Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr5
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: 39371879
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2227820 characters in sequence are not A, C, G, or T
File 17 of 103
Found at i:6147450 original size:27 final size:27
Alignment explanation
Indices: 6147335--6147463 Score: 104
Period size: 27 Copynumber: 4.8 Consensus size: 27
6147325 AAAAATGTAA
* *
6147335 TGTTACATGCCATGTTCTAAAATTTAGT
1 TGTTACATGTCATGTT-GAAAATTTAGT
* * * *
6147363 TATTTACA-CTCTATGTTGGAAA--TAAT
1 T-GTTACATGTC-ATGTTGAAAATTTAGT
* **
6147389 TGTTACACGTCATACTGAAAATGTTA-T
1 TGTTACATGTCATGTTGAAAAT-TTAGT
6147416 TGTTACATGTCATGTTGAAAATTTAGT
1 TGTTACATGTCATGTTGAAAATTTAGT
*
6147443 TGTTACATGCCATGTTGAAAA
1 TGTTACATGTCATGTTGAAAA
6147464 ATGTTTGACT
Statistics
Matches: 79, Mismatches: 15, Indels: 15
0.72 0.14 0.14
Matches are distributed among these distances:
25 12 0.15
26 9 0.11
27 41 0.52
28 7 0.09
29 10 0.13
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (27 bp):
TGTTACATGTCATGTTGAAAATTTAGT
Found at i:6150172 original size:39 final size:39
Alignment explanation
Indices: 6150129--6150250 Score: 100
Period size: 39 Copynumber: 3.1 Consensus size: 39
6150119 GACATTCGTT
*
6150129 ATATGAATAAACCAAAACATTCTTAAAACAATGTTCATC
1 ATATGAATAAACCAAAACATTCATAAAACAATGTTCATC
* * * * * * * *
6150168 ATATGTATAAATCAAACCATTCGTAAATCCATTTTTCGTC
1 ATATGAATAAACCAAAACATTCATAAA-ACAATGTTCATC
** * ** *
6150208 ACGTGAGTAAACCAATTCATTCATAAATCAATGTTCATC
1 ATATGAATAAACCAAAACATTCATAAAACAATGTTCATC
6150247 ATAT
1 ATAT
6150251 TATTAAGCCC
Statistics
Matches: 60, Mismatches: 22, Indels: 2
0.71 0.26 0.02
Matches are distributed among these distances:
39 33 0.55
40 27 0.45
ACGTcount: A:0.41, C:0.19, G:0.07, T:0.33
Consensus pattern (39 bp):
ATATGAATAAACCAAAACATTCATAAAACAATGTTCATC
Found at i:6152207 original size:21 final size:21
Alignment explanation
Indices: 6152181--6152220 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
6152171 AATGTAAAAA
6152181 TATTATGTTATT-TTTTAATGT
1 TATTAT-TTATTGTTTTAATGT
6152202 TATTATTTATTGTTTTAAT
1 TATTATTTATTGTTTTAAT
6152221 TGCTTAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (21 bp):
TATTATTTATTGTTTTAATGT
Found at i:6156423 original size:20 final size:20
Alignment explanation
Indices: 6156383--6156424 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
6156373 TAAGACACAC
* *
6156383 TTTAATCAGTTAGGACCTCT
1 TTTAATCAGTTAGAACATCT
*
6156403 TTTAATCATTTAGAACATCT
1 TTTAATCAGTTAGAACATCT
6156423 TT
1 TT
6156425 GTCTTAAGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.17, G:0.10, T:0.45
Consensus pattern (20 bp):
TTTAATCAGTTAGAACATCT
Found at i:6160099 original size:49 final size:49
Alignment explanation
Indices: 6160027--6160137 Score: 186
Period size: 49 Copynumber: 2.3 Consensus size: 49
6160017 CATTCATCGT
* *
6160027 CATAGCTGGGTCATCATCATCATCGACTTATGCGCACTCCCTACTCGCA
1 CATAGCCGGGTCATCATCATCATCGACTTATGCGCACTCCCTACTCACA
* *
6160076 CATAGCCGAGTCATCATCATCATCGGCTTATGCGCACTCCCTACTCACA
1 CATAGCCGGGTCATCATCATCATCGACTTATGCGCACTCCCTACTCACA
6160125 CATAGCCGGGTCA
1 CATAGCCGGGTCA
6160138 ATGTCATCAC
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 57 1.00
ACGTcount: A:0.23, C:0.35, G:0.17, T:0.24
Consensus pattern (49 bp):
CATAGCCGGGTCATCATCATCATCGACTTATGCGCACTCCCTACTCACA
Found at i:6161549 original size:16 final size:17
Alignment explanation
Indices: 6161528--6161564 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
6161518 ATTGGATAAT
6161528 TTTAAGAGG-GCACATA
1 TTTAAGAGGTGCACATA
*
6161544 TTTAAGGGGTGCACATA
1 TTTAAGAGGTGCACATA
6161561 TTTA
1 TTTA
6161565 GGGGGAGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.32
Consensus pattern (17 bp):
TTTAAGAGGTGCACATA
Found at i:6161567 original size:16 final size:17
Alignment explanation
Indices: 6161528--6161568 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
6161518 ATTGGATAAT
*
6161528 TTTAAGAGG-GCACATA
1 TTTAAGGGGTGCACATA
6161544 TTTAAGGGGTGCACATA
1 TTTAAGGGGTGCACATA
6161561 TTT-AGGGG
1 TTTAAGGGG
6161569 GAGCAATCCC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.29, C:0.10, G:0.32, T:0.29
Consensus pattern (17 bp):
TTTAAGGGGTGCACATA
Found at i:6171243 original size:14 final size:14
Alignment explanation
Indices: 6171224--6171253 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
6171214 GAGGAACGAG
6171224 GAGTGTACTTTGTT
1 GAGTGTACTTTGTT
6171238 GAGTGTACTTTGTT
1 GAGTGTACTTTGTT
6171252 GA
1 GA
6171254 TTGTTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.17, C:0.07, G:0.30, T:0.47
Consensus pattern (14 bp):
GAGTGTACTTTGTT
Found at i:6173354 original size:21 final size:22
Alignment explanation
Indices: 6173328--6173368 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
6173318 ACTTTAAGTA
*
6173328 ATTAAAATAATAA-ATAATAAC
1 ATTAAAAAAATAACATAATAAC
6173349 ATTAAAAAAATAACATAATA
1 ATTAAAAAAATAACATAATA
6173369 CTTTTATATT
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:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (22 bp):
ATTAAAAAAATAACATAATAAC
Found at i:6173489 original size:20 final size:20
Alignment explanation
Indices: 6173466--6173505 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
6173456 AACATTATCC
6173466 AAAAAAATCTATCGATAGAT
1 AAAAAAATCTATCGATAGAT
*
6173486 AAAAAATTCTATCGATAGAT
1 AAAAAAATCTATCGATAGAT
6173506 TATACTATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.53, C:0.10, G:0.10, T:0.28
Consensus pattern (20 bp):
AAAAAAATCTATCGATAGAT
Found at i:6173987 original size:27 final size:27
Alignment explanation
Indices: 6173931--6173992 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 27
6173921 AAAAAGCCAT
* * *
6173931 AAGGTAAGAAGGAAGAAAGTGGTGAAG
1 AAGGTAAGAAGAAAGAAAGTGATCAAG
*
6173958 AAGGTAAGAAGAAGAGAAAG-GATCAGG
1 AAGGTAAGAAGAA-AGAAAGTGATCAAG
*
6173985 AAGTTAAG
1 AAGGTAAG
6173993 TTAGGGAACA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
27 23 0.79
28 6 0.21
ACGTcount: A:0.50, C:0.02, G:0.37, T:0.11
Consensus pattern (27 bp):
AAGGTAAGAAGAAAGAAAGTGATCAAG
Found at i:6181762 original size:57 final size:57
Alignment explanation
Indices: 6181674--6181791 Score: 157
Period size: 57 Copynumber: 2.1 Consensus size: 57
6181664 GAATTGAACG
*
6181674 ATATACTTTCAATTTTAATTAAATATGATATAACAAATCAATCCACAT-TATTTTTTT
1 ATATACTTTCAATTTTAATTAAATATGATATAACAAATCAATCCACATCT-TATTTTT
* * * * * *
6181731 ATATATTTTTAATTTTAATTAAATATTATATAACATATCGATTCACATCTTATTTTT
1 ATATACTTTCAATTTTAATTAAATATGATATAACAAATCAATCCACATCTTATTTTT
6181788 ATAT
1 ATAT
6181792 CATATCATAT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
57 52 0.98
58 1 0.02
ACGTcount: A:0.39, C:0.10, G:0.02, T:0.49
Consensus pattern (57 bp):
ATATACTTTCAATTTTAATTAAATATGATATAACAAATCAATCCACATCTTATTTTT
Found at i:6182044 original size:16 final size:16
Alignment explanation
Indices: 6182019--6182066 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
6182009 CAATTATTTT
6182019 CAAA-ATTAAAAAATA
1 CAAATATTAAAAAATA
* *
6182034 CAAATATTAAATATTA
1 CAAATATTAAAAAATA
*
6182050 GAAATATGTAAAAAATA
1 CAAATAT-TAAAAAATA
6182067 TATTTTTTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 4 0.15
16 15 0.58
17 7 0.27
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (16 bp):
CAAATATTAAAAAATA
Found at i:6186664 original size:71 final size:71
Alignment explanation
Indices: 6186534--6186665 Score: 167
Period size: 71 Copynumber: 1.9 Consensus size: 71
6186524 AAAATAGCTA
* * * * *
6186534 TTGAAAATTATTAAATATATCTTACCGTTAGTTGATTGAAAATAAAAGACATAGGTGAGAAAAAA
1 TTGAAAATTATTAAATACATATTACCATTAGTTGATTGAAAATAAAAGAAATACGTGAGAAAAAA
6186599 TAATAG
66 TAATAG
* * * *
6186605 TTGAAGATTATTAAATACATATTACTATTAGTTGATT-AGAAATAAGAGAAATACTTGAGAA
1 TTGAAAATTATTAAATACATATTACCATTAGTTGATTGA-AAATAAAAGAAATACGTGAGAA
6186666 TTAATAGCAT
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
70 1 0.02
71 50 0.98
ACGTcount: A:0.47, C:0.05, G:0.15, T:0.33
Consensus pattern (71 bp):
TTGAAAATTATTAAATACATATTACCATTAGTTGATTGAAAATAAAAGAAATACGTGAGAAAAAA
TAATAG
Found at i:6186943 original size:21 final size:21
Alignment explanation
Indices: 6186904--6186943 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
6186894 CTTATTTTTA
*
6186904 TATATTTTTAATATAATTAAT
1 TATATTATTAATATAATTAAT
* *
6186925 TATATTATTATTATTATTA
1 TATATTATTAATATAATTA
6186944 TAAAAATATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATATTATTAATATAATTAAT
Found at i:6190869 original size:15 final size:15
Alignment explanation
Indices: 6190849--6190893 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
6190839 TTTTACAATA
*
6190849 TAATGTGATTATAGG
1 TAATGTGATTGTAGG
* *
6190864 TAATGTGATTGCAAG
1 TAATGTGATTGTAGG
6190879 TAATGTGATTGTAGG
1 TAATGTGATTGTAGG
6190894 AAAAATAACA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.31, C:0.02, G:0.29, T:0.38
Consensus pattern (15 bp):
TAATGTGATTGTAGG
Found at i:6191160 original size:33 final size:30
Alignment explanation
Indices: 6191084--6191241 Score: 109
Period size: 33 Copynumber: 5.2 Consensus size: 30
6191074 CTTAAATATA
* *
6191084 TTTTTA-ATATCATATATTTTATTTTCATTT
1 TTTTTATATATTATATATTTTATTTT-AATT
6191114 TTTATTATAATATTATATATTTTATTTTAATT
1 TTT-TTAT-ATATTATATATTTTATTTTAATT
* *
6191146 TCTTTTACCTATATTATGTA---AATTTTAA-T
1 T-TTTTA--TATATTATATATTTTATTTTAATT
*
6191175 TTCTT-T-TATT-T-TATTTTATTTTAATT
1 TTTTTATATATTATATATTTTATTTTAATT
*
6191201 TTTAATTCTTATATTATATATTTTATTTTAATAT
1 TTT--TT-ATATATTATATATTTTATTTTAAT-T
6191235 TTTTTAT
1 TTTTTAT
6191242 TTTAATTATA
Statistics
Matches: 102, Mismatches: 8, Indels: 35
0.70 0.06 0.24
Matches are distributed among these distances:
22 2 0.02
23 1 0.01
24 4 0.04
25 8 0.08
26 3 0.03
28 5 0.05
29 2 0.02
30 11 0.11
31 8 0.08
32 10 0.10
33 43 0.42
34 5 0.05
ACGTcount: A:0.28, C:0.04, G:0.01, T:0.66
Consensus pattern (30 bp):
TTTTTATATATTATATATTTTATTTTAATT
Found at i:6191187 original size:15 final size:15
Alignment explanation
Indices: 6191167--6191248 Score: 64
Period size: 15 Copynumber: 5.6 Consensus size: 15
6191157 TATTATGTAA
*
6191167 ATTTTAATTTCTTTT
1 ATTTTAATTTATTTT
*
6191182 ATTTTATTTTATTTT
1 ATTTTAATTTATTTT
* *
6191197 AATTT--TTAATTCTT
1 ATTTTAATTTATT-TT
* *
6191211 ATATT-ATATATTTT
1 ATTTTAATTTATTTT
6191225 ATTTTAATATT-TTTT
1 ATTTTAAT-TTATTTT
6191240 ATTTTAATT
1 ATTTTAATT
6191249 ATAAAATTAC
Statistics
Matches: 53, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
13 5 0.09
14 12 0.23
15 35 0.66
16 1 0.02
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (15 bp):
ATTTTAATTTATTTT
Found at i:6191188 original size:5 final size:5
Alignment explanation
Indices: 6191167--6191245 Score: 54
Period size: 5 Copynumber: 15.2 Consensus size: 5
6191157 TATTATGTAA
* * *
6191167 ATTTT AATTT CTTTT ATTTT ATTTT ATTTT AATTTTT AATTCTT ATATT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT -A-TTTT -ATT-TT ATTTT
* *
6191216 A-TAT ATTTT ATTTT AATATT -TTTT ATTTT A
1 ATTTT ATTTT ATTTT -ATTTT ATTTT ATTTT A
6191246 ATTATAAAAT
Statistics
Matches: 58, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
4 5 0.09
5 36 0.62
6 9 0.16
7 8 0.14
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.71
Consensus pattern (5 bp):
ATTTT
Found at i:6199233 original size:22 final size:22
Alignment explanation
Indices: 6199190--6199233 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
6199180 TTTAAAACTA
* *
6199190 CTTTAAAACTAAAAACTTTGAT
1 CTTTAAAACCAAAAACTCTGAT
*
6199212 CTTTAAAACCAAAAGCTCTGAT
1 CTTTAAAACCAAAAACTCTGAT
6199234 ACCAATCAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (22 bp):
CTTTAAAACCAAAAACTCTGAT
Found at i:6201854 original size:19 final size:19
Alignment explanation
Indices: 6201830--6201867 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
6201820 ACTTCTAAAC
*
6201830 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
*
6201849 CTCAAATCATACTTCAATA
1 CTCAAATCATACTCCAATA
6201868 AGTCAAATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.42, C:0.26, G:0.00, T:0.32
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:6205463 original size:17 final size:17
Alignment explanation
Indices: 6205441--6205484 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
6205431 TGAGAAGCTC
*
6205441 TTAAAAAAAGTAGCTTT
1 TTAAAAAAAATAGCTTT
**
6205458 TTAAAAAAAATATTTTT
1 TTAAAAAAAATAGCTTT
6205475 TTAAAAAAAA
1 TTAAAAAAAA
6205485 AGTTTCAAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (17 bp):
TTAAAAAAAATAGCTTT
Found at i:6205968 original size:13 final size:13
Alignment explanation
Indices: 6205950--6205974 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6205940 AAGTTGTTTC
6205950 ATTTTTTTTATTG
1 ATTTTTTTTATTG
6205963 ATTTTTTTTATT
1 ATTTTTTTTATT
6205975 TTAATATTTG
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:0.16, C:0.00, G:0.04, T:0.80
Consensus pattern (13 bp):
ATTTTTTTTATTG
Found at i:6225543 original size:81 final size:81
Alignment explanation
Indices: 6225408--6225570 Score: 258
Period size: 81 Copynumber: 2.0 Consensus size: 81
6225398 ATTGGCAGGT
** * *
6225408 TAGTTTTCCCCTTTTCTATGTATTACTAAAGCATCAGATGATATTTTTTTGGATTCTTTATTC-T
1 TAGTTTTCCCCCGTTCCATGTATTACTAAAGCATCAGATGATATTTTTTTGGATTCTTTAATCTT
6225472 TAAATGTATAACATGCA
66 TAAATGTAT-ACATGCA
6225489 TAGTTTTCCCCCGTTCCATGTATTACTAAAGCATC-GTATGATATTTTTTTGGATTCTTTAATCT
1 TAGTTTTCCCCCGTTCCATGTATTACTAAAGCATCAG-ATGATATTTTTTTGGATTCTTTAATCT
6225553 TTAAATGTATACATGCA
65 TTAAATGTATACATGCA
6225570 T
1 T
6225571 CTGGTTTTGA
Statistics
Matches: 76, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
80 1 0.01
81 65 0.86
82 10 0.13
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.46
Consensus pattern (81 bp):
TAGTTTTCCCCCGTTCCATGTATTACTAAAGCATCAGATGATATTTTTTTGGATTCTTTAATCTT
TAAATGTATACATGCA
Found at i:6231448 original size:2 final size:2
Alignment explanation
Indices: 6231404--6231430 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6231394 TCACATCAAC
6231404 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
6231431 CTCATTCTGA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6234967 original size:53 final size:53
Alignment explanation
Indices: 6234886--6235233 Score: 426
Period size: 53 Copynumber: 6.6 Consensus size: 53
6234876 GTGGGCGTCA
* * * * *
6234886 GATTTGAGGTTTGGGTTACCGTCAGTTAGAGGGAGAGAGAGAAGCCAGCGCCG
1 GATTTGGGGCTTGGGTTACCGCCGGTTAGAGGGAGAAAGAGAAGCCAGCGCCG
* ** * *
6234939 AATTTGGGGCTTGGGTTGTCGCCAGTTAGAGGGAGAAAGAGAAGCCAGCGTCG
1 GATTTGGGGCTTGGGTTACCGCCGGTTAGAGGGAGAAAGAGAAGCCAGCGCCG
* * * * *
6234992 AATTTGGGGCTTGGGTTGCCACTGGTTAGAGGGAGAAAGAGAAGCCAGCTCCG
1 GATTTGGGGCTTGGGTTACCGCCGGTTAGAGGGAGAAAGAGAAGCCAGCGCCG
* * * * *
6235045 GATTTGGGGCTTGGGTTACCGTCGGTTAAAGGGAGAGAGAAAAGCCAGCTCCG
1 GATTTGGGGCTTGGGTTACCGCCGGTTAGAGGGAGAAAGAGAAGCCAGCGCCG
** * *
6235098 GATTTGGGGCTTGGGTTACCATCGGTTAGAGGGAGAAAGAGAAGCCAGCACTG
1 GATTTGGGGCTTGGGTTACCGCCGGTTAGAGGGAGAAAGAGAAGCCAGCGCCG
* * * *
6235151 GATTTGGGGCTTGGGTTATCGTCGGTTAGAGGGAGAGAGAGAAGCCAGCGACG
1 GATTTGGGGCTTGGGTTACCGCCGGTTAGAGGGAGAAAGAGAAGCCAGCGCCG
**
6235204 GATTTGGGGCTTGGGTTGTCGCCGGTTAGA
1 GATTTGGGGCTTGGGTTACCGCCGGTTAGA
6235234 AGTCGAATTT
Statistics
Matches: 259, Mismatches: 36, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 259 1.00
ACGTcount: A:0.23, C:0.15, G:0.40, T:0.22
Consensus pattern (53 bp):
GATTTGGGGCTTGGGTTACCGCCGGTTAGAGGGAGAAAGAGAAGCCAGCGCCG
Found at i:6236047 original size:20 final size:20
Alignment explanation
Indices: 6236019--6236056 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
6236009 TAATAAATAA
*
6236019 ATAACAATAGATA-AAAAAGG
1 ATAAAAATA-ATATAAAAAGG
6236039 ATAAAAATAATATAAAAA
1 ATAAAAATAATATAAAAA
6236057 TAAAAAATAA
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:0.71, C:0.03, G:0.08, T:0.18
Consensus pattern (20 bp):
ATAAAAATAATATAAAAAGG
Found at i:6236105 original size:17 final size:20
Alignment explanation
Indices: 6236065--6236106 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 20
6236055 AATAAAAAAT
*
6236065 AAAATAATTCAAATATATAT
1 AAAATAATTCAAATATATAA
6236085 AAAATAA-T-AAAT-TATAA
1 AAAATAATTCAAATATATAA
6236102 AAAAT
1 AAAAT
6236107 GCAACATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 9 0.43
18 4 0.19
19 1 0.05
20 7 0.33
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAATAATTCAAATATATAA
Found at i:6236367 original size:18 final size:17
Alignment explanation
Indices: 6236338--6236422 Score: 70
Period size: 18 Copynumber: 5.0 Consensus size: 17
6236328 TGCTTACGAA
6236338 AAAAATAT-AATAACAAT
1 AAAAATATAAATAA-AAT
* *
6236355 AAAAATATAAAT-ATAC
1 AAAAATATAAATAAAAT
6236371 AAAAATATACAA-AAATAT
1 AAAAATATA-AATAAA-AT
*
6236389 GAAAATATAAAATAAAAT
1 AAAAATAT-AAATAAAAT
*
6236407 AAAAA-ATATATAAAAT
1 AAAAATATAAATAAAAT
6236423 TTATGTCGTT
Statistics
Matches: 55, Mismatches: 7, Indels: 13
0.73 0.09 0.17
Matches are distributed among these distances:
16 18 0.33
17 14 0.25
18 19 0.35
19 4 0.07
ACGTcount: A:0.72, C:0.04, G:0.01, T:0.24
Consensus pattern (17 bp):
AAAAATATAAATAAAAT
Found at i:6236378 original size:10 final size:9
Alignment explanation
Indices: 6236363--6236422 Score: 59
Period size: 10 Copynumber: 6.4 Consensus size: 9
6236353 ATAAAAATAT
6236363 AAATATACAA
1 AAATATA-AA
6236373 AAATATACAA
1 AAATATA-AA
*
6236383 AAATAT-GA
1 AAATATAAA
6236391 AAATATAAA
1 AAATATAAA
*
6236400 ATAAAATAAA
1 A-AATATAAA
*
6236410 AAATATATA
1 AAATATAAA
6236419 AAAT
1 AAAT
6236423 TTATGTCGTT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
8 7 0.16
9 12 0.28
10 24 0.56
ACGTcount: A:0.72, C:0.03, G:0.02, T:0.23
Consensus pattern (9 bp):
AAATATAAA
Found at i:6236421 original size:28 final size:29
Alignment explanation
Indices: 6236355--6236422 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 29
6236345 TAATAACAAT
*
6236355 AAAA-ATAT-AAATATACAAAAATATACA
1 AAAATATATAAAATATACAAAAAAATACA
*
6236382 AAAATAT-GAAAATATA-AAATAAAATA-A
1 AAAATATATAAAATATACAAA-AAAATACA
6236409 AAAATATATAAAAT
1 AAAATATATAAAAT
6236423 TTATGTCGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
27 15 0.44
28 19 0.56
ACGTcount: A:0.72, C:0.03, G:0.01, T:0.24
Consensus pattern (29 bp):
AAAATATATAAAATATACAAAAAAATACA
Found at i:6239041 original size:67 final size:67
Alignment explanation
Indices: 6238933--6239068 Score: 245
Period size: 67 Copynumber: 2.0 Consensus size: 67
6238923 TATCATTTTC
*
6238933 AAGGTATTAATGAAGGTAATAACTAATAGATTGAAACCATATATGTTTACACTAGTAGCAAAAAC
1 AAGGTATTAATGAAGGTAATAACTAATAGATTGAAACCATATATGTCTACACTAGTAGCAAAAAC
6238998 AT
66 AT
* *
6239000 AAGGTATTAATGAAGGTAATAACTAATAGATTGAAACCATATATGTCTACATTAGTAGCAGAAAC
1 AAGGTATTAATGAAGGTAATAACTAATAGATTGAAACCATATATGTCTACACTAGTAGCAAAAAC
6239065 AT
66 AT
6239067 AA
1 AA
6239069 TCTAGCTTCA
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.28
Consensus pattern (67 bp):
AAGGTATTAATGAAGGTAATAACTAATAGATTGAAACCATATATGTCTACACTAGTAGCAAAAAC
AT
Found at i:6241902 original size:22 final size:22
Alignment explanation
Indices: 6241859--6241900 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
6241849 ATAAAAATCA
* *
6241859 TATTAATGTTTTAATAATAAAT
1 TATTAATGATTTAAAAATAAAT
6241881 TATTAAT-ATTTAAAAATAAA
1 TATTAATGATTTAAAAATAAA
6241901 ATACTAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
TATTAATGATTTAAAAATAAAT
Found at i:6241910 original size:22 final size:21
Alignment explanation
Indices: 6241868--6241931 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
6241858 ATATTAATGT
* * *
6241868 TTTAATAATAAATTATTAATA
1 TTTAAAAATAAAATATAAATA
6241889 TTTAAAAATAAAATACTAAATA
1 TTTAAAAATAAAATA-TAAATA
*
6241911 TTT-CAAATAAAA-AGTAAATA
1 TTTAAAAATAAAATA-TAAATA
6241931 T
1 T
6241932 CCAAGAATCA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
20 8 0.22
21 21 0.57
22 8 0.22
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.38
Consensus pattern (21 bp):
TTTAAAAATAAAATATAAATA
Found at i:6241918 original size:21 final size:21
Alignment explanation
Indices: 6241885--6241931 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
6241875 ATAAATTATT
6241885 AATATTTAAAAATAAAATACTA
1 AATATTTAAAAATAAAA-ACTA
* *
6241907 AATATTT-CAAATAAAAAGTA
1 AATATTTAAAAATAAAAACTA
6241927 AATAT
1 AATAT
6241932 CCAAGAATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 8 0.35
21 8 0.35
22 7 0.30
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (21 bp):
AATATTTAAAAATAAAAACTA
Found at i:6243155 original size:13 final size:12
Alignment explanation
Indices: 6243122--6243164 Score: 50
Period size: 14 Copynumber: 3.3 Consensus size: 12
6243112 AACAAGGTCT
6243122 TTTAATTTATAAA
1 TTTAATTT-TAAA
6243135 TTTAAATTTTGAAA
1 TTT-AATTTT-AAA
*
6243149 TTTAATTTTCAA
1 TTTAATTTTAAA
6243161 TTTA
1 TTTA
6243165 TCATTTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 6 0.22
13 10 0.37
14 11 0.41
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (12 bp):
TTTAATTTTAAA
Found at i:6243585 original size:19 final size:19
Alignment explanation
Indices: 6243561--6243607 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
6243551 AGCTCTTAAA
6243561 AAAAAAAAGCT-TTTTTTTT
1 AAAAAAAA-CTATTTTTTTT
*
6243580 AAAAAAAATTATTTTTTTT
1 AAAAAAAACTATTTTTTTT
6243599 AAAATAAAA
1 AAAA-AAAA
6243608 AAAAGAGCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 1 0.04
19 20 0.80
20 4 0.16
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (19 bp):
AAAAAAAACTATTTTTTTT
Found at i:6243694 original size:17 final size:17
Alignment explanation
Indices: 6243674--6243706 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
6243664 AAAANATATA
6243674 TTTTTTAAAAAAATAAT
1 TTTTTTAAAAAAATAAT
6243691 TTTTTTAAAAAAATAA
1 TTTTTTAAAAAAATAA
6243707 ATCTTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTTTTAAAAAAATAAT
Found at i:6243728 original size:12 final size:13
Alignment explanation
Indices: 6243698--6243732 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
6243688 AATTTTTTTA
*
6243698 AAAAAATAAATCTT
1 AAAAAA-AAAGCTT
6243712 AAAAAAAAAGCTT
1 AAAAAAAAAGCTT
6243725 AAAAAAAA
1 AAAAAAAA
6243733 CTCCAATTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 14 0.70
14 6 0.30
ACGTcount: A:0.74, C:0.06, G:0.03, T:0.17
Consensus pattern (13 bp):
AAAAAAAAAGCTT
Found at i:6245173 original size:26 final size:27
Alignment explanation
Indices: 6245099--6245270 Score: 133
Period size: 27 Copynumber: 6.4 Consensus size: 27
6245089 GACTATAATA
* * *
6245099 TTTTTTCAACATGACGTATAACAATAATAT
1 TTTTTTCAACAAGACATGTAACAAT--T-T
* * * *
6245129 TTTTTT-AATATGACTTGTAATAATTT
1 TTTTTTCAACAAGACATGTAACAATTT
*
6245155 TTTTTT-AACAAGACATGT-A-AA-CT
1 TTTTTTCAACAAGACATGTAACAATTT
* *
6245178 TTTTTTCAACAGGACAAGTAACAATTTT
1 TTTTTTCAACAAGACATGTAACAA-TTT
*
6245206 TTTTTTCAACAAGGA-GTGTAACAATTT
1 TTTTTTCAACAA-GACATGTAACAATTT
*
6245233 TTTTTTCAACAATG-CGTGTAACAATTT
1 TTTTTTCAACAA-GACATGTAACAATTT
6245260 TTTTTTCAACA
1 TTTTTTCAACA
6245271 TAATGTGTAA
Statistics
Matches: 120, Mismatches: 15, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
23 7 0.06
24 12 0.10
25 2 0.02
26 18 0.15
27 40 0.33
28 19 0.16
29 16 0.13
30 6 0.05
ACGTcount: A:0.34, C:0.12, G:0.09, T:0.44
Consensus pattern (27 bp):
TTTTTTCAACAAGACATGTAACAATTT
Found at i:6245180 original size:24 final size:25
Alignment explanation
Indices: 6245153--6245209 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
6245143 TTGTAATAAT
* *
6245153 TTTTTTTTAACAAGACATGTAA-AC
1 TTTTTTTTAACAAGACAAGTAACAA
* *
6245177 TTTTTTTCAACAGGACAAGTAACAA
1 TTTTTTTTAACAAGACAAGTAACAA
6245202 TTTTTTTT
1 TTTTTTTT
6245210 TTCAACAAGG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 19 0.70
25 8 0.30
ACGTcount: A:0.33, C:0.12, G:0.09, T:0.46
Consensus pattern (25 bp):
TTTTTTTTAACAAGACAAGTAACAA
Found at i:6245209 original size:28 final size:28
Alignment explanation
Indices: 6245144--6245270 Score: 135
Period size: 27 Copynumber: 4.8 Consensus size: 28
6245134 TAATATGACT
* *
6245144 TGTAATAATTTTTTTTT-AACAA-GACA
1 TGTAACAATTTTTTTTTCAACAAGGACG
* *
6245170 TGT-A-AA-CTTTTTTTCAAC-AGGACA
1 TGTAACAATTTTTTTTTCAACAAGGACG
*
6245194 AGTAACAATTTTTTTTTTCAACAAGGA-G
1 TGTAACAA-TTTTTTTTTCAACAAGGACG
*
6245222 TGTAACAATTTTTTTTTCAACAATG-CG
1 TGTAACAATTTTTTTTTCAACAAGGACG
6245249 TGTAACAATTTTTTTTTCAACA
1 TGTAACAATTTTTTTTTCAACA
6245271 TAATGTGTAA
Statistics
Matches: 87, Mismatches: 6, Indels: 15
0.81 0.06 0.14
Matches are distributed among these distances:
23 8 0.09
24 11 0.13
25 2 0.02
26 5 0.06
27 39 0.45
28 18 0.21
29 4 0.05
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (28 bp):
TGTAACAATTTTTTTTTCAACAAGGACG
Found at i:6245278 original size:27 final size:26
Alignment explanation
Indices: 6245195--6245294 Score: 114
Period size: 27 Copynumber: 3.7 Consensus size: 26
6245185 AACAGGACAA
6245195 GTAACAATTTTTTTTTTCAACAAGGA-GT
1 GTAACAA-TTTTTTTTTCAACAA--ATGT
6245223 GTAACAATTTTTTTTTCAAC-AATGCGT
1 GTAACAATTTTTTTTTCAACAAAT--GT
6245250 GTAACAATTTTTTTTTCAACATAATGT
1 GTAACAATTTTTTTTTCAACA-AATGT
**
6245277 GTAACAACATTTTTTTCA
1 GTAACAATTTTTTTTTCA
6245295 TGTGCGTTTG
Statistics
Matches: 65, Mismatches: 2, Indels: 11
0.83 0.03 0.14
Matches are distributed among these distances:
24 1 0.02
26 1 0.02
27 53 0.82
28 7 0.11
29 3 0.05
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.45
Consensus pattern (26 bp):
GTAACAATTTTTTTTTCAACAAATGT
Found at i:6251675 original size:133 final size:132
Alignment explanation
Indices: 6251510--6251773 Score: 383
Period size: 133 Copynumber: 2.0 Consensus size: 132
6251500 GGATAAGGGA
*
6251510 TGACCATGTGCTGAAAAAATGTCCTGGTGATGAAAAATTACCGTTTTACCCCTA-AGGTGGTAAA
1 TGACCATGTGCTGAAAAAATGTCCTGGTGATGAAAAATTAACGTTTTACCCCTAGA-GTGGTAAA
*
6251574 ATTATC-ATTTTAG-CCTTATACTTC-AAATTATACCGGAATTAAAATTTTTCACTTCTAAACCT
65 ATTA-CGATTTT-GCCCCTATA-TTCTAAATTATACCGGAATTAAAATTTTTCACTTCTAAACCT
6251636 CAAATC
127 CAAATC
* * * *
6251642 NTGACCTTGTGCTGGAAAAATGTCCTGGTGATGAAAAATTAATGTTTTGCCCCTAGAGTGGTAAA
1 -TGACCATGTGCTGAAAAAATGTCCTGGTGATGAAAAATTAACGTTTTACCCCTAGAGTGGTAAA
* *
6251707 ATTACGATTTTGCCCCTATATTCTGAATTATACCGGAATTAAATTTTTTCACTTCTAAACCTCAA
65 ATTACGATTTTGCCCCTATATTCTAAATTATACCGGAATTAAAATTTTTCACTTCTAAACCTCAA
6251772 AT
130 AT
6251774 ATATACTCCA
Statistics
Matches: 119, Mismatches: 8, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
132 5 0.04
133 113 0.95
134 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.35
Consensus pattern (132 bp):
TGACCATGTGCTGAAAAAATGTCCTGGTGATGAAAAATTAACGTTTTACCCCTAGAGTGGTAAAA
TTACGATTTTGCCCCTATATTCTAAATTATACCGGAATTAAAATTTTTCACTTCTAAACCTCAAA
TC
Found at i:6253929 original size:16 final size:17
Alignment explanation
Indices: 6253898--6253935 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
6253888 CTTCTTCTTT
6253898 CTATTTATATTATTTAA
1 CTATTTATATTATTTAA
6253915 CTATTTATA-TATTTAA
1 CTATTTATATTATTTAA
*
6253931 TTATT
1 CTATT
6253936 ATGTAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (17 bp):
CTATTTATATTATTTAA
Found at i:6253978 original size:7 final size:7
Alignment explanation
Indices: 6253966--6254005 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
6253956 TATTTAATTA
6253966 TTTATAT
1 TTTATAT
6253973 TTTATAT
1 TTTATAT
*
6253980 ATTATAAT
1 TTTAT-AT
6253988 TTTATAT
1 TTTATAT
*
6253995 TTAATAT
1 TTTATAT
6254002 TTTA
1 TTTA
6254006 AGTTTAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 22 0.79
8 6 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (7 bp):
TTTATAT
Found at i:6253984 original size:14 final size:14
Alignment explanation
Indices: 6253943--6254005 Score: 58
Period size: 14 Copynumber: 4.4 Consensus size: 14
6253933 ATTATGTAAA
* *
6253943 ATTTTACATATTGT
1 ATTTTATATATTAT
*
6253957 ATTTAAT-TATTTAT
1 ATTTTATATA-TTAT
6253971 ATTTTATATATTAT
1 ATTTTATATATTAT
6253985 AATTTTATAT-TTAAT
1 -ATTTTATATATT-AT
6254000 ATTTTA
1 ATTTTA
6254006 AGTTTAAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
13 2 0.05
14 26 0.63
15 13 0.32
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (14 bp):
ATTTTATATATTAT
Found at i:6254784 original size:9 final size:9
Alignment explanation
Indices: 6254770--6254802 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
6254760 GGCTCTAGGT
*
6254770 AATAAATGA
1 AATAAATAA
6254779 AATAAATAA
1 AATAAATAA
6254788 AATAAATAA
1 AATAAATAA
6254797 AATAAA
1 AATAAA
6254803 AAATGTCTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (9 bp):
AATAAATAA
Found at i:6261766 original size:2 final size:2
Alignment explanation
Indices: 6261747--6261799 Score: 79
Period size: 2 Copynumber: 26.5 Consensus size: 2
6261737 GATAAGCATT
* * *
6261747 TA TA TA CA TA TG TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6261789 TA TA TA TA TA T
1 TA TA TA TA TA T
6261800 TATTTCAATT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (2 bp):
TA
Found at i:6264614 original size:15 final size:15
Alignment explanation
Indices: 6264594--6264639 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
6264584 TTCTTAAAAC
6264594 AACTTTAAAACCAAA
1 AACTTTAAAACCAAA
6264609 AACTTTAAAATCC-AA
1 AACTTTAAAA-CCAAA
* *
6264624 AGCTTTAAAATCAAA
1 AACTTTAAAACCAAA
6264639 A
1 A
6264640 TCTCTGATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 1 0.04
15 24 0.89
16 2 0.07
ACGTcount: A:0.57, C:0.17, G:0.02, T:0.24
Consensus pattern (15 bp):
AACTTTAAAACCAAA
Found at i:6266010 original size:13 final size:13
Alignment explanation
Indices: 6265992--6266017 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6265982 TGTCAAAAAA
6265992 TTTATAAAATCAT
1 TTTATAAAATCAT
6266005 TTTATAAAATCAT
1 TTTATAAAATCAT
6266018 AATTTCTCCT
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:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:6267272 original size:19 final size:19
Alignment explanation
Indices: 6267248--6267285 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
6267238 ACTTCTAAAC
*
6267248 CTCAAATTGTACTCCAATA
1 CTCAAATTATACTCCAATA
6267267 CTCAAATTATACTCCAATA
1 CTCAAATTATACTCCAATA
6267286 AGTCAAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.39, C:0.26, G:0.03, T:0.32
Consensus pattern (19 bp):
CTCAAATTATACTCCAATA
Found at i:6269623 original size:5 final size:5
Alignment explanation
Indices: 6269609--6269648 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
6269599 CTATTCAACC
* * *
6269609 TAACC TAACT TAACT TAATT TAATT TAACT TAACT TAACT
1 TAACT TAACT TAACT TAACT TAACT TAACT TAACT TAACT
6269649 AGGGGCCACG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.42
Consensus pattern (5 bp):
TAACT
Found at i:6269705 original size:15 final size:15
Alignment explanation
Indices: 6269685--6269735 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
6269675 TTCTTAAAAC
6269685 AACTTTAAAACCAAA
1 AACTTTAAAACCAAA
*
6269700 AACTTTAAAATTC-AA
1 AACTTTAAAA-CCAAA
*
6269715 AGCTTTAAAACCAAA
1 AACTTTAAAACCAAA
*
6269730 ATCTTT
1 AACTTT
6269736 GATCTTTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
14 1 0.03
15 28 0.93
16 1 0.03
ACGTcount: A:0.51, C:0.18, G:0.02, T:0.29
Consensus pattern (15 bp):
AACTTTAAAACCAAA
Found at i:6271985 original size:21 final size:21
Alignment explanation
Indices: 6271959--6272002 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
6271949 TGGGCTGATT
6271959 TATGCTGATTTTTAAATTAAA
1 TATGCTGATTTTTAAATTAAA
6271980 TATGCTGATTTTTAAATTAAA
1 TATGCTGATTTTTAAATTAAA
6272001 TA
1 TA
6272003 ATAAAATATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.48
Consensus pattern (21 bp):
TATGCTGATTTTTAAATTAAA
Found at i:6272273 original size:19 final size:19
Alignment explanation
Indices: 6272249--6272286 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
6272239 ACTTCTAAAC
6272249 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
*
6272268 CTCAAATCATAGTCCAATA
1 CTCAAATCATACTCCAATA
6272287 AGTCAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.03, T:0.26
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:6278647 original size:2 final size:2
Alignment explanation
Indices: 6278640--6278681 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
6278630 AATTTTACTT
* *
6278640 TA TA TA TA TA TA TA TA TA AA TA AA 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 TA TA TA TA
6278681 T
1 T
6278682 GGATATTTAC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:6281955 original size:30 final size:30
Alignment explanation
Indices: 6281921--6281978 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
6281911 AACAATCATC
* *
6281921 AAAGAATGTATGAGTTTTCTACACTTAGTT
1 AAAGAATGCATGAGTTTTCTACAATTAGTT
*
6281951 AAAGATTGCATGAGTTTTCTACAATTAG
1 AAAGAATGCATGAGTTTTCTACAATTAG
6281979 ATACAATTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.38
Consensus pattern (30 bp):
AAAGAATGCATGAGTTTTCTACAATTAGTT
Found at i:6282914 original size:22 final size:22
Alignment explanation
Indices: 6282886--6282934 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
6282876 GATAAGCTTG
6282886 AGCTTTTTATCATATTTCCAGT
1 AGCTTTTTATCATATTTCCAGT
6282908 AGCTTTTTATCATATTTCCAGT
1 AGCTTTTTATCATATTTCCAGT
6282930 AGCTT
1 AGCTT
6282935 CTTCTTCTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.22, C:0.18, G:0.10, T:0.49
Consensus pattern (22 bp):
AGCTTTTTATCATATTTCCAGT
Found at i:6283801 original size:43 final size:43
Alignment explanation
Indices: 6283715--6283850 Score: 177
Period size: 43 Copynumber: 3.2 Consensus size: 43
6283705 TTTTGTGTGA
* * * *
6283715 TGATGATGACCCAGCTATGTGCGTAT-AGGAGTGCACATGAGC
1 TGATGATGACCCAACTATATGCGAATGGGGAGTGCACATGAGC
* *
6283757 TGATGATGACCTAGCTATATGC-AAGTGGGGAGTGCACATGAGC
1 TGATGATGACCCAACTATATGCGAA-TGGGGAGTGCACATGAGC
* *
6283800 TGATGATGACCCAACTATGTGCGAATGGGGAGTGCACATGAGT
1 TGATGATGACCCAACTATATGCGAATGGGGAGTGCACATGAGC
6283843 TGATGATG
1 TGATGATG
6283851 GTGGGATGGT
Statistics
Matches: 83, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
41 1 0.01
42 21 0.25
43 59 0.71
44 2 0.02
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.24
Consensus pattern (43 bp):
TGATGATGACCCAACTATATGCGAATGGGGAGTGCACATGAGC
Found at i:6284107 original size:21 final size:21
Alignment explanation
Indices: 6284055--6284110 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
6284045 GTGTCCTGTT
*
6284055 TCTCGCTACAACAAGAATGAA
1 TCTCGCTACAGCAAGAATGAA
*
6284076 TCTCGCTACAGTAAGAATGAA
1 TCTCGCTACAGCAAGAATGAA
*
6284097 TGTCGCTACAGCAA
1 TCTCGCTACAGCAA
6284111 AAAACTCTCG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (21 bp):
TCTCGCTACAGCAAGAATGAA
Found at i:6285168 original size:23 final size:23
Alignment explanation
Indices: 6285137--6285183 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
6285127 GAAAAGGTCT
* *
6285137 ATTATTTTTA-TAATAATAATATA
1 ATTAATTTTATTAAAAAT-ATATA
6285160 ATTAATTTTATTAAAAATATATA
1 ATTAATTTTATTAAAAATATATA
6285183 A
1 A
6285184 AAATTAAGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
ATTAATTTTATTAAAAATATATA
Found at i:6287002 original size:16 final size:16
Alignment explanation
Indices: 6286978--6287015 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
6286968 TGAGAAAATA
6286978 TTTTAAAAAT-ATTAGT
1 TTTTAAAAATAATTA-T
*
6286994 TTTTTAAAATAATTAT
1 TTTTAAAAATAATTAT
6287010 TTTTAA
1 TTTTAA
6287016 TTTATTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
TTTTAAAAATAATTAT
Found at i:6287769 original size:14 final size:14
Alignment explanation
Indices: 6287725--6287771 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
6287715 TGTTACAAAT
6287725 AAATAAATTACACC
1 AAATAAATTACACC
6287739 TAATATAAA-TA-ACC
1 -AA-ATAAATTACACC
*
6287753 AAATAAATTACATC
1 AAATAAATTACACC
6287767 AAATA
1 AAATA
6287772 TAAGTAAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
12 5 0.18
13 4 0.14
14 10 0.36
15 4 0.14
16 5 0.18
ACGTcount: A:0.60, C:0.15, G:0.00, T:0.26
Consensus pattern (14 bp):
AAATAAATTACACC
Found at i:6296473 original size:990 final size:991
Alignment explanation
Indices: 6294830--6296759 Score: 3096
Period size: 990 Copynumber: 1.9 Consensus size: 991
6294820 ACCGACTATT
* *
6294830 AATCTATTATTATCTATGTTCACTTCATTTTTACTACTTTGTAAGTAGAAACTTGACTAAGAAAT
1 AATCTATTATTATCTATGTTCACTTCATTTATACTACTTGGTAAGTAGAAACTTGACTAAGAAAT
*
6294895 GTTGGGTCGTCCCAATCTTTTTTCTTATGTCATCACTAATGTCTTTCTTTATTATGTTCTCTTTT
66 GTAGGGTCGTCCCAA------TTCTTATGT-ATCACTAATGTCTTTCTTTATTATGTTCTCTTTT
*
6294960 TAAAAATTTATTCTTTTTTATGGTCAGAAAAATGAAATGTAGTTGAAGACCTTCTGTTATGCTTT
124 TAAAAATTTATTCTTGTTTATGGTCAGAAAAATGAAATGTAGTTGAAGACC-TCTGTTATGCTTT
6295025 AATTCTAAGTACAATTCTAGAATTGTGGGCTTCACGTGACTTAATCACAAATGTCAAACCAAAGG
188 AATTCTAAGTACAATTCTAGAATTGTGGGCTTCACGTGACTTAATCACAAATGTCAAACCAAAGG
* * *
6295090 CCCAATTAAATAACTAAAAATCAAAATGTTTGTGACAAATTCTACTGCTACCTTCTCTTTTTTCA
253 CCCAATTAAATAACCAAAAATCAAAATGTTTGTGACAAATTCTACTGCCACCTACTCTTTTTTCA
*
6295155 TCTCATTCACACTATTTTTTAGATTTCATAAATTTCAACCTCTTAGTGGAACTTTAATTTAATTT
318 CCTCATTCACACTATTTTTTAGATTTCATAAATTTCAACCTCTTAGTGGAACTTTAATTTAATTT
*
6295220 AAAGCTTGTAATGTTGTAATTGGAATTGTCAAAGTCCTTGAATTCTACTATAAATATACAATTAA
383 AAAGCTTGTAATGTTGTAATTGGAATTGTCAAAGTCCTTGAATTCTACTATAAATACACAATTAA
*
6295285 ATAAGGAAAAAATTTTATCCAATTTTAAGATGTCATCTATCCTTTGAAATTTATCCAAGGTTTTG
448 ATAAGGAAAAAATTTTATCCAATTTTAAGATGTCATCAATCCTTTGAAATTTATCCAAGGTTTTG
* *
6295350 GGACCTTTTTGTAATTGGAGTTTGATGAACCAAGATTTCAATTAAGGAAGGTAGAGGGCTTTTGA
513 AGACCTTTTTGTAATTGGAGTTTGATGAACCAAGATTTCAATTAAGGAAGGTAAAGGGCTTTTGA
*
6295415 GAAAGTTAGTCAAAATCAAATCCATTAGTTTATGTAATTGATGCAAAGATACATACAACATGGTC
578 GAAAGTTAGTCAAAAACAAATCCATTAGTTTATGTAATTGATGCAAAGATACATACAACATGGTC
6295480 ATAAATTAATAATATTTATTTATTTATTATGTTTTATTTTCTTACAGTTTGTATGCCATAAGTTT
643 ATAAATTAATAATATTTATTTATTTATTATGTTTTATTTTCTTACAGTTTGTATGCCATAAGTTT
6295545 TCAATATTTTTTGTACATAATAAAATAGATTAAAACATTTATTTTTTGCAAG-CATGGTTCATTT
708 TCAATATTTTTTGTACATAATAAAATAGATTAAAACATTTATTTTTTGC-AGTCATGGTTCATTT
*
6295609 GTGTTTGA-AAAGAGATGCTGAACGACAAAAAA-GTTACTAGCTATATTAAATTTTATATAGAGA
772 GTGTTTGAGAAA-AGATGCTGAACGACAAAAAAGGCTACTAGCTATATTAAATTTTATATAGAGA
* *
6295672 TTTGTCGTGTTGCTAGTTCG-TTCTGCACTTTGTTGTCTCTGGCGTCGACTTTATGTACTTATGG
836 TTTGTCGTGTTGCTAGTTCGTTTCTG-ACTTTGTTGTCTCTAGCGTCGACTTTATGTACTTATAG
*
6295736 GCCAAGAGTTAGATCTTATGCACTAGATTTTGTTGCGAATTGGCAATATGTGAAGTGACTTGTGT
900 GCCAAGAGTTAGATCATATGCACTAGATTTTGTTGCGAATTGGCAATATGTGAAGTGACTTGTGT
6295801 ATGATAATGATATTTCATGTATTTCAC
965 ATGATAATGATATTTCATGTATTTCAC
* *
6295828 AATCTATTATTCTCTATGTTCACTTCATTTATACTACTTGGTAAGTAGAAACTTGACTAAGAATT
1 AATCTATTATTATCTATGTTCACTTCATTTATACTACTTGGTAAGTAGAAACTTGACTAAGAAAT
* * *
6295893 GTAGGGTGGTCCCAA-TCTT-T-T-TCACTAATGTCTTTCTTTATTTTGTTCT-TTCTTT-TAAA
66 GTAGGGTCGTCCCAATTCTTATGTATCACTAATGTCTTTCTTTATTATGTTCTCTT-TTTAAAAA
*
6295952 TTTATTCTTGTTTATGGTCAGAAAAATGAAATGTAGTTGAATA-C-CTGTTATGCTTTAATTCTA
130 TTTATTCTTGTTTATGGTCAGAAAAATGAAATGTAGTTGAAGACCTCTGTTATGCTTTAATTCTA
* *
6296015 AGTACAATTCTAGAATTGTGGGCTTGACTTGACTTAATACTTAATCACAAATGTCATAA-CAAAG
195 AGTACAATTCTAGAATTGTGGGCTT--C---ACGT--GACTTAATCACAAATGTCA-AACCAAAG
*
6296079 GCCCAATTAAATAACCAAAAATCAAAATGTTTGTGACAAATTCTTCTGCCACCTACTCTTTTTTC
252 GCCCAATTAAATAACCAAAAATCAAAATGTTTGTGACAAATTCTACTGCCACCTACTCTTTTTTC
*
6296144 ACCTCATTCACACTCATTTTTTAGATTTCATAAATTTCAACCTCTTAGTTGAACTTTAATTTAAT
317 ACCTCATTCACACT-ATTTTTTAGATTTCATAAATTTCAACCTCTTAGTGGAACTTTAATTTAAT
* *
6296209 TTAAAGCTTGTAATGTTGTAATTGGAATTGTCAAAGTCCTTGAATTCTACTCTAAATACACACTT
381 TTAAAGCTTGTAATGTTGTAATTGGAATTGTCAAAGTCCTTGAATTCTACTATAAATACACAATT
* ** * *
6296274 GAATAAGGAAAATTTTTTATCCAATTTTAAGATGTCATCAAT-CTTTGAAATTTGTCCAATGTTT
446 AAATAAGGAAAAAATTTTATCCAATTTTAAGATGTCATCAATCCTTTGAAATTTATCCAAGGTTT
*
6296338 TGAGACTTTTTTGTAATTGGAGTTTGATGAACCAAGATTTCAATTAAGGAAGGTAAAGGGCTTTT
511 TGAGACCTTTTTGTAATTGGAGTTTGATGAACCAAGATTTCAATTAAGGAAGGTAAAGGGCTTTT
* * *
6296403 GGGAAAGTTAGTCAAAAACAAATCCATTATTTTATGTAATTGATGCAAAGATACATATAACATGG
576 GAGAAAGTTAGTCAAAAACAAATCCATTAGTTTATGTAATTGATGCAAAGATACATACAACATGG
* ** *
6296468 TCATAAATTAATAATATTTATTTATTTATTTTGTTTTATTTTCTTACTTTTTGTATGCCATATGT
641 TCATAAATTAATAATATTTATTTATTTATTATGTTTTATTTTCTTACAGTTTGTATGCCATAAGT
*
6296533 TTTCAATATTTTTTGTACGTAATAAAATAGATTAAAACATTTATTTTTTGCAGTCATGGTTCATT
706 TTTCAATATTTTTTGTACATAATAAAATAGATTAAAACATTTATTTTTTGCAGTCATGGTTCATT
* *
6296598 TGTGTTTGAGAAAAGATGTTGAACGGCAAAAAAGGCTACTAGCTATATTAAATTTTATATAGAGA
771 TGTGTTTGAGAAAAGATGCTGAACGACAAAAAAGGCTACTAGCTATATTAAATTTTATATAGAGA
* * * * *
6296663 TTTTTTGTGTTGTTAGTTCGTTTTTGACTTTGTTGTCTCTAGCTTCGACTTTATGTACTTATAGG
836 TTTGTCGTGTTGCTAGTTCGTTTCTGACTTTGTTGTCTCTAGCGTCGACTTTATGTACTTATAGG
* * *
6296728 CCATGAGTTAGGTCATATGTACTAGATTTTGT
901 CCAAGAGTTAGATCATATGCACTAGATTTTGT
6296760 AGCAAATCAA
Statistics
Matches: 865, Mismatches: 53, Indels: 35
0.91 0.06 0.04
Matches are distributed among these distances:
983 44 0.05
985 2 0.00
986 46 0.05
987 30 0.03
988 3 0.00
989 3 0.00
990 390 0.45
991 269 0.31
992 4 0.00
998 74 0.09
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.41
Consensus pattern (991 bp):
AATCTATTATTATCTATGTTCACTTCATTTATACTACTTGGTAAGTAGAAACTTGACTAAGAAAT
GTAGGGTCGTCCCAATTCTTATGTATCACTAATGTCTTTCTTTATTATGTTCTCTTTTTAAAAAT
TTATTCTTGTTTATGGTCAGAAAAATGAAATGTAGTTGAAGACCTCTGTTATGCTTTAATTCTAA
GTACAATTCTAGAATTGTGGGCTTCACGTGACTTAATCACAAATGTCAAACCAAAGGCCCAATTA
AATAACCAAAAATCAAAATGTTTGTGACAAATTCTACTGCCACCTACTCTTTTTTCACCTCATTC
ACACTATTTTTTAGATTTCATAAATTTCAACCTCTTAGTGGAACTTTAATTTAATTTAAAGCTTG
TAATGTTGTAATTGGAATTGTCAAAGTCCTTGAATTCTACTATAAATACACAATTAAATAAGGAA
AAAATTTTATCCAATTTTAAGATGTCATCAATCCTTTGAAATTTATCCAAGGTTTTGAGACCTTT
TTGTAATTGGAGTTTGATGAACCAAGATTTCAATTAAGGAAGGTAAAGGGCTTTTGAGAAAGTTA
GTCAAAAACAAATCCATTAGTTTATGTAATTGATGCAAAGATACATACAACATGGTCATAAATTA
ATAATATTTATTTATTTATTATGTTTTATTTTCTTACAGTTTGTATGCCATAAGTTTTCAATATT
TTTTGTACATAATAAAATAGATTAAAACATTTATTTTTTGCAGTCATGGTTCATTTGTGTTTGAG
AAAAGATGCTGAACGACAAAAAAGGCTACTAGCTATATTAAATTTTATATAGAGATTTGTCGTGT
TGCTAGTTCGTTTCTGACTTTGTTGTCTCTAGCGTCGACTTTATGTACTTATAGGCCAAGAGTTA
GATCATATGCACTAGATTTTGTTGCGAATTGGCAATATGTGAAGTGACTTGTGTATGATAATGAT
ATTTCATGTATTTCAC
Found at i:6302485 original size:15 final size:15
Alignment explanation
Indices: 6302465--6302498 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
6302455 ATTATGGATA
6302465 AAAATTATAAGTTT-T
1 AAAATTATAA-TTTAT
6302480 AAAATTATAATTTAT
1 AAAATTATAATTTAT
6302495 AAAA
1 AAAA
6302499 AAAAATGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 3 0.17
15 15 0.83
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (15 bp):
AAAATTATAATTTAT
Found at i:6304930 original size:2 final size:2
Alignment explanation
Indices: 6304923--6304948 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6304913 TCAATTCAAG
6304923 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
6304949 TATCATTAAT
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:6305970 original size:42 final size:42
Alignment explanation
Indices: 6305923--6306004 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
6305913 TGTAATTTGC
*
6305923 TAATTAGTCCTTACACTTAATTGAACCATTCAATTAAGTTGT
1 TAATTAGTCCTTACACTTAATTAAACCATTCAATTAAGTTGT
* * *
6305965 TAATTAGTCCTTATACTTAATTAAATCATTTAATTAAGTT
1 TAATTAGTCCTTACACTTAATTAAACCATTCAATTAAGTT
6306005 CAATTGAAGC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.44
Consensus pattern (42 bp):
TAATTAGTCCTTACACTTAATTAAACCATTCAATTAAGTTGT
Found at i:6308399 original size:86 final size:86
Alignment explanation
Indices: 6308254--6308427 Score: 330
Period size: 86 Copynumber: 2.0 Consensus size: 86
6308244 ATAATTAAAT
6308254 ATGATATAATTATTCCAAATAATTATTCAAACATGAAAAATAAAAGTTTTAACATCTACATGCTA
1 ATGATATAATTATTCCAAATAATTATTCAAACATGAAAAATAAAAGTTTTAACATCTACATGCTA
6308319 AATTTAGATGTTTCATCAACC
66 AATTTAGATGTTTCATCAACC
*
6308340 ATGATATAATTATTCCAAATAATTATTCAAACATGAAAAATAAAAGTTTTAACATCTACATGTTA
1 ATGATATAATTATTCCAAATAATTATTCAAACATGAAAAATAAAAGTTTTAACATCTACATGCTA
*
6308405 AATTTAGATGTTTCATCAGCC
66 AATTTAGATGTTTCATCAACC
6308426 AT
1 AT
6308428 CCATATGGCA
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
86 86 1.00
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.36
Consensus pattern (86 bp):
ATGATATAATTATTCCAAATAATTATTCAAACATGAAAAATAAAAGTTTTAACATCTACATGCTA
AATTTAGATGTTTCATCAACC
Found at i:6312111 original size:25 final size:25
Alignment explanation
Indices: 6312083--6312132 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
6312073 TGGGTAAGGT
6312083 AGATCTTAAGCTAAATCGTGAAATC
1 AGATCTTAAGCTAAATCGTGAAATC
* *
6312108 AGATCTTAAGTTAAATTGTGAAATC
1 AGATCTTAAGCTAAATCGTGAAATC
6312133 TTACCTCCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (25 bp):
AGATCTTAAGCTAAATCGTGAAATC
Found at i:6313135 original size:20 final size:23
Alignment explanation
Indices: 6313107--6313151 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
6313097 ATTTCTATTT
6313107 AAACTTATAATAC-T-AAATATA
1 AAACTTATAATACATAAAATATA
*
6313128 AAAC-TATAATGCATAAAATATA
1 AAACTTATAATACATAAAATATA
6313150 AA
1 AA
6313152 TAGTTAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 7 0.33
21 5 0.24
22 9 0.43
ACGTcount: A:0.60, C:0.09, G:0.02, T:0.29
Consensus pattern (23 bp):
AAACTTATAATACATAAAATATA
Found at i:6314684 original size:38 final size:38
Alignment explanation
Indices: 6314576--6314689 Score: 129
Period size: 38 Copynumber: 3.0 Consensus size: 38
6314566 CACACTCAGC
* * * ***
6314576 TCATGTGCACTTCCTACACGCATAAGGCAATATCATCA
1 TCATGTGCACTCCCTACTCGCACATTTCAATATCATCA
* * *
6314614 TCATGTGCACTCCCTACTTGTATATTTCAATATCATCA
1 TCATGTGCACTCCCTACTCGCACATTTCAATATCATCA
* *
6314652 TCATGTGCACTCCTTACTCGCACATTTTAATATCATCA
1 TCATGTGCACTCCCTACTCGCACATTTCAATATCATCA
6314690 CACGCACTCC
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 64 1.00
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.34
Consensus pattern (38 bp):
TCATGTGCACTCCCTACTCGCACATTTCAATATCATCA
Found at i:6316674 original size:14 final size:15
Alignment explanation
Indices: 6316649--6316690 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
6316639 TATTAATTTT
6316649 TAAAAATCAAAAT-CA
1 TAAAAAT-AAAATCCA
6316664 TAAAAATAAAATCCA
1 TAAAAATAAAATCCA
*
6316679 TATAATATAAAA
1 TA-AAAATAAAA
6316691 AAAGAAAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 5 0.21
15 11 0.46
16 8 0.33
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.24
Consensus pattern (15 bp):
TAAAAATAAAATCCA
Found at i:6317367 original size:16 final size:17
Alignment explanation
Indices: 6317342--6317384 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
6317332 TTTAAAATCT
*
6317342 ATAATTATAAAA-AAAA
1 ATAATAATAAAACAAAA
* *
6317358 TTTATAATAAAACAAAA
1 ATAATAATAAAACAAAA
6317375 ATAATAATAA
1 ATAATAATAA
6317385 CATCAAATAA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (17 bp):
ATAATAATAAAACAAAA
Found at i:6317583 original size:18 final size:18
Alignment explanation
Indices: 6317560--6317598 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
6317550 GTATATACGT
*
6317560 TTAAACACGACAACACGA
1 TTAAACACAACAACACGA
*
6317578 TTAAACACAATAACACGA
1 TTAAACACAACAACACGA
6317596 TTA
1 TTA
6317599 GGTAAACGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.23, G:0.08, T:0.18
Consensus pattern (18 bp):
TTAAACACAACAACACGA
Found at i:6317616 original size:10 final size:10
Alignment explanation
Indices: 6317601--6317632 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
6317591 CACGATTAGG
6317601 TAAACGTGTT
1 TAAACGTGTT
6317611 TAAACGTGTTT
1 TAAACGTG-TT
6317622 TAAACGTGTT
1 TAAACGTGTT
6317632 T
1 T
6317633 GTCATGTCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 11 0.52
11 10 0.48
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.44
Consensus pattern (10 bp):
TAAACGTGTT
Found at i:6317625 original size:11 final size:11
Alignment explanation
Indices: 6317601--6317632 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
6317591 CACGATTAGG
6317601 TAAACGTG-TT
1 TAAACGTGTTT
6317611 TAAACGTGTTT
1 TAAACGTGTTT
6317622 TAAACGTGTTT
1 TAAACGTGTTT
6317633 GTCATGTCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.38
11 13 0.62
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.44
Consensus pattern (11 bp):
TAAACGTGTTT
Found at i:6322433 original size:17 final size:18
Alignment explanation
Indices: 6322413--6322447 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
6322403 ATCAAGACCG
6322413 ATCAAAAATATT-ATTTA
1 ATCAAAAATATTAATTTA
6322430 ATCAAAAATATTAATTTA
1 ATCAAAAATATTAATTTA
6322448 TGGAGTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (18 bp):
ATCAAAAATATTAATTTA
Found at i:6322894 original size:17 final size:18
Alignment explanation
Indices: 6322852--6322899 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
6322842 CGCTTTCTTC
6322852 TTTCAATTTATATTATTAT
1 TTTC-ATTTATATTATTAT
*
6322871 TTT-ATTTATATT-TTTT
1 TTTCATTTATATTATTAT
*
6322887 TTTCATTTTTATT
1 TTTCATTTATATT
6322900 CTATTTACTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 6 0.23
17 17 0.65
19 3 0.12
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTCATTTATATTATTAT
Found at i:6325364 original size:20 final size:19
Alignment explanation
Indices: 6325339--6325378 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
6325329 CGCGAATTCC
6325339 CCTTTGAATTTTCTACTTTT
1 CCTTTGAATTTTCT-CTTTT
**
6325359 CCTTTGGTTTTTCTCTTTT
1 CCTTTGAATTTTCTCTTTT
6325378 C
1 C
6325379 TTCCTTTCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.07, C:0.23, G:0.07, T:0.62
Consensus pattern (19 bp):
CCTTTGAATTTTCTCTTTT
Found at i:6329353 original size:56 final size:55
Alignment explanation
Indices: 6329253--6329397 Score: 220
Period size: 56 Copynumber: 2.6 Consensus size: 55
6329243 AACCACAGGC
* *
6329253 TCATCAGCTCATGTGCACTCCCACATCGCACATAGCTAGAATCATCATCCATCAG
1 TCATTAGCTCATGTGCACTCCCACATCGCACATAGCTAGAATCATCATCCACCAG
* * *
6329308 TCATTAGCTCATGTGCATTCCCACAGTCGCACATAGCTGGAATCATCATCCACCGG
1 TCATTAGCTCATGTGCACTCCCACA-TCGCACATAGCTAGAATCATCATCCACCAG
6329364 TCATTAGCTCATGTGCACTCCCACA-CAGCACATA
1 TCATTAGCTCATGTGCACTCCCACATC-GCACATA
6329398 ACTGAAATCA
Statistics
Matches: 82, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
54 1 0.01
55 30 0.37
56 51 0.62
ACGTcount: A:0.28, C:0.34, G:0.14, T:0.24
Consensus pattern (55 bp):
TCATTAGCTCATGTGCACTCCCACATCGCACATAGCTAGAATCATCATCCACCAG
Found at i:6332409 original size:48 final size:48
Alignment explanation
Indices: 6332344--6332468 Score: 128
Period size: 48 Copynumber: 2.6 Consensus size: 48
6332334 TCATCAGTAG
* * * *
6332344 CAACTCCGACATTATGAACAACCTCAA-CATTCGAAGTAATTCTAGCAT
1 CAACTCCGACATCATGAACAACCTCAATAATT-GAAGTAACTCCAGCAT
*
6332392 CAACTCC-AGCATCATGAATAACCTCAATAATTGAAGTAACTCCAGCAT
1 CAACTCCGA-CATCATGAACAACCTCAATAATTGAAGTAACTCCAGCAT
** * * *
6332440 CAACTTTGACATCAAGGACAACTTCAATA
1 CAACTCCGACATCATGAACAACCTCAATA
6332469 GCATGAATAG
Statistics
Matches: 63, Mismatches: 11, Indels: 6
0.79 0.14 0.08
Matches are distributed among these distances:
47 1 0.02
48 58 0.92
49 4 0.06
ACGTcount: A:0.39, C:0.26, G:0.10, T:0.24
Consensus pattern (48 bp):
CAACTCCGACATCATGAACAACCTCAATAATTGAAGTAACTCCAGCAT
Found at i:6353443 original size:2 final size:2
Alignment explanation
Indices: 6353436--6353476 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
6353426 NNNNNNNATA
* *
6353436 AT AT AT AT -T AT AT AT AT AT AC AT AT AT AT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6353477 TATTCTCTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:6353740 original size:19 final size:19
Alignment explanation
Indices: 6353716--6353752 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
6353706 GACTTTGCTC
6353716 TGAATTTTG-TTTAGCTTTT
1 TGAATTTTGCTTTA-CTTTT
6353735 TGAATTTTGCTTTACTTT
1 TGAATTTTGCTTTACTTT
6353753 GAATCTGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.16, C:0.08, G:0.14, T:0.62
Consensus pattern (19 bp):
TGAATTTTGCTTTACTTTT
Found at i:6353984 original size:30 final size:30
Alignment explanation
Indices: 6353945--6354020 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 30
6353935 TTACACTAAC
*
6353945 ATGTTACTACCTAAGGCATTACTGCTTCAG
1 ATGTTACTACCTAAGGCATTACTACTTCAG
* *
6353975 ATGTAACTACCTAAGGCATTACTATTTCAG
1 ATGTTACTACCTAAGGCATTACTACTTCAG
* *
6354005 GTGTTACTATCTAAGG
1 ATGTTACTACCTAAGG
6354021 TGGTATTGCT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (30 bp):
ATGTTACTACCTAAGGCATTACTACTTCAG
Found at i:6354273 original size:32 final size:32
Alignment explanation
Indices: 6354231--6354297 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
6354221 TAATGAGAAC
*
6354231 AACTAGAACAAGTGAAGCACTACTTCACACAA
1 AACTAGAACAAGTGAAACACTACTTCACACAA
* * *
6354263 AACTATAACAAGTGAAATACTACTTCACATAA
1 AACTAGAACAAGTGAAACACTACTTCACACAA
6354295 AAC
1 AAC
6354298 AACTACTTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.49, C:0.22, G:0.09, T:0.19
Consensus pattern (32 bp):
AACTAGAACAAGTGAAACACTACTTCACACAA
Found at i:6373068 original size:18 final size:17
Alignment explanation
Indices: 6373031--6373098 Score: 65
Period size: 17 Copynumber: 4.2 Consensus size: 17
6373021 CTTGTGAAGC
*
6373031 TTATCTTTATTTTA-TTT
1 TTAT-TTTATTATATTTT
6373048 TTATTATTATTATATTTT
1 TTATT-TTATTATATTTT
6373066 TTATTTTA-T-T-TTTT
1 TTATTTTATTATATTTT
*
6373080 ATATTTTATTA-ATTTT
1 TTATTTTATTATATTTT
6373096 TTA
1 TTA
6373099 ACTAATTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
14 11 0.26
15 2 0.05
16 8 0.19
17 14 0.33
18 8 0.19
ACGTcount: A:0.24, C:0.01, G:0.00, T:0.75
Consensus pattern (17 bp):
TTATTTTATTATATTTT
Found at i:6373070 original size:29 final size:30
Alignment explanation
Indices: 6373036--6373098 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 30
6373026 GAAGCTTATC
6373036 TTTATTTTA-TTTTTAT-TATTATTATATTT
1 TTTATTTTATTTTTTATATATTATTA-ATTT
*
6373065 TTTATTTTATTTTTTATATTTTATTAATTT
1 TTTATTTTATTTTTTATATATTATTAATTT
6373095 TTTA
1 TTTA
6373099 ACTAATTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
29 9 0.29
30 15 0.48
31 7 0.23
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (30 bp):
TTTATTTTATTTTTTATATATTATTAATTT
Found at i:6373094 original size:23 final size:23
Alignment explanation
Indices: 6373040--6373095 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
6373030 CTTATCTTTA
6373040 TTTTATTTTTATTATTATTATATT
1 TTTTA-TTTTATTATTATTATATT
6373064 TTTTATTTTATT-TT-TTATATT
1 TTTTATTTTATTATTATTATATT
6373085 TTATTAATTTT
1 TT-TT-ATTTT
6373096 TTAACTAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.30
22 4 0.13
23 12 0.40
24 5 0.17
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTTATTTTATTATTATTATATT
Found at i:6373107 original size:30 final size:30
Alignment explanation
Indices: 6373045--6373108 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
6373035 CTTTATTTTA
** *
6373045 TTTTTATTATTATTATATTTTTTATTTTAT
1 TTTTTATTATTATTATATTTTTTAACTAAT
*
6373075 TTTTTATATTTTATTA-ATTTTTTAACTAAT
1 TTTTTAT-TATTATTATATTTTTTAACTAAT
6373105 TTTT
1 TTTT
6373109 ATGTAGTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 22 0.76
31 7 0.24
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (30 bp):
TTTTTATTATTATTATATTTTTTAACTAAT
Found at i:6374138 original size:88 final size:87
Alignment explanation
Indices: 6374005--6374172 Score: 255
Period size: 88 Copynumber: 1.9 Consensus size: 87
6373995 TTTTTCCTGC
* * * *
6374005 CTTTTGCTCGACAACTCTAGATCTCTCTCAAAATGTCACCGACCGACTCTCCCCTTTAGTGCTGA
1 CTTTCGCTCGACAACTCTAGATCTCTCCCAAAATGTCACCGACCGACTCT-CCCTTTAGGGCCGA
*
6374070 TTGGTTTTCTCTCTCTATCCTTT
65 TTGGTTCTCTCTCTCTATCCTTT
* * *
6374093 CTTTCGCTCGACAACTCTAGATCTCTCCCAAAATGTCGCCGACCGACTCTTCCTTTGGGGCCGAT
1 CTTTCGCTCGACAACTCTAGATCTCTCCCAAAATGTCACCGACCGACTCTCCCTTTAGGGCCGAT
6374158 TGGTTCTCTCTCTCT
66 TGGTTCTCTCTCTCT
6374173 CNTCTTCCTT
Statistics
Matches: 72, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
87 25 0.35
88 47 0.65
ACGTcount: A:0.16, C:0.33, G:0.15, T:0.36
Consensus pattern (87 bp):
CTTTCGCTCGACAACTCTAGATCTCTCCCAAAATGTCACCGACCGACTCTCCCTTTAGGGCCGAT
TGGTTCTCTCTCTCTATCCTTT
Found at i:6374186 original size:35 final size:36
Alignment explanation
Indices: 6374139--6374213 Score: 127
Period size: 37 Copynumber: 2.1 Consensus size: 36
6374129 CGCCGACCGA
6374139 CTCTTCCTTTGGGG-CC-GATTGGTTCTCTCTCTCT
1 CTCTTCCTTTGGGGTCCGGATTGGTTCTCTCTCTCT
6374173 CNTCTTCCTTTGGGGTCCGGATTGGTTCTCTCTCTCT
1 C-TCTTCCTTTGGGGTCCGGATTGGTTCTCTCTCTCT
6374210 CTCT
1 CTCT
6374214 CTCTCTCTCT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
34 1 0.03
35 13 0.34
36 5 0.13
37 19 0.50
ACGTcount: A:0.03, C:0.32, G:0.20, T:0.44
Consensus pattern (36 bp):
CTCTTCCTTTGGGGTCCGGATTGGTTCTCTCTCTCT
Found at i:6374206 original size:2 final size:2
Alignment explanation
Indices: 6374199--6374226 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6374189 CCGGATTGGT
6374199 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
6374227 CCTTTCCTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:6375066 original size:15 final size:16
Alignment explanation
Indices: 6375034--6375067 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
6375024 ATTTTTTTTG
*
6375034 AAATTTTTTTTATGTT
1 AAATTTTTTTTATATT
6375050 AAATTTTTTTTA-ATT
1 AAATTTTTTTTATATT
6375065 AAA
1 AAA
6375068 AAATTATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (16 bp):
AAATTTTTTTTATATT
Found at i:6375321 original size:22 final size:22
Alignment explanation
Indices: 6375296--6375342 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
6375286 TTTATTTATT
6375296 AAAAATAAATTTTA-AAAATATA
1 AAAAAT-AATTTTATAAAATATA
* *
6375318 AAAAATATTTTTATATAATATA
1 AAAAATAATTTTATAAAATATA
6375340 AAA
1 AAA
6375343 TTTATAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
AAAAATAATTTTATAAAATATA
Found at i:6395796 original size:47 final size:47
Alignment explanation
Indices: 6395718--6396036 Score: 349
Period size: 47 Copynumber: 6.8 Consensus size: 47
6395708 GTCATGTTGA
* * *
6395718 GAATGTGTGACACGTCAGCA-TTCAGAATTGGTGAGACGCTATGGAGG
1 GAATCTGTGACACGCCAG-AGTTCAGAGTTGGTGAGACGCTATGGAGG
* * * *
6395765 GAATCTGTGACACGCCAGAATTAAGAGTTGGTGACACG-TCATGGTGG
1 GAATCTGTGACACGCCAGAGTTCAGAGTTGGTGAGACGCT-ATGGAGG
* ** * *
6395812 AAATCTGTGACACGTTAGCGTTCAGAGTTGGTGAGACGCCATGGAGG
1 GAATCTGTGACACGCCAGAGTTCAGAGTTGGTGAGACGCTATGGAGG
* * *
6395859 GAATTTGTGACACACCAGAGTTCAGAGTTGGTGACACGGC-ATGGAGG
1 GAATCTGTGACACGCCAGAGTTCAGAGTTGGTGAGAC-GCTATGGAGG
* * * *
6395906 GAATCTGTGACACGTCAGCGTTCAGAGTTCGTGAGACGCCATGGAGG
1 GAATCTGTGACACGCCAGAGTTCAGAGTTGGTGAGACGCTATGGAGG
* * * *
6395953 GAATCTGTGACACGCTAGAGTTCAGAGTTGGTGACACACTAAGGAGG
1 GAATCTGTGACACGCCAGAGTTCAGAGTTGGTGAGACGCTATGGAGG
* *
6396000 GAAGT-TGTGACAAGCCCGAGTTCAGAGTTGGTGAGAC
1 GAA-TCTGTGACACGCCAGAGTTCAGAGTTGGTGAGAC
6396037 ACCATGTTTA
Statistics
Matches: 226, Mismatches: 40, Indels: 12
0.81 0.14 0.04
Matches are distributed among these distances:
46 4 0.02
47 219 0.97
48 3 0.01
ACGTcount: A:0.27, C:0.17, G:0.34, T:0.22
Consensus pattern (47 bp):
GAATCTGTGACACGCCAGAGTTCAGAGTTGGTGAGACGCTATGGAGG
Found at i:6395958 original size:141 final size:141
Alignment explanation
Indices: 6395738--6396033 Score: 389
Period size: 141 Copynumber: 2.1 Consensus size: 141
6395728 CACGTCAGCA
* * *
6395738 TTCAGAATTGGTGAGACGCTATGGAGGGAATCTGTGACACGCCAGAATTAAGAGTTGGTGACACG
1 TTCAGAGTTGGTGACACGCTATGGAGGGAATCTGTGACACGCCAGAATTAAGAGTTCGTGACACG
* * * * * * * *
6395803 TCATGGTGGAAATCTGTGACACGTTAGCGTTCAGAGTTGGTGAGACGCCATGGAGGGAATTTGTG
66 CCATGGAGGAAATCTGTGACACGCTAGAGTTCAGAGTTGGTGACACACCAAGGAGGGAAGTTGTG
6395868 ACACA-CCAGAG
131 ACA-AGCCAGAG
* ** * *
6395879 TTCAGAGTTGGTGACACGGC-ATGGAGGGAATCTGTGACACGTCAGCGTTCAGAGTTCGTGAGAC
1 TTCAGAGTTGGTGACAC-GCTATGGAGGGAATCTGTGACACGCCAGAATTAAGAGTTCGTGACAC
* *
6395943 GCCATGGAGGGAATCTGTGACACGCTAGAGTTCAGAGTTGGTGACACACTAAGGAGGGAAGTTGT
65 GCCATGGAGGAAATCTGTGACACGCTAGAGTTCAGAGTTGGTGACACACCAAGGAGGGAAGTTGT
*
6396008 GACAAGCCCGAG
130 GACAAGCCAGAG
6396020 TTCAGAGTTGGTGA
1 TTCAGAGTTGGTGA
6396034 GACACCATGT
Statistics
Matches: 134, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
140 1 0.01
141 131 0.98
142 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.34, T:0.23
Consensus pattern (141 bp):
TTCAGAGTTGGTGACACGCTATGGAGGGAATCTGTGACACGCCAGAATTAAGAGTTCGTGACACG
CCATGGAGGAAATCTGTGACACGCTAGAGTTCAGAGTTGGTGACACACCAAGGAGGGAAGTTGTG
ACAAGCCAGAG
Found at i:6395999 original size:94 final size:93
Alignment explanation
Indices: 6395718--6396042 Score: 411
Period size: 94 Copynumber: 3.5 Consensus size: 93
6395708 GTCATGTTGA
* * * *
6395718 GAATGTGTGACACGTCAGCATTCAGAATTGGTGAGACGCTATGGAGGGAATCTGTGACACGCCAG
1 GAATCTGTGACACGTCAGCGTTCAGAGTTGGTGAGACGCCATGGAGGGAATCTGTGACACGCCAG
* * * *
6395783 AATTAAGAGTTGGTGACACGTCATGGTGG
66 AGTTCAGAGTTGGTGACACCT-ATGGAGG
* * * *
6395812 AAATCTGTGACACGTTAGCGTTCAGAGTTGGTGAGACGCCATGGAGGGAATTTGTGACACACCAG
1 GAATCTGTGACACGTCAGCGTTCAGAGTTGGTGAGACGCCATGGAGGGAATCTGTGACACGCCAG
6395877 AGTTCAGAGTTGGTGACACGGC-ATGGAGG
66 AGTTCAGAGTTGGTGACAC--CTATGGAGG
* *
6395906 GAATCTGTGACACGTCAGCGTTCAGAGTTCGTGAGACGCCATGGAGGGAATCTGTGACACGCTAG
1 GAATCTGTGACACGTCAGCGTTCAGAGTTGGTGAGACGCCATGGAGGGAATCTGTGACACGCCAG
*
6395971 AGTTCAGAGTTGGTGACACACTAAGGAGG
66 AGTTCAGAGTTGGTGACAC-CTATGGAGG
* * * * *
6396000 GAAGT-TGTGACAAGCCCGAGTTCAGAGTTGGTGAGACACCATG
1 GAA-TCTGTGACACGTCAGCGTTCAGAGTTGGTGAGACGCCATG
6396043 TTTAGAGTGT
Statistics
Matches: 201, Mismatches: 26, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
93 1 0.00
94 199 0.99
95 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.33, T:0.22
Consensus pattern (93 bp):
GAATCTGTGACACGTCAGCGTTCAGAGTTGGTGAGACGCCATGGAGGGAATCTGTGACACGCCAG
AGTTCAGAGTTGGTGACACCTATGGAGG
Found at i:6396093 original size:47 final size:47
Alignment explanation
Indices: 6396035--6396139 Score: 158
Period size: 47 Copynumber: 2.3 Consensus size: 47
6396025 AGTTGGTGAG
*
6396035 ACACCAT-GTTTAGAGTGTGTGACATGGCATTGCATGAAAAGCTGAC
1 ACACCATGGTTTAGAGTGTGTGACACGGCATTGCATGAAAAGCTGAC
* *
6396081 ACACCATGGTTTAGAGTGTGTGACACGGCATTGCTTGAATAGCTGAC
1 ACACCATGGTTTAGAGTGTGTGACACGGCATTGCATGAAAAGCTGAC
**
6396128 ACGTCATGGTTT
1 ACACCATGGTTT
6396140 GAAATAGAGA
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
46 7 0.13
47 46 0.87
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.29
Consensus pattern (47 bp):
ACACCATGGTTTAGAGTGTGTGACACGGCATTGCATGAAAAGCTGAC
Found at i:6396667 original size:31 final size:31
Alignment explanation
Indices: 6396629--6396761 Score: 144
Period size: 31 Copynumber: 4.3 Consensus size: 31
6396619 TTAACATGTG
*
6396629 ACAACATTTGAATCGATATGCATGGCGTGTC
1 ACAACATTTGACTCGATATGCATGGCGTGTC
*
6396660 ACAACATTTTACTCGATATGCATGGCGTGTC
1 ACAACATTTGACTCGATATGCATGGCGTGTC
* * * * *
6396691 ACAATATTTTACTTGTTATGCATGACGTGTC
1 ACAACATTTGACTCGATATGCATGGCGTGTC
* * *
6396722 ACAATATTTTG-CT-TATTATGCATGGCGTTTC
1 ACAACA-TTTGACTCGA-TATGCATGGCGTGTC
6396753 ACAACATTT
1 ACAACATTT
6396762 ATTCCTTATT
Statistics
Matches: 88, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
30 3 0.03
31 82 0.93
32 3 0.03
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (31 bp):
ACAACATTTGACTCGATATGCATGGCGTGTC
Found at i:6396742 original size:62 final size:62
Alignment explanation
Indices: 6396645--6396761 Score: 164
Period size: 62 Copynumber: 1.9 Consensus size: 62
6396635 TTTGAATCGA
* *
6396645 TATGCATGGCGTGTCACAACATTTTACTCGATATGCATGGCGTGTCACAATATTTTACTTGT
1 TATGCATGACGTGTCACAACATTTTACTCGATATGCATGGCGTGTCACAACATTTTACTTGT
* * * *
6396707 TATGCATGACGTGTCACAATATTTTGCT-TATTATGCATGGCGTTTCACAACATTT
1 TATGCATGACGTGTCACAACATTTTACTCGA-TATGCATGGCGTGTCACAACATTT
6396762 ATTCCTTATT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
61 1 0.02
62 47 0.98
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (62 bp):
TATGCATGACGTGTCACAACATTTTACTCGATATGCATGGCGTGTCACAACATTTTACTTGT
Found at i:6398997 original size:31 final size:31
Alignment explanation
Indices: 6398955--6399222 Score: 320
Period size: 31 Copynumber: 8.6 Consensus size: 31
6398945 TTAGCATGTG
* *
6398955 ACAAAATTTTACTTGTTATGCATGGCATGTC
1 ACAACATTTTACTTGTTATGCATGGCGTGTC
* * *
6398986 AGAACAATTTACTTGTTATGCATGGTGTGTC
1 ACAACATTTTACTTGTTATGCATGGCGTGTC
* * * *
6399017 ACAACGTTTAACTTGTTATGCATGGTGTGTT
1 ACAACATTTTACTTGTTATGCATGGCGTGTC
* * * **
6399048 AGAACATTTTGCTTGTTATCCATGATGTGTC
1 ACAACATTTTACTTGTTATGCATGGCGTGTC
*
6399079 ACAACATTTTTCTTGTTATGCATGGCGTGTC
1 ACAACATTTTACTTGTTATGCATGGCGTGTC
* *
6399110 AGAACATTTTGCTTGTTATGCATGGCGTGTC
1 ACAACATTTTACTTGTTATGCATGGCGTGTC
** * *
6399141 ACAATGTTTTACTTGCTATCCATGGCGTGTC
1 ACAACATTTTACTTGTTATGCATGGCGTGTC
* *
6399172 ACAACATTTTACTTGTTATGCATGACGCGTC
1 ACAACATTTTACTTGTTATGCATGGCGTGTC
*
6399203 ACAACATTTTACTGGTTATG
1 ACAACATTTTACTTGTTATG
6399223 GTTTGTGGTA
Statistics
Matches: 200, Mismatches: 37, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 200 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.40
Consensus pattern (31 bp):
ACAACATTTTACTTGTTATGCATGGCGTGTC
Found at i:6400828 original size:16 final size:16
Alignment explanation
Indices: 6400769--6400828 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
6400759 TTATATAGAA
*
6400769 TTATTTT-TATACAAT
1 TTATTTTATACACAAT
* * *
6400784 TAACTTTATACATAAT
1 TTATTTTATACACAAT
*
6400800 TTTTTTGTATACACAAT
1 TTATTT-TATACACAAT
6400817 TTATTTTATACA
1 TTATTTTATACA
6400829 ATTCATTGTA
Statistics
Matches: 34, Mismatches: 9, Indels: 3
0.74 0.20 0.07
Matches are distributed among these distances:
15 5 0.15
16 15 0.44
17 14 0.41
ACGTcount: A:0.35, C:0.10, G:0.02, T:0.53
Consensus pattern (16 bp):
TTATTTTATACACAAT
Found at i:6400942 original size:53 final size:52
Alignment explanation
Indices: 6400754--6400932 Score: 185
Period size: 52 Copynumber: 3.5 Consensus size: 52
6400744 TGTCTGTACA
* * * *
6400754 TTTTTT-TATATAGAATTATTTTTATACAATTAACTTTATAC---A-TAA-T
1 TTTTTTGTATACACAATTAATTTTATACAATTAATTTTATACAAAATTAATT
* * *
6400800 TTTTTTGTATACACAATTTATTTTATACAATTCATTGTATACAAAATTAATT
1 TTTTTTGTATACACAATTAATTTTATACAATTAATTTTATACAAAATTAATT
* * *
6400852 CTTTTTGTATACACAA-TATATTTTATATAATTAATTTTATACACAATT-ATT
1 TTTTTTGTATACACAATTA-ATTTTATACAATTAATTTTATACAAAATTAATT
6400903 TTTTTTGTTTATACACAATTAATTTTATAC
1 TTTTTTG--TATACACAATTAATTTTATAC
6400933 CAAGAATTTT
Statistics
Matches: 108, Mismatches: 15, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
46 6 0.06
47 28 0.26
50 1 0.01
51 13 0.12
52 41 0.38
53 17 0.16
54 2 0.02
ACGTcount: A:0.36, C:0.09, G:0.03, T:0.53
Consensus pattern (52 bp):
TTTTTTGTATACACAATTAATTTTATACAATTAATTTTATACAAAATTAATT
Found at i:6402006 original size:31 final size:31
Alignment explanation
Indices: 6401931--6402159 Score: 329
Period size: 31 Copynumber: 7.5 Consensus size: 31
6401921 TGGCGTGTCA
* * * *
6401931 GTGTGACAACATTTCACTTGATATGTATGGC
1 GTGTCACAACATTTTACTTGTTATGCATGGC
*
6401962 -TGTGACAACATTTTACTTGTTATGCATGGC
1 GTGTCACAACATTTTACTTGTTATGCATGGC
* *
6401992 GTGTTAGAACATTTTACTTGTTATGCATGGC
1 GTGTCACAACATTTTACTTGTTATGCATGGC
6402023 -TGTCACAA-ATTTTTACTTGTTATGCATGGC
1 GTGTCACAACA-TTTTACTTGTTATGCATGGC
6402053 GTGTCACAACATTTTACTTGTTATGCATGGC
1 GTGTCACAACATTTTACTTGTTATGCATGGC
* *
6402084 ATGTCACAATATTTTACTTGTTATGCATGGC
1 GTGTCACAACATTTTACTTGTTATGCATGGC
* *
6402115 GTGTCATAACATTTTGCTTGTTATGCATGGC
1 GTGTCACAACATTTTACTTGTTATGCATGGC
6402146 GTGTCACAACATTT
1 GTGTCACAACATTT
6402160 ATTCCTTATT
Statistics
Matches: 180, Mismatches: 14, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
29 1 0.01
30 53 0.29
31 125 0.69
32 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.40
Consensus pattern (31 bp):
GTGTCACAACATTTTACTTGTTATGCATGGC
Found at i:6402117 original size:62 final size:61
Alignment explanation
Indices: 6401931--6402159 Score: 334
Period size: 61 Copynumber: 3.7 Consensus size: 61
6401921 TGGCGTGTCA
* * * * *
6401931 GTGTGACAACATTTCACTTGATATGTATGGCTGTGACAACATTTTACTTGTTATGCATGGC
1 GTGTCACAACATTTTACTTGTTATGCATGGCTGTCACAACATTTTACTTGTTATGCATGGC
* *
6401992 GTGTTAGAACATTTTACTTGTTATGCATGGCTGTCACAA-ATTTTTACTTGTTATGCATGGC
1 GTGTCACAACATTTTACTTGTTATGCATGGCTGTCACAACA-TTTTACTTGTTATGCATGGC
*
6402053 GTGTCACAACATTTTACTTGTTATGCATGGCATGTCACAATATTTTACTTGTTATGCATGGC
1 GTGTCACAACATTTTACTTGTTATGCATGGC-TGTCACAACATTTTACTTGTTATGCATGGC
* *
6402115 GTGTCATAACATTTTGCTTGTTATGCATGGCGTGTCACAACATTT
1 GTGTCACAACATTTTACTTGTTATGCATGGC-TGTCACAACATTT
6402160 ATTCCTTATT
Statistics
Matches: 153, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
60 1 0.01
61 82 0.54
62 69 0.45
63 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.40
Consensus pattern (61 bp):
GTGTCACAACATTTTACTTGTTATGCATGGCTGTCACAACATTTTACTTGTTATGCATGGC
Found at i:6407230 original size:54 final size:54
Alignment explanation
Indices: 6407171--6407276 Score: 185
Period size: 54 Copynumber: 2.0 Consensus size: 54
6407161 TGTAACCGTG
*
6407171 CATGAGCTGGGTGAGATGTGGTGTCCGGCTATGTGTACAATGTGGTGGGATGCA
1 CATGAGCTGGGTGAGATGTGGTGTCCGGCTATGTGCACAATGTGGTGGGATGCA
* *
6407225 CATGAGCTGGGTGAGATGTGGTGTCTGGCTATGTGCACGATGTGGTGGGATG
1 CATGAGCTGGGTGAGATGTGGTGTCCGGCTATGTGCACAATGTGGTGGGATG
6407277 ATGTCCGACT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.17, C:0.12, G:0.42, T:0.28
Consensus pattern (54 bp):
CATGAGCTGGGTGAGATGTGGTGTCCGGCTATGTGCACAATGTGGTGGGATGCA
Found at i:6407337 original size:86 final size:86
Alignment explanation
Indices: 6407192--6407362 Score: 288
Period size: 86 Copynumber: 2.0 Consensus size: 86
6407182 TGAGATGTGG
* * *
6407192 TGTCCGGCTATGTGTACAATGTGGTGGGATGCACATGAGCTGGGTGAGATGTGGTGTCTGGCTAT
1 TGTCCGACTATGTGCACAATGTGGTGGGATGCACATGAGCTGGGTGAGATGTGGTGTCTGACTAT
6407257 GTGCACGATGTGGTGGGATGA
66 GTGCACGATGTGGTGGGATGA
* * *
6407278 TGTCCGACTATGTGCACGATGTGGTGGGATGCACATGAGTTGGGTGAGGTGTGGTGTCTGACTAT
1 TGTCCGACTATGTGCACAATGTGGTGGGATGCACATGAGCTGGGTGAGATGTGGTGTCTGACTAT
6407343 GTGCACGATGTGGTGGGATG
66 GTGCACGATGTGGTGGGATG
6407363 CACATGAGCT
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
86 79 1.00
ACGTcount: A:0.17, C:0.13, G:0.41, T:0.29
Consensus pattern (86 bp):
TGTCCGACTATGTGCACAATGTGGTGGGATGCACATGAGCTGGGTGAGATGTGGTGTCTGACTAT
GTGCACGATGTGGTGGGATGA
Found at i:6407345 original size:54 final size:54
Alignment explanation
Indices: 6407278--6407435 Score: 262
Period size: 54 Copynumber: 2.9 Consensus size: 54
6407268 GGTGGGATGA
* *
6407278 TGTCCGACTATGTGCACGATGTGGTGGGATGCACATGAGTTGGGTGAGGTGTGG
1 TGTCCGACTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGATGTGG
*
6407332 TGTCTGACTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGATGTGG
1 TGTCCGACTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGATGTGG
* * *
6407386 TGTCCGGCTATGTGCAAGATGTGGTGGGATGCACATGAGCTGGGCGAGAT
1 TGTCCGACTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGAT
6407436 AAAATGTTTT
Statistics
Matches: 97, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 97 1.00
ACGTcount: A:0.18, C:0.14, G:0.41, T:0.27
Consensus pattern (54 bp):
TGTCCGACTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGATGTGG
Found at i:6409621 original size:31 final size:31
Alignment explanation
Indices: 6409583--6409782 Score: 310
Period size: 31 Copynumber: 6.5 Consensus size: 31
6409573 ATTATTACAT
* *
6409583 GCCATGCATATAACTTAAAATGTAGTAACAC
1 GCCATGCATATAACGTAAAATGTGGTAACAC
6409614 GCCATGCATATAACGTAAAATGTGGTAACAC
1 GCCATGCATATAACGTAAAATGTGGTAACAC
*
6409645 GCCATGCATATAACGGAAAATGTGGTAACAC
1 GCCATGCATATAACGTAAAATGTGGTAACAC
* *
6409676 GCCATGCATATAACGTAAAATATTGTAACAC
1 GCCATGCATATAACGTAAAATGTGGTAACAC
* * * *
6409707 GCCATGCATATAATGTTAAATATTGTAACAC
1 GCCATGCATATAACGTAAAATGTGGTAACAC
*
6409738 GCCATGCATATAACGTAAAATGTTGTAACAC
1 GCCATGCATATAACGTAAAATGTGGTAACAC
6409769 GCCATGCATATAAC
1 GCCATGCATATAAC
6409783 CAATGTCATG
Statistics
Matches: 158, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 158 1.00
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.25
Consensus pattern (31 bp):
GCCATGCATATAACGTAAAATGTGGTAACAC
Found at i:6413303 original size:28 final size:29
Alignment explanation
Indices: 6413259--6413313 Score: 94
Period size: 28 Copynumber: 1.9 Consensus size: 29
6413249 TATGATTTAA
*
6413259 AATAAAAATATAAAAATTTAATTAAATAT
1 AATAAAAATATAAAAATTTAAATAAATAT
6413288 AATAAAAA-ATAAAAATTTAAATAAAT
1 AATAAAAATATAAAAATTTAAATAAAT
6413314 TTAAAATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 17 0.68
29 8 0.32
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (29 bp):
AATAAAAATATAAAAATTTAAATAAATAT
Found at i:6414442 original size:80 final size:80
Alignment explanation
Indices: 6414309--6414457 Score: 237
Period size: 80 Copynumber: 1.9 Consensus size: 80
6414299 TTTTCTTTTT
* * * *
6414309 GTTTCATCAAAATCTAGGTGTTGAGTAATTACAAATTTAAAAGGTCTTCATTTTTGGGTTTATAG
1 GTTTCATCAAAATCTAGATGTTGAGTAATTACAAAATTAAAAAGTCTTAATTTTTGGGTTTATAG
6414374 TATGTTAAATTTGGC
66 TATGTTAAATTTGGC
*
6414389 GTTTCATCAAAAT-TCAGATGTTGAGTAATTACAAAATTAAAAAGTCTTAATTTTTGGGTTTATG
1 GTTTCATCAAAATCT-AGATGTTGAGTAATTACAAAATTAAAAAGTCTTAATTTTTGGGTTTATA
6414453 GTATG
65 GTATG
6414458 CTAATTATGG
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
79 1 0.02
80 62 0.98
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (80 bp):
GTTTCATCAAAATCTAGATGTTGAGTAATTACAAAATTAAAAAGTCTTAATTTTTGGGTTTATAG
TATGTTAAATTTGGC
Found at i:6421433 original size:8 final size:8
Alignment explanation
Indices: 6421420--6421454 Score: 52
Period size: 8 Copynumber: 4.1 Consensus size: 8
6421410 CATTTCATTT
6421420 ATAAAAAA
1 ATAAAAAA
6421428 ATAAAAAA
1 ATAAAAAA
6421436 ATAAAAAAAA
1 AT--AAAAAA
6421446 ATAAAAAA
1 ATAAAAAA
6421454 A
1 A
6421455 AGAACTAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 17 0.68
10 8 0.32
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (8 bp):
ATAAAAAA
Found at i:6421443 original size:10 final size:10
Alignment explanation
Indices: 6421422--6421455 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
6421412 TTTCATTTAT
6421422 AAAAAAAT--
1 AAAAAAATAA
6421430 AAAAAAATAA
1 AAAAAAATAA
6421440 AAAAAAATAA
1 AAAAAAATAA
6421450 AAAAAA
1 AAAAAA
6421456 GAACTAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.33
10 16 0.67
ACGTcount: A:0.91, C:0.00, G:0.00, T:0.09
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:6425205 original size:40 final size:40
Alignment explanation
Indices: 6425161--6425270 Score: 184
Period size: 40 Copynumber: 2.8 Consensus size: 40
6425151 GATAGTGCCC
*
6425161 ATGTGCACGATGTGGGGGGATGCACATGATGACTCCGGCT
1 ATGTGCACGATGTGGGGGGATGCACATGAGGACTCCGGCT
*
6425201 ATGTGCACGATGTGGGGGGATGCACACGAGGACTCCGGCT
1 ATGTGCACGATGTGGGGGGATGCACATGAGGACTCCGGCT
* *
6425241 ATGTGCATGATGTGAGGGGATGCACATGAG
1 ATGTGCACGATGTGGGGGGATGCACATGAG
6425271 TTGGGTGTGA
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 65 1.00
ACGTcount: A:0.22, C:0.18, G:0.39, T:0.21
Consensus pattern (40 bp):
ATGTGCACGATGTGGGGGGATGCACATGAGGACTCCGGCT
Found at i:6429419 original size:20 final size:20
Alignment explanation
Indices: 6429394--6429438 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
6429384 TACTTCTTTG
*
6429394 TATGTTGATGTGGACCCGGC
1 TATGTTGATGTGGACCCGAC
6429414 TATGTTGATGTGGACCCGAC
1 TATGTTGATGTGGACCCGAC
6429434 TATGT
1 TATGT
6429439 GCGAGTAGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.18, C:0.18, G:0.31, T:0.33
Consensus pattern (20 bp):
TATGTTGATGTGGACCCGAC
Found at i:6429556 original size:2 final size:2
Alignment explanation
Indices: 6429549--6429598 Score: 55
Period size: 2 Copynumber: 25.0 Consensus size: 2
6429539 ACGATGATTG
* * * *
6429549 AT AT AT AT AT GT AT AT AT AC AT AT AT AT GT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
6429591 AC AT AT AT
1 AT AT AT AT
6429599 GGTATATGGT
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (2 bp):
AT
Found at i:6429572 original size:16 final size:16
Alignment explanation
Indices: 6429553--6429598 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
6429543 TGATTGATAT
*
6429553 ATATATGTATATATAC
1 ATATATATATATATAC
*
6429569 ATATATATGTATATAC
1 ATATATATATATATAC
*
6429585 ATATATACATATAT
1 ATATATATATATAT
6429599 GGTATATGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (16 bp):
ATATATATATATATAC
Found at i:6429907 original size:60 final size:60
Alignment explanation
Indices: 6429834--6429969 Score: 182
Period size: 60 Copynumber: 2.3 Consensus size: 60
6429824 AAGAATGCAT
* * * * * *
6429834 TTTCGCTGCAGCGAAATTTATTCTCGTTGCAGCGAGAAACTTTTTGTTTTTGGATTACAA
1 TTTCGCTGCAGCGAAATTGAATCTCGCTGCAGCGAGAAACATTTTGTTTATGGATCACAA
* * * *
6429894 TTTCGCTGTAGCGAGATTGAATCTCGCTGCAGCGAGAAACATTTTGTTTATGGGTCATAA
1 TTTCGCTGCAGCGAAATTGAATCTCGCTGCAGCGAGAAACATTTTGTTTATGGATCACAA
6429954 TTTCGCTGCAGCGAAA
1 TTTCGCTGCAGCGAAA
6429970 AACTTTCTGT
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 64 1.00
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (60 bp):
TTTCGCTGCAGCGAAATTGAATCTCGCTGCAGCGAGAAACATTTTGTTTATGGATCACAA
Found at i:6434438 original size:17 final size:18
Alignment explanation
Indices: 6434408--6434441 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
6434398 CTACATTCAT
6434408 TTATCATACATACCATTC
1 TTATCATACATACCATTC
6434426 TTATCAT-CATACCATT
1 TTATCATACATACCATT
6434442 GGGATCGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.32, C:0.26, G:0.00, T:0.41
Consensus pattern (18 bp):
TTATCATACATACCATTC
Done.