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 19 of 135
Found at i:5109566 original size:5 final size:5
Alignment explanation
Indices: 5109556--5109584 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
5109546 TATTAAATAT
5109556 TAAAA TAAAA TAAAA TAAAA TAAAA TAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAA
5109585 TATTTTTAAA
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:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:5115752 original size:19 final size:19
Alignment explanation
Indices: 5115728--5115770 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
5115718 CTTTTCATTT
*
5115728 TATATATCTATAGTGGAGA
1 TATATATCTATAGTGGAAA
5115747 TATATATCTATAGTGGAAA
1 TATATATCTATAGTGGAAA
5115766 TATAT
1 TATAT
5115771 CCATATCTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.40, C:0.05, G:0.16, T:0.40
Consensus pattern (19 bp):
TATATATCTATAGTGGAAA
Found at i:5125665 original size:17 final size:17
Alignment explanation
Indices: 5125645--5125678 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5125635 ATCACTCACT
*
5125645 ATTTCAATAGCATTTTC
1 ATTTCAATAACATTTTC
5125662 ATTTCAATAACATTTTC
1 ATTTCAATAACATTTTC
5125679 CATATCAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.18, G:0.03, T:0.47
Consensus pattern (17 bp):
ATTTCAATAACATTTTC
Found at i:5126394 original size:13 final size:13
Alignment explanation
Indices: 5126376--5126419 Score: 61
Period size: 13 Copynumber: 3.2 Consensus size: 13
5126366 CTTTATTTTT
5126376 TTATTATAATATA
1 TTATTATAATATA
5126389 TTATTATAATACTA
1 TTATTATAATA-TA
*
5126403 TTATTTAGAATATA
1 TTA-TTATAATATA
5126417 TTA
1 TTA
5126420 ACACCAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 11 0.39
14 10 0.36
15 7 0.25
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (13 bp):
TTATTATAATATA
Found at i:5128381 original size:53 final size:53
Alignment explanation
Indices: 5128299--5128403 Score: 183
Period size: 53 Copynumber: 2.0 Consensus size: 53
5128289 ATCGTGCAAC
* *
5128299 AATTTTTATTACCATCTTCCAATTGTCAAGCTTTATTAAATGGGGCTATTAAA
1 AATTATTATTACCATCTTCCAATTGTCAAGCTTTATTAAATGGAGCTATTAAA
*
5128352 AATTATTATTACCATCTTCCAATTGTCAAGCTTTATTAAATGTAGCTATTAA
1 AATTATTATTACCATCTTCCAATTGTCAAGCTTTATTAAATGGAGCTATTAA
5128404 CTTCAATCTC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (53 bp):
AATTATTATTACCATCTTCCAATTGTCAAGCTTTATTAAATGGAGCTATTAAA
Found at i:5132103 original size:57 final size:57
Alignment explanation
Indices: 5131970--5132148 Score: 245
Period size: 57 Copynumber: 3.1 Consensus size: 57
5131960 AAACTCATCT
* ** *
5131970 ATAAACTAAACCAAAATATTTTTAAACCCATTTTTAATTTCATTATTCAAAAACACTC
1 ATAAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATT-TTCAAAAACACTC
*
5132028 ATAAACTAAATCCAAATATTTTTAAACCCAAATATAATTTCATTTTCAAAAACACTC
1 ATAAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTTTCAAAAACACTC
* *
5132085 ATAAATTAAACCCAAATATTTTTAAACCCAAATATAATGTT-A-TTCCTAAATAACACTC
1 ATAAACTAAACCCAAATATTTTTAAACCCAAATATAAT-TTCATTTTC-AAA-AACACTC
5132143 ATAAAC
1 ATAAAC
5132149 AACTCATTTT
Statistics
Matches: 109, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
56 3 0.03
57 53 0.49
58 53 0.49
ACGTcount: A:0.47, C:0.19, G:0.01, T:0.34
Consensus pattern (57 bp):
ATAAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCATTTTCAAAAACACTC
Found at i:5132728 original size:18 final size:18
Alignment explanation
Indices: 5132705--5132743 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
5132695 CATGAATAAA
5132705 TATATTTGATTCAAATTC
1 TATATTTGATTCAAATTC
5132723 TATATTTGATTCAAATTC
1 TATATTTGATTCAAATTC
5132741 TAT
1 TAT
5132744 CTCACTCAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.51
Consensus pattern (18 bp):
TATATTTGATTCAAATTC
Found at i:5132833 original size:50 final size:50
Alignment explanation
Indices: 5132778--5132875 Score: 178
Period size: 50 Copynumber: 2.0 Consensus size: 50
5132768 TTTCAAATCG
* *
5132778 AATTAAAATGATGAAATAAGATTCGAAAATTCAATTAATTCAAAAAATGA
1 AATTAAAATGATGAAATAAAATTCAAAAATTCAATTAATTCAAAAAATGA
5132828 AATTAAAATGATGAAATAAAATTCAAAAATTCAATTAATTCAAAAAAT
1 AATTAAAATGATGAAATAAAATTCAAAAATTCAATTAATTCAAAAAAT
5132876 TTTCATTCGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.58, C:0.06, G:0.07, T:0.29
Consensus pattern (50 bp):
AATTAAAATGATGAAATAAAATTCAAAAATTCAATTAATTCAAAAAATGA
Found at i:5133170 original size:148 final size:148
Alignment explanation
Indices: 5132897--5133198 Score: 595
Period size: 148 Copynumber: 2.0 Consensus size: 148
5132887 TCAATCAAAT
*
5132897 ACTCACACTTCTACACACTTCTATTTTTAAGGATTGCTTGAATTAGTTAAACTTTATGAACTGAA
1 ACTCTCACTTCTACACACTTCTATTTTTAAGGATTGCTTGAATTAGTTAAACTTTATGAACTGAA
5132962 ATTGGGTGTGGTGCGCCAGGCCCAAGCAATAGTGCAGAACTTGGGCGACACTCGAGAGCCCCAGT
66 ATTGGGTGTGGTGCGCCAGGCCCAAGCAATAGTGCAGAACTTGGGCGACACTCGAGAGCCCCAGT
5133027 AGCAAGCTACTGTGAAGG
131 AGCAAGCTACTGTGAAGG
5133045 ACTCTCACTTCTACACACTTCTATTTTTAAGGATTGCTTGAATTAGTTAAACTTTATGAACTGAA
1 ACTCTCACTTCTACACACTTCTATTTTTAAGGATTGCTTGAATTAGTTAAACTTTATGAACTGAA
5133110 ATTGGGTGTGGTGCGCCAGGCCCAAGCAATAGTGCAGAACTTGGGCGACACTCGAGAGCCCCAGT
66 ATTGGGTGTGGTGCGCCAGGCCCAAGCAATAGTGCAGAACTTGGGCGACACTCGAGAGCCCCAGT
5133175 AGCAAGCTACTGTGAAGG
131 AGCAAGCTACTGTGAAGG
5133193 ACTCTC
1 ACTCTC
5133199 CCACTCAATA
Statistics
Matches: 153, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
148 153 1.00
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (148 bp):
ACTCTCACTTCTACACACTTCTATTTTTAAGGATTGCTTGAATTAGTTAAACTTTATGAACTGAA
ATTGGGTGTGGTGCGCCAGGCCCAAGCAATAGTGCAGAACTTGGGCGACACTCGAGAGCCCCAGT
AGCAAGCTACTGTGAAGG
Found at i:5133992 original size:9 final size:9
Alignment explanation
Indices: 5133980--5134023 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
5133970 TTATTTTAGG
5133980 ATTTTTTAA
1 ATTTTTTAA
5133989 ATTTTTTATA
1 ATTTTTTA-A
* *
5133999 TATTCTTTAG
1 -ATTTTTTAA
5134009 ATTTTTTAA
1 ATTTTTTAA
5134018 ATTTTT
1 ATTTTT
5134024 AATATTTTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
9 21 0.72
10 1 0.03
11 7 0.24
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (9 bp):
ATTTTTTAA
Found at i:5143180 original size:161 final size:164
Alignment explanation
Indices: 5143009--5143322 Score: 458
Period size: 162 Copynumber: 1.9 Consensus size: 164
5142999 TAATTTAGTC
* * *
5143009 CTTTGACTGTTTGATTGTACCATAGACTGCCACGTGTCA-CTTTTTGGATCATTTTTGCATTTAG
1 CTTTGACTGTTTGATTGCACCAGAGACTGCCACGTGTCATCTTTTTGGATCATTTCTGCATTTAG
* * *
5143073 TCCTTTTTATTTTTTATTTGTTTTAATTTAATCC-CAAATCAAC-TTTATTTTAATTACGAAATT
66 TCCTTTTTATTTTTAATTTGTTCTAATTTAATCCTCAAATCAACTTTTA-TTTAATTACAAAATT
5143136 GGCCCAATAA-TTTTTCAAG-TTTTATAAACCAGTT
130 GGCCCAA-AATTTTTTCAAGATTTTATAAACCAGTT
** * *
5143170 CTTTGACTGTTTGATTGCACCAGAGGTTGCCACGTGTCATCTTTTTGGATTATTTCTGTATTTAG
1 CTTTGACTGTTTGATTGCACCAGAGACTGCCACGTGTCATCTTTTTGGATCATTTCTGCATTTAG
* *
5143235 TCCTTTTTATTTTTAATTTGTTCTAATTTAATCCTTAAATCGACTTTTATTTAATTACAAAATTG
66 TCCTTTTTATTTTTAATTTGTTCTAATTTAATCCTCAAATCAACTTTTATTTAATTACAAAATTG
*
5143300 GTCCAAAATTTTTTCAAGATTTT
131 GCCCAAAATTTTTTCAAGATTTT
5143323 CAAATTGGTC
Statistics
Matches: 135, Mismatches: 13, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
161 35 0.26
162 56 0.41
163 36 0.27
164 8 0.06
ACGTcount: A:0.25, C:0.15, G:0.12, T:0.48
Consensus pattern (164 bp):
CTTTGACTGTTTGATTGCACCAGAGACTGCCACGTGTCATCTTTTTGGATCATTTCTGCATTTAG
TCCTTTTTATTTTTAATTTGTTCTAATTTAATCCTCAAATCAACTTTTATTTAATTACAAAATTG
GCCCAAAATTTTTTCAAGATTTTATAAACCAGTT
Found at i:5143449 original size:30 final size:29
Alignment explanation
Indices: 5143399--5143516 Score: 137
Period size: 30 Copynumber: 3.9 Consensus size: 29
5143389 GCTTTGTAAG
* *
5143399 CCCCTAAATTATCCAGAAATTACATTTTGA
1 CCCCAAAATTTTCCA-AAATTACATTTTGA
* *
5143429 TCCTAAAATTTTCCTAAAATTACATTTTGA
1 CCCCAAAATTTTCC-AAAATTACATTTTGA
* * *
5143459 CCCCGAAACTTTACCAAAATTACGTTTTGA
1 CCCC-AAAATTTTCCAAAATTACATTTTGA
5143489 CCCCAAAACTTTTCCAAAATTACATTTT
1 CCCCAAAA-TTTTCCAAAATTACATTTT
5143517 TAACCCCGAT
Statistics
Matches: 73, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
29 3 0.04
30 61 0.84
31 9 0.12
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.36
Consensus pattern (29 bp):
CCCCAAAATTTTCCAAAATTACATTTTGA
Found at i:5143575 original size:59 final size:59
Alignment explanation
Indices: 5143504--5143966 Score: 712
Period size: 59 Copynumber: 7.9 Consensus size: 59
5143494 AAACTTTTCC
* * * **
5143504 AAAATTACATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCTCGAAGCTTCA
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAGCTTTT
**
5143563 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAGCTTCG
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAGCTTTT
* * * * *
5143622 AAAATTCCGTCTTTAACACCGATTTCACCAAAAATTACCATTTTACCCCCGAATCTTTT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAGCTTTT
**
5143681 AAAATTCTGTTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAGCTTTT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAGCTTTT
5143740 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAGCTTTT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAGCTTTT
* * * * *
5143799 AAAATTCCGTTTTTAACCCCAATTTCACCGAGAATTACCATTTTACCCCCAAATCTTTT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAGCTTTT
*
5143858 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAGCTTTT
* * *
5143917 AAAATTCCATTTTTAATCCCGATTACACC-AAAATTACCATTTTGCCCCCG
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCG
5143967 GGTATCCATA
Statistics
Matches: 374, Mismatches: 30, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
58 20 0.05
59 354 0.95
ACGTcount: A:0.31, C:0.29, G:0.06, T:0.34
Consensus pattern (59 bp):
AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAGCTTTT
Found at i:5143949 original size:29 final size:29
Alignment explanation
Indices: 5143502--5143959 Score: 187
Period size: 30 Copynumber: 15.6 Consensus size: 29
5143492 CAAAACTTTT
5143502 CCAAAATTA-CATTTTTAACCCCGATTTCA
1 CCAAAATTACCATTTTTAACCCCGA-TTCA
5143531 CCAAAAATTACCA-TTTT-ACCCTCGAAGCTTCA
1 CC-AAAATTACCATTTTTAACCC-CG-A--TTCA
5143563 --AAAATT-CCATTTTTAACCCCGATTTCA
1 CCAAAATTACCATTTTTAACCCCGA-TTCA
* ** *
5143590 CCGAAAATTACCA-TTTTACCCCCGAAGCTT
1 CC-AAAATTACCATTTTTAACCCCGATTC-A
* * * *
5143620 CGAAAATT-CCGTCTTTAACACCGATTTCA
1 CCAAAATTACCATTTTTAACCCCGA-TTCA
* * *
5143649 CCAAAAATTACCA-TTTTACCCCCGAATCTT
1 CC-AAAATTACCATTTTTAACCCCGATTC-A
** **
5143679 TTAAAATT-CTGTTTTTAACCCCGATTTCA
1 CCAAAATTACCATTTTTAACCCCGA-TTCA
* ** *
5143708 CCGAAAATTACCA-TTTTACCCCCGAAGCTT
1 CC-AAAATTACCATTTTTAACCCCGATTC-A
**
5143738 TTAAAATT-CCATTTTTAACCCCGATTTCA
1 CCAAAATTACCATTTTTAACCCCGA-TTCA
* ** *
5143767 CCGAAAATTACCA-TTTTACCCCCGAAGCTT
1 CC-AAAATTACCATTTTTAACCCCGATTC-A
** * *
5143797 TTAAAATT-CCGTTTTTAACCCCAATTTCA
1 CCAAAATTACCATTTTTAACCCCGA-TTCA
* * * * *
5143826 CCGAGAATTACCA-TTTTACCCCCAAATCTT
1 CC-AAAATTACCATTTTTAACCCCGATTC-A
**
5143856 TTAAAATT-CCATTTTTAACCCCGATTTCA
1 CCAAAATTACCATTTTTAACCCCGA-TTCA
* * *
5143885 CCGAAAATTACCA-TTTTACCCCCGAATCTT
1 CC-AAAATTACCATTTTTAACCCCGATTC-A
** *
5143915 TTAAAATT-CCATTTTTAATCCCGATTACA
1 CCAAAATTACCATTTTTAACCCCGATT-CA
5143944 CCAAAATTACCATTTT
1 CCAAAATTACCATTTT
5143960 GCCCCCGGGT
Statistics
Matches: 306, Mismatches: 83, Indels: 79
0.65 0.18 0.17
Matches are distributed among these distances:
27 4 0.01
28 18 0.06
29 131 0.43
30 132 0.43
31 17 0.06
32 4 0.01
ACGTcount: A:0.32, C:0.28, G:0.06, T:0.34
Consensus pattern (29 bp):
CCAAAATTACCATTTTTAACCCCGATTCA
Found at i:5155343 original size:6 final size:6
Alignment explanation
Indices: 5155325--5155432 Score: 89
Period size: 6 Copynumber: 18.0 Consensus size: 6
5155315 TTAAATTGAT
* * *
5155325 TTTAAA TTT--A TTTAAA TTTAGA TTT-AT TTTAAA TTTAAAA TTAAATA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAA-A
* ** *
5155372 TTTAAA TTT-AA TTTGAA TTTAAA TTTAAA TAAAAA TTAAAA TATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA
5155420 TTTAACA TTTAAA
1 TTTAA-A TTTAAA
5155433 AGTCCAAATG
Statistics
Matches: 83, Mismatches: 11, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
4 4 0.05
5 8 0.10
6 50 0.60
7 21 0.25
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:5155355 original size:17 final size:17
Alignment explanation
Indices: 5155325--5155401 Score: 77
Period size: 17 Copynumber: 4.4 Consensus size: 17
5155315 TTAAATTGAT
5155325 TTTAAATTTA-TTTAAA
1 TTTAAATTTATTTTAAA
*
5155341 TTTAGATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
5155358 TTTAAAATTAAATATTTAAA
1 TTT-AAATT-TAT-TTTAAA
*
5155378 TTT-AATTTGAATTTAAA
1 TTTAAATTT-ATTTTAAA
5155395 TTTAAAT
1 TTTAAAT
5155402 AAAAATTAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
16 9 0.18
17 18 0.36
18 12 0.24
19 2 0.04
20 9 0.18
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:5155390 original size:11 final size:11
Alignment explanation
Indices: 5155315--5155401 Score: 61
Period size: 11 Copynumber: 7.5 Consensus size: 11
5155305 GACTTTTGAG
* *
5155315 TTAAATTGATT
1 TTAAATTTAAT
5155326 TTAAATTT-AT
1 TTAAATTTAAT
5155336 TTAAATTTAGAT
1 TTAAATTTA-AT
*
5155348 TT-ATTTTAAAT
1 TTAAATTT-AAT
*
5155359 TTAAAATTAAATAT
1 TT-AAATT-TA-AT
5155373 TTAAATTTAAT
1 TTAAATTTAAT
*
5155384 TTGAATTTAAAT
1 TTAAATTT-AAT
5155396 TTAAAT
1 TTAAAT
5155402 AAAAATTAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 15
0.72 0.10 0.18
Matches are distributed among these distances:
10 9 0.15
11 24 0.40
12 14 0.23
13 9 0.15
14 4 0.07
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:5155422 original size:31 final size:30
Alignment explanation
Indices: 5155352--5155432 Score: 83
Period size: 31 Copynumber: 2.6 Consensus size: 30
5155342 TTAGATTTAT
* * *
5155352 TTTAAATTTAAAATTAAATATTTAAATTTAA
1 TTTAAATTTAAATTTAAATA-TAAAATTAAA
*
5155383 TTTGAATTTAAATTTAAATA-AAAATTAAAA
1 TTTAAATTTAAATTTAAATATAAAATT-AAA
5155413 TATTAAATTTAACATTTAAA
1 T-TTAAATTTAA-ATTTAAA
5155433 AGTCCAAATG
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
29 5 0.12
30 3 0.07
31 27 0.64
32 7 0.17
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (30 bp):
TTTAAATTTAAATTTAAATATAAAATTAAA
Found at i:5156241 original size:29 final size:29
Alignment explanation
Indices: 5156204--5156278 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
5156194 CCCTAAATTA
5156204 TTTAAAAATTACATTTCAACCCCAAAA-T
1 TTTAAAAATTACATTTCAACCCCAAAACT
** **
5156232 TTTAGAAAATTATGTTTTGACCCCAAAACT
1 TTTA-AAAATTACATTTCAACCCCAAAACT
*
5156262 TTCAAAAATTACCATTT
1 TTTAAAAATTA-CATTT
5156279 TACACCCAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
28 4 0.11
29 26 0.70
30 7 0.19
ACGTcount: A:0.41, C:0.19, G:0.04, T:0.36
Consensus pattern (29 bp):
TTTAAAAATTACATTTCAACCCCAAAACT
Found at i:5156298 original size:30 final size:29
Alignment explanation
Indices: 5156257--5156535 Score: 145
Period size: 30 Copynumber: 9.4 Consensus size: 29
5156247 TTTGACCCCA
*
5156257 AAACTTTCAAAAATTACCATTTTACACCC
1 AAACTTTCCAAAATTACCATTTTACACCC
5156286 AAACTTTCCAAAATT-CCATTTTTA-ACCC
1 AAACTTTCCAAAATTACCA-TTTTACACCC
**
5156314 TGA-TTTCACCTAAAATTACCATTTTAC-CCC
1 AAACTTT--CC-AAAATTACCATTTTACACCC
*
5156344 TAAACTTTCCTAAATT-CCATTTTTA-ACCC
1 -AAACTTTCCAAAATTACCA-TTTTACACCC
** *
5156373 CGATTTTACCCAAAATTACCATTTTAC-CCC
1 AAACTTT--CCAAAATTACCATTTTACACCC
* *
5156403 TAACTTTCCTAAATT-CCAATTTTA-ACCC
1 AAACTTTCCAAAATTACC-ATTTTACACCC
** * *
5156431 CGA-TTTCACCAAAAATTACCATCTTACCCCTC
1 AAACTTT--CC-AAAATTACCATTTTACACC-C
5156463 AAACTTTCCAAAATT-CCATTTTTA-ACCTC
1 AAACTTTCCAAAATTACCA-TTTTACACC-C
* *
5156492 -GATTTTCACCAAAAGTTACCATTTTAC-CCC
1 AAACTTT--CCAAAA-TTACCATTTTACACCC
*
5156522 TAAGCTTTCCAAAA
1 -AAACTTTCCAAAA
5156536 AGCCTAACAT
Statistics
Matches: 191, Mismatches: 28, Indels: 61
0.68 0.10 0.22
Matches are distributed among these distances:
27 8 0.04
28 36 0.19
29 43 0.23
30 68 0.36
31 22 0.12
32 11 0.06
33 3 0.02
ACGTcount: A:0.33, C:0.30, G:0.02, T:0.35
Consensus pattern (29 bp):
AAACTTTCCAAAATTACCATTTTACACCC
Found at i:5156436 original size:58 final size:58
Alignment explanation
Indices: 5156266--5156535 Score: 380
Period size: 59 Copynumber: 4.6 Consensus size: 58
5156256 AAAACTTTCA
* * *
5156266 AAAATTACCATTTTACACCCAAACTTTCCAAAATTCCATTTTTAACCCTGATTTCACCT
1 AAAATTACCATTTTAC-CCCTAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCC
* *
5156325 AAAATTACCATTTTACCCCTAAACTTTCCTAAATTCCATTTTTAACCCCGATTTTACCC
1 AAAATTACCATTTTACCCCT-AACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCC
* * *
5156384 AAAATTACCATTTTACCCCTAACTTTCCTAAATTCCAATTTTAACCCCGATTTCACCA
1 AAAATTACCATTTTACCCCTAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCC
* *
5156442 AAAATTACCATCTTACCCCTCAAACTTTCCAAAATTCCATTTTTAACCTCGATTTTCA-CC
1 AAAATTACCATTTTACCCCT--AACTTTCCAAAATTCCATTTTTAACCCCGA-TTTCACCC
5156502 AAAAGTTACCATTTTACCCCTAAGCTTTCCAAAA
1 AAAA-TTACCATTTTACCCCTAA-CTTTCCAAAA
5156536 AGCCTAACAT
Statistics
Matches: 191, Mismatches: 14, Indels: 11
0.88 0.06 0.05
Matches are distributed among these distances:
58 57 0.30
59 72 0.38
60 42 0.22
61 20 0.10
ACGTcount: A:0.33, C:0.30, G:0.02, T:0.35
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCTAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCC
Found at i:5172694 original size:18 final size:17
Alignment explanation
Indices: 5172673--5172713 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
5172663 ATGATTTTTG
*
5172673 AATTTATTTCTAAAATTA
1 AATTTACTT-TAAAATTA
*
5172691 AATTTACTTTAAATTTA
1 AATTTACTTTAAAATTA
5172708 AATTTA
1 AATTTA
5172714 AATTCATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (17 bp):
AATTTACTTTAAAATTA
Found at i:5172707 original size:6 final size:6
Alignment explanation
Indices: 5172683--5172751 Score: 63
Period size: 6 Copynumber: 11.8 Consensus size: 6
5172673 AATTTATTTC
* * * *
5172683 TAAAAT TAAATT T-ACTT TAAATT TAAATT TAAA-T TCATTT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
*
5172729 TAAATT T-AGTT TAAATT TGAAAT
1 TAAATT TAAATT TAAATT T-AAAT
5172752 AATTTTTAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 7
0.76 0.14 0.11
Matches are distributed among these distances:
5 11 0.22
6 35 0.70
7 4 0.08
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (6 bp):
TAAATT
Found at i:5172708 original size:17 final size:17
Alignment explanation
Indices: 5172704--5172751 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
5172694 TTACTTTAAA
*
5172704 TTTAAATTTAAATTCAT
1 TTTAAATTTAAATTCAG
*
5172721 TTTAAATTTAAATTTAG
1 TTTAAATTTAAATTCAG
5172738 TTTAAATTTGAAAT
1 TTTAAATTT-AAAT
5172752 AATTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
17 24 0.86
18 4 0.14
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (17 bp):
TTTAAATTTAAATTCAG
Found at i:5172733 original size:23 final size:23
Alignment explanation
Indices: 5172683--5172736 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
5172673 AATTTATTTC
* *
5172683 TAAAATTAAATTTACTTTAAATT
1 TAAATTTAAATTCACTTTAAATT
*
5172706 TAAATTTAAATTCATTTTAAATT
1 TAAATTTAAATTCACTTTAAATT
5172729 TAAATTTA
1 TAAATTTA
5172737 GTTTAAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (23 bp):
TAAATTTAAATTCACTTTAAATT
Found at i:5172746 original size:11 final size:11
Alignment explanation
Indices: 5172688--5172736 Score: 53
Period size: 11 Copynumber: 4.3 Consensus size: 11
5172678 ATTTCTAAAA
*
5172688 TTAAATTTACT
1 TTAAATTTAAT
5172699 TTAAATTTAAAT
1 TTAAATTT-AAT
* *
5172711 TTAAATTCATT
1 TTAAATTTAAT
5172722 TTAAATTTAAAT
1 TTAAATTT-AAT
5172734 TTA
1 TTA
5172737 GTTTAAATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
11 17 0.55
12 14 0.45
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:5173561 original size:9 final size:9
Alignment explanation
Indices: 5173523--5173578 Score: 67
Period size: 9 Copynumber: 6.0 Consensus size: 9
5173513 CAATAATGCT
*
5173523 TTAATAGTA
1 TTAATAATA
*
5173532 TTAATTAACA
1 TTAA-TAATA
5173542 TTAATTAATA
1 TTAA-TAATA
5173552 TTAATAATA
1 TTAATAATA
5173561 TTAATAATA
1 TTAATAATA
*
5173570 ATAATAATA
1 TTAATAATA
5173579 AATATTTTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
9 26 0.62
10 16 0.38
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (9 bp):
TTAATAATA
Found at i:5174744 original size:28 final size:27
Alignment explanation
Indices: 5174712--5174820 Score: 87
Period size: 28 Copynumber: 3.8 Consensus size: 27
5174702 TTTGACCCCA
5174712 AAACTTTCAAAAATTACCATTTTACACC
1 AAACTTTCAAAAATT-CCATTTTACACC
*
5174740 AAACTTTCCAAAATTCCATTTTTA-ACCC
1 AAACTTTCAAAAATTCCA-TTTTACA-CC
* *
5174768 CAA-TTTCACCCAAAATTACCATTTTACCCC
1 AAACTTTCA---AAAATT-CCATTTTACACC
**
5174798 TAAACTTTCTTAAATTCCATTTT
1 -AAACTTTCAAAAATTCCATTTT
5174821 TAACCACGAT
Statistics
Matches: 65, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
27 8 0.12
28 30 0.46
29 5 0.08
30 13 0.20
31 5 0.08
32 4 0.06
ACGTcount: A:0.36, C:0.28, G:0.00, T:0.37
Consensus pattern (27 bp):
AAACTTTCAAAAATTCCATTTTACACC
Found at i:5174881 original size:29 final size:28
Alignment explanation
Indices: 5174701--5175063 Score: 135
Period size: 29 Copynumber: 12.3 Consensus size: 28
5174691 GAAAATTATG
*
5174701 TTTTGACCCCAAAACTTTCAAAAATTACCA
1 TTTT-ACCCC-AAACTTTCCAAAATTACCA
*
5174731 TTTTACACCAAACTTTCCAAAATT-CCA
1 TTTTACCCCAAACTTTCCAAAATTACCA
5174758 TTTTTAACCCC-AA-TTTCACCCAAAATTACCA
1 -TTTT-ACCCCAAACTTT---CCAAAATTACCA
**
5174789 TTTTACCCCTAAACTTTCTTAAATT-CCA
1 TTTTACCCC-AAACTTTCCAAAATTACCA
* *
5174817 TTTTTA-ACCACGA-TTTCACCCAAAATTACCA
1 -TTTTACCCCA-AACTTT---CCAAAATTACCA
* *
5174848 CTTTACCCCTAAACTTTCCTAAATT-CCAA
1 TTTTACCCC-AAACTTTCCAAAATTACC-A
*
5174877 TTTTAACCCC-GA-TTTCACCAAAAATTACCA
1 TTTT-ACCCCAAACTTT--CC-AAAATTACCA
* *
5174907 TCTTACCCCTCGAACTTTCCAAAATT-CCA
1 TTTTA-CCC-CAAACTTTCCAAAATTACCA
* *
5174936 TTTTTAACCTC-GA-TTTCACCAAAAATTACCA
1 -TTTT-ACCCCAAACTTT--CC-AAAATTACCA
* * *
5174967 TATTACCCCTAAGCTTTCCAAAATT-CTA
1 TTTTACCCC-AAACTTTCCAAAATTACCA
* *
5174995 TTTTTGACCTC-GA-TTTCACCAAAAGTTACCA
1 -TTTT-ACCCCAAACTTT--CCAAAA-TTACCA
* *
5175026 TTTTACCCCTGAACTTTTCAAAATTACCA
1 TTTTACCCC-AAACTTTCCAAAATTACCA
*
5175055 TTTTGCCCC
1 TTTTACCCC
5175064 CGGGTACCCA
Statistics
Matches: 252, Mismatches: 35, Indels: 93
0.66 0.09 0.24
Matches are distributed among these distances:
27 19 0.08
28 32 0.13
29 81 0.32
30 80 0.32
31 23 0.09
32 14 0.06
33 3 0.01
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.34
Consensus pattern (28 bp):
TTTTACCCCAAACTTTCCAAAATTACCA
Found at i:5174963 original size:178 final size:176
Alignment explanation
Indices: 5174719--5175042 Score: 479
Period size: 178 Copynumber: 1.8 Consensus size: 176
5174709 CCAAAACTTT
* *
5174719 CAAAAATTACCATTTTACACCAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCCAAAAT
1 CAAAAATTACCATCTTACACCAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCAAAAAT
* **
5174784 TACCATTTTACCCCTAAACTTTCTTAAATTCCATTTTTAACCACGATTTCACCCAAAA-TTACCA
66 TACCATATTACCCCTAAACTTTCCAAAATTCCATTTTTAACCACGATTTCA-CCAAAAGTTACCA
5174848 CTTTACCCCTAAACTTTCCTAAATTCCAATTTTAACCCCGATTTCAC
130 CTTTACCCCTAAACTTTCCTAAATTCCAATTTTAACCCCGATTTCAC
* * * *
5174895 CAAAAATTACCATCTTACCCCTCGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCAAAA
1 CAAAAATTACCATCTTA-CAC-CAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCAAAA
* * * *
5174960 ATTACCATATTACCCCTAAGCTTTCCAAAATTCTATTTTTGACCTCGATTTCACCAAAAGTTACC
64 ATTACCATATTACCCCTAAACTTTCCAAAATTCCATTTTTAACCACGATTTCACCAAAAGTTACC
* *
5175025 ATTTTACCCCTGAACTTT
129 ACTTTACCCCTAAACTTT
5175043 TCAAAATTAC
Statistics
Matches: 130, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
176 16 0.12
177 8 0.06
178 106 0.82
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.34
Consensus pattern (176 bp):
CAAAAATTACCATCTTACACCAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCAAAAAT
TACCATATTACCCCTAAACTTTCCAAAATTCCATTTTTAACCACGATTTCACCAAAAGTTACCAC
TTTACCCCTAAACTTTCCTAAATTCCAATTTTAACCCCGATTTCAC
Found at i:5174973 original size:119 final size:117
Alignment explanation
Indices: 5174719--5175058 Score: 475
Period size: 119 Copynumber: 2.9 Consensus size: 117
5174709 CCAAAACTTT
* * *
5174719 CAAAAATTACCATTTTACACC-AAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCCAAAA
1 CAAAAATTACCA-TTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAA
* **
5174783 TTACCATTTTACCCCTAAACTTTCTTAAATTCCATTTTTAACCACGATTTCAC
65 TTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCACGATTTCAC
* * *
5174836 CCAAAATTACCACTTTACCCCTAAACTTTCCTAAATTCCAATTTTAACCCCGATTTCACCAAAAA
1 CAAAAATTACCA-TTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAA
* *
5174901 TTACCATCTTACCCCTCGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCAC
65 TTACCATTTTACCCCT-GAACTTTCCAAAATTCCATTTTTAACCACGATTTCAC
* * * * *
5174955 CAAAAATTACCATATTACCCCTAAGCTTTCCAAAATTCTATTTTTGACCTCGATTTCACCAAAAG
1 CAAAAATTACCAT-TTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAA
*
5175020 TTACCATTTTACCCCTGAACTTTTCAAAATTACCATTTT
65 TTACCATTTTACCCCTGAACTTTCCAAAATT-CCATTTT
5175059 GCCCCCGGGT
Statistics
Matches: 197, Mismatches: 22, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
117 18 0.09
118 69 0.35
119 110 0.56
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (117 bp):
CAAAAATTACCATTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAAT
TACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCACGATTTCAC
Found at i:5175059 original size:59 final size:59
Alignment explanation
Indices: 5174719--5175058 Score: 466
Period size: 59 Copynumber: 5.7 Consensus size: 59
5174709 CCAAAACTTT
* *
5174719 CAAAAATTACCATTTTACACC-AAACTTTCCAAAATTCCATTTTTAACCCCAATTTCAC
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAC
* ** *
5174777 CCAAAATTACCATTTTACCCCTAAACTTTCTTAAATTCCATTTTTAACCACGATTTCAC
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAC
* * * *
5174836 CCAAAATTACCACTTTACCCCTAAACTTTCCTAAATTCCAATTTTAACCCCGATTTCAC
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAC
* * *
5174895 CAAAAATTACCATCTTACCCCTCGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCAC
1 CAAAAATTACCATTTTACCCCT-AAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAC
* * * * *
5174955 CAAAAATTACCATATTACCCCTAAGCTTTCCAAAATTCTATTTTTGACCTCGATTTCAC
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAC
* * *
5175014 CAAAAGTTACCATTTTACCCCTGAACTTTTCAAAATTACCATTTT
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATT-CCATTTT
5175059 GCCCCCGGGT
Statistics
Matches: 251, Mismatches: 28, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
58 19 0.08
59 172 0.69
60 60 0.24
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (59 bp):
CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAC
Found at i:5175166 original size:15 final size:16
Alignment explanation
Indices: 5175139--5175184 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 16
5175129 ATTTATTTGC
*
5175139 ATCTGCATTTTATATT
1 ATCTGCATATTATATT
*
5175155 TTC-GCATATTAT-TT
1 ATCTGCATATTATATT
*
5175169 ATCTGCTTATTATATT
1 ATCTGCATATTATATT
5175185 GCTTCGTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
14 4 0.17
15 16 0.67
16 4 0.17
ACGTcount: A:0.24, C:0.13, G:0.07, T:0.57
Consensus pattern (16 bp):
ATCTGCATATTATATT
Found at i:5180698 original size:21 final size:21
Alignment explanation
Indices: 5180674--5180716 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
5180664 TAATAAATCT
5180674 TGAACACAGATACAGGCTAAG
1 TGAACACAGATACAGGCTAAG
5180695 TGAACACAGATACAGGCTAAG
1 TGAACACAGATACAGGCTAAG
5180716 T
1 T
5180717 CAGCTTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.19, G:0.23, T:0.16
Consensus pattern (21 bp):
TGAACACAGATACAGGCTAAG
Found at i:5200476 original size:21 final size:21
Alignment explanation
Indices: 5200451--5200501 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
5200441 GGATTATATA
5200451 ATTTGGATTTATAAACTTTAT
1 ATTTGGATTTATAAACTTTAT
* *
5200472 TTTTGGATTTCTAAACTTTAT
1 ATTTGGATTTATAAACTTTAT
5200493 ATTTGGATT
1 ATTTGGATT
5200502 GCTATTATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.27, C:0.06, G:0.12, T:0.55
Consensus pattern (21 bp):
ATTTGGATTTATAAACTTTAT
Found at i:5202998 original size:2 final size:2
Alignment explanation
Indices: 5202986--5203033 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
5202976 GCATAAACAC
*
5202986 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT 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
5203027 AT AT AT A
1 AT AT AT A
5203034 GGAGGATAGA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5208663 original size:36 final size:36
Alignment explanation
Indices: 5208615--5208714 Score: 173
Period size: 36 Copynumber: 2.8 Consensus size: 36
5208605 TGATATCTGA
*
5208615 TTTACTCTCTGTTGACCCAAAGGTCATGATGCTCAT
1 TTTACTCCCTGTTGACCCAAAGGTCATGATGCTCAT
*
5208651 TTTACTCCCTGTTAACCCAAAGGTCATGATGCTCAT
1 TTTACTCCCTGTTGACCCAAAGGTCATGATGCTCAT
*
5208687 TTTACTCCCTATTGACCCAAAGGTCATG
1 TTTACTCCCTGTTGACCCAAAGGTCATG
5208715 CCTGTTTCCA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 60 1.00
ACGTcount: A:0.24, C:0.27, G:0.15, T:0.34
Consensus pattern (36 bp):
TTTACTCCCTGTTGACCCAAAGGTCATGATGCTCAT
Found at i:5210482 original size:23 final size:23
Alignment explanation
Indices: 5210407--5210529 Score: 142
Period size: 23 Copynumber: 5.4 Consensus size: 23
5210397 AAGCACTGGG
* *
5210407 GAAACAGTAAGCACACACAGTGC
1 GAAACAGTAGGCACACAAAGTGC
* ** * *
5210430 -AATCAGTAGGCGTACATAGCGC
1 GAAACAGTAGGCACACAAAGTGC
*
5210452 -AAATCAGTAGGCACACGAAGTGC
1 GAAA-CAGTAGGCACACAAAGTGC
5210475 GAAACAGTAGGCACACAAAGTGC
1 GAAACAGTAGGCACACAAAGTGC
*
5210498 GAAACAGTAAGCACACAAAGTGC
1 GAAACAGTAGGCACACAAAGTGC
5210521 GAAACAGTA
1 GAAACAGTA
5210530 AGTACACACA
Statistics
Matches: 84, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
22 18 0.21
23 63 0.75
24 3 0.04
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.11
Consensus pattern (23 bp):
GAAACAGTAGGCACACAAAGTGC
Found at i:5210555 original size:46 final size:46
Alignment explanation
Indices: 5210407--5210543 Score: 127
Period size: 46 Copynumber: 3.0 Consensus size: 46
5210397 AAGCACTGGG
* * * ** *
5210407 GAAACAGTAAGCACACACAGTGC-AATCAGTAGGCGTACATAG--C
1 GAAACAGTAAGCACACAAAGTGCGAAACAGTAAGCACACAAAGTAC
* * * *
5210450 GCAAATCAGTAGGCACACGAAGTGCGAAACAGTAGGCACACAAAGTGC
1 G-AAA-CAGTAAGCACACAAAGTGCGAAACAGTAAGCACACAAAGTAC
* *
5210498 GAAACAGTAAGCACACAAAGTGCGAAACAGTAAGTACACACAGTAC
1 GAAACAGTAAGCACACAAAGTGCGAAACAGTAAGCACACAAAGTAC
5210544 TGAACGATAA
Statistics
Matches: 76, Mismatches: 13, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
43 1 0.01
44 3 0.04
45 16 0.21
46 51 0.67
47 3 0.04
48 2 0.03
ACGTcount: A:0.42, C:0.23, G:0.23, T:0.12
Consensus pattern (46 bp):
GAAACAGTAAGCACACAAAGTGCGAAACAGTAAGCACACAAAGTAC
Found at i:5229601 original size:20 final size:21
Alignment explanation
Indices: 5229549--5229612 Score: 69
Period size: 20 Copynumber: 3.0 Consensus size: 21
5229539 ATTGAACCGG
5229549 TTTTATAAATTCTTTAGTATATTC
1 TTTTATAAATT-TTTA-T-TATTC
*
5229573 TTTT-GAAATTTTTATTATT-
1 TTTTATAAATTTTTATTATTC
5229592 TTTTATAAATTTTTAATTATT
1 TTTTATAAATTTTT-ATTATT
5229613 GTTAGACGGA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
19 4 0.11
20 12 0.33
21 7 0.19
22 4 0.11
23 5 0.14
24 4 0.11
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (21 bp):
TTTTATAAATTTTTATTATTC
Found at i:5229810 original size:14 final size:15
Alignment explanation
Indices: 5229791--5229823 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
5229781 ATTTTTCGAA
*
5229791 TTTTCA-AAATGTTT
1 TTTTCATAAATATTT
5229805 TTTTCATAAATATTT
1 TTTTCATAAATATTT
5229820 TTTT
1 TTTT
5229824 AAATAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.27, C:0.06, G:0.03, T:0.64
Consensus pattern (15 bp):
TTTTCATAAATATTT
Found at i:5236480 original size:23 final size:23
Alignment explanation
Indices: 5236454--5236578 Score: 112
Period size: 23 Copynumber: 5.4 Consensus size: 23
5236444 ACACTAGCGC
*
5236454 GCTTATTGTTCAGCACTGTGTGT
1 GCTTACTGTTCAGCACTGTGTGT
*
5236477 GCTTATTGGATT--GCACTGTGTGT
1 GCTTACT-G-TTCAGCACTGTGTGT
*
5236500 GCTTACTGATCAGCACTGTGTGT
1 GCTTACTGTTCAGCACTGTGTGT
* *
5236523 GCTTACTGATCAACACTGTGTGT
1 GCTTACTGTTCAGCACTGTGTGT
* ** * *
5236546 GTTTA-TAGGACTGCATTGTGTGT
1 GCTTACT-GTTCAGCACTGTGTGT
5236569 GCTTACTGTT
1 GCTTACTGTT
5236579 GCCAAACACT
Statistics
Matches: 84, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
21 1 0.01
22 2 0.02
23 77 0.92
24 2 0.02
25 2 0.02
ACGTcount: A:0.16, C:0.17, G:0.26, T:0.41
Consensus pattern (23 bp):
GCTTACTGTTCAGCACTGTGTGT
Found at i:5239686 original size:18 final size:18
Alignment explanation
Indices: 5239663--5239699 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5239653 TTTGTGATCA
5239663 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
5239681 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
5239699 A
1 A
5239700 TATGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:5239849 original size:41 final size:40
Alignment explanation
Indices: 5239801--5239901 Score: 109
Period size: 38 Copynumber: 2.6 Consensus size: 40
5239791 TCGACCTTGA
* ** *
5239801 GTCGATGAGACACTGGGTGTCATTATTTTACTTCGGATAG
1 GTCGATGAGGCACTGGGTGTCACCACTTTACTTCGGATAG
* * *
5239841 ATTCGATGAGGTACT-GG-GT-ACCACTTTACTTCGGCTAG
1 -GTCGATGAGGCACTGGGTGTCACCACTTTACTTCGGATAG
5239879 GTCGATGAGGCACTGGGTGTCAC
1 GTCGATGAGGCACTGGGTGTCAC
5239902 TTTATTGCTT
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
37 12 0.25
38 17 0.35
39 4 0.08
40 4 0.08
41 11 0.23
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.31
Consensus pattern (40 bp):
GTCGATGAGGCACTGGGTGTCACCACTTTACTTCGGATAG
Found at i:5239894 original size:37 final size:38
Alignment explanation
Indices: 5239827--5239905 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 38
5239817 GTGTCATTAT
* *
5239827 TTTACTTCGGATAGATTCGATGAGGTACTGGGTACCAC
1 TTTACTTCGGATAGAGTCGATGAGGCACTGGGTACCAC
* **
5239865 TTTACTTCGGCTAG-GTCGATGAGGCACTGGGTGTCAC
1 TTTACTTCGGATAGAGTCGATGAGGCACTGGGTACCAC
5239902 TTTA
1 TTTA
5239906 TTGCTTCGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
37 23 0.64
38 13 0.36
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.33
Consensus pattern (38 bp):
TTTACTTCGGATAGAGTCGATGAGGCACTGGGTACCAC
Found at i:5244291 original size:25 final size:23
Alignment explanation
Indices: 5244254--5244299 Score: 56
Period size: 25 Copynumber: 1.9 Consensus size: 23
5244244 CCAAACATGA
5244254 TAAAATTACTTATTCATTGTATTAT
1 TAAAATTACTTATT-A-TGTATTAT
**
5244279 TAAAATTTGTTATTATGTATT
1 TAAAATTACTTATTATGTATT
5244300 TTTTTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.32
24 1 0.05
25 12 0.63
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (23 bp):
TAAAATTACTTATTATGTATTAT
Found at i:5244386 original size:15 final size:15
Alignment explanation
Indices: 5244366--5244401 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
5244356 TTTGACAACG
5244366 CACACACACCTTGCA
1 CACACACACCTTGCA
5244381 CACACACACCTTGCA
1 CACACACACCTTGCA
5244396 CACACA
1 CACACA
5244402 GGTGCTCGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.36, C:0.47, G:0.06, T:0.11
Consensus pattern (15 bp):
CACACACACCTTGCA
Found at i:5245288 original size:27 final size:26
Alignment explanation
Indices: 5245258--5245311 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
5245248 CTTAAGAAAC
* *
5245258 TAATTCCAAACCCTAACCTTCAAACAT
1 TAATTCCAAACCCAAACCCT-AAACAT
* *
5245285 TAATTTCTAACCCAAACCCTAAACAT
1 TAATTCCAAACCCAAACCCTAAACAT
5245311 T
1 T
5245312 GATTTAACCA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.41, C:0.31, G:0.00, T:0.28
Consensus pattern (26 bp):
TAATTCCAAACCCAAACCCTAAACAT
Found at i:5255290 original size:14 final size:14
Alignment explanation
Indices: 5255271--5255298 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5255261 TCTCTTTTTT
5255271 CTTCAAATCATTTG
1 CTTCAAATCATTTG
5255285 CTTCAAATCATTTG
1 CTTCAAATCATTTG
5255299 TTTTTATCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.21, G:0.07, T:0.43
Consensus pattern (14 bp):
CTTCAAATCATTTG
Found at i:5256942 original size:22 final size:22
Alignment explanation
Indices: 5256917--5256959 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
5256907 AATTAATAAA
*
5256917 AAAAGTAAAATTAT-TAAATATT
1 AAAA-TAAAATAATATAAATATT
*
5256939 AAAATAATATAATATAAATAT
1 AAAATAAAATAATATAAATAT
5256960 ATTTTTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
AAAATAAAATAATATAAATATT
Found at i:5257118 original size:32 final size:32
Alignment explanation
Indices: 5257077--5257145 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
5257067 TCGGGTTGAG
5257077 CTTAGACAAGCATAAAGTATGTTAATACCATA
1 CTTAGACAAGCATAAAGTATGTTAATACCATA
* * *
5257109 CTTAGACAAGCATTAAGTATGTTAATATCATG
1 CTTAGACAAGCATAAAGTATGTTAATACCATA
5257141 CTTAG
1 CTTAG
5257146 GTCTAACCCA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.32
Consensus pattern (32 bp):
CTTAGACAAGCATAAAGTATGTTAATACCATA
Found at i:5260447 original size:18 final size:18
Alignment explanation
Indices: 5260411--5260455 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
5260401 AATTATAATC
5260411 TTTTA-ATAA-AATAAAT
1 TTTTATATAATAATAAAT
* *
5260427 TTTTATTTAATAATAATT
1 TTTTATATAATAATAAAT
5260445 TTTTATATAAT
1 TTTTATATAAT
5260456 GTTTATAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 5 0.21
17 3 0.12
18 16 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTTATATAATAATAAAT
Found at i:5260705 original size:37 final size:37
Alignment explanation
Indices: 5260659--5260733 Score: 107
Period size: 37 Copynumber: 2.0 Consensus size: 37
5260649 AAATTTTAAT
**
5260659 TAATTTTTT-AAAATTTTAAAAATTCAAAAAAAAATTA
1 TAATTTTTTAAAAAAATTAAAAATT-AAAAAAAAATTA
*
5260696 TAATTTTTTAAAAAAATTAAAAATTATAAAAAAATTA
1 TAATTTTTTAAAAAAATTAAAAATTAAAAAAAAATTA
5260733 T
1 T
5260734 CTTTTTAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 21 0.62
38 13 0.38
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (37 bp):
TAATTTTTTAAAAAAATTAAAAATTAAAAAAAAATTA
Found at i:5260708 original size:18 final size:19
Alignment explanation
Indices: 5260685--5260733 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
5260675 TAAAAATTCA
* *
5260685 AAAAAAAATTATAATTTTT
1 AAAAAAAATTATAAATTAT
* *
5260704 TAAAAAAATTAAAAATTAT
1 AAAAAAAATTATAAATTAT
5260723 -AAAAAAATTAT
1 AAAAAAAATTAT
5260734 CTTTTTAATA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAAAAAATTATAAATTAT
Found at i:5260708 original size:19 final size:19
Alignment explanation
Indices: 5260686--5260733 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
5260676 AAAAATTCAA
** *
5260686 AAAAAAATTATAATTTTTT
1 AAAAAAATTATAAAATTAT
5260705 AAAAAAATTA-AAAATTAT
1 AAAAAAATTATAAAATTAT
5260723 AAAAAAATTAT
1 AAAAAAATTAT
5260734 CTTTTTAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 15 0.60
19 10 0.40
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAAAAATTATAAAATTAT
Found at i:5264062 original size:26 final size:28
Alignment explanation
Indices: 5263996--5264062 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 28
5263986 TATACAAAAT
5263996 TTTTATTGAATTATATATATAAATTTTCA
1 TTTTATT-AATTATATATATAAATTTTCA
5264025 TTTTATATAATT-T-TATA-AAAGTTTT-A
1 TTTTAT-TAATTATATATATAAA-TTTTCA
5264051 TTTTATTCAATT
1 TTTTATT-AATT
5264063 CTCATATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
25 1 0.03
26 14 0.40
27 8 0.23
28 1 0.03
29 10 0.29
30 1 0.03
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (28 bp):
TTTTATTAATTATATATATAAATTTTCA
Found at i:5264088 original size:12 final size:12
Alignment explanation
Indices: 5264071--5264099 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
5264061 TTCTCATATT
5264071 TTATTAATATAA
1 TTATTAATATAA
5264083 TTATTAATATAA
1 TTATTAATATAA
5264095 -TATTA
1 TTATTA
5264100 TTTTATATTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTATTAATATAA
Found at i:5266078 original size:29 final size:29
Alignment explanation
Indices: 5266046--5266147 Score: 82
Period size: 30 Copynumber: 3.5 Consensus size: 29
5266036 TTCGGGGGCA
* *
5266046 AAAATGTAATTTTGGGAAAATTTGAGGTT
1 AAAATGGAATTTTGGGAAAATTAGAGGTT
* ** * *
5266075 AAAAATGGGATTTT-GGAAGGTTCGAGGGT
1 -AAAATGGAATTTTGGGAAAATTAGAGGTT
* *
5266104 AAAATGGTAATTTTTGGTAAAATCAG-GGTT
1 AAAATGG-AA-TTTTGGGAAAATTAGAGGTT
5266134 AAAATGGAATTTTG
1 AAAATGGAATTTTG
5266148 AAAAGTTCGG
Statistics
Matches: 56, Mismatches: 13, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
28 12 0.21
29 14 0.25
30 25 0.45
31 5 0.09
ACGTcount: A:0.36, C:0.02, G:0.27, T:0.34
Consensus pattern (29 bp):
AAAATGGAATTTTGGGAAAATTAGAGGTT
Found at i:5266114 original size:59 final size:59
Alignment explanation
Indices: 5266036--5266401 Score: 420
Period size: 59 Copynumber: 6.2 Consensus size: 59
5266026 ACTTTTGACT
* * * * *
5266036 TTCGGGGGCAAAAAT-GTAA-TTTTGG-GAAAATTTGAGGTTAAAAATGGGATTTTGGAAGG
1 TTCGGGGG-TAAAATGGTAATTTTTGGTG-AAA-TCGAGGTCAAAAATGGAATTTTGGAAAG
* * * *
5266095 TTCGAGGGTAAAATGGTAATTTTTGGTAAAATC-AGGGT-TAAAATGGAATTTTGAAAAG
1 TTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGA-GGTCAAAAATGGAATTTTGGAAAG
* * *
5266153 TTCGGGGGTAAAATAGTAGTTTTTGGTAAAATCGAGGTCAAAAATGGAATTTTGGAAAG
1 TTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAG
* * * * * *
5266212 TTCGGGGATAAAATGGTAATCTTTGGTGAAATCGGGGTTAGAAATGGAATTTTAGAAAG
1 TTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAG
* *
5266271 CTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATAGAATTTTGGAAAG
1 TTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAG
* * * *
5266330 TTCGAGGGTAAAATGGTAATTTTTGGTGAAATTTG-GGTCAAAGATGGGATTTTGGAAAG
1 TTCGGGGGTAAAATGGTAATTTTTGGTGAAA-TCGAGGTCAAAAATGGAATTTTGGAAAG
*
5266389 TTTGGGGGTAAAA
1 TTCGGGGGTAAAA
5266402 ACATAATTTT
Statistics
Matches: 262, Mismatches: 38, Indels: 14
0.83 0.12 0.04
Matches are distributed among these distances:
58 55 0.21
59 196 0.75
60 11 0.04
ACGTcount: A:0.34, C:0.04, G:0.30, T:0.31
Consensus pattern (59 bp):
TTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAG
Found at i:5266161 original size:29 final size:27
Alignment explanation
Indices: 5266071--5266293 Score: 96
Period size: 30 Copynumber: 7.6 Consensus size: 27
5266061 GAAAATTTGA
* * *
5266071 GGTTAAAAATGGGATTTTGGAAGGTTCGAG
1 GGTT-AAAATGGAATTTTGAAAAG-TCG-G
*
5266101 GG-TAAAATGGTAATTTTTGGTAAAA-TCAG
1 GGTTAAAATGG-AA-TTTT-G-AAAAGTCGG
5266130 GGTTAAAATGGAATTTTGAAAAGTTCGG
1 GGTTAAAATGGAATTTTGAAAAG-TCGG
* * * *
5266158 GGGTAAAATAGTAGTTTTTGGTAAAA-TCGA
1 GGTTAAAAT-GGA-ATTTT-G-AAAAGTCGG
* *
5266188 GGTCAAAAATGGAATTTTGGAAAGTTCGG
1 GGT-TAAAATGGAATTTTGAAAAG-TCGG
* *
5266217 GGATAAAATGGTAATCTTTGGTGAAA-TCGG
1 GGTTAAAATGG-AAT-TTT-G-AAAAGTCGG
5266247 GGTTAGAAATGGAATTTT-AGAAAGCTCGG
1 GGTTA-AAATGGAATTTTGA-AAAG-TCGG
*
5266276 GGGTAAAATGGTAATTTT
1 GGTTAAAATGG-AATTTT
5266294 TGGTGAAATC
Statistics
Matches: 150, Mismatches: 20, Indels: 47
0.69 0.09 0.22
Matches are distributed among these distances:
26 4 0.03
27 7 0.05
28 36 0.24
29 38 0.25
30 41 0.27
31 14 0.09
32 10 0.07
ACGTcount: A:0.35, C:0.04, G:0.30, T:0.31
Consensus pattern (27 bp):
GGTTAAAATGGAATTTTGAAAAGTCGG
Found at i:5266409 original size:118 final size:116
Alignment explanation
Indices: 5266036--5266462 Score: 472
Period size: 118 Copynumber: 3.6 Consensus size: 116
5266026 ACTTTTGACT
* * * * * *
5266036 TTCGGGGGCAAAAATGTAA-TTTTGGGAAAATTTGAGGTTAAAAATGGGATTTTGGAAGGTTCGA
1 TTCGGGGGTAAAAA-GTAATTTTTGGTAAAA-TCGAGGTCAAAAATGGAATTTTGGAAAGTTCGA
* *
5266100 GGGTAAAATGGTAATTTTTGGTAAAATCAGGGTTAAAATGGAATTTTGAAAAG
64 GGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAATGGAATTTTGGAAAG
*
5266153 TTCGGGGGTAAAATAGTAGTTTTTGGTAAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTCG-G
1 TTCGGGGGTAAAA-AGTAATTTTTGGTAAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTCGAG
* * *
5266217 GGATAAAATGGTAATCTTTGGTGAAATCGGGGTTAGAAATGGAATTTTAGAAAG
65 GG-TAAAATGGTAATTTTTGGTGAAATCAGGGTTA-AAATGGAATTTTGGAAAG
* * * *
5266271 CTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATAGAATTTTGGAAAGTTCGAG
1 TTCGGGGGTAAAA-AGTAATTTTTGGTAAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTCGAG
** * *
5266336 GGTAAAATGGTAATTTTTGGTGAAATTTGGGTCAAAGATGGGATTTTGGAAAG
65 GGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAA-ATGGAATTTTGGAAAG
* * *
5266389 TTTGGGGGTAAAAACATAATTTTT-G-AAAAGCTCGAAGGT-AAAAATGTAATTTTTGG-AAGTT
1 TTCGGGGGTAAAAA-GTAATTTTTGGTAAAA--TCG-AGGTCAAAAATGGAA-TTTTGGAAAG-T
5266450 TCG-GGGTCAAAAT
60 TCGAGGGT-AAAAT
5266463 ATAATTTCTG
Statistics
Matches: 267, Mismatches: 30, Indels: 24
0.83 0.09 0.07
Matches are distributed among these distances:
116 6 0.02
117 75 0.28
118 164 0.61
119 22 0.08
ACGTcount: A:0.35, C:0.05, G:0.29, T:0.31
Consensus pattern (116 bp):
TTCGGGGGTAAAAAGTAATTTTTGGTAAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTCGAGG
GTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAATGGAATTTTGGAAAG
Found at i:5268361 original size:17 final size:17
Alignment explanation
Indices: 5268335--5268396 Score: 81
Period size: 17 Copynumber: 3.6 Consensus size: 17
5268325 TTTAATATTG
* *
5268335 ATTTAAATTTTAATTAA
1 ATTTAAATTTAAAGTAA
*
5268352 ATTTAGATTTAAAGTAA
1 ATTTAAATTTAAAGTAA
5268369 ATTTAAATTTACAA-TAA
1 ATTTAAATTTA-AAGTAA
5268386 ATTTAAATTTA
1 ATTTAAATTTA
5268397 TTTAAACCCA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
17 38 0.95
18 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (17 bp):
ATTTAAATTTAAAGTAA
Found at i:5268375 original size:6 final size:6
Alignment explanation
Indices: 5268335--5268396 Score: 60
Period size: 6 Copynumber: 10.8 Consensus size: 6
5268325 TTTAATATTG
* * *
5268335 ATTTAA ATTTTA A-TTAA ATTTAG ATTTAA A-GTAA ATTTAA ATTTACA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTA-A
5268382 A--TAA ATTTAA ATTTA
1 ATTTAA ATTTAA ATTTA
5268397 TTTAAACCCA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
4 2 0.04
5 10 0.22
6 31 0.69
7 2 0.04
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (6 bp):
ATTTAA
Found at i:5270510 original size:19 final size:20
Alignment explanation
Indices: 5270486--5270536 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
5270476 ATATTATGTT
5270486 AAAAATAAT-AAATATGATC
1 AAAAATAATAAAATATGATC
* * *
5270505 AAAAATTATAAAATATTATT
1 AAAAATAATAAAATATGATC
5270525 AAAAATAA-AAAA
1 AAAAATAATAAAA
5270537 GAGAATTTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (20 bp):
AAAAATAATAAAATATGATC
Found at i:5271359 original size:6 final size:6
Alignment explanation
Indices: 5271338--5271372 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
5271328 TCCCATTTTT
*
5271338 TTTAAA TTTCAAA TTTAAA TTTAAA TTTACA TTTA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTA
5271373 TTTTATTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:5272372 original size:19 final size:19
Alignment explanation
Indices: 5272348--5272385 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5272338 CCAAACTCAA
5272348 AAATAAATTAAAAATAAAT
1 AAATAAATTAAAAATAAAT
* *
5272367 AAATAAATTTAAATTAAAT
1 AAATAAATTAAAAATAAAT
5272386 TTATTTGATT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
AAATAAATTAAAAATAAAT
Found at i:5273557 original size:49 final size:49
Alignment explanation
Indices: 5273433--5273868 Score: 322
Period size: 49 Copynumber: 8.9 Consensus size: 49
5273423 TCACCGCAAG
* * *
5273433 GATATGGAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTATCTCA-GAA
1 GATATGGAGGGAAAAGTTTAAGTCGCAACGGCGAACCTAGTA-C-CACGAA
* * * *
5273483 G-CAT-GAAGG-AAAGATTTAAGCCGCAATGGCGAATCC-AGTACCACGAA
1 GATATGGAGGGAAAAG-TTTAAGTCGCAACGGCGAA-CCTAGTACCACGAA
* *
5273530 GATATGGAGGGAAAAGTTTAAGTCGCAACGACGAACCTTA-TACCTCAGAA
1 GATATGGAGGGAAAAGTTTAAGTCGCAACGGCGAACC-TAGTACCAC-GAA
* * *
5273580 G--ATGAGATGGG-AAAGATTTAAGCCACAACGGTGAACCTAGTACCACGAA
1 GATATG-GA-GGGAAAAG-TTTAAGTCGCAACGGCGAACCTAGTACCACGAA
* ** * * * *
5273629 GATATTGAGGGAATGGTTTAAGTCGCAACAGTGAACCTTGTACCTCAGAA
1 GATATGGAGGGAAAAGTTTAAGTCGCAACGGCGAACCTAGTACCAC-GAA
* * * *
5273679 -ACATGAAGGG-AAAGATTTAAGTCGCAACGGCGAATCTAGCACCACGAA
1 GATATGGAGGGAAAAG-TTTAAGTCGCAACGGCGAACCTAGTACCACGAA
* * * * * *
5273727 GATACGGAGGGAAAGGTTTAAGTCGCAATGGCGAAACTTGTACCTCAGAA
1 GATATGGAGGGAAAAGTTTAAGTCGCAACGGCGAACCTAGTACCAC-GAA
* * * * *
5273777 G-CATGAAGGG-AAAGATTTAAGCCGCAACGACGAATCTAGTACCACGAA
1 GATATGGAGGGAAAAG-TTTAAGTCGCAACGGCGAACCTAGTACCACGAA
* * * *
5273825 GATATGGAGGGAAAGGTTTAAGTCGTAATGGCGAACCTTGTACC
1 GATATGGAGGGAAAAGTTTAAGTCGCAACGGCGAACCTAGTACC
5273869 TCAGAAACAT
Statistics
Matches: 299, Mismatches: 63, Indels: 49
0.73 0.15 0.12
Matches are distributed among these distances:
46 2 0.01
47 8 0.03
48 44 0.15
49 191 0.64
50 52 0.17
51 2 0.01
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.19
Consensus pattern (49 bp):
GATATGGAGGGAAAAGTTTAAGTCGCAACGGCGAACCTAGTACCACGAA
Found at i:5273738 original size:98 final size:98
Alignment explanation
Indices: 5273433--5273901 Score: 656
Period size: 98 Copynumber: 4.8 Consensus size: 98
5273423 TCACCGCAAG
* *
5273433 GATATGGAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTATCTCAGAAGCATGAA-GGAAAGA
1 GATATGGAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAGAAACATGAAGGGAAAGA
* *
5273497 TTTAAGCCGCAATGGCGAATCCAGTACCACGAA
66 TTTAAGCCGCAACGGCGAATCTAGTACCACGAA
* * * * *
5273530 GATATGGAGGGAAAAGTTTAAGTCGCAACGACGAACCTTATACCTCAG-AAGATGAGATGGGAAA
1 GATATGGAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAGAAACATGA-A-GGGAAA
* * *
5273594 GATTTAAGCCACAACGGTGAACCTAGTACCACGAA
64 GATTTAAGCCGCAACGGCGAATCTAGTACCACGAA
* * ** *
5273629 GATATTGAGGGAATGGTTTAAGTCGCAACAGTGAACCTTGTACCTCAGAAACATGAAGGGAAAGA
1 GATATGGAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAGAAACATGAAGGGAAAGA
* *
5273694 TTTAAGTCGCAACGGCGAATCTAGCACCACGAA
66 TTTAAGCCGCAACGGCGAATCTAGTACCACGAA
* * *
5273727 GATACGGAGGGAAAGGTTTAAGTCGCAATGGCGAAACTTGTACCTCAGAAGCATGAAGGGAAAGA
1 GATATGGAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAGAAACATGAAGGGAAAGA
*
5273792 TTTAAGCCGCAACGACGAATCTAGTACCACGAA
66 TTTAAGCCGCAACGGCGAATCTAGTACCACGAA
* *
5273825 GATATGGAGGGAAAGGTTTAAGTCGTAATGGCGAACCTTGTACCTCAGAAACATG-AGAGAAAGA
1 GATATGGAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAGAAACATGAAGGGAAAGA
* *
5273889 TTGAAGTCGCAAC
66 TTTAAGCCGCAAC
5273902 TGCAAGTCCG
Statistics
Matches: 325, Mismatches: 43, Indels: 8
0.86 0.11 0.02
Matches are distributed among these distances:
96 5 0.02
97 63 0.19
98 174 0.54
99 77 0.24
100 6 0.02
ACGTcount: A:0.36, C:0.17, G:0.27, T:0.19
Consensus pattern (98 bp):
GATATGGAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAGAAACATGAAGGGAAAGA
TTTAAGCCGCAACGGCGAATCTAGTACCACGAA
Found at i:5274055 original size:49 final size:49
Alignment explanation
Indices: 5273909--5274055 Score: 206
Period size: 48 Copynumber: 3.0 Consensus size: 49
5273899 AACTGCAAGT
5273909 CCGATACCATGAAGATTTGAAGGGAAAGGTTACGACCGCGATGGCGAAC
1 CCGATACCATGAAGATTTGAAGGGAAAGGTTACGACCGCGATGGCGAAC
* * * * *
5273958 CCGATGCCATAAAG-TTTGAAGGGAAAGATTACGACCACGATGGTGAAC
1 CCGATACCATGAAGATTTGAAGGGAAAGGTTACGACCGCGATGGCGAAC
* * **
5274006 CCGGTACCATGAAGATTTAAAGGGAAAGGTTACGACCGCGACAGCGAAC
1 CCGATACCATGAAGATTTGAAGGGAAAGGTTACGACCGCGATGGCGAAC
5274055 C
1 C
5274056 AGTACCTTAA
Statistics
Matches: 83, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
48 42 0.51
49 41 0.49
ACGTcount: A:0.34, C:0.21, G:0.29, T:0.16
Consensus pattern (49 bp):
CCGATACCATGAAGATTTGAAGGGAAAGGTTACGACCGCGATGGCGAAC
Found at i:5274093 original size:97 final size:97
Alignment explanation
Indices: 5273913--5274094 Score: 215
Period size: 97 Copynumber: 1.9 Consensus size: 97
5273903 GCAAGTCCGA
* ** * * ***
5273913 TACCATGAAGATTTGAAGGGAAAGGTTACGACCGCGATGGCGAACCCGATGCCATAAAGTTTGAA
1 TACCATGAAGATTTAAAGGGAAAGGTTACGACCGCGACAGCGAACCAGATACCATAAAACATGAA
* * *
5273978 GGGAAAGATTACGACCACGATGGTGAACCCGG
66 GAGAAAGATCACAACCACGATGGTGAACCCGG
*
5274010 TACCATGAAGATTTAAAGGGAAAGGTTACGACCGCGACAGCGAACCAG-TACCTTAAAAACATGA
1 TACCATGAAGATTTAAAGGGAAAGGTTACGACCGCGACAGCGAACCAGATACCAT-AAAACATGA
*
5274074 CGAGAAAGATCA-AACCCACGA
65 AGAGAAAGATCACAA-CCACGA
5274095 CGGTAAAACT
Statistics
Matches: 70, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
96 5 0.07
97 65 0.93
ACGTcount: A:0.37, C:0.21, G:0.26, T:0.16
Consensus pattern (97 bp):
TACCATGAAGATTTAAAGGGAAAGGTTACGACCGCGACAGCGAACCAGATACCATAAAACATGAA
GAGAAAGATCACAACCACGATGGTGAACCCGG
Found at i:5274396 original size:102 final size:102
Alignment explanation
Indices: 5274140--5275042 Score: 1208
Period size: 102 Copynumber: 9.0 Consensus size: 102
5274130 ATCAAAACTA
* *
5274140 AAATAGCAAGTCTTTATCTCTATGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATTC
1 AAATAGCAAGTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATCC
5274205 TATCCTCTTGAAGTTGCAGTAAAGTTGGATT----A-
66 TATCCTCTTGAAGTTGCAGTAAAGTTGGATTAAAAAC
* * * *
5274237 ATATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGAGGAAGCTTTAACGTCAAATCC
1 AAATAGCAAGTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATCC
* * *
5274302 TATCCTCTTGAAGTAGTAGTAAAGTTGGATTAAAAAT
66 TATCCTCTTGAAGTTGCAGTAAAGTTGGATTAAAAAC
** * * *
5274339 AAATAATAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAACTTCAACGTCAAATTC
1 AAATAGCAAGTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATCC
*
5274404 TATCCTCTTGAAGTTGCAGTAAAGTTAGATT----A-
66 TATCCTCTTGAAGTTGCAGTAAAGTTGGATTAAAAAC
*
5274436 AAATAGTAAGTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATCC
1 AAATAGCAAGTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATCC
* * *
5274501 TATCCTCTTGAAGTTGTATTAAAGTTCGATTAAAAAC
66 TATCCTCTTGAAGTTGCAGTAAAGTTGGATTAAAAAC
* **
5274538 AAATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAATATTCAACGTCAAATCC
1 AAATAGCAAGTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATCC
5274603 TATCCTCTTGAAGTTGCAGTAAAGTTGGATTAAAAAC
66 TATCCTCTTGAAGTTGCAGTAAAGTTGGATTAAAAAC
* *
5274640 AAATAGCAAGTCTTTATCTCTCTTAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATTC
1 AAATAGCAAGTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATCC
* * *
5274705 TATTCTCTTGAAGTTGCAATAAGGTTGGATT----A-
66 TATCCTCTTGAAGTTGCAGTAAAGTTGGATTAAAAAC
* *
5274737 AAATAGCAAGTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACATCAAATTC
1 AAATAGCAAGTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATCC
* * *
5274802 TATCCTCTTAAAGCTGCAATAAAGTTGGATTAAAAAC
66 TATCCTCTTGAAGTTGCAGTAAAGTTGGATTAAAAAC
* * * * * *
5274839 AAATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGTAAGATGAAGTTTTAACATCAAATCT
1 AAATAGCAAGTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATCC
* * *
5274904 TATCTTCCTGAAGTTGCAGTGAAGTTGGATTAAAAAC
66 TATCCTCTTGAAGTTGCAGTAAAGTTGGATTAAAAAC
* * * * * *
5274941 AAAAATAACAGGTCTTTATCTCTCTGAAGTTGCAATAAGTGCAAGATGAAGCTTTAACATCAAAT
1 --AAATAGCAAGTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAAT
* * * *
5275006 CCTATCTTCCTGAAGTTGCGGTGAAA-TTGGATCAAAA
64 CCTATCCTCTTGAAGTTGCAGT-AAAGTTGGATTAAAA
5275043 CCACAGTAGC
Statistics
Matches: 719, Mismatches: 69, Indels: 29
0.88 0.08 0.04
Matches are distributed among these distances:
97 267 0.37
98 2 0.00
101 3 0.00
102 359 0.50
104 86 0.12
105 2 0.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (102 bp):
AAATAGCAAGTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATCC
TATCCTCTTGAAGTTGCAGTAAAGTTGGATTAAAAAC
Found at i:5274449 original size:199 final size:201
Alignment explanation
Indices: 5274140--5275037 Score: 1195
Period size: 199 Copynumber: 4.5 Consensus size: 201
5274130 ATCAAAACTA
* *
5274140 AAATAGCAAGTCTTTATCTCTATGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATTC
1 AAATAACAAGTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATTC
* *
5274205 TATCCTCTTGAAGTTGCAGTAAAGTTGGATT-A-ATATAGCAAGTCTTTATCTCTCTGAAGTTGT
66 TATCCTCTTGAAGTTGCAGTAAAGTTGGATTAACAAATAGCAAGTCTTTATCTCTCTGAAGTTGC
* * * *
5274268 AGTAAGAGCAAGAGGAAGCTTTAACGTCAAATCCTATCCTCTTGAAGTAGTAGTAAAGTTGGATT
131 AGTAAGAGCAAGATGAAGCTTCAACGTCAAATCCTATCCTCTTGAAGTTGCAGTAAAGTTGGATT
*
5274333 AAAAAT
196 AAAAAC
* * *
5274339 AAATAATAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAACTTCAACGTCAAATTC
1 AAATAACAAGTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATTC
* *
5274404 TATCCTCTTGAAGTTGCAGTAAAGTTAGATT-A-AAATAGTAAGTCTTTATCTCTCTGAAGTTGC
66 TATCCTCTTGAAGTTGCAGTAAAGTTGGATTAACAAATAGCAAGTCTTTATCTCTCTGAAGTTGC
* * *
5274467 AGTAAGAGCAAGATGAAGCTTCAACGTCAAATCCTATCCTCTTGAAGTTGTATTAAAGTTCGATT
131 AGTAAGAGCAAGATGAAGCTTCAACGTCAAATCCTATCCTCTTGAAGTTGCAGTAAAGTTGGATT
5274532 AAAAAC
196 AAAAAC
* * ** *
5274538 AAATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAATATTCAACGTCAAATCC
1 AAATAACAAGTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATTC
*
5274603 TATCCTCTTGAAGTTGCAGTAAAGTTGGATTAAAAACAAATAGCAAGTCTTTATCTCTCTTAAGT
66 TATCCTCTTGAAGTTGCAGTAAAGTTGGATT---AACAAATAGCAAGTCTTTATCTCTCTGAAGT
* * * *
5274668 TGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATTCTATTCTCTTGAAGTTGCAATAAGGTTGG
128 TGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATCCTATCCTCTTGAAGTTGCAGTAAAGTTGG
5274733 ATT----A-
193 ATTAAAAAC
* *
5274737 AAATAGCAAGTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACATCAAATTC
1 AAATAACAAGTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATTC
* * *
5274802 TATCCTCTTAAAGCTGCAATAAAGTTGGATTAAAAACAAATAGCAAGTCTTTATCTCTCTGAAGT
66 TATCCTCTTGAAGTTGCAGTAAAGTTGGATT---AACAAATAGCAAGTCTTTATCTCTCTGAAGT
* * * * * * * * *
5274867 TGTAGTAAGAGTAAGATGAAGTTTTAACATCAAATCTTATCTTCCTGAAGTTGCAGTGAAGTTGG
128 TGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATCCTATCCTCTTGAAGTTGCAGTAAAGTTGG
5274932 ATTAAAAAC
193 ATTAAAAAC
* * * * *
5274941 AAAAATAACAGGTCTTTATCTCTCTGAAGTTGCAATAAGTGCAAGATGAAGCTTTAACATCAAAT
1 --AAATAACAAGTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAAT
* * * *
5275006 CCTATCTTCCTGAAGTTGCGGTGAAA-TTGGAT
64 TCTATCCTCTTGAAGTTGCAGT-AAAGTTGGAT
5275038 CAAAACCACA
Statistics
Matches: 623, Mismatches: 63, Indels: 19
0.88 0.09 0.03
Matches are distributed among these distances:
199 450 0.72
200 1 0.00
203 2 0.00
204 88 0.14
206 79 0.13
207 3 0.00
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.31
Consensus pattern (201 bp):
AAATAACAAGTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAATTC
TATCCTCTTGAAGTTGCAGTAAAGTTGGATTAACAAATAGCAAGTCTTTATCTCTCTGAAGTTGC
AGTAAGAGCAAGATGAAGCTTCAACGTCAAATCCTATCCTCTTGAAGTTGCAGTAAAGTTGGATT
AAAAAC
Found at i:5274653 original size:301 final size:300
Alignment explanation
Indices: 5274138--5275024 Score: 1334
Period size: 301 Copynumber: 3.0 Consensus size: 300
5274128 AGATCAAAAC
*
5274138 TAAAATAGCAAGTCTTTATCTCTATGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAAT
1 TAAAATAGCAAGTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAAT
* *
5274203 TCTATCCTCTTGAAGTTGCAGTAAAGTTGGATT----A-ATATAGCAAGTCTTTATCTCTCTGAA
66 TCTATCCTCTTGAAGTTGCAATAAAGTTGGATTAAAAACAAATAGCAAGTCTTTATCTCTCTGAA
* * * *
5274263 GTTGTAGTAAGAGCAAGAGGAAGCTTTAACGTCAAATCCTATCCTCTTGAAGTAGTAGTAAAGTT
131 GTTGTAGTAAGAGCAAGATGAA-TTTTAACGTCAAATCCTATCCTCTTGAAGTTGCAGTAAAGTT
* * * *
5274328 GGATTAAAAATAAATAATAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAACTTCA
195 GGATTAAAAACAAATAACAAGTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCA
*
5274393 ACGTCAAATTCTATCCTCTTGAAGTTGCAGTAAAGTTAGAT
260 ACGTCAAATTCTATCCTCTTGAAGTTGCAATAAAGTTAGAT
*
5274434 TAAAATAGTAAGTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAAT
1 TAAAATAGCAAGTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAAT
* * * *
5274499 CCTATCCTCTTGAAGTTGTATTAAAGTTCGATTAAAAACAAATAGCAAGTCTTTATCTCTCTGAA
66 TCTATCCTCTTGAAGTTGCAATAAAGTTGGATTAAAAACAAATAGCAAGTCTTTATCTCTCTGAA
*
5274564 GTTGTAGTAAGAGCAAGATGAATATTCAACGTCAAATCCTATCCTCTTGAAGTTGCAGTAAAGTT
131 GTTGTAGTAAGAGCAAGATGAAT-TTTAACGTCAAATCCTATCCTCTTGAAGTTGCAGTAAAGTT
* *
5274629 GGATTAAAAACAAATAGCAAGTCTTTATCTCTCTTAAGTTGCAGTAAGAGCAAGATGAAGCTTCA
195 GGATTAAAAACAAATAACAAGTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCA
* * *
5274694 ACGTCAAATTCTATTCTCTTGAAGTTGCAATAAGGTTGGAT
260 ACGTCAAATTCTATCCTCTTGAAGTTGCAATAAAGTTAGAT
*
5274735 TAAAATAGCAAGTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACATCAAAT
1 TAAAATAGCAAGTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAAT
* *
5274800 TCTATCCTCTTAAAGCTGCAATAAAGTTGGATTAAAAACAAATAGCAAGTCTTTATCTCTCTGAA
66 TCTATCCTCTTGAAGTTGCAATAAAGTTGGATTAAAAACAAATAGCAAGTCTTTATCTCTCTGAA
* * * * * *
5274865 GTTGTAGTAAGAGTAAGATGAAGTTTTAACATCAAATCTTATCTTCCTGAAGTTGCAGTGAAGTT
131 GTTGTAGTAAGAGCAAGATGAA-TTTTAACGTCAAATCCTATCCTCTTGAAGTTGCAGTAAAGTT
* * *
5274930 GGATTAAAAACAAAAATAACAGGTCTTTATCTCTCTGAAGTTGCAATAAGTGCAAGATGAAGCTT
195 GGATTAAAAAC--AAATAACAAGTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTT
* * * * *
5274995 TAACATCAAATCCTATCTTCCTGAAGTTGC
258 CAACGTCAAATTCTATCCTCTTGAAGTTGC
5275025 GGTGAAATTG
Statistics
Matches: 534, Mismatches: 48, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
296 92 0.17
300 1 0.00
301 369 0.69
302 1 0.00
303 71 0.13
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (300 bp):
TAAAATAGCAAGTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAACGTCAAAT
TCTATCCTCTTGAAGTTGCAATAAAGTTGGATTAAAAACAAATAGCAAGTCTTTATCTCTCTGAA
GTTGTAGTAAGAGCAAGATGAATTTTAACGTCAAATCCTATCCTCTTGAAGTTGCAGTAAAGTTG
GATTAAAAACAAATAACAAGTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTCAA
CGTCAAATTCTATCCTCTTGAAGTTGCAATAAAGTTAGAT
Found at i:5277153 original size:20 final size:19
Alignment explanation
Indices: 5277128--5277173 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
5277118 ACTATAGGCC
* *
5277128 AAATAGTAATGTGGTGGTTG
1 AAATAG-AATATGGTAGTTG
*
5277148 AAATAGAGTATGGTAGTTG
1 AAATAGAATATGGTAGTTG
5277167 AAATAGA
1 AAATAGA
5277174 GCAAGTGGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.39, C:0.00, G:0.30, T:0.30
Consensus pattern (19 bp):
AAATAGAATATGGTAGTTG
Found at i:5278108 original size:21 final size:23
Alignment explanation
Indices: 5278046--5278114 Score: 61
Period size: 24 Copynumber: 3.0 Consensus size: 23
5278036 CATTAAATTG
* * * *
5278046 ATAAAATTATATATTTTAACTCTC
1 ATAAAA-TAAATAATTTAACTTTT
5278070 ATAAAAATAAATAATTTAA-TTTT
1 AT-AAAATAAATAATTTAACTTTT
*
5278093 ATAAAA-AAATATTTTAACTTTT
1 ATAAAATAAATAATTTAACTTTT
5278115 CCCTTAAAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
21 10 0.26
22 8 0.21
23 4 0.11
24 12 0.32
25 4 0.11
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (23 bp):
ATAAAATAAATAATTTAACTTTT
Found at i:5280514 original size:28 final size:29
Alignment explanation
Indices: 5280452--5280531 Score: 126
Period size: 28 Copynumber: 2.8 Consensus size: 29
5280442 ACAAAATACT
* *
5280452 AACATAAGTGACTAAAACGTAACATTTCA
1 AACATAAGTGTCTAAAATGTAACATTTCA
*
5280481 AGCATAAGTGTCT-AAATGTAACATTTCA
1 AACATAAGTGTCTAAAATGTAACATTTCA
5280509 AACATAAGTGTCTAAAATGTAAC
1 AACATAAGTGTCTAAAATGTAAC
5280532 TTGAAATAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
28 26 0.57
29 20 0.43
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (29 bp):
AACATAAGTGTCTAAAATGTAACATTTCA
Found at i:5286558 original size:25 final size:27
Alignment explanation
Indices: 5286507--5286560 Score: 69
Period size: 25 Copynumber: 2.1 Consensus size: 27
5286497 AGTTTATATA
*
5286507 TAATATACACAAATAATTATATTTATT
1 TAATATACACAAATAATTATATGTATT
5286534 TAATATA-A-AAATAATT-TGATGTATT
1 TAATATACACAAATAATTAT-ATGTATT
5286559 TA
1 TA
5286561 TTTTTTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 1 0.04
25 16 0.64
26 1 0.04
27 7 0.28
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (27 bp):
TAATATACACAAATAATTATATGTATT
Found at i:5306595 original size:23 final size:23
Alignment explanation
Indices: 5306565--5306610 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
5306555 TGAAGAGTGA
5306565 GTGAAGGCCTCATTTATAGGCAG
1 GTGAAGGCCTCATTTATAGGCAG
5306588 GTGAAGGCCTCATTTATAGGCAG
1 GTGAAGGCCTCATTTATAGGCAG
5306611 AGACCCGCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.26
Consensus pattern (23 bp):
GTGAAGGCCTCATTTATAGGCAG
Found at i:5308250 original size:60 final size:60
Alignment explanation
Indices: 5308157--5308273 Score: 162
Period size: 60 Copynumber: 1.9 Consensus size: 60
5308147 ATTGAATTGG
* * * *
5308157 ACAAAAAAAAAAACTATATACCAAATTAAGAAAAAGTGTTAAATTCAGTTACCAAATTAA
1 ACAAAAAAAAAAACTAAATACCAAATCAAGAAAAAATATTAAATTCAGTTACCAAATTAA
** * *
5308217 ACAAAAAAAAAATTTAAATACCTAATCAAGAAAAAATATTAAATTCAGTTATCAAAT
1 ACAAAAAAAAAAACTAAATACCAAATCAAGAAAAAATATTAAATTCAGTTACCAAAT
5308274 GTTAATTTAA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.59, C:0.11, G:0.05, T:0.25
Consensus pattern (60 bp):
ACAAAAAAAAAAACTAAATACCAAATCAAGAAAAAATATTAAATTCAGTTACCAAATTAA
Found at i:5311520 original size:15 final size:16
Alignment explanation
Indices: 5311495--5311528 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
5311485 AAAATTTAAT
5311495 TTTATTATTTTAATAA
1 TTTATTATTTTAATAA
*
5311511 TTTA-TATTTTTATAA
1 TTTATTATTTTAATAA
5311526 TTT
1 TTT
5311529 TTAAATGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTATTATTTTAATAA
Found at i:5319205 original size:59 final size:62
Alignment explanation
Indices: 5319107--5319229 Score: 180
Period size: 60 Copynumber: 2.0 Consensus size: 62
5319097 TTGATGCTTG
* * * * *
5319107 AACTTGACATTTTTTTCTTAATTTGGTATCTAAA-TTTTTTTTT-ACTCAATTTGGTATTTA
1 AACTTGACAATTATTTCTTAATTTGGTACCTAAACTTTTTTTTTGACACAATTTGGTATCTA
5319167 AACTTGACAATTATTTC-TAATTTGGTACCTAAACTTTTTTTTTGACACAATTTGGTATCTA
1 AACTTGACAATTATTTCTTAATTTGGTACCTAAACTTTTTTTTTGACACAATTTGGTATCTA
5319228 AA
1 AA
5319230 TTTATTAAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
59 15 0.27
60 24 0.43
61 17 0.30
ACGTcount: A:0.28, C:0.12, G:0.09, T:0.50
Consensus pattern (62 bp):
AACTTGACAATTATTTCTTAATTTGGTACCTAAACTTTTTTTTTGACACAATTTGGTATCTA
Found at i:5319466 original size:31 final size:31
Alignment explanation
Indices: 5319431--5319510 Score: 124
Period size: 31 Copynumber: 2.6 Consensus size: 31
5319421 GGACCCTAAA
* *
5319431 AAGTTTAAGTACCAACTTAAAAAAAAATGTC
1 AAGTTTAAGTACCAAATTAAAAAAAAATATC
* *
5319462 AAGTTTAGGTACCAAATTAAGAAAAAATATC
1 AAGTTTAAGTACCAAATTAAAAAAAAATATC
5319493 AAGTTTAAGTACCAAATT
1 AAGTTTAAGTACCAAATT
5319511 GAATCCAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.28
Consensus pattern (31 bp):
AAGTTTAAGTACCAAATTAAAAAAAAATATC
Found at i:5330782 original size:23 final size:23
Alignment explanation
Indices: 5330752--5330830 Score: 104
Period size: 23 Copynumber: 3.4 Consensus size: 23
5330742 GAACGCTAGC
*
5330752 GTGCTTACTATTTCGCACTTTGT
1 GTGCTTACTATTTCGCACTTCGT
*
5330775 GTGCTTACTATTTTGCACTTCGT
1 GTGCTTACTATTTCGCACTTCGT
* * *
5330798 GTTCTTACTGTTTCGCACCTCGT
1 GTGCTTACTATTTCGCACTTCGT
*
5330821 GTGCCTACTA
1 GTGCTTACTA
5330831 ATTTGCGCTA
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.13, C:0.25, G:0.18, T:0.44
Consensus pattern (23 bp):
GTGCTTACTATTTCGCACTTCGT
Found at i:5330888 original size:21 final size:21
Alignment explanation
Indices: 5330820--5330888 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
5330810 TCGCACCTCG
* *
5330820 TGTGCCTACTAATTTGCGC-TA
1 TGTGCCTACTGA-TTGCACGTA
*
5330841 TGTGCGCCTACTGATTGCACGTG
1 TGT--GCCTACTGATTGCACGTA
*
5330864 TGTGCCTACTGGATTGTAC-TA
1 TGTGCCTACT-GATTGCACGTA
5330885 TGTG
1 TGTG
5330889 TGCTTATTGT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
21 15 0.38
22 12 0.31
23 12 0.31
ACGTcount: A:0.16, C:0.22, G:0.26, T:0.36
Consensus pattern (21 bp):
TGTGCCTACTGATTGCACGTA
Found at i:5330888 original size:23 final size:22
Alignment explanation
Indices: 5330819--5330891 Score: 76
Period size: 23 Copynumber: 3.3 Consensus size: 22
5330809 TTCGCACCTC
* *
5330819 GTGTGCCTACTAATTTGCGCTAT
1 GTGTGCCTACTGA-TTGCACTAT
* *
5330842 GTGCGCCTACTGATTGCAC-GT
1 GTGTGCCTACTGATTGCACTAT
*
5330863 GTGTGCCTACTGGATTGTACTAT
1 GTGTGCCTACT-GATTGCACTAT
5330886 GTGTGC
1 GTGTGC
5330892 TTATTGTTTC
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
21 11 0.27
22 12 0.29
23 18 0.44
ACGTcount: A:0.15, C:0.22, G:0.27, T:0.36
Consensus pattern (22 bp):
GTGTGCCTACTGATTGCACTAT
Found at i:5332114 original size:188 final size:187
Alignment explanation
Indices: 5331759--5332116 Score: 583
Period size: 188 Copynumber: 1.9 Consensus size: 187
5331749 GTGGATACTG
5331759 TCAAGTAGGCGACACCACCCCTAATTTCTGCCATGTGTCAGATAAAAATTAAAAAAATAATATTT
1 TCAAGTAGGCGACACCACCCCTAATTTCTGCCATGTGTCAGATAAAAATTAAAAAAATAATATTT
* * * *
5331824 TAATGGATGGAGGTTGTCAGATAGGCAGCACTCATTTTTTATACGGGTCATATACGAGGTATAAT
66 TAATGGATGGAGGCTGCCAGATAGACAGCACCCATTTTTTATACGGGTCATATACGAGGTATAAT
*
5331889 ACAAAAAATTGTACTTTTTTGTGGAGGCTATCTGACAGGCACCACAGGTGGTAGCTA
131 ACAAAAAATTGTACTTTGTTGTGGAGGCTATCTGACAGGCACCACAGGTGGTAGCTA
*
5331946 TCAAGTAGGCGACACCACCCCTAATTTTTGCCATGTGTCAGATAAAAATTAAAAAAAATAATATT
1 TCAAGTAGGCGACACCACCCCTAATTTCTGCCATGTGTCAGATAAAAATT-AAAAAAATAATATT
* * * *
5332011 TTAATGGGTGGAGGCTGCCAGATAGACGGCACCCATTTTTTTATATGGGTCATATACGGGGTATA
65 TTAATGGATGGAGGCTGCCAGATAGACAGCACCCA-TTTTTTATACGGGTCATATACGAGGTATA
**
5332076 ATACCGAAAATTGTAC-TTGTTGTGGAGGCTATCTGACAGGC
129 ATACAAAAAATTGTACTTTGTTGTGGAGGCTATCTGACAGGC
5332117 GGCACCTAGG
Statistics
Matches: 157, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
187 49 0.31
188 67 0.43
189 41 0.26
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (187 bp):
TCAAGTAGGCGACACCACCCCTAATTTCTGCCATGTGTCAGATAAAAATTAAAAAAATAATATTT
TAATGGATGGAGGCTGCCAGATAGACAGCACCCATTTTTTATACGGGTCATATACGAGGTATAAT
ACAAAAAATTGTACTTTGTTGTGGAGGCTATCTGACAGGCACCACAGGTGGTAGCTA
Found at i:5332749 original size:39 final size:39
Alignment explanation
Indices: 5332671--5333000 Score: 344
Period size: 39 Copynumber: 8.4 Consensus size: 39
5332661 AGTTGTGCGA
* *
5332671 TGTTTACAGTGTCACTGCCTAA-TCA-TAATAATATTGCAG
1 TGTTTACAGTGTCACTGCC-AATTCAGT-ATAGTATCGCAG
* * * *
5332710 TGGTCACAGTGTCACTGTCAGA-TCAGTGTAGTATCGCAG
1 TGTTTACAGTGTCACTGCCA-ATTCAGTATAGTATCGCAG
* * ** *
5332749 TGTTTACAGTGTCATTGTCAATTCAGTATAGCGTCACAG
1 TGTTTACAGTGTCACTGCCAATTCAGTATAGTATCGCAG
* * *
5332788 TGTTTACAGTGTCACTGCCCATTTCAGTATAGCATTGCAG
1 TGTTTACAGTGTCACTG-CCAATTCAGTATAGTATCGCAG
* *
5332828 TGTTTACAGTGTCACTGCCAATTCAGTATTGTATCGTAG
1 TGTTTACAGTGTCACTGCCAATTCAGTATAGTATCGCAG
* *
5332867 TGTTTACAGTGTCACTACCAATTCAGTATAGTGTCGCAG
1 TGTTTACAGTGTCACTGCCAATTCAGTATAGTATCGCAG
* * *
5332906 TGTTTACAGTGTCACTGCCAATTCAGTATAGTGTTGTAG
1 TGTTTACAGTGTCACTGCCAATTCAGTATAGTATCGCAG
* * * * *
5332945 TGTTTACAATATCACTGCCAATTCAATATAGCTA-CACGG
1 TGTTTACAGTGTCACTGCCAATTCAGTATAG-TATCGCAG
*
5332984 TGTTTACAATGTCACTG
1 TGTTTACAGTGTCACTG
5333001 TCAGCTCAAT
Statistics
Matches: 246, Mismatches: 40, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
38 2 0.01
39 208 0.85
40 36 0.15
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (39 bp):
TGTTTACAGTGTCACTGCCAATTCAGTATAGTATCGCAG
Found at i:5332947 original size:157 final size:156
Alignment explanation
Indices: 5332671--5332976 Score: 375
Period size: 157 Copynumber: 2.0 Consensus size: 156
5332661 AGTTGTGCGA
* **
5332671 TGTTTACAGTGTCACTGCCTAATCATAATAATATTGCAGTGGTCACAGTGTCACTGTCAGATCAG
1 TGTTTACAGTGTCACTGCCTAATCATAATAATATCGCAGTGGTCACAGTGTCACTACCAGATCAG
* * * * *
5332736 TGTAGTATCGCAGTGTTTACAGTGTCATTGTCAATTCAGTATAGCGTCACAGTGTTTACAGTGTC
66 TATAGTATCGCAGTGTTTACAGTGTCACTGCCAATTCAGTATAGCGTCACAGTGTTTACAATATC
* *
5332801 ACTGCCCATTTCAGTATAGCATTGCAG
131 ACTG-CCAATTCAATATAGCATTGCAG
** * * *
5332828 TGTTTACAGTGTCACTGCC-AATTCAGT-ATTGTATCGTAGTGTTTACAGTGTCACTACCA-ATT
1 TGTTTACAGTGTCACTGCCTAA-TCA-TAATAATATCGCAGTGGTCACAGTGTCACTACCAGA-T
* * ***
5332890 CAGTATAGTGTCGCAGTGTTTACAGTGTCACTGCCAATTCAGTATAGTGTTGTAGTGTTTACAAT
63 CAGTATAGTATCGCAGTGTTTACAGTGTCACTGCCAATTCAGTATAGCGTCACAGTGTTTACAAT
5332955 ATCACTGCCAATTCAATATAGC
128 ATCACTGCCAATTCAATATAGC
5332977 TACACGGTGT
Statistics
Matches: 126, Mismatches: 20, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
156 16 0.13
157 109 0.87
158 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (156 bp):
TGTTTACAGTGTCACTGCCTAATCATAATAATATCGCAGTGGTCACAGTGTCACTACCAGATCAG
TATAGTATCGCAGTGTTTACAGTGTCACTGCCAATTCAGTATAGCGTCACAGTGTTTACAATATC
ACTGCCAATTCAATATAGCATTGCAG
Found at i:5335411 original size:6 final size:6
Alignment explanation
Indices: 5335402--5335428 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5335392 ATCAAAATTA
5335402 AAAGTG AAAGTG AAAGTG AAAGTG AAA
1 AAAGTG AAAGTG AAAGTG AAAGTG AAA
5335429 TTAGAATTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.30, T:0.15
Consensus pattern (6 bp):
AAAGTG
Found at i:5336754 original size:13 final size:13
Alignment explanation
Indices: 5336723--5336760 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
5336713 TTGTTTAACT
*
5336723 AAATAAAATAAA-
1 AAATAAAAAAAAC
5336735 AAA-AAAAAAAAC
1 AAATAAAAAAAAC
5336747 AAATAAAAAAAAC
1 AAATAAAAAAAAC
5336760 A
1 A
5336761 CCAATGAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 7 0.30
12 6 0.26
13 10 0.43
ACGTcount: A:0.87, C:0.05, G:0.00, T:0.08
Consensus pattern (13 bp):
AAATAAAAAAAAC
Found at i:5337279 original size:27 final size:27
Alignment explanation
Indices: 5337241--5337294 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
5337231 TATTAAAAAT
*
5337241 TTGGTGTCGCCTGTCAGGTAGGCACCA
1 TTGGTGTCGCCTATCAGGTAGGCACCA
*
5337268 TTGGTG-CAGCCTATTAGGTAGGCACCA
1 TTGGTGTC-GCCTATCAGGTAGGCACCA
5337295 CCCTCGTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 1 0.04
27 23 0.96
ACGTcount: A:0.19, C:0.24, G:0.31, T:0.26
Consensus pattern (27 bp):
TTGGTGTCGCCTATCAGGTAGGCACCA
Found at i:5350728 original size:27 final size:27
Alignment explanation
Indices: 5350687--5350754 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 27
5350677 ATATTTGGAG
* *
5350687 ATATT-TTTCATTAAT-TAATTAGTTAA
1 ATATTATTTTATTAATAT-ATTACTTAA
*
5350713 ATATTATTTTATTAATATTTTACTTAA
1 ATATTATTTTATTAATATATTACTTAA
5350740 ATATTTATTATTATT
1 ATA-TTATT-TTATT
5350755 TTATTTAGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 5 0.14
27 19 0.54
28 6 0.17
29 5 0.14
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (27 bp):
ATATTATTTTATTAATATATTACTTAA
Found at i:5350744 original size:13 final size:11
Alignment explanation
Indices: 5350717--5350759 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
5350707 AGTTAAATAT
5350717 TATTTTATTAA
1 TATTTTATTAA
5350728 TATTTTACTTAA
1 TATTTTA-TTAA
*
5350740 -ATATTTATTAT
1 TAT-TTTATTAA
5350751 TATTTTATT
1 TATTTTATT
5350760 TAGAAAATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
11 18 0.64
12 10 0.36
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:5354559 original size:35 final size:34
Alignment explanation
Indices: 5354499--5354569 Score: 99
Period size: 35 Copynumber: 2.1 Consensus size: 34
5354489 TAAAAAAATA
*
5354499 TTTATTTACTAAATAATATACAAAAATTATTTAT
1 TTTATTTACTAAATAATATACAAAAATTATTAAT
*
5354533 TTTATTTGACTAAAGTAATAT-TAAAAATTATTAAT
1 TTTATTT-ACTAAA-TAATATACAAAAATTATTAAT
5354568 TT
1 TT
5354570 AATAAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
34 7 0.21
35 20 0.61
36 6 0.18
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (34 bp):
TTTATTTACTAAATAATATACAAAAATTATTAAT
Found at i:5355396 original size:24 final size:24
Alignment explanation
Indices: 5355369--5355415 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
5355359 TGTGGAACTT
5355369 GTAGAAAATGAAGATCCAACTCCA
1 GTAGAAAATGAAGATCCAACTCCA
*
5355393 GTAGAAAATGAAGATTCAACTCC
1 GTAGAAAATGAAGATCCAACTCC
5355416 GTGTATGGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.45, C:0.19, G:0.17, T:0.19
Consensus pattern (24 bp):
GTAGAAAATGAAGATCCAACTCCA
Found at i:5357861 original size:7 final size:7
Alignment explanation
Indices: 5357838--5357888 Score: 59
Period size: 7 Copynumber: 7.1 Consensus size: 7
5357828 TTGTTTTCAA
5357838 TTTAAGG
1 TTTAAGG
5357845 TTTATA-G
1 TTTA-AGG
*
5357852 TTTAGGG
1 TTTAAGG
*
5357859 TTTAGGG
1 TTTAAGG
5357866 TTTAAGG
1 TTTAAGG
5357873 TTTAAGG
1 TTTAAGG
5357880 TTTATAGG
1 TTTA-AGG
5357888 T
1 T
5357889 ATGAAACTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
7 34 0.87
8 5 0.13
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.47
Consensus pattern (7 bp):
TTTAAGG
Found at i:5358340 original size:6 final size:6
Alignment explanation
Indices: 5358303--5358366 Score: 56
Period size: 6 Copynumber: 10.7 Consensus size: 6
5358293 CATCCAATGC
* * * * * *
5358303 CTCTTC CTCTTC CTCTTC CTCTTG CCCTTG CTCTTG CTCTGG CTCTAG
1 CTCTTG CTCTTG CTCTTG CTCTTG CTCTTG CTCTTG CTCTTG CTCTTG
* *
5358351 CTCTAG CTCTGG CTCT
1 CTCTTG CTCTTG CTCT
5358367 GGGGTAGGAG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 52 1.00
ACGTcount: A:0.03, C:0.41, G:0.14, T:0.42
Consensus pattern (6 bp):
CTCTTG
Found at i:5360245 original size:16 final size:16
Alignment explanation
Indices: 5360224--5360272 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
5360214 GGATGGGGAT
5360224 ATTATTTTGGTAATTA
1 ATTATTTTGGTAATTA
5360240 ATTATTTT--TCATATT-
1 ATTATTTTGGT-A-ATTA
5360255 A-TATTTTGGTAATTA
1 ATTATTTTGGTAATTA
5360270 ATT
1 ATT
5360273 TAGAGTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 12
0.69 0.00 0.31
Matches are distributed among these distances:
14 10 0.37
15 4 0.15
16 13 0.48
ACGTcount: A:0.31, C:0.02, G:0.08, T:0.59
Consensus pattern (16 bp):
ATTATTTTGGTAATTA
Found at i:5364910 original size:22 final size:22
Alignment explanation
Indices: 5364875--5364916 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
5364865 ATTTTACGTA
5364875 TATTCTTTAGAATTTTATTTATT
1 TATTCTTTAGAATTTT-TTTATT
*
5364898 TATT-TTTATAATTTTTTTA
1 TATTCTTTAGAATTTTTTTA
5364917 AAAATATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 10 0.56
23 4 0.22
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (22 bp):
TATTCTTTAGAATTTTTTTATT
Found at i:5364965 original size:26 final size:26
Alignment explanation
Indices: 5364901--5364966 Score: 62
Period size: 26 Copynumber: 2.5 Consensus size: 26
5364891 ATTTATTTAT
5364901 TTTTATAATTTTTT-TAAAAATATAAA
1 TTTT-TAATTTTTTATAAAAATATAAA
* ** * * *
5364927 TTTTGAAAATTTTATAAATATTTGAA
1 TTTTTAATTTTTTATAAAAATATAAA
5364953 TTTTTAATTTTTTA
1 TTTTTAATTTTTTA
5364967 AATTTTTGTT
Statistics
Matches: 30, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
25 6 0.20
26 24 0.80
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (26 bp):
TTTTTAATTTTTTATAAAAATATAAA
Found at i:5368178 original size:24 final size:24
Alignment explanation
Indices: 5368145--5368197 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
5368135 AATGTGAGAT
* * * *
5368145 ATTTGCGGAGTATGATTTCTAATA
1 ATTTGAGGAGGATGATTTATAACA
*
5368169 ATTTGAGGAGGGTGATTTATAACA
1 ATTTGAGGAGGATGATTTATAACA
5368193 ATTTG
1 ATTTG
5368198 GCTTCGATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.30, C:0.06, G:0.25, T:0.40
Consensus pattern (24 bp):
ATTTGAGGAGGATGATTTATAACA
Found at i:5370328 original size:6 final size:6
Alignment explanation
Indices: 5370304--5370337 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
5370294 ATCGGTATAT
* *
5370304 TCTCCC TCTCTC TCCCCC TCTCCC TCTCCC TCTC
1 TCTCCC TCTCCC TCTCCC TCTCCC TCTCCC TCTC
5370338 TCAGCTCCTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (6 bp):
TCTCCC
Found at i:5371663 original size:2 final size:2
Alignment explanation
Indices: 5371656--5371689 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5371646 TTACATAATG
5371656 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5371690 TTGATGAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5372295 original size:21 final size:22
Alignment explanation
Indices: 5372270--5372324 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
5372260 TTAATACATG
5372270 ATAAAATTATAATTTA-TCATT
1 ATAAAATTATAATTTACTCATT
* *
5372291 ATAAAATTTTAATTTACTTATT
1 ATAAAATTATAATTTACTCATT
*
5372313 TTAAAATTATAA
1 ATAAAATTATAA
5372325 AGATATATGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 15 0.52
22 14 0.48
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (22 bp):
ATAAAATTATAATTTACTCATT
Found at i:5372374 original size:23 final size:21
Alignment explanation
Indices: 5372348--5372403 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 21
5372338 TACATTGGTG
5372348 AAATATTATTTTAACTATCATAA
1 AAATATTATTTTAA-TATCA-AA
* *
5372371 AAATATATAATTTAATGTCAAA
1 AAATAT-TATTTTAATATCAAA
5372393 AAA-ATTATTTT
1 AAATATTATTTT
5372404 GGACTCACCC
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 5 0.17
21 2 0.07
22 5 0.17
23 10 0.34
24 7 0.24
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (21 bp):
AAATATTATTTTAATATCAAA
Found at i:5372812 original size:58 final size:58
Alignment explanation
Indices: 5372750--5372869 Score: 170
Period size: 58 Copynumber: 2.1 Consensus size: 58
5372740 ACCCATCAAC
*
5372750 AAACTAAACCC-AAATATTTTTAAACCCAAATATAATTTCATTCTTAAAAAACACTCAT
1 AAACTAAACCCAAAAT-TTTTTAAACCCAAATATAATTTCATTCCTAAAAAACACTCAT
* * * * *
5372808 AAACTAAACTCAAAATTTTTTAAACCCAAATATGATTTTATTCCTAAATAGCACTCAT
1 AAACTAAACCCAAAATTTTTTAAACCCAAATATAATTTCATTCCTAAAAAACACTCAT
5372866 AAAC
1 AAAC
5372870 AACTTCATTT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
58 51 0.93
59 4 0.07
ACGTcount: A:0.47, C:0.20, G:0.02, T:0.32
Consensus pattern (58 bp):
AAACTAAACCCAAAATTTTTTAAACCCAAATATAATTTCATTCCTAAAAAACACTCAT
Found at i:5373099 original size:21 final size:21
Alignment explanation
Indices: 5373075--5373124 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
5373065 GTGTTATTAC
5373075 TGTTCGTTTTTA-CTTTTGTTG
1 TGTT-GTTTTTATCTTTTGTTG
* *
5373096 TGTTGTTTTTATTTTTTGTTT
1 TGTTGTTTTTATCTTTTGTTG
5373117 TGTTGTTT
1 TGTTGTTT
5373125 GGCATGGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 7 0.27
21 19 0.73
ACGTcount: A:0.04, C:0.04, G:0.18, T:0.74
Consensus pattern (21 bp):
TGTTGTTTTTATCTTTTGTTG
Found at i:5377233 original size:28 final size:28
Alignment explanation
Indices: 5377202--5377289 Score: 90
Period size: 28 Copynumber: 3.1 Consensus size: 28
5377192 TAAATTAAAA
5377202 AATAATTTTTATATTTTTTAATAATTTT
1 AATAATTTTTATATTTTTTAATAATTTT
* *
5377230 AATAACTTTTA-ATTTTTAGAATAATTTTT
1 AATAATTTTTATATTTTT-TAATAA-TTTT
* *
5377259 ACAT-ATTTTTAATTTTTTTTAAAAATTTT
1 A-ATAATTTTT-ATATTTTTTAATAATTTT
5377288 AA
1 AA
5377290 AAAAATAATT
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
27 6 0.12
28 16 0.33
29 15 0.31
30 7 0.14
31 5 0.10
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (28 bp):
AATAATTTTTATATTTTTTAATAATTTT
Found at i:5377239 original size:19 final size:19
Alignment explanation
Indices: 5377202--5377242 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
5377192 TAAATTAAAA
* **
5377202 AATAATTTTTATATTTTTT
1 AATAATTTTAATAACTTTT
5377221 AATAATTTTAATAACTTTT
1 AATAATTTTAATAACTTTT
5377240 AAT
1 AAT
5377243 TTTTAGAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (19 bp):
AATAATTTTAATAACTTTT
Found at i:5377432 original size:17 final size:18
Alignment explanation
Indices: 5377407--5377440 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5377397 ATACAAGTTT
5377407 AAAAATTAAA-AAAAATG
1 AAAAATTAAATAAAAATG
*
5377424 AAAATTTAAATAAAAAT
1 AAAAATTAAATAAAAAT
5377441 TTAAAATACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (18 bp):
AAAAATTAAATAAAAATG
Found at i:5377853 original size:21 final size:20
Alignment explanation
Indices: 5377829--5377876 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 20
5377819 TATTTCCTGT
*
5377829 TATTTATAAAATTTTTATGAA
1 TATTTATAAAATTTTTA-AAA
*
5377850 TATTTTTAAAATTTTTAAAA
1 TATTTATAAAATTTTTAAAA
5377870 TATTTAT
1 TATTTAT
5377877 TGACATGACG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
TATTTATAAAATTTTTAAAA
Found at i:5387961 original size:12 final size:12
Alignment explanation
Indices: 5387944--5388049 Score: 85
Period size: 12 Copynumber: 9.2 Consensus size: 12
5387934 ATAACATCCA
5387944 AACAACAAAAAT
1 AACAACAAAAAT
5387956 AACAACAAAAAT
1 AACAACAAAAAT
* *
5387968 AGCAGCAAAAAT
1 AACAACAAAAAT
**
5387980 AAC-AGTAAAAT
1 AACAACAAAAAT
**
5387991 AAC-A-TTAAA-
1 AACAACAAAAAT
5388000 AACAACAAAAAT
1 AACAACAAAAAT
* * *
5388012 AGCAATAAAAAC
1 AACAACAAAAAT
*
5388024 AGCAACAAAAAT
1 AACAACAAAAAT
*
5388036 AACAGCAAAAAT
1 AACAACAAAAAT
5388048 AA
1 AA
5388050 TACGAAAATA
Statistics
Matches: 75, Mismatches: 16, Indels: 6
0.77 0.16 0.06
Matches are distributed among these distances:
9 3 0.04
10 5 0.07
11 12 0.16
12 55 0.73
ACGTcount: A:0.69, C:0.15, G:0.06, T:0.10
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:5387983 original size:44 final size:44
Alignment explanation
Indices: 5387930--5388015 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 44
5387920 AAAACGCATA
*
5387930 AAAAATAACA-TCCAAACAACA-AAAATAACAACAAAAATAGCAGC
1 AAAAATAACAGT-AAAACAACATAAAA-AACAACAAAAATAGCAGC
* *
5387974 AAAAATAACAGTAAAATAACATTAAAAACAACAAAAATAGCA
1 AAAAATAACAGTAAAACAACATAAAAAACAACAAAAATAGCA
5388016 ATAAAAACAG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
44 33 0.89
45 4 0.11
ACGTcount: A:0.67, C:0.16, G:0.05, T:0.12
Consensus pattern (44 bp):
AAAAATAACAGTAAAACAACATAAAAAACAACAAAAATAGCAGC
Found at i:5388051 original size:15 final size:16
Alignment explanation
Indices: 5388015--5388051 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
5388005 CAAAAATAGC
*
5388015 AATAAAAACAGCAACA
1 AATAATAACAGCAACA
5388031 AA-AATAACAGCAA-A
1 AATAATAACAGCAACA
5388045 AATAATA
1 AATAATA
5388052 CGAAAATAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 3 0.16
15 14 0.74
16 2 0.11
ACGTcount: A:0.70, C:0.14, G:0.05, T:0.11
Consensus pattern (16 bp):
AATAATAACAGCAACA
Found at i:5388090 original size:68 final size:69
Alignment explanation
Indices: 5387949--5388093 Score: 172
Period size: 68 Copynumber: 2.1 Consensus size: 69
5387939 ATCCAAACAA
* * * *
5387949 CAAAAATAACAACAAAAATAGCAGCAAAAATAACAGTAAAATAACATTAAAAACAACAAAAATAG
1 CAAAAACAGCAACAAAAATAACAGCAAAAATAACAGTAAAATAACAATAAAAACAACAAAAATAG
5388014 CAAT
66 CAAT
* * * *
5388018 -AAAAACAGCAACAAAAATAACAGCAAAAATAATACG-AAAATAGCAATCAAAACAATAAAAA-A
1 CAAAAACAGCAACAAAAATAACAGCAAAAATAACA-GTAAAATAACAATAAAAACAACAAAAATA
5388080 -CAATT
65 GCAA-T
5388085 CAAAAACAG
1 CAAAAACAG
5388094 TAAAAACACA
Statistics
Matches: 65, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
66 3 0.05
67 2 0.03
68 59 0.91
69 1 0.02
ACGTcount: A:0.67, C:0.15, G:0.06, T:0.12
Consensus pattern (69 bp):
CAAAAACAGCAACAAAAATAACAGCAAAAATAACAGTAAAATAACAATAAAAACAACAAAAATAG
CAAT
Found at i:5391812 original size:20 final size:20
Alignment explanation
Indices: 5391763--5391812 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
5391753 ATTTCATAAG
**
5391763 TTTTATTA-GAATAAAGTTA
1 TTTTATTATGAATAAAGAAA
*
5391782 TTTTAATTATGAATATAGAAA
1 TTTT-ATTATGAATAAAGAAA
5391803 TTTTATTATG
1 TTTTATTATG
5391813 TTTATTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 4 0.15
20 10 0.38
21 12 0.46
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (20 bp):
TTTTATTATGAATAAAGAAA
Found at i:5392256 original size:10 final size:9
Alignment explanation
Indices: 5392219--5392263 Score: 51
Period size: 9 Copynumber: 5.1 Consensus size: 9
5392209 ATCAAGTTTT
5392219 TTTTTATAA
1 TTTTTATAA
5392228 TTTTTA-AA
1 TTTTTATAA
5392236 TTTTT-TGAA
1 TTTTTAT-AA
5392245 TTTTTAATAA
1 TTTTT-ATAA
5392255 TTTTT-TAA
1 TTTTTATAA
5392263 T
1 T
5392264 CGAATTGATT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
8 11 0.34
9 13 0.41
10 7 0.22
11 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (9 bp):
TTTTTATAA
Found at i:5393330 original size:21 final size:22
Alignment explanation
Indices: 5393294--5393336 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
5393284 CAGCAAATGA
*
5393294 TTTTAAAATTATTAAAATTATT
1 TTTTAAAAATATTAAAATTATT
5393316 TTTTAAAAATA-TAAAATTATT
1 TTTTAAAAATATTAAAATTATT
5393337 AAAATTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTTAAAAATATTAAAATTATT
Found at i:5393361 original size:31 final size:30
Alignment explanation
Indices: 5393297--5393377 Score: 114
Period size: 30 Copynumber: 2.7 Consensus size: 30
5393287 CAAATGATTT
5393297 TAAAATTATTAAAATTATTTTTTAAAAATA
1 TAAAATTATTAAAATTATTTTTTAAAAATA
*
5393327 TAAAATTATTAAAATTATATTTTTGAAACA-A
1 TAAAATTATTAAAATTAT-TTTTT-AAAAATA
5393358 TAAAATTATT-AAA-TATTTTT
1 TAAAATTATTAAAATTATTTTT
5393378 AATTTCCAAT
Statistics
Matches: 48, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
28 4 0.08
29 3 0.06
30 21 0.44
31 16 0.33
32 4 0.08
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (30 bp):
TAAAATTATTAAAATTATTTTTTAAAAATA
Found at i:5394590 original size:29 final size:29
Alignment explanation
Indices: 5394490--5394590 Score: 102
Period size: 28 Copynumber: 3.5 Consensus size: 29
5394480 AATTAAAATT
5394490 ATTTAATAAATTTATTATTCCA-AAAAAATAA
1 ATTTAATAAATTTA-TATT--ATAAAAAATAA
* *
5394521 TTTTAAT-AATTATATATT-TTAAAAAT-A
1 ATTTAATAAATT-TATATTATAAAAAATAA
*
5394548 ATTTAAAAAATTTATATTATAAAAAATAA
1 ATTTAATAAATTTATATTATAAAAAATAA
*
5394577 ATTTAATAATTTTA
1 ATTTAATAAATTTA
5394591 AAATCATTTG
Statistics
Matches: 58, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
27 12 0.21
28 17 0.29
29 13 0.22
30 8 0.14
31 8 0.14
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (29 bp):
ATTTAATAAATTTATATTATAAAAAATAA
Done.