Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D01
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: 62811768
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 736185 characters in sequence are not A, C, G, or T
File 8 of 211
Found at i:2502892 original size:18 final size:18
Alignment explanation
Indices: 2502828--2502891 Score: 78
Period size: 19 Copynumber: 3.5 Consensus size: 18
2502818 ATAAAAAAAA
2502828 TTAAT-TTTTAT-TAAAAT
1 TTAATATTTTATCT-AAAT
*
2502845 TTAAATTTTTTATCTAAAT
1 TT-AATATTTTATCTAAAT
2502864 TTAATATTTTATCTAAATT
1 TTAATATTTTATCTAAA-T
2502883 TTAATATTT
1 TTAATATTT
2502892 AATATTTTTA
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
17 2 0.05
18 17 0.40
19 22 0.52
20 1 0.02
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (18 bp):
TTAATATTTTATCTAAAT
Found at i:2509101 original size:31 final size:31
Alignment explanation
Indices: 2509036--2509101 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
2509026 AATATCAGTA
* *
2509036 TTTTAATTTGATTAATTTTAATCTTTTAATT
1 TTTTAATTTGATTAATTTTAATCCTGTAATT
* *
2509067 TTTTGATTTGGTTAATTTTAATTCCTGTAATT
1 TTTTAATTTGATTAATTTTAA-TCCTGTAATT
2509099 TTT
1 TTT
2509102 AAAATTTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 19 0.63
32 11 0.37
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.64
Consensus pattern (31 bp):
TTTTAATTTGATTAATTTTAATCCTGTAATT
Found at i:2510077 original size:20 final size:21
Alignment explanation
Indices: 2510038--2510079 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
2510028 ATTAATATTC
2510038 AATAAATTATTCAATATTTTAA
1 AATAAATTA-TCAATATTTTAA
*
2510060 AATAAATTA-CAATTTTTTAA
1 AATAAATTATCAATATTTTAA
2510080 GTGAAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
22 9 0.47
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (21 bp):
AATAAATTATCAATATTTTAA
Found at i:2510972 original size:91 final size:91
Alignment explanation
Indices: 2510854--2511019 Score: 244
Period size: 91 Copynumber: 1.8 Consensus size: 91
2510844 CGAGATTCTT
* ***
2510854 TTTTTGTTCCGTGGTTAAGAAAATGTTTGGCTTGAATTCGCACTAGAATTTTCTGTTT-CTTTGC
1 TTTTCGTTCCGTGGTTAAGAAAATGTTTAAATTGAATTCGCACTAGAATTTTCTGTTTGC-TTGC
*
2510918 TGCGAAACACTGTTTGAATTCTTTTTA
65 TGAGAAACACTGTTTGAATTCTTTTTA
* * *
2510945 TTTTCGTTGCGTGGTTAAGAAACTGTTTAAATTGAATTCGCACTAGAATTTTTTGTTTGCTTGCT
1 TTTTCGTTCCGTGGTTAAGAAAATGTTTAAATTGAATTCGCACTAGAATTTTCTGTTTGCTTGCT
2511010 GAGAAACACT
66 GAGAAACACT
2511020 CTGAGAAAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
91 65 0.98
92 1 0.02
ACGTcount: A:0.23, C:0.14, G:0.19, T:0.44
Consensus pattern (91 bp):
TTTTCGTTCCGTGGTTAAGAAAATGTTTAAATTGAATTCGCACTAGAATTTTCTGTTTGCTTGCT
GAGAAACACTGTTTGAATTCTTTTTA
Found at i:2511220 original size:100 final size:100
Alignment explanation
Indices: 2510921--2511305 Score: 418
Period size: 106 Copynumber: 3.8 Consensus size: 100
2510911 TCTTTGCTGC
* * * *
2510921 GAAACACTGTTTGAATTCTTTTTATTTTCGTTGCGTGGTTAAGAAACTGTTTAAATTGAATTCGC
1 GAAAAACTGTTTGAATTC-TTTT-TTTTCGTTGCGCGGTTAAGAAAATGTTTAATTTGAATTCGC
* *
2510986 ACTAGAATTTTTTGTTTGCTTGCTGAGAAACACTCTGA
64 ACTAGAATTTTCTGATTGCTTGCTGAGAAACACT-TGA
* * * * *
2511024 GAAAAACTGGTTGAATTCCTTGTTTTTT-TTTGGTCGCGTGGATAAGAAAATGTTTGATTCGAAT
1 GAAAAACTGTTTGAATT-CTT-TTTTTTCGTT-G-CGC--GGTTAAGAAAATGTTTAATTTGAAT
** * *
2511088 TCGCGTTAGAGTTTTCTGATTGTTTGCTGAGAAACACTGTGA
60 TCGCACTAGAATTTTCTGATTGCTTGCTGAGAAACACT-TGA
* * *
2511130 GAAAAACTGTTTGAGTTCTTTTTTTTCGTTGCGCGGTTAAGAAAATG-TTAGTTTTAATTCGCAC
1 GAAAAACTGTTTGAATTCTTTTTTTTCGTTGCGCGGTTAAGAAAATGTTTAATTTGAATTCGCAC
* *
2511194 TAGAATTATCTGATTGGTTGCTGAGAAACAC-TGA
66 TAGAATTTTCTGATTGCTTGCTGAGAAACACTTGA
* * * *
2511228 GAAAAAATCGTTTGAATT-TTTTTATTTCGTTGCGTGGTTAAGAAATTGTTTAATTTGAACTCGC
1 GAAAAACT-GTTTGAATTCTTTTT-TTTCGTTGCGCGGTTAAGAAAATGTTTAATTTGAATTCGC
2511292 ACTAGAATTTTCTG
64 ACTAGAATTTTCTG
2511306 TTTCTGGTTG
Statistics
Matches: 235, Mismatches: 37, Indels: 23
0.80 0.13 0.08
Matches are distributed among these distances:
98 15 0.06
99 30 0.13
100 64 0.27
101 12 0.05
102 2 0.01
103 25 0.11
104 12 0.05
105 5 0.02
106 70 0.30
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.41
Consensus pattern (100 bp):
GAAAAACTGTTTGAATTCTTTTTTTTCGTTGCGCGGTTAAGAAAATGTTTAATTTGAATTCGCAC
TAGAATTTTCTGATTGCTTGCTGAGAAACACTTGA
Found at i:2511318 original size:56 final size:56
Alignment explanation
Indices: 2511256--2511361 Score: 160
Period size: 56 Copynumber: 1.9 Consensus size: 56
2511246 TTTTTATTTC
2511256 GTTGCGTGGTTAAGAA-ATTGTTTAATTTGAACTCGCACTAGAATTTTCTGTTTCTG
1 GTTGCGTGGTTAAGAAGA-TGTTTAATTTGAACTCGCACTAGAATTTTCTGTTTCTG
* * * *
2511312 GTTGCGTGGTTAATAAGATGTTTAATTTGAATTCGGATTAGAATTTTCTG
1 GTTGCGTGGTTAAGAAGATGTTTAATTTGAACTCGCACTAGAATTTTCTG
2511362 ATTGTTTCCC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
56 44 0.98
57 1 0.02
ACGTcount: A:0.25, C:0.09, G:0.23, T:0.43
Consensus pattern (56 bp):
GTTGCGTGGTTAAGAAGATGTTTAATTTGAACTCGCACTAGAATTTTCTGTTTCTG
Found at i:2511460 original size:158 final size:155
Alignment explanation
Indices: 2511157--2511444 Score: 362
Period size: 156 Copynumber: 1.8 Consensus size: 155
2511147 CTTTTTTTTC
* * * *
2511157 GTTGCGCGGTTAAGAAAATGTTAGTTTTAATTCGCACTAGAATTATCTGATTGGTTGCTGAGAAA
1 GTTGCGCGGTTAAGAAAATGTTAATTTGAATTCGCACTAGAATTATCTGATTGGTTCCCGAGAAA
* * * **
2511222 CACTGAGAAAAAATCGTTTGAATTTTTTTATTTCGTTGCGTGGTTAAGAAATTGTTTAATTTGAA
66 CACTGAGAAAAAATCGTTTGAATTTTTTTATTTCGTTGCATGGTTAAGAAAATATTTAATTCAAA
2511287 CTCGCACTAGAATTTTCTGTTTCTG
131 CTCGCACTAGAATTTTCTGTTTCTG
* * * * * * *
2511312 GTTGCGTGGTTAATAAGATGTTTAATTTGAATTCGGATTAGAATTTTCTGATTGTTTCCCGAGAA
1 GTTGCGCGGTTAAGAAAATG-TTAATTTGAATTCGCACTAGAATTATCTGATTGGTTCCCGAGAA
* * *
2511377 ACACTGAG-AAAAATTGTTTGAATTTCTTTTTTTTTTCGTTGCATGGTTAAGAAAATATTTGATT
65 ACACTGAGAAAAAATCGTTTGAA--T-TTTTTTATTTCGTTGCATGGTTAAGAAAATATTTAATT
2511441 CAAA
127 CAAA
2511445 TTCGGATCAG
Statistics
Matches: 110, Mismatches: 19, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
155 30 0.27
156 44 0.40
157 1 0.01
158 35 0.32
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.41
Consensus pattern (155 bp):
GTTGCGCGGTTAAGAAAATGTTAATTTGAATTCGCACTAGAATTATCTGATTGGTTCCCGAGAAA
CACTGAGAAAAAATCGTTTGAATTTTTTTATTTCGTTGCATGGTTAAGAAAATATTTAATTCAAA
CTCGCACTAGAATTTTCTGTTTCTG
Found at i:2517120 original size:13 final size:13
Alignment explanation
Indices: 2517102--2517128 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2517092 AATTTAAAAG
2517102 TTAGATATGATTA
1 TTAGATATGATTA
2517115 TTAGATATGATTA
1 TTAGATATGATTA
2517128 T
1 T
2517129 ATAATAAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (13 bp):
TTAGATATGATTA
Found at i:2529853 original size:20 final size:20
Alignment explanation
Indices: 2529830--2529871 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
2529820 ACGTTTTCGC
* *
2529830 ATAATTTTTTTAATTTTTTT
1 ATAAATTTTATAATTTTTTT
2529850 ATAAATTTTATAATTTTTTT
1 ATAAATTTTATAATTTTTTT
2529870 AT
1 AT
2529872 TCTTAAATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
ATAAATTTTATAATTTTTTT
Found at i:2530242 original size:39 final size:37
Alignment explanation
Indices: 2530166--2530257 Score: 114
Period size: 39 Copynumber: 2.4 Consensus size: 37
2530156 GCATTTAATT
* * *
2530166 AAAT-TTTTTAAATTTTAAAAATTATAAAAATTCAAAA
1 AAATATTTTTAAA-ATTAAAAATCATAAAAATTAAAAA
*
2530203 AAATATTTTTAAAATTAAAAATCATTAAAATTATAAAAA
1 AAATATTTTTAAAATTAAAAATCA-TAAAAAT-TAAAAA
2530242 AAATATTTTTAAAATT
1 AAATATTTTTAAAATT
2530258 TTAAAAATTA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
37 13 0.27
38 14 0.29
39 21 0.44
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (37 bp):
AAATATTTTTAAAATTAAAAATCATAAAAATTAAAAA
Found at i:2533603 original size:18 final size:18
Alignment explanation
Indices: 2533577--2533629 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
2533567 TTGGTTAAAA
* *
2533577 ATTAACCGAGTTAACCGG
1 ATTACCCGAATTAACCGG
2533595 ATTACCCGAATTAACCGG
1 ATTACCCGAATTAACCGG
*
2533613 ATTACCCAAATTAACCG
1 ATTACCCGAATTAACCG
2533630 AATTGAATCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.23
Consensus pattern (18 bp):
ATTACCCGAATTAACCGG
Found at i:2533633 original size:9 final size:9
Alignment explanation
Indices: 2533576--2533633 Score: 62
Period size: 9 Copynumber: 6.4 Consensus size: 9
2533566 CTTGGTTAAA
2533576 AATTAACCG
1 AATTAACCG
*
2533585 AGTTAACCG
1 AATTAACCG
* *
2533594 GATTACCCG
1 AATTAACCG
2533603 AATTAACCG
1 AATTAACCG
* * *
2533612 GATTACCCA
1 AATTAACCG
2533621 AATTAACCG
1 AATTAACCG
2533630 AATT
1 AATT
2533634 GAATCACTAC
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:2533862 original size:107 final size:107
Alignment explanation
Indices: 2533748--2533951 Score: 399
Period size: 107 Copynumber: 1.9 Consensus size: 107
2533738 GAGTTGGGTA
*
2533748 ATTGGGTTGGGTTGAATACTTGAGTTTGGATTGGGTTTAGGTGAATAATGGGCCTATTTATATAT
1 ATTGGGTTGGGTTGAATACTTGAGTTTGGATTGAGTTTAGGTGAATAATGGGCCTATTTATATAT
2533813 TATAATTTTATTTATTAATTTTTTCGGTTAACTGAATTTATG
66 TATAATTTTATTTATTAATTTTTTCGGTTAACTGAATTTATG
2533855 ATTGGGTTGGGTTGAATACTTGAGTTTGGATTGAGTTTAGGTGAATAATGGGCCTATTTATATAT
1 ATTGGGTTGGGTTGAATACTTGAGTTTGGATTGAGTTTAGGTGAATAATGGGCCTATTTATATAT
2533920 TATAATTTTATTTATTAATTTTTTCGGTTAAC
66 TATAATTTTATTTATTAATTTTTTCGGTTAAC
2533952 CGACCGGTTT
Statistics
Matches: 96, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
107 96 1.00
ACGTcount: A:0.25, C:0.05, G:0.22, T:0.48
Consensus pattern (107 bp):
ATTGGGTTGGGTTGAATACTTGAGTTTGGATTGAGTTTAGGTGAATAATGGGCCTATTTATATAT
TATAATTTTATTTATTAATTTTTTCGGTTAACTGAATTTATG
Found at i:2534746 original size:3 final size:3
Alignment explanation
Indices: 2534738--2534802 Score: 58
Period size: 3 Copynumber: 21.7 Consensus size: 3
2534728 CGAAGAGGAA
* * * * * * * *
2534738 GAC GAC GAC GAC GAC GAC GAG GAT GAT GAA GGC GAA GAT GGC GAC GAC
1 GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC
2534786 GAC GAC GAC GAC GAC GA
1 GAC GAC GAC GAC GAC GA
2534803 AGGAGAGGAG
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.34, C:0.23, G:0.38, T:0.05
Consensus pattern (3 bp):
GAC
Found at i:2534929 original size:6 final size:6
Alignment explanation
Indices: 2534920--2534958 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
2534910 AAGGCGACGG
* *
2534920 CGATGA CGATGA CGATGA CGACGA CGACGA CGATGA CGA
1 CGATGA CGATGA CGATGA CGATGA CGATGA CGATGA CGA
2534959 CAGTGATGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.33, C:0.23, G:0.33, T:0.10
Consensus pattern (6 bp):
CGATGA
Found at i:2534959 original size:12 final size:12
Alignment explanation
Indices: 2534891--2534958 Score: 64
Period size: 12 Copynumber: 5.7 Consensus size: 12
2534881 GGATGTTAAA
*
2534891 GACGATGATGAC
1 GACGACGATGAC
* * *
2534903 GACGATGAAGGC
1 GACGACGATGAC
*
2534915 GACGGCGATGAC
1 GACGACGATGAC
*
2534927 GATGACGATGAC
1 GACGACGATGAC
*
2534939 GACGACGACGAC
1 GACGACGATGAC
*
2534951 GATGACGA
1 GACGACGA
2534959 CAGTGATGAA
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 45 1.00
ACGTcount: A:0.32, C:0.21, G:0.37, T:0.10
Consensus pattern (12 bp):
GACGACGATGAC
Found at i:2535973 original size:12 final size:12
Alignment explanation
Indices: 2535956--2535981 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2535946 GGTGTGTTAG
2535956 AAAAAACAAAAA
1 AAAAAACAAAAA
2535968 AAAAAACAAAAA
1 AAAAAACAAAAA
2535980 AA
1 AA
2535982 GTAGAAAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAACAAAAA
Found at i:2536262 original size:3 final size:3
Alignment explanation
Indices: 2536254--2536279 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2536244 CCATTTTTGC
2536254 ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG AT
2536280 AGCCATTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:2543274 original size:60 final size:59
Alignment explanation
Indices: 2543193--2543369 Score: 196
Period size: 61 Copynumber: 2.9 Consensus size: 59
2543183 CGAAATTGAA
**
2543193 TCCAAAAAAAAGCTTGGGTACCAAATTAGAAAAAAATGGCAAGTTCAAGTACCAAATTTGG
1 TCCAAAAAAAAG-TTCAGTACCAAATTAGAAAAAAATGGCAAGTTCAAGTACCAAA-TTGG
* *
2543254 TCCAAAAAAAAGTTCAGTACCAAATTTTA-AAAAAAATGGCAAGTTCAGGTACCTAATTGG
1 TCCAAAAAAAAGTTCAGTACCAAA--TTAGAAAAAAATGGCAAGTTCAAGTACCAAATTGG
* * * * *
2543314 -GCAAAAAAAATTTTAGATACCAAATTAGAAAAAAAAGTGTCAAGTTCAAGAACCAA
1 TCCAAAAAAAAGTTCAG-TACCAAATTAG-AAAAAAA-TGGCAAGTTCAAGTACCAA
2543370 TGTTATATTA
Statistics
Matches: 99, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
58 3 0.03
59 13 0.13
60 28 0.28
61 52 0.53
62 3 0.03
ACGTcount: A:0.49, C:0.14, G:0.15, T:0.22
Consensus pattern (59 bp):
TCCAAAAAAAAGTTCAGTACCAAATTAGAAAAAAATGGCAAGTTCAAGTACCAAATTGG
Found at i:2543301 original size:31 final size:31
Alignment explanation
Indices: 2543210--2543311 Score: 90
Period size: 31 Copynumber: 3.3 Consensus size: 31
2543200 AAAAGCTTGG
2543210 GTACCAAA--TTAGAAAAAAATGGCAAGTTCAA
1 GTACCAAATTTTA-AAAAAAATGGCAAGTTC-A
**
2543241 GTACCAAATTTGGTCCAAAAAA----AAGTTCA
1 GTACCAAATTT--TAAAAAAAATGGCAAGTTCA
2543270 GTACCAAATTTTAAAAAAAATGGCAAGTTCA
1 GTACCAAATTTTAAAAAAAATGGCAAGTTCA
*
2543301 GGTACCTAATT
1 -GTACCAAATT
2543312 GGGCAAAAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 17
0.72 0.06 0.22
Matches are distributed among these distances:
27 7 0.12
29 12 0.21
30 6 0.11
31 15 0.26
32 9 0.16
33 1 0.02
34 6 0.11
35 1 0.02
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.25
Consensus pattern (31 bp):
GTACCAAATTTTAAAAAAAATGGCAAGTTCA
Found at i:2549123 original size:14 final size:14
Alignment explanation
Indices: 2549104--2549131 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2549094 GGCCTGTGAT
2549104 TCAAGATTTTAAAC
1 TCAAGATTTTAAAC
2549118 TCAAGATTTTAAAC
1 TCAAGATTTTAAAC
2549132 AACTAAGAAC
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:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (14 bp):
TCAAGATTTTAAAC
Found at i:2552759 original size:2 final size:2
Alignment explanation
Indices: 2552752--2552781 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2552742 CATTTGACTC
2552752 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2552782 TAATATTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2565795 original size:11 final size:11
Alignment explanation
Indices: 2565775--2565811 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
2565765 AGCCCTGCCC
*
2565775 ATATTAAATAT
1 ATATTTAATAT
2565786 ATATTTAATAT
1 ATATTTAATAT
2565797 ATA--TAATAT
1 ATATTTAATAT
2565806 ATATTT
1 ATATTT
2565812 GATTAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
9 9 0.39
11 14 0.61
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
ATATTTAATAT
Found at i:2571281 original size:9 final size:9
Alignment explanation
Indices: 2571264--2571294 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
2571254 TCGAGTTGAT
2571264 TCGAATAAC
1 TCGAATAAC
*
2571273 TCGATTAAC
1 TCGAATAAC
2571282 TCGAATAAC
1 TCGAATAAC
2571291 TCGA
1 TCGA
2571295 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:2573082 original size:29 final size:29
Alignment explanation
Indices: 2573041--2573124 Score: 80
Period size: 31 Copynumber: 2.8 Consensus size: 29
2573031 ATAAATTTCA
2573041 AAAT-TACACATGAACTTTGATTTGGTGC
1 AAATATACACATGAACTTTGATTTGGTGC
* * *
2573069 AATTATACACATGAAACCTTGATTGTGGTTC
1 AAATATACACATG-AACTTTGATT-TGGTGC
* * *
2573100 AAATATATATATGAAGCTTTAATTT
1 AAATATACACATGAA-CTTTGATTT
2573125 CAATTAAATC
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
28 3 0.07
29 8 0.18
30 12 0.27
31 21 0.48
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (29 bp):
AAATATACACATGAACTTTGATTTGGTGC
Found at i:2577001 original size:29 final size:31
Alignment explanation
Indices: 2576968--2577040 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
2576958 GTGAAAATAC
*
2576968 AAATATATATATAT-ATATATAA-ATTTTTA
1 AAATATATATATATCATATAAAATATTTTTA
* * *
2576997 AAATATAAATATGTCATCTAAAATATTTTTA
1 AAATATATATATATCATATAAAATATTTTTA
*
2577028 AAATAAATATATA
1 AAATATATATATA
2577041 ATTTTCCAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
29 12 0.34
30 6 0.17
31 17 0.49
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.42
Consensus pattern (31 bp):
AAATATATATATATCATATAAAATATTTTTA
Found at i:2577478 original size:19 final size:19
Alignment explanation
Indices: 2577442--2577477 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
2577432 ATGAACTTTA
2577442 TTTTATTTTATTTATATAT
1 TTTTATTTTATTTATATAT
2577461 TTTTA-TTTATTTA-ATAT
1 TTTTATTTTATTTATATAT
2577478 AAAAAAAGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 8 0.47
19 5 0.29
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTATTTTATTTATATAT
Found at i:2585500 original size:20 final size:21
Alignment explanation
Indices: 2585477--2585515 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
2585467 AATAGAAAAT
2585477 AAAGAA-A-AAAAATAAAGTTA
1 AAAGAACATAAAAA-AAAGTTA
2585497 AAAGAACATAAAAAAAAGT
1 AAAGAACATAAAAAAAAGT
2585516 GCTCAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 6 0.35
22 5 0.29
ACGTcount: A:0.74, C:0.03, G:0.10, T:0.13
Consensus pattern (21 bp):
AAAGAACATAAAAAAAAGTTA
Found at i:2585644 original size:16 final size:16
Alignment explanation
Indices: 2585620--2585653 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2585610 CTTATCATTA
*
2585620 TACCGTTAAGGGCAAT
1 TACCATTAAGGGCAAT
2585636 TACCATTAAGGGCAAT
1 TACCATTAAGGGCAAT
2585652 TA
1 TA
2585654 ATAGCTCAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (16 bp):
TACCATTAAGGGCAAT
Found at i:2587718 original size:10 final size:10
Alignment explanation
Indices: 2587699--2587728 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
2587689 ATTTTACTAT
2587699 TATATATATG
1 TATATATATG
*
2587709 TATATGTATG
1 TATATATATG
2587719 TATATATATG
1 TATATATATG
2587729 CTTCAGTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (10 bp):
TATATATATG
Found at i:2596980 original size:19 final size:19
Alignment explanation
Indices: 2596956--2597032 Score: 72
Period size: 19 Copynumber: 4.1 Consensus size: 19
2596946 TGATTTTTTT
2596956 TATAATTTTTATAAGTTTA
1 TATAATTTTTATAAGTTTA
* *
2596975 TATAA-TTTTA-ATGTTTT
1 TATAATTTTTATAAGTTTA
2596992 TATTAATTTTTAATAA-TTT-
1 TA-TAATTTTT-ATAAGTTTA
*
2597011 TATGATTTTTTATAAGTTTA
1 TAT-AATTTTTATAAGTTTA
2597031 TA
1 TA
2597033 AGAATGTTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
17 7 0.15
18 13 0.28
19 20 0.43
20 6 0.13
21 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (19 bp):
TATAATTTTTATAAGTTTA
Found at i:2597049 original size:29 final size:28
Alignment explanation
Indices: 2596953--2597054 Score: 102
Period size: 29 Copynumber: 3.6 Consensus size: 28
2596943 TTATGATTTT
*
2596953 TTTTATAATTTTTATAAGTTTAT-ATAA
1 TTTTATAGTTTTTATAAGTTTATAATAA
*
2596980 TTTTA-ATGTTTTTATTAA-TTTTTAATAA
1 TTTTATA-GTTTTTA-TAAGTTTATAATAA
* *
2597008 TTTTATGATTTTTTATAAGTTTATAAGAA
1 TTTTAT-AGTTTTTATAAGTTTATAATAA
*
2597037 TGTTATACGTTTTTATAA
1 TTTTATA-GTTTTTATAA
2597055 AATTTTAGAT
Statistics
Matches: 61, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
26 1 0.02
27 15 0.25
28 16 0.26
29 28 0.46
30 1 0.02
ACGTcount: A:0.33, C:0.01, G:0.07, T:0.59
Consensus pattern (28 bp):
TTTTATAGTTTTTATAAGTTTATAATAA
Found at i:2597087 original size:19 final size:19
Alignment explanation
Indices: 2596971--2597115 Score: 75
Period size: 19 Copynumber: 7.5 Consensus size: 19
2596961 TTTTTATAAG
2596971 TTTATATAATTT-TAATGTT
1 TTTATATAATTTATAAT-TT
* *
2596990 TTTAT-TAATTTTTAATAAT
1 TTTATATAATTTATAAT-TT
** *
2597009 TTTATGATTTTTTATAAGTT
1 TTTAT-ATAATTTATAATTT
* * **
2597029 TATA-AGAATGTTATACGTT
1 TTTATATAAT-TTATAATTT
* *
2597048 TTTATAAAATTTTAGATATTT
1 TTTATATAA-TTTATA-ATTT
2597069 TTTAT-TAATTCTATAATTT
1 TTTATATAATT-TATAATTT
* *
2597088 TTTTTATAATTTATTATTT
1 TTTATATAATTTATAATTT
2597107 TTT-TATAAT
1 TTTATATAAT
2597116 ATTTATAAGT
Statistics
Matches: 96, Mismatches: 21, Indels: 19
0.71 0.15 0.14
Matches are distributed among these distances:
18 14 0.15
19 46 0.48
20 21 0.22
21 15 0.16
ACGTcount: A:0.32, C:0.01, G:0.05, T:0.61
Consensus pattern (19 bp):
TTTATATAATTTATAATTT
Found at i:2597107 original size:18 final size:20
Alignment explanation
Indices: 2597066--2597115 Score: 68
Period size: 18 Copynumber: 2.5 Consensus size: 20
2597056 ATTTTAGATA
2597066 TTTTTTATTAATTCTATAATT
1 TTTTTTA-TAATTCTATAATT
*
2597087 TTTTTTATAATT-TATTA-T
1 TTTTTTATAATTCTATAATT
2597105 TTTTTTATAAT
1 TTTTTTATAAT
2597116 ATTTATAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 12 0.43
19 4 0.14
20 5 0.18
21 7 0.25
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTTTATAATTCTATAATT
Found at i:2597267 original size:7 final size:7
Alignment explanation
Indices: 2597257--2597297 Score: 55
Period size: 7 Copynumber: 5.7 Consensus size: 7
2597247 ATTTTATATT
2597257 TTTAATA
1 TTTAATA
2597264 TTTAATA
1 TTTAATA
2597271 TTTAATA
1 TTTAATA
*
2597278 TTTTATA
1 TTTAATA
*
2597285 TTTTATAA
1 TTTAAT-A
2597293 TTTAA
1 TTTAA
2597298 AACAAGTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
7 26 0.84
8 5 0.16
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (7 bp):
TTTAATA
Found at i:2597282 original size:22 final size:23
Alignment explanation
Indices: 2597246--2597297 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
2597236 TATTAAAATA
*
2597246 AATTTTATATTTTTAATATTTAAT
1 AATTTAATATTTTT-ATATTTAAT
*
2597270 -ATTTAATA-TTTTATATTTTAT
1 AATTTAATATTTTTATATTTAAT
2597291 AATTTAA
1 AATTTAA
2597298 AACAAGTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 8 0.32
22 10 0.40
23 7 0.28
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
AATTTAATATTTTTATATTTAAT
Found at i:2597383 original size:21 final size:21
Alignment explanation
Indices: 2597359--2597399 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2597349 GATCAAATAG
*
2597359 TAGTTCAATGTGATCTACTTC
1 TAGTTCAATGTGATCCACTTC
2597380 TAGTTCAATGTGATCCACTT
1 TAGTTCAATGTGATCCACTT
2597400 TTAGATTGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (21 bp):
TAGTTCAATGTGATCCACTTC
Found at i:2598197 original size:54 final size:55
Alignment explanation
Indices: 2598111--2598224 Score: 194
Period size: 54 Copynumber: 2.1 Consensus size: 55
2598101 TCAAACTTCT
* *
2598111 TCAGCCTCCTTCGAGCACTACTCGTCGGCTAACATTGCTT-ACACCTATGCTCTA
1 TCAGCCTCCTTAGAGCACTACTCGTCGCCTAACATTGCTTAACACCTATGCTCTA
2598165 TCAGCCTCCTTAGAGCACTACTCGTCGCCTAACATTGCTTAGACACCTATGCTCTA
1 TCAGCCTCCTTAGAGCACTACTCGTCGCCTAACATTGCTTA-ACACCTATGCTCTA
2598221 TCAG
1 TCAG
2598225 GAATTGGTCG
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
54 38 0.68
56 18 0.32
ACGTcount: A:0.22, C:0.34, G:0.15, T:0.29
Consensus pattern (55 bp):
TCAGCCTCCTTAGAGCACTACTCGTCGCCTAACATTGCTTAACACCTATGCTCTA
Found at i:2602230 original size:29 final size:30
Alignment explanation
Indices: 2602196--2602263 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
2602186 TTGAAAATGT
2602196 AAAATTTAGATC-CTATA-TTTTTA-TTTTC
1 AAAATTTAG-TCACTATACTTTTTAGTTTTC
*
2602224 AAGAATTTAGTCACTCTACTTTTTAGTTTTTC
1 AA-AATTTAGTCACTATACTTTTTAG-TTTTC
2602256 AAAATTTA
1 AAAATTTA
2602264 AGTCCAATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
28 4 0.12
29 11 0.32
30 6 0.18
31 6 0.18
32 7 0.21
ACGTcount: A:0.32, C:0.12, G:0.06, T:0.50
Consensus pattern (30 bp):
AAAATTTAGTCACTATACTTTTTAGTTTTC
Found at i:2602937 original size:17 final size:17
Alignment explanation
Indices: 2602911--2602953 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
2602901 TAAAAAACCA
2602911 ACTT-AATAATCAAATT
1 ACTTAAATAATCAAATT
*
2602927 ATTTAAATAATCAAATT
1 ACTTAAATAATCAAATT
2602944 ACTTAAATAA
1 ACTTAAATAA
2602954 ACACTCTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.37
Consensus pattern (17 bp):
ACTTAAATAATCAAATT
Found at i:2606427 original size:13 final size:13
Alignment explanation
Indices: 2606409--2606433 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2606399 CCTTATTTAA
2606409 ATAAAATACAATG
1 ATAAAATACAATG
2606422 ATAAAATACAAT
1 ATAAAATACAAT
2606434 AAAAGTAAAA
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:0.64, C:0.08, G:0.04, T:0.24
Consensus pattern (13 bp):
ATAAAATACAATG
Found at i:2608463 original size:18 final size:19
Alignment explanation
Indices: 2608440--2608478 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
2608430 AAAGAAGAAA
2608440 AAATATG-CATATATATAT
1 AAATATGACATATATATAT
*
2608458 AAATATGTACGTATATATAT
1 AAATATG-ACATATATATAT
2608478 A
1 A
2608479 GGTGTATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
20 11 0.61
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.38
Consensus pattern (19 bp):
AAATATGACATATATATAT
Found at i:2608919 original size:3 final size:3
Alignment explanation
Indices: 2608908--2608965 Score: 80
Period size: 3 Copynumber: 19.3 Consensus size: 3
2608898 CAATAATACC
* * * *
2608908 AAT ACT AAT AAT AGT AAA AAT GAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2608956 AAT AAT AAT A
1 AAT AAT AAT A
2608966 GCAAAAGTAC
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2609458 original size:12 final size:12
Alignment explanation
Indices: 2609441--2609468 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
2609431 AGCTTCAGTC
2609441 GCCGTCCGTCGT
1 GCCGTCCGTCGT
2609453 GCCGTCCGTCGT
1 GCCGTCCGTCGT
2609465 GCCG
1 GCCG
2609469 GCGTTGCTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.43, G:0.36, T:0.21
Consensus pattern (12 bp):
GCCGTCCGTCGT
Found at i:2610605 original size:131 final size:128
Alignment explanation
Indices: 2610471--2610990 Score: 431
Period size: 131 Copynumber: 4.0 Consensus size: 128
2610461 AGTGTCTTCG
* *
2610471 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATC-CTGTCTTTAATCTGCTCCACTGTAACCTCA
* *
2610536 GGGAGATAAGATCCGAAATTCTTTGGTCTATTCCACTGTAATCTCAGGGAGATAAGA-CCTGATG
65 GGGAGATAAGATCCG-AATTCTTTGATCTGTTCCACTGTAATCTCAGGGAGATAAGATCCTG-T-
*
2610600 TG
127 TA
* * * * * *
2610602 ATCTTCTCTACTGTAA-CTTCAGGGAGATAAGATCCTTTAATTTAATCCGCTCCACTGTAACTTC
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCCTGT-CTTTAATCTGCTCCACTGTAACCTC
* * * * *
2610666 AGGGAGATAGGAT---AGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGG
64 AGGGAGATAAGATCCGAAT-TCTTTGATCTGTTCCACTGTAATCTCAGGGAGATAAGATC-CT-G
2610728 CTTCA
126 -TT-A
* ** ** *
2610733 ATCTGCTCCACTGTAACCTCAGGGAGATAAGATCC-GAAATTCTTTGGTCTATTCCACTGTAATC
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCCTG----TCTTTAATCTGCTCCACTGTAACC
* *
2610797 TCAGGGAGATAAGA-CCTG-A---TGTGATCT-TCTCTACTGTAA-CTTCAGGGAGATAAGATCC
62 TCAGGGAGATAAGATCC-GAATTCTTTGATCTGT-TCCACTGTAATC-TCAGGGAGATAAGATCC
2610855 T-TTA
124 TGTTA
* * * * * * * * *
2610859 ATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCTTTGATCTGCTCCGCTGTAATCTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGA-TCCTGTCTTTAATCTGCTCCACTGTAACCTCA
* *
2610924 GGGAGATAAGATCTGAAATTCTTTGGTCTGTTCCACTGTAATCTCAGGGAGATAAGA-CCTGTAT
65 GGGAGATAAGATCCG-AATTCTTTGATCTGTTCCACTGTAATCTCAGGGAGATAAGATCCTGT-T
2610988 A
128 A
2610989 AT
1 AT
2610991 AAACCTAACT
Statistics
Matches: 309, Mismatches: 50, Indels: 61
0.74 0.12 0.15
Matches are distributed among these distances:
124 35 0.11
125 1 0.00
126 29 0.09
127 6 0.02
128 36 0.12
129 31 0.10
130 15 0.05
131 126 0.41
132 1 0.00
133 28 0.09
134 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.31
Consensus pattern (128 bp):
ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCCTGTCTTTAATCTGCTCCACTGTAACCTCAG
GGAGATAAGATCCGAATTCTTTGATCTGTTCCACTGTAATCTCAGGGAGATAAGATCCTGTTA
Found at i:2610618 original size:218 final size:217
Alignment explanation
Indices: 2610363--2610937 Score: 971
Period size: 218 Copynumber: 2.7 Consensus size: 217
2610353 ACTACTGCTT
* ** * * *
2610363 AGGGAGATAAGACTTGATGTGATCCACTCTGCTGTAACCTCAGAGAGATAAGATCCTTTATTTTA
1 AGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGGGAGATAAGATCCTTTA-TTTA
*
2610428 ATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCACTGTAATCTCAG
65 ATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAG
2610493 GGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCCGAAATTCT
130 GGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCCGAAATTCT
2610558 TTGGTCTATTCCACTGTAATCTC
195 TTGGTCTATTCCACTGTAATCTC
2610581 AGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGGGAGATAAGATCCTTTAATTTA
1 AGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGGGAGATAAGATCCTTT-ATTTA
2610646 ATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAG
65 ATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAG
2610711 GGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCCGAAATTCT
130 GGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCCGAAATTCT
2610776 TTGGTCTATTCCACTGTAATCTC
195 TTGGTCTATTCCACTGTAATCTC
2610799 AGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGGGAGATAAGATCC----TTTAA
1 AGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGGGAGATAAGATCCTTTATTTAA
* * * * *
2610860 TCCGCTCCATTGTAA-TCTCAAGGAGATAGGATTACTATCTTTGATCTGCTCCGCTGTAATCTCA
66 TCCGCTCCACTGTAACT-TCAGGGAGATAGGA-TAGTGTCTTCGATCTGCTCCGCTGTAATCTCA
2610924 GGGAGATAAGATCT
129 GGGAGATAAGATCT
2610938 GAAATTCTTT
Statistics
Matches: 342, Mismatches: 12, Indels: 10
0.94 0.03 0.03
Matches are distributed among these distances:
212 1 0.00
213 32 0.09
214 43 0.13
218 265 0.77
219 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.31
Consensus pattern (217 bp):
AGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGGGAGATAAGATCCTTTATTTAA
TCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGG
GAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCCGAAATTCTT
TGGTCTATTCCACTGTAATCTC
Found at i:2610692 original size:87 final size:87
Alignment explanation
Indices: 2610601--2610810 Score: 210
Period size: 87 Copynumber: 2.4 Consensus size: 87
2610591 GACCTGATGT
* * * * *
2610601 GATCTTCTCTACTGTAA-CTTCAGGGAGATAAGATC-CTTTAATTTAATCCGCTCCACTGTAACT
1 GATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCTC-TGAATTCAATCCGCTCCACTGTAACC
2610664 TCAGGGAGATAGGATAGTGTCTTC
64 TCAGGGAGATAGGATAGTGTCTTC
* ** *
2610688 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTC
1 GATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCTGAATTCAATCCGCTCCACTGTAACCTC
* * *
2610753 AGGGAGATAAGATCCGAAAT-TCTTT
66 AGGGAGATAGGAT----AGTGTCTTC
* **
2610778 GGTCTATTCCACTGTAATCTCAGGGAGATAAGA
1 GATCTGCTCCACTGTAATCTCAGGGAGATAAGA
2610811 CCTGATGTGA
Statistics
Matches: 101, Mismatches: 16, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
87 64 0.63
88 2 0.02
90 33 0.33
91 2 0.02
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (87 bp):
GATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCTGAATTCAATCCGCTCCACTGTAACCTC
AGGGAGATAGGATAGTGTCTTC
Found at i:2610929 original size:44 final size:43
Alignment explanation
Indices: 2610394--2610980 Score: 396
Period size: 44 Copynumber: 13.5 Consensus size: 43
2610384 ATCCACTCTG
* * * *
2610394 CTGTAACCTCAGAGAGATAAGATCCTTTAT-TTTAATCCGCTCCA
1 CTGTAATCTCAGGGAGATAAGATCC--TATCTTTGATCTGCTCCA
* ** * *
2610438 CTGTAA-CTTCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCA
1 CTGTAATC-TCAGGGAGATAAGATCCTATCTTTGATCTGCTCCA
** **
2610481 CTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCA
1 CTGTAATCTCAGGGAGATAAGATC-CTATCTTTGATCTGCTCCA
* * * **
2610525 CTGTAACCTCAGGGAGATAAGATCCGAAATTCTTTGGTCTATTCCA
1 CTGTAATCTCAGGGAGATAAGATCC--TA-TCTTTGATCTGCTCCA
* * *
2610571 CTGTAATCTCAGGGAGATAAGA-CCTGA--TGTGATCTTCTCTA
1 CTGTAATCTCAGGGAGATAAGATCCT-ATCTTTGATCTGCTCCA
* * * *
2610612 CTGTAA-CTTCAGGGAGATAAGATCCTTTAATTTAATCCGCTCCA
1 CTGTAATC-TCAGGGAGATAAGATCCTAT-CTTTGATCTGCTCCA
* ** * * *
2610656 CTGTAA-CTTCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCG
1 CTGTAATC-TCAGGGAGATAAGATCCTATCTTTGATCTGCTCCA
** **
2610699 CTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCA
1 CTGTAATCTCAGGGAGATAAGATC-CTATCTTTGATCTGCTCCA
* * * **
2610743 CTGTAACCTCAGGGAGATAAGATCCGAAATTCTTTGGTCTATTCCA
1 CTGTAATCTCAGGGAGATAAGATCC--TA-TCTTTGATCTGCTCCA
* * *
2610789 CTGTAATCTCAGGGAGATAAGA-CCTGA--TGTGATCTTCTCTA
1 CTGTAATCTCAGGGAGATAAGATCCT-ATCTTTGATCTGCTCCA
* *
2610830 CTGTAA-CTTCAGGGAGATAAGAT-C---CTTTAATCCGCTCCA
1 CTGTAATC-TCAGGGAGATAAGATCCTATCTTTGATCTGCTCCA
* * * * *
2610869 TTGTAATCTCAAGGAGATAGGATTACTATCTTTGATCTGCTCCG
1 CTGTAATCTCAGGGAGATAAGA-TCCTATCTTTGATCTGCTCCA
* *
2610913 CTGTAATCTCAGGGAGATAAGAT-CTGAAATTCTTTGGTCTGTTCCA
1 CTGTAATCTCAGGGAGATAAGATCCT---A-TCTTTGATCTGCTCCA
2610959 CTGTAATCTCAGGGAGATAAGA
1 CTGTAATCTCAGGGAGATAAGA
2610981 CCTGTATAAT
Statistics
Matches: 428, Mismatches: 83, Indels: 62
0.75 0.14 0.11
Matches are distributed among these distances:
39 26 0.06
40 4 0.01
41 60 0.14
42 7 0.02
43 65 0.15
44 164 0.38
45 5 0.01
46 97 0.23
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (43 bp):
CTGTAATCTCAGGGAGATAAGATCCTATCTTTGATCTGCTCCA
Found at i:2623557 original size:36 final size:36
Alignment explanation
Indices: 2623517--2623596 Score: 92
Period size: 36 Copynumber: 2.2 Consensus size: 36
2623507 ATACATATAA
* *
2623517 ATATATATACT-TATAAAAATAAAAAT-ATGTATATGT
1 ATATATATA-TATATAAAAAGAAAAATGA-GTATACGT
* *
2623553 ATATAGATATATATAAAAAGAAATATGAGTATACGT
1 ATATATATATATATAAAAAGAAAAATGAGTATACGT
2623589 ATATATAT
1 ATATATAT
2623597 TAAACAAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
35 1 0.03
36 35 0.95
37 1 0.03
ACGTcount: A:0.53, C:0.03, G:0.09, T:0.36
Consensus pattern (36 bp):
ATATATATATATATAAAAAGAAAAATGAGTATACGT
Found at i:2623738 original size:3 final size:3
Alignment explanation
Indices: 2623727--2623772 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
2623717 CAATAATACC
*
2623727 AAT ACT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2623773 GCAAAAGTAC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2633809 original size:24 final size:23
Alignment explanation
Indices: 2633756--2633809 Score: 54
Period size: 24 Copynumber: 2.3 Consensus size: 23
2633746 ACAGTTGAAT
* **
2633756 TGAAGTTATTTTTTTTGCTTTTA
1 TGAATTTATTTTTTTTAATTTTA
**
2633779 TTTATTTATTTATTTTTAATTTTA
1 TGAATTTATTT-TTTTTAATTTTA
2633803 TGAATTT
1 TGAATTT
2633810 TTAATGATTT
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.22, C:0.02, G:0.07, T:0.69
Consensus pattern (23 bp):
TGAATTTATTTTTTTTAATTTTA
Found at i:2640552 original size:22 final size:21
Alignment explanation
Indices: 2640525--2640585 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 21
2640515 TTCTAATAAA
2640525 AATATAAATATATATTTAATC
1 AATATAAATATATATTTAATC
* *
2640546 AACTAT-AATATAAAATTAAATC
1 AA-TATAAATAT-ATATTTAATC
*
2640568 AATATAAA-ATATAATTAA
1 AATATAAATATATATTTAA
2640586 CAAAAAATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
20 5 0.16
21 12 0.38
22 15 0.47
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (21 bp):
AATATAAATATATATTTAATC
Found at i:2640556 original size:21 final size:20
Alignment explanation
Indices: 2640525--2640585 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
2640515 TTCTAATAAA
2640525 AATATAAATATATATTTAATC
1 AATAT-AATATATATTTAATC
* *
2640546 AACTATAATATAAAATTAAATC
1 AA-TATAATAT-ATATTTAATC
* *
2640568 AATATAAAATATAATTAA
1 AATATAATATATATTTAA
2640586 CAAAAAATTA
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
20 5 0.16
21 14 0.44
22 13 0.41
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (20 bp):
AATATAATATATATTTAATC
Found at i:2640930 original size:6 final size:6
Alignment explanation
Indices: 2640919--2640943 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2640909 CCGAATATAA
2640919 TATATT TATATT TATATT TATATT T
1 TATATT TATATT TATATT TATATT T
2640944 TTAATTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TATATT
Found at i:2640964 original size:20 final size:20
Alignment explanation
Indices: 2640941--2640983 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
2640931 TATATTTATA
2640941 TTTTTAATTTTAAAAT-AAT
1 TTTTTAATTTTAAAATAAAT
*
2640960 TTTTTATTTTTAAAATAAAT
1 TTTTTAATTTTAAAATAAAT
2640980 TTTT
1 TTTT
2640984 GGTGTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTTAATTTTAAAATAAAT
Found at i:2640991 original size:20 final size:19
Alignment explanation
Indices: 2640940--2640991 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
2640930 TTATATTTAT
*
2640940 ATTTTTAAT-TTTAAAATA
1 ATTTTTGATGTTTAAAATA
* *
2640958 ATTTTTTATTTTTAAAATAA
1 ATTTTTGATGTTTAAAAT-A
*
2640978 ATTTTTGGTGTTTA
1 ATTTTTGATGTTTA
2640992 TTAAAAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 8 0.29
19 8 0.29
20 12 0.43
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.60
Consensus pattern (19 bp):
ATTTTTGATGTTTAAAATA
Found at i:2641392 original size:13 final size:13
Alignment explanation
Indices: 2641374--2641398 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2641364 AAAAAAGTAA
2641374 TTAAATTTTTTAG
1 TTAAATTTTTTAG
2641387 TTAAATTTTTTA
1 TTAAATTTTTTA
2641399 TCAATTTTTA
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:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
TTAAATTTTTTAG
Found at i:2641825 original size:23 final size:23
Alignment explanation
Indices: 2641799--2641859 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 23
2641789 AAAAATAAAT
2641799 TTTAAAATTTATGTTTTT-TATTG
1 TTTAAAATTTAT-TTTTTGTATTG
* *
2641822 TTT-AAATCTCATTTTTTGTATTT
1 TTTAAAAT-TTATTTTTTGTATTG
2641845 TTTAAAGATTTATTT
1 TTTAAA-ATTTATTT
2641860 ATTAGCTTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
22 9 0.29
23 13 0.42
24 7 0.23
25 2 0.06
ACGTcount: A:0.26, C:0.03, G:0.07, T:0.64
Consensus pattern (23 bp):
TTTAAAATTTATTTTTTGTATTG
Found at i:2644293 original size:13 final size:13
Alignment explanation
Indices: 2644253--2644303 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
2644243 TTTTTCATTA
2644253 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
* ** *
2644266 CTGTAAAAAAATG
1 CTTTTGAAAAGTG
*
2644279 CTTTTGAGAAGTG
1 CTTTTGAAAAGTG
2644292 CTTTTGAAAAGT
1 CTTTTGAAAAGT
2644304 TTGGTTTAAA
Statistics
Matches: 28, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.35, C:0.08, G:0.22, T:0.35
Consensus pattern (13 bp):
CTTTTGAAAAGTG
Found at i:2648178 original size:25 final size:23
Alignment explanation
Indices: 2648133--2648180 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
2648123 AGCAAAGCAA
*
2648133 AGCAAAACCCATTATTAATCTAC
1 AGCAAAACCCATTAGTAATCTAC
*
2648156 AGCAAAACCACCATTAGTCATCTAC
1 AGCAAAA-C-CCATTAGTAATCTAC
2648181 TACAGTTGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 7 0.33
24 1 0.05
25 13 0.62
ACGTcount: A:0.42, C:0.29, G:0.06, T:0.23
Consensus pattern (23 bp):
AGCAAAACCCATTAGTAATCTAC
Found at i:2648676 original size:26 final size:26
Alignment explanation
Indices: 2648624--2648676 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
2648614 ATGAGATTAA
*
2648624 TATTCAAAAACAAATCCATAATATTG
1 TATTCAAAAACAAATCCAGAATATTG
*
2648650 TATTCAATAACAAATCCGAGAAT-TTG
1 TATTCAAAAACAAATCC-AGAATATTG
2648676 T
1 T
2648677 TGTTGGAGGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 20 0.83
27 4 0.17
ACGTcount: A:0.45, C:0.15, G:0.08, T:0.32
Consensus pattern (26 bp):
TATTCAAAAACAAATCCAGAATATTG
Found at i:2651344 original size:19 final size:20
Alignment explanation
Indices: 2651311--2651365 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
2651301 AATTTAGTCT
*
2651311 TTAATATTTGTATTTTTTTAA
1 TTAA-ATTTGGATTTTTTTAA
*
2651332 TT-AATTTGGATTTTTTTAG
1 TTAAATTTGGATTTTTTTAA
2651351 TTAAATTTGG-TTTTT
1 TTAAATTTGGATTTTT
2651366 AATTTTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 21 0.68
20 8 0.26
21 2 0.06
ACGTcount: A:0.24, C:0.00, G:0.11, T:0.65
Consensus pattern (20 bp):
TTAAATTTGGATTTTTTTAA
Found at i:2662960 original size:31 final size:32
Alignment explanation
Indices: 2662896--2662965 Score: 83
Period size: 31 Copynumber: 2.2 Consensus size: 32
2662886 TAACAGTGAA
*
2662896 TGACT-AAAATAGAAATGATCTAAATCGTGAG
1 TGACTAAAAATAGAAATGATCTAAATCATGAG
* *
2662927 TGA-TAAAAATAGAAATTATCTAAAAT-ATTAG
1 TGACTAAAAATAGAAATGATCT-AAATCATGAG
2662958 TGACTAAA
1 TGACTAAA
2662966 TTAAATATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
30 1 0.03
31 24 0.73
32 8 0.24
ACGTcount: A:0.50, C:0.07, G:0.14, T:0.29
Consensus pattern (32 bp):
TGACTAAAAATAGAAATGATCTAAATCATGAG
Found at i:2666264 original size:30 final size:30
Alignment explanation
Indices: 2666196--2666267 Score: 81
Period size: 31 Copynumber: 2.4 Consensus size: 30
2666186 GATTAATTCA
* * * *
2666196 AAATTACAGTTTCATATATATATTTGAACT
1 AAATTAAAGTTTCATATAGATAATTGAACC
* *
2666226 ATAATTAAAGTTTCATGTAGATAATTGCACC
1 A-AATTAAAGTTTCATATAGATAATTGAACC
2666257 AAATTAAAGTT
1 AAATTAAAGTT
2666268 CGTGTATCAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
30 11 0.31
31 24 0.69
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.39
Consensus pattern (30 bp):
AAATTAAAGTTTCATATAGATAATTGAACC
Found at i:2672965 original size:14 final size:14
Alignment explanation
Indices: 2672948--2672977 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2672938 GAAACATAAA
2672948 AATTTACATGTACC
1 AATTTACATGTACC
2672962 AATTTACATGTACC
1 AATTTACATGTACC
2672976 AA
1 AA
2672978 ATCGAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (14 bp):
AATTTACATGTACC
Found at i:2680875 original size:2 final size:2
Alignment explanation
Indices: 2680868--2680902 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2680858 ACTCATATTT
2680868 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2680903 ACTAATTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2682055 original size:6 final size:7
Alignment explanation
Indices: 2682038--2682065 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
2682028 ACATGTAATA
2682038 TTTTTTG
1 TTTTTTG
2682045 TTTTTTG
1 TTTTTTG
2682052 TTTTTTG
1 TTTTTTG
2682059 TTTTTTG
1 TTTTTTG
2682066 GTGATGGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (7 bp):
TTTTTTG
Found at i:2693681 original size:28 final size:28
Alignment explanation
Indices: 2693641--2693698 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
2693631 TAACCTACTG
2693641 AAGGGTTATTTCATTGGATTCCAATATT
1 AAGGGTTATTTCATTGGATTCCAATATT
2693669 AAGGGTTATTTCATTGGATTCCAATATT
1 AAGGGTTATTTCATTGGATTCCAATATT
2693697 AA
1 AA
2693699 AGTTCGAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.41
Consensus pattern (28 bp):
AAGGGTTATTTCATTGGATTCCAATATT
Found at i:2695679 original size:22 final size:20
Alignment explanation
Indices: 2695643--2695683 Score: 64
Period size: 20 Copynumber: 1.9 Consensus size: 20
2695633 AGGCAGTGTA
2695643 ATATATATACACATGTATAC
1 ATATATATACACATGTATAC
2695663 ATATATATACATGCATGTATA
1 ATATATATACA--CATGTATA
2695684 GTTTTACTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.58
22 8 0.42
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (20 bp):
ATATATATACACATGTATAC
Found at i:2698288 original size:16 final size:18
Alignment explanation
Indices: 2698255--2698293 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
2698245 AATAACTCTC
2698255 CTTTTGAGAAAAAAAATA
1 CTTTTGAGAAAAAAAATA
*
2698273 -TTTTGA-AAATAAAATA
1 CTTTTGAGAAAAAAAATA
2698289 CTTTT
1 CTTTT
2698294 CTATTATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.38
Consensus pattern (18 bp):
CTTTTGAGAAAAAAAATA
Found at i:2698920 original size:22 final size:22
Alignment explanation
Indices: 2698895--2698936 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2698885 TATTTATTTT
2698895 TAAT-TTTAAAATATTTTTTACA
1 TAATATTT-AAATATTTTTTACA
*
2698917 TAATATTTTAATATTTTTTA
1 TAATATTTAAATATTTTTTA
2698937 ATTTTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
TAATATTTAAATATTTTTTACA
Found at i:2698956 original size:30 final size:29
Alignment explanation
Indices: 2698922--2699008 Score: 102
Period size: 30 Copynumber: 2.9 Consensus size: 29
2698912 TTACATAATA
2698922 TTTTAATATTTTTTAATTTTAAAATACTTT
1 TTTTAATATTTTTTAATTTTAAAATA-TTT
* *
2698952 TTTTAAATTTTTTTTAAATTTAAAATATTT
1 TTTT-AATATTTTTTAATTTTAAAATATTT
** *
2698982 TTAAAATATTTTTAAAATTTTAAAATA
1 TTTTAATATTTTT-TAATTTTAAAATA
2699009 AAAATAGGCC
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
29 8 0.17
30 20 0.42
31 20 0.42
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (29 bp):
TTTTAATATTTTTTAATTTTAAAATATTT
Found at i:2698981 original size:9 final size:10
Alignment explanation
Indices: 2698970--2699008 Score: 53
Period size: 11 Copynumber: 3.9 Consensus size: 10
2698960 TTTTTTTAAA
2698970 TTTAAAATATT
1 TTTAAAATA-T
2698981 TTTAAAATAT
1 TTTAAAATAT
*
2698991 TTTTAAA-AT
1 TTTAAAATAT
2699000 TTTAAAATA
1 TTTAAAATA
2699009 AAAATAGGCC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 8 0.32
10 8 0.32
11 9 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (10 bp):
TTTAAAATAT
Found at i:2698984 original size:11 final size:11
Alignment explanation
Indices: 2698970--2698999 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
2698960 TTTTTTTAAA
2698970 TTTAAAATATT
1 TTTAAAATATT
2698981 TTTAAAATATT
1 TTTAAAATATT
2698992 TTTAAAAT
1 TTTAAAAT
2699000 TTTAAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
TTTAAAATATT
Found at i:2702397 original size:19 final size:18
Alignment explanation
Indices: 2702364--2702399 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2702354 TGTTGTTTGT
2702364 TGTTGTTTATTGCTATTA
1 TGTTGTTTATTGCTATTA
*
2702382 TGTTGCTTTTTTGCTATT
1 TGTTG-TTTATTGCTATT
2702400 GTTATGTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.11, C:0.08, G:0.17, T:0.64
Consensus pattern (18 bp):
TGTTGTTTATTGCTATTA
Found at i:2704876 original size:44 final size:44
Alignment explanation
Indices: 2704813--2704900 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
2704803 TTGCTCCTAT
2704813 GCCTAATCCATATGGGGTGCGAATCAGAAGAAACTTAAATCCAA
1 GCCTAATCCATATGGGGTGCGAATCAGAAGAAACTTAAATCCAA
2704857 GCCTAATCCATATGGGGTGCGAATCAGAAGAAACTTAAATCCAA
1 GCCTAATCCATATGGGGTGCGAATCAGAAGAAACTTAAATCCAA
2704901 TTTGATTTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.20
Consensus pattern (44 bp):
GCCTAATCCATATGGGGTGCGAATCAGAAGAAACTTAAATCCAA
Found at i:2716893 original size:35 final size:33
Alignment explanation
Indices: 2716854--2716918 Score: 80
Period size: 35 Copynumber: 1.9 Consensus size: 33
2716844 AACCTCTAAT
2716854 CTTGAACTC-TAAACC-CTGAACCTTAAATCTCACAA
1 CTTGAA-TCATAAACCAC-GAACC-TAAA-CTCACAA
2716889 CTTGAATCATAAACCACGAACCTAAACTCA
1 CTTGAATCATAAACCACGAACCTAAACTCA
2716919 GAGTCTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
33 4 0.14
34 6 0.21
35 17 0.61
36 1 0.04
ACGTcount: A:0.40, C:0.31, G:0.06, T:0.23
Consensus pattern (33 bp):
CTTGAATCATAAACCACGAACCTAAACTCACAA
Found at i:2717797 original size:22 final size:21
Alignment explanation
Indices: 2717753--2717798 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
2717743 AATTATTTAA
* **
2717753 ATTTATATATAATAATTTTTT
1 ATTTATATATAAAAATTAATT
2717774 ATTTAATATATAAAAATTAATT
1 ATTT-ATATATAAAAATTAATT
2717796 ATT
1 ATT
2717799 GAAGTTATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTTATATATAAAAATTAATT
Found at i:2720983 original size:20 final size:21
Alignment explanation
Indices: 2720960--2721000 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2720950 AAATAGGGAG
2720960 AAAACA-AAAAAAATAGCATT
1 AAAACAGAAAAAAATAGCATT
* *
2720980 AAAACAGCAAATAATAGCATT
1 AAAACAGAAAAAAATAGCATT
2721001 TTTTTGTCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.63, C:0.12, G:0.07, T:0.17
Consensus pattern (21 bp):
AAAACAGAAAAAAATAGCATT
Found at i:2723968 original size:12 final size:11
Alignment explanation
Indices: 2723953--2723991 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
2723943 TTTATATATA
2723953 TATATAGATTT
1 TATATAGATTT
2723964 ATATATAGATTT
1 -TATATAGATTT
*
2723976 T-TTTAGATTT
1 TATATAGATTT
2723986 TATATA
1 TATATA
2723992 AAAATATTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 9 0.38
11 4 0.17
12 11 0.46
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (11 bp):
TATATAGATTT
Found at i:2730051 original size:23 final size:23
Alignment explanation
Indices: 2730040--2730118 Score: 78
Period size: 21 Copynumber: 3.7 Consensus size: 23
2730030 ACATTAGGGG
2730040 CTTTATGTGTCGTATCTCAGGCA
1 CTTTATGTGTCGTATCTCAGGCA
*
2730063 CTTTATGTGTCGTA--TCAGGTA
1 CTTTATGTGTCGTATCTCAGGCA
* **
2730084 CCTCGTGTGTCGT-T-TCAGGCA
1 CTTTATGTGTCGTATCTCAGGCA
*
2730105 C-TTATGTGCCGTAT
1 CTTTATGTGTCGTAT
2730119 ACTGATCAAG
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
20 8 0.17
21 24 0.52
23 14 0.30
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.39
Consensus pattern (23 bp):
CTTTATGTGTCGTATCTCAGGCA
Found at i:2736122 original size:30 final size:30
Alignment explanation
Indices: 2736086--2736146 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
2736076 ATTCATGAGC
2736086 TGTTCAAATTTATTTTGTTATGGGTCTGGT
1 TGTTCAAATTTATTTTGTTATGGGTCTGGT
2736116 TGTTCAAATTTATTTTGTTATGGGTCTGGT
1 TGTTCAAATTTATTTTGTTATGGGTCTGGT
2736146 T
1 T
2736147 ATATTTCGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.16, C:0.07, G:0.23, T:0.54
Consensus pattern (30 bp):
TGTTCAAATTTATTTTGTTATGGGTCTGGT
Found at i:2741804 original size:26 final size:26
Alignment explanation
Indices: 2741775--2741826 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
2741765 ACCCAAAATA
2741775 AAATAGAATGAGCTA-ACTGGACCCAG
1 AAATAGAATGAGC-AGACTGGACCCAG
2741801 AAATAGAATGAGCAGACTGGACCCAG
1 AAATAGAATGAGCAGACTGGACCCAG
2741827 CAAAGCGCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 1 0.04
26 24 0.96
ACGTcount: A:0.42, C:0.19, G:0.25, T:0.13
Consensus pattern (26 bp):
AAATAGAATGAGCAGACTGGACCCAG
Found at i:2745814 original size:11 final size:11
Alignment explanation
Indices: 2745798--2745822 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2745788 TAAATATATT
2745798 AATGTATGGTA
1 AATGTATGGTA
2745809 AATGTATGGTA
1 AATGTATGGTA
2745820 AAT
1 AAT
2745823 TTGTTAGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.24, T:0.36
Consensus pattern (11 bp):
AATGTATGGTA
Found at i:2745888 original size:13 final size:14
Alignment explanation
Indices: 2745847--2745888 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
2745837 TTGAAATTCT
2745847 AATTCTATTAGTTA
1 AATTCTATTAGTTA
*
2745861 AATT-TGTTAGGTTA
1 AATTCTATTA-GTTA
2745875 AATTCTATTA-TTA
1 AATTCTATTAGTTA
2745888 A
1 A
2745889 CCCGGTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
13 8 0.33
14 12 0.50
15 4 0.17
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.50
Consensus pattern (14 bp):
AATTCTATTAGTTA
Found at i:2746386 original size:5 final size:5
Alignment explanation
Indices: 2746378--2746405 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
2746368 TCGTTTCAGT
2746378 TTTTA TTTTA TTTTA TTTTA TTTTA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTT
2746406 ACATTATAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:2753315 original size:16 final size:17
Alignment explanation
Indices: 2753280--2753321 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
2753270 CAAATAAATC
2753280 TAACCGAAACCCAGAAA
1 TAACCGAAACCCAGAAA
* *
2753297 TAACCTAAACCTA-AAA
1 TAACCGAAACCCAGAAA
*
2753313 TAACTGAAA
1 TAACCGAAA
2753322 ATTAAATTCA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.55, C:0.24, G:0.07, T:0.14
Consensus pattern (17 bp):
TAACCGAAACCCAGAAA
Found at i:2754281 original size:9 final size:9
Alignment explanation
Indices: 2754267--2754292 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
2754257 GGGATTTAAT
2754267 TGAAAATAA
1 TGAAAATAA
2754276 TGAAAATAA
1 TGAAAATAA
2754285 TGAAAATA
1 TGAAAATA
2754293 TGACTATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.23
Consensus pattern (9 bp):
TGAAAATAA
Found at i:2764311 original size:13 final size:13
Alignment explanation
Indices: 2764295--2764323 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2764285 AATTGTTAGG
2764295 TTAAATTCTATTA
1 TTAAATTCTATTA
2764308 TTAAATTCTATTA
1 TTAAATTCTATTA
2764321 TTA
1 TTA
2764324 GGTTAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (13 bp):
TTAAATTCTATTA
Found at i:2764426 original size:13 final size:13
Alignment explanation
Indices: 2764408--2764436 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2764398 ATTTGTTAGG
2764408 TTAAATTCTATTA
1 TTAAATTCTATTA
2764421 TTAAATTCTATTA
1 TTAAATTCTATTA
2764434 TTA
1 TTA
2764437 GGTTAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (13 bp):
TTAAATTCTATTA
Found at i:2764458 original size:113 final size:114
Alignment explanation
Indices: 2764223--2764540 Score: 593
Period size: 113 Copynumber: 2.8 Consensus size: 114
2764213 ACATACAAAC
* *
2764223 GTCTCGTATCAACTTACAATACCATGTAGGTTAAAACATGTTCTAAAACCCTTGAAGAAAAAAAT
1 GTCTCGTATCAACTTACAATACCATGTAGGTTAAAACGTGTTCTAAAACCCTTGAAGAAAAAATT
2764288 TGTTAGGTTAAATTCTATTATTAAATTCTATTATTAGGTTAAAAAATTT
66 TGTTAGGTTAAATTCTATTATTAAATTCTATTATTAGGTTAAAAAATTT
**
2764337 GTCTCGTATTTACTTACAATACCATGTAGGTTAAAACGTGTTCTAAAACCCTTGAAG-AAAAATT
1 GTCTCGTATCAACTTACAATACCATGTAGGTTAAAACGTGTTCTAAAACCCTTGAAGAAAAAATT
2764401 TGTTAGGTTAAATTCTATTATTAAATTCTATTATTAGGTTAAAAAATTT
66 TGTTAGGTTAAATTCTATTATTAAATTCTATTATTAGGTTAAAAAATTT
2764450 GTCTCGTATCAACTTACAATACCATGTAGGTTAAAACGTGTTCTAAAACCCTTGAAGAAAAAATT
1 GTCTCGTATCAACTTACAATACCATGTAGGTTAAAACGTGTTCTAAAACCCTTGAAGAAAAAATT
2764515 TGTTAGGTTAAATTCTATTATTAAAT
66 TGTTAGGTTAAATTCTATTATTAAAT
2764541 ATATAAATGT
Statistics
Matches: 197, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
113 110 0.56
114 87 0.44
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (114 bp):
GTCTCGTATCAACTTACAATACCATGTAGGTTAAAACGTGTTCTAAAACCCTTGAAGAAAAAATT
TGTTAGGTTAAATTCTATTATTAAATTCTATTATTAGGTTAAAAAATTT
Found at i:2766704 original size:21 final size:19
Alignment explanation
Indices: 2766658--2766728 Score: 87
Period size: 19 Copynumber: 3.8 Consensus size: 19
2766648 AATCTTCGAG
*
2766658 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
2766677 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
2766696 GATATATGCAATCTTAGA-A-
1 G--ATATGCAATCTTAGATAT
2766715 GATATG--ATCTTAGA
1 GATATGCAATCTTAGA
2766729 GATTTAATTT
Statistics
Matches: 49, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
15 8 0.16
17 5 0.10
19 20 0.41
20 1 0.02
21 15 0.31
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:2768320 original size:98 final size:98
Alignment explanation
Indices: 2768199--2768389 Score: 346
Period size: 98 Copynumber: 1.9 Consensus size: 98
2768189 ATCATGAAGG
*
2768199 AAATATTCCGAGTTTGAGATTCTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTCTTAAAT
1 AAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTTAAAT
2768264 CTTGGATAAGTGGATGTTCTTTTAAAGTGAATA
66 CTTGGATAAGTGGATGTTCTTTTAAAGTGAATA
* *
2768297 AAATATTCCGAGTTTGGGATTCTAAAGGGATCGTGCCCTAACGTATTGGGTGTGATTTCTTAAAT
1 AAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTTAAAT
*
2768362 CTTGGATGAGTGGATGTTCTTTTAAAGT
66 CTTGGATAAGTGGATGTTCTTTTAAAGT
2768390 TTTATTGTAT
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 89 1.00
ACGTcount: A:0.27, C:0.11, G:0.24, T:0.38
Consensus pattern (98 bp):
AAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTTAAAT
CTTGGATAAGTGGATGTTCTTTTAAAGTGAATA
Found at i:2779882 original size:11 final size:11
Alignment explanation
Indices: 2779855--2779897 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
2779845 TGACCTTTCC
2779855 AAGGTATGGG-
1 AAGGTATGGGA
*
2779865 TAGGTATGGGA
1 AAGGTATGGGA
*
2779876 AAGGTATGGGC
1 AAGGTATGGGA
2779887 AAGGTATGGGA
1 AAGGTATGGGA
2779898 TATATTCTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.30, C:0.02, G:0.47, T:0.21
Consensus pattern (11 bp):
AAGGTATGGGA
Found at i:2779894 original size:22 final size:21
Alignment explanation
Indices: 2779855--2779897 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2779845 TGACCTTTCC
*
2779855 AAGGTATGGGTAGGTATGGGA
1 AAGGTATGGGAAGGTATGGGA
2779876 AAGGTATGGGCAAGGTATGGGA
1 AAGGTATGGG-AAGGTATGGGA
2779898 TATATTCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.30, C:0.02, G:0.47, T:0.21
Consensus pattern (21 bp):
AAGGTATGGGAAGGTATGGGA
Found at i:2783962 original size:18 final size:18
Alignment explanation
Indices: 2783939--2784031 Score: 150
Period size: 18 Copynumber: 5.2 Consensus size: 18
2783929 CCCAACTACT
*
2783939 GTATACGTGAACAGTGCC
1 GTATACGTGAATAGTGCC
2783957 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTGCC
*
2783975 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTGCC
*
2783993 ATATACGTGAATAGTGCC
1 GTATACGTGAATAGTGCC
*
2784011 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTGCC
2784029 GTA
1 GTA
2784032 AACAGTCTTA
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 69 1.00
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (18 bp):
GTATACGTGAATAGTGCC
Found at i:2784591 original size:11 final size:11
Alignment explanation
Indices: 2784564--2784606 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
2784554 TGACCTTTCC
2784564 AAGGTATGGG-
1 AAGGTATGGGA
*
2784574 TAGGTATGGGA
1 AAGGTATGGGA
*
2784585 AAGGTATGGGC
1 AAGGTATGGGA
2784596 AAGGTATGGGA
1 AAGGTATGGGA
2784607 TATATTCTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.30, C:0.02, G:0.47, T:0.21
Consensus pattern (11 bp):
AAGGTATGGGA
Found at i:2784603 original size:22 final size:21
Alignment explanation
Indices: 2784564--2784606 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2784554 TGACCTTTCC
*
2784564 AAGGTATGGGTAGGTATGGGA
1 AAGGTATGGGAAGGTATGGGA
2784585 AAGGTATGGGCAAGGTATGGGA
1 AAGGTATGGG-AAGGTATGGGA
2784607 TATATTCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.30, C:0.02, G:0.47, T:0.21
Consensus pattern (21 bp):
AAGGTATGGGAAGGTATGGGA
Found at i:2793865 original size:33 final size:33
Alignment explanation
Indices: 2793823--2793890 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
2793813 ACTTTTCTCT
2793823 TAGCCTTGAATATTTTAACATCCCAGAGGGTGC
1 TAGCCTTGAATATTTTAACATCCCAGAGGGTGC
2793856 TAGCCTTGAATATTTTAACATCCCAGAGGGTGC
1 TAGCCTTGAATATTTTAACATCCCAGAGGGTGC
2793889 TA
1 TA
2793891 TTTGGGACAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (33 bp):
TAGCCTTGAATATTTTAACATCCCAGAGGGTGC
Found at i:2804330 original size:105 final size:105
Alignment explanation
Indices: 2804148--2804358 Score: 395
Period size: 105 Copynumber: 2.0 Consensus size: 105
2804138 ACTAAATGAA
* *
2804148 ATCAATTTTTTTATACATTAATGTATAGAGTCACGCACACATAATTCGTCACTTACTTAAAATTG
1 ATCAAATTTTTTATACATTAAAGTATAGAGTCACGCACACATAATTCGTCACTTACTTAAAATTG
2804213 AAGTATGCCACATTATAAAAGTTACAATGAATAAATTCAT
66 AAGTATGCCACATTATAAAAGTTACAATGAATAAATTCAT
*
2804253 ATCAAATTTTTTATACATTAAAGTATATAGTCACGCACACATAATTCGTCACTTACTTAAAATTG
1 ATCAAATTTTTTATACATTAAAGTATAGAGTCACGCACACATAATTCGTCACTTACTTAAAATTG
2804318 AAGTATGCCACATTATAAAAGTTACAATGAATAAATTCAT
66 AAGTATGCCACATTATAAAAGTTACAATGAATAAATTCAT
2804358 A
1 A
2804359 AACGAATCTA
Statistics
Matches: 103, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
105 103 1.00
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.35
Consensus pattern (105 bp):
ATCAAATTTTTTATACATTAAAGTATAGAGTCACGCACACATAATTCGTCACTTACTTAAAATTG
AAGTATGCCACATTATAAAAGTTACAATGAATAAATTCAT
Found at i:2815124 original size:30 final size:30
Alignment explanation
Indices: 2815090--2815148 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
2815080 TTCTTTAAGA
2815090 GTTTACTTAGGGTAAAATTGGATTTAAAGG
1 GTTTACTTAGGGTAAAATTGGATTTAAAGG
2815120 GTTTACTTAGGGTAAAATTGGATTTAAAG
1 GTTTACTTAGGGTAAAATTGGATTTAAAG
2815149 TTATTTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.03, G:0.25, T:0.37
Consensus pattern (30 bp):
GTTTACTTAGGGTAAAATTGGATTTAAAGG
Found at i:2820549 original size:6 final size:6
Alignment explanation
Indices: 2820538--2820568 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
2820528 GTTAAATTAA
2820538 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT A
2820569 TTATTACAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:2825096 original size:15 final size:15
Alignment explanation
Indices: 2825074--2825133 Score: 52
Period size: 15 Copynumber: 4.0 Consensus size: 15
2825064 AAGATAATGG
2825074 AAAA-TAAATAAATA
1 AAAATTAAATAAATA
*
2825088 AAAATTAAAGAACATAA
1 AAAATTAAATAA-AT-A
* * *
2825105 AAAATTAAATTACTC
1 AAAATTAAATAAATA
2825120 AAAATTAAA-AAATA
1 AAAATTAAATAAATA
2825134 TGGGGATCGA
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
14 6 0.17
15 15 0.43
16 3 0.09
17 11 0.31
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (15 bp):
AAAATTAAATAAATA
Found at i:2825825 original size:12 final size:12
Alignment explanation
Indices: 2825808--2825834 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2825798 ACAAAATTAT
2825808 ATTATATCAATA
1 ATTATATCAATA
2825820 ATTATATCAATA
1 ATTATATCAATA
2825832 ATT
1 ATT
2825835 TATAAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (12 bp):
ATTATATCAATA
Found at i:2829192 original size:27 final size:27
Alignment explanation
Indices: 2829077--2829198 Score: 104
Period size: 27 Copynumber: 4.5 Consensus size: 27
2829067 TGGAGGGGTT
* * *
2829077 CTGATTGGCGGCACCAAAGGTGCCAAA
1 CTGATTGGCGGCACCGATGGTGCCATA
*
2829104 CTGATTGGCGGCATCGATGGTGCCA-A
1 CTGATTGGCGGCACCGATGGTGCCATA
** * *
2829130 -TGAGGTTGGAAGCACTGATGATGCCATA
1 CTGA--TTGGCGGCACCGATGGTGCCATA
* * * *
2829158 CAGGTTGGCAGCACCGACGGTGCCATA
1 CTGATTGGCGGCACCGATGGTGCCATA
2829185 CTGATTGGCGGCAC
1 CTGATTGGCGGCAC
2829199 TACTCGTCTT
Statistics
Matches: 74, Mismatches: 17, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
25 3 0.04
26 1 0.01
27 68 0.92
28 1 0.01
29 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.33, T:0.20
Consensus pattern (27 bp):
CTGATTGGCGGCACCGATGGTGCCATA
Found at i:2829422 original size:3 final size:3
Alignment explanation
Indices: 2829414--2829453 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
2829404 GATAGTTTTA
* *
2829414 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT GTT AGT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
2829454 AGATGTTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:2830316 original size:15 final size:18
Alignment explanation
Indices: 2830288--2830332 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
2830278 TTGATATGGT
* *
2830288 TGGTGGTGAAGAAGAAAG
1 TGGTGGCGAAGAAGAAGG
2830306 TGGTGGCGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
2830324 TGGTGGCGA
1 TGGTGGCGA
2830333 TCATTGGGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.31, C:0.04, G:0.49, T:0.16
Consensus pattern (18 bp):
TGGTGGCGAAGAAGAAGG
Found at i:2832972 original size:162 final size:159
Alignment explanation
Indices: 2832740--2833294 Score: 591
Period size: 162 Copynumber: 3.5 Consensus size: 159
2832730 TTTCTCCGCA
* * * *
2832740 TTTTATTACTTTA-AAAAATATCTTAATTTCTAATTTTATAAGTTTACATTATTTCAGTGCATAA
1 TTTTATTACTTTATAAAAATATTTTATTTTCTAATTTTATAATTTTACATTATTCCAGTGCATAA
2832804 TGTTTGAAATTTATTAATTTAGTGTGTTTTTTAAATTAAGTTGGTGTAAGAAAAAAACCCTTATC
66 TGTTTGAAATTTATTAATTTAGTGTGTTTTTTAAATTAA-TTGGTGTAAGAAAAAAACCCTTATC
2832869 CCTGCCCTTTGCTCGTATTATTTTCCCAAT
130 CCTGCCCTTTGCTCGTATTATTTTCCCAAT
* *
2832899 TTTTATTACTTTCAATAAAAATATTTTATTTTCGT-ATTTTATTATTTTATATTATTCCAGTGCA
1 TTTTATTACTTT--ATAAAAATATTTTATTTTC-TAATTTTATAATTTTACATTATTCCAGTGCA
** * * * *
2832963 TTTTGTTTGAAATATTTGTATTAA-TTATTCCTGAATTTTTAAA--AA---GT-T-AGTAAAAAA
63 TAATGTTTG-AA-A-TT-TATTAATTTAGT-GTG-TTTTTTAAATTAATTGGTGTAAGAAAAAAA
* * * * * * * *
2833020 CTCTTA-CTTCGGCCATTTGTTTGTATTTTTTTCTCCGCAT
122 CCCTTATC-CCTGCCCTTTGCTCGTATTATTTTC-CC-AAT
* *
2833060 TTTT-TTA--TTATAGAAAATATTATAATTTT-TAATTTTATAATTTTACATTATTTCAGTGCAT
1 TTTTATTACTTTATA-AAAATATT-TTATTTTCTAATTTTATAATTTTACATTATTCCAGTGCAT
2833121 AATGTTTGAAATTTATTAATTTAGTGTGTTTTTTAAATTAATTTGGTGTAAGAAAAAAACCCTTA
64 AATGTTTGAAATTTATTAATTTAGTGTGTTTTTTAAATTAA-TTGGTGTAAGAAAAAAACCCTTA
*
2833186 TCCCTGCCCTTTGCTCGTATTATTTTCCCGAT
128 TCCCTGCCCTTTGCTCGTATTATTTTCCCAAT
* * *
2833218 TTTTATTACTTTCAATAAAAATATTTTATTTTCGAATTTTATTATTTTATATTATTCCAGTGCAT
1 TTTTATTACTTT--ATAAAAATATTTTATTTTCTAATTTTATAATTTTACATTATTCCAGTGCAT
**
2833283 TTTGTTTGAAAT
64 AATGTTTGAAAT
2833295 ATTTGTATTA
Statistics
Matches: 319, Mismatches: 45, Indels: 61
0.75 0.11 0.14
Matches are distributed among these distances:
152 8 0.03
153 8 0.03
154 8 0.03
155 1 0.00
156 6 0.02
157 41 0.13
158 17 0.05
159 50 0.16
160 38 0.12
161 18 0.06
162 93 0.29
163 6 0.02
164 1 0.00
165 8 0.03
166 8 0.03
167 8 0.03
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.50
Consensus pattern (159 bp):
TTTTATTACTTTATAAAAATATTTTATTTTCTAATTTTATAATTTTACATTATTCCAGTGCATAA
TGTTTGAAATTTATTAATTTAGTGTGTTTTTTAAATTAATTGGTGTAAGAAAAAAACCCTTATCC
CTGCCCTTTGCTCGTATTATTTTCCCAAT
Found at i:2833263 original size:319 final size:318
Alignment explanation
Indices: 2832685--2833459 Score: 1340
Period size: 319 Copynumber: 2.4 Consensus size: 318
2832675 AAGTTGAAAA
2832685 AAAAAGTTAGTAAAAAACTCTTACTTCGGCCATTTGTTCGTA-TTTTTTCTCCGCATTTTATTAC
1 AAAAAGTTAGTAAAAAACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTA-
* *
2832749 TTTAAAAAATATCTTAATTTCTAATTTTATAAGTTTACATTATTTCAGTGCATAATGTTTGAAAT
65 TTTAAAAAATAT-TTAATTTTTAATTTTATAATTTTACATTATTTCAGTGCATAATGTTTGAAAT
2832814 TTATTAATTTAGTGTGTTTTTTAAATTAAGTTGGTGTAAGAAAAAAACCCTTATCCCTGCCCTTT
129 TTATTAATTTAGTGTGTTTTTTAAATTAAGTTGGTGTAAGAAAAAAACCCTTATCCCTGCCCTTT
*
2832879 GCTCGTATTATTTTCCCAATTTTTATTACTTTCAATAAAAATATTTTATTTTCGTATTTTATTAT
194 GCTCGTATTATTTTCCCAATTTTTATTACTTTCAATAAAAATATTTTATTTTCGAATTTTATTAT
2832944 TTTATATTATTCCAGTGCATTTTGTTTGAAATATTTGTATTAATTAT-TCCTGAA-TTTTT
259 TTTATATTATTCCAGTGCATTTTGTTTGAAATATTTGTATTAATTATCT-CTGAATTTTTT
* *
2833003 AAAAAGTTAGTAAAAAACTCTTACTTCGGCCATTTGTTTGTATTTTTTTCTCCGCATTTTTTTAT
1 AAAAAGTTAGTAAAAAACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTAT
*
2833068 TATAGAAAATATTATAATTTTTAATTTTATAATTTTACATTATTTCAGTGCATAATGTTTGAAAT
66 T-TAAAAAATATT-TAATTTTTAATTTTATAATTTTACATTATTTCAGTGCATAATGTTTGAAAT
*
2833133 TTATTAATTTAGTGTGTTTTTTAAATTAATTTGGTGTAAGAAAAAAACCCTTATCCCTGCCCTTT
129 TTATTAATTTAGTGTGTTTTTTAAATTAAGTTGGTGTAAGAAAAAAACCCTTATCCCTGCCCTTT
*
2833198 GCTCGTATTATTTTCCCGATTTTTATTACTTTCAATAAAAATATTTTATTTTCGAATTTTATTAT
194 GCTCGTATTATTTTCCCAATTTTTATTACTTTCAATAAAAATATTTTATTTTCGAATTTTATTAT
2833263 TTTATATTATTCCAGTGCATTTTGTTTGAAATATTTGTATTAATTATCTCTGAATTTTTT
259 TTTATATTATTCCAGTGCATTTTGTTTGAAATATTTGTATTAATTATCTCTGAATTTTTT
* * *
2833323 AAAAAGTTAGTAAAAAACTCTTATTTCGACCATTTGTTCGTATTTTTTTATCCGCATTTTATTAT
1 AAAAAGTTAGTAAAAAACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTA-
* * *
2833388 TTTAAAAAATATCGTAATTTTTAATTTTATCATTTTACATTATTTCAGTGCATTATGTTTGAAAT
65 TTTAAAAAATAT-TTAATTTTTAATTTTATAATTTTACATTATTTCAGTGCATAATGTTTGAAAT
2833453 TTATTAA
129 TTATTAA
2833460 ATATACAATT
Statistics
Matches: 433, Mismatches: 17, Indels: 12
0.94 0.04 0.03
Matches are distributed among these distances:
318 44 0.10
319 257 0.59
320 130 0.30
321 2 0.00
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.49
Consensus pattern (318 bp):
AAAAAGTTAGTAAAAAACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTAT
TTAAAAAATATTTAATTTTTAATTTTATAATTTTACATTATTTCAGTGCATAATGTTTGAAATTT
ATTAATTTAGTGTGTTTTTTAAATTAAGTTGGTGTAAGAAAAAAACCCTTATCCCTGCCCTTTGC
TCGTATTATTTTCCCAATTTTTATTACTTTCAATAAAAATATTTTATTTTCGAATTTTATTATTT
TATATTATTCCAGTGCATTTTGTTTGAAATATTTGTATTAATTATCTCTGAATTTTTT
Found at i:2833829 original size:4 final size:4
Alignment explanation
Indices: 2833822--2833973 Score: 85
Period size: 4 Copynumber: 38.8 Consensus size: 4
2833812 TTCCCTCTTC
* * *
2833822 TTCT TTCT TT-T TTTT TTCT CTTCT CTTC- TCCT TTCTT TTCT TTCC TTC-
1 TTCT TTCT TTCT TTCT TTCT -TTCT -TTCT TTCT TTC-T TTCT TTCT TTCT
*
2833870 TT-T TTCT TTCT TT-T TTC- TTC- TTC- TTCT TTCCTT TTCT TTCC TTC-
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TT-C-T TTCT TTCT TTCT
* *
2833914 TT-T TTCT TTCT TTCCT CTCCT GTCCTT TTCT TTCT TTCT TTCT TTCT
1 TTCT TTCT TTCT TT-CT -TTCT -TTC-T TTCT TTCT TTCT TTCT TTCT
2833961 TTC- TTC- TTCT TTC
1 TTCT TTCT TTCT TTC
2833974 CCTCTCCTTC
Statistics
Matches: 124, Mismatches: 8, Indels: 32
0.76 0.05 0.20
Matches are distributed among these distances:
3 31 0.25
4 65 0.52
5 23 0.19
6 5 0.04
ACGTcount: A:0.00, C:0.29, G:0.01, T:0.70
Consensus pattern (4 bp):
TTCT
Found at i:2833830 original size:10 final size:10
Alignment explanation
Indices: 2833817--2833973 Score: 88
Period size: 10 Copynumber: 16.2 Consensus size: 10
2833807 CTTCCTTCCC
2833817 TCTTCTTCTT
1 TCTTCTTCTT
2833827 TCTT-TT-TT
1 TCTTCTTCTT
*
2833835 TTTTC-TCTT
1 TCTTCTTCTT
*
2833844 CTCTTCTCCTT
1 -TCTTCTTCTT
2833855 TCTT-TTCTT
1 TCTTCTTCTT
2833864 TCCTTCTT-TT
1 T-CTTCTTCTT
*
2833874 TCTTTCTTTTT
1 TC-TTCTTCTT
2833885 TCTTCTTC-T
1 TCTTCTTCTT
*
2833894 TCTT-TCCTTT
1 TCTTCTTC-TT
2833904 TCTTTCCTTCTT
1 TC-TT-CTTCTT
2833916 T-TTCTTTCTT
1 TCTTC-TTCTT
* *
2833926 TCCTCTCCTGT
1 TCTTCTTCT-T
*
2833937 CCTT-TTCTT
1 TCTTCTTCTT
2833946 TC-T-TTCTT
1 TCTTCTTCTT
2833954 TC-T-TTCTT
1 TCTTCTTCTT
2833962 TCTTCTTCTT
1 TCTTCTTCTT
2833972 TC
1 TC
2833974 CCTCTCCTTC
Statistics
Matches: 116, Mismatches: 13, Indels: 36
0.70 0.08 0.22
Matches are distributed among these distances:
8 24 0.21
9 19 0.16
10 52 0.45
11 16 0.14
12 3 0.03
13 2 0.02
ACGTcount: A:0.00, C:0.29, G:0.01, T:0.70
Consensus pattern (10 bp):
TCTTCTTCTT
Found at i:2833847 original size:28 final size:28
Alignment explanation
Indices: 2833794--2833972 Score: 94
Period size: 31 Copynumber: 6.2 Consensus size: 28
2833784 TTACCTTTTT
2833794 TTTCTTTTTTTTCCTTC-CTTCCCTCTTCTTC
1 TTTCTTTTTTTT--TTCTCTT--CTCTTCTTC
*
2833825 TTTCTTTTTTTTTTCTCTTCTCTTCTCC
1 TTTCTTTTTTTTTTCTCTTCTCTTCTTC
*
2833853 TTTC--TTTTCTTTC-CTTCT-TT-TTC
1 TTTCTTTTTTTTTTCTCTTCTCTTCTTC
2833876 TTTCTTTTTTCTTCTTCTTCTT-TCCTT-TTC
1 TTTCTTTTTT-TT-TTC-TCTTCT-CTTCTTC
*
2833906 TTTCCTTCTTTTTCTTTCT-TTCCTCTCCTGTCC
1 TTT-CTT-TTTTT-TTTCTCTT-CTCTTCT-T-C
*
2833939 TTTTCTTTCTTTCTTTCT-TTCT-TTCTTC
1 -TTTCTTT-TTTTTTTCTCTTCTCTTCTTC
2833967 -TTCTTT
1 TTTCTTT
2833973 CCCTCTCCTT
Statistics
Matches: 122, Mismatches: 7, Indels: 43
0.71 0.04 0.25
Matches are distributed among these distances:
23 6 0.05
24 2 0.02
25 9 0.07
26 15 0.12
27 3 0.02
28 14 0.11
29 9 0.07
30 17 0.14
31 23 0.19
32 14 0.11
33 7 0.06
34 3 0.02
ACGTcount: A:0.00, C:0.30, G:0.01, T:0.70
Consensus pattern (28 bp):
TTTCTTTTTTTTTTCTCTTCTCTTCTTC
Found at i:2833874 original size:14 final size:14
Alignment explanation
Indices: 2833857--2833923 Score: 73
Period size: 14 Copynumber: 4.6 Consensus size: 14
2833847 TTCTCCTTTC
2833857 TTTTCTTTCCTTCT
1 TTTTCTTTCCTTCT
*
2833871 TTTTCTTT-CTTTT
1 TTTTCTTTCCTTCT
* *
2833884 TTCTTCTTCTTCTTTCC
1 TT-TTC-T-TTCCTTCT
2833901 TTTTCTTTCCTTCT
1 TTTTCTTTCCTTCT
2833915 TTTTCTTTC
1 TTTTCTTTC
2833924 TTTCCTCTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
13 6 0.14
14 26 0.60
15 2 0.05
16 5 0.12
17 4 0.09
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTTCTTTCCTTCT
Found at i:2841126 original size:16 final size:17
Alignment explanation
Indices: 2841090--2841131 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
2841080 TCCAAACTTG
2841090 AAAATAATTTAAAACTA
1 AAAATAATTTAAAACTA
*
2841107 AAAATAATTTAAAA-TT
1 AAAATAATTTAAAACTA
2841123 AAAATAATT
1 AAAATAATT
2841132 CAAACCCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 10 0.42
17 14 0.58
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATAATTTAAAACTA
Found at i:2841944 original size:43 final size:43
Alignment explanation
Indices: 2841883--2842149 Score: 430
Period size: 43 Copynumber: 6.3 Consensus size: 43
2841873 GATATGTTTT
*
2841883 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
*
2841926 TAGCGGCGTTTGTGGGAAAAGCGCCACTAAAGGTCCTGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
* * *
2841969 TAGCGGCGTTTGTGCGAAAAGCGCTGCTAAAGGTCCTGGTCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
* * *
2842012 TAGCGGCGTTTGTTGTAAAAGCGCCGCTAAAGGTCCTGCTCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
2842055 TAGCGGCGTTTGT-GGAAAAGCGCCGCTAAAGGTCCTGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
* *
2842097 TAGCGGCGTTTG-GGAAAAAGCGCCGCTAAAGGTCTTGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
2842139 TAGCGGCGTTT
1 TAGCGGCGTTT
2842150 ATTTCTATAA
Statistics
Matches: 208, Mismatches: 15, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
42 77 0.37
43 131 0.63
ACGTcount: A:0.23, C:0.21, G:0.31, T:0.25
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
Found at i:2842590 original size:30 final size:31
Alignment explanation
Indices: 2842554--2842614 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
2842544 ATACATGAAT
* *
2842554 TTTGATT-TGATGCAATTGTACACATCAAAC
1 TTTGATTATGATGCAAATGTACACATAAAAC
* *
2842584 TTTGATTATGATTCAAATGTATACATAAAAC
1 TTTGATTATGATGCAAATGTACACATAAAAC
2842615 ATTTAAAGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 7 0.27
31 19 0.73
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (31 bp):
TTTGATTATGATGCAAATGTACACATAAAAC
Found at i:2843691 original size:20 final size:20
Alignment explanation
Indices: 2843653--2843706 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
2843643 CCTAGCCTCT
* *
2843653 GCCACCGCCACCAAC-GTCAT
1 GCCACCACCACC-ACGGTCAC
*
2843673 GCCACCACCGCCACGGTCAC
1 GCCACCACCACCACGGTCAC
*
2843693 GTCACCACCACCAC
1 GCCACCACCACCAC
2843707 TTGCACCGTC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.07
20 26 0.93
ACGTcount: A:0.24, C:0.54, G:0.15, T:0.07
Consensus pattern (20 bp):
GCCACCACCACCACGGTCAC
Found at i:2845069 original size:18 final size:17
Alignment explanation
Indices: 2845046--2845084 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
2845036 TGCTTTAATT
2845046 TTTTATTTGTTT-ATTTAC
1 TTTTATTT-TTTGATTT-C
2845064 TTTTATTTTTTGATTTC
1 TTTTATTTTTTGATTTC
2845081 TTTT
1 TTTT
2845085 CATTATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.13, C:0.05, G:0.05, T:0.77
Consensus pattern (17 bp):
TTTTATTTTTTGATTTC
Found at i:2845470 original size:111 final size:109
Alignment explanation
Indices: 2845233--2845578 Score: 541
Period size: 111 Copynumber: 3.2 Consensus size: 109
2845223 CAGAAAAATG
* *
2845233 GGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTTAAACT
1 GGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTCAAAAT
2845298 AAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAA
66 AAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAA
2845342 GGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAAAATTTCAAA
1 GGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTT--AAAAATTTCAAA
* * * *
2845407 ATATGACAATATTTTGCGTTTGAAAATTCGAGAAAACATGCCCTAA
64 ATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAA
* * * *
2845453 GGTGTTGGGTGTTGATTTTTCTCATTCAACCAAATGGCTAAATATCCTTTTAAAAATTTCAAAAT
1 GGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTCAAAAT
* *
2845518 AAGGCAATGTTTTGCATTTGGAAATTCGAG-GAACATGCCCTAA
66 AAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAA
* *
2845561 TGTGCTGGGTTTCGATTT
1 GGTGCTGGGTGTCGATTT
2845579 CTCGATTGAC
Statistics
Matches: 215, Mismatches: 20, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
108 26 0.12
109 90 0.42
111 99 0.46
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.36
Consensus pattern (109 bp):
GGTGCTGGGTGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTCAAAAT
AAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAA
Found at i:2846672 original size:13 final size:13
Alignment explanation
Indices: 2846654--2846692 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
2846644 TGAAAAAATT
*
2846654 CAATATTCTAATA
1 CAATATTCTAAAA
*
2846667 CAATATTTTAAAA
1 CAATATTCTAAAA
2846680 CAATATTCATAAA
1 CAATATTC-TAAA
2846693 TCAGACATGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 18 0.82
14 4 0.18
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (13 bp):
CAATATTCTAAAA
Done.