Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008527.1 Hibiscus syriacus cultivar Beakdansim tig00111402_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: 9057482
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 37
Found at i:1486624 original size:12 final size:10
Alignment explanation
Indices: 1486610--1486650 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
1486600 ACCTTAAAAA
*
1486610 GAGAGTATTT
1 GAGAGAATTT
1486620 GAGAGAAATTT
1 GAGAG-AATTT
1486631 -AGAGAATTT
1 GAGAGAATTT
1486640 GAGAGAATTT
1 GAGAGAATTT
1486650 G
1 G
1486651 GTGTGATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 5 0.18
10 19 0.68
11 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:1486814 original size:50 final size:50
Alignment explanation
Indices: 1486760--1486886 Score: 148
Period size: 51 Copynumber: 2.5 Consensus size: 50
1486750 AGATATACAT
* **
1486760 GTATAGCGCGCTGCAGGGGCCGCGCTATA-CCCACGTGGCGCCAGCTCACC
1 GTATAGCGCGGTGCAGGGG-CGCGCTATACCCCACGTGGCGCCAAATCACC
* * *
1486810 GTATAGCGCGGTGCAGGTGGCGCGTTATACCCCACGTGGTGCCAAATCATC
1 GTATAGCGCGGTGCAGG-GGCGCGCTATACCCCACGTGGCGCCAAATCACC
* *
1486861 GTATAACGCGGTGGAGGGGGCGCGCT
1 GTATAGCGCGGTGCA-GGGGCGCGCT
1486887 TTACTGCTAA
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
50 24 0.37
51 39 0.60
52 2 0.03
ACGTcount: A:0.17, C:0.30, G:0.35, T:0.17
Consensus pattern (50 bp):
GTATAGCGCGGTGCAGGGGCGCGCTATACCCCACGTGGCGCCAAATCACC
Found at i:1487389 original size:9 final size:9
Alignment explanation
Indices: 1487371--1487403 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
1487361 TTATTATTAA
1487371 TAAT-TAAT
1 TAATATAAT
1487379 TAATATAAT
1 TAATATAAT
1487388 TAATATAAT
1 TAATATAAT
1487397 TACATAT
1 TA-ATAT
1487404 TTAAATATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 4 0.17
9 15 0.65
10 4 0.17
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (9 bp):
TAATATAAT
Found at i:1491450 original size:24 final size:24
Alignment explanation
Indices: 1491423--1491498 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
1491413 TATATCAAAA
*
1491423 ATCAAAACATAAATCAGGTCAAGT
1 ATCAAAACAGAAATCAGGTCAAGT
* *
1491447 ATCATATCAGAAATCAGGTCAAGT
1 ATCAAAACAGAAATCAGGTCAAGT
* * * *
1491471 AACATATCAG-AATCCAAGTCAAGT
1 ATCAAAACAGAAAT-CAGGTCAAGT
1491495 ATCA
1 ATCA
1491499 GATCAGAATC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 3 0.07
24 42 0.93
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (24 bp):
ATCAAAACAGAAATCAGGTCAAGT
Found at i:1491503 original size:24 final size:24
Alignment explanation
Indices: 1491440--1491555 Score: 146
Period size: 24 Copynumber: 4.8 Consensus size: 24
1491430 CATAAATCAG
* *
1491440 GTCAAGTATCATATCAGAAAT-CAG
1 GTCAAGTATCAGATCAG-AATCCAT
* * *
1491464 GTCAAGTAACATATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
1491488 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
*
1491512 GTC-AGATATCAGATCAGAATCTAT
1 GTCAAG-TATCAGATCAGAATCCAT
1491536 GTCAAGTATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
1491556 TCAAATCGAA
Statistics
Matches: 83, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
23 5 0.06
24 76 0.92
25 2 0.02
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:1491571 original size:48 final size:48
Alignment explanation
Indices: 1491476--1491573 Score: 126
Period size: 48 Copynumber: 2.0 Consensus size: 48
1491466 CAAGTAACAT
** *
1491476 ATCAGAATCCAAGTCAAGTATCAGATCAGAATCCATGTCAGATATCAG
1 ATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAGAAATCAG
* * *
1491524 ATCAGAATCTATGTCAAGTATCAGATCAGAATTCAAATC-GAAAATCAG
1 ATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAG-AAATCAG
1491572 AT
1 AT
1491574 AAAATATTCA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
47 1 0.02
48 42 0.98
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.24
Consensus pattern (48 bp):
ATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAAATCAGAAATCAG
Found at i:1494101 original size:18 final size:18
Alignment explanation
Indices: 1494078--1494119 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
1494068 AACGGTCAAT
1494078 GGGTCGGGTCAACGGGTC
1 GGGTCGGGTCAACGGGTC
1494096 GGGTCGGGTCAACGGGTC
1 GGGTCGGGTCAACGGGTC
1494114 GGGTCG
1 GGGTCG
1494120 TGACCGGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.10, C:0.21, G:0.52, T:0.17
Consensus pattern (18 bp):
GGGTCGGGTCAACGGGTC
Found at i:1494118 original size:13 final size:13
Alignment explanation
Indices: 1494071--1494100 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1494061 GCCGGTCAAC
*
1494071 GGTCAATGGGTCG
1 GGTCAACGGGTCG
1494084 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1494097 GGTC
1 GGTC
1494101 GGGTCAACGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.13, C:0.20, G:0.47, T:0.20
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1496083 original size:2 final size:2
Alignment explanation
Indices: 1496076--1496176 Score: 202
Period size: 2 Copynumber: 50.5 Consensus size: 2
1496066 CTTTTAAAAC
1496076 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
1496118 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
1496160 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
1496177 GCCCCATCCC
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 99 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1496386 original size:24 final size:24
Alignment explanation
Indices: 1496359--1496474 Score: 155
Period size: 24 Copynumber: 4.8 Consensus size: 24
1496349 CATAAATCAG
*
1496359 GTCAAGTAACAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAA
1496383 GTCAAGTAAT-AGATCAGAATCCAA
1 GTCAAGT-ATCAGATCAGAATCCAA
* *
1496407 GTCAAGTATCATATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAA
* *
1496431 GTC-AGATATCATATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAA
1496455 GTCAAGTATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
1496475 TCAAATCGAA
Statistics
Matches: 84, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.05
24 77 0.92
25 3 0.04
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAA
Found at i:1498978 original size:13 final size:13
Alignment explanation
Indices: 1498960--1499002 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
1498950 GGTCAACGGT
1498960 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1498973 GGTCAACGGGTCG
1 GGTCAACGGGTCG
* *
1498986 GGTAAACGAGTCG
1 GGTCAACGGGTCG
1498999 GGTC
1 GGTC
1499003 GTGACCGGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.19, C:0.21, G:0.44, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1500709 original size:33 final size:33
Alignment explanation
Indices: 1500660--1500737 Score: 129
Period size: 33 Copynumber: 2.4 Consensus size: 33
1500650 TCTTGTGTGT
*
1500660 TTAGGAATCTTTTATGATAAGAAAGTACAAGTC
1 TTAGGAGTCTTTTATGATAAGAAAGTACAAGTC
* *
1500693 TTGGGAGTCTTTTATGATAAGAAAGTATAAGTC
1 TTAGGAGTCTTTTATGATAAGAAAGTACAAGTC
1500726 TTAGGAGTCTTT
1 TTAGGAGTCTTT
1500738 GTAATCTCTA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.33, C:0.08, G:0.22, T:0.37
Consensus pattern (33 bp):
TTAGGAGTCTTTTATGATAAGAAAGTACAAGTC
Found at i:1518967 original size:20 final size:20
Alignment explanation
Indices: 1518911--1518970 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
1518901 GAGTCGAGGG
*
1518911 TTCATAGGTCTTTCGAGACA
1 TTCATAGGTCTTTCGGGACA
* * * * *
1518931 TACAGAGATCCTTCGGGATA
1 TTCATAGGTCTTTCGGGACA
1518951 TTCATAGGTCTTTCGGGACA
1 TTCATAGGTCTTTCGGGACA
1518971 AGATTTCACA
Statistics
Matches: 29, Mismatches: 11, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (20 bp):
TTCATAGGTCTTTCGGGACA
Found at i:1522239 original size:43 final size:39
Alignment explanation
Indices: 1522174--1522256 Score: 96
Period size: 43 Copynumber: 2.0 Consensus size: 39
1522164 AAATAAATCA
1522174 AAATAATAAATAATAATAAGTTAACTAATCTATTATTTTTAAT
1 AAATAATAAATAATAATAAGTTAA-TAA--TATTA-TTTTAAT
* *
1522217 AAATAATAAA-ATATTATTAGTTAATAATATTATTTTAAT
1 AAATAATAAATA-ATAATAAGTTAATAATATTATTTTAAT
1522256 A
1 A
1522257 CAAAAAGAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
39 8 0.22
40 5 0.14
42 4 0.11
43 20 0.54
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (39 bp):
AAATAATAAATAATAATAAGTTAATAATATTATTTTAAT
Found at i:1524736 original size:30 final size:31
Alignment explanation
Indices: 1524690--1524753 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 31
1524680 TAATCTCATA
* * *
1524690 ATCAGACTATTTCTTCTGTTTTAGGGAACAT
1 ATCAGACTAATTCTTCTCTTTTAGGGAAAAT
*
1524721 ATCA-ACTAATTCTTCTCTTTTATGGAAAAT
1 ATCAGACTAATTCTTCTCTTTTAGGGAAAAT
1524751 ATC
1 ATC
1524754 GTCGCTAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 25 0.86
31 4 0.14
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.42
Consensus pattern (31 bp):
ATCAGACTAATTCTTCTCTTTTAGGGAAAAT
Found at i:1524891 original size:30 final size:31
Alignment explanation
Indices: 1524828--1524894 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
1524818 TAATATTTTA
* * *
1524828 ATTAAACTATTGTAAAATATTTATTACATTT
1 ATTAAACTATTATAAAATATCTATTAAATTT
1524859 ATTAAACTATTATAAAATATCT-TTAAATTT
1 ATTAAACTATTATAAAATATCTATTAAATTT
1524889 ATTAAA
1 ATTAAA
1524895 ATTTATCACT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 13 0.39
31 20 0.61
ACGTcount: A:0.46, C:0.06, G:0.01, T:0.46
Consensus pattern (31 bp):
ATTAAACTATTATAAAATATCTATTAAATTT
Found at i:1525314 original size:32 final size:30
Alignment explanation
Indices: 1525202--1525315 Score: 79
Period size: 32 Copynumber: 3.7 Consensus size: 30
1525192 TTTTAAAAGC
* *
1525202 TATAAATTAATCATTAAATTTATTTAAATT-T
1 TATAAAATAATCA-TGAATTTA-TTAAATTAT
* * * * * *
1525233 TATAAAATTATTAT-ATTTTATCAAACTAC
1 TATAAAATAATCATGAATTTATTAAATTAT
*
1525262 TATAAAATGATCATGAAATTTCATTAAATTAT
1 TATAAAATAATCATG-AATTT-ATTAAATTAT
*
1525294 TATAAAATAATTATTGAATTTA
1 TATAAAATAATCA-TGAATTTA
1525316 CCAATTTTTT
Statistics
Matches: 63, Mismatches: 15, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
28 5 0.08
29 17 0.27
30 1 0.02
31 15 0.24
32 23 0.37
33 2 0.03
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (30 bp):
TATAAAATAATCATGAATTTATTAAATTAT
Found at i:1527988 original size:10 final size:10
Alignment explanation
Indices: 1527936--1528027 Score: 50
Period size: 11 Copynumber: 9.2 Consensus size: 10
1527926 CGATAATATG
1527936 ATAATTATTTT
1 ATAA-TATTTT
*
1527947 ATAGTA-TTT
1 ATAATATTTT
* * *
1527956 AGAAAAATTT
1 ATAATATTTT
1527966 ATTAATAATTTT
1 A-TAAT-ATTTT
1527978 ATAATATTTT
1 ATAATATTTT
*
1527988 AATAA-ATTTA
1 -ATAATATTTT
*
1527998 ACAAGTATTTT
1 ATAA-TATTTT
1528009 ATAAT-TTTT
1 ATAATATTTT
1528018 -TAA-ATTTT
1 ATAATATTTT
1528026 AT
1 AT
1528028 TAACGAAAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 18
0.68 0.12 0.20
Matches are distributed among these distances:
8 7 0.11
9 14 0.23
10 16 0.26
11 20 0.32
12 5 0.08
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.53
Consensus pattern (10 bp):
ATAATATTTT
Found at i:1527991 original size:19 final size:19
Alignment explanation
Indices: 1527967--1528026 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
1527957 GAAAAATTTA
1527967 TTAATAATTTTATAATATT
1 TTAATAATTTTATAATATT
* *
1527986 TTAATAAATTTAACAAGTATT
1 TTAAT-AATTTTATAA-TATT
*
1528007 TT-ATAATTTTTTAA-ATT
1 TTAATAATTTTATAATATT
1528024 TTA
1 TTA
1528027 TTAACGAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
17 5 0.15
19 12 0.36
20 10 0.30
21 6 0.18
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (19 bp):
TTAATAATTTTATAATATT
Found at i:1527995 original size:31 final size:30
Alignment explanation
Indices: 1527936--1528021 Score: 84
Period size: 31 Copynumber: 2.8 Consensus size: 30
1527926 CGATAATATG
*
1527936 ATAATTATTTTATAGTA-TTTAGAAAAATTTA
1 ATAA-TATTTTATAATATTTTA-AAAAATTTA
* *
1527967 TTAATAATTTTATAATATTTTAATAAATTTA
1 ATAAT-ATTTTATAATATTTTAAAAAATTTA
* *
1527998 ACAAGTATTTTATAATTTTTTAAA
1 ATAA-TATTTTATAATATTTTAAA
1528022 TTTTATTAAC
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
30 1 0.02
31 39 0.87
32 5 0.11
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (30 bp):
ATAATATTTTATAATATTTTAAAAAATTTA
Found at i:1528115 original size:26 final size:26
Alignment explanation
Indices: 1528082--1528153 Score: 85
Period size: 27 Copynumber: 2.8 Consensus size: 26
1528072 ACTTTATTTG
1528082 AAAA-TATATATTAAACTTAGTAAAA
1 AAAATTATATATTAAACTTAGTAAAA
* *
1528107 AATATTATACAATTAAACTTAGTAAAA
1 AAAATTATA-TATTAAACTTAGTAAAA
*
1528134 AAAATT-TATATAAAAACTTA
1 AAAATTATATAT-TAAACTTA
1528154 AAAAATCATG
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
25 5 0.13
26 13 0.33
27 21 0.54
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.33
Consensus pattern (26 bp):
AAAATTATATATTAAACTTAGTAAAA
Found at i:1528792 original size:20 final size:18
Alignment explanation
Indices: 1528748--1528798 Score: 50
Period size: 20 Copynumber: 2.7 Consensus size: 18
1528738 ATAAAGTTTA
*
1528748 AAAATTTATAAAATATTT
1 AAAATTTATAAAAGATTT
1528766 ATTAAATTTATTAAAAGATTGT
1 A--AAATTTA-TAAAAGATT-T
1528788 AAAA-TTATAAA
1 AAAATTTATAAA
1528799 TAAATTTATC
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
18 5 0.18
19 3 0.11
20 10 0.36
21 8 0.29
22 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (18 bp):
AAAATTTATAAAAGATTT
Found at i:1532253 original size:23 final size:23
Alignment explanation
Indices: 1532227--1532271 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1532217 CACCACAGCT
*
1532227 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
1532250 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
1532272 ATATAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:1539099 original size:23 final size:23
Alignment explanation
Indices: 1539073--1539117 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1539063 CACCACAGCT
*
1539073 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
1539096 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
1539118 ATATAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:1539791 original size:19 final size:20
Alignment explanation
Indices: 1539754--1539791 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1539744 TTTTTTTATA
*
1539754 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
1539774 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
1539792 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:1543471 original size:22 final size:22
Alignment explanation
Indices: 1543446--1543490 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
1543436 GTCAACAAAT
1543446 AGTCATAACGATCCTACAACTG
1 AGTCATAACGATCCTACAACTG
*
1543468 AGTCATAACGATCTTACAACTG
1 AGTCATAACGATCCTACAACTG
1543490 A
1 A
1543491 CATTTACACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.24
Consensus pattern (22 bp):
AGTCATAACGATCCTACAACTG
Found at i:1544068 original size:16 final size:16
Alignment explanation
Indices: 1544047--1544089 Score: 70
Period size: 15 Copynumber: 2.8 Consensus size: 16
1544037 TGTGCAAATC
1544047 CGGGTACCCGGATTTT
1 CGGGTACCCGGATTTT
1544063 CGGGTACCC-GATTTT
1 CGGGTACCCGGATTTT
*
1544078 TGGGTACCCGGA
1 CGGGTACCCGGA
1544090 ACTTCCGGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 14 0.56
16 11 0.44
ACGTcount: A:0.14, C:0.26, G:0.33, T:0.28
Consensus pattern (16 bp):
CGGGTACCCGGATTTT
Found at i:1544147 original size:17 final size:16
Alignment explanation
Indices: 1544125--1544193 Score: 63
Period size: 15 Copynumber: 4.3 Consensus size: 16
1544115 CCGTGTCCCG
*
1544125 ACCCGGATGTTACGGGT
1 ACCCGGATATT-CGGGT
*
1544142 ACCCGG-TAATCGGGT
1 ACCCGGATATTCGGGT
*
1544157 ACCCGGATTTTGCGGGT
1 ACCCGGATATT-CGGGT
1544174 ACCCAGGA-A-TCGGGT
1 ACCC-GGATATTCGGGT
1544189 ACCCG
1 ACCCG
1544194 ATACCCGGTT
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
14 1 0.02
15 20 0.45
16 5 0.11
17 15 0.34
18 3 0.07
ACGTcount: A:0.19, C:0.28, G:0.33, T:0.20
Consensus pattern (16 bp):
ACCCGGATATTCGGGT
Found at i:1544161 original size:32 final size:32
Alignment explanation
Indices: 1544125--1544193 Score: 104
Period size: 32 Copynumber: 2.2 Consensus size: 32
1544115 CCGTGTCCCG
1544125 ACCCGGATGTTACGGGTACCC-GGTAATCGGGT
1 ACCCGGATGTTACGGGTACCCAGG-AATCGGGT
* *
1544157 ACCCGGATTTTGCGGGTACCCAGGAATCGGGT
1 ACCCGGATGTTACGGGTACCCAGGAATCGGGT
1544189 ACCCG
1 ACCCG
1544194 ATACCCGGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 32 0.94
33 2 0.06
ACGTcount: A:0.19, C:0.28, G:0.33, T:0.20
Consensus pattern (32 bp):
ACCCGGATGTTACGGGTACCCAGGAATCGGGT
Found at i:1547496 original size:24 final size:24
Alignment explanation
Indices: 1547468--1547584 Score: 171
Period size: 24 Copynumber: 4.9 Consensus size: 24
1547458 TTTCGACTTT
* * *
1547468 AATTCTGTTCTGATTTCTGATATG
1 AATTCTGTTATGATATCTGATCTG
*
1547492 GATTCTGTTATGATATCTGATCTG
1 AATTCTGTTATGATATCTGATCTG
1547516 AATTCTGTTATGATATCTGATCTG
1 AATTCTGTTATGATATCTGATCTG
*
1547540 AATTCTGTTTTGATATCTGATCTG
1 AATTCTGTTATGATATCTGATCTG
* *
1547564 AATTCTGTTTTGATTTCTGAT
1 AATTCTGTTATGATATCTGAT
1547585 ATCTCCGTTT
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 86 1.00
ACGTcount: A:0.21, C:0.12, G:0.17, T:0.50
Consensus pattern (24 bp):
AATTCTGTTATGATATCTGATCTG
Found at i:1547558 original size:12 final size:12
Alignment explanation
Indices: 1547471--1547582 Score: 61
Period size: 12 Copynumber: 9.3 Consensus size: 12
1547461 CGACTTTAAT
*
1547471 TCTGTTCTGATT
1 TCTGTTCTGATA
* *
1547483 TCTGATATGGAT-
1 TCTGTTCT-GATA
*
1547495 TCTGTTATGATA
1 TCTGTTCTGATA
*
1547507 TCTGATCTGA-A
1 TCTGTTCTGATA
*
1547518 TTCTGTTATGATA
1 -TCTGTTCTGATA
*
1547531 TCTGATCTGA-A
1 TCTGTTCTGATA
*
1547542 TTCTGTTTTGATA
1 -TCTGTTCTGATA
*
1547555 TCTGATCTGA-A
1 TCTGTTCTGATA
* *
1547566 TTCTGTTTTGATT
1 -TCTGTTCTGATA
1547579 TCTG
1 TCTG
1547583 ATATCTCCGT
Statistics
Matches: 76, Mismatches: 16, Indels: 16
0.70 0.15 0.15
Matches are distributed among these distances:
11 6 0.08
12 65 0.86
13 5 0.07
ACGTcount: A:0.20, C:0.12, G:0.18, T:0.50
Consensus pattern (12 bp):
TCTGTTCTGATA
Found at i:1548860 original size:50 final size:50
Alignment explanation
Indices: 1548803--1548899 Score: 167
Period size: 50 Copynumber: 1.9 Consensus size: 50
1548793 AAAATGACAC
* *
1548803 AAAAAATATTATGTTTATTTAAAAAATTTAACGCATTGAGTTTGAATGCT
1 AAAAAATATTATATTTATTTAAAAAATTTAACGCATTAAGTTTGAATGCT
*
1548853 AAAAAATATTATATTTATTTAAAAAATTTAACGTATTAAGTTTGAAT
1 AAAAAATATTATATTTATTTAAAAAATTTAACGCATTAAGTTTGAAT
1548900 ACTTATATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.41
Consensus pattern (50 bp):
AAAAAATATTATATTTATTTAAAAAATTTAACGCATTAAGTTTGAATGCT
Found at i:1548919 original size:50 final size:50
Alignment explanation
Indices: 1548816--1548919 Score: 136
Period size: 50 Copynumber: 2.1 Consensus size: 50
1548806 AAATATTATG
* * * *
1548816 TTTATTTAAAAAATTTAACGCATTGAGTTTGAATGCTAAAAAATATTATA
1 TTTATTTAAAAAATTTAACGCATTAAGTTTGAATACTAAAAAATATAAAA
* * * *
1548866 TTTATTTAAAAAATTTAACGTATTAAGTTTGAATACTTATATATATAAAA
1 TTTATTTAAAAAATTTAACGCATTAAGTTTGAATACTAAAAAATATAAAA
1548916 TTTA
1 TTTA
1548920 AAGTCAGGTG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.43
Consensus pattern (50 bp):
TTTATTTAAAAAATTTAACGCATTAAGTTTGAATACTAAAAAATATAAAA
Found at i:1554729 original size:12 final size:11
Alignment explanation
Indices: 1554695--1554737 Score: 54
Period size: 12 Copynumber: 3.9 Consensus size: 11
1554685 TCCTTGGTCC
1554695 CCGTTGACCGA
1 CCGTTGACCGA
1554706 CC--TGACCCGA
1 CCGTTGA-CCGA
1554716 CCGTTGACCTGA
1 CCGTTGACC-GA
1554728 CCGTTGACCG
1 CCGTTGACCG
1554738 TTGTCCTGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
9 3 0.11
10 6 0.21
11 5 0.18
12 14 0.50
ACGTcount: A:0.16, C:0.40, G:0.26, T:0.19
Consensus pattern (11 bp):
CCGTTGACCGA
Found at i:1554886 original size:29 final size:29
Alignment explanation
Indices: 1554750--1554878 Score: 190
Period size: 29 Copynumber: 4.5 Consensus size: 29
1554740 GTCCTGGTGT
* * * *
1554750 TATTTTAGTAATTAATTCGAAATAGGTGT
1 TATTTTAGTAATTAATTCAAAACATGTGC
*
1554779 TATTTTAGTAATTAATTC-GAA-ATGGTGC
1 TATTTTAGTAATTAATTCAAAACAT-GTGC
1554807 TATTTTAGTAATTAATTCAAAACATGTGC
1 TATTTTAGTAATTAATTCAAAACATGTGC
1554836 TATTTTAGTAATTAATTCAAAACATGTGC
1 TATTTTAGTAATTAATTCAAAACATGTGC
1554865 TATTTTAGTAATTA
1 TATTTTAGTAATTA
1554879 TTTAAAAAAA
Statistics
Matches: 93, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
27 1 0.01
28 23 0.25
29 67 0.72
30 2 0.02
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44
Consensus pattern (29 bp):
TATTTTAGTAATTAATTCAAAACATGTGC
Found at i:1554897 original size:57 final size:57
Alignment explanation
Indices: 1554744--1554897 Score: 195
Period size: 57 Copynumber: 2.7 Consensus size: 57
1554734 ACCGTTGTCC
* * * * *
1554744 TGGTGTTATTTTAGTAATTAATTCGAAATAGGTGTTATTTTAGTAATTAATTCGAAA
1 TGGTGCTATTTTAGTAATTAATTCAAAAAAAGTGTTATTTTAGTAATTAATTCAAAA
* * *
1554801 TGGTGCTATTTTAGTAATTAATTCAAAACATGTGCTATTTTAGTAATTAATTCAAAACA
1 TGGTGCTATTTTAGTAATTAATTCAAAAAAAGTGTTATTTTAGTAATTAATTC-AAA-A
*
1554860 T-GTGCTATTTTAGTAATT-ATTTAAAAAAAGTGTTATTT
1 TGGTGCTATTTTAGTAATTAATTCAAAAAAAGTGTTATTT
1554898 CTGTAAAATG
Statistics
Matches: 85, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
57 64 0.75
58 19 0.22
59 2 0.02
ACGTcount: A:0.35, C:0.06, G:0.14, T:0.45
Consensus pattern (57 bp):
TGGTGCTATTTTAGTAATTAATTCAAAAAAAGTGTTATTTTAGTAATTAATTCAAAA
Found at i:1564089 original size:24 final size:24
Alignment explanation
Indices: 1564044--1564108 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 24
1564034 AAACATAATT
* * * *
1564044 CAGGTCAGGTAACAGATCAAAATC
1 CAGGTCAAGTATCATATAAAAATC
* *
1564068 CATGTCAAGTATCATATAAAAATT
1 CAGGTCAAGTATCATATAAAAATC
*
1564092 TAGGTCAAGTATCATAT
1 CAGGTCAAGTATCATAT
1564109 CAGATAACTA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (24 bp):
CAGGTCAAGTATCATATAAAAATC
Found at i:1564830 original size:29 final size:29
Alignment explanation
Indices: 1564798--1564975 Score: 220
Period size: 29 Copynumber: 6.2 Consensus size: 29
1564788 CATTTTACAG
** *
1564798 AAATAACACCATTTTTAAAATAATTACTA
1 AAATAACACCATTTTCGAATTAATTACTA
*
1564827 AAATAGCACCTATTTT-GAATTAATTACTA
1 AAATAACACC-ATTTTCGAATTAATTACTA
* *
1564856 AAATAGCACCA-TTTCAAATTAATTACTA
1 AAATAACACCATTTTCGAATTAATTACTA
1564884 AAATAACA-CATATTTCGAATTAATTACTA
1 AAATAACACCAT-TTTCGAATTAATTACTA
* *
1564913 AAATATCACCAATTTCGAATTAATTACTA
1 AAATAACACCATTTTCGAATTAATTACTA
*
1564942 AAATAACA-CTTATTTCGAATTAATTACTA
1 AAATAACACCAT-TTTCGAATTAATTACTA
1564971 AAATA
1 AAATA
1564976 GAACCTGATC
Statistics
Matches: 132, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
27 5 0.04
28 21 0.16
29 99 0.75
30 7 0.05
ACGTcount: A:0.47, C:0.15, G:0.03, T:0.35
Consensus pattern (29 bp):
AAATAACACCATTTTCGAATTAATTACTA
Found at i:1564956 original size:58 final size:57
Alignment explanation
Indices: 1564798--1564976 Score: 259
Period size: 58 Copynumber: 3.1 Consensus size: 57
1564788 CATTTTACAG
* * * * * *
1564798 AAATAACACCATTTTTAAAATAATTACTAAAATAGCACCTATTTTGAATTAATTACTA
1 AAATAGCACCA-TTTCAAATTAATTACTAAAATAACACATATTTCGAATTAATTACTA
1564856 AAATAGCACCATTTCAAATTAATTACTAAAATAACACATATTTCGAATTAATTACTA
1 AAATAGCACCATTTCAAATTAATTACTAAAATAACACATATTTCGAATTAATTACTA
* * *
1564913 AAATATCACCAATTTCGAATTAATTACTAAAATAACACTTATTTCGAATTAATTACTA
1 AAATAGCACC-ATTTCAAATTAATTACTAAAATAACACATATTTCGAATTAATTACTA
1564971 AAATAG
1 AAATAG
1564977 AACCTGATCA
Statistics
Matches: 110, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
57 50 0.45
58 60 0.55
ACGTcount: A:0.47, C:0.15, G:0.04, T:0.35
Consensus pattern (57 bp):
AAATAGCACCATTTCAAATTAATTACTAAAATAACACATATTTCGAATTAATTACTA
Found at i:1575081 original size:22 final size:24
Alignment explanation
Indices: 1575042--1575086 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
1575032 TTCAAGTGAA
*
1575042 TTAATCTATTTTAAAAA-TATTTT
1 TTAATCTATTATAAAAATTATTTT
*
1575065 TTAAT-TATTATATAAATTATTT
1 TTAATCTATTATAAAAATTATTT
1575087 AAACACTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (24 bp):
TTAATCTATTATAAAAATTATTTT
Found at i:1586199 original size:3 final size:3
Alignment explanation
Indices: 1586186--1586246 Score: 113
Period size: 3 Copynumber: 20.0 Consensus size: 3
1586176 ATTTATTCAA
1586186 AAT AGAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1586232 AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT
1586247 GCATTTTTAC
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 54 0.95
4 3 0.05
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1586553 original size:40 final size:40
Alignment explanation
Indices: 1586466--1586580 Score: 112
Period size: 40 Copynumber: 2.9 Consensus size: 40
1586456 GGTTTGACAT
* * *
1586466 AACCTAAAATATTACCATCTTCAT-A-ATATTATCGATT--C
1 AACCGAAAATATTACAATCTTCATAACATTTTAT-G-TTGGC
* * * * *
1586504 AACCTAAAATGTTATATTCTTCATAACATTTTTTGTTGGC
1 AACCGAAAATATTACAATCTTCATAACATTTTATGTTGGC
1586544 AACCGAAAATATTACAATCTTCATAACATTTTATGTT
1 AACCGAAAATATTACAATCTTCATAACATTTTATGTT
1586581 TAACAAAAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
38 22 0.35
39 2 0.03
40 38 0.61
ACGTcount: A:0.37, C:0.17, G:0.06, T:0.40
Consensus pattern (40 bp):
AACCGAAAATATTACAATCTTCATAACATTTTATGTTGGC
Found at i:1588549 original size:2 final size:2
Alignment explanation
Indices: 1588544--1588571 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1588534 CGACACACAA
1588544 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
1588572 TATTTTCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1588731 original size:21 final size:21
Alignment explanation
Indices: 1588705--1588750 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
1588695 TATCGCAGTT
1588705 GCGGACATAACGAATTCCATC
1 GCGGACATAACGAATTCCATC
*
1588726 GCGGACATAACGAATTCCATT
1 GCGGACATAACGAATTCCATC
1588747 GCGG
1 GCGG
1588751 TCACTAGGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.30, C:0.26, G:0.24, T:0.20
Consensus pattern (21 bp):
GCGGACATAACGAATTCCATC
Found at i:1589217 original size:13 final size:13
Alignment explanation
Indices: 1589201--1589225 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1589191 AACATCACCT
1589201 TAAAACTAAAAAC
1 TAAAACTAAAAAC
1589214 TAAAACTAAAAA
1 TAAAACTAAAAA
1589226 TTAATATCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.12, G:0.00, T:0.16
Consensus pattern (13 bp):
TAAAACTAAAAAC
Found at i:1589604 original size:76 final size:77
Alignment explanation
Indices: 1589507--1589656 Score: 248
Period size: 77 Copynumber: 2.0 Consensus size: 77
1589497 ACCAAGCACA
* *
1589507 AGCTGAAAATCGGAGAAATAGGGAAAAGTGTA-TTTTTTGGCTTTAACTATGTGAATTTGTCAGG
1 AGCTGAAAATCAGAGAAATAGGGAAAAGGGTATTTTTTTGGCTTTAACTATGTGAATTTGTCAGG
*
1589571 TTCGATTTAATG
66 TTCAATTTAATG
* *
1589583 AGCTGAAAATCAGAGAAATAGGGAAAAGGGTATTTTTTTTGCTTTAATTATGTGAATTTGTCAGG
1 AGCTGAAAATCAGAGAAATAGGGAAAAGGGTATTTTTTTGGCTTTAACTATGTGAATTTGTCAGG
1589648 TTCAATTTA
66 TTCAATTTA
1589657 CTGTTAAACA
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
76 30 0.44
77 38 0.56
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.37
Consensus pattern (77 bp):
AGCTGAAAATCAGAGAAATAGGGAAAAGGGTATTTTTTTGGCTTTAACTATGTGAATTTGTCAGG
TTCAATTTAATG
Found at i:1590898 original size:25 final size:25
Alignment explanation
Indices: 1590864--1590913 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
1590854 TTACACTCTC
1590864 ACAATCATAGATCACAAATGAATTG
1 ACAATCATAGATCACAAATGAATTG
*
1590889 ACAATCATAGATCACAATTGAATTG
1 ACAATCATAGATCACAAATGAATTG
1590914 TAATATGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.46, C:0.16, G:0.12, T:0.26
Consensus pattern (25 bp):
ACAATCATAGATCACAAATGAATTG
Found at i:1600154 original size:9 final size:9
Alignment explanation
Indices: 1600140--1600238 Score: 81
Period size: 9 Copynumber: 10.3 Consensus size: 9
1600130 GCTGCTGGAA
1600140 ACCGGTTTG
1 ACCGGTTTG
*
1600149 ACCGGTTTTCA
1 ACCGG-TTT-G
*
1600160 ACCTGTTCTG
1 ACCGGTT-TG
1600170 ACCGGTTTG
1 ACCGGTTTG
*
1600179 ACCGGTTTCA
1 ACCGGTTT-G
*
1600189 ACCGGTTCG
1 ACCGGTTTG
1600198 AACCGGTTTG
1 -ACCGGTTTG
*
1600208 ACCGGTCTG
1 ACCGGTTTG
*
1600217 AATCGGTTTG
1 -ACCGGTTTG
*
1600227 ACCGGTCTG
1 ACCGGTTTG
1600236 ACC
1 ACC
1600239 CGACCGTTGA
Statistics
Matches: 71, Mismatches: 13, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
9 33 0.46
10 33 0.46
11 5 0.07
ACGTcount: A:0.15, C:0.27, G:0.27, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:1600194 original size:19 final size:19
Alignment explanation
Indices: 1600139--1600232 Score: 84
Period size: 19 Copynumber: 4.8 Consensus size: 19
1600129 GGCTGCTGGA
1600139 AACCGGTTTGACCGGTTTTC
1 AACCGGTTTGACCGG-TTTC
*
1600159 AACCTGTTCTGACCGGTTT-
1 AACCGGTT-TGACCGGTTTC
* *
1600178 GACCGGTTTCAACCGG-TTC
1 AACCGGTTT-GACCGGTTTC
* *
1600197 GAACCGGTTTGACCGGTCTG
1 -AACCGGTTTGACCGGTTTC
*
1600217 AATCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
1600233 CTGACCCGAC
Statistics
Matches: 60, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
18 3 0.05
19 31 0.52
20 19 0.32
21 7 0.12
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.31
Consensus pattern (19 bp):
AACCGGTTTGACCGGTTTC
Found at i:1600202 original size:29 final size:30
Alignment explanation
Indices: 1600139--1600238 Score: 118
Period size: 29 Copynumber: 3.4 Consensus size: 30
1600129 GGCTGCTGGA
*
1600139 AACCGGTTTGACCGGTTTTCAACCTGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
1600170 -ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
* * *
1600198 AACCGGTTTGACCGGTCTGAATCGGTT-TG
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
*
1600227 -ACCGGTCTGACC
1 AACCGGTTTGACC
1600239 CGACCGTTGA
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
28 12 0.19
29 36 0.58
30 14 0.23
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:1600257 original size:17 final size:17
Alignment explanation
Indices: 1600252--1600289 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
1600242 CCGTTGACCC
1600252 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
1600269 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
1600286 GACC
1 GACC
1600290 GTTGACCGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.18, C:0.47, G:0.24, T:0.11
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:1600262 original size:22 final size:22
Alignment explanation
Indices: 1600235--1600296 Score: 97
Period size: 22 Copynumber: 2.7 Consensus size: 22
1600225 TGACCGGTCT
1600235 GACCCGACCGTTGACCCGACCC
1 GACCCGACCGTTGACCCGACCC
1600257 GACCCGACCGTTGACCCGACCC
1 GACCCGACCGTTGACCCGACCC
*
1600279 GACCGTTGACCGTTGACC
1 GACC--CGACCGTTGACC
1600297 GTTGACCGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
22 26 0.70
24 11 0.30
ACGTcount: A:0.18, C:0.45, G:0.24, T:0.13
Consensus pattern (22 bp):
GACCCGACCGTTGACCCGACCC
Found at i:1600289 original size:7 final size:7
Alignment explanation
Indices: 1600279--1600316 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
1600269 GACCCGACCC
1600279 GACCGTT
1 GACCGTT
1600286 GACCGTT
1 GACCGTT
1600293 GACCGTT
1 GACCGTT
1600300 GACCGTT
1 GACCGTT
1600307 GACCGTT
1 GACCGTT
1600314 GAC
1 GAC
1600317 TTTCTTTGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:1600289 original size:12 final size:12
Alignment explanation
Indices: 1600234--1600277 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
1600224 TTGACCGGTC
1600234 TGACCCGACCGT
1 TGACCCGACCGT
1600246 TGACCCGACC--
1 TGACCCGACCGT
*
1600256 CGACCCGACCGT
1 TGACCCGACCGT
1600268 TGACCCGACC
1 TGACCCGACC
1600278 CGACCGTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 9 0.32
12 19 0.68
ACGTcount: A:0.18, C:0.48, G:0.23, T:0.11
Consensus pattern (12 bp):
TGACCCGACCGT
Found at i:1601261 original size:32 final size:31
Alignment explanation
Indices: 1601177--1601253 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
1601167 CTAATGTGAC
* *
1601177 TCTTAGGTAGGCTCTGCGGCCCTGAGATTAT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGATTAT
** *
1601208 TCTCGGGTAGGCCCTGCGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGAT-TAT
1601240 TCTTAGGTAGGCCC
1 TCTTAGGTAGGCCC
1601254 CACGGCCCCG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 24 0.63
32 14 0.37
ACGTcount: A:0.14, C:0.26, G:0.31, T:0.29
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCGGCCCTAAGATTAT
Found at i:1607507 original size:9 final size:9
Alignment explanation
Indices: 1607493--1607583 Score: 74
Period size: 10 Copynumber: 9.4 Consensus size: 9
1607483 GCTGCTGGAA
1607493 ACCGGTTTG
1 ACCGGTTTG
*
1607502 ACCGGTTTTCA
1 ACCGG-TTT-G
1607513 ACCGGTTCTG
1 ACCGGTT-TG
1607523 ACCGGTTTG
1 ACCGGTTTG
*
1607532 ACCGGTTTCA
1 ACCGGTTT-G
* *
1607542 ATCGGTTCG
1 ACCGGTTTG
1607551 AACCGGTTTG
1 -ACCGGTTTG
*
1607561 ACCGGTCTG
1 ACCGGTTTG
*
1607570 AATCGGTTTG
1 -ACCGGTTTG
1607580 ACCG
1 ACCG
1607584 CTCCGCTCCG
Statistics
Matches: 64, Mismatches: 12, Indels: 12
0.73 0.14 0.14
Matches are distributed among these distances:
9 26 0.41
10 32 0.50
11 6 0.09
ACGTcount: A:0.15, C:0.25, G:0.29, T:0.31
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:1607517 original size:20 final size:21
Alignment explanation
Indices: 1607492--1607530 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1607482 GGCTGCTGGA
1607492 AACCGGTT-TGACCGGTTTTC
1 AACCGGTTCTGACCGGTTTTC
1607512 AACCGGTTCTGACCGGTTT
1 AACCGGTTCTGACCGGTTT
1607531 GACCGGTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.15, C:0.26, G:0.26, T:0.33
Consensus pattern (21 bp):
AACCGGTTCTGACCGGTTTTC
Found at i:1607537 original size:19 final size:20
Alignment explanation
Indices: 1607492--1607583 Score: 93
Period size: 19 Copynumber: 4.7 Consensus size: 20
1607482 GGCTGCTGGA
* *
1607492 AACCGGTTTGACCGGTTTTC
1 AACCGGTTTGACCGGTTCTG
1607512 AACCGGTTCTGACCGGTT-TG
1 AACCGGTT-TGACCGGTTCTG
* *
1607532 -ACCGGTTTCAATCGGTTC-G
1 AACCGGTTT-GACCGGTTCTG
1607551 AACCGGTTTGACCGG-TCTG
1 AACCGGTTTGACCGGTTCTG
*
1607570 AATCGGTTTGACCG
1 AACCGGTTTGACCG
1607584 CTCCGCTCCG
Statistics
Matches: 61, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
18 3 0.05
19 32 0.52
20 17 0.28
21 9 0.15
ACGTcount: A:0.16, C:0.25, G:0.28, T:0.30
Consensus pattern (20 bp):
AACCGGTTTGACCGGTTCTG
Found at i:1607555 original size:29 final size:30
Alignment explanation
Indices: 1607492--1607577 Score: 122
Period size: 29 Copynumber: 2.9 Consensus size: 30
1607482 GGCTGCTGGA
*
1607492 AACCGGTTTGACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAATCGGTTCTG
1607523 -ACCGGTTTGACCGGTTTCAATCGGTTC-G
1 AACCGGTTTGACCGGTTTCAATCGGTTCTG
* *
1607551 AACCGGTTTGACCGGTCTGAATCGGTT
1 AACCGGTTTGACCGGTTTCAATCGGTT
1607578 TGACCGCTCC
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
28 1 0.02
29 36 0.71
30 14 0.27
ACGTcount: A:0.16, C:0.24, G:0.28, T:0.31
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAATCGGTTCTG
Found at i:1608588 original size:32 final size:31
Alignment explanation
Indices: 1608504--1608580 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
1608494 CTAATGTGAC
* *
1608504 TCTTAGGTAGGCTCTGCGGCCCTGAGATTAT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGATTAT
** *
1608535 TCTCGGGTAGGCCCTGCGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGAT-TAT
1608567 TCTTAGGTAGGCCC
1 TCTTAGGTAGGCCC
1608581 CACGGCCCCG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 24 0.63
32 14 0.37
ACGTcount: A:0.14, C:0.26, G:0.31, T:0.29
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCGGCCCTAAGATTAT
Found at i:1624820 original size:18 final size:18
Alignment explanation
Indices: 1624794--1624828 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1624784 TCCGTCCGAT
1624794 CTTAATATTTAATTCAAA
1 CTTAATATTTAATTCAAA
* *
1624812 CTTATTATTTACTTCAA
1 CTTAATATTTAATTCAA
1624829 TCCTTTCGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.14, G:0.00, T:0.49
Consensus pattern (18 bp):
CTTAATATTTAATTCAAA
Found at i:1627798 original size:89 final size:91
Alignment explanation
Indices: 1627638--1627821 Score: 293
Period size: 89 Copynumber: 2.0 Consensus size: 91
1627628 GAACTATGTT
* * * * *
1627638 CGTAGGGCTTACCCTAAGCACATAGCAAAAGGGATCCAACCTAAGGATATTCCTTGGGGCCTATG
1 CGTAGGGCTTACCCTAAGCACACAACAAAAGGAAACCAACATAAGGATATTCCTTGGGGCCTATG
1627703 GGCCTACCCAAGGGTATCCTT-AGATC
66 GGCCTACCCAAGGGTATCCTTAAG-TC
1627729 CGTAGGG-TTACCCTAAGCACACAAC-AAAGGAAACCAACATAAGGATATTCCTTGGGGCCTATG
1 CGTAGGGCTTACCCTAAGCACACAACAAAAGGAAACCAACATAAGGATATTCCTTGGGGCCTATG
1627792 GGCCTACCCAAGGGTATCCTTAAGTC
66 GGCCTACCCAAGGGTATCCTTAAGTC
1627818 CGTA
1 CGTA
1627822 AGGTCTTATC
Statistics
Matches: 87, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
89 62 0.71
90 18 0.21
91 7 0.08
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.21
Consensus pattern (91 bp):
CGTAGGGCTTACCCTAAGCACACAACAAAAGGAAACCAACATAAGGATATTCCTTGGGGCCTATG
GGCCTACCCAAGGGTATCCTTAAGTC
Found at i:1631965 original size:101 final size:101
Alignment explanation
Indices: 1631790--1631991 Score: 404
Period size: 101 Copynumber: 2.0 Consensus size: 101
1631780 CAAACCAGCT
1631790 GCAGAAAGTTCAAATTGTTAACGAAGTTAATAAGGTAATAGAAACTTACTCCTTTACTATTGTTA
1 GCAGAAAGTTCAAATTGTTAACGAAGTTAATAAGGTAATAGAAACTTACTCCTTTACTATTGTTA
1631855 TTACTGCAGTTATAATTTACCATGTATTGTCTCCCC
66 TTACTGCAGTTATAATTTACCATGTATTGTCTCCCC
1631891 GCAGAAAGTTCAAATTGTTAACGAAGTTAATAAGGTAATAGAAACTTACTCCTTTACTATTGTTA
1 GCAGAAAGTTCAAATTGTTAACGAAGTTAATAAGGTAATAGAAACTTACTCCTTTACTATTGTTA
1631956 TTACTGCAGTTATAATTTACCATGTATTGTCTCCCC
66 TTACTGCAGTTATAATTTACCATGTATTGTCTCCCC
1631992 TCATATTTTT
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 101 1.00
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.37
Consensus pattern (101 bp):
GCAGAAAGTTCAAATTGTTAACGAAGTTAATAAGGTAATAGAAACTTACTCCTTTACTATTGTTA
TTACTGCAGTTATAATTTACCATGTATTGTCTCCCC
Found at i:1640644 original size:55 final size:55
Alignment explanation
Indices: 1640577--1640682 Score: 167
Period size: 55 Copynumber: 1.9 Consensus size: 55
1640567 TCGACCTTTT
* * **
1640577 TTTTTTTTAATTATTGATAGTTATCTTTTAAAACATTCATCATTCTTTGCATCTA
1 TTTTTTTCAATTATTGACAGACATCTTTTAAAACATTCATCATTCTTTGCATCTA
*
1640632 TTTTTTTCAATTATTGACAGACATCTTTTAAAACATTCATCATTTTTTGCA
1 TTTTTTTCAATTATTGACAGACATCTTTTAAAACATTCATCATTCTTTGCA
1640683 CAAATATAAG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 46 1.00
ACGTcount: A:0.28, C:0.14, G:0.06, T:0.52
Consensus pattern (55 bp):
TTTTTTTCAATTATTGACAGACATCTTTTAAAACATTCATCATTCTTTGCATCTA
Found at i:1648743 original size:22 final size:24
Alignment explanation
Indices: 1648702--1648745 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
1648692 AACTAATTAG
1648702 ATATAATTAAAAGAAATAAAAATA
1 ATATAATTAAAAGAAATAAAAATA
1648726 ATATAATT-AAA-AAATAAAAA
1 ATATAATTAAAAGAAATAAAAA
1648746 ATGTTAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 9 0.45
23 3 0.15
24 8 0.40
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (24 bp):
ATATAATTAAAAGAAATAAAAATA
Found at i:1653282 original size:42 final size:42
Alignment explanation
Indices: 1653224--1653409 Score: 194
Period size: 42 Copynumber: 4.4 Consensus size: 42
1653214 TGCTTATATA
* * * *
1653224 AAAACACCACGAAAGTATGAGTATTTAGCGGCGTTTATGCTT
1 AAAACGCCACTAAAGTAAGAGTATTTAGCGGCGTTTGTGCTT
* * *
1653266 AAAATGACACTAAAGTAAGAGTCTTTAGCGGCGTTTGTGCTT
1 AAAACGCCACTAAAGTAAGAGTATTTAGCGGCGTTTGTGCTT
* * * * *
1653308 AAAACGCCGCTAAAGCACGAGTATTTATCGGCGTTTGTTCTT
1 AAAACGCCACTAAAGTAAGAGTATTTAGCGGCGTTTGTGCTT
* * * * * *
1653350 AAAGCGTCGCTAAAG-AAGGAGTATTCAGCGGCATTTGTTCTT
1 AAAACGCCACTAAAGTAA-GAGTATTTAGCGGCGTTTGTGCTT
1653392 AAAACGCCACTAAAGTAA
1 AAAACGCCACTAAAGTAA
1653410 TGTGATACTA
Statistics
Matches: 118, Mismatches: 24, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
41 1 0.01
42 115 0.97
43 2 0.02
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (42 bp):
AAAACGCCACTAAAGTAAGAGTATTTAGCGGCGTTTGTGCTT
Found at i:1657313 original size:42 final size:42
Alignment explanation
Indices: 1657261--1657564 Score: 333
Period size: 42 Copynumber: 7.1 Consensus size: 42
1657251 GTTTTAATTC
* * *
1657261 GCGGCGTTTGTAT-AAAAAACGCTGCTATAGATCTGACTTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCTGACCTTTT
* *
1657303 GCGGCATTTGTTTCAAAAACGCCGCTATAGATCTGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTT
* * * *
1657345 GCGGTGTTTGTTCCAAAAACACTGCTATAGATCTGACATTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTT
** * *
1657387 GTTGCCTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCTGACCTTTT
* * * *
1657430 ACGGCGTTTGTTCCAAAAACGCCGTTATCGATATGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTT
* **
1657472 GCGGCGTTTTATATCCAAAAACGCCGCTATAGATCTCGGTCTTTT
1 GCGGCG-TTTGT-TCCAAAAACGCCGCTATAGATCT-GACCTTTT
* *
1657517 GCGGCGTTTGTTCCAAAAACGTCGCGATAGATCTTGA-CTTATT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATC-TGACCTT-TT
1657560 GCGGC
1 GCGGC
1657565 ATTTTTTGTT
Statistics
Matches: 220, Mismatches: 35, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
41 1 0.00
42 116 0.53
43 66 0.30
44 25 0.11
45 12 0.05
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (42 bp):
GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTT
Found at i:1657427 original size:85 final size:85
Alignment explanation
Indices: 1657261--1657568 Score: 354
Period size: 85 Copynumber: 3.6 Consensus size: 85
1657251 GTTTTAATTC
* * *
1657261 GCGGCGTTTGTAT-AAAAAACGCTGCTATAGATCTGACTTTTTGCGGCATTTGT-TTCAAAAACG
1 GCGGCGTTTGT-TCCAAAAACGCTGCTATAGATCTGACATTTTGCGGCATTTGTATCCAAAAACG
1657324 CCGCTATAGATCTGACCTTTT
65 CCGCTATAGATCTGACCTTTT
* * ** *
1657345 GCGGTGTTTGTTCCAAAAACACTGCTATAGATCTGACATTTTGTTGCCTTTGTATCCAAAAACGC
1 GCGGCGTTTGTTCCAAAAACGCTGCTATAGATCTGACATTTTGCGGCATTTGTATCCAAAAACGC
*
1657410 CGCTATAGATATGACCTTTT
66 CGCTATAGATCTGACCTTTT
* * * * * * * *
1657430 ACGGCGTTTGTTCCAAAAACGCCGTTATCGATATGACCTTTTGCGGCGTTTTATATCCAAAAACG
1 GCGGCGTTTGTTCCAAAAACGCTGCTATAGATCTGACATTTTGCGGC-ATTTGTATCCAAAAACG
**
1657495 CCGCTATAGATCTCGGTCTTTT
65 CCGCTATAGATCT-GACCTTTT
*
1657517 GCGGCGTTTGTTCCAAAAACG-TCGCGATAGATCTTGAC-TTATTGCGGCATTT
1 GCGGCGTTTGTTCCAAAAACGCT-GCTATAGATC-TGACATT-TTGCGGCATTT
1657569 TTTGTTCACA
Statistics
Matches: 186, Mismatches: 31, Indels: 11
0.82 0.14 0.05
Matches are distributed among these distances:
83 1 0.01
84 44 0.24
85 66 0.35
86 27 0.15
87 37 0.20
88 11 0.06
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (85 bp):
GCGGCGTTTGTTCCAAAAACGCTGCTATAGATCTGACATTTTGCGGCATTTGTATCCAAAAACGC
CGCTATAGATCTGACCTTTT
Found at i:1658622 original size:29 final size:29
Alignment explanation
Indices: 1658580--1658638 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1658570 TATAGTATGC
1658580 CTTTCAAAAACACATTTAACTTGATATAT
1 CTTTCAAAAACACATTTAACTTGATATAT
1658609 CTTTCAAAAACACATTTAACTTGATATAT
1 CTTTCAAAAACACATTTAACTTGATATAT
1658638 C
1 C
1658639 GTTATCTATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.41, C:0.19, G:0.03, T:0.37
Consensus pattern (29 bp):
CTTTCAAAAACACATTTAACTTGATATAT
Found at i:1667400 original size:31 final size:31
Alignment explanation
Indices: 1667362--1667486 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
1667352 CCCGAAGGAC
* *
1667362 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
1667393 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1667424 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1667455 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1667486 C
1 C
1667487 CCTCGACCCT
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 86 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:1667689 original size:23 final size:24
Alignment explanation
Indices: 1667663--1667709 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
1667653 ATATACTTGT
*
1667663 TTTCACATATATA-TTTCATATCA
1 TTTCACATATACACTTTCATATCA
1667686 TTTCACATATACACTTTCATATCA
1 TTTCACATATACACTTTCATATCA
1667710 CATGCCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTCACATATACACTTTCATATCA
Found at i:1671370 original size:31 final size:31
Alignment explanation
Indices: 1671332--1671456 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
1671322 CCCGAAGGAC
* *
1671332 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
1671363 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1671394 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1671425 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1671456 C
1 C
1671457 CCTCGACCCT
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 86 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:1671660 original size:23 final size:22
Alignment explanation
Indices: 1671633--1671677 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1671623 CATATACTTG
*
1671633 TTTCACATATATATTTCATATCA
1 TTTCACATACA-ATTTCATATCA
*
1671656 TTTCACATACACTTTCATATCA
1 TTTCACATACAATTTCATATCA
1671678 CATGCCATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.33, C:0.22, G:0.00, T:0.44
Consensus pattern (22 bp):
TTTCACATACAATTTCATATCA
Found at i:1672302 original size:21 final size:21
Alignment explanation
Indices: 1672272--1672316 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1672262 ATTCTGTCGT
*
1672272 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
1672293 TTGAATGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
1672314 TTG
1 TTG
1672317 CCCAGAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.16, C:0.22, G:0.29, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:1675333 original size:31 final size:31
Alignment explanation
Indices: 1675295--1675419 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
1675285 CCCGAAGGAC
* *
1675295 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
1675326 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1675357 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1675388 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1675419 C
1 C
1675420 CCTCGACCCT
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 86 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:1675623 original size:23 final size:24
Alignment explanation
Indices: 1675597--1675643 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
1675587 ATATACTTGT
*
1675597 TTTCACATATATA-TTTCATATCA
1 TTTCACATATACACTTTCATATCA
1675620 TTTCACATATACACTTTCATATCA
1 TTTCACATATACACTTTCATATCA
1675644 CATGCCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTCACATATACACTTTCATATCA
Found at i:1676274 original size:21 final size:21
Alignment explanation
Indices: 1676244--1676288 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1676234 ATTCTGTCGT
* *
1676244 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1676265 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1676286 TTG
1 TTG
1676289 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1680312 original size:18 final size:18
Alignment explanation
Indices: 1680289--1680328 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
1680279 ATCCGGCCCA
1680289 TTGACATCCTAGACCTAG
1 TTGACATCCTAGACCTAG
1680307 TTGACATCCTAGACCTAG
1 TTGACATCCTAGACCTAG
1680325 TTGA
1 TTGA
1680329 TGTGGAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (18 bp):
TTGACATCCTAGACCTAG
Found at i:1691607 original size:99 final size:99
Alignment explanation
Indices: 1691436--1691635 Score: 373
Period size: 99 Copynumber: 2.0 Consensus size: 99
1691426 CGAGTACCAC
*
1691436 GGAGGGCATTTCATAATTCGGAGGTCTCTTACGGAAGCTGCTCTCAACGTGGTGTTGGGGGTAGC
1 GGAGGGCATTTCATAATTCGGAAGTCTCTTACGGAAGCTGCTCTCAACGTGGTGTTGGGGGTAGC
1691501 CTACTATCTTACCTCCCCCTTACCCCATACATAT
66 CTACTATCTTACCTCCCCCTTACCCCATACATAT
* *
1691535 GGAGGGTATTTCATAATTCGGAAGTCTCTTACGGAAGCTGCTCTCAACGTTGTGTTGGGGGTAGC
1 GGAGGGCATTTCATAATTCGGAAGTCTCTTACGGAAGCTGCTCTCAACGTGGTGTTGGGGGTAGC
1691600 CTACTATCTTACCTCCCCCTTACCCCATACATAT
66 CTACTATCTTACCTCCCCCTTACCCCATACATAT
1691634 GG
1 GG
1691636 GAAAAAGGGA
Statistics
Matches: 98, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
99 98 1.00
ACGTcount: A:0.20, C:0.27, G:0.23, T:0.30
Consensus pattern (99 bp):
GGAGGGCATTTCATAATTCGGAAGTCTCTTACGGAAGCTGCTCTCAACGTGGTGTTGGGGGTAGC
CTACTATCTTACCTCCCCCTTACCCCATACATAT
Found at i:1698437 original size:20 final size:20
Alignment explanation
Indices: 1698414--1698494 Score: 126
Period size: 20 Copynumber: 4.0 Consensus size: 20
1698404 AAGATTATCG
1698414 GTGGGAATAAAATATTACCA
1 GTGGGAATAAAATATTACCA
1698434 GTGGGAATAAAATATTACCA
1 GTGGGAATAAAATATTACCA
* * *
1698454 GTGAGAATAAAAGATTTCCA
1 GTGGGAATAAAATATTACCA
*
1698474 GTGGGAATAAAAAATTACCA
1 GTGGGAATAAAATATTACCA
1698494 G
1 G
1698495 GGAATAGGAT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.46, C:0.10, G:0.21, T:0.23
Consensus pattern (20 bp):
GTGGGAATAAAATATTACCA
Found at i:1698688 original size:17 final size:15
Alignment explanation
Indices: 1698650--1698680 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1698640 AAATTCTAAA
*
1698650 TATTTAAATAAAAAT
1 TATTTATATAAAAAT
1698665 TATTTATATAAAAAT
1 TATTTATATAAAAAT
1698680 T
1 T
1698681 TTATTTATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTATATAAAAAT
Found at i:1699861 original size:58 final size:58
Alignment explanation
Indices: 1699771--1699887 Score: 234
Period size: 58 Copynumber: 2.0 Consensus size: 58
1699761 TATTAACCAA
1699771 TATACGCTATATAAACAATGCACTCCATTATGAAGGGTCAAAACCTCAAAAACTAACT
1 TATACGCTATATAAACAATGCACTCCATTATGAAGGGTCAAAACCTCAAAAACTAACT
1699829 TATACGCTATATAAACAATGCACTCCATTATGAAGGGTCAAAACCTCAAAAACTAACT
1 TATACGCTATATAAACAATGCACTCCATTATGAAGGGTCAAAACCTCAAAAACTAACT
1699887 T
1 T
1699888 TTCAAATCCA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.43, C:0.22, G:0.10, T:0.25
Consensus pattern (58 bp):
TATACGCTATATAAACAATGCACTCCATTATGAAGGGTCAAAACCTCAAAAACTAACT
Found at i:1703442 original size:23 final size:23
Alignment explanation
Indices: 1703404--1703447 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1703394 TGGAGGGGTA
*
1703404 CTGTAATCTGCTGATTACAAGCT
1 CTGTAATCTGCGGATTACAAGCT
*
1703427 CTGTAATTTGCGGATTACAAG
1 CTGTAATCTGCGGATTACAAG
1703448 AATACGTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (23 bp):
CTGTAATCTGCGGATTACAAGCT
Found at i:1703683 original size:22 final size:22
Alignment explanation
Indices: 1703655--1703733 Score: 140
Period size: 22 Copynumber: 3.6 Consensus size: 22
1703645 ATAATAATTT
*
1703655 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCAATA
*
1703677 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCAATA
1703699 TTTTAAAATAAATCAATCAATA
1 TTTTAAAATAAATCAATCAATA
1703721 TTTTAAAATAAAT
1 TTTTAAAATAAAT
1703734 TTTTTCATAT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 55 1.00
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCAATA
Found at i:1703743 original size:22 final size:22
Alignment explanation
Indices: 1703655--1703750 Score: 106
Period size: 22 Copynumber: 4.4 Consensus size: 22
1703645 ATAATAATTT
*
1703655 TTTTAAAATAAATCAA-TCTATA
1 TTTTAAAATAAATTAATTC-ATA
* *
1703677 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATTAATTCATA
*
1703699 TTTTAAAATAAATCAA-TCAATA
1 TTTTAAAATAAATTAATTC-ATA
**
1703721 TTTTAAAATAAATTTTTTCATA
1 TTTTAAAATAAATTAATTCATA
1703743 TTTTAAAA
1 TTTTAAAA
1703751 AAAAAATTTA
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
21 1 0.02
22 62 0.94
23 3 0.05
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (22 bp):
TTTTAAAATAAATTAATTCATA
Found at i:1707320 original size:106 final size:106
Alignment explanation
Indices: 1707135--1707560 Score: 681
Period size: 106 Copynumber: 4.0 Consensus size: 106
1707125 TGTATTGTTC
* * * * * * *
1707135 CGAGTCCAATATCCTCCGCCGTGAAGTTGAATTTGGTTCTGGAACTGGGAAATTGTTTATTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
*
1707200 ACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * *
1707241 CGAGTCTAATATCCTTCGATGTGAAGTTGAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* *
1707306 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCG
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
*
1707347 CGAGTCCAATACCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* *
1707412 ACCAGTCGTCCCTTCGTTGTGAAGTCGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * *
1707453 TGAGTCCAATATCCTTCGCTGTGAAGCTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
1707518 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
1707559 CG
1 CG
1707561 GGTGGGGCGA
Statistics
Matches: 294, Mismatches: 26, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
106 294 1.00
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (106 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:1708410 original size:36 final size:38
Alignment explanation
Indices: 1708356--1708432 Score: 122
Period size: 36 Copynumber: 2.1 Consensus size: 38
1708346 GAAACAATTT
*
1708356 CAAAGGTTTTTTTCCAAGGGAAACTGTCTCAAGAGAGA
1 CAAAGGTTTGTTTCCAAGGGAAACTGTCTCAAGAGAGA
*
1708394 CAAA-GTTTGTTT-CAAGGGAAACTGTCTTAAGAGAGA
1 CAAAGGTTTGTTTCCAAGGGAAACTGTCTCAAGAGAGA
1708430 CAA
1 CAA
1708433 TGGTGAGCAC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 26 0.70
37 7 0.19
38 4 0.11
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.26
Consensus pattern (38 bp):
CAAAGGTTTGTTTCCAAGGGAAACTGTCTCAAGAGAGA
Found at i:1708946 original size:18 final size:18
Alignment explanation
Indices: 1708919--1708954 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1708909 TGTTGAATCC
*
1708919 CCAAAGATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
1708937 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
1708955 TTGATGTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.33, G:0.08, T:0.17
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:1710024 original size:21 final size:19
Alignment explanation
Indices: 1710007--1710063 Score: 73
Period size: 18 Copynumber: 3.1 Consensus size: 19
1709997 TTCCTTTTGA
1710007 TTTTTGCTTCTTTTCTTTT
1 TTTTTGCTTCTTTTCTTTT
* * *
1710026 TTGTT-CTTGTTTT-TTCT
1 TTTTTGCTTCTTTTCTTTT
1710043 TTTTTGCTTCTTTTCTTTT
1 TTTTTGCTTCTTTTCTTTT
1710062 TT
1 TT
1710064 GTTCTTGATT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
17 7 0.23
18 14 0.47
19 9 0.30
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (19 bp):
TTTTTGCTTCTTTTCTTTT
Found at i:1710032 original size:15 final size:16
Alignment explanation
Indices: 1710007--1710069 Score: 74
Period size: 16 Copynumber: 3.8 Consensus size: 16
1709997 TTCCTTTTGA
1710007 TTTTTGCTTCTTTTCT
1 TTTTTGCTTCTTTTCT
*
1710023 TTTTTGTTCTTGTTTTTTCT
1 TTTTTG--C-T-TCTTTTCT
1710043 TTTTTGCTTCTTTTCT
1 TTTTTGCTTCTTTTCT
1710059 TTTTTG-TTCTT
1 TTTTTGCTTCTT
1710070 GATTGAATCT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
15 5 0.12
16 19 0.46
17 1 0.02
18 2 0.05
19 1 0.02
20 13 0.32
ACGTcount: A:0.00, C:0.14, G:0.08, T:0.78
Consensus pattern (16 bp):
TTTTTGCTTCTTTTCT
Found at i:1710069 original size:10 final size:10
Alignment explanation
Indices: 1710019--1710056 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
1710009 TTTGCTTCTT
1710019 TTCTTTTTTG
1 TTCTTTTTTG
1710029 TTCTTGTTTT-
1 TTCTT-TTTTG
1710039 TTCTTTTTTG
1 TTCTTTTTTG
1710049 CTTCTTTT
1 -TTCTTTT
1710057 CTTTTTTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 4 0.16
10 10 0.40
11 11 0.44
ACGTcount: A:0.00, C:0.13, G:0.08, T:0.79
Consensus pattern (10 bp):
TTCTTTTTTG
Found at i:1712501 original size:14 final size:14
Alignment explanation
Indices: 1712482--1712509 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1712472 ATCAGGGGGC
1712482 TCTCCAGGTAATAT
1 TCTCCAGGTAATAT
1712496 TCTCCAGGTAATAT
1 TCTCCAGGTAATAT
1712510 CCTGATCTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (14 bp):
TCTCCAGGTAATAT
Found at i:1714646 original size:9 final size:9
Alignment explanation
Indices: 1714622--1714694 Score: 51
Period size: 9 Copynumber: 7.7 Consensus size: 9
1714612 AAGATAATGG
*
1714622 AATAAGATA
1 AATAAAATA
1714631 AAT-AAATA
1 AATAAAATA
1714639 AATAAAATA
1 AATAAAATA
*
1714648 GGA-AAAATGA
1 -AATAAAAT-A
*
1714658 ATCAAAAAATA
1 A--ATAAAATA
1714669 AATAAAATAAA
1 AATAAAAT--A
1714680 AATAAAATA
1 AATAAAATA
1714689 AATAAA
1 AATAAA
1714695 CAAAACGAAG
Statistics
Matches: 52, Mismatches: 4, Indels: 16
0.72 0.06 0.22
Matches are distributed among these distances:
8 7 0.13
9 26 0.50
10 2 0.04
11 12 0.23
12 5 0.10
ACGTcount: A:0.74, C:0.01, G:0.05, T:0.19
Consensus pattern (9 bp):
AATAAAATA
Found at i:1714646 original size:13 final size:13
Alignment explanation
Indices: 1714587--1714699 Score: 58
Period size: 13 Copynumber: 8.6 Consensus size: 13
1714577 GAGATTATGA
*
1714587 AAATAAAATGAAT
1 AAATAAAATAAAT
*
1714600 ATAT-AAA-AAAT
1 AAATAAAATAAAT
* * *
1714611 AAAGATAATGGAAT
1 AAATAAAAT-AAAT
1714625 AAGAT-AAATAAAT
1 AA-ATAAAATAAAT
1714638 AAATAAAATAGGAA-
1 AAATAAAATA--AAT
*
1714652 AAATGAATCAAAAAAT
1 AAAT-AA--AATAAAT
1714668 AAATAAAAT-AA-
1 AAATAAAATAAAT
1714679 AAATAAAATAAAT
1 AAATAAAATAAAT
*
1714692 AAACAAAA
1 AAATAAAA
1714700 CGAAGGGAAA
Statistics
Matches: 75, Mismatches: 12, Indels: 26
0.66 0.11 0.23
Matches are distributed among these distances:
11 14 0.19
12 11 0.15
13 22 0.29
14 12 0.16
15 9 0.12
16 4 0.05
17 3 0.04
ACGTcount: A:0.72, C:0.02, G:0.07, T:0.19
Consensus pattern (13 bp):
AAATAAAATAAAT
Found at i:1714682 original size:15 final size:15
Alignment explanation
Indices: 1714662--1714694 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1714652 AAATGAATCA
1714662 AAAAAT-AAATAAAAT
1 AAAAATAAAAT-AAAT
1714677 AAAAATAAAATAAAT
1 AAAAATAAAATAAAT
1714692 AAA
1 AAA
1714695 CAAAACGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (15 bp):
AAAAATAAAATAAAT
Found at i:1714794 original size:2 final size:2
Alignment explanation
Indices: 1714787--1714834 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
1714777 AAATAACGTA
1714787 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
1714829 A- AT AT A
1 AT AT AT A
1714835 AATAAAATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1718574 original size:30 final size:30
Alignment explanation
Indices: 1718519--1718576 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1718509 CCGAAATTTA
* **
1718519 TTCGGTTCGGTTAATATTTTCAAAAAAAAG
1 TTCGGTTCGGTTAATAGTTAAAAAAAAAAG
*
1718549 TTCGGTTCGGTTAATGGTTAAAAAAAAA
1 TTCGGTTCGGTTAATAGTTAAAAAAAAA
1718577 TTCGATTAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (30 bp):
TTCGGTTCGGTTAATAGTTAAAAAAAAAAG
Found at i:1729760 original size:2 final size:2
Alignment explanation
Indices: 1729720--1729745 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1729710 TAAGTCGAAT
1729720 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1729746 ATTTTAAATA
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):
TA
Found at i:1735233 original size:206 final size:211
Alignment explanation
Indices: 1734850--1735233 Score: 670
Period size: 206 Copynumber: 1.8 Consensus size: 211
1734840 AGTTCACTGA
*
1734850 GCGAGTTTGCAATCGGTTCAGCCGATGGCTATGCAGAACTCATAGCGAAGCTGCCACAAACTTTA
1 GCGAGTTTGCAATCGGTTCAGCCGATGGCTATGCAGAACTCATAGCGAAGCTACCACAAACTTTA
1734915 AGTGGCTCCCAGCATAATGATAGGGAAGATACCGATGCCAAAAGATTTTAAGATTTTAAGGAGTT
66 AGTGGCTCCCAGCATAATGATAGGGAAGATACCGATGCC--AAGA---TAAGATTTTAAGGAGTT
*
1734980 TTCATGTAAATGCAGTTAGTATGGTTAACAAATATGCCTTGCAATATTTCCGTAAGGGTACTCTG
126 TTCATGTAAATGCAGTTAGTATGGTTAACAAATATGCCTTACAATATTTCCGTAAGGGTACTCTG
1735045 TGCCGGAATGTGTGTTGCAAT
191 TGCCGGAATGTGTGTTGCAAT
1735066 GCGAGTTTGCAATCGGTTCAGCCGATGGCTATGCAGAACTCATAGCGAAGCTACCACAAAC-TT-
1 GCGAGTTTGCAATCGGTTCAGCCGATGGCTATGCAGAACTCATAGCGAAGCTACCACAAACTTTA
1735129 AGTGGCTCCCAGCATAATGATAGGGAAGATACCGATGCC-A-A-AAGATTTTAAGGAGTTTTCAT
66 AGTGGCTCCCAGCATAATGATAGGGAAGATACCGATGCCAAGATAAGATTTTAAGGAGTTTTCAT
1735191 GTAAATGCAGTTAGTATGGTTAACAAATATGCCTTACAATATT
131 GTAAATGCAGTTAGTATGGTTAACAAATATGCCTTACAATATT
1735234 ACTAAATCAA
Statistics
Matches: 166, Mismatches: 2, Indels: 10
0.93 0.01 0.06
Matches are distributed among these distances:
206 63 0.38
210 1 0.01
211 1 0.01
214 39 0.23
215 2 0.01
216 60 0.36
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (211 bp):
GCGAGTTTGCAATCGGTTCAGCCGATGGCTATGCAGAACTCATAGCGAAGCTACCACAAACTTTA
AGTGGCTCCCAGCATAATGATAGGGAAGATACCGATGCCAAGATAAGATTTTAAGGAGTTTTCAT
GTAAATGCAGTTAGTATGGTTAACAAATATGCCTTACAATATTTCCGTAAGGGTACTCTGTGCCG
GAATGTGTGTTGCAAT
Found at i:1739088 original size:38 final size:38
Alignment explanation
Indices: 1739041--1739150 Score: 175
Period size: 39 Copynumber: 2.9 Consensus size: 38
1739031 GTTTTTGAAA
*
1739041 ATATATTATATAGTTTTGAAAATGATTTTTGAAAAGAT
1 ATATATTATATAGTTTTGAAAATGATTTTTGAAAAAAT
* *
1739079 ATATATTATATAGTTTTAAAAATTATTTTTTGAAAAAAT
1 ATATATTATATAGTTTTGAAAATGA-TTTTTGAAAAAAT
*
1739118 ATATATTATATGGTTTTGAAAATGATTTTTGAA
1 ATATATTATATAGTTTTGAAAATGATTTTTGAA
1739151 TATATATTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
38 31 0.48
39 34 0.52
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (38 bp):
ATATATTATATAGTTTTGAAAATGATTTTTGAAAAAAT
Found at i:1739149 original size:13 final size:13
Alignment explanation
Indices: 1739131--1739210 Score: 51
Period size: 13 Copynumber: 6.1 Consensus size: 13
1739121 TATTATATGG
1739131 TTTTGAAAATGAT-
1 TTTTGAAAAT-ATA
*
1739144 TTTTGAATATATA
1 TTTTGAAAATATA
*
1739157 TTTTGAATATATA
1 TTTTGAAAATATA
* *
1739170 -TAT-ATATATATTA
1 TTTTGA-AAATA-TA
1739183 GTTTTGAAAAT-TA
1 -TTTTGAAAATATA
1739196 TTTTTGAAAATATA
1 -TTTTGAAAATATA
1739210 T
1 T
1739211 ATATTATATA
Statistics
Matches: 55, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
11 1 0.02
12 9 0.16
13 37 0.67
14 2 0.04
15 5 0.09
16 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (13 bp):
TTTTGAAAATATA
Found at i:1739187 original size:53 final size:51
Alignment explanation
Indices: 1739092--1739210 Score: 148
Period size: 53 Copynumber: 2.3 Consensus size: 51
1739082 TATTATATAG
* * *
1739092 TTTTAAAAATTATTTTTTGAAAAAATATATATTATATGGTTTTGAAAATGAT
1 TTTTGAAAA-TATATTTTGAAAAAATATATATTATATAGTTTTGAAAATGAT
* * * *
1739144 TTTTGAATATATATTTTGAATATATATATATATATATTAGTTTTGAAAATTAT
1 TTTTGAAAATATATTTTGAAAAAATATATAT-TATA-TAGTTTTGAAAATGAT
1739197 TTTTGAAAATATAT
1 TTTTGAAAATATAT
1739211 ATATTATATA
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
51 19 0.33
52 11 0.19
53 27 0.47
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.50
Consensus pattern (51 bp):
TTTTGAAAATATATTTTGAAAAAATATATATTATATAGTTTTGAAAATGAT
Found at i:1739188 original size:40 final size:38
Alignment explanation
Indices: 1739144--1739271 Score: 156
Period size: 38 Copynumber: 3.4 Consensus size: 38
1739134 TGAAAATGAT
*
1739144 TTTTGAATATATATTTTGAATATATATATATATATATTAG
1 TTTTGAAAATATATTTTGAATATATATATAT-TATA-TAG
*
1739184 TTTTGAAAAT-TATTTTTGAAAATATATATATTATATAG
1 TTTTGAAAATATA-TTTTGAATATATATATATTATATAG
*
1739222 ATTTGAAAATGAT-TTTTGAATATATATATA-T-TATAG
1 TTTTGAAAAT-ATATTTTGAATATATATATATTATATAG
*
1739258 TTTTGAAAACATAT
1 TTTTGAAAATATAT
1739272 ATATAATATA
Statistics
Matches: 78, Mismatches: 6, Indels: 12
0.81 0.06 0.12
Matches are distributed among these distances:
35 2 0.03
36 14 0.18
37 1 0.01
38 28 0.36
39 6 0.08
40 27 0.35
ACGTcount: A:0.41, C:0.01, G:0.09, T:0.49
Consensus pattern (38 bp):
TTTTGAAAATATATTTTGAATATATATATATTATATAG
Found at i:1739213 original size:91 final size:90
Alignment explanation
Indices: 1739054--1739248 Score: 286
Period size: 91 Copynumber: 2.2 Consensus size: 90
1739044 TATTATATAG
*
1739054 TTTTGAAAATGAT-TTTTGAAAAGATATATATTATATAGTTTTAAAAATTATTTTTTGAAAAAAT
1 TTTTGAATAT-ATATTTTGAAAAGATATATATTATATAGTTTTAAAAATTATTTTTTGAAAAAAT
* *
1739118 ATATATTATATGGTTTTGAAAATGAT
65 ATATATTATATAGATTTGAAAATGAT
* * * *
1739144 TTTTGAATATATATTTTGAATATATATATATATATATTAGTTTTGAAAATTA-TTTTTGAAAATA
1 TTTTGAATATATATTTTGAAAAGATATATAT-TATA-TAGTTTTAAAAATTATTTTTTGAAAAAA
1739208 TATATATTATATAGATTTGAAAATGAT
64 TATATATTATATAGATTTGAAAATGAT
1739235 TTTTGAATATATAT
1 TTTTGAATATATAT
1739249 ATATTATAGT
Statistics
Matches: 95, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
89 2 0.02
90 25 0.26
91 54 0.57
92 14 0.15
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.49
Consensus pattern (90 bp):
TTTTGAATATATATTTTGAAAAGATATATATTATATAGTTTTAAAAATTATTTTTTGAAAAAATA
TATATTATATAGATTTGAAAATGAT
Found at i:1739227 original size:38 final size:39
Alignment explanation
Indices: 1739157--1739256 Score: 157
Period size: 38 Copynumber: 2.6 Consensus size: 39
1739147 TGAATATATA
* *
1739157 TTTTGAATATATATATATATATATTAGTTTTGAAAATTAT
1 TTTTGAATATATATATAT-TATATTAGATTTGAAAATGAT
*
1739197 TTTTGAAAATATATATATTATA-TAGATTTGAAAATGAT
1 TTTTGAATATATATATATTATATTAGATTTGAAAATGAT
1739235 TTTTGAATATATATATATTATA
1 TTTTGAATATATATATATTATA
1739257 GTTTTGAAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
38 35 0.62
39 4 0.07
40 17 0.30
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (39 bp):
TTTTGAATATATATATATTATATTAGATTTGAAAATGAT
Found at i:1739244 original size:36 final size:37
Alignment explanation
Indices: 1739144--1739266 Score: 144
Period size: 40 Copynumber: 3.2 Consensus size: 37
1739134 TGAAAATGAT
*
1739144 TTTTGAATAT-ATATTTTGAATATATATATATATATATTAG
1 TTTTGAAAATGAT-TTTTGAA-ATATATATAT-TATA-TAG
*
1739184 TTTTGAAAATTATTTTTGAAAATATATATATTATATAG
1 TTTTGAAAATGATTTTTG-AAATATATATATTATATAG
*
1739222 ATTTGAAAATGATTTTTG-AATATATATA-TATTATAG
1 TTTTGAAAATGATTTTTGAAATATATATATTA-TATAG
1739258 TTTTGAAAA
1 TTTTGAAAA
1739267 CATATATATA
Statistics
Matches: 76, Mismatches: 4, Indels: 10
0.84 0.04 0.11
Matches are distributed among these distances:
35 2 0.03
36 23 0.30
38 19 0.25
39 4 0.05
40 24 0.32
41 4 0.05
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (37 bp):
TTTTGAAAATGATTTTTGAAATATATATATTATATAG
Found at i:1739271 original size:27 final size:29
Alignment explanation
Indices: 1739241--1739306 Score: 95
Period size: 27 Copynumber: 2.4 Consensus size: 29
1739231 TGATTTTTGA
1739241 ATATATATATAT-TATAG-TTTTGAAAAC
1 ATATATATATATATATAGTTTTTGAAAAC
*
1739268 ATATATATA-ATATATAGTTTTTGAAAAT
1 ATATATATATATATATAGTTTTTGAAAAC
1739296 ATATA-ATATAT
1 ATATATATATAT
1739307 GGTTTTAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
26 2 0.06
27 17 0.49
28 16 0.46
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (29 bp):
ATATATATATATATATAGTTTTTGAAAAC
Found at i:1739283 original size:38 final size:38
Alignment explanation
Indices: 1739168--1739283 Score: 116
Period size: 38 Copynumber: 3.1 Consensus size: 38
1739158 TTTGAATATA
* *
1739168 TATATATATATAT-TAGTTTTGAAAATTATTTTTGAAAA
1 TATATATATATATATAGTTTTGAAAAATATTTTT-AATA
* *
1739206 TATATATAT-TATATAGATTTG-AAAATGATTTTTGA-A
1 TATATATATATATATAGTTTTGAAAAAT-ATTTTTAATA
* *
1739242 TATATATATAT-TATAGTTTTGAAAACATATATATAATA
1 TATATATATATATATAGTTTTGAAAA-ATATTTTTAATA
1739280 TATA
1 TATA
1739284 GTTTTTGAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
36 19 0.29
37 17 0.26
38 29 0.45
ACGTcount: A:0.44, C:0.01, G:0.08, T:0.47
Consensus pattern (38 bp):
TATATATATATATATAGTTTTGAAAAATATTTTTAATA
Found at i:1739316 original size:22 final size:24
Alignment explanation
Indices: 1739235--1739317 Score: 73
Period size: 23 Copynumber: 3.4 Consensus size: 24
1739225 TGAAAATGAT
*
1739235 TTTTGAATATATAT-ATATTATA-G
1 TTTTGAAAATATATAATA-TATAGG
*
1739258 TTTTGAAAACATATATATAATATATAGT
1 TTTTG--AA-A-ATATATAATATATAGG
1739286 TTTTGAAAATATATAATATAT-GG
1 TTTTGAAAATATATAATATATAGG
*
1739309 TTTTAAAAA
1 TTTTGAAAA
1739318 CATTTTGGAA
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
23 14 0.28
24 13 0.26
25 3 0.06
26 2 0.04
27 10 0.20
28 8 0.16
ACGTcount: A:0.45, C:0.01, G:0.08, T:0.46
Consensus pattern (24 bp):
TTTTGAAAATATATAATATATAGG
Found at i:1739382 original size:15 final size:16
Alignment explanation
Indices: 1739364--1739404 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
1739354 TTAAATAATA
1739364 TTATTTTTATTA-TTT
1 TTATTTTTATTATTTT
*
1739379 TTATTTATATTATTTT
1 TTATTTTTATTATTTT
1739395 TTATTTTTAT
1 TTATTTTTAT
1739405 ATTATTGCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (16 bp):
TTATTTTTATTATTTT
Found at i:1739389 original size:24 final size:23
Alignment explanation
Indices: 1739361--1739409 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 23
1739351 TATTTAAATA
1739361 ATATTATTTTTATTATTTTTAT-TT
1 ATATTA-TTTT-TTATTTTTATATT
1739385 ATATTATTTTTTATTTTTATATT
1 ATATTATTTTTTATTTTTATATT
1739408 AT
1 AT
1739410 TGCTTATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 10 0.42
23 8 0.33
24 6 0.25
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (23 bp):
ATATTATTTTTTATTTTTATATT
Found at i:1739391 original size:18 final size:18
Alignment explanation
Indices: 1739370--1739410 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1739360 AATATTATTT
1739370 TTATTATTTT-TATTTATA
1 TTATT-TTTTATATTTATA
*
1739388 TTATTTTTTATTTTTATA
1 TTATTTTTTATATTTATA
1739406 TTATT
1 TTATT
1739411 GCTTATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (18 bp):
TTATTTTTTATATTTATA
Found at i:1739407 original size:15 final size:15
Alignment explanation
Indices: 1739364--1739407 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
1739354 TTAAATAATA
1739364 TTATTTTTAT-TATTT
1 TTATTTTTATAT-TTT
*
1739379 TTATTTATATTATTTT
1 TTATTTTTA-TATTTT
1739395 TTATTTTTATATT
1 TTATTTTTATATT
1739408 ATTGCTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 12 0.48
16 12 0.48
17 1 0.04
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTATTTTTATATTTT
Found at i:1739416 original size:18 final size:18
Alignment explanation
Indices: 1739382--1739418 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1739372 ATTATTTTTA
**
1739382 TTTATATTATTTTTTATT
1 TTTATATTATTGCTTATT
1739400 TTTATATTATTGCTTATT
1 TTTATATTATTGCTTATT
1739418 T
1 T
1739419 ATTTAATTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.73
Consensus pattern (18 bp):
TTTATATTATTGCTTATT
Found at i:1739419 original size:22 final size:21
Alignment explanation
Indices: 1739361--1739422 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 21
1739351 TATTTAAATA
*
1739361 ATATTATTTTTA-TTATTTTT
1 ATATTATTATTATTTATTTTT
* *
1739381 ATTTATATTATTTTTTATTTTT
1 ATAT-TATTATTATTTATTTTT
*
1739403 ATATTATTGCTTATTTATTT
1 ATATTATT-ATTATTTATTT
1739423 AATTCTAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
20 3 0.09
21 10 0.30
22 20 0.61
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (21 bp):
ATATTATTATTATTTATTTTT
Found at i:1740507 original size:29 final size:30
Alignment explanation
Indices: 1740474--1740531 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
1740464 TTTTTAGTAA
*
1740474 CAATTTAATCC-CTAAATTTCAATTTATTT
1 CAATTTAATCCTCTAAATTTCAAGTTATTT
* * *
1740503 CAATTTGATCCTTTAAATTTTAAGTTATT
1 CAATTTAATCCTCTAAATTTCAAGTTATT
1740532 CATTTTCCTC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 10 0.42
30 14 0.58
ACGTcount: A:0.33, C:0.14, G:0.03, T:0.50
Consensus pattern (30 bp):
CAATTTAATCCTCTAAATTTCAAGTTATTT
Found at i:1740609 original size:14 final size:13
Alignment explanation
Indices: 1740560--1740608 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 13
1740550 TTAGTATGTT
1740560 TTTTATTTGTTTTA
1 TTTTATTT-TTTTA
1740574 TTTTA-TTTTTTA
1 TTTTATTTTTTTA
1740586 CTTCTTATTATTTTTA
1 -TT-TTATT-TTTTTA
1740602 TTTTATT
1 TTTTATT
1740609 ACTTTTAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
12 5 0.16
13 4 0.13
14 13 0.42
15 3 0.10
16 6 0.19
ACGTcount: A:0.16, C:0.04, G:0.02, T:0.78
Consensus pattern (13 bp):
TTTTATTTTTTTA
Found at i:1740614 original size:14 final size:13
Alignment explanation
Indices: 1740542--1740615 Score: 53
Period size: 14 Copynumber: 5.4 Consensus size: 13
1740532 CATTTTCCTC
*
1740542 TTTTAATTTTAGTA
1 TTTT-ATTTTATTA
* *
1740556 TGTT-TTTTATTTG
1 TTTTATTTTA-TTA
1740569 TTTTATTTTATT-
1 TTTTATTTTATTA
1740581 TTTTACTTCTTATTA
1 TTTTA-TT-TTATTA
1740596 TTTTTATTTTATTA
1 -TTTTATTTTATTA
1740610 CTTTTA
1 -TTTTA
1740616 AAATTTAACA
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
12 10 0.20
13 8 0.16
14 24 0.49
15 2 0.04
16 5 0.10
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.73
Consensus pattern (13 bp):
TTTTATTTTATTA
Found at i:1740621 original size:23 final size:23
Alignment explanation
Indices: 1740574--1740621 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1740564 ATTTGTTTTA
**
1740574 TTTTATTTTTTACTTCTTATTAT
1 TTTTATTTTTTACTTCTTAAAAT
1740597 TTTTATTTTATTACTT-TTAAAAT
1 TTTTATTTT-TTACTTCTTAAAAT
1740620 TT
1 TT
1740622 AACATTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (23 bp):
TTTTATTTTTTACTTCTTAAAAT
Found at i:1740703 original size:42 final size:41
Alignment explanation
Indices: 1740630--1740718 Score: 126
Period size: 42 Copynumber: 2.1 Consensus size: 41
1740620 TTAACATTTA
1740630 TTTTA-TTTTATTTTATTTTCCCCTTTGATTTATTTAATAT
1 TTTTATTTTTATTTTATTTTCCCCTTTGATTTATTTAATAT
* **
1740670 TTTTATTTTTATTTTTTTCTTTTCCTTTGATTTATTTAATAT
1 TTTTATTTTTATTTTATT-TTCCCCTTTGATTTATTTAATAT
1740712 TTCTTAT
1 TT-TTAT
1740719 ATAATATTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
40 5 0.12
41 11 0.26
42 23 0.53
43 4 0.09
ACGTcount: A:0.18, C:0.09, G:0.02, T:0.71
Consensus pattern (41 bp):
TTTTATTTTTATTTTATTTTCCCCTTTGATTTATTTAATAT
Done.