Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A12
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: 103038859
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4950000 characters in sequence are not A, C, G, or T
File 10 of 320
Found at i:2734201 original size:45 final size:45
Alignment explanation
Indices: 2734145--2734259 Score: 117
Period size: 44 Copynumber: 2.6 Consensus size: 45
2734135 ATATGCTTCG
* * **
2734145 CTGCAATTTTAGGGAAATAAGATTTGCTATCTTCAGTCTACTCCA
1 CTGCAACTTTAGGGAAATAAGATTTGCTAACTTCAACCTACTCCA
* * * *
2734190 CTGCAACTTTAGGGAGATAAGA-CTACTAACTTCAACCTGCTCCA
1 CTGCAACTTTAGGGAAATAAGATTTGCTAACTTCAACCTACTCCA
* *
2734234 CTGCAACTTCA-GGAAGATAAGGTTTG
1 CTGCAACTTTAGGGAA-ATAAGATTTG
2734260 TTTTGATCTG
Statistics
Matches: 55, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
43 3 0.05
44 31 0.56
45 21 0.38
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (45 bp):
CTGCAACTTTAGGGAAATAAGATTTGCTAACTTCAACCTACTCCA
Found at i:2734301 original size:55 final size:55
Alignment explanation
Indices: 2734226--2734337 Score: 188
Period size: 55 Copynumber: 2.0 Consensus size: 55
2734216 TAACTTCAAC
*
2734226 CTGCTCCACTGCAACTTCAGGAAGATAAGGTTTGTTTTGATCTGCTCTACTGCAA
1 CTGCTCCACTGCAACTTCAGGAAGATAAGGTTTGTTTTGACCTGCTCTACTGCAA
* * *
2734281 CTGCTCCACTGTAACTTCAGGGAGATAAGGTTTGTTTTGACCTGTTCTACTGCAA
1 CTGCTCCACTGCAACTTCAGGAAGATAAGGTTTGTTTTGACCTGCTCTACTGCAA
2734336 CT
1 CT
2734338 TCAGAGAGAT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (55 bp):
CTGCTCCACTGCAACTTCAGGAAGATAAGGTTTGTTTTGACCTGCTCTACTGCAA
Found at i:2734518 original size:85 final size:85
Alignment explanation
Indices: 2734417--2734573 Score: 224
Period size: 85 Copynumber: 1.8 Consensus size: 85
2734407 GCTATCTTCT
* *
2734417 ATTTGCTCCACTGCAACTTTAGGGAGATAAGACTAGTAACTTCAACCTACTCCACTGCAACTTTA
1 ATTTGCTCCACTGCAACTTCAGGGAGATAAGACTAGTAACTTCAACCTACTCCACTGAAACTTTA
*
2734482 GGGAGATTAGGTTTGTTTTG
66 AGGAGATTAGGTTTGTTTTG
* * * * * **
2734502 ATTTGCTCTACTGCAACTTCAGGGAGATAAGATTTGTGACTTCAATCTACTCTGCTGAAACTTTA
1 ATTTGCTCCACTGCAACTTCAGGGAGATAAGACTAGTAACTTCAACCTACTCCACTGAAACTTTA
2734567 AGGAGAT
66 AGGAGAT
2734574 CTGCTGTGGC
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
85 62 1.00
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (85 bp):
ATTTGCTCCACTGCAACTTCAGGGAGATAAGACTAGTAACTTCAACCTACTCCACTGAAACTTTA
AGGAGATTAGGTTTGTTTTG
Found at i:2734767 original size:86 final size:86
Alignment explanation
Indices: 2734608--2735448 Score: 1004
Period size: 86 Copynumber: 9.7 Consensus size: 86
2734598 ACGCCATTTC
* * * *
2734608 AGGGAGA-AGAGATTTGTAATTCCCAGCCTGTTACCCTATTGCTTAGGGGGTTAAGGCTTACCGT
1 AGGGAGATA-AGATCTGTAATT--CAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCATCGT
**
2734672 CTTTAATCTGCTCCACTACTGCTT
63 CTTCGATCTGCTCCACTACTGCTT
* * **
2734696 AGGGAGATAAGATCTGTAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCACCTT
1 AGGGAGATAAGATCTGTAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCATCGTCTT
* *
2734761 CGATCTGTTCCCCTACTGCTT
66 CGATCTGCTCCACTACTGCTT
* * * * *
2734782 AGGGTGATAAGATCTATAAATTCAGCCTGTTACCCTACTGCTTAAGGGGTTAAGGCTTATTGTCT
1 AGGGAGATAAGATCTGT-AATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCATCGTCT
* *
2734847 TCGATCCGCTACACTACTGCTT
65 TCGATCTGCTCCACTACTGCTT
* ** * * * **
2734869 AGAGAGATAAGATCTAAAATTTTCAACCTGTTACCATACTGCTTA-GGGGTTAAGGCCCATTATC
1 AGGGAGATAAGATCTGTAA--TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCATCGTC
2734933 TTCGATCTGCTCCACTACTGCTT
64 TTCGATCTGCTCCACTACTGCTT
* * * * **
2734956 AGAGAGACAAGATCTGAAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATTATC
1 AGGGAGATAAGATCTGTAA--TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCATCGTC
* *
2735021 TTCGATCCGTTCCACTACTGCTT
64 TTCGATCTGCTCCACTACTGCTT
* * * * * *
2735044 AGGGTGACAAGATCTGTAATTCGGCCTGTTACCCTACTGCTTAGAGGGTTAAGGCTTATTGTCTT
1 AGGGAGATAAGATCTGTAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCATCGTCTT
**
2735109 CGATCCACTCCACTACTGCTT
66 CGATCTGCTCCACTACTGCTT
** * * *
2735130 AGGGAGATAAGATCTAAAATTTCCAGCCTGTTACACTA-TCGCTTAGGAGGTTAAGGCTCACCGT
1 AGGGAGATAAGATCTGTAA-TT-CAGCCTGTTACCCTACT-GCTTAGGGGGTTAAGGCTCATCGT
*
2735194 CTTTGATCTGCTCCACTACTGCTT
63 CTTCGATCTGCTCCACTACTGCTT
* * * ** * *
2735218 AGGGAGACAATATCTGTAATTCAGCCTGTTACCTTACTATTTAGGGGGTTAAGGCTCACCGCCTT
1 AGGGAGATAAGATCTGTAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCATCGTCTT
2735283 CGATCTGCTCCACTACTGCTT
66 CGATCTGCTCCACTACTGCTT
* *
2735304 AGGGAGATAAGATCTGTAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCATCTT
1 AGGGAGATAAGATCTGTAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCATCGTCTT
*
2735369 CGATCTGCTCTACTACTGCTT
66 CGATCTGCTCCACTACTGCTT
*
2735390 AGGGAGACAAGATCTGTAATTCTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTC
1 AGGGAGATAAGATCTGTAA-T-TCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTC
2735449 GTGAATTCAC
Statistics
Matches: 657, Mismatches: 85, Indels: 22
0.86 0.11 0.03
Matches are distributed among these distances:
86 298 0.45
87 157 0.24
88 201 0.31
89 1 0.00
ACGTcount: A:0.23, C:0.24, G:0.21, T:0.31
Consensus pattern (86 bp):
AGGGAGATAAGATCTGTAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCATCGTCTT
CGATCTGCTCCACTACTGCTT
Found at i:2735126 original size:174 final size:173
Alignment explanation
Indices: 2734631--2735448 Score: 1032
Period size: 174 Copynumber: 4.7 Consensus size: 173
2734621 TTGTAATTCC
* * **
2734631 CAGCCTGTTACCCTATTGCTTAGGGGGTTAAGGCTTACCGTCTTTAATCTGCTCCACTACTGCTT
1 CAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTGCTT
* * *
2734696 AGGGAGATAAGATCTGTAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAAGCCCATCACCTT
66 AGGGAGACAAGATCTGTAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCATCACCTT
* * * *
2734761 CGATCTGTTCCCCTACTGCTTAGGGTGATAAGATCT-ATAAATT
131 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGA-AATTT
* * ** * *
2734804 CAGCCTGTTACCCTACTGCTTAAGGGGTTAAGGCTTATTGTCTTCGATCCGCTACACTACTGCTT
1 CAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTGCTT
* * ** * * * * *
2734869 AGAGAGATAAGATCTAAAATTTTCAACCTGTTACCATACTGCTTA-GGGGTTAAGGCCCATTATC
66 AGGGAGACAAGATCTGTAA--TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCATCACC
* *
2734933 TTCGATCTGCTCCACTACTGCTTAGAGAGACAAGATCTGAAATTTT
129 TTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAA-TTT
* *** * *
2734979 CAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATTATCTTCGATCCGTTCCACTACTGCTT
1 CAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTGCTT
* * * * ***
2735044 AGGGTGACAAGATCTGTAATTCGGCCTGTTACCCTACTGCTTAGAGGGTTAAGGCTTATTGTCTT
66 AGGGAGACAAGATCTGTAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCATCACCTT
** *
2735109 CGATCCACTCCACTACTGCTTAGGGAGATAAGATCTAAAATTT
131 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATTT
* * *
2735152 CCAGCCTGTTACACTA-TCGCTTAGGAGGTTAAGGCTCACCGTCTTTGATCTGCTCCACTACTGC
1 -CAGCCTGTTACCCTACT-GCTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTGC
* * ** * *
2735216 TTAGGGAGACAATATCTGTAATTCAGCCTGTTACCTTACTATTTAGGGGGTTAAGGCTCACCGCC
64 TTAGGGAGACAAGATCTGTAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCATCACC
*
2735281 TTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAA-TT
129 TTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATTT
* *
2735325 CAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCATCTTCGATCTGCTCTACTACTGCTT
1 CAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTGCTT
2735390 AGGGAGACAAGATCTGTAATTCTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTC
66 AGGGAGACAAGATCTGTAA-T-TCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTC
2735449 GTGAATTCAC
Statistics
Matches: 557, Mismatches: 78, Indels: 19
0.85 0.12 0.03
Matches are distributed among these distances:
172 76 0.14
173 102 0.18
174 281 0.50
175 98 0.18
ACGTcount: A:0.23, C:0.24, G:0.21, T:0.32
Consensus pattern (173 bp):
CAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTGCTT
AGGGAGACAAGATCTGTAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCATCACCTT
CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATTT
Found at i:2735167 original size:44 final size:44
Alignment explanation
Indices: 2734685--2735176 Score: 167
Period size: 44 Copynumber: 11.3 Consensus size: 44
2734675 TAATCTGCTC
*
2734685 CACTACTGCTTAGGGAGATAAGATCTGTAA-TT-CAGCCTGTTA
1 CACTACTGCTTAGGGAGATAAGATCTATAATTTCCAGCCTGTTA
* * * * * ** * * *
2734727 CCCTACTGCTTAGGGGGTTAA-AGCCCATCACCTTCGA-TCTGTTC
1 CACTACTGCTTAGGGAGATAAGA-TCTAT-AATTTCCAGCCTGTTA
* * *
2734771 CCCTACTGCTTAGGGTGATAAGATCTATAAATT-CAGCCTGTTA
1 CACTACTGCTTAGGGAGATAAGATCTATAATTTCCAGCCTGTTA
* * * ** * * *
2734814 CCCTACTGCTTAAGGG-GTTAAG-GCTTATTGTCTTCGATCC-GCTA
1 CACTACTGCTT-AGGGAGATAAGATC-TATAAT-TTCCAGCCTGTTA
* * * *
2734858 CACTACTGCTTAGAGAGATAAGATCTAAAATTTTCAACCTGTTA
1 CACTACTGCTTAGGGAGATAAGATCTATAATTTCCAGCCTGTTA
* ** * * * * * *
2734902 C-CATACTGCTTAGGG-GTTAAGGCCCATTATCTTCGA-TCTGCTC
1 CAC-TACTGCTTAGGGAGATAAGATCTATAAT-TTCCAGCCTGTTA
* * *
2734945 CACTACTGCTTAGAGAGACAAGATCTGA-AATTTTCAGCCTGTTA
1 CACTACTGCTTAGGGAGATAAGATCT-ATAATTTCCAGCCTGTTA
* * * ** * * * * *
2734989 CCCTACTGCTTAGGGGGTTAAGGCCCATTATCTTCGATCC-GTTC
1 CACTACTGCTTAGGGAGATAAGATCTATAAT-TTCCAGCCTGTTA
* * * *
2735033 CACTACTGCTTAGGGTGACAAGATCTGTAA-TT-CGGCCTGTTA
1 CACTACTGCTTAGGGAGATAAGATCTATAATTTCCAGCCTGTTA
* * * ** * * ** *
2735075 CCCTACTGCTTAGAGG-GTTAAG-GCTTATTGTCTTCGATCC-ACTC
1 CACTACTGCTTAG-GGAGATAAGATC-TATAAT-TTCCAGCCTGTTA
*
2735119 CACTACTGCTTAGGGAGATAAGATCTAAAATTTCCAGCCTGTTA
1 CACTACTGCTTAGGGAGATAAGATCTATAATTTCCAGCCTGTTA
2735163 CACTA-TCGCTTAGG
1 CACTACT-GCTTAGG
2735177 AGGTTAAGGC
Statistics
Matches: 307, Mismatches: 112, Indels: 60
0.64 0.23 0.13
Matches are distributed among these distances:
41 4 0.01
42 45 0.15
43 77 0.25
44 166 0.54
45 15 0.05
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (44 bp):
CACTACTGCTTAGGGAGATAAGATCTATAATTTCCAGCCTGTTA
Found at i:2735347 original size:260 final size:261
Alignment explanation
Indices: 2734625--2735448 Score: 1140
Period size: 260 Copynumber: 3.2 Consensus size: 261
2734615 AGAGATTTGT
* * *
2734625 AATTCCCAGCCTGTTACCCTAT-TGCTTAGGGGGTTAAGGCTTACCGTCTTTAATCTGCTCCACT
1 AATTTCCAGCCTGTTACCCTATCTGCTTAGGGGGTTAAGGCTCACCGTCTTTGATCTGCTCCACT
* *
2734689 ACTGCTTAGGGAGATAAGATCTGTAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAAGCCCA
66 ACTGCTTAGGGAGACAAGATCTGTAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCA
* *
2734754 TCACCTTCGATCTGTTCCCCTACTGCTTAGGGTGATAAGATCTATAAATTCAGCCTGTTACCCTA
131 TCACCTTCGATCTGTTCCACTACTGCTTAGGGTGATAAGATCTGT-AATTCAGCCTGTTACCCTA
* *
2734819 CTGCTTA-AGGGGTTAAGGCTTATTGTCTTCGATCCGCTACACTACTGCTTAGAGAGATAAGATC
195 CTGCTTAGA-GGGTTAAGGCTTATTGTCTTCGATCCGCTCCACTACTGCTTAGGGAGATAAGATC
2734883 TAA
259 TAA
* * * * *** *
2734886 AATTTTCAACCTGTTACCATA-CTGCTTA-GGGGTTAAGGCCCATTATCTTCGATCTGCTCCACT
1 AATTTCCAGCCTGTTACCCTATCTGCTTAGGGGGTTAAGGCTCACCGTCTTTGATCTGCTCCACT
* *
2734949 ACTGCTTAGAGAGACAAGATCTGAAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCC
66 ACTGCTTAGGGAGACAAGATCTGTAA--TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCC
* * * * *
2735014 CATTATCTTCGATCCGTTCCACTACTGCTTAGGGTGACAAGATCTGTAATTCGGCCTGTTACCCT
129 CATCACCTTCGATCTGTTCCACTACTGCTTAGGGTGATAAGATCTGTAATTCAGCCTGTTACCCT
*
2735079 ACTGCTTAGAGGGTTAAGGCTTATTGTCTTCGATCCACTCCACTACTGCTTAGGGAGATAAGATC
194 ACTGCTTAGAGGGTTAAGGCTTATTGTCTTCGATCCGCTCCACTACTGCTTAGGGAGATAAGATC
2735144 TAA
259 TAA
* *
2735147 AATTTCCAGCCTGTTACACTATC-GCTTAGGAGGTTAAGGCTCACCGTCTTTGATCTGCTCCACT
1 AATTTCCAGCCTGTTACCCTATCTGCTTAGGGGGTTAAGGCTCACCGTCTTTGATCTGCTCCACT
* * ** *
2735211 ACTGCTTAGGGAGACAATATCTGTAATTCAGCCTGTTACCTTACTATTTAGGGGGTTAAGGCTCA
66 ACTGCTTAGGGAGACAAGATCTGTAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCA
* * * *
2735276 CCGCCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTCAGCCTGTTACCCTAC
131 TCACCTTCGATCTGTTCCACTACTGCTTAGGGTGATAAGATCTGTAATTCAGCCTGTTACCCTAC
* * *** * * * *
2735341 TGCTTAGGGGGTTAAGGCTCACCATCTTCGATCTGCTCTACTACTGCTTAGGGAGACAAGATCTG
196 TGCTTAGAGGGTTAAGGCTTATTGTCTTCGATCCGCTCCACTACTGCTTAGGGAGATAAGATCTA
*
2735406 T
261 A
2735407 AA-TTCTCAGCCTGTTACCCTA-CTGCTTAGGGGGTTAAGGCTC
1 AATTTC-CAGCCTGTTACCCTATCTGCTTAGGGGGTTAAGGCTC
2735449 GTGAATTCAC
Statistics
Matches: 491, Mismatches: 64, Indels: 17
0.86 0.11 0.03
Matches are distributed among these distances:
259 4 0.01
260 231 0.47
261 125 0.25
262 131 0.27
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.32
Consensus pattern (261 bp):
AATTTCCAGCCTGTTACCCTATCTGCTTAGGGGGTTAAGGCTCACCGTCTTTGATCTGCTCCACT
ACTGCTTAGGGAGACAAGATCTGTAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCA
TCACCTTCGATCTGTTCCACTACTGCTTAGGGTGATAAGATCTGTAATTCAGCCTGTTACCCTAC
TGCTTAGAGGGTTAAGGCTTATTGTCTTCGATCCGCTCCACTACTGCTTAGGGAGATAAGATCTA
A
Found at i:2735601 original size:64 final size:64
Alignment explanation
Indices: 2735500--2735627 Score: 211
Period size: 64 Copynumber: 2.0 Consensus size: 64
2735490 TCATGTATCT
* *
2735500 ATGCTTATGCCAAATAGTTAGGATGCTATAATCGAAATGAATCAAATGCTCCTAACTAGATGTG
1 ATGCTTATGCCAAATAATTAGGATGCTATAATCGAAATAAATCAAATGCTCCTAACTAGATGTG
* * *
2735564 ATGCTTGTGTCAAATAATTAGGATGCTATGATCGAAATAAATCAAATGCTCCTAACTAGATGTG
1 ATGCTTATGCCAAATAATTAGGATGCTATAATCGAAATAAATCAAATGCTCCTAACTAGATGTG
2735628 TTATGAATGA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 59 1.00
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (64 bp):
ATGCTTATGCCAAATAATTAGGATGCTATAATCGAAATAAATCAAATGCTCCTAACTAGATGTG
Found at i:2740744 original size:14 final size:16
Alignment explanation
Indices: 2740718--2740751 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
2740708 AAATAAAAAC
2740718 ATAAAATATGACAA-A
1 ATAAAATATGACAATA
2740733 ATAAAA-ATGACAATA
1 ATAAAATATGACAATA
2740748 ATAA
1 ATAA
2740752 TGAAAACAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.68, C:0.06, G:0.06, T:0.21
Consensus pattern (16 bp):
ATAAAATATGACAATA
Found at i:2740767 original size:3 final size:3
Alignment explanation
Indices: 2740761--2741083 Score: 169
Period size: 3 Copynumber: 107.7 Consensus size: 3
2740751 ATGAAAACAG
* * * * * *
2740761 TAA TAA TAA TAA TAC TAA TAG TAG TAA TAA TAA TAG TAA AAA GTAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA
* ** * *
2740807 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TGG CAA TAA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
** * * * *
2740855 TAA TAA T-A TGC TAAA TAA TAA TAA GAA -AA -AA AAA TAG TAA TAG
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * **
2740898 TAA TTA CAA -AA GTGA TAA TAA TAA TAA -AA TAGGA TGC TAA TAA TAA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TA--A TAA TAA TAA TAA
* * * * * * * *
2740944 TAC TAA TGAA -AC TAA AAA TAG TAG TAA TAG TAA TAA TAA TAA GACCG
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA--A
* * * * * *
2740991 TAA TAA AAA GAA AAA GAAA TAA TAA TAA TAA T-A TAT TAA TAA GAA
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
2741036 -AA TAA TAA T-C TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2741082 TA
1 TA
2741084 GAAATGGAAT
Statistics
Matches: 242, Mismatches: 61, Indels: 34
0.72 0.18 0.10
Matches are distributed among these distances:
2 16 0.07
3 215 0.89
4 8 0.03
5 3 0.01
ACGTcount: A:0.60, C:0.03, G:0.08, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:2743294 original size:16 final size:17
Alignment explanation
Indices: 2743259--2743295 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
2743249 TTTTTTTTGT
2743259 TTTTCATTGTTAATAAG
1 TTTTCATTGTTAATAAG
2743276 TTTTCAATT-TTAA-AAG
1 TTTTC-ATTGTTAATAAG
2743292 TTTT
1 TTTT
2743296 TATCTAACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.37
17 9 0.47
18 3 0.16
ACGTcount: A:0.30, C:0.05, G:0.08, T:0.57
Consensus pattern (17 bp):
TTTTCATTGTTAATAAG
Found at i:2743773 original size:32 final size:32
Alignment explanation
Indices: 2743732--2743793 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
2743722 TTAAAGATTC
2743732 GTTGGTTTTGATAGACGAAGAAATGAATTTGT
1 GTTGGTTTTGATAGACGAAGAAATGAATTTGT
2743764 GTTGGTTTTGATAGACGAAGAAATGAATTT
1 GTTGGTTTTGATAGACGAAGAAATGAATTT
2743794 ATTTTTAGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.32, C:0.03, G:0.27, T:0.37
Consensus pattern (32 bp):
GTTGGTTTTGATAGACGAAGAAATGAATTTGT
Found at i:2751178 original size:27 final size:27
Alignment explanation
Indices: 2751140--2751193 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
2751130 TTGCTTTGTA
*
2751140 ACACTGTTAAATATACATAGCAGAAAT
1 ACACTGTTAAATATACACAGCAGAAAT
2751167 ACACTGTTAAATATACACAGCAGAAAT
1 ACACTGTTAAATATACACAGCAGAAAT
2751194 CATAATTATG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.48, C:0.17, G:0.11, T:0.24
Consensus pattern (27 bp):
ACACTGTTAAATATACACAGCAGAAAT
Found at i:2761486 original size:4 final size:4
Alignment explanation
Indices: 2761477--2761501 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2761467 TCAAATTATA
2761477 TAAT TAAT TAAT TAAT TAAT TAAT T
1 TAAT TAAT TAAT TAAT TAAT TAAT T
2761502 GAGTTTATAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TAAT
Found at i:2779503 original size:133 final size:133
Alignment explanation
Indices: 2779244--2779626 Score: 631
Period size: 133 Copynumber: 2.9 Consensus size: 133
2779234 TAGGTACATA
* * * * *
2779244 AGTTAATCATGGCTATTTTTTTAAATCATGTGTGTTATACTTATTCTATTATCTGATTTGATAAG
1 AGTTAAGCATGACTA-TTTTGTAAATCATGTGTGTTATACTTATTCTGTTATCTGTTTTGATAAG
* *
2779309 CTATTTGATTCAGTTATGTAATATGAACATATGATATTATGATTTTGCATGTCCATGTGCATTGA
65 CTATTTGATTCAATTATGTAATATGAACATATGATATTATGATTCTGCATGTCCATGTGCATTGA
2779374 GGTG
130 GGTG
* * *
2779378 AGTTAAGCATGATTGTTTTGTAAATCATGTGCGTTATACTTATTCTGTTATCTGTTTTGATAAGC
1 AGTTAAGCATGACTATTTTGTAAATCATGTGTGTTATACTTATTCTGTTATCTGTTTTGATAAGC
* * *
2779443 TATTTGATTCAATTATGTAATATGAACCTATGATATTATGATTCTACATGTCCATGTGCATTGGG
66 TATTTGATTCAATTATGTAATATGAACATATGATATTATGATTCTGCATGTCCATGTGCATTGAG
2779508 GTG
131 GTG
2779511 AGTTAAGCATGACTATTTTGTAAATCATGTGTGTTATACTTATTCTGTTATCTGTTTTGATAAGC
1 AGTTAAGCATGACTATTTTGTAAATCATGTGTGTTATACTTATTCTGTTATCTGTTTTGATAAGC
*
2779576 TATTTGATTCAATTATGTAATATGAACATATGATATTATGATCCTGCATGT
66 TATTTGATTCAATTATGTAATATGAACATATGATATTATGATTCTGCATGT
2779627 GCATTGGGCC
Statistics
Matches: 230, Mismatches: 19, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
133 219 0.95
134 11 0.05
ACGTcount: A:0.28, C:0.10, G:0.17, T:0.45
Consensus pattern (133 bp):
AGTTAAGCATGACTATTTTGTAAATCATGTGTGTTATACTTATTCTGTTATCTGTTTTGATAAGC
TATTTGATTCAATTATGTAATATGAACATATGATATTATGATTCTGCATGTCCATGTGCATTGAG
GTG
Found at i:2782655 original size:192 final size:192
Alignment explanation
Indices: 2782328--2783085 Score: 1318
Period size: 192 Copynumber: 3.9 Consensus size: 192
2782318 GATAAATGTG
* * *
2782328 GCTTAATGGAGTTTCCTAAGCCTAGGCCTCCCCATGCTTCTTGCAACTCTCTCTCCCTTGCTTCT
1 GCTTAATGGAGTTTCCTAAGCTTAAGCCGCCCCATGCTTCTTGCAACTCTCTCTCCCTTGCTTCT
*
2782393 CTACGAGATAGAGAGAATCTAATCTGCTCACTTGGTTGCTCAGAAGTAGCCATCTTCTCTTTCTC
66 CTACGAGATACAGAGAATCTAATCTGCTCACTTGGTTGCTCAGAAGTAGCCATCTTCTCTTTCTC
*
2782458 TAATTTTGATTTGTGTTTAACCAAAATTTGGTCCAGACTACCCCGATCATCCGCCACCTGTT
131 TAATTTTGATTTGTGTTTAACCAAAATTTGGTCCAGACTACCCTGATCATCCGCCACCTGTT
* *
2782520 GCTTAATGGAGTTTCCTAAGCTTAAACCGCCCCATGCTTCTTGCAACTCTCTCTCCCTTGCTTGT
1 GCTTAATGGAGTTTCCTAAGCTTAAGCCGCCCCATGCTTCTTGCAACTCTCTCTCCCTTGCTTCT
*
2782585 CTACGAGATACAGAGAATCTAATCTGCTCACTTGGTTGCTCAGAAGTAGCCATCTTCTCTTTTTC
66 CTACGAGATACAGAGAATCTAATCTGCTCACTTGGTTGCTCAGAAGTAGCCATCTTCTCTTTCTC
*
2782650 TAATTTTGATTTGTGTTTAACTAAAATTTGGTCCAGACTACCCTGATCATCCGCCACCTGTT
131 TAATTTTGATTTGTGTTTAACCAAAATTTGGTCCAGACTACCCTGATCATCCGCCACCTGTT
* *
2782712 GCTTAATGGAGTTTTCTAAGCTTAAGCCGCCCCATGCTTCTTGCAACTCTCTCTCCCTTGCTTGT
1 GCTTAATGGAGTTTCCTAAGCTTAAGCCGCCCCATGCTTCTTGCAACTCTCTCTCCCTTGCTTCT
*
2782777 CTACGAGATACAGAGAATCTAATCTGCTCACTTGGTTGCTCAGAAGTAGCCATCTTCTCTTTTTC
66 CTACGAGATACAGAGAATCTAATCTGCTCACTTGGTTGCTCAGAAGTAGCCATCTTCTCTTTCTC
*
2782842 TAATTTTGATTTGTGTTTAACTAAAATTTGGTCCAGACTACCCTGATCATCCGCCACCTGTT
131 TAATTTTGATTTGTGTTTAACCAAAATTTGGTCCAGACTACCCTGATCATCCGCCACCTGTT
*
2782904 GCTTAATGGAGTTTTCTAAGCTTAAGCCGCCCCATGCTTCTTGCAACTCTCTCTCCCTTGCTTCT
1 GCTTAATGGAGTTTCCTAAGCTTAAGCCGCCCCATGCTTCTTGCAACTCTCTCTCCCTTGCTTCT
* * * * * * *
2782969 CTACGAGATACAGATAATCTAATTTGCTCGCTTGCTTGCTCAGAACTTGTCATCTTCTCTTTCTC
66 CTACGAGATACAGAGAATCTAATCTGCTCACTTGGTTGCTCAGAAGTAGCCATCTTCTCTTTCTC
*
2783034 TAATTTTGATTTGTGTTTAACCAAAATTTGATCCAGACTACCCTGATCATCC
131 TAATTTTGATTTGTGTTTAACCAAAATTTGGTCCAGACTACCCTGATCATCC
2783086 ACTTGTGGCG
Statistics
Matches: 544, Mismatches: 22, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
192 544 1.00
ACGTcount: A:0.21, C:0.27, G:0.15, T:0.36
Consensus pattern (192 bp):
GCTTAATGGAGTTTCCTAAGCTTAAGCCGCCCCATGCTTCTTGCAACTCTCTCTCCCTTGCTTCT
CTACGAGATACAGAGAATCTAATCTGCTCACTTGGTTGCTCAGAAGTAGCCATCTTCTCTTTCTC
TAATTTTGATTTGTGTTTAACCAAAATTTGGTCCAGACTACCCTGATCATCCGCCACCTGTT
Found at i:2789512 original size:19 final size:20
Alignment explanation
Indices: 2789475--2789512 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
2789465 TCTAAATTTT
* *
2789475 TTTTTTACAATTTATAATAA
1 TTTTTTACAAGTTAGAATAA
2789495 TTTTTTA-AAGTTAGAATA
1 TTTTTTACAAGTTAGAATA
2789513 GGGGAATTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (20 bp):
TTTTTTACAAGTTAGAATAA
Found at i:2795645 original size:19 final size:21
Alignment explanation
Indices: 2795607--2795659 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 21
2795597 TCATATCAAC
*
2795607 AAATAATTTAAAAATTATAAA
1 AAATAATTTAAAAATAATAAA
2795628 AAAT-ATTT-AAAATAATAAA
1 AAATAATTTAAAAATAATAAA
2795647 TAAA-AATTATAAA
1 -AAATAATT-TAAA
2795660 TTTCAGAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
19 10 0.37
20 10 0.37
21 5 0.19
22 2 0.07
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
AAATAATTTAAAAATAATAAA
Found at i:2797450 original size:33 final size:33
Alignment explanation
Indices: 2797411--2797481 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
2797401 AATATATATA
* *
2797411 TAAATTAGTTTAAATTGTGAGTAAAAATAAATT
1 TAAATTAGTTTAAATTGTGAATAAAAATAAAAT
2797444 TAAATTAGTTTAAATTGTGAATAAAAATAAAAT
1 TAAATTAGTTTAAATTGTGAATAAAAATAAAAT
2797477 TAAAT
1 TAAAT
2797482 AGGTAAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (33 bp):
TAAATTAGTTTAAATTGTGAATAAAAATAAAAT
Found at i:2806470 original size:39 final size:39
Alignment explanation
Indices: 2806412--2806488 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 39
2806402 TAGGGTTTCA
*
2806412 GTTTAGCTCTAATGAGCTTCAGTTAGCCTTCGGGCTTCT
1 GTTTAGCACTAATGAGCTTCAGTTAGCCTTCGGGCTTCT
* * *
2806451 GTTTAGCACTTATGTGCTTCAGTTAGCCTTCTGGCTTC
1 GTTTAGCACTAATGAGCTTCAGTTAGCCTTCGGGCTTC
2806489 AGATCACGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.14, C:0.23, G:0.22, T:0.40
Consensus pattern (39 bp):
GTTTAGCACTAATGAGCTTCAGTTAGCCTTCGGGCTTCT
Found at i:2806489 original size:18 final size:18
Alignment explanation
Indices: 2806427--2806490 Score: 74
Period size: 18 Copynumber: 3.4 Consensus size: 18
2806417 GCTCTAATGA
*
2806427 GCTTCAGTTAGCCTTCGG
1 GCTTCAGTTAGCCTTCTG
* *
2806445 GCTTCTGTTTAGCACTTATG
1 GCTTCAG-TTAGC-CTTCTG
2806465 TGCTTCAGTTAGCCTTCTG
1 -GCTTCAGTTAGCCTTCTG
2806484 GCTTCAG
1 GCTTCAG
2806491 ATCACGATGT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
18 13 0.34
19 10 0.26
20 9 0.24
21 6 0.16
ACGTcount: A:0.12, C:0.25, G:0.23, T:0.39
Consensus pattern (18 bp):
GCTTCAGTTAGCCTTCTG
Found at i:2809750 original size:32 final size:32
Alignment explanation
Indices: 2809709--2809772 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
2809699 TATCATGACA
2809709 TAGTTCAACAATTCCGGGTCAATAAGTAATGT
1 TAGTTCAACAATTCCGGGTCAATAAGTAATGT
2809741 TAGTTCAACAATTCCGGGTCAATAAGTAATGT
1 TAGTTCAACAATTCCGGGTCAATAAGTAATGT
2809773 ACATACAGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (32 bp):
TAGTTCAACAATTCCGGGTCAATAAGTAATGT
Found at i:2812527 original size:24 final size:24
Alignment explanation
Indices: 2812500--2812561 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 24
2812490 GGAGTGCAAC
*
2812500 GGAGACGAAGATGAAGTCGATGGT
1 GGAGACGAAGATGAAGACGATGGT
* * *
2812524 GGAGACAAAAATAAAGACGATGGT
1 GGAGACGAAGATGAAGACGATGGT
* *
2812548 AGAGATGAAGATGA
1 GGAGACGAAGATGA
2812562 CTACAATGAT
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.35, T:0.15
Consensus pattern (24 bp):
GGAGACGAAGATGAAGACGATGGT
Found at i:2814082 original size:8 final size:8
Alignment explanation
Indices: 2814069--2814101 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
2814059 TAAAAATAAA
2814069 TTTATTTT
1 TTTATTTT
2814077 TTTATTTT
1 TTTATTTT
*
2814085 TTTATATT
1 TTTATTTT
2814093 TTTATTTT
1 TTTATTTT
2814101 T
1 T
2814102 GAATTTGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (8 bp):
TTTATTTT
Found at i:2820130 original size:19 final size:19
Alignment explanation
Indices: 2820093--2820130 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2820083 CCCCTTGGCT
*
2820093 GTGTGTGCTCCAAGCCAAG
1 GTGTGTGCTCCAAGACAAG
2820112 GTGTGTGCCTCCAA-ACAAG
1 GTGTGTG-CTCCAAGACAAG
2820131 CTTCCCGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.24, C:0.26, G:0.29, T:0.21
Consensus pattern (19 bp):
GTGTGTGCTCCAAGACAAG
Found at i:2825358 original size:33 final size:33
Alignment explanation
Indices: 2825316--2825414 Score: 162
Period size: 33 Copynumber: 3.0 Consensus size: 33
2825306 TATTACAAAC
* *
2825316 GAGTGTTTGGTTGCTAGACGGGAGCTGGAATGT
1 GAGTGTTTGGTTGCTGGACAGGAGCTGGAATGT
*
2825349 GAGTGTTTGGTTGCTGGATAGGAGCTGGAATGT
1 GAGTGTTTGGTTGCTGGACAGGAGCTGGAATGT
*
2825382 GAGTGTTTGGTTGCTGGACAGTAGCTGGAATGT
1 GAGTGTTTGGTTGCTGGACAGGAGCTGGAATGT
2825415 CAAGAAGAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 61 1.00
ACGTcount: A:0.18, C:0.08, G:0.41, T:0.32
Consensus pattern (33 bp):
GAGTGTTTGGTTGCTGGACAGGAGCTGGAATGT
Found at i:2833602 original size:3 final size:3
Alignment explanation
Indices: 2833594--2833642 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
2833584 TTTAATTTAG
2833594 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2833641 AT
1 AT
2833643 GAAATAAGTT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 43 0.96
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2834188 original size:3 final size:3
Alignment explanation
Indices: 2834173--2834216 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
2834163 TATTTATTAA
*
2834173 ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2834217 CAAATAAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2834573 original size:17 final size:15
Alignment explanation
Indices: 2834551--2834584 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 15
2834541 AGGGGAGAAA
2834551 GAAAGAAAGGAAAAAGG
1 GAAAGAAA-G-AAAAGG
2834568 GAAAGAAAGAAAAGG
1 GAAAGAAAGAAAAGG
2834583 GA
1 GA
2834585 GAAATAGGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 1 0.06
17 8 0.47
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (15 bp):
GAAAGAAAGAAAAGG
Found at i:2834588 original size:17 final size:18
Alignment explanation
Indices: 2834550--2834588 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
2834540 CAGGGGAGAA
2834550 AGAAAGAAAGGAAAAAGG
1 AGAAAGAAAGGAAAAAGG
*
2834568 -GAAAGAAA-GAAAAGGG
1 AGAAAGAAAGGAAAAAGG
2834584 AGAAA
1 AGAAA
2834589 TAGGGATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (18 bp):
AGAAAGAAAGGAAAAAGG
Found at i:2835466 original size:18 final size:18
Alignment explanation
Indices: 2835445--2835508 Score: 85
Period size: 18 Copynumber: 3.6 Consensus size: 18
2835435 AACGACTAAC
*
2835445 TGTTATTGAATAATTGAT
1 TGTTACTGAATAATTGAT
2835463 TGTTACTGAATAATTGAT
1 TGTTACTGAATAATTGAT
* *
2835481 TGCTACTGAAAAATTGAT
1 TGTTACTGAATAATTGAT
*
2835499 T-TTAATGAAT
1 TGTTACTGAAT
2835509 GATATTGATA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
17 6 0.15
18 34 0.85
ACGTcount: A:0.36, C:0.05, G:0.16, T:0.44
Consensus pattern (18 bp):
TGTTACTGAATAATTGAT
Found at i:2849590 original size:3 final size:3
Alignment explanation
Indices: 2849571--2849649 Score: 65
Period size: 3 Copynumber: 25.7 Consensus size: 3
2849561 AACGTAATAG
* *
2849571 TAT TTT TAT TAT T-T TAT TAT TAT T-T TCACCT T-T TAT TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-A--T TAT TAT TAT TAT TAT
*
2849616 TAT TAACC TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT T-A-T TAT TAT TAT TAT TAT TAT TAT TAT TA
2849650 ATATAGTGTT
Statistics
Matches: 62, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
2 6 0.10
3 51 0.82
4 2 0.03
5 1 0.02
6 2 0.03
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:2849629 original size:23 final size:23
Alignment explanation
Indices: 2849580--2849643 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
2849570 GTATTTTTAT
*
2849580 TATT-TTATTATTATT-TTCACC
1 TATTATTATTATTATTATTAACC
* *
2849601 TTTTATTACTATTATTATTAACC
1 TATTATTATTATTATTATTAACC
2849624 TATTATTATTATTATTATTA
1 TATTATTATTATTATTATTA
2849644 TTATTAATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
21 3 0.08
22 10 0.28
23 23 0.64
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (23 bp):
TATTATTATTATTATTATTAACC
Found at i:2849661 original size:29 final size:29
Alignment explanation
Indices: 2849603--2849662 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
2849593 TTTTCACCTT
* *
2849603 TTATTACTATTATTATTAACCTATTATTA
1 TTATTACTATTATTATTAACATAGTATTA
* * *
2849632 TTATTATTATTATTATTAATATAGTGTTA
1 TTATTACTATTATTATTAACATAGTATTA
2849661 TT
1 TT
2849663 TTCATTTCTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.58
Consensus pattern (29 bp):
TTATTACTATTATTATTAACATAGTATTA
Found at i:2849723 original size:29 final size:29
Alignment explanation
Indices: 2849659--2849724 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
2849649 AATATAGTGT
* *
2849659 TATTTTCATTTCTTTTATTATCATTATTA
1 TATTATCATTTCTTTTATTATCATTAATA
*
2849688 -ACATATCATTTCTATTT-TTATCATTAATA
1 TA-TTATCATTTCT-TTTATTATCATTAATA
2849717 TATTATCA
1 TATTATCA
2849725 CGCTTATTAG
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
28 1 0.03
29 25 0.83
30 4 0.13
ACGTcount: A:0.30, C:0.12, G:0.00, T:0.58
Consensus pattern (29 bp):
TATTATCATTTCTTTTATTATCATTAATA
Found at i:2849888 original size:22 final size:20
Alignment explanation
Indices: 2849830--2849889 Score: 54
Period size: 22 Copynumber: 2.9 Consensus size: 20
2849820 CCTTTTTGTA
2849830 TTTATTTA-TTC-ATTTTAT
1 TTTATTTATTTCAATTTTAT
2849848 TTTCATTT-TTTACAAATTTCTAT
1 TTT-ATTTATTT-C-AATTT-TAT
2849871 TTTATTTATTTCAGATTTT
1 TTTATTTATTTCA-ATTTT
2849890 TACATAATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
18 3 0.09
19 6 0.18
20 1 0.03
21 2 0.06
22 13 0.38
23 9 0.26
ACGTcount: A:0.23, C:0.08, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTATTTATTTCAATTTTAT
Found at i:2851534 original size:40 final size:39
Alignment explanation
Indices: 2851485--2851570 Score: 156
Period size: 40 Copynumber: 2.2 Consensus size: 39
2851475 ATGAAAAAAA
2851485 TATATTTTTTATTTTAAAAAATTAATAATTTAATTTAAG
1 TATATTTTTTATTTTAAAAAATTAATAATTTAATTTAAG
2851524 TATACTTTTTTATTTTAAAAAATTAATAATTTAATTTAAG
1 TATA-TTTTTTATTTTAAAAAATTAATAATTTAATTTAAG
2851564 TAT-TTTT
1 TATATTTT
2851571 AATACAAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
38 4 0.09
39 4 0.09
40 38 0.83
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (39 bp):
TATATTTTTTATTTTAAAAAATTAATAATTTAATTTAAG
Found at i:2851580 original size:36 final size:38
Alignment explanation
Indices: 2851500--2851583 Score: 109
Period size: 40 Copynumber: 2.2 Consensus size: 38
2851490 TTTTTATTTT
* **
2851500 AAAAAATTAATAATTTAATTTAAGTATACTTTTTTATTTT
1 AAAAAATTAATAATTTAATTTAAG-ATAC-TTTTTAATAC
2851540 AAAAAATTAATAATTTAATTTAAG-TA-TTTTTAATAC
1 AAAAAATTAATAATTTAATTTAAGATACTTTTTAATAC
2851576 AAAAAATT
1 AAAAAATT
2851584 TAATTTTATC
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
36 15 0.37
38 2 0.05
40 24 0.59
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (38 bp):
AAAAAATTAATAATTTAATTTAAGATACTTTTTAATAC
Found at i:2854050 original size:22 final size:23
Alignment explanation
Indices: 2854003--2854061 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 23
2853993 AAAGCCAAGC
*
2854003 TATATACGAATAATTTTAAAGAAAA
1 TATATAC-AATAAATTT-AAGAAAA
2854028 TATATACAATAAATTT-AGAAAA
1 TATATACAATAAATTTAAGAAAA
*
2854050 TATTTAC-ATAAA
1 TATATACAATAAA
2854062 ATAATATGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 5 0.16
22 12 0.38
24 8 0.25
25 7 0.22
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.34
Consensus pattern (23 bp):
TATATACAATAAATTTAAGAAAA
Found at i:2856098 original size:46 final size:45
Alignment explanation
Indices: 2856048--2856374 Score: 213
Period size: 46 Copynumber: 7.2 Consensus size: 45
2856038 TGCCGATACA
*
2856048 TGAAGATAAGACTTGCCAAAATTTGATCTGCTTCACTCCTGCTCAG
1 TGAAGATAAGACTTGCCAAAATTT-ATCTGCTCCACTCCTGCTCAG
** ** * *
2856094 TGAAGATAAGA-TCTG-GTATGTTTAGCCTGCTCCACTCTTGCTCAG
1 TGAAGATAAGACT-TGCCAAAATTTA-TCTGCTCCACTCCTGCTCAG
* **** *
2856139 TGAAGATAAGGCTGGTGGTTGAA---ATCTACTCCACTCCTGCTCAG
1 TGAAGATAAGACT--TGCCAAAATTTATCTGCTCCACTCCTGCTCAG
* * *
2856183 TGAAGATAAGACTCGCCAAAATTTGATCTGCTTCACTCTTGCTCAG
1 TGAAGATAAGACTTGCCAAAATTT-ATCTGCTCCACTCCTGCTCAG
* * *** ** *
2856229 TAAAGATAAGA-TCGGGTATGTTTAGCCTGCTCCACTCCTGCTCAG
1 TGAAGATAAGACTTGCCAAAATTTA-TCTGCTCCACTCCTGCTCAG
* * * **
2856274 TGAAGATAAGGCTGGAGGCTGAA---ATCTGCTCCACTCCTGCTCAG
1 TGAAGATAAGACT--TGCCAAAATTTATCTGCTCCACTCCTGCTCAG
* * *
2856318 TGAAGATAAGACTCGCCAAAATTTAATCTGCTTCACTCCTGCTTAG
1 TGAAGATAAGACTTGCCAAAATTT-ATCTGCTCCACTCCTGCTCAG
2856364 TGAAGATAAGA
1 TGAAGATAAGA
2856375 TCAGGTATGT
Statistics
Matches: 215, Mismatches: 49, Indels: 34
0.72 0.16 0.11
Matches are distributed among these distances:
42 7 0.03
44 62 0.29
45 67 0.31
46 73 0.34
47 2 0.01
48 4 0.02
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (45 bp):
TGAAGATAAGACTTGCCAAAATTTATCTGCTCCACTCCTGCTCAG
Found at i:2856147 original size:135 final size:135
Alignment explanation
Indices: 2855961--2856385 Score: 662
Period size: 135 Copynumber: 3.2 Consensus size: 135
2855951 AGCCGATACA
*
2855961 TGAAGATAAGATCTGGTA--TTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATAGCT
1 TGAAGATAAGATCTGGTATGTTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGGCT
* * *
2856024 GAAATCTGCTCCATTGCC-GATACA-TGAAGATAAGACTTGCCAAAATTTGATCTGCTTCACTCC
66 GAAATCTGCTCCACT-CCTGCT-CAGTGAAGATAAGACTCGCCAAAATTTGATCTGCTTCACTCC
2856087 TGCTCAG
129 TGCTCAG
* * *
2856094 TGAAGATAAGATCTGGTATGTTTAGCCTGCTCCACTCTTGCTCAGTGAAGATAAGGCTGGTGGTT
1 TGAAGATAAGATCTGGTATGTTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGGCT
* *
2856159 GAAATCTACTCCACTCCTGCTCAGTGAAGATAAGACTCGCCAAAATTTGATCTGCTTCACTCTTG
66 GAAATCTGCTCCACTCCTGCTCAGTGAAGATAAGACTCGCCAAAATTTGATCTGCTTCACTCCTG
2856224 CTCAG
131 CTCAG
* *
2856229 TAAAGATAAGATCGGGTATGTTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGGA-GGC
1 TGAAGATAAGATCTGGTATGTTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGCT-GATGGC
*
2856293 TGAAATCTGCTCCACTCCTGCTCAGTGAAGATAAGACTCGCCAAAATTTAATCTGCTTCACTCCT
65 TGAAATCTGCTCCACTCCTGCTCAGTGAAGATAAGACTCGCCAAAATTTGATCTGCTTCACTCCT
*
2856358 GCTTAG
130 GCTCAG
*
2856364 TGAAGATAAGATCAGGTATGTT
1 TGAAGATAAGATCTGGTATGTT
2856386 CACGATTCCA
Statistics
Matches: 267, Mismatches: 20, Indels: 8
0.91 0.07 0.03
Matches are distributed among these distances:
133 18 0.07
134 4 0.01
135 244 0.91
136 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (135 bp):
TGAAGATAAGATCTGGTATGTTTAGCCTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGATGGCT
GAAATCTGCTCCACTCCTGCTCAGTGAAGATAAGACTCGCCAAAATTTGATCTGCTTCACTCCTG
CTCAG
Found at i:2856173 original size:44 final size:44
Alignment explanation
Indices: 2855985--2856327 Score: 209
Period size: 44 Copynumber: 7.7 Consensus size: 44
2855975 GGTATTTAGC
* *
2855985 CTGCTCCACTCCTGCTCAGTGAAGATAAGGCT-GATAGCTGAAAT
1 CTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGGA-GGTTGAAAT
* * * * **
2856029 CTGCTCCATTGCC-GATACA-TGAAGATAAGACTTGCCAAAATTTG--AT
1 CTGCTCCACT-CCTGCT-CAGTGAAGATAAGGC-TG---GAGGTTGAAAT
* * * * **
2856075 CTGCTTCACTCCTGCTCAGTGAAGATAAGATCTGGTATGTT-TAGC
1 CTGCTCCACTCCTGCTCAGTGAAGATAAG-GCTGG-AGGTTGAAAT
* *
2856120 CTGCTCCACTCTTGCTCAGTGAAGATAAGGCTGGTGGTTGAAAT
1 CTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGGAGGTTGAAAT
* * * **
2856164 CTACTCCACTCCTGCTCAGTGAAGATAAGACTCGCCAAAATTTG--AT
1 CTGCTCCACTCCTGCTCAGTGAAGATAAGGCT-G---GAGGTTGAAAT
* * * * * * * **
2856210 CTGCTTCACTCTTGCTCAGTAAAGATAAGATCGGGTATGTT-TAGC
1 CTGCTCCACTCCTGCTCAGTGAAGATAAG-GCTGG-AGGTTGAAAT
*
2856255 CTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGGAGGCTGAAAT
1 CTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGGAGGTTGAAAT
2856299 CTGCTCCACTCCTGCTCAGTGAAGATAAG
1 CTGCTCCACTCCTGCTCAGTGAAGATAAG
2856328 ACTCGCCAAA
Statistics
Matches: 225, Mismatches: 51, Indels: 46
0.70 0.16 0.14
Matches are distributed among these distances:
43 6 0.03
44 95 0.42
45 63 0.28
46 52 0.23
47 2 0.01
48 6 0.03
49 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (44 bp):
CTGCTCCACTCCTGCTCAGTGAAGATAAGGCTGGAGGTTGAAAT
Found at i:2861707 original size:22 final size:23
Alignment explanation
Indices: 2861660--2861718 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 23
2861650 AAAGCCAAGC
*
2861660 TATATACGAATAATTTTAAAGAAAA
1 TATATAC-AATAAATTT-AAGAAAA
2861685 TATATACAATAAATTT-AGAAAA
1 TATATACAATAAATTTAAGAAAA
*
2861707 TATTTAC-ATAAA
1 TATATACAATAAA
2861719 ATAATATGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 5 0.16
22 12 0.38
24 8 0.25
25 7 0.22
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.34
Consensus pattern (23 bp):
TATATACAATAAATTTAAGAAAA
Found at i:2861826 original size:7 final size:7
Alignment explanation
Indices: 2861814--2861846 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
2861804 AATAACATAC
2861814 AAATAAA
1 AAATAAA
2861821 AAATAAA
1 AAATAAA
2861828 AAATAAA
1 AAATAAA
*
2861835 ATA-AAA
1 AAATAAA
2861841 AAATAA
1 AAATAA
2861847 TGTTTTTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
AAATAAA
Found at i:2861841 original size:13 final size:14
Alignment explanation
Indices: 2861814--2861846 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2861804 AATAACATAC
2861814 AAATAAAAAATAAA
1 AAATAAAAAATAAA
*
2861828 AAATAAAATA-AAA
1 AAATAAAAAATAAA
2861841 AAATAA
1 AAATAA
2861847 TGTTTTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (14 bp):
AAATAAAAAATAAA
Found at i:2870660 original size:25 final size:28
Alignment explanation
Indices: 2870616--2870667 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 28
2870606 ATATATTAAA
*
2870616 AAAATCTTAAGAACTATTT-AAGAAATC
1 AAAATCTTAAGAACAATTTAAAGAAATC
2870643 AAAAT-TTAA-AACAATTTAAAGAAAT
1 AAAATCTTAAGAACAATTTAAAGAAAT
2870668 TATAAAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 7 0.30
26 11 0.48
27 5 0.22
ACGTcount: A:0.58, C:0.08, G:0.06, T:0.29
Consensus pattern (28 bp):
AAAATCTTAAGAACAATTTAAAGAAATC
Found at i:2873269 original size:29 final size:32
Alignment explanation
Indices: 2873236--2873299 Score: 89
Period size: 29 Copynumber: 2.1 Consensus size: 32
2873226 TGTTACTTGG
* *
2873236 AATTACAATAAA-AAATACAAAG-AAA-GATT
1 AATTACAATAAAGAAAAAAAAAGAAAACGATT
2873265 AATTACAATAAAGAAAAAAAAAGAAAACGATT
1 AATTACAATAAAGAAAAAAAAAGAAAACGATT
2873297 AAT
1 AAT
2873300 CACATTATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 12 0.40
30 8 0.27
31 3 0.10
32 7 0.23
ACGTcount: A:0.67, C:0.06, G:0.08, T:0.19
Consensus pattern (32 bp):
AATTACAATAAAGAAAAAAAAAGAAAACGATT
Found at i:2885317 original size:73 final size:73
Alignment explanation
Indices: 2885231--2885377 Score: 249
Period size: 73 Copynumber: 2.0 Consensus size: 73
2885221 ATCAAGTTCA
* * *
2885231 AACTTAATATTATTAATAAGAATAAAAATACTCTTTTTGCTTATATGGTTGAATCTTCTTTATGA
1 AACTCAATATTATTAATAAGAATAAAAATACTCTCTCTGCTTATATGGTTGAATCTTCTTTATGA
2885296 CATTATAG
66 CATTATAG
* *
2885304 AACTCAATATTATTAATAAGAATAAAAATACTCTCTCTGTTTATATGGTTGAATCTTCTTTATGG
1 AACTCAATATTATTAATAAGAATAAAAATACTCTCTCTGCTTATATGGTTGAATCTTCTTTATGA
2885369 CATTATAG
66 CATTATAG
2885377 A
1 A
2885378 TTAGGTCATT
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
73 69 1.00
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.42
Consensus pattern (73 bp):
AACTCAATATTATTAATAAGAATAAAAATACTCTCTCTGCTTATATGGTTGAATCTTCTTTATGA
CATTATAG
Found at i:2889797 original size:48 final size:48
Alignment explanation
Indices: 2889722--2889868 Score: 231
Period size: 48 Copynumber: 3.1 Consensus size: 48
2889712 GTGTCATTAA
* *
2889722 GAGCTTCATTGATTTGGCTTCGGGCCATGATACTAGCACTTTGGGTGC
1 GAGCTTCATTGATTTGGCTTCGGGCCATGATATTAGCACTTAGGGTGC
* * *
2889770 GAGCTTCATTGATTTGGCTTCGAGCCATGATATTAGCACTTCGGGTGT
1 GAGCTTCATTGATTTGGCTTCGGGCCATGATATTAGCACTTAGGGTGC
* *
2889818 GAGCTTCATTGATTTGGCTTCGGGCCATGATATTGGCACCTAGGGTGC
1 GAGCTTCATTGATTTGGCTTCGGGCCATGATATTAGCACTTAGGGTGC
2889866 GAG
1 GAG
2889869 ACTTTCGAGT
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 90 1.00
ACGTcount: A:0.18, C:0.20, G:0.30, T:0.33
Consensus pattern (48 bp):
GAGCTTCATTGATTTGGCTTCGGGCCATGATATTAGCACTTAGGGTGC
Found at i:2891127 original size:43 final size:43
Alignment explanation
Indices: 2891066--2891171 Score: 194
Period size: 43 Copynumber: 2.5 Consensus size: 43
2891056 ACGGGGTTAG
* *
2891066 ACATGGGCTGGGACACGGCCATGTGCTCCTATTTTGAATGTCC
1 ACATGGCCTGTGACACGGCCATGTGCTCCTATTTTGAATGTCC
2891109 ACATGGCCTGTGACACGGCCATGTGCTCCTATTTTGAATGTCC
1 ACATGGCCTGTGACACGGCCATGTGCTCCTATTTTGAATGTCC
2891152 ACATGGCCTGTGACACGGCC
1 ACATGGCCTGTGACACGGCC
2891172 TTGTCTTTGG
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 61 1.00
ACGTcount: A:0.19, C:0.28, G:0.26, T:0.26
Consensus pattern (43 bp):
ACATGGCCTGTGACACGGCCATGTGCTCCTATTTTGAATGTCC
Found at i:2906015 original size:36 final size:36
Alignment explanation
Indices: 2905967--2906039 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
2905957 CATTCTACTT
* *
2905967 ATATAAAGATACCAAGTTACATAAGTTCATGTTTTA
1 ATATAAACATACCAAGTTAAATAAGTTCATGTTTTA
*
2906003 ATATAAACATACCAAGTTAAATAAGTTTATGTTTTA
1 ATATAAACATACCAAGTTAAATAAGTTCATGTTTTA
2906039 A
1 A
2906040 CTTCGCTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.37
Consensus pattern (36 bp):
ATATAAACATACCAAGTTAAATAAGTTCATGTTTTA
Found at i:2914126 original size:16 final size:17
Alignment explanation
Indices: 2914091--2914128 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
2914081 AAAGAAAAGA
2914091 AAAAGTAAAAAAGAATG
1 AAAAGTAAAAAAGAATG
* *
2914108 AAAATTAAAACAGAA-G
1 AAAAGTAAAAAAGAATG
2914124 AAAAG
1 AAAAG
2914129 GATGGAAACG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.71, C:0.03, G:0.16, T:0.11
Consensus pattern (17 bp):
AAAAGTAAAAAAGAATG
Found at i:2916613 original size:95 final size:95
Alignment explanation
Indices: 2916431--2916721 Score: 345
Period size: 95 Copynumber: 3.0 Consensus size: 95
2916421 TCAATTAATT
* *
2916431 CATGAATAATAGTAAAAAATGTAAAATTTCTAACTTTTT-TACTAAAAT-GATAATAAATAATAA
1 CATGAATAATA-TTAAAAATATAAAATTTCTAACTTTTTAT-C-AAAATAG-TAATAAATAATAA
* * *
2916494 AAACTCATACCGAAACATTATGCATCGGCTCGTG
62 AAACTTATACTGGAACATTATGCATCGGCTCGTG
* * * *
2916528 CATGAATAATATTAAAAATATAAAATTTCAAACTTTTTATCGAAATAGTAATAAATAACAAGAAC
1 CATGAATAATATTAAAAATATAAAATTTCTAACTTTTTATCAAAATAGTAATAAATAATAAAAAC
* * * *
2916593 TTATATTGGAACATTGTGCATTGGCTCGTA
66 TTATACTGGAACATTATGCATCGGCTCGTG
* * *
2916623 TATGAATAATATTAAAAATATAAAATTTCTAATTTTTTA-CAAAAATGGTAATAAATAATAAAAA
1 CATGAATAATATTAAAAATATAAAATTTCTAACTTTTTATC-AAAATAGTAATAAATAATAAAAA
* * *
2916687 ATTTTACTAGAACATTATGCATCGGCTCGTG
65 CTTATACTGGAACATTATGCATCGGCTCGTG
2916718 CATG
1 CATG
2916722 GCTATTTTAT
Statistics
Matches: 163, Mismatches: 28, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
94 1 0.01
95 124 0.76
96 26 0.16
97 12 0.07
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (95 bp):
CATGAATAATATTAAAAATATAAAATTTCTAACTTTTTATCAAAATAGTAATAAATAATAAAAAC
TTATACTGGAACATTATGCATCGGCTCGTG
Found at i:2919607 original size:68 final size:66
Alignment explanation
Indices: 2919535--2919706 Score: 170
Period size: 67 Copynumber: 2.6 Consensus size: 66
2919525 CATCATGTGT
** * *
2919535 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTA-TG-TGTACACCA
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCATGATACTAGTGAAGGACACCA
2919598 TGTAG
62 TGTAG
** * *
2919603 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCATGGTTCTAGGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCATGATACTA-GTGAAGGACACCATGT
2919668 AG
65 AG
* * * *
2919670 ACAAGAGAGCTACGAGATAAAT-TGGCTAGGTCACATG
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATG
2919707 GGTGGTACTG
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
64 24 0.27
65 3 0.03
66 17 0.19
67 32 0.36
68 13 0.15
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.23
Consensus pattern (66 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCATGATACTAGTGAAGGACACCATGTA
G
Found at i:2919640 original size:64 final size:64
Alignment explanation
Indices: 2919559--2919730 Score: 195
Period size: 67 Copynumber: 2.7 Consensus size: 64
2919549 AGACATTATG
* * *
2919559 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
** * * *
2919623 ATGTAGCTAGGTCGCATGCATGGTTCTAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
2919688 AA
63 AA
* * *
2919690 AT-TGGCTAGGTCACATGGGTGGTACTGA-GTGTTCACCATGT
1 ATGTAGCTAGGTCGCATGGGTGGTACT-ATGTGTACACCATGT
2919731 GTACTAGAGA
Statistics
Matches: 88, Mismatches: 16, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
63 9 0.10
64 25 0.28
66 21 0.24
67 33 0.38
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.25
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:2920837 original size:12 final size:12
Alignment explanation
Indices: 2920822--2920847 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2920812 TCATGACATG
2920822 TGTATATATATA
1 TGTATATATATA
2920834 TGTATATATATA
1 TGTATATATATA
2920846 TG
1 TG
2920848 ACTAGTCTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (12 bp):
TGTATATATATA
Found at i:2929120 original size:5 final size:5
Alignment explanation
Indices: 2929112--2929150 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
2929102 TATTAAAGAC
* *
2929112 ATTAC ATTAC ATTAA ATTAA ATTAA ATTAA ATTAA ATTA
1 ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTA
2929151 TATATGTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (5 bp):
ATTAA
Found at i:2929359 original size:9 final size:9
Alignment explanation
Indices: 2929345--2929382 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
2929335 TACAATAAAC
2929345 ATATAATTT
1 ATATAATTT
2929354 ATATAATTT
1 ATATAATTT
2929363 ATAATAAATTT
1 AT-AT-AATTT
2929374 ATAT-ATTT
1 ATATAATTT
2929382 A
1 A
2929383 CTACATCAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 5 0.19
9 11 0.41
10 4 0.15
11 7 0.26
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
ATATAATTT
Found at i:2931774 original size:3 final size:3
Alignment explanation
Indices: 2931766--2931791 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2931756 GTAAGGGTAA
2931766 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
2931792 AGGAAACCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2938632 original size:15 final size:15
Alignment explanation
Indices: 2938612--2938642 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2938602 CTATCATCTT
*
2938612 TAACTGTTAACAGAC
1 TAACTGCTAACAGAC
2938627 TAACTGCTAACAGAC
1 TAACTGCTAACAGAC
2938642 T
1 T
2938643 TACATCGGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (15 bp):
TAACTGCTAACAGAC
Found at i:2938676 original size:20 final size:20
Alignment explanation
Indices: 2938651--2938692 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
2938641 CTTACATCGG
*
2938651 TACAACGGTTTTGACTATAT
1 TACAACGGCTTTGACTATAT
*
2938671 TACAACTGCTTTGACTATAT
1 TACAACGGCTTTGACTATAT
2938691 TA
1 TA
2938693 ACTCTAACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (20 bp):
TACAACGGCTTTGACTATAT
Found at i:2940550 original size:18 final size:18
Alignment explanation
Indices: 2940517--2940551 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2940507 ACCAGCAGAT
* *
2940517 GGCATACTGACTTGTTGG
1 GGCATACTAACCTGTTGG
2940535 GGCATACTAACCTGTTG
1 GGCATACTAACCTGTTG
2940552 TGGAGAGCTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.31
Consensus pattern (18 bp):
GGCATACTAACCTGTTGG
Found at i:2941813 original size:15 final size:15
Alignment explanation
Indices: 2941793--2941823 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2941783 CTATCATCTT
2941793 TAACTGCTAACAGAC
1 TAACTGCTAACAGAC
2941808 TAACTGCTAACAGAC
1 TAACTGCTAACAGAC
2941823 T
1 T
2941824 TACATCGGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.26, G:0.13, T:0.23
Consensus pattern (15 bp):
TAACTGCTAACAGAC
Found at i:2941857 original size:20 final size:20
Alignment explanation
Indices: 2941832--2941873 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
2941822 CTTACATCGG
*
2941832 TACAACGGTTTTGACTATAT
1 TACAACGGCTTTGACTATAT
*
2941852 TACAACTGCTTTGACTATAT
1 TACAACGGCTTTGACTATAT
2941872 TA
1 TA
2941874 ACTCTAACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (20 bp):
TACAACGGCTTTGACTATAT
Found at i:2943056 original size:24 final size:24
Alignment explanation
Indices: 2943024--2943070 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2943014 TAATTTTATA
* * *
2943024 GCTTGCACTTGCTTTTCCATGTCT
1 GCTTACACTTGATTTTCAATGTCT
2943048 GCTTACACTTGATTTTCAATGTC
1 GCTTACACTTGATTTTCAATGTC
2943071 AAGGACAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.15, C:0.26, G:0.15, T:0.45
Consensus pattern (24 bp):
GCTTACACTTGATTTTCAATGTCT
Found at i:2954886 original size:24 final size:24
Alignment explanation
Indices: 2954852--2954905 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
2954842 TTCTAATTAA
* *
2954852 ATTTTATAAATAATTAATATTTAT
1 ATTTTAAAAATAATTAAAATTTAT
* *
2954876 TTTTTAAAAATATTTAAAATTTAT
1 ATTTTAAAAATAATTAAAATTTAT
2954900 ATTTTA
1 ATTTTA
2954906 TATATTAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
ATTTTAAAAATAATTAAAATTTAT
Found at i:2956780 original size:23 final size:23
Alignment explanation
Indices: 2956750--2956793 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
2956740 TTACAAATTT
2956750 AAATTTTAAAAACAACATCATTC
1 AAATTTTAAAAACAACATCATTC
*
2956773 AAATTTTAAAGACAACATCAT
1 AAATTTTAAAAACAACATCAT
2956794 ATTCGATCCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.52, C:0.16, G:0.02, T:0.30
Consensus pattern (23 bp):
AAATTTTAAAAACAACATCATTC
Found at i:2958128 original size:7 final size:7
Alignment explanation
Indices: 2958113--2958151 Score: 69
Period size: 7 Copynumber: 5.6 Consensus size: 7
2958103 AATCCCAGCG
2958113 TTCAACC
1 TTCAACC
*
2958120 TTCAGCC
1 TTCAACC
2958127 TTCAACC
1 TTCAACC
2958134 TTCAACC
1 TTCAACC
2958141 TTCAACC
1 TTCAACC
2958148 TTCA
1 TTCA
2958152 GCTTCTTGTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.26, C:0.41, G:0.03, T:0.31
Consensus pattern (7 bp):
TTCAACC
Found at i:2958130 original size:14 final size:14
Alignment explanation
Indices: 2958108--2958153 Score: 74
Period size: 14 Copynumber: 3.3 Consensus size: 14
2958098 AGCCCAATCC
*
2958108 CAGCGTTCAACCTT
1 CAGCCTTCAACCTT
2958122 CAGCCTTCAACCTT
1 CAGCCTTCAACCTT
*
2958136 CAACCTTCAACCTT
1 CAGCCTTCAACCTT
2958150 CAGC
1 CAGC
2958154 TTCTTGTCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.24, C:0.41, G:0.09, T:0.26
Consensus pattern (14 bp):
CAGCCTTCAACCTT
Found at i:2959190 original size:95 final size:95
Alignment explanation
Indices: 2959027--2959217 Score: 355
Period size: 95 Copynumber: 2.0 Consensus size: 95
2959017 CAAATAATAA
2959027 CTATTAAATTCATTATGTTATTTTCAAAATTTGATGTATCAAACATATTATCGCATATGTACCGC
1 CTATTAAATTCATTATGTTATTTTCAAAATTTGATGTATCAAACATATTATCGCATATGTACCGC
*
2959092 TATGTTTGTTTGTTATTTTTACATATTACT
66 TATGTTTGTTTATTATTTTTACATATTACT
* *
2959122 CTATTAAATTCATTATGTTATTTTCAAAATTTGATGTGTCAAACATATTATCGCATGTGTACCGC
1 CTATTAAATTCATTATGTTATTTTCAAAATTTGATGTATCAAACATATTATCGCATATGTACCGC
2959187 TATGTTTGTTTATTATTTTTACATATTACT
66 TATGTTTGTTTATTATTTTTACATATTACT
2959217 C
1 C
2959218 ACAAAAAAAT
Statistics
Matches: 93, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
95 93 1.00
ACGTcount: A:0.29, C:0.13, G:0.10, T:0.48
Consensus pattern (95 bp):
CTATTAAATTCATTATGTTATTTTCAAAATTTGATGTATCAAACATATTATCGCATATGTACCGC
TATGTTTGTTTATTATTTTTACATATTACT
Found at i:2960189 original size:18 final size:18
Alignment explanation
Indices: 2960135--2960192 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 18
2960125 TTACTTTCCA
2960135 TATATATATTAATTATT-AT
1 TATAT-TATTAATT-TTAAT
* *
2960154 TACATTACTAATTTTTAAT
1 TATATTATTAA-TTTTAAT
2960173 TATATTATTAATTTTAAT
1 TATATTATTAATTTTAAT
2960191 TA
1 TA
2960193 ATCATGCTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
18 16 0.48
19 17 0.52
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (18 bp):
TATATTATTAATTTTAAT
Found at i:2962371 original size:307 final size:306
Alignment explanation
Indices: 2961781--2962538 Score: 1022
Period size: 307 Copynumber: 2.5 Consensus size: 306
2961771 ACCCATATGG
* * * *
2961781 TGAAATCACTTTCATGGCAAGACCTTAACAAGAATGCCACAATGGAAAAG-CTCAAAATGAATTC
1 TGAAATCACTCTCATGGCAAGACCTCAACAAGAA-GGCACAATGG-AAAGCCTCAGAATGAATTC
* * * * * * *
2961845 AAGATTCTGATTAAAAGGAAAATAAGATTATTCGGACAAGATATCTGGGAAGAGGTCATGATGTA
64 AAGATTTTGATTAAAAGGAAAATAAGATTATTTGGGCAAGACATTTGGGGAGAGGTCATGGTGTA
** * * **
2961910 AATTGTCAAAAGTTTTTTACACCATTGTTGGGGGGAGCCATTAGAAAATAAGAGTAGGTACTAAA
129 AATTACCAAAAGCTTTTTACACCATTGTTGGGGGGAACCATTAGAAAATAAGAACAGGTACTAAA
* * *
2961975 GCTATGTCTTTCATGTCCTGAATATTTCTTCATATTGAATAAAACCCGTGGTTTCAAATATATAT
194 GCTATGTCTTTCATATCCTAAATATTTCTTCATACTGAATAAAACCCGTGGTTTCAAATATATAT
*
2962040 TAATTATCTTCTCTCTTTTATTCATTACAAATATTGGCTACAATATAA
259 TAATTATCTTCTCCCTTTTATTCATTACAAATATTGGCTACAATATAA
* * * **
2962088 TGAAATCACTCTCATGGCAAGACCTCGACATGAAGGCGACAATTGAGTGCCTCAGAATGAATTCA
1 TGAAATCACTCTCATGGCAAGACCTCAACAAGAAGGC-ACAATGGAAAGCCTCAGAATGAATTCA
* *
2962153 AGATTTTCATTAAAAGGAAAATAAGATTGTTTGGGCAAGACATTTTGGGGAGAGGTCATGGTGTA
65 AGATTTTGATTAAAAGGAAAATAAGATTATTTGGGCAAGACA-TTTGGGGAGAGGTCATGGTGTA
*
2962218 AATTACCAAAAGCTTTTTACGCCATTGTTGGGGGGAACCATTAGAAAATAAGAACAGGTACTAAA
129 AATTACCAAAAGCTTTTTACACCATTGTTGGGGGGAACCATTAGAAAATAAGAACAGGTACTAAA
* * *
2962283 GTTATGTCTTTCATATACC-AAATGTTT-TCTCATACTGAATAAAACTCGTGG-TTCAAATATAT
194 GCTATGTCTTTCATAT-CCTAAATATTTCT-TCATACTGAATAAAACCCGTGGTTTCAAATATAT
* *
2962345 ATTAATTATCTTCTCCCTTTTATTCATTACAAATATTGGCTACCATATGA
257 ATTAATTATCTTCTCCCTTTTATTCATTACAAATATTGGCTACAATATAA
* *
2962395 CGAAATCACTCTCATGGCAAGACCTCAACAAGAAGGCAGCAATGGAAAGCGC-CAGAATAAATTC
1 TGAAATCACTCTCATGGCAAGACCTCAACAAGAAGGCA-CAATGGAAAGC-CTCAGAATGAATTC
* * * * * *
2962459 AAGGTTTTGATTAAAAGAAAAATAAGATTATTTGGGTAAGACATTTGGGGAGAGATTATCGTGTA
64 AAGATTTTGATTAAAAGGAAAATAAGATTATTTGGGCAAGACATTTGGGGAGAGGTCATGGTGTA
*
2962524 AATTACAAAAAGCTT
129 AATTACCAAAAGCTT
2962539 CATTTGAAGA
Statistics
Matches: 394, Mismatches: 50, Indels: 15
0.86 0.11 0.03
Matches are distributed among these distances:
306 38 0.10
307 236 0.60
308 118 0.30
309 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (306 bp):
TGAAATCACTCTCATGGCAAGACCTCAACAAGAAGGCACAATGGAAAGCCTCAGAATGAATTCAA
GATTTTGATTAAAAGGAAAATAAGATTATTTGGGCAAGACATTTGGGGAGAGGTCATGGTGTAAA
TTACCAAAAGCTTTTTACACCATTGTTGGGGGGAACCATTAGAAAATAAGAACAGGTACTAAAGC
TATGTCTTTCATATCCTAAATATTTCTTCATACTGAATAAAACCCGTGGTTTCAAATATATATTA
ATTATCTTCTCCCTTTTATTCATTACAAATATTGGCTACAATATAA
Found at i:2966705 original size:31 final size:31
Alignment explanation
Indices: 2966638--2966725 Score: 113
Period size: 31 Copynumber: 2.7 Consensus size: 31
2966628 AACTTAATGT
* *
2966638 TGTTTTAAACTCAGTTTGAAATATTTTATGTTTA
1 TGTTCTAAACTCAGTTTGAAA-A--TTAAGTTTA
2966672 TGTTCTAAACTCAGTTTGAAAATTAAGTTTA
1 TGTTCTAAACTCAGTTTGAAAATTAAGTTTA
* *
2966703 TGTTCTAAGCTGAGTTTGAAAAT
1 TGTTCTAAACTCAGTTTGAAAAT
2966726 AAAAAATTTA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
31 29 0.58
33 1 0.02
34 20 0.40
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.45
Consensus pattern (31 bp):
TGTTCTAAACTCAGTTTGAAAATTAAGTTTA
Found at i:2969062 original size:31 final size:31
Alignment explanation
Indices: 2969024--2969090 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
2969014 ATAATAAAAT
2969024 TCTTAGCCAATGTTTCCCAATTTTATTGTGA
1 TCTTAGCCAATGTTTCCCAATTTTATTGTGA
* *
2969055 TCTTAGCCAATGTTTGCCAATTTTCTTGTGA
1 TCTTAGCCAATGTTTCCCAATTTTATTGTGA
2969086 TCTTA
1 TCTTA
2969091 TTCTTCCATG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.21, C:0.19, G:0.13, T:0.46
Consensus pattern (31 bp):
TCTTAGCCAATGTTTCCCAATTTTATTGTGA
Found at i:2969611 original size:21 final size:21
Alignment explanation
Indices: 2969585--2969624 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2969575 ATTATTCCCT
*
2969585 TTTTGATGATATGACATTTCA
1 TTTTGATGATATAACATTTCA
2969606 TTTTGATGATATAACATTT
1 TTTTGATGATATAACATTT
2969625 TTATGTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.07, G:0.12, T:0.50
Consensus pattern (21 bp):
TTTTGATGATATAACATTTCA
Found at i:2981128 original size:26 final size:26
Alignment explanation
Indices: 2981097--2981254 Score: 271
Period size: 26 Copynumber: 6.1 Consensus size: 26
2981087 TGAAATGCCC
*
2981097 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
2981123 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
2981149 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
2981175 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
2981201 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
2981227 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
2981253 AT
1 AT
2981255 GAATTTGTAC
Statistics
Matches: 123, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 123 1.00
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.34
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:2985397 original size:19 final size:18
Alignment explanation
Indices: 2985373--2985416 Score: 70
Period size: 19 Copynumber: 2.4 Consensus size: 18
2985363 TATTTATATA
2985373 TTAATTATATTACTAATTT
1 TTAATTATATTACTAA-TT
*
2985392 TTAATTATATTATTAATT
1 TTAATTATATTACTAATT
2985410 TTAATTA
1 TTAATTA
2985417 ATCATGCTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (18 bp):
TTAATTATATTACTAATT
Found at i:2985868 original size:84 final size:84
Alignment explanation
Indices: 2985727--2985896 Score: 241
Period size: 84 Copynumber: 2.0 Consensus size: 84
2985717 GTCAATAATA
** * * *
2985727 TCCATAAAAAACAAACGTCATTCTTGAGACTCGAAAAATGAAGCAACAGACATGAAAGGGAAAAA
1 TCCATAAAAAACAAACACCATTCTTGAAAATCGAAAAATGAAGAAACAGACATGAAAGGGAAAAA
*
2985792 TAGTATGCATCGTTCTACT
66 CAGTATGCATCGTTCTACT
* * * *
2985811 TCCATGAAAAACAAACACCATTCTTGAAAATTGAAAAATGCAGAAATAGACATGAAAGGGAAAAA
1 TCCATAAAAAACAAACACCATTCTTGAAAATCGAAAAATGAAGAAACAGACATGAAAGGGAAAAA
*
2985876 CGGTATGCATCGTTCTACT
66 CAGTATGCATCGTTCTACT
2985895 TC
1 TC
2985897 ACTTTGAATC
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
84 75 1.00
ACGTcount: A:0.44, C:0.18, G:0.16, T:0.22
Consensus pattern (84 bp):
TCCATAAAAAACAAACACCATTCTTGAAAATCGAAAAATGAAGAAACAGACATGAAAGGGAAAAA
CAGTATGCATCGTTCTACT
Found at i:2986262 original size:17 final size:17
Alignment explanation
Indices: 2986240--2986276 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
2986230 CCCCTTATGT
2986240 TTCAGGCTACATATTGG
1 TTCAGGCTACATATTGG
2986257 TTCAGGCTACATATTGG
1 TTCAGGCTACATATTGG
2986274 TTC
1 TTC
2986277 TAACTTCTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.38
Consensus pattern (17 bp):
TTCAGGCTACATATTGG
Found at i:2990903 original size:27 final size:25
Alignment explanation
Indices: 2990852--2990904 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 25
2990842 TTGTTAAAGG
*
2990852 TGATTTTTTAGTTTCTTTCCCTTTC
1 TGATTTTTTAGTTTCTTTCACTTTC
* *
2990877 TGATTTTGTTATTATTCTTTCATTTTC
1 TGATTTT-TTAGT-TTCTTTCACTTTC
2990904 T
1 T
2990905 TCTTGCGTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 4 0.17
27 12 0.52
ACGTcount: A:0.11, C:0.15, G:0.08, T:0.66
Consensus pattern (25 bp):
TGATTTTTTAGTTTCTTTCACTTTC
Found at i:2991477 original size:11 final size:11
Alignment explanation
Indices: 2991461--2991485 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2991451 TAAAATATCC
2991461 ATTTTATTTTA
1 ATTTTATTTTA
2991472 ATTTTATTTTA
1 ATTTTATTTTA
2991483 ATT
1 ATT
2991486 GAGTTTTTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
ATTTTATTTTA
Found at i:2991781 original size:24 final size:22
Alignment explanation
Indices: 2991736--2991782 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
2991726 TATTATTTTA
*
2991736 TGTAAATATTTTCTAAATTTAT
1 TGTAAATATTTTCTAAAATTAT
*
2991758 TGTATATATTTTCTTTAAAATTAT
1 TGTAAATATTTTC--TAAAATTAT
2991782 T
1 T
2991783 CATATATAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 12 0.57
24 9 0.43
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.57
Consensus pattern (22 bp):
TGTAAATATTTTCTAAAATTAT
Found at i:2995226 original size:7 final size:7
Alignment explanation
Indices: 2995210--2995261 Score: 52
Period size: 7 Copynumber: 7.6 Consensus size: 7
2995200 AAAGGCGGCC
*
2995210 AAAAAGA
1 AAAAACA
2995217 AAAAACA
1 AAAAACA
**
2995224 AAAAAGG
1 AAAAACA
*
2995231 AAAGACA
1 AAAAACA
2995238 AAAAACA
1 AAAAACA
2995245 AAAAA-A
1 AAAAACA
*
2995251 AATAACA
1 AAAAACA
2995258 AAAA
1 AAAA
2995262 GAGATTGTAG
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
6 5 0.14
7 30 0.86
ACGTcount: A:0.83, C:0.08, G:0.08, T:0.02
Consensus pattern (7 bp):
AAAAACA
Found at i:2995261 original size:21 final size:20
Alignment explanation
Indices: 2995210--2995261 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
2995200 AAAGGCGGCC
*
2995210 AAAAAGAAAAAACAAAAAAGG
1 AAAAACAAAAAACAAAAAA-G
*
2995231 AAAGACAAAAAACAAAAAA-
1 AAAAACAAAAAACAAAAAAG
2995250 AAATAACAAAAA
1 AAA-AACAAAAA
2995262 GAGATTGTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 3 0.11
20 7 0.26
21 17 0.63
ACGTcount: A:0.83, C:0.08, G:0.08, T:0.02
Consensus pattern (20 bp):
AAAAACAAAAAACAAAAAAG
Found at i:2996981 original size:64 final size:65
Alignment explanation
Indices: 2996869--2996997 Score: 188
Period size: 64 Copynumber: 2.0 Consensus size: 65
2996859 TATACAATAG
* * *
2996869 CACATCTAGTTAGGAGCATTTGATTTTATTTCGATCATAGCATCCTAATTATTTGACATAAGCAT
1 CACATCTAGGTAGGAGCATTTGATTTCATTTCAATCATAGCATCCTAATTATTTGACATAAGCAT
* * * *
2996934 CACATTTAGGTAGGAGCATTTGA-TTCATTTCAATCATTGCATCCTAATTATTTGGCATAGGCAT
1 CACATCTAGGTAGGAGCATTTGATTTCATTTCAATCATAGCATCCTAATTATTTGACATAAGCAT
2996998 AGATACATGA
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
64 36 0.63
65 21 0.37
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (65 bp):
CACATCTAGGTAGGAGCATTTGATTTCATTTCAATCATAGCATCCTAATTATTTGACATAAGCAT
Found at i:2997492 original size:135 final size:133
Alignment explanation
Indices: 2997236--2997985 Score: 969
Period size: 133 Copynumber: 5.6 Consensus size: 133
2997226 GCTAAAATTA
* * * * * *
2997236 CAGATCTTAT-TTCGCTGAGCAAGAGCGGAGCAGATCAAATTTTGGTAAATCTTATCTCCATGTA
1 CAGATCTTATCTTCACTGAGCAGGAGTGAAGCAGATCAAATTTTGGCAAGTCTTATCTCCATGTA
* * * *
2997300 TAGGCAATGGAGCATATTCCAATCATCAGCCTTATCTTTACTGAGCAGGAGTGGAGCAGGCTAAA
66 TCGGCAATGGAGCAGATTCCAACCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCT-AA
2997365 CATAC
130 -ATAC
* *
2997370 CAGATCTTTTCTTCACTGAGCAGGAGTGAAGCAGATCAAATTTTGGCAAGTCTTATCTTCATGTA
1 CAGATCTTATCTTCACTGAGCAGGAGTGAAGCAGATCAAATTTTGGCAAGTCTTATCTCCATGTA
* *
2997435 TCGGCAATGGAGCAGATTTCAACCATCAGTCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAA
66 TCGGCAATGGAGCAGATTCCAACCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAA
2997500 TAC
131 TAC
* * * *
2997503 CAGATCTTATCTTCACTGATCAGGAGTGAAGCAGATCAAACTTTGG-AGAATCTTATCTCCACGT
1 CAGATCTTATCTTCACTGAGCAGGAGTGAAGCAGATCAAATTTTGGCA-AGTCTTATCTCCATGT
* *
2997567 ACCGGCAATGGAGCAGATTCCAATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAA
65 ATCGGCAATGGAGCAGATTCCAACCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCT-A
2997632 ACATAC
129 A-ATAC
*
2997638 CAGATCTTATCTTCACTGAGCAGGAGTGAAGCAGATCAAATTTTGGCAAGTCTTATCTTCATGTA
1 CAGATCTTATCTTCACTGAGCAGGAGTGAAGCAGATCAAATTTTGGCAAGTCTTATCTCCATGTA
* * * *
2997703 TCGGCAATGGAGCAGATTTCAGCCATCAGCCTTATCTTTACTGAGCACGAGTGGAGCAGGCTAAA
66 TCGGCAATGGAGCAGATTCCAACCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAA
2997768 TAC
131 TAC
* * * *
2997771 CAGATCTTATCTTCACTGAGCAGGAGTGAAGCAGATCGAACTTT-G-AAGAATCTTATCTTCACG
1 CAGATCTTATCTTCACTGAGCAGGAGTGAAGCAGATCAAATTTTGGCAAG--TCTTATCTCCATG
* * * * * *
2997834 TACCGACGATGGAGCAGATTCCAATCATCGGCCTTATCTTCACTGAGCAGGAGTGGAGTAGGCTA
64 TATCGGCAATGGAGCAGATTCCAACCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTA
2997899 AATAC
129 AATAC
* * * * *
2997904 CAGATCTTATCTCCA-TGTATC-GGCTA-TGGAGCAGATCAGAA--ATGGCGAGTCTTATCTCCA
1 CAGATCTTATCTTCACTG-AGCAGG--AGTGAAGCAGATCA-AATTTTGGCAAGTCTTATCTCCA
*
2997964 TGTATCGGCTATGGAGCAGATT
62 TGTATCGGCAATGGAGCAGATT
2997986 TTAGCCACAA
Statistics
Matches: 544, Mismatches: 59, Indels: 28
0.86 0.09 0.04
Matches are distributed among these distances:
131 3 0.01
132 35 0.06
133 264 0.49
134 20 0.04
135 221 0.41
136 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (133 bp):
CAGATCTTATCTTCACTGAGCAGGAGTGAAGCAGATCAAATTTTGGCAAGTCTTATCTCCATGTA
TCGGCAATGGAGCAGATTCCAACCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAA
TAC
Found at i:2997701 original size:268 final size:268
Alignment explanation
Indices: 2997236--2998006 Score: 1139
Period size: 268 Copynumber: 2.9 Consensus size: 268
2997226 GCTAAAATTA
* * * * * *
2997236 CAGATCTTAT-TTCGCTGAGCAAGAGCGGAGCAGATCAAATTTTGGTA-AATCTTATCTCCATGT
1 CAGATCTTATCTTCACTGAGCAGGAGTGAAGCAGATCAAACTTTGG-AGAATCTTATCTCCACGT
** * *
2997299 ATAGGCAATGGAGCATATTCCAATCATCAGCCTTATCTTTACTGAGCAGGAGTGGAGCAGGCTAA
65 ACCGGCAATGGAGCAGATTCCAATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAA
*
2997364 ACATACCAGATCTTTTCTTCACTGAGCAGGAGTGAAGCAGATCAAATTTTGGCAAGTCTTATCTT
130 ACATACCAGATCTTATCTTCACTGAGCAGGAGTGAAGCAGATCAAATTTTGGCAAGTCTTATCTT
* *
2997429 CATGTATCGGCAATGGAGCAGATTTCAACCATCAGTCTTATCTTCACTGAGCAGGAGTGGAGCAG
195 CATGTATCGGCAATGGAGCAGATTTCAGCCATCAGTCTTATCTTCACTGAGCACGAGTGGAGCAG
2997494 GCTAAATAC
260 GCTAAATAC
*
2997503 CAGATCTTATCTTCACTGATCAGGAGTGAAGCAGATCAAACTTTGGAGAATCTTATCTCCACGTA
1 CAGATCTTATCTTCACTGAGCAGGAGTGAAGCAGATCAAACTTTGGAGAATCTTATCTCCACGTA
2997568 CCGGCAATGGAGCAGATTCCAATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAA
66 CCGGCAATGGAGCAGATTCCAATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAA
2997633 CATACCAGATCTTATCTTCACTGAGCAGGAGTGAAGCAGATCAAATTTTGGCAAGTCTTATCTTC
131 CATACCAGATCTTATCTTCACTGAGCAGGAGTGAAGCAGATCAAATTTTGGCAAGTCTTATCTTC
* *
2997698 ATGTATCGGCAATGGAGCAGATTTCAGCCATCAGCCTTATCTTTACTGAGCACGAGTGGAGCAGG
196 ATGTATCGGCAATGGAGCAGATTTCAGCCATCAGTCTTATCTTCACTGAGCACGAGTGGAGCAGG
2997763 CTAAATAC
261 CTAAATAC
* * *
2997771 CAGATCTTATCTTCACTGAGCAGGAGTGAAGCAGATCGAACTTTGAAGAATCTTATCTTCACGTA
1 CAGATCTTATCTTCACTGAGCAGGAGTGAAGCAGATCAAACTTTGGAGAATCTTATCTCCACGTA
* * * *
2997836 CCGACGATGGAGCAGATTCCAATCATCGGCCTTATCTTCACTGAGCAGGAGTGGAGTAGGCT-AA
66 CCGGCAATGGAGCAGATTCCAATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAA
* * * * *
2997900 -ATACCAGATCTTATCTCCA-TGTATC-GGCTA-TGGAGCAGATCAGAA--ATGGCGAGTCTTAT
131 CATACCAGATCTTATCTTCACTG-AGCAGG--AGTGAAGCAGATCA-AATTTTGGCAAGTCTTAT
* * *
2997959 CTCCATGTATCGGCTATGGAGCAGATTTTAGCCA-CAAGTCTTATCTTC
192 CTTCATGTATCGGCAATGGAGCAGATTTCAGCCATC-AGTCTTATCTTC
2998007 CTAAAGTTGC
Statistics
Matches: 463, Mismatches: 34, Indels: 16
0.90 0.07 0.03
Matches are distributed among these distances:
264 1 0.00
265 57 0.12
266 31 0.07
267 16 0.03
268 358 0.77
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (268 bp):
CAGATCTTATCTTCACTGAGCAGGAGTGAAGCAGATCAAACTTTGGAGAATCTTATCTCCACGTA
CCGGCAATGGAGCAGATTCCAATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAA
CATACCAGATCTTATCTTCACTGAGCAGGAGTGAAGCAGATCAAATTTTGGCAAGTCTTATCTTC
ATGTATCGGCAATGGAGCAGATTTCAGCCATCAGTCTTATCTTCACTGAGCACGAGTGGAGCAGG
CTAAATAC
Found at i:2998239 original size:133 final size:133
Alignment explanation
Indices: 2997904--2998224 Score: 527
Period size: 133 Copynumber: 2.4 Consensus size: 133
2997894 GGCTAAATAC
* *
2997904 CAGATCTTATCTCCATGTATCGGCTATGGAGCAGATCAGAAATGGCGAGTCTTATCTCCATGTAT
1 CAGATCTTATCTCCATGTATCGACTATGGAGCAGATCAGAAATGGCGAGTCTTATCTCTATGTAT
* *
2997969 CGGCTATGGAGCAGATTTTAGCCACAAGTCTTATCTTCCTAAAGTTGCAGGAAGCAGACTGAAAA
66 CAGATATGGAGCAGATTTTAGCCACAAGTCTTATCTTCCTAAAGTTGCAGGAAGCAGACTGAAAA
2998034 TTA
131 TTA
* *
2998037 CAGATCTTATCTCCATGTATCGACTATGGAGAAAATCAGAAATGGCGAGTCTTATCTCTATGTAT
1 CAGATCTTATCTCCATGTATCGACTATGGAGCAGATCAGAAATGGCGAGTCTTATCTCTATGTAT
* * *
2998102 CAGATATGGAGCAGATTTTAGCCACAAGTCTTATCTTCTTGAAGTTGTAGGAAGCAGACTGAAAA
66 CAGATATGGAGCAGATTTTAGCCACAAGTCTTATCTTCCTAAAGTTGCAGGAAGCAGACTGAAAA
2998167 TTA
131 TTA
* * *
2998170 CAGATCATATCTCCATGTATCGACTATGGAGCAGATCAGGAATGG-TAGTCTTATC
1 CAGATCTTATCTCCATGTATCGACTATGGAGCAGATCAGAAATGGCGAGTCTTATC
2998225 GGCTATGAAG
Statistics
Matches: 174, Mismatches: 14, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
132 9 0.05
133 165 0.95
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.30
Consensus pattern (133 bp):
CAGATCTTATCTCCATGTATCGACTATGGAGCAGATCAGAAATGGCGAGTCTTATCTCTATGTAT
CAGATATGGAGCAGATTTTAGCCACAAGTCTTATCTTCCTAAAGTTGCAGGAAGCAGACTGAAAA
TTA
Found at i:2999232 original size:27 final size:25
Alignment explanation
Indices: 2999181--2999233 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 25
2999171 TTGTTAAAGG
*
2999181 TGATTTTTTAGTTTCTTTCCCTTTC
1 TGATTTTTTAGTTTCTTTCACTTTC
* *
2999206 TGATTTTGTTATTATTCTTTCATTTTC
1 TGATTTT-TTAGT-TTCTTTCACTTTC
2999233 T
1 T
2999234 TCTTGCGTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 4 0.17
27 12 0.52
ACGTcount: A:0.11, C:0.15, G:0.08, T:0.66
Consensus pattern (25 bp):
TGATTTTTTAGTTTCTTTCACTTTC
Found at i:3000119 original size:25 final size:22
Alignment explanation
Indices: 3000068--3000122 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
3000058 TATTATTTTA
* *
3000068 TGTAAATATTTTCTAAATTTAT
1 TGTATATATTTTCTAAAATTAT
3000090 TGTATATATTTTCTTTAAAATTAT
1 TGTATATATTTTC--TAAAATTAT
3000114 TCGTATATA
1 T-GTATATA
3000123 GCTTGGCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 12 0.43
24 9 0.32
25 7 0.25
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (22 bp):
TGTATATATTTTCTAAAATTAT
Found at i:3004859 original size:27 final size:27
Alignment explanation
Indices: 3004821--3004877 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
3004811 CCTAGGACTA
3004821 AGGCGAATGATACAATGAAAAGATTTG
1 AGGCGAATGATACAATGAAAAGATTTG
*
3004848 AGGCGAATGATACCATGAAAAGATTTG
1 AGGCGAATGATACAATGAAAAGATTTG
3004875 AGG
1 AGG
3004878 TAAGGAAACA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.42, C:0.09, G:0.28, T:0.21
Consensus pattern (27 bp):
AGGCGAATGATACAATGAAAAGATTTG
Found at i:3014492 original size:22 final size:21
Alignment explanation
Indices: 3014467--3014523 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
3014457 TAACTAAGGC
*
3014467 ATGTCTCGAGACAAAAGCTCTT
1 ATGTCTCGAGACAAAA-CTCAT
* * *
3014489 ATGTCTTGAGACCTATACTCAT
1 ATGTCTCGAGA-CAAAACTCAT
3014511 ATGTCTCGAGACA
1 ATGTCTCGAGACA
3014524 GGGTACCTTC
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
21 1 0.04
22 24 0.86
23 3 0.11
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.30
Consensus pattern (21 bp):
ATGTCTCGAGACAAAACTCAT
Found at i:3015941 original size:17 final size:17
Alignment explanation
Indices: 3015919--3015952 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3015909 ACAAAAATTT
*
3015919 TTAAAAAGATAGAAGAG
1 TTAAAAAGATAAAAGAG
3015936 TTAAAAAGATAAAAGAG
1 TTAAAAAGATAAAAGAG
3015953 AGAATAGTCA
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:0.62, C:0.00, G:0.21, T:0.18
Consensus pattern (17 bp):
TTAAAAAGATAAAAGAG
Found at i:3017831 original size:101 final size:101
Alignment explanation
Indices: 3017656--3017858 Score: 316
Period size: 101 Copynumber: 2.0 Consensus size: 101
3017646 ATTTTCCATA
* * * * *
3017656 ATAAATTGAATGGCTAAACAAGATACGAAAGCAGAAGCAACTTGGCTTCTAGCACCTATTAAAAC
1 ATAAATTGAAAGGCTAAACAAGATACAAAAGCAGAAGCAACTTAGCTTCTAGCACATACTAAAAC
* *
3017721 AGTATAGACTAGGATGGAACTATATCTAAAGATGAC
66 AGTATAGACTAAGATGGAACTATAACTAAAGATGAC
*
3017757 ATAAATTGAAAGGCTAAACAAGATTCAAAAGCAGAAGCAACTTAGCTTCTAGCACATACTAAAAC
1 ATAAATTGAAAGGCTAAACAAGATACAAAAGCAGAAGCAACTTAGCTTCTAGCACATACTAAAAC
* *
3017822 AGTATAGACTAAGATGGAATTATAAGTAAAGATGAC
66 AGTATAGACTAAGATGGAACTATAACTAAAGATGAC
3017858 A
1 A
3017859 AACTAAAAAG
Statistics
Matches: 92, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
101 92 1.00
ACGTcount: A:0.45, C:0.15, G:0.18, T:0.22
Consensus pattern (101 bp):
ATAAATTGAAAGGCTAAACAAGATACAAAAGCAGAAGCAACTTAGCTTCTAGCACATACTAAAAC
AGTATAGACTAAGATGGAACTATAACTAAAGATGAC
Found at i:3022066 original size:22 final size:21
Alignment explanation
Indices: 3022041--3022097 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
3022031 TAACTGAGGC
*
3022041 ATGTCTCGAGACAAAAGCTCTT
1 ATGTCTCGAGACAAAA-CTCAT
* *
3022063 ATGTCTCGAGACTTATACTCAT
1 ATGTCTCGAGAC-AAAACTCAT
3022085 ATGTCTCGAGACA
1 ATGTCTCGAGACA
3022098 GAGCACCTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 28 0.93
23 2 0.07
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.30
Consensus pattern (21 bp):
ATGTCTCGAGACAAAACTCAT
Found at i:3026853 original size:11 final size:11
Alignment explanation
Indices: 3026846--3026870 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3026836 CATTTTTTAT
3026846 TTTATTTTTTG
1 TTTATTTTTTG
3026857 TTTATTTTTTG
1 TTTATTTTTTG
3026868 TTT
1 TTT
3026871 TCTAATTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.84
Consensus pattern (11 bp):
TTTATTTTTTG
Found at i:3029488 original size:231 final size:231
Alignment explanation
Indices: 3029079--3029529 Score: 787
Period size: 231 Copynumber: 2.0 Consensus size: 231
3029069 TATGAGGACG
* * * *
3029079 AAGCCTAATAGAGCAGCCAGTGTTTTCAATCTAGATGTAGTCACCATATTATCAAACCAGATAGA
1 AAGCCTAACAGACCAACCAATGTTTTCAATCTAGATGTAGTCACCATATTATCAAACCAGATAGA
* * *
3029144 ATAATTAAATAAGAAAATTGATTGTTTATGTGTTTCTATGTAGGTACATCCGGTGATGCAGTGTG
66 ATAATTAAATAAGAAAATTGATTGTTTATGTGTTTCTACGCAAGTACATCCGGTGATGCAGTGTG
* *
3029209 ATACAAATGGAGGAGGAATGAACAATTCAGAATATTTACCCTACGGTCCTAGCACAGAGAACAAA
131 ATACAAACGGAGGAGGAATGAACAATTCAGAATATTTACCCTACGGTCCTAACACAGAGAACAAA
3029274 CAAGTCAACTATATGGGTAATAATTATCAGAGGATA
196 CAAGTCAACTATATGGGTAATAATTATCAGAGGATA
3029310 AAGCCTAACAGACCAACCAATGTTTTCAATCTAGATGTAGTCACCATATTATCAAACCAGATAGA
1 AAGCCTAACAGACCAACCAATGTTTTCAATCTAGATGTAGTCACCATATTATCAAACCAGATAGA
3029375 ATAATTAAATAAGAAAATTGATTGTTTATGTGTTTCTACGCAAGTACATCCGGTGATGCAGTGTG
66 ATAATTAAATAAGAAAATTGATTGTTTATGTGTTTCTACGCAAGTACATCCGGTGATGCAGTGTG
**
3029440 ATACAAACGGAGGAGGAATGAACAATTCAGAATATTTACACC-ACGGTCCTAACACAGAGAATGA
131 ATACAAACGGAGGAGGAATGAACAATTCAGAATATTTAC-CCTACGGTCCTAACACAGAGAACAA
3029504 ACAAGTCAACTATATGGGTAATAATT
195 ACAAGTCAACTATATGGGTAATAATT
3029530 CTACGTCTCA
Statistics
Matches: 208, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
231 206 0.99
232 2 0.01
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (231 bp):
AAGCCTAACAGACCAACCAATGTTTTCAATCTAGATGTAGTCACCATATTATCAAACCAGATAGA
ATAATTAAATAAGAAAATTGATTGTTTATGTGTTTCTACGCAAGTACATCCGGTGATGCAGTGTG
ATACAAACGGAGGAGGAATGAACAATTCAGAATATTTACCCTACGGTCCTAACACAGAGAACAAA
CAAGTCAACTATATGGGTAATAATTATCAGAGGATA
Found at i:3034116 original size:23 final size:22
Alignment explanation
Indices: 3034075--3034117 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
3034065 GCAATCTTAG
*
3034075 ATATGATATGTAATCTTAGAAC
1 ATATGATATGTAATATTAGAAC
*
3034097 ATATGATTTTGTAATATTAGA
1 ATATGA-TATGTAATATTAGA
3034118 GATTTGATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.42
Consensus pattern (22 bp):
ATATGATATGTAATATTAGAAC
Found at i:3034368 original size:15 final size:16
Alignment explanation
Indices: 3034350--3034381 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
3034340 GTCGTTTAGC
3034350 TTTGAGTT-GTTTTCG
1 TTTGAGTTGGTTTTCG
3034365 TTTGAGTTGGTTTTCG
1 TTTGAGTTGGTTTTCG
3034381 T
1 T
3034382 AGAGGAATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.06, C:0.06, G:0.28, T:0.59
Consensus pattern (16 bp):
TTTGAGTTGGTTTTCG
Found at i:3036368 original size:9 final size:9
Alignment explanation
Indices: 3036342--3036376 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
3036332 TAAAATAAAG
*
3036342 AAATGGAAT
1 AAATGAAAT
3036351 AAA-GAAAT
1 AAATGAAAT
3036359 AAATGAAAT
1 AAATGAAAT
3036368 AAATGAAAT
1 AAATGAAAT
3036377 GAAAAAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 7 0.29
9 17 0.71
ACGTcount: A:0.66, C:0.00, G:0.14, T:0.20
Consensus pattern (9 bp):
AAATGAAAT
Found at i:3036368 original size:17 final size:18
Alignment explanation
Indices: 3036342--3036376 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
3036332 TAAAATAAAG
*
3036342 AAATGGAATAAA-GAAAT
1 AAATGAAATAAATGAAAT
3036359 AAATGAAATAAATGAAAT
1 AAATGAAATAAATGAAAT
3036377 GAAAAAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.66, C:0.00, G:0.14, T:0.20
Consensus pattern (18 bp):
AAATGAAATAAATGAAAT
Found at i:3037251 original size:22 final size:22
Alignment explanation
Indices: 3037193--3037251 Score: 91
Period size: 22 Copynumber: 2.6 Consensus size: 22
3037183 TTACCGATCG
*
3037193 GGCACTTTATGTGCCGTATCTTA
1 GGCAC-TTATGTGCTGTATCTTA
*
3037216 GGCACTTATGTGCTGTATGTTA
1 GGCACTTATGTGCTGTATCTTA
3037238 GGCACTTATGTGCT
1 GGCACTTATGTGCT
3037252 AGTTACTGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 29 0.85
23 5 0.15
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.39
Consensus pattern (22 bp):
GGCACTTATGTGCTGTATCTTA
Found at i:3037339 original size:45 final size:45
Alignment explanation
Indices: 3037267--3037502 Score: 339
Period size: 45 Copynumber: 5.2 Consensus size: 45
3037257 CTGTTACCGC
* *
3037267 TACTGCTACTGTTTACCGATTCAGCACTTTGTGTGTCGAATATTGT
1 TACTGTTACTG-TTACCGATTCGGCACTTTGTGTGTCGAATATTGT
*
3037313 TACTGCTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
* * *
3037358 TACTGTTACCGTTACCGATTCGGCACTGTGTATGTCGAATATTGT
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
* *
3037403 TACTGTTA-TCATTACCGATTCGGCACTTTGTGTGTGGAATATTGT
1 TACTGTTACT-GTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
* * * *
3037448 TACTGTTACCGTTACCGATTCAGCACTTTGTGTGTTGAATACTGT
1 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
3037493 TACTGTTACT
1 TACTGTTACT
3037503 ATTCCAGATT
Statistics
Matches: 172, Mismatches: 16, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
45 161 0.94
46 11 0.06
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.41
Consensus pattern (45 bp):
TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
Found at i:3037702 original size:18 final size:18
Alignment explanation
Indices: 3037681--3037872 Score: 153
Period size: 18 Copynumber: 10.7 Consensus size: 18
3037671 TAACTGATTA
3037681 TTACTGAATAATTGACTG
1 TTACTGAATAATTGACTG
* *
3037699 TTACCGGATAATTGACTG
1 TTACTGAATAATTGACTG
*
3037717 TTACTGGAT-ATTAGACTG
1 TTACTGAATAATT-GACTG
* * *
3037735 TTACTGAATAACTGAATA
1 TTACTGAATAATTGACTG
*
3037753 TTACTGAATAATTGA-TCA
1 TTACTGAATAATTGACT-G
* * *
3037771 TTATTGAATAACTGATTG
1 TTACTGAATAATTGACTG
*
3037789 TCACTGAATGAA-TGACTG
1 TTACTGAAT-AATTGACTG
* *
3037807 CTACTGAATAACTT-AATAG
1 TTACTGAATAA-TTGACT-G
* *
3037826 TTACTAAAT-ATCTGA-TT
1 TTACTGAATAAT-TGACTG
3037843 TTACTGAATAATTGACTG
1 TTACTGAATAATTGACTG
3037861 TTACTGAATAAT
1 TTACTGAATAAT
3037873 CGATCAATTG
Statistics
Matches: 140, Mismatches: 22, Indels: 24
0.75 0.12 0.13
Matches are distributed among these distances:
17 18 0.13
18 107 0.76
19 15 0.11
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (18 bp):
TTACTGAATAATTGACTG
Found at i:3037757 original size:36 final size:36
Alignment explanation
Indices: 3037669--3037951 Score: 144
Period size: 36 Copynumber: 7.6 Consensus size: 36
3037659 AAAGGTATAA
*
3037669 AATAACTGATTATTACTGAATAATTGACTGTTACCG
1 AATAACTGAATATTACTGAATAATTGACTGTTACCG
* * * * * *
3037705 GATAATTGACTGTTACTGGAT-ATTAGACTGTTACTG
1 AATAACTGAATATTACTGAATAATT-GACTGTTACCG
* **
3037741 AATAACTGAATATTACTGAATAATTGA-TCATTATTG
1 AATAACTGAATATTACTGAATAATTGACT-GTTACCG
* * * * *
3037777 AATAACTGATTGTCACTGAATGAA-TGACTGCTACTG
1 AATAACTGAATATTACTGAAT-AATTGACTGTTACCG
* * * *
3037813 AATAACTTAATAGTTACTAAAT-ATCTGA-TTTTACTG
1 AATAACTGAATA-TTACTGAATAAT-TGACTGTTACCG
* * * * *
3037849 AATAATTGACTGTTACTGAATAATCGATCAATTGATCGATACTG
1 AATAACTGAATATTACTGAATAATTGA-C---TG-T---TACCG
* * * *
3037893 AATAACTGATTATTATTGAATAATTGATTGTTATCG
1 AATAACTGAATATTACTGAATAATTGACTGTTACCG
* *
3037929 AATAACTGATTGTTACTGAATAA
1 AATAACTGAATATTACTGAATAA
3037952 ATAATTATTC
Statistics
Matches: 186, Mismatches: 43, Indels: 36
0.70 0.16 0.14
Matches are distributed among these distances:
35 15 0.08
36 123 0.66
37 16 0.09
39 1 0.01
40 3 0.02
41 1 0.01
44 27 0.15
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.37
Consensus pattern (36 bp):
AATAACTGAATATTACTGAATAATTGACTGTTACCG
Found at i:3037795 original size:54 final size:53
Alignment explanation
Indices: 3037669--3037951 Score: 169
Period size: 54 Copynumber: 5.4 Consensus size: 53
3037659 AAAGGTATAA
* * * * * *
3037669 AATAACTGATTATTACTGAATAATTGACTGTTACCGGATAATTGA-CTGTTACTG
1 AATAACTGATT-TTACTGAATAACTGACTATTACTGAATAATTGATC-ATTATTG
* * * *
3037723 GAT-ATTAGACTGTTACTGAATAACTGAATATTACTGAATAATTGATCATTATTG
1 AATAACT-GA-TTTTACTGAATAACTGACTATTACTGAATAATTGATCATTATTG
* ** * * *
3037777 AATAACTGATTGTCACTGAATGAA-TGACTGCTACTGAATAACTTAAT-AGTTACTA
1 AATAACTGATT-TTACTGAAT-AACTGACTATTACTGAATAA-TTGATCA-TTATTG
* * * *
3037832 AATATCTGATTTTACTGAATAATTGACTGTTACTGAATAATCGATCA--ATTG
1 AATAACTGATTTTACTGAATAACTGACTATTACTGAATAATTGATCATTATTG
* * ** *
3037883 -AT--C-GA---TACTGAATAACTGATTATTATTGAATAATTGATTGTTATCG
1 AATAACTGATTTTACTGAATAACTGACTATTACTGAATAATTGATCATTATTG
3037929 AATAACTGATTGTTACTGAATAA
1 AATAACTGATT-TTACTGAATAA
3037952 ATAATTATTC
Statistics
Matches: 174, Mismatches: 35, Indels: 40
0.70 0.14 0.16
Matches are distributed among these distances:
44 28 0.16
46 3 0.02
47 4 0.02
48 1 0.01
49 1 0.01
50 4 0.02
51 2 0.01
53 8 0.05
54 99 0.57
55 24 0.14
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.37
Consensus pattern (53 bp):
AATAACTGATTTTACTGAATAACTGACTATTACTGAATAATTGATCATTATTG
Found at i:3037912 original size:18 final size:18
Alignment explanation
Indices: 3037891--3037951 Score: 86
Period size: 18 Copynumber: 3.4 Consensus size: 18
3037881 TGATCGATAC
*
3037891 TGAATAACTGATTATTAT
1 TGAATAACTGATTGTTAT
*
3037909 TGAATAATTGATTGTTAT
1 TGAATAACTGATTGTTAT
* *
3037927 CGAATAACTGATTGTTAC
1 TGAATAACTGATTGTTAT
3037945 TGAATAA
1 TGAATAA
3037952 ATAATTATTC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.41
Consensus pattern (18 bp):
TGAATAACTGATTGTTAT
Found at i:3038097 original size:2 final size:2
Alignment explanation
Indices: 3038090--3038114 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3038080 TGAATAGTTC
3038090 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3038115 TAATATGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3042300 original size:5 final size:5
Alignment explanation
Indices: 3042292--3042331 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
3042282 ATAAAATAAA
3042292 GAAAT GAAAT -AAA- GAAAT -AAAT GAAAT -AAAT GAAAT GAAA
1 GAAAT GAAAT GAAAT GAAAT GAAAT GAAAT GAAAT GAAAT GAAA
3042332 AAGAAAAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
4 14 0.45
5 17 0.55
ACGTcount: A:0.68, C:0.00, G:0.15, T:0.17
Consensus pattern (5 bp):
GAAAT
Found at i:3042303 original size:13 final size:13
Alignment explanation
Indices: 3042285--3042327 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
3042275 TTTAATAATA
3042285 AAATAAAGAAATG
1 AAATAAAGAAATG
3042298 AAATAAAGAAAT-
1 AAATAAAGAAATG
*
3042310 AAATGAAATAAATG
1 AAAT-AAAGAAATG
3042324 AAAT
1 AAAT
3042328 GAAAAAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 4 0.15
13 19 0.70
14 4 0.15
ACGTcount: A:0.70, C:0.00, G:0.12, T:0.19
Consensus pattern (13 bp):
AAATAAAGAAATG
Found at i:3042315 original size:17 final size:18
Alignment explanation
Indices: 3042293--3042327 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
3042283 TAAAATAAAG
3042293 AAATGAAATAAA-GAAAT
1 AAATGAAATAAATGAAAT
3042310 AAATGAAATAAATGAAAT
1 AAATGAAATAAATGAAAT
3042328 GAAAAAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.69, C:0.00, G:0.11, T:0.20
Consensus pattern (18 bp):
AAATGAAATAAATGAAAT
Found at i:3042319 original size:9 final size:9
Alignment explanation
Indices: 3042293--3042327 Score: 63
Period size: 9 Copynumber: 4.0 Consensus size: 9
3042283 TAAAATAAAG
3042293 AAATGAAAT
1 AAATGAAAT
3042302 AAA-GAAAT
1 AAATGAAAT
3042310 AAATGAAAT
1 AAATGAAAT
3042319 AAATGAAAT
1 AAATGAAAT
3042328 GAAAAAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.32
9 17 0.68
ACGTcount: A:0.69, C:0.00, G:0.11, T:0.20
Consensus pattern (9 bp):
AAATGAAAT
Found at i:3042761 original size:5 final size:5
Alignment explanation
Indices: 3042753--3042801 Score: 80
Period size: 5 Copynumber: 9.8 Consensus size: 5
3042743 AAGTGAATTT
* *
3042753 GAATT GAATT GAATG GAATG GAATG GAATG GAATG GAATG GAATG GAAT
1 GAATG GAATG GAATG GAATG GAATG GAATG GAATG GAATG GAATG GAAT
3042802 TATGATTAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
5 43 1.00
ACGTcount: A:0.41, C:0.00, G:0.35, T:0.24
Consensus pattern (5 bp):
GAATG
Found at i:3043281 original size:45 final size:45
Alignment explanation
Indices: 3043211--3043450 Score: 354
Period size: 45 Copynumber: 5.3 Consensus size: 45
3043201 CTGTTACCGC
* * *
3043211 TACTGCTACTGTTACCGATTTGGCACTTTGTGTGTCGAATATTGT
1 TACTGTTACCGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
* * * *
3043256 TACTGCTATCGTTACTGATTCGGCACTTTGTGTGTCGGATATTGT
1 TACTGTTACCGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
*
3043301 TACTGTTACCGTTACCGATTCGGCACTGTGTGTGTCGAATATTGT
1 TACTGTTACCGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
* *
3043346 TACTGTTACCGTTACCGATTCGGTACTTTGTGTGTGGAATATTGT
1 TACTGTTACCGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
* * *
3043391 TACTGTTACCGTTACCGATTCAGCACTTTGTGTGTTGAATACTGT
1 TACTGTTACCGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
*
3043436 TACTGTTACTGTTAC
1 TACTGTTACCGTTAC
3043451 TATTCCGGAT
Statistics
Matches: 177, Mismatches: 18, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 177 1.00
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.41
Consensus pattern (45 bp):
TACTGTTACCGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
Found at i:3043651 original size:18 final size:18
Alignment explanation
Indices: 3043630--3043820 Score: 160
Period size: 18 Copynumber: 10.6 Consensus size: 18
3043620 TAACTGATTA
3043630 TTACTGAATAATTGACTG
1 TTACTGAATAATTGACTG
* *
3043648 TTACCGGATAATTGACTG
1 TTACTGAATAATTGACTG
*
3043666 TTACTGGAT-ATTAGACTG
1 TTACTGAATAATT-GACTG
* * *
3043684 TTACTGAATAACTGAATA
1 TTACTGAATAATTGACTG
*
3043702 TTACTGAATAATTGA-TCA
1 TTACTGAATAATTGACT-G
* *
3043720 TTACTGAATAACTGATTG
1 TTACTGAATAATTGACTG
3043738 TTACTGAATGAA-TGACTG
1 TTACTGAAT-AATTGACTG
* *
3043756 CTACTGAATAACTT-AATAG
1 TTACTGAATAA-TTGACT-G
*
3043775 TTACTGAAT-ATCTGA-TT
1 TTACTGAATAAT-TGACTG
*
3043792 TTACTGAATAATTGACTA
1 TTACTGAATAATTGACTG
*
3043810 TTACTGGATAA
1 TTACTGAATAA
3043821 CCGATCAATT
Statistics
Matches: 144, Mismatches: 17, Indels: 24
0.78 0.09 0.13
Matches are distributed among these distances:
17 19 0.13
18 109 0.76
19 16 0.11
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (18 bp):
TTACTGAATAATTGACTG
Found at i:3043706 original size:36 final size:36
Alignment explanation
Indices: 3043618--3043900 Score: 182
Period size: 36 Copynumber: 7.6 Consensus size: 36
3043608 AAAGGTATAA
* *
3043618 AATAACTGATTATTACTGAATAATTGACTGTTACCG
1 AATAACTGAATATTACTGAATAATTGACTGTTACTG
* * * * *
3043654 GATAATTGACTGTTACTGGAT-ATTAGACTGTTACTG
1 AATAACTGAATATTACTGAATAATT-GACTGTTACTG
*
3043690 AATAACTGAATATTACTGAATAATTGA-TCATTACTG
1 AATAACTGAATATTACTGAATAATTGACT-GTTACTG
* * *
3043726 AATAACTGATTGTTACTGAATGAA-TGACTGCTACTG
1 AATAACTGAATATTACTGAAT-AATTGACTGTTACTG
* *
3043762 AATAACTTAATAGTTACTGAAT-ATCTGA-TTTTACTG
1 AATAACTGAATA-TTACTGAATAAT-TGACTGTTACTG
* * *
3043798 AATAATTGACTATTACTGGATAACCGATCAATTGA-TCGATACTG
1 AATAACTGAATATTACT-G---A---AT-AATTGACT-GTTACTG
** * * *
3043842 AATAACTGGTTATTATTGAATAATTGATTGTTACCG
1 AATAACTGAATATTACTGAATAATTGACTGTTACTG
* * *
3043878 AATAACTGACTGTTACTAAATAA
1 AATAACTGAATATTACTGAATAA
3043901 ATAATTATTC
Statistics
Matches: 191, Mismatches: 37, Indels: 38
0.72 0.14 0.14
Matches are distributed among these distances:
35 10 0.05
36 131 0.69
37 21 0.11
39 1 0.01
40 1 0.01
42 2 0.01
43 5 0.03
44 20 0.10
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (36 bp):
AATAACTGAATATTACTGAATAATTGACTGTTACTG
Found at i:3043740 original size:72 final size:71
Alignment explanation
Indices: 3043618--3043820 Score: 232
Period size: 72 Copynumber: 2.8 Consensus size: 71
3043608 AAAGGTATAA
* * * * *
3043618 AATAACTGATTATTACTGAATAATTGA-CTGTTACCGGATAATTGACTGTTACTGGATATTAGAC
1 AATAACTGAATATTACTGAATAATTGATC-ATTACTGAATAATTGACTGTTACTGGATAAT-GAC
*
3043682 TGTTACTG
64 TGCTACTG
* * *
3043690 AATAACTGAATATTACTGAATAATTGATCATTACTGAATAACTGATTGTTACTGAATGAATGACT
1 AATAACTGAATATTACTGAATAATTGATCATTACTGAATAATTGACTGTTACTGGAT-AATGACT
3043755 GCTACTG
65 GCTACTG
* * *
3043762 AATAACTTAATAGTTACTGAAT-ATCTGAT-TTTACTGAATAATTGACTATTACTGGATAA
1 AATAACTGAATA-TTACTGAATAAT-TGATCATTACTGAATAATTGACTGTTACTGGATAA
3043821 CCGATCAATT
Statistics
Matches: 112, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
71 2 0.02
72 94 0.84
73 16 0.14
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (71 bp):
AATAACTGAATATTACTGAATAATTGATCATTACTGAATAATTGACTGTTACTGGATAATGACTG
CTACTG
Found at i:3043880 original size:18 final size:18
Alignment explanation
Indices: 3043859--3043893 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3043849 GGTTATTATT
* *
3043859 GAATAATTGATTGTTACC
1 GAATAACTGACTGTTACC
3043877 GAATAACTGACTGTTAC
1 GAATAACTGACTGTTAC
3043894 TAAATAAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (18 bp):
GAATAACTGACTGTTACC
Found at i:3045479 original size:13 final size:13
Alignment explanation
Indices: 3045461--3045486 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3045451 GTAAATGATG
3045461 TTAAAATAAATAT
1 TTAAAATAAATAT
3045474 TTAAAATAAATAT
1 TTAAAATAAATAT
3045487 ATTATAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TTAAAATAAATAT
Found at i:3045605 original size:12 final size:12
Alignment explanation
Indices: 3045588--3045618 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
3045578 GAAGCAGGGG
3045588 AGAAAAAGAGAA
1 AGAAAAAGAGAA
*
3045600 AGAAAAAGGGAA
1 AGAAAAAGAGAA
3045612 AGAAAAA
1 AGAAAAA
3045619 TAAAAGAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
AGAAAAAGAGAA
Done.