Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008746.1 Hibiscus syriacus cultivar Beakdansim tig00111835_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: 2013901
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 10
Found at i:1165348 original size:288 final size:293
Alignment explanation
Indices: 1164804--1165390 Score: 1121
Period size: 288 Copynumber: 2.0 Consensus size: 293
1164794 GTAACCTTTT
1164804 TCTTGTCCTGCCCCTGCACCTTTCACCATCTCGTTCTGGAAAAGTTGACTTTTGATGAGCTTGGT
1 TCTTGTCCTGCCCCTGCACCTTT--CCATCTCGTTCTGGAAAAGTTGACTTTTGATGAGCTTGGT
1164869 GGAAACCCGGTCCATTCCGAGTCTTTTCTTACTATAGCTGGACTTCTGAGCTTTTCATCTCTTGT
64 GGAAACCCGGTCCATTCCGAGTCTTTTCTTACTATAGCTGGACTTCTGAGCTTTTCATCTCTTGT
1164934 ATTATAACCCCTTTGTCCATTAATGCAGATTATTCATGTTTAACAAACACGATTTTGGTGGATCA
129 ATTATAACCCCTTTGTCCATTAATGCAGATTATTCATGTTTAACAAACACGATTTTGGTGGATCA
1164999 ACACCTCTTTTAAAAGATGCGAATGATGAAAACAAAATAAAAGAGAACAAAAATAAAAATAGTTG
194 ACACCTCTTTTAAAAGATGCGAATGATGAAAACAAAATAAAAGAGAACAAAAATAAAAATAGTTG
1165064 GTGAGGTAAATC-AAACAATAATAAAAATG-AAAA
259 GTGAGGTAAATCAAAACAATAATAAAAATGAAAAA
1165097 TCTTGTCCTGCCCCTGCACCTTT-CATCTCGTTCTGGAAAAGTTGACTTTTGATGAGCTTGGTGG
1 TCTTGTCCTGCCCCTGCACCTTTCCATCTCGTTCTGGAAAAGTTGACTTTTGATGAGCTTGGTGG
1165161 AAACCCGGTCCATTCCGAGTCTTTTCTTACTATAGCTGGACTTCTGAGCTTTTCATCT-TTGT-T
66 AAACCCGGTCCATTCCGAGTCTTTTCTTACTATAGCTGGACTTCTGAGCTTTTCATCTCTTGTAT
1165224 TATAACCCCTTTGTCCATTAATGCAGATTATTCATGTTTAACAAACACGATTTTGGTGGATCAAC
131 TATAACCCCTTTGTCCATTAATGCAGATTATTCATGTTTAACAAACACGATTTTGGTGGATCAAC
1165289 ACCTCTTTTAAAAGATGCGAATGATGAAAACAAAATAAAAGAGAACAAAAATAAAAATAGTTGGT
196 ACCTCTTTTAAAAGATGCGAATGATGAAAACAAAATAAAAGAGAACAAAAATAAAAATAGTTGGT
1165354 GAGGTAAATCAAAACAATAATAAAAATGAAAAA
261 GAGGTAAATCAAAACAATAATAAAAATGAAAAA
1165387 TCTT
1 TCTT
1165391 ACCCCACATG
Statistics
Matches: 292, Mismatches: 0, Indels: 7
0.98 0.00 0.02
Matches are distributed among these distances:
288 141 0.48
289 21 0.07
290 107 0.37
293 23 0.08
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (293 bp):
TCTTGTCCTGCCCCTGCACCTTTCCATCTCGTTCTGGAAAAGTTGACTTTTGATGAGCTTGGTGG
AAACCCGGTCCATTCCGAGTCTTTTCTTACTATAGCTGGACTTCTGAGCTTTTCATCTCTTGTAT
TATAACCCCTTTGTCCATTAATGCAGATTATTCATGTTTAACAAACACGATTTTGGTGGATCAAC
ACCTCTTTTAAAAGATGCGAATGATGAAAACAAAATAAAAGAGAACAAAAATAAAAATAGTTGGT
GAGGTAAATCAAAACAATAATAAAAATGAAAAA
Found at i:1167191 original size:14 final size:13
Alignment explanation
Indices: 1167172--1167202 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
1167162 AAAAAAAAGT
1167172 AATAATAATAGATA
1 AATAATAATA-ATA
1167186 AATAATAATAATA
1 AATAATAATAATA
1167199 AATA
1 AATA
1167203 TAAAAAAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (13 bp):
AATAATAATAATA
Found at i:1167273 original size:40 final size:39
Alignment explanation
Indices: 1167214--1167564 Score: 190
Period size: 38 Copynumber: 9.3 Consensus size: 39
1167204 AAAAAAAGTA
**
1167214 TTTTTTAAAAAAAACTATATAATATAAATTTTTAAAAATG
1 TTTTTTAAAAACTA-TATATAATATAAATTTTTAAAAATG
*
1167254 TTTTTTAAAAAACTATATATTATATATAAATTTTTAAAAATA
1 TTTTTT-AAAAACTATATA-TA-ATATAAATTTTTAAAAATG
* *
1167296 TTTTTTTAAAAC------T-ATAT-AA-TTTCAAAAATG
1 TTTTTTAAAAACTATATATAATATAAATTTTTAAAAATG
* * *
1167326 -TTTTAAAAATTA-TATAT-TACATATAAGTTTTCAAAAATG
1 TTTTTTAAAA--ACTATATATA-ATATAAATTTTTAAAAATG
* * * *
1167365 -TTTTCAAAAACTATATATTATATAAGTTTTCAAAAATG
1 TTTTTTAAAAACTATATATAATATAAATTTTTAAAAATG
* * * *
1167403 -TTTTCAAAAACTATATATTATAT-AAGTTTTCAAAATG
1 TTTTTTAAAAACTATATATAATATAAATTTTTAAAAATG
* *
1167440 -ATTTT-AAAACTATATATTATATATATATTTTT-AAAA--
1 TTTTTTAAAAACTATATA-TA-ATATAAATTTTTAAAAATG
* * * * *
1167476 TATTTTAAAAACTATATATCATAT--AGTTTT-CAAAGG
1 TTTTTTAAAAACTATATATAATATAAATTTTTAAAAATG
* * * *
1167512 TATTTTAAAAACTATATATTATATACATTTTTAATATATG
1 TTTTTTAAAAACTATATATAATATAAATTTTTAA-AAATG
*
1167552 TATTTTCAAAAAC
1 T-TTTTTAAAAAC
1167565 CGTTTGCAAA
Statistics
Matches: 253, Mismatches: 30, Indels: 55
0.75 0.09 0.16
Matches are distributed among these distances:
29 7 0.03
30 9 0.04
31 3 0.01
32 4 0.02
34 9 0.04
35 1 0.00
36 38 0.15
37 25 0.10
38 72 0.28
39 25 0.10
40 14 0.06
41 22 0.09
42 24 0.09
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (39 bp):
TTTTTTAAAAACTATATATAATATAAATTTTTAAAAATG
Found at i:1167282 original size:42 final size:40
Alignment explanation
Indices: 1167206--1167313 Score: 139
Period size: 42 Copynumber: 2.6 Consensus size: 40
1167196 ATAAATATAA
*
1167206 AAAAAGTATTTTTTAAAAAA-AACTATATAATATAAATTTTT
1 AAAAA-TATTTTTTAAAAAACTA-TATATAATATAAATTTTT
*
1167247 AAAAATGTTTTTTAAAAAACTATATATTATATATAAATTTTT
1 AAAAATATTTTTTAAAAAACTATATA-TA-ATATAAATTTTT
*
1167289 AAAAATATTTTTT-TAAAACTATATA
1 AAAAATATTTTTTAAAAAACTATATA
1167314 ATTTCAAAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
40 17 0.28
41 19 0.32
42 24 0.40
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (40 bp):
AAAAATATTTTTTAAAAAACTATATATAATATAAATTTTT
Found at i:1167369 original size:12 final size:12
Alignment explanation
Indices: 1167352--1167412 Score: 54
Period size: 12 Copynumber: 4.9 Consensus size: 12
1167342 TTACATATAA
1167352 GTTTTCAAAAAT
1 GTTTTCAAAAAT
1167364 GTTTTCAAAAACT
1 GTTTTCAAAAA-T
* *
1167377 ATATATT-ATATAA-
1 GT-T-TTCA-AAAAT
1167390 GTTTTCAAAAAT
1 GTTTTCAAAAAT
1167402 GTTTTCAAAAA
1 GTTTTCAAAAA
1167413 CTATATATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
11 5 0.13
12 24 0.62
13 3 0.08
14 2 0.05
15 5 0.13
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.41
Consensus pattern (12 bp):
GTTTTCAAAAAT
Found at i:1167449 original size:36 final size:37
Alignment explanation
Indices: 1167308--1167536 Score: 281
Period size: 38 Copynumber: 6.2 Consensus size: 37
1167298 TTTTTAAAAC
*
1167308 TATATAA--TTTCAAAAATGTTTTAAAAATTATATAT
1 TATATAAGTTTTCAAAAATGTTTTAAAAACTATATAT
1167343 TACATATAAGTTTTCAAAAATGTTTTCAAAAACTATATAT
1 T--ATATAAGTTTTCAAAAATGTTTT-AAAAACTATATAT
1167383 TATATAAGTTTTCAAAAATGTTTTCAAAAACTATATAT
1 TATATAAGTTTTCAAAAATGTTTT-AAAAACTATATAT
1167421 TATATAAGTTTTC-AAAATGATTTT-AAAACTATATAT
1 TATATAAGTTTTCAAAAATG-TTTTAAAAACTATATAT
** *
1167457 TATATATA-TATTTTTAAAATATTTTAAAAACTATATAT
1 TATATA-AGT-TTTCAAAAATGTTTTAAAAACTATATAT
* ** *
1167495 CATAT-AGTTTTCAAAGGTATTTTAAAAACTATATAT
1 TATATAAGTTTTCAAAAATGTTTTAAAAACTATATAT
1167531 TATATA
1 TATATA
1167537 CATTTTTAAT
Statistics
Matches: 173, Mismatches: 9, Indels: 22
0.85 0.04 0.11
Matches are distributed among these distances:
35 1 0.01
36 48 0.28
37 21 0.12
38 75 0.43
39 15 0.09
40 13 0.08
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.44
Consensus pattern (37 bp):
TATATAAGTTTTCAAAAATGTTTTAAAAACTATATAT
Found at i:1167492 original size:74 final size:74
Alignment explanation
Indices: 1167308--1167536 Score: 283
Period size: 74 Copynumber: 3.1 Consensus size: 74
1167298 TTTTTAAAAC
*
1167308 TATATAA--TTTCAAAAATGTTTTAAAAATTATATATTACATATAAGTTTTCAAAAATG-TTTTC
1 TATATAAGTTTTCAAAAATGTTTTAAAAACTATATATT--ATATAAGTTTTC-AAAATGATTTT-
1167370 AAAAACTATATAT
62 AAAAACTATATAT
1167383 TATATAAGTTTTCAAAAATGTTTTCAAAAACTATATATTATATAAGTTTTCAAAATGATTTT-AA
1 TATATAAGTTTTCAAAAATGTTTT-AAAAACTATATATTATATAAGTTTTCAAAATGATTTTAAA
1167447 AACTATATAT
65 AACTATATAT
** * * *
1167457 TATATATA-TATTTTTAAAATATTTTAAAAACTATATATCATAT-AGTTTTC-AAAGGTATTTTA
1 TATATA-AGT-TTTCAAAAATGTTTTAAAAACTATATATTATATAAGTTTTCAAAATG-ATTTTA
1167519 AAAACTATATAT
63 AAAACTATATAT
1167531 TATATA
1 TATATA
1167537 CATTTTTAAT
Statistics
Matches: 140, Mismatches: 6, Indels: 17
0.86 0.04 0.10
Matches are distributed among these distances:
72 4 0.03
73 12 0.09
74 54 0.39
75 26 0.19
76 16 0.11
77 15 0.11
78 13 0.09
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.44
Consensus pattern (74 bp):
TATATAAGTTTTCAAAAATGTTTTAAAAACTATATATTATATAAGTTTTCAAAATGATTTTAAAA
ACTATATAT
Found at i:1171716 original size:2 final size:2
Alignment explanation
Indices: 1171711--1171741 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1171701 CATACACACA
1171711 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
1171742 CTTGTGGAGG
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:1177155 original size:33 final size:33
Alignment explanation
Indices: 1177095--1177193 Score: 171
Period size: 33 Copynumber: 3.0 Consensus size: 33
1177085 CTCATGTGCA
* *
1177095 AAGTTGGCCACCTACCAAAGATTAATTTTCCAAT
1 AAGTTGGCCACCAACC-AAGATGAATTTTCCAAT
1177129 AAGTTGGCCACCAACCAAGATGAATTTTCCAAT
1 AAGTTGGCCACCAACCAAGATGAATTTTCCAAT
1177162 AAGTTGGCCACCAACCAAGATGAATTTTCCAA
1 AAGTTGGCCACCAACCAAGATGAATTTTCCAA
1177194 CTTGCCAAAT
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
33 48 0.76
34 15 0.24
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.25
Consensus pattern (33 bp):
AAGTTGGCCACCAACCAAGATGAATTTTCCAAT
Found at i:1183024 original size:2 final size:2
Alignment explanation
Indices: 1183014--1183143 Score: 66
Period size: 2 Copynumber: 69.0 Consensus size: 2
1183004 AATTGAAAAA
* *
1183014 AT AT A- AT AT AT AT AT AT AT A- AT AT A- AGT TT AT AT AT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
* * *
1183054 -T AT AT AT AT AA ACT AT AT AT AT AA ACT AT AT TT AT AT -T AT A-
1 AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
* * * *
1183095 AA AT AT AT A- AT -T AT -T AT A- AG CT AT AT AT AT AT AT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1183133 -T AT AT TT AT AT
1 AT AT AT AT AT AT
1183144 GAACTATATT
Statistics
Matches: 96, Mismatches: 18, Indels: 28
0.68 0.13 0.20
Matches are distributed among these distances:
1 11 0.11
2 83 0.86
3 2 0.02
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1183048 original size:17 final size:15
Alignment explanation
Indices: 1183014--1183142 Score: 90
Period size: 15 Copynumber: 8.3 Consensus size: 15
1183004 AATTGAAAAA
1183014 ATATAATATATATAT
1 ATATAATATATATAT
*
1183029 ATATAATATAAGTTTAT
1 ATATAATAT-A-TATAT
1183046 ATATAA-AT-TATAT
1 ATATAATATATATAT
1183059 ATATAA-ACTATATAT
1 ATATAATA-TATATAT
*
1183074 ATA-AACTATATTTAT
1 ATATAA-TATATATAT
*
1183089 ATTATAAAATATATAATT
1 A-TATAATATATAT-A-T
1183107 ATTATAAGCTATATATAT
1 A-TATAA--TATATATAT
1183125 ATATAA-AT-TATAT
1 ATATAATATATATAT
*
1183138 TTATA
1 ATATA
1183143 TGAACTATAT
Statistics
Matches: 95, Mismatches: 7, Indels: 26
0.74 0.05 0.20
Matches are distributed among these distances:
13 20 0.21
14 5 0.05
15 24 0.25
16 11 0.12
17 18 0.19
18 10 0.11
19 1 0.01
20 6 0.06
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (15 bp):
ATATAATATATATAT
Found at i:1183096 original size:18 final size:18
Alignment explanation
Indices: 1183067--1183143 Score: 77
Period size: 18 Copynumber: 4.3 Consensus size: 18
1183057 ATATATAAAC
1183067 TATATATATAAACTATATT
1 TATAT-TATAAACTATATT
*
1183086 TATATTATAAAATATA-T
1 TATATTATAAACTATATT
* * *
1183103 AATTATTATAAGCTATATA
1 TA-TATTATAAACTATATT
*
1183122 TATA-TATAAATTATATT
1 TATATTATAAACTATATT
1183139 TATAT
1 TATAT
1183144 GAACTATATT
Statistics
Matches: 46, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
17 16 0.35
18 24 0.52
19 6 0.13
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (18 bp):
TATATTATAAACTATATT
Found at i:1183136 original size:13 final size:13
Alignment explanation
Indices: 1183019--1183142 Score: 82
Period size: 13 Copynumber: 9.7 Consensus size: 13
1183009 AAAAAATATA
*
1183019 ATATATATATA-T
1 ATATATATAAATT
*
1183031 ATA-ATATAAGTT
1 ATATATATAAATT
1183043 -TATATATAAATT
1 ATATATATAAATT
*
1183055 ATATATATAAACT
1 ATATATATAAATT
*
1183068 ATATATATAAACT
1 ATATATATAAATT
*
1183081 ATAT-T-TATATT
1 ATATATATAAATT
*
1183092 ATAAAATATATAATT
1 AT-ATATATA-AATT
*
1183107 AT-TATA-AGCTATAT
1 ATATATATA--AAT-T
1183121 ATATATATAAATT
1 ATATATATAAATT
*
1183134 ATATTTATA
1 ATATATATA
1183143 TGAACTATAT
Statistics
Matches: 88, Mismatches: 13, Indels: 21
0.72 0.11 0.17
Matches are distributed among these distances:
11 13 0.15
12 15 0.17
13 43 0.49
14 7 0.08
15 9 0.10
16 1 0.01
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (13 bp):
ATATATATAAATT
Found at i:1183256 original size:13 final size:13
Alignment explanation
Indices: 1183238--1183282 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
1183228 AGGAGTGACA
1183238 ATATATATAAACT
1 ATATATATAAACT
*
1183251 ATATATGTAAACT
1 ATATATATAAACT
1183264 ATATAGGTATAAACT
1 ATATA--TATAAACT
1183279 ATAT
1 ATAT
1183283 TATTTTCGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 17 0.61
15 11 0.39
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.38
Consensus pattern (13 bp):
ATATATATAAACT
Found at i:1183815 original size:15 final size:15
Alignment explanation
Indices: 1183797--1183841 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
1183787 TTAATCATGT
*
1183797 TTTATATAATTTATA
1 TTTAAATAATTTATA
1183812 TTTAAATAATTT-TA
1 TTTAAATAATTTATA
1183826 -TTAAATAATTTTATA
1 TTTAAATAA-TTTATA
1183841 T
1 T
1183842 AATATGTATG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 8 0.31
14 5 0.19
15 13 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTAAATAATTTATA
Found at i:1183845 original size:13 final size:13
Alignment explanation
Indices: 1183802--1183839 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
1183792 CATGTTTTAT
1183802 ATAATTTATATTTAA
1 ATAATTT-TA-TTAA
1183817 ATAATTTTATTAA
1 ATAATTTTATTAA
1183830 ATAATTTTAT
1 ATAATTTTAT
1183840 ATAATATGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 14 0.61
14 2 0.09
15 7 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATAATTTTATTAA
Found at i:1183923 original size:2 final size:2
Alignment explanation
Indices: 1183863--1183914 Score: 61
Period size: 2 Copynumber: 26.0 Consensus size: 2
1183853 ATAAACCATG
*
1183863 TA TA -A TA TA TA TA AA CTA 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
**
1183905 CC TA TA TA TA
1 TA TA TA TA TA
1183915 AACTATATAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
1 1 0.02
2 40 0.95
3 1 0.02
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:1184055 original size:28 final size:28
Alignment explanation
Indices: 1183998--1184068 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 28
1183988 TAAATTATAG
* ***
1183998 AAACCCTAAACTCT-AATCATAAAGTTT
1 AAACCCTAAACTTTAAATCATAAACCCT
*
1184025 AAACCTTAAACTTTAAATCATAAACCCT
1 AAACCCTAAACTTTAAATCATAAACCCT
*
1184053 AAACCCTAAACCTTAA
1 AAACCCTAAACTTTAA
1184069 TATAAATGAA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
27 12 0.33
28 24 0.67
ACGTcount: A:0.46, C:0.25, G:0.01, T:0.27
Consensus pattern (28 bp):
AAACCCTAAACTTTAAATCATAAACCCT
Found at i:1184480 original size:16 final size:16
Alignment explanation
Indices: 1184461--1184509 Score: 91
Period size: 16 Copynumber: 3.1 Consensus size: 16
1184451 AAATATCAGA
1184461 TCAGGTTGAAAACAGG
1 TCAGGTTGAAAACAGG
1184477 TCAGGTTGAAAACAGG
1 TCAGGTTGAAAACAGG
1184493 TC-GGTTGAAAACAGG
1 TCAGGTTGAAAACAGG
1184508 TC
1 TC
1184510 GGGTAATACC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
15 15 0.45
16 18 0.55
ACGTcount: A:0.35, C:0.14, G:0.31, T:0.20
Consensus pattern (16 bp):
TCAGGTTGAAAACAGG
Found at i:1184500 original size:15 final size:15
Alignment explanation
Indices: 1184464--1184511 Score: 87
Period size: 15 Copynumber: 3.1 Consensus size: 15
1184454 TATCAGATCA
1184464 GGTTGAAAACAGGTC
1 GGTTGAAAACAGGTC
1184479 AGGTTGAAAACAGGTC
1 -GGTTGAAAACAGGTC
1184495 GGTTGAAAACAGGTC
1 GGTTGAAAACAGGTC
1184510 GG
1 GG
1184512 GTAATACCAG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
15 17 0.53
16 15 0.47
ACGTcount: A:0.33, C:0.12, G:0.35, T:0.19
Consensus pattern (15 bp):
GGTTGAAAACAGGTC
Found at i:1192372 original size:179 final size:179
Alignment explanation
Indices: 1192072--1192430 Score: 718
Period size: 179 Copynumber: 2.0 Consensus size: 179
1192062 CTTAGAACTG
1192072 AGAGTCATACTGTTAAAATCCATTAAAACTGGACTGTATTTCTTCATCCAGTCAACTCCCAAGAC
1 AGAGTCATACTGTTAAAATCCATTAAAACTGGACTGTATTTCTTCATCCAGTCAACTCCCAAGAC
1192137 CATATCACTACCTCCAAGGTTTAACACCCTGAAATCATGAATAAAAATGAAGTCTTGCATTTCCC
66 CATATCACTACCTCCAAGGTTTAACACCCTGAAATCATGAATAAAAATGAAGTCTTGCATTTCCC
1192202 AACTCAATTGTTTACTCTTTGCTGTACTATAAAGCTTATCACCATTAGC
131 AACTCAATTGTTTACTCTTTGCTGTACTATAAAGCTTATCACCATTAGC
1192251 AGAGTCATACTGTTAAAATCCATTAAAACTGGACTGTATTTCTTCATCCAGTCAACTCCCAAGAC
1 AGAGTCATACTGTTAAAATCCATTAAAACTGGACTGTATTTCTTCATCCAGTCAACTCCCAAGAC
1192316 CATATCACTACCTCCAAGGTTTAACACCCTGAAATCATGAATAAAAATGAAGTCTTGCATTTCCC
66 CATATCACTACCTCCAAGGTTTAACACCCTGAAATCATGAATAAAAATGAAGTCTTGCATTTCCC
1192381 AACTCAATTGTTTACTCTTTGCTGTACTATAAAGCTTATCACCATTAGC
131 AACTCAATTGTTTACTCTTTGCTGTACTATAAAGCTTATCACCATTAGC
1192430 A
1 A
1192431 ACTGTAATGA
Statistics
Matches: 180, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
179 180 1.00
ACGTcount: A:0.33, C:0.25, G:0.11, T:0.31
Consensus pattern (179 bp):
AGAGTCATACTGTTAAAATCCATTAAAACTGGACTGTATTTCTTCATCCAGTCAACTCCCAAGAC
CATATCACTACCTCCAAGGTTTAACACCCTGAAATCATGAATAAAAATGAAGTCTTGCATTTCCC
AACTCAATTGTTTACTCTTTGCTGTACTATAAAGCTTATCACCATTAGC
Found at i:1202537 original size:162 final size:162
Alignment explanation
Indices: 1202270--1202594 Score: 650
Period size: 162 Copynumber: 2.0 Consensus size: 162
1202260 GGCTGACTTC
1202270 AGATTTCTTTCTGATTAGATACACCCAGGTATGTCTGCTGAACACATCAATAAATGATACATAAT
1 AGATTTCTTTCTGATTAGATACACCCAGGTATGTCTGCTGAACACATCAATAAATGATACATAAT
1202335 ATACGTAACCTTCAGTCGAAACTACAGGAGCAGGTCCCCACACATCTGACACAACCAGCTGAAAA
66 ATACGTAACCTTCAGTCGAAACTACAGGAGCAGGTCCCCACACATCTGACACAACCAGCTGAAAA
1202400 ATTTCTTTGTATTCAGTCAACGAATTACAAAA
131 ATTTCTTTGTATTCAGTCAACGAATTACAAAA
1202432 AGATTTCTTTCTGATTAGATACACCCAGGTATGTCTGCTGAACACATCAATAAATGATACATAAT
1 AGATTTCTTTCTGATTAGATACACCCAGGTATGTCTGCTGAACACATCAATAAATGATACATAAT
1202497 ATACGTAACCTTCAGTCGAAACTACAGGAGCAGGTCCCCACACATCTGACACAACCAGCTGAAAA
66 ATACGTAACCTTCAGTCGAAACTACAGGAGCAGGTCCCCACACATCTGACACAACCAGCTGAAAA
1202562 ATTTCTTTGTATTCAGTCAACGAATTACAAAA
131 ATTTCTTTGTATTCAGTCAACGAATTACAAAA
1202594 A
1 A
1202595 AGGTAGCTTG
Statistics
Matches: 163, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
162 163 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (162 bp):
AGATTTCTTTCTGATTAGATACACCCAGGTATGTCTGCTGAACACATCAATAAATGATACATAAT
ATACGTAACCTTCAGTCGAAACTACAGGAGCAGGTCCCCACACATCTGACACAACCAGCTGAAAA
ATTTCTTTGTATTCAGTCAACGAATTACAAAA
Found at i:1224785 original size:28 final size:28
Alignment explanation
Indices: 1224753--1224808 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
1224743 TCATCATGAC
* *
1224753 TTATT-TTATTAATATTTATGTATGATTA
1 TTATTCTTATT-ATATTAATATATGATTA
*
1224781 TTATTCTTATTTTATTAATATATGATTA
1 TTATTCTTATTATATTAATATATGATTA
1224809 AAATAATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 19 0.79
29 5 0.21
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (28 bp):
TTATTCTTATTATATTAATATATGATTA
Found at i:1228008 original size:31 final size:32
Alignment explanation
Indices: 1227948--1228008 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
1227938 TAATAAATTA
* * **
1227948 TAAAATTTTGATAAATTTCATTATTATTTTTT
1 TAAAATTTTGATAAATTTAATGACCATTTTTT
1227980 TAAAA-TTTGATAAATTTAATGACCATTTT
1 TAAAATTTTGATAAATTTAATGACCATTTT
1228009 GTAATTTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 20 0.80
32 5 0.20
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (32 bp):
TAAAATTTTGATAAATTTAATGACCATTTTTT
Found at i:1229624 original size:10 final size:10
Alignment explanation
Indices: 1229605--1229733 Score: 81
Period size: 10 Copynumber: 13.0 Consensus size: 10
1229595 CATATATACT
*
1229605 TAATATTTAA
1 TAATAATTAA
1229615 TAATAATTAA
1 TAATAATTAA
*
1229625 CAATAA-TAA
1 TAATAATTAA
1229634 TAATTAA-TAA
1 TAA-TAATTAA
* *
1229644 TAACAATAAA
1 TAATAATTAA
*
1229654 T-ATAAATAA
1 TAATAATTAA
*
1229663 TAGTAATTAA
1 TAATAATTAA
*
1229673 TAATCA-TAA
1 TAATAATTAA
1229682 TAATTAATACTAA
1 TAA-TAAT--TAA
*
1229695 TAACAATTAA
1 TAATAATTAA
* *
1229705 TATTGATTAA
1 TAATAATTAA
1229715 TAAT-ATTATA
1 TAATAATTA-A
1229725 TAA-AATTAA
1 TAATAATTAA
1229734 CTTTTGGACA
Statistics
Matches: 92, Mismatches: 18, Indels: 19
0.71 0.14 0.15
Matches are distributed among these distances:
9 24 0.26
10 59 0.64
12 3 0.03
13 6 0.07
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (10 bp):
TAATAATTAA
Found at i:1229633 original size:16 final size:16
Alignment explanation
Indices: 1229612--1229706 Score: 111
Period size: 16 Copynumber: 5.9 Consensus size: 16
1229602 ACTTAATATT
*
1229612 TAATAATAATTAACAA
1 TAATAATAATTAATAA
1229628 TAATAATAATTAATAA
1 TAATAATAATTAATAA
* *
1229644 TAACAATAAAT-ATAAA
1 TAATAATAATTAAT-AA
*
1229660 TAATAGTAATTAATAA
1 TAATAATAATTAATAA
* *
1229676 TCATAATAATTAATAC
1 TAATAATAATTAATAA
*
1229692 TAATAACAATTAATA
1 TAATAATAATTAATA
1229707 TTGATTAATA
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
15 2 0.03
16 62 0.94
17 2 0.03
ACGTcount: A:0.60, C:0.05, G:0.01, T:0.34
Consensus pattern (16 bp):
TAATAATAATTAATAA
Found at i:1229642 original size:13 final size:12
Alignment explanation
Indices: 1229612--1229697 Score: 66
Period size: 13 Copynumber: 6.8 Consensus size: 12
1229602 ACTTAATATT
1229612 TAATAATAATTAA
1 TAATAATAA-TAA
*
1229625 CAATAATAATAA
1 TAATAATAATAA
*
1229637 TTAATAATAACAA
1 -TAATAATAATAA
1229650 TAA-ATATAAATAA
1 TAATA-AT-AATAA
*
1229663 TAGTAATTAATAA
1 TAATAA-TAATAA
*
1229676 TCATAATAATTAA
1 TAATAATAA-TAA
*
1229689 TACTAATAA
1 TAATAATAA
1229698 CAATTAATAT
Statistics
Matches: 58, Mismatches: 9, Indels: 12
0.73 0.11 0.15
Matches are distributed among these distances:
11 1 0.02
12 11 0.19
13 44 0.76
14 2 0.03
ACGTcount: A:0.60, C:0.05, G:0.01, T:0.34
Consensus pattern (12 bp):
TAATAATAATAA
Found at i:1231652 original size:134 final size:134
Alignment explanation
Indices: 1231412--1231679 Score: 520
Period size: 134 Copynumber: 2.0 Consensus size: 134
1231402 TGAAAAGTCC
1231412 AAGGACTAATTTTGGGAATTATGTATAGGAACTATTAGCAAGGATTGAAGAGTGGAAGGGAATTA
1 AAGGACTAATTTTGGGAATTATGTATAGGAACTATTAGCAAGGATTGAAGAGTGGAAGGGAATTA
1231477 TGGTATTTTTGTAGGAAATGAATTTAAAATTTATTTCCAAGGATATTTAAGCATGTGTGG-CTTG
66 TGGTATTTTTGTAGGAAATGAATTTAAAATTTATTTCCAAGGATATTTAAGCATGTG-GGACTTG
1231541 AAAAA
130 AAAAA
1231546 AAGGACTAATTTTGGGAATTATGTATAGGAACTATTAGCAAGGATTGAAGAGTGGAAGGGAATTA
1 AAGGACTAATTTTGGGAATTATGTATAGGAACTATTAGCAAGGATTGAAGAGTGGAAGGGAATTA
1231611 TGGTATTTTTGTAGGAAATGAATTTAAAATTTATTTCCAAGGATATTTAAGCATGTGGGACTTGA
66 TGGTATTTTTGTAGGAAATGAATTTAAAATTTATTTCCAAGGATATTTAAGCATGTGGGACTTGA
1231676 AAAA
131 AAAA
1231680 TGGGGAAAAG
Statistics
Matches: 133, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
133 2 0.02
134 131 0.98
ACGTcount: A:0.37, C:0.05, G:0.25, T:0.33
Consensus pattern (134 bp):
AAGGACTAATTTTGGGAATTATGTATAGGAACTATTAGCAAGGATTGAAGAGTGGAAGGGAATTA
TGGTATTTTTGTAGGAAATGAATTTAAAATTTATTTCCAAGGATATTTAAGCATGTGGGACTTGA
AAAA
Found at i:1235607 original size:20 final size:21
Alignment explanation
Indices: 1235555--1235615 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
1235545 TTCCCCTGTG
1235555 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
*
1235578 GGGGGAATCGGTTCCCTC-AT
1 GGGGGAATCGGTTCCCTCAAA
* *
1235598 GGGGGTATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
1235616 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 17 0.49
21 2 0.06
22 3 0.09
23 13 0.37
ACGTcount: A:0.16, C:0.26, G:0.33, T:0.25
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:1246508 original size:23 final size:23
Alignment explanation
Indices: 1246479--1246606 Score: 136
Period size: 23 Copynumber: 5.7 Consensus size: 23
1246469 TCGAGGGTTA
* * *
1246479 TATGTGGTCCTTCGAGATAAACC
1 TATGTGGTCATTCGGGACAAACC
* *
1246502 TTTGTGGTCCTTCGGGACAAACC
1 TATGTGGTCATTCGGGACAAACC
* *
1246525 TTTGTGGTCATTCGGGACAAATC
1 TATGTGGTCATTCGGGACAAACC
* *
1246548 TATGTGGTCATTCGTGACAAAAC
1 TATGTGGTCATTCGGGACAAACC
*
1246571 TATGTGGTCATTTGGGACAAA--
1 TATGTGGTCATTCGGGACAAACC
1246592 TATGTGG-CACTTCGG
1 TATGTGGTCA-TTCGG
1246607 TGCAAATTAT
Statistics
Matches: 93, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
20 2 0.02
21 11 0.12
23 80 0.86
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (23 bp):
TATGTGGTCATTCGGGACAAACC
Found at i:1247939 original size:104 final size:104
Alignment explanation
Indices: 1247805--1248013 Score: 418
Period size: 104 Copynumber: 2.0 Consensus size: 104
1247795 TTTCCTTCAT
1247805 TAAGTCATTATTCAAATTTAATGCATTATATGAAATGATTCTTTCTGGTGTTCCATATCTACAAA
1 TAAGTCATTATTCAAATTTAATGCATTATATGAAATGATTCTTTCTGGTGTTCCATATCTACAAA
1247870 TGATTTCCCTTTTTAGGAATCTGCAAACTGCTCCTTTCG
66 TGATTTCCCTTTTTAGGAATCTGCAAACTGCTCCTTTCG
1247909 TAAGTCATTATTCAAATTTAATGCATTATATGAAATGATTCTTTCTGGTGTTCCATATCTACAAA
1 TAAGTCATTATTCAAATTTAATGCATTATATGAAATGATTCTTTCTGGTGTTCCATATCTACAAA
1247974 TGATTTCCCTTTTTAGGAATCTGCAAACTGCTCCTTTCG
66 TGATTTCCCTTTTTAGGAATCTGCAAACTGCTCCTTTCG
1248013 T
1 T
1248014 GACATTGGCG
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
104 105 1.00
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.42
Consensus pattern (104 bp):
TAAGTCATTATTCAAATTTAATGCATTATATGAAATGATTCTTTCTGGTGTTCCATATCTACAAA
TGATTTCCCTTTTTAGGAATCTGCAAACTGCTCCTTTCG
Found at i:1252611 original size:404 final size:404
Alignment explanation
Indices: 1251862--1252667 Score: 1171
Period size: 404 Copynumber: 2.0 Consensus size: 404
1251852 CGATCCATTG
* *
1251862 CAGTGGGTAGTAATAAACAAAGCCTTGCATCTACCCTTACCTTCATAAGGTATCTCATCATCATA
1 CAGTGGGTAGTAATAAACAAAGCATTGCATCTACCATTACCTTCATAAGGTATCTCATCATCATA
** *
1251927 GAAATAAATGAAGTTATCTACATTAATGTGATTTACCATCCTATCCACATGCTCCATCGGTATAT
66 GAAATAAATGAAGTTATCTACATTAATGTGATTTACCATCCTATCCACACACTCCACCGGTATAT
* * * ** * *
1251992 CCTTTCCCACAGAAGTTTCATTTAAAACCTTTATTAGTGTATTTTGATGTACCTCATAATGTAAG
131 CATTTCCCACAAAAGTTTCATTCAAAACCTTTATTAGTGTATTTCAATGTACCTCAGAATGTAAC
* * ** ***
1252057 AGAAGAGATAACATTGAAATCCGTTCTGGAGTTTTATGGAGTTGCTCTACAATGTTGTACTTGTT
196 AGAAGAGATAACATTGAAATCCATGCCAGAGTTTTATGGAGTTGCTCTACAATGTTGTACTCACT
* * *
1252122 GTGTTTTAAAAACTTCTAAAATTCCTGAGCTTCCTCAATCTTGACGGGTTCATTCACTCTGTCCT
261 GTGTTTTAAAAACTTCAAAAATTCCTGAGCTTCATCAATCTTGACGGGTTCATTCACTCTATCCT
* * * **
1252187 CAAGCTCATCGATTACCACAACTTTTACTTTTTCAAATCTGTCAGGGGTGTAACATCTCCCACTC
326 CAAGCTCATCAATTACCACAACTCTTACTTTTTCAAATCTGCCAGGGACGTAACATCTCCCACTC
*
1252252 CTAGTGAAACCTTA
391 ATAGTGAAACCTTA
** * * * * * **
1252266 CAGTGGGTAGTAATGTACAAAGCATTGCATCTACCATTACTTTCCTTAGTTATTTTGTCATCATA
1 CAGTGGGTAGTAATAAACAAAGCATTGCATCTACCATTACCTTCATAAGGTATCTCATCATCATA
* * * *
1252331 TAAATAAATGATGTTATCTGCATTAGTGTGATTTACCATCCTATCCACACACTCCACCGGTATAT
66 GAAATAAATGAAGTTATCTACATTAATGTGATTTACCATCCTATCCACACACTCCACCGGTATAT
* *
1252396 CATTTCCCACAAAAGTTTCATTCAGAACCTTTATTAGTGTATTTCAATGTACCTTAGAATGTAAC
131 CATTTCCCACAAAAGTTTCATTCAAAACCTTTATTAGTGTATTTCAATGTACCTCAGAATGTAAC
1252461 AGAAGAGATAACATTGAAATCCATGCCAGAGTTTTATGGAGTTGCTCTACAATGTTGTACTCACT
196 AGAAGAGATAACATTGAAATCCATGCCAGAGTTTTATGGAGTTGCTCTACAATGTTGTACTCACT
*
1252526 GTGTTTTAAAAACTTCAAAAATTCCTGAGCTTCATCAATCTTGACGGGTTTATTCACTCTATCCT
261 GTGTTTTAAAAACTTCAAAAATTCCTGAGCTTCATCAATCTTGACGGGTTCATTCACTCTATCCT
* ** *
1252591 CAAGCTCATCAATTACCACAACTCTTGCTTTTTCAGTTCTGCCAGGGACGTACCATCTCCCACTC
326 CAAGCTCATCAATTACCACAACTCTTACTTTTTCAAATCTGCCAGGGACGTAACATCTCCCACTC
*
1252656 ATGGTGAAACCT
391 ATAGTGAAACCT
1252668 CCAAATTTAT
Statistics
Matches: 353, Mismatches: 49, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
404 353 1.00
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (404 bp):
CAGTGGGTAGTAATAAACAAAGCATTGCATCTACCATTACCTTCATAAGGTATCTCATCATCATA
GAAATAAATGAAGTTATCTACATTAATGTGATTTACCATCCTATCCACACACTCCACCGGTATAT
CATTTCCCACAAAAGTTTCATTCAAAACCTTTATTAGTGTATTTCAATGTACCTCAGAATGTAAC
AGAAGAGATAACATTGAAATCCATGCCAGAGTTTTATGGAGTTGCTCTACAATGTTGTACTCACT
GTGTTTTAAAAACTTCAAAAATTCCTGAGCTTCATCAATCTTGACGGGTTCATTCACTCTATCCT
CAAGCTCATCAATTACCACAACTCTTACTTTTTCAAATCTGCCAGGGACGTAACATCTCCCACTC
ATAGTGAAACCTTA
Found at i:1255912 original size:64 final size:65
Alignment explanation
Indices: 1255810--1255938 Score: 251
Period size: 64 Copynumber: 2.0 Consensus size: 65
1255800 GTTTCAGGCC
1255810 ATTCTTTTTATAAGATACTCTACAATAAGAGAATAATCCTTCAGAAAGTGATTGTAATTGACTTT
1 ATTCTTTTTATAAGATACTCTACAATAAGAGAATAATCCTTCAGAAAGTGATTGTAATTGACTTT
1255875 ATTC-TTTTATAAGATACTCTACAATAAGAGAATAATCCTTCAGAAAGTGATTGTAATTGACTTT
1 ATTCTTTTTATAAGATACTCTACAATAAGAGAATAATCCTTCAGAAAGTGATTGTAATTGACTTT
1255939 TTATTCTCTC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
64 60 0.94
65 4 0.06
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.38
Consensus pattern (65 bp):
ATTCTTTTTATAAGATACTCTACAATAAGAGAATAATCCTTCAGAAAGTGATTGTAATTGACTTT
Found at i:1256016 original size:44 final size:44
Alignment explanation
Indices: 1255966--1256057 Score: 157
Period size: 44 Copynumber: 2.1 Consensus size: 44
1255956 GACTTATAAT
* *
1255966 CCAAATAGTGAGCAATTGAGAGCAACCTATAAAGCGTCCTCCTC
1 CCAAATAGGGAGCAATTGAGAGCAACCCATAAAGCGTCCTCCTC
*
1256010 CCAAATAGGGAGCAATTGAGCGCAACCCATAAAGCGTCCTCCTC
1 CCAAATAGGGAGCAATTGAGAGCAACCCATAAAGCGTCCTCCTC
1256054 CCAA
1 CCAA
1256058 CCTCCTACAG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.34, C:0.30, G:0.18, T:0.17
Consensus pattern (44 bp):
CCAAATAGGGAGCAATTGAGAGCAACCCATAAAGCGTCCTCCTC
Found at i:1260270 original size:13 final size:13
Alignment explanation
Indices: 1260254--1260283 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1260244 CTTAATATTT
1260254 AATAATAATTAAC
1 AATAATAATTAAC
*
1260267 AATAATAATTAAT
1 AATAATAATTAAC
1260280 AATA
1 AATA
1260284 GCAATAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (13 bp):
AATAATAATTAAC
Found at i:1260319 original size:19 final size:19
Alignment explanation
Indices: 1260253--1260321 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
1260243 ACTTAATATT
*
1260253 TAATAATAATTAACAAT-AA
1 TAATAATAA-TAGCAATAAA
1260272 TAATTAATAATAGCAATAAA
1 TAA-TAATAATAGCAATAAA
* * *
1260292 TATTAATAATAGTAATTAA
1 TAATAATAATAGCAATAAA
*
1260311 TAATCATAATA
1 TAATAATAATA
1260322 ATTAATACTA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
19 32 0.76
20 10 0.24
ACGTcount: A:0.58, C:0.04, G:0.03, T:0.35
Consensus pattern (19 bp):
TAATAATAATAGCAATAAA
Found at i:1260335 original size:16 final size:16
Alignment explanation
Indices: 1260253--1260335 Score: 78
Period size: 16 Copynumber: 5.2 Consensus size: 16
1260243 ACTTAATATT
*
1260253 TAATAA-TAATTAACAA
1 TAATAATTAA-TAATAA
*
1260269 TAATAATTAATAATAG
1 TAATAATTAATAATAA
* * *
1260285 CAATAAATATTAATAA
1 TAATAATTAATAATAA
* *
1260301 TAGTAATTAATAATCA
1 TAATAATTAATAATAA
*
1260317 TAATAATTAATACTAA
1 TAATAATTAATAATAA
1260333 TAA
1 TAA
1260336 CAATAAATAT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
16 49 0.94
17 3 0.06
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (16 bp):
TAATAATTAATAATAA
Found at i:1262497 original size:19 final size:19
Alignment explanation
Indices: 1262440--1262499 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
1262430 TATTTTTTTT
*
1262440 ATTTTTTTTA-TTTCATAAA
1 ATTTTTTTTATTTTTA-AAA
* * *
1262459 ATTTTTATT-TGTTT-ATA
1 ATTTTTTTTATTTTTAAAA
1262476 ATTTTTTTTATTTTTAAAA
1 ATTTTTTTTATTTTTAAAA
1262495 ATTTT
1 ATTTT
1262500 AGAAGGCGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
17 10 0.32
18 4 0.13
19 17 0.55
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (19 bp):
ATTTTTTTTATTTTTAAAA
Found at i:1263507 original size:77 final size:76
Alignment explanation
Indices: 1263365--1263517 Score: 297
Period size: 77 Copynumber: 2.0 Consensus size: 76
1263355 GTCATAATTG
1263365 ACAAGACGACGACAACGACAGTGACGATCAAAGGTACGAACCCGATGTACTTGACGAGCTCCGTG
1 ACAAGACGACGACAACGACAGTGACGATCAAAGGTACGAACCCGATGTACTTGACGAGCTCCGTG
1263430 ACATTATCATT
66 ACATTATCATT
1263441 ACAAGACGACGACAACGACAGTGACGATCAAAGTGTACGAACCCGATGTACTTGACGAGCTCCGT
1 ACAAGACGACGACAACGACAGTGACGATCAAAG-GTACGAACCCGATGTACTTGACGAGCTCCGT
1263506 GACATTATCATT
65 GACATTATCATT
1263518 CGACCACTCC
Statistics
Matches: 76, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
76 33 0.43
77 43 0.57
ACGTcount: A:0.34, C:0.25, G:0.22, T:0.19
Consensus pattern (76 bp):
ACAAGACGACGACAACGACAGTGACGATCAAAGGTACGAACCCGATGTACTTGACGAGCTCCGTG
ACATTATCATT
Found at i:1266341 original size:31 final size:31
Alignment explanation
Indices: 1266306--1266375 Score: 131
Period size: 31 Copynumber: 2.3 Consensus size: 31
1266296 AAAAAATAAT
1266306 ATATGGTCATTTTCGTTTATATTTAATTAAG
1 ATATGGTCATTTTCGTTTATATTTAATTAAG
*
1266337 ATATGATCATTTTCGTTTATATTTAATTAAG
1 ATATGGTCATTTTCGTTTATATTTAATTAAG
1266368 ATATGGTC
1 ATATGGTC
1266376 TCCACGAGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.30, C:0.07, G:0.13, T:0.50
Consensus pattern (31 bp):
ATATGGTCATTTTCGTTTATATTTAATTAAG
Found at i:1266547 original size:16 final size:16
Alignment explanation
Indices: 1266526--1266556 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1266516 TCGAATAATA
*
1266526 CCACGTGTCATTGGTG
1 CCACGTGTCACTGGTG
1266542 CCACGTGTCACTGGT
1 CCACGTGTCACTGGT
1266557 ACCATATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.29, G:0.29, T:0.29
Consensus pattern (16 bp):
CCACGTGTCACTGGTG
Found at i:1267446 original size:31 final size:31
Alignment explanation
Indices: 1267411--1267488 Score: 138
Period size: 31 Copynumber: 2.5 Consensus size: 31
1267401 TTAAATAACA
*
1267411 TAAGTTTTGGTCACTTACATTATTGTTTTAT
1 TAAGTTTTGGTCACTTACATTATCGTTTTAT
*
1267442 TAAGTTTTGGTCACTTACGTTATCGTTTTAT
1 TAAGTTTTGGTCACTTACATTATCGTTTTAT
1267473 TAAGTTTTGGTCACTT
1 TAAGTTTTGGTCACTT
1267489 GGACGTTGAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.21, C:0.12, G:0.15, T:0.53
Consensus pattern (31 bp):
TAAGTTTTGGTCACTTACATTATCGTTTTAT
Found at i:1268886 original size:31 final size:31
Alignment explanation
Indices: 1268851--1268929 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
1268841 AATTAACGTC
*
1268851 TAAGTGACCAAAACTTAATAAAACGATAACA
1 TAAGTGACCAAAACTTAATAAAACAATAACA
* * *
1268882 TAAGTGACAAAAAGTTAATAAAACAATAACG
1 TAAGTGACCAAAACTTAATAAAACAATAACA
*
1268913 TAAGTAACCAAAACTTA
1 TAAGTGACCAAAACTTA
1268930 TGTTTTTTTA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.56, C:0.14, G:0.10, T:0.20
Consensus pattern (31 bp):
TAAGTGACCAAAACTTAATAAAACAATAACA
Found at i:1270810 original size:13 final size:13
Alignment explanation
Indices: 1270792--1270821 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1270782 CACTTGAAAA
1270792 GTTAATATCAGTT
1 GTTAATATCAGTT
1270805 GTTAATATCAGTT
1 GTTAATATCAGTT
1270818 GTTA
1 GTTA
1270822 GAGAGATATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.47
Consensus pattern (13 bp):
GTTAATATCAGTT
Found at i:1272487 original size:96 final size:95
Alignment explanation
Indices: 1272380--1272566 Score: 302
Period size: 96 Copynumber: 2.0 Consensus size: 95
1272370 ATATCGGGTA
* ** *
1272380 ACATCGAATCTAATTTTGGTATCGATACCATATAGGGATATCGGTACCATAGTATAATAGTATCG
1 ACATCAAATCTAATTTTGGTATCGATACCATATAGGGATATCAATACCATAATATAATAGTATCG
1272445 ATACCATGGAAGGGGGTATCGATACTGGGCC
66 ATACCATGGAA-GGGGTATCGATACTGGGCC
* *
1272476 ACATCAAATCTAATTTTGGTATCGATACCATATAGGGGTATCAATACCATAATATAGTAGTATCG
1 ACATCAAATCTAATTTTGGTATCGATACCATATAGGGATATCAATACCATAATATAATAGTATCG
*
1272541 ATACCATGGTAGGGGTATCGATACTG
66 ATACCATGGAAGGGGTATCGATACTG
1272567 AAGGGCCAAA
Statistics
Matches: 84, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
95 15 0.18
96 69 0.82
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (95 bp):
ACATCAAATCTAATTTTGGTATCGATACCATATAGGGATATCAATACCATAATATAATAGTATCG
ATACCATGGAAGGGGTATCGATACTGGGCC
Found at i:1272517 original size:19 final size:19
Alignment explanation
Indices: 1272493--1272564 Score: 72
Period size: 22 Copynumber: 3.6 Consensus size: 19
1272483 ATCTAATTTT
1272493 GGTATCGATACCATATAGG
1 GGTATCGATACCATATAGG
* *
1272512 GGTATCAATACCATAATATAGT
1 GGTATCGATACC---ATATAGG
* *
1272534 AGTATCGATACCATGGTAGG
1 GGTATCGATACCAT-ATAGG
1272554 GGTATCGATAC
1 GGTATCGATAC
1272565 TGAAGGGCCA
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
19 13 0.31
20 13 0.31
22 16 0.38
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (19 bp):
GGTATCGATACCATATAGG
Found at i:1273148 original size:79 final size:79
Alignment explanation
Indices: 1272963--1273140 Score: 257
Period size: 79 Copynumber: 2.3 Consensus size: 79
1272953 AAAACAAATG
* * *
1272963 AAAAAAATAATGCATATGGGTGTATTATTGGCATGAAAGGATGTCATAGCTAAAATGTATATGGG
1 AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTAAAATGTATATGGG
*
1273028 TACATTGTTAGCAT
66 TACATTGTCAGCAT
* ** * *
1273042 AAAATAATAATGCATATCAGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATTGG
1 AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTAAAATGTATATGGG
*
1273107 TGCATTGTCAGCAT
66 TACATTGTCAGCAT
*
1273121 CAAAGAATAATGCATATGGG
1 AAAAGAATAATGCATATGGG
1273141 ACCATTATCA
Statistics
Matches: 86, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
79 86 1.00
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30
Consensus pattern (79 bp):
AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTAAAATGTATATGGG
TACATTGTCAGCAT
Found at i:1276725 original size:25 final size:27
Alignment explanation
Indices: 1276697--1276756 Score: 70
Period size: 31 Copynumber: 2.1 Consensus size: 27
1276687 ATTTCACAAA
1276697 ATATAA-T-ATATGGTCATTTTCGTTT
1 ATATAATTAATATGGTCATTTTCGTTT
1276722 ATATTTAATTAAGATATGGTCATTTTCGTTT
1 ATA--TAATT-A-ATATGGTCATTTTCGTTT
1276753 ATAT
1 ATAT
1276757 TTAATTAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
25 3 0.10
27 3 0.10
28 1 0.03
29 1 0.03
31 21 0.72
ACGTcount: A:0.30, C:0.07, G:0.12, T:0.52
Consensus pattern (27 bp):
ATATAATTAATATGGTCATTTTCGTTT
Found at i:1276739 original size:31 final size:31
Alignment explanation
Indices: 1276704--1276769 Score: 132
Period size: 31 Copynumber: 2.1 Consensus size: 31
1276694 AAAATATAAT
1276704 ATATGGTCATTTTCGTTTATATTTAATTAAG
1 ATATGGTCATTTTCGTTTATATTTAATTAAG
1276735 ATATGGTCATTTTCGTTTATATTTAATTAAG
1 ATATGGTCATTTTCGTTTATATTTAATTAAG
1276766 ATAT
1 ATAT
1276770 AGTCTCCACG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.30, C:0.06, G:0.12, T:0.52
Consensus pattern (31 bp):
ATATGGTCATTTTCGTTTATATTTAATTAAG
Found at i:1276948 original size:16 final size:16
Alignment explanation
Indices: 1276924--1276958 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1276914 TCGAATAATA
*
1276924 CCACATGTCATTGGTG
1 CCACATGTCACTGGTG
*
1276940 CCACGTGTCACTGGTG
1 CCACATGTCACTGGTG
1276956 CCA
1 CCA
1276959 TATATTACCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.17, C:0.31, G:0.26, T:0.26
Consensus pattern (16 bp):
CCACATGTCACTGGTG
Found at i:1277837 original size:31 final size:31
Alignment explanation
Indices: 1277802--1277879 Score: 129
Period size: 31 Copynumber: 2.5 Consensus size: 31
1277792 TTAAATAACA
*
1277802 TAAGTTTTGGTCACTTACATTATTGTTTTAT
1 TAAGTTTTGGTCACTTACATTATCGTTTTAT
* *
1277833 TAAGTTGTGGTCACTTACGTTATCGTTTTAT
1 TAAGTTTTGGTCACTTACATTATCGTTTTAT
1277864 TAAGTTTTGGTCACTT
1 TAAGTTTTGGTCACTT
1277880 GGACGTTGAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.21, C:0.12, G:0.17, T:0.51
Consensus pattern (31 bp):
TAAGTTTTGGTCACTTACATTATCGTTTTAT
Found at i:1283587 original size:24 final size:24
Alignment explanation
Indices: 1283555--1283624 Score: 71
Period size: 24 Copynumber: 3.2 Consensus size: 24
1283545 TATGGTAATG
1283555 GTATCGGTACTACTATACATAGTA
1 GTATCGGTACTACTATACATAGTA
* **
1283579 GTATTGGTACCCCT-T---T-G-A
1 GTATCGGTACTACTATACATAGTA
1283597 GTATCGGTACTACTATACATAGTA
1 GTATCGGTACTACTATACATAGTA
1283621 GTAT
1 GTAT
1283625 TGATGCCCCT
Statistics
Matches: 34, Mismatches: 6, Indels: 12
0.65 0.12 0.23
Matches are distributed among these distances:
18 12 0.35
19 2 0.06
20 1 0.03
22 1 0.03
23 2 0.06
24 16 0.47
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (24 bp):
GTATCGGTACTACTATACATAGTA
Found at i:1283614 original size:42 final size:42
Alignment explanation
Indices: 1283555--1283648 Score: 170
Period size: 42 Copynumber: 2.2 Consensus size: 42
1283545 TATGGTAATG
*
1283555 GTATCGGTACTACTATACATAGTAGTATTGGTACCCCTTTGA
1 GTATCGGTACTACTATACATAGTAGTATTGATACCCCTTTGA
*
1283597 GTATCGGTACTACTATACATAGTAGTATTGATGCCCCTTTGA
1 GTATCGGTACTACTATACATAGTAGTATTGATACCCCTTTGA
1283639 GTATCGGTAC
1 GTATCGGTAC
1283649 CATTTTTGCA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (42 bp):
GTATCGGTACTACTATACATAGTAGTATTGATACCCCTTTGA
Found at i:1285157 original size:16 final size:16
Alignment explanation
Indices: 1285136--1285170 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1285126 TCGAATAATA
*
1285136 CCACGTGTCATTGGTG
1 CCACGTGTCACTGGTG
1285152 CCACGTGTCACTGGTG
1 CCACGTGTCACTGGTG
1285168 CCA
1 CCA
1285171 TATATTTCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.14, C:0.31, G:0.29, T:0.26
Consensus pattern (16 bp):
CCACGTGTCACTGGTG
Found at i:1286059 original size:31 final size:31
Alignment explanation
Indices: 1286023--1286100 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
1286013 TTAAATAACA
*
1286023 TAAGTTTTAGTCACTTAAATTAT-AGTTTTAT
1 TAAGTTTTGGTCACTTAAATTATCA-TTTTAT
**
1286054 TAAGTTTTGGTCACTTACGTTATCATTTTAT
1 TAAGTTTTGGTCACTTAAATTATCATTTTAT
1286085 TAAGTTTTGGTCACTT
1 TAAGTTTTGGTCACTT
1286101 GGACGTTGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
31 42 0.98
32 1 0.02
ACGTcount: A:0.26, C:0.10, G:0.13, T:0.51
Consensus pattern (31 bp):
TAAGTTTTGGTCACTTAAATTATCATTTTAT
Found at i:1287375 original size:31 final size:31
Alignment explanation
Indices: 1287340--1287418 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
1287330 AATTAATGTC
**
1287340 TAAGTGACCAAAACTTAATAAAATGATAACA
1 TAAGTGACCAAAACTTAATAAAACAATAACA
* * *
1287371 TAAGTGACAAAAAGTTAATAAAACAATAACG
1 TAAGTGACCAAAACTTAATAAAACAATAACA
*
1287402 TAAGTAACCAAAACTTA
1 TAAGTGACCAAAACTTA
1287419 TGTTTTTTGA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.56, C:0.13, G:0.10, T:0.22
Consensus pattern (31 bp):
TAAGTGACCAAAACTTAATAAAACAATAACA
Found at i:1291132 original size:96 final size:96
Alignment explanation
Indices: 1290984--1291159 Score: 262
Period size: 96 Copynumber: 1.8 Consensus size: 96
1290974 ATATCAGGTA
* * * *
1290984 ACATCGAATCTAATTTTGGTATTGATACCATATAGGGATATCGGTACCATAGTATAATAATATTG
1 ACATCAAATCTAATTTTGGTATCGATACCATATAGGGATATCAGTACCATAGTATAATAATATCG
1291049 ATACCATGGAAGGGGGTATTTATACTGGGCC
66 ATACCATGGAAGGGGGTATTTATACTGGGCC
* * * * *
1291080 ACATCAAATCTAATTTTTGTATCGATACCATATAGGGGTATCAGTACTATAGTATAGTAGTATCG
1 ACATCAAATCTAATTTTGGTATCGATACCATATAGGGATATCAGTACCATAGTATAATAATATCG
*
1291145 ATACCATGGTAGGGG
66 ATACCATGGAAGGGG
1291160 TATCGATACT
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
96 70 1.00
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (96 bp):
ACATCAAATCTAATTTTGGTATCGATACCATATAGGGATATCAGTACCATAGTATAATAATATCG
ATACCATGGAAGGGGGTATTTATACTGGGCC
Found at i:1291752 original size:79 final size:79
Alignment explanation
Indices: 1291568--1291753 Score: 302
Period size: 79 Copynumber: 2.4 Consensus size: 79
1291558 AAACAAATGA
1291568 AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATTCCATAGCTAAAATGTATATGGG
1 AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATTCCATAGCTAAAATGTATATGGG
1291633 TACATTGTCAGCAT
66 TACATTGTCAGCAT
* ** *
1291647 AAAATAATAATGCATATCAGTGCATTATTGGCATGAAAGG-TTGCCATAGCTGAAATGTATATGG
1 AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATT-CCATAGCTAAAATGTATATGG
1291711 GTACATTGTCAGCAT
65 GTACATTGTCAGCAT
* *
1291726 CAAAGAATAATGCATATGGGTCCATTAT
1 AAAAGAATAATGCATATGGGTGCATTAT
1291754 CAGCATAAGA
Statistics
Matches: 97, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
78 2 0.02
79 95 0.98
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.30
Consensus pattern (79 bp):
AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATTCCATAGCTAAAATGTATATGGG
TACATTGTCAGCAT
Found at i:1291757 original size:34 final size:32
Alignment explanation
Indices: 1291700--1291766 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 32
1291690 CCATAGCTGA
* *
1291700 AATGTATATGGGTACATTGTCAGCATCAAAGAAT
1 AATGCATATGGGTACATTATCAGCAT--AAGAAT
*
1291734 AATGCATATGGGTCCATTATCAGCATAAGAAT
1 AATGCATATGGGTACATTATCAGCATAAGAAT
1291766 A
1 A
1291767 TATTTTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 7 0.23
34 23 0.77
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.28
Consensus pattern (32 bp):
AATGCATATGGGTACATTATCAGCATAAGAAT
Found at i:1294099 original size:42 final size:43
Alignment explanation
Indices: 1294006--1294100 Score: 165
Period size: 43 Copynumber: 2.2 Consensus size: 43
1293996 TATGGAAATG
*
1294006 GTATCGGTACTACTATACATAGTAGTATTGGTACCCCCTTTGA
1 GTATCGGTACTACTATACATAGTAGTATTGATACCCCCTTTGA
*
1294049 GTATCGGTACTATTATACATAGTAGTATTGATA-CCCCTTTGA
1 GTATCGGTACTACTATACATAGTAGTATTGATACCCCCTTTGA
1294091 GTATCGGTAC
1 GTATCGGTAC
1294101 CATTTTTGCA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
42 19 0.38
43 31 0.62
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (43 bp):
GTATCGGTACTACTATACATAGTAGTATTGATACCCCCTTTGA
Found at i:1295441 original size:31 final size:31
Alignment explanation
Indices: 1295398--1295467 Score: 113
Period size: 31 Copynumber: 2.3 Consensus size: 31
1295388 AAAATATAAT
*
1295398 ATATGGTTATTTTCATTTATATTTAATTAAG
1 ATATGGTCATTTTCATTTATATTTAATTAAG
**
1295429 ATATGGTCATTTTTGTTTATATTTAATTAAG
1 ATATGGTCATTTTCATTTATATTTAATTAAG
1295460 ATATGGTC
1 ATATGGTC
1295468 TCCACTAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.30, C:0.04, G:0.13, T:0.53
Consensus pattern (31 bp):
ATATGGTCATTTTCATTTATATTTAATTAAG
Found at i:1295640 original size:16 final size:16
Alignment explanation
Indices: 1295619--1295649 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1295609 CGAATAATAC
1295619 CACGTGTCACTGGTGT
1 CACGTGTCACTGGTGT
1295635 CACGTGTCACTGGTG
1 CACGTGTCACTGGTG
1295650 CCATATATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.13, C:0.26, G:0.32, T:0.29
Consensus pattern (16 bp):
CACGTGTCACTGGTGT
Found at i:1296539 original size:31 final size:31
Alignment explanation
Indices: 1296504--1296581 Score: 138
Period size: 31 Copynumber: 2.5 Consensus size: 31
1296494 TTAAATAACA
*
1296504 TAAGTTTTGGTCACTTACATTATTGTTTTAT
1 TAAGTTTTGGTCACTTACATTATCGTTTTAT
*
1296535 TAAGTTTTGGTCACTTACGTTATCGTTTTAT
1 TAAGTTTTGGTCACTTACATTATCGTTTTAT
1296566 TAAGTTTTGGTCACTT
1 TAAGTTTTGGTCACTT
1296582 GGACGTTGAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.21, C:0.12, G:0.15, T:0.53
Consensus pattern (31 bp):
TAAGTTTTGGTCACTTACATTATCGTTTTAT
Found at i:1297976 original size:31 final size:31
Alignment explanation
Indices: 1297941--1298019 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
1297931 AATTAACGTC
*
1297941 TAAGTGACCAAAACTTAATAAAACGATAACA
1 TAAGTGACCAAAACTTAATAAAACAATAACA
* * *
1297972 TAAGTGACAAAAAGTTAATAAAACAATAACG
1 TAAGTGACCAAAACTTAATAAAACAATAACA
*
1298003 TAAGTAACCAAAACTTA
1 TAAGTGACCAAAACTTA
1298020 TGTTTTTTGA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.56, C:0.14, G:0.10, T:0.20
Consensus pattern (31 bp):
TAAGTGACCAAAACTTAATAAAACAATAACA
Found at i:1302256 original size:79 final size:79
Alignment explanation
Indices: 1302072--1302257 Score: 309
Period size: 79 Copynumber: 2.4 Consensus size: 79
1302062 AAAACAAATG
*
1302072 AAAAAAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTAAAATGTATATGGG
1 AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTAAAATGTATATGGG
1302137 TACATTGTCAGCAT
66 TACATTGTCAGCAT
* ** *
1302151 AAAATAATAATGCATATCAGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGGG
1 AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTAAAATGTATATGGG
1302216 TACATTGTCAGCAT
66 TACATTGTCAGCAT
* *
1302230 CAAAGAATAATGCATATGGGTCCATTAT
1 AAAAGAATAATGCATATGGGTGCATTAT
1302258 CAGCATAAGA
Statistics
Matches: 98, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
79 98 1.00
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (79 bp):
AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTAAAATGTATATGGG
TACATTGTCAGCAT
Found at i:1302261 original size:34 final size:32
Alignment explanation
Indices: 1302204--1302270 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 32
1302194 CCATAGCTGA
* *
1302204 AATGTATATGGGTACATTGTCAGCATCAAAGAAT
1 AATGCATATGGGTACATTATCAGCAT--AAGAAT
*
1302238 AATGCATATGGGTCCATTATCAGCATAAGAAT
1 AATGCATATGGGTACATTATCAGCATAAGAAT
1302270 A
1 A
1302271 TATTTTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 7 0.23
34 23 0.77
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.28
Consensus pattern (32 bp):
AATGCATATGGGTACATTATCAGCATAAGAAT
Found at i:1304540 original size:24 final size:23
Alignment explanation
Indices: 1304508--1304583 Score: 63
Period size: 24 Copynumber: 3.4 Consensus size: 23
1304498 TATGGTAATG
1304508 GTATCGGTACTACTATACATAGTA
1 GTATCGGTACTACTATACATAG-A
* **
1304532 GTATTGGTACCCCT-T---T-GA
1 GTATCGGTACTACTATACATAGA
1304550 GTATCGGTACTACTATACATAGCA
1 GTATCGGTACTACTATACATAG-A
*
1304574 GTATTGGTAC
1 GTATCGGTAC
1304584 CCCTTTTAGT
Statistics
Matches: 39, Mismatches: 7, Indels: 12
0.67 0.12 0.21
Matches are distributed among these distances:
18 12 0.31
19 2 0.05
20 1 0.03
22 1 0.03
23 2 0.05
24 21 0.54
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (23 bp):
GTATCGGTACTACTATACATAGA
Found at i:1304555 original size:42 final size:42
Alignment explanation
Indices: 1304508--1304601 Score: 170
Period size: 42 Copynumber: 2.2 Consensus size: 42
1304498 TATGGTAATG
*
1304508 GTATCGGTACTACTATACATAGTAGTATTGGTACCCCTTTGA
1 GTATCGGTACTACTATACATAGCAGTATTGGTACCCCTTTGA
*
1304550 GTATCGGTACTACTATACATAGCAGTATTGGTACCCCTTTTA
1 GTATCGGTACTACTATACATAGCAGTATTGGTACCCCTTTGA
1304592 GTATCGGTAC
1 GTATCGGTAC
1304602 CATTTTTGCA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (42 bp):
GTATCGGTACTACTATACATAGCAGTATTGGTACCCCTTTGA
Found at i:1309656 original size:14 final size:14
Alignment explanation
Indices: 1309626--1309669 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
1309616 AAGTTAACTC
1309626 TATATTAAAATAAAAA
1 TATATTAAAAT--AAA
1309642 TATATTAAAATAAA
1 TATATTAAAATAAA
* *
1309656 TAAATAAAAATAAA
1 TATATTAAAATAAA
1309670 GTTAGTCCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 15 0.58
16 11 0.42
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
TATATTAAAATAAA
Found at i:1310045 original size:26 final size:26
Alignment explanation
Indices: 1310016--1310066 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
1310006 AAAGTATAAT
*
1310016 ATTTGATCATTTTTATGTTGTTTTAG
1 ATTTGATCATTTTCATGTTGTTTTAG
* *
1310042 ATTTGGTCATTTTCATTTTGTTTTA
1 ATTTGATCATTTTCATGTTGTTTTA
1310067 ATTAAGATGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.18, C:0.06, G:0.14, T:0.63
Consensus pattern (26 bp):
ATTTGATCATTTTCATGTTGTTTTAG
Found at i:1315693 original size:31 final size:30
Alignment explanation
Indices: 1315658--1315736 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 30
1315648 ATTCAACATC
*
1315658 TAAGTGATCAAAACTTAATAAAACGATAACA
1 TAAGTGA-CAAAACTTAATAAAACAATAACA
* *
1315689 TAAGTGACAAAAATTTAATAAAACAATAACG
1 TAAGTGAC-AAAACTTAATAAAACAATAACA
*
1315720 TAAGTAACCAAAACTTA
1 TAAGTGA-CAAAACTTA
1315737 TGTTTTTTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
30 1 0.02
31 39 0.95
32 1 0.02
ACGTcount: A:0.56, C:0.13, G:0.09, T:0.23
Consensus pattern (30 bp):
TAAGTGACAAAACTTAATAAAACAATAACA
Found at i:1322074 original size:76 final size:76
Alignment explanation
Indices: 1321949--1322148 Score: 323
Period size: 76 Copynumber: 2.6 Consensus size: 76
1321939 GTTATGAGAT
* *
1321949 GGGGTATCGGTA-CCTCCTGGGAGGTATCAGTACCCTCCGAGCAATCTGTTATTTCTCGGAGCCA
1 GGGGTATCGGTACCCTCTTGGGGGGTATCAGTACCCTCCGAGCAATCTGTTATTTCTCGGAGCCA
1322013 AA-CTTTACATG
66 AATC-TTACATG
1322024 GGGGTATCGGTACCCTCTTGGGGGGTATCAGTACCCTCCGAGCAATCTGTTATTTCTCGGAGCCA
1 GGGGTATCGGTACCCTCTTGGGGGGTATCAGTACCCTCCGAGCAATCTGTTATTTCTCGGAGCCA
1322089 AATCTTACATG
66 AATCTTACATG
* * * *
1322100 GGGGTATCGGTACCCTCTTGGGGAGTATCGGTACCCTCTGGGCAATCTG
1 GGGGTATCGGTACCCTCTTGGGGGGTATCAGTACCCTCCGAGCAATCTG
1322149 GTTTTTCAGT
Statistics
Matches: 117, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
75 12 0.10
76 104 0.89
77 1 0.01
ACGTcount: A:0.19, C:0.25, G:0.28, T:0.28
Consensus pattern (76 bp):
GGGGTATCGGTACCCTCTTGGGGGGTATCAGTACCCTCCGAGCAATCTGTTATTTCTCGGAGCCA
AATCTTACATG
Found at i:1322141 original size:20 final size:20
Alignment explanation
Indices: 1322098--1322138 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 20
1322088 AAATCTTACA
1322098 TGGGGGTATCGGTACCCTCT
1 TGGGGGTATCGGTACCCTCT
1322118 TGGGGAGTATCGGTACCCTCT
1 TGGGG-GTATCGGTACCCTCT
1322139 GGGCAATCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.12, C:0.24, G:0.34, T:0.29
Consensus pattern (20 bp):
TGGGGGTATCGGTACCCTCT
Found at i:1324886 original size:23 final size:22
Alignment explanation
Indices: 1324837--1324909 Score: 80
Period size: 23 Copynumber: 3.4 Consensus size: 22
1324827 GAACCCGTGA
*
1324837 AGGGTATCAGTA-CC-CTCAAG
1 AGGGTATCGGTACCCACTCAAG
*
1324857 GGGGTATCGGTACCCACTCAAAG
1 AGGGTATCGGTACCCACTC-AAG
1324880 AGGGTATCGGTACCCA-TGCAAG
1 AGGGTATCGGTACCCACT-CAAG
*
1324902 AAGGTATC
1 AGGGTATC
1324910 AATACCTAGT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
20 10 0.22
21 2 0.04
22 14 0.31
23 19 0.42
ACGTcount: A:0.29, C:0.23, G:0.29, T:0.19
Consensus pattern (22 bp):
AGGGTATCGGTACCCACTCAAG
Found at i:1330669 original size:21 final size:21
Alignment explanation
Indices: 1330645--1330684 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1330635 AATCTTATAT
*
1330645 GGGAGTATTGGTACCCTCTTG
1 GGGAGTATCGGTACCCTCTTG
1330666 GGGAGTATCGGTACCCTCT
1 GGGAGTATCGGTACCCTCT
1330685 GGGCAATCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.23, G:0.33, T:0.30
Consensus pattern (21 bp):
GGGAGTATCGGTACCCTCTTG
Found at i:1331199 original size:53 final size:53
Alignment explanation
Indices: 1331118--1331237 Score: 206
Period size: 53 Copynumber: 2.3 Consensus size: 53
1331108 TTTACGGTGT
*
1331118 TACAAGAGA-ATTCAAATAACATGGCATTTCACTTCATTTTCTCTAACACACT
1 TACAAGAGACATTCAAATAACATGGCATTTCACTTCATTTTCTCTAACACACC
* *
1331170 TGCAAGAGACATTCAAATAACTTGGCATTTCACTTCATTTTCTCTAACACACC
1 TACAAGAGACATTCAAATAACATGGCATTTCACTTCATTTTCTCTAACACACC
1331223 TACAAGAGACATTCA
1 TACAAGAGACATTCA
1331238 TTTTGATTTT
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
52 8 0.13
53 55 0.87
ACGTcount: A:0.36, C:0.24, G:0.09, T:0.31
Consensus pattern (53 bp):
TACAAGAGACATTCAAATAACATGGCATTTCACTTCATTTTCTCTAACACACC
Found at i:1340616 original size:125 final size:125
Alignment explanation
Indices: 1340394--1340777 Score: 644
Period size: 125 Copynumber: 3.1 Consensus size: 125
1340384 AATACACACA
* * * *
1340394 TTGGGGCAAGATTGAACCCATATCACGTTGAGATGACAAGATTCAGACCAAGGAGGCATTAAGAA
1 TTGGGGCATGACTGAACCCACATCATGTTGAGATGACAAGATTCAGACCAAGGAGGCATTAAGAA
1340459 TGAGCCTTACAATTTGAGGTGTTGGGGCATTTTGAAGGCCCGTACCAGTATAAGATAATG
66 TGAGCCTTACAATTTGAGGTGTTGGGGCATTTTGAAGGCCCGTACCAGTATAAGATAATG
* *
1340519 TTGGGGCATGACTGAACCCACATCATGTTGAGATGACAAGATTCAGTCCAAGGAGACATTAAGAA
1 TTGGGGCATGACTGAACCCACATCATGTTGAGATGACAAGATTCAGACCAAGGAGGCATTAAGAA
* * *
1340584 TGAGCCTTACAATTTGAGGTGTTTGGGCATTTTGAAGGCTCGTACCAGTTTAAGATAATG
66 TGAGCCTTACAATTTGAGGTGTTGGGGCATTTTGAAGGCCCGTACCAGTATAAGATAATG
*
1340644 TTGGGGCATGACTGAACCCACATCATGTTGAGATGACAAGATTCAGACCAA-GAGGGCATTGAGA
1 TTGGGGCATGACTGAACCCACATCATGTTGAGATGACAAGATTCAGACCAAGGA-GGCATTAAGA
* *
1340708 ATGAGCCTTACGATTTGAGGTGTTGGGGCATTTTGAAGGCCCGTACCAATATAAGATAATG
65 ATGAGCCTTACAATTTGAGGTGTTGGGGCATTTTGAAGGCCCGTACCAGTATAAGATAATG
1340769 TTGGGGCAT
1 TTGGGGCAT
1340778 TAGTGGGCCT
Statistics
Matches: 241, Mismatches: 17, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
124 2 0.01
125 239 0.99
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.26
Consensus pattern (125 bp):
TTGGGGCATGACTGAACCCACATCATGTTGAGATGACAAGATTCAGACCAAGGAGGCATTAAGAA
TGAGCCTTACAATTTGAGGTGTTGGGGCATTTTGAAGGCCCGTACCAGTATAAGATAATG
Found at i:1341755 original size:6 final size:6
Alignment explanation
Indices: 1341744--1341775 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
1341734 TTACATTTAG
1341744 TTGCAT TTGCAT TTGCAT TTGCAT TTGCAT TT
1 TTGCAT TTGCAT TTGCAT TTGCAT TTGCAT TT
1341776 AGACACATGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.53
Consensus pattern (6 bp):
TTGCAT
Found at i:1342366 original size:55 final size:55
Alignment explanation
Indices: 1342282--1343042 Score: 1012
Period size: 55 Copynumber: 13.8 Consensus size: 55
1342272 TGAAGCAAAT
* * * * ** *
1342282 GAAGATTGTTCGAGTTCTATAATCCCTAAATAAAGAGGGATCAAACCCGTAGGCA
1 GAAGATTGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGTA
* * * ** *
1342337 GAAGATCGTTTGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGGAA
1 GAAGATTGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGTA
1342392 GAAGA-TGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGTA
1 GAAGATTGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGTA
*
1342446 GAAGATTGTTCGAGTTCCATACTCCCTAAAAGAAAGAGGGAGCGAACCCGTTTGTA
1 GAAGATTGTTCGAGTTCTATACTCCCT-AAAGAAAGAGGGAGCGAACCCGTTTGTA
** * * ** *
1342502 GAAGATTGTTATAGTTCTATACTCCCTGAAAGAAAAAGGGAGCGAACCCATAGGAA
1 GAAGATTGTTCGAGTTCTATACTCCCT-AAAGAAAGAGGGAGCGAACCCGTTTGTA
** * *
1342558 GAAGA-TGGACGAGTTCTATACTCCCTAAAGAAAGAGAGAGCGAACCCGTTTGCA
1 GAAGATTGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGTA
* * * * ** *
1342612 TAAGAATGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGAGAACGTGTTTGCA
1 GAAGATTGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGTA
* *
1342667 GAAGA-TGTTCGAGTTTTATACTCCCTAAAGAAAGAGGGAGCGAACCCATTTGTA
1 GAAGATTGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGTA
* *
1342721 GAAGATTGATCGAGTTCTATACTCCCTAAAGAAAGAGGGAACGAACCCGTTTGCT-
1 GAAGATTGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTG-TA
*
1342776 GAAGATTGTTCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCCATTTGTA
1 GAAGATTGTTCGAGTTCTATACTCCCT-AAAGAAAGAGGGAGCGAACCCGTTTGTA
* *
1342832 GAAGATTGTTCGAGTTCTATAATCCCTAAAGAAAGAGGGAACGAACCCGTTTGTA
1 GAAGATTGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGTA
* *
1342887 GAAGATTGATCGAGTTCTATACTCCCTAAAGAAATAGGGAGCGAACCCGTTTGTA
1 GAAGATTGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGTA
*
1342942 GAAGATTGTTTGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTTTGTA
1 GAAGATTGTTCGAGTTCTATACTCCCT-AAAGAAAGAGGGAGCGAACCCGTTTGTA
* * * *
1342998 GAGGAATTGTTCGAGTTC--TACTCCCTGAAGCAAGAGGGAGTGAAC
1 GAAG-ATTGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAAC
1343043 ATGTTTTTCA
Statistics
Matches: 625, Mismatches: 72, Indels: 19
0.87 0.10 0.03
Matches are distributed among these distances:
54 137 0.22
55 315 0.50
56 161 0.26
57 12 0.02
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (55 bp):
GAAGATTGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGTA
Found at i:1342563 original size:166 final size:165
Alignment explanation
Indices: 1342282--1343042 Score: 1030
Period size: 166 Copynumber: 4.6 Consensus size: 165
1342272 TGAAGCAAAT
* * * * ** * *
1342282 GAAGATTGTTCGAGTTCTATAATCCCTAAATAAAGAGGGATCAAACCCGTAGGCAGAAGATCGTT
1 GAAGATTGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGTAGAAGATTGTT
* * * *
1342347 TGAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGGAAGAAGA-TGTTCGAGTTCTAT
66 CGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCATAGGAAGAAGATTGATCGAGTTCTAT
1342411 ACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGTA
131 ACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGTA
*
1342446 GAAGATTGTTCGAGTTCCATACTCCCTAAAAGAAAGAGGGAGCGAACCCGTTTGTAGAAGATTGT
1 GAAGATTGTTCGAGTTCTATACTCCCT-AAAGAAAGAGGGAGCGAACCCGTTTGTAGAAGATTGT
** * *
1342511 TATAGTTCTATACTCCCTGAAAGAAAAAGGGAGCGAACCCATAGGAAGAAGATGGA-CGAGTTCT
65 TCGAGTTCTATACTCCCT-AAAGAAAGAGGGAGCGAACCCATAGGAAGAAGATTGATCGAGTTCT
* *
1342575 ATACTCCCTAAAGAAAGAGAGAGCGAACCCGTTTGCA
129 ATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGTA
* * * * ** *
1342612 TAAGAATGTTCGAGTTCCATACTCCCTAAAGAAAGAGGGAGAGAACGTGTTTGCAGAAGA-TGTT
1 GAAGATTGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGTAGAAGATTGTT
* ** *
1342676 CGAGTTTTATACTCCCTAAAGAAAGAGGGAGCGAACCCATTTGTAGAAGATTGATCGAGTTCTAT
66 CGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCATAGGAAGAAGATTGATCGAGTTCTAT
*
1342741 ACTCCCTAAAGAAAGAGGGAACGAACCCGTTTGCT-
131 ACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTG-TA
*
1342776 GAAGATTGTTCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCCATTTGTAGAAGATTGT
1 GAAGATTGTTCGAGTTCTATACTCCCT-AAAGAAAGAGGGAGCGAACCCGTTTGTAGAAGATTGT
* * * ** *
1342841 TCGAGTTCTATAATCCCTAAAGAAAGAGGGAACGAACCCGTTTGTAGAAGATTGATCGAGTTCTA
65 TCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCATAGGAAGAAGATTGATCGAGTTCTA
*
1342906 TACTCCCTAAAGAAATAGGGAGCGAACCCGTTTGTA
130 TACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGTA
* *
1342942 GAAGATTGTTTGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTTTGTAGAGGAATTG
1 GAAGATTGTTCGAGTTCTATACTCCCT-AAAGAAAGAGGGAGCGAACCCGTTTGTAGAAG-ATTG
* * *
1343007 TTCGAGTTC--TACTCCCTGAAGCAAGAGGGAGTGAAC
64 TTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAAC
1343043 ATGTTTTTCA
Statistics
Matches: 531, Mismatches: 57, Indels: 17
0.88 0.09 0.03
Matches are distributed among these distances:
163 32 0.06
164 108 0.20
165 125 0.24
166 252 0.47
167 14 0.03
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (165 bp):
GAAGATTGTTCGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGTAGAAGATTGTT
CGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCATAGGAAGAAGATTGATCGAGTTCTAT
ACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGTA
Found at i:1343352 original size:2 final size:2
Alignment explanation
Indices: 1343345--1343370 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1343335 AGGGTGTTTA
1343345 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
1343371 GTTATGATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1349050 original size:1 final size:1
Alignment explanation
Indices: 1349046--1349070 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1349036 AATGTACCTG
1349046 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
1349071 GCGAAGAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1358778 original size:21 final size:22
Alignment explanation
Indices: 1358754--1358794 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1358744 TGATTTTTGC
1358754 ATATGA-TGTTATCATGAATAT
1 ATATGATTGTTATCATGAATAT
*
1358775 ATATGATTTTTATCATGAAT
1 ATATGATTGTTATCATGAAT
1358795 GTTATTTCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.46
Consensus pattern (22 bp):
ATATGATTGTTATCATGAATAT
Found at i:1363129 original size:34 final size:32
Alignment explanation
Indices: 1363059--1363143 Score: 98
Period size: 34 Copynumber: 2.6 Consensus size: 32
1363049 GTTTTCCGGT
* * *
1363059 TCGGATCAATATCAGATCGGTTGATTTTTAGA
1 TCGGGTCAATACCAGATCGATTGATTTTTAGA
* *
1363091 TCGGGTCAATACCAGATCGATTGATTTTTTTTGG
1 TCGGGTCAATACCAGATCGATTGA--TTTTTAGA
*
1363125 TCGGGTTAATACCAGATCG
1 TCGGGTCAATACCAGATCG
1363144 GTTATATTTC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
32 21 0.47
34 24 0.53
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (32 bp):
TCGGGTCAATACCAGATCGATTGATTTTTAGA
Found at i:1363186 original size:32 final size:32
Alignment explanation
Indices: 1363018--1363187 Score: 128
Period size: 32 Copynumber: 5.2 Consensus size: 32
1363008 GATCGGGTAA
* * **
1363018 ATTTTCGGGTCGGGTGATTATTGGATCGGTTG
1 ATTTTCGGGTCGGGTCAATATCAGATCGGTTG
* *
1363050 -TTTTCCGGTTCGGATCAATATCAGATCGGTTG
1 ATTTT-CGGGTCGGGTCAATATCAGATCGGTTG
** * * *
1363082 ATTTTTAGATCGGGTCAATACCAGATCGATTG
1 ATTTTCGGGTCGGGTCAATATCAGATCGGTTG
** * *
1363114 ATTTTTTTTGGTCGGGTTAATACCAGATCGGTT-
1 A--TTTTCGGGTCGGGTCAATATCAGATCGGTTG
** *
1363147 ATATTTCGGGTCGGGTCAATATTGGATCTGTTG
1 AT-TTTCGGGTCGGGTCAATATCAGATCGGTTG
1363180 ATTTTCGG
1 ATTTTCGG
1363188 TTTAGGTAAA
Statistics
Matches: 109, Mismatches: 23, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
31 5 0.05
32 71 0.65
33 7 0.06
34 26 0.24
ACGTcount: A:0.19, C:0.14, G:0.28, T:0.40
Consensus pattern (32 bp):
ATTTTCGGGTCGGGTCAATATCAGATCGGTTG
Found at i:1363792 original size:17 final size:17
Alignment explanation
Indices: 1363767--1363832 Score: 57
Period size: 17 Copynumber: 3.9 Consensus size: 17
1363757 CTTAAACTTT
* *
1363767 ATATTATTTTGTTATAA
1 ATATAATTTTATTATAA
*
1363784 ATATAATTTTTTTAATAA
1 ATATAATTTTATT-ATAA
1363802 ATTATTAATTTTATT-TAA
1 A-TA-TAATTTTATTATAA
1363820 AT-TAA-TTTATTAT
1 ATATAATTTTATTAT
1363833 TGAAAATAAC
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
14 6 0.14
15 4 0.10
17 12 0.29
18 9 0.21
19 2 0.05
20 9 0.21
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (17 bp):
ATATAATTTTATTATAA
Found at i:1363810 original size:20 final size:19
Alignment explanation
Indices: 1363767--1363819 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 19
1363757 CTTAAACTTT
*
1363767 ATATT-ATTTTGTT-ATAA
1 ATATTAATTTTTTTAATAA
1363784 ATA-TAATTTTTTTAATAA
1 ATATTAATTTTTTTAATAA
1363802 ATTATTAATTTTATTTAA
1 A-TATTAATTTT-TTTAA
1363820 ATTAATTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
16 1 0.03
17 10 0.33
18 5 0.17
19 2 0.07
20 7 0.23
21 5 0.17
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
ATATTAATTTTTTTAATAA
Found at i:1363925 original size:16 final size:16
Alignment explanation
Indices: 1363906--1363941 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
1363896 TCAGGTTAAA
*
1363906 TTCGGTTTGGGTTGCT
1 TTCGGTTTGGGCTGCT
1363922 TTCGGTTTGGGCTGCT
1 TTCGGTTTGGGCTGCT
1363938 TTCG
1 TTCG
1363942 ATTCGAGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.00, C:0.17, G:0.36, T:0.47
Consensus pattern (16 bp):
TTCGGTTTGGGCTGCT
Found at i:1363994 original size:21 final size:22
Alignment explanation
Indices: 1363953--1364000 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
1363943 TTCGAGTTAT
*
1363953 TTTCGGTTTGAGTTAATTTCAA
1 TTTCGATTTGAGTTAATTTCAA
* *
1363975 TTTCGATTTGA-TTGATTTCAG
1 TTTCGATTTGAGTTAATTTCAA
1363996 TTTCG
1 TTTCG
1364001 CTAAATTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.19, C:0.10, G:0.19, T:0.52
Consensus pattern (22 bp):
TTTCGATTTGAGTTAATTTCAA
Found at i:1364683 original size:16 final size:16
Alignment explanation
Indices: 1364659--1364691 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1364649 ATTGAATTCT
1364659 TGTTCTTGACTTGGTG
1 TGTTCTTGACTTGGTG
*
1364675 TGTTGTTGACTTGGTG
1 TGTTCTTGACTTGGTG
1364691 T
1 T
1364692 AACGGGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.09, G:0.33, T:0.52
Consensus pattern (16 bp):
TGTTCTTGACTTGGTG
Found at i:1366750 original size:73 final size:73
Alignment explanation
Indices: 1366673--1366823 Score: 275
Period size: 73 Copynumber: 2.1 Consensus size: 73
1366663 AATTATGAAT
* *
1366673 TTAGGTATAATTTCAAAAACTATTCTATAAATCTTAAGATTTTATAGGACATAAATTGTAATTTA
1 TTAGGTATAATTTCAAAAACTATTCTATAAATCTTAAGATTTTATAAGACATAAATTATAATTTA
1366738 ACCAAATG
66 ACCAAATG
*
1366746 TTAGGTATAATTTCAAAAACTATTCTATAAATCTTAAGATTTTATAAGACATAAGTTATAATTTA
1 TTAGGTATAATTTCAAAAACTATTCTATAAATCTTAAGATTTTATAAGACATAAATTATAATTTA
1366811 ACCAAATG
66 ACCAAATG
1366819 TTAGG
1 TTAGG
1366824 ACATAAACTC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 75 1.00
ACGTcount: A:0.42, C:0.09, G:0.10, T:0.38
Consensus pattern (73 bp):
TTAGGTATAATTTCAAAAACTATTCTATAAATCTTAAGATTTTATAAGACATAAATTATAATTTA
ACCAAATG
Found at i:1369784 original size:355 final size:347
Alignment explanation
Indices: 1369139--1369847 Score: 1030
Period size: 355 Copynumber: 2.0 Consensus size: 347
1369129 GTATTTCACT
*
1369139 CAACGTTCTTCTCCTAGGATTAGTTTTCCACGAAATACACTCAAAATTAACAAAATTAAACAAAA
1 CAACGTTCTTCTCCTAGGATTAGTTTTCCACGAAACACACTCAAAATTAACAAAATTAAACAAAA
*
1369204 AAATTACTATTTTTAGGGGTTTGAGTACTTTTTTAGATTTGAGGGATCTTGAGTATTTGTTCAAA
66 AAATTACTATTTTTAGGGGTTTGAGGACTTTTTTAGATTTGAGGGATCTTGAGTATTTGTTCAAA
1369269 AATACGAACAATGAAAAACATTATTTCAAAAAAAAAACTAATAACATAACTCAAAACTAGCCTCA
131 AATACGAACAATGAAAAACATTATTT--AAAAAAAAACTAATAACATAACTCAAAACTAGCCTCA
*
1369334 TCAGAAGAGATCAAAGTATTATTTTAAATGAAATTTTATCGATTTTGAGTGAGTTTTATAGAAAA
194 TCAGAAGAGATCAAAGTATTATTTTAAATGAAATTTTATCGATTTTGAGTGAGTTTCATAGAAAA
* *
1369399 GCAATCCTAGAAGAAAAAATAAGAGTGATTAATAGTTTAGTACCTATCTTGATGCGAAAGAGAAT
259 ACAATCCTAGAAGAAAAAATAAGAGTGATTAATAGTTTAGTACCTATCTTGATGCGAAAGAGAAC
1369464 CAATGACGGGCAATGATTTGTTAC
324 CAATGACGGGCAATGATTTGTTAC
* * * * * * *
1369488 CAACGTTCTTCTCCTATGATTAGTTTTCTATGAACCACACTCAAAATTGACGAAATTAAA-TAAA
1 CAACGTTCTTCTCCTAGGATTAGTTTTCCACGAAACACACTCAAAATTAACAAAATTAAACAAAA
* * * *
1369552 AAATTATTATTTTTAGGGGTTTGAGGATTTTTTTAGATTTGAGGGATCTTGGGTGTTTGTTCAAA
66 AAATTACTATTTTTAGGGGTTTGAGGACTTTTTTAGATTTGAGGGATCTTGAGTATTTGTTCAAA
* * * * *
1369617 AATTCGAACAATGGAAAGCATTA-TT-AAAAAAAAGTAATAATATAACTCAAAACTAGCCTCATC
131 AATACGAACAATGAAAAACATTATTTAAAAAAAAACTAATAACATAACTCAAAACTAG---C--C
* *
1369680 AAATGGTCATCAGAAGAGATCGAAGTATTATTTTAAATG-AATTTGTATTGATTTTGAGTGAGTT
191 ------TCATCAGAAGAGATCAAAGTATTATTTTAAATGAAATTT-TATCGATTTTGAGTGAGTT
* * *
1369744 TCATAGAAAAACAATCCTATAAGAAGAAATAAGAGTGATTAATAGTTTAGTATCTATCTTGATGC
249 TCATAGAAAAACAATCCTAGAAGAAAAAATAAGAGTGATTAATAGTTTAGTACCTATCTTGATGC
1369809 GAAAGAGAACCAATGACGGGCAATGATTTGTTAC
314 GAAAGAGAACCAATGACGGGCAATGATTTGTTAC
1369843 CAACG
1 CAACG
1369848 ACGATCGAAA
Statistics
Matches: 322, Mismatches: 26, Indels: 18
0.88 0.07 0.05
Matches are distributed among these distances:
344 29 0.09
347 3 0.01
348 83 0.26
349 54 0.17
354 5 0.02
355 148 0.46
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.32
Consensus pattern (347 bp):
CAACGTTCTTCTCCTAGGATTAGTTTTCCACGAAACACACTCAAAATTAACAAAATTAAACAAAA
AAATTACTATTTTTAGGGGTTTGAGGACTTTTTTAGATTTGAGGGATCTTGAGTATTTGTTCAAA
AATACGAACAATGAAAAACATTATTTAAAAAAAAACTAATAACATAACTCAAAACTAGCCTCATC
AGAAGAGATCAAAGTATTATTTTAAATGAAATTTTATCGATTTTGAGTGAGTTTCATAGAAAAAC
AATCCTAGAAGAAAAAATAAGAGTGATTAATAGTTTAGTACCTATCTTGATGCGAAAGAGAACCA
ATGACGGGCAATGATTTGTTAC
Found at i:1370085 original size:31 final size:29
Alignment explanation
Indices: 1370049--1370114 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
1370039 TGACTCGGTG
1370049 TTATAATTGAAGTTAAAA-TAAAAATTTAATA
1 TTATAATTGAA---AAAATTAAAAATTTAATA
*
1370080 TTATAATTGAAAAAATTAAAAATTTATTA
1 TTATAATTGAAAAAATTAAAAATTTAATA
*
1370109 ATATAA
1 TTATAA
1370115 ATAATACGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 4 0.12
29 17 0.53
31 11 0.34
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (29 bp):
TTATAATTGAAAAAATTAAAAATTTAATA
Found at i:1372341 original size:4 final size:4
Alignment explanation
Indices: 1372332--1372367 Score: 63
Period size: 4 Copynumber: 8.8 Consensus size: 4
1372322 AATTGGGCCT
1372332 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTT
1372368 TCTTTTGGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 27 0.87
5 4 0.13
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:1372442 original size:16 final size:15
Alignment explanation
Indices: 1372421--1372472 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
1372411 TTTAACCATG
1372421 TTTATTATTATTATTA
1 TTTATT-TTATTATTA
1372437 TTTATTTTATTTCATTA
1 TTTATTTTA-TT-ATTA
1372454 TTT-TTTTATT-TT-
1 TTTATTTTATTATTA
1372466 TTTATTT
1 TTTATTT
1372473 GTACTCCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
12 3 0.09
13 5 0.15
15 5 0.15
16 13 0.39
17 7 0.21
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTATTTTATTATTA
Found at i:1372462 original size:8 final size:8
Alignment explanation
Indices: 1372434--1372472 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
1372424 ATTATTATTA
1372434 TTATTTATT
1 TTATTT-TT
**
1372443 TTATTTCA
1 TTATTTTT
1372451 TTATTTTT
1 TTATTTTT
1372459 TTATTTTT
1 TTATTTTT
1372467 TTATTT
1 TTATTT
1372473 GTACTCCATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
8 20 0.77
9 6 0.23
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (8 bp):
TTATTTTT
Found at i:1372999 original size:6 final size:6
Alignment explanation
Indices: 1372988--1373028 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
1372978 GAAAATGGTA
1372988 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTT
1373029 ATTCATTTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
AATTTT
Found at i:1373591 original size:16 final size:16
Alignment explanation
Indices: 1373570--1373615 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
1373560 AGGAATAATA
1373570 AGCATGTGGGGTAGAT
1 AGCATGTGGGGTAGAT
*
1373586 AGCATGTGGGGCAGAT
1 AGCATGTGGGGTAGAT
* *
1373602 ATCATATGGGGTAG
1 AGCATGTGGGGTAG
1373616 GATTTTTCAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.26, C:0.09, G:0.41, T:0.24
Consensus pattern (16 bp):
AGCATGTGGGGTAGAT
Found at i:1375673 original size:15 final size:14
Alignment explanation
Indices: 1375637--1375679 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
1375627 ACAAAAAGAG
1375637 AAAAAAGAGAAAAA
1 AAAAAAGAGAAAAA
*
1375651 AAGCAAAGAGAAAATA
1 AA-AAAAGAGAAAA-A
1375667 AAAAAAGA-AAAAA
1 AAAAAAGAGAAAAA
1375680 CAAAGGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
13 1 0.04
14 6 0.24
15 15 0.60
16 3 0.12
ACGTcount: A:0.81, C:0.02, G:0.14, T:0.02
Consensus pattern (14 bp):
AAAAAAGAGAAAAA
Found at i:1375900 original size:69 final size:69
Alignment explanation
Indices: 1375763--1375893 Score: 235
Period size: 69 Copynumber: 1.9 Consensus size: 69
1375753 ATTCAAACTA
*
1375763 TGAGATTGATCAAGCACAATCATTTCCGAATCACTGAACCACTTCACTCGAAGATCATAGAGCAT
1 TGAGATTGATCAAGCACAATCATTTCCGAATCACTGAACCACTCCACTCGAAGATCATAGAGCAT
1375828 CAAG
66 CAAG
* *
1375832 TGAGATTGATCAAGCACAATCATTTCTGAATCACTGAATCACTCCACTCGAAGATCATAGAG
1 TGAGATTGATCAAGCACAATCATTTCCGAATCACTGAACCACTCCACTCGAAGATCATAGAG
1375894 AGTCAAGAGA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 59 1.00
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (69 bp):
TGAGATTGATCAAGCACAATCATTTCCGAATCACTGAACCACTCCACTCGAAGATCATAGAGCAT
CAAG
Found at i:1376826 original size:32 final size:32
Alignment explanation
Indices: 1376789--1376904 Score: 121
Period size: 32 Copynumber: 3.6 Consensus size: 32
1376779 GGAACAATAA
*
1376789 GGGCA-TCTTTGAAGATTCAACGTCAAATGATG
1 GGGCATTCTTTG-AGATTCAACATCAAATGATG
* * *
1376821 GGGCATTTTTTGAGATTTAACATCAAATGTTG
1 GGGCATTCTTTGAGATTCAACATCAAATGATG
* *
1376853 GGGCATTTTTTGAGATTCAACATCGAAT-ATTG
1 GGGCATTCTTTGAGATTCAACATCAAATGA-TG
*
1376885 GGGCA-TCTTTGGGAATTCAA
1 GGGCATTCTTTGAG-ATTCAA
1376905 TATCCTGATG
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
31 6 0.08
32 61 0.85
33 5 0.07
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.34
Consensus pattern (32 bp):
GGGCATTCTTTGAGATTCAACATCAAATGATG
Found at i:1378463 original size:36 final size:36
Alignment explanation
Indices: 1378369--1378837 Score: 580
Period size: 36 Copynumber: 13.2 Consensus size: 36
1378359 AATTTACTCA
** * * * *
1378369 AAACAAATTCCGTCTCCCTTGAGACAATTTCTTCTAG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTC-CCTTG
*
1378406 -AACTAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * *
1378442 AAACAAATTTGGCCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
*
1378478 AAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
*
1378514 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
*
1378550 AAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
*
1378586 AAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1378622 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* ** * *
1378658 AAACAAA------ATCT-TTGA-ATTTGTTTTCCTTA
1 AAACAAATTTTGTCTCTCTTGAGA-CAGTTTCCCTTG
* * **
1378687 AAACTAATTTTGTCTC-CTTGAGATAGTTTCTTTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * * *
1378722 GAACTAAGTTTTGTCTCTCTTGAGAAAGTTTCTCTTG
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
*
1378759 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTGG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1378795 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1378831 AAACAAA
1 AAACAAA
1378838 ATCTTTGAAT
Statistics
Matches: 374, Mismatches: 45, Indels: 27
0.84 0.10 0.06
Matches are distributed among these distances:
28 1 0.00
29 18 0.05
30 3 0.01
35 16 0.04
36 291 0.78
37 45 0.12
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
Found at i:1378777 original size:21 final size:21
Alignment explanation
Indices: 1378752--1378816 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
1378742 TGAGAAAGTT
1378752 TCTCTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
* *
1378773 TCTCTTGAGAC--A-GTT-TC
1 TCTCTTGAAACAAATTTTGTC
*
1378790 -C-CTGGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
1378809 TCTCTTGA
1 TCTCTTGA
1378817 GACAGTTTCC
Statistics
Matches: 32, Mismatches: 6, Indels: 12
0.64 0.12 0.24
Matches are distributed among these distances:
15 6 0.19
16 1 0.03
17 3 0.09
18 4 0.12
19 3 0.09
20 1 0.03
21 14 0.44
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.40
Consensus pattern (21 bp):
TCTCTTGAAACAAATTTTGTC
Found at i:1378792 original size:173 final size:172
Alignment explanation
Indices: 1378413--1378889 Score: 661
Period size: 173 Copynumber: 2.7 Consensus size: 172
1378403 TAGAACTAAG
* * *
1378413 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTGGCCTCTCTTGAGACAGTTTCTCTTG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
** * * *
1378478 AAAC-AAAT-TTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
66 AAACAAAATCTTTG--AAT-TT--G----TTTTCCTTAAAACTAATTTTGTCTC-CTTGAGACAG
*
1378541 TTTCTCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAA
121 TTTCTCTTGAAACAAATTTTATCTCTCTTGAGAAAGTTTCCCTTGAAACAAA
*
1378593 TTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * *
1378658 AAACAAAATCTTTGAATTTGTTTTCCTTAAAACTAATTTTGTCTCCTTGAGATAGTTTCTTTTGG
66 AAACAAAATCTTTGAATTTGTTTTCCTTAAAACTAATTTTGTCTCCTTGAGACAGTTTCTCTTGA
* * *
1378723 AACTAAGTTTTGTCTCTCTTGAGAAAGTTTCTCTTGAAACAAA
131 AAC-AAATTTTATCTCTCTTGAGAAAGTTTCCCTTGAAACAAA
*
1378766 TTTTGTCTCTCTTGAGACAGTTTCCCTGGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* *
1378831 AAACAAAATCTTTGAATATGTTTTTCTTAAAACTAATTTTGTCTCCCTTGAGACAGTTT
66 AAACAAAATCTTTGAATTTGTTTTCCTTAAAACTAATTTTGTCT-CCTTGAGACAGTTT
1378890 TGTCTTTCTT
Statistics
Matches: 272, Mismatches: 21, Indels: 14
0.89 0.07 0.05
Matches are distributed among these distances:
172 20 0.07
173 162 0.60
174 13 0.05
177 1 0.00
179 2 0.01
180 66 0.24
181 4 0.01
182 4 0.01
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (172 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
AAACAAAATCTTTGAATTTGTTTTCCTTAAAACTAATTTTGTCTCCTTGAGACAGTTTCTCTTGA
AACAAATTTTATCTCTCTTGAGAAAGTTTCCCTTGAAACAAA
Found at i:1378900 original size:20 final size:19
Alignment explanation
Indices: 1378866--1378914 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
1378856 CTTAAAACTA
*
1378866 ATTTTGTCTCCCTTGAGAC
1 ATTTTGTCTTCCTTGAGAC
* *
1378885 AGTTTTGTCTTTCTTGTGAC
1 A-TTTTGTCTTCCTTGAGAC
*
1378905 ATTTTCTCTT
1 ATTTTGTCTT
1378915 GAAACACCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.12, C:0.20, G:0.14, T:0.53
Consensus pattern (19 bp):
ATTTTGTCTTCCTTGAGAC
Found at i:1378914 original size:19 final size:20
Alignment explanation
Indices: 1378877--1378914 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
1378867 TTTTGTCTCC
*
1378877 CTTGAGACAGTTTTGTCTTT
1 CTTGAGACAGTTTTCTCTTT
*
1378897 CTTGTGACA-TTTTCTCTT
1 CTTGAGACAGTTTTCTCTT
1378915 GAAACACCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.13, C:0.18, G:0.16, T:0.53
Consensus pattern (20 bp):
CTTGAGACAGTTTTCTCTTT
Found at i:1378916 original size:85 final size:87
Alignment explanation
Indices: 1378802--1378966 Score: 244
Period size: 85 Copynumber: 1.9 Consensus size: 87
1378792 TGGAAACAAA
* *
1378802 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA-AAATCTTTGAATATGTTTTTCTTAAAAC-T
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACACAAATCTTTGAATATGTTTCTCTTAAAACAA
*
1378865 AATTTTGTCTCCCTTGAGACAG
66 AATTTTGCCTCCCTTGAGACAG
* * * * *
1378887 TTTTGTCTTTCTTGTGACATTTTCTCTTGAAACACCAATCTTTGAATATGTTTCTCTTAAAACAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACACAAATCTTTGAATATGTTTCTCTTAAAACAA
1378952 AATTTTGCCTCCCTT
66 AATTTTGCCTCCCTT
1378967 TAGATAATTT
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
85 30 0.43
86 26 0.37
87 14 0.20
ACGTcount: A:0.25, C:0.20, G:0.11, T:0.44
Consensus pattern (87 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACACAAATCTTTGAATATGTTTCTCTTAAAACAA
AATTTTGCCTCCCTTGAGACAG
Found at i:1391643 original size:219 final size:216
Alignment explanation
Indices: 1391085--1391925 Score: 999
Period size: 216 Copynumber: 3.9 Consensus size: 216
1391075 AAACCTTTTC
* * * * * * * *
1391085 TATCTTAGAATCCATATCTGAAGTAGTGCCCTCAATTTTTCCAATTCCCTCTCCACTTTCCTCAG
1 TATCTTAGACTCCATATTTGAAGTGGTACCCTCAATTTTACCAATTCTCTCCCCATTTTCCTCAG
* * ** * *
1391150 CACCACTGCTTTCTTCCTCCTTCAGCTTAACACTG-GAGGGAACTTCGCTTTTGGAACTAGATTC
66 CACTAGTATTTTCTTCCTCCTCCAGCTTAACACTGTG-GGGAACTTCGCTTTTGGAACTAGACTC
* * * * * *
1391214 TGAAGCAGCTAATTCATTTCTAATTTCACTTTCAATAGCACGAGCTTCCAGTGGAGGAGAAGCCG
130 TGAAGAAGCTAATTCAGTTCTAATTTCACTTTCAATAGCAGGAGCTGCCAATGGAGGAGAAGCCT
1391279 GTTCTACATCAGGAACTAAATT
195 GTTCTACATCAGGAACTAAATT
* * * * *
1391301 TATCTTAGGCTCCTTATTTGAGGTGGTGCCCTCAATTTTACCAACTCTCTCCCCATTTTCCTCAG
1 TATCTTAGACTCCATATTTGAAGTGGTACCCTCAATTTTACCAATTCTCTCCCCATTTTCCTCAG
* * * * *
1391366 CACCAGTATTTTCTTCCTCCTCCGGCTTAACATTGTGGGGAACTTTGCTTTTGGAACTAGACTCA
66 CACTAGTATTTTCTTCCTCCTCCAGCTTAACACTGTGGGGAACTTCGCTTTTGGAACTAGACTCT
* * **
1391431 GCAGAAGCTAATTCGGTTCTAGCTTCACTTTCAATAGCAGGAGCTGCCAATGGAGGAGCAA-CCT
131 GAAGAAGCTAATTCAGTTCTAATTTCACTTTCAATAGCAGGAGCTGCCAATGGAGGAG-AAGCCT
*
1391495 GTTCTACATCAGGAACTAAATC
195 GTTCTACATCAGGAACTAAATT
* * * *
1391517 TATCTTAGACCCTTCCGTATTTGAAGTGGTACCCTCAATTTTACCAATTATCTCTCCGTTTTCCT
1 TATCTTAGA--C-TCCATATTTGAAGTGGTACCCTCAATTTTACCAATTCTCTCCCCATTTTCCT
* * * *
1391582 CGGCACTGGT-TTTTCCTTCCTCCTCCAACTTAACACTGTGGGAAACTTCGCTTTTGGAACTAGA
63 CAGCACTAGTATTTT-CTTCCTCCTCCAGCTTAACACTGTGGGGAACTTCGCTTTTGGAACTAGA
* * *
1391646 CTCTGGAGAAGCTAATTCAGTCCTAATTTCACTTTCAATTGCAGGAGCTGCCAATGGAGGAGAAG
127 CTCTGAAGAAGCTAATTCAGTTCTAATTTCACTTTCAATAGCAGGAGCTGCCAATGGAGGAGAAG
* *
1391711 CCTGTCCTACATCAGGGACTAAATT
192 CCTGTTCTACATCAGGAACTAAATT
* * *
1391736 TATCTTAGACTCCATATTTGGAGTGGTACTCTCAGTTTTACCAATTCTCTCCCCATTTTCCTCAG
1 TATCTTAGACTCCATATTTGAAGTGGTACCCTCAATTTTACCAATTCTCTCCCCATTTTCCTCAG
* * *
1391801 CA-TCAGTATTTTCTTCCTCCTCCAGCTTAACACCGTGGGGAGCTTTGCTTTTGGAACTAGACTC
66 CACT-AGTATTTTCTTCCTCCTCCAGCTTAACACTGTGGGGAACTTCGCTTTTGGAACTAGACTC
* * * ** * * * * *
1391865 T-AAGGAATCTAGTTCAGTTATAATTTCTGTTTCAGTAGCAGAAGATTCCAGTGGAGGAGAA
130 TGAA-GAAGCTAATTCAGTTCTAATTTCACTTTCAATAGCAGGAGCTGCCAATGGAGGAGAA
1391926 ACCTTCTTTA
Statistics
Matches: 531, Mismatches: 84, Indels: 20
0.84 0.13 0.03
Matches are distributed among these distances:
215 2 0.00
216 332 0.63
217 8 0.02
218 7 0.01
219 182 0.34
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (216 bp):
TATCTTAGACTCCATATTTGAAGTGGTACCCTCAATTTTACCAATTCTCTCCCCATTTTCCTCAG
CACTAGTATTTTCTTCCTCCTCCAGCTTAACACTGTGGGGAACTTCGCTTTTGGAACTAGACTCT
GAAGAAGCTAATTCAGTTCTAATTTCACTTTCAATAGCAGGAGCTGCCAATGGAGGAGAAGCCTG
TTCTACATCAGGAACTAAATT
Found at i:1395015 original size:18 final size:18
Alignment explanation
Indices: 1394992--1395041 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
1394982 AAAATTCAGA
1394992 GTGCATCGATGCATGGCT
1 GTGCATCGATGCATGGCT
* *
1395010 GTGCATCGGTGCATGGGT
1 GTGCATCGATGCATGGCT
1395028 GTGCATCGATGCAT
1 GTGCATCGATGCAT
1395042 AAAATGCATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.16, C:0.20, G:0.36, T:0.28
Consensus pattern (18 bp):
GTGCATCGATGCATGGCT
Found at i:1396165 original size:18 final size:17
Alignment explanation
Indices: 1396126--1396168 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
1396116 ATAAAATAAA
1396126 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
1396142 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
1396160 TATTATTAT
1 TATTATTAT
1396169 ACATATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:1396178 original size:2 final size:2
Alignment explanation
Indices: 1396166--1396195 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1396156 TTATTATTAT
*
1396166 TA TA CA 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
1396196 ATTATTTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1396498 original size:23 final size:22
Alignment explanation
Indices: 1396441--1396499 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 22
1396431 TATAACTTTA
1396441 TATATATATTATTTTTATTATTAT
1 TATAT-TATT-TTTTTATTATTAT
*
1396465 T-T-TCA-TTTTTTATTCATTAT
1 TATATTATTTTTTTATT-ATTAT
1396485 TATATTATTTTTTTA
1 TATATTATTTTTTTA
1396500 AAACCTTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
19 8 0.28
20 7 0.24
21 2 0.07
22 3 0.10
23 8 0.28
24 1 0.03
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.69
Consensus pattern (22 bp):
TATATTATTTTTTTATTATTAT
Found at i:1396614 original size:41 final size:39
Alignment explanation
Indices: 1396569--1396645 Score: 109
Period size: 41 Copynumber: 1.9 Consensus size: 39
1396559 ATGACCCATT
* *
1396569 TTTTTGTTTTATTTCTAACTAAAGTCTCTCCCACTTTCCTC
1 TTTTTGTCTTATTTCTAACTAAAG-C-CCCCCACTTTCCTC
*
1396610 TTTTTGTCTTATTTCTGACTAAAGCCCCCCACTTTC
1 TTTTTGTCTTATTTCTAACTAAAGCCCCCCACTTTC
1396646 GGTGAAGTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 10 0.30
40 1 0.03
41 22 0.67
ACGTcount: A:0.17, C:0.29, G:0.06, T:0.48
Consensus pattern (39 bp):
TTTTTGTCTTATTTCTAACTAAAGCCCCCCACTTTCCTC
Found at i:1396712 original size:38 final size:40
Alignment explanation
Indices: 1396661--1396739 Score: 110
Period size: 40 Copynumber: 2.0 Consensus size: 40
1396651 AGTGAGAAGG
*
1396661 TAGCTTTTCTATTTT-TAAAT-ATTTGTTGTATATATATA
1 TAGCTTTTCTATTTTATAAATAATTTGATGTATATATATA
*
1396699 TAGCTTATT-TATTTTATTAATAATTTGATGTATATATATA
1 TAGCTT-TTCTATTTTATAAATAATTTGATGTATATATATA
1396739 T
1 T
1396740 TTTTTTTTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
38 12 0.33
39 6 0.17
40 18 0.50
ACGTcount: A:0.32, C:0.04, G:0.08, T:0.57
Consensus pattern (40 bp):
TAGCTTTTCTATTTTATAAATAATTTGATGTATATATATA
Found at i:1396753 original size:40 final size:39
Alignment explanation
Indices: 1396661--1396762 Score: 102
Period size: 40 Copynumber: 2.6 Consensus size: 39
1396651 AGTGAGAAGG
* *
1396661 TAGCTTTTCT-ATTTTTAAATATTTGTTGTATATATATA
1 TAGCTTTTTTCATTTTTAAATATTTGATGTATATATATA
* *
1396699 TAGCTTATTT-ATTTTATTAATAATTTGATGTATATATATA
1 TAGCTTTTTTCATTTT-TAAAT-ATTTGATGTATATATATA
**
1396739 T-TTTTTTTTCATTTTTCAAATATT
1 TAGCTTTTTTCATTTTT-AAATATT
1396763 ACTATATATA
Statistics
Matches: 52, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
38 13 0.25
39 13 0.25
40 26 0.50
ACGTcount: A:0.29, C:0.05, G:0.06, T:0.60
Consensus pattern (39 bp):
TAGCTTTTTTCATTTTTAAATATTTGATGTATATATATA
Found at i:1405866 original size:212 final size:214
Alignment explanation
Indices: 1405079--1406045 Score: 1424
Period size: 216 Copynumber: 4.5 Consensus size: 214
1405069 ATATTGCGCC
* * * *
1405079 ACTCGAGACAAAACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACCATTACCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
* *
1405144 AATTTCAGAGCTAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACT
* * *
1405209 TCACAACGAATGGACGACTGGTTGTCAACAAACCACTTTTTAGTTTCATTCAGAGTCAATTTCAA
131 TCACAACGAAGGGACGACTGGTTGTCAACAAACCACTTTTCAG-TT-ATTCAGAGCCAATTTCAA
*
1405274 CTTCACAGCGTAGGATATTGA
194 CTTCACAGCGAAGGATATTGA
* * * * * *
1405295 ACTCAAGATAACACAAGTTCAACTTCACAATGAAGGGACGGTTGGTTGTCAACAAACCATTACTC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
**
1405360 AATTTCAGAGCCAATTTCAACTTCACAGCGAATTATATTGGACTCAAGACAACACAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACT
* *
1405425 TCACAACGAAGGGACGACTGGTTGTCAATAAACCACTTTTCAGTTTTATTCAGAGTCAATTTCAA
131 TCACAACGAAGGGACGACTGGTTGTCAACAAACCACTTTTCAG--TTATTCAGAGCCAATTTCAA
*
1405490 CTTCACAGCGAAGGATATTGG
194 CTTCACAGCGAAGGATATTGA
*
1405511 ACTTAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAAACAATTTCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-AAACAATTTCC
* * *
1405576 CAGTTTCAGAGCTAATTTCAACTTCACAGCGAATGATATTGGACTCAAGACAACACAAGTTCAAC
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAAC
* *
1405641 TTCACAACGAAGGGACGGCTGGTTGTCAACAAACCACTTTTCAG-T-TTCAGAGCCAATTTCAGC
130 TTCACAACGAAGGGACGACTGGTTGTCAACAAACCACTTTTCAGTTATTCAGAGCCAATTTCAAC
*
1405704 TTCACAGCGAAGGATATTGG
195 TTCACAGCGAAGGATATTGA
* *
1405724 ACTCAAGACAACACAAGTTCAACTTCACAACGAAAGGACGGCTGGTTGTCAGCAAACAATTTCCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
* *
1405789 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACGACACAAGTTCAAAT
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACT
* * * *
1405854 TCACAACGAAGGGACGACTGGTTGTCAACAAA-TAATTTCCCA-AT-TTCAGAGCCAATTTCAAC
131 TCACAACGAAGGGACGACTGGTTGTCAACAAACCACTTT-TCAGTTATTCAGAGCCAATTTCAAC
1405916 TTCACAGCGAAGGATATTGA
195 TTCACAGCGAAGGATATTGA
* * * * *
1405936 ACTCGAGACAACACAAGCTCAACTTCACAACGAAGGGGCGGCTAGCTGTCAACAAACAATTTCCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
* * * *
1406001 AGTTCCGGAGCCAATTTCAACTTCAC-GACGGAGGATATTGGACTC
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGGACTC
1406046 GGAACAATAC
Statistics
Matches: 692, Mismatches: 54, Indels: 14
0.91 0.07 0.02
Matches are distributed among these distances:
211 5 0.01
212 239 0.35
213 86 0.12
214 1 0.00
216 246 0.36
217 115 0.17
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.24
Consensus pattern (214 bp):
ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACT
TCACAACGAAGGGACGACTGGTTGTCAACAAACCACTTTTCAGTTATTCAGAGCCAATTTCAACT
TCACAGCGAAGGATATTGA
Found at i:1406046 original size:106 final size:106
Alignment explanation
Indices: 1405048--1406045 Score: 1322
Period size: 106 Copynumber: 9.3 Consensus size: 106
1405038 GCCATCAGCG
* * * *
1405048 ATTTCAACTCCAC-GACGGAGGATATTGCGCCACTCGAGACAAAACAAGTTCAACTTCACAACGA
1 ATTTCAACTTCACAG-CGAAGGATATTG-G--ACTCAAGACAACACAAGTTCAACTTCACAACGA
* * * *
1405112 AGGGACGGCTGGTTGTCAACAAACCATTACCCAATTTCAGAGCTA
62 AGGGACGGCTGGTTGTCAACAAACAATTTCCCAGTTTCAGAGCCA
* *
1405157 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAATGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGG
* * ** *
1405222 ACGACTGGTTGTCAACAAACCACTTT-TTAGTTTCATTCAGAGTCA
66 ACGGCTGGTTGTCAACAAA-CAATTTCCCAG--T--TTCAGAGCCA
* * * *
1405267 ATTTCAACTTCACAGCGTAGGATATTGAACTCAAGATAACACAAGTTCAACTTCACAATGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGG
* * * * *
1405332 ACGGTTGGTTGTCAACAAACCATTACTCAATTTCAGAGCCA
66 ACGGCTGGTTGTCAACAAACAATTTCCCAGTTTCAGAGCCA
**
1405373 ATTTCAACTTCACAGCGAATTATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGG
* * * * *
1405438 ACGACTGGTTGTCAATAAACCACTTT-TCAGTTTTATTCAGAGTCA
66 ACGGCTGGTTGTCAACAAA-CAATTTCCCAG---T-TTCAGAGCCA
*
1405483 ATTTCAACTTCACAGCGAAGGATATTGGACTTAAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGG
*
1405548 ACGGCTGGTTGTCAACAAAACAATTTCCCAGTTTCAGAGCTA
66 ACGGCTGGTTGTCAAC-AAACAATTTCCCAGTTTCAGAGCCA
*
1405590 ATTTCAACTTCACAGCGAATGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGG
* *
1405655 ACGGCTGGTTGTCAACAAACCACTTT-TCAGTTTCAGAGCCA
66 ACGGCTGGTTGTCAACAAA-CAATTTCCCAGTTTCAGAGCCA
* *
1405696 ATTTCAGCTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAAGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGG
* *
1405761 ACGGCTGGTTGTCAGCAAACAATTTCCCAATTTCAGAGCCA
66 ACGGCTGGTTGTCAACAAACAATTTCCCAGTTTCAGAGCCA
* *
1405802 ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACGACACAAGTTCAAATTCACAACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGG
* * *
1405867 ACGACTGGTTGTCAACAAATAATTTCCCAATTTCAGAGCCA
66 ACGGCTGGTTGTCAACAAACAATTTCCCAGTTTCAGAGCCA
* * *
1405908 ATTTCAACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGCTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGG
* * * * *
1405973 GCGGCTAGCTGTCAACAAACAATTTCCCAGTTCCGGAGCCA
66 ACGGCTGGTTGTCAACAAACAATTTCCCAGTTTCAGAGCCA
*
1406014 ATTTCAACTTCAC-GACGGAGGATATTGGACTC
1 ATTTCAACTTCACAG-CGAAGGATATTGGACTC
1406046 GGAACAATAC
Statistics
Matches: 788, Mismatches: 84, Indels: 37
0.87 0.09 0.04
Matches are distributed among these distances:
105 6 0.01
106 470 0.60
107 98 0.12
108 4 0.01
109 27 0.03
110 177 0.22
111 6 0.01
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.24
Consensus pattern (106 bp):
ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGG
ACGGCTGGTTGTCAACAAACAATTTCCCAGTTTCAGAGCCA
Found at i:1407373 original size:18 final size:17
Alignment explanation
Indices: 1407334--1407376 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
1407324 ATTATATGGA
1407334 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
1407350 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
1407368 TATTATTAT
1 TATTATTAT
1407377 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:1407645 original size:2 final size:2
Alignment explanation
Indices: 1407640--1407664 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1407630 CTTATAACTT
1407640 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 T
1407665 TATTATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1409422 original size:14 final size:15
Alignment explanation
Indices: 1409397--1409431 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
1409387 ATTACATCAT
1409397 ATAATAATATATATG
1 ATAATAATATATATG
1409412 ATAATATATATATAT-
1 ATAATA-ATATATATG
1409427 ATAAT
1 ATAAT
1409432 TTCAAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (15 bp):
ATAATAATATATATG
Done.