Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 129432109
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: 129432109
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 423 of 425
Found at i:128565847 original size:22 final size:21
Alignment explanation
Indices: 128565822--128565877 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
128565812 TTTATTCGAG
*
128565822 TTAATTAATTAATTATAATTAT
1 TTAATTAATTAATTATAA-TAA
* * *
128565844 TTAATTCAGTATTTATAATAA
1 TTAATTAATTAATTATAATAA
128565865 TTAATTATATTAA
1 TTAATTA-ATTAA
128565878 AATTATAAAT
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
21 8 0.31
22 18 0.69
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (21 bp):
TTAATTAATTAATTATAATAA
Found at i:128572778 original size:25 final size:27
Alignment explanation
Indices: 128572736--128572796 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 27
128572726 ATGATGTGTC
*
128572736 ATTATTATTCACTGACAATACA-TAAAT
1 ATTA-TATTCACTAACAATACATTAAAT
*
128572763 CTTATATT-ACTAACAATACATTAAAT
1 ATTATATTCACTAACAATACATTAAAT
128572789 ATTATATT
1 ATTATATT
128572797 TAAATAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
25 11 0.37
26 16 0.53
27 3 0.10
ACGTcount: A:0.44, C:0.13, G:0.02, T:0.41
Consensus pattern (27 bp):
ATTATATTCACTAACAATACATTAAAT
Found at i:128573137 original size:29 final size:29
Alignment explanation
Indices: 128573105--128573167 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 29
128573095 TTATATCCGT
128573105 AATTACAC-CAAATCAAAATTTATATATCA
1 AATTACACGCAAATCAAAATTTATATAT-A
* *
128573134 AATTACACGTTAAATCAAAATTTTTATATA
1 AATTACACG-CAAATCAAAATTTATATATA
128573164 AATT
1 AATT
128573168 TAATATTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 8 0.27
30 5 0.17
31 17 0.57
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.37
Consensus pattern (29 bp):
AATTACACGCAAATCAAAATTTATATATA
Found at i:128575003 original size:19 final size:19
Alignment explanation
Indices: 128574997--128575044 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
128574987 TAAATTATTT
*
128574997 AATTATTTAATTACAAATT
1 AATTATTTAATTACAAATA
**
128575016 AATTATTTAATTATTAATA
1 AATTATTTAATTACAAATA
128575035 AATTTATTTA
1 AA-TTATTTA
128575045 TTTTTGTCAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
AATTATTTAATTACAAATA
Found at i:128591231 original size:160 final size:156
Alignment explanation
Indices: 128590887--128591510 Score: 712
Period size: 160 Copynumber: 4.0 Consensus size: 156
128590877 TCCGGACCCA
* * *
128590887 GGACTTATTTCGATTGATTCATTCAGTTACCTTTAAAAGATGGCATCAGATATATATGGGGTTCA
1 GGACTTATTTCGATTGATTCATCCAGTCACCTTTAAAAGATGGCATCA-ACATATATGGGGTTC-
* *
128590952 GAA-ACCAATATCTATACCAAAAGGTAAACTTTTAATCATTTGGGGTGTATTG-----A-A-AA-
64 GAATCCCAATATCTATACCAAAAGGGAAACTTTTAATCATTT-GGGTGTATTGAAATCAGAGAAT
* *
128591008 GTGTCGTGGAGCTAAGAATGTGCTCGGATG
128 GTGTCATGGAGCTAAAAATGTGCTC-GATG
* * * *
128591038 GGATTTATTTCGATTGATTCATCCAGTCACCTTTAAAAGATGGTAGTCGACATATATGGGGTTTG
1 GGACTTATTTCGATTGATTCATCCAGTCACCTTTAAAAGATGGCA-TCAACATATATGGGGTTCG
*
128591103 AATCCCAATATCTATA-CAATAAGGGAAAGTTTTAATCATTTGGGTGTATTGAAAACTCAGAGAA
65 AATCCCAATATCTATACCAA-AAGGGAAACTTTTAATCATTTGGGTGTATTG-AAA-TCAGAGAA
* *
128591167 TGTGTCGTGGTGCTAAAAATGTGCTCAGATG
127 TGTGTCATGGAGCTAAAAATGTGCTC-GATG
* ** * * * * *
128591198 GGACTTATTTCGAGTGATTCATTTAGCCACCTTTAAAAGATGACACCCAACAGATTTGGGG-TCG
1 GGACTTATTTCGATTGATTCATCCAGTCACCTTTAAAAGATGGCA-TCAACATATATGGGGTTCG
* *
128591262 AATCCCAATATCTGTACCAAAAGGGAAACTTTTAATCATTTGGGTGTACTGAAAATTCAGAGAAT
65 AATCCCAATATCTATACCAAAAGGGAAACTTTTAATCATTTGGGTGTATTG-AAA-TCAGAGAAT
* **
128591327 GAGTCACAGAGCTAAAAATGTGCTCGAATG
128 GTGTCATGGAGCTAAAAATGTGCTCG-ATG
* * * * *
128591357 GGACTTCTTTCGATTGATTCATCCAATTATCTTTAAAAGATGGCATCCAACATATTTGGGGTTCG
1 GGACTTATTTCGATTGATTCATCCAGTCACCTTTAAAAGATGGCAT-CAACATATATGGGGTTCG
* *
128591422 AATCCCAATATCTATACCAAAAGGGAAACTTCTAATCATTCGGGTGTATTGAAAGTCTAGAGAAT
65 AATCCCAATATCTATACCAAAAGGGAAACTTTTAATCATTTGGGTGTATTGAAA-TC-AGAGAAT
*
128591487 GTGTCATGGTGCTAAAAATGTGCT
128 GTGTCATGGAGCTAAAAATGTGCT
128591511 TGGATGACAA
Statistics
Matches: 400, Mismatches: 55, Indels: 27
0.83 0.11 0.06
Matches are distributed among these distances:
150 16 0.04
151 85 0.21
152 2 0.00
157 1 0.00
158 2 0.00
159 138 0.34
160 156 0.39
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.31
Consensus pattern (156 bp):
GGACTTATTTCGATTGATTCATCCAGTCACCTTTAAAAGATGGCATCAACATATATGGGGTTCGA
ATCCCAATATCTATACCAAAAGGGAAACTTTTAATCATTTGGGTGTATTGAAATCAGAGAATGTG
TCATGGAGCTAAAAATGTGCTCGATG
Found at i:128597995 original size:18 final size:19
Alignment explanation
Indices: 128597959--128597996 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
128597949 GCAGCAGTAC
*
128597959 TCTTCTATTTTGCTCTAAG
1 TCTTCTATTTTCCTCTAAG
*
128597978 TCTTC-ATTTTCCTTTAAG
1 TCTTCTATTTTCCTCTAAG
128597996 T
1 T
128597997 ATCCTTGTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.16, C:0.21, G:0.08, T:0.55
Consensus pattern (19 bp):
TCTTCTATTTTCCTCTAAG
Found at i:128600780 original size:104 final size:103
Alignment explanation
Indices: 128600499--128600796 Score: 395
Period size: 102 Copynumber: 2.9 Consensus size: 103
128600489 CTTGTTAAAG
* * *
128600499 ACTTGAAGTCAATTGCAAAAACCAATTTTTTTAATTTGATGGTATAATTTTTCCCCAAGTCCCTG
1 ACTTGAAGTCAGTTGCAAAAA-C--TTTTTTTAATTTGATGGTCTAATTTTTCCCCAAGTCCCTA
* * *
128600564 TACTCTTTTAAATTTTGAAATTCAA-CTTTTTTATAAGAGA
63 TACCCTTTGAAATTTTGAAATTTAATCTTTTTTATAAGAGA
* * *
128600604 ACTTGAAGCCAGTTGCAAAAACTTTTTTTAATTTGATGGTCTAATTTTTACCCAAGTCTCTAT-C
1 ACTTGAAGTCAGTTGCAAAAACTTTTTTTAATTTGATGGTCTAATTTTTCCCCAAGTCCCTATAC
* * *
128600668 CTCTTTGAAATTTTGAAATTTAATTTTTTTTATATGATA
66 C-CTTTGAAATTTTGAAATTTAATCTTTTTTATAAGAGA
* *
128600707 ACTTGAAGTCAGTTGCAAAAACTTTTTTTAAATTT-AGTGGTCTAATTTTGCCCCAAATCCCTAT
1 ACTTGAAGTCAGTTGCAAAAACTTTTTTT-AATTTGA-TGGTCTAATTTTTCCCCAAGTCCCTAT
128600771 ACCCTTTGAAATTTTGAAATTTAATC
64 ACCCTTTGAAATTTTGAAATTTAATC
128600797 ATTCTTTTTC
Statistics
Matches: 170, Mismatches: 18, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
101 1 0.01
102 56 0.33
103 41 0.24
104 51 0.30
105 21 0.12
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (103 bp):
ACTTGAAGTCAGTTGCAAAAACTTTTTTTAATTTGATGGTCTAATTTTTCCCCAAGTCCCTATAC
CCTTTGAAATTTTGAAATTTAATCTTTTTTATAAGAGA
Found at i:128602817 original size:26 final size:23
Alignment explanation
Indices: 128602769--128602817 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 23
128602759 TTACGGTGTA
*
128602769 AATTATTTTCTTTCTTTTGTTTT
1 AATTATTTTCTTTCTTTTCTTTT
128602792 AATTATTTTTCTTATGCTTTTCTTTT
1 AATTA-TTTTCTT-T-CTTTTCTTTT
128602818 TTAGTTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 5 0.23
24 7 0.32
25 1 0.05
26 9 0.41
ACGTcount: A:0.14, C:0.10, G:0.04, T:0.71
Consensus pattern (23 bp):
AATTATTTTCTTTCTTTTCTTTT
Found at i:128603923 original size:17 final size:15
Alignment explanation
Indices: 128603896--128603937 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 15
128603886 ATATATATTC
128603896 AAAAATT-ATATTAA
1 AAAAATTAATATTAA
128603910 AAATAATATAATA-TAA
1 AAA-AAT-TAATATTAA
128603926 AAAAATTAATAT
1 AAAAATTAATAT
128603938 GGGGGGGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
14 8 0.33
15 6 0.25
16 7 0.29
17 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAAATTAATATTAA
Found at i:128604731 original size:11 final size:11
Alignment explanation
Indices: 128604715--128604744 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
128604705 CCATAGGATT
128604715 GCGTGGAATCC
1 GCGTGGAATCC
128604726 GCGTGGAATCC
1 GCGTGGAATCC
128604737 GCGTGGAA
1 GCGTGGAA
128604745 ATGTGTGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.20, C:0.23, G:0.40, T:0.17
Consensus pattern (11 bp):
GCGTGGAATCC
Found at i:128607826 original size:27 final size:27
Alignment explanation
Indices: 128607783--128607835 Score: 63
Period size: 26 Copynumber: 1.9 Consensus size: 27
128607773 TTACACCTAA
*
128607783 TAAAAAGTTAACAGTTA-AATTTAATT
1 TAAAAAATTAACAGTTACAATTTAATT
*
128607809 TAAAAAATTAAACCGTTACTAATTTAA
1 TAAAAAATT-AACAGTTAC-AATTTAA
128607836 GATTTAAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 8 0.36
27 7 0.32
29 7 0.32
ACGTcount: A:0.51, C:0.08, G:0.06, T:0.36
Consensus pattern (27 bp):
TAAAAAATTAACAGTTACAATTTAATT
Found at i:128608033 original size:29 final size:30
Alignment explanation
Indices: 128607973--128608033 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 30
128607963 GAAAATTTAA
* * * * *
128607973 TTTTATATTAATATTTATATAAATTTATTC
1 TTTTATAATAATATTTAAATAAAATAAGTC
128608003 TTTTATAATAA-ATTTAAATAAAATAAGTC
1 TTTTATAATAATATTTAAATAAAATAAGTC
128608032 TT
1 TT
128608034 AAATTTTGGG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (30 bp):
TTTTATAATAATATTTAAATAAAATAAGTC
Found at i:128617398 original size:2 final size:2
Alignment explanation
Indices: 128617391--128617422 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
128617381 GTTGAAATAC
128617391 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
128617423 GTGTGTGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:128620333 original size:9 final size:9
Alignment explanation
Indices: 128620321--128620512 Score: 100
Period size: 9 Copynumber: 20.1 Consensus size: 9
128620311 TTATGAATTT
128620321 TTTTTATAA
1 TTTTTATAA
128620330 TTTTTATAA
1 TTTTTATAA
*
128620339 GTTTATATCAA
1 -TTTTTAT-AA
* *
128620350 TTTTAATATT
1 TTTTTATA-A
*
128620360 TTTTTCATATT
1 TTTTT-ATA-A
*
128620371 TTTTTACAA
1 TTTTTATAA
*
128620380 TTTTTTATTA
1 -TTTTTATAA
128620390 TTTTTAAGTAA
1 TTTTT-A-TAA
*
128620401 TATGTTTTTAA
1 T-T-TTTATAA
**
128620412 TTTAAAT-A
1 TTTTTATAA
* * *
128620420 TTGTAAAAA
1 TTTTTATAA
*
128620429 TTTTTATTA
1 TTTTTATAA
*
128620438 CTTTTATAA
1 TTTTTATAA
128620447 TTTTTATAA
1 TTTTTATAA
*
128620456 TTTATTAGAA
1 TTT-TTATAA
128620466 TTTATTAT-A
1 TTT-TTATAA
128620475 TTTTTATAA
1 TTTTTATAA
*
128620484 TATTTATAA
1 TTTTTATAA
128620493 GTTTTTATAA
1 -TTTTTATAA
*
128620503 TTTTTTTAA
1 TTTTTATAA
128620512 T
1 T
128620513 AAATTTAATA
Statistics
Matches: 141, Mismatches: 29, Indels: 26
0.72 0.15 0.13
Matches are distributed among these distances:
8 9 0.06
9 63 0.45
10 46 0.33
11 19 0.13
12 1 0.01
13 3 0.02
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:128620333 original size:11 final size:10
Alignment explanation
Indices: 128620320--128620512 Score: 79
Period size: 10 Copynumber: 20.1 Consensus size: 10
128620310 TTTATGAATT
128620320 TTTTTTATAA
1 TTTTTTATAA
128620330 -TTTTTATAA
1 TTTTTTATAA
* *
128620339 GTTTATATCAA
1 TTTTTTAT-AA
* *
128620350 -TTTTAATAT
1 TTTTTTATAA
*
128620359 TTTTTTCATAT
1 TTTTTT-ATAA
*
128620370 TTTTTTACAA
1 TTTTTTATAA
*
128620380 TTTTTTATTA
1 TTTTTTATAA
*
128620390 TTTTTAAGTAA
1 TTTTTTA-TAA
128620401 TATGTTTT-TAA
1 T-T-TTTTATAA
128620412 ---TTTA-AA
1 TTTTTTATAA
* * *
128620418 TATTGTAAAA
1 TTTTTTATAA
* *
128620428 ATTTTTATTA
1 TTTTTTATAA
*
128620438 -CTTTTATAA
1 TTTTTTATAA
128620447 -TTTTTATAA
1 TTTTTTATAA
* *
128620456 TTTATTAGAA
1 TTTTTTATAA
*
128620466 TTTATTAT-A
1 TTTTTTATAA
128620475 -TTTTTATAA
1 TTTTTTATAA
*
128620484 -TATTTATAA
1 TTTTTTATAA
*
128620493 GTTTTTATAA
1 TTTTTTATAA
128620503 TTTTTT-TAA
1 TTTTTTATAA
128620512 T
1 T
128620513 AAATTTAATA
Statistics
Matches: 140, Mismatches: 28, Indels: 31
0.70 0.14 0.16
Matches are distributed among these distances:
6 5 0.04
8 6 0.04
9 42 0.30
10 65 0.46
11 18 0.13
12 1 0.01
13 3 0.02
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:128623926 original size:9 final size:9
Alignment explanation
Indices: 128623912--128623947 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
128623902 TAAAATTTAA
*
128623912 TAAAAATAT
1 TAAAAATTT
128623921 TAAAAATTT
1 TAAAAATTT
128623930 TAATAAATTT
1 TAA-AAATTT
128623940 TAAAAATT
1 TAAAAATT
128623948 CATCCATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 16 0.64
10 9 0.36
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
TAAAAATTT
Found at i:128624790 original size:60 final size:60
Alignment explanation
Indices: 128624715--128624833 Score: 211
Period size: 60 Copynumber: 2.0 Consensus size: 60
128624705 ATACTAAACT
* *
128624715 AAACACAACAGTTTATAATATAATCCTAAATTACTAATAAATTAATTTTAAAATAATTAC
1 AAACACAACAATTTATAATATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTAC
*
128624775 AAACACAATAATTTATAATATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
1 AAACACAACAATTTATAATATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
128624834 TTAAAAAAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.53, C:0.11, G:0.01, T:0.35
Consensus pattern (60 bp):
AAACACAACAATTTATAATATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTAC
Found at i:128627186 original size:239 final size:228
Alignment explanation
Indices: 128626768--128627225 Score: 553
Period size: 239 Copynumber: 2.0 Consensus size: 228
128626758 TTCAAAATCT
* * * * *
128626768 TATATATATGAACTAGAAGATCAAACATCACCAGAAGTCCTTCACTATGTATGCACTATGAACTT
1 TATATATATGAACTAGAAAATCAAACATCACCAGAACTCCATCACTATGCATGAACTATGAACTT
* * **
128626833 ACCATTGTTATATTTTGCTACTAAAATCTACACTTGAAATAAATTACAGTTTCATTTCAAATTTT
66 ACCATTGTTATATTTTACTACTAAAATCTACACTTGAAATAAATTACAGTTTCATTCCAAATTCA
* * * *
128626898 GAACTTCCTCAAATAATTTCCATTCAAACACTCATATGATACTAATCAAGTTAAAAAATTAGCCA
131 AAACTTCCTCAAATAAGTTCCATTCAAACACTCATATGATACTAATCAAGTT--AAAATTAACAA
*
128626963 AA-AAACTTCAAAATATTATATATATGTGTATATA
194 AAGAAACATCAAAATATTATATATATGTGTATATA
* * *
128626997 TATATATATGAACTAGAAAATCAATAAAACATCACTAGCACTCCATCACTATGCATGAATTATGA
1 TATATATATGAACTAGAAAATC----AAACATCACCAGAACTCCATCACTATGCATGAACTATGA
* *
128627062 ACTTAACCATTGTTATATTTTACTACTAAAATCTACACCTGAACCTGATATAAATTACAGTTTTA
62 ACTT-ACCATTGTTATATTTTACTACTAAAATCTACA-CT-----TGAAATAAATTACAGTTTCA
* ** *
128627127 TTCCAAGTTCAAAACTT-CTCAAATGGGTTCCATTCAAACTCTCATATGATA-TCAATCAAGTTA
120 TTCCAAATTCAAAACTTCCTCAAATAAGTTCCATTCAAACACTCATATGATACT-AATCAAGTTA
*
128627190 AATTTAACAAAAGAAACATCAAAATATTATATATAT
184 AAATTAACAAAAGAAACATCAAAATATTATATATAT
128627226 ATATATATGA
Statistics
Matches: 192, Mismatches: 24, Indels: 17
0.82 0.10 0.07
Matches are distributed among these distances:
229 21 0.11
233 36 0.19
234 31 0.16
235 2 0.01
237 10 0.05
238 23 0.12
239 39 0.20
240 30 0.16
ACGTcount: A:0.41, C:0.17, G:0.08, T:0.34
Consensus pattern (228 bp):
TATATATATGAACTAGAAAATCAAACATCACCAGAACTCCATCACTATGCATGAACTATGAACTT
ACCATTGTTATATTTTACTACTAAAATCTACACTTGAAATAAATTACAGTTTCATTCCAAATTCA
AAACTTCCTCAAATAAGTTCCATTCAAACACTCATATGATACTAATCAAGTTAAAATTAACAAAA
GAAACATCAAAATATTATATATATGTGTATATA
Found at i:128627493 original size:197 final size:196
Alignment explanation
Indices: 128627020--128627590 Score: 556
Period size: 197 Copynumber: 2.9 Consensus size: 196
128627010 TAGAAAATCA
* * *
128627020 ATAAAACATCACTAGCACTCCATCACTATGCATGAATTATGAACTTAACCATTGTTATATTTTAC
1 ATAAAATATCACTAGAACTCCATCACTATGCATGAACTATGAACTT-ACCATTGTTATATTTTAC
* * *
128627085 TACTAAAATCTACACCTGAACCTGATATAAATTACAGTTTTATTCCAAGTTCAAAACTTCTCAAA
65 TACTAAAATCTACA--T----CTGATAT-AATTACAGTTTCATTTCAAATTCAAAACTTCTCAAA
* * * *
128627150 TGGGTTCCATTCAAACTCTCATATGATATCAATCAAGTTAAATTTAACAAAAGAAACATCAAAAT
123 TAGGTTCCATTCAAACTCTAATATGATACCAATCAAGTTAAAATTAACAAAAGAAACATCAAAAT
128627215 ATTATATAT
188 ATTATATAT
* * * * ** * * * *
128627224 ATATATATATGAACTAGAA---GATCAATAAAACAT-CACTAT-TACTCTACTA-AG-TATGAAC
1 ATA-AAATAT-CACTAGAACTCCATCACT-ATGCATGAACTATGAACT-TACCATTGTTAT--A-
* * * * *
128627282 TATGACTGCTAAAATCTGCATCTGATATAATTTACAGTTTCATTTCAAATTCAAAACTTCTTAAA
59 TTTTACTACTAAAATCTACATCTGATATAA-TTACAGTTTCATTTCAAATTCAAAACTTCTCAAA
* * *
128627347 TAGGTTCCATTCAAACTCTTATATGATACCAATCAAGTTAAAATTAGCAAAAGAAACTTCAAAAT
123 TAGGTTCCATTCAAACTCTAATATGATACCAATCAAGTTAAAATTAACAAAAGAAACATCAAAAT
128627412 ATTATCA-AGT
188 ATTAT-ATA-T
* * *
128627422 -TAAAATATCACCAGAACTCCTTCACTGTGCATGAACTATGAACTTACCATTGTTATATTTTACT
1 ATAAAATATCACTAGAACTCCATCACTATGCATGAACTATGAACTTACCATTGTTATATTTTACT
* * * *
128627486 ACTAAAATCTACACCTGATATAAATACAGTTTGATTTCAAATTCAAAACTTCTCAAATAGTTTCC
66 ACTAAAATCTACATCTGATATAATTACAGTTTCATTTCAAATTCAAAACTTCTCAAATAGGTTCC
* *
128627551 ATTC--A--CTAATATGATGCCAATCAAGTTGAAATTAACAAAA
131 ATTCAAACTCTAATATGATACCAATCAAGTTAAAATTAACAAAA
128627591 AATTTGAAAA
Statistics
Matches: 297, Mismatches: 53, Indels: 46
0.75 0.13 0.12
Matches are distributed among these distances:
192 31 0.10
194 1 0.00
195 6 0.02
196 49 0.16
197 132 0.44
198 16 0.05
199 4 0.01
200 6 0.02
201 2 0.01
202 7 0.02
203 26 0.09
204 7 0.02
205 4 0.01
206 6 0.02
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (196 bp):
ATAAAATATCACTAGAACTCCATCACTATGCATGAACTATGAACTTACCATTGTTATATTTTACT
ACTAAAATCTACATCTGATATAATTACAGTTTCATTTCAAATTCAAAACTTCTCAAATAGGTTCC
ATTCAAACTCTAATATGATACCAATCAAGTTAAAATTAACAAAAGAAACATCAAAATATTATATA
T
Found at i:128628885 original size:10 final size:10
Alignment explanation
Indices: 128628862--128628946 Score: 50
Period size: 10 Copynumber: 8.4 Consensus size: 10
128628852 CTAATTCAAA
*
128628862 TTTTTATGATT
1 TTTTTAT-AAT
128628873 TTTTTATAA-
1 TTTTTATAAT
*
128628882 TTTTTATAAG
1 TTTTTATAAT
*
128628892 TTTATATCAA-
1 TTTTTAT-AAT
* *
128628902 TTTTAATATT
1 TTTTTATAAT
128628912 TTTTTCAT-AT
1 TTTTT-ATAAT
*
128628922 TTTTTACAATT
1 TTTTTATAA-T
*
128628933 TTTTTATTAT
1 TTTTTATAAT
128628943 TTTT
1 TTTT
128628947 AAAGTAATAT
Statistics
Matches: 58, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
9 11 0.19
10 28 0.48
11 19 0.33
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:128628885 original size:20 final size:19
Alignment explanation
Indices: 128628860--128628947 Score: 77
Period size: 20 Copynumber: 4.4 Consensus size: 19
128628850 GTCTAATTCA
128628860 AATTTTTATGATTTTTTTAT
1 AATTTTTAT-ATTTTTTTAT
** *
128628880 AATTTTTATAAGTTTATAT
1 AATTTTTATATTTTTTTAT
*
128628899 CAATTTTAATATTTTTTTCAT
1 -AATTTTTATATTTTTTT-AT
* *
128628920 ATTTTTTACAATTTTTTTAT
1 AATTTTTA-TATTTTTTTAT
*
128628940 TATTTTTA
1 AATTTTTA
128628948 AAGTAATATG
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
19 7 0.13
20 36 0.68
21 10 0.19
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.66
Consensus pattern (19 bp):
AATTTTTATATTTTTTTAT
Found at i:128628995 original size:10 final size:9
Alignment explanation
Indices: 128628979--128629056 Score: 52
Period size: 10 Copynumber: 8.0 Consensus size: 9
128628969 AATATTGTAA
128628979 ATAATTTTT
1 ATAATTTTT
128628988 ATTAA-TTTT
1 A-TAATTTTT
128628997 ATAATTTTTTTCT
1 ATAA---TTTT-T
128629010 ATAATTTATT
1 ATAATTT-TT
*
128629020 AT-AGTTTT
1 ATAATTTTT
*
128629028 ATAGTTTTT
1 ATAATTTTT
128629037 ATAAGTTTTT
1 ATAA-TTTTT
128629047 ATAAATTTTT
1 AT-AATTTTT
128629057 TTATTGTTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 19
0.71 0.05 0.24
Matches are distributed among these distances:
8 7 0.13
9 16 0.29
10 21 0.38
11 3 0.05
12 3 0.05
13 5 0.09
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.64
Consensus pattern (9 bp):
ATAATTTTT
Found at i:128629037 original size:20 final size:21
Alignment explanation
Indices: 128629014--128629067 Score: 53
Period size: 20 Copynumber: 2.7 Consensus size: 21
128629004 TTTTCTATAA
*
128629014 TTTATTATAGTTTTAT-AGTT
1 TTTATTATAGTTTTATAAATT
128629034 TTTA-TA-AGTTTTTATAAATT
1 TTTATTATAG-TTTTATAAATT
*
128629054 TTT-TTATTGTTTTA
1 TTTATTATAGTTTTA
128629068 ATAACTTTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
18 2 0.07
19 8 0.29
20 17 0.61
21 1 0.04
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (21 bp):
TTTATTATAGTTTTATAAATT
Found at i:128629957 original size:3 final size:3
Alignment explanation
Indices: 128629949--128629985 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
128629939 ATATCTACCA
128629949 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG C
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG C
128629986 AACCATAATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.35, G:0.32, T:0.32
Consensus pattern (3 bp):
CTG
Found at i:128630454 original size:150 final size:150
Alignment explanation
Indices: 128630189--128630463 Score: 433
Period size: 150 Copynumber: 1.8 Consensus size: 150
128630179 ATAATTCGAA
*
128630189 TGTTGCCAACATCTTCCATTTCCACTAACCGGTCTCTCACAAGGAGCACCATCGCAGGTGGGTGC
1 TGTTGCCAACACCTTCCATTTCCACTAACCGGTCTCTCACAAGGAGCACCATCGCAGGTGGGTGC
* * * * *
128630254 TCCACAAACGGATGTAATATCACCACCACCGTGGTCCAACCATTGTGGAGTAAAACTGCTACCGC
66 TCCACAAACGAATATAATATCACCACCACCATGGTCCAACCACTGCGGAGTAAAACTGCTACCGC
128630319 CGTCCCTGCCATAATCCAAG
131 CGTCCCTGCCATAATCCAAG
* * * *
128630339 TGTTGCCAACACCTTCCATTTCCACTAACCGGTCTCTCGCAAGGAGCACCATTGTAGGTGGTTGC
1 TGTTGCCAACACCTTCCATTTCCACTAACCGGTCTCTCACAAGGAGCACCATCGCAGGTGGGTGC
** *
128630404 TCCACAAATTAATATAATATCATCACCACCATGGTCCAACCACTGCGGAGTAAAACTGCT
66 TCCACAAACGAATATAATATCACCACCACCATGGTCCAACCACTGCGGAGTAAAACTGCT
128630464 GCCATAGCCG
Statistics
Matches: 112, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
150 112 1.00
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (150 bp):
TGTTGCCAACACCTTCCATTTCCACTAACCGGTCTCTCACAAGGAGCACCATCGCAGGTGGGTGC
TCCACAAACGAATATAATATCACCACCACCATGGTCCAACCACTGCGGAGTAAAACTGCTACCGC
CGTCCCTGCCATAATCCAAG
Found at i:128630608 original size:339 final size:341
Alignment explanation
Indices: 128629988--128630678 Score: 1233
Period size: 339 Copynumber: 2.0 Consensus size: 341
128629978 GCTGCTGCAA
128629988 CCATAATCCAAGTGTTGCCAACACCTTCCATTTCCAATAACCGGTCTCTCGCAAGGAGCACCATT
1 CCATAATCCAAGTGTTGCCAACACCTTCCATTTCCAATAACCGGTCTCTCGCAAGGAGCACCATT
128630053 GCAGGTGGTTGCTCCACAAATTAATATAATATCATCACCACCATGGTCCAACCACCGCGGAGTAA
66 GCAGGTGGTTGCTCCACAAATTAATATAATATCATCACCACCATGGTCCAACCACCGCGGAGTAA
*
128630118 AACTGCTACCATAGCCGCCATAATTTAAGTTCCGTGAAGTAAAACAACTACTACTGCGACCATAA
131 AACTGCTACCATAGCCGCCATAATTTAAGCTCCGTGAAGTAAAACAACTACTACTGCGACCATAA
*
128630183 TTCGAATGTTGCCAACATCTTCCATTTCCACTAACCGGTCTCTCACAAGGAGCACCATCGCAGGT
196 TTCGAATGTTGCCAACATCTTCCATTTCCACTAACCGGTCTCTCACAAGGAGCACCATCGCAAGT
* *
128630248 GGGTGCTCCACAAACGGATGT-AAT-ATCACCACCACCGTGGTCCAACCATTGTGGAGTAAAACT
261 GGGTGCTCCACAAACGGATGTAAATCACCACCACCACCGTGGTCCAACCATCGTGGAGTAAAACT
*
128630311 GCTACCGCCGTCCCTG
326 GCTACCGCCGTCCCCG
*
128630327 CCATAATCCAAGTGTTGCCAACACCTTCCATTTCCACTAACCGGTCTCTCGCAAGGAGCACCATT
1 CCATAATCCAAGTGTTGCCAACACCTTCCATTTCCAATAACCGGTCTCTCGCAAGGAGCACCATT
* *
128630392 GTAGGTGGTTGCTCCACAAATTAATATAATATCATCACCACCATGGTCCAACCACTGCGGAGTAA
66 GCAGGTGGTTGCTCCACAAATTAATATAATATCATCACCACCATGGTCCAACCACCGCGGAGTAA
*
128630457 AACTGCTGCCATAGCCGCCATAATTTAAGCTCCGTGAAGTAAAACAACTACTACTGCGACCATAA
131 AACTGCTACCATAGCCGCCATAATTTAAGCTCCGTGAAGTAAAACAACTACTACTGCGACCATAA
*
128630522 TTCGAATGTTGCCAACATCTTCCATTTCCATTAACCGGTCTCTCACAAGGAGCACCATCGCAAGT
196 TTCGAATGTTGCCAACATCTTCCATTTCCACTAACCGGTCTCTCACAAGGAGCACCATCGCAAGT
*
128630587 GGGTGCTCCACAAATGGATGTAAAATCACCACCACCACCACCGTGGTCCAACCATCGTGGAGTAA
261 GGGTGCTCCACAAACGGATGT-AAAT---CACCACCACCACCGTGGTCCAACCATCGTGGAGTAA
128630652 AACTGCTACCGCCGTCCCCG
322 AACTGCTACCGCCGTCCCCG
128630672 CCATAAT
1 CCATAAT
128630679 TTAAGTGGCT
Statistics
Matches: 335, Mismatches: 11, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
339 273 0.81
341 3 0.01
345 59 0.18
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (341 bp):
CCATAATCCAAGTGTTGCCAACACCTTCCATTTCCAATAACCGGTCTCTCGCAAGGAGCACCATT
GCAGGTGGTTGCTCCACAAATTAATATAATATCATCACCACCATGGTCCAACCACCGCGGAGTAA
AACTGCTACCATAGCCGCCATAATTTAAGCTCCGTGAAGTAAAACAACTACTACTGCGACCATAA
TTCGAATGTTGCCAACATCTTCCATTTCCACTAACCGGTCTCTCACAAGGAGCACCATCGCAAGT
GGGTGCTCCACAAACGGATGTAAATCACCACCACCACCGTGGTCCAACCATCGTGGAGTAAAACT
GCTACCGCCGTCCCCG
Found at i:128631356 original size:21 final size:20
Alignment explanation
Indices: 128631319--128631357 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
128631309 CCAAAAAATC
*
128631319 AAAATAAAAAACTAATATGA
1 AAAATAAAAAACAAATATGA
128631339 AAAATAAAAAATCAAATAT
1 AAAATAAAAAA-CAAATAT
128631358 AGTTATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.72, C:0.05, G:0.03, T:0.21
Consensus pattern (20 bp):
AAAATAAAAAACAAATATGA
Found at i:128634310 original size:15 final size:15
Alignment explanation
Indices: 128634286--128634324 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
128634276 GCATCTCCAT
128634286 TTTTTC-TCTTCTCC
1 TTTTTCTTCTTCTCC
* *
128634300 TTTTTCTTCTTTTTC
1 TTTTTCTTCTTCTCC
128634315 TTTTTCTTCT
1 TTTTTCTTCT
128634325 CTATGTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 6 0.27
15 16 0.73
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTTCTTCTTCTCC
Found at i:128634490 original size:30 final size:31
Alignment explanation
Indices: 128634438--128634505 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 31
128634428 CTGTTAACCG
*
128634438 GTGACTGTTTTGTCACTTTTTTATAACG-TTA
1 GTGACTGTTTTGTCACTTTTTTA-AAAGTTTA
*
128634469 GTGACTGTTTTGTTA-TTTTTTAAAAGTTTA
1 GTGACTGTTTTGTCACTTTTTTAAAAGTTTA
128634499 GTGACTG
1 GTGACTG
128634506 AAATGAAACC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 3 0.09
30 17 0.50
31 14 0.41
ACGTcount: A:0.21, C:0.09, G:0.19, T:0.51
Consensus pattern (31 bp):
GTGACTGTTTTGTCACTTTTTTAAAAGTTTA
Found at i:128641614 original size:2 final size:2
Alignment explanation
Indices: 128641607--128641631 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
128641597 AGATTGAAAA
128641607 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
128641632 ATAACGAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:128643568 original size:29 final size:30
Alignment explanation
Indices: 128643523--128643579 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
128643513 AAATACTAAA
* *
128643523 AAAAATAATTATATAAATGA-TTAAAATTT
1 AAAAACAATTATATAAATAACTTAAAATTT
128643552 AAAAACAATTACT-TAAATAACTTAAAAT
1 AAAAACAATTA-TATAAATAACTTAAAAT
128643580 AAACAGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (30 bp):
AAAAACAATTATATAAATAACTTAAAATTT
Found at i:128646366 original size:60 final size:61
Alignment explanation
Indices: 128646269--128646391 Score: 151
Period size: 60 Copynumber: 2.0 Consensus size: 61
128646259 TATTGATATA
* * ** *
128646269 TTAATAAATTTAGCTCTTCAATATTTATATATTTTATTAATTTGA-TTTTAAATCTAAAAAT
1 TTAATAAATTTAACTCTTCAATATTTATAAAAATTATT-ATTTGAGTTCTAAATCTAAAAAT
* * *
128646330 TTAATAAATTTAACT-TTTAATATTTATAAAAATTATTATTTTAGTTCTAATTCTAAAAAT
1 TTAATAAATTTAACTCTTCAATATTTATAAAAATTATTATTTGAGTTCTAAATCTAAAAAT
128646390 TT
1 TT
128646392 TAAAAATAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
59 5 0.09
60 34 0.64
61 14 0.26
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.51
Consensus pattern (61 bp):
TTAATAAATTTAACTCTTCAATATTTATAAAAATTATTATTTGAGTTCTAAATCTAAAAAT
Found at i:128654666 original size:22 final size:22
Alignment explanation
Indices: 128654627--128654674 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
128654617 TCTTTAAATT
*
128654627 GATT-TTTTTGTTGATTGAATC
1 GATTCTTTTTATTGATTGAATC
*
128654648 GATTCTTTTTATTGTTTGAATC
1 GATTCTTTTTATTGATTGAATC
*
128654670 AATTC
1 GATTC
128654675 ATTGGTGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.21, C:0.08, G:0.15, T:0.56
Consensus pattern (22 bp):
GATTCTTTTTATTGATTGAATC
Found at i:128654932 original size:15 final size:15
Alignment explanation
Indices: 128654912--128654963 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
128654902 ACTACAAAAG
128654912 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
128654927 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
128654946 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
128654961 ATT
1 ATT
128654964 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:128655307 original size:5 final size:5
Alignment explanation
Indices: 128655297--128655322 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
128655287 ATATTGTTAC
128655297 TATTT TATTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT T
128655323 TGTTGTTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TATTT
Found at i:128659734 original size:3 final size:3
Alignment explanation
Indices: 128659726--128659793 Score: 61
Period size: 3 Copynumber: 23.0 Consensus size: 3
128659716 ATTTTCGGCA
* * *
128659726 AAG AAG AAG AAG AAA AAG AGAG AAG AAG -GG AAG AAG -GG AAG AAG
1 AAG AAG AAG AAG AAG AAG A-AG AAG AAG AAG AAG AAG AAG AAG AAG
*
128659770 -AG AAG AAG AAG AAAG AAA AAG AAG
1 AAG AAG AAG AAG -AAG AAG AAG AAG
128659794 GAGAGGAGGA
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
2 4 0.08
3 42 0.81
4 6 0.12
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:128659751 original size:16 final size:15
Alignment explanation
Indices: 128659725--128659793 Score: 61
Period size: 16 Copynumber: 4.5 Consensus size: 15
128659715 CATTTTCGGC
128659725 AAAGAAGAAGAAGAA
1 AAAGAAGAAGAAGAA
128659740 AAAGAGAGAAGAAGGGAA
1 AAAGA-AGAAGAA--GAA
* *
128659758 GAAG-GGAAGAAG-A
1 AAAGAAGAAGAAGAA
*
128659771 GAAGAAGAAGAAAGAA
1 AAAGAAGAAG-AAGAA
128659787 AAAGAAG
1 AAAGAAG
128659794 GAGAGGAGGA
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
13 5 0.11
14 5 0.11
15 8 0.18
16 20 0.45
18 6 0.14
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (15 bp):
AAAGAAGAAGAAGAA
Found at i:128659778 original size:8 final size:8
Alignment explanation
Indices: 128659726--128659778 Score: 58
Period size: 8 Copynumber: 6.9 Consensus size: 8
128659716 ATTTTCGGCA
128659726 AAGAAGAAG
1 AAGAAG-AG
128659735 AAGAA-A-
1 AAGAAGAG
128659741 AAG-AGAG
1 AAGAAGAG
*
128659748 AAGAAGGG
1 AAGAAGAG
*
128659756 AAGAAGGG
1 AAGAAGAG
128659764 AAGAAGAG
1 AAGAAGAG
128659772 AAGAAGA
1 AAGAAGA
128659779 AGAAAGAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
5 1 0.03
6 4 0.10
7 4 0.10
8 25 0.64
9 5 0.13
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (8 bp):
AAGAAGAG
Found at i:128659879 original size:14 final size:14
Alignment explanation
Indices: 128659830--128659892 Score: 58
Period size: 14 Copynumber: 4.4 Consensus size: 14
128659820 TGAGAGAAGA
128659830 AAAAAGAA--AAAG
1 AAAAAGAAGGAAAG
128659842 AAAAAGAGAAGGAGAAG
1 -AAAA-AGAAGGA-AAG
* * *
128659859 AAGAAGAGGGAAGG
1 AAAAAGAAGGAAAG
128659873 AAAAAGAAGGAAAG
1 AAAAAGAAGGAAAG
128659887 AAAAAG
1 AAAAAG
128659893 GTAATTTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
13 4 0.10
14 23 0.57
15 6 0.15
16 4 0.10
17 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (14 bp):
AAAAAGAAGGAAAG
Found at i:128659879 original size:17 final size:17
Alignment explanation
Indices: 128659835--128659892 Score: 50
Period size: 19 Copynumber: 3.4 Consensus size: 17
128659825 GAAGAAAAAA
*
128659835 GAAAAAGAAAAAGAGAAG
1 GAAAAAG-AAGAGAGAAG
*
128659853 GAGAAGAAGAAGAGGGAAG
1 GA-AA-AAGAAGAGAGAAG
128659872 GAAAAAGAAG-GA-AA-
1 GAAAAAGAAGAGAGAAG
128659886 GAAAAAG
1 GAAAAAG
128659893 GTAATTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
14 7 0.20
15 2 0.06
16 1 0.03
17 6 0.17
18 4 0.11
19 12 0.34
20 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (17 bp):
GAAAAAGAAGAGAGAAG
Found at i:128660375 original size:30 final size:31
Alignment explanation
Indices: 128660335--128660393 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
128660325 TTTTGTTAAA
*
128660335 ATAATATAAAAAAATAAAATATGAAAATAGT
1 ATAATATAAAAAAATAAAATACGAAAATAGT
*
128660366 ATAAT-TAAAAAAATAAAATCCGAAAATA
1 ATAATATAAAAAAATAAAATACGAAAATA
128660394 AAAAAATACG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (31 bp):
ATAATATAAAAAAATAAAATACGAAAATAGT
Found at i:128660485 original size:136 final size:132
Alignment explanation
Indices: 128660345--128660600 Score: 327
Period size: 131 Copynumber: 1.9 Consensus size: 132
128660335 ATAATATAAA
** * * *
128660345 AAAATAAAATATGAAAATAGTATAATTAAAAAAATAAAATCCGAAAATAAAAAAATACGAACAAG
1 AAAATAAAATACCAAAATAATATAATTAAAAAAATAAAATACG-----AAAAAAATACGAACAAA
* *
128660410 GTGCCAAAGTCA-GGTTACTTATTAAATTAATATAAAAAA-ACTTAAATAATACATTTGAAAGAT
61 GTGCCAAAATCAGGGTTACTTATTAAA-AAATATAAAAAATACTTAAATAATACATTTGAAAGAT
128660473 TTTATGCT
125 TTTATGCT
* * * * *
128660481 AAAATAAAATACCAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
1 AAAATAAAATACCAAAATAATATAATTAAAAAAATAAAATACGAAAAAAATACGAACAAAGTGCC
*
128660546 AAAATCAGGGTTATTTATTAAAAAATATAAAAAATACTTAAATAATACATTTGAA
66 AAAATCAGGGTTACTTATTAAAAAATATAAAAAATACTTAAATAATACATTTGAA
128660601 GCATTATGTA
Statistics
Matches: 105, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
131 36 0.34
132 33 0.31
136 36 0.34
ACGTcount: A:0.57, C:0.07, G:0.08, T:0.28
Consensus pattern (132 bp):
AAAATAAAATACCAAAATAATATAATTAAAAAAATAAAATACGAAAAAAATACGAACAAAGTGCC
AAAATCAGGGTTACTTATTAAAAAATATAAAAAATACTTAAATAATACATTTGAAAGATTTTATG
CT
Found at i:128660643 original size:145 final size:145
Alignment explanation
Indices: 128660481--128661390 Score: 1013
Period size: 145 Copynumber: 6.1 Consensus size: 145
128660471 ATTTTATGCT
*
128660481 AAAATAAAATACCAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
1 AAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
*
128660546 -AAAATCAGGGTTATTTATTAAAAAATATAAAAAATACTTAAATAATACATTTGAAGCATTATGT
66 CAAAATCAGGGTTATTTATTAAAAAATATAAAAAATACTTAAATAATACATTTGAAACATTATGT
128660610 ACTAAAATAATATAA
131 ACTAAAATAATATAA
*
128660625 AGAAATAAAATACGAAAATAATATATTTT-AAAAATAATATACGAAATAAAAAAATTACGAAGAA
1 A-AAATAAAATACGAAAATAATATATTTTAAAAAATAATATACG----AAAAAAA-TACGAATAA
* * *
128660689 AGT-ATCAAAATCAGGGTTATTTAGTAAAAAACCCTTAATATAAAGAA-ACAGTTAATTAATACA
60 AGTGCTCAAAATCAGGGTTATTTATTAAAAAA----T-ATA-AAA-AATAC--TTAAATAATACA
*** * * *
128660752 TTTGAATTTTTTTTTGCTAAAATAATATAA
116 TTTGAAACATTATGTACTAAAATAATATAA
*
128660782 AAAATAAAATAAGAAAATAATATATTTTAAAAAATAATATAC-AAAAAAATACGAATAAAGTGCT
1 AAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
* *
128660846 -AAAATCAGGGATATTTATTGAAAAAATATAAAAAATACTGAAATAATACATTTGAAACATTATG
66 CAAAATCAGGGTTATTTATT-AAAAAATATAAAAAATACTTAAATAATACATTTGAAACATTATG
128660910 TACTAAAATAATATGAA
130 TACTAAAATAATAT-AA
* * *
128660927 GAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATAC-AAAAAAATACGAAAAAAGTG-T
1 AAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
* *
128660990 CAAAATCAGGGTTATTTATTAAATTAGTATAAAAAAACACTTACATAATATACATAATACATTTG
66 CAAAATCAGGGTTATTTATTAAA--A-AATATAAAAA-A--TAC-T--TA-A-ATAATACATTTG
* * *
128661055 AAACATTTTTTGCTAAAATAATATAA
120 AAACATTATGTACTAAAATAATATAA
* *
128661081 AAAATAAAATAGGAAAATAATATATTTTAAAAAATAATATACG-AAAAAATATGAATAAAGTGCT
1 AAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
** * * *
128661145 -AAAATCAGGGTTATTTATTAAAAAAATATTTAAAACACTTAAATAATATATTTAAAACATTATG
66 CAAAATCAGGGTTATTTATT-AAAAAATATAAAAAATACTTAAATAATACATTTGAAACATTATG
* *
128661209 TACTAAAATAAGGTTTTA
130 TACTAAAATAA--TATAA
* * *
128661227 AAATTAAATAATACGAAAGTAATATA-TTTAAAAAA-AAGATACGAAAAAAAATACGAA-AAAGT
1 AAAAT-AA-AATACGAAAATAATATATTTTAAAAAATAATATACG-AAAAAAATACGAATAAAGT
* * * *
128661289 G-TCAAAATCAGTGTTATTTATTAAATTAATATAAAAAAATACTTACATAATACATTTAAAACAT
63 GCTCAAAATCAGGGTTATTTATTAAA-AAATAT-AAAAAATACTTAAATAATACATTTGAAACAT
* *
128661353 T-TTTGCTAAAATAATATAA
126 TATGTACTAAAATAATATAA
*
128661372 AAAATAATATACGAAAATA
1 AAAATAAAATACGAAAATA
128661391 TTTTACTTAT
Statistics
Matches: 650, Mismatches: 71, Indels: 91
0.80 0.09 0.11
Matches are distributed among these distances:
143 10 0.02
144 81 0.12
145 114 0.18
146 26 0.04
147 62 0.10
148 64 0.10
149 37 0.06
150 3 0.00
151 30 0.05
152 20 0.03
153 3 0.00
154 81 0.12
155 42 0.06
156 28 0.04
157 49 0.08
ACGTcount: A:0.56, C:0.06, G:0.08, T:0.30
Consensus pattern (145 bp):
AAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
CAAAATCAGGGTTATTTATTAAAAAATATAAAAAATACTTAAATAATACATTTGAAACATTATGT
ACTAAAATAATATAA
Found at i:128660647 original size:29 final size:29
Alignment explanation
Indices: 128660615--128660670 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
128660605 TATGTACTAA
128660615 AATA-ATATAAAGAAATAAAATACGAAAAT
1 AATATATATAAA-AAATAAAATACGAAAAT
* * *
128660644 AATATATTTTAAAAATAATATACGAAA
1 AATATATATAAAAAATAAAATACGAAA
128660671 TAAAAAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 18 0.78
30 5 0.22
ACGTcount: A:0.64, C:0.04, G:0.05, T:0.27
Consensus pattern (29 bp):
AATATATATAAAAAATAAAATACGAAAAT
Found at i:128660683 original size:16 final size:18
Alignment explanation
Indices: 128660653--128660685 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
128660643 TAATATATTT
128660653 TAAAAATAATATACGAAA
1 TAAAAATAATATACGAAA
128660671 TAAAAA-AAT-TACGAA
1 TAAAAATAATATACGAA
128660686 GAAAGTATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 3 0.20
18 6 0.40
ACGTcount: A:0.67, C:0.06, G:0.06, T:0.21
Consensus pattern (18 bp):
TAAAAATAATATACGAAA
Found at i:128660785 original size:12 final size:13
Alignment explanation
Indices: 128660770--128660805 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
128660760 TTTTTTTGCT
128660770 AAAATAATATAA-
1 AAAATAATATAAG
*
128660782 AAAATAAAATAAG
1 AAAATAATATAAG
128660795 AAAATAATATA
1 AAAATAATATA
128660806 TTTTAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (13 bp):
AAAATAATATAAG
Found at i:128660807 original size:301 final size:292
Alignment explanation
Indices: 128660481--128661390 Score: 1205
Period size: 301 Copynumber: 3.1 Consensus size: 292
128660471 ATTTTATGCT
*
128660481 AAAATAAAATACCAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
1 AAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
*
128660546 AAAATCAGGGTTATTTATT-AAAAAATATAAAAAATACTTAAATAATACATTTGAAGCATTATGT
66 AAAATCAGGGTTATTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAAACATTATGT
128660610 ACTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAATAATATACGAAATAAA
131 ACTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAA-AATATACG-AA-AAA
* * * *
128660675 AAAATTACGAAGAAAGTATCAAAATCAGGGTTATTTAGTAAAAAACCCTTAATATAAAGAAACAG
193 AAAA-TACGAA-AAAGTGTCAAAATCAGGGTTATTTA-T--TAAA---TTAATATAAAAAAACAC
***
128660740 TTA-ATTAATACATTTGAATTTTTTTTTGCTAAAATAATATAA
250 TTACATTAATACATTTGAAAAATTTTTTGCTAAAATAATATAA
*
128660782 AAAATAAAATAAGAAAATAATATATTTTAAAAAATAATATAC-AAAAAAATACGAATAAAGTGCT
1 AAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
* * *
128660846 AAAATCAGGGATATTTATTGAAAAAATATAAAAAATACTGAAATAATACATTTGAAACATTATGT
66 AAAATCAGGGTTATTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAAACATTATGT
*
128660911 ACTAAAATAATATGAAGAAATAAAATACGAAAATAATATATTTT-AAAAAATA-A-GATACAAAA
131 ACTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAAATATACGA-A-AAAA
*
128660973 AAATACGAAAAAAGTGTCAAAATCAGGGTTATTTATTAAATTAGTATAAAAAAACACTTACATAA
194 AAATACG-AAAAAGTGTCAAAATCAGGGTTATTTATTAAATTAATATAAAAAAACACTTAC----
*
128661038 TATACATAATACATTTGAAACATTTTTTGCTAAAATAATATAA
254 -AT---TAATACATTTGAAAAATTTTTTGCTAAAATAATATAA
* *
128661081 AAAATAAAATAGGAAAATAATATATTTTAAAAAATAATATACG-AAAAAATATGAATAAAGTGCT
1 AAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
** * * *
128661145 AAAATCAGGGTTATTTATTAAAAAAATATTTAAAACACTTAAATAATATATTTAAAACATTATGT
66 AAAATCAGGGTTATTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAAACATTATGT
* * * * * *
128661210 ACTAAAATAAGGTTTTAA-AATTAAATAATACGAAAGTAATATATTTAAAAAAAAGATACG-AAA
131 ACTAAAATAA--TATAAAGAAAT-AA-AATACGAAAATAATATATTTTAAAAAAATATACGAAAA
* *
128661273 AAAAATACGAAAAAGTGTCAAAATCAGTGTTATTTATTAAATTAATATAAAAAAATACTTACA-T
192 AAAAATACGAAAAAGTGTCAAAATCAGGGTTATTTATTAAATTAATATAAAAAAACACTTACATT
128661337 AATACATTT-AAAACA-TTTTTGCTAAAATAATATAA
257 AATACATTTGAAAA-ATTTTTTGCTAAAATAATATAA
*
128661372 AAAATAATATACGAAAATA
1 AAAATAAAATACGAAAATA
128661391 TTTTACTTAT
Statistics
Matches: 551, Mismatches: 37, Indels: 52
0.86 0.06 0.08
Matches are distributed among these distances:
290 17 0.03
291 40 0.07
292 11 0.02
293 3 0.01
295 1 0.00
296 32 0.06
297 11 0.02
298 1 0.00
299 166 0.30
300 47 0.09
301 182 0.33
302 30 0.05
303 8 0.01
304 1 0.00
305 1 0.00
ACGTcount: A:0.56, C:0.06, G:0.08, T:0.30
Consensus pattern (292 bp):
AAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
AAAATCAGGGTTATTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAAACATTATGT
ACTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAAATATACGAAAAAAAA
ATACGAAAAAGTGTCAAAATCAGGGTTATTTATTAAATTAATATAAAAAAACACTTACATTAATA
CATTTGAAAAATTTTTTGCTAAAATAATATAA
Found at i:128661128 original size:154 final size:151
Alignment explanation
Indices: 128660888--128661390 Score: 565
Period size: 154 Copynumber: 3.4 Consensus size: 151
128660878 AAATACTGAA
* *
128660888 ATAATACATTTGAAACATTATGTACTAAAATAATATGAAGAAATAAAATACGAAAATAATATATT
1 ATAATACATTTAAAACATTATGTACTAAAATAATAT-AAAAAATAAAATACGAAAATAATATATT
* *
128660953 TTAAAAAATAAGATACAAAAAAATACGAAAAAAGTGTCAAAATCAGGGTTATTTATTAAATTAGT
65 TTAAAAAATAAGATACGAAAAAATACGAAAAAAGTGTCAAAATCAGGGTTATTTATTAAATTAAT
128661018 ATAAAAAAACACTTACATAATATAC
130 AT-AAAAAACAC-TAC-TAATATAC
* * * * *
128661043 ATAATACATTTGAAACATTTTTTGCTAAAATAATATAAAAAATAAAATAGGAAAATAATATATTT
1 ATAATACATTTAAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATAATATATTT
* * * **
128661108 TAAAAAATAATATACGAAAAAATATGAATAAAGTG-CTAAAATCAGGGTTATTTATTAAAAAAAT
66 TAAAAAATAAGATACGAAAAAATACGAAAAAAGTGTC-AAAATCAGGGTTATTTATTAAATTAAT
**
128661172 ATTTAAAACACT--TAA-ATA-
130 ATAAAAAACACTACTAATATAC
* * * *
128661190 AT-AT--ATTTAAAACATTATGTACTAAAATAAGGTTTTAAAATTAAATAATACGAAAGTAATAT
1 ATAATACATTTAAAACATTATGTACTAAAATAA--TATAAAAAAT-AA-AATACGAAAATAATAT
*
128661252 A-TTTAAAAAA-AAGATACGAAAAAAAATACG-AAAAAGTGTCAAAATCAGTGTTATTTATTAAA
62 ATTTTAAAAAATAAGATACG--AAAAAATACGAAAAAAGTGTCAAAATCAGGGTTATTTATTAAA
128661314 TTAATATAAAAAA-A-TAC---T-TAC
125 TTAATATAAAAAACACTACTAATATAC
* * *
128661335 ATAATACATTTAAAACATT-TTTGCTAAAATAATATAAAAAATAATATACGAAAATA
1 ATAATACATTTAAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATA
128661391 TTTTACTTAT
Statistics
Matches: 295, Mismatches: 38, Indels: 42
0.79 0.10 0.11
Matches are distributed among these distances:
143 10 0.03
144 26 0.09
145 10 0.03
146 19 0.06
147 61 0.21
148 40 0.14
149 3 0.01
152 1 0.00
153 8 0.03
154 84 0.28
155 33 0.11
ACGTcount: A:0.55, C:0.07, G:0.08, T:0.31
Consensus pattern (151 bp):
ATAATACATTTAAAACATTATGTACTAAAATAATATAAAAAATAAAATACGAAAATAATATATTT
TAAAAAATAAGATACGAAAAAATACGAAAAAAGTGTCAAAATCAGGGTTATTTATTAAATTAATA
TAAAAAACACTACTAATATAC
Found at i:128661186 original size:21 final size:22
Alignment explanation
Indices: 128661162--128661203 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
128661152 GGGTTATTTA
128661162 TTAAA-AAAATATTTAAAACAC
1 TTAAATAAAATATTTAAAACAC
*
128661183 TTAAATAATATATTTAAAACA
1 TTAAATAAAATATTTAAAACA
128661204 TTATGTACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (22 bp):
TTAAATAAAATATTTAAAACAC
Found at i:128661275 original size:13 final size:12
Alignment explanation
Indices: 128661257--128661286 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
128661247 AATATATTTA
128661257 AAAAAAAGATACG
1 AAAAAAA-ATACG
128661270 AAAAAAAATACG
1 AAAAAAAATACG
128661282 AAAAA
1 AAAAA
128661287 GTGTCAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.77, C:0.07, G:0.10, T:0.07
Consensus pattern (12 bp):
AAAAAAAATACG
Found at i:128663346 original size:72 final size:72
Alignment explanation
Indices: 128663257--128663392 Score: 200
Period size: 72 Copynumber: 1.9 Consensus size: 72
128663247 CGAGCAGTCG
* * *
128663257 CATTCACATTCGACTGATACTTCTTATCATCCGGATTTGGCAGGCAATGACTATTTCTCGGGCTC
1 CATTCACATTCGACTGATACTTCTTATCATCCAGATTTGACAGGCAATGACAATTTCTCGGGCTC
128663322 GTCATCA
66 GTCATCA
* * * * *
128663329 CATTCACTTTCGGCTGATACTTCTTATCATCCATATTTTACGGGCAATGACAATTTCTCGGGCT
1 CATTCACATTCGACTGATACTTCTTATCATCCAGATTTGACAGGCAATGACAATTTCTCGGGCT
128663393 TATCGAGAGG
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
72 56 1.00
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.35
Consensus pattern (72 bp):
CATTCACATTCGACTGATACTTCTTATCATCCAGATTTGACAGGCAATGACAATTTCTCGGGCTC
GTCATCA
Found at i:128667868 original size:24 final size:25
Alignment explanation
Indices: 128667814--128667874 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 25
128667804 TACCTTCTTT
*
128667814 TTTTCTTCTCC-TTCTTTTTCTTCC
1 TTTTCTTCTCCTTTCTTTTTCTTCA
*
128667838 TTCTCTTCTCCTTTCTTTCTT-TT-A
1 TTTTCTTCTCCTTTCTTT-TTCTTCA
128667862 TTTTCTTCTCCTT
1 TTTTCTTCTCCTT
128667875 GCTGCTGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
24 22 0.69
25 8 0.25
26 2 0.06
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (25 bp):
TTTTCTTCTCCTTTCTTTTTCTTCA
Found at i:128668802 original size:22 final size:23
Alignment explanation
Indices: 128668759--128668804 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
128668749 TTAATTTTGA
*
128668759 ATTTTTGAAATTTAATTAAATTT
1 ATTTATGAAATTTAATTAAATTT
*
128668782 ATTTATGAAA-TTAATTTAATTT
1 ATTTATGAAATTTAATTAAATTT
128668804 A
1 A
128668805 AGTTTAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (23 bp):
ATTTATGAAATTTAATTAAATTT
Found at i:128671477 original size:42 final size:42
Alignment explanation
Indices: 128671431--128671573 Score: 101
Period size: 42 Copynumber: 3.1 Consensus size: 42
128671421 AAAATCAGAG
128671431 TGAATTGAAGATGGAAATTGTGAAATTGAAGCAAAAAAATGA
1 TGAATTGAAGATGGAAATTGTGAAATTGAAGCAAAAAAATGA
* * ** *
128671473 TGAATCTAATGATAAACTGGAAGCTGAGATTGGGATTTTGAAG-AAAAATCAAAG-
1 TGAA--T--TGA-AGA-TGG-A----A-ATTGTGAAATTGAAGCAAAAA--AATGA
128671527 TGAATTGAAGATGGAAATTGTGAAATTGAAGCAAAAAAATGA
1 TGAATTGAAGATGGAAATTGTGAAATTGAAGCAAAAAAATGA
128671569 TGAAT
1 TGAAT
128671574 CTAATGATAA
Statistics
Matches: 75, Mismatches: 10, Indels: 32
0.64 0.09 0.27
Matches are distributed among these distances:
41 3 0.04
42 21 0.28
43 6 0.08
44 1 0.01
46 3 0.04
47 3 0.04
48 6 0.08
49 3 0.04
50 3 0.04
52 1 0.01
53 6 0.08
54 16 0.21
55 3 0.04
ACGTcount: A:0.47, C:0.04, G:0.24, T:0.25
Consensus pattern (42 bp):
TGAATTGAAGATGGAAATTGTGAAATTGAAGCAAAAAAATGA
Found at i:128671519 original size:96 final size:96
Alignment explanation
Indices: 128671394--128671587 Score: 379
Period size: 96 Copynumber: 2.0 Consensus size: 96
128671384 AATACTGAAT
*
128671394 TGGAAGCTGAGATTGGGATTTTGAAGAAAAATCAGAGTGAATTGAAGATGGAAATTGTGAAATTG
1 TGGAAGCTGAGATTGGGATTTTGAAGAAAAATCAAAGTGAATTGAAGATGGAAATTGTGAAATTG
128671459 AAGCAAAAAAATGATGAATCTAATGATAAAC
66 AAGCAAAAAAATGATGAATCTAATGATAAAC
128671490 TGGAAGCTGAGATTGGGATTTTGAAGAAAAATCAAAGTGAATTGAAGATGGAAATTGTGAAATTG
1 TGGAAGCTGAGATTGGGATTTTGAAGAAAAATCAAAGTGAATTGAAGATGGAAATTGTGAAATTG
128671555 AAGCAAAAAAATGATGAATCTAATGATAAAC
66 AAGCAAAAAAATGATGAATCTAATGATAAAC
128671586 TG
1 TG
128671588 ACTGTATTCG
Statistics
Matches: 97, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 97 1.00
ACGTcount: A:0.45, C:0.05, G:0.25, T:0.25
Consensus pattern (96 bp):
TGGAAGCTGAGATTGGGATTTTGAAGAAAAATCAAAGTGAATTGAAGATGGAAATTGTGAAATTG
AAGCAAAAAAATGATGAATCTAATGATAAAC
Found at i:128671847 original size:42 final size:41
Alignment explanation
Indices: 128671771--128672152 Score: 291
Period size: 42 Copynumber: 9.1 Consensus size: 41
128671761 TGAGACACAA
* * * * * *
128671771 GTCACTAAGAGTTTGCTTGAGCTTATGGGAACTGATCAAACG
1 GTCACAAAGAGCTTGCCTGAGCCTATGGG-ACTGACCAAAGG
** **
128671813 GTCACAAAGAGCTTGAATGAGCCTATGGAGACTGACCGGAGG
1 GTCACAAAGAGCTTGCCTGAGCCTATGG-GACTGACCAAAGG
* * * *
128671855 GGCACCAAGAACTTGCCTGAGCCTATAGGGACTGACCAGAGG
1 GTCACAAAGAGCTTGCCTGAGCCTAT-GGGACTGACCAAAGG
* * * * *
128671897 GTCACCAAGAACTTGCCTGGGCCTATGGGGAATGACCAAAGT
1 GTCACAAAGAGCTTGCCTGAGCCTAT-GGGACTGACCAAAGG
* *
128671939 GTCACAAAGAGCTTGCCTGAGCCTATGGGGACTGACCGAAGT
1 GTCACAAAGAGCTTGCCTGAGCCTAT-GGGACTGACCAAAGG
*
128671981 GT-AGCAAAGAGCTTGCCTGAGCCTATAGGGACTGACCAGAGG
1 GTCA-CAAAGAGCTTGCCTGAGCCTAT-GGGACTGACCAAAGG
* * * *
128672023 GTCACCAAAGA-CTTGGCTGAGCCTACGGGGACTGACCAATGT
1 GTCA-CAAAGAGCTTGCCTGAGCCTA-TGGGACTGACCAAAGG
* * * * ** * *
128672065 GTCCCAAAGACCTTGCCTAAGCCAATGGAGACCAACCAACGT
1 GTCACAAAGAGCTTGCCTGAGCCTATGG-GACTGACCAAAGG
* * * * * *
128672107 ATCACAAAGACCTTGCCTAAGCCTATGGAGATTGGCCAAAGT
1 GTCACAAAGAGCTTGCCTGAGCCTATGG-GACTGACCAAAGG
128672149 GTCA
1 GTCA
128672153 TCAACTCTAA
Statistics
Matches: 280, Mismatches: 53, Indels: 14
0.81 0.15 0.04
Matches are distributed among these distances:
41 9 0.03
42 261 0.93
43 10 0.04
ACGTcount: A:0.29, C:0.24, G:0.28, T:0.19
Consensus pattern (41 bp):
GTCACAAAGAGCTTGCCTGAGCCTATGGGACTGACCAAAGG
Found at i:128671996 original size:126 final size:125
Alignment explanation
Indices: 128671813--128672096 Score: 383
Period size: 126 Copynumber: 2.3 Consensus size: 125
128671803 TGATCAAACG
** * *
128671813 GTCACAAAGAGCTTGAATGAGCCTATGGAGACTGACCGGAGGGGCACCAAGAACTTGCCTGAGCC
1 GTCACAAAGAGCTTGCCTGAGCCTATGGAGACTGACCGAAGGAGCA-CAAGAACTTGCCTGAGCC
* *
128671878 TATAGGGACTGACCAGAGGGTCACC-AAGAACTTGCCTGGGCCTATGGGGAATGACCAAAGT
65 TATAGGGACTGACCAGAGGGTCACCAAAG-ACTTGCCTGAGCCTACGGGGAATGACCAAAGT
* *
128671939 GTCACAAAGAGCTTGCCTGAGCCTATGGGGACTGACCGAAGTGTAGCA-AAGAGCTTGCCTGAGC
1 GTCACAAAGAGCTTGCCTGAGCCTATGGAGACTGACCGAAG-G-AGCACAAGAACTTGCCTGAGC
* * *
128672003 CTATAGGGACTGACCAGAGGGTCACCAAAGACTTGGCTGAGCCTACGGGGACTGACCAATGT
64 CTATAGGGACTGACCAGAGGGTCACCAAAGACTTGCCTGAGCCTACGGGGAATGACCAAAGT
* * * *
128672065 GTCCCAAAGACCTTGCCTAAGCCAATGGAGAC
1 GTCACAAAGAGCTTGCCTGAGCCTATGGAGAC
128672097 CAACCAACGT
Statistics
Matches: 139, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
126 132 0.95
127 4 0.03
128 3 0.02
ACGTcount: A:0.29, C:0.24, G:0.30, T:0.17
Consensus pattern (125 bp):
GTCACAAAGAGCTTGCCTGAGCCTATGGAGACTGACCGAAGGAGCACAAGAACTTGCCTGAGCCT
ATAGGGACTGACCAGAGGGTCACCAAAGACTTGCCTGAGCCTACGGGGAATGACCAAAGT
Found at i:128672115 original size:126 final size:126
Alignment explanation
Indices: 128671861--128672132 Score: 352
Period size: 126 Copynumber: 2.2 Consensus size: 126
128671851 GAGGGGCACC
* *
128671861 AAGAACTTGCCTGAGCCTATAGGGACTGACCAGAGGGTCACCAAGAACTTGCCTGGGCCTATGGG
1 AAGAACTTGCCTGAGCCTATAGGGACTGACCAGAGGGTCACCAAGAACTTGCCTGAGCCTACGGG
* * * * ** *
128671926 GAATGACCAAAGTGTCACAAAGAGCTTGCCTGAGCCTATGGGGACTGACCGAAGTGTAGCA
66 GAATGACCAAAGTGTCACAAAGACCTTGCCTAAGCCAATGGAGACCAACCGAAGTATAGCA
* *
128671987 AAGAGCTTGCCTGAGCCTATAGGGACTGACCAGAGGGTCACCAA-AGACTTGGCTGAGCCTACGG
1 AAGAACTTGCCTGAGCCTATAGGGACTGACCAGAGGGTCACCAAGA-ACTTGCCTGAGCCTACGG
* * *
128672051 GGACTGACCAATGTGTCCCAAAGACCTTGCCTAAGCCAATGGAGACCAACC-AACGTATCA-CA
65 GGAATGACCAAAGTGTCACAAAGACCTTGCCTAAGCCAATGGAGACCAACCGAA-GTAT-AGCA
* *
128672113 AAGACCTTGCCTAAGCCTAT
1 AAGAACTTGCCTGAGCCTAT
128672133 GGAGATTGGC
Statistics
Matches: 127, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
125 3 0.02
126 123 0.97
127 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.27, T:0.18
Consensus pattern (126 bp):
AAGAACTTGCCTGAGCCTATAGGGACTGACCAGAGGGTCACCAAGAACTTGCCTGAGCCTACGGG
GAATGACCAAAGTGTCACAAAGACCTTGCCTAAGCCAATGGAGACCAACCGAAGTATAGCA
Found at i:128677244 original size:30 final size:31
Alignment explanation
Indices: 128677183--128677245 Score: 83
Period size: 30 Copynumber: 2.0 Consensus size: 31
128677173 GGTCAAGATT
*
128677183 AAATTGAAAATTTGAAAAAAGTATAGGGACTA
1 AAATTAAAAATTTG-AAAAAGTATAGGGACTA
* *
128677215 AAATTAAAAATTTG-AAACGTATGGGGACTA
1 AAATTAAAAATTTGAAAAAGTATAGGGACTA
128677245 A
1 A
128677246 TTGTGATCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 15 0.54
32 13 0.46
ACGTcount: A:0.51, C:0.05, G:0.19, T:0.25
Consensus pattern (31 bp):
AAATTAAAAATTTGAAAAAGTATAGGGACTA
Found at i:128678871 original size:2 final size:2
Alignment explanation
Indices: 128678864--128678890 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
128678854 TAAATTTCTC
128678864 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
128678891 CACACACAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:128679491 original size:42 final size:42
Alignment explanation
Indices: 128679430--128679591 Score: 191
Period size: 42 Copynumber: 3.7 Consensus size: 42
128679420 TCGTTTTCTA
** *
128679430 GATGCCATAGTTCAACTATGGTCTTACACATCTTCACATTAT-
1 GATGCCATAGCCCAGCTATGGTCTTACACATCTTCACA-TATC
* *
128679472 GATGCCATAGCCCAGCTATGGTCTTACACATATTCATATATC
1 GATGCCATAGCCCAGCTATGGTCTTACACATCTTCACATATC
*
128679514 GATGCCATATCCCAGCTATGGTCTTACACGTAATCACATATCACATATC
1 GATGCCATAGCCCAGCTATGGTCTTACAC---AT--C-T-TCACATATC
128679563 GATGCCATAGCCCAGCTATGGTCTTACAC
1 GATGCCATAGCCCAGCTATGGTCTTACAC
128679592 GAATCACATA
Statistics
Matches: 103, Mismatches: 9, Indels: 9
0.85 0.07 0.07
Matches are distributed among these distances:
41 3 0.03
42 61 0.59
45 2 0.02
48 1 0.01
49 36 0.35
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.30
Consensus pattern (42 bp):
GATGCCATAGCCCAGCTATGGTCTTACACATCTTCACATATC
Found at i:128679571 original size:49 final size:48
Alignment explanation
Indices: 128679511--128679681 Score: 197
Period size: 47 Copynumber: 3.6 Consensus size: 48
128679501 ATATTCATAT
*
128679511 ATCGATGCCATATCCCAGCTATGGTCTTACACGTAATCACATATCACA
1 ATCGATGCCATATCCCAGATATGGTCTTACACGTAATCACATATCACA
* * *
128679559 TATCGATGCCATAGCCCAGCTATGGTCTTACACG-AATCACATATCTCA
1 -ATCGATGCCATATCCCAGATATGGTCTTACACGTAATCACATATCACA
* * * * * *
128679607 CT-GATGCCATATCCTAGATATGGTATTATACAGT-AGCATATATCAC-
1 ATCGATGCCATATCCCAGATATGGTCTTACAC-GTAATCACATATCACA
*
128679653 ACCGATGCCATATCCCAGATATGGTCTTA
1 ATCGATGCCATATCCCAGATATGGTCTTA
128679682 TACGGAAATC
Statistics
Matches: 104, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
46 24 0.23
47 35 0.34
48 13 0.12
49 32 0.31
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (48 bp):
ATCGATGCCATATCCCAGATATGGTCTTACACGTAATCACATATCACA
Found at i:128681018 original size:44 final size:45
Alignment explanation
Indices: 128680970--128681058 Score: 126
Period size: 46 Copynumber: 2.0 Consensus size: 45
128680960 CATGAATTAT
*
128680970 TCCTGTCTCCAATGCCATA-TATAATATGGACTTACATGGCTCAA
1 TCCTGTCTCCAAAGCCATATTATAATATGGACTTACATGGCTCAA
* * *
128681014 TCCTGTCTCTAAAGCTATATTTCTAATATGGACTTACATGGCTCA
1 TCCTGTCTCCAAAGCCATA-TTATAATATGGACTTACATGGCTCA
128681059 TTTCTGTTCT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 16 0.41
46 23 0.59
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (45 bp):
TCCTGTCTCCAAAGCCATATTATAATATGGACTTACATGGCTCAA
Found at i:128686783 original size:44 final size:45
Alignment explanation
Indices: 128686688--128686802 Score: 144
Period size: 44 Copynumber: 2.6 Consensus size: 45
128686678 ACAGGACAGA
*
128686688 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTATGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCTATGGAG
* *
128686734 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGC-ATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCTA-TGGAG
* **
128686778 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
128686803 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
43 1 0.02
44 34 0.56
46 26 0.43
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCTATGGAG
Found at i:128692609 original size:46 final size:44
Alignment explanation
Indices: 128692505--128692612 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
128692495 TGTCTTTGAC
** * * *
128692505 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
128692549 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
128692595 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
128692613 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:128693869 original size:31 final size:31
Alignment explanation
Indices: 128693826--128693943 Score: 209
Period size: 31 Copynumber: 3.8 Consensus size: 31
128693816 TGTTACACTT
*
128693826 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
128693857 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
128693888 GTAGCCGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
128693919 GTAGCAGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
128693944 TGTCATTTGT
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 83 1.00
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.25
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:128697870 original size:18 final size:18
Alignment explanation
Indices: 128697843--128697878 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
128697833 TTTTTAAATG
128697843 TTAAAAATAACATAATAT
1 TTAAAAATAACATAATAT
*
128697861 TTAAATATAACATAATAT
1 TTAAAAATAACATAATAT
128697879 AAAATATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (18 bp):
TTAAAAATAACATAATAT
Found at i:128698099 original size:59 final size:59
Alignment explanation
Indices: 128698029--128698145 Score: 216
Period size: 59 Copynumber: 2.0 Consensus size: 59
128698019 ACCCTTTTAA
*
128698029 ACTTCAAATAAACTTTTAAACATAGATAGTTAATCTAATTCACGAACAAATCGAATATT
1 ACTTCAAATAAACTTTTAAACATAGATAGATAATCTAATTCACGAACAAATCGAATATT
*
128698088 ACTTCAAATAAACTTTTAAACATAGATAGATAATCTAATTCCCGAACAAATCGAATAT
1 ACTTCAAATAAACTTTTAAACATAGATAGATAATCTAATTCACGAACAAATCGAATAT
128698146 AAAAAATGGC
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.46, C:0.16, G:0.07, T:0.31
Consensus pattern (59 bp):
ACTTCAAATAAACTTTTAAACATAGATAGATAATCTAATTCACGAACAAATCGAATATT
Found at i:128708184 original size:6 final size:6
Alignment explanation
Indices: 128708175--128708204 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
128708165 ATTATAATTA
128708175 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
128708205 GTCAGCTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
ATTTTT
Found at i:128709019 original size:21 final size:21
Alignment explanation
Indices: 128708980--128709020 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
128708970 TCCTCAACAA
*
128708980 ATAAATATATAATTTTTTAAT
1 ATAAATATATAATTATTTAAT
128709001 ATAAATAT-TAATATATTTAA
1 ATAAATATATAAT-TATTTAA
128709021 GTAATTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATAAATATATAATTATTTAAT
Found at i:128712734 original size:141 final size:141
Alignment explanation
Indices: 128712454--128712725 Score: 481
Period size: 141 Copynumber: 1.9 Consensus size: 141
128712444 GCCGCCAACT
*
128712454 CCGCCTCCTGCAGCTGCATATCGTAAACCAAGGCGAAGTTATCAAGCTGTTGGCCGGAACGAGAA
1 CCGCCTCCTGCAGCTGCATATCGTAAACCAAGGCGAAGTTATCAAGCTGTTGGCCGGAAAGAGAA
*
128712519 TGTGAATAATACTCAGAAGTTTCATGTTAAGTACGATGGAAGTGAGTCTCCGGCTCCGCAGCCAG
66 TGTGAATAATACTCAAAAGTTTCATGTTAAGTACGATGGAAGTGAGTCTCCGGCTCCGCAGCCAG
128712584 TGAAGCCACCG
131 TGAAGCCACCG
* *
128712595 CCGCCTCCTGCATCTGGATATCGTAAACCAAGGCGAAGTTATCAAGCTGTTGGCCGGAAAGAGAA
1 CCGCCTCCTGCAGCTGCATATCGTAAACCAAGGCGAAGTTATCAAGCTGTTGGCCGGAAAGAGAA
* * *
128712660 TGTGAATAATGCTCAAAAGTTTCATGTTGAGTACGATGGAAGTGAGTCTCCGGCTCCTCAGCCAG
66 TGTGAATAATACTCAAAAGTTTCATGTTAAGTACGATGGAAGTGAGTCTCCGGCTCCGCAGCCAG
128712725 T
131 T
128712726 AACTCCACCT
Statistics
Matches: 124, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
141 124 1.00
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.23
Consensus pattern (141 bp):
CCGCCTCCTGCAGCTGCATATCGTAAACCAAGGCGAAGTTATCAAGCTGTTGGCCGGAAAGAGAA
TGTGAATAATACTCAAAAGTTTCATGTTAAGTACGATGGAAGTGAGTCTCCGGCTCCGCAGCCAG
TGAAGCCACCG
Found at i:128713137 original size:3 final size:3
Alignment explanation
Indices: 128713129--128713174 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
128713119 CACTCAATCC
* * * *
128713129 CCA CCA CCA CCA CCA CCA CCA CCA CCT GCA CCG CCA ACA CCA CCA C
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA C
128713175 TCAGACCGTC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.30, C:0.63, G:0.04, T:0.02
Consensus pattern (3 bp):
CCA
Found at i:128722144 original size:29 final size:30
Alignment explanation
Indices: 128722111--128722169 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
128722101 GATGCCATAG
128722111 GTCTTTATAC-TTTC-ATTTCTTGAAATTTA
1 GTCTTTATACTTTTCAATTT-TTGAAATTTA
*
128722140 GTCTTTCTACTTTTCAATTTTTGAAATTTA
1 GTCTTTATACTTTTCAATTTTTGAAATTTA
128722170 AGTCAAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 9 0.33
30 14 0.52
31 4 0.15
ACGTcount: A:0.24, C:0.14, G:0.07, T:0.56
Consensus pattern (30 bp):
GTCTTTATACTTTTCAATTTTTGAAATTTA
Found at i:128736827 original size:22 final size:23
Alignment explanation
Indices: 128736795--128736878 Score: 53
Period size: 23 Copynumber: 3.5 Consensus size: 23
128736785 AATCATTGTA
*
128736795 TTTTTATTTTTAGAAAATTAGTT
1 TTTTTACTTTTAGAAAATTAGTT
** * *
128736818 TTTTTA-TTTTTTAATATTAAATT
1 TTTTTACTTTTAGAAAATT-AGTT
*
128736841 TTAGATTTAACTTTTAGAAATTTAGTT
1 TT---TTT-ACTTTTAGAAAATTAGTT
*
128736868 TTTTTATTTTT
1 TTTTTACTTTT
128736879 CAAATATTAA
Statistics
Matches: 45, Mismatches: 10, Indels: 12
0.67 0.15 0.18
Matches are distributed among these distances:
22 9 0.20
23 16 0.36
24 3 0.07
26 3 0.07
27 6 0.13
28 8 0.18
ACGTcount: A:0.29, C:0.01, G:0.06, T:0.64
Consensus pattern (23 bp):
TTTTTACTTTTAGAAAATTAGTT
Found at i:128736877 original size:50 final size:51
Alignment explanation
Indices: 128736802--128736910 Score: 184
Period size: 51 Copynumber: 2.2 Consensus size: 51
128736792 GTATTTTTAT
* *
128736802 TTTTAGAAAATTAGTTTTTTTATTTTT-TAATATTAAATTTTAGATTTAAC
1 TTTTAGAAAATTAGTTTTTTTATTTTTCAAATATTAAATTTTAGATTTAAA
*
128736852 TTTTAGAAATTTAGTTTTTTTATTTTTCAAATATTAAATTTTAGATTTAAA
1 TTTTAGAAAATTAGTTTTTTTATTTTTCAAATATTAAATTTTAGATTTAAA
128736903 TTTTAGAA
1 TTTTAGAA
128736911 GTGTTAACAT
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
50 26 0.47
51 29 0.53
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.57
Consensus pattern (51 bp):
TTTTAGAAAATTAGTTTTTTTATTTTTCAAATATTAAATTTTAGATTTAAA
Found at i:128736903 original size:13 final size:13
Alignment explanation
Indices: 128736885--128736909 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
128736875 TTTTCAAATA
128736885 TTAAATTTTAGAT
1 TTAAATTTTAGAT
128736898 TTAAATTTTAGA
1 TTAAATTTTAGA
128736910 AGTGTTAACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (13 bp):
TTAAATTTTAGAT
Found at i:128737291 original size:143 final size:143
Alignment explanation
Indices: 128737079--128737364 Score: 500
Period size: 143 Copynumber: 2.0 Consensus size: 143
128737069 TTTTAACTTA
128737079 TTTTATAAATAGTTAATGCAATCTCGTTTGGGTTAAGGCTTTGAATATAAAAATTTGAGTCCAAA
1 TTTTATAAATAGTTAATGCAATCTCGTTTGGGTTAAGGCTTTGAATATAAAAATTTGAGTCCAAA
* * **
128737144 CTATATTTAAATCGGAACTGTTTTTCTTTAAATTTGATTTTATTTTTTTGTACATAACGAAGGAA
66 CTATATTTAAACCGGAACTATTTTTCTCCAAATTTGATTTTATTTTTTTGTACATAACGAAGGAA
128737209 AAACTAATGAAAG
131 AAACTAATGAAAG
* * *
128737222 TTTTATAAATAGTTAATGCAATCTCGTTTGGGTTCAGGCTTTGAATATAAAAATTTGAGTTCAAC
1 TTTTATAAATAGTTAATGCAATCTCGTTTGGGTTAAGGCTTTGAATATAAAAATTTGAGTCCAAA
*
128737287 CTATATTTAAACCGGAACTATTTTTCTCCAAATTTGTTTTTATTTTTTTGTACATAACGAAGGAA
66 CTATATTTAAACCGGAACTATTTTTCTCCAAATTTGATTTTATTTTTTTGTACATAACGAAGGAA
128737352 AAACTAATGAAAG
131 AAACTAATGAAAG
128737365 CTTGCGAAGC
Statistics
Matches: 135, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
143 135 1.00
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.40
Consensus pattern (143 bp):
TTTTATAAATAGTTAATGCAATCTCGTTTGGGTTAAGGCTTTGAATATAAAAATTTGAGTCCAAA
CTATATTTAAACCGGAACTATTTTTCTCCAAATTTGATTTTATTTTTTTGTACATAACGAAGGAA
AAACTAATGAAAG
Found at i:128738938 original size:3 final size:3
Alignment explanation
Indices: 128738930--128738965 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
128738920 CTCCATGATC
* *
128738930 ATT ATT ATT GTT ATT ATT ATT ACT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
128738966 TAATCGTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:128739956 original size:3 final size:3
Alignment explanation
Indices: 128739948--128739991 Score: 54
Period size: 3 Copynumber: 14.3 Consensus size: 3
128739938 GCCGCCATGG
*
128739948 CTT CTT CTT CTT CTT CTT CTT CTAAT -TT CTT CTT CAT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CT--T CTT CTT CTT CTT CTT CTT C
128739992 CTCGTGTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
2 1 0.03
3 33 0.92
4 1 0.03
5 1 0.03
ACGTcount: A:0.07, C:0.32, G:0.00, T:0.61
Consensus pattern (3 bp):
CTT
Found at i:128744553 original size:20 final size:20
Alignment explanation
Indices: 128744528--128744566 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
128744518 CTCAATATCC
128744528 AAAATGGTAACAGTTGAAAA
1 AAAATGGTAACAGTTGAAAA
128744548 AAAATGGTAACAGTTGAAA
1 AAAATGGTAACAGTTGAAA
128744567 CCATTAGGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.54, C:0.05, G:0.21, T:0.21
Consensus pattern (20 bp):
AAAATGGTAACAGTTGAAAA
Found at i:128750218 original size:26 final size:26
Alignment explanation
Indices: 128750189--128750238 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
128750179 TGATTTTTTT
128750189 GTTGTTCTTGTTTGGTTCTTTGGGGG
1 GTTGTTCTTGTTTGGTTCTTTGGGGG
* * **
128750215 GTTGTTTTTTTTTTTTTCTTTGGG
1 GTTGTTCTTGTTTGGTTCTTTGGG
128750239 TTAATTTTGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.00, C:0.06, G:0.30, T:0.64
Consensus pattern (26 bp):
GTTGTTCTTGTTTGGTTCTTTGGGGG
Found at i:128751007 original size:2 final size:2
Alignment explanation
Indices: 128751000--128751030 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
128750990 GATCAGTTTG
128751000 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
128751031 GTGTGTGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:128768782 original size:18 final size:18
Alignment explanation
Indices: 128768738--128768784 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
128768728 AATTTTATAA
128768738 AATAGTTTAAAAATTAAAT
1 AATA-TTTAAAAATTAAAT
**
128768757 AATA-TTAAAAATTATTT
1 AATATTTAAAAATTAAAT
*
128768774 TATATTTAAAA
1 AATATTTAAAA
128768785 GATGTTAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 14 0.58
18 6 0.25
19 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
AATATTTAAAAATTAAAT
Found at i:128772165 original size:4 final size:4
Alignment explanation
Indices: 128772156--128772209 Score: 108
Period size: 4 Copynumber: 13.5 Consensus size: 4
128772146 TTGACCCTAT
128772156 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
128772204 ATAC AT
1 ATAC AT
128772210 GCACACACAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 50 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:128772218 original size:2 final size:2
Alignment explanation
Indices: 128772211--128772252 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
128772201 TACATACATG
*
128772211 CA CA CA CA CA CA CA CA CT CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
128772253 TATACATATG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.50, G:0.00, T:0.02
Consensus pattern (2 bp):
CA
Found at i:128776849 original size:21 final size:21
Alignment explanation
Indices: 128776825--128776888 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
128776815 CGAAATTAAA
128776825 CTTAACCCAATCGAATTTCAT
1 CTTAACCCAATCGAATTTCAT
** * * *
128776846 CTTAA-AAAAGC-AA--TAAA
1 CTTAACCCAATCGAATTTCAT
128776863 CTTAACCCAATCGAATTTCAT
1 CTTAACCCAATCGAATTTCAT
128776884 CTTAA
1 CTTAA
128776889 AAAAGCAATA
Statistics
Matches: 29, Mismatches: 10, Indels: 8
0.62 0.21 0.17
Matches are distributed among these distances:
17 7 0.24
18 3 0.10
19 4 0.14
20 3 0.10
21 12 0.41
ACGTcount: A:0.42, C:0.23, G:0.05, T:0.30
Consensus pattern (21 bp):
CTTAACCCAATCGAATTTCAT
Found at i:128776872 original size:38 final size:38
Alignment explanation
Indices: 128776821--128776899 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
128776811 AATTCGAAAT
128776821 TAAACTTAACCCAATCGAATTTCATCTTAAAAAAGCAA
1 TAAACTTAACCCAATCGAATTTCATCTTAAAAAAGCAA
128776859 TAAACTTAACCCAATCGAATTTCATCTTAAAAAAGCAA
1 TAAACTTAACCCAATCGAATTTCATCTTAAAAAAGCAA
128776897 TAA
1 TAA
128776900 TCTAAAGTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.48, C:0.20, G:0.05, T:0.27
Consensus pattern (38 bp):
TAAACTTAACCCAATCGAATTTCATCTTAAAAAAGCAA
Found at i:128776973 original size:18 final size:18
Alignment explanation
Indices: 128776952--128777008 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
128776942 ATGATAATTA
128776952 ATTTTGTGGAAATTCAAT
1 ATTTTGTGGAAATTCAAT
128776970 A-TTTGTGATGATAATT--A-
1 ATTTTGTG--GA-AATTCAAT
128776987 ATTTTGTGGAAATTCAAT
1 ATTTTGTGGAAATTCAAT
128777005 ATTT
1 ATTT
128777009 GTACTTTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 14
0.70 0.00 0.30
Matches are distributed among these distances:
15 4 0.12
16 2 0.06
17 8 0.25
18 12 0.38
19 2 0.06
20 4 0.12
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (18 bp):
ATTTTGTGGAAATTCAAT
Found at i:128776976 original size:17 final size:17
Alignment explanation
Indices: 128776954--128777010 Score: 73
Period size: 17 Copynumber: 3.3 Consensus size: 17
128776944 GATAATTAAT
128776954 TTTGTGGAAATTCAATA
1 TTTGTGGAAATTCAATA
128776971 TTTGTGATGATAATT-AAT-
1 TTTGTG--GA-AATTCAATA
128776989 TTTGTGGAAATTCAATA
1 TTTGTGGAAATTCAATA
128777006 TTTGT
1 TTTGT
128777011 ACTTTATAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
15 4 0.11
16 5 0.14
17 11 0.31
18 6 0.17
19 5 0.14
20 4 0.11
ACGTcount: A:0.32, C:0.04, G:0.18, T:0.47
Consensus pattern (17 bp):
TTTGTGGAAATTCAATA
Found at i:128776976 original size:35 final size:35
Alignment explanation
Indices: 128776937--128777010 Score: 148
Period size: 35 Copynumber: 2.1 Consensus size: 35
128776927 AATGTGCCAA
128776937 TTGTGATGATAATTAATTTTGTGGAAATTCAATAT
1 TTGTGATGATAATTAATTTTGTGGAAATTCAATAT
128776972 TTGTGATGATAATTAATTTTGTGGAAATTCAATAT
1 TTGTGATGATAATTAATTTTGTGGAAATTCAATAT
128777007 TTGT
1 TTGT
128777011 ACTTTATAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.32, C:0.03, G:0.18, T:0.47
Consensus pattern (35 bp):
TTGTGATGATAATTAATTTTGTGGAAATTCAATAT
Found at i:128781802 original size:26 final size:28
Alignment explanation
Indices: 128781773--128781834 Score: 65
Period size: 28 Copynumber: 2.3 Consensus size: 28
128781763 TTAAATTTTA
*
128781773 TTTATTGT-ATAATTTA-ATATATAAAT
1 TTTATTGTAATAATATACATATATAAAT
* * *
128781799 TTTAGTGTAATTATATACATATATAACT
1 TTTATTGTAATAATATACATATATAAAT
*
128781827 TTGATTGT
1 TTTATTGT
128781835 GGTATTAACT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
26 7 0.25
27 6 0.21
28 15 0.54
ACGTcount: A:0.37, C:0.03, G:0.08, T:0.52
Consensus pattern (28 bp):
TTTATTGTAATAATATACATATATAAAT
Found at i:128782382 original size:10 final size:10
Alignment explanation
Indices: 128782354--128782383 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
128782344 CACATGCATG
*
128782354 CTCTCTCTCT
1 CTCTCTCTTT
128782364 CTCTCTCTTT
1 CTCTCTCTTT
128782374 CTCTCTCTTT
1 CTCTCTCTTT
128782384 TTAAGAACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (10 bp):
CTCTCTCTTT
Found at i:128786241 original size:192 final size:192
Alignment explanation
Indices: 128785887--128786285 Score: 568
Period size: 192 Copynumber: 2.1 Consensus size: 192
128785877 CCACCTTGCT
* *
128785887 CAACACTAAGCACGCTACTTGCTAGTTCATTAATCAATGATCCGATCTGTTCATTGGAATTGTGA
1 CAACACTAAGCATGCTACTTGCTAGTTCATTAATCAATGATCCGATCTGTTCACTGGAATTGTGA
* * *
128785952 TTGTAAACCGATGCGTGAATGATGTTATTCATTATGATTTGAAGCGTCGGAAACTCTTTAGTTTG
66 TTGTAAACCGATGCGTGAATGATGTTACTCATTATGATTTGAAGAGTCGGAAACTCTTTACTTTG
* * * *
128786017 ATGCTTAGTCTGTTTCGGTATGAGAGGAATTGTTGAAAAACTGAATCAGTGACTGCATCGAC
131 ATGCATAGTCTGTTTCGGTACGAGAAGAATTGTTGAAAAACTGAATCAGTAACTGCATCGAC
* *
128786079 CAACACTGAGCATGCTACTTGTTAGTTCAATT-ATCAATGATCCGATCTGTTCACTGGAATTGTG
1 CAACACTAAGCATGCTACTTGCTAGTTC-ATTAATCAATGATCCGATCTGTTCACTGGAATTGTG
* * * * *
128786143 ATTGTAAATCGATGCGTGAATGATGTTACTCTTTATGATTTGAAGAGTCTGAAGCTTTTTACTTT
65 ATTGTAAACCGATGCGTGAATGATGTTACTCATTATGATTTGAAGAGTCGGAAACTCTTTACTTT
* * * * * *
128786208 GATGCATATTTTGTTTCTGTACGAGAAGAATTGTTGAAAAATTGAATCAGTAACTGCATCTAT
130 GATGCATAGTCTGTTTCGGTACGAGAAGAATTGTTGAAAAACTGAATCAGTAACTGCATCGAC
128786271 CAACAC-ACAGCATGC
1 CAACACTA-AGCATGC
128786286 AAATGCGTAA
Statistics
Matches: 182, Mismatches: 23, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
192 179 0.98
193 3 0.02
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (192 bp):
CAACACTAAGCATGCTACTTGCTAGTTCATTAATCAATGATCCGATCTGTTCACTGGAATTGTGA
TTGTAAACCGATGCGTGAATGATGTTACTCATTATGATTTGAAGAGTCGGAAACTCTTTACTTTG
ATGCATAGTCTGTTTCGGTACGAGAAGAATTGTTGAAAAACTGAATCAGTAACTGCATCGAC
Found at i:128786849 original size:39 final size:39
Alignment explanation
Indices: 128786795--128786874 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
128786785 AAAAAATGAG
*
128786795 CAAATTAGTCTTTATCATTACATTAAAAAGCAAATTGAT
1 CAAATTAGTCTTTATCATTACATCAAAAAGCAAATTGAT
128786834 CAAATTAGTCTTTATCATTACATCAAAAAGCAAATTGAT
1 CAAATTAGTCTTTATCATTACATCAAAAAGCAAATTGAT
128786873 CA
1 CA
128786875 TTCTTTTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.34
Consensus pattern (39 bp):
CAAATTAGTCTTTATCATTACATCAAAAAGCAAATTGAT
Found at i:128790175 original size:25 final size:25
Alignment explanation
Indices: 128790128--128790175 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
128790118 ATCACAATTC
* *
128790128 AATAATTAATATATGATTTTAAAAA
1 AATAATTAATATATGAGTATAAAAA
128790153 AATAA-TAATATATTGAGTATAAA
1 AATAATTAATATA-TGAGTATAAA
128790176 TACATACATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (25 bp):
AATAATTAATATATGAGTATAAAAA
Found at i:128805228 original size:3 final size:3
Alignment explanation
Indices: 128805222--128805266 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
128805212 GAAGATTTTT
128805222 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
128805267 CTATAAATTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:128806443 original size:20 final size:20
Alignment explanation
Indices: 128806416--128806460 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
128806406 AAAAACATCT
* *
128806416 TTTG-AATGCTTTGCAAATC
1 TTTGAAATGCTTTGAAAATA
*
128806435 TTTGAAATGTTTTGAAAATA
1 TTTGAAATGCTTTGAAAATA
128806455 TTTGAA
1 TTTGAA
128806461 CACTAAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (20 bp):
TTTGAAATGCTTTGAAAATA
Found at i:128806561 original size:23 final size:22
Alignment explanation
Indices: 128806513--128806561 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
128806503 GAGTAACAAT
* *
128806513 TTCTCAATTTAGGGTTCAGCCT
1 TTCTCAATTTAGGGGTCAGCCC
128806535 TTCTCAATTTAGGGGGTCAGCCC
1 TTCTCAATTTA-GGGGTCAGCCC
128806558 TTCT
1 TTCT
128806562 TCCTTTTTCG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.39
Consensus pattern (22 bp):
TTCTCAATTTAGGGGTCAGCCC
Found at i:128807668 original size:27 final size:27
Alignment explanation
Indices: 128807630--128807696 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
128807620 ATGCCTGAAT
* *
128807630 CTAATTCAGTGGGCGTTTCGATAAAAG
1 CTAACTCAGTGGGCGTTTCAATAAAAG
*
128807657 CTAACTCAGTGGGTGTTTCAATAAAAG
1 CTAACTCAGTGGGCGTTTCAATAAAAG
128807684 CTAACTCAGTGGG
1 CTAACTCAGTGGG
128807697 ACTTTCCATT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.28
Consensus pattern (27 bp):
CTAACTCAGTGGGCGTTTCAATAAAAG
Found at i:128809529 original size:13 final size:13
Alignment explanation
Indices: 128809506--128809547 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
128809496 ATAAACATGT
*
128809506 TATTTTCAATTTA
1 TATTTTTAATTTA
* *
128809519 TCTTTTTAATTAA
1 TATTTTTAATTTA
128809532 TATTTTTAATTTA
1 TATTTTTAATTTA
128809545 TAT
1 TAT
128809548 AATAAAATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (13 bp):
TATTTTTAATTTA
Found at i:128809566 original size:19 final size:19
Alignment explanation
Indices: 128809542--128809579 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
128809532 TATTTTTAAT
128809542 TTATATAATAAAATAATAA
1 TTATATAATAAAATAATAA
* *
128809561 TTATATAATTATATAATAA
1 TTATATAATAAAATAATAA
128809580 AAATATATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TTATATAATAAAATAATAA
Found at i:128809585 original size:19 final size:19
Alignment explanation
Indices: 128809544--128809586 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
128809534 TTTTTAATTT
**
128809544 ATATAATAAAATAATAATT
1 ATATAATAAAATAATAAAA
* *
128809563 ATATAATTATATAATAAAA
1 ATATAATAAAATAATAAAA
128809582 ATATA
1 ATATA
128809587 TTTGATATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
ATATAATAAAATAATAAAA
Found at i:128810543 original size:23 final size:22
Alignment explanation
Indices: 128810503--128810551 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
128810493 TTATTTTCAC
*
128810503 TATTATTTGAGATATTTAGTTAT
1 TATTATTTGAGATATTTA-CTAT
*
128810526 TATTATTTGATAGT-TTTACTAT
1 TATTATTTGAGA-TATTTACTAT
128810548 TATT
1 TATT
128810552 TAATTTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 7 0.30
23 15 0.65
24 1 0.04
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.59
Consensus pattern (22 bp):
TATTATTTGAGATATTTACTAT
Found at i:128812163 original size:53 final size:53
Alignment explanation
Indices: 128812096--128812246 Score: 207
Period size: 53 Copynumber: 2.8 Consensus size: 53
128812086 ACAAGTGTGC
*
128812096 CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGA-AATGTGATAATGTGACT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGT-ATAATGTGATAATGTGACT
* *
128812149 CCGTATAAGACCATAGCTGGGCTATGGCATTGGTATAATGTGATAATGTGATT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
* *
128812202 CCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGATATGTGA
1 CCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A-ATGTGA
128812247 ACCGTGTAAG
Statistics
Matches: 88, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
52 2 0.02
53 79 0.90
54 1 0.01
55 6 0.07
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.30
Consensus pattern (53 bp):
CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
Found at i:128815736 original size:7 final size:7
Alignment explanation
Indices: 128815724--128815750 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
128815714 CGTATACCCT
128815724 TGGCTGG
1 TGGCTGG
128815731 TGGCTGG
1 TGGCTGG
128815738 TGGCTGG
1 TGGCTGG
128815745 TGGCTG
1 TGGCTG
128815751 CTAATGGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.56, T:0.30
Consensus pattern (7 bp):
TGGCTGG
Found at i:128816482 original size:4 final size:4
Alignment explanation
Indices: 128816473--128816503 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
128816463 TTCAACAGTT
128816473 TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
128816504 ATGTTTTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:128825521 original size:2 final size:2
Alignment explanation
Indices: 128825514--128825545 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
128825504 TATAATGTAA
128825514 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
128825546 TAGTATGTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:128829746 original size:27 final size:26
Alignment explanation
Indices: 128829678--128829746 Score: 61
Period size: 32 Copynumber: 2.5 Consensus size: 26
128829668 AAGATAAAAA
128829678 TTTTAAT-AAAAAATAATTTATTCTT
1 TTTTAATAAAAAAATAATTTATTCTT
128829703 TAATTTAATATATAAAAAATTAATTTA-TCATT
1 T--TTT-A-ATA-AAAAAA-TAATTTATTC-TT
128829735 TTTTAATAAAAA
1 TTTTAATAAAAA
128829747 TAATCTAACT
Statistics
Matches: 36, Mismatches: 0, Indels: 14
0.72 0.00 0.28
Matches are distributed among these distances:
25 1 0.03
27 7 0.19
28 4 0.11
29 3 0.08
30 3 0.08
31 8 0.22
32 10 0.28
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (26 bp):
TTTTAATAAAAAAATAATTTATTCTT
Found at i:128834214 original size:29 final size:27
Alignment explanation
Indices: 128834173--128834231 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 27
128834163 TTCCACTAAA
*
128834173 AAATGATTAGTTTTAATTTTAGTCAAAAT
1 AAATAATTAG-TTTAATTTTAGTC-AAAT
128834202 AAATAATTAGTTTAATTTTAGTCAAAT
1 AAATAATTAGTTTAATTTTAGTCAAAT
128834229 AAA
1 AAA
128834232 AAAATATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 7 0.24
28 13 0.45
29 9 0.31
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.42
Consensus pattern (27 bp):
AAATAATTAGTTTAATTTTAGTCAAAT
Found at i:128834223 original size:28 final size:28
Alignment explanation
Indices: 128834147--128834231 Score: 95
Period size: 26 Copynumber: 3.1 Consensus size: 28
128834137 TTAAATTTTA
* ** *
128834147 AAATAATTAATTTTAATTCCACT-AAA-
1 AAATAATTAGTTTTAATTTTAGTCAAAT
*
128834173 AAATGATTAGTTTTAATTTTAGTCAAAAT
1 AAATAATTAGTTTTAATTTTAGTC-AAAT
128834202 AAATAATTAG-TTTAATTTTAGTCAAAT
1 AAATAATTAGTTTTAATTTTAGTCAAAT
128834229 AAA
1 AAA
128834232 AAAATATTTA
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
26 18 0.36
27 7 0.14
28 16 0.32
29 9 0.18
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (28 bp):
AAATAATTAGTTTTAATTTTAGTCAAAT
Found at i:128843821 original size:6 final size:6
Alignment explanation
Indices: 128843810--128843837 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
128843800 TGAATTCAGA
128843810 ATTTGG ATTTGG ATTTGG ATTTGG ATTT
1 ATTTGG ATTTGG ATTTGG ATTTGG ATTT
128843838 CAACAGTGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.29, T:0.54
Consensus pattern (6 bp):
ATTTGG
Found at i:128852889 original size:3 final size:3
Alignment explanation
Indices: 128852881--128852906 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
128852871 CAACTATTTA
128852881 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
128852907 CAAAAGAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:128856147 original size:16 final size:17
Alignment explanation
Indices: 128856123--128856157 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
128856113 TTAATTATTC
*
128856123 AAATTATTTTAAA-TTT
1 AAATAATTTTAAACTTT
128856139 AAATAATTTTAAACTTT
1 AAATAATTTTAAACTTT
128856156 AA
1 AA
128856158 TTTTGACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (17 bp):
AAATAATTTTAAACTTT
Found at i:128863221 original size:31 final size:31
Alignment explanation
Indices: 128863186--128863250 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
128863176 AAAAAACCTT
* *
128863186 AATAGCCTAGTGTCTTAAATAAAAGCTTTCA
1 AATAGCCTAGTGACTTAAATAAAAACTTTCA
** *
128863217 AATAGTTTAGTGACTTAAATAAAAACTTTTA
1 AATAGCCTAGTGACTTAAATAAAAACTTTCA
128863248 AAT
1 AAT
128863251 TGTTTGTTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.35
Consensus pattern (31 bp):
AATAGCCTAGTGACTTAAATAAAAACTTTCA
Found at i:128864011 original size:2 final size:2
Alignment explanation
Indices: 128864000--128864030 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
128863990 CACTCTCATT
128864000 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
128864031 GGTGAGAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:128864561 original size:6 final size:6
Alignment explanation
Indices: 128864552--128864577 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
128864542 ATCACCACCT
128864552 TCTTCC TCTTCC TCTTCC TCTTCC TC
1 TCTTCC TCTTCC TCTTCC TCTTCC TC
128864578 CAACACCACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (6 bp):
TCTTCC
Found at i:128878498 original size:15 final size:16
Alignment explanation
Indices: 128878468--128878507 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 16
128878458 TGAACTTTCT
*
128878468 AATTGTTATA-TAT-A
1 AATTGTTAAATTATAA
128878482 AATTGTTAAATTATAA
1 AATTGTTAAATTATAA
128878498 AATT-TTAAAT
1 AATTGTTAAAT
128878508 GGGTAAACTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 9 0.39
15 9 0.39
16 5 0.22
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (16 bp):
AATTGTTAAATTATAA
Found at i:128880668 original size:3 final size:3
Alignment explanation
Indices: 128880662--128880696 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
128880652 ATGATAATAA
128880662 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
128880697 TCTACAACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.66, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:128881676 original size:144 final size:140
Alignment explanation
Indices: 128881427--128881688 Score: 310
Period size: 144 Copynumber: 1.8 Consensus size: 140
128881417 GAGCTCCTTG
* * ** *
128881427 TCATTATGGTTTTAGTCCCTCGATATTTGGTAGTTACATTGGGCTCGAATTTTTAAACGAGGATG
1 TCATTATGGTTTTAGTCCCTCGATATTTAGTAGTTACATTAGGCTCGAATTCCTAAACGAGGATA
* * * * *
128881492 ATGTTTTCTCAACGTTATTTTTTGTATTTATAAGACTTGAACTCTAAACTTAGTTTAAAGAGCAT
66 AAGTTCTCCCAACGTTATTTTTTG-ATTCACAAGACTTGAACTCTAAACTTAGTTTAAAGAGCAT
128881557 TGAGTTCTTTA
130 TGAGTTCTTTA
* * *
128881568 TCATTATGGTTTTAGCCATCGCTTGATATTTAGTAGTTACATTAGGCTCGAATTCCTAAATGAGG
1 TCATTATGGTTTTAG---TCCCTCGATATTTAGTAGTTACATTAGGCTCGAATTCCTAAACGAGG
* * * *
128881633 GTAAAGTTCTCCCAACGTTCTTTTTCTCG-TTCACAAGAGTTGAACTCTAAATTTAG
63 ATAAAGTTCTCCCAACGTTATTTTT-T-GATTCACAAGACTTGAACTCTAAACTTAG
128881689 AGTATTGAGT
Statistics
Matches: 99, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
141 15 0.15
144 82 0.83
145 1 0.01
146 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (140 bp):
TCATTATGGTTTTAGTCCCTCGATATTTAGTAGTTACATTAGGCTCGAATTCCTAAACGAGGATA
AAGTTCTCCCAACGTTATTTTTTGATTCACAAGACTTGAACTCTAAACTTAGTTTAAAGAGCATT
GAGTTCTTTA
Found at i:128888781 original size:82 final size:82
Alignment explanation
Indices: 128888609--128888784 Score: 275
Period size: 82 Copynumber: 2.2 Consensus size: 82
128888599 TTTTCCCTCT
* *
128888609 TTTTG-TTGAATATGAATTACATGGACTTAAAGATCTTGTTTTTATTTAATGTGTTGTGATATTT
1 TTTTGATTGAATATGAATTACATGGACTTAAAGATCTTGTTTTTATTTAATGTATGGTGATATTT
128888673 TTTCTGGGTTTTGCTTG
66 TTTCTGGGTTTTGCTTG
* * * *
128888690 TTTTGATTGAGTATGCATTACTTGGACTTAAAGATCTTGTTTTTATTTGATGTATGGTGATATTT
1 TTTTGATTGAATATGAATTACATGGACTTAAAGATCTTGTTTTTATTTAATGTATGGTGATATTT
128888755 TTTCTGGGTTTTGCTTG
66 TTTCTGGGTTTTGCTTG
128888772 -TTTGAATTGAATA
1 TTTTG-ATTGAATA
128888785 CTGTTACGTA
Statistics
Matches: 86, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
81 9 0.10
82 77 0.90
ACGTcount: A:0.21, C:0.06, G:0.20, T:0.52
Consensus pattern (82 bp):
TTTTGATTGAATATGAATTACATGGACTTAAAGATCTTGTTTTTATTTAATGTATGGTGATATTT
TTTCTGGGTTTTGCTTG
Done.