Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007851.1 Hibiscus syriacus cultivar Beakdansim tig00110210_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: 1608033
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 9
Found at i:1137856 original size:2 final size:2
Alignment explanation
Indices: 1137849--1137880 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1137839 TCCAATCAAT
1137849 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1137881 ATTTTTTGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1139593 original size:162 final size:162
Alignment explanation
Indices: 1139443--1139754 Score: 509
Period size: 162 Copynumber: 1.9 Consensus size: 162
1139433 AACGGTACTG
* * *
1139443 GATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTGTGAATTTAAAAGAGAATCA
1 GATATATTGAAAATGTCAATACTTTAATATAAGTATCGACACTTTGTGAATTTAAAAGAGAAGCA
*
1139508 GTTTTAG-AGCCTATAAAGTGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACATG
66 GTTTTAGCA-CCTATAAAGTGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACAGG
*
1139572 CAAAAATATGACAAAACCGGTATAGAGCGACCA
130 CAAAAATATGACAAAACCGGTATAAAGCGACCA
* * *
1139605 TATATATTGAAAATGTTAATACTTTAATATAAGTATCGACACTTTGTGAATTTAGAAGAGAAGCA
1 GATATATTGAAAATGTCAATACTTTAATATAAGTATCGACACTTTGTGAATTTAAAAGAGAAGCA
*
1139670 GTTTTAGCACCTATAAAGTGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACAGGT
66 GTTTTAGCACCTATAAAGTGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACAGGC
* *
1139735 AAAAATATGATAAAATCGGT
131 AAAAATATGACAAAACCGGT
1139755 CTCTAAAGGA
Statistics
Matches: 139, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
162 138 0.99
163 1 0.01
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.30
Consensus pattern (162 bp):
GATATATTGAAAATGTCAATACTTTAATATAAGTATCGACACTTTGTGAATTTAAAAGAGAAGCA
GTTTTAGCACCTATAAAGTGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACAGGC
AAAAATATGACAAAACCGGTATAAAGCGACCA
Found at i:1139888 original size:182 final size:182
Alignment explanation
Indices: 1139581--1140179 Score: 905
Period size: 182 Copynumber: 3.3 Consensus size: 182
1139571 GCAAAAATAT
* * * **
1139581 GACAAAACCGGTATAGAGCGACCATATATATTGAAAATGTTAATACTTTAATATAAGTATCGACA
1 GACAAAACCAGTATAGAGCGACCAGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACA
* *
1139646 CTTTGTGAATTTAGAAGAGAAGCAGTTTTAGCACCTATAAAGTGTCGATACTTTATAACAATGTA
66 CTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTATAACAATGTA
*
1139711 TCGATCCACAACGATATAACAGGTAAAAATATGATAAAATCGGTCTCTAAAG
131 TCGATCCACAACGATATAACAGGTAAAAATATGACAAAATCGGTCTCTAAAG
*
1139763 GACAAAATCAGTATAGAGCGACC-GAATATATTGAAAGTGTCGATACTTTAATATAAGTATCGAC
1 GACAAAACCAGTATAGAGCGACCAG-ATATATTGAAAGTGTCGATACTTTAATATAAGTATCGAC
* *
1139827 ACTTTGTGAATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAGAGTCGATACTTTATAACAATGT
65 ACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTATAACAATGT
* * *
1139892 ATCGATCCAAAATGATATAACAGGTAAAAATATGACAAAAGCGGTCTCTAAAG
130 ATCGATCCACAACGATATAACAGGTAAAAATATGACAAAATCGGTCTCTAAAG
* * * ** **
1139945 GACAAAATCGGTATAGAGCGACCAGATATATTTAAAGTGTCGATACTTTAATATATTTATTAACA
1 GACAAAACCAGTATAGAGCGACCAGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACA
*
1140010 CTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTTTCGATACTTTATAACAATGTA
66 CTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTATAACAATGTA
* *
1140075 TC-AGTCCACAACGATATAACAGGTAAAAATATGACAAAATCGGTCTCGAAAT
131 TCGA-TCCACAACGATATAACAGGTAAAAATATGACAAAATCGGTCTCTAAAG
* * * * *
1140127 GACAAAACCAGTAAAGCGCTACCGGATATATTGAAAGTGTTGATACTTTAATA
1 GACAAAACCAGTATAGAGCGACCAGATATATTGAAAGTGTCGATACTTTAATA
1140180 AGTACGCATA
Statistics
Matches: 378, Mismatches: 36, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
181 1 0.00
182 376 0.99
183 1 0.00
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (182 bp):
GACAAAACCAGTATAGAGCGACCAGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACA
CTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTATAACAATGTA
TCGATCCACAACGATATAACAGGTAAAAATATGACAAAATCGGTCTCTAAAG
Found at i:1142479 original size:19 final size:19
Alignment explanation
Indices: 1142455--1142493 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1142445 TCGAATGCAT
1142455 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
1142474 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
1142493 T
1 T
1142494 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:1148101 original size:20 final size:21
Alignment explanation
Indices: 1148072--1148127 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
1148062 TTTGTGCTTC
*
1148072 ATGCACCGATGCAT-TT-AACA
1 ATGCATCGATGCATCTTGAA-A
*
1148092 ATGCATCGATGCATCCTTGAAT
1 ATGCATCGATGCAT-CTTGAAA
1148114 ATGCATCGATGCAT
1 ATGCATCGATGCAT
1148128 AATACCATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.42
22 16 0.52
23 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGCATCGATGCATCTTGAAA
Found at i:1149705 original size:21 final size:21
Alignment explanation
Indices: 1149663--1149706 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1149653 ACCCCAGGAG
*
1149663 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
*
1149684 CTAGTTCTT-ATCGTGCTCCTC
1 CTAGTTCTTCA-CGAGCTCCTC
1149705 CT
1 CT
1149707 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.11, C:0.34, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:1150791 original size:65 final size:64
Alignment explanation
Indices: 1150674--1150884 Score: 239
Period size: 65 Copynumber: 3.3 Consensus size: 64
1150664 ATTCAAAGGA
* * * *
1150674 ATGCACCGATGCATCAGTCCATGCATCGATGCATCTATGAAT-TAATT-GAACATCGAATGCATT
1 ATGCACCGATGCA-CACTCCATGCATCGATGCA-CTCTGAATAT-TTTCAAACATCGAATGCATT
*
1150737 CC
63 TC
*
1150739 ATGCACCGATGCACACTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTTG
1 ATGCACCGATGCACACTCCATGCATCGATGCACTCTGAATATTTTC-AAACATCGAATGCATTTC
* ** * **
1150804 ATGCATCGATGCACAAGCCATGCATCGATGCA-TCAGGCTATTTTTCAAACATCGAATGCATTTC
1 ATGCACCGATGCACACTCCATGCATCGATGCACTCTGAATA-TTTTCAAACATCGAATGCATTTC
*
1150868 ATGCATCGATGCACACT
1 ATGCACCGATGCACACT
1150885 TGGTGCACCG
Statistics
Matches: 127, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
63 9 0.07
64 56 0.44
65 62 0.49
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (64 bp):
ATGCACCGATGCACACTCCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTTC
Found at i:1150897 original size:64 final size:64
Alignment explanation
Indices: 1150674--1150902 Score: 232
Period size: 64 Copynumber: 3.5 Consensus size: 64
1150664 ATTCAAAGGA
* * * *
1150674 ATGCACCGATGCATCAGTCCATGCATCGATGCATCTATGAAT-TAATT--GAACATCGAATGCAT
1 ATGCATCGATGCA-CACTCCATGCATCGATGCATC-A-GAATAT-TTTCAAAACATCGAATGCAT
*
1150736 TCC
62 TTC
* * *
1150739 ATGCACCGATGCACACTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTTG
1 ATGCATCGATGCACACTCCATGCATCGATGCA-TCAGAATATTTTCAAAACATCGAATGCATTTC
** **
1150804 ATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTTTC-AAACATCGAATGCATTTC
1 ATGCATCGATGCACACTCCATGCATCGATGCATCAGAATA-TTTTCAAAACATCGAATGCATTTC
*** *
1150868 ATGCATCGATGCACACTTGGTGCACCGATGCATCA
1 ATGCATCGATGCACACTCCATGCATCGATGCATCA
1150903 AGTGTTCCAA
Statistics
Matches: 140, Mismatches: 19, Indels: 11
0.82 0.11 0.06
Matches are distributed among these distances:
63 6 0.04
64 70 0.50
65 64 0.46
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (64 bp):
ATGCATCGATGCACACTCCATGCATCGATGCATCAGAATATTTTCAAAACATCGAATGCATTTC
Found at i:1153546 original size:18 final size:18
Alignment explanation
Indices: 1153519--1153609 Score: 119
Period size: 18 Copynumber: 4.9 Consensus size: 18
1153509 ACTGAATATT
1153519 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
1153537 TGTCCTGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
1153555 TGTCCCGAAGGACCACTGTT
1 TGTCCCGAAGGACCAC--TA
* * *
1153575 TGTTCCGAAGAACCACCA
1 TGTCCCGAAGGACCACTA
1153593 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
1153610 GTTTATCCCT
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
18 46 0.75
20 15 0.25
ACGTcount: A:0.26, C:0.32, G:0.22, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1153599 original size:38 final size:38
Alignment explanation
Indices: 1153519--1153613 Score: 133
Period size: 38 Copynumber: 2.6 Consensus size: 38
1153509 ACTGAATATT
* * *
1153519 TGTCCCGAAGGACCAC--TATGTCCTGAAGGACCACTA
1 TGTCCCGAAGGACCACTGTTTGTCCTGAAGAACCACCA
1153555 TGTCCCGAAGGACCACTGTTTGTTCC-GAAGAACCACCA
1 TGTCCCGAAGGACCACTGTTTG-TCCTGAAGAACCACCA
1153593 TGTCCCGAAGGACCACTGTTT
1 TGTCCCGAAGGACCACTGTTT
1153614 ATCCCTAGAC
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
36 16 0.30
38 34 0.64
39 3 0.06
ACGTcount: A:0.25, C:0.31, G:0.22, T:0.22
Consensus pattern (38 bp):
TGTCCCGAAGGACCACTGTTTGTCCTGAAGAACCACCA
Found at i:1154455 original size:65 final size:64
Alignment explanation
Indices: 1154382--1154517 Score: 193
Period size: 64 Copynumber: 2.1 Consensus size: 64
1154372 ACTACATGTA
**
1154382 CATCGATACAAAAATTACATTCGATGTTTTCT-TCTTAAGGGGGGTGCATCGATGCACTCCTTAT
1 CATCGATACAAAAACGACATTCGATGTTTT-TATCTTAA-GGGGGTGCATCGATGCACTCCTTAT
1154446 G
64 G
*** *
1154447 CATCGATACACTGACGACATTCGATGTTTTTATTTTAAGGGGGTGCATCGATGCACTCCTTATG
1 CATCGATACAAAAACGACATTCGATGTTTTTATCTTAAGGGGGTGCATCGATGCACTCCTTATG
1154511 CATCGAT
1 CATCGAT
1154518 GCACTGGTGA
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
64 34 0.53
65 30 0.47
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.34
Consensus pattern (64 bp):
CATCGATACAAAAACGACATTCGATGTTTTTATCTTAAGGGGGTGCATCGATGCACTCCTTATG
Found at i:1154517 original size:64 final size:65
Alignment explanation
Indices: 1154398--1154538 Score: 223
Period size: 64 Copynumber: 2.2 Consensus size: 65
1154388 TACAAAAATT
1154398 ACATTCGATGTTTTCTTCTTAAGGGGGGTGCATCGATGCACTCCTTATGCATCGATACACTGACG
1 ACATTCGATGTTTTCTTCTTAAGGGGGGTGCATCGATGCACTCCTTATGCATCGATACACTGACG
* * **
1154463 ACATTCGATGTTTT-TATTTTAA-GGGGGTGCATCGATGCACTCCTTATGCATCGATGCACTGGT
1 ACATTCGATGTTTTCT-TCTTAAGGGGGGTGCATCGATGCACTCCTTATGCATCGATACACTGAC
1154526 G
65 G
1154527 ACATTCGATGTT
1 ACATTCGATGTT
1154539 CATTATTTGA
Statistics
Matches: 71, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
64 52 0.73
65 19 0.27
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (65 bp):
ACATTCGATGTTTTCTTCTTAAGGGGGGTGCATCGATGCACTCCTTATGCATCGATACACTGACG
Found at i:1166285 original size:18 final size:18
Alignment explanation
Indices: 1166262--1166300 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
1166252 GAAAAAATAT
*
1166262 GAAGAAGAAATGATGGAG
1 GAAGAAGAAAAGATGGAG
1166280 GAAGAAGAAAAGATGGAG
1 GAAGAAGAAAAGATGGAG
1166298 GAA
1 GAA
1166301 ATGAGGAGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.38, T:0.08
Consensus pattern (18 bp):
GAAGAAGAAAAGATGGAG
Found at i:1169793 original size:55 final size:55
Alignment explanation
Indices: 1169712--1170234 Score: 411
Period size: 55 Copynumber: 9.6 Consensus size: 55
1169702 ATACTTGAAA
* *
1169712 AATCTTCAA-ATAACGGGTCTGCTCCCTTTTCTTTCAAGGAGTATAAGACTCGAAC
1 AATCTTCAACA-AACGGGTCTGCTCCCTATTCATTCAAGGAGTATAAGACTCGAAC
** * * *
1169767 AATCCTT-GGCAAACGTGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCAAAC
1 AAT-CTTCAACAAACGGGTCTGCTCCCTATTCATTCAAGGAGTATAAGACTCGAAC
* * * *
1169822 AATCTTCAACAAACGTGTCTGCTCCCTATTCGTTCAGGGAGTATAAGACTCGAAT
1 AATCTTCAACAAACGGGTCTGCTCCCTATTCATTCAAGGAGTATAAGACTCGAAC
* *
1169877 AATCTTCAACAAACGGGTCCGCTCCCTATTCCTTC-AGAGAGTATAAGACT----C
1 AATCTTCAACAAACGGGTCTGCTCCCTATTCATTCAAG-GAGTATAAGACTCGAAC
* * * * * *
1169928 AATCTTCAATAAACGTGTCCGCTCCCTATTCCTTC-AGAGAGTATAGGACTCAAAC
1 AATCTTCAACAAACGGGTCTGCTCCCTATTCATTCAAG-GAGTATAAGACTCGAAC
* * ** * *
1169983 AATCTTCAAAAAACAGGTCCACTCTCTATTCCTTC-AGAGAGTAT-AGAACTCGAAC
1 AATCTTCAACAAACGGGTCTGCTCCCTATTCATTCAAG-GAGTATAAG-ACTCGAAC
* * *
1170038 AATCTTCATA-AAACGGGTCCGCTCTCTATTCCTTC-AGAGAGTAT-AGAACTCGAAC
1 AATCTTCA-ACAAACGGGTCTGCTCCCTATTCATTCAAG-GAGTATAAG-ACTCGAAC
* * * *
1170093 AATCTTCATA-AAATGGGTCCGCTCTCTATTCCTTC-AGAGAGTAT-AGAACTCGAAC
1 AATCTTCA-ACAAACGGGTCTGCTCCCTATTCATTCAAG-GAGTATAAG-ACTCGAAC
* ** *
1170148 AATCTTCATA-AAACGGGTCCGCTCTTTATTCCTTC-AGAGAGTAT-AGAACTCGAAC
1 AATCTTCA-ACAAACGGGTCTGCTCCCTATTCATTCAAG-GAGTATAAG-ACTCGAAC
* *
1170203 AATCTTCATA-AAACGGGTTTGCTTCACTATTC
1 AATCTTCA-ACAAACGGGTCTGC-TCCCTATTC
1170235 TTTCGTGAAG
Statistics
Matches: 421, Mismatches: 36, Indels: 21
0.88 0.08 0.04
Matches are distributed among these distances:
51 47 0.11
54 5 0.01
55 357 0.85
56 12 0.03
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (55 bp):
AATCTTCAACAAACGGGTCTGCTCCCTATTCATTCAAGGAGTATAAGACTCGAAC
Found at i:1169905 original size:110 final size:108
Alignment explanation
Indices: 1169712--1170220 Score: 577
Period size: 110 Copynumber: 4.7 Consensus size: 108
1169702 ATACTTGAAA
* * * **
1169712 AATCTTCAAATAACGGGTCTGCTCCCTTTTCTTTCA-AGGAGTATAAGACTCGAACAATCCTTGG
1 AATCTTCAAA-AACGGGTCCGCTCCCTATTCCTTCAGA-GAGTATAAGACTCGAACAAT-CTTCA
* * * * * *
1169776 CAAACGTGTCTGCTCCCTATTCATTCAGGGAGTATA-AGACTCAAAC
63 AAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAAC
* * * * *
1169822 AATCTTCAACAAACGTGTCTGCTCCCTATTCGTTCAGGGAGTATAAGACTCGAATAATCTTCAAC
1 AATCTTCAA-AAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAA-
1169887 AAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATA-AGACT----C
64 AAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAAC
* * *
1169928 AATCTTCAATAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAAACAATCTTCAAA
1 AATCTTCAA-AAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTC-AA
* * *
1169993 AAACAGGTCCACTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
64 AAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAAC
*
1170038 AATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAACAATCTTCAT
1 AATCTTCA-AAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCA-
* *
1170102 AAAATGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
63 AAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAAC
**
1170148 AATCTTCATAAAACGGGTCCGCTCTTTATTCCTTCAGAGAGTAT-AGAACTCGAACAATCTTCAT
1 AATCTTCA-AAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCA-
1170212 AAAACGGGT
63 AAAACGGGT
1170221 TTGCTTCACT
Statistics
Matches: 356, Mismatches: 31, Indels: 24
0.87 0.08 0.06
Matches are distributed among these distances:
106 91 0.26
107 3 0.01
109 5 0.01
110 255 0.72
111 2 0.01
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (108 bp):
AATCTTCAAAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAAAA
ACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAAC
Found at i:1170180 original size:165 final size:160
Alignment explanation
Indices: 1169777--1170220 Score: 574
Period size: 161 Copynumber: 2.7 Consensus size: 160
1169767 AATCCTTGGC
* * * * *
1169777 AAACGTGTCTGCTCCCTATTCATTCAGGGAGTATA-AGACTCAAACAATCTTCAACAAACGTGTC
1 AAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAGA-ACTCAAACAATCTTCAA-AAACGGGTC
* * * * *
1169841 TGCTCCCTATTCGTTCAGGGAGTATA-AGACTCGAATAATCTTCA-ACAAACGGGTCCGCTCCCT
64 CGCTCTCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCATA-AAACGGGTCCGCTCCCT
1169904 ATTCCTTCAGAGAGTATAAGACTCAATCTTCAAT
127 ATTCCTTCAGAGAGTATAAGACTCAATCTTCAAT
* * *
1169938 AAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAAACAATCTTCAAAAAACAGGTCC
1 AAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCAAACAATCTTC-AAAAACGGGTCC
* *
1170003 ACTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTATT
65 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCCCTATT
1170068 CCTTCAGAGAGTAT-AGAACTCGAACAATCTTC-AT
130 CCTTCAGAGAGTATAAG-ACT----CAATCTTCAAT
* * *
1170102 AAAATGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTC
1 -AAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCAAACAATCTTCA-AAAACGGGTC
*
1170167 CGCTCTTTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGT
64 CGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGT
1170221 TTGCTTCACT
Statistics
Matches: 251, Mismatches: 21, Indels: 18
0.87 0.07 0.06
Matches are distributed among these distances:
160 2 0.01
161 126 0.50
162 4 0.02
164 3 0.01
165 116 0.46
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (160 bp):
AAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCAAACAATCTTCAAAAACGGGTCCG
CTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCCCTATTC
CTTCAGAGAGTATAAGACTCAATCTTCAAT
Found at i:1170280 original size:37 final size:37
Alignment explanation
Indices: 1170220--1170302 Score: 116
Period size: 37 Copynumber: 2.2 Consensus size: 37
1170210 ATAAAACGGG
*
1170220 TTTGCTTCACTATTCTTTCGTGAAGGCTTATAGA-TGA
1 TTTGCTTCACTACTCTTTCGTGAAGGCTTA-AGATTGA
1170257 TTTGCTTCACTACTC-TTCTGTGAAGGCTTAAGATTGA
1 TTTGCTTCACTACTCTTTC-GTGAAGGCTTAAGATTGA
*
1170294 TTTGTTTCA
1 TTTGCTTCA
1170303 AAGATCCAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
36 6 0.14
37 36 0.86
ACGTcount: A:0.20, C:0.17, G:0.18, T:0.45
Consensus pattern (37 bp):
TTTGCTTCACTACTCTTTCGTGAAGGCTTAAGATTGA
Found at i:1171600 original size:15 final size:15
Alignment explanation
Indices: 1171569--1171631 Score: 56
Period size: 16 Copynumber: 4.1 Consensus size: 15
1171559 TGAACCCTCC
* *
1171569 TTTT-ATTTCTCTTT
1 TTTTCATTTTTCTCT
1171583 TTTTCATTTTTCTCTT
1 TTTTCATTTTTCTC-T
*
1171599 TTTTCATTTTTCATTT
1 TTTTCATTTTTC-TCT
*
1171615 TTTCTCATTTTTTTCT
1 TTT-TCATTTTTCTCT
1171631 T
1 T
1171632 CTTTTTCTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
14 4 0.10
15 7 0.17
16 20 0.50
17 9 0.22
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTCATTTTTCTCT
Found at i:1171652 original size:50 final size:49
Alignment explanation
Indices: 1171578--1171686 Score: 125
Period size: 50 Copynumber: 2.2 Consensus size: 49
1171568 CTTTTATTTC
* *
1171578 TCTTTTTTTCATTTTTCTC-TTTTTTCATTTTTCATTTTTTCTCATTTTTT
1 TCTTTTTTTCATTCTTCTCATTTTTTCA-TATT-ATTTTTTCTCATTTTTT
*
1171628 TCTTCTTTTTC-TTCTTCTCATTTTTTTCATATTATTTTTTTTCA-TTTTT
1 TCTT-TTTTTCATTCTTCTCA-TTTTTTCATATTATTTTTTCTCATTTTTT
*
1171677 TCATTTTTTC
1 TCTTTTTTTC
1171687 TCTTTTATTT
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
48 6 0.12
49 8 0.15
50 21 0.40
51 9 0.17
52 8 0.15
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.74
Consensus pattern (49 bp):
TCTTTTTTTCATTCTTCTCATTTTTTCATATTATTTTTTCTCATTTTTT
Found at i:1171657 original size:9 final size:9
Alignment explanation
Indices: 1171580--1171685 Score: 79
Period size: 9 Copynumber: 12.7 Consensus size: 9
1171570 TTTATTTCTC
1171580 TTTTTTTCA
1 TTTTTTTCA
*
1171589 TTTTTCTC-
1 TTTTTTTCA
1171597 -TTTTTTCA
1 TTTTTTTCA
1171605 --TTTTTCA
1 TTTTTTTCA
1171612 TTTTTTCTCA
1 TTTTTT-TCA
1171622 TTTTTTTC-
1 TTTTTTTCA
1171630 TTCTTTTTC-
1 TT-TTTTTCA
* *
1171639 TTCTTCTCA
1 TTTTTTTCA
1171648 TTTTTTTCA
1 TTTTTTTCA
* *
1171657 -TATTAT--
1 TTTTTTTCA
1171663 TTTTTTTCA
1 TTTTTTTCA
1171672 -TTTTTTCA
1 TTTTTTTCA
1171680 TTTTTT
1 TTTTTT
1171686 CTCTTTTATT
Statistics
Matches: 77, Mismatches: 10, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
7 17 0.22
8 18 0.23
9 33 0.43
10 9 0.12
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTTTTTCA
Found at i:1171681 original size:68 final size:67
Alignment explanation
Indices: 1171575--1171702 Score: 190
Period size: 68 Copynumber: 1.9 Consensus size: 67
1171565 CTCCTTTTAT
*
1171575 TTCTCTTTTTTTCATTTTTCTCTTTTTTCATTTTTCATTTTTTCTCATTTT-TTTCTTCTTTTTC
1 TTCTCTTTTTTTCATTTATCTCTTTTTTCATTTTTCATTTTTTCTC-TTTTATTTCTTCTTTTTC
1171639 TTC
65 TTC
1171642 TTCTCATTTTTTTCATATTAT-T-TTTTTTCATTTTTTCATTTTTTCTCTTTTATTTCTTCTT
1 TTCTC-TTTTTTTCAT-TTATCTCTTTTTTCA-TTTTTCATTTTTTCTCTTTTATTTCTTCTT
1171703 CAAGCGAAAT
Statistics
Matches: 56, Mismatches: 1, Indels: 7
0.88 0.02 0.11
Matches are distributed among these distances:
67 17 0.30
68 36 0.64
69 3 0.05
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.74
Consensus pattern (67 bp):
TTCTCTTTTTTTCATTTATCTCTTTTTTCATTTTTCATTTTTTCTCTTTTATTTCTTCTTTTTCT
TC
Found at i:1171683 original size:7 final size:8
Alignment explanation
Indices: 1171581--1171686 Score: 78
Period size: 8 Copynumber: 12.9 Consensus size: 8
1171571 TTATTTCTCT
1171581 TTTTTTCA
1 TTTTTTCA
1171589 TTTTTCTC-
1 TTTTT-TCA
1171597 TTTTTTCA
1 TTTTTTCA
1171605 -TTTTTCA
1 TTTTTTCA
1171612 TTTTTTCTCA
1 -TTTTT-TCA
*
1171622 TTTTTTTCT
1 -TTTTTTCA
1171631 TCTTTTTC-
1 T-TTTTTCA
*
1171639 TTCTTCTCA
1 TT-TTTTCA
1171648 TTTTTTTCA
1 -TTTTTTCA
*
1171657 TATTATT--
1 T-TTTTTCA
1171664 TTTTTTCA
1 TTTTTTCA
1171672 TTTTTTCA
1 TTTTTTCA
1171680 TTTTTTC
1 TTTTTTC
1171687 TCTTTTATTT
Statistics
Matches: 81, Mismatches: 5, Indels: 24
0.74 0.05 0.22
Matches are distributed among these distances:
6 4 0.05
7 11 0.14
8 32 0.40
9 23 0.28
10 11 0.14
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (8 bp):
TTTTTTCA
Found at i:1181402 original size:45 final size:47
Alignment explanation
Indices: 1181333--1181443 Score: 145
Period size: 45 Copynumber: 2.3 Consensus size: 47
1181323 CCATGCTTTG
* *
1181333 TTATTCACAAAAATAAATCTTAACCGCATGATATCTAATTCGCAT-AC
1 TTATTCA-AAAAATGAATCCTAACCGCATGATATCTAATTCGCATCAC
* *
1181380 TTATTCAAAAAATGAA-CCTAACCGCATGATATCTAGTTCGCATGCAT
1 TTATTCAAAAAATGAATCCTAACCGCATGATATCTAATTCGCAT-CAC
1181427 TTATTCGAAAAAATGAA
1 TTATTC-AAAAAATGAA
1181444 AATAAATTAC
Statistics
Matches: 57, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
45 25 0.44
46 8 0.14
47 14 0.25
48 10 0.18
ACGTcount: A:0.41, C:0.19, G:0.10, T:0.31
Consensus pattern (47 bp):
TTATTCAAAAAATGAATCCTAACCGCATGATATCTAATTCGCATCAC
Found at i:1184501 original size:19 final size:19
Alignment explanation
Indices: 1184477--1184525 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1184467 AATGTAGGGT
1184477 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
1184496 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
1184515 TAATTTTGTAT
1 TAATTTTGTAT
1184526 GTGAATGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:1185392 original size:200 final size:200
Alignment explanation
Indices: 1184877--1186033 Score: 1420
Period size: 200 Copynumber: 5.8 Consensus size: 200
1184867 GTAATAAGAT
* * * * *
1184877 GTGTCGATACATTTATAAAAGGTATCGATCCCAAAAATATTGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTTTAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* *
1184942 GGTAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGTGAGAATAGGTCAACATAATGT
66 GGTAATTTTGTAATGTAACCGGTATAAATATACCGGTTTTATGTGAGAATAGGTCTACATAATGT
* * * *
1185007 ATCGACACTTTTGAAATTAGTGTCGATAATTTTTGTCCAGAATGAAT-CCCAAAATGGTGAACGC
131 ATCGACACTTATGAAATTTGTGTCGATACTGTTTGTCCAGAATGAATGCCCAAAATGGTGAACGC
1185071 ATAAA
196 ATAAA
* * * * *
1185076 GTGTCGATACATTTATAAAAAGTATCGAT-CCAGAAACATTGAAACCCATAATTATAATGTAAAA
1 GTGTCGATACATTTTTAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * * *
1185140 GGCAATTTT-CAATGTAACCGGTATAACTATACCGGTTTTATGAGAAAATAGGTCTACATAATGT
66 GGTAATTTTGTAATGTAACCGGTATAAATATACCGGTTTTATGTGAGAATAGGTCTACATAATGT
* * * * * * **
1185204 ATCGACACTTATGGAATTTGTTTCAATACTGTTTGTCCAGAAGGAATGCCCAAAAGGGTGCACAA
131 ATCGACACTTATGAAATTTGTGTCGATACTGTTTGTCCAGAATGAATGCCCAAAATGGTGAACGC
1185269 ATAAA
196 ATAAA
* * * * *
1185274 ATGTCGATACTTTTTTTAAAAGTGTCGATCCCATAGACATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTTTAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* *
1185339 TGTAATTTTGTAATGTAACCGGTATAAATATACTGGTTTTATGTGAGAATAGGTCTACATAATGT
66 GGTAATTTTGTAATGTAACCGGTATAAATATACCGGTTTTATGTGAGAATAGGTCTACATAATGT
*
1185404 ATCGACACATT-TGAAATTGGTGTCGATAC-GTTTTGTCCAGAATGAATGCCCAAAATGGTGAAC
131 ATCGACAC-TTATGAAATTTGTGTCGATACTG-TTTGTCCAGAATGAATGCCCAAAATGGTGAAC
1185467 GCATAAA
194 GCATAAA
* * *
1185474 GTGTCGATACATTTTTTAAAAGTGTCGATCCCAGAGACATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTTTAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * * *
1185539 TGCAATTTTGTAATGTAACTGGTATAATTATACTGGTTTTATGTGAGAATAGGTCTACATAATGT
66 GGTAATTTTGTAATGTAACCGGTATAAATATACCGGTTTTATGTGAGAATAGGTCTACATAATGT
* * *
1185604 ATCGACACATT-TGAAATTGGTGTCGATACAT-TTTGCCCAGAATGAATGCCTAAAATATGGTGA
131 ATCGACAC-TTATGAAATTTGTGTCGATAC-TGTTTGTCCAGAATGAATGCC-CAAA-ATGGTGA
1185667 ACGCATAAA
192 ACGCATAAA
* * * **
1185676 GTGTCGATACATTTATAAAAAGTGTCGATCCCATAAACATCGAAACCCATGATTATAAAATAATA
1 GTGTCGATACATTTTTAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* ** * * * *
1185741 GGTAATTTT-TCAATGTAACCAGTATAAATATACTAGTTTTATGCGAGAATAGGTATAGAAAATG
66 GGTAATTTTGT-AATGTAACCGGTATAAATATACCGGTTTTATGTGAGAATAGGTCTACATAATG
* * * * *
1185805 TATCGACACTTATGGAATTTGTGTTGATACTTTTTGTCCAGAAGGAATG-CCAAAAGGGTGCAAC
130 TATCGACACTTATGAAATTTGTGTCGATACTGTTTGTCCAGAATGAATGCCCAAAATGGTG-AAC
*
1185869 -CATTAA
194 GCATAAA
* * **
1185875 GTGTCAATACATTTTTAAAAAGTGTCGATCCCAAAAATATCGAAACCGGTAATTATAATGTAATA
1 GTGTCGATACATTTTTAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* ** * * * * *
1185940 GGTAAATTTCCAATGTGATCGATATAAATATACCGGTTTTATGAT-AAAATAGGTC-AGCATAAA
66 GGTAATTTTGTAATGTAACCGGTATAAATATACCGGTTTTATG-TGAGAATAGGTCTA-CATAAT
* *
1186003 GTATCGACAATTATTAAATTTGTGTCGATAC
129 GTATCGACACTTATGAAATTTGTGTCGATAC
1186034 CATTTTAAAA
Statistics
Matches: 834, Mismatches: 108, Indels: 32
0.86 0.11 0.03
Matches are distributed among these distances:
197 88 0.11
198 83 0.10
199 205 0.25
200 283 0.34
201 10 0.01
202 165 0.20
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (200 bp):
GTGTCGATACATTTTTAAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
GGTAATTTTGTAATGTAACCGGTATAAATATACCGGTTTTATGTGAGAATAGGTCTACATAATGT
ATCGACACTTATGAAATTTGTGTCGATACTGTTTGTCCAGAATGAATGCCCAAAATGGTGAACGC
ATAAA
Found at i:1186706 original size:199 final size:199
Alignment explanation
Indices: 1186366--1186856 Score: 790
Period size: 199 Copynumber: 2.5 Consensus size: 199
1186356 ACATTTTTAG
* * *
1186366 ATTTACAATGTAACCAGTATAAATTTACCAATTTTATAAGAAAATAGGTGAACATAATGTATCGA
1 ATTTACAATGTAACCGGTATAAATTTACCGATTTTATGAGAAAATAGGTGAACATAATGTATCGA
* * **
1186431 CACGTTTTAGATTTGTGTCGATACATTTTGTCCAAAATGAATGTCAAACGTTGTGCAGGCAAAAA
66 CACGTTTTAGATTTGTGTCGATACATTTTTTCCAAAATGAATGCCAAACGGGGTGCAGGCAAAAA
* * *
1186496 GTGTCGATACATTTGAAATTGTATCGATCCTAAAAATATCGAAACCGATAATTATAATGTAATAG
131 GTGTCGATACATTTGAAATTGTATCGATCCCAAAAACATCGAAACCGATAATTATAACGTAATAG
1186561 GTAA
196 GTAA
*
1186565 ATTTACAATGTAACCGGTATGAATTTACCGATTTTATGAGAAAATAGGTGAACATAATGTATCGA
1 ATTTACAATGTAACCGGTATAAATTTACCGATTTTATGAGAAAATAGGTGAACATAATGTATCGA
* *
1186630 CACGTTTTAGATTTATGTCGATACATTTTTTCCAGAATGAATGCCAAACGGGGTGCAGG-AACAA
66 CACGTTTTAGATTTGTGTCGATACATTTTTTCCAAAATGAATGCCAAACGGGGTGCAGGCAA-AA
1186694 AGTGTCGATACATTTGAAATTGTATCGATCCCAAAAACATCGAAACCGATAATTATAACGTAATA
130 AGTGTCGATACATTTGAAATTGTATCGATCCCAAAAACATCGAAACCGATAATTATAACGTAATA
1186759 GGTAA
195 GGTAA
* * * *
1186764 ATTTACAATGTAACCGATATAAATATACCGATTTTATGAGAGAATAGGTCAACATAATGTATCGA
1 ATTTACAATGTAACCGGTATAAATTTACCGATTTTATGAGAAAATAGGTGAACATAATGTATCGA
*
1186829 CAC-TTTTAAATTTGTGTCGATAC-TTTTT
66 CACGTTTTAGATTTGTGTCGATACATTTTT
1186857 AAATAACACG
Statistics
Matches: 271, Mismatches: 20, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
197 5 0.02
198 20 0.07
199 246 0.91
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (199 bp):
ATTTACAATGTAACCGGTATAAATTTACCGATTTTATGAGAAAATAGGTGAACATAATGTATCGA
CACGTTTTAGATTTGTGTCGATACATTTTTTCCAAAATGAATGCCAAACGGGGTGCAGGCAAAAA
GTGTCGATACATTTGAAATTGTATCGATCCCAAAAACATCGAAACCGATAATTATAACGTAATAG
GTAA
Found at i:1187612 original size:19 final size:19
Alignment explanation
Indices: 1187588--1187632 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
1187578 AATGTAGGGT
*
1187588 TAATTTTATATAAGATTTA
1 TAATTTTACATAAGATTTA
*
1187607 TAATTTTACATACGATTTA
1 TAATTTTACATAAGATTTA
1187626 TAATTTT
1 TAATTTT
1187633 GTATGTGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.53
Consensus pattern (19 bp):
TAATTTTACATAAGATTTA
Found at i:1190664 original size:199 final size:198
Alignment explanation
Indices: 1190112--1190813 Score: 748
Period size: 199 Copynumber: 3.5 Consensus size: 198
1190102 ACCTAAATAT
* *
1190112 GTGTCGATACATTT-TCTAAAAGTATCGACCCAAAAAACATTGAAACCAATAATTATAATGTAAT
1 GTGTCGATACATTTAT-TAAAAGTATCGACCCAAAAAACATCGAAACCGATAATTATAATGTAAT
* * * * * *
1190176 AGGTAAATTAACAATGTAACCGGTATAAATATAACGG-TTAATTAGAAAACATGTC-AACATAAT
65 AGGTAAATTTACAATGTAACCGGTATAAATAT-ACGGTTTTATGAGAAAATAGGTCTGA-ATAAT
1190239 GTATCGACACTTGTGTAATTTGTGTCGATAC-TTATTGTCCAGAATGAATGCCCAAACGAGGTGC
128 GTATCGACACTT-TGTAATTTGTGTCGATACATT-TTGTCCAGAATGAATG-CCAAACGAGGTGC
1190303 ACGCATAAA
190 ACGCATAAA
* * *** * *
1190312 GTGTCGATACATTTATTAAAAGTATCGATCCCAATAAA-ATCGATACTTTTAAATT-TGTATATA
1 GTGTCGATACATTTATTAAAAGTATCGA-CCCAAAAAACATCGAAACCGAT-AATTAT-AATGTA
* * *
1190375 ATATGTAAATTTACAATGTAACCGGTATAAAAATACTGGTTTTATGAGAAAATAGGT-TAGCATA
63 ATAGGTAAATTTACAATGTAACCGGTATAAATATAC-GGTTTTATGAGAAAATAGGTCT-GAATA
* * *
1190439 AAGTATCGACAC-TTGTTAAATTTGTGTCGATACATTTTGTCCATAATGAATGCTAAAC-AGGTG
126 ATGTATCGACACTTTG-T-AATTTGTGTCGATACATTTTGTCCAGAATGAATGCCAAACGAGGTG
1190502 CACGCATAAA
189 CACGCATAAA
* * * * *
1190512 GTGTAGATACATTTATTAAAAGTATCGATTCC-AAAAACATCGAAACCGATATTTACAATGTGAT
1 GTGTCGATACATTTATTAAAAGTATCGA-CCCAAAAAACATCGAAACCGATAATTATAATGTAAT
* * * *
1190576 AAGTAAATTTACAATGTACCCGATAGAAATATATCGGTTTTATGAGAAAATAGGTCTGAATAATG
65 AGGTAAATTTACAATGTAACCGGTATAAATATA-CGGTTTTATGAGAAAATAGGTCTGAATAATG
** * *
1190641 TATTAACACTTTGTAAGTTTGTGTCGATACTATTTT-T-CAGAATGAATGCCCAACGAGATGCAC
129 TATCGACACTTTGTAA-TTTGTGTCGATAC-ATTTTGTCCAGAATGAATGCCAAACGAGGTGCAC
1190704 GCATAAA
192 GCATAAA
** * * *
1190711 GTGTCGATACATTTCA--AATTGTATCGATCCAAAAAATATCAAAACCGATAATTATAATGTAAT
1 GTGTCGATACATTT-ATTAAAAGTATCGACCCAAAAAACATCGAAACCGATAATTATAATGTAAT
* * * *
1190774 AGGTAAATTTATAATTTTACCGTTATAAATATACCGGTTT
65 AGGTAAATTTACAATGTAACCGGTATAAATATA-CGGTTT
1190814 ACTTATAAAA
Statistics
Matches: 420, Mismatches: 61, Indels: 44
0.80 0.12 0.08
Matches are distributed among these distances:
197 3 0.01
198 84 0.20
199 115 0.27
200 102 0.24
201 57 0.14
202 57 0.14
203 2 0.00
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (198 bp):
GTGTCGATACATTTATTAAAAGTATCGACCCAAAAAACATCGAAACCGATAATTATAATGTAATA
GGTAAATTTACAATGTAACCGGTATAAATATACGGTTTTATGAGAAAATAGGTCTGAATAATGTA
TCGACACTTTGTAATTTGTGTCGATACATTTTGTCCAGAATGAATGCCAAACGAGGTGCACGCAT
AAA
Found at i:1190940 original size:87 final size:87
Alignment explanation
Indices: 1190831--1190993 Score: 254
Period size: 87 Copynumber: 1.9 Consensus size: 87
1190821 AAATAGGTCG
* * * **
1190831 ATATAAGTGCTACTTATCACATTATATAAGCGTTACCTAATATGTTATTGTACTTGCTAATATTT
1 ATATAAGCGCTACCTATCACATTATATAAGCGCTACCTAATATGTTATTGTACTTAATAATATTT
*
1190896 CCTGTTAAATGCCTATTTTATT
66 CCGGTTAAATGCCTATTTTATT
* *
1190918 ATATAAGCGCTACCTATTACATTATATAAGTGCTACCTAATATGTTATTGTACTTAATAATATTT
1 ATATAAGCGCTACCTATCACATTATATAAGCGCTACCTAATATGTTATTGTACTTAATAATATTT
1190983 CCGGTTAAATG
66 CCGGTTAAATG
1190994 ATATAACATA
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
87 68 1.00
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (87 bp):
ATATAAGCGCTACCTATCACATTATATAAGCGCTACCTAATATGTTATTGTACTTAATAATATTT
CCGGTTAAATGCCTATTTTATT
Found at i:1190965 original size:23 final size:23
Alignment explanation
Indices: 1190915--1190959 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1190905 TGCCTATTTT
*
1190915 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
*
1190938 ATTATATAAGTGCTACCTAATA
1 ATTATATAAGCGCTACCTAATA
1190960 TGTTATTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.36
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:1197998 original size:180 final size:180
Alignment explanation
Indices: 1197696--1198055 Score: 720
Period size: 180 Copynumber: 2.0 Consensus size: 180
1197686 TATATTCACA
1197696 AAATAATCAACAGAAATGCGCATTATATCATGTTTACCAATCCTCCAAATCCCTTGAACATCATA
1 AAATAATCAACAGAAATGCGCATTATATCATGTTTACCAATCCTCCAAATCCCTTGAACATCATA
1197761 AAGGCCATGAATACGATTCTTTTTTTCTCCCATTCGCCCTAGCATGGAAGTAAGATGCATTATGA
66 AAGGCCATGAATACGATTCTTTTTTTCTCCCATTCGCCCTAGCATGGAAGTAAGATGCATTATGA
1197826 TCTCCATGGGATAACCACGCCACCCTCGATCGCCGAAGCCAATAAATCTC
131 TCTCCATGGGATAACCACGCCACCCTCGATCGCCGAAGCCAATAAATCTC
1197876 AAATAATCAACAGAAATGCGCATTATATCATGTTTACCAATCCTCCAAATCCCTTGAACATCATA
1 AAATAATCAACAGAAATGCGCATTATATCATGTTTACCAATCCTCCAAATCCCTTGAACATCATA
1197941 AAGGCCATGAATACGATTCTTTTTTTCTCCCATTCGCCCTAGCATGGAAGTAAGATGCATTATGA
66 AAGGCCATGAATACGATTCTTTTTTTCTCCCATTCGCCCTAGCATGGAAGTAAGATGCATTATGA
1198006 TCTCCATGGGATAACCACGCCACCCTCGATCGCCGAAGCCAATAAATCTC
131 TCTCCATGGGATAACCACGCCACCCTCGATCGCCGAAGCCAATAAATCTC
1198056 TCATTATCAA
Statistics
Matches: 180, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
180 180 1.00
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.27
Consensus pattern (180 bp):
AAATAATCAACAGAAATGCGCATTATATCATGTTTACCAATCCTCCAAATCCCTTGAACATCATA
AAGGCCATGAATACGATTCTTTTTTTCTCCCATTCGCCCTAGCATGGAAGTAAGATGCATTATGA
TCTCCATGGGATAACCACGCCACCCTCGATCGCCGAAGCCAATAAATCTC
Found at i:1200040 original size:38 final size:38
Alignment explanation
Indices: 1199998--1200082 Score: 136
Period size: 38 Copynumber: 2.2 Consensus size: 38
1199988 AACTTTTTTC
*
1199998 TAACATTTTCGATTCAACAAAAAATATTACGAAAAATA-
1 TAACATTTTCGATTCAACAAAAAATATTA-GAAAAAAAT
*
1200036 TAACATTTTCGATTCAACTAAAAATATTAGAAAAAAAT
1 TAACATTTTCGATTCAACAAAAAATATTAGAAAAAAAT
1200074 TAACATTTT
1 TAACATTTT
1200083 AGGTTGCGTC
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
37 7 0.16
38 37 0.84
ACGTcount: A:0.51, C:0.12, G:0.05, T:0.33
Consensus pattern (38 bp):
TAACATTTTCGATTCAACAAAAAATATTAGAAAAAAAT
Found at i:1202779 original size:13 final size:13
Alignment explanation
Indices: 1202761--1202794 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
1202751 ATCCAAAACA
1202761 AAAGATAATTCCT
1 AAAGATAATTCCT
1202774 AAAGATAATTCCT
1 AAAGATAATTCCT
*
1202787 AAAAATAA
1 AAAGATAA
1202795 AAATAAGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.56, C:0.12, G:0.06, T:0.26
Consensus pattern (13 bp):
AAAGATAATTCCT
Found at i:1206281 original size:23 final size:23
Alignment explanation
Indices: 1206255--1206302 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1206245 ATAAAGTACA
*
1206255 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
1206278 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
1206301 AT
1 AT
1206303 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:1206694 original size:20 final size:20
Alignment explanation
Indices: 1206669--1206707 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1206659 TTCCACAGTA
* *
1206669 AAAAAAGTATGGACACTTTT
1 AAAAAAGGATAGACACTTTT
1206689 AAAAAAGGATAGACACTTT
1 AAAAAAGGATAGACACTTT
1206708 ACAATATAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.26
Consensus pattern (20 bp):
AAAAAAGGATAGACACTTTT
Found at i:1206774 original size:22 final size:22
Alignment explanation
Indices: 1206711--1206780 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 22
1206701 ACACTTTACA
* *
1206711 ATATAACCACTACCTATACATT
1 ATATAAACGCTACCTATACATT
*
1206733 ATATAAACGATACCTATACATT
1 ATATAAACGCTACCTATACATT
* *
1206755 ATAT-AGCGCTACCTATTACATC
1 ATATAAACGCTACCTA-TACATT
1206777 ATAT
1 ATAT
1206781 TTTTACCTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
21 9 0.22
22 32 0.78
ACGTcount: A:0.40, C:0.23, G:0.04, T:0.33
Consensus pattern (22 bp):
ATATAAACGCTACCTATACATT
Found at i:1207156 original size:21 final size:21
Alignment explanation
Indices: 1207126--1207196 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
1207116 GATAGACACT
*
1207126 TTACAATATAACCACTACCTA
1 TTACATTATAACCACTACCTA
* *
1207147 TTACATTATATACGA-TACATA
1 TTACATTATA-ACCACTACCTA
* *
1207168 TTACATTATATAAGCGCTACCTA
1 TTACA-T-TATAACCACTACCTA
1207191 TTACAT
1 TTACAT
1207197 CATATTTTTA
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
21 19 0.49
22 6 0.15
23 14 0.36
ACGTcount: A:0.39, C:0.21, G:0.04, T:0.35
Consensus pattern (21 bp):
TTACATTATAACCACTACCTA
Found at i:1207179 original size:23 final size:23
Alignment explanation
Indices: 1207145--1207201 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
1207135 AACCACTACC
1207145 TATTACATTATAT-A-CGATACA
1 TATTACATTATATAAGCGATACA
* *
1207166 TATTACATTATATAAGCGCTACC
1 TATTACATTATATAAGCGATACA
*
1207189 TATTACATCATAT
1 TATTACATTATAT
1207202 TTTTACCTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 13 0.42
22 1 0.03
23 17 0.55
ACGTcount: A:0.39, C:0.18, G:0.05, T:0.39
Consensus pattern (23 bp):
TATTACATTATATAAGCGATACA
Found at i:1207579 original size:21 final size:22
Alignment explanation
Indices: 1207554--1207605 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
1207544 ACACTTTACA
*
1207554 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
1207577 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
1207600 ATATAA
1 ATATAA
1207606 GTGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:1207590 original size:23 final size:23
Alignment explanation
Indices: 1207564--1207626 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1207554 ATATAACCAC
1207564 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
1207587 TACCTATTACATTATATAAGTGC
1 TACCTATTACATTATATAAACGA
*
1207610 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1207627 TTTACCTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1207769 original size:422 final size:428
Alignment explanation
Indices: 1206369--1207823 Score: 2613
Period size: 423 Copynumber: 3.5 Consensus size: 428
1206359 TATTACATTA
1206369 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1206434 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
66 TTATGTTTCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
*
1206499 ATTTGCACAAAAAATTATTTGATTAATTGATATTTTATAAAATATTATTTAGAATTTTTAA-TT-
130 ATTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
1206562 -TAATAATATATATCGTAACGTAAAAAAT--TCATTA-ACGCCTATAATTACTAAATTAATATCT
195 ATAATAATATATATCGTAACGTAAAAAATAATCATTAGACGCCTATAATTACTAAATTAATATCT
*
1206623 TAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTAAAAAAAGTATGGACACTTT
260 TAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTT
1206688 TA-AAAAAGGATAGACACTTTACAATATAACCACTACCTA-TACATTATATAAACGATACCTA-T
325 TATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATT
1206750 ACATTATAT-AGCGCTACCTATTACATCATATTTTTACC
390 ACATTATATAAGCGCTACCTATTACATCATATTTTTACC
1206788 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAA-
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1206852 TTATGTTTCAATTTTTTTAATA-TGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
66 TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
*
1206916 TTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAA-TTTTAATTTAA
131 TTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAA
1206980 TAAT-A-ATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCT
196 TAATAATATATATCGTAACGTAAAAAAT-AATCATTAGACGCCTATAATTACTAAATTAATATCT
*
1207043 T-AAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTA
260 TAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTT
*
1207107 TATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATAT--ACGATACATATT
325 TATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATT
1207170 ACATTATATAAGCGCTACCTATTACATCATATTTTTACC
390 ACATTATATAAGCGCTACCTATTACATCATATTTTTACC
*
1207209 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAATGATCGATACTTCTTTTAAAGTTATGTAA
1 TATTATATTGAAAGTGTCCATACTTTTTAT-AAAAAGGATCGATACTTCTTTTAAAGTTATGTAA
1207274 TTTATGTTTCAA-TTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAA-TTAATAATTTC
65 TTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
1207337 ATTTGCAC-AAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
130 ATTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
1207401 ATAATAATATATATCGTAACGTAAAAAATAATCATTAGACGCCTATAATTACT-AATTAATATCT
195 ATAATAATATATATCGTAACGTAAAAAATAATCATTAGACGCCTATAATTACTAAATTAATATCT
*
1207465 TAAAACTTACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTT
260 TAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTT
1207530 TATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATT
325 TATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATT
*
1207595 ACATTATATAAGTGCTACCTATTACATCATA-TTTTACC
390 ACATTATATAAGCGCTACCTATTACATCATATTTTTACC
*
1207633 TATTATATTGAAAGTGTCAATACTTTTTAT-AAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1207697 TTATGTTTCAATTTTTTTAATAGTGTTTCATG-TTTCCACCTACAATA-TAATTTAATAATTTCA
66 TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
1207760 TTTGCACAAAAAATTATTTGATTA-TTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAA
131 TTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAA
1207824 CAACATTAAC
Statistics
Matches: 1000, Mismatches: 13, Indels: 43
0.95 0.01 0.04
Matches are distributed among these distances:
415 6 0.01
416 116 0.12
417 12 0.01
418 15 0.01
419 142 0.14
420 75 0.08
421 116 0.12
422 207 0.21
423 213 0.21
424 57 0.06
425 41 0.04
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (428 bp):
TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
TTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAA
TAATAATATATATCGTAACGTAAAAAATAATCATTAGACGCCTATAATTACTAAATTAATATCTT
AAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTT
ATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTA
CATTATATAAGCGCTACCTATTACATCATATTTTTACC
Found at i:1208087 original size:38 final size:39
Alignment explanation
Indices: 1208036--1208120 Score: 136
Period size: 39 Copynumber: 2.2 Consensus size: 39
1208026 CAAGTTGTAG
*
1208036 ATTTTGATTTCC-TTTGCTTGGCATCATATGAGATTTGA
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
* *
1208074 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTGG
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
1208113 ATTTTGAT
1 ATTTTGAT
1208121 GAGCATCGGA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
38 12 0.28
39 31 0.72
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.48
Consensus pattern (39 bp):
ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
Found at i:1208886 original size:22 final size:23
Alignment explanation
Indices: 1208825--1208891 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
1208815 GATACTTACA
* *
1208825 ATATAACCACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
*
1208848 ATATAAACGATACCTATTACATT
1 ATATAAACGCTACCTATTACATT
*
1208871 ATAT-AGCGCTACCTATTACAT
1 ATATAAACGCTACCTATTACAT
1208892 CATGTTTACC
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
22 15 0.38
23 24 0.62
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.34
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:1211253 original size:3 final size:3
Alignment explanation
Indices: 1211245--1211325 Score: 72
Period size: 3 Copynumber: 27.0 Consensus size: 3
1211235 ACTTGTTTGG
* * * **
1211245 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * *
1211293 AGC TTC ATC GTC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1211326 GTCAGCTTCA
Statistics
Matches: 59, Mismatches: 19, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.23, C:0.35, G:0.06, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:1211262 original size:12 final size:12
Alignment explanation
Indices: 1211249--1211337 Score: 88
Period size: 12 Copynumber: 7.4 Consensus size: 12
1211239 GTTTGGATCA
* *
1211249 TCATCTTCATCA
1 TCATCGTCATCT
* *
1211261 TCATCATCATCA
1 TCATCGTCATCT
* *
1211273 TCGTCATCATCT
1 TCATCGTCATCT
* *
1211285 TCATCGCCAGCT
1 TCATCGTCATCT
*
1211297 TCATCGTCATCA
1 TCATCGTCATCT
1211309 TCATCGTCATCT
1 TCATCGTCATCT
*
1211321 TCATCGTCAGCT
1 TCATCGTCATCT
1211333 TCATC
1 TCATC
1211338 TTCTGCGACC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 65 1.00
ACGTcount: A:0.21, C:0.35, G:0.08, T:0.36
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:1211268 original size:18 final size:18
Alignment explanation
Indices: 1211249--1211340 Score: 76
Period size: 18 Copynumber: 5.1 Consensus size: 18
1211239 GTTTGGATCA
* *
1211249 TCATCTTCATCATCATCA
1 TCATCATCATCATCATCT
*
1211267 TCATCATCGTCATCATCT
1 TCATCATCATCATCATCT
** * * *
1211285 TCATCGCCAGCTTCATCG
1 TCATCATCATCATCATCT
*
1211303 TCATCATCATCGTCATCT
1 TCATCATCATCATCATCT
* * *
1211321 TCATCGTCAGCTTCATCT
1 TCATCATCATCATCATCT
1211339 TC
1 TC
1211341 TGCGACCGCT
Statistics
Matches: 57, Mismatches: 17, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 57 1.00
ACGTcount: A:0.21, C:0.35, G:0.08, T:0.37
Consensus pattern (18 bp):
TCATCATCATCATCATCT
Found at i:1211301 original size:36 final size:36
Alignment explanation
Indices: 1211261--1211337 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 36
1211251 ATCTTCATCA
*
1211261 TCATCATCATCATCGTCATCATCTTCATCGCCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGCCAGCT
* * *
1211297 TCATCGTCATCATCATCGTCATCTTCATCGTCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGCCAGCT
1211333 TCATC
1 TCATC
1211338 TTCTGCGACC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.21, C:0.35, G:0.09, T:0.35
Consensus pattern (36 bp):
TCATCATCATCATCATCATCATCTTCATCGCCAGCT
Found at i:1211340 original size:6 final size:6
Alignment explanation
Indices: 1211249--1211340 Score: 67
Period size: 6 Copynumber: 15.3 Consensus size: 6
1211239 GTTTGGATCA
* * * * * * * *
1211249 TCATCT TCATCA TCATCA TCATCA TCGTCA TCATCT TCATCG CCAGCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* * * * *
1211297 TCATCG TCATCA TCATCG TCATCT TCATCG TCAGCT TCATCT TC
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TC
1211341 TGCGACCGCT
Statistics
Matches: 68, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 68 1.00
ACGTcount: A:0.21, C:0.35, G:0.08, T:0.37
Consensus pattern (6 bp):
TCATCT
Found at i:1213522 original size:200 final size:199
Alignment explanation
Indices: 1212789--1213760 Score: 1763
Period size: 198 Copynumber: 4.9 Consensus size: 199
1212779 TTTAAATTAG
1212789 TATCGACACAAACTATA--ACGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAT
1 TATCGACACAAACTATATTA-GTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAT
*
1212852 ACTTGTACCGGTTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
65 AATTGTACCGG-TTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
*
1212917 ATCGACACTTTTTATATATGGATCGACACTTTATAGGTGCACCCTGTTTTCCATTCATTCTGGAA
129 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAA
1212982 AAAAAA
194 AAAAAA
1212988 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1213053 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
1213118 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
1213182 AAAA
196 AAAA
1213186 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1213251 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
1213316 CGACACTTTTTATATATGGATCGATACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
1213381 AAAAA
195 AAAAA
* * * *
1213386 TATCGACATAAACTATATTAGTGTCGGCACATTATTTATACATATTATCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1213451 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
1213516 CGACACTTTTTATATATGAATCGACACTTTATGGGTGCACCCT-TTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
1213580 AAAA
196 AAAA
*
1213584 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAGA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* * *
1213649 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGGA
*
1213714 TTGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
130 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
1213761 GGCCATATTG
Statistics
Matches: 748, Mismatches: 19, Indels: 11
0.96 0.02 0.01
Matches are distributed among these distances:
198 311 0.42
199 206 0.28
200 230 0.31
201 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.37
Consensus pattern (199 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
AAAA
Found at i:1213524 original size:398 final size:397
Alignment explanation
Indices: 1212789--1213760 Score: 1770
Period size: 398 Copynumber: 2.4 Consensus size: 397
1212779 TTTAAATTAG
1212789 TATCGACACAAACTATA--ACGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAT
1 TATCGACACAAACTATATTA-GTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAT
1212852 ACTTGTACCGGTTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
65 ACTTGTACCGG-TTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGG
*
1212917 ATCGACACTTTTTATATATGGATCGACACTTTATAGGTGCACCCTGTTTTCCATTCATTCTGGAA
129 ATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAA
*
1212982 AAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACC
194 AAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACC
1213047 GGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTT
259 GGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTT
*
1213112 TGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCT
324 TGGGATCGACACTTTTTATATATGAATCGACACTTTATGGGTGCACCCT-TTTTCCATTCATTCT
1213177 GG-AAAAAAA
388 GGAAAAAAAA
1213186 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
1213251 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
1213316 CGACACTTTTTATATATGGATCGATACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
* * *
1213381 AAAAATATCGACATAAACTATATTAGTGTCGGCACATTATTTATACATATTATCTCATAAAACCG
195 AAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCG
1213446 GTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
260 GTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTT
1213511 GGGATCGACACTTTTTATATATGAATCGACACTTTATGGGTGCACCCTTTTTCCATTCATTCTGG
325 GGGATCGACACTTTTTATATATGAATCGACACTTTATGGGTGCACCCTTTTTCCATTCATTCTGG
1213576 AAAAAAAA
390 AAAAAAAA
*
1213584 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAGA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* *
1213649 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGGA
*
1213714 TTGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
130 TCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
1213761 GGCCATATTG
Statistics
Matches: 556, Mismatches: 14, Indels: 8
0.96 0.02 0.01
Matches are distributed among these distances:
397 148 0.27
398 347 0.62
399 61 0.11
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.37
Consensus pattern (397 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGG
TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
GGATCGACACTTTTTATATATGAATCGACACTTTATGGGTGCACCCTTTTTCCATTCATTCTGGA
AAAAAAA
Found at i:1213902 original size:18 final size:18
Alignment explanation
Indices: 1213876--1213921 Score: 74
Period size: 18 Copynumber: 2.5 Consensus size: 18
1213866 TTATATTCAC
1213876 ATACAAAAATATAAATCGT
1 ATAC-AAAATATAAATCGT
*
1213895 ATACAAAATATAAATCTT
1 ATACAAAATATAAATCGT
1213913 ATACAAAAT
1 ATACAAAAT
1213922 TAACCCTACA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 22 0.85
19 4 0.15
ACGTcount: A:0.59, C:0.11, G:0.02, T:0.28
Consensus pattern (18 bp):
ATACAAAATATAAATCGT
Found at i:1215737 original size:33 final size:33
Alignment explanation
Indices: 1215700--1215765 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1215690 CATCTTAATA
*
1215700 TCACCCCTTAACAC-CCTAACTTCTTTCACCACT
1 TCACCCCTCAACACACCT-ACTTCTTTCACCACT
*
1215733 TCACCCCTCAACACATCTACTTCTTTCACCACT
1 TCACCCCTCAACACACCTACTTCTTTCACCACT
1215766 CCATCTATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.93
34 2 0.07
ACGTcount: A:0.24, C:0.45, G:0.00, T:0.30
Consensus pattern (33 bp):
TCACCCCTCAACACACCTACTTCTTTCACCACT
Found at i:1215824 original size:21 final size:21
Alignment explanation
Indices: 1215799--1215863 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
1215789 CCTCTTATGC
* *
1215799 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
* *
1215820 CTCTCGAGTTTCTCTACGACT
1 CTCTCAAGTTTCTCTTCGACT
**
1215841 CGATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
1215862 CT
1 CT
1215864 TGATTATCTT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.17, C:0.31, G:0.14, T:0.38
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:1218301 original size:20 final size:20
Alignment explanation
Indices: 1218274--1218320 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
1218264 TCCGGTAACG
1218274 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
1218293 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
1218314 TTTTACC
1 TTTTACC
1218321 TGGTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:1218547 original size:182 final size:179
Alignment explanation
Indices: 1218063--1218532 Score: 674
Period size: 182 Copynumber: 2.6 Consensus size: 179
1218053 CGTACTTACG
* * * *
1218063 AAAGTATCGACACTTTCAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATATCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
1218128 TATCATATTTTACCTGTTATATCG-TGTGGATCGATATATTTTTTAAAGTATCGACGCATTATAG
66 TATCATATTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAGTATCGACACATTATAG
* *
1218192 GCGCTATAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
131 GAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
* *
1218241 AAAGTATCGACACTTTTAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGTTACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
1218306 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATA-TTTTACCTGTTATATCGTTTTGGATCGATACATTTTTT-AAAGTATCGACACATTAT
** *
1218371 AGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
129 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
* * * * *
1218423 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTGACCGGTTTTATCATTTCT-ATACCGGTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTT-TGATACCGGTT
* *
1218487 TTGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
65 TTATCATA-TTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
1218533 AATTTGGATC
Statistics
Matches: 261, Mismatches: 26, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
178 67 0.26
179 16 0.06
180 18 0.07
181 61 0.23
182 98 0.38
183 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (179 bp):
AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAGTATCGACACATTATAG
GAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
Found at i:1219002 original size:230 final size:229
Alignment explanation
Indices: 1218599--1219087 Score: 879
Period size: 230 Copynumber: 2.1 Consensus size: 229
1218589 ACCTACTTTT
**
1218599 ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCA
1 ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTCGAAAGTTATGTAATTTATGTTTCA
*
1218664 ATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTACACAA
66 ATTTTTTTTAATAGTGTTTCATGTTTTCCACATACAATATTAATTTAATAATTTAATTTACACAA
*
1218729 AATATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAA
131 AAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAA
* *
1218794 CCAAATATAATAATAAATATGTTTTCAACAGTGAA
196 CCAAAGATAATAATAAATATATTTTC-ACAGTGAA
1218829 ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTCGAAAGTTATGTAATTTATGTTTCA
1 ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTCGAAAGTTATGTAATTTATGTTTCA
*
1218894 ATTTTTTTTAATAGTGTTTCATGTTTTCCACATACAATATTAATTTAATAATTTCATTTACACAA
66 ATTTTTTTTAATAGTGTTTCATGTTTTCCACATACAATATTAATTTAATAATTTAATTTACACAA
*
1218959 AAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGATTTTAAATTTAACAATATTAA
131 AAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAA
*
1219024 CTAAAGATAATAATAAATATATTTTCACAGTGAA
196 CCAAAGATAATAATAAATATATTTTCACAGTGAA
*
1219058 ATAAGTATGGACACTTTTATAAAAAAGATA
1 ATAAGTATGGACACTTTTATAAAAATGATA
1219088 GATAATTTAC
Statistics
Matches: 249, Mismatches: 10, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
229 37 0.15
230 212 0.85
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (229 bp):
ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTCGAAAGTTATGTAATTTATGTTTCA
ATTTTTTTTAATAGTGTTTCATGTTTTCCACATACAATATTAATTTAATAATTTAATTTACACAA
AAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAA
CCAAAGATAATAATAAATATATTTTCACAGTGAA
Found at i:1225550 original size:11 final size:11
Alignment explanation
Indices: 1225525--1225567 Score: 68
Period size: 11 Copynumber: 3.8 Consensus size: 11
1225515 CGGAAAATAC
1225525 TGTAGCAGTTAT
1 TGTAGCAG-TAT
1225537 TGTAGCAGTAT
1 TGTAGCAGTAT
*
1225548 TGTAGCAGTAC
1 TGTAGCAGTAT
1225559 TGTAGCAGT
1 TGTAGCAGT
1225568 GCATCGATAC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
11 22 0.73
12 8 0.27
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.35
Consensus pattern (11 bp):
TGTAGCAGTAT
Found at i:1230869 original size:54 final size:54
Alignment explanation
Indices: 1230786--1230962 Score: 223
Period size: 54 Copynumber: 3.3 Consensus size: 54
1230776 GTGTACTATA
* * *
1230786 GGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAATGATCGTA-C
1 GGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAAGGACCATATC
* * *
1230839 ATGCACTAAGTGTACAACCCAC-GAAATTCATCATATATTGATGAAGGACCATATC
1 -GGCACTAAGTGTGCAACCCACAG-AATTCATCATATGTTGATGAAGGACCATATC
* * * *
1230894 GGCACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACCGTATC
1 GGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAAGGACCATATC
*
1230948 GGCACTACGTGTGCA
1 GGCACTAAGTGTGCA
1230963 TCTCAAAGAA
Statistics
Matches: 106, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
53 1 0.01
54 103 0.97
55 2 0.02
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.25
Consensus pattern (54 bp):
GGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAAGGACCATATC
Found at i:1237573 original size:54 final size:54
Alignment explanation
Indices: 1237488--1237722 Score: 319
Period size: 54 Copynumber: 4.4 Consensus size: 54
1237478 CTATGTGTAA
1237488 TATAGGCACTAAGTGTGCAACCCAC-AGAATTCATCATATGTTGATGAACGACCG
1 TATAGGCACTAAGTGTGCAACCCACGA-AATTCATCATATGTTGATGAACGACCG
* *
1237542 TATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTAATGAACGACAG
1 TATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCG
* * *
1237596 TATAAGCACTAAGTGTGCAACCCACGGAATTCATCATATGTTGATGAACGACCA
1 TATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCG
* * * * * * *
1237650 TATTGACACTAAGTGTGCAACCCACAAAATTCATAATATGTTTATGAACAACCC
1 TATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCG
* * *
1237704 TATCGACACTACGTGTGCA
1 TATAGGCACTAAGTGTGCA
1237723 TCTCAAAGAA
Statistics
Matches: 162, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
54 161 0.99
55 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.25
Consensus pattern (54 bp):
TATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCG
Found at i:1238126 original size:14 final size:14
Alignment explanation
Indices: 1238107--1238134 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1238097 GTTTTATGAA
1238107 AAGAAACAAAATTT
1 AAGAAACAAAATTT
1238121 AAGAAACAAAATTT
1 AAGAAACAAAATTT
1238135 TACGGGTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.07, G:0.07, T:0.21
Consensus pattern (14 bp):
AAGAAACAAAATTT
Found at i:1239385 original size:2 final size:2
Alignment explanation
Indices: 1239378--1239412 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1239368 TTGGGAGTTA
* *
1239378 CT CT CT CT CT CT CT CT CT CT CT CT AT CT AT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1239413 AAACACATGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.06, C:0.46, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1250400 original size:20 final size:19
Alignment explanation
Indices: 1250377--1250425 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
1250367 TTTAAGTTAA
*
1250377 TTAAAATATGTTTAAAGTGT
1 TTAAAATATGTTTAAA-TCT
**
1250397 TTAAAATGCGTTTAAATCT
1 TTAAAATATGTTTAAATCT
*
1250416 TTTAAATATG
1 TTAAAATATG
1250426 AAAAACACTA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.39, C:0.04, G:0.12, T:0.45
Consensus pattern (19 bp):
TTAAAATATGTTTAAATCT
Found at i:1259174 original size:22 final size:22
Alignment explanation
Indices: 1259144--1259224 Score: 90
Period size: 22 Copynumber: 3.6 Consensus size: 22
1259134 TGGTGTAGAT
*
1259144 GGAATCGATACCCCCTTGAAGG
1 GGAACCGATACCCCCTTGAAGG
*
1259166 GGAACCGATTCCCCCTTTGAAGG
1 GGAACCGATACCCCC-TTGAAGG
* ** *
1259189 GGAACCGATTCCCCCTACAGGG
1 GGAACCGATACCCCCTTGAAGG
*
1259211 GGAATCGATACCCC
1 GGAACCGATACCCC
1259225 ATGGGGTTCT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
22 29 0.57
23 22 0.43
ACGTcount: A:0.25, C:0.32, G:0.26, T:0.17
Consensus pattern (22 bp):
GGAACCGATACCCCCTTGAAGG
Found at i:1259185 original size:23 final size:23
Alignment explanation
Indices: 1259144--1259204 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
1259134 TGGTGTAGAT
* *
1259144 GGAATCGATACCCCC-TTGAAGG
1 GGAACCGATTCCCCCTTTGAAGG
1259166 GGAACCGATTCCCCCTTTGAAGG
1 GGAACCGATTCCCCCTTTGAAGG
1259189 GGAACCGATTCCCCCT
1 GGAACCGATTCCCCCT
1259205 ACAGGGGGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 13 0.36
23 23 0.64
ACGTcount: A:0.23, C:0.33, G:0.25, T:0.20
Consensus pattern (23 bp):
GGAACCGATTCCCCCTTTGAAGG
Found at i:1261145 original size:17 final size:17
Alignment explanation
Indices: 1261116--1261153 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1261106 CATTTTGGAT
1261116 ATTT-TGGAATGTTTGA
1 ATTTGTGGAATGTTTGA
*
1261132 ATTTGTGGATTGTTTGA
1 ATTTGTGGAATGTTTGA
*
1261149 CTTTG
1 ATTTG
1261154 AATTTGTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.18, C:0.03, G:0.26, T:0.53
Consensus pattern (17 bp):
ATTTGTGGAATGTTTGA
Found at i:1263126 original size:16 final size:15
Alignment explanation
Indices: 1263094--1263122 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1263084 ACATCCACAT
1263094 TGGTATCGATACCCA
1 TGGTATCGATACCCA
1263109 TGGTATCGATACCC
1 TGGTATCGATACCC
1263123 CATGAAGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.28
Consensus pattern (15 bp):
TGGTATCGATACCCA
Found at i:1270388 original size:25 final size:25
Alignment explanation
Indices: 1270360--1270410 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
1270350 ATAAAACAGT
* *
1270360 TTAGTTTAATCATCTAAACCATAAG
1 TTAGTTTAATCATCAAAACCACAAG
1270385 TTAGTTTAATCATCAAAACCACAAG
1 TTAGTTTAATCATCAAAACCACAAG
1270410 T
1 T
1270411 AAAGTGTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (25 bp):
TTAGTTTAATCATCAAAACCACAAG
Found at i:1271940 original size:20 final size:20
Alignment explanation
Indices: 1271915--1271975 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
1271905 CTAGACTACC
1271915 AGGAAAAGAATCAAAAGCAA
1 AGGAAAAGAATCAAAAGCAA
*
1271935 AGGAAAAGAATCAAAAGTAA
1 AGGAAAAGAATCAAAAGCAA
*
1271955 AGGAAAAGAATCAAAATCAA
1 AGGAAAAGAATCAAAAGCAA
1271975 A
1 A
1271976 AGCAAAGTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.66, C:0.08, G:0.18, T:0.08
Consensus pattern (20 bp):
AGGAAAAGAATCAAAAGCAA
Found at i:1273552 original size:30 final size:30
Alignment explanation
Indices: 1273480--1273588 Score: 121
Period size: 30 Copynumber: 3.7 Consensus size: 30
1273470 AAAAAAAGTA
* * **
1273480 AAGGACCAAAATAGGATTAACAAAAAC-TT
1 AAGGACTAAAATAGCAAAAACAAAAACTTT
* *
1273509 GAGGACCAAAATAGCAAAAACAAAAACTTT
1 AAGGACTAAAATAGCAAAAACAAAAACTTT
* * *
1273539 AAGGATTAAAATAGCAAAAACTAAAACTTA
1 AAGGACTAAAATAGCAAAAACAAAAACTTT
*
1273569 AAGGACTAAAATAGTAAAAA
1 AAGGACTAAAATAGCAAAAA
1273589 TAGAAACCTA
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
29 23 0.34
30 45 0.66
ACGTcount: A:0.59, C:0.12, G:0.13, T:0.17
Consensus pattern (30 bp):
AAGGACTAAAATAGCAAAAACAAAAACTTT
Found at i:1273608 original size:30 final size:30
Alignment explanation
Indices: 1273510--1273615 Score: 99
Period size: 30 Copynumber: 3.6 Consensus size: 30
1273500 CAAAAACTTG
* * * * *
1273510 AGGACCAAAATAGCAAAAACAAAAACTTTA
1 AGGACTAAAATAGTAAAAACTAAAACCTAA
* * *
1273540 AGGATTAAAATAGCAAAAACTAAAACTTAA
1 AGGACTAAAATAGTAAAAACTAAAACCTAA
1273570 AGGACTAAAATAGTAAAAA-TAGAAACCTAA
1 AGGACTAAAATAGTAAAAACTA-AAACCTAA
* *
1273600 GGGGCT-AAATAGTAAA
1 AGGACTAAAATAGTAAA
1273616 TACAGACATT
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
29 12 0.18
30 54 0.82
ACGTcount: A:0.58, C:0.11, G:0.14, T:0.17
Consensus pattern (30 bp):
AGGACTAAAATAGTAAAAACTAAAACCTAA
Found at i:1273636 original size:29 final size:29
Alignment explanation
Indices: 1273566--1273698 Score: 115
Period size: 29 Copynumber: 4.5 Consensus size: 29
1273556 AAACTAAAAC
* *
1273566 TTAAAGGACTAAAATAGTAAAAATAGAAAC
1 TTAAAGGACTAAAATAGTAAAAA-AGACAT
* * * *
1273596 CTAAGGGGCT-AAATAGTAAATACAGACAT
1 TTAAAGGACTAAAATAGTAAA-AAAGACAT
**
1273625 TTAAAGGACTAAAATAACAAAAAAGACAT
1 TTAAAGGACTAAAATAGTAAAAAAGACAT
* * * *
1273654 TTAAAGGACTTATATAGTAAAAATAGAAAC
1 TTAAAGGACTAAAATAGTAAAAA-AGACAT
*
1273684 TTAAGGGACTAAAAT
1 TTAAAGGACTAAAAT
1273699 TGTATTAACA
Statistics
Matches: 79, Mismatches: 21, Indels: 6
0.75 0.20 0.06
Matches are distributed among these distances:
29 47 0.59
30 32 0.41
ACGTcount: A:0.54, C:0.09, G:0.15, T:0.22
Consensus pattern (29 bp):
TTAAAGGACTAAAATAGTAAAAAAGACAT
Found at i:1275209 original size:3 final size:3
Alignment explanation
Indices: 1275201--1275235 Score: 52
Period size: 3 Copynumber: 11.0 Consensus size: 3
1275191 ATATGTAAAT
1275201 TAA TAA TAA TAA TAA TAA TAA TAAA TAAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA T-AA TAA TAA
1275236 GTGTAACACC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 24 0.77
4 7 0.23
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:1276107 original size:23 final size:23
Alignment explanation
Indices: 1276089--1276149 Score: 113
Period size: 23 Copynumber: 2.7 Consensus size: 23
1276079 CTCGTATAAA
1276089 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
1276112 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
1276135 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
1276150 TATAATAATG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:1278415 original size:40 final size:40
Alignment explanation
Indices: 1278329--1278423 Score: 115
Period size: 40 Copynumber: 2.4 Consensus size: 40
1278319 AACACAATTC
*
1278329 CTACGTGATGAGGATGGTTGGTTATCAGGATGACACGACTT
1 CTACGTGATGAGGATGGTTGGTCA-CAGGATGACACGACTT
*
1278370 CTACGTGATGAGGA-GGTCTGGTCA-AGGGATGACACG-GTT
1 CTACGTGATGAGGATGGT-TGGTCACA-GGATGACACGACTT
1278409 CTTACGTGATGAGGA
1 C-TACGTGATGAGGA
1278424 CGGGAGGCAA
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
39 4 0.08
40 26 0.53
41 19 0.39
ACGTcount: A:0.24, C:0.15, G:0.35, T:0.26
Consensus pattern (40 bp):
CTACGTGATGAGGATGGTTGGTCACAGGATGACACGACTT
Found at i:1278536 original size:132 final size:131
Alignment explanation
Indices: 1278090--1278555 Score: 487
Period size: 131 Copynumber: 3.5 Consensus size: 131
1278080 ATGGTCGTCT
* ** * * * *
1278090 AAGGGTGACATAACTCCTACGTGATGAGGATATCTGGTCGGGGGATGAAACTGCTCATACGTGAT
1 AAGGGTGACACAACTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGGTTCTTACGTGAT
* * *
1278155 GAAGA-GTTCTTG-GCCATCTTTAGGGAGGGTGATAACACGGTTCCTACGCGATGAGGATGGTTG
66 GAGGACG--C--GAGCCATCTTTA-GGAGGGTGATAACACAGTTCCTACGTGATGAGGATGGTTG
1278218 GTTATC
126 GTTATC
* * * * *
1278224 TAGGGGTGATACGGA-TACTACGTGATGAGGAGGTCTGGTCGGGGGATGACATGGTT-TCTACGT
1 -AAGGGTGACAC-AACTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGGTTCT-TACGT
* * ** * *
1278287 GATGAGGATGACAAGTTATCTTTA-G-GGATGATAACACAATTCCTACGTGATGAGGATGGTTGG
63 GATGAGGACG-CGAGCCATCTTTAGGAGGGTGATAACACAGTTCCTACGTGATGAGGATGGTTGG
1278350 TTATC
127 TTATC
* * * **
1278355 -AGGATGACACGACTTCTACGTGATGAGGAGGTCTGGTCAAGGGATGACACGGTTCTTACGTGAT
1 AAGGGTGACACAACTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGGTTCTTACGTGAT
* * * * * *
1278419 GAGGACGGGAGGCAACCTTAGGAAGGGTGATAACACAGTTCCTACATGATGAGGACGGTTGGTTA
66 GAGGACGCGAGCCATCTTTAGG-AGGGTGATAACACAGTTCCTACGTGATGAGGATGGTTGGTTA
1278484 TC
130 TC
* *
1278486 AAGGGTGACACAACTCCTACGTGATGAGGAGGTCTGGTTGGGGGATGACACGGTTCCTACGTGAT
1 AAGGGTGACACAACTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGGTTCTTACGTGAT
1278551 GAGGA
66 GAGGA
1278556 TAGCATACCA
Statistics
Matches: 275, Mismatches: 46, Indels: 23
0.80 0.13 0.07
Matches are distributed among these distances:
128 9 0.03
129 59 0.21
130 1 0.00
131 78 0.28
132 63 0.23
134 8 0.03
135 55 0.20
136 2 0.01
ACGTcount: A:0.25, C:0.15, G:0.34, T:0.26
Consensus pattern (131 bp):
AAGGGTGACACAACTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGGTTCTTACGTGAT
GAGGACGCGAGCCATCTTTAGGAGGGTGATAACACAGTTCCTACGTGATGAGGATGGTTGGTTAT
C
Found at i:1278813 original size:63 final size:63
Alignment explanation
Indices: 1278712--1278864 Score: 222
Period size: 63 Copynumber: 2.4 Consensus size: 63
1278702 TGTGTTAAAT
* * *
1278712 TTTGTTTCCAAAGAAACAGACTCAAAGATTTTTCTAAAA-AAACTGTCTTAAGAGAGACAAAAA
1 TTTGTTT-CAAAGAAACAAACTCAAAGATTTTTCTAAAAGAAACTGTCTCAAAAGAGACAAAAA
1278775 TTTGTTTGCAAAGAAACAAACTCAAAGATTTCTT-TAAAAGAAACTGTCTCAAAAGAGACAAAAA
1 TTTGTTT-CAAAGAAACAAACTCAAAGATTT-TTCTAAAAGAAACTGTCTCAAAAGAGACAAAAA
1278839 TTTGTTTCAAGAGAAAC-AACTCAAAG
1 TTTGTTTCAA-AGAAACAAACTCAAAG
1278865 GATACTGATA
Statistics
Matches: 83, Mismatches: 4, Indels: 6
0.89 0.04 0.06
Matches are distributed among these distances:
63 46 0.55
64 37 0.45
ACGTcount: A:0.46, C:0.14, G:0.13, T:0.26
Consensus pattern (63 bp):
TTTGTTTCAAAGAAACAAACTCAAAGATTTTTCTAAAAGAAACTGTCTCAAAAGAGACAAAAA
Found at i:1284227 original size:20 final size:20
Alignment explanation
Indices: 1284202--1284243 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1284192 CATTATTCCC
* *
1284202 TAACCATATACCATAGACAA
1 TAACCATAAACAATAGACAA
1284222 TAACCATAAACAATAGACAA
1 TAACCATAAACAATAGACAA
1284242 TA
1 TA
1284244 GTCCAATGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.21, G:0.05, T:0.19
Consensus pattern (20 bp):
TAACCATAAACAATAGACAA
Found at i:1287717 original size:29 final size:31
Alignment explanation
Indices: 1287659--1287829 Score: 124
Period size: 30 Copynumber: 5.7 Consensus size: 31
1287649 AAAATAATAA
* **
1287659 AAAATTTAAAGGACCAAAATA-AGATTAACAT
1 AAAACTTAAAGGACCAAAATAGA-AAAAACAT
*
1287690 AAAA-TT-GAGGACCAAAATAGAAAAAACA-
1 AAAACTTAAAGGACCAAAATAGAAAAAACAT
* *
1287718 AAAACTTAAAGGACTAAAATAGAAAAAA-TT
1 AAAACTTAAAGGACCAAAATAGAAAAAACAT
* *
1287748 AAAACTTAAAGGACTAAAATAGTAAAAACA-
1 AAAACTTAAAGGACCAAAATAGAAAAAACAT
* ** * *
1287778 AAAAATGT-AAGGGGCTAAATAGAAAATACAT
1 AAAACT-TAAAGGACCAAAATAGAAAAAACAT
* * *
1287809 -ACATTTAAAGGACTAAAATAG
1 AAAACTTAAAGGACCAAAATAG
1287830 TAATAATAGA
Statistics
Matches: 111, Mismatches: 21, Indels: 17
0.74 0.14 0.11
Matches are distributed among these distances:
28 4 0.04
29 20 0.18
30 82 0.74
31 5 0.05
ACGTcount: A:0.60, C:0.09, G:0.13, T:0.19
Consensus pattern (31 bp):
AAAACTTAAAGGACCAAAATAGAAAAAACAT
Found at i:1287737 original size:30 final size:30
Alignment explanation
Indices: 1287697--1287885 Score: 164
Period size: 30 Copynumber: 6.3 Consensus size: 30
1287687 CATAAAATTG
*
1287697 AGGACCAAAATAGAAAAAACAAAAACTTAA
1 AGGACTAAAATAGAAAAAACAAAAACTTAA
**
1287727 AGGACTAAAATAGAAAAAATTAAAACTTAA
1 AGGACTAAAATAGAAAAAACAAAAACTTAA
* *
1287757 AGGACTAAAATAGTAAAAACAAAAAATGTAA
1 AGGACTAAAATAGAAAAAACAAAAACT-TAA
* * * * * *
1287788 GGGGCT-AAATAGAAAATACATACATTTAA
1 AGGACTAAAATAGAAAAAACAAAAACTTAA
* * * *
1287817 AGGACTAAAATAGTAATAATAGAAACTTAA
1 AGGACTAAAATAGAAAAAACAAAAACTTAA
* * * ** *
1287847 GGGACTAAAATGGTATTAACAAAAACTAAA
1 AGGACTAAAATAGAAAAAACAAAAACTTAA
*
1287877 AGGGCTAAA
1 AGGACTAAA
1287886 CATTAATTAC
Statistics
Matches: 126, Mismatches: 31, Indels: 4
0.78 0.19 0.02
Matches are distributed among these distances:
29 7 0.06
30 112 0.89
31 7 0.06
ACGTcount: A:0.58, C:0.09, G:0.14, T:0.19
Consensus pattern (30 bp):
AGGACTAAAATAGAAAAAACAAAAACTTAA
Found at i:1287737 original size:59 final size:60
Alignment explanation
Indices: 1287658--1287781 Score: 146
Period size: 60 Copynumber: 2.1 Consensus size: 60
1287648 CAAAATAATA
* * * *
1287658 AAAAATTTAAAGGACCAAAATAAGATTAACA-TAAAA-TT-GAGGACCAAAATAGAAAAAAC
1 AAAAACTTAAAGGACCAAAAT-AGA-AAAAATTAAAACTTAAAGGACCAAAATAGAAAAAAC
* * *
1287717 AAAAACTTAAAGGACTAAAATAGAAAAAATTAAAACTTAAAGGACTAAAATAGTAAAAAC
1 AAAAACTTAAAGGACCAAAATAGAAAAAATTAAAACTTAAAGGACCAAAATAGAAAAAAC
1287777 AAAAA
1 AAAAA
1287782 ATGTAAGGGG
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
57 3 0.05
58 8 0.15
59 21 0.38
60 23 0.42
ACGTcount: A:0.64, C:0.09, G:0.10, T:0.17
Consensus pattern (60 bp):
AAAAACTTAAAGGACCAAAATAGAAAAAATTAAAACTTAAAGGACCAAAATAGAAAAAAC
Found at i:1287775 original size:60 final size:60
Alignment explanation
Indices: 1287697--1287857 Score: 184
Period size: 60 Copynumber: 2.7 Consensus size: 60
1287687 CATAAAATTG
* * *
1287697 AGGACCAAAATAGAAAAAACAAAAACTTAAAGGACTAAAATAGAAAA-A-ATTAAAACTTAA
1 AGGACTAAAATAGTAAAAACAAAAACTTAAGGGACTAAAATAGAAAATACA-T-AAACTTAA
* * * *
1287757 AGGACTAAAATAGTAAAAACAAAAAATGTAAGGGGCT-AAATAGAAAATACATACATTTAA
1 AGGACTAAAATAGTAAAAACAAAAACT-TAAGGGACTAAAATAGAAAATACATAAACTTAA
* * *
1287817 AGGACTAAAATAGTAATAATAGAAACTTAAGGGACTAAAAT
1 AGGACTAAAATAGTAAAAACAAAAACTTAAGGGACTAAAAT
1287858 GGTATTAACA
Statistics
Matches: 85, Mismatches: 12, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
59 8 0.09
60 67 0.79
61 9 0.11
62 1 0.01
ACGTcount: A:0.59, C:0.09, G:0.14, T:0.19
Consensus pattern (60 bp):
AGGACTAAAATAGTAAAAACAAAAACTTAAGGGACTAAAATAGAAAATACATAAACTTAA
Found at i:1287825 original size:90 final size:90
Alignment explanation
Indices: 1287704--1287871 Score: 230
Period size: 90 Copynumber: 1.9 Consensus size: 90
1287694 TTGAGGACCA
1287704 AAATAGAAAAAACAAAAACTTAAAGGACTAAAATAGAAAAAATTA-AAACTTAAAGGACTAAAAT
1 AAATAGAAAAAACAAAAACTTAAAGGACTAAAATAGAAAAAA-TAGAAACTTAAAGGACTAAAAT
1287768 AGTAAAAACAAAAAATGTAAGGGGCT
65 AGTAAAAACAAAAAATGTAAGGGGCT
* * * * * * * *
1287794 AAATAGAAAATACATACATTTAAAGGACTAAAATAGTAATAATAGAAACTTAAGGGACTAAAATG
1 AAATAGAAAAAACAAAAACTTAAAGGACTAAAATAGAAAAAATAGAAACTTAAAGGACTAAAATA
**
1287859 GTATTAACAAAAA
66 GTAAAAACAAAAA
1287872 CTAAAAGGGC
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
89 2 0.03
90 65 0.97
ACGTcount: A:0.60, C:0.08, G:0.13, T:0.20
Consensus pattern (90 bp):
AAATAGAAAAAACAAAAACTTAAAGGACTAAAATAGAAAAAATAGAAACTTAAAGGACTAAAATA
GTAAAAACAAAAAATGTAAGGGGCT
Found at i:1288193 original size:4 final size:4
Alignment explanation
Indices: 1288184--1288210 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1288174 TGACCTCAGT
1288184 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1288211 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:1288215 original size:2 final size:2
Alignment explanation
Indices: 1288208--1288271 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
1288198 AAATAAATAA
1288208 AT AT AT AT AT AT 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 AT AT AT AT AT AT
1288250 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
1288272 GCTTAAAGGC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1289450 original size:3 final size:3
Alignment explanation
Indices: 1289442--1289472 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
1289432 ATTAATTAAT
1289442 TAA TAA TAA TAA TAA TAA TAAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
1289473 ATATAATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1289478 original size:16 final size:16
Alignment explanation
Indices: 1289442--1289472 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1289432 ATTAATTAAT
1289442 TAAT-AATAATAATAA
1 TAATAAATAATAATAA
1289457 TAATAAATAATAATAA
1 TAATAAATAATAATAA
1289473 ATATAATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
TAATAAATAATAATAA
Found at i:1311871 original size:2 final size:2
Alignment explanation
Indices: 1311864--1311897 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1311854 CTGCCTTCTA
1311864 AT AT 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 AT AT
1311898 TCATTCTTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1312399 original size:50 final size:50
Alignment explanation
Indices: 1312280--1312405 Score: 135
Period size: 50 Copynumber: 2.5 Consensus size: 50
1312270 GTAGCAATAA
* * * *
1312280 AGCGCGCCCTCTGAACCGCGCTATACGCTGATTTGGCACCACGTGGGTAT
1 AGCGCGCCCCCTGAACCACGATATACGCTGATCTGGCACCACGTGGGTAT
* ** * **
1312330 AGCCCGCCCCCTGCCCCACGATATACGGTGATCTGGCGTCACGTGGGTAT
1 AGCGCGCCCCCTGAACCACGATATACGCTGATCTGGCACCACGTGGGTAT
* * *
1312380 AGTGCGCCCCCTGATCCACGTTATAC
1 AGCGCGCCCCCTGAACCACGATATAC
1312406 TTGGGTATCT
Statistics
Matches: 61, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
50 61 1.00
ACGTcount: A:0.17, C:0.35, G:0.26, T:0.21
Consensus pattern (50 bp):
AGCGCGCCCCCTGAACCACGATATACGCTGATCTGGCACCACGTGGGTAT
Found at i:1312887 original size:111 final size:111
Alignment explanation
Indices: 1312693--1313024 Score: 567
Period size: 110 Copynumber: 3.0 Consensus size: 111
1312683 TGGAAATCAT
* ** ** *
1312693 ATATCTCTACACTTTGTTGATACATTAACATTTTAACGATTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
1312758 TATTTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
*
1312804 ATATCTCGACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTATTAA
1 ATATCTCGACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1312869 TAATTAGTTGATTTATTTAATGCATGATTATTAG-TTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
*
1312914 ATATCTCGACACTTTACTAATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
1312979 TAATTAGTTGATTTATTTAATGCATGATTATTAGAGTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
1313025 TTTTTGTAAT
Statistics
Matches: 209, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
110 108 0.52
111 101 0.48
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:1318366 original size:12 final size:12
Alignment explanation
Indices: 1318333--1318369 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1318323 ATTTATAAAA
*
1318333 GAGGAGAGATGC
1 GAGGAGAGATGT
1318345 GA-G-GAGATGT
1 GAGGAGAGATGT
1318355 GAGGAGAGATGT
1 GAGGAGAGATGT
1318367 GAG
1 GAG
1318370 AACCGGAGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
10 8 0.36
11 2 0.09
12 12 0.55
ACGTcount: A:0.32, C:0.03, G:0.51, T:0.14
Consensus pattern (12 bp):
GAGGAGAGATGT
Found at i:1318621 original size:51 final size:50
Alignment explanation
Indices: 1318516--1318639 Score: 153
Period size: 51 Copynumber: 2.5 Consensus size: 50
1318506 CTACGTGGCG
* * *
1318516 TATAGCGCGG-AGCAGGGGGCGCGCTATACCCACGTGTAGCCTAGTCAGCG
1 TATAGCGCGGTA-CAGGGGGCGCGCTATACCCACGTGTAGCCAAATCAGCA
* *
1318566 TATAGCGCGGTACAGGGGGCGTGTTATACTCCACGTGGT-GCCAAATCAGCA
1 TATAGCGCGGTACAGGGGGCGCGCTATAC-CCACGT-GTAGCCAAATCAGCA
*
1318617 TATAGCGCGGTTCAGGGGGCGCG
1 TATAGCGCGGTACAGGGGGCGCG
1318640 ATTTACTGCT
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
50 25 0.39
51 37 0.58
52 2 0.03
ACGTcount: A:0.20, C:0.25, G:0.36, T:0.19
Consensus pattern (50 bp):
TATAGCGCGGTACAGGGGGCGCGCTATACCCACGTGTAGCCAAATCAGCA
Found at i:1319413 original size:37 final size:37
Alignment explanation
Indices: 1319360--1319464 Score: 140
Period size: 37 Copynumber: 2.8 Consensus size: 37
1319350 TCTTTTCGTC
1319360 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAA-TT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATA-AAGTT
* * *
1319397 TTGCTAGGATTCAAACTCCTAAAAATATGATAAAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAGTT
* * *
1319434 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
1319465 CAACAAGCAA
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
36 2 0.03
37 56 0.97
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAGTT
Found at i:1320245 original size:5 final size:6
Alignment explanation
Indices: 1320219--1320257 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
1320209 TATATATTTA
*
1320219 TTTGTT TTTGTT TTTGGTT TTTGTT TTTTTT ATTTGTT T
1 TTTGTT TTTGTT TTT-GTT TTTGTT TTTGTT -TTTGTT T
1320258 ATATTATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 18 0.62
7 11 0.38
ACGTcount: A:0.03, C:0.00, G:0.15, T:0.82
Consensus pattern (6 bp):
TTTGTT
Found at i:1320257 original size:13 final size:13
Alignment explanation
Indices: 1320222--1320246 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1320212 ATATTTATTT
1320222 GTTTTTGTTTTTG
1 GTTTTTGTTTTTG
1320235 GTTTTTGTTTTT
1 GTTTTTGTTTTT
1320247 TTTATTTGTT
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:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (13 bp):
GTTTTTGTTTTTG
Found at i:1320360 original size:4 final size:4
Alignment explanation
Indices: 1320347--1320376 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
1320337 TATATATTAA
1320347 TATT TCATT TATT TATT TATT TATT TATT T
1 TATT T-ATT TATT TATT TATT TATT TATT T
1320377 TTCCTTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:1320394 original size:30 final size:32
Alignment explanation
Indices: 1320358--1320441 Score: 95
Period size: 30 Copynumber: 2.7 Consensus size: 32
1320348 ATTTCATTTA
1320358 TTTATTTATTTATTTATTTTTCCTT-TT-ATT
1 TTTATTTATTTATTTATTTTTCCTTCTTCATT
* * *
1320388 TTTATTTTTTTACTTATTTTT-ATTCTTCATT
1 TTTATTTATTTATTTATTTTTCCTTCTTCATT
*
1320419 TTT-TTTCATTTATTCATTTTTCC
1 TTTATTT-ATTTATTTATTTTTCC
1320442 CTCTAACACA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
29 2 0.05
30 24 0.56
31 17 0.40
ACGTcount: A:0.15, C:0.11, G:0.00, T:0.74
Consensus pattern (32 bp):
TTTATTTATTTATTTATTTTTCCTTCTTCATT
Found at i:1324865 original size:29 final size:28
Alignment explanation
Indices: 1324833--1324897 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 28
1324823 AATCAAGAAC
*
1324833 AAAAAAGAAA-AGAAGCAAAAAAACAAAGA
1 AAAAAAGAAACAAAAG--AAAAAACAAAGA
*
1324862 AAAAAGAGAAACAAAAGAAAAAAGAAAGA
1 AAAAA-AGAAACAAAAGAAAAAACAAAGA
1324891 ACAAAAA
1 A-AAAAA
1324898 TCAAAAAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
29 18 0.58
30 9 0.29
31 4 0.13
ACGTcount: A:0.80, C:0.06, G:0.14, T:0.00
Consensus pattern (28 bp):
AAAAAAGAAACAAAAGAAAAAACAAAGA
Found at i:1324876 original size:25 final size:26
Alignment explanation
Indices: 1324830--1324908 Score: 78
Period size: 25 Copynumber: 3.1 Consensus size: 26
1324820 TCCAATCAAG
*
1324830 AACAAA-AAAGAAAAGAAGCAAAA-A
1 AACAAAGAAAGAAAAGAAACAAAAGA
1324854 AACAAAGAAA-AAAGAGAAACAAAAGA
1 AACAAAGAAAGAAA-AGAAACAAAAGA
1324880 AA-AAAGAAAGAACAA-AAATCAAAAAGA
1 AACAAAGAAAGAA-AAGAAA-C-AAAAGA
1324907 AA
1 AA
1324909 AAGGGACAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 11
0.80 0.02 0.19
Matches are distributed among these distances:
24 9 0.19
25 22 0.47
26 7 0.15
27 9 0.19
ACGTcount: A:0.78, C:0.08, G:0.13, T:0.01
Consensus pattern (26 bp):
AACAAAGAAAGAAAAGAAACAAAAGA
Found at i:1324880 original size:18 final size:18
Alignment explanation
Indices: 1324835--1324910 Score: 73
Period size: 18 Copynumber: 3.9 Consensus size: 18
1324825 TCAAGAACAA
*
1324835 AAAAGAAAAGAAGCAAAAAA
1 AAAAGAAAA-AAG-AAAAAC
*
1324855 ACAAAGAAAAAAGAGAAAC
1 A-AAAGAAAAAAGAAAAAC
1324874 AAAAGAAAAAAGAAAGAAC
1 AAAAGAAAAAAGAAA-AAC
1324893 AAAA-ATCAAAAAGAAAAA
1 AAAAGA--AAAAAGAAAAA
1324911 GGGACAAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
18 14 0.29
19 14 0.29
20 13 0.27
21 8 0.16
ACGTcount: A:0.79, C:0.07, G:0.13, T:0.01
Consensus pattern (18 bp):
AAAAGAAAAAAGAAAAAC
Found at i:1324883 original size:30 final size:31
Alignment explanation
Indices: 1324827--1324897 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
1324817 AGATCCAATC
*
1324827 AAGAACAAAAAAGAAAAGAAGCAAAAAAACA
1 AAGAACAAAAAAGAAAAAAAGCAAAAAAACA
* *
1324858 AAGAA-AAAAGAGAAACAAAAG--AAAAAAGA
1 AAGAACAAAAAAGAAA-AAAAGCAAAAAAACA
1324887 AAGAACAAAAA
1 AAGAACAAAAA
1324898 TCAAAAAGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
29 12 0.35
30 13 0.38
31 9 0.26
ACGTcount: A:0.79, C:0.07, G:0.14, T:0.00
Consensus pattern (31 bp):
AAGAACAAAAAAGAAAAAAAGCAAAAAAACA
Found at i:1324897 original size:20 final size:19
Alignment explanation
Indices: 1324834--1324910 Score: 77
Period size: 20 Copynumber: 3.9 Consensus size: 19
1324824 ATCAAGAACA
1324834 AAAAAGAAAAGAAGCAAAAA-
1 AAAAAGAAAA-AAG-AAAAAC
*
1324854 AACAAAGAAAAAAGAGAAAC
1 AA-AAAGAAAAAAGAAAAAC
1324874 -AAAAGAAAAAAGAAAGAAC
1 AAAAAGAAAAAAGAAA-AAC
**
1324893 AAAAATCAAAAAGAAAAA
1 AAAAAGAAAAAAGAAAAA
1324911 GGGACAAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
18 13 0.27
19 10 0.20
20 18 0.37
21 8 0.16
ACGTcount: A:0.79, C:0.06, G:0.13, T:0.01
Consensus pattern (19 bp):
AAAAAGAAAAAAGAAAAAC
Found at i:1326590 original size:106 final size:106
Alignment explanation
Indices: 1326377--1327539 Score: 1624
Period size: 106 Copynumber: 11.0 Consensus size: 106
1326367 ATATCGTGCC
* * * ** * *
1326377 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACAACTGGTTGTCAA-CAACAATTTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* *
1326441 AATTTCGGAGCCAATTTCAACTTCACAGCGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
1326482 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* * *
1326547 AATTTCATATCCAATTTAAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
1326588 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1326653 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
1326694 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
1326759 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
1326800 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGATCGCTGGTTGTCAACAACCAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* *
1326865 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGAAATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
1326906 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTTAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1326971 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
1327012 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAAAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* *
1327077 AATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
1327118 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* *
1327183 AATTTCAGAGCCAATTTCAACTTCACATCGTAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
1327224 ACTCAAGACAACACAAATTCAACTTCACGACGAAGGGACCGCTGTTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* * *
1327289 AATTTTAGAGCCAATTTCAACTTCTCAGCGAAGGATCTTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * *
1327330 AC-CCAAGACAACACAAGCTCAACTTCACGACGAAGGGGCGGCTGATTGTTAA-CAA-AATTT--
1 ACTCC-AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCC
* * * *
1327390 C-A-TTCAAAGTCAATTTCAACTTCACAACAAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * * * *
1327430 ACTCGAGACAACACAAGTTCATCTTCACAACGAATGGACGGCTAGTTGTCAACAAACAATTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
** * ** *
1327495 GGTTCCAGAGTTAATTTCAACTTCAC-GACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
1327536 ACTC
1 ACTC
1327540 GGAACAATAC
Statistics
Matches: 955, Mismatches: 93, Indels: 19
0.90 0.09 0.02
Matches are distributed among these distances:
100 72 0.08
101 4 0.00
102 6 0.01
104 5 0.01
105 50 0.05
106 818 0.86
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:1328291 original size:37 final size:37
Alignment explanation
Indices: 1328238--1328342 Score: 140
Period size: 37 Copynumber: 2.8 Consensus size: 37
1328228 CCTTTTCGTC
*
1328238 CTACTAGGATTCAAACTCCTAAAAATATGATAGAA-TT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATA-AAGTT
* *
1328275 TTGCTAGGATTCAAACTCCTAAAAATAGGATAAAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAGTT
* * *
1328312 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
1328343 CCACAAGCAC
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
36 2 0.03
37 57 0.97
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAGTT
Found at i:1328858 original size:18 final size:17
Alignment explanation
Indices: 1328837--1328893 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 17
1328827 TATATATACA
*
1328837 TATATTTATTTATTTATT
1 TATATTAATTTA-TTATT
*
1328855 TATATTCATTTGATTATT
1 TATATTAATTT-ATTATT
1328873 T-T-TTAATATTATTATT
1 TATATTAAT-TTATTATT
1328889 TATAT
1 TATAT
1328894 ATATATATAC
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
16 11 0.33
17 4 0.12
18 17 0.52
19 1 0.03
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (17 bp):
TATATTAATTTATTATT
Found at i:1329183 original size:2 final size:2
Alignment explanation
Indices: 1329176--1329201 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1329166 TATTTTACTC
1329176 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
1329202 TTTAATATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1329252 original size:30 final size:31
Alignment explanation
Indices: 1329218--1329299 Score: 87
Period size: 30 Copynumber: 2.7 Consensus size: 31
1329208 ATTTCATTTA
* * *
1329218 TTTATTTATTTATTTCTTTTTCTTTTTC-TT
1 TTTATTTATTTATTTATTTTTATTCTTCATT
* *
1329248 TTTATTTTTTTACTTATTTTTATTCTTCATT
1 TTTATTTATTTATTTATTTTTATTCTTCATT
*
1329279 TTT-TTTCATTTATTCATTTTT
1 TTTATTT-ATTTATTTATTTTT
1329300 TTCCTCTAAC
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
30 26 0.62
31 16 0.38
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (31 bp):
TTTATTTATTTATTTATTTTTATTCTTCATT
Found at i:1329264 original size:12 final size:11
Alignment explanation
Indices: 1329234--1329283 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 11
1329224 TATTTATTTC
1329234 TTTTTCTT-TT
1 TTTTTCTTATT
*
1329244 TCTTT-TTATT
1 TTTTTCTTATT
1329254 TTTTTACTTATT
1 TTTTT-CTTATT
1329266 TTTATTCTTCATT
1 TTT-TTCTT-ATT
1329279 TTTTT
1 TTTTT
1329284 TCATTTATTC
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
9 2 0.06
10 10 0.30
12 13 0.39
13 8 0.24
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTTCTTATT
Found at i:1329284 original size:34 final size:34
Alignment explanation
Indices: 1329214--1329292 Score: 90
Period size: 34 Copynumber: 2.3 Consensus size: 34
1329204 TAATATTTCA
* *
1329214 TTTATTTATTTATTTATTTCTTTTTCTTTTTCTT
1 TTTATTTATTTACTTATTTCTTATTCTTTTTCTT
*
1329248 TTTATTTTTTTACTTATTT-TTATTCTTCATTT-TT
1 TTTATTTATTTACTTATTTCTTATTCTT--TTTCTT
1329282 TTTCATTTATT
1 TTT-ATTTATT
1329293 CATTTTTTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
33 7 0.18
34 22 0.58
35 9 0.24
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (34 bp):
TTTATTTATTTACTTATTTCTTATTCTTTTTCTT
Found at i:1332742 original size:16 final size:16
Alignment explanation
Indices: 1332695--1332744 Score: 64
Period size: 16 Copynumber: 3.0 Consensus size: 16
1332685 TATTTTTTTT
1332695 CAAAAACAAAACAAAAAA
1 CAAAAA-AAAAC-AAAAA
**
1332713 CAAAAAAAGGCAAAAA
1 CAAAAAAAAACAAAAA
1332729 CAAAAAAAAACAAAAA
1 CAAAAAAAAACAAAAA
1332745 AAAGTCAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 19 0.68
17 3 0.11
18 6 0.21
ACGTcount: A:0.82, C:0.14, G:0.04, T:0.00
Consensus pattern (16 bp):
CAAAAAAAAACAAAAA
Found at i:1332748 original size:27 final size:28
Alignment explanation
Indices: 1332695--1332746 Score: 90
Period size: 26 Copynumber: 1.9 Consensus size: 28
1332685 TATTTTTTTT
1332695 CAAAAACAAAACAAAAAACAAAAAAAGG
1 CAAAAACAAAACAAAAAACAAAAAAAGG
1332723 CAAAAAC-AAA-AAAAAACAAAAAAA
1 CAAAAACAAAACAAAAAACAAAAAAA
1332747 AGTCAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 14 0.58
27 3 0.12
28 7 0.29
ACGTcount: A:0.83, C:0.13, G:0.04, T:0.00
Consensus pattern (28 bp):
CAAAAACAAAACAAAAAACAAAAAAAGG
Found at i:1332753 original size:27 final size:28
Alignment explanation
Indices: 1332694--1332754 Score: 90
Period size: 27 Copynumber: 2.2 Consensus size: 28
1332684 CTATTTTTTT
1332694 TCAAAAACAAAACAAAAAACAAAAAAAG
1 TCAAAAACAAAACAAAAAACAAAAAAAG
*
1332722 GCAAAAAC-AAA-AAAAAACAAAAAAAAG
1 TCAAAAACAAAACAAAAAAC-AAAAAAAG
1332749 TCAAAA
1 TCAAAA
1332755 TTTTAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
26 7 0.23
27 16 0.53
28 7 0.23
ACGTcount: A:0.79, C:0.13, G:0.05, T:0.03
Consensus pattern (28 bp):
TCAAAAACAAAACAAAAAACAAAAAAAG
Found at i:1332754 original size:11 final size:10
Alignment explanation
Indices: 1332695--1332747 Score: 54
Period size: 10 Copynumber: 4.9 Consensus size: 10
1332685 TATTTTTTTT
1332695 CAAAAACAAAA
1 CAAAAA-AAAA
1332706 CAAAAAACAAA
1 CAAAAAA-AAA
1332717 -AAAAGGCAAAAA
1 CAAAA---AAAAA
1332729 CAAAAAAAAA
1 CAAAAAAAAA
1332739 CAAAAAAAA
1 CAAAAAAAA
1332748 GTCAAAATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
10 19 0.51
11 9 0.24
12 3 0.08
13 6 0.16
ACGTcount: A:0.83, C:0.13, G:0.04, T:0.00
Consensus pattern (10 bp):
CAAAAAAAAA
Found at i:1337862 original size:32 final size:32
Alignment explanation
Indices: 1337818--1337894 Score: 109
Period size: 32 Copynumber: 2.4 Consensus size: 32
1337808 ATCTAATTTG
* * *
1337818 ACCCGAATCGAAAACAATCTAAACCAAAATTA
1 ACCCGAATCGAAAACAATCCAAACAAAAAATA
* *
1337850 ACCCGAACCGAAAGCAATCCAAACAAAAAATA
1 ACCCGAATCGAAAACAATCCAAACAAAAAATA
1337882 ACCCGAATCGAAA
1 ACCCGAATCGAAA
1337895 TTGAATTTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.53, C:0.27, G:0.09, T:0.10
Consensus pattern (32 bp):
ACCCGAATCGAAAACAATCCAAACAAAAAATA
Found at i:1340544 original size:13 final size:13
Alignment explanation
Indices: 1340514--1340552 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
1340504 CCGTGTTTGT
* *
1340514 AATAATAATATTT
1 AATAATAATAATA
*
1340527 TATAATAATAATA
1 AATAATAATAATA
1340540 AATAATAATAATA
1 AATAATAATAATA
1340553 TAACAATGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AATAATAATAATA
Found at i:1340547 original size:16 final size:16
Alignment explanation
Indices: 1340513--1340552 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
1340503 TCCGTGTTTG
** *
1340513 TAATAATAATATTTTA
1 TAATAATAATAAATAA
1340529 TAATAATAATAAATAA
1 TAATAATAATAAATAA
1340545 TAATAATA
1 TAATAATA
1340553 TAACAATGGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TAATAATAATAAATAA
Found at i:1340759 original size:32 final size:31
Alignment explanation
Indices: 1340722--1340855 Score: 90
Period size: 32 Copynumber: 4.2 Consensus size: 31
1340712 TGACCCAAAT
*
1340722 CGAAAATCAATCGATCCGATATTGACCCGATC
1 CGAAAATCAA-CGATCCGATATTGACCCGACC
* * *
1340754 TGAAAATCAACTGATTCGATATTGATCCGACC
1 CGAAAATCAAC-GATCCGATATTGACCCGACC
* * ** **
1340786 CAAAAATCAACCAATCC-ATATTGATTCGAAT
1 CGAAAATCAA-CGATCCGATATTGACCCGACC
* ** * *
1340817 CGAAAAACAAACGATTGGATAGTCACCCGACC
1 CGAAAATC-AACGATCCGATATTGACCCGACC
1340849 CGAAAAT
1 CGAAAAT
1340856 TGATCCAACC
Statistics
Matches: 75, Mismatches: 23, Indels: 8
0.71 0.22 0.08
Matches are distributed among these distances:
31 21 0.28
32 53 0.71
33 1 0.01
ACGTcount: A:0.40, C:0.25, G:0.14, T:0.22
Consensus pattern (31 bp):
CGAAAATCAACGATCCGATATTGACCCGACC
Found at i:1341205 original size:20 final size:20
Alignment explanation
Indices: 1341180--1341218 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1341170 TTTTAAAATC
1341180 CGAAATTTTTATATTAATTT
1 CGAAATTTTTATATTAATTT
1341200 CGAAATTTTTATATTAATT
1 CGAAATTTTTATATTAATT
1341219 GTTTATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (20 bp):
CGAAATTTTTATATTAATTT
Found at i:1342141 original size:19 final size:18
Alignment explanation
Indices: 1342103--1342157 Score: 67
Period size: 18 Copynumber: 3.0 Consensus size: 18
1342093 ATCTTTCAAA
1342103 TTATTTTTAAGATATTTT
1 TTATTTTTAAGATATTTT
1342121 TTATTTTTAA-ATATGTATT
1 TTATTTTTAAGATAT-T-TT
* *
1342140 TTATCTTTACGATATTTT
1 TTATTTTTAAGATATTTT
1342158 AATACAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
17 4 0.12
18 13 0.41
19 11 0.34
20 4 0.12
ACGTcount: A:0.27, C:0.04, G:0.05, T:0.64
Consensus pattern (18 bp):
TTATTTTTAAGATATTTT
Found at i:1346674 original size:15 final size:15
Alignment explanation
Indices: 1346643--1346676 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1346633 TATGGAAGAT
*
1346643 GAAAGGAAATGATAA
1 GAAAGGAAATGACAA
*
1346658 GAAAGGAAATGGCAA
1 GAAAGGAAATGACAA
1346673 GAAA
1 GAAA
1346677 TGATAACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.59, C:0.03, G:0.29, T:0.09
Consensus pattern (15 bp):
GAAAGGAAATGACAA
Found at i:1346864 original size:14 final size:14
Alignment explanation
Indices: 1346833--1346872 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
1346823 ATGGGTTTGA
*
1346833 ATGGTGATGG-AGG
1 ATGGTGATGGAAAG
1346846 ATGGTGATGGAAAG
1 ATGGTGATGGAAAG
1346860 ATGGTGATGGAAA
1 ATGGTGATGGAAA
1346873 TAGTATCTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.33, C:0.00, G:0.45, T:0.23
Consensus pattern (14 bp):
ATGGTGATGGAAAG
Done.