Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002660.1 Hibiscus syriacus cultivar Beakdansim tig00005459_pilon, whole genome shotgun sequence
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: 2211860
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 9
Found at i:1495124 original size:2 final size:2
Alignment explanation
Indices: 1495112--1495160 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
1495102 TACACAACTC
1495112 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1495153 AT AT AT AT
1 AT AT AT AT
1495161 TGTAACATGT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1497662 original size:17 final size:18
Alignment explanation
Indices: 1497628--1497680 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 18
1497618 TAAAATTTGT
1497628 AATATTATTTACTAATTTA
1 AATATTATTTA-TAATTTA
1497647 AATATTATTT-TAATTTA
1 AATATTATTTATAATTTA
*
1497664 TATAATATATTTATAAT
1 AAT-AT-TATTTATAAT
1497681 GTTCAGTCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 9 0.30
18 2 0.07
19 15 0.50
20 4 0.13
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
AATATTATTTATAATTTA
Found at i:1501683 original size:2 final size:2
Alignment explanation
Indices: 1501676--1501713 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1501666 AGATTAATCC
1501676 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1501714 TTATTTTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1510775 original size:19 final size:19
Alignment explanation
Indices: 1510751--1510789 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1510741 TAATAGTGGC
1510751 CTTGTACCTCTATTCTTCA
1 CTTGTACCTCTATTCTTCA
1510770 CTTGTACCTCTATTCTTCA
1 CTTGTACCTCTATTCTTCA
1510789 C
1 C
1510790 GTGTCATGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.33, G:0.05, T:0.46
Consensus pattern (19 bp):
CTTGTACCTCTATTCTTCA
Found at i:1515395 original size:31 final size:30
Alignment explanation
Indices: 1515306--1515414 Score: 121
Period size: 30 Copynumber: 3.6 Consensus size: 30
1515296 TAAAGAACAC
* * *
1515306 TAATTTGATCATAAGTTTTAGATAAAATAT
1 TAATTTAATCTTAAATTTTAGATAAAATAT
*
1515336 TAATTTAATCTTAAATTTTAGATGAAATAT
1 TAATTTAATCTTAAATTTTAGATAAAATAT
*
1515366 TAATTTAATTCTT-AATATTTAAATAAAATAT
1 TAATTTAA-TCTTAAAT-TTTAGATAAAATAT
* *
1515397 CAATTTGACTCTTAAATT
1 TAATTT-AATCTTAAATT
1515415 CAGTTAAAGT
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
30 37 0.55
31 26 0.39
32 4 0.06
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.46
Consensus pattern (30 bp):
TAATTTAATCTTAAATTTTAGATAAAATAT
Found at i:1518151 original size:6 final size:6
Alignment explanation
Indices: 1518106--1518148 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
1518096 TAAAGGTAAC
* * *
1518106 GGGAGA GGGAGA GGGAGA GGGAGA GGGGGA GAGAGA GAGAGA G
1 GGGAGA GGGAGA GGGAGA GGGAGA GGGAGA GGGAGA GGGAGA G
1518149 AGATATGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (6 bp):
GGGAGA
Found at i:1518272 original size:15 final size:15
Alignment explanation
Indices: 1518254--1518283 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1518244 TTGATATATC
1518254 ATATTTTTTTATTTA
1 ATATTTTTTTATTTA
1518269 ATATTTTTTTATTTA
1 ATATTTTTTTATTTA
1518284 TTCAGATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
ATATTTTTTTATTTA
Found at i:1525745 original size:16 final size:16
Alignment explanation
Indices: 1525703--1525747 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
1525693 TGTTAGTCAA
*
1525703 CTCGTTGTTCATTAAG
1 CTCGTTGCTCATTAAG
* * *
1525719 TTTGTTACTCATTAAG
1 CTCGTTGCTCATTAAG
1525735 CTCGTTGCTCATT
1 CTCGTTGCTCATT
1525748 TCTAGTCTCG
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.18, C:0.20, G:0.16, T:0.47
Consensus pattern (16 bp):
CTCGTTGCTCATTAAG
Found at i:1533086 original size:32 final size:29
Alignment explanation
Indices: 1533021--1533091 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 29
1533011 TTTTATTAAT
*
1533021 AAAATTTAATAAATAAATTAGAAAAATTG
1 AAAATTTAATAAATAAATTAGAAAAATAG
*
1533050 AAAATATAATAAATAAAGTATAAGAAAAA-AG
1 AAAATTTAATAAATAAA-T-T-AGAAAAATAG
1533081 AAAAATTTAAT
1 -AAAATTTAAT
1533092 GGAAAACGGT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 16 0.46
30 1 0.03
31 2 0.06
32 16 0.46
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (29 bp):
AAAATTTAATAAATAAATTAGAAAAATAG
Found at i:1536778 original size:21 final size:21
Alignment explanation
Indices: 1536754--1536793 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1536744 TCAGATAATC
1536754 AATAAAAAATACAAAGGAAAA
1 AATAAAAAATACAAAGGAAAA
* *
1536775 AATATAAAATATAAAGGAA
1 AATAAAAAATACAAAGGAA
1536794 TTTAAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.72, C:0.03, G:0.10, T:0.15
Consensus pattern (21 bp):
AATAAAAAATACAAAGGAAAA
Found at i:1549188 original size:310 final size:311
Alignment explanation
Indices: 1548386--1549315 Score: 1718
Period size: 310 Copynumber: 3.0 Consensus size: 311
1548376 TAAATTACGT
*
1548386 GTTTAGTACTTAAACTATCAGTTTTAGTTCTTTTTAGTTCCTAAACTTTCATTTTTTTTTAAAAT
1 GTTTAGTACTTAAACTATCAGTTTTAGTTCTTTTTAGTTCCTAAACTTTCATTTTTTTTCAAAAT
*
1548451 CATACCTAAAGTTTAG-TTTTATTTCATTTTAGTTTCACGTCGTTAAAAATTTTAGTTTTTGTTT
66 CATACCTAAAGTTTAGTTTTTATTTCATTTTAGTTCCACGTCGTTAAAAATTTTAGTTTTTGTTT
1548515 CATTTTAGTACCTCCGTTCAAATTCAATGTTAAGTTTGAAAAAATTGAAAGTTTAAGTACTAAAA
131 CATTTTAGTACCTCCGTTCAAATTCAATGTTAAGTTTGAAAAAATTGAAAGTTTAAGTACTAAAA
* *
1548580 TAGACCAAAACTGATAG---A-TTACATCTTCATATGAAAACCTACATGAACCGGAAACAAACTA
196 TGGACCAAAACTGATAGATTAGTTACATCTTCATATGAAAACCTACGTGAACCGGAAACAAACTA
1548641 GGGATTTGTAAATAACTTAAGCTTGAAGACAGTGATGGAGCAAGGATTTTA
261 GGGATTTGTAAATAACTTAAGCTTGAAGACAGTGATGGAGCAAGGATTTTA
*
1548692 GTTTAGTACTTAAATTATCAGTTTTAGTTCTTTTTAGTTCCTAAACTTT--TTTTTTTTCAAAAT
1 GTTTAGTACTTAAACTATCAGTTTTAGTTCTTTTTAGTTCCTAAACTTTCATTTTTTTTCAAAAT
*
1548755 CATACATAAAGTTTAGTTTTTATTTCATTTTAGTTCCACGTCGTT-AAAATTTTAGTTTTTGTTT
66 CATACCTAAAGTTTAGTTTTTATTTCATTTTAGTTCCACGTCGTTAAAAATTTTAGTTTTTGTTT
1548819 CATTTTAGTACCTCCGTTCAAATTCAATGTTAAGTTTGAAAAAATTGAAAGTTTAAGTACTAAAA
131 CATTTTAGTACCTCCGTTCAAATTCAATGTTAAGTTTGAAAAAATTGAAAGTTTAAGTACTAAAA
1548884 TGGACCAAAAACTGATAGATTAGTTACATCTTCATATG-AAACCTACGTGAACCGGAAACAAACT
196 TGGACC-AAAACTGATAGATTAGTTACATCTTCATATGAAAACCTACGTGAACCGGAAACAAACT
1548948 AGGGATTTGTAAATAACTTAAGCTTGAAGACAGTGATGGAGCAAGGA-TTTA
260 AGGGATTTGTAAATAACTTAAGCTTGAAGACAGTGATGGAGCAAGGATTTTA
1548999 GTTTAGTACTTAAACTATCAGTTTTAGTTCTTTTTAGTTCCTAAACTTTCATTTTTTTTCAAAAT
1 GTTTAGTACTTAAACTATCAGTTTTAGTTCTTTTTAGTTCCTAAACTTTCATTTTTTTTCAAAAT
1549064 CATACCTAAAGTTTAGTTTTTATTTCATTTTAGTTCCACGTCGTTAAAAATTTTAGTTTTTGTTT
66 CATACCTAAAGTTTAGTTTTTATTTCATTTTAGTTCCACGTCGTTAAAAATTTTAGTTTTTGTTT
1549129 CATTTTAGTACCTCCGTTCAAATTCAATGTTAAGTTTGAAAAAATTGAAAGTTTAAGTACTAAAA
131 CATTTTAGTACCTCCGTTCAAATTCAATGTTAAGTTTGAAAAAATTGAAAGTTTAAGTACTAAAA
1549194 TGGACCAAAACTGATAGATTAGTTACATCTTCATATGAAAACCTACGTGAACCGGAAACAAACTA
196 TGGACCAAAACTGATAGATTAGTTACATCTTCATATGAAAACCTACGTGAACCGGAAACAAACTA
1549259 GGGATTTTGTAAATAACTTAAGCTTGAAGACAGTGATGGAGCAAGGATTTTA
261 GGGA-TTTGTAAATAACTTAAGCTTGAAGACAGTGATGGAGCAAGGATTTTA
1549311 GTTTA
1 GTTTA
1549316 AGGGGACAAA
Statistics
Matches: 604, Mismatches: 8, Indels: 18
0.96 0.01 0.03
Matches are distributed among these distances:
304 117 0.19
305 38 0.06
306 48 0.08
307 52 0.09
308 73 0.12
309 104 0.17
310 121 0.20
311 42 0.07
312 9 0.01
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (311 bp):
GTTTAGTACTTAAACTATCAGTTTTAGTTCTTTTTAGTTCCTAAACTTTCATTTTTTTTCAAAAT
CATACCTAAAGTTTAGTTTTTATTTCATTTTAGTTCCACGTCGTTAAAAATTTTAGTTTTTGTTT
CATTTTAGTACCTCCGTTCAAATTCAATGTTAAGTTTGAAAAAATTGAAAGTTTAAGTACTAAAA
TGGACCAAAACTGATAGATTAGTTACATCTTCATATGAAAACCTACGTGAACCGGAAACAAACTA
GGGATTTGTAAATAACTTAAGCTTGAAGACAGTGATGGAGCAAGGATTTTA
Found at i:1551322 original size:101 final size:102
Alignment explanation
Indices: 1551157--1551340 Score: 286
Period size: 102 Copynumber: 1.8 Consensus size: 102
1551147 ACCAAATAAT
1551157 CTGTGTCAAAGTAACACAAGCATCAATTTAGTAAGATTCATACAATAGTAAAATAAAATACGTCA
1 CTGTGTCAAAGTAACACAAGCATCAATTTAGT-AGATTCATACAATAGTAAAATAAAATACGTCA
* *
1551222 T-AAATTAGTGTATCAAATATACAAATGACATCAAAAA
65 TAAAATTAGCGTACCAAATATACAAATGACATCAAAAA
1551259 CTGTGTCAAAGT-A-ACAAGCATCAATTTAGT-GATTCATACATCAATAGTAAAATAAAATACGT
1 CTGTGTCAAAGTAACACAAGCATCAATTTAGTAGATTCAT--A-CAATAGTAAAATAAAATACGT
1551321 CATAAAATTAGCGTACCAAA
63 CATAAAATTAGCGTACCAAA
1551341 ATAAAGACAG
Statistics
Matches: 76, Mismatches: 2, Indels: 8
0.88 0.02 0.09
Matches are distributed among these distances:
98 7 0.09
100 18 0.24
101 25 0.33
102 26 0.34
ACGTcount: A:0.47, C:0.15, G:0.11, T:0.27
Consensus pattern (102 bp):
CTGTGTCAAAGTAACACAAGCATCAATTTAGTAGATTCATACAATAGTAAAATAAAATACGTCAT
AAAATTAGCGTACCAAATATACAAATGACATCAAAAA
Found at i:1553393 original size:11 final size:12
Alignment explanation
Indices: 1553362--1553405 Score: 53
Period size: 11 Copynumber: 4.1 Consensus size: 12
1553352 TCAAAAATCA
1553362 TAAAATAATTAT
1 TAAAATAATTAT
1553374 T-AAAT--TTAT
1 TAAAATAATTAT
1553383 TAAAAT-ATTA-
1 TAAAATAATTAT
1553393 TAAAATAATTAT
1 TAAAATAATTAT
1553405 T
1 T
1553406 TTGTAGCAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
9 5 0.18
10 10 0.36
11 11 0.39
12 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TAAAATAATTAT
Found at i:1553992 original size:23 final size:23
Alignment explanation
Indices: 1553957--1554005 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
1553947 TTACTTAGAG
1553957 AAAAGGAGAAAGA-AGACTCCTAA
1 AAAAGGAGAAAGACAG-CTCCTAA
*
1553980 AAAAGGA-ATAAGACTGCTCCTAA
1 AAAAGGAGA-AAGACAGCTCCTAA
1554003 AAA
1 AAA
1554006 GGCGTAAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 1 0.04
23 21 0.91
24 1 0.04
ACGTcount: A:0.55, C:0.14, G:0.18, T:0.12
Consensus pattern (23 bp):
AAAAGGAGAAAGACAGCTCCTAA
Found at i:1554197 original size:2 final size:2
Alignment explanation
Indices: 1554192--1554229 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1554182 TCTCTCTCTC
1554192 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1554230 GCTACGATTC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1554720 original size:295 final size:299
Alignment explanation
Indices: 1554204--1554784 Score: 924
Period size: 297 Copynumber: 2.0 Consensus size: 299
1554194 TATATATATA
* * *
1554204 TATATATATATATATATATATTATATGCTACGATTCAATTACATAGTTTAAAACTTCTTAGTTTT
1 TATATATATATATATATATATTATAGGCCACGATTCAATTACATAGTTTAAAACTTATTAGTTTT
1554269 TACACTTTTTAGGATCATTAGATGATAAGAAATCAAAGACTGAGATTAACATTAATAAATGAGAA
66 TACACTTTTTAGGATCATTAGATGATAAGAAATCAAAGACTGAGATTAACATTAATAAATGAGAA
*
1554334 GATATTCACTGAAAAAGAAAAACAAAAAGTTAATCTTAGTCTTTGATTTCCCTCATTCAACTATT
131 GATATTCACTGAAAAAGAAAAACAAAAAGTTAATCTTAGTCTTTGATTTCCCTCATCCAACTATT
* *
1554399 TTAAGGTGTAAAACTAAAAC-TTTTTTTATAT-ACCACTGGTATCTGATTTATTAATCGGCTAAA
196 TTAAGGTGTAAAACTAAAACTTTTTTTTATATAACCACTAGTATCTGAGTTATTAATCGGCTAAA
* *
1554462 ATTTTTACATTATGTAATTGGATTCTCTCTCTCTCTCTC
261 AATTTTACACTATGTAATTGGATTCTCTCTCTCTCTCTC
* **
1554501 TATATATATATATATATGTATGTATAGGCCGTGATTCAATTAC-T-GTTTAAAACTTATTAGTTT
1 TATATATATATATATATATAT-TATAGGCCACGATTCAATTACATAGTTTAAAACTTATTAGTTT
* * * * *
1554564 TTACACTTTTTTAATGATCGTTGGATGAT-A-AAATCAAAGGCTGAGATTAACATTAGTAAATGA
65 TTACAC-TTTTT-AGGATCATTAGATGATAAGAAATCAAAGACTGAGATTAACATTAATAAATGA
1554627 GAAGATA-TCACTGAAAAAGAAAAACAAAAAGTTAATCTTAGTCTTTGATTTCCCTCATCCAACT
128 GAAGATATTCACTGAAAAAGAAAAACAAAAAGTTAATCTTAGTCTTTGATTTCCCTCATCCAACT
* *
1554691 ATTTTAAGGTGTAAAACTAAAAGTTTTTTTTATATAACCACTAGTATCTGAGTTATTAATCTGCT
193 ATTTTAAGGTGTAAAACTAAAACTTTTTTTTATATAACCACTAGTATCTGAGTTATTAATCGGCT
1554756 AAAAATTTTACACTATGTAATTGGATTCT
258 AAAAATTTTACACTATGTAATTGGATTCT
1554785 TTCCTCTATA
Statistics
Matches: 261, Mismatches: 18, Indels: 10
0.90 0.06 0.03
Matches are distributed among these distances:
295 78 0.30
296 73 0.28
297 80 0.31
298 30 0.11
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.39
Consensus pattern (299 bp):
TATATATATATATATATATATTATAGGCCACGATTCAATTACATAGTTTAAAACTTATTAGTTTT
TACACTTTTTAGGATCATTAGATGATAAGAAATCAAAGACTGAGATTAACATTAATAAATGAGAA
GATATTCACTGAAAAAGAAAAACAAAAAGTTAATCTTAGTCTTTGATTTCCCTCATCCAACTATT
TTAAGGTGTAAAACTAAAACTTTTTTTTATATAACCACTAGTATCTGAGTTATTAATCGGCTAAA
AATTTTACACTATGTAATTGGATTCTCTCTCTCTCTCTC
Found at i:1555459 original size:27 final size:27
Alignment explanation
Indices: 1555420--1555486 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
1555410 TCAAAATTCT
**
1555420 CCCTCCCAATCCTAGTAACCGTCGTCC
1 CCCTCCCCCTCCTAGTAACCGTCGTCC
1555447 CCCTCCCCCTCCTAGTAACCGTCGTCC
1 CCCTCCCCCTCCTAGTAACCGTCGTCC
*
1555474 TCCTCCCCCTCCT
1 CCCTCCCCCTCCT
1555487 CCACGGCCAC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.12, C:0.55, G:0.09, T:0.24
Consensus pattern (27 bp):
CCCTCCCCCTCCTAGTAACCGTCGTCC
Found at i:1555645 original size:21 final size:21
Alignment explanation
Indices: 1555621--1555691 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
1555611 CTCCACCTAC
1555621 TCCCCCTCCTCGCGCACCTCT
1 TCCCCCTCCTCGCGCACCTCT
*
1555642 TCCCCCTCC-C-CTGCTCCTAC-
1 TCCCCCTCCTCGC-GCACCT-CT
**
1555662 TCCCCCTCCTCGTACACCTCT
1 TCCCCCTCCTCGCGCACCTCT
*
1555683 TCCACCTCC
1 TCCCCCTCC
1555692 CCTACTCCCC
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
19 1 0.03
20 16 0.40
21 23 0.57
ACGTcount: A:0.07, C:0.62, G:0.06, T:0.25
Consensus pattern (21 bp):
TCCCCCTCCTCGCGCACCTCT
Found at i:1555664 original size:41 final size:41
Alignment explanation
Indices: 1555616--1555934 Score: 265
Period size: 41 Copynumber: 8.3 Consensus size: 41
1555606 TACCCCTCCA
1555616 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCTGCT
1 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCTGCT
** *
1555657 CCTACTCCCCCTCCTCGTACACCTCTTCCACCT---C--C-
1 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCTGCT
* *
1555692 CCTACT-CCCC-CCTAGCTCACCTCTTCCCCCTCCCCCTGCT
1 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCT-CCCCTGCT
** * *
1555732 CCTACTCCCCCTCCT--C-CA-C-C-T---CCTATCCTCCA
1 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCTGCT
*
1555764 CCTACTCCCCCTCCTCGCGCACCT-TTCCCCCCTCCTCCTCCT
1 CCTACTCCCCCTCCTCGCGCACCTCTT-CCCCCTCC-CCTGCT
1555806 CCTACTCCCCCTCCTCGCGCACCTCTT-CCCCTCCCCCTGCT
1 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCT-CCCCTGCT
** * * *
1555847 CCTACTCCCCCTCCTCGTACA-C-C-T---CCTACCCTCCA
1 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCTGCT
* *
1555882 CCTACTCCTCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCT
1 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCT-CCCCTGCT
1555924 CCTACTCCCCC
1 CCTACTCCCCC
1555935 CACCTACTCC
Statistics
Matches: 221, Mismatches: 28, Indels: 57
0.72 0.09 0.19
Matches are distributed among these distances:
32 19 0.09
33 20 0.09
34 5 0.02
35 30 0.14
36 7 0.03
37 4 0.02
38 4 0.02
39 4 0.02
40 8 0.04
41 69 0.31
42 49 0.22
43 2 0.01
ACGTcount: A:0.08, C:0.62, G:0.05, T:0.25
Consensus pattern (41 bp):
CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCTGCT
Found at i:1555665 original size:20 final size:21
Alignment explanation
Indices: 1555614--1555673 Score: 72
Period size: 20 Copynumber: 2.9 Consensus size: 21
1555604 CCTACCCCTC
1555614 CACCTACTCCCCCTCCTCGCG
1 CACCTACTCCCCCTCCTCGCG
1555635 CACCT-CTTCCCCCTCC-C-CTG
1 CACCTAC-TCCCCCTCCTCGC-G
*
1555655 CTCCTACTCCCCCTCCTCG
1 CACCTACTCCCCCTCCTCG
1555674 TACACCTCTT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
19 1 0.03
20 16 0.48
21 16 0.48
ACGTcount: A:0.07, C:0.63, G:0.07, T:0.23
Consensus pattern (21 bp):
CACCTACTCCCCCTCCTCGCG
Found at i:1555725 original size:74 final size:76
Alignment explanation
Indices: 1555583--1555848 Score: 330
Period size: 74 Copynumber: 3.5 Consensus size: 76
1555573 AACACGCCTC
*
1555583 CTCCCCCTCCTCGTACAACCTCCTACCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCC
1 CTCCCCCTCCTCGTAC-ACCT-CTTCCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCC
1555648 TCCCCTGCTCCTA
64 TCCCCTGCTCCTA
* *
1555661 CTCCCCCTCCTCGTACACCTCTTCCACCTCC-CCTACT-CCCC-CCTAGCTCACCTCTTCCCCCT
1 CTCCCCCTCCTCGTACACCTCTTCC-CCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCCT
1555723 CCCCCTGCTCCTA
65 -CCCCTGCTCCTA
* **
1555736 CTCCCCCTCCTC---CACCTCCTATCCTCCACCTACTCCCCCTCCTCGCGCACCT-TTCCCCCCT
1 CTCCCCCTCCTCGTACACCTCTTCCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTT-CCCCCT
*
1555797 CCTCCTCCTCCTA
65 CC-CCTGCTCCTA
** * *
1555810 CTCCCCCTCCTCGCGCACCTCTTCCCCTCCCCCTGCTCC
1 CTCCCCCTCCTCGTACACCTCTTCCCCTCCACCTACTCC
1555849 TACTCCCCCT
Statistics
Matches: 164, Mismatches: 14, Indels: 21
0.82 0.07 0.11
Matches are distributed among these distances:
71 5 0.03
72 13 0.08
73 8 0.05
74 56 0.34
75 28 0.17
76 10 0.06
77 28 0.17
78 16 0.10
ACGTcount: A:0.08, C:0.63, G:0.05, T:0.24
Consensus pattern (76 bp):
CTCCCCCTCCTCGTACACCTCTTCCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTC
CCCTGCTCCTA
Found at i:1555742 original size:21 final size:21
Alignment explanation
Indices: 1555716--1555860 Score: 78
Period size: 21 Copynumber: 6.4 Consensus size: 21
1555706 GCTCACCTCT
*
1555716 TCCCCCTCCCCCTGCTCCTAC
1 TCCCCCTCCCCCTCCTCCTAC
* *
1555737 TCCCCCTCCTCCACCTCCTATCC
1 TCCCCCTCCCCCTCCTCCTA--C
*
1555760 TCCACCTACTCCCCCTCCTCGCGCACC
1 TCC-CC--CTCCCCCTCCTC-C-TA-C
*
1555787 TTTCCCCCCTCCTCCTCCTCCTAC
1 --T-CCCCCTCCCCCTCCTCCTAC
* * *
1555811 TCCCCCTCCTCGC-GCACCT-C
1 TCCCCCTCC-CCCTCCTCCTAC
* *
1555831 TTCCCCTCCCCCTGCTCCTAC
1 TCCCCCTCCCCCTCCTCCTAC
1555852 TCCCCCTCC
1 TCCCCCTCC
1555861 TCGTACACCT
Statistics
Matches: 95, Mismatches: 16, Indels: 26
0.69 0.12 0.19
Matches are distributed among these distances:
19 2 0.02
20 14 0.15
21 38 0.40
22 2 0.02
23 4 0.04
24 3 0.03
25 1 0.01
26 11 0.12
27 14 0.15
28 1 0.01
29 3 0.03
30 2 0.02
ACGTcount: A:0.06, C:0.65, G:0.04, T:0.25
Consensus pattern (21 bp):
TCCCCCTCCCCCTCCTCCTAC
Found at i:1555754 original size:15 final size:16
Alignment explanation
Indices: 1555720--1555862 Score: 59
Period size: 15 Copynumber: 8.8 Consensus size: 16
1555710 ACCTCTTCCC
*
1555720 CCTCCCCCTGCTCCTA
1 CCTCCCCCTCCTCCTA
1555736 -CTCCCCCTCCTCC-A
1 CCTCCCCCTCCTCCTA
* *
1555750 CCTCCTATCCTCCACCTA
1 CCTCC--CCCTCCTCCTA
*
1555768 -CTCCCCCTCCTCGCGCA
1 CCTCCCCCTCCTC-C-TA
1555785 CCTTTCCCCCCTCCTCCT-
1 CC--T-CCCCCTCCTCCTA
** *
1555803 CCTCCTACTCCCCCT-
1 CCTCCCCCTCCTCCTA
*
1555818 CCTCGCGCACCTCTTCC--
1 CCTC-C-C-CCTCCTCCTA
*
1555835 CCTCCCCCTGCTCCTA
1 CCTCCCCCTCCTCCTA
1555851 -CTCCCCCTCCTC
1 CCTCCCCCTCCTC
1555863 GTACACCTCC
Statistics
Matches: 95, Mismatches: 17, Indels: 31
0.66 0.12 0.22
Matches are distributed among these distances:
14 7 0.07
15 47 0.49
16 4 0.04
17 16 0.17
18 9 0.09
20 2 0.02
21 10 0.11
ACGTcount: A:0.06, C:0.64, G:0.04, T:0.25
Consensus pattern (16 bp):
CCTCCCCCTCCTCCTA
Found at i:1555950 original size:55 final size:56
Alignment explanation
Indices: 1555875--1555993 Score: 213
Period size: 55 Copynumber: 2.1 Consensus size: 56
1555865 ACACCTCCTA
* *
1555875 CCCTCCACCTACTCCTCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTC
1 CCCTCCACCTACTCCCCCTCCTAGCACACCTCTTCCCCCTCCCCCTGCTCCTACTC
1555931 CCC-CCACCTACTCCCCCTCCTAGCACACCTCTTCCCCCTCCCCCTGCTCCTACTC
1 CCCTCCACCTACTCCCCCTCCTAGCACACCTCTTCCCCCTCCCCCTGCTCCTACTC
1555986 CCCTCCAC
1 CCCTCCAC
1555994 GTACACCTCC
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
55 53 0.88
56 7 0.12
ACGTcount: A:0.10, C:0.63, G:0.04, T:0.23
Consensus pattern (56 bp):
CCCTCCACCTACTCCCCCTCCTAGCACACCTCTTCCCCCTCCCCCTGCTCCTACTC
Found at i:1556011 original size:21 final size:21
Alignment explanation
Indices: 1555985--1556024 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1555975 TGCTCCTACT
*
1555985 CCCCTCCACGTACACCTCCTA
1 CCCCTCCACCTACACCTCCTA
*
1556006 CCCCTCCACCTACTCCTCC
1 CCCCTCCACCTACACCTCC
1556025 CCCTCCCCCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.62, G:0.03, T:0.20
Consensus pattern (21 bp):
CCCCTCCACCTACACCTCCTA
Found at i:1556031 original size:6 final size:6
Alignment explanation
Indices: 1556006--1556082 Score: 84
Period size: 6 Copynumber: 13.0 Consensus size: 6
1555996 ACACCTCCTA
* * * *
1556006 CCCCTC CACCTA CTCCTC CCCCTC CCCCTC CCTCTC CCCC-C CCCCTC
1 CCCCTC CCCCTC CCCCTC CCCCTC CCCCTC CCCCTC CCCCTC CCCCTC
* * *
1556053 CCCCTC CACCTC CACCTC CCCCTC CACCTC
1 CCCCTC CCCCTC CCCCTC CCCCTC CCCCTC
1556083 ACCTCCACCA
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
5 5 0.08
6 55 0.92
ACGTcount: A:0.06, C:0.75, G:0.00, T:0.18
Consensus pattern (6 bp):
CCCCTC
Found at i:1556049 original size:23 final size:24
Alignment explanation
Indices: 1556023--1556091 Score: 81
Period size: 23 Copynumber: 3.0 Consensus size: 24
1556013 ACCTACTCCT
1556023 CCCCCTCCCCCTCCCTCTCC-CCC
1 CCCCCTCCCCCTCCCTCTCCACCC
*
1556046 CCCCCTCCCCCTCCAC-CTCCACCT
1 CCCCCTCCCCCTCC-CTCTCCACCC
* *
1556070 CCCCCTCCACCTCAC-CTCCACC
1 CCCCCTCCCCCTCCCTCTCCACC
1556092 AGCTACCTGC
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
23 26 0.63
24 15 0.37
ACGTcount: A:0.07, C:0.77, G:0.00, T:0.16
Consensus pattern (24 bp):
CCCCCTCCCCCTCCCTCTCCACCC
Found at i:1556050 original size:131 final size:131
Alignment explanation
Indices: 1555806--1556051 Score: 372
Period size: 131 Copynumber: 1.9 Consensus size: 131
1555796 TCCTCCTCCT
* * *
1555806 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACCT
1 CCTACTCCCCCTCCTAGCACACCTCTTCCCCTCCCCCTGCTCCTACTCCCCCTCCACGTACACCT
* * *
1555871 CCTACCCTCCACCTACTCCTCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCC
66 CCTACCCTCCACCTACTCCTCCCCCTACCCCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCC
1555936 A
131 A
1555937 CCTACTCCCCCTCCTAGCACACCTCTTCCCCCTCCCCCTGCTCCTACT-CCCCTCCACGTACACC
1 CCTACTCCCCCTCCTAGCACACCTCTT-CCCCTCCCCCTGCTCCTACTCCCCCTCCACGTACACC
* *
1556001 TCCTACCCCTCCACCTACTCCTCCCCCTCCCCCTCC-CTCTCCCCC-CCCCCT
65 TCCTA-CCCTCCACCTACTCCTCCCCCTACCCCACCTCT-TCCCCCTCCCCCT
1556052 CCCCCTCCAC
Statistics
Matches: 104, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
131 53 0.51
132 51 0.49
ACGTcount: A:0.09, C:0.64, G:0.04, T:0.23
Consensus pattern (131 bp):
CCTACTCCCCCTCCTAGCACACCTCTTCCCCTCCCCCTGCTCCTACTCCCCCTCCACGTACACCT
CCTACCCTCCACCTACTCCTCCCCCTACCCCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCC
A
Found at i:1556064 original size:12 final size:12
Alignment explanation
Indices: 1556020--1556091 Score: 76
Period size: 12 Copynumber: 6.2 Consensus size: 12
1556010 TCCACCTACT
*
1556020 CCTCCCCCTCCC
1 CCTCCCCCTCCA
*
1556032 CCTCCCTCTCC-
1 CCTCCCCCTCCA
* *
1556043 CCCCCCCCTCCC
1 CCTCCCCCTCCA
*
1556055 CCTCCACCTCCA
1 CCTCCCCCTCCA
1556067 CCTCCCCCTCCA
1 CCTCCCCCTCCA
*
1556079 CCT-CACCTCCA
1 CCTCCCCCTCCA
1556090 CC
1 CC
1556092 AGCTACCTGC
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
11 18 0.35
12 33 0.65
ACGTcount: A:0.07, C:0.76, G:0.00, T:0.17
Consensus pattern (12 bp):
CCTCCCCCTCCA
Found at i:1556091 original size:6 final size:6
Alignment explanation
Indices: 1556008--1556091 Score: 66
Period size: 6 Copynumber: 14.3 Consensus size: 6
1555998 ACCTCCTACC
* * * * * * *
1556008 CCTCCA CCTACT CCTCCC CCTCCC CCTCC- CTCTCC- CCCCCC CCTCCC
1 CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA C-CTCCA CCTCCA CCTCCA
*
1556055 CCTCCA CCTCCA CCTCCC CCTCCA CCT-CA CCTCCA CC
1 CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA CCTCCA CC
1556092 AGCTACCTGC
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
5 9 0.14
6 57 0.86
ACGTcount: A:0.08, C:0.74, G:0.00, T:0.18
Consensus pattern (6 bp):
CCTCCA
Found at i:1559799 original size:20 final size:20
Alignment explanation
Indices: 1559774--1559844 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
1559764 CTTTTTAAGC
1559774 GTTTCGAAACTATCTCAAGA
1 GTTTCGAAACTATCTCAAGA
*
1559794 GTTTCGAAACTATCTAAAGA
1 GTTTCGAAACTATCTCAAGA
* *
1559814 GTTTTGAAACTATCTCAAGG
1 GTTTCGAAACTATCTCAAGA
1559834 GTTTCGAAACT
1 GTTTCGAAACT
1559845 TTCCCTAAAG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (20 bp):
GTTTCGAAACTATCTCAAGA
Found at i:1560995 original size:2 final size:2
Alignment explanation
Indices: 1560988--1561057 Score: 113
Period size: 2 Copynumber: 35.0 Consensus size: 2
1560978 TAATAAGTGA
* * *
1560988 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AG AT AT AT AT AT CT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1561030 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1561058 CCACTTTAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1563710 original size:41 final size:43
Alignment explanation
Indices: 1563665--1563748 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
1563655 AACACGATAA
1563665 ACAA-TTTTT-AAAGATTACTACCATAATTTTTTGTGAAGCAC
1 ACAATTTTTTAAAAGATTACTACCATAATTTTTTGTGAAGCAC
1563706 ACAATTTTTTAAAAGATTACTACCATAATTTTTTGTGAAGCAC
1 ACAATTTTTTAAAAGATTACTACCATAATTTTTTGTGAAGCAC
1563749 GCACCCTTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
41 4 0.10
42 5 0.12
43 32 0.78
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (43 bp):
ACAATTTTTTAAAAGATTACTACCATAATTTTTTGTGAAGCAC
Found at i:1565471 original size:16 final size:15
Alignment explanation
Indices: 1565450--1565487 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 15
1565440 CATGATCCAA
1565450 TTACACTGTGTAAATT
1 TTACACT-TGTAAATT
1565466 TTACACCTTGTAAATT
1 TTACA-CTTGTAAATT
1565482 TTACAC
1 TTACAC
1565488 ATTTTTAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 1 0.05
16 18 0.86
17 2 0.10
ACGTcount: A:0.32, C:0.18, G:0.08, T:0.42
Consensus pattern (15 bp):
TTACACTTGTAAATT
Found at i:1566935 original size:27 final size:27
Alignment explanation
Indices: 1566905--1566961 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
1566895 GACCTCCCAA
*
1566905 TCCTAGTAACCGTCGTCCCCCTCCCCC
1 TCCTAGTAACCGTCATCCCCCTCCCCC
*
1566932 TCCTAGTAACCGTCATCCTCCTCCCCC
1 TCCTAGTAACCGTCATCCCCCTCCCCC
1566959 TCC
1 TCC
1566962 CCCTCCTCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.12, C:0.54, G:0.09, T:0.25
Consensus pattern (27 bp):
TCCTAGTAACCGTCATCCCCCTCCCCC
Found at i:1567159 original size:42 final size:42
Alignment explanation
Indices: 1567113--1567531 Score: 307
Period size: 42 Copynumber: 10.5 Consensus size: 42
1567103 ACACCTCCTA
1567113 CCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTC
1 CCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTC
* * **
1567155 CCCCTTCTCCTACTCCCCCTCCTCGTACACCTC-T-----TC
1 CCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTC
** * *
1567191 AACCTCCACCTACTCCCCCTCCTAGCTCACCTCTTCCCCCTC
1 CCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTC
* * ** * * *
1567233 CCCCTCCCCCTGCTCCTACTCC-C-C-CTCCTCGTACACCTCCTA
1 CCCCTCCACCTACTCCCCCTCCTCGCGCACCTC-TTC-CC-CCTC
*
1567275 TCCCTCCACCTACTCCCCCTCCTCGCGCA-CT-TTCCCCCCTC
1 CCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTT-CCCCCTC
** * *
1567316 ATCCTGCTCCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTC
1 CCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTC
* * * *
1567358 CCCCTGCTCCTACT--CCC-CCTC-CGTA-C-C-T---CCTA
1 CCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTC
* *
1567390 CCCCTCCACCTACTCCTCCTCCTAGCGCACCTCTTCCCCCTC
1 CCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTC
* * * * *
1567432 CCCCTGCTCCTACTCCCCCTCCT--CGTACATC-T---CCTA
1 CCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTC
*
1567468 CCCCTCCACCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTC
1 CCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTC
* *
1567510 CCCCTGCTCCTACTCCCCCTCC
1 CCCCTCCACCTACTCCCCCTCC
1567532 ACGTACACCT
Statistics
Matches: 290, Mismatches: 56, Indels: 62
0.71 0.14 0.15
Matches are distributed among these distances:
32 15 0.05
34 2 0.01
35 4 0.01
36 56 0.19
37 3 0.01
38 10 0.03
39 12 0.04
40 12 0.04
41 31 0.11
42 137 0.47
43 4 0.01
44 3 0.01
45 1 0.00
ACGTcount: A:0.09, C:0.62, G:0.05, T:0.25
Consensus pattern (42 bp):
CCCCTCCACCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTC
Found at i:1567171 original size:21 final size:21
Alignment explanation
Indices: 1567086--1567598 Score: 102
Period size: 21 Copynumber: 24.8 Consensus size: 21
1567076 CACGCCTCCT
* * *
1567086 CCCCTCCCCCTCCTCGTACAC
1 CCCCTCCCCCTCCACCTACTC
* *
1567107 CTCCTACCCCTCCACCTACTC
1 CCCCTCCCCCTCCACCTACTC
* *
1567128 CCCCTCCTCGC-GCACCT-CTTC
1 CCCCTCC-CCCTCCACCTAC-TC
* *
1567149 CCCCTCCCCCTTCTCCTACTC
1 CCCCTCCCCCTCCACCTACTC
* * *
1567170 CCCCTCCTCGTACACCT-CT-
1 CCCCTCCCCCTCCACCTACTC
**
1567189 ----TCAACCTCCACCTACTC
1 CCCCTCCCCCTCCACCTACTC
**
1567206 CCCCTCCTAGCT-CACCT-CTTC
1 CCCCTCC-CCCTCCACCTAC-TC
* *
1567227 CCCCTCCCCCTCCCCCTGCTC
1 CCCCTCCCCCTCCACCTACTC
** * * *
1567248 CTACTCCCCCTCCTCGTACAC
1 CCCCTCCCCCTCCACCTACTC
* **
1567269 CTCCTATCCCTCCACCTACTC
1 CCCCTCCCCCTCCACCTACTC
* * * *
1567290 CCCCTCCTCGC-GCACTTTC-C
1 CCCCTCC-CCCTCCACCTACTC
** * *
1567310 CCCCTCATCCTGCTCCTACTC
1 CCCCTCCCCCTCCACCTACTC
* *
1567331 CCCCTCCTCGC-GCACCT-CTTC
1 CCCCTCC-CCCTCCACCTAC-TC
* *
1567352 CCCCTCCCCCTGCTCCTACTC
1 CCCCTCCCCCTCCACCTACTC
* *
1567373 CCCCTCCGTACCTCCTACC-CCTC
1 CCCCTCC--CCCTCC-ACCTACTC
* * * * *
1567396 CACCTACTCCTCCTCCTAGCGC
1 CCCCTCCCCCTCCACCTA-CTC
* * *
1567418 ACCTCTTCCCCCTCCCCCTGCTC
1 -CC-CCTCCCCCTCCACCTACTC
** * *
1567441 CTACTCCCCCTCCTCGTACAT-
1 CCCCTCCCCCTCCACCTAC-TC
* *
1567462 CTCCTACCCCTCCACCTACTC
1 CCCCTCCCCCTCCACCTACTC
** *
1567483 CCCCTCCTAGC-GCACCT-CTTC
1 CCCCTCC-CCCTCCACCTAC-TC
* *
1567504 CCCCTCCCCCTGCTCCTACTC
1 CCCCTCCCCCTCCACCTACTC
* * * * *
1567525 CCCCTCCACGTACACCTCCTA
1 CCCCTCCCCCTCCACCTACTC
* *
1567546 CCCCTCCACCT--A-CTCCTC
1 CCCCTCCCCCTCCACCTACTC
*
1567564 CCCCTCCCTCTCCA-C--CTC
1 CCCCTCCCCCTCCACCTACTC
*
1567582 CCCCTCCACCTCCACCT
1 CCCCTCCCCCTCCACCT
1567599 CCACCTCCAC
Statistics
Matches: 351, Mismatches: 103, Indels: 77
0.66 0.19 0.15
Matches are distributed among these distances:
15 9 0.03
16 2 0.01
18 29 0.08
19 3 0.01
20 30 0.09
21 233 0.66
22 17 0.05
23 15 0.04
24 13 0.04
ACGTcount: A:0.10, C:0.62, G:0.04, T:0.24
Consensus pattern (21 bp):
CCCCTCCCCCTCCACCTACTC
Found at i:1567233 original size:36 final size:36
Alignment explanation
Indices: 1567089--1567233 Score: 148
Period size: 36 Copynumber: 3.9 Consensus size: 36
1567079 GCCTCCTCCC
* *
1567089 CTCCCCCTCCTCGTACACCTCCTACCCCTCCACCTA
1 CTCCCCCTCCTCGTACACCTCTTCCCCCTCCACCTA
** *
1567125 CTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTTCTCCTA
1 CTCCCCCTCCTCGTACACCTCTTCCCCCT----C--CACCTA
**
1567167 CTCCCCCTCCTCGTACACCTCTTCAACCTCCACCTA
1 CTCCCCCTCCTCGTACACCTCTTCCCCCTCCACCTA
*
1567203 CTCCCCCTCCTAGCT-CACCTCTTCCCCCTCC
1 CTCCCCCTCCTCG-TACACCTCTTCCCCCTCC
1567234 CCCTCCCCCT
Statistics
Matches: 89, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
36 56 0.63
37 1 0.01
38 1 0.01
40 1 0.01
42 30 0.34
ACGTcount: A:0.10, C:0.61, G:0.03, T:0.25
Consensus pattern (36 bp):
CTCCCCCTCCTCGTACACCTCTTCCCCCTCCACCTA
Found at i:1567314 original size:20 final size:20
Alignment explanation
Indices: 1567289--1567355 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 20
1567279 TCCACCTACT
1567289 CCCCCTCCTCGCGCACTTTC
1 CCCCCTCCTCGCGCACTTTC
* * * *
1567309 CCCCCTCATC-CTGCTCCTAC
1 CCCCCTCCTCGC-GCACTTTC
1567329 TCCCCCTCCTCGCGCACCTCTTC
1 -CCCCCTCCTCGCGCA-CT-TTC
1567352 CCCC
1 CCCC
1567356 TCCCCCTGCT
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
19 1 0.03
20 14 0.41
21 11 0.32
22 6 0.18
23 2 0.06
ACGTcount: A:0.06, C:0.63, G:0.07, T:0.24
Consensus pattern (20 bp):
CCCCCTCCTCGCGCACTTTC
Found at i:1567502 original size:78 final size:76
Alignment explanation
Indices: 1567324--1567561 Score: 408
Period size: 78 Copynumber: 3.1 Consensus size: 76
1567314 TCATCCTGCT
*
1567324 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCT-CCGTAC-CTC
1 CCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCCGTACACTC
1567387 CTACCCCTCCA
66 CTACCCCTCCA
*
1567398 CCTACTCCTCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACATC
1 CCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCC-CGTACA-C
1567463 TCCTACCCCTCCA
64 TCCTACCCCTCCA
1567476 CCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCACGTACACC
1 CCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCC-CGTACA-C
1567541 TCCTACCCCTCCA
64 TCCTACCCCTCCA
1567554 CCTACTCC
1 CCTACTCC
1567562 TCCCCCTCCC
Statistics
Matches: 155, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
74 52 0.34
75 1 0.01
76 5 0.03
78 97 0.63
ACGTcount: A:0.10, C:0.61, G:0.05, T:0.24
Consensus pattern (76 bp):
CCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCCGTACACTC
CTACCCCTCCA
Found at i:1567541 original size:42 final size:42
Alignment explanation
Indices: 1567417--1567562 Score: 146
Period size: 42 Copynumber: 3.6 Consensus size: 42
1567407 CCTCCTAGCG
*
1567417 CACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTA
1 CACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCACGTA
* * *
1567459 CA--TC-T---CCTACCCCTCCACCTACTCCCCCTCCTAGCG--
1 CACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCC-A-CGTA
1567495 CACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCACGTA
1 CACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCACGTA
* * * *
1567537 CACCTCCTACCCCTCCACCTACTCCT
1 CACCTCTTCCCCCTCCCCCTGCTCCT
1567563 CCCCCTCCCT
Statistics
Matches: 83, Mismatches: 11, Indels: 20
0.73 0.10 0.18
Matches are distributed among these distances:
36 25 0.30
38 4 0.05
39 2 0.02
40 4 0.05
41 1 0.01
42 47 0.57
ACGTcount: A:0.11, C:0.61, G:0.04, T:0.24
Consensus pattern (42 bp):
CACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCACGTA
Found at i:1567561 original size:18 final size:18
Alignment explanation
Indices: 1567462--1567609 Score: 72
Period size: 18 Copynumber: 7.9 Consensus size: 18
1567452 CCTCGTACAT
*
1567462 CTCCTACCCCTCCACCTA
1 CTCCTCCCCCTCCACCTA
1567480 CTCC-CCCTCCTAGCGCACCT-
1 CTCCTCCC-CCT--C-CACCTA
* *
1567500 CT--TCCCCCTCCCCCTG
1 CTCCTCCCCCTCCACCTA
*
1567516 CTCCTACTCCCCCTCCACGTACA
1 CT-C--CTCCCCCTCCACCT--A
*
1567539 CCTCCTACCCCTCCACCTA
1 -CTCCTCCCCCTCCACCTA
*
1567558 CTCCTCCCCCTCC-CTCTC
1 CTCCTCCCCCTCCAC-CTA
* *
1567576 CACCTCCCCCTCCACCTC
1 CTCCTCCCCCTCCACCTA
* *
1567594 CACCTCCACCTCCACC
1 CTCCTCCCCCTCCACC
1567610 AGTTACCTGC
Statistics
Matches: 103, Mismatches: 11, Indels: 32
0.71 0.08 0.22
Matches are distributed among these distances:
15 4 0.04
16 3 0.03
17 3 0.03
18 54 0.52
19 5 0.05
20 3 0.03
21 28 0.27
23 1 0.01
24 2 0.02
ACGTcount: A:0.11, C:0.65, G:0.03, T:0.21
Consensus pattern (18 bp):
CTCCTCCCCCTCCACCTA
Found at i:1567571 original size:6 final size:6
Alignment explanation
Indices: 1567548--1567609 Score: 72
Period size: 6 Copynumber: 10.3 Consensus size: 6
1567538 ACCTCCTACC
* * * *
1567548 CCTCCA CCTACT CCTCCC CCTCC- CTCTCCA CCTCCC CCTCCA CCTCCA
1 CCTCCA CCTCCA CCTCCA CCTCCA C-CTCCA CCTCCA CCTCCA CCTCCA
1567596 CCTCCA CCTCCA CC
1 CCTCCA CCTCCA CC
1567610 AGTTACCTGC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
5 1 0.02
6 46 0.96
7 1 0.02
ACGTcount: A:0.11, C:0.69, G:0.00, T:0.19
Consensus pattern (6 bp):
CCTCCA
Found at i:1570940 original size:20 final size:20
Alignment explanation
Indices: 1570878--1570950 Score: 71
Period size: 20 Copynumber: 3.7 Consensus size: 20
1570868 ATAGTCCAAA
* *
1570878 AGTTTCGATACTTT-TTAAG
1 AGTTTCGAAACTTTCCTAAG
*
1570897 AGTTTCGAAACTAT-CTCAAG
1 AGTTTCGAAACTTTCCT-AAG
1570917 AGTTTCGAAACTTTCCCTAA-
1 AGTTTCGAAACTTT-CCTAAG
*
1570937 AGTTTCGATACTTT
1 AGTTTCGAAACTTT
1570951 GGCTTCAACG
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 13 0.28
20 29 0.63
21 2 0.04
22 2 0.04
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.40
Consensus pattern (20 bp):
AGTTTCGAAACTTTCCTAAG
Found at i:1576444 original size:25 final size:24
Alignment explanation
Indices: 1576403--1576477 Score: 66
Period size: 25 Copynumber: 3.1 Consensus size: 24
1576393 TCATTTTGTC
*
1576403 TATAAATTGTATAAATTAATAATTA
1 TATATATT-TATAAATTAATAATTA
*
1576428 TAT-TATTTAATAAAATTAGACAA-TA
1 TATATATTT-AT-AAATTA-ATAATTA
*
1576453 TATATATTTATTAATTAAT-ATTA
1 TATATATTTATAAATTAATAATTA
1576476 TA
1 TA
1576478 ATGAATCAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
22 1 0.02
23 6 0.15
24 10 0.24
25 16 0.39
26 8 0.20
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (24 bp):
TATATATTTATAAATTAATAATTA
Found at i:1576539 original size:2 final size:2
Alignment explanation
Indices: 1576524--1576639 Score: 195
Period size: 2 Copynumber: 60.0 Consensus size: 2
1576514 TAACTATTAA
*
1576524 AT AT -T AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1576564 A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1576605 AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1576640 GGGAATGATC
Statistics
Matches: 108, Mismatches: 2, Indels: 8
0.92 0.02 0.07
Matches are distributed among these distances:
1 4 0.04
2 104 0.96
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1577166 original size:16 final size:16
Alignment explanation
Indices: 1577142--1577172 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1577132 AATTACACAG
1577142 TTTAAAACTTTTTAGT
1 TTTAAAACTTTTTAGT
*
1577158 TTTATAACTTTTTAG
1 TTTAAAACTTTTTAG
1577173 GATCGTTGGA
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:0.29, C:0.06, G:0.06, T:0.58
Consensus pattern (16 bp):
TTTAAAACTTTTTAGT
Found at i:1578034 original size:27 final size:27
Alignment explanation
Indices: 1578004--1578060 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
1577994 GACCTCTCAA
1578004 TCCTAATAACCGTCGTCCCCCTCCCCC
1 TCCTAATAACCGTCGTCCCCCTCCCCC
* *
1578031 TCCTAGTAACCGTCGTCCTCCTCCCCC
1 TCCTAATAACCGTCGTCCCCCTCCCCC
1578058 TCC
1 TCC
1578061 CCCTCCTCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.12, C:0.54, G:0.09, T:0.25
Consensus pattern (27 bp):
TCCTAATAACCGTCGTCCCCCTCCCCC
Found at i:1578287 original size:21 final size:21
Alignment explanation
Indices: 1578223--1578288 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
1578213 TCCACCTACT
**
1578223 CCCCTCCTCGCGCACCTCTTC
1 CCCCTCCTCGTACACCTCTTC
* * * *
1578244 CCCCTCCCCCTTCTCCTAC-TC
1 CCCCTCCTCGTACACCT-CTTC
1578265 CCCCTCCTCGTACACCTCTTC
1 CCCCTCCTCGTACACCTCTTC
1578286 CCC
1 CCC
1578289 TCCACCTACT
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
20 1 0.03
21 32 0.94
22 1 0.03
ACGTcount: A:0.06, C:0.64, G:0.05, T:0.26
Consensus pattern (21 bp):
CCCCTCCTCGTACACCTCTTC
Found at i:1578315 original size:21 final size:22
Alignment explanation
Indices: 1578291--1578350 Score: 54
Period size: 21 Copynumber: 2.8 Consensus size: 22
1578281 TCTTCCCCTC
*
1578291 CACCTACTCCCCCTCCTAGCT-
1 CACCTACTCCCCCTCCTACCTG
*
1578312 CACCT-CTTCCCCCCTCC-CCCTG
1 CACCTAC-T-CCCCCTCCTACCTG
*
1578334 CTCCTACTCCCCCTCCT
1 CACCTACTCCCCCTCCT
1578351 CGTACACCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
20 1 0.03
21 16 0.52
22 13 0.42
23 1 0.03
ACGTcount: A:0.08, C:0.63, G:0.03, T:0.25
Consensus pattern (22 bp):
CACCTACTCCCCCTCCTACCTG
Found at i:1578445 original size:21 final size:21
Alignment explanation
Indices: 1578377--1578447 Score: 78
Period size: 21 Copynumber: 3.4 Consensus size: 21
1578367 CTCCACCTAC
1578377 TCCCCC-CCTCGCGCACCT-T
1 TCCCCCTCCTCGCGCACCTCT
*
1578396 TCCCCCCTCCTC-CTGCTCCTAC-
1 T-CCCCCTCCTCGC-GCACCT-CT
1578418 TCCCCCTCCTCGCGCACCTCT
1 TCCCCCTCCTCGCGCACCTCT
1578439 TCCCCCTCC
1 TCCCCCTCC
1578448 CCCTGCTCCT
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
19 1 0.02
20 7 0.16
21 33 0.77
22 2 0.05
ACGTcount: A:0.04, C:0.65, G:0.07, T:0.24
Consensus pattern (21 bp):
TCCCCCTCCTCGCGCACCTCT
Found at i:1578446 original size:77 final size:78
Alignment explanation
Indices: 1578180--1578456 Score: 400
Period size: 77 Copynumber: 3.6 Consensus size: 78
1578170 CCGAACACGC
* *
1578180 CTCCTCCTCCCCCTCCTCGTACACCTC-TACCCCTCCACCTACTCCCCTCCTCGCGCACCTCTT-
1 CTCCTACTCCCCCTCCTCGTACACCTCTTACCCCTCCACCTACTCCCCCCCTCGCGCACCTCTTC
*
1578243 CCCCCTCCCCCTT
66 CCCCCTCCCCCTG
* *
1578256 CTCCTACTCCCCCTCCTCGTACACCTCTT-CCCCTCCACCTACTCCCCCTCCTAGCTCACCTCTT
1 CTCCTACTCCCCCTCCTCGTACACCTCTTACCCCTCCACCTACTCCCCC-CCTCGCGCACCTCTT
1578320 CCCCCCTCCCCCTG
65 CCCCCCTCCCCCTG
* *
1578334 CTCCTACTCCCCCTCCTCGTACACCTCCTATCCCTCCACCTACTCCCCCCCTCGCGCACCT-TTC
1 CTCCTACTCCCCCTCCTCGTACACCTCTTACCCCTCCACCTACTCCCCCCCTCGCGCACCTCTTC
*
1578398 CCCCCTCCTCCTG
66 CCCCCTCCCCCTG
** * * *
1578411 CTCCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCC
1 CTCCTACTCCCCCTCCTCGTACACCTCTTACCCCTCCACCTACTCC
1578457 TACTCCCCCT
Statistics
Matches: 180, Mismatches: 17, Indels: 7
0.88 0.08 0.03
Matches are distributed among these distances:
76 44 0.24
77 68 0.38
78 50 0.28
79 18 0.10
ACGTcount: A:0.08, C:0.62, G:0.05, T:0.25
Consensus pattern (78 bp):
CTCCTACTCCCCCTCCTCGTACACCTCTTACCCCTCCACCTACTCCCCCCCTCGCGCACCTCTTC
CCCCCTCCCCCTG
Found at i:1578463 original size:21 final size:21
Alignment explanation
Indices: 1578398--1578468 Score: 83
Period size: 21 Copynumber: 3.4 Consensus size: 21
1578388 CGCACCTTTC
*
1578398 CCCCCTCCTCCTGCTCCTACT
1 CCCCCTCCCCCTGCTCCTACT
* *
1578419 CCCCCTCCTCGC-GCACCT-CTT
1 CCCCCTCC-CCCTGCTCCTAC-T
1578440 CCCCCTCCCCCTGCTCCTACT
1 CCCCCTCCCCCTGCTCCTACT
1578461 CCCCCTCC
1 CCCCCTCC
1578469 TCGTACACCT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
20 3 0.07
21 36 0.88
22 2 0.05
ACGTcount: A:0.04, C:0.66, G:0.06, T:0.24
Consensus pattern (21 bp):
CCCCCTCCCCCTGCTCCTACT
Found at i:1578500 original size:21 final size:21
Alignment explanation
Indices: 1578441--1578502 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 21
1578431 GCACCTCTTC
* * * *
1578441 CCCCTCCCCCTGCTCCTACTC
1 CCCCTCCACCTACTCCTCCTA
* * *
1578462 CCCCTCCTCGTACACCTCCTA
1 CCCCTCCACCTACTCCTCCTA
1578483 CCCCTCCACCTACTCCTCCT
1 CCCCTCCACCTACTCCTCCT
1578503 CCTAGCGCAC
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.10, C:0.63, G:0.03, T:0.24
Consensus pattern (21 bp):
CCCCTCCACCTACTCCTCCTA
Found at i:1578546 original size:77 final size:78
Alignment explanation
Indices: 1578413--1578656 Score: 438
Period size: 77 Copynumber: 3.1 Consensus size: 78
1578403 TCCTCCTGCT
* *
1578413 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
1 CCTACTCCTCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
1578478 TCCTACCCCTCCA
66 TCCTACCCCTCCA
1578491 CCTACTCCTCCTCCTAGCGCACCTCTT-CCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
1 CCTACTCCTCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
1578555 TCCTACCCCTCCA
66 TCCTACCCCTCCA
*
1578568 CCTACTCC-CCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCACGTACACC
1 CCTACTCCTCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
1578632 TCCTACCCCTCCA
66 TCCTACCCCTCCA
1578645 CCTACCTCCTCC
1 CCTA-CTCCTCC
1578657 CCCTCCCTCT
Statistics
Matches: 160, Mismatches: 3, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
76 18 0.11
77 111 0.69
78 29 0.18
79 2 0.01
ACGTcount: A:0.10, C:0.61, G:0.05, T:0.23
Consensus pattern (78 bp):
CCTACTCCTCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
TCCTACCCCTCCA
Found at i:1578640 original size:21 final size:19
Alignment explanation
Indices: 1578629--1578700 Score: 64
Period size: 17 Copynumber: 3.9 Consensus size: 19
1578619 CTCCACGTAC
1578629 ACCTCCTACCCCTCCACCT
1 ACCTCCTACCCCTCCACCT
*
1578648 ACCTCCTCCCCCTCC-CTCT
1 ACCTCCTACCCCTCCAC-CT
*
1578667 -CCACCT-CCCCTCCACCT
1 ACCTCCTACCCCTCCACCT
*
1578684 -CCACCT-CCACCTCCACC
1 ACCTCCTACC-CCTCCACC
1578701 AGTTACCTGC
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
17 17 0.35
18 15 0.31
19 16 0.33
ACGTcount: A:0.12, C:0.68, G:0.00, T:0.19
Consensus pattern (19 bp):
ACCTCCTACCCCTCCACCT
Found at i:1578643 original size:196 final size:196
Alignment explanation
Indices: 1578217--1578622 Score: 692
Period size: 196 Copynumber: 2.1 Consensus size: 196
1578207 TACCCCTCCA
*
1578217 CCTACT-CCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTTCTCCTACTCCCCCTCCTCGTACACC
1 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
* *
1578281 TCTTCCCCTCCACCTACTCCCCCTCCTAGCTCACCTCTTCCCCCCTCCCCCTGCTCCTACTCCCC
66 TCTACCCCTCCACCTACTCCCCCTCCTAGCGCACCTCTT-CCCCCTCCCCCTGCTCCTACTCCCC
* * *
1578346 CTCCTCGTACACCTCCTATCCCTCCACCTACTCCCCCCCTCGCGCACCTTTCCCCCCTCCTCCTG
130 CTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCCCTAGCGCACCTTTCCCCCCTCCCCCTG
1578411 CT
195 CT
1578413 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
1 CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
*
1578478 TCCTACCCCTCCACCTACTCCTCCTCCTAGCGCACCTCTT-CCCCTCCCCCTGCTCCTACTCCCC
66 T-CTACCCCTCCACCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCC
*
1578542 CTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCTCCTAGCGCACCTCTT-CCCCCTCCCCCT
130 CTCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCCCTAGCGCACCT-TTCCCCCCTCCCCCT
1578606 GCT
194 GCT
1578609 CCTACTCCCCCTCC
1 CCTACTCCCCCTCC
1578623 ACGTACACCT
Statistics
Matches: 199, Mismatches: 8, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
196 104 0.52
197 60 0.30
198 35 0.18
ACGTcount: A:0.09, C:0.62, G:0.05, T:0.25
Consensus pattern (196 bp):
CCTACTCCCCCTCCTCGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC
TCTACCCCTCCACCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCC
TCCTCGTACACCTCCTACCCCTCCACCTACTCCCCCCCTAGCGCACCTTTCCCCCCTCCCCCTGC
T
Found at i:1578663 original size:6 final size:6
Alignment explanation
Indices: 1578639--1578700 Score: 74
Period size: 6 Copynumber: 10.3 Consensus size: 6
1578629 ACCTCCTACC
* *
1578639 CCTCCA CCTACCT CCTCCC CCTCC- CTCTCCA CCTCC- CCTCCA CCTCCA
1 CCTCCA CCT-CCA CCTCCA CCTCCA C-CTCCA CCTCCA CCTCCA CCTCCA
1578687 CCTCCA CCTCCA CC
1 CCTCCA CCTCCA CC
1578701 AGTTACCTGC
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
5 6 0.12
6 38 0.76
7 6 0.12
ACGTcount: A:0.11, C:0.69, G:0.00, T:0.19
Consensus pattern (6 bp):
CCTCCA
Found at i:1578678 original size:17 final size:17
Alignment explanation
Indices: 1578637--1578700 Score: 76
Period size: 17 Copynumber: 3.6 Consensus size: 17
1578627 ACACCTCCTA
*
1578637 CCCCTCCACCTACCTCCT
1 CCCCTCCACCT-CCACCT
1578655 CCCCCTCC-CTCTCCACCT
1 -CCCCTCCAC-CTCCACCT
1578673 CCCCTCCACCTCCACCT
1 CCCCTCCACCTCCACCT
1578690 CCACCTCCACC
1 CC-CCTCCACC
1578701 AGTTACCTGC
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
17 17 0.41
18 15 0.37
19 9 0.22
ACGTcount: A:0.11, C:0.70, G:0.00, T:0.19
Consensus pattern (17 bp):
CCCCTCCACCTCCACCT
Found at i:1578678 original size:23 final size:24
Alignment explanation
Indices: 1578639--1578697 Score: 77
Period size: 23 Copynumber: 2.5 Consensus size: 24
1578629 ACCTCCTACC
*
1578639 CCTCCACCTACCTCCTCCCCCTCC-
1 CCTCCACCT-CCTCCTCCACCTCCA
1578663 CTCTCCACCTCC-CCTCCACCTCCA
1 C-CTCCACCTCCTCCTCCACCTCCA
1578687 CCTCCACCTCC
1 CCTCCACCTCC
1578698 ACCAGTTACC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
23 20 0.62
24 4 0.12
25 8 0.25
ACGTcount: A:0.10, C:0.69, G:0.00, T:0.20
Consensus pattern (24 bp):
CCTCCACCTCCTCCTCCACCTCCA
Found at i:1582427 original size:20 final size:20
Alignment explanation
Indices: 1582402--1582476 Score: 132
Period size: 20 Copynumber: 3.8 Consensus size: 20
1582392 GATACTTTTT
1582402 AAGAGTTTCGAAACTATCTC
1 AAGAGTTTCGAAACTATCTC
*
1582422 AAGAGTTTCGAAACTATCTA
1 AAGAGTTTCGAAACTATCTC
1582442 AAGAGTTTCGAAACTATCTC
1 AAGAGTTTCGAAACTATCTC
*
1582462 AAGAGTTTTGAAACT
1 AAGAGTTTCGAAACT
1582477 TTCCCTAAAG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (20 bp):
AAGAGTTTCGAAACTATCTC
Found at i:1587256 original size:11 final size:12
Alignment explanation
Indices: 1587225--1587268 Score: 53
Period size: 11 Copynumber: 4.1 Consensus size: 12
1587215 TCAAAAATCA
1587225 TAAAATAATTAT
1 TAAAATAATTAT
1587237 T-AAAT--TTAT
1 TAAAATAATTAT
1587246 TAAAAT-ATTA-
1 TAAAATAATTAT
1587256 TAAAATAATTAT
1 TAAAATAATTAT
1587268 T
1 T
1587269 TTGTAGCAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
9 5 0.18
10 10 0.36
11 11 0.39
12 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TAAAATAATTAT
Found at i:1588185 original size:2 final size:2
Alignment explanation
Indices: 1588178--1588212 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1588168 ATTAAAATTT
1588178 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1588213 GGGAAGGATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1588692 original size:2 final size:2
Alignment explanation
Indices: 1588687--1588727 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1588677 TCTCTCTCTC
1588687 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1588728 GTTTATAAGC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1589037 original size:2 final size:2
Alignment explanation
Indices: 1589030--1589057 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1589020 CTAACTTAAG
1589030 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1589058 CTCAAATTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1589720 original size:27 final size:27
Alignment explanation
Indices: 1589690--1589742 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
1589680 CTCCCAATCC
1589690 TAGTAACCGTCGTCCCCCTCCCCCTCT
1 TAGTAACCGTCGTCCCCCTCCCCCTCT
*
1589717 TAGTAACCGTCGTCCTCCTCCCCCTC
1 TAGTAACCGTCGTCCCCCTCCCCCTC
1589743 CTCCACGACC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.11, C:0.51, G:0.11, T:0.26
Consensus pattern (27 bp):
TAGTAACCGTCGTCCCCCTCCCCCTCT
Found at i:1589914 original size:36 final size:36
Alignment explanation
Indices: 1589869--1590505 Score: 307
Period size: 36 Copynumber: 16.3 Consensus size: 36
1589859 CCTCCCCTCC
* *
1589869 CCCCCTCCTCGTACACCTCCTACCCCTCCACCTACT
1 CCCCCTCCTCGTACACCTCCTCCCCCTCCTCCTACT
* *
1589905 CCCCCTCCTCGTGCACCTCTTCCCCCTCCCCCTGCTCTTACT
1 CCCCCTCCTCGTACACCTCCTCCCCCT---CCT-C-C-TACT
** *
1589947 CCCCCTCCTCGCGCACCTCTCCCCCTCCCCCTGCTCCTACT
1 CCCCCTCCTCGTACA-C-CT---CCTCCCCCTCCTCCTACT
* * *
1589988 CCCCCTCCTCGTACACCTCTTCCACCTCCACCTACT
1 CCCCCTCCTCGTACACCTCCTCCCCCTCCTCCTACT
* *
1590024 CCCCCTCCTAGCT-CACCTCTTCCCCCTCCCCCTGCTCCTACT
1 CCCCCTCCTCG-TACA-C-C-T---CCTCCCCCTCCTCCTACT
* * *
1590066 CCACCTCCTCGTGCACCTTTCCCCCCTCCTCCTGCTCCTACT
1 CCCCCTCCTCGTACACC--TCCTCCC-CCT-C--CTCCTACT
* * * *
1590108 CCCACTCCTCACGCCCT-CTTCCCCCTCCCCCTGCTCCTACT
1 CCCCCTCCT--CG---TAC-ACCTCCTCCCCCTCCTCCTACT
* * *
1590149 CCCCCTCCTCGTGCACCTCCTACCCCTCCACCTACT
1 CCCCCTCCTCGTACACCTCCTCCCCCTCCTCCTACT
* *
1590185 CCCCCTCCTAGCGCAC-CTCTTCCCCCTCCCCCTGCTCCTACT
1 CCCCCTCCT--CGTACAC-C-T---CCTCCCCCTCCTCCTACT
** *
1590227 CCCCCTCCTCGTACACCTCCTAACCCTCCGCCTACT
1 CCCCCTCCTCGTACACCTCCTCCCCCTCCTCCTACT
* * *
1590263 CCCCCTCCTAGTGCACCTCTTCCGCCTCCCCCTGCTCCTACT
1 CCCCCTCCTCGTACA-C-C-T---CCTCCCCCTCCTCCTACT
* * *
1590305 CCCCTTCCTCGTACACCTCCTACCCCTCCACCTACT
1 CCCCCTCCTCGTACACCTCCTCCCCCTCCTCCTACT
* * *
1590341 CCTCCTCCTAGCGCAC-CTCTTCCCCCTCCCCCTGCTCCTACT
1 CCCCCTCCT--CGTACAC-C-T---CCTCCCCCTCCTCCTACT
* * *
1590383 CCCCCTCCTCATACACCTCCTACCCCTCCACCTACT
1 CCCCCTCCTCGTACACCTCCTCCCCCTCCTCCTACT
* *
1590419 CCCCCTCCTAGCGCAC-CTCTTCCCCCTCCCCCTGCTCCTACT
1 CCCCCTCCT--CGTACAC-C-T---CCTCCCCCTCCTCCTACT
* * *
1590461 CCCCCTCCACGTACACCTCCT-ACCCTCCACCTACT
1 CCCCCTCCTCGTACACCTCCTCCCCCTCCTCCTACT
1590496 CCTCCC-CCTC
1 CC-CCCTCCTC
1590506 CCTCTCCACC
Statistics
Matches: 460, Mismatches: 79, Indels: 125
0.69 0.12 0.19
Matches are distributed among these distances:
35 16 0.03
36 156 0.34
37 7 0.02
38 20 0.04
39 18 0.04
40 18 0.04
41 42 0.09
42 155 0.34
43 2 0.00
44 9 0.02
45 5 0.01
46 1 0.00
47 11 0.02
ACGTcount: A:0.10, C:0.61, G:0.05, T:0.24
Consensus pattern (36 bp):
CCCCCTCCTCGTACACCTCCTCCCCCTCCTCCTACT
Found at i:1589947 original size:42 final size:42
Alignment explanation
Indices: 1589899--1590479 Score: 555
Period size: 42 Copynumber: 14.6 Consensus size: 42
1589889 TACCCCTCCA
1589899 CCTACTCCCCCTCCTCGTGCACCTCTTCCCCCTCCCCCTGCT
1 CCTACTCCCCCTCCTCGTGCACCTCTTCCCCCTCCCCCTGCT
* *
1589941 CTTACTCCCCCTCCTCGCGCACCTC-TCCCCCTCCCCCTGCT
1 CCTACTCCCCCTCCTCGTGCACCTCTTCCCCCTCCCCCTGCT
* * *
1589982 CCTACTCCCCCTCCTCGTACACCTCTTCCACCT----C--CA
1 CCTACTCCCCCTCCTCGTGCACCTCTTCCCCCTCCCCCTGCT
*
1590018 CCTACTCCCCCTCCTAGCT-CACCTCTTCCCCCTCCCCCTGCT
1 CCTACTCCCCCTCCTCG-TGCACCTCTTCCCCCTCCCCCTGCT
* *
1590060 CCTACTCCACCTCCTCGTGCACCT-TTCCCCCCTCCTCCTGCT
1 CCTACTCCCCCTCCTCGTGCACCTCTT-CCCCCTCCCCCTGCT
* **
1590102 CCTACTCCCACTCCTCACGC-CCTCTTCCCCCTCCCCCTGCT
1 CCTACTCCCCCTCCTCGTGCACCTCTTCCCCCTCCCCCTGCT
* * *
1590143 CCTACTCCCCCTCCTCGTGCA-C-C-T---CCTACCCCTCCA
1 CCTACTCCCCCTCCTCGTGCACCTCTTCCCCCTCCCCCTGCT
* *
1590179 CCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCT
1 CCTACTCCCCCTCCTCGTGCACCTCTTCCCCCTCCCCCTGCT
* * **
1590221 CCTACTCCCCCTCCTCGTACACCTCCTAACCCT---CC-G--
1 CCTACTCCCCCTCCTCGTGCACCTCTTCCCCCTCCCCCTGCT
* *
1590257 CCTACTCCCCCTCCTAGTGCACCTCTTCCGCCTCCCCCTGCT
1 CCTACTCCCCCTCCTCGTGCACCTCTTCCCCCTCCCCCTGCT
* * * * *
1590299 CCTACTCCCCTTCCTCGTACA-C-C-T---CCTACCCCTCCA
1 CCTACTCCCCCTCCTCGTGCACCTCTTCCCCCTCCCCCTGCT
* * *
1590335 CCTACTCCTCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCT
1 CCTACTCCCCCTCCTCGTGCACCTCTTCCCCCTCCCCCTGCT
* * * * *
1590377 CCTACTCCCCCTCCTCATACA-C-C-T---CCTACCCCTCCA
1 CCTACTCCCCCTCCTCGTGCACCTCTTCCCCCTCCCCCTGCT
* *
1590413 CCTACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCT
1 CCTACTCCCCCTCCTCGTGCACCTCTTCCCCCTCCCCCTGCT
* *
1590455 CCTACTCCCCCTCCACGTACACCTC
1 CCTACTCCCCCTCCTCGTGCACCTC
1590480 CTACCCTCCA
Statistics
Matches: 429, Mismatches: 74, Indels: 72
0.75 0.13 0.13
Matches are distributed among these distances:
36 136 0.32
37 4 0.01
38 5 0.01
39 10 0.02
40 5 0.01
41 78 0.18
42 191 0.45
ACGTcount: A:0.09, C:0.60, G:0.06, T:0.25
Consensus pattern (42 bp):
CCTACTCCCCCTCCTCGTGCACCTCTTCCCCCTCCCCCTGCT
Found at i:1590215 original size:78 final size:78
Alignment explanation
Indices: 1589943--1590497 Score: 841
Period size: 78 Copynumber: 7.1 Consensus size: 78
1589933 CCCCTGCTCT
*
1589943 TACTCCCCCTCCTCGCGCACCTC-TCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACCT-
1 TACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACCTC
*
1590006 CTTCCACCTCCACC
66 CTACC-CCTCCACC
* * *
1590020 TACTCCCCCTCCTAGCTCACCTCTTCCCCCTCCCCCTGCTCCTACTCCACCTCCTCGTGCACCTT
1 TACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACC--
** *
1590085 TCCCCCCTCCTCCTGCTCC
64 TCCTACC-CCT-C--CACC
* *
1590104 TACTCCCACTCCTCA-CGC-CCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTGCACCT
1 TACTCCCCCTCCT-AGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACCT
1590167 CCTACCCCTCCACC
65 CCTACCCCTCCACC
1590181 TACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACCTC
1 TACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACCTC
* *
1590246 CTAACCCTCCGCC
66 CTACCCCTCCACC
* * *
1590259 TACTCCCCCTCCTAGTGCACCTCTTCCGCCTCCCCCTGCTCCTACTCCCCTTCCTCGTACACCTC
1 TACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACCTC
1590324 CTACCCCTCCACC
66 CTACCCCTCCACC
* *
1590337 TACTCCTCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCATACACCTC
1 TACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACCTC
1590402 CTACCCCTCCACC
66 CTACCCCTCCACC
*
1590415 TACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCACGTACACCTC
1 TACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACCTC
1590480 CTA-CCCTCCACC
66 CTACCCCTCCACC
1590492 TACTCC
1 TACTCC
1590498 TCCCCCTCCC
Statistics
Matches: 437, Mismatches: 31, Indels: 20
0.90 0.06 0.04
Matches are distributed among these distances:
76 1 0.00
77 54 0.12
78 304 0.70
79 1 0.00
80 4 0.01
81 11 0.03
82 1 0.00
83 43 0.10
84 17 0.04
85 1 0.00
ACGTcount: A:0.10, C:0.60, G:0.05, T:0.24
Consensus pattern (78 bp):
TACTCCCCCTCCTAGCGCACCTCTTCCCCCTCCCCCTGCTCCTACTCCCCCTCCTCGTACACCTC
CTACCCCTCCACC
Found at i:1590506 original size:18 final size:18
Alignment explanation
Indices: 1590399--1590545 Score: 79
Period size: 18 Copynumber: 7.9 Consensus size: 18
1590389 CCTCATACAC
*
1590399 CTCCTACCCCTCCACCTA
1 CTCCTCCCCCTCCACCTA
1590417 CTCC-CCCTCCTAGCGCACCT-
1 CTCCTCCC-CCT--C-CACCTA
* *
1590437 CT--TCCCCCTCCCCCTG
1 CTCCTCCCCCTCCACCTA
*
1590453 CTCCTACTCCCCCTCCACGTA
1 CT-C--CTCCCCCTCCACCTA
*
1590474 CACCTCCTACCCTCCACCTA
1 CTCCTCC--CCCTCCACCTA
*
1590494 CTCCTCCCCCTCC-CTCTC
1 CTCCTCCCCCTCCAC-CTA
* *
1590512 CACCTCCCCCTCCACCTC
1 CTCCTCCCCCTCCACCTA
* *
1590530 CACCTCCACCTCCACC
1 CTCCTCCCCCTCCACC
1590546 AGTTACCTGC
Statistics
Matches: 103, Mismatches: 11, Indels: 30
0.72 0.08 0.21
Matches are distributed among these distances:
15 4 0.04
16 3 0.03
17 3 0.03
18 52 0.50
19 4 0.04
20 20 0.19
21 17 0.17
ACGTcount: A:0.12, C:0.65, G:0.03, T:0.21
Consensus pattern (18 bp):
CTCCTCCCCCTCCACCTA
Found at i:1590507 original size:6 final size:6
Alignment explanation
Indices: 1590459--1590545 Score: 77
Period size: 6 Copynumber: 14.2 Consensus size: 6
1590449 CCTGCTCCTA
* * * * * *
1590459 CTCCCC CTCCAC GTACAC CTCCTACC CTCCAC CTACTC CTCCCC CTCC-C
1 CTCCAC CTCCAC CTCCAC CTCC-A-C CTCCAC CTCCAC CTCCAC CTCCAC
*
1590508 TCTCCAC CTCCCC CTCCAC CTCCAC CTCCAC CTCCAC C
1 -CTCCAC CTCCAC CTCCAC CTCCAC CTCCAC CTCCAC C
1590546 AGTTACCTGC
Statistics
Matches: 66, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
5 1 0.02
6 57 0.86
7 3 0.05
8 5 0.08
ACGTcount: A:0.13, C:0.67, G:0.01, T:0.20
Consensus pattern (6 bp):
CTCCAC
Found at i:1603563 original size:172 final size:172
Alignment explanation
Indices: 1603277--1603620 Score: 688
Period size: 172 Copynumber: 2.0 Consensus size: 172
1603267 GGGTGAACTA
1603277 CCCTCGAGAACTTTCACTCAGTTGTCTTTCTCTTGAAAGATACAACTTTTTCAAATTTTAGGCTA
1 CCCTCGAGAACTTTCACTCAGTTGTCTTTCTCTTGAAAGATACAACTTTTTCAAATTTTAGGCTA
1603342 TCTTCTCTTGTCAAGCAACAACATACTTCACTATGTAGCATCTACCAAAACATTAATTCTTTCTT
66 TCTTCTCTTGTCAAGCAACAACATACTTCACTATGTAGCATCTACCAAAACATTAATTCTTTCTT
1603407 TATCATTTCGATGCATAAATTAAAATAAAAACATATTGCAGT
131 TATCATTTCGATGCATAAATTAAAATAAAAACATATTGCAGT
1603449 CCCTCGAGAACTTTCACTCAGTTGTCTTTCTCTTGAAAGATACAACTTTTTCAAATTTTAGGCTA
1 CCCTCGAGAACTTTCACTCAGTTGTCTTTCTCTTGAAAGATACAACTTTTTCAAATTTTAGGCTA
1603514 TCTTCTCTTGTCAAGCAACAACATACTTCACTATGTAGCATCTACCAAAACATTAATTCTTTCTT
66 TCTTCTCTTGTCAAGCAACAACATACTTCACTATGTAGCATCTACCAAAACATTAATTCTTTCTT
1603579 TATCATTTCGATGCATAAATTAAAATAAAAACATATTGCAGT
131 TATCATTTCGATGCATAAATTAAAATAAAAACATATTGCAGT
1603621 TTATAGAACA
Statistics
Matches: 172, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
172 172 1.00
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.37
Consensus pattern (172 bp):
CCCTCGAGAACTTTCACTCAGTTGTCTTTCTCTTGAAAGATACAACTTTTTCAAATTTTAGGCTA
TCTTCTCTTGTCAAGCAACAACATACTTCACTATGTAGCATCTACCAAAACATTAATTCTTTCTT
TATCATTTCGATGCATAAATTAAAATAAAAACATATTGCAGT
Found at i:1619942 original size:19 final size:19
Alignment explanation
Indices: 1619902--1619942 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1619892 GATTTATTTT
** *
1619902 TATTTATTTTAATTTAATA
1 TATTTATTTTAACATAAAA
1619921 TATTTATTTTAACATAAAA
1 TATTTATTTTAACATAAAA
1619940 TAT
1 TAT
1619943 ATTAAATAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
TATTTATTTTAACATAAAA
Found at i:1634408 original size:31 final size:32
Alignment explanation
Indices: 1634342--1634412 Score: 135
Period size: 32 Copynumber: 2.2 Consensus size: 32
1634332 TCGAGGGTTC
1634342 CCTATGTTCTTCGGGACATATGGACTGTTTTA
1 CCTATGTTCTTCGGGACATATGGACTGTTTTA
1634374 CCTATGTTCTTCGGGACATATGGACTG-TTTA
1 CCTATGTTCTTCGGGACATATGGACTGTTTTA
1634405 CCTATGTT
1 CCTATGTT
1634413 AGGGTATAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
31 12 0.31
32 27 0.69
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (32 bp):
CCTATGTTCTTCGGGACATATGGACTGTTTTA
Found at i:1634483 original size:30 final size:31
Alignment explanation
Indices: 1634443--1634515 Score: 132
Period size: 31 Copynumber: 2.4 Consensus size: 31
1634433 AGGGTCGAGG
1634443 GTTTA-CTATGTTCTTC-GGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1634472 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1634503 GTTTACCTATGTT
1 GTTTACCTATGTT
1634516 TAGATGGTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
29 5 0.12
30 11 0.26
31 26 0.62
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.42
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1634689 original size:31 final size:31
Alignment explanation
Indices: 1634651--1634837 Score: 331
Period size: 31 Copynumber: 6.0 Consensus size: 31
1634641 AGGGTCGAGG
1634651 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1634682 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1634713 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1634744 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1634775 GTTTACATATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
1634806 GTTTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
1634837 G
1 G
1634838 GTCCTTCGGG
Statistics
Matches: 151, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
31 150 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1639342 original size:31 final size:31
Alignment explanation
Indices: 1639125--1639327 Score: 379
Period size: 31 Copynumber: 6.5 Consensus size: 31
1639115 AGGGTCGAGG
1639125 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1639156 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1639187 GTTTACCTATGTTCTTCGGGACATATTGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1639218 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1639249 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1639280 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1639311 GTTTACCTAGGTTCTTC
1 GTTTACCTATGTTCTTC
1639328 AGAATCTATG
Statistics
Matches: 167, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 167 1.00
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1639816 original size:21 final size:21
Alignment explanation
Indices: 1639792--1639834 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1639782 TGTCGAAGTT
1639792 ACTGTAGCAGTGCATCGATGC
1 ACTGTAGCAGTGCATCGATGC
1639813 ACTGTAGCAGTGCATCGATGC
1 ACTGTAGCAGTGCATCGATGC
1639834 A
1 A
1639835 TAATTCATAC
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:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (21 bp):
ACTGTAGCAGTGCATCGATGC
Found at i:1643398 original size:31 final size:31
Alignment explanation
Indices: 1643356--1643498 Score: 241
Period size: 31 Copynumber: 4.6 Consensus size: 31
1643346 AGGGTAGAGG
*
1643356 GTTTACGTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1643387 CTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1643418 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1643449 GTTTACCTATGTTCTTCGGGACATATAGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
1643480 GATTACCTAGGTTCTTCGG
1 GTTTACCTATGTTCTTCGG
1643499 AATCTATGGA
Statistics
Matches: 106, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 106 1.00
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1646523 original size:75 final size:75
Alignment explanation
Indices: 1646359--1646566 Score: 249
Period size: 75 Copynumber: 2.8 Consensus size: 75
1646349 CAAAGCCAAA
* * * * **
1646359 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATT-CCCCCTGAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATT--CCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
1646423 TTTGGCTCCGAG
64 TTTGGCTCCGAG
* *
1646435 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACTGATTCCCCCCTAAACAGTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
* *
1646500 TTGTTCCGAG
66 TGGCTCCGAG
* * * *
1646510 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGAT-TCCCCCATAGGAGGAACCGATTCCCCCCT
1646567 GTTCAATGGT
Statistics
Matches: 114, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
74 20 0.18
75 63 0.55
76 31 0.27
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.21
Consensus pattern (75 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
TGGCTCCGAG
Found at i:1650441 original size:24 final size:24
Alignment explanation
Indices: 1650409--1650456 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1650399 CCAAGAGAGT
1650409 ACAACTATGTCAAAGATGGTGAAA
1 ACAACTATGTCAAAGATGGTGAAA
1650433 ACAACTATGTCAAAGATGGTGAAA
1 ACAACTATGTCAAAGATGGTGAAA
1650457 TTATAGGTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.12, G:0.21, T:0.21
Consensus pattern (24 bp):
ACAACTATGTCAAAGATGGTGAAA
Found at i:1652349 original size:21 final size:22
Alignment explanation
Indices: 1652313--1652373 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 22
1652303 TTTGGTGCAG
*
1652313 AGGGAATCGA-TCCCCCCTTGA
1 AGGGAACCGATTCCCCCCTTGA
*
1652334 A-GGAACCGATTCCCCCTTTGA
1 AGGGAACCGATTCCCCCCTTGA
*
1652355 AGGGGAACTGATTCCCCCC
1 A-GGGAACCGATTCCCCCC
1652374 ACAGGGGAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 7 0.21
21 12 0.36
23 14 0.42
ACGTcount: A:0.23, C:0.34, G:0.23, T:0.20
Consensus pattern (22 bp):
AGGGAACCGATTCCCCCCTTGA
Found at i:1652392 original size:21 final size:21
Alignment explanation
Indices: 1652355--1652394 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1652345 CCCCCTTTGA
*
1652355 AGGGGAACTGATTCCCCCCAC
1 AGGGGAACTGATACCCCCCAC
1652376 AGGGGAA-TCGATACCCCCC
1 AGGGGAACT-GATACCCCCC
1652395 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.25, C:0.38, G:0.25, T:0.12
Consensus pattern (21 bp):
AGGGGAACTGATACCCCCCAC
Found at i:1654143 original size:73 final size:75
Alignment explanation
Indices: 1654003--1654145 Score: 231
Period size: 73 Copynumber: 1.9 Consensus size: 75
1653993 ATGAAGCCGA
1654003 ATGAGCCTGACTCACCCAAGAGCAGCCCGAGGAGCAAAGCACAACAAACGCATCAAATGCCTCCA
1 ATGAGCCTGACTCACCCAAGAGCAGCCCGAGGAGCAAAGCACAAC-AACGCATCAAATGCCTCCA
1654068 TATTTCCGAAG
65 TATTTCCGAAG
1654079 ATGAGCCTGA-TCAACCCGAAGAGCAG-CCGAGGAGC-AAGCACAAC-ACGCATCAAATGCCTCC
1 ATGAGCCTGACTC-ACCC-AAGAGCAGCCCGAGGAGCAAAGCACAACAACGCATCAAATGCCTCC
1654140 ATATTT
64 ATATTT
1654146 TCAATCCTTT
Statistics
Matches: 65, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
73 23 0.35
75 11 0.17
76 23 0.35
77 8 0.12
ACGTcount: A:0.35, C:0.31, G:0.20, T:0.14
Consensus pattern (75 bp):
ATGAGCCTGACTCACCCAAGAGCAGCCCGAGGAGCAAAGCACAACAACGCATCAAATGCCTCCAT
ATTTCCGAAG
Found at i:1654441 original size:15 final size:15
Alignment explanation
Indices: 1654421--1654462 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 15
1654411 CTTTTTGAAT
*
1654421 ATTTTGGATTGTTTG
1 ATTTTGGATTGTTGG
1654436 ATTTTGTGGATTGTTGG
1 A-TTT-TGGATTGTTGG
1654453 ATTTTGGATT
1 ATTTTGGATT
1654463 TATGAATGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 7 0.29
16 6 0.25
17 11 0.46
ACGTcount: A:0.14, C:0.00, G:0.29, T:0.57
Consensus pattern (15 bp):
ATTTTGGATTGTTGG
Found at i:1654447 original size:17 final size:17
Alignment explanation
Indices: 1654425--1654458 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1654415 TTGAATATTT
*
1654425 TGGATTGTTTGATTTTG
1 TGGATTGTTGGATTTTG
1654442 TGGATTGTTGGATTTTG
1 TGGATTGTTGGATTTTG
1654459 GATTTATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.32, T:0.56
Consensus pattern (17 bp):
TGGATTGTTGGATTTTG
Found at i:1655213 original size:75 final size:75
Alignment explanation
Indices: 1655064--1655270 Score: 245
Period size: 75 Copynumber: 2.7 Consensus size: 75
1655054 CAAAGCCAAA
* * * * * * **
1655064 AATTACAGATTGCTCAGAGGGAACTGATTCCCCCCATAGGAGGAACCGATTCCCCTCTGAATGGT
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
1655129 TTGGCTCCGAG
65 TTGGCTCCGAG
*
1655140 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
* *
1655205 TTGTTCCGAG
66 TGGCTCCGAG
* * * *
1655215 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCCA-AGGGGGTACCGATTCCCCC
1 AATTCCAGAATGCTCGGAGGGAACCGAT--TCCCCCATAGGAGGAACCGATTCCCCC
1655271 ATGTTCAACG
Statistics
Matches: 113, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
75 66 0.58
76 41 0.36
77 6 0.05
ACGTcount: A:0.24, C:0.30, G:0.24, T:0.21
Consensus pattern (75 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
TGGCTCCGAG
Found at i:1663807 original size:37 final size:37
Alignment explanation
Indices: 1663757--1663832 Score: 116
Period size: 37 Copynumber: 2.1 Consensus size: 37
1663747 ATGGTGTGAA
*
1663757 AGAAAGATTCACCTTTGACATCTCTAGATTATCACGC
1 AGAAAGATTCACCTTTGACATCTCCAGATTATCACGC
* * *
1663794 AGAAAGCTTCACCTTTGACCTCTCCAGATTATTACGC
1 AGAAAGATTCACCTTTGACATCTCCAGATTATCACGC
1663831 AG
1 AG
1663833 TTTTTTCAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.29
Consensus pattern (37 bp):
AGAAAGATTCACCTTTGACATCTCCAGATTATCACGC
Found at i:1672641 original size:129 final size:130
Alignment explanation
Indices: 1672492--1672750 Score: 511
Period size: 129 Copynumber: 2.0 Consensus size: 130
1672482 GATATAATTA
1672492 TAGTTGAGGATGGCTTGTCTCACGTTGTACATTTTTGTCATAATTTAATAAACAATTTAGAATTT
1 TAGTTGAGGATGGCTTGTCTCACGTTGTACATTTTTGTCATAATTTAATAAACAATTTAGAATTT
1672557 AAAATACTTTTTTTTGACCATTTTTGCTAAAAGAATAATAGTATTTACTTTCTTTTTA-TTATTT
66 AAAATACTTTTTTTTGACCATTTTTGCTAAAAGAATAATAGTATTTACTTTCTTTTTATTTATTT
1672621 TAGTTGAGGATGGCTTGTCTCACGTTGTACATTTTTGTCATAATTTAATAAACAATTTAGAATTT
1 TAGTTGAGGATGGCTTGTCTCACGTTGTACATTTTTGTCATAATTTAATAAACAATTTAGAATTT
1672686 AAAATACTTTTTTTTGACCATTTTTGCTAAAAGAATAATAGTATTTACTTTCTTTTTATTTATTT
66 AAAATACTTTTTTTTGACCATTTTTGCTAAAAGAATAATAGTATTTACTTTCTTTTTATTTATTT
1672751 CTGTAATTAA
Statistics
Matches: 129, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
129 123 0.95
130 6 0.05
ACGTcount: A:0.30, C:0.10, G:0.12, T:0.48
Consensus pattern (130 bp):
TAGTTGAGGATGGCTTGTCTCACGTTGTACATTTTTGTCATAATTTAATAAACAATTTAGAATTT
AAAATACTTTTTTTTGACCATTTTTGCTAAAAGAATAATAGTATTTACTTTCTTTTTATTTATTT
Found at i:1673523 original size:256 final size:249
Alignment explanation
Indices: 1673075--1673619 Score: 765
Period size: 256 Copynumber: 2.1 Consensus size: 249
1673065 TTTTATTATT
* *
1673075 TCGGGTCGGGTGAAACTTTATTTTAGTCGGGTCGGGTCGGTTTTTTTAAGTGTGATATTCGGGTC
1 TCGGGTCGGGTGAAACTTTATTTTGGTCGGGTC-GGT--GTTTTTTTAAGTATGATATTCGGGTC
* * * *
1673140 GGGTCGATTTCAGGTTTAGGGTGAAAAATATCCGACCCGAAAATATATATAATTTTACCTTATAT
63 GGGTCGAGTTCAGGTTTAGAGTGAAAAATAACCGACCCGAAAAAATATATAATTTTACCTTATAT
* *
1673205 ATTTAGGAATAATTACAATAATATCCCTCTATATATAATTTTTCCAATTAAGTCACTGTTTTTAT
128 ATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTTTCCAATTAAGTCAATGTTTTTAT
*
1673270 TGAATAAAAATA-TTTTTTTATTATT-TCGGGTCGGGTTTCTAATTCATATATTCGGG
193 TGAATAAAAATATTTTTTTTATT-TTGTCGGGTCGGATTTCTAATTCATATATTCGGG
*
1673326 TCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGT-TTTTTTTAAGTATGATATTCGGGTTGGG
1 TCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGTGTTTTTTTAAGTATGATATTCGGGTCGGG
*
1673390 TCGAGTTCGGGTTTAGAGTGAAAAATACCCGACCTGACCCGACCAAAAAAATATATAATTTTACC
66 TCGAGTTCAGGTTTAGAGTGAAAAATA----ACC-GACCCG----AAAAAATATATAATTTTACC
*
1673455 TTATATATTTAGGAATAATTACAATAATACCCCTCTATATATATATTTTT-TAATTAAGTCAATG
122 TTATATATTTAGGAATAATTACAATAATACCCCTCTATATATA-ATTTTTCCAATTAAGTCAATG
*
1673519 TTTTTATTGAATAAAAATATTTTTTTTATTTTGGGTCGGGTCGGATTTCTAATTCATATATTTGG
186 TTTTTATTGAATAAAAATATTTTTTTTATTTT--GTCGGGTCGGATTTCTAATTCATATATTCGG
1673584 G
249 G
* * * *
1673585 TTGAGTCAGGTGAAACTTTATTTTGGTTGGGTCGG
1 TCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGG
1673620 GTCTCGGATG
Statistics
Matches: 263, Mismatches: 17, Indels: 20
0.88 0.06 0.07
Matches are distributed among these distances:
247 50 0.19
250 3 0.01
251 34 0.13
252 6 0.02
256 94 0.36
257 16 0.06
259 60 0.23
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (249 bp):
TCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGTGTTTTTTTAAGTATGATATTCGGGTCGGG
TCGAGTTCAGGTTTAGAGTGAAAAATAACCGACCCGAAAAAATATATAATTTTACCTTATATATT
TAGGAATAATTACAATAATACCCCTCTATATATAATTTTTCCAATTAAGTCAATGTTTTTATTGA
ATAAAAATATTTTTTTTATTTTGTCGGGTCGGATTTCTAATTCATATATTCGGG
Found at i:1680224 original size:18 final size:18
Alignment explanation
Indices: 1680201--1680235 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1680191 GATGATGGCT
*
1680201 TATTAAGCTTTATTTCCG
1 TATTAAGCTTTACTTCCG
*
1680219 TATTAAGGTTTACTTCC
1 TATTAAGCTTTACTTCC
1680236 AGAATAAGGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.17, G:0.11, T:0.49
Consensus pattern (18 bp):
TATTAAGCTTTACTTCCG
Found at i:1680490 original size:14 final size:13
Alignment explanation
Indices: 1680470--1680512 Score: 54
Period size: 12 Copynumber: 3.4 Consensus size: 13
1680460 AAGTTTAGGT
1680470 TTTTTAAAATATA
1 TTTTTAAAATATA
*
1680483 TATTTTAAAGTAT-
1 T-TTTTAAAATATA
1680496 TTTTTAAAA-ATA
1 TTTTTAAAATATA
1680508 TTTTT
1 TTTTT
1680513 TCAAGATTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 2 0.08
12 12 0.46
13 2 0.08
14 10 0.38
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (13 bp):
TTTTTAAAATATA
Found at i:1683303 original size:17 final size:17
Alignment explanation
Indices: 1683283--1683315 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1683273 ATATTTATTT
1683283 ATAT-AAAATATAATATA
1 ATATGAAAA-ATAATATA
1683300 ATATGAAAAATAATAT
1 ATATGAAAAATAATAT
1683316 TATAATCTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
ATATGAAAAATAATATA
Found at i:1700824 original size:2 final size:2
Alignment explanation
Indices: 1700817--1700844 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1700807 ACGTATAAGC
1700817 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1700845 TTTTTGATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1700958 original size:35 final size:35
Alignment explanation
Indices: 1700907--1700982 Score: 143
Period size: 35 Copynumber: 2.2 Consensus size: 35
1700897 AATTATGTTT
*
1700907 AGACAACACTTGATCTTCTTATTATAGGGGAAGAA
1 AGACTACACTTGATCTTCTTATTATAGGGGAAGAA
1700942 AGACTACACTTGATCTTCTTATTATAGGGGAAGAA
1 AGACTACACTTGATCTTCTTATTATAGGGGAAGAA
1700977 AGACTA
1 AGACTA
1700983 TTTGATTGGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (35 bp):
AGACTACACTTGATCTTCTTATTATAGGGGAAGAA
Found at i:1701640 original size:14 final size:14
Alignment explanation
Indices: 1701617--1701647 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1701607 ATATACATAC
1701617 ATACACACATATAT
1 ATACACACATATAT
*
1701631 ATACATACATATAT
1 ATACACACATATAT
1701645 ATA
1 ATA
1701648 AATAACACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (14 bp):
ATACACACATATAT
Found at i:1701646 original size:18 final size:18
Alignment explanation
Indices: 1701606--1701647 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1701596 AAATTATATG
1701606 TATATACATACATACACA
1 TATATACATACATACACA
* * *
1701624 CATATATATACATACATA
1 TATATACATACATACACA
1701642 TATATA
1 TATATA
1701648 AATAACACAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (18 bp):
TATATACATACATACACA
Found at i:1711705 original size:20 final size:19
Alignment explanation
Indices: 1711672--1711710 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
1711662 ATTTCTAGTT
* *
1711672 TCCCTTTAATTAAATAATTA
1 TCCCTATAACTAAA-AATTA
1711692 TCCCTATAACTAAAAATTA
1 TCCCTATAACTAAAAATTA
1711711 GGGTTAGAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (19 bp):
TCCCTATAACTAAAAATTA
Found at i:1718277 original size:45 final size:44
Alignment explanation
Indices: 1718164--1718408 Score: 218
Period size: 44 Copynumber: 5.6 Consensus size: 44
1718154 TTTTGTTACT
* *
1718164 TTTATAATTGAGGCCCCTAA--TTTTGTAATCTCA-TTAT-TAAC
1 TTTACAATTGAGGCCCCTAAGTTTTTTTAATCTCACTT-TCTAAC
* * *** *
1718205 TTTATAATTGAAGCTTTTAAGTTTTTTCAATCTCACTTTCTACAC
1 TTTACAATTGAGGCCCCTAAGTTTTTTTAATCTCACTTTCTA-AC
* *
1718250 TTT-CAATTGAGGCCCCTAAGTTTTTTTCAATCTCAATTTCTACC
1 TTTACAATTGAGGCCCCTAAGTTTTTTT-AATCTCACTTTCTAAC
* * * * *
1718294 TTTATAATTGAGGCCTCTAA--TTTTTTAATCCCACTTTTTTAAT
1 TTTACAATTGAGGCCCCTAAGTTTTTTTAATCTCAC-TTTCTAAC
* **
1718337 TTTATAATTGAGGCCTTTAAGTTTTTTTAATCTCACTTTCTAAC
1 TTTACAATTGAGGCCCCTAAGTTTTTTTAATCTCACTTTCTAAC
*
1718381 TTT-CTAATTGAGGTCCCTAAGTTTTTTT
1 TTTAC-AATTGAGGCCCCTAAGTTTTTTT
1718409 TATCACAATT
Statistics
Matches: 164, Mismatches: 29, Indels: 19
0.77 0.14 0.09
Matches are distributed among these distances:
41 16 0.10
42 6 0.04
43 42 0.26
44 55 0.34
45 45 0.27
ACGTcount: A:0.25, C:0.18, G:0.09, T:0.48
Consensus pattern (44 bp):
TTTACAATTGAGGCCCCTAAGTTTTTTTAATCTCACTTTCTAAC
Found at i:1718377 original size:87 final size:87
Alignment explanation
Indices: 1718052--1718495 Score: 324
Period size: 87 Copynumber: 5.1 Consensus size: 87
1718042 TTTTTCATCT
* * * * *
1718052 TAATTTTTTAAATCTTA-TTTTTTACCTTTATAATTGAGG-TCCTAA-TATTATTCAATCTCACT
1 TAATTTTTT-AATC-CACTTTTTTAACTTTATAATTGAGGCCCCTAAGTTTTTTTCAATCTCACT
* * * *
1718114 TTTTATCTTTATAATTGAAGTCTC
64 TTCTAACTTTATAATTGAGGCCTC
*
1718138 TAATTTTTTCAATCC-CTTTTGTT-ACTTTTATAATTGAGGCCCCTAA--TTTTGT-AATCTCA-
1 TAATTTTTT-AATCCACTTTT-TTAAC-TTTATAATTGAGGCCCCTAAGTTTTTTTCAATCTCAC
* * *
1718197 TTAT-TAACTTTATAATTGAAGCTTT
63 TT-TCTAACTTTATAATTGAGGCCTC
* *
1718222 TAAGTTTTTTCAATCTCAC-TTTCTACACTTT-CAATTGAGGCCCCTAAGTTTTTTTCAATCTCA
1 TAA-TTTTTT-AATC-CACTTTTTTA-ACTTTATAATTGAGGCCCCTAAGTTTTTTTCAATCTCA
* *
1718285 ATTTCTACCTTTATAATTGAGGCCTC
62 CTTTCTAACTTTATAATTGAGGCCTC
* **
1718311 TAATTTTTTAATCCCACTTTTTTAATTTTATAATTGAGGCCTTTAAGTTTTTTT-AATCTCACTT
1 TAATTTTTTAAT-CCACTTTTTTAACTTTATAATTGAGGCCCCTAAGTTTTTTTCAATCTCACTT
*
1718375 TCTAACTTTCTAATTGAGGTCC-C
65 TCTAACTTTATAATTGAGG-CCTC
* ** * * * * ** * **
1718398 TAAGTTTTTTTTAT-CACAATTATACCTTTATAATTGATGCCTCTATTTTTTTTTCAATATCGTT
1 TAA--TTTTTTAATCCACTTTTTTAACTTTATAATTGAGGCCCCTAAGTTTTTTTCAATCTCACT
* * *
1718462 TTCTACCTTTATAATTAAGCCCTC
64 TTCTAACTTTATAATTGAGGCCTC
*
1718486 TATTTTTTTA
1 TAATTTTTTA
1718496 CAATTTCATA
Statistics
Matches: 290, Mismatches: 45, Indels: 46
0.76 0.12 0.12
Matches are distributed among these distances:
84 22 0.08
85 40 0.14
86 44 0.15
87 86 0.30
88 68 0.23
89 30 0.10
ACGTcount: A:0.25, C:0.17, G:0.07, T:0.50
Consensus pattern (87 bp):
TAATTTTTTAATCCACTTTTTTAACTTTATAATTGAGGCCCCTAAGTTTTTTTCAATCTCACTTT
CTAACTTTATAATTGAGGCCTC
Found at i:1718409 original size:45 final size:44
Alignment explanation
Indices: 1718077--1718495 Score: 294
Period size: 43 Copynumber: 9.7 Consensus size: 44
1718067 TATTTTTTAC
* * * * *
1718077 CTTTATAATTGAGGTC-CTAA-TATTATTCAATCTCACTTTTTAT
1 CTTTATAATTGAGGCCTCTAAGT-TTTTTTAATCTCACTTTCTAA
* * * * *
1718120 CTTTATAATTGAAGTCTCTAA-TTTTTTCAATC-C-CTTTTGTTA
1 CTTTATAATTGAGGCCTCTAAGTTTTTTTAATCTCAC-TTTCTAA
* *
1718162 CTTTTATAATTGAGGCCCCTAA--TTTTGTAATCTCA-TTAT-TAA
1 C-TTTATAATTGAGGCCTCTAAGTTTTTTTAATCTCACTT-TCTAA
* * * *
1718204 CTTTATAATTGAAGCTTTTAAGTTTTTTCAATCTCACTTTCTACA
1 CTTTATAATTGAGGCCTCTAAGTTTTTTTAATCTCACTTTCTA-A
* * * *
1718249 CTTT-CAATTGAGGCCCCTAAGTTTTTTTCAATCTCAATTTCTAC
1 CTTTATAATTGAGGCCTCTAAGTTTTTTT-AATCTCACTTTCTAA
* *
1718293 CTTTATAATTGAGGCCTCTAA--TTTTTTAATCCCACTTTTTTAA
1 CTTTATAATTGAGGCCTCTAAGTTTTTTTAATCTCAC-TTTCTAA
* *
1718336 TTTTATAATTGAGGCCTTTAAGTTTTTTTAATCTCACTTTCTAA
1 CTTTATAATTGAGGCCTCTAAGTTTTTTTAATCTCACTTTCTAA
* * * * * *
1718380 CTTTCTAATTGAGGTCC-CTAAGTTTTTTTTATCACA-ATTATAC
1 CTTTATAATTGAGG-CCTCTAAGTTTTTTTAATCTCACTTTCTAA
* ** * ** *
1718423 CTTTATAATTGATGCCTCTATTTTTTTTTCAATATCGTTTTCTAC
1 CTTTATAATTGAGGCCTCTAAGTTTTTTT-AATCTCACTTTCTAA
* *
1718468 CTTTATAATTAAGCCCTCT-A-TTTTTTTA
1 CTTTATAATTGAGGCCTCTAAGTTTTTTTA
1718496 CAATTTCATA
Statistics
Matches: 299, Mismatches: 57, Indels: 41
0.75 0.14 0.10
Matches are distributed among these distances:
41 17 0.06
42 28 0.09
43 118 0.39
44 68 0.23
45 68 0.23
ACGTcount: A:0.25, C:0.18, G:0.08, T:0.49
Consensus pattern (44 bp):
CTTTATAATTGAGGCCTCTAAGTTTTTTTAATCTCACTTTCTAA
Found at i:1718451 original size:132 final size:132
Alignment explanation
Indices: 1718164--1718449 Score: 402
Period size: 132 Copynumber: 2.2 Consensus size: 132
1718154 TTTTGTTACT
* * * * *
1718164 TTTATAATTGAGGCCCCTAATTTTGTAATCTCA--TTATTAACTTTATAATTGAAGCTTTTAAGT
1 TTTATAATTGAGGCCTCTAATTTTTTAATCCCACTTTTTTAACTTTATAATTGAAGCCTTTAAGT
* *
1718227 TTTTTCAATCTCACTTTCTACACTTTCAATTGAGGCCCCTAAGTTTTTTTCAATCTCAATTTCTA
66 TTTTTCAATCTCACTTTCTACACTTTCAATTGAGGCCCCTAAGTTTTTTTCAATCACAATTTATA
1718292 CC
131 CC
* *
1718294 TTTATAATTGAGGCCTCTAATTTTTTAATCCCACTTTTTTAATTTTATAATTGAGGCCTTTAAGT
1 TTTATAATTGAGGCCTCTAATTTTTTAATCCCACTTTTTTAACTTTATAATTGAAGCCTTTAAGT
* * *
1718359 TTTTTTAATCTCACTTTCTA-ACTTTCTAATTGAGGTCCCTAAGTTTTTTT-TATCACAA-TTAT
66 TTTTTCAATCTCACTTTCTACACTTTC-AATTGAGGCCCCTAAGTTTTTTTCAATCACAATTTAT
1718421 ACC
130 ACC
* *
1718424 TTTATAATTGATGCCTCTATTTTTTT
1 TTTATAATTGAGGCCTCTAATTTTTT
1718450 TTCAATATCG
Statistics
Matches: 139, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
130 60 0.43
131 12 0.09
132 67 0.48
ACGTcount: A:0.25, C:0.18, G:0.08, T:0.49
Consensus pattern (132 bp):
TTTATAATTGAGGCCTCTAATTTTTTAATCCCACTTTTTTAACTTTATAATTGAAGCCTTTAAGT
TTTTTCAATCTCACTTTCTACACTTTCAATTGAGGCCCCTAAGTTTTTTTCAATCACAATTTATA
CC
Found at i:1718494 original size:132 final size:132
Alignment explanation
Indices: 1718164--1718487 Score: 349
Period size: 132 Copynumber: 2.5 Consensus size: 132
1718154 TTTTGTTACT
* * * * *
1718164 TTTATAATTGAGGCCCCTAATTTTGTAAT-CTCA-TTAT-TAACTTTATAATTGAAG-CTTTTAA
1 TTTATAATTGAGGCCTCTAATTTTTTAATAC-CACTTTTCTAACTTTATAATT-AAGCCCTCTAA
* *
1718225 GTTTTTTCAATCTCACTTTCTACACTTTCAATTGAGGCCCCTAAGTTTTTTTCAATCTCAATTTC
64 GTTTTTTCAATCTCACTTTCTACACTTTCAATTGAGGCCCCTAAGTTTTTTTCAATCACAATTTA
1718290 TACC
129 TACC
* * * * * *
1718294 TTTATAATTGAGGCCTCTAATTTTTTAATCCCACTTTTTTAATTTTATAATTGAGGCCTTTAAGT
1 TTTATAATTGAGGCCTCTAATTTTTTAATACCACTTTTCTAACTTTATAATTAAGCCCTCTAAGT
* * *
1718359 TTTTTTAATCTCACTTTCTA-ACTTTCTAATTGAGGTCCCTAAGTTTTTTT-TATCACAA-TTAT
66 TTTTTCAATCTCACTTTCTACACTTTC-AATTGAGGCCCCTAAGTTTTTTTCAATCACAATTTAT
1718421 ACC
130 ACC
* * * * *
1718424 TTTATAATTGATGCCTCTATTTTTTTTTCAATATC-GTTTTCTACCTTTATAATTAAGCCCTCTA
1 TTTATAATTGAGGCCTCTA--ATTTTTT-AATACCACTTTTCTAACTTTATAATTAAGCCCTCTA
1718488 TTTTTTTACA
Statistics
Matches: 164, Mismatches: 22, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
130 53 0.32
131 18 0.11
132 89 0.54
133 4 0.02
ACGTcount: A:0.25, C:0.19, G:0.08, T:0.48
Consensus pattern (132 bp):
TTTATAATTGAGGCCTCTAATTTTTTAATACCACTTTTCTAACTTTATAATTAAGCCCTCTAAGT
TTTTTCAATCTCACTTTCTACACTTTCAATTGAGGCCCCTAAGTTTTTTTCAATCACAATTTATA
CC
Found at i:1719346 original size:2 final size:2
Alignment explanation
Indices: 1719339--1719375 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1719329 CACGTTGTAA
1719339 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1719376 GAGAGAGAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1719380 original size:2 final size:2
Alignment explanation
Indices: 1719375--1719402 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1719365 ATATATATAT
1719375 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1719403 TTTTGTCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1727124 original size:20 final size:21
Alignment explanation
Indices: 1727095--1727147 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
1727085 TAATATAATA
*
1727095 TTATTTAAAATATCAGTTTT-
1 TTATTTAAAATATCAATTTTG
* *
1727115 TTATTAAAAATATTAATTTTG
1 TTATTTAAAATATCAATTTTG
1727136 TTATTTAAAATA
1 TTATTTAAAATA
1727148 AATATTTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (21 bp):
TTATTTAAAATATCAATTTTG
Found at i:1739231 original size:17 final size:16
Alignment explanation
Indices: 1739209--1739242 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1739199 TAAAGACAGT
1739209 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
1739226 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
1739242 A
1 A
1739243 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:1739761 original size:24 final size:24
Alignment explanation
Indices: 1739717--1739763 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1739707 ATAAAGAACC
*
1739717 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAATAAACCATTA
*
1739741 AAAATAAAGTTTAAA-AAACCATT
1 AAAATAAA-CTTAAATAAACCATT
1739764 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.60, C:0.11, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAATAAACCATTA
Found at i:1743101 original size:19 final size:20
Alignment explanation
Indices: 1743079--1743122 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1743069 GAGAAAAGGT
1743079 AAAAGTTAA-AATGAAAGAG
1 AAAAGTTAATAATGAAAGAG
* *
1743098 AAAAATTAATAATGAAAGAT
1 AAAAGTTAATAATGAAAGAG
1743118 AAAAG
1 AAAAG
1743123 AAAAAGTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.18
Consensus pattern (20 bp):
AAAAGTTAATAATGAAAGAG
Found at i:1750022 original size:24 final size:24
Alignment explanation
Indices: 1749978--1750024 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1749968 ATAAAGAACC
*
1749978 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
1750002 AAAATAAAGTTCAAACA-ACCATT
1 AAAATAAACTT-AAACATACCATT
1750025 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.57, C:0.15, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:1755534 original size:2 final size:2
Alignment explanation
Indices: 1755524--1755555 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1755514 TTTTATAACC
1755524 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1755556 AATTCGAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1760700 original size:3 final size:3
Alignment explanation
Indices: 1760692--1760719 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1760682 AGGCTACGTT
1760692 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1760720 CTTTCTACAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:1763810 original size:11 final size:11
Alignment explanation
Indices: 1763794--1763836 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
1763784 AGTAACTTTC
1763794 TATAATATATA
1 TATAATATATA
1763805 TATAATATATA
1 TATAATATATA
1763816 TTATTAATATA-A
1 -TA-TAATATATA
1763828 T-TAATATAT
1 TATAATATAT
1763837 TAATTAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
9 7 0.24
11 12 0.41
12 3 0.10
13 7 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
TATAATATATA
Found at i:1763842 original size:24 final size:24
Alignment explanation
Indices: 1763796--1763846 Score: 72
Period size: 21 Copynumber: 2.2 Consensus size: 24
1763786 TAACTTTCTA
1763796 TAATATATATATAATATATATTAT
1 TAATATATATATAATATATATTAT
*
1763820 TAATATA-AT-TAATATAT-TAAT
1 TAATATATATATAATATATATTAT
1763841 TAATAT
1 TAATAT
1763847 TTCAAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 9 0.35
22 8 0.31
23 2 0.08
24 7 0.27
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TAATATATATATAATATATATTAT
Found at i:1770285 original size:18 final size:18
Alignment explanation
Indices: 1770262--1770298 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1770252 AATAGTATAC
1770262 AAATTAAAATATAAACTA
1 AAATTAAAATATAAACTA
1770280 AAATTAAAATATAAACTA
1 AAATTAAAATATAAACTA
1770298 A
1 A
1770299 TACTAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (18 bp):
AAATTAAAATATAAACTA
Found at i:1770305 original size:18 final size:18
Alignment explanation
Indices: 1770266--1770306 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1770256 GTATACAAAT
*
1770266 TAAAATATAAACTAAAAT
1 TAAAATATAAACTAAAAC
*
1770284 TAAAATATAAACTAATAC
1 TAAAATATAAACTAAAAC
1770302 TAAAA
1 TAAAA
1770307 AAACATTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (18 bp):
TAAAATATAAACTAAAAC
Found at i:1770636 original size:24 final size:24
Alignment explanation
Indices: 1770599--1770665 Score: 107
Period size: 24 Copynumber: 2.8 Consensus size: 24
1770589 GAGTTGTATG
* *
1770599 AGGTGATATTTATAGGGGAGGAGT
1 AGGTGGTAATTATAGGGGAGGAGT
*
1770623 ATGTGGTAATTATAGGGGAGGAGT
1 AGGTGGTAATTATAGGGGAGGAGT
1770647 AGGTGGTAATTATAGGGGA
1 AGGTGGTAATTATAGGGGA
1770666 AAGACGAGCG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.30, C:0.00, G:0.42, T:0.28
Consensus pattern (24 bp):
AGGTGGTAATTATAGGGGAGGAGT
Found at i:1790268 original size:185 final size:186
Alignment explanation
Indices: 1790031--1790408 Score: 625
Period size: 186 Copynumber: 2.0 Consensus size: 186
1790021 ATAAAAATTA
**
1790031 AATATTTTTTAATTCAAAAAAACAGTTTCTAATTAATTTTAATAATATATAATTATAAAATAAAA
1 AATATTTTTTAATTCAAAAAAACAGTTTCTAATTAATTGAAATAATATATAATTATAAAATAAAA
1790096 A-TTTATATAAAATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATT
66 ATTTTATATAAAATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATT
1790160 ATTAATTAAGTTTTAAATAGTTTGGGCTGAACCCATATGTTATACATAATATATTT
131 ATTAATTAAGTTTTAAATAGTTTGGGCTGAACCCATATGTTATACATAATATATTT
* **
1790216 AATATTTTTTAATTCAAGAAAATTGTTTAC-AATTAATTGAAATAATATATAATTATAAAATAAA
1 AATATTTTTTAATTCAAAAAAACAGTTT-CTAATTAATTGAAATAATATATAATTATAAAATAAA
* *
1790280 AATTTTATATAAATTTTTTAATTAATTAATATTTATTTAGGTTTAAAAGTTATTGGATCTTAAAT
65 AATTTTATATAAAATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAAT
* * * *
1790345 TATTAATTGAGTTTTAAATGGTTTGGGCTGAGCCCATATGTTATATATAATATATTT
130 TATTAATTAAGTTTTAAATAGTTTGGGCTGAACCCATATGTTATACATAATATATTT
*
1790402 AAAATTT
1 AATATTT
1790409 AAAATTTAAT
Statistics
Matches: 179, Mismatches: 12, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
185 59 0.33
186 120 0.67
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (186 bp):
AATATTTTTTAATTCAAAAAAACAGTTTCTAATTAATTGAAATAATATATAATTATAAAATAAAA
ATTTTATATAAAATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATT
ATTAATTAAGTTTTAAATAGTTTGGGCTGAACCCATATGTTATACATAATATATTT
Found at i:1792739 original size:34 final size:34
Alignment explanation
Indices: 1792697--1792799 Score: 172
Period size: 34 Copynumber: 3.1 Consensus size: 34
1792687 AGGTTTGTAT
*
1792697 TATATAATTAATATAAAATATATAAAATATTATA
1 TATATAATTAATATAAAAAATATAAAATATTATA
*
1792731 TATATAATTGATATAAAAAATATAAAATATTATA
1 TATATAATTAATATAAAAAATATAAAATATTATA
*
1792765 TATATAATTAATATAAAAAATGTAAAATA-TATA
1 TATATAATTAATATAAAAAATATAAAATATTATA
1792798 TA
1 TA
1792800 ATCAGGGCGG
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
33 6 0.09
34 59 0.91
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (34 bp):
TATATAATTAATATAAAAAATATAAAATATTATA
Found at i:1792760 original size:25 final size:25
Alignment explanation
Indices: 1792706--1792782 Score: 68
Period size: 25 Copynumber: 3.1 Consensus size: 25
1792696 TTATATAATT
* *
1792706 AATATAAAATATATAAAATAT-TATA
1 AATATAATATATATAAAAAATATA-A
*
1792731 TATATAAT-TGATATAAAAAATATAA
1 AATATAATAT-ATATAAAAAATATAA
* **
1792756 AATATTATATATATAATTAATATAA
1 AATATAATATATATAAAAAATATAA
1792781 AA
1 AA
1792783 AATGTAAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
24 1 0.02
25 38 0.90
26 3 0.07
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (25 bp):
AATATAATATATATAAAAAATATAA
Done.