Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 115 of 135
Found at i:34463847 original size:30 final size:29
Alignment explanation
Indices: 34463779--34463834 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
34463769 AACATTAAAC
*
34463779 AAACGAACATGAACACAAATAATTTAAAAT
1 AAACGAACATGAACACAAAT-ATTGAAAAT
34463809 AAACGAACATGAACACAAAT-TTGAAA
1 AAACGAACATGAACACAAATATTGAAA
34463835 TTCTTAACGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 5 0.20
30 20 0.80
ACGTcount: A:0.59, C:0.14, G:0.09, T:0.18
Consensus pattern (29 bp):
AAACGAACATGAACACAAATATTGAAAAT
Found at i:34473636 original size:80 final size:80
Alignment explanation
Indices: 34473444--34473638 Score: 259
Period size: 80 Copynumber: 2.4 Consensus size: 80
34473434 TAAACCAACG
* * ** * *
34473444 ATCCTGGCACCCAGTGCCTAGCAGATAAATTGCAAAAGTGAGCCCAGCTCTAGTTGGATTAACCA
1 ATCCTGACACTCAGTGCCTAGCAGATAAACCGCAAAAGTGAGCCCAACTCTAATTGGATTAACCA
34473509 ACAAATATCCGTCAA
66 ACAAATATCCGTCAA
* * *
34473524 ATCTTGACACCTAATGTG--TAGCAGATAGACCGCAAAAGTGAGCCCAACTCTAATTGGATTAAC
1 ATCCTGACA-CTCA-GTGCCTAGCAGATAAACCGCAAAAGTGAGCCCAACTCTAATTGGATTAAC
*
34473587 CAACGAATATCCGTCAA
64 CAACAAATATCCGTCAA
*
34473604 ATCCTGACACTCAGTGCCTAGCGGATAAACCGCAA
1 ATCCTGACACTCAGTGCCTAGCAGATAAACCGCAA
34473639 TTGTGTGCCT
Statistics
Matches: 97, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
78 3 0.03
79 3 0.03
80 86 0.89
81 2 0.02
82 3 0.03
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.21
Consensus pattern (80 bp):
ATCCTGACACTCAGTGCCTAGCAGATAAACCGCAAAAGTGAGCCCAACTCTAATTGGATTAACCA
ACAAATATCCGTCAA
Found at i:34475445 original size:4 final size:4
Alignment explanation
Indices: 34475436--34475463 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
34475426 TCTCTTATGG
34475436 CTTT CTTT CTTT CTTT CTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT
34475464 TTTTTTTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
CTTT
Found at i:34482997 original size:21 final size:22
Alignment explanation
Indices: 34482979--34483020 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
34482969 TATCTTTTGT
34482979 ATTAAACTTAATT-AATTTTATG
1 ATTAAA-TTAATTAAATTTTATG
*
34483001 ATTTAATTAATTAAATTTTA
1 ATTAAATTAATTAAATTTTA
34483021 ATTTTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (22 bp):
ATTAAATTAATTAAATTTTATG
Found at i:34483499 original size:29 final size:26
Alignment explanation
Indices: 34483432--34483499 Score: 66
Period size: 29 Copynumber: 2.5 Consensus size: 26
34483422 CAAAAATAAA
* *
34483432 ATGTAAAACAAATTTTTATTTTATAT
1 ATGTAAAATAAATTTTTATTTAATAT
*
34483458 ATG-AAATTAAAATTGTTTATCTTAAATAT
1 ATGTAAAAT-AAATT-TTTAT-TT-AATAT
34483487 ATGTAAAATAAAT
1 ATGTAAAATAAAT
34483500 AACATATAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
25 3 0.09
26 8 0.24
27 5 0.15
28 2 0.06
29 11 0.33
30 4 0.12
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (26 bp):
ATGTAAAATAAATTTTTATTTAATAT
Found at i:34484296 original size:16 final size:16
Alignment explanation
Indices: 34484275--34484317 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
34484265 AAATGAACTC
34484275 AATAAAAATAATTAAA
1 AATAAAAATAATTAAA
*
34484291 AATAAATAA-AATTTAA
1 AATAAA-AATAATTAAA
*
34484307 TATAAAAATAA
1 AATAAAAATAA
34484318 AAATACAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 2 0.09
16 19 0.83
17 2 0.09
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
AATAAAAATAATTAAA
Found at i:34484301 original size:9 final size:10
Alignment explanation
Indices: 34484275--34484318 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
34484265 AAATGAACTC
34484275 AATAAAAATA
1 AATAAAAATA
*
34484285 ATTAAAAATA
1 AATAAAAATA
*
34484295 AATAAAATTTA
1 AATAAAA-ATA
34484306 ATATAAAAATA
1 A-ATAAAAATA
34484317 AA
1 AA
34484319 AATACAACAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
10 16 0.57
11 6 0.21
12 6 0.21
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
AATAAAAATA
Found at i:34484330 original size:26 final size:21
Alignment explanation
Indices: 34484275--34484318 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
34484265 AAATGAACTC
*
34484275 AATAAAA-ATAATTAAAAATA
1 AATAAAATTTAATTAAAAATA
34484295 AATAAAATTTAATATAAAAATA
1 AATAAAATTTAAT-TAAAAATA
34484317 AA
1 AA
34484319 AATACAACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.33
21 4 0.19
22 10 0.48
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (21 bp):
AATAAAATTTAATTAAAAATA
Found at i:34494261 original size:16 final size:16
Alignment explanation
Indices: 34494233--34494272 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
34494223 TACAGTTATA
*
34494233 AAATTTATATTTATATT
1 AAATTT-TATTTAAATT
34494250 AAATTTTATTTAAATT
1 AAATTTTATTTAAATT
*
34494266 ATATTTT
1 AAATTTT
34494273 GTTGAGTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
AAATTTTATTTAAATT
Found at i:34495640 original size:14 final size:15
Alignment explanation
Indices: 34495621--34495653 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
34495611 TTTTAATATT
34495621 TAATAA-TTTTTATA
1 TAATAATTTTTTATA
34495635 TAATAATTTTTTATA
1 TAATAATTTTTTATA
34495650 TAAT
1 TAAT
34495654 CATCTTAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TAATAATTTTTTATA
Found at i:34496984 original size:123 final size:123
Alignment explanation
Indices: 34496850--34497349 Score: 343
Period size: 123 Copynumber: 4.1 Consensus size: 123
34496840 CTTTGCAGGA
*
34496850 AGCTTTGCTTCGTTTTGCTCAGTTTCCGCTATTGATACG-CGGCCATT-AGTGACCTCATCATAA
1 AGCTTTACTTCGTTTTGCTCAGTTTCCGCTATTGATACGTC-GCCATTGA-TGACCTCATCATAA
*** *
34496913 GCTGTGTCTTTGACAAGCTTT-TCATTGTCATCATGCTCAATATTAAAGAATTCTACGGGG
64 GCTGTGTCAACGACAAGCTTTCT-ATTATCATCATGCTCAATATTAAAGAATTCTACGGGG
* ** * * * ** *
34496973 AGCTTTACTTCGTTATGCTCAGTTTCAACTATTAATATGTCGCCCTTGATGACCTCATGGTAAGT
1 AGCTTTACTTCGTTTTGCTCAGTTTCCGCTATTGATACGTCGCCATTGATGACCTCATCATAAGC
* * ** **
34497038 TGTGTCAACGACAAGCTTTCTGTTATCATCATGCTCATTATTAAAGGGTTCTGTGGGG
66 TGTGTCAACGACAAGCTTTCTATTATCATCATGCTCAATATTAAAGAATTCTACGGGG
* * * * * ** * * * **
34497096 AGCTTCACTTTGTTTTGCTCAGTTTCCGCTACTGATATGCCATCGTTGATGACTTCATTATAAAT
1 AGCTTTACTTCGTTTTGCTCAGTTTCCGCTATTGATACGTCGCCATTGATGACCTCATCATAAGC
* * * * * *
34497161 TGTGTCAATGACGAAGCTTTC-GTTATCATCATACCCAACATT-AAGAGATTC-ACTGGCG
66 TGTGTCAACGAC-AAGCTTTCTATTATCATCATGCTCAATATTAAAGA-ATTCTAC-GGGG
* * * * * * * * **
34497219 ATCTTTGCTTTGTTTTTCTCAATTTCCGCTACTGATA-GGCTGCCATTCG-TGACATCATTGTAA
1 AGCTTTACTTCGTTTTGCTCAGTTTCCGCTATTGATACGTC-GCCATT-GATGACCTCATCATAA
* * * * * * * **
34497282 GTTGTGTCAAAGACAAGTTTTTTATTATCATCATGC-CGAACATTAAGGGATTCTGTGGGG
64 GCTGTGTCAACGACAAGCTTTCTATTATCATCATGCTC-AATATTAAAGAATTCTACGGGG
34497342 AGCTTTAC
1 AGCTTTAC
34497350 GTCGCCATTG
Statistics
Matches: 296, Mismatches: 69, Indels: 24
0.76 0.18 0.06
Matches are distributed among these distances:
122 12 0.04
123 270 0.91
124 14 0.05
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.37
Consensus pattern (123 bp):
AGCTTTACTTCGTTTTGCTCAGTTTCCGCTATTGATACGTCGCCATTGATGACCTCATCATAAGC
TGTGTCAACGACAAGCTTTCTATTATCATCATGCTCAATATTAAAGAATTCTACGGGG
Found at i:34497585 original size:123 final size:120
Alignment explanation
Indices: 34497406--34497687 Score: 363
Period size: 123 Copynumber: 2.3 Consensus size: 120
34497396 TTGTTATCGC
* * * * * *
34497406 CATGCCCAACATTCAGGGGTTCTCTGGGGAGCTTCGCTACGTTTTGCTCCATTTCCACTATTGAT
1 CATGCCCAACATTAAAGGATTCTCTGGGGAGCTTTGCTTCGTTTTGCTCCATTTCCACTACTGAT
* * *
34497471 TCGCCGTCATTCATGACTTCATTATAAG-CTGCGTTAATGT-CAAACTTTCCATCAT
66 ACGCCGTCATTCATGACATCATTATAAGTC-GAGTTAAT-TACAAACTTTCCATCAT
* * *
34497526 CATCCTGCGCAACATTAAAGGATTCTCTGGAGAGCTTTGCTTCGTTTTGCT-TAGTTTCCACTAC
1 CA---TGCCCAACATTAAAGGATTCTCTGGGGAGCTTTGCTTCGTTTTGCTCCA-TTTCCACTAC
*
34497590 TGATACGCCGTCATTGATGACATCATTATAAGTCGAGTTAATTACAAACTTTCCATCAT
62 TGATACGCCGTCATTCATGACATCATTATAAGTCGAGTTAATTACAAACTTTCCATCAT
*
34497649 CATGCCCAACATTAAAGGATTCTTTGGGGAGCTTTGCTT
1 CATGCCCAACATTAAAGGATTCTCTGGGGAGCTTTGCTT
34497688 TGATATGCTC
Statistics
Matches: 140, Mismatches: 16, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
120 36 0.26
122 2 0.01
123 101 0.72
124 1 0.01
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.35
Consensus pattern (120 bp):
CATGCCCAACATTAAAGGATTCTCTGGGGAGCTTTGCTTCGTTTTGCTCCATTTCCACTACTGAT
ACGCCGTCATTCATGACATCATTATAAGTCGAGTTAATTACAAACTTTCCATCAT
Found at i:34497614 original size:339 final size:339
Alignment explanation
Indices: 34497011--34497622 Score: 721
Period size: 339 Copynumber: 1.8 Consensus size: 339
34497001 CTATTAATAT
* * * * * * *
34497011 GTCGCCCTTGATGACCTCATGGTAAGTTGTGTCAACGACAAGCTTTCTGTTATCATCATGCTCAT
1 GTCGCCATTGATGACCTCATGGTAAGTCGTATCAACGACAAACTTTCTGTTATCACCATGCCCAA
* * ** * *
34497076 TATTAAAGGGTTCTGTGGGGAGCTTCACTTTGTTTTGCTCAGTTTCCGCTACTGATATGCCATCG
66 CATTAAAGGGTTCTCTGGGGAGCTTCACTACGTTTTGCTCAGTTTCCACTACTGATATGCCATCA
* * * * * *
34497141 TTGATGACTTCATTATAAATTGTGTCAATGACGAAGCTTTCGTTATCATCATACCCAACATTAAG
131 TTCATGACTTCATTATAAACTGCGTCAATGACGAAACTTTCATCATCATCATACCCAACATTAAG
* * * * * * *
34497206 AGATTCACTGGCGATCTTTGCTTTGTTTTTCTCAATTTCCGCTACTGATAGGCTGCCATTCGTGA
196 AGATTCACTGGAGAGCTTTGCTTCGTTTTGCTCAATTTCCACTACTGATACGCCGCCATTCGTGA
*
34497271 CATCATTGTAAGTTGTGTCAAAGACAAGTTTTTTATTATCATCATGCCGAACATTAAGGGATTCT
261 CATCATTATAAGTTGTGTCAAAGACAAGTTTTTTATTATCATCATGCCGAACATTAAGGGATTCT
34497336 GTGGGGAGCTTTAC
326 GTGGGGAGCTTTAC
* * * * *
34497350 GTCGCCATTGATGATCTCATTGTAAGTCGTATCAATGACAAACTTTTTGTTATCGCCATGCCCAA
1 GTCGCCATTGATGACCTCATGGTAAGTCGTATCAACGACAAACTTTCTGTTATCACCATGCCCAA
* * * * *
34497415 CATTCAGGGGTTCTCTGGGGAGCTTCGCTACGTTTTGCTCCA-TTTCCACTATTGAT-TCGCCGT
66 CATTAAAGGGTTCTCTGGGGAGCTTCACTACGTTTTGCT-CAGTTTCCACTACTGATAT-GCCAT
* * * * * *
34497478 CATTCATGACTTCATTATAAGCTGCGTTAATGTC-AAACTTTCCATCATCATCCTGCGCAACATT
129 CATTCATGACTTCATTATAAACTGCGTCAATGACGAAACTTT-CATCATCATCATACCCAACATT
* * * *
34497542 AA-AGGATTCTCTGGAGAGCTTTGCTTCGTTTTGCTTAGTTTCCACTACTGATACGCCGTCATT-
193 AAGA-GATTCACTGGAGAGCTTTGCTTCGTTTTGCTCAATTTCCACTACTGATACGCCGCCATTC
34497605 GATGACATCATTATAAGT
257 G-TGACATCATTATAAGT
34497623 CGAGTTAATT
Statistics
Matches: 221, Mismatches: 47, Indels: 10
0.79 0.17 0.04
Matches are distributed among these distances:
338 9 0.04
339 210 0.95
340 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (339 bp):
GTCGCCATTGATGACCTCATGGTAAGTCGTATCAACGACAAACTTTCTGTTATCACCATGCCCAA
CATTAAAGGGTTCTCTGGGGAGCTTCACTACGTTTTGCTCAGTTTCCACTACTGATATGCCATCA
TTCATGACTTCATTATAAACTGCGTCAATGACGAAACTTTCATCATCATCATACCCAACATTAAG
AGATTCACTGGAGAGCTTTGCTTCGTTTTGCTCAATTTCCACTACTGATACGCCGCCATTCGTGA
CATCATTATAAGTTGTGTCAAAGACAAGTTTTTTATTATCATCATGCCGAACATTAAGGGATTCT
GTGGGGAGCTTTAC
Found at i:34497725 original size:120 final size:122
Alignment explanation
Indices: 34497408--34497742 Score: 322
Period size: 123 Copynumber: 2.8 Consensus size: 122
34497398 GTTATCGCCA
* * * * * * * * * * * *
34497408 TGCCCAACATTCAGGGGTTCTCTGGGGAGCTTCGCTACGTTTTGCTCCA-TTTCCACTATTGATT
1 TGCCCAACATTAAAGGATTCTCTGGAGAGCTTTGCTTCGATATGCT-CAGGTTCCACTACTAATA
* * * *
34497472 CGCCGTCATTCATGACTTCATTATAAG-CTGCGTTAATGTCAAACTTTCCATCATCATCC
65 CGCCGCCATTGATGACATCATTATAAGTCTGAGTTAATGTCAAACTTTCCATCATCA--C
* * * * * *
34497531 TGCGCAACATTAAAGGATTCTCTGGAGAGCTTTGCTTCGTTTTGCTTAGTTTCCACTACTGATAC
1 TGCCCAACATTAAAGGATTCTCTGGAGAGCTTTGCTTCGATATGCTCAGGTTCCACTACTAATAC
*
34497596 GCCGTCATTGATGACATCATTATAAGTC-GAGTTAAT-TACAAACTTTCCATCATCA-
66 GCCGCCATTGATGACATCATTATAAGTCTGAGTTAATGT-CAAACTTTCCATCATCAC
* * *
34497651 TGCCCAACATTAAAGGATTCTTTGGGGAGCTTTGCTTTGATATGCTCAGGTT-CATCTACTAATA
1 TGCCCAACATTAAAGGATTCTCTGGAGAGCTTTGCTTCGATATGCTCAGGTTCCA-CTACTAATA
* * *
34497715 CGTCGCCATTGATGACCTCATTGTAAGT
65 CGCCGCCATTGATGACATCATTATAAGT
34497743 TGTGTCAACG
Statistics
Matches: 182, Mismatches: 26, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
119 2 0.01
120 76 0.42
122 2 0.01
123 101 0.55
124 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.35
Consensus pattern (122 bp):
TGCCCAACATTAAAGGATTCTCTGGAGAGCTTTGCTTCGATATGCTCAGGTTCCACTACTAATAC
GCCGCCATTGATGACATCATTATAAGTCTGAGTTAATGTCAAACTTTCCATCATCAC
Found at i:34498063 original size:120 final size:120
Alignment explanation
Indices: 34497727--34498111 Score: 336
Period size: 120 Copynumber: 3.2 Consensus size: 120
34497717 TCGCCATTGA
*
34497727 TGACCTCATTGTAAGTTGTGTCAACGATAAGCTTATTT-TTATCGTCATGTCC-AACATTAAGGG
1 TGACCTCATTGTAAGTTGTGTCAACGACAAGCTT-TTTGTTATCGTCATG-CCTAACATTAAGGG
* * * * * * * *
34497790 ACAT-TGTGGAGAGCTTTACTTCCTTCGGCTTAGTTTCCGCTATGGATACGCCGCCAT
64 A-TTCTGTGGGGAGCTTTGCTTCGTTCCGCTCAGTTTCCGCTATGGATACACCACCAT
* * * * * * **
34497847 TGACCTCGTTATAAACTT-T-TCCGATGACAAGCTTTTTGTTATCATCATGCCTAACATTAAACG
1 TGACCTCATTGT-AAGTTGTGT-CAACGACAAGCTTTTTGTTATCGTCATGCCTAACATTAAGGG
* * * *
34497910 ATTCTGTGGAGG-GCTTTGCTTCGTTCCGGTCAG-TTCTCGCTATTGATACATCACCGT
64 ATTCTGTGG-GGAGCTTTGCTTCGTTCCGCTCAGTTTC-CGCTATGGATACACCACCAT
** *
34497967 TGACCTCATTGTAAGTTGTGTCAACGACAAGCTTTTTGTTATCGTCATGCCTAATGTTAGGGGAT
1 TGACCTCATTGTAAGTTGTGTCAACGACAAGCTTTTTGTTATCGTCATGCCTAACATTAAGGGAT
** * **
34498032 TCTGTGGGGAGCTTTGCTTCGTTATGCTCAGTTTCAGCTACTGGA-ACATCGCCATTAT
66 TCTGTGGGGAGCTTTGCTTCGTTCCGCTCAGTTTCCGCTA-TGGATACA---CCACCAT
* *
34498090 TGACCTCATCGTAAGCTGTGTC
1 TGACCTCATTGTAAGTTGTGTC
34498112 GACTGCAATA
Statistics
Matches: 207, Mismatches: 43, Indels: 27
0.75 0.16 0.10
Matches are distributed among these distances:
119 16 0.08
120 156 0.75
121 12 0.06
123 23 0.11
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (120 bp):
TGACCTCATTGTAAGTTGTGTCAACGACAAGCTTTTTGTTATCGTCATGCCTAACATTAAGGGAT
TCTGTGGGGAGCTTTGCTTCGTTCCGCTCAGTTTCCGCTATGGATACACCACCAT
Found at i:34510928 original size:2 final size:2
Alignment explanation
Indices: 34510921--34510955 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
34510911 AGGCAAGCTT
*
34510921 TC TC TC TC TC TC TC TC TC TC TC TC T- TT TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
34510956 ACTTCTTGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Found at i:34522516 original size:21 final size:20
Alignment explanation
Indices: 34522490--34522543 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 20
34522480 TTAAGATTCG
34522490 GGGTTTGAAGTTTGATG-TTTA
1 GGGTTTG-AGTTTGA-GATTTA
34522511 GGGTTTGAGATTTGAGATTTA
1 GGGTTTGAG-TTTGAGATTTA
*
34522532 AGGTTTGGAGTT
1 GGGTTT-GAGTT
34522544 CAGAATTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
20 3 0.10
21 23 0.79
22 3 0.10
ACGTcount: A:0.20, C:0.00, G:0.35, T:0.44
Consensus pattern (20 bp):
GGGTTTGAGTTTGAGATTTA
Found at i:34534611 original size:22 final size:22
Alignment explanation
Indices: 34534570--34534610 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
34534560 ATTTAAATAT
34534570 TTTTTATTTTTTAAAGTTTTAA
1 TTTTTATTTTTTAAAGTTTTAA
*
34534592 TTTTTA-TTTTTAAATTTTT
1 TTTTTATTTTTTAAAGTTTT
34534611 TTTAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (22 bp):
TTTTTATTTTTTAAAGTTTTAA
Found at i:34543324 original size:31 final size:30
Alignment explanation
Indices: 34543260--34543327 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
34543250 AATTTTTTAT
*
34543260 ATTTTATAATTTTTAAAAGATTAAATTAAA
1 ATTTTATAATTTTTAAAAGATTAAAGTAAA
* * **
34543290 ATTTTATCATTTTTAAAAGGGTTAAAGTGTA
1 ATTTTATAATTTTTAAAA-GATTAAAGTAAA
34543321 ATTTTAT
1 ATTTTAT
34543328 TTTAATTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 17 0.53
31 15 0.47
ACGTcount: A:0.41, C:0.01, G:0.09, T:0.49
Consensus pattern (30 bp):
ATTTTATAATTTTTAAAAGATTAAAGTAAA
Found at i:34545230 original size:29 final size:29
Alignment explanation
Indices: 34545194--34545258 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 29
34545184 AAATACATAA
* * *
34545194 ATAT-TTTTTAAAATATTTATTTGTTTTT
1 ATATATTTTAAAAATATTTATGTATTTTT
34545222 ATATATTTTAAAAATATTTATGTATTTTT
1 ATATATTTTAAAAATATTTATGTATTTTT
*
34545251 ATACATTT
1 ATATATTT
34545259 CTTGGATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 4 0.12
29 28 0.88
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.62
Consensus pattern (29 bp):
ATATATTTTAAAAATATTTATGTATTTTT
Found at i:34546540 original size:22 final size:22
Alignment explanation
Indices: 34546489--34546590 Score: 132
Period size: 22 Copynumber: 4.5 Consensus size: 22
34546479 AAGTACTTAA
*
34546489 CAGTAAGCACACACAGTGCAAT
1 CAGTAGGCACACACAGTGCAAT
34546511 CCAGTAGGCACACACAGTGCAAT
1 -CAGTAGGCACACACAGTGCAAT
* *
34546534 CAGTAGGCGCACATAGTGCAAT
1 CAGTAGGCACACACAGTGCAAT
* * *
34546556 CAGTAGGCGCACATAGCGCAAAT
1 CAGTAGGCACACACAGTGC-AAT
34546579 CAGTAGGCACAC
1 CAGTAGGCACAC
34546591 GAAGTGCGAA
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
22 38 0.52
23 35 0.48
ACGTcount: A:0.35, C:0.27, G:0.24, T:0.14
Consensus pattern (22 bp):
CAGTAGGCACACACAGTGCAAT
Found at i:34546597 original size:45 final size:45
Alignment explanation
Indices: 34546489--34546590 Score: 134
Period size: 45 Copynumber: 2.3 Consensus size: 45
34546479 AAGTACTTAA
* *
34546489 CAGTAAGCACACACAGTGCAATCCAGTAGGCACACACAGTGCAAT
1 CAGTAGGCACACACAGTGCAATCCAGTAGGCACACACAGCGCAAT
* * * *
34546534 CAGTAGGCGCACATAGTGCAAT-CAGTAGGCGCACATAGCGCAAAT
1 CAGTAGGCACACACAGTGCAATCCAGTAGGCACACACAGCGC-AAT
34546579 CAGTAGGCACAC
1 CAGTAGGCACAC
34546591 GAAGTGCGAA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
44 16 0.33
45 33 0.67
ACGTcount: A:0.35, C:0.27, G:0.24, T:0.14
Consensus pattern (45 bp):
CAGTAGGCACACACAGTGCAATCCAGTAGGCACACACAGCGCAAT
Found at i:34548471 original size:5 final size:5
Alignment explanation
Indices: 34548461--34548489 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
34548451 TGTTACCATT
34548461 AGAGA AGAGA AGAGA AGAGA AGAGA AGAG
1 AGAGA AGAGA AGAGA AGAGA AGAGA AGAG
34548490 CAGAACAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (5 bp):
AGAGA
Found at i:34549072 original size:31 final size:29
Alignment explanation
Indices: 34549011--34549074 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 29
34549001 ATAACTTAAA
* *
34549011 TGACTAAAATGTAACATTTCAAACATAAG
1 TGACTAAAATGTAACATGTCAAACAAAAG
*
34549040 TGACTAAAATGTAACCTGAGTCAAACAAAAG
1 TGACTAAAATGTAACAT--GTCAAACAAAAG
34549071 TGAC
1 TGAC
34549075 CATTTCGGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 16 0.53
31 14 0.47
ACGTcount: A:0.47, C:0.16, G:0.14, T:0.23
Consensus pattern (29 bp):
TGACTAAAATGTAACATGTCAAACAAAAG
Found at i:34563142 original size:23 final size:26
Alignment explanation
Indices: 34563102--34563148 Score: 64
Period size: 23 Copynumber: 1.9 Consensus size: 26
34563092 ATTTGTTTTT
*
34563102 AAAAAACTTCGTTTAAATT-TAAAAA
1 AAAAAACTTCGTTAAAATTGTAAAAA
34563127 AAAAAAC-T-GTTAAAATTGTAAA
1 AAAAAACTTCGTTAAAATTGTAAA
34563149 TCTAATCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 8 0.40
24 5 0.25
25 7 0.35
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.30
Consensus pattern (26 bp):
AAAAAACTTCGTTAAAATTGTAAAAA
Found at i:34564837 original size:2 final size:2
Alignment explanation
Indices: 34564830--34564855 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
34564820 AACCACATAC
34564830 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
34564856 TTTTTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34571704 original size:8 final size:8
Alignment explanation
Indices: 34571691--34571715 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
34571681 TACCTTTACT
34571691 AATTTTAA
1 AATTTTAA
34571699 AATTTTAA
1 AATTTTAA
34571707 AATTTTAA
1 AATTTTAA
34571715 A
1 A
34571716 GGGTTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
AATTTTAA
Found at i:34576015 original size:30 final size:30
Alignment explanation
Indices: 34575979--34576047 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
34575969 AAGTGTGAGG
*
34575979 AAAGCTCGTCTAGTTGAACGT-GCTTTCCAA
1 AAAGCTCGTCCAGTTGAAC-TCGCTTTCCAA
* *
34576009 AAAGCTCATCCAGTTGAACTCGTTTTCCAA
1 AAAGCTCGTCCAGTTGAACTCGCTTTCCAA
*
34576039 AAAACTCGT
1 AAAGCTCGT
34576048 TCAACTCCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 1 0.03
30 32 0.97
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (30 bp):
AAAGCTCGTCCAGTTGAACTCGCTTTCCAA
Found at i:34576853 original size:6 final size:6
Alignment explanation
Indices: 34576842--34576869 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
34576832 GGATTTTAGA
34576842 TTTTCT TTTTCT TTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTT
34576870 TGTCATCTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTCT
Found at i:34581259 original size:5 final size:5
Alignment explanation
Indices: 34581249--34581293 Score: 90
Period size: 5 Copynumber: 9.0 Consensus size: 5
34581239 ATATAACACC
34581249 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
34581294 TCCTTTATCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 40 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:34582919 original size:18 final size:18
Alignment explanation
Indices: 34582893--34582952 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
34582883 ATTAAAAATA
34582893 TTTTCAATAATTATTAAT
1 TTTTCAATAATTATTAAT
* *
34582911 TTTAT-AATAAATATAAAT
1 TTT-TCAATAATTATTAAT
34582929 TGTTTCAATAATTTATTTAAT
1 T-TTTCAATAA-TTA-TTAAT
34582950 TTT
1 TTT
34582953 GATTTAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
18 16 0.48
19 8 0.24
20 4 0.12
21 5 0.15
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (18 bp):
TTTTCAATAATTATTAAT
Found at i:34609443 original size:7 final size:8
Alignment explanation
Indices: 34609425--34609453 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
34609415 TAGAGGAGTC
34609425 AAAAATGA
1 AAAAATGA
34609433 AAAAATGA
1 AAAAATGA
34609441 AAAAATGA
1 AAAAATGA
34609449 AAAAA
1 AAAAA
34609454 AGGTTGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.10
Consensus pattern (8 bp):
AAAAATGA
Found at i:34612086 original size:24 final size:23
Alignment explanation
Indices: 34612027--34612090 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 23
34612017 TGAAATTAAT
*
34612027 TAATAATAACATTAAAAATATATA
1 TAATAATAAAATT-AAAATATATA
* *
34612051 TGATAATAAAATTAAAATGTATA
1 TAATAATAAAATTAAAATATATA
*
34612074 TAATAAATTAAATTAAA
1 TAAT-AATAAAATTAAA
34612091 GTTCATTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 12 0.35
24 22 0.65
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (23 bp):
TAATAATAAAATTAAAATATATA
Found at i:34630608 original size:18 final size:18
Alignment explanation
Indices: 34630573--34630606 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
34630563 GGTTTATATT
*
34630573 TTTATTTTTTGATCTTTA
1 TTTATTTTTTGACCTTTA
34630591 TTTATTTTTT-ACCTTT
1 TTTATTTTTTGACCTTT
34630607 TAAAAAAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.15, C:0.09, G:0.03, T:0.74
Consensus pattern (18 bp):
TTTATTTTTTGACCTTTA
Found at i:34634073 original size:16 final size:17
Alignment explanation
Indices: 34634045--34634086 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
34634035 CCTTAAAATG
34634045 ATAAAA-TTT-TAATTT
1 ATAAAATTTTATAATTT
*
34634060 A-AATATTTTATAATTT
1 ATAAAATTTTATAATTT
34634076 ATAAAATTTTA
1 ATAAAATTTTA
34634087 AAATAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 3 0.14
15 4 0.18
16 7 0.32
17 8 0.36
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATAAAATTTTATAATTT
Found at i:34635151 original size:17 final size:15
Alignment explanation
Indices: 34635129--34635179 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
34635119 TAATAAAAAT
34635129 ATAATTTTATTATTTTA
1 ATAA-TTTA-TATTTTA
34635146 ATAATTTATATTTTA
1 ATAATTTATATTTTA
**
34635161 TATGTTTTA-ATTTTA
1 -ATAATTTATATTTTA
34635176 ATAA
1 ATAA
34635180 ATATGAATGG
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
14 2 0.07
15 13 0.45
16 10 0.34
17 4 0.14
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (15 bp):
ATAATTTATATTTTA
Found at i:34635717 original size:60 final size:61
Alignment explanation
Indices: 34635645--34635767 Score: 203
Period size: 60 Copynumber: 2.0 Consensus size: 61
34635635 AAATTTAAAA
*
34635645 TCTTTAAATATTTAGATTTGAGTTTTACTATTTTTAATTTTAATTTTTATTTT-TATTTTC
1 TCTTTAAATATTTAGATTTGAGTTTTACTATTTTTAATTTTAATTTTTATTTTCTAATTTC
* * *
34635705 TCTTTAAATATTTAGATTTGAGTTTTACTGTTTTTATTTTTTATTTTTATTTTCTAATTTC
1 TCTTTAAATATTTAGATTTGAGTTTTACTATTTTTAATTTTAATTTTTATTTTCTAATTTC
34635766 TC
1 TC
34635768 CTATAAATGG
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
60 50 0.86
61 8 0.14
ACGTcount: A:0.23, C:0.07, G:0.06, T:0.65
Consensus pattern (61 bp):
TCTTTAAATATTTAGATTTGAGTTTTACTATTTTTAATTTTAATTTTTATTTTCTAATTTC
Found at i:34638623 original size:20 final size:20
Alignment explanation
Indices: 34638600--34638647 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
34638590 TAAAAAATCA
34638600 AAATATATTA-ATAATTAAAT
1 AAAT-TATTATATAATTAAAT
*
34638620 AAATTATTATTTAATTAAAT
1 AAATTATTATATAATTAAAT
*
34638640 GAATTATT
1 AAATTATT
34638648 GAAAAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
AAATTATTATATAATTAAAT
Found at i:34639243 original size:12 final size:12
Alignment explanation
Indices: 34639224--34639392 Score: 57
Period size: 12 Copynumber: 14.8 Consensus size: 12
34639214 TAATGCATAA
34639224 AATA-ATAATAT
1 AATATATAATAT
34639235 AATATATAA-A-
1 AATATATAATAT
34639245 AATCA-ATAATA-
1 AAT-ATATAATAT
*
34639256 CATGATAT-A-AT
1 AAT-ATATAATAT
34639267 AATATATAACTAT
1 AATATATAA-TAT
34639280 --TAT-TAA-A-
1 AATATATAATAT
34639287 AATAT-TAATA-
1 AATATATAATAT
*
34639297 CATATATAACTAT
1 AATATATAA-TAT
*
34639310 TAT-TATAATAT
1 AATATATAATAT
*
34639321 AGAT-TATAATAA
1 A-ATATATAATAT
34639333 AATATATAATAT
1 AATATATAATAT
* * *
34639345 TACATGATATTAT
1 AATAT-ATAATAT
* *
34639358 AATGTTTAATCAT
1 AATATATAAT-AT
34639371 CAATATAT-ATAT
1 -AATATATAATAT
34639383 ATATATATAA
1 A-ATATATAA
34639393 GCGGATTTTT
Statistics
Matches: 119, Mismatches: 18, Indels: 40
0.67 0.10 0.23
Matches are distributed among these distances:
8 1 0.01
9 6 0.05
10 20 0.17
11 26 0.22
12 44 0.37
13 17 0.14
14 5 0.04
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (12 bp):
AATATATAATAT
Found at i:34639263 original size:22 final size:21
Alignment explanation
Indices: 34639222--34639305 Score: 61
Period size: 22 Copynumber: 4.0 Consensus size: 21
34639212 ACTAATGCAT
34639222 AAAATAATAATATAATATATA
1 AAAATAATAATATAATATATA
*
34639243 AAAATCAATAATA-CATGATATA
1 AAAAT-AATAATATAAT-ATATA
*
34639265 ATAATATATAACTAT--TAT-TA
1 AAAATA-ATAA-TATAATATATA
* *
34639285 AAAATATTAATA-CATATATA
1 AAAATAATAATATAATATATA
34639305 A
1 A
34639306 CTATTATTAT
Statistics
Matches: 51, Mismatches: 4, Indels: 17
0.71 0.06 0.24
Matches are distributed among these distances:
18 2 0.04
19 6 0.12
20 10 0.20
21 10 0.20
22 21 0.41
23 2 0.04
ACGTcount: A:0.60, C:0.05, G:0.01, T:0.35
Consensus pattern (21 bp):
AAAATAATAATATAATATATA
Found at i:34663947 original size:5 final size:5
Alignment explanation
Indices: 34663932--34663975 Score: 81
Period size: 5 Copynumber: 9.0 Consensus size: 5
34663922 GTTCATAGAG
34663932 TTGGA -TGGA TTGGA TTGGA TTGGA TTGGA TTGGA TTGGA TTGGA
1 TTGGA TTGGA TTGGA TTGGA TTGGA TTGGA TTGGA TTGGA TTGGA
34663976 CCTTTTACGT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 4 0.11
5 34 0.89
ACGTcount: A:0.20, C:0.00, G:0.41, T:0.39
Consensus pattern (5 bp):
TTGGA
Found at i:34673239 original size:59 final size:57
Alignment explanation
Indices: 34673165--34673368 Score: 248
Period size: 59 Copynumber: 3.5 Consensus size: 57
34673155 AGACATCCGG
* *
34673165 GGGT-AAAATGGTAATTTTTGAAAGTTTCGAGGTCAAAAATGGAATCTTTGGAATTTTA
1 GGGTAAAAAT-GTAATTTTTGAAAGTTT-TAGGTCAAAAATGGAATTTTTGGAATTTTA
* * *
34673223 TGGGTAAAAATGTAATTTTTGAAAGTGTTTTGGTCAAAAATGGAATTTTTGAAATTTTG
1 -GGGTAAAAATGTAATTTTTGAAAGT-TTTAGGTCAAAAATGGAATTTTTGGAATTTTA
* ** * *
34673282 GGGATAAAAATGTAATTTTTGGAAGTTTTAGGATCAAAAATAAAATTTTTAGAATTTCGA
1 GGG-TAAAAATGTAATTTTTGAAAGTTTTAGG-TCAAAAATGGAATTTTTGGAATTT-TA
34673342 GGGTAAAAATGTAATTTTTGAAAGTTT
1 GGGTAAAAATGTAATTTTTGAAAGTTT
34673369 GGGGGTAAAA
Statistics
Matches: 126, Mismatches: 14, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
58 8 0.06
59 108 0.86
60 10 0.08
ACGTcount: A:0.37, C:0.03, G:0.22, T:0.39
Consensus pattern (57 bp):
GGGTAAAAATGTAATTTTTGAAAGTTTTAGGTCAAAAATGGAATTTTTGGAATTTTA
Found at i:34673389 original size:29 final size:29
Alignment explanation
Indices: 34673165--34673390 Score: 169
Period size: 29 Copynumber: 7.7 Consensus size: 29
34673155 AGACATCCGG
34673165 GGGT-AAAATGGTAATTTTTGAAAGTTTCGA
1 GGGTAAAAAT-GTAATTTTTGAAAGTTT-GA
* * * *
34673195 -GGTCAAAAATGGAATCTTTGGAA-TTTTA
1 GGGT-AAAAATGTAATTTTTGAAAGTTTGA
*
34673223 TGGGTAAAAATGTAATTTTTGAAAGTGTT-T
1 -GGGTAAAAATGTAATTTTTGAAAGT-TTGA
* * *
34673253 TGGTCAAAAATGGAATTTTTGAAATTTTG-
1 GGGT-AAAAATGTAATTTTTGAAAGTTTGA
* *
34673282 GGGATAAAAATGTAATTTTTGGAAGTTTTA
1 GGG-TAAAAATGTAATTTTTGAAAGTTTGA
* **
34673312 GGATCAAAAATAAAATTTTT-AGAA-TTTCGA
1 GGGT-AAAAATGTAATTTTTGA-AAGTTT-GA
*
34673342 GGGTAAAAATGTAATTTTTGAAAGTTTGG
1 GGGTAAAAATGTAATTTTTGAAAGTTTGA
* *
34673371 GGGTAAAAATATAAATTTTG
1 GGGTAAAAATGTAATTTTTG
34673391 GACAGTTTAG
Statistics
Matches: 154, Mismatches: 27, Indels: 31
0.73 0.13 0.15
Matches are distributed among these distances:
28 1 0.01
29 87 0.56
30 59 0.38
31 7 0.05
ACGTcount: A:0.37, C:0.03, G:0.22, T:0.38
Consensus pattern (29 bp):
GGGTAAAAATGTAATTTTTGAAAGTTTGA
Found at i:34675283 original size:6 final size:6
Alignment explanation
Indices: 34675274--34675369 Score: 82
Period size: 6 Copynumber: 17.0 Consensus size: 6
34675264 TTAATACTAT
* *
34675274 TTTAAA TTT-AA -TTAAA TTTAAA CTTAAA -GTAAA TTTAAA TTTAAGA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A
* *
34675320 --TAAA TTTAAA TTTAAA ATTAAGA --TAAA TTTAAA TTTAAA -ATAAA
1 TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA
34675364 TTTAAA
1 TTTAAA
34675370 ACAAATTTAA
Statistics
Matches: 74, Mismatches: 6, Indels: 20
0.74 0.06 0.20
Matches are distributed among these distances:
4 4 0.05
5 18 0.24
6 50 0.68
7 2 0.03
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (6 bp):
TTTAAA
Found at i:34675292 original size:17 final size:16
Alignment explanation
Indices: 34675274--34675380 Score: 90
Period size: 17 Copynumber: 6.4 Consensus size: 16
34675264 TTAATACTAT
*
34675274 TTTAAATTTAATTAAA
1 TTTAAATTTAAATAAA
*
34675290 TTTAAACTTAAAGTAAA
1 TTTAAATTTAAA-TAAA
34675307 TTTAAATTTAAGATAAA
1 TTTAAATTTAA-ATAAA
*
34675324 TTTAAATTTAAAATTAA
1 TTTAAATTT-AAATAAA
**
34675341 GATAAATTTAAATTTAAA
1 TTTAAATTTAAA--TAAA
* *
34675359 -ATAAATTTAAAACAAA
1 TTTAAATTT-AAATAAA
34675375 TTTAAA
1 TTTAAA
34675381 CCTCAATTAA
Statistics
Matches: 75, Mismatches: 9, Indels: 13
0.77 0.09 0.13
Matches are distributed among these distances:
16 16 0.21
17 50 0.67
18 9 0.12
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (16 bp):
TTTAAATTTAAATAAA
Found at i:34675315 original size:23 final size:22
Alignment explanation
Indices: 34675285--34675363 Score: 71
Period size: 23 Copynumber: 3.7 Consensus size: 22
34675275 TTAAATTTAA
34675285 TTAAATTTAAACTTAAAGTAAAT
1 TTAAATTTAAA-TTAAAGTAAAT
*
34675308 TTAAATTT--A--AGA-TAAAT
1 TTAAATTTAAATTAAAGTAAAT
34675325 TTAAATTTAAAATT-AAGATAAAT
1 TTAAATTT-AAATTAAAG-TAAAT
*
34675348 TTAAATTTAAAATAAA
1 TTAAATTTAAATTAAA
34675364 TTTAAAACAA
Statistics
Matches: 45, Mismatches: 3, Indels: 16
0.70 0.05 0.25
Matches are distributed among these distances:
17 13 0.29
18 2 0.04
20 1 0.02
21 2 0.04
22 4 0.09
23 23 0.51
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.39
Consensus pattern (22 bp):
TTAAATTTAAATTAAAGTAAAT
Found at i:34675363 original size:11 final size:11
Alignment explanation
Indices: 34675326--34675380 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
34675316 AAGATAAATT
34675326 TAAATTTAAAA
1 TAAATTTAAAA
* ** *
34675337 TTAAGATAAATT
1 TAAATTTAAA-A
34675349 TAAATTTAAAA
1 TAAATTTAAAA
34675360 TAAATTTAAAA
1 TAAATTTAAAA
*
34675371 CAAATTTAAA
1 TAAATTTAAA
34675381 CCTCAATTAA
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
11 27 0.79
12 7 0.21
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:34675369 original size:23 final size:23
Alignment explanation
Indices: 34675303--34675358 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
34675293 AAACTTAAAG
34675303 TAAATTTAAATTTAAGATAAATT
1 TAAATTTAAATTTAAGATAAATT
*
34675326 TAAATTTAAAATTAAGATAAATT
1 TAAATTTAAATTTAAGATAAATT
34675349 TAAATTTAAA
1 TAAATTTAAA
34675359 ATAAATTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (23 bp):
TAAATTTAAATTTAAGATAAATT
Found at i:34676371 original size:11 final size:11
Alignment explanation
Indices: 34676357--34676382 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
34676347 TTCAAAACTC
34676357 ATAAAATTAAT
1 ATAAAATTAAT
34676368 ATAAAATTAAT
1 ATAAAATTAAT
34676379 ATAA
1 ATAA
34676383 TTAATCATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
ATAAAATTAAT
Found at i:34677184 original size:18 final size:18
Alignment explanation
Indices: 34677158--34677192 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
34677148 TAAATAGTAA
* *
34677158 AATATTATTATTTATTAT
1 AATACTATTATTAATTAT
34677176 AATACTATTATTAATTA
1 AATACTATTATTAATTA
34677193 ATATATAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (18 bp):
AATACTATTATTAATTAT
Found at i:34681327 original size:22 final size:22
Alignment explanation
Indices: 34681270--34681327 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
34681260 CATAAAGCAG
34681270 AAGCGTGCCACAAGGCAGAGAA
1 AAGCGTGCCACAAGGCAGAGAA
* *
34681292 AATGCGTACCACAA-GTAGAGGAA
1 AA-GCGTGCCACAAGGCAGA-GAA
*
34681315 AAGCGTGCAACAA
1 AAGCGTGCCACAA
34681328 AGTTAGATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
22 15 0.50
23 15 0.50
ACGTcount: A:0.43, C:0.21, G:0.28, T:0.09
Consensus pattern (22 bp):
AAGCGTGCCACAAGGCAGAGAA
Found at i:34681330 original size:23 final size:22
Alignment explanation
Indices: 34681270--34681339 Score: 61
Period size: 23 Copynumber: 3.1 Consensus size: 22
34681260 CATAAAGCAG
* *
34681270 AAGCGTGCCACAAGGCAGAGAA
1 AAGCGTGCCACAAAGTAGAGAA
*
34681292 AATGCGTACCAC-AAGTAGAGGAA
1 AA-GCGTGCCACAAAGTAGA-GAA
* *
34681315 AAGCGTGCAACAAAGTTAGATAA
1 AAGCGTGCCACAAAG-TAGAGAA
34681338 AA
1 AA
34681340 TATAAAAGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
22 14 0.37
23 20 0.53
24 4 0.11
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (22 bp):
AAGCGTGCCACAAAGTAGAGAA
Found at i:34681356 original size:18 final size:17
Alignment explanation
Indices: 34681334--34681374 Score: 73
Period size: 18 Copynumber: 2.4 Consensus size: 17
34681324 ACAAAGTTAG
34681334 ATAAAATATAAAAGAAA
1 ATAAAATATAAAAGAAA
34681351 ATTAAAATATAAAAGAAA
1 A-TAAAATATAAAAGAAA
34681369 ATAAAA
1 ATAAAA
34681375 ACTGAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (17 bp):
ATAAAATATAAAAGAAA
Found at i:34682504 original size:12 final size:13
Alignment explanation
Indices: 34682487--34682516 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
34682477 AAATAATTTA
34682487 ATTTTTA-AAATT
1 ATTTTTATAAATT
34682499 ATTTTTATAAATT
1 ATTTTTATAAATT
34682512 ATTTT
1 ATTTT
34682517 AAATTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
ATTTTTATAAATT
Found at i:34683803 original size:24 final size:24
Alignment explanation
Indices: 34683757--34683805 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
34683747 TTTCATCTAA
*
34683757 CTAGTAGTTGTAGACATGGAAATT
1 CTAGTAGTTGTAGACATGAAAATT
* *
34683781 CTAGTAGTTGTATATATGAAAATT
1 CTAGTAGTTGTAGACATGAAAATT
34683805 C
1 C
34683806 AACTGTTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.37
Consensus pattern (24 bp):
CTAGTAGTTGTAGACATGAAAATT
Found at i:34687010 original size:11 final size:11
Alignment explanation
Indices: 34686994--34687018 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
34686984 TGCATCTAGG
34686994 TTTTGTATTAC
1 TTTTGTATTAC
34687005 TTTTGTATTAC
1 TTTTGTATTAC
34687016 TTT
1 TTT
34687019 GTGGAATATA
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:0.16, C:0.08, G:0.08, T:0.68
Consensus pattern (11 bp):
TTTTGTATTAC
Found at i:34691020 original size:9 final size:9
Alignment explanation
Indices: 34691006--34691030 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
34690996 ACTCCTTAAT
34691006 GGAGTTATA
1 GGAGTTATA
34691015 GGAGTTATA
1 GGAGTTATA
34691024 GGAGTTA
1 GGAGTTA
34691031 ATAAGGGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (9 bp):
GGAGTTATA
Found at i:34700143 original size:2 final size:2
Alignment explanation
Indices: 34700136--34700185 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
34700126 ACGTTGGTTG
34700136 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
34700178 GT GT GT GT
1 GT GT GT GT
34700186 AATATAAATA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:34707471 original size:17 final size:18
Alignment explanation
Indices: 34707447--34707489 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
34707437 GTTTTGGTGC
*
34707447 TGTTTTTTACTATTTTGG
1 TGTTTTTTAATATTTTGG
*
34707465 T-TTTTTTAATGTTTTGG
1 TGTTTTTTAATATTTTGG
34707482 TGTTTTTT
1 TGTTTTTT
34707490 TACTGTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.09, C:0.02, G:0.16, T:0.72
Consensus pattern (18 bp):
TGTTTTTTAATATTTTGG
Found at i:34707486 original size:19 final size:19
Alignment explanation
Indices: 34707436--34707498 Score: 76
Period size: 19 Copynumber: 3.3 Consensus size: 19
34707426 ATTATATTGT
34707436 TGTTTTGGTGCTGTTTTTTAC
1 TGTTTTGGTG-T-TTTTTTAC
* *
34707457 TATTTT-G-GTTTTTTTAA
1 TGTTTTGGTGTTTTTTTAC
34707474 TGTTTTGGTGTTTTTTTAC
1 TGTTTTGGTGTTTTTTTAC
34707493 TGTTTT
1 TGTTTT
34707499 AGTTATTGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
17 12 0.33
18 2 0.06
19 16 0.44
20 1 0.03
21 5 0.14
ACGTcount: A:0.08, C:0.05, G:0.19, T:0.68
Consensus pattern (19 bp):
TGTTTTGGTGTTTTTTTAC
Found at i:34707496 original size:11 final size:11
Alignment explanation
Indices: 34707482--34707541 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 11
34707472 AATGTTTTGG
*
34707482 TGTTTTTTTAC
1 TGTTTTGTTAC
*
34707493 TGTTTTAGTTAT
1 TGTTTT-GTTAC
* *
34707505 TGTTTTGGTGC
1 TGTTTTGTTAC
34707516 TGCTTTT-TTAC
1 TG-TTTTGTTAC
*
34707527 TGTTTTGATAC
1 TGTTTTGTTAC
34707538 TGTT
1 TGTT
34707542 ATTTTTGTTG
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
10 4 0.11
11 21 0.55
12 13 0.34
ACGTcount: A:0.10, C:0.08, G:0.18, T:0.63
Consensus pattern (11 bp):
TGTTTTGTTAC
Found at i:34707567 original size:20 final size:20
Alignment explanation
Indices: 34707544--34707586 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
34707534 ATACTGTTAT
* *
34707544 TTTTGTTGCTATTTTTGTTG
1 TTTTGCTGCTATTTTAGTTG
*
34707564 TTTTGCTGCTGTTTTAGTTG
1 TTTTGCTGCTATTTTAGTTG
34707584 TTT
1 TTT
34707587 GGATGTTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.05, C:0.07, G:0.21, T:0.67
Consensus pattern (20 bp):
TTTTGCTGCTATTTTAGTTG
Found at i:34708257 original size:21 final size:19
Alignment explanation
Indices: 34708232--34708281 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 19
34708222 TTGTATATTT
34708232 TAATTTTTTATAATTGTTTC
1 TAATTTTTTATAA-TGTTTC
*
34708252 ATAATTTTCTATAATGTTTC
1 -TAATTTTTTATAATGTTTC
34708272 TAATATTTTT
1 TAAT-TTTTT
34708282 TTAAAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 4 0.15
20 10 0.38
21 12 0.46
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.62
Consensus pattern (19 bp):
TAATTTTTTATAATGTTTC
Found at i:34708319 original size:19 final size:18
Alignment explanation
Indices: 34708297--34708338 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
34708287 AAATTATAAG
34708297 TTTTAT-ACTTTTATAACAT
1 TTTTATGACTTTTA-AAC-T
*
34708316 TTTTATGATTTTTAAACT
1 TTTTATGACTTTTAAACT
34708334 TTTTA
1 TTTTA
34708339 ATTTTTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 6 0.29
19 9 0.43
20 6 0.29
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTTATGACTTTTAAACT
Found at i:34708345 original size:18 final size:18
Alignment explanation
Indices: 34708324--34708375 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
34708314 ATTTTTATGA
34708324 TTTTTA-AACTTTTTAA-T
1 TTTTTATAA-TTTTTAATT
*
34708341 TTTTTATAATTATTAATT
1 TTTTTATAATTTTTAATT
*
34708359 ATTTTATAATTTTTAAT
1 TTTTTATAATTTTTAAT
34708376 ATATATCAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
17 12 0.40
18 18 0.60
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTTATAATTTTTAATT
Found at i:34708869 original size:28 final size:28
Alignment explanation
Indices: 34708833--34708890 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
34708823 TATACCGTGC
34708833 ATCTTAACTCACTTTTAATTTTAATGCA
1 ATCTTAACTCACTTTTAATTTTAATGCA
34708861 ATCTTAACTCACTTTTAATTTTAATGCA
1 ATCTTAACTCACTTTTAATTTTAATGCA
34708889 AT
1 AT
34708891 AATGAGAAAC
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:0.33, C:0.17, G:0.03, T:0.47
Consensus pattern (28 bp):
ATCTTAACTCACTTTTAATTTTAATGCA
Found at i:34710970 original size:15 final size:17
Alignment explanation
Indices: 34710949--34710989 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
34710939 AATTTATTTA
34710949 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATAAT
*
34710965 -AAATTATTAAAATAAT
1 AAAATTATAAAAATAAT
34710981 AAAATTATA
1 AAAATTATA
34710990 TTTTTATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATAAT
Found at i:34713742 original size:18 final size:18
Alignment explanation
Indices: 34713709--34713761 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
34713699 GTTGAGATGA
34713709 AAATAAATTT--TTAATT
1 AAATAAATTTAATTAATT
34713725 AAATAAATTTAATTAATT
1 AAATAAATTTAATTAATT
*
34713743 AAA-AATTTTAAATTAATT
1 AAATAAATTT-AATTAATT
34713761 A
1 A
34713762 CAACTGAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
16 10 0.30
17 5 0.15
18 18 0.55
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AAATAAATTTAATTAATT
Found at i:34718486 original size:21 final size:21
Alignment explanation
Indices: 34718462--34718517 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 21
34718452 CGATCTGAGG
34718462 AAAAATAAAAGAAACAGAATT
1 AAAAATAAAAGAAACAGAATT
* *
34718483 AAAAATAAAATAAAATAGAATT
1 AAAAATAAAA-GAAACAGAATT
*
34718505 AAAAA-AATAGAAA
1 AAAAATAAAAGAAA
34718518 ATAGGAAAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 3 0.10
21 13 0.43
22 14 0.47
ACGTcount: A:0.75, C:0.02, G:0.07, T:0.16
Consensus pattern (21 bp):
AAAAATAAAAGAAACAGAATT
Found at i:34718518 original size:21 final size:22
Alignment explanation
Indices: 34718462--34718521 Score: 79
Period size: 21 Copynumber: 2.8 Consensus size: 22
34718452 CGATCTGAGG
*
34718462 AAAAATAAAAG-AAACAGAATT
1 AAAAATAAAAGAAAATAGAATT
*
34718483 AAAAATAAAATAAAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
*
34718505 AAAAA-AATAGAAAATAG
1 AAAAATAAAAGAAAATAG
34718522 GAAAGTCGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 20 0.59
22 14 0.41
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.17
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:34719770 original size:21 final size:22
Alignment explanation
Indices: 34719746--34719786 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
34719736 AAATATAATT
*
34719746 ATAAACAATATAATT-AAGAAC
1 ATAAACAACATAATTCAAGAAC
*
34719767 ATAAATAACATAATTCAAGA
1 ATAAACAACATAATTCAAGA
34719787 GGAGAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.61, C:0.10, G:0.05, T:0.24
Consensus pattern (22 bp):
ATAAACAACATAATTCAAGAAC
Found at i:34730129 original size:14 final size:15
Alignment explanation
Indices: 34730112--34730140 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
34730102 AAAAGAATAC
34730112 TAAAAAA-CATAAAA
1 TAAAAAACCATAAAA
34730126 TAAAAAACCATAAAA
1 TAAAAAACCATAAAA
34730141 GAATAGTGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.76, C:0.10, G:0.00, T:0.14
Consensus pattern (15 bp):
TAAAAAACCATAAAA
Found at i:34747148 original size:16 final size:15
Alignment explanation
Indices: 34747129--34747171 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
34747119 TCAATTTCAG
34747129 AATTGATTAATTTTAA
1 AATTGATTAATTTT-A
*
34747145 AATTGATTAA-ATTA
1 AATTGATTAATTTTA
34747159 AATTGAATTAATT
1 AATTG-ATTAATT
34747172 AAAATTTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 6 0.26
15 7 0.30
16 10 0.43
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (15 bp):
AATTGATTAATTTTA
Found at i:34747176 original size:15 final size:15
Alignment explanation
Indices: 34747129--34747177 Score: 57
Period size: 14 Copynumber: 3.3 Consensus size: 15
34747119 TCAATTTCAG
*
34747129 AATTGATTAATTTTAA
1 AATTGATTAA-ATTAA
34747145 AATTGATTAAATT-A
1 AATTGATTAAATTAA
34747159 AATTGAATT-AATTAA
1 AATTG-ATTAAATTAA
34747174 AATT
1 AATT
34747178 TATAAGTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 10 0.33
15 10 0.33
16 10 0.33
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (15 bp):
AATTGATTAAATTAA
Found at i:34748189 original size:15 final size:15
Alignment explanation
Indices: 34748169--34748214 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
34748159 ACAAAATAAT
34748169 AACATAAATGATTAA
1 AACATAAATGATTAA
*
34748184 AACATAACAT--TTCA
1 AACATAA-ATGATTAA
*
34748198 AACATAAGTGATTAA
1 AACATAAATGATTAA
34748213 AA
1 AA
34748215 TGTAACCTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
13 1 0.04
14 10 0.40
15 12 0.48
16 2 0.08
ACGTcount: A:0.57, C:0.11, G:0.07, T:0.26
Consensus pattern (15 bp):
AACATAAATGATTAA
Found at i:34748500 original size:21 final size:22
Alignment explanation
Indices: 34748476--34748521 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
34748466 TTGTAGAAGA
*
34748476 ATATT-ATTTCTTAAAAGATGT
1 ATATTGATTTCTTAAAAAATGT
*
34748497 ATATTGGATTTTTTAAAAAATGT
1 ATATT-GATTTCTTAAAAAATGT
34748520 AT
1 AT
34748522 TGCAGCACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 5 0.24
23 16 0.76
ACGTcount: A:0.39, C:0.02, G:0.11, T:0.48
Consensus pattern (22 bp):
ATATTGATTTCTTAAAAAATGT
Found at i:34751739 original size:14 final size:14
Alignment explanation
Indices: 34751722--34751762 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
34751712 ATATTATTTT
34751722 ATTTTTAATATATC
1 ATTTTTAATATATC
* * *
34751736 ATTTATATTATATT
1 ATTTTTAATATATC
34751750 ATTTTTAATATAT
1 ATTTTTAATATAT
34751763 GTGTGCATAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (14 bp):
ATTTTTAATATATC
Found at i:34751751 original size:28 final size:28
Alignment explanation
Indices: 34751708--34751762 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
34751698 TAAATCGTGT
*
34751708 ATTTATATTATTTTATTTTTAATATATC
1 ATTTATATTATATTATTTTTAATATATC
34751736 ATTTATATTATATTATTTTTAATATAT
1 ATTTATATTATATTATTTTTAATATAT
34751763 GTGTGCATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (28 bp):
ATTTATATTATATTATTTTTAATATATC
Found at i:34751831 original size:25 final size:25
Alignment explanation
Indices: 34751772--34751832 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 25
34751762 TGTGTGCATA
*
34751772 AAATTAGTATAAATAAATGATAAAT
1 AAATTATTATAAATAAATGATAAAT
34751797 AAA-TAGTTATAAA-AAAGTGAT-AAT
1 AAATTA-TTATAAATAAA-TGATAAAT
34751821 AGAATTATTATA
1 A-AATTATTATA
34751833 TACAAATTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
24 9 0.29
25 20 0.65
26 2 0.06
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (25 bp):
AAATTATTATAAATAAATGATAAAT
Found at i:34755613 original size:21 final size:21
Alignment explanation
Indices: 34755587--34755654 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 21
34755577 TAATAAAATT
34755587 TTATATGCATAATAAATTTAA
1 TTATATGCATAATAAATTTAA
*
34755608 TTATAT-C--GATAAATTTAA
1 TTATATGCATAATAAATTTAA
* *
34755626 TAAT-TGAATAATTAAAATATTAA
1 TTATATGCATAA-T-AAAT-TTAA
34755649 TTATAT
1 TTATAT
34755655 AAAAACATGA
Statistics
Matches: 35, Mismatches: 5, Indels: 11
0.69 0.10 0.22
Matches are distributed among these distances:
17 1 0.03
18 13 0.37
20 2 0.06
21 7 0.20
22 4 0.11
23 7 0.20
24 1 0.03
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44
Consensus pattern (21 bp):
TTATATGCATAATAAATTTAA
Found at i:34756392 original size:30 final size:31
Alignment explanation
Indices: 34756353--34756415 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 31
34756343 ATTTTAACAC
34756353 AACAATCACTCAAC-TT-T-AAAAATGTGACAA
1 AACAATCACT-AACATTATCAAAAA-GTGACAA
*
34756383 AACAGTCACTAACATTATCAAAAAGTGACAA
1 AACAATCACTAACATTATCAAAAAGTGACAA
34756414 AA
1 AA
34756416 TAGTTACTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 3 0.10
30 11 0.38
31 10 0.34
32 5 0.17
ACGTcount: A:0.52, C:0.19, G:0.08, T:0.21
Consensus pattern (31 bp):
AACAATCACTAACATTATCAAAAAGTGACAA
Found at i:34756813 original size:47 final size:47
Alignment explanation
Indices: 34756707--34756818 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
34756697 GTTATTTTGT
* * *
34756707 GTTTATTCGAATTTGATGTCGATATTGATTGTGATTTTTGATTTAGG
1 GTTTATTCGATTTTGATTTCGATATTGATTGTCATTTTTGATTTAGG
* *
34756754 GTTTATTCGATTTTGATTTGGATATTGATTTTCATTTTTGATTTAGG
1 GTTTATTCGATTTTGATTTCGATATTGATTGTCATTTTTGATTTAGG
*
34756801 G-TTATTTTGATTTTGATT
1 GTTTA-TTCGATTTTGATT
34756819 GGGTTATGGT
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
46 3 0.05
47 55 0.95
ACGTcount: A:0.20, C:0.04, G:0.21, T:0.56
Consensus pattern (47 bp):
GTTTATTCGATTTTGATTTCGATATTGATTGTCATTTTTGATTTAGG
Found at i:34756974 original size:30 final size:30
Alignment explanation
Indices: 34756938--34757007 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 30
34756928 ACTATTAATC
34756938 AGTGACTGTTTTG-CAC-TTTTCGATAACGTT-
1 AGTGACTGTTTTGTCACATTTTC-A-AA-GTTG
*
34756968 AGTGACTATTTTGTCACATTTTCAAAGTTG
1 AGTGACTGTTTTGTCACATTTTCAAAGTTG
34756998 AGTGACTGTT
1 AGTGACTGTT
34757008 GTGTTAAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
29 3 0.09
30 23 0.66
31 4 0.11
32 5 0.14
ACGTcount: A:0.23, C:0.14, G:0.20, T:0.43
Consensus pattern (30 bp):
AGTGACTGTTTTGTCACATTTTCAAAGTTG
Found at i:34757482 original size:31 final size:29
Alignment explanation
Indices: 34757433--34757514 Score: 96
Period size: 29 Copynumber: 2.8 Consensus size: 29
34757423 TAAATCTCAA
*
34757433 AATTATAT--ATGAATTTTAATTTAATGTGC
1 AATTATATACATGAACTTTAATTTAA--TGC
*
34757462 AATTATATACATGAACTTTAATTTGATGC
1 AATTATATACATGAACTTTAATTTAATGC
*
34757491 AATTATATACGTGAAACTTTAATT
1 AATTATATACATG-AACTTTAATT
34757515 GTGGCTCAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
29 23 0.49
30 10 0.21
31 14 0.30
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.44
Consensus pattern (29 bp):
AATTATATACATGAACTTTAATTTAATGC
Found at i:34757537 original size:31 final size:30
Alignment explanation
Indices: 34757459--34757546 Score: 90
Period size: 31 Copynumber: 2.9 Consensus size: 30
34757449 TAATTTAATG
*
34757459 TGCAATTATATACATG-AACTTTAATTTGA
1 TGCAAATATATACATGAAACTTTAATTTGA
* * *
34757488 TGCAATTATATACGTGAAACTTTAATTGTGGC
1 TGCAAATATATACATGAAACTTTAATT-T-GA
* *
34757520 T-CAAATATATACTTGAAACGTTAATTT
1 TGCAAATATATACATGAAACTTTAATTT
34757547 TGATTTAATT
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
29 15 0.29
30 11 0.22
31 23 0.45
32 2 0.04
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.40
Consensus pattern (30 bp):
TGCAAATATATACATGAAACTTTAATTTGA
Found at i:34758084 original size:12 final size:12
Alignment explanation
Indices: 34758064--34758092 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
34758054 TAAATTTATG
34758064 TTTTT-AGTTTT
1 TTTTTAAGTTTT
34758075 TTTTTAAGTTTT
1 TTTTTAAGTTTT
34758087 TTTTTA
1 TTTTTA
34758093 TGTTCACCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (12 bp):
TTTTTAAGTTTT
Found at i:34764830 original size:29 final size:29
Alignment explanation
Indices: 34764798--34764875 Score: 72
Period size: 29 Copynumber: 2.7 Consensus size: 29
34764788 ACCCGGGGGG
34764798 CAAAATGGTAATTTTGGACACTTCGA-GGT
1 CAAAATGGTAATTTTGGA-ACTTCGAGGGT
* * *
34764827 CAAAAAT-GAAATTTTTGGAAGTTTGAGGGT
1 C-AAAATGGTAA-TTTTGGAACTTCGAGGGT
34764857 -AAAATGGTAATTTTTGGAA
1 CAAAATGGTAA-TTTTGGAA
34764876 AAAATTGGGG
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
28 5 0.12
29 21 0.51
30 15 0.37
ACGTcount: A:0.36, C:0.06, G:0.24, T:0.33
Consensus pattern (29 bp):
CAAAATGGTAATTTTGGAACTTCGAGGGT
Found at i:34764890 original size:59 final size:59
Alignment explanation
Indices: 34764827--34764989 Score: 163
Period size: 59 Copynumber: 2.8 Consensus size: 59
34764817 ACTTCGAGGT
* *
34764827 CAAAAATGAAATTTTTGGAAGTTTGAGGGT-AAAATGGTAATTTTTGGAAAAA-ATTGGGG
1 CAAAAATGAAATTTTTGGAAGTTTGAGGGTAAAAAT-GTAATTTTT-CAAAAAGATTAGGG
* * * * *
34764886 CAAAAATGGAATTTTTAGAGGTTTGGGGGTAAAAATGTAA-TTTTCAAAAAGTTTAGGG
1 CAAAAATGAAATTTTTGGAAGTTTGAGGGTAAAAATGTAATTTTTCAAAAAGATTAGGG
** * *
34764944 TTAAAATGTAATTTTTGGAAAGTTT-AGGGGTCAAAATGTAATTTTT
1 CAAAAATGAAATTTTTGG-AAGTTTGA-GGGTAAAAATGTAATTTTT
34764990 AGAATGTTTG
Statistics
Matches: 85, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
57 5 0.06
58 23 0.27
59 48 0.56
60 9 0.11
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.36
Consensus pattern (59 bp):
CAAAAATGAAATTTTTGGAAGTTTGAGGGTAAAAATGTAATTTTTCAAAAAGATTAGGG
Found at i:34764982 original size:30 final size:30
Alignment explanation
Indices: 34764824--34765060 Score: 209
Period size: 30 Copynumber: 8.0 Consensus size: 30
34764814 GACACTTCGA
*
34764824 GGTCAAAAATGAAATTTTTGG-AAGTTT-GAG
1 GGTC-AAAATGTAATTTTTGGAAAGTTTAG-G
**
34764854 GGT-AAAATGGTAATTTTTGGAAAAAATT-GG
1 GGTCAAAAT-GTAATTTTTGG-AAAGTTTAGG
* * * *
34764884 GG-CAAAAATGGAATTTTTAG-AGGTTTGGG
1 GGTC-AAAATGTAATTTTTGGAAAGTTTAGG
* ***
34764913 GGTAAAAATGTAATTTTCAAAAAGTTTA-G
1 GGTCAAAATGTAATTTTTGGAAAGTTTAGG
*
34764942 GGTTAAAATGTAATTTTTGGAAAGTTTAGG
1 GGTCAAAATGTAATTTTTGGAAAGTTTAGG
* * *
34764972 GGTCAAAATGTAATTTTTAGAATGTTTGGG
1 GGTCAAAATGTAATTTTTGGAAAGTTTAGG
*
34765002 GGTCAAAATGTAATTTTTGGAAAGTTTAAG
1 GGTCAAAATGTAATTTTTGGAAAGTTTAGG
* * *
34765032 GGTCAAAATATGATTTTTGGATAGTTTAG
1 GGTCAAAATGTAATTTTTGGAAAGTTTAG
34765061 AGACCTTCAG
Statistics
Matches: 168, Mismatches: 30, Indels: 18
0.78 0.14 0.08
Matches are distributed among these distances:
28 8 0.05
29 52 0.31
30 98 0.58
31 10 0.06
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (30 bp):
GGTCAAAATGTAATTTTTGGAAAGTTTAGG
Found at i:34766137 original size:3 final size:3
Alignment explanation
Indices: 34766124--34766182 Score: 102
Period size: 3 Copynumber: 20.0 Consensus size: 3
34766114 AGATTTCTTT
34766124 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
34766171 TTA TCA TTA TTA
1 TTA TTA TTA TTA
34766183 CTACTACTAC
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 51 0.96
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:34766187 original size:3 final size:3
Alignment explanation
Indices: 34766181--34766206 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
34766171 TTATCATTAT
34766181 TAC TAC TAC TAC TAC TAC TAC TAC TA
1 TAC TAC TAC TAC TAC TAC TAC TAC TA
34766207 AATATTGCAA
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:0.31, G:0.00, T:0.35
Consensus pattern (3 bp):
TAC
Found at i:34766908 original size:17 final size:17
Alignment explanation
Indices: 34766886--34766953 Score: 79
Period size: 17 Copynumber: 4.1 Consensus size: 17
34766876 TATTTCAAAT
*
34766886 TTTAAATTTAAAATAAA
1 TTTAAACTTAAAATAAA
34766903 TTTAAACTT--AATAAA
1 TTTAAACTTAAAATAAA
*
34766918 TTTAAATTTAAAAT-AA
1 TTTAAACTTAAAATAAA
*
34766934 TTCTAAACTTAGAATAAA
1 TT-TAAACTTAAAATAAA
34766952 TT
1 TT
34766954 GAAAATAAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
15 14 0.33
16 4 0.09
17 21 0.49
18 4 0.09
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.41
Consensus pattern (17 bp):
TTTAAACTTAAAATAAA
Found at i:34766917 original size:15 final size:15
Alignment explanation
Indices: 34766897--34766944 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
34766887 TTAAATTTAA
34766897 AATAAATTTAAACTT
1 AATAAATTTAAACTT
*
34766912 AATAAATTTAAATTT
1 AATAAATTTAAACTT
*
34766927 AAAATAATTCTAAACTT
1 AATA-AATT-TAAACTT
34766944 A
1 A
34766945 GAATAAATTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 17 0.61
16 4 0.14
17 7 0.25
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (15 bp):
AATAAATTTAAACTT
Found at i:34766924 original size:32 final size:33
Alignment explanation
Indices: 34766886--34766953 Score: 104
Period size: 32 Copynumber: 2.1 Consensus size: 33
34766876 TATTTCAAAT
34766886 TTTAAATTTAAAATAAATT-TAAACTT-AATAAA
1 TTTAAATTTAAAAT-AATTCTAAACTTAAATAAA
34766918 TTTAAATTTAAAATAATTCTAAACTTAGAATAAA
1 TTTAAATTTAAAATAATTCTAAACTTA-AATAAA
34766952 TT
1 TT
34766954 GAAAATAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
31 4 0.12
32 21 0.64
34 8 0.24
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.41
Consensus pattern (33 bp):
TTTAAATTTAAAATAATTCTAAACTTAAATAAA
Found at i:34767043 original size:21 final size:21
Alignment explanation
Indices: 34767019--34767109 Score: 105
Period size: 21 Copynumber: 4.3 Consensus size: 21
34767009 CTTCAACAGT
34767019 TGTTTTGGTGCTTTTTTTTAC
1 TGTTTTGGTGCTTTTTTTTAC
* *
34767040 TGTTTTGGTTACTATTTTTTAC
1 TGTTTTGG-TGCTTTTTTTTAC
* *
34767062 TGTTTTTGTG-TTGTTTTTTAT
1 TGTTTTGGTGCTT-TTTTTTAC
*
34767083 TATTTTGGTGC-TTTTTTTAC
1 TGTTTTGGTGCTTTTTTTTAC
34767103 TGTTTTG
1 TGTTTTG
34767110 ATTGTTGTTT
Statistics
Matches: 57, Mismatches: 10, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
20 14 0.25
21 25 0.44
22 18 0.32
ACGTcount: A:0.08, C:0.07, G:0.18, T:0.68
Consensus pattern (21 bp):
TGTTTTGGTGCTTTTTTTTAC
Found at i:34767118 original size:12 final size:11
Alignment explanation
Indices: 34767103--34767196 Score: 52
Period size: 12 Copynumber: 8.5 Consensus size: 11
34767093 CTTTTTTTAC
34767103 TGTTTTGATTGT
1 TGTTTT-ATTGT
*
34767115 TG-TTT-TTGC
1 TGTTTTATTGT
*
34767124 TGTTATTTTTGT
1 TGTT-TTATTGT
*
34767136 TGTTATTTTTGT
1 TGTT-TTATTGT
*
34767148 TGTTTTTAATGT
1 TG-TTTTATTGT
**
34767160 TGTTTTGCTGT
1 TGTTTTATTGT
34767171 TGTTTTGATTGT
1 TGTTTT-ATTGT
*
34767183 T-ATTT-TTGT
1 TGTTTTATTGT
34767192 TGTTT
1 TGTTT
34767197 GGATGTTATT
Statistics
Matches: 66, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
9 10 0.15
10 3 0.05
11 21 0.32
12 30 0.45
13 2 0.03
ACGTcount: A:0.07, C:0.02, G:0.20, T:0.70
Consensus pattern (11 bp):
TGTTTTATTGT
Found at i:34767120 original size:22 final size:21
Alignment explanation
Indices: 34767019--34767121 Score: 84
Period size: 21 Copynumber: 4.9 Consensus size: 21
34767009 CTTCAACAGT
* *
34767019 TGTTTTGGTGCTTTTTTTTAC
1 TGTTTTGTTGCTGTTTTTTAC
* *
34767040 TGTTTTGGTTACTATTTTTTAC
1 TGTTTT-GTTGCTGTTTTTTAC
* *
34767062 TGTTTT-TGTGTTGTTTTTTAT
1 TGTTTTGT-TGCTGTTTTTTAC
* *
34767083 TATTTTGGTGCT-TTTTTTAC
1 TGTTTTGTTGCTGTTTTTTAC
*
34767103 TGTTTTGATTGTTGTTTTT
1 TGTTTTG-TTGCTGTTTTT
34767122 GCTGTTATTT
Statistics
Matches: 63, Mismatches: 14, Indels: 9
0.73 0.16 0.10
Matches are distributed among these distances:
20 14 0.22
21 26 0.41
22 23 0.37
ACGTcount: A:0.08, C:0.06, G:0.17, T:0.69
Consensus pattern (21 bp):
TGTTTTGTTGCTGTTTTTTAC
Found at i:34767121 original size:63 final size:65
Alignment explanation
Indices: 34767021--34767144 Score: 164
Period size: 63 Copynumber: 1.9 Consensus size: 65
34767011 TCAACAGTTG
*
34767021 TTTTGGTGCTTTTTTTTACTGTTTTGGTTACTATTTTTTACTGTT-TTTGTGTTGTT-TTTTATT
1 TTTTGGTGCTTTTTTTTACTGTTTTGATTACTA-TTTTTACTGTTATTTGTGTTGTTATTTTATT
34767084 A
65 A
** * * *
34767085 TTTTGGTGC-TTTTTTTACTGTTTTGATTGTTGTTTTTGCTGTTATTTTTGTTGTTATTTT
1 TTTTGGTGCTTTTTTTTACTGTTTTGATTACTATTTTTACTGTTATTTGTGTTGTTATTTT
34767145 TGTTGTTTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
62 10 0.19
63 29 0.56
64 13 0.25
ACGTcount: A:0.08, C:0.06, G:0.17, T:0.69
Consensus pattern (65 bp):
TTTTGGTGCTTTTTTTTACTGTTTTGATTACTATTTTTACTGTTATTTGTGTTGTTATTTTATTA
Found at i:34767148 original size:21 final size:20
Alignment explanation
Indices: 34767130--34767209 Score: 81
Period size: 21 Copynumber: 3.8 Consensus size: 20
34767120 TTGCTGTTAT
34767130 TTTTGTTGTTATTTTTGTTG
1 TTTTGTTGTTATTTTTGTTG
*
34767150 TTTT-TAATGTTGTTTTGCTGTTG
1 TTTTGT--TGTTATTTT--TGTTG
34767173 TTTTGATTGTTATTTTTGTTG
1 TTTTG-TTGTTATTTTTGTTG
* *
34767194 TTTGGATGTTATTTTT
1 TTTTGTTGTTATTTTT
34767210 TTAATGCATT
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
19 1 0.02
20 14 0.28
21 17 0.34
23 17 0.34
25 1 0.02
ACGTcount: A:0.09, C:0.01, G:0.20, T:0.70
Consensus pattern (20 bp):
TTTTGTTGTTATTTTTGTTG
Found at i:34767166 original size:44 final size:45
Alignment explanation
Indices: 34767103--34767209 Score: 139
Period size: 44 Copynumber: 2.4 Consensus size: 45
34767093 CTTTTTTTAC
* *
34767103 TGTTTTGATTGTTGTTTTTGCTGTTATTTTTG-TTGTTATTTTTGT
1 TGTTTTGAATGTTGTTTTTGCTGTT-GTTTTGATTGTTATTTTTGT
*
34767148 TGTTTTTAATGTTG-TTTTGCTGTTGTTTTGATTGTTATTTTTGT
1 TGTTTTGAATGTTGTTTTTGCTGTTGTTTTGATTGTTATTTTTGT
* *
34767192 TG-TTTGGATGTTATTTTT
1 TGTTTTGAATGTTGTTTTT
34767210 TTAATGCATT
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
43 13 0.24
44 29 0.54
45 12 0.22
ACGTcount: A:0.08, C:0.02, G:0.21, T:0.69
Consensus pattern (45 bp):
TGTTTTGAATGTTGTTTTTGCTGTTGTTTTGATTGTTATTTTTGT
Found at i:34768084 original size:7 final size:7
Alignment explanation
Indices: 34768072--34768096 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
34768062 CAATTATTCT
34768072 CCAAATG
1 CCAAATG
34768079 CCAAATG
1 CCAAATG
34768086 CCAAATG
1 CCAAATG
34768093 CCAA
1 CCAA
34768097 CCAACCAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.32, G:0.12, T:0.12
Consensus pattern (7 bp):
CCAAATG
Found at i:34769617 original size:14 final size:15
Alignment explanation
Indices: 34769598--34769626 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
34769588 GATATTTTAA
34769598 TTTTAC-ATAATATT
1 TTTTACAATAATATT
34769612 TTTTACAATAATATT
1 TTTTACAATAATATT
34769627 AAATACACGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTTACAATAATATT
Found at i:34771827 original size:20 final size:21
Alignment explanation
Indices: 34771788--34771827 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
34771778 GGAGATTCCA
* *
34771788 AAATCAAAAGAAATGGAAAAT
1 AAATCAAAAGAAAAGAAAAAT
34771809 AAAT-AAAAGAAAAGAAAAA
1 AAATCAAAAGAAAAGAAAAA
34771828 AAGAGAAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.75, C:0.03, G:0.12, T:0.10
Consensus pattern (21 bp):
AAATCAAAAGAAAAGAAAAAT
Found at i:34787654 original size:19 final size:20
Alignment explanation
Indices: 34787595--34787655 Score: 56
Period size: 19 Copynumber: 3.1 Consensus size: 20
34787585 TTAAACATTT
*
34787595 AAAAAA-TATTAAAATGATTA
1 AAAAAATTATT-AAATAATTA
* * *
34787615 TAAAAATT-TTCAATAAATA
1 AAAAAATTATTAAATAATTA
34787634 AAAAAATTATTAAAT-ATTA
1 AAAAAATTATTAAATAATTA
34787653 AAA
1 AAA
34787656 TAAAATAATA
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
19 19 0.59
20 12 0.38
21 1 0.03
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (20 bp):
AAAAAATTATTAAATAATTA
Found at i:34787669 original size:22 final size:24
Alignment explanation
Indices: 34787629--34787673 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
34787619 AATTTTCAAT
34787629 AAATAAAAAAATTATTAAATATTA
1 AAATAAAAAAATTATTAAATATTA
*
34787653 AAATAAAATAA-TA-TAAATATT
1 AAATAAAAAAATTATTAAATATT
34787674 TTTTTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 8 0.40
23 2 0.10
24 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (24 bp):
AAATAAAAAAATTATTAAATATTA
Found at i:34788237 original size:12 final size:12
Alignment explanation
Indices: 34788220--34788245 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
34788210 ATGAAAGGTT
34788220 AATTTAAATTAA
1 AATTTAAATTAA
34788232 AATTTAAATTAA
1 AATTTAAATTAA
34788244 AA
1 AA
34788246 ATAATTTAAT
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:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AATTTAAATTAA
Found at i:34789937 original size:22 final size:22
Alignment explanation
Indices: 34789910--34789969 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
34789900 TCGACTTCCC
34789910 TATTTTCTATTT-CTTTTAATTT
1 TATTTTCT-TTTACTTTTAATTT
* *
34789932 TATTTTCTTTTATTTTTAATTC
1 TATTTTCTTTTACTTTTAATTT
* *
34789954 T-GTTTCTTTTATTTTT
1 TATTTTCTTTTACTTTT
34789970 CCTTATATAC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 17 0.50
22 17 0.50
ACGTcount: A:0.15, C:0.08, G:0.02, T:0.75
Consensus pattern (22 bp):
TATTTTCTTTTACTTTTAATTT
Found at i:34789940 original size:16 final size:16
Alignment explanation
Indices: 34789919--34789949 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
34789909 CTATTTTCTA
34789919 TTTCTTTTAATTTTAT
1 TTTCTTTTAATTTTAT
*
34789935 TTTCTTTTATTTTTA
1 TTTCTTTTAATTTTA
34789950 ATTCTGTTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTCTTTTAATTTTAT
Found at i:34795625 original size:74 final size:74
Alignment explanation
Indices: 34795540--34795679 Score: 203
Period size: 74 Copynumber: 1.9 Consensus size: 74
34795530 ATGTATTCAT
* *
34795540 TTTTTTTCA-TTTTTGAGTAAATTGTAAATAAGTATAGTATTGATGTAAAAATACAATAG-AATA
1 TTTTTTTCATTTTTTCA-TAAATTGTAAATAAGTATAGTATTGATGCAAAAATACAAT-GCAATA
34795603 CAATACAAATA
64 CAATACAAATA
* * *
34795614 TTTTTTTCATTTTTTCATAAATTGTAAATAAGTTTATTGTTGATGCAAAAATACAATGCAATACA
1 TTTTTTTCATTTTTTCATAAATTGTAAATAAGTATAGTATTGATGCAAAAATACAATGCAATACA
34795679 A
66 A
34795680 ATAAATTTTC
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
73 1 0.02
74 52 0.88
75 6 0.10
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.41
Consensus pattern (74 bp):
TTTTTTTCATTTTTTCATAAATTGTAAATAAGTATAGTATTGATGCAAAAATACAATGCAATACA
ATACAAATA
Found at i:34795949 original size:18 final size:18
Alignment explanation
Indices: 34795918--34795955 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
34795908 GGTTTCGGCT
*
34795918 CTTCATCTTCATCTTCAC
1 CTTCATCTTCATCTCCAC
34795936 CTTCATC-TCAATCTCCAC
1 CTTCATCTTC-ATCTCCAC
34795954 CT
1 CT
34795956 CTATCTTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.18, C:0.42, G:0.00, T:0.39
Consensus pattern (18 bp):
CTTCATCTTCATCTCCAC
Found at i:34799214 original size:14 final size:14
Alignment explanation
Indices: 34799178--34799214 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
34799168 CAAAACAAGA
34799178 AAATA-AAAA-TAC
1 AAATAGAAAATTAC
*
34799190 AATTAGAAAATTAC
1 AAATAGAAAATTAC
34799204 AAATAGAAAAT
1 AAATAGAAAAT
34799215 AGTACTAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
12 4 0.19
13 4 0.19
14 13 0.62
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.22
Consensus pattern (14 bp):
AAATAGAAAATTAC
Found at i:34807384 original size:3 final size:3
Alignment explanation
Indices: 34807376--34807428 Score: 79
Period size: 3 Copynumber: 17.7 Consensus size: 3
34807366 GCAATTTGTG
* *
34807376 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA ATA GTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
34807424 GTA AT
1 ATA AT
34807429 GTTCTTCACA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:34814090 original size:16 final size:18
Alignment explanation
Indices: 34814069--34814108 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
34814059 ATGAAAAAAT
*
34814069 TTAAAAATA-T-AATACA
1 TTAAAAATATTAAAAACA
34814085 TTAAAAATATTAAAAACA
1 TTAAAAATATTAAAAACA
34814103 TTAAAA
1 TTAAAA
34814109 CAAATATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.43
17 1 0.05
18 11 0.52
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (18 bp):
TTAAAAATATTAAAAACA
Found at i:34814217 original size:17 final size:17
Alignment explanation
Indices: 34814197--34814229 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
34814187 AACAAATTCT
34814197 ATTAA-AATAATAACAAA
1 ATTAACAATAA-AACAAA
34814214 ATTAACAATAAAACAA
1 ATTAACAATAAAACAA
34814230 GAGTTATACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.21
Consensus pattern (17 bp):
ATTAACAATAAAACAAA
Found at i:34814264 original size:11 final size:11
Alignment explanation
Indices: 34814250--34814340 Score: 64
Period size: 11 Copynumber: 8.5 Consensus size: 11
34814240 ATATTCAAAC
34814250 AATAACAATAA
1 AATAACAATAA
*
34814261 AATAATAATAA
1 AATAACAATAA
* * *
34814272 CATAATAATGA
1 AATAACAATAA
*
34814283 AATAA-TATCAA
1 AATAACAAT-AA
34814294 AATAACGAA-AA
1 AATAAC-AATAA
*
34814305 AATAATAA-AA
1 AATAACAATAA
*
34814315 AATAACAACAA
1 AATAACAATAA
*
34814326 AACAACAA-AA
1 AATAACAATAA
34814336 AATAA
1 AATAA
34814341 TAATTCTTTT
Statistics
Matches: 65, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
10 19 0.29
11 45 0.69
13 1 0.02
ACGTcount: A:0.71, C:0.09, G:0.02, T:0.18
Consensus pattern (11 bp):
AATAACAATAA
Found at i:34814276 original size:22 final size:22
Alignment explanation
Indices: 34814250--34814340 Score: 82
Period size: 22 Copynumber: 4.2 Consensus size: 22
34814240 ATATTCAAAC
34814250 AATAACAATAAAATAATAATAA
1 AATAACAATAAAATAATAATAA
* * *
34814272 CATAATAATGAAATAAT-ATCAA
1 AATAACAATAAAATAATAAT-AA
34814294 AATAACGAA-AAAATAATAA-AA
1 AATAAC-AATAAAATAATAATAA
* * *
34814315 AATAACAACAAAACAACAA-AA
1 AATAACAATAAAATAATAATAA
34814336 AATAA
1 AATAA
34814341 TAATTCTTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
20 2 0.04
21 25 0.44
22 27 0.47
23 3 0.05
ACGTcount: A:0.71, C:0.09, G:0.02, T:0.18
Consensus pattern (22 bp):
AATAACAATAAAATAATAATAA
Found at i:34814286 original size:19 final size:19
Alignment explanation
Indices: 34814264--34814314 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 19
34814254 ACAATAAAAT
* *
34814264 AATAATAACATAATAATGA
1 AATAATAACAAAATAACGA
*
34814283 AATAATATCAAAATAACGA
1 AATAATAACAAAATAACGA
* *
34814302 AAAAATAATAAAA
1 AATAATAACAAAA
34814315 AATAACAACA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.69, C:0.06, G:0.04, T:0.22
Consensus pattern (19 bp):
AATAATAACAAAATAACGA
Found at i:34818134 original size:30 final size:30
Alignment explanation
Indices: 34818095--34818155 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
34818085 AATATTATTG
* *
34818095 TCAAGTGAATTTATTTCCATATTATTACTA
1 TCAAATGAATTTATTTCCATATCATTACTA
*
34818125 TCAAATGAATTTATTTCTATATCATTACTA
1 TCAAATGAATTTATTTCCATATCATTACTA
34818155 T
1 T
34818156 ATCTAACCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.34, C:0.13, G:0.05, T:0.48
Consensus pattern (30 bp):
TCAAATGAATTTATTTCCATATCATTACTA
Found at i:34824650 original size:15 final size:16
Alignment explanation
Indices: 34824613--34824652 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
34824603 TTAGATTCTT
*
34824613 TTAAAATTTATAAAAA
1 TTAAAATTAATAAAAA
*
34824629 TTTAAATTAATAAAAA
1 TTAAAATTAATAAAAA
34824645 -TAAAATTA
1 TTAAAATTA
34824653 TACTCTTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TTAAAATTAATAAAAA
Found at i:34825231 original size:23 final size:23
Alignment explanation
Indices: 34825198--34825241 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
34825188 AGTCATTGTA
*
34825198 TTTTTATTTTTAAGAATTTAATT
1 TTTTTACTTTTAAGAATTTAATT
* *
34825221 TTTTTACTTTTTAGATTTTAA
1 TTTTTACTTTTAAGAATTTAA
34825242 AATTTAAGTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (23 bp):
TTTTTACTTTTAAGAATTTAATT
Done.