Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008702.1 Hibiscus syriacus cultivar Beakdansim tig00111741_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: 3201804
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 14
Found at i:1329339 original size:90 final size:91
Alignment explanation
Indices: 1329208--1329377 Score: 207
Period size: 90 Copynumber: 1.9 Consensus size: 91
1329198 CTCTAACAAC
* * * ** * *
1329208 TTTTCTGTTGATAATACGCCCATATGCATTTCAACTATAGTATATTTTTATGTTGATAATGTACC
1 TTTTCTGTTGATAATACACCCATATACATTTAAACTATAGTATACATTTATATTGATAATGCACC
1329273 CATATACATCTCAACCATAGCATATA
66 CATATACATCTCAACCATAGCATATA
** * * *
1329299 TTTT-TGTTGATAATGTACCCATATACATTTAAACTCTAGTATACATTTCTATTGATGATGCACC
1 TTTTCTGTTGATAATACACCCATATACATTTAAACTATAGTATACATTTATATTGATAATGCACC
* *
1329363 CATATGCATTTCAAC
66 CATATACATCTCAAC
1329378 TCTGGCATTT
Statistics
Matches: 65, Mismatches: 14, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
90 61 0.94
91 4 0.06
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.40
Consensus pattern (91 bp):
TTTTCTGTTGATAATACACCCATATACATTTAAACTATAGTATACATTTATATTGATAATGCACC
CATATACATCTCAACCATAGCATATA
Found at i:1329491 original size:79 final size:79
Alignment explanation
Indices: 1329388--1329585 Score: 310
Period size: 79 Copynumber: 2.5 Consensus size: 79
1329378 TCTGGCATTT
*
1329388 TTTCATGCCAATAATGCACCCATATGCATTATTCTGTTATGCCGATAATGTACCCATATACATAT
1 TTTCATGCCAATAATGCACCCATATGCATTATTCTGTTATGACGATAATGTACCCATATACATAT
1329453 C-GTCTAAGGCATCC
66 CAG-CTAAGGCATCC
* * *
1329467 TTTCATGCCACTAATGAACCCATATGCATTATTATGTTATGACGATAATGTACCCATATACATAT
1 TTTCATGCCAATAATGCACCCATATGCATTATTCTGTTATGACGATAATGTACCCATATACATAT
1329532 CAGCTAAGGCATCC
66 CAGCTAAGGCATCC
* *
1329546 TTTCATGCCATTAATGCACCCATATG-ATTTATTCTTTTAT
1 TTTCATGCCAATAATGCACCCATATGCA-TTATTCTGTTAT
1329586 TCATTAGTTT
Statistics
Matches: 109, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
78 1 0.01
79 107 0.98
80 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (79 bp):
TTTCATGCCAATAATGCACCCATATGCATTATTCTGTTATGACGATAATGTACCCATATACATAT
CAGCTAAGGCATCC
Found at i:1330716 original size:14 final size:13
Alignment explanation
Indices: 1330697--1330735 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
1330687 TATATGGATA
1330697 TTTTATTCATTTAT
1 TTTTATT-ATTTAT
1330711 TTTTATTATTTAT
1 TTTTATTATTTAT
1330724 GTTATTATTATT
1 -TT-TTATTATT
1330736 ATATGTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.26
14 9 0.39
15 8 0.35
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (13 bp):
TTTTATTATTTAT
Found at i:1330734 original size:18 final size:17
Alignment explanation
Indices: 1330695--1330737 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1330685 ATTATATGGA
1330695 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
* *
1330711 TTTTATTATTTATGTTAT
1 TATTATTATTCAT-TTAT
1330729 TATTATTAT
1 TATTATTAT
1330738 ATGTATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 7 0.32
18 12 0.55
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:1330748 original size:2 final size:2
Alignment explanation
Indices: 1330735--1330779 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1330725 TTATTATTAT
*
1330735 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1330777 TA T
1 TA T
1330780 TCTATTATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1330800 original size:13 final size:14
Alignment explanation
Indices: 1330782--1330813 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1330772 ATATATATTC
1330782 TATTATAA-TCTAT
1 TATTATAAGTCTAT
1330795 TATTATAAGTCTAT
1 TATTATAAGTCTAT
1330809 TATTA
1 TATTA
1330814 CTATATATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.53
Consensus pattern (14 bp):
TATTATAAGTCTAT
Found at i:1331170 original size:2 final size:2
Alignment explanation
Indices: 1331163--1331187 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1331153 TACTTTGACG
1331163 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
1331188 TTTTCCTTTT
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:1331263 original size:9 final size:9
Alignment explanation
Indices: 1331242--1331275 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
1331232 TTTTTTTTCC
1331242 TTTATCTTA-
1 TTTAT-TTAT
1331251 TTTATTTAT
1 TTTATTTAT
1331260 TTTATTTAT
1 TTTATTTAT
1331269 TTTATTT
1 TTTATTT
1331276 TTCCCTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 3 0.12
9 21 0.88
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTATTTAT
Found at i:1331264 original size:13 final size:14
Alignment explanation
Indices: 1331242--1331276 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
1331232 TTTTTTTTCC
*
1331242 TTTATCTTATTTA-
1 TTTATTTTATTTAT
1331255 TTTATTTTATTTAT
1 TTTATTTTATTTAT
1331269 TTTATTTT
1 TTTATTTT
1331277 TCCCTTTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTATTTTATTTAT
Found at i:1334325 original size:22 final size:22
Alignment explanation
Indices: 1334302--1334363 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 22
1334292 CAAAAAGGGC
1334302 AAAAAGAAAAAAGAAAAGAAGCA
1 AAAAAGAAAAAA-AAAAGAAGCA
* *
1334325 AAAAAGGAAAAAACAAGAA-CA
1 AAAAAGAAAAAAAAAAGAAGCA
1334346 AAAAAGAAAGAACAAAAA
1 AAAAAGAAA-AA-AAAAA
1334364 TAAAAAAGGG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 10 0.30
22 8 0.24
23 15 0.45
ACGTcount: A:0.79, C:0.06, G:0.15, T:0.00
Consensus pattern (22 bp):
AAAAAGAAAAAAAAAAGAAGCA
Found at i:1334354 original size:20 final size:20
Alignment explanation
Indices: 1334302--1334371 Score: 68
Period size: 20 Copynumber: 3.3 Consensus size: 20
1334292 CAAAAAGGGC
*
1334302 AAAAAGAAAAAAGAAAAGAAGCA
1 AAAAAG-AAAAA-ACAAGAA-CA
1334325 AAAAAGGAAAAAACAAGAACA
1 AAAAA-GAAAAAACAAGAACA
* * *
1334346 AAAAAGAAAGAACAAAAATA
1 AAAAAGAAAAAACAAGAACA
1334366 AAAAAG
1 AAAAAG
1334372 GGAACAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
20 18 0.43
21 7 0.17
22 6 0.14
23 10 0.24
24 1 0.02
ACGTcount: A:0.79, C:0.06, G:0.14, T:0.01
Consensus pattern (20 bp):
AAAAAGAAAAAACAAGAACA
Found at i:1335000 original size:29 final size:29
Alignment explanation
Indices: 1334958--1335020 Score: 126
Period size: 29 Copynumber: 2.2 Consensus size: 29
1334948 CCAGTAGAGA
1334958 AGCATGCAAGCTACCCCATCAATCCTTTG
1 AGCATGCAAGCTACCCCATCAATCCTTTG
1334987 AGCATGCAAGCTACCCCATCAATCCTTTG
1 AGCATGCAAGCTACCCCATCAATCCTTTG
1335016 AGCAT
1 AGCAT
1335021 CAAATGCCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.29, C:0.33, G:0.14, T:0.24
Consensus pattern (29 bp):
AGCATGCAAGCTACCCCATCAATCCTTTG
Found at i:1335478 original size:18 final size:18
Alignment explanation
Indices: 1335455--1335489 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1335445 TCAACATCAA
* *
1335455 ATATTGGGGCATTTTTGT
1 ATATTGAGGCATCTTTGT
1335473 ATATTGAGGCATCTTTG
1 ATATTGAGGCATCTTTG
1335490 GGGATTCAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.09, G:0.26, T:0.46
Consensus pattern (18 bp):
ATATTGAGGCATCTTTGT
Found at i:1335997 original size:36 final size:36
Alignment explanation
Indices: 1335949--1336230 Score: 312
Period size: 36 Copynumber: 8.0 Consensus size: 36
1335939 ACTAGAAGAG
*
1335949 TTTTTTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
*
1335985 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * *
1336021 TTTCGTCTATCTTGAGACAGTTTCCCTTGAAATAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1336057 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * * * *
1336093 ------ATAT-TTGA-ATATGTTTTCTTTGAAACAAA
1 TTTTGTCTCTCTTGAGACA-GTTTCCCTTGAAACAAA
* * ** * *
1336122 TTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAA
*
1336159 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
*
1336194 TTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTT-GTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1336231 ACCTTTGAAT
Statistics
Matches: 205, Mismatches: 29, Indels: 23
0.80 0.11 0.09
Matches are distributed among these distances:
28 2 0.01
29 19 0.09
30 2 0.01
35 6 0.03
36 141 0.69
37 35 0.17
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.41
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:1335999 original size:71 final size:73
Alignment explanation
Indices: 1335907--1336230 Score: 239
Period size: 72 Copynumber: 4.6 Consensus size: 73
1335897 GTTTTTCTTA
* * * * ** *
1335907 AAACAAGA-TTTGTCTCACTTGAGACCGTTTTCACTAG-AA-GAGTTTTTTCTCTCTTGAGACAG
1 AAACAA-ATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAG
1335969 TTTCCCTTG
65 TTTCCCTTG
* *
1335978 AAACAAATTTTGTCTCTCTTGAGACAG-TTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAGT
1336042 TTCCCTTG
66 TTCCCTTG
* * * * *
1336050 AAATAAATTTTGTCTCTCTTGAGACAG-TTTCCCTTGAAACAAA------ATAT-TTGA-ATATG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACA-G
* *
1336106 TTTTCTTTG
65 TTTCCCTTG
* * ** * * * * *
1336115 AAACAAATTTCGTCTCCCTTGAGACAG-TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAAC-AAATTTCGTCTATCTTGAGACAG
*
1336179 TTTCTCTTG
65 TTTCCCTTG
* * *
1336188 AAAC-AATTTTCGTCTATCTTGAGACAG-TTTCCCTTGAAACAAA
1 AAACAAATTTT-GTCTCTCTTGAGACAGTTTTCACTAGAAACAAA
1336231 ACCTTTGAAT
Statistics
Matches: 204, Mismatches: 35, Indels: 27
0.77 0.13 0.10
Matches are distributed among these distances:
64 2 0.01
65 46 0.23
66 5 0.02
70 8 0.04
71 25 0.12
72 77 0.38
73 39 0.19
74 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (73 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTTCACTAGAAACAAATTTCGTCTATCTTGAGACAGT
TTCCCTTG
Found at i:1336144 original size:101 final size:103
Alignment explanation
Indices: 1336005--1336193 Score: 301
Period size: 102 Copynumber: 1.9 Consensus size: 103
1335995 CTTGAGACAG
*
1336005 TTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTT-GAAATAAATTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTCGTCTACCTTGAGACAGTTTCCCTTGGAAATAAATTTTGTCTCTCT
1336069 TGAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
66 TGAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
* ** * *
1336107 TTTCT-TTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTCGTCTACCTTGAGACAGTTTCCCTTGGAAATAAATTTTGTCTCTCT
*
1336171 TGAGACAGTTTCTCTTGAAACAA
66 TGAGACAGTTTCCCTTGAAACAA
1336194 TTTTCGTCTA
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 34 0.43
102 45 0.57
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.41
Consensus pattern (103 bp):
TTTCTCTTGAAACAAATTTCGTCTACCTTGAGACAGTTTCCCTTGGAAATAAATTTTGTCTCTCT
TGAGACAGTTTCCCTTGAAACAAAATATTTGAATATGT
Found at i:1336222 original size:138 final size:137
Alignment explanation
Indices: 1335969--1336293 Score: 438
Period size: 138 Copynumber: 2.4 Consensus size: 137
1335959 CTTGAGACAG
*
1335969 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
* *
1336034 GAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATTT
66 GAGACAGTTTCCCTTGAAATAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAACATTT
*
1336099 GAATATG
131 GAATATA
* * * * * * * *
1336106 TTTTCTTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC-AAATTTCGTCTATCT
* * *
1336171 TGAGACAGTTTCTCTTGAAA-CAATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAACCT
65 TGAGACAGTTTCCCTTGAAATAAATTTT-GTCTATCTTGAGACAGTTTCCCTTGAAACAAAACAT
*
1336235 TTGAATTTA
129 TTGAATATA
* * *
1336244 TTTCCCCT-AAAAATAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACA
1 TTTCCCTTGAAACA-AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1336294 CAAAATCTTC
Statistics
Matches: 161, Mismatches: 24, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
137 54 0.34
138 107 0.66
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (137 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
GAGACAGTTTCCCTTGAAATAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAACATTT
GAATATA
Found at i:1336322 original size:67 final size:68
Alignment explanation
Indices: 1336205--1336361 Score: 203
Period size: 68 Copynumber: 2.4 Consensus size: 68
1336195 TTTCGTCTAT
* **
1336205 CTTGAGACAGTTTCCCTTG-AA-ACAAAACCTTTGAATTTATTTCCCCTAAAA-ATAATTTTGTC
1 CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTGTC
1336267 TCC
66 TCC
* * * *
1336270 CTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCTTAAAACATAATTTTGTT
1 CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTGTC
1336335 TCC
66 TCC
* * *
1336338 CTTGAAACTGTTTCTCATGAAACA
1 CTTGAGACAGTTTCTCTTGAAACA
1336362 ACAGATATCT
Statistics
Matches: 78, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
65 17 0.22
66 2 0.03
67 26 0.33
68 33 0.42
ACGTcount: A:0.32, C:0.22, G:0.09, T:0.37
Consensus pattern (68 bp):
CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTGTC
TCC
Found at i:1337605 original size:205 final size:205
Alignment explanation
Indices: 1336964--1338035 Score: 1601
Period size: 205 Copynumber: 5.2 Consensus size: 205
1336954 GCCATCCGCG
* * * * * *
1336964 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
1337029 GGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
63 GGGACCGCTGCTTGTCAAC-AA-AA-TT-TC-A-TTCAGAGCCAATTTCAACTTCACAACGAAGG
* * *
1337094 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACA
122 ATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAA-CAACA
* * *
1337159 ATTTTCCCAATTTCAGAGCTA
186 ACTTT-CCAATCTCAGAGCCA
* *
1337180 ATTTCAACTTCACAGCGAAGGATATTGTACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
1337245 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
66 ACCGCTGCTTGTCAACAA-AA-TT-TC-AT-TCAGAGCCAATTTCAACTTCACAACGAAGGATAT
1337310 TGGACTCCAGA-AATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTT
126 TGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTT
1337374 CCAATCTCAGAGCCA
191 CCAATCTCAGAGCCA
*
1337389 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
1337454 ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGGAC
66 ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
1337519 TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAAT
131 TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAAT
1337584 CTCAGAGCCA
196 CTCAGAGCCA
1337594 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
1337659 ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
66 ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
* * *
1337724 TCCAGACAATGGAAGTTCAACTTCACGACGAAGGGACCGCTGTTTGTCAACAACAACTTCCCAAT
131 TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAAT
*
1337789 CCCAGAGCCA
196 CTCAGAGCCA
*
1337799 ATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
**
1337864 ACCGCTGCTTGTCAACAAAATTTCATTCAGATTCAATTTCAACTTCACAACGAAGGATATTGGAC
66 ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
* ** * * * *
1337929 TCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAA-TTTCCCG
131 TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTT-CCA
*
1337993 GT-TCCAGAGCCA
194 ATCT-CAGAGCCA
* *
1338005 ATTTCAACTTCACGACGGAGGATATTGGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
1338036 TGGAACAATG
Statistics
Matches: 804, Mismatches: 47, Indels: 20
0.92 0.05 0.02
Matches are distributed among these distances:
204 43 0.05
205 441 0.55
206 45 0.06
207 2 0.00
208 2 0.00
209 92 0.11
210 8 0.01
211 42 0.05
212 57 0.07
213 49 0.06
214 2 0.00
216 21 0.03
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.22
Consensus pattern (205 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAAT
CTCAGAGCCA
Found at i:1337654 original size:105 final size:104
Alignment explanation
Indices: 1336964--1338035 Score: 1544
Period size: 105 Copynumber: 10.3 Consensus size: 104
1336954 GCCATCCGCG
* * * * * *
1336964 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
1337029 GGGACGGCTGGTTGTCAACAAACAAC-TTCTCAATTTCAGAGCCA
63 GGGACCGCTGCTTGTCAAC-AACAACTTTC-CAA-TTCAGAGCCA
1337073 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * *
1337138 ACCGCTGGTTGTCAATAAACAATTTTCCCAATTTCAGAGCTA
66 ACCGCTGCTTGTCAA-CAACAACTTT-CCAA-TTCAGAGCCA
* *
1337180 ATTTCAACTTCACAGCGAAGGATATTGTACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
1337245 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTTCCAAT-TCAGAGCCA
*
1337285 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGA-AATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1337349 ACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTTCCAAT-TCAGAGCCA
*
1337389 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1337454 ACCGCTGCTTGTCAACAA-AA-TTT-C-ATTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTTCCAATTCAGAGCCA
* * *
1337489 ATTTCAACTTCACAGCAAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1337554 ACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTTCCAAT-TCAGAGCCA
1337594 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1337659 ACCGCTGCTTGTCAACAA-AA-TTT-C-ATTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTTCCAATTCAGAGCCA
* * *
1337694 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGGAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * *
1337759 ACCGCTGTTTGTCAACAACAACTTCCCAATCCCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTTCCAAT-TCAGAGCCA
*
1337799 ATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
**
1337864 ACCGCTGCTTGTCAACAA-AA-TTT-C-ATTCAGATTCA
66 ACCGCTGCTTGTCAACAACAACTTTCCAATTCAGAGCCA
* * *
1337899 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * **
1337964 ACGGCTGGTTGTCAACAAACAA-TTTCCCGGTTCCAGAGCCA
66 ACCGCTGCTTGTCAAC-AACAACTTT-CCAATT-CAGAGCCA
* *
1338005 ATTTCAACTTCACGACGGAGGATATTGGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
1338036 TGGAACAATG
Statistics
Matches: 890, Mismatches: 52, Indels: 45
0.90 0.05 0.05
Matches are distributed among these distances:
100 259 0.29
101 12 0.01
102 13 0.01
103 10 0.01
104 113 0.13
105 269 0.30
106 95 0.11
107 96 0.11
108 1 0.00
109 22 0.02
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.22
Consensus pattern (104 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTTCCAATTCAGAGCCA
Found at i:1339053 original size:14 final size:13
Alignment explanation
Indices: 1339034--1339072 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
1339024 TATATGGATA
1339034 TTTTATTCATTTAT
1 TTTTATT-ATTTAT
1339048 TTTTATTATTTAT
1 TTTTATTATTTAT
1339061 GTTATTATTATT
1 -TT-TTATTATT
1339073 ATATGTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.26
14 9 0.39
15 8 0.35
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (13 bp):
TTTTATTATTTAT
Found at i:1339071 original size:18 final size:17
Alignment explanation
Indices: 1339032--1339074 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1339022 ATTATATGGA
1339032 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
* *
1339048 TTTTATTATTTATGTTAT
1 TATTATTATTCAT-TTAT
1339066 TATTATTAT
1 TATTATTAT
1339075 ATGTATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 7 0.32
18 12 0.55
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:1339085 original size:2 final size:2
Alignment explanation
Indices: 1339072--1339106 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1339062 TTATTATTAT
*
1339072 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1339107 TTCTTTAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1339292 original size:2 final size:2
Alignment explanation
Indices: 1339287--1339341 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
1339277 CTTATAACTT
1339287 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1339329 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
1339342 TATTTTTGTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1339647 original size:31 final size:31
Alignment explanation
Indices: 1339599--1339658 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
1339589 CTTTACTATT
* *
1339599 TTTTTTCCTTTATCTTATTT-ATTTATTTTA
1 TTTTTCCCTTTACCTTATTTGATTTATTTTA
*
1339629 TTTTTCCCTTTTACCTTATTTGTTTTATTT
1 TTTTTCCC-TTTACCTTATTTGATTTATTT
1339659 ACCTTGTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 7 0.28
31 11 0.44
32 7 0.28
ACGTcount: A:0.13, C:0.13, G:0.02, T:0.72
Consensus pattern (31 bp):
TTTTTCCCTTTACCTTATTTGATTTATTTTA
Found at i:1344243 original size:45 final size:46
Alignment explanation
Indices: 1344194--1344383 Score: 163
Period size: 45 Copynumber: 4.2 Consensus size: 46
1344184 AATACATCAT
* *
1344194 TATGCATTTTAAACTCTAACAT-CATTTCTGTTGATAATGCACCCA
1 TATGCATTTTAAACTATAACATACTTTTCTGTTGATAATGCACCCA
* * * *
1344239 TATGCA-TTTCAACTATAGCATACTTTTATGTTGATAATGTACCCA
1 TATGCATTTTAAACTATAACATACTTTTCTGTTGATAATGCACCCA
* * * * *** * *
1344284 TATACA-TCTCAACCATTGTATACTTTTTGTGTTGATAATGTACCCA
1 TATGCATTTTAAACTATAACATAC-TTTTCTGTTGATAATGCACCCA
* * ** *
1344330 TATACA-TTTCAACTATAGTATACTTTTCTATTGATAATGCACCCA
1 TATGCATTTTAAACTATAACATACTTTTCTGTTGATAATGCACCCA
1344375 TATGCATTT
1 TATGCATTT
1344384 CAAATCTGGC
Statistics
Matches: 123, Mismatches: 19, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
44 12 0.10
45 68 0.55
46 43 0.35
ACGTcount: A:0.31, C:0.19, G:0.09, T:0.41
Consensus pattern (46 bp):
TATGCATTTTAAACTATAACATACTTTTCTGTTGATAATGCACCCA
Found at i:1344384 original size:45 final size:45
Alignment explanation
Indices: 1344218--1344386 Score: 230
Period size: 45 Copynumber: 3.7 Consensus size: 45
1344208 TCTAACATCA
* *
1344218 TTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGCATACT
1 TTTCTGTTGATAATGCACCCATATACATTTCAACTATAGTATACT
* * * * *
1344263 TTTATGTTGATAATGTACCCATATACATCTCAACCATTGTATACTT
1 TTTCTGTTGATAATGCACCCATATACATTTCAACTATAGTATAC-T
* *
1344309 TTTGTGTTGATAATGTACCCATATACATTTCAACTATAGTATACT
1 TTTCTGTTGATAATGCACCCATATACATTTCAACTATAGTATACT
* *
1344354 TTTCTATTGATAATGCACCCATATGCATTTCAA
1 TTTCTGTTGATAATGCACCCATATACATTTCAA
1344387 ATCTGGCATC
Statistics
Matches: 108, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
45 67 0.62
46 41 0.38
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (45 bp):
TTTCTGTTGATAATGCACCCATATACATTTCAACTATAGTATACT
Found at i:1352461 original size:7 final size:7
Alignment explanation
Indices: 1352449--1352499 Score: 68
Period size: 7 Copynumber: 7.4 Consensus size: 7
1352439 GTCAAAGGAC
1352449 GTCAACG
1 GTCAACG
1352456 GTCAACG
1 GTCAACG
*
1352463 GTC-ACA
1 GTCAACG
*
1352469 GTCAACA
1 GTCAACG
1352476 GTCAACG
1 GTCAACG
1352483 GTCAACG
1 GTCAACG
*
1352490 GTTAACG
1 GTCAACG
1352497 GTC
1 GTC
1352500 GGGTCGGGTC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
6 5 0.13
7 34 0.87
ACGTcount: A:0.29, C:0.27, G:0.25, T:0.18
Consensus pattern (7 bp):
GTCAACG
Found at i:1352474 original size:20 final size:20
Alignment explanation
Indices: 1352449--1352486 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1352439 GTCAAAGGAC
*
1352449 GTCAACGGTCAACGGTCACA
1 GTCAACAGTCAACGGTCACA
1352469 GTCAACAGTCAACGGTCA
1 GTCAACAGTCAACGGTCA
1352487 ACGGTTAACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.29, G:0.24, T:0.16
Consensus pattern (20 bp):
GTCAACAGTCAACGGTCACA
Found at i:1352596 original size:20 final size:20
Alignment explanation
Indices: 1352571--1352619 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1352561 CAGACCGGTC
1352571 AAACCGGTTCGAACCAG-TCA
1 AAACCGGTTCGAACC-GCTCA
1352591 AAACCGGTTCGAACCGCTCA
1 AAACCGGTTCGAACCGCTCA
*
1352611 GAACCGGTT
1 AAACCGGTT
1352620 GAAAACTGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.31, C:0.31, G:0.22, T:0.16
Consensus pattern (20 bp):
AAACCGGTTCGAACCGCTCA
Found at i:1359858 original size:20 final size:20
Alignment explanation
Indices: 1359833--1359878 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
1359823 AGACCGGTTC
*
1359833 GAACCGTTCAAAACTAGTCA
1 GAACCGTTCAAAACCAGTCA
*
1359853 GAACCGGTTGAAAACCAGTCA
1 GAACC-GTTCAAAACCAGTCA
1359874 -AACCG
1 GAACCG
1359879 GTTTCCAGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 1 0.04
20 9 0.39
21 13 0.57
ACGTcount: A:0.39, C:0.26, G:0.20, T:0.15
Consensus pattern (20 bp):
GAACCGTTCAAAACCAGTCA
Found at i:1359879 original size:20 final size:21
Alignment explanation
Indices: 1359833--1359881 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
1359823 AGACCGGTTC
* *
1359833 GAACC-GTTCAAAACTAGTCA
1 GAACCGGTTGAAAACCAGTCA
1359853 GAACCGGTTGAAAACCAGTCA
1 GAACCGGTTGAAAACCAGTCA
1359874 -AACCGGTT
1 GAACCGGTT
1359882 TCCAGCCCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.18
Consensus pattern (21 bp):
GAACCGGTTGAAAACCAGTCA
Found at i:1380119 original size:14 final size:15
Alignment explanation
Indices: 1380083--1380120 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
1380073 TTTATTGGTT
*
1380083 TAATAATACATATAA
1 TAATAATATATATAA
1380098 T-ATAATATAT-TAA
1 TAATAATATATATAA
1380111 TAATAATATA
1 TAATAATATA
1380121 GGTAGAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 4 0.19
14 16 0.76
15 1 0.05
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (15 bp):
TAATAATATATATAA
Found at i:1382578 original size:31 final size:31
Alignment explanation
Indices: 1382543--1382605 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
1382533 TTAACGTTCG
* *
1382543 AGTGACCAATTTATTATAAATTGATAATGTT
1 AGTGACAAATTTATTATAAATTGATAAAGTT
*
1382574 AGTGATAAATTTATTATAAATTGATAAAGTT
1 AGTGACAAATTTATTATAAATTGATAAAGTT
1382605 A
1 A
1382606 ATAAATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.43, C:0.03, G:0.13, T:0.41
Consensus pattern (31 bp):
AGTGACAAATTTATTATAAATTGATAAAGTT
Found at i:1382619 original size:31 final size:31
Alignment explanation
Indices: 1382550--1382620 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
1382540 TCGAGTGACC
* * *
1382550 AATTTATTATAAATTGATAATGTTAGTGATA
1 AATTTATTATAAATTGATAAAGTTAATAATA
1382581 AATTTATTATAAATTGATAAAGTTAATAAATA
1 AATTTATTATAAATTGATAAAGTTAAT-AATA
1382613 AA-TTATTA
1 AATTTATTA
1382621 CTTTTGAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 31 0.86
32 5 0.14
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (31 bp):
AATTTATTATAAATTGATAAAGTTAATAATA
Found at i:1383419 original size:118 final size:119
Alignment explanation
Indices: 1383211--1383469 Score: 369
Period size: 118 Copynumber: 2.2 Consensus size: 119
1383201 AAATATAGAT
* *
1383211 GATAACATAACTGGTTAATTACTAGAAACATTATCAAGCATAATAACATATTAGGTAGCGCTTAT
1 GATAACATAACAGGTTAATTACTAGAAACATTATCAAGCATAATAACATATTAGGTAGCGATTAT
* * *
1383276 ATAACGTAATTGGTAGCGCCTTTTTAAAGCTGACAGGGC-TTTGGAAATCCGAC
66 ATAACGTAATAGGCAGCACCTTTTTAAAGCTGACAGGGCTTTTGGAAATCCGAC
* * *
1383329 GATAACATAACCGGTTAATTATTGGAAACATTATCAAGCATAATAACATATTAGGTAGCGATTAT
1 GATAACATAACAGGTTAATTACTAGAAACATTATCAAGCATAATAACATATTAGGTAGCGATTAT
* ** *
1383394 A-AATCGTAATAGGCAGCACCTTTTTAAAGTTGATGGGGCTTTTGGAAATCTGAC
66 ATAA-CGTAATAGGCAGCACCTTTTTAAAGCTGACAGGGCTTTTGGAAATCCGAC
* *
1383448 GATAACAAAATAGGTTAATTAC
1 GATAACATAACAGGTTAATTAC
1383470 ATAATTTTTT
Statistics
Matches: 124, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
117 2 0.02
118 91 0.73
119 31 0.25
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (119 bp):
GATAACATAACAGGTTAATTACTAGAAACATTATCAAGCATAATAACATATTAGGTAGCGATTAT
ATAACGTAATAGGCAGCACCTTTTTAAAGCTGACAGGGCTTTTGGAAATCCGAC
Found at i:1383726 original size:226 final size:225
Alignment explanation
Indices: 1383319--1383800 Score: 675
Period size: 226 Copynumber: 2.1 Consensus size: 225
1383309 CAGGGCTTTG
1383319 GAAATCCGACGATAACATAACCGGTTAATTATTGGAAACATTATCAAGCATAATAACATATTAGG
1 GAAATCCGACGATAACATAACCGGTTAATTATTGGAAACATTATCAAGCATAATAACATATTAGG
* * * * * *
1383384 TAGCGATTATAAATCGTAATAGGCAGCACCTTTTTAAAGTTGATGGGGCTTTTGGAAATCTGACG
66 TAGCGATTATAAATCGTAATAGGCAGCACATTATTAAAGCTGATGGGGCTTTTAGAAATCCGACA
* * * **
1383449 ATAACAAAATAGGTTAATTACATAATTTTTTGTTAGTATTATCAAATATTAGGTAATGCCTAAAA
131 ATAACAAAATAGGTTAATTACATAATTTGTTATCAGTATTATCAAATATTAGGTAACACCT-AAA
*
1383514 TATTACCAAAATTTAAACTGATAT-AGCCTTA
195 TATTAACAAAATTTAAACTGAT-TGAGCCTTA
* *
1383545 GAAATCCAACGATAACATAACCGGTTAATTATTGGAAACATTATCAAGCATAATAACATCTTAGG
1 GAAATCCGACGATAACATAACCGGTTAATTATTGGAAACATTATCAAGCATAATAACATATTAGG
* * *
1383610 TAGCGCTTATGTAA-CGTAATAGGTAG-AGCATTATTAAAGCTGATGGGGC-TTTAGAAATCCGA
66 TAGCGATTAT-AAATCGTAATAGGCAGCA-CATTATTAAAGCTGATGGGGCTTTTAGAAATCCGA
* *
1383672 TAATAACAAAATAGGTTAATTACTTAATTTGTTATCAGTATTATCAACATATTAGGTAACACCTA
129 CAATAACAAAATAGGTTAATTACATAATTTGTTATCAGTATTATCAA-ATATTAGGTAACACCTA
* * *
1383737 AATGTTAACAAAATTTAAGCTGATTGAGTCTTA
193 AATATTAACAAAATTTAAACTGATTGAGCCTTA
* *
1383770 GGAATCCGATGATAACATAACCGGTTAATTA
1 GAAATCCGACGATAACATAACCGGTTAATTA
1383801 CTTTAAAGTA
Statistics
Matches: 227, Mismatches: 25, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
224 1 0.00
225 109 0.48
226 115 0.51
227 2 0.01
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (225 bp):
GAAATCCGACGATAACATAACCGGTTAATTATTGGAAACATTATCAAGCATAATAACATATTAGG
TAGCGATTATAAATCGTAATAGGCAGCACATTATTAAAGCTGATGGGGCTTTTAGAAATCCGACA
ATAACAAAATAGGTTAATTACATAATTTGTTATCAGTATTATCAAATATTAGGTAACACCTAAAT
ATTAACAAAATTTAAACTGATTGAGCCTTA
Found at i:1383832 original size:2 final size:2
Alignment explanation
Indices: 1383825--1383865 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1383815 GTTTCGAAAT
1383825 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1383866 TTCTCTGATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1386346 original size:6 final size:6
Alignment explanation
Indices: 1386335--1386417 Score: 51
Period size: 6 Copynumber: 13.7 Consensus size: 6
1386325 TAGTGGTGAC
* * * * *
1386335 GAAATT GAAATT AAAATT CAAACT CAAATT GAAATTT AAAATT GAAATT
1 GAAATT GAAATT GAAATT GAAATT GAAATT GAAA-TT GAAATT GAAATT
* * * * *
1386384 CAAACTC G-AATT AAAATT AAAATT GAAAAT GAAA
1 GAAA-TT GAAATT GAAATT GAAATT GAAATT GAAA
1386418 ACTGCATAAA
Statistics
Matches: 60, Mismatches: 14, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
5 1 0.02
6 53 0.88
7 6 0.10
ACGTcount: A:0.55, C:0.07, G:0.08, T:0.29
Consensus pattern (6 bp):
GAAATT
Found at i:1386401 original size:37 final size:37
Alignment explanation
Indices: 1386336--1386417 Score: 94
Period size: 37 Copynumber: 2.2 Consensus size: 37
1386326 AGTGGTGACG
* * * *
1386336 AAATTGAAATTAAAATTCAAACTCAAATTGAAATTTA
1 AAATTGAAATTAAAACTCAAACTAAAATTAAAATTGA
* * *
1386373 AAATTGAAATTCAAACTCGAATTAAAATTAAAATTGA
1 AAATTGAAATTAAAACTCAAACTAAAATTAAAATTGA
1386410 AAA-TGAAA
1 AAATTGAAA
1386418 ACTGCATAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
36 5 0.13
37 33 0.87
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.29
Consensus pattern (37 bp):
AAATTGAAATTAAAACTCAAACTAAAATTAAAATTGA
Found at i:1386420 original size:31 final size:32
Alignment explanation
Indices: 1386336--1386413 Score: 108
Period size: 31 Copynumber: 2.5 Consensus size: 32
1386326 AGTGGTGACG
*
1386336 AAATTGAAATT-AAAATTCAAACTCAAATTGA
1 AAATTAAAATTGAAAATTCAAACTCAAATTGA
* *
1386367 AATTTAAAATTG-AAATTCAAACTCGAATT-A
1 AAATTAAAATTGAAAATTCAAACTCAAATTGA
1386397 AAATTAAAATTGAAAAT
1 AAATTAAAATTGAAAAT
1386414 GAAAACTGCA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
30 12 0.29
31 29 0.71
ACGTcount: A:0.55, C:0.08, G:0.06, T:0.31
Consensus pattern (32 bp):
AAATTAAAATTGAAAATTCAAACTCAAATTGA
Found at i:1387806 original size:17 final size:18
Alignment explanation
Indices: 1387781--1387815 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1387771 TCAAATACAT
1387781 TTTACAACATATA-AATG
1 TTTACAACATATATAATG
*
1387798 TTTAGAACATATATAATG
1 TTTACAACATATATAATG
1387816 AATTACCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.37
Consensus pattern (18 bp):
TTTACAACATATATAATG
Found at i:1391153 original size:48 final size:48
Alignment explanation
Indices: 1391082--1391177 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 48
1391072 ACTTCAAAAG
* *
1391082 TTGAAGGAACTTGATCAAGATCTTCAATTATCAAGGACTTTTTTTTAA
1 TTGAAGGAACTTGATCAAGATCTTCAATTATCAAAGACTTTTTCTTAA
1391130 TTGAAGGAACTTGATCAAGATCTTCAATTATCAAAGACTTTTTCTTAA
1 TTGAAGGAACTTGATCAAGATCTTCAATTATCAAAGACTTTTTCTTAA
1391178 ATAAAAGAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.39
Consensus pattern (48 bp):
TTGAAGGAACTTGATCAAGATCTTCAATTATCAAAGACTTTTTCTTAA
Found at i:1395149 original size:2 final size:2
Alignment explanation
Indices: 1395142--1395172 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1395132 CAAGAGGTAT
1395142 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1395173 TACATGCATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1395638 original size:9 final size:8
Alignment explanation
Indices: 1395618--1395671 Score: 58
Period size: 9 Copynumber: 6.5 Consensus size: 8
1395608 ACCCTTTTAC
1395618 TTTT-TTA
1 TTTTATTA
1395625 TTTTATTCA
1 TTTTATT-A
1395634 TTTTATTTTA
1 TTTTA--TTA
1395644 TTTT-TTA
1 TTTTATTA
1395651 TTTTCATTA
1 TTTT-ATTA
1395660 TTTTATTA
1 TTTTATTA
1395668 TTTT
1 TTTT
1395672 TGTTTATTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
7 11 0.27
8 10 0.24
9 13 0.32
10 5 0.12
11 2 0.05
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTATTA
Found at i:1395639 original size:14 final size:13
Alignment explanation
Indices: 1395620--1395666 Score: 69
Period size: 14 Copynumber: 3.5 Consensus size: 13
1395610 CCTTTTACTT
1395620 TTTTATTTTATTCA
1 TTTTATTTTATT-A
1395634 TTTTATTTTATT-
1 TTTTATTTTATTA
1395646 TTTTATTTTCATTA
1 TTTTATTTT-ATTA
1395660 TTTTATT
1 TTTTATT
1395667 ATTTTTGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
12 9 0.29
13 3 0.10
14 19 0.61
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTATTTTATTA
Found at i:1395647 original size:26 final size:26
Alignment explanation
Indices: 1395612--1395679 Score: 86
Period size: 26 Copynumber: 2.5 Consensus size: 26
1395602 AAACTAACCC
1395612 TTTTACTTTTTTATTTT-ATTCATTTTA
1 TTTTA-TTTTTTATTTTCATT-ATTTTA
1395639 TTTTATTTTTTATTTTCATTATTTTA
1 TTTTATTTTTTATTTTCATTATTTTA
1395665 TTATT-TTTGTTTATT
1 TT-TTATTT-TTTATT
1395680 ATCTTTTTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
26 22 0.58
27 16 0.42
ACGTcount: A:0.18, C:0.04, G:0.01, T:0.76
Consensus pattern (26 bp):
TTTTATTTTTTATTTTCATTATTTTA
Found at i:1397483 original size:7 final size:7
Alignment explanation
Indices: 1397466--1397499 Score: 59
Period size: 7 Copynumber: 4.7 Consensus size: 7
1397456 GAACATCTCA
1397466 TGCATTTT
1 TGCA-TTT
1397474 TGCATTT
1 TGCATTT
1397481 TGCATTT
1 TGCATTT
1397488 TGCATTT
1 TGCATTT
1397495 TGCAT
1 TGCAT
1397500 CTACATTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 22 0.85
8 4 0.15
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.56
Consensus pattern (7 bp):
TGCATTT
Found at i:1398715 original size:22 final size:22
Alignment explanation
Indices: 1398676--1398744 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 22
1398666 CAAGAACAAA
1398676 AAAGAA-AAGAAGCAAAAAAACAACG
1 AAAGAACAA-AAG-AAAAAAA-AA-G
1398701 AAA-AACAAAAGAAAAAAAAAG
1 AAAGAACAAAAGAAAAAAAAAG
*
1398722 AAAGAAC-AAA-AATAAAAAAG
1 AAAGAACAAAAGAAAAAAAAAG
1398742 AAA
1 AAA
1398745 AAGGGACAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
20 12 0.29
21 7 0.17
22 5 0.12
23 7 0.17
24 5 0.12
25 5 0.12
ACGTcount: A:0.80, C:0.07, G:0.12, T:0.01
Consensus pattern (22 bp):
AAAGAACAAAAGAAAAAAAAAG
Found at i:1398725 original size:14 final size:15
Alignment explanation
Indices: 1398707--1398746 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1398697 AACGAAAAAC
1398707 AAAAGAAAAAAA-AA
1 AAAAGAAAAAAATAA
*
1398721 GAAAGAACAAAAATAA
1 AAAAGAA-AAAAATAA
1398737 AAAAGAAAAA
1 AAAAGAAAAA
1398747 GGGACAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 6 0.27
15 8 0.36
16 8 0.36
ACGTcount: A:0.85, C:0.03, G:0.10, T:0.03
Consensus pattern (15 bp):
AAAAGAAAAAAATAA
Found at i:1398745 original size:27 final size:25
Alignment explanation
Indices: 1398667--1398746 Score: 70
Period size: 28 Copynumber: 2.9 Consensus size: 25
1398657 ATATCCAATC
*
1398667 AAGAACAAAAAAGAAAAGAAGCAAAAA
1 AAGAACAAAAAAAAAAAGAA--AAAAA
* *
1398694 AACAACGAAAAACAAAAGAAAAAAAAAGA
1 AAGAAC-AAAAA-AAAA-AAGAAAAAA-A
1398723 AAGAACAAAAATAAAAAAGAAAAA
1 AAGAACAAAAA-AAAAAAGAAAAA
1398747 GGGACAAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
27 12 0.28
28 18 0.42
29 9 0.21
30 4 0.09
ACGTcount: A:0.80, C:0.07, G:0.11, T:0.01
Consensus pattern (25 bp):
AAGAACAAAAAAAAAAAGAAAAAAA
Found at i:1398745 original size:41 final size:42
Alignment explanation
Indices: 1398667--1398746 Score: 110
Period size: 41 Copynumber: 1.9 Consensus size: 42
1398657 ATATCCAATC
* * *
1398667 AAGAACAAAAAAGAAAAGAAGCAAAAAAACAACGAAAAACAA
1 AAGAAAAAAAAAGAAAAGAAGCAAAAAAAAAAAGAAAAACAA
1398709 AAGAAAAAAAAAG-AAAGAA-CAAAAATAAAAAAGAAAAA
1 AAGAAAAAAAAAGAAAAGAAGCAAAAA-AAAAAAGAAAAA
1398747 GGGACAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
40 6 0.18
41 16 0.47
42 12 0.35
ACGTcount: A:0.80, C:0.07, G:0.11, T:0.01
Consensus pattern (42 bp):
AAGAAAAAAAAAGAAAAGAAGCAAAAAAAAAAAGAAAAACAA
Found at i:1399825 original size:18 final size:18
Alignment explanation
Indices: 1399802--1399836 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1399792 TCAACATCAA
* *
1399802 ATATTGGGGCATTTTTGG
1 ATATTGAGGCATCTTTGG
1399820 ATATTGAGGCATCTTTG
1 ATATTGAGGCATCTTTG
1399837 AAGATTCAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.09, G:0.29, T:0.43
Consensus pattern (18 bp):
ATATTGAGGCATCTTTGG
Found at i:1400478 original size:106 final size:106
Alignment explanation
Indices: 1400349--1401093 Score: 1094
Period size: 106 Copynumber: 7.0 Consensus size: 106
1400339 ATATCGTGCT
* * * * *
1400349 ACTCGAGACAACGCAAGTTCAACTTCATGACGAATGTACCACTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1400414 AATTTCAGAGTCAATTTCAACTTCATAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
1400455 ACTCCAAACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTATCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1400520 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
1400561 ACTCCAGACAACGTAAGTTCAACTTCACGACGACGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1400626 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * **
1400667 ACTCCAGAAAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTTTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1400732 AATTTCAGAGCCAATTTCAACTTCACAACGTAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
1400773 ACTCGAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1400838 AATTTCAGAGCCAATTTTAACTTCATAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * *
1400879 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCACTAGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1400944 AATTTTAGAGCCAATTTCAACTTCACAACGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
1400985 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * ** *
1401050 AGTTCCAGAGCCAATTTCAGCTTCACGGCGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
1401091 ACT
1 ACT
1401094 TGGAACAATA
Statistics
Matches: 579, Mismatches: 60, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
106 579 1.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:1401310 original size:84 final size:83
Alignment explanation
Indices: 1401214--1401744 Score: 490
Period size: 84 Copynumber: 6.4 Consensus size: 83
1401204 AATCGTTCCA
* * *
1401214 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTTAAGG
1 ACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGT
* *
1401279 CTAGAAGGGTTATCTATC
66 CGAGAAGGGTTATCTGTC
** * * *
1401297 ACCAAAAGACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCTCATCATTTGTAGCATAGCTTAAG
1 ACC-AAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAG
* *
1401362 TTGAGAAGGGCTATCTG--
65 TCGAGAAGGGTTATCTGTC
* * * * * * *
1401379 -CCAAAGACC-CCTGAGTTCGATTACACTCATCTTCGAGGGCATATCATTAT-CAGCAAAACTTA
1 ACCAAAGACCTTC-GAGTTCGACTACACTCAGC-TCCAAGGCACATCATT-TGCAGCATAACTTA
*
1401441 AGTCTAGAAGGGTTATCTGTC
63 AGTCGAGAAGGGTTATCTGTC
* * * *
1401462 ACCAAAAGACCTTTGAGTTCGACTACACTCAGCT-CAACGGCACATAATTTGCATCATAGCTTAA
1 ACC-AAAGACCTTCGAGTTCGACTACACTCAGCTCCAA-GGCACATCATTTGCAGCATAACTTAA
* *
1401526 GTCGATAAGGGCTATCTG--
64 GTCGAGAAGGGTTATCTGTC
* * ** * * *
1401544 -CCAAAGA-CTCCCGAGTTCGATTACACTCAGCTTTGAGGGCACGTCATTTGCAACATAACTTAA
1 ACCAAAGACCT-TCGAGTTCGACTACACTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAA
* *
1401607 GTCGAGAAGGTTTATCTGCC
64 GTCGAGAAGGGTTATCTGTC
* * * *
1401627 AACCAAATACCTTCGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTGCAGCATAGCTTAAG
1 -ACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAG
* *
1401692 TCGA-AAAGGTCTATCTGCC
65 TCGAGAAGGGT-TATCTGTC
* * *
1401711 AACAGAAAACCTTCGAGTTCGATTACACTCAGCT
1 ACCA-AAGACCTTCGAGTTCGACTACACTCAGCT
1401745 AAGAGGCAAA
Statistics
Matches: 359, Mismatches: 68, Indels: 41
0.77 0.15 0.09
Matches are distributed among these distances:
79 3 0.01
80 45 0.13
81 79 0.22
82 2 0.01
83 12 0.03
84 168 0.47
85 48 0.13
86 2 0.01
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (83 bp):
ACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGT
CGAGAAGGGTTATCTGTC
Found at i:1401486 original size:165 final size:165
Alignment explanation
Indices: 1401227--1401744 Score: 650
Period size: 165 Copynumber: 3.1 Consensus size: 165
1401217 AAAGACCTTC
* * * * *
1401227 GAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTACAGCATAACTTAAGGCTAGAAGGGTTA
1 GAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTTAAGTCTAGAAGGGTTA
* * * *
1401291 TCTATCACCAAAAGACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCTCATCATTTGTAGCATAG
66 TCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAG
* *
1401356 CTTAAGTTGAGAAGGGCTATCTGCCAAAGACCCCT
131 CTTAAGTCGAAAAGGGCTATCTGCCAAAGACCCCT
* * *
1401391 GAGTTCGATTACACTCATCTTCGAGGGCATATCA-TTATCAGCAAAACTTAAGTCTAGAAGGGTT
1 GAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTA-CAGCATAACTTAAGTCTAGAAGGGTT
* * * *
1401455 ATCTGTCACCAAAAGACCTTTGAGTTCGACTACACTCAGCT-CAACGGCACATAATTTGCATCAT
65 ATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGCAT
*
1401519 AGCTTAAGTCGATAAGGGCTATCTGCCAAAGACTCCC-
129 AGCTTAAGTCGAAAAGGGCTATCTGCCAAAGAC-CCCT
* * * * * *
1401556 GAGTTCGATTACACTCAGCTTTGAGGGCACGTCATTTGCAACATAACTTAAGTCGAGAAGGTTTA
1 GAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTTAAGTCTAGAAGGGTTA
* * *
1401621 TCTGCCAACC-AAATACCTTCGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTGCAGCATA
66 TCTGTC-ACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATA
* * *
1401685 GCTTAAGTCGAAAAGGTCTATCTGCCAACAGAAAACCTT
130 GCTTAAGTCGAAAAGGGCTATCTGCCAA-AG--ACCCCT
1401724 CGAGTTCGATTACACTCAGCT
1 -GAGTTCGATTACACTCAGCT
1401745 AAGAGGCAAA
Statistics
Matches: 304, Mismatches: 38, Indels: 19
0.84 0.11 0.05
Matches are distributed among these distances:
164 22 0.07
165 246 0.81
166 13 0.04
167 2 0.01
168 1 0.00
169 20 0.07
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (165 bp):
GAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTTAAGTCTAGAAGGGTTA
TCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAG
CTTAAGTCGAAAAGGGCTATCTGCCAAAGACCCCT
Found at i:1403451 original size:5 final size:5
Alignment explanation
Indices: 1403441--1403509 Score: 51
Period size: 5 Copynumber: 14.4 Consensus size: 5
1403431 CCTTTTACTT
* *
1403441 TTTTA TTTTA -TTCA TTTTA TTTTA -TTTA TTTTTA TTTTTA TTTT- TATT-
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA -TTTTA TTTTA TTTTA
1403489 TTTTA TTTTCA --TTA TTTTA TT
1 TTTTA TTTT-A TTTTA TTTTA TT
1403510 ATTTTTGTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
3 1 0.02
4 15 0.28
5 26 0.49
6 11 0.21
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:1403468 original size:9 final size:9
Alignment explanation
Indices: 1403442--1403514 Score: 53
Period size: 9 Copynumber: 7.9 Consensus size: 9
1403432 CTTTTACTTT
1403442 TTTATTTTA
1 TTTATTTTA
*
1403451 TTCATTTTA
1 TTTATTTTA
*
1403460 TTTTATTTATT
1 -TTTATTT-TA
1403471 TTTATTTTTA
1 TTTA-TTTTA
*
1403481 TTT-TTATTT
1 TTTATT-TTA
1403490 TTTATTTTCA
1 TTTATTTT-A
1403500 -TTATTTTA
1 TTTATTTTA
1403508 -TTATTTT
1 TTTATTTT
1403515 TGTTTATTAT
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
8 10 0.19
9 22 0.42
10 16 0.31
11 4 0.08
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTATTTTA
Found at i:1403480 original size:43 final size:44
Alignment explanation
Indices: 1403433--1403531 Score: 109
Period size: 41 Copynumber: 2.3 Consensus size: 44
1403423 AAACTAACCC
1403433 TTTTACTTTTTTATTTTATTCATTTT-ATT-TTAT-TTATTTTTAT
1 TTTTACTTTTTTATTTT-TT-ATTTTCATTATTATATTATTTTTAT
* *
1403476 TTTTA--TTTTTATTTTTTATTTTCATTATTTTATTATTTTTGT
1 TTTTACTTTTTTATTTTTTATTTTCATTATTATATTATTTTTAT
1403518 TTATTATCTTTTTT
1 TT-TTA-CTTTTTT
1403532 CACTAACTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
39 5 0.11
40 5 0.11
41 13 0.28
42 11 0.23
43 8 0.17
46 5 0.11
ACGTcount: A:0.17, C:0.04, G:0.01, T:0.78
Consensus pattern (44 bp):
TTTTACTTTTTTATTTTTTATTTTCATTATTATATTATTTTTAT
Found at i:1403486 original size:18 final size:18
Alignment explanation
Indices: 1403465--1403529 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 18
1403455 TTTTATTTTA
1403465 TTTATTTTTATTTTTATT
1 TTTATTTTTATTTTTATT
*
1403483 TTTATTTTTTATTTTCATT
1 TTTA-TTTTTATTTTTATT
* * *
1403502 ATT-TTATTATTTTTGTT
1 TTTATTTTTATTTTTATT
1403519 TATTATCTTTT
1 T-TTAT-TTTT
1403530 TTCACTAACT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
17 11 0.31
18 6 0.17
19 16 0.44
20 3 0.08
ACGTcount: A:0.17, C:0.03, G:0.02, T:0.78
Consensus pattern (18 bp):
TTTATTTTTATTTTTATT
Found at i:1403504 original size:34 final size:36
Alignment explanation
Indices: 1403440--1403530 Score: 100
Period size: 36 Copynumber: 2.5 Consensus size: 36
1403430 CCCTTTTACT
1403440 TTTTTA-TTTTATTCATTTTATTTTATTTA-TTT-TTA
1 TTTTTATTTTTATT--TTTTATTTTATTTATTTTATTA
1403475 TTTTTATTTTTATTTTTTATTTTCA-TTATTTTATTA
1 TTTTTATTTTTATTTTTTATTTT-ATTTATTTTATTA
*
1403511 TTTTTGTTTATTATCTTTTT
1 TTTTTATTT-TTAT-TTTTT
1403531 TCACTAACTT
Statistics
Matches: 49, Mismatches: 1, Indels: 9
0.83 0.02 0.15
Matches are distributed among these distances:
34 12 0.24
35 10 0.20
36 18 0.37
37 4 0.08
38 5 0.10
ACGTcount: A:0.18, C:0.03, G:0.01, T:0.78
Consensus pattern (36 bp):
TTTTTATTTTTATTTTTTATTTTATTTATTTTATTA
Found at i:1403523 original size:13 final size:13
Alignment explanation
Indices: 1403440--1403529 Score: 67
Period size: 14 Copynumber: 6.4 Consensus size: 13
1403430 CCCTTTTACT
1403440 TTTTTATTTTATTCA
1 TTTTTA-TTTATT-A
1403455 -TTTTATTTTATTTA
1 TTTTTA-TTTA-TTA
1403469 TTTTTATTT-TTA
1 TTTTTATTTATTA
*
1403481 TTTTTATTTTTTA
1 TTTTTATTTATTA
1403494 TTTTCATTATTTTATTA
1 -TTT--TTA-TTTATTA
*
1403511 TTTTTGTTTATTA
1 TTTTTATTTATTA
1403524 TCTTTT
1 T-TTTT
1403530 TTCACTAACT
Statistics
Matches: 65, Mismatches: 2, Indels: 17
0.77 0.02 0.20
Matches are distributed among these distances:
12 12 0.18
13 11 0.17
14 23 0.35
15 7 0.11
16 6 0.09
17 6 0.09
ACGTcount: A:0.18, C:0.03, G:0.01, T:0.78
Consensus pattern (13 bp):
TTTTTATTTATTA
Found at i:1406449 original size:61 final size:60
Alignment explanation
Indices: 1406374--1406496 Score: 160
Period size: 61 Copynumber: 2.0 Consensus size: 60
1406364 CCAGGCGACC
* * * *
1406374 ATTTTGTAACTTTTAGTAGTCAAGA-GACTCAATAAAG-AACTTCCCTTGTAGTCAAGGGACT
1 ATTTTGTAACTTTTAATAGT-AAGATGACTCAACAAAGAAAC--ACCTTATAGTCAAGGGACT
*
1406435 ATTTTGTAACTTTTAATAGTTAGATGACTCAACAAAGAAACACCTTATAGTCAAGGGACT
1 ATTTTGTAACTTTTAATAGTAAGATGACTCAACAAAGAAACACCTTATAGTCAAGGGACT
1406495 AT
1 AT
1406497 CTATGTACTT
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
60 22 0.40
61 30 0.55
62 3 0.05
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (60 bp):
ATTTTGTAACTTTTAATAGTAAGATGACTCAACAAAGAAACACCTTATAGTCAAGGGACT
Found at i:1407535 original size:12 final size:11
Alignment explanation
Indices: 1407513--1407540 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1407503 GGGTTATTTA
1407513 TTTTCTTTTTT
1 TTTTCTTTTTT
1407524 TTTTCTTTTTT
1 TTTTCTTTTTT
1407535 TTTTCT
1 TTTTCT
1407541 CATCAAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:1407537 original size:350 final size:347
Alignment explanation
Indices: 1406895--1407589 Score: 1160
Period size: 350 Copynumber: 2.0 Consensus size: 347
1406885 TATGTTATAA
* * * *
1406895 TATAAATTATAAATATGTATGTATAAAGATAAATTGAGGGTTGTTGGGGTCCGATCCATAATTTT
1 TATAAATTATAAATATGTATGTACAAAGATAAACTGAGGGGTGTTAGGGTCCGATCCATAATTTT
*
1406960 CAAATTCATATATGGTTTCGATATTTTCTTTGTATTTTCTATTATTTATCTAATTTTGCATCCCT
66 CAAATTCATATATGGTTTCAATATTTTCTTTGTATTTTCTATTATTTATCTAATTTTGCATCCCT
* *
1407025 AAATTCTTAATATAACTTCTTAAATTAGCACCACTTGACATGAAATCTTGTGTCCTGTGTATTCA
131 AAATGCTTAATATAACTTCTTAAATTAGCACCACTTGACATGAAATCTTATGTCCTGTGTATTCA
* *
1407090 CGTTATGCATGAACAAATTAGATTTGACATGCTAAAAAGTAGGTTATGATATTAAAACTCTATAG
196 CGTTATGCATGAACAAATTAGATTTGACATGCTAAAAAGTAGGATATGATATTAAAACTCTACAG
1407155 GGTTATTTATTTTCTTCCTTTCTATCTTTTTTTTTACTCATCAAAATGATTTTTATTAATCGAGC
261 GGTTATTTATTTTCTTCCTTTCTATCTTTTTTTTT-CTCATCAAAATGATTTTTATTAATCGAGC
*
1407220 CTAAGTCAAAAGTCTCATTAAAT
325 CTAAGTCAAAAGTATCATTAAAT
1407243 TATAAATTATAAATATGTATGTACAAAGATAAACTGAGGGGTGTTAGGGTGCACGATCCATAATT
1 TATAAATTATAAATATGTATGTACAAAGATAAACTGAGGGGTGTTAGGGT-C-CGATCCATAATT
1407308 TTCAAATTCATATATGGTTTCAATATTTTCTTTGTATTTTCTATTATTTATCTAATTTTGCATCC
64 TTCAAATTCATATATGGTTTCAATATTTTCTTTGTATTTTCTATTATTTATCTAATTTTGCATCC
* *
1407373 CTAAATGCTTAATATAACTTCTTACATTTGCACCACTTGACATGAAATCTTATGTCCTGTGTATT
129 CTAAATGCTTAATATAACTTCTTAAATTAGCACCACTTGACATGAAATCTTATGTCCTGTGTATT
* * * *
1407438 CACGTTATGCATGAACAAATTGGATTTGACCTGCTAAAAAGTAGGATGTGGTATT-AAACTCTAC
194 CACGTTATGCATGAACAAATTAGATTTGACATGCTAAAAAGTAGGATATGATATTAAAACTCTAC
* * *
1407502 AGGGTTATTTATTTTCTT-TTTTTTTTCTTTTTTTTTTCTCATCAAAATGATTTTTATTAATCGA
259 AGGGTTATTTATTTTCTTCCTTTCTATC-TTTTTTTTTCTCATCAAAATGATTTTTATTAATCGA
*
1407566 GCCTAAGTCAAAAGTATCGTTAAA
323 GCCTAAGTCAAAAGTATCATTAAA
1407590 AACATCCCTA
Statistics
Matches: 324, Mismatches: 20, Indels: 6
0.93 0.06 0.02
Matches are distributed among these distances:
348 101 0.31
349 36 0.11
350 187 0.58
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.43
Consensus pattern (347 bp):
TATAAATTATAAATATGTATGTACAAAGATAAACTGAGGGGTGTTAGGGTCCGATCCATAATTTT
CAAATTCATATATGGTTTCAATATTTTCTTTGTATTTTCTATTATTTATCTAATTTTGCATCCCT
AAATGCTTAATATAACTTCTTAAATTAGCACCACTTGACATGAAATCTTATGTCCTGTGTATTCA
CGTTATGCATGAACAAATTAGATTTGACATGCTAAAAAGTAGGATATGATATTAAAACTCTACAG
GGTTATTTATTTTCTTCCTTTCTATCTTTTTTTTTCTCATCAAAATGATTTTTATTAATCGAGCC
TAAGTCAAAAGTATCATTAAAT
Found at i:1409579 original size:10 final size:10
Alignment explanation
Indices: 1409566--1409593 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
1409556 ACCCGAACCA
1409566 ACCCGACCTG
1 ACCCGACCTG
1409576 ACCCGACCTG
1 ACCCGACCTG
1409586 ACCCGACC
1 ACCCGACC
1409594 GTTGACCGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.21, C:0.54, G:0.18, T:0.07
Consensus pattern (10 bp):
ACCCGACCTG
Found at i:1409678 original size:29 final size:29
Alignment explanation
Indices: 1409627--1409739 Score: 92
Period size: 29 Copynumber: 4.0 Consensus size: 29
1409617 ATTATTTTGA
* * * *
1409627 AAAATAGTGGTATTTTGGAAATTATATTT
1 AAAATGGTGATATTTTCGTAATTATATTT
* *
1409656 AAAATGGTGCTATTTTCGTAATT-TTTTT
1 AAAATGGTGATATTTTCGTAATTATATTT
* * *
1409684 AAAA-GGTTATAATTTT-GTAATTTTTTTT
1 AAAATGGTGAT-ATTTTCGTAATTATATTT
*
1409712 AAAAGGGTGATATTTTCGTAA--ATATTT
1 AAAATGGTGATATTTTCGTAATTATATTT
1409739 A
1 A
1409740 TTCAAAAGGG
Statistics
Matches: 70, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
27 15 0.21
28 27 0.39
29 28 0.40
ACGTcount: A:0.34, C:0.03, G:0.15, T:0.49
Consensus pattern (29 bp):
AAAATGGTGATATTTTCGTAATTATATTT
Found at i:1409698 original size:28 final size:29
Alignment explanation
Indices: 1409653--1409754 Score: 111
Period size: 28 Copynumber: 3.5 Consensus size: 29
1409643 GGAAATTATA
* *
1409653 TTTAAAATGGTGCTATTTTCGTAA-TTTT
1 TTTAAAAGGGTGATATTTTCGTAATTTTT
*
1409681 TTTAAAA-GGTTATAATTTT-GTAATTTTT
1 TTTAAAAGGGTGAT-ATTTTCGTAATTTTT
*
1409709 TTTAAAAGGGTGATATTTTCGTAAATATTTA
1 TTTAAAAGGGTGATATTTTCGT-AAT-TTTT
*
1409740 TTCAAAAGGGTGATA
1 TTTAAAAGGGTGATA
1409755 ATTGTGTAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
27 8 0.13
28 28 0.44
29 7 0.11
30 3 0.05
31 17 0.27
ACGTcount: A:0.32, C:0.04, G:0.16, T:0.48
Consensus pattern (29 bp):
TTTAAAAGGGTGATATTTTCGTAATTTTT
Found at i:1427622 original size:79 final size:79
Alignment explanation
Indices: 1427527--1427928 Score: 579
Period size: 79 Copynumber: 5.1 Consensus size: 79
1427517 AAAAGAAGGA
* *
1427527 ATAAAAGAATAATGCATATGGGTGCATTATTAGCATGAAAGGATGCCATAGTTGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATG
*
1427592 GGTGCATTATCGGT
66 GGTGCATTATCGGC
* * * *
1427606 ATACAAGAATAATGCATATGGGTGCATTATTGACATGAAATGATACCATAGCTGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATG
* *
1427671 GGTACATTATCAGC
66 GGTGCATTATCGGC
* * * * *
1427685 ATAAAAGAATAATACATATGGGTGCATTATTGGCAAGAAAGGATGCCATAACTAAAATGCATATA
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATG
*
1427750 GGTGCATTATCGAC
66 GGTGCATTATCGGC
* **
1427764 ATAAAAGAATAATGCATATGGGTGTATTATTGGCATGAAAGGATGTTATAGCTGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATG
1427829 GGTGCATTATCGGC
66 GGTGCATTATCGGC
* * ** *
1427843 ATAAATGAATAATGCATATGGGTGCGTTATTGGCATGAAACAATGCCATAGCTGAGATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATG
* *
1427908 GGTGTATTATCGGT
66 GGTGCATTATCGGC
1427922 ATAAAAG
1 ATAAAAG
1427929 TATACCACAT
Statistics
Matches: 282, Mismatches: 41, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
79 282 1.00
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.28
Consensus pattern (79 bp):
ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATG
GGTGCATTATCGGC
Found at i:1434006 original size:75 final size:74
Alignment explanation
Indices: 1433891--1434030 Score: 185
Period size: 75 Copynumber: 1.9 Consensus size: 74
1433881 CGTTGAGGCA
* * *
1433891 GTATCGATACCATTATAAGGGTATGGATACCAAGCAAACATCGAATCTAATATTGGTATCGATAC
1 GTATCGATACCATTATAAGGGTATCGATACCAAGCAAACATCAAACCTAATATTGGTATCGATAC
1433956 CGTAAGTGG
66 CGTAAGTGG
* * *
1433965 GTATCGATACCA-TAGTATGGTAGTATCGATACCAGGC-AACATCAAACCTAATTTTGGTATCGA
1 GTATCGATACCATTA-TAAGG--GTATCGATACCAAGCAAACATCAAACCTAATATTGGTATCGA
1434028 TAC
63 TAC
1434031 TTAGAGGAAG
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
73 2 0.04
74 16 0.28
75 26 0.46
76 13 0.23
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (74 bp):
GTATCGATACCATTATAAGGGTATCGATACCAAGCAAACATCAAACCTAATATTGGTATCGATAC
CGTAAGTGG
Found at i:1434051 original size:75 final size:76
Alignment explanation
Indices: 1433911--1434075 Score: 183
Period size: 75 Copynumber: 2.2 Consensus size: 76
1433901 CATTATAAGG
* * * * *
1433911 GTATGGATACCAAGCAAACATCGAATCTAATATTGGTATCGATACCGTAAGTGGGTATCGATACC
1 GTATCGATACCAAGCAAACATCAAACCTAATATTGGTATCGATACCGTAAGTGAGTATAGATACC
*
1433976 ATAGTATGGTA
66 ATAGTATGGAA
* * * *
1433987 GTATCGATACCAGGC-AACATCAAACCTAATTTTGGTATCGATA-CTTAGAG-GAAGTATAGGTA
1 GTATCGATACCAAGCAAACATCAAACCTAATATTGGTATCGATACCGTA-AGTG-AGTATAGATA
*
1434049 CCATAGTATTGAA
64 CCATAGTATGGAA
*
1434062 GTATCGGTACCAAG
1 GTATCGATACCAAG
1434076 TTAGTAGTGT
Statistics
Matches: 74, Mismatches: 13, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
74 4 0.05
75 57 0.77
76 13 0.18
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (76 bp):
GTATCGATACCAAGCAAACATCAAACCTAATATTGGTATCGATACCGTAAGTGAGTATAGATACC
ATAGTATGGAA
Found at i:1434612 original size:78 final size:79
Alignment explanation
Indices: 1434479--1434632 Score: 247
Period size: 78 Copynumber: 2.0 Consensus size: 79
1434469 AAATGAATGA
* * *
1434479 ATAAAAGAATAATGCATATGGGTGTATTATTGGCATGAAAGGATGCCATAACTGAAATGTATA-G
1 ATAAAAGAATAATGCATATGAGTGCATTATTGGCATGAAAGGATGCCATAACTGAAATGGATATG
1434543 GGTGCATTATAGGT
66 GGTGCATTATAGGT
* * *
1434557 ATAAAAGAATAATGCATATGAGTGCATTATTGGCATGAATGGATGGCATAGCTGAAATGGATATG
1 ATAAAAGAATAATGCATATGAGTGCATTATTGGCATGAAAGGATGCCATAACTGAAATGGATATG
1434622 GGTGCATTATA
66 GGTGCATTATA
1434633 TGCATGAATG
Statistics
Matches: 69, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
78 57 0.83
79 12 0.17
ACGTcount: A:0.37, C:0.08, G:0.26, T:0.29
Consensus pattern (79 bp):
ATAAAAGAATAATGCATATGAGTGCATTATTGGCATGAAAGGATGCCATAACTGAAATGGATATG
GGTGCATTATAGGT
Found at i:1434638 original size:45 final size:45
Alignment explanation
Indices: 1434567--1434885 Score: 279
Period size: 45 Copynumber: 7.6 Consensus size: 45
1434557 ATAAAAGAAT
* *
1434567 AATGCATATGAGTGCATTATTGGCATGAATGGATGGCATAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAATGGATGCCATAGCTGA
*
1434612 AATGGATATGGGTGCATTATAT-GCATGAATGGATGCCATAGCTGA
1 AATGCATATGGGTGCATTAT-TGGCATGAATGGATGCCATAGCTGA
* * * * *
1434657 AATGCATCTGGGTTCATTATCGGC-TTAA---AAG--A-A--T--
1 AATGCATATGGGTGCATTATTGGCATGAATGGATGCCATAGCTGA
* * *
1434691 AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCGTAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAATGGATGCCATAGCTGA
* * *
1434736 AATGCATATGGGTGCATTATCGACAT-AA---AAG--A-A--T--
1 AATGCATATGGGTGCATTATTGGCATGAATGGATGCCATAGCTGA
* *
1434770 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTTA
1 AATGCATATGGGTGCATTATTGGCATGAATGGATGCCATAGCTGA
* * *
1434815 AATTCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGTTGA
1 AATGCATATGGGTGCATTATTGGCATGAATGGATGCCATAGCTGA
* *
1434860 AATGCATATGGGTCCATTATTAGCAT
1 AATGCATATGGGTGCATTATTGGCAT
1434886 AAAAGTATAC
Statistics
Matches: 222, Mismatches: 28, Indels: 48
0.74 0.09 0.16
Matches are distributed among these distances:
34 45 0.20
35 5 0.02
36 2 0.01
38 6 0.03
39 1 0.00
40 1 0.00
41 6 0.03
43 2 0.01
44 5 0.02
45 148 0.67
46 1 0.00
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (45 bp):
AATGCATATGGGTGCATTATTGGCATGAATGGATGCCATAGCTGA
Found at i:1434706 original size:79 final size:79
Alignment explanation
Indices: 1434612--1434834 Score: 340
Period size: 79 Copynumber: 2.8 Consensus size: 79
1434602 GCATAGCTGA
* * * *
1434612 AATGGATATGGGTGCATTATAT-GCATGAATGGATGCCATAGCTGAAATGCATCTGGGTTCATTA
1 AATGCATATGGGTGCATTAT-TGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTA
* *
1434676 TCGGCTTAAAAGAAT
65 TCGACATAAAAGAAT
* *
1434691 AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCGTAGCTGAAATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTAT
1434756 CGACATAAAAGAAT
66 CGACATAAAAGAAT
* *
1434770 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTTAAATTCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTAT
1434835 TGGCATGAAA
Statistics
Matches: 131, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
78 1 0.01
79 130 0.99
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (79 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTGCATTAT
CGACATAAAAGAAT
Found at i:1434715 original size:124 final size:123
Alignment explanation
Indices: 1434489--1434755 Score: 385
Period size: 124 Copynumber: 2.2 Consensus size: 123
1434479 ATAAAAGAAT
* *
1434489 AATGCATATGGGTGTATTATTGGCATGAAAGGATGCCATAACTGAAATGTATAGGGTGCATTATA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAACTGAAATGCATAGGGTGCATTATA
*
1434554 GGTATAAAAGAATAATGCATATGAGTGCATTATTGGCATGAATGGATGGCATAGCTGA
66 GGTATAAAAGAATAATGCATATGAGTGCATTATTGGCATGAAAGGATGGCATAGCTGA
* * * * *
1434612 AATGGATATGGGTGCATTATAT-GCATGAATGGATGCCATAGCTGAAATGCATCTGGGTTCATTA
1 AATGCATATGGGTGCATTAT-TGGCATGAAAGGATGCCATAACTGAAATGCAT-AGGGTGCATTA
* * * *
1434676 TCGGCT-TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGTCGTAGCTGA
64 TAGG-TATAAAAGAATAATGCATATGAGTGCATTATTGGCATGAAAGGATGGCATAGCTGA
1434736 AATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTAT
1434756 CGACATAAAA
Statistics
Matches: 128, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
123 45 0.35
124 82 0.64
125 1 0.01
ACGTcount: A:0.33, C:0.10, G:0.27, T:0.30
Consensus pattern (123 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAACTGAAATGCATAGGGTGCATTATA
GGTATAAAAGAATAATGCATATGAGTGCATTATTGGCATGAAAGGATGGCATAGCTGA
Found at i:1443437 original size:40 final size:40
Alignment explanation
Indices: 1443382--1443543 Score: 297
Period size: 40 Copynumber: 4.0 Consensus size: 40
1443372 TGTAGGTTTA
1443382 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
1443422 TAATACACTTCGGTGTATATGGTGTGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
1443462 TAATACACTTCGGTGTATATGGTGGGCACGGCCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
1443502 TAATACACTTCGATGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1443542 TA
1 TA
1443544 GCACCACGGT
Statistics
Matches: 117, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 117 1.00
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:1443748 original size:47 final size:46
Alignment explanation
Indices: 1443648--1443816 Score: 184
Period size: 47 Copynumber: 3.7 Consensus size: 46
1443638 ATAAGCTTAC
* * * *
1443648 AAATAAGCTTACAAGCTT-TTGGAAT-AATGGCAAGTATATGGGA-A
1 AAATAAGCTTACGAGCTTATGGGATTAAATGGCAAGTATAT-TGATA
* *
1443692 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATCTTGTATA
1 AAATAAGCTTACGAGCTTATGGGATTAAATGGCAAGTATATTG-ATA
* * * * *
1443739 AAATAAGCTTATGAGCTTATGGAATTTATATGGCAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGGA-TTAAATGGCAAGTATATTGATA
1443786 AAATAAGCTTACGAGCTTATGGGA-TAAATGG
1 AAATAAGCTTACGAGCTTATGGGATTAAATGG
1443817 TAAAAGATTT
Statistics
Matches: 105, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
44 17 0.16
45 12 0.11
46 13 0.12
47 47 0.45
48 16 0.15
ACGTcount: A:0.37, C:0.08, G:0.22, T:0.32
Consensus pattern (46 bp):
AAATAAGCTTACGAGCTTATGGGATTAAATGGCAAGTATATTGATA
Found at i:1443789 original size:94 final size:90
Alignment explanation
Indices: 1443648--1443819 Score: 254
Period size: 94 Copynumber: 1.9 Consensus size: 90
1443638 ATAAGCTTAC
*
1443648 AAATAAGCTTACAAGCTTTTGGAATAATGGCAAGTATATGGGAAAAATAAGCTTACGAGCTTATG
1 AAATAAGCTTACAAGCTTATGGAATAATGGCAAGTATATGGGAAAAATAAGCTTACGAGCTTATG
1443713 GGATTAAATGGTAAGTATCTTGTATA
66 GGA-TAAATGGTAAGTATCTTGTATA
** * * *
1443739 AAATAAGCTTATGAGCTTATGGAATTTATATGGCAAGTATTTTGGTAAAATAAGCTTACGAGCTT
1 AAATAAGCTTACAAGCTTATGGAA--TA-ATGGCAAGTATATGGGAAAAATAAGCTTACGAGCTT
1443804 ATGGGATAAATGGTAA
63 ATGGGATAAATGGTAA
1443820 AAGATTTTAT
Statistics
Matches: 72, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
91 21 0.29
93 12 0.17
94 39 0.54
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.32
Consensus pattern (90 bp):
AAATAAGCTTACAAGCTTATGGAATAATGGCAAGTATATGGGAAAAATAAGCTTACGAGCTTATG
GGATAAATGGTAAGTATCTTGTATA
Found at i:1446182 original size:257 final size:255
Alignment explanation
Indices: 1445705--1446388 Score: 867
Period size: 257 Copynumber: 2.7 Consensus size: 255
1445695 TTTTTTTTTT
* * ** *
1445705 GAAAATGATAAAGTGATTTCCAAAGTTTCTCATTTAATACTTCCAGAAAATGAAATTTTTAAAAA
1 GAAAATGAGAAAGAGATTTCCAAAGTTTCTCATTTAATA-TTTTAGAAAATGAAATTTTTGAAAA
* *
1445770 GTAAGAAAGCGATTTCCAAAATTTCTTACCGAGTAAATTATTTCCAAAATTTG-TAAGTCCTTCG
65 GTAAGAAAGCTATTTCCAAAATTTCTTACCCAGTAAATTATTTCCAAAA-TTGATAAGTCCTTCG
* ** *
1445834 GGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCGTTCTGGTCATCTGTAAGTCTTTCGAAC
129 GGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCTGGTCATCACTAAGTCTTTCCAAC
* * *
1445899 AAGGTGATAATTCCATCGGCCCATCCGTAAGACCTTCGGTTAGGATGTTTTCACATGAAGTTG
194 AAGATGATAAGTCCATCGGCCCATCCGTAAGACCTTCGGGTAGGATGTTTTCACATGAA-TTG
*
1445962 GAAAATGAGAAAGAGATTTCCAAAGTTTCGCATTTAATGATTTTAGAAAATGAAATTTTTGAAAA
1 GAAAATGAGAAAGAGATTTCCAAAGTTTCTCATTTAAT-ATTTTAGAAAATGAAATTTTTGAAAA
* ** * * *
1446027 GTAAGAAAGCTATTTCCAAAGTTTCTTACATAGTAAACTATTTCCCAAATTGATAAGTTCTTCGG
65 GTAAGAAAGCTATTTCCAAAATTTCTTACCCAGTAAATTATTTCCAAAATTGATAAGTCCTTCGG
* *
1446092 GCCATCAGTAATTCTTTCGAGCATGATGATTAAATCCTTC-GATTCATCACTCAA-T-TTTCCAA
130 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCTG-GTCATCACT-AAGTCTTTCCAA
* * * * *
1446154 GCAAGATGATAAGTCCTTTGGGCCATCCGTAAGACCTTTGGGTAGGATGTTTTCACATGAATTT
193 -CAAGATGATAAGTCCATCGGCCCATCCGTAAGACCTTCGGGTAGGATGTTTTCACATGAATTG
* * * * *
1446218 GAAATATAAGAAAGCGATTTCCAAAGTTTCTCATTTAGTATTTTCAGAAAATGAAAATTTCGAAA
1 GAAA-ATGAGAAAGAGATTTCCAAAGTTTCTCATTTAATATTTT-AGAAAATGAAATTTTTGAAA
* * * *
1446283 AGTAAGAAAG-TGATTTCCAAATTTTCTCACCCAATAAATTATTTCTAAAATT-AGTAAGTCCTT
64 AGTAAGAAAGCT-ATTTCCAAAATTTCTTACCCAGTAAATTATTTCCAAAATTGA-TAAGTCCTT
* * *
1446346 CGGGCCATGATTAAGTCTTTCGAGCATGATGATTAATTCCTTC
127 CGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTC
1446389 AAGGTATTTT
Statistics
Matches: 372, Mismatches: 46, Indels: 18
0.85 0.11 0.04
Matches are distributed among these distances:
256 23 0.06
257 346 0.93
258 3 0.01
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (255 bp):
GAAAATGAGAAAGAGATTTCCAAAGTTTCTCATTTAATATTTTAGAAAATGAAATTTTTGAAAAG
TAAGAAAGCTATTTCCAAAATTTCTTACCCAGTAAATTATTTCCAAAATTGATAAGTCCTTCGGG
CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCTGGTCATCACTAAGTCTTTCCAACAA
GATGATAAGTCCATCGGCCCATCCGTAAGACCTTCGGGTAGGATGTTTTCACATGAATTG
Found at i:1446375 original size:19 final size:20
Alignment explanation
Indices: 1446337--1446375 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1446327 CTAAAATTAG
*
1446337 TAAGTCCTTCGGGCCATGAT
1 TAAGTCCTTCGAGCCATGAT
*
1446357 TAAGTCTTTCGAG-CATGAT
1 TAAGTCCTTCGAGCCATGAT
1446376 GATTAATTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (20 bp):
TAAGTCCTTCGAGCCATGAT
Found at i:1450971 original size:15 final size:15
Alignment explanation
Indices: 1450951--1450987 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
1450941 CTCCCTTTAT
1450951 ACCAAGGTGATCCGA
1 ACCAAGGTGATCCGA
*
1450966 ACCAAGGTGATCTGA
1 ACCAAGGTGATCCGA
1450981 ACCAAGG
1 ACCAAGG
1450988 GGCTCACAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.35, C:0.24, G:0.27, T:0.14
Consensus pattern (15 bp):
ACCAAGGTGATCCGA
Found at i:1459279 original size:136 final size:137
Alignment explanation
Indices: 1459011--1459283 Score: 372
Period size: 136 Copynumber: 2.0 Consensus size: 137
1459001 ACCTTTGGGT
**
1459011 CAATACCTTAGAATCAGTAATGCCTCGCTTGAGGGTTTGACATATCTAATAAAGAGTTCATAATG
1 CAATACCTTAGAATCAGTAATGCCTCGCTTGAGGGACTGACATATCTAATAAAGAGTTCATAATG
* * *
1459076 AGAAGAACTCATACGACAGGGAGAGAAGAAATTCATAATAAGAATAACTTATTCAACCTGTTACT
66 AGAAGAACACATACGACAGGGAGAGAAGAAATTCATAATAAGAAGAACTTATTCAACCTATTACT
1459141 CGATTCA
131 CGATTCA
* * * *
1459148 CAATA-CTTTGAATCAGTAATGCCTCGCTTTAGGGACTGACATTTCTAATAGAGAGTTCATAATG
1 CAATACCTTAGAATCAGTAATGCCTCGCTTGAGGGACTGACATATCTAATAAAGAGTTCATAATG
* * * * * *
1459212 AGAAGAACACATCCGACAGAGG-GAGAATAAGTTCATAATGAGAAGAACTTGTTCGAA-CTATTG
66 AGAAGAACACATACGACAG-GGAGAGAAGAAATTCATAATAAGAAGAACTTATTC-AACCTATTA
1459275 CTCGATTCA
129 CTCGATTCA
1459284 AGGTATTTCA
Statistics
Matches: 119, Mismatches: 15, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
136 110 0.92
137 9 0.08
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (137 bp):
CAATACCTTAGAATCAGTAATGCCTCGCTTGAGGGACTGACATATCTAATAAAGAGTTCATAATG
AGAAGAACACATACGACAGGGAGAGAAGAAATTCATAATAAGAAGAACTTATTCAACCTATTACT
CGATTCA
Found at i:1459326 original size:136 final size:136
Alignment explanation
Indices: 1459011--1459328 Score: 333
Period size: 136 Copynumber: 2.3 Consensus size: 136
1459001 ACCTTTGGGT
* * * ** * *
1459011 CAATACCTTAGAATCAGTAATGCCTCGCTTGAGGGTTTGACATATCTAATAAAGAGTTCATAATG
1 CAATACTTTA-AATCAGCAATGCCTCGCTTTAGGGACTAACATTTCTAATAAAGAGTTCATAATG
* * *
1459076 AGAAGAACTCATACGACAGGGAGAGAAGAAATTCATAATAAGAATAACTTATTCAACCTGTTACT
65 AGAAGAACACATACGACAGGGAGAGAAGAAATTCATAATAAGAAGAACTTATTCAACCTATTACT
1459141 CGATTCA
130 CGATTCA
* * * *
1459148 CAATACTTTGAATCAGTAATGCCTCGCTTTAGGGACTGACATTTCTAATAGAGAGTTCATAATGA
1 CAATACTTTAAATCAGCAATGCCTCGCTTTAGGGACTAACATTTCTAATAAAGAGTTCATAATGA
* * * * * *
1459213 GAAGAACACATCCGACAGAGG-GAGAATAAGTTCATAATGAGAAGAACTTGTTCGAA-CTATTGC
66 GAAGAACACATACGACAG-GGAGAGAAGAAATTCATAATAAGAAGAACTTATTC-AACCTATTAC
1459276 TCGATTCA
129 TCGATTCA
* *
1459284 -AGGTA-TTTCAAATCAGCAATGCCTTG-TTTAAGGGA-TCAACATTTC
1 CA-ATACTTT-AAATCAGCAATGCCTCGCTTT-AGGGACT-AACATTTC
1459329 CAGTAGAAAG
Statistics
Matches: 154, Mismatches: 21, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
135 8 0.05
136 134 0.87
137 12 0.08
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (136 bp):
CAATACTTTAAATCAGCAATGCCTCGCTTTAGGGACTAACATTTCTAATAAAGAGTTCATAATGA
GAAGAACACATACGACAGGGAGAGAAGAAATTCATAATAAGAAGAACTTATTCAACCTATTACTC
GATTCA
Found at i:1460981 original size:20 final size:21
Alignment explanation
Indices: 1460958--1460996 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1460948 TGTACTTGTA
1460958 TTTAAGTT-TATTTTATTTAT
1 TTTAAGTTGTATTTTATTTAT
* *
1460978 TTTATGTTGTTTTTTATTT
1 TTTAAGTTGTATTTTATTT
1460997 TTATTATTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.18, C:0.00, G:0.08, T:0.74
Consensus pattern (21 bp):
TTTAAGTTGTATTTTATTTAT
Found at i:1461013 original size:21 final size:22
Alignment explanation
Indices: 1460965--1461014 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
1460955 GTATTTAAGT
*
1460965 TTATTTTATTTATTTTATGTTG
1 TTATTTTATTTATTTTATGTTC
1460987 TT-TTTTATTT-TTATTAT-TTC
1 TTATTTTATTTATT-TTATGTTC
1461007 TTATTTTA
1 TTATTTTA
1461015 ATTAGGTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 6 0.24
21 17 0.68
22 2 0.08
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.76
Consensus pattern (22 bp):
TTATTTTATTTATTTTATGTTC
Found at i:1462128 original size:43 final size:42
Alignment explanation
Indices: 1462058--1462168 Score: 141
Period size: 42 Copynumber: 2.6 Consensus size: 42
1462048 CAAAAACGAT
* * * **
1462058 AAAGTCTTATCCTTGCACATAGCAAAAGAGTCTGGGGAAACTA
1 AAAGGCTTATCCTTGCACACAGTAAAAGAACCT-GGGAAACTA
*
1462101 AAAGGCTTATCCTTGCACACAGTAAAAGAACCTGGGAAACTG
1 AAAGGCTTATCCTTGCACACAGTAAAAGAACCTGGGAAACTA
* *
1462143 TAAGGCTTACCCTTGCACACAGTAAA
1 AAAGGCTTATCCTTGCACACAGTAAA
1462169 GGGGAAACTG
Statistics
Matches: 60, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
42 32 0.53
43 28 0.47
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (42 bp):
AAAGGCTTATCCTTGCACACAGTAAAAGAACCTGGGAAACTA
Found at i:1462181 original size:36 final size:37
Alignment explanation
Indices: 1462091--1462198 Score: 137
Period size: 36 Copynumber: 2.8 Consensus size: 37
1462081 AAAAGAGTCT
** *
1462091 GGGGAAACTAAAAGGCTTATCCTTGCACACAGTAAAA
1 GGGGAAACTGTAAGGCTTACCCTTGCACACAGTAAAA
1462128 GAACCTGGGAAACTGTAAGGCTTACCCTTGCACACAGT-AAA
1 G-----GGGAAACTGTAAGGCTTACCCTTGCACACAGTAAAA
1462169 GGGGAAACTGTAAGGCTTACCCTTGCACAC
1 GGGGAAACTGTAAGGCTTACCCTTGCACAC
1462199 GACAAAGGGA
Statistics
Matches: 63, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
36 29 0.46
37 1 0.02
41 4 0.06
42 29 0.46
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.19
Consensus pattern (37 bp):
GGGGAAACTGTAAGGCTTACCCTTGCACACAGTAAAA
Found at i:1462206 original size:36 final size:36
Alignment explanation
Indices: 1462134--1462383 Score: 124
Period size: 44 Copynumber: 6.1 Consensus size: 36
1462124 AAAAGAACCT
*
1462134 GGGAAACTGTAAGGCTTACCCTTGCACACAGTAAAG
1 GGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAG
1462170 GGGAAACTGTAAGGCTTACCCTTGCACAC-GACAAAGGGACCTG
1 GGGAAACTGTAAGGCTTACCCTTGCACACAG-C-AA---A---G
* * *
1462213 GGGTAAACTGTAAGGCTTACTCTTGCACAAAACAAAGGGGCCTGG
1 GGG-AAACTGTAAGGCTTACCCTTGCACACAGCAAA--------G
* *
1462258 GGGAAACTGTAAGGCTTACCCTTGTACATAGCAAAGGGACCTGG
1 GGGAAACTGTAAGGCTTACCCTTGCACACAGC-AA---A----G
*
1462302 GGGAAATTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGG
1 GGGAAACTGTAAGGCTTACCCTTGCACACAGC-AA---A----G
*
1462346 GGGAAACTGTAAGGCTTACCCTTGCACACAACAAAG
1 GGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAG
1462382 GG
1 GG
1462384 ACCTGGGGGA
Statistics
Matches: 180, Mismatches: 15, Indels: 38
0.77 0.06 0.16
Matches are distributed among these distances:
35 1 0.01
36 32 0.18
37 2 0.01
40 3 0.02
43 8 0.04
44 126 0.70
45 7 0.04
48 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.28, T:0.18
Consensus pattern (36 bp):
GGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAG
Found at i:1462238 original size:44 final size:44
Alignment explanation
Indices: 1462169--1462400 Score: 367
Period size: 44 Copynumber: 5.3 Consensus size: 44
1462159 ACACAGTAAA
*
1462169 GGGGAAACTGTAAGGCTTACCCTTGCACACGACAAAGGGACCTG
1 GGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTG
* * * *
1462213 GGGTAAACTGTAAGGCTTACTCTTGCACAAAACAAAGGGGCCTG
1 GGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTG
* * *
1462257 GGGGAAACTGTAAGGCTTACCCTTGTACATAGCAAAGGGACCTG
1 GGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTG
* *
1462301 GGGGAAATTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTG
1 GGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTG
1462345 GGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTG
1 GGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTG
1462389 GGGG-AACTGTAA
1 GGGGAAACTGTAA
1462401 CGGTAATTAA
Statistics
Matches: 172, Mismatches: 16, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
43 8 0.05
44 164 0.95
ACGTcount: A:0.31, C:0.22, G:0.29, T:0.18
Consensus pattern (44 bp):
GGGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTG
Found at i:1465296 original size:18 final size:18
Alignment explanation
Indices: 1465272--1465342 Score: 108
Period size: 18 Copynumber: 3.9 Consensus size: 18
1465262 CCGGTCAACG
1465272 GTCAACGGGTCAGGTCG-
1 GTCAACGGGTCAGGTCGA
*
1465289 GATCAACGGGTCAGGTCAA
1 G-TCAACGGGTCAGGTCGA
1465308 GTCAACGGGTCAGGTCGA
1 GTCAACGGGTCAGGTCGA
*
1465326 GTCAACGGGTCGGGTCG
1 GTCAACGGGTCAGGTCG
1465343 GGTTGTAACC
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
17 1 0.02
18 47 0.96
19 1 0.02
ACGTcount: A:0.21, C:0.23, G:0.39, T:0.17
Consensus pattern (18 bp):
GTCAACGGGTCAGGTCGA
Found at i:1476352 original size:2 final size:2
Alignment explanation
Indices: 1476345--1476369 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1476335 AGTTGGAACC
1476345 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
1476370 TTCTCATCAA
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:1476831 original size:21 final size:21
Alignment explanation
Indices: 1476801--1476858 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 21
1476791 ATAACGTATC
*
1476801 AAAAAT-AAAAATACTTTTATT
1 AAAAATAAAAAATA-TTATATT
1476822 -AAAATAAAAAAATATTATATT
1 AAAAAT-AAAAAATATTATATT
1476843 AAAAATAAAATAATAT
1 AAAAATAAAA-AATAT
1476859 GGGAAGACTT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
20 5 0.16
21 10 0.31
22 17 0.53
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAAATAAAAAATATTATATT
Found at i:1476835 original size:22 final size:22
Alignment explanation
Indices: 1476807--1476858 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
1476797 TATCAAAAAT
*
1476807 AAAAATACTTTTATT-AAAATAA
1 AAAAATA-TTATATTAAAAATAA
1476829 AAAAATATTATATTAAAAATAA
1 AAAAATATTATATTAAAAATAA
*
1476851 AATAATAT
1 AAAAATAT
1476859 GGGAAGACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 6 0.22
22 21 0.78
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (22 bp):
AAAAATATTATATTAAAAATAA
Found at i:1477687 original size:28 final size:28
Alignment explanation
Indices: 1477655--1477708 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
1477645 CGTATTCTTT
1477655 ATGGTACACATTGATAGTTGGTAAATGC
1 ATGGTACACATTGATAGTTGGTAAATGC
1477683 ATGGTACACATTGATAGTTGGTAAAT
1 ATGGTACACATTGATAGTTGGTAAAT
1477709 ACATCAATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.33, C:0.09, G:0.24, T:0.33
Consensus pattern (28 bp):
ATGGTACACATTGATAGTTGGTAAATGC
Found at i:1482294 original size:19 final size:18
Alignment explanation
Indices: 1482244--1482304 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 18
1482234 AACCGAGTCA
*
1482244 ACCTAACCCTTTGACTTTG
1 ACCTAA-CCGTTGACTTTG
* *
1482263 ACATGACCTGTTGACTTTG
1 ACCTAACC-GTTGACTTTG
*
1482282 ACCTAAGCCGTTGAATTTG
1 ACCTAA-CCGTTGACTTTG
1482301 ACCT
1 ACCT
1482305 GACCATTAAC
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
18 2 0.06
19 30 0.88
20 2 0.06
ACGTcount: A:0.23, C:0.26, G:0.16, T:0.34
Consensus pattern (18 bp):
ACCTAACCGTTGACTTTG
Found at i:1483931 original size:35 final size:35
Alignment explanation
Indices: 1483892--1483958 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
1483882 TGGATTATGG
1483892 AGGTTCAG-CTGGATCAAACTGGTAATTCCTTATAT
1 AGGTTCAGACT-GATCAAACTGGTAATTCCTTATAT
* *
1483927 AGGTTCAGACTGATCGAGCTGGTAATTCCTTA
1 AGGTTCAGACTGATCAAACTGGTAATTCCTTA
1483959 CGGACCTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 27 0.93
36 2 0.07
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (35 bp):
AGGTTCAGACTGATCAAACTGGTAATTCCTTATAT
Found at i:1498421 original size:13 final size:13
Alignment explanation
Indices: 1498403--1498427 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1498393 CATAGTTGAA
1498403 CAGTCTTCATATG
1 CAGTCTTCATATG
1498416 CAGTCTTCATAT
1 CAGTCTTCATAT
1498428 ACGCATCTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.40
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:1500432 original size:69 final size:69
Alignment explanation
Indices: 1500321--1500459 Score: 260
Period size: 69 Copynumber: 2.0 Consensus size: 69
1500311 TAAGACCTTG
*
1500321 AATTATTTTTATAACATCTAGAACCATATAAAATTTTCTTGGTGTAAGTCCTGTAGCTGAATCAA
1 AATTATGTTTATAACATCTAGAACCATATAAAATTTTCTTGGTGTAAGTCCTGTAGCTGAATCAA
1500386 AGTA
66 AGTA
*
1500390 AATTATGTTTATAACATCTAGAACCATATAAATTTTTCTTGGTGTAAGTCCTGTAGCTGAATCAA
1 AATTATGTTTATAACATCTAGAACCATATAAAATTTTCTTGGTGTAAGTCCTGTAGCTGAATCAA
1500455 AGTA
66 AGTA
1500459 A
1 A
1500460 GAAACTATGT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (69 bp):
AATTATGTTTATAACATCTAGAACCATATAAAATTTTCTTGGTGTAAGTCCTGTAGCTGAATCAA
AGTA
Found at i:1504962 original size:54 final size:53
Alignment explanation
Indices: 1504884--1505125 Score: 272
Period size: 54 Copynumber: 4.5 Consensus size: 53
1504874 AGCATATGTT
* * * * * *
1504884 ACGATCGTATATGCAATAACTGTGCAACCCATGAAATTTATCATATGCTGATGA
1 ACGACCGTATAGGCACTAAGTGTGCAACCCA-GAAATTCATCATATGTTGATGA
* * * *
1504938 ATGACCGTATAGGCACTAAATGTGCAACCCACATAATTCATCATATGTTGACGA
1 ACGACCGTATAGGCACTAAGTGTGCAACCCAGA-AATTCATCATATGTTGATGA
* *
1504992 ATGACCGTATAGGCTCTAAGTGTGCAACACACAG-AATTCATCATATGTTGATGA
1 ACGACCGTATAGGCACTAAGTGTGCAAC-C-CAGAAATTCATCATATGTTGATGA
* * *
1505046 ACGACCGTATAAGCACTAAGTGTGCAACCCACAAAATTAATCATATGTTGATGA
1 ACGACCGTATAGGCACTAAGTGTGCAACCCA-GAAATTCATCATATGTTGATGA
*
1505100 ACGACCGTATCA-GCACTACGTGTGCA
1 ACGACCGTAT-AGGCACTAAGTGTGCA
1505126 TCTCAAAAAA
Statistics
Matches: 163, Mismatches: 19, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
52 2 0.01
53 2 0.01
54 155 0.95
55 2 0.01
56 2 0.01
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (53 bp):
ACGACCGTATAGGCACTAAGTGTGCAACCCAGAAATTCATCATATGTTGATGA
Found at i:1505123 original size:108 final size:108
Alignment explanation
Indices: 1504884--1505125 Score: 301
Period size: 108 Copynumber: 2.2 Consensus size: 108
1504874 AGCATATGTT
* * * * * *
1504884 ACGATCGTATATGCAATAACTGTGCAAC-C-CATGAAATTTATCATATGCTGATGAATGACCGTA
1 ACGACCGTATAGGCACTAAGTGTGCAACACACA-G-AATTCATCATATGCTGATGAACGACCGTA
* * *
1504947 TAGGCACTAAATGTGCAACCCACATAATTCATCATATGTTGACGA
64 TAAGCACTAAATGTGCAACCCACAAAATTAATCATATGTTGACGA
* * *
1504992 ATGACCGTATAGGCTCTAAGTGTGCAACACACAGAATTCATCATATGTTGATGAACGACCGTATA
1 ACGACCGTATAGGCACTAAGTGTGCAACACACAGAATTCATCATATGCTGATGAACGACCGTATA
* *
1505057 AGCACTAAGTGTGCAACCCACAAAATTAATCATATGTTGATGA
66 AGCACTAAATGTGCAACCCACAAAATTAATCATATGTTGACGA
*
1505100 ACGACCGTATCA-GCACTACGTGTGCA
1 ACGACCGTAT-AGGCACTAAGTGTGCA
1505126 TCTCAAAAAA
Statistics
Matches: 114, Mismatches: 17, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
108 109 0.96
109 3 0.03
110 2 0.02
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (108 bp):
ACGACCGTATAGGCACTAAGTGTGCAACACACAGAATTCATCATATGCTGATGAACGACCGTATA
AGCACTAAATGTGCAACCCACAAAATTAATCATATGTTGACGA
Found at i:1508146 original size:30 final size:29
Alignment explanation
Indices: 1508112--1508305 Score: 223
Period size: 29 Copynumber: 6.7 Consensus size: 29
1508102 ACCCGATCCG
1508112 GTGACATTTTGGGAATTTTTTTGAAAAAAT
1 GTGACATTTTGGGAATTTTTTTG-AAAAAT
* * *
1508142 GTGACATTCTGGGATTTTTTTTTGAAAAAG
1 GTGACATTTTGGGA-ATTTTTTTGAAAAAT
*
1508172 GTAACATTTTGGGAATTTTTTTGAAAAAT
1 GTGACATTTTGGGAATTTTTTTGAAAAAT
* * *
1508201 GTAACATTCTGGGAATTATTTTGAAAAA-
1 GTGACATTTTGGGAATTTTTTTGAAAAAT
*
1508229 GATGACATTTTGGGAATTATTTTGAAAAA-
1 G-TGACATTTTGGGAATTTTTTTGAAAAAT
* *
1508258 GATG-CATTCTGGGAATTATTTTGAAAAAT
1 G-TGACATTTTGGGAATTTTTTTGAAAAAT
**
1508287 GTGACATTTCCGGAATTTT
1 GTGACATTTTGGGAATTTT
1508306 CGGATGTGGA
Statistics
Matches: 144, Mismatches: 16, Indels: 9
0.85 0.09 0.05
Matches are distributed among these distances:
28 26 0.18
29 80 0.56
30 30 0.21
31 8 0.06
ACGTcount: A:0.33, C:0.06, G:0.20, T:0.41
Consensus pattern (29 bp):
GTGACATTTTGGGAATTTTTTTGAAAAAT
Found at i:1508292 original size:57 final size:56
Alignment explanation
Indices: 1508112--1508305 Score: 230
Period size: 57 Copynumber: 3.3 Consensus size: 56
1508102 ACCCGATCCG
* *
1508112 GTGACATTTTGGGAATTTTTTTGAAAAA-ATGTGACATTCTGGGATTTTTTTTTGAAAAA
1 GTGACATTTTGGGAATTTTTTTGAAAAAGA--TG-CATTCTGGGA-ATTATTTTGAAAAA
* *
1508171 GGTAACATTTTGGGAATTTTTTTGAAAAATG-TAACATTCTGGGAATTATTTTGAAAAA
1 -GTGACATTTTGGGAATTTTTTTGAAAAA-GAT-GCATTCTGGGAATTATTTTGAAAAA
*
1508229 GATGACATTTTGGGAATTATTTTGAAAAAGATGCATTCTGGGAATTATTTTGAAAAA
1 G-TGACATTTTGGGAATTTTTTTGAAAAAGATGCATTCTGGGAATTATTTTGAAAAA
**
1508286 TGTGACATTTCCGGAATTTT
1 -GTGACATTTTGGGAATTTT
1508306 CGGATGTGGA
Statistics
Matches: 118, Mismatches: 10, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
57 41 0.35
58 39 0.33
59 11 0.09
60 27 0.23
ACGTcount: A:0.33, C:0.06, G:0.20, T:0.41
Consensus pattern (56 bp):
GTGACATTTTGGGAATTTTTTTGAAAAAGATGCATTCTGGGAATTATTTTGAAAAA
Found at i:1509296 original size:26 final size:26
Alignment explanation
Indices: 1509243--1509298 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
1509233 AAGGTAATTC
* * *
1509243 TTTTATGGGATTTACTGTAGTATAAT
1 TTTTATGAGATTTACTGGACTATAAT
*
1509269 TTTTATGAGATTTACTGGACTATGAT
1 TTTTATGAGATTTACTGGACTATAAT
1509295 TTTT
1 TTTT
1509299 TTAGTGTACC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.25, C:0.05, G:0.18, T:0.52
Consensus pattern (26 bp):
TTTTATGAGATTTACTGGACTATAAT
Found at i:1515575 original size:29 final size:29
Alignment explanation
Indices: 1515497--1515628 Score: 185
Period size: 29 Copynumber: 4.6 Consensus size: 29
1515487 CCCGACCCGA
*
1515497 TGACATTTTGGGAATTATTTTGAAAAAAGA
1 TGACATTTTGGGAATTATTTTG-AAAAAGG
* *
1515527 TTACATTTTGGGAATT-TTTTGATAAAGG
1 TGACATTTTGGGAATTATTTTGAAAAAGG
*
1515555 TGACATTTCGGGAATTATTTTGAAAAAGG
1 TGACATTTTGGGAATTATTTTGAAAAAGG
* * *
1515584 TAACATTCTGGGAATTATTTTGAAAATGG
1 TGACATTTTGGGAATTATTTTGAAAAAGG
1515613 TGACATTTTGGGAATT
1 TGACATTTTGGGAATT
1515629 TTTGAATGTA
Statistics
Matches: 89, Mismatches: 12, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
28 19 0.21
29 55 0.62
30 15 0.17
ACGTcount: A:0.33, C:0.05, G:0.22, T:0.39
Consensus pattern (29 bp):
TGACATTTTGGGAATTATTTTGAAAAAGG
Found at i:1520990 original size:54 final size:54
Alignment explanation
Indices: 1520915--1521134 Score: 320
Period size: 54 Copynumber: 4.1 Consensus size: 54
1520905 AGAATATGTT
* *
1520915 ACGACCGTAAAGGAACCAAGTGTGCAACCCACGAAATTCATCATATGTTGATGA
1 ACGACCGTATAGGAACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGA
*
1520969 ACGACCGTATAGGCACTAAGTGTGCAACCCACCG-AATTCATCATATGTTGATGA
1 ACGACCGTATAGGAACTAAGTGTGCAACCCA-CGAAATTCATCATATGTTGATGA
* *
1521023 ACGACCGTATAGGAACTAAGTGTGCAACCGCA--AAATTCATTATATGCTGATGA
1 ACGACCGTATAGGAACTAAGTGTGCAACC-CACGAAATTCATCATATGTTGATGA
* * * *
1521076 ACAACCGTATAGGCACTAAGTGTGCAACCCCCGTAATTCATCATATGTTGATGA
1 ACGACCGTATAGGAACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGA
1521130 ACGAC
1 ACGAC
1521135 TATATCGATA
Statistics
Matches: 148, Mismatches: 13, Indels: 10
0.87 0.08 0.06
Matches are distributed among these distances:
52 1 0.01
53 45 0.30
54 98 0.66
55 4 0.03
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (54 bp):
ACGACCGTATAGGAACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGA
Found at i:1521102 original size:107 final size:107
Alignment explanation
Indices: 1520915--1521134 Score: 354
Period size: 107 Copynumber: 2.0 Consensus size: 107
1520905 AGAATATGTT
* *
1520915 ACGACCGTAAAGGAACCAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCGTATA
1 ACGACCGTAAAGGAACCAAGTGTGCAACCCAC-AAATTCATCATATGCTGATGAACAACCGTATA
1520980 GGCACTAAGTGTGCAACCCACCG-AATTCATCATATGTTGATGA
65 GGCACTAAGTGTGCAACCC-CCGTAATTCATCATATGTTGATGA
* * *
1521023 ACGACCGTATAGGAACTAAGTGTGCAACCGCA-AAATTCATTATATGCTGATGAACAACCGTATA
1 ACGACCGTAAAGGAACCAAGTGTGCAACC-CACAAATTCATCATATGCTGATGAACAACCGTATA
1521087 GGCACTAAGTGTGCAACCCCCGTAATTCATCATATGTTGATGA
65 GGCACTAAGTGTGCAACCCCCGTAATTCATCATATGTTGATGA
1521130 ACGAC
1 ACGAC
1521135 TATATCGATA
Statistics
Matches: 105, Mismatches: 5, Indels: 5
0.91 0.04 0.04
Matches are distributed among these distances:
106 3 0.03
107 73 0.70
108 27 0.26
109 2 0.02
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (107 bp):
ACGACCGTAAAGGAACCAAGTGTGCAACCCACAAATTCATCATATGCTGATGAACAACCGTATAG
GCACTAAGTGTGCAACCCCCGTAATTCATCATATGTTGATGA
Found at i:1527255 original size:20 final size:20
Alignment explanation
Indices: 1527230--1527280 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
1527220 TACTCATACG
1527230 GGTATCGATACAATGAAGAA
1 GGTATCGATACAATGAAGAA
1527250 GGTATCGATACAATGAAGAA
1 GGTATCGATACAATGAAGAA
1527270 GGTATCGATAC
1 GGTATCGATAC
1527281 CATGGTTTCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.41, C:0.12, G:0.25, T:0.22
Consensus pattern (20 bp):
GGTATCGATACAATGAAGAA
Found at i:1527698 original size:54 final size:54
Alignment explanation
Indices: 1527631--1528046 Score: 465
Period size: 54 Copynumber: 7.7 Consensus size: 54
1527621 CATATGGAAT
* * *
1527631 GACCGTATAGGCACTAAGTGTACAACACAAAAAATTCATCATATATTGATGAAC
1 GACCGTATAGGCACTAAGTGTGCAACCCAAAAAATTCATCATATGTTGATGAAC
* *
1527685 GACCGTATAGGCACTTAGTGTGCAA-CCAACAAAATTCATCATATGTTAATGAAC
1 GACCGTATAGGCACTAAGTGTGCAACCCAA-AAAATTCATCATATGTTGATGAAC
* * * *
1527739 GACTGTATAGGCACTAAGTGTACAACCCACAAAATTCATCATGTGTTGATGAAC
1 GACCGTATAGGCACTAAGTGTGCAACCCAAAAAATTCATCATATGTTGATGAAC
* ** * **
1527793 AATTGTATAGGCACTGAGTGTGCAACCCACGAAATTCATCATATGTTGATGAAC
1 GACCGTATAGGCACTAAGTGTGCAACCCAAAAAATTCATCATATGTTGATGAAC
* * *** *
1527847 GACCGTATAGGCAATAAGGGTGCAACCCATGGAATTCATCATATGTTAATGAAC
1 GACCGTATAGGCACTAAGTGTGCAACCCAAAAAATTCATCATATGTTGATGAAC
* * * * * * *
1527901 AACAGGATATGCACTAAGTGTCCAACCCATAAAATTCATCATATGTTGATGAAA
1 GACCGTATAGGCACTAAGTGTGCAACCCAAAAAATTCATCATATGTTGATGAAC
* * * * *
1527955 GACCATATGGGCACTAAGTGTGCAACCCAAGAAATTCGTCATATGTTTATGAAC
1 GACCGTATAGGCACTAAGTGTGCAACCCAAAAAATTCATCATATGTTGATGAAC
* * * * *
1528009 GACCGTATCGACACTACGTGTGCATCTCAAAGAAATTC
1 GACCGTATAGGCACTAAGTGTGCAACCCAAA-AAATTC
1528047 TAATGATTTG
Statistics
Matches: 303, Mismatches: 56, Indels: 5
0.83 0.15 0.01
Matches are distributed among these distances:
53 3 0.01
54 291 0.96
55 9 0.03
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.25
Consensus pattern (54 bp):
GACCGTATAGGCACTAAGTGTGCAACCCAAAAAATTCATCATATGTTGATGAAC
Found at i:1527917 original size:162 final size:162
Alignment explanation
Indices: 1527631--1528016 Score: 522
Period size: 162 Copynumber: 2.4 Consensus size: 162
1527621 CATATGGAAT
* * * *
1527631 GACCGTATAGGCACTAAGTGTACAACACAAAAAATTCATCATATATTGATGAACGACCGTATAGG
1 GACCGTATAGGCACTAAGTGTGCAACCCAAGAAATTCATCATATGTTGATGAACGACCGTATAGG
* * * * * *
1527696 CACTTAGTGTGCAACCAACAAAATTCATCATATGTTAATGAACGACTGTATAGGCACTAAGTGTA
66 CAATAAGGGTGCAACCAACAAAATTCATCATATGTTAATGAACAACAGGATAGGCACTAAGTGTA
*
1527761 CAACCCACAAAATTCATCATGTGTTGATGAACA
131 CAACCCACAAAATTCATCATATGTTGATGAA-A
** * *
1527794 -ATTGTATAGGCACTGAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCGTATAGG
1 GACCGTATAGGCACTAAGTGTGCAACCCAAGAAATTCATCATATGTTGATGAACGACCGTATAGG
* *** * *
1527858 CAATAAGGGTGCAACCCATGGAATTCATCATATGTTAATGAACAACAGGATATGCACTAAGTGTC
66 CAATAAGGGTGCAACCAACAAAATTCATCATATGTTAATGAACAACAGGATAGGCACTAAGTGTA
*
1527923 CAACCCATAAAATTCATCATATGTTGATGAAA
131 CAACCCACAAAATTCATCATATGTTGATGAAA
* * * *
1527955 GACCATATGGGCACTAAGTGTGCAACCCAAGAAATTCGTCATATGTTTATGAACGACCGTAT
1 GACCGTATAGGCACTAAGTGTGCAACCCAAGAAATTCATCATATGTTGATGAACGACCGTAT
1528017 CGACACTACG
Statistics
Matches: 192, Mismatches: 30, Indels: 3
0.85 0.13 0.01
Matches are distributed among these distances:
161 1 0.01
162 191 0.99
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (162 bp):
GACCGTATAGGCACTAAGTGTGCAACCCAAGAAATTCATCATATGTTGATGAACGACCGTATAGG
CAATAAGGGTGCAACCAACAAAATTCATCATATGTTAATGAACAACAGGATAGGCACTAAGTGTA
CAACCCACAAAATTCATCATATGTTGATGAAA
Found at i:1537329 original size:16 final size:16
Alignment explanation
Indices: 1537308--1537347 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
1537298 ACGGGTTATC
1537308 AGGATACAACCAAATT
1 AGGATACAACCAAATT
1537324 AGGATACAACCAAATT
1 AGGATACAACCAAATT
*
1537340 AAGATACA
1 AGGATACA
1537348 TCCAGAAGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.53, C:0.17, G:0.12, T:0.17
Consensus pattern (16 bp):
AGGATACAACCAAATT
Found at i:1540398 original size:11 final size:11
Alignment explanation
Indices: 1540382--1540408 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1540372 ATTTGGGAGA
1540382 CACAAACAGCT
1 CACAAACAGCT
1540393 CACAAACAGCT
1 CACAAACAGCT
1540404 CACAA
1 CACAA
1540409 GAATCTGGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.48, C:0.37, G:0.07, T:0.07
Consensus pattern (11 bp):
CACAAACAGCT
Found at i:1541150 original size:29 final size:30
Alignment explanation
Indices: 1541112--1541174 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 30
1541102 ATTCATCTTG
1541112 AAAAAAAAATTCCGAAAA-TAAAA-AAAAC
1 AAAAAAAAATTCCGAAAATTAAAAGAAAAC
* *
1541140 AAAAACAAAATTCTGAAAATTAAAAGAAAAG
1 AAAAA-AAAATTCCGAAAATTAAAAGAAAAC
1541171 AAAA
1 AAAA
1541175 GTTATGGTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 5 0.17
29 12 0.40
30 5 0.17
31 8 0.27
ACGTcount: A:0.73, C:0.08, G:0.06, T:0.13
Consensus pattern (30 bp):
AAAAAAAAATTCCGAAAATTAAAAGAAAAC
Found at i:1549259 original size:117 final size:116
Alignment explanation
Indices: 1549060--1549275 Score: 290
Period size: 117 Copynumber: 1.9 Consensus size: 116
1549050 CTTTTGAAAG
* *
1549060 CTAAAATAGACTTGGAAAATCAAAATGAAATGTTGAAAAAGGAGTTATAGCTTTCAAAAATGAAA
1 CTAAAATAGACTTGGAAAATCAAAATGAAATATTGAAAAAGGAGTTAGAGCTTTCAAAAATGAAA
*
1549125 TCTGAAAACTTTAAAAAAGAAATTTTCGAATTAAACAAACTTCTTCTAAAAA
66 TCTGAAAACTTTAAAAAAAAAATTTT-GAATTAAACAAACTTCTTCTAAAAA
* * * * * *
1549177 CTAAAATGGATTTTGAAAATCAAAATGAAATATTGAAGAAGTATTTAGAGCTTTCAAAAATGAAA
1 CTAAAATAGACTTGGAAAATCAAAATGAAATATTGAAAAAGGAGTTAGAGCTTTCAAAAATGAAA
* * * *
1549242 TTTG-AAAGTATTGAAAAAAAAATTTTGATTTAAA
66 TCTGAAAACT-TTAAAAAAAAAATTTTGAATTAAA
1549276 AGTTAGGCTT
Statistics
Matches: 85, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
116 11 0.13
117 74 0.87
ACGTcount: A:0.50, C:0.07, G:0.13, T:0.30
Consensus pattern (116 bp):
CTAAAATAGACTTGGAAAATCAAAATGAAATATTGAAAAAGGAGTTAGAGCTTTCAAAAATGAAA
TCTGAAAACTTTAAAAAAAAAATTTTGAATTAAACAAACTTCTTCTAAAAA
Found at i:1555301 original size:13 final size:13
Alignment explanation
Indices: 1555283--1555307 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1555273 ACCATTACAA
1555283 ATTGATTATGAAT
1 ATTGATTATGAAT
1555296 ATTGATTATGAA
1 ATTGATTATGAA
1555308 CTAATGGCTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (13 bp):
ATTGATTATGAAT
Found at i:1556993 original size:37 final size:36
Alignment explanation
Indices: 1556934--1557164 Score: 215
Period size: 37 Copynumber: 6.4 Consensus size: 36
1556924 AATAATATAG
* * * *
1556934 TATAGTTTTTTAATATATTTTTGAAAATATATAATA
1 TATAGGTTTTAAAAATATTTTTGAAAACATATAATA
*
1556970 TATAGCTTTTAAAAACTATTTTTGGAAAACATAT-A-A
1 TATAGGTTTTAAAAA-TATTTTT-GAAAACATATAATA
* * *
1557006 TAT-GGTTTTGAAAACACATTTTTGAAAACGTGTAATA
1 TATAGGTTTT-AAAA-ATATTTTTGAAAACATATAATA
*
1557043 TATA-GTTTT-TAAATATTTTTGAAAACATAT-ATAA
1 TATAGGTTTTAAAAATATTTTTGAAAACATATAAT-A
*
1557077 TATAGGTTTTGAAAAATTATTTTTG-AAACATATAATG
1 TATAGGTTTT-AAAAA-TATTTTTGAAAACATATAATA
* * *
1557114 TATAGTTTTTTTAAAATATTTTTGAAAACATATAGTA
1 TATAG-GTTTTAAAAATATTTTTGAAAACATATAATA
*
1557151 TATAGTTTTTAAAA
1 TATAGGTTTTAAAA
1557165 TGGGTTTTGT
Statistics
Matches: 161, Mismatches: 19, Indels: 30
0.77 0.09 0.14
Matches are distributed among these distances:
33 2 0.01
34 20 0.12
35 20 0.12
36 43 0.27
37 53 0.33
38 23 0.14
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.45
Consensus pattern (36 bp):
TATAGGTTTTAAAAATATTTTTGAAAACATATAATA
Found at i:1557134 original size:36 final size:36
Alignment explanation
Indices: 1556934--1557185 Score: 230
Period size: 36 Copynumber: 7.0 Consensus size: 36
1556924 AATAATATAG
* *
1556934 TATAGTTTTTTAATATATTTTTGAAAATATATAATA
1 TATAGTTTTTTAAAATATTTTTGAAAACATATAATA
* *
1556970 TATAGCTTTTAAAAACTATTTTTGGAAAACATAT-A-A
1 TATAGTTTTTTAAAA-TATTTTT-GAAAACATATAATA
* ** * * *
1557006 TATGGTTTTGAAAACACATTTTTGAAAACGTGTAATA
1 TATAGTTTTTTAAA-ATATTTTTGAAAACATATAATA
1557043 TATAG-TTTTT-AAATATTTTTGAAAACATAT-ATAA
1 TATAGTTTTTTAAAATATTTTTGAAAACATATAAT-A
** *
1557077 TATAGGTTTTGAAAAATTATTTTTG-AAACATATAATG
1 TATA-GTTTTTTAAAA-TATTTTTGAAAACATATAATA
*
1557114 TATAGTTTTTTTAAAATATTTTTGAAAACATATAGTA
1 TATAG-TTTTTTAAAATATTTTTGAAAACATATAATA
** *
1557151 TATAG-TTTTTAAAATGGGTTTTGTAAACATATAAT
1 TATAGTTTTTTAAAAT-ATTTTTGAAAACATATAAT
1557186 TTTTAAAAAA
Statistics
Matches: 175, Mismatches: 27, Indels: 28
0.76 0.12 0.12
Matches are distributed among these distances:
33 2 0.01
34 20 0.11
35 21 0.12
36 61 0.35
37 52 0.30
38 19 0.11
ACGTcount: A:0.41, C:0.04, G:0.10, T:0.45
Consensus pattern (36 bp):
TATAGTTTTTTAAAATATTTTTGAAAACATATAATA
Found at i:1557221 original size:32 final size:32
Alignment explanation
Indices: 1557150--1557241 Score: 91
Period size: 32 Copynumber: 2.9 Consensus size: 32
1557140 AACATATAGT
** *
1557150 ATATAGTTTTT--AAAATGGGTTTTG-TAAAC
1 ATATAGTTTTTAAAAAATGATTTTTGAAAAAC
*
1557179 ATATAATTTTTAAAAAATGATTTTTGAAAAAC
1 ATATAGTTTTTAAAAAATGATTTTTGAAAAAC
* *
1557211 ATATAGTTTTTGAAAACATGTTTTTTCGAAA
1 ATATAGTTTTT-AAAAAATGATTTTT-GAAA
1557242 GATATACATA
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
29 10 0.20
31 11 0.22
32 14 0.27
33 12 0.24
34 4 0.08
ACGTcount: A:0.40, C:0.04, G:0.12, T:0.43
Consensus pattern (32 bp):
ATATAGTTTTTAAAAAATGATTTTTGAAAAAC
Found at i:1557226 original size:17 final size:17
Alignment explanation
Indices: 1557169--1557229 Score: 58
Period size: 17 Copynumber: 3.7 Consensus size: 17
1557159 TTAAAATGGG
* *
1557169 TTTTGTAAACATATAAT
1 TTTTGAAAACATATAGT
1557186 TTTT-AAAA-A-AT-GAT
1 TTTTGAAAACATATAG-T
1557200 TTTTGAAAAACATATAGT
1 TTTTG-AAAACATATAGT
1557218 TTTTGAAAACAT
1 TTTTGAAAACAT
1557230 GTTTTTTCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
14 7 0.19
15 1 0.03
16 7 0.19
17 12 0.33
18 8 0.22
19 1 0.03
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.43
Consensus pattern (17 bp):
TTTTGAAAACATATAGT
Found at i:1557288 original size:18 final size:18
Alignment explanation
Indices: 1557265--1557328 Score: 64
Period size: 18 Copynumber: 3.6 Consensus size: 18
1557255 ATATTATTAG
1557265 TATTTTATTTTATGTT-TT
1 TATTTTATTTTAT-TTATT
*
1557283 TATTTTAATTTATTTATT
1 TATTTTATTTTATTTATT
1557301 TATTTT-TATTTA-TTATT
1 TATTTTAT-TTTATTTATT
1557318 CT-TTTTATTTT
1 -TATTTTATTTT
1557329 TCAGTCAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
17 14 0.35
18 26 0.65
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.77
Consensus pattern (18 bp):
TATTTTATTTTATTTATT
Found at i:1565506 original size:16 final size:16
Alignment explanation
Indices: 1565485--1565524 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
1565475 TTTATTTATA
1565485 TGTGTATAATCATAAT
1 TGTGTATAATCATAAT
1565501 TGTGTATAATCATAAT
1 TGTGTATAATCATAAT
1565517 TGTGTATA
1 TGTGTATA
1565525 CCCAAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (16 bp):
TGTGTATAATCATAAT
Done.