Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000186.1 Hibiscus syriacus cultivar Beakdansim tig00000329_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3152351
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 7 of 17
Found at i:1233586 original size:24 final size:24
Alignment explanation
Indices: 1233549--1233601 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1233539 CCGTTCAATC
1233549 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA-CTTA
** *
1233573 TATTTTCATCGGATATGTTATTTA
1 TATTTTCAGAGGATATGTTACTTA
1233597 TATTT
1 TATTT
1233602 AATCGATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (24 bp):
TATTTTCAGAGGATATGTTACTTA
Found at i:1234199 original size:182 final size:179
Alignment explanation
Indices: 1233713--1234184 Score: 651
Period size: 180 Copynumber: 2.6 Consensus size: 179
1233703 CGTACTTACG
* * *
1233713 AAAGTATCGACACTTTCAATATATCCGGTATCATTTTACCGGTTTTATCATTTTAATACCGATTT
1 AAAGTATCGACACTTTAAATATATCCGGTAAC-CTTTACCGGTTTTATCATTTTAATACCGATTT
* * *
1233778 TATCATATTTTTACATGTTATATCGTTGTGGATCGATATATTTTTTAAAGTATCGACACATTATA
65 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAGTATCGACACATTATA
* *
1233843 GGCGCTAAAACTGTTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
130 GGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
* * * *
1233893 AAAGTATCGACACTTTTAATATATCTGGTAACCTTTTACCGGTTTTATCGTTTTGATACCGATTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACC-TTTACCGGTTTTATCATTTTAATACCGATTT
* *
1233958 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
65 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTT-AAAGTATCGACACATTAT
** *
1234023 AGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
129 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
* * * *
1234075 AAAGTA-CATACACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCATTTCT-ATACCGGT
1 AAAGTATC-GACACTTTAAATATATCCGGTAAC-CTTTACCGGTTTTATCATTT-TAATACCGAT
* * *
1234138 TTTGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
63 TTTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
1234185 AATTTGGATC
Statistics
Matches: 259, Mismatches: 27, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
180 100 0.39
181 63 0.24
182 94 0.36
183 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (179 bp):
AAAGTATCGACACTTTAAATATATCCGGTAACCTTTACCGGTTTTATCATTTTAATACCGATTTT
ATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAGTATCGACACATTATAG
GAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
Found at i:1240010 original size:12 final size:12
Alignment explanation
Indices: 1239993--1240022 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1239983 TAGGGCTATT
1239993 AGTTTTACATCA
1 AGTTTTACATCA
*
1240005 AGTTTTACATTA
1 AGTTTTACATCA
1240017 AGTTTT
1 AGTTTT
1240023 CTTTATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (12 bp):
AGTTTTACATCA
Found at i:1244931 original size:9 final size:9
Alignment explanation
Indices: 1244917--1244946 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
1244907 CTTTCATTGA
1244917 AAAAAAAAG
1 AAAAAAAAG
1244926 AAAAAAAAG
1 AAAAAAAAG
1244935 AAAAAAAGAG
1 AAAAAAA-AG
1244945 AA
1 AA
1244947 GCAAAAATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 16 0.80
10 4 0.20
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:1246053 original size:12 final size:12
Alignment explanation
Indices: 1246036--1246065 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1246026 TAGGGCCATT
1246036 AGTTTTACATCA
1 AGTTTTACATCA
*
1246048 AGTTTTACATTA
1 AGTTTTACATCA
1246060 AGTTTT
1 AGTTTT
1246066 CTTTATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (12 bp):
AGTTTTACATCA
Found at i:1248296 original size:22 final size:22
Alignment explanation
Indices: 1248271--1248354 Score: 66
Period size: 22 Copynumber: 3.9 Consensus size: 22
1248261 AAAAAATTTA
1248271 TATAAAAT-TTTTATTTTATAAT
1 TATAAAATATTTTATTTT-TAAT
* * **
1248293 TATATATTA-TTTA-AATTAAT
1 TATAAAATATTTTATTTTTAAT
* * *
1248313 TATAAACTGTTTTTTTTTTAAT
1 TATAAAATATTTTATTTTTAAT
*
1248335 TATAAAATATTTAATTTTTA
1 TATAAAATATTTTATTTTTA
1248355 TATAAATTAG
Statistics
Matches: 45, Mismatches: 14, Indels: 6
0.69 0.22 0.09
Matches are distributed among these distances:
20 10 0.22
21 4 0.09
22 31 0.69
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (22 bp):
TATAAAATATTTTATTTTTAAT
Found at i:1248359 original size:42 final size:41
Alignment explanation
Indices: 1248264--1248360 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 41
1248254 ACTAATTAAA
* *
1248264 AAATTTATATAAAATTTTTATTTTATAATTATATATTATTT
1 AAATTTATATAAAATTTTTATTTTATAATTATAAAATATTT
* * *
1248305 AAATTAATTATAAACTGTTTT-TTTTTTAATTATAAAATATTT
1 AAATTTA-TATAAAAT-TTTTATTTTATAATTATAAAATATTT
*
1248347 AATTTTTATATAAA
1 AA-ATTTATATAAA
1248361 TTAGAAAATT
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
41 6 0.13
42 33 0.72
43 7 0.15
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (41 bp):
AAATTTATATAAAATTTTTATTTTATAATTATAAAATATTT
Found at i:1248359 original size:185 final size:185
Alignment explanation
Indices: 1247966--1248328 Score: 611
Period size: 185 Copynumber: 2.0 Consensus size: 185
1247956 ATAAAATTTT
* * *
1247966 AAATTTTAAATATATTATATATAACATATGAGCTCAGCCCGAACCATTTAAAACTCAATTAATAA
1 AAATATTATATATATTATATATAACATATGAGCTCAGCCCAAACCATTTAAAACTCAATTAATAA
* * * * *
1248031 TTTAAGATCTAATAACTTTTAAACCTAAATTAATATTAATTAATTAAAATATTTATATAAAAGTT
66 TTTAAGATCCAATAACATTTAAACCTAAATCAATATTAACTAATTAAAAAATTTATATAAAAGTT
1248096 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTTGAATTAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTTGAATTAA
* *
1248151 AAATATTATATATATTATATATAACATATGGGCTTAGCCCAAACCATTTAAAAC-CTAATTAATA
1 AAATATTATATATATTATATATAACATATGAGCTCAGCCCAAACCATTTAAAACTC-AATTAATA
*
1248215 ATTTAAGATCCAATAACATTTAAACCTAAATCAATATTAACTAATTAAAAAATTTATATAAAATT
65 ATTTAAGATCCAATAACATTTAAACCTAAATCAATATTAACTAATTAAAAAATTTATATAAAAGT
1248280 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTT
130 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTT
1248329 TTTAATTATA
Statistics
Matches: 166, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
184 1 0.01
185 165 0.99
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.43
Consensus pattern (185 bp):
AAATATTATATATATTATATATAACATATGAGCTCAGCCCAAACCATTTAAAACTCAATTAATAA
TTTAAGATCCAATAACATTTAAACCTAAATCAATATTAACTAATTAAAAAATTTATATAAAAGTT
TTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTTGAATTAA
Found at i:1250346 original size:22 final size:22
Alignment explanation
Indices: 1250321--1250362 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1250311 TAAGCTGTTA
* *
1250321 TAACTCCTGAAATTATATCATG
1 TAACCCCTGAAATTAAATCATG
*
1250343 TAACCCCTGGAATTAAATCA
1 TAACCCCTGAAATTAAATCA
1250363 AATAACTCAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (22 bp):
TAACCCCTGAAATTAAATCATG
Found at i:1250368 original size:22 final size:22
Alignment explanation
Indices: 1250320--1250368 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
1250310 TTAAGCTGTT
* * *
1250320 ATAACTCCTGAAATTATATCAT
1 ATAACCCCTGAAATTAAATCAA
* *
1250342 GTAACCCCTGGAATTAAATCAA
1 ATAACCCCTGAAATTAAATCAA
1250364 ATAAC
1 ATAAC
1250369 TCATGTAATC
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.29
Consensus pattern (22 bp):
ATAACCCCTGAAATTAAATCAA
Found at i:1256143 original size:26 final size:26
Alignment explanation
Indices: 1256107--1256161 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
1256097 TAGGATTAAA
*
1256107 TCTCTTCTTTTGTAACAGTTGAAACG
1 TCTCTTCTTTTGTAACAGCTGAAACG
1256133 TCTCTTCTTTTGTAACAGCTGAAACG
1 TCTCTTCTTTTGTAACAGCTGAAACG
1256159 TCT
1 TCT
1256162 AGATGAACCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.42
Consensus pattern (26 bp):
TCTCTTCTTTTGTAACAGCTGAAACG
Found at i:1256702 original size:23 final size:23
Alignment explanation
Indices: 1256668--1256738 Score: 117
Period size: 23 Copynumber: 3.1 Consensus size: 23
1256658 ATTACCAACA
*
1256668 ATAAAGACATATGAAAATGTGTC
1 ATAAAGAAATATGAAAATGTGTC
1256691 ATAAAGAAATATGAAAATGTGTC
1 ATAAAGAAATATGAAAATGTGTC
*
1256714 ATAAA-AAAGATGAAAATGTGTC
1 ATAAAGAAATATGAAAATGTGTC
1256736 ATA
1 ATA
1256739 CATGCAAATT
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
22 19 0.41
23 27 0.59
ACGTcount: A:0.52, C:0.06, G:0.17, T:0.25
Consensus pattern (23 bp):
ATAAAGAAATATGAAAATGTGTC
Found at i:1256989 original size:13 final size:13
Alignment explanation
Indices: 1256971--1256997 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1256961 ATAGATTTTA
1256971 TATTTTATTTAAG
1 TATTTTATTTAAG
1256984 TATTTTATTTAAG
1 TATTTTATTTAAG
1256997 T
1 T
1256998 TATAGAGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (13 bp):
TATTTTATTTAAG
Found at i:1257081 original size:18 final size:18
Alignment explanation
Indices: 1257034--1257081 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 18
1257024 GGTTTAAGGT
*
1257034 AAATAGATATATTATGTA
1 AAATAGATATATTATGAA
1257052 AAAT--A-A-ATTATGAA
1 AAATAGATATATTATGAA
1257066 AAATAGATATATTATG
1 AAATAGATATATTATG
1257082 TAAATTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
14 11 0.44
15 1 0.04
16 2 0.08
17 1 0.04
18 10 0.40
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.35
Consensus pattern (18 bp):
AAATAGATATATTATGAA
Found at i:1257560 original size:60 final size:60
Alignment explanation
Indices: 1257491--1257638 Score: 165
Period size: 60 Copynumber: 2.5 Consensus size: 60
1257481 GGATGAATTT
* * ** *
1257491 GGGATGAAATTGGAAGATTCAAAAGTTTGGGGACTAATTTAGAATGAGGGTCATAGTTTG
1 GGGATGAAATTGGAAAATTCAAAAGTTTAGGGACTAATTTAGAATGAAAGCCATAGTTTG
* * *
1257551 GGGATGAAATTGGAACAATT-AAAAGTTTATGGATTGATTTAGAATGAAAGCCATAGTTTG
1 GGGATGAAATTGGAA-AATTCAAAAGTTTAGGGACTAATTTAGAATGAAAGCCATAGTTTG
* * *
1257611 AGGATAAAATT-AAAATATTCAAAAGTTT
1 GGGATGAAATTGGAAA-ATTCAAAAGTTT
1257639 TAAAACAAAT
Statistics
Matches: 74, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
58 1 0.01
59 5 0.07
60 65 0.88
61 3 0.04
ACGTcount: A:0.39, C:0.05, G:0.25, T:0.31
Consensus pattern (60 bp):
GGGATGAAATTGGAAAATTCAAAAGTTTAGGGACTAATTTAGAATGAAAGCCATAGTTTG
Found at i:1266307 original size:33 final size:34
Alignment explanation
Indices: 1266235--1266319 Score: 127
Period size: 36 Copynumber: 2.5 Consensus size: 34
1266225 CGAGGGTTTG
* *
1266235 GTGTTTCAAGAGAAATATTTTCAAAGGTTTTTTTTT
1 GTGTTTCAAGAGAAACAATTTCAAAGG--TTTTTTT
1266271 GTGTTTCAAGAGAAACAATTTCAAAGG-TTTTTT
1 GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTT
1266304 GTGTTTCAAGAGAAAC
1 GTGTTTCAAGAGAAAC
1266320 TGTATTCAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
33 22 0.47
36 25 0.53
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.41
Consensus pattern (34 bp):
GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTT
Found at i:1266386 original size:36 final size:34
Alignment explanation
Indices: 1266335--1266435 Score: 130
Period size: 36 Copynumber: 2.9 Consensus size: 34
1266325 TCAAAGATTG
*
1266335 AAGTTTCAAGGGAAACTGTCTCAAGAGAGACAAA
1 AAGTTTCAAGAGAAACTGTCTCAAGAGAGACAAA
*
1266369 ATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAA
1 A--AGTTTCAAGAGAAACTGTCTCAAGAGAGACAAA
* * * *
1266405 AACTTCCAAAAGAAACTGTCTCAAGTGAGAC
1 AAGTTTCAAGAGAAACTGTCTCAAGAGAGAC
1266436 GCGATTTGTT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
34 26 0.45
36 32 0.55
ACGTcount: A:0.43, C:0.17, G:0.20, T:0.21
Consensus pattern (34 bp):
AAGTTTCAAGAGAAACTGTCTCAAGAGAGACAAA
Found at i:1266419 original size:34 final size:35
Alignment explanation
Indices: 1266346--1266435 Score: 119
Period size: 34 Copynumber: 2.6 Consensus size: 35
1266336 AGTTTCAAGG
** * *
1266346 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGA
1 GAAACTGTCTCAAGAGAGACAAAA-TACTTCCAAAA
1266382 GAAACTGTCTCAAGAGAGACAAAA-ACTTCCAAAA
1 GAAACTGTCTCAAGAGAGACAAAATACTTCCAAAA
*
1266416 GAAACTGTCTCAAGTGAGAC
1 GAAACTGTCTCAAGAGAGAC
1266436 GCGATTTGTT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
34 25 0.51
36 24 0.49
ACGTcount: A:0.43, C:0.18, G:0.19, T:0.20
Consensus pattern (35 bp):
GAAACTGTCTCAAGAGAGACAAAATACTTCCAAAA
Found at i:1266657 original size:37 final size:37
Alignment explanation
Indices: 1266602--1267007 Score: 149
Period size: 37 Copynumber: 12.0 Consensus size: 37
1266592 TCAATGTTTA
*
1266602 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
* *
1266639 TGTTTCAAGGGAACCTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
** * * * * * *
1266675 CATCTCAAGGGAAA-TGTTTTC-A-A-TG-C----TTA
1 TGTTTCAAGAGAAACT-ATCTCAAGAGAGACAAAATTT
*
1266704 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
* * * * * *
1266741 AGTTCCAAAAGAAAATGTCTCAAGGGAGACAAAA-TT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
* *
1266777 TGTTTCAAGGGAAACAGAT-TC-A-A-AG-----ATTT
1 TGTTTCAAGAGAAAC-TATCTCAAGAGAGACAAAATTT
*
1266806 TGTTTCAAGAGAAACTATCTTAAGAGAGACAAAA-TT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
** * * * *
1266842 CATTTCAAGGGAAA-TGTTTTC-A-A-TG------TTT
1 TGTTTCAAGAGAAACT-ATCTCAAGAGAGACAAAATTT
*
1266870 ATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTT
1 -TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
* * * * * *
1266908 AGTTCCAAAAGAAAATGTCTCAAGGGAGACAAAA-TT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
* *
1266944 TGTTTCAAGGGAAACATAT-TC-A-A-AG-----ATTC
1 TGTTTCAAGAGAAAC-TATCTCAAGAGAGACAAAATTT
1266973 TGTTTCAAGAGAAACTA-CTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
1267008 CATTTCAAGG
Statistics
Matches: 257, Mismatches: 66, Indels: 93
0.62 0.16 0.22
Matches are distributed among these distances:
28 10 0.04
29 61 0.24
30 6 0.02
31 5 0.02
32 5 0.02
33 7 0.03
34 2 0.01
35 6 0.02
36 61 0.24
37 92 0.36
38 2 0.01
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
Found at i:1266671 original size:102 final size:102
Alignment explanation
Indices: 1266473--1266855 Score: 459
Period size: 102 Copynumber: 3.8 Consensus size: 102
1266463 AAAGATTTGG
* * * * * *
1266473 TTTCAAAGGAAACTGTTTTCAAAGTTTATGCTTAAAGAGAAATTGTCTCAAGGGAGACAAAATTT
1 TTTCAAGGGAAACTGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
* *
1266538 GTTTCAAGGGAAACTATCTCATGAGTGACAAAATTCA
66 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
* *
1266575 TTTCAAGGGAAA-TGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTT
1 TTTCAAGGGAAACTGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAA-TT
*
1266639 TGTTTCAAGGGAACCTATCTCAAGAGAGACAAAATTCA
65 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
* * *
1266677 TCTCAAGGGAAA-TGTTTTCAATGCTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTT
1 TTTCAAGGGAAACTGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAA-TT
* * ** * * * **
1266741 AGTTCCAAAAGAAAATGTCTCAAGGGAGACAAAATTTG
65 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
* * *
1266779 TTTCAAGGGAAACAG-ATTCAAAGATTT-TGTTTCAAGAGAAACTATCTTAAGAGAGACAAAATT
1 TTTCAAGGGAAACTGTTTTCAAAG-TTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
**
1266842 CATTTCAAGGGAAA
65 TGTTTCAAGGGAAA
1266856 TGTTTTCAAT
Statistics
Matches: 244, Mismatches: 34, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
101 55 0.23
102 186 0.76
103 3 0.01
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (102 bp):
TTTCAAGGGAAACTGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
GTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
Found at i:1266854 original size:65 final size:65
Alignment explanation
Indices: 1266758--1266904 Score: 199
Period size: 65 Copynumber: 2.3 Consensus size: 65
1266748 AAAGAAAATG
* **
1266758 TCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAG-ATTCAAAGATTT-TGTTTCAAGAGAAAC
1 TCTCAAGAGAGACAAAATTCATTTCAAGGGAAA-AGTATTCAAAG-TTTATGTTTCAAGAGAAAC
1266821 TA
64 TA
* * * *
1266823 TCTTAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTA
1 TCTCAAGAGAGACAAAATTCATTTCAAGGGAAAAGTATTCAAAGTTTATGTTTCAAGAGAAACTA
1266888 TCTCAAGAGAGACAAAA
1 TCTCAAGAGAGACAAAA
1266905 CTTAGTTCCA
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
64 4 0.06
65 68 0.94
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (65 bp):
TCTCAAGAGAGACAAAATTCATTTCAAGGGAAAAGTATTCAAAGTTTATGTTTCAAGAGAAACTA
Found at i:1266921 original size:102 final size:101
Alignment explanation
Indices: 1266815--1267005 Score: 265
Period size: 102 Copynumber: 1.9 Consensus size: 101
1266805 TTGTTTCAAG
* * ** * * *
1266815 AGAAACTATCTTAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAG
1 AGAAAATATCTCAAGAGAGACAAAATTCATTTCAAGGGAAACATATTCAAAGATTATGTTTCAAG
1266880 AGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAA
66 AGAAACTA-CTCAAGAGAGACAAAACTTAGTTCCAAA
* * ** *
1266917 AGAAAATGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACATATTCAAAGATTCTGTTTCAAG
1 AGAAAATATCTCAAGAGAGACAAAATTCATTTCAAGGGAAACATATTCAAAGATTATGTTTCAAG
1266982 AGAAACTACTCAAGAGAGACAAAA
66 AGAAACTACTCAAGAGAGACAAAA
1267006 TTCATTTCAA
Statistics
Matches: 77, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
101 16 0.21
102 61 0.79
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (101 bp):
AGAAAATATCTCAAGAGAGACAAAATTCATTTCAAGGGAAACATATTCAAAGATTATGTTTCAAG
AGAAACTACTCAAGAGAGACAAAACTTAGTTCCAAA
Found at i:1267030 original size:64 final size:65
Alignment explanation
Indices: 1266917--1267072 Score: 188
Period size: 64 Copynumber: 2.4 Consensus size: 65
1266907 TAGTTCCAAA
* * ** *
1266917 AGAAAATGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACATATTCAAAGATTCTGTTTCAAG
1 AGAAACTGACTCAAGGGAGACAAAATTCATTTCAAGGGAAACATATTCAAAGATTATGTTTCAAG
* ** * * * *
1266982 AGAAACT-ACTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAT
1 AGAAACTGACTCAAGGGAGACAAAATTCATTTCAAGGGAAACATATTCAAAGATTATGTTTCAAG
*
1267046 AGAAACTGTCTCAAGGGAGACAAAATT
1 AGAAACTGACTCAAGGGAGACAAAATT
1267073 TAGTTCCAAA
Statistics
Matches: 76, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
64 53 0.70
65 23 0.30
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (65 bp):
AGAAACTGACTCAAGGGAGACAAAATTCATTTCAAGGGAAACATATTCAAAGATTATGTTTCAAG
Found at i:1267101 original size:166 final size:167
Alignment explanation
Indices: 1266631--1267154 Score: 863
Period size: 167 Copynumber: 3.1 Consensus size: 167
1266621 TCAAGGGAGA
* * *
1266631 CAAA-ATTTTGTTTCAAGGGAACCTATCTCAAGAGAGACAAAATTCATCTCAAGGGAAATGTTTT
1 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTT
*
1266695 CAATGCTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTC
66 CAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTC
*
1266760 TCAAGGGAGACAAAATTTGTTTCAAGGGAAACAGATT
131 TCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATT
*
1266797 CAAAGATTTTGTTTCAAGAGAAACTATCTTAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTT
1 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTT
1266862 CAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTC
66 CAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTC
*
1266927 TCAAGGGAGACAAAATTTGTTTCAAGGGAAACATATT
131 TCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATT
*
1266964 CAAAGATTCTGTTTCAAGAGAAACTA-CTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTT
1 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTT
* * * *
1267028 CAATGTTTATGTTTCAATAGAAACTGTCTCAAGGGAGACAAAATTTAGTTCCAAAAGAAAATGTC
66 CAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTC
* * * *
1267093 TCAAGGGAGACGAAATTAGTTTCAATGAAAACAAATT
131 TCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATT
* * *
1267130 TAAATATTTTGTTTCAAGGGAAACT
1 CAAAGATTTTGTTTCAAGAGAAACT
1267155 TGGAAACTGT
Statistics
Matches: 336, Mismatches: 21, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
166 155 0.46
167 181 0.54
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (167 bp):
CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTT
CAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGTC
TCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATT
Found at i:1267494 original size:106 final size:105
Alignment explanation
Indices: 1267302--1267623 Score: 441
Period size: 106 Copynumber: 3.0 Consensus size: 105
1267292 TGTATTGTTC
* * * * ** *
1267302 CGAGTCCAATATCCTCCGCCGTGAAGTTAAAATTGGCTCTGGAACTAAGAAATTGTTTGTTCACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-GAATTGGGAAATTGTTTGTTGACA
* * * * * *
1267367 GCCAGCCGCCCCTT-TTCTGTGAAGTTGAGCTTGTGCTGTCT
65 ACCAGCTGTCCCTTCAT-TGTGAAGTTGAACTTGTGTTGTCT
*
1267408 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTG-AATTGGGAAATTGTTTGTTGACA
*
1267473 ACCAGCTGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
65 ACCAGCTGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCT
*
1267514 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTGGGAAATTGTTTGTTGACAA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATTGGGAAATTGTTTGTTGACAA
*
1267579 CCAG-TCGTCCCTTCATTGTGGAGTTGAACTTGTGTTGTCT
66 CCAGCT-GTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCT
1267619 CGAGT
1 CGAGT
1267624 GGCACGATAT
Statistics
Matches: 195, Mismatches: 18, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
104 1 0.01
105 66 0.34
106 127 0.65
107 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.34
Consensus pattern (105 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATTGGGAAATTGTTTGTTGACAA
CCAGCTGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCT
Found at i:1268273 original size:32 final size:32
Alignment explanation
Indices: 1268187--1268274 Score: 99
Period size: 32 Copynumber: 2.8 Consensus size: 32
1268177 TTTGCATCAG
* * *
1268187 GATGTTGAAT-TCCCAAAGATTCCCCAATATTC
1 GATGTTGAATCT-TCAAAGATGCCCCAACATTC
* *
1268219 GATGTTGAATC-TCAAAAAATGCCCCAACATTT
1 GATGTTGAATCTTC-AAAGATGCCCCAACATTC
1268251 GATGTTGAATCTTCAAAGATGCCC
1 GATGTTGAATCTTCAAAGATGCCC
1268275 TCATTGTTCC
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
31 1 0.02
32 44 0.94
33 2 0.04
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.30
Consensus pattern (32 bp):
GATGTTGAATCTTCAAAGATGCCCCAACATTC
Found at i:1269380 original size:13 final size:13
Alignment explanation
Indices: 1269339--1269381 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
1269329 TTTTCTTCAA
1269339 TTTTC-CTTTGTT
1 TTTTCTCTTTGTT
1269351 TTTTCTCTTT-TT
1 TTTTCTCTTTGTT
1269363 ATTTTCTCTTTGCTT
1 -TTTTCTCTTTG-TT
1269378 TTTT
1 TTTT
1269382 TTTCTCTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 7 0.26
13 14 0.52
14 4 0.15
15 2 0.07
ACGTcount: A:0.02, C:0.16, G:0.05, T:0.77
Consensus pattern (13 bp):
TTTTCTCTTTGTT
Found at i:1269384 original size:17 final size:18
Alignment explanation
Indices: 1269357--1269390 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1269347 TGTTTTTTCT
1269357 CTTTTTATTTTCTCTTTG
1 CTTTTTATTTTCTCTTTG
1269375 CTTTTT-TTTTCTCTTT
1 CTTTTTATTTTCTCTTT
1269391 TTTTCTGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (18 bp):
CTTTTTATTTTCTCTTTG
Found at i:1269392 original size:13 final size:13
Alignment explanation
Indices: 1269339--1269394 Score: 51
Period size: 13 Copynumber: 4.1 Consensus size: 13
1269329 TTTTCTTCAA
*
1269339 TTTTC-CTTTGTT
1 TTTTCTCTTTTTT
1269351 TTTTCTCTTTTTAT
1 TTTTCTCTTTTT-T
*
1269365 TTTCTCTTTGCTTTTT
1 TTT-TCTCT--TTTTT
1269381 TTTTCTCTTTTTT
1 TTTTCTCTTTTTT
1269394 T
1 T
1269395 CTGATTGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
12 5 0.14
13 11 0.31
14 4 0.11
15 8 0.22
16 4 0.11
17 4 0.11
ACGTcount: A:0.02, C:0.16, G:0.04, T:0.79
Consensus pattern (13 bp):
TTTTCTCTTTTTT
Found at i:1272446 original size:4 final size:4
Alignment explanation
Indices: 1272437--1272467 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
1272427 AAAAGGTAAG
1272437 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1272468 ATTAAAATGA
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:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:1272554 original size:13 final size:13
Alignment explanation
Indices: 1272536--1272560 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1272526 ATACTAAGTA
1272536 AAATAAATAAAAC
1 AAATAAATAAAAC
1272549 AAATAAATAAAA
1 AAATAAATAAAA
1272561 TAATAATAAA
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:0.80, C:0.04, G:0.00, T:0.16
Consensus pattern (13 bp):
AAATAAATAAAAC
Found at i:1272579 original size:32 final size:31
Alignment explanation
Indices: 1272457--1272579 Score: 78
Period size: 32 Copynumber: 4.0 Consensus size: 31
1272447 ATAAATAAAT
* *
1272457 AAATAAATAAAATTAA-AATGAAGAA-AAAAC
1 AAATAAATAAAA-TAATAATAAAAAAGAAAAC
* * *
1272487 AAATTAAATAAAA-GATAA-GATAAAGAAAAC
1 AAA-TAAATAAAATAATAATAAAAAAGAAAAC
* * *
1272517 -AA-AGATAAAATACTAAGTAAAATAAATAAAAC
1 AAATAAATAAAATAATAA-T-AAA-AAAGAAAAC
1272549 AAATAAATAAAATAATAATAAAAAAGTAAAA
1 AAATAAATAAAATAATAATAAAAAAG-AAAA
1272580 ATAATATATA
Statistics
Matches: 70, Mismatches: 12, Indels: 20
0.69 0.12 0.20
Matches are distributed among these distances:
27 7 0.10
28 3 0.04
29 7 0.10
30 10 0.14
31 13 0.19
32 15 0.21
33 3 0.04
34 12 0.17
ACGTcount: A:0.72, C:0.03, G:0.07, T:0.18
Consensus pattern (31 bp):
AAATAAATAAAATAATAATAAAAAAGAAAAC
Found at i:1272717 original size:2 final size:2
Alignment explanation
Indices: 1272583--1272697 Score: 223
Period size: 2 Copynumber: 58.0 Consensus size: 2
1272573 AGTAAAAATA
1272583 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1272625 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1272667 AT AT AT AT A- 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
1272698 CTAAAAAATA
Statistics
Matches: 112, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 111 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1280534 original size:30 final size:30
Alignment explanation
Indices: 1280468--1280536 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
1280458 GATTTATTGA
* * *
1280468 GTGACCAAATTATAAATTTGGTAAATTTTG
1 GTGACCAAAGTATAAATTTGGAAAATTTAG
1280498 GTGACCAAAGTATAAACTTT-GAAAAGTTTAG
1 GTGACCAAAGTATAAA-TTTGGAAAA-TTTAG
1280529 G-GACCAAA
1 GTGACCAAA
1280537 ATGTAATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 26 0.76
31 8 0.24
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.30
Consensus pattern (30 bp):
GTGACCAAAGTATAAATTTGGAAAATTTAG
Found at i:1282810 original size:15 final size:15
Alignment explanation
Indices: 1282782--1282830 Score: 80
Period size: 15 Copynumber: 3.3 Consensus size: 15
1282772 CCGTAGGACC
* *
1282782 ACTACATCCTGAAGG
1 ACTACGTCCCGAAGG
1282797 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
1282812 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
1282827 ACTA
1 ACTA
1282831 TTATACCCTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.31, C:0.31, G:0.22, T:0.16
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Found at i:1283426 original size:64 final size:63
Alignment explanation
Indices: 1283357--1283513 Score: 167
Period size: 64 Copynumber: 2.5 Consensus size: 63
1283347 TAATGAAGGT
* **
1283357 ATGCATCGATGCACTACTTGTGCATCGGTGCA-TAAAATGCATTCGATG-TTTTATTATTAATGG
1 ATGCATCGATGCACTACTTGTGCATCGATGCACT-AAATGCATTCGATGTTTTTATT-TTAA-AA
*
1283420 G
63 C
* * * *
1283421 ATGCATCGATACA-TGCCTTATGCATCGATGCACTAATTGCATTCGATGTTTTTATTTTAAAAC
1 ATGCATCGATGCACT-ACTTGTGCATCGATGCACTAAATGCATTCGATGTTTTTATTTTAAAAC
*
1283484 AGTGCATCGATGCACTACCTGTGCATCGAT
1 A-TGCATCGATGCACTACTTGTGCATCGAT
1283514 ACACCTTCAA
Statistics
Matches: 76, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
63 2 0.03
64 65 0.86
65 9 0.12
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCACTAAATGCATTCGATGTTTTTATTTTAAAAC
Found at i:1289757 original size:15 final size:15
Alignment explanation
Indices: 1289733--1289766 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1289723 CCGTAGGACC
1289733 ACTACATCCCGAAGG
1 ACTACATCCCGAAGG
* *
1289748 ACTACGTCCCGAATG
1 ACTACATCCCGAAGG
1289763 ACTA
1 ACTA
1289767 TTATACCCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.32, C:0.32, G:0.18, T:0.18
Consensus pattern (15 bp):
ACTACATCCCGAAGG
Found at i:1294566 original size:12 final size:12
Alignment explanation
Indices: 1294549--1294639 Score: 182
Period size: 12 Copynumber: 7.6 Consensus size: 12
1294539 GCCAAATCAT
1294549 TCATTGAGTCAC
1 TCATTGAGTCAC
1294561 TCATTGAGTCAC
1 TCATTGAGTCAC
1294573 TCATTGAGTCAC
1 TCATTGAGTCAC
1294585 TCATTGAGTCAC
1 TCATTGAGTCAC
1294597 TCATTGAGTCAC
1 TCATTGAGTCAC
1294609 TCATTGAGTCAC
1 TCATTGAGTCAC
1294621 TCATTGAGTCAC
1 TCATTGAGTCAC
1294633 TCATTGA
1 TCATTGA
1294640 TTATTTACTT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 79 1.00
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.34
Consensus pattern (12 bp):
TCATTGAGTCAC
Found at i:1311341 original size:35 final size:34
Alignment explanation
Indices: 1311256--1311342 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
1311246 AATATAATTT
*
1311256 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
* *
1311290 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--G-TATTAAATGG
1311328 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
1311343 ACCAAAATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 4 0.09
38 11 0.24
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:1311375 original size:34 final size:33
Alignment explanation
Indices: 1311337--1311411 Score: 82
Period size: 34 Copynumber: 2.2 Consensus size: 33
1311327 GTAATAAACA
* *
1311337 AAATTAACCAAAATACATTAACAA-AAAGTCCAA-C
1 AAATTAA-CAAAAAAAATTAA-AATAAA-TCCAACC
1311371 AAATTTAACAAAAAAAATTAAAATAAATCCAACC
1 AAA-TTAACAAAAAAAATTAAAATAAATCCAACC
1311405 AAATTAA
1 AAATTAA
1311412 TGAAATAAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
33 11 0.31
34 21 0.58
35 4 0.11
ACGTcount: A:0.63, C:0.16, G:0.01, T:0.20
Consensus pattern (33 bp):
AAATTAACAAAAAAAATTAAAATAAATCCAACC
Found at i:1311468 original size:12 final size:13
Alignment explanation
Indices: 1311441--1311471 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1311431 AATGATAAAT
1311441 AATAAAAAATTAC
1 AATAAAAAATTAC
1311454 AATAAAAAATT-C
1 AATAAAAAATTAC
1311466 AATAAA
1 AATAAA
1311472 CAACTAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (13 bp):
AATAAAAAATTAC
Found at i:1313699 original size:17 final size:17
Alignment explanation
Indices: 1313674--1313706 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
1313664 AAATTAAATA
1313674 AAATATTAAA-AAATTT
1 AAATATTAAATAAATTT
1313690 AAATACTTAAATAAATT
1 AAATA-TTAAATAAATT
1313707 AAAAAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATATTAAATAAATTT
Found at i:1313708 original size:17 final size:16
Alignment explanation
Indices: 1313668--1313709 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
1313658 AAAAAAAAAT
*
1313668 TAAATAAAATATTAAA
1 TAAATTAAATATTAAA
1313684 -AAATTTAAATACTTAAA
1 TAAA-TTAAATA-TTAAA
1313701 TAAATTAAA
1 TAAATTAAA
1313710 AAAATATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
15 3 0.14
16 6 0.27
17 10 0.45
18 3 0.14
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (16 bp):
TAAATTAAATATTAAA
Found at i:1313850 original size:47 final size:47
Alignment explanation
Indices: 1313781--1313878 Score: 178
Period size: 47 Copynumber: 2.1 Consensus size: 47
1313771 GAGAAGTTGA
*
1313781 GAGGATTTGGTGTGATGAAAGTGATTGAGAATGAGGGTATTTATAGG
1 GAGGATTTGGTATGATGAAAGTGATTGAGAATGAGGGTATTTATAGG
*
1313828 GAGGATTTGGTATGATGAAAGTGATTGAGAATGGGGGTATTTATAGG
1 GAGGATTTGGTATGATGAAAGTGATTGAGAATGAGGGTATTTATAGG
1313875 GAGG
1 GAGG
1313879 GATGGTGGGT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.30, C:0.00, G:0.40, T:0.31
Consensus pattern (47 bp):
GAGGATTTGGTATGATGAAAGTGATTGAGAATGAGGGTATTTATAGG
Found at i:1314584 original size:14 final size:14
Alignment explanation
Indices: 1314567--1314658 Score: 51
Period size: 14 Copynumber: 6.3 Consensus size: 14
1314557 AAATAGAGTA
*
1314567 AAAAAAGAATAAGT
1 AAAAAAGAATAAAT
*
1314581 AAAAAAGGATAAAT
1 AAAAAAGAATAAAT
*
1314595 AAATAAATAAATAAAT
1 AAA-AAA-GAATAAAT
** *
1314611 AACCATGAATAAAT
1 AAAAAAGAATAAAT
* *
1314625 AAATGAA-AATAAAG
1 AAA-AAAGAATAAAT
*
1314639 AAAATAAAAATAAAAT
1 AAAA-AAGAAT-AAAT
1314655 AAAA
1 AAAA
1314659 CAAAGAGAAG
Statistics
Matches: 58, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
14 35 0.60
15 8 0.14
16 15 0.26
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.17
Consensus pattern (14 bp):
AAAAAAGAATAAAT
Found at i:1314598 original size:4 final size:4
Alignment explanation
Indices: 1314589--1314628 Score: 53
Period size: 4 Copynumber: 9.5 Consensus size: 4
1314579 GTAAAAAAGG
*
1314589 ATAA ATAA ATAA ATAA ATAA ATAA CCATGA ATAA ATAA AT
1 ATAA ATAA ATAA ATAA ATAA ATAA --ATAA ATAA ATAA AT
1314629 GAAAATAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 29 0.91
6 3 0.09
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.25
Consensus pattern (4 bp):
ATAA
Found at i:1314603 original size:26 final size:26
Alignment explanation
Indices: 1314574--1314637 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
1314564 GTAAAAAAAG
* **
1314574 AATAAGTAAAAAAGGATAAATAAATA
1 AATAAATAAAAAACCATAAATAAATA
* *
1314600 AATAAATAAATAACCATGAATAAATA
1 AATAAATAAAAAACCATAAATAAATA
1314626 AATGAAAATAAA
1 AAT--AAATAAA
1314638 GAAAATAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 24 0.77
28 7 0.23
ACGTcount: A:0.69, C:0.03, G:0.08, T:0.20
Consensus pattern (26 bp):
AATAAATAAAAAACCATAAATAAATA
Found at i:1314931 original size:20 final size:20
Alignment explanation
Indices: 1314906--1314959 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
1314896 GTTAGGTTAG
1314906 ATATATATAATAATAATAAT
1 ATATATATAATAATAATAAT
*
1314926 ATATATAT-ATATATACTAAT
1 ATATATATAATA-ATAATAAT
*
1314946 ATAAATGATAATAA
1 ATATAT-ATAATAA
1314960 AGAAAAGAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 3 0.10
20 20 0.69
21 3 0.10
22 3 0.10
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (20 bp):
ATATATATAATAATAATAAT
Found at i:1315892 original size:12 final size:12
Alignment explanation
Indices: 1315875--1315900 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1315865 TTTCGTATCA
1315875 ACCGTGTCAAAT
1 ACCGTGTCAAAT
1315887 ACCGTGTCAAAT
1 ACCGTGTCAAAT
1315899 AC
1 AC
1315901 AATGGATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.23
Consensus pattern (12 bp):
ACCGTGTCAAAT
Found at i:1317235 original size:95 final size:95
Alignment explanation
Indices: 1317069--1317245 Score: 259
Period size: 95 Copynumber: 1.9 Consensus size: 95
1317059 AAATTGTTTG
* * * *
1317069 TTGACAGTCAGCCGCCTCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGAGTCTAATATCATTCG
1 TTGACAATCAGCCGCCCCTTCGCTGCGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCATTCG
1317134 TCGTGAAGTTGAAATTGACTCTGAATGAAT
66 TCGTGAAGTTGAAATTGACTCTGAATGAAT
* * *
1317164 TTGACAATCAGCCGCCCCTTCG-TCGCGAAGTTGAGCTTGTGTTGTCTTGGGTCCAATATCCTTC
1 TTGACAATCAGCCGCCCCTTCGCT-GCGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCATTC
1317228 G-CTGTGAAGTTGAAATTG
65 GTC-GTGAAGTTGAAATTG
1317246 GCTATGAAAT
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
94 2 0.03
95 71 0.97
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.34
Consensus pattern (95 bp):
TTGACAATCAGCCGCCCCTTCGCTGCGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATATCATTCG
TCGTGAAGTTGAAATTGACTCTGAATGAAT
Found at i:1318406 original size:6 final size:6
Alignment explanation
Indices: 1318391--1318441 Score: 50
Period size: 6 Copynumber: 7.8 Consensus size: 6
1318381 ACTCACCTTA
1318391 TTTTTC -TTTTC TTTTTC TTTTGTTC TTTTTCTC TTTTTTC TTTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC -TTT-TTC -TTTT-TC -TTTTTC TTTTTC TTTTT
1318442 TCAATTTAGG
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
5 5 0.12
6 16 0.39
7 6 0.15
8 14 0.34
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (6 bp):
TTTTTC
Found at i:1318418 original size:8 final size:7
Alignment explanation
Indices: 1318397--1318443 Score: 62
Period size: 8 Copynumber: 6.7 Consensus size: 7
1318387 CTTATTTTTC
1318397 TTTTC-T
1 TTTTCTT
1318403 TTTTCTT
1 TTTTCTT
1318410 TTGTTCTT
1 TT-TTCTT
1318418 TTTCTCTT
1 TTT-TCTT
1318426 TTTTC-T
1 TTTTCTT
1318432 TTTTCTT
1 TTTTCTT
1318439 TTTTC
1 TTTTC
1318444 AATTTAGGGT
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
6 11 0.30
7 12 0.32
8 14 0.38
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (7 bp):
TTTTCTT
Found at i:1318431 original size:15 final size:14
Alignment explanation
Indices: 1318397--1318442 Score: 74
Period size: 14 Copynumber: 3.2 Consensus size: 14
1318387 CTTATTTTTC
1318397 TTTTCTTTTTCTTT
1 TTTTCTTTTTCTTT
*
1318411 TGTTCTTTTTCTCTT
1 TTTTCTTTTTCT-TT
1318426 TTTTCTTTTTCTTT
1 TTTTCTTTTTCTTT
1318440 TTT
1 TTT
1318443 CAATTTAGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 16 0.55
15 13 0.45
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (14 bp):
TTTTCTTTTTCTTT
Found at i:1328947 original size:4 final size:4
Alignment explanation
Indices: 1328938--1328985 Score: 60
Period size: 4 Copynumber: 11.5 Consensus size: 4
1328928 GTAAAAAAGG
* *
1328938 ATAA ATAA ATAA ATAA ATGA ATAA ATAA ATAA CCATGA ATAA ATAA AT
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA --ATAA ATAA ATAA AT
1328986 GAAAATAAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
4 35 0.92
6 3 0.08
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.25
Consensus pattern (4 bp):
ATAA
Found at i:1329134 original size:2 final size:2
Alignment explanation
Indices: 1329127--1329176 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1329117 GTATTAATAA
1329127 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1329169 AT AT AT AT
1 AT AT AT AT
1329177 TTTTACACAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1329282 original size:2 final size:2
Alignment explanation
Indices: 1329275--1329319 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
1329265 GTTAGGTTAG
1329275 AT AT AT AT A- AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1329315 AT AT A
1 AT AT A
1329320 CTAATATAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1329292 original size:10 final size:9
Alignment explanation
Indices: 1329275--1329327 Score: 63
Period size: 10 Copynumber: 5.6 Consensus size: 9
1329265 GTTAGGTTAG
1329275 ATATATATA
1 ATATATATA
1329284 ATA-ATATA
1 ATATATATA
1329292 TATATATATA
1 -ATATATATA
1329302 TATATATATA
1 -ATATATATA
1329312 TATATATACTA
1 -ATATATA-TA
1329323 ATATA
1 ATATA
1329328 AATGATAATA
Statistics
Matches: 41, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
8 5 0.12
9 6 0.15
10 28 0.68
11 2 0.05
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (9 bp):
ATATATATA
Found at i:1329292 original size:12 final size:12
Alignment explanation
Indices: 1329275--1329337 Score: 67
Period size: 12 Copynumber: 5.2 Consensus size: 12
1329265 GTTAGGTTAG
1329275 ATATATATAATA
1 ATATATATAATA
1329287 ATATATAT-AT-
1 ATATATATAATA
1329297 ATATATATATATA
1 ATATATATA-ATA
*
1329310 TATATATATACTA
1 -ATATATATAATA
* *
1329323 ATATAAATGATA
1 ATATATATAATA
1329335 ATA
1 ATA
1329338 AAGACAAGAG
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
10 8 0.19
11 2 0.05
12 22 0.51
13 2 0.05
14 9 0.21
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (12 bp):
ATATATATAATA
Found at i:1329326 original size:8 final size:7
Alignment explanation
Indices: 1329275--1329327 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 7
1329265 GTTAGGTTAG
1329275 ATATAT-
1 ATATATA
1329281 ATA-ATA
1 ATATATA
1329287 ATATAT-
1 ATATATA
1329293 ATATAT-
1 ATATATA
1329299 ATATATA
1 ATATATA
1329306 TATATATA
1 -ATATATA
1329314 TATATACTA
1 -ATATA-TA
1329323 ATATA
1 ATATA
1329328 AATGATAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
5 2 0.05
6 18 0.43
7 2 0.05
8 18 0.43
9 2 0.05
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (7 bp):
ATATATA
Found at i:1329489 original size:2 final size:2
Alignment explanation
Indices: 1329482--1329512 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1329472 AATAAATAGA
1329482 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1329513 CACAATTATA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1341236 original size:36 final size:35
Alignment explanation
Indices: 1341196--1341294 Score: 99
Period size: 35 Copynumber: 2.8 Consensus size: 35
1341186 AAGAATAACG
* * *
1341196 AAAGGAAGTATCGGCACTTTCGATTCACGAAGAACA
1 AAAGGAAGAATCAGCACTTTCGATTCAAG-AGAACA
* * * *
1341232 AAAGGAAGAATCAGTACTTTTGATTCAAGTGAACG
1 AAAGGAAGAATCAGCACTTTCGATTCAAGAGAACA
* * *
1341267 GAAGGAAGCATCAACACTTTCGATTCAA
1 AAAGGAAGAATCAGCACTTTCGATTCAA
1341295 TTATTCATCT
Statistics
Matches: 51, Mismatches: 12, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
35 27 0.53
36 24 0.47
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.22
Consensus pattern (35 bp):
AAAGGAAGAATCAGCACTTTCGATTCAAGAGAACA
Found at i:1353813 original size:35 final size:35
Alignment explanation
Indices: 1353774--1353892 Score: 148
Period size: 36 Copynumber: 3.3 Consensus size: 35
1353764 ATGAACAATC
* *
1353774 GAATCGAAAGTGATGACGCTTCCTTCCGTTCACTT
1 GAATCGAAAGTGACGATGCTTCCTTCCGTTCACTT
* * *
1353809 GAATCGAAAGTGACGATGCTTCATTTCGTTCTTCTT
1 GAATCGAAAGTGACGATGCTTCCTTCCGTTC-ACTT
* * *
1353845 GAATCGAAAGTGCCGATGCTTCCTTCCATCCACTTT
1 GAATCGAAAGTGACGATGCTTCCTTCCGTTCAC-TT
1353881 GAATCGAAAGTG
1 GAATCGAAAGTG
1353893 CTAATGTTTC
Statistics
Matches: 71, Mismatches: 11, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
35 28 0.39
36 43 0.61
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (35 bp):
GAATCGAAAGTGACGATGCTTCCTTCCGTTCACTT
Found at i:1353866 original size:71 final size:72
Alignment explanation
Indices: 1353774--1353916 Score: 191
Period size: 72 Copynumber: 2.0 Consensus size: 72
1353764 ATGAACAATC
* * * *
1353774 GAATCGAAAGTGATGACGCTTCCTTCCGTTCAC-TTGAATCGAAAGTGAC-GATGCTTCATTTCG
1 GAATCGAAAGTGACGACGCTTCCTTCCATCCACTTTGAATCGAAAGTG-CTAATGCTTCATTTCG
1353837 TTCTTCTT
65 TTCTTCTT
* * * *
1353845 GAATCGAAAGTGCCGATGCTTCCTTCCATCCACTTTGAATCGAAAGTGCTAATGTTTCCTTTCGT
1 GAATCGAAAGTGACGACGCTTCCTTCCATCCACTTTGAATCGAAAGTGCTAATGCTTCATTTCGT
1353910 TCTTCTT
66 TCTTCTT
1353917 ATTCACCTTC
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
71 29 0.47
72 33 0.53
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (72 bp):
GAATCGAAAGTGACGACGCTTCCTTCCATCCACTTTGAATCGAAAGTGCTAATGCTTCATTTCGT
TCTTCTT
Found at i:1356586 original size:50 final size:50
Alignment explanation
Indices: 1356523--1356624 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
1356513 TTTATCCTAT
1356523 TTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
1 TTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
1356573 TTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
1 TTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
1356623 TT
1 TT
1356625 CAATAATTTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.25, C:0.02, G:0.16, T:0.57
Consensus pattern (50 bp):
TTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
Found at i:1357680 original size:24 final size:24
Alignment explanation
Indices: 1357620--1357685 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 24
1357610 AATAAAAATA
* * *
1357620 TATTTTTTCTATTTTTGTGACACG
1 TATTTTATCTGTTCTTGTGACACG
*
1357644 TATTTTATCTGTTCTTGTGGCACG
1 TATTTTATCTGTTCTTGTGACACG
* * *
1357668 TGTTTTCTTTGTTCTTGT
1 TATTTTATCTGTTCTTGT
1357686 AAGACGATCT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.11, C:0.14, G:0.17, T:0.59
Consensus pattern (24 bp):
TATTTTATCTGTTCTTGTGACACG
Found at i:1358838 original size:54 final size:54
Alignment explanation
Indices: 1358737--1358901 Score: 285
Period size: 54 Copynumber: 3.0 Consensus size: 54
1358727 ATCTGGATTA
*
1358737 ACATTTTGGAACATTTGTATACAATAATCATATGAAGAATAAGGCAAAAGAAAGT
1 ACATTTTAGAACATTTGTATACAAT-ATCATATGAAGAATAAGGCAAAAGAAAGT
*
1358792 ACATTTTAGAACATTTGTATACACTATCATATGAAGAATAAGGCAAAAGAAAGT
1 ACATTTTAGAACATTTGTATACAATATCATATGAAGAATAAGGCAAAAGAAAGT
* *
1358846 ACATTTTAGAATATTTGTATACAATATCATATGAGGAATAAGGCAAAAGAAAGT
1 ACATTTTAGAACATTTGTATACAATATCATATGAAGAATAAGGCAAAAGAAAGT
1358900 AC
1 AC
1358902 CCCAGAATTC
Statistics
Matches: 105, Mismatches: 5, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
54 82 0.78
55 23 0.22
ACGTcount: A:0.47, C:0.10, G:0.16, T:0.28
Consensus pattern (54 bp):
ACATTTTAGAACATTTGTATACAATATCATATGAAGAATAAGGCAAAAGAAAGT
Found at i:1362170 original size:41 final size:41
Alignment explanation
Indices: 1362066--1362185 Score: 125
Period size: 41 Copynumber: 2.9 Consensus size: 41
1362056 ACTTGCACGA
* * ***
1362066 CACTAAATTACGAGTCTATAGCAGCGTTCGCATAAAAACGC
1 CACTAAATTACGAGTCTTTAGCGGCGTTTTAATAAAAACGC
* ** *
1362107 CACTAAAGTATTAGT-TTATAGCGGCGTTTTTATAAAAACGC
1 CACTAAATTACGAGTCTT-TAGCGGCGTTTTAATAAAAACGC
* *
1362148 TACTAAATTACGAATCTTTAGCGGCGTTTTAATAAAAA
1 CACTAAATTACGAGTCTTTAGCGGCGTTTTAATAAAAA
1362186 AACGCCGCAA
Statistics
Matches: 63, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
40 1 0.02
41 60 0.95
42 2 0.03
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (41 bp):
CACTAAATTACGAGTCTTTAGCGGCGTTTTAATAAAAACGC
Found at i:1362808 original size:36 final size:34
Alignment explanation
Indices: 1362768--1362835 Score: 84
Period size: 36 Copynumber: 1.9 Consensus size: 34
1362758 AGTTAATATA
*
1362768 TAATTGAACTATATA-TAATTTTAAAATGTTTAATTT
1 TAATTGAACTA-AAAGTAA-TTTAAAAT-TTTAATTT
*
1362804 TAATTGAAGTAAAAGTAATTTAAAATTTTAAT
1 TAATTGAACTAAAAGTAATTTAAAATTTTAAT
1362836 ATAATTACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 6 0.21
35 10 0.34
36 13 0.45
ACGTcount: A:0.46, C:0.01, G:0.07, T:0.46
Consensus pattern (34 bp):
TAATTGAACTAAAAGTAATTTAAAATTTTAATTT
Found at i:1367498 original size:19 final size:19
Alignment explanation
Indices: 1367474--1367518 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
1367464 CTTTTAAATA
*
1367474 TTTATTTAAAAATATTTAT
1 TTTATTTAAAAATATATAT
*
1367493 TTTATTAAAAAATATATAT
1 TTTATTTAAAAATATATAT
*
1367512 ATTATTT
1 TTTATTT
1367519 TTAAAAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTATTTAAAAATATATAT
Found at i:1367520 original size:25 final size:22
Alignment explanation
Indices: 1367485--1367529 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 22
1367475 TTATTTAAAA
*
1367485 ATATTTATTTTATTAAAAAATAT
1 ATATTTATTTTA-AAAAAAATAT
1367508 ATATATTATTTTTAAAAAAAAT
1 ATAT-TTA-TTTTAAAAAAAAT
1367530 CTTTTTTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 4 0.21
24 10 0.53
25 5 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATATTTATTTTAAAAAAAATAT
Found at i:1368354 original size:25 final size:25
Alignment explanation
Indices: 1368320--1368372 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
1368310 GCCTTTTCCC
1368320 TTCGTTCTGGCTGATTATGTGAAAT
1 TTCGTTCTGGCTGATTATGTGAAAT
1368345 TTCGTTCTGGCTGATTATGTGAAAT
1 TTCGTTCTGGCTGATTATGTGAAAT
1368370 TTC
1 TTC
1368373 CGTCGTGCGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.19, C:0.13, G:0.23, T:0.45
Consensus pattern (25 bp):
TTCGTTCTGGCTGATTATGTGAAAT
Found at i:1371108 original size:17 final size:17
Alignment explanation
Indices: 1371086--1371122 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
1371076 GGTTGCTGTG
*
1371086 ATTAGCGTTGGCAAGTA
1 ATTAGCATTGGCAAGTA
1371103 ATTAGCATTGGCAAGTA
1 ATTAGCATTGGCAAGTA
1371120 ATT
1 ATT
1371123 TCTTTTCTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.32
Consensus pattern (17 bp):
ATTAGCATTGGCAAGTA
Found at i:1372512 original size:21 final size:21
Alignment explanation
Indices: 1372488--1372597 Score: 57
Period size: 21 Copynumber: 5.2 Consensus size: 21
1372478 TAATAAAATA
1372488 ATATATTATCGATGAATTTTT
1 ATATATTATCGATGAATTTTT
* ** ** **
1372509 ATATAAATAT-TTTTTATTTAA
1 ATAT-ATTATCGATGAATTTTT
1372530 ATATATTATCGATGAATTTTT
1 ATATATTATCGATGAATTTTT
* * **
1372551 ATATA-AAT-AAT-TTTTATTT
1 ATATATTATCGATGAATT-TTT
1372570 AAATATATTATCGATGAATTTTT
1 --ATATATTATCGATGAATTTTT
1372593 ATATA
1 ATATA
1372598 AATAATTTAT
Statistics
Matches: 59, Mismatches: 22, Indels: 16
0.61 0.23 0.16
Matches are distributed among these distances:
18 2 0.03
19 5 0.08
20 6 0.10
21 33 0.56
22 6 0.10
23 5 0.08
24 2 0.03
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (21 bp):
ATATATTATCGATGAATTTTT
Found at i:1372534 original size:42 final size:42
Alignment explanation
Indices: 1372487--1372605 Score: 229
Period size: 42 Copynumber: 2.8 Consensus size: 42
1372477 ATAATAAAAT
*
1372487 AATATATTATCGATGAATTTTTATATAAATATTTTTTATTTA
1 AATATATTATCGATGAATTTTTATATAAATAATTTTTATTTA
1372529 AATATATTATCGATGAATTTTTATATAAATAATTTTTATTTA
1 AATATATTATCGATGAATTTTTATATAAATAATTTTTATTTA
1372571 AATATATTATCGATGAATTTTTATATAAATAATTT
1 AATATATTATCGATGAATTTTTATATAAATAATTT
1372606 ATGGTTTAGG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (42 bp):
AATATATTATCGATGAATTTTTATATAAATAATTTTTATTTA
Found at i:1372564 original size:15 final size:15
Alignment explanation
Indices: 1372502--1372574 Score: 55
Period size: 15 Copynumber: 5.1 Consensus size: 15
1372492 ATTATCGATG
1372502 AATTTTTATATAAAT
1 AATTTTTATATAAAT
* *
1372517 ATTTTTTATTTAAAT
1 AATTTTTATATAAAT
* **
1372532 -A--TAT-TATCGAT
1 AATTTTTATATAAAT
1372543 GAATTTTTATATAAAT
1 -AATTTTTATATAAAT
*
1372559 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
1372574 A
1 A
1372575 TATTATCGAT
Statistics
Matches: 42, Mismatches: 11, Indels: 10
0.67 0.17 0.16
Matches are distributed among these distances:
11 4 0.10
12 2 0.05
13 1 0.02
15 30 0.71
16 5 0.12
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:1375315 original size:2 final size:2
Alignment explanation
Indices: 1375308--1375383 Score: 108
Period size: 2 Copynumber: 40.5 Consensus size: 2
1375298 TTTACATTGT
1375308 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1375350 TA T- TT TA TA TA TA TA TA T- TA T- TA TA T- TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1375384 TTTTTTATTC
Statistics
Matches: 68, Mismatches: 1, Indels: 10
0.86 0.01 0.13
Matches are distributed among these distances:
1 5 0.07
2 63 0.93
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:1375392 original size:16 final size:17
Alignment explanation
Indices: 1375320--1375392 Score: 67
Period size: 19 Copynumber: 4.1 Consensus size: 17
1375310 TATATATATA
*
1375320 TATATATATATATATATAT
1 TATATATAT-TAT-TTTAT
1375339 ATATATATATATATTTTAT
1 -TATATATAT-TATTTTAT
*
1375358 ATATATATATTATTATAT
1 -TATATATATTATTTTAT
*
1375376 TAT-TATATTTTTTTAT
1 TATATATATTATTTTAT
1375392 T
1 T
1375393 CTTTTTTCAT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
16 12 0.24
17 3 0.06
18 7 0.14
19 14 0.29
20 13 0.27
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TATATATATTATTTTAT
Found at i:1379220 original size:110 final size:110
Alignment explanation
Indices: 1379072--1379727 Score: 987
Period size: 110 Copynumber: 6.0 Consensus size: 110
1379062 TATGGTGGTT
* *
1379072 GCTCAACTTCACAGCGAAGGGGCAACTGACGGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
* *
1379137 AATTTCAACTTCACAACGAATGATATTGGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* * * *
1379182 TCTCAACTTCACAGTGAAGGGGCGATTGACTGTCAACAAATAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
*
1379247 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGATAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* * *
1379292 GCTCAACTTCAAAGCGAAGGGGCGACTGACTGTCAACAAATAACTTTTTAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
*
1379357 AATTTCAATTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* *
1379402 GCACAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTTAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
* * *
1379467 AATTCCAACTTCACAGTGAAGGATATTAGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* *
1379512 GCTCAACTTCACAGCGAAGGGGCGACTGACTATTAACAAACAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
* * *
1379577 AATTTCAACTTCACAGTGAAAGATATTGGACTCGAGACAATACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* * * *
1379622 GCTCAACTTCACAACGAATGGGCGGCTGGCTGTCAACAAACAACTTTTCAG--T--TTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
* * * * * *
1379683 AATTTAAACTTCACGGCGAAGGATATTAGCCTTGAAACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
1379728 ATATTTGGAT
Statistics
Matches: 500, Mismatches: 46, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
106 45 0.09
108 1 0.00
110 454 0.91
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.25
Consensus pattern (110 bp):
GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
Found at i:1380094 original size:84 final size:83
Alignment explanation
Indices: 1379834--1380928 Score: 1054
Period size: 84 Copynumber: 13.2 Consensus size: 83
1379824 AATCATGCCC
* *
1379834 ACCAAAGGCCTTCGAGTTCGACTACGCTCAACTCTAAGGCACATCATTTGCAGCATAACTTAAGT
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTGCAGCATAACTTAAGT
*
1379899 CAAGAAGGGTTATCTGCTA
66 CGAGAAGGGTTATCTGC-A
* * * * * * * * * * *
1379918 ATCGAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAG
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAAC-TCCAAGGCACATCATTTGCAGCATAACTTAAG
* * **
1379983 GCTAGAAGGGTTATCTGTG
65 TCGAGAAGGGTTATCTGCA
* * * *
1380002 ACCAAAAGACCTTCGAGTTTGACTACACTCAACTCCAAGGCATATCATTTACAGCATAACTTAAG
1 ACC-AAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTGCAGCATAACTTAAG
*
1380067 TTGAGAAGGGTTATCTGCCA
65 TCGAGAAGGGTTATCTG-CA
* *
1380087 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGT
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTGCAGCATAACTTAAGT
*
1380152 CGAGAAGGGCTATCTG--
66 CGAGAAGGGTTATCTGCA
* * * * * * * * * * *
1380168 -GCAAAGACCCTCTAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAG
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAAC-TCCAAGGCACATCATTTGCAGCATAACTTAAG
* * *
1380232 GCTA-AAGGGTTATCTGTA
65 TCGAGAAGGGTTATCTGCA
* * * *
1380250 ACCAAAAGACCTTCGAGTTAGACTACGCTTAACT-CAAGGCATATCATTTGCAGCATAACATAAG
1 ACC-AAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTGCAGCATAACTTAAG
1380314 TCGAGAAGGGTTATCTGTCA
65 TCGAGAAGGGTTATCTG-CA
* * * *
1380334 ACCAAAGACCTTTGAGTTCGACTACGCTCATCTCTAAGGCACATCATTTGCAGCATAGCTTAAGT
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTGCAGCATAACTTAAGT
*
1380399 CGAGAAGGGCTATCT---
66 CGAGAAGGGTTATCTGCA
* * * * * * * * *
1380414 TCCAAAGACCCTT-AAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAA
1 ACCAAAGA-CCTTCGAGTTCGACTACGCTCAAC-TCCAAGGCACATCATTTGCAGCATAACTTAA
* * * **
1380478 GGCTAAAAGGGTTATCTGTG
64 GTCGAGAAGGGTTATCTGCA
* * * *
1380498 ACCAAAAGACCTTTGAGTTCGACTACGCTTAACT-CAAGGCATATCATTTGCAACATAACTTAAG
1 ACC-AAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTGCAGCATAACTTAAG
*
1380562 TCGAGAAAGGTTATCTGCCA
65 TCGAGAAGGGTTATCTG-CA
* * *
1380582 ACCAAAGACCTTCGAGTTCGATTACGCTCGACTCCAAGGCACATCATTTTCAGCATAACTTAAGT
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTGCAGCATAACTTAAGT
* *
1380647 TGAGAAGGGCTATCTG--
66 CGAGAAGGGTTATCTGCA
* * * * * * * * * *
1380663 -TCAAAGACCCTCGAGTTTGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAG
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAAC-TCCAAGGCACATCATTTGCAGCATAACTTAAG
* * **
1380727 GCTAGAAGGGTTATCTGTG
65 TCGAGAAGGGTTATCTGCA
* * * *
1380746 ACCAAAAGACATTCGAGTTCGACTACACTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAG
1 ACC-AAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTGCAGCATAACTTAAG
* *
1380811 TCAAGAAGGGTTATCTACCA
65 TCGAGAAGGGTTATCT-GCA
*
1380831 ACCAAAGACCTTCGAGTTCGACTACGCTCAGA-TCCAAGGCACATCATTTGCAGCATAGCTTAAG
1 ACCAAAGACCTTCGAGTTCGACTACGCTCA-ACTCCAAGGCACATCATTTGCAGCATAACTTAAG
* * *
1380895 GCAAGAAGAGTTATCTG--
65 TCGAGAAGGGTTATCTGCA
*
1380912 -CCAAAGACCTTAGAGTT
1 ACCAAAGACCTTCGAGTT
1380929 TGATTCCATT
Statistics
Matches: 823, Mismatches: 161, Indels: 58
0.79 0.15 0.06
Matches are distributed among these distances:
80 100 0.12
81 112 0.14
82 25 0.03
83 103 0.13
84 367 0.45
85 116 0.14
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (83 bp):
ACCAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTGCAGCATAACTTAAGT
CGAGAAGGGTTATCTGCA
Found at i:1380623 original size:248 final size:248
Alignment explanation
Indices: 1379829--1380950 Score: 1619
Period size: 248 Copynumber: 4.5 Consensus size: 248
1379819 AAGGGAATCA
* * * *
1379829 TGCCCACCAAAGGCCTTCGAGTTCGACTACGCTCAACTCTAAGGCACATCATTTGCAGCATAACT
1 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTC-ACTCCAAGGCACATCATTTGCAGCATAGCT
* * * * **
1379894 TAAGTCAAGAAGGGTTATCTGCTAATCGAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGC
65 TAAGTCGAGAAGGGCTATCT--T--CCAAAGACCCTTAAGTTCGATTACACTCAGCTTCGAGGGC
* *
1379959 ACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTTGA
126 ACATCATTTACAACATAACTCAAGGCTAAAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGA
* *
1380024 CTACACTCAACTCCAAGGCATATCATTTACAGCATAACTTAAGTTGAGAAGGGTTATC
191 CTACACTCAACTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATC
1380082 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCT
1 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCA-CTCCAAGGCACATCATTTGCAGCATAGCT
**
1380147 TAAGTCGAGAAGGGCTATCTGGCAAAGACCCTCT-AGTTCGATTACACTCAGCTTCGAGGGCACA
65 TAAGTCGAGAAGGGCTATCTTCCAAAGACCCT-TAAGTTCGATTACACTCAGCTTCGAGGGCACA
* *
1380211 TCATTTACAACATAACTCAAGGCT-AAAGGGTTATCTGTAACCAAAAGACCTTCGAGTTAGACTA
129 TCATTTACAACATAACTCAAGGCTAAAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTA
* * *
1380275 CGCTTAACT-CAAGGCATATCATTTGCAGCATAACATAAGTCGAGAAGGGTTATC
194 CACTCAACTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATC
* * *
1380329 TGTCAACCAAAGACCTTTGAGTTCGACTACGCTCATCTCTAAGGCACATCATTTGCAGCATAGCT
1 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCA-CTCCAAGGCACATCATTTGCAGCATAGCT
1380394 TAAGTCGAGAAGGGCTATCTTCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCGAGGGCACAT
65 TAAGTCGAGAAGGGCTATCTTCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCGAGGGCACAT
* *
1380459 CATTTACAGCATAACTCAAGGCTAAAAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCGACTAC
130 CATTTACAACATAACTCAAGGCTAAAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTAC
* * * *
1380524 GCTTAACT-CAAGGCATATCATTTGCAACATAACTTAAGTCGAGAAAGGTTATC
195 ACTCAACTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATC
* * *
1380577 TGCCAACCAAAGACCTTCGAGTTCGATTACGCTCGACTCCAAGGCACATCATTTTCAGCATAACT
1 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTC-ACTCCAAGGCACATCATTTGCAGCATAGCT
* ** *
1380642 TAAGTTGAGAAGGGCTATCTGT-CAAAGACCCTCGAGTTTGATTACACTCAGCTTCGAGGGCACA
65 TAAGTCGAGAAGGGCTATCT-TCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCGAGGGCACA
* * *
1380706 TCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACATTCGAGTTCGACTA
129 TCATTTACAACATAACTCAAGGCTAAAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTA
* *
1380771 CACTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATC
194 CACTCAACTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATC
* *
1380826 TACCAACCAAAGACCTTCGAGTTCGACTACGCTCAGATCCAAGGCACATCATTTGCAGCATAGCT
1 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCA-CTCCAAGGCACATCATTTGCAGCATAGCT
* * * * * * * *
1380891 TAAGGCAAGAAGAGTTATCTGCCAAAGA-CCTTAGAGTTTGATTCCATTCAGC-TCGAGGGC
65 TAAGTCGAGAAGGGCTATCTTCCAAAGACCCTTA-AGTTCGATTACACTCAGCTTCGAGGGC
1380951 GTATCAACCG
Statistics
Matches: 794, Mismatches: 65, Indels: 25
0.90 0.07 0.03
Matches are distributed among these distances:
246 1 0.00
247 186 0.23
248 327 0.41
249 202 0.25
252 1 0.00
253 77 0.10
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.25
Consensus pattern (248 bp):
TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCACTCCAAGGCACATCATTTGCAGCATAGCTT
AAGTCGAGAAGGGCTATCTTCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCGAGGGCACATC
ATTTACAACATAACTCAAGGCTAAAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACA
CTCAACTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATC
Found at i:1381302 original size:14 final size:14
Alignment explanation
Indices: 1381273--1381321 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 14
1381263 TCTACAAAAA
1381273 TATT-TTATTATAT
1 TATTATTATTATAT
1381286 TA-TA-TA-TATAT
1 TATTATTATTATAT
1381297 TATTATTATTATAT
1 TATTATTATTATAT
*
1381311 TTTTATT-TTAT
1 TATTATTATTAT
1381322 TATTTTTGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
11 7 0.23
12 5 0.16
13 8 0.26
14 11 0.35
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTATTATTATAT
Found at i:1381311 original size:11 final size:11
Alignment explanation
Indices: 1381272--1381325 Score: 56
Period size: 11 Copynumber: 4.7 Consensus size: 11
1381262 GTCTACAAAA
1381272 ATATT-TTATT
1 ATATTATTATT
1381282 ATATTATATATAT
1 ATATTAT-TAT-T
1381295 ATTATTATTATT
1 A-TATTATTATT
*
1381307 ATATTTTTATT
1 ATATTATTATT
*
1381318 TTATTATT
1 ATATTATT
1381326 TTTGCAGGCC
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
10 5 0.14
11 16 0.43
12 5 0.14
13 5 0.14
14 6 0.16
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
ATATTATTATT
Found at i:1381321 original size:22 final size:20
Alignment explanation
Indices: 1381272--1381325 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 20
1381262 GTCTACAAAA
1381272 ATATTTTATTA-TATTATAT
1 ATATTTTATTATTATTATAT
*
1381291 ATATATTATTATTATTATATTT
1 ATATTTTATTATTATTATA--T
*
1381313 TTATTTTATTATT
1 ATATTTTATTATT
1381326 TTTGCAGGCC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 10 0.34
20 7 0.24
22 12 0.41
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
ATATTTTATTATTATTATAT
Found at i:1381416 original size:33 final size:33
Alignment explanation
Indices: 1381379--1381445 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
1381369 GAAAATAAAT
*
1381379 CAACGTATTTGAGTCCTATTGAAACACTAAAAC
1 CAACGTATTTGAGTCCTATTAAAACACTAAAAC
1381412 CAACGTATTTGAGTCCTATTAAAACACTAAAAC
1 CAACGTATTTGAGTCCTATTAAAACACTAAAAC
1381445 C
1 C
1381446 GAAGCATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.22, G:0.10, T:0.27
Consensus pattern (33 bp):
CAACGTATTTGAGTCCTATTAAAACACTAAAAC
Found at i:1381993 original size:12 final size:12
Alignment explanation
Indices: 1381976--1382002 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1381966 GAATTGAATT
1381976 TTTAAATTTTAA
1 TTTAAATTTTAA
1381988 TTTAAATTTTAA
1 TTTAAATTTTAA
1382000 TTT
1 TTT
1382003 TTGCGATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TTTAAATTTTAA
Found at i:1386789 original size:11 final size:11
Alignment explanation
Indices: 1386775--1386799 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1386765 ATTATCGTTT
1386775 TATTTTTTATA
1 TATTTTTTATA
1386786 TATTTTTTATA
1 TATTTTTTATA
1386797 TAT
1 TAT
1386800 AAAAGAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TATTTTTTATA
Found at i:1387478 original size:29 final size:28
Alignment explanation
Indices: 1387362--1387485 Score: 97
Period size: 29 Copynumber: 4.3 Consensus size: 28
1387352 AACAATAAAA
* *
1387362 TTAGAATGTTCAAAAGCTTTAGGACCAAT
1 TTAGAATATTCAAAAG-TTTAGGATCAAT
* * *
1387391 TTAGAATGTCCAAAAGTTTAGGGATTAAT
1 TTAGAATATTCAAAAGTTTA-GGATCAAT
* * * *
1387420 TTAGAATGAGTC-ATAGTTTAAGAATGAAT
1 TTAGAAT-ATTCAAAAGTTT-AGGATCAAT
*
1387449 TTGGAATATTCAAAAGTTTAGGCATCAAT
1 TTAGAATATTCAAAAGTTTAGG-ATCAAT
*
1387478 TTAAAATA
1 TTAGAATA
1387486 ATTATCATAG
Statistics
Matches: 74, Mismatches: 16, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
28 9 0.12
29 63 0.85
30 2 0.03
ACGTcount: A:0.40, C:0.08, G:0.18, T:0.34
Consensus pattern (28 bp):
TTAGAATATTCAAAAGTTTAGGATCAAT
Found at i:1387569 original size:3 final size:3
Alignment explanation
Indices: 1387561--1387613 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
1387551 TCTTTTATCC
1387561 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1387609 ATA AT
1 ATA AT
1387614 TATGTTATTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1392692 original size:24 final size:25
Alignment explanation
Indices: 1392665--1392724 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 25
1392655 TAAATTAAAT
* *
1392665 TTTTAATAATTTAATTTTTTG-CTA
1 TTTTAATAATTTAATTTATTGAATA
*
1392689 TTTTTAT-ATTTAATTTATTGAATA
1 TTTTAATAATTTAATTTATTGAATA
*
1392713 TCTTAATAATTT
1 TTTTAATAATTT
1392725 TCTATATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 12 0.41
24 13 0.45
25 4 0.14
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (25 bp):
TTTTAATAATTTAATTTATTGAATA
Found at i:1392860 original size:21 final size:20
Alignment explanation
Indices: 1392834--1392902 Score: 68
Period size: 21 Copynumber: 3.4 Consensus size: 20
1392824 TCCATCGAGT
1392834 ACTGTCAAAATAATATTGTGA
1 ACTGTC-AAATAATATTGTGA
* *
1392855 ACTGTCACATCAATATTGTAA
1 ACTGTCAAAT-AATATTGTGA
* *
1392876 ATTGTCATATAAGT-TTGTGA
1 ACTGTCAAATAA-TATTGTGA
1392896 ACTGTCA
1 ACTGTCA
1392903 TGTAAGCGTC
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
20 16 0.40
21 24 0.60
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.36
Consensus pattern (20 bp):
ACTGTCAAATAATATTGTGA
Found at i:1394205 original size:30 final size:31
Alignment explanation
Indices: 1394169--1394227 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
1394159 TAATAGTAAG
*
1394169 GTATCAAAATT-AAAGTTTAGGTACTAAAAC
1 GTATCAAAATTGAAAGTTTAGATACTAAAAC
*
1394199 GTATCAAAATTGATAGTTTAGATACTAAA
1 GTATCAAAATTGAAAGTTTAGATACTAAA
1394228 CATGTTAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.46, C:0.08, G:0.14, T:0.32
Consensus pattern (31 bp):
GTATCAAAATTGAAAGTTTAGATACTAAAAC
Found at i:1394718 original size:2 final size:2
Alignment explanation
Indices: 1394711--1394738 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1394701 TAATAAAAAT
1394711 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1394739 AATAAAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1394912 original size:30 final size:30
Alignment explanation
Indices: 1394877--1394936 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
1394867 TATATGTGTC
1394877 ATAATTTAGTAGGCCATGATCTAT-ATATAT
1 ATAATTTAGTAGGCCATGATCT-TCATATAT
1394907 ATAATTTAGTAGGCCATGATCTTCATATAT
1 ATAATTTAGTAGGCCATGATCTTCATATAT
1394937 GACCAAAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 1 0.03
30 28 0.97
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (30 bp):
ATAATTTAGTAGGCCATGATCTTCATATAT
Found at i:1397079 original size:21 final size:20
Alignment explanation
Indices: 1397024--1397080 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
1397014 TGTGATCTAT
*
1397024 ACCTGGTATCGATACTTCAC
1 ACCTGGTATTGATACTTCAC
*
1397044 ACTTGGTATCT-ATACTTCAC
1 ACCTGGTAT-TGATACTTCAC
*
1397064 CCCTGAGTATTGATACT
1 ACCTG-GTATTGATACT
1397081 CTACTAACAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
20 21 0.70
21 9 0.30
ACGTcount: A:0.25, C:0.26, G:0.14, T:0.35
Consensus pattern (20 bp):
ACCTGGTATTGATACTTCAC
Found at i:1397759 original size:20 final size:20
Alignment explanation
Indices: 1397736--1397774 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1397726 ATCGGTACCG
*
1397736 ACCCCTAATTATCAATACTC
1 ACCCCTAAGTATCAATACTC
* *
1397756 ACCCTTTAGTATCAATACT
1 ACCCCTAAGTATCAATACT
1397775 GAAATGGCTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.31, G:0.03, T:0.33
Consensus pattern (20 bp):
ACCCCTAAGTATCAATACTC
Found at i:1398066 original size:21 final size:21
Alignment explanation
Indices: 1398011--1398067 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 21
1398001 TGTGATCTAT
*
1398011 ACCTGGCATC-GATACTTCAC
1 ACCTGGTATCTGATACTTCAC
*
1398031 ACTTGGTATCT-ATACTTCAC
1 ACCTGGTATCTGATACTTCAC
*
1398051 CCCTGAGTAT-TGATACT
1 ACCTG-GTATCTGATACT
1398068 CTACTAACAG
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
20 21 0.70
21 9 0.30
ACGTcount: A:0.25, C:0.28, G:0.14, T:0.33
Consensus pattern (21 bp):
ACCTGGTATCTGATACTTCAC
Found at i:1398295 original size:987 final size:989
Alignment explanation
Indices: 1396381--1398359 Score: 3838
Period size: 987 Copynumber: 2.0 Consensus size: 989
1396371 GATCCAGAAC
1396381 TGCATCGGAAGTGTACGTTTGGTCAACTTACTTCATCGAGTCTTAGGGCATTTGCACCCAGTTGA
1 TGCATCGGAAGTGTACGTTTGGTCAACTTACTTCATCGAGTCTTAGGGCATTTGCACCCAGTTGA
1396446 CAACTGTAGTTCCTTGGCACTAACTAGTATATATTCAGATGTTGCTACAACGAGACGATCGTCAT
66 CAACTGTAGTTCCTTGGCACTAACTAGTATATATTCAGATGTTGCTACAACGAGACGATCGTCAT
1396511 TGTCTAAAGTAACTCAGTCTCCTAATTGTTTCTCGAGTATCAAACAAGGCTAGTTTTATGTTATC
131 TGTCTAAAGTAACTCAGTCTCCTAATTGTTTCTCGAGTATCAAACAAGGCTAGTTTTATGTTATC
1396576 CTAGATGTTATTGTTTCTACCTATATTGCTTTTTTATTATTTTCATTTGTAGTTTTATTTGATGG
196 CTAGATGTTATTGTTTCTACCTATATTGCTTTTTTATTATTTTCATTTGTAGTTTTATTTGATGG
1396641 CGTTTTGGTGTTATTGGGCCCTTCAAGTCTAATCCTTTAACCATTTGGATTTTTTTTATCAAAAA
261 CGTTTTGGTGTTATTGGGCCCTTCAAGTCTAATCCTTTAACCATTTGGATTTTTTTTATCAAAAA
1396706 CTATACGTTGGTACCGACACTGAGCCCTTTGGTATCGGTACCGACCCCTAATTATCAATACTCAA
326 CTATACGTTGGTACCGACACTGAGCCCTTTGGTATCGGTACCGACCCCTAATTATCAATACTCAA
1396771 CCTTTAGCATCAATACTGAAATGGCTATGTGAGCTGAGAATGAAGGGTAGTATTCGATACTCTTG
391 CCTTTAGCATCAATACTGAAATGGCTATGTGAGCTGAGAATGAAGGGTAGTATTCGATACTCTTG
1396836 GACCAAGTATCTATACTTCTAAACTAGGATATCAATACTATCTTGAGTATCAGTACCAAAATTTG
456 GACCAAGTATCTATACTTCTAAACTAGGATATCAATACTATCTTGAGTATCAGTACCAAAATTTG
1396901 CTTCGATGTATTGAATATTGGCTCGATATCAATACTCGTACTGAGGGTATTGACACATTTTCCTC
521 CTTCGATGTATTGAATATTGGCTCGATATCAATACTCGTACTGAGGGTATTGACACATTTTCCTC
*
1396966 AGTATCGATACTCTCATGAGTACGATCCCAAAAATGACTACTGGAATCTGTGATCTATACCTGGT
586 AGTATCGATACTCTCATGAGTACGATCCCAAAAATGACTACTGGAATCTGTGATCTATACCTGGC
*
1397031 ATCGATACTTCACACTTGGTATCTATACTTCACCCCTGAGTATTGATACTCTACTAACATTATCG
651 ATCGATACTTCACACTTGGTATCTATACTTCACCCCTGAGTATTGATACTCTACTAACAGTATCG
*
1397096 ATACACGATGAAAGAGTTTCGGTACTCCCAATCTAAAAGCTCTTTACTTTTTAGGCTATTTAACG
716 ATACACGATGAAAGAGTTTCAGTACTCCCAATCTAAAAGCTCTTTACTTTTTAGGCTATTTAACG
*
1397161 AACAATATCAGTACTGTTCTTCTAATACCGAGACTCAAACTCATAAATGTCCTGTTTGGGAACAA
781 AAAAATATCAGTACTGTTCTTCTAATACCGAGACTCAAACTCATAAATGTCCTGTTTGGGAACAA
1397226 AAATGACTCCCCATTTCTCCTAAAAGCCATACTTAGGTTCCTAAATGTTATTAACATTTTATGTA
846 AAATGACTCCCCATTTCTCCTAAAAGCCATACTTAGGTTCCTAAATGTTATTAACATTTTATGTA
1397291 TGATAGAAGAGGTCATGATAGGCCAATAAACATGCT-AAAAAACACCCAATACTAGGATTTACCA
911 TGATAGAAGAGGTCATGATAGGCCAATAAACATGCTAAAAAAACACCCAATACTAGGATTTACCA
1397355 TGAACATGCTTATA
976 TGAACATGCTTATA
1397369 TGCATCGGAAGTGTACGTTTGGTCAACTTACTTCATCGAGTCTTAGGGCATTTGCACCCAGTTGA
1 TGCATCGGAAGTGTACGTTTGGTCAACTTACTTCATCGAGTCTTAGGGCATTTGCACCCAGTTGA
1397434 CAACTGTAGTTCCTTGGCACTAACTAGTATATATTCAGATGTTGCTACAACGAGACGATCGTCAT
66 CAACTGTAGTTCCTTGGCACTAACTAGTATATATTCAGATGTTGCTACAACGAGACGATCGTCAT
*
1397499 TGTCTAAAGTAACTCAGTCAT-CTAATTGTTTCTTGAGTATCAAACAAGGCTAGTTTTATGTTAT
131 TGTCTAAAGTAACTCAGTC-TCCTAATTGTTTCTCGAGTATCAAACAAGGCTAGTTTTATGTTAT
1397563 CCTAGATGTTATTGTTTCTACCTATATTGCTTTTTTATTATTTTCATTTGTAG-TTTATTTGATG
195 CCTAGATGTTATTGTTTCTACCTATATTGCTTTTTTATTATTTTCATTTGTAGTTTTATTTGATG
1397627 GCGTTTTGGTGTTATTGGGCCCTTCAAGTCTAATCCTTTAACCATTTGGATTTTTTTTATCAAAA
260 GCGTTTTGGTGTTATTGGGCCCTTCAAGTCTAATCCTTTAACCATTTGGATTTTTTTTATCAAAA
1397692 ACTATACGTTGGTACCGACACTGAGCCCTTTGGTATCGGTACCGACCCCTAATTATCAATACTCA
325 ACTATACGTTGGTACCGACACTGAGCCCTTTGGTATCGGTACCGACCCCTAATTATCAATACTCA
* *
1397757 CCCTTTAGTATCAATACTGAAATGGCTATGTGAGCTGAGAATGAAGGGTAGTATTCGATACTCTT
390 ACCTTTAGCATCAATACTGAAATGGCTATGTGAGCTGAGAATGAAGGGTAGTATTCGATACTCTT
1397822 GGACCAAGTATCTATACTTCTAAACTAGGATATCAATACTATCTTGAGTATCAGTACCAAAATTT
455 GGACCAAGTATCTATACTTCTAAACTAGGATATCAATACTATCTTGAGTATCAGTACCAAAATTT
1397887 GCTTCGATGTATTGAATATTGGCTCGATATCAATACTCGTACTGAGGGTATTGACACATTTTCCT
520 GCTTCGATGTATTGAATATTGGCTCGATATCAATACTCGTACTGAGGGTATTGACACATTTTCCT
1397952 CAGTATCGATACTCTCATGAGTACGATCCCAAAAATGACTACTGGAATCTGTGATCTATACCTGG
585 CAGTATCGATACTCTCATGAGTACGATCCCAAAAATGACTACTGGAATCTGTGATCTATACCTGG
1398017 CATCGATACTTCACACTTGGTATCTATACTTCACCCCTGAGTATTGATACTCTACTAACAGTATC
650 CATCGATACTTCACACTTGGTATCTATACTTCACCCCTGAGTATTGATACTCTACTAACAGTATC
1398082 GATACACGATGAAAGAGTTTCAGTACTCCCAATCTAAAAGCTCTTTACTTTTTAGGCTATTTAAC
715 GATACACGATGAAAGAGTTTCAGTACTCCCAATCTAAAAGCTCTTTACTTTTTAGGCTATTTAAC
* *
1398147 GAAAAATATCGGTATTGTTCTTCTAATACCGAGACTCAAACTCATAAATGTCCTGTTTGGGAACA
780 GAAAAATATCAGTACTGTTCTTCTAATACCGAGACTCAAACTCATAAATGTCCTGTTTGGGAACA
1398212 AAAATGACTCCCCATTTCTCCTAAAAGCCATACTTAGGTTCCTAAATGTTATTAACATTTTATGT
845 AAAATGACTCCCCATTTCTCCTAAAAGCCATACTTAGGTTCCTAAATGTTATTAACATTTTATGT
*
1398277 ATGATAGAAGAGGTCATGATAGGCTAATAAACATGCTAAAAAAACACCCAATACTAGGATTTACC
910 ATGATAGAAGAGGTCATGATAGGCCAATAAACATGCTAAAAAAACACCCAATACTAGGATTTACC
1398342 ATGAACATGCTTATA
975 ATGAACATGCTTATA
1398357 TGC
1 TGC
1398360 TTCATAACTC
Statistics
Matches: 979, Mismatches: 10, Indels: 4
0.99 0.01 0.00
Matches are distributed among these distances:
987 689 0.70
988 289 0.30
989 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (989 bp):
TGCATCGGAAGTGTACGTTTGGTCAACTTACTTCATCGAGTCTTAGGGCATTTGCACCCAGTTGA
CAACTGTAGTTCCTTGGCACTAACTAGTATATATTCAGATGTTGCTACAACGAGACGATCGTCAT
TGTCTAAAGTAACTCAGTCTCCTAATTGTTTCTCGAGTATCAAACAAGGCTAGTTTTATGTTATC
CTAGATGTTATTGTTTCTACCTATATTGCTTTTTTATTATTTTCATTTGTAGTTTTATTTGATGG
CGTTTTGGTGTTATTGGGCCCTTCAAGTCTAATCCTTTAACCATTTGGATTTTTTTTATCAAAAA
CTATACGTTGGTACCGACACTGAGCCCTTTGGTATCGGTACCGACCCCTAATTATCAATACTCAA
CCTTTAGCATCAATACTGAAATGGCTATGTGAGCTGAGAATGAAGGGTAGTATTCGATACTCTTG
GACCAAGTATCTATACTTCTAAACTAGGATATCAATACTATCTTGAGTATCAGTACCAAAATTTG
CTTCGATGTATTGAATATTGGCTCGATATCAATACTCGTACTGAGGGTATTGACACATTTTCCTC
AGTATCGATACTCTCATGAGTACGATCCCAAAAATGACTACTGGAATCTGTGATCTATACCTGGC
ATCGATACTTCACACTTGGTATCTATACTTCACCCCTGAGTATTGATACTCTACTAACAGTATCG
ATACACGATGAAAGAGTTTCAGTACTCCCAATCTAAAAGCTCTTTACTTTTTAGGCTATTTAACG
AAAAATATCAGTACTGTTCTTCTAATACCGAGACTCAAACTCATAAATGTCCTGTTTGGGAACAA
AAATGACTCCCCATTTCTCCTAAAAGCCATACTTAGGTTCCTAAATGTTATTAACATTTTATGTA
TGATAGAAGAGGTCATGATAGGCCAATAAACATGCTAAAAAAACACCCAATACTAGGATTTACCA
TGAACATGCTTATA
Found at i:1399973 original size:29 final size:29
Alignment explanation
Indices: 1399922--1400143 Score: 273
Period size: 29 Copynumber: 7.6 Consensus size: 29
1399912 ATAGTCAACT
* * * *
1399922 ATTACGAAAATAACACTTTTTTTTAAAATA
1 ATTACCAAAATATCAC-CTTTTTAAAAATA
*
1399952 ATTACAAAAATATCACCTTTTTAAAAATA
1 ATTACCAAAATATCACCTTTTTAAAAATA
* *
1399981 ATTACCAAAATATCATCGTTTTAAAAATA
1 ATTACCAAAATATCACCTTTTTAAAAATA
* *
1400010 TTTACCAAAATATCACCGTTTTAAAAATA
1 ATTACCAAAATATCACCTTTTTAAAAATA
* **
1400039 ATTACCAAAATGTCACAATTTTAAAAATA
1 ATTACCAAAATATCACCTTTTTAAAAATA
**
1400068 ATTACCAAAATATCACCTTTTTCGAAATA
1 ATTACCAAAATATCACCTTTTTAAAAATA
* * *
1400097 ATTACTAAAATATCACATTTTTCAAAATA
1 ATTACCAAAATATCACCTTTTTAAAAATA
*
1400126 ATTACTAAAATATCACCT
1 ATTACCAAAATATCACCT
1400144 GATCGGGTCG
Statistics
Matches: 170, Mismatches: 22, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
29 156 0.92
30 14 0.08
ACGTcount: A:0.47, C:0.15, G:0.02, T:0.35
Consensus pattern (29 bp):
ATTACCAAAATATCACCTTTTTAAAAATA
Found at i:1400169 original size:18 final size:18
Alignment explanation
Indices: 1400146--1400188 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
1400136 TATCACCTGA
* *
1400146 TCGGGTCGGGTCAACGGG
1 TCGGGTCGGATCAACAGG
1400164 TCGGGTCGGATCAACAGG
1 TCGGGTCGGATCAACAGG
1400182 TCGGGTC
1 TCGGGTC
1400189 AAACCGGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.23, G:0.44, T:0.19
Consensus pattern (18 bp):
TCGGGTCGGATCAACAGG
Found at i:1407564 original size:29 final size:28
Alignment explanation
Indices: 1407487--1407673 Score: 225
Period size: 29 Copynumber: 6.5 Consensus size: 28
1407477 ACAGTCAACT
* *
1407487 ATTACGAAAATAACAT-TTTTTAAATATA
1 ATTACCAAAATATCATCTTTTTAAA-ATA
* *
1407515 ATTACGAAAATATCACCTTTTTAAAATA
1 ATTACCAAAATATCATCTTTTTAAAATA
*
1407543 ATTACCAAAATATCATCGTTTTAAAAATA
1 ATTACCAAAATATCATC-TTTTTAAAATA
* *
1407572 ATTACCAAAATATCACCATTTTAAAAATA
1 ATTACCAAAATATCATC-TTTTTAAAATA
1407601 ATTACCAAAATATCA-CTTTTTTCAAAATA
1 ATTACCAAAATATCATC-TTTTT-AAAATA
*
1407630 ATTACTAAAATATCATCTTTTTAAAAATA
1 ATTACCAAAATATCATCTTTTT-AAAATA
*
1407659 ATTACTAAAATATCA
1 ATTACCAAAATATCA
1407674 CCGGGCCGGG
Statistics
Matches: 144, Mismatches: 11, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
28 37 0.26
29 106 0.74
30 1 0.01
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (28 bp):
ATTACCAAAATATCATCTTTTTAAAATA
Found at i:1407655 original size:87 final size:86
Alignment explanation
Indices: 1407504--1407675 Score: 281
Period size: 87 Copynumber: 2.0 Consensus size: 86
1407494 AAATAACATT
* *
1407504 TTTTAAATATAATTACGAAAATATCACCTTTTTAAAATAATTACCAAAATATCATCGTTTTAAAA
1 TTTTAAAAATAATTACCAAAATATCACCTTTTTAAAATAATTACCAAAATATCATCGTTTTAAAA
1407569 ATAATTACCAAAATATCACCA
66 ATAATTACCAAAATATCACCA
* * *
1407590 TTTTAAAAATAATTACCAAAATATCACTTTTTTCAAAATAATTACTAAAATATCATCTTTTTAAA
1 TTTTAAAAATAATTACCAAAATATCACCTTTTT-AAAATAATTACCAAAATATCATCGTTTTAAA
*
1407655 AATAATTACTAAAATATCACC
65 AATAATTACCAAAATATCACC
1407676 GGGCCGGGTC
Statistics
Matches: 79, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
86 30 0.38
87 49 0.62
ACGTcount: A:0.48, C:0.15, G:0.01, T:0.37
Consensus pattern (86 bp):
TTTTAAAAATAATTACCAAAATATCACCTTTTTAAAATAATTACCAAAATATCATCGTTTTAAAA
ATAATTACCAAAATATCACCA
Found at i:1407674 original size:58 final size:56
Alignment explanation
Indices: 1407487--1407673 Score: 250
Period size: 58 Copynumber: 3.3 Consensus size: 56
1407477 ACAGTCAACT
* * *
1407487 ATTACGAAAATAACATTTTTTAAATATAATTACGAAAATATCACCTTTTT-AAAATA
1 ATTACCAAAATATCATTTTTTAAA-ATAATTACCAAAATATCACCTTTTTAAAAATA
* *
1407543 ATTACCAAAATATCATCGTTTTAAAAATAATTACCAAAATATCACCATTTTAAAAATA
1 ATTACCAAAATATCAT--TTTTTAAAATAATTACCAAAATATCACCTTTTTAAAAATA
* *
1407601 ATTACCAAAATATCACTTTTTTCAAAATAATTACTAAAATATCATCTTTTTAAAAATA
1 ATTACCAAAATATCA-TTTTTT-AAAATAATTACCAAAATATCACCTTTTTAAAAATA
*
1407659 ATTACTAAAATATCA
1 ATTACCAAAATATCA
1407674 CCGGGCCGGG
Statistics
Matches: 116, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
56 14 0.12
57 27 0.23
58 74 0.64
59 1 0.01
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (56 bp):
ATTACCAAAATATCATTTTTTAAAATAATTACCAAAATATCACCTTTTTAAAAATA
Found at i:1408389 original size:10 final size:10
Alignment explanation
Indices: 1408374--1408400 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1408364 TTTAATTTAG
1408374 TCACCAAATT
1 TCACCAAATT
1408384 TCACCAAATT
1 TCACCAAATT
1408394 TCACCAA
1 TCACCAA
1408401 TATAAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.33, G:0.00, T:0.26
Consensus pattern (10 bp):
TCACCAAATT
Found at i:1413409 original size:30 final size:31
Alignment explanation
Indices: 1413375--1413436 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
1413365 CGCTATTCTA
*
1413375 AGCTTTGCTAAGCTTT-ACTCAATTCTCTCT
1 AGCTTTGCTAAGCTTTCACTCAAATCTCTCT
* *
1413405 AGCTTTTCTAAGCTTTCTCTCAAATCTCTCT
1 AGCTTTGCTAAGCTTTCACTCAAATCTCTCT
1413436 A
1 A
1413437 ATATTTTTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 15 0.54
31 13 0.46
ACGTcount: A:0.21, C:0.27, G:0.08, T:0.44
Consensus pattern (31 bp):
AGCTTTGCTAAGCTTTCACTCAAATCTCTCT
Found at i:1416550 original size:31 final size:31
Alignment explanation
Indices: 1416515--1416581 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
1416505 ACCTCGCTAT
*
1416515 TCTAACCTTTGCTAAGCTTT-ACTCAATTCTC
1 TCTAA-CTTTGCTAAGCTTTCACTCAAATCTC
* *
1416546 TCTAACTTTTCTAAGCTTTCTCTCAAATCTC
1 TCTAACTTTGCTAAGCTTTCACTCAAATCTC
1416577 TCTAA
1 TCTAA
1416582 TATTTTTCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 13 0.41
31 19 0.59
ACGTcount: A:0.24, C:0.28, G:0.04, T:0.43
Consensus pattern (31 bp):
TCTAACTTTGCTAAGCTTTCACTCAAATCTC
Found at i:1417769 original size:48 final size:48
Alignment explanation
Indices: 1417693--1417809 Score: 207
Period size: 48 Copynumber: 2.4 Consensus size: 48
1417683 GTAGATTAAA
* *
1417693 TTTACAAGTTCTATCAATTTAGTCCTAGTTCTAAGTTTAGCCCTCATT
1 TTTATAAGTTCTATCAATTTGGTCCTAGTTCTAAGTTTAGCCCTCATT
1417741 TTTATAAGTTCTATCAATTTGGTCCTAGTTCTAAGTTTAGCCCTCATT
1 TTTATAAGTTCTATCAATTTGGTCCTAGTTCTAAGTTTAGCCCTCATT
*
1417789 TTTATAAATTCTATCAATTTG
1 TTTATAAGTTCTATCAATTTG
1417810 ACCCTCCACA
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 66 1.00
ACGTcount: A:0.26, C:0.18, G:0.10, T:0.46
Consensus pattern (48 bp):
TTTATAAGTTCTATCAATTTGGTCCTAGTTCTAAGTTTAGCCCTCATT
Found at i:1430348 original size:20 final size:20
Alignment explanation
Indices: 1430323--1430364 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
1430313 TTATTTGAAT
1430323 GATGTTATATTGTAATGGTG
1 GATGTTATATTGTAATGGTG
*
1430343 GATGTTATTTTGTAATGGTG
1 GATGTTATATTGTAATGGTG
1430363 GA
1 GA
1430365 ATTATGAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.31, T:0.45
Consensus pattern (20 bp):
GATGTTATATTGTAATGGTG
Found at i:1434958 original size:29 final size:29
Alignment explanation
Indices: 1434918--1434997 Score: 117
Period size: 29 Copynumber: 2.8 Consensus size: 29
1434908 TGTCAAATTT
*
1434918 TATAC-TTAAACCAAAGTAAAGGGTCAAAA
1 TATACATT-AACCAAAGTCAAGGGTCAAAA
*
1434947 TATACATTAACCAAAGTCAACGGTCAAAA
1 TATACATTAACCAAAGTCAAGGGTCAAAA
*
1434976 TATACATTAACTAAAGTCAAGG
1 TATACATTAACCAAAGTCAAGG
1434998 TTTAAATTGA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 44 0.96
30 2 0.04
ACGTcount: A:0.49, C:0.16, G:0.12, T:0.23
Consensus pattern (29 bp):
TATACATTAACCAAAGTCAAGGGTCAAAA
Found at i:1438917 original size:2 final size:2
Alignment explanation
Indices: 1438910--1438948 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1438900 ATTTATTTAT
1438910 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1438949 TTAATTTTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1442272 original size:16 final size:16
Alignment explanation
Indices: 1442251--1442287 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
1442241 AATAAAAGGT
1442251 CTAGTAATTGATCATG
1 CTAGTAATTGATCATG
1442267 CTAGTAATTGATCATG
1 CTAGTAATTGATCATG
1442283 CTAGT
1 CTAGT
1442288 CGCGTCATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.38
Consensus pattern (16 bp):
CTAGTAATTGATCATG
Found at i:1443038 original size:106 final size:106
Alignment explanation
Indices: 1442897--1444704 Score: 2797
Period size: 106 Copynumber: 17.2 Consensus size: 106
1442887 TTCAGTTTCA
*
1442897 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* *
1442962 CGACGAAGGGACCACTGGTTGTCAATAAACAATTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAAT
*
1443003 TTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* * *
1443068 CGACGAAGGGACCGCTGGTTGTCAA-CAATAACTTCCCAAA
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAAT
*
1443108 TTCAGAGCCAATTTCAATTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* *
1443173 CGACGAAGGGATCGCTGGTTGTCAA-CAACAACTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAAT
*
1443213 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* * *
1443278 TGACGAAGGGACCGCTGGTTGTCAA-CAATAACTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAAT
*
1443318 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
*
1443383 CGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAAT
*
1443424 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* * *
1443489 CGACGAAGGGACCGCTGGTTGTCAACAAATAACTTCTCAAT
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAAT
* *
1443530 TTCAGAGCC-ATTTCAAC-TCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTTA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* * * *
1443593 CGACTAAGGGACCACTGGTTGTCAATAAACAATTTCACAAT
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAAT
* *
1443634 TTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
*
1443699 CGACGAAGGGACCGCTGGTTGTTAATAAACAACTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAAT
*
1443740 TTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
*
1443805 CGACGAAGGGACCGCTGGTTGTCAA-CAAC-ACTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAAT
*
1443844 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
*
1443909 CGACGAAGGGA-CGCTGGTTGTCAA-CAA-AACTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAAT
*
1443947 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
*
1444012 CGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAAT
* *
1444053 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* * *
1444118 CGACGAAGGGACCGCTGGTTGTCAACAAATAACTTCTCAAT
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAAT
* * *
1444159 TTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTTA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* * * *
1444224 CGACTAAGGGACCACTGGTTGTCAATAAACAATTTCACAAT
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAAT
* *
1444265 TTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1444330 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAAT
*
1444371 TTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* *
1444436 TGACGAAGGGACCGTTGGTTGTCAATAAACAACTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAAT
* * * * *
1444477 TTCAGAGCCAATTTCAACTTCTCAGTGAAGGATCTTGGAC-CCAAGACAACACAAGCTCAACTTC
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC-AGACAACGCAAGTTCAACTTC
* * * * *
1444541 ACGACGAAGGGGCGGCTGATTGTCAA-CAA-AA-TT-TC-A-
65 ACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAAT
* * * *
1444577 TTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* * * * * **
1444642 CAACGAAAGGA-CGTTTGGTTGTCAACAAACAATTTCCCGGT
66 CGACGAAGGGACCG-CTGGTTGTCAATAAACAACTTCCCAAT
* *
1444683 TCCAGAGCTAATTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCA
1444705 TGACAGAGGA
Statistics
Matches: 1566, Mismatches: 120, Indels: 32
0.91 0.07 0.02
Matches are distributed among these distances:
99 1 0.00
100 73 0.05
101 4 0.00
102 3 0.00
103 104 0.07
104 187 0.12
105 323 0.21
106 871 0.56
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAAT
Found at i:1443293 original size:210 final size:211
Alignment explanation
Indices: 1442897--1444704 Score: 2895
Period size: 210 Copynumber: 8.6 Consensus size: 211
1442887 TTCAGTTTCA
* *
1442897 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
*
1442962 CGACGAAGGGACCACTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACA
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACA
* *
1443027 GTGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
131 GCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
*
1443092 ACAATAACTTCCCAAA
196 ACAATAACTTCCCAAT
* *
1443108 TTCAGAGCCAATTTCAATTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* * *
1443173 CGACGAAGGGATCGCTGGTTGTCAA-CAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACA
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACA
*
1443237 GCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCA
131 GCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
1443302 ACAATAACTTCCCAAT
196 ACAATAACTTCCCAAT
1443318 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1443383 CGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACA
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACA
* *
1443448 GCGAAGGATATTGGACTCCAGACAACGCAAGCTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
131 GCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
*
1443513 ACAAATAACTTCTCAAT
196 AC-AATAACTTCCCAAT
*
1443530 TTCAGAGCC-ATTTCAAC-TCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTTA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* * *
1443593 CGACTAAGGGACCACTGGTTGTCAATAAACAATTTCACAATTTCAGAGCCAATTTCAACTTCACA
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACA
* *
1443658 TCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTTA
131 GCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
* *
1443723 ATAAACAACTTCCCAAT
196 A-CAATAACTTCCCAAT
* *
1443740 TTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* *
1443805 CGACGAAGGGACCGCTGGTTGTCAA-CAAC-ACTTCCCAATTTCAGAGCCAATTTCAACTTCACA
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACA
1443868 GCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGA-CGCTGGTTGTCA
131 GCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
1443932 ACAA-AACTTCCCAAT
196 ACAATAACTTCCCAAT
1443947 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1444012 CGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACA
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACA
* * *
1444077 GCGAAGGATATTGGACTCCAGACAATGCAAGCTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
131 GCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
*
1444142 ACAAATAACTTCTCAAT
196 AC-AATAACTTCCCAAT
* *
1444159 TTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTTA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* * *
1444224 CGACTAAGGGACCACTGGTTGTCAATAAACAATTTCACAATTTCAGAGCCAATTTCAACTTCACA
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACA
*
1444289 TCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
131 GCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
* *
1444354 ATAAACAACTTCCCAAT
196 A-CAATAACTTCCCAAT
* *
1444371 TTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* * * *
1444436 TGACGAAGGGACCGTTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCTCA
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACA
* * * * * * * *
1444501 GTGAAGGATCTTGGACCCAAGACAACACAAGCTCAACTTCACGACGAAGGGGCGGCTGATTGTCA
131 GCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
*
1444566 ACAA-AA-TT-TC-A-
196 ACAATAACTTCCCAAT
* * *
1444577 TTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* * * * ** * *
1444642 CAACGAAAGGA-CGTTTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCTAATTTCAACTTCA
66 CGACGAAGGGACCG-CTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCA
1444705 TGACAGAGGA
Statistics
Matches: 1487, Mismatches: 98, Indels: 29
0.92 0.06 0.02
Matches are distributed among these distances:
205 2 0.00
206 110 0.07
207 100 0.07
208 6 0.00
209 96 0.06
210 490 0.33
211 209 0.14
212 474 0.32
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (211 bp):
TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
CGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACA
GCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
ACAATAACTTCCCAAT
Found at i:1444184 original size:631 final size:632
Alignment explanation
Indices: 1442897--1444704 Score: 3141
Period size: 631 Copynumber: 2.9 Consensus size: 632
1442887 TTCAGTTTCA
* * *
1442897 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTTA
* *
1442962 CGACGAAGGGACCACTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACA
66 CGACTAAGGGACCACTGGTTGTCAATAAACAATTTCACAATTTCAGAGCCAATTTCAACTTCACA
*
1443027 GT-GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC
131 -TCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC
* * * * *
1443091 AA-CAATAACTTCCCAAATTCAGAGCCAATTTCAATTTCACAGCGAAGGATATTGGACTCCAGAC
195 AATAAACAACTTCCCAATTTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGGACTCCAGAC
*
1443155 AACGCAAGTTCAACTTCACGACGAAGGGATCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAG
260 AACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAG
*
1443220 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCATGACGAA
325 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAA
1443285 GGGACCGCTGGTTGTCAACAATAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGA
390 GGGA-CGCTGGTTGTCAACAA-AACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGA
1443350 TATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAA
453 TATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAA
1443415 TTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGC
518 TTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGC
1443480 TCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAACTTCTCAAT
583 TCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAACTTCTCAAT
1443530 TTCAGAGCC-ATTTCAAC-TCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTTA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTTA
1443593 CGACTAAGGGACCACTGGTTGTCAATAAACAATTTCACAATTTCAGAGCCAATTTCAACTTCACA
66 CGACTAAGGGACCACTGGTTGTCAATAAACAATTTCACAATTTCAGAGCCAATTTCAACTTCACA
*
1443658 TCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTTA
131 TCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
1443723 ATAAACAACTTCCCAATTTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGGACTCCAGACA
196 ATAAACAACTTCCCAATTTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGGACTCCAGACA
1443788 ACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAC-ACTTCCCAATTTCAGAGC
261 ACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGC
1443852 CAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAG
326 CAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAG
1443917 GGACGCTGGTTGTCAACAAAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
391 GGACGCTGGTTGTCAACAAAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
1443982 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTT
456 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTT
*
1444047 CCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGCTCA
521 CCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGCTCA
1444112 ACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAACTTCTCAAT
586 ACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAACTTCTCAAT
*
1444159 TTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTTA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTTA
1444224 CGACTAAGGGACCACTGGTTGTCAATAAACAATTTCACAATTTCAGAGCCAATTTCAACTTCACA
66 CGACTAAGGGACCACTGGTTGTCAATAAACAATTTCACAATTTCAGAGCCAATTTCAACTTCACA
1444289 TCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
131 TCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
1444354 ATAAACAACTTCCCAATTTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGGACTCCAGACA
196 ATAAACAACTTCCCAATTTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGGACTCCAGACA
* * *
1444419 ACGCAAGTTCAACTTCATGACGAAGGGACCGTTGGTTGTCAATAAACAACTTCCCAATTTCAGAG
261 ACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA-CAACAACTTCCCAATTTCAGAG
* * * * * *
1444484 CCAATTTCAACTTCTCAGTGAAGGATCTTGGACCCAAGACAACACAAGCTCAACTTCACGACGAA
325 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAA
* * * *
1444549 GGGGCGGCTGATTGTCAACAAAA-TT-TC-A-TTCAGAGTCAATTTCAACTTCACAACGAAGGAT
390 GGGAC-GCTGGTTGTCAACAAAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
* * * * * *
1444610 ATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAAGGA-CGTTTGGTTGTCAACAAACAA
454 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAATAAACAA
** * *
1444674 TTTCCCGGTTCCAGAGCTAATTTCAACTTCA
518 TTTCCCAATTTCAGAGCCAATTTCAACTTCA
1444705 TGACAGAGGA
Statistics
Matches: 1127, Mismatches: 40, Indels: 19
0.95 0.03 0.02
Matches are distributed among these distances:
629 232 0.21
630 139 0.12
631 535 0.47
632 115 0.10
633 90 0.08
634 16 0.01
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (632 bp):
TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTTA
CGACTAAGGGACCACTGGTTGTCAATAAACAATTTCACAATTTCAGAGCCAATTTCAACTTCACA
TCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
ATAAACAACTTCCCAATTTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGGACTCCAGACA
ACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGC
CAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAG
GGACGCTGGTTGTCAACAAAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTT
CCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGCTCA
ACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAACTTCTCAAT
Found at i:1445032 original size:84 final size:84
Alignment explanation
Indices: 1444904--1445412 Score: 396
Period size: 84 Copynumber: 6.2 Consensus size: 84
1444894 TCCAACTCAA
* * * *
1444904 AGAAGGGTTATCTGTCACCAAAGA-CTTTCGAGTTTGACTACGCTCAGCTCCCA-GGCATATCAT
1 AGAAGGGTTATCTGCCAACAAAGACCTTT-GAGTTCGACTACGCTCAGCTCCAACGGCATATCAT
* *
1444967 TTGCAGTACAACTTAAGTCT
65 TTGCAGCATAACTTAAGTCT
* * *
1444987 AGAAGGGTTGTCTGCCAACAACAGACCTTTGAGTTCGACTACGCTCA-CTTCAACGGCACATCAT
1 AGAAGGGTTATCTGCCAACAA-AGACCTTTGAGTTCGACTACGCTCAGCTCCAACGGCATATCAT
* * *
1445051 TTGCGGCATAGCTTAAGTCG
65 TTGCAGCATAACTTAAGTCT
* * * **** * * ** * * *
1445071 AGGAGGGCTATATG-C--CAAAG-CCCCCCAGTCCGATTACATTCAGCTTCGAGGGCATATCATT
1 AGAAGGGTTATCTGCCAACAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAACGGCATATCATT
* * *
1445132 TACAGCATAACTCAAGGCT
66 TGCAGCATAACTTAAGTCT
* * * * * *
1445151 AGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTTGATTACGCTCAGCTCCCA-GGCATATCATT
1 AGAAGGGTTATCTGCCAACAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAACGGCATATCATT
* *
1445215 TGCAGTACAACTTAAGTCT
66 TGCAGCATAACTTAAGTCT
* *
1445234 AGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCT-CAACGGCACATCAT
1 AGAAGGGTTATCTGCCAAC-AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAACGGCATATCAT
*
1445298 TTGCAGCATAACTTAAGTCG
65 TTGCAGCATAACTTAAGTCT
* * * * * * * * * *
1445318 ATG-AGGGCTATCTG-C--CAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATTAT
1 A-GAAGGGTTATCTGCCAACAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAACGGCATATCAT
* ** * *
1445379 TTACAATATAACTCAAGGCT
65 TTGCAGCATAACTTAAGTCT
1445399 AGAAGGGTTATCTG
1 AGAAGGGTTATCTG
1445413 TCACCAAATT
Statistics
Matches: 336, Mismatches: 77, Indels: 28
0.76 0.17 0.06
Matches are distributed among these distances:
79 14 0.04
80 68 0.20
81 41 0.12
83 72 0.21
84 136 0.40
85 5 0.01
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (84 bp):
AGAAGGGTTATCTGCCAACAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAACGGCATATCATT
TGCAGCATAACTTAAGTCT
Found at i:1446543 original size:4 final size:4
Alignment explanation
Indices: 1446534--1446573 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
1446524 TTTAATCCTT
* *
1446534 TTTA TTTA TTTA TTTA TTATA TATA TATA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TT-TA TTTA TTTA TTTA TTTA TTT
1446574 TAATTTTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
4 30 0.91
5 3 0.09
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (4 bp):
TTTA
Found at i:1447224 original size:21 final size:23
Alignment explanation
Indices: 1447200--1447252 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 23
1447190 AATTGAGTCA
*
1447200 TTTTCTA-TAGATTATATCAA-T
1 TTTTCTATTAGATTAAATCAACT
* *
1447221 TTTTTTATTTGATTAAATCAACT
1 TTTTCTATTAGATTAAATCAACT
*
1447244 TTTTTTATT
1 TTTTCTATT
1447253 TTATTTAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 6 0.22
22 11 0.41
23 10 0.37
ACGTcount: A:0.28, C:0.08, G:0.04, T:0.60
Consensus pattern (23 bp):
TTTTCTATTAGATTAAATCAACT
Found at i:1447234 original size:22 final size:23
Alignment explanation
Indices: 1447209--1447253 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1447199 ATTTTCTATA
*
1447209 GATTATATCAA-TTTTTTTATTT
1 GATTAAATCAACTTTTTTTATTT
1447231 GATTAAATCAACTTTTTTTATTT
1 GATTAAATCAACTTTTTTTATTT
1447254 TATTTAGTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.29, C:0.07, G:0.04, T:0.60
Consensus pattern (23 bp):
GATTAAATCAACTTTTTTTATTT
Found at i:1448172 original size:16 final size:16
Alignment explanation
Indices: 1448139--1448174 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1448129 TTTCGAAGGT
**
1448139 ATAAATTAATAATTTA
1 ATAAATTAATAAGATA
1448155 ATAAATTAATAAGATA
1 ATAAATTAATAAGATA
1448171 ATAA
1 ATAA
1448175 TTTTTTGGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
ATAAATTAATAAGATA
Found at i:1448907 original size:41 final size:42
Alignment explanation
Indices: 1448841--1448924 Score: 134
Period size: 41 Copynumber: 2.0 Consensus size: 42
1448831 CCATAGGGTG
1448841 ACCCACTTGTAACCCTCTAAATACAAG-AAACAATTTAAAGA
1 ACCCACTTGTAACCCTCTAAATACAAGAAAACAATTTAAAGA
* * *
1448882 ACCCACTTGTAACTCTTTAATTACAAGAAAACAATTTAAAGA
1 ACCCACTTGTAACCCTCTAAATACAAGAAAACAATTTAAAGA
1448924 A
1 A
1448925 AGTTAGGATT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 24 0.62
42 15 0.38
ACGTcount: A:0.46, C:0.21, G:0.07, T:0.25
Consensus pattern (42 bp):
ACCCACTTGTAACCCTCTAAATACAAGAAAACAATTTAAAGA
Found at i:1449244 original size:30 final size:30
Alignment explanation
Indices: 1449208--1449375 Score: 119
Period size: 30 Copynumber: 5.6 Consensus size: 30
1449198 AGTTAATAAT
1449208 AAATATATTTTTTAAGTTAATAAAAGAATA
1 AAATATATTTTTTAAGTTAATAAAAGAATA
* * * * * *
1449238 AAATATATATTTGAAGTTGAGATAATAATA
1 AAATATATTTTTTAAGTTAATAAAAGAATA
* *
1449268 AATTATATATTTTAAGTTAATAAAAGAATTA
1 AAATATATTTTTTAAGTTAATAAAAGAA-TA
* * * * * *
1449299 TATATATATATATATTGAAGTTAA-GATATAA-C
1 -A-A-ATATAT-TTTTTAAGTTAATAAAAGAATA
*
1449331 AAATATATTTTTTAAGTTAGT-AAA-AATA
1 AAATATATTTTTTAAGTTAATAAAAGAATA
*
1449359 AAATATATTTTTAAAGT
1 AAATATATTTTTTAAGT
1449376 CATATTAATA
Statistics
Matches: 105, Mismatches: 26, Indels: 16
0.71 0.18 0.11
Matches are distributed among these distances:
27 2 0.02
28 27 0.26
29 6 0.06
30 47 0.45
31 3 0.03
32 1 0.01
33 1 0.01
34 9 0.09
35 9 0.09
ACGTcount: A:0.50, C:0.01, G:0.08, T:0.41
Consensus pattern (30 bp):
AAATATATTTTTTAAGTTAATAAAAGAATA
Done.