Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 120 of 335
Found at i:36436998 original size:2 final size:2
Alignment explanation
Indices: 36436991--36437020 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
36436981 ATAAATTTAT
36436991 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
36437021 AAGTAAACTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:36437186 original size:14 final size:14
Alignment explanation
Indices: 36437167--36437233 Score: 89
Period size: 14 Copynumber: 4.7 Consensus size: 14
36437157 CCAGAAAAGT
36437167 AAATCATTTTCCAG
1 AAATCATTTTCCAG
*
36437181 AAATCATTTTTCAAG
1 AAATCA-TTTTCCAG
*
36437196 AAATTATTTTCCAG
1 AAATCATTTTCCAG
*
36437210 AAATTATTTTCCAG
1 AAATCATTTTCCAG
*
36437224 AAAACATTTT
1 AAATCATTTT
36437234 ACCTGCGAAC
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
14 35 0.74
15 12 0.26
ACGTcount: A:0.39, C:0.15, G:0.06, T:0.40
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:36438589 original size:3 final size:3
Alignment explanation
Indices: 36438581--36438606 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
36438571 TTAACCTATC
36438581 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
36438607 TATCCTTCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:36455929 original size:21 final size:23
Alignment explanation
Indices: 36455893--36455936 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
36455883 ATCAATAATA
36455893 ATAAATATTCTATAATATAAAAT
1 ATAAATATTCTATAATATAAAAT
*
36455916 ATAAATATT-T-TAATTTAAAAT
1 ATAAATATTCTATAATATAAAAT
36455937 TGCTTATCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 10 0.50
22 1 0.05
23 9 0.45
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
ATAAATATTCTATAATATAAAAT
Found at i:36456105 original size:2 final size:2
Alignment explanation
Indices: 36456100--36456128 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
36456090 AATGTCAACT
36456100 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
36456129 TTATGATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:36456209 original size:36 final size:33
Alignment explanation
Indices: 36456148--36456215 Score: 91
Period size: 36 Copynumber: 2.0 Consensus size: 33
36456138 TACAATCATG
36456148 ATAAAATTAAATTTTATAAAAATATATTTTTAA
1 ATAAAATTAAATTTTATAAAAATATATTTTTAA
* *
36456181 ATAAATTTAATATTTTAGTCAACAATATATTTTTA
1 ATAAAATTAA-ATTTTA-T-AAAAATATATTTTTA
36456216 TTAAAGGGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
33 9 0.30
34 6 0.20
35 1 0.03
36 14 0.47
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (33 bp):
ATAAAATTAAATTTTATAAAAATATATTTTTAA
Found at i:36456735 original size:25 final size:25
Alignment explanation
Indices: 36456707--36456754 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
36456697 AATTAAAAAT
36456707 ATTT-AAATGTTATTTTTACATATAA
1 ATTTCAAATGTTATTTTT-CATATAA
* *
36456732 ATTTCTACTGTTATTTTTCATAT
1 ATTTCAAATGTTATTTTTCATAT
36456755 CAGTAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 9 0.45
26 11 0.55
ACGTcount: A:0.31, C:0.08, G:0.04, T:0.56
Consensus pattern (25 bp):
ATTTCAAATGTTATTTTTCATATAA
Found at i:36458280 original size:23 final size:22
Alignment explanation
Indices: 36458254--36458298 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
36458244 ATTTTAATTT
*
36458254 TTTTTAAAATATTTAATTAAATA
1 TTTTTAAAATA-TTAAATAAATA
* *
36458277 TTTTTTATATATTAAATAAATA
1 TTTTTAAAATATTAAATAAATA
36458299 AAACTAGCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTTTAAAATATTAAATAAATA
Found at i:36458434 original size:23 final size:22
Alignment explanation
Indices: 36458376--36458434 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 22
36458366 ATAATTTTGA
36458376 ATTTTAAATAATATTCTTAATAT
1 ATTTT-AATAATATTCTTAATAT
* *
36458399 ATTATTAAAAATATT-TATATTAAT
1 ATT-TTAATAATATTCT-TAAT-AT
36458423 ATTTTAATAATA
1 ATTTTAATAATA
36458435 AATATATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
22 1 0.03
23 22 0.73
24 7 0.23
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
ATTTTAATAATATTCTTAATAT
Found at i:36458438 original size:15 final size:15
Alignment explanation
Indices: 36458420--36458476 Score: 62
Period size: 15 Copynumber: 3.6 Consensus size: 15
36458410 TATTTATATT
36458420 AATATTTTAATAATA
1 AATATTTTAATAATA
*
36458435 AATATATATTACATTTATA
1 AATAT-T-TTA-A-TAATA
36458454 AATA-TTTAATAATA
1 AATATTTTAATAATA
36458468 AATATTTTA
1 AATATTTTA
36458477 TGCATTGTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 8 0.23
15 10 0.29
16 4 0.11
17 4 0.11
18 1 0.03
19 8 0.23
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:36458470 original size:14 final size:14
Alignment explanation
Indices: 36458394--36458474 Score: 51
Period size: 14 Copynumber: 5.5 Consensus size: 14
36458384 TAATATTCTT
*
36458394 AATATATTATTAA-A
1 AATAT-TTAATAATA
*
36458408 AATATTT-AT-ATT
1 AATATTTAATAATA
36458420 AATATTTTAATAATAA
1 AATA-TTTAATAAT-A
*
36458436 ATATATATTACATTTATA
1 A-ATAT-TTA-A-TAATA
36458454 AATATTTAATAATA
1 AATATTTAATAATA
36458468 AATATTT
1 AATATTT
36458475 TATGCATTGT
Statistics
Matches: 53, Mismatches: 5, Indels: 18
0.70 0.07 0.24
Matches are distributed among these distances:
11 1 0.02
12 5 0.09
13 5 0.09
14 18 0.34
15 3 0.06
16 5 0.09
17 10 0.19
18 3 0.06
19 3 0.06
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (14 bp):
AATATTTAATAATA
Found at i:36462525 original size:13 final size:13
Alignment explanation
Indices: 36462509--36462534 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
36462499 GGATTTTACT
36462509 TGTTTAATATTAA
1 TGTTTAATATTAA
36462522 TGTTTAATATTAA
1 TGTTTAATATTAA
36462535 GGATTAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
TGTTTAATATTAA
Found at i:36465946 original size:41 final size:41
Alignment explanation
Indices: 36465883--36465962 Score: 115
Period size: 41 Copynumber: 2.0 Consensus size: 41
36465873 CCTTGAGTCC
* * *
36465883 AACAAGCTTTGTGCCGGAGATTTATATCAGGCTTTGTGCCT
1 AACAAGCTTCGTGCAGGAGATTTATATCAAGCTTTGTGCCT
* *
36465924 AACAGGCTTCGTGCAGGTGATTTATATCAAGCTTTGTGC
1 AACAAGCTTCGTGCAGGAGATTTATATCAAGCTTTGTGC
36465963 TGATGATATA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.34
Consensus pattern (41 bp):
AACAAGCTTCGTGCAGGAGATTTATATCAAGCTTTGTGCCT
Found at i:36466001 original size:66 final size:66
Alignment explanation
Indices: 36465885--36466018 Score: 173
Period size: 66 Copynumber: 2.0 Consensus size: 66
36465875 TTGAGTCCAA
* * * *
36465885 CAAGCTTTGTGCCGGAGATTTATATCAGGCTTTGTGCCTAACAGGCTTCGTG-CAGGTGATTTAT
1 CAAGCTTTGTGCCGGAGATATATATAAGACTGTGTGCCTAACAGGCTTCGTGTCA-GTGATTTAT
36465949 AT
65 AT
* * *
36465951 CAAGCTTTGTG-CTGATGATATATATAAGACTGTGTGCCTAGCAGGTTTCGTGTCAGTGATTTAT
1 CAAGCTTTGTGCCGGA-GATATATATAAGACTGTGTGCCTAACAGGCTTCGTGTCAGTGATTTAT
36466015 AT
65 AT
36466017 CA
1 CA
36466019 GGCTCTATGC
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
65 3 0.05
66 54 0.92
67 2 0.03
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.36
Consensus pattern (66 bp):
CAAGCTTTGTGCCGGAGATATATATAAGACTGTGTGCCTAACAGGCTTCGTGTCAGTGATTTATA
T
Found at i:36468514 original size:27 final size:27
Alignment explanation
Indices: 36468472--36468526 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
36468462 TATAATTTGA
36468472 TGCATGACATTCAAAGTTGTTTATTAT
1 TGCATGACATTCAAAGTTGTTTATTAT
*
36468499 TGCATGACATTTAAAGTTGTTTATTAT
1 TGCATGACATTCAAAGTTGTTTATTAT
36468526 T
1 T
36468527 TAAAAAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.29, C:0.09, G:0.15, T:0.47
Consensus pattern (27 bp):
TGCATGACATTCAAAGTTGTTTATTAT
Found at i:36472141 original size:5 final size:6
Alignment explanation
Indices: 36472126--36472165 Score: 53
Period size: 6 Copynumber: 6.3 Consensus size: 6
36472116 AGAGAGAGGA
*
36472126 AAAAAT AAAAAT AAAAAT AAAATT AAGATAAT AAAAAT AA
1 AAAAAT AAAAAT AAAAAT AAAAAT AA-A-AAT AAAAAT AA
36472166 TATCTCAACT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 24 0.80
7 2 0.07
8 4 0.13
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.20
Consensus pattern (6 bp):
AAAAAT
Found at i:36477781 original size:44 final size:44
Alignment explanation
Indices: 36477718--36477808 Score: 148
Period size: 44 Copynumber: 2.1 Consensus size: 44
36477708 ATTGGTCAAA
*
36477718 TAATATTAAAATAAACTACACTAATTA-AAGTTTAAGTGGGAAAC
1 TAATATTAAAATAAACTACACTAATTAGAA-TTTAAGTAGGAAAC
*
36477762 TAATATTAAAATAACCTACACTAATTAGAATTTAAGTAGGAAAC
1 TAATATTAAAATAAACTACACTAATTAGAATTTAAGTAGGAAAC
36477806 TAA
1 TAA
36477809 AAACCAGAGA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 42 0.95
45 2 0.05
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.30
Consensus pattern (44 bp):
TAATATTAAAATAAACTACACTAATTAGAATTTAAGTAGGAAAC
Found at i:36479608 original size:42 final size:42
Alignment explanation
Indices: 36479558--36479684 Score: 161
Period size: 42 Copynumber: 3.0 Consensus size: 42
36479548 CTTCATTTTC
** ** *
36479558 TCGATGCCATAGTTCAATTATGGTCTTACACATCTTCACATAA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACAT-A
*
36479601 T-GATGCCATAGCCCAGCTATGGTCTTACACATATTCATATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
36479642 TCGATGCCATAGCCCAGCTATGGTCTTACACGA-A-TCACATA
1 TCGATGCCATAGCCCAGCTATGGTCTTACAC-ATATTCACATA
36479683 TC
1 TC
36479685 TCACTGATGC
Statistics
Matches: 75, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
41 10 0.13
42 63 0.84
43 2 0.03
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (42 bp):
TCGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATA
Found at i:36479746 original size:47 final size:46
Alignment explanation
Indices: 36479643--36479766 Score: 167
Period size: 47 Copynumber: 2.7 Consensus size: 46
36479633 ATTCATATAT
* * * * *
36479643 CGATGCCATAGCCCAGCTATGGTCTTACACGAATCACATATCTCAC
1 CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACAC
* * *
36479689 TGATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
1 CGATGCCATATCCCAGATATGGTCTTATAC-GAAGCACATATCACAC
36479736 CGATGCCATATCCCAGATATGGTCTTATACG
1 CGATGCCATATCCCAGATATGGTCTTATACG
36479767 GAAATCACTT
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
46 27 0.40
47 41 0.60
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.27
Consensus pattern (46 bp):
CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACAC
Found at i:36479826 original size:31 final size:31
Alignment explanation
Indices: 36479791--36480000 Score: 327
Period size: 31 Copynumber: 6.8 Consensus size: 31
36479781 CTTGTCACTT
*
36479791 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
36479822 GTAGCCGAAGCTA-CAATTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
36479852 GTAGCTGGAA-CTACCACTTTTCACTGATCAG
1 GTAGC-CGAAGCTACCACTTTTCACTGATCAG
*
36479883 GTAGCAGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
36479914 GTAGCCGGAA-CTACCACTTTTCACTGATCAG
1 GTAGCC-GAAGCTACCACTTTTCACTGATCAG
*
36479945 GTAGCAGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
36479976 GTAGCTGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
36480001 TGTCATTTGC
Statistics
Matches: 166, Mismatches: 8, Indels: 10
0.90 0.04 0.05
Matches are distributed among these distances:
30 29 0.17
31 134 0.81
32 3 0.02
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.27
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:36480080 original size:50 final size:51
Alignment explanation
Indices: 36479976--36480104 Score: 190
Period size: 50 Copynumber: 2.5 Consensus size: 51
36479966 CACTGATCAG
* * *
36479976 GTAGCTGAAGCTACCACTTTTCACTTGTCATTTGCCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCATTTGCCATTGATCAGATAAGT
* *
36480027 GTAGTCGAAGCTATCACTTATCACTT-TCACTTTTCC-TTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCA-TTTGCCATTGATCAGATAAGT
36480077 GTAGCCGAAGCTATCACTTATCACTTGT
1 GTAGCCGAAGCTATCACTTATCACTTGT
36480105 TGCCATGGTC
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
50 42 0.60
51 28 0.40
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (51 bp):
GTAGCCGAAGCTATCACTTATCACTTGTCATTTGCCATTGATCAGATAAGT
Found at i:36499213 original size:40 final size:38
Alignment explanation
Indices: 36499169--36499257 Score: 133
Period size: 40 Copynumber: 2.3 Consensus size: 38
36499159 TTACAGCACC
36499169 ACTTGGTGTGTAGGGCTGGATGGGTCGATTTTATCCCCAT
1 ACTTGGTGTGTAGGGCTGGATGGGTCGATTTTAT-CCC-T
* *
36499209 ACTTGGTGTGTAGGGCTGGGTGGGTTGATTTTATCCCT
1 ACTTGGTGTGTAGGGCTGGATGGGTCGATTTTATCCCT
*
36499247 ACATGGTGTGT
1 ACTTGGTGTGT
36499258 TGGATTAGAC
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
38 11 0.24
39 3 0.07
40 32 0.70
ACGTcount: A:0.13, C:0.15, G:0.35, T:0.37
Consensus pattern (38 bp):
ACTTGGTGTGTAGGGCTGGATGGGTCGATTTTATCCCT
Found at i:36506343 original size:40 final size:40
Alignment explanation
Indices: 36506299--36506375 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
36506289 TTATAGTACC
36506299 ACTTGGTGTCTAGGGCTGGATGGGTCGATTTTATCCCCAT
1 ACTTGGTGTCTAGGGCTGGATGGGTCGATTTTATCCCCAT
* * *
36506339 ACTTGGTGTGTAGGGCTGGGTGGGTTGATTTTATCCC
1 ACTTGGTGTCTAGGGCTGGATGGGTCGATTTTATCCC
36506376 TACATGGTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.13, C:0.17, G:0.34, T:0.36
Consensus pattern (40 bp):
ACTTGGTGTCTAGGGCTGGATGGGTCGATTTTATCCCCAT
Found at i:36508128 original size:17 final size:17
Alignment explanation
Indices: 36508106--36508141 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
36508096 TATTAAAATT
*
36508106 ATTATTATGGTTTTATA
1 ATTATTATGATTTTATA
*
36508123 ATTATTATGATTTTTTA
1 ATTATTATGATTTTATA
36508140 AT
1 AT
36508142 GAATATTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (17 bp):
ATTATTATGATTTTATA
Found at i:36508510 original size:23 final size:24
Alignment explanation
Indices: 36508474--36508520 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
36508464 ATAAAGAAAC
*
36508474 AAAAGGGAAGAGAAACAGAAAAGA
1 AAAAGGGAAGAGAAAAAGAAAAGA
*
36508498 AAAAGGGAA-AGAAAAATAAAAGA
1 AAAAGGGAAGAGAAAAAGAAAAGA
36508521 GAACTAAGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.70, C:0.02, G:0.26, T:0.02
Consensus pattern (24 bp):
AAAAGGGAAGAGAAAAAGAAAAGA
Found at i:36509680 original size:18 final size:18
Alignment explanation
Indices: 36509657--36509697 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
36509647 AAAAAAAAAA
36509657 AGAAATT-GAATTATGAAT
1 AGAAATTGGAATTATG-AT
*
36509675 AGAAATTGGAATTGTGAT
1 AGAAATTGGAATTATGAT
36509693 AGAAA
1 AGAAA
36509698 GAGAAAAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.49, C:0.00, G:0.22, T:0.29
Consensus pattern (18 bp):
AGAAATTGGAATTATGAT
Found at i:36510208 original size:20 final size:20
Alignment explanation
Indices: 36510185--36510222 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
36510175 GTTATTAAGT
36510185 TAAAAATTATGTTA-ATGATA
1 TAAAAATTA-GTTATATGATA
*
36510205 TAAATATTAGTTATATGA
1 TAAAAATTAGTTATATGA
36510223 ATGTGAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (20 bp):
TAAAAATTAGTTATATGATA
Found at i:36510642 original size:2 final size:2
Alignment explanation
Indices: 36510631--36510664 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
36510621 CTTACTTCGA
36510631 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
36510665 AGCCCTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36518234 original size:6 final size:6
Alignment explanation
Indices: 36518223--36518293 Score: 80
Period size: 6 Copynumber: 12.3 Consensus size: 6
36518213 CAACCCAATC
36518223 TTTATT TTTATT TTTA-- TTTATT TTT-TT TTTATT ATTTATT TTT-TT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT -TTTATT TTTATT
*
36518268 TTTTTCT TTTATT TTTA-T TTTATT TT
1 TTTAT-T TTTATT TTTATT TTTATT TT
36518294 AGTTAAATAT
Statistics
Matches: 57, Mismatches: 1, Indels: 14
0.79 0.01 0.19
Matches are distributed among these distances:
4 4 0.07
5 15 0.26
6 27 0.47
7 11 0.19
ACGTcount: A:0.14, C:0.01, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:36518257 original size:18 final size:17
Alignment explanation
Indices: 36518223--36518292 Score: 81
Period size: 16 Copynumber: 4.2 Consensus size: 17
36518213 CAACCCAATC
*
36518223 TTTA-TTTTTATTTTTA
1 TTTATTTTTTTTTTTTA
36518239 TTTATTTTTTTTTTATTA
1 TTTATTTTTTTTTT-TTA
*
36518257 TTTATTTTTTTTTTTTC
1 TTTATTTTTTTTTTTTA
* *
36518274 TTT-TATTTTTATTTTA
1 TTTATTTTTTTTTTTTA
36518290 TTT
1 TTT
36518293 TAGTTAAATA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
16 17 0.36
17 13 0.28
18 17 0.36
ACGTcount: A:0.14, C:0.01, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTATTTTTTTTTTTTA
Found at i:36518446 original size:40 final size:42
Alignment explanation
Indices: 36518390--36518490 Score: 125
Period size: 40 Copynumber: 2.4 Consensus size: 42
36518380 AAAACAACCC
* * *
36518390 TATCCATGCTGCCAAACAGTTCTATTCCAGCC-AGAAT-GCCA
1 TATCC-TGCAGCCAAACAGTCCTATTCCAGCCTAGAATCCCCA
36518431 TATCCTGCAGCCAAACAGTCCTATTCCAGCCTTAGAATCCCCA
1 TATCCTGCAGCCAAACAGTCCTATTCCAGCC-TAGAATCCCCA
* *
36518474 AAACCTGCAGCCAAACA
1 TATCCTGCAGCCAAACA
36518491 CCCCTTTTCA
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
40 24 0.46
41 5 0.10
42 5 0.10
43 18 0.35
ACGTcount: A:0.32, C:0.35, G:0.13, T:0.21
Consensus pattern (42 bp):
TATCCTGCAGCCAAACAGTCCTATTCCAGCCTAGAATCCCCA
Found at i:36519459 original size:118 final size:118
Alignment explanation
Indices: 36519251--36519481 Score: 390
Period size: 118 Copynumber: 2.0 Consensus size: 118
36519241 TGTTTTCCAT
* *
36519251 GGTTATGAGTACAGCTTAGATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
1 GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
36519316 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGA
66 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGA
**
36519369 GGTTATGAGTATGGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
1 GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
****
36519434 CTACTTCGCGTCAAAAGGTTGTGTGACGTGTTGGGTAAAACTCCGCTA
66 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTA
36519482 ACCGGAAATA
Statistics
Matches: 105, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
118 105 1.00
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.29
Consensus pattern (118 bp):
GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGA
Found at i:36522777 original size:21 final size:20
Alignment explanation
Indices: 36522738--36522779 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
36522728 AATATGCTGT
* *
36522738 AAAATGAAATTTTTTGATAG
1 AAAATGAAAATTATTGATAG
36522758 AAAATGAAAGATTATTGATAG
1 AAAATGAAA-ATTATTGATAG
36522779 A
1 A
36522780 TAAACTACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (20 bp):
AAAATGAAAATTATTGATAG
Found at i:36523510 original size:32 final size:32
Alignment explanation
Indices: 36523468--36523650 Score: 147
Period size: 32 Copynumber: 5.7 Consensus size: 32
36523458 AAATGATACA
* *
36523468 ACTTGAAAAGGTTATGTACACTTTGTGTGTAC
1 ACTTGAAAAGGTAAGGTACACTTTGTGTGTAC
* * * *
36523500 ACTTGGAAAGGTTAGGTATACTTTGTGTATAC
1 ACTTGAAAAGGTAAGGTACACTTTGTGTGTAC
*
36523532 -CATATGAAAAGGAAAGGTACACTTTGTGTGTAC
1 AC-T-TGAAAAGGTAAGGTACACTTTGTGTGTAC
* * * * *
36523565 ACTTGGAAAGGTTAGGTATACTTTTTGTATAC
1 ACTTGAAAAGGTAAGGTACACTTTGTGTGTAC
* * *
36523597 -CATATGAAAAGGAAAGGTATACTTTGTGAGTACC
1 AC-T-TGAAAAGGTAAGGTACACTTTGTGTGTA-C
* *
36523631 ACTTGGAAAGG-AATGTACAC
1 ACTTGAAAAGGTAAGGTACAC
36523651 CTCAAGTGTA
Statistics
Matches: 120, Mismatches: 24, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
31 2 0.02
32 60 0.50
33 54 0.45
34 3 0.03
35 1 0.01
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.32
Consensus pattern (32 bp):
ACTTGAAAAGGTAAGGTACACTTTGTGTGTAC
Found at i:36523543 original size:65 final size:65
Alignment explanation
Indices: 36523483--36523641 Score: 282
Period size: 65 Copynumber: 2.4 Consensus size: 65
36523473 AAAAGGTTAT
36523483 GTACACTTTGTGTGTACACTTGGAAAGGTTAGGTATACTTTGTGTATACCATATGAAAAGGAAAG
1 GTACACTTTGTGTGTACACTTGGAAAGGTTAGGTATACTTTGTGTATACCATATGAAAAGGAAAG
*
36523548 GTACACTTTGTGTGTACACTTGGAAAGGTTAGGTATACTTTTTGTATACCATATGAAAAGGAAAG
1 GTACACTTTGTGTGTACACTTGGAAAGGTTAGGTATACTTTGTGTATACCATATGAAAAGGAAAG
* *
36523613 GTATACTTTGTGAGTACCACTTGGAAAGG
1 GTACACTTTGTGTGTA-CACTTGGAAAGG
36523642 AATGTACACC
Statistics
Matches: 90, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
65 78 0.87
66 12 0.13
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (65 bp):
GTACACTTTGTGTGTACACTTGGAAAGGTTAGGTATACTTTGTGTATACCATATGAAAAGGAAAG
Found at i:36523631 original size:33 final size:33
Alignment explanation
Indices: 36523513--36523624 Score: 147
Period size: 33 Copynumber: 3.4 Consensus size: 33
36523503 TGGAAAGGTT
36523513 AGGTATACTTTGTGTATACCATATGAAAAGGAA
1 AGGTATACTTTGTGTATACCATATGAAAAGGAA
* * * **
36523546 AGGTACACTTTGTGTGTA-CACT-TGGAAAGGTT
1 AGGTATACTTTGTGTATACCA-TATGAAAAGGAA
*
36523578 AGGTATACTTTTTGTATACCATATGAAAAGGAA
1 AGGTATACTTTGTGTATACCATATGAAAAGGAA
36523611 AGGTATACTTTGTG
1 AGGTATACTTTGTG
36523625 AGTACCACTT
Statistics
Matches: 64, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
32 25 0.39
33 39 0.61
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.34
Consensus pattern (33 bp):
AGGTATACTTTGTGTATACCATATGAAAAGGAA
Found at i:36523641 original size:33 final size:33
Alignment explanation
Indices: 36523487--36523643 Score: 146
Period size: 33 Copynumber: 4.8 Consensus size: 33
36523477 GGTTATGTAC
* **
36523487 ACTTTGTGTGTA-CACTTGGAAAGGTTAGGTAT
1 ACTTTGTGAGTACCACTTGGAAAGGAAAGGTAT
* *
36523519 ACTTTGTGTA-TACCA-TATGAAAAGGAAAGGTAC
1 ACTTTGTG-AGTACCACT-TGGAAAGGAAAGGTAT
* **
36523552 ACTTTGTGTGTA-CACTTGGAAAGGTTAGGTAT
1 ACTTTGTGAGTACCACTTGGAAAGGAAAGGTAT
* *
36523584 ACTTTTTGTA-TACCA-TATGAAAAGGAAAGGTAT
1 ACTTTGTG-AGTACCACT-TGGAAAGGAAAGGTAT
36523617 ACTTTGTGAGTACCACTTGGAAAGGAA
1 ACTTTGTGAGTACCACTTGGAAAGGAA
36523644 TGTACACCTC
Statistics
Matches: 98, Mismatches: 17, Indels: 19
0.73 0.13 0.14
Matches are distributed among these distances:
32 36 0.37
33 61 0.62
34 1 0.01
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.32
Consensus pattern (33 bp):
ACTTTGTGAGTACCACTTGGAAAGGAAAGGTAT
Found at i:36527712 original size:2 final size:2
Alignment explanation
Indices: 36527705--36527739 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
36527695 TTAAAACTGT
36527705 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
36527740 CAATAATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:36528517 original size:15 final size:15
Alignment explanation
Indices: 36528497--36528533 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
36528487 CGAGGGTTAG
36528497 ATTATTACTATTACT
1 ATTATTACTATTACT
**
36528512 ATTATTTTTATTACT
1 ATTATTACTATTACT
36528527 ATTATTA
1 ATTATTA
36528534 TTACTATTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTATTACTATTACT
Found at i:36540091 original size:45 final size:45
Alignment explanation
Indices: 36540033--36540122 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 45
36540023 TTCATCTTAT
* * * *
36540033 TCATTTTGTATTTTGGAAAAATGTGCTATCTTGATTAATTTATTC
1 TCATGTTGTATTTTAGAAAAATGTGCTATCGTGATTAATTCATTC
* *
36540078 TCATGTTGTATTTTAGCAAAATTTGCTATCGTGATTAATTCATTC
1 TCATGTTGTATTTTAGAAAAATGTGCTATCGTGATTAATTCATTC
36540123 CGAGCTTTGT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.27, C:0.11, G:0.13, T:0.49
Consensus pattern (45 bp):
TCATGTTGTATTTTAGAAAAATGTGCTATCGTGATTAATTCATTC
Found at i:36540790 original size:89 final size:87
Alignment explanation
Indices: 36540687--36541204 Score: 383
Period size: 89 Copynumber: 5.9 Consensus size: 87
36540677 GACCATGGCG
* * * *
36540687 AATCTTATCTCCCTGAAGTTGCAGTGTAGCAGATTGATGTCACAAACCTTATCTCTCTAAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTCACAAACCTTATCTCCCTGAAGTTG
36540752 CAGTGGAGCAGGTTAAAAATAACA
66 CAGTGGAGCAGGTT-AAAAT-ACA
* * * * * * *
36540776 AATCTTATCACCCTGAAGTTTCAGTGGGGTAGATTGTAGTTACAGATCC-TATCTCCCTGAAGTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTCACA-AACCTTATCTCCCTGAAGTT
* * **
36540840 GCAGTGGAGTAGGTCGAAGTTAGCA
65 GCAGTGGAGCAGGT-TAAAATA-CA
* * * * *
36540865 AACCTTATCCCCCTGAAGTTGCAGTGGAGTAGGTTGAAGTTAGCAAACCTTATC-CCCTTGAAGT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTCA-CAAACCTTATCTCCC-TGAAGT
* *
36540929 TGCAATGGAGCAGG-T----T-GA
64 TGCAGTGGAGCAGGTTAAAATACA
* * * *
36540947 AGT-TTATCTCCCT-AGAGTTGCAGTGGAGCAGACTGAAAGTTACAAACTTTATCTCCCTGAAGT
1 AATCTTATCTCCCTGA-AGTTGCAGTGGAGCAGATTG-AAGTCACAAACCTTATCTCCCTGAAGT
**
36541010 TGCAGTGGAGCAGGTTGAAGTTACA
64 TGCAGTGGAGCAGGTT-AAAATACA
** * * * * ** *
36541035 AATCTTATCTATCTGAAGTTGCAGTAGAGCAGATTAAAG-CTATAAATCTTATCTATCTAAAGTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTC-ACAAACCTTATCTCCCTGAAGTT
* * * * *
36541099 GCAGTAGAGTAGATTAAAGCTATA
65 GCAGTGGAGCAGGTTAAA-ATACA
* * * * * ** *
36541123 AACCTTATCTCCCTGAAGTTGCAGTGAAGTAGATTGAAGCCACTAGTCTTGTCTCCCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTCACAAACCTTATCTCCCTGAAGTTG
* *
36541188 CAGTGGAACAGATTAAA
66 CAGTGGAGCAGGTTAAA
36541205 GCTATGAGTT
Statistics
Matches: 337, Mismatches: 71, Indels: 43
0.75 0.16 0.10
Matches are distributed among these distances:
80 1 0.00
81 55 0.16
82 12 0.04
84 1 0.00
87 3 0.01
88 102 0.30
89 135 0.40
90 28 0.08
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.29
Consensus pattern (87 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTCACAAACCTTATCTCCCTGAAGTTG
CAGTGGAGCAGGTTAAAATACA
Found at i:36540795 original size:45 final size:43
Alignment explanation
Indices: 36540687--36541205 Score: 356
Period size: 44 Copynumber: 11.9 Consensus size: 43
36540677 GACCATGGCG
* * *
36540687 AATCTTATCTCCCTGAAGTTGCAGTGTAGCAGATTGATGTCACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGT-ACA
* * * * *
36540731 AACCTTATCTCTCTAAAGTTGCAGTGGAGCAGGTTAAAAATAACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGT-ACA
* * * * **
36540776 AATCTTATCACCCTGAAGTTTCAGTGGGGTAGATTGTAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-TACA
* * * * **
36540820 GATCCTATCTCCCTGAAGTTGCAGTGGAGTAGGTCGAAGTTAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-TA-CA
* * * * *
36540865 AACCTTATCCCCCTGAAGTTGCAGTGGAGTAGGTTGAAGTTAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-TA-CA
* * *
36540910 AACCTTATC-CCCTTGAAGTTGCAATGGAGCAGGTT---G---A
1 AATCTTATCTCCC-TGAAGTTGCAGTGGAGCAGATTAAAGTACA
* *
36540947 AGT-TTATCTCCCT-AGAGTTGCAGTGGAGCAGACTGAAAGTTACA
1 AATCTTATCTCCCTGA-AGTTGCAGTGGAGCAGA-TTAAAG-TACA
* *
36540991 AA-CTTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTACA
1 AATC-TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-TACA
** * *
36541035 AATCTTATCTATCTGAAGTTGCAGTAGAGCAGATTAAAGCTATA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-TACA
** * * * *
36541079 AATCTTATCTATCTAAAGTTGCAGTAGAGTAGATTAAAGCTATA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-TACA
* * * * * *
36541123 AACCTTATCTCCCTGAAGTTGCAGTGAAGTAGATTGAAGCCACT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-TACA
* * *
36541167 AGTCTTGTCTCCCTGAAGTTGCAGTGGAACAGATTAAAG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG
36541206 CTATGAGTTA
Statistics
Matches: 387, Mismatches: 70, Indels: 36
0.78 0.14 0.07
Matches are distributed among these distances:
35 1 0.00
36 21 0.05
37 6 0.02
40 1 0.00
42 1 0.00
44 225 0.58
45 131 0.34
46 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (43 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTACA
Found at i:36541008 original size:81 final size:81
Alignment explanation
Indices: 36540881--36541031 Score: 225
Period size: 81 Copynumber: 1.9 Consensus size: 81
36540871 ATCCCCCTGA
* **
36540881 AGTTGCAGTGGAGTAGGTTGAAGTTAGCAAACCTTATCCCCTTGAAGTTGCAATGGAGCAGGTTG
1 AGTTGCAGTGGAGCAGACTGAAGTTAGCAAACCTTATCCCCTTGAAGTTGCAATGGAGCAGGTTG
36540946 AAGTTTATCTCCCTAG
66 AAGTTTATCTCCCTAG
* *
36540962 AGTTGCAGTGGAGCAGACTGAAAGTTA-CAAACTTTATCTCCC-TGAAGTTGCAGTGGAGCAGGT
1 AGTTGCAGTGGAGCAGACTG-AAGTTAGCAAACCTTATC-CCCTTGAAGTTGCAATGGAGCAGGT
36541025 TGAAGTT
64 TGAAGTT
36541032 ACAAATCTTA
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
81 54 0.86
82 9 0.14
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (81 bp):
AGTTGCAGTGGAGCAGACTGAAGTTAGCAAACCTTATCCCCTTGAAGTTGCAATGGAGCAGGTTG
AAGTTTATCTCCCTAG
Found at i:36541800 original size:23 final size:23
Alignment explanation
Indices: 36541773--36541816 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
36541763 GCAGAGAAAT
*
36541773 AACAGTAGCAAAATCAAGTCATG
1 AACAGTAACAAAATCAAGTCATG
36541796 AACAGTAACAAAATCAAGTCA
1 AACAGTAACAAAATCAAGTCA
36541817 AGTGTAACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.52, C:0.18, G:0.14, T:0.16
Consensus pattern (23 bp):
AACAGTAACAAAATCAAGTCATG
Found at i:36542029 original size:2 final size:2
Alignment explanation
Indices: 36542022--36542050 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
36542012 TTAAAACTGT
36542022 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
36542051 CAGTAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:36542875 original size:12 final size:12
Alignment explanation
Indices: 36542860--36542889 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
36542850 CTATTACTAT
36542860 TATTTTTATTAC
1 TATTTTTATTAC
*
36542872 TATTATTATTAC
1 TATTTTTATTAC
36542884 TATTTT
1 TATTTT
36542890 CGTTATTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.67
Consensus pattern (12 bp):
TATTTTTATTAC
Found at i:36543082 original size:44 final size:44
Alignment explanation
Indices: 36543033--36543121 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
36543023 TTATTTATTA
*
36543033 TTTGTATTTGTTATAATTATTATTATTAGTATTATATTTAAAAC
1 TTTGTATTTGTTATAATTATTATTATAAGTATTATATTTAAAAC
36543077 TTTGTATTTGTTATAATTATTATTATAAGTATTATATTTAAAAC
1 TTTGTATTTGTTATAATTATTATTATAAGTATTATATTTAAAAC
36543121 T
1 T
36543122 ACTTTACTTA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.56
Consensus pattern (44 bp):
TTTGTATTTGTTATAATTATTATTATAAGTATTATATTTAAAAC
Found at i:36550069 original size:25 final size:22
Alignment explanation
Indices: 36550026--36550077 Score: 52
Period size: 22 Copynumber: 2.2 Consensus size: 22
36550016 AATTACTTGA
*
36550026 TTTTTATAAAAAAAAA-TTTAT
1 TTTTTACAAAAAAAAATTTTAT
36550047 GTTTTTACAAGAAAAAACCATTTTAT
1 -TTTTTACAA-AAAAAA--ATTTTAT
36550073 TTTTT
1 TTTTT
36550078 CAATTTCCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 8 0.32
23 6 0.24
25 6 0.24
26 5 0.20
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (22 bp):
TTTTTACAAAAAAAAATTTTAT
Found at i:36553499 original size:16 final size:15
Alignment explanation
Indices: 36553467--36553518 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
36553457 TAATTTCATG
*
36553467 TTGAAACATATAAAT
1 TTGAAACATATATAT
36553482 TTGAAACTATATATAT
1 TTGAAAC-ATATATAT
* *
36553498 TTAAAAAAATATATAT
1 TT-GAAACATATATAT
36553514 TTGAA
1 TTGAA
36553519 TCATTAATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
15 9 0.29
16 19 0.61
17 3 0.10
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (15 bp):
TTGAAACATATATAT
Found at i:36556358 original size:26 final size:26
Alignment explanation
Indices: 36556324--36556375 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
36556314 TTAAATACAT
* *
36556324 ATATTAGTAATTATTAT-TTACTTATA
1 ATATAAGTAAATATTATATTA-TTATA
36556350 ATATAAGTAAATATTATATTATTATA
1 ATATAAGTAAATATTATATTATTATA
36556376 TTATTATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 20 0.87
27 3 0.13
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (26 bp):
ATATAAGTAAATATTATATTATTATA
Found at i:36557967 original size:44 final size:44
Alignment explanation
Indices: 36557881--36557972 Score: 105
Period size: 44 Copynumber: 2.1 Consensus size: 44
36557871 TGTTCAGGGA
* * * * *
36557881 TACTTCGACCTTGAGTCGATGAGGCACTATAAGTTTCGTACTGT
1 TACTTCGACCTTGAGTCAATGAGGCACCATAAGTGTCATACTGC
**
36557925 TACTTCGA-CTTCGAGTCAATGAGGCACCATGTGTGTCATACTGC
1 TACTTCGACCTT-GAGTCAATGAGGCACCATAAGTGTCATACTGC
36557969 TACT
1 TACT
36557973 GTTACATTAG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
43 3 0.08
44 37 0.93
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.33
Consensus pattern (44 bp):
TACTTCGACCTTGAGTCAATGAGGCACCATAAGTGTCATACTGC
Found at i:36559313 original size:14 final size:14
Alignment explanation
Indices: 36559296--36559324 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
36559286 GAGAAATGAA
36559296 ATTATTTGGAAATG
1 ATTATTTGGAAATG
36559310 ATTATTTGGAAATG
1 ATTATTTGGAAATG
36559324 A
1 A
36559325 ATATAGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (14 bp):
ATTATTTGGAAATG
Found at i:36559652 original size:29 final size:29
Alignment explanation
Indices: 36559617--36559676 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
36559607 TAAAGTGTTG
36559617 GGTTAAAAGTCCATGAAGTACTTGTTATT
1 GGTTAAAAGTCCATGAAGTACTTGTTATT
36559646 GGTTAAAAGTCCATGAAGTACTTGTTATT
1 GGTTAAAAGTCCATGAAGTACTTGTTATT
36559675 GG
1 GG
36559677 ACTCGATATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.30, C:0.10, G:0.23, T:0.37
Consensus pattern (29 bp):
GGTTAAAAGTCCATGAAGTACTTGTTATT
Found at i:36561762 original size:21 final size:21
Alignment explanation
Indices: 36561736--36561778 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
36561726 AAATAATTTT
36561736 ATTTTATTAATCATATGTATA
1 ATTTTATTAATCATATGTATA
*
36561757 ATTTTATTAATCGTATGTATA
1 ATTTTATTAATCATATGTATA
36561778 A
1 A
36561779 AGCTTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (21 bp):
ATTTTATTAATCATATGTATA
Found at i:36562304 original size:2 final size:2
Alignment explanation
Indices: 36562297--36562331 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
36562287 TTTGGAAAGA
36562297 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
36562332 AAACCATGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:36563185 original size:3 final size:3
Alignment explanation
Indices: 36563179--36563239 Score: 113
Period size: 3 Copynumber: 20.3 Consensus size: 3
36563169 TATCAATTGT
*
36563179 TTA TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
36563227 TTA TTA TTA TTA T
1 TTA TTA TTA TTA T
36563240 CGATTACCAA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:36564542 original size:26 final size:25
Alignment explanation
Indices: 36564493--36564548 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
36564483 TTTGTTATTA
* * * *
36564493 AATTTTAATTAAATTATTATTAAAT
1 AATTTTAATAAAAATAATAATAAAT
36564518 ATATTTTAATAAAAATAATAATAAAT
1 A-ATTTTAATAAAAATAATAATAAAT
36564544 AATTT
1 AATTT
36564549 AATCATATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 5 0.19
26 21 0.81
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
AATTTTAATAAAAATAATAATAAAT
Found at i:36564559 original size:61 final size:60
Alignment explanation
Indices: 36564494--36564666 Score: 178
Period size: 61 Copynumber: 2.9 Consensus size: 60
36564484 TTGTTATTAA
*
36564494 ATTTTAATTAAATTATTATTAAATATATTTTAATAAAAATAATAATAAATAATTTAATCAT
1 ATTTTAATTAAATTATTATTAAATATATTTTAATAAAAATAATAAT-AATAATTTAATAAT
* * * *
36564555 ATTTTAA-CACGATTATTATTAAATACAATTTAAT-AAAATAAT-AT-ATAATTTAATAAT
1 ATTTTAATTA-AATTATTATTAAATATATTTTAATAAAAATAATAATAATAATTTAATAAT
* *
36564612 ATTCTTAATATAAA-TATTATTAAA-ATATGAATTAATAAAAATCATAATATATAAT
1 ATT-TTAAT-TAAATTATTATTAAATATAT--TTTAATAAAAATAATAATA-ATAAT
36564667 ATTATAAAAA
Statistics
Matches: 91, Mismatches: 11, Indels: 18
0.76 0.09 0.15
Matches are distributed among these distances:
57 17 0.19
58 14 0.15
59 8 0.09
60 17 0.19
61 30 0.33
63 5 0.05
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (60 bp):
ATTTTAATTAAATTATTATTAAATATATTTTAATAAAAATAATAATAATAATTTAATAAT
Found at i:36568972 original size:22 final size:22
Alignment explanation
Indices: 36568947--36568992 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
36568937 CACACTACCA
36568947 AAGAAAATGAACAATACATATT
1 AAGAAAATGAACAATACATATT
** **
36568969 AAGAATCTTTACAATACATATT
1 AAGAAAATGAACAATACATATT
36568991 AA
1 AA
36568993 AAATCTTTGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.54, C:0.11, G:0.07, T:0.28
Consensus pattern (22 bp):
AAGAAAATGAACAATACATATT
Found at i:36568997 original size:22 final size:22
Alignment explanation
Indices: 36568957--36569000 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
36568947 AAGAAAATGA
*
36568957 ACAATACATATTAAGAATCTTT
1 ACAATACATATTAAAAATCTTT
36568979 ACAATACATATTAAAAATCTTT
1 ACAATACATATTAAAAATCTTT
36569001 GCAAAGCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.48, C:0.14, G:0.02, T:0.36
Consensus pattern (22 bp):
ACAATACATATTAAAAATCTTT
Found at i:36573856 original size:22 final size:19
Alignment explanation
Indices: 36573811--36573886 Score: 68
Period size: 19 Copynumber: 3.8 Consensus size: 19
36573801 CTTTAGAAAT
36573811 TTTTTAAAAAT-TTTAAT-AA
1 TTTTTAAAAATATTT--TGAA
36573830 TTTTTAAAAATAAATTTTGGAA
1 TTTTTAAAAAT--ATTTT-GAA
*
36573852 TTTTTATAAATATTTTGAA
1 TTTTTAAAAATATTTTGAA
36573871 -TTTTAAAAATTATTTT
1 TTTTTAAAAA-TATTTT
36573887 TTTATTCTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
18 8 0.16
19 20 0.41
20 6 0.12
22 15 0.31
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (19 bp):
TTTTTAAAAATATTTTGAA
Found at i:36573873 original size:19 final size:21
Alignment explanation
Indices: 36573828--36573886 Score: 70
Period size: 22 Copynumber: 2.9 Consensus size: 21
36573818 AAATTTTAAT
36573828 AATTTTTAAAAATAAATTTTGG
1 AATTTTTAAAAAT-AATTTTGG
*
36573850 AATTTTTATAAAT-ATTTT-G
1 AATTTTTAAAAATAATTTTGG
*
36573869 AA-TTTTAAAAATTATTTT
1 AATTTTTAAAAATAATTTT
36573887 TTTATTCTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 9 0.26
19 8 0.24
20 5 0.15
22 12 0.35
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (21 bp):
AATTTTTAAAAATAATTTTGG
Found at i:36575072 original size:3 final size:3
Alignment explanation
Indices: 36575064--36575109 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
36575054 TGACTCAAAT
36575064 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
36575110 CCACATGATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:36581811 original size:21 final size:21
Alignment explanation
Indices: 36581785--36581846 Score: 106
Period size: 21 Copynumber: 3.0 Consensus size: 21
36581775 AAACTTGAAG
36581785 GCTAAACAAAAGCACATAAGT
1 GCTAAACAAAAGCACATAAGT
36581806 GCTAAACAAAAGCACATAAGT
1 GCTAAACAAAAGCACATAAGT
* *
36581827 GCTAAACAAAAACCCATAAG
1 GCTAAACAAAAGCACATAAG
36581847 GGTTGAATGG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.53, C:0.21, G:0.13, T:0.13
Consensus pattern (21 bp):
GCTAAACAAAAGCACATAAGT
Found at i:36581904 original size:42 final size:42
Alignment explanation
Indices: 36581815--36581949 Score: 130
Period size: 42 Copynumber: 3.2 Consensus size: 42
36581805 TGCTAAACAA
* * *
36581815 AAGCACATAAGTGCTAAACAAAAACCCATAAGGGTTGAA-TGG
1 AAGCTCATAAGTGCTAAACAGAAACCCATAAGGGTTAAACT-G
* * * *
36581857 TAGCTCATAAGAGCTAAACGGAAACCCATAAAGGTTAAACTG
1 AAGCTCATAAGTGCTAAACAGAAACCCATAAGGGTTAAACTG
* * * *
36581899 AAGCTCAAAAGTGCTGAACTGAAATCCC-TTAGGGTTAAACTG
1 AAGCTCATAAGTGCTAAACAGAAA-CCCATAAGGGTTAAACTG
*
36581941 AAACTCATA
1 AAGCTCATA
36581950 TGAGTTAATG
Statistics
Matches: 75, Mismatches: 16, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
42 71 0.95
43 4 0.05
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.20
Consensus pattern (42 bp):
AAGCTCATAAGTGCTAAACAGAAACCCATAAGGGTTAAACTG
Found at i:36584977 original size:25 final size:25
Alignment explanation
Indices: 36584949--36585049 Score: 130
Period size: 25 Copynumber: 4.0 Consensus size: 25
36584939 CCACAGCTTA
* *
36584949 TATGAGCTTCCTGATTTACAGGTCG
1 TATGAGCTTCCTAATTTACAGCTCG
*
36584974 TATGAGCTTCCTAATTTACAGCTCA
1 TATGAGCTTCCTAATTTACAGCTCG
* *
36584999 TATGAGCTTCCTAATTTGCAGCTCT
1 TATGAGCTTCCTAATTTACAGCTCG
** *
36585024 TATGAGCTTCCCGATTCACAGCTCG
1 TATGAGCTTCCTAATTTACAGCTCG
36585049 T
1 T
36585050 GAGAGCATAT
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 66 1.00
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.36
Consensus pattern (25 bp):
TATGAGCTTCCTAATTTACAGCTCG
Found at i:36585045 original size:50 final size:50
Alignment explanation
Indices: 36584940--36585047 Score: 144
Period size: 50 Copynumber: 2.2 Consensus size: 50
36584930 GCAGACACAC
* * * *
36584940 CACAGCTTATATGAGCTTCCTGATTTACAGGTCGTATGAGCTTCCTAATT
1 CACAGCTCATATGAGCTTCCTAATTTACAGCTCGTATGAGCTTCCCAATT
* * * *
36584990 TACAGCTCATATGAGCTTCCTAATTTGCAGCTCTTATGAGCTTCCCGATT
1 CACAGCTCATATGAGCTTCCTAATTTACAGCTCGTATGAGCTTCCCAATT
36585040 CACAGCTC
1 CACAGCTC
36585048 GTGAGAGCAT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (50 bp):
CACAGCTCATATGAGCTTCCTAATTTACAGCTCGTATGAGCTTCCCAATT
Found at i:36585064 original size:25 final size:25
Alignment explanation
Indices: 36585036--36585083 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
36585026 TGAGCTTCCC
36585036 GATTCACAGCTCGTGA-GAGCATATT
1 GATTCACAGCTCGT-ATGAGCATATT
*
36585061 GATTCATAGCTCGTATGAGCATA
1 GATTCACAGCTCGTATGAGCATA
36585084 CATGAATATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (25 bp):
GATTCACAGCTCGTATGAGCATATT
Found at i:36586697 original size:17 final size:17
Alignment explanation
Indices: 36586675--36586708 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
36586665 TCCATCAATT
36586675 GAATGAGCATTTTCTTA
1 GAATGAGCATTTTCTTA
36586692 GAATGAGCATTTTCTTA
1 GAATGAGCATTTTCTTA
36586709 AGCCTTTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (17 bp):
GAATGAGCATTTTCTTA
Found at i:36594475 original size:32 final size:32
Alignment explanation
Indices: 36594432--36594516 Score: 109
Period size: 32 Copynumber: 2.7 Consensus size: 32
36594422 TCACAGTATA
*
36594432 AATTGGGCCTAGCCCATTTCAGAATCAATATC
1 AATTGGGCCTAGCCCATTTCAGAACCAATATC
* * *
36594464 AGTTGGGCCTAGCCC-TTATCAGAACCATTATT
1 AATTGGGCCTAGCCCATT-TCAGAACCAATATC
*
36594496 AATTGGGCCTGGCCCATTTCA
1 AATTGGGCCTAGCCCATTTCA
36594517 ATATCCAACC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
31 2 0.04
32 41 0.91
33 2 0.04
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (32 bp):
AATTGGGCCTAGCCCATTTCAGAACCAATATC
Found at i:36599881 original size:14 final size:16
Alignment explanation
Indices: 36599857--36599902 Score: 65
Period size: 18 Copynumber: 2.7 Consensus size: 16
36599847 ATCCGTTTTT
36599857 CCAACAACAACACCAC
1 CCAACAACAACACCAC
36599873 CCAAACAACCAACACCAC
1 CC-AACAA-CAACACCAC
36599891 CCAAACAACAAC
1 CC-AACAACAAC
36599903 TATCTTAACC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 2 0.07
17 9 0.32
18 17 0.61
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (16 bp):
CCAACAACAACACCAC
Found at i:36599887 original size:18 final size:18
Alignment explanation
Indices: 36599859--36599899 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
36599849 CCGTTTTTCC
36599859 AACAA-CAACACCACCCA
1 AACAACCAACACCACCCA
36599876 AACAACCAACACCACCCA
1 AACAACCAACACCACCCA
36599894 AACAAC
1 AACAAC
36599900 AACTATCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.54, C:0.46, G:0.00, T:0.00
Consensus pattern (18 bp):
AACAACCAACACCACCCA
Found at i:36602639 original size:29 final size:29
Alignment explanation
Indices: 36602580--36602639 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
36602570 TTTTTGCAAT
* *
36602580 TTTTTAAAAAATTTAAATACTTTTTTTTA
1 TTTTTAAAAAATTGAAATACTTTTTTATA
36602609 TTTTTATAAAAATTGAAA-A-TTTTTATATA
1 TTTTTA-AAAAATTGAAATACTTTTT-TATA
36602638 TT
1 TT
36602640 ATTTGACTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 5 0.19
29 12 0.44
30 10 0.37
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (29 bp):
TTTTTAAAAAATTGAAATACTTTTTTATA
Found at i:36602689 original size:10 final size:9
Alignment explanation
Indices: 36602674--36602710 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
36602664 TACATATTTC
36602674 AAAATTTTAT
1 AAAATTTT-T
36602684 AAAATTTTT
1 AAAATTTTT
*
36602693 AAATTTTTT
1 AAAATTTTT
36602702 AAAATTTTT
1 AAAATTTTT
36602711 TTGAATTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 17 0.68
10 8 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
AAAATTTTT
Found at i:36602696 original size:18 final size:18
Alignment explanation
Indices: 36602675--36602710 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
36602665 ACATATTTCA
36602675 AAATTTTATAAAATTTTT
1 AAATTTTATAAAATTTTT
*
36602693 AAATTTTTTAAAATTTTT
1 AAATTTTATAAAATTTTT
36602711 TTGAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
AAATTTTATAAAATTTTT
Found at i:36602711 original size:10 final size:10
Alignment explanation
Indices: 36602674--36602711 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
36602664 TACATATTTC
*
36602674 AAAATTTTAT
1 AAAATTTTTT
36602684 AAAA-TTTTT
1 AAAATTTTTT
36602693 -AAATTTTTT
1 AAAATTTTTT
36602702 AAAATTTTTT
1 AAAATTTTTT
36602712 TGAATTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
8 3 0.12
9 9 0.36
10 13 0.52
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
AAAATTTTTT
Found at i:36605780 original size:46 final size:45
Alignment explanation
Indices: 36605730--36605978 Score: 338
Period size: 46 Copynumber: 5.5 Consensus size: 45
36605720 TATTCATTTC
36605730 TATCTTTCAACCATGGTCTTATTCATTTCCTGTCATGTTGCCATGG
1 TATCTTTCAACCATGGTCTTATTCATTT-CTGTCATGTTGCCATGG
* *
36605776 TATCTTTCAACCATGGTCTTATTCATTTCCTGTCATGTGGCCATAG
1 TATCTTTCAACCATGGTCTTATTCATTT-CTGTCATGTTGCCATGG
* *
36605822 TATCTTTCAACCATGGTCTTATTCATTT-TATCATGTTACCATGG
1 TATCTTTCAACCATGGTCTTATTCATTTCTGTCATGTTGCCATGG
*
36605866 TATCTTTCAACCATGGTCTTATTCATTTTCTATCATGTTGCCATGG
1 TATCTTTCAACCATGGTCTTATTCA-TTTCTGTCATGTTGCCATGG
* ** * **
36605912 TATCTTTCAACCATAGTCTTATTTGTTTCTCGTCATATTGCCATAA
1 TATCTTTCAACCATGGTCTTATTCATTTCT-GTCATGTTGCCATGG
* *
36605958 TATCTTTCAACTATGGCCTTA
1 TATCTTTCAACCATGGTCTTA
36605979 CATATCTTAA
Statistics
Matches: 183, Mismatches: 17, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
44 37 0.20
45 8 0.04
46 138 0.75
ACGTcount: A:0.21, C:0.22, G:0.12, T:0.44
Consensus pattern (45 bp):
TATCTTTCAACCATGGTCTTATTCATTTCTGTCATGTTGCCATGG
Found at i:36605885 original size:90 final size:91
Alignment explanation
Indices: 36605730--36605934 Score: 331
Period size: 90 Copynumber: 2.3 Consensus size: 91
36605720 TATTCATTTC
* *
36605730 TATCTTTCAACCATGGTCTTATTCATTTCCTGTCATGTTGCCATGGTATCTTTCAACCATGGTCT
1 TATCTTTCAACCATGGTCTTATTCATTT-CTATCATGTTACCATGGTATCTTTCAACCATGGTCT
*
36605795 TATTCATTTCCTGTCATGTGGCCATAG
65 TATTCATTTCCTATCATGTGGCCATAG
36605822 TATCTTTCAACCATGGTCTTATTCATTT-TATCATGTTACCATGGTATCTTTCAACCATGGTCTT
1 TATCTTTCAACCATGGTCTTATTCATTTCTATCATGTTACCATGGTATCTTTCAACCATGGTCTT
* * *
36605886 ATTCATTTTCTATCATGTTGCCATGG
66 ATTCATTTCCTATCATGTGGCCATAG
*
36605912 TATCTTTCAACCATAGTCTTATT
1 TATCTTTCAACCATGGTCTTATT
36605935 TGTTTCTCGT
Statistics
Matches: 106, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
90 78 0.74
92 28 0.26
ACGTcount: A:0.20, C:0.22, G:0.13, T:0.44
Consensus pattern (91 bp):
TATCTTTCAACCATGGTCTTATTCATTTCTATCATGTTACCATGGTATCTTTCAACCATGGTCTT
ATTCATTTCCTATCATGTGGCCATAG
Found at i:36605902 original size:136 final size:136
Alignment explanation
Indices: 36605730--36605978 Score: 392
Period size: 136 Copynumber: 1.8 Consensus size: 136
36605720 TATTCATTTC
* *
36605730 TATCTTTCAACCATGGTCTTATTCATTTCCTGTCATGTTGCCATGGTATCTTTCAACCATGGTCT
1 TATCTTTCAACCATGGTCTTATTCATTTCCTATCATGTTGCCATGGTATCTTTCAACCATAGTCT
* * *
36605795 TATTCATTTC-CTGTCATGTGGCCATAGTATCTTTCAACCATGGTCTTATTCATTTTATCATGTT
66 TATTCATTTCTC-GTCATATGGCCATAATATCTTTCAACCATGGCCTTATTCATTTTATCATGTT
36605859 ACCATGG
130 ACCATGG
*
36605866 TATCTTTCAACCATGGTCTTATTCATTTTCTATCATGTTGCCATGGTATCTTTCAACCATAGTCT
1 TATCTTTCAACCATGGTCTTATTCATTTCCTATCATGTTGCCATGGTATCTTTCAACCATAGTCT
** * *
36605931 TATTTGTTTCTCGTCATATTGCCATAATATCTTTCAACTATGGCCTTA
66 TATTCATTTCTCGTCATATGGCCATAATATCTTTCAACCATGGCCTTA
36605979 CATATCTTAA
Statistics
Matches: 102, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
136 101 0.99
137 1 0.01
ACGTcount: A:0.21, C:0.22, G:0.12, T:0.44
Consensus pattern (136 bp):
TATCTTTCAACCATGGTCTTATTCATTTCCTATCATGTTGCCATGGTATCTTTCAACCATAGTCT
TATTCATTTCTCGTCATATGGCCATAATATCTTTCAACCATGGCCTTATTCATTTTATCATGTTA
CCATGG
Found at i:36606009 original size:45 final size:45
Alignment explanation
Indices: 36605950--36606073 Score: 160
Period size: 45 Copynumber: 2.8 Consensus size: 45
36605940 CTCGTCATAT
** * * * *
36605950 TGCCATAATATCTTTCAACTATGGCCTTACAT-ATCTTAATCGTGA
1 TGCCATAACGTCTTTCAGCTATGGTCTTAC-TCATCTGAATCGCGA
36605995 TGCCATAACGTCTTTCAGCTATGGTCTTACTCATCTGAATCGCGA
1 TGCCATAACGTCTTTCAGCTATGGTCTTACTCATCTGAATCGCGA
**
36606040 TGCCATTGCGTCTTTCAGCTATGGTCTTACTCAT
1 TGCCATAACGTCTTTCAGCTATGGTCTTACTCAT
36606074 TTCTGGTATG
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
44 1 0.01
45 69 0.99
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.37
Consensus pattern (45 bp):
TGCCATAACGTCTTTCAGCTATGGTCTTACTCATCTGAATCGCGA
Found at i:36606087 original size:45 final size:42
Alignment explanation
Indices: 36605992--36606091 Score: 119
Period size: 45 Copynumber: 2.2 Consensus size: 42
36605982 ATCTTAATCG
36605992 TGATGCCATAACGTCTTTCAGCTATGGTCTTACTCATCTGAA
1 TGATGCCATAACGTCTTTCAGCTATGGTCTTACTCATCTGAA
** *
36606034 TCGCGATGCCATTGCGTCTTTCAGCTATGGTCTTACTCATTTCTGGTA
1 T---GATGCCATAACGTCTTTCAGCTATGGTCTTACTCA--TCT-GAA
36606082 TGATGCCATA
1 TGATGCCATA
36606092 GTCCAACTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
42 1 0.02
45 41 0.85
47 3 0.06
48 3 0.06
ACGTcount: A:0.20, C:0.24, G:0.19, T:0.37
Consensus pattern (42 bp):
TGATGCCATAACGTCTTTCAGCTATGGTCTTACTCATCTGAA
Found at i:36606140 original size:33 final size:33
Alignment explanation
Indices: 36606085--36606240 Score: 120
Period size: 33 Copynumber: 4.7 Consensus size: 33
36606075 TCTGGTATGA
* * * *
36606085 TGCCATAGTCCAACTATAGTCTTACACATGTAT
1 TGCCATAGCCCAGCCATGGTCTTACACATGTAT
* * *
36606118 TGCCATGGCGCAGCCATGGTCTTACAC-TCGTAG
1 TGCCATAGCCCAGCCATGGTCTTACACAT-GTAT
* ** *
36606151 TGCCATATCCCAGATATGGTCTTATCATCA-GGA-
1 TGCCATAGCCCAGCCATGGTCTTA-CA-CATGTAT
* * * *
36606184 TCCCATAGCCTAGCTATGGTCTTACACATATAT
1 TGCCATAGCCCAGCCATGGTCTTACACATGTAT
*
36606217 TGCCATGGCCCAGCCATGGTCTTA
1 TGCCATAGCCCAGCCATGGTCTTA
36606241 TCCGTCAATT
Statistics
Matches: 94, Mismatches: 23, Indels: 12
0.73 0.18 0.09
Matches are distributed among these distances:
31 2 0.02
32 4 0.04
33 83 0.88
34 4 0.04
35 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (33 bp):
TGCCATAGCCCAGCCATGGTCTTACACATGTAT
Found at i:36607842 original size:11 final size:11
Alignment explanation
Indices: 36607826--36607850 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
36607816 CTTTCTTTAT
36607826 ATACTAATAAA
1 ATACTAATAAA
36607837 ATACTAATAAA
1 ATACTAATAAA
36607848 ATA
1 ATA
36607851 ATAACAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (11 bp):
ATACTAATAAA
Found at i:36608192 original size:30 final size:31
Alignment explanation
Indices: 36608124--36608182 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
36608114 CACCCTTAAA
** *
36608124 ATATTTACACTTTTAGTCCTTCAAATTTTTC
1 ATATTTACACTTTTAACCCCTCAAATTTTTC
36608155 ATATTTACAC-TTTAACCCCTCAAATTTT
1 ATATTTACACTTTTAACCCCTCAAATTTT
36608183 GAGTATTTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.29, C:0.22, G:0.02, T:0.47
Consensus pattern (31 bp):
ATATTTACACTTTTAACCCCTCAAATTTTTC
Found at i:36613324 original size:29 final size:30
Alignment explanation
Indices: 36613279--36613348 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 30
36613269 TTATATTATC
36613279 TAAATATATTTTA-TTTTGTGATTGAA-AAAT
1 TAAA-ATATTTTATTTTTGTGATT-AAGAAAT
*
36613309 TAAAATATTTTATTTTTGTGGTTAAGAAAT
1 TAAAATATTTTATTTTTGTGATTAAGAAAT
*
36613339 TCAAATATTT
1 TAAAATATTT
36613349 GAATTTAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
29 10 0.28
30 26 0.72
ACGTcount: A:0.39, C:0.01, G:0.10, T:0.50
Consensus pattern (30 bp):
TAAAATATTTTATTTTTGTGATTAAGAAAT
Found at i:36613420 original size:13 final size:13
Alignment explanation
Indices: 36613402--36613426 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36613392 TAACTTTATT
36613402 TTTAAATATTTTG
1 TTTAAATATTTTG
36613415 TTTAAATATTTT
1 TTTAAATATTTT
36613427 TCTACTTTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
TTTAAATATTTTG
Found at i:36616732 original size:2 final size:2
Alignment explanation
Indices: 36616725--36616751 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
36616715 TACTATGAGT
36616725 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
36616752 TCATTTATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:36620190 original size:17 final size:18
Alignment explanation
Indices: 36620164--36620207 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
36620154 CAATTCTTGT
*
36620164 TTTCTGTTTTCTTATT-G
1 TTTCTTTTTTCTTATTGG
*
36620181 TTTCTTTTTTCTTTTTGG
1 TTTCTTTTTTCTTATTGG
36620199 TTT-TTTTTT
1 TTTCTTTTTT
36620208 TGGGGTTGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 20 0.83
18 4 0.17
ACGTcount: A:0.02, C:0.09, G:0.09, T:0.80
Consensus pattern (18 bp):
TTTCTTTTTTCTTATTGG
Found at i:36625055 original size:2 final size:2
Alignment explanation
Indices: 36625048--36625086 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
36625038 TCAATGTTCA
*
36625048 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
36625087 GAAACTAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:36626433 original size:37 final size:38
Alignment explanation
Indices: 36626369--36626447 Score: 92
Period size: 37 Copynumber: 2.2 Consensus size: 38
36626359 AATATCAATT
*
36626369 TCACA-TTTTATCTTTAAGATAACTTTT-ATTTAAAAA
1 TCACATTTTTATATTTAAGATAACTTTTAATTTAAAAA
* ** *
36626405 TCACATTTTTATATTTAATATATTTTTTAATTTCAAAA
1 TCACATTTTTATATTTAAGATAACTTTTAATTTAAAAA
36626443 T-ACAT
1 TCACAT
36626448 AGTGACGAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
36 5 0.14
37 22 0.61
38 9 0.25
ACGTcount: A:0.38, C:0.10, G:0.01, T:0.51
Consensus pattern (38 bp):
TCACATTTTTATATTTAAGATAACTTTTAATTTAAAAA
Found at i:36642518 original size:29 final size:31
Alignment explanation
Indices: 36642477--36642536 Score: 70
Period size: 29 Copynumber: 2.0 Consensus size: 31
36642467 AATTTACCGA
* *
36642477 TAGATAAACTAAATCTAAAAACATTAAAATT
1 TAGATAAACTAAAACCAAAAACATTAAAATT
**
36642508 TAGA-AAA-TAAAACCAAAAGTATTAAAATT
1 TAGATAAACTAAAACCAAAAACATTAAAATT
36642537 ATAATATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
29 18 0.72
30 3 0.12
31 4 0.16
ACGTcount: A:0.60, C:0.08, G:0.05, T:0.27
Consensus pattern (31 bp):
TAGATAAACTAAAACCAAAAACATTAAAATT
Found at i:36642830 original size:16 final size:16
Alignment explanation
Indices: 36642809--36642847 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
36642799 TCAATGTAGC
36642809 TTAAAAAAATAAAATT
1 TTAAAAAAATAAAATT
* *
36642825 TTAAAATATTAAAATT
1 TTAAAAAAATAAAATT
*
36642841 CTAAAAA
1 TTAAAAA
36642848 TTAACTAGTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (16 bp):
TTAAAAAAATAAAATT
Found at i:36647012 original size:26 final size:26
Alignment explanation
Indices: 36646976--36647084 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
36646966 TGATACAAAT
36646976 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
36647002 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
36647028 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
36647054 TGATAATGGGTTAGGTAAATGTT-CA
1 TGATAATAGGTTAGGTAAATGTTCCA
36647079 TGATAA
1 TGATAA
36647085 GAATTTCATG
Statistics
Matches: 81, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
25 8 0.10
26 73 0.90
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:36648741 original size:27 final size:27
Alignment explanation
Indices: 36648700--36648812 Score: 129
Period size: 27 Copynumber: 4.2 Consensus size: 27
36648690 GAGGAAGCGT
*
36648700 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
36648727 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
36648754 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
36648782 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
36648808 TCTGG
1 TCTGG
36648813 CAGCCATGCT
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
26 5 0.07
27 55 0.73
28 15 0.20
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.36
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:36648805 original size:54 final size:54
Alignment explanation
Indices: 36648698--36648812 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
36648688 TGGAGGAAGC
*
36648698 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
* * * *
36648752 GTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCT
1 GTTCTGGTGGCTATGCCACAAATATCTG-ATCTGGTGACTCTGCCACATATATCT
36648806 GTTCTGG
1 GTTCTGG
36648813 CAGCCATGCT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 37 0.67
55 18 0.33
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (54 bp):
GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
Found at i:36652810 original size:26 final size:26
Alignment explanation
Indices: 36652774--36652882 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
36652764 TGATACAAAT
36652774 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
36652800 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
36652826 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
36652852 TGATAATGGGTTAGGTAAATGTT-CA
1 TGATAATAGGTTAGGTAAATGTTCCA
36652877 TGATAA
1 TGATAA
36652883 GAATTTCATG
Statistics
Matches: 81, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
25 8 0.10
26 73 0.90
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:36654598 original size:27 final size:26
Alignment explanation
Indices: 36654494--36654608 Score: 140
Period size: 27 Copynumber: 4.3 Consensus size: 26
36654484 TGGAGGAAGC
* *
36654494 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTCTGCCAC-ATTATCT
*
36654521 GATCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTCTGCCACAT-TATCT
36654548 GTTCTGGTGGCTCTGCCACGATTATCT
1 GTTCTGGTGGCTCTGCCAC-ATTATCT
* **
36654575 GTATCTGGTGACTCTATCACATTATCT
1 GT-TCTGGTGGCTCTGCCACATTATCT
36654602 GTTCTGG
1 GTTCTGG
36654609 CAGCCATGCT
Statistics
Matches: 78, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
26 6 0.08
27 56 0.72
28 16 0.21
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (26 bp):
GTTCTGGTGGCTCTGCCACATTATCT
Found at i:36654601 original size:54 final size:54
Alignment explanation
Indices: 36654494--36654608 Score: 160
Period size: 54 Copynumber: 2.1 Consensus size: 54
36654484 TGGAGGAAGC
* *
36654494 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTACCACATATATCT
* * * *
36654548 GTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTATCACAT-TATCT
1 GTTCTGGTGGCTATGCCACAAATATCTG-ATCTGGTGACTCTACCACATATATCT
36654602 GTTCTGG
1 GTTCTGG
36654609 CAGCCATGCT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
54 37 0.69
55 17 0.31
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (54 bp):
GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTACCACATATATCT
Found at i:36656222 original size:10 final size:10
Alignment explanation
Indices: 36656209--36656244 Score: 72
Period size: 10 Copynumber: 3.6 Consensus size: 10
36656199 ACATAAATAC
36656209 AGATAATTAA
1 AGATAATTAA
36656219 AGATAATTAA
1 AGATAATTAA
36656229 AGATAATTAA
1 AGATAATTAA
36656239 AGATAA
1 AGATAA
36656245 AAGCTAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.28
Consensus pattern (10 bp):
AGATAATTAA
Found at i:36658220 original size:27 final size:26
Alignment explanation
Indices: 36658189--36658254 Score: 64
Period size: 27 Copynumber: 2.5 Consensus size: 26
36658179 ACTAATATCC
*
36658189 AAAAAAATAAAA-TAATAAATAATAAA
1 AAAAAAATAAAAGGAA-AAATAATAAA
*
36658215 AGAAAAAGA-AAAAGGAAGAATAATAAA
1 A-AAAAA-ATAAAAGGAAAAATAATAAA
36658242 AAATAAAATAAAA
1 AAA-AAAATAAAA
36658255 AAATTGGGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
26 4 0.12
27 26 0.79
28 3 0.09
ACGTcount: A:0.79, C:0.00, G:0.08, T:0.14
Consensus pattern (26 bp):
AAAAAAATAAAAGGAAAAATAATAAA
Found at i:36661121 original size:10 final size:10
Alignment explanation
Indices: 36661104--36661142 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
36661094 TTAAATTCTA
36661104 AAAGATAAAT
1 AAAGATAAAT
* *
36661114 ACAGATAATT
1 AAAGATAAAT
36661124 AAAGATAAAT
1 AAAGATAAAT
36661134 AAAGATAAA
1 AAAGATAAA
36661143 AGCTAGAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.67, C:0.03, G:0.10, T:0.21
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:36661129 original size:20 final size:20
Alignment explanation
Indices: 36661104--36661141 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
36661094 TTAAATTCTA
*
36661104 AAAGATAAATACAGATAATT
1 AAAGATAAATAAAGATAATT
36661124 AAAGATAAATAAAGATAA
1 AAAGATAAATAAAGATAA
36661142 AAGCTAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.66, C:0.03, G:0.11, T:0.21
Consensus pattern (20 bp):
AAAGATAAATAAAGATAATT
Found at i:36664779 original size:21 final size:21
Alignment explanation
Indices: 36664755--36664794 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
36664745 TGCAAGTTAG
*
36664755 ATAAAGAAAAGACA-GTAAATA
1 ATAAACAAAAG-CATGTAAATA
36664776 ATAAACAAAAGCATGTAAA
1 ATAAACAAAAGCATGTAAA
36664795 ATGGCTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.65, C:0.07, G:0.12, T:0.15
Consensus pattern (21 bp):
ATAAACAAAAGCATGTAAATA
Found at i:36666007 original size:28 final size:29
Alignment explanation
Indices: 36665975--36666032 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
36665965 TTTCTAATAT
36665975 TATTA-CAAATATATTATTTCTT-TTATTA
1 TATTATCAAA-ATATTATTTCTTATTATTA
* *
36666003 TATTATTAAAATATTATTTTTTATTATTA
1 TATTATCAAAATATTATTTCTTATTATTA
36666032 T
1 T
36666033 TTTCTTTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.60
Consensus pattern (29 bp):
TATTATCAAAATATTATTTCTTATTATTA
Found at i:36666009 original size:31 final size:29
Alignment explanation
Indices: 36665971--36666032 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 29
36665961 GTATTTTCTA
*
36665971 ATATTATTACAAATA-TATTATTTCTTTTATT
1 ATATTATTA-AAATATTATT-TTT-TATTATT
36666002 ATATTATTAAAATATTATTTTTTATTATT
1 ATATTATTAAAATATTATTTTTTATTATT
36666031 AT
1 AT
36666033 TTTCTTTATC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 8 0.28
30 8 0.28
31 13 0.45
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (29 bp):
ATATTATTAAAATATTATTTTTTATTATT
Found at i:36666147 original size:2 final size:2
Alignment explanation
Indices: 36666140--36666177 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
36666130 ATTGCAAATG
*
36666140 AT AT AT AT AT AT AT AT AA 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 AT AT
36666178 TTAATTAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:36675914 original size:93 final size:91
Alignment explanation
Indices: 36675792--36675963 Score: 263
Period size: 93 Copynumber: 1.9 Consensus size: 91
36675782 TGATATTTTT
* * **
36675792 ATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGCCACATGCTGA
1 ATTTCTGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGACCCTCGAGCCACACACTGA
*
36675857 GGTATTTTCAATTTCTATTTTTTAAA
66 GGTATCTTCAATTTCTATTTTTTAAA
* *
36675883 ATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGACCCTCGGGTCACACACT
1 ATTTCTGCTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGACCCTCGAGCCACACACT
36675948 GAGGTATCTTCAATTT
64 GAGGTATCTTCAATTT
36675964 ATGTTTCAAA
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
91 12 0.17
93 60 0.83
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (91 bp):
ATTTCTGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGACCCTCGAGCCACACACTGA
GGTATCTTCAATTTCTATTTTTTAAA
Found at i:36676015 original size:79 final size:77
Alignment explanation
Indices: 36675896--36676171 Score: 331
Period size: 78 Copynumber: 3.5 Consensus size: 77
36675886 TCTGCTTTTC
* * * * *
36675896 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGACCCTCGGGTCACACACTGAGGTATCTTCAA
1 AAAAAAATCAACTCATATTGCAAGAAGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTCAA
*
36675961 TTTATGTTTCAAAA
66 TTTATTTTTC--AA
* *
36675975 AAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTTTA
1 AAAAAAATCAACTCATATTGCAAGAAGTGAGTTGAGCCTCGGGTCACACGCTGAGGTA-TTTTCA
*
36676040 GTTTGTATTTTTC--
65 -ATT-TATTTTTCAA
* * * *
36676053 AAAAAAATCAACTCATATTACAAGAGGTGAGTTGAGTCTCGGGACACACGCTGAGGTATTTTCAA
1 AAAAAAATCAACTCATATTGCAAGAAGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTCAA
36676118 TTTACATTTTTTCAA
66 TTT--A-TTTTTCAA
**
36676133 AAAAAAATTGACTCATATTGCAAGAAGTGAGTTGAGCCT
1 AAAAAAATCAACTCATATTGCAAGAAGTGAGTTGAGCCT
36676172 TTTAGTCTCT
Statistics
Matches: 170, Mismatches: 19, Indels: 15
0.83 0.09 0.07
Matches are distributed among these distances:
75 1 0.01
76 2 0.01
77 6 0.04
78 59 0.35
79 55 0.32
80 38 0.22
81 2 0.01
82 7 0.04
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (77 bp):
AAAAAAATCAACTCATATTGCAAGAAGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTCAA
TTTATTTTTCAA
Found at i:36678291 original size:28 final size:29
Alignment explanation
Indices: 36678259--36678316 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
36678249 TTTCTACTAT
36678259 TATTA-CAAATATATTATTTCTT-TTATTA
1 TATTATCAAA-ATATTATTTCTTATTATTA
* *
36678287 TATTATTAAAATATTATTTTTTATTATTA
1 TATTATCAAAATATTATTTCTTATTATTA
36678316 T
1 T
36678317 TTTCTTTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.60
Consensus pattern (29 bp):
TATTATCAAAATATTATTTCTTATTATTA
Found at i:36678348 original size:24 final size:23
Alignment explanation
Indices: 36678308--36678366 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 23
36678298 TATTATTTTT
36678308 TATTATTATTT-TCTTTA-TCATGAA
1 TATTATT-TTTATCTTTATTC-T-AA
*
36678332 TATTATTTTTATTTTTATTCTAA
1 TATTATTTTTATCTTTATTCTAA
36678355 TATTATATTTTA
1 TATTAT-TTTTA
36678367 ATATTTTTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
23 11 0.35
24 18 0.58
25 2 0.06
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (23 bp):
TATTATTTTTATCTTTATTCTAA
Found at i:36678967 original size:25 final size:25
Alignment explanation
Indices: 36678939--36678993 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
36678929 ACGTAGCTAC
*
36678939 AAATATTTTATTTTAATTATTAT-TT
1 AAATATTTGATTTTAATT-TTATATT
*
36678964 AAAT-TTTGGTTTTAATTTTATACTT
1 AAATATTTGATTTTAATTTTATA-TT
36678989 AAATA
1 AAATA
36678994 ATAAATTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 4 0.16
24 11 0.44
25 10 0.40
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (25 bp):
AAATATTTGATTTTAATTTTATATT
Found at i:36680004 original size:2 final size:2
Alignment explanation
Indices: 36679997--36680022 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
36679987 AAATAAAAAT
36679997 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
36680023 AAAGGAGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:36680822 original size:20 final size:20
Alignment explanation
Indices: 36680785--36680821 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
36680775 TATTTTTCTG
*
36680785 AAAAAGTTAATTATTTTTAA
1 AAAAAATTAATTATTTTTAA
36680805 AAAAAATTAA-TATTTTT
1 AAAAAATTAATTATTTTT
36680822 TGGTGTTTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (20 bp):
AAAAAATTAATTATTTTTAA
Found at i:36681409 original size:20 final size:22
Alignment explanation
Indices: 36681380--36681421 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
36681370 AATAAAATAG
*
36681380 AAATATTAAA-TA-ATTTATTA
1 AAATAATAAATTATATTTATTA
36681400 AAATAATAAATTATATTTATTA
1 AAATAATAAATTATATTTATTA
36681422 TATTAACAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 2 0.11
22 8 0.42
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AAATAATAAATTATATTTATTA
Found at i:36681435 original size:22 final size:22
Alignment explanation
Indices: 36681392--36681435 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
36681382 ATATTAAATA
*
36681392 ATTTATTAAAATAATAAATTAT
1 ATTTATTAAAATAACAAATTAT
* * *
36681414 ATTTATTATATTAACAATTTAT
1 ATTTATTAAAATAACAAATTAT
36681436 CGTATAACTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
ATTTATTAAAATAACAAATTAT
Found at i:36682901 original size:67 final size:67
Alignment explanation
Indices: 36682777--36682903 Score: 177
Period size: 67 Copynumber: 1.9 Consensus size: 67
36682767 GTTTGTCTAG
* * *
36682777 TGGACTTCATAGCCCCCACATGTGAACTCCTTAGTATATGCGAGCTGCTACCACGAACTTTCCTT
1 TGGACTTCATAGCCCCCACATGTCAACTCCTTAGTATATACGAGCTGCGACCACGAACTTTCCTT
36682842 GC
66 GC
* *
36682844 TGGACTTCATAGCCCCCACATG-CAATCTCCTTGGTATATACGAGCTAG-GACCGCGAACTT
1 TGGACTTCATAGCCCCCACATGTCAA-CTCCTTAGTATATACGAGCT-GCGACCACGAACTT
36682904 CCCTCGCGAA
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
66 2 0.04
67 50 0.94
68 1 0.02
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.27
Consensus pattern (67 bp):
TGGACTTCATAGCCCCCACATGTCAACTCCTTAGTATATACGAGCTGCGACCACGAACTTTCCTT
GC
Found at i:36684036 original size:54 final size:54
Alignment explanation
Indices: 36683954--36684067 Score: 210
Period size: 54 Copynumber: 2.1 Consensus size: 54
36683944 AAGAATGTGA
* *
36683954 AGGAAACGTACCATATTGTTATGGAGTTTGATATCAACCTTAAAAAATGGCAGG
1 AGGAAACGTACCATATAGTTATGGAGTTTGATATCAACCTTAAAAAATGGCAGC
36684008 AGGAAACGTACCATATAGTTATGGAGTTTGATATCAACCTTAAAAAATGGCAGC
1 AGGAAACGTACCATATAGTTATGGAGTTTGATATCAACCTTAAAAAATGGCAGC
36684062 AGGAAA
1 AGGAAA
36684068 ACTACAATAA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 58 1.00
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.25
Consensus pattern (54 bp):
AGGAAACGTACCATATAGTTATGGAGTTTGATATCAACCTTAAAAAATGGCAGC
Found at i:36692473 original size:14 final size:14
Alignment explanation
Indices: 36692454--36692483 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
36692444 CATAGTAACC
*
36692454 CTTATGCTATGCAT
1 CTTATGCTATACAT
36692468 CTTATGCTATACAT
1 CTTATGCTATACAT
36692482 CT
1 CT
36692484 CGGTGGTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.43
Consensus pattern (14 bp):
CTTATGCTATACAT
Found at i:36697583 original size:27 final size:27
Alignment explanation
Indices: 36697539--36697627 Score: 82
Period size: 25 Copynumber: 3.5 Consensus size: 27
36697529 AATGCTCATA
* *
36697539 CGAGCACATA-AACTGGAAGCTCCCTCT
1 CGAGC-CATATAACAGGAAGCTCCATCT
*
36697566 CGAGCCATATAACAGGAAGCT-CATGT
1 CGAGCCATATAACAGGAAGCTCCATCT
* *
36697592 -GAGCCATATAACAAGAAGCT-CAT-A
1 CGAGCCATATAACAGGAAGCTCCATCT
36697616 CGAGCCA-ATAAC
1 CGAGCCATATAAC
36697628 GGGTAGTTCT
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
24 5 0.09
25 28 0.51
26 7 0.13
27 15 0.27
ACGTcount: A:0.37, C:0.27, G:0.19, T:0.17
Consensus pattern (27 bp):
CGAGCCATATAACAGGAAGCTCCATCT
Found at i:36697599 original size:25 final size:25
Alignment explanation
Indices: 36697566--36697627 Score: 90
Period size: 25 Copynumber: 2.5 Consensus size: 25
36697556 AGCTCCCTCT
* *
36697566 CGAGCCATATAACAGGAAGCTCATG
1 CGAGCCATATAACAAGAAGCTCATA
*
36697591 TGAGCCATATAACAAGAAGCTCATA
1 CGAGCCATATAACAAGAAGCTCATA
36697616 CGAGCCA-ATAAC
1 CGAGCCATATAAC
36697628 GGGTAGTTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
24 5 0.15
25 28 0.85
ACGTcount: A:0.40, C:0.24, G:0.19, T:0.16
Consensus pattern (25 bp):
CGAGCCATATAACAAGAAGCTCATA
Done.