Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold465
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: 646967
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
File 4 of 4
Found at i:478442 original size:51 final size:51
Alignment explanation
Indices: 478387--478489 Score: 129
Period size: 51 Copynumber: 2.0 Consensus size: 51
478377 CTCACCTCGA
* * *
478387 TTTTA-TTTCTAAAATATCAACTTT-TCACCTTCGGGGATACTCCAACCCCAT
1 TTTTATTTTC-AAAATACCAA-TTTCTCACCATCAGGGATACTCCAACCCCAT
* *
478438 TTTTATTTTCAAAATACCAATTTCTCACCATCAGGTATACTCTAACCCCAT
1 TTTTATTTTCAAAATACCAATTTCTCACCATCAGGGATACTCCAACCCCAT
478489 T
1 T
478490 ATTTTTGAGG
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
50 3 0.07
51 38 0.84
52 4 0.09
ACGTcount: A:0.29, C:0.27, G:0.06, T:0.38
Consensus pattern (51 bp):
TTTTATTTTCAAAATACCAATTTCTCACCATCAGGGATACTCCAACCCCAT
Found at i:480612 original size:14 final size:14
Alignment explanation
Indices: 480593--480620 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
480583 ATTTCGTACA
480593 GTCACTAATTCATT
1 GTCACTAATTCATT
480607 GTCACTAATTCATT
1 GTCACTAATTCATT
480621 TTCCTTTTTG
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):
GTCACTAATTCATT
Found at i:484631 original size:28 final size:28
Alignment explanation
Indices: 484557--484633 Score: 120
Period size: 28 Copynumber: 2.8 Consensus size: 28
484547 GAAATAAGGT
*
484557 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
484585 TGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
484613 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
484634 TATGAAAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
27 1 0.02
28 44 0.98
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:484659 original size:107 final size:107
Alignment explanation
Indices: 484473--484681 Score: 271
Period size: 107 Copynumber: 2.0 Consensus size: 107
484463 TTTTGGAGAT
* * *
484473 AATAACGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTGTCCCCGATTGTGAGAAATC
1 AATAACGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATC
** *
484538 AATATTTTAGAAATAAGGTCGGGGTTGGAGTATCCCCTCAGA
66 AATATTTTAGAAATAAAATCGGAGTTGGAGTATCCCCTCAGA
*
484580 AATAATGGGGTTGGAGTAT-CCC-CGATGAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAA
1 AATAACGGGGTTGGAGTATCCCCTCGA--AAATAACGGGGTTGGAGTATCCCCGATTATGAAAAA
* * * *
484643 TTAGTGTTTT-GAAAATAAAATCGGAGTTGGAGTGTCCCC
64 TCAATATTTTAG-AAATAAAATCGGAGTTGGAGTATCCCC
484682 GATTATGGAG
Statistics
Matches: 88, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
105 3 0.03
106 4 0.05
107 81 0.92
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.26
Consensus pattern (107 bp):
AATAACGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATC
AATATTTTAGAAATAAAATCGGAGTTGGAGTATCCCCTCAGA
Found at i:484686 original size:51 final size:51
Alignment explanation
Indices: 484617--484728 Score: 147
Period size: 51 Copynumber: 2.2 Consensus size: 51
484607 AAATAACGGG
484617 GTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTT-GAAAATAAAA-TCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAG-AAATAAAACT-GGA
* * * * *
484668 GTTGGAGTGTCCCCGATTATGGAGAATTGGTGTTTTAGAAATAAAACTGGG
1 GTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAACTGGA
484719 GTTGGAGTAT
1 GTTGGAGTAT
484729 TCCCTCAAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
51 51 0.96
52 2 0.04
ACGTcount: A:0.31, C:0.09, G:0.28, T:0.32
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAACTGGA
Found at i:484751 original size:79 final size:77
Alignment explanation
Indices: 484668--484959 Score: 347
Period size: 76 Copynumber: 3.8 Consensus size: 77
484658 TAAAATCGGA
* * * * * *
484668 GTTGGAGTGTCCCCGATTATGGAGAATTGGTGTTTTAGAAATAAAACTGGGGTTGGAGTATTCCC
1 GTTGGAGTATCCCCGA--ATGAAAAATTGATGTTTTAGAAATAAAACCGAGGTTGGAGTATTCCC
484733 TCAAAAATAACGGG
64 TCAAAAATAACGGG
*
484747 GTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCG-GAGTTGGAGTGTTCC
1 GTTGGAGTATCCCCGA--ATGAAAAATTGATGTTTTAGAAATAAAACCGAG-GTTGGAGTATTCC
*
484811 CTCAAAAATAATGGG
63 CTCAAAAATAACGGG
* * * * *
484826 GTTGGAATATCCCCG-ATGAAAAATTGATGTTTTAGAAATAAAACCAAGGTTAGAGTGTCCCCTC
1 GTTGGAGTATCCCCGAATGAAAAATTGATGTTTTAGAAATAAAACCGAGGTTGGAGTATTCCCTC
**
484890 GGAAATAACGGG
66 AAAAATAACGGG
* * * *
484902 GTTAGAGTATCCTC-AATGAAAAATTGATGTTTTAGAAATAAAACTGAGGTTGAAGTAT
1 GTTGGAGTATCCCCGAATGAAAAATTGATGTTTTAGAAATAAAACCGAGGTTGGAGTAT
484960 CCCCGATTAT
Statistics
Matches: 188, Mismatches: 22, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
76 102 0.54
77 1 0.01
78 1 0.01
79 84 0.45
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (77 bp):
GTTGGAGTATCCCCGAATGAAAAATTGATGTTTTAGAAATAAAACCGAGGTTGGAGTATTCCCTC
AAAAATAACGGG
Found at i:484984 original size:51 final size:51
Alignment explanation
Indices: 484921--485067 Score: 160
Period size: 51 Copynumber: 2.9 Consensus size: 51
484911 TCCTCAATGA
*
484921 AAAATTGATGTTTTAGAAATAAAA-CTGAGGTTGAAGTATCCCCGATTATGG
1 AAAATTGATGTTTTAGAAATAAAATCGGA-GTTGAAGTATCCCCGATTATGG
* *
484972 AAAATGTG-TGTTTTAGAAATAAAATCGGAGTTGGAGTATCCCCGATTA-AG
1 AAAAT-TGATGTTTTAGAAATAAAATCGGAGTTGAAGTATCCCCGATTATGG
* * *
485022 AGAAATTGATGTTTT-GAAAATGAAACCAGGA-TTGGAGTATCCCCGA
1 A-AAATTGATGTTTTAG-AAATAAAATC-GGAGTTGAAGTATCCCCGA
485068 GATGAAAAAT
Statistics
Matches: 85, Mismatches: 5, Indels: 12
0.83 0.05 0.12
Matches are distributed among these distances:
50 5 0.06
51 72 0.85
52 8 0.09
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (51 bp):
AAAATTGATGTTTTAGAAATAAAATCGGAGTTGAAGTATCCCCGATTATGG
Found at i:487391 original size:20 final size:21
Alignment explanation
Indices: 487366--487408 Score: 79
Period size: 20 Copynumber: 2.1 Consensus size: 21
487356 AAAATGCCTG
487366 AATGTATCGATACAT-TGGGT
1 AATGTATCGATACATCTGGGT
487386 AATGTATCGATACATCTGGGT
1 AATGTATCGATACATCTGGGT
487407 AA
1 AA
487409 AATTTTCAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.33
Consensus pattern (21 bp):
AATGTATCGATACATCTGGGT
Found at i:487456 original size:13 final size:13
Alignment explanation
Indices: 487438--487462 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
487428 ACAAAAGATC
487438 AATGTATCGATAT
1 AATGTATCGATAT
487451 AATGTATCGATA
1 AATGTATCGATA
487463 CATTTCCTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (13 bp):
AATGTATCGATAT
Found at i:487476 original size:21 final size:21
Alignment explanation
Indices: 487450--487492 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
487440 TGTATCGATA
487450 TAATGTATCGATACATTTCCT
1 TAATGTATCGATACATTTCCT
487471 TAATGTATCGATACATTTCCT
1 TAATGTATCGATACATTTCCT
487492 T
1 T
487493 GGTAGTAGCT
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:0.28, C:0.19, G:0.09, T:0.44
Consensus pattern (21 bp):
TAATGTATCGATACATTTCCT
Found at i:487527 original size:13 final size:13
Alignment explanation
Indices: 487509--487624 Score: 70
Period size: 13 Copynumber: 7.5 Consensus size: 13
487499 AGCTTCGTAG
487509 CGATACATTGTAT
1 CGATACATTGTAT
487522 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
487541 CGATACATTGTAT
1 CGATACATTGTAT
487554 CGATACAACACTTATGTAT
1 CGAT---ACA--T-TGTAT
487573 CGATACATTGTAT
1 CGATACATTGTAT
487586 CGATACAACACTTATGTAT
1 CGAT---ACA--T-TGTAT
487605 CGATACATTGTAT
1 CGATACATTGTAT
487618 CGATACA
1 CGATACA
487625 ACACTTATGT
Statistics
Matches: 85, Mismatches: 0, Indels: 36
0.70 0.00 0.30
Matches are distributed among these distances:
13 35 0.41
14 2 0.02
15 2 0.02
16 14 0.16
17 2 0.02
18 2 0.02
19 28 0.33
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:487541 original size:19 final size:18
Alignment explanation
Indices: 487517--487666 Score: 114
Period size: 19 Copynumber: 8.8 Consensus size: 18
487507 AGCGATACAT
487517 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
487536 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
487549 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
487568 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
487581 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
487600 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
487613 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
* *
487632 TGTATCGATACATTTACTGTT
1 TGTATCGATACA--AACT-TA
487653 TGTATCGATACAAA
1 TGTATCGATACAAA
487667 TTGTTTGAAA
Statistics
Matches: 107, Mismatches: 3, Indels: 42
0.70 0.02 0.28
Matches are distributed among these distances:
13 33 0.31
14 3 0.03
16 6 0.06
18 3 0.03
19 46 0.43
20 3 0.03
21 13 0.12
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:487550 original size:32 final size:32
Alignment explanation
Indices: 487509--487645 Score: 265
Period size: 32 Copynumber: 4.3 Consensus size: 32
487499 AGCTTCGTAG
*
487509 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
487541 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
487573 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
487605 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
487637 CGATACATT
1 CGATACATT
487646 TACTGTTTGT
Statistics
Matches: 104, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
32 104 1.00
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.34
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:487673 original size:19 final size:19
Alignment explanation
Indices: 487612--487673 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
487602 TATCGATACA
487612 TTGTATCGATACAACACT-T
1 TTGTATCGATACAA-ACTGT
* *
487631 ATGTATCGATACATTTACTGT
1 TTGTATCGATACA--AACTGT
*
487652 TTGTATCGATACAAATTGT
1 TTGTATCGATACAAACTGT
487671 TTG
1 TTG
487674 AAATTCAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
19 19 0.54
20 3 0.09
21 13 0.37
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.42
Consensus pattern (19 bp):
TTGTATCGATACAAACTGT
Found at i:494134 original size:23 final size:24
Alignment explanation
Indices: 494108--494155 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
494098 AGTTATGACA
494108 GCCCCATGGCC-TTTTTCTATGTG
1 GCCCCATGGCCTTTTTTCTATGTG
*
494131 GCCCCATGGCCTTTTTTCTCTGTG
1 GCCCCATGGCCTTTTTTCTATGTG
494155 G
1 G
494156 GGCATGGACA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.06, C:0.31, G:0.23, T:0.40
Consensus pattern (24 bp):
GCCCCATGGCCTTTTTTCTATGTG
Found at i:496236 original size:59 final size:59
Alignment explanation
Indices: 496048--496541 Score: 571
Period size: 59 Copynumber: 8.4 Consensus size: 59
496038 AACCTTTTAT
* * * * * * ** *
496048 CCTTTTAGTCCTTAAAGAGTAAGACACCTT-CTTTTAAAGCCCACACAGGTTAATGACA
1 CCTTCTAGTCCTCAAAGAGCAGGACACTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * *
496106 CCTT-TAGTCCTCAAAGAGAAGGACACGTTCTCCTTTCAAAGCCAACACAGGTTGATGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACAC-TT-TCCTTTTAAAGCCCACACAAGTTGGTGGCA
* *
496166 ACTTTTAGTCCTCAAAGAGCAGGACACTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACACTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * *
496225 CCTTCTTGTCCTCAAAGAGCAGGACACTTTCTTTTTAAAGCTCACACAAGTTGATGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACACTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * *
496284 CCTTCTAGCCCTCAAAGAGTAGGACACTTT-CTTTTAAAGCCCACACAAGTTAGTGGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACACTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * * *
496342 CATTCTAGTCCTCAAACAGCAGGACACCTTCTCTTTCTAAAGCCCATAAAAGTTGGTAGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACACTTTC-CTTT-TAAAGCCCACACAAGTTGGTGGCA
* * * *
496403 CCTTCTAGTCCTCAAAGAGTAGGACATTTTCCTTTTAAAGCCCACACAAGTTAGTGACA
1 CCTTCTAGTCCTCAAAGAGCAGGACACTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * *
496462 CCTTCTAGTCCTCAAAGTGCAGGACACTTTCCTTTCAAAGCCCACACAGGTTGCTAGCA
1 CCTTCTAGTCCTCAAAGAGCAGGACACTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* *
496521 CCTTCTAGTCTTTAAAGAGCA
1 CCTTCTAGTCCTCAAAGAGCA
496542 TGATGCCTTC
Statistics
Matches: 371, Mismatches: 58, Indels: 13
0.84 0.13 0.03
Matches are distributed among these distances:
57 19 0.05
58 54 0.15
59 194 0.52
60 37 0.10
61 67 0.18
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (59 bp):
CCTTCTAGTCCTCAAAGAGCAGGACACTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:496397 original size:178 final size:175
Alignment explanation
Indices: 496048--496530 Score: 596
Period size: 178 Copynumber: 2.7 Consensus size: 175
496038 AACCTTTTAT
* * * * *
496048 CCTTTTAGTCCTTAAAGAGTAAGACACCTTCTTTTAAAGCCCACACAGGTTAATGACACCTT-TA
1 CCTTCTAGTCCTCAAAGAGTAGGACACTTTCTTTTAAAGCCCACACAAGTT-ATGACACCTTCTA
* * *
496112 GTCCTCAAAGAGAAGGACACGTTCTCCTTTCAAAGCCAACACAGGTTGATGGCAACTTTTAGTCC
65 GTCCTCAAAGAGAAGGACAC-TT-TCCTTTCAAAGCCCACACAAGTTGATGGCAACTTCTAGTCC
* * * *
496177 TCAAAGAGCAGGACACTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
128 TCAAACAGCAGGACACCTTCCTTTTAAAGCCCACAAAAGTTGGTAGCA
* * * *
496225 CCTTCTTGTCCTCAAAGAGCAGGACACTTTCTTTTTAAAGCTCACACAAGTTGATGGCACCTTCT
1 CCTTCTAGTCCTCAAAGAGTAGGACACTTTC-TTTTAAAGCCCACACAAGTT-ATGACACCTTCT
* * *
496290 AGCCCTCAAAGAGTAGGACACTTT-CTTTTAAAGCCCACACAAGTT-AGTGGC-ACATTCTAGTC
64 AGTCCTCAAAGAGAAGGACACTTTCCTTTCAAAGCCCACACAAGTTGA-TGGCAAC-TTCTAGTC
*
496352 CTCAAACAGCAGGACACCTTCTCTTTCTAAAGCCCATAAAAGTTGGTAGCA
127 CTCAAACAGCAGGACACCTTC-CTTT-TAAAGCCCACAAAAGTTGGTAGCA
*
496403 CCTTCTAGTCCTCAAAGAGTAGGACATTTTCCTTTTAAAGCCCACACAAGTTAGTGACACCTTCT
1 CCTTCTAGTCCTCAAAGAGTAGGACACTTT-CTTTTAAAGCCCACACAAGTTA-TGACACCTTCT
* * * * * *
496468 AGTCCTCAAAGTGCAGGACACTTTCCTTTCAAAGCCCACACAGGTTGCTAGCACCTTCTAGTC
64 AGTCCTCAAAGAGAAGGACACTTTCCTTTCAAAGCCCACACAAGTTGATGGCAACTTCTAGTC
496531 TTTAAAGAGC
Statistics
Matches: 261, Mismatches: 34, Indels: 20
0.83 0.11 0.06
Matches are distributed among these distances:
175 3 0.01
176 48 0.18
177 31 0.12
178 127 0.49
179 51 0.20
180 1 0.00
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (175 bp):
CCTTCTAGTCCTCAAAGAGTAGGACACTTTCTTTTAAAGCCCACACAAGTTATGACACCTTCTAG
TCCTCAAAGAGAAGGACACTTTCCTTTCAAAGCCCACACAAGTTGATGGCAACTTCTAGTCCTCA
AACAGCAGGACACCTTCCTTTTAAAGCCCACAAAAGTTGGTAGCA
Found at i:496475 original size:237 final size:236
Alignment explanation
Indices: 496061--496528 Score: 650
Period size: 237 Copynumber: 2.0 Consensus size: 236
496051 TTTAGTCCTT
* * *
496061 AAAGAGTAAGACACCTTCTTTTAAAGCCCACACAGGTTAATGACACCTTTAGTCCTCAAAGAGAA
1 AAAGAGTAAGACACCTTCTTTTAAAGCCCACACAAGTTAATGACACATTTAGTCCTCAAACAGAA
* * * * *
496126 GGACACGTTCTCCTTTCAAAGCCAACACAGGTTGATGGCAACTTTTAGTCCTCAAAGAGCAGGAC
66 GGACACCTTCTCCTTTCAAAGCCAACAAAAGTTGATAGCAACTTCTAGTCCTCAAAGAGCAGGAC
* * *
496191 ACTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTTGTCCTCAAAGAGCAGGACACTTTC
131 ACTTTCCTTTTAAAGCCCACACAAGTTAGTGACACCTTCTAGTCCTCAAAGAGCAGGACACTTTC
* * * *
496256 TTTTTAAAGCTCACACAAGTTGATGGCACCTTCTAGCCCTC
196 CTTTCAAAGCCCACACAAGTTGATAGCACCTTCTAGCCCTC
* * * * *
496297 AAAGAGTAGGACACTTTCTTTTAAAGCCCACACAAGTTAGTGGCACATTCTAGTCCTCAAACAGC
1 AAAGAGTAAGACACCTTCTTTTAAAGCCCACACAAGTTAATGACACATT-TAGTCCTCAAACAGA
* * * * *
496362 AGGACACCTTCT-CTTTCTAAAGCCCATAAAAGTTGGTAGCACCTTCTAGTCCTCAAAGAGTAGG
65 AGGACACCTTCTCCTTTC-AAAGCCAACAAAAGTTGATAGCAACTTCTAGTCCTCAAAGAGCAGG
* *
496426 ACATTTTCCTTTTAAAGCCCACACAAGTTAGTGACACCTTCTAGTCCTCAAAGTGCAGGACACTT
129 ACACTTTCCTTTTAAAGCCCACACAAGTTAGTGACACCTTCTAGTCCTCAAAGAGCAGGACACTT
* *
496491 TCCTTTCAAAGCCCACACAGGTTGCTAGCACCTTCTAG
194 TCCTTTCAAAGCCCACACAAGTTGATAGCACCTTCTAG
496529 TCTTTAAAGA
Statistics
Matches: 201, Mismatches: 29, Indels: 3
0.86 0.12 0.01
Matches are distributed among these distances:
236 48 0.24
237 153 0.76
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (236 bp):
AAAGAGTAAGACACCTTCTTTTAAAGCCCACACAAGTTAATGACACATTTAGTCCTCAAACAGAA
GGACACCTTCTCCTTTCAAAGCCAACAAAAGTTGATAGCAACTTCTAGTCCTCAAAGAGCAGGAC
ACTTTCCTTTTAAAGCCCACACAAGTTAGTGACACCTTCTAGTCCTCAAAGAGCAGGACACTTTC
CTTTCAAAGCCCACACAAGTTGATAGCACCTTCTAGCCCTC
Found at i:496881 original size:13 final size:13
Alignment explanation
Indices: 496863--496887 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
496853 CATTATGCTT
496863 TGTATCGATACAC
1 TGTATCGATACAC
496876 TGTATCGATACA
1 TGTATCGATACA
496888 TGGACAATTG
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:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:501192 original size:13 final size:13
Alignment explanation
Indices: 501174--501199 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
501164 CAATTTTTTG
501174 TGTATCGATACAT
1 TGTATCGATACAT
501187 TGTATCGATACAT
1 TGTATCGATACAT
501200 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:501264 original size:21 final size:20
Alignment explanation
Indices: 501238--501314 Score: 91
Period size: 21 Copynumber: 3.8 Consensus size: 20
501228 CTGCCAAGAA
501238 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACAT-TTTTTT
*****
501259 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTTTTTT
501279 ATGTATCGATACATTTTTTT
1 ATGTATCGATACATTTTTTT
501299 CATGTATCGATACATT
1 -ATGTATCGATACATT
501315 GCAACATGTA
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTTT
Found at i:501284 original size:20 final size:20
Alignment explanation
Indices: 501259--501331 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
501249 CATCTTTTTT
501259 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
501279 ATGTATCGATACATTTTTTTC
1 ATGTATCGATACA-TTGCAAC
501300 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
501320 ATGTATCGATAC
1 ATGTATCGATAC
501332 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:501298 original size:41 final size:41
Alignment explanation
Indices: 501238--501331 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
501228 CTGCCAAGAA
*
501238 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
*
501279 ATGTATCGATACATTTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
501320 ATGTATCGATAC
1 ATGTATCGATAC
501332 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:503795 original size:13 final size:13
Alignment explanation
Indices: 503777--503815 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
503767 ATAATCACCC
*
503777 TGTATCGATACAG
1 TGTATCGATACAA
503790 TGTATCGATACAA
1 TGTATCGATACAA
503803 TGTATCGATACAA
1 TGTATCGATACAA
503816 GGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:510077 original size:13 final size:13
Alignment explanation
Indices: 510059--510084 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
510049 CAATTTTTTG
510059 TGTATCGATACAT
1 TGTATCGATACAT
510072 TGTATCGATACAT
1 TGTATCGATACAT
510085 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:510169 original size:20 final size:20
Alignment explanation
Indices: 510144--510216 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
510134 CATCCTTTTT
510144 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
510164 ATGTATCGATACATTTTTTTC
1 ATGTATCGATACA-TTGCAAC
510185 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
510205 ATGTATCGATAC
1 ATGTATCGATAC
510217 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:510189 original size:21 final size:21
Alignment explanation
Indices: 510123--510199 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
510113 CTGCCAAGAA
*
510123 ATGTATCGATACATCCTTTTT-
1 ATGTATCGATACAT-TTTTTTC
****
510144 ATGTATCGATACA-TTGCAAC
1 ATGTATCGATACATTTTTTTC
510164 ATGTATCGATACATTTTTTTC
1 ATGTATCGATACATTTTTTTC
510185 ATGTATCGATACATT
1 ATGTATCGATACATT
510200 GCAACATGTA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
19 1 0.02
20 13 0.29
21 31 0.69
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.43
Consensus pattern (21 bp):
ATGTATCGATACATTTTTTTC
Found at i:510189 original size:41 final size:41
Alignment explanation
Indices: 510123--510216 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
510113 CTGCCAAGAA
510123 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
*
510164 ATGTATCGATACAT-TTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCCTTTTT-ATGTATCGATACATTGCAAC
510205 ATGTATCGATAC
1 ATGTATCGATAC
510217 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 5 0.10
41 46 0.90
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
Found at i:512125 original size:20 final size:21
Alignment explanation
Indices: 512081--512130 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
512071 CTACCACTCT
*
512081 TTGTATCGATATATGGTATAA
1 TTGTATCGATACATGGTATAA
512102 -TGTATCGATACAT-G-ATGAA
1 TTGTATCGATACATGGTAT-AA
512121 TTGTATCGAT
1 TTGTATCGAT
512131 GCATTGCTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 2 0.08
19 3 0.12
20 21 0.81
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (21 bp):
TTGTATCGATACATGGTATAA
Found at i:514333 original size:21 final size:21
Alignment explanation
Indices: 514316--514356 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
514306 AAGATGATAT
514316 TAAAAAATTAGCTAATGAAAA
1 TAAAAAATTAGCTAATGAAAA
**
514337 TAATGAATTAGCTAA-GAAAA
1 TAAAAAATTAGCTAATGAAAA
514357 ACACAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.59, C:0.05, G:0.12, T:0.24
Consensus pattern (21 bp):
TAAAAAATTAGCTAATGAAAA
Found at i:514365 original size:20 final size:21
Alignment explanation
Indices: 514320--514365 Score: 51
Period size: 20 Copynumber: 2.2 Consensus size: 21
514310 TGATATTAAA
*
514320 AAATTAGCTAATGAAAATAAT
1 AAATTAGCTAATGAAAATAAC
*
514341 GAATTAGCTAA-GAAAA-ACAC
1 AAATTAGCTAATGAAAATA-AC
514361 AAATT
1 AAATT
514366 TGCATGATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.05
20 10 0.48
21 10 0.48
ACGTcount: A:0.57, C:0.09, G:0.11, T:0.24
Consensus pattern (21 bp):
AAATTAGCTAATGAAAATAAC
Found at i:520189 original size:22 final size:22
Alignment explanation
Indices: 520164--520226 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 22
520154 TTTTTTAATT
*
520164 TTTGACAAAGGGGGAGAAATGC
1 TTTGACAAAGGGAGAGAAATGC
** *
520186 TTTGATTAAGGGAGAGAAATTC
1 TTTGACAAAGGGAGAGAAATGC
* **
520208 TTTAATTAAGGGAGAGAAA
1 TTTGACAAAGGGAGAGAAA
520227 AATGAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.40, C:0.05, G:0.30, T:0.25
Consensus pattern (22 bp):
TTTGACAAAGGGAGAGAAATGC
Found at i:520200 original size:20 final size:21
Alignment explanation
Indices: 520174--520226 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 21
520164 TTTGACAAAG
*
520174 GGGGAGAAATGCTTTGATTAA
1 GGGGAGAAATGCTTTAATTAA
*
520195 GGGAGAGAAATTCTTTAATTAA
1 GGG-GAGAAATGCTTTAATTAA
520217 GGGAGAGAAA
1 GGG-GAGAAA
520227 AATGAAAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 3 0.10
22 26 0.90
ACGTcount: A:0.40, C:0.04, G:0.32, T:0.25
Consensus pattern (21 bp):
GGGGAGAAATGCTTTAATTAA
Found at i:520788 original size:13 final size:13
Alignment explanation
Indices: 520770--520796 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
520760 ACATTATGCT
520770 TTGTATCGATACA
1 TTGTATCGATACA
520783 TTGTATCGATACA
1 TTGTATCGATACA
520796 T
1 T
520797 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:525223 original size:79 final size:79
Alignment explanation
Indices: 525139--525582 Score: 402
Period size: 79 Copynumber: 5.6 Consensus size: 79
525129 TTTTCCATTA
* * *
525139 GGGATACTCCAACCCCATTATTTTCGAGAGAATATTCCAACCCCGTTTTTTTCCCAAAATATCAA
1 GGGATACTCCAACCCCATTATTTTCGAGAGGATACTCCAACCCCGTTTTTTTTCCAAAATATCAA
*
525204 ATTTTTCACCATTG
66 ATTTTTCACCATCG
* * * * * ** *
525218 GGGATACTTCAACCCCATCATTTCCGAGGGGATACTCCAACCCCATTTTTAACTCCAAAATATTA
1 GGGATACTCCAACCCCATTATTTTCGAGAGGATACTCCAACCCCGTTTTT-TTTCCAAAATATCA
*
525283 AATTTTTCATC-TCG
65 AATTTTTCACCATCG
* * *
525297 AGGATACTCCAACCCCGTTATTTTCGA-AGGGATACTCCAGCCCC-TTTTTTAGTTCCAAAATAT
1 GGGATACTCCAACCCCATTATTTTCGAGA-GGATACTCCAACCCCGTTTTTT--TTCCAAAATAT
* *
525360 TAAA-TTTTCATC-TCG
63 CAAATTTTTCACCATCG
** ** * * *
525375 GGGATACTTTAACCCCATTATTCCCAAGGGGATACTCCAGCCCCGTTTTTTATTTCCAAAATATC
1 GGGATACTCCAACCCCATTATTTTCGAGAGGATACTCCAACCCCG-TTTTT-TTTCCAAAATATC
*
525440 -AATTTTTCACTATCG
64 AAATTTTTCACCATCG
* ** * ** *
525455 GGGATACTTCAACCCCATTATTTTTAAG-GAGATACTCTAACCTTGTTTTTATTTTCAAAATATC
1 GGGATACTCCAACCCCATTATTTTCGAGAG-GATACTCCAACCCCGTTTTT-TTTCCAAAATATC
*
525519 -GATTTTTCACCATCG
64 AAATTTTTCACCATCG
* * * * *
525534 GGGATACTCCAACCCTATCACTTTCAAG-GGATACTCCAACCCTGTTTTT
1 GGGATACTCCAACCCCATTATTTTCGAGAGGATACTCCAACCCCGTTTTT
525583 ACTTATAAAA
Statistics
Matches: 303, Mismatches: 51, Indels: 23
0.80 0.14 0.06
Matches are distributed among these distances:
78 71 0.23
79 168 0.55
80 63 0.21
81 1 0.00
ACGTcount: A:0.27, C:0.26, G:0.12, T:0.35
Consensus pattern (79 bp):
GGGATACTCCAACCCCATTATTTTCGAGAGGATACTCCAACCCCGTTTTTTTTCCAAAATATCAA
ATTTTTCACCATCG
Found at i:525368 original size:158 final size:155
Alignment explanation
Indices: 525140--525624 Score: 462
Period size: 158 Copynumber: 3.1 Consensus size: 155
525130 TTTCCATTAG
* * *
525140 GGATACTCCAACCCCATTATTTTCG-AGAGAATATTCCAACCCCGTTTTTT-TCCCAAAATATCA
1 GGATACTCCAACCCCATTATTTTCGAAG-GGATACTCC-ACCCC-TTTTTTATTCCAAAATATCA
*
525203 AATTTTTCACCATTGGGGATACTTCAACCCCATCATTTCCGAGGGGATACTCCAACCCCATTTTT
63 AA-TTTTCACCATCGGGGATACTTCAACCCCATCATTTCC-AGGGGATACTCCAACCCCATTTTT
525268 AACTCCAAAATATTAAATTTTTCATCTCGA
126 AACTCCAAAATATTAAATTTTTCATCTCGA
* *
525298 GGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAGCCCCTTTTTTAGTTCCAAAATATTAA
1 GGATACTCCAACCCCATTATTTTCGAAGGGATACTCCA-CCCCTTTTTTA-TTCCAAAATATCAA
* * * * * *
525363 ATTTTCATC-TCGGGGATACTTTAACCCCATTATTCCCAAGGGGATACTCCAGCCCCGTTTTTTA
64 ATTTTCACCATCGGGGATACTTCAACCCCATCATTTCC-AGGGGATACTCCAACCCC-ATTTTTA
** * * *
525427 TTTCCAAAATA-TCAATTTTTCACTATCGG
127 ACTCCAAAATATTAAATTTTTCA-TCTCGA
* * * * * * *
525456 GGATACTTCAACCCCATTATTTT-TAAGGAGATACTCTAACCTTGTTTTTATTTTCAAAATATCG
1 GGATACTCCAACCCCATTATTTTCGAAGG-GATACTCCACCCCT-TTTTTA-TTCCAAAATATCA
* * * * **
525520 ATTTTTCACCATCGGGGATACTCCAACCCTATCACTTT-CAAGGGATACTCCAACCCTGTTTTT-
63 AATTTTCACCATCGGGGATACTTCAACCCCATCA-TTTCCAGGGGATACTCCAACCCCATTTTTA
** *
525583 ACTTATAAAATATTAAATTTTTTTCATCTCAA
127 AC-TCCAAAATATTAAA--TTTTTCATCTCGA
*
525615 GGGTACTCCA
1 GGATACTCCA
525625 CCCATATCCC
Statistics
Matches: 264, Mismatches: 49, Indels: 27
0.78 0.14 0.08
Matches are distributed among these distances:
157 77 0.29
158 132 0.50
159 46 0.17
160 9 0.03
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.35
Consensus pattern (155 bp):
GGATACTCCAACCCCATTATTTTCGAAGGGATACTCCACCCCTTTTTTATTCCAAAATATCAAAT
TTTCACCATCGGGGATACTTCAACCCCATCATTTCCAGGGGATACTCCAACCCCATTTTTAACTC
CAAAATATTAAATTTTTCATCTCGA
Found at i:530505 original size:52 final size:52
Alignment explanation
Indices: 530420--530544 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
530410 ATATGAAAAG
* *
530420 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
530472 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
530524 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
530545 AAGATCAGTG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:530557 original size:52 final size:51
Alignment explanation
Indices: 530420--530564 Score: 211
Period size: 52 Copynumber: 2.8 Consensus size: 51
530410 ATATGAAAAG
*
530420 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
530472 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
530524 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
530565 ATGTATCGAT
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 83 0.98
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:530571 original size:13 final size:13
Alignment explanation
Indices: 530553--530577 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
530543 CAAAGATCAG
530553 TGTATCGATACAA
1 TGTATCGATACAA
530566 TGTATCGATACA
1 TGTATCGATACA
530578 TGTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:530660 original size:33 final size:33
Alignment explanation
Indices: 530618--530687 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
530608 GGCAGTAGCT
530618 TACATTGTATCGATACAAAAAAATATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
* ***
530651 TACATTGTATCGATACAACATTTTATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
530684 TACA
1 TACA
530688 AATCGTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (33 bp):
TACATTGTATCGATACAAAAAAATATGTATCGA
Found at i:530661 original size:13 final size:13
Alignment explanation
Indices: 530643--530667 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
530633 CAAAAAAATA
530643 TGTATCGATACAT
1 TGTATCGATACAT
530656 TGTATCGATACA
1 TGTATCGATACA
530668 ACATTTTATG
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:532725 original size:155 final size:155
Alignment explanation
Indices: 532398--532736 Score: 405
Period size: 155 Copynumber: 2.2 Consensus size: 155
532388 GCCTTCGACA
* * *
532398 TAAAAGTACCTA-ATACCCCTAAAAGACTTAAAAAGGATAATAGATGGGATGAACCTATCCTAAA
1 TAAAAGTACC-AGATACCCCTAAAGGACTTAAAAAGGATAATAGATGAGATAAACCTATCCTAAA
* **
532462 TATAAACCTTTGGCATAAAAGCGGACCCAGTGACAACCTAGGACTCAATCCTAAAAAATTATGAA
65 TATAAACCTTCGGCATAAAAGCGGACCCAGTGACAACCTAGGACTCAATCCTAAAAAATTACAAA
* *
532527 AATGCCCCTAAGGGATACCTTTGACG
130 AATGCCCCTAAGAGATACCTTTAACG
** * * *
532553 TAAAAGTAAAAGGTACCCCTAAAGGACTTAAAAAGGATAATATATGAGATAAACCTGTCCTAAAT
1 TAAAAGTACCAGATACCCCTAAAGGACTTAAAAAGGATAATAGATGAGATAAACCTATCCTAAAT
* * * * *** *
532618 ATCTAA-CTTCGGCATAAAAGTGGACCCTGTGTCAACCTAGGACTTGGTTCTAAAAAATTACAAA
66 AT-AAACCTTCGGCATAAAAGCGGACCCAGTGACAACCTAGGACTCAATCCTAAAAAATTACAAA
* *
532682 AATGCTCCTAAGAGATGTCC-TTAACG
130 AATGCCCCTAAGAGAT-ACCTTTAACG
* *
532708 TAAAAGTACCCGATACCCCTAAGGGACTT
1 TAAAAGTACCAGATACCCCTAAAGGACTT
532737 GGGATAATGC
Statistics
Matches: 153, Mismatches: 28, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
154 1 0.01
155 148 0.97
156 4 0.03
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (155 bp):
TAAAAGTACCAGATACCCCTAAAGGACTTAAAAAGGATAATAGATGAGATAAACCTATCCTAAAT
ATAAACCTTCGGCATAAAAGCGGACCCAGTGACAACCTAGGACTCAATCCTAAAAAATTACAAAA
ATGCCCCTAAGAGATACCTTTAACG
Found at i:533282 original size:159 final size:162
Alignment explanation
Indices: 533050--533475 Score: 630
Period size: 164 Copynumber: 2.6 Consensus size: 162
533040 TTATTATTAA
* * *
533050 ACCTTAATGGAAGCCTGAAAAGATAC-AAGAAG--TTTCAAAGTCTTTTAATACCCCTACGGATA
1 ACCTTAATGGAAGCCCGAAAAGATACGAA-AAGTTTTTGAAAATCTTTT-ATACCCCTACGGATA
* *
533112 CCCATAGGAATATAAAAGATTAGAAAAATGATTAAAATTTACCTCAATAGCGAAAGTGTTAATTT
64 CCCATAGGAATATAAAAGATTAGAAAAATGATTAAAATTGACCTCAATAACGAAAGTGTTAATTT
*
533177 AA-TTTA-ATTTATTTTCAAAAATACCATTTCGT
129 AATTTTATATTTATTTTCAAAAATACCATTTCAT
* * *
533209 ACCTTAATGGAAGCCCGAAAAGATACGAAAAGTTTTTGGAAATCTTTTATACCCCTATGGATGCC
1 ACCTTAATGGAAGCCCGAAAAGATACGAAAAGTTTTTGAAAATCTTTTATACCCCTACGGATACC
* *
533274 CATA-GAATATAAAAGATTAGAAAAATGATTAAAATTGATCTCAATAACGAATGTGTTAATTTAA
66 CATAGGAATATAAAAGATTAGAAAAATGATTAAAATTGACCTCAATAACGAAAGTGTTAATTTAA
533338 TTTTATTTTATTTATTTTCAAAAATACCATTTCAT
131 TTTTA---TATTTATTTTCAAAAATACCATTTCAT
*
533373 ACCTTAATGGAAGCCCGAAAAGATACGAAAAGTTTTTGAAAATCTTTTATACCCCTACGGATTCC
1 ACCTTAATGGAAGCCCGAAAAGATACGAAAAGTTTTTGAAAATCTTTTATACCCCTACGGATACC
* *
533438 CATAGGAATATAAAAAATTAAAAAGAATGATTAAAATT
66 CATAGGAATATAAAAGATTAGAAA-AATGATTAAAATT
533476 CAACTTTGCC
Statistics
Matches: 241, Mismatches: 16, Indels: 13
0.89 0.06 0.05
Matches are distributed among these distances:
159 84 0.35
160 25 0.10
161 11 0.05
164 91 0.38
165 17 0.07
166 13 0.05
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.32
Consensus pattern (162 bp):
ACCTTAATGGAAGCCCGAAAAGATACGAAAAGTTTTTGAAAATCTTTTATACCCCTACGGATACC
CATAGGAATATAAAAGATTAGAAAAATGATTAAAATTGACCTCAATAACGAAAGTGTTAATTTAA
TTTTATATTTATTTTCAAAAATACCATTTCAT
Found at i:535821 original size:19 final size:20
Alignment explanation
Indices: 535797--535837 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
535787 AAAAACATTC
*
535797 AAAATTAACGAAA-TAAATT
1 AAAATTAACAAAACTAAATT
*
535816 AAAATTATCAAAACTAAATT
1 AAAATTAACAAAACTAAATT
535836 AA
1 AA
535838 TGAGAGTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.27
Consensus pattern (20 bp):
AAAATTAACAAAACTAAATT
Found at i:535835 original size:20 final size:19
Alignment explanation
Indices: 535784--535837 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
535774 ATCAATATAT
535784 ACAAAA-AACATTCAAAATTA
1 ACAAAATAA-ATT-AAAATTA
*
535804 ACGAAATAAATTAAAATTA
1 ACAAAATAAATTAAAATTA
*
535823 TCAAAACTAAATTAA
1 ACAAAA-TAAATTAA
535838 TGAGAGTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 11 0.38
20 16 0.55
21 2 0.07
ACGTcount: A:0.63, C:0.11, G:0.02, T:0.24
Consensus pattern (19 bp):
ACAAAATAAATTAAAATTA
Found at i:536351 original size:327 final size:332
Alignment explanation
Indices: 535888--536707 Score: 967
Period size: 327 Copynumber: 2.5 Consensus size: 332
535878 TAGACCAAAG
** * * *
535888 AAAATCCCCCCGAAAATATTTATGGA-ATAGAAAACT-TG-ATTTTTCG-AAGAAATGG-GAATT
1 AAAATCCCCCTAAAAAAATTTACGGAGA-AGAAAACTCTGTA-TTTTAGAAAGAAA-GGAGAATT
* * * * *
535948 TTAAGGAAAAAATTAAAAATTCATG-AAATGAATGAATTTTTGAAAACTGAATTTATATAAAATA
63 TCAAAGAAAAAATTCAAAATTCATGAAAATGAATGAATTTTTGAAAACTAAATTAATATAAAATA
* * * *
536012 AATAATAATATTTGATGAATTTTACAAATTAAAAACCAAGAAAAATTCC-CTTGAAAAAATTTAC
128 AATAATAATATTTGATGAATTTTAAAAATAAAAAAACAAGAAAAA-TCCTCTCGAAAAAATTTAC
*
536076 GAAGTAGAAAACTCTATA-TTT-CAAAAAAAAAAATTTCAAGGAAAAAAATT-AAA-TTATGGAA
192 GAAGTAGAAAACTCCATATTTTGCAAAAAAAAAAATTTCAAGG-AAAAAATTGAAATTTATGGAA
*
536137 ATGAATG-AATTTT-CAAAAACTAAATTAATGTGGAA-TAAATAATAATATTTTATAAATGTTAA
256 ATGAATGAAATTTTGC--AAACTAAATTAAT-TGGAAGTAAATAATAATATTTAATAAATGTTAA
536199 AAATCAAAAATA-AGA
318 AAATCAAAAA-ACAGA
* * * * *
536214 AAAAT-CTCTTCGAAAAAATTTATGGAGAAGAAAACTCTTTA-TTT-GAAAGAAAGGAGAATTTC
1 AAAATCCCCCT-AAAAAAATTTACGGAGAAGAAAACTCTGTATTTTAGAAAGAAAGGAGAATTTC
* * ** * *
536276 AAAGAAAAAATTCAAGATTCATGAAAATGAATGAATTATTGAAATTTAAATTAATAAAAAATAAC
65 AAAGAAAAAATTCAAAATTCATGAAAATGAATGAATTTTTGAAAACTAAATTAATATAAAATAAA
* * *
536341 TAAAAATATTTAATGAATTTTAAAAATAAAAAAACAAGAAAAATCCTCTCGAAAAAATTTACGGA
130 TAATAATATTTGATGAATTTTAAAAATAAAAAAACAAGAAAAATCCTCTCGAAAAAATTTACGAA
* ** * *
536406 GTAGAAAACTCCATATTTTGGAAAAAAAAGGATTTCAAGGAAAAAATTGAAATTTATGTACATGA
195 GTAGAAAACTCCATATTTTGCAAAAAAAAAAATTTCAAGGAAAAAATTGAAATTTATGGAAATGA
* * * * *
536471 ATGAAATTTTGCAAACTATATTAATTTGAAGTAAATAATAATATTTAATGAATTTTAAAATTCAA
260 ATGAAATTTTGCAAACTAAATTAATTGGAAGTAAATAATAATATTTAATAAATGTTAAAAATCAA
536536 AAAACAGA
325 AAAACAGA
* *
536544 AAAATCCCCCTAAAAAAATTTACGGAGCAGAAAACTCTGTATTTTAGAAA-AAAAGAGAATTTCA
1 AAAATCCCCCTAAAAAAATTTACGGAGAAGAAAACTCTGTATTTTAGAAAGAAAGGAGAATTTCA
* * *
536608 AAGAAAAAATTCAAAATTTATGAAAATGAATAAATTTTTAAAAACTAAATTAATATAAAATAAAT
66 AAGAAAAAATTCAAAATTCATGAAAATGAATGAATTTTTGAAAACTAAATTAATATAAAATAAAT
* * *
536673 AATAATATTGGGTGAATTTAAAAAAATCAAAAAAA
131 AATAATATTTGATGAATTT-TAAAAAT-AAAAAAA
536708 GATCCCCTCG
Statistics
Matches: 417, Mismatches: 56, Indels: 35
0.82 0.11 0.07
Matches are distributed among these distances:
325 5 0.01
326 65 0.16
327 104 0.25
328 12 0.03
329 25 0.06
330 92 0.22
331 96 0.23
332 11 0.03
333 7 0.02
ACGTcount: A:0.53, C:0.07, G:0.11, T:0.29
Consensus pattern (332 bp):
AAAATCCCCCTAAAAAAATTTACGGAGAAGAAAACTCTGTATTTTAGAAAGAAAGGAGAATTTCA
AAGAAAAAATTCAAAATTCATGAAAATGAATGAATTTTTGAAAACTAAATTAATATAAAATAAAT
AATAATATTTGATGAATTTTAAAAATAAAAAAACAAGAAAAATCCTCTCGAAAAAATTTACGAAG
TAGAAAACTCCATATTTTGCAAAAAAAAAAATTTCAAGGAAAAAATTGAAATTTATGGAAATGAA
TGAAATTTTGCAAACTAAATTAATTGGAAGTAAATAATAATATTTAATAAATGTTAAAAATCAAA
AAACAGA
Found at i:536367 original size:165 final size:161
Alignment explanation
Indices: 535898--536709 Score: 771
Period size: 165 Copynumber: 4.9 Consensus size: 161
535888 AAAATCCCCC
* * * * * * *
535898 CGAAAATATTTATGGAATAGAAAACT-TGAT-TTTTCGAAGAAATGGGAATTTTAAGGAAAAAAT
1 CGAAAAAATTTACGGAGTAGAAAACTCT-ATATTTTAGAA-AAAAGAGAATTTCAAGGAAAAAAT
* * *
535961 TAAAAATTCATG-AAATGAATGAATTTTTGAAAACTGAATTTATATAAAATAAATAATAATATTT
64 T-CAAATTCATGAAAATGAATGAA-TTTTGAAAACTAAATTAATATAAAATAAATAATAATATTT
* * *
536025 GATGAATTTTACAAATTAAAAACCAAGAAAAATTCCCTT
127 AATGAATTTTAAAAATCAAAAA--AAGAAAAA-T-CCTT
* * *
536064 -GAAAAAATTTACGAAGTAGAAAACTCTATATTTCA-AAAAAA-AAAATTTCAAGGAAAAAAATT
1 CGAAAAAATTTACGGAGTAGAAAACTCTATATTTTAGAAAAAAGAGAATTTCAAGG-AAAAAATT
* * * ** *
536126 -AAATT-ATGGAAATGAATGAATTTTCAAAAACTAAATTAATGTGGAATAAATAATAATATTTTA
65 CAAATTCATGAAAATGAATGAATTTT-GAAAACTAAATTAATATAAAATAAATAATAATATTTAA
* *
536189 TAAATGTTAAAAATCAAAAATAAGAAAAATCTCTT
129 TGAATTTTAAAAATCAAAAA-AAGAAAAATC-CTT
* * * *
536224 CGAAAAAATTTATGGAGAAGAAAACTCTTTA-TTT-GAAAGAAAGGAGAATTTCAAAGAAAAAAT
1 CGAAAAAATTTACGGAGTAGAAAACTCTATATTTTAGAAA-AAA-GAGAATTTCAAGGAAAAAAT
** * * *
536287 TCAAGATTCATGAAAATGAATGAATTATTGAAATTTAAATTAATAAAAAATAACTAAAAATATTT
64 TCAA-ATTCATGAAAATGAATGAATT-TTGAAAACTAAATTAATATAAAATAAATAATAATATTT
*
536352 AATGAATTTTAAAAATAAAAAAACAAGAAAAATCCTCT
127 AATGAATTTTAAAAAT-CAAAAA-AAGAAAAATCCT-T
* * * * *
536390 CGAAAAAATTTACGGAGTAGAAAACTCCATATTTTGGAAAAAAAAGGATTTCAAGGAAAAAATTG
1 CGAAAAAATTTACGGAGTAGAAAACTCTATATTTTAGAAAAAAGAGAATTTCAAGGAAAAAATTC
* * * * * * * *
536455 AAATTTATGTACATGAATGAAATTTTGCAAACTATATTAATTTGAAGTAAATAATAATATTTAAT
66 AAATTCATGAAAATGAATG-AATTTTGAAAACTAAATTAATATAAAATAAATAATAATATTTAAT
* **
536520 GAATTTTAAAATTCAAAAAACAGAAAAATCCCC
130 GAATTTTAAAAATCAAAAAA-AGAAAAATCCTT
* * * *
536553 CTAAAAAAATTTACGGAGCAGAAAACTCTGTATTTTAGAAAAAAAGAGAATTTCAAAGAAAAAAT
1 C-GAAAAAATTTACGGAGTAGAAAACTCTATATTTTAG-AAAAAAGAGAATTTCAAGGAAAAAAT
* * * *
536618 TCAAAATTTATGAAAATGAATAAATTTTTAAAAACTAAATTAATATAAAATAAATAATAATATTG
64 TC-AAATTCATGAAAATGAATGAA-TTTTGAAAACTAAATTAATATAAAATAAATAATAATATTT
** *
536683 GGTGAATTTAAAAAAATCAAAAAAAGA
127 AATGAATTT-TAAAAATCAAAAAAAGA
536710 TCCCCTCGAA
Statistics
Matches: 528, Mismatches: 92, Indels: 52
0.79 0.14 0.08
Matches are distributed among these distances:
159 1 0.00
160 9 0.02
161 44 0.08
162 71 0.13
163 23 0.04
164 60 0.11
165 166 0.31
166 132 0.25
167 18 0.03
168 4 0.01
ACGTcount: A:0.53, C:0.07, G:0.11, T:0.29
Consensus pattern (161 bp):
CGAAAAAATTTACGGAGTAGAAAACTCTATATTTTAGAAAAAAGAGAATTTCAAGGAAAAAATTC
AAATTCATGAAAATGAATGAATTTTGAAAACTAAATTAATATAAAATAAATAATAATATTTAATG
AATTTTAAAAATCAAAAAAAGAAAAATCCTT
Found at i:538092 original size:44 final size:44
Alignment explanation
Indices: 538020--538716 Score: 236
Period size: 44 Copynumber: 15.9 Consensus size: 44
538010 CTGAATAGGG
*
538020 TGAGAAGAGTTTGACCAGGGTGGTAACCATACATCAAA-CAAAAA
1 TGAGAAGAGTTTGACTAGGGTGGTAACCATACATCAAATC-AAAA
* *
538064 TGAGGCATA-TTTGACTAGGGTGGTAACCATACATCAAATCAAAA
1 TGA-GAAGAGTTTGACTAGGGTGGTAACCATACATCAAATCAAAA
* ** * *
538108 TGAGAAGAGTTTGACTAAGGTGGTAACCATATGTTAAAT-AGGAA
1 TGAGAAGAGTTTGACTAGGGTGGTAACCATACATCAAATCA-AAA
* * * * *** * * *
538152 -G-GAAGTAGATTTGACCAAGCTAGTAACCATGTGTGAAATTAGAA
1 TGAGAAG-AG-TTTGACTAGGGTGGTAACCATACATCAAATCAAAA
* * * * * * *
538196 TGAAAAGAATCTAACCTAGGGTGGTAACCATACATCAGACCGAAA
1 TGAGAAGAGTTTGA-CTAGGGTGGTAACCATACATCAAATCAAAA
* * *
538241 TGAGAAGAGTTTGACCAGGGTGGTAACCATACATTAAA-CATGAA
1 TGAGAAGAGTTTGACTAGGGTGGTAACCATACATCAAATCA-AAA
* ** * * ** * **
538285 TGAAAAGAACTTGACCAAGGTGGTAACCATATGTCAAGT-AGGA
1 TGAGAAGAGTTTGACTAGGGTGGTAACCATACATCAAATCAAAA
* * * * * * * *
538328 TGAAAAGAATCTGACCAGGGTGGTAACCATACGTCAGACCCAAA
1 TGAGAAGAGTTTGACTAGGGTGGTAACCATACATCAAATCAAAA
* * * * ** *
538372 TGAAAAGAGTTTGACCAAGGTGGTAACCATGCGCCAAAT-AGGAA
1 TGAGAAGAGTTTGACTAGGGTGGTAACCATACATCAAATCA-AAA
* * * * * *
538416 GGAGGCAA-A-TTTAACCATGGTGGTAACCATACGTCAAATCGAAA
1 TGA-G-AAGAGTTTGACTAGGGTGGTAACCATACATCAAATCAAAA
* * * ** * *
538460 TAAGAAGAGTTTGACCAAGGTGGTAACCATATGTTAAA-CATGAA
1 TGAGAAGAGTTTGACTAGGGTGGTAACCATACATCAAATCA-AAA
* * ** * * ** * **
538504 TGAAAATAACTTAACAAGGGTGGTAACCATATGTC-AAGCAGGA
1 TGAGAAGAGTTTGACTAGGGTGGTAACCATACATCAAATCAAAA
* * * * * * * * *
538547 TGAAAAGAATCT-AATCAAGGTGGTAACCATACGTCAGACCGAAA
1 TGAGAAGAGTTTGACT-AGGGTGGTAACCATACATCAAATCAAAA
* * * *
538591 TGAGAAGAGTTTGACCAGGGTGGTAATCATACGTCAAA-CATGAA
1 TGAGAAGAGTTTGACTAGGGTGGTAACCATACATCAAATCA-AAA
* ** * * * * * **
538635 TGAAAAGAACTTGACCAGAGTGATAACCATACGTC-AAGCAGGA
1 TGAGAAGAGTTTGACTAGGGTGGTAACCATACATCAAATCAAAA
* * * *
538678 TGAAAAGAATCTGACTAGGGTGGTAACCATACGTCAAAT
1 TGAGAAGAGTTTGACTAGGGTGGTAACCATACATCAAAT
538717 GAGGGATGAA
Statistics
Matches: 496, Mismatches: 130, Indels: 54
0.73 0.19 0.08
Matches are distributed among these distances:
42 7 0.01
43 110 0.22
44 338 0.68
45 36 0.07
46 5 0.01
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (44 bp):
TGAGAAGAGTTTGACTAGGGTGGTAACCATACATCAAATCAAAA
Found at i:538178 original size:88 final size:87
Alignment explanation
Indices: 538024--538716 Score: 414
Period size: 88 Copynumber: 7.9 Consensus size: 87
538014 ATAGGGTGAG
* ** * ** * * * *
538024 AAGAGTTTGACCAGGGTGGTAACCATACATCAAACAAAAATGAGGCATATTTGACTAGGGTGGTA
1 AAGAGTTTGACCAAGGTGGTAACCATATGTCAAATAGGAAGGAAG-AGATTTGACCAGGGTGGTA
* *
538089 ACCATACATCAAATCAAAATGAG
65 ACCATACGTCAAATCAAAATGAA
* * * * *
538112 AAGAGTTTGACTAAGGTGGTAACCATATGTTAAATAGGAAGGAAGTAGATTTGACCAAGCTAGTA
1 AAGAGTTTGACCAAGGTGGTAACCATATGTCAAATAGGAAGGAAG-AGATTTGACCAGGGTGGTA
** * * *
538177 ACCATGTGTGAAATTAGAATGAA
65 ACCATACGTCAAATCAAAATGAA
* * * * ** * ** *
538200 AAGAATCTAACCTAGGGTGGTAACCATACATCAGACCGAAATGAGAAGAG-TTTGACCAGGGTGG
1 AAGAGTTTGACC-AAGGTGGTAACCATATGTCAAATAGGAA-G-GAAGAGATTTGACCAGGGTGG
* * *
538264 TAACCATACATTAAA-CATGAATGAA
63 TAACCATACGTCAAATCA-AAATGAA
** * * * *
538289 AAGAACTTGACCAAGGTGGTAACCATATGTCAAGTAGG-ATGAAAAGAATCTGACCAGGGTGGTA
1 AAGAGTTTGACCAAGGTGGTAACCATATGTCAAATAGGAAGGAAGAG-ATTTGACCAGGGTGGTA
* * *
538353 ACCATACGTCAGACCCAAATGAA
65 ACCATACGTCAAATCAAAATGAA
** * * * * *
538376 AAGAGTTTGACCAAGGTGGTAACCATGCGCCAAATAGGAAGGAGGCAAATTTAACCATGGTGGTA
1 AAGAGTTTGACCAAGGTGGTAACCATATGTCAAATAGGAAGGAAG-AGATTTGACCAGGGTGGTA
*
538441 ACCATACGTCAAATCGAAAT-AA
65 ACCATACGTCAAATCAAAATGAA
* * * * * * * * *
538463 GAAGAGTTTGACCAAGGTGGTAACCATATGTTAAACATGAATGAAAATAACTTAACAAGGGTGGT
1 -AAGAGTTTGACCAAGGTGGTAACCATATGTCAAATAGGAAGGAAGA-GATTTGACCAGGGTGGT
* * **
538528 AACCATATGTC-AAGCAGGATGAA
64 AACCATACGTCAAATCAAAATGAA
* * * * * * ** *
538551 AAGAATCTAATCAAGGTGGTAACCATACGTCAGACCGAAATGAGAAGAG-TTTGACCAGGGTGGT
1 AAGAGTTTGACCAAGGTGGTAACCATATGTCAAATAGGAA-G-GAAGAGATTTGACCAGGGTGGT
* *
538615 AATCATACGTCAAA-CATGAATGAA
64 AACCATACGTCAAATCA-AAATGAA
** * * ** * * * *
538639 AAGAACTTGACC-AGAGTGATAACCATACGTCAAGCAGG-ATGAAAAGAATCTGACTAGGGTGGT
1 AAGAGTTTGACCAAG-GTGGTAACCATATGTCAAATAGGAAGGAAGAG-ATTTGACCAGGGTGGT
538702 AACCATACGTCAAAT
64 AACCATACGTCAAAT
538717 GAGGGATGAA
Statistics
Matches: 457, Mismatches: 128, Indels: 40
0.73 0.20 0.06
Matches are distributed among these distances:
85 10 0.02
87 154 0.34
88 223 0.49
89 63 0.14
90 3 0.01
91 4 0.01
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (87 bp):
AAGAGTTTGACCAAGGTGGTAACCATATGTCAAATAGGAAGGAAGAGATTTGACCAGGGTGGTAA
CCATACGTCAAATCAAAATGAA
Found at i:538266 original size:133 final size:132
Alignment explanation
Indices: 538078--538401 Score: 418
Period size: 133 Copynumber: 2.5 Consensus size: 132
538068 GCATATTTGA
* * * **
538078 CTAGGGTGGTAACCATACATCAAATCAAAATGAGAAGAGTTTGACTAAGGTGGTAACCATATGTT
1 CTAGGGTGGTAACCATACATCAGACCAAAATGAGAAGAGTTTGACCAAGGTGGTAACCATACATT
* * * * *
538143 AAATAGGAAGGAAGTAG-ATTTGACCAAGCTAGTAACCATGTGTGAAATTAGAATGAAAAGAATC
66 AAACAGGAAGGAA-AAGAACTTGACCAAGCTAGTAACCATATGT-AAAGTAGAATGAAAAGAATC
538207 TAAC
129 TAAC
* *
538211 CTAGGGTGGTAACCATACATCAGACCGAAATGAGAAGAGTTTGACCAGGGTGGTAACCATACATT
1 CTAGGGTGGTAACCATACATCAGACCAAAATGAGAAGAGTTTGACCAAGGTGGTAACCATACATT
* * * * * * *
538276 AAACATGAATGAAAAGAACTTGACCAAGGTGGTAACCATATGTCAAGTAGGATGAAAAGAATCTG
66 AAACAGGAAGGAAAAGAACTTGACCAAGCTAGTAACCATATGTAAAGTAGAATGAAAAGAATCTA
538341 AC
131 AC
* * *
538343 C-AGGGTGGTAACCATACGTCAGACCCAAATGAAAAGAGTTTGACCAAGGTGGTAACCAT
1 CTAGGGTGGTAACCATACATCAGACCAAAATGAGAAGAGTTTGACCAAGGTGGTAACCAT
538402 GCGCCAAATA
Statistics
Matches: 167, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
131 54 0.32
132 23 0.14
133 90 0.54
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.22
Consensus pattern (132 bp):
CTAGGGTGGTAACCATACATCAGACCAAAATGAGAAGAGTTTGACCAAGGTGGTAACCATACATT
AAACAGGAAGGAAAAGAACTTGACCAAGCTAGTAACCATATGTAAAGTAGAATGAAAAGAATCTA
AC
Found at i:538506 original size:219 final size:219
Alignment explanation
Indices: 538215--538616 Score: 644
Period size: 219 Copynumber: 1.8 Consensus size: 219
538205 TCTAACCTAG
* * *
538215 GGTGGTAACCATACATCAGACCGAAATGAGAAGAGTTTGACCAGGGTGGTAACCATACATTAAAC
1 GGTGGTAACCATACATCAAACCGAAATAAGAAGAGTTTGACCAAGGTGGTAACCATACATTAAAC
* * *
538280 ATGAATGAAAAGAACTTGACCAA-GGTGGTAACCATATGTCAAGTAGGATGAAAAGAATCTGACC
66 ATGAATGAAAAGAACTT-AACAAGGGTGGTAACCATATGTCAAGCAGGATGAAAAGAATCTAACC
*
538344 AGGGTGGTAACCATACGTCAGACCCAAATGAAAAGAGTTTGACCAAGGTGGTAACCATGCGCCAA
130 AAGGTGGTAACCATACGTCAGACCCAAATGAAAAGAGTTTGACCAAGGTGGTAACCATGCGCCAA
538409 ATAGGAAGGAGGCAAATTTAACCAT
195 ATAGGAAGGAGGCAAATTTAACCAT
* * **
538434 GGTGGTAACCATACGTCAAATCGAAATAAGAAGAGTTTGACCAAGGTGGTAACCATATGTTAAAC
1 GGTGGTAACCATACATCAAACCGAAATAAGAAGAGTTTGACCAAGGTGGTAACCATACATTAAAC
* *
538499 ATGAATGAAAATAACTTAACAAGGGTGGTAACCATATGTCAAGCAGGATGAAAAGAATCTAATCA
66 ATGAATGAAAAGAACTTAACAAGGGTGGTAACCATATGTCAAGCAGGATGAAAAGAATCTAACCA
* * *
538564 AGGTGGTAACCATACGTCAGACCGAAATGAGAAGAGTTTGACCAGGGTGGTAA
131 AGGTGGTAACCATACGTCAGACCCAAATGAAAAGAGTTTGACCAAGGTGGTAA
538617 TCATACGTCA
Statistics
Matches: 166, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
218 4 0.02
219 162 0.98
ACGTcount: A:0.39, C:0.16, G:0.25, T:0.20
Consensus pattern (219 bp):
GGTGGTAACCATACATCAAACCGAAATAAGAAGAGTTTGACCAAGGTGGTAACCATACATTAAAC
ATGAATGAAAAGAACTTAACAAGGGTGGTAACCATATGTCAAGCAGGATGAAAAGAATCTAACCA
AGGTGGTAACCATACGTCAGACCCAAATGAAAAGAGTTTGACCAAGGTGGTAACCATGCGCCAAA
TAGGAAGGAGGCAAATTTAACCAT
Found at i:538522 original size:131 final size:130
Alignment explanation
Indices: 538339--538715 Score: 378
Period size: 131 Copynumber: 2.9 Consensus size: 130
538329 GAAAAGAATC
* * *** ** * *
538339 TGACCAGGGTGGTAACCATACGTCAGACCCAAATGAAAAGAGTTTGACCAAGGTGGTAACCATGC
1 TGACCAAGGTGGTAACCATACGTCAAACATGAATGAAAAGAACTT-AACAAGGTGGTAACCATAC
* ** * * *
538404 GCCAAATAGGAAGGAGGCA-AATTTAACCATGGTGGTAACCATACGTCAAATCGAAATAAGAAGA
65 GCCAAACAGG-AGGA-AAAGAATCTAACCAAGGTGGTAACCATACGTCAAACCGAAATAAGAAGA
538468 GTT
128 GTT
* * * *
538471 TGACCAAGGTGGTAACCATATGTTAAACATGAATGAAAATAACTTAACAAGGGTGGTAACCATAT
1 TGACCAAGGTGGTAACCATACGTCAAACATGAATGAAAAGAACTTAACAA-GGTGGTAACCATAC
* * * * * *
538536 GTCAAGCAGGATGAAAAGAATCTAATCAAGGTGGTAACCATACGTCAGACCGAAATGAGAAGAGT
65 GCCAAACAGGAGGAAAAGAATCTAACCAAGGTGGTAACCATACGTCAAACCGAAATAAGAAGAGT
538601 T
130 T
* * * * *
538602 TGACCAGGGTGGTAATCATACGTCAAACATGAATGAAAAGAACTTGACCAGAGTGATAACCATAC
1 TGACCAAGGTGGTAACCATACGTCAAACATGAATGAAAAGAACTTAACAAG-GTGGTAACCATAC
* * * * * *
538667 GTCAAGCAGGATGAAAAGAATCTGACTAGGGTGGTAACCATACGTCAAA
65 GCCAAACAGGAGGAAAAGAATCTAACCAAGGTGGTAACCATACGTCAAA
538716 TGAGGGATGA
Statistics
Matches: 203, Mismatches: 39, Indels: 7
0.82 0.16 0.03
Matches are distributed among these distances:
130 2 0.01
131 147 0.72
132 54 0.27
ACGTcount: A:0.40, C:0.17, G:0.24, T:0.20
Consensus pattern (130 bp):
TGACCAAGGTGGTAACCATACGTCAAACATGAATGAAAAGAACTTAACAAGGTGGTAACCATACG
CCAAACAGGAGGAAAAGAATCTAACCAAGGTGGTAACCATACGTCAAACCGAAATAAGAAGAGTT
Found at i:538664 original size:219 final size:217
Alignment explanation
Indices: 538193--538671 Score: 629
Period size: 219 Copynumber: 2.2 Consensus size: 217
538183 TGTGAAATTA
* * *
538193 GAATGAAAAGAATCTAACCTAGGGTGGTAACCATACATCAGACCGAAATGAGAAGAGTTTGACCA
1 GAATGAAAAGAAT-TAACC-A-GGTGGTAACCATACGTCAAACCGAAATAAGAAGAGTTTGACCA
* *
538258 GGGTGGTAACCATACATTAAACATGAATGAAAAGAACTTGACCAAGGTGGTAACCATATGTCAAG
63 AGGTGGTAACCATACATTAAACATGAATGAAAAGAACTTGAACAAGGTGGTAACCATATGTCAAG
* * *
538323 TAGGATGAAAAGAATCTGACCAGGGTGGTAACCATACGTCAGACCCAAATGAAAAGAGTTTGACC
128 CAGGATGAAAAGAATCTAACCAAGGTGGTAACCATACGTCAGACCCAAATGAAAAGAGTTTGACC
* *
538388 AAGGTGGTAACCATGCGCCAAATAG
193 AAGGTGGTAACCATACGCCAAACAG
* * * *
538413 GAAGGAGGCAA-ATTTAACCATGGTGGTAACCATACGTCAAATCGAAATAAGAAGAGTTTGACCA
1 GAATGA--AAAGAATTAACCA-GGTGGTAACCATACGTCAAACCGAAATAAGAAGAGTTTGACCA
** *
538477 AGGTGGTAACCATATGTTAAACATGAATGAAAATAACTT-AACAAGGGTGGTAACCATATGTCAA
63 AGGTGGTAACCATACATTAAACATGAATGAAAAGAACTTGAACAA-GGTGGTAACCATATGTCAA
* * *
538541 GCAGGATGAAAAGAATCTAATCAAGGTGGTAACCATACGTCAGACCGAAATGAGAAGAGTTTGAC
127 GCAGGATGAAAAGAATCTAACCAAGGTGGTAACCATACGTCAGACCCAAATGAAAAGAGTTTGAC
* * * *
538606 CAGGGTGGTAATCATACGTCAAACAT
192 CAAGGTGGTAACCATACGCCAAACAG
* *
538632 GAATGAAAAGAACTTGACCAGAGTGATAACCATACGTCAA
1 GAATGAAAAGAA-TTAACCAG-GTGGTAACCATACGTCAA
538672 GCAGGATGAA
Statistics
Matches: 223, Mismatches: 30, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
217 2 0.01
218 6 0.03
219 201 0.90
220 10 0.04
221 2 0.01
222 2 0.01
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.20
Consensus pattern (217 bp):
GAATGAAAAGAATTAACCAGGTGGTAACCATACGTCAAACCGAAATAAGAAGAGTTTGACCAAGG
TGGTAACCATACATTAAACATGAATGAAAAGAACTTGAACAAGGTGGTAACCATATGTCAAGCAG
GATGAAAAGAATCTAACCAAGGTGGTAACCATACGTCAGACCCAAATGAAAAGAGTTTGACCAAG
GTGGTAACCATACGCCAAACAG
Found at i:538773 original size:48 final size:48
Alignment explanation
Indices: 538710--538861 Score: 218
Period size: 48 Copynumber: 3.2 Consensus size: 48
538700 GTAACCATAC
* *
538710 GTCAAATGAGGGATGAAAAAAGTTTAACCAGGCCCTAACACCAATATA
1 GTCAAACGAGGGATGAAAAAAGTTTGACCAGGCCCTAACACCAATATA
* ** * *
538758 GTTAAACGAGGGATGAAATGAGTTTGACTAGGCCCTAACACCAATACA
1 GTCAAACGAGGGATGAAAAAAGTTTGACCAGGCCCTAACACCAATATA
*
538806 GTCAAACGAGGAATG--AAAAGTTTGACCAGGCCCTAACACCAATATA
1 GTCAAACGAGGGATGAAAAAAGTTTGACCAGGCCCTAACACCAATATA
538852 GTCAAACGAG
1 GTCAAACGAG
538862 AAAGGTCTTG
Statistics
Matches: 91, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
46 37 0.41
48 54 0.59
ACGTcount: A:0.41, C:0.20, G:0.21, T:0.18
Consensus pattern (48 bp):
GTCAAACGAGGGATGAAAAAAGTTTGACCAGGCCCTAACACCAATATA
Found at i:538952 original size:35 final size:35
Alignment explanation
Indices: 538894--538973 Score: 99
Period size: 35 Copynumber: 2.3 Consensus size: 35
538884 AAAAAGGAGT
* * * **
538894 AAGA-TTTGATCAAGTACAGTCAAATTAGGATGGA
1 AAGAGTTTGACCAAATACAATCAAACGAGGATGGA
*
538928 AAGAGTTTGACCAAATACAATCAAACGATGATGGA
1 AAGAGTTTGACCAAATACAATCAAACGAGGATGGA
538963 AAGAGTTTGAC
1 AAGAGTTTGAC
538974 ATAGTTAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
34 4 0.10
35 35 0.90
ACGTcount: A:0.42, C:0.11, G:0.23, T:0.24
Consensus pattern (35 bp):
AAGAGTTTGACCAAATACAATCAAACGAGGATGGA
Found at i:539388 original size:22 final size:21
Alignment explanation
Indices: 539344--539386 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
539334 GATTTTCAAT
539344 ATCAAAGATTTCAAGATAAAA
1 ATCAAAGATTTCAAGATAAAA
*
539365 ATCATAAGTTTTCAAG-TAAAA
1 ATCA-AAGATTTCAAGATAAAA
539386 A
1 A
539387 ATAATCCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.53, C:0.09, G:0.09, T:0.28
Consensus pattern (21 bp):
ATCAAAGATTTCAAGATAAAA
Found at i:545754 original size:20 final size:21
Alignment explanation
Indices: 545729--545770 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
545719 AAAATTTCCC
545729 AGAATGTATCGATACAT-TGA
1 AGAATGTATCGATACATCTGA
*
545749 AGAATGTATTGATACATCTGA
1 AGAATGTATCGATACATCTGA
545770 A
1 A
545771 AAACCCAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (21 bp):
AGAATGTATCGATACATCTGA
Found at i:547557 original size:17 final size:17
Alignment explanation
Indices: 547535--547569 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
547525 TGATATTTTC
547535 TACATGAATCCAATATA
1 TACATGAATCCAATATA
*
547552 TACATGAATGCAATATA
1 TACATGAATCCAATATA
547569 T
1 T
547570 TTTCTGCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.31
Consensus pattern (17 bp):
TACATGAATCCAATATA
Found at i:547694 original size:23 final size:20
Alignment explanation
Indices: 547673--547717 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
547663 ATAAATTTGA
*
547673 TGAAAAAAGGAGAGATACTT
1 TGAAAAAAAGAGAGATACTT
* *
547693 TGAAAGAAATAGAGATACTT
1 TGAAAAAAAGAGAGATACTT
547713 TGAAA
1 TGAAA
547718 GAATTTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.51, C:0.04, G:0.22, T:0.22
Consensus pattern (20 bp):
TGAAAAAAAGAGAGATACTT
Found at i:547706 original size:20 final size:20
Alignment explanation
Indices: 547683--547720 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
547673 TGAAAAAAGG
547683 AGAGATACTTTGAAAGAAAT
1 AGAGATACTTTGAAAGAAAT
547703 AGAGATACTTTGAAAGAA
1 AGAGATACTTTGAAAGAA
547721 TTTTTTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.05, G:0.21, T:0.24
Consensus pattern (20 bp):
AGAGATACTTTGAAAGAAAT
Found at i:548452 original size:21 final size:20
Alignment explanation
Indices: 548426--548465 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
548416 AAGGTAAAAA
548426 ACCTAGAAAGTATCGATACAC
1 ACCTAG-AAGTATCGATACAC
*
548447 ACCTAGATGTATCGATACA
1 ACCTAGAAGTATCGATACA
548466 TATTGCTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.23
Consensus pattern (20 bp):
ACCTAGAAGTATCGATACAC
Found at i:549484 original size:91 final size:91
Alignment explanation
Indices: 549383--549659 Score: 410
Period size: 91 Copynumber: 3.0 Consensus size: 91
549373 TGCCCTAGGA
* * * * *
549383 AAATCAAGCTTTCTAATGCATCAATACCATCTAGTGGTTGGATGAAGGAGATATAATTGGGGAAT
1 AAATCAAGCTTTATGATGCATCAATACCATCTAGTGGTTAGATGAAAGAGATATGATTGGGGAAT
*
549448 GTGTGGGCTGCACCTTGCCCCCATGG
66 GTGTGGGCTGCACCTTGCCCCCAAGG
* * *
549474 AAATCAAGCTTTATGATGCATCAATATCTTCTAGTGGTTAGATGAAAGAGATATGATTGGGTAAT
1 AAATCAAGCTTTATGATGCATCAATACCATCTAGTGGTTAGATGAAAGAGATATGATTGGGGAAT
549539 GTGTGGGCTGCACCTTGCCCCCAAGG
66 GTGTGGGCTGCACCTTGCCCCCAAGG
* * * * *
549565 AAATCAGGCTTTGTGATGCATTAATACCATCTAGAGGTTAGATGAAAGAGATGTGATTGGGGAAT
1 AAATCAAGCTTTATGATGCATCAATACCATCTAGTGGTTAGATGAAAGAGATATGATTGGGGAAT
* *
549630 ATGTGGGCTGCACCTTGCCTCCAAGG
66 GTGTGGGCTGCACCTTGCCCCCAAGG
549656 AAAT
1 AAAT
549660 TGTTAAGCTT
Statistics
Matches: 167, Mismatches: 19, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
91 167 1.00
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (91 bp):
AAATCAAGCTTTATGATGCATCAATACCATCTAGTGGTTAGATGAAAGAGATATGATTGGGGAAT
GTGTGGGCTGCACCTTGCCCCCAAGG
Found at i:550110 original size:21 final size:21
Alignment explanation
Indices: 550084--550136 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
550074 CCCTCGATTT
*
550084 TATCGATACATGTTGAAATTG
1 TATCGATACATGTTAAAATTG
** *
550105 TATCGATATGTTTTAAAATTG
1 TATCGATACATGTTAAAATTG
550126 TATCGATACAT
1 TATCGATACAT
550137 CAAGAATTGT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.42
Consensus pattern (21 bp):
TATCGATACATGTTAAAATTG
Found at i:559614 original size:13 final size:13
Alignment explanation
Indices: 559596--559635 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
559586 ACAATGTTTT
559596 TTGTATCGATACA
1 TTGTATCGATACA
* *
559609 TTGTATTGATGCA
1 TTGTATCGATACA
*
559622 ATGTATCGATACA
1 TTGTATCGATACA
559635 T
1 T
559636 GGGTTACTAT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.40
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:561130 original size:33 final size:33
Alignment explanation
Indices: 561093--561159 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
561083 CGAGAGTTGA
*
561093 TCACTTCACTTTCGCAGCACATGAATGAGCACT
1 TCACTTCACTCTCGCAGCACATGAATGAGCACT
*
561126 TCACTTCACTCTCGCAGCACATGGATGAGCACT
1 TCACTTCACTCTCGCAGCACATGAATGAGCACT
561159 T
1 T
561160 TAGCTCTCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.25, C:0.31, G:0.16, T:0.27
Consensus pattern (33 bp):
TCACTTCACTCTCGCAGCACATGAATGAGCACT
Found at i:562102 original size:13 final size:13
Alignment explanation
Indices: 562084--562108 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
562074 CATTATGCTT
562084 TGTATCGATACAA
1 TGTATCGATACAA
562097 TGTATCGATACA
1 TGTATCGATACA
562109 TGTTCATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:562121 original size:19 final size:20
Alignment explanation
Indices: 562095--562151 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
562085 GTATCGATAC
**
562095 AATGTATCGATACATGTTC-
1 AATGTATCGATACATGAACA
* *
562114 ATTGTATCAATACATGAACA
1 AATGTATCGATACATGAACA
562134 AATGTATCGATACATGAA
1 AATGTATCGATACATGAA
562152 ACTGGTAGTA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (20 bp):
AATGTATCGATACATGAACA
Found at i:565607 original size:20 final size:20
Alignment explanation
Indices: 565568--565608 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
565558 GTTTTCTAGA
*
565568 TTGTATCGATACAATGAAAT
1 TTGTATCGATACAATAAAAT
*
565588 TTGTATCGATACATTAAAAT
1 TTGTATCGATACAATAAAAT
565608 T
1 T
565609 ATATCGAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (20 bp):
TTGTATCGATACAATAAAAT
Found at i:565615 original size:19 final size:20
Alignment explanation
Indices: 565571--565615 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
565561 TTCTAGATTG
* *
565571 TATCGATACAATGAAATTTG
1 TATCGATACAATGAAAATTA
*
565591 TATCGATAC-ATTAAAATTA
1 TATCGATACAATGAAAATTA
565610 TATCGA
1 TATCGA
565616 AATAATTTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (20 bp):
TATCGATACAATGAAAATTA
Found at i:565758 original size:21 final size:21
Alignment explanation
Indices: 565709--565764 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
565699 ATTTTCCAGT
*
565709 CATCAAA-TTCTTCAAATACA
1 CATCAAATTTCTTCAAAAACA
* **
565729 CTTTGAATTTCTTCAAAAACA
1 CATCAAATTTCTTCAAAAACA
*
565750 CATCAAATTCCTTCA
1 CATCAAATTTCTTCA
565765 TTTCCTTATC
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.39, C:0.25, G:0.02, T:0.34
Consensus pattern (21 bp):
CATCAAATTTCTTCAAAAACA
Found at i:568242 original size:20 final size:19
Alignment explanation
Indices: 568179--568243 Score: 52
Period size: 20 Copynumber: 3.6 Consensus size: 19
568169 CACACCCAGA
568179 TGTATCGATACAAATTGCT
1 TGTATCGATACAAATTGCT
*
568198 AAGTATCGATAC--ATTG--
1 -TGTATCGATACAAATTGCT
*
568214 TAT-TC-ATACAAATTGCTT
1 TGTATCGATACAAATTGC-T
568232 TGTATCGATACA
1 TGTATCGATACA
568244 CTTGAAATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 14
0.65 0.08 0.27
Matches are distributed among these distances:
13 4 0.12
14 2 0.06
15 5 0.15
18 6 0.18
19 2 0.06
20 15 0.44
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (19 bp):
TGTATCGATACAAATTGCT
Found at i:568269 original size:18 final size:19
Alignment explanation
Indices: 568234--568270 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
568224 AATTGCTTTG
568234 TATCGATACACTTGAAATTA
1 TATCGATACAC-TGAAATTA
568254 TATCGATACA-TGAAATT
1 TATCGATACACTGAAATT
568271 GGAAGTAGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.35
Consensus pattern (19 bp):
TATCGATACACTGAAATTA
Found at i:569803 original size:50 final size:51
Alignment explanation
Indices: 569672--569805 Score: 189
Period size: 50 Copynumber: 2.6 Consensus size: 51
569662 TTTTACTATT
* * * * *
569672 TGTATCGATGCATTATTCATTGCATCGATAAATTCTGGGCTTTTACCTAGA
1 TGTATCGATACATTATTCATTGTATCGATACATTCTGAGATTTTACCTAGA
*
569723 TGTATCGATACATTCTTCATTGTATCGATACATTCT-AGATTTTACCTAGA
1 TGTATCGATACATTATTCATTGTATCGATACATTCTGAGATTTTACCTAGA
* *
569773 TGTATCGATATATTATTCAATGTATCGATACAT
1 TGTATCGATACATTATTCATTGTATCGATACAT
569806 GCAGGCAAAT
Statistics
Matches: 74, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
50 42 0.57
51 32 0.43
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.41
Consensus pattern (51 bp):
TGTATCGATACATTATTCATTGTATCGATACATTCTGAGATTTTACCTAGA
Found at i:579386 original size:13 final size:13
Alignment explanation
Indices: 579368--579407 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
579358 GCAATGTTCT
*
579368 TTGTATTGATACA
1 TTGTATCGATACA
*
579381 TTGTATCGATATA
1 TTGTATCGATACA
*
579394 ATGTATCGATACA
1 TTGTATCGATACA
579407 T
1 T
579408 GGGCTACTAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:586843 original size:18 final size:18
Alignment explanation
Indices: 586809--586842 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
586799 CTTGTACGCT
586809 TTTTCATTTTCATTTTTC
1 TTTTCATTTTCATTTTTC
*
586827 TTTTCTTTTTC-TTTTT
1 TTTTCATTTTCATTTTT
586843 TTGTTTTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTCATTTTCATTTTTC
Found at i:587217 original size:15 final size:14
Alignment explanation
Indices: 587181--587219 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
587171 AGCACTTTAA
587181 TTTTCTTTTTCTTT
1 TTTTCTTTTTCTTT
*
587195 TTCCTCTTTTTCCTTT
1 TT-TTCTTTTT-CTTT
587211 TTTTCTTTT
1 TTTTCTTTT
587220 AATGAATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 2 0.10
15 13 0.62
16 6 0.29
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTCTTTTTCTTT
Found at i:590676 original size:155 final size:153
Alignment explanation
Indices: 590157--590684 Score: 546
Period size: 155 Copynumber: 3.4 Consensus size: 153
590147 ATTTTGTAGG
** * * * *
590157 AAAATTATGAAAATGCTCTTAGGGGATACCTTCGACGTAAAAGTACTCAATACCACTAAAGGACT
1 AAAATTACAAAAATGCTCTTAGGGGATACCTTTGACGTAAAAGTACCCGATACCCCTAAA-GACT
* * * * *
590222 TAAAAAGGTTTAA-A-ATGGGATGAACATATCCTAACTGTCCACCTTTGGCATAAAAGCGGACCC
65 TAAAAAGG-ATAATAGATGAGATGAACATATCCTAAATATCTACCTTTGGCATAAAAGCGGACCC
* * * * *
590285 GGCGACAACCTTAGAGTTAGTT-T-T
129 AGTGACAACC-TAGACTTGGTTCTGA
* ** * **
590309 AAAATTACGAAAATGC-CTCTAAAGGATA-CTTTCAACAAAAAAGTACCCGATACCCCTAAAGAA
1 AAAATTACAAAAATGCTCT-TAGGGGATACCTTT-GACGTAAAAGTACCCGATACCCCTAAAG-A
* * * * **
590372 CTTAAAAAGGATAATAGATAAGACGAGCCTATCCTAAATATCTACCTTCAGCATAAAAGCGGACC
63 CTTAAAAAGGATAATAGATGAGATGAACATATCCTAAATATCTACCTTTGGCATAAAAGCGGACC
* *
590437 CAGTGACAACCAAAGACTCGGTTCTGA
128 CAGTGACAACC-TAGACTTGGTTCTGA
* * * * *
590464 AAAATTACAAAAATGCCCGTAGGGGATACTTTTGACGTAAAATTACCCGACACCCCTAAATGACT
1 AAAATTACAAAAATGCTCTTAGGGGATACCTTTGACGTAAAAGTACCCGATACCCCTAAA-GACT
* * *
590529 TAAAAAGGATAATAGATGAGATGAACTTATCCTAAATATCTACCTTTGGCATAAAAGCGAACCTA
65 TAAAAAGGATAATAGATGAGATGAACATATCCTAAATATCTACCTTTGGCATAAAAGCGGACCCA
590594 GTGACAACCTAGGACTTGGTTCTGA
130 GTGACAACCTA-GACTTGGTTCTGA
* * * *
590619 AAAATTACAAAAATGCTCTTAGGGAATACCTTTGACGTAAAAGTACCTGGTATCCCTAAGAGACT
1 AAAATTACAAAAATGCTCTTAGGGGATACCTTTGACGTAAAAGTACCCGATACCCCTAA-AGACT
590684 T
65 T
590685 GGGATAATGC
Statistics
Matches: 306, Mismatches: 58, Indels: 21
0.79 0.15 0.05
Matches are distributed among these distances:
151 9 0.03
152 55 0.18
153 54 0.18
154 2 0.01
155 180 0.59
156 6 0.02
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (153 bp):
AAAATTACAAAAATGCTCTTAGGGGATACCTTTGACGTAAAAGTACCCGATACCCCTAAAGACTT
AAAAAGGATAATAGATGAGATGAACATATCCTAAATATCTACCTTTGGCATAAAAGCGGACCCAG
TGACAACCTAGACTTGGTTCTGA
Found at i:591265 original size:155 final size:158
Alignment explanation
Indices: 590995--591585 Score: 801
Period size: 165 Copynumber: 3.7 Consensus size: 158
590985 AATTTATCTT
* * *
590995 GTACCTTAATGGAAGCCCGAAAAGATACGAGAAGTTTTTGAAATTCTTTTAATACCCCTACGGAT
1 GTACCTTAATGGAAGCCCGAAAAGATACGAAAAGTTTTTAAAAATCTTTT-ATACCCCTACGGAT
* * * *
591060 GCCCATAGGAATATAAAAGATTAGAAAAATTATTAAAGTTGATCTCAATAATGAAAATGTT-A-A
65 GCCCATAGGAATATAAAAGATTAGAAAAATGATTAAAATTGATCTCAATAACGAAAGTGTTAATA
*
591123 TTTTA-TTTATTTTCAAAAATATCATTTT
130 TTTTATTTTATTTTCAAAAATATCATTTC
* * *
591151 GTACCTTAATGAAAACCCGAAAAGATACGAAAAGTTTTTAAAAATCTTTTATACCCCTATGGATG
1 GTACCTTAATGGAAGCCCGAAAAGATACGAAAAGTTTTTAAAAATCTTTTATACCCCTACGGATG
591216 CCCATAGGAATATAAAAGATTAGAAAAATGATTAAAATTGATCTCAATAACGAAAGTGTTAATTT
66 CCCATAGGAATATAAAAGATTAGAAAAATGATTAAAATTGATCTCAATAACGAAAGTGTTAA---
*
591281 TATTTTATTTTATTAATTTTCAAAAATACCATTTC
128 TATTTTA--TT-TT-ATTTTCAAAAATATCATTTC
* * **
591316 GTACCTTAATGGAAGCCCAAAAAGATACGAAAAGTTTTTAAAAATCTTTTATACCCTTATAGATG
1 GTACCTTAATGGAAGCCCGAAAAGATACGAAAAGTTTTTAAAAATCTTTTATACCCCTACGGATG
*
591381 CCCATAGGAATATAAAAGATTAGAAAAATGATTAAAATTAATCTCAATAACGAAAGTGTTAATTT
66 CCCATAGGAATATAAAAGATTAGAAAAATGATTAAAATTGATCTCAATAACGAAAGTGTTAA---
591446 TATTTTATTTTATTTTATTTCAAAAATATCATTTC
128 TATTTTATTTTA---T-TTTCAAAAATATCATTTC
* * * * * *
591481 GTACCTCAATGGAAGCCCGAAAAAATATGAAAAGTTTTTGAAAATATTTTATGCCCCTACGGATG
1 GTACCTTAATGGAAGCCCGAAAAGATACGAAAAGTTTTTAAAAATCTTTTATACCCCTACGGATG
*
591546 CCCATAGGAATATAAAAGATTAAAAAGAATGATTAAAATT
66 CCCATAGGAATATAAAAGATTAGAAA-AATGATTAAAATT
591586 CAATTTTGCC
Statistics
Matches: 390, Mismatches: 30, Indels: 20
0.89 0.07 0.05
Matches are distributed among these distances:
155 70 0.18
156 46 0.12
160 6 0.02
161 1 0.00
162 2 0.01
163 3 0.01
164 3 0.01
165 246 0.63
166 13 0.03
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (158 bp):
GTACCTTAATGGAAGCCCGAAAAGATACGAAAAGTTTTTAAAAATCTTTTATACCCCTACGGATG
CCCATAGGAATATAAAAGATTAGAAAAATGATTAAAATTGATCTCAATAACGAAAGTGTTAATAT
TTTATTTTATTTTCAAAAATATCATTTC
Found at i:592552 original size:22 final size:22
Alignment explanation
Indices: 592527--592568 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
592517 AATTTTCTCC
* *
592527 TTTTT-TTCTTTCTTTTCTTTA
1 TTTTTCTTTTTTCTCTTCTTTA
592548 TTTTTCTTTTTTCTCTTCTTT
1 TTTTTCTTTTTTCTCTTCTTT
592569 CAGCTGAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (22 bp):
TTTTTCTTTTTTCTCTTCTTTA
Found at i:592564 original size:19 final size:18
Alignment explanation
Indices: 592519--592564 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
592509 TTTCACTCAA
*
592519 TTTTCTCCTTTTTTTCTT
1 TTTTCTCTTTTTTTTCTT
592537 TCTTT-TCTTTATTTTTCTT
1 T-TTTCTCTTT-TTTTTCTT
592556 TTTTCTCTT
1 TTTTCTCTT
592565 CTTTCAGCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTCTCTTTTTTTTCTT
Found at i:593520 original size:162 final size:163
Alignment explanation
Indices: 593198--593974 Score: 842
Period size: 162 Copynumber: 4.9 Consensus size: 163
593188 AATTTAAAGA
* *
593198 AAAAAATTCAAAATTCATGGAAATGAATAAATTTTTGAAAA-TGGAAATAATATGAAATAAATAA
1 AAAAAATTCAAAATTCATGGAAATGAATGAATTTTTGAAAACT-GAATTAATATGAAATAAATAA
* * * *
593262 TAATATTTGATGAATTTTAAAAATTAAAAACTAGGAAAAATCCCCTTGAAATAATTTACGGAGTA
65 TAATATTTGATGAATTTTAAAAATCAAAAAC-AAGAAAAAT-CCCTCGAAAAAATTTACGGAGTA
* * * *
593327 AAAAACTCTGTATTTTGAAAAA-AAAAATTTCA-GG
128 GAAAACTCTGTATTTCGAAAAATGAGAATTTCATGG
* * * *
593361 GAAAAA-TAAAAATTTATGGAAATGAATGAATTTTTGAAAACTGAATTAATGTGAAATAAATAAT
1 AAAAAATTCAAAATTCATGGAAATGAATGAATTTTTGAAAACTGAATTAATATGAAATAAATAAT
* *
593425 AAT-TTTGATGAATTTTGAAAATCAGAAAACATGAAAAATCCCTCGAAAAAATTTACGGAGTAGA
66 AATATTTGATGAATTTTAAAAATCA-AAAACAAGAAAAATCCCTCGAAAAAATTTACGGAGTAGA
*
593489 AAACTCTGTATTTCGAAGAAATGAGAATTTCA-AG
130 AAACTCTGTATTTCGAA-AAATGAGAATTTCATGG
* *
593523 AAAAAATTCAAAATTCATGGAAATTAATGAATTTTTGAAAACTGAATTAA-ATTGAAGT-AATAA
1 AAAAAATTCAAAATTCATGGAAATGAATGAATTTTTGAAAACTGAATTAATA-TGAAATAAATAA
* *
593586 TAATATTTTATGAATTTTAAAAAT---AAA-AA-AAAAAT-CCTC--------TT---GA--AAA
65 TAATATTTGATGAATTTTAAAAATCAAAAACAAGAAAAATCCCTCGAAAAAATTTACGGAGTAGA
* *
593632 AAA-TCTGTATTTCAAAAAAATGAGAATTTCATGA
130 AAACTCTGTATTTC-GAAAAATGAGAATTTCATGG
* * *
593666 AAAAAATTCAAAATTTATGGAAATGAATGACTTTTTAAAAACTGAATTAATATGAAATAAATAAT
1 AAAAAATTCAAAATTCATGGAAATGAATGAATTTTTGAAAACTGAATTAATATGAAATAAATAAT
* * *
593731 AATATTTAATGAATTTTAAAAATTAAAATCAAGAAAAATCTGCCT-GAAAAAATTTACGGAGTAG
66 AATATTTGATGAATTTTAAAAATCAAAAACAAGAAAAATC--CCTCGAAAAAATTTACGGAGTAG
* * * *
593795 AAAACTCCGTATTTCGGATAAATAGGGAATTTGATGG
129 AAAACTCTGTATTTC-GAAAAAT-GAGAATTTCATGG
* * * * *
593832 AAAAAAATTTAAAATTCATGGAAATGAATAAATTTTTGAAAATTGAATTAAAATGAATTAAATAA
1 -AAAAAATTCAAAATTCATGGAAATGAATGAATTTTTGAAAACTGAATTAATATGAAATAAATAA
* *
593897 TAATATTTTATGAATTTAAAAAATCAAAAAACAAGAAAAATCCC-C-AAAAGAATTTACGGAGTA
65 TAATATTTGATGAATTTTAAAAATC-AAAAACAAGAAAAATCCCTCGAAAA-AATTTACGGAGTA
*
593960 GAAAGCTCTGTATTT
128 GAAAACTCTGTATTT
593975 TAGAAAAAGA
Statistics
Matches: 518, Mismatches: 58, Indels: 73
0.80 0.09 0.11
Matches are distributed among these distances:
142 24 0.05
143 58 0.11
144 29 0.06
145 2 0.00
147 2 0.00
148 4 0.01
149 6 0.01
152 3 0.01
156 4 0.01
157 6 0.01
158 1 0.00
159 5 0.01
160 38 0.07
161 30 0.06
162 84 0.16
163 68 0.13
164 5 0.01
165 18 0.03
166 38 0.07
167 78 0.15
168 15 0.03
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.31
Consensus pattern (163 bp):
AAAAAATTCAAAATTCATGGAAATGAATGAATTTTTGAAAACTGAATTAATATGAAATAAATAAT
AATATTTGATGAATTTTAAAAATCAAAAACAAGAAAAATCCCTCGAAAAAATTTACGGAGTAGAA
AACTCTGTATTTCGAAAAATGAGAATTTCATGG
Found at i:593656 original size:142 final size:144
Alignment explanation
Indices: 593488--593758 Score: 413
Period size: 143 Copynumber: 1.9 Consensus size: 144
593478 TACGGAGTAG
* * * *
593488 AAAACTCTGTATTTCGAAGAAATGAGAATTTCAAG-AAAAAATTCAAAATTCATGGAAATTAATG
1 AAAAATCTGTATTTCAAAAAAATGAGAATTTCAAGAAAAAAATTCAAAATTCATGGAAATGAATG
* * *
593552 AATTTTTGAAAACTGAATTAA-ATTGAAGT-AATAATAATATTTTATGAATTTTAAAAATAAAAA
66 AATTTTTAAAAACTGAATTAATA-TGAAATAAATAATAATATTTAATGAATTTTAAAAATAAAAA
593615 AAAAATCCTCTTGAA
130 AAAAATCCTCTTGAA
* *
593630 AAAAATCTGTATTTCAAAAAAATGAGAATTTCATGAAAAAAATTCAAAATTTATGGAAATGAATG
1 AAAAATCTGTATTTCAAAAAAATGAGAATTTCAAGAAAAAAATTCAAAATTCATGGAAATGAATG
* *
593695 ACTTTTTAAAAACTGAATTAATATGAAATAAATAATAATATTTAATGAATTTTAAAAATTAAAA
66 AATTTTTAAAAACTGAATTAATATGAAATAAATAATAATATTTAATGAATTTTAAAAATAAAAA
593759 TCAAGAAAAA
Statistics
Matches: 115, Mismatches: 11, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
142 31 0.27
143 51 0.44
144 33 0.29
ACGTcount: A:0.52, C:0.06, G:0.10, T:0.33
Consensus pattern (144 bp):
AAAAATCTGTATTTCAAAAAAATGAGAATTTCAAGAAAAAAATTCAAAATTCATGGAAATGAATG
AATTTTTAAAAACTGAATTAATATGAAATAAATAATAATATTTAATGAATTTTAAAAATAAAAAA
AAAATCCTCTTGAA
Found at i:593855 original size:167 final size:165
Alignment explanation
Indices: 593655--593974 Score: 446
Period size: 167 Copynumber: 1.9 Consensus size: 165
593645 AAAAAAATGA
* * * *
593655 GAATTTCATGAAAAAAATTCAAAATTTATGGAAATGAATGACTTTTTAAAAACTGAATTAATATG
1 GAATTTCATGAAAAAAATTCAAAATTCATGGAAATGAATAAATTTTTAAAAACTGAATTAAAATG
* * * *
593720 AAATAAATAATAATATTTAATGAATTTTAAAAAT-TAAAATCAAGAAAAATCTGCCTGAAAA-AA
66 AAATAAATAATAATATTTAATGAATTTAAAAAATCAAAAAACAAGAAAAATC--CC-CAAAAGAA
593783 TTTACGGAGTAGAAAACTCCGTATTTCGGATAAATAGG
128 TTTACGGAGTAGAAAACTCCGTATTTCGGATAAATAGG
* * * *
593821 GAATTTGATGGAAAAAAATTTAAAATTCATGGAAATGAATAAATTTTTGAAAATTGAATTAAAAT
1 GAATTTCAT-GAAAAAAATTCAAAATTCATGGAAATGAATAAATTTTTAAAAACTGAATTAAAAT
* *
593886 GAATTAAATAATAATATTTTATGAATTTAAAAAATCAAAAAACAAGAAAAATCCCCAAAAGAATT
65 GAAATAAATAATAATATTTAATGAATTTAAAAAATCAAAAAACAAGAAAAATCCCCAAAAGAATT
* *
593951 TACGGAGTAGAAAGCTCTGTATTT
130 TACGGAGTAGAAAACTCCGTATTT
593975 TAGAAAAAGA
Statistics
Matches: 135, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
165 4 0.03
166 36 0.27
167 80 0.59
168 15 0.11
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.31
Consensus pattern (165 bp):
GAATTTCATGAAAAAAATTCAAAATTCATGGAAATGAATAAATTTTTAAAAACTGAATTAAAATG
AAATAAATAATAATATTTAATGAATTTAAAAAATCAAAAAACAAGAAAAATCCCCAAAAGAATTT
ACGGAGTAGAAAACTCCGTATTTCGGATAAATAGG
Found at i:596026 original size:33 final size:32
Alignment explanation
Indices: 595989--596086 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 32
595979 TACCACTGTT
595989 TGTATCGATACATG-GCACATTGTATCGATACAA
1 TGTATCGATACATGAG-A-ATTGTATCGATACAA
596022 TGTATCGATACATGAAGAATTGTATCGATACAA
1 TGTATCGATACATG-AGAATTGTATCGATACAA
*
596055 TGTATCGATACATAAAGAATTGTATCGATACA
1 TGTATCGATACAT-GAGAATTGTATCGATACA
596087 TTAACTCAAA
Statistics
Matches: 61, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
33 59 0.97
34 1 0.02
35 1 0.02
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (32 bp):
TGTATCGATACATGAGAATTGTATCGATACAA
Found at i:596027 original size:13 final size:13
Alignment explanation
Indices: 596009--596066 Score: 56
Period size: 13 Copynumber: 4.9 Consensus size: 13
595999 CATGGCACAT
596009 TGTATCGATACAA
1 TGTATCGATACAA
596022 TGTATCGATAC-A
1 TGTATCGATACAA
* *
596034 TG-A---AGA-AT
1 TGTATCGATACAA
596042 TGTATCGATACAA
1 TGTATCGATACAA
596055 TGTATCGATACA
1 TGTATCGATACA
596067 TAAAGAATTG
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
8 4 0.11
9 1 0.03
11 1 0.03
12 5 0.14
13 24 0.69
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:596047 original size:20 final size:19
Alignment explanation
Indices: 596022--596087 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 19
596012 ATCGATACAA
596022 TGTATCGATACATGAAGAAT
1 TGTATCGATACAT-AAGAAT
596042 TGTATCGATAC-----AA-
1 TGTATCGATACATAAGAAT
596055 TGTATCGATACATAAAGAAT
1 TGTATCGATACAT-AAGAAT
596075 TGTATCGATACAT
1 TGTATCGATACAT
596088 TAACTCAAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 11 0.28
14 2 0.05
19 2 0.05
20 24 0.62
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (19 bp):
TGTATCGATACATAAGAAT
Found at i:600778 original size:16 final size:16
Alignment explanation
Indices: 600754--600784 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
600744 AAAAGCTTTC
*
600754 AAAATTTTTAATAGAA
1 AAAAGTTTTAATAGAA
600770 AAAAGTTTTAATAGA
1 AAAAGTTTTAATAGA
600785 GGAAATGTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (16 bp):
AAAAGTTTTAATAGAA
Found at i:606141 original size:20 final size:20
Alignment explanation
Indices: 606116--606161 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
606106 GGTAATTTTT
606116 ATGTAATTCGATAATAATTA
1 ATGTAATTCGATAATAATTA
* * *
606136 ATGTAATTTGATAATATTTT
1 ATGTAATTCGATAATAATTA
606156 ATGTAA
1 ATGTAA
606162 CTTAAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.46
Consensus pattern (20 bp):
ATGTAATTCGATAATAATTA
Found at i:606915 original size:32 final size:33
Alignment explanation
Indices: 606839--606916 Score: 113
Period size: 33 Copynumber: 2.4 Consensus size: 33
606829 TTAAGAAATT
*
606839 TGATCAAAGTTAACCAAAAGTGTATAATATCTA
1 TGATCAAAGTTAAACAAAAGTGTATAATATCTA
* *
606872 GGATCAGAGTTAAACAAAAGTGTATAA-ATCTA
1 TGATCAAAGTTAAACAAAAGTGTATAATATCTA
*
606904 TGATTAAAGTTAA
1 TGATCAAAGTTAA
606917 CAGCTTTAGA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
32 15 0.38
33 24 0.62
ACGTcount: A:0.46, C:0.09, G:0.15, T:0.29
Consensus pattern (33 bp):
TGATCAAAGTTAAACAAAAGTGTATAATATCTA
Found at i:608575 original size:295 final size:299
Alignment explanation
Indices: 607958--608867 Score: 1387
Period size: 295 Copynumber: 3.0 Consensus size: 299
607948 TCAGAATATC
* *
607958 CATGCTGAAATTAAAAATCAGAATTATTACCTACCTGCTGCCTCTTAGTGTGGAAGTTGAATTGA
1 CATGCTGAAATTAAAAATCAGAATTATTACCTGCCTGCTGCCTCTTGGTGTGGAAGTTGAATTGA
* ** * **
608023 TATCCATACTTGACACATGTGGAAATCTCCTTTGCATGGCAGTTGCAAATTTAACAAGTTCAGTA
66 TGTCCATGTTTGACACATGTGGAAA------TTGCATGGCAGTTGCAAATTTAATAAGTTCAACA
*
608088 TTTATCTTTGAAAGTGAATCTACCTTAGCCTCTAGTTCACTCATTTTAGATACTTTTTCCTCTAA
125 TTTATCTTTGAAAGTGAATCTACCTTAGCCTCTAGTTCACTCATTTTAGATAC-TTTTCTTCTAA
*
608153 CTCTGACACTTTAGCTGCTTTTTCTTCCAAAGTAGTCACTTCATCTATCATGACCTCTAACTTCT
189 CTCTGACACTTTAGCTGCTTTTTCTTCCAAAGTAGTCACTTTATCTATCATGACCTCTAACTTCT
608218 CTTACAATTTGAGTACCTCTTCTTCTCTTCCATTATCAACCTCATT
254 CTTACAATTTGAGTACCTCTTCTTCTCTTCCATTATCAACCTCATT
*
608264 CATGCTGAAATTAAAAATCAGAATTATTACCTGCTTGCTGCCTCTTGGTGTGGAAGTTGAATTGA
1 CATGCTGAAATTAAAAATCAGAATTATTACCTGCCTGCTGCCTCTTGGTGTGGAAGTTGAATTGA
*
608329 TGTCCATGTTTGACATATGTGGAAA-T-C-TGGCAGTTGCAAATTTAATAAGTTCAACATTTATC
66 TGTCCATGTTTGACACATGTGGAAATTGCATGGCAGTTGCAAATTTAATAAGTTCAACATTTATC
* * *
608391 TTCGAAAGTGAATCTACCTTAGCCTCTAGTTCACTCATTTTAGATACGTTTCTTTTAACTCTGAC
131 TTTGAAAGTGAATCTACCTTAGCCTCTAGTTCACTCATTTTAGATACTTTTCTTCTAACTCTGAC
** *
608456 ACTTTAGCTATTTTTTCTTCCAAAGTAGTCACTTTATCTAT-ATGACCTCTAGCTTCTCTTACAA
196 ACTTTAGCTGCTTTTTCTTCCAAAGTAGTCACTTTATCTATCATGACCTCTAACTTCTCTTACAA
608520 TTTGAGTACCTCTTCTTCTCTTCCATTATCAACCTCATT
261 TTTGAGTACCTCTTCTTCTCTTCCATTATCAACCTCATT
* * * *
608559 CATGCTGAAATTAAAAATCAGAATTATTACTTGCCTACTTCCTCTTGGTGTAGAAGTTGAATTGA
1 CATGCTGAAATTAAAAATCAGAATTATTACCTGCCTGCTGCCTCTTGGTGTGGAAGTTGAATTGA
608624 TGTCCATGTTTGACACATGTGGAAATCTCCTTTGCATGGCAGTTGCAAATTTAATAAGTTCAACA
66 TGTCCATGTTTGACACATGTGGAAA------TTGCATGGCAGTTGCAAATTTAATAAGTTCAACA
*** * * * * *
608689 TTTATCTTTGAAAACAAATTTACCTTAGCGTTTAGTTCACTCATTTTAGATATTTTTCTTCTAAT
125 TTTATCTTTGAAAGTGAATCTACCTTAGCCTCTAGTTCACTCATTTTAGATACTTTTCTTCTAAC
*
608754 TTTGACACTTTAGCTGCTTTTTCTTCCAAAGTAGTCACTTTATCTATCATGACCTCTAACTTCTC
190 TCTGACACTTTAGCTGCTTTTTCTTCCAAAGTAGTCACTTTATCTATCATGACCTCTAACTTCTC
*
608819 TTGCAATTTGAGTACCTCTTCTTCTCTTCCATTATCAACCTCATT
255 TTACAATTTGAGTACCTCTTCTTCTCTTCCATTATCAACCTCATT
608864 CATG
1 CATG
608868 GCTTGAAAGT
Statistics
Matches: 554, Mismatches: 40, Indels: 21
0.90 0.07 0.03
Matches are distributed among these distances:
295 145 0.26
296 53 0.10
297 78 0.14
298 1 0.00
299 1 0.00
302 1 0.00
303 1 0.00
304 127 0.23
305 64 0.12
306 83 0.15
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (299 bp):
CATGCTGAAATTAAAAATCAGAATTATTACCTGCCTGCTGCCTCTTGGTGTGGAAGTTGAATTGA
TGTCCATGTTTGACACATGTGGAAATTGCATGGCAGTTGCAAATTTAATAAGTTCAACATTTATC
TTTGAAAGTGAATCTACCTTAGCCTCTAGTTCACTCATTTTAGATACTTTTCTTCTAACTCTGAC
ACTTTAGCTGCTTTTTCTTCCAAAGTAGTCACTTTATCTATCATGACCTCTAACTTCTCTTACAA
TTTGAGTACCTCTTCTTCTCTTCCATTATCAACCTCATT
Found at i:616216 original size:2 final size:2
Alignment explanation
Indices: 616209--616234 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
616199 TTTTGTCTCC
616209 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
616235 CTTTTACTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:616250 original size:148 final size:148
Alignment explanation
Indices: 616069--616339 Score: 445
Period size: 148 Copynumber: 1.8 Consensus size: 148
616059 TTGTCTCCAC
616069 ATATATATATATATATATCTTCTACTAAATTATTTTA-TTCAGGATTTAGTTCCCCTAAAACCTT
1 ATATATATATATATATATCTTCTACTAAATTATTTTATTTC-GGATTTAGTTCCCCTAAAACCTT
* *
616133 TTTCTAATTTCAATTTCTTTTTTGTTTCTTTTTCTAATGTTGACTTCTCGATAGGCTAGGATTGC
65 TTTCTAATTTCAATTTCTTTTTTGTTTCTTTCTCTAATGTTGACTTCTCAATAGGCTAGGATTGC
616198 ATTTTGTCTCCATATATAT
130 ATTTTGTCTCCATATATAT
* ** *
616217 ATATATATATATATATATCTTTTACTAAATTATTTTATTTCGGATTTAGTTCCTTTAATACCTTT
1 ATATATATATATATATATCTTCTACTAAATTATTTTATTTCGGATTTAGTTCCCCTAAAACCTTT
* * *
616282 TTCTAATTTCGATTTCTTTTTTGTTTCTTTCTCTACTGTTGACTTCTCAATGGGCTAG
66 TTCTAATTTCAATTTCTTTTTTGTTTCTTTCTCTAATGTTGACTTCTCAATAGGCTAG
616340 TTTCTAAGTA
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
148 110 0.97
149 3 0.03
ACGTcount: A:0.24, C:0.15, G:0.09, T:0.52
Consensus pattern (148 bp):
ATATATATATATATATATCTTCTACTAAATTATTTTATTTCGGATTTAGTTCCCCTAAAACCTTT
TTCTAATTTCAATTTCTTTTTTGTTTCTTTCTCTAATGTTGACTTCTCAATAGGCTAGGATTGCA
TTTTGTCTCCATATATAT
Found at i:617368 original size:13 final size:13
Alignment explanation
Indices: 617350--617375 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
617340 ACACCAAAGT
617350 ATGTATCGATACA
1 ATGTATCGATACA
617363 ATGTATCGATACA
1 ATGTATCGATACA
617376 CAAAAAAATT
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:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:617373 original size:33 final size:34
Alignment explanation
Indices: 617331--617396 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 34
617321 TAGCCAAACT
* **
617331 TGTATCGATACACCAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAAATTGTATCGATACAA
617364 TGTATCGATACACAAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAAATTGTATCGATACA
617397 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 17 0.59
34 12 0.41
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (34 bp):
TGTATCGATACACAAAAAAATTGTATCGATACAA
Found at i:623297 original size:13 final size:13
Alignment explanation
Indices: 623279--623303 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
623269 GATGTTGAAA
623279 TGAATGATTTTGG
1 TGAATGATTTTGG
623292 TGAATGATTTTG
1 TGAATGATTTTG
623304 TGTTTTTATA
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:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (13 bp):
TGAATGATTTTGG
Found at i:623626 original size:20 final size:20
Alignment explanation
Indices: 623583--623628 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
623573 AAATCTTTTG
623583 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
623604 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
623624 CAAAA
1 CAAAA
623629 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:626054 original size:13 final size:13
Alignment explanation
Indices: 626036--626061 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
626026 ACACCAAAGT
626036 ATGTATCGATACA
1 ATGTATCGATACA
626049 ATGTATCGATACA
1 ATGTATCGATACA
626062 CAAAAAAATT
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:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:626059 original size:33 final size:34
Alignment explanation
Indices: 626017--626082 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 34
626007 TAGCCAAACT
* **
626017 TGTATCGATACACCAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAAATTGTATCGATACAA
626050 TGTATCGATACACAAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAAATTGTATCGATACA
626083 TTGGCTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 17 0.59
34 12 0.41
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (34 bp):
TGTATCGATACACAAAAAAATTGTATCGATACAA
Found at i:627293 original size:21 final size:21
Alignment explanation
Indices: 627269--627313 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
627259 AAAAATTATT
*
627269 ATTAGGTAAT-ATTTTTATGTA
1 ATTA-GTAATGATTTTTATATA
*
627290 ATTAGTAATGTTTTTTATATA
1 ATTAGTAATGATTTTTATATA
627311 ATT
1 ATT
627314 CTAATGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (21 bp):
ATTAGTAATGATTTTTATATA
Found at i:627318 original size:20 final size:21
Alignment explanation
Indices: 627280--627319 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
627270 TTAGGTAATA
* *
627280 TTTTTATGTAATTAGTAATGT
1 TTTTTATATAATTACTAATGT
627301 TTTTTATATAATT-CTAATG
1 TTTTTATATAATTACTAATG
627320 AAAAATATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.30, C:0.03, G:0.10, T:0.57
Consensus pattern (21 bp):
TTTTTATATAATTACTAATGT
Found at i:627560 original size:21 final size:20
Alignment explanation
Indices: 627530--627608 Score: 81
Period size: 20 Copynumber: 4.0 Consensus size: 20
627520 AAATTATTTT
*
627530 TAGGTAAT-TTTAATGTAAC
1 TAGGTAATATTTTATGTAAC
*
627549 TAGTTAATATTTTTATGTAAC
1 TAGGTAATA-TTTTATGTAAC
* *
627570 T-GGTAATATATTTATATAAT
1 TAGGTAATAT-TTTATGTAAC
*
627590 TAGGCAATATTTTATGTAA
1 TAGGTAATATTTTATGTAA
627609 TTCGATGAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
19 8 0.16
20 23 0.47
21 18 0.37
ACGTcount: A:0.37, C:0.04, G:0.13, T:0.47
Consensus pattern (20 bp):
TAGGTAATATTTTATGTAAC
Found at i:627607 original size:259 final size:261
Alignment explanation
Indices: 627084--627610 Score: 548
Period size: 259 Copynumber: 2.0 Consensus size: 261
627074 TAATGATTTG
* * *
627084 TGTAATTTGTAATCTTTTTAGGTAATTAGGTAATATTTTATGTAATTTTGTTGAAACAATATTTT
1 TGTAATTTGTAATCTTTTTAAGTAAATAGGTAATATTTTATATAATTTTGTTGAAACAATATTTT
* * * * * * *
627149 AAAATCGATGGGCCATTTTGAAACCAAGGTGGTGTTTTTATCTTCGAGTAAAGTTTTTTATAACT
66 AAAATCAATAGGCCATTTTGAAACCAAGGTAGCGTTTTTATCTACAAGTAAAGTTTTATATAACT
*
627214 TGCAATGTTTATATCTATTATGGTAATGTCTTATGTAATTCAAATAAAAATTATTATTAGGTAAT
131 TGCAATGTTTATATCTAATATGGTAATGTCTTATGTAATTCAAATAAAAATTATTATTAGGTAAT
* * * * ** * *
627279 ATTTTTATGTAATTAGTAATGTTTTTTATATAATTCTAATGAAAAATATTTTTAAGTAATGTATT
196 ATTTTAATGTAACTAGTAATGATTTTTATATAATGCTAATGAAAAATATAATTAAGCAATATATT
627344 A
261 A
* * *
627345 TGTAATTTGTAGTGC-TTTTAAGTAAAT-GGTAATGTTTTATATAGTTTCT-TT-AAACAATATT
1 TGTAATTTGTAAT-CTTTTTAAGTAAATAGGTAATATTTTATATAATTT-TGTTGAAACAATATT
* * * * * *
627406 TTAAAATCAATAGGCTATTTTGAAATCTATGTAGCGTTTTTATCTACAAGTAAAGTTTTATGTGA
64 TTAAAATCAATAGGCCATTTTGAAACCAAGGTAGCGTTTTTATCTACAAGTAAAGTTTTATATAA
* * * * * *** * *
627471 CTTGTAATGTTTATATGTAATGTGGTAATTTTTTATGTAATTTTGATGAAAATTATTTTTAGGT-
129 CTTGCAATGTTTATATCTAATATGGTAATGTCTTATGTAATTCAAATAAAAATTATTATTAGGTA
* * ** *
627535 A-ATTTTAATGTAACTAGTTAAT-ATTTTTATGTAACTGGTAAT-ATATTTATATAATTAGGCAA
194 ATATTTTAATGTAACTAG-TAATGATTTTTATATAA-TGCTAATGA-A-AAATATAATTAAGCAA
*
627597 TATTTTA
255 TATATTA
627604 TGTAATT
1 TGTAATT
627611 CGATGAAAAT
Statistics
Matches: 216, Mismatches: 44, Indels: 14
0.79 0.16 0.05
Matches are distributed among these distances:
257 25 0.12
258 11 0.05
259 137 0.63
260 19 0.09
261 23 0.11
262 1 0.00
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.47
Consensus pattern (261 bp):
TGTAATTTGTAATCTTTTTAAGTAAATAGGTAATATTTTATATAATTTTGTTGAAACAATATTTT
AAAATCAATAGGCCATTTTGAAACCAAGGTAGCGTTTTTATCTACAAGTAAAGTTTTATATAACT
TGCAATGTTTATATCTAATATGGTAATGTCTTATGTAATTCAAATAAAAATTATTATTAGGTAAT
ATTTTAATGTAACTAGTAATGATTTTTATATAATGCTAATGAAAAATATAATTAAGCAATATATT
A
Found at i:627734 original size:20 final size:19
Alignment explanation
Indices: 627694--627734 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
627684 GTAATATATA
*
627694 TTTATGTAACTTAAAAAAT
1 TTTATGTAAATTAAAAAAT
*
627713 TTTATGTAAATATAATAAAT
1 TTTATGTAAAT-TAAAAAAT
627733 TT
1 TT
627735 ATCTATTACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (19 bp):
TTTATGTAAATTAAAAAAT
Found at i:628326 original size:2 final size:2
Alignment explanation
Indices: 628319--628344 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
628309 AGATTTATTT
628319 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
628345 AACAAACTGT
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:629621 original size:23 final size:23
Alignment explanation
Indices: 629569--629621 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
629559 AATTTAATTT
**
629569 AATTAATATAAATCTCATTATGA
1 AATTAATATAAATAACATTATGA
* *
629592 AAATAATATAAAATAACCTTAT-A
1 AATTAATAT-AAATAACATTATGA
629615 AATTAAT
1 AATTAAT
629622 TGTAAAAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.36
Consensus pattern (23 bp):
AATTAATATAAATAACATTATGA
Found at i:630109 original size:2 final size:2
Alignment explanation
Indices: 630102--630142 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
630092 TACATATCTT
*
630102 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
630143 CCATGCCTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:631833 original size:29 final size:29
Alignment explanation
Indices: 631780--631847 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
631770 TATATTAAAA
*
631780 ATTAAAAATTATTTTATTATTAAATAATT
1 ATTAAAAATTATTTTATTATAAAATAATT
631809 ATTAAAATATTA-TTTA-TATAAAAATAATTT
1 ATTAAAA-ATTATTTTATTAT-AAAATAA-TT
*
631839 AATAAAAAT
1 ATTAAAAAT
631848 AGATAAAGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
28 3 0.09
29 19 0.56
30 12 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
ATTAAAAATTATTTTATTATAAAATAATT
Found at i:631838 original size:15 final size:15
Alignment explanation
Indices: 631801--631848 Score: 57
Period size: 14 Copynumber: 3.3 Consensus size: 15
631791 TTTTATTATT
631801 AAATAA-TTAT-TAA
1 AAATAATTTATATAA
*
631814 AATATTATTTATATAA
1 AA-ATAATTTATATAA
631830 AAATAATTTA-ATAA
1 AAATAATTTATATAA
631844 AAATA
1 AAATA
631849 GATAAAGAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
13 2 0.07
14 12 0.40
15 11 0.37
16 5 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AAATAATTTATATAA
Found at i:635460 original size:13 final size:13
Alignment explanation
Indices: 635441--635479 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
635431 AATAATCACC
635441 CTGTATCGATACA
1 CTGTATCGATACA
*
635454 GTGTATCGATACA
1 CTGTATCGATACA
635467 CTGTATCGATACA
1 CTGTATCGATACA
635480 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31
Consensus pattern (13 bp):
CTGTATCGATACA
Found at i:637579 original size:15 final size:15
Alignment explanation
Indices: 637559--637589 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
637549 ATTTCGTTTG
*
637559 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
637574 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
637589 G
1 G
637590 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:641682 original size:13 final size:13
Alignment explanation
Indices: 641664--641689 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
641654 CAATTTTTTG
641664 TGTATCGATACAT
1 TGTATCGATACAT
641677 TGTATCGATACAT
1 TGTATCGATACAT
641690 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:645127 original size:22 final size:23
Alignment explanation
Indices: 645101--645143 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
645091 TTAATCATGT
645101 TTAAAAGTG-TTTAAATAATTGA
1 TTAAAAGTGTTTTAAATAATTGA
* *
645123 TTAAAATTGTTTTAATTAATT
1 TTAAAAGTGTTTTAAATAATT
645144 TAGGTTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (23 bp):
TTAAAAGTGTTTTAAATAATTGA
Done.