Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007979.1 Hibiscus syriacus cultivar Beakdansim tig00110418_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: 2767453
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 13
Found at i:1268127 original size:105 final size:105
Alignment explanation
Indices: 1267941--1269090 Score: 1842
Period size: 105 Copynumber: 11.0 Consensus size: 105
1267931 GCACTCGAGG
* * * *
1267941 CAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAG
*
1268006 AGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
1268047 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCCTGTCAACAACAAATTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* *
1268112 GCCAATTTCAACTTCACAATGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
1268152 CAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGCTGCTTGTCAACAACAACTTCTCAATTTC
1 CAACGCAAGTTCAACTTCACGACGAAGGGA-C-C-GCTGCTTGTCAACAACAACTTCTCAATTTC
1268217 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
63 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
1268260 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCATA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
1268325 GCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * *
1268365 CAACGCATGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
1268430 GCCAATTTCAACTTCACAACGAAGAATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
1268470 CAACGCAAGTTCAACTTCACGGCGAAGGGACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
1268535 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
1268575 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTTAACAACAACTTCTCAATTTCATA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
1268640 GCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
1268680 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
1268745 GCTAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * *
1268785 CAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTAAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
1268850 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
1268890 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
** *
1268950 TTCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * * * * ** *
1268990 CAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAG
* *
1269055 AGCCAATTTCAACTTCACGACGGAGGATATTGGACT
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACT
1269091 TGGAACAATG
Statistics
Matches: 974, Mismatches: 61, Indels: 18
0.92 0.06 0.02
Matches are distributed among these distances:
100 82 0.08
101 3 0.00
102 3 0.00
103 4 0.00
104 3 0.00
105 701 0.72
106 78 0.08
107 2 0.00
108 98 0.10
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.22
Consensus pattern (105 bp):
CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
Found at i:1269682 original size:34 final size:36
Alignment explanation
Indices: 1269638--1269739 Score: 172
Period size: 34 Copynumber: 2.9 Consensus size: 36
1269628 TTTCGTCCTA
1269638 CTAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
*
1269673 -TAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
1269708 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
1269740 GTTCTACTAT
Statistics
Matches: 62, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
34 30 0.48
35 3 0.05
37 29 0.47
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:1270341 original size:16 final size:18
Alignment explanation
Indices: 1270320--1270354 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
1270310 TTTACTCATT
1270320 TATTTAT-CTAT-TTTTA
1 TATTTATCCTATATTTTA
1270336 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
1270354 T
1 T
1270355 GTTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Found at i:1270914 original size:13 final size:13
Alignment explanation
Indices: 1270896--1270920 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1270886 GTATAAAGTC
1270896 ATAAAATATAAAT
1 ATAAAATATAAAT
1270909 ATAAAATATAAA
1 ATAAAATATAAA
1270921 CTTAATGTTA
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
ATAAAATATAAAT
Found at i:1271946 original size:24 final size:23
Alignment explanation
Indices: 1271894--1271983 Score: 110
Period size: 23 Copynumber: 3.9 Consensus size: 23
1271884 TTTTCATTTA
**
1271894 TGTTCGTTTACGTTCATTTATTG
1 TGTTCGTTTACGTTTGTTTATTG
1271917 TGTTCGTTTACGTTTGTTCGT-TTG
1 TGTTCGTTTACGTTTGTT--TATTG
*
1271941 TGTTCGTTTACGTTCGTTTATTG
1 TGTTCGTTTACGTTTGTTTATTG
* *
1271964 TGTTCGTTTATGTTTATTTA
1 TGTTCGTTTACGTTTGTTTA
1271984 CATTCATTCG
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
22 1 0.02
23 36 0.62
24 20 0.34
25 1 0.02
ACGTcount: A:0.10, C:0.11, G:0.20, T:0.59
Consensus pattern (23 bp):
TGTTCGTTTACGTTTGTTTATTG
Found at i:1275189 original size:20 final size:20
Alignment explanation
Indices: 1275123--1275189 Score: 62
Period size: 20 Copynumber: 3.1 Consensus size: 20
1275113 ATTATCTAAT
*
1275123 ATATTATTTTTCTACCGAAA
1 ATATTATTTTTCTACTGAAA
*
1275143 ATATTAATATTGTGTGCTACTTAAA
1 ATATT-AT-TT-T-T-CTACTGAAA
*
1275168 ATATTATTTTTCTACTGGAA
1 ATATTATTTTTCTACTGAAA
1275188 AT
1 AT
1275190 TAGGGTGCGA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
20 14 0.37
21 3 0.08
22 3 0.08
23 3 0.08
24 3 0.08
25 12 0.32
ACGTcount: A:0.34, C:0.10, G:0.09, T:0.46
Consensus pattern (20 bp):
ATATTATTTTTCTACTGAAA
Found at i:1279719 original size:18 final size:19
Alignment explanation
Indices: 1279696--1279760 Score: 91
Period size: 18 Copynumber: 3.6 Consensus size: 19
1279686 GTTCTTAAGG
*
1279696 AGTGGTCCTT-CGAGACAT
1 AGTGGTCATTCCGAGACAT
1279714 AGTGGTCATTCCG-GACAT
1 AGTGGTCATTCCGAGACAT
*
1279732 AGTGGTCCTTCCGA-ACAT
1 AGTGGTCATTCCGAGACAT
1279750 AGTGGTCATTC
1 AGTGGTCATTC
1279761 GGAACAAGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
18 40 0.95
19 2 0.05
ACGTcount: A:0.22, C:0.23, G:0.26, T:0.29
Consensus pattern (19 bp):
AGTGGTCATTCCGAGACAT
Found at i:1283413 original size:20 final size:21
Alignment explanation
Indices: 1283390--1283428 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1283380 TCTTAAGATT
1283390 TGAA-GTCACTACTTATATGG
1 TGAACGTCACTACTTATATGG
* *
1283410 TGAACGTTACTATTTATAT
1 TGAACGTCACTACTTATAT
1283429 ACCGATAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (21 bp):
TGAACGTCACTACTTATATGG
Found at i:1286752 original size:20 final size:20
Alignment explanation
Indices: 1286727--1286775 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
1286717 ATCCTTCGGG
1286727 ACATATATGTAATCTTTGGA
1 ACATATATGTAATCTTTGGA
*
1286747 ACATATATATAATCTTTGGA
1 ACATATATGTAATCTTTGGA
1286767 ACATATATG
1 ACATATATG
1286776 CGATACTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (20 bp):
ACATATATGTAATCTTTGGA
Found at i:1290443 original size:18 final size:18
Alignment explanation
Indices: 1290420--1290459 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
1290410 AAAGAGGCCT
1290420 GCCTTTCTGACTCACTGA
1 GCCTTTCTGACTCACTGA
1290438 GCCTTTCTGACTCACTGA
1 GCCTTTCTGACTCACTGA
1290456 GCCT
1 GCCT
1290460 CTCTTTGTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.15, C:0.35, G:0.17, T:0.33
Consensus pattern (18 bp):
GCCTTTCTGACTCACTGA
Found at i:1290960 original size:3 final size:3
Alignment explanation
Indices: 1290952--1290997 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
1290942 TATTTCATTT
* * *
1290952 TTA TTA TTA -AA TTA TTA TTA TTA TTA TTA TTA -TA ATA TTA TGA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1290998 ATTGTTCCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
2 3 0.08
3 33 0.92
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:1298052 original size:21 final size:22
Alignment explanation
Indices: 1298016--1298059 Score: 81
Period size: 21 Copynumber: 2.0 Consensus size: 22
1298006 AAGCCCTATG
1298016 TTTATCCTATTGGTTGAGTTAA
1 TTTATCCTATTGGTTGAGTTAA
1298038 TTTATCCTA-TGGTTGAGTTAA
1 TTTATCCTATTGGTTGAGTTAA
1298059 T
1 T
1298060 ATTTTACGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.23, C:0.09, G:0.18, T:0.50
Consensus pattern (22 bp):
TTTATCCTATTGGTTGAGTTAA
Found at i:1302151 original size:110 final size:110
Alignment explanation
Indices: 1301905--1302163 Score: 271
Period size: 110 Copynumber: 2.4 Consensus size: 110
1301895 CATATTGCTC
* ** * * *
1301905 CGAGTCCAATATC-TTCCGCCGTGAAGTTGAAATTGGTTCTG---GAACTGGGAAA-TTGTTTGT
1 CGAGTCCAATATCATT-CGCTGTGAAGTTGAAATTGACTCTGAATGAAATTGAAAAGTTGTTTGT
*
1301965 TGACAGTCAGCTGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
65 TGACAATCAGCTGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
* * * * * *
1302011 CGAGTCTAATATCCTTTGTTGTTAAGTTGAAATTTACTCTGAATGAAATTGAAAAGTTGTTTGTT
1 CGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAATTGAAAAGTTGTTTGTT
* *
1302076 GACAATCAG-TCGCCCCTTCG-TCGTGAAGTTGAGCTTGTGTTGTCT
66 GACAATCAGCT-GCCCCTTCGCT-GTGAAGTTGAACTTGTGCTGTCT
* * * *
1302121 TGGGTCCAATATCATTCGCTGTGAATTTGAAATTGGCTCTGAA
1 CGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAA
1302164 ATTGGGAAGC
Statistics
Matches: 122, Mismatches: 24, Indels: 10
0.78 0.15 0.06
Matches are distributed among these distances:
106 30 0.25
107 2 0.02
109 10 0.08
110 80 0.66
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (110 bp):
CGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTCTGAATGAAATTGAAAAGTTGTTTGTT
GACAATCAGCTGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
Found at i:1303315 original size:17 final size:17
Alignment explanation
Indices: 1303293--1303332 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1303283 CTTACTTTTC
*
1303293 TTTTTCT-TTTTTGTTCT
1 TTTTTCTCTTTTT-TCCT
1303310 TTTTTCTCTTTTTTCCT
1 TTTTTCTCTTTTTTCCT
1303327 TTTTTC
1 TTTTTC
1303333 AATTTAGGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (17 bp):
TTTTTCTCTTTTTTCCT
Found at i:1303319 original size:9 final size:9
Alignment explanation
Indices: 1303293--1303332 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
1303283 CTTACTTTTC
1303293 TTTTTCT-T
1 TTTTTCTCT
1303301 TTTTGT-TCT
1 TTTT-TCTCT
1303310 TTTTTCTCT
1 TTTTTCTCT
1303319 TTTTTC-CT
1 TTTTTCTCT
1303327 TTTTTC
1 TTTTTC
1303333 AATTTAGGGC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
8 14 0.48
9 15 0.52
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (9 bp):
TTTTTCTCT
Found at i:1313492 original size:4 final size:4
Alignment explanation
Indices: 1313483--1313528 Score: 51
Period size: 4 Copynumber: 11.8 Consensus size: 4
1313473 TAAAGTGATA
* *
1313483 AAAT AAAT AAAC ATA- AAAT AAAAT AAA- AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAA
1313529 GGAAAAACAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
3 5 0.14
4 27 0.75
5 4 0.11
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:1313500 original size:15 final size:14
Alignment explanation
Indices: 1313480--1313528 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
1313470 AAATAAAGTG
1313480 ATAAAATAAATAAA
1 ATAAAATAAATAAA
1313494 CATAAAATAAAATAAA
1 -ATAAAAT-AAATAAA
*
1313510 AAATAAATAAAT-AA
1 ATA-AAATAAATAAA
1313524 ATAAA
1 ATAAA
1313529 GGAAAAACAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
13 2 0.07
14 4 0.13
15 13 0.43
16 11 0.37
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (14 bp):
ATAAAATAAATAAA
Found at i:1313503 original size:11 final size:10
Alignment explanation
Indices: 1313480--1313528 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
1313470 AAATAAAGTG
1313480 ATAAAAT-AA
1 ATAAAATAAA
1313489 ATAAACATAAA
1 ATAAA-ATAAA
1313500 ATAAAATAAA
1 ATAAAATAAA
*
1313510 AAATAAAT-AA
1 ATA-AAATAAA
1313520 AT-AAATAAA
1 ATAAAATAAA
1313529 GGAAAAACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
8 4 0.12
9 7 0.21
10 12 0.35
11 11 0.32
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (10 bp):
ATAAAATAAA
Found at i:1313505 original size:20 final size:18
Alignment explanation
Indices: 1313444--1313528 Score: 61
Period size: 17 Copynumber: 4.8 Consensus size: 18
1313434 TGAAAATGAT
**
1313444 AATAAAATAAATAGCATA
1 AATAAAATAAATAAAATA
** * *
1313462 AGGAAAACAAATAAAGT-
1 AATAAAATAAATAAAATA
*
1313479 GATAAAATAAATAAACATAA
1 AATAAAATAAATAAA-AT-A
1313499 AATAAAAT-AA-AAAATA
1 AATAAAATAAATAAAATA
1313515 AAT-AAATAAATAAA
1 AATAAAATAAATAAA
1313529 GGAAAAACAA
Statistics
Matches: 50, Mismatches: 12, Indels: 11
0.68 0.16 0.15
Matches are distributed among these distances:
15 4 0.08
16 6 0.12
17 16 0.32
18 15 0.30
19 2 0.04
20 7 0.14
ACGTcount: A:0.72, C:0.04, G:0.06, T:0.19
Consensus pattern (18 bp):
AATAAAATAAATAAAATA
Found at i:1313752 original size:26 final size:26
Alignment explanation
Indices: 1313723--1313772 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1313713 AAGGTATAAT
*
1313723 AATAAAA-ATAAATAAAAAATAAAAGG
1 AATAAAATAGAAAT-AAAAATAAAAGG
*
1313749 AATAAAATAGAAATAGAAATAAAA
1 AATAAAATAGAAATAAAAATAAAA
1313773 TATATACATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 16 0.76
27 5 0.24
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (26 bp):
AATAAAATAGAAATAAAAATAAAAGG
Found at i:1315226 original size:32 final size:31
Alignment explanation
Indices: 1315190--1315269 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 31
1315180 TACAGTGCTT
* *
1315190 AAATAATAATGTGATATGTATTACATCATCTA
1 AAATAATAATATGATATGTATAACATCA-CTA
* * *
1315222 AAATAATGATATGATATGTATAATATTACTA
1 AAATAATAATATGATATGTATAACATCACTA
*
1315253 AAGTAATAATATGATAT
1 AAATAATAATATGATAT
1315270 ACGAACCAAC
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
31 18 0.44
32 23 0.56
ACGTcount: A:0.47, C:0.05, G:0.10, T:0.38
Consensus pattern (31 bp):
AAATAATAATATGATATGTATAACATCACTA
Found at i:1325252 original size:21 final size:21
Alignment explanation
Indices: 1325226--1325276 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
1325216 AGTAAGTTTG
1325226 GGATCGATCCTCTAGGCCAAA
1 GGATCGATCCTCTAGGCCAAA
*
1325247 GGATCGATCCTCTAGGCCAAG
1 GGATCGATCCTCTAGGCCAAA
1325268 GGATCGATC
1 GGATCGATC
1325277 ATTTTGTGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.25, C:0.27, G:0.27, T:0.20
Consensus pattern (21 bp):
GGATCGATCCTCTAGGCCAAA
Found at i:1325294 original size:40 final size:40
Alignment explanation
Indices: 1325245--1325321 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
1325235 CTCTAGGCCA
**
1325245 AAGGATCGATCCTCTAGGCC-AAGGGATCGATCATTTTGTG
1 AAGGATCGATCCT-TACCCCTAAGGGATCGATCATTTTGTG
*
1325285 AAGGATCGATCCTTTCCCCTAAGGGATCGATCATTTT
1 AAGGATCGATCCTTACCCCTAAGGGATCGATCATTTT
1325322 CCTGGAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 3 0.09
40 30 0.91
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (40 bp):
AAGGATCGATCCTTACCCCTAAGGGATCGATCATTTTGTG
Found at i:1331964 original size:31 final size:31
Alignment explanation
Indices: 1331929--1332030 Score: 120
Period size: 31 Copynumber: 3.4 Consensus size: 31
1331919 TTCATCACCT
1331929 GTCCTTAAACTATGACTCTCATTTCAAATTA
1 GTCCTTAAACTATGACTCTCATTTCAAATTA
* * ** * *
1331960 GTCCTTAAACTTTTA-AAT-ATTCCAATTTCA
1 GTCCTTAAACTATGACTCTCATTTCAAATT-A
1331990 -TCCTTAAACTATGACTCTCATTTCAAATTA
1 GTCCTTAAACTATGACTCTCATTTCAAATTA
1332020 GTCCTTAAACT
1 GTCCTTAAACT
1332031 TTTGAAAATT
Statistics
Matches: 55, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
29 20 0.36
30 4 0.07
31 31 0.56
ACGTcount: A:0.32, C:0.23, G:0.05, T:0.40
Consensus pattern (31 bp):
GTCCTTAAACTATGACTCTCATTTCAAATTA
Found at i:1332003 original size:60 final size:60
Alignment explanation
Indices: 1331930--1332112 Score: 244
Period size: 60 Copynumber: 3.0 Consensus size: 60
1331920 TCATCACCTG
1331930 TCCTTAAACTATGACTCTCATTTCAAATTAGTCCTTAAACTTTTAAATATTCCAATTTCA
1 TCCTTAAACTATGACTCTCATTTCAAATTAGTCCTTAAACTTTTAAATATTCCAATTTCA
* *
1331990 TCCTTAAACTATGACTCTCATTTCAAATTAGTCCTTAAACTTTTGAAA-ATTCAAATTTTA
1 TCCTTAAACTATGACTCTCATTTCAAATTAGTCCTTAAACTTTT-AAATATTCCAATTTCA
** * ** * * *
1332050 TCCCCAAACTATGAATCTCA-TTCTAAATCGGTCCTTAAACTTTTAGATCTTTCAATTTCA
1 TCCTTAAACTATGACTCTCATTTC-AAATTAGTCCTTAAACTTTTAAATATTCCAATTTCA
1332110 TCC
1 TCC
1332113 CCAAATTCAT
Statistics
Matches: 108, Mismatches: 12, Indels: 6
0.86 0.10 0.05
Matches are distributed among these distances:
59 5 0.05
60 100 0.93
61 3 0.03
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.40
Consensus pattern (60 bp):
TCCTTAAACTATGACTCTCATTTCAAATTAGTCCTTAAACTTTTAAATATTCCAATTTCA
Found at i:1337512 original size:28 final size:29
Alignment explanation
Indices: 1337471--1337530 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
1337461 TATGATTATT
*
1337471 TTTCACAAT-TAAAAACGCTTGAAAATAG
1 TTTCACAATAAAAAAACGCTTGAAAATAG
* *
1337499 TTTCAGAATAAAAAAATGCTTGAAAATAG
1 TTTCACAATAAAAAAACGCTTGAAAATAG
1337528 TTT
1 TTT
1337531 ATGCAAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 8 0.29
29 20 0.71
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.32
Consensus pattern (29 bp):
TTTCACAATAAAAAAACGCTTGAAAATAG
Found at i:1341517 original size:20 final size:20
Alignment explanation
Indices: 1341492--1341542 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
1341482 GCCAGAGCTT
1341492 GGCTCAGTGGAGTTCTTTCG
1 GGCTCAGTGGAGTTCTTTCG
1341512 GGCTCAGTGGAGTTCTTTCG
1 GGCTCAGTGGAGTTCTTTCG
1341532 GGCTCAGTGGA
1 GGCTCAGTGGA
1341543 ATATTGGGCA
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:0.12, C:0.20, G:0.37, T:0.31
Consensus pattern (20 bp):
GGCTCAGTGGAGTTCTTTCG
Found at i:1362920 original size:40 final size:40
Alignment explanation
Indices: 1362876--1362960 Score: 93
Period size: 40 Copynumber: 2.1 Consensus size: 40
1362866 TTTAAATTAT
**
1362876 TTAAAATGTCTTTTTGATTTAACA-AAAAAGGGGAGAAGTG
1 TTAAAATGTCTTTTAAATTTAA-AGAAAAAGGGGAGAAGTG
* * *
1362916 TT-AAATGTGTTTTAAATTTAAATGATAAATGGGAGAAGTG
1 TTAAAATGTCTTTTAAATTTAAA-GAAAAAGGGGAGAAGTG
1362956 TTAAA
1 TTAAA
1362961 GTAAGGGGGA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
38 1 0.03
39 16 0.43
40 18 0.49
41 2 0.05
ACGTcount: A:0.41, C:0.02, G:0.21, T:0.35
Consensus pattern (40 bp):
TTAAAATGTCTTTTAAATTTAAAGAAAAAGGGGAGAAGTG
Found at i:1364606 original size:2 final size:2
Alignment explanation
Indices: 1364599--1364639 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1364589 TTGACTACTA
1364599 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1364640 GCGTTTAAGT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1371198 original size:5 final size:5
Alignment explanation
Indices: 1371184--1371227 Score: 63
Period size: 5 Copynumber: 8.8 Consensus size: 5
1371174 AAGGAGTGAC
*
1371184 ATCA- ATCAT ATCAT ATCAT ATCAT ATCAT ATCAAT ACCAT ATCA
1 ATCAT ATCAT ATCAT ATCAT ATCAT ATCAT ATC-AT ATCAT ATCA
1371228 GTAACTTTGA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
4 4 0.11
5 28 0.78
6 4 0.11
ACGTcount: A:0.43, C:0.23, G:0.00, T:0.34
Consensus pattern (5 bp):
ATCAT
Found at i:1376451 original size:16 final size:16
Alignment explanation
Indices: 1376430--1376464 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
1376420 ATTTATATAT
1376430 ATACAAGGATGATTGC
1 ATACAAGGATGATTGC
1376446 ATACAAGGATGATTGC
1 ATACAAGGATGATTGC
1376462 ATA
1 ATA
1376465 ATTTTCCTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.40, C:0.11, G:0.23, T:0.26
Consensus pattern (16 bp):
ATACAAGGATGATTGC
Found at i:1377337 original size:36 final size:36
Alignment explanation
Indices: 1377290--1377358 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
1377280 AACGATTTCA
*
1377290 CCTGCCAGCTCCTCTCGGTCCATCCCGGATTATTCC
1 CCTGCCAGCTCCCCTCGGTCCATCCCGGATTATTCC
*
1377326 CCTGCCAGCTCCCCTCGGTCCATCCCTGATTAT
1 CCTGCCAGCTCCCCTCGGTCCATCCCGGATTAT
1377359 GTTGTCAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.12, C:0.45, G:0.16, T:0.28
Consensus pattern (36 bp):
CCTGCCAGCTCCCCTCGGTCCATCCCGGATTATTCC
Found at i:1377573 original size:149 final size:149
Alignment explanation
Indices: 1377303--1377597 Score: 572
Period size: 149 Copynumber: 2.0 Consensus size: 149
1377293 GCCAGCTCCT
*
1377303 CTCGGTCCATCCCGGATTATTCCCCTGCCAGCTCCCCTCGGTCCATCCCTGATTATGTTGTCAAT
1 CTCGGTCCATCCCGGATTATTCCCCTGCCAGCTCCCCTCGGTCCATCCCGGATTATGTTGTCAAT
*
1377368 TGAATCAGTTCTTTATTTGTTACCTTTTTAGTATTAGTGTTGTTGTAGACATTGATGAACCATCC
66 TGAATCAGTTCTTTATTTGTAACCTTTTTAGTATTAGTGTTGTTGTAGACATTGATGAACCATCC
1377433 AAAGTCCTATGTATGGCCC
131 AAAGTCCTATGTATGGCCC
1377452 CTCGGTCCATCCCGGATTATTCCCCTGCCAGCTCCCCTCGGTCCATCCCGGATTATGTTGTCAAT
1 CTCGGTCCATCCCGGATTATTCCCCTGCCAGCTCCCCTCGGTCCATCCCGGATTATGTTGTCAAT
1377517 TGAATCAGTTCTTTATTTGTAACCTTTTTAGTATTAGTGTTGTTGTAGACATTGATGAACCATCC
66 TGAATCAGTTCTTTATTTGTAACCTTTTTAGTATTAGTGTTGTTGTAGACATTGATGAACCATCC
1377582 AAAGTCCTATGTATGG
131 AAAGTCCTATGTATGG
1377598 ATGTTTGTAT
Statistics
Matches: 144, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 144 1.00
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.37
Consensus pattern (149 bp):
CTCGGTCCATCCCGGATTATTCCCCTGCCAGCTCCCCTCGGTCCATCCCGGATTATGTTGTCAAT
TGAATCAGTTCTTTATTTGTAACCTTTTTAGTATTAGTGTTGTTGTAGACATTGATGAACCATCC
AAAGTCCTATGTATGGCCC
Found at i:1378724 original size:113 final size:113
Alignment explanation
Indices: 1378526--1378751 Score: 443
Period size: 113 Copynumber: 2.0 Consensus size: 113
1378516 CACTGAACCT
1378526 ATGCTTGCCTCTGCCTCAACTTTCTCCTTTCGTTCCCTCCTCCTAAAGCAATAGTCACTAGCCTT
1 ATGCTTGCCTCTGCCTCAACTTTCTCCTTTCGTTCCCTCCTCCTAAAGCAATAGTCACTAGCCTT
1378591 ACTCATAACTACAAATAGAATTCTTGTCCTATTTATTAGGATTTTGTA
66 ACTCATAACTACAAATAGAATTCTTGTCCTATTTATTAGGATTTTGTA
*
1378639 ATGCTTGCCTCTGCCTCGACTTTCTCCTTTCGTTCCCTCCTCCTAAAGCAATAGTCACTAGCCTT
1 ATGCTTGCCTCTGCCTCAACTTTCTCCTTTCGTTCCCTCCTCCTAAAGCAATAGTCACTAGCCTT
1378704 ACTCATAACTACAAATAGAATTCTTGTCCTATTTATTAGGATTTTGTA
66 ACTCATAACTACAAATAGAATTCTTGTCCTATTTATTAGGATTTTGTA
1378752 TAGGCAAGAT
Statistics
Matches: 112, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
113 112 1.00
ACGTcount: A:0.23, C:0.27, G:0.11, T:0.38
Consensus pattern (113 bp):
ATGCTTGCCTCTGCCTCAACTTTCTCCTTTCGTTCCCTCCTCCTAAAGCAATAGTCACTAGCCTT
ACTCATAACTACAAATAGAATTCTTGTCCTATTTATTAGGATTTTGTA
Found at i:1379872 original size:39 final size:38
Alignment explanation
Indices: 1379790--1379872 Score: 96
Period size: 39 Copynumber: 2.1 Consensus size: 38
1379780 AACGGATATT
**
1379790 AAAATGAAACAAAAATTAAAGTTTTTAATAGATGGTATT
1 AAAATGAAACAAAAATTAAAG-TTTTAATAGATGGTAAA
**
1379829 AAAATGAAACAAAAATTAAA-TTTTAAGTATGATTTTAAA
1 AAAATGAAACAAAAATTAAAGTTTTAA-TA-GATGGTAAA
1379868 AAAAT
1 AAAAT
1379873 TAAAAATTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
37 6 0.16
38 2 0.05
39 30 0.79
ACGTcount: A:0.55, C:0.02, G:0.10, T:0.33
Consensus pattern (38 bp):
AAAATGAAACAAAAATTAAAGTTTTAATAGATGGTAAA
Found at i:1380068 original size:57 final size:57
Alignment explanation
Indices: 1379999--1380114 Score: 232
Period size: 57 Copynumber: 2.0 Consensus size: 57
1379989 AATTCTCGGC
1379999 TTTCAAACACATCCTATACGACACGTCAAATACAACATTAATGACCTTAAACGAAGT
1 TTTCAAACACATCCTATACGACACGTCAAATACAACATTAATGACCTTAAACGAAGT
1380056 TTTCAAACACATCCTATACGACACGTCAAATACAACATTAATGACCTTAAACGAAGT
1 TTTCAAACACATCCTATACGACACGTCAAATACAACATTAATGACCTTAAACGAAGT
1380113 TT
1 TT
1380115 ACACACGTTT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 59 1.00
ACGTcount: A:0.41, C:0.24, G:0.09, T:0.26
Consensus pattern (57 bp):
TTTCAAACACATCCTATACGACACGTCAAATACAACATTAATGACCTTAAACGAAGT
Found at i:1381493 original size:116 final size:115
Alignment explanation
Indices: 1381361--1381597 Score: 361
Period size: 116 Copynumber: 2.1 Consensus size: 115
1381351 AAAAAAGAGA
* * *
1381361 AAAAATTATTAGATTTAATTCAAAATTGAATGAATAAATAAGAGAAATGGAAAAAGAGTGTCAAA
1 AAAAATGATTAAATTTAATTCAAAATTGAATGAATAAATAAGAGAAATGGAAAAAGAGGGT-AAA
* * *
1381426 AACTAAATATTTTATGAAATTATAA-AAATTAGGGG-TACTAATTATTAATAT
65 AACTAAAAAATTTATGAAATTATAAGAAATTAGGGGCT--TAATTATAAATAT
* *
1381477 AAAAATGATTAAATTTAATTCAAAATTGAATGAATTAATAAGAGAAATGGAAAATGAGGGTAAAA
1 AAAAATGATTAAATTTAATTCAAAATTGAATGAATAAATAAGAGAAATGGAAAAAGAGGGTAAAA
1381542 ACTAAAAAATTTATGAAATTATAAGAAATTAGGGGCTTAATTATAAATAT
66 ACTAAAAAATTTATGAAATTATAAGAAATTAGGGGCTTAATTATAAATAT
1381592 AAAAAT
1 AAAAAT
1381598 TGGGGATTCT
Statistics
Matches: 111, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
115 44 0.40
116 66 0.59
117 1 0.01
ACGTcount: A:0.53, C:0.03, G:0.14, T:0.30
Consensus pattern (115 bp):
AAAAATGATTAAATTTAATTCAAAATTGAATGAATAAATAAGAGAAATGGAAAAAGAGGGTAAAA
ACTAAAAAATTTATGAAATTATAAGAAATTAGGGGCTTAATTATAAATAT
Found at i:1386174 original size:64 final size:63
Alignment explanation
Indices: 1386038--1386198 Score: 180
Period size: 64 Copynumber: 2.5 Consensus size: 63
1386028 AATTGTTCAG
* * * *
1386038 TGTGTATCGATGCACAGGAAGTGCATCGATGCACCTATTAAAATGGAAACATCGAATGCAATT
1 TGTGTATCGATGCAAAGGAAGTGCATCGATGCACCCATTAAAATGAAAACATCGAAAGCAATT
* * * **
1386101 GGTGCATCGATGCATAAGG-AGTGCATCGATGCATCCCCTTAAAATGAAAACATCGAAAGTGATT
1 TGTGTATCGATGCA-AAGGAAGTGCATCGATGCA-CCCATTAAAATGAAAACATCGAAAGCAATT
** * *
1386165 TGTGTATCGATGCACGGGTACTGCATCGATGCAC
1 TGTGTATCGATGCAAAGGAAGTGCATCGATGCAC
1386199 ATGCTAAAGA
Statistics
Matches: 81, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
63 29 0.36
64 52 0.64
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (63 bp):
TGTGTATCGATGCAAAGGAAGTGCATCGATGCACCCATTAAAATGAAAACATCGAAAGCAATT
Found at i:1387097 original size:4 final size:4
Alignment explanation
Indices: 1387081--1389531 Score: 4689
Period size: 4 Copynumber: 618.2 Consensus size: 4
1387071 AAATGATGAC
*
1387081 ATGT ATAT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1387129 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1387177 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1387225 ATGT ATGT A-GT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1387272 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1387320 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1387368 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1387416 ATGT ATGT ATGT ATGT ATGT ATGT ATGT A--T ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1387462 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT -TGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1387509 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1387557 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1387605 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1387653 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1387701 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1387749 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1387797 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1387845 ATGT ATGT ATGT ATGT A--T ATGT ATGT ATGT ATG- -TGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1387889 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1387937 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1387985 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1388033 ATGT ATGT ATGT ATGT ATGT ATGT AATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT -ATGT ATGT ATGT ATGT ATGT ATGT
1388082 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1388130 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1388178 ATGT ATGT ATGT ATGT ATGT ATG- -TGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1388224 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1388272 ATGT ATGT ATGT ATG- -TGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1388318 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1388366 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1388414 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
1388462 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AGGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1388510 ATGT ATGT ATGT ATGT A-GT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1388557 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG- -TGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1388603 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A-GT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1388650 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1388698 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1388746 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1388794 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1388842 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1388890 ATGT ATGT ATGT ATGT ATGT ATGT A-GT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1388937 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1388985 ATGT A-GT A-GT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1389031 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1389079 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1389127 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1389175 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1389223 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1389271 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1389319 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1389367 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1389415 A--T ATGT ATG- ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT-GT
*
1389461 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A-GT ATGC
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1389508 ATGT ATGT ATGT ATG- ATGT ATGT A
1 ATGT ATGT ATGT ATGT ATGT ATGT A
1389532 ATGGTATATG
Statistics
Matches: 2416, Mismatches: 6, Indels: 50
0.98 0.00 0.02
Matches are distributed among these distances:
2 14 0.01
3 30 0.01
4 2364 0.98
5 8 0.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:1389809 original size:30 final size:30
Alignment explanation
Indices: 1389775--1389877 Score: 170
Period size: 30 Copynumber: 3.4 Consensus size: 30
1389765 GGTTCTTCAG
* *
1389775 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAAGATCTTTAT
* *
1389805 GACCTCTTGATAGTTACCGATGATCTTTAT
1 GACCTCTGGATAGTTACCGAAGATCTTTAT
1389835 GACCTCTGGATAGTTACCGAAGATCTTTAT
1 GACCTCTGGATAGTTACCGAAGATCTTTAT
1389865 GACCTCTGGATAG
1 GACCTCTGGATAG
1389878 GTCCTTCGGA
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 68 1.00
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.33
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAAGATCTTTAT
Found at i:1392923 original size:14 final size:13
Alignment explanation
Indices: 1392876--1392919 Score: 54
Period size: 14 Copynumber: 3.4 Consensus size: 13
1392866 TTTAACCCAA
*
1392876 AATT-TATTTTTT
1 AATTATATTTATT
*
1392888 AATTATAGTTATAT
1 AATTATATTTAT-T
1392902 AATTATATTTATT
1 AATTATATTTATT
1392915 AATTA
1 AATTA
1392920 ATATGTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 4 0.15
13 11 0.41
14 12 0.44
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (13 bp):
AATTATATTTATT
Found at i:1399122 original size:191 final size:193
Alignment explanation
Indices: 1398795--1399167 Score: 660
Period size: 191 Copynumber: 1.9 Consensus size: 193
1398785 CAAGAAGAGA
*
1398795 CTGAGCAAAAATAACCTTAAATTTGAACTACCATTATGCCCATCCAATTATAACAATAACAGAGA
1 CTGAGCAAAAATAACCTTAAATTTGAACTACCATTATGCCCATCCAATTATAACAATAACAAAGA
* * *
1398860 CAACAGGATAGCATGCATTAGCCATCAGAAAAAGAATACGAGTGTCTCTGATATTAAGTGTCATA
66 CAACAAGATAACATGCATTAGCCATCAGAAAAAGAATACGAGTGTCTCTGATAATAAGTGTCATA
1398925 TTCTTGGAGAT-AAACAGCAATCTTCCACAAGG-CATCCCTCAAAGGATAACTTCTTGAGACT
131 TTCTTGGAGATCAAACAGCAATCTTCCACAAGGCCATCCCTCAAAGGATAACTTCTTGAGACT
* *
1398986 CTGAGCAAAAGTAACCTTAAATTTGAACTACCATTATGCCCATCCAATTATAATAATAACAAAGA
1 CTGAGCAAAAATAACCTTAAATTTGAACTACCATTATGCCCATCCAATTATAACAATAACAAAGA
* *
1399051 CAACAAGATAACATGTATTAGCCATCAGAAAAAGAATACGAGTGTCTCTGATAATAAGTGTCATT
66 CAACAAGATAACATGCATTAGCCATCAGAAAAAGAATACGAGTGTCTCTGATAATAAGTGTCATA
1399116 TTCTTGGAGATCAAACAGCAATCTTCCACAAGGCCATCCCTCAAAGGATAAC
131 TTCTTGGAGATCAAACAGCAATCTTCCACAAGGCCATCCCTCAAAGGATAAC
1399168 GATTAGATAA
Statistics
Matches: 172, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
191 133 0.77
192 21 0.12
193 18 0.10
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.25
Consensus pattern (193 bp):
CTGAGCAAAAATAACCTTAAATTTGAACTACCATTATGCCCATCCAATTATAACAATAACAAAGA
CAACAAGATAACATGCATTAGCCATCAGAAAAAGAATACGAGTGTCTCTGATAATAAGTGTCATA
TTCTTGGAGATCAAACAGCAATCTTCCACAAGGCCATCCCTCAAAGGATAACTTCTTGAGACT
Found at i:1402664 original size:19 final size:19
Alignment explanation
Indices: 1402640--1402676 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1402630 ATTATCTTAT
*
1402640 AATAATCTCACTATTAAAA
1 AATAATCTCAATATTAAAA
*
1402659 AATAATCTTAATATTAAA
1 AATAATCTCAATATTAAA
1402677 TTTTAAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (19 bp):
AATAATCTCAATATTAAAA
Found at i:1405371 original size:119 final size:119
Alignment explanation
Indices: 1405178--1405401 Score: 378
Period size: 119 Copynumber: 1.9 Consensus size: 119
1405168 TGATTTCATG
* * * *
1405178 TCATCTTCTCATGATTTTATTAAAAATCATGTAAATCAATATTAAATATTATAAACAATTCATAT
1 TCATCTTCTCATGATTTTATCAAAAATCATGTAAATCAACATCAAATATCATAAACAATTCATAT
*
1405243 TTCTTTCATTCGTACATATTTCAGAACTTTCATTTCATTTAAAAATCATGAAAA
66 TTCTTTCATTCGTACATATTTCAAAACTTTCATTTCATTTAAAAATCATGAAAA
*
1405297 TCATCATT-TCATGATTTTATCAAAAATCATGTAAATCAACATCAAATATCATAAACAATTTATA
1 TCATC-TTCTCATGATTTTATCAAAAATCATGTAAATCAACATCAAATATCATAAACAATTCATA
1405361 TTTCTTTCATTCGTACATATTTCAAAACTTTCATTTCATTT
65 TTTCTTTCATTCGTACATATTTCAAAACTTTCATTTCATTT
1405402 TCATATTCTT
Statistics
Matches: 98, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
119 96 0.98
120 2 0.02
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.42
Consensus pattern (119 bp):
TCATCTTCTCATGATTTTATCAAAAATCATGTAAATCAACATCAAATATCATAAACAATTCATAT
TTCTTTCATTCGTACATATTTCAAAACTTTCATTTCATTTAAAAATCATGAAAA
Found at i:1406518 original size:24 final size:24
Alignment explanation
Indices: 1406491--1406544 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
1406481 AACATTATGA
1406491 GTCACTTCTTACCGTAGTAACTTC
1 GTCACTTCTTACCGTAGTAACTTC
1406515 GTCACTTCTTACCGTAGTAACTTC
1 GTCACTTCTTACCGTAGTAACTTC
1406539 GTCACT
1 GTCACT
1406545 GGTTCATCGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.20, C:0.30, G:0.13, T:0.37
Consensus pattern (24 bp):
GTCACTTCTTACCGTAGTAACTTC
Found at i:1408994 original size:23 final size:24
Alignment explanation
Indices: 1408955--1409002 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
1408945 AAAAACCTAG
* *
1408955 ACCGGTTTTTTTACCGGATAAAAA
1 ACCGGTTTTTATACCGGAAAAAAA
1408979 ACCGGTTTTTAT-CCGGAAAAAAA
1 ACCGGTTTTTATACCGGAAAAAAA
1409002 A
1 A
1409003 TTGGTTTGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.29
Consensus pattern (24 bp):
ACCGGTTTTTATACCGGAAAAAAA
Found at i:1411312 original size:21 final size:21
Alignment explanation
Indices: 1411288--1411329 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1411278 AGTTTATTTT
1411288 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
1411309 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
1411330 AACTTGAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:1411378 original size:33 final size:32
Alignment explanation
Indices: 1411324--1411422 Score: 153
Period size: 33 Copynumber: 3.0 Consensus size: 32
1411314 TTTGTTTCAA
1411324 TTATCGAACTTGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGAAGTTTTTAAGTATTTGAAT
1411356 TTATCGAACTTGAAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTG-AAGTTTTTAAGTATTTGAAT
* * *
1411389 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1411422 T
1 T
1411423 ATGTTGAGTT
Statistics
Matches: 62, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
32 12 0.19
33 49 0.79
34 1 0.02
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.45
Consensus pattern (32 bp):
TTATCGAACTTGAAGTTTTTAAGTATTTGAAT
Found at i:1412566 original size:17 final size:17
Alignment explanation
Indices: 1412546--1412579 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1412536 ATTTTTTTAT
*
1412546 AACCGATTTTTTTAAAA
1 AACCAATTTTTTTAAAA
1412563 AACCAATTTTTTTAAAA
1 AACCAATTTTTTTAAAA
1412580 TCGAAACCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.03, T:0.41
Consensus pattern (17 bp):
AACCAATTTTTTTAAAA
Found at i:1412579 original size:15 final size:15
Alignment explanation
Indices: 1412536--1412579 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 15
1412526 ATTAAAATTG
* *
1412536 ATTTTTTTATAACCG
1 ATTTTTTTAAAACCA
1412551 ATTTTTTTAAAAAACCA
1 ATTTTTTT--AAAACCA
1412568 ATTTTTTTAAAA
1 ATTTTTTTAAAA
1412580 TCGAAACCAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 12 0.48
17 13 0.52
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.50
Consensus pattern (15 bp):
ATTTTTTTAAAACCA
Found at i:1414403 original size:30 final size:29
Alignment explanation
Indices: 1414369--1414453 Score: 82
Period size: 30 Copynumber: 2.9 Consensus size: 29
1414359 ATGTTAATAC
*
1414369 TATTTTTATCCTTTAAATTTATGTTTGTAA
1 TATTTTAATCCTTTAAATTTATGTTT-TAA
** * * **
1414399 TATTTTGGTACTTTAAATTTCTGTTTTTT
1 TATTTTAATCCTTTAAATTTATGTTTTAA
*
1414428 TA-TTTAATCCCTTAAATTTATGTTTT
1 TATTTTAATCCTTTAAATTTATGTTTT
1414454 TCTCTTGCAG
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
28 19 0.43
29 3 0.07
30 22 0.50
ACGTcount: A:0.24, C:0.08, G:0.07, T:0.61
Consensus pattern (29 bp):
TATTTTAATCCTTTAAATTTATGTTTTAA
Found at i:1417642 original size:22 final size:22
Alignment explanation
Indices: 1417617--1417667 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
1417607 TTGGTATATG
*
1417617 TATATGGTTCTTAAGGA-ATTT
1 TATATGGTCCTTAAGGACATTT
*
1417638 CTATATGGTCCTTATGGACATTT
1 -TATATGGTCCTTAAGGACATTT
1417661 TATATGG
1 TATATGG
1417668 CATTTCGGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 22 0.85
23 4 0.15
ACGTcount: A:0.25, C:0.10, G:0.20, T:0.45
Consensus pattern (22 bp):
TATATGGTCCTTAAGGACATTT
Found at i:1417710 original size:23 final size:23
Alignment explanation
Indices: 1417666--1417733 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 23
1417656 CATTTTATAT
* * * *
1417666 GGCATTTCGGTGTATTTCTACGC
1 GGCACTTCGGTGCAATTATACGC
* *
1417689 GTCACTTCGGTGCAATTATACGT
1 GGCACTTCGGTGCAATTATACGC
* *
1417712 GGCACTTTGGTGCATTTATACG
1 GGCACTTCGGTGCAATTATACG
1417734 AGCTGTGGTG
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.37
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTATACGC
Found at i:1423670 original size:34 final size:36
Alignment explanation
Indices: 1423612--1423679 Score: 86
Period size: 34 Copynumber: 1.9 Consensus size: 36
1423602 ATGAAGTTAA
** * *
1423612 TCTCACTTGAGATTGTTTTTCTTAA-A-ACAAACTG
1 TCTCACTTGAGACAGTCTTCCTTAAGATACAAACTG
1423646 TCTCACTTGAGACAGTCTTCCTTAAGATACAAAC
1 TCTCACTTGAGACAGTCTTCCTTAAGATACAAAC
1423680 ATTTGATATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 21 0.75
35 1 0.04
36 6 0.21
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (36 bp):
TCTCACTTGAGACAGTCTTCCTTAAGATACAAACTG
Found at i:1423873 original size:67 final size:68
Alignment explanation
Indices: 1423761--1423905 Score: 195
Period size: 67 Copynumber: 2.2 Consensus size: 68
1423751 AGTTGTTTTA
* * * *
1423761 CTTGAAATAT-AATACATTTGAGATTGTTTCTCTTGAAAAAAATTTTGTCTCTCTTGAGACAGTT
1 CTTGAAACATAAAAACATTTGAGATTATTTCCCTTGAAAAAAATTTTGTCTCTCTTGAGACAGTT
*
1423825 TCT
66 TCC
* * * *
1423828 CTTGAAACATAAAAACA-TTGAGATTATTTCCCTTGAAACATATTTTGTCTCTTTTGAGACATTT
1 CTTGAAACATAAAAACATTTGAGATTATTTCCCTTGAAAAAAATTTTGTCTCTCTTGAGACAGTT
1423892 TCC
66 TCC
1423895 CTTGAAACATA
1 CTTGAAACATA
1423906 TTTTGTCTCG
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
67 63 0.93
68 5 0.07
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.41
Consensus pattern (68 bp):
CTTGAAACATAAAAACATTTGAGATTATTTCCCTTGAAAAAAATTTTGTCTCTCTTGAGACAGTT
TCC
Found at i:1423966 original size:36 final size:36
Alignment explanation
Indices: 1423854--1423965 Score: 143
Period size: 36 Copynumber: 3.1 Consensus size: 36
1423844 ATTGAGATTA
** *
1423854 TTTCCCTTGAAACATATTTTGTCTCTTTTGAGACAT
1 TTTCCCTTGAAACATATTTTGTCTCAATTGAGACAG
** *
1423890 TTTCCCTTGAAACATATTTTGTCTCGCTTGAGACCG
1 TTTCCCTTGAAACATATTTTGTCTCAATTGAGACAG
* * *
1423926 TTTCTCTTGAAACAAATTTTGTCTCAATCGAGACAG
1 TTTCCCTTGAAACATATTTTGTCTCAATTGAGACAG
1423962 TTTC
1 TTTC
1423966 TTATTAAGCA
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 66 1.00
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.42
Consensus pattern (36 bp):
TTTCCCTTGAAACATATTTTGTCTCAATTGAGACAG
Found at i:1424070 original size:69 final size:69
Alignment explanation
Indices: 1423978--1424110 Score: 171
Period size: 69 Copynumber: 1.9 Consensus size: 69
1423968 ATTAAGCATA
* * * *
1423978 AAACTTTGAGATTGTTCCCTTGAAACAAGTTTTAGTTTCCTTGAGA-CTGTTTCTCATGAAACAA
1 AAACTTTAAGATTGTTCCCTTGAAACAAATCTCAGTTTCCTTGAGATC-GTTTCTCATGAAACAA
1424042 CAACC
65 CAACC
* * *
1424047 AAACTTTAAGA-TGTTCCTCTTGAAACAAATCTCATTTTCTTTGAGATCGTTTCTCTTGAAACAA
1 AAACTTTAAGATTGTTCC-CTTGAAACAAATCTCAGTTTCCTTGAGATCGTTTCTCATGAAACAA
1424111 ATCATATTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
68 6 0.11
69 48 0.87
70 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.37
Consensus pattern (69 bp):
AAACTTTAAGATTGTTCCCTTGAAACAAATCTCAGTTTCCTTGAGATCGTTTCTCATGAAACAAC
AACC
Found at i:1424106 original size:36 final size:35
Alignment explanation
Indices: 1424050--1424146 Score: 133
Period size: 36 Copynumber: 2.7 Consensus size: 35
1424040 AACAACCAAA
* *
1424050 CTTTAAGATGTTCCTCTTGAAACAAATC-TCATTTT
1 CTTTGAGATGTTTCTCTTGAAACAAATCAT-ATTTT
1424085 CTTTGAGATCGTTTCTCTTGAAACAAATCATATTTT
1 CTTTGAGAT-GTTTCTCTTGAAACAAATCATATTTT
*
1424121 CTTTGAGATTGTTTCTCATGAAACAA
1 CTTTGAGA-TGTTTCTCTTGAAACAA
1424147 CAAATAAATT
Statistics
Matches: 56, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
35 8 0.14
36 46 0.82
37 2 0.04
ACGTcount: A:0.29, C:0.18, G:0.11, T:0.42
Consensus pattern (35 bp):
CTTTGAGATGTTTCTCTTGAAACAAATCATATTTT
Found at i:1424168 original size:33 final size:36
Alignment explanation
Indices: 1424086--1424177 Score: 100
Period size: 33 Copynumber: 2.6 Consensus size: 36
1424076 TCTCATTTTC
* ***
1424086 TTTGAGATCGTTTCTCTTGAAACAAATCATATTTTC
1 TTTGAGATCGTTTCTCTTGAAACAAATCATAATAAA
* *
1424122 TTTGAGATTGTTTCTCATGAAAC-AA-CA-AATAAA
1 TTTGAGATCGTTTCTCTTGAAACAAATCATAATAAA
*
1424155 TTTGAGATCGTTTCCCTTGAAAC
1 TTTGAGATCGTTTCTCTTGAAAC
1424178 GAATTTTGTC
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
33 22 0.47
34 2 0.04
35 2 0.04
36 21 0.45
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (36 bp):
TTTGAGATCGTTTCTCTTGAAACAAATCATAATAAA
Found at i:1424428 original size:88 final size:88
Alignment explanation
Indices: 1424288--1424466 Score: 295
Period size: 88 Copynumber: 2.0 Consensus size: 88
1424278 ATAAAAACCA
* * *
1424288 TGTTATCATCCCTAATAATGGCCTACCGTCCTCATCACGTATGAACTATGTCATCCCTCGACCAG
1 TGTTATCATCCCTAATAATGGCCTACCATCCTCATCACGTAGGAACCATGTCATCCCTCGACCAG
1424353 ATCTCCTCATCACGTAGGAGCCG
66 ATCTCCTCATCACGTAGGAGCCG
* * *
1424376 TGTTATCATCCCTAATGATGGCCTTCCATCCTCATCACGTAGGAACCGTGTCATCCCTCGACCAG
1 TGTTATCATCCCTAATAATGGCCTACCATCCTCATCACGTAGGAACCATGTCATCCCTCGACCAG
*
1424441 ATCTCCTCATCACGTAGGAGTCG
66 ATCTCCTCATCACGTAGGAGCCG
1424464 TGT
1 TGT
1424467 CAACCTTAGA
Statistics
Matches: 84, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
88 84 1.00
ACGTcount: A:0.22, C:0.32, G:0.17, T:0.28
Consensus pattern (88 bp):
TGTTATCATCCCTAATAATGGCCTACCATCCTCATCACGTAGGAACCATGTCATCCCTCGACCAG
ATCTCCTCATCACGTAGGAGCCG
Found at i:1424459 original size:40 final size:41
Alignment explanation
Indices: 1424316--1424509 Score: 137
Period size: 40 Copynumber: 4.6 Consensus size: 41
1424306 TGGCCTACCG
* **
1424316 TCCTCATCACGTATGAACTATGTCATCCCTCGACCAGATC-
1 TCCTCATCACGTAGGAACCGTGTCATCCCTCGACCAGATCA
* * *
1424356 TCCTCATCACGTAGGAGCCGTGTTATCATCCCTAATGATGGCC--TTCCA
1 TCCTCATCACGTAGGAACCGTG---TCATCCCT--CGA---CCAGAT-CA
1424404 TCCTCATCACGTAGGAACCGTGTCATCCCTCGACCAGATC-
1 TCCTCATCACGTAGGAACCGTGTCATCCCTCGACCAGATCA
** * * * *
1424444 TCCTCATCACGTAGGAGTCGTGTCAACCTTAGATAACCAG-TCG
1 TCCTCATCACGTAGGAACCGTGTCATCCCTCG---ACCAGATCA
1424487 TCCTCATCACGTAGGAACCGTGT
1 TCCTCATCACGTAGGAACCGTGT
1424510 TATCATCCTT
Statistics
Matches: 122, Mismatches: 16, Indels: 29
0.73 0.10 0.17
Matches are distributed among these distances:
40 47 0.39
41 1 0.01
42 3 0.02
43 36 0.30
45 10 0.08
46 1 0.01
47 1 0.01
48 23 0.19
ACGTcount: A:0.23, C:0.32, G:0.18, T:0.26
Consensus pattern (41 bp):
TCCTCATCACGTAGGAACCGTGTCATCCCTCGACCAGATCA
Found at i:1425944 original size:30 final size:30
Alignment explanation
Indices: 1425910--1425970 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
1425900 CTGTTAATAC
* * *
1425910 TATTTTTATCCTTTAAATTTTTGTTTGTAT
1 TATTTTGATACTTTAAATTTCTGTTTGTAT
* *
1425940 TATTTTGGTACTTTAAATTTCTGTTTTTAT
1 TATTTTGATACTTTAAATTTCTGTTTGTAT
1425970 T
1 T
1425971 TAATCCCTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.20, C:0.07, G:0.08, T:0.66
Consensus pattern (30 bp):
TATTTTGATACTTTAAATTTCTGTTTGTAT
Found at i:1426582 original size:22 final size:18
Alignment explanation
Indices: 1426522--1426585 Score: 60
Period size: 22 Copynumber: 3.4 Consensus size: 18
1426512 AAATATAAAA
*
1426522 ATTCAACTTAAAATTTT-T
1 ATTCAAATT-AAATTTTAT
1426540 A-TCAAATTAAATTTTAT
1 ATTCAAATTAAATTTTAT
1426557 ATTCAAATTCAAATATTTGAAT
1 ATTCAAATT-AAAT-TTT--AT
1426579 ATTCAAA
1 ATTCAAA
1426586 AAGTGATCAG
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
16 7 0.18
17 8 0.21
18 8 0.21
19 4 0.10
20 3 0.08
22 9 0.23
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.44
Consensus pattern (18 bp):
ATTCAAATTAAATTTTAT
Found at i:1430867 original size:21 final size:21
Alignment explanation
Indices: 1430842--1430898 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
1430832 ACCCTAAGGT
1430842 CAGTATCGATACTGATAGGCC
1 CAGTATCGATACTGATAGGCC
1430863 CAGTATCGATACTGATAGGCC
1 CAGTATCGATACTGATAGGCC
*
1430884 CAGTATCGGTACTGA
1 CAGTATCGATACTGA
1430899 CGTCTTGTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.25
Consensus pattern (21 bp):
CAGTATCGATACTGATAGGCC
Found at i:1431187 original size:22 final size:23
Alignment explanation
Indices: 1431153--1431222 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 23
1431143 TCTTCCCCAA
*
1431153 TGCT-ATTGTACTTTTGTATTAG
1 TGCTGATTGCACTTTTGTATTAG
* * *
1431175 TGC-GATTGCACTTTTTTATCAA
1 TGCTGATTGCACTTTTGTATTAG
* *
1431197 TGCTGA-GGCACTTTAGTATTAG
1 TGCTGATTGCACTTTTGTATTAG
1431219 TGCT
1 TGCT
1431223 AAGGCACTTC
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
22 35 0.95
23 2 0.05
ACGTcount: A:0.20, C:0.14, G:0.20, T:0.46
Consensus pattern (23 bp):
TGCTGATTGCACTTTTGTATTAG
Found at i:1438051 original size:26 final size:26
Alignment explanation
Indices: 1438021--1438085 Score: 123
Period size: 25 Copynumber: 2.5 Consensus size: 26
1438011 AGTTTTACTC
1438021 TTATTTTCTTAAGTTTTTTTTATAGA
1 TTATTTTCTTAAGTTTTTTTTATAGA
1438047 TTATTTTCTTAAG-TTTTTTTATAGA
1 TTATTTTCTTAAGTTTTTTTTATAGA
1438072 TTATTTTCTTAAGT
1 TTATTTTCTTAAGT
1438086 GTAATGAGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 25 0.66
26 13 0.34
ACGTcount: A:0.23, C:0.05, G:0.08, T:0.65
Consensus pattern (26 bp):
TTATTTTCTTAAGTTTTTTTTATAGA
Found at i:1444196 original size:95 final size:96
Alignment explanation
Indices: 1444015--1444212 Score: 265
Period size: 95 Copynumber: 2.1 Consensus size: 96
1444005 TACCGTTGAG
* * * *
1444015 GTAGTATTTATACCATTATAAGGGTATCGATACCAAGCAAACATCGAATCTAATTTTGGTATCGA
1 GTAGTATTGATACCATGATAAGGGTATCGATACCAAGCAAACATCGAAGCTAATTTCGGTATCGA
* *
1444080 TACCGTAAGGGGGTACCGGTAC-CATAGTATA
66 TACCGAAAGAGGGTACCGGTACTC-TAGTATA
* *
1444111 GTAGTATTGATACCATGGTAAGGGTATCGATACCATGC-AACATCGAAGCTAATTTCGGTATCGA
1 GTAGTATTGATACCATGATAAGGGTATCGATACCAAGCAAACATCGAAGCTAATTTCGGTATCGA
* **
1444175 TACCGAAAGATGGTATTGGTACTCTAGTATA
66 TACCGAAAGAGGGTACCGGTACTCTAGTATA
*
1444206 GAAGTAT
1 GTAGTAT
1444213 CAGTACTAGG
Statistics
Matches: 89, Mismatches: 12, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
95 54 0.61
96 35 0.39
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (96 bp):
GTAGTATTGATACCATGATAAGGGTATCGATACCAAGCAAACATCGAAGCTAATTTCGGTATCGA
TACCGAAAGAGGGTACCGGTACTCTAGTATA
Found at i:1444233 original size:95 final size:96
Alignment explanation
Indices: 1444033--1444238 Score: 231
Period size: 95 Copynumber: 2.2 Consensus size: 96
1444023 TATACCATTA
* * * * *
1444033 TAAGGGTATCGATACCAAGCAAACATCGAATCTAATTTTGGTATCGATACCGTAAGGGGGTACCG
1 TAAGAGTATCGATACCAAGCAAACATCGAAGCTAATTTCGGTATCGATACCGAAAGAGGGTACCG
* * *
1444098 GTACCATAGTATAGTAGTATTGATACCATGG
66 GTACCATAGTATAGAAGTATAGATACCAGGG
* * * **
1444129 TAAGGGTATCGATACCATGC-AACATCGAAGCTAATTTCGGTATCGATACCGAAAGATGGTATTG
1 TAAGAGTATCGATACCAAGCAAACATCGAAGCTAATTTCGGTATCGATACCGAAAGAGGGTACCG
*
1444193 GTACTC-TAGTATAGAAGTATCAG-TACTAGGG
66 GTAC-CATAGTATAGAAGTAT-AGATACCAGGG
1444224 T-AGTAGTATCGATAC
1 TAAG-AGTATCGATAC
1444239 TATGGAGCCT
Statistics
Matches: 94, Mismatches: 13, Indels: 7
0.82 0.11 0.06
Matches are distributed among these distances:
94 2 0.02
95 71 0.76
96 21 0.22
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.28
Consensus pattern (96 bp):
TAAGAGTATCGATACCAAGCAAACATCGAAGCTAATTTCGGTATCGATACCGAAAGAGGGTACCG
GTACCATAGTATAGAAGTATAGATACCAGGG
Found at i:1450624 original size:6 final size:6
Alignment explanation
Indices: 1450609--1450702 Score: 52
Period size: 6 Copynumber: 15.2 Consensus size: 6
1450599 AGAGAAATAT
* * *
1450609 AGAAAG AGAAAA AG-AAA AGATAAA A-AAAA TG-AAA TGAAAA AGAAAA
1 AGAAAA AGAAAA AGAAAA AGA-AAA AGAAAA AGAAAA AGAAAA AGAAAA
* *
1450655 TA-AAAA AGGAAA AGAAAG AGAAAA TGAGAAAA TGAGAAAA ATGAAAA
1 -AGAAAA AGAAAA AGAAAA AGAAAA --AGAAAA --AGAAAA A-GAAAA
1450702 A
1 A
1450703 AAGAATGAAA
Statistics
Matches: 72, Mismatches: 7, Indels: 17
0.75 0.07 0.18
Matches are distributed among these distances:
5 14 0.19
6 33 0.46
7 11 0.15
8 14 0.19
ACGTcount: A:0.73, C:0.00, G:0.19, T:0.07
Consensus pattern (6 bp):
AGAAAA
Found at i:1450633 original size:12 final size:11
Alignment explanation
Indices: 1450588--1450678 Score: 51
Period size: 12 Copynumber: 7.7 Consensus size: 11
1450578 CTGACATCAT
*
1450588 AAAGAGAAAGA
1 AAAGAAAAAGA
*
1450599 AGAGAAATATAGA
1 AAAGAAA-A-AGA
1450612 AAGAGAAAAAGA
1 AA-AGAAAAAGA
1450624 AAAGATAAAA-A
1 AAAGA-AAAAGA
*
1450635 AAATG-AAATGAA
1 AAA-GAAAAAG-A
*
1450647 AAAGAAAATAAA
1 AAAGAAAA-AGA
*
1450659 AAAGGAAAAGA
1 AAAGAAAAAGA
1450670 AAGAGAAAA
1 AA-AGAAAA
1450679 TGAGAAAATG
Statistics
Matches: 61, Mismatches: 9, Indels: 19
0.69 0.10 0.21
Matches are distributed among these distances:
10 3 0.05
11 17 0.28
12 31 0.51
13 5 0.08
14 5 0.08
ACGTcount: A:0.74, C:0.00, G:0.20, T:0.07
Consensus pattern (11 bp):
AAAGAAAAAGA
Found at i:1450666 original size:24 final size:24
Alignment explanation
Indices: 1450618--1450679 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 24
1450608 TAGAAAGAGA
* *
1450618 AAAAG-AAAAGATAA-AAAAAATG
1 AAAAGAAAAAGAAAATAAAAAAGG
*
1450640 AAATGAAAAAGAAAATAAAAAAGG
1 AAAAGAAAAAGAAAATAAAAAAGG
*
1450664 AAAAGAAAGAGAAAAT
1 AAAAGAAAAAGAAAAT
1450680 GAGAAAATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
22 4 0.12
23 8 0.24
24 21 0.64
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (24 bp):
AAAAGAAAAAGAAAATAAAAAAGG
Found at i:1450703 original size:17 final size:17
Alignment explanation
Indices: 1450657--1450706 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
1450647 AAAGAAAATA
*
1450657 AAAAAGGAAAAGAAAGAG
1 AAAAATGAAAA-AAAGAG
* *
1450675 -AAAATGAGAAAATGAG
1 AAAAATGAAAAAAAGAG
1450691 AAAAATGAAAAAAAGA
1 AAAAATGAAAAAAAGA
1450707 ATGAAAGAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
16 5 0.19
17 21 0.81
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (17 bp):
AAAAATGAAAAAAAGAG
Found at i:1453442 original size:36 final size:36
Alignment explanation
Indices: 1453396--1453661 Score: 299
Period size: 36 Copynumber: 7.4 Consensus size: 36
1453386 AGCAAAGTCA
*
1453396 ATCTTAAGCCTTCACCGAAGAGA-AGTGAAGCAAACC
1 ATCTGAAGCCTTCACCGAAGA-ATAGTGAAGCAAACC
* *
1453432 ATCTGAAGCCTTCACTGGAGAATAGTGAAGCAAACC
1 ATCTGAAGCCTTCACCGAAGAATAGTGAAGCAAACC
*
1453468 ATCCT-AAGCCTTCACCGGAGAATAGTGAAGCAAACC
1 AT-CTGAAGCCTTCACCGAAGAATAGTGAAGCAAACC
* * *
1453504 ATCTGAAGCCTTCACCGGAGAATAGTGAAGCAATCA
1 ATCTGAAGCCTTCACCGAAGAATAGTGAAGCAAACC
*
1453540 ATCTGAAGCCTTCACCGGAGAATAGTGAAGCAAACC
1 ATCTGAAGCCTTCACCGAAGAATAGTGAAGCAAACC
* *
1453576 ATCAT-AAGTCTTCACC-AGAGAGTAGTGAAGCAAACC
1 ATC-TGAAGCCTTCACCGA-AGAATAGTGAAGCAAACC
* * * *
1453612 ATCTTAAGTCTTCACC-AAAAAGTAGTGAAGCAGATCC
1 ATCTGAAGCCTTCACCGAAGAA-TAGTGAAGCA-AACC
* *
1453649 ATTTTAAGCCTTC
1 ATCTGAAGCCTTC
1453662 TCAGAAGAGT
Statistics
Matches: 206, Mismatches: 16, Indels: 15
0.87 0.07 0.06
Matches are distributed among these distances:
35 6 0.03
36 183 0.89
37 17 0.08
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (36 bp):
ATCTGAAGCCTTCACCGAAGAATAGTGAAGCAAACC
Found at i:1453531 original size:108 final size:108
Alignment explanation
Indices: 1453396--1453643 Score: 363
Period size: 108 Copynumber: 2.3 Consensus size: 108
1453386 AGCAAAGTCA
* *
1453396 ATCTTAAGCCTTCACCGAAGAGAAGTGAAGCAAACCATCTGAAGCCTTCACTGGAGAATAGTGAA
1 ATCTTAAGCCTTCACCGAAGAGAAGTGAAGCAAACAATCTGAAGCCTTCACCGGAGAATAGTGAA
* *
1453461 GCAAACCATCCTAAGCCTTCACCGGAGAATAGTGAAGCAAACC
66 GCAAACCATCATAAGCCTTCACCAGAGAATAGTGAAGCAAACC
* * *
1453504 ATCTGAAGCCTTCACCGGAGA-ATAGTGAAGCAATCAATCTGAAGCCTTCACCGGAGAATAGTGA
1 ATCTTAAGCCTTCACCGAAGAGA-AGTGAAGCAAACAATCTGAAGCCTTCACCGGAGAATAGTGA
* *
1453568 AGCAAACCATCATAAGTCTTCACCAGAGAGTAGTGAAGCAAACC
65 AGCAAACCATCATAAGCCTTCACCAGAGAATAGTGAAGCAAACC
* * * *
1453612 ATCTTAAGTCTTCACCAAAAAGTAGTGAAGCA
1 ATCTTAAGCCTTCACCGAAGAGAAGTGAAGCA
1453644 GATCCATTTT
Statistics
Matches: 123, Mismatches: 15, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
107 1 0.01
108 122 0.99
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.19
Consensus pattern (108 bp):
ATCTTAAGCCTTCACCGAAGAGAAGTGAAGCAAACAATCTGAAGCCTTCACCGGAGAATAGTGAA
GCAAACCATCATAAGCCTTCACCAGAGAATAGTGAAGCAAACC
Found at i:1454177 original size:51 final size:50
Alignment explanation
Indices: 1454043--1454594 Score: 534
Period size: 51 Copynumber: 10.5 Consensus size: 50
1454033 AAGATTATTT
* *
1454043 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGA-GATGTC
1 GAGTTCTATACTCCTTA-AGAAAGAGGGAGCGAACCCGTTTGAAGATG-T-TC
* * * * *
1454095 TGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTATGAAGATATCC
1 -GAGTTCTATACTCCTTA-AGAAAGAGGGAGCGAACCCGTTTGAAGATGTTC
* *
1454147 GAGTTCCATACTCCTTAATGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
1 GAGTTCTATACTCCTTAA-GAAAGAGGGAGCGAACCCGTTTGAAGATGTTC
* * * ** * *
1454198 GAGTTCTATACTCTTTAAAGAGAGAAGGAGCGAACCCGTAAGAAGAAGATTTTT
1 GAGTTCTATACTCCTT-AAGAAAGAGGGAGCGAACCCGT---TTGAAGATGTTC
*
1454252 GAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCCAG-TTGAAGATGTTC
1 GAGTTCTATACT-CCTTAAGAAAGAGGGAGCGAACCC-GTTTGAAGATGTTC
*
1454303 GAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTC
1 GAGTTCTATACT-CCTTAAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTC
*
1454354 GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTC
1 GAGTTCTATACTCCTT-AAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTC
* **
1454405 GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACTAGTTTGAAGAGATGTTC
1 GAGTTCTATACTCCTT-AAGAAAGAGGGAGCGAACCCGTTTG-A-AGATGTTC
* * * *
1454458 AAGTTCTATACTCCCTAGAGAAAGGGGGAGCGAACCCGTTTGAAGAATATGTC
1 GAGTTCTATACTCCTTA-AGAAAGAGGGAGCGAACCCGTTTGAAG-ATGT-TC
* * * * *
1454511 TGAGTTCCATACTCCCTAGAGAAATAGGGAGTGAACCCATTTGTTGAAGATTGTTC
1 -GAGTTCTATACTCCTTA-AGAAAGAGGGAGCGAACCC--GT-TTGAAGA-TGTTC
* *
1454567 GAG-TCTTATACTCTCTGAAGAAATAGGG
1 GAGTTC-TATACTC-CTTAAGAAAGAGGG
1454595 GGCAGACGCG
Statistics
Matches: 432, Mismatches: 45, Indels: 42
0.83 0.09 0.08
Matches are distributed among these distances:
50 5 0.01
51 220 0.51
52 9 0.02
53 90 0.21
54 72 0.17
55 22 0.05
56 6 0.01
57 8 0.02
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.24
Consensus pattern (50 bp):
GAGTTCTATACTCCTTAAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTC
Found at i:1454315 original size:156 final size:152
Alignment explanation
Indices: 1454043--1454548 Score: 570
Period size: 156 Copynumber: 3.2 Consensus size: 152
1454033 AAGATTATTT
* * * * * *
1454043 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAG-AGATGTCTGAGTTCCATAC
1 GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCG--TGAAGAAGATGTTTGAGTTCTATAC
* * * *
1454107 TCCCTAGAGAAAGAGGGAGCGAACCC-GTATGAAGATATCCGAGTTCCATACTCCTTAATGAAAG
64 TCCCTA-AGAAAGAGGGAGCGAACCCAGT-TGAAGATGTTCGAGTTCTATACTCCCTAA-GAAAG
*
1454171 AAGGAGCGAACCCGTTTGAAGATGTTC
126 AGGGAGCGAACCCGTTTGAAGATGTTC
* * *
1454198 GAGTTCTATACTCTTTAAAGAGAGAAGGAGCGAACCCGTAAGAAGAAGATTTTTGAGTTCTATAC
1 GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGT--GAAGAAGATGTTTGAGTTCTATAC
1454263 TCCCTGAAGAAAGAGGGAGCGAACCCAGTTGAAGATGTTCGAGTTCTATACTCCCTAAAGAAAGA
64 TCCCT-AAGAAAGAGGGAGCGAACCCAGTTGAAGATGTTCGAGTTCTATACTCCCT-AAGAAAGA
1454328 GGGAGCGAACCCGTTTGAAGATGTTC
127 GGGAGCGAACCCGTTTGAAGATGTTC
** *
1454354 GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGT-TTGAAGATGTTCGAGTTCTATACTC
1 GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTGAAGAAGATGTTTGAGTTCTATACTC
* * * *
1454418 CTTAAAGAAAGAAGGAGCGAA-CTAGTTTGAAGAGATGTTCAAGTTCTATACTCCCTAGAGAAAG
66 CCT-AAGAAAGAGGGAGCGAACCCAG-TTG-A-AGATGTTCGAGTTCTATACTCCCTA-AGAAAG
* *
1454482 GGGGAGCGAACCCGTTTGAAGAATATGTC
126 AGGGAGCGAACCCGTTTGAAG-ATGT-TC
* * * * * *
1454511 TGAGTTCCATACTCCCTAGAGAAATAGGGAGTGAACCC
1 -GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCC
1454549 ATTTGTTGAA
Statistics
Matches: 305, Mismatches: 33, Indels: 23
0.84 0.09 0.06
Matches are distributed among these distances:
152 3 0.01
153 43 0.14
154 2 0.01
155 85 0.28
156 134 0.44
157 7 0.02
158 31 0.10
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (152 bp):
GAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTGAAGAAGATGTTTGAGTTCTATACTC
CCTAAGAAAGAGGGAGCGAACCCAGTTGAAGATGTTCGAGTTCTATACTCCCTAAGAAAGAGGGA
GCGAACCCGTTTGAAGATGTTC
Found at i:1454397 original size:207 final size:209
Alignment explanation
Indices: 1454032--1454579 Score: 759
Period size: 207 Copynumber: 2.6 Consensus size: 209
1454022 TGAAGCAAAT
*
1454032 GAAGATTATTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGA-GATGTCT
1 GAAGATT-TTTGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATG-TGTCT
* * * *
1454096 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTATGAAGATATCCGAGTTCCATACTCC
64 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTCTATACTCC
* * *
1454161 TTAATGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTCTATACTCTTTAAAGAGAGAAGG
129 TTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGG
*
1454226 AGCGAACCCGTAAGAA
194 AGCGAACCAGTAAGAA
1454242 GAAGATTTTTGAGTTCTATACTCCCT-GAAGAAAGAGGGAGCGAACCCAG-TTGAAGATGT-TC-
1 GAAGATTTTTGAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCC-GTTTGAAGATGTGTCT
* *
1454303 GAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTCTATACTCC
64 GAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTCTATACTCC
1454368 TTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGG
129 TTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGG
* **
1454433 AGCGAACTAGTTTGAA
194 AGCGAACCAGTAAGAA
* ** * *
1454449 G-AGATGTTCAAGTTCTATACTCCCTAGAGAAAGGGGGAGCGAACCCGTTTGAAGAATATGTCTG
1 GAAGATTTTTGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAG-ATGTGTCTG
* * *
1454513 AGTTCCATACTCCCTAGAGAAATAGGGAGTGAACCCATTTGTTGAAGATTGTTCGAG-TCTTATA
65 AGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCC--GT-TTGAAGA-TGTTCGAGTTC-TATA
1454577 CTC
125 CTC
1454580 TCTGAAGAAA
Statistics
Matches: 301, Mismatches: 24, Indels: 23
0.86 0.07 0.07
Matches are distributed among these distances:
205 1 0.00
206 45 0.15
207 138 0.46
208 5 0.02
209 78 0.26
210 9 0.03
211 1 0.00
212 9 0.03
213 15 0.05
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (209 bp):
GAAGATTTTTGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTGTCTGA
GTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTCTATACTCCTT
AAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTCTATACTCCTTAAAGAAAGAAGGAG
CGAACCAGTAAGAA
Found at i:1454589 original size:55 final size:55
Alignment explanation
Indices: 1454553--1454777 Score: 328
Period size: 55 Copynumber: 4.1 Consensus size: 55
1454543 GAACCCATTT
*
1454553 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATC
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATC
* * *
1454608 GTTGAAGATTGTTTGAGTCTTATACTCTTTGAAGATATAGGGGGCAGACACGATC
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATC
* ** *
1454663 GTTGAAGATTGTTCGAGTCTTATACTCTCTAAAGAAATAGGGGGCAGATGCGATT
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATC
* * *
1454718 GATGAAGATTG-T-GGGTCTTATACTCTCTGAAGATATAGGGGGCAGACACGATC
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATC
*
1454771 GTGGAAG
1 GTTGAAG
1454778 CAATAGGGAG
Statistics
Matches: 150, Mismatches: 20, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
53 40 0.27
54 1 0.01
55 109 0.73
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.29
Consensus pattern (55 bp):
GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATC
Found at i:1454633 original size:110 final size:109
Alignment explanation
Indices: 1454519--1454777 Score: 305
Period size: 110 Copynumber: 2.4 Consensus size: 109
1454509 TCTGAGTTCC
*
1454519 ATACTCCCTAG-AGAAATAGGGAGTG-A-AC-CCATTTGTTGAAGATTGTTCGAGTCTTATACTC
1 ATACTCCCTAGAAGAAATAGGG-G-GCAGACACCA-TCGTTGAAGATTGTTCGAGTCTTATACTC
* *
1454580 TCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTGTTTGAGTCTT
63 TCTAAAGAAATAGGGGGCAGACGCGATCGATGAAGATTG--TGAGTCTT
* * * *
1454629 ATACT-CTTTGAAGATATAGGGGGCAGACACGATCGTTGAAGATTGTTCGAGTCTTATACTCTCT
1 ATACTCCCTAGAAGAAATAGGGGGCAGACACCATCGTTGAAGATTGTTCGAGTCTTATACTCTCT
* * *
1454693 AAAGAAATAGGGGGCAGATGCGATTGATGAAGATTGTGGGTCTT
66 AAAGAAATAGGGGGCAGACGCGATCGATGAAGATTGTGAGTCTT
* * * *
1454737 ATACTCTCT-GAAGATATAGGGGGCAGACACGATCGTGGAAG
1 ATACTCCCTAGAAGAAATAGGGGGCAGACACCATCGTTGAAG
1454778 CAATAGGGAG
Statistics
Matches: 131, Mismatches: 13, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
108 44 0.34
109 6 0.05
110 79 0.60
111 2 0.02
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (109 bp):
ATACTCCCTAGAAGAAATAGGGGGCAGACACCATCGTTGAAGATTGTTCGAGTCTTATACTCTCT
AAAGAAATAGGGGGCAGACGCGATCGATGAAGATTGTGAGTCTT
Found at i:1458416 original size:46 final size:46
Alignment explanation
Indices: 1458349--1458577 Score: 341
Period size: 46 Copynumber: 5.0 Consensus size: 46
1458339 TAAATCGAAA
* * *
1458349 CATAATTAAAATGCATGAAAGGATGCATGAAGGCATTAACGGATGC
1 CATAACTAAAATGCATGAAATGATGCATGAAGGCATGAACGGATGC
* * *
1458395 CATAACTAAAATGCATGAAAGGATGCATGAAGGTATGAACGAATGC
1 CATAACTAAAATGCATGAAATGATGCATGAAGGCATGAACGGATGC
* * * * *
1458441 AATAACTAAAATACATGAAATGATGTATGAAGGCATGAACAGATAC
1 CATAACTAAAATGCATGAAATGATGCATGAAGGCATGAACGGATGC
1458487 CATAACTAAAATGCATGAAATGATGCATGAAGGCATGAACGGATGC
1 CATAACTAAAATGCATGAAATGATGCATGAAGGCATGAACGGATGC
* *
1458533 CATAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
1 CATAACTAAAATGCATGAAATGATGCATGAAGGCATGAACGGATG
1458578 TGGGATATAA
Statistics
Matches: 164, Mismatches: 19, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 164 1.00
ACGTcount: A:0.44, C:0.13, G:0.22, T:0.21
Consensus pattern (46 bp):
CATAACTAAAATGCATGAAATGATGCATGAAGGCATGAACGGATGC
Found at i:1458557 original size:26 final size:26
Alignment explanation
Indices: 1458473--1458558 Score: 69
Period size: 26 Copynumber: 3.5 Consensus size: 26
1458463 ATGTATGAAG
*
1458473 GCATGAACA-GATACCATAACTAAAAT
1 GCATGAA-ATGATGCCATAACTAAAAT
* *
1458499 GCATGAAATGATG-C---A-T-GAAG
1 GCATGAAATGATGCCATAACTAAAAT
**
1458519 GCATGAACGGATGCCATAACTAAAAT
1 GCATGAAATGATGCCATAACTAAAAT
1458545 GCATGAAATGATGC
1 GCATGAAATGATGC
1458559 ATTAAGGCAT
Statistics
Matches: 44, Mismatches: 9, Indels: 14
0.66 0.13 0.21
Matches are distributed among these distances:
20 13 0.30
21 2 0.05
22 1 0.02
24 1 0.02
25 3 0.07
26 24 0.55
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.20
Consensus pattern (26 bp):
GCATGAAATGATGCCATAACTAAAAT
Found at i:1458570 original size:20 final size:20
Alignment explanation
Indices: 1458499--1458577 Score: 59
Period size: 20 Copynumber: 3.6 Consensus size: 20
1458489 TAACTAAAAT
* *
1458499 GCATGAAATGATGCATGAAG
1 GCATGAAAGGATGCATTAAG
* *
1458519 GCATGAACGGATGCCATAACTAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
*
1458545 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
1458565 GCATGAAAGGATG
1 GCATGAAAGGATG
1458578 TGGGATATAA
Statistics
Matches: 45, Mismatches: 8, Indels: 12
0.69 0.12 0.18
Matches are distributed among these distances:
20 25 0.56
21 3 0.07
22 1 0.02
25 3 0.07
26 13 0.29
ACGTcount: A:0.41, C:0.13, G:0.27, T:0.20
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:1459212 original size:24 final size:24
Alignment explanation
Indices: 1459169--1459224 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
1459159 CACCACAGCT
* * *
1459169 CATATAAATTGCACCAAAGTGCCG
1 CATAGAAACTGCACCAAAGTGCCA
* *
1459193 CGTAGAAACTGCACCGAAGTGCCA
1 CATAGAAACTGCACCAAAGTGCCA
1459217 CATAGAAA
1 CATAGAAA
1459225 TGTCTCGAAG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.39, C:0.25, G:0.20, T:0.16
Consensus pattern (24 bp):
CATAGAAACTGCACCAAAGTGCCA
Found at i:1459315 original size:23 final size:23
Alignment explanation
Indices: 1459206--1459307 Score: 109
Period size: 23 Copynumber: 4.4 Consensus size: 23
1459196 AGAAACTGCA
1459206 CCGAAGTG-CCACATAGAAATGTC
1 CCGAAG-GACCACATAGAAATGTC
* * *
1459229 TCGAAGGACCACATAGTATTGT-
1 CCGAAGGACCACATAGAAATGTC
* * *
1459251 CCTAAAGATCCGCATAGAAATGTC
1 CCGAAGGA-CCACATAGAAATGTC
*
1459275 CCGAAGGACCACATAGAATTGTC
1 CCGAAGGACCACATAGAAATGTC
1459298 CCGAAGGACC
1 CCGAAGGACC
1459308 GCGTAGAACC
Statistics
Matches: 63, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
22 6 0.10
23 51 0.81
24 6 0.10
ACGTcount: A:0.34, C:0.25, G:0.22, T:0.19
Consensus pattern (23 bp):
CCGAAGGACCACATAGAAATGTC
Found at i:1459315 original size:46 final size:46
Alignment explanation
Indices: 1459217--1459315 Score: 137
Period size: 46 Copynumber: 2.2 Consensus size: 46
1459207 CGAAGTGCCA
* * *
1459217 CATAGAAATGTCTCGAAGGACCACATAGTATTGTCCTAAAGATCCG
1 CATAGAAATGTCCCGAAGGACCACATAGAATTGTCCGAAAGATCCG
*
1459263 CATAGAAATGTCCCGAAGGACCACATAGAATTGTCCCGAAGGA-CCG
1 CATAGAAATGTCCCGAAGGACCACATAGAATTGT-CCGAAAGATCCG
*
1459309 CGTAGAA
1 CATAGAA
1459316 CCTTTGACTC
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
46 41 0.87
47 6 0.13
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.19
Consensus pattern (46 bp):
CATAGAAATGTCCCGAAGGACCACATAGAATTGTCCGAAAGATCCG
Found at i:1459461 original size:17 final size:17
Alignment explanation
Indices: 1459439--1459499 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
1459429 TATCTTATTC
*
1459439 TCATATATTCACATAGA
1 TCATATATACACATAGA
1459456 TCATATA-ACACATAGAA
1 TCATATATACACATAG-A
* *
1459473 TAATATATAACACATAGC
1 TCATATAT-ACACATAGA
*
1459491 TCATGTATA
1 TCATATATA
1459500 ACAGTGCATA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
16 7 0.19
17 15 0.42
18 6 0.17
19 8 0.22
ACGTcount: A:0.46, C:0.16, G:0.07, T:0.31
Consensus pattern (17 bp):
TCATATATACACATAGA
Found at i:1474031 original size:4 final size:4
Alignment explanation
Indices: 1474022--1474052 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
1474012 CTGAAATGTT
1474022 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1474053 TATAATAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:1480928 original size:20 final size:20
Alignment explanation
Indices: 1480865--1480936 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
1480855 ATCCAATTTT
* *
1480865 AGTAACGATACTCAGTCT--
1 AGTATCGATACTCAGCCTAG
* *
1480883 AGTATCGATACCCTAGCACCAG
1 AGTATCGATACTC-AGC-CTAG
1480905 AGTATCGATACTCAGCCTAG
1 AGTATCGATACTCAGCCTAG
*
1480925 AGTATTGATACT
1 AGTATCGATACT
1480937 TCCTCAATCA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
18 11 0.26
19 2 0.05
20 15 0.35
21 3 0.07
22 12 0.28
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (20 bp):
AGTATCGATACTCAGCCTAG
Found at i:1482263 original size:3 final size:3
Alignment explanation
Indices: 1482255--1482308 Score: 99
Period size: 3 Copynumber: 18.0 Consensus size: 3
1482245 TAACCTTACT
*
1482255 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAC TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1482303 TAA TAA
1 TAA TAA
1482309 CTTACAATTA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1482515 original size:17 final size:17
Alignment explanation
Indices: 1482493--1482526 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1482483 TATGAGAGTA
1482493 ATACTCTCAATTCAATT
1 ATACTCTCAATTCAATT
1482510 ATACTCTCAATTCAATT
1 ATACTCTCAATTCAATT
1482527 TTATCCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.24, G:0.00, T:0.41
Consensus pattern (17 bp):
ATACTCTCAATTCAATT
Found at i:1495829 original size:28 final size:28
Alignment explanation
Indices: 1495792--1495857 Score: 132
Period size: 28 Copynumber: 2.4 Consensus size: 28
1495782 TTGAATTAAA
1495792 TTAAAATTCAGAATAAAAATCAAATAAT
1 TTAAAATTCAGAATAAAAATCAAATAAT
1495820 TTAAAATTCAGAATAAAAATCAAATAAT
1 TTAAAATTCAGAATAAAAATCAAATAAT
1495848 TTAAAATTCA
1 TTAAAATTCA
1495858 ATGCCGAAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.59, C:0.08, G:0.03, T:0.30
Consensus pattern (28 bp):
TTAAAATTCAGAATAAAAATCAAATAAT
Found at i:1495858 original size:16 final size:16
Alignment explanation
Indices: 1495805--1495858 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
1495795 AAATTCAGAA
*
1495805 TAAAAATCAAATAATT
1 TAAAATTCAAATAATT
1495821 TAAAATTCAGAAT-A--
1 TAAAATTCA-AATAATT
1495835 -AAAA-TCAAATAATT
1 TAAAATTCAAATAATT
1495849 TAAAATTCAA
1 TAAAATTCAA
1495859 TGCCGAAACC
Statistics
Matches: 31, Mismatches: 1, Indels: 12
0.70 0.02 0.27
Matches are distributed among these distances:
11 3 0.10
12 4 0.13
13 4 0.13
15 4 0.13
16 13 0.42
17 3 0.10
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (16 bp):
TAAAATTCAAATAATT
Found at i:1497335 original size:30 final size:30
Alignment explanation
Indices: 1497296--1497365 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
1497286 ATTTTATGTT
*
1497296 GGAGAACGAACTTGAATTTATAAAACTTT-A
1 GGAGAACGAACTTGAACTTATAAAA-TTTCA
* * *
1497326 GGGGAACGAATTTGAACTTATGAAATTTCA
1 GGAGAACGAACTTGAACTTATAAAATTTCA
1497356 GGAGAACGAA
1 GGAGAACGAA
1497366 AACAGATTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 3 0.09
30 31 0.91
ACGTcount: A:0.41, C:0.10, G:0.23, T:0.26
Consensus pattern (30 bp):
GGAGAACGAACTTGAACTTATAAAATTTCA
Found at i:1505036 original size:83 final size:83
Alignment explanation
Indices: 1504935--1505096 Score: 281
Period size: 83 Copynumber: 2.0 Consensus size: 83
1504925 GAATTTCGAT
*
1504935 AGAGTTTTACACCAACTAAA-ACTCTTTTAATATCTAAATTTAAATAGATAATAATATCTTTTAA
1 AGAGTTTTACACCAACTAAATA-TCTTTTAATATCTAAATTTAAACAGATAATAATATCTTTTAA
1504999 ATTTAAAATATTAAAAATG
65 ATTTAAAATATTAAAAATG
* *
1505018 AGAGTTTTACTCCAACTAAATATCTTTTAATATCTAAATTTAAGCAGATAATAATATCTTTTAAA
1 AGAGTTTTACACCAACTAAATATCTTTTAATATCTAAATTTAAACAGATAATAATATCTTTTAAA
1505083 TTTAAAATATTAAA
66 TTTAAAATATTAAA
1505097 CAGATATACA
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
83 74 0.99
84 1 0.01
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.40
Consensus pattern (83 bp):
AGAGTTTTACACCAACTAAATATCTTTTAATATCTAAATTTAAACAGATAATAATATCTTTTAAA
TTTAAAATATTAAAAATG
Found at i:1511876 original size:4 final size:4
Alignment explanation
Indices: 1511867--1511891 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1511857 CACGGTGAAG
1511867 AAGA AAGA AAGA AAGA AAGA AAGA A
1 AAGA AAGA AAGA AAGA AAGA AAGA A
1511892 TATGAAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:1518040 original size:17 final size:17
Alignment explanation
Indices: 1518014--1518046 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1518004 GGTTAAGCGT
1518014 TAAATAATTTAAAGATC
1 TAAATAATTTAAAGATC
*
1518031 TAAATGATTTAAAGAT
1 TAAATAATTTAAAGAT
1518047 TCTGTATGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.03, G:0.09, T:0.36
Consensus pattern (17 bp):
TAAATAATTTAAAGATC
Found at i:1524445 original size:76 final size:76
Alignment explanation
Indices: 1524318--1524469 Score: 286
Period size: 76 Copynumber: 2.0 Consensus size: 76
1524308 CGATTAAATT
1524318 ACGAAATTCCCCCTAAATTATTATAGCCAATGCCAAATGATTTTTCATTTTTCAAGTTAACCTAA
1 ACGAAATTCCCCCTAAATTATTATAGCCAATGCCAAATGATTTTTCATTTTTCAAGTTAACCTAA
1524383 TATAACCAAAC
66 TATAACCAAAC
* *
1524394 ACGAAATTCGCCCTAAATTATTATAGCCAATGCCAAATGATTTTTCGTTTTTCAAGTTAACCTAA
1 ACGAAATTCCCCCTAAATTATTATAGCCAATGCCAAATGATTTTTCATTTTTCAAGTTAACCTAA
1524459 TATAACCAAAC
66 TATAACCAAAC
1524470 TTCTCTCTTG
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 74 1.00
ACGTcount: A:0.38, C:0.22, G:0.08, T:0.33
Consensus pattern (76 bp):
ACGAAATTCCCCCTAAATTATTATAGCCAATGCCAAATGATTTTTCATTTTTCAAGTTAACCTAA
TATAACCAAAC
Found at i:1524778 original size:21 final size:21
Alignment explanation
Indices: 1524745--1524790 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
1524735 GTTGTACTTT
1524745 TTTTAAGTGTTTAATATTTAAA
1 TTTTAAGTGTTTAATA-TTAAA
* *
1524767 TTTTCAGT-TTTAGTATTAAA
1 TTTTAAGTGTTTAATATTAAA
1524787 TTTT
1 TTTT
1524791 TAATTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 9 0.41
21 6 0.27
22 7 0.32
ACGTcount: A:0.30, C:0.02, G:0.09, T:0.59
Consensus pattern (21 bp):
TTTTAAGTGTTTAATATTAAA
Found at i:1524791 original size:21 final size:23
Alignment explanation
Indices: 1524744--1524793 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 23
1524734 AGTTGTACTT
1524744 TTTTTAAGTGTTTAATATTTAAA
1 TTTTTAAGTGTTTAATATTTAAA
* *
1524767 -TTTTCAGT-TTTAGTA-TTAAA
1 TTTTTAAGTGTTTAATATTTAAA
1524787 TTTTTAA
1 TTTTTAA
1524794 TTTTTTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 5 0.22
21 11 0.48
22 7 0.30
ACGTcount: A:0.32, C:0.02, G:0.08, T:0.58
Consensus pattern (23 bp):
TTTTTAAGTGTTTAATATTTAAA
Found at i:1526361 original size:16 final size:17
Alignment explanation
Indices: 1526311--1526362 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
1526301 AAAAAAATTA
1526311 AATTTGAAAGTTAGAGT
1 AATTTGAAAGTTAGAGT
*
1526328 GA-TT-AAA-TTAAGAGT
1 AATTTGAAAGTT-AGAGT
1526343 AATTTGAAAGTTA-AGT
1 AATTTGAAAGTTAGAGT
1526359 AATT
1 AATT
1526363 AAATTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 2 0.07
15 9 0.31
16 11 0.38
17 5 0.17
18 2 0.07
ACGTcount: A:0.44, C:0.00, G:0.19, T:0.37
Consensus pattern (17 bp):
AATTTGAAAGTTAGAGT
Found at i:1527261 original size:78 final size:78
Alignment explanation
Indices: 1527168--1527329 Score: 315
Period size: 78 Copynumber: 2.1 Consensus size: 78
1527158 CAACATATAA
1527168 ATACTAATTCAACAACAACTTTTATATTTACTTTAATGTAATATGTACATTCTGTACTTTATAAA
1 ATACTAATTCAACAACAACTTTTATATTTACTTTAATGTAATATGTACATTCTGTACTTTATAAA
1527233 ATTATTAGAAATT
66 ATTATTAGAAATT
*
1527246 ATACTAATTCAACAACAACTTTTATATTTACTTTAATGTAATATGTACATTCTGTATTTTATAAA
1 ATACTAATTCAACAACAACTTTTATATTTACTTTAATGTAATATGTACATTCTGTACTTTATAAA
1527311 ATTATTAGAAATT
66 ATTATTAGAAATT
1527324 ATACTA
1 ATACTA
1527330 TCAAAAAATA
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 83 1.00
ACGTcount: A:0.40, C:0.11, G:0.05, T:0.44
Consensus pattern (78 bp):
ATACTAATTCAACAACAACTTTTATATTTACTTTAATGTAATATGTACATTCTGTACTTTATAAA
ATTATTAGAAATT
Found at i:1528352 original size:16 final size:16
Alignment explanation
Indices: 1528331--1528365 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1528321 TTGGTATTTG
1528331 TTAATTTTTGTT-TAAA
1 TTAATTTTT-TTATAAA
1528347 TTAATTTTTTTATAAA
1 TTAATTTTTTTATAAA
1528363 TTA
1 TTA
1528366 TATTAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 2 0.11
16 16 0.89
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (16 bp):
TTAATTTTTTTATAAA
Found at i:1529008 original size:28 final size:29
Alignment explanation
Indices: 1528956--1529016 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 29
1528946 AATATTGTTT
*
1528956 AGAA-TTTAATTTGATTCATTCAAAA-AA
1 AGAATTTTAATTTCATTCATTCAAAATAA
*
1528983 AGAATTTTAATTTCATT-ATTATAAAATAA
1 AGAATTTTAATTTCATTCATT-CAAAATAA
1529012 A-AATT
1 AGAATT
1529017 GGTGAATTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
27 7 0.24
28 19 0.66
29 3 0.10
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (29 bp):
AGAATTTTAATTTCATTCATTCAAAATAA
Found at i:1529546 original size:11 final size:11
Alignment explanation
Indices: 1529532--1529572 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
1529522 GTCAACGTTA
*
1529532 AAATAAAATTT
1 AAATAAAAATT
*
1529543 AAATAAAAAAT
1 AAATAAAAATT
*
1529554 AGATAAAAATT
1 AAATAAAAATT
1529565 AAATAAAA
1 AAATAAAA
1529573 TTCTAATTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (11 bp):
AAATAAAAATT
Found at i:1534828 original size:125 final size:124
Alignment explanation
Indices: 1534278--1534930 Score: 829
Period size: 124 Copynumber: 5.3 Consensus size: 124
1534268 TTGCTTCCGA
* * * *
1534278 TTTCATGCTTGTATTACAAGTAATTCAGTTCTCGTCAAAGTACGTTCAAATTCAAACCAATTAAC
1 TTTCATGCTTGTATTACAAGTAATGCAGTTCTCGTCAAACTACATTCGAATTCAAACCAATTAAC
* * * *
1534343 ACAAAATAGTAGTTATAACAGATCGTGCCACAGTCTTGGATTGATTTCATTGTTCTTTG
66 ACGATATAGTAGTTATAACAGATCATGCCACAGTCTTGGATTGATTTCATTGTTTTTTG
* * * * * * *
1534402 TTTCATGCTTGTACTACAAGCAATACAGTTCTCATCAAAGTACATGC-ATATTCAACCCAATTAA
1 TTTCATGCTTGTATTACAAGTAATGCAGTTCTCGTCAAACTACATTCGA-ATTCAAACCAATTAA
* * * * *
1534466 CACGTTATTGTAGTTATAATAGATCATGCCACACCACAGTCTTGGATTGATTTCTTTGTTTTCTG
65 CACGATATAGTAGTTATAACAGATCATG-----CCACAGTCTTGGATTGATTTCATTGTTTTTTG
* *
1534531 TTTCATGCTTGTATTAAAAGTAATGCAGTTCTCATCAAAGC-ACATTCGAATTCAAACCAATTAA
1 TTTCATGCTTGTATTACAAGTAATGCAGTTCTCGTCAAA-CTACATTCGAATTCAAACCAATTAA
*
1534595 CACGATATA-TAG-TAGT--TAGATCATG-C-CAGTCTTGGATTGATTTCATTGTTTTTTG
65 CACGATATAGTAGTTA-TAACAGATCATGCCACAGTCTTGGATTGATTTCATTGTTTTTTG
* * * * * *
1534650 TTTCACGCTTGTATTACAAGTAATTCAATTCTTG-CTGAACTACATTCGAATTCAAACCAAATAA
1 TTTCATGCTTGTATTACAAGTAATGCAGTTCTCGTC-AAACTACATTCGAATTCAAACCAATTAA
* * *
1534714 CACGATATAGTAGTTATAACAGATCATGCCACCGTCTTGAATTGATTTCACTGTTTTTTG
65 CACGATATAGTAGTTATAACAGATCATGCCACAGTCTTGGATTGATTTCATTGTTTTTTG
1534774 TTTCATGCTTGTATTACAAGTAATGCAGTTCTCGTCAAAACTACATTCGAATTCAAACCAATTAA
1 TTTCATGCTTGTATTACAAGTAATGCAGTTCTCGTC-AAACTACATTCGAATTCAAACCAATTAA
** *
1534839 CATAATATAGTAGCTATAACAGATCATGCCACAGTCTTGGATTGATTTCATTGTTTTTTG
65 CACGATATAGTAGTTATAACAGATCATGCCACAGTCTTGGATTGATTTCATTGTTTTTTG
*
1534899 TTTCATGCTTGTATTACAAGTAATGCAATTCT
1 TTTCATGCTTGTATTACAAGTAATGCAGTTCT
1534931 TGCTGAAGTA
Statistics
Matches: 458, Mismatches: 53, Indels: 35
0.84 0.10 0.06
Matches are distributed among these distances:
118 2 0.00
119 88 0.19
120 5 0.01
121 2 0.00
122 8 0.02
123 2 0.00
124 133 0.29
125 112 0.24
126 9 0.02
127 2 0.00
128 4 0.01
129 90 0.20
130 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (124 bp):
TTTCATGCTTGTATTACAAGTAATGCAGTTCTCGTCAAACTACATTCGAATTCAAACCAATTAAC
ACGATATAGTAGTTATAACAGATCATGCCACAGTCTTGGATTGATTTCATTGTTTTTTG
Found at i:1541198 original size:31 final size:31
Alignment explanation
Indices: 1541163--1541224 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
1541153 ATTTCTTGCA
*
1541163 TATTTTTATTTGAATGAAT-TTTTGTAAATAT
1 TATTTCTATTTGAATGAATATTTT-TAAATAT
1541194 TATTTCTATTTGAATGAATATTTTTAAATAT
1 TATTTCTATTTGAATGAATATTTTTAAATAT
1541225 AAATTTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 25 0.86
32 4 0.14
ACGTcount: A:0.34, C:0.02, G:0.08, T:0.56
Consensus pattern (31 bp):
TATTTCTATTTGAATGAATATTTTTAAATAT
Found at i:1541533 original size:102 final size:105
Alignment explanation
Indices: 1541330--1541562 Score: 273
Period size: 106 Copynumber: 2.2 Consensus size: 105
1541320 TGATTGTTGC
* *
1541330 CCCCACGTGAATACTTCTCAAAACATACATGCAATGACAATCATTTAATATAAAAAAACAATTCA
1 CCCCACGTGAATGCTTCCCAAAACATACATGCAATGACAATCATTTAATATAAAAAAACAATTCA
*
1541395 CATACATTTAATAAAAAAAAAACCAAAAAGTTGTTGC-CTCCA
66 CATACATTT-AT--AAAAAAAACCAAAAAGTCGTTGCACTCCA
* *
1541437 -CCTACGTGAATGCTTCCCAAAACATGCATGCAATGAC-ATGCATTTAATA-AAAAAAACCAAAA
1 CCCCACGTGAATGCTTCCCAAAACATACATGCAATGACAAT-CATTTAATATAAAAAAA-C--AA
* *
1541499 TTCACATGCA-TT-T-AAAAAAACCAAAAAGTCGTTGCACTCTA
62 TTCACATACATTTATAAAAAAAACCAAAAAGTCGTTGCACTCCA
*
1541540 TCCCCACGTGAATGTTTCCCAAA
1 -CCCCACGTGAATGCTTCCCAAA
1541563 GATCTAGGAG
Statistics
Matches: 110, Mismatches: 9, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
102 21 0.19
103 4 0.04
105 29 0.26
106 43 0.39
107 2 0.02
108 11 0.10
ACGTcount: A:0.44, C:0.23, G:0.09, T:0.24
Consensus pattern (105 bp):
CCCCACGTGAATGCTTCCCAAAACATACATGCAATGACAATCATTTAATATAAAAAAACAATTCA
CATACATTTATAAAAAAAACCAAAAAGTCGTTGCACTCCA
Found at i:1548265 original size:33 final size:33
Alignment explanation
Indices: 1548228--1548290 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
1548218 ATCAAATGGT
* *
1548228 GGTGCTTCTCTTGGCTCTAATGACTCGACTAAC
1 GGTGCCTCCCTTGGCTCTAATGACTCGACTAAC
* *
1548261 GGTGCCTCCCTTGGTTCTACTGACTCGACT
1 GGTGCCTCCCTTGGCTCTAATGACTCGACT
1548291 GGTGGTGCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.14, C:0.30, G:0.22, T:0.33
Consensus pattern (33 bp):
GGTGCCTCCCTTGGCTCTAATGACTCGACTAAC
Found at i:1548298 original size:33 final size:33
Alignment explanation
Indices: 1548224--1548298 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 33
1548214 CTGAATCAAA
* *
1548224 TGGTGGTGCTTCTCTTGGCTCTAATGACTCGAC
1 TGGTGGTGCCTCCCTTGGCTCTAATGACTCGAC
*** * *
1548257 TAACGGTGCCTCCCTTGGTTCTACTGACTCGAC
1 TGGTGGTGCCTCCCTTGGCTCTAATGACTCGAC
1548290 TGGTGGTGC
1 TGGTGGTGC
1548299 TTTCCTTGAT
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.12, C:0.27, G:0.28, T:0.33
Consensus pattern (33 bp):
TGGTGGTGCCTCCCTTGGCTCTAATGACTCGAC
Found at i:1550812 original size:27 final size:27
Alignment explanation
Indices: 1550746--1550812 Score: 62
Period size: 27 Copynumber: 2.5 Consensus size: 27
1550736 TTTAAATAGT
* * * *
1550746 AATTCTAAAAAATTAGATTTTTTTTAA
1 AATTATAAAAAAATAAATTATTTTTAA
* **
1550773 AAATATATGAAAATAAATTATTTTTAA
1 AATTATAAAAAAATAAATTATTTTTAA
*
1550800 AATTTTAAAAAAA
1 AATTATAAAAAAA
1550813 ATATTTCAAA
Statistics
Matches: 29, Mismatches: 11, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (27 bp):
AATTATAAAAAAATAAATTATTTTTAA
Found at i:1551668 original size:15 final size:15
Alignment explanation
Indices: 1551648--1551692 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
1551638 TATTAAGATT
1551648 AATAAAAAAATAAAA
1 AATAAAAAAATAAAA
***
1551663 AATAAAAAAATATTT
1 AATAAAAAAATAAAA
1551678 AATAAAAAAATAAAA
1 AATAAAAAAATAAAA
1551693 TCTTAACCAC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (15 bp):
AATAAAAAAATAAAA
Found at i:1552353 original size:17 final size:17
Alignment explanation
Indices: 1552317--1552354 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1552307 ATTCGGAGTC
1552317 CGATTCGAATCATCAAAT
1 CGATTCGAATCA-CAAAT
1552335 CGATTGCGAATCA-AAAT
1 CGATT-CGAATCACAAAT
1552352 CGA
1 CGA
1552355 AACGGCAGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
18 5 0.26
19 7 0.37
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.24
Consensus pattern (17 bp):
CGATTCGAATCACAAAT
Found at i:1554743 original size:15 final size:16
Alignment explanation
Indices: 1554723--1554768 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 16
1554713 TCGATAAGAT
1554723 TATTTTTTTA-AATAA
1 TATTTTTTTATAATAA
*
1554738 TATTTTTTTATAATAG
1 TATTTTTTTATAATAA
*
1554754 TTTATTTTTTATAAT
1 TAT-TTTTTTATAAT
1554769 CAATTTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 10 0.37
16 6 0.22
17 11 0.41
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (16 bp):
TATTTTTTTATAATAA
Found at i:1555462 original size:13 final size:14
Alignment explanation
Indices: 1555446--1555474 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1555436 AACTAAATAA
1555446 AAGTAAAAAAT-TT
1 AAGTAAAAAATATT
1555459 AAGTAAAAAATATT
1 AAGTAAAAAATATT
1555473 AA
1 AA
1555475 AGATTTAGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.28
Consensus pattern (14 bp):
AAGTAAAAAATATT
Found at i:1556041 original size:60 final size:61
Alignment explanation
Indices: 1555915--1556041 Score: 152
Period size: 60 Copynumber: 2.1 Consensus size: 61
1555905 AAATGATCCC
1555915 CAACTATAGAGTAATGCTTTGTTGAGTCTCCTGGCTATTAAAAGTTACAAAATAGTCCAAT
1 CAACTATAGAGTAATGCTTTGTTGAGTCTCCTGGCTATTAAAAGTTACAAAATAGTCCAAT
* ** * * * * *
1555976 -GACTATAGAGTGTTGCTTTGTTGAGTC-CTTTGGCTGTTAAAATTTACAAAATGGT-CACT
1 CAACTATAGAGTAATGCTTTGTTGAGTCTC-CTGGCTATTAAAAGTTACAAAATAGTCCAAT
1556035 CAACTAT
1 CAACTAT
1556042 TCATTATGTT
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
59 4 0.07
60 51 0.93
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (61 bp):
CAACTATAGAGTAATGCTTTGTTGAGTCTCCTGGCTATTAAAAGTTACAAAATAGTCCAAT
Found at i:1556703 original size:2 final size:2
Alignment explanation
Indices: 1556696--1556728 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1556686 TCGTCTCATT
*
1556696 TA TA TA TA TA GA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1556729 GTTTAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1556840 original size:36 final size:36
Alignment explanation
Indices: 1556711--1557027 Score: 265
Period size: 36 Copynumber: 8.7 Consensus size: 36
1556701 ATATAGATAT
* *
1556711 ATATATATATATATTATAG-TTTAAAAATATTTTTAAA
1 ATATATATA-ATA-TATAGTTTTTAAAATATTTTGAAA
* *
1556748 ACCTATATATAATATATAGTTTTGAAAACATGTTTGAAA
1 A--TATATATAATATATAGTTTTTAAAATAT-TTTGAAA
*
1556787 ATATTTATATATTATATAGTTTTTAAAATATTTTGAAA
1 ATA--TATATAATATATAGTTTTTAAAATATTTTGAAA
* *
1556825 ATAAATATAATATATAGTTTTT-ACATATTTTTGAAA
1 ATATATATAATATATAGTTTTTAAAATA-TTTTGAAA
* * *
1556861 ATATATGTATTATATAGTTTTTAAAGTATTTTGAAA
1 ATATATATAATATATAGTTTTTAAAATATTTTGAAA
* * * * *
1556897 ATAAATATACTATATAATTTTTAAAACATTTTTTTAAA
1 ATATATATAATATATAGTTTTT-AAA-ATATTTTGAAA
*
1556935 ATATATAT--TATATAGTTTTT-AAACATTTTGAAA
1 ATATATATAATATATAGTTTTTAAAATATTTTGAAA
* ***
1556968 ATATATATAGT-T-T--TTAAAAAAATATTTTGAAGAA
1 ATATATATAATATATAGTTTTTAAAATATTTTG-A-AA
*
1557002 CATATATATATTATATAGTTTTTAAA
1 -ATATATATAATATATAGTTTTTAAA
1557028 TCATTTCAAA
Statistics
Matches: 226, Mismatches: 34, Indels: 38
0.76 0.11 0.13
Matches are distributed among these distances:
31 2 0.01
32 9 0.04
33 18 0.08
34 5 0.02
35 15 0.07
36 82 0.36
37 15 0.07
38 37 0.16
39 43 0.19
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (36 bp):
ATATATATAATATATAGTTTTTAAAATATTTTGAAA
Found at i:1557105 original size:30 final size:31
Alignment explanation
Indices: 1557047--1557114 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
1557037 AAACTTATAA
*
1557047 TATATAATTTTAAAAAACATTTT-TAAAAAC
1 TATATAATTTTAAAAAACATTTTAAAAAAAC
* *
1557077 TATATAATTTT-GAAAACGTTTTAAAAAAAAC
1 TATATAATTTTAAAAAACATTTT-AAAAAAAC
1557108 -ATATAAT
1 TATATAAT
1557115 ATATAATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 9 0.27
30 18 0.55
31 6 0.18
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (31 bp):
TATATAATTTTAAAAAACATTTTAAAAAAAC
Found at i:1557228 original size:29 final size:28
Alignment explanation
Indices: 1557178--1557243 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 28
1557168 GTTTTTTAGT
1557178 TTATTTA-TTTACCTTTTGTTATGTATTTA
1 TTATTTATTTTACCTTTTGTTAT-T-TTTA
1557207 TTATTTATTTTA-CTTATT-TTATTTTTA
1 TTATTTATTTTACCTT-TTGTTATTTTTA
1557234 TT-TTTATTTT
1 TTATTTATTTT
1557244 GTTGCAGGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
26 8 0.23
27 6 0.17
28 1 0.03
29 14 0.40
30 6 0.17
ACGTcount: A:0.20, C:0.05, G:0.03, T:0.73
Consensus pattern (28 bp):
TTATTTATTTTACCTTTTGTTATTTTTA
Found at i:1563826 original size:165 final size:165
Alignment explanation
Indices: 1563554--1564883 Score: 1628
Period size: 165 Copynumber: 8.0 Consensus size: 165
1563544 TAAATAACAA
* * * * ** *
1563554 ATCATTTGCAGTACAACTTAAGTCTAGAAGGGTTGTCTGCCAATAAAAGACCTTTGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
* * *
1563619 ACGCTCAGCT-CAACGACACATCATTTGTAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAG
66 ACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAG
1563683 ACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
130 ACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
1563719 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
* *
1563784 ACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTTCCAAAGA
66 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA
1563849 CCCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
131 CCCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
* *
1563884 ATCATTTGCAACATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
* * *
1563949 ACGCTCAGCT-CAACGGCACATCATTTGCAGTATAGCTTAAGTCGAAAAGGGTTATCTGCCAAAG
66 ACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAG
1564013 ACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
130 ACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
* * * * **
1564049 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG-TGACCAAAAGACCTTCGAGTTCGAC
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGAC
*
1564113 TACGCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAG
65 TACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAG
1564178 ACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
130 ACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
* *
1564214 ATCATTTGCAGCATAACTTAAGTTGAGAAGGGTTATCTGCCAACCAAAGACATTCGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
* * *
1564279 ACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCA
66 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG----CCA
*** * * * *
1564344 AAGACCTTTGAGTTCGACTACGCTCAGC-TCAACGGCAC
127 AAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
* * * ** *
1564382 ATCATTTGCAGTATAGCTTAAGTCGAAAAGGGTTATCTG----CCAAAGACCCCCGAGTTCGATT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
* * * * * * * * * * *
1564443 ACACTCAACTTCGAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTGACCA
66 ACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATC--TG-CC-
** * * * *
1564508 AAAGACCTTCGAGTTCGACTACGCTCAGC-TCTAAGGCAC
126 AAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
* * * *
1564547 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGA-CTCCCGAGTTCGAT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCT-TCGAGTTCGAC
* * * * *
1564607 TACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAC
65 TACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG----C
** * * * * *
1564672 CAAAGACCTTCGAGTTCGACTACACTAAGC-TCCAAGGCAT
125 CAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
* * * * *
1564712 ATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
1564777 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA
66 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA
* * * * *
1564842 CCCTCGAGTTCGATTACACTCAACCTCGAGGTCAT
131 CCCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
1564877 ATCATTT
1 ATCATTT
1564884 ACAACATAGC
Statistics
Matches: 1040, Mismatches: 102, Indels: 46
0.88 0.09 0.04
Matches are distributed among these distances:
163 2 0.00
164 62 0.06
165 824 0.79
166 11 0.01
167 2 0.00
168 88 0.08
169 49 0.05
170 2 0.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (165 bp):
ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA
CCCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
Done.