Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007772.1 Hibiscus syriacus cultivar Beakdansim tig00110053_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: 1636317
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 9
Found at i:1204779 original size:47 final size:47
Alignment explanation
Indices: 1204710--1204810 Score: 125
Period size: 47 Copynumber: 2.1 Consensus size: 47
1204700 GAGTCAAGGG
* *
1204710 TTCTACCCAGTCCTTCAGGACAATTCTATATGGTCA-TTCGG-GACAAA
1 TTCTACGCAGTCCTTCAGGACAAATCTATATGG-CACTTCGGTG-CAAA
* * *
1204757 TTCTACGCGGTCCTTCAGGACAAATCTATGTGGCACTTCGGTGCATA
1 TTCTACGCAGTCCTTCAGGACAAATCTATATGGCACTTCGGTGCAAA
1204804 TTCTACG
1 TTCTACG
1204811 TGGCACTTCG
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
46 2 0.04
47 44 0.94
48 1 0.02
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.31
Consensus pattern (47 bp):
TTCTACGCAGTCCTTCAGGACAAATCTATATGGCACTTCGGTGCAAA
Found at i:1204795 original size:23 final size:24
Alignment explanation
Indices: 1204722--1204795 Score: 73
Period size: 23 Copynumber: 3.2 Consensus size: 24
1204712 CTACCCAGTC
* *
1204722 CTTCAGGACAATTCTATATGGTCA
1 CTTCAGGACAAATCTATGTGGTCA
* * *
1204746 -TTCGGGACAAATTCTACGCGGTC-
1 CTTCAGGACAAA-TCTATGTGGTCA
1204769 CTTCAGGACAAATCTATGTGG-CA
1 CTTCAGGACAAATCTATGTGGTCA
1204792 CTTC
1 CTTC
1204796 GGTGCATATT
Statistics
Matches: 39, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
22 1 0.03
23 20 0.51
24 18 0.46
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (24 bp):
CTTCAGGACAAATCTATGTGGTCA
Found at i:1204808 original size:24 final size:24
Alignment explanation
Indices: 1204777--1204834 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
1204767 TCCTTCAGGA
1204777 CAAA-TCTATGTGGCACTTCGGTG
1 CAAATTCTATGTGGCACTTCGGTG
* *
1204800 CATATTCTACGTGGCACTTCGGTG
1 CAAATTCTATGTGGCACTTCGGTG
1204824 CAAATTCTATG
1 CAAATTCTATG
1204835 CGTCAATTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 3 0.10
24 27 0.90
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (24 bp):
CAAATTCTATGTGGCACTTCGGTG
Found at i:1205531 original size:13 final size:13
Alignment explanation
Indices: 1205513--1205537 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1205503 TACATACACA
1205513 ATATGAAGACTGC
1 ATATGAAGACTGC
1205526 ATATGAAGACTG
1 ATATGAAGACTG
1205538 TTCAACTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (13 bp):
ATATGAAGACTGC
Found at i:1206937 original size:36 final size:36
Alignment explanation
Indices: 1206863--1206937 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
1206853 TTTTTATATT
*
1206863 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
*
1206899 TTTAATTTTTTAAAGAAAA-TATATAAATATT-TACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
1206935 TTT
1 TTT
1206938 GTAATATTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 1 0.03
36 30 0.86
37 4 0.11
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:1207120 original size:19 final size:18
Alignment explanation
Indices: 1207078--1207120 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
1207068 CAGTAATCCT
**
1207078 ATTCCCTGGTAATCTTTT
1 ATTCCCTGGTAATCTTAC
1207096 ATTTCCACTGGTAATCTTAC
1 A-TTCC-CTGGTAATCTTAC
1207116 ATTCC
1 ATTCC
1207121 GTGAACCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 8 0.38
20 12 0.57
ACGTcount: A:0.21, C:0.26, G:0.09, T:0.44
Consensus pattern (18 bp):
ATTCCCTGGTAATCTTAC
Found at i:1207317 original size:37 final size:38
Alignment explanation
Indices: 1207264--1207351 Score: 99
Period size: 38 Copynumber: 2.3 Consensus size: 38
1207254 AATTATACTC
** * *
1207264 TATATTTTAACTTAAA-T-TCACATATTAACATTAAAAA
1 TATATTTTATTTTAAATTATCAAATATTAAC-CTAAAAA
* *
1207301 TATTTTTTATTTTAAATTATTAAATATTAACCTAAAAA
1 TATATTTTATTTTAAATTATCAAATATTAACCTAAAAA
1207339 TATATTTTATTTT
1 TATATTTTATTTT
1207352 TATTTTAACT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
37 13 0.31
38 19 0.45
39 10 0.24
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (38 bp):
TATATTTTATTTTAAATTATCAAATATTAACCTAAAAA
Found at i:1207458 original size:31 final size:31
Alignment explanation
Indices: 1207369--1207463 Score: 73
Period size: 31 Copynumber: 2.9 Consensus size: 31
1207359 ACTTAAAATA
*
1207369 TATTTTAATCTTATCATAATTTATATATTTTATTTT
1 TATTTTAA-CTTATCAT-A--T-TATATCTTATTTT
** * * * *
1207405 TATCCTAACTTTTAAAAGTATATCTTATTTT
1 TATTTTAACTTATCATATTATATCTTATTTT
1207436 TATTTTAACTTATCATATTATATTCTTA
1 TATTTTAACTTATCATATTATA-TCTTA
1207464 AATTAAATCA
Statistics
Matches: 45, Mismatches: 13, Indels: 6
0.70 0.20 0.09
Matches are distributed among these distances:
31 28 0.62
32 5 0.11
34 1 0.02
35 5 0.11
36 6 0.13
ACGTcount: A:0.32, C:0.09, G:0.01, T:0.58
Consensus pattern (31 bp):
TATTTTAACTTATCATATTATATCTTATTTT
Found at i:1207485 original size:31 final size:30
Alignment explanation
Indices: 1207450--1207518 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 30
1207440 TTAACTTATC
*
1207450 ATATTATATTCTTAAATTAAATCATTAAAAT
1 ATATTATAGTCTTAAATTAAATCATT-AAAT
** *
1207481 ATATTATAGTCTTACCTTAAATTATTAAAT
1 ATATTATAGTCTTAAATTAAATCATTAAAT
1207511 ATAATTAT
1 AT-ATTAT
1207519 CCTTATTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 6 0.18
31 27 0.82
ACGTcount: A:0.45, C:0.07, G:0.01, T:0.46
Consensus pattern (30 bp):
ATATTATAGTCTTAAATTAAATCATTAAAT
Found at i:1207736 original size:31 final size:31
Alignment explanation
Indices: 1207629--1207746 Score: 115
Period size: 31 Copynumber: 4.0 Consensus size: 31
1207619 TTAAAATATT
* * *
1207629 ATAAGAATAAAATATAAATATTTAAGTTAAG
1 ATAAGAATAAAATATATATTTTTAAGTTAAA
* *
1207660 GTAAGAAT-AAAT-TAT-TTTTTAA-TT-TA
1 ATAAGAATAAAATATATATTTTTAAGTTAAA
*
1207686 ATAA-ATATTAAA-ATATATTTTTAAGTTAAA
1 ATAAGA-ATAAAATATATATTTTTAAGTTAAA
1207716 ATAAGAATAAAATATATATTTTTAATGTTAA
1 ATAAGAATAAAATATATATTTTTAA-GTTAA
1207747 GATGTTAATT
Statistics
Matches: 70, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
25 1 0.01
26 5 0.07
27 8 0.11
28 13 0.19
29 4 0.06
30 14 0.20
31 20 0.29
32 5 0.07
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.42
Consensus pattern (31 bp):
ATAAGAATAAAATATATATTTTTAAGTTAAA
Found at i:1207769 original size:18 final size:18
Alignment explanation
Indices: 1207736--1207782 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
1207726 AATATATATT
*
1207736 TTTAATGTTAAGATGTTAA
1 TTTAAT-TTAAGATGTGAA
*
1207755 TTTAATTTAATATGTGAA
1 TTTAATTTAAGATGTGAA
*
1207773 TTTAAGTTAA
1 TTTAATTTAA
1207783 AAATTTATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 19 0.76
19 6 0.24
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (18 bp):
TTTAATTTAAGATGTGAA
Found at i:1215234 original size:58 final size:57
Alignment explanation
Indices: 1215045--1215258 Score: 155
Period size: 58 Copynumber: 3.7 Consensus size: 57
1215035 AAACAAAATA
* ** * * **** *
1215045 ATACAAGATTCTATGAAAATAAATTTAACAATTTATTTCCTTATACAAAATGGAATT
1 ATACAAGATTCTAAGAAAATAAATTTAATGATTTATTTACTTTTACAATCCAGAATC
* * * * *
1215102 GTTCAAGATTTCTAAGAAAATAAATTTGATGTTTTATTTTCTTTTACAATCCAGAATC
1 ATACAAGA-TTCTAAGAAAATAAATTTAATGATTTATTTACTTTTACAATCCAGAATC
* * *
1215160 ATATAAGATTCATAAGAAAAAAAATTTAATGATTTATTTACTTTT-CAAAGT-TAGAATC
1 ATACAAGATTC-TAAGAAAATAAATTTAATGATTTATTTACTTTTAC-AA-TCCAGAATC
* *
1215218 A-ACGCAAGATTCTAAGATGAAATAAATTCAATAATTTATTT
1 ATA--CAAGATTCTAAGA--AAATAAATTTAATGATTTATTT
1215259 CTCTTTTCCA
Statistics
Matches: 123, Mismatches: 26, Indels: 13
0.76 0.16 0.08
Matches are distributed among these distances:
57 11 0.09
58 85 0.69
59 8 0.07
60 19 0.15
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.38
Consensus pattern (57 bp):
ATACAAGATTCTAAGAAAATAAATTTAATGATTTATTTACTTTTACAATCCAGAATC
Found at i:1216132 original size:157 final size:158
Alignment explanation
Indices: 1215808--1216490 Score: 776
Period size: 157 Copynumber: 4.4 Consensus size: 158
1215798 GGTATATGAG
* * * *
1215808 CATGTGGTTCAAATTTGGTAAAAACATACTTAAAAT-AAGGATGAATTAAAGAAATAAGGAATTT
1 CATGTGGTTCAAATTTGGTAAAAACAAACTTAAAATAAAGGATGAATTGAAGAAATAAGAAAATT
* *
1215872 ATGAAAAAA--TGAGGGACTAAATTGAAAAATAG-AAATTTCATTAT--AAAAAA-GAGTTTGAA
66 AT-AAAAAATTTGAGGGACTAAATTGAAAAATAGAAAATTT-GTTATCAAAAAAAGGA-ATTGAA
* * * *
1215931 AATACATATGTATTATACGAAGGTTTAGGAA
128 AGTACATATGTATTCTACGATGATTTAGGAA
*
1215962 CATGTAGTTCAAATTTGGTAAAAACAAACTTAAAATAAAGGATGAATTGAAGAAATAAGAAAATT
1 CATGTGGTTCAAATTTGGTAAAAACAAACTTAAAATAAAGGATGAATTGAAGAAATAAGAAAATT
* *
1216027 AT-AAAAATTTGAGGGAGTAAATTGGAAAATAGAAAATTTGTTATCAAAAAAAGGAATTGAAAGT
66 ATAAAAAATTTGAGGGACTAAATTGAAAAATAGAAAATTTGTTATCAAAAAAAGGAATTGAAAGT
* *
1216091 ACATATGTATTCTACGATGTTTTAGGAG
131 ACATATGTATTCTACGATGATTTAGGAA
* * * *
1216119 CATGTGGTTCAAATTTGATAAAAACAGACTTAAAATAAAGGATGAATTGAAGAAACAAGGAAATT
1 CATGTGGTTCAAATTTGGTAAAAACAAACTTAAAATAAAGGATGAATTGAAGAAATAAGAAAATT
* *
1216184 ATAAAAAAAGTTAAGGGACTAAATTGAAAAATAGAAAATTTGTTATCAAAAAGAGAGGAATTGAA
66 AT-AAAAAATTTGAGGGACTAAATTGAAAAATAGAAAATTTGTTATCAAAAA-A-AGGAATTGAA
* * * *
1216249 AGTACATATATATTCTACAATGATTTACGAT
128 AGTACATATGTATTCTACGATGATTTAGGAA
*
1216280 CATGTGGTTCAAATTTGGTAAAAA-AAGAATTAAAATAAAGGATGAATTGAA-AAATAA-AGAAA
1 CATGTGGTTCAAATTTGGTAAAAACAA-ACTTAAAATAAAGGATGAATTGAAGAAATAAGA-AAA
* * * **
1216342 TTATAAGAAATTT-AGGGAGTAAA-T-----A-A-AAAATTTGTTATCAAAAAGATTAATTGAAA
64 TTATAAAAAATTTGAGGGACTAAATTGAAAAATAGAAAATTTGTTATCAAAAAAAGGAATTGAAA
* *
1216398 GTACATATATATTCTACGATGATTTAAGAA
129 GTACATATGTATTCTACGATGATTTAGGAA
* * ** * ** *
1216428 TATGTAGTTCAAATTTAATAAAAATAAACTTAAAATAAAACATGAATTGAAGGAATAATGAAA
1 CATGTGGTTCAAATTTGGTAAAAACAAACTTAAAATAAAGGATGAATTGAAGAAATAA-GAAA
1216491 TAAGGGACCA
Statistics
Matches: 462, Mismatches: 50, Indels: 38
0.84 0.09 0.07
Matches are distributed among these distances:
148 77 0.17
149 7 0.02
150 20 0.04
151 2 0.00
152 1 0.00
153 5 0.01
154 34 0.07
155 52 0.11
156 6 0.01
157 100 0.22
158 11 0.02
159 51 0.11
160 14 0.03
161 82 0.18
ACGTcount: A:0.50, C:0.05, G:0.17, T:0.28
Consensus pattern (158 bp):
CATGTGGTTCAAATTTGGTAAAAACAAACTTAAAATAAAGGATGAATTGAAGAAATAAGAAAATT
ATAAAAAATTTGAGGGACTAAATTGAAAAATAGAAAATTTGTTATCAAAAAAAGGAATTGAAAGT
ACATATGTATTCTACGATGATTTAGGAA
Found at i:1216440 original size:309 final size:308
Alignment explanation
Indices: 1215808--1216479 Score: 853
Period size: 309 Copynumber: 2.2 Consensus size: 308
1215798 GGTATATGAG
* * * * *
1215808 CATGTGGTTCAAATTTGGTAAAAACATACTTAAAAT-AAGGATGAATTAAAGAAATAAGGAATTT
1 CATGTGGTTCAAATTTGATAAAAACAAACTTAAAATAAAGGATGAATTGAAGAAACAAGGAAATT
* * *
1215872 ATGAAAAAATGAGGGACTAAATTGAAAAATAGAAATTTCATTATAAAAAAGAGTTTGAAAATACA
66 ATAAAAAAATAAGGGACTAAATTGAAAAATAGAAATTTCATTATAAAAAAGAGATTGAAAATACA
* * * *
1215937 TATGTATTATACGAAGGTTTAGGAACATGTAGTTCAAATTTGGTAAAAACAAACTTAAAATAAAG
131 TATATATTATACGAAGATTTACGAACATGTAGTTCAAATTTGGTAAAAACAAAATTAAAATAAAG
1216002 GATGAATTGAAGAAATAAGAAAATTATAAAAATTTGAGGGAGTAAATTGGAAAATAGAAAATTTG
196 GATGAATTGAAGAAATAAGAAAATTATAAAAATTTGAGGGAGTAAATT----AATAGAAAATTTG
* * * *
1216067 TTATCAAAAAAAGGAATTGAAAGTACATATGTATTCTACGATGTTTTAGGAG
257 TTATCAAAAAAAGGAATTGAAAGTACATATATATTCTACGATGATTTAAGAA
*
1216119 CATGTGGTTCAAATTTGATAAAAACAGACTTAAAATAAAGGATGAATTGAAGAAACAAGGAAATT
1 CATGTGGTTCAAATTTGATAAAAACAAACTTAAAATAAAGGATGAATTGAAGAAACAAGGAAATT
*
1216184 ATAAAAAAAGTTAAGGGACTAAATTGAAAAATAGAAAATTT-GTTATCAAAAAGAGAGGAATTGA
66 ATAAAAAAA--TAAGGGACTAAATTGAAAAATAG-AAATTTCATTAT-AAAAA-AGA-G-ATTGA
* * * *
1216248 AAGTACATATATATTCTAC-AATGATTTACGATCATGTGGTTCAAATTTGGTAAAAA-AAGAATT
124 AAATACATATATATTATACGAA-GATTTACGAACATGTAGTTCAAATTTGGTAAAAACAA-AATT
1216311 AAAATAAAGGATGAATTGAA-AAATAA-AGAAATTATAAGAAATTT-AGGGAGTAAA-T-A-A-A
187 AAAATAAAGGATGAATTGAAGAAATAAGA-AAATTATAA-AAATTTGAGGGAGTAAATTAATAGA
* **
1216369 AAATTTGTTATCAAAAAGATTAATTGAAAGTACATATATATTCTACGATGATTTAAGAA
250 AAATTTGTTATCAAAAAAAGGAATTGAAAGTACATATATATTCTACGATGATTTAAGAA
* * * * **
1216428 TATGTAGTTCAAATTTAATAAAAATAAACTTAAAATAAAACATGAATTGAAG
1 CATGTGGTTCAAATTTGATAAAAACAAACTTAAAATAAAGGATGAATTGAAG
1216480 GAATAATGAA
Statistics
Matches: 318, Mismatches: 31, Indels: 26
0.85 0.08 0.07
Matches are distributed among these distances:
309 98 0.31
310 1 0.00
311 35 0.11
312 33 0.10
314 26 0.08
315 11 0.03
316 5 0.02
317 30 0.09
318 79 0.25
ACGTcount: A:0.50, C:0.05, G:0.17, T:0.29
Consensus pattern (308 bp):
CATGTGGTTCAAATTTGATAAAAACAAACTTAAAATAAAGGATGAATTGAAGAAACAAGGAAATT
ATAAAAAAATAAGGGACTAAATTGAAAAATAGAAATTTCATTATAAAAAAGAGATTGAAAATACA
TATATATTATACGAAGATTTACGAACATGTAGTTCAAATTTGGTAAAAACAAAATTAAAATAAAG
GATGAATTGAAGAAATAAGAAAATTATAAAAATTTGAGGGAGTAAATTAATAGAAAATTTGTTAT
CAAAAAAAGGAATTGAAAGTACATATATATTCTACGATGATTTAAGAA
Found at i:1216798 original size:20 final size:20
Alignment explanation
Indices: 1216773--1216904 Score: 194
Period size: 20 Copynumber: 6.6 Consensus size: 20
1216763 GATTCTTGAC
* *
1216773 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
1216793 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1216813 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1216833 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1216853 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1216873 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1216893 AACCGCAACGCG
1 AATCGCAACGCG
1216905 ATTTTTAAAG
Statistics
Matches: 102, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
20 100 0.98
21 2 0.02
ACGTcount: A:0.32, C:0.30, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1216835 original size:40 final size:40
Alignment explanation
Indices: 1216751--1216904 Score: 195
Period size: 40 Copynumber: 3.8 Consensus size: 40
1216741 TCAGTTTCCA
* * * *
1216751 AAATCGCAACGCG-ATTCTTGACAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATCCGT-A-AATCGCAACGCGTATC-CGT
*
1216792 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGT
*
1216832 AAATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGT
* *
1216872 ATATCGCAACGCGTATCCGTAAACCGCAACGCG
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG
1216905 ATTTTTAAAG
Statistics
Matches: 101, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
40 81 0.80
41 16 0.16
42 4 0.04
ACGTcount: A:0.32, C:0.29, G:0.19, T:0.19
Consensus pattern (40 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGT
Found at i:1216857 original size:60 final size:60
Alignment explanation
Indices: 1216751--1216905 Score: 197
Period size: 60 Copynumber: 2.6 Consensus size: 60
1216741 TCAGTTTCCA
* *
1216751 AAATCGCAACGCG-ATTCTTGACAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT-A-AATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
* * * *
1216812 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATC-CGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACACATAAATCGCAACGCGTATCCGT
* *
1216872 ATATCGCAACGCGTATCCGTAAACCGCAACGCGA
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1216906 TTTTTAAAGC
Statistics
Matches: 83, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
59 1 0.01
60 63 0.76
61 15 0.18
62 4 0.05
ACGTcount: A:0.32, C:0.29, G:0.19, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
Found at i:1217323 original size:33 final size:33
Alignment explanation
Indices: 1217284--1217354 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1217274 TTCACTTAGA
1217284 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1217317 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1217350 TTTCA
1 TTTCA
1217355 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1217501 original size:21 final size:21
Alignment explanation
Indices: 1217434--1217506 Score: 87
Period size: 21 Copynumber: 3.5 Consensus size: 21
1217424 TGCAGAAGAG
*
1217434 TCGCAACGAGATAAATG-AAA
1 TCGCAACGAGAAAAATGAAAA
* **
1217454 TCGCAACGTG-AAAATGACTA
1 TCGCAACGAGAAAAATGAAAA
1217474 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAGAAAAATGAAAA
1217496 TCGCAACGAGA
1 TCGCAACGAGA
1217507 GAATCGCAAC
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
19 5 0.12
20 12 0.28
21 16 0.37
22 10 0.23
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.15
Consensus pattern (21 bp):
TCGCAACGAGAAAAATGAAAA
Found at i:1217513 original size:14 final size:14
Alignment explanation
Indices: 1217494--1217550 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1217484 GAAAAATGAA
1217494 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1217508 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1217527 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1217541 AATCGCAACG
1 AATCGCAACG
1217551 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1217525 original size:33 final size:33
Alignment explanation
Indices: 1217487--1217566 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
1217477 GCAACGAGAA
1217487 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1217520 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
1217553 AAACCAAAATCGCA
1 AAATGAAAATCGCA
1217567 TTGTGATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:1217532 original size:19 final size:20
Alignment explanation
Indices: 1217434--1217536 Score: 69
Period size: 19 Copynumber: 5.4 Consensus size: 20
1217424 TGCAGAAGAG
*
1217434 TCGCAACGAGATAAATG-AAA
1 TCGCAACGCGA-AAATGAAAA
* **
1217454 TCGCAACGTGAAAATGACTA
1 TCGCAACGCGAAAATGAAAA
*
1217474 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGCG-AAAATGAAAA
*
1217496 TCGCAA--CG---A-GAGAA
1 TCGCAACGCGAAAATGAAAA
1217510 TCGCAACGCG-AAATGAAAA
1 TCGCAACGCGAAAATGAAAA
1217529 TCGCAACG
1 TCGCAACG
1217537 AGAGAATCGC
Statistics
Matches: 66, Mismatches: 9, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
14 10 0.15
15 1 0.02
16 2 0.03
18 1 0.02
19 18 0.27
20 13 0.20
21 11 0.17
22 10 0.15
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.14
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:1217618 original size:21 final size:21
Alignment explanation
Indices: 1217592--1217656 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
1217582 CGCGTTGCGA
*
1217592 TTCTCTCGTTGCAATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
1217613 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
1217633 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
1217654 TTC
1 TTC
1217657 AACCAAAAGA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 17 0.47
21 19 0.53
ACGTcount: A:0.12, C:0.26, G:0.14, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:1217653 original size:20 final size:20
Alignment explanation
Indices: 1217591--1217654 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
1217581 TCGCGTTGCG
*
1217591 ATTCTCTCGTTGCAATTTTC
1 ATTCTCTCGTTGCGATTTTC
***
1217611 ATTTCTCTCGTTGCGACAGTC
1 A-TTCTCTCGTTGCGATTTTC
1217632 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
1217652 ATT
1 ATT
1217655 TCAACCAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 20 0.56
21 16 0.44
ACGTcount: A:0.14, C:0.25, G:0.14, T:0.47
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:1219513 original size:93 final size:93
Alignment explanation
Indices: 1219354--1219665 Score: 615
Period size: 93 Copynumber: 3.4 Consensus size: 93
1219344 ATTGCTTAGT
*
1219354 AATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
1 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
1219419 TCTTTGTTTTGTCTTTTGGTTGAAAGTA
66 TCTTTGTTTTGTCTTTTGGTTGAAAGTA
1219447 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
1 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
1219512 TCTTTGTTTTGTCTTTTGGTTGAAAGTA
66 TCTTTGTTTTGTCTTTTGGTTGAAAGTA
1219540 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
1 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
1219605 TCTTTGTTTTGTCTTTTGGTTGAAAGTA
66 TCTTTGTTTTGTCTTTTGGTTGAAAGTA
1219633 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1219666 AATACCCTGA
Statistics
Matches: 218, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 218 1.00
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.46
Consensus pattern (93 bp):
AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
TCTTTGTTTTGTCTTTTGGTTGAAAGTA
Found at i:1219822 original size:33 final size:33
Alignment explanation
Indices: 1219779--1219886 Score: 171
Period size: 33 Copynumber: 3.3 Consensus size: 33
1219769 CACTGAACTT
* **
1219779 AAAATCGCAACGAGAGAATCGCAACGCGAAATG
1 AAAATCGCAACGACAGAATCGCAACGCGAAACC
*
1219812 AAAATTGCAACGACAGAATCGCAACGCGAAACC
1 AAAATCGCAACGACAGAATCGCAACGCGAAACC
*
1219845 AAAATCGCAACGACAAAATCGCAACGCGAAACC
1 AAAATCGCAACGACAGAATCGCAACGCGAAACC
1219878 AAAATCGCA
1 AAAATCGCA
1219887 TTGCGATTTT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 69 1.00
ACGTcount: A:0.47, C:0.26, G:0.19, T:0.08
Consensus pattern (33 bp):
AAAATCGCAACGACAGAATCGCAACGCGAAACC
Found at i:1219852 original size:19 final size:19
Alignment explanation
Indices: 1219828--1219886 Score: 83
Period size: 19 Copynumber: 3.4 Consensus size: 19
1219818 GCAACGACAG
1219828 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
1219847 AATCGCAA--CG--A-CAA
1 AATCGCAACGCGAAACCAA
1219861 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
1219880 AATCGCA
1 AATCGCA
1219887 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 11 0.31
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 18 0.51
ACGTcount: A:0.47, C:0.31, G:0.15, T:0.07
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:1219904 original size:19 final size:19
Alignment explanation
Indices: 1219882--1220054 Score: 141
Period size: 19 Copynumber: 9.6 Consensus size: 19
1219872 GAAACCAAAA
*
1219882 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1219901 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
1219915 TCTCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
1219934 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
1219950 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1219967 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
1219986 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
1220005 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
* *
1220024 TTGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1220044 TCGTGTTGCGA
1 TCGCGTTGCGA
1220055 AAGTAAACTA
Statistics
Matches: 124, Mismatches: 19, Indels: 21
0.76 0.12 0.13
Matches are distributed among these distances:
14 18 0.15
16 7 0.06
17 7 0.06
19 81 0.65
20 11 0.09
ACGTcount: A:0.09, C:0.19, G:0.25, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1219956 original size:14 final size:14
Alignment explanation
Indices: 1219904--1219960 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1219894 TTTCATTTCG
*
1219904 CGTTGCGATTCTCT
1 CGTTGCGATTCTGT
*
1219918 CGTTGCGATTTTGGTTT
1 CGTTGCGATTCT-G--T
1219935 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTGT
1219951 CGTTGCGATT
1 CGTTGCGATT
1219961 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 21 0.60
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.31
ACGTcount: A:0.07, C:0.21, G:0.28, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTGT
Found at i:1219974 original size:52 final size:54
Alignment explanation
Indices: 1219918--1220054 Score: 179
Period size: 52 Copynumber: 2.5 Consensus size: 54
1219908 GCGATTCTCT
*
1219918 CGTTGCGATTTTGGTTTCGCGTTGCGATTCT-G-TCGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTGGTTTCGCGTTGCGATTCTGGTTCGTTGCGATTCTCATTTCG
* *
1219970 CGTTGCGATTTTGGTTTCGCGTTGCGATTTTGGTTTCTCGTTGCGATTCTCATTTTG
1 CGTTGCGATTTTGGTTTCGCGTTGCGATTCTGG--T-TCGTTGCGATTCTCATTTCG
* *
1220027 CGTTGCGATTTTAAGTTTCGTGTTGCGA
1 CGTTGCGATTTT-GGTTTCGCGTTGCGA
1220055 AAGTAAACTA
Statistics
Matches: 74, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
52 30 0.41
53 1 0.01
57 30 0.41
58 13 0.18
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.47
Consensus pattern (54 bp):
CGTTGCGATTTTGGTTTCGCGTTGCGATTCTGGTTCGTTGCGATTCTCATTTCG
Found at i:1220012 original size:38 final size:36
Alignment explanation
Indices: 1219887--1220054 Score: 159
Period size: 33 Copynumber: 4.7 Consensus size: 36
1219877 CAAAATCGCA
** *
1219887 TTGCGATTTTCATTTCGCGTTGCGATTC--TCT-CG
1 TTGCGATTTTGGTTTCGCGTTGCGATTCTGTTTGCG
1219920 TTGCGATTTTGGTTTCGCGTTGCGATTCTG--T-CG
1 TTGCGATTTTGGTTTCGCGTTGCGATTCTGTTTGCG
** *
1219953 TTGCGATTTTCATTTCGCGTTGCGATTTTGGTTTCGCG
1 TTGCGATTTTGGTTTCGCGTTGCGATTCT-GTTT-GCG
* *
1219991 TTGCGATTTTGGTTTCTCGTTGCGATTCTCATTTTGCG
1 TTGCGATTTTGGTTTCGCGTTGCGATTCT--GTTTGCG
* *
1220029 TTGCGATTTTAAGTTTCGTGTTGCGA
1 TTGCGATTTT-GGTTTCGCGTTGCGA
1220055 AAGTAAACTA
Statistics
Matches: 112, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
33 55 0.49
34 1 0.01
36 1 0.01
38 40 0.36
39 15 0.13
ACGTcount: A:0.09, C:0.18, G:0.26, T:0.47
Consensus pattern (36 bp):
TTGCGATTTTGGTTTCGCGTTGCGATTCTGTTTGCG
Found at i:1221998 original size:14 final size:14
Alignment explanation
Indices: 1221979--1222014 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1221969 ATTGTTTAAT
1221979 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1221993 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1222007 TGATTTGT
1 TGATTTGT
1222015 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1222129 original size:19 final size:19
Alignment explanation
Indices: 1222105--1222192 Score: 123
Period size: 19 Copynumber: 4.8 Consensus size: 19
1222095 GCATTATGTT
1222105 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
1222124 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAATGC
*
1222141 G--A-GAGAATCGCAATGC
1 GAAATGAAAATCGCAATGC
1222157 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
1222176 GGAAATGAAAATCGCAA
1 -GAAATGAAAATCGCAA
1222193 CGAGAGAATC
Statistics
Matches: 61, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
14 10 0.16
15 1 0.02
16 2 0.03
17 2 0.03
18 1 0.02
19 29 0.48
20 16 0.26
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAATGC
Found at i:1222224 original size:53 final size:53
Alignment explanation
Indices: 1222105--1222211 Score: 207
Period size: 53 Copynumber: 2.0 Consensus size: 53
1222095 GCATTATGTT
1222105 GAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
1222157 GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
1222210 GA
1 GA
1222212 TTTTCATTTC
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 19 0.35
53 35 0.65
ACGTcount: A:0.46, C:0.17, G:0.24, T:0.13
Consensus pattern (53 bp):
GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
Found at i:1222288 original size:72 final size:69
Alignment explanation
Indices: 1222202--1222495 Score: 280
Period size: 72 Copynumber: 4.2 Consensus size: 69
1222192 ACGAGAGAAT
*
1222202 CGCAATGCGATTTTCATTTCGCATTGCGATTTTCATTTACGCATTGCGATTCTCTCGTTGCGATT
1 CGCATTGCGATTTTC-TTTCG--TTGCGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATT
1222267 TTCATTT-
62 TTCATTTC
* * * * *
1222274 CGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCATTGCGA
1 CGCATTGCGATTTTC-TTTCG--TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGTTGCGA
1222336 TTTTCATTTC
60 TTTTCATTTC
* *
1222346 CGCATTGCGA--TTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
1 CGCATTGCGATTTTCTTTCGTTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGAT
1222409 TTTCATTTC
61 TTTCATTTC
* * *
1222418 CGCATTGCGATTTTC-TT-GTTGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTGTAA
1 CGCATTGCGATTTTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
1222481 TTTC
66 TTTC
**
1222485 CGTGTTGCGAT
1 CGCATTGCGAT
1222496 AGTCAAATGC
Statistics
Matches: 188, Mismatches: 20, Indels: 33
0.78 0.08 0.14
Matches are distributed among these distances:
65 9 0.05
66 3 0.02
67 31 0.16
68 2 0.01
69 8 0.04
70 8 0.04
71 18 0.10
72 95 0.51
73 7 0.04
74 7 0.04
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.45
Consensus pattern (69 bp):
CGCATTGCGATTTTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
TTTC
Found at i:1222327 original size:105 final size:108
Alignment explanation
Indices: 1222207--1222476 Score: 423
Period size: 105 Copynumber: 2.5 Consensus size: 108
1222197 AGAATCGCAA
1222207 TGCGATTTTCATTTCGCATTGCGATTTTCATTTACGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATTTTCAT
1222272 TTCGCATTGCGATTTTCATTTCGCATTGCGA-TTC-TCT-CG-T
65 TTCGCATTGCGATTTTCATTTCGCATTGCGATTTCATCTCCGAT
1222312 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATTTTCAT
*
1222377 TTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCAT
65 TTCGCATTGCGATTTTCATTTCGCATTGCGA-TTTCATCTCCG-AT
*
1222423 TGCGATTTTC--TT-G--TTGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
1222477 GTAATTTCCG
Statistics
Matches: 156, Mismatches: 3, Indels: 12
0.91 0.02 0.07
Matches are distributed among these distances:
105 121 0.78
106 14 0.09
107 3 0.02
108 3 0.02
109 4 0.03
111 11 0.07
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (108 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
TCGCATTGCGATTTTCATTTCGCATTGCGATTTCATCTCCGAT
Found at i:1222491 original size:53 final size:52
Alignment explanation
Indices: 1222207--1222476 Score: 415
Period size: 53 Copynumber: 5.1 Consensus size: 52
1222197 AGAATCGCAA
1222207 TGCGATTTTCATTTCGCATTGCGATTTTCATTTACGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
1222260 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1222312 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
*
1222365 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG--T
*
1222423 TGCGATTTTC--TT-G--TTGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1222470 TGCGATT
1 TGCGATT
1222477 GTAATTTCCG
Statistics
Matches: 207, Mismatches: 3, Indels: 20
0.90 0.01 0.09
Matches are distributed among these distances:
47 8 0.04
49 2 0.01
50 2 0.01
51 3 0.01
52 62 0.30
53 109 0.53
54 3 0.01
55 3 0.01
56 4 0.02
58 11 0.05
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (52 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:1224776 original size:12 final size:12
Alignment explanation
Indices: 1224759--1224783 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1224749 TCTTCGGGGA
1224759 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1224771 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1224783 C
1 C
1224784 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1224991 original size:24 final size:24
Alignment explanation
Indices: 1224957--1225003 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1224947 CTGAAACATC
1224957 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1224981 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1225004 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:1225723 original size:20 final size:20
Alignment explanation
Indices: 1225695--1225923 Score: 253
Period size: 20 Copynumber: 11.4 Consensus size: 20
1225685 AAATTTCAGT
* * *
1225695 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1225715 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
1225735 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1225755 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
1225775 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1225795 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1225815 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1225835 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
1225855 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
1225875 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
1225895 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
1225915 GTTGCGATT
1 GTTGCGATT
1225924 ATGGAAAATC
Statistics
Matches: 185, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
20 184 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:1225941 original size:21 final size:20
Alignment explanation
Indices: 1225917--1225964 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
1225907 ATATTCGCGT
1225917 TGCGATTATGGAAAATCGCAA
1 TGCGATTAT-GAAAATCGCAA
* *
1225938 TGCGAATATGAAAATCGCAT
1 TGCGATTATGAAAATCGCAA
1225958 TGCGATT
1 TGCGATT
1225965 GTCAAGAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (20 bp):
TGCGATTATGAAAATCGCAA
Found at i:1227958 original size:19 final size:19
Alignment explanation
Indices: 1227894--1227960 Score: 55
Period size: 19 Copynumber: 3.3 Consensus size: 19
1227884 GCTATAAAGT
*
1227894 TAACTGACTAACCAAAAAAAC
1 TAACTGA-TAA-CAAACAAAC
*
1227915 T-ACTGCTAACAAATCAGCTAAC
1 TAACTGATAACAAA-CA---AAC
1227937 TAACTGATAACAAACAAAC
1 TAACTGATAACAAACAAAC
1227956 TAACT
1 TAACT
1227961 ACAAGCTGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
18 4 0.11
19 12 0.32
20 4 0.11
21 1 0.03
22 6 0.16
23 11 0.29
ACGTcount: A:0.51, C:0.24, G:0.06, T:0.19
Consensus pattern (19 bp):
TAACTGATAACAAACAAAC
Found at i:1232562 original size:26 final size:23
Alignment explanation
Indices: 1232492--1232563 Score: 67
Period size: 23 Copynumber: 3.0 Consensus size: 23
1232482 TAACCAAAAA
* *
1232492 AACT-ACTGCTAACAAATCAACT
1 AACTAACTGATAACTAATCAACT
*
1232514 AACTAACTGATAA-TAAACAAACT
1 AACTAACTGATAACTAATC-AACT
1232537 AACTACAAGCTGATAACTAATCAACT
1 AACT--AA-CTGATAACTAATCAACT
1232563 A
1 A
1232564 TAAGCTATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
22 7 0.17
23 15 0.38
25 2 0.05
26 12 0.30
27 4 0.10
ACGTcount: A:0.50, C:0.22, G:0.06, T:0.22
Consensus pattern (23 bp):
AACTAACTGATAACTAATCAACT
Found at i:1232850 original size:19 final size:19
Alignment explanation
Indices: 1232826--1232862 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1232816 ATCATAAAAT
*
1232826 TTATAATTACAATTTGAAC
1 TTATAATCACAATTTGAAC
1232845 TTATAATCACAATTTGAA
1 TTATAATCACAATTTGAA
1232863 ATTTATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (19 bp):
TTATAATCACAATTTGAAC
Found at i:1232917 original size:16 final size:18
Alignment explanation
Indices: 1232885--1232931 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 18
1232875 TTTCAATTGT
1232885 ATAAAAATAAA-AGAT-A
1 ATAAAAATAAATAGATAA
1232901 ATAAAAATAAATA-ATAA
1 ATAAAAATAAATAGATAA
1232918 ATAGAAAATCAAAT
1 ATA-AAAAT-AAAT
1232932 CAAGTAATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 13 0.48
17 5 0.19
18 5 0.19
19 4 0.15
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.21
Consensus pattern (18 bp):
ATAAAAATAAATAGATAA
Found at i:1232984 original size:117 final size:116
Alignment explanation
Indices: 1232744--1232963 Score: 325
Period size: 117 Copynumber: 1.8 Consensus size: 116
1232734 ACCGAAAACA
1232744 AAATTTATTTTAAATTTCAATTGTATAAAAATAAAAGATAATAAATAATAAATAGAAAAATCAAA
1 AAATTTATTTTAAATTTCAATTGTATAAAAATAAAAGATAATAAATAATAAATAGAAAAATCAAA
* *
1232809 TCAAATAATCATAAAATTTATAATTACAATTTGAACTTATAATCACAATTTG
66 TCAAATAATCATAAAATTTATAATTAAAATATGAACTTATAATCACAA-TTG
1232861 AAATTTATTTTAAATTTCAATTGTATAAAAATAAAAGATAATAAAAATAAATAATAAATAG-AAA
1 AAATTTATTTTAAATTTCAATTGTATAAAAATAAAAG---AT---AATAAATAATAAATAGAAAA
* *
1232925 ATCAAATCAAGTAATCATTAAATTTATAATTATAAATAT
60 ATCAAATCAAATAATCATAAAATTTATAATTA-AAATAT
1232964 ATTTTAAATA
Statistics
Matches: 92, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
117 37 0.40
120 2 0.02
122 33 0.36
123 20 0.22
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.35
Consensus pattern (116 bp):
AAATTTATTTTAAATTTCAATTGTATAAAAATAAAAGATAATAAATAATAAATAGAAAAATCAAA
TCAAATAATCATAAAATTTATAATTAAAATATGAACTTATAATCACAATTG
Found at i:1233797 original size:3 final size:3
Alignment explanation
Indices: 1233789--1233823 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1233779 TATTATATTA
1233789 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1233824 AATGTCAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1234337 original size:16 final size:19
Alignment explanation
Indices: 1234317--1234358 Score: 63
Period size: 16 Copynumber: 2.4 Consensus size: 19
1234307 ATTAACGTAA
1234317 ATAAAATATA-TTAT-ATT
1 ATAAAATATATTTATAATT
1234334 -TAAAATATATTTATAATT
1 ATAAAATATATTTATAATT
1234352 ATAAAAT
1 ATAAAAT
1234359 GGTATTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 9 0.41
17 4 0.18
18 3 0.14
19 6 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATAAAATATATTTATAATT
Found at i:1234457 original size:14 final size:12
Alignment explanation
Indices: 1234427--1234451 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1234417 TATACAATTG
1234427 AAATTTTAAAAT
1 AAATTTTAAAAT
1234439 AAATTTTAAAAT
1 AAATTTTAAAAT
1234451 A
1 A
1234452 TAAATTACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAATTTTAAAAT
Found at i:1241636 original size:17 final size:17
Alignment explanation
Indices: 1241614--1241647 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1241604 TGGCCACCAA
*
1241614 CCAACTTGTCAACTTTG
1 CCAACTTGTCAAATTTG
1241631 CCAACTTGTCAAATTTG
1 CCAACTTGTCAAATTTG
1241648 ACAATTTACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.12, T:0.35
Consensus pattern (17 bp):
CCAACTTGTCAAATTTG
Found at i:1244953 original size:19 final size:19
Alignment explanation
Indices: 1244929--1244966 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1244919 TTATATGTGT
1244929 GACACGTGTCAGGTAACAA
1 GACACGTGTCAGGTAACAA
*
1244948 GACACGTGTTAGGTAACAA
1 GACACGTGTCAGGTAACAA
1244967 CCAAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.18
Consensus pattern (19 bp):
GACACGTGTCAGGTAACAA
Found at i:1245919 original size:57 final size:58
Alignment explanation
Indices: 1245845--1245959 Score: 178
Period size: 57 Copynumber: 2.0 Consensus size: 58
1245835 ATATAAAGAA
* *
1245845 ATTCGGATTTTAAAGGAGCACATTTTCATC-TTAGACAAGCCTTGCATCCGTCAGTGT
1 ATTCGGATTTCAAAGGAGCACATGTTCATCTTTAGACAAGCCTTGCATCCGTCAGTGT
* *
1245902 ATTCGGATTTCAGAGGAGCACGTGTTCATCTTTTAGACAAGCCTTGCATCCGTCAGTG
1 ATTCGGATTTCAAAGGAGCACATGTTCATC-TTTAGACAAGCCTTGCATCCGTCAGTG
1245960 CATGGAGAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
57 26 0.50
59 26 0.50
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (58 bp):
ATTCGGATTTCAAAGGAGCACATGTTCATCTTTAGACAAGCCTTGCATCCGTCAGTGT
Found at i:1249810 original size:16 final size:18
Alignment explanation
Indices: 1249778--1249812 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
1249768 GGTATCGCAG
1249778 AACGAATTTTGTCTTAAA
1 AACGAATTTTGTCTTAAA
1249796 AACG-ATTTT-TCTTAAA
1 AACGAATTTTGTCTTAAA
1249812 A
1 A
1249813 TTGTTTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 5 0.29
18 4 0.24
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (18 bp):
AACGAATTTTGTCTTAAA
Found at i:1263032 original size:51 final size:51
Alignment explanation
Indices: 1262956--1263086 Score: 244
Period size: 51 Copynumber: 2.6 Consensus size: 51
1262946 TTTTACCTTA
1262956 GCACTGTAAGAGCATCGAGAGATAGCCTTGGGTTTTGGTAAACACGTCTTG
1 GCACTGTAAGAGCATCGAGAGATAGCCTTGGGTTTTGGTAAACACGTCTTG
1263007 GCACTGTAAGAGCATCGAGAGATAGCCTTGGGTTTTGGTAAACACGTCTTG
1 GCACTGTAAGAGCATCGAGAGATAGCCTTGGGTTTTGGTAAACACGTCTTG
* *
1263058 GCATTGTAAGAGCATCGAGAGATAACCTT
1 GCACTGTAAGAGCATCGAGAGATAGCCTT
1263087 TTGTCTAGAT
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
51 78 1.00
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.27
Consensus pattern (51 bp):
GCACTGTAAGAGCATCGAGAGATAGCCTTGGGTTTTGGTAAACACGTCTTG
Found at i:1265358 original size:15 final size:13
Alignment explanation
Indices: 1265334--1265382 Score: 66
Period size: 13 Copynumber: 3.8 Consensus size: 13
1265324 ATATCAAATC
1265334 AAAACAAAGAAAA
1 AAAACAAAGAAAA
1265347 AAGAAGCAAAG-AAA
1 AA-AA-CAAAGAAAA
1265361 AAAACAAAGAAAA
1 AAAACAAAGAAAA
1265374 AAAA-AAAGA
1 AAAACAAAGA
1265383 CAAGAAGCAC
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
12 10 0.30
13 11 0.33
14 7 0.21
15 5 0.15
ACGTcount: A:0.82, C:0.06, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAACAAAGAAAA
Found at i:1265370 original size:12 final size:12
Alignment explanation
Indices: 1265334--1265382 Score: 62
Period size: 12 Copynumber: 3.8 Consensus size: 12
1265324 ATATCAAATC
1265334 AAAACAAAGAAAA
1 AAAACAAAG-AAA
1265347 AAGAAGCAAAGAAA
1 AA-AA-CAAAGAAA
1265361 AAAACAAAGAAA
1 AAAACAAAGAAA
*
1265373 AAAAAAAAGA
1 AAAACAAAGA
1265383 CAAGAAGCAC
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
12 17 0.52
13 4 0.12
14 7 0.21
15 5 0.15
ACGTcount: A:0.82, C:0.06, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAACAAAGAAA
Found at i:1266643 original size:35 final size:38
Alignment explanation
Indices: 1266560--1266653 Score: 106
Period size: 35 Copynumber: 2.6 Consensus size: 38
1266550 ACGAAGCGTC
* *
1266560 GTCTCGCTAGAGATAGTTTTTCTAAAAAATAAAATTTT
1 GTCTCGCTTGAGACAGTTTTTCTAAAAAATAAAATTTT
* *
1266598 GTCTCGCTTGAGACAGTTTTT-T-AAAAA-CAATTTTT
1 GTCTCGCTTGAGACAGTTTTTCTAAAAAATAAAATTTT
* *
1266633 TTCTCGCTTGAGATA-TTTTTC
1 GTCTCGCTTGAGACAGTTTTTC
1266654 CTCTGAGATA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
34 5 0.10
35 19 0.39
36 5 0.10
37 1 0.02
38 19 0.39
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.44
Consensus pattern (38 bp):
GTCTCGCTTGAGACAGTTTTTCTAAAAAATAAAATTTT
Found at i:1266808 original size:65 final size:65
Alignment explanation
Indices: 1266733--1266920 Score: 209
Period size: 65 Copynumber: 2.9 Consensus size: 65
1266723 AATAAACTTT
* *
1266733 GTCTCACTTGAGACTGACTTC-CTT-AAGACATCATCTTTGAGATCGTTTCTCTTGAAACAAATT
1 GTCTCACTTGAGACAG-CTTCTCTTGAA-ACATCATCTTTGAGATCGTTTCCCTTGAAACAAATT
1266796 TC
64 TC
* * * *
1266798 GTCTCTCTTGAGACAGTTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAACAAGTTTT
1 GTCTCACTTGAGACAGCTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAACAAATTTC
* * * * * * * *
1266863 GTCTCCCTCGAGATAGTTTATCTTGAAACACCCATCTTTGAGATTGTTTCTCTTGAAA
1 GTCTCACTTGAGACAGCTTCTCTTGAAACA-TCATCTTTGAGATCGTTTCCCTTGAAA
1266921 TGAATTTTAT
Statistics
Matches: 107, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
64 3 0.03
65 78 0.73
66 26 0.24
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.38
Consensus pattern (65 bp):
GTCTCACTTGAGACAGCTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAACAAATTTC
Found at i:1267214 original size:131 final size:131
Alignment explanation
Indices: 1266975--1267329 Score: 369
Period size: 131 Copynumber: 2.7 Consensus size: 131
1266965 CTTGAAAAAA
* * * * *
1266975 ATCCCTAAAGATGGTATGTCATCCTCATCGCATAGGAACCATATCATCCACCGACCAGACCTCCT
1 ATCCCTAAAGATGGCATATCATCCTCATCACGTAGGAACCATATCATCCACCGACTAGACCTCCT
** * * * * *
1267040 CATCACA-TACAAGCCGTGTCACCACTAGATAACCAGTCGTCCTCA-TCACGTAGGAACCGTGTT
66 CATCA-AGTAGGA-TCGTGTCACCCCTAGATAACCAGCCATCCTCATTCA-GGAGGAACCGTGTT
1267103 AT-C
128 ATCC
* * *
1267106 ATCCCTAAAGATGGCATATCATCCTCATCACGTAGGAACCGTGTCATCCACCGACTAGACCTCTT
1 ATCCCTAAAGATGGCATATCATCCTCATCACGTAGGAACCATATCATCCACCGACTAGACCTCCT
* * *
1267171 CATCAAGTAGGATCTGTGTCACCCCTAGATAACTAGCCATCCTCATTGAGGAGGAACTGTGTTAT
66 CATCAAGTAGGATC-GTGTCACCCCTAGATAACCAGCCATCCTCATTCAGGAGGAACCGTGTTAT
1267236 CACC
130 --CC
* * ** *
1267240 ATCCCTAAAGATGGCCA-AGACGTCCTCATCACGTAGGAATAATATCATCCACCGA-TCAGATCT
1 ATCCCTAAAGATGG-CATA-TCATCCTCATCACGTAGGAACCATATCATCCACCGACT-AGACCT
*
1267303 CCTCATCACGTAGGAGTCGTGTCACCC
63 CCTCATCAAGTAGGA-TCGTGTCACCC
1267330 TTAAATGACC
Statistics
Matches: 187, Mismatches: 27, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
130 2 0.01
131 105 0.56
132 2 0.01
134 17 0.09
135 59 0.32
136 2 0.01
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (131 bp):
ATCCCTAAAGATGGCATATCATCCTCATCACGTAGGAACCATATCATCCACCGACTAGACCTCCT
CATCAAGTAGGATCGTGTCACCCCTAGATAACCAGCCATCCTCATTCAGGAGGAACCGTGTTATC
C
Found at i:1267537 original size:3 final size:3
Alignment explanation
Indices: 1267529--1267572 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
1267519 AAAACAATTG
* * * *
1267529 TTA TTA TTA TTG TTG TTG TTA TTA TTA TTA TTA TTA CTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1267573 TAACATATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.25, C:0.02, G:0.07, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1268163 original size:20 final size:21
Alignment explanation
Indices: 1268120--1268178 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
1268110 AAAAATACAG
*
1268120 AGAGAAACTAAAAGAAAAC--C
1 AGAGAAA-TAAAAGAAAACAAA
1268140 AGAGAAA-AAAAGAAAACAAA
1 AGAGAAATAAAAGAAAACAAA
*
1268160 AGAGAAATAAAAGGAAACA
1 AGAGAAATAAAAGAAAACA
1268179 CATTCGAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 10 0.29
20 14 0.41
21 10 0.29
ACGTcount: A:0.71, C:0.08, G:0.17, T:0.03
Consensus pattern (21 bp):
AGAGAAATAAAAGAAAACAAA
Found at i:1268177 original size:21 final size:20
Alignment explanation
Indices: 1268140--1268178 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1268130 AAAGAAAACC
1268140 AGAGAAAAAAAGAAAACAAA
1 AGAGAAAAAAAGAAAACAAA
*
1268160 AGAGAAATAAAAGGAAACA
1 AGAGAAA-AAAAGAAAACA
1268179 CATTCGAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.74, C:0.05, G:0.18, T:0.03
Consensus pattern (20 bp):
AGAGAAAAAAAGAAAACAAA
Found at i:1270715 original size:33 final size:33
Alignment explanation
Indices: 1270668--1270771 Score: 174
Period size: 33 Copynumber: 3.2 Consensus size: 33
1270658 ACAAAGTTTA
* *
1270668 CGAT-AATTGAAATACTTAAATACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
*
1270700 CGATAAATTCAAATACTTAAAAATTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
1270733 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
1270766 CGATAA
1 CGATAA
1270772 TTGAAACAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 4 0.06
33 63 0.94
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (33 bp):
CGATAAATTCAAATACTTAAAAACTTCCAAGTT
Found at i:1270790 original size:21 final size:21
Alignment explanation
Indices: 1270766--1270807 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1270756 CTTCCAAGTT
1270766 CGATAATTGAAACAAAATTTA
1 CGATAATTGAAACAAAATTTA
* *
1270787 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAATTTA
1270808 AAAATAAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAATTTA
Found at i:1275429 original size:26 final size:26
Alignment explanation
Indices: 1275400--1275550 Score: 85
Period size: 26 Copynumber: 5.5 Consensus size: 26
1275390 GAAAAACATT
1275400 ATTATATAATATAGTTTTTTAAAATA
1 ATTATATAATATAGTTTTTTAAAATA
* * **
1275426 A-T-TATCATGTAGTTTTAAAAACCATTA
1 ATTATATAATATAGTTTTTTAAA--A-TA
*
1275453 TTCTATATAATATAG-TTTTTAAAATA
1 AT-TATATAATATAGTTTTTTAAAATA
**
1275479 ATTATTATAATATAG-TTTAGAAAACTA
1 ATTA-TATAATATAGTTTTTTAAAA-TA
*
1275506 TTATTATATATAGTATAGTTTTTTTAATATA
1 --ATTATATA-A-TATAG-TTTTTTAAAATA
*
1275537 ATTATTATTATATA
1 ATTA-TATAATATA
1275551 TAGCATAGTT
Statistics
Matches: 94, Mismatches: 16, Indels: 28
0.68 0.12 0.20
Matches are distributed among these distances:
24 15 0.16
25 3 0.03
26 22 0.23
27 5 0.05
28 8 0.09
29 17 0.18
30 16 0.17
31 2 0.02
32 6 0.06
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.49
Consensus pattern (26 bp):
ATTATATAATATAGTTTTTTAAAATA
Found at i:1275471 original size:30 final size:29
Alignment explanation
Indices: 1275350--1275527 Score: 112
Period size: 30 Copynumber: 6.4 Consensus size: 29
1275340 CGAAACCTCC
* * *
1275350 AATATAGTTTTTAGAAATATTTATTATGTA-
1 AATATAG-TTTTAAAAACA-TTATTATATAT
1275380 AA-ATAGTTTTGAAAAACATTA-T-TATAT
1 AATATAGTTTT-AAAAACATTATTATATAT
**
1275407 AATATAGTTTTTTAAA-A-TA--AT-TAT
1 AATATAGTTTTAAAAACATTATTATATAT
* * *
1275431 CATGTAGTTTTAAAAACCATTATTCTATAT
1 AATATAGTTTTAAAAA-CATTATTATATAT
* *
1275461 AATATAGTTTT-TAAA-ATAATTAT-TAT
1 AATATAGTTTTAAAAACATTATTATATAT
1275487 AATATAG-TTTAGAAAACTATTATTATATAT
1 AATATAGTTTTA-AAAAC-ATTATTATATAT
*
1275517 AGTATAGTTTT
1 AATATAGTTTT
1275528 TTTAATATAA
Statistics
Matches: 114, Mismatches: 18, Indels: 31
0.70 0.11 0.19
Matches are distributed among these distances:
24 15 0.13
25 6 0.05
26 15 0.13
27 17 0.15
28 15 0.13
29 20 0.18
30 23 0.20
31 3 0.03
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (29 bp):
AATATAGTTTTAAAAACATTATTATATAT
Found at i:1275509 original size:56 final size:55
Alignment explanation
Indices: 1275350--1275550 Score: 191
Period size: 56 Copynumber: 3.6 Consensus size: 55
1275340 CGAAACCTCC
* * *
1275350 AATATAG-TTTTTAGAAATATTTATTATGTAAAATAGTTTTGAAAAACATTA-TTATAT
1 AATATAGTTTTTTA-AAATAATTATTA--TAATATAGTTTAG-AAAACATTATTTATAT
* *
1275407 AATATAGTTTTTTAAAAT-A--ATTATCATGTAGTTTTA-AAAACCATTATTCTATAT
1 AATATAGTTTTTTAAAATAATTATTATAATATAG-TTTAGAAAA-CATTATT-TATAT
1275461 AATATAG-TTTTTAAAATAATTATTATAATATAGTTTAGAAAACTATTATTATATAT
1 AATATAGTTTTTTAAAATAATTATTATAATATAGTTTAGAAAAC-ATTATT-TATAT
* * *
1275517 AGTATAGTTTTTTTAATATAATTATTATTATATA
1 AATATAG-TTTTTTAAAATAATTATTATAATATA
1275551 TAGCATAGTT
Statistics
Matches: 121, Mismatches: 11, Indels: 23
0.78 0.07 0.15
Matches are distributed among these distances:
51 4 0.03
52 10 0.08
53 14 0.12
54 17 0.14
55 5 0.04
56 31 0.26
57 11 0.09
58 29 0.24
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (55 bp):
AATATAGTTTTTTAAAATAATTATTATAATATAGTTTAGAAAACATTATTTATAT
Found at i:1278089 original size:21 final size:21
Alignment explanation
Indices: 1278065--1278106 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1278055 AATTTATTTT
1278065 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
1278086 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
1278107 AACTTGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:1278143 original size:33 final size:32
Alignment explanation
Indices: 1278095--1278171 Score: 109
Period size: 33 Copynumber: 2.4 Consensus size: 32
1278085 GTAAACTTTG
*
1278095 TTTCAATTATCGAACTTGAAAATTTTTAAGTA
1 TTTCAATTATCGAACTTGAAAATATTTAAGTA
* * *
1278127 TTTGAATTTATCGAACTTGGAAGTATTTAAGTA
1 TTTCAA-TTATCGAACTTGAAAATATTTAAGTA
1278160 TTTCAATTATCG
1 TTTCAATTATCG
1278172 TAACCTTTGT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
32 11 0.28
33 28 0.72
ACGTcount: A:0.34, C:0.09, G:0.13, T:0.44
Consensus pattern (32 bp):
TTTCAATTATCGAACTTGAAAATATTTAAGTA
Found at i:1279664 original size:15 final size:15
Alignment explanation
Indices: 1279627--1279713 Score: 129
Period size: 15 Copynumber: 5.7 Consensus size: 15
1279617 TCCAGAGCCT
*
1279627 CTTAATCATTCAGCA
1 CTTAATCATTCAGCG
*
1279642 TTTAAATCATTCAGCG
1 CTT-AATCATTCAGCG
*
1279658 TTTAATCATTCAGCG
1 CTTAATCATTCAGCG
*
1279673 CTTAATTATTCAGCG
1 CTTAATCATTCAGCG
1279688 CTTAATCATTCAGCG
1 CTTAATCATTCAGCG
1279703 CTTAATCATTC
1 CTTAATCATTC
1279714 TAAAATAAAC
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
15 52 0.79
16 14 0.21
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38
Consensus pattern (15 bp):
CTTAATCATTCAGCG
Found at i:1281707 original size:14 final size:14
Alignment explanation
Indices: 1281688--1281714 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1281678 ACCAGTTAAA
1281688 GTTAATTAATTTTT
1 GTTAATTAATTTTT
1281702 GTTAATTAATTTT
1 GTTAATTAATTTT
1281715 ACTTTAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (14 bp):
GTTAATTAATTTTT
Found at i:1281723 original size:11 final size:11
Alignment explanation
Indices: 1281707--1281740 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
1281697 TTTTTGTTAA
1281707 TTAATTTTACT
1 TTAATTTTACT
*
1281718 TTAATTACTACT
1 TTAATT-TTACT
1281730 TTAATTTTACT
1 TTAATTTTACT
1281741 AACTTATTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.59
Consensus pattern (11 bp):
TTAATTTTACT
Found at i:1286065 original size:17 final size:17
Alignment explanation
Indices: 1286006--1286065 Score: 50
Period size: 17 Copynumber: 3.2 Consensus size: 17
1285996 ATTGTCTCTA
1286006 AAAATTCAAAATATATTT
1 AAAATT-AAAATATATTT
*
1286024 -AATTTAAATTTATATTATTT
1 AAAATTAAA---ATA-TATTT
1286044 CAAAATTAAAATATATTT
1 -AAAATTAAAATATATTT
1286062 AAAA
1 AAAA
1286066 ATATCGGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 13
0.69 0.04 0.27
Matches are distributed among these distances:
16 3 0.09
17 8 0.24
18 5 0.15
19 6 0.18
20 5 0.15
22 7 0.21
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (17 bp):
AAAATTAAAATATATTT
Found at i:1286901 original size:13 final size:13
Alignment explanation
Indices: 1286883--1286911 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1286873 CCACCGTACT
1286883 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
1286896 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
1286909 CCG
1 CCG
1286912 TAACGGTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.62, G:0.31, T:0.00
Consensus pattern (13 bp):
CCGCCGCCGGCCA
Found at i:1287634 original size:3 final size:3
Alignment explanation
Indices: 1287626--1287749 Score: 194
Period size: 3 Copynumber: 40.7 Consensus size: 3
1287616 TTATTTATTA
*
1287626 AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAAT AAT AAT AAT AAT AAT
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT
*
1287673 AAT AAT AAT AAT AAT TAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
**
1287721 AAT AAT AAT AAT AAT TTT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1287750 CTTTAAATGA
Statistics
Matches: 111, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
3 105 0.95
4 6 0.05
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:1288012 original size:76 final size:76
Alignment explanation
Indices: 1287878--1289356 Score: 2762
Period size: 76 Copynumber: 19.5 Consensus size: 76
1287868 GATGGAAATG
* * *
1287878 TTTGAAAACATCATGCACTGAAGAACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1287943 CCCGAAGGCTT
66 CCCGAAGGCTT
1287954 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1288019 CCCGAAGGCTT
66 CCCGAAGGCTT
1288030 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
*
1288095 CACGAAGGCTT
66 CCCGAAGGCTT
*
1288106 TTTGGAAACATCATGCACTGAAGGACTTACAGATGATCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
*
1288171 CACGAAGGCTT
66 CCCGAAGGCTT
*
1288182 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1288247 CCCGAAGGCTT
66 CCCGAAGGCTT
*
1288258 TTTGGAAACATCATGCACTGAAGGACTTACAGATGATCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1288323 CCCGAAGGCTT
66 CCCGAAGGCTT
1288334 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1288399 CCCGAAGGCTT
66 CCCGAAGGCTT
*
1288410 TTTGGAAACATCATGCACTGAAGGACTTACAGATGATCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1288475 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
1288486 TTTGGAAACATCATGCACTGAAGAACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1288551 CCCGAAGGCTT
66 CCCGAAGGCTT
1288562 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1288627 CCCGAAGGCTT
66 CCCGAAGGCTT
1288638 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
**
1288703 CATGAAGGCTT
66 CCCGAAGGCTT
*
1288714 TTTGGAAACATCATGCACTGAAGGACTTACAGATGATCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
*
1288779 CACGAAGGCTT
66 CCCGAAGGCTT
*
1288790 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAATATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1288855 CCCGAAGGCTT
66 CCCGAAGGCTT
*
1288866 TTTGGAAACATCATGCACTGAAGGACTTACAGATGATCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1288931 CCCGAAGGCTT
66 CCCGAAGGCTT
1288942 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1289007 CCCGAAGGCTT
66 CCCGAAGGCTT
*
1289018 TTTGGAAACATCATGCACTGAAGGACTTACAGATGATCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1289083 CCCGAAGGCTT
66 CCCGAAGGCTT
1289094 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1289159 CCCGAAGGCTT
66 CCCGAAGGCTT
1289170 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1289235 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
1289246 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAATATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1289311 CCC-AACGGCTT
66 CCCGAA-GGCTT
1289322 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
1289357 TGAGAAATAG
Statistics
Matches: 1371, Mismatches: 31, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
75 2 0.00
76 1369 1.00
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.22
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:1290498 original size:59 final size:59
Alignment explanation
Indices: 1290406--1290552 Score: 260
Period size: 59 Copynumber: 2.5 Consensus size: 59
1290396 GGTTCGTAAA
* *
1290406 ACATTCAT-CTTTTCATGTGGTTTCTGCTCGGATTATTGGTCAAGGAAGCATTTGACAAC
1 ACATTCATCCTTTCCGT-TGGTTTCTGCTCGGATTATTGGTCAAGGAAGCATTTGACAAC
1290465 ACATTCATCCTTTCCGTTGGTTTCTGCTCGGATTATTGGTCAAGGAAGCATTTGACAAC
1 ACATTCATCCTTTCCGTTGGTTTCTGCTCGGATTATTGGTCAAGGAAGCATTTGACAAC
1290524 ACATTCATCCTTTCCGTTGGTTTCTGCTC
1 ACATTCATCCTTTCCGTTGGTTTCTGCTC
1290553 AGATGTTCTC
Statistics
Matches: 85, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
59 79 0.93
60 6 0.07
ACGTcount: A:0.20, C:0.22, G:0.19, T:0.38
Consensus pattern (59 bp):
ACATTCATCCTTTCCGTTGGTTTCTGCTCGGATTATTGGTCAAGGAAGCATTTGACAAC
Found at i:1292712 original size:83 final size:83
Alignment explanation
Indices: 1292570--1292873 Score: 538
Period size: 83 Copynumber: 3.7 Consensus size: 83
1292560 ACTGAATCAT
* *
1292570 ATCAGATAACTCAAAGAACACTTCCAGAAGATGATATTGGCAAATTTATCTTCTGAATTCAATGA
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGATATTGGCAAATTCATCTTCTAAATTCAATGA
1292635 TTGGTTCTGTTCAACCAG
66 TTGGTTCTGTTCAACCAG
*
1292653 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAATGA
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGATATTGGCAAATTCATCTTCTAAATTCAATGA
*
1292718 TTGGTTCTG-CCAAACCAG
66 TTGGTTCTGTTC-AACCAG
*
1292736 ATCAGATAACTCAAAGAACACTTCCAGAAGATGATATTGGCAAATTCATCTTCTGAATTCAATGA
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGATATTGGCAAATTCATCTTCTAAATTCAATGA
1292801 TTGGTTCTGTTCAACCAG
66 TTGGTTCTGTTCAACCAG
*
1292819 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTA
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGATATTGGCAAATTCATCTTCTA
1292874 GTTAATGTTT
Statistics
Matches: 210, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
82 1 0.00
83 208 0.99
84 1 0.00
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (83 bp):
ATCAGATAACTCAAAGAACACTTCCAGAAGATGATATTGGCAAATTCATCTTCTAAATTCAATGA
TTGGTTCTGTTCAACCAG
Found at i:1292844 original size:166 final size:166
Alignment explanation
Indices: 1292570--1292873 Score: 599
Period size: 166 Copynumber: 1.8 Consensus size: 166
1292560 ACTGAATCAT
*
1292570 ATCAGATAACTCAAAGAACACTTCCAGAAGATGATATTGGCAAATTTATCTTCTGAATTCAATGA
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGATATTGGCAAATTCATCTTCTGAATTCAATGA
1292635 TTGGTTCTGTTCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTC
66 TTGGTTCTGTTCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTC
1292700 ATCTTCTAAATTCAATGATTGGTTCTGCCAAACCAG
131 ATCTTCTAAATTCAATGATTGGTTCTGCCAAACCAG
1292736 ATCAGATAACTCAAAGAACACTTCCAGAAGATGATATTGGCAAATTCATCTTCTGAATTCAATGA
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGATATTGGCAAATTCATCTTCTGAATTCAATGA
1292801 TTGGTTCTGTTCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTC
66 TTGGTTCTGTTCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTC
1292866 ATCTTCTA
131 ATCTTCTA
1292874 GTTAATGTTT
Statistics
Matches: 137, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
166 137 1.00
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (166 bp):
ATCAGATAACTCAAAGAACACTTCCAGAAGATGATATTGGCAAATTCATCTTCTGAATTCAATGA
TTGGTTCTGTTCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTC
ATCTTCTAAATTCAATGATTGGTTCTGCCAAACCAG
Found at i:1300112 original size:17 final size:17
Alignment explanation
Indices: 1300053--1300112 Score: 50
Period size: 17 Copynumber: 3.2 Consensus size: 17
1300043 ATTGTCTCTA
1300053 AAAATTCAAAATATATTT
1 AAAATT-AAAATATATTT
*
1300071 -AATTTAAATTTATATTATTT
1 AAAATTAAA---ATA-TATTT
1300091 CAAAATTAAAATATATTT
1 -AAAATTAAAATATATTT
1300109 AAAA
1 AAAA
1300113 ATATCGGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 13
0.69 0.04 0.27
Matches are distributed among these distances:
16 3 0.09
17 8 0.24
18 5 0.15
19 6 0.18
20 5 0.15
22 7 0.21
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (17 bp):
AAAATTAAAATATATTT
Found at i:1300931 original size:13 final size:13
Alignment explanation
Indices: 1300913--1300941 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1300903 CCACCGTACT
1300913 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
1300926 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
1300939 CCG
1 CCG
1300942 TAACGGTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.62, G:0.31, T:0.00
Consensus pattern (13 bp):
CCGCCGCCGGCCA
Found at i:1301661 original size:3 final size:3
Alignment explanation
Indices: 1301653--1301761 Score: 132
Period size: 3 Copynumber: 36.0 Consensus size: 3
1301643 AATTATTTAT
* *
1301653 TAA TAA TAA TATA TAA TAT TAAA TAA TAA TAA TAA TAA TAA T-A TAT
1 TAA TAA TAA TA-A TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
* *
1301699 TAA TAA TAA TAC TAA TAA TAA TAA TAA TAC TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1301747 -ATT TAA TAA TAA TAA
1 TA-A TAA TAA TAA TAA
1301762 CTTTAAATGA
Statistics
Matches: 91, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
2 3 0.03
3 82 0.90
4 6 0.07
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1306704 original size:44 final size:44
Alignment explanation
Indices: 1306527--1307050 Score: 655
Period size: 44 Copynumber: 12.0 Consensus size: 44
1306517 AAAAGAGCCT
* * * ** * *
1306527 GGGAAACGGTAAGGTCTTATCCTTGCACATAGTAGAGGAGCCT--
1 GGGAAACTGTAAGG-CTTACCCTTGCACACAACAAAGGAACCTGG
* *
1306570 GGGAAACAGTAAGGCTTACCCTTGCACACAGCAAAGGAACCT-G
1 GGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGG
*
1306613 GGAAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCT-G
1 GGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGG
* * * **
1306656 GGGAAACTGTAAGGCTTACCTTTGCACATAGCAAATAAACCTGG
1 GGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGG
*
1306700 GGGAAACTGTAAGGCTTACCCTTACACACAACAAAGGAACCTGG
1 GGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGG
*
1306744 GGGAAACTGTAAGGCTTACCCTTCCACACAACAAAGGAACCTGG
1 GGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGG
* * * * **
1306788 GGGAAATTGTAAGGCATACCCTTGCACACAATAAAGCAACCTAA
1 GGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGG
* * *
1306832 GGGAAACTGTAAGGCATACCCTTGCACACAACAAAGCAACCTAG
1 GGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGG
* * * *
1306876 GGAAAACTCTAAGGCTTACCCTTTCATACAACAAAGGAACCTGG
1 GGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGG
* *
1306920 GGGAAAGTGTAAGGCTTACCCGTT-CACACAACAAAGGAACCTGA
1 GGGAAACTGTAAGGCTTACCC-TTGCACACAACAAAGGAACCTGG
* * *
1306964 GGGAAACTTTAAGGCTTACCCATGCACGCAACAAAGGAACCT-G
1 GGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGG
* *
1307007 GGGAAACTGTAAGCCTTACCCTTGCACACAGCAAAGGAACCTGG
1 GGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGG
1307051 AGAAAACAGG
Statistics
Matches: 422, Mismatches: 54, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
42 23 0.05
43 127 0.30
44 270 0.64
45 2 0.00
ACGTcount: A:0.35, C:0.24, G:0.23, T:0.17
Consensus pattern (44 bp):
GGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGG
Found at i:1307531 original size:38 final size:37
Alignment explanation
Indices: 1307489--1307593 Score: 110
Period size: 39 Copynumber: 2.8 Consensus size: 37
1307479 AGAAATGCAT
1307489 AAATATGAAAATAATAAACAAAAAAAATAACAAAGGAA
1 AAATATGAAAATAATAAACAAAAAAAATAA-AAAGGAA
* * * *
1307527 AAATATTGAAAAAAATAAAACAAAATAAATAAAATGGTA
1 AAATA-TGAAAATAAT-AAACAAAAAAAATAAAAAGGAA
1307566 AAATA-G-AAAT-A-AAACAAAACAAAATAAA
1 AAATATGAAAATAATAAACAAAA-AAAATAAA
1307594 TAAAAATAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
33 8 0.14
34 7 0.12
35 1 0.02
36 3 0.05
37 1 0.02
38 5 0.09
39 19 0.33
40 14 0.24
ACGTcount: A:0.73, C:0.05, G:0.07, T:0.15
Consensus pattern (37 bp):
AAATATGAAAATAATAAACAAAAAAAATAAAAAGGAA
Found at i:1307594 original size:38 final size:38
Alignment explanation
Indices: 1307489--1307616 Score: 129
Period size: 38 Copynumber: 3.4 Consensus size: 38
1307479 AGAAATGCAT
* * *
1307489 AAATATGAAAATAA-TAAACAAAAAAAATAACAAAGGAA
1 AAATATGAAAAAAACAAAACAAAATAAATAA-AAAGGAA
* * *
1307527 AAATATTGAAAAAAATAAAACAAAATAAATAAAATGGTA
1 AAATA-TGAAAAAAACAAAACAAAATAAATAAAAAGGAA
*
1307566 AAATA-GAAATAAAACAAAACAAAATAAATAAAAA-TAA
1 AAATATGAAA-AAAACAAAACAAAATAAATAAAAAGGAA
1307603 AAATA-GAACAAAAA
1 AAATATGAA-AAAAA
1307617 TAAGAATAAA
Statistics
Matches: 77, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
37 17 0.22
38 28 0.36
39 18 0.23
40 14 0.18
ACGTcount: A:0.74, C:0.05, G:0.06, T:0.15
Consensus pattern (38 bp):
AAATATGAAAAAAACAAAACAAAATAAATAAAAAGGAA
Found at i:1307722 original size:2 final size:2
Alignment explanation
Indices: 1307715--1307770 Score: 89
Period size: 2 Copynumber: 29.0 Consensus size: 2
1307705 AAAATAATAG
*
1307715 AT AT AT AT A- AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1307756 AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT
1307771 TAATGATAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
1 2 0.04
2 48 0.96
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1307774 original size:6 final size:7
Alignment explanation
Indices: 1307708--1307774 Score: 61
Period size: 8 Copynumber: 9.7 Consensus size: 7
1307698 AAAAATAAAA
*
1307708 ATAATAG
1 ATAATAT
1307715 AT-ATAT
1 ATAATAT
*
1307721 ATAATAA
1 ATAATAT
1307728 AT-ATAT
1 ATAATAT
1307734 AT-ATAT
1 ATAATAT
1307740 ATATATAT
1 ATA-ATAT
1307748 ATATATAT
1 ATA-ATAT
1307756 ATATATAT
1 ATA-ATAT
1307764 ATAATAT
1 ATAATAT
1307771 -TAAT
1 ATAAT
1307775 GATAATAATG
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
6 20 0.37
7 11 0.20
8 23 0.43
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (7 bp):
ATAATAT
Found at i:1309881 original size:21 final size:21
Alignment explanation
Indices: 1309855--1309899 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1309845 GATTTCTGGG
* *
1309855 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
1309876 CAAGGGGAACCGATACCCATT
1 CAAGGGGAACCGATACCCATT
1309897 CAA
1 CAA
1309900 ACGAACAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.27, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1315079 original size:21 final size:21
Alignment explanation
Indices: 1315053--1315097 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1315043 GATTTATGGG
* *
1315053 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1315074 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1315095 CAA
1 CAA
1315098 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1316965 original size:23 final size:23
Alignment explanation
Indices: 1316920--1316965 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1316910 CATCATTATA
*
1316920 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTATACG
* *
1316943 TGGCACTTCGGTGCATTTATACG
1 TGGCACTACGGTGCAATTATACG
1316966 AGCTGTGGTG
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:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTATACG
Found at i:1324493 original size:10 final size:10
Alignment explanation
Indices: 1324487--1324527 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
1324477 GGAAAAATAT
1324487 TGAAAAAAAA
1 TGAAAAAAAA
1324497 TGAAAAAAAA
1 TGAAAAAAAA
1324507 T-AAAACAAAA
1 TGAAAA-AAAA
*
1324517 T-AAATAAAA
1 TGAAAAAAAA
1324526 TG
1 TG
1324528 GTAAAATAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 9 0.32
10 19 0.68
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.15
Consensus pattern (10 bp):
TGAAAAAAAA
Found at i:1324577 original size:12 final size:12
Alignment explanation
Indices: 1324556--1324594 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
1324546 AAAACAAATA
1324556 AAAAAT-AGAAC
1 AAAAATAAGAAC
1324567 AAAAATAAGAAC
1 AAAAATAAGAAC
1324579 AAAAATAAGAA-
1 AAAAATAAGAAC
1324590 AAAAA
1 AAAAA
1324595 AACAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 11 0.41
12 16 0.59
ACGTcount: A:0.79, C:0.05, G:0.08, T:0.08
Consensus pattern (12 bp):
AAAAATAAGAAC
Found at i:1324580 original size:33 final size:31
Alignment explanation
Indices: 1324491--1324611 Score: 97
Period size: 33 Copynumber: 3.8 Consensus size: 31
1324481 AAATATTGAA
*
1324491 AAAAAAT-GAAAAAAAATAAAACAAAATAAAT
1 AAAAAATAGAACAAAAATAAAACAAAA-AAAT
** * * *
1324522 AAAATGGTAAAATAGAAATAAAACAAAACAAAT
1 AAAA-AATAGAACAAAAATAAAACAAAA-AAAT
*
1324555 AAAAAATAGAACAAAAATAAGAACAAAAATAAG
1 AAAAAATAGAACAAAAATAA-AACAAAAA-AAT
1324588 AAAAAA-A-AACAAAAA-AAACACAAA
1 AAAAAATAGAACAAAAATAAA-ACAAA
1324612 TATAACGAAA
Statistics
Matches: 73, Mismatches: 12, Indels: 11
0.76 0.12 0.11
Matches are distributed among these distances:
29 1 0.01
30 7 0.10
31 12 0.16
32 14 0.19
33 39 0.53
ACGTcount: A:0.78, C:0.07, G:0.06, T:0.10
Consensus pattern (31 bp):
AAAAAATAGAACAAAAATAAAACAAAAAAAT
Found at i:1324611 original size:30 final size:30
Alignment explanation
Indices: 1324541--1324622 Score: 78
Period size: 31 Copynumber: 2.7 Consensus size: 30
1324531 AAATAGAAAT
* * *
1324541 AAAACAAAACAAATAA-AAAATAGAACAAAA
1 AAAACACAA-AAATAAGAAAAAAAAACAAAA
1324571 ATAAGA-ACAAAAATAAGAAAAAAAAACAAAA
1 A-AA-ACACAAAAATAAGAAAAAAAAACAAAA
*
1324602 AAAACACAAATATAACGAAAA
1 AAAACACAAAAATAA-GAAAA
1324623 GTGAAAACAA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
29 1 0.02
30 18 0.42
31 23 0.53
32 1 0.02
ACGTcount: A:0.78, C:0.10, G:0.05, T:0.07
Consensus pattern (30 bp):
AAAACACAAAAATAAGAAAAAAAAACAAAA
Found at i:1325099 original size:3 final size:3
Alignment explanation
Indices: 1325091--1325163 Score: 64
Period size: 3 Copynumber: 24.7 Consensus size: 3
1325081 ATAAACAAAA
* *
1325091 AAT AAT AAT AAGT AAT CA- AAT AAA AAT AA- AAT AA- ACA- AAT AAAT
1 AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT -AAT
*
1325135 AAT AAT AAT AAT AAT AAT AAT ATT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1325164 AATGATTAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
2 5 0.09
3 47 0.81
4 6 0.10
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:1325171 original size:12 final size:12
Alignment explanation
Indices: 1325134--1325172 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
1325124 AACAAATAAA
*
1325134 TAATAATAATAA
1 TAATAATAATAT
1325146 TAATAATAATAT
1 TAATAATAATAT
1325158 TAATAA-AATGAT
1 TAATAATAAT-AT
1325170 TAA
1 TAA
1325173 AAAGCTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 3 0.12
12 22 0.88
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (12 bp):
TAATAATAATAT
Found at i:1325228 original size:21 final size:21
Alignment explanation
Indices: 1325198--1325241 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1325188 ATAATGTAAC
*
1325198 TATATGATATAAATAAATATA
1 TATATGATATAAACAAATATA
*
1325219 TATATTATATAAACAAATATA
1 TATATGATATAAACAAATATA
1325240 TA
1 TA
1325242 CAAAAATGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (21 bp):
TATATGATATAAACAAATATA
Found at i:1325345 original size:27 final size:27
Alignment explanation
Indices: 1325256--1325348 Score: 68
Period size: 27 Copynumber: 3.5 Consensus size: 27
1325246 AATGTTAGGT
* * * *
1325256 AAAAACAAATAAACAAATAAACATATA
1 AAAAATAATTAAATAAATAAATATATA
*
1325283 AAATAA-AA-TAAA-AAATATATATAT-
1 AAA-AATAATTAAATAAATAAATATATA
***
1325307 AACGTTAGATTAAATAAATAAATATATA
1 AAAAATA-ATTAAATAAATAAATATATA
1325335 AAAAATAATTAAAT
1 AAAAATAATTAAAT
1325349 CGTAAATTAA
Statistics
Matches: 51, Mismatches: 9, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
24 3 0.06
25 11 0.22
26 8 0.16
27 23 0.45
28 6 0.12
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.26
Consensus pattern (27 bp):
AAAAATAATTAAATAAATAAATATATA
Found at i:1326391 original size:2 final size:2
Alignment explanation
Indices: 1326384--1326435 Score: 67
Period size: 2 Copynumber: 27.5 Consensus size: 2
1326374 AATAAATAAT
1326384 TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA -A TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1326423 TA TGA TA TA -A TA T
1 TA T-A TA TA TA TA T
1326436 TGATGGACAA
Statistics
Matches: 45, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
1 4 0.09
2 39 0.87
3 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1326402 original size:15 final size:15
Alignment explanation
Indices: 1326382--1326435 Score: 71
Period size: 15 Copynumber: 3.9 Consensus size: 15
1326372 TAAATAAATA
1326382 ATTATATATATATAT
1 ATTATATATATATAT
1326397 ATTATATATATATAT
1 ATTATATATATATAT
1326412 A-TATA-ATAT-TAT
1 ATTATATATATATAT
*
1326424 ATGATATA-ATAT
1 ATTATATATATAT
1326436 TGATGGACAA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
12 4 0.11
13 9 0.26
14 6 0.17
15 16 0.46
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (15 bp):
ATTATATATATATAT
Found at i:1326406 original size:17 final size:17
Alignment explanation
Indices: 1326379--1326435 Score: 73
Period size: 17 Copynumber: 3.4 Consensus size: 17
1326369 AAATAAATAA
1326379 ATAATTATATATATATAT
1 ATAA-TATATATATATAT
*
1326397 ATTATATATATATATAT
1 ATAATATATATATATAT
*
1326414 ATAATAT-TATAT-GAT
1 ATAATATATATATATAT
1326429 ATAATAT
1 ATAATAT
1326436 TGATGGACAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
15 9 0.25
16 5 0.14
17 19 0.53
18 3 0.08
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (17 bp):
ATAATATATATATATAT
Found at i:1326436 original size:15 final size:14
Alignment explanation
Indices: 1326382--1326436 Score: 66
Period size: 11 Copynumber: 4.2 Consensus size: 14
1326372 TAAATAAATA
1326382 ATTATATATAT-AT
1 ATTATATATATAAT
1326395 A-TAT-TATAT-AT
1 ATTATATATATAAT
1326406 A-TATATATATAAT
1 ATTATATATATAAT
1326419 ATTATATGATATAAT
1 ATTATAT-ATATAAT
1326434 ATT
1 ATT
1326437 GATGGACAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
11 11 0.29
12 8 0.21
13 4 0.11
14 5 0.13
15 10 0.26
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (14 bp):
ATTATATATATAAT
Found at i:1331203 original size:129 final size:129
Alignment explanation
Indices: 1330979--1331533 Score: 584
Period size: 129 Copynumber: 4.3 Consensus size: 129
1330969 AATTCCATTT
* ** * *
1330979 TCTATCTTGATCTGACCTACCCTGAAGAGCAATTGAGCAAATCCTATTTTCTTTGAATCTGACTT
1 TCTATCTTGATCTAACCTACCCTGAAGAGCAACGGAGCAAATCCTCTTTTCTTTGAATCTGACCT
* * * * * * *
1331044 ACCCT-AAAAAGTAACAAATCATATTCCATTAGATTTGACCTACCCTGAAGAGTAGTGGAGTAAA
66 ACCTTGAAGAA-CAACGAAGCAAATTCCATTAGATTTGACCTACCCTGAAGAGTAGTGGAGCAAA
* * * *
1331108 TCTATCTTAATCAAACCTACCCTGAAGAGCAGCAGAGCAAATCCTCTTTTCTTTGAATCTGACCT
1 TCTATCTTGATCTAACCTACCCTGAAGAGCAACGGAGCAAATCCTCTTTTCTTTGAATCTGACCT
* * *
1331173 ACCTTGAAGAACAACGAAGCAAATTTCATTAGATTTGACCTACCCTGAAGAGTAATAGAGCAAA
66 ACCTTGAAGAACAACGAAGCAAATTCCATTAGATTTGACCTACCCTGAAGAGTAGTGGAGCAAA
* * * * * * * *
1331237 TTTATCTTGATTTGACCTACCCTGAAGAGCAACGAAGCATATCC-CTTTTTCTTTAAATCTTACA
1 TCTATCTTGATCTAACCTACCCTGAAGAGCAACGGAGCAAATCCTC-TTTTCTTTGAATCTGACC
* **** *
1331301 TGCCTTGAAGAGTGGC-ATAGCACATTCCA-TAGATTTGACCTACCCTGAAGAGTAGT-GAGGCA
65 TACCTTGAAGAACAACGA-AGCAAATTCCATTAGATTTGACCTACCCTGAAGAGTAGTGGA-GCA
1331363 AA
128 AA
* * * * *
1331365 TCTATCTTGATCTAACATACCCTGAAGTA-CAATGGAGCATATCCCCTTTTCTTTGAATTTGACC
1 TCTATCTTGATCTAACCTACCCTGAAG-AGCAACGGAGCAAATCCTCTTTTCTTTGAATCTGACC
* * * * * * *
1331429 TACCTTGAAGAGCAGCGGAGCAGATTCCATTAGATTTGACATACCATGAAGAGTAGTGAAGCAAA
65 TACCTTGAAGAACAACGAAGCAAATTCCATTAGATTTGACCTACCCTGAAGAGTAGTGGAGCAAA
*
1331494 TCTATCTTGAATCTAACCTACCCTAAAGAG-AAGCGGAGCA
1 TCTATCTTG-ATCTAACCTACCCTGAAGAGCAA-CGGAGCA
1331534 GATTCCATTA
Statistics
Matches: 355, Mismatches: 59, Indels: 23
0.81 0.14 0.05
Matches are distributed among these distances:
127 2 0.01
128 106 0.30
129 220 0.62
130 27 0.08
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.29
Consensus pattern (129 bp):
TCTATCTTGATCTAACCTACCCTGAAGAGCAACGGAGCAAATCCTCTTTTCTTTGAATCTGACCT
ACCTTGAAGAACAACGAAGCAAATTCCATTAGATTTGACCTACCCTGAAGAGTAGTGGAGCAAA
Found at i:1331416 original size:257 final size:258
Alignment explanation
Indices: 1330979--1331523 Score: 670
Period size: 257 Copynumber: 2.1 Consensus size: 258
1330969 AATTCCATTT
* * *
1330979 TCTATCTTGATCTGACCTACCCTGAAGAGCAATTGAGCAAATCCTATTTTCTTTGAATCTGACTT
1 TCTATCTTGATCTGACCTACCCTGAAGAGCAATCGAGCAAATCCTATTTTCTTTAAATCTGACAT
* * *
1331044 ACCCTAAAAAGTAACAAATCATATTCCATTAGATTTGACCTACCCTGAAGAGTAGTGGAGTAAAT
66 ACCCTAAAAAGTAACAAAGCACATTCCATTAGATTTGACCTACCCTGAAGAGTAGTGGAGCAAAT
* * *
1331109 CTATCTTAATCAAACCTACCCTGAAGAGCAGCAGAGCAAATCCTCTTTTCTTTGAATCTGACCTA
131 CTATCTTAATCAAACATACCCTGAAGAGCAACAGAGCAAATCCCCTTTTCTTTGAATCTGACCTA
* * *
1331174 CCTTGAAGAACAACGAAGCAAATTTCATTAGATTTGACCTACCCTGAAGAGTAAT-AGAGCAAA
196 CCTTGAAGAACAACGAAGCAAATTCCATTAGATTTGACATACCATGAAGAGTAATGA-AGCAAA
* * * *
1331237 TTTATCTTGATTTGACCTACCCTGAAGAGCAA-CGAAGCATATCCCT-TTTTCTTTAAATCTTAC
1 TCTATCTTGATCTGACCTACCCTGAAGAGCAATCG-AGCAAAT-CCTATTTTCTTTAAATCTGAC
* * * * ** *
1331300 ATGCCTTGAAGAGTGGCATAGCACATTCCA-TAGATTTGACCTACCCTGAAGAGTAGT-GAGGCA
64 ATACCCTAAAAAGTAACAAAGCACATTCCATTAGATTTGACCTACCCTGAAGAGTAGTGGA-GCA
* * ** * *
1331363 AATCTATCTTGATCTAACATACCCTGAAGTA-CAATGGAGCATATCCCCTTTTCTTTGAATTTGA
128 AATCTATCTTAATCAAACATACCCTGAAG-AGCAACAGAGCAAATCCCCTTTTCTTTGAATCTGA
* * * * *
1331427 CCTACCTTGAAGAGCAGCGGAGCAGATTCCATTAGATTTGACATACCATGAAGAGTAGTGAAGCA
192 CCTACCTTGAAGAACAACGAAGCAAATTCCATTAGATTTGACATACCATGAAGAGTAATGAAGCA
1331492 AA
257 AA
* *
1331494 TCTATCTTGAATCTAACCTACCCTAAAGAG
1 TCTATCTTG-ATCTGACCTACCCTGAAGAG
1331524 AAGCGGAGCA
Statistics
Matches: 243, Mismatches: 38, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
256 2 0.01
257 148 0.61
258 90 0.37
259 3 0.01
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (258 bp):
TCTATCTTGATCTGACCTACCCTGAAGAGCAATCGAGCAAATCCTATTTTCTTTAAATCTGACAT
ACCCTAAAAAGTAACAAAGCACATTCCATTAGATTTGACCTACCCTGAAGAGTAGTGGAGCAAAT
CTATCTTAATCAAACATACCCTGAAGAGCAACAGAGCAAATCCCCTTTTCTTTGAATCTGACCTA
CCTTGAAGAACAACGAAGCAAATTCCATTAGATTTGACATACCATGAAGAGTAATGAAGCAAA
Found at i:1331466 original size:41 final size:41
Alignment explanation
Indices: 1331421--1331563 Score: 135
Period size: 41 Copynumber: 3.5 Consensus size: 41
1331411 TTTTCTTTGA
* *
1331421 ATTTGACCTACCTTGAAGAGCAGCGGAGCAGATTCCATTAG
1 ATTTGACCTACCCTGAAGAGAAGCGGAGCAGATTCCATTAG
* * * * * * * *
1331462 ATTTGACATACCATGAAGAGTAGTGAAGCA-AATCTATCTTG
1 ATTTGACCTACCCTGAAGAGAAGCGGAGCAGATTCCAT-TAG
* * * *
1331503 AATCTAACCTACCCTAAAGAGAAGCGGAGCAGATTCCATTAA
1 -ATTTGACCTACCCTGAAGAGAAGCGGAGCAGATTCCATTAG
1331545 ATTTGACCTACCCTGAAGA
1 ATTTGACCTACCCTGAAGA
1331564 ATAGTAGAGC
Statistics
Matches: 76, Mismatches: 23, Indels: 6
0.72 0.22 0.06
Matches are distributed among these distances:
40 5 0.07
41 43 0.57
42 23 0.30
43 5 0.07
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (41 bp):
ATTTGACCTACCCTGAAGAGAAGCGGAGCAGATTCCATTAG
Found at i:1331529 original size:83 final size:83
Alignment explanation
Indices: 1331417--1331615 Score: 267
Period size: 83 Copynumber: 2.4 Consensus size: 83
1331407 CCCCTTTTCT
* * * * *
1331417 TTGAATTTGACCTACCTTGAAGAGCAGCGGAGCAGATTCCATTAGATTTGACATACCATGAAGAG
1 TTGAATATAACCTACCTTGAAGAGAAGCGGAGCAGATTCCATTAAATTTGACATACCATGAAGAA
1331482 TAGT-GAAGCAAATCTATC
66 TAGTAG-AGCAAATCTATC
* * * * *
1331500 TTGAATCTAACCTACCCTAAAGAGAAGCGGAGCAGATTCCATTAAATTTGACCTACCCTGAAGAA
1 TTGAATATAACCTACCTTGAAGAGAAGCGGAGCAGATTCCATTAAATTTGACATACCATGAAGAA
1331565 TAGTAGAGCAAATCTATC
66 TAGTAGAGCAAATCTATC
* *
1331583 TTG-ATATAACCTACCTTGAAGAGTAGCGAAGCA
1 TTGAATATAACCTACCTTGAAGAGAAGCGGAGCA
1331616 TATCCCCTTT
Statistics
Matches: 101, Mismatches: 14, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
82 25 0.25
83 75 0.74
84 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.25
Consensus pattern (83 bp):
TTGAATATAACCTACCTTGAAGAGAAGCGGAGCAGATTCCATTAAATTTGACATACCATGAAGAA
TAGTAGAGCAAATCTATC
Found at i:1331586 original size:212 final size:211
Alignment explanation
Indices: 1331319--1331712 Score: 519
Period size: 212 Copynumber: 1.9 Consensus size: 211
1331309 AGAGTGGCAT
* * *
1331319 AGCACATTCCATAGATTTGACCTACCCTGAAGAGTAGTGAGGCAAATCTATCTTGATCTAACATA
1 AGCACATTCCATAAATTTGACCTACCCTGAAGAATAGTGAGGCAAATCTATCTTGATATAACATA
* * *
1331384 CCCTGAAGTACAATG-G-AGCATATCCCCTTTTCTTTGAATTTGACCTACCTTGAAGAGCAGCGG
66 CCCTGAAG-ACAA-GCGAAGCATATCCCCTTTTCTTTGAATATGACCTACCCTGAAGAGCAACGG
*
1331447 AGCAGATTCCA-TTAGATTTGACATACCATGAAGAGTAGT-GAAGCAAATCTATCTTGAATCTAA
129 AGCA-ATTCCATTTAGATTTGACATACCATAAAGAGTAGTCG-AGCAAATCTATCTTGAATCTAA
1331510 CCTACCCTAAAGAGAAGCGG
192 CCTACCCTAAAGAGAAGCGG
* *
1331530 AGCAGATTCCATTAAATTTGACCTACCCTGAAGAATAGT-AGAGCAAATCTATCTTGATATAACC
1 AGCACATTCCA-TAAATTTGACCTACCCTGAAGAATAGTGAG-GCAAATCTATCTTGATATAACA
* ** * *
1331594 TACCTTGAAGAGTAGCGAAGCATATCCCCTTTTCTTTGAATATGACCTACCCTGAAGATCAATGG
64 TACCCTGAAGACAAGCGAAGCATATCCCCTTTTCTTTGAATATGACCTACCCTGAAGAGCAACGG
* * * * * *
1331659 AGCATTTTCATTTAGATTTGACCTACCCTAAAGAGTATTCGAGCAAATTTATCT
129 AGCAATTCCATTTAGATTTGACATACCATAAAGAGTAGTCGAGCAAATCTATCT
1331713 AGATTTTACC
Statistics
Matches: 157, Mismatches: 20, Indels: 11
0.84 0.11 0.06
Matches are distributed among these distances:
210 1 0.01
211 19 0.12
212 136 0.87
213 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (211 bp):
AGCACATTCCATAAATTTGACCTACCCTGAAGAATAGTGAGGCAAATCTATCTTGATATAACATA
CCCTGAAGACAAGCGAAGCATATCCCCTTTTCTTTGAATATGACCTACCCTGAAGAGCAACGGAG
CAATTCCATTTAGATTTGACATACCATAAAGAGTAGTCGAGCAAATCTATCTTGAATCTAACCTA
CCCTAAAGAGAAGCGG
Found at i:1331681 original size:41 final size:39
Alignment explanation
Indices: 1331636--1331745 Score: 105
Period size: 41 Copynumber: 2.7 Consensus size: 39
1331626 TCTTTGAATA
*
1331636 TGACCTACCCTGAAGATCAATGGAGCATTTTCATTTAGATT
1 TGACCTACCCT-AAGATCAATGGAGCATTTT-ATCTAGATT
* * *
1331677 TGACCTACCCTAAAGAGT-ATTCGAGCAAATTTATCTAGATT
1 TGACCTACCCT-AAGA-TCAATGGAGC-ATTTTATCTAGATT
* *
1331718 TTACCTACCCATAAGAGCAATGGAGCAT
1 TGACCTACCC-TAAGATCAATGGAGCAT
1331746 ATCTTTCTTT
Statistics
Matches: 55, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
40 1 0.02
41 48 0.87
42 6 0.11
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (39 bp):
TGACCTACCCTAAGATCAATGGAGCATTTTATCTAGATT
Found at i:1331970 original size:21 final size:21
Alignment explanation
Indices: 1331940--1331981 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1331930 GCTATATTAT
1331940 ATATAATAAA-TATATGTATAG
1 ATATAATAAAGTATA-GTATAG
*
1331961 ATATATTAAAGTATAGTATAG
1 ATATAATAAAGTATAGTATAG
1331982 TTTTTGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (21 bp):
ATATAATAAAGTATAGTATAG
Found at i:1332035 original size:30 final size:31
Alignment explanation
Indices: 1331972--1332098 Score: 118
Period size: 30 Copynumber: 4.1 Consensus size: 31
1331962 TATATTAAAG
* * *
1331972 TATAGTATAGTTTTTGAAAATAATTA-T-TA
1 TATAATATAGTTTTTAAAAACAATTATTATA
* *
1332001 TATAATATAG-TTTTGAAAACCATTATTATA
1 TATAATATAGTTTTTAAAAACAATTATTATA
*
1332031 TATAATATAGTTTTTTAAAAATAATAATTATTATA
1 TATAATATAG-TTTTT--AAA-AACAATTATTATA
* *
1332066 TATAATATAG-TTTCAAAAACAATTATTACA
1 TATAATATAGTTTTTAAAAACAATTATTATA
1332096 TAT
1 TAT
1332099 TAAGTATTTT
Statistics
Matches: 82, Mismatches: 9, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
28 13 0.16
29 10 0.12
30 26 0.32
31 3 0.04
32 4 0.05
33 3 0.04
34 2 0.02
35 21 0.26
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.45
Consensus pattern (31 bp):
TATAATATAGTTTTTAAAAACAATTATTATA
Found at i:1332084 original size:33 final size:34
Alignment explanation
Indices: 1331990--1332093 Score: 105
Period size: 35 Copynumber: 3.2 Consensus size: 34
1331980 AGTTTTTGAA
*
1331990 AATAATTA-T-TATATAATATAGTTTT-GAAAAC
1 AATAATTATTATATATAATATAGTTTTCAAAAAC
* * *
1332021 ---CATTATTATATATAATATAGTTTTTTAAAAAT
1 AATAATTATTATATATAATATAG-TTTTCAAAAAC
1332053 AATAATTATTATATATAATATAG-TTTCAAAAAC
1 AATAATTATTATATATAATATAGTTTTCAAAAAC
*
1332086 AATTATTA
1 AATAATTA
1332094 CATATTAAGT
Statistics
Matches: 59, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
28 4 0.07
29 1 0.02
30 12 0.20
31 4 0.07
32 4 0.07
33 15 0.25
35 19 0.32
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (34 bp):
AATAATTATTATATATAATATAGTTTTCAAAAAC
Found at i:1333041 original size:36 final size:37
Alignment explanation
Indices: 1333001--1333076 Score: 102
Period size: 36 Copynumber: 2.1 Consensus size: 37
1332991 TTTTTATATT
1333001 TTTAATTTTGTAAA-AAAATTATATAAATATTATG-AA
1 TTTAATTTTGTAAAGAAAA-TATATAAATATTATGTAA
* * *
1333037 TTTAATTTTTTAAAGAAAATGTATAAATATTTTGTAA
1 TTTAATTTTGTAAAGAAAATATATAAATATTATGTAA
1333074 TTT
1 TTT
1333077 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.49
Consensus pattern (37 bp):
TTTAATTTTGTAAAGAAAATATATAAATATTATGTAA
Found at i:1337814 original size:18 final size:17
Alignment explanation
Indices: 1337759--1337878 Score: 98
Period size: 17 Copynumber: 6.9 Consensus size: 17
1337749 ATGTTTACAG
*
1337759 TTTACAGTTAT-ATGACA
1 TTTACAGTTATCA-GATA
* * *
1337776 TTTCACATTTATTATATA
1 TTT-ACAGTTATCAGATA
*
1337794 TTTACAGTTATTAGATGA
1 TTTACAGTTATCAGAT-A
* * *
1337812 TTTTCAATCATCAGATA
1 TTTACAGTTATCAGATA
*
1337829 TTTACAGTTATCAGATGT
1 TTTACAGTTATCAGAT-A
* *
1337847 TTTTCAGTTATAAGATA
1 TTTACAGTTATCAGATA
1337864 TTTACAGTTATCAGA
1 TTTACAGTTATCAGA
1337879 CGTAGATTAA
Statistics
Matches: 81, Mismatches: 18, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
17 41 0.51
18 39 0.48
19 1 0.01
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.45
Consensus pattern (17 bp):
TTTACAGTTATCAGATA
Found at i:1337830 original size:35 final size:35
Alignment explanation
Indices: 1337791--1337878 Score: 131
Period size: 35 Copynumber: 2.5 Consensus size: 35
1337781 CATTTATTAT
* *
1337791 ATATTTACAGTTATTAGATGATTTTCAATCATCAG
1 ATATTTACAGTTATCAGATGATTTTCAATCATAAG
* * *
1337826 ATATTTACAGTTATCAGATGTTTTTCAGTTATAAG
1 ATATTTACAGTTATCAGATGATTTTCAATCATAAG
1337861 ATATTTACAGTTATCAGA
1 ATATTTACAGTTATCAGA
1337879 CGTAGATTAA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 48 1.00
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.43
Consensus pattern (35 bp):
ATATTTACAGTTATCAGATGATTTTCAATCATAAG
Found at i:1338767 original size:2 final size:2
Alignment explanation
Indices: 1338760--1338789 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1338750 TTAGGCAGTG
1338760 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1338790 TTATGAACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1340300 original size:114 final size:114
Alignment explanation
Indices: 1339590--1340301 Score: 801
Period size: 114 Copynumber: 6.3 Consensus size: 114
1339580 TAATATTTAA
* * ** * * *
1339590 AAATGAAAAAGAATCTTAACTATTCACATCTTTTTATATTCAGTGAAATATCACCTTAAATTAGA
1 AAATGACAGAGAATCTTAACTATTCATGTCCTTTTGTATTCAGTGAAATATCACCTTAAATCAGA
* * * *
1339655 ACTTCTTTCATATTGAATGAAAAATCTTATCTAGCATAATAATGATTTC
66 ACTTCTTTCATATTGAATGAAAAATCTTATCTGGTACAATAATAATTTC
* * * * * * * *
1339704 AGATGATAGAGAATCTTAAATATTAATGCCCCTTTGTATTCAGTGAAATAT-ATCTTAAATCAAA
1 AAATGACAGAGAATCTTAACTATTCATGTCCTTTTGTATTCAGTGAAATATCACCTTAAATCAGA
* * * * * *
1339768 ACTTTTTTTATATTAAATGAAAATTTTTATCTGGTATAATAATAATTTC
66 ACTTCTTTCATATTGAATGAAAAATCTTATCTGGTACAATAATAATTTC
* * * * * * *
1339817 AAATTACAGAGAATCTTAACTTTTTATGT-CTTTT-T-TTC-GTAAAATTTCACCTCAAATAAGA
1 AAATGACAGAGAATCTTAACTATTCATGTCCTTTTGTATTCAGTGAAATATCACCTTAAATCAGA
* *
1339878 ACTTATTTCATATTGAATGAAAAATCTTATCTGGTATAATAAT-ATTTC
66 ACTTCTTTCATATTGAATGAAAAATCTTATCTGGTACAATAATAATTTC
* * * * * * * *
1339926 AAATGAAAGAGAATCTTAACTAATCACGTCCTTTTGTATTAATTAAAATAACACCTTAAATCAAA
1 AAATGACAGAGAATCTTAACTATTCATGTCCTTTTGTATTCAGTGAAATATCACCTTAAATCAGA
* ** *
1339991 ACTTCTTTCATATTGAATGAACAATCTTATAAGGTACAATAACAATTTC
66 ACTTCTTTCATATTGAATGAAAAATCTTATCTGGTACAATAATAATTTC
* *
1340040 AAATGACAGAGAATCTTAACTATTCATGTCCTTTTGTATTCAGTGAAATATCACCTCAAATAAGA
1 AAATGACAGAGAATCTTAACTATTCATGTCCTTTTGTATTCAGTGAAATATCACCTTAAATCAGA
*
1340105 ACTT-TTTCTATATTGAATGAAAAATCTTATTTGGTACAATAATAATTTC
66 ACTTCTTTC-ATATTGAATGAAAAATCTTATCTGGTACAATAATAATTTC
* * ** * * * *
1340154 AAATGATAGAGAATGTTAACTATTCACATCTTTTTCTTTTCAGTGATATATCACCTTAAATCAGA
1 AAATGACAGAGAATCTTAACTATTCATGTCCTTTTGTATTCAGTGAAATATCACCTTAAATCAGA
* **
1340219 ACTTGTTTCATATTGAATGAAAAATCTTATC-GGTACAATAATAACCTC
66 ACTTCTTTCATATTGAATGAAAAATCTTATCTGGTACAATAATAATTTC
* *
1340267 AAATGACAGATAATCTTAACTATTCATGTTCTTTT
1 AAATGACAGAGAATCTTAACTATTCATGTCCTTTT
1340302 CTTTTTAGTG
Statistics
Matches: 496, Mismatches: 94, Indels: 17
0.82 0.15 0.03
Matches are distributed among these distances:
109 35 0.07
110 55 0.11
111 2 0.00
112 6 0.01
113 174 0.35
114 220 0.44
115 4 0.01
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (114 bp):
AAATGACAGAGAATCTTAACTATTCATGTCCTTTTGTATTCAGTGAAATATCACCTTAAATCAGA
ACTTCTTTCATATTGAATGAAAAATCTTATCTGGTACAATAATAATTTC
Found at i:1340327 original size:227 final size:224
Alignment explanation
Indices: 1339590--1340350 Score: 802
Period size: 227 Copynumber: 3.4 Consensus size: 224
1339580 TAATATTTAA
* * ** * * * *
1339590 AAATGAAAAAGAATCTTAACTATTCA-CATCTTTTTATATTCAGTGAAATATCACCTTAAATTAG
1 AAATGACAGAGAATCTTAACTATTCATGTTCTTTTT-T-TTTAGTG-ATTATCACCTCAAATAAG
* * * *
1339654 AACTTCTTTCATATTGAATGAAAAATCTTATCTAGCATAATAATGATTTCAGATGATAGAGAATC
63 AACTTATTTCATATTGAATGAAAAATCTTATCTGGTATAATAAT-ATTTCAAATGATAGAGAATC
* * * * *
1339719 TTAAATATT-A-ATGCCCCTTTGTATTCAGTGAAATAT-ATCTTAAATCAAAACTTTTTTTATAT
127 TTAACTATTCACAT--CCTTTTGTATTCAGTGAAATATCACCTTAAATCAAAACTTCTTTCATAT
* * * *
1339781 TAAATGAAAATTTTTATCTGGTATAATAATAATTTC
190 TGAATGAAAAATCTTATC-GGTACAATAATAATTTC
* * * * **
1339817 AAATTACAGAGAATCTTAACTTTTTATG-TCTTTTTTTCGTA-AAATT-TCACCTCAAATAAGAA
1 AAATGACAGAGAATCTTAACTATTCATGTTCTTTTTTT-TTAGTGATTATCACCTCAAATAAGAA
*
1339879 CTTATTTCATATTGAATGAAAAATCTTATCTGGTATAATAATATTTCAAATGAAAGAGAATCTTA
65 CTTATTTCATATTGAATGAAAAATCTTATCTGGTATAATAATATTTCAAATGATAGAGAATCTTA
* * * * * *
1339944 ACTAATCACGTCCTTTTGTATTAATTAAAATAACACCTTAAATCAAAACTTCTTTCATATTGAAT
130 ACTATTCACATCCTTTTGTATTCAGTGAAATATCACCTTAAATCAAAACTTCTTTCATATTGAAT
* * *
1340009 GAACAATCTTATAAGGTACAATAACAATTTC
195 GAAAAATCTTAT-CGGTACAATAATAATTTC
* * * *
1340040 AAATGACAGAGAATCTTAACTATTCATGTCCTTTTGTATTCAGTGAAATATCACCTCAAATAAGA
1 AAATGACAGAGAATCTTAACTATTCATGTTCTTTT-TTTTTAGTG-ATTATCACCTCAAATAAGA
* * *
1340105 ACTT-TTTCTATATTGAATGAAAAATCTTATTTGGTACAATAATAATTTCAAATGATAGAGAATG
64 ACTTATTTC-ATATTGAATGAAAAATCTTATCTGGTATAATAAT-ATTTCAAATGATAGAGAATC
* * * * * *
1340169 TTAACTATTCACATCTTTTTCTTTTCAGTGATATATCACCTTAAATCAGAACTTGTTTCATATTG
127 TTAACTATTCACATCCTTTTGTATTCAGTGAAATATCACCTTAAATCAAAACTTCTTTCATATTG
**
1340234 AATGAAAAATCTTATCGGTACAATAATAACCTC
192 AATGAAAAATCTTATCGGTACAATAATAATTTC
* *
1340267 AAATGACAGATAATCTTAACTATTCATGTTCTTTTCTTTTTAGTGATTCATCATCTCAAATCAA-
1 AAATGACAGAGAATCTTAACTATTCATGTTCTTTT-TTTTTAGTGATT-ATCACCTCAAAT-AAG
* * *
1340331 AACTTTTTTAATATTAAATG
63 AACTTATTTCATATTGAATG
1340351 TAACACCCTA
Statistics
Matches: 442, Mismatches: 76, Indels: 32
0.80 0.14 0.06
Matches are distributed among these distances:
222 42 0.10
223 130 0.29
224 9 0.02
225 3 0.01
226 10 0.02
227 158 0.36
228 90 0.20
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (224 bp):
AAATGACAGAGAATCTTAACTATTCATGTTCTTTTTTTTTAGTGATTATCACCTCAAATAAGAAC
TTATTTCATATTGAATGAAAAATCTTATCTGGTATAATAATATTTCAAATGATAGAGAATCTTAA
CTATTCACATCCTTTTGTATTCAGTGAAATATCACCTTAAATCAAAACTTCTTTCATATTGAATG
AAAAATCTTATCGGTACAATAATAATTTC
Found at i:1341007 original size:21 final size:20
Alignment explanation
Indices: 1340983--1341052 Score: 95
Period size: 21 Copynumber: 3.4 Consensus size: 20
1340973 TAGTATCTAG
*
1340983 AATCACAAAGTGGCTCGATAT
1 AATCACAAAGAGGC-CGATAT
1341004 AATCACAAAGAGGCCCGATAT
1 AATCACAAAGAGG-CCGATAT
*
1341025 ATTCACAAAGAGGCCTGATAT
1 AATCACAAAGAGGCC-GATAT
1341046 AATCACA
1 AATCACA
1341053 CAATAACAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
20 2 0.05
21 41 0.93
22 1 0.02
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.20
Consensus pattern (20 bp):
AATCACAAAGAGGCCGATAT
Found at i:1343880 original size:17 final size:17
Alignment explanation
Indices: 1343858--1343893 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1343848 GTTAAATGTT
* *
1343858 TGTAATGTGTAATTTAA
1 TGTAATGCGTAATGTAA
1343875 TGTAATGCGTAATGTAA
1 TGTAATGCGTAATGTAA
1343892 TG
1 TG
1343894 CAATATAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.33, C:0.03, G:0.22, T:0.42
Consensus pattern (17 bp):
TGTAATGCGTAATGTAA
Found at i:1344142 original size:34 final size:34
Alignment explanation
Indices: 1344099--1344166 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
1344089 TCACCATTTC
1344099 CTTTGACGAAGACATTTGACTTGATAACGAAAAT
1 CTTTGACGAAGACATTTGACTTGATAACGAAAAT
1344133 CTTTGACGAAGACATTTGACTTGATAACGAAAAT
1 CTTTGACGAAGACATTTGACTTGATAACGAAAAT
1344167 TTCAAACAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (34 bp):
CTTTGACGAAGACATTTGACTTGATAACGAAAAT
Done.