Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 79 of 97
Found at i:31384419 original size:124 final size:126
Alignment explanation
Indices: 31384174--31384440 Score: 398
Period size: 124 Copynumber: 2.1 Consensus size: 126
31384164 NNNNNNNATT
*
31384174 AATTATTAATA-TTTAAAAAATAAAATAAAATAATTAATCATAAGAATATTTAAATTAAATAAAT
1 AATTATTAATATTTTAAAAAATAAAATAAAATAATTAATCATAAGAATATTTAAATTAAATAAAA
* * *
31384238 TATTAATATTTTAAATAAATTAATGATTAAATTGGAAATAAATTATTAATATTTAAATTATC
66 TATGAATATTTTAAAT-AATTAATGATTAAATTAGAAATAAAATATTAATATTTAAATTATC
* * *
31384300 AATTATTAATATTTTAAAAAATATAAT-AAA-AATTAATTATAATAATATTTAAATTAAATAAAA
1 AATTATTAATATTTTAAAAAATAAAATAAAATAATTAATCATAAGAATATTTAAATTAAATAAAA
* * *
31384363 TATGAATATTTTAACAT-ATTAATGATTAAATTATAAATAAAATATTAATGTTTAAATTATT
66 TATGAATATTTTAA-ATAATTAATGATTAAATTAGAAATAAAATATTAATATTTAAATTATC
31384424 AATTATTAATATTTTAA
1 AATTATTAATATTTTAA
31384441 TTAAATTCTA
Statistics
Matches: 129, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
124 56 0.43
125 43 0.33
126 16 0.12
127 14 0.11
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (126 bp):
AATTATTAATATTTTAAAAAATAAAATAAAATAATTAATCATAAGAATATTTAAATTAAATAAAA
TATGAATATTTTAAATAATTAATGATTAAATTAGAAATAAAATATTAATATTTAAATTATC
Found at i:31384432 original size:15 final size:15
Alignment explanation
Indices: 31384379--31384443 Score: 52
Period size: 15 Copynumber: 4.6 Consensus size: 15
31384369 TATTTTAACA
*
31384379 TATTAATGATTAAAT
1 TATTAATTATTAAAT
*
31384394 TA-TAA--A-TAAAA
1 TATTAATTATTAAAT
31384405 TATTAATGT-TTAAAT
1 TATTAAT-TATTAAAT
31384420 TATTAATTATTAATAT
1 TATTAATTATTAA-AT
31384436 T-TTAATTA
1 TATTAATTA
31384444 AATTCTAGAT
Statistics
Matches: 41, Mismatches: 2, Indels: 14
0.72 0.04 0.25
Matches are distributed among these distances:
11 6 0.15
12 4 0.10
14 4 0.10
15 24 0.59
16 3 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (15 bp):
TATTAATTATTAAAT
Found at i:31385625 original size:45 final size:45
Alignment explanation
Indices: 31385508--31385629 Score: 145
Period size: 45 Copynumber: 2.7 Consensus size: 45
31385498 CACGCTATGA
* * *
31385508 TGTTACACGCCCTGTACAAAAATATGTTACACGCCATAATTAGCT
1 TGTTACACGCCATGTACAAAAATATGTGACACACCATAATTAGCT
* * * * * *
31385553 TGTTACACGTCATATGCAAAAACATGTGACACACCATGATTAGGT
1 TGTTACACGCCATGTACAAAAATATGTGACACACCATAATTAGCT
* *
31385598 TGTTACACACCATGTACAGAAATATGTGACAC
1 TGTTACACGCCATGTACAAAAATATGTGACAC
31385630 GTCATGTACA
Statistics
Matches: 62, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
45 62 1.00
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (45 bp):
TGTTACACGCCATGTACAAAAATATGTGACACACCATAATTAGCT
Found at i:31385635 original size:24 final size:24
Alignment explanation
Indices: 31385608--31385731 Score: 176
Period size: 24 Copynumber: 5.2 Consensus size: 24
31385598 TGTTACACAC
* * *
31385608 CATGTACAGAAATATGTGACACGT
1 CATGTACAAAAACATGTGAGACGT
31385632 CATGTACAAAAACATGTGAGACGT
1 CATGTACAAAAACATGTGAGACGT
* *
31385656 TATGTACAAAAACATGTGAGACGC
1 CATGTACAAAAACATGTGAGACGT
*
31385680 CATGTACAAAAACATGTGAGACGC
1 CATGTACAAAAACATGTGAGACGT
* *
31385704 CATGTACAAAAACATATGACACGT
1 CATGTACAAAAACATGTGAGACGT
31385728 CATG
1 CATG
31385732 ATTAGGTTGT
Statistics
Matches: 91, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 91 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (24 bp):
CATGTACAAAAACATGTGAGACGT
Found at i:31385807 original size:26 final size:26
Alignment explanation
Indices: 31385768--31385817 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
31385758 AAAAATATTG
*
31385768 TTGTTACACGCCATTGTT-AAAAAAGA
1 TTGTTACACACCA-TGTTGAAAAAAGA
31385794 TTGTTACACACCATGTTGAAAAAA
1 TTGTTACACACCATGTTGAAAAAA
31385818 AAATACTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (26 bp):
TTGTTACACACCATGTTGAAAAAAGA
Found at i:31385846 original size:29 final size:30
Alignment explanation
Indices: 31385738--31385861 Score: 107
Period size: 29 Copynumber: 4.2 Consensus size: 30
31385728 CATGATTAGG
* * *
31385738 TTGTTACATGTCATGTTAAAAAAAATATTG
1 TTGTTACACGCCATGTTAAAAAAAATATTA
*
31385768 TTGTTACACGCCATTGTT---AAAAA-A-GA
1 TTGTTACACGCCA-TGTTAAAAAAAATATTA
* *
31385794 TTGTTACACACCATGTTGAAAAAAAAATACTA
1 TTGTTACACGCCATGTT--AAAAAAAATATTA
* *
31385826 TCGTTACACGTCATGTT-AAAAAAATATTA
1 TTGTTACACGCCATGTTAAAAAAAATATTA
31385855 TTGTTAC
1 TTGTTAC
31385862 TTACGAACCA
Statistics
Matches: 75, Mismatches: 11, Indels: 17
0.73 0.11 0.17
Matches are distributed among these distances:
25 4 0.05
26 12 0.16
27 1 0.01
28 5 0.07
29 17 0.23
30 16 0.21
31 5 0.07
32 15 0.20
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (30 bp):
TTGTTACACGCCATGTTAAAAAAAATATTA
Found at i:31385847 original size:30 final size:27
Alignment explanation
Indices: 31385738--31385861 Score: 90
Period size: 30 Copynumber: 4.3 Consensus size: 27
31385728 CATGATTAGG
* *
31385738 TTGTTACATGTCATGTTAAAAAAAATA
1 TTGTTACACGCCATGTTAAAAAAAATA
*
31385765 TTGTTGTTACACGCCATTGTT--AAAAAAGA
1 ---TTGTTACACGCCA-TGTTAAAAAAAATA
*
31385794 TTGTTACACACCATGTTGAAAAAAAAATA
1 TTGTTACACGCCATGTT--AAAAAAAATA
*
31385823 CTATCGTTACACGTCATGTTAAAAAAATATTA
1 -T-T-GTTACACGCCATGTTAAAAAAA-A-TA
31385855 TTGTTAC
1 TTGTTAC
31385862 TTACGAACCA
Statistics
Matches: 77, Mismatches: 7, Indels: 21
0.73 0.07 0.20
Matches are distributed among these distances:
25 4 0.05
26 12 0.16
29 19 0.25
30 20 0.26
31 7 0.09
32 15 0.19
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (27 bp):
TTGTTACACGCCATGTTAAAAAAAATA
Found at i:31387816 original size:20 final size:18
Alignment explanation
Indices: 31387788--31387847 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
31387778 ACAAAAAATT
*
31387788 TAAACTATAATAAAACCAAA
1 TAAAATATAATAAAA--AAA
31387808 TAAAATAT-ATAAAAAAA
1 TAAAATATAATAAAAAAA
* *
31387825 TAAAA-ATATATATATAAA
1 TAAAATATA-ATAAAAAAA
31387843 TAAAA
1 TAAAA
31387848 AAAAAAGGGT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
16 2 0.06
17 8 0.23
18 12 0.34
19 6 0.17
20 7 0.20
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (18 bp):
TAAAATATAATAAAAAAA
Found at i:31387850 original size:20 final size:18
Alignment explanation
Indices: 31387805--31387848 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
31387795 TAATAAAACC
31387805 AAAT-AAAATATATAAAA
1 AAATAAAAATATATAAAA
* *
31387822 AAATAAAAATATATATAT
1 AAATAAAAATATATAAAA
31387840 AAATAAAAA
1 AAATAAAAA
31387849 AAAAAGGGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 4 0.17
18 20 0.83
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (18 bp):
AAATAAAAATATATAAAA
Found at i:31388164 original size:9 final size:9
Alignment explanation
Indices: 31388150--31388189 Score: 53
Period size: 9 Copynumber: 4.1 Consensus size: 9
31388140 CGCCCCGGCA
31388150 AAGAGAAAG
1 AAGAGAAAG
31388159 AAGAGAAAGAG
1 AAGAG-AA-AG
31388170 AAGGAGAAAG
1 AA-GAGAAAG
31388180 AAGAGAAAG
1 AAGAGAAAG
31388189 A
1 A
31388190 GAAGAAGGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 13 0.46
10 6 0.21
11 6 0.21
12 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (9 bp):
AAGAGAAAG
Found at i:31388178 original size:21 final size:21
Alignment explanation
Indices: 31388152--31388193 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
31388142 CCCCGGCAAA
31388152 GAGAAAGAAGAGAAAGAGAAG
1 GAGAAAGAAGAGAAAGAGAAG
31388173 GAGAAAGAAGAGAAAGAGAAG
1 GAGAAAGAAGAGAAAGAGAAG
31388194 AAGGGGGGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (21 bp):
GAGAAAGAAGAGAAAGAGAAG
Found at i:31388224 original size:4 final size:4
Alignment explanation
Indices: 31388215--31388276 Score: 57
Period size: 4 Copynumber: 17.2 Consensus size: 4
31388205 CGGCTAGGAG
*
31388215 AGAA AGAA AGAA AGAA AG-- AGAA AGAA AG-A AGAA AGAG A-AA AG-A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
*
31388258 A-AA AGAA AGAG A-AA AGAA A
1 AGAA AGAA AGAA AGAA AGAA A
31388277 AGGGGAGCGG
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
2 2 0.04
3 11 0.23
4 34 0.72
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:31388248 original size:17 final size:17
Alignment explanation
Indices: 31388213--31388356 Score: 103
Period size: 17 Copynumber: 7.7 Consensus size: 17
31388203 AGCGGCTAGG
31388213 AGAGAAAGAAAGAAAGAA
1 AGAGAAAGAAAG-AAGAA
31388231 AGAGAAAGAAAGAAGAA
1 AGAGAAAGAAAGAAGAA
31388248 AGAGAAAAGAAA-AAGAA
1 AGAG-AAAGAAAGAAGAA
* **
31388265 AGAGAAAAGAAAAGGGGAGCGGCTGGG
1 AGAG-AAAG-AAA---GA-----AGAA
*
31388292 AGAGAAAGAAAGAGAAAA
1 AGAGAAAGAAAGA-AGAA
31388310 AGAGAAAGAAAGAAGAA
1 AGAGAAAGAAAGAAGAA
31388327 AGAGAAAAGAAA-AAGAA
1 AGAG-AAAGAAAGAAGAA
31388344 AGAGAGAAGAAAG
1 AGAGA-AAGAAAG
31388357 GGGGAGCGGC
Statistics
Matches: 103, Mismatches: 9, Indels: 28
0.74 0.06 0.20
Matches are distributed among these distances:
16 1 0.01
17 45 0.44
18 42 0.41
22 3 0.03
25 3 0.03
26 4 0.04
27 5 0.05
ACGTcount: A:0.66, C:0.01, G:0.32, T:0.01
Consensus pattern (17 bp):
AGAGAAAGAAAGAAGAA
Found at i:31388315 original size:18 final size:18
Alignment explanation
Indices: 31388292--31388356 Score: 80
Period size: 18 Copynumber: 3.7 Consensus size: 18
31388282 AGCGGCTGGG
31388292 AGAGAAAGAAAGAGAAAA
1 AGAGAAAGAAAGAGAAAA
*
31388310 AGAGAAAGAAAGA-AGAA
1 AGAGAAAGAAAGAGAAAA
* *
31388327 AGAGAAAAGAAAAAGAAAG
1 AGAG-AAAGAAAGAGAAAA
31388346 AGAG-AAGAAAG
1 AGAGAAAGAAAG
31388357 GGGGAGCGGC
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
17 13 0.32
18 21 0.52
19 6 0.15
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (18 bp):
AGAGAAAGAAAGAGAAAA
Found at i:31388317 original size:6 final size:6
Alignment explanation
Indices: 31388298--31388353 Score: 53
Period size: 6 Copynumber: 9.2 Consensus size: 6
31388288 TGGGAGAGAA
* *
31388298 AGAAAG AGAAAA AGAGAA- AGAAAG AAGAAAG AGAAA- AGAAAA AGAAAG
1 AGAAAG AGAAAG AGA-AAG AGAAAG -AGAAAG AGAAAG AGAAAG AGAAAG
31388346 AGAGAAG A
1 AGA-AAG A
31388354 AAGGGGGAGC
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
5 7 0.16
6 24 0.56
7 12 0.28
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (6 bp):
AGAAAG
Found at i:31388328 original size:11 final size:10
Alignment explanation
Indices: 31388292--31388356 Score: 62
Period size: 10 Copynumber: 6.2 Consensus size: 10
31388282 AGCGGCTGGG
31388292 AGAGAAAGAA
1 AGAGAAAGAA
31388302 AGAG-AA-AA
1 AGAGAAAGAA
31388310 AGAGAAAGAA
1 AGAGAAAGAA
31388320 AGAAGAAAGAGAAA
1 AG-AG-AA-AG-AA
*
31388334 AGAAAAAGAA
1 AGAGAAAGAA
31388344 AGAGAGAAGAA
1 AGAGA-AAGAA
31388355 AG
1 AG
31388357 GGGGAGCGGC
Statistics
Matches: 46, Mismatches: 2, Indels: 13
0.75 0.03 0.21
Matches are distributed among these distances:
8 6 0.13
9 4 0.09
10 14 0.30
11 11 0.24
12 4 0.09
13 3 0.07
14 4 0.09
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (10 bp):
AGAGAAAGAA
Found at i:31388353 original size:24 final size:25
Alignment explanation
Indices: 31388297--31388351 Score: 85
Period size: 24 Copynumber: 2.2 Consensus size: 25
31388287 CTGGGAGAGA
*
31388297 AAGAAAGAGAAAAAGAGAAAGAAAG
1 AAGAAAGAGAAAAAGAAAAAGAAAG
31388322 AAGAAAGAG-AAAAGAAAAAGAAAG
1 AAGAAAGAGAAAAAGAAAAAGAAAG
31388346 AGAGAA
1 A-AGAA
31388352 GAAAGGGGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
24 15 0.54
25 13 0.46
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (25 bp):
AAGAAAGAGAAAAAGAAAAAGAAAG
Found at i:31388410 original size:12 final size:11
Alignment explanation
Indices: 31388387--31388420 Score: 59
Period size: 11 Copynumber: 3.0 Consensus size: 11
31388377 AGAAAGAGAG
31388387 AAAGAAAAAAA
1 AAAGAAAAAAA
31388398 AAAGAAAAGAAA
1 AAAGAAAA-AAA
31388410 AAAGAAAAAAA
1 AAAGAAAAAAA
31388421 TGGAGAAAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAAA
Found at i:31388419 original size:79 final size:79
Alignment explanation
Indices: 31388149--31388418 Score: 379
Period size: 79 Copynumber: 3.4 Consensus size: 79
31388139 ACGCCCCGGC
* * *
31388149 AAAGAGAAAG-AAG-AGAAAGAGAAGGAGAAAGAAGAGAA-AGAGAAGAAGGGGGGGAGCGGCTA
1 AAAGAGAAAGAAAGAAGAAAGAGAA-AAGAAA-AAGA-AAGAGAGAAGAA-AGGGGGAGCGGCTG
*
31388211 GGAGAGAAAGAAAGAAAG
62 GGAGAGAAAGAAAGAGAG
* *
31388229 AAAGAGAAAGAAAGAAGAAAGAGAAAAGAAAAAGAAAGAGAAAAGAAAAGGGGAGCGGCTGGGAG
1 AAAGAGAAAGAAAGAAGAAAGAGAAAAGAAAAAGAAAGAGAGAAGAAAGGGGGAGCGGCTGGGAG
*
31388294 AGAAAGAAAGAGAA
66 AGAAAGAAAGAGAG
31388308 AAAGAGAAAGAAAGAAGAAAGAGAAAAGAAAAAGAAAGAGAGAAGAAAGGGGGAGCGGCTGGGAG
1 AAAGAGAAAGAAAGAAGAAAGAGAAAAGAAAAAGAAAGAGAGAAGAAAGGGGGAGCGGCTGGGAG
31388373 AGAAAGAAAGAGAG
66 AGAAAGAAAGAGAG
* *
31388387 AAAGA-AAA-AAAAAAGAAAAGAAAAAAGAAAAA
1 AAAGAGAAAGAAAGAAG-AAAGAGAAAAGAAAAA
31388419 AATGGAGAAA
Statistics
Matches: 174, Mismatches: 12, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
77 6 0.03
78 18 0.10
79 110 0.63
80 22 0.13
81 8 0.05
82 10 0.06
ACGTcount: A:0.62, C:0.02, G:0.35, T:0.01
Consensus pattern (79 bp):
AAAGAGAAAGAAAGAAGAAAGAGAAAAGAAAAAGAAAGAGAGAAGAAAGGGGGAGCGGCTGGGAG
AGAAAGAAAGAGAG
Found at i:31388429 original size:23 final size:23
Alignment explanation
Indices: 31388375--31388420 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
31388365 GCTGGGAGAG
*
31388375 AAAGAAAGAGAGAAAGAAAAAAA
1 AAAGAAAGAGAAAAAGAAAAAAA
31388398 AAAGAAA-AGAAAAAAGAAAAAAA
1 AAAGAAAGAG-AAAAAGAAAAAAA
31388421 TGGAGAAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 2 0.10
23 19 0.90
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (23 bp):
AAAGAAAGAGAAAAAGAAAAAAA
Found at i:31390082 original size:30 final size:29
Alignment explanation
Indices: 31390047--31390146 Score: 100
Period size: 29 Copynumber: 3.5 Consensus size: 29
31390037 CGTTAAAGTG
* *
31390047 TAACAAAATGTTTTTGAATATGTCGTGTAA
1 TAACAATAT-TTTTTCAATATGTCGTGTAA
* *
31390077 TAACAATATTTTTTCAACATGGCGTGTAA
1 TAACAATATTTTTTCAATATGTCGTGTAA
*
31390106 TAATAATATTTTTTTCAATATGAT-GTG---
1 TAACAATA-TTTTTTCAATATG-TCGTGTAA
31390133 TAACAATATTTTTT
1 TAACAATATTTTTT
31390147 AATCATAGCA
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
26 6 0.10
27 7 0.12
29 24 0.40
30 23 0.38
ACGTcount: A:0.35, C:0.08, G:0.12, T:0.45
Consensus pattern (29 bp):
TAACAATATTTTTTCAATATGTCGTGTAA
Found at i:31390283 original size:45 final size:45
Alignment explanation
Indices: 31390225--31390342 Score: 155
Period size: 45 Copynumber: 2.6 Consensus size: 45
31390215 TTTGTTTTCA
* * * *
31390225 ACATGGCTTGTAACAACCTAACCATGGCTTATCACATGTTTTTGT
1 ACATGGCATGTAACAACCTAACCATGACTTATCACATATTTTTAT
* ** * *
31390270 ACATTGTGTGTAACAATCTAACCATAACTTATCACATATTTTTAT
1 ACATGGCATGTAACAACCTAACCATGACTTATCACATATTTTTAT
31390315 ACATGGCATGTAACAACCTAACCATGAC
1 ACATGGCATGTAACAACCTAACCATGAC
31390343 ATGTAACATC
Statistics
Matches: 60, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 60 1.00
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (45 bp):
ACATGGCATGTAACAACCTAACCATGACTTATCACATATTTTTAT
Found at i:31399040 original size:98 final size:98
Alignment explanation
Indices: 31398906--31399103 Score: 315
Period size: 98 Copynumber: 2.0 Consensus size: 98
31398896 ATTTTCAATA
* * *
31398906 TCATATATTAACATGCTATCCCATTTAATAATATTTGCATTTCAGACCACTTAATGGGATACTTG
1 TCATAAATTAACATGCTATCCCATTTAATAACATTTGCATTTCAGACAACTTAATGGGATACTTG
* *
31398971 AACATGAGTAATACACATTTTGCATGCTTAACC
66 AACATGAGCAATAAACATTTTGCATGCTTAACC
* *
31399004 TCATAAATTAACATGCTATTCCATTTGATAACATTTGCATTTCAGACAACTTAATGGGATACTTG
1 TCATAAATTAACATGCTATCCCATTTAATAACATTTGCATTTCAGACAACTTAATGGGATACTTG
* *
31399069 AACATGGGCAATAAACATTTTGGATGCTTAACC
66 AACATGAGCAATAAACATTTTGCATGCTTAACC
31399102 TC
1 TC
31399104 CAACCTTAAT
Statistics
Matches: 91, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
98 91 1.00
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.35
Consensus pattern (98 bp):
TCATAAATTAACATGCTATCCCATTTAATAACATTTGCATTTCAGACAACTTAATGGGATACTTG
AACATGAGCAATAAACATTTTGCATGCTTAACC
Found at i:31420600 original size:23 final size:23
Alignment explanation
Indices: 31420547--31420598 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
31420537 ATCGTTAGTT
*
31420547 ATAAAAATTTATTTTTACTTAAC
1 ATAAAAATTTATTTTTACTTAAA
*
31420570 ATAAAAATTTA-TTTTATTTAAA
1 ATAAAAATTTATTTTTACTTAAA
31420592 ATAAAAA
1 ATAAAAA
31420599 ATAAAAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 16 0.59
23 11 0.41
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (23 bp):
ATAAAAATTTATTTTTACTTAAA
Found at i:31424801 original size:22 final size:23
Alignment explanation
Indices: 31424759--31424801 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
31424749 CGTGATTGAA
* *
31424759 TATTTGTTGAGCATTGTGTGATC
1 TATTTGTAGAGCATTGCGTGATC
31424782 TATTTGTAG-GCATTGCGTGA
1 TATTTGTAGAGCATTGCGTGA
31424802 CTTTAGCTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.19, C:0.09, G:0.28, T:0.44
Consensus pattern (23 bp):
TATTTGTAGAGCATTGCGTGATC
Found at i:31425771 original size:22 final size:22
Alignment explanation
Indices: 31425696--31425773 Score: 129
Period size: 22 Copynumber: 3.5 Consensus size: 22
31425686 TGAGTGGATG
*
31425696 TTAGGCATTGGGTGACTTATTA
1 TTAGGTATTGGGTGACTTATTA
* *
31425718 TTAAGTATTAGGTGACTTATTA
1 TTAGGTATTGGGTGACTTATTA
31425740 TTAGGTATTGGGTGACTTATTA
1 TTAGGTATTGGGTGACTTATTA
31425762 TTAGGTATTGGG
1 TTAGGTATTGGG
31425774 AGAATGGGTT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.24, C:0.05, G:0.27, T:0.44
Consensus pattern (22 bp):
TTAGGTATTGGGTGACTTATTA
Found at i:31426631 original size:196 final size:197
Alignment explanation
Indices: 31426084--31426881 Score: 1303
Period size: 197 Copynumber: 4.1 Consensus size: 197
31426074 CGTGACTGAT
* *
31426084 TTGTGCAATTTATGTGTTGCTTTTAGGCTTTTGTTCAGTAGTTTTTTAGGCAGTGCGTGACTGGT
1 TTGTGCAATTCATGTGTTGCTTTGAGGCTTTTGTTCAGTAGTTTTTTAGGCAGTGCGTGACTGGT
31426149 TTTTATATATTGCGTTACCTGTTGAAGCGAGAGTGGTGGCGCGTGACTTGTGCAATTCATGTGTT
66 TTTTATATATTGCGTTACCTGTTGAAGCGAGAGTGGTGGCGCGTGACTTGTGCAATTCATGTGTT
* *
31426214 ATTTTGAGGTTTTTGTTCAGTAGTTTTTTAGGCTTGCACATATGTATGGAGTCTGACCGTGGATT
131 ATTTTGAGGCTTTTGTTCAGTAGTTTTTTAGGCTTGCACATATGTGTGGAGTCTGACCGTGGATT
31426279 AC
196 AC
*
31426281 TTGTGCAATTCATCTGTTGCTTTGAGGCTTTTGTTCAGTAGTTTTTTAGGCAGTGCGTGACTGGT
1 TTGTGCAATTCATGTGTTGCTTTGAGGCTTTTGTTCAGTAGTTTTTTAGGCAGTGCGTGACTGGT
* * *
31426346 TTTTATATATTGCGTTACCTGTTGAAGCGAGAGTGGCGGCGCGTAACTTGTGCAATTCATGTATT
66 TTTTATATATTGCGTTACCTGTTGAAGCGAGAGTGGTGGCGCGTGACTTGTGCAATTCATGTGTT
* * * **
31426411 GTTTTGAGGCTTTTGTTCAGTAGTTTTTTAGGCTTGCGCATATGTGTGGAGTTTGACTATGGATT
131 ATTTTGAGGCTTTTGTTCAGTAGTTTTTTAGGCTTGCACATATGTGTGGAGTCTGACCGTGGATT
31426476 AC
196 AC
* *
31426478 TTGTGCAATTCATGTGTTACTTTGAGGCTTTTTTTCAGTAGTTTTTTAGGCA-TGCGTGACTGGT
1 TTGTGCAATTCATGTGTTGCTTTGAGGCTTTTGTTCAGTAGTTTTTTAGGCAGTGCGTGACTGGT
* *
31426542 TTTTATATATTACGTTACCTGTTGAAGCGAGAGTGGTGACGCGTGACTTGTGCAATTCATGTGTT
66 TTTTATATATTGCGTTACCTGTTGAAGCGAGAGTGGTGGCGCGTGACTTGTGCAATTCATGTGTT
* * * *
31426607 ATTTTGAGACTTTTGTTCAGTAGTTTTTTAGGCTTGCGCATATGTGTGGAGTCTAACCGTAGATT
131 ATTTTGAGGCTTTTGTTCAGTAGTTTTTTAGGCTTGCACATATGTGTGGAGTCTGACCGTGGATT
31426672 AC
196 AC
* *
31426674 TTGTGCAATTCATGTATTGCTTTGATGCTTTTGTTCAGTAGTTTTTTAGGCAGTGCGTGACTGGT
1 TTGTGCAATTCATGTGTTGCTTTGAGGCTTTTGTTCAGTAGTTTTTTAGGCAGTGCGTGACTGGT
* *
31426739 TTTTATATATTGCGTTACCTGTTGAAGCGAGAGTGGTGGTGCATGACTTGTGCAATTCATGTGTT
66 TTTTATATATTGCGTTACCTGTTGAAGCGAGAGTGGTGGCGCGTGACTTGTGCAATTCATGTGTT
* * * * *
31426804 GTTTTGAGGCTTTTGTTCAG-AGTTTTTTAAGCTTACACATATGTTTGGAGTTTGACCGTGGATT
131 ATTTTGAGGCTTTTGTTCAGTAGTTTTTTAGGCTTGCACATATGTGTGGAGTCTGACCGTGGATT
31426868 AC
196 AC
*
31426870 TTGTGCAGTTCA
1 TTGTGCAATTCA
31426882 CCTCTTGTTT
Statistics
Matches: 554, Mismatches: 46, Indels: 3
0.92 0.08 0.00
Matches are distributed among these distances:
196 230 0.42
197 324 0.58
ACGTcount: A:0.18, C:0.13, G:0.26, T:0.43
Consensus pattern (197 bp):
TTGTGCAATTCATGTGTTGCTTTGAGGCTTTTGTTCAGTAGTTTTTTAGGCAGTGCGTGACTGGT
TTTTATATATTGCGTTACCTGTTGAAGCGAGAGTGGTGGCGCGTGACTTGTGCAATTCATGTGTT
ATTTTGAGGCTTTTGTTCAGTAGTTTTTTAGGCTTGCACATATGTGTGGAGTCTGACCGTGGATT
AC
Found at i:31435646 original size:10 final size:10
Alignment explanation
Indices: 31435631--31435655 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
31435621 GAGAGAGAAG
31435631 AAAAAGAAAA
1 AAAAAGAAAA
31435641 AAAAAGAAAA
1 AAAAAGAAAA
31435651 AAAAA
1 AAAAA
31435656 ATAAGAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:31436283 original size:21 final size:22
Alignment explanation
Indices: 31436259--31436299 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
31436249 AAAAAATACT
*
31436259 TTTTATTAAAA-TTAAAAATTA
1 TTTTATTAAAAGATAAAAATTA
*
31436280 TTTTGTTAAAAGATAAAAAT
1 TTTTATTAAAAGATAAAAAT
31436300 ATTCTAAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (22 bp):
TTTTATTAAAAGATAAAAATTA
Found at i:31436392 original size:22 final size:22
Alignment explanation
Indices: 31436341--31436394 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
31436331 CTATAATTAA
31436341 AATAATATTTTCATAAAAATAC
1 AATAATATTTTCATAAAAATAC
* * **
31436363 AA-ATATATTTTTATAATAATTT
1 AATA-ATATTTTCATAAAAATAC
31436385 AATAATATTT
1 AATAATATTT
31436395 GTATTAGAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 1 0.04
22 24 0.92
23 1 0.04
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (22 bp):
AATAATATTTTCATAAAAATAC
Found at i:31436523 original size:42 final size:41
Alignment explanation
Indices: 31436474--31436579 Score: 131
Period size: 45 Copynumber: 2.4 Consensus size: 41
31436464 TTCATTAAAT
* *
31436474 TTAAATAATACTAAATATTATTCTTTATTATATTTATTATA
1 TTAAATAATATTAAATATTATTCTTTATAATATTTATTATA
*
31436515 TTCAAATAATATTATTAAATAATATTCTTTATAATATTTATTATA
1 TT-AAAT-A-A-TATTAAATATTATTCTTTATAATATTTATTATA
31436560 GTTAAATAATATTAATATAT
1 -TTAAATAATATTAA-ATAT
31436580 AAAATAATAT
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
41 2 0.04
42 10 0.18
43 5 0.09
44 2 0.04
45 34 0.62
46 2 0.04
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.51
Consensus pattern (41 bp):
TTAAATAATATTAAATATTATTCTTTATAATATTTATTATA
Found at i:31436534 original size:45 final size:45
Alignment explanation
Indices: 31436485--31436573 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
31436475 TAAATAATAC
* *
31436485 TAAATATTATTCTTTATTATATTTATTATA-TTCAAATAATATTAT
1 TAAATAATATTCTTTATAATATTTATTATAGTT-AAATAATATTAT
31436530 TAAATAATATTCTTTATAATATTTATTATAGTTAAATAATATTA
1 TAAATAATATTCTTTATAATATTTATTATAGTTAAATAATATTA
31436574 ATATATAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
45 39 0.95
46 2 0.05
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (45 bp):
TAAATAATATTCTTTATAATATTTATTATAGTTAAATAATATTAT
Found at i:31450781 original size:42 final size:43
Alignment explanation
Indices: 31450722--31450802 Score: 119
Period size: 42 Copynumber: 1.9 Consensus size: 43
31450712 GAGGCATACG
*
31450722 AGAACAAGTTAAGAGAAAA-AGATGTACGTGAAAAGGTACAAA
1 AGAACAAGGTAAGAGAAAAGAGATGTACGTGAAAAGGTACAAA
* **
31450764 AGAACAAGGTAAGAGAAAAGAGGTGTATTTGAAAAGGTA
1 AGAACAAGGTAAGAGAAAAGAGATGTACGTGAAAAGGTA
31450803 AGAGGGAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
42 18 0.53
43 16 0.47
ACGTcount: A:0.52, C:0.05, G:0.27, T:0.16
Consensus pattern (43 bp):
AGAACAAGGTAAGAGAAAAGAGATGTACGTGAAAAGGTACAAA
Found at i:31456872 original size:21 final size:20
Alignment explanation
Indices: 31456813--31456876 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 20
31456803 TTTAAAAATA
*
31456813 TTAAAATTTTAAATATTATTTT
1 TTAAAA-TTTAAATATTA-ATT
*
31456835 TTAAAATTTTAAT-TTAATT
1 TTAAAATTTAAATATTAATT
*
31456854 TTAAAATATAAAATATTAATT
1 TTAAAAT-TTAAATATTAATT
31456875 TT
1 TT
31456877 TAGCTTTTCT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
19 9 0.25
20 7 0.19
21 14 0.39
22 6 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTAAAATTTAAATATTAATT
Found at i:31461794 original size:538 final size:537
Alignment explanation
Indices: 31460777--31461840 Score: 2092
Period size: 538 Copynumber: 2.0 Consensus size: 537
31460767 GCAGGAATTA
*
31460777 AAAAAAAATTTCAAAAACAAAAATGAGGGAAATCCTTCACGTACAAGGTGGGCAGTGCGGGAACC
1 AAAAAAAATTTCAAAAAAAAAAATGAGGGAAATCCTTCACGTACAAGGTGGGCAGTGCGGGAACC
31460842 AGATCGGATCCAAGTTCTGGGAAGTGGTCTGCGACGAGCACGGCATCGACCCCACAGGACGTTAC
66 AGATCGGATCCAAGTTCTGGGAAGTGGTCTGCGACGAGCACGGCATCGACCCCACAGGACGTTAC
31460907 ATCGGAAACTCCGATCTGCAATTGGAGCGCGTAAATGTTTACTACAATGAGGCTTCGTGTGGAAG
131 ATCGGAAACTCCGATCTGCAATTGGAGCGCGTAAATGTTTACTACAATGAGGCTTCGTGTGGAAG
31460972 GTTTGTCCCACGCGCCGTGCTCATGGATCTCGAGCCGGGAACTATGGATAGTGTGAGGACTGGAC
196 GTTTGTCCCACGCGCCGTGCTCATGGATCTCGAGCCGGGAACTATGGATAGTGTGAGGACTGGAC
31461037 CTTACGGACAGATCTTTAGGCCTGATAACTTCGTGTTTGGACAATCTGGAGCTGGGAATAATTGG
261 CTTACGGACAGATCTTTAGGCCTGATAACTTCGTGTTTGGACAATCTGGAGCTGGGAATAATTGG
31461102 GCTAAGGGGCATTACACTGAAGGAGCTGAGCTTATTGATGCTGTTCTTGATGTTGTTAGAAAGGA
326 GCTAAGGGGCATTACACTGAAGGAGCTGAGCTTATTGATGCTGTTCTTGATGTTGTTAGAAAGGA
31461167 GGCTGAGAATTGTGACTGTCTCCAAGGTATAATTTTTTTAGTTCTTCTTTTAATACAAGTTTAAC
391 GGCTGAGAATTGTGACTGTCTCCAAGGTATAATTTTTTTAGTTCTTCTTTTAATACAAGTTTAAC
31461232 TGTTTTTTTCTTTAATATTGATGCTTTAAACGACATTTTAATGTCTGTAAAAGCATTTGGCTCAT
456 TGTTTTTTTCTTTAATATTGATGCTTTAAACGACATTTTAATGTCTGTAAAAGCATTTGGCTCAT
31461297 TAGTTNACATGGCAGATT
521 TAGTT-ACATGGCAGATT
*
31461315 AAAAAAATTTTCAAAAAAAAAAATGAGGGAAATCCTTCACGTACAAGGTGGGCAGTGCGGGAACC
1 AAAAAAAATTTCAAAAAAAAAAATGAGGGAAATCCTTCACGTACAAGGTGGGCAGTGCGGGAACC
31461380 AGATCGGATCCAAGTTCTGGGAAGTGGTCTGCGACGAGCACGGCATCGACCCCACAGGACGTTAC
66 AGATCGGATCCAAGTTCTGGGAAGTGGTCTGCGACGAGCACGGCATCGACCCCACAGGACGTTAC
*
31461445 ATCGGAAACTCCGATCTGCAATTGGAGCGTGTAAATGTTTACTACAATGAGGCTTCGTGTGGAAG
131 ATCGGAAACTCCGATCTGCAATTGGAGCGCGTAAATGTTTACTACAATGAGGCTTCGTGTGGAAG
31461510 GTTTGTCCCACGCGCCGTGCTCATGGATCTCGAGCCGGGAACTATGGATAGTGTGAGGACTGGAC
196 GTTTGTCCCACGCGCCGTGCTCATGGATCTCGAGCCGGGAACTATGGATAGTGTGAGGACTGGAC
31461575 CTTACGGACAGATCTTTAGGCCTGATAACTTCGTGTTTGGACAATCTGGAGCTGGGAATAATTGG
261 CTTACGGACAGATCTTTAGGCCTGATAACTTCGTGTTTGGACAATCTGGAGCTGGGAATAATTGG
31461640 GCTAAGGGGCATTACACTGAAGGAGCTGAGCTTATTGATGCTGTTCTTGATGTTGTTAGAAAGGA
326 GCTAAGGGGCATTACACTGAAGGAGCTGAGCTTATTGATGCTGTTCTTGATGTTGTTAGAAAGGA
31461705 GGCTGAGAATTGTGACTGTCTCCAAGGTATAATTTTTTTAGTTCTTCTTTTAATACAAGTTTAAC
391 GGCTGAGAATTGTGACTGTCTCCAAGGTATAATTTTTTTAGTTCTTCTTTTAATACAAGTTTAAC
31461770 TGTTTTTTTCTTTAATATTGATGCTTTAAACGACATTTTAATGTCTGTAAAAGCATTTGGCTCAT
456 TGTTTTTTTCTTTAATATTGATGCTTTAAACGACATTTTAATGTCTGTAAAAGCATTTGGCTCAT
31461835 TAGTTA
521 TAGTTA
31461841 ATGTAGAAAG
Statistics
Matches: 523, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
537 1 0.00
538 522 1.00
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.30
Consensus pattern (537 bp):
AAAAAAAATTTCAAAAAAAAAAATGAGGGAAATCCTTCACGTACAAGGTGGGCAGTGCGGGAACC
AGATCGGATCCAAGTTCTGGGAAGTGGTCTGCGACGAGCACGGCATCGACCCCACAGGACGTTAC
ATCGGAAACTCCGATCTGCAATTGGAGCGCGTAAATGTTTACTACAATGAGGCTTCGTGTGGAAG
GTTTGTCCCACGCGCCGTGCTCATGGATCTCGAGCCGGGAACTATGGATAGTGTGAGGACTGGAC
CTTACGGACAGATCTTTAGGCCTGATAACTTCGTGTTTGGACAATCTGGAGCTGGGAATAATTGG
GCTAAGGGGCATTACACTGAAGGAGCTGAGCTTATTGATGCTGTTCTTGATGTTGTTAGAAAGGA
GGCTGAGAATTGTGACTGTCTCCAAGGTATAATTTTTTTAGTTCTTCTTTTAATACAAGTTTAAC
TGTTTTTTTCTTTAATATTGATGCTTTAAACGACATTTTAATGTCTGTAAAAGCATTTGGCTCAT
TAGTTACATGGCAGATT
Found at i:31464876 original size:21 final size:21
Alignment explanation
Indices: 31464852--31464902 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
31464842 TTTTAAAATA
*
31464852 TTAAAAATATTTTTTA-TATAT
1 TTAAAAATATTATTTAGTA-AT
*
31464873 TTAAATATATTATTTAGTAAT
1 TTAAAAATATTATTTAGTAAT
*
31464894 TTAATAATA
1 TTAAAAATA
31464903 ATATAAAATC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
TTAAAAATATTATTTAGTAAT
Found at i:31469296 original size:15 final size:16
Alignment explanation
Indices: 31469276--31469305 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
31469266 TGGTAAGAGA
31469276 GAAAGAGAG-AGAAAG
1 GAAAGAGAGAAGAAAG
31469291 GAAAGAGAGAAGAAA
1 GAAAGAGAGAAGAAA
31469306 AGTATTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (16 bp):
GAAAGAGAGAAGAAAG
Found at i:31469530 original size:178 final size:178
Alignment explanation
Indices: 31469321--31469665 Score: 615
Period size: 178 Copynumber: 1.9 Consensus size: 178
31469311 TTTTGTCTTT
31469321 CCCTTCTTTCCTTGGCTACGAGGGAAATAAGAAAAATATTTTTTATTTAAGATTTACATAATATT
1 CCCTTCTTTCCTTGGCTACGAGGGAAATAAGAAAAATATTTTTTATTTAAGATTTACATAATATT
* *
31469386 TGAAAAAGTTTTGAATAATTTAAAAAATTTAAATAAATCTT-TTTTTTTATTGTGTTCAA-TAAG
66 TGAAAAAGTTTTGAATAATTTAAAAAATTTAAATAAATCTTATTGTTTTATTATGTTCAATTAAG
31469449 TTTTTATATTTTTA-TTTGAATCAAATAAAATTTTATAAAAAATTCTTAA
131 -TTTTATATTTTTATTTTG-ATCAAATAAAATTTTATAAAAAATTCTTAA
31469498 NCCCTTCTTTCCTTGGCTACGAGGGAAATAAGAAAAATATTTTTTATTTAAGATTTACATAATAT
1 -CCCTTCTTTCCTTGGCTACGAGGGAAATAAGAAAAATATTTTTTATTTAAGATTTACATAATAT
31469563 TTGAAAAAGTTTTGAATAATTTAAAAAATTTAAATAAATCTTATTGTTTTATTATGTTCAATTAA
65 TTGAAAAAGTTTTGAATAATTTAAAAAATTTAAATAAATCTTATTGTTTTATTATGTTCAATTAA
*
31469628 GTTTTATATTTTTATTTTGATCAAATAAACTTTTATAA
130 GTTTTATATTTTTATTTTGATCAAATAAAATTTTATAA
31469666 CTAAAATTGT
Statistics
Matches: 161, Mismatches: 3, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
178 106 0.66
179 47 0.29
180 8 0.05
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.45
Consensus pattern (178 bp):
CCCTTCTTTCCTTGGCTACGAGGGAAATAAGAAAAATATTTTTTATTTAAGATTTACATAATATT
TGAAAAAGTTTTGAATAATTTAAAAAATTTAAATAAATCTTATTGTTTTATTATGTTCAATTAAG
TTTTATATTTTTATTTTGATCAAATAAAATTTTATAAAAAATTCTTAA
Found at i:31469899 original size:20 final size:19
Alignment explanation
Indices: 31469871--31469908 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
31469861 ACAATAATTA
31469871 ATTAATTTTTAATAATAAAT
1 ATTAATTTTTAA-AATAAAT
*
31469891 ATTATTTTTTAAAATAAA
1 ATTAATTTTTAAAATAAA
31469909 AAATAAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTAATTTTTAAAATAAAT
Found at i:31470725 original size:2 final size:2
Alignment explanation
Indices: 31470718--31470752 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
31470708 GTTACTGTAC
31470718 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
31470753 CACACCTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:31471799 original size:24 final size:24
Alignment explanation
Indices: 31471768--31471816 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
31471758 AATGTGTGTG
*
31471768 TATATATACACACATATATATATA
1 TATATATACACACACATATATATA
31471792 TATATATACACACACATATATATA
1 TATATATACACACACATATATATA
31471816 T
1 T
31471817 GTTCTACCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (24 bp):
TATATATACACACACATATATATA
Found at i:31476912 original size:32 final size:31
Alignment explanation
Indices: 31476844--31476918 Score: 87
Period size: 32 Copynumber: 2.4 Consensus size: 31
31476834 GTGGTACTTG
* * *
31476844 CATGATGACGTGGCATGCCATGTGGCATTGA
1 CATGATGACGTGGCATACCATGTGGCACTAA
* *
31476875 CATGATGACGTGGTAGTACCATGTGGTACTAA
1 CATGATGACGTGGCA-TACCATGTGGCACTAA
*
31476907 TATGATGACGTG
1 CATGATGACGTG
31476919 ATATTGACAT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
31 14 0.38
32 23 0.62
ACGTcount: A:0.25, C:0.16, G:0.31, T:0.28
Consensus pattern (31 bp):
CATGATGACGTGGCATACCATGTGGCACTAA
Found at i:31477675 original size:31 final size:31
Alignment explanation
Indices: 31477640--31477701 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
31477630 TGCAAGCATC
*
31477640 AATTTGGCCAATAATAGTATGTTATGAATTA
1 AATTTAGCCAATAATAGTATGTTATGAATTA
* *
31477671 AATTTAGTCAATGATAGTATGTTATGAATTA
1 AATTTAGCCAATAATAGTATGTTATGAATTA
31477702 TACAGAGACT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.39, C:0.05, G:0.16, T:0.40
Consensus pattern (31 bp):
AATTTAGCCAATAATAGTATGTTATGAATTA
Found at i:31478552 original size:23 final size:23
Alignment explanation
Indices: 31478516--31478595 Score: 97
Period size: 23 Copynumber: 3.5 Consensus size: 23
31478506 GTTTAGAGTT
*
31478516 TGTGAAACGACATGGTGGGAATG
1 TGTGAAACGGCATGGTGGGAATG
*
31478539 TGTGACACGGCATGGTGGGAATG
1 TGTGAAACGGCATGGTGGGAATG
* ** * *
31478562 TGTGACACATCATGGTGAGAATA
1 TGTGAAACGGCATGGTGGGAATG
31478585 TGTGAAACGGC
1 TGTGAAACGGC
31478596 TATGACACGC
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.29, C:0.12, G:0.36, T:0.23
Consensus pattern (23 bp):
TGTGAAACGGCATGGTGGGAATG
Found at i:31478649 original size:23 final size:23
Alignment explanation
Indices: 31478620--31478730 Score: 96
Period size: 23 Copynumber: 4.8 Consensus size: 23
31478610 GTATAATGTT
* * *
31478620 TGTGACACGGCATGGTGGGAATG
1 TGTGACACGTCATGGTGAGAATA
*
31478643 TGTGACACGTCATGTTGAGAATA
1 TGTGACACGTCATGGTGAGAATA
* * * * * *
31478666 TGTGACATGACAAGGTTTAGAGTG
1 TGTGACACGTCATGG-TGAGAATA
* * *
31478690 TGTGACACGCCATGGAGGGAATA
1 TGTGACACGTCATGGTGAGAATA
31478713 TGTGACACGTCATGGTGA
1 TGTGACACGTCATGGTGA
31478731 TAATGTATGA
Statistics
Matches: 65, Mismatches: 22, Indels: 2
0.73 0.25 0.02
Matches are distributed among these distances:
23 48 0.74
24 17 0.26
ACGTcount: A:0.27, C:0.14, G:0.34, T:0.25
Consensus pattern (23 bp):
TGTGACACGTCATGGTGAGAATA
Found at i:31478846 original size:23 final size:23
Alignment explanation
Indices: 31478813--31478869 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
31478803 ATGGTCAGAC
* * *
31478813 GTGTGACACGGCAATGTTATAAT
1 GTGTGACACGGCAAGGTGAGAAT
*
31478836 GTGTGAAACGGCAAGGTGAGAAT
1 GTGTGACACGGCAAGGTGAGAAT
31478859 GTGTGACACGG
1 GTGTGACACGG
31478870 GTGTGATACG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.30, C:0.12, G:0.35, T:0.23
Consensus pattern (23 bp):
GTGTGACACGGCAAGGTGAGAAT
Found at i:31478990 original size:23 final size:23
Alignment explanation
Indices: 31478964--31479018 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
31478954 GGTCAGAACA
*
31478964 TGTGACACGACAGGGTCATAATG
1 TGTGACACGACAGGATCATAATG
* * *
31478987 TGTGAAACGACATGATGATAATG
1 TGTGACACGACAGGATCATAATG
*
31479010 TGCGACACG
1 TGTGACACG
31479019 GGAGTTACAC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.22
Consensus pattern (23 bp):
TGTGACACGACAGGATCATAATG
Found at i:31479237 original size:23 final size:23
Alignment explanation
Indices: 31479171--31479231 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
31479161 TAATCAGACG
*
31479171 TGTGACACGGCATGGGTTGAATA
1 TGTGACACGCCATGGGTTGAATA
*
31479194 TGTGACACTCCATGGGTTGAATA
1 TGTGACACGCCATGGGTTGAATA
31479217 TGTGACACGCCATGG
1 TGTGACACGCCATGG
31479232 TGTGAAAGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (23 bp):
TGTGACACGCCATGGGTTGAATA
Found at i:31479712 original size:55 final size:55
Alignment explanation
Indices: 31479628--31479900 Score: 377
Period size: 55 Copynumber: 5.0 Consensus size: 55
31479618 CGTCTACATA
* * *
31479628 TGGCGTGTTGTGGGTTAATTGGTTTTTTGGGTTTTTAGCTTGTCACGGCTGTTCT
1 TGGCGTGTTGTGGGTTAACTGGTTTTTTGGGTTTTTAGCGTGTCACGGCTGTTCC
* *
31479683 TGGCGTGTTGTAGGTTAACTGGTTTTTTGGGTTTTTAGCGTGTCACGGTTGCTT-C
1 TGGCGTGTTGTGGGTTAACTGGTTTTTTGGGTTTTTAGCGTGTCACGGCTG-TTCC
* * * *
31479738 TGGGGTGTTATGGGTTAACTGATTTTTTGGGTTTTTAGCGTGTCACGGCTGCTCC
1 TGGCGTGTTGTGGGTTAACTGGTTTTTTGGGTTTTTAGCGTGTCACGGCTGTTCC
* ** * * *
31479793 TGGTGTGTCATGGGTTAACTGGTTTTTTAGGTTTTTAGCGTGTCACGACTGCTCC
1 TGGCGTGTTGTGGGTTAACTGGTTTTTTGGGTTTTTAGCGTGTCACGGCTGTTCC
* *
31479848 TGGAGTGTTGTGGGTTAACTGATTTTTTGGGTTTTTAGCGTGTCACGGCTGTT
1 TGGCGTGTTGTGGGTTAACTGGTTTTTTGGGTTTTTAGCGTGTCACGGCTGTT
31479901 GGTGTAACGA
Statistics
Matches: 193, Mismatches: 23, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
54 1 0.01
55 190 0.98
56 2 0.01
ACGTcount: A:0.10, C:0.13, G:0.32, T:0.45
Consensus pattern (55 bp):
TGGCGTGTTGTGGGTTAACTGGTTTTTTGGGTTTTTAGCGTGTCACGGCTGTTCC
Found at i:31479963 original size:25 final size:25
Alignment explanation
Indices: 31479929--31479993 Score: 121
Period size: 25 Copynumber: 2.6 Consensus size: 25
31479919 TTATAGTGAT
31479929 TGGCGTGTCACGACACTGATATGCA
1 TGGCGTGTCACGACACTGATATGCA
31479954 TGGCGTGTCACGACACTGATATGCA
1 TGGCGTGTCACGACACTGATATGCA
*
31479979 TGGTGTGTCACGACA
1 TGGCGTGTCACGACA
31479994 TTTGACTTGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (25 bp):
TGGCGTGTCACGACACTGATATGCA
Found at i:31480008 original size:31 final size:31
Alignment explanation
Indices: 31479970--31480120 Score: 196
Period size: 31 Copynumber: 4.9 Consensus size: 31
31479960 GTCACGACAC
*
31479970 TGATATGCATGGTGTGTCACGACATTTGACT
1 TGATATGCATGGTGTGTCACAACATTTGACT
* *
31480001 TGATATGCATGGCGTGTTACAACATTTGACT
1 TGATATGCATGGTGTGTCACAACATTTGACT
*
31480032 TGATATGCATGGTGTGTCACGACATTTGACT
1 TGATATGCATGGTGTGTCACAACATTTGACT
* * *
31480063 TAATATGCATTGTGTGTTACAACA-TTGTACT
1 TGATATGCATGGTGTGTCACAACATTTG-ACT
* * *
31480094 TGATATGCATGGCGTGTAATAACATTT
1 TGATATGCATGGTGTGTCACAACATTT
31480121 ATTTGTTTCT
Statistics
Matches: 103, Mismatches: 15, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
30 3 0.03
31 98 0.95
32 2 0.02
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.37
Consensus pattern (31 bp):
TGATATGCATGGTGTGTCACAACATTTGACT
Found at i:31480120 original size:62 final size:62
Alignment explanation
Indices: 31479970--31480110 Score: 230
Period size: 62 Copynumber: 2.3 Consensus size: 62
31479960 GTCACGACAC
*
31479970 TGATATGCATGGTGTGTCACGACATTTGACTTGATATGCATGGCGTGTTACAACATTTGACT
1 TGATATGCATGGTGTGTCACGACATTTGACTTAATATGCATGGCGTGTTACAACATTTGACT
* *
31480032 TGATATGCATGGTGTGTCACGACATTTGACTTAATATGCATTGTGTGTTACAACA-TTGTACT
1 TGATATGCATGGTGTGTCACGACATTTGACTTAATATGCATGGCGTGTTACAACATTTG-ACT
*
31480094 TGATATGCATGGCGTGT
1 TGATATGCATGGTGTGT
31480111 AATAACATTT
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
61 3 0.04
62 71 0.96
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (62 bp):
TGATATGCATGGTGTGTCACGACATTTGACTTAATATGCATGGCGTGTTACAACATTTGACT
Found at i:31484024 original size:86 final size:86
Alignment explanation
Indices: 31483903--31484490 Score: 702
Period size: 86 Copynumber: 6.8 Consensus size: 86
31483893 GGGCATGGCT
* * * * * *
31483903 TGTCA-CCCACAATACTGCAATAAGTTAGCGTGTCATGTCAGAAATTTGCATGCACTCAGCGTGT
1 TGTCACCCCACAAGACTGCAACAAGTCAACGTGTCATGTCAGAAGTCTGCATGCACTCAGCGTGT
*
31483967 CACCACAATTGGCCCTTACCA
66 CACCACAATTGGCCCTTGCCA
** * *
31483988 TGTCACCCCACAAGACTATACCAAGTCAACATGTCATG-CTAGAAGTCTGCATGCACTCAGCGTG
1 TGTCACCCCACAAGACTGCAACAAGTCAACGTGTCATGTC-AGAAGTCTGCATGCACTCAGCGTG
* *
31484052 TCACCACAATTGGCCCATGCCG
65 TCACCACAATTGGCCCTTGCCA
* * * * *
31484074 TGTCACCCCACAATATTGCAACAAGTCAACGT-TGCACG-CTAGAAGTCTGCATGCACTCAACAT
1 TGTCACCCCACAAGACTGCAACAAGTCAACGTGT-CATGTC-AGAAGTCTGCATGCACTCAGCGT
*
31484137 GTCACCACAATTGACCCTTG-CA
64 GTCACCACAATTGGCCCTTGCCA
* * * *
31484159 GTGTCACCCCATAAGACTGCAACAAGTCAACGTGTCACGCCAGAAGTCTGCATGCACTTAGCGTG
1 -TGTCACCCCACAAGACTGCAACAAGTCAACGTGTCATGTCAGAAGTCTGCATGCACTCAGCGTG
*
31484224 TCACCACAATTGG-CCTGTGTCA
65 TCACCACAATTGGCCCT-TGCCA
* * * * *
31484246 TGTCACCCCACAATACTGCAACAAGTCAGCGTGTAATGTTAGAAGTCTGCATGCACTCAGTGTGT
1 TGTCACCCCACAAGACTGCAACAAGTCAACGTGTCATGTCAGAAGTCTGCATGCACTCAGCGTGT
* *
31484311 CACCACAATTGGCCCTTGTCG
66 CACCACAATTGGCCCTTGCCA
* * * * *
31484332 TGTCACCCCATAAGACTACAACAAGTCAGCGTGTCATGCCAAAAGTCTGCATGCACTCAGCGTGT
1 TGTCACCCCACAAGACTGCAACAAGTCAACGTGTCATGTCAGAAGTCTGCATGCACTCAGCGTGT
* *
31484397 CACCACAATTGGCCCGTGCCG
66 CACCACAATTGGCCCTTGCCA
* * ** *
31484418 TGTCACCCCACAATATTGCAACAAGTCAACGTGTCACATTAGAAGTCTGCATGCACTCAGCGTGT
1 TGTCACCCCACAAGACTGCAACAAGTCAACGTGTCATGTCAGAAGTCTGCATGCACTCAGCGTGT
31484483 CACCACAA
66 CACCACAA
31484491 GATGTCATTA
Statistics
Matches: 432, Mismatches: 62, Indels: 17
0.85 0.12 0.03
Matches are distributed among these distances:
85 11 0.03
86 414 0.96
87 7 0.02
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (86 bp):
TGTCACCCCACAAGACTGCAACAAGTCAACGTGTCATGTCAGAAGTCTGCATGCACTCAGCGTGT
CACCACAATTGGCCCTTGCCA
Found at i:31484206 original size:172 final size:172
Alignment explanation
Indices: 31483903--31484490 Score: 824
Period size: 172 Copynumber: 3.4 Consensus size: 172
31483893 GGGCATGGCT
* * * * * * * *
31483903 TGTCA-CCCACAATACTGCAATAAGTTAGCGTGTCATGTCAGAAATTTGCATGCACTCAGCGTGT
1 TGTCACCCCACAATATTGCAACAAGTCAACGTGTCACGTTAGAAGTCTGCATGCACTCAGCGTGT
* * * * * *
31483967 CACCACAATTGGCCCTTACCA-TGTCACCCCACAAGACTATACCAAGTCAACATGTCATGCTAGA
66 CACCACAATTGGCCCTT-GCAGTGTCACCCCATAAGACTACAACAAGTCAACGTGTCATGCCAGA
*
31484031 AGTCTGCATGCACTCAGCGTGTCACCACAATTGGCCCATGCCG
130 AGTCTGCATGCACTCAGCGTGTCACCACAATTGGCCCGTGCCG
* * *
31484074 TGTCACCCCACAATATTGCAACAAGTCAACGT-TGCACGCTAGAAGTCTGCATGCACTCAACATG
1 TGTCACCCCACAATATTGCAACAAGTCAACGTGT-CACGTTAGAAGTCTGCATGCACTCAGCGTG
* * *
31484138 TCACCACAATTGACCCTTGCAGTGTCACCCCATAAGACTGCAACAAGTCAACGTGTCACGCCAGA
65 TCACCACAATTGGCCCTTGCAGTGTCACCCCATAAGACTACAACAAGTCAACGTGTCATGCCAGA
* * * *
31484203 AGTCTGCATGCACTTAGCGTGTCACCACAATTGGCCTGTGTCA
130 AGTCTGCATGCACTCAGCGTGTCACCACAATTGGCCCGTGCCG
* * * * *
31484246 TGTCACCCCACAATACTGCAACAAGTCAGCGTGTAATGTTAGAAGTCTGCATGCACTCAGTGTGT
1 TGTCACCCCACAATATTGCAACAAGTCAACGTGTCACGTTAGAAGTCTGCATGCACTCAGCGTGT
* *
31484311 CACCACAATTGGCCCTTGTC-GTGTCACCCCATAAGACTACAACAAGTCAGCGTGTCATGCCAAA
66 CACCACAATTGGCCCTTG-CAGTGTCACCCCATAAGACTACAACAAGTCAACGTGTCATGCCAGA
31484375 AGTCTGCATGCACTCAGCGTGTCACCACAATTGGCCCGTGCCG
130 AGTCTGCATGCACTCAGCGTGTCACCACAATTGGCCCGTGCCG
*
31484418 TGTCACCCCACAATATTGCAACAAGTCAACGTGTCACATTAGAAGTCTGCATGCACTCAGCGTGT
1 TGTCACCCCACAATATTGCAACAAGTCAACGTGTCACGTTAGAAGTCTGCATGCACTCAGCGTGT
31484483 CACCACAA
66 CACCACAA
31484491 GATGTCATTA
Statistics
Matches: 364, Mismatches: 48, Indels: 9
0.86 0.11 0.02
Matches are distributed among these distances:
171 8 0.02
172 354 0.97
173 2 0.01
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (172 bp):
TGTCACCCCACAATATTGCAACAAGTCAACGTGTCACGTTAGAAGTCTGCATGCACTCAGCGTGT
CACCACAATTGGCCCTTGCAGTGTCACCCCATAAGACTACAACAAGTCAACGTGTCATGCCAGAA
GTCTGCATGCACTCAGCGTGTCACCACAATTGGCCCGTGCCG
Found at i:31484380 original size:258 final size:258
Alignment explanation
Indices: 31483903--31484490 Score: 786
Period size: 258 Copynumber: 2.3 Consensus size: 258
31483893 GGGCATGGCT
* * * * * *
31483903 TGTCA-CCCACAATACTGCAATAAGTTAGCGTGTCATGTCAGAAATTTGCATGCACTCAGCGTGT
1 TGTCACCCCACAATACTGCAACAAGTCAACGTGTCACGTCAGAAGTCTGCATGCACTCAGCGTGT
* * *
31483967 CACCACAATTGGCCCTTACCATGTCACCCCACAAGACTATACCAAGTCAACATGTCATGCTAGAA
66 CACCACAATTGGCCCTTACCATGTCACCCCACAAGACTACAACAAGTCAACATGTAATGCTAGAA
* * *
31484032 GTCTGCATGCACTCAGCGTGTCACCACAATTGGCCCATGCCGTGTCACCCCACAATATTGCAACA
131 GTCTGCATGCACTCAGCGTGTCACCACAATTGGCCCATGCCGTGTCACCCCACAAGACTACAACA
* * *
31484097 AGTCAACGTTGCACGCTAGAAGTCTGCATGCACTCAACATGTCACCACAATTGACCCTTGCAG
196 AGTCAACGTTGCACGCCAAAAGTCTGCATGCACTCAACATGTCACCACAATTGACCCGTGCAG
* * * *
31484160 TGTCACCCCATAAGACTGCAACAAGTCAACGTGTCACGCCAGAAGTCTGCATGCACTTAGCGTGT
1 TGTCACCCCACAATACTGCAACAAGTCAACGTGTCACGTCAGAAGTCTGCATGCACTCAGCGTGT
** * * * * *
31484225 CACCACAATTGG-CCTGTGTCATGTCACCCCACAATACTGCAACAAGTCAGCGTGTAATGTTAGA
66 CACCACAATTGGCCCT-TACCATGTCACCCCACAAGACTACAACAAGTCAACATGTAATGCTAGA
* * * *
31484289 AGTCTGCATGCACTCAGTGTGTCACCACAATTGGCCCTTGTCGTGTCACCCCATAAGACTACAAC
130 AGTCTGCATGCACTCAGCGTGTCACCACAATTGGCCCATGCCGTGTCACCCCACAAGACTACAAC
* * * * * *
31484354 AAGTCAGCG-TGTCATGCCAAAAGTCTGCATGCACTCAGCGTGTCACCACAATTGGCCCGTGCCG
195 AAGTCAACGTTG-CACGCCAAAAGTCTGCATGCACTCAACATGTCACCACAATTGACCCGTGCAG
* * *
31484418 TGTCACCCCACAATATTGCAACAAGTCAACGTGTCACATTAGAAGTCTGCATGCACTCAGCGTGT
1 TGTCACCCCACAATACTGCAACAAGTCAACGTGTCACGTCAGAAGTCTGCATGCACTCAGCGTGT
31484483 CACCACAA
66 CACCACAA
31484491 GATGTCATTA
Statistics
Matches: 285, Mismatches: 43, Indels: 5
0.86 0.13 0.02
Matches are distributed among these distances:
257 10 0.04
258 275 0.96
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (258 bp):
TGTCACCCCACAATACTGCAACAAGTCAACGTGTCACGTCAGAAGTCTGCATGCACTCAGCGTGT
CACCACAATTGGCCCTTACCATGTCACCCCACAAGACTACAACAAGTCAACATGTAATGCTAGAA
GTCTGCATGCACTCAGCGTGTCACCACAATTGGCCCATGCCGTGTCACCCCACAAGACTACAACA
AGTCAACGTTGCACGCCAAAAGTCTGCATGCACTCAACATGTCACCACAATTGACCCGTGCAG
Found at i:31488060 original size:31 final size:31
Alignment explanation
Indices: 31488007--31488332 Score: 512
Period size: 31 Copynumber: 10.5 Consensus size: 31
31487997 TTTGTCAGTC
* *
31488007 ATGTTGTTACACACCATGCATATAACGTAAA
1 ATGTTGTAACACGCCATGCATATAACGTAAA
* * *
31488038 ATGTTGCAACACGCCATACATATAATGTAAA
1 ATGTTGTAACACGCCATGCATATAACGTAAA
31488069 ATGTTGTAACACGCCATGCATATAACGTAAA
1 ATGTTGTAACACGCCATGCATATAACGTAAA
* *
31488100 ATGTGGTAACACGCCATGCATATAATAGT-AA
1 ATGTTGTAACACGCCATGCATATAA-CGTAAA
31488131 ATGTTAGTAACACGCCATGCATATAACGT-AA
1 ATGTT-GTAACACGCCATGCATATAACGTAAA
*
31488162 ATGTGGTAACACGCCATGCATATAACGTAAA
1 ATGTTGTAACACGCCATGCATATAACGTAAA
31488193 ATGTTGTAACACGCCATGCATATAACGTAAA
1 ATGTTGTAACACGCCATGCATATAACGTAAA
*
31488224 ATGTTGTAACACGCCATGCATATAATGTAAA
1 ATGTTGTAACACGCCATGCATATAACGTAAA
*
31488255 ATATTGTAACACGCCATGCATATAACGTAAA
1 ATGTTGTAACACGCCATGCATATAACGTAAA
*
31488286 ATGTTGTAACTCGCCATGCATATAACGTAAA
1 ATGTTGTAACACGCCATGCATATAACGTAAA
*
31488317 ATGTTGTAACATGCCA
1 ATGTTGTAACACGCCA
31488333 ACGCTGACAC
Statistics
Matches: 271, Mismatches: 21, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
30 23 0.08
31 226 0.83
32 22 0.08
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.27
Consensus pattern (31 bp):
ATGTTGTAACACGCCATGCATATAACGTAAA
Found at i:31491466 original size:10 final size:9
Alignment explanation
Indices: 31491427--31491460 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
31491417 GTTACTGTAG
*
31491427 AAGAAAGAA
1 AAGAAAAAA
31491436 AAGAAAGAAA
1 AAGAAA-AAA
31491446 AAGAAAAAA
1 AAGAAAAAA
31491455 AAGAAA
1 AAGAAA
31491461 TTAAAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:31491819 original size:16 final size:16
Alignment explanation
Indices: 31491782--31491841 Score: 52
Period size: 16 Copynumber: 3.7 Consensus size: 16
31491772 TATTTTAAAT
*
31491782 AAATTTTAAATTATTA
1 AAATTTTAAATTATAA
*
31491798 ATATTTTAATATT-TAA
1 AAATTTTAA-ATTATAA
*
31491814 AAATTTTAAAATAGTGAA
1 AAATTTTAAATTA-T-AA
31491832 AAA-TTTAAAT
1 AAATTTTAAAT
31491842 AAAAAATAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
15 2 0.06
16 18 0.51
17 10 0.29
18 5 0.14
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
AAATTTTAAATTATAA
Found at i:31491854 original size:208 final size:203
Alignment explanation
Indices: 31491575--31492176 Score: 747
Period size: 205 Copynumber: 3.0 Consensus size: 203
31491565 AAATTTCTAA
* *
31491575 TATTTTAAACAAATTATAAATTATTAATATTTTAATATTTAAAAATT-----T--A-AAAAA-TA
1 TATTTTAAATAAATTATTAATTATTAATATTTTAATATTTAAAAATTAAAAATAGAGAAAAATTA
*
31491631 GAA-AAAAATTAAATGATCATATTAAAATTTTAATTAAAAATTATTAATATTTTAATAAATTATA
66 -AATAAAAAATAAATGATCATATTAAAATTTTAATTAAAAATTATTAATATTTTAATAAATTATA
*
31491695 AAAATAAATATTTCAATTAAAAAGGATAAATTATAATAAAAATATATTTATATCTTTTTTATCAC
130 AAAAT-AATATTTCAATTAAAAA-CATAAATTATAATAAAAAT-TATTTATATCTTTTTTATCAC
31491760 TTAATATTTTGT
192 TTAATATTTTGT
* *
31491772 TATTTTAAATAAATT-TTAAATTATTAATATTTTAATATTTAAAAATTTTAAAATAGTGAAAAAT
1 TATTTTAAATAAATTATT-AATTATTAATATTTTAATATTTAAAAA-TTAAAAATAGAGAAAAA-
* * ** * *
31491836 TTAAATAAAAAATAAATGATGATATTGAACCTGTAATTAAAAATTATTAATATTTTAATAAAATA
63 TTAAATAAAAAATAAATGATCATATTAAAATTTTAATTAAAAATTATTAATATTTTAAT-AAATT
* * *
31491901 ATAAAAATGATGTTTCAA--AAAAACATAAATTATAGTAAAAATGTATTTATATCTTTTTTATCA
127 ATAAAAATAATATTTCAATTAAAAACATAAATTATAATAAAAAT-TATTTATATCTTTTTTATCA
31491964 CTTAATATTTTGT
191 CTTAATATTTTGT
* *
31491977 TTTTTTAAATAAATTATTAATTATTAATATTTTTATATTTAAAAATTAAAAATAGAGAAAAATTA
1 TATTTTAAATAAATTATTAATTATTAATATTTTAATATTTAAAAATTAAAAATAGAGAAAAATTA
* * * * * *
31492042 AAT-AAAAATAAATGATCATGTTAATATTTTTATTAGAAATTATTAACATTTTAATATATTA-AA
66 AATAAAAAATAAATGATCATATTAAAATTTTAATTAAAAATTATTAATATTTTAATAAATTATAA
*
31492105 AAATAATATTTCAAATTAAAAAACATAAATTATAAT-AAAATTA--TATAT-ATTTTTATCACTT
131 AAATAATATTTC-AATT-AAAAACATAAATTATAATAAAAATTATTTATATCTTTTTTATCACTT
*
31492166 AATCTTTTGT
194 AATATTTTGT
31492176 T
1 T
31492177 CTTTCAAAGC
Statistics
Matches: 350, Mismatches: 36, Indels: 36
0.83 0.09 0.09
Matches are distributed among these distances:
196 1 0.00
197 41 0.12
198 2 0.01
199 22 0.06
200 17 0.05
201 6 0.02
202 44 0.13
203 12 0.03
204 32 0.09
205 90 0.26
206 12 0.03
207 2 0.01
208 57 0.16
209 12 0.03
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.43
Consensus pattern (203 bp):
TATTTTAAATAAATTATTAATTATTAATATTTTAATATTTAAAAATTAAAAATAGAGAAAAATTA
AATAAAAAATAAATGATCATATTAAAATTTTAATTAAAAATTATTAATATTTTAATAAATTATAA
AAATAATATTTCAATTAAAAACATAAATTATAATAAAAATTATTTATATCTTTTTTATCACTTAA
TATTTTGT
Found at i:31495192 original size:1 final size:1
Alignment explanation
Indices: 31495186--31495219 Score: 59
Period size: 1 Copynumber: 34.0 Consensus size: 1
31495176 NNNNCTATTT
*
31495186 CCCCCCCCCCCCCCCCCCCCCCCCCCCGCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
31495220 ATCTTAACAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.97, G:0.03, T:0.00
Consensus pattern (1 bp):
C
Found at i:31503610 original size:18 final size:19
Alignment explanation
Indices: 31503587--31503632 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 19
31503577 GGCACCTCTA
31503587 TTTTTTTGTCTTG-TTTTG
1 TTTTTTTGTCTTGTTTTTG
*
31503605 -TTTTTTGTTTTTGTTTTTG
1 TTTTTTTG-TCTTGTTTTTG
31503624 TTTTTTTGT
1 TTTTTTTGT
31503633 GATGACCAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 7 0.29
18 4 0.17
19 6 0.25
20 7 0.29
ACGTcount: A:0.00, C:0.02, G:0.15, T:0.83
Consensus pattern (19 bp):
TTTTTTTGTCTTGTTTTTG
Found at i:31506082 original size:36 final size:36
Alignment explanation
Indices: 31506035--31506103 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
31506025 TCTTCCAGAG
* *
31506035 GTTAGTGCTGCATG-TTTTCTAAACTTGGTTGCTCCT
1 GTTAGGGCTGCA-GCTTTCCTAAACTTGGTTGCTCCT
*
31506071 GTTAGGGCTGCAGCTTTCCTAGACTTGGTTGCT
1 GTTAGGGCTGCAGCTTTCCTAAACTTGGTTGCT
31506104 GGTCTTGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 1 0.03
36 28 0.97
ACGTcount: A:0.13, C:0.20, G:0.26, T:0.41
Consensus pattern (36 bp):
GTTAGGGCTGCAGCTTTCCTAAACTTGGTTGCTCCT
Found at i:31518773 original size:23 final size:23
Alignment explanation
Indices: 31518743--31518790 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
31518733 TCTGACATGG
*
31518743 CTTTTAACTCATTTAGAATGTTT
1 CTTTTAACTCATTCAGAATGTTT
31518766 CTTTTAACTCATTCAGAATGTTT
1 CTTTTAACTCATTCAGAATGTTT
31518789 CT
1 CT
31518791 GGTTATTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.25, C:0.17, G:0.08, T:0.50
Consensus pattern (23 bp):
CTTTTAACTCATTCAGAATGTTT
Found at i:31522489 original size:53 final size:54
Alignment explanation
Indices: 31522416--31522519 Score: 149
Period size: 53 Copynumber: 1.9 Consensus size: 54
31522406 ATTCTCTTAC
* * *
31522416 AAATGATGAGATTAATCCCTTAAAAGG-TGTGGCTA-ATCATTATCCTAGAGTAT
1 AAATAATGAGACTAACCCCTTAAAAGGTTGTGGC-AGATCATTATCCTAGAGTAT
*
31522469 AAATAATGAGACTAACCCCTTAAAAGGTTTTGGCAGATCATTATCCTAGAG
1 AAATAATGAGACTAACCCCTTAAAAGGTTGTGGCAGATCATTATCCTAGAG
31522520 GTTACAAAGA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
53 25 0.56
54 20 0.44
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (54 bp):
AAATAATGAGACTAACCCCTTAAAAGGTTGTGGCAGATCATTATCCTAGAGTAT
Found at i:31553846 original size:35 final size:34
Alignment explanation
Indices: 31553761--31553852 Score: 89
Period size: 35 Copynumber: 2.6 Consensus size: 34
31553751 AAAAAAATAA
* *
31553761 TAAAAAATATCTTGATAAATTAATTTTTTATTAAT
1 TAAATAATATCTTGATAAATT-ATTATTTATTAAT
* *
31553796 T-AAT-GTATGAATTGATAAATTATTAATTTATTAAT
1 TAAATAATAT--CTTGATAAATTATT-ATTTATTAAT
*
31553831 TAAATAATATCTTGATTAATTA
1 TAAATAATATCTTGATAAATTA
31553853 ATAAATTTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
33 3 0.07
34 5 0.11
35 31 0.69
36 3 0.07
37 3 0.07
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (34 bp):
TAAATAATATCTTGATAAATTATTATTTATTAAT
Found at i:31555022 original size:28 final size:28
Alignment explanation
Indices: 31554991--31555227 Score: 167
Period size: 27 Copynumber: 8.6 Consensus size: 28
31554981 CATCGTAACG
* *
31554991 TGTAATAACTACATTTTTCAACATAGCA
1 TGTAACAACTACATTTTTCAACATGGCA
* * **
31555019 TGTAACAATTA-AATTTTCAACATTACA
1 TGTAACAACTACATTTTTCAACATGGCA
* * *
31555046 TGTAACACCTACATTTTTCAATATGGCG
1 TGTAACAACTACATTTTTCAACATGGCA
* * * * **
31555074 TGTAATAACTA-AATCTTCAATATGGTG
1 TGTAACAACTACATTTTTCAACATGGCA
* * * *
31555101 TATAACAATTAGATTTTTCAACATGACA
1 TGTAACAACTACATTTTTCAACATGGCA
* * ***
31555129 TGTAACAATTAGA-TTTTCAACATGATG
1 TGTAACAACTACATTTTTCAACATGGCA
* *
31555156 TGTAACAATTACATTTTTCAACATGGCG
1 TGTAACAACTACATTTTTCAACATGGCA
* ***
31555184 TGTAACAACTAAATTTTT-AACATGATG
1 TGTAACAACTACATTTTTCAACATGGCA
*
31555211 TGTAACAACTATATTTT
1 TGTAACAACTACATTTT
31555228 CAAAAAGATT
Statistics
Matches: 169, Mismatches: 37, Indels: 7
0.79 0.17 0.03
Matches are distributed among these distances:
27 90 0.53
28 79 0.47
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.37
Consensus pattern (28 bp):
TGTAACAACTACATTTTTCAACATGGCA
Found at i:31555058 original size:55 final size:55
Alignment explanation
Indices: 31554990--31555227 Score: 269
Period size: 55 Copynumber: 4.3 Consensus size: 55
31554980 TCATCGTAAC
* * * * *
31554990 GTGTAATAACTACATTTTTCAACATAGCATGTAACAATTAAATTTTCAACATTAC
1 GTGTAACAACTACATTTTTCAACATGGCATGTAACAACTAAATTTTCAACATGAT
* * * * * * * *
31555045 ATGTAACACCTACATTTTTCAATATGGCGTGTAATAACTAAATCTTCAATATGGT
1 GTGTAACAACTACATTTTTCAACATGGCATGTAACAACTAAATTTTCAACATGAT
* * * * * *
31555100 GTATAACAATTAGATTTTTCAACATGACATGTAACAATTAGATTTTCAACATGAT
1 GTGTAACAACTACATTTTTCAACATGGCATGTAACAACTAAATTTTCAACATGAT
* * *
31555155 GTGTAACAATTACATTTTTCAACATGGCGTGTAACAACTAAATTTTTAACATGAT
1 GTGTAACAACTACATTTTTCAACATGGCATGTAACAACTAAATTTTCAACATGAT
*
31555210 GTGTAACAACTATATTTT
1 GTGTAACAACTACATTTT
31555228 CAAAAAGATT
Statistics
Matches: 147, Mismatches: 36, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
55 147 1.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (55 bp):
GTGTAACAACTACATTTTTCAACATGGCATGTAACAACTAAATTTTCAACATGAT
Found at i:31555217 original size:110 final size:110
Alignment explanation
Indices: 31554997--31555227 Score: 302
Period size: 110 Copynumber: 2.1 Consensus size: 110
31554987 AACGTGTAAT
* * *
31554997 AACTACATTTTTCAACATAGCATGTAACAATTAAATTTTCAACATTACATGTAACACCTACATTT
1 AACTAGATTTTTCAACATAGCATGTAACAATTAAATTTTCAACATGACATGTAACAACTACATTT
* * * *
31555062 TTCAATATGGCGTGTAATAACTAAATCTTCAATATGGTGTATAAC
66 TTCAACATGGCGTGTAACAACTAAATCTTCAACATGATGTATAAC
* * ** *
31555107 AATTAGATTTTTCAACAT-GACATGTAACAATTAGATTTTCAACATGATGTGTAACAATTACATT
1 AACTAGATTTTTCAACATAG-CATGTAACAATTAAATTTTCAACATGACATGTAACAACTACATT
* * *
31555171 TTTCAACATGGCGTGTAACAACTAAATTTTTAACATGATGTGTAAC
65 TTTCAACATGGCGTGTAACAACTAAATCTTCAACATGATGTATAAC
*
31555217 AACTATATTTT
1 AACTAGATTTT
31555228 CAAAAAGATT
Statistics
Matches: 103, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
109 1 0.01
110 102 0.99
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (110 bp):
AACTAGATTTTTCAACATAGCATGTAACAATTAAATTTTCAACATGACATGTAACAACTACATTT
TTCAACATGGCGTGTAACAACTAAATCTTCAACATGATGTATAAC
Found at i:31555390 original size:2 final size:2
Alignment explanation
Indices: 31555383--31555418 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
31555373 GTGTTAAGAA
31555383 AT AT AT 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
31555419 TCTTAATTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31558388 original size:26 final size:26
Alignment explanation
Indices: 31558358--31558438 Score: 117
Period size: 26 Copynumber: 3.1 Consensus size: 26
31558348 ACATCATTGA
* **
31558358 AAACCCCACTAAGGTGAAAAATTGCC
1 AAACCCTACTAAGGTGAAAAATAACC
*
31558384 AAACCCTACTAAGGTGAAAAACAACC
1 AAACCCTACTAAGGTGAAAAATAACC
*
31558410 AAACCATACTAAGGTGAAAAATAACC
1 AAACCCTACTAAGGTGAAAAATAACC
31558436 AAA
1 AAA
31558439 ATCCTATTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 49 1.00
ACGTcount: A:0.51, C:0.23, G:0.12, T:0.14
Consensus pattern (26 bp):
AAACCCTACTAAGGTGAAAAATAACC
Found at i:31558839 original size:158 final size:158
Alignment explanation
Indices: 31558551--31558867 Score: 526
Period size: 158 Copynumber: 2.0 Consensus size: 158
31558541 AATTCTCAGC
* *
31558551 TTGAATGTGAATAATAACTAAGCCTGAGGGTCCTATTTATAGTATTATAGGCCCATGTCTTAATA
1 TTGAATGAGAATAATAACTAAGCCTAAGGGTCCTATTTATAGTATTATAGGCCCATGTCTTAATA
* * * * *
31558616 AAACTCTACTTCTAGTTGTTTACTACAATTAAAATAGTTAACAAGAGATTTAAATAAAGTACAAC
66 AAACTCTACTTCTAATTGTCTAATACAATTAAAATAGTTAACAAAAGATTTAAATAAAATACAAC
*
31558681 ATGACTAGTCTAATCAAATAATAGTCTT
131 ATGACTAGCCTAATCAAATAATAGTCTT
* **
31558709 TTGAATGAGAATAATAACTAAGCCTAATGGTCCTATTTATAGTATTATAGGCTTATGTCTTAATA
1 TTGAATGAGAATAATAACTAAGCCTAAGGGTCCTATTTATAGTATTATAGGCCCATGTCTTAATA
31558774 AAACTCTACTTCTAATTGTCTAATACAATTAAAATAGTTAACAAAAGATTTAAATAAAATACAAC
66 AAACTCTACTTCTAATTGTCTAATACAATTAAAATAGTTAACAAAAGATTTAAATAAAATACAAC
*
31558839 ATGATTAGCCTAATCAAATAATAGTCTT
131 ATGACTAGCCTAATCAAATAATAGTCTT
31558867 T
1 T
31558868 AAAAGTATTA
Statistics
Matches: 147, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
158 147 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (158 bp):
TTGAATGAGAATAATAACTAAGCCTAAGGGTCCTATTTATAGTATTATAGGCCCATGTCTTAATA
AAACTCTACTTCTAATTGTCTAATACAATTAAAATAGTTAACAAAAGATTTAAATAAAATACAAC
ATGACTAGCCTAATCAAATAATAGTCTT
Found at i:31558962 original size:19 final size:18
Alignment explanation
Indices: 31558938--31558974 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
31558928 AATAAATCCT
*
31558938 AAATTAACTAAAATTAAAA
1 AAATTAAATAAAA-TAAAA
31558957 AAATTAAATAAAATAAAA
1 AAATTAAATAAAATAAAA
31558975 TACAATCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (18 bp):
AAATTAAATAAAATAAAA
Found at i:31558975 original size:10 final size:10
Alignment explanation
Indices: 31558938--31558976 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
31558928 AATAAATCCT
*
31558938 AAATTAACTA
1 AAATTAAATA
31558948 AAATTAAA-A
1 AAATTAAATA
31558957 AAATTAAATA
1 AAATTAAATA
*
31558967 AAATAAAATA
1 AAATTAAATA
31558977 CAATCATAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
9 9 0.35
10 17 0.65
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (10 bp):
AAATTAAATA
Found at i:31560310 original size:23 final size:21
Alignment explanation
Indices: 31560271--31560316 Score: 65
Period size: 23 Copynumber: 2.1 Consensus size: 21
31560261 CCACTAGCTT
*
31560271 AATTATTTATATCTTGGTTGC
1 AATTATTTATATATTGGTTGC
31560292 AATTATATTATATTATTGGTTGC
1 AATTAT-TTATA-TATTGGTTGC
31560315 AA
1 AA
31560317 GCTATATTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.27
22 5 0.23
23 11 0.50
ACGTcount: A:0.30, C:0.07, G:0.13, T:0.50
Consensus pattern (21 bp):
AATTATTTATATATTGGTTGC
Found at i:31564355 original size:2 final size:2
Alignment explanation
Indices: 31564348--31564397 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
31564338 TTGTTTGAAC
31564348 AT AT AT AT AT AT 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 AT AT AT
31564390 AT AT AT AT
1 AT AT AT AT
31564398 GCATAAAAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31565321 original size:29 final size:29
Alignment explanation
Indices: 31565288--31565352 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 29
31565278 CTACTTTTAC
* *
31565288 CTTCTTCTCTTGTACCTGTTCATGTACAA
1 CTTCTTCTCTTGTACCTATTCACGTACAA
* *
31565317 CTTCTTTTCTTGTACCTATTCACGTACAG
1 CTTCTTCTCTTGTACCTATTCACGTACAA
31565346 C-TCTTCT
1 CTTCTTCT
31565353 TTATTAGCTC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
28 5 0.16
29 26 0.84
ACGTcount: A:0.15, C:0.29, G:0.09, T:0.46
Consensus pattern (29 bp):
CTTCTTCTCTTGTACCTATTCACGTACAA
Found at i:31566964 original size:10 final size:10
Alignment explanation
Indices: 31566944--31566984 Score: 59
Period size: 10 Copynumber: 4.2 Consensus size: 10
31566934 ATACAATTAT
31566944 TATATTAAAAA
1 TATA-TAAAAA
31566955 TATATAAAAA
1 TATATAAAAA
31566965 T-TA-AAAAA
1 TATATAAAAA
31566973 TATATAAAAA
1 TATATAAAAA
31566983 TA
1 TA
31566985 AAAAATAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
8 6 0.21
9 4 0.14
10 14 0.50
11 4 0.14
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
TATATAAAAA
Found at i:31566973 original size:18 final size:17
Alignment explanation
Indices: 31566950--31566991 Score: 75
Period size: 18 Copynumber: 2.4 Consensus size: 17
31566940 TTATTATATT
31566950 AAAAATATATAAAAATTA
1 AAAAATATATAAAAA-TA
31566968 AAAAATATATAAAAATA
1 AAAAATATATAAAAATA
31566985 AAAAATA
1 AAAAATA
31566992 ATTAATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAAATATATAAAAATA
Found at i:31571502 original size:2 final size:2
Alignment explanation
Indices: 31571495--31571585 Score: 82
Period size: 2 Copynumber: 46.0 Consensus size: 2
31571485 GGAGAATGGA
*
31571495 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
31571536 AT ANC AA ACT -T GGT GT AT AT -T AT AT AT AT AT AT -T AT AT AT
1 AT A-T AT A-T AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31571576 AT AT AT AT AT
1 AT AT AT AT AT
31571586 TATGTTTTTC
Statistics
Matches: 76, Mismatches: 6, Indels: 14
0.79 0.06 0.15
Matches are distributed among these distances:
1 4 0.05
2 70 0.92
3 2 0.03
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31571569 original size:13 final size:13
Alignment explanation
Indices: 31571551--31571585 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
31571541 AAACTTGGTG
31571551 TATATTATATATA
1 TATATTATATATA
31571564 TATATTATATATA
1 TATATTATATATA
31571577 TATA-TATAT
1 TATATTATAT
31571586 TATGTTTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 5 0.23
13 17 0.77
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATTATATATA
Found at i:31571576 original size:15 final size:15
Alignment explanation
Indices: 31571551--31571588 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
31571541 AAACTTGGTG
31571551 TATATTATATATATA
1 TATATTATATATATA
31571566 TAT-TATATATATATA
1 TATAT-TATATATATA
31571581 TATATTAT
1 TATATTAT
31571589 GTTTTTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 1 0.05
15 19 0.90
16 1 0.05
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATATTATATATATA
Found at i:31575157 original size:21 final size:22
Alignment explanation
Indices: 31575127--31575170 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
31575117 TTTCTTAACT
31575127 CCTTAATTTGGTGCAACGTTCA
1 CCTTAATTTGGTGCAACGTTCA
*
31575149 CCTT-ATTTGGTGCAATGTTCA
1 CCTTAATTTGGTGCAACGTTCA
31575170 C
1 C
31575171 TTTACTCCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.39
Consensus pattern (22 bp):
CCTTAATTTGGTGCAACGTTCA
Found at i:31582251 original size:27 final size:27
Alignment explanation
Indices: 31582209--31582260 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
31582199 GGTAGGTAAT
31582209 TAATTAAGTTGATAGAAGCGTGCTTAC
1 TAATTAAGTTGATAGAAGCGTGCTTAC
*
31582236 TAATTAAGTTGGTAGAAGCGTGCTT
1 TAATTAAGTTGATAGAAGCGTGCTT
31582261 TGTATTAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.31, C:0.10, G:0.25, T:0.35
Consensus pattern (27 bp):
TAATTAAGTTGATAGAAGCGTGCTTAC
Found at i:31585473 original size:16 final size:16
Alignment explanation
Indices: 31585452--31585484 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
31585442 CGGTTTATCT
31585452 TTATTTTTTTTATTTG
1 TTATTTTTTTTATTTG
*
31585468 TTATTTTTTTTCTTTG
1 TTATTTTTTTTATTTG
31585484 T
1 T
31585485 CTATCAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.09, C:0.03, G:0.06, T:0.82
Consensus pattern (16 bp):
TTATTTTTTTTATTTG
Found at i:31598638 original size:27 final size:27
Alignment explanation
Indices: 31598599--31598653 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
31598589 CACAATAACC
31598599 TGGACACAGGATAAGCACCCGAGCATT
1 TGGACACAGGATAAGCACCCGAGCATT
* *
31598626 TGGACAC-GTGATAGGCATCCGAGCATT
1 TGGACACAG-GATAAGCACCCGAGCATT
31598653 T
1 T
31598654 AGCTCATTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 1 0.04
27 24 0.96
ACGTcount: A:0.29, C:0.24, G:0.27, T:0.20
Consensus pattern (27 bp):
TGGACACAGGATAAGCACCCGAGCATT
Found at i:31601997 original size:18 final size:18
Alignment explanation
Indices: 31601971--31602007 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
31601961 ATTGCATAAG
31601971 TTAACAATGCAAAAAACC
1 TTAACAATGCAAAAAACC
*
31601989 TTAAGAATGCAAAAAACC
1 TTAACAATGCAAAAAACC
31602007 T
1 T
31602008 CTTTCATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.54, C:0.19, G:0.08, T:0.19
Consensus pattern (18 bp):
TTAACAATGCAAAAAACC
Found at i:31609366 original size:2 final size:2
Alignment explanation
Indices: 31609359--31609472 Score: 171
Period size: 2 Copynumber: 57.5 Consensus size: 2
31609349 GGAGCATGGA
31609359 AT AT AT AT AT AT 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 AT AT AT
**
31609401 AT AT AT AT NGG AGT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT -AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31609444 AT AT AT AT AT AT -T AT AT AT -T AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
31609473 GTTTGTTTTC
Statistics
Matches: 103, Mismatches: 4, Indels: 10
0.88 0.03 0.09
Matches are distributed among these distances:
1 3 0.03
2 99 0.96
3 1 0.01
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:31610027 original size:24 final size:24
Alignment explanation
Indices: 31609982--31610027 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
31609972 CCATAACAAA
* *
31609982 CCAAGAAAAGCCCAATCTTCTAAG
1 CCAAGAAAAGCCCAACCCTCTAAG
* *
31610006 CCAAGAGAGGCCCAACCCTCTA
1 CCAAGAAAAGCCCAACCCTCTA
31610028 GAAGACCATG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.37, C:0.35, G:0.15, T:0.13
Consensus pattern (24 bp):
CCAAGAAAAGCCCAACCCTCTAAG
Found at i:31611906 original size:21 final size:22
Alignment explanation
Indices: 31611852--31611908 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
31611842 TAATCACCGT
* *
31611852 GTGACTAGTTTTTAGTCATTAC
1 GTGACTAGATTTTAGCCATTAC
*
31611874 GTGA-TTGATTTTAGCCATTAC
1 GTGACTAGATTTTAGCCATTAC
*
31611895 GTGACTAGTTTTTA
1 GTGACTAGATTTTA
31611909 TACATTGCAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.46
Consensus pattern (22 bp):
GTGACTAGATTTTAGCCATTAC
Found at i:31611980 original size:23 final size:23
Alignment explanation
Indices: 31611942--31612264 Score: 173
Period size: 26 Copynumber: 13.7 Consensus size: 23
31611932 GCAATGCCTA
* * *
31611942 AGTCACACGATGCCTTACGAACT
1 AGTCACGCAATGCCTTACTAACT
* *
31611965 AGTCACGCAATACCTTACTAACA
1 AGTCACGCAATGCCTTACTAACT
* *
31611988 AGTCACACGATGCCTTACTAA-T
1 AGTCACGCAATGCCTTACTAACT
*
31612010 AAGTCACGCAATGCCTTACTAACA
1 -AGTCACGCAATGCCTTACTAACT
*
31612034 AGTCACGCAATGTC-TA-TCAACT
1 AGTCACGCAATGCCTTACT-AACT
* * *
31612056 AGTCATGCAATACCTTATCAGAAACT
1 AGTCACGCAATGCCTTA-C--TAACT
*
31612082 AGTCACGCAATGCCTTATCAAAAACT
1 AGTCACGCAATGCCTTA-C--TAACT
* *
31612108 AGTCACGCAATGCC---CAAAGTT
1 AGTCACGCAATGCCTTACTAA-CT
* * *
31612129 AGTCATGCAATGCTTTATTAGAAACT
1 AGTCACGCAATGCCTTACT---AACT
31612155 AGTCACGCAATGCCTTA-TAAAAACCT
1 AGTCACGCAATGCCTTACT---AA-CT
* *
31612181 AGTCACGCAATGCC---CAAAGT
1 AGTCACGCAATGCCTTACTAACT
* *
31612201 CAGTCACGTAATGCC-TATTAACT
1 -AGTCACGCAATGCCTTACTAACT
* *
31612224 AGTCACACAATGCCTTATCAGAAACT
1 AGTCACGCAATGCCTTA-C--TAACT
31612250 AGTCACGCAATGCCT
1 AGTCACGCAATGCCT
31612265 CATCAAAAAT
Statistics
Matches: 235, Mismatches: 41, Indels: 45
0.73 0.13 0.14
Matches are distributed among these distances:
20 4 0.02
21 29 0.12
22 29 0.12
23 75 0.32
25 5 0.02
26 91 0.39
27 2 0.01
ACGTcount: A:0.35, C:0.27, G:0.14, T:0.24
Consensus pattern (23 bp):
AGTCACGCAATGCCTTACTAACT
Found at i:31612015 original size:46 final size:46
Alignment explanation
Indices: 31611941--31612072 Score: 171
Period size: 46 Copynumber: 2.9 Consensus size: 46
31611931 AGCAATGCCT
31611941 AAGTCACACGATGCCTTACGAACTAGTCACGCAATACCTTACTAAC
1 AAGTCACACGATGCCTTACGAACTAGTCACGCAATACCTTACTAAC
* *
31611987 AAGTCACACGATGCCTTACTAA-TAAGTCACGCAATGCCTTACTAAC
1 AAGTCACACGATGCCTTACGAACT-AGTCACGCAATACCTTACTAAC
* * * *
31612033 AAGTCACGCAATGTC-TATC-AACTAGTCATGCAATACCTTA
1 AAGTCACACGATGCCTTA-CGAACTAGTCACGCAATACCTTA
31612073 TCAGAAACTA
Statistics
Matches: 76, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
45 20 0.26
46 56 0.74
ACGTcount: A:0.35, C:0.28, G:0.13, T:0.24
Consensus pattern (46 bp):
AAGTCACACGATGCCTTACGAACTAGTCACGCAATACCTTACTAAC
Found at i:31612081 original size:26 final size:26
Alignment explanation
Indices: 31612011--31612382 Score: 198
Period size: 26 Copynumber: 15.5 Consensus size: 26
31612001 CTTACTAATA
* *
31612011 AGTCACGCAATGCCTTA-C--TAACA
1 AGTCACGCAATGCCTTATCAAAAACT
*
31612034 AGTCACGCAATGTC-TATC---AACT
1 AGTCACGCAATGCCTTATCAAAAACT
* * *
31612056 AGTCATGCAATACCTTATCAGAAACT
1 AGTCACGCAATGCCTTATCAAAAACT
31612082 AGTCACGCAATGCCTTATCAAAAACT
1 AGTCACGCAATGCCTTATCAAAAACT
**
31612108 AGTCACGCAATGCC----C-AAAGTT
1 AGTCACGCAATGCCTTATCAAAAACT
* * * *
31612129 AGTCATGCAATGCTTTATTAGAAACT
1 AGTCACGCAATGCCTTATCAAAAACT
31612155 AGTCACGCAATGCCTTAT-AAAAACCT
1 AGTCACGCAATGCCTTATCAAAAA-CT
**
31612181 AGTCACGCAATGCC----CAAAGTC-
1 AGTCACGCAATGCCTTATCAAAAACT
* *
31612202 AGTCACGTAATGCC-TAT---TAACT
1 AGTCACGCAATGCCTTATCAAAAACT
* *
31612224 AGTCACACAATGCCTTATCAGAAACT
1 AGTCACGCAATGCCTTATCAAAAACT
*
31612250 AGTCACGCAATGCCTCATCAAAAA-T
1 AGTCACGCAATGCCTTATCAAAAACT
* * * ***
31612275 CAATCACGTAATACC----CAAGGTC-
1 -AGTCACGCAATGCCTTATCAAAAACT
* * *
31612297 AGTCACACAATACC-TAT---TAACT
1 AGTCACGCAATGCCTTATCAAAAACT
*
31612319 AGTCATGCAATGCCTTATCAAAAACT
1 AGTCACGCAATGCCTTATCAAAAACT
**
31612345 AGTCACATAATGCCTTATCAAAAA-T
1 AGTCACGCAATGCCTTATCAAAAACT
*
31612370 CAGTCACGTAATG
1 -AGTCACGCAATG
31612383 TTCAAAGTCA
Statistics
Matches: 267, Mismatches: 51, Indels: 59
0.71 0.14 0.16
Matches are distributed among these distances:
21 42 0.16
22 44 0.16
23 27 0.10
25 6 0.02
26 148 0.55
ACGTcount: A:0.37, C:0.26, G:0.13, T:0.24
Consensus pattern (26 bp):
AGTCACGCAATGCCTTATCAAAAACT
Found at i:31612152 original size:73 final size:72
Alignment explanation
Indices: 31612055--31612263 Score: 291
Period size: 73 Copynumber: 2.9 Consensus size: 72
31612045 GTCTATCAAC
* *
31612055 TAGTCATGCAATACCTTATCAGAAACTAGTCACGCAATGCCTTATCAAAAACTAGTCACGCAATG
1 TAGTCATGCAAT-GCTTATTAGAAACTAGTCACGCAATGCCTTATCAAAAACTAGTCACGCAATG
31612120 CCCAAAGT
65 CCCAAAGT
31612128 TAGTCATGCAATGCTTTATTAGAAACTAGTCACGCAATGCCTTAT-AAAAACCTAGTCACGCAAT
1 TAGTCATGCAATGC-TTATTAGAAACTAGTCACGCAATGCCTTATCAAAAA-CTAGTCACGCAAT
31612192 GCCCAAAGT
64 GCCCAAAGT
* * * * * *
31612201 CAGTCACGTAATGCCTATT---AACTAGTCACACAATGCCTTATCAGAAACTAGTCACGCAATGC
1 TAGTCATGCAATGCTTATTAGAAACTAGTCACGCAATGCCTTATCAAAAACTAGTCACGCAATGC
31612263 C
66 C
31612264 TCATCAAAAA
Statistics
Matches: 125, Mismatches: 8, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
69 37 0.30
70 4 0.03
72 10 0.08
73 74 0.59
ACGTcount: A:0.35, C:0.26, G:0.14, T:0.24
Consensus pattern (72 bp):
TAGTCATGCAATGCTTATTAGAAACTAGTCACGCAATGCCTTATCAAAAACTAGTCACGCAATGC
CCAAAGT
Found at i:31612414 original size:95 final size:95
Alignment explanation
Indices: 31612011--31612404 Score: 372
Period size: 95 Copynumber: 4.1 Consensus size: 95
31612001 CTTACTAATA
* * * * * *
31612011 AGTCACGCAATGCCTTACTAACAAGTCACGCAATGTC-TATC---AACTAGTCATGCAATACCTT
1 AGTCACGCAATGCC-TATTAACTAGTCATGCAATGCCTTATCAGAAACTAGTCACGCAATGCCTT
* * **
31612072 ATCAGAAA-CTAGTCACGCAATGCCTTATCAAAAAC
65 ATCAAAAATC-AGTCACGTAATGCC----CAAAGTC
* * * *
31612107 TAGTCACGCAATGCCCA--AAGTTAGTCATGCAATGCTTTATTAGAAACTAGTCACGCAATGCCT
1 -AGTCACGCAATGCCTATTAA-CTAGTCATGCAATGCCTTATCAGAAACTAGTCACGCAATGCCT
* *
31612170 TAT-AAAAACCTAGTCACGCAATGCCCAAAGTC
64 TATCAAAAATC-AGTCACGTAATGCCCAAAGTC
* ** *
31612202 AGTCACGTAATGCCTATTAACTAGTCACACAATGCCTTATCAGAAACTAGTCACGCAATGCCTCA
1 AGTCACGCAATGCCTATTAACTAGTCATGCAATGCCTTATCAGAAACTAGTCACGCAATGCCTTA
* * *
31612267 TCAAAAATCAATCACGTAATACCCAAGGTC
66 TCAAAAATCAGTCACGTAATGCCCAAAGTC
* * * **
31612297 AGTCACACAATACCTATTAACTAGTCATGCAATGCCTTATCAAAAACTAGTCACATAATGCCTTA
1 AGTCACGCAATGCCTATTAACTAGTCATGCAATGCCTTATCAGAAACTAGTCACGCAATGCCTTA
**
31612362 TCAAAAATCAGTCACGTAATGTTCAAAGTC
66 TCAAAAATCAGTCACGTAATGCCCAAAGTC
*
31612392 AGTCATGCAATGC
1 AGTCACGCAATGC
31612405 TTAAAAACTA
Statistics
Matches: 246, Mismatches: 42, Indels: 20
0.80 0.14 0.06
Matches are distributed among these distances:
94 16 0.07
95 164 0.67
96 12 0.05
97 14 0.06
98 4 0.02
99 36 0.15
ACGTcount: A:0.37, C:0.26, G:0.13, T:0.25
Consensus pattern (95 bp):
AGTCACGCAATGCCTATTAACTAGTCATGCAATGCCTTATCAGAAACTAGTCACGCAATGCCTTA
TCAAAAATCAGTCACGTAATGCCCAAAGTC
Found at i:31613743 original size:24 final size:24
Alignment explanation
Indices: 31613715--31613760 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
31613705 GAAGCACATA
31613715 GAATGAAGT-TAAAGGAATCCTATT
1 GAATGAA-TATAAAGGAATCCTATT
*
31613739 GAATGAATATATAGGAATCCTA
1 GAATGAATATAAAGGAATCCTA
31613761 AGATCAATCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.43, C:0.09, G:0.20, T:0.28
Consensus pattern (24 bp):
GAATGAATATAAAGGAATCCTATT
Found at i:31616545 original size:2 final size:2
Alignment explanation
Indices: 31616540--31616564 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31616530 TTGTTTGAAC
31616540 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 A
31616565 CATAAAAAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31618333 original size:29 final size:29
Alignment explanation
Indices: 31618288--31618364 Score: 109
Period size: 29 Copynumber: 2.7 Consensus size: 29
31618278 AGGTAATAGA
*
31618288 AAAAAGGTGTACAAGAATAGGTACAAAAG
1 AAAAAGCTGTACAAGAATAGGTACAAAAG
* *
31618317 AAAAAGCTGTACGAGAATAGGTACAAGAG
1 AAAAAGCTGTACAAGAATAGGTACAAAAG
* *
31618346 AATAAGCTGTACATGAATA
1 AAAAAGCTGTACAAGAATA
31618365 AGTATACGAG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.51, C:0.09, G:0.23, T:0.17
Consensus pattern (29 bp):
AAAAAGCTGTACAAGAATAGGTACAAAAG
Found at i:31618670 original size:26 final size:25
Alignment explanation
Indices: 31618641--31618713 Score: 94
Period size: 26 Copynumber: 2.8 Consensus size: 25
31618631 GTTCTACTTT
*
31618641 AAGTAGTACTTCACTTATTCTGCGTG
1 AAGTAGT-CTTCACTTGTTCTGCGTG
31618667 AAGTAG-CGTTTCACTTGTTCTGCGTG
1 AAGTAGTC--TTCACTTGTTCTGCGTG
31618693 AAGTAGCTCTTCACTTGTTCT
1 AAGTAG-TCTTCACTTGTTCT
31618714 AATTATTCTG
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
24 1 0.02
26 40 0.95
28 1 0.02
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.40
Consensus pattern (25 bp):
AAGTAGTCTTCACTTGTTCTGCGTG
Found at i:31643144 original size:29 final size:29
Alignment explanation
Indices: 31643111--31643188 Score: 113
Period size: 29 Copynumber: 2.7 Consensus size: 29
31643101 CGTATACTTG
* *
31643111 TTCACATACACCTTCTTCTCTTGTATCTA
1 TTCACATACAGCTTCTTCTCTTGTACCTA
* *
31643140 TTCACATATAGCTTCTTCTCTTGTACCTG
1 TTCACATACAGCTTCTTCTCTTGTACCTA
31643169 TTCACATACAGC-TCTTCTCT
1 TTCACATACAGCTTCTTCTCT
31643189 ATCAGCTCTT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
28 8 0.18
29 36 0.82
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (29 bp):
TTCACATACAGCTTCTTCTCTTGTACCTA
Found at i:31644968 original size:16 final size:17
Alignment explanation
Indices: 31644947--31644980 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
31644937 GATTTCTCAC
31644947 AATAATTAAAT-ATATA
1 AATAATTAAATAATATA
31644963 AATAATTAAATAATATA
1 AATAATTAAATAATATA
31644980 A
1 A
31644981 TTAGAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AATAATTAAATAATATA
Found at i:31647290 original size:15 final size:15
Alignment explanation
Indices: 31647270--31647300 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
31647260 CATGATAATG
31647270 ATAATAATAAATATA
1 ATAATAATAAATATA
*
31647285 ATAATAATAAGTATA
1 ATAATAATAAATATA
31647300 A
1 A
31647301 GAGAATAAAT
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:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (15 bp):
ATAATAATAAATATA
Found at i:31649062 original size:21 final size:21
Alignment explanation
Indices: 31649037--31649148 Score: 103
Period size: 21 Copynumber: 5.5 Consensus size: 21
31649027 TGAGATGGGA
31649037 TAAATTTAAATTTAATTTGTT
1 TAAATTTAAATTTAATTTGTT
31649058 TAAATTTAAATTATACA-TTG--
1 TAAATTTAAATT-TA-ATTTGTT
31649078 T--ATTTAAATTTAATTTGTT
1 TAAATTTAAATTTAATTTGTT
* **
31649097 TAAATTTAAA--TAAGGATTAAT
1 TAAATTTAAATTTAA--TTTGTT
*
31649118 TATATTTAAATTTAATTTGTT
1 TAAATTTAAATTTAATTTGTT
31649139 TAAATTTAAA
1 TAAATTTAAA
31649149 CATAATATCC
Statistics
Matches: 72, Mismatches: 8, Indels: 22
0.71 0.08 0.22
Matches are distributed among these distances:
16 1 0.01
17 5 0.07
18 9 0.12
19 4 0.06
20 1 0.01
21 43 0.60
22 5 0.07
23 4 0.06
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (21 bp):
TAAATTTAAATTTAATTTGTT
Found at i:31649137 original size:42 final size:39
Alignment explanation
Indices: 31649040--31649148 Score: 157
Period size: 42 Copynumber: 2.7 Consensus size: 39
31649030 GATGGGATAA
* *
31649040 ATTTAAATTTAATTTGTTTAAATTTAAATTATACATTGT
1 ATTTAAATTTAATTTGTTTAAATTTAAATGATACATTAT
31649079 ATTTAAATTTAATTTGTTTAAATTTAAATAAGGATTA-ATTAT
1 ATTTAAATTTAATTTGTTTAAATTTAAAT---GA-TACATTAT
31649121 ATTTAAATTTAATTTGTTTAAATTTAAA
1 ATTTAAATTTAATTTGTTTAAATTTAAA
31649149 CATAATATCC
Statistics
Matches: 64, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
39 29 0.45
42 33 0.52
43 2 0.03
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.52
Consensus pattern (39 bp):
ATTTAAATTTAATTTGTTTAAATTTAAATGATACATTAT
Found at i:31650210 original size:47 final size:47
Alignment explanation
Indices: 31650143--31650550 Score: 586
Period size: 47 Copynumber: 8.9 Consensus size: 47
31650133 ACATATGTTG
31650143 TAAAATGC-T-ATGTAATTATTTTACTTATTTGTTAGGTAAAATTTA
1 TAAAATGCATGATGTAATTATTTTACTTATTTGTTAGGTAAAATTTA
31650188 TAAAATGCATGATGTAATTATTTTACTTATTTGTTAGGTAAAA--T-
1 TAAAATGCATGATGTAATTATTTTACTTATTTGTTAGGTAAAATTTA
*
31650232 T----T--ATGATGTAATTATTTTACATATTTGTTAGGTAAAATTTA
1 TAAAATGCATGATGTAATTATTTTACTTATTTGTTAGGTAAAATTTA
* * *
31650273 TAAAATGCATGATGTATTTATTTTACTCATTTGTTAGGTAAATTTTA
1 TAAAATGCATGATGTAATTATTTTACTTATTTGTTAGGTAAAATTTA
*
31650320 TAAAATGCATGATGTAATTATTTTACTTATTTGTTAGGTAAATTTTA
1 TAAAATGCATGATGTAATTATTTTACTTATTTGTTAGGTAAAATTTA
*
31650367 TAAAATGCATGATGTAATTATTTTACTTATTTGTTAAGTAAAATTTA
1 TAAAATGCATGATGTAATTATTTTACTTATTTGTTAGGTAAAATTTA
* *
31650414 TAAAATGCATGATGTATTTATTTTACTTATTTGTTACGTAAAATTTA
1 TAAAATGCATGATGTAATTATTTTACTTATTTGTTAGGTAAAATTTA
* ** *
31650461 TAAAATGCATAATGTAATTATTTTACTTATTTGAAAAGGCAAAATTTA
1 TAAAATGCATGATGTAATTATTTTACTTATTTG-TTAGGTAAAATTTA
* * * *
31650509 TAAAATACATGGTGCAATTATTTTACTTATTTGTTAAGTAAA
1 TAAAATGCATGATGTAATTATTTTACTTATTTGTTAGGTAAA
31650551 CTTATATGCA
Statistics
Matches: 326, Mismatches: 25, Indels: 22
0.87 0.07 0.06
Matches are distributed among these distances:
38 34 0.10
40 2 0.01
41 1 0.00
44 1 0.00
45 10 0.03
46 1 0.00
47 238 0.73
48 39 0.12
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.47
Consensus pattern (47 bp):
TAAAATGCATGATGTAATTATTTTACTTATTTGTTAGGTAAAATTTA
Found at i:31650245 original size:141 final size:135
Alignment explanation
Indices: 31650092--31650512 Score: 394
Period size: 141 Copynumber: 3.0 Consensus size: 135
31650082 TTCTAAAACA
* * *
31650092 TATATATGAATTAAGCAAATGTTTGTTAATGCAATTATTTTACATATGTTGTAAAATGC-T-ATG
1 TATAAATGAATTATG-AAAT-TTTGTTAATG--ATTA-TTTA-A-AT-TTATAAAATGCATGATG
*
31650155 TAATTATTTTACTTATTTGTTAGGTAAAATTTATAAAATGCATGATGTAATTATTTTACTTATTT
58 TATTTATTTTACTTATTTGTTAGGTAAAATTTATAAAATGCATGATGTAATTATTTTACTTATTT
31650220 GTTAGGTAAAATT
123 GTTAGGTAAAATT
* * * *
31650233 TAT-GATGTAATTATTTTACATATTTGTT-A-G-GTA---AAATTTATAAAATGCATGATGTATT
1 TATAAATG-AATTA--TGAAAT-TTTGTTAATGATTATTTAAATTTATAAAATGCATGATGTATT
* *
31650291 TATTTTACTCATTTGTTAGGTAAATTTTATAAAATGCATGATGTAATTATTTTACTTATTTGTTA
62 TATTTTACTTATTTGTTAGGTAAAATTTATAAAATGCATGATGTAATTATTTTACTTATTTGTTA
*
31650356 GGTAAATTT
127 GGTAAAATT
* * * * * *
31650365 TATAAAATGCATGATGTAATTATTTTACTTATTTG-TTAAGTAAAATTTATAAAATGCATGATGT
1 TAT-AAATGAATTATG-AA--ATTTT-GTTA-ATGATT-ATTTAAATTTATAAAATGCATGATGT
* *
31650429 ATTTATTTTACTTATTTGTTACGTAAAATTTATAAAATGCATAATGTAATTATTTTACTTATTTG
59 ATTTATTTTACTTATTTGTTAGGTAAAATTTATAAAATGCATGATGTAATTATTTTACTTATTTG
** *
31650494 AAAAGGCAAAATT
124 -TTAGGTAAAATT
31650507 TATAAA
1 TATAAA
31650513 ATACATGGTG
Statistics
Matches: 234, Mismatches: 27, Indels: 38
0.78 0.09 0.13
Matches are distributed among these distances:
130 10 0.04
131 4 0.02
132 82 0.35
133 7 0.03
134 7 0.03
137 4 0.02
138 1 0.00
140 4 0.02
141 95 0.41
142 20 0.09
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.47
Consensus pattern (135 bp):
TATAAATGAATTATGAAATTTTGTTAATGATTATTTAAATTTATAAAATGCATGATGTATTTATT
TTACTTATTTGTTAGGTAAAATTTATAAAATGCATGATGTAATTATTTTACTTATTTGTTAGGTA
AAATT
Found at i:31650343 original size:25 final size:25
Alignment explanation
Indices: 31650314--31650391 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 25
31650304 TGTTAGGTAA
31650314 ATTTTATAAAATGCATGATGTAATT
1 ATTTTATAAAATGCATGATGTAATT
* ** * *
31650339 ATTTTACTTATTTG--TTAGGTAA--
1 ATTTTA-TAAAATGCATGATGTAATT
31650361 ATTTTATAAAATGCATGATGTAATT
1 ATTTTATAAAATGCATGATGTAATT
31650386 ATTTTA
1 ATTTTA
31650392 CTTATTTGTT
Statistics
Matches: 38, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
21 4 0.11
22 6 0.16
23 6 0.16
24 6 0.16
25 12 0.32
26 4 0.11
ACGTcount: A:0.36, C:0.04, G:0.12, T:0.49
Consensus pattern (25 bp):
ATTTTATAAAATGCATGATGTAATT
Found at i:31654732 original size:19 final size:19
Alignment explanation
Indices: 31654694--31654732 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
31654684 AAATTTTTGA
**
31654694 AATAAAATAATATTTTAAT
1 AATAAAATAATATTAAAAT
*
31654713 AATACAATAATATTAAAAT
1 AATAAAATAATATTAAAAT
31654732 A
1 A
31654733 TTAATATTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (19 bp):
AATAAAATAATATTAAAAT
Found at i:31661815 original size:23 final size:21
Alignment explanation
Indices: 31661770--31661880 Score: 99
Period size: 21 Copynumber: 5.5 Consensus size: 21
31661760 TGAAATAGGA
*
31661770 TAAATTTAAATTTAATTTGTT
1 TAAATTTAAATTTAATTTATT
**
31661791 TAAATTTAAA-TT-ATACATT
1 TAAATTTAAATTTAATTTATT
*
31661810 T--ATTTAAATTTAATTTGTT
1 TAAATTTAAATTTAATTTATT
* *
31661829 TAAATTTAAA--TAAGGATTAAT
1 TAAATTTAAATTTAA--TTTATT
*
31661850 TATATTTAAATTTAATTTATT
1 TAAATTTAAATTTAATTTATT
31661871 TAAATTTAAA
1 TAAATTTAAA
31661881 CATAATATCC
Statistics
Matches: 69, Mismatches: 13, Indels: 16
0.70 0.13 0.16
Matches are distributed among these distances:
17 7 0.10
18 2 0.03
19 13 0.19
20 2 0.03
21 42 0.61
23 3 0.04
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (21 bp):
TAAATTTAAATTTAATTTATT
Found at i:31661823 original size:38 final size:40
Alignment explanation
Indices: 31661773--31661880 Score: 150
Period size: 42 Copynumber: 2.7 Consensus size: 40
31661763 AATAGGATAA
*
31661773 ATTTAAATTTAATTTGTTTAAATTTAAAT-TA-TACATT-T
1 ATTTAAATTTAATTTGTTTAAATTTAAATAGATTA-ATTAT
31661811 ATTTAAATTTAATTTGTTTAAATTTAAATAAGGATTAATTAT
1 ATTTAAATTTAATTTGTTTAAATTTAAAT-A-GATTAATTAT
*
31661853 ATTTAAATTTAATTTATTTAAATTTAAA
1 ATTTAAATTTAATTTGTTTAAATTTAAA
31661881 CATAATATCC
Statistics
Matches: 63, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
38 29 0.46
41 4 0.06
42 30 0.48
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.53
Consensus pattern (40 bp):
ATTTAAATTTAATTTGTTTAAATTTAAATAGATTAATTAT
Found at i:31661830 original size:15 final size:15
Alignment explanation
Indices: 31661794--31661879 Score: 76
Period size: 15 Copynumber: 5.8 Consensus size: 15
31661784 ATTTGTTTAA
31661794 ATTTAAATTATACATTT
1 ATTTAAATT-TA-ATTT
31661811 ATTTAAATTTAATTT
1 ATTTAAATTTAATTT
*
31661826 GTTTAAATTTAA---
1 ATTTAAATTTAATTT
31661838 A--TAAGGA-TTAATTAT
1 ATTTAA--ATTTAATT-T
31661853 ATTTAAATTTAATTT
1 ATTTAAATTTAATTT
31661868 ATTTAAATTTAA
1 ATTTAAATTTAA
31661880 ACATAATATC
Statistics
Matches: 58, Mismatches: 2, Indels: 20
0.73 0.03 0.25
Matches are distributed among these distances:
10 3 0.05
11 4 0.07
12 1 0.02
15 30 0.52
16 8 0.14
17 12 0.21
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.52
Consensus pattern (15 bp):
ATTTAAATTTAATTT
Found at i:31662231 original size:2 final size:2
Alignment explanation
Indices: 31662224--31662250 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
31662214 CAATATGTAT
31662224 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
31662251 TATTAAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31663952 original size:16 final size:16
Alignment explanation
Indices: 31663922--31663962 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
31663912 AAATGTAGTC
31663922 ACTTGAAAAAGTATTT
1 ACTTGAAAAAGTATTT
31663938 ACTTGAAAACA-TATTT
1 ACTTGAAAA-AGTATTT
*
31663954 AATTGAAAA
1 ACTTGAAAA
31663963 TGTACCCCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 22 0.96
17 1 0.04
ACGTcount: A:0.49, C:0.07, G:0.10, T:0.34
Consensus pattern (16 bp):
ACTTGAAAAAGTATTT
Found at i:31667825 original size:42 final size:42
Alignment explanation
Indices: 31667778--31667861 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
31667768 TATTCTCTGT
31667778 ATAATATTATGCTATAAAATAATTCTTCAGATAATAGGTATC
1 ATAATATTATGCTATAAAATAATTCTTCAGATAATAGGTATC
31667820 ATAATATTATGCTATAAAATAATTCTTCAGATAATAGGTATC
1 ATAATATTATGCTATAAAATAATTCTTCAGATAATAGGTATC
31667862 GACCAAAATC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.38
Consensus pattern (42 bp):
ATAATATTATGCTATAAAATAATTCTTCAGATAATAGGTATC
Found at i:31673122 original size:22 final size:22
Alignment explanation
Indices: 31673097--31673143 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
31673087 TTCACTAGGA
31673097 GATGTTAATATTTATAAAATTT
1 GATGTTAATATTTATAAAATTT
*
31673119 GATGTTAGTATTTATAAAATTT
1 GATGTTAATATTTATAAAATTT
31673141 GAT
1 GAT
31673144 CTCTTTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (22 bp):
GATGTTAATATTTATAAAATTT
Found at i:31679909 original size:32 final size:33
Alignment explanation
Indices: 31679844--31679913 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 33
31679834 AGTGATTTCG
*
31679844 GAAAATATTTTCCGAAAGATGATCCAAATAACA
1 GAAAATATTTTCCGAAAGATGATCCAAACAACA
* * *
31679877 GAAAATATTTT-CGACAGTTTATCCAAACAACA
1 GAAAATATTTTCCGAAAGATGATCCAAACAACA
31679909 GAAAA
1 GAAAA
31679914 CATTAAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
32 22 0.67
33 11 0.33
ACGTcount: A:0.49, C:0.16, G:0.11, T:0.24
Consensus pattern (33 bp):
GAAAATATTTTCCGAAAGATGATCCAAACAACA
Found at i:31688452 original size:22 final size:22
Alignment explanation
Indices: 31688424--31688474 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
31688414 GACTTAGATA
31688424 TTAGGTATTGCGTAACTAATTT
1 TTAGGTATTGCGTAACTAATTT
31688446 TTAGGTATTGCGTAACTAATTT
1 TTAGGTATTGCGTAACTAATTT
31688468 TTAGGTA
1 TTAGGTA
31688475 ATGCCTAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.27, C:0.08, G:0.20, T:0.45
Consensus pattern (22 bp):
TTAGGTATTGCGTAACTAATTT
Found at i:31688619 original size:22 final size:22
Alignment explanation
Indices: 31688594--31688698 Score: 111
Period size: 22 Copynumber: 4.8 Consensus size: 22
31688584 AACCATTAAC
*
31688594 ACAATACCTAAAAATCAGTCAT
1 ACAATACTTAAAAATCAGTCAT
** * * *
31688616 ACAATGTTTAAAAATTAGTAAC
1 ACAATACTTAAAAATCAGTCAT
* *
31688638 GCAATACCTAAAAATCAGTCAT
1 ACAATACTTAAAAATCAGTCAT
* * *
31688660 ATAATACTTAAAAATCAATTAT
1 ACAATACTTAAAAATCAGTCAT
31688682 ACAATACTTAAAAATCA
1 ACAATACTTAAAAATCA
31688699 CCAAAACTAT
Statistics
Matches: 64, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 64 1.00
ACGTcount: A:0.51, C:0.16, G:0.05, T:0.28
Consensus pattern (22 bp):
ACAATACTTAAAAATCAGTCAT
Found at i:31688649 original size:44 final size:44
Alignment explanation
Indices: 31688590--31688698 Score: 137
Period size: 44 Copynumber: 2.5 Consensus size: 44
31688580 TATCAACCAT
**
31688590 TAACACAATACCTAAAAATCAGTCATACAATGTTTAAAAATTAG
1 TAACACAATACCTAAAAATCAGTCATACAATACTTAAAAATTAG
* * * *
31688634 TAACGCAATACCTAAAAATCAGTCATATAATACTTAAAAATCAA
1 TAACACAATACCTAAAAATCAGTCATACAATACTTAAAAATTAG
* * *
31688678 TTATACAATACTTAAAAATCA
1 TAACACAATACCTAAAAATCA
31688699 CCAAAACTAT
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 55 1.00
ACGTcount: A:0.51, C:0.17, G:0.05, T:0.28
Consensus pattern (44 bp):
TAACACAATACCTAAAAATCAGTCATACAATACTTAAAAATTAG
Found at i:31691386 original size:53 final size:53
Alignment explanation
Indices: 31691306--31691414 Score: 209
Period size: 53 Copynumber: 2.1 Consensus size: 53
31691296 TTAAATTTCG
31691306 ATTAAATCAATGATAATTATTTGCATTATAATCTTGAATTTCATATCTTTATA
1 ATTAAATCAATGATAATTATTTGCATTATAATCTTGAATTTCATATCTTTATA
*
31691359 ATTAAATCAATGATAATTATTTGCATTATAATCTTTAATTTCATATCTTTATA
1 ATTAAATCAATGATAATTATTTGCATTATAATCTTGAATTTCATATCTTTATA
31691412 ATT
1 ATT
31691415 TATTGATGTA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.38, C:0.09, G:0.05, T:0.49
Consensus pattern (53 bp):
ATTAAATCAATGATAATTATTTGCATTATAATCTTGAATTTCATATCTTTATA
Found at i:31692629 original size:2 final size:2
Alignment explanation
Indices: 31692547--31692611 Score: 109
Period size: 2 Copynumber: 34.0 Consensus size: 2
31692537 AAAGAAATAC
31692547 TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31692587 T- TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
31692612 ACAAGGNNNN
Statistics
Matches: 60, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
1 3 0.05
2 57 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Done.