Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr10
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: 21822658
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.32
Warning! 1067834 characters in sequence are not A, C, G, or T
File 7 of 59
Found at i:2331855 original size:177 final size:177
Alignment explanation
Indices: 2331552--2331904 Score: 562
Period size: 177 Copynumber: 2.0 Consensus size: 177
2331542 GTGTACCTTA
* * * *
2331552 TCAAGTATAAACATCACAAATTATAACCACATGACCTACAACTCAATTATTAGGCCCCTCAGCAC
1 TCAAGTATAAACATCACAAAATATAACCACATGACCTACAACTCAACTACTAGGCCCCCCAGCAC
* * *
2331617 ACAAATATGACCATTCACACATCATATATATTCATATGGCATGTAACATAGGTGATATGGCCCTT
66 ACAAATATAACCATTCACACATCATATATATTCATATGGCATGTAACACAAGTGATATGGCCCTT
*
2331682 AGTAAATCTCAATTCACCAATTCACATCAATAAGCATTGATCATATC
131 AGTAAATCTCAAATCACCAATTCACATCAATAAGCATTGATCATATC
* * * * **
2331729 TCAAGTCTAAACATCACAAAATATAGCCTCATGACCTATAGTTCAACTACTAGGCCCCCCAGCAC
1 TCAAGTATAAACATCACAAAATATAACCACATGACCTACAACTCAACTACTAGGCCCCCCAGCAC
2331794 ACAAATATAACCATTCACACATCATATATATTCATATGGCATGTAACACAAGTGATATGGCCCTT
66 ACAAATATAACCATTCACACATCATATATATTCATATGGCATGTAACACAAGTGATATGGCCCTT
* *
2331859 AGTAAATCTCAAATCGCCAATTCATATCAATAAGCATTGATCATAT
131 AGTAAATCTCAAATCACCAATTCACATCAATAAGCATTGATCATAT
2331905 ATATATATAT
Statistics
Matches: 160, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
177 160 1.00
ACGTcount: A:0.38, C:0.25, G:0.10, T:0.27
Consensus pattern (177 bp):
TCAAGTATAAACATCACAAAATATAACCACATGACCTACAACTCAACTACTAGGCCCCCCAGCAC
ACAAATATAACCATTCACACATCATATATATTCATATGGCATGTAACACAAGTGATATGGCCCTT
AGTAAATCTCAAATCACCAATTCACATCAATAAGCATTGATCATATC
Found at i:2335504 original size:59 final size:59
Alignment explanation
Indices: 2335441--2335556 Score: 146
Period size: 59 Copynumber: 2.0 Consensus size: 59
2335431 TTTAGGTCTC
*
2335441 CCTTTACCTACTCGTGAGAACTCCCCACAG-CACCAAATATGAGCTGA-GGCTTCAAGTTT
1 CCTTTACCTACTCGTGAGAACTCCCCAC-GTCACCAAATATCAG-TGAGGGCTTCAAGTTT
* * * * *
2335500 CCTTTACCTACTTGTGGGAACTCTCTACGTCACCAAATATCAGTTAGGGCTTCAAGT
1 CCTTTACCTACTCGTGAGAACTCCCCACGTCACCAAATATCAGTGAGGGCTTCAAGT
2335557 CCCTCTTTAT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
58 3 0.06
59 46 0.94
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.28
Consensus pattern (59 bp):
CCTTTACCTACTCGTGAGAACTCCCCACGTCACCAAATATCAGTGAGGGCTTCAAGTTT
Found at i:2339082 original size:4 final size:4
Alignment explanation
Indices: 2339073--2339109 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
2339063 AAGACTCAAA
2339073 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG A
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG A
2339110 TAAATACGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:2346067 original size:52 final size:52
Alignment explanation
Indices: 2345986--2346089 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
2345976 GATGCTAACC
*
2345986 CTCTTCCAGCATAGTAAACATTTTTAACCATAAGCACGAAGAAATCCAGGAT
1 CTCTTCCAGCATAGTAAACATTTTCAACCATAAGCACGAAGAAATCCAGGAT
2346038 CTCTTCCAGCATAGTAAACATTTTCAACCATAAGCACGAAGAAATCCAGGAT
1 CTCTTCCAGCATAGTAAACATTTTCAACCATAAGCACGAAGAAATCCAGGAT
2346090 TGGGGAATCG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.24
Consensus pattern (52 bp):
CTCTTCCAGCATAGTAAACATTTTCAACCATAAGCACGAAGAAATCCAGGAT
Found at i:2353376 original size:24 final size:24
Alignment explanation
Indices: 2353349--2353402 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
2353339 AAAAAAATTA
*
2353349 TTAAATAT-TTATTTTTTTAATTTT
1 TTAAATATGTAATTTTTTT-ATTTT
2353373 TTAAA-ATGTAATTTTTTTATTTT
1 TTAAATATGTAATTTTTTTATTTT
2353396 TTAAATA
1 TTAAATA
2353403 ATTAATACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 12 0.44
24 15 0.56
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (24 bp):
TTAAATATGTAATTTTTTTATTTT
Found at i:2353504 original size:24 final size:21
Alignment explanation
Indices: 2353487--2353529 Score: 59
Period size: 24 Copynumber: 1.9 Consensus size: 21
2353477 AATATAATAT
2353487 AAATAAAAAATTAAAATAAAA
1 AAATAAAAAATTAAAATAAAA
2353508 AAATATATAAATATTAAAATAA
1 AAATA-A-AAA-ATTAAAATAA
2353530 TAGTACTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 1 0.05
23 3 0.16
24 10 0.53
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (21 bp):
AAATAAAAAATTAAAATAAAA
Found at i:2353518 original size:17 final size:18
Alignment explanation
Indices: 2353477--2353518 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
2353467 ATAATATAAT
*
2353477 AATATAATATAAATAAAA
1 AATATAAAATAAATAAAA
2353495 AAT-TAAAATAAA-AAAA
1 AATATAAAATAAATAAAA
*
2353511 TATATAAA
1 AATATAAA
2353519 TATTAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 6 0.29
17 12 0.57
18 3 0.14
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AATATAAAATAAATAAAA
Found at i:2353526 original size:17 final size:15
Alignment explanation
Indices: 2353483--2353520 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
2353473 TAATAATATA
2353483 ATATAAATAAAAAAT
1 ATATAAATAAAAAAT
2353498 -TA-AAATAAAAAAAT
1 ATATAAAT-AAAAAAT
2353512 ATATAAATA
1 ATATAAATA
2353521 TTAAAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
13 4 0.20
14 9 0.45
15 3 0.15
16 4 0.20
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
ATATAAATAAAAAAT
Found at i:2353962 original size:17 final size:17
Alignment explanation
Indices: 2353940--2353983 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
2353930 TTTTATTAAT
* *
2353940 TATTTTTTATTTTTATG
1 TATTTTTAATTTTTATA
2353957 TATTTTTAATTTTTATA
1 TATTTTTAATTTTTATA
2353974 TATTTTTAAT
1 TATTTTTAAT
2353984 ATAATAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (17 bp):
TATTTTTAATTTTTATA
Found at i:2355364 original size:26 final size:25
Alignment explanation
Indices: 2355332--2355381 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
2355322 TAAAAATTTA
2355332 TTTAATTTAAA-ATAAAAATAAAATAG
1 TTTAA-TTAAATATAAAAA-AAAATAG
*
2355358 TTTAATTAAATATAATAAAAAATA
1 TTTAATTAAATATAAAAAAAAATA
2355382 AAAATTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (25 bp):
TTTAATTAAATATAAAAAAAAATAG
Found at i:2367110 original size:20 final size:20
Alignment explanation
Indices: 2367084--2367124 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
2367074 AGTAAGAATC
*
2367084 TTTTTTTAATTAATAAATATA
1 TTTTTTAAATTAA-AAATATA
2367105 TTTTTTAAATTAAAAATATA
1 TTTTTTAAATTAAAAATATA
2367125 AATTCATGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTTTTAAATTAAAAATATA
Found at i:2380882 original size:2 final size:2
Alignment explanation
Indices: 2380875--2380912 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2380865 AGTAAATCTA
2380875 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2380913 GAAGTCCAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2386232 original size:2 final size:2
Alignment explanation
Indices: 2386220--2386261 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
2386210 CATATCAAAT
* *
2386220 TA TA AA TA TA TA TA TA TA TA TA TA TA T- TA AA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2386260 TA
1 TA
2386262 AAACAAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2386237 original size:14 final size:14
Alignment explanation
Indices: 2386220--2386263 Score: 60
Period size: 12 Copynumber: 3.4 Consensus size: 14
2386210 CATATCAAAT
2386220 TATAAATATATATA
1 TATAAATATATATA
2386234 TAT--ATATATATA
1 TATAAATATATATA
2386246 T-TAAAT-TATATA
1 TATAAATATATATA
2386258 TATAAA
1 TATAAA
2386264 ACAAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
11 1 0.04
12 17 0.63
13 6 0.22
14 3 0.11
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TATAAATATATATA
Found at i:2407980 original size:40 final size:40
Alignment explanation
Indices: 2407931--2408076 Score: 184
Period size: 40 Copynumber: 3.6 Consensus size: 40
2407921 CAAAGATCTT
*
2407931 AAACATAAACTTAAATAACTAAAAATAAATATCCACACAA
1 AAACATAAACTTAAATAACTAAAAATAAATATCCAAACAA
** * * * *
2407971 CGATATAAACTTAAATAACTATACATAAATATCCAAATAA
1 AAACATAAACTTAAATAACTAAAAATAAATATCCAAACAA
* * *
2408011 AAACATAAACTTAAATAACTAAACACAAAAATCCAAACAA
1 AAACATAAACTTAAATAACTAAAAATAAATATCCAAACAA
*
2408051 ATAACATAAACTTAAATAACAAAAAA
1 A-AACATAAACTTAAATAACTAAAAA
2408077 ATATAATTTT
Statistics
Matches: 89, Mismatches: 16, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
40 67 0.75
41 22 0.25
ACGTcount: A:0.62, C:0.16, G:0.01, T:0.21
Consensus pattern (40 bp):
AAACATAAACTTAAATAACTAAAAATAAATATCCAAACAA
Found at i:2408290 original size:21 final size:21
Alignment explanation
Indices: 2408251--2408299 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
2408241 ACATTACAAT
*
2408251 TTAATTAATAATCATAATTTTA
1 TTAATTAATAA-CATAATTATA
2408273 TTAATTAATTAA-ATAATTATA
1 TTAATTAA-TAACATAATTATA
*
2408294 TGAATT
1 TTAATT
2408300 GGTCCCTAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 13 0.54
22 8 0.33
23 3 0.12
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
TTAATTAATAACATAATTATA
Found at i:2408546 original size:2 final size:2
Alignment explanation
Indices: 2408541--2408587 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
2408531 TGTATATATA
2408541 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2408583 TG TG T
1 TG TG T
2408588 ATTACAATTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:2408618 original size:15 final size:17
Alignment explanation
Indices: 2408598--2408630 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2408588 ATTACAATTA
2408598 ATAA-TTTTATAA-GTT
1 ATAATTTTTATAATGTT
2408613 ATAATTTTTATAATGTT
1 ATAATTTTTATAATGTT
2408630 A
1 A
2408631 ACACAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 8 0.50
17 4 0.25
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (17 bp):
ATAATTTTTATAATGTT
Found at i:2408676 original size:17 final size:17
Alignment explanation
Indices: 2408646--2408696 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
2408636 AAATAAAAAA
*
2408646 TAAA-TATATTTATATT
1 TAAAGTATATATATATT
*
2408662 TAAAGTATATATATACT
1 TAAAGTATATATATATT
*
2408679 AAAAGTATTAGTATATAT
1 TAAAGTA-TA-TATATAT
2408697 ATATTATAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
16 4 0.14
17 16 0.57
18 2 0.07
19 6 0.21
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (17 bp):
TAAAGTATATATATATT
Found at i:2415184 original size:10 final size:10
Alignment explanation
Indices: 2415154--2415178 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2415144 TATCATGGCC
2415154 TTTAAAAATT
1 TTTAAAAATT
2415164 TTTAAAAATT
1 TTTAAAAATT
2415174 TTTAA
1 TTTAA
2415179 TTATTTATAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
TTTAAAAATT
Found at i:2415359 original size:16 final size:15
Alignment explanation
Indices: 2415338--2415371 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
2415328 GTTTTTTATT
*
2415338 TAATAATTAATATAAA
1 TAATAAATAATA-AAA
2415354 TAATAAATAATAAAA
1 TAATAAATAATAAAA
2415369 TAA
1 TAA
2415372 CTCTACAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
TAATAAATAATAAAA
Found at i:2415459 original size:18 final size:19
Alignment explanation
Indices: 2415436--2415473 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
2415426 TCCCTCTCCC
2415436 TCTCTT-TTTTTTTCTTTT
1 TCTCTTCTTTTTTTCTTTT
*
2415454 TCTCTTCTTTTTTTGTTTT
1 TCTCTTCTTTTTTTCTTTT
2415473 T
1 T
2415474 TTATTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.82
Consensus pattern (19 bp):
TCTCTTCTTTTTTTCTTTT
Found at i:2426705 original size:18 final size:18
Alignment explanation
Indices: 2426675--2426709 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2426665 TATTCTAAAA
2426675 ATAATAAATAATAATATG
1 ATAATAAATAATAATATG
2426693 ATAA-AAATAAATAATAT
1 ATAATAAAT-AATAATAT
2426710 TTTAATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (18 bp):
ATAATAAATAATAATATG
Found at i:2427090 original size:26 final size:26
Alignment explanation
Indices: 2427034--2427091 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
2427024 TTTTCTTATA
* *
2427034 TGTGCTAATATCGTAATTCGTATTTC
1 TGTGTTAATATCATAATTCGTATTTC
* *
2427060 TGTGTTAATATCATAATTTGTATTTT
1 TGTGTTAATATCATAATTCGTATTTC
2427086 TGTGTT
1 TGTGTT
2427092 TTAATTGTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.22, C:0.09, G:0.16, T:0.53
Consensus pattern (26 bp):
TGTGTTAATATCATAATTCGTATTTC
Found at i:2429998 original size:21 final size:22
Alignment explanation
Indices: 2429956--2429998 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
2429946 TAATAAATTA
* *
2429956 TTAAAATAATAAATTTTTTAAT
1 TTAAAATAATAAATATTATAAT
*
2429978 TTAAAA-ATTAAATATTATAAT
1 TTAAAATAATAAATATTATAAT
2429999 AAAAGTTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TTAAAATAATAAATATTATAAT
Found at i:2451506 original size:20 final size:20
Alignment explanation
Indices: 2451481--2451519 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2451471 TCTTAGATTA
*
2451481 TTTTTTGTTTTTTA-ATGTTC
1 TTTTTT-TTTATTATATGTTC
2451501 TTTTTTTTTATTATATGTT
1 TTTTTTTTTATTATATGTT
2451520 TATGATTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.13, C:0.03, G:0.08, T:0.77
Consensus pattern (20 bp):
TTTTTTTTTATTATATGTTC
Found at i:2454983 original size:18 final size:18
Alignment explanation
Indices: 2454946--2455029 Score: 82
Period size: 18 Copynumber: 4.7 Consensus size: 18
2454936 CATTGTAGGC
* * *
2454946 GCTTCATTACCTGTAAGT
1 GCTTCATTACTTGCAGGT
2454964 GCTTCATTACTTGCAGGT
1 GCTTCATTACTTGCAGGT
* *
2454982 GCTTC-TTCAATTGCTGGT
1 GCTTCATT-ACTTGCAGGT
*
2455000 GCTTCTTTAAC-TGCAGGT
1 GCTTCATT-ACTTGCAGGT
2455018 GCTTCATTACTT
1 GCTTCATTACTT
2455030 TTAGGGACTT
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
17 4 0.07
18 47 0.87
19 3 0.06
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.42
Consensus pattern (18 bp):
GCTTCATTACTTGCAGGT
Found at i:2477230 original size:25 final size:26
Alignment explanation
Indices: 2477202--2477258 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
2477192 ATTTTTTATT
2477202 ATCTCAAAATAAGG-TATTCATAGCC
1 ATCTCAAAATAAGGTTATTCATAGCC
2477227 ATCTCAAAATAAGGTTATTCATAGCC
1 ATCTCAAAATAAGGTTATTCATAGCC
2477253 ATCTCA
1 ATCTCA
2477259 TAATGGCACA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 14 0.45
26 17 0.55
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.30
Consensus pattern (26 bp):
ATCTCAAAATAAGGTTATTCATAGCC
Found at i:2478275 original size:46 final size:43
Alignment explanation
Indices: 2478222--2478330 Score: 123
Period size: 46 Copynumber: 2.5 Consensus size: 43
2478212 CCCACCACAC
*
2478222 TCAGCTCATGTGCACTCCCTACA-CGCACA-ATGCAATATCATCATTA
1 TCAGCTCATGTGCACTCCC-ACACCGCACATA-G--ATA-CATCATCA
* **
2478268 TCAGCTCATGTGCACTCTCACACCGCACATAGATAGGTCATCA
1 TCAGCTCATGTGCACTCCCACACCGCACATAGATACATCATCA
2478311 TCAGCTCATGTGCACTCCCA
1 TCAGCTCATGTGCACTCCCA
2478331 TAATGCACAT
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
43 24 0.43
44 3 0.05
45 3 0.05
46 25 0.45
47 1 0.02
ACGTcount: A:0.28, C:0.34, G:0.14, T:0.25
Consensus pattern (43 bp):
TCAGCTCATGTGCACTCCCACACCGCACATAGATACATCATCA
Found at i:2478339 original size:43 final size:43
Alignment explanation
Indices: 2478262--2478354 Score: 123
Period size: 43 Copynumber: 2.2 Consensus size: 43
2478252 TGCAATATCA
* * *
2478262 TCATTATCAGCTCATGTGCACTCTCACACCGCACATAGATAGG
1 TCATCATCAGCTCATGTGCACTCCCACAACGCACATAGATAGG
* * *
2478305 TCATCATCAGCTCATGTGCACTCCCATAATGCACATAGCTAGG
1 TCATCATCAGCTCATGTGCACTCCCACAACGCACATAGATAGG
*
2478348 TCCTCAT
1 TCATCAT
2478355 TATCACACAA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (43 bp):
TCATCATCAGCTCATGTGCACTCCCACAACGCACATAGATAGG
Found at i:2480525 original size:2 final size:2
Alignment explanation
Indices: 2480520--2480547 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2480510 CACACACGTG
2480520 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2480548 ACAATTTGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2482016 original size:30 final size:30
Alignment explanation
Indices: 2481982--2482039 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
2481972 AAGAGGCAAC
*
2481982 CCTATGAAAGCTGAAGGAAAGATGGGAAGG
1 CCTATGAAAGCTGAAGGAAAGAGGGGAAGG
2482012 CCTATGAAAGCTGAAGGAAAGAGGGGAA
1 CCTATGAAAGCTGAAGGAAAGAGGGGAA
2482040 AGAAGAATCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.41, C:0.10, G:0.36, T:0.12
Consensus pattern (30 bp):
CCTATGAAAGCTGAAGGAAAGAGGGGAAGG
Found at i:2482099 original size:44 final size:44
Alignment explanation
Indices: 2482050--2482139 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
2482040 AGAAGAATCC
*
2482050 AGAGACAGAACATGATCCAGATGACAGCCAAAGAAACACTGCAA
1 AGAGACAGAACATGATCCAGATGACAGCCAAAGAAACAATGCAA
2482094 AGAGACAGAACATGATCCAGATGACAGCCAAAGAAACAATGCAA
1 AGAGACAGAACATGATCCAGATGACAGCCAAAGAAACAATGCAA
2482138 AG
1 AG
2482140 GAACGATGGT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.49, C:0.21, G:0.21, T:0.09
Consensus pattern (44 bp):
AGAGACAGAACATGATCCAGATGACAGCCAAAGAAACAATGCAA
Found at i:2484054 original size:32 final size:32
Alignment explanation
Indices: 2484013--2484074 Score: 108
Period size: 32 Copynumber: 1.9 Consensus size: 32
2484003 ACGGGAGTCG
2484013 TTCGAGGTGTCTGGTAAAGGTG-CCTAAGCTCA
1 TTCGAGGTGTCTGGTAAAGGTGTCC-AAGCTCA
2484045 TTCGAGGTGTCTGGTAAAGGTGTCCAAGCT
1 TTCGAGGTGTCTGGTAAAGGTGTCCAAGCT
2484075 GGAGAAGGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 27 0.93
33 2 0.07
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (32 bp):
TTCGAGGTGTCTGGTAAAGGTGTCCAAGCTCA
Found at i:2493497 original size:20 final size:19
Alignment explanation
Indices: 2493444--2493500 Score: 96
Period size: 19 Copynumber: 2.9 Consensus size: 19
2493434 ACTGACGCAG
*
2493444 GGGCGTTGTAAAGACACTT
1 GGGCGTTGTAAAGACACCT
2493463 GGGCGTTGTAAAGACACCT
1 GGGCGTTGTAAAGACACCT
2493482 GGGCGTTGTGAAAGACACC
1 GGGCGTTGT-AAAGACACC
2493501 AATCATGGCG
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
19 27 0.75
20 9 0.25
ACGTcount: A:0.26, C:0.19, G:0.33, T:0.21
Consensus pattern (19 bp):
GGGCGTTGTAAAGACACCT
Found at i:2493941 original size:15 final size:15
Alignment explanation
Indices: 2493902--2493943 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
2493892 GCTATAATTC
*
2493902 TTAAATCAAATAAAA
1 TTAAATAAAATAAAA
*
2493917 TTAACA-AAAATTAAA
1 TTAA-ATAAAATAAAA
2493932 TTAAATAAAATA
1 TTAAATAAAATA
2493944 TAATCCTAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
14 1 0.05
15 20 0.91
16 1 0.05
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.29
Consensus pattern (15 bp):
TTAAATAAAATAAAA
Found at i:2497550 original size:21 final size:22
Alignment explanation
Indices: 2497507--2497550 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
2497497 GGAGAGAACT
*
2497507 GAAACAACACCCAATACAGCAAA
1 GAAACAACACCC-ATACAACAAA
2497530 GAAACAACACCC-TACAACAAA
1 GAAACAACACCCATACAACAAA
2497551 AACCATAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 8 0.40
23 12 0.60
ACGTcount: A:0.57, C:0.32, G:0.07, T:0.05
Consensus pattern (22 bp):
GAAACAACACCCATACAACAAA
Found at i:2499667 original size:21 final size:21
Alignment explanation
Indices: 2499641--2499698 Score: 116
Period size: 21 Copynumber: 2.8 Consensus size: 21
2499631 AATATATTAA
2499641 TAAGGAATGTAAGGTGAATAT
1 TAAGGAATGTAAGGTGAATAT
2499662 TAAGGAATGTAAGGTGAATAT
1 TAAGGAATGTAAGGTGAATAT
2499683 TAAGGAATGTAAGGTG
1 TAAGGAATGTAAGGTG
2499699 GTGTATTATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.41, C:0.00, G:0.31, T:0.28
Consensus pattern (21 bp):
TAAGGAATGTAAGGTGAATAT
Found at i:2500924 original size:2 final size:2
Alignment explanation
Indices: 2500912--2500955 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
2500902 AATTTTAATC
*
2500912 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2500954 TA
1 TA
2500956 AGAACTAACA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2502882 original size:77 final size:76
Alignment explanation
Indices: 2502751--2502896 Score: 166
Period size: 77 Copynumber: 1.9 Consensus size: 76
2502741 CAAAAGTTTG
* * * * * * *
2502751 GATATAAAAAGTTTTTTTTTAATATTATAGTTCAAAAGGCATGTCTTGTGGAATGAGTGGTTGTT
1 GATATAAAAAGTTATCTTTTAATATTATACTTCAAAAGGCATGTCTTATAGAATGAATGATTG-T
2502816 CTTTTATAGCGT
65 CTTTTATAGCGT
* * * ***
2502828 GATATGAAAAGTTATCTTTTCATATTATACTTTAAAAGTTGTGTCTTATAGAATGAATGATTGTC
1 GATATAAAAAGTTATCTTTTAATATTATACTTCAAAAGGCATGTCTTATAGAATGAATGATTGTC
2502893 TTTT
66 TTTT
2502897 TATAAGATAA
Statistics
Matches: 56, Mismatches: 13, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
76 6 0.11
77 50 0.89
ACGTcount: A:0.30, C:0.07, G:0.18, T:0.45
Consensus pattern (76 bp):
GATATAAAAAGTTATCTTTTAATATTATACTTCAAAAGGCATGTCTTATAGAATGAATGATTGTC
TTTTATAGCGT
Found at i:2504070 original size:21 final size:21
Alignment explanation
Indices: 2504032--2504071 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2504022 TTTAAATGTT
*
2504032 GTCATACATTTTAGGATTGCA
1 GTCATACATTATAGGATTGCA
* *
2504053 GTCATATATTATATGATTG
1 GTCATACATTATAGGATTG
2504072 GATATTAATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.10, G:0.17, T:0.42
Consensus pattern (21 bp):
GTCATACATTATAGGATTGCA
Found at i:2508584 original size:28 final size:28
Alignment explanation
Indices: 2508523--2508586 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 28
2508513 GAGTTAATGG
* *
2508523 CGTGTAATAACTTTTTTTTTCAACATAA
1 CGTGTAACAACTCTTTTTTTCAACATAA
* * * *
2508551 CTTGTAACAACTCTTTTTTTGAATATGA
1 CGTGTAACAACTCTTTTTTTCAACATAA
2508579 CGTGTAAC
1 CGTGTAAC
2508587 TTGGTTTCTA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.44
Consensus pattern (28 bp):
CGTGTAACAACTCTTTTTTTCAACATAA
Found at i:2518771 original size:45 final size:45
Alignment explanation
Indices: 2518704--2518808 Score: 174
Period size: 45 Copynumber: 2.3 Consensus size: 45
2518694 CGTCTGGATG
2518704 CAGCATGAACTCCCTTTATAACCGTTAGGATCAAAATATTCTTTTA
1 CAGCATGAAC-CCCTTTATAACCGTTAGGATCAAAATATTCTTTTA
* * *
2518750 CAGCATGAACCCCTTTGTAACCGTTAGGATCAAAGTATTCTTTTG
1 CAGCATGAACCCCTTTATAACCGTTAGGATCAAAATATTCTTTTA
2518795 CAGCATGAACCCCT
1 CAGCATGAACCCCT
2518809 CCCAGGTTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 46 0.82
46 10 0.18
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (45 bp):
CAGCATGAACCCCTTTATAACCGTTAGGATCAAAATATTCTTTTA
Found at i:2519063 original size:58 final size:59
Alignment explanation
Indices: 2518993--2519110 Score: 184
Period size: 58 Copynumber: 2.0 Consensus size: 59
2518983 ATACCCCCTT
* *
2518993 CTGTTTATTATGGGAACTGAAACACCATCTTACCTTCCTATTTTTCAGTGT-AAAAGTG
1 CTGTTTATTATGGGAACTGAAACACCATCTTACCTTCATATTTTTCACTGTAAAAAGTG
* * *
2519051 CTGTTTATTATGGGAACTGAAACTCCATCTTATCTTCATTTTTTTCACTGTAAAAAGTG
1 CTGTTTATTATGGGAACTGAAACACCATCTTACCTTCATATTTTTCACTGTAAAAAGTG
2519110 C
1 C
2519111 ATTTAAATGA
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
58 46 0.85
59 8 0.15
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (59 bp):
CTGTTTATTATGGGAACTGAAACACCATCTTACCTTCATATTTTTCACTGTAAAAAGTG
Found at i:2526419 original size:17 final size:17
Alignment explanation
Indices: 2526397--2526430 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2526387 TTCATTTTCT
2526397 CAAAACATATCCCATGC
1 CAAAACATATCCCATGC
*
2526414 CAAAACATATCTCATGC
1 CAAAACATATCCCATGC
2526431 ATATAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.41, C:0.32, G:0.06, T:0.21
Consensus pattern (17 bp):
CAAAACATATCCCATGC
Found at i:2536050 original size:45 final size:46
Alignment explanation
Indices: 2535955--2536058 Score: 165
Period size: 45 Copynumber: 2.3 Consensus size: 46
2535945 CGTCTGGATG
* *
2535955 CAGCATGAACTCCCTTTATAACCGTTAGGACCAAAGTATTCTTTTA
1 CAGCATGAACCCCCTTTATAACCGTCAGGACCAAAGTATTCTTTTA
* *
2536001 CAGCATGAACCCCCTTTGTAACCG-CAGGATCAAAGTATTCTTTTA
1 CAGCATGAACCCCCTTTATAACCGTCAGGACCAAAGTATTCTTTTA
2536046 CAGCATGAACCCC
1 CAGCATGAACCCC
2536059 TTCCAGGTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
45 32 0.59
46 22 0.41
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (46 bp):
CAGCATGAACCCCCTTTATAACCGTCAGGACCAAAGTATTCTTTTA
Found at i:2536330 original size:58 final size:59
Alignment explanation
Indices: 2536237--2536356 Score: 206
Period size: 58 Copynumber: 2.1 Consensus size: 59
2536227 ATAATACCCC
* *
2536237 TGCTGTTTATTATGGGAACTGAAACACCATTTTATCTTCATGTTTTTCAGTGT-AAAAG
1 TGCTGTTCATTATGGGAACTGAAACACCATCTTATCTTCATGTTTTTCAGTGTAAAAAG
*
2536295 TGCTGTTCATTATGGGAACTGAAACACCATCTTATCTTCATTTTTTTCAGTGTAAAAAG
1 TGCTGTTCATTATGGGAACTGAAACACCATCTTATCTTCATGTTTTTCAGTGTAAAAAG
2536354 TGC
1 TGC
2536357 ATTTAAATGA
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
58 50 0.86
59 8 0.14
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.40
Consensus pattern (59 bp):
TGCTGTTCATTATGGGAACTGAAACACCATCTTATCTTCATGTTTTTCAGTGTAAAAAG
Found at i:2542993 original size:17 final size:17
Alignment explanation
Indices: 2542971--2543004 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2542961 AACATTGCTC
2542971 TTAATGTTAGAAAAAAT
1 TTAATGTTAGAAAAAAT
2542988 TTAATGTTAGAAAAAAT
1 TTAATGTTAGAAAAAAT
2543005 AAAAGAAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (17 bp):
TTAATGTTAGAAAAAAT
Found at i:2545071 original size:45 final size:46
Alignment explanation
Indices: 2545011--2545117 Score: 162
Period size: 45 Copynumber: 2.3 Consensus size: 46
2545001 CGTCTGGATG
*
2545011 CAGCAAGAACTCCCTTTATAACCGTTAGGATCAAAGTA-TTCTTTTA
1 CAGCATGAAC-CCCTTTATAACCGTTAGGATCAAAGTACTTCTTTTA
*
2545057 CAGCATGAACCCCTTTGTAACCGTTAGGATCAAAGTATCTTCTTTTA
1 CAGCATGAACCCCTTTATAACCGTTAGGATCAAAGTA-CTTCTTTTA
*
2545104 CAGCGTGAACCCCT
1 CAGCATGAACCCCT
2545118 ACCTTACGGG
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
45 26 0.46
46 9 0.16
47 21 0.38
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (46 bp):
CAGCATGAACCCCTTTATAACCGTTAGGATCAAAGTACTTCTTTTA
Found at i:2545392 original size:58 final size:58
Alignment explanation
Indices: 2545271--2545401 Score: 140
Period size: 58 Copynumber: 2.3 Consensus size: 58
2545261 CAACATCTAT
* * *** * **
2545271 CAAAACTGCTGTTTATTATGGGAATTGAAAGACCATCTTATCTTCATGTTTTTCAAGG
1 CAAAAGTGCTATTTATTATGGGAACAAAAACACCATCTTATCTTCATGTTTGACAAGG
* *
2545329 TAAAAGTGCTATTTATTATGGGAACAAAAACACCATTTTATCTTCATGTTTGAC-AGTG
1 CAAAAGTGCTATTTATTATGGGAACAAAAACACCATCTTATCTTCATGTTTGACAAG-G
2545387 CAAAAGGTGC-ATTTA
1 CAAAA-GTGCTATTTA
2545402 AAAGGAAAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
57 2 0.03
58 54 0.90
59 4 0.07
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.36
Consensus pattern (58 bp):
CAAAAGTGCTATTTATTATGGGAACAAAAACACCATCTTATCTTCATGTTTGACAAGG
Found at i:2551105 original size:33 final size:33
Alignment explanation
Indices: 2551067--2551140 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
2551057 TTTCTTAATC
* * *
2551067 TATCACGTTAACATTATCATATCATTATGTTAA
1 TATCACGTTAACATTATCATATAATCATGTCAA
* **
2551100 TATCACATTAGTATTATCATATAATCATGTCAA
1 TATCACGTTAACATTATCATATAATCATGTCAA
*
2551133 TGTCACGT
1 TATCACGT
2551141 GATACTACCA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.41
Consensus pattern (33 bp):
TATCACGTTAACATTATCATATAATCATGTCAA
Found at i:2554159 original size:2 final size:2
Alignment explanation
Indices: 2554152--2554181 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2554142 NNNNNNNNNN
2554152 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
2554182 CGATTATGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2554714 original size:12 final size:12
Alignment explanation
Indices: 2554697--2554734 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
2554687 CTTGAATAAG
2554697 ATACGTGAGGAA
1 ATACGTGAGGAA
2554709 ATACGTG-GGAAA
1 ATACGTGAGG-AA
*
2554721 ATACGTGAAGAA
1 ATACGTGAGGAA
2554733 AT
1 AT
2554735 GAGAAATGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
11 2 0.09
12 20 0.87
13 1 0.04
ACGTcount: A:0.45, C:0.08, G:0.29, T:0.18
Consensus pattern (12 bp):
ATACGTGAGGAA
Found at i:2564618 original size:20 final size:21
Alignment explanation
Indices: 2564588--2564637 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
2564578 AGGTTGCTTG
*
2564588 GGCTATTTGCTAGCCCACCAA
1 GGCTATTTGCTAGCACACCAA
* *
2564609 GGCT-TTTGCTTGCATACCAA
1 GGCTATTTGCTAGCACACCAA
*
2564629 GGCTGTTTG
1 GGCTATTTG
2564638 GGTTGTCTGC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.18, C:0.26, G:0.24, T:0.32
Consensus pattern (21 bp):
GGCTATTTGCTAGCACACCAA
Found at i:2566254 original size:23 final size:23
Alignment explanation
Indices: 2566228--2566273 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2566218 ATACAATAAC
* * *
2566228 CTTATCCTGATATAATTAGGAAT
1 CTTATCCTAATAGAATTAAGAAT
2566251 CTTATCCTAATAGAATTAAGAAT
1 CTTATCCTAATAGAATTAAGAAT
2566274 TGTTATTCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (23 bp):
CTTATCCTAATAGAATTAAGAAT
Found at i:2576264 original size:2 final size:2
Alignment explanation
Indices: 2576257--2576288 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2576247 CATCGCACTA
2576257 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
2576289 CATCATCATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2583147 original size:162 final size:162
Alignment explanation
Indices: 2582857--2583148 Score: 362
Period size: 162 Copynumber: 1.8 Consensus size: 162
2582847 CACATTTAAC
* * * *
2582857 ATGAAGGGCAAACTTGCATATGGAACAACAATACACAAATCCTTGACCTTGGGTTTCTTGGCATA
1 ATGAAGGGCAAACTTGCATAGGGAACAACAATAAACAAATCCCTGACCTTGGGTTTCTTGACATA
** * ** *
2582922 TTTGGCAAGGGAGAGATTTTGGATTGAACTGTAGAATAAGAGGATGTATGCGGTGGCAAAGGTGA
66 TTTGGCAAGGGAGAGATTTACGATTGAACTGTAAAATAAGAGGATGTATGCAATGGAAAAGGTGA
2582987 TTAATTTTAATTGGTAGCTCTGCACATGCAAT
131 TTAATTTTAATTGGTAGCTCTGCACATGCAAT
**
2583019 ATGAAGGGCAAAC-TGACA-AGGTGAACAACAATAAACAAATCCCCT-AGGTTGGG-TTCTTTGA
1 ATGAAGGGCAAACTTG-CATAGG-GAACAACAATAAACAAAT-CCCTGACCTTGGGTTTC-TTGA
* *
2583080 CATATTTGGCAAGGGAGACG-TTTACTATTGAACTGTAAAATTAGAGGATGT-TGGCAATGGAAA
62 CATATTTGGCAAGGGAGA-GATTTACGATTGAACTGTAAAATAAGAGGATGTAT-GCAATGGAAA
2583143 AGGTGA
125 AGGTGA
2583149 CTGATTTCAA
Statistics
Matches: 110, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
161 8 0.07
162 98 0.89
163 4 0.04
ACGTcount: A:0.34, C:0.13, G:0.26, T:0.27
Consensus pattern (162 bp):
ATGAAGGGCAAACTTGCATAGGGAACAACAATAAACAAATCCCTGACCTTGGGTTTCTTGACATA
TTTGGCAAGGGAGAGATTTACGATTGAACTGTAAAATAAGAGGATGTATGCAATGGAAAAGGTGA
TTAATTTTAATTGGTAGCTCTGCACATGCAAT
Found at i:2585130 original size:55 final size:55
Alignment explanation
Indices: 2585064--2585178 Score: 212
Period size: 55 Copynumber: 2.1 Consensus size: 55
2585054 CCTTTCTTGC
*
2585064 TCCTTGGTCTCTTGGAATGGTATCAATATTCTCTTTCTCTTTCTCTTTAATCTTT
1 TCCTTGGTCTCTTGGAATGGTATCAATATTCTCTTTCTCTTTCTCTTTAATCATT
*
2585119 TCCTTGGTCTCTTGGAATGGTATCAGTATTCTCTTTCTCTTTCTCTTTAATCATT
1 TCCTTGGTCTCTTGGAATGGTATCAATATTCTCTTTCTCTTTCTCTTTAATCATT
2585174 TCCTT
1 TCCTT
2585179 TAATAAAAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
55 58 1.00
ACGTcount: A:0.14, C:0.23, G:0.11, T:0.52
Consensus pattern (55 bp):
TCCTTGGTCTCTTGGAATGGTATCAATATTCTCTTTCTCTTTCTCTTTAATCATT
Found at i:2586225 original size:2 final size:2
Alignment explanation
Indices: 2586220--2586255 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2586210 TAGTGTGTTA
2586220 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
2586256 GTATGTATAA
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:2586731 original size:84 final size:85
Alignment explanation
Indices: 2586632--2586798 Score: 248
Period size: 84 Copynumber: 2.0 Consensus size: 85
2586622 TAACTAAAGC
* *
2586632 AAATAAACTGCATATTAATAAGATTCAACAATAGAACAAAGGCGACCAA-CATAAAGCAGATGTT
1 AAATAAACCGCATATTAATAAGATTCAACAATAGAACAAAGACGA-CAATCATAAAGCAGATGTT
* *
2586696 ACACGGTTTTTA-TTTAGAGT
65 ACAAGGCTTTTACTTTAGAGT
* * *
2586716 AAATAAACCGCATATTAATAAGATTCAACAATAGAACAAAGATGAGAATCATAAAGTAGATGTTA
1 AAATAAACCGCATATTAATAAGATTCAACAATAGAACAAAGACGACAATCATAAAGCAGATGTTA
2586781 CAAGGCTTTTACTTTAGA
66 CAAGGCTTTTACTTTAGA
2586799 TTCTTGTTTA
Statistics
Matches: 74, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
83 2 0.03
84 66 0.89
85 6 0.08
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.26
Consensus pattern (85 bp):
AAATAAACCGCATATTAATAAGATTCAACAATAGAACAAAGACGACAATCATAAAGCAGATGTTA
CAAGGCTTTTACTTTAGAGT
Found at i:2587945 original size:18 final size:18
Alignment explanation
Indices: 2587922--2587957 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2587912 AGATCCTTCT
2587922 CCCGAACTTGATAAATGG
1 CCCGAACTTGATAAATGG
2587940 CCCGAACTTGATAAATGG
1 CCCGAACTTGATAAATGG
2587958 GTAATCTCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (18 bp):
CCCGAACTTGATAAATGG
Found at i:2600647 original size:19 final size:17
Alignment explanation
Indices: 2600623--2600668 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 17
2600613 GTAAATAAAC
*
2600623 ATAAAATTAAAATAAATT
1 ATAAAAATAAAAT-AATT
*
2600641 AATAAAAATAAACTAATT
1 -ATAAAAATAAAATAATT
2600659 ATAAAAATAA
1 ATAAAAATAA
2600669 CCAAAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 10 0.40
18 4 0.16
19 11 0.44
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (17 bp):
ATAAAAATAAAATAATT
Found at i:2605540 original size:30 final size:30
Alignment explanation
Indices: 2605504--2605566 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
2605494 AATCATTAAT
2605504 TATAAGAACTTATTTGACTTAAAAA-AAAAG
1 TATAAGAACTTATTTGAC-TAAAAATAAAAG
*
2605534 TATAAGAACTTATTTGGCTAAAAATAAAAG
1 TATAAGAACTTATTTGACTAAAAATAAAAG
2605564 TAT
1 TAT
2605567 TAGAGTTTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 6 0.19
30 25 0.81
ACGTcount: A:0.51, C:0.06, G:0.11, T:0.32
Consensus pattern (30 bp):
TATAAGAACTTATTTGACTAAAAATAAAAG
Found at i:2609210 original size:125 final size:124
Alignment explanation
Indices: 2608986--2609236 Score: 405
Period size: 125 Copynumber: 2.0 Consensus size: 124
2608976 TTCTTGAAGT
* *
2608986 AAATCAAAACAATCTTTTTGATAACATATGTGAGTGACAAAAGTAGAATCTAAATACCAATCAAA
1 AAATCAAAACAATCCTTTTGATAACATATGTGAGTGACAAAAGCAGAATCTAAATACCAATCAAA
*
2609051 ATTTGCATCCATATTTTCTGAGATTGTAAAGACATCACAATCATCACCTTCAGCAATGA
66 ATTTGCATCCATATTTTCTGAAATTGTAAAGACATCACAATCATCACCTTCAGCAATGA
*
2609110 ANAATCAAAACAATCCTTTTGATAACATATGTGAGT-AGCAGAAGCAGAATCTAAATACCAATCA
1 A-AATCAAAACAATCCTTTTGATAACATATGTGAGTGA-CAAAAGCAGAATCTAAATACCAATCA
* * * *
2609174 GAATTTGCATCTATATTTTCTGAAATTGTAAGGACATCACAATCATCACCTTCAGCAACGA
64 AAATTTGCATCCATATTTTCTGAAATTGTAAAGACATCACAATCATCACCTTCAGCAATGA
2609235 AA
1 AA
2609237 GTACACTCAC
Statistics
Matches: 117, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
124 3 0.03
125 114 0.97
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.28
Consensus pattern (124 bp):
AAATCAAAACAATCCTTTTGATAACATATGTGAGTGACAAAAGCAGAATCTAAATACCAATCAAA
ATTTGCATCCATATTTTCTGAAATTGTAAAGACATCACAATCATCACCTTCAGCAATGA
Found at i:2615622 original size:20 final size:20
Alignment explanation
Indices: 2615587--2615638 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
2615577 GCAGTGATTG
2615587 TTTTT-TTTTTT-C-TTTCT
1 TTTTTCTTTTTTCCTTTTCT
2615604 TTTTTCTTTTTTCCTTTTCT
1 TTTTTCTTTTTTCCTTTTCT
* *
2615624 CTTTCCTTTTTTCCT
1 TTTTTCTTTTTTCCT
2615639 CTTTAATCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
17 5 0.17
18 6 0.20
19 1 0.03
20 18 0.60
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTTCTTTTTTCCTTTTCT
Found at i:2625293 original size:4 final size:4
Alignment explanation
Indices: 2625284--2625310 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2625274 AAAGTGATCA
2625284 AATT AATT AATT AATT AATT AATT AAT
1 AATT AATT AATT AATT AATT AATT AAT
2625311 GGTTGCTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:2633842 original size:30 final size:30
Alignment explanation
Indices: 2633806--2633863 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
2633796 CAGTAAAATT
2633806 TAAATAAGTAC-TTATACTTTTATATTGAGC
1 TAAATAAG-ACTTTATACTTTTATATTGAGC
* *
2633836 TAAATAAGCCTTTATACTTTTATTTTGA
1 TAAATAAGACTTTATACTTTTATATTGA
2633864 ATCAAAGAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 24 0.96
ACGTcount: A:0.34, C:0.10, G:0.09, T:0.47
Consensus pattern (30 bp):
TAAATAAGACTTTATACTTTTATATTGAGC
Found at i:2633875 original size:30 final size:30
Alignment explanation
Indices: 2633817--2633880 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
2633807 AAATAAGTAC
*
2633817 TTATACTTTTATATTGAGCTAAATAAGCCT
1 TTATACTTTTATATTGAGCTAAAGAAGCCT
* *
2633847 TTATACTTTTATTTTGA-ATCAAAGAAGCCT
1 TTATACTTTTATATTGAGCT-AAAGAAGCCT
2633877 TTAT
1 TTAT
2633881 TATTAATAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 1 0.03
30 29 0.97
ACGTcount: A:0.33, C:0.12, G:0.09, T:0.45
Consensus pattern (30 bp):
TTATACTTTTATATTGAGCTAAAGAAGCCT
Found at i:2633974 original size:33 final size:33
Alignment explanation
Indices: 2633937--2634016 Score: 106
Period size: 33 Copynumber: 2.4 Consensus size: 33
2633927 CGTTACACTA
*
2633937 ATGTGATATACTAAAATATCATAATTGATGATG
1 ATGTGACATACTAAAATATCATAATTGATGATG
* * * *
2633970 ATGTGACATACTGACATATCATAATTGATGGTA
1 ATGTGACATACTAAAATATCATAATTGATGATG
*
2634003 ATATGACATACTAA
1 ATGTGACATACTAA
2634017 TTTAGTATAA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (33 bp):
ATGTGACATACTAAAATATCATAATTGATGATG
Found at i:2646408 original size:75 final size:75
Alignment explanation
Indices: 2646285--2646437 Score: 306
Period size: 75 Copynumber: 2.0 Consensus size: 75
2646275 GTCTTAAACA
2646285 CTTAGTGAATGAGTGGTCATGACTACTATCTTCAACAAAAGGTGATGGTGACACACATTCAATGT
1 CTTAGTGAATGAGTGGTCATGACTACTATCTTCAACAAAAGGTGATGGTGACACACATTCAATGT
2646350 GAAAGGCAAC
66 GAAAGGCAAC
2646360 CTTAGTGAATGAGTGGTCATGACTACTATCTTCAACAAAAGGTGATGGTGACACACATTCAATGT
1 CTTAGTGAATGAGTGGTCATGACTACTATCTTCAACAAAAGGTGATGGTGACACACATTCAATGT
2646425 GAAAGGCAAC
66 GAAAGGCAAC
2646435 CTT
1 CTT
2646438 GCACATTGAA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 78 1.00
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (75 bp):
CTTAGTGAATGAGTGGTCATGACTACTATCTTCAACAAAAGGTGATGGTGACACACATTCAATGT
GAAAGGCAAC
Found at i:2655653 original size:17 final size:16
Alignment explanation
Indices: 2655627--2655677 Score: 59
Period size: 17 Copynumber: 3.2 Consensus size: 16
2655617 CCAGCCGTGA
2655627 TTTTTCTTCTTTTATC
1 TTTTTCTTCTTTTATC
*
2655643 TTTTTCTTTCTTTTTTC
1 TTTTTC-TTCTTTTATC
* *
2655660 TTTTT-TACTTTTCTC
1 TTTTTCTTCTTTTATC
2655675 TTT
1 TTT
2655678 CCTTTTTTCC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
15 11 0.35
16 6 0.19
17 14 0.45
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTCTTCTTTTATC
Found at i:2655672 original size:20 final size:19
Alignment explanation
Indices: 2655633--2655718 Score: 70
Period size: 20 Copynumber: 4.5 Consensus size: 19
2655623 GTGATTTTTC
*
2655633 TTCTTTTATC-TTTTTC-T
1 TTCTTTTTTCTTTTTTCTT
2655650 TTCTTTTTTCTTTTTTACTT
1 TTCTTTTTTCTTTTTT-CTT
* *
2655670 TTCTCTTTCCTTTTTTCCTCT
1 TTCTTTTTTCTTTTTT-CT-T
** *
2655691 TTAATTTTTCTTGTTTCTT
1 TTCTTTTTTCTTTTTTCTT
2655710 TT-TTTTTTC
1 TTCTTTTTTC
2655719 ATTGACTTAG
Statistics
Matches: 55, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
17 9 0.16
18 11 0.20
19 4 0.07
20 19 0.35
21 12 0.22
ACGTcount: A:0.05, C:0.19, G:0.01, T:0.76
Consensus pattern (19 bp):
TTCTTTTTTCTTTTTTCTT
Found at i:2655693 original size:27 final size:25
Alignment explanation
Indices: 2655627--2655702 Score: 89
Period size: 27 Copynumber: 2.9 Consensus size: 25
2655617 CCAGCCGTGA
2655627 TTTTTCTTCTTTTATCTTTTTCTTTCT
1 TTTTTCTTC-TTTA-CTTTTTCTTTCT
*
2655654 TTTTTCTTTTTTACTTTTCTCTTTCCT
1 TTTTTCTTCTTTACTTTT-TCTTT-CT
* *
2655681 TTTTTCCTCTTTAATTTTTCTT
1 TTTTTCTTCTTTACTTTTTCTT
2655703 GTTTCTTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
25 5 0.12
26 13 0.30
27 25 0.58
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (25 bp):
TTTTTCTTCTTTACTTTTTCTTTCT
Found at i:2659656 original size:35 final size:35
Alignment explanation
Indices: 2659617--2659693 Score: 109
Period size: 37 Copynumber: 2.1 Consensus size: 35
2659607 GACTTTAAGA
2659617 GACAGAACTTGAATTTTCTTGATTTCTCTCCTCCT
1 GACAGAACTTGAATTTTCTTGATTTCTCTCCTCCT
** *
2659652 GACAGTGATTTTTAATTTTCTTGATTTCTCTCCTCCT
1 GACA--GAACTTGAATTTTCTTGATTTCTCTCCTCCT
2659689 GACAG
1 GACAG
2659694 TGATTTTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
35 5 0.14
37 32 0.86
ACGTcount: A:0.19, C:0.23, G:0.13, T:0.44
Consensus pattern (35 bp):
GACAGAACTTGAATTTTCTTGATTTCTCTCCTCCT
Found at i:2659669 original size:37 final size:37
Alignment explanation
Indices: 2659628--2659708 Score: 162
Period size: 37 Copynumber: 2.2 Consensus size: 37
2659618 ACAGAACTTG
2659628 AATTTTCTTGATTTCTCTCCTCCTGACAGTGATTTTT
1 AATTTTCTTGATTTCTCTCCTCCTGACAGTGATTTTT
2659665 AATTTTCTTGATTTCTCTCCTCCTGACAGTGATTTTT
1 AATTTTCTTGATTTCTCTCCTCCTGACAGTGATTTTT
2659702 AATTTTC
1 AATTTTC
2659709 CTACATTTCT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.17, C:0.21, G:0.10, T:0.52
Consensus pattern (37 bp):
AATTTTCTTGATTTCTCTCCTCCTGACAGTGATTTTT
Found at i:2666662 original size:23 final size:23
Alignment explanation
Indices: 2666632--2666676 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
2666622 TACAATAACA
2666632 ATTCCTAATTATATTAGGATAAG
1 ATTCCTAATTATATTAGGATAAG
2666655 ATTCCTAATTATATTAGGATAA
1 ATTCCTAATTATATTAGGATAA
2666677 AGTTATTGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (23 bp):
ATTCCTAATTATATTAGGATAAG
Found at i:2670162 original size:23 final size:23
Alignment explanation
Indices: 2670132--2670177 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
2670122 TAGAATAACA
*
2670132 ATTCCTAATTCTATTAGGATAAG
1 ATTCCTAATTATATTAGGATAAG
2670155 ATTCCTAATTATATTAGGATAAG
1 ATTCCTAATTATATTAGGATAAG
2670178 GTTATTGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (23 bp):
ATTCCTAATTATATTAGGATAAG
Found at i:2685250 original size:18 final size:18
Alignment explanation
Indices: 2685227--2685263 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2685217 AGGCGGCTCA
*
2685227 ATCTCTTCCGCCTCCTCC
1 ATCTCTTCCGCCGCCTCC
*
2685245 ATCTCTTCCTCCGCCTCC
1 ATCTCTTCCGCCGCCTCC
2685263 A
1 A
2685264 CCTGCGCCGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.08, C:0.54, G:0.05, T:0.32
Consensus pattern (18 bp):
ATCTCTTCCGCCGCCTCC
Found at i:2707761 original size:19 final size:20
Alignment explanation
Indices: 2707737--2707774 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
2707727 ATTTAAAAAT
*
2707737 ATTATTTTTTA-TAATTTTA
1 ATTATTTTTAATTAATTTTA
2707756 ATTATTTTTAATTAATTTT
1 ATTATTTTTAATTAATTTT
2707775 TGATATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
ATTATTTTTAATTAATTTTA
Found at i:2708628 original size:22 final size:22
Alignment explanation
Indices: 2708563--2708644 Score: 94
Period size: 22 Copynumber: 3.8 Consensus size: 22
2708553 ATTTAATTAC
* *
2708563 TACGTGACTGATTTTTAGAAAA
1 TACGTGACTGATTTTTAGACAT
* * * *
2708585 TACATTATTGATTTTAAG-CAT
1 TACGTGACTGATTTTTAGACAT
*
2708606 TATGTGACTGATTTTTAGACAT
1 TACGTGACTGATTTTTAGACAT
2708628 TACGTGACTGATTTTTA
1 TACGTGACTGATTTTTA
2708645 AGTAATACCT
Statistics
Matches: 47, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
21 14 0.30
22 33 0.70
ACGTcount: A:0.30, C:0.10, G:0.16, T:0.44
Consensus pattern (22 bp):
TACGTGACTGATTTTTAGACAT
Found at i:2708726 original size:26 final size:26
Alignment explanation
Indices: 2708697--2708765 Score: 102
Period size: 26 Copynumber: 2.7 Consensus size: 26
2708687 AATACCTATC
**
2708697 AACTAGTCACGTAATACCTTATCAAA
1 AACTAGTCACACAATACCTTATCAAA
* *
2708723 AACTAGTCACACAATGCTTTATCAAA
1 AACTAGTCACACAATACCTTATCAAA
2708749 AACTAGTCACACAATAC
1 AACTAGTCACACAATAC
2708766 TTAAAGTCAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.43, C:0.25, G:0.07, T:0.25
Consensus pattern (26 bp):
AACTAGTCACACAATACCTTATCAAA
Found at i:2708974 original size:11 final size:10
Alignment explanation
Indices: 2708962--2708995 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
2708952 TTCATATATC
2708962 AAAAATATTT
1 AAAAATATTT
* *
2708972 CAAAATACTT
1 AAAAATATTT
2708982 AAAAATATTT
1 AAAAATATTT
2708992 AAAA
1 AAAA
2708996 CGCTCACAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (10 bp):
AAAAATATTT
Found at i:2720855 original size:25 final size:25
Alignment explanation
Indices: 2720827--2720911 Score: 91
Period size: 25 Copynumber: 3.4 Consensus size: 25
2720817 AGTAGTGGAT
2720827 AATAATTTTACCATCAGAATCTAAG
1 AATAATTTTACCATCAGAATCTAAG
* ** *
2720852 AATAATTTTACCACCAGAAGTGGATG
1 AATAATTTTACCATCAGAA-TCTAAG
* *
2720878 GATAATTTTACTATCAGAATCTAA-
1 AATAATTTTACCATCAGAATCTAAG
2720902 AGATAATTTT
1 A-ATAATTTT
2720912 GCTACCAGAA
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
25 28 0.60
26 19 0.40
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.34
Consensus pattern (25 bp):
AATAATTTTACCATCAGAATCTAAG
Found at i:2720895 original size:26 final size:26
Alignment explanation
Indices: 2720853--2720953 Score: 98
Period size: 25 Copynumber: 4.0 Consensus size: 26
2720843 GAATCTAAGA
*
2720853 ATAATTTTACCACCAGAAGTGGATGG
1 ATAATTTTACTACCAGAAGTGGATGG
* ** **
2720879 ATAATTTTACTATCAGAA-TCTAAAG
1 ATAATTTTACTACCAGAAGTGGATGG
*
2720904 ATAATTTTGCTACCAGAAGTGGATGG
1 ATAATTTTACTACCAGAAGTGGATGG
* * *
2720930 ATAA-TTTACCACAAGTAGTGGATG
1 ATAATTTTACTACCAGAAGTGGATG
2720954 AATGTCATCA
Statistics
Matches: 58, Mismatches: 16, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
25 35 0.60
26 23 0.40
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.31
Consensus pattern (26 bp):
ATAATTTTACTACCAGAAGTGGATGG
Found at i:2720901 original size:51 final size:51
Alignment explanation
Indices: 2720803--2720940 Score: 201
Period size: 51 Copynumber: 2.7 Consensus size: 51
2720793 AATTCTAATT
* *
2720803 ATAATTTTGCCACCAGTAGTGGAT-AATAATTTTACCATCAGAATCT-AAG
1 ATAATTTTGCCACCAGAAGTGGATGGATAATTTTACCATCAGAATCTAAAG
* *
2720852 AATAATTTTACCACCAGAAGTGGATGGATAATTTTACTATCAGAATCTAAAG
1 -ATAATTTTGCCACCAGAAGTGGATGGATAATTTTACCATCAGAATCTAAAG
*
2720904 ATAATTTTGCTACCAGAAGTGGATGGATAA-TTTACCA
1 ATAATTTTGCCACCAGAAGTGGATGGATAATTTTACCA
2720941 CAAGTAGTGG
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
50 28 0.35
51 48 0.61
52 3 0.04
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (51 bp):
ATAATTTTGCCACCAGAAGTGGATGGATAATTTTACCATCAGAATCTAAAG
Found at i:2740627 original size:3 final size:3
Alignment explanation
Indices: 2740621--2740659 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
2740611 CTACTTATAC
* * *
2740621 ATT ATT AGT ATT GTT ATT ATT ATT ATT ATT ACT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2740660 TTTAAAACGG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:2741317 original size:6 final size:6
Alignment explanation
Indices: 2741302--2741347 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
2741292 GTTAGCCACA
* *
2741302 AAAAAG AAAAAC AAAAGAG AAAAAC -AAAAC AAAAA- AAAAAC AAAAA
1 AAAAAC AAAAAC AAAA-AC AAAAAC AAAAAC AAAAAC AAAAAC AAAAA
2741348 AGAAGAGGGG
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
5 10 0.29
6 19 0.56
7 5 0.15
ACGTcount: A:0.85, C:0.09, G:0.07, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:2741317 original size:13 final size:13
Alignment explanation
Indices: 2741299--2741351 Score: 61
Period size: 13 Copynumber: 3.8 Consensus size: 13
2741289 GCAGTTAGCC
2741299 ACAAAAAAGAAAA
1 ACAAAAAAGAAAA
*
2741312 ACAAAAGAGAAAA
1 ACAAAAAAGAAAA
*
2741325 ACAAAACAAAAAAAAA
1 AC--AA-AAAAGAAAA
2741341 ACAAAAAAGAA
1 ACAAAAAAGAA
2741352 GAGGGGGGGA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
13 20 0.61
14 2 0.06
15 2 0.06
16 9 0.27
ACGTcount: A:0.83, C:0.09, G:0.08, T:0.00
Consensus pattern (13 bp):
ACAAAAAAGAAAA
Found at i:2741348 original size:11 final size:11
Alignment explanation
Indices: 2741301--2741348 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
2741291 AGTTAGCCAC
*
2741301 AAAAAAGAAAA
1 AAAAAACAAAA
*
2741312 ACAAAAGAGAAAA
1 A-AAAA-ACAAAA
*
2741325 ACAAAACAAAA
1 AAAAAACAAAA
2741336 AAAAAACAAAA
1 AAAAAACAAAA
2741347 AA
1 AA
2741349 GAAGAGGGGG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
11 18 0.56
12 7 0.22
13 7 0.22
ACGTcount: A:0.85, C:0.08, G:0.06, T:0.00
Consensus pattern (11 bp):
AAAAAACAAAA
Found at i:2741465 original size:71 final size:71
Alignment explanation
Indices: 2741367--2741546 Score: 261
Period size: 71 Copynumber: 2.5 Consensus size: 71
2741357 GGGGAGATCT
* *
2741367 GAGAAAAGAGAGGAAGAGAGGCCGACGAAAGAGAGGGATCGGCCGACAGAAGGCGAAGAGATCCG
1 GAGAGAAGAGA-G-AGAGAGGCCGACGAAAGAGAGGGATCGGCCGACAGAAGACGAAGAGATCCG
* *
2741432 TCGGGAGA
64 CCGAGAGA
* *
2741440 GAGAGAAGAGAGAGAGAGGCTGACGAAAGAGAGGGATCGGCCGACAGAAGACGAAGAGATCTGCC
1 GAGAGAAGAGAGAGAGAGGCCGACGAAAGAGAGGGATCGGCCGACAGAAGACGAAGAGATCCGCC
2741505 GAGAGA
66 GAGAGA
* *
2741511 GAGAGAAGAGAGAGAGAAGCCGACGGGAAGAGAGGG
1 GAGAGAAGAGAGAGAGAGGCCGAC-GAAAGAGAGGG
2741547 GAAGATGTCG
Statistics
Matches: 97, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
71 76 0.78
72 11 0.11
73 10 0.10
ACGTcount: A:0.39, C:0.13, G:0.43, T:0.04
Consensus pattern (71 bp):
GAGAGAAGAGAGAGAGAGGCCGACGAAAGAGAGGGATCGGCCGACAGAAGACGAAGAGATCCGCC
GAGAGA
Found at i:2741500 original size:23 final size:23
Alignment explanation
Indices: 2741474--2741521 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
2741464 GAAAGAGAGG
2741474 GATCGGCCGACAGA-AGACGAAGA
1 GATCGGCCGACAGAGAGA-GAAGA
* *
2741497 GATCTGCCGAGAGAGAGAGAAGA
1 GATCGGCCGACAGAGAGAGAAGA
2741520 GA
1 GA
2741522 GAGAGAAGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 19 0.86
24 3 0.14
ACGTcount: A:0.40, C:0.17, G:0.38, T:0.06
Consensus pattern (23 bp):
GATCGGCCGACAGAGAGAGAAGA
Found at i:2742130 original size:17 final size:16
Alignment explanation
Indices: 2742112--2742174 Score: 72
Period size: 17 Copynumber: 3.8 Consensus size: 16
2742102 ATAAGTAAAT
* *
2742112 AAATAAAAAAAATTCA
1 AAATAAAAAAAAATAA
*
2742128 TAATAAATAAAAAATAA
1 AAATAAA-AAAAAATAA
2742145 AAATAAAAATAAAATAAA
1 AAATAAAAA-AAAAT-AA
2742163 AAATAAAAAAAA
1 AAATAAAAAAAA
2742175 TATATATAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
16 8 0.20
17 21 0.52
18 11 0.28
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.17
Consensus pattern (16 bp):
AAATAAAAAAAAATAA
Found at i:2742135 original size:24 final size:25
Alignment explanation
Indices: 2742102--2742171 Score: 76
Period size: 24 Copynumber: 2.9 Consensus size: 25
2742092 TATATATAAA
2742102 ATAAGTAAATAAATAAA-AAAAATTC
1 ATAAGTAAATAAA-AAATAAAAATTC
2742127 ATAA-TAAATAAAAAATAAAAA-T-
1 ATAAGTAAATAAAAAATAAAAATTC
* *
2742149 AAAAATAAAATAAAAAATAAAAA
1 ATAAGT-AAATAAAAAATAAAAA
2742172 AAATATATAT
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
22 3 0.07
23 5 0.12
24 29 0.71
25 4 0.10
ACGTcount: A:0.77, C:0.01, G:0.01, T:0.20
Consensus pattern (25 bp):
ATAAGTAAATAAAAAATAAAAATTC
Found at i:2742142 original size:7 final size:7
Alignment explanation
Indices: 2742127--2742172 Score: 55
Period size: 7 Copynumber: 7.1 Consensus size: 7
2742117 AAAAAAATTC
*
2742127 ATAATAA
1 ATAAAAA
2742134 ATAAAAA
1 ATAAAAA
2742141 AT-AAAA
1 ATAAAAA
2742147 AT-AAAA
1 ATAAAAA
2742153 AT--AAA
1 ATAAAAA
2742158 ATAAAAA
1 ATAAAAA
2742165 ATAAAAA
1 ATAAAAA
2742172 A
1 A
2742173 AATATATATA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
5 5 0.14
6 12 0.33
7 19 0.53
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (7 bp):
ATAAAAA
Found at i:2742148 original size:6 final size:6
Alignment explanation
Indices: 2742127--2742171 Score: 56
Period size: 6 Copynumber: 7.2 Consensus size: 6
2742117 AAAAAAATTC
2742127 ATAATAA ATAAAAA ATAAAA ATAAAA AT-AAA ATAAAAA ATAAAA A
1 ATAA-AA AT-AAAA ATAAAA ATAAAA ATAAAA AT-AAAA ATAAAA A
2742172 AAATATATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.14
6 17 0.49
7 11 0.31
8 2 0.06
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
ATAAAA
Found at i:2742167 original size:51 final size:53
Alignment explanation
Indices: 2742099--2742201 Score: 135
Period size: 51 Copynumber: 2.0 Consensus size: 53
2742089 ACATATATAT
*
2742099 AAAATAAGTAAATAAATAAAAAAAAT-TCATAATAAATAA-AA-AATAA-AAATA
1 AAAATAAATAAATAAATAAAAAAAATAT-AT-ATAAATAACAACAATAACAAATA
2742150 AAAATAAAATAAA-AAATAAAAAAAATATATATAAATAACAACAATAACAAAT
1 AAAAT-AAATAAATAAATAAAAAAAATATATATAAATAACAACAATAACAAAT
2742202 GAATAAAAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 8
0.84 0.02 0.15
Matches are distributed among these distances:
50 8 0.17
51 22 0.48
52 12 0.26
53 4 0.09
ACGTcount: A:0.75, C:0.04, G:0.01, T:0.20
Consensus pattern (53 bp):
AAAATAAATAAATAAATAAAAAAAATATATATAAATAACAACAATAACAAATA
Found at i:2742210 original size:37 final size:34
Alignment explanation
Indices: 2742133--2742219 Score: 95
Period size: 33 Copynumber: 2.5 Consensus size: 34
2742123 ATTCATAATA
* * *
2742133 AATAAAAAATAAAAATAAAAATAAAATAAAAAAT
1 AATAAAAAATATATATAAAAACAAAATAAAAAAT
*
2742167 AA-AAAAAATATATATAAATAACAACAATAACAAAT
1 AATAAAAAATATATATAAA-AACAA-AATAAAAAAT
*
2742202 GAATAAAAAATATTTATA
1 -AATAAAAAATATATATA
2742220 TTATAAATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
33 14 0.32
34 6 0.14
35 9 0.20
36 2 0.05
37 13 0.30
ACGTcount: A:0.74, C:0.03, G:0.01, T:0.22
Consensus pattern (34 bp):
AATAAAAAATATATATAAAAACAAAATAAAAAAT
Found at i:2747581 original size:36 final size:36
Alignment explanation
Indices: 2747534--2747605 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
2747524 AATGGATTGG
2747534 AGGATGAGTGAGGCTGCTCAAACAGGAAACATCAAC
1 AGGATGAGTGAGGCTGCTCAAACAGGAAACATCAAC
2747570 AGGATGAGTGAGGCTGCTCAAACAGGAAACATCAAC
1 AGGATGAGTGAGGCTGCTCAAACAGGAAACATCAAC
2747606 GTATTGTATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.39, C:0.19, G:0.28, T:0.14
Consensus pattern (36 bp):
AGGATGAGTGAGGCTGCTCAAACAGGAAACATCAAC
Found at i:2750151 original size:23 final size:23
Alignment explanation
Indices: 2750123--2750174 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
2750113 TTGTTATTAG
2750123 CATTGCGTGACTTGTTTATAGAT
1 CATTGCGTGACTTGTTTATAGAT
2750146 CATTGCGTGACTTGTTTATAGAT
1 CATTGCGTGACTTGTTTATAGAT
2750169 CATTGC
1 CATTGC
2750175 ATGATTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.42
Consensus pattern (23 bp):
CATTGCGTGACTTGTTTATAGAT
Found at i:2754105 original size:23 final size:23
Alignment explanation
Indices: 2754079--2754128 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
2754069 ACTCAAATTT
*
2754079 GAATAACGTGAGTAGTTAATATG
1 GAATAACGTGACTAGTTAATATG
** *
2754102 GAATCGCGTGACTAGTTATTATG
1 GAATAACGTGACTAGTTAATATG
2754125 GAAT
1 GAAT
2754129 CGCATTACAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.34, C:0.08, G:0.26, T:0.32
Consensus pattern (23 bp):
GAATAACGTGACTAGTTAATATG
Found at i:2754129 original size:23 final size:23
Alignment explanation
Indices: 2754085--2754131 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
2754075 ATTTGAATAA
*
2754085 CGTGAGTAGTTAATATGGAATCG
1 CGTGACTAGTTAATATGGAATCG
*
2754108 CGTGACTAGTTATTATGGAATCG
1 CGTGACTAGTTAATATGGAATCG
2754131 C
1 C
2754132 ATTACAAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.32
Consensus pattern (23 bp):
CGTGACTAGTTAATATGGAATCG
Found at i:2754141 original size:23 final size:23
Alignment explanation
Indices: 2754092--2754146 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
2754082 TAACGTGAGT
* *
2754092 AGTTAATATGGAATCGCGTGACT
1 AGTTAATATGGAATCGCATGACA
* *
2754115 AGTTATTATGGAATCGCATTACA
1 AGTTAATATGGAATCGCATGACA
*
2754138 AGTTGATAT
1 AGTTAATAT
2754147 TGAGTCATGT
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:0.11, G:0.22, T:0.35
Consensus pattern (23 bp):
AGTTAATATGGAATCGCATGACA
Found at i:2763420 original size:20 final size:22
Alignment explanation
Indices: 2763392--2763437 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 22
2763382 TATTTCTATT
*
2763392 TAAACTTATAATAT-T-AAATA
1 TAAAATTATAATATGTAAAATA
2763412 TAAAATTATAATATGTAAAATA
1 TAAAATTATAATATGTAAAATA
2763434 TAAA
1 TAAA
2763438 TACTTAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.57
21 1 0.04
22 9 0.39
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (22 bp):
TAAAATTATAATATGTAAAATA
Found at i:2789113 original size:57 final size:55
Alignment explanation
Indices: 2789052--2789158 Score: 160
Period size: 57 Copynumber: 1.9 Consensus size: 55
2789042 CGTTTCCATT
* **
2789052 ATTTATTTTATTTATTATCATTATTTACCTCTTTTTATTCAAACAGTCAATTTCATA
1 ATTTATATTATTTATTATCATTA-TTACCTCTTCCTATTCAAACAG-CAATTTCATA
*
2789109 ATTTATATTATTTATTATCGTTATTACCTCTTCCTATTCAAACAGCAATT
1 ATTTATATTATTTATTATCATTATTACCTCTTCCTATTCAAACAGCAATT
2789159 GACTGACCAA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
55 5 0.11
56 20 0.43
57 21 0.46
ACGTcount: A:0.30, C:0.16, G:0.03, T:0.51
Consensus pattern (55 bp):
ATTTATATTATTTATTATCATTATTACCTCTTCCTATTCAAACAGCAATTTCATA
Found at i:2793877 original size:35 final size:35
Alignment explanation
Indices: 2793838--2793905 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
2793828 CTTTTGTCTT
* *
2793838 AATCACTTCCACCGGCACCATATTGTTTAACTCTC
1 AATCACTTCCACCGGCACCATACTGTTCAACTCTC
**
2793873 AATCACTTCCATTGGCACCATACTGTTCAACTC
1 AATCACTTCCACCGGCACCATACTGTTCAACTC
2793906 AAATATCACC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.26, C:0.34, G:0.09, T:0.31
Consensus pattern (35 bp):
AATCACTTCCACCGGCACCATACTGTTCAACTCTC
Found at i:2807650 original size:15 final size:15
Alignment explanation
Indices: 2807630--2807659 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2807620 TCTTTGTTGT
*
2807630 TTTTTTTCTTTTTAA
1 TTTTTTTATTTTTAA
2807645 TTTTTTTATTTTTAA
1 TTTTTTTATTTTTAA
2807660 ATTGTAGTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTTTATTTTTAA
Found at i:2807961 original size:3 final size:3
Alignment explanation
Indices: 2807953--2807994 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
2807943 GGGAGTCTCT
2807953 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2807995 AGTGGGTGAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2808835 original size:17 final size:18
Alignment explanation
Indices: 2808813--2808856 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
2808803 AATTTTATTA
2808813 ATATTTTTTA-CTTTTAT
1 ATATTTTTTAGCTTTTAT
*
2808830 ATATTTTTTTAGTTTTTAT
1 ATA-TTTTTTAGCTTTTAT
2808849 ATATTTTT
1 ATATTTTT
2808857 AATATAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 3 0.12
18 12 0.50
19 9 0.38
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (18 bp):
ATATTTTTTAGCTTTTAT
Found at i:2808839 original size:19 final size:19
Alignment explanation
Indices: 2808816--2808856 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
2808806 TTTATTAATA
2808816 TTTTTTA-CTTTTATATAT
1 TTTTTTAGCTTTTATATAT
*
2808834 TTTTTTAGTTTTTATATAT
1 TTTTTTAGCTTTTATATAT
2808853 TTTT
1 TTTT
2808857 AATATAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (19 bp):
TTTTTTAGCTTTTATATAT
Found at i:2810129 original size:58 final size:59
Alignment explanation
Indices: 2810004--2810130 Score: 150
Period size: 58 Copynumber: 2.2 Consensus size: 59
2809994 AGAAAAGCCT
* * *
2810004 TTAAGCATTTTAAGTATTTTGAAGTGGTTTTTAATACATGAAGAAAAACCGTTGAGCATT
1 TTAAGCATTTTAAGCATTTTGAAGTGATTTTT-ATACATGAAGAAAAACCGTTGAGCATA
* * * * *
2810064 TTTAGCATTTTAAAGCATTTTGGAGTGATTTTT-T-TATGAAGAAAAACCTTTGAGTATA
1 TTAAGCATTTT-AAGCATTTTGAAGTGATTTTTATACATGAAGAAAAACCGTTGAGCATA
2810122 TTAAGCATT
1 TTAAGCATT
2810131 CTTCATCAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
58 28 0.49
59 1 0.02
60 10 0.18
61 18 0.32
ACGTcount: A:0.34, C:0.08, G:0.17, T:0.41
Consensus pattern (59 bp):
TTAAGCATTTTAAGCATTTTGAAGTGATTTTTATACATGAAGAAAAACCGTTGAGCATA
Found at i:2810339 original size:22 final size:23
Alignment explanation
Indices: 2810296--2810341 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
2810286 AGTACATGAT
*
2810296 TGGTTGATATGACATTATGTGAC
1 TGGTTGATATGACATTACGTGAC
*
2810319 TGGTTGAT-TGGCATTACGTGAC
1 TGGTTGATATGACATTACGTGAC
2810341 T
1 T
2810342 AGTTAGTAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.22, C:0.11, G:0.28, T:0.39
Consensus pattern (23 bp):
TGGTTGATATGACATTACGTGAC
Found at i:2810356 original size:23 final size:23
Alignment explanation
Indices: 2810328--2810391 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
2810318 CTGGTTGATT
*
2810328 GGCATTACGTGACTAGTTAGTAA
1 GGCATTACATGACTAGTTAGTAA
*
2810351 GGCATTGCATGACTAGTTAGTAA
1 GGCATTACATGACTAGTTAGTAA
*
2810374 GGCATTATATGACTAGTT
1 GGCATTACATGACTAGTT
2810392 TTTAGCTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (23 bp):
GGCATTACATGACTAGTTAGTAA
Found at i:2810484 original size:22 final size:22
Alignment explanation
Indices: 2810458--2810504 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
2810448 TACAATGCTT
**
2810458 TAAAAACCAGTGACACAATACC
1 TAAAAACCAGCAACACAATACC
* *
2810480 TAAAAACTAGCAACGCAATACC
1 TAAAAACCAGCAACACAATACC
2810502 TAA
1 TAA
2810505 TAACTAATTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.26, G:0.09, T:0.15
Consensus pattern (22 bp):
TAAAAACCAGCAACACAATACC
Found at i:2822271 original size:2 final size:2
Alignment explanation
Indices: 2822264--2822291 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2822254 GTACTAGATT
2822264 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2822292 CATGGAAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2822863 original size:2 final size:2
Alignment explanation
Indices: 2822856--2822908 Score: 72
Period size: 2 Copynumber: 27.0 Consensus size: 2
2822846 TTTATTTGTA
* * *
2822856 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT GT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2822898 AT A- AT AT AT AT
1 AT AT AT AT AT AT
2822909 TTCTTTTTGG
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2828199 original size:34 final size:36
Alignment explanation
Indices: 2828144--2828238 Score: 108
Period size: 35 Copynumber: 2.7 Consensus size: 36
2828134 ACGTTATCAC
*
2828144 ATTTAAAAGAAAATCAATCAATTTTACCTTAT-TGT
1 ATTTAAAAGAAAAACAATCAATTTTACCTTATATGT
* *
2828179 ATTTAAAA-AAAAACAATCAA-TTAATCTTATCATGT
1 ATTTAAAAGAAAAACAATCAATTTTACCTTAT-ATGT
* *
2828214 -TTTAAAATAAAAATAATCAATTTTA
1 ATTTAAAAGAAAAACAATCAATTTTA
2828239 TCTCAATACG
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
33 8 0.16
34 18 0.35
35 22 0.43
36 3 0.06
ACGTcount: A:0.49, C:0.09, G:0.03, T:0.38
Consensus pattern (36 bp):
ATTTAAAAGAAAAACAATCAATTTTACCTTATATGT
Found at i:2848689 original size:56 final size:56
Alignment explanation
Indices: 2848622--2848736 Score: 149
Period size: 56 Copynumber: 2.1 Consensus size: 56
2848612 GTTCGGGTTA
* * * * *
2848622 TTTTTAATTTAAGTGTTGACTTTTTAAGTCAAATGAAATTGGATTTAGATGAATTG
1 TTTTCAATTTAAGTGTTGACCTTTTAAGTCAAATGAAATTAGATTTAAACGAATTG
* * * *
2848678 TTTTCAATTTAAGTGTTGGCCTTTTAAGTCACATGGATTTAGATTTAAACGAATTG
1 TTTTCAATTTAAGTGTTGACCTTTTAAGTCAAATGAAATTAGATTTAAACGAATTG
2848734 TTT
1 TTT
2848737 GAATTAGAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
56 50 1.00
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.46
Consensus pattern (56 bp):
TTTTCAATTTAAGTGTTGACCTTTTAAGTCAAATGAAATTAGATTTAAACGAATTG
Found at i:2855598 original size:6 final size:7
Alignment explanation
Indices: 2855583--2855607 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2855573 CTATATAAAC
2855583 TTTTATT
1 TTTTATT
2855590 TTTTATT
1 TTTTATT
2855597 TTTTATT
1 TTTTATT
2855604 TTTT
1 TTTT
2855608 TCTTAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTATT
Found at i:2855723 original size:22 final size:22
Alignment explanation
Indices: 2855697--2855743 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
2855687 CTCCCTTCTG
*
2855697 AGGGAACTGTTGTGCTCCATCA
1 AGGGAACTGTCGTGCTCCATCA
* *
2855719 AGGGAATTGTCGTGCTCCCTCA
1 AGGGAACTGTCGTGCTCCATCA
2855741 AGG
1 AGG
2855744 AAGCGCCAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.21, C:0.23, G:0.30, T:0.26
Consensus pattern (22 bp):
AGGGAACTGTCGTGCTCCATCA
Found at i:2856272 original size:17 final size:18
Alignment explanation
Indices: 2856229--2856275 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
2856219 TTTCAACATA
*
2856229 AAATGTTGAGTTGAATTTG
1 AAATGTTCA-TTGAATTTG
2856248 ATAATGTTCATTGAA-TTG
1 A-AATGTTCATTGAATTTG
2856266 AAATGTTCAT
1 AAATGTTCAT
2856276 CTTCTTCCCC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 9 0.35
18 4 0.15
19 6 0.23
20 7 0.27
ACGTcount: A:0.34, C:0.04, G:0.19, T:0.43
Consensus pattern (18 bp):
AAATGTTCATTGAATTTG
Done.