Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 9 of 210
Found at i:3547633 original size:15 final size:15
Alignment explanation
Indices: 3547615--3547648 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3547605 GTTGTTCGAG
3547615 AATAGCTATGTCCAA
1 AATAGCTATGTCCAA
* *
3547630 AATAGTTATGTTCAA
1 AATAGCTATGTCCAA
3547645 AATA
1 AATA
3547649 TGATTTTAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (15 bp):
AATAGCTATGTCCAA
Found at i:3547922 original size:15 final size:16
Alignment explanation
Indices: 3547888--3547934 Score: 60
Period size: 15 Copynumber: 2.9 Consensus size: 16
3547878 CAGTTATTCG
*
3547888 GAACAACCTCAATATTGA
1 GAACAA-CTC-ATGTTGA
3547906 GAACAACT-ATGTTGA
1 GAACAACTCATGTTGA
3547921 GAACAACTCATGTT
1 GAACAACTCATGTT
3547935 TGGAACAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 14 0.52
16 5 0.19
17 2 0.07
18 6 0.22
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (16 bp):
GAACAACTCATGTTGA
Found at i:3551449 original size:2 final size:2
Alignment explanation
Indices: 3551442--3551467 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3551432 TGCCTTTTAC
3551442 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
3551468 TATTTAAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3554414 original size:24 final size:24
Alignment explanation
Indices: 3554359--3554415 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
3554349 GTTACATAAA
* *
3554359 AATTCAAAATACTAATTCAAAAAT
1 AATTTAAAATAATAATTCAAAAAT
** *
3554383 AAGATAAAATAATAATTCAAAATT
1 AATTTAAAATAATAATTCAAAAAT
3554407 AATTTAAAA
1 AATTTAAAA
3554416 CTAAGATAAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (24 bp):
AATTTAAAATAATAATTCAAAAAT
Found at i:3554421 original size:35 final size:37
Alignment explanation
Indices: 3554354--3554429 Score: 102
Period size: 35 Copynumber: 2.1 Consensus size: 37
3554344 AGATAGTTAC
3554354 ATAAAAATTCAAAATACTAATTCAAAAATAAGATAA-A
1 ATAAAAATTCAAAATA-TAATTCAAAAATAAGATAATA
* * *
3554391 ATAATAATTCAAAAT-TAATTTAAAACTAAGATAATA
1 ATAAAAATTCAAAATATAATTCAAAAATAAGATAATA
3554427 ATA
1 ATA
3554430 GCTAATCTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
35 17 0.49
36 4 0.11
37 14 0.40
ACGTcount: A:0.62, C:0.07, G:0.03, T:0.29
Consensus pattern (37 bp):
ATAAAAATTCAAAATATAATTCAAAAATAAGATAATA
Found at i:3556650 original size:28 final size:29
Alignment explanation
Indices: 3556592--3556656 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 29
3556582 TTATAAAAGT
*
3556592 TATATATATTATATAAAGAAATACGTATA
1 TATATATACTATATAAAGAAATACGTATA
* *
3556621 TATATATACTATAT-AAGAAATGCGTGTA
1 TATATATACTATATAAAGAAATACGTATA
*
3556649 TAAATATA
1 TATATATA
3556657 GAAATAGTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 19 0.59
29 13 0.41
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.37
Consensus pattern (29 bp):
TATATATACTATATAAAGAAATACGTATA
Found at i:3558293 original size:28 final size:28
Alignment explanation
Indices: 3558243--3558296 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
3558233 AACTCAACCT
**
3558243 TTCTCTTCCCTTTTTTTTTTCTTTTCCA
1 TTCTCTTCCCTTTTTTAGTTCTTTTCCA
3558271 TTCT-TTCCCTTTTATTAGTTCTTTTC
1 TTCTCTTCCCTTTT-TTAGTTCTTTTC
3558297 TTCAGCTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.06, C:0.26, G:0.02, T:0.67
Consensus pattern (28 bp):
TTCTCTTCCCTTTTTTAGTTCTTTTCCA
Found at i:3565274 original size:35 final size:35
Alignment explanation
Indices: 3565228--3565297 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
3565218 AAGTTCTCAA
3565228 AAATGATTTTTATGCATTTTGAATAAAAATATTCT
1 AAATGATTTTTATGCATTTTGAATAAAAATATTCT
3565263 AAATGATTTTTATGCATTTTGAATAAAAATATTCT
1 AAATGATTTTTATGCATTTTGAATAAAAATATTCT
3565298 CGGTCATTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.46
Consensus pattern (35 bp):
AAATGATTTTTATGCATTTTGAATAAAAATATTCT
Found at i:3565962 original size:17 final size:18
Alignment explanation
Indices: 3565932--3565967 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
3565922 GTATAAATAC
3565932 GTATATATAAAATATAAG
1 GTATATATAAAATATAAG
3565950 GTATATA-AAAATATAAG
1 GTATATATAAAATATAAG
3565967 G
1 G
3565968 GATAAAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.56, C:0.00, G:0.14, T:0.31
Consensus pattern (18 bp):
GTATATATAAAATATAAG
Found at i:3566713 original size:16 final size:16
Alignment explanation
Indices: 3566692--3566723 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3566682 CTAGCGTCCT
3566692 CGCGCCGCCGCCGCAA
1 CGCGCCGCCGCCGCAA
*
3566708 CGCGCCTCCGCCGCAA
1 CGCGCCGCCGCCGCAA
3566724 TTTCACCGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.12, C:0.56, G:0.28, T:0.03
Consensus pattern (16 bp):
CGCGCCGCCGCCGCAA
Found at i:3577019 original size:17 final size:18
Alignment explanation
Indices: 3576989--3577024 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
3576979 GTATAAATAC
3576989 GTATATATAAAATATAAG
1 GTATATATAAAATATAAG
3577007 GTATATA-AAAATATAAG
1 GTATATATAAAATATAAG
3577024 G
1 G
3577025 GATAAAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.56, C:0.00, G:0.14, T:0.31
Consensus pattern (18 bp):
GTATATATAAAATATAAG
Found at i:3577771 original size:16 final size:16
Alignment explanation
Indices: 3577750--3577781 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3577740 CTAGCGTCCT
3577750 CGCGCCGCCGCCGCAA
1 CGCGCCGCCGCCGCAA
*
3577766 CGCGCCTCCGCCGCAA
1 CGCGCCGCCGCCGCAA
3577782 TTTCACCGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.12, C:0.56, G:0.28, T:0.03
Consensus pattern (16 bp):
CGCGCCGCCGCCGCAA
Found at i:3593250 original size:31 final size:31
Alignment explanation
Indices: 3593183--3593248 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 31
3593173 TTAATAAAAG
*
3593183 TAAAATTGTACTTTAATCTCCTTAAAAATTA
1 TAAAATTGTAATTTAATCTCCTTAAAAATTA
* *
3593214 TAAAATTTTAATTTAATC-CTTTAAAAATTA
1 TAAAATTGTAATTTAATCTCCTTAAAAATTA
3593244 TAAAA
1 TAAAA
3593249 ATATAGGCTA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 16 0.50
31 16 0.50
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.42
Consensus pattern (31 bp):
TAAAATTGTAATTTAATCTCCTTAAAAATTA
Found at i:3594526 original size:33 final size:34
Alignment explanation
Indices: 3594458--3594526 Score: 79
Period size: 33 Copynumber: 2.0 Consensus size: 34
3594448 AAATAAAGAT
* **
3594458 AAAAAAATGTATATGTGTATATATTTACAAAATAA
1 AAAAAAATGTATA-GAGTATATACATACAAAATAA
3594493 AAAAAAATGTATA-AGTATATACATA-AAATATAA
1 AAAAAAATGTATAGAGTATATACATACAAA-ATAA
3594526 A
1 A
3594527 GCATATAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
32 3 0.10
33 14 0.47
35 13 0.43
ACGTcount: A:0.59, C:0.03, G:0.07, T:0.30
Consensus pattern (34 bp):
AAAAAAATGTATAGAGTATATACATACAAAATAA
Found at i:3594562 original size:2 final size:2
Alignment explanation
Indices: 3594557--3594587 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3594547 TAAATATAAA
*
3594557 AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3594588 AAAACGTATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3594652 original size:17 final size:17
Alignment explanation
Indices: 3594630--3594678 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
3594620 CAAAAAGTTT
*
3594630 AAAAATACATATATAAA
1 AAAAATATATATATAAA
* **
3594647 AAAAATGTATATATTTA
1 AAAAATATATATATAAA
3594664 AAAAATATATATATA
1 AAAAATATATATATA
3594679 CGTATAAGAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (17 bp):
AAAAATATATATATAAA
Found at i:3594665 original size:19 final size:19
Alignment explanation
Indices: 3594638--3594678 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
3594628 TTAAAAATAC
*
3594638 ATATATAAAAAAAATGTAT
1 ATATATAAAAAAAATATAT
* *
3594657 ATATTTAAAAAATATATAT
1 ATATATAAAAAAAATATAT
3594676 ATA
1 ATA
3594679 CGTATAAGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (19 bp):
ATATATAAAAAAAATATAT
Found at i:3594703 original size:3 final size:3
Alignment explanation
Indices: 3594695--3594738 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
3594685 AGAATATAGA
* *
3594695 AAT AAT AAT AAT AAT CAT AAT AAT AAAT AAT -AT AAC AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AA
3594739 ATATTTTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
2 2 0.06
3 30 0.86
4 3 0.09
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:3594739 original size:18 final size:19
Alignment explanation
Indices: 3594695--3594741 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
3594685 AGAATATAGA
* *
3594695 AATAAT-AATAATAATCAT
1 AATAATAAATAATAATAAC
3594713 AATAATAAATAAT-ATAAC
1 AATAATAAATAATAATAAC
3594731 AATAATAAATA
1 AATAATAAATA
3594742 TTTTAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 20 0.77
19 6 0.23
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (19 bp):
AATAATAAATAATAATAAC
Found at i:3595172 original size:13 final size:14
Alignment explanation
Indices: 3595154--3595183 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3595144 AAGCCGAATG
3595154 AAAG-AAAAAAATA
1 AAAGAAAAAAAATA
3595167 AAAGAAAAAAAATA
1 AAAGAAAAAAAATA
3595181 AAA
1 AAA
3595184 CGTTTCTCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.87, C:0.00, G:0.07, T:0.07
Consensus pattern (14 bp):
AAAGAAAAAAAATA
Found at i:3596357 original size:44 final size:45
Alignment explanation
Indices: 3596280--3596397 Score: 168
Period size: 44 Copynumber: 2.6 Consensus size: 45
3596270 AAGACTTGTA
3596280 TCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCTT
1 TCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCTT
* *
3596325 TCTTTGATCTACTTCA-CGCCAGTA-GGTGAAGACAAGATCTGCTT
1 TCTTCGATCTACTTCACCACCAGTATGG-GAAGACAAGATCTGCTT
* * *
3596369 TCTTCAATCTACTCCACCACTAGTATGGG
1 TCTTCGATCTACTTCACCACCAGTATGGG
3596398 GAGATAGAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
43 2 0.03
44 37 0.59
45 22 0.35
46 2 0.03
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (45 bp):
TCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCTT
Found at i:3596565 original size:50 final size:50
Alignment explanation
Indices: 3596503--3596765 Score: 201
Period size: 50 Copynumber: 5.3 Consensus size: 50
3596493 GATCTGTAAT
* ** *
3596503 CTTCAATTTGTTCAACTGCAATGTTGGGGAAACCAGATCCGCCGTCGTAG
1 CTTCAATCTGTTCAACTGCAATGTCAGGGAAACCAGATCCGCCGTCGTGG
* ** ** ***
3596553 CTTCAATCTGTTCCACCACACCGTCAGGGAAGTAAGATCCGCCGTCGTGG
1 CTTCAATCTGTTCAACTGCAATGTCAGGGAAACCAGATCCGCCGTCGTGG
* * *
3596603 CTTTAATCT-TTTAAATCGCAA-GATCAGGGAAACCAGATCCGCCGTCGTGG
1 CTTCAATCTGTTCAACT-GCAATG-TCAGGGAAACCAGATCCGCCGTCGTGG
* * ** * * *** *
3596653 CTTCAACCTGCTCCGCTGCACTGGT-AAGGAAGTAAGATCCGCCGTTGTGG
1 CTTCAATCTGTTCAACTGCAAT-GTCAGGGAAACCAGATCCGCCGTCGTGG
* * * *
3596703 CTTCAATCT-TTTAAATCGCAATATCAGGGAAACCAGATCCGCCGTCGTAG
1 CTTCAATCTGTTCAACT-GCAATGTCAGGGAAACCAGATCCGCCGTCGTGG
3596753 CTTCAATCTGTTC
1 CTTCAATCTGTTC
3596766 CGCTGCATTG
Statistics
Matches: 155, Mismatches: 50, Indels: 15
0.70 0.23 0.07
Matches are distributed among these distances:
49 7 0.05
50 142 0.92
51 5 0.03
52 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.26
Consensus pattern (50 bp):
CTTCAATCTGTTCAACTGCAATGTCAGGGAAACCAGATCCGCCGTCGTGG
Found at i:3596644 original size:100 final size:100
Alignment explanation
Indices: 3596529--3596814 Score: 378
Period size: 100 Copynumber: 2.9 Consensus size: 100
3596519 TGCAATGTTG
*
3596529 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACCACAC-CGTCAGGGAAGTAAGATCC
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACCACACTCGT-AAGGAAGTAAGATCC
*
3596593 GCCGTCGTGGCTTTAATCTTTTAAATCGCAAGATCA
65 GCCGTCGTGGCTTCAATCTTTTAAATCGCAAGATCA
* * * * ** *
3596629 GGGAAACCAGATCCGCCGTCGTGGCTTCAACCTGCTCCGCTGCACTGGTAAGGAAGTAAGATCCG
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACCACACTCGTAAGGAAGTAAGATCCG
* *
3596694 CCGTTGTGGCTTCAATCTTTTAAATCGCAATATCA
66 CCGTCGTGGCTTCAATCTTTTAAATCGCAAGATCA
* ** * * *
3596729 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCGCTGCA-TTGCTAAAGAAGTAAGATCT
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACCACACTCG-TAAGGAAGTAAGATCC
*
3596793 GCCGTTGTGGCTTCAATCTTTT
65 GCCGTCGTGGCTTCAATCTTTT
3596815 CAGTTTTCAA
Statistics
Matches: 167, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
99 2 0.01
100 163 0.98
101 2 0.01
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (100 bp):
GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACCACACTCGTAAGGAAGTAAGATCCG
CCGTCGTGGCTTCAATCTTTTAAATCGCAAGATCA
Found at i:3602715 original size:20 final size:20
Alignment explanation
Indices: 3602690--3602729 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
3602680 TAAAGGTCCT
*
3602690 TAATGCATATGATGTGATGC
1 TAATGCATATGATGCGATGC
3602710 TAATGCATATGATGCGATGC
1 TAATGCATATGATGCGATGC
3602730 ATGAGATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (20 bp):
TAATGCATATGATGCGATGC
Found at i:3606437 original size:32 final size:33
Alignment explanation
Indices: 3606367--3606437 Score: 83
Period size: 34 Copynumber: 2.2 Consensus size: 33
3606357 TAAAATAAAG
* **
3606367 ATAAAAAAAATGTATATGTGTATATATTTACAAA
1 ATAAAAAAAATGTATA-GAGTATATACATACAAA
3606401 ATAAAAAAAATGTATA-AGTATATACATA-AAA
1 ATAAAAAAAATGTATAGAGTATATACATACAAA
3606432 TATAAA
1 -ATAAA
3606438 GCATATAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 3 0.09
32 14 0.42
34 16 0.48
ACGTcount: A:0.59, C:0.03, G:0.07, T:0.31
Consensus pattern (33 bp):
ATAAAAAAAATGTATAGAGTATATACATACAAA
Found at i:3606620 original size:3 final size:3
Alignment explanation
Indices: 3606612--3606655 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
3606602 AGAATATAGA
* *
3606612 AAT AAT AAT AAT AAT CAT AAT AAT AAAT AAT -AT AAC AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AA
3606656 ATATTTAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
2 2 0.06
3 30 0.86
4 3 0.09
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:3606656 original size:18 final size:19
Alignment explanation
Indices: 3606612--3606658 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
3606602 AGAATATAGA
* *
3606612 AATAAT-AATAATAATCAT
1 AATAATAAATAATAATAAC
3606630 AATAATAAATAAT-ATAAC
1 AATAATAAATAATAATAAC
3606648 AATAATAAATA
1 AATAATAAATA
3606659 TTTAAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 20 0.77
19 6 0.23
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (19 bp):
AATAATAAATAATAATAAC
Found at i:3607093 original size:13 final size:13
Alignment explanation
Indices: 3607075--3607099 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3607065 CGAATGAAAG
3607075 AAAAAAATAAAAT
1 AAAAAAATAAAAT
3607088 AAAAAAATAAAA
1 AAAAAAATAAAA
3607100 CGTTTCTCTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAAATAAAAT
Found at i:3609065 original size:46 final size:45
Alignment explanation
Indices: 3609013--3609209 Score: 234
Period size: 46 Copynumber: 4.6 Consensus size: 45
3609003 TTTGAGTACT
3609013 TCTGATCAAGTGACAAAGTGATAAGTGGTAGTTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAG-TTTAGCTACACTTA
**
3609059 TCTGATCAAGAAACAAAGTGATAA---GT-G----GCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGTTTAGCTACACTTA
* *
3609096 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTCAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAG-TTTAGCTACACTTA
** **
3609142 TCTGATCAAGTGGTAAAGTGATAAGTGGTAGCCTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGTTTAGCTACACTTA
3609187 TCTGATCAAG-GAC-AAGTGATAAG
1 TCTGATCAAGTGACAAAGTGATAAG
3609210 AGGTCATATG
Statistics
Matches: 131, Mismatches: 11, Indels: 21
0.80 0.07 0.13
Matches are distributed among these distances:
37 31 0.24
40 2 0.02
41 1 0.01
42 1 0.01
43 12 0.09
44 1 0.01
45 21 0.16
46 62 0.47
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (45 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGTTTAGCTACACTTA
Found at i:3609090 original size:37 final size:37
Alignment explanation
Indices: 3609049--3609123 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
3609039 GGTAGTTTTA
3609049 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
** *
3609086 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
3609123 G
1 G
3609124 TAGCTTCAGC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:3609117 original size:83 final size:83
Alignment explanation
Indices: 3609013--3609169 Score: 251
Period size: 83 Copynumber: 1.9 Consensus size: 83
3609003 TTTGAGTACT
* *
3609013 TCTGATCAAGTGACAAAGTGATAAGTGGTAGTTTTAGCTACACTTATCTGATCAAGAAACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAAGAAACAAAGT
3609078 GATAAGTGGCTACACTTA
66 GATAAGTGGCTACACTTA
* ****
3609096 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAAGTGGTAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAAGAAACAAAGT
3609161 GATAAGTGG
66 GATAAGTGG
3609170 TAGCCTAGCT
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
83 67 1.00
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.29
Consensus pattern (83 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAAGAAACAAAGT
GATAAGTGGCTACACTTA
Found at i:3612363 original size:22 final size:23
Alignment explanation
Indices: 3612334--3612384 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
3612324 AATTTATTTT
* *
3612334 ATAA-TAAGATGATAT-TTTATA
1 ATAATTAAGATCATATATATATA
3612355 ATAATTAAGATCATATATATATA
1 ATAATTAAGATCATATATATATA
3612378 A-AATTAA
1 ATAATTAA
3612385 TGATAAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 4 0.15
22 16 0.62
23 6 0.23
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.39
Consensus pattern (23 bp):
ATAATTAAGATCATATATATATA
Found at i:3616858 original size:29 final size:29
Alignment explanation
Indices: 3616826--3616882 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
3616816 AATCATCATC
* *
3616826 TCAAACATAAGTGACTAAAATGTAACATT
1 TCAAACATAAATAACTAAAATGTAACATT
3616855 TCAAACATAAATAACTAAAATGTAACAT
1 TCAAACATAAATAACTAAAATGTAACAT
3616883 AATGTAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.53, C:0.14, G:0.07, T:0.26
Consensus pattern (29 bp):
TCAAACATAAATAACTAAAATGTAACATT
Found at i:3620163 original size:6 final size:6
Alignment explanation
Indices: 3620152--3620202 Score: 95
Period size: 6 Copynumber: 8.7 Consensus size: 6
3620142 GGAGGAAAAT
3620152 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAA-G
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
3620199 AGAA
1 AGAA
3620203 TGAAAAATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.11
6 40 0.89
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (6 bp):
AGAAGG
Found at i:3636060 original size:2 final size:2
Alignment explanation
Indices: 3636055--3636083 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3636045 ACACATGCAT
3636055 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3636084 TCTGTACTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3642935 original size:17 final size:17
Alignment explanation
Indices: 3642913--3642946 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3642903 AAGGAGGACT
3642913 ATAATAAT-ATAATCATA
1 ATAATAATCAT-ATCATA
3642930 ATAATAATCATATCATA
1 ATAATAATCATATCATA
3642947 GGAATAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.88
18 2 0.12
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (17 bp):
ATAATAATCATATCATA
Found at i:3643259 original size:37 final size:36
Alignment explanation
Indices: 3643184--3643292 Score: 85
Period size: 37 Copynumber: 2.9 Consensus size: 36
3643174 AATAAAGGCA
* **
3643184 AAAAGAAAAATAAAAAAATAAAAATGAATACACGAC
1 AAAAGAAAAATAAAAAAATAAAAATGAATAAAAAAC
* *
3643220 AAAAGAAAGAATAAAAAAATTTAAAAT-ATTAAAAAAC
1 AAAAGAAA-AATAAAAAAA-TAAAAATGAATAAAAAAC
* *
3643257 AAAGAAGTAATAACTAAATAAAATAAAAATAAATAA
1 -AA-AAG-AA-AAATAAA-AAAATAAAAATGAATAA
3643293 TCTAGGAAGG
Statistics
Matches: 57, Mismatches: 8, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
36 8 0.14
37 16 0.28
38 8 0.14
39 3 0.05
40 13 0.23
41 9 0.16
ACGTcount: A:0.72, C:0.05, G:0.06, T:0.17
Consensus pattern (36 bp):
AAAAGAAAAATAAAAAAATAAAAATGAATAAAAAAC
Found at i:3643923 original size:89 final size:89
Alignment explanation
Indices: 3643809--3644107 Score: 445
Period size: 89 Copynumber: 3.4 Consensus size: 89
3643799 GTGGATCCTA
3643809 GCTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAATATTTTCTACTGCAACTTCATGG
1 GCTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAATATTTTCTACTGCAACTTCATGG
3643874 AGATAAGATTTATAGCTTTAATCT
66 AGATAAGATTTATAGCTTTAATCT
* *
3643898 GCTCTACTGCAATTTCAGAGAGATAATATTTGCTATCTTCAATATTTTCTACTGCAACTTCATGG
1 GCTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAATATTTTCTACTGCAACTTCATGG
3643963 AGATAAGATTTATAGCTTTAATCT
66 AGATAAGATTTATAGCTTTAATCT
* * * ** * *
3643987 GCTCTACTACAATTTCAGAGAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTCAGGG
1 GCTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAATATTTTCTACTGCAACTTCATGG
* * *
3644052 AGATAAGATTTGTATCTTCAATCT
66 AGATAAGATTTATAGCTTTAATCT
* * * * *
3644076 ACTCCACTGCCACTTCAGGGAGATAATATTTG
1 GCTCTACTGCAACTTCAGAGAGATAAGATTTG
3644108 TAACTTATAG
Statistics
Matches: 191, Mismatches: 19, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
89 191 1.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (89 bp):
GCTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAATATTTTCTACTGCAACTTCATGG
AGATAAGATTTATAGCTTTAATCT
Found at i:3644108 original size:44 final size:44
Alignment explanation
Indices: 3643809--3644109 Score: 341
Period size: 44 Copynumber: 6.8 Consensus size: 44
3643799 GTGGATCCTA
* *
3643809 GCTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAATAT
1 GCTCTACTGCAACTTCAGGGAGATAAGATTTG-TATCTTCAATCT
** * * * *
3643854 TTTCTACTGCAACTTCATGGAGATAAGATTTATAGCTTTAATCT
1 GCTCTACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCT
* * * *
3643898 GCTCTACTGCAATTTCAGAGAGATAATATTTGCTATCTTCAATAT
1 GCTCTACTGCAACTTCAGGGAGATAAGATTTG-TATCTTCAATCT
** * * * *
3643943 TTTCTACTGCAACTTCATGGAGATAAGATTTATAGCTTTAATCT
1 GCTCTACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCT
* * *
3643987 GCTCTACTACAATTTCAGAGAGATAAGATTTGCTATCTTCAATCT
1 GCTCTACTGCAACTTCAGGGAGATAAGATTTG-TATCTTCAATCT
*
3644032 GCTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCT
1 GCTCTACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCT
* * * *
3644076 ACTCCACTGCCACTTCAGGGAGATAATATTTGTA
1 GCTCTACTGCAACTTCAGGGAGATAAGATTTGTA
3644110 ACTTATAGCT
Statistics
Matches: 210, Mismatches: 44, Indels: 5
0.81 0.17 0.02
Matches are distributed among these distances:
44 111 0.53
45 99 0.47
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (44 bp):
GCTCTACTGCAACTTCAGGGAGATAAGATTTGTATCTTCAATCT
Found at i:3646333 original size:44 final size:44
Alignment explanation
Indices: 3646270--3646425 Score: 222
Period size: 44 Copynumber: 3.4 Consensus size: 44
3646260 GGCTGTTACA
3646270 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATC
1 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATC
3646314 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATCAGTGAC
1 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTG---A-T--C
* *
3646364 AAGTGACAAGTGATAAGTAGTAGCTTTAGCTACACTTATCTGACC
1 -AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATC
*
3646409 AGTGACAAGTGACAAGT
1 AGTGACAAGTGATAAGT
3646426 GACAAGTGAT
Statistics
Matches: 102, Mismatches: 3, Indels: 14
0.86 0.03 0.12
Matches are distributed among these distances:
44 57 0.56
45 1 0.01
47 1 0.01
48 2 0.02
50 1 0.01
51 40 0.39
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (44 bp):
AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATC
Found at i:3646369 original size:51 final size:51
Alignment explanation
Indices: 3646314--3646539 Score: 337
Period size: 51 Copynumber: 4.3 Consensus size: 51
3646304 TTATCTGATC
*
3646314 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTAGTAGCTTTAGCTACACTTATCTGATCAGTGACA
3646365 AGTGACAAGTGATAAGTAGTAGCTTTAGCTACACTTATCTGACCAGTGACAAGTGACA
1 AGTGACAAGTGATAAGTAGTAGCTTTAGCTACACTTATCTG---A-T--C-AGTGACA
*
3646423 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTAGTAGCTTTAGCTACACTTATCTGATCAGTGACA
* *
3646474 AGTAACAAGTGATAAGT-GATAGCTTTAGCTACACTTATCTGATCAGGGACA
1 AGTGACAAGTGATAAGTAG-TAGCTTTAGCTACACTTATCTGATCAGTGACA
3646525 AGTGACAAGTGATAA
1 AGTGACAAGTGATAA
3646540 ATGTGATCCG
Statistics
Matches: 162, Mismatches: 5, Indels: 16
0.89 0.03 0.09
Matches are distributed among these distances:
50 1 0.01
51 108 0.67
52 1 0.01
54 2 0.01
55 2 0.01
57 1 0.01
58 47 0.29
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.27
Consensus pattern (51 bp):
AGTGACAAGTGATAAGTAGTAGCTTTAGCTACACTTATCTGATCAGTGACA
Found at i:3646419 original size:7 final size:7
Alignment explanation
Indices: 3646404--3646440 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
3646394 TACACTTATC
*
3646404 TGACCAG
1 TGACAAG
3646411 TGACAAG
1 TGACAAG
3646418 TGACAAG
1 TGACAAG
3646425 TGACAAG
1 TGACAAG
*
3646432 TGATAAG
1 TGACAAG
3646439 TG
1 TG
3646441 GTAGCTTTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.38, C:0.14, G:0.30, T:0.19
Consensus pattern (7 bp):
TGACAAG
Found at i:3646453 original size:109 final size:109
Alignment explanation
Indices: 3646314--3646536 Score: 385
Period size: 109 Copynumber: 2.0 Consensus size: 109
3646304 TTATCTGATC
*
3646314 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATCAGTGACAAGTGACAAGTGATA
1 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATCAGTGACAAGTAACAAGTGATA
*
3646379 AGT-AGTAGCTTTAGCTACACTTATCTGACCAGTGACAAGTGACA
66 AGTGA-TAGCTTTAGCTACACTTATCTGACCAGGGACAAGTGACA
* *
3646423 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTAACAAGTGATA
1 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATCAGTGACAAGTAACAAGTGATA
*
3646488 AGTGATAGCTTTAGCTACACTTATCTGATCAGGGACAAGTGACA
66 AGTGATAGCTTTAGCTACACTTATCTGACCAGGGACAAGTGACA
3646532 AGTGA
1 AGTGA
3646537 TAAATGTGAT
Statistics
Matches: 108, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
109 107 0.99
110 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (109 bp):
AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATCAGTGACAAGTAACAAGTGATA
AGTGATAGCTTTAGCTACACTTATCTGACCAGGGACAAGTGACA
Found at i:3647273 original size:45 final size:45
Alignment explanation
Indices: 3647182--3647279 Score: 124
Period size: 45 Copynumber: 2.2 Consensus size: 45
3647172 GGGTAAGGGG
* **
3647182 TGTTACACTGCAACTTCAGGGAAATAAGATTCGCTATCTTTAATC
1 TGTTACACTGCAACTTCAGGGAAATAAGATTAGCTATCACTAATC
* * * * *
3647227 TGTTACACTGCAACTTTAGGGAGATAAGATTAGGTTTCACTGATC
1 TGTTACACTGCAACTTCAGGGAAATAAGATTAGCTATCACTAATC
3647272 TGTTACAC
1 TGTTACAC
3647280 CATTCTCTAG
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (45 bp):
TGTTACACTGCAACTTCAGGGAAATAAGATTAGCTATCACTAATC
Found at i:3649647 original size:24 final size:22
Alignment explanation
Indices: 3649604--3649648 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 22
3649594 ACTATTTTTT
3649604 TACTGTTTGCTTTTGTTTCTGC
1 TACTGTTTGCTTTTGTTTCTGC
*
3649626 TACTGTTTCTCTTGTTGTTTCTG
1 TACTGTTT-GCTT-TTGTTTCTG
3649649 TGTTCCTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 8 0.40
23 3 0.15
24 9 0.45
ACGTcount: A:0.04, C:0.18, G:0.18, T:0.60
Consensus pattern (22 bp):
TACTGTTTGCTTTTGTTTCTGC
Found at i:3650484 original size:17 final size:17
Alignment explanation
Indices: 3650458--3650500 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
3650448 TCCCATATTT
3650458 CGGG-CGGGCTGTCGGG
1 CGGGCCGGGCTGTCGGG
3650474 CGGGCCGGGCTGTCGGG
1 CGGGCCGGGCTGTCGGG
3650491 CGGGCCGGGC
1 CGGGCCGGGC
3650501 CGCCCGGCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 4 0.15
17 22 0.85
ACGTcount: A:0.00, C:0.30, G:0.60, T:0.09
Consensus pattern (17 bp):
CGGGCCGGGCTGTCGGG
Found at i:3660939 original size:16 final size:16
Alignment explanation
Indices: 3660918--3660948 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3660908 TGCCATTTCG
3660918 GAATTTCCTTTTTCAT
1 GAATTTCCTTTTTCAT
3660934 GAATTTCCTTTTTCA
1 GAATTTCCTTTTTCA
3660949 GATAGTTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.19, G:0.06, T:0.55
Consensus pattern (16 bp):
GAATTTCCTTTTTCAT
Found at i:3662140 original size:25 final size:27
Alignment explanation
Indices: 3662105--3662154 Score: 77
Period size: 25 Copynumber: 1.9 Consensus size: 27
3662095 TTTTAAATGT
3662105 GATTATAAAAAA-TAA-TTAAAATAAA
1 GATTATAAAAAATTAATTTAAAATAAA
*
3662130 GATTATTAAAAATTAATTTAAAATA
1 GATTATAAAAAATTAATTTAAAATA
3662155 TGACAACATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 11 0.50
26 3 0.14
27 8 0.36
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (27 bp):
GATTATAAAAAATTAATTTAAAATAAA
Found at i:3662146 original size:26 final size:26
Alignment explanation
Indices: 3662105--3662154 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
3662095 TTTTAAATGT
3662105 GATTATAAAAAATAA-TTAAAATAAA
1 GATTATAAAAAATAATTTAAAATAAA
*
3662130 GATTATTAAAAATTAATTTAAAATA
1 GATTA-TAAAAAATAATTTAAAATA
3662155 TGACAACATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 5 0.23
26 9 0.41
27 8 0.36
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (26 bp):
GATTATAAAAAATAATTTAAAATAAA
Found at i:3662856 original size:27 final size:28
Alignment explanation
Indices: 3662826--3662885 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 28
3662816 TTCTTCCTTG
3662826 TTTTTAAAAC-AAAAACGAAATAGATTT
1 TTTTTAAAACAAAAAACGAAATAGATTT
*
3662853 TTTTTAAAACAGAAAAATGAAATAGATTT
1 TTTTTAAAACA-AAAAACGAAATAGATTT
3662882 TTTT
1 TTTT
3662886 GTTTTAATCA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 10 0.33
29 20 0.67
ACGTcount: A:0.48, C:0.05, G:0.08, T:0.38
Consensus pattern (28 bp):
TTTTTAAAACAAAAAACGAAATAGATTT
Found at i:3663343 original size:23 final size:21
Alignment explanation
Indices: 3663313--3663365 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 21
3663303 CCTTAGCCTC
3663313 TCCATTTTTACTTTTTTCCATTT
1 TCCATTTTTA-TTTTTTCCA-TT
*
3663336 TCCATTTTTTATTTTTTTCATT
1 TCCA-TTTTTATTTTTTCCATT
3663358 T-CATTTTT
1 TCCATTTTT
3663366 TTACGACTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 5 0.18
21 2 0.07
22 3 0.11
23 12 0.43
24 6 0.21
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (21 bp):
TCCATTTTTATTTTTTCCATT
Found at i:3663853 original size:1 final size:1
Alignment explanation
Indices: 3663839--3663936 Score: 52
Period size: 1 Copynumber: 98.0 Consensus size: 1
3663829 CCGGTAGAGG
* * * * * * * * * * *
3663839 TTTTTGTTTCTTTTTGTTTTTATTTTTTTGTTCTTGTTCTTTTCTTTTTTTTTCTTTTTTTCTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * *
3663904 TCTTTTCTTTTCTTTTCTTTTTTTCTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3663937 GGAATTGAAT
Statistics
Matches: 65, Mismatches: 32, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
1 65 1.00
ACGTcount: A:0.01, C:0.11, G:0.04, T:0.84
Consensus pattern (1 bp):
T
Found at i:3663854 original size:10 final size:9
Alignment explanation
Indices: 3663839--3663936 Score: 85
Period size: 9 Copynumber: 10.6 Consensus size: 9
3663829 CCGGTAGAGG
*
3663839 TTTTTGTTT
1 TTTTTCTTT
*
3663848 CTTTTTGTTT
1 -TTTTTCTTT
*
3663858 TTATT-TTT
1 TTTTTCTTT
*
3663866 TTGTTCTTGT
1 TTTTTCTT-T
3663876 TCTTTTCTTT
1 T-TTTTCTTT
3663886 TTTTT-TCTT
1 TTTTTCT-TT
3663895 TTTTTCTTT
1 TTTTTCTTT
3663904 TCTTTTCTTT
1 T-TTTTCTTT
3663914 TCTTTTC-TT
1 T-TTTTCTTT
3663923 TTTTTCTTT
1 TTTTTCTTT
3663932 TTTTT
1 TTTTT
3663937 GGAATTGAAT
Statistics
Matches: 78, Mismatches: 3, Indels: 15
0.81 0.03 0.16
Matches are distributed among these distances:
8 13 0.17
9 30 0.38
10 29 0.37
11 6 0.08
ACGTcount: A:0.01, C:0.11, G:0.04, T:0.84
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:3663872 original size:23 final size:22
Alignment explanation
Indices: 3663839--3663936 Score: 108
Period size: 23 Copynumber: 4.4 Consensus size: 22
3663829 CCGGTAGAGG
* * *
3663839 TTTTTGTTTCTTTTTGTTTTTA
1 TTTTTTTTTCTTTTTTTTTTTC
* *
3663861 TTTTTTTGTTC-TTGTTCTTTTC
1 TTTTTTT-TTCTTTTTTTTTTTC
3663883 TTTTTTTTTCTTTTTTTCTTTTC
1 TTTTTTTTTCTTTTTTT-TTTTC
*
3663906 TTTTCTTTTCTTTTCTTTTTTTC
1 TTTTTTTTTCTTTT-TTTTTTTC
3663929 TTTTTTTT
1 TTTTTTTT
3663937 GGAATTGAAT
Statistics
Matches: 63, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
21 3 0.05
22 24 0.38
23 33 0.52
24 3 0.05
ACGTcount: A:0.01, C:0.11, G:0.04, T:0.84
Consensus pattern (22 bp):
TTTTTTTTTCTTTTTTTTTTTC
Found at i:3663883 original size:5 final size:5
Alignment explanation
Indices: 3663869--3663936 Score: 83
Period size: 5 Copynumber: 14.4 Consensus size: 5
3663859 TATTTTTTTG
*
3663869 TTCTT GTTCTT TTCTT TTTTT TTC-T TT-TT TTCTT TTCTT TTCTT TTCTT
1 TTCTT -TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT
3663918 TTC-T TT-TT TTCTT TT-TT TT
1 TTCTT TTCTT TTCTT TTCTT TT
3663937 GGAATTGAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
4 16 0.29
5 35 0.62
6 5 0.09
ACGTcount: A:0.00, C:0.15, G:0.01, T:0.84
Consensus pattern (5 bp):
TTCTT
Found at i:3663886 original size:28 final size:28
Alignment explanation
Indices: 3663845--3663936 Score: 100
Period size: 28 Copynumber: 3.3 Consensus size: 28
3663835 GAGGTTTTTG
*
3663845 TTTCTTTTTGTTTTTATTT-TTTTGTTCT
1 TTTC-TTTTCTTTTTATTTCTTTTGTTCT
* *
3663873 TGTTCTTTTCTTTTTTTTTCTTTTTTTCT
1 T-TTCTTTTCTTTTTATTTCTTTTGTTCT
*
3663902 TTTCTTTTCTTTTCT-TTTCTTTTTTTCT
1 TTTCTTTTCTTTT-TATTTCTTTTGTTCT
3663930 TTT-TTTT
1 TTTCTTTT
3663937 GGAATTGAAT
Statistics
Matches: 58, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
27 4 0.07
28 41 0.71
29 13 0.22
ACGTcount: A:0.01, C:0.12, G:0.03, T:0.84
Consensus pattern (28 bp):
TTTCTTTTCTTTTTATTTCTTTTGTTCT
Found at i:3668989 original size:22 final size:22
Alignment explanation
Indices: 3668943--3668990 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
3668933 CCGGCCCGTT
* *
3668943 TTTAAAATAAACATTAAAATTA
1 TTTAAAATAAAAATTAAAATAA
3668965 TTTAAAATAAAAATATAAAA-AA
1 TTTAAAATAAAAAT-TAAAATAA
3668987 TTTA
1 TTTA
3668991 TTTTAAAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAAAATTAAAATAA
Found at i:3669743 original size:44 final size:44
Alignment explanation
Indices: 3669626--3669872 Score: 135
Period size: 44 Copynumber: 5.7 Consensus size: 44
3669616 ACTTGATGCG
*
3669626 ATCTACTCTACTGCAACTTTAGAGAGATAAGATCTGGATGTTTTA
1 ATCTACTCTACTGCAACTTCA-AGAGATAAGATCTGGATGTTTTA
** * * * * * *
3669671 ATCCGCTCCACTACAACTTCAGGGAGATAGGAT-T-GATTTCTTTT
1 ATCTACTCTACTGCAACTTCA-AGAGATAAGATCTGGATGT-TTTA
* *
3669715 ATCTACTCTACTGCAACTTCAAGCAGATAAGA-CTGTATG---TG
1 ATCTACTCTACTGCAACTTCAAG-AGATAAGATCTGGATGTTTTA
* *
3669756 ATCTGCTCT-CTGCAACTTCAGAGAGATAAGATAT--ATGGTTTTA
1 ATCTACTCTACTGCAACTTCA-AGAGATAAGATCTGGAT-GTTTTA
** * * *
3669799 ATCCGCTCCACTGCAACTTCAGGAAGAT-AGAAT-TGGATG---TG
1 ATCTACTCTACTGCAACTTCAAG-AGATAAG-ATCTGGATGTTTTA
* *
3669840 ATCTACTCTACTGTAACTTTAGAGAGATAAGAT
1 ATCTACTCTACTGCAACTTCA-AGAGATAAGAT
3669873 TTGTGGTTTT
Statistics
Matches: 154, Mismatches: 31, Indels: 38
0.69 0.14 0.17
Matches are distributed among these distances:
39 2 0.01
40 20 0.13
41 35 0.23
42 3 0.02
43 17 0.11
44 47 0.31
45 30 0.19
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (44 bp):
ATCTACTCTACTGCAACTTCAAGAGATAAGATCTGGATGTTTTA
Found at i:3669883 original size:85 final size:85
Alignment explanation
Indices: 3669724--3669913 Score: 240
Period size: 85 Copynumber: 2.2 Consensus size: 85
3669714 TATCTACTCT
* * * *
3669724 ACTGCAACTTCAAGCAGATA-AGACTGTATGTGATCTGCTCTCTGCAACTTCAGAGAGATAAGAT
1 ACTGCAACTTCAGGAAGATAGAGACTGGATGTGATCTACTCTCTGCAACTTCAGAGAGATAAGAT
*
3669788 ATATGGTTTTAATCCGCTCC
66 ATATGGTTTTAACCCGCTCC
* * *
3669808 ACTGCAACTTCAGGAAGATAGA-ATTGGATGTGATCTACTCTACTGTAACTTTAGAGAGATAAGA
1 ACTGCAACTTCAGGAAGATAGAGACTGGATGTGATCTACTCT-CTGCAACTTCAGAGAGATAAGA
* *
3669872 TTTGTGGTTTTAACCCGCTCC
65 TATATGGTTTTAACCCGCTCC
* * *
3669893 ACTACAACTTTAGGGAGATAG
1 ACTGCAACTTCAGGAAGATAG
3669914 GATCATTGGC
Statistics
Matches: 91, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
84 34 0.37
85 57 0.63
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.30
Consensus pattern (85 bp):
ACTGCAACTTCAGGAAGATAGAGACTGGATGTGATCTACTCTCTGCAACTTCAGAGAGATAAGAT
ATATGGTTTTAACCCGCTCC
Found at i:3670057 original size:50 final size:50
Alignment explanation
Indices: 3669992--3670582 Score: 233
Period size: 50 Copynumber: 11.8 Consensus size: 50
3669982 ATTGCAATGT
** *
3669992 CGGGGAAACAAGATTCACCTTCGTAGCTTCAATCTGTTCCACTACACCAC
1 CGGGGAAGTAAGATTCACCTTCGTAGCTTCAATCTGTTCCACTACACCGC
* * * ** ** ** *
3670042 CAGAGAAGTAAGATTCGCCATT-GTTTCTTCAATCTGTTTAACTACAATGT
1 CGGGGAAGTAAGATTCACC-TTCGTAGCTTCAATCTGTTCCACTACACCGC
** * *
3670092 CGGGGAAACAAGATTCGA-CATCCTAGCTTCAATCTGTTCCACTACACCGC
1 CGGGGAAGTAAGATTC-ACCTTCGTAGCTTCAATCTGTTCCACTACACCGC
** * * * ** * ** *
3670142 CGGGGAAGTAAGATTTGTCGTT-ATAGCTTCAATCTATTTAACTGCAATGT
1 CGGGGAAGTAAGA-TTCACCTTCGTAGCTTCAATCTGTTCCACTACACCGC
** * * *
3670192 CGGGGAAACAAGATTCGCCATCGTAGCTTCAATCTGTTTCACTACACCGC
1 CGGGGAAGTAAGATTCACCTTCGTAGCTTCAATCTGTTCCACTACACCGC
** * * * * * * ** ** *
3670242 TAGAGAAGTAAGACTCGCCGTT-GTGGCTTCAATTTATTTAACTACAATGT
1 CGGGGAAGTAAGATTCACC-TTCGTAGCTTCAATCTGTTCCACTACACCGC
* ** * * *
3670292 CGTGGAAACAAGATTCGCCGTCGTAGCTTCAATCTATTCCACTACACCGC
1 CGGGGAAGTAAGATTCACCTTCGTAGCTTCAATCTGTTCCACTACACCGC
* * * * * ** * ** *
3670342 CAGGGAAGTAAGATTC-GCTGTTGTGGCTTCAATCTTTTTAACTGCAATGT
1 CGGGGAAGTAAGATTCACCT-TCGTAGCTTCAATCTGTTCCACTACACCGC
** * * *
3670392 CGGGGAAACAAGATTCGCCATCGTAGCTTCAATCTGTTCCATTACACCGC
1 CGGGGAAGTAAGATTCACCTTCGTAGCTTCAATCTGTTCCACTACACCGC
* ** * * * ** ** ** *
3670442 CAGGGAAGTAAGATTC-GTTATTGTGGCTTCAATCTTTTTAACTGTAATGT
1 CGGGGAAGTAAGATTCACCT-TCGTAGCTTCAATCTGTTCCACTACACCGC
** * * * * *
3670492 CGGGGAAACAAGATTCGCCGTCGTAGATTCAATCTATTCCACTACACTGC
1 CGGGGAAGTAAGATTCACCTTCGTAGCTTCAATCTGTTCCACTACACCGC
** * * *
3670542 TAGGGAAGTAAGATTCACCGTT-GTGGTTTCAATCTATTCCA
1 CGGGGAAGTAAGATTCACC-TTCGTAGCTTCAATCTGTTCCA
3670583 TTGTAATGCC
Statistics
Matches: 374, Mismatches: 154, Indels: 26
0.68 0.28 0.05
Matches are distributed among these distances:
49 7 0.02
50 359 0.96
51 8 0.02
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (50 bp):
CGGGGAAGTAAGATTCACCTTCGTAGCTTCAATCTGTTCCACTACACCGC
Found at i:3670590 original size:100 final size:100
Alignment explanation
Indices: 3669972--3670579 Score: 838
Period size: 100 Copynumber: 6.1 Consensus size: 100
3669962 TGCCATCTTT
* * * *
3669972 AATCTGTTTAATTGCAATGTCGGGGAAACAAGATTCACCTTCGTAGCTTCAATCTGTTCCACTAC
1 AATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCATCGTAGCTTCAATCTGTTCCACTAC
* * * **
3670037 ACCACCAGAGAAGTAAGATTCGCCATTGTTTCTTC
66 ACCGCCAGGGAAGTAAGATTCGCCGTTGTGGCTTC
* * * *
3670072 AATCTGTTTAACTACAATGTCGGGGAAACAAGATTCGACATCCTAGCTTCAATCTGTTCCACTAC
1 AATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCATCGTAGCTTCAATCTGTTCCACTAC
* * * * *
3670137 ACCGCCGGGGAAGTAAGATTTGTCGTTATAGCTTC
66 ACCGCCAGGGAAGTAAGATTCGCCGTTGTGGCTTC
*
3670172 AATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCATCGTAGCTTCAATCTGTTTCACTAC
1 AATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCATCGTAGCTTCAATCTGTTCCACTAC
* * *
3670237 ACCGCTAGAGAAGTAAGACTCGCCGTTGTGGCTTC
66 ACCGCCAGGGAAGTAAGATTCGCCGTTGTGGCTTC
* * * * *
3670272 AATTTATTTAACTACAATGTCGTGGAAACAAGATTCGCCGTCGTAGCTTCAATCTATTCCACTAC
1 AATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCATCGTAGCTTCAATCTGTTCCACTAC
*
3670337 ACCGCCAGGGAAGTAAGATTCGCTGTTGTGGCTTC
66 ACCGCCAGGGAAGTAAGATTCGCCGTTGTGGCTTC
* *
3670372 AATCTTTTTAACTGCAATGTCGGGGAAACAAGATTCGCCATCGTAGCTTCAATCTGTTCCATTAC
1 AATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCATCGTAGCTTCAATCTGTTCCACTAC
***
3670437 ACCGCCAGGGAAGTAAGATTCGTTATTGTGGCTTC
66 ACCGCCAGGGAAGTAAGATTCGCCGTTGTGGCTTC
* * * * *
3670472 AATCTTTTTAACTGTAATGTCGGGGAAACAAGATTCGCCGTCGTAGATTCAATCTATTCCACTAC
1 AATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCATCGTAGCTTCAATCTGTTCCACTAC
* * * *
3670537 ACTGCTAGGGAAGTAAGATTCACCGTTGTGGTTTC
66 ACCGCCAGGGAAGTAAGATTCGCCGTTGTGGCTTC
3670572 AATCTATT
1 AATCTATT
3670580 CCATTGTAAT
Statistics
Matches: 448, Mismatches: 60, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
100 448 1.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (100 bp):
AATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCCATCGTAGCTTCAATCTGTTCCACTAC
ACCGCCAGGGAAGTAAGATTCGCCGTTGTGGCTTC
Found at i:3670942 original size:88 final size:88
Alignment explanation
Indices: 3670777--3671119 Score: 463
Period size: 88 Copynumber: 3.9 Consensus size: 88
3670767 TAAGACTGGT
* ** * * *
3670777 GTCTTCGATCTGCTTCATTGCCAGTACAGGAAGGCAAGATCTGCCATTTTTCAACCTACTCCACT
1 GTCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA-TTTTCAACCTACTCCACT
*
3670842 GCTGCTCAGGGAGACAAGGCT-AG
65 ACTGCTCAGGGAGACAAGGCTGAG
* * * * *
3670865 TATCTTCAATCTACTTTGCTGCCAATACAGGAAAACAAGATCTTCTATTTTCAACCTACTCCACT
1 -GTCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACT
* *
3670930 GCTGCTCAGGGAGATAAGGCTGAG
65 ACTGCTCAGGGAGACAAGGCTGAG
* **
3670954 GTCTTCGATCTACTTCACTGTGAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTA
1 GTCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTA
* *
3671019 CTGCTCAAGGAGACAAGACTGAG
66 CTGCTCAGGGAGACAAGGCTGAG
* *
3671042 GTCTTCGATCTACTTCGCTGCCAATACATGAAGACAAGATTTGCTATTTTCAACCTACTCCACTA
1 GTCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTA
*
3671107 CTGCTTAGGGAGA
66 CTGCTCAGGGAGA
3671120 TAGGATTTAT
Statistics
Matches: 222, Mismatches: 31, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
88 185 0.83
89 37 0.17
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.28
Consensus pattern (88 bp):
GTCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAACCTACTCCACTA
CTGCTCAGGGAGACAAGGCTGAG
Found at i:3674175 original size:22 final size:23
Alignment explanation
Indices: 3674137--3674179 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
3674127 AAAGAATCAT
3674137 AAAAATTATAGACAAAATTTATG
1 AAAAATTATAGACAAAATTTATG
3674160 AAAAAGTTATA-A-AAAATTTA
1 AAAAA-TTATAGACAAAATTTA
3674180 AAATTATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 8 0.42
23 6 0.32
24 5 0.26
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.30
Consensus pattern (23 bp):
AAAAATTATAGACAAAATTTATG
Found at i:3674338 original size:11 final size:12
Alignment explanation
Indices: 3674317--3674353 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
3674307 TAAATTTAAA
3674317 TTTTTATAACTT
1 TTTTTATAACTT
3674329 TTTTTA-AACTT
1 TTTTTATAACTT
*
3674340 TGTTTATAA-TT
1 TTTTTATAACTT
3674351 TTT
1 TTT
3674354 ATGATTTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 14 0.64
12 8 0.36
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (12 bp):
TTTTTATAACTT
Found at i:3676050 original size:44 final size:44
Alignment explanation
Indices: 3675991--3676075 Score: 109
Period size: 44 Copynumber: 1.9 Consensus size: 44
3675981 CCTCATAGAT
*
3675991 ACGGCACAGGATTCTGCTCAAACAGACTGCGCATGGTGTCATAC
1 ACGGCACAGGATTCTGCTCAAACAGACTGCGCATAGTGTCATAC
* * * *
3676035 ACGGCACA-GATTTCTGTTCAAAGAGGCTGCGGATAGTGTCA
1 ACGGCACAGGA-TTCTGCTCAAACAGACTGCGCATAGTGTCA
3676076 GCTATCGGGT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 2 0.06
44 33 0.94
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (44 bp):
ACGGCACAGGATTCTGCTCAAACAGACTGCGCATAGTGTCATAC
Found at i:3676592 original size:20 final size:20
Alignment explanation
Indices: 3676567--3676606 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3676557 CTTTATATAT
3676567 TTTTTATAATTTTTGTAAAA
1 TTTTTATAATTTTTGTAAAA
* *
3676587 TTTTTATAGTTTTTTTAAAA
1 TTTTTATAATTTTTGTAAAA
3676607 ATATAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (20 bp):
TTTTTATAATTTTTGTAAAA
Found at i:3676655 original size:19 final size:19
Alignment explanation
Indices: 3676611--3676657 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
3676601 TTAAAAATAT
*
3676611 AAATTTTGAAATTTTTATA
1 AAATTTTGAAATTTTTAAA
* **
3676630 AATTTTTGATTTTTTTAAA
1 AAATTTTGAAATTTTTAAA
3676649 AAATTTTGA
1 AAATTTTGA
3676658 GAGAGAGTGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.55
Consensus pattern (19 bp):
AAATTTTGAAATTTTTAAA
Found at i:3688781 original size:37 final size:38
Alignment explanation
Indices: 3688713--3688792 Score: 94
Period size: 37 Copynumber: 2.1 Consensus size: 38
3688703 AAATAGTCCC
* * *
3688713 TAAAATTTTAATTTTATAGTTTTTACGATTTAA-TCTT
1 TAAAATTTTAATTTTATAGTTCTTACAATTTAATTCCT
3688750 TAAAATTTTAATTTTTACTA-TTCTT-CAATTTAATTCCT
1 TAAAATTTTAA-TTTTA-TAGTTCTTACAATTTAATTCCT
3688788 TAAAA
1 TAAAA
3688793 ACAGATTTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
37 18 0.49
38 17 0.46
39 2 0.05
ACGTcount: A:0.35, C:0.09, G:0.03, T:0.54
Consensus pattern (38 bp):
TAAAATTTTAATTTTATAGTTCTTACAATTTAATTCCT
Found at i:3689764 original size:21 final size:20
Alignment explanation
Indices: 3689738--3689791 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 20
3689728 TCTAGTAAAA
3689738 TAAAAAAATAATTCATGAAGT
1 TAAAAAAATAATTC-TGAAGT
* *
3689759 TAAAAAAATTAATTCTTAATT
1 TAAAAAAA-TAATTCTGAAGT
3689780 TAAAGAAAATAA
1 TAAA-AAAATAA
3689792 ATGTAATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 19 0.66
22 10 0.34
ACGTcount: A:0.59, C:0.04, G:0.06, T:0.31
Consensus pattern (20 bp):
TAAAAAAATAATTCTGAAGT
Found at i:3710108 original size:27 final size:26
Alignment explanation
Indices: 3710076--3710173 Score: 115
Period size: 27 Copynumber: 3.7 Consensus size: 26
3710066 AAAAAGTATT
3710076 TTAAAAATATTTTAAAATTTAAAAAAA
1 TTAAAAATATTTTAAAA-TTAAAAAAA
3710103 TTAAAAATATTTTAAAATTAAAAATAA
1 TTAAAAATATTTTAAAATTAAAAA-AA
* * **
3710130 TAAAAAAGTATTTTAAAAATATTAAAA
1 TTAAAAA-TATTTTAAAATTAAAAAAA
* *
3710157 TTAAAAAAAATTTAAAA
1 TTAAAAATATTTTAAAA
3710174 AATAAATATA
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
26 15 0.24
27 33 0.53
28 14 0.23
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (26 bp):
TTAAAAATATTTTAAAATTAAAAAAA
Found at i:3710799 original size:11 final size:11
Alignment explanation
Indices: 3710783--3710816 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
3710773 TCAATTATTT
3710783 TCTCAATTTCC
1 TCTCAATTTCC
*
3710794 TCTCAATTTGC
1 TCTCAATTTCC
3710805 TCTCAATTTCC
1 TCTCAATTTCC
3710816 T
1 T
3710817 TCCAAATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.18, C:0.32, G:0.03, T:0.47
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:3710811 original size:22 final size:22
Alignment explanation
Indices: 3710779--3710832 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
3710769 TCTCTCAATT
3710779 ATTT-TCTCAATTTCC-TCTC-A
1 ATTTCTCTCAATTTCCTTC-CAA
3710799 ATTTGCTCTCAATTTCCTTCCAA
1 ATTT-CTCTCAATTTCCTTCCAA
3710822 ATTTCTCTCAA
1 ATTTCTCTCAA
3710833 ATCTATATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
20 4 0.13
22 19 0.63
23 7 0.23
ACGTcount: A:0.22, C:0.30, G:0.02, T:0.46
Consensus pattern (22 bp):
ATTTCTCTCAATTTCCTTCCAA
Found at i:3713327 original size:21 final size:21
Alignment explanation
Indices: 3713280--3713353 Score: 123
Period size: 21 Copynumber: 3.6 Consensus size: 21
3713270 AAACCCTAAC
3713280 AAAAACCCTAACCCTTAACTT
1 AAAAACCCTAACCCTTAACTT
*
3713301 -AAAACCCTATCCCTTAACTT
1 AAAAACCCTAACCCTTAACTT
*
3713321 AAAAACCCTAACCTTTAACTT
1 AAAAACCCTAACCCTTAACTT
3713342 AAAAACCCTAAC
1 AAAAACCCTAAC
3713354 TGTAACTCTT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
20 19 0.39
21 30 0.61
ACGTcount: A:0.43, C:0.32, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAACCCTAACCCTTAACTT
Found at i:3713329 original size:15 final size:15
Alignment explanation
Indices: 3713330--3713389 Score: 65
Period size: 15 Copynumber: 4.2 Consensus size: 15
3713320 TAAAAACCCT
*
3713330 AACCTTTAACTTAAA
1 AACCCTTAACTTAAA
3713345 AACCC-TAACTGT---
1 AACCCTTAACT-TAAA
*
3713357 AACTCTTAACTTAAA
1 AACCCTTAACTTAAA
3713372 AACCCTTAACTTAAA
1 AACCCTTAACTTAAA
3713387 AAC
1 AAC
3713390 ACCAAAACCT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
12 5 0.14
13 5 0.14
14 5 0.14
15 22 0.59
ACGTcount: A:0.45, C:0.25, G:0.02, T:0.28
Consensus pattern (15 bp):
AACCCTTAACTTAAA
Found at i:3713333 original size:27 final size:26
Alignment explanation
Indices: 3713303--3713377 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 26
3713293 CTTAACTTAA
3713303 AACCCTATCCCTTAACTTAAAAACCCT
1 AACCCTAT-CCTTAACTTAAAAACCCT
3713330 AA-CC--T--TTAACTTAAAAACCCT
1 AACCCTATCCTTAACTTAAAAACCCT
** *
3713351 AACTGTAACTCTTAACTTAAAAACCCT
1 AACCCTATC-CTTAACTTAAAAACCCT
3713378 TAACTTAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
21 18 0.46
24 1 0.03
26 2 0.05
27 18 0.46
ACGTcount: A:0.40, C:0.31, G:0.01, T:0.28
Consensus pattern (26 bp):
AACCCTATCCTTAACTTAAAAACCCT
Found at i:3713360 original size:41 final size:40
Alignment explanation
Indices: 3713280--3713360 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 40
3713270 AAACCCTAAC
*
3713280 AAAAACCCTAACCCTTAACTTAAAACCCTATCCCTTAACTT
1 AAAAACCCTAACCCTTAACTTAAAACCCTA-CACTTAACTT
*
3713321 AAAAACCCTAACCTTTAACTTAAAAACCCTA-ACTGTAACT
1 AAAAACCCTAACCCTTAACTT-AAAACCCTACACT-TAACT
3713361 CTTAACTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
40 2 0.06
41 25 0.69
42 9 0.25
ACGTcount: A:0.42, C:0.31, G:0.01, T:0.26
Consensus pattern (40 bp):
AAAAACCCTAACCCTTAACTTAAAACCCTACACTTAACTT
Found at i:3713577 original size:104 final size:103
Alignment explanation
Indices: 3713443--3713665 Score: 299
Period size: 104 Copynumber: 2.2 Consensus size: 103
3713433 CCCTAATATG
3713443 ATATAATTTGATA-AA-TTTACTAACAATTAATACAATTAACAATTAATAATTTGACTAACAAA-
1 ATATAATTTGATACAATTTTACTAACAATTAATACAATTAACAATTAATAATTTGACTAACAAAT
** * *
3713505 ATGTTAGATTGTACAAAATGTTTTGACTGGTACTAACAA
66 A-GCCAGATTGTACAAAATGTTTTGACTGGTACAAAAAA
* * * **
3713544 TTAATAATTTGATACAATTTTACTAACAATTAATACAATTAATAATTAATAATTTTACTAACATT
1 AT-ATAATTTGATACAATTTTACTAACAATTAATACAATTAACAATTAATAATTTGACTAACAAA
* *
3713609 TAGCCATATTTTACAAAATGTTTTGACTGGTACAAAAAA
65 TAGCCAGATTGTACAAAATGTTTTGACTGGTACAAAAAA
3713648 ATATAATTTGATTACAAT
1 ATATAATTTGA-TACAAT
3713666 GACATTCAAC
Statistics
Matches: 105, Mismatches: 12, Indels: 7
0.85 0.10 0.06
Matches are distributed among these distances:
101 1 0.01
102 11 0.10
103 11 0.10
104 81 0.77
105 1 0.01
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (103 bp):
ATATAATTTGATACAATTTTACTAACAATTAATACAATTAACAATTAATAATTTGACTAACAAAT
AGCCAGATTGTACAAAATGTTTTGACTGGTACAAAAAA
Found at i:3716833 original size:125 final size:125
Alignment explanation
Indices: 3716611--3716927 Score: 517
Period size: 125 Copynumber: 2.5 Consensus size: 125
3716601 CCCAAACATG
* * * * *
3716611 CTACTGTAGCAAAAACGCGTCTACGAGGGCGCGATTTCATAAATTCATCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
* *
3716676 TTGAAGCGTTTTTTATATTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
66 TTGAAGCATTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
* * *
3716736 CTACTGTAGCAAAAGCACGTCCACGTTGGCGCGATTTCAAAAATTCTTTTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
* *
3716801 TTGAAGCATTTTTTATACTATTTTCTCAGAAACGTCAACTCGAAATTATTTTTTCAGTAC
66 TTGAAGCATTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
*
3716861 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
3716926 TT
66 TT
3716928 TGATTTTATC
Statistics
Matches: 176, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
125 176 1.00
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.32
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCAAAAATTCTTCTGATAAAGCATCCTGC
TTGAAGCATTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
Found at i:3717610 original size:55 final size:55
Alignment explanation
Indices: 3717530--3717643 Score: 221
Period size: 55 Copynumber: 2.1 Consensus size: 55
3717520 GAAAAGAACA
3717530 ACTTTAATGAATGCTCGAATCCTATTATTATGCATAAATTATGAATTTAGTCTTT
1 ACTTTAATGAATGCTCGAATCCTATTATTATGCATAAATTATGAATTTAGTCTTT
3717585 ACTTTAATGAATGCTCGAATCCTATTATTATGCATAAATTATGAATTTAGTCTTT
1 ACTTTAATGAATGCTCGAATCCTATTATTATGCATAAATTATGAATTTAGTCTTT
3717640 -CTTT
1 ACTTT
3717644 GTAATTTTTT
Statistics
Matches: 59, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
54 4 0.07
55 55 0.93
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.45
Consensus pattern (55 bp):
ACTTTAATGAATGCTCGAATCCTATTATTATGCATAAATTATGAATTTAGTCTTT
Found at i:3719574 original size:3 final size:3
Alignment explanation
Indices: 3719540--3719604 Score: 53
Period size: 3 Copynumber: 21.3 Consensus size: 3
3719530 ATTAAATTGC
* * *
3719540 ATT ATT GTT ATT -GT ATT ATT -GT ATT ATCT ATT ATTT ATT ATAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT A-TT ATT AT-T ATT
*
3719586 ATT ATT ATT AGT ATT ATT A
1 ATT ATT ATT ATT ATT ATT A
3719605 CTTCCATACG
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
2 2 0.04
3 38 0.78
4 9 0.18
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:3719578 original size:14 final size:14
Alignment explanation
Indices: 3719553--3719603 Score: 59
Period size: 14 Copynumber: 3.5 Consensus size: 14
3719543 ATTGTTATTG
*
3719553 TATTATTGTATTATC
1 TATTATT-TATTATA
3719568 TATTATTTATTATA
1 TATTATTTATTATA
3719582 TATTA-TTATTATTA
1 TATTATTTATTA-TA
3719596 GTATTATT
1 -TATTATT
3719604 ACTTCCATAC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
13 6 0.19
14 13 0.41
15 12 0.38
16 1 0.03
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (14 bp):
TATTATTTATTATA
Found at i:3722918 original size:21 final size:22
Alignment explanation
Indices: 3722892--3722938 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
3722882 CTCTGCTCAA
*
3722892 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
3722913 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
3722935 ACTC
1 ACTC
3722939 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:3729183 original size:41 final size:41
Alignment explanation
Indices: 3729124--3729363 Score: 270
Period size: 41 Copynumber: 5.9 Consensus size: 41
3729114 GATTTTTTAA
* *
3729124 ACCTTTAGCGTCGTTTTTATCTAAGCGCCACTAATGCTCGG
1 ACCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCGG
* * *
3729165 ATCTTTAGCGGCGTTTTTATCTAAGCCCCGCTAATGCACGG
1 ACCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCGG
* * * *
3729206 ATCTTTAGCGGTGTTTTTATCTAAGCGCCGCTAATTCTC-T
1 ACCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCGG
* * *
3729246 AGCCTTTAGCGGCGTTTTTATCTGAGCGCCACTAATTCTCTGG
1 A-CCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTC-GG
* * **
3729289 -CCTTTAGCGGCGTTTGTAGCTAAGCGCCGCTAATGCAT-TT
1 ACCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGC-TCGG
* *
3729329 ACCTTTAGCGGCGTTTTTACCGAAGCGCCGCTAAT
1 ACCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAAT
3729364 AGTAACAAAA
Statistics
Matches: 169, Mismatches: 25, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
40 1 0.01
41 167 0.99
42 1 0.01
ACGTcount: A:0.18, C:0.26, G:0.22, T:0.34
Consensus pattern (41 bp):
ACCTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCGG
Found at i:3729345 original size:123 final size:123
Alignment explanation
Indices: 3729125--3729363 Score: 336
Period size: 123 Copynumber: 1.9 Consensus size: 123
3729115 ATTTTTTAAA
* * * *
3729125 CCTTTAGCGTCGTTTTTATCTAAGCGCCACTAATGCTCGGATCTTTAGCGGCGTTTTTATCTAAG
1 CCTTTAGCGGCGTTTTTATCTAAGCGCCACTAATGCTCGGACCTTTAGCGGCGTTTGTAGCTAAG
* * * *
3729190 CCCCGCTAATGCACGGATCTTTAGCGGTGTTTTTATCTAAGCGCCGCTAATTCTCTAG
66 CCCCGCTAATGCACGGACCTTTAGCGGCGTTTTTACCGAAGCGCCGCTAATTCTCTAG
* *
3729248 CCTTTAGCGGCGTTTTTATCTGAGCGCCACTAATTCTCTGG-CCTTTAGCGGCGTTTGTAGCTAA
1 CCTTTAGCGGCGTTTTTATCTAAGCGCCACTAATGCTC-GGACCTTTAGCGGCGTTTGTAGCTAA
* ***
3729312 GCGCCGCTAATGCATTTACCTTTAGCGGCGTTTTTACCGAAGCGCCGCTAAT
65 GCCCCGCTAATGCACGGACCTTTAGCGGCGTTTTTACCGAAGCGCCGCTAAT
3729364 AGTAACAAAA
Statistics
Matches: 101, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
123 99 0.98
124 2 0.02
ACGTcount: A:0.18, C:0.26, G:0.22, T:0.34
Consensus pattern (123 bp):
CCTTTAGCGGCGTTTTTATCTAAGCGCCACTAATGCTCGGACCTTTAGCGGCGTTTGTAGCTAAG
CCCCGCTAATGCACGGACCTTTAGCGGCGTTTTTACCGAAGCGCCGCTAATTCTCTAG
Found at i:3732102 original size:12 final size:10
Alignment explanation
Indices: 3732072--3732100 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
3732062 TAAATTTTTT
3732072 GATATATATG
1 GATATATATG
3732082 GATATATATG
1 GATATATATG
3732092 GATATATAT
1 GATATATAT
3732101 ATATAGTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.17, T:0.41
Consensus pattern (10 bp):
GATATATATG
Found at i:3732200 original size:27 final size:27
Alignment explanation
Indices: 3732170--3732221 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
3732160 AATAAACAAA
* *
3732170 TAAATAAGTAAGTAATTATTTATTTGT
1 TAAATAAATAAGTAATTAATTATTTGT
**
3732197 TAAATAAATTGGTAATTAATTATTT
1 TAAATAAATAAGTAATTAATTATTT
3732222 AAATGTAAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (27 bp):
TAAATAAATAAGTAATTAATTATTTGT
Found at i:3734610 original size:13 final size:14
Alignment explanation
Indices: 3734592--3734624 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
3734582 TTGTTTTTAA
*
3734592 TTATTTTTAGT-GT
1 TTATTTTTAATGGT
3734605 TTATTTTTAATGGT
1 TTATTTTTAATGGT
3734619 TTATTT
1 TTATTT
3734625 CATCTATTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.18, C:0.00, G:0.12, T:0.70
Consensus pattern (14 bp):
TTATTTTTAATGGT
Found at i:3735088 original size:21 final size:21
Alignment explanation
Indices: 3735063--3735111 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
3735053 CTGCAGCTTA
*
3735063 AAGCAGAGGCGGCAGCGAGAG
1 AAGCAGAGGCGGCAGCAAGAG
* *
3735084 AAGCAGAGGCTGCAGCAAGGG
1 AAGCAGAGGCGGCAGCAAGAG
3735105 AAGCAGA
1 AAGCAGA
3735112 CCAGCATAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.37, C:0.18, G:0.43, T:0.02
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCAAGAG
Found at i:3735239 original size:19 final size:19
Alignment explanation
Indices: 3735215--3735252 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3735205 GTAAATATTT
3735215 TTATCATTTTAACTTTTAA
1 TTATCATTTTAACTTTTAA
3735234 TTATCATTTTAACTTTTAA
1 TTATCATTTTAACTTTTAA
3735253 CATTTTTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.58
Consensus pattern (19 bp):
TTATCATTTTAACTTTTAA
Found at i:3735482 original size:43 final size:43
Alignment explanation
Indices: 3735429--3735655 Score: 276
Period size: 43 Copynumber: 5.3 Consensus size: 43
3735419 ACTGCCAAAA
* * * * ** *
3735429 TTAGTGGCGTTTTTTAAAAAAGCGCCGTTAAAGGTTAGGGTCT
1 TTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGACAAGGTCT
* *
3735472 TTAGCGGCGTTTGTGAAAAAAGTGCCGCTAAATGACAAGGTCT
1 TTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGACAAGGTCT
** * * *
3735515 TTAGCGGCGTTTGTGGGAAAAGCACTGCTAAAGGTCAAGGTCT
1 TTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGACAAGGTCT
3735558 TTAGCGGCGTTTGTAGAAAAAA-CGCCGCTAAAGGACAAGGTCT
1 TTAGCGGCGTTTGT-GAAAAAAGCGCCGCTAAAGGACAAGGTCT
** * *
3735601 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGACATGATCT
1 TTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGACAAGGTCT
3735644 TTAGCGGCGTTT
1 TTAGCGGCGTTT
3735656 TTAGCGGCGC
Statistics
Matches: 157, Mismatches: 25, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
42 5 0.03
43 147 0.94
44 5 0.03
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.27
Consensus pattern (43 bp):
TTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGACAAGGTCT
Found at i:3735557 original size:86 final size:86
Alignment explanation
Indices: 3735446--3735655 Score: 305
Period size: 86 Copynumber: 2.4 Consensus size: 86
3735436 CGTTTTTTAA
* * * * * *
3735446 AAAAGCGCCGTTAAAGGTTAGGGTCTTTAGCGGCGTTTGT-GAAAAAAGTGCCGCTAAATGACAA
1 AAAAGCACCGCTAAAGGTCAAGGTCTTTAGCGGCGTTTGTAGAAAAAA-CGCCGCTAAAGGACAA
3735510 GGTCTTTAGCGGCGTTTGTGGG
65 GGTCTTTAGCGGCGTTTGTGGG
*
3735532 AAAAGCACTGCTAAAGGTCAAGGTCTTTAGCGGCGTTTGTAGAAAAAACGCCGCTAAAGGACAAG
1 AAAAGCACCGCTAAAGGTCAAGGTCTTTAGCGGCGTTTGTAGAAAAAACGCCGCTAAAGGACAAG
3735597 GTCTTTAGCGGCGTTTGTGGG
66 GTCTTTAGCGGCGTTTGTGGG
* * * *
3735618 AAAAGCGCCGCTAAAGGACATGATCTTTAGCGGCGTTT
1 AAAAGCACCGCTAAAGGTCAAGGTCTTTAGCGGCGTTT
3735656 TTAGCGGCGC
Statistics
Matches: 111, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
86 104 0.94
87 7 0.06
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.25
Consensus pattern (86 bp):
AAAAGCACCGCTAAAGGTCAAGGTCTTTAGCGGCGTTTGTAGAAAAAACGCCGCTAAAGGACAAG
GTCTTTAGCGGCGTTTGTGGG
Found at i:3738722 original size:2 final size:2
Alignment explanation
Indices: 3738709--3738744 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
3738699 CTCACAACCA
*
3738709 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3738745 CAATAACTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3749629 original size:88 final size:88
Alignment explanation
Indices: 3749473--3749648 Score: 316
Period size: 88 Copynumber: 2.0 Consensus size: 88
3749463 TTGAAACATC
*
3749473 CCATGCATGTTCATATCAAAAGTAGAGAGCAATGATCAGCAATTATTGCTCAACGCCAATGACGA
1 CCATGCATGTTCATATCAAAAGTAGAGAGCAATGATCAGCAATTATTGCTCAACGCCAATGACAA
3749538 CAGAAAATCCGGAAGAAAGCCAT
66 CAGAAAATCCGGAAGAAAGCCAT
* **
3749561 CCATGCATGTTCATATCAAAAGTAGAGAGTAATGATCAGCAATTATTGCTCAACGCCAATGGTAA
1 CCATGCATGTTCATATCAAAAGTAGAGAGCAATGATCAGCAATTATTGCTCAACGCCAATGACAA
3749626 CAGAAAATCCGGAAGAAAGCCAT
66 CAGAAAATCCGGAAGAAAGCCAT
3749649 TACAACCCAA
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
88 84 1.00
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.20
Consensus pattern (88 bp):
CCATGCATGTTCATATCAAAAGTAGAGAGCAATGATCAGCAATTATTGCTCAACGCCAATGACAA
CAGAAAATCCGGAAGAAAGCCAT
Found at i:3752103 original size:13 final size:13
Alignment explanation
Indices: 3752085--3752114 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3752075 TTTCCTTCTC
3752085 TTTTTTTCTTTGT
1 TTTTTTTCTTTGT
*
3752098 TTTTTTTTTTTGT
1 TTTTTTTCTTTGT
3752111 TTTT
1 TTTT
3752115 GTTTTCCCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.03, G:0.07, T:0.90
Consensus pattern (13 bp):
TTTTTTTCTTTGT
Found at i:3754850 original size:6 final size:6
Alignment explanation
Indices: 3754841--3754867 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3754831 AATAGTAAAA
3754841 TATAAT TATAAT TATAAT TATAAT TAT
1 TATAAT TATAAT TATAAT TATAAT TAT
3754868 CACAACATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TATAAT
Found at i:3756009 original size:5 final size:5
Alignment explanation
Indices: 3755999--3756023 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3755989 AACGTGAAGC
3755999 AAATA AAATA AAATA AAATA AAATA
1 AAATA AAATA AAATA AAATA AAATA
3756024 TATACATGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:3762429 original size:9 final size:9
Alignment explanation
Indices: 3762395--3762433 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
3762385 TAAAATGTAA
*
3762395 TATTATTTT
1 TATTATATT
*
3762404 TAATATATT
1 TATTATATT
3762413 TATCTATATT
1 TAT-TATATT
3762423 TATTATATT
1 TATTATATT
3762432 TA
1 TA
3762434 AAGTTTCGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
9 17 0.65
10 9 0.35
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (9 bp):
TATTATATT
Found at i:3766854 original size:29 final size:29
Alignment explanation
Indices: 3766821--3766901 Score: 94
Period size: 29 Copynumber: 2.8 Consensus size: 29
3766811 ATTTATCCAC
*
3766821 CATCGGTACATAGTAG-TTGATAAATATAA
1 CATCGGTACATAGT-GCCTGATAAATATAA
**
3766850 CATCGACACATAGTGCCTGATAAATATAA
1 CATCGGTACATAGTGCCTGATAAATATAA
*
3766879 CA-CTGGTACAAAGTGCCTGATAA
1 CATC-GGTACATAGTGCCTGATAA
3766902 TATGGTCACC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
28 2 0.05
29 42 0.95
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (29 bp):
CATCGGTACATAGTGCCTGATAAATATAA
Found at i:3768113 original size:19 final size:20
Alignment explanation
Indices: 3768080--3768117 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3768070 TTATTTGCTT
3768080 AAATTATAACATATAATATA
1 AAATTATAACATATAATATA
*
3768100 AAATTATAA-TTATAATAT
1 AAATTATAACATATAATAT
3768118 TAACATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (20 bp):
AAATTATAACATATAATATA
Found at i:3769931 original size:42 final size:45
Alignment explanation
Indices: 3769878--3769963 Score: 106
Period size: 47 Copynumber: 1.9 Consensus size: 45
3769868 AATAAATTAT
* *
3769878 AAATTTTTAAAA-AAATAT-AAT-TAATAACCATAAATTTATCGG
1 AAATTTATAAAATAAATATGAATAAAATAACCATAAATTTATCGG
*
3769920 AAATTTATAAAATAATTATGGAAATAAAATAACCATAAATTTAT
1 AAATTTATAAAATAAATAT-G-AATAAAATAACCATAAATTTAT
3769964 AAATATTGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
42 11 0.31
43 5 0.14
46 3 0.08
47 17 0.47
ACGTcount: A:0.55, C:0.06, G:0.05, T:0.35
Consensus pattern (45 bp):
AAATTTATAAAATAAATATGAATAAAATAACCATAAATTTATCGG
Found at i:3770640 original size:22 final size:22
Alignment explanation
Indices: 3770613--3770654 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
3770603 ATTGGAAATA
3770613 GAAATTTCAAA-TTTTGTTTTCC
1 GAAATTTCAAAGTTTT-TTTTCC
3770635 GAAATTTCAAAGTTTTTTTT
1 GAAATTTCAAAGTTTTTTTT
3770655 AAAGCTGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.52
Consensus pattern (22 bp):
GAAATTTCAAAGTTTTTTTTCC
Found at i:3771109 original size:31 final size:31
Alignment explanation
Indices: 3771060--3771125 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
3771050 AGTCTTAATG
** *
3771060 TTTTAATTTGATTCATTTTAGTTCTTGTATT
1 TTTTAATTTGATAAATTTTAGTCCTTGTATT
* * *
3771091 TTTTGATTTGATAAATTTTCGTCCTTGTGTT
1 TTTTAATTTGATAAATTTTAGTCCTTGTATT
3771122 TTTT
1 TTTT
3771126 CGAATATTGA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.17, C:0.08, G:0.12, T:0.64
Consensus pattern (31 bp):
TTTTAATTTGATAAATTTTAGTCCTTGTATT
Found at i:3773148 original size:143 final size:143
Alignment explanation
Indices: 3772762--3773257 Score: 698
Period size: 143 Copynumber: 3.4 Consensus size: 143
3772752 GTAGAACTCT
*
3772762 AAATTAAAAAAATAGTATATTTTTTAAAAGTAATAAAATCCGAGAAAATAAATACGAACATAGGG
1 AAATT-AAAAAATAGTATATTTTTTAAAAGTAATAAAAT-CGAGGAAA-AAATACGAACATAGGG
3772827 CCGAAATAAGGGTTTTTTT--AATTTATTTAAAAATCACACTAAATTAATACATTTCAAATATAA
63 CCGAAATAAGGGTTTTTTTAAAATTTATTTAAAAAT-ACACTAAATTAATACATTTCAAATATAA
3772890 TATACTAAAATAATGTAAAATTAGA
127 TATACTAAAATAA--T---A-T--A
* *
3772915 AAATTAGAAAATAGTATATTTTTTAAAAGTAATAAAATC-TGGAAAAAATACGAACATAGGGCCG
1 AAATTAAAAAATAGTATATTTTTTAAAAGTAATAAAATCGAGGAAAAAATACGAACATAGGGCCG
*
3772979 AAATAAGGGTTTTTTTAAAAATTTATTTAAAAATACACTAAATTAATACATTTCAAATGTAATAT
66 AAATAAGGGTTTTTTT-AAAATTTATTTAAAAATACACTAAATTAATACATTTCAAATATAATAT
3773044 ACTAAAATAATATA
130 ACTAAAATAATATA
* * *
3773058 AAATTAAAAAATAATATATTTTTTAAAAGTAATAAAATCGGGGGAAAAATACGAACATAGGGCCG
1 AAATTAAAAAATAGTATATTTTTTAAAAGTAATAAAATCGAGGAAAAAATACGAACATAGGGCCG
* * *
3773123 AAATAAGAGTTTTTTTAAAATTTATTTAAAAACT-CATTAAATTAATACATTTCAAATATAATGT
66 AAATAAGGGTTTTTTTAAAATTTATTTAAAAA-TACACTAAATTAATACATTTCAAATATAATAT
*
3773187 ACTAAAATAATGTA
130 ACTAAAATAATATA
*
3773201 AAA-TAAAAAATAGTATA-TTTTTAAAAGTAATAAAATCCGAAGAAAAAAATACGAACA
1 AAATTAAAAAATAGTATATTTTTTAAAAGTAATAAAAT-CG-AGGAAAAAATACGAACA
3773258 AATGGGGGGT
Statistics
Matches: 319, Mismatches: 17, Indels: 24
0.89 0.05 0.07
Matches are distributed among these distances:
141 19 0.06
142 15 0.05
143 111 0.35
144 39 0.12
145 1 0.00
146 1 0.00
149 36 0.11
150 4 0.01
151 41 0.13
152 47 0.15
153 5 0.02
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.31
Consensus pattern (143 bp):
AAATTAAAAAATAGTATATTTTTTAAAAGTAATAAAATCGAGGAAAAAATACGAACATAGGGCCG
AAATAAGGGTTTTTTTAAAATTTATTTAAAAATACACTAAATTAATACATTTCAAATATAATATA
CTAAAATAATATA
Found at i:3773313 original size:27 final size:27
Alignment explanation
Indices: 3773265--3773324 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
3773255 ACAAATGGGG
* * **
3773265 GGTGCCGCCTGTGGCAGTGGCACCATT
1 GGTGCCGCCTCTGCCACAGGCACCATT
3773292 GGTGCCGCCTCTGCCACAGGCACCATT
1 GGTGCCGCCTCTGCCACAGGCACCATT
3773319 GGTGCC
1 GGTGCC
3773325 ACCTGTGGCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.12, C:0.35, G:0.33, T:0.20
Consensus pattern (27 bp):
GGTGCCGCCTCTGCCACAGGCACCATT
Found at i:3775035 original size:2 final size:2
Alignment explanation
Indices: 3775022--3775059 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
3775012 ACACCCATGA
* *
3775022 AT AT AT AC AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3775060 GCTTATGTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3779362 original size:30 final size:31
Alignment explanation
Indices: 3779321--3779394 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
3779311 AATTAAATTT
* *
3779321 TTTTAAAAAAATTAA-AAAGCATAA-TGAAAA
1 TTTTCAAAAAATTAAGAAAACATAACT-AAAA
* *
3779351 TTTTCAAAAAATTAAGAAAACTTAACTAAAG
1 TTTTCAAAAAATTAAGAAAACATAACTAAAA
3779382 TTTTCAAAAAATT
1 TTTTCAAAAAATT
3779395 TAGAGGGCCC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 14 0.37
31 23 0.61
32 1 0.03
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.31
Consensus pattern (31 bp):
TTTTCAAAAAATTAAGAAAACATAACTAAAA
Found at i:3791539 original size:18 final size:19
Alignment explanation
Indices: 3791497--3791543 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
3791487 TTTTGTGAAT
* *
3791497 TATATATTTATAAATTATC
1 TATATATTAATAAATTAAC
3791516 TATATATTAAT-AATTAAC
1 TATATATTAATAAATTAAC
*
3791534 TTTATATTAA
1 TATATATTAA
3791544 ACTTTTGATG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 15 0.60
19 10 0.40
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (19 bp):
TATATATTAATAAATTAAC
Found at i:3802762 original size:9 final size:9
Alignment explanation
Indices: 3802748--3802824 Score: 102
Period size: 9 Copynumber: 8.4 Consensus size: 9
3802738 TTTGGTTAAA
3802748 AATTACCCG
1 AATTACCCG
3802757 AATTACCCG
1 AATTACCCG
3802766 AATTACCCG
1 AATTACCCG
*
3802775 AATTAACCG
1 AATTACCCG
*
3802784 AATTAACCG
1 AATTACCCG
3802793 AATTA-CCG
1 AATTACCCG
*
3802801 AAAAATACCCG
1 --AATTACCCG
3802812 AATTACCCG
1 AATTACCCG
3802821 AATT
1 AATT
3802825 TTTTTATTTT
Statistics
Matches: 62, Mismatches: 3, Indels: 6
0.87 0.04 0.08
Matches are distributed among these distances:
8 3 0.05
9 52 0.84
10 4 0.06
11 3 0.05
ACGTcount: A:0.40, C:0.27, G:0.10, T:0.22
Consensus pattern (9 bp):
AATTACCCG
Found at i:3802942 original size:40 final size:39
Alignment explanation
Indices: 3802898--3802996 Score: 121
Period size: 39 Copynumber: 2.5 Consensus size: 39
3802888 ACTTTAGTAA
**
3802898 ATTGGGTTGGTAAATTGGGTAGTCTTTTAGTTTTAGTTTT
1 ATTGGGTTGGTAAATTGGGTAAAC-TTTAGTTTTAGTTTT
*
3802938 ATTGGATTGGGT-AATTGGGTAAACTTTAGTTTTAGTTTT
1 ATTGGGTT-GGTAAATTGGGTAAACTTTAGTTTTAGTTTT
*
3802977 ATCGGGTTGG-ATAATTGGGT
1 ATTGGGTTGGTA-AATTGGGT
3802997 TTGGGTTGGG
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
38 2 0.04
39 29 0.57
40 17 0.33
41 3 0.06
ACGTcount: A:0.20, C:0.03, G:0.29, T:0.47
Consensus pattern (39 bp):
ATTGGGTTGGTAAATTGGGTAAACTTTAGTTTTAGTTTT
Found at i:3805795 original size:2 final size:2
Alignment explanation
Indices: 3805788--3805820 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3805778 GGTAAAAATA
3805788 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3805821 CACACTAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3809807 original size:94 final size:94
Alignment explanation
Indices: 3809457--3809817 Score: 270
Period size: 94 Copynumber: 3.8 Consensus size: 94
3809447 AAGTAATATC
* * * * * * * * * *
3809457 CACTTTGGGGTGTCTACTTTATAACTTTGTAAAATTTAACTGAGTGCATT-GAGAGGCTAGTAGT
1 CACTTTGAGATGTTTACTTTATAACTTTGTAAAATTTAGCTAAGTGCCTTAAAGAGGTTAGCA-A
* * * * * *
3809521 TTTTCTGCTATTGACTTGATAAA-TAGTTT
65 TTTTCTGCTATTAACGTAACAAACAATTTT
* * * *
3809550 CTACTTT-AGAGTGTTTGCTTTATAACTTTGTAAAATTTAGCTAAGTGCTTTAAA-AGGCTAGTA
1 C-ACTTTGAGA-TGTTTACTTTATAACTTTGTAAAATTTAGCTAAGTGCCTTAAAGAGGTTAGCA
** * ***
3809613 ATGTTT-TAGCTATGGACTTAGTGAACAATTTT
64 AT-TTTCT-GCTATTAACGTAACAAACAATTTT
* * * * * *
3809645 CACTTTGAGGTGTTTACTTTATAACTTTGTAAATTTTAGCTAAGTACC-TCAAGTGGTTAACAAT
1 CACTTTGAGATGTTTACTTTATAACTTTGTAAAATTTAGCTAAGTGCCTTAAAGAGGTTAGCAA-
3809709 TTTTCTGCTATTAACGTAACAAACAATTTT
65 TTTTCTGCTATTAACGTAACAAACAATTTT
* **
3809739 CACTTTG-GAATGTCTT-TTTTATAACTTTGTAAAACATAGCTAAGTGCCTTAAAGAGGTTAGCA
1 CACTTTGAG-ATGT-TTACTTTATAACTTTGTAAAATTTAGCTAAGTGCCTTAAAGAGGTTAGCA
*
3809802 ATTTTCTACTATTAAC
64 ATTTTCTGCTATTAAC
3809818 TTAGCGAGCT
Statistics
Matches: 214, Mismatches: 41, Indels: 25
0.76 0.15 0.09
Matches are distributed among these distances:
93 8 0.04
94 182 0.85
95 24 0.11
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.41
Consensus pattern (94 bp):
CACTTTGAGATGTTTACTTTATAACTTTGTAAAATTTAGCTAAGTGCCTTAAAGAGGTTAGCAAT
TTTCTGCTATTAACGTAACAAACAATTTT
Found at i:3818507 original size:36 final size:36
Alignment explanation
Indices: 3818467--3818537 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
3818457 ATCAAGGACT
*
3818467 ACAATTAAAAGTTGTATACAATTAGAACTCTAAGAC
1 ACAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
*
3818503 ACAATTAGAAGCTGTATACAATTAGAACTCTAAGA
1 ACAATTAAAAGCTGTATACAATTAGAACTCTAAGA
3818538 TTATATAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.46, C:0.14, G:0.13, T:0.27
Consensus pattern (36 bp):
ACAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
Found at i:3818508 original size:19 final size:19
Alignment explanation
Indices: 3818484--3818537 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 19
3818474 AAAGTTGTAT
3818484 ACAATTAGAACTCTAAGAC
1 ACAATTAGAACTCTAAGAC
* *
3818503 ACAATTAGAA-GCT--GTAT
1 ACAATTAGAACTCTAAG-AC
3818520 ACAATTAGAACTCTAAGA
1 ACAATTAGAACTCTAAGA
3818538 TTATATAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
16 1 0.04
17 11 0.39
18 4 0.14
19 11 0.39
20 1 0.04
ACGTcount: A:0.46, C:0.17, G:0.13, T:0.24
Consensus pattern (19 bp):
ACAATTAGAACTCTAAGAC
Found at i:3818525 original size:17 final size:17
Alignment explanation
Indices: 3818466--3818529 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
3818456 TATCAAGGAC
* *
3818466 TACAATTAAAAGTTGTA
1 TACAATTAGAAGCTGTA
*
3818483 TACAATTAGAA-CTCTAAGA
1 TACAATTAGAAGCTGT---A
*
3818502 CACAATTAGAAGCTGTA
1 TACAATTAGAAGCTGTA
3818519 TACAATTAGAA
1 TACAATTAGAA
3818530 CTCTAAGATT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
16 2 0.05
17 21 0.57
19 11 0.30
20 3 0.08
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.28
Consensus pattern (17 bp):
TACAATTAGAAGCTGTA
Found at i:3823842 original size:90 final size:90
Alignment explanation
Indices: 3823689--3823961 Score: 465
Period size: 90 Copynumber: 3.0 Consensus size: 90
3823679 TTTAGGGATA
* * *
3823689 AAAAACAGGTCACCAGGAAAGAGGGCCCAGCTATGATGTCAAAGGAGATGAATGTGAAGTCTACA
1 AAAAACAGGTCACCAGGAAAGAGGGCTCAGCTATGATCTCAAAGGAGATAAATGTGAAGTCTACA
* *
3823754 TCATTCAGCAAGGAGAATAGCAACC
66 TCATTCAGCAAGGGGAATAGCAGCC
3823779 AAAAACAGGTCACCAGGAAAGAGGGCTCAGCTATGATCTCAAAGGAGATAAATGTGAAGTCTACA
1 AAAAACAGGTCACCAGGAAAGAGGGCTCAGCTATGATCTCAAAGGAGATAAATGTGAAGTCTACA
* * *
3823844 TCATCCAGTAAGGGGAATAGCTGCC
66 TCATTCAGCAAGGGGAATAGCAGCC
*
3823869 AAAAACAGGTCACCAGGAAAGAGGGCTCAGCTATGAGCTCAAAGGAGATAAATGTGAAGTCTACA
1 AAAAACAGGTCACCAGGAAAGAGGGCTCAGCTATGATCTCAAAGGAGATAAATGTGAAGTCTACA
3823934 TCATTCAGCAAGGGGAATAGCAGCC
66 TCATTCAGCAAGGGGAATAGCAGCC
3823959 AAA
1 AAA
3823962 GACCTGGAGA
Statistics
Matches: 171, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
90 171 1.00
ACGTcount: A:0.40, C:0.19, G:0.26, T:0.16
Consensus pattern (90 bp):
AAAAACAGGTCACCAGGAAAGAGGGCTCAGCTATGATCTCAAAGGAGATAAATGTGAAGTCTACA
TCATTCAGCAAGGGGAATAGCAGCC
Found at i:3828514 original size:2 final size:2
Alignment explanation
Indices: 3828509--3828538 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3828499 AAAGAGAGAA
3828509 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3828539 CCCATATGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3830243 original size:18 final size:20
Alignment explanation
Indices: 3830222--3830263 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
3830212 ATTAAGAAAT
*
3830222 TTTTATAAA-TATTTTG-AA
1 TTTTAAAAATTATTTTGTAA
3830240 TTTTAAAAATTATTTTGTAA
1 TTTTAAAAATTATTTTGTAA
3830260 TTTT
1 TTTT
3830264 TGTTGAGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.38
19 7 0.33
20 6 0.29
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (20 bp):
TTTTAAAAATTATTTTGTAA
Found at i:3830243 original size:19 final size:21
Alignment explanation
Indices: 3830219--3830264 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
3830209 TAAATTAAGA
*
3830219 AATTTTTATAAA-TATTTTG-
1 AATTTTTAAAAATTATTTTGT
3830238 AA-TTTTAAAAATTATTTTGT
1 AATTTTTAAAAATTATTTTGT
3830258 AATTTTT
1 AATTTTT
3830265 GTTGAGGGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 8 0.35
19 9 0.39
20 2 0.09
21 4 0.17
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (21 bp):
AATTTTTAAAAATTATTTTGT
Found at i:3831165 original size:2 final size:2
Alignment explanation
Indices: 3831152--3831186 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3831142 ATTACCTTTC
*
3831152 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3831187 GTAGCCATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:3837049 original size:7 final size:7
Alignment explanation
Indices: 3837037--3837101 Score: 51
Period size: 7 Copynumber: 9.4 Consensus size: 7
3837027 TGTGATAATA
3837037 AAATTTT
1 AAATTTT
3837044 AAATTTT
1 AAATTTT
**
3837051 AAATAAT
1 AAATTTT
*
3837058 AAATCTT
1 AAATTTT
**
3837065 AAATCAT
1 AAATTTT
3837072 AAATTTT
1 AAATTTT
**
3837079 AAATAGT
1 AAATTTT
*
3837086 AAA-CTT
1 AAATTTT
3837092 AAATTTT
1 AAATTTT
3837099 AAA
1 AAA
3837102 AGATTATCTT
Statistics
Matches: 45, Mismatches: 12, Indels: 2
0.76 0.20 0.03
Matches are distributed among these distances:
6 4 0.09
7 41 0.91
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.42
Consensus pattern (7 bp):
AAATTTT
Done.