Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008610.1 Hibiscus syriacus cultivar Beakdansim tig00111566_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: 2108335
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 11
Found at i:1074029 original size:105 final size:105
Alignment explanation
Indices: 1073847--1074669 Score: 1282
Period size: 105 Copynumber: 7.9 Consensus size: 105
1073837 GAGAATAGAT
*
1073847 TTCAACTTCACGACGAAGGGACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTC
1 TTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTC
* *
1073912 AACTTTACAATGAAGGATATTGGACTTCAGACAACGCAAG
66 AACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAG
1073952 TTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTC
1 TTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTC
* *
1074017 AACTTCACAATGAAGGATATTAGACTTCAGACAACGCAAG
66 AACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAG
* *
1074057 TTGAACTTCACGACGAAGGGACCGTTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTC
1 TTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTC
*
1074122 AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
66 AACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAG
1074162 TTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTC
1 TTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTC
1074227 AACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAG
66 AACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAG
* * * *
1074267 GTCAACTTCACGACGAAGGGACCGCTGCTTGTCAATAACAACTTCCCAATCTCAGAGCCAATTTC
1 TTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTC
* *
1074332 AACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAG
66 AACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAG
* * * *
1074372 TTCAACTTCGCGACGAAGGGACCGCTGCTTGTTAACAACAACTTCCCAATCTCAGAGCCAATTTC
1 TTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTC
1074437 AACTTCACAACGAAGGATATTGGAC-TCTAGACAACGCAAG
66 AACTTCACAACGAAGGATATTGGACTTC-AGACAACGCAAG
**
1074477 TTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGATTCAATTTC
1 TTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTC
* *
1074537 AACTTCATAACGAAGGATATTGGAC-TCGAGACAACACAAG
66 AACTTCACAACGAAGGATATTGGACTTC-AGACAACGCAAG
* * * * * ** *
1074577 TTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAGAGCCAATTT
* *
1074642 CAACTTCACGACGGAGGATATTGGACTT
65 CAACTTCACAACGAAGGATATTGGACTT
1074670 GGAACAATGC
Statistics
Matches: 667, Mismatches: 43, Indels: 14
0.92 0.06 0.02
Matches are distributed among these distances:
100 82 0.12
101 3 0.00
102 3 0.00
103 4 0.01
104 4 0.01
105 536 0.80
106 34 0.05
107 1 0.00
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (105 bp):
TTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTC
AACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAG
Found at i:1075260 original size:34 final size:37
Alignment explanation
Indices: 1075216--1075317 Score: 167
Period size: 34 Copynumber: 2.8 Consensus size: 37
1075206 TTTCGTCCTA
1075216 CTAGGATTCAAACTCCTAAAAATAGGATAGA-A-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
1075251 -TAGGATTCAAACTCCTAAAAATAGGATA-ACATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
1075286 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
1075318 GTTCTACTAA
Statistics
Matches: 62, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
33 1 0.02
34 29 0.47
35 3 0.05
37 28 0.45
38 1 0.02
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (37 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
Found at i:1075301 original size:37 final size:35
Alignment explanation
Indices: 1075216--1075351 Score: 168
Period size: 37 Copynumber: 3.8 Consensus size: 35
1075206 TTTCGTCCTA
1075216 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1075251 -TAGGATTCAAACTCCTAAAAATAGGATA-ACATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGA-A-TTT
*
1075286 GCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTCT
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGAATT-T
* * * *
1075323 ACTAAGATTTAAATTCCTAAAGATAGGAT
1 -CTAGGATTCAAACTCCTAAAAATAGGAT
1075352 CCACAAGCAC
Statistics
Matches: 89, Mismatches: 6, Indels: 10
0.85 0.06 0.10
Matches are distributed among these distances:
33 1 0.01
34 29 0.33
35 3 0.03
36 2 0.02
37 53 0.60
38 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.29
Consensus pattern (35 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:1075747 original size:18 final size:17
Alignment explanation
Indices: 1075708--1075750 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
1075698 ATTATATGGA
1075708 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
1075724 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
1075742 TATTATTAT
1 TATTATTAT
1075751 GTATATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:1075782 original size:57 final size:55
Alignment explanation
Indices: 1075720--1075828 Score: 125
Period size: 57 Copynumber: 1.9 Consensus size: 55
1075710 TTTTATTCAT
*
1075720 TTATTTTTA-TTATTCATGTTA-T-TATTATTATGTATATATATATATATATATATTAAA
1 TTATTTTCATTTATT-ATGTTACTATATT-TTAT-TAT-TAT-TATATATATATATTAAA
* *
1075777 TTATTTTCATTTATTTTTTTACTATATTTTATTATTATTATATATATATATT
1 TTATTTTCATTTATTATGTTACTATATTTTATTATTATTATATATATATATT
1075829 TCTTTAATAT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
55 14 0.30
56 3 0.07
57 15 0.33
58 10 0.22
59 4 0.09
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (55 bp):
TTATTTTCATTTATTATGTTACTATATTTTATTATTATTATATATATATATTAAA
Found at i:1077809 original size:15 final size:15
Alignment explanation
Indices: 1077791--1077840 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
1077781 TAGCCCCTAG
1077791 TATTTTAATAATTCA
1 TATTTTAATAATTCA
* ** *
1077806 TATTTTAGT--CCCG
1 TATTTTAATAATTCA
1077819 TATTTTAATAATTCA
1 TATTTTAATAATTCA
1077834 TATTTTA
1 TATTTTA
1077841 GTCCCGAATT
Statistics
Matches: 25, Mismatches: 8, Indels: 4
0.68 0.22 0.11
Matches are distributed among these distances:
13 9 0.36
15 16 0.64
ACGTcount: A:0.32, C:0.10, G:0.04, T:0.54
Consensus pattern (15 bp):
TATTTTAATAATTCA
Found at i:1077822 original size:28 final size:28
Alignment explanation
Indices: 1077790--1077855 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 28
1077780 TTAGCCCCTA
1077790 GTATTTTAATAATTCATATTTTAGTCCC
1 GTATTTTAATAATTCATATTTTAGTCCC
1077818 GTATTTTAATAATTCATATTTTAGTCCC
1 GTATTTTAATAATTCATATTTTAGTCCC
* *
1077846 GAATTATAAT
1 GTATTTTAAT
1077856 TTAGGTTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.48
Consensus pattern (28 bp):
GTATTTTAATAATTCATATTTTAGTCCC
Found at i:1079607 original size:2 final size:2
Alignment explanation
Indices: 1079600--1079678 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
1079590 ATTATAACAA
1079600 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
1079642 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1079679 GTTTAGAGTT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1080099 original size:38 final size:38
Alignment explanation
Indices: 1080052--1080136 Score: 89
Period size: 38 Copynumber: 2.2 Consensus size: 38
1080042 CTTCTAAACG
* * *
1080052 AGTTTATAAAGAAGCTTATTCATGAACATAAATGAATA
1 AGTTGATAAAGAAGCTTATTCATGAACATAAACGAACA
*** * * *
1080090 AGTTGATAAATTGGTTTATTTATGAACATAAACGAACG
1 AGTTGATAAAGAAGCTTATTCATGAACATAAACGAACA
1080128 AGTTGATAA
1 AGTTGATAA
1080137 GTGAATTTGT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.44, C:0.07, G:0.16, T:0.33
Consensus pattern (38 bp):
AGTTGATAAAGAAGCTTATTCATGAACATAAACGAACA
Found at i:1081998 original size:64 final size:65
Alignment explanation
Indices: 1081852--1082007 Score: 201
Period size: 65 Copynumber: 2.4 Consensus size: 65
1081842 TACACTAAGG
* * * *
1081852 GTGCATCGATTCATAAAATACATTTGATATTTTAAATAAGCCTGGAGTGCATCGATACATGGTCT
1 GTGCATCGATGCATAAAATGCATTCGATATTTTAAAAAAGCCTGGAGTGCATCGATACATGGTCT
* * *
1081917 TTGCATCGATGCATAAAATGCATTCGAT-TTTTCAATAAAATCCT-GAGTGCATCGATGCATGG-
1 GTGCATCGATGCATAAAATGCATTCGATATTTT-AA-AAAAGCCTGGAGTGCATCGATACATGGT
1081979 CT
64 CT
*
1081981 GTGCATCGGTGCATAAAATGCATTCGA
1 GTGCATCGATGCATAAAATGCATTCGA
1082008 AATGGGGTGT
Statistics
Matches: 80, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
64 31 0.39
65 43 0.54
66 6 0.08
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCGATATTTTAAAAAAGCCTGGAGTGCATCGATACATGGTCT
Found at i:1083003 original size:27 final size:27
Alignment explanation
Indices: 1082973--1083027 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
1082963 AGCCGGTGCC
* *
1082973 GGTGGAGGTGGAGCACGAGAAGATCTA
1 GGTGGAGGAGGAGCACGAGAAGAACTA
* * *
1083000 GGTGTAGGAGGAGCTCGTGAAGAACTA
1 GGTGGAGGAGGAGCACGAGAAGAACTA
1083027 G
1 G
1083028 CGCCCGTTGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.29, C:0.11, G:0.44, T:0.16
Consensus pattern (27 bp):
GGTGGAGGAGGAGCACGAGAAGAACTA
Found at i:1084586 original size:23 final size:23
Alignment explanation
Indices: 1084555--1084637 Score: 64
Period size: 23 Copynumber: 3.7 Consensus size: 23
1084545 ATGCACTGCT
*
1084555 GAGTCCATCGATGCACATTCAAG
1 GAGTGCATCGATGCACATTCAAG
* ** *
1084578 GAGTGCATCGGTGCAC-TTTTAT
1 GAGTGCATCGATGCACATTCAAG
* *
1084600 G-GTGTATCGATGCATATTCAAAG
1 GAGTGCATCGATGCACATTC-AAG
*
1084623 GA-TACATCGATGCAC
1 GAGTGCATCGATGCAC
1084638 TGGCGAGTGT
Statistics
Matches: 43, Mismatches: 14, Indels: 6
0.68 0.22 0.10
Matches are distributed among these distances:
21 11 0.26
22 6 0.14
23 26 0.60
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (23 bp):
GAGTGCATCGATGCACATTCAAG
Found at i:1090975 original size:20 final size:21
Alignment explanation
Indices: 1090950--1090988 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
1090940 TTGTATTATG
1090950 ATTTATTGAGA-AGAAAAACA
1 ATTTATTGAGAGAGAAAAACA
1090970 ATTTATTGAGAGAGAAAAA
1 ATTTATTGAGAGAGAAAAA
1090989 TATGTTTGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.54, C:0.03, G:0.18, T:0.26
Consensus pattern (21 bp):
ATTTATTGAGAGAGAAAAACA
Found at i:1093440 original size:30 final size:30
Alignment explanation
Indices: 1093406--1093465 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
1093396 CCCGAAGGAC
*
1093406 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGACCCTCGGTAA
1093436 CTATCCAGAGGTCATAAAGACCCTCGGTAA
1 CTATCCAGAGGTCATAAAGACCCTCGGTAA
1093466 ACTGTCCATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGACCCTCGGTAA
Found at i:1095735 original size:2 final size:2
Alignment explanation
Indices: 1095728--1095767 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1095718 TAAACTGATC
1095728 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
1095768 TCCCCAAACT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1100498 original size:27 final size:26
Alignment explanation
Indices: 1100425--1100499 Score: 62
Period size: 27 Copynumber: 2.8 Consensus size: 26
1100415 TCTTGACATG
* *
1100425 TAAATGATGTGAACATTAATAAATTT
1 TAAATGATATGAATATTAATAAATTT
* * * **
1100451 CAAATGATAT-CATCATGAATACTTTTT
1 TAAATGATATGAAT-ATTAATA-AATTT
1100478 TAAATGATATGAATATTAATAA
1 TAAATGATATGAATATTAATAA
1100500 GTACAATAAT
Statistics
Matches: 35, Mismatches: 11, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
25 1 0.03
26 14 0.40
27 18 0.51
28 2 0.06
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (26 bp):
TAAATGATATGAATATTAATAAATTT
Found at i:1112691 original size:21 final size:20
Alignment explanation
Indices: 1112645--1112691 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
1112635 TAGGGGTGAG
*
1112645 TATCGATACTCAGAGGTCAG
1 TATCGATACTCAGAGGTCAA
1112665 TATCGATACTCA-AGGGATCAA
1 TATCGATACTCAGA-GG-TCAA
1112686 TATCGA
1 TATCGA
1112692 AACCAACGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 14 0.58
21 9 0.38
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (20 bp):
TATCGATACTCAGAGGTCAA
Found at i:1112725 original size:14 final size:14
Alignment explanation
Indices: 1112706--1112737 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
1112696 AACGAATTAA
1112706 TTAAGGGGTTATAC
1 TTAAGGGGTTATAC
1112720 TTAAGGGGTTATAC
1 TTAAGGGGTTATAC
1112734 TTAA
1 TTAA
1112738 TATCAGAACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.38
Consensus pattern (14 bp):
TTAAGGGGTTATAC
Found at i:1120458 original size:19 final size:20
Alignment explanation
Indices: 1120435--1120498 Score: 76
Period size: 22 Copynumber: 3.1 Consensus size: 20
1120425 AATGGTATTG
1120435 ATACCATAGTA-GGGTATCA
1 ATACCATAGTAGGGGTATCA
* *
1120454 TTACCATAGTATGGTAGTATCA
1 ATACCATAGTA-GG-GGTATCA
*
1120476 ATACCATGGTAGGGGTATCA
1 ATACCATAGTAGGGGTATCA
1120496 ATA
1 ATA
1120499 TTGAGGAGCC
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
19 10 0.27
20 9 0.24
21 3 0.08
22 15 0.41
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (20 bp):
ATACCATAGTAGGGGTATCA
Found at i:1120911 original size:55 final size:55
Alignment explanation
Indices: 1120839--1121387 Score: 882
Period size: 55 Copynumber: 10.0 Consensus size: 55
1120829 AGTGTGCCAA
* * *
1120839 AAACCTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGACACTATATGTGC
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
1120894 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
*
1120949 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCTTATGGGCACTATATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* * *
1121004 AAACTTAAGAAATTCATACTACGAGGATGAATTTTCGTATGGGCACTATATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* * *
1121059 AAACTTAAGAAATTCATACTACGAGGATGAATTTTCGTATGGGCACTATATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
*
1121114 AAACTTAAGAAATTCATACTAAGTAGATGAATTTCCGTATGGGCACTATATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* *
1121169 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGTATGAGCACTATATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* * * *
1121224 AAACTTAAGAAATTTATATTAAGTGGATGAATTTCTGTATGGGTACTATATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* * *
1121279 AAACTTAAGAAATTCATACTAAGTGGACGAATTTCCGTATTGGCACTTTATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* * **
1121334 AAACTTCAGAAATTCATACTAAGTGGACGAATTTATGTATGGGCACTATATGTG
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTG
1121388 CAAAACTAGA
Statistics
Matches: 463, Mismatches: 31, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 463 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (55 bp):
AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
Found at i:1123837 original size:20 final size:20
Alignment explanation
Indices: 1123812--1123856 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
1123802 AGACAAGAAT
1123812 CTTAGGACTAATTAGTGACA
1 CTTAGGACTAATTAGTGACA
1123832 CTTAGGACTAATTAGTGACA
1 CTTAGGACTAATTAGTGACA
1123852 CTTAG
1 CTTAG
1123857 TTCTAGTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (20 bp):
CTTAGGACTAATTAGTGACA
Found at i:1126666 original size:15 final size:15
Alignment explanation
Indices: 1126553--1126676 Score: 55
Period size: 15 Copynumber: 8.1 Consensus size: 15
1126543 TTATTATAAA
1126553 TTATATATAAATATAT
1 TTATATAT-AATATAT
1126569 TATATGCATATTAATATTAT
1 T-TAT--ATA-TAATA-TAT
1126589 TTATA-ATAATATA-
1 TTATATATAATATAT
* *
1126602 GTATA-ATCATACTAT
1 TTATATATAATA-TAT
* *
1126617 TTATTCTATAGAAATA-
1 TTA-TATATA-ATATAT
*
1126633 TTATATAT-AT-TAG
1 TTATATATAATATAT
*
1126646 TAATATATAATATAT
1 TTATATATAATATAT
1126661 TTATATTATAA-ATAT
1 TTATA-TATAATATAT
1126676 T
1 T
1126677 ATTTTAATTT
Statistics
Matches: 83, Mismatches: 11, Indels: 29
0.67 0.09 0.24
Matches are distributed among these distances:
12 2 0.02
13 17 0.20
14 6 0.07
15 22 0.27
16 11 0.13
17 8 0.10
18 2 0.02
19 10 0.12
20 5 0.06
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (15 bp):
TTATATATAATATAT
Found at i:1126670 original size:18 final size:19
Alignment explanation
Indices: 1126630--1126680 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
1126620 TTCTATAGAA
*
1126630 ATATTATATATATTAGTAAT
1 ATATAATATAT-TTAGTAAT
*
1126650 ATATAATATATTTA-TATT
1 ATATAATATATTTAGTAAT
1126668 ATA-AATATTATTT
1 ATATAATA-TATTT
1126681 TAATTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 4 0.14
18 11 0.39
19 3 0.11
20 10 0.36
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
ATATAATATATTTAGTAAT
Found at i:1129904 original size:15 final size:16
Alignment explanation
Indices: 1129884--1129924 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
1129874 TTTGTTTGGC
1129884 TTTTGGTTTTGATT-T
1 TTTTGGTTTTGATTGT
* *
1129899 TTTTGG-CTTGGTTGT
1 TTTTGGTTTTGATTGT
1129914 TTTTGGTTTTG
1 TTTTGGTTTTG
1129925 GCCAAATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
14 5 0.24
15 13 0.62
16 3 0.14
ACGTcount: A:0.02, C:0.02, G:0.27, T:0.68
Consensus pattern (16 bp):
TTTTGGTTTTGATTGT
Found at i:1130473 original size:3 final size:3
Alignment explanation
Indices: 1130465--1130527 Score: 69
Period size: 3 Copynumber: 20.7 Consensus size: 3
1130455 ATTAATGATA
1130465 AAT AAT AAT AAT AAT AAT AAT AAT -AT ATAT ATAT ATAT ATAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT A-AT A-AT A-AT AAT AAT
1130513 AAT -AT AAT -AT AAT AA
1 AAT AAT AAT AAT AAT AA
1130528 CTATATATAA
Statistics
Matches: 56, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
2 6 0.11
3 35 0.62
4 15 0.27
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:1130593 original size:72 final size:70
Alignment explanation
Indices: 1130477--1130650 Score: 127
Period size: 62 Copynumber: 2.7 Consensus size: 70
1130467 TAATAATAAT
1130477 AATAATAATAATATATATATA-TATATATATAATA-ATA-ATATA-AT-ATAATAACTAT-ATAT
1 AATAATAA-AATATATATATACTATATATATAATATATATATATATATAATAATAA-TATAATAT
1130536 AATA-TA
64 AATACTA
* ** * *
1130542 TAT-ATATGA-CTATATATA-TA-ATA-CT-ATATATATATATA-AT-AT-A-AATATAATATAA
1 AATAATAAAATATATATATACTATATATATAATATATATATATATATAATAATAATATAATATAA
1130597 TACTA
66 TACTA
* *
1130602 AATAATAAAATATATATATACTATATA-CT-ATATATAT-TCTATATAATAA
1 AATAATAAAATATATATATACTATATATATAATATATATATATATATAATAA
1130651 AAACAAAAAG
Statistics
Matches: 88, Mismatches: 10, Indels: 21
0.74 0.08 0.18
Matches are distributed among these distances:
58 3 0.03
59 13 0.15
60 9 0.10
61 16 0.18
62 18 0.20
63 6 0.07
64 18 0.20
65 4 0.05
66 1 0.01
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.41
Consensus pattern (70 bp):
AATAATAAAATATATATATACTATATATATAATATATATATATATATAATAATAATATAATATAA
TACTA
Found at i:1130646 original size:2 final size:2
Alignment explanation
Indices: 1130487--1130638 Score: 123
Period size: 2 Copynumber: 79.0 Consensus size: 2
1130477 AATAATAATA
1130487 AT AT AT AT AT AT AT AT AT AT A- AT A- AT A- AT AT A- AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1130524 AT A- ACT AT AT AT A- AT AT AT AT AT AT GACT AT AT AT AT A- AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT -A-T AT AT AT AT AT AT
* *
1130564 ACT AT AT AT AT AT AT A- AT AT AA AT AT A- AT AT A- AT ACT AA AT
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
*
1130605 A- AT A- AA AT AT AT AT AT ACT AT AT ACT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT
1130639 TCTATATAAT
Statistics
Matches: 125, Mismatches: 5, Indels: 40
0.74 0.03 0.24
Matches are distributed among these distances:
1 13 0.10
2 100 0.80
3 11 0.09
4 1 0.01
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (2 bp):
AT
Found at i:1149095 original size:24 final size:24
Alignment explanation
Indices: 1149063--1149122 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
1149053 ACAAAGGCAT
*
1149063 GTGCGTTTGCAGCAGACAAAACTA
1 GTGCTTTTGCAGCAGACAAAACTA
* *
1149087 GTGCTTTTGCAACAGATAAAACTA
1 GTGCTTTTGCAGCAGACAAAACTA
1149111 GTGCTTTTGCAG
1 GTGCTTTTGCAG
1149123 TAGATGAAGC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.28
Consensus pattern (24 bp):
GTGCTTTTGCAGCAGACAAAACTA
Found at i:1151687 original size:6 final size:6
Alignment explanation
Indices: 1151668--1151712 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
1151658 AGTTAGTAAG
* * *
1151668 ATAAAA ATCAAAA ATCAAA ATAATA ATGAAA ATAAAA ATAAAA AT
1 ATAAAA AT-AAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA AT
1151713 TCCTACCCAC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
6 26 0.81
7 6 0.19
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.20
Consensus pattern (6 bp):
ATAAAA
Found at i:1152667 original size:19 final size:18
Alignment explanation
Indices: 1152626--1152661 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1152616 TTAATTACGA
1152626 AAATTAAAAAGTTAAATT
1 AAATTAAAAAGTTAAATT
* *
1152644 AAATTTAAAAGTTTAATT
1 AAATTAAAAAGTTAAATT
1152662 CGAATTACTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.39
Consensus pattern (18 bp):
AAATTAAAAAGTTAAATT
Found at i:1155347 original size:54 final size:53
Alignment explanation
Indices: 1155261--1155435 Score: 208
Period size: 54 Copynumber: 3.2 Consensus size: 53
1155251 GGCACTAAAA
** * *
1155261 GTGCAACCCACAAAATTCATAATTAGTCTATGAAAGACTGTATCGGCATTAAGT
1 GTGCAACCCACGGAATTCATAATAAGTTTATGAAAGACTGTATC-GCATTAAGT
* * * * *
1155315 GTGCAACCCATGTAATTCATAATAAGTTTATGAACGACTGTATAAGCACTAAGT
1 GTGCAACCCACGGAATTCATAATAAGTTTATGAAAGACTGTAT-CGCATTAAGT
**
1155369 GTGCAACCCACGGAATTCATAATAAGTTTATGAATA-ACCATATTCGCATTAAGT
1 GTGCAACCCACGGAATTCATAATAAGTTTATGAA-AGACTGTA-TCGCATTAAGT
1155423 GTGCAACCCACGG
1 GTGCAACCCACGG
1155436 GTTGGCTTTG
Statistics
Matches: 103, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
54 102 0.99
55 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.27
Consensus pattern (53 bp):
GTGCAACCCACGGAATTCATAATAAGTTTATGAAAGACTGTATCGCATTAAGT
Found at i:1156799 original size:54 final size:54
Alignment explanation
Indices: 1156721--1156895 Score: 217
Period size: 54 Copynumber: 3.2 Consensus size: 54
1156711 GGCACTAAAA
** * * *
1156721 GTGCAACCCACAAAATTCGTAATAAGTCTATGAAAGACTGTATCGGCATTAAGT
1 GTGCAACCCACGGAATTCATAATAAGTTTATGAAAGACTGTATCAGCATTAAGT
* * * * *
1156775 GTGCAACCCATGTAATTCATAATAAGTTTATGAACGACTGTATAAGCACTAAGT
1 GTGCAACCCACGGAATTCATAATAAGTTTATGAAAGACTGTATCAGCATTAAGT
** *
1156829 GTGCAACCCACGGAATTCATAATAAGTTTATGAATA-ACCATATCCGCATTAAGT
1 GTGCAACCCACGGAATTCATAATAAGTTTATGAA-AGACTGTATCAGCATTAAGT
1156883 GTGCAACCCACGG
1 GTGCAACCCACGG
1156896 GTTGGCTTTG
Statistics
Matches: 103, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
54 103 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (54 bp):
GTGCAACCCACGGAATTCATAATAAGTTTATGAAAGACTGTATCAGCATTAAGT
Found at i:1158258 original size:54 final size:53
Alignment explanation
Indices: 1158180--1158354 Score: 244
Period size: 54 Copynumber: 3.2 Consensus size: 53
1158170 GGCACTAAAA
* *
1158180 GTGCAACCCACGAAATTCATAATAAGTCTATGAAAGACTGTATCGGCATTAAGT
1 GTGCAACCCACGGAATTCATAATAAGTTTATGAAAGACTGTATC-GCATTAAGT
* * * *
1158234 GTGCAACCCATGGAATTCATAATAAGTTTATGAACGACTGTATAAGCACTAAGT
1 GTGCAACCCACGGAATTCATAATAAGTTTATGAAAGACTGTAT-CGCATTAAGT
*
1158288 GTGCAACCCACGGAATTCATAATAAGTTTATGAATA-ACCGTATTCGCATTAAGT
1 GTGCAACCCACGGAATTCATAATAAGTTTATGAA-AGACTGTA-TCGCATTAAGT
1158342 GTGCAACCCACGG
1 GTGCAACCCACGG
1158355 GTTGGATTTG
Statistics
Matches: 107, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
54 106 0.99
55 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.26
Consensus pattern (53 bp):
GTGCAACCCACGGAATTCATAATAAGTTTATGAAAGACTGTATCGCATTAAGT
Found at i:1159707 original size:54 final size:54
Alignment explanation
Indices: 1159624--1159934 Score: 374
Period size: 54 Copynumber: 5.7 Consensus size: 54
1159614 TTTACGTATA
* *
1159624 GGCACTAAGTGTGCAACCCACAAAATTCATAATAAGTTTATGAACGGCCATATC
1 GGCACTAAGTGTGCAACCCACATAATTCATAATAAGTTTATGAACGACCATATC
* * * *
1159678 AGCACTAAGTGTGCAACCAACATAATTCATAATAAGTTTATGAACGATCATATA
1 GGCACTAAGTGTGCAACCCACATAATTCATAATAAGTTTATGAACGACCATATC
* * *** * * *
1159732 AGCACTAAGTGTACAACCCATGGAATTTATAATAAGTTTATAAACGACCGTATC
1 GGCACTAAGTGTGCAACCCACATAATTCATAATAAGTTTATGAACGACCATATC
* * ** * *
1159786 GGCATTAAATGTGCAACCCACGGAATTCAAAATAAGTTTATGAACGACCGTATC
1 GGCACTAAGTGTGCAACCCACATAATTCATAATAAGTTTATGAACGACCATATC
*
1159840 GGCACTAAGTGTGCAACCCACAAAATTCATAATAAGTTTATGAACGA-CAGTATC
1 GGCACTAAGTGTGCAACCCACATAATTCATAATAAGTTTATGAACGACCA-TATC
* *
1159894 GGCACCAAGTGTGCAACCCATGA-AATTCATAATAAGGTTTA
1 GGCACTAAGTGTGCAACCCA-CATAATTCATAATAA-GTTTA
1159935 CAAATGATCG
Statistics
Matches: 222, Mismatches: 32, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
53 1 0.00
54 215 0.97
55 6 0.03
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (54 bp):
GGCACTAAGTGTGCAACCCACATAATTCATAATAAGTTTATGAACGACCATATC
Found at i:1159814 original size:108 final size:108
Alignment explanation
Indices: 1159620--1159934 Score: 416
Period size: 108 Copynumber: 2.9 Consensus size: 108
1159610 CATTTTTACG
* * *
1159620 TATAGGCACTAAGTGTGCAACCCACAAAATTCATAATAAGTTTATGAACGGCCATATCAGCACTA
1 TATAGGCACTAAGTGTGCAACCCACAAAATTCATAATAAGTTTATGAACGACCGTATCGGCACTA
* *
1159685 AGTGTGCAACCAAC-ATAATTCATAATAAGTTTATGAACGATCA
66 AGTGTGCAACCCACGA-AATTCATAATAAGTTTATGAACGACCA
* * *** * * *
1159728 TATAAGCACTAAGTGTACAACCCATGGAATTTATAATAAGTTTATAAACGACCGTATCGGCATTA
1 TATAGGCACTAAGTGTGCAACCCACAAAATTCATAATAAGTTTATGAACGACCGTATCGGCACTA
* * * *
1159793 AATGTGCAACCCACGGAATTCAAAATAAGTTTATGAACGACCG
66 AGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCA
* * *
1159836 TATCGGCACTAAGTGTGCAACCCACAAAATTCATAATAAGTTTATGAACGACAGTATCGGCACCA
1 TATAGGCACTAAGTGTGCAACCCACAAAATTCATAATAAGTTTATGAACGACCGTATCGGCACTA
*
1159901 AGTGTGCAACCCATGAAATTCATAATAAGGTTTA
66 AGTGTGCAACCCACGAAATTCATAATAA-GTTTA
1159935 CAAATGATCG
Statistics
Matches: 173, Mismatches: 32, Indels: 3
0.83 0.15 0.01
Matches are distributed among these distances:
108 168 0.97
109 5 0.03
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.26
Consensus pattern (108 bp):
TATAGGCACTAAGTGTGCAACCCACAAAATTCATAATAAGTTTATGAACGACCGTATCGGCACTA
AGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCA
Found at i:1159913 original size:162 final size:163
Alignment explanation
Indices: 1159618--1159955 Score: 464
Period size: 162 Copynumber: 2.1 Consensus size: 163
1159608 TGCATTTTTA
* * * *
1159618 CGTATAGGCACTAAGTGTGCAACCCACAAAATTCATAATAAGTTTATGAACGGCCATATCAGCAC
1 CGTATCGGCACTAAATGTGCAACCCACAAAATTCAAAATAAGTTTATGAACGACCATATCAGCAC
* *
1159683 TAAGTGTGCAACCAACATAATTCATAATAAGTTTATGAACGATCATATAAGCACTAAGTGTACAA
66 TAAGTGTGCAACCAACAAAATTCATAATAAGTTTATGAACGATCATATAAGCACCAAGTGTACAA
* * *
1159748 CCCATGGAATTTATAATAA-GTTTATAAACGAC
131 CCCATGAAATTCATAATAAGGTTTACAAACGAC
* ** * *
1159780 CGTATCGGCATTAAATGTGCAACCCACGGAATTCAAAATAAGTTTATGAACGACCGTATCGGCAC
1 CGTATCGGCACTAAATGTGCAACCCACAAAATTCAAAATAAGTTTATGAACGACCATATCAGCAC
* ** *
1159845 TAAGTGTGCAACCCACAAAATTCATAATAAGTTTATGAACGA-CAGTATCGGCACCAAGTGTGCA
66 TAAGTGTGCAACCAACAAAATTCATAATAAGTTTATGAACGATCA-TATAAGCACCAAGTGTACA
* *
1159909 ACCCATGAAATTCATAATAAGGTTTACAAATGAT
130 ACCCATGAAATTCATAATAAGGTTTACAAACGAC
*
1159943 CGTTTCGGCACTA
1 CGTATCGGCACTA
1159956 CGTGTGCACC
Statistics
Matches: 152, Mismatches: 22, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
161 2 0.01
162 129 0.85
163 21 0.14
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.26
Consensus pattern (163 bp):
CGTATCGGCACTAAATGTGCAACCCACAAAATTCAAAATAAGTTTATGAACGACCATATCAGCAC
TAAGTGTGCAACCAACAAAATTCATAATAAGTTTATGAACGATCATATAAGCACCAAGTGTACAA
CCCATGAAATTCATAATAAGGTTTACAAACGAC
Found at i:1167130 original size:74 final size:73
Alignment explanation
Indices: 1167006--1167194 Score: 256
Period size: 74 Copynumber: 2.5 Consensus size: 73
1166996 GACCGTTAAA
*
1167006 TGAC-TAGGGGTATCGGTACCTCTA-GGGGGTATCGGTACCCATTAGGCATTCTGTTATTCTCGG
1 TGACATAGGGGTATCGGTACC-CTATAGGGGTATCGGTACCCATTAGGCATTCTGTTATTCTCGG
1167069 AGCCAAAAT
65 AGCCAAAAT
* * * * *
1167078 TGGCATAGGGGTATCGGTACCCTGTCAGGGGTATCGATACCCATTTGGCATTCTGTTTTTCTCGG
1 TGACATAGGGGTATCGGTACCCTAT-AGGGGTATCGGTACCCATTAGGCATTCTGTTATTCTCGG
*
1167143 AGCCAACAT
65 AGCCAAAAT
1167152 TGACATAGGGGTATCGGTACACCCTATGAGGGGTATCGGTACC
1 TGACATAGGGGTATCGGT--ACCCTAT-AGGGGTATCGGTACC
1167195 TCCTTATTTA
Statistics
Matches: 101, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
72 5 0.05
73 16 0.16
74 60 0.59
76 20 0.20
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.29
Consensus pattern (73 bp):
TGACATAGGGGTATCGGTACCCTATAGGGGTATCGGTACCCATTAGGCATTCTGTTATTCTCGGA
GCCAAAAT
Found at i:1169296 original size:13 final size:13
Alignment explanation
Indices: 1169273--1169318 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
1169263 ATCCTAATGG
1169273 ACAAT-TTTGAAA
1 ACAATATTTGAAA
*
1169285 ACTATATTTGAAA
1 ACAATATTTGAAA
*
1169298 ACAATGTTTGAAA
1 ACAATATTTGAAA
1169311 ATCAATAT
1 A-CAATAT
1169319 GTAGTTTTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 4 0.14
13 19 0.68
14 5 0.18
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.35
Consensus pattern (13 bp):
ACAATATTTGAAA
Found at i:1169849 original size:21 final size:22
Alignment explanation
Indices: 1169775--1169896 Score: 87
Period size: 21 Copynumber: 5.7 Consensus size: 22
1169765 TAAACCCGAC
* *
1169775 AGGGGTATCGATACCCA-TC-G
1 AGGGGTATCGATACACATTCAA
1169795 AGGGGTATCGATACACATTCAA
1 AGGGGTATCGATACACATTCAA
* *
1169817 AGAGGGTATCGATACACGTT-GA
1 AG-GGGTATCGATACACATTCAA
* *
1169839 AGGGATATCGATAC-C-TAGCAA
1 AGGGGTATCGATACACAT-TCAA
* **
1169860 GGGGGTATCGATAC-CAGTT-TT
1 AGGGGTATCGATACACA-TTCAA
1169881 AGGGGTATCGATACAC
1 AGGGGTATCGATACAC
1169897 TATGCACAAA
Statistics
Matches: 81, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
19 1 0.01
20 17 0.21
21 40 0.49
22 6 0.07
23 17 0.21
ACGTcount: A:0.30, C:0.18, G:0.29, T:0.23
Consensus pattern (22 bp):
AGGGGTATCGATACACATTCAA
Found at i:1174994 original size:18 final size:19
Alignment explanation
Indices: 1174971--1175007 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1174961 CCGTTAAATG
1174971 TCTA-GGGATATCGGTACC
1 TCTAGGGGATATCGGTACC
*
1174989 TCTAGGGGGTATCGGTACC
1 TCTAGGGGATATCGGTACC
1175008 CATTAGGCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.19, C:0.22, G:0.32, T:0.27
Consensus pattern (19 bp):
TCTAGGGGATATCGGTACC
Found at i:1175093 original size:74 final size:74
Alignment explanation
Indices: 1174973--1175157 Score: 248
Period size: 74 Copynumber: 2.5 Consensus size: 74
1174963 GTTAAATGTC
* *
1174973 TAGGGATATCGGTACCTCTA-G-GGGGTATCGGTACCCATTAGGCATTCTATTTTTCTCGGAGCC
1 TAGGGGTATCGGTACC-CTATGAGGGGTATCGGTACCCATTAGGCATTCTATTTTTCTCAGAGCC
*
1175036 AAAATTGGCA
65 AAAATTAGCA
* * * * *
1175046 TAGGGGTATCGGTACCCTATGAGGGGTATCAGTACCCATTTGGCATTCTGTTTTTCTCATAGTCA
1 TAGGGGTATCGGTACCCTATGAGGGGTATCGGTACCCATTAGGCATTCTATTTTTCTCAGAGCCA
1175111 AAATTAGCA
66 AAATTAGCA
*
1175120 TAGGGGTGTCGGTACACCCTATGAGGGGTATCGGTACC
1 TAGGGGTATCGGT--ACCCTATGAGGGGTATCGGTACC
1175158 TCCTTATTTA
Statistics
Matches: 98, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
72 3 0.03
73 16 0.16
74 57 0.58
76 22 0.22
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (74 bp):
TAGGGGTATCGGTACCCTATGAGGGGTATCGGTACCCATTAGGCATTCTATTTTTCTCAGAGCCA
AAATTAGCA
Found at i:1175490 original size:54 final size:54
Alignment explanation
Indices: 1175431--1175703 Score: 336
Period size: 54 Copynumber: 5.1 Consensus size: 54
1175421 GTACCAAATA
*
1175431 TGCAACCCACGAAATTAATAATAAGTTTATGAACGACCGTATCGGCACTAAGTG
1 TGCAACCCACGAAATTCATAATAAGTTTATGAACGACCGTATCGGCACTAAGTG
* * *
1175485 TGCAACCTAAGAAATTCATAATAAGTTTATGAACGATCGTATCGGCACTAAGTG
1 TGCAACCCACGAAATTCATAATAAGTTTATGAACGACCGTATCGGCACTAAGTG
* * *
1175539 TGCAACCCACGGAATTTATAATAATTTTATGAACGACCGTATCGGCACTAAGTG
1 TGCAACCCACGAAATTCATAATAAGTTTATGAACGACCGTATCGGCACTAAGTG
* * * * **
1175593 TGCAACTCAC-AGAATTTATAATAATTTTATGAACGACCGAATCGAAACTAAGTG
1 TGCAACCCACGA-AATTCATAATAAGTTTATGAACGACCGTATCGGCACTAAGTG
* * * * * *
1175647 TGCAACCCAGGGAATTCATAATAAGGTTTACGAATGA--TTATCGGCACTACGTG
1 TGCAACCCACGAAATTCATAATAA-GTTTATGAACGACCGTATCGGCACTAAGTG
1175700 TGCA
1 TGCA
1175704 TACCATGAAA
Statistics
Matches: 189, Mismatches: 27, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
53 15 0.08
54 165 0.87
55 9 0.05
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.27
Consensus pattern (54 bp):
TGCAACCCACGAAATTCATAATAAGTTTATGAACGACCGTATCGGCACTAAGTG
Found at i:1176328 original size:2 final size:2
Alignment explanation
Indices: 1176323--1176543 Score: 146
Period size: 2 Copynumber: 118.5 Consensus size: 2
1176313 ATAATAACAC
1176323 AT AT AT -T AT AT A- AT AT AT A- AT AT A- AT AT AT AT ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
* *
1176362 A- AT AT AA AT AT A- AT AT A- AT ACT AA AT A- AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
*
1176400 AT AT AC ACT AT AT AT AT AT -T AT AT A- AT AT AT A- AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1176440 ACT AT AT A- AT AT A- AT AT -T A- AT AT AT AT AT AC ACT AT AT A-
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
* * *
1176479 AT AT A- AT CT AT A- AC AT GT AT AT A- AT AT A- AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1176516 CGT AT AT AT AT AT A- AT AT AT ACT AT AT A
1 -AT AT AT AT AT AT AT AT AT AT A-T AT AT A
1176544 ATAAAAATAA
Statistics
Matches: 174, Mismatches: 15, Indels: 60
0.70 0.06 0.24
Matches are distributed among these distances:
1 23 0.13
2 140 0.80
3 11 0.06
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.43
Consensus pattern (2 bp):
AT
Found at i:1176339 original size:7 final size:7
Alignment explanation
Indices: 1176293--1176546 Score: 152
Period size: 7 Copynumber: 35.6 Consensus size: 7
1176283 ATTAATGATA
1176293 AATA-AT
1 AATATAT
1176299 AATA-AT
1 AATATAT
*
1176305 ACTATAT
1 AATATAT
1176312 AATA-AT
1 AATATAT
*
1176318 AACACATAT
1 -A-ATATAT
*
1176327 ATTATAT
1 AATATAT
1176334 AATATAT
1 AATATAT
1176341 AATATA-
1 AATATAT
1176347 ATATATAT
1 A-ATATAT
*
1176355 ACTATAT
1 AATATAT
*
1176362 AATATAA
1 AATATAT
1176369 ATATAATAT
1 A-AT-ATAT
1176378 AATACTA-
1 AATA-TAT
1176385 AATAATAT
1 AAT-ATAT
1176393 AATATAT
1 AATATAT
*
1176400 ATATACACT
1 A-ATATA-T
1176409 ATATATAT
1 A-ATATAT
*
1176417 ATTATAT
1 AATATAT
1176424 AATATAT
1 AATATAT
1176431 AATATAT
1 AATATAT
1176438 -ATACTAT
1 AATA-TAT
1176445 -ATAATAT
1 AAT-ATAT
1176452 AATAT-T
1 AATATAT
1176458 AATATAT
1 AATATAT
*
1176465 -ATATAC
1 AATATAT
*
1176471 ACTATAT
1 AATATAT
1176478 -A-ATAT
1 AATATAT
*
1176483 AATCTAT
1 AATATAT
* *
1176490 AACATGT
1 AATATAT
1176497 ATATAATAT
1 A-AT-ATAT
1176506 AATATAT
1 AATATAT
* *
1176513 TATCGTAT
1 AAT-ATAT
1176521 ATATATAT
1 A-ATATAT
1176529 AATATAT
1 AATATAT
*
1176536 ACTATAT
1 AATATAT
1176543 AATA
1 AATA
1176547 AAAATAAAAA
Statistics
Matches: 194, Mismatches: 30, Indels: 47
0.72 0.11 0.17
Matches are distributed among these distances:
5 4 0.02
6 27 0.14
7 111 0.57
8 33 0.17
9 19 0.10
ACGTcount: A:0.53, C:0.06, G:0.01, T:0.41
Consensus pattern (7 bp):
AATATAT
Found at i:1183497 original size:20 final size:20
Alignment explanation
Indices: 1183472--1183515 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
1183462 AAGGTCCACT
*
1183472 TTCGCAATGCGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
1183492 TTCGCAACGCGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
1183512 TTCG
1 TTCG
1183516 AGTTACGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.20
Consensus pattern (20 bp):
TTCGCAACGCGAAAGTCAAA
Found at i:1183618 original size:29 final size:29
Alignment explanation
Indices: 1183584--1183639 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
1183574 TTTCGCGTTT
1183584 CGAATTTGACTTTCACAATAATCGCAACG
1 CGAATTTGACTTTCACAATAATCGCAACG
**
1183613 CGAATTTGACTTTTGCAATAATCGCAA
1 CGAATTTGACTTTCACAATAATCGCAA
1183640 TAAAAAATCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.30
Consensus pattern (29 bp):
CGAATTTGACTTTCACAATAATCGCAACG
Found at i:1187202 original size:21 final size:22
Alignment explanation
Indices: 1187177--1187236 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 22
1187167 TTACGAAATT
* *
1187177 AAAATTCGTGTTGTGAATTC-G
1 AAAATTCGAGTTGCGAATTCAG
1187198 AAAA-TCGAGTTGCGAATTCAG
1 AAAATTCGAGTTGCGAATTCAG
*
1187219 AAAA-TCAAGTTGCGAATT
1 AAAATTCGAGTTGCGAATT
1187237 TGAAATTCAG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
20 13 0.37
21 22 0.63
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.30
Consensus pattern (22 bp):
AAAATTCGAGTTGCGAATTCAG
Found at i:1187214 original size:20 final size:20
Alignment explanation
Indices: 1187186--1187241 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 20
1187176 TAAAATTCGT
* *
1187186 GTTGTGAATTCGAAAATCGA
1 GTTGCGAATTCGAAAATCAA
1187206 GTTGCGAATTCAGAAAATCAA
1 GTTGCGAATTC-GAAAATCAA
*
1187227 GTTGCGAATTTGAAA
1 GTTGCGAATTCGAAA
1187242 TTCAGTATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 14 0.44
21 18 0.56
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.29
Consensus pattern (20 bp):
GTTGCGAATTCGAAAATCAA
Found at i:1187291 original size:20 final size:20
Alignment explanation
Indices: 1187252--1187301 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
1187242 TTCAGTATTA
*
1187252 CGAATTTAGAAATTGCGTTG
1 CGAATTTAGAAACTGCGTTG
* *
1187272 CGAATTTGGAAACTGTGTTG
1 CGAATTTAGAAACTGCGTTG
* *
1187292 TGAAATTAGA
1 CGAATTTAGA
1187302 GTTCATTTTG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.32, C:0.08, G:0.26, T:0.34
Consensus pattern (20 bp):
CGAATTTAGAAACTGCGTTG
Found at i:1189895 original size:2 final size:2
Alignment explanation
Indices: 1189888--1189913 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1189878 TGCATCATAC
1189888 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
1189914 GAACTATAAC
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:1191365 original size:18 final size:18
Alignment explanation
Indices: 1191342--1191378 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1191332 AAGGAATAAC
1191342 ATTTTAAAATTAAATTTA
1 ATTTTAAAATTAAATTTA
1191360 ATTTTAAAATTAAATTTA
1 ATTTTAAAATTAAATTTA
1191378 A
1 A
1191379 ATTCATATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTTTAAAATTAAATTTA
Found at i:1192462 original size:4 final size:4
Alignment explanation
Indices: 1192455--1192763 Score: 81
Period size: 4 Copynumber: 74.8 Consensus size: 4
1192445 TATTCTTGTT
* * * * *
1192455 TTTA TTTA -TTA TATA TATA TATA TATA TATTA TTTT TTCTA TTCTA TTCT-
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TT-TA TT-TA TT-TA
* *
1192505 TTT- TTTA TATA TATT- TTTA TTTTC TTTA TCTATA TTGTA TTTA TCTTA
1 TTTA TTTA TTTA T-TTA TTTA -TTTA TTTA T-T-TA TT-TA TTTA T-TTA
* *
1192553 TTTA TCTTTA TTT- TATT- TTTA TTTTT TTTA TTTT TTTAA TTT- TTTA
1 TTTA --TTTA TTTA T-TTA TTTA -TTTA TTTA TTTA TTT-A TTTA TTTA
* * * * *
1192599 TGTTC TTTA TCTTTA TTTTC TTTA TTTT TTTC TTTA TTTT TTTCA -TTA
1 T-TTA TTTA --TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTT-A TTTA
* * * * *
1192647 TTTA TTTTC TTTA TCT- TTTC TTTA TTT- TTTA TTT- TCTT- TATA TTTT
1 TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA
* *
1192693 TTTA TTTC TTTA TTTA -TT- TTTA TTT- TATTA TTGTT TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TT-TA TTTA TTTA TTTA
* *
1192740 TTAA TTATA TATA TTTA TTTA TTT
1 TTTA TT-TA TTTA TTTA TTTA TTT
1192764 TCTTTATTTT
Statistics
Matches: 232, Mismatches: 40, Indels: 66
0.69 0.12 0.20
Matches are distributed among these distances:
3 28 0.12
4 145 0.62
5 48 0.21
6 11 0.05
ACGTcount: A:0.20, C:0.06, G:0.01, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:1192519 original size:17 final size:18
Alignment explanation
Indices: 1192476--1192529 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 18
1192466 TATATATATA
1192476 TATATATATTATTTTTTC
1 TATATATATTATTTTTTC
* *
1192494 TAT-TCTATTCTTTTTT-
1 TATATATATTATTTTTTC
*
1192510 TATATATATTTTTATTTTC
1 TATATATATTATT-TTTTC
1192529 T
1 T
1192530 TTATCTATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
16 3 0.10
17 18 0.62
18 7 0.24
19 1 0.03
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.70
Consensus pattern (18 bp):
TATATATATTATTTTTTC
Found at i:1192540 original size:15 final size:13
Alignment explanation
Indices: 1192520--1192922 Score: 158
Period size: 12 Copynumber: 31.2 Consensus size: 13
1192510 TATATATATT
1192520 TTTATTTTCTTTA
1 TTTATTTTCTTTA
* *
1192533 TCTATATTGTATTTA
1 T-T-TATTTTCTTTA
1192548 TCTTATTTATCTTTA
1 T-TTATTT-TCTTTA
*
1192563 TTT-TATT-TTTA
1 TTTATTTTCTTTA
1192574 --T-TTTT-TTTA
1 TTTATTTTCTTTA
*
1192583 TTT-TTTTAATTT-
1 TTTATTTT-CTTTA
*
1192595 TTTATGTTCTTTA
1 TTTATTTTCTTTA
1192608 TCTTTATTTTCTTTA
1 --TTTATTTTCTTTA
1192623 TTT-TTTTCTTTA
1 TTTATTTTCTTTA
*
1192635 TTT-TTTTCATTA
1 TTTATTTTCTTTA
1192647 TTTATTTTCTTTA
1 TTTATTTTCTTTA
* *
1192660 TCTTTTCTTTATTT-
1 T-TTAT-TTTCTTTA
1192674 TTTATTTTCTTTA
1 TTTATTTTCTTTA
1192687 --TATTTT-TTTA
1 TTTATTTTCTTTA
* *
1192697 TTT-CTTTATTTA
1 TTTATTTTCTTTA
*
1192709 TTT-TTAT-TTTA
1 TTTATTTTCTTTA
1192720 -TTATTGTT-TTTA
1 TTTATT-TTCTTTA
*
1192732 TTTA-TTT-ATTA
1 TTTATTTTCTTTA
* * *
1192743 ATTATATATATTTA
1 TTTAT-TTTCTTTA
1192757 TTTATTTTCTTTA
1 TTTATTTTCTTTA
* *
1192770 TTT-TTATCATTA
1 TTTATTTTCTTTA
1192782 TTT-TTTTCTTTTA
1 TTTATTTTC-TTTA
*
1192795 TTT-TCTGTATC-TTG
1 TTTAT-T-T-TCTTTA
*
1192809 TTTATTTTATTTA
1 TTTATTTTCTTTA
1192822 CTTT-TTTATCTTTA
1 -TTTATTT-TCTTTA
* *
1192836 CATTATCTTTATTTA
1 -TTTAT-TTTCTTTA
* *
1192851 TTTTTCTTTATATTTA
1 --TTTATTT-TCTTTA
1192867 TTTTATTTTCTTTA
1 -TTTATTTTCTTTA
*
1192881 TCTCATTTTCTTTA
1 T-TTATTTTCTTTA
* * *
1192895 TTTAATTTGTTTT
1 TTTATTTTCTTTA
1192908 TTTATTTT-TTTA
1 TTTATTTTCTTTA
1192920 TTT
1 TTT
1192923 TCGTTACTTT
Statistics
Matches: 305, Mismatches: 48, Indels: 75
0.71 0.11 0.18
Matches are distributed among these distances:
9 8 0.03
10 6 0.02
11 32 0.10
12 73 0.24
13 67 0.22
14 53 0.17
15 53 0.17
16 13 0.04
ACGTcount: A:0.17, C:0.07, G:0.01, T:0.74
Consensus pattern (13 bp):
TTTATTTTCTTTA
Found at i:1192556 original size:9 final size:10
Alignment explanation
Indices: 1192520--1192898 Score: 117
Period size: 9 Copynumber: 39.8 Consensus size: 10
1192510 TATATATATT
1192520 TTTATTT-TC
1 TTTATTTATC
* *
1192529 TTTATCTATA
1 TTTATTTATC
1192539 TTGTATTTATC
1 TT-TATTTATC
1192550 -TTATTTATC
1 TTTATTTATC
*
1192559 TTTATTTTATT
1 TTTA-TTTATC
*
1192570 TTTATTT-TT
1 TTTATTTATC
1192579 TTTATTT-T-
1 TTTATTTATC
* *
1192587 TTTAATTTTTTA
1 TTT-A-TTTATC
*
1192599 TGTTCTTTATC
1 T-TTATTTATC
1192610 TTTATTT-TC
1 TTTATTTATC
1192619 TTTATTT-T-
1 TTTATTTATC
*
1192627 TTTCTTTAT-
1 TTTATTTATC
*
1192636 TTT-TTTCATTA
1 TTTATTT-A-TC
1192647 TTTATTT-TC
1 TTTATTTATC
*
1192656 TTTATCTTTTC
1 TTTAT-TTATC
1192667 TTTA-TT-T-
1 TTTATTTATC
1192674 TTTATTT-TC
1 TTTATTTATC
*
1192683 TTTATATT-TT
1 TTTAT-TTATC
1192693 TTTA-TT-TC
1 TTTATTTATC
*
1192701 TTTATTTATT
1 TTTATTTATC
1192711 TTTATTT-T-
1 TTTATTTATC
*
1192719 ATTATTGT-T-
1 TTTATT-TATC
*
1192728 TTTATTTATT
1 TTTATTTATC
* *
1192738 TATTAATTATA
1 T-TTATTTATC
*
1192749 TATATTTA--
1 TTTATTTATC
1192757 TTTATTT-TC
1 TTTATTTATC
1192766 TTTATTTTTATC
1 TTTA--TTTATC
*
1192778 ATTATTT-T-
1 TTTATTTATC
*
1192786 TTTCTTTTAT-
1 TTT-ATTTATC
* *
1192796 TTTCTGTATC
1 TTTATTTATC
*
1192806 -TTGTTTAT-
1 TTTATTTATC
1192814 TTTATTTA-C
1 TTTATTTATC
1192823 TTT-TTTATC
1 TTTATTTATC
*
1192832 TTTACATTATC
1 TTTA-TTTATC
*
1192843 TTTATTTATT
1 TTTATTTATC
* *
1192853 TTTCTTTATA
1 TTTATTTATC
1192863 TTTATTTTAT-
1 TTTA-TTTATC
*
1192873 TTTCTTTATC
1 TTTATTTATC
*
1192883 -TCATTT-TC
1 TTTATTTATC
1192891 TTTATTTA
1 TTTATTTA
1192899 ATTTGTTTTT
Statistics
Matches: 289, Mismatches: 39, Indels: 83
0.70 0.09 0.20
Matches are distributed among these distances:
7 4 0.01
8 43 0.15
9 109 0.38
10 67 0.23
11 55 0.19
12 9 0.03
13 2 0.01
ACGTcount: A:0.18, C:0.07, G:0.01, T:0.74
Consensus pattern (10 bp):
TTTATTTATC
Found at i:1192657 original size:52 final size:52
Alignment explanation
Indices: 1192542--1192798 Score: 210
Period size: 52 Copynumber: 4.9 Consensus size: 52
1192532 ATCTATATTG
* * *
1192542 TATTTATCTTATTTATCTTTATTTTATTT-TTATTTTT-TTTATTTTTTTAAT
1 TATTTATTTTCTTTATCTTTATTTTATTTATT-TTTTTCTTTATTTTTTTCAT
* * *
1192593 TTTTTATGTTCTTTATCTTTATTTTCTTTATTTTTTTCTTTATTTTTTTCAT
1 TATTTATTTTCTTTATCTTTATTTTATTTATTTTTTTCTTTATTTTTTTCAT
*
1192645 TATTTATTTTCTTTATCTTT-TCTTTATTT-TTTATTTTCTTTATATTTTT--T
1 TATTTATTTTCTTTATCTTTAT-TTTATTTATTT-TTTTCTTTATTTTTTTCAT
* * * * *
1192695 TATTT-CTTTATTTATTTTTATTTTA-TTATTGTTTTTATTTATTTATTAATTATAT
1 TATTTATTTTCTTTATCTTTATTTTATTTATT-TTTTTCTTTATTT-TT--TT-CAT
*
1192750 ATATTTA-TTTATTT-TCTTTATTTTTATCATTATTTTTTTCTTTTATTTT
1 -TATTTATTTTCTTTATCTTTA-TTTTAT--TTATTTTTTTC-TTTATTTT
1192799 CTGTATCTTG
Statistics
Matches: 170, Mismatches: 16, Indels: 33
0.78 0.07 0.15
Matches are distributed among these distances:
48 2 0.01
49 27 0.16
50 10 0.06
51 34 0.20
52 56 0.33
55 6 0.04
56 17 0.10
58 6 0.04
59 12 0.07
ACGTcount: A:0.18, C:0.06, G:0.01, T:0.76
Consensus pattern (52 bp):
TATTTATTTTCTTTATCTTTATTTTATTTATTTTTTTCTTTATTTTTTTCAT
Found at i:1192701 original size:34 final size:34
Alignment explanation
Indices: 1192564--1192937 Score: 126
Period size: 34 Copynumber: 10.9 Consensus size: 34
1192554 TTATCTTTAT
1192564 TTTA-TTTTTATTTT-TTT-TATTTTTTTAATTT-
1 TTTATTTTTTATTTTCTTTATATTTTTTT-ATTTC
* *
1192595 TTTATGTTCTTTATCTTTATTT-TCTTTATTTT-TTTC
1 TTTAT-TT-TTTAT-TTTCTTTATATTT-TTTTATTTC
* * *
1192631 TTTATTTTTT-TCATTATTTAT-TTTCTTTATCTTTTC
1 TTTATTTTTTAT-TTTCTTTATATTT-TTT-T-ATTTC
1192667 TTTATTTTTTATTTTCTTTATATTTTTTTATTTC
1 TTTATTTTTTATTTTCTTTATATTTTTTTATTTC
* *
1192701 TTTATTTATTT-TTAT-TTTATTATTGTTTTTATTTA
1 TTTATTT-TTTATTTTCTTTA-TATT-TTTTTATTTC
* *
1192736 TTTATTAATTATATATATTTATTTAT-TTTCTTTATTT-
1 TTTATT--TT-T-TAT-TTTCTTTATATTTTTTTATTTC
* * *
1192773 TTATCATTATTT-TTTTCTTT-TATTTTCTGTATCTTG
1 TT-T-ATTTTTTATTTTCTTTATATTTT-TTTAT-TTC
* * * **
1192809 TTTA--TTTTATTTACTTTTTTATCTTTACATTATC
1 TTTATTTTTTATTTTC-TTTATATTTTTTTATT-TC
*
1192843 TTTA-TTTAT-TTTTCTTTATATTTATTTTATTTTC
1 TTTATTTTTTATTTTCTTTATATTT-TTTTA-TTTC
* * ** * *
1192877 TTTA--TCTCATTTTCTTTAT-TTAATTTGTTTT
1 TTTATTTTTTATTTTCTTTATATTTTTTTATTTC
*
1192908 TTTATTTTTTTATTTTCGTTACT-TTTTTTT
1 TTTA-TTTTTTATTTTCTTTA-TATTTTTTT
1192938 CCTTTTTTCT
Statistics
Matches: 264, Mismatches: 38, Indels: 78
0.69 0.10 0.21
Matches are distributed among these distances:
31 11 0.04
32 7 0.03
33 44 0.17
34 79 0.30
35 47 0.18
36 40 0.15
37 13 0.05
38 10 0.04
39 6 0.02
40 3 0.01
41 4 0.02
ACGTcount: A:0.17, C:0.07, G:0.02, T:0.75
Consensus pattern (34 bp):
TTTATTTTTTATTTTCTTTATATTTTTTTATTTC
Found at i:1192858 original size:25 final size:26
Alignment explanation
Indices: 1192809--1192883 Score: 75
Period size: 25 Copynumber: 2.8 Consensus size: 26
1192799 CTGTATCTTG
1192809 TTTATTTTATTTACTTTTTTATCTTTACA
1 TTTATTTTATTTA---TTTTATCTTTACA
*
1192838 -TTATCTTTATTTATTTT-TCTTTATA
1 TTTAT-TTTATTTATTTTATCTTTACA
1192863 TTTATTTTATTT-TCTTTATCT
1 TTTATTTTATTTAT-TTTATCT
1192884 CATTTTCTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
24 1 0.02
25 17 0.41
26 11 0.27
28 4 0.10
29 8 0.20
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (26 bp):
TTTATTTTATTTATTTTATCTTTACA
Found at i:1192872 original size:152 final size:148
Alignment explanation
Indices: 1192544--1192873 Score: 345
Period size: 147 Copynumber: 2.2 Consensus size: 148
1192534 CTATATTGTA
* * * ** * *
1192544 TTTATCTTATTTATCTTTATTTTA-TTT-TTATTTTTTTTATTTTTTTAATTTTTTATGTTCTTT
1 TTTAT-TTATTTTTCTTTATTTTATTTTATTATTGTTTTTATTTATTTAATTAATTATATTATTT
* * *
1192607 ATCTTTATTTTCTTTATTTTTTTCTTTATTTTTTTCATTATTTATTTTCTTTATCTTTTCTTTAT
65 A-CTTTATTTTCTTTATTTTTATCATTATTTTTTTCA-TATTTATTTTCTGTATCTTTTCTTTAT
* *
1192672 TTTTTATTTTCTTTATATTTT
128 TTTTTATTTTCTTTACATTTC
* *
1192693 TTTA-TT-TCTTTATTTATTTTTATTTTATTATTGTTTTTATTTATTT-ATTAATTATATATATT
1 TTTATTTATTTTTCTTTA-TTTTATTTTATTATTGTTTTTATTTATTTAATTAATTATAT-TATT
*
1192755 TA-TTTATTTTCTTTATTTTTATCATTATTTTTTTC-T-TTTATTTTCTGTATCTTGTTTATTTT
64 TACTTTATTTTCTTTATTTTTATCATTATTTTTTTCATATTTATTTTCTGTATC-T-TTT-CTTT
1192817 ATTTACTTT-TTTATCTTTACATTATC
126 ATTT--TTTATTT-TCTTTACATT-TC
1192843 TTTATTTATTTTTCTTTATATTTATTTTATT
1 TTTATTTATTTTTCTTTAT-TTTATTTTATT
1192874 TTCTTTATCT
Statistics
Matches: 150, Mismatches: 17, Indels: 25
0.78 0.09 0.13
Matches are distributed among these distances:
144 14 0.09
145 2 0.01
146 10 0.07
147 45 0.30
148 14 0.09
149 38 0.25
150 5 0.03
151 3 0.02
152 19 0.13
ACGTcount: A:0.18, C:0.07, G:0.01, T:0.75
Consensus pattern (148 bp):
TTTATTTATTTTTCTTTATTTTATTTTATTATTGTTTTTATTTATTTAATTAATTATATTATTTA
CTTTATTTTCTTTATTTTTATCATTATTTTTTTCATATTTATTTTCTGTATCTTTTCTTTATTTT
TTATTTTCTTTACATTTC
Found at i:1192895 original size:48 final size:47
Alignment explanation
Indices: 1192552--1192924 Score: 145
Period size: 49 Copynumber: 7.9 Consensus size: 47
1192542 TATTTATCTT
* * ** *
1192552 ATTTATCTTTATTTTATTTTTATTT-TTTTTATTTT-TTTAATTT-TTT
1 ATTT-TCTTTA-TTTATTTTTCTTTATATTTATTTTATTTTCTTTATTC
* * *
1192598 ATGTTCTTTATCTTTA-TTTTCTTTATTTTTTTCTTTATTTT-TTTCATT-
1 ATTTTCTTTA--TTTATTTTTCTTTATATTTAT-TTTATTTTCTTT-ATTC
* * * * * *
1192646 ATTTAT-TTTCTTTATCTTTTCTTTATTTTTTATTTTCTTTATATTTTTTT
1 ATTT-TCTTTATTTAT-TTTTCTTTA-TATTTATTTTATTT-TCTTTATTC
* *
1192696 A-TTTCTTTATTTATTTTTATTTTATTATTGT-TTTTATTTATTTATTAATT-
1 ATTTTCTTTATTTATTTTT-CTTTA-TATT-TATTTTATTT-TCT-TT-ATTC
* * * * * *
1192746 ATATATATTTATTTA-TTTTCTTTATTTTTATCATTATTTT-TTTCTTTT
1 AT-TTTCTTTATTTATTTTTCTTTATATTTAT-TTTATTTTCTTT-ATTC
* * * * *
1192794 ATTTTCTGTATCT-TGTTTATTT-TATTTACTTTT-TTATCTTTA--C
1 ATTTTCTTTATTTATTTTTCTTTATATTTA-TTTTATTTTCTTTATTC
*
1192837 ATTATCTTTATTTATTTTTCTTTATATTTATTTTATTTTCTTTATCTC
1 ATTTTCTTTATTTATTTTTCTTTATATTTATTTTATTTTCTTTAT-TC
*
1192885 ATTTTCTTTATTTAATTTGTT-TTTTTATTT-TTTTATTTTC
1 ATTTTCTTTATTT-ATTT-TTCTTTATATTTATTTTATTTTC
1192925 GTTACTTTTT
Statistics
Matches: 251, Mismatches: 42, Indels: 66
0.70 0.12 0.18
Matches are distributed among these distances:
43 10 0.04
44 11 0.04
45 30 0.12
46 27 0.11
47 24 0.10
48 56 0.22
49 57 0.23
50 20 0.08
51 6 0.02
52 10 0.04
ACGTcount: A:0.17, C:0.07, G:0.01, T:0.75
Consensus pattern (47 bp):
ATTTTCTTTATTTATTTTTCTTTATATTTATTTTATTTTCTTTATTC
Found at i:1192916 original size:9 final size:9
Alignment explanation
Indices: 1192504--1192937 Score: 116
Period size: 9 Copynumber: 45.9 Consensus size: 9
1192494 TATTCTATTC
1192504 TTTTTTTATA
1 TTTTTTT-TA
*
1192514 TATATTTTTA
1 T-TTTTTTTA
*
1192524 TTTTCTTTA
1 TTTTTTTTA
* *
1192533 TCTATATTGTA
1 T-T-TTTTTTA
* *
1192544 TTTATCTTA
1 TTTTTTTTA
*
1192553 TTTATCTTTA
1 TTT-TTTTTA
1192563 TTTTATTTTTA
1 -TTT-TTTTTA
1192574 TTTTTTTTA
1 TTTTTTTTA
*
1192583 TTTTTTTAA
1 TTTTTTTTA
1192592 TTTTTTATGT-
1 TTTTTT-T-TA
1192602 TCTTTATCTTTA
1 T-TTT-T-TTTA
*
1192614 TTTTCTTTA
1 TTTTTTTTA
1192623 TTTTTTTCT-
1 TTTTTTT-TA
1192632 TTATTTTTT-
1 TT-TTTTTTA
* *
1192641 TCATTATTTA
1 T-TTTTTTTA
*
1192651 TTTTCTTTA
1 TTTTTTTTA
1192660 TCTTTTCTTTA
1 T-TTTT-TTTA
1192671 --TTTTTTA
1 TTTTTTTTA
*
1192678 TTTTCTTTA
1 TTTTTTTTA
1192687 TATTTTTTTA
1 T-TTTTTTTA
*
1192697 -TTTCTTTA
1 TTTTTTTTA
1192705 TTTATTTTTA
1 TTT-TTTTTA
*
1192715 -TTTTATTA
1 TTTTTTTTA
*
1192723 TTGTTTTTA
1 TTTTTTTTA
1192732 TTTATTTATTA
1 TTT-TTT-TTA
* * *
1192743 -ATTATATA
1 TTTTTTTTA
*
1192751 TATTTATTTA
1 T-TTTTTTTA
*
1192761 TTTTCTTTA
1 TTTTTTTTA
* *
1192770 TTTTTATCA
1 TTTTTTTTA
*
1192779 -TTATTTT-
1 TTTTTTTTA
*
1192786 TTTCTTTTA
1 TTTTTTTTA
* *
1192795 TTTTCTGTA
1 TTTTTTTTA
* *
1192804 TCTTGTTTA
1 TTTTTTTTA
*
1192813 TTTTATTTA
1 TTTTTTTTA
*
1192822 -CTTTTTTA
1 TTTTTTTTA
**
1192830 TCTTTACATTA
1 T-TTT-TTTTA
*
1192841 TCTTTATTTA
1 T-TTTTTTTA
1192851 TTTTTCTTTA
1 TTTTT-TTTA
1192861 TATTTATTTTA
1 T-TTT-TTTTA
*
1192872 TTTTCTTTA
1 TTTTTTTTA
** *
1192881 TCTCATTTTC
1 T-TTTTTTTA
* *
1192891 TTTATTTAA
1 TTTTTTTTA
*
1192900 TTTGTTTTTT
1 TTT-TTTTTA
1192910 TATTTTTTTA
1 T-TTTTTTTA
**
1192920 TTTTCGTTA
1 TTTTTTTTA
1192929 CTTTTTTTT
1 -TTTTTTTT
1192938 CCTTTTTTCT
Statistics
Matches: 311, Mismatches: 74, Indels: 78
0.67 0.16 0.17
Matches are distributed among these distances:
7 4 0.01
8 33 0.11
9 136 0.44
10 82 0.26
11 51 0.16
12 4 0.01
13 1 0.00
ACGTcount: A:0.17, C:0.07, G:0.02, T:0.74
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:1195582 original size:46 final size:45
Alignment explanation
Indices: 1195428--1195591 Score: 199
Period size: 46 Copynumber: 3.6 Consensus size: 45
1195418 ATTTGCATAT
*
1195428 CCAATAT-TTTACCATTTATTAACCATAAGCTCATAAGCTTATTTTA
1 CCAATATACTTACCATTTATT--CCATAAGCTCATAAGCTTATTTTA
* *
1195474 CCAAAAATACTTACCATTTA-TCTCATAAGCTTATAAGCTTATTTTA
1 CC-AATATACTTACCATTTATTC-CATAAGCTCATAAGCTTATTTTA
* *
1195520 CCCATATACTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTA
1 CCAATATACTTACCATTT-ATTCCATAAGCTCATAAGCTTATTTTA
* *
1195566 CCAATACACTTGCCA-TTATTCCATAA
1 CCAATATACTTACCATTTATTCCATAA
1195592 CCATATACCA
Statistics
Matches: 103, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
44 9 0.09
45 17 0.17
46 60 0.58
47 7 0.07
48 10 0.10
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.38
Consensus pattern (45 bp):
CCAATATACTTACCATTTATTCCATAAGCTCATAAGCTTATTTTA
Found at i:1195727 original size:33 final size:33
Alignment explanation
Indices: 1195690--1195753 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
1195680 ACCGTAGTGC
*
1195690 TAATCTGTATGACACATAAGGTCGTGTCCACTA
1 TAATCCGTATGACACATAAGGTCGTGTCCACTA
1195723 TAATCCGTATGACACATAAGGTCGTGTCCAC
1 TAATCCGTATGACACATAAGGTCGTGTCCAC
1195754 CATCTATTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (33 bp):
TAATCCGTATGACACATAAGGTCGTGTCCACTA
Found at i:1204162 original size:50 final size:50
Alignment explanation
Indices: 1204108--1204331 Score: 151
Period size: 50 Copynumber: 4.4 Consensus size: 50
1204098 CTCTGTTTTA
1204108 TTCTTGTTTTTATTTATTTATTATATATATATATTATT-TTTACTATTATT
1 TTCTTGTTTTTATTTATTTATTATATATATATATTATTATTTACT-TTATT
* * * * *
1204158 TTCTTTTTTTTATTATTATGTT-TTCTTTAT-TTTATT-TTATTTTCTTTATCT
1 TTCTTGTTTTTA-T-TTAT-TTATTATATATATATATTATTATTTACTTTAT-T
* * * * * *
1204209 TTATTGTATTTATCTTATTTATCTTTATCT-TAT-TTTTTA-TTATTTTTATT
1 TTCTTGTTTTTAT-TTATTTAT-TATATATATATATTATTATTTA-CTTTATT
*
1204259 TTCTT-TATCTTTATTTATTTATTATATATATATTATTATTATTTTCTTTATT
1 TTCTTGT-T-TTTATTTATTTATTATATATATA-TATTATTATTTACTTTATT
* * *
1204311 TTC-TATCTTTATTTTTTTATT
1 TTCTTGTTTTTATTTATTTATT
1204332 TCTTTTATTT
Statistics
Matches: 134, Mismatches: 24, Indels: 32
0.71 0.13 0.17
Matches are distributed among these distances:
49 8 0.06
50 55 0.41
51 42 0.31
52 25 0.19
53 4 0.03
ACGTcount: A:0.21, C:0.06, G:0.01, T:0.72
Consensus pattern (50 bp):
TTCTTGTTTTTATTTATTTATTATATATATATATTATTATTTACTTTATT
Found at i:1204171 original size:17 final size:17
Alignment explanation
Indices: 1204151--1204192 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1204141 TTATTTTTAC
* *
1204151 TATTATTTTCTTTTTTT
1 TATTATTATCTTTTCTT
*
1204168 TATTATTATGTTTTCTT
1 TATTATTATCTTTTCTT
1204185 TATT-TTAT
1 TATTATTAT
1204193 TTTATTTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76
Consensus pattern (17 bp):
TATTATTATCTTTTCTT
Found at i:1204175 original size:32 final size:32
Alignment explanation
Indices: 1204139--1204200 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
1204129 TATATATATA
*
1204139 TATTAT-TTTTACTATTATTTTCTTTT-TTTTAT
1 TATTATGTTTT-CT-TTATTTTATTTTATTTTAT
1204171 TATTATGTTTTCTTTATTTTATTTTATTTT
1 TATTATGTTTTCTTTATTTTATTTTATTTT
1204201 CTTTATCTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 11 0.41
32 12 0.44
33 4 0.15
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.76
Consensus pattern (32 bp):
TATTATGTTTTCTTTATTTTATTTTATTTTAT
Found at i:1204205 original size:9 final size:9
Alignment explanation
Indices: 1204178--1204462 Score: 109
Period size: 9 Copynumber: 30.6 Consensus size: 9
1204168 TATTATTATG
1204178 TTTTCTTTA
1 TTTTCTTTA
*
1204187 TTTTATTTTA
1 TTTT-CTTTA
1204197 TTTTCTTTA
1 TTTTCTTTA
*
1204206 TCTTTATTGTA
1 T-TTTCTT-TA
1204217 TTTATC-TTA
1 TTT-TCTTTA
1204226 TTTATCTTTA
1 TTT-TCTTTA
*
1204236 TCTTATTTTTTA
1 --TT-TTCTTTA
1204248 TTATT-TTTA
1 TT-TTCTTTA
1204257 TTTTCTTTA
1 TTTTCTTTA
*
1204266 TCTTTATTTA
1 T-TTTCTTTA
1204276 TTTAT-TATATA
1 TTT-TCT-T-TA
*
1204287 TATATTATTATTA
1 T-T-TT-CT-TTA
1204300 TTTTCTTTA
1 TTTTCTTTA
1204309 TTTTC--TA
1 TTTTCTTTA
1204316 ---TCTTTA
1 TTTTCTTTA
1204322 TTTT-TTTA
1 TTTTCTTTA
1204330 -TTTCTTTTA
1 TTTTC-TTTA
1204339 TTTTCTTTA
1 TTTTCTTTA
*
1204348 TCTTTATTTCA
1 T-TTTCTTT-A
*
1204359 TTTACTTT-
1 TTTTCTTTA
*
1204367 TTATCTTTA
1 TTTTCTTTA
1204376 CTTTATCTTTA
1 -TTT-TCTTTA
*
1204387 TTTT-TTTC
1 TTTTCTTTA
1204395 TTTATCTTTA
1 TTT-TCTTTA
1204405 --TT-TTTA
1 TTTTCTTTA
1204411 TTTTCTTTA
1 TTTTCTTTA
*
1204420 TCTCATTTTTTA
1 T-T--TTCTTTA
*
1204432 -TTTCATTTG
1 TTTTC-TTTA
1204441 TTTT-TTTA
1 TTTTCTTTA
1204449 TTTTCTTTA
1 TTTTCTTTA
1204458 TTTTC
1 TTTTC
1204463 ATTAACTTTT
Statistics
Matches: 216, Mismatches: 19, Indels: 82
0.68 0.06 0.26
Matches are distributed among these distances:
4 2 0.01
6 6 0.03
7 6 0.03
8 30 0.14
9 68 0.31
10 63 0.29
11 17 0.08
12 16 0.07
13 5 0.02
14 3 0.01
ACGTcount: A:0.17, C:0.09, G:0.01, T:0.73
Consensus pattern (9 bp):
TTTTCTTTA
Found at i:1204213 original size:15 final size:15
Alignment explanation
Indices: 1204188--1204422 Score: 145
Period size: 15 Copynumber: 15.5 Consensus size: 15
1204178 TTTTCTTTAT
1204188 TTTAT-TTTATTTTC
1 TTTATCTTTATTTTC
* *
1204202 TTTATCTTTATTGTA
1 TTTATCTTTATTTTC
1204217 TTTATC-TTATTTATC
1 TTTATCTTTATTT-TC
*
1204232 TTTATC-TTATTTTT
1 TTTATCTTTATTTTC
*
1204246 TATTATTTTTATTTTC
1 T-TTATCTTTATTTTC
*
1204262 TTTATCTTTATTTATT
1 TTTATCTTTATTT-TC
* *
1204278 TATTATATATATATTATTAT
1 T-TTATCT-T-TATT-TT-C
*
1204298 TATTTTCTTTATTTTC
1 T-TTATCTTTATTTTC
1204314 --TATCTTTATTTT-
1 TTTATCTTTATTTTC
1204326 TTTATTTCTTTTATTTTC
1 TTTA--TC-TTTATTTTC
1204344 TTTATCTTTA-TTTC
1 TTTATCTTTATTTTC
*
1204358 ATTTACTTTTTATCTTTAC
1 -TTTA-TCTTTAT-TTT-C
1204377 TTTATCTTTA-TTT-
1 TTTATCTTTATTTTC
1204390 TTT-TCTTTA---TC
1 TTTATCTTTATTTTC
*
1204401 TTTATTTTTATTTTC
1 TTTATCTTTATTTTC
1204416 TTTATCT
1 TTTATCT
1204423 CATTTTTTAT
Statistics
Matches: 177, Mismatches: 18, Indels: 51
0.72 0.07 0.21
Matches are distributed among these distances:
10 1 0.01
11 3 0.02
12 11 0.06
13 14 0.08
14 18 0.10
15 60 0.34
16 19 0.11
17 20 0.11
18 16 0.09
19 7 0.04
20 8 0.05
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTATCTTTATTTTC
Found at i:1204331 original size:33 final size:32
Alignment explanation
Indices: 1204294--1204408 Score: 96
Period size: 33 Copynumber: 3.6 Consensus size: 32
1204284 ATATATATTA
1204294 TTATTATTTTCTTTATTTTCTATCTTTATTTTT
1 TTATT-TTTTCTTTATTTTCTATCTTTATTTTT
* *
1204327 TTA-TTTCT-TTTATTTTCTTTATCTTTATTTCAT
1 TTATTTTTTCTTTATTTTC--TATCTTTATTT-TT
*
1204360 TTACTTTTTATCTTTA-CTT-TATCTTTATTTTT
1 TTA-TTTTT-TCTTTATTTTCTATCTTTATTTTT
* *
1204392 TT-CTTTATCTTTATTTT
1 TTATTTTTTCTTTATTTT
1204409 TATTTTCTTT
Statistics
Matches: 66, Mismatches: 8, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
29 6 0.09
30 14 0.21
31 3 0.05
32 15 0.23
33 18 0.27
35 3 0.05
36 3 0.05
37 4 0.06
ACGTcount: A:0.15, C:0.11, G:0.00, T:0.74
Consensus pattern (32 bp):
TTATTTTTTCTTTATTTTCTATCTTTATTTTT
Found at i:1204353 original size:6 final size:6
Alignment explanation
Indices: 1204342--1204422 Score: 62
Period size: 6 Copynumber: 13.5 Consensus size: 6
1204332 TCTTTTATTT
* * *
1204342 TCTTTA TCTTTA TTTCATTTA CTTTTTA TCTTTA -CTTTA TCTTTA TTTTTT
1 TCTTTA TCTTTA --TC-TTTA -TCTTTA TCTTTA TCTTTA TCTTTA TCTTTA
*
1204393 TCTTTA TCTTTA T-TTT- TATTT- TCTTTA TCT
1 TCTTTA TCTTTA TCTTTA TCTTTA TCTTTA TCT
1204423 CATTTTTTAT
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
4 1 0.02
5 15 0.25
6 34 0.56
7 4 0.07
8 3 0.05
9 4 0.07
ACGTcount: A:0.15, C:0.14, G:0.00, T:0.72
Consensus pattern (6 bp):
TCTTTA
Found at i:1204432 original size:33 final size:34
Alignment explanation
Indices: 1204334--1204432 Score: 103
Period size: 33 Copynumber: 2.8 Consensus size: 34
1204324 TTTTTATTTC
*
1204334 TTTTATTTTCTTTATCTTTATTTCATTTACTTTTTAT
1 TTTTATTTTCTTTATC-TTATTTC-TTTA-TCTTTAT
* *
1204371 CTTTACTTTATCTTTAT-TTTTTTCTTTATCTTTAT
1 TTTTA-TTT-TCTTTATCTTATTTCTTTATCTTTAT
*
1204406 TTTTATTTTCTTTATCTCATTT-TTTAT
1 TTTTATTTTCTTTATCTTATTTCTTTAT
1204433 TTCATTTGTT
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
33 12 0.23
34 7 0.13
35 10 0.19
36 4 0.08
37 10 0.19
38 3 0.06
39 7 0.13
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (34 bp):
TTTTATTTTCTTTATCTTATTTCTTTATCTTTAT
Found at i:1207936 original size:23 final size:23
Alignment explanation
Indices: 1207908--1207983 Score: 89
Period size: 23 Copynumber: 3.3 Consensus size: 23
1207898 GAGTCGAGGG
1207908 TTCTATGCGGTCATTCGAGACAA
1 TTCTATGCGGTCATTCGAGACAA
* *
1207931 TTCTATGTGGTCATTCGAGACAT
1 TTCTATGCGGTCATTCGAGACAA
* * * *
1207954 TTCTACGCAGTCCTTTGAGACAA
1 TTCTATGCGGTCATTCGAGACAA
*
1207977 TACTATG
1 TTCTATG
1207984 TGATTCTTCG
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (23 bp):
TTCTATGCGGTCATTCGAGACAA
Found at i:1208307 original size:387 final size:387
Alignment explanation
Indices: 1207641--1208416 Score: 1507
Period size: 387 Copynumber: 2.0 Consensus size: 387
1207631 GGTATAATTG
*
1207641 ACCTATGTGATTAAATGAAAAAACGAGATAAGCTAAATAACATTTACCTATGTGATTACATGAGA
1 ACCTATGTGATTAAATGAAAAAACAAGATAAGCTAAATAACATTTACCTATGTGATTACATGAGA
1207706 ATATGATATAAGCTATGTGAGATTGACATAAGTGATTATATGAACATGTGATGTAACCTACGTGA
66 ATATGATATAAGCTATGTGAGATTGACATAAGTGATTATATGAACATGTGATGTAACCTACGTGA
1207771 TAACAACTTATGTGATTATATGTCCATATGATATTGAACTACGTGATTATATGAATATGTGAAAT
131 TAACAACTTATGTGATTATATGTCCATATGATATTGAACTACGTGATTATATGAATATGTGAAAT
*
1207836 GTGTAAATAGTAAAGCCCATAAGTATGTGATATGAGAGCTAAATGTATAATTGACATGCCAAGAG
196 ATGTAAATAGTAAAGCCCATAAGTATGTGATATGAGAGCTAAATGTATAATTGACATGCCAAGAG
*
1207901 TCGAGGGTTCTATGCGGTCATTCGAGACAATTCTATGTGGTCATTCGAGACATTTCTACGCAGTC
261 TCGAGGGTTCTACGCGGTCATTCGAGACAATTCTATGTGGTCATTCGAGACATTTCTACGCAGTC
*
1207966 CTTTGAGACAATACTATGTGATTCTTCGGGATATATCTATGTGGCACTTCAGTGTAATTGAT
326 CTTTGAGACAATACTATGTGATCCTTCGGGATATATCTATGTGGCACTTCAGTGTAATTGAT
1208028 ACCTATGTGATTAAATGAAAAAACAAGATAAGCTAAATAACATTTACCTATGTGATTACATGAGA
1 ACCTATGTGATTAAATGAAAAAACAAGATAAGCTAAATAACATTTACCTATGTGATTACATGAGA
1208093 ATATGATATAAGCTATGTGAGATTGACATAAGTGATTATATGAACATGTGATGTAACCTACGTGA
66 ATATGATATAAGCTATGTGAGATTGACATAAGTGATTATATGAACATGTGATGTAACCTACGTGA
1208158 TAACAACTTATGTGATTATATGTCCATATGATATTGAACTACGTGATTATATGAATATGTGAAAT
131 TAACAACTTATGTGATTATATGTCCATATGATATTGAACTACGTGATTATATGAATATGTGAAAT
1208223 ATGTAAATAGTAAAGCCCATAAGTATGTGATATGAGAGCTAAATGTATAATTGACATGCCAAGAG
196 ATGTAAATAGTAAAGCCCATAAGTATGTGATATGAGAGCTAAATGTATAATTGACATGCCAAGAG
1208288 TCGAGGGTTCTACGCGGTCATTCGAGACAATTCTATGTGGTCATTCGAGACATTTCTACGCAGTC
261 TCGAGGGTTCTACGCGGTCATTCGAGACAATTCTATGTGGTCATTCGAGACATTTCTACGCAGTC
*
1208353 CTTTGAGACAATACTATGTGATCCTTCGGGATATATCTATGTGGCACTTCGGTGTAATTGAT
326 CTTTGAGACAATACTATGTGATCCTTCGGGATATATCTATGTGGCACTTCAGTGTAATTGAT
1208415 AC
1 AC
1208417 GAGTTGTGGT
Statistics
Matches: 384, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
387 384 1.00
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (387 bp):
ACCTATGTGATTAAATGAAAAAACAAGATAAGCTAAATAACATTTACCTATGTGATTACATGAGA
ATATGATATAAGCTATGTGAGATTGACATAAGTGATTATATGAACATGTGATGTAACCTACGTGA
TAACAACTTATGTGATTATATGTCCATATGATATTGAACTACGTGATTATATGAATATGTGAAAT
ATGTAAATAGTAAAGCCCATAAGTATGTGATATGAGAGCTAAATGTATAATTGACATGCCAAGAG
TCGAGGGTTCTACGCGGTCATTCGAGACAATTCTATGTGGTCATTCGAGACATTTCTACGCAGTC
CTTTGAGACAATACTATGTGATCCTTCGGGATATATCTATGTGGCACTTCAGTGTAATTGAT
Found at i:1208322 original size:23 final size:23
Alignment explanation
Indices: 1208295--1208364 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
1208285 GAGTCGAGGG
1208295 TTCTACGCGGTCATTCGAGACAA
1 TTCTACGCGGTCATTCGAGACAA
* * *
1208318 TTCTATGTGGTCATTCGAGACAT
1 TTCTACGCGGTCATTCGAGACAA
* * *
1208341 TTCTACGCAGTCCTTTGAGACAA
1 TTCTACGCGGTCATTCGAGACAA
1208364 T
1 T
1208365 ACTATGTGAT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (23 bp):
TTCTACGCGGTCATTCGAGACAA
Found at i:1208531 original size:6 final size:6
Alignment explanation
Indices: 1208520--1208590 Score: 79
Period size: 6 Copynumber: 11.8 Consensus size: 6
1208510 ATAATGAACT
* * * * *
1208520 ATGATA ATGATA ATGATA GTGACA ATGATA ATGGTG TTGATA ATGATA
1 ATGATA ATGATA ATGATA ATGATA ATGATA ATGATA ATGATA ATGATA
* *
1208568 TTGATA ATGATG ATGATA ATGAT
1 ATGATA ATGATA ATGATA ATGAT
1208591 GCTGATGTTG
Statistics
Matches: 51, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.41, C:0.01, G:0.23, T:0.35
Consensus pattern (6 bp):
ATGATA
Found at i:1210799 original size:16 final size:16
Alignment explanation
Indices: 1210770--1210809 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
1210760 ATTGAGTTTA
*
1210770 AAGGATTCAATATGAC
1 AAGGATTAAATATGAC
*
1210786 AAGTATTAAATATGAC
1 AAGGATTAAATATGAC
1210802 AAGGATTA
1 AAGGATTA
1210810 TTACAAGGTG
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:0.47, C:0.07, G:0.17, T:0.28
Consensus pattern (16 bp):
AAGGATTAAATATGAC
Found at i:1213067 original size:16 final size:17
Alignment explanation
Indices: 1213041--1213099 Score: 63
Period size: 16 Copynumber: 3.6 Consensus size: 17
1213031 TACGTGACAA
1213041 GAACTTATGTGATTATAT
1 GAAC-TATGTGATTATAT
*
1213059 G-TCTATGTGA-TAT-T
1 GAACTATGTGATTATAT
*
1213073 GAACTACGTGATTATAT
1 GAACTATGTGATTATAT
1213090 GAA-TATGTGA
1 GAACTATGTGA
1213100 AATGTGTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
14 2 0.06
15 10 0.29
16 16 0.47
17 5 0.15
18 1 0.03
ACGTcount: A:0.32, C:0.07, G:0.20, T:0.41
Consensus pattern (17 bp):
GAACTATGTGATTATAT
Found at i:1213211 original size:23 final size:23
Alignment explanation
Indices: 1213185--1213276 Score: 105
Period size: 23 Copynumber: 4.0 Consensus size: 23
1213175 TTCTACGCGA
1213185 TCCTTCGGGACAATTCTATGTGG
1 TCCTTCGGGACAATTCTATGTGG
* * * * *
1213208 TCCTTTGAGACATTTCTACGCGG
1 TCCTTCGGGACAATTCTATGTGG
* *
1213231 TTCTTCGGGACAATACTATGTGG
1 TCCTTCGGGACAATTCTATGTGG
1213254 TCCTTCGGGAC-ATATCTATGTGG
1 TCCTTCGGGACAAT-TCTATGTGG
1213277 CACTTCGATG
Statistics
Matches: 54, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
22 2 0.04
23 52 0.96
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.35
Consensus pattern (23 bp):
TCCTTCGGGACAATTCTATGTGG
Found at i:1213266 original size:46 final size:46
Alignment explanation
Indices: 1213175--1213271 Score: 140
Period size: 46 Copynumber: 2.1 Consensus size: 46
1213165 GAGTCGAGGG
* *
1213175 TTCTACGCGATCCTTCGGGACAATTCTATGTGGTCCTTTGAGACAT
1 TTCTACGCGATCCTTCGGGACAATACTATGTGGTCCTTCGAGACAT
* * *
1213221 TTCTACGCGGTTCTTCGGGACAATACTATGTGGTCCTTCGGGACAT
1 TTCTACGCGATCCTTCGGGACAATACTATGTGGTCCTTCGAGACAT
*
1213267 ATCTA
1 TTCTA
1213272 TGTGGCACTT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.34
Consensus pattern (46 bp):
TTCTACGCGATCCTTCGGGACAATACTATGTGGTCCTTCGAGACAT
Found at i:1213283 original size:46 final size:46
Alignment explanation
Indices: 1213187--1213283 Score: 122
Period size: 46 Copynumber: 2.1 Consensus size: 46
1213177 CTACGCGATC
* * * **
1213187 CTTCGGGACAATTCTATGTGGTCCTTTGAGACATTTCTACGCGGTT
1 CTTCGGGACAATACTATGTGGTCCTTCGAGACATATCTACGCGGCA
* * *
1213233 CTTCGGGACAATACTATGTGGTCCTTCGGGACATATCTATGTGGCA
1 CTTCGGGACAATACTATGTGGTCCTTCGAGACATATCTACGCGGCA
1213279 CTTCG
1 CTTCG
1213284 ATGCAATTTA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.19, C:0.23, G:0.25, T:0.34
Consensus pattern (46 bp):
CTTCGGGACAATACTATGTGGTCCTTCGAGACATATCTACGCGGCA
Found at i:1213409 original size:6 final size:6
Alignment explanation
Indices: 1213388--1213462 Score: 69
Period size: 6 Copynumber: 12.3 Consensus size: 6
1213378 AAGAAAAGAT
* * * **
1213388 ATAATG AAATATG ATAATG ATAGTG ACAATG ATAATG ATGTTG ATAATG
1 ATAATG ATA-ATG ATAATG ATAATG ATAATG ATAATG ATAATG ATAATG
* * *
1213437 ATATTG ATGATG ATGATG ATAATG AT
1 ATAATG ATAATG ATAATG ATAATG AT
1213463 GCTGATGCTG
Statistics
Matches: 54, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
6 49 0.91
7 5 0.09
ACGTcount: A:0.43, C:0.01, G:0.21, T:0.35
Consensus pattern (6 bp):
ATAATG
Found at i:1213421 original size:18 final size:18
Alignment explanation
Indices: 1213398--1213468 Score: 81
Period size: 18 Copynumber: 3.9 Consensus size: 18
1213388 ATAATGAAAT
*
1213398 ATGATAATGAT-AGTGACA
1 ATGATAATGATGA-TGATA
*
1213416 ATGATAATGATGTTGATA
1 ATGATAATGATGATGATA
* *
1213434 ATGATATTGATGATGATG
1 ATGATAATGATGATGATA
*
1213452 ATGATAATGATGCTGAT
1 ATGATAATGATGATGAT
1213469 GCTGATGAGG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.35
Consensus pattern (18 bp):
ATGATAATGATGATGATA
Found at i:1213432 original size:12 final size:12
Alignment explanation
Indices: 1213417--1213468 Score: 68
Period size: 12 Copynumber: 4.3 Consensus size: 12
1213407 ATAGTGACAA
1213417 TGATAATGATGT
1 TGATAATGATGT
*
1213429 TGATAATGATAT
1 TGATAATGATGT
* *
1213441 TGATGATGATGA
1 TGATAATGATGT
*
1213453 TGATAATGATGC
1 TGATAATGATGT
1213465 TGAT
1 TGAT
1213469 GCTGATGAGG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.35, C:0.02, G:0.25, T:0.38
Consensus pattern (12 bp):
TGATAATGATGT
Found at i:1215019 original size:20 final size:22
Alignment explanation
Indices: 1214970--1215025 Score: 71
Period size: 20 Copynumber: 2.6 Consensus size: 22
1214960 AATACTCAGA
* *
1214970 AAAGTATCAATACCCTAACATC
1 AAAGTATCGATACTCTAACATC
*
1214992 AGAGTATCGATACTC-AACAT-
1 AAAGTATCGATACTCTAACATC
1215012 AAAGTATCGATACT
1 AAAGTATCGATACT
1215026 ACCTTACCCA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 13 0.43
21 5 0.17
22 12 0.40
ACGTcount: A:0.43, C:0.21, G:0.11, T:0.25
Consensus pattern (22 bp):
AAAGTATCGATACTCTAACATC
Found at i:1216041 original size:36 final size:36
Alignment explanation
Indices: 1215994--1216072 Score: 158
Period size: 36 Copynumber: 2.2 Consensus size: 36
1215984 TATGGGTTAC
1215994 TATTCGGTAGTCCCGTGTGACATTGTAATCCATGGA
1 TATTCGGTAGTCCCGTGTGACATTGTAATCCATGGA
1216030 TATTCGGTAGTCCCGTGTGACATTGTAATCCATGGA
1 TATTCGGTAGTCCCGTGTGACATTGTAATCCATGGA
1216066 TATTCGG
1 TATTCGG
1216073 ATTGGACTGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (36 bp):
TATTCGGTAGTCCCGTGTGACATTGTAATCCATGGA
Found at i:1224842 original size:17 final size:17
Alignment explanation
Indices: 1224822--1224858 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
1224812 ACCAAAATAC
1224822 CCCTGTAATGAAAATGA
1 CCCTGTAATGAAAATGA
1224839 CCCTGTAATGAAAATGA
1 CCCTGTAATGAAAATGA
1224856 CCC
1 CCC
1224859 AAGAATACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.22
Consensus pattern (17 bp):
CCCTGTAATGAAAATGA
Found at i:1225307 original size:19 final size:19
Alignment explanation
Indices: 1225285--1225328 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
1225275 TTGTATTACT
*
1225285 CTGGAAAATCCTGAAGTAA
1 CTGGAAAATCCCGAAGTAA
1225304 CTGGAAAATCCCGAAGTAA
1 CTGGAAAATCCCGAAGTAA
1225323 CTGGAA
1 CTGGAA
1225329 TGGACTTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.18
Consensus pattern (19 bp):
CTGGAAAATCCCGAAGTAA
Found at i:1236772 original size:20 final size:20
Alignment explanation
Indices: 1236610--1236862 Score: 158
Period size: 20 Copynumber: 12.7 Consensus size: 20
1236600 GCGATTTTCC
*
1236610 TAAATCGCAATGCGAATTAGG
1 TAAATCGCAATGCG-ATTACG
* * *
1236631 AAAATCACAACGCGATTACG
1 TAAATCGCAATGCGATTACG
*
1236651 TAAATCGCAATGTGATTACG
1 TAAATCGCAATGCGATTACG
* * * *
1236671 T-ATTCGCATTGCGATTTTCC
1 TAAATCGCAATGCGA-TTACG
* *
1236691 TAATTCGCATTGCGATTTACG
1 TAAATCGCAATGCGA-TTACG
* * * *
1236712 T-ATTCGCATTGCGATTTTCC
1 TAAATCGCAATGCGA-TTACG
* * *
1236732 TAATTCGCAA----AATATG
1 TAAATCGCAATGCGATTACG
*
1236748 TAAATCGCAACGCGATTACG
1 TAAATCGCAATGCGATTACG
* *
1236768 TAAATCACAACGCGATTACG
1 TAAATCGCAATGCGATTACG
* *
1236788 TAAATCGTAATGCGAATTAGG
1 TAAATCGCAATGCG-ATTACG
* * *
1236809 AAAATTGCAATGCGAATACG
1 TAAATCGCAATGCGATTACG
*
1236829 TAAATCGCAATGCGAATTAGG
1 TAAATCGCAATGCG-ATTACG
*
1236850 AAAATCGCAATGC
1 TAAATCGCAATGC
1236863 AATTTACATA
Statistics
Matches: 183, Mismatches: 40, Indels: 18
0.76 0.17 0.07
Matches are distributed among these distances:
16 10 0.05
17 1 0.01
19 10 0.05
20 94 0.51
21 68 0.37
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (20 bp):
TAAATCGCAATGCGATTACG
Found at i:1236832 original size:41 final size:41
Alignment explanation
Indices: 1236742--1236862 Score: 154
Period size: 41 Copynumber: 3.0 Consensus size: 41
1236732 TAATTCGCAA
* * * * * *
1236742 AATATGTAAATCGCAACGCG-ATTACGTAAATCACAACGCG
1 AATACGTAAATCGCAATGCGAATTAGGAAAATCGCAATGCG
* * *
1236782 ATTACGTAAATCGTAATGCGAATTAGGAAAATTGCAATGCG
1 AATACGTAAATCGCAATGCGAATTAGGAAAATCGCAATGCG
1236823 AATACGTAAATCGCAATGCGAATTAGGAAAATCGCAATGC
1 AATACGTAAATCGCAATGCGAATTAGGAAAATCGCAATGC
1236863 AATTTACATA
Statistics
Matches: 68, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
40 16 0.24
41 52 0.76
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.22
Consensus pattern (41 bp):
AATACGTAAATCGCAATGCGAATTAGGAAAATCGCAATGCG
Found at i:1237095 original size:25 final size:27
Alignment explanation
Indices: 1237073--1237125 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1237063 GTCCCCATCG
1237073 CCGAC-GAAATCCCTCACAACCATTCA
1 CCGACAGAAATCCCTCACAACCATTCA
* * *
1237099 CGGTCAGAAATCCCTCACAATCATTCA
1 CCGACAGAAATCCCTCACAACCATTCA
1237126 GAAATAGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 3 0.13
27 20 0.87
ACGTcount: A:0.34, C:0.38, G:0.09, T:0.19
Consensus pattern (27 bp):
CCGACAGAAATCCCTCACAACCATTCA
Found at i:1237423 original size:20 final size:19
Alignment explanation
Indices: 1237398--1237469 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 19
1237388 TTCTAAACTT
1237398 AAAATCGCAACATGAAAATG
1 AAAATCGCAACA-GAAAATG
*
1237418 AAAATCGCAATACGAAAATG
1 AAAATCGCAACA-GAAAATG
**
1237438 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAAC-AGA-AAATG
1237459 AAAATCGCAAC
1 AAAATCGCAAC
1237470 GAGATAATCA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
20 28 0.65
21 15 0.35
ACGTcount: A:0.51, C:0.18, G:0.17, T:0.14
Consensus pattern (19 bp):
AAAATCGCAACAGAAAATG
Found at i:1237543 original size:20 final size:19
Alignment explanation
Indices: 1237496--1237555 Score: 93
Period size: 19 Copynumber: 3.1 Consensus size: 19
1237486 GAAACAAAAA
*
1237496 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1237515 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1237534 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1237554 TC
1 TC
1237556 AACCAAAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
19 20 0.53
20 18 0.47
ACGTcount: A:0.12, C:0.23, G:0.17, T:0.48
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1239410 original size:94 final size:94
Alignment explanation
Indices: 1239220--1239572 Score: 563
Period size: 94 Copynumber: 3.8 Consensus size: 94
1239210 TAGATTGCTT
* * *
1239220 AGTAAATTTATTCGGTTGCTGCCAATACTGCTCAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
1239281 ATTTGTCTTTTGTTTTATCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
1239310 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1239375 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
1239404 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAATTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1239469 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * * *
1239498 AGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAACTATGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1239563 ATTTGTCTTT
66 ATTTGTCTTT
1239573 TGGTTGAAGT
Statistics
Matches: 247, Mismatches: 11, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
90 34 0.14
92 3 0.01
93 21 0.09
94 189 0.77
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1239701 original size:20 final size:19
Alignment explanation
Indices: 1239674--1239731 Score: 89
Period size: 19 Copynumber: 3.0 Consensus size: 19
1239664 TCTTTTGGTT
*
1239674 GAAATGAAAATTGCAACGA
1 GAAATGAAAATCGCAACGA
*
1239693 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGA
1239713 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
1239732 CAAAATCGCA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
19 18 0.51
20 17 0.49
ACGTcount: A:0.50, C:0.16, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:1239742 original size:33 final size:34
Alignment explanation
Indices: 1239700--1239764 Score: 105
Period size: 33 Copynumber: 1.9 Consensus size: 34
1239690 CGAGAGAATG
**
1239700 AAAATCGCAACGCGAAA-TGAAAATCGCAACGAC
1 AAAATCGCAACGCGAAACCAAAAATCGCAACGAC
1239733 AAAATCGCAACGCGAAACCAAAAATCGCAACG
1 AAAATCGCAACGCGAAACCAAAAATCGCAACG
1239765 CGAAACCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 17 0.59
34 12 0.41
ACGTcount: A:0.49, C:0.26, G:0.17, T:0.08
Consensus pattern (34 bp):
AAAATCGCAACGCGAAACCAAAAATCGCAACGAC
Found at i:1239756 original size:20 final size:20
Alignment explanation
Indices: 1239733--1239782 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
1239723 TCGCAACGAC
1239733 AAAATCGCAACGCGAAACCA
1 AAAATCGCAACGCGAAACCA
1239753 AAAATCGCAACGCGAAACCA
1 AAAATCGCAACGCGAAACCA
1239773 AAAATCGCAA
1 AAAATCGCAA
1239783 TTCGATTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.52, C:0.28, G:0.14, T:0.06
Consensus pattern (20 bp):
AAAATCGCAACGCGAAACCA
Found at i:1239837 original size:19 final size:20
Alignment explanation
Indices: 1239813--1239864 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
1239803 ACGATTCTCT
*
1239813 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTTCATTTTCA
**
1239832 CGTTGCGATAGTCATTTTTCA
1 CGTTGCGATTTTCA-TTTTCA
1239853 CGTTGCGATTTT
1 CGTTGCGATTTT
1239865 AAGTTCCATA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 12 0.46
21 14 0.54
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.46
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTTCA
Found at i:1241879 original size:19 final size:19
Alignment explanation
Indices: 1241863--1241916 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
1241853 AAAAATGACT
*
1241863 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCAAAATGAAA
*
1241882 ATCACAATGCAAAATGAAA
1 ATCGCAATGCAAAATGAAA
1241901 ATCGCAATGACAAAAT
1 ATCGCAATG-CAAAAT
1241917 CACAACGCGA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 25 0.81
20 6 0.19
ACGTcount: A:0.52, C:0.17, G:0.15, T:0.17
Consensus pattern (19 bp):
ATCGCAATGCAAAATGAAA
Found at i:1241956 original size:19 final size:19
Alignment explanation
Indices: 1241934--1242084 Score: 71
Period size: 19 Copynumber: 8.7 Consensus size: 19
1241924 CGAAACTAAA
1241934 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1241953 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* * * *
1241968 -CCTCGTTGTGTTTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1241986 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
1242001 -TCTCGTTGCGATTTTTAT
1 TTCGCGTTGCGATTTTCAT
*
1242019 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
1242034 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* **
1242052 TTCGCATTGCGATAGTCAT
1 TTCGCGTTGCGATTTTCAT
1242071 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
1242085 AGACATTAAG
Statistics
Matches: 92, Mismatches: 24, Indels: 31
0.63 0.16 0.21
Matches are distributed among these distances:
14 24 0.26
16 8 0.09
17 8 0.09
19 42 0.46
20 10 0.11
ACGTcount: A:0.11, C:0.23, G:0.20, T:0.46
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1241983 original size:33 final size:33
Alignment explanation
Indices: 1241938--1242064 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
1241928 ACTAAATTCG
* * *
1241938 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGTTTTTCATTTCGCATTGCGATTCTCT
*
1241971 CGTTGTGTTTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGTTTTTCATTTCGCATTGCGATTCTCT
1242004 CGTTGCGATTTTT-ATTTCGCATTGCGATTCTCT
1 CGTTGCG-TTTTTCATTTCGCATTGCGATTCTCT
*
1242037 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGTTTTTCATTTCGCATTGCGAT
1242065 AGTCATTTCC
Statistics
Matches: 86, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
32 4 0.05
33 77 0.90
34 5 0.06
ACGTcount: A:0.11, C:0.23, G:0.19, T:0.47
Consensus pattern (33 bp):
CGTTGCGTTTTTCATTTCGCATTGCGATTCTCT
Found at i:1242083 original size:20 final size:20
Alignment explanation
Indices: 1242037--1242130 Score: 68
Period size: 20 Copynumber: 4.7 Consensus size: 20
1242027 GCGATTCTCT
**
1242037 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTCCG
*
1242056 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* **
1242076 CGTTGCGATAGACA-TTAAG
1 CGTTGCGATAGTCATTTCCG
*
1242095 ATGATTGCGA-ACGTCATTTCCG
1 -CG-TTGCGATA-GTCATTTCCG
*
1242117 TGTTGCGATAGTCA
1 CGTTGCGATAGTCA
1242131 AATGAATGCC
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
19 17 0.29
20 26 0.45
21 12 0.21
22 3 0.05
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:1244669 original size:24 final size:24
Alignment explanation
Indices: 1244618--1244669 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
1244608 ATCCGAGTAT
* *
1244618 TGACCAAGATCAAAGTTCAGGTAT
1 TGACCAAGATCAAAGTTCAGATAC
*
1244642 TGACCAAGATCAAATTTC-GAATAC
1 TGACCAAGATCAAAGTTCAG-ATAC
1244666 TGAC
1 TGAC
1244670 TAGTACTCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.25
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCAGATAC
Found at i:1245550 original size:20 final size:21
Alignment explanation
Indices: 1245523--1245610 Score: 101
Period size: 21 Copynumber: 4.3 Consensus size: 21
1245513 TCGTTGCAAT
*
1245523 TTAC-TAAATCGTAATGCG-A
1 TTACGTAAATCGCAATGCGAA
1245542 TTACGTAAATCGCAATGCGAA
1 TTACGTAAATCGCAATGCGAA
* *
1245563 TTAGGAAAATCGCAATGCGAA
1 TTACGTAAATCGCAATGCGAA
* * *
1245584 TTAGGAAAATCTCAATGCG-A
1 TTACGTAAATCGCAATGCGAA
1245604 TTACGTA
1 TTACGTA
1245611 TTCGCATTGC
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
19 4 0.07
20 19 0.31
21 38 0.62
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (21 bp):
TTACGTAAATCGCAATGCGAA
Found at i:1245572 original size:21 final size:21
Alignment explanation
Indices: 1245528--1245603 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
1245518 GCAATTTACT
* * *
1245528 AAATCGTAATGCG-ATTACGT
1 AAATCGCAATGCGAATTAGGA
1245548 AAATCGCAATGCGAATTAGGA
1 AAATCGCAATGCGAATTAGGA
1245569 AAATCGCAATGCGAATTAGGA
1 AAATCGCAATGCGAATTAGGA
*
1245590 AAATCTCAATGCGA
1 AAATCGCAATGCGA
1245604 TTACGTATTC
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
20 12 0.24
21 39 0.76
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (21 bp):
AAATCGCAATGCGAATTAGGA
Found at i:1245668 original size:22 final size:21
Alignment explanation
Indices: 1245643--1245685 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1245633 TCGTGTTGCG
1245643 ATTTAGGAAAATCGCAACGCGA
1 ATTT-GGAAAATCGCAACGCGA
* *
1245665 ATTTGGGAAATCGCAATGCGA
1 ATTTGGAAAATCGCAACGCGA
1245686 TAGTCAGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.21
Consensus pattern (21 bp):
ATTTGGAAAATCGCAACGCGA
Found at i:1246315 original size:22 final size:23
Alignment explanation
Indices: 1246281--1246323 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
1246271 ATATAATAAA
1246281 TAATATTATTTATTATAAAAACT
1 TAATATTATTTATTATAAAAACT
*
1246304 TAATATTA-TTATTTTAAAAA
1 TAATATTATTTATTATAAAAA
1246324 TATTAGAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TAATATTATTTATTATAAAAACT
Found at i:1246491 original size:21 final size:23
Alignment explanation
Indices: 1246461--1246507 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1246451 TCAATATCTA
*
1246461 TAAAAATATT-AT-ATTATATTT
1 TAAAAATATTAATAAATATATTT
*
1246482 TAAAATTATTAATAAATATATTT
1 TAAAAATATTAATAAATATATTT
1246505 TAA
1 TAA
1246508 GGAATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 9 0.41
22 2 0.09
23 11 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TAAAAATATTAATAAATATATTT
Found at i:1246522 original size:23 final size:22
Alignment explanation
Indices: 1246461--1246523 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
1246451 TCAATATCTA
* *
1246461 TAAAAATA-TTATATTATATTT
1 TAAAATTATTTATAATATATTT
*
1246482 TAAAATTATTAATAAATATATTT
1 TAAAATTATTTAT-AATATATTT
1246505 TAAGGAATT-TTTATAATAT
1 TAA--AATTATTTATAATAT
1246524 TATTAGACTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 7 0.21
22 3 0.09
23 16 0.47
24 4 0.12
25 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (22 bp):
TAAAATTATTTATAATATATTT
Found at i:1247439 original size:23 final size:23
Alignment explanation
Indices: 1247397--1247452 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
1247387 GATATTATAT
1247397 TATATTGTTAAAAATATTAATAAA
1 TATATT-TTAAAAATATTAATAAA
* * *
1247421 TATATTTTAAATATCTTAATAAT
1 TATATTTTAAAAATATTAATAAA
1247444 TAATATTTT
1 T-ATATTTT
1247453 TATTAAAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 15 0.54
24 13 0.46
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATAAA
Found at i:1250399 original size:183 final size:183
Alignment explanation
Indices: 1250091--1250448 Score: 707
Period size: 183 Copynumber: 2.0 Consensus size: 183
1250081 ATGGACCTGG
1250091 TGCTTGTCCAACTTCGATATATCTACCATAATACTCACCACCTCTATCAGTTCTCACCATCTTAA
1 TGCTTGTCCAACTTCGATATATCTACCATAATACTCACCACCTCTATCAGTTCTCACCATCTTAA
1250156 TTTGCTTATTGCATTGTTTCTCTACTTCAACCTTGAAAATTTTAAAGGCTTATAATGTTTTGCTC
66 TTTGCTTATTGCATTGTTTCTCTACTTCAACCTTGAAAATTTTAAAGGCTTATAATGTTTTGCTC
1250221 TTATAATGAAGCATGTACAGATACATGTATCGTGAGTAATCATCATCTTAATT
131 TTATAATGAAGCATGTACAGATACATGTATCGTGAGTAATCATCATCTTAATT
1250274 TGCTTGTCCAACTTCGATATATCTACCATAATACTCACCACCTCTATCAGTTCTCACCATCTTAA
1 TGCTTGTCCAACTTCGATATATCTACCATAATACTCACCACCTCTATCAGTTCTCACCATCTTAA
*
1250339 TTTGCTTATTGCATTGTTTCTCTACTTCAACCTTGAAAATTTTAAAGGCTTATAATGTTTTTCTC
66 TTTGCTTATTGCATTGTTTCTCTACTTCAACCTTGAAAATTTTAAAGGCTTATAATGTTTTGCTC
1250404 TTATAATGAAGCATGTACAGATACATGTATCGTGAGTAATCATCA
131 TTATAATGAAGCATGTACAGATACATGTATCGTGAGTAATCATCA
1250449 ATAAAAGTGA
Statistics
Matches: 174, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
183 174 1.00
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (183 bp):
TGCTTGTCCAACTTCGATATATCTACCATAATACTCACCACCTCTATCAGTTCTCACCATCTTAA
TTTGCTTATTGCATTGTTTCTCTACTTCAACCTTGAAAATTTTAAAGGCTTATAATGTTTTGCTC
TTATAATGAAGCATGTACAGATACATGTATCGTGAGTAATCATCATCTTAATT
Found at i:1250819 original size:31 final size:31
Alignment explanation
Indices: 1250783--1250846 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
1250773 TTTAAAGAGT
1250783 AAAGACCATCGGATAAAATTTCATTTCCAAC
1 AAAGACCATCGGATAAAATTTCATTTCCAAC
1250814 AAAGACCATCGGATAAAATTTCATTTCCAAC
1 AAAGACCATCGGATAAAATTTCATTTCCAAC
1250845 AA
1 AA
1250847 TTTCTGATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.44, C:0.22, G:0.09, T:0.25
Consensus pattern (31 bp):
AAAGACCATCGGATAAAATTTCATTTCCAAC
Found at i:1254110 original size:31 final size:31
Alignment explanation
Indices: 1254074--1254132 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1254064 AACTTAAAAG
* *
1254074 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
1254105 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
1254133 CAATATAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:1254168 original size:21 final size:22
Alignment explanation
Indices: 1254144--1254194 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
1254134 AATATAACTA
1254144 AAAT-AATAAAT-TATTTAAAAT
1 AAATCAATAAATAT-TTTAAAAT
**
1254165 AAATCAATCCATATTTTAAAAT
1 AAATCAATAAATATTTTAAAAT
1254187 AAATCAAT
1 AAATCAAT
1254195 CATACTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 4 0.15
22 21 0.81
23 1 0.04
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (22 bp):
AAATCAATAAATATTTTAAAAT
Found at i:1254206 original size:22 final size:22
Alignment explanation
Indices: 1254159--1254206 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1254149 ATAAATTATT
**
1254159 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
1254181 TAAAATAAATCAAT-CATACTAA
1 TAAAATAAATCAATCCATA-TAA
1254203 TAAA
1 TAAA
1254207 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:1254220 original size:14 final size:14
Alignment explanation
Indices: 1254201--1254253 Score: 61
Period size: 14 Copynumber: 3.5 Consensus size: 14
1254191 CAATCATACT
1254201 AATAAATTATTTAA
1 AATAAATTATTTAA
*
1254215 AATAAATCAATTTATA
1 AATAAAT-TATTTA-A
1254231 CTAATAAATTATTTAA
1 --AATAAATTATTTAA
1254247 AATAAAT
1 AATAAAT
1254254 CAATCCATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
14 14 0.42
15 5 0.15
16 2 0.06
17 5 0.15
18 7 0.21
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.40
Consensus pattern (14 bp):
AATAAATTATTTAA
Found at i:1254232 original size:32 final size:32
Alignment explanation
Indices: 1254179--1254633 Score: 199
Period size: 32 Copynumber: 15.5 Consensus size: 32
1254169 CAATCCATAT
1254179 TTTAAAATAAATCAA-TCATACTAATAAATTA
1 TTTAAAATAAATCAATTCATACTAATAAATTA
*
1254210 TTTAAAATAAATCAATTTATACTAATAAATTA
1 TTTAAAATAAATCAATTCATACTAATAAATTA
1254242 TTTAAAATAAATCAA-TC---C--AT--A-T-
1 TTTAAAATAAATCAATTCATACTAATAAATTA
*
1254264 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATTCATACTAATAAATTA
*
1254296 TTTAAAATAAATCAATCCATAC-AACTACAA-TA
1 TTTAAAATAAATCAATTCATACTAA-TA-AATTA
* * * * * *
1254328 -AT-ATATCAATCCATATT-TTA-AAATAAATCAA
1 TTTAAAATAAAT-CA-ATTCATACTAATAAAT-TA
* * * *
1254359 TCTATACTAATAAAT-TATT--TA-AAATAAATCAA
1 T-T-TA-AAATAAATCAATTCATACTAATAAAT-TA
* * ** ** *
1254391 TCCATACAACTACAAT-AATAAAT-C-AATCCATTT
1 T--TTA-AAATA-AATCAATTCATACTAATAAATTA
*
1254424 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATTCATACTAATAAATTA
1254456 TTTAAAATAAATCAA-TC---C--AT--A-T-
1 TTTAAAATAAATCAATTCATACTAATAAATTA
* *
1254478 TTTAAAATAAATCAATCCATACTAATAAATTT
1 TTTAAAATAAATCAATTCATACTAATAAATTA
1254510 TTTAAAATAAATCAA-TC---C--AT--A-T-
1 TTTAAAATAAATCAATTCATACTAATAAATTA
*
1254532 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATTCATACTAATAAATTA
1254564 TTTAAAATAAATCAA-T--T-C--AT--A-T-
1 TTTAAAATAAATCAATTCATACTAATAAATTA
1254586 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATTCATACTAATAAATTA
1254618 TTTAAAATAAATCAAT
1 TTTAAAATAAATCAAT
1254634 CTATACAACT
Statistics
Matches: 328, Mismatches: 35, Indels: 121
0.68 0.07 0.25
Matches are distributed among these distances:
22 60 0.18
23 8 0.02
24 4 0.01
25 1 0.00
26 12 0.04
28 12 0.04
29 6 0.02
30 21 0.06
31 35 0.11
32 145 0.44
33 12 0.04
34 6 0.02
35 1 0.00
36 5 0.02
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.36
Consensus pattern (32 bp):
TTTAAAATAAATCAATTCATACTAATAAATTA
Found at i:1254270 original size:22 final size:22
Alignment explanation
Indices: 1254242--1254284 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1254232 TAATAAATTA
1254242 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
1254264 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
1254285 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:1254278 original size:54 final size:54
Alignment explanation
Indices: 1254210--1255005 Score: 669
Period size: 54 Copynumber: 14.9 Consensus size: 54
1254200 TAATAAATTA
**
1254210 TTTAAAATAAATCAATTTATACTAATAAATTATTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
*
1254264 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAAC
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCAT---AT
** * * * * * * *
1254321 TACAATAATATATCAATCCATATTTTAAAATAAATCAATCTATACT-AATAAAT---TA-
1 TTTAA-AATAAATCAATCCATA--CT--AATAAAT-TATTTAAAATAAATCAATCCATAT
* *
1254376 TTTAAAATAAATCAATCCATAC-AACTACA--A--T--AATAAATCAATCCATTT
1 TTTAAAATAAATCAATCCATACTAA-TAAATTATTTAAAATAAATCAATCCATAT
1254424 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
*
1254478 TTTAAAATAAATCAATCCATACTAATAAATTTTTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
*
1254532 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
* * *
1254586 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCTATACAAC
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCAT---AT
** * * * * * *
1254643 TACAATAATAAATCAATCCATATTTTAAAATAAATCAATTCATACT-AATAAAT---TA-
1 TTTAA-AATAAATCAATCCATA--CT--AATAAAT-TATTTAAAATAAATCAATCCATAT
* *
1254698 TTTAAAATAAATCAATCCATAC------A--A-CTACAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
* *
1254743 TTTAAAATAAATAAATCCATACTAATAAATTATTTAAAATAAATCAATCTATAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
* * *
1254797 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCTATACAAC
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCAT---AT
** * * * * * *
1254854 TACAATAATAAATCAATCCATATTTTAAAATAAATCAATTCATACT-AATAAAT---TA-
1 TTTAA-AATAAATCAATCCATA--CT--AATAAAT-TATTTAAAATAAATCAATCCATAT
*
1254909 TTTAAAATAAATCAATCCATAC-AACTACA--A--T--AATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATACTAA-TAAATTATTTAAAATAAATCAATCCATAT
*
1254957 TTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATC
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATC
1255006 TATGCAACTA
Statistics
Matches: 604, Mismatches: 71, Indels: 134
0.75 0.09 0.17
Matches are distributed among these distances:
40 3 0.00
41 7 0.01
43 4 0.01
44 15 0.02
45 22 0.04
47 5 0.01
48 49 0.08
49 8 0.01
50 8 0.01
51 1 0.00
52 2 0.00
53 1 0.00
54 347 0.57
55 9 0.01
56 3 0.00
57 12 0.02
58 45 0.07
59 3 0.00
60 3 0.00
62 39 0.06
63 18 0.03
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (54 bp):
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
Found at i:1254293 original size:22 final size:22
Alignment explanation
Indices: 1254244--1254292 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1254234 ATAAATTATT
**
1254244 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
1254266 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
1254289 TAAA
1 TAAA
1254293 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:1254366 original size:80 final size:80
Alignment explanation
Indices: 1254162--1254791 Score: 782
Period size: 80 Copynumber: 7.8 Consensus size: 80
1254152 AATTATTTAA
1254162 AATAAATCAATCCATATTTTAAAATAAATCAAT-CATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
** *
1254226 TTATACTAA-TAAATTATTT
66 CCATAC-AACTACA--A--T
1254245 AAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
1 --AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
1254310 ATCCATACAACTACAAT
64 ATCCATACAACTACAAT
* *
1254327 AATATATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1254392 CCATACAACTACAAT
66 CCATACAACTACAAT
*
1254407 AATAAATCAATCCATTTTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
* **
1254472 CCAT---ATTTTAA-
66 CCATACAACTACAAT
** * *** * ** **
1254483 AATAAATCAATCCATACTAATAAATTTTTTAAAATAAAT-C-AATCCA-TATTTTAAAATAAATC
1 AATAAATCAATCCATA-TTTTAAAATAAAT-CAATCCATACTAATAAATTA-TTTAAAATAAATC
*
1254545 AATCCATACTAA-TAAATTATTT
63 AATCCATAC-AACTACA--A--T
* *
1254567 AAAATAAATCAATTCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCA
1 --AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
*
1254632 ATCTATACAACTACAAT
64 ATCCATACAACTACAAT
*
1254649 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1254714 CCATACAACTAC---
66 CCATACAACTACAAT
*
1254726 AATAAATCAATCCATATTTTAAAATAAATAAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1254791 C
66 C
1254792 TATATTTTAA
Statistics
Matches: 482, Mismatches: 43, Indels: 48
0.84 0.08 0.08
Matches are distributed among these distances:
75 2 0.00
76 39 0.08
77 76 0.16
78 5 0.01
79 2 0.00
80 220 0.46
81 1 0.00
82 2 0.00
84 7 0.01
85 45 0.09
86 81 0.17
87 2 0.00
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (80 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
CCATACAACTACAAT
Done.