Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009274.1 Hibiscus syriacus cultivar Beakdansim tig00112957_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: 585551
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:203759 original size:26 final size:27
Alignment explanation
Indices: 203724--203776 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
203714 TAATTGCAAA
203724 AAAAAAAAAACTATAAG-TACCAAATTG
1 AAAAAAAAAACT-TAAGCTACCAAATTG
* *
203751 AAAAGAAAAACTTCAGCTACCAAATT
1 AAAAAAAAAACTTAAGCTACCAAATT
203777 AAACATTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 3 0.13
27 20 0.87
ACGTcount: A:0.58, C:0.15, G:0.08, T:0.19
Consensus pattern (27 bp):
AAAAAAAAAACTTAAGCTACCAAATTG
Found at i:229557 original size:24 final size:25
Alignment explanation
Indices: 229505--229557 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
229495 ATAATAATAT
*
229505 TTTAAATAAATTATATATTTATAAC
1 TTTAAATAAATTATATATTTATAAA
*
229530 TTTAAA-AAATTATTTA-TTATTAAA
1 TTTAAATAAATTATATATTTA-TAAA
229554 TTTA
1 TTTA
229558 TAATTAAGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 3 0.12
24 16 0.64
25 6 0.24
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (25 bp):
TTTAAATAAATTATATATTTATAAA
Found at i:232757 original size:18 final size:18
Alignment explanation
Indices: 232710--232760 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
232700 GGATTATCAG
*
232710 TGGTCCTTCGGAACATAA
1 TGGTCCTTCGGGACATAA
232728 TGGTCCTTCGGGACATAA
1 TGGTCCTTCGGGACATAA
*
232746 TGGTCATTCGGGACA
1 TGGTCCTTCGGGACA
232761 AATATTCAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (18 bp):
TGGTCCTTCGGGACATAA
Found at i:233088 original size:15 final size:15
Alignment explanation
Indices: 233068--233109 Score: 75
Period size: 15 Copynumber: 2.8 Consensus size: 15
233058 GACTTAGCGT
233068 GTAAGTGATTTACAC
1 GTAAGTGATTTACAC
*
233083 GTAAGTGATTTACAT
1 GTAAGTGATTTACAC
233098 GTAAGTGATTTA
1 GTAAGTGATTTA
233110 GACAAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.33, C:0.07, G:0.21, T:0.38
Consensus pattern (15 bp):
GTAAGTGATTTACAC
Found at i:233501 original size:31 final size:32
Alignment explanation
Indices: 233439--233518 Score: 99
Period size: 31 Copynumber: 2.5 Consensus size: 32
233429 GAAAAAAATC
* *
233439 TTTAGACACCAAAAAAATAAAAGTAGGTATAA
1 TTTAGACACCAAAAAATTAAAAGTAGATATAA
* * *
233471 TTTAAACACC-AAAAATTAATATTAGATATAA
1 TTTAGACACCAAAAAATTAAAAGTAGATATAA
*
233502 TTTAGACACCTAAAAAT
1 TTTAGACACCAAAAAAT
233519 GTATTAAGCC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
31 26 0.63
32 15 0.37
ACGTcount: A:0.54, C:0.11, G:0.07, T:0.28
Consensus pattern (32 bp):
TTTAGACACCAAAAAATTAAAAGTAGATATAA
Found at i:234540 original size:18 final size:18
Alignment explanation
Indices: 234516--234556 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
234506 ATGTATATTT
*
234516 AATATGTATTTAATTATA
1 AATATGTATTTAACTATA
*
234534 TATATGTATTTAACTATA
1 AATATGTATTTAACTATA
234552 AATAT
1 AATAT
234557 AAATAAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (18 bp):
AATATGTATTTAACTATA
Found at i:235266 original size:17 final size:16
Alignment explanation
Indices: 235246--235280 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
235236 GAAGAAGAAA
235246 AATATTAAAAAAATGTT
1 AATA-TAAAAAAATGTT
*
235263 AATATATAAAAATGTT
1 AATATAAAAAAATGTT
235279 AA
1 AA
235281 AAGAAAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (16 bp):
AATATAAAAAAATGTT
Found at i:235354 original size:31 final size:30
Alignment explanation
Indices: 235268--235361 Score: 89
Period size: 31 Copynumber: 3.1 Consensus size: 30
235258 ATGTTAATAT
* *
235268 ATAAAAATGTTAAAAGAAAAACAAAAGAAA
1 ATAAAAATGTTAAAAGAAAAAAAAAACAAA
* **** * *
235298 AGAAAAAATGTTAAATTTCAGAAAAAATAAA
1 A-TAAAAATGTTAAAAGAAAAAAAAAACAAA
235329 ATAAAAATGTTAAAAGAGAAAAAAAAACAAA
1 ATAAAAATGTTAAAAGA-AAAAAAAAACAAA
235360 AT
1 AT
235362 GGAATGAAAA
Statistics
Matches: 47, Mismatches: 15, Indels: 3
0.72 0.23 0.05
Matches are distributed among these distances:
30 13 0.28
31 34 0.72
ACGTcount: A:0.70, C:0.03, G:0.10, T:0.17
Consensus pattern (30 bp):
ATAAAAATGTTAAAAGAAAAAAAAAACAAA
Found at i:236703 original size:3 final size:3
Alignment explanation
Indices: 236695--236753 Score: 95
Period size: 3 Copynumber: 20.3 Consensus size: 3
236685 TAAATAAATA
*
236695 AAT AAT AAT AAT AAT AAT AAT AAT AA- AAG AA- AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
236741 AAT AAT AAT AAT A
1 AAT AAT AAT AAT A
236754 TATTATTATA
Statistics
Matches: 54, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 4 0.07
3 50 0.93
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:236804 original size:37 final size:36
Alignment explanation
Indices: 236760--236961 Score: 135
Period size: 37 Copynumber: 5.2 Consensus size: 36
236750 AATATATTAT
236760 TATATATATTTTCAAAAACATTTCCAAAACTATATAA
1 TATATATATTTTCAAAAACATTT-CAAAACTATATAA
* *
236797 TATATATATATTCAAAAACATTTTAAAACTATAT-A
1 TATATATATTTTCAAAAACATTTCAAAACTATATAA
* * *
236832 T-TATAT-TTTTTAAAAAAATGTTTTTAAAAAAACTATAT-A
1 TATATATATTTTCAAAAACA----TTT--CAAAACTATATAA
** *
236871 T-TATATATTTTCAAAATGATTTTAAAACTATATACTATATA
1 TATATATATTTTCAAAAACATTTCAAAAC----TA-TATA-A
236912 TATATATATATATTCAAAAATCATTTTCAAAACTATATATA
1 TATATATAT-T-TTCAAAAA-CATT-TCAAAACTATATA-A
236953 TATATATAT
1 TATATATAT
236962 AACCGATAAA
Statistics
Matches: 133, Mismatches: 13, Indels: 34
0.74 0.07 0.19
Matches are distributed among these distances:
33 9 0.07
34 10 0.08
35 2 0.02
36 13 0.10
37 25 0.19
38 2 0.02
39 20 0.15
40 9 0.07
41 17 0.13
42 9 0.07
43 1 0.01
44 7 0.05
45 3 0.02
46 6 0.05
ACGTcount: A:0.48, C:0.08, G:0.01, T:0.43
Consensus pattern (36 bp):
TATATATATTTTCAAAAACATTTCAAAACTATATAA
Found at i:236932 original size:45 final size:44
Alignment explanation
Indices: 236865--236962 Score: 146
Period size: 45 Copynumber: 2.2 Consensus size: 44
236855 TTAAAAAAAC
* *
236865 TATATAT-TATATATTTTCAAAATGATTTT-AAAACTATATACTA
1 TATATATATATATATATTCAAAATCATTTTCAAAACTATATA-TA
236908 TATATATATATATATATTCAAAAATCATTTTCAAAACTATATATA
1 TATATATATATATATATTC-AAAATCATTTTCAAAACTATATATA
236953 TATATATATA
1 TATATATATA
236963 ACCGATAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
43 7 0.14
44 10 0.20
45 22 0.44
46 11 0.22
ACGTcount: A:0.47, C:0.07, G:0.01, T:0.45
Consensus pattern (44 bp):
TATATATATATATATATTCAAAATCATTTTCAAAACTATATATA
Found at i:239598 original size:16 final size:16
Alignment explanation
Indices: 239579--239613 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
239569 CGAGTATTGC
*
239579 TGAGTTCGACTCGACT
1 TGAGCTCGACTCGACT
239595 TGAGCTCGACTCGACT
1 TGAGCTCGACTCGACT
239611 TGA
1 TGA
239614 AAACTCTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.29
Consensus pattern (16 bp):
TGAGCTCGACTCGACT
Found at i:241747 original size:124 final size:124
Alignment explanation
Indices: 241515--241758 Score: 402
Period size: 124 Copynumber: 2.0 Consensus size: 124
241505 CATGCCACGT
*
241515 CATCCAACTAATAGCAGCTAACGTCCCAGTGACCGCATCTTAATTAAAACGAAACAAAAATAGCC
1 CATCCAACTAATAGCAGCTAACGTCCCAGTGACCACATCTTAATTAAAACGAAACAAAAATAGCC
241580 ATATATTATTTTTTTGGATTGAGTGACCATACGTTTATAAAAATTAAAACAAAAGCGAC
66 ATATATTATTTTTTTGGATTGAGTGACCATACGTTTATAAAAATTAAAACAAAAGCGAC
* * * *
241639 CATCTAACTAATGGCAGCTAACGTCCCAGTGACCACATCTTAATTAAAACGAAAC-AAAATCGAT
1 CATCCAACTAATAGCAGCTAACGTCCCAGTGACCACATCTTAATTAAAACGAAACAAAAATAG-C
*
241703 CATATATTATTTTTTTTGGATTGAGTGACCATACGTTTAT-AAAATTGAAACAAAAG
65 CATATATTA-TTTTTTTGGATTGAGTGACCATACGTTTATAAAAATTAAAACAAAAG
241759 TGACTAACCC
Statistics
Matches: 112, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
123 6 0.05
124 76 0.68
125 30 0.27
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.28
Consensus pattern (124 bp):
CATCCAACTAATAGCAGCTAACGTCCCAGTGACCACATCTTAATTAAAACGAAACAAAAATAGCC
ATATATTATTTTTTTGGATTGAGTGACCATACGTTTATAAAAATTAAAACAAAAGCGAC
Found at i:245573 original size:21 final size:22
Alignment explanation
Indices: 245535--245587 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 22
245525 ACGTATAATT
245535 ATAAATTAGTTAAAAATTTAAA-G
1 ATAAATTA-TTAAAAA-TTAAAGG
245558 ATAAATTATT-AAAATTAAAGG
1 ATAAATTATTAAAAATTAAAGG
*
245579 GTAAATTAT
1 ATAAATTAT
245588 ACTAGTACCA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 5 0.18
21 13 0.46
22 2 0.07
23 8 0.29
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (22 bp):
ATAAATTATTAAAAATTAAAGG
Found at i:247416 original size:14 final size:15
Alignment explanation
Indices: 247397--247425 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
247387 TATAATTTAC
247397 CATTTAT-TTTAAAT
1 CATTTATCTTTAAAT
247411 CATTTATCTTTAAAT
1 CATTTATCTTTAAAT
247426 TTTTATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.55
Consensus pattern (15 bp):
CATTTATCTTTAAAT
Found at i:248206 original size:23 final size:23
Alignment explanation
Indices: 248169--248218 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
248159 GTGTTGCACG
248169 TTTTCATATGCCTTTATGGCATAT
1 TTTTCATATGCCTTTATGGCAT-T
* *
248193 TTTTCTTATG-CTTTTTGGCATT
1 TTTTCATATGCCTTTATGGCATT
248215 TTTT
1 TTTT
248219 GGTTCTTTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 5 0.21
23 10 0.42
24 9 0.38
ACGTcount: A:0.14, C:0.14, G:0.12, T:0.60
Consensus pattern (23 bp):
TTTTCATATGCCTTTATGGCATT
Found at i:248846 original size:200 final size:202
Alignment explanation
Indices: 248502--248896 Score: 625
Period size: 200 Copynumber: 2.0 Consensus size: 202
248492 TGGTTAGATT
* *
248502 TAATCTTTCATTGTATAGTCCTTATGTTATCTTAAATTACTAGTTTTTGTTTCAATGATTATAGG
1 TAATCTTTCATTGTATAGTCCTTATGTGATCTTAAACTACTAGTTTTTGTTTCAATGATTATAGG
* * * *
248567 AAATTTTCCTAATTATGTGCTTAATTTACGATTGTAATTGTAAATCTTTATTGTAATTTGGGATA
66 AAAATTTCATAATTATATGCTTAATTTACGATTGTAATTGTAAATCCTTATTGTAATTTGGGATA
* * *
248632 TTTTCTATTTTAAATAAAATTAATTGCTTCTAT-AAAAAAATCATCAAACTATTAACGGAGGTTG
131 TTTTCTATTTTAAATAAAATTAATCGCTTCTATAAAAAAAATCATCAAAATATCAACGGAGGTTG
248696 GTTCAAG
196 GTTCAAG
* **
248703 TAATCTTTCCTTGTATAGTCCTTATGTGATCTTATGCTACTAG-TTTTGTTTCAATGATTATAGG
1 TAATCTTTCATTGTATAGTCCTTATGTGATCTTAAACTACTAGTTTTTGTTTCAATGATTATAGG
*
248767 AAAATTTCATAATTATATGCTTAATTTACGATTGTAATTTTAAATCCTTATTGTAATTTGGGATA
66 AAAATTTCATAATTATATGCTTAATTTACGATTGTAATTGTAAATCCTTATTGTAATTTGGGATA
* *
248832 -TTTCATATTTTAAATAAAATTAGTCGCTTCTATAAAAAAAATCATCAAAATATCAATGGAGGTT
131 TTTTC-TATTTTAAATAAAATTAATCGCTTCTATAAAAAAAATCATCAAAATATCAACGGAGGTT
248896 G
195 G
248897 ATTAAAGTGG
Statistics
Matches: 177, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
199 4 0.02
200 107 0.60
201 66 0.37
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.44
Consensus pattern (202 bp):
TAATCTTTCATTGTATAGTCCTTATGTGATCTTAAACTACTAGTTTTTGTTTCAATGATTATAGG
AAAATTTCATAATTATATGCTTAATTTACGATTGTAATTGTAAATCCTTATTGTAATTTGGGATA
TTTTCTATTTTAAATAAAATTAATCGCTTCTATAAAAAAAATCATCAAAATATCAACGGAGGTTG
GTTCAAG
Found at i:250352 original size:20 final size:21
Alignment explanation
Indices: 250311--250354 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
250301 ATTGTCAAAG
*
250311 AGTATTGATACTCGGGGGTTT
1 AGTATTGATACTCGGAGGTTT
250332 AGTATTGATACTC-GAGGTTT
1 AGTATTGATACTCGGAGGTTT
250352 AGT
1 AGT
250355 TCAGATTCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.23, C:0.09, G:0.30, T:0.39
Consensus pattern (21 bp):
AGTATTGATACTCGGAGGTTT
Found at i:250876 original size:98 final size:97
Alignment explanation
Indices: 250695--250888 Score: 307
Period size: 98 Copynumber: 2.0 Consensus size: 97
250685 TACAAGTGAT
250695 AAAATTAATAATCGTGTGATAACATAAGGTAATTATGAAGTAAATTTCCATAAGACTTATGCCTT
1 AAAATTAATAATCGTGTGATAACATAAGGTAATTATGAAGTAAATTTCCATAAGACTTATGCCTT
*
250760 GTTTGATGATCAAAAAACATTGAGGACACCCG
66 GTTTGATGATCAAAAAACATCGAGGACACCCG
* * * *
250792 AAAACTTAATAATTGTGTGATAACATAAGGTCATTATGAAGTAAATTTTCATAAGACTTATGTCT
1 AAAA-TTAATAATCGTGTGATAACATAAGGTAATTATGAAGTAAATTTCCATAAGACTTATGCCT
* **
250857 TGTTTGATGCTCAGGAAACATCGAGGACACCC
65 TGTTTGATGATCAAAAAACATCGAGGACACCC
250889 AAGTTACTTG
Statistics
Matches: 88, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
97 4 0.05
98 84 0.95
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (97 bp):
AAAATTAATAATCGTGTGATAACATAAGGTAATTATGAAGTAAATTTCCATAAGACTTATGCCTT
GTTTGATGATCAAAAAACATCGAGGACACCCG
Found at i:256716 original size:165 final size:166
Alignment explanation
Indices: 256422--256754 Score: 614
Period size: 165 Copynumber: 2.0 Consensus size: 166
256412 GTAATGTTTC
*
256422 TTAAAATCTGAACGATTTACGACTTATAATAATGTGTATCATATTTAATAGTCATAATCCAAAAA
1 TTAAAATCTGAACGATTTACGACTTACAATAATGTGTATCATATTTAATAGTCATAATCC-AAAA
256487 AAAATTCAAAAACACGGAGTACACTTTTAATTATGTGTCATATGTAAAAGTCATCTTTTAATTTC
65 AAAATTCAAAAACACGGAGTACACTTTTAATTATGTGTCATATGTAAAAGTCATCTTTTAATTTC
256552 GCCATTATTTTCATCATGTACGCATGCTTTCTCTCTT
130 GCCATTATTTTCATCATGTACGCATGCTTTCTCTCTT
256589 TTAAAATCTGAACGATTTACGACTTACAATAATGTGTATCATATTTAATAGTCATAATCC-AAAA
1 TTAAAATCTGAACGATTTACGACTTACAATAATGTGTATCATATTTAATAGTCATAATCCAAAAA
* *
256653 AAATTCAAAAACACGGAGTACACTTTTAATTGTGTGTCATATGTAAAAGTCGTCTTTTAATTTCG
66 AAATTCAAAAACACGGAGTACACTTTTAATTATGTGTCATATGTAAAAGTCATCTTTTAATTTCG
*
256718 CCATTATTTTCATCATGTACGTATGCTTTCTCTCTT
131 CCATTATTTTCATCATGTACGCATGCTTTCTCTCTT
256754 T
1 T
256755 AAATGCTTTT
Statistics
Matches: 162, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
165 103 0.64
167 59 0.36
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (166 bp):
TTAAAATCTGAACGATTTACGACTTACAATAATGTGTATCATATTTAATAGTCATAATCCAAAAA
AAATTCAAAAACACGGAGTACACTTTTAATTATGTGTCATATGTAAAAGTCATCTTTTAATTTCG
CCATTATTTTCATCATGTACGCATGCTTTCTCTCTT
Found at i:260240 original size:13 final size:13
Alignment explanation
Indices: 260204--260255 Score: 68
Period size: 13 Copynumber: 4.0 Consensus size: 13
260194 AATGACGCTC
260204 AATGCGCGTCATA
1 AATGCGCGTCATA
* *
260217 AATGTGAGTCATA
1 AATGCGCGTCATA
* *
260230 AATGCGTGTCATC
1 AATGCGCGTCATA
260243 AATGCGCGTCATA
1 AATGCGCGTCATA
260256 GATTTATGAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:269131 original size:20 final size:19
Alignment explanation
Indices: 269106--269152 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
269096 TTTAGGTATT
269106 GATACCAAGGCTTCGATATG
1 GATACCAA-GCTTCGATATG
* *
269126 GATACCTAATCTTTGATATG
1 GATACC-AAGCTTCGATATG
269146 GATACCA
1 GATACCA
269153 GTTTACCCAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 1 0.04
20 21 0.88
21 2 0.08
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (19 bp):
GATACCAAGCTTCGATATG
Found at i:270042 original size:10 final size:10
Alignment explanation
Indices: 270027--270080 Score: 54
Period size: 10 Copynumber: 5.0 Consensus size: 10
270017 TGAGTGGGAA
270027 AAAAAAGAAG
1 AAAAAAGAAG
270037 AAAAAAGAAAG
1 AAAAAAG-AAG
*
270048 ATAATGAAGAAG
1 A-AA-AAAGAAG
*
270060 AGAAAAGGAAG
1 A-AAAAAGAAG
270071 AAAAAAGAAG
1 AAAAAAGAAG
270081 CCCTCTATAG
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
10 15 0.42
11 10 0.28
12 8 0.22
13 3 0.08
ACGTcount: A:0.72, C:0.00, G:0.24, T:0.04
Consensus pattern (10 bp):
AAAAAAGAAG
Found at i:270207 original size:7 final size:7
Alignment explanation
Indices: 270197--270318 Score: 60
Period size: 7 Copynumber: 17.4 Consensus size: 7
270187 TCTTTTAAGG
270197 TTAGAGT
1 TTAGAGT
*
270204 TTAGGGT
1 TTAGAGT
* *
270211 TTAAAAT
1 TTAGAGT
270218 TTA-AGAT
1 TTAGAG-T
*
270225 TTAGGGT
1 TTAGAGT
270232 TTATGA-T
1 TTA-GAGT
270239 TTA-AGT
1 TTAGAGT
270245 TATATG-GT
1 T-TA-GAGT
*
270253 TTAGAAT
1 TTAGAGT
*
270260 TTAGGGT
1 TTAGAGT
270267 TTAGAGT
1 TTAGAGT
270274 TTA-AGAT
1 TTAGAG-T
270281 TTAGAGT
1 TTAGAGT
270288 TT-GAG-
1 TTAGAGT
*
270293 GTAGGAGTT
1 TTA-GAG-T
270302 TTAGAGT
1 TTAGAGT
*
270309 TTAGGGT
1 TTAGAGT
270316 TTA
1 TTA
270319 AGATTTGAGA
Statistics
Matches: 87, Mismatches: 14, Indels: 28
0.67 0.11 0.22
Matches are distributed among these distances:
5 2 0.02
6 9 0.10
7 64 0.74
8 10 0.11
9 2 0.02
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (7 bp):
TTAGAGT
Found at i:270228 original size:21 final size:20
Alignment explanation
Indices: 270201--270289 Score: 79
Period size: 21 Copynumber: 4.2 Consensus size: 20
270191 TTAAGGTTAG
270201 AGTTTAGGGTTTAAAATTTA
1 AGTTTAGGGTTTAAAATTTA
**
270221 AGATTTAGGGTTTATGATTTA
1 AG-TTTAGGGTTTAAAATTTA
* *
270242 AGTTATATGGTTTAGAATTTA
1 AGTT-TAGGGTTTAAAATTTA
* * *
270263 GGGTTTAGAGTTTAAGATTTA
1 -AGTTTAGGGTTTAAAATTTA
270284 GAGTTT
1 -AGTTT
270290 GAGGTAGGAG
Statistics
Matches: 55, Mismatches: 11, Indels: 5
0.77 0.15 0.07
Matches are distributed among these distances:
20 4 0.07
21 48 0.87
22 3 0.05
ACGTcount: A:0.30, C:0.00, G:0.24, T:0.46
Consensus pattern (20 bp):
AGTTTAGGGTTTAAAATTTA
Found at i:270234 original size:14 final size:14
Alignment explanation
Indices: 270197--270324 Score: 73
Period size: 14 Copynumber: 9.1 Consensus size: 14
270187 TCTTTTAAGG
* *
270197 TTAGAGTTTAGGGT
1 TTAGAGTTTAAGAT
* *
270211 TTAAAATTTAAGAT
1 TTAGAGTTTAAGAT
* *
270225 TTAGGGTTTATGAT
1 TTAGAGTTTAAGAT
* *
270239 TTA-AGTTATATGGT
1 TTAGAGTT-TAAGAT
* * *
270253 TTAGAATTTAGGGT
1 TTAGAGTTTAAGAT
270267 TTAGAGTTTAAGAT
1 TTAGAGTTTAAGAT
*
270281 TTAGAGTTT--GAG
1 TTAGAGTTTAAGAT
* *
270293 GTAGGAGTTTTAGAGT
1 TTA-GAGTTTAAGA-T
*
270309 TTAGGGTTTAAGAT
1 TTAGAGTTTAAGAT
270323 TT
1 TT
270325 GAGATTGAGG
Statistics
Matches: 87, Mismatches: 21, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
12 4 0.05
13 9 0.10
14 59 0.68
15 13 0.15
16 2 0.02
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.45
Consensus pattern (14 bp):
TTAGAGTTTAAGAT
Found at i:276522 original size:310 final size:311
Alignment explanation
Indices: 275685--276620 Score: 1865
Period size: 311 Copynumber: 3.0 Consensus size: 311
275675 AGAAAGTATA
275685 AACTACTGAAAACTCTCAAGGATCTAGCATTTTTGTCAAGATGGTCCTAATTTTAAATTAGTCCC
1 AACTACTGAAAACTCTCAAGGATCTAGCATTTTTGTCAAGATGGTCCTAATTTTAAATTAGTCCC
275750 TAAATTTTTTAACATTTCAATAATGTTTGCAAAATCATTCAAGATTTTGTGGATTAAATTGGAAC
66 TAAATTTTTTAACATTTCAATAATGTTTGCAAAATCATTCAAGATTTTGTGGATTAAATTGGAAC
275815 ATTAATAAGTTTGGGGGATCAATATAGAATGAAAGTCATATTTGGAGATGAATTTAGAATGTTCA
131 ATTAATAAGTTTGGGGGATCAATATAGAATGAAAGTCATATTTGGAGATGAATTTAGAATGTTCA
275880 AGAGTTTAGGGACTAATATAGAATAAAAATCAACATTTGAGGATAAAATTAGAACAATTATAAGT
196 AGAGTTTAGGGACTAATATAGAATAAAAATCAACATTTGAGGATAAAATTAGAACAATTATAAGT
275945 TTAAGGACCAATTTAAAAAATTATCATTATTTAAATATGTTTAATGCAATT
261 TTAAGGACCAATTTAAAAAATTATCATTATTTAAATATGTTTAATGCAATT
275996 AACTACTGAAAACTCTCAAGGATCTAGCATTTTTGTCAAGATGGTCCTAATTTTAAATTAGTCCC
1 AACTACTGAAAACTCTCAAGGATCTAGCATTTTTGTCAAGATGGTCCTAATTTTAAATTAGTCCC
276061 TAAATTTTTTAACATTTCAATAATGTTTGCAAAATCATTCAAGATTTTGTGGATTAAATTGGAAC
66 TAAATTTTTTAACATTTCAATAATGTTTGCAAAATCATTCAAGATTTTGTGGATTAAATTGGAAC
276126 ATTAATAAGTTTGGGGGATCAATATAGAATGAAAGTCATATTTGGAGATGAATTTAGAATGTTCA
131 ATTAATAAGTTTGGGGGATCAATATAGAATGAAAGTCATATTTGGAGATGAATTTAGAATGTTCA
276191 AGAGTTTAGGGACTAATATAGAATAAAAATCAACATTTGAGGATAAAATTAGAACAATTATAAGT
196 AGAGTTTAGGGACTAATATAGAATAAAAATCAACATTTGAGGATAAAATTAGAACAATTATAAGT
276256 TTAAGGACCAATTT-AAAAATTATCATTATTTAAATATGTTTAATGCAATT
261 TTAAGGACCAATTTAAAAAATTATCATTATTTAAATATGTTTAATGCAATT
276306 AACTACTGAAAACTCTCAAGGATCTAGCATTTTTGTCAAGATGGTCCTAATTTTAAATTAGTCCC
1 AACTACTGAAAACTCTCAAGGATCTAGCATTTTTGTCAAGATGGTCCTAATTTTAAATTAGTCCC
276371 TAAATTTTTTAACATTTCAATAATGTTTGCAAAATCATTCAAGATTTTGTGGATTAAATTGGAAC
66 TAAATTTTTTAACATTTCAATAATGTTTGCAAAATCATTCAAGATTTTGTGGATTAAATTGGAAC
276436 ATTAATAAGTTTGGGGGATCAATATAGAATGAAAGTCATATTTGGAGATGAATTTAGAATGTTCA
131 ATTAATAAGTTTGGGGGATCAATATAGAATGAAAGTCATATTTGGAGATGAATTTAGAATGTTCA
276501 AGAGTTTAGGGACTAATATAGAATAAAAATCAACATTTGAGGATAAAATTAGAACAATTATAAGT
196 AGAGTTTAGGGACTAATATAGAATAAAAATCAACATTTGAGGATAAAATTAGAACAATTATAAGT
276566 TTAAGGACCAATTTAAAAAATTATCATTATTTAAATATGTTTAATGCAATT
261 TTAAGGACCAATTTAAAAAATTATCATTATTTAAATATGTTTAATGCAATT
276617 AACT
1 AACT
276621 TTCTATATTA
Statistics
Matches: 624, Mismatches: 0, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
310 310 0.50
311 314 0.50
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (311 bp):
AACTACTGAAAACTCTCAAGGATCTAGCATTTTTGTCAAGATGGTCCTAATTTTAAATTAGTCCC
TAAATTTTTTAACATTTCAATAATGTTTGCAAAATCATTCAAGATTTTGTGGATTAAATTGGAAC
ATTAATAAGTTTGGGGGATCAATATAGAATGAAAGTCATATTTGGAGATGAATTTAGAATGTTCA
AGAGTTTAGGGACTAATATAGAATAAAAATCAACATTTGAGGATAAAATTAGAACAATTATAAGT
TTAAGGACCAATTTAAAAAATTATCATTATTTAAATATGTTTAATGCAATT
Found at i:277437 original size:2 final size:2
Alignment explanation
Indices: 277430--277473 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
277420 TGTTAACATG
277430 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
277472 TA
1 TA
277474 AACATTATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:278366 original size:17 final size:17
Alignment explanation
Indices: 278332--278383 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
278322 ACCGGACAAA
* *
278332 TTTATTATTTTAGAGAG
1 TTTATTAATTTACAGAG
*
278349 TTTATTAATTTACCGAG
1 TTTATTAATTTACAGAG
*
278366 --TATTAATTTAAAGAG
1 TTTATTAATTTACAGAG
278381 TTT
1 TTT
278384 CTACTGTATA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.50
Consensus pattern (17 bp):
TTTATTAATTTACAGAG
Found at i:279463 original size:26 final size:24
Alignment explanation
Indices: 279405--279467 Score: 65
Period size: 27 Copynumber: 2.4 Consensus size: 24
279395 AGAGATTCGC
279405 TATTTTCAAAATAAAAAATTATATT
1 TATTTT-AAAATAAAAAATTATATT
279430 TCACTTTTATAAATAAAAATAATT-TATT
1 T-A-TTTTA-AAAT-AAAA-AATTATATT
279458 TATTTTAAAA
1 TATTTTAAAA
279468 CTTTAGTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
25 4 0.12
26 7 0.21
27 9 0.27
28 9 0.27
29 4 0.12
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (24 bp):
TATTTTAAAATAAAAAATTATATT
Found at i:286877 original size:32 final size:32
Alignment explanation
Indices: 286812--286896 Score: 106
Period size: 32 Copynumber: 2.8 Consensus size: 32
286802 GTTCTACGGA
* **
286812 ACATATGGACAGAATTACC--TGTCTTTTGGG
1 ACATATGGACATAATTACCTATGTCTTTTAAG
286842 ACATATGGACATAATTACCTATGTCTTTTAAG
1 ACATATGGACATAATTACCTATGTCTTTTAAG
286874 ACATATGGACAGT-A-TACCTATGT
1 ACATATGGACA-TAATTACCTATGT
286897 TCTAATGAGC
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
30 18 0.37
31 9 0.18
32 21 0.43
33 1 0.02
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (32 bp):
ACATATGGACATAATTACCTATGTCTTTTAAG
Found at i:286895 original size:31 final size:32
Alignment explanation
Indices: 286812--286924 Score: 114
Period size: 31 Copynumber: 3.7 Consensus size: 32
286802 GTTCTACGGA
* **
286812 ACATATGGACAGAATTACC--TGTCTTTTGGG
1 ACATATGGACAGTATTACCTATGTCTTTTAAG
286842 ACATATGGACA-TAATTACCTATGTCTTTTAAG
1 ACATATGGACAGT-ATTACCTATGTCTTTTAAG
*
286874 ACATATGGACAGTA-TACCTATG--TTCTAATG
1 ACATATGGACAGTATTACCTATGTCTTTTAA-G
286904 AGCATATGGACAGT-TTACCTA
1 A-CATATGGACAGTATTACCTA
286925 GGTTCTTTGG
Statistics
Matches: 72, Mismatches: 4, Indels: 13
0.81 0.04 0.15
Matches are distributed among these distances:
29 5 0.07
30 19 0.26
31 26 0.36
32 21 0.29
33 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Consensus pattern (32 bp):
ACATATGGACAGTATTACCTATGTCTTTTAAG
Found at i:287791 original size:21 final size:21
Alignment explanation
Indices: 287765--287815 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
287755 CTGTAGCAGT
* *
287765 ACTGTATCAGTGCATCGGTGC
1 ACTGTATCAATGCATCGATGC
* *
287786 ACTGTAGCAATGCATCGATGT
1 ACTGTATCAATGCATCGATGC
287807 ACTGTATCA
1 ACTGTATCA
287816 CTGTTCACAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (21 bp):
ACTGTATCAATGCATCGATGC
Found at i:289114 original size:3 final size:3
Alignment explanation
Indices: 289106--289131 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
289096 TATAACAAAA
289106 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
289132 TTCCCAATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:292490 original size:2 final size:2
Alignment explanation
Indices: 292483--292509 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
292473 GACATTTTTA
292483 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
292510 CACTCTCCTC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:294228 original size:20 final size:20
Alignment explanation
Indices: 294199--294239 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
294189 CGTTTTTAAA
*
294199 TATTATATAT-TTTATTTTT
1 TATTATATATATTGATTTTT
294218 TATTCATATATATTGATTTTT
1 TATT-ATATATATTGATTTTT
294239 T
1 T
294240 TATCAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 6 0.32
21 9 0.47
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (20 bp):
TATTATATATATTGATTTTT
Found at i:297520 original size:17 final size:17
Alignment explanation
Indices: 297480--297524 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
297470 ATAATCATTT
* *
297480 TATTTTTTATTTTTTAA
1 TATTTTTTAATTTCTAA
*
297497 -ATATTTTAATTTCTAA
1 TATTTTTTAATTTCTAA
297513 TATTTTTTAATT
1 TATTTTTTAATT
297525 AAAAATAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (17 bp):
TATTTTTTAATTTCTAA
Found at i:298559 original size:41 final size:41
Alignment explanation
Indices: 298440--298539 Score: 164
Period size: 41 Copynumber: 2.4 Consensus size: 41
298430 TTTTGAAAAA
* *
298440 ATACCTTGGTATCGATACCCCTATATGGAGTATCAATAGTC
1 ATACCATGGTATCGATACCCCTATATGGAGTATCAATAATC
*
298481 ATACCCTGGTATCGATACCCCTATATGGAGTATCAATAATC
1 ATACCATGGTATCGATACCCCTATATGGAGTATCAATAATC
*
298522 CTACCATGGTATCGATAC
1 ATACCATGGTATCGATAC
298540 TCTATGAATG
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (41 bp):
ATACCATGGTATCGATACCCCTATATGGAGTATCAATAATC
Found at i:299890 original size:16 final size:16
Alignment explanation
Indices: 299871--299909 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
299861 ATATGATATA
299871 TATTATTATCAT-TTAT
1 TATTATTA-CATATTAT
299887 TATTATTACATATTAT
1 TATTATTACATATTAT
*
299903 TTTTATT
1 TATTATT
299910 TATTTTTACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 3 0.14
16 18 0.86
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (16 bp):
TATTATTACATATTAT
Found at i:299912 original size:23 final size:23
Alignment explanation
Indices: 299882--299937 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
299872 ATTATTATCA
299882 TTTA-TTATTATTACATA-TTATT
1 TTTATTTATTATTACATATTTA-T
* *
299904 TTTATTTATTTTTACTTATTTAT
1 TTTATTTATTATTACATATTTAT
299927 TTTACTTTATT
1 TTTA-TTTATT
299938 TTGTTTTCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 4 0.14
23 16 0.55
24 9 0.31
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (23 bp):
TTTATTTATTATTACATATTTAT
Found at i:299913 original size:13 final size:13
Alignment explanation
Indices: 299871--299927 Score: 60
Period size: 13 Copynumber: 4.3 Consensus size: 13
299861 ATATGATATA
*
299871 TATTATTATCATT
1 TATTATTATTATT
**
299884 TATTATTATTACA
1 TATTATTATTATT
*
299897 TATTATTTTTATT
1 TATTATTATTATT
*
299910 TATTTTTACTTATT
1 TATTATTA-TTATT
299924 TATT
1 TATT
299928 TTACTTTATT
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
13 26 0.74
14 9 0.26
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (13 bp):
TATTATTATTATT
Found at i:299924 original size:14 final size:14
Alignment explanation
Indices: 299904--299938 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
299894 ACATATTATT
299904 TTTATTTATTTTTAC
1 TTTATTTA-TTTTAC
299919 -TTATTTATTTTAC
1 TTTATTTATTTTAC
299932 TTTATTT
1 TTTATTT
299939 TGTTTTCCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTATTTATTTTAC
Found at i:301248 original size:3 final size:3
Alignment explanation
Indices: 301234--301272 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
301224 TTTAATTTTA
*
301234 ATT ATT -TT ATT ATT ATT ATT ATT ATT ATT ATT AGT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
301273 GCTCATTAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:304435 original size:12 final size:12
Alignment explanation
Indices: 304415--304444 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
304405 ATACGGTATA
*
304415 AACAATACCGTG
1 AACAGTACCGTG
304427 AACAGTACCGTG
1 AACAGTACCGTG
304439 AACAGT
1 AACAGT
304445 GCTAGAGTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.40, C:0.23, G:0.20, T:0.17
Consensus pattern (12 bp):
AACAGTACCGTG
Found at i:307447 original size:14 final size:15
Alignment explanation
Indices: 307428--307460 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
307418 GTGGTACTCT
307428 GCTGAAA-GTAATAA
1 GCTGAAAGGTAATAA
307442 GCTGAAAGGTAATAA
1 GCTGAAAGGTAATAA
307457 GCTG
1 GCTG
307461 TTAATCTTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.42, C:0.09, G:0.27, T:0.21
Consensus pattern (15 bp):
GCTGAAAGGTAATAA
Found at i:310651 original size:13 final size:13
Alignment explanation
Indices: 310635--310679 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
310625 TCAAAGAATT
310635 TTTATTTTACTTG
1 TTTATTTTACTTG
310648 TTTATTTT--TTG
1 TTTATTTTACTTG
*
310659 TATAGTTTTACTTG
1 TTTA-TTTTACTTG
310673 -TTATTTT
1 TTTATTTT
310680 CCTTTTCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
11 6 0.22
12 8 0.30
13 10 0.37
14 3 0.11
ACGTcount: A:0.16, C:0.04, G:0.09, T:0.71
Consensus pattern (13 bp):
TTTATTTTACTTG
Found at i:317343 original size:16 final size:16
Alignment explanation
Indices: 317322--317352 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
317312 AGTGTTTTTA
*
317322 TATTTATGATATATAC
1 TATTTATAATATATAC
317338 TATTTATAATATATA
1 TATTTATAATATATA
317353 TATATAGGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (16 bp):
TATTTATAATATATAC
Found at i:317503 original size:150 final size:150
Alignment explanation
Indices: 317213--317506 Score: 414
Period size: 150 Copynumber: 2.0 Consensus size: 150
317203 AAAATCGGAT
* * * * *
317213 GAAATCTCATGTCTTTTTATATTTGCTCTATTGTCGTTACATGACAATGGACAATGAGGGACAAC
1 GAAAACTCATGTCTTTTTATATTTGCCCTATTATCGTTACACGACAATGGACAATAAGGGACAAC
* *
317278 TGTAGACACTCAAAATTCGTCCGGAGTTGTTCCAAGTGTTTTTATATTTATGATATATACTATTT
66 TGTAGACACACAAAATTCGTCCGGAGTTGTTCCAAGGGTTTTTATATTTATGATATATACTATTT
317343 ATAATATATATATATAGGAA
131 ATAATATATATATATAGGAA
* * * *
317363 GAAAACTCGTGTCTTTTTATCTTTTCCCTATTATCGTTACACGGCAATGGACAATTAAGGG-CAA
1 GAAAACTCATGTCTTTTTATATTTGCCCTATTATCGTTACACGACAATGGACAA-TAAGGGACAA
* * * *
317427 CTGTAGACACAC-ATATTCGTCCGGAGTTGTTCCAAGGGTTTTTATATTTATGCTATATAGTGTT
65 CTGTAGACACACAAAATTCGTCCGGAGTTGTTCCAAGGGTTTTTATATTTATGATATATACTATT
*
317491 TATAAT-TTTATATATA
130 TATAATATATATATATA
317507 ATATAAATAA
Statistics
Matches: 127, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
148 9 0.07
149 53 0.42
150 60 0.47
151 5 0.04
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.39
Consensus pattern (150 bp):
GAAAACTCATGTCTTTTTATATTTGCCCTATTATCGTTACACGACAATGGACAATAAGGGACAAC
TGTAGACACACAAAATTCGTCCGGAGTTGTTCCAAGGGTTTTTATATTTATGATATATACTATTT
ATAATATATATATATAGGAA
Found at i:317551 original size:42 final size:44
Alignment explanation
Indices: 317503--317586 Score: 109
Period size: 42 Copynumber: 1.9 Consensus size: 44
317493 TAATTTTATA
* *
317503 TATAATATAAATAATTTTT-AAA-ATATAGTTTTTAAAAATGCG
1 TATAATATAAACAATTTTTAAAACATATAGTTTTGAAAAATGCG
* *
317545 TATAATATATACAATTTTTGAAAACATATTGTTTTGAAAAAT
1 TATAATATAAACAATTTTT-AAAACATATAGTTTTGAAAAAT
317587 ATAATATATT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
42 17 0.49
44 3 0.09
45 15 0.43
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (44 bp):
TATAATATAAACAATTTTTAAAACATATAGTTTTGAAAAATGCG
Found at i:317680 original size:2 final size:2
Alignment explanation
Indices: 317675--317711 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
317665 TAGTTTTTTA
317675 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT
317712 TATTATTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:317732 original size:10 final size:10
Alignment explanation
Indices: 317709--317778 Score: 53
Period size: 10 Copynumber: 7.4 Consensus size: 10
317699 ATATGATATA
317709 TATTATTA-T
1 TATTATTACT
317718 TATTATTACT
1 TATTATTACT
317728 TATTATGTA-T
1 TATTAT-TACT
317738 TATTA-TAC-
1 TATTATTACT
*
317746 -AGTATTTAC-
1 TATTA-TTACT
*
317755 TATTATTATT
1 TATTATTACT
*
317765 TATTTTTACT
1 TATTATTACT
317775 TATT
1 TATT
317779 TATTTTACTT
Statistics
Matches: 49, Mismatches: 5, Indels: 13
0.73 0.07 0.19
Matches are distributed among these distances:
7 3 0.06
8 2 0.04
9 14 0.29
10 28 0.57
11 2 0.04
ACGTcount: A:0.30, C:0.06, G:0.03, T:0.61
Consensus pattern (10 bp):
TATTATTACT
Found at i:317763 original size:3 final size:3
Alignment explanation
Indices: 317709--317743 Score: 52
Period size: 3 Copynumber: 11.0 Consensus size: 3
317699 ATATGATATA
317709 TAT TAT TAT TAT TAT TACT TAT TAT GTAT TAT TAT
1 TAT TAT TAT TAT TAT TA-T TAT TAT -TAT TAT TAT
317744 ACAGTATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 24 0.80
4 6 0.20
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:317779 original size:14 final size:14
Alignment explanation
Indices: 317760--317793 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
317750 TTTACTATTA
317760 TTATTTATTTTTAC-
1 TTATTTA-TTTTACT
317774 TTATTTATTTTACT
1 TTATTTATTTTACT
317788 TTATTT
1 TTATTT
317794 TGTTTTCAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (14 bp):
TTATTTATTTTACT
Found at i:323945 original size:21 final size:21
Alignment explanation
Indices: 323921--323963 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
323911 GTTGATCGGT
*
323921 TAGAATGTCACATGGAACCAC
1 TAGAATGCCACATGGAACCAC
*
323942 TAGAATGCCACTTGGAACCAC
1 TAGAATGCCACATGGAACCAC
323963 T
1 T
323964 TTAAAAATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.21
Consensus pattern (21 bp):
TAGAATGCCACATGGAACCAC
Found at i:327864 original size:27 final size:27
Alignment explanation
Indices: 327834--327918 Score: 152
Period size: 27 Copynumber: 3.1 Consensus size: 27
327824 AGGGAAAATG
*
327834 GATTTCATTCATTCTATGATGAAATTC
1 GATTTCATCCATTCTATGATGAAATTC
327861 GATTTCATCCATTCTATGATGAAATTC
1 GATTTCATCCATTCTATGATGAAATTC
*
327888 GATTTCATCCATTCTATGATGAAATTA
1 GATTTCATCCATTCTATGATGAAATTC
327915 GATT
1 GATT
327919 CCCTTGTTAG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 56 1.00
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (27 bp):
GATTTCATCCATTCTATGATGAAATTC
Found at i:328520 original size:247 final size:249
Alignment explanation
Indices: 328069--328815 Score: 951
Period size: 265 Copynumber: 2.9 Consensus size: 249
328059 TTTATTTTGG
328069 TCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGAATATATATATATATATAT
1 TCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGAA-A-ATATATATA-A-AT
* * *
328134 TTACCTTATATATTTAGAAATAATTACAATAATACCCCTCTATATATAA--TTTTTTCAATTAAA
62 TTACCTTATATATTTAGGAATAATTACAATAATACCTCTCTATATATAATTTTTTTTCAATTAAG
*
328197 TCACTATTTTTATTGAATAAAAATAAGTTTTTTATTAT---TTCGGGTCGGGTTTCTAATTCATA
127 TCACTATTTTTATTGAATAAAAATAATTTTTTTATT-TCGGTTC-GGTCGGGTTTCTAATTCATA
328259 TATTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGG-TTTTTTTAAATGTGATA-T
190 TATT---GTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGTTTTTTTTAAATGTGATACT
* *
328320 TCGGGTCGAGTCGAGTTCGGGTTTAGGGTGAAAAATATCCGACCCGAAAATATATATAAATTTAC
1 TCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGAAAATATATATAAATTTAC
328385 CTTATATATTTAGGAATAATTACAATAATACCTCTCTATATATAATTTTTTTTTCAATTAAGTCA
66 CTTATATATTTAGGAATAATTACAATAATACCTCTCTATATATAA-TTTTTTTTCAATTAAGTCA
*
328450 CTATTTTTATTGAATAAAAATAATTTTTTTATTTCGGTTCGGATCGGATTTCTAATTCATATATT
130 CTATTTTTATTGAATAAAAATAATTTTTTTATTTCGGTTCGG-TCGGGTTTCTAATTCATATATT
*
328515 CGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGTGTCGGTTTTTTTTAAGTGTGATACT
194 ---GTCGGGTCGGGTGAAACTTTATTTTGGTC--G--G-GTCGGTTTTTTTTAAATGTGATACT
* * *
328579 T-GGGTCGGGTCG-GGTCGGGTTTAGGGTGAAAAATACCCGACCCGACCCGACCCAAAAAAATAT
1 TCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAAT-----ACCCGACCCGA---AAATATATAT
* * * *
328642 AATTTTACCTTATATATTTATGAAAAATTACAATAATAACTCTCTCTATATAT-ATTTGTTTTCA
58 AAATTTACCTTATATATTTAGGAATAATTACAATAAT-AC-CTCTCTATATATAATTTTTTTTCA
* * *
328706 ATTAAGCCACTGTTTTTATTGAATAAAAATAATTTTTTATTATTTCGGGTCAGGTCGGGTTTCTA
121 ATTAAGTCACTATTTTTATTGAATAAAAATAA-TTTTT-TTATTTCGGTTC-GGTCGGGTTTCTA
*
328771 ATTCATATA-T-TCGGGTTGGGTGAAACTTTATTTTGGTCGGGTCGG
183 ATTCATATATTGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGG
328816 GTCTCGGATG
Statistics
Matches: 447, Mismatches: 22, Indels: 48
0.86 0.04 0.09
Matches are distributed among these distances:
247 49 0.11
248 1 0.00
249 10 0.02
250 49 0.11
251 48 0.11
252 56 0.13
254 1 0.00
256 1 0.00
257 31 0.07
258 27 0.06
259 2 0.00
260 1 0.00
262 37 0.08
265 81 0.18
266 9 0.02
267 42 0.09
268 2 0.00
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.40
Consensus pattern (249 bp):
TCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGAAAATATATATAAATTTAC
CTTATATATTTAGGAATAATTACAATAATACCTCTCTATATATAATTTTTTTTCAATTAAGTCAC
TATTTTTATTGAATAAAAATAATTTTTTTATTTCGGTTCGGTCGGGTTTCTAATTCATATATTGT
CGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGTTTTTTTTAAATGTGATACT
Found at i:328882 original size:10 final size:10
Alignment explanation
Indices: 328867--328896 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
328857 GGACCAAAAA
328867 CCCGACCCAT
1 CCCGACCCAT
*
328877 CCCGACCCAA
1 CCCGACCCAT
328887 CCCGACCCAT
1 CCCGACCCAT
328897 GGCCATCCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.23, C:0.60, G:0.10, T:0.07
Consensus pattern (10 bp):
CCCGACCCAT
Found at i:329061 original size:15 final size:15
Alignment explanation
Indices: 329041--329070 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
329031 ATTTATAAAA
*
329041 CAAAAAAAAATTAAG
1 CAAAAAAAAAATAAG
329056 CAAAAAAAAAATAAG
1 CAAAAAAAAAATAAG
329071 AAGGGCAATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.07, G:0.07, T:0.10
Consensus pattern (15 bp):
CAAAAAAAAAATAAG
Found at i:329230 original size:18 final size:17
Alignment explanation
Indices: 329193--329239 Score: 67
Period size: 18 Copynumber: 2.7 Consensus size: 17
329183 TATGGAATTG
329193 GATTCCAATTCCTAACA
1 GATTCCAATTCCTAACA
* *
329210 GATTCAAATTCCTTCACA
1 GATTCCAATTCC-TAACA
329228 GATTCCAATTCC
1 GATTCCAATTCC
329240 CTCATAAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.32, C:0.30, G:0.06, T:0.32
Consensus pattern (17 bp):
GATTCCAATTCCTAACA
Found at i:330106 original size:20 final size:21
Alignment explanation
Indices: 330073--330135 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
330063 CCTTTAACTG
*
330073 AATTGTACTAATTAATATAAA
1 AATTATACTAATTAATATAAA
* * *
330094 AATT-TATTAATTAAAATTTAA
1 AATTATACTAATTAATA-TAAA
*
330115 TATTATACTAATTAATATAAA
1 AATTATACTAATTAATATAAA
330136 GGTCAATATA
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
20 10 0.30
21 13 0.39
22 10 0.30
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (21 bp):
AATTATACTAATTAATATAAA
Found at i:331345 original size:18 final size:19
Alignment explanation
Indices: 331309--331357 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
331299 TATGGGGAGG
*
331309 ATAAAATTATATTTTTAAA
1 ATAAAATTATATTTATAAA
331328 A-AAAATTAT-TATTATAAA
1 ATAAAATTATAT-TTATAAA
*
331346 ATAAAAATATAT
1 ATAAAATTATAT
331358 AAATTATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 1 0.04
18 15 0.60
19 8 0.32
20 1 0.04
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
ATAAAATTATATTTATAAA
Found at i:331791 original size:70 final size:70
Alignment explanation
Indices: 331703--331844 Score: 257
Period size: 70 Copynumber: 2.0 Consensus size: 70
331693 AAATTTTCCC
*
331703 TCGTACCAATAGATAATAACTTGAAAATGATCAAATTAATAATTATAAAATGATACCAACGACTA
1 TCGTACCAATAGATAATAACTTGAAAATGATCAAATTAATAATTATAAAATGATACCAACAACTA
331768 ATTTG
66 ATTTG
* *
331773 TCGTACCATTAGATAATAACTTGAAAATGATCAAATTAATAATTATAAAATGATACTAACAACTA
1 TCGTACCAATAGATAATAACTTGAAAATGATCAAATTAATAATTATAAAATGATACCAACAACTA
331838 ATTTG
66 ATTTG
331843 TC
1 TC
331845 TAATAAGACG
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.32
Consensus pattern (70 bp):
TCGTACCAATAGATAATAACTTGAAAATGATCAAATTAATAATTATAAAATGATACCAACAACTA
ATTTG
Found at i:335630 original size:20 final size:20
Alignment explanation
Indices: 335608--335646 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
335598 TTTAAATATT
335608 TTTTA-TTTTTATAAATTTA
1 TTTTACTTTTTATAAATTTA
335627 TTTTACTTTTTATAAATTTA
1 TTTTACTTTTTATAAATTTA
335647 AATTTTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTACTTTTTATAAATTTA
Found at i:343929 original size:3 final size:3
Alignment explanation
Indices: 343915--343975 Score: 113
Period size: 3 Copynumber: 20.0 Consensus size: 3
343905 CAGATCATTT
343915 AGG AGTG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
1 AGG AG-G AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
343961 AGG AGG AGG AGG AGG
1 AGG AGG AGG AGG AGG
343976 GTTAACTGCC
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 54 0.95
4 3 0.05
ACGTcount: A:0.33, C:0.00, G:0.66, T:0.02
Consensus pattern (3 bp):
AGG
Found at i:344640 original size:55 final size:57
Alignment explanation
Indices: 344561--344732 Score: 190
Period size: 55 Copynumber: 3.0 Consensus size: 57
344551 AATTATGATC
* * *
344561 CTTATTCTAAATTAGTTCCT-AAACTTTTAAATATTTCAATTTCATCCCTAAATTATGA
1 CTTATTCTAAATTAG-TCCTCAAACTTTTGAACATTTCAATTTCATCCC-AAATTATAA
* * *
344619 -TT-TTC-AGATTAGTCCTCAAACTTTTGACCATTTCAATTTCATCCCCAAACTATAA
1 CTTATTCTAAATTAGTCCTCAAACTTTTGAACATTTCAATTTCAT-CCCAAATTATAA
* *
344674 TCTTCATTCTAAATTGGTCCCCAAACTTTTTGAACATTTCAATTTCATCCCAAATTATA
1 -CTT-ATTCTAAATTAGTCCTCAAAC-TTTTGAACATTTCAATTTCATCCCAAATTATA
344733 TGTATATACT
Statistics
Matches: 95, Mismatches: 11, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
54 4 0.04
55 35 0.37
56 6 0.06
57 4 0.04
59 3 0.03
60 23 0.24
61 20 0.21
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (57 bp):
CTTATTCTAAATTAGTCCTCAAACTTTTGAACATTTCAATTTCATCCCAAATTATAA
Found at i:344957 original size:60 final size:60
Alignment explanation
Indices: 344852--345005 Score: 184
Period size: 60 Copynumber: 2.6 Consensus size: 60
344842 TTTGGATGAA
* *** *
344852 TTTAGGGATAAAATTGGAATATTCAAAAGTTTGGGGACAAATTTAGAATAAGAGTCATAG
1 TTTAGGGATAAAATTAGAATATTCAAAAGTTTAAAGACAAATTTAGAATAAGAGTAATAG
* * * *
344912 TTT-GAGGATAAAATTAGAATGTTCAAAAGTTTAAAGACTAGTTTAGAATGAGAGTAATAG
1 TTTAG-GGATAAAATTAGAATATTCAAAAGTTTAAAGACAAATTTAGAATAAGAGTAATAG
* * *
344972 TTTAGGGATGAAATTAAAATATTTAAAAGTTTAA
1 TTTAGGGATAAAATTAGAATATTCAAAAGTTTAA
345006 GGATTATTTT
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
59 1 0.01
60 77 0.97
61 1 0.01
ACGTcount: A:0.44, C:0.03, G:0.21, T:0.32
Consensus pattern (60 bp):
TTTAGGGATAAAATTAGAATATTCAAAAGTTTAAAGACAAATTTAGAATAAGAGTAATAG
Found at i:345671 original size:23 final size:23
Alignment explanation
Indices: 345645--345695 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
345635 TAAAATATCA
*
345645 AAAGACAAAGAAAAACATGTCAT
1 AAAGACAAAGAAAAACATGCCAT
* * *
345668 AAAGACAGAGATAAACGTGCCAT
1 AAAGACAAAGAAAAACATGCCAT
345691 AAAGA
1 AAAGA
345696 AAGAGAACAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.57, C:0.14, G:0.18, T:0.12
Consensus pattern (23 bp):
AAAGACAAAGAAAAACATGCCAT
Found at i:349421 original size:23 final size:22
Alignment explanation
Indices: 349394--349465 Score: 63
Period size: 23 Copynumber: 3.1 Consensus size: 22
349384 ATTTCATCTT
349394 AACATGTTAGCAGACATTAAATG
1 AACATGTTAGCA-ACATTAAATG
* ** *
349417 AACATATTCAAAAACATTAAACG
1 AACATGTT-AGCAACATTAAATG
* *
349440 AACATGTTTGCCAACACTAAATG
1 AACATGTTAG-CAACATTAAATG
349463 AAC
1 AAC
349466 TAACATGAAC
Statistics
Matches: 37, Mismatches: 10, Indels: 4
0.73 0.20 0.08
Matches are distributed among these distances:
23 35 0.95
24 2 0.05
ACGTcount: A:0.47, C:0.18, G:0.11, T:0.24
Consensus pattern (22 bp):
AACATGTTAGCAACATTAAATG
Found at i:349518 original size:41 final size:40
Alignment explanation
Indices: 349462--349542 Score: 126
Period size: 41 Copynumber: 2.0 Consensus size: 40
349452 AACACTAAAT
* *
349462 GAACTAACATGAACATATTCAAAAATAAATAAAGGAACAC
1 GAACTAACATAAACATATTCAAAAATAAATAAACGAACAC
*
349502 GAACTGAACATAAACATCTTCAAAAATAAATAAACGAACAC
1 GAACT-AACATAAACATATTCAAAAATAAATAAACGAACAC
349543 AAACGAAACA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
40 5 0.14
41 32 0.86
ACGTcount: A:0.57, C:0.17, G:0.09, T:0.17
Consensus pattern (40 bp):
GAACTAACATAAACATATTCAAAAATAAATAAACGAACAC
Found at i:349549 original size:45 final size:43
Alignment explanation
Indices: 349452--349549 Score: 112
Period size: 41 Copynumber: 2.3 Consensus size: 43
349442 CATGTTTGCC
* *
349452 AACACTAAATGAACTAACATGAACATATTCAAAAATAAATAAAG
1 AACAC-AAACGAACTAACATAAACATATTCAAAAATAAATAAAG
* *
349496 GA-AC--ACGAACTGAACATAAACATCTTCAAAAATAAATAAACG
1 AACACAAACGAACT-AACATAAACATATTCAAAAATAAATAAA-G
349538 AACACAAACGAA
1 AACACAAACGAA
349550 ACATTATTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
40 6 0.14
41 26 0.59
42 2 0.05
43 4 0.09
44 1 0.02
45 5 0.11
ACGTcount: A:0.58, C:0.17, G:0.08, T:0.16
Consensus pattern (43 bp):
AACACAAACGAACTAACATAAACATATTCAAAAATAAATAAAG
Found at i:351789 original size:21 final size:21
Alignment explanation
Indices: 351748--351789 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
351738 GTTTACATAA
* *
351748 TTTATCAGTTTAATCATATTT
1 TTTATCAATTTAATCAAATTT
351769 TTTATTCAATTTAAT-AAATTT
1 TTTA-TCAATTTAATCAAATTT
351790 AATCTCCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.57
Consensus pattern (21 bp):
TTTATCAATTTAATCAAATTT
Found at i:351860 original size:30 final size:28
Alignment explanation
Indices: 351824--351882 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 28
351814 TATCATCACC
351824 TAATTAATTTT-TTTTAATATTTCAATTAAT
1 TAATTAATTTTATTTT--TATTT-AATTAAT
351854 TAATTAATTTTATTTTTATTTAATTAAT
1 TAATTAATTTTATTTTTATTTAATTAAT
351882 T
1 T
351883 GGTATAGCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
28 8 0.29
29 5 0.18
30 11 0.39
31 4 0.14
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.63
Consensus pattern (28 bp):
TAATTAATTTTATTTTTATTTAATTAAT
Found at i:356007 original size:3 final size:3
Alignment explanation
Indices: 355993--356044 Score: 52
Period size: 3 Copynumber: 17.7 Consensus size: 3
355983 ATCCCGGTTC
* * * * *
355993 TAT TAT TTT TAT TAT AAT AAT TAT AAT TAT AAT TAT T-T TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
356040 TAT TA
1 TAT TA
356045 AATAATTTTA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:358076 original size:125 final size:124
Alignment explanation
Indices: 357849--358078 Score: 313
Period size: 125 Copynumber: 1.8 Consensus size: 124
357839 AATATTTTAG
* * *
357849 TTATTTATTTTTTAATGTTGAAGGAAAGAGCTGTCTTAAAGCAACTAGAAGTCCTTTTCTAAATA
1 TTATTTATTTTTTAATGATCAAAGAAAGAGCTGTCTTAAAGCAACTAGAAGTCCTTTTCTAAATA
* *
357914 TTTTTAAATAAATAAATATCTTACTATATTAAAATAAATTTTTTAATTGTTTTAATTAT
66 TTTCTAAATAAATAAATATCTTACTATATAAAAATAAATTTTTTAATTGTTTTAATTAT
* * *
357973 TTATTTATTTTTTTAAT-ATCAAAGAAGAGAGCTGTCTTAAGGCACCTAGAAGTCCTTTTCT-TA
1 TTATTTA-TTTTTTAATGATCAAAGAA-AGAGCTGTCTTAAAGCAACTAGAAGTCCTTTTCTAAA
* *
358036 TATTTCTAAATAAATAAATATTTTA-TTTATAAATATATAAATT
64 TATTTCTAAATAAATAAATATCTTACTATATAAA-A-ATAAATT
358079 AATATATATT
Statistics
Matches: 92, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
123 6 0.07
124 38 0.41
125 48 0.52
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.45
Consensus pattern (124 bp):
TTATTTATTTTTTAATGATCAAAGAAAGAGCTGTCTTAAAGCAACTAGAAGTCCTTTTCTAAATA
TTTCTAAATAAATAAATATCTTACTATATAAAAATAAATTTTTTAATTGTTTTAATTAT
Found at i:358105 original size:27 final size:31
Alignment explanation
Indices: 358042--358102 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
358032 CTTATATTTC
* *
358042 TAAATAAATAAATATTTTATTTATAAATATA
1 TAAATTAATAAATATTTTATTCATAAATATA
* *
358073 TAAATTAATATATATTTT-TTCATAATTATA
1 TAAATTAATAAATATTTTATTCATAAATATA
358103 ATTTTAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 10 0.38
31 16 0.62
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (31 bp):
TAAATTAATAAATATTTTATTCATAAATATA
Found at i:360148 original size:7 final size:7
Alignment explanation
Indices: 360132--360173 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
360122 TTTTCATACA
360132 TGCA-TT
1 TGCATTT
360138 TGCATTT
1 TGCATTT
360145 TGCATATT
1 TGCAT-TT
360153 TGCATTT
1 TGCATTT
* *
360160 TTCATTG
1 TGCATTT
360167 TGCATTT
1 TGCATTT
360174 ATACTCTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.17, C:0.14, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:360155 original size:15 final size:15
Alignment explanation
Indices: 360135--360173 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
360125 TCATACATGC
360135 ATTTGCATTTTGCAT
1 ATTTGCATTTTGCAT
*
360150 ATTTGCATTTTTCAT
1 ATTTGCATTTTGCAT
*
360165 -TGTGCATTT
1 ATTTGCATTT
360174 ATACTCTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.18, C:0.13, G:0.13, T:0.56
Consensus pattern (15 bp):
ATTTGCATTTTGCAT
Found at i:364459 original size:115 final size:115
Alignment explanation
Indices: 364299--364870 Score: 930
Period size: 115 Copynumber: 5.0 Consensus size: 115
364289 AAGTGCCATG
364299 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * *
364364 TGATTTGGTATGAACCCCAAAAACCAATCATTAGATTTGAAAAATGAATG
66 TGGTTTGGTATGAACCCCAAAAACCAATCATTAGATTTGAAAGATGAATT
*
364414 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * *
364479 TGATTTGGTATGAACCCAAAAAACCAATCATTGGATTTGAAAGATGAATT
66 TGGTTTGGTATGAACCCCAAAAACCAATCATTAGATTTGAAAGATGAATT
*
364529 TGCTCAGAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * *
364594 TGGTTTGGTATGAATCACAAAAACCAATCATTGGATTTGAAAGATGAATT
66 TGGTTTGGTATGAACCCCAAAAACCAATCATTAGATTTGAAAGATGAATT
364644 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
*
364709 TGGTTTGGTATGAACCCCAAAAACTAATCATTAGATTTGAAAGATGAATT
66 TGGTTTGGTATGAACCCCAAAAACCAATCATTAGATTTGAAAGATGAATT
* * * *
364759 TGCTCATGGTAGAAATAAGGAGGCCCAATAGTATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * * * * * *
364824 TGGTTCGGTAGGAACCAC-AGAACCAATCATTGGAATTAAAAGATGAA
66 TGGTTTGGTATGAACCCCAAAAACCAATCATTAGATTTGAAAGATGAA
364871 CTGCATGATC
Statistics
Matches: 429, Mismatches: 28, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
114 24 0.06
115 405 0.94
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (115 bp):
TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGGTTTGGTATGAACCCCAAAAACCAATCATTAGATTTGAAAGATGAATT
Found at i:366879 original size:54 final size:54
Alignment explanation
Indices: 366797--367060 Score: 393
Period size: 54 Copynumber: 4.9 Consensus size: 54
366787 AGAAATCTTG
* * * * * *
366797 GCAGAAGCCACAGAAAAAGACGAATGTGTTGTCAAACGCTTTACGAACGTCTGA
1 GCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
* * * * *
366851 GCAGAAGCCACAGAAAAGGACGAATGTGTTGTCAAACGCTTTACGAACGTCTGA
1 GCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
*
366905 GCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
1 GCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
*
366959 GCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
1 GCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
* *
367013 GCAGAAGCCACAGGAAAGGATGAATGCGCTGTCAAATGTTTTACGAAC
1 GCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
367061 CTGCTATTCT
Statistics
Matches: 200, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 200 1.00
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (54 bp):
GCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
Found at i:367452 original size:22 final size:22
Alignment explanation
Indices: 367424--367483 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
367414 TCTACATCTA
*
367424 CACTCTTCAAAGATGATAGATT
1 CACTCTTCAAAGATGACAGATT
367446 CACTCTTCAAAGATGACAGATT
1 CACTCTTCAAAGATGACAGATT
* *
367468 CTCTTTTCAAAGATGA
1 CACTCTTCAAAGATGA
367484 AAGCTTTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (22 bp):
CACTCTTCAAAGATGACAGATT
Found at i:368425 original size:37 final size:37
Alignment explanation
Indices: 368337--368542 Score: 134
Period size: 37 Copynumber: 5.6 Consensus size: 37
368327 TTTTCAAATA
** ** *
368337 AAATTTATCTCACTTGAGATTGTTTTTCTT-AAA-AC
1 AAATTTATCTCACTTGAGACAGTTTCACTTGAAACAG
* * *
368372 AAATTTGTCTCGCTTGAGACAGTTTCACTCGAAACAG
1 AAATTTATCTCACTTGAGACAGTTTCACTTGAAACAG
** ** ** *
368409 AACCTTATCTCACTTGAGATTGTTTTTCTTAAAACA-
1 AAATTTATCTCACTTGAGACAGTTTCACTTGAAACAG
* * *
368445 AATTTTGTCTCGCTTGAGACAGTTTCACTTGAAAC-G
1 AAATTTATCTCACTTGAGACAGTTTCACTTGAAACAG
** ** *
368481 AAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACA-
1 -AAATTTATCTCACTTGAGACAGTTTCACTTGAAACAG
* *
368518 AAGATTTGTCTCGCTTGAGACAGTT
1 AA-ATTTATCTCACTTGAGACAGTT
368543 ATTTTGAGTT
Statistics
Matches: 126, Mismatches: 39, Indels: 10
0.72 0.22 0.06
Matches are distributed among these distances:
35 23 0.18
36 31 0.25
37 72 0.57
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (37 bp):
AAATTTATCTCACTTGAGACAGTTTCACTTGAAACAG
Found at i:368491 original size:73 final size:71
Alignment explanation
Indices: 368336--368542 Score: 342
Period size: 73 Copynumber: 2.8 Consensus size: 71
368326 GTTTTCAAAT
368336 AAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTGTCTCGCTTGAGACAGTTTCACT
1 AAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTGTCTCGCTTGAGACAGTTTCACT
368401 CGAAAC
66 CGAAAC
**
368407 AGAACCTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTTGTCTCGCTTGAGACAGTTTCA
1 A-AAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAA-TTTGTCTCGCTTGAGACAGTTTCA
*
368472 CTTGAAAC
64 CTCGAAAC
368480 GAAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAGATTTGTCTCGCTTGAGACAGTT
1 -AAAATTTATCTCACTTGAGATTGTTTTTCTTAAAAC-AA-ATTTGTCTCGCTTGAGACAGTT
368543 ATTTTGAGTT
Statistics
Matches: 126, Mismatches: 5, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
71 1 0.01
72 36 0.29
73 64 0.51
74 24 0.19
75 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (71 bp):
AAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTGTCTCGCTTGAGACAGTTTCACT
CGAAAC
Found at i:368838 original size:76 final size:76
Alignment explanation
Indices: 368712--368942 Score: 372
Period size: 76 Copynumber: 3.0 Consensus size: 76
368702 TATTTCCCAT
*
368712 ATCTGTAAGTTCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
1 ATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
368777 GCCTTAGGGTC
66 GCCTTAGGGTC
*
368788 ATCTGTAAGTCCTGCATTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
1 ATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
368853 GCCTTAGGGTC
66 GCCTTAGGGTC
* * * * * *
368864 ATTTATAAATCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTAATATTTTCAAA
1 ATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
* *
368929 ACCTTCGGGTC
66 GCCTTAGGGTC
368940 ATC
1 ATC
368943 AGCATTACCA
Statistics
Matches: 143, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
76 143 1.00
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.35
Consensus pattern (76 bp):
ATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
GCCTTAGGGTC
Found at i:369099 original size:112 final size:112
Alignment explanation
Indices: 368959--369709 Score: 999
Period size: 112 Copynumber: 6.6 Consensus size: 112
368949 ACCAGGTAGA
* * *
368959 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAGCTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
*
369024 AACTTTTGCTCAAATTCATCACTTGATGGATCAACATTTCCAGAAGT
66 ACCTTTTGCTCAAATTCATCACTTGATGGATCAACATTTCCAGAAGT
369071 GTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
369136 ACCTTTTGCTCAAATTCATCACTTGATGGATCAACATTTCCAGAAGT
66 ACCTTTTGCTCAAATTCATCACTTGATGGATCAACATTTCCAGAAGT
*
369183 GTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* *
369248 ACATTTTGCTCTAATTCATCACTTGATGGATCAACATTTCCAGAAGT
66 ACCTTTTGCTCAAATTCATCACTTGATGGATCAACATTTCCAGAAGT
* * *
369295 GTTCATAATGAGAAGAACCCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* * **
369360 ACCTTTTGCTCTAATTCATCACTTGATAGATCAACATTTCCAGAGAAA
66 ACCTTTTGCTCAAATTCATCACTTGATGGATCAACATTTCCAGA-AGT
* * * *
369408 GTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* * * * **
369472 ACCTTTTGC-CTGAATTCATCACTTGATGAATTAACTTTTCCAGAGAAA
66 ACCTTTTGCTC-AAATTCATCACTTGATGGATCAACATTTCCAGA-AGT
* * * *
369520 GTTCATAATGAGAAGAACTTATCTGAAG-ATGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
** * * * **
369584 ACCTTTGTTTGACTCTATCACA-GAATGAGATAGATCAACATCAACATTTCCAGAAGT
66 ACC--T-TTTG-CTC-A--A-ATTCATCA-CTTGAT--GGATCAACATTTCCAGAAGT
* * *
369641 GTTCATAATGAGAAGAACTCATCTTAAGAAAGAA-AAGAAATTCATAATGAGAAGAATTTGTTCA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
369705 ACCTT
66 ACCTT
369710 GCCTTAATTT
Statistics
Matches: 582, Mismatches: 43, Indels: 22
0.90 0.07 0.03
Matches are distributed among these distances:
111 1 0.00
112 460 0.79
113 27 0.05
114 1 0.00
115 4 0.01
116 1 0.00
117 2 0.00
118 1 0.00
119 5 0.01
120 5 0.01
121 58 0.10
122 17 0.03
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (112 bp):
GTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
ACCTTTTGCTCAAATTCATCACTTGATGGATCAACATTTCCAGAAGT
Found at i:370028 original size:3 final size:3
Alignment explanation
Indices: 370014--370065 Score: 52
Period size: 3 Copynumber: 17.7 Consensus size: 3
370004 ATCCCGGTTC
* * * * *
370014 TAT TAT TTT TAT TAT AAT AAT TAT AAT TAT AAT TAT T-T TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
370061 TAT TA
1 TAT TA
370066 AATAATTTTA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:371759 original size:20 final size:19
Alignment explanation
Indices: 371730--371785 Score: 58
Period size: 23 Copynumber: 2.7 Consensus size: 19
371720 TTTGCAATAT
371730 TATTTTATTATTACTTTTA
1 TATTTTATTATTACTTTTA
*
371749 TATTTTAATTATTGCTTTAATTA
1 TATTTT-ATTATTAC-TT--TTA
371772 TTATTTTATTATTA
1 -TATTTTATTATTA
371786 TCTTAGTCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 6 0.20
20 7 0.23
21 2 0.07
23 9 0.30
24 6 0.20
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.66
Consensus pattern (19 bp):
TATTTTATTATTACTTTTA
Found at i:371784 original size:11 final size:11
Alignment explanation
Indices: 371727--371786 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
371717 TTATTTGCAA
371727 TATTATTTTAT
1 TATTATTTTAT
371738 TATTACTTTTA-
1 TATTA-TTTTAT
*
371749 TA-T-TTTAAT
1 TATTATTTTAT
* *
371758 TATTGCTTTAAT
1 TATT-ATTTTAT
371770 TATTATTTTAT
1 TATTATTTTAT
371781 TATTAT
1 TATTAT
371787 CTTAGTCATA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
8 4 0.10
9 2 0.05
10 2 0.05
11 18 0.44
12 15 0.37
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (11 bp):
TATTATTTTAT
Found at i:372141 original size:125 final size:124
Alignment explanation
Indices: 371914--372143 Score: 286
Period size: 125 Copynumber: 1.8 Consensus size: 124
371904 AATATTTTAG
* * *
371914 TTATTTATTTTTTAATGTTGAAGGAAAGAGTTGTCTTAAAGCAACTAGAAGCCCTTTTCTAAATA
1 TTATTTATTTTTTAATGATCAAAGAAAGAGTTGTCTTAAAGCAACTAGAAGCCCTTTTCTAAATA
* *
371979 TTTTTAAAAAAATAAATATCTTACTATATTAAAATAAATTTTTTAATTGTTTTAATTAA
66 TTTCTAAAAAAATAAATATCTTACTATATAAAAATAAATTTTTTAATTGTTTTAATTAA
* * ** *
372038 TTATTTATTTTTTTAAT-ATCAAAGAAGAGAGTTGTCTTAAGGCACCTAGAAGTTCTTTTCT-TA
1 TTATTTA-TTTTTTAATGATCAAAGAA-AGAGTTGTCTTAAAGCAACTAGAAGCCCTTTTCTAAA
* * *
372101 TATTTCTAAATAAATAAATATTTTA-TTTATAAATATATAAATT
64 TATTTCTAAAAAAATAAATATCTTACTATATAAA-A-ATAAATT
372144 AATATATATT
Statistics
Matches: 89, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
123 6 0.07
124 37 0.42
125 46 0.52
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.45
Consensus pattern (124 bp):
TTATTTATTTTTTAATGATCAAAGAAAGAGTTGTCTTAAAGCAACTAGAAGCCCTTTTCTAAATA
TTTCTAAAAAAATAAATATCTTACTATATAAAAATAAATTTTTTAATTGTTTTAATTAA
Found at i:376552 original size:24 final size:25
Alignment explanation
Indices: 376499--376552 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
376489 ATTATCATGA
376499 TTCATTAATGGCAATTTTAAAATTT
1 TTCATTAATGGCAATTTTAAAATTT
* *
376524 CTCATTAATTG-AATTTT-AAATTCT
1 TTCATTAATGGCAATTTTAAAATT-T
376548 TTCAT
1 TTCAT
376553 ATTATAAAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 5 0.20
24 11 0.44
25 9 0.36
ACGTcount: A:0.33, C:0.11, G:0.06, T:0.50
Consensus pattern (25 bp):
TTCATTAATGGCAATTTTAAAATTT
Found at i:381131 original size:60 final size:54
Alignment explanation
Indices: 381065--381185 Score: 152
Period size: 60 Copynumber: 2.1 Consensus size: 54
381055 AAAATCTTGC
* *
381065 GTTACAAAAAGCGATGCTATATAAAGACCAACAGAAGGAGGAGTTAACAACTACTCTTCA
1 GTTACAAAAACCAATGCTATATAAAGACCAAC---A--A-GAGTTAACAACTACTCTTCA
* *
381125 GTTACAACAACCAATGCTATATAAAGACCAACAAGAGTTAACAACTATTCTTCA
1 GTTACAAAAACCAATGCTATATAAAGACCAACAAGAGTTAACAACTACTCTTCA
381179 GTTACAA
1 GTTACAA
381186 CAACTTAACC
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
54 26 0.46
55 1 0.02
57 1 0.02
60 29 0.51
ACGTcount: A:0.44, C:0.20, G:0.14, T:0.22
Consensus pattern (54 bp):
GTTACAAAAACCAATGCTATATAAAGACCAACAAGAGTTAACAACTACTCTTCA
Found at i:381169 original size:54 final size:57
Alignment explanation
Indices: 381078--381189 Score: 167
Period size: 54 Copynumber: 2.0 Consensus size: 57
381068 ACAAAAAGCG
381078 ATGCTATATAAAGACCAACAGAAGGAGGAGTTAACAACTACTCTTCAGTTACAACAACCA
1 ATGCTATATAAAGACCAAC--AA-GAGGAGTTAACAACTACTCTTCAGTTACAACAACCA
*
381138 ATGCTATATAAAGACCAAC-A-A-GAGTTAACAACTATTCTTCAGTTACAACAAC
1 ATGCTATATAAAGACCAACAAGAGGAGTTAACAACTACTCTTCAGTTACAACAAC
381190 TTAACCACCT
Statistics
Matches: 51, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
54 30 0.59
55 1 0.02
57 1 0.02
60 19 0.37
ACGTcount: A:0.44, C:0.21, G:0.12, T:0.22
Consensus pattern (57 bp):
ATGCTATATAAAGACCAACAAGAGGAGTTAACAACTACTCTTCAGTTACAACAACCA
Found at i:381544 original size:21 final size:20
Alignment explanation
Indices: 381520--381558 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
381510 TAATGAATCA
*
381520 CTATGTATTTATAAATATGAT
1 CTATATATTT-TAAATATGAT
*
381541 CTATATATTTTAATTATG
1 CTATATATTTTAAATATG
381559 TTTCAGCTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.36, C:0.05, G:0.08, T:0.51
Consensus pattern (20 bp):
CTATATATTTTAAATATGAT
Found at i:384019 original size:18 final size:18
Alignment explanation
Indices: 383998--384056 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
383988 GATATACTGG
383998 AATTGGTTCCTATAACAT
1 AATTGGTTCCTATAACAT
* * *
384016 AATT--TACTTGATATACTGT
1 AATTGGTTCCT-ATA-AC-AT
384035 AATTGGTTCCTATAACAT
1 AATTGGTTCCTATAACAT
384053 AATT
1 AATT
384057 TACGTAAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 10
0.65 0.13 0.22
Matches are distributed among these distances:
16 3 0.10
17 3 0.10
18 11 0.37
19 7 0.23
20 3 0.10
21 3 0.10
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (18 bp):
AATTGGTTCCTATAACAT
Found at i:384027 original size:37 final size:37
Alignment explanation
Indices: 383986--384059 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
383976 AGGGGTCCGT
383986 TTGATATACTGGAATTGGTTCCTATAACATAATTTAC
1 TTGATATACTGGAATTGGTTCCTATAACATAATTTAC
*
384023 TTGATATACTGTAATTGGTTCCTATAACATAATTTAC
1 TTGATATACTGGAATTGGTTCCTATAACATAATTTAC
384060 GTAAAATGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (37 bp):
TTGATATACTGGAATTGGTTCCTATAACATAATTTAC
Found at i:384235 original size:30 final size:29
Alignment explanation
Indices: 384201--384270 Score: 86
Period size: 30 Copynumber: 2.4 Consensus size: 29
384191 TTAATTTTAT
* * *
384201 AAAATTTATTTACGTGAATTGAATTATTTG
1 AAAATTAATTTACATGAAATGAATTA-TTG
*
384231 AAAATTAATTTACATTAAATGAATTATTG
1 AAAATTAATTTACATGAAATGAATTATTG
*
384260 AAAAATAATTT
1 AAAATTAATTT
384271 TTAAAAAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 13 0.37
30 22 0.63
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.43
Consensus pattern (29 bp):
AAAATTAATTTACATGAAATGAATTATTG
Found at i:384279 original size:29 final size:30
Alignment explanation
Indices: 384220--384279 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 30
384210 TTACGTGAAT
* **
384220 TGAATTATTTGAAAATTAATTTACATTAAA
1 TGAATTATTTGAAAAATAATTTACAAAAAA
**
384250 TGAATTA-TTGAAAAATAATTTTTAAAAAA
1 TGAATTATTTGAAAAATAATTTACAAAAAA
384279 T
1 T
384280 ATTTTATGGT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.42
Consensus pattern (30 bp):
TGAATTATTTGAAAAATAATTTACAAAAAA
Found at i:385102 original size:15 final size:15
Alignment explanation
Indices: 385051--385107 Score: 57
Period size: 15 Copynumber: 3.8 Consensus size: 15
385041 TCAAAAAATA
385051 TAATATTATTAA-AAT
1 TAATATT-TTAATAAT
*
385066 TAA-ATTAT-ATATAT
1 TAATATTTTAATA-AT
385080 TAAATATTTTAATAAT
1 T-AATATTTTAATAAT
385096 TAATATTTTAAT
1 TAATATTTTAAT
385108 TAAAATAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
12 1 0.03
13 2 0.06
14 6 0.17
15 16 0.46
16 7 0.20
17 3 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TAATATTTTAATAAT
Found at i:386306 original size:22 final size:22
Alignment explanation
Indices: 386278--386319 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
386268 ATATTTTTTA
386278 ATTTTTTAAT-AATAAAAATATT
1 ATTTTTTAATGAA-AAAAATATT
386300 ATTTTTTAATGAAAAAAATA
1 ATTTTTTAATGAAAAAAATA
386320 AAAAAACTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
ATTTTTTAATGAAAAAAATATT
Found at i:396920 original size:2 final size:2
Alignment explanation
Indices: 396913--396937 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
396903 ATCGTCCCTA
396913 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
396938 GTTTCAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:400721 original size:15 final size:15
Alignment explanation
Indices: 400701--400733 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
400691 TAAAATCTTT
*
400701 TTTTCCCGTTCTTGA
1 TTTTCCCGTTCTGGA
400716 TTTTCCCGTTCTGGA
1 TTTTCCCGTTCTGGA
400731 TTT
1 TTT
400734 CAATCTGCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.24, G:0.15, T:0.55
Consensus pattern (15 bp):
TTTTCCCGTTCTGGA
Found at i:402540 original size:12 final size:12
Alignment explanation
Indices: 402523--402548 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
402513 ATATTTTTGG
402523 TAAAATGTTATT
1 TAAAATGTTATT
402535 TAAAATGTTATT
1 TAAAATGTTATT
402547 TA
1 TA
402549 TTATTGGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
TAAAATGTTATT
Found at i:402999 original size:63 final size:63
Alignment explanation
Indices: 402846--402972 Score: 236
Period size: 63 Copynumber: 2.0 Consensus size: 63
402836 AAGTTAGAAC
*
402846 AAATATCAAAGTAAAATATAATTTTTAAACTTTATTTCTCATACACAATATTTAGATTCAAAA
1 AAATATCAAAGTAAAATATAATTTTTAAACATTATTTCTCATACACAATATTTAGATTCAAAA
*
402909 AAATATCAAAGTAAAATATAATTTTTAAACATTATTTTTCATACACAATATTTAGATTCAAAA
1 AAATATCAAAGTAAAATATAATTTTTAAACATTATTTCTCATACACAATATTTAGATTCAAAA
402972 A
1 A
402973 TTTATTTAAG
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.38
Consensus pattern (63 bp):
AAATATCAAAGTAAAATATAATTTTTAAACATTATTTCTCATACACAATATTTAGATTCAAAA
Found at i:412506 original size:3 final size:3
Alignment explanation
Indices: 412500--412547 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
412490 ATGATTTTTT
* *
412500 TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA T-A TAA TGA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
412547 T
1 T
412548 TATTAGTAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:415742 original size:15 final size:15
Alignment explanation
Indices: 415719--415754 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
415709 AATACTTTTT
* *
415719 TATATTTAATTTATA
1 TATAATTAATCTATA
415734 TATAATTAATCTATA
1 TATAATTAATCTATA
415749 TATAAT
1 TATAAT
415755 ACTGTAGAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (15 bp):
TATAATTAATCTATA
Found at i:416605 original size:21 final size:21
Alignment explanation
Indices: 416576--416618 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
416566 GGTAATAAGA
*
416576 TTATGATTTAGGATTTAAAGT
1 TTATAATTTAGGATTTAAAGT
* *
416597 TTATAATTTAGGGTTTTAAGT
1 TTATAATTTAGGATTTAAAGT
416618 T
1 T
416619 AGATGCAGGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.51
Consensus pattern (21 bp):
TTATAATTTAGGATTTAAAGT
Found at i:419212 original size:17 final size:17
Alignment explanation
Indices: 419185--419217 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
419175 TTTAGAAAAA
419185 ATAAGTATTTTTATAAAT
1 ATAAGTATTTTT-TAAAT
419203 ATAA-TATTTTTTAAA
1 ATAAGTATTTTTTAAA
419218 AAAATTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 7 0.47
18 4 0.27
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (17 bp):
ATAAGTATTTTTTAAAT
Found at i:424996 original size:39 final size:39
Alignment explanation
Indices: 424942--425186 Score: 373
Period size: 39 Copynumber: 6.3 Consensus size: 39
424932 ATTTGGTCAC
* * **
424942 AGGCCAAGTGACTACGACTCGAGTTATAGATGGGGTAAT
1 AGGCCGAGTGACTACGACTCCAGCCATAGATGGGGTAAT
424981 AGGCCGAGTGACTACGACTCCAGCCATAGATGGGGTAAT
1 AGGCCGAGTGACTACGACTCCAGCCATAGATGGGGTAAT
* * *
425020 AGGTCGAGTGACTACGACTCCTGCCATAGATGGGATAAT
1 AGGCCGAGTGACTACGACTCCAGCCATAGATGGGGTAAT
*
425059 AGGCCGAGTGACTACGACTCCTGCCATAGATGGGGTAAT
1 AGGCCGAGTGACTACGACTCCAGCCATAGATGGGGTAAT
* * *
425098 AGGCCAAGTGACTACGACACCAGCCATAGATGGCGTAAT
1 AGGCCGAGTGACTACGACTCCAGCCATAGATGGGGTAAT
* *
425137 AGACCAAGTGACTACGACTCCAGCCATAGATGGGGTAAT
1 AGGCCGAGTGACTACGACTCCAGCCATAGATGGGGTAAT
425176 AGGCCGAGTGA
1 AGGCCGAGTGA
425187 TTACTCCCGA
Statistics
Matches: 188, Mismatches: 18, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 188 1.00
ACGTcount: A:0.30, C:0.22, G:0.29, T:0.19
Consensus pattern (39 bp):
AGGCCGAGTGACTACGACTCCAGCCATAGATGGGGTAAT
Found at i:425211 original size:18 final size:18
Alignment explanation
Indices: 425188--425229 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
425178 GCCGAGTGAT
425188 TACTCCCGACCTAGCGAC
1 TACTCCCGACCTAGCGAC
*
425206 TACTCCCGACCTAGCGAT
1 TACTCCCGACCTAGCGAC
425224 TACTCC
1 TACTCC
425230 AGATGGGGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.43, G:0.14, T:0.21
Consensus pattern (18 bp):
TACTCCCGACCTAGCGAC
Found at i:434090 original size:20 final size:20
Alignment explanation
Indices: 434054--434091 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
434044 ATCCTATTCC
**
434054 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
434074 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
434092 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:434153 original size:26 final size:26
Alignment explanation
Indices: 434124--434230 Score: 137
Period size: 26 Copynumber: 4.2 Consensus size: 26
434114 GTCTTGGTTC
*
434124 AAATAGCACTTTCGAGTGCGAGTGAT
1 AAATAGCACTTTCGAGTGCAAGTGAT
* *
434150 AAATAACACTTTCGAGTGCGAGTGAT
1 AAATAGCACTTTCGAGTGCAAGTGAT
434176 AAATAGCAC-TTCGAGTGCAAGTGAT
1 AAATAGCACTTTCGAGTGCAAGTGAT
* * *
434201 AAAT-GATATTTTCTAGTGCAAGTGAT
1 AAATAG-CACTTTCGAGTGCAAGTGAT
434227 AAAT
1 AAAT
434231 GACACTATAT
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
24 1 0.01
25 20 0.27
26 52 0.71
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (26 bp):
AAATAGCACTTTCGAGTGCAAGTGAT
Found at i:434199 original size:51 final size:52
Alignment explanation
Indices: 434124--434230 Score: 153
Period size: 51 Copynumber: 2.1 Consensus size: 52
434114 GTCTTGGTTC
* *
434124 AAATAGCACTTTCGAGTGCGAGTGATAAATAACACTTTCGAGTGCGAGTGAT
1 AAATAGCACTTTCGAGTGCAAGTGATAAATAACACTTTCGAGTGCAAGTGAT
* * * *
434176 AAATAGCAC-TTCGAGTGCAAGTGATAAATGATATTTTCTAGTGCAAGTGAT
1 AAATAGCACTTTCGAGTGCAAGTGATAAATAACACTTTCGAGTGCAAGTGAT
434227 AAAT
1 AAAT
434231 GACACTATAT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
51 40 0.82
52 9 0.18
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (52 bp):
AAATAGCACTTTCGAGTGCAAGTGATAAATAACACTTTCGAGTGCAAGTGAT
Found at i:434627 original size:25 final size:25
Alignment explanation
Indices: 434599--434648 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
434589 TTAATAAGTC
*
434599 TGTTTTACCTGTTCATATATTTATA
1 TGTTTTACCTATTCATATATTTATA
*
434624 TGTTTTACCTATTTATATATTTATA
1 TGTTTTACCTATTCATATATTTATA
434649 CAATATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.26, C:0.10, G:0.06, T:0.58
Consensus pattern (25 bp):
TGTTTTACCTATTCATATATTTATA
Found at i:434655 original size:19 final size:17
Alignment explanation
Indices: 434615--434659 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
434605 ACCTGTTCAT
*
434615 ATATTTATATGTTTTAC
1 ATATTTATATATTTTAC
*
434632 CTATTTATATATTTATAC
1 ATATTTATATATTT-TAC
434650 AATATTTATA
1 -ATATTTATA
434660 GTAATATAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 12 0.52
18 3 0.13
19 8 0.35
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.56
Consensus pattern (17 bp):
ATATTTATATATTTTAC
Found at i:435448 original size:26 final size:26
Alignment explanation
Indices: 435419--435499 Score: 119
Period size: 26 Copynumber: 3.1 Consensus size: 26
435409 TTTAAATAGT
* *
435419 ACTTTCGAGGGCGAGTGATAAATGAC
1 ACTTTTGAGGGCAAGTGATAAATGAC
435445 ACTTTTGAGTGG-AAGTGATAAATGAC
1 ACTTTTGAG-GGCAAGTGATAAATGAC
*
435471 ACTTTTGAGTGCAAGTGATAAATGAC
1 ACTTTTGAGGGCAAGTGATAAATGAC
435497 ACT
1 ACT
435500 ATATGTGCAA
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
25 1 0.02
26 47 0.94
27 2 0.04
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.28
Consensus pattern (26 bp):
ACTTTTGAGGGCAAGTGATAAATGAC
Found at i:438627 original size:6 final size:6
Alignment explanation
Indices: 438616--438642 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
438606 AAGGTTCATA
438616 TTTGAG TTTGAG TTTGAG TTTGAG TTT
1 TTTGAG TTTGAG TTTGAG TTTGAG TTT
438643 AAGGCTTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.30, T:0.56
Consensus pattern (6 bp):
TTTGAG
Found at i:440294 original size:54 final size:54
Alignment explanation
Indices: 440211--440492 Score: 321
Period size: 54 Copynumber: 5.2 Consensus size: 54
440201 GATTTAAATT
* * * * * *
440211 AGTTTGTGAAATATCGTATTGACATTATGTGTGCAACCCGCGTAATTCATATTT
1 AGTTTGTGAATTACCGTATTGACACTATGTGTGCAACCCACGTAATTCATAATG
* ** * **
440265 AGTTTGTGAATTACCTTATTGGTACTATGTGTGCAACCTAATTAATTCATAATG
1 AGTTTGTGAATTACCGTATTGACACTATGTGTGCAACCCACGTAATTCATAATG
* * *
440319 AATATGTGAATTACCGTATTGACACTATGTGTGCAATCCACGTAATTCATAATG
1 AGTTTGTGAATTACCGTATTGACACTATGTGTGCAACCCACGTAATTCATAATG
* * * * * * *
440373 AGTTTATGAATTACCGTATCGGCACTATATGTGCAACTCACGTAATTTATAACG
1 AGTTTGTGAATTACCGTATTGACACTATGTGTGCAACCCACGTAATTCATAATG
* * * * *
440427 AGTTTGTGAATTACTGTATCGACACTATGTGTGCAACCCATGAAATTCATAACG
1 AGTTTGTGAATTACCGTATTGACACTATGTGTGCAACCCACGTAATTCATAATG
440481 AGTTTGTGAATT
1 AGTTTGTGAATT
440493 TCTATATCGG
Statistics
Matches: 189, Mismatches: 39, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 189 1.00
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (54 bp):
AGTTTGTGAATTACCGTATTGACACTATGTGTGCAACCCACGTAATTCATAATG
Found at i:444890 original size:50 final size:50
Alignment explanation
Indices: 444828--444927 Score: 191
Period size: 50 Copynumber: 2.0 Consensus size: 50
444818 TTCTTGGCAA
444828 GATTTTCGAATTCATCTTGCAAGAGTTGGAGTCATGGAATTCGGTGGTTC
1 GATTTTCGAATTCATCTTGCAAGAGTTGGAGTCATGGAATTCGGTGGTTC
*
444878 GATTTTCGAATTCATCTTGCAAGAGTTGGAGTCATGGCATTCGGTGGTTC
1 GATTTTCGAATTCATCTTGCAAGAGTTGGAGTCATGGAATTCGGTGGTTC
444928 TAGAAACATT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.21, C:0.15, G:0.28, T:0.36
Consensus pattern (50 bp):
GATTTTCGAATTCATCTTGCAAGAGTTGGAGTCATGGAATTCGGTGGTTC
Found at i:449557 original size:16 final size:16
Alignment explanation
Indices: 449536--449566 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
449526 AATCACTAAC
449536 AAAATAACTATTTATT
1 AAAATAACTATTTATT
*
449552 AAAATAATTATTTAT
1 AAAATAACTATTTAT
449567 CGAACTAGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
AAAATAACTATTTATT
Found at i:450159 original size:121 final size:122
Alignment explanation
Indices: 449945--450189 Score: 402
Period size: 121 Copynumber: 2.0 Consensus size: 122
449935 TAAAAACACA
*
449945 TAATTACCCAAGCACAAACTGGAACAAGCAACAACGACAATACACATATATTAACCCATATTATT
1 TAATTACCCAAGCACAAACCGGAACAAGCAACAACGACAATACACATATATTAACCCATATTATT
* *
450010 TAGAAATATTAGTTTTCAGGCATTTTTATCAAAAC-ATTACCATAATAATAAAATAT
66 TAGAAATATTAATTTTCAGGCATTTTTATCAAAACAATTACCATAAAAATAAAATAT
* * **
450066 TAATTACCCAAGCACAAACCGGAGCAAGCAACAATGGTAATACACATATATTAACCCATATTATT
1 TAATTACCCAAGCACAAACCGGAACAAGCAACAACGACAATACACATATATTAACCCATATTATT
* *
450131 TAGATATGTTAATTTTCAGGCATTTTTATCAAAACAATTACCATAAAAATAAAATAT
66 TAGAAATATTAATTTTCAGGCATTTTTATCAAAACAATTACCATAAAAATAAAATAT
450188 TA
1 TA
450190 CTTGTGGGGC
Statistics
Matches: 114, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
121 92 0.81
122 22 0.19
ACGTcount: A:0.45, C:0.18, G:0.08, T:0.29
Consensus pattern (122 bp):
TAATTACCCAAGCACAAACCGGAACAAGCAACAACGACAATACACATATATTAACCCATATTATT
TAGAAATATTAATTTTCAGGCATTTTTATCAAAACAATTACCATAAAAATAAAATAT
Found at i:453885 original size:15 final size:15
Alignment explanation
Indices: 453865--453894 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
453855 GAGCATCACA
*
453865 ATGAAATTTTAGTTT
1 ATGAAATCTTAGTTT
453880 ATGAAATCTTAGTTT
1 ATGAAATCTTAGTTT
453895 GTGTTATTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.50
Consensus pattern (15 bp):
ATGAAATCTTAGTTT
Done.