Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 179 of 185
Found at i:54535449 original size:25 final size:26
Alignment explanation
Indices: 54535419--54535468 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
54535409 ATATAAATAT
54535419 GAAAATATTC-ATTAAAAAAATATAG
1 GAAAATATTCGATTAAAAAAATATAG
* *
54535444 GAAAATATTCGTTTTAAAAAATATA
1 GAAAATATTCGATTAAAAAAATATA
54535469 TATACATGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.56, C:0.04, G:0.08, T:0.32
Consensus pattern (26 bp):
GAAAATATTCGATTAAAAAAATATAG
Found at i:54536250 original size:19 final size:19
Alignment explanation
Indices: 54536226--54536338 Score: 163
Period size: 19 Copynumber: 5.8 Consensus size: 19
54536216 AATCATATAT
54536226 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
54536245 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
*
54536264 TCTAATATTGCATATCATA
1 TCTAAGATTGCATATCATA
54536283 TCTAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
**
54536304 TCTTGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
54536323 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
54536339 CTAAAAAATT
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
19 65 0.79
21 17 0.21
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:54536314 original size:40 final size:40
Alignment explanation
Indices: 54536226--54536337 Score: 183
Period size: 40 Copynumber: 2.9 Consensus size: 40
54536216 AATCATATAT
54536226 TCTAAGATTGCATATCATATCTAAGATT--ATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
*
54536264 TCTAATATTGCATATCATATCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
**
54536304 TCTTGGATTGCATATCATATCTAAGATTGCATAT
1 TCTAAGATTGCATATCATATCTAAGATTGCATAT
54536338 CCTAAAAAAT
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
38 27 0.40
40 41 0.60
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (40 bp):
TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
Found at i:54536319 original size:59 final size:56
Alignment explanation
Indices: 54536219--54536338 Score: 161
Period size: 59 Copynumber: 2.1 Consensus size: 56
54536209 ATTACAAAAT
* *
54536219 CATAT-ATTCTAAGATTGCATATCATATCTAAGATTATATATCATATCTAATATTG
1 CATATCATTCTAAGATTGCATATCATATCTAAGATTACATATCATATCTAAGATTG
** *
54536274 CATATCATATCTAAGATTGCATATATCATATCTTGGATTGCATATCATATCTAAGATTG
1 CATATCAT-TCTAAGATTGC--ATATCATATCTAAGATTACATATCATATCTAAGATTG
54536333 CATATC
1 CATATC
54536339 CTAAAAAATT
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
55 5 0.09
56 2 0.04
57 11 0.20
59 38 0.68
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (56 bp):
CATATCATTCTAAGATTGCATATCATATCTAAGATTACATATCATATCTAAGATTG
Found at i:54536654 original size:44 final size:43
Alignment explanation
Indices: 54536552--54536886 Score: 256
Period size: 44 Copynumber: 7.7 Consensus size: 43
54536542 CTTCAATCTA
*
54536552 CTCCACTGTAACTTCAGGGAGATAAGACTTGCTATCTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCT-TCTT-AGTCTG
*
54536597 C-CTCACTACAACTTCA-GGAGGATAAGACTTGCTTCCTTAGTCTG
1 CTC-CACTGCAACTTCAGGGA-GATAAGACTTGCTT-CTTAGTCTG
* * * *
54536641 CTCCACTGCAACTTCAGGGAGATAAGACTAG-ATGTGA-TCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGCTTCTTAGTCTG
* * * * * *
54536682 -TTCTCTGCAACTTCAGAGAGATAAGATCTGTGATT-TTAATCCG
1 CTCCACTGCAACTTCAGGGAGATAAGA-CT-TGCTTCTTAGTCTG
* * * ** *
54536725 CTCCACTGCAACTTCAGGGAAACAGGA-TTGTCGGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTG-CTTC-TTAGTCTG
* * * *
54536769 CTCCACTGTAACTTCAGGGAGTTAAGATTTGTCATCTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTG-CTTCTT-AGTCTG
* *
54536814 C-CTCACTGTAACTTCA-GGAGGATAAGACTTACTTACTTAGTCTG
1 CTC-CACTGCAACTTCAGGGA-GATAAGACTTGCTT-CTTAGTCTG
*
54536858 CTCCACTGCAACTTCAGGAAGATAAGACT
1 CTCCACTGCAACTTCAGGGAGATAAGACT
54536887 AGATGCGATC
Statistics
Matches: 232, Mismatches: 38, Indels: 41
0.75 0.12 0.13
Matches are distributed among these distances:
40 23 0.10
41 8 0.03
42 6 0.03
43 5 0.02
44 119 0.51
45 71 0.31
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.30
Consensus pattern (43 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTTGCTTCTTAGTCTG
Found at i:54536927 original size:217 final size:217
Alignment explanation
Indices: 54536541--54536987 Score: 718
Period size: 217 Copynumber: 2.1 Consensus size: 217
54536531 AGGAATTAGT
* *
54536541 GCTTCAATCTACTCCACTGTAACTTCAGGGAGATAAGACTTGCTATCTTCAGTCTGCCTCACTAC
1 GCTTTAATCTGCTCCACTGTAACTTCAGGGAGATAAGACTTGCTATCTTCAGTCTGCCTCACTAC
* * *
54536606 AACTTCAGGAGGATAAGACTTGCTTCCTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTA
66 AACTTCAGGAGGATAAGACTTACTTACTTAGTCTGCTCCACTGCAACTTCAGGAAGATAAGACTA
* * *
54536671 GATGTGATCTGTTCTCTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTCCACTGCAA
131 GATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCACTCCACTGCAA
54536736 CTTCAGGGAA-ACAGGATTGTCG
196 CTTCA-GGAAGACAGGATTGTCG
* * *
54536758 GCTTTAATCTGCTCCACTGTAACTTCAGGGAGTTAAGATTTG-TCATCTTCAGTCTGCCTCACTG
1 GCTTTAATCTGCTCCACTGTAACTTCAGGGAGATAAGACTTGCT-ATCTTCAGTCTGCCTCACTA
*
54536822 TAACTTCAGGAGGATAAGACTTACTTACTTAGTCTGCTCCACTGCAACTTCAGGAAGATAAGACT
65 CAACTTCAGGAGGATAAGACTTACTTACTTAGTCTGCTCCACTGCAACTTCAGGAAGATAAGACT
* *
54536887 AGATGCGATCTGCTCTCTGTAACTTCAGAGAGATAAGATCTGTGATTTTAATCCACTCTACTGCA
130 AGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCACTCCACTGCA
*
54536952 ACTTCAGGAAGATAGGATTGTCG
195 ACTTCAGGAAGACAGGATTGTCG
*
54536975 ACTTTAATCTGCT
1 GCTTTAATCTGCT
54536988 TCCCACTATC
Statistics
Matches: 212, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
216 5 0.02
217 207 0.98
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.31
Consensus pattern (217 bp):
GCTTTAATCTGCTCCACTGTAACTTCAGGGAGATAAGACTTGCTATCTTCAGTCTGCCTCACTAC
AACTTCAGGAGGATAAGACTTACTTACTTAGTCTGCTCCACTGCAACTTCAGGAAGATAAGACTA
GATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCACTCCACTGCAA
CTTCAGGAAGACAGGATTGTCG
Found at i:54536958 original size:44 final size:43
Alignment explanation
Indices: 54536600--54536983 Score: 163
Period size: 44 Copynumber: 8.9 Consensus size: 43
54536590 CAGTCTGCCT
* * * *
54536600 CACTACAACTTCAGGAGGATAAGA-CT-TGCTTCCTTAGTCTGCTC
1 CACTGCAACTTCAGGA-GATAAGATCTGTGATT--TTAATCCGCTC
* * * * *
54536644 CACTGCAACTTCAGGGAGATAAGA-CT-AGA-TGTGATCTG-TT
1 CACTGCAACTTCA-GGAGATAAGATCTGTGATTTTAATCCGCTC
*
54536684 CTCTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTC
1 CACTGCAACTTCAG-GAGATAAGATCTGTGATTTTAATCCGCTC
* ** *
54536728 CACTGCAACTTCAGG-GAAACAGGAT-TGTCGGCTTTAATCTGCTC
1 CACTGCAACTTCAGGAGATA-A-GATCTGT-GATTTTAATCCGCTC
* * * * * * *
54536772 CACTGTAACTTCAGGGAGTTAAGATTTGTCATCTTCAGTCTGC-C
1 CACTGCAACTTCA-GGAGATAAGATCTGTGAT-TTTAATCCGCTC
* * *
54536816 TCACTGTAACTTCAGGAGGATAAGA-CT-T-ACTTACTTAGTCTGCTC
1 -CACTGCAACTTCAGGA-GATAAGATCTGTGA-TT--TTAATCCGCTC
* *** *
54536861 CACTGCAACTTCAGGAAGATAAGA-CT-AGA-TGCGATCTGCT-
1 CACTGCAACTTCAGG-AGATAAGATCTGTGATTTTAATCCGCTC
* * *
54536901 CTCTGTAACTTCAGAGAGATAAGATCTGTGATTTTAATCCACTC
1 CACTGCAACTTCAG-GAGATAAGATCTGTGATTTTAATCCGCTC
* * *
54536945 TACTGCAACTTCAGGAAGATAGGAT-TGTCGACTTTAATC
1 CACTGCAACTTCAGG-AGATAAGATCTGT-GATTTTAATC
54536984 TGCTTCCCAC
Statistics
Matches: 264, Mismatches: 48, Indels: 56
0.72 0.13 0.15
Matches are distributed among these distances:
39 1 0.00
40 42 0.16
41 16 0.06
42 9 0.03
43 25 0.09
44 130 0.49
45 39 0.15
46 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (43 bp):
CACTGCAACTTCAGGAGATAAGATCTGTGATTTTAATCCGCTC
Found at i:54537133 original size:132 final size:132
Alignment explanation
Indices: 54536980--54537854 Score: 1374
Period size: 132 Copynumber: 6.6 Consensus size: 132
54536970 TGTCGACTTT
* *
54536980 AATCTGCTTCCCACTATCTTGGAAAGATATGATTTGTCGTCTTCGATCTGCTCCACTACTGCTTA
1 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTA
* * * *
54537045 GGGAGATAAGATCTACAATCTTTAACCTACTCCGCTGCTGCTCAGGGAAAGAAGACTTGGTGGCT
66 GGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAAACAAGGCTTGGTGGCT
*
54537110 TG
131 TA
*
54537112 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTTACCGTCTTCGATCTGCTCCACTACTGCTTA
1 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTA
** * * * *
54537177 GGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTATTGCTTAGGGAGACAAAGCTTGTTGGCT
66 GGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAAACAAGGCTTGGTGGCT
54537242 TA
131 TA
* *
54537244 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTTACCGTCTTCGATCTGCTCCACTACTACTTA
1 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTA
54537309 GGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAGAA-AAGGCTTGGTGGC
66 GGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGA-AACAAGGCTTGGTGGC
54537373 TTA
130 TTA
* * *
54537376 AATCTGTTTCCCACTATCTTGGAAAGATAAGATTTGCTGTCTTCGATATGCTCCACTACTGCTTA
1 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTA
* * * * *
54537441 GGGAGATAAGATCTATAATCTTCAACCTTTTCCACTGCTGCTCAGAGAGACAAGGCTTGGTGGCT
66 GGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAAACAAGGCTTGGTGGCT
54537506 TA
131 TA
* *
54537508 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTTACCGTCTTCGATCTGCTCTACTACTGCTTA
1 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTA
* * * * * * *
54537573 GGGAGATAAGATCTACAATTTTTAACTTTCTCCGCTACTACTCAGGGAGACAAGGCTTGGTGCCT
66 GGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAAACAAGGCTTGGTGGCT
54537638 TA
131 TA
* *
54537640 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCTGTCTTCGATCTGCTCCACTACTGCTTA
1 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTA
** *
54537705 GGGAGATAAGATCTACAATCTTCAACCTTCTCCTTTGCTGCTCAGGGAGACAAGGCTTGGTGGCT
66 GGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAAACAAGGCTTGGTGGCT
54537770 TA
131 TA
* *
54537772 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGTTTA
1 AATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTA
54537837 GGGAGATAAGATCTACAA
66 GGGAGATAAGATCTACAA
54537855 ATTTCACTGA
Statistics
Matches: 681, Mismatches: 60, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
131 1 0.00
132 679 1.00
133 1 0.00
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.31
Consensus pattern (132 bp):
AATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTA
GGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTGCTCAGGGAAACAAGGCTTGGTGGCT
TA
Found at i:54537163 original size:44 final size:46
Alignment explanation
Indices: 54537113--54537584 Score: 124
Period size: 44 Copynumber: 10.7 Consensus size: 46
54537103 GGTGGCTTGA
54537113 ATCTGCTTCCCACTA-T-CTT-GGAAAGATAAGATTTACCGTCTTCG
1 ATCTGCTTCCCACTACTGCTTAGG-AAGATAAGATTTACCGTCTTCG
* * **
54537157 ATCTGC-T-CCACTACTGCTTAGGGAGATAAGATCTACAATCTTC-
1 ATCTGCTTCCCACTACTGCTTAGGAAGATAAGATTTACCGTCTTCG
* * * * * * * * **
54537200 AAC--CTTCTCCGCTATTGCTTAGGGAGACAAAGCTTGT--TGGCTTAA
1 ATCTGCTTC-CCACTACTGCTTAGGAAGA-TAAGATT-TACCGTCTTCG
54537245 ATCTGCTTCCCACTA-T-CTT-GGAAAGATAAGATTTACCGTCTTCG
1 ATCTGCTTCCCACTACTGCTTAGG-AAGATAAGATTTACCGTCTTCG
* * * **
54537289 ATCTGC-T-CCACTACTACTTAGGGAGATAAGATCTACAATCTTC-
1 ATCTGCTTCCCACTACTGCTTAGGAAGATAAGATTTACCGTCTTCG
* * * * * * ** *** * **
54537332 AAC--CTTCTCCGCTGCTGCTCAGGGAGAAAAGGCTTGGTGGCTTAA
1 ATCTGCTTC-CCACTACTGCTTAGGAAGATAAGATTTACCGTCTTCG
* * *
54537377 ATCTGTTTCCCACTA-T-CTT-GGAAAGATAAGATTTGCTGTCTTCG
1 ATCTGCTTCCCACTACTGCTTAGG-AAGATAAGATTTACCGTCTTCG
* * * *** *
54537421 ATATGC-T-CCACTACTGCTTAGGGAGATAAGATCTATAATCTTCA
1 ATCTGCTTCCCACTACTGCTTAGGAAGATAAGATTTACCGTCTTCG
* * * * * ** *** * **
54537465 ACCT--TTTCCACTGCTGCTCA-GAGAGACAAGGCTTGGTGGCTTAA
1 ATCTGCTTCCCACTACTGCTTAGGA-AGATAAGATTTACCGTCTTCG
54537509 ATCTGCTTCCCACTA-T-CTT-GGAAAGATAAGATTTACCGTCTTCG
1 ATCTGCTTCCCACTACTGCTTAGG-AAGATAAGATTTACCGTCTTCG
* *
54537553 ATCTGC-T-CTACTACTGCTTAGGGAGATAAGAT
1 ATCTGCTTCCCACTACTGCTTAGGAAGATAAGAT
54537585 CTACAATTTT
Statistics
Matches: 297, Mismatches: 94, Indels: 74
0.64 0.20 0.16
Matches are distributed among these distances:
41 2 0.01
42 26 0.09
43 23 0.08
44 202 0.68
45 20 0.07
46 17 0.06
47 7 0.02
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.32
Consensus pattern (46 bp):
ATCTGCTTCCCACTACTGCTTAGGAAGATAAGATTTACCGTCTTCG
Found at i:54539044 original size:21 final size:19
Alignment explanation
Indices: 54539020--54539068 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 19
54539010 TTCTTTTCTC
54539020 TTTTATTTTTTATTTTTTTTG
1 TTTT-TTTTTTA-TTTTTTTG
54539041 TTTTTGTTTTTATTTTTTTG
1 TTTTT-TTTTTATTTTTTTG
54539061 TTTTTTTT
1 TTTTTTTT
54539069 AATCTGAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 3 0.11
20 14 0.52
21 10 0.37
ACGTcount: A:0.06, C:0.00, G:0.06, T:0.88
Consensus pattern (19 bp):
TTTTTTTTTTATTTTTTTG
Found at i:54539044 original size:28 final size:29
Alignment explanation
Indices: 54539008--54539068 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
54538998 GGCCTTTCCA
54539008 TTTTCTTTTCT-CTTTTA-TTTTTTATTTT
1 TTTTCTTTT-TGCTTTTATTTTTTTATTTT
* * *
54539036 TTTTGTTTTTGTTTTTATTTTTTTGTTTT
1 TTTTCTTTTTGCTTTTATTTTTTTATTTT
54539065 TTTT
1 TTTT
54539069 AATCTGAACT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 1 0.04
28 13 0.46
29 14 0.50
ACGTcount: A:0.05, C:0.05, G:0.05, T:0.85
Consensus pattern (29 bp):
TTTTCTTTTTGCTTTTATTTTTTTATTTT
Found at i:54543082 original size:98 final size:98
Alignment explanation
Indices: 54542913--54543109 Score: 349
Period size: 98 Copynumber: 2.0 Consensus size: 98
54542903 ATACAATAAA
* *
54542913 ACTTTAAAATAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATC
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
54542978 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
* *
54543011 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
*
54543076 CCTTTAGAATCTCAAACTCGGAATATTTCCTTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
54543109 A
1 A
54543110 TGATTTTTTT
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.37, C:0.25, G:0.10, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
Found at i:54543811 original size:24 final size:25
Alignment explanation
Indices: 54543782--54543830 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
54543772 ATATAAATAT
54543782 GAAAATATTC-ATTAAAAAATATAG
1 GAAAATATTCGATTAAAAAATATAG
*
54543806 GAAAATATTCGTTTTAAAAAATATA
1 GAAAATATTCG-ATTAAAAAATATA
54543831 TACATGTACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 10 0.45
26 12 0.55
ACGTcount: A:0.55, C:0.04, G:0.08, T:0.33
Consensus pattern (25 bp):
GAAAATATTCGATTAAAAAATATAG
Found at i:54544623 original size:19 final size:19
Alignment explanation
Indices: 54544599--54544711 Score: 136
Period size: 19 Copynumber: 5.8 Consensus size: 19
54544589 AATCATATAT
54544599 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
54544618 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
* *
54544637 TCTAATATTGCATATTATA
1 TCTAAGATTGCATATCATA
54544656 TCTAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
** *
54544677 TCTTGGATTGTATATCATA
1 TCTAAGATTGCATATCATA
*
54544696 TCTAAGATTGTATATC
1 TCTAAGATTGCATATC
54544712 CTAAAAAATT
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
19 64 0.81
21 15 0.19
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.42
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:54544691 original size:59 final size:58
Alignment explanation
Indices: 54544594--54544710 Score: 164
Period size: 59 Copynumber: 2.0 Consensus size: 58
54544584 TACAAAATCA
*
54544594 TATATTCTAAGATTGCATATCATATCTAAGATTATATATCATATCTAATATTGCATAT
1 TATATTCTAAGATTGCATATCATATCTAAGATTATATATCATATCTAAGATTGCATAT
** * *
54544652 TATA-TCTAAGATTGCATATATCATATCTTGGATTGTATATCATATCTAAGATTGTATAT
1 TATATTCTAAGATTGC--ATATCATATCTAAGATTATATATCATATCTAAGATTGCATAT
54544711 CCTAAAAAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
57 11 0.21
58 4 0.08
59 37 0.71
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.44
Consensus pattern (58 bp):
TATATTCTAAGATTGCATATCATATCTAAGATTATATATCATATCTAAGATTGCATAT
Found at i:54544697 original size:40 final size:39
Alignment explanation
Indices: 54544599--54544711 Score: 158
Period size: 40 Copynumber: 2.9 Consensus size: 39
54544589 AATCATATAT
54544599 TCTAAGATTGCATATCATATCTAAGATT-ATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTGATATATCATA
* *
54544637 TCTAATATTGCATATTATATCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTG-ATATATCATA
** *
54544677 TCTTGGATTGTATATCATATCTAAGATTG-TATATC
1 TCTAAGATTGCATATCATATCTAAGATTGATATATC
54544712 CTAAAAAATT
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
38 32 0.48
40 34 0.52
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.42
Consensus pattern (39 bp):
TCTAAGATTGCATATCATATCTAAGATTGATATATCATA
Found at i:54545445 original size:16 final size:16
Alignment explanation
Indices: 54545424--54545483 Score: 61
Period size: 16 Copynumber: 3.6 Consensus size: 16
54545414 ACTTAAATTT
54545424 AAATTTATTATTATTA
1 AAATTTATTATTATTA
54545440 AAATTTATTATTAATATA
1 AAATTTATTATT-AT-TA
*
54545458 AAA-TTA-TAATATTAA
1 AAATTTATTATTATT-A
54545473 ATAATTTATTA
1 A-AATTTATTA
54545484 AAATAATAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 1 0.03
15 4 0.11
16 17 0.46
17 8 0.22
18 7 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AAATTTATTATTATTA
Found at i:54569419 original size:17 final size:16
Alignment explanation
Indices: 54569397--54569429 Score: 57
Period size: 16 Copynumber: 2.0 Consensus size: 16
54569387 TAATTAAATT
54569397 ATTATAAATTTATAAAA
1 ATTATAAA-TTATAAAA
54569414 ATTATAAATTATAAAA
1 ATTATAAATTATAAAA
54569430 TCCGATTCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTATAAATTATAAAA
Found at i:54573090 original size:2 final size:2
Alignment explanation
Indices: 54573083--54573108 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
54573073 ATATCTAATC
54573083 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
54573109 TTAATATAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54574870 original size:43 final size:43
Alignment explanation
Indices: 54574807--54574973 Score: 212
Period size: 43 Copynumber: 3.9 Consensus size: 43
54574797 CCACTATAGA
* *
54574807 ACATGACATTTAGCGGTGC-TTTACCCACAAACGCCGCTAAAGG
1 ACATGACCTTTAGCGGTGCTTTTA-TCACAAACGCCGCTAAAGG
* * * * *
54574850 TCATGATCTTTAGCGTTGCTTTTATCACAAACTCCGCTAAAGA
1 ACATGACCTTTAGCGGTGCTTTTATCACAAACGCCGCTAAAGG
*
54574893 ACATGACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAA-G
1 ACATGACCTTTAGCGGTGCTTTTATCACAAACGCCGCTAAAGG
** *
54574935 ACATGACCTTTAGCGACGCTTTTATCACAAACGCTGCTA
1 ACATGACCTTTAGCGGTGCTTTTATCACAAACGCCGCTA
54574974 TAAATACCGT
Statistics
Matches: 108, Mismatches: 15, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
42 37 0.34
43 67 0.62
44 4 0.04
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (43 bp):
ACATGACCTTTAGCGGTGCTTTTATCACAAACGCCGCTAAAGG
Found at i:54576119 original size:17 final size:17
Alignment explanation
Indices: 54576099--54576136 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
54576089 TTTGATTATA
54576099 AAATATGA-AAAATGTAT
1 AAATATGATAAAA-GTAT
*
54576116 AAATATTATAAAAGTAT
1 AAATATGATAAAAGTAT
54576133 AAAT
1 AAAT
54576137 GTACATACGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.32
Consensus pattern (17 bp):
AAATATGATAAAAGTAT
Found at i:54576291 original size:3 final size:3
Alignment explanation
Indices: 54576283--54576309 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
54576273 ACAATACTAT
54576283 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
54576310 GTAAAAAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:54579063 original size:4 final size:4
Alignment explanation
Indices: 54579054--54579092 Score: 71
Period size: 4 Copynumber: 10.0 Consensus size: 4
54579044 TAGAAAGGAC
54579054 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAA- TAAT TAAT
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT
54579093 ACAAGTCATA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.09
4 31 0.91
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (4 bp):
TAAT
Found at i:54580738 original size:31 final size:31
Alignment explanation
Indices: 54580703--54580771 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
54580693 TTTTAAAAAA
** *
54580703 TAGTGACTTAAATAAAAAATTTTGAATAGTT
1 TAGTGACTTAAATAAAAAATTTCAAATAATT
* *
54580734 TAGTGACTTAAATGAAAACTTTCAAATAATT
1 TAGTGACTTAAATAAAAAATTTCAAATAATT
54580765 TAGTGAC
1 TAGTGAC
54580772 CAAATTATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.36
Consensus pattern (31 bp):
TAGTGACTTAAATAAAAAATTTCAAATAATT
Found at i:54589274 original size:21 final size:19
Alignment explanation
Indices: 54589250--54589293 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
54589240 TATTTAAGTT
54589250 TTTATTAATTTAGCATATAAA
1 TTTATTAATTT--CATATAAA
* *
54589271 TTTATTTATTTTATATAAA
1 TTTATTAATTTCATATAAA
54589290 TTTA
1 TTTA
54589294 GTATTAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 11 0.52
21 10 0.48
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (19 bp):
TTTATTAATTTCATATAAA
Found at i:54590399 original size:20 final size:20
Alignment explanation
Indices: 54590362--54590401 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
54590352 AAATTTTTAT
* *
54590362 TTTTTAAAAAATTATAAAAA
1 TTTTAAAAAAAATATAAAAA
*
54590382 TTTTAAAAAAAATCTAAAAA
1 TTTTAAAAAAAATATAAAAA
54590402 AATGTATATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (20 bp):
TTTTAAAAAAAATATAAAAA
Found at i:54597910 original size:28 final size:27
Alignment explanation
Indices: 54597869--54597925 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
54597859 AGGAAGAAGA
*
54597869 AATTTAAAATATTTTTAAAT-TAAAAAT
1 AATTTAAAACA-TTTTAAATATAAAAAT
*
54597896 AATTTATAAACATTTTAAATATGAAAAT
1 AATTTA-AAACATTTTAAATATAAAAAT
54597924 AA
1 AA
54597926 ACTATGTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 14 0.54
28 12 0.46
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (27 bp):
AATTTAAAACATTTTAAATATAAAAAT
Found at i:54598875 original size:11 final size:11
Alignment explanation
Indices: 54598859--54598884 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
54598849 TAGAAGAGAC
54598859 GAAACAGGGGA
1 GAAACAGGGGA
54598870 GAAACAGGGGA
1 GAAACAGGGGA
54598881 GAAA
1 GAAA
54598885 GAAGAAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.08, G:0.42, T:0.00
Consensus pattern (11 bp):
GAAACAGGGGA
Found at i:54601566 original size:17 final size:17
Alignment explanation
Indices: 54601539--54601578 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
54601529 AACTTCAATT
*
54601539 AATTT-TAAATATTTTA
1 AATTTATAAATACTTTA
54601555 AATTTATAAATACTTTA
1 AATTTATAAATACTTTA
*
54601572 AAATTAT
1 AATTTAT
54601579 TTTTTATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
AATTTATAAATACTTTA
Found at i:54606904 original size:83 final size:83
Alignment explanation
Indices: 54606765--54606931 Score: 325
Period size: 83 Copynumber: 2.0 Consensus size: 83
54606755 AATGTCATTC
*
54606765 TCCTGCCCCTTCTCTTTCGTTTGTTTTTCTTTTCTGATAGTGCAATCCTCATTGCAACCATAAAT
1 TCCTGCCCCTTCTCTTTCGTTTGTTTTTCTTTTCTGATAGTGCAATCCTCATTGCAACCATAAAC
54606830 GATGATTTAGAGAACATG
66 GATGATTTAGAGAACATG
54606848 TCCTGCCCCTTCTCTTTCGTTTGTTTTTCTTTTCTGATAGTGCAATCCTCATTGCAACCATAAAC
1 TCCTGCCCCTTCTCTTTCGTTTGTTTTTCTTTTCTGATAGTGCAATCCTCATTGCAACCATAAAC
54606913 GATGATTTAGAGAACATG
66 GATGATTTAGAGAACATG
54606931 T
1 T
54606932 TTCCCTTTTC
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 83 1.00
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.41
Consensus pattern (83 bp):
TCCTGCCCCTTCTCTTTCGTTTGTTTTTCTTTTCTGATAGTGCAATCCTCATTGCAACCATAAAC
GATGATTTAGAGAACATG
Found at i:54613352 original size:43 final size:44
Alignment explanation
Indices: 54613278--54613382 Score: 124
Period size: 43 Copynumber: 2.4 Consensus size: 44
54613268 TCAAAAGTGT
* * *
54613278 ATGGCACTAAGTGTGCGAATTCAAGATAGCTTCAGTTGGAT-AA
1 ATGGCACTAAGTGTGCGAACTCAAGAGAGCTTCAGTTGAATGAA
* * **
54613321 ATGGCACTAAGTGTGCGATACT-AAGAGAGCTTCGGTTTAATGTG
1 ATGGCACTAAGTGTGCGA-ACTCAAGAGAGCTTCAGTTGAATGAA
54613365 ATGGCACTAAGTGTGCGA
1 ATGGCACTAAGTGTGCGA
54613383 CATTGTTATA
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
43 33 0.62
44 20 0.38
ACGTcount: A:0.30, C:0.14, G:0.29, T:0.28
Consensus pattern (44 bp):
ATGGCACTAAGTGTGCGAACTCAAGAGAGCTTCAGTTGAATGAA
Found at i:54613607 original size:19 final size:19
Alignment explanation
Indices: 54613571--54613608 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
54613561 ATGGAATATA
*
54613571 TATATAAATGAGTAATGAT
1 TATATAAATGAATAATGAT
54613590 TATATGAAATGAAT-ATGAT
1 TATAT-AAATGAATAATGAT
54613609 GATCCTTCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.37
Consensus pattern (19 bp):
TATATAAATGAATAATGAT
Found at i:54616001 original size:40 final size:40
Alignment explanation
Indices: 54615957--54616090 Score: 164
Period size: 40 Copynumber: 3.3 Consensus size: 40
54615947 CTGTGTTTAT
*
54615957 CACTTAGTGTGCGAATTGAGATAACTTCGGCTATTTATGG
1 CACTTAGTGTGCGAATTGAGATAGCTTCGGCTATTTATGG
* *
54615997 CACTTAGTGTGCG-ATTGGGAATAGCTTTGGCTATATT-TGG
1 CACTTAGTGTGCGAATTGAG-ATAGCTTCGGCTAT-TTATGG
* * * *
54616037 CACTTAGTGTGTGAGACTGAGATAGCTTCGGCTATGTAAGG
1 CACTTAGTGTGCGA-ATTGAGATAGCTTCGGCTATTTATGG
54616078 CACTTAGTGTGCG
1 CACTTAGTGTGCG
54616091 GGATTATAAT
Statistics
Matches: 79, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
39 5 0.06
40 41 0.52
41 29 0.37
42 4 0.05
ACGTcount: A:0.22, C:0.15, G:0.29, T:0.34
Consensus pattern (40 bp):
CACTTAGTGTGCGAATTGAGATAGCTTCGGCTATTTATGG
Found at i:54620049 original size:4 final size:4
Alignment explanation
Indices: 54620040--54620075 Score: 63
Period size: 4 Copynumber: 8.8 Consensus size: 4
54620030 TAATGGACAC
54620040 ATAA ATAA ATAA ATAA ATAA ATAA ATAAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA AT-AA ATAA ATA
54620076 TCAAGTAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 27 0.87
5 4 0.13
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAA
Found at i:54620271 original size:13 final size:14
Alignment explanation
Indices: 54620247--54620275 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
54620237 AAAAGATATA
54620247 AATAATTATATAAT
1 AATAATTATATAAT
54620261 AATAA-TATATAAT
1 AATAATTATATAAT
54620274 AA
1 AA
54620276 GACAAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AATAATTATATAAT
Found at i:54621219 original size:13 final size:15
Alignment explanation
Indices: 54621189--54621226 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 15
54621179 TAAGTTTTGT
*
54621189 TTTTTTGTTTTCTAA
1 TTTTTTGTTGTCTAA
54621204 TTTTTTGTTGT-T-A
1 TTTTTTGTTGTCTAA
54621217 TTTTTTGTTG
1 TTTTTTGTTG
54621227 AATCTGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.50
14 1 0.05
15 10 0.45
ACGTcount: A:0.08, C:0.03, G:0.13, T:0.76
Consensus pattern (15 bp):
TTTTTTGTTGTCTAA
Found at i:54629971 original size:124 final size:116
Alignment explanation
Indices: 54629759--54630428 Score: 565
Period size: 114 Copynumber: 5.9 Consensus size: 116
54629749 AAATTTACAA
54629759 ATTTTTTT-GTGTCAGAATCAGATAT-AAAATACGAAAAAAATTAAAAAAAAATTTTGGGTGCTG
1 ATTTTTTTCGTGTCAGAATCAGATATAAAAATACGAAAAAAATTAAAAAAAAATTTTGGGTGCTG
* *
54629822 GCCTGTCAATGGCCGGCACCCAGTACACAGTACAAAAAAAATTGTTTTTTTTTT
66 GCCTGTCAATGGCCGGCACCCAGTACACAGTACAAAAAAAA---ATTTTCTTTT
*
54629876 ATTTTTTTCATGTCAGAATCAGATATAAAAATACG-AAAAAATTAAAATATATATATATTTTTGG
1 ATTTTTTTCGTGTCAGAATCAGATATAAAAATACGAAAAAAATTAAAA-A-A-A-A-A-TTTTGG
*
54629940 GTGCTGGCCTGTCAATGGCCGGCACCTAGTACACAGTACAAAAAAAAATTTTCTTTT
60 GTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACAAAAAAAAATTTTCTTTT
**
54629997 ATTTTTTTCGTGTCAGAATCAGATATAAAAATACGAAAAAAATT-AAAAAAAA--TT--G-GCCA
1 ATTTTTTTCGTGTCAGAATCAGATATAAAAATACGAAAAAAATTAAAAAAAAATTTTGGGTGCTG
* * * * ******* *** *
54630056 GCAC--CCAAT-------ACACAGTACAAAATTTTTTTTATTTTTTTCG---
66 GC-CTGTCAATGGCCGGCACCCAGTACACAGTACAAAAAAAAATTTTCTTTT
* ***
54630096 ----------TGTCAGAATCAGATATAAAAATATGAAAAAAAAATTTAAAAAATTTTTTTTGGGT
1 ATTTTTTTCGTGTCAGAATCAGATATAAAAATACG--AAAAAAA-TTAAAAAA-AAATTTTGGGT
* *
54630151 GCTGGCCTGTCAACGGCCGGCACCCAGTACACAGTAC--AAAAAAATTTATTTTTT
62 GCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACAAAAAAAAATTT-TCTTTT
*
54630205 ATTTTTTTCGTGTCAGAATCAGATATAAAAATACGAAAAAAATTAAAAAATATATATTTTTTGAG
1 ATTTTTTTCGTGTCAGAATCAGATATAAAAATACGAAAAAAATTAAAAAA-A-A-A--TTTTGGG
*** * *
54630270 TGCAAACTTGTCAATGGCCGGCACCCAGTACACAGTAC-------AATTTTTTTTT
61 TGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACAAAAAAAAATTTTCTTTT
54630319 ATTTTTTTCGTGTCAGAATCAGATATAAAAATACGAAAAAAATTAAAAAAAAATTTTTTGGGTGC
1 ATTTTTTTCGTGTCAGAATCAGATATAAAAATACGAAAAAAATTAAAAAAAAA--TTTTGGGTGC
54630384 TGGCCTGTCAATGGCCGGCACCCAGTACACAGTACAAAAAAAAAT
64 TGGCCTGTCAATGGCCGGCACCCAGTACACAGTACAAAAAAAAAT
54630429 CAGCACCCAA
Statistics
Matches: 440, Mismatches: 59, Indels: 107
0.73 0.10 0.18
Matches are distributed among these distances:
89 24 0.05
91 7 0.02
92 2 0.00
93 5 0.01
96 2 0.00
98 2 0.00
99 4 0.01
100 3 0.01
102 16 0.04
105 4 0.01
106 1 0.00
107 11 0.03
109 4 0.01
110 4 0.01
111 45 0.10
112 1 0.00
113 3 0.01
114 56 0.13
115 5 0.01
116 10 0.02
117 16 0.04
118 32 0.07
119 34 0.08
120 41 0.09
121 46 0.10
122 9 0.02
123 1 0.00
124 52 0.12
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.32
Consensus pattern (116 bp):
ATTTTTTTCGTGTCAGAATCAGATATAAAAATACGAAAAAAATTAAAAAAAAATTTTGGGTGCTG
GCCTGTCAATGGCCGGCACCCAGTACACAGTACAAAAAAAAATTTTCTTTT
Found at i:54630139 original size:329 final size:316
Alignment explanation
Indices: 54629759--54630370 Score: 920
Period size: 329 Copynumber: 1.9 Consensus size: 316
54629749 AAATTTACAA
*
54629759 ATTTTTTTGTGTCAGAATCAGATATAAAATACGAAAAAAATTAAAAAAAAATTTTGGGTGCTGGC
1 ATTTTTTTGTGTCAGAATCAGATATAAAATACGAAAAAAATTAAAAAAAATTTTTGGGTGCTGGC
* *
54629824 CTGTCAATGGCCGGCACCCAGTACACAGTACAAAAAAAATTGTTTTTTTTTTATTTTTTTCATGT
66 CTGTCAACGGCCGGCACCCAGTACACAGTAC-AAAAAAA---TTTATTTTTTATTTTTTTCATGT
* * ***
54629889 CAGAATCAGATATAAAAATACG-AAAAAATTAAAATATATATATATTTTTGGGTGCTGGCCTGTC
127 CAGAATCAGATATAAAAATACGAAAAAAATTAAAAAATATATAT-TTTTTGAGTGCAAACCTGTC
*
54629953 AATGGCCGGCACCTAGTACACAGTACAAAAAAAAATTTTCTTTTATTTTTTTCGTGTCAGAATCA
191 AATGGCCGGCACCCAGTACACAGTAC-------AATTTTCTTTTATTTTTTTCGTGTCAGAATCA
54630018 GATATAAAAATACGAAAAAAATTAAAAAAAATTGGCCAGCACCCAATACACAGTACAAAATTTTT
249 GATATAAAAATACGAAAAAAATTAAAAAAAATTGGCCAGCACCCAATACACAGTACAAAATTTTT
54630083 TTT
314 TTT
* **
54630086 ATTTTTTTCGTGTCAGAATCAGATATAAAAATATGAAAAAAAAATTTAAAAAATTTTTTTTGGGT
1 ATTTTTTT-GTGTCAGAATCAGATAT-AAAATACG--AAAAAAA-TTAAAAAA-AATTTTTGGGT
*
54630151 GCTGGCCTGTCAACGGCCGGCACCCAGTACACAGTACAAAAAAATTTATTTTTTATTTTTTTCGT
60 GCTGGCCTGTCAACGGCCGGCACCCAGTACACAGTACAAAAAAATTTATTTTTTATTTTTTTCAT
*
54630216 GTCAGAATCAGATATAAAAATACGAAAAAAATTAAAAAATATATATTTTTTGAGTGCAAACTTGT
125 GTCAGAATCAGATATAAAAATACGAAAAAAATTAAAAAATATATATTTTTTGAGTGCAAACCTGT
*
54630281 CAATGGCCGGCACCCAGTACACAGTACAATTTTTTTTTATTTTTTTCGTGTCAGAATCAGATATA
190 CAATGGCCGGCACCCAGTACACAGTACAATTTTCTTTTATTTTTTTCGTGTCAGAATCAGATATA
54630346 AAAATACGAAAAAAATTAAAAAAAA
255 AAAATACGAAAAAAATTAAAAAAAA
54630371 ATTTTTTGGG
Statistics
Matches: 263, Mismatches: 15, Indels: 19
0.89 0.05 0.06
Matches are distributed among these distances:
322 62 0.24
327 8 0.03
328 17 0.06
329 90 0.34
330 20 0.08
331 7 0.03
332 15 0.06
333 44 0.17
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.33
Consensus pattern (316 bp):
ATTTTTTTGTGTCAGAATCAGATATAAAATACGAAAAAAATTAAAAAAAATTTTTGGGTGCTGGC
CTGTCAACGGCCGGCACCCAGTACACAGTACAAAAAAATTTATTTTTTATTTTTTTCATGTCAGA
ATCAGATATAAAAATACGAAAAAAATTAAAAAATATATATTTTTTGAGTGCAAACCTGTCAATGG
CCGGCACCCAGTACACAGTACAATTTTCTTTTATTTTTTTCGTGTCAGAATCAGATATAAAAATA
CGAAAAAAATTAAAAAAAATTGGCCAGCACCCAATACACAGTACAAAATTTTTTTT
Found at i:54630564 original size:117 final size:118
Alignment explanation
Indices: 54630429--54630734 Score: 415
Period size: 117 Copynumber: 2.6 Consensus size: 118
54630419 AAAAAAAAAT
* * *
54630429 CAGCACCCAAAAAATTTTTTTAAAATTATTTTTCGTATTTTTATATCTGATTCTAACACGAAAAA
1 CAGCACCCAAAAATTTTTTTTTAAATT-TTTTTCGTATTTTTATATCTGATTCTGACACGAAAAA
* *
54630494 AAT-AAAAGA-AAATTTTTTTGTACTGTGTACTGGGTGCCGGCCATTGACAGTC
65 AATAAAAAAACAAATTTTTTTGTACTGTGTACTGGGTGCCGGCCATTGACAGGC
54630546 CAGCACCCAAAAATTTTTTTTTAAATTTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAA
1 CAGCACCCAAAAATTTTTTTTTAAA-TTTTTTTCGTATTTTTATATCTGATTCTGACACG-AAAA
* *
54630611 AAATAAAAAAAAAAACAAATTTTTTTGTATTGTGTACTGGGTGTCGGCCATTGACAGGC
64 AAAT----AAAAAAACAAATTTTTTTGTACTGTGTACTGGGTGCCGGCCATTGACAGGC
* * *
54630670 AAGCACCCAAAATTTTTTTTTTTAAA-TTTTTTCGTATTTTTATATTTGATTCTGACA--AAAAA
1 CAGCACCCAAAA-ATTTTTTTTTAAATTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAA
54630732 AAT
65 AAT
54630735 TTGTACTGTG
Statistics
Matches: 170, Mismatches: 10, Indels: 15
0.87 0.05 0.08
Matches are distributed among these distances:
117 54 0.32
118 10 0.06
120 8 0.05
123 35 0.21
124 51 0.30
125 12 0.07
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.40
Consensus pattern (118 bp):
CAGCACCCAAAAATTTTTTTTTAAATTTTTTTCGTATTTTTATATCTGATTCTGACACGAAAAAA
ATAAAAAAACAAATTTTTTTGTACTGTGTACTGGGTGCCGGCCATTGACAGGC
Found at i:54637376 original size:3 final size:3
Alignment explanation
Indices: 54637368--54637396 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
54637358 TGATTGCTTT
54637368 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
54637397 TTTTTGTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:54638824 original size:108 final size:109
Alignment explanation
Indices: 54638632--54639053 Score: 570
Period size: 109 Copynumber: 3.9 Consensus size: 109
54638622 ATTCAAGAGG
* * * * *
54638632 ATATTTGACTATTTGGTTAAACGAG--AAATCGAAACCCAGCACATTAGGGCAAG-CTCCTCGAA
1 ATATTTGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAA
54638694 TTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTGAAAGA
66 TTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTGAAAGA
* *
54638738 ATATTTGGCTATTTGGTTGAGCGAGAAAAATCGAAACCCAGCATATT-GGGACACGTTTTCTCGA
1 ATATTTGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGG-CACGTTTTCTCGA
*** * *
54638802 ATTTCCAAACGC-TTTCATTGCCTTATTTTGAAATTTTTAAAAGG
65 ATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTGAAAGA
* * *
54638846 ATACTTAGCTATTTGGTTGAATGAGAAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGA
1 ATATTTGGCTATTTGGTTGAACGAG-AAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGA
*
54638911 ATTTTCAAACGCAAAACATTGCCTTATTTTGAAATTTTTGAAAGA
65 ATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTGAAAGA
*
54638956 ATATTTGGCTATTTGGTTGAGA-GAGAAAAATCGAAACCCAGCATATT-GGGACACGTTTTCTCG
1 ATATTTGGCTATTTGGTTGA-ACGAGAAAAATCGAAACCCAGCACATTAGGG-CACGTTTTCTCG
* * * *
54639019 AATTTCCAAACGCTAAATATTGCCTCATTTAGAAA
64 AATTTCCAAACGCAAAACATTGCCTTATTTTGAAA
54639054 AAATTTCCTT
Statistics
Matches: 276, Mismatches: 31, Indels: 15
0.86 0.10 0.05
Matches are distributed among these distances:
106 22 0.08
107 3 0.01
108 73 0.26
109 126 0.46
110 51 0.18
111 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (109 bp):
ATATTTGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAA
TTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTGAAAGA
Found at i:54639200 original size:18 final size:18
Alignment explanation
Indices: 54639172--54639216 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
54639162 TGTATATATC
54639172 ATAACAAATAAA-TAAATAA
1 ATAA-AAATAAACTAAA-AA
*
54639191 ATAAAAATAAACTAAAAC
1 ATAAAAATAAACTAAAAA
54639209 ATAAAAAT
1 ATAAAAAT
54639217 GGACATATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (18 bp):
ATAAAAATAAACTAAAAA
Found at i:54639589 original size:14 final size:15
Alignment explanation
Indices: 54639565--54639593 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
54639555 TGTAAGATGA
54639565 AAAATATATACATAT
1 AAAATATATACATAT
54639580 AAAA-ATATACATAT
1 AAAATATATACATAT
54639594 TTTAATACGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (15 bp):
AAAATATATACATAT
Found at i:54639822 original size:3 final size:3
Alignment explanation
Indices: 54639811--54639918 Score: 71
Period size: 3 Copynumber: 36.3 Consensus size: 3
54639801 TAAAAAAAAC
* * * * *
54639811 ATA ACA ATA ATA CTA ATA ATA ATA CTT ATA ATA ATA GTA A-A TATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA
* * * *
54639856 ATA ATA ATA ATA ATA GTA ATA ATA AAA GATG ATA AT- ATA TTA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA
*
54639900 ATA ATGA AGA A-A ATA ATA A
1 ATA AT-A ATA ATA ATA ATA A
54639919 AAATGTTGAA
Statistics
Matches: 79, Mismatches: 19, Indels: 14
0.71 0.17 0.12
Matches are distributed among these distances:
2 7 0.09
3 68 0.86
4 4 0.05
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:54641505 original size:112 final size:114
Alignment explanation
Indices: 54641308--54641724 Score: 419
Period size: 126 Copynumber: 3.5 Consensus size: 114
54641298 GAATCTATGG
* * * * * * *
54641308 TCTTCGATCTATTCCACTGCTACCCAAGGAGATAGAATTACTGGCTTCAATATACTCCACTGTAA
1 TCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATTGGCTTCAATGTACTCCACTGTAG
* * *
54641373 TCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCC-T-CTCTGAAA
66 TCACAGTGAGGTAAAATCTGCCATCTTCGATCTACTCCGTAATCTGAAA
*
54641420 TCTTCAATCTATTCTACTGCCAACCAGGGAGATAGAATTATTGGCTTCAATGTACTCCACTGTAG
1 TCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATTGGCTTCAATGTACTCCACTGTAG
*
54641485 TCACAGTGAGGTAAAATCTGCCATCTTCGATCTTCTCCACTTTGGGAGATAAGATCTGAAA
66 TCACAGTGAGGTAAAATCTGCCATCTTCGATCTACT-C-C-------G-T-A-ATCTGAAA
* *
54641546 TCTTCAATTTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCCACTGTAG
1 TCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATTGGCTTCAATGTACTCCACTGTAG
54641611 TCACA-TAGAGGTAAAATCCT-CCATCTTCGATCTACTCCACTTTGGGAGATAATATCTGAAA
66 TCACAGT-GAGGTAAAAT-CTGCCATCTTCGATCTACT-C-C-------G-T-A-ATCTGAAA
* * *
54641672 TCTTCAATCTATTCCACTGCCAACCAGAGAGATAGAATTACTGGATTCAATGT
1 TCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATTGGCTTCAATGT
54641725 CTGTTTAACT
Statistics
Matches: 268, Mismatches: 21, Indels: 18
0.87 0.07 0.06
Matches are distributed among these distances:
112 91 0.34
113 1 0.00
114 1 0.00
123 1 0.00
125 1 0.00
126 171 0.64
127 2 0.01
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (114 bp):
TCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATTGGCTTCAATGTACTCCACTGTAG
TCACAGTGAGGTAAAATCTGCCATCTTCGATCTACTCCGTAATCTGAAA
Found at i:54641638 original size:126 final size:126
Alignment explanation
Indices: 54641413--54641724 Score: 513
Period size: 126 Copynumber: 2.5 Consensus size: 126
54641403 TCTGCTCCTC
* *
54641413 TCTGAAATCTTCAATCTATTCTACTGCCAACCAGGGAGATAGAATTATTGGCTTCAATGTACTCC
1 TCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCC
*
54641478 ACTGTAGTCACAGTGAGGTAAAATCTGCCATCTTCGATCTTCTCCACTTTGGGAGATAAGA
66 ACTGTAGTCACAGTGAGGTAAAATCTGCCATCTTCGATCTACTCCACTTTGGGAGATAAGA
*
54641539 TCTGAAATCTTCAATTTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCC
1 TCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCC
*
54641604 ACTGTAGTCACA-TAGAGGTAAAATCCT-CCATCTTCGATCTACTCCACTTTGGGAGATAATA
66 ACTGTAGTCACAGT-GAGGTAAAAT-CTGCCATCTTCGATCTACTCCACTTTGGGAGATAAGA
* *
54641665 TCTGAAATCTTCAATCTATTCCACTGCCAACCAGAGAGATAGAATTA-CTGGATTCAATGT
1 TCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATC-GGCTTCAATGT
54641725 CTGTTTAACT
Statistics
Matches: 175, Mismatches: 8, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
125 2 0.01
126 171 0.98
127 2 0.01
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (126 bp):
TCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCC
ACTGTAGTCACAGTGAGGTAAAATCTGCCATCTTCGATCTACTCCACTTTGGGAGATAAGA
Found at i:54641856 original size:100 final size:100
Alignment explanation
Indices: 54641736--54642337 Score: 816
Period size: 100 Copynumber: 6.0 Consensus size: 100
54641726 TGTTTAACTA
* * * * **
54641736 CAATGTTGGGGAAGTA-AGATTCGCCGTCGTAGCTTCAATCTATTCCACTACACCGCTTGGGAAA
1 CAATGTCGGGGAAG-AGAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAA
* *
54641800 GTAAGATTCACCGTTGTGGCCTCAATCTTTTAATTG
65 GTAAGATTCGCCGTTGTGGCTTCAATCTTTTAATTG
* * * * *
54641836 CAATGTCGAGGAAGAGAGATTCACCGTTGTAGCTTCAATCTGTTCCACAGCACTGCCAGGAAAAG
1 CAATGTCGGGGAAGAGAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAAG
*
54641901 TAAGATTCGCCGTTGTGGCTTCAATCTTTTAATTA
66 TAAGATTCGCCGTTGTGGCTTCAATCTTTTAATTG
* * * ** *
54641936 CAATGTCGGGGAAGCGAGATTCGCTGTTGTAGCTTCAATCTGTTCCATTGCACTTCCTGGGAAAG
1 CAATGTCGGGGAAGAGAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAAG
* *
54642001 TAAGATTCGCCGTTATGGCTTGAATCTTTTAATTG
66 TAAGATTCGCCGTTGTGGCTTCAATCTTTTAATTG
** * * *
54642036 CAATGTTAGGGAAGCGAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACTGCCTGGGAAAG
1 CAATGTCGGGGAAGAGAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAAG
*
54642101 TAAGATTCGCCGTTGTGGCTTGAATCTTTTAATTG
66 TAAGATTCGCCGTTGTGGCTTCAATCTTTTAATTG
* * * *
54642136 CAATGTCGGGGAAGTGAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCATCGCCAGAG-AAG
1 CAATGTCGGGGAAGAGAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAAG
54642200 TAAGATTCGCCGTTGTGGCTTCAATCTTTTAATTG
66 TAAGATTCGCCGTTGTGGCTTCAATCTTTTAATTG
* * * *
54642235 CAATGTCGGGGAAGCA-AGATTTGCCGTTGTAGCTTCAATATGTTCCACTGCATCGCCAGAG-AA
1 CAATGTCGGGGAAG-AGAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAA
*
54642298 GTAAGATTCGCCATTGTGGCTTCAATCCTTTTAATTG
65 GTAAGATTCGCCGTTGTGGCTTCAAT-CTTTTAATTG
54642335 CAA
1 CAA
54642338 ACTATGGTGT
Statistics
Matches: 453, Mismatches: 46, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
99 121 0.27
100 332 0.73
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (100 bp):
CAATGTCGGGGAAGAGAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAGGGAAAG
TAAGATTCGCCGTTGTGGCTTCAATCTTTTAATTG
Found at i:54642320 original size:50 final size:50
Alignment explanation
Indices: 54641744--54642324 Score: 373
Period size: 49 Copynumber: 11.6 Consensus size: 50
54641734 TACAATGTTG
* * * * **
54641744 GGGAAGTAAGATTCGCCGTCGTAGCTTCAATCTATTCCACTACACCGCTT
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCATCGCCA
* * * ** * *
54641794 GGGAAAGTAAGATTCACCGTTGTGGCCTCAATCT-TTTAATTGCAAT-GTC-
1 GGG-AAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGC-ATCGCCA
* *
54641843 GAGGAAG-AGAGATTCACCGTTGTAGCTTCAATCTGTTCCACAGCA-CTGCCA
1 G-GGAAGTA-AGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCATC-GCCA
* * ** * * * *
54641894 GGAAAAGTAAGATTCGCCGTTGTGGCTTCAATCT-TTTAATTACAAT-GTCG
1 GG-GAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGC-ATCGCCA
** * * * *
54641944 GGGAAGCGAGATTCGCTGTTGTAGCTTCAATCTGTTCCATTGCA-CTTCCT
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCATC-GCCA
* * * ** * **
54641994 GGGAAAGTAAGATTCGCCGTTATGGCTTGAATCT-TTTAATTGCAAT-GTTA
1 GGG-AAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGC-ATCGCCA
** *
54642044 GGGAAGCGAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCA-CTGCCT
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCATC-GCCA
* * ** * * *
54642094 GGGAAAGTAAGATTCGCCGTTGTGGCTTGAATCT-TTTAATTGCAAT-GTCG
1 GGG-AAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGC-ATCGCCA
* *
54642144 GGGAAGTGAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCATCGCCA
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCATCGCCA
* * ** * * *
54642194 GAGAAGTAAGATTCGCCGTTGTGGCTTCAATCT-TTTAATTGCAAT-GTCG
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGC-ATCGCCA
* * *
54642243 GGGAAGCAAGATTTGCCGTTGTAGCTTCAATATGTTCCACTGCATCGCCA
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCATCGCCA
* * *
54642293 GAGAAGTAAGATTCGCCATTGTGGCTTCAATC
1 GGGAAGTAAGATTCGCCGTTGTAGCTTCAATC
54642325 CTTTTAATTG
Statistics
Matches: 397, Mismatches: 105, Indels: 58
0.71 0.19 0.10
Matches are distributed among these distances:
48 1 0.00
49 147 0.37
50 141 0.36
51 107 0.27
52 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (50 bp):
GGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCATCGCCA
Found at i:54652680 original size:27 final size:27
Alignment explanation
Indices: 54652624--54652694 Score: 108
Period size: 27 Copynumber: 2.6 Consensus size: 27
54652614 ATAAAAAATA
**
54652624 ACCAAAATATTATAACTTTTTTTTATTT
1 ACCAAAATATTATAA-AATTTTTTATTT
54652652 ACCAAAATATTATAAAATTTTTTATTT
1 ACCAAAATATTATAAAATTTTTTATTT
54652679 ACCAAAATA-TATAAAA
1 ACCAAAATATTATAAAA
54652695 AAAAAACAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
26 7 0.17
27 19 0.46
28 15 0.37
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (27 bp):
ACCAAAATATTATAAAATTTTTTATTT
Found at i:54653149 original size:29 final size:27
Alignment explanation
Indices: 54653117--54653182 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 27
54653107 AAAATAGTTT
*
54653117 AATTTAATAACTCTATTTTAATTTTAAAA
1 AATTTAATAA-ACTATTTTAATTTT-AAA
* *
54653146 AATTAAATTAAACTATTTTAATTTTATA
1 AATTTAA-TAAACTATTTTAATTTTAAA
54653174 AATTTAATA
1 AATTTAATA
54653183 TATTCCCTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 2 0.06
28 8 0.25
29 19 0.59
30 3 0.09
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (27 bp):
AATTTAATAAACTATTTTAATTTTAAA
Found at i:54653407 original size:18 final size:19
Alignment explanation
Indices: 54653368--54653463 Score: 124
Period size: 19 Copynumber: 5.2 Consensus size: 19
54653358 ATTTTATATT
54653368 TTAAATGAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
* *
54653387 TTAAATGAGAATAG-TTTA
1 TTAAATGAAAATAGAGTTA
*
54653405 TTAAATTAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
* *
54653424 TTAAATGAGAATAG-TTTA
1 TTAAATGAAAATAGAGTTA
*
54653442 TTAAATTAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
54653461 TTA
1 TTA
54653464 CTTAATTAGA
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
18 30 0.47
19 34 0.53
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.38
Consensus pattern (19 bp):
TTAAATGAAAATAGAGTTA
Found at i:54653409 original size:37 final size:37
Alignment explanation
Indices: 54653368--54653463 Score: 183
Period size: 37 Copynumber: 2.6 Consensus size: 37
54653358 ATTTTATATT
*
54653368 TTAAATGAAAATAGAGTTATTAAATGAGAATAGTTTA
1 TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
54653405 TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
1 TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
54653442 TTAAATTAAAATAGAGTTATTA
1 TTAAATTAAAATAGAGTTATTA
54653464 CTTAATTAGA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.38
Consensus pattern (37 bp):
TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
Found at i:54654075 original size:27 final size:27
Alignment explanation
Indices: 54654037--54654112 Score: 102
Period size: 27 Copynumber: 2.9 Consensus size: 27
54654027 TTTTAGTCTT
54654037 TTGGCACCATTGGTGCCGCCAATCACA
1 TTGGCACCATTGGTGCCGCCAATCACA
* * *
54654064 TTGGCACCATTGGTGCCG-CAAACTCT
1 TTGGCACCATTGGTGCCGCCAATCACA
54654090 TTGGCACC-TTGAGTGCCGCCAAT
1 TTGGCACCATTG-GTGCCGCCAAT
54654113 GTGATTGGCC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
25 3 0.07
26 19 0.44
27 21 0.49
ACGTcount: A:0.20, C:0.32, G:0.24, T:0.25
Consensus pattern (27 bp):
TTGGCACCATTGGTGCCGCCAATCACA
Found at i:54654105 original size:26 final size:26
Alignment explanation
Indices: 54654036--54654108 Score: 94
Period size: 26 Copynumber: 2.8 Consensus size: 26
54654026 ATTTTAGTCT
*
54654036 TTTGGCACCATTGGTGCCGCCAATCAC
1 TTTGGCACCATTGGTGCCG-CAAACAC
* *
54654063 ATTGGCACCATTGGTGCCGCAAACTC
1 TTTGGCACCATTGGTGCCGCAAACAC
54654089 TTTGGCACC-TTGAGTGCCGC
1 TTTGGCACCATTG-GTGCCGC
54654109 CAATGTGATT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
25 3 0.07
26 20 0.49
27 18 0.44
ACGTcount: A:0.18, C:0.32, G:0.25, T:0.26
Consensus pattern (26 bp):
TTTGGCACCATTGGTGCCGCAAACAC
Found at i:54654196 original size:27 final size:28
Alignment explanation
Indices: 54654166--54654227 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 28
54654156 TTTTTTCGGT
54654166 ATATTTTGGTAAAT-AAAAAAAATTATA
1 ATATTTTGGTAAATAAAAAAAAATTATA
54654193 ATATTTTGGTAAATAAAAAAAAATTATA
1 ATATTTTGGTAAATAAAAAAAAATTATA
54654221 ATATTTT
1 ATATTTT
54654228 AGTTATTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 14 0.41
28 20 0.59
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.40
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAATTATA
Found at i:54658113 original size:21 final size:19
Alignment explanation
Indices: 54658087--54658125 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
54658077 TTTCTTTCAA
54658087 TTCCTTATATACTATTATTCC
1 TTCCTTATAT--TATTATTCC
*
54658108 TTCCTTCTATTATTATTC
1 TTCCTTATATTATTATTC
54658126 TTCAGCTGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
21 9 0.53
ACGTcount: A:0.21, C:0.23, G:0.00, T:0.56
Consensus pattern (19 bp):
TTCCTTATATTATTATTCC
Found at i:54663817 original size:17 final size:17
Alignment explanation
Indices: 54663784--54663821 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
54663774 TAACCTACCT
54663784 AATATATCACATCTATA
1 AATATATCACATCTATA
*
54663801 AATA-ATCATATCATATA
1 AATATATCACATC-TATA
54663818 AATA
1 AATA
54663822 CATAAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (17 bp):
AATATATCACATCTATA
Found at i:54666739 original size:374 final size:374
Alignment explanation
Indices: 54666050--54667169 Score: 2159
Period size: 374 Copynumber: 3.0 Consensus size: 374
54666040 GCAGTTGTGG
*
54666050 CATATGAAGTTGGGACATGCCAGCGAAAAATCCTTGCAAATTCTGGAAAAGCAAGGATTGTTGAA
1 CATATGAAGTTGGGACATGCCAGCGAAAAATCCTTGCAAATTCTGGCAAAGCAAGGATTGTTGAA
*
54666115 AGGTGCAAAGGCTTACAAATTAAAATTTTGTGAGCATTGTGTTCTGGGAAAGCAAAAGAGAGTGA
66 AGGTGCAAAGGCTTACAAATTAAAATTTTGCGAGCATTGTGTTCTGGGAAAGCAAAAGAGAGTGA
54666180 AATTCGGTACTGCTATCCATAATACAAAAGGTATTTTGGAATATGTTCACTCAGATGTGTGGGGG
131 AATTCGGTACTGCTATCCATAATACAAAAGGTATTTTGGAATATGTTCACTCAGATGTGTGGGGG
54666245 CCTTCCAAGACACCTTCATTGGGAGGAAAACACTACTTTGTTACTTTTGTTGATGACTTTTCCAG
196 CCTTCCAAGACACCTTCATTGGGAGGAAAACACTACTTTGTTACTTTTGTTGATGACTTTTCCAG
54666310 AAGAGTTTGGGTGTATACCATGAGAACTAAGGATGAAGTGCTTAGAGTTTTTCTTAAATGGAAAA
261 AAGAGTTTGGGTGTATACCATGAGAACTAAGGATGAAGTGCTTAGAGTTTTTCTTAAATGGAAAA
54666375 CTATGATCGAAAACCAGACTGGCAAGAAAATCAAGCGGCTTAGGACGGA
326 CTATGATCGAAAACCAGACTGGCAAGAAAATCAAGCGGCTTAGGACGGA
*
54666424 CATATGAAGTTGGGACATGCCAGCGAAAAATCTTTGCAAATTCTGGCAAAGCAAGGATTGTTGAA
1 CATATGAAGTTGGGACATGCCAGCGAAAAATCCTTGCAAATTCTGGCAAAGCAAGGATTGTTGAA
54666489 AGGTGCAAAGGCTTACAAATTAAAATTTTGCGAGCATTGTGTTCTGGGAAAGCAAAAGAGAGTGA
66 AGGTGCAAAGGCTTACAAATTAAAATTTTGCGAGCATTGTGTTCTGGGAAAGCAAAAGAGAGTGA
*
54666554 AATTCGGTACTGCTATCCATAATACAAAAGGTACTTTGGAATATGTTCACTCAGATGTGTGGGGG
131 AATTCGGTACTGCTATCCATAATACAAAAGGTATTTTGGAATATGTTCACTCAGATGTGTGGGGG
54666619 CCTTCCAAGACACCTTCATTGGGAGGAAAACACTACTTTGTTACTTTTGTTGATGACTTTTCCAG
196 CCTTCCAAGACACCTTCATTGGGAGGAAAACACTACTTTGTTACTTTTGTTGATGACTTTTCCAG
54666684 AAGAGTTTGGGTGTATACCATGAGAACTAAGGATGAAGTGCTTAGAGTTTTTCTTAAATGGAAAA
261 AAGAGTTTGGGTGTATACCATGAGAACTAAGGATGAAGTGCTTAGAGTTTTTCTTAAATGGAAAA
54666749 CTATGATCGAAAACCAGACTGGCAAGAAAATCAAGCGGCTTAGGACGGA
326 CTATGATCGAAAACCAGACTGGCAAGAAAATCAAGCGGCTTAGGACGGA
54666798 CATATGAAGTTGGGACATGCCAGCGAAAAATCCTTGCAAATTCTGGCAAAGCAAGGATTGTTGAA
1 CATATGAAGTTGGGACATGCCAGCGAAAAATCCTTGCAAATTCTGGCAAAGCAAGGATTGTTGAA
* *
54666863 AGGTGCAAAGGCTTACAAATTAAAATCTTGCGAGCATTGTATTCTGGGAAAGCAAAAGAGAGTGA
66 AGGTGCAAAGGCTTACAAATTAAAATTTTGCGAGCATTGTGTTCTGGGAAAGCAAAAGAGAGTGA
* * *
54666928 AATTTGGTACTGCTATCCATAATACAAAAGGTATTTTGGAATATGTTTACTCAGATGTATGGGGG
131 AATTCGGTACTGCTATCCATAATACAAAAGGTATTTTGGAATATGTTCACTCAGATGTGTGGGGG
54666993 CCTTCCAAGACACCTTCATTGGGAGGAAAACACTACTTTGTTACTTTTGTTGATGACTTTTCCAG
196 CCTTCCAAGACACCTTCATTGGGAGGAAAACACTACTTTGTTACTTTTGTTGATGACTTTTCCAG
54667058 AAGAGTTTGGGTGTATACCATGAGAACTAAGGATGAAGTGCTTAGAGTTTTTCTTAAATGGAAAA
261 AAGAGTTTGGGTGTATACCATGAGAACTAAGGATGAAGTGCTTAGAGTTTTTCTTAAATGGAAAA
54667123 CTATGATCGAAAACCAGACTGGCAAGAAAATCAAGCGGCTTAGGACG
326 CTATGATCGAAAACCAGACTGGCAAGAAAATCAAGCGGCTTAGGACG
54667170 AACAATGGAG
Statistics
Matches: 735, Mismatches: 11, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
374 735 1.00
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (374 bp):
CATATGAAGTTGGGACATGCCAGCGAAAAATCCTTGCAAATTCTGGCAAAGCAAGGATTGTTGAA
AGGTGCAAAGGCTTACAAATTAAAATTTTGCGAGCATTGTGTTCTGGGAAAGCAAAAGAGAGTGA
AATTCGGTACTGCTATCCATAATACAAAAGGTATTTTGGAATATGTTCACTCAGATGTGTGGGGG
CCTTCCAAGACACCTTCATTGGGAGGAAAACACTACTTTGTTACTTTTGTTGATGACTTTTCCAG
AAGAGTTTGGGTGTATACCATGAGAACTAAGGATGAAGTGCTTAGAGTTTTTCTTAAATGGAAAA
CTATGATCGAAAACCAGACTGGCAAGAAAATCAAGCGGCTTAGGACGGA
Found at i:54667708 original size:21 final size:21
Alignment explanation
Indices: 54667682--54667722 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
54667672 AGACGAGCAA
* *
54667682 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
54667703 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
54667723 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:54678423 original size:88 final size:87
Alignment explanation
Indices: 54678194--54678569 Score: 259
Period size: 90 Copynumber: 4.3 Consensus size: 87
54678184 AAAATGTCAA
* * * * *
54678194 CATCGTAGATAAAACAAACCAAAACAATCCA-ACTAT-TGATAATAAACCAAACATGAAAGATGT
1 CATCATAGAAAAAACAAACCAAAACAA-CCAGAATATGT-ATAATAAAACAAACATGAAAGATGC
* *
54678257 CGAT-AAAAGAAA-TTTACTCA-A-
64 CGATAAAAAAAAACATTA-TCACAT
** * * *** * * * **
54678278 CATCATAGCTAAAACAAACTAAAACCATTTGAACATGAACAATAAAACTGACATGAAAGATGCCG
1 CATCATAGAAAAAACAAACCAAAACAACCAGAATATGTATAATAAAACAAACATGAAAGATGCCG
54678343 ATAAAAGAAAAACATTATCA-AT
66 ATAAAA-AAAAACATTATCACAT
* * * *
54678365 GGCATCCTA-AAAAAACAAACCAAAGCAACTCA-AATATAG-ATAATAAAACAAATATGAAAAAT
1 --CATCATAGAAAAAACAAACCAAAACAAC-CAGAATAT-GTATAATAAAACAAACATGAAAGAT
* *
54678427 GCCGATTAGAAAAAACTATTATCAGCAT
62 GCCGATAAAAAAAAAC-ATTATCA-CAT
* * *
54678455 CATCATAGGGAAAAACAAACCAAAACAACCAGAATATGTGTAGTAAAACAAACATGAAAGATGCC
1 CATCATA-GAAAAAACAAACCAAAACAACCAGAATATGTATAATAAAACAAACATGAAAGATGCC
* * *
54678520 GACAAAACAAAAACACTATCTGCAT
65 GATAAAA-AAAAACATTATC-ACAT
**
54678545 CATCATAGGTAAAACAAACCCAAAA
1 CATCATAGAAAAAACAAA-CCAAAA
54678570 AAGAAAAAAA
Statistics
Matches: 225, Mismatches: 47, Indels: 34
0.74 0.15 0.11
Matches are distributed among these distances:
84 50 0.22
85 3 0.01
86 8 0.04
87 9 0.04
88 57 0.25
89 20 0.09
90 72 0.32
91 6 0.03
ACGTcount: A:0.53, C:0.18, G:0.11, T:0.18
Consensus pattern (87 bp):
CATCATAGAAAAAACAAACCAAAACAACCAGAATATGTATAATAAAACAAACATGAAAGATGCCG
ATAAAAAAAAACATTATCACAT
Found at i:54692596 original size:23 final size:23
Alignment explanation
Indices: 54692566--54692613 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
54692556 GTGCAACTAC
54692566 TTAATTTGCTGGTTACTCGCCAT
1 TTAATTTGCTGGTTACTCGCCAT
54692589 TTAATTTGCTGGTTACTCGCCAT
1 TTAATTTGCTGGTTACTCGCCAT
54692612 TT
1 TT
54692614 TTAGAAGACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.17, C:0.21, G:0.17, T:0.46
Consensus pattern (23 bp):
TTAATTTGCTGGTTACTCGCCAT
Found at i:54692666 original size:23 final size:24
Alignment explanation
Indices: 54692625--54692680 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
54692615 TAGAAGACTT
*
54692625 TTTATATTAGTAAACTTATATATA
1 TTTATATTAGTAAAATTATATATA
*
54692649 TTTAT-TTATTAAAATTATATATAA
1 TTTATATTAGTAAAATTATATAT-A
54692673 TTT-TATTA
1 TTTATATTA
54692681 ACAATTTTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 16 0.57
24 12 0.43
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (24 bp):
TTTATATTAGTAAAATTATATATA
Found at i:54693216 original size:21 final size:21
Alignment explanation
Indices: 54693192--54693231 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
54693182 ATGGGACAGT
*
54693192 TGACATGGCTAGTTAACTAAC
1 TGACATGGCCAGTTAACTAAC
*
54693213 TGACGTGGCCAGTTAACTA
1 TGACATGGCCAGTTAACTA
54693232 CTTGATATGA
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:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (21 bp):
TGACATGGCCAGTTAACTAAC
Found at i:54695352 original size:31 final size:29
Alignment explanation
Indices: 54695282--54695355 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
54695272 GGCTCAGGTT
*
54695282 ACATTTTAGTCACTTATGTTTAAAATGTT
1 ACATTTTAGTCACTTATGTTTAAAATGTA
* ***
54695311 ACGTTTTAGTCACTTATGTTATCACGTTGTA
1 ACATTTTAGTCACTTATGTT-T-AAAATGTA
54695342 ACATTTTAGTCACT
1 ACATTTTAGTCACT
54695356 GAGCCGTTAG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 19 0.51
30 1 0.03
31 17 0.46
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (29 bp):
ACATTTTAGTCACTTATGTTTAAAATGTA
Found at i:54695589 original size:18 final size:18
Alignment explanation
Indices: 54695562--54695601 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
54695552 CCATTCTCCA
54695562 TTTC-TTTCAACGTAGTT
1 TTTCTTTTCAACGTAGTT
54695579 TTTCTTTTCAACGTAGTT
1 TTTCTTTTCAACGTAGTT
54695597 TTTCT
1 TTTCT
54695602 ATGTTTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.15, C:0.17, G:0.10, T:0.57
Consensus pattern (18 bp):
TTTCTTTTCAACGTAGTT
Found at i:54700795 original size:13 final size:13
Alignment explanation
Indices: 54700777--54700803 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
54700767 TAACCAAAAG
54700777 ATTAGTTAAATTA
1 ATTAGTTAAATTA
54700790 ATTAGTTAAATTA
1 ATTAGTTAAATTA
54700803 A
1 A
54700804 CTTTTTGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (13 bp):
ATTAGTTAAATTA
Found at i:54700942 original size:152 final size:153
Alignment explanation
Indices: 54700638--54700913 Score: 383
Period size: 152 Copynumber: 1.8 Consensus size: 153
54700628 TAACCAAAAG
* * *
54700638 ATTAGTCAAATTAACTTTTTGAATTTTTTGTGAATATGTCTATCCCCGAGGTGGAGAAAAGTATT
1 ATTAGTCAAATTAACTTTTTGAAGTTTTTGTGAATATGTCCATCCCCGAGGTGGAGAAAAATATT
* * * **
54700703 TATAGAGGGCAAACATCATTAAATTCTTCGATGTAGTTCTAAAATATAAATATTAATTGGGGTTT
66 TATAGAGGGCAAACATCATTAAATTCTTCGAAGTAGTTCTAAAATATAAATATCAATTGGAGAGT
*
54700768 AACCAAAAGATTAGTTAAATT-A
131 AACCAAAAGAATAGTTAAATTAA
*
54700790 ATTAGTTAAATTAACTTTTTGAAGTTTTTGTGAATATGTCCATCCCCGAGGTGGAGAAAAATATT
1 ATTAGTCAAATTAACTTTTTGAAGTTTTTGTGAATATGTCCATCCCCGAGGTGGAGAAAAATATT
* *** * * *
54700855 TATGGAGGGCTCTCAATCATTAAATTCTTCGAAGTAGTTTTAAAATGTAGATATCAATT
66 TATAGAGGGCAAAC-ATCATTAAATTCTTCGAAGTAGTTCTAAAATATAAATATCAATT
54700914 AATGAGAGTA
Statistics
Matches: 110, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
152 71 0.65
153 39 0.35
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (153 bp):
ATTAGTCAAATTAACTTTTTGAAGTTTTTGTGAATATGTCCATCCCCGAGGTGGAGAAAAATATT
TATAGAGGGCAAACATCATTAAATTCTTCGAAGTAGTTCTAAAATATAAATATCAATTGGAGAGT
AACCAAAAGAATAGTTAAATTAA
Found at i:54704223 original size:2 final size:2
Alignment explanation
Indices: 54704213--54704247 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
54704203 AAATATATAT
*
54704213 AC AC CC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
54704248 AAAGAGATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.51, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:54711316 original size:13 final size:13
Alignment explanation
Indices: 54711298--54711322 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54711288 ATTATTAATA
54711298 TTATTTTGTGTGT
1 TTATTTTGTGTGT
54711311 TTATTTTGTGTG
1 TTATTTTGTGTG
54711323 CATTTGATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:54713115 original size:41 final size:41
Alignment explanation
Indices: 54712979--54713142 Score: 186
Period size: 41 Copynumber: 4.0 Consensus size: 41
54712969 GTGAAATTAT
* * *
54712979 TCAGACTATACGTCTAGCAGGCTAAGTGCCGGTGAATTGAA
1 TCAGACTATAAGCCTAGCAGGCTAAGTGCCGGTGAACTGAA
* * * *
54713020 TCGGACTATACGTCTAGCATGCTAAGTGCCGGTGAACTGAA
1 TCAGACTATAAGCCTAGCAGGCTAAGTGCCGGTGAACTGAA
* *
54713061 TCAGGCTACAAGCCTAGCAGGCTAAGTGCCGGTGAACTGAA
1 TCAGACTATAAGCCTAGCAGGCTAAGTGCCGGTGAACTGAA
* * * *
54713102 TTAAACTATAAGCCTATCAGG-TGAAGTGCCAGTGAATCTGA
1 TCAGACTATAAGCCTAGCAGGCT-AAGTGCCGGTGAA-CTGA
54713143 TTCTATGCAT
Statistics
Matches: 106, Mismatches: 15, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
40 1 0.01
41 101 0.95
42 4 0.04
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.23
Consensus pattern (41 bp):
TCAGACTATAAGCCTAGCAGGCTAAGTGCCGGTGAACTGAA
Found at i:54721580 original size:425 final size:425
Alignment explanation
Indices: 54720790--54721641 Score: 1704
Period size: 425 Copynumber: 2.0 Consensus size: 425
54720780 TCAATTGGTG
54720790 TCTCGTAAGTTTTTGGCATCCTAGTGCAAATTAGGATTCTTTGGTAGTTTGGTTCACACTCTCTA
1 TCTCGTAAGTTTTTGGCATCCTAGTGCAAATTAGGATTCTTTGGTAGTTTGGTTCACACTCTCTA
54720855 ATTGGTTGATATAAACTCTGATAAAGAACTCACAAGATTGAATTCGACCTCATTGAGAATTTGAT
66 ATTGGTTGATATAAACTCTGATAAAGAACTCACAAGATTGAATTCGACCTCATTGAGAATTTGAT
54720920 TTTTTCTTTTTGAGTGATTAACGGTGAGGTTTGATAACTTTTATTTTTGAGTGTTGAGTGTTTTG
131 TTTTTCTTTTTGAGTGATTAACGGTGAGGTTTGATAACTTTTATTTTTGAGTGTTGAGTGTTTTG
54720985 CAGGTTTTAAAAAAAATGTCTACAGGTGATAATACTAGTGACATATTTAAAAAATTCCAACAACA
196 CAGGTTTTAAAAAAAATGTCTACAGGTGATAATACTAGTGACATATTTAAAAAATTCCAACAACA
54721050 GTTGGACGAACAGGCTGCTGCACTTCGAGCGTTGACTGCTACTATCAATGAGGTGCGGTTGAATC
261 GTTGGACGAACAGGCTGCTGCACTTCGAGCGTTGACTGCTACTATCAATGAGGTGCGGTTGAATC
54721115 AAGAGCCTCAATATCGAGATCAAATTAAAGACGATGTGGATAACCAGCCTCCTGCTCATAGGCGC
326 AAGAGCCTCAATATCGAGATCAAATTAAAGACGATGTGGATAACCAGCCTCCTGCTCATAGGCGC
54721180 GCTCCTCGGCGTGTCCTTAGAACTGATTATGATCT
391 GCTCCTCGGCGTGTCCTTAGAACTGATTATGATCT
54721215 TCTCGTAAGTTTTTGGCATCCTAGTGCAAATTAGGATTCTTTGGTAGTTTGGTTCACACTCTCTA
1 TCTCGTAAGTTTTTGGCATCCTAGTGCAAATTAGGATTCTTTGGTAGTTTGGTTCACACTCTCTA
54721280 ATTGGTTGATATAAACTCTGATAAAGAACTCACAAGATTGAATTCGACCTCATTGAGAATTTGAT
66 ATTGGTTGATATAAACTCTGATAAAGAACTCACAAGATTGAATTCGACCTCATTGAGAATTTGAT
54721345 TTTTTCTTTTTGAGTGATTAACGGTGAGGTTTGATAACTTTTATTTTTGAGTGTTGAGTGTTTTG
131 TTTTTCTTTTTGAGTGATTAACGGTGAGGTTTGATAACTTTTATTTTTGAGTGTTGAGTGTTTTG
54721410 CAGGTTTTAAAAAAAATGTCTACAGGTGATAATACTAGTGACATATTTAAAAAATTCCAACAACA
196 CAGGTTTTAAAAAAAATGTCTACAGGTGATAATACTAGTGACATATTTAAAAAATTCCAACAACA
54721475 GTTGGACGAACAGGCTGCTGCACTTCGAGCGTTGACTGCTACTATCAATGAGGTGCGGTTGAATC
261 GTTGGACGAACAGGCTGCTGCACTTCGAGCGTTGACTGCTACTATCAATGAGGTGCGGTTGAATC
54721540 AAGAGCCTCAATATCGAGATCAAATTAAAGACGATGTGGATAACCAGCCTCCTGCTCATAGGCGC
326 AAGAGCCTCAATATCGAGATCAAATTAAAGACGATGTGGATAACCAGCCTCCTGCTCATAGGCGC
54721605 GCTCCTCGGCGTGTCCTTAGAACTGATTATGATCT
391 GCTCCTCGGCGTGTCCTTAGAACTGATTATGATCT
54721640 TC
1 TC
54721642 ATGATCGTGG
Statistics
Matches: 427, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
425 427 1.00
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (425 bp):
TCTCGTAAGTTTTTGGCATCCTAGTGCAAATTAGGATTCTTTGGTAGTTTGGTTCACACTCTCTA
ATTGGTTGATATAAACTCTGATAAAGAACTCACAAGATTGAATTCGACCTCATTGAGAATTTGAT
TTTTTCTTTTTGAGTGATTAACGGTGAGGTTTGATAACTTTTATTTTTGAGTGTTGAGTGTTTTG
CAGGTTTTAAAAAAAATGTCTACAGGTGATAATACTAGTGACATATTTAAAAAATTCCAACAACA
GTTGGACGAACAGGCTGCTGCACTTCGAGCGTTGACTGCTACTATCAATGAGGTGCGGTTGAATC
AAGAGCCTCAATATCGAGATCAAATTAAAGACGATGTGGATAACCAGCCTCCTGCTCATAGGCGC
GCTCCTCGGCGTGTCCTTAGAACTGATTATGATCT
Found at i:54722190 original size:18 final size:18
Alignment explanation
Indices: 54722169--54722207 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
54722159 GATTGAGAGT
*
54722169 GAAAAGAAATGTGAAACA
1 GAAAAGAAATGTGAAAAA
*
54722187 GAAAAGAAATTTGAAAAA
1 GAAAAGAAATGTGAAAAA
54722205 GAA
1 GAA
54722208 GTTGAAGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.64, C:0.03, G:0.21, T:0.13
Consensus pattern (18 bp):
GAAAAGAAATGTGAAAAA
Found at i:54727847 original size:29 final size:29
Alignment explanation
Indices: 54727746--54727885 Score: 104
Period size: 30 Copynumber: 4.7 Consensus size: 29
54727736 AAGCAAAAAA
* *
54727746 TAAAGATTACATTTTAACCCCTATACTTTT-
1 TAAA-ATTACATTTTAACCCC-AAAATTTTC
* * * *
54727776 TGAAATTTCTATTTTGACCCCAAACCTTTT-
1 TAAAATTAC-ATTTTAACCCCAAA-ATTTTC
54727806 TAAAATTCACATTTTAACCCCAAAATTTTC
1 TAAAATT-ACATTTTAACCCCAAAATTTTC
* * **
54727836 TAAAAGTACATTTTGACCCTTAAATTTTC
1 TAAAATTACATTTTAACCCCAAAATTTTC
* *
54727865 TTAAAATTGCACTTTAACCCC
1 -TAAAATTACATTTTAACCCC
54727886 TAAACTCTCA
Statistics
Matches: 88, Mismatches: 17, Indels: 10
0.77 0.15 0.09
Matches are distributed among these distances:
29 29 0.33
30 58 0.66
31 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.04, T:0.40
Consensus pattern (29 bp):
TAAAATTACATTTTAACCCCAAAATTTTC
Found at i:54729514 original size:3 final size:3
Alignment explanation
Indices: 54729506--54729538 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
54729496 TTAAAAGAGT
*
54729506 ATA ATA ATA ATA ATA ATG ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
54729539 TGAAATTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:54730234 original size:20 final size:20
Alignment explanation
Indices: 54730205--54730248 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
54730195 AGTTACGAAA
*
54730205 AAAAGAAAAAA-AATAAAGAG
1 AAAAGAAAAAATAAAAAAG-G
*
54730225 AAAAGTAAAAATAAAAAAGG
1 AAAAGAAAAAATAAAAAAGG
54730245 AAAA
1 AAAA
54730249 TAGAACTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.07
Consensus pattern (20 bp):
AAAAGAAAAAATAAAAAAGG
Found at i:54730980 original size:40 final size:40
Alignment explanation
Indices: 54730936--54731047 Score: 118
Period size: 44 Copynumber: 2.7 Consensus size: 40
54730926 ACACTGCGCT
* *
54730936 TTAGGGAAATAAGACTTGATGCGATCTGCTCTACTACTGC
1 TTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGC
* * *
54730976 TTAGGGAGATAAGATCTGGTTTCTTTTG-TCTGCTCCACTACTGC
1 TTAGGGAGATAAGA-CTTGATGC----GATCTGCTCCACTACTGC
*
54731020 TTAGGGAGATAATACTTGATGCGATCTG
1 TTAGGGAGATAAGACTTGATGCGATCTG
54731048 TGGTTTTAAT
Statistics
Matches: 57, Mismatches: 9, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
39 1 0.02
40 17 0.30
41 5 0.09
43 5 0.09
44 28 0.49
45 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (40 bp):
TTAGGGAGATAAGACTTGATGCGATCTGCTCCACTACTGC
Found at i:54731356 original size:174 final size:173
Alignment explanation
Indices: 54731051--54731659 Score: 645
Period size: 174 Copynumber: 3.5 Consensus size: 173
54731041 CGATCTGTGG
54731051 TTTTAATCCGCTCCGCTGTAACTTCAGGGAGATAGGA-TAGTGTCTTCGATCTGCTCCGCTGTAA
1 TTTTAATCCGCTCCGCTGTAACTTCAGGGAGATAGGATTA-TGTCTTCGATCTGCTCCGCTGTAA
* * *
54731115 CCTCAGGGGGATAAGATCTGAAATTCTTCGGTCTACTCTACTGTAACCTCAGGGAGATAAGACCT
65 CCTCAGGGAGATAAGATCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCT
* *
54731180 GGTGCGATCTGCTCTACTGTAACTTCAGAGAGATAAGGTCCTTT
130 GGTGCGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCCTGT
* * * *
54731224 ATTTTAAACCGTTCCACTGTAACTTCAGGGAGATAGGATTATGTCTTCAATCTGCTCCGCTGTAA
1 -TTTTAATCCGCTCCGCTGTAACTTCAGGGAGATAGGATTATGTCTTCGATCTGCTCCGCTGTAA
54731289 CCTCAGGGAGATAAGATCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCT
65 CCTCAGGGAGATAAGATCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCT
54731354 GGTGCGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCCTGT
130 GGTGCGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCCTGT
* ** * * * * * * *
54731398 CTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGAAAGTCTTCGGTCTACTCCACTGT
1 TTTTAATCCGCTCCGCTGTAACTTCAGGGAGATAGGAT-T--ATGTCTTCGATCTGCTCCGCTGT
* * * * * * *
54731463 AACCTCAGGGAGATAAGACCTG---G--TGCGATCTGCTCTACTGTAACTTCAGAGAGATAAGAT
63 AACCTCAGGGAGATAAGATCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGA-
* ** *** * * * * **
54731523 CTTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAATATTATGT
127 C--CTGGTGCGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCCTGT
* * * * * * * * *
54731572 CTTCAATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGAAAGTCTTCGGTCTACTCCACTGT
1 TTTTAATCCGCTCCGCTGTAACTTCAGGGAGATAGGAT-T--ATGTCTTCGATCTGCTCCGCTGT
*
54731637 AACCTCAGGGAGATAAGACCTGA
63 AACCTCAGGGAGATAAGATCTGA
54731660 TGCGATCTAC
Statistics
Matches: 384, Mismatches: 43, Indels: 15
0.87 0.10 0.03
Matches are distributed among these distances:
171 30 0.08
172 1 0.00
173 30 0.08
174 282 0.73
175 2 0.01
176 39 0.10
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (173 bp):
TTTTAATCCGCTCCGCTGTAACTTCAGGGAGATAGGATTATGTCTTCGATCTGCTCCGCTGTAAC
CTCAGGGAGATAAGATCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTG
GTGCGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCCTGT
Found at i:54731407 original size:130 final size:129
Alignment explanation
Indices: 54731239--54731958 Score: 683
Period size: 130 Copynumber: 5.5 Consensus size: 129
54731229 AAACCGTTCC
* ** * * *
54731239 ACTGTAACTTCAGGGAGATAGGATTATGTCTTCAATCTGCTCCGCTGTAACCTCAGGGAGATAAG
1 ACTGTAACTTCAGGGAGATAAGATCCTGTCTTCGATCTGCTCCACTGTAACTTCAGGGAGATAAG
* * *
54731304 ATCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTG-G-TGCGATCTGCT
66 ATCT---AGTCTTCGATCTACTCCGCTGTAACCTCAGGGAGATAAGACCTGAGCTGCGATCTACT
54731367 CT
128 CT
* * *
54731369 ACTGTAACTTCAGAGAGATAAGATCCTGTCTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAG
1 ACTGTAACTTCAGGGAGATAAGATCCTGTCTTCGATCTGCTCCACTGTAACTTCAGGGAGATAAG
* * *
54731434 ATCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTG-G-TGCGATCTGCT
66 ATCT---AGTCTTCGATCTACTCCGCTGTAACCTCAGGGAGATAAGACCTGAGCTGCGATCTACT
54731497 CT
128 CT
* * * * ** *
54731499 ACTGTAACTTCAGAGAGATAAGATCTTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAA
1 ACTGTAACTTCAGGGAGATAAGATCCTGT-CTTCGATCTGCTCCACTGTAACTTCAGGGAGATAA
* * * * * *
54731564 TAT-TATGTCTTCAATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGAAAGTCTTCGGTCTA
65 GATCTA-GTCTTCGATCTACTCCGCTGTAACCTCAGGGAGATAAGACCTG--AG-CTGCGATCTA
*
54731628 CTCC
126 CTCT
* * * * * *
54731632 ACTGTAACCTCAGGGAGATAAGA-CCTG-ATGCGATCTACTCTACTGTAACTTCAGAGAGATAAG
1 ACTGTAACTTCAGGGAGATAAGATCCTGTCTTCGATCTGCTCCACTGTAACTTCAGGGAGATAAG
* * *
54731695 ATTCT-GTCTTCGATCTACTCCGCTGTAACCTCAGGGAGATAAGATCTGAAAGTCTTCGGTCTAC
66 A-TCTAGTCTTCGATCTACTCCGCTGTAACCTCAGGGAGATAAGACCTG--AG-CTGCGATCTAC
54731759 TCT
127 TCT
* * * * * *
54731762 ACTGTAACCTCAGGGAGATAAGA-CCTG-GTGCGATCTGCTCTACTGTAACTTTAGAGAGATAAG
1 ACTGTAACTTCAGGGAGATAAGATCCTGTCTTCGATCTGCTCCACTGTAACTTCAGGGAGATAAG
* * * * *
54731825 ATCCT-GTCTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTAC
66 AT-CTAGTCTTCGATCTACTCCGCTGTAACCTCAGGGAGATAAGACCTG--A-GCTGCGATCTAC
*
54731889 TCC
127 TCT
* * * * *
54731892 ACTGTAACCTCAGGGAGATAAGA-CCTG-GTGCGATCTGCTCTACTGTAACTTCAGAGAGATAAG
1 ACTGTAACTTCAGGGAGATAAGATCCTGTCTTCGATCTGCTCCACTGTAACTTCAGGGAGATAAG
54731955 ATCT
66 ATCT
54731959 TTTATTTTAA
Statistics
Matches: 533, Mismatches: 46, Indels: 23
0.89 0.08 0.04
Matches are distributed among these distances:
127 1 0.00
128 38 0.07
129 3 0.01
130 425 0.80
131 33 0.06
132 3 0.01
133 30 0.06
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (129 bp):
ACTGTAACTTCAGGGAGATAAGATCCTGTCTTCGATCTGCTCCACTGTAACTTCAGGGAGATAAG
ATCTAGTCTTCGATCTACTCCGCTGTAACCTCAGGGAGATAAGACCTGAGCTGCGATCTACTCT
Found at i:54731551 original size:44 final size:44
Alignment explanation
Indices: 54731055--54732046 Score: 387
Period size: 46 Copynumber: 22.8 Consensus size: 44
54731045 CTGTGGTTTT
* *
54731055 AATCCGCTCCGCTGTAACTTCAGGGAGATAGGA--TAGTGTCTTC
1 AATCCGCTCCACTGTAACTTCAGGGAGATAAGATCTA-TGTCTTC
* * * * *
54731098 GATCTGCTCCGCTGTAACCTCAGGGGGATAAGATCTGAAAT-TCTTC
1 AATCCGCTCCACTGTAACTTCAGGGAGATAAGATCT---ATGTCTTC
** ** * * * * *
54731144 GGTCTACTCTACTGTAACCTCAGGGAGATAAGA-C-CTG-GTGC
1 AATCCGCTCCACTGTAACTTCAGGGAGATAAGATCTATGTCTTC
* * * * * * * *
54731185 GATCTGCTCTACTGTAACTTCAGAGAGATAAGGTCCTTTAT-TTT
1 AATCCGCTCCACTGTAACTTCAGGGAGATAAGAT-CTATGTCTTC
* * *
54731229 AAACCGTTCCACTGTAACTTCAGGGAGATAGGAT-TATGTCTTC
1 AATCCGCTCCACTGTAACTTCAGGGAGATAAGATCTATGTCTTC
* * * *
54731272 AATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGAAAGTCTTC
1 AATCCGCTCCACTGTAACTTCAGGGAGATAAGATCT--ATGTCTTC
** ** * * * *
54731318 GGTCTACTCCACTGTAACCTCAGGGAGATAAGA-C-CTG-GTGC
1 AATCCGCTCCACTGTAACTTCAGGGAGATAAGATCTATGTCTTC
* * * * *
54731359 GATCTGCTCTACTGTAACTTCAGAGAGATAAGATC-CTGTCTTC
1 AATCCGCTCCACTGTAACTTCAGGGAGATAAGATCTATGTCTTC
* * * * *
54731402 GATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGAAAGTCTTC
1 AATCCGCTCCACTGTAACTTCAGGGAGATAAGATCT--ATGTCTTC
** ** * * * *
54731448 GGTCTACTCCACTGTAACCTCAGGGAGATAAGA-C-CTG-GTGC
1 AATCCGCTCCACTGTAACTTCAGGGAGATAAGATCTATGTCTTC
* * * * * * *
54731489 GATCTGCTCTACTGTAACTTCAGAGAGATAAGATCT-TTTATTTT
1 AATCCGCTCCACTGTAACTTCAGGGAGATAAGATCTATGT-CTTC
*
54731533 AATCCGCTCCACTGTAACTTCAGGGAGATAATAT-TATGTCTTC
1 AATCCGCTCCACTGTAACTTCAGGGAGATAAGATCTATGTCTTC
* * * *
54731576 AATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGAAAGTCTTC
1 AATCCGCTCCACTGTAACTTCAGGGAGATAAGATCT--ATGTCTTC
** ** * *
54731622 GGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATG----C
1 AATCCGCTCCACTGTAACTTCAGGGAGATAAGATCT-ATGTCTTC
* ** * * *
54731663 GATCTACTCTACTGTAACTTCAGAGAGATAAGAT-TCTGTCTTC
1 AATCCGCTCCACTGTAACTTCAGGGAGATAAGATCTATGTCTTC
* ** * * *
54731706 GATCTACTCCGCTGTAACCTCAGGGAGATAAGATCTGAAAGTCTTC
1 AATCCGCTCCACTGTAACTTCAGGGAGATAAGATCT--ATGTCTTC
** ** * * * * *
54731752 GGTCTACTCTACTGTAACCTCAGGGAGATAAGA-C-CTG-GTGC
1 AATCCGCTCCACTGTAACTTCAGGGAGATAAGATCTATGTCTTC
* * * * * *
54731793 GATCTGCTCTACTGTAACTTTAGAGAGATAAGATC-CTGTCTTC
1 AATCCGCTCCACTGTAACTTCAGGGAGATAAGATCTATGTCTTC
* * * *
54731836 GATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGAAAT-TCTTC
1 AATCCGCTCCACTGTAACTTCAGGGAGATAAGATCT---ATGTCTTC
** ** * * * *
54731882 GGTCTACTCCACTGTAACCTCAGGGAGATAAGA-C-CTG-GTGC
1 AATCCGCTCCACTGTAACTTCAGGGAGATAAGATCTATGTCTTC
* * * * * * *
54731923 GATCTGCTCTACTGTAACTTCAGAGAGATAAGATCT-TTTATTTT
1 AATCCGCTCCACTGTAACTTCAGGGAGATAAGATCTATGT-CTTC
* * * * **
54731967 AAACCGTTCCACTATAA-TCTCAGGGAGATAGGAT-TACTAACTTC
1 AATCCGCTCCACTGTAACT-TCAGGGAGATAAGATCTA-TGTCTTC
* *
54732011 AATCTGCTCCGCTGTAA-TCTCAGGGAGATAAGATCT
1 AATCCGCTCCACTGTAACT-TCAGGGAGATAAGATCT
54732047 GAAATTCTTC
Statistics
Matches: 738, Mismatches: 162, Indels: 96
0.74 0.16 0.10
Matches are distributed among these distances:
39 2 0.00
40 1 0.00
41 182 0.25
42 18 0.02
43 190 0.26
44 118 0.16
45 10 0.01
46 214 0.29
47 2 0.00
48 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.29
Consensus pattern (44 bp):
AATCCGCTCCACTGTAACTTCAGGGAGATAAGATCTATGTCTTC
Found at i:54731615 original size:304 final size:304
Alignment explanation
Indices: 54731066--54731914 Score: 1387
Period size: 304 Copynumber: 2.8 Consensus size: 304
54731056 ATCCGCTCCG
* * * *
54731066 CTGTAACTTCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAACCTCAGGGGGATAAGA
1 CTGTAACTTCAGAGAGATAAGATACTGTCTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAGA
*
54731131 TCTGAAATTCTTCGGTCTACTCTACTGTAACCTCAGGGAGATAAGACCTGGTGCGATCTGCTCTA
66 TCTGAAAGTCTTCGGTCTACTCTACTGTAACCTCAGGGAGATAAGACCTGGTGCGATCTGCTCTA
* * * *
54731196 CTGTAACTTCAGAGAGATAAGGTCCTTTATTTTAAACCGTTCCACTGTAACTTCAGGGAGATAGG
131 CTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAAG
54731261 ATTATGTCTTCAATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGAAAGTCTTCGGTCTACT
196 ATTATGTCTTCAATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGAAAGTCTTCGGTCTACT
* *
54731326 CCACTGTAACCTCAGGGAGATAAGACCTGGTGCGATCTGCTCTA
261 CCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTA
*
54731370 CTGTAACTTCAGAGAGATAAGATCCTGTCTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAGA
1 CTGTAACTTCAGAGAGATAAGATACTGTCTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAGA
*
54731435 TCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGGTGCGATCTGCTCTA
66 TCTGAAAGTCTTCGGTCTACTCTACTGTAACCTCAGGGAGATAAGACCTGGTGCGATCTGCTCTA
* *
54731500 CTGTAACTTCAGAGAGATAAGATCTTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAAT
131 CTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAAG
54731565 ATTATGTCTTCAATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGAAAGTCTTCGGTCTACT
196 ATTATGTCTTCAATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGAAAGTCTTCGGTCTACT
54731630 CCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTA
261 CCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTA
* *
54731674 CTGTAACTTCAGAGAGATAAGATTCTGTCTTCGATCTACTCCGCTGTAACCTCAGGGAGATAAGA
1 CTGTAACTTCAGAGAGATAAGATACTGTCTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAGA
54731739 TCTGAAAGTCTTCGGTCTACTCTACTGTAACCTCAGGGAGATAAGACCTGGTGCGATCTGCTCTA
66 TCTGAAAGTCTTCGGTCTACTCTACTGTAACCTCAGGGAGATAAGACCTGGTGCGATCTGCTCTA
* * * ** * * *
54731804 CTGTAACTTTAGAGAGATAAGATCCTGT-CTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAG
131 CTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAAG
** * *
54731868 ATCTGAAAT-TCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGA
196 AT-T---ATGTCTTCAATCTGCTCCGCTGTAACCTCAGGGAGATAAGA
54731915 CCTGGTGCGA
Statistics
Matches: 509, Mismatches: 32, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
303 31 0.06
304 442 0.87
306 34 0.07
307 2 0.00
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (304 bp):
CTGTAACTTCAGAGAGATAAGATACTGTCTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAGA
TCTGAAAGTCTTCGGTCTACTCTACTGTAACCTCAGGGAGATAAGACCTGGTGCGATCTGCTCTA
CTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAAG
ATTATGTCTTCAATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGAAAGTCTTCGGTCTACT
CCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTA
Found at i:54731666 original size:174 final size:174
Alignment explanation
Indices: 54731364--54731696 Score: 594
Period size: 174 Copynumber: 1.9 Consensus size: 174
54731354 GGTGCGATCT
* * *
54731364 GCTCTACTGTAACTTCAGAGAGATAAGATCCTGTCTTCGATCTGCTCCGCTGTAACCTCAGGGAG
1 GCTCCACTGTAACTTCAGAGAGATAAGATCATGTCTTCAATCTGCTCCGCTGTAACCTCAGGGAG
*
54731429 ATAAGATCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGGTGCGATCT
66 ATAAGATCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCT
*
54731494 GCTCTACTGTAACTTCAGAGAGATAAGATCTTTTATTTTAATCC
131 ACTCTACTGTAACTTCAGAGAGATAAGATCTTTTATTTTAATCC
* * *
54731538 GCTCCACTGTAACTTCAGGGAGATAATATTATGTCTTCAATCTGCTCCGCTGTAACCTCAGGGAG
1 GCTCCACTGTAACTTCAGAGAGATAAGATCATGTCTTCAATCTGCTCCGCTGTAACCTCAGGGAG
54731603 ATAAGATCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCT
66 ATAAGATCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCT
54731668 ACTCTACTGTAACTTCAGAGAGATAAGAT
131 ACTCTACTGTAACTTCAGAGAGATAAGAT
54731697 TCTGTCTTCG
Statistics
Matches: 151, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
174 151 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.29
Consensus pattern (174 bp):
GCTCCACTGTAACTTCAGAGAGATAAGATCATGTCTTCAATCTGCTCCGCTGTAACCTCAGGGAG
ATAAGATCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCT
ACTCTACTGTAACTTCAGAGAGATAAGATCTTTTATTTTAATCC
Found at i:54731874 original size:434 final size:435
Alignment explanation
Indices: 54731239--54732056 Score: 1460
Period size: 434 Copynumber: 1.9 Consensus size: 435
54731229 AAACCGTTCC
* * *
54731239 ACTGTAACTTCAGGGAGATAGGATTATGTCTTCAATCTGCTCCGCTGTAACCTCAGGGAGATAAG
1 ACTGTAACTTCAGAGAGATAAGATTATGTCTTCAATCTACTCCGCTGTAACCTCAGGGAGATAAG
54731304 ATCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGGTGCGATCTGCTCT
66 ATCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGGTGCGATCTGCTCT
54731369 ACTGTAACTTCAGAGAGATAAGATCCTGTCTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAG
131 ACTGTAACTTCAGAGAGATAAGATCCTGTCTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAG
54731434 ATCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGGTGCGATCTGCTCT
196 ATCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGGTGCGATCTGCTCT
* *
54731499 ACTGTAACTTCAGAGAGATAAGATCTTTTATTTTAATCCGCTCCACTGTAA-CTTCAGGGAGATA
261 ACTGTAACTTCAGAGAGATAAGATCTTTTATTTTAAACCGCTCCACTATAATC-TCAGGGAGATA
* **
54731563 ATATTA-TGTCTTCAATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGAAAGTCTTCGGTCT
325 AGATTACTAACTTCAATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGAAAGTCTTCGGTCT
54731627 ACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCT
390 ACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCT
* *
54731673 ACTGTAACTTCAGAGAGATAAGATTCTGTCTTCGATCTACTCCGCTGTAACCTCAGGGAGATAAG
1 ACTGTAACTTCAGAGAGATAAGATTATGTCTTCAATCTACTCCGCTGTAACCTCAGGGAGATAAG
*
54731738 ATCTGAAAGTCTTCGGTCTACTCTACTGTAACCTCAGGGAGATAAGACCTGGTGCGATCTGCTCT
66 ATCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGGTGCGATCTGCTCT
*
54731803 ACTGTAACTTTAGAGAGATAAGATCCTGTCTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAG
131 ACTGTAACTTCAGAGAGATAAGATCCTGTCTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAG
*
54731868 ATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGGTGCGATCTGCTCT
196 ATCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGGTGCGATCTGCTCT
* *
54731933 ACTGTAACTTCAGAGAGATAAGATCTTTTATTTTAAACCGTTCCACTATAATCTCAGGGAGATAG
261 ACTGTAACTTCAGAGAGATAAGATCTTTTATTTTAAACCGCTCCACTATAATCTCAGGGAGATAA
* *
54731998 GATTACTAACTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTC
326 GATTACTAACTTCAATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGAAAGTCTTC
54732057 AGCCAGCTCC
Statistics
Matches: 365, Mismatches: 17, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
434 315 0.86
435 50 0.14
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (435 bp):
ACTGTAACTTCAGAGAGATAAGATTATGTCTTCAATCTACTCCGCTGTAACCTCAGGGAGATAAG
ATCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGGTGCGATCTGCTCT
ACTGTAACTTCAGAGAGATAAGATCCTGTCTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAG
ATCTGAAAGTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGGTGCGATCTGCTCT
ACTGTAACTTCAGAGAGATAAGATCTTTTATTTTAAACCGCTCCACTATAATCTCAGGGAGATAA
GATTACTAACTTCAATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGAAAGTCTTCGGTCTA
CTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCT
Found at i:54732172 original size:44 final size:44
Alignment explanation
Indices: 54732113--54732241 Score: 120
Period size: 44 Copynumber: 2.9 Consensus size: 44
54732103 GCTTCGCTGT
**
54732113 CAATGCAAAAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCA
1 CAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCA
* * * * * **
54732157 CAAATG-AGGGAGGCAAGGTTTG-TGTCTTCGACCTGCTTCGC-TGT
1 C-AATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGC-TC-CATCA
*
54732201 CAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCA
1 CAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCA
54732242 CTGCAACCAA
Statistics
Matches: 64, Mismatches: 15, Indels: 12
0.70 0.16 0.13
Matches are distributed among these distances:
43 17 0.27
44 30 0.47
45 17 0.27
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.26
Consensus pattern (44 bp):
CAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCA
Found at i:54732175 original size:86 final size:85
Alignment explanation
Indices: 54732051--54732663 Score: 734
Period size: 86 Copynumber: 7.1 Consensus size: 85
54732041 AGATCTGAAA
* * * * * * *
54732051 TTCTTCAGCCAGCTCCACTACAACCGA-GAGAGGTAAGG-TTCGTCTTCGACCTGCTTCGCTGTC
1 TTCTTCAACCAGCTCCACT-CAACCAATGA-AGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTT
* ** *
54732114 AATGCAAAAAGGCAAGATCTGT
64 AACGCAGGAAGGCAAGATCTGC
* *
54732136 TGTCTTCAACCAGCTCCA-TC-ACAAATGAGGGAGGCAAGG-TTTGTGTCTTCGACCTGCTTCGC
1 T-TCTTCAACCAGCTCCACTCAACCAATGA---AGGCAAGGCTTTGT-T-TTCGATCTGCTTCGC
* * **
54732198 TGTCAATGCAGGAAGGCAAGATCTTT
60 TGTTAACGCAGGAAGGCAAGATCTGC
54732224 TGTCTTCAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTT
1 T-TCTTCAACCAGCTCCACT-CAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTT
54732289 AACGCAGGAAGGCAAGATCTGC
64 AACGCAGGAAGGCAAGATCTGC
* *
54732311 TTCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTATTA
1 TTCTTCAACCAGCTCCACT-CAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTA
54732376 ACGCAGGAAGGCAAGATCTGC
65 ACGCAGGAAGGCAAGATCTGC
* *
54732397 TTCTTTAACCAGCTCCACTGTAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTA
1 TTCTTCAACCAGCTCCACT-CAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTA
54732462 ACGCAGGAAGGCAAGATCTGC
65 ACGCAGGAAGGCAAGATCTGC
* * *
54732483 TTCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTTGTTTTCAATCTGCTTCACTGTTA
1 TTCTTCAACCAGCTCCACT-CAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTA
54732548 ACGCAGGAAGG-AAGGATCTGC
65 ACGCAGGAAGGCAA-GATCTGC
* * * * * * *
54732569 TATATTCAACCAGCTCCACTGCAACCGATGGAGGTAAGGATTTGTTTTCGATATGCTTCACTGTT
1 T-TCTTCAACCAGCTCCACT-CAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTT
* *
54732634 AACGCAGGAAGGTAAGATCTGA
64 AACGCAGGAAGGCAAGATCTGC
54732656 TGTCTTCA
1 T-TCTTCA
54732664 TTGATCTGTT
Statistics
Matches: 482, Mismatches: 33, Indels: 24
0.89 0.06 0.04
Matches are distributed among these distances:
83 3 0.01
84 3 0.01
85 4 0.01
86 275 0.57
87 116 0.24
88 67 0.14
89 6 0.01
90 1 0.00
91 7 0.01
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.28
Consensus pattern (85 bp):
TTCTTCAACCAGCTCCACTCAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAA
CGCAGGAAGGCAAGATCTGC
Found at i:54732304 original size:43 final size:43
Alignment explanation
Indices: 54732253--54732645 Score: 209
Period size: 43 Copynumber: 9.1 Consensus size: 43
54732243 TGCAACCAAT
* *
54732253 GAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAG
1 GAAGGCAAGGCTTTGTTTTCAATCTGCTTCACTGTTAACGCAG
* * * * * * * *
54732296 GAAGGCAA-GATCTGCTTCTTTAACCAGCTCCACTG-CAAC-CAAT
1 GAAGGCAAGGCTTTG-TT-TTCAATCTGCTTCACTGTTAACGC-AG
* * *
54732339 GAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTATTAACGCAG
1 GAAGGCAAGGCTTTGTTTTCAATCTGCTTCACTGTTAACGCAG
* * * * * * *
54732382 GAAGGCAA-GATCTGCTTCTTTAACCAGCTCCACTG-TAAC-CAAT
1 GAAGGCAAGGCTTTG-TT-TTCAATCTGCTTCACTGTTAACGC-AG
* *
54732425 GAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAG
1 GAAGGCAAGGCTTTGTTTTCAATCTGCTTCACTGTTAACGCAG
* * * * * * * *
54732468 GAAGGCAA-GATCTGCTTCTTTAACCAGCTCCACTG-CAAC-CAAT
1 GAAGGCAAGGCTTTG-TT-TTCAATCTGCTTCACTGTTAACGC-AG
54732511 GAAGGCAAGGCTTTGTTTTCAATCTGCTTCACTGTTAACGCAG
1 GAAGGCAAGGCTTTGTTTTCAATCTGCTTCACTGTTAACGCAG
* * * * * *
54732554 GAAGG-AAGGATCTGCTATATTCAACCAGCTCCACTG-CAAC-CGATG
1 GAAGGCAAGGCTTTG-T-T-TTCAATCTGCTTCACTGTTAACGC-A-G
* * * *
54732599 G-AGGTAAGGATTTGTTTTCGATATGCTTCACTGTTAACGCAG
1 GAAGGCAAGGCTTTGTTTTCAATCTGCTTCACTGTTAACGCAG
54732641 GAAGG
1 GAAGG
54732646 TAAGATCTGA
Statistics
Matches: 252, Mismatches: 71, Indels: 54
0.67 0.19 0.14
Matches are distributed among these distances:
42 70 0.28
43 101 0.40
44 57 0.23
45 24 0.10
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.28
Consensus pattern (43 bp):
GAAGGCAAGGCTTTGTTTTCAATCTGCTTCACTGTTAACGCAG
Found at i:54732653 original size:259 final size:258
Alignment explanation
Indices: 54732054--54732663 Score: 793
Period size: 259 Copynumber: 2.3 Consensus size: 258
54732044 TCTGAAATTC
* * * * * * *
54732054 TTCAGCCAGCTCCACTACAACCGA-GAGAGGTAAGGTTCGTCTTCGACCTGCTTCGCTGTCAATG
1 TTCAACCAGCTCCACTGCAACCGATG-GAGGTAAGGTTTGTTTTCGATCTGCTTCGCTGTTAACG
** * *
54732118 CAAAAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAAATGAGGGAGGCAAGGTTTGTGTC
65 CAGGAAGGCAAGATCTGCTGTCTTCAACCAGCTCCATAACAAATGA--GAGGCAAGGTTTGTGTC
* **
54732183 TTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCACTGCAA
128 TTCGACCTGCTTCGCTGTCAACGCAGGAAGGCAAGATCTGCTGTCTTCAACCAGCTCCACTGCAA
* *
54732248 CCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTT
193 CCAATGAAGGCAAGGCTTTGTTTTCAATCTGCTTCACTGTTAACGCAGGAAGGCAAGATCTGCTT
*
54732313 C
258 A
* * * * *
54732314 TTTAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTATTAACG
1 TTCAACCAGCTCCACTGCAACCGATGGAGGTAAGG-TTTGTTTTCGATCTGCTTCGCTGTTAACG
* *
54732379 CAGGAAGGCAAGATCTGCT-TCTTTAACCAGCTCCACTGTAACCAATGA-AGGCAAGGCTTTGT-
65 CAGGAAGGCAAGATCTGCTGTCTTCAACCAGCTCCA---TAACAAATGAGAGGCAAGG-TTTGTG
* * *
54732441 T-TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCT-TCTTTAACCAGCTCCACTGC
126 TCTTCGACCTGCTTCGCTGTCAACGCAGGAAGGCAAGATCTGCTGTCTTCAACCAGCTCCACTGC
54732504 AACCAATGAAGGCAAGGCTTTGTTTTCAATCTGCTTCACTGTTAACGCAGGAAGG-AAGGATCTG
191 AACCAATGAAGGCAAGGCTTTGTTTTCAATCTGCTTCACTGTTAACGCAGGAAGGCAA-GATCTG
54732568 CTATA
255 CT-TA
* *
54732573 TTCAACCAGCTCCACTGCAACCGATGGAGGTAAGGATTTGTTTTCGATATGCTTCACTGTTAACG
1 TTCAACCAGCTCCACTGCAACCGATGGAGGTAAGG-TTTGTTTTCGATCTGCTTCGCTGTTAACG
* *
54732638 CAGGAAGGTAAGATCTGATGTCTTCA
65 CAGGAAGGCAAGATCTGCTGTCTTCA
54732664 TTGATCTGTT
Statistics
Matches: 303, Mismatches: 38, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
257 2 0.01
258 80 0.26
259 112 0.37
260 56 0.18
261 45 0.15
263 8 0.03
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (258 bp):
TTCAACCAGCTCCACTGCAACCGATGGAGGTAAGGTTTGTTTTCGATCTGCTTCGCTGTTAACGC
AGGAAGGCAAGATCTGCTGTCTTCAACCAGCTCCATAACAAATGAGAGGCAAGGTTTGTGTCTTC
GACCTGCTTCGCTGTCAACGCAGGAAGGCAAGATCTGCTGTCTTCAACCAGCTCCACTGCAACCA
ATGAAGGCAAGGCTTTGTTTTCAATCTGCTTCACTGTTAACGCAGGAAGGCAAGATCTGCTTA
Found at i:54733907 original size:13 final size:12
Alignment explanation
Indices: 54733891--54733924 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
54733881 ATTTTTACTT
54733891 TTTTATTTTTTCA
1 TTTT-TTTTTTCA
54733904 TTTTTTTATTTCA
1 TTTTTTT-TTTCA
54733917 TTTTTTTT
1 TTTTTTTT
54733925 GACTCAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 4 0.20
13 16 0.80
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTTTTTTCA
Found at i:54734807 original size:19 final size:17
Alignment explanation
Indices: 54734783--54734817 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
54734773 TTTTTAATTT
54734783 TTTTTTGATGATTTTTTTA
1 TTTTTTGA--ATTTTTTTA
54734802 TTTTTTGAATTTTTTT
1 TTTTTTGAATTTTTTT
54734818 TTTGAGTCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
19 8 0.50
ACGTcount: A:0.14, C:0.00, G:0.09, T:0.77
Consensus pattern (17 bp):
TTTTTTGAATTTTTTTA
Found at i:54735569 original size:27 final size:27
Alignment explanation
Indices: 54735531--54735582 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
54735521 ATGCAAAATT
*
54735531 AATTTGGAAGAAAATCTAAAAGAATAA
1 AATTTGGAAGAAAATCGAAAAGAATAA
54735558 AATTTGGAAGAAAATCGAAAAGAAT
1 AATTTGGAAGAAAATCGAAAAGAAT
54735583 CAAAGAATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.58, C:0.04, G:0.17, T:0.21
Consensus pattern (27 bp):
AATTTGGAAGAAAATCGAAAAGAATAA
Found at i:54738375 original size:3 final size:3
Alignment explanation
Indices: 54738367--54738402 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
54738357 TTAAAAGAGT
*
54738367 ATA ATA ATA ATA ATA ATA ATG ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
54738403 TGAAATTTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:54739789 original size:6 final size:6
Alignment explanation
Indices: 54739782--54739840 Score: 64
Period size: 6 Copynumber: 9.3 Consensus size: 6
54739772 CGGCCCGAAG
* * *
54739782 AAGAAG AAGAAA AAGAAA AAGAAA GAAGGAAA AAGAGAG AAGAAA AAGAGA
1 AAGAAA AAGAAA AAGAAA AAGAAA -AA-GAAA AAGA-AA AAGAAA AAGAAA
54739833 AAGAAA AA
1 AAGAAA AA
54739841 AAGAAATATA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
6 32 0.71
7 9 0.20
8 4 0.09
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:54739993 original size:24 final size:24
Alignment explanation
Indices: 54739956--54740023 Score: 79
Period size: 23 Copynumber: 2.9 Consensus size: 24
54739946 AAAAAAAACC
* **
54739956 AAAACAGAAA-AAAGAAGCAGCGG
1 AAAAAAGAAAGAAAGAAGCAGCAA
54739979 AAAAAAGAAAGAAAGAAGCAG-AA
1 AAAAAAGAAAGAAAGAAGCAGCAA
54740002 AAAATAAG-AAGAAAGAAGCAGC
1 AAAA-AAGAAAGAAAGAAGCAGC
54740024 CCAAATGCAG
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
23 26 0.67
24 13 0.33
ACGTcount: A:0.66, C:0.09, G:0.24, T:0.01
Consensus pattern (24 bp):
AAAAAAGAAAGAAAGAAGCAGCAA
Found at i:54740100 original size:22 final size:24
Alignment explanation
Indices: 54740054--54740104 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
54740044 GCAGCAGGCC
54740054 CAGCAGGCCCCCAGGCCCAGTGCAG
1 CAGCAGGCCCCCAGGCCCAG-GCAG
*
54740079 CAGCA-GCCCCCAGGCCTA-GCAG
1 CAGCAGGCCCCCAGGCCCAGGCAG
54740101 CAGC
1 CAGC
54740105 CCAACAGGCC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 8 0.32
24 12 0.48
25 5 0.20
ACGTcount: A:0.22, C:0.45, G:0.29, T:0.04
Consensus pattern (24 bp):
CAGCAGGCCCCCAGGCCCAGGCAG
Found at i:54740114 original size:20 final size:19
Alignment explanation
Indices: 54740077--54740114 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
54740067 GGCCCAGTGC
*
54740077 AGCAGCAGCCCCCAGGCCT
1 AGCAGCAGCCCACAGGCCT
54740096 AGCAGCAGCCCAACAGGCC
1 AGCAGCAGCCC-ACAGGCC
54740115 AGCCCAGTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.26, C:0.45, G:0.26, T:0.03
Consensus pattern (19 bp):
AGCAGCAGCCCACAGGCCT
Found at i:54740140 original size:10 final size:10
Alignment explanation
Indices: 54740127--54740185 Score: 64
Period size: 10 Copynumber: 5.9 Consensus size: 10
54740117 CCCAGTCCAG
54740127 AAAAAAAAGA
1 AAAAAAAAGA
*
54740137 AAAAAAGAGA
1 AAAAAAAAGA
**
54740147 GGAAAAAAGA
1 AAAAAAAAGA
* *
54740157 AGATAAAAGA
1 AAAAAAAAGA
*
54740167 AGAAAAAAGA
1 AAAAAAAAGA
54740177 AAAAAAAAG
1 AAAAAAAAG
54740186 GTTTTAATTT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 41 1.00
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.02
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:54740184 original size:20 final size:20
Alignment explanation
Indices: 54740125--54740185 Score: 79
Period size: 20 Copynumber: 3.1 Consensus size: 20
54740115 AGCCCAGTCC
*
54740125 AGAA-AAAAAAGAAAAAAAG
1 AGAAGAAAAAAGAAAAAAAA
* * *
54740144 AGAGGAAAAAAGAAGATAAA
1 AGAAGAAAAAAGAAAAAAAA
54740164 AGAAGAAAAAAGAAAAAAAA
1 AGAAGAAAAAAGAAAAAAAA
54740184 AG
1 AG
54740186 GTTTTAATTT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 3 0.09
20 31 0.91
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.02
Consensus pattern (20 bp):
AGAAGAAAAAAGAAAAAAAA
Found at i:54740374 original size:11 final size:11
Alignment explanation
Indices: 54740343--54740391 Score: 50
Period size: 10 Copynumber: 4.6 Consensus size: 11
54740333 GTATTTATAT
54740343 TTTTAATTTAA
1 TTTTAATTTAA
*
54740354 -TTCAATTTTAA
1 TTTTAA-TTTAA
54740365 TTTTAATTT-A
1 TTTTAATTTAA
*
54740375 TTTTAA-ATAA
1 TTTTAATTTAA
54740385 TTTTAAT
1 TTTTAAT
54740392 AAATAAGACA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
9 1 0.03
10 18 0.58
11 8 0.26
12 4 0.13
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTTAATTTAA
Found at i:54740685 original size:18 final size:18
Alignment explanation
Indices: 54740660--54740934 Score: 168
Period size: 17 Copynumber: 15.5 Consensus size: 18
54740650 AAAAATCAGG
*
54740660 TTTCAAAAATTGTCGTGT
1 TTTCAAAAATTCTCGTGT
* *
54740678 TTT-AAAAATTTTCATG-
1 TTTCAAAAATTCTCGTGT
*
54740694 TTTCTAAAATGT-T--TGT
1 TTTCAAAAAT-TCTCGTGT
*
54740710 ATTTCAAAAAATCCTCGTGT
1 -TTTC-AAAAATTCTCGTGT
*
54740730 TTTCAAAAATTCTCATG-
1 TTTCAAAAATTCTCGTGT
54740747 TTTCAAAAA-TCTTCGTGT
1 TTTCAAAAATTC-TCGTGT
*
54740765 TTTC-AAAATTCTAGTG-
1 TTTCAAAAATTCTCGTGT
* *
54740781 TTTCAAAAATTTTCATGT
1 TTTCAAAAATTCTCGTGT
* **
54740799 TTTCAAAAATTTTTATGT
1 TTTCAAAAATTCTCGTGT
*
54740817 TTTCAAAAATTCTCGTAT
1 TTTCAAAAATTCTCGTGT
* * *
54740835 TTT-GAAAATTTTCTTGT
1 TTTCAAAAATTCTCGTGT
54740852 TTTCAAAAAAAAACTT-TCGTGT
1 TTTC----AAAAA-TTCTCGTGT
*
54740874 TTT-ATAAA-TCTCCGTGT
1 TTTCAAAAATTCT-CGTGT
*
54740891 TTTCAAAAAATTCTCGT-C
1 TTTC-AAAAATTCTCGTGT
54740909 TTTCAAAAATT-TCCGTG-
1 TTTCAAAAATTCT-CGTGT
54740926 TTTCAAAAA
1 TTTCAAAAA
54740935 AAAATCCTCG
Statistics
Matches: 205, Mismatches: 26, Indels: 53
0.72 0.09 0.19
Matches are distributed among these distances:
15 3 0.01
16 11 0.05
17 95 0.46
18 65 0.32
19 11 0.05
20 6 0.03
22 12 0.06
23 2 0.01
ACGTcount: A:0.32, C:0.13, G:0.09, T:0.45
Consensus pattern (18 bp):
TTTCAAAAATTCTCGTGT
Found at i:54740750 original size:87 final size:86
Alignment explanation
Indices: 54740659--54740830 Score: 206
Period size: 87 Copynumber: 2.0 Consensus size: 86
54740649 AAAAAATCAG
* *
54740659 GTTTCAAAAAT-TGTCGTGTTTTAAAAATTTTCA-TGTTTCTAAAATGTT-TGTATTTCAAAAAA
1 GTTTCAAAAATCT-TCGTGTTTTAAAAATTCT-AGTGTTTCAAAAATGTTATGT-TTTC-AAAAA
*
54740721 TCCTCGTGTTTTCAAAAATTCTCAT
62 TCCTCATGTTTTCAAAAATTCTCAT
* * **
54740746 GTTTCAAAAATCTTCGTGTTTTCAAAATTCTAGTGTTTCAAAAATTTTCATGTTTTCAAAAATTT
1 GTTTCAAAAATCTTCGTGTTTTAAAAATTCTAGTGTTTCAAAAATGTT-ATGTTTTCAAAAATCC
*
54740811 TTATGTTTTCAAAAATTCTC
65 TCATGTTTTCAAAAATTCTC
54740831 GTATTTTGAA
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
86 1 0.01
87 64 0.88
88 5 0.07
89 3 0.04
ACGTcount: A:0.32, C:0.13, G:0.09, T:0.46
Consensus pattern (86 bp):
GTTTCAAAAATCTTCGTGTTTTAAAAATTCTAGTGTTTCAAAAATGTTATGTTTTCAAAAATCCT
CATGTTTTCAAAAATTCTCAT
Found at i:54740755 original size:35 final size:36
Alignment explanation
Indices: 54740711--54740860 Score: 148
Period size: 35 Copynumber: 4.2 Consensus size: 36
54740701 AATGTTTGTA
54740711 TTTCAAAAAATCCTCGTGTTTTCAAAAATTCTCATG-
1 TTTC-AAAAATCCTCGTGTTTTCAAAAATTCTCATGT
*
54740747 TTTCAAAAATCTTCGTGTTTTC-AAAATTCT-A-GT
1 TTTCAAAAATCCTCGTGTTTTCAAAAATTCTCATGT
** * * *
54740780 GTTTCAAAAATTTTCATGTTTTCAAAAATTTTTATGT
1 -TTTCAAAAATCCTCGTGTTTTCAAAAATTCTCATGT
* * * * *
54740817 TTTCAAAAATTCTCGTATTTT-GAAAATTTTCTTGT
1 TTTCAAAAATCCTCGTGTTTTCAAAAATTCTCATGT
54740852 TTTCAAAAA
1 TTTCAAAAA
54740861 AAAACTTTCG
Statistics
Matches: 99, Mismatches: 10, Indels: 11
0.82 0.08 0.09
Matches are distributed among these distances:
32 1 0.01
33 1 0.01
34 28 0.28
35 44 0.44
36 23 0.23
37 2 0.02
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (36 bp):
TTTCAAAAATCCTCGTGTTTTCAAAAATTCTCATGT
Found at i:54740786 original size:16 final size:16
Alignment explanation
Indices: 54740730--54740788 Score: 57
Period size: 16 Copynumber: 3.5 Consensus size: 16
54740720 ATCCTCGTGT
54740730 TTTCAAAAATTCTCA-TG
1 TTTC-AAAATTCT-AGTG
* *
54740747 TTTCAAAAATCTTCGTG
1 TTTCAAAATTC-TAGTG
54740764 TTTTCAAAATTCTAGTG
1 -TTTCAAAATTCTAGTG
54740781 TTTCAAAA
1 TTTCAAAA
54740789 ATTTTCATGT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
16 14 0.40
17 11 0.31
18 10 0.29
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.42
Consensus pattern (16 bp):
TTTCAAAATTCTAGTG
Found at i:54740930 original size:35 final size:35
Alignment explanation
Indices: 54740659--54740935 Score: 135
Period size: 35 Copynumber: 7.8 Consensus size: 35
54740649 AAAAAATCAG
* * *
54740659 GTTTCAAAAATTGT-CGTGTTT-TAAAAATTTTCAT
1 GTTTCAAAAATT-TCCGTGTTTCAAAAAATTCTCGT
* * * *
54740693 GTTTCTAAAATGTT-TGTATTTCAAAAAATCCTCGT
1 GTTTCAAAAAT-TTCCGTGTTTCAAAAAATTCTCGT
*
54740728 GTTTTCAAAAA-TTCTCATGTTTC-AAAAA-TCTTCGT
1 G-TTTCAAAAATTTC-CGTGTTTCAAAAAATTC-TCGT
* * *
54740763 GTTTTC-AAAA-TTCTAGTGTTTC-AAAAATTTTCAT
1 G-TTTCAAAAATTTC-CGTGTTTCAAAAAATTCTCGT
***
54740797 GTTTTCAAAAATTTTTATGTTTTC-AAAAATTCTCGT
1 G-TTTCAAAAATTTCCGTG-TTTCAAAAAATTCTCGT
* ** * *
54740833 ATTTTGAAAATTTTCTTGTTTTCAAAAAAAAACTT-TCGT
1 GTTTCAAAAATTTCCGTG-TTTC---AAAAAA-TTCTCGT
* * *
54740872 GTTTTATAAATCTCCGTGTTTTCAAAAAATTCTCGT
1 GTTTCAAAAATTTCCGTG-TTTCAAAAAATTCTCGT
*
54740908 CTTTCAAAAATTTCCGTGTTTCAAAAAA
1 GTTTCAAAAATTTCCGTGTTTCAAAAAA
54740936 AAATCCTCGT
Statistics
Matches: 191, Mismatches: 36, Indels: 31
0.74 0.14 0.12
Matches are distributed among these distances:
34 47 0.25
35 63 0.33
36 53 0.28
39 26 0.14
40 2 0.01
ACGTcount: A:0.32, C:0.13, G:0.09, T:0.45
Consensus pattern (35 bp):
GTTTCAAAAATTTCCGTGTTTCAAAAAATTCTCGT
Found at i:54740935 original size:18 final size:18
Alignment explanation
Indices: 54740879--54740935 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
54740869 CGTGTTTTAT
*
54740879 AAATCTCCGTGTTTTCAAA
1 AAATTTCCGTG-TTTCAAA
*
54740898 AAA-TTCTCGTCTTTC-AA
1 AAATTTC-CGTGTTTCAAA
54740915 AAATTTCCGTGTTTCAAA
1 AAATTTCCGTGTTTCAAA
54740933 AAA
1 AAA
54740936 AAATCCTCGT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
17 12 0.38
18 14 0.44
19 6 0.19
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (18 bp):
AAATTTCCGTGTTTCAAA
Found at i:54740946 original size:74 final size:74
Alignment explanation
Indices: 54740814--54740954 Score: 187
Period size: 74 Copynumber: 1.9 Consensus size: 74
54740804 AAAATTTTTA
** * * * *
54740814 TGTTTTCAAAAATTCTCGTATTTTGAAAATTTTCTTGTTTTCAAAAAAAAACTTTCGTGTTTTAT
1 TGTTTTCAAAAATTCTCGTATTTCAAAAATTTCCGTGTTTTCAAAAAAAAACTCTCGTGTTTCAT
54740879 AAATCTCCG
66 AAATCTCCG
*
54740888 TGTTTTCAAAAAATTCTCGTCTTTCAAAAATTTCCGTG-TTTCAAAAAAAAA-TCCTCGTGTTTC
1 TGTTTTC-AAAAATTCTCGTATTTCAAAAATTTCCGTGTTTTCAAAAAAAAACT-CTCGTGTTTC
54740951 ATAA
64 ATAA
54740955 TTTATCAAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
73 1 0.02
74 32 0.55
75 25 0.43
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.43
Consensus pattern (74 bp):
TGTTTTCAAAAATTCTCGTATTTCAAAAATTTCCGTGTTTTCAAAAAAAAACTCTCGTGTTTCAT
AAATCTCCG
Found at i:54741004 original size:22 final size:22
Alignment explanation
Indices: 54740961--54741002 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
54740951 ATAATTTATC
*
54740961 AAAATTTTTGTGTTTTCAAAAT
1 AAAATTTTTGTGTTTTAAAAAT
54740983 AAAA-TTTTGTGTTTTAAAAA
1 AAAATTTTTGTGTTTTAAAAA
54741003 ATTCTCATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (22 bp):
AAAATTTTTGTGTTTTAAAAAT
Found at i:54741019 original size:17 final size:18
Alignment explanation
Indices: 54740992--54741041 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
54740982 TAAAATTTTG
*
54740992 TGTTTTAAAAAATTCTCA
1 TGTTTTCAAAAATTCTCA
* * *
54741010 TG-TTTCAAAAACTGTCG
1 TGTTTTCAAAAATTCTCA
54741027 TGTTTTCAAAAATTC
1 TGTTTTCAAAAATTC
54741042 CCGTGTTAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (18 bp):
TGTTTTCAAAAATTCTCA
Found at i:54741036 original size:121 final size:120
Alignment explanation
Indices: 54740839--54741055 Score: 275
Period size: 121 Copynumber: 1.8 Consensus size: 120
54740829 TCGTATTTTG
* *
54740839 AAAATTTTCTTGTTTTCAAAAAAAAACTTTCGTGTTTTATAAATCTCCGTGTTTTCAAAAAATTC
1 AAAATTTTCTTGTTTTCAAAAAAAAACTTTCGTGTTTTAAAAATCTCCATGTTTTCAAAAAATTC
*
54740904 TCGTCTTTCAAAAATTTCCGTGTTTCAAAAAAAAATCCTCGTGTTTCATAATTTATC
66 TCGTCTTTCAAAAATTCCCGTG-TT-AAAAAAAAATCCTCGTGTTTCATAATTTATC
* * *
54740961 AAAATTTT-TGTGTTTTCAAAATAAAA-TTTTGTGTTTTAAAAAAT-TCTCATG-TTTCAAAAAC
1 AAAATTTTCT-TGTTTTCAAAAAAAAACTTTCGTGTTTT-AAAAATCTC-CATGTTTTCAAAAAA
54741022 TGTCGT-GT-TTTCAAAAATTCCCGTGTTAAAAAAA
63 T-TC-TCGTCTTTCAAAAATTCCCGTGTTAAAAAAA
54741056 TTTATGTTTT
Statistics
Matches: 84, Mismatches: 6, Indels: 13
0.82 0.06 0.13
Matches are distributed among these distances:
119 7 0.08
120 2 0.02
121 39 0.46
122 35 0.42
123 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.41
Consensus pattern (120 bp):
AAAATTTTCTTGTTTTCAAAAAAAAACTTTCGTGTTTTAAAAATCTCCATGTTTTCAAAAAATTC
TCGTCTTTCAAAAATTCCCGTGTTAAAAAAAAATCCTCGTGTTTCATAATTTATC
Found at i:54741098 original size:17 final size:18
Alignment explanation
Indices: 54740983--54741117 Score: 96
Period size: 18 Copynumber: 7.3 Consensus size: 18
54740973 TTTTCAAAAT
*
54740983 AAAATTTT-GTGTTTTAA
1 AAAATTTTCGTGTTTTCA
* *
54741000 AAAATTCTCATG-TTTCA
1 AAAATTTTCGTGTTTTCA
* *
54741017 AAAACTGTCGTGTTTTCA
1 AAAATTTTCGTGTTTTCA
** ***
54741035 AAAATTCCCGTGTTAAAA
1 AAAATTTTCGTGTTTTCA
54741053 AAATTTATGTTTTCGTGTTTTCAA
1 AAA---A--TTTTCGTGTTTTC-A
54741077 AAAATTTTCGTG-TTTCA
1 AAAATTTTCGTGTTTTCA
*
54741094 AAAATCTTCGTGTTTTCA
1 AAAATTTTCGTGTTTTCA
54741112 AAAATT
1 AAAATT
54741118 ATTATTTTGT
Statistics
Matches: 90, Mismatches: 19, Indels: 17
0.71 0.15 0.13
Matches are distributed among these distances:
17 32 0.36
18 36 0.40
19 8 0.09
21 2 0.02
23 8 0.09
24 4 0.04
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (18 bp):
AAAATTTTCGTGTTTTCA
Found at i:54744316 original size:16 final size:16
Alignment explanation
Indices: 54744290--54744328 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
54744280 TTAAGAAATA
*
54744290 ATAATTATTATGTTAAT
1 ATAA-TATTATATTAAT
54744307 ATAATATTATATTAAT
1 ATAATATTATATTAAT
54744323 ATAATA
1 ATAATA
54744329 AACATAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (16 bp):
ATAATATTATATTAAT
Found at i:54744347 original size:9 final size:9
Alignment explanation
Indices: 54744335--54744360 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
54744325 AATAAACATA
54744335 AAATGAAAC
1 AAATGAAAC
54744344 AAATGAAAC
1 AAATGAAAC
54744353 AAATGAAA
1 AAATGAAA
54744361 TAGAAAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.69, C:0.08, G:0.12, T:0.12
Consensus pattern (9 bp):
AAATGAAAC
Found at i:54747502 original size:36 final size:36
Alignment explanation
Indices: 54747416--54747502 Score: 129
Period size: 36 Copynumber: 2.4 Consensus size: 36
54747406 AGGTTTAATG
* *
54747416 AAACTACGTCATTTTGGCCTCGCTTCAAAAGCCACA
1 AAACAACGTCGTTTTGGCCTCGCTTCAAAAGCCACA
*
54747452 AAACAACGTCGTTTTGGCCTCGCTTCAAAAGCCCCA
1 AAACAACGTCGTTTTGGCCTCGCTTCAAAAGCCACA
* *
54747488 AAACGACGTTGTTTT
1 AAACAACGTCGTTTT
54747503 AATGCTGACC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (36 bp):
AAACAACGTCGTTTTGGCCTCGCTTCAAAAGCCACA
Found at i:54754734 original size:89 final size:89
Alignment explanation
Indices: 54754583--54754756 Score: 330
Period size: 89 Copynumber: 2.0 Consensus size: 89
54754573 ACCACCTGGA
*
54754583 ACAAAACATGATCAAATGATAAAACATATGGCAATGGCATACATCTCGACATGTCGAAGATCGCA
1 ACAAAACATGATCAAATGATAAAACATATGGCAATGGCATACATCTAGACATGTCGAAGATCGCA
*
54754648 TGAGGCAGAGCCACATCGACGTAG
66 TGAGGCAGAACCACATCGACGTAG
54754672 ACAAAACATGATCAAATGATAAAACATATGGCAATGGCATACATCTAGACATGTCGAAGATCGCA
1 ACAAAACATGATCAAATGATAAAACATATGGCAATGGCATACATCTAGACATGTCGAAGATCGCA
54754737 TGAGGCAGAACCACATCGAC
66 TGAGGCAGAACCACATCGAC
54754757 CCAGACAATC
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 83 1.00
ACGTcount: A:0.41, C:0.21, G:0.20, T:0.18
Consensus pattern (89 bp):
ACAAAACATGATCAAATGATAAAACATATGGCAATGGCATACATCTAGACATGTCGAAGATCGCA
TGAGGCAGAACCACATCGACGTAG
Found at i:54762799 original size:18 final size:18
Alignment explanation
Indices: 54762759--54762802 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
54762749 AATTTTTATG
**
54762759 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGAATA
54762777 ATTGGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
54762795 CTTGGGTT
1 ATTGGGTT
54762803 TGGATTGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.02, G:0.43, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Found at i:54769558 original size:9 final size:9
Alignment explanation
Indices: 54769544--54769568 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
54769534 ACCATTTGCT
54769544 GATAAATAA
1 GATAAATAA
54769553 GATAAATAA
1 GATAAATAA
54769562 GATAAAT
1 GATAAAT
54769569 GTAGTTCAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (9 bp):
GATAAATAA
Found at i:54773152 original size:93 final size:92
Alignment explanation
Indices: 54773020--54773214 Score: 286
Period size: 93 Copynumber: 2.1 Consensus size: 92
54773010 TTGATTTTAG
* *
54773020 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTA-TATAATTA
1 TAAATTCATATAAGAAAATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTA-AATTA
* *
54773084 TATTTAAT-ATTAATTATTTTAAATTGTA
65 TATGTAATAATT-ATTATTTTAAATTATA
* *
54773112 TAAATTCATATAAGAAAATTTTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTA
1 TAAATTCATATAAGAAAA-TTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTA
54773177 TATGTAATAATTATTATTTTAAATTATA
65 TATGTAATAATTATTATTTTAAATTATA
*
54773205 CAAATTCATA
1 TAAATTCATA
54773215 AACTATAATC
Statistics
Matches: 93, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
92 17 0.18
93 71 0.76
94 5 0.05
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (92 bp):
TAAATTCATATAAGAAAATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTAT
ATGTAATAATTATTATTTTAAATTATA
Found at i:54773272 original size:17 final size:17
Alignment explanation
Indices: 54773247--54773280 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
54773237 ATAATTTTAA
*
54773247 ATTTTATTAAATCATAT
1 ATTTAATTAAATCATAT
54773264 ATTTAATTAAATCATAT
1 ATTTAATTAAATCATAT
54773281 TTAATATTAA
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:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTAATTAAATCATAT
Found at i:54773282 original size:15 final size:16
Alignment explanation
Indices: 54773247--54773285 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
54773237 ATAATTTTAA
*
54773247 ATTTTATTAAATCATAT
1 ATTTAATTAAATCA-AT
54773264 ATTTAATTAAATC-AT
1 ATTTAATTAAATCAAT
54773279 ATTTAAT
1 ATTTAAT
54773286 ATTAATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.43
17 12 0.57
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTTAATTAAATCAAT
Found at i:54773289 original size:17 final size:18
Alignment explanation
Indices: 54773251--54773290 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
54773241 TTTTAAATTT
*
54773251 TATTAAATCATATATTTA
1 TATTAAATCATATATTAA
54773269 -ATTAAATCATAT-TTAA
1 TATTAAATCATATATTAA
54773285 TATTAA
1 TATTAA
54773291 TTATTTGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTAAATCATATATTAA
Found at i:54773405 original size:15 final size:15
Alignment explanation
Indices: 54773370--54773421 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
54773360 TTAAGAATTT
*
54773370 TATTAAATTAT-ATA
1 TATTTAATTATAATA
54773384 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
54773398 TATTTAATAATAAT-
1 TATTTAATTATAATA
54773412 TATGTTAATT
1 TAT-TTAATT
54773422 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:54773412 original size:120 final size:120
Alignment explanation
Indices: 54773246--54773537 Score: 459
Period size: 120 Copynumber: 2.4 Consensus size: 120
54773236 AATAATTTTA
* * *
54773246 AATTTTATTAAATCATATA-TTTAATTA-AATCATATTTAATATTAATTAT-TTGAAATTT-TCT
1 AATTTTATTAAATTATATATTTTAATTATAAT-ATATTTAATAATAATTATGTT--AATTTATAT
* *
54773307 TTTATAGTATCATATATTATGATTTGAGTAAATTCATAGAAGAAT-TTTATTTATTAAG
63 TTTACAGTATCATATATTATGATTTGAGTAAATTCATAGAAGAATATTAATTT-TTAAG
54773365 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
*
54773430 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTTTTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATAGAAGAATATTAATTTTTAAG
54773485 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
54773538 TAAATATGAT
Statistics
Matches: 162, Mismatches: 6, Indels: 9
0.92 0.03 0.05
Matches are distributed among these distances:
119 23 0.14
120 128 0.79
121 11 0.07
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATAGAAGAATATTAATTTTTAAG
Done.