Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167937.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_2, 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: 35885061
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 165000 characters in sequence are not A, C, G, or T
File 11 of 195
Found at i:2314514 original size:20 final size:20
Alignment explanation
Indices: 2314477--2314514 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2314467 CTTTCATTCA
*
2314477 TGGTAGTAAGAAATTACAAT
1 TGGTAGTAAGAAAATACAAT
2314497 TGGTAG-AAGAGAAATACA
1 TGGTAGTAAGA-AAATACA
2314515 CTTACTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.47, C:0.05, G:0.24, T:0.24
Consensus pattern (20 bp):
TGGTAGTAAGAAAATACAAT
Found at i:2315634 original size:156 final size:156
Alignment explanation
Indices: 2315435--2315740 Score: 427
Period size: 157 Copynumber: 2.0 Consensus size: 156
2315425 GGCATATACA
* * *
2315435 TGCGACAGAAAGATAACATACTAACTCTCATTCATGTGTATTCTTTAATGA-TAAATTTTATTAA
1 TGCGACAGAAAGATAACATACTAACTATCATTCAGGTGTATTCTTTAATAATTAAATTTTATTAA
* * ** *
2315499 AAATCTCATCTATCTA-TCTAATTTATAATCATTCCATCAATCTTCTAAGATAAGTGTGCATTAT
66 AAATCTCATCTATCTACT-TAATTCATAATCATTCCATCAATCTTCTAAGACAAACGCGCATTAT
*
2315563 TCACAATGAATATTATTATATGTCAAG
130 TCACAATAAATATTATTATATGTCAAG
* *
2315590 TGCGACAGAGAGATAAACATACTAACTATCATTTAGGTGTATTCTTTAATAATTAAATTTTATTA
1 TGCGACAGAAAGAT-AACATACTAACTATCATTCAGGTGTATTCTTTAATAATTAAATTTTATTA
* * * * *
2315655 AGAATCTCATTTATCTACTTAATTCATAATCATTCCGTTAATCTTCTAAGACAAACGCGTATTAT
65 AAAATCTCATCTATCTACTTAATTCATAATCATTCCATCAATCTTCTAAGACAAACGCGCATTAT
*
2315720 TCACCATAAATATTATTATAT
130 TCACAATAAATATTATTATAT
2315741 ACCATGTTTT
Statistics
Matches: 131, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
155 13 0.10
156 33 0.25
157 84 0.64
158 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (156 bp):
TGCGACAGAAAGATAACATACTAACTATCATTCAGGTGTATTCTTTAATAATTAAATTTTATTAA
AAATCTCATCTATCTACTTAATTCATAATCATTCCATCAATCTTCTAAGACAAACGCGCATTATT
CACAATAAATATTATTATATGTCAAG
Found at i:2318194 original size:31 final size:29
Alignment explanation
Indices: 2318159--2318224 Score: 78
Period size: 31 Copynumber: 2.2 Consensus size: 29
2318149 ACATTGTTAA
2318159 TAAATATGATGATATCATTTCATTAATGAAG
1 TAAATAT-ATGATATCATTTCATTAATG-AG
* * *
2318190 TAAATTATATGATGTTATTTTATTAATGAG
1 TAAA-TATATGATATCATTTCATTAATGAG
2318220 TAAAT
1 TAAAT
2318225 TTTTTAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 1 0.03
30 6 0.19
31 21 0.68
32 3 0.10
ACGTcount: A:0.41, C:0.03, G:0.12, T:0.44
Consensus pattern (29 bp):
TAAATATATGATATCATTTCATTAATGAG
Found at i:2333990 original size:34 final size:34
Alignment explanation
Indices: 2333947--2334016 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
2333937 TAAATACTCG
2333947 TATATAACCTTATATCATACTAAGACGATTAGTT
1 TATATAACCTTATATCATACTAAGACGATTAGTT
2333981 TATATAACCTTATATCATACTAAGACGATTAGTT
1 TATATAACCTTATATCATACTAAGACGATTAGTT
2334015 TA
1 TA
2334017 CTCTTAACAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.39
Consensus pattern (34 bp):
TATATAACCTTATATCATACTAAGACGATTAGTT
Found at i:2344585 original size:62 final size:59
Alignment explanation
Indices: 2344509--2344659 Score: 149
Period size: 59 Copynumber: 2.5 Consensus size: 59
2344499 GGTAGGCTAA
** *
2344509 CCAACCTCAATGACGAAGGCTGAGGTTAGGTGAGGAAGAATCTCACAGACCTAAAAAAGAGT
1 CCAACCTCCGTGACGAAGGCTGAGGTT-GG-G-GGAAGAATCGCACAGACCTAAAAAAGAGT
* * * * * * *
2344571 CTAACCTCCGTGACGAGGGCTGAGGTTGGGTGTAGAATGGCACGGACCTAAAGAAGAGT
1 CCAACCTCCGTGACGAAGGCTGAGGTTGGGGGAAGAATCGCACAGACCTAAAAAAGAGT
* * * *
2344630 CCAGCCTCCGTGACGAGGGTTGAGTTTGGG
1 CCAACCTCCGTGACGAAGGCTGAGGTTGGG
2344660 TGGATGAAAA
Statistics
Matches: 75, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
59 49 0.65
60 1 0.01
61 2 0.03
62 23 0.31
ACGTcount: A:0.29, C:0.20, G:0.32, T:0.19
Consensus pattern (59 bp):
CCAACCTCCGTGACGAAGGCTGAGGTTGGGGGAAGAATCGCACAGACCTAAAAAAGAGT
Found at i:2345163 original size:3 final size:3
Alignment explanation
Indices: 2345155--2345182 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2345145 GGACGGTGTC
2345155 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2345183 ACTGGTAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2345405 original size:28 final size:28
Alignment explanation
Indices: 2345346--2345404 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 28
2345336 ATTGATCATT
* *
2345346 AAATTAATTTTGATAAAATGATTTTAAA
1 AAATTAATTTTGATAAAATCAATTTAAA
* *
2345374 AAATTAATTTTTGATTAATTCAATTTAAA
1 AAATTAA-TTTTGATAAAATCAATTTAAA
2345403 AA
1 AA
2345405 TGAAATTAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 7 0.27
29 19 0.73
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (28 bp):
AAATTAATTTTGATAAAATCAATTTAAA
Found at i:2345740 original size:20 final size:20
Alignment explanation
Indices: 2345717--2345755 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2345707 GAACACCTCT
2345717 AATAA-AATATTAATTAAAAC
1 AATAATAAT-TTAATTAAAAC
*
2345737 AATAATAATTTTATTAAAA
1 AATAATAATTTAATTAAAA
2345756 TATAAGCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (20 bp):
AATAATAATTTAATTAAAAC
Found at i:2352693 original size:2 final size:2
Alignment explanation
Indices: 2352686--2352710 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2352676 ACATACAAAC
2352686 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2352711 GAGGGGGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2352903 original size:7 final size:7
Alignment explanation
Indices: 2352893--2352938 Score: 92
Period size: 7 Copynumber: 6.6 Consensus size: 7
2352883 ACAAAAGGAG
2352893 AAAGGTA
1 AAAGGTA
2352900 AAAGGTA
1 AAAGGTA
2352907 AAAGGTA
1 AAAGGTA
2352914 AAAGGTA
1 AAAGGTA
2352921 AAAGGTA
1 AAAGGTA
2352928 AAAGGTA
1 AAAGGTA
2352935 AAAG
1 AAAG
2352939 ACTTTAACAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 39 1.00
ACGTcount: A:0.59, C:0.00, G:0.28, T:0.13
Consensus pattern (7 bp):
AAAGGTA
Found at i:2352909 original size:21 final size:21
Alignment explanation
Indices: 2352885--2352938 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
2352875 GAACAAAGAC
2352885 AAAAGG-AGAAAGGTAAAAGGT
1 AAAAGGTA-AAAGGTAAAAGGT
2352906 AAAAGGTAAAAGGTAAAAGGT
1 AAAAGGTAAAAGGTAAAAGGT
2352927 AAAAGGTAAAAG
1 AAAAGGTAAAAG
2352939 ACTTTAACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 31 0.97
22 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.30, T:0.11
Consensus pattern (21 bp):
AAAAGGTAAAAGGTAAAAGGT
Found at i:2354184 original size:17 final size:17
Alignment explanation
Indices: 2354162--2354198 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
2354152 TTCATTCACC
2354162 TTTATATTACAGGAAAG
1 TTTATATTACAGGAAAG
* *
2354179 TTTATATTGCTGGAAAG
1 TTTATATTACAGGAAAG
2354196 TTT
1 TTT
2354199 TGAAATGTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.43
Consensus pattern (17 bp):
TTTATATTACAGGAAAG
Found at i:2355977 original size:20 final size:20
Alignment explanation
Indices: 2355954--2355995 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
2355944 AACATAGGGT
2355954 AGATTTTGTATATTCTAAGA
1 AGATTTTGTATATTCTAAGA
*
2355974 AGATTTTGTATGTTCTAAGA
1 AGATTTTGTATATTCTAAGA
2355994 AG
1 AG
2355996 CTCCTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (20 bp):
AGATTTTGTATATTCTAAGA
Found at i:2360886 original size:2 final size:2
Alignment explanation
Indices: 2360879--2360911 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2360869 CTCCTTAAAA
2360879 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2360912 AAAAAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2361559 original size:2 final size:2
Alignment explanation
Indices: 2361552--2361588 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2361542 ATAGTTTGTT
2361552 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2361589 ACGTGGTGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2361950 original size:18 final size:18
Alignment explanation
Indices: 2361911--2361952 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2361901 TAAATAATAA
*
2361911 AAAATATAAGAAAAAAATT
1 AAAA-ATAAGAAAAAAAGT
*
2361930 AAAAATAAGAAAAATAGT
1 AAAAATAAGAAAAAAAGT
2361948 AAAAA
1 AAAAA
2361953 AGATATAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (18 bp):
AAAAATAAGAAAAAAAGT
Found at i:2362842 original size:175 final size:174
Alignment explanation
Indices: 2362551--2362905 Score: 674
Period size: 175 Copynumber: 2.0 Consensus size: 174
2362541 CCGAGGTATC
2362551 TAAAAACTGTAACTTCTGTTTTTGGCCGTTTGAAATTGTATAATAAAGGTTTAAAGCTGCTAATT
1 TAAAAACTGTAACTTCTGTTTTTGGCCGTTTGAAATTGTATAATAAAGGTTTAAAGCTGCTAATT
2362616 GTAAGCATATCGATTAGGTTTATACCTCTTTATGTAATTAACCTATGTTTGGCTGTTCTTATTGG
66 GTAAGCATATCGATTAGGTTTATACCTCTTTATGTAATTAACCTATGTTTGGCTGTTCTTATTGG
2362681 CGCATTTGGATTCAAAGGTAAAATACTAACAATTTTGAATGATTA
131 CGCATTTGGATTCAAAGGT-AAATACTAACAATTTTGAATGATTA
*
2362726 TAAAAACTGTAACTTTTGTTTTTGGCCGTTTGAAATTGTATAATAAAGGTTTAAAGCTGCTAATT
1 TAAAAACTGTAACTTCTGTTTTTGGCCGTTTGAAATTGTATAATAAAGGTTTAAAGCTGCTAATT
*
2362791 GTAAGCATATCGATTAGGTTTATACCTCTTTATGTAATTAACCTCTGTTTGGCTGTTCTTATTGG
66 GTAAGCATATCGATTAGGTTTATACCTCTTTATGTAATTAACCTATGTTTGGCTGTTCTTATTGG
*
2362856 CGCATTTGGATTCAAAGGTAAATACTAACAATTTTGAATGATTG
131 CGCATTTGGATTCAAAGGTAAATACTAACAATTTTGAATGATTA
2362900 TAAAAA
1 TAAAAA
2362906 GTTTTTCTTA
Statistics
Matches: 177, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
174 30 0.17
175 147 0.83
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (174 bp):
TAAAAACTGTAACTTCTGTTTTTGGCCGTTTGAAATTGTATAATAAAGGTTTAAAGCTGCTAATT
GTAAGCATATCGATTAGGTTTATACCTCTTTATGTAATTAACCTATGTTTGGCTGTTCTTATTGG
CGCATTTGGATTCAAAGGTAAATACTAACAATTTTGAATGATTA
Found at i:2365546 original size:16 final size:16
Alignment explanation
Indices: 2365525--2365558 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
2365515 CTCTAGTCAG
2365525 CTAGTTGTGCTTAATT
1 CTAGTTGTGCTTAATT
2365541 CTAGTTGTGCTTAATT
1 CTAGTTGTGCTTAATT
2365557 CT
1 CT
2365559 GTATTTCTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.18, C:0.15, G:0.18, T:0.50
Consensus pattern (16 bp):
CTAGTTGTGCTTAATT
Found at i:2367834 original size:123 final size:123
Alignment explanation
Indices: 2367610--2367852 Score: 423
Period size: 123 Copynumber: 2.0 Consensus size: 123
2367600 CCATAGATTA
* * *
2367610 ATCTTTTCTGTAGATTTCCATTAACTGGTTACCATGCTCAATGCAGTTTTACTTTTCCCTTTTTA
1 ATCTTTTCTATAGATTTCCATTAACTGGTTACAATGATCAATGCAGTTTTACTTTTCCCTTTTTA
2367675 TCATTTTGTTTTGGTTTCTTCTTTATCTCCAATTGTATTCTGAATCTGCTTCTCTGTT
66 TCATTTTGTTTTGGTTTCTTCTTTATCTCCAATTGTATTCTGAATCTGCTTCTCTGTT
**
2367733 ATCTTTTCTATAGATTTCCATTAACTGGTTACAATGATCAATGCAGTTTTACTTTTCTTTTTTTA
1 ATCTTTTCTATAGATTTCCATTAACTGGTTACAATGATCAATGCAGTTTTACTTTTCCCTTTTTA
**
2367798 TCATTTTGTTTTGGTTTCTTCTTTATCTCCTCTTGTATTCTGAATCTGCTTCTCT
66 TCATTTTGTTTTGGTTTCTTCTTTATCTCCAATTGTATTCTGAATCTGCTTCTCT
2367853 ATCTTTCAGA
Statistics
Matches: 113, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
123 113 1.00
ACGTcount: A:0.17, C:0.19, G:0.11, T:0.53
Consensus pattern (123 bp):
ATCTTTTCTATAGATTTCCATTAACTGGTTACAATGATCAATGCAGTTTTACTTTTCCCTTTTTA
TCATTTTGTTTTGGTTTCTTCTTTATCTCCAATTGTATTCTGAATCTGCTTCTCTGTT
Found at i:2383961 original size:13 final size:13
Alignment explanation
Indices: 2383936--2383961 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2383926 TATTTATATC
2383936 TATTATTATTATT
1 TATTATTATTATT
2383949 TATTATTATTATT
1 TATTATTATTATT
2383962 CTGCAGAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TATTATTATTATT
Found at i:2395871 original size:16 final size:16
Alignment explanation
Indices: 2395846--2395882 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
2395836 GGTATTGACA
*
2395846 AATATTCTCTATAGTT
1 AATATACTCTATAGTT
2395862 AATATACTCTATAGTT
1 AATATACTCTATAGTT
2395878 AATAT
1 AATAT
2395883 TATCTACAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (16 bp):
AATATACTCTATAGTT
Found at i:2395888 original size:16 final size:16
Alignment explanation
Indices: 2395846--2395888 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
2395836 GGTATTGACA
*
2395846 AATATTCTCTATAGTT
1 AATATTATCTATAGTT
2395862 AATA-TACTCTATAGTT
1 AATATTA-TCTATAGTT
2395878 AATATTATCTA
1 AATATTATCTA
2395889 CAGTGTGCAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 1 0.04
16 21 0.88
17 2 0.08
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.47
Consensus pattern (16 bp):
AATATTATCTATAGTT
Found at i:2407979 original size:2 final size:2
Alignment explanation
Indices: 2407965--2408001 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
2407955 TTATTGACAT
*
2407965 TC TC TC T- TT TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2408002 AATTTGAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Found at i:2419747 original size:23 final size:24
Alignment explanation
Indices: 2419710--2419761 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
2419700 TTCTCTTTCT
* * *
2419710 TTTTCTTTTTTTTTTAAATTTTAA
1 TTTTCATTTTTTTTCAAAATTTAA
*
2419734 TTTTCATTTTTTTTCAAAATTTAT
1 TTTTCATTTTTTTTCAAAATTTAA
2419758 TTTT
1 TTTT
2419762 TAAAAAATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (24 bp):
TTTTCATTTTTTTTCAAAATTTAA
Found at i:2420298 original size:12 final size:12
Alignment explanation
Indices: 2420281--2420318 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
2420271 CTGATAAATG
2420281 TTTCTTTTTCCT
1 TTTCTTTTTCCT
*
2420293 TTTCTTTTT-TT
1 TTTCTTTTTCCT
*
2420304 TTTTTTTTTCCT
1 TTTCTTTTTCCT
2420316 TTT
1 TTT
2420319 TCTGATAGGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
11 9 0.41
12 13 0.59
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTCTTTTTCCT
Found at i:2421432 original size:99 final size:98
Alignment explanation
Indices: 2421254--2421452 Score: 353
Period size: 99 Copynumber: 2.0 Consensus size: 98
2421244 TTTGATGAAA
* * *
2421254 TCATTGCTTTGAAAAGCAATAAATAAATTTAATTTCCAGAGATGCTGAATAGTCAAAATGGTATA
1 TCATTGCTTGGAAAAACAATAAATAAATTTAATTTCCAGAAATGCTGAATAGTCAAAATGGTATA
2421319 GCATGTATGTAGCTAGGGTTTCTTTAATTATTG
66 GCATGTATGTAGCTAGGGTTTCTTTAATTATTG
*
2421352 TCATTGCTTGGAAAAACAATAAATAAATTTAATTTCCAGAAAATGCTGAATATTCAAAATGGTAT
1 TCATTGCTTGGAAAAACAATAAATAAATTTAATTTCCAG-AAATGCTGAATAGTCAAAATGGTAT
2421417 AGCATGTATGTAGCTAGGGTTTCTTTAATTATTG
65 AGCATGTATGTAGCTAGGGTTTCTTTAATTATTG
2421451 TC
1 TC
2421453 TTAATTATCG
Statistics
Matches: 96, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
98 37 0.39
99 59 0.61
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.37
Consensus pattern (98 bp):
TCATTGCTTGGAAAAACAATAAATAAATTTAATTTCCAGAAATGCTGAATAGTCAAAATGGTATA
GCATGTATGTAGCTAGGGTTTCTTTAATTATTG
Found at i:2427278 original size:25 final size:24
Alignment explanation
Indices: 2427237--2427289 Score: 79
Period size: 25 Copynumber: 2.2 Consensus size: 24
2427227 ATTAATAATT
* *
2427237 TAAATATTTATATTATATTTTATA
1 TAAAAATTTATATTATAATTTATA
2427261 TAAAAATTATATATTATAATTTATA
1 TAAAAATT-TATATTATAATTTATA
2427286 TAAA
1 TAAA
2427290 TATAAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 7 0.27
25 19 0.73
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TAAAAATTTATATTATAATTTATA
Found at i:2428909 original size:2 final size:2
Alignment explanation
Indices: 2428902--2428933 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
2428892 TTTATTAGAT
2428902 TA TA TA TA TA TA TA -A TA T- TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2428934 CAAGAAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2433021 original size:13 final size:13
Alignment explanation
Indices: 2433003--2433028 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2432993 CTATTTTGGT
2433003 GGAATTTCAAGAG
1 GGAATTTCAAGAG
2433016 GGAATTTCAAGAG
1 GGAATTTCAAGAG
2433029 AGAAATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.31, T:0.23
Consensus pattern (13 bp):
GGAATTTCAAGAG
Found at i:2437742 original size:21 final size:21
Alignment explanation
Indices: 2437716--2437755 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2437706 TATTAAAAAT
*
2437716 AATTAAATTAAAATAAATAAA
1 AATTAAAATAAAATAAATAAA
*
2437737 AATTAAAATAAAATTAATA
1 AATTAAAATAAAATAAATA
2437756 GATTATAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (21 bp):
AATTAAAATAAAATAAATAAA
Found at i:2445578 original size:31 final size:30
Alignment explanation
Indices: 2445521--2445583 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 30
2445511 ATTATATTTT
* *
2445521 ATATAAAAATTATGTATTATAATTTATATAA
1 ATATAAAAAATATATATTATAATTTAT-TAA
*
2445552 ATATAAAAAATATAT-TTTTAATTTTATTAA
1 ATATAAAAAATATATATTATAA-TTTATTAA
2445582 AT
1 AT
2445584 TTAGTTATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 10 0.36
31 18 0.64
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (30 bp):
ATATAAAAAATATATATTATAATTTATTAA
Found at i:2445583 original size:30 final size:31
Alignment explanation
Indices: 2445521--2445583 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 31
2445511 ATTATATTTT
* *
2445521 ATATAAAAATTATGTATTATAATTTATATAA
1 ATATAAAAAATATATATTATAATTTATATAA
*
2445552 ATATAAAAAATATAT-TTTTAATTT-TATTAA
1 ATATAAAAAATATATATTATAATTTATA-TAA
2445582 AT
1 AT
2445584 TTAGTTATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 2 0.07
30 13 0.46
31 13 0.46
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (31 bp):
ATATAAAAAATATATATTATAATTTATATAA
Found at i:2447189 original size:2 final size:2
Alignment explanation
Indices: 2447184--2447219 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
2447174 TTTATTAGAT
2447184 TA TA TA TA TA TA TA TA -A TA T- TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2447220 AAGGAAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2447207 original size:20 final size:20
Alignment explanation
Indices: 2447182--2447220 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
2447172 TTTTTATTAG
2447182 ATTATATATATATATATAAT
1 ATTATATATATATATATAAT
2447202 ATTATATATATATATATAA
1 ATTATATATATATATATAA
2447221 AGGAAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTATATATATATATATAAT
Found at i:2448694 original size:8 final size:8
Alignment explanation
Indices: 2448681--2448717 Score: 74
Period size: 8 Copynumber: 4.6 Consensus size: 8
2448671 AAGGAAAAAA
2448681 ATAATACT
1 ATAATACT
2448689 ATAATACT
1 ATAATACT
2448697 ATAATACT
1 ATAATACT
2448705 ATAATACT
1 ATAATACT
2448713 ATAAT
1 ATAAT
2448718 TATGAGGCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (8 bp):
ATAATACT
Found at i:2449011 original size:21 final size:22
Alignment explanation
Indices: 2448969--2449011 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
2448959 TAATTACTTT
*
2448969 TTTTTAATAATATAAGTTTATA
1 TTTTTAATAATATAAGTATATA
2448991 TTTTT-ATAATATCAA-TATATA
1 TTTTTAATAATAT-AAGTATATA
2449012 AATATTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTTTAATAATATAAGTATATA
Found at i:2449586 original size:2 final size:2
Alignment explanation
Indices: 2449581--2449607 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2449571 ATATATATAT
2449581 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
2449608 TATGAACTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2451135 original size:17 final size:16
Alignment explanation
Indices: 2451100--2451137 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
2451090 CAAATTAATG
*
2451100 ATAT-TAAAGATAAAA
1 ATATATAAAAATAAAA
2451115 ATATATAAAAAT-AAA
1 ATATATAAAAATAAAA
2451130 ATATATAA
1 ATATATAA
2451138 TATGAGTATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (16 bp):
ATATATAAAAATAAAA
Found at i:2451350 original size:13 final size:13
Alignment explanation
Indices: 2451332--2451356 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2451322 CTATTTTGGT
2451332 GAATTTCAAGAGG
1 GAATTTCAAGAGG
2451345 GAATTTCAAGAG
1 GAATTTCAAGAG
2451357 AGAAAGTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.28, T:0.24
Consensus pattern (13 bp):
GAATTTCAAGAGG
Found at i:2457558 original size:23 final size:26
Alignment explanation
Indices: 2457520--2457567 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 26
2457510 GAATATTTCA
2457520 ACGTATAATTGTTTTA-AAATTAAAC
1 ACGTATAATTGTTTTACAAATTAAAC
*
2457545 ACGTA-AATT-TTTTACATATTAAA
1 ACGTATAATTGTTTTACAAATTAAA
2457568 AGAAACATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 5 0.24
24 11 0.52
25 5 0.24
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (26 bp):
ACGTATAATTGTTTTACAAATTAAAC
Found at i:2458014 original size:2 final size:2
Alignment explanation
Indices: 2458007--2458042 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2457997 TCATTCCTGC
*
2458007 TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2458043 ACCTCAGTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2458277 original size:11 final size:11
Alignment explanation
Indices: 2458261--2458314 Score: 54
Period size: 11 Copynumber: 4.6 Consensus size: 11
2458251 ATAAAAATAT
2458261 AAATTTTTTTA
1 AAATTTTTTTA
2458272 AAATTTTTTTA
1 AAATTTTTTTA
* *
2458283 TTAAATTTATGTA
1 --AAATTTTTTTA
*
2458296 TAATTTTTATTA
1 AAATTTTT-TTA
2458308 AAATTTT
1 AAATTTT
2458315 AAAATAAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
11 17 0.50
12 8 0.24
13 9 0.26
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (11 bp):
AAATTTTTTTA
Found at i:2459327 original size:26 final size:25
Alignment explanation
Indices: 2459273--2459327 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
2459263 CTCACTTAAG
*
2459273 AATTTTATAAAAATTTACCATTTGA
1 AATTTTATAAAAATTTACCATTGGA
* *
2459298 AATTTT-TATAAATTCTATCATTGGA
1 AATTTTATAAAAATT-TACCATTGGA
2459323 TAATT
1 -AATT
2459328 ACTATTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 7 0.28
25 14 0.56
26 4 0.16
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.47
Consensus pattern (25 bp):
AATTTTATAAAAATTTACCATTGGA
Found at i:2459852 original size:8 final size:8
Alignment explanation
Indices: 2459839--2459873 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
2459829 CTCAACTATC
2459839 TATTTTTT
1 TATTTTTT
2459847 TA-TTTTT
1 TATTTTTT
*
2459854 TATTTTCT
1 TATTTTTT
2459862 TATTTTTT
1 TATTTTTT
2459870 TATT
1 TATT
2459874 AGCAAAAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 7 0.29
8 17 0.71
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.83
Consensus pattern (8 bp):
TATTTTTT
Found at i:2459859 original size:15 final size:15
Alignment explanation
Indices: 2459839--2459869 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2459829 CTCAACTATC
*
2459839 TATTTTTTTATTTTT
1 TATTTTCTTATTTTT
2459854 TATTTTCTTATTTTT
1 TATTTTCTTATTTTT
2459869 T
1 T
2459870 TATTAGCAAA
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:0.13, C:0.03, G:0.00, T:0.84
Consensus pattern (15 bp):
TATTTTCTTATTTTT
Found at i:2460160 original size:41 final size:41
Alignment explanation
Indices: 2460061--2460312 Score: 252
Period size: 41 Copynumber: 6.1 Consensus size: 41
2460051 AGTAAACAAA
* * * * * *
2460061 GCTCCTTTAAATAGAGGCTCAACGACTTTGAAAAAAATAAAT
1 GCTCCTCTAAACAGAGGCACCACAACTTTGAAAAATA-AAAT
* *
2460103 GCTCCTCTAAACAGAGGCACCACAACGTTGAAAAGTAAAAT
1 GCTCCTCTAAACAGAGGCACCACAACTTTGAAAAATAAAAT
* * * *
2460144 GCTCCTTTAAATAGAGGCATCACAACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACAACTTTGAAAAATAAAAT
* *
2460185 GTTCCTCTAAACAGAAGCACCACAACTTTGAAAAATAAAAT
1 GCTCCTCTAAACAGAGGCACCACAACTTTGAAAAATAAAAT
* * * **
2460226 TCTCCTCTAAACAGAGGTACCACAACTTTGAAAAGTAAAGC
1 GCTCCTCTAAACAGAGGCACCACAACTTTGAAAAATAAAAT
* * * * * * *
2460267 ACTCTTCTAAATAGAGGTATCACAACTTTTGAAAAGTAAAAG
1 GCTCCTCTAAACAGAGGCACCACAAC-TTTGAAAAATAAAAT
2460309 GCTC
1 GCTC
2460313 TTCGATAATC
Statistics
Matches: 175, Mismatches: 34, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
41 130 0.74
42 45 0.26
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.24
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACCACAACTTTGAAAAATAAAAT
Found at i:2460532 original size:22 final size:23
Alignment explanation
Indices: 2460488--2460534 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
2460478 AAGAATTTAA
*
2460488 ATTTGCAAGATTTCAAGATTCGC
1 ATTTGCAAGATTTCAAGACTCGC
2460511 ATTTGCAA-ATTGT-AAGACTCGC
1 ATTTGCAAGATT-TCAAGACTCGC
2460533 AT
1 AT
2460535 CCAACATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (23 bp):
ATTTGCAAGATTTCAAGACTCGC
Found at i:2461969 original size:10 final size:11
Alignment explanation
Indices: 2461949--2461987 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
2461939 TTAATTTGAG
2461949 TCTTATTTTTC-
1 TCTT-TTTTTCA
2461960 TCTTTTTTTCA
1 TCTTTTTTTCA
2461971 TCTTTTTTTCA
1 TCTTTTTTTCA
2461982 TTCTTT
1 -TCTTT
2461988 CATTTTTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 6 0.23
11 15 0.58
12 5 0.19
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (11 bp):
TCTTTTTTTCA
Found at i:2461993 original size:28 final size:27
Alignment explanation
Indices: 2461960--2462022 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 27
2461950 CTTATTTTTC
*
2461960 TCTTTTTTTCATCTTTTTTTCATTCTT
1 TCTTTTTTTCATCTTTTTTTCACTCTT
* * *
2461987 TCATTTTTTTCTTTTTTTTTTTACTCTT
1 TC-TTTTTTTCATCTTTTTTTCACTCTT
2462015 TCTTTTTT
1 TCTTTTTT
2462023 CTTTTTCATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 8 0.26
28 23 0.74
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (27 bp):
TCTTTTTTTCATCTTTTTTTCACTCTT
Found at i:2462006 original size:11 final size:11
Alignment explanation
Indices: 2461949--2462028 Score: 52
Period size: 11 Copynumber: 6.6 Consensus size: 11
2461939 TTAATTTGAG
* *
2461949 TCTTATTTTTC
1 TCTTTTTTTTT
**
2461960 TCTTTTTTTCA
1 TCTTTTTTTTT
*
2461971 TCTTTTTTTCAT
1 TCTTTTTTT-TT
2461983 TCTTTCATTTTTT
1 TCTTT--TTTTTT
2461996 TCTTTTTTTTTT
1 TC-TTTTTTTTT
2462008 TACTCTTTCTTTTT
1 T-CT-TTT-TTTTT
2462022 TCTTTTT
1 TCTTTTT
2462029 CATATTTTCC
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
11 18 0.32
12 16 0.29
13 9 0.16
14 13 0.23
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (11 bp):
TCTTTTTTTTT
Found at i:2466449 original size:25 final size:25
Alignment explanation
Indices: 2466419--2466477 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
2466409 AAATTTAGAC
2466419 AAAATTTCT-CACTTAAAAATTTTAT
1 AAAATTT-TACACTTAAAAATTTTAT
* *
2466444 AAAATTTTACCATTTAAAATTTTTAT
1 AAAATTTTA-CACTTAAAAATTTTAT
2466470 -AAATTTTA
1 AAAATTTTA
2466478 TCATTAGATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 1 0.03
25 15 0.50
26 14 0.47
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (25 bp):
AAAATTTTACACTTAAAAATTTTAT
Found at i:2466490 original size:26 final size:26
Alignment explanation
Indices: 2466431--2466482 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
2466421 AATTTCTCAC
*
2466431 TTAAAAATTTTATAAAATTTTACCAT
1 TTAAAATTTTTATAAAATTTTACCAT
*
2466457 TTAAAATTTTTAT-AAATTTTATCAT
1 TTAAAATTTTTATAAAATTTTACCAT
2466482 T
1 T
2466483 AGATAATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 12 0.50
26 12 0.50
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (26 bp):
TTAAAATTTTTATAAAATTTTACCAT
Found at i:2466768 original size:12 final size:11
Alignment explanation
Indices: 2466741--2466767 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2466731 AATCTGGAAA
2466741 TTTTTCAAATT
1 TTTTTCAAATT
2466752 TTTTTCAAATT
1 TTTTTCAAATT
2466763 TTTTT
1 TTTTT
2466768 TTAAAACCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTTTCAAATT
Found at i:2469731 original size:20 final size:21
Alignment explanation
Indices: 2469684--2469731 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
2469674 TAAAACTAAA
2469684 AAAAT-AATAATAAAAGAAAT
1 AAAATGAATAATAAAAGAAAT
**
2469704 AAAA-GAATAAT-AAAGACCT
1 AAAATGAATAATAAAAGAAAT
2469723 AAAATGAAT
1 AAAATGAAT
2469732 TTACTTCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.69, C:0.04, G:0.08, T:0.19
Consensus pattern (21 bp):
AAAATGAATAATAAAAGAAAT
Found at i:2469935 original size:20 final size:20
Alignment explanation
Indices: 2469899--2469936 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2469889 CGTTTTCATT
*
2469899 TTTTGAGCTCTTTATTTTTA
1 TTTTGAGATCTTTATTTTTA
2469919 TTTTGAGAT-TTTGATTTT
1 TTTTGAGATCTTT-ATTTT
2469937 AGCAAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.16, C:0.05, G:0.13, T:0.66
Consensus pattern (20 bp):
TTTTGAGATCTTTATTTTTA
Found at i:2470330 original size:27 final size:27
Alignment explanation
Indices: 2470299--2470365 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
2470289 TTTCGATTTG
*
2470299 AATTTAAATAATTAGCTAAACATATTA
1 AATTTAAATAATTAGCCAAACATATTA
* *
2470326 AATTTACATAATTATCCAAACATATTA
1 AATTTAAATAATTAGCCAAACATATTA
2470353 AATTTAAATAATT
1 AATTTAAATAATT
2470366 TATTAAATAG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.51, C:0.09, G:0.01, T:0.39
Consensus pattern (27 bp):
AATTTAAATAATTAGCCAAACATATTA
Found at i:2470566 original size:29 final size:28
Alignment explanation
Indices: 2470509--2470571 Score: 65
Period size: 29 Copynumber: 2.2 Consensus size: 28
2470499 TCTTCTTTTG
* * *
2470509 TATTTTATGTATTGTATTATTTATTTAT
1 TATTTTATGTATTATATTATGTATATAT
2470537 TATTATTATGTATTA-ATATATGTATATATT
1 TATT-TTATGTATTATAT-TATGTATATA-T
2470567 TATTT
1 TATTT
2470572 ATTTATTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
28 6 0.21
29 18 0.62
30 5 0.17
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.63
Consensus pattern (28 bp):
TATTTTATGTATTATATTATGTATATAT
Found at i:2470588 original size:35 final size:39
Alignment explanation
Indices: 2470521--2470612 Score: 101
Period size: 37 Copynumber: 2.5 Consensus size: 39
2470511 TTTTATGTAT
2470521 TGTAT-TATTTATTTA-TTATTATTATGTATTAATA-TA
1 TGTATATATTTATTTATTTATTATTATGTATTAATATTA
*
2470557 TGTATATATTTATTTATTTATT-TT-T-TGTTAATATTTA
1 TGTATATATTTATTTATTTATTATTATGTATTAATA-TTA
*
2470594 TGTGTAT-TTTA-TTATTTAT
1 TGTATATATTTATTTATTTAT
2470613 GTATATATAT
Statistics
Matches: 50, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
35 15 0.30
36 10 0.20
37 20 0.40
38 5 0.10
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (39 bp):
TGTATATATTTATTTATTTATTATTATGTATTAATATTA
Found at i:2470627 original size:18 final size:17
Alignment explanation
Indices: 2470512--2470627 Score: 52
Period size: 16 Copynumber: 7.1 Consensus size: 17
2470502 TCTTTTGTAT
2470512 TTTATGTAT-TGTAT-TA
1 TTTATGTATAT-TATATA
2470528 TTTAT-T-TATTAT-TA
1 TTTATGTATATTATATA
*
2470542 -TTATGTAT-TAATATA
1 TTTATGTATATTATATA
* * *
2470557 TGTATATAT-TTATTTA
1 TTTATGTATATTATATA
* * *
2470573 TTTATTTTTTGTTA-ATA
1 TTTA-TGTATATTATATA
* *
2470590 TTTATGTGTATTTTATTA
1 TTTATGTATATTATA-TA
2470608 TTTATGTATATATATATA
1 TTTATGTATAT-TATATA
2470626 TT
1 TT
2470628 ATATTTTTTT
Statistics
Matches: 75, Mismatches: 15, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
13 4 0.05
14 10 0.13
15 5 0.07
16 24 0.32
17 10 0.13
18 19 0.25
19 3 0.04
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (17 bp):
TTTATGTATATTATATA
Found at i:2470663 original size:63 final size:63
Alignment explanation
Indices: 2470553--2470714 Score: 151
Period size: 61 Copynumber: 2.6 Consensus size: 63
2470543 TATGTATTAA
* * * * * *
2470553 TATATGTATATATT-TATTTATTTATTTTTTGTTAATATTTATGTGTA-TTTTA-TTAT-TTAT
1 TATATATATATATTATATTTTTTTATTTTTTATT-TTATTCATGTGTATTTTTACTTATCTAAT
*
2470613 GTATATATATATATTATATTTTTTTATCTTTTTATTTTATTCATTTTGTATTTTTACTTATCTAA
1 -TATATATATATATTATATTTTTTTAT-TTTTTATTTTATTCA-TGTGTATTTTTACTTATCTAA
2470678 T
63 T
*
2470679 TATATAT-T-TGA-TATATTTTTTTA-TTATTATTTTATT
1 TATATATATAT-ATTATATTTTTTTATTTTTTATTTTATT
2470715 TATCCTATAA
Statistics
Matches: 86, Mismatches: 8, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
61 25 0.29
62 15 0.17
63 25 0.29
64 7 0.08
65 11 0.13
66 3 0.03
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (63 bp):
TATATATATATATTATATTTTTTTATTTTTTATTTTATTCATGTGTATTTTTACTTATCTAAT
Found at i:2471070 original size:24 final size:23
Alignment explanation
Indices: 2471039--2471093 Score: 67
Period size: 26 Copynumber: 2.3 Consensus size: 23
2471029 GGGTGTGAGA
2471039 AAAATTTTT-TAGAAATTTTTGGCG
1 AAAATTTTTCTAGAAATTTTT-G-G
*
2471063 AAAATTTTTTCTGGAAATTTTTGG
1 AAAA-TTTTTCTAGAAATTTTTGG
2471087 AAAATTT
1 AAAATTT
2471094 CCAGATTCTG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 3 0.11
24 9 0.32
25 6 0.21
26 10 0.36
ACGTcount: A:0.35, C:0.04, G:0.15, T:0.47
Consensus pattern (23 bp):
AAAATTTTTCTAGAAATTTTTGG
Found at i:2471876 original size:60 final size:59
Alignment explanation
Indices: 2471716--2472183 Score: 569
Period size: 60 Copynumber: 7.9 Consensus size: 59
2471706 AAAAATAAAA
* * *
2471716 AAATTCCAAAAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
1 AAATTTCAAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
*
2471775 AAATTTTC---AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAAT
1 AAA-TTTCAAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
2471832 AAA-TTCAAAAAAAAAATATTTTTAGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
1 AAATTTC-AAAAAAAAATATTTTT-GGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
* * * *
2471892 AAATTTC--CAAAAAATATTTTTGAGGAAGAGTTGAAAGTATCAATTTTCCTCAGAAAT
1 AAATTTCAAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
*
2471949 AAATTTCAAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAAT
1 AAATTTC-AAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT---AG--AAAT
* *
2472014 AAATTTCCAAAAAAAATATTGTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
1 AAATTTCAAAAAAAAATATT-TTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
** *** *
2472074 AAATTTTTAAAAAAAGGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT-GAAAAT
1 AAATTTCAAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAG-AAAT
* *
2472133 CGAAATTTC--CAAAAAATA-TTTTGGGAAAAAGTTGAAAGTAATCAATTTTCC
1 --AAATTTCAAAAAAAAATATTTTTGGGGAAAAGTTGAAAGT-ATCAATTTTCC
2472184 CTACAAAAAA
Statistics
Matches: 358, Mismatches: 31, Indels: 40
0.83 0.07 0.09
Matches are distributed among these distances:
55 3 0.01
57 89 0.25
58 33 0.09
59 67 0.19
60 99 0.28
61 9 0.03
62 2 0.01
63 2 0.01
64 12 0.03
65 42 0.12
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.33
Consensus pattern (59 bp):
AAATTTCAAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
Found at i:2471878 original size:117 final size:117
Alignment explanation
Indices: 2471716--2472183 Score: 660
Period size: 117 Copynumber: 3.9 Consensus size: 117
2471706 AAAAATAAAA
* *
2471716 AAATTCCAAAAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAG-AAATAAATT
1 AAATTCAAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAATAAATT
* *
2471780 TTCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAGAAAT
66 TCCAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTCAGAAAT
2471832 AAATTCAAAAAAAAAATATTTTTAGGGGAAAAGTTGAAAGTATCAATTTTCCTTAG-AAATAAAT
1 AAATTCAAAAAAAAAATATTTTTA-GGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAATAAAT
*
2471896 TTCCAAAAAATATTTTTGAGG-AAGAGTTGAAAGTATCAATTTTCCTCAGAAAT
65 TTCCAAAAAATATTTTTG-GGAAAAAGTTGAAAGTATCAATTTTCCTCAGAAAT
2471949 AAATTTCAAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAAT
1 AAA-TTCAAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT---AG-AAAAT
*
2472014 AAATTTCCAAAAAAAATATTGTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT
61 AAATTTCC--AAAAAATATT-TTTGGGAAAAAGTTGAAAGTATCAATTTTCCTCAGAAAT
*** ***
2472074 AAATTTTTAAAAAAAGGGTTTTT-GAGGAAAAGTTGAAAGTATCAATTTTCCTT-GAAAATCGAA
1 AAATTCAAAAAAAAAATATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAAT--AA
2472137 ATTTCCAAAAAATA-TTTTGGGAAAAAGTTGAAAGTAATCAATTTTCC
63 ATTTCCAAAAAATATTTTTGGGAAAAAGTTGAAAGT-ATCAATTTTCC
2472184 CTACAAAAAA
Statistics
Matches: 324, Mismatches: 12, Indels: 30
0.89 0.03 0.08
Matches are distributed among these distances:
116 22 0.07
117 139 0.43
118 35 0.11
119 13 0.04
120 3 0.01
121 8 0.02
122 12 0.04
123 1 0.00
124 54 0.17
125 37 0.11
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.33
Consensus pattern (117 bp):
AAATTCAAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAATAAATT
TCCAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTCAGAAAT
Found at i:2473048 original size:2 final size:2
Alignment explanation
Indices: 2473041--2473081 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
2473031 GTTATTGGAT
* *
2473041 TA TA TA TA TA TA TA TT TA TA TA T- TA T- TA TA CA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2473081 T
1 T
2473082 GTACAAGAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:2475520 original size:18 final size:18
Alignment explanation
Indices: 2475486--2475521 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2475476 ACATATTTGA
**
2475486 CATAAAGTAAAGGTGACT
1 CATAAAGTAAACATGACT
2475504 CATAAAGTAAACATGACT
1 CATAAAGTAAACATGACT
2475522 TAACTTAGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.47, C:0.14, G:0.17, T:0.22
Consensus pattern (18 bp):
CATAAAGTAAACATGACT
Found at i:2481434 original size:21 final size:22
Alignment explanation
Indices: 2481392--2481434 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
2481382 TAATTACTTT
*
2481392 TTTTTAATAATATAAGTTTATA
1 TTTTTAATAATATAAGTATATA
2481414 TTTTT-ATAATATCAA-TATATA
1 TTTTTAATAATAT-AAGTATATA
2481435 AATATTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTTTAATAATATAAGTATATA
Found at i:2492721 original size:15 final size:15
Alignment explanation
Indices: 2492699--2492749 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
2492689 ATATTATTTT
2492699 TATT-AATATAATAA
1 TATTAAATATAATAA
*
2492713 TATTAAATATAGTAA
1 TATTAAATATAATAA
*
2492728 TATTTAATATTAA-AA
1 TATTAAATA-TAATAA
2492743 TATTAAA
1 TATTAAA
2492750 AATATTTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
14 4 0.13
15 25 0.81
16 2 0.06
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (15 bp):
TATTAAATATAATAA
Found at i:2493173 original size:20 final size:19
Alignment explanation
Indices: 2493138--2493175 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
2493128 TTTAATTAAA
2493138 ATTAAATAAAATTATTTTT
1 ATTAAATAAAATTATTTTT
2493157 ATTAATATAATAA-TATTTT
1 ATTAA-ATAA-AATTATTTT
2493176 AGTCGGGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.29
20 10 0.59
21 2 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTAAATAAAATTATTTTT
Found at i:2493296 original size:23 final size:23
Alignment explanation
Indices: 2493230--2493298 Score: 68
Period size: 25 Copynumber: 2.9 Consensus size: 23
2493220 CTCTTTAGAG
2493230 TAAAAT-TATAAAATTATTTAAAAT
1 TAAAATAT-TAAAATT-TTTAAAAT
*
2493254 TAAAATATTAAAATACTTTTAATAT
1 TAAAATATTAAAAT--TTTTAAAAT
* *
2493279 TAATATTTTAAAATTTTTAA
1 TAAAATATTAAAATTTTTAA
2493299 GTAAAATTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
23 6 0.15
24 12 0.31
25 20 0.51
26 1 0.03
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (23 bp):
TAAAATATTAAAATTTTTAAAAT
Found at i:2493326 original size:19 final size:20
Alignment explanation
Indices: 2493304--2493341 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2493294 TTTAAGTAAA
2493304 ATTAA-ATAAAAATATTTTT
1 ATTAATATAAAAATATTTTT
*
2493323 ATTAATATAATAATATTTT
1 ATTAATATAAAAATATTTT
2493342 AAATCGAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTAATATAAAAATATTTTT
Found at i:2493341 original size:46 final size:50
Alignment explanation
Indices: 2493248--2493341 Score: 115
Period size: 46 Copynumber: 1.9 Consensus size: 50
2493238 TAAAATTATT
**
2493248 TAAAATTAAAATATTAAAATACTTTTAATATTAATATTTTAAAATTTTTAAG
1 TAAAATTAAAATA-TAAAATACTTTT-ATATTAATATAATAAAATTTTTAAG
*
2493300 TAAAATT-AAATA-AAAATA-TTTT-TATTAATATAATAATATTTT
1 TAAAATTAAAATATAAAATACTTTTATATTAATATAATAAAATTTT
2493342 AAATCGAATC
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
46 17 0.44
48 4 0.10
49 6 0.15
51 5 0.13
52 7 0.18
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (50 bp):
TAAAATTAAAATATAAAATACTTTTATATTAATATAATAAAATTTTTAAG
Found at i:2493484 original size:20 final size:19
Alignment explanation
Indices: 2493441--2493485 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
2493431 CACCCATAAA
2493441 TAATTTTTTTTCAAAAAAT
1 TAATTTTTTTTCAAAAAAT
**
2493460 T-ATTTTTTTCTTTAAAAAT
1 TAATTTTTTT-TCAAAAAAT
2493479 TAATTTT
1 TAATTTT
2493486 CAAAAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 8 0.36
19 9 0.41
20 5 0.23
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (19 bp):
TAATTTTTTTTCAAAAAAT
Found at i:2494300 original size:7 final size:7
Alignment explanation
Indices: 2494270--2494314 Score: 54
Period size: 7 Copynumber: 6.4 Consensus size: 7
2494260 CTCAACTCAC
2494270 TTCAATG
1 TTCAATG
*
2494277 TTCGATG
1 TTCAATG
*
2494284 TTAAATG
1 TTCAATG
2494291 TTCAATG
1 TTCAATG
*
2494298 TTCAAAG
1 TTCAATG
*
2494305 TTCAAAG
1 TTCAATG
2494312 TTC
1 TTC
2494315 CAACCTTTCT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (7 bp):
TTCAATG
Found at i:2501606 original size:2 final size:2
Alignment explanation
Indices: 2501599--2501631 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2501589 GAAAATCGGG
2501599 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
2501632 GTACTTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2506953 original size:25 final size:26
Alignment explanation
Indices: 2506925--2506975 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
2506915 TCAATATATA
2506925 TCAGTAA-AATATTAAATTTTTAATT
1 TCAGTAACAATATTAAATTTTTAATT
* *
2506950 TCAGTAATCAATATTCATTTTTTAAT
1 TCAGTAA-CAATATTAAATTTTTAAT
2506976 AATCCCAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 7 0.32
27 15 0.68
ACGTcount: A:0.39, C:0.08, G:0.04, T:0.49
Consensus pattern (26 bp):
TCAGTAACAATATTAAATTTTTAATT
Found at i:2507080 original size:2 final size:2
Alignment explanation
Indices: 2507073--2507117 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
2507063 AGCATTTCCC
*
2507073 TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2507115 TA T
1 TA T
2507118 CTACATCTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2510392 original size:15 final size:15
Alignment explanation
Indices: 2510362--2510406 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
2510352 AAATTTTAAT
* *
2510362 TTTATATTTATAATA
1 TTTATATTTTTTATA
2510377 TTTATATTTTTTATA
1 TTTATATTTTTTATA
* *
2510392 TTGAGATTTTTTATA
1 TTTATATTTTTTATA
2510407 AAAAAATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (15 bp):
TTTATATTTTTTATA
Found at i:2510965 original size:26 final size:25
Alignment explanation
Indices: 2510919--2511008 Score: 65
Period size: 26 Copynumber: 3.4 Consensus size: 25
2510909 TCATTATTTA
*
2510919 TTTTAAAATATATATTAATTATAAT
1 TTTTAAAATATATATTAATTAAAAT
*
2510944 TTTTATAAATAT-TATTGTATTAAAAT
1 TTTTA-AAATATATATT-AATTAAAAT
*** *
2510970 TTTATCTTATATATATCTTATTAAAAT
1 TTT-TAAAATATATAT-TAATTAAAAT
2510997 ATATTTAAAATA
1 -T-TTTAAAATA
2511009 ATTAATAAAC
Statistics
Matches: 50, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
25 9 0.18
26 20 0.40
27 13 0.26
28 6 0.12
29 2 0.04
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.52
Consensus pattern (25 bp):
TTTTAAAATATATATTAATTAAAAT
Found at i:2511315 original size:22 final size:22
Alignment explanation
Indices: 2511288--2511330 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2511278 CAGCCTCCCG
2511288 ACCAACCACCCTACAGCCACCA
1 ACCAACCACCCTACAGCCACCA
* **
2511310 ACCAACTATTCTACAGCCACC
1 ACCAACCACCCTACAGCCACC
2511331 TAGATCCCTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.35, C:0.49, G:0.05, T:0.12
Consensus pattern (22 bp):
ACCAACCACCCTACAGCCACCA
Found at i:2511447 original size:24 final size:24
Alignment explanation
Indices: 2511420--2511467 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
2511410 AAAGGAAGCT
*
2511420 CTCTCGGAATCCCCTTCAATCTCC
1 CTCTAGGAATCCCCTTCAATCTCC
*
2511444 CTCTAGGAATTCCCTTCAATCTCC
1 CTCTAGGAATCCCCTTCAATCTCC
2511468 TTAAAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.19, C:0.42, G:0.08, T:0.31
Consensus pattern (24 bp):
CTCTAGGAATCCCCTTCAATCTCC
Found at i:2514010 original size:29 final size:29
Alignment explanation
Indices: 2513955--2514010 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
2513945 TATCATTTAT
* **
2513955 ATAATAGTAATTAAATATTAAATAAAATA
1 ATAATAATAATTAAATAACAAATAAAATA
2513984 ATAATAATAATTAGAATAACAAA-AAAA
1 ATAATAATAATTA-AATAACAAATAAAA
2514011 GAGGGAAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 16 0.70
30 7 0.30
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.29
Consensus pattern (29 bp):
ATAATAATAATTAAATAACAAATAAAATA
Found at i:2515173 original size:12 final size:11
Alignment explanation
Indices: 2515137--2515175 Score: 51
Period size: 12 Copynumber: 3.3 Consensus size: 11
2515127 TCAATTCAAG
2515137 TATTTATTTTTT
1 TATTT-TTTTTT
2515149 TATTTTTTATTT
1 TATTTTTT-TTT
2515161 TATTTTTATTTT
1 TATTTTT-TTTT
2515173 TAT
1 TAT
2515176 CATTTTAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.12
12 21 0.84
13 1 0.04
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (11 bp):
TATTTTTTTTT
Found at i:2515262 original size:3 final size:3
Alignment explanation
Indices: 2515254--2515289 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
2515244 GGTTACCTTT
2515254 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2515290 AGTTTAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2515357 original size:3 final size:3
Alignment explanation
Indices: 2515349--2515390 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
2515339 TTATAAGATA
2515349 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2515391 GAAAATGATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2516235 original size:32 final size:31
Alignment explanation
Indices: 2516197--2516256 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
2516187 TAAACCCTCC
*
2516197 AAAATCCTAAACGTTCGAAACCTTAAAATTTT
1 AAAATCCTAAA-GTTCGAAACCCTAAAATTTT
* *
2516229 AAAATCCTAAATTTTGAAACCCTAAAAT
1 AAAATCCTAAAGTTCGAAACCCTAAAAT
2516257 CTCAAACCCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 14 0.56
32 11 0.44
ACGTcount: A:0.47, C:0.18, G:0.05, T:0.30
Consensus pattern (31 bp):
AAAATCCTAAAGTTCGAAACCCTAAAATTTT
Found at i:2516309 original size:23 final size:23
Alignment explanation
Indices: 2516283--2516362 Score: 69
Period size: 23 Copynumber: 3.5 Consensus size: 23
2516273 TCAAAACTCA
2516283 AAACCTTAAAACCATAAACCTTG
1 AAACCTTAAAACCATAAACCTTG
* *
2516306 AAACTTTAAAACCA-AAA-CTCTA
1 AAACCTTAAAACCATAAACCT-TG
*
2516328 AAACC-TAAAAGCC-TAAAACCCTG
1 AAACCTTAAAA-CCAT-AAACCTTG
*
2516351 AAATCTTAAAAC
1 AAACCTTAAAAC
2516363 GATACCCTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
21 7 0.16
22 10 0.22
23 22 0.49
24 6 0.13
ACGTcount: A:0.51, C:0.25, G:0.04, T:0.20
Consensus pattern (23 bp):
AAACCTTAAAACCATAAACCTTG
Found at i:2516329 original size:14 final size:15
Alignment explanation
Indices: 2516275--2516347 Score: 57
Period size: 15 Copynumber: 4.9 Consensus size: 15
2516265 CTAAGCCTTC
2516275 AAAACTC-AAAACCTT
1 AAAACTCTAAAACC-T
2516290 AAAAC-C-ATAAACCTT
1 AAAACTCTA-AAACC-T
* *
2516305 GAAACTTTAAAACC-
1 AAAACTCTAAAACCT
2516319 AAAACTCTAAAACCT
1 AAAACTCTAAAACCT
2516334 AAAAGC-CTAAAACC
1 AAAA-CTCTAAAACC
2516348 CTGAAATCTT
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
14 14 0.29
15 28 0.57
16 6 0.12
17 1 0.02
ACGTcount: A:0.53, C:0.26, G:0.03, T:0.18
Consensus pattern (15 bp):
AAAACTCTAAAACCT
Found at i:2516343 original size:15 final size:14
Alignment explanation
Indices: 2516306--2516347 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
2516296 ATAAACCTTG
*
2516306 AAACTTTAAAACCA
1 AAACTCTAAAACCA
2516320 AAACTCTAAAACCTA
1 AAACTCTAAAACC-A
2516335 AAAGC-CTAAAACC
1 AAA-CTCTAAAACC
2516348 CTGAAATCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 12 0.48
15 12 0.48
16 1 0.04
ACGTcount: A:0.55, C:0.26, G:0.02, T:0.17
Consensus pattern (14 bp):
AAACTCTAAAACCA
Found at i:2517679 original size:20 final size:21
Alignment explanation
Indices: 2517632--2517682 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
2517622 CAAATACATA
*
2517632 TTTTATTAT-TATTTTAATAT
1 TTTTATTATAAATTTTAATAT
* *
2517652 TATCATTATAAATTTTAAT-T
1 TTTTATTATAAATTTTAATAT
2517672 TTTTATTATAA
1 TTTTATTATAA
2517683 TAATTAATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTTATTATAAATTTTAATAT
Found at i:2518756 original size:3 final size:3
Alignment explanation
Indices: 2518750--2518775 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2518740 ATTGTTATTA
2518750 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
2518776 AGCTAACAAC
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:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:2524439 original size:17 final size:17
Alignment explanation
Indices: 2524419--2524453 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
2524409 TGTATTATAA
2524419 TTCATAAAATTTTATTT
1 TTCATAAAATTTTATTT
*
2524436 TTCATATAATTTTATTT
1 TTCATAAAATTTTATTT
2524453 T
1 T
2524454 ATAATCTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (17 bp):
TTCATAAAATTTTATTT
Found at i:2525206 original size:22 final size:23
Alignment explanation
Indices: 2525180--2525226 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
2525170 TGAGTGCTGG
* *
2525180 CGATTTAGGATTTGG-GATTTTT
1 CGATTAAGGATTGGGTGATTTTT
*
2525202 CGATTAAGGCTTGGGTGATTTTT
1 CGATTAAGGATTGGGTGATTTTT
2525225 CG
1 CG
2525227 TTTTTTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.17, C:0.09, G:0.30, T:0.45
Consensus pattern (23 bp):
CGATTAAGGATTGGGTGATTTTT
Found at i:2527718 original size:13 final size:13
Alignment explanation
Indices: 2527700--2527724 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2527690 CTTTGTTTTT
2527700 TTTTTTTTTTTCC
1 TTTTTTTTTTTCC
2527713 TTTTTTTTTTTC
1 TTTTTTTTTTTC
2527725 AGTTCTTATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTTTTTTCC
Found at i:2528966 original size:51 final size:51
Alignment explanation
Indices: 2528890--2528991 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
2528880 TTAATGACAT
2528890 AACCTTTCTTAATTGATTCCCAACTCATATTCCACCAAAATTGTTATTGTG
1 AACCTTTCTTAATTGATTCCCAACTCATATTCCACCAAAATTGTTATTGTG
2528941 AACCTTTCTTAATTGATTCCCAACTCATATTCCACCAAAATTGTTATTGTG
1 AACCTTTCTTAATTGATTCCCAACTCATATTCCACCAAAATTGTTATTGTG
2528992 TTTGAACCTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.29, C:0.24, G:0.08, T:0.39
Consensus pattern (51 bp):
AACCTTTCTTAATTGATTCCCAACTCATATTCCACCAAAATTGTTATTGTG
Found at i:2532730 original size:4 final size:4
Alignment explanation
Indices: 2532723--2532748 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2532713 TTCTTCAAAA
2532723 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
2532749 TAATAATAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:2545192 original size:19 final size:17
Alignment explanation
Indices: 2545166--2545209 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
2545156 TATTATTTTT
*
2545166 AATT-TTATATTTATAA
1 AATTATTATATTAATAA
2545182 ATATATATTATATTAATAA
1 A-AT-TATTATATTAATAA
2545201 AATTATTAT
1 AATTATTAT
2545210 GCAATACTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 1 0.04
17 8 0.33
18 3 0.12
19 12 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
AATTATTATATTAATAA
Found at i:2545293 original size:42 final size:41
Alignment explanation
Indices: 2545217--2545297 Score: 96
Period size: 41 Copynumber: 2.0 Consensus size: 41
2545207 TATGCAATAC
2545217 TTTAATTTAAGATATTAACTTAATAAAAATATTATATTTACA
1 TTTAATTTAAGATATTAACTTAATAAAAATATTAT-TTTACA
*
2545259 TTTAA-TTAAGATA-TAATTTATATTAAGAAA-ATTATTTTA
1 TTTAATTTAAGATATTAACTTA-A-TAA-AAATATTATTTTA
2545298 TGAATATTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
40 6 0.17
41 13 0.37
42 13 0.37
43 3 0.09
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (41 bp):
TTTAATTTAAGATATTAACTTAATAAAAATATTATTTTACA
Found at i:2545536 original size:11 final size:11
Alignment explanation
Indices: 2545512--2545575 Score: 53
Period size: 11 Copynumber: 5.7 Consensus size: 11
2545502 ATTTAAATTC
2545512 AAATATATATTTA
1 AAATAT-TA-TTA
2545525 AAATATTATTA
1 AAATATTATTA
*
2545536 AAATTACTATTGA
1 AAA-TATTATT-A
2545549 AAATA-TATTA
1 AAATATTATTA
2545559 AAA-A-TATTA
1 AAATATTATTA
*
2545568 AAGTATTA
1 AAATATTA
2545576 ATAATTTTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
9 8 0.18
10 5 0.11
11 12 0.27
12 10 0.22
13 10 0.22
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.41
Consensus pattern (11 bp):
AAATATTATTA
Found at i:2545546 original size:12 final size:10
Alignment explanation
Indices: 2545516--2545569 Score: 56
Period size: 11 Copynumber: 5.0 Consensus size: 10
2545506 AAATTCAAAT
2545516 ATATATTTAAA
1 ATATA-TTAAA
2545527 ATATTATTAAA
1 ATA-TATTAAA
2545538 ATTACTATTGAAA
1 A-TA-TATT-AAA
2545551 ATATATTAAA
1 ATATATTAAA
2545561 A-ATATTAAA
1 ATATATTAAA
2545570 GTATTAATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
9 8 0.21
10 4 0.10
11 13 0.33
12 10 0.26
13 4 0.10
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (10 bp):
ATATATTAAA
Found at i:2549898 original size:21 final size:23
Alignment explanation
Indices: 2549862--2549903 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
2549852 TATTAAGCTA
*
2549862 TTGATGTTGTGTTTATTCTTTAT
1 TTGATGTTGTGTTTATGCTTTAT
2549885 TTGAT-TTG-GTTTATGCTTT
1 TTGATGTTGTGTTTATGCTTT
2549904 TGGGATCATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 3 0.17
23 5 0.28
ACGTcount: A:0.12, C:0.05, G:0.19, T:0.64
Consensus pattern (23 bp):
TTGATGTTGTGTTTATGCTTTAT
Found at i:2555699 original size:3 final size:3
Alignment explanation
Indices: 2555691--2555724 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2555681 ACCAAAATCA
2555691 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2555725 TAGTAAAACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2556608 original size:22 final size:22
Alignment explanation
Indices: 2556580--2556621 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
2556570 AGAGCATAAC
*
2556580 ATTATATCTGTTGATGACATGA
1 ATTATATCTGTCGATGACATGA
2556602 ATTATATCTGTCGATGACAT
1 ATTATATCTGTCGATGACAT
2556622 AAAACAGAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (22 bp):
ATTATATCTGTCGATGACATGA
Found at i:2558948 original size:18 final size:18
Alignment explanation
Indices: 2558910--2558951 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2558900 AGTATAAAAT
* **
2558910 TAAATATATATATATGTA
1 TAAATATATATAAATAAA
2558928 TAAATATATATAAATAAA
1 TAAATATATATAAATAAA
2558946 TAAATA
1 TAAATA
2558952 ATTATTTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
TAAATATATATAAATAAA
Found at i:2563169 original size:31 final size:33
Alignment explanation
Indices: 2563125--2563213 Score: 91
Period size: 30 Copynumber: 2.9 Consensus size: 33
2563115 AAAAATAAAA
* *
2563125 AAATTAT-TTTTTAGTTTTTTTTA-AAAT-TTT
1 AAATTATATATTTAGTTTTTTTTATAAATATAT
*
2563155 AAATTATATATTTAGATTTTTTTATAAATATAT
1 AAATTATATATTTAGTTTTTTTTATAAATATAT
* *
2563188 ATATTA-ATATTTA--TTTTTCTATAAAT
1 AAATTATATATTTAGTTTTTTTTATAAAT
2563214 TTATTTTAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
30 19 0.37
31 14 0.27
32 11 0.22
33 7 0.14
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.60
Consensus pattern (33 bp):
AAATTATATATTTAGTTTTTTTTATAAATATAT
Found at i:2563199 original size:26 final size:26
Alignment explanation
Indices: 2563154--2563204 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
2563144 TTTAAAATTT
*
2563154 TAAATTATATATTTAGATTT-TTTTA
1 TAAATTATATATTAAGATTTATTTTA
*
2563179 TAAATATATATATTAATATTTATTTT
1 TAAAT-TATATATTAAGATTTATTTT
2563205 TCTATAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 5 0.23
26 13 0.59
27 4 0.18
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (26 bp):
TAAATTATATATTAAGATTTATTTTA
Found at i:2563272 original size:17 final size:17
Alignment explanation
Indices: 2563252--2563284 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2563242 ATGATTTATA
2563252 TTATTTAATAAAAAAAT
1 TTATTTAATAAAAAAAT
*
2563269 TTATTTACTAAAAAAA
1 TTATTTAATAAAAAAA
2563285 ATAAATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (17 bp):
TTATTTAATAAAAAAAT
Found at i:2567671 original size:30 final size:30
Alignment explanation
Indices: 2567625--2567716 Score: 109
Period size: 30 Copynumber: 3.1 Consensus size: 30
2567615 TATTGTACCC
2567625 AATT-AACTCATT-AAATTGTTA-TTTTATTT
1 AATTAAACTC-TTAAAATT-TTATTTTTATTT
* *
2567654 AATTAAACTCTTAAAATTCTATTTTTATCT
1 AATTAAACTCTTAAAATTTTATTTTTATTT
* *
2567684 AATTAAACTCTAAAAATATTATTTTTATTT
1 AATTAAACTCTTAAAATTTTATTTTTATTT
2567714 AAT
1 AAT
2567717 GGAACTTTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
29 8 0.15
30 46 0.85
ACGTcount: A:0.39, C:0.09, G:0.01, T:0.51
Consensus pattern (30 bp):
AATTAAACTCTTAAAATTTTATTTTTATTT
Found at i:2567934 original size:2 final size:2
Alignment explanation
Indices: 2567927--2567959 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2567917 AACTTTTGTA
2567927 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2567960 GAGGAAGGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2569535 original size:25 final size:25
Alignment explanation
Indices: 2569468--2569535 Score: 70
Period size: 25 Copynumber: 2.7 Consensus size: 25
2569458 AAAATTTTAA
*
2569468 ATTAAAATTTTAAGTTTT-TAATTTT
1 ATTAAAA-TTTAAGTTTTATAATTAT
*
2569493 TTTAAAAATTATAA--TTTATAATTAT
1 ATT-AAAATT-TAAGTTTTATAATTAT
2569518 ATTAAAATTTAAGTTTTA
1 ATTAAAATTTAAGTTTTA
2569536 AATCAATTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
23 3 0.09
24 9 0.26
25 16 0.46
26 7 0.20
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (25 bp):
ATTAAAATTTAAGTTTTATAATTAT
Found at i:2574447 original size:4 final size:4
Alignment explanation
Indices: 2574440--2574496 Score: 114
Period size: 4 Copynumber: 14.2 Consensus size: 4
2574430 GGCTGGCATG
2574440 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2574488 CATA CATA C
1 CATA CATA C
2574497 TATGTATATG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 53 1.00
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:2598869 original size:28 final size:30
Alignment explanation
Indices: 2598837--2598895 Score: 104
Period size: 28 Copynumber: 2.0 Consensus size: 30
2598827 AACGAAATCA
2598837 TTAATATAATATTTAAATT-T-AAATTTTT
1 TTAATATAATATTTAAATTATGAAATTTTT
2598865 TTAATATAATATTTAAATTATGAAATTTTT
1 TTAATATAATATTTAAATTATGAAATTTTT
2598895 T
1 T
2598896 AATTATTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 19 0.66
29 1 0.03
30 9 0.31
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (30 bp):
TTAATATAATATTTAAATTATGAAATTTTT
Found at i:2598906 original size:33 final size:29
Alignment explanation
Indices: 2598836--2598908 Score: 94
Period size: 28 Copynumber: 2.4 Consensus size: 29
2598826 TAACGAAATC
2598836 ATTAATATAATATTTAAATTTAAATTTTT
1 ATTAATATAATATTTAAATTTAAATTTTT
2598865 -TTAATATAATATTTAAATTATGAAATTTTTT
1 ATTAATATAATATTTAAATT-T-AAA-TTTTT
*
2598896 AATTATTATAATA
1 -ATTAATATAATA
2598909 ATTACTTTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
28 19 0.50
29 1 0.03
30 3 0.08
31 5 0.13
33 10 0.26
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (29 bp):
ATTAATATAATATTTAAATTTAAATTTTT
Found at i:2601986 original size:4 final size:4
Alignment explanation
Indices: 2601967--2602005 Score: 60
Period size: 4 Copynumber: 9.2 Consensus size: 4
2601957 CCTTGAAATC
2601967 CCTT CCCTT CCCTT CCTT CCTT CCTT CCTT CCTT CCTT C
1 CCTT -CCTT -CCTT CCTT CCTT CCTT CCTT CCTT CCTT C
2602006 TTCTTCTTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 25 0.74
5 9 0.26
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (4 bp):
CCTT
Found at i:2605246 original size:29 final size:27
Alignment explanation
Indices: 2605209--2605271 Score: 90
Period size: 29 Copynumber: 2.3 Consensus size: 27
2605199 TTATTATAAT
*
2605209 AAAATATTTAATATAATATTTGAATATTA
1 AAAATATTTAATATAATAGTTG-A-ATTA
*
2605238 AAAATATTTAATATATTAGTTGAATTA
1 AAAATATTTAATATAATAGTTGAATTA
2605265 AAAATAT
1 AAAATAT
2605272 GTTATCACCC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 11 0.34
28 1 0.03
29 20 0.62
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (27 bp):
AAAATATTTAATATAATAGTTGAATTA
Found at i:2611390 original size:5 final size:5
Alignment explanation
Indices: 2611380--2611430 Score: 52
Period size: 5 Copynumber: 10.2 Consensus size: 5
2611370 ATTATTTTGT
* *
2611380 TATTA TATTA TATTA TATTA TA-T- TACTA TATTA CATTA CTATTA TTATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA -TATTA -TATTA
2611430 T
1 T
2611431 TATATAGTGT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
3 2 0.05
4 2 0.05
5 26 0.67
6 9 0.23
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (5 bp):
TATTA
Found at i:2611395 original size:13 final size:14
Alignment explanation
Indices: 2611379--2611432 Score: 58
Period size: 15 Copynumber: 3.8 Consensus size: 14
2611369 TATTATTTTG
2611379 TTATTATATTA-TA
1 TTATTATATTACTA
2611392 TTATATTATATTACTA
1 -T-TATTATATTACTA
*
2611408 -TATTACATTACTA
1 TTATTATATTACTA
2611421 TTATTATTATTA
1 TTATTA-TATTA
2611433 TATAGTGTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
13 12 0.35
14 6 0.18
15 14 0.41
16 2 0.06
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (14 bp):
TTATTATATTACTA
Found at i:2612365 original size:19 final size:18
Alignment explanation
Indices: 2612338--2612436 Score: 65
Period size: 19 Copynumber: 5.3 Consensus size: 18
2612328 AGTTTTTCTA
2612338 TTTTATTTTTATATTATTT
1 TTTTATTTTTAT-TTATTT
*
2612357 TTTTGTTTTTATTTATTT
1 TTTTATTTTTATTTATTT
** * * *
2612375 TCATATTTTAAGTT-TTG
1 TTTTATTTTTATTTATTT
*
2612392 TTTTATTTTTAATTTTTAATT
1 TTTTATTTTT-A--TTTATTT
*
2612413 TTTTATTGGTTATTTATTT
1 TTTTATT-TTTATTTATTT
*
2612432 ATTTA
1 TTTTA
2612437 CTCAATAAAA
Statistics
Matches: 59, Mismatches: 16, Indels: 10
0.69 0.19 0.12
Matches are distributed among these distances:
17 9 0.15
18 16 0.27
19 21 0.36
20 2 0.03
21 9 0.15
22 2 0.03
ACGTcount: A:0.20, C:0.01, G:0.05, T:0.74
Consensus pattern (18 bp):
TTTTATTTTTATTTATTT
Found at i:2612383 original size:25 final size:24
Alignment explanation
Indices: 2612355--2612414 Score: 59
Period size: 25 Copynumber: 2.5 Consensus size: 24
2612345 TTTATATTAT
*
2612355 TTTTTTGTTTT-TATTTATTTTCATA
1 TTTTTAGTTTTGT-TTTATTTTCA-A
* *
2612380 TTTTAAGTTTTGTTTTATTTTTAA
1 TTTTTAGTTTTGTTTTATTTTCAA
*
2612404 TTTTTAATTTT
1 TTTTTAGTTTT
2612415 TTATTGGTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
24 10 0.34
25 18 0.62
26 1 0.03
ACGTcount: A:0.18, C:0.02, G:0.05, T:0.75
Consensus pattern (24 bp):
TTTTTAGTTTTGTTTTATTTTCAA
Found at i:2612407 original size:17 final size:16
Alignment explanation
Indices: 2612338--2612408 Score: 54
Period size: 18 Copynumber: 4.1 Consensus size: 16
2612328 AGTTTTTCTA
2612338 TTTTATTTTTATATTATT
1 TTTTATTTTTA-ATT-TT
*
2612356 TTTT-TGTTTTTATTTAT
1 TTTTAT-TTTTAATTT-T
*
2612373 TTTCATATTTTAAGTTTT
1 TTTTAT-TTTTAA-TTTT
2612391 GTTTTATTTTTAATTTT
1 -TTTTATTTTTAATTTT
2612408 T
1 T
2612409 AATTTTTTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
16 2 0.05
17 12 0.28
18 21 0.49
19 8 0.19
ACGTcount: A:0.18, C:0.01, G:0.04, T:0.76
Consensus pattern (16 bp):
TTTTATTTTTAATTTT
Found at i:2616743 original size:22 final size:21
Alignment explanation
Indices: 2616718--2616762 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
2616708 TATATCATAT
2616718 TTCTTTTTTTGA-ATATTTAAAA
1 TTCTTTTTTT-ATAT-TTTAAAA
2616740 TTCTTTTTTTATATTTTAAAA
1 TTCTTTTTTTATATTTTAAAA
2616761 TT
1 TT
2616763 ATGTTAACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.64
Consensus pattern (21 bp):
TTCTTTTTTTATATTTTAAAA
Done.