Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007867.1 Hibiscus syriacus cultivar Beakdansim tig00110239_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3477501
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 18
Found at i:2977086 original size:20 final size:20
Alignment explanation
Indices: 2977061--2977110 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
2977051 GCAATGTGCG
2977061 TTTATTTTCGCAACGCGAAT
1 TTTATTTTCGCAACGCGAAT
*
2977081 TTTATTTTCGCAACGTGAAT
1 TTTATTTTCGCAACGCGAAT
2977101 TTTATTTTCG
1 TTTATTTTCG
2977111 AATTCGAAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.22, C:0.16, G:0.14, T:0.48
Consensus pattern (20 bp):
TTTATTTTCGCAACGCGAAT
Found at i:2977257 original size:22 final size:22
Alignment explanation
Indices: 2977232--2977303 Score: 126
Period size: 22 Copynumber: 3.3 Consensus size: 22
2977222 CACTCTCTAT
2977232 GGCGACATCCGTCCCCATCTCC
1 GGCGACATCCGTCCCCATCTCC
2977254 GGCGACATCCGTCCCCATCTCC
1 GGCGACATCCGTCCCCATCTCC
*
2977276 GGCGACATCCGTCCCCATATCC
1 GGCGACATCCGTCCCCATCTCC
*
2977298 GACGAC
1 GGCGAC
2977304 CCCCCCTCCA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.17, C:0.47, G:0.19, T:0.17
Consensus pattern (22 bp):
GGCGACATCCGTCCCCATCTCC
Found at i:2977718 original size:34 final size:34
Alignment explanation
Indices: 2977680--2977745 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
2977670 GCAATTTTAG
*
2977680 TTTTCGCGTTGCAAATTCCGTGTTGCGAATTTCA
1 TTTTCGAGTTGCAAATTCCGTGTTGCGAATTTCA
* * * *
2977714 TTTTCGAGTTGCGATTTTCTTGTTGCGAATTT
1 TTTTCGAGTTGCAAATTCCGTGTTGCGAATTT
2977746 AAGTTTCAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.15, C:0.17, G:0.21, T:0.47
Consensus pattern (34 bp):
TTTTCGAGTTGCAAATTCCGTGTTGCGAATTTCA
Found at i:2979334 original size:42 final size:42
Alignment explanation
Indices: 2979249--2979351 Score: 129
Period size: 42 Copynumber: 2.5 Consensus size: 42
2979239 CCCCACTTCA
* * *
2979249 ACACCGAGATCCATCACCTGATCGAGTCTCTTCTTTACTTCG
1 ACACCGAGATCCATCACCTGATCGAGTCTATTCTTCACCTCG
*
2979291 ACACCGAGATTCATCACCTGATCGAGT-TGATT-TTACACCTCG
1 ACACCGAGATCCATCACCTGATCGAGTCT-ATTCTT-CACCTCG
*
2979333 ACACCGAGAGCCATCACCT
1 ACACCGAGATCCATCACCT
2979352 ATTCCATCAC
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
41 3 0.06
42 50 0.94
ACGTcount: A:0.25, C:0.33, G:0.16, T:0.26
Consensus pattern (42 bp):
ACACCGAGATCCATCACCTGATCGAGTCTATTCTTCACCTCG
Found at i:2979490 original size:21 final size:20
Alignment explanation
Indices: 2979466--2979641 Score: 100
Period size: 21 Copynumber: 8.4 Consensus size: 20
2979456 GTTAGGGGAG
2979466 TTACGTGATGAGGTCAGTGCT
1 TTACGTGATGAGGT-AGTGCT
*
2979487 TTACGTGATGAGGTCGGTGCT
1 TTACGTGATGAGGT-AGTGCT
* * * * *
2979508 TTACATGACGAGAATGGTGCA
1 TTACGTGATGAG-GTAGTGCT
** *
2979529 TGGCGTGATGAGGTAGGGTCT
1 TTACGTGATGAGGTAGTG-CT
* *
2979550 TTACGTGGTGAGGTAGTTGTT
1 TTACGTGATGAGGTAG-TGCT
** * *
2979571 TTACGTGATGACAATGGTACT
1 TTACGTGATGA-GGTAGTGCT
* *
2979592 TTACGTGGTGAGGTATCTGCT
1 TTACGTGATGAGGTA-GTGCT
* *
2979613 TTATGTGATGAGGTTGTTGCT
1 TTACGTGATGAGGTAG-TGCT
*
2979634 CTACGTGA
1 TTACGTGA
2979642 GATTGTTTCA
Statistics
Matches: 113, Mismatches: 36, Indels: 12
0.70 0.22 0.07
Matches are distributed among these distances:
20 4 0.04
21 105 0.93
22 4 0.04
ACGTcount: A:0.19, C:0.12, G:0.34, T:0.35
Consensus pattern (20 bp):
TTACGTGATGAGGTAGTGCT
Found at i:2979574 original size:63 final size:63
Alignment explanation
Indices: 2979469--2979588 Score: 152
Period size: 63 Copynumber: 1.9 Consensus size: 63
2979459 AGGGGAGTTA
* * *
2979469 CGTGATGAGGTCAGTGCTTTACGTGATGAGGTCGGTGCTTTACATGACGAGAATGGTGCATGG
1 CGTGATGAGGTCAGGGCTTTACGTGATGAGGTAGGTGCTTTACATGACGACAATGGTGCATGG
* * * * *
2979532 CGTGATGAGGT-AGGGTCTTTACGTGGTGAGGTAGTTGTTTTACGTGATGACAATGGT
1 CGTGATGAGGTCAGGG-CTTTACGTGATGAGGTAGGTGCTTTACATGACGACAATGGT
2979589 ACTTTACGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
62 3 0.06
63 45 0.94
ACGTcount: A:0.20, C:0.12, G:0.37, T:0.32
Consensus pattern (63 bp):
CGTGATGAGGTCAGGGCTTTACGTGATGAGGTAGGTGCTTTACATGACGACAATGGTGCATGG
Found at i:2979578 original size:42 final size:43
Alignment explanation
Indices: 2979532--2979626 Score: 115
Period size: 42 Copynumber: 2.3 Consensus size: 43
2979522 TGGTGCATGG
*
2979532 CGTGATGAGGTAGGGT-CTTTACGTGGTGAGGTAGT-TGTTTTA
1 CGTGATGAGGTAGGGTACTTTACGTGGTGAGGTA-TCTGCTTTA
** *
2979574 CGTGATGA-CAATGGTACTTTACGTGGTGAGGTATCTGCTTTA
1 CGTGATGAGGTAGGGTACTTTACGTGGTGAGGTATCTGCTTTA
*
2979616 TGTGATGAGGT
1 CGTGATGAGGT
2979627 TGTTGCTCTA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
41 5 0.12
42 38 0.88
ACGTcount: A:0.19, C:0.09, G:0.35, T:0.37
Consensus pattern (43 bp):
CGTGATGAGGTAGGGTACTTTACGTGGTGAGGTATCTGCTTTA
Found at i:2979951 original size:21 final size:21
Alignment explanation
Indices: 2979925--2980099 Score: 158
Period size: 21 Copynumber: 8.3 Consensus size: 21
2979915 GAAGAAGCTC
* *
2979925 GATCCACCTACCATTGTTCAG
1 GATCCACCTCCCATCGTTCAG
* *
2979946 GATCCACCTACCATTGTTCAG
1 GATCCACCTCCCATCGTTCAG
* **
2979967 GATCTACCTCCCATTATTCAG
1 GATCCACCTCCCATCGTTCAG
* ** *
2979988 GATTCACCTGTCATCGTTCAA
1 GATCCACCTCCCATCGTTCAG
* *
2980009 GAGGCC-CCTCCCATCGTTCAA
1 GA-TCCACCTCCCATCGTTCAG
* *
2980030 GAGGCC-CCTTCCATCGTTCAG
1 GA-TCCACCTCCCATCGTTCAG
*
2980051 GATCCACCTCCCACCGTTCAG
1 GATCCACCTCCCATCGTTCAG
2980072 GATCCACCTCCCA-CTGTTCAG
1 GATCCACCTCCCATC-GTTCAG
2980093 GATCCAC
1 GATCCAC
2980100 ATGGCATACT
Statistics
Matches: 132, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
20 3 0.02
21 128 0.97
22 1 0.01
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (21 bp):
GATCCACCTCCCATCGTTCAG
Found at i:2981531 original size:16 final size:16
Alignment explanation
Indices: 2981502--2981537 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2981492 TGTAAATAAA
* *
2981502 AATTGTTTTTTTGTTT
1 AATTGATTTGTTGTTT
2981518 AATTGATTTGTTGTTT
1 AATTGATTTGTTGTTT
2981534 AATT
1 AATT
2981538 TCAATCTGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.14, T:0.67
Consensus pattern (16 bp):
AATTGATTTGTTGTTT
Found at i:2984238 original size:24 final size:24
Alignment explanation
Indices: 2984204--2984259 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
2984194 CTGAAACATC
*
2984204 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAATTCCGAGTATTGACCAAG
*
2984228 ATCAAATTCCGGGTATTGACCAAG
1 ATCAAATTCCGAGTATTGACCAAG
2984252 ATCAAATT
1 ATCAAATT
2984260 TCGAATACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (24 bp):
ATCAAATTCCGAGTATTGACCAAG
Found at i:2984271 original size:24 final size:24
Alignment explanation
Indices: 2984204--2984271 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
2984194 CTGAAACATC
* * *
2984204 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAATTCCGAATACTGACCAAG
** *
2984228 ATCAAATTCCGGGTATTGACCAAG
1 ATCAAATTCCGAATACTGACCAAG
*
2984252 ATCAAATTTCGAATACTGAC
1 ATCAAATTCCGAATACTGAC
2984272 TAGTACTCAC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.25
Consensus pattern (24 bp):
ATCAAATTCCGAATACTGACCAAG
Found at i:2985045 original size:15 final size:16
Alignment explanation
Indices: 2985009--2985046 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
2984999 AAATCATTGA
*
2985009 AAAATTATATAGAAAT
1 AAAATTATATAGAAAC
*
2985025 AAAATTATGTA-AAAC
1 AAAATTATATAGAAAC
2985040 AAAATTA
1 AAAATTA
2985047 GAGATGGGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (16 bp):
AAAATTATATAGAAAC
Found at i:2985210 original size:18 final size:18
Alignment explanation
Indices: 2985187--2985221 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2985177 CAAAACATTT
2985187 TTGTTGCGAAAATAAAAG
1 TTGTTGCGAAAATAAAAG
* *
2985205 TTGTTGTGAAATTAAAA
1 TTGTTGCGAAAATAAAA
2985222 TTCGTGTTGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.03, G:0.20, T:0.34
Consensus pattern (18 bp):
TTGTTGCGAAAATAAAAG
Found at i:2985266 original size:40 final size:39
Alignment explanation
Indices: 2985218--2985358 Score: 140
Period size: 40 Copynumber: 3.5 Consensus size: 39
2985208 TTGTGAAATT
*
2985218 AAAATTCGTGTTGCGAATTCGGAAATCGAGTTGCGAAAA
1 AAAATTCGTGTTGCGAATTCGAAAATCGAGTTGCGAAAA
* * **
2985257 CAAAATTCGTGTTGTGAATTAGAAAATCTTGTTGCGAAAA
1 -AAAATTCGTGTTGCGAATTCGAAAATCGAGTTGCGAAAA
* ** * *
2985297 GGAAACTT-GTGTTGCGAATTTAAAAATCGCGTTGCTAAAA
1 --AAAATTCGTGTTGCGAATTCGAAAATCGAGTTGCGAAAA
*
2985337 ATAAATTCGCGTTGCGAATTCG
1 A-AAATTCGTGTTGCGAATTCG
2985359 CAACGCAAAT
Statistics
Matches: 81, Mismatches: 17, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
38 1 0.01
39 4 0.05
40 71 0.88
41 5 0.06
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.30
Consensus pattern (39 bp):
AAAATTCGTGTTGCGAATTCGAAAATCGAGTTGCGAAAA
Found at i:2985270 original size:20 final size:20
Alignment explanation
Indices: 2985188--2985354 Score: 69
Period size: 20 Copynumber: 8.4 Consensus size: 20
2985178 AAAACATTTT
*
2985188 TGTTGCGAAAATAAAAGT--
1 TGTTGCGAAAATAAAATTCG
* *
2985206 TGTTGTGAAATTAAAATTCG
1 TGTTGCGAAAATAAAATTCG
* *
2985226 TGTTGCG-AATTCGGAAA-TCG
1 TGTTGCGAAAAT--AAAATTCG
* *
2985246 AGTTGCGAAAACAAAATTCG
1 TGTTGCGAAAATAAAATTCG
* * * *
2985266 TGTTGTG-AATTAGAAAATCT
1 TGTTGCGAAAATA-AAATTCG
* *
2985286 TGTTGCGAAAAGGAAACTT-G
1 TGTTGCGAAAA-TAAAATTCG
** *
2985306 TGTTGCGAATTTAAAAATCG
1 TGTTGCGAAAATAAAATTCG
* *
2985326 CGTTGCTAAAA-ATAAATTCG
1 TGTTGCGAAAATA-AAATTCG
*
2985346 CGTTGCGAA
1 TGTTGCGAA
2985355 TTCGCAACGC
Statistics
Matches: 106, Mismatches: 32, Indels: 20
0.67 0.20 0.13
Matches are distributed among these distances:
18 15 0.14
19 15 0.14
20 65 0.61
21 10 0.09
22 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.31
Consensus pattern (20 bp):
TGTTGCGAAAATAAAATTCG
Found at i:2985311 original size:60 final size:58
Alignment explanation
Indices: 2985188--2985314 Score: 132
Period size: 60 Copynumber: 2.2 Consensus size: 58
2985178 AAAACATTTT
* * **
2985188 TGTTGCGAAAATAAAAGTTGTTGTGAAATTAAAATTCGTGTTGCGAATTCGGAAATCG
1 TGTTGCGAAAACAAAAGTTGTTGTGAAATTAAAAATCGTGTTGCGAATAAGGAAATCG
* * * *
2985246 AGTTGCGAAAACAAAATTCGTGTTGTG-AATTAGAAAATCTTGTTGCGAA-AAGGAAACTTG
1 TGTTGCGAAAACAAAAGT--TGTTGTGAAATTA-AAAATCGTGTTGCGAATAAGGAAA-TCG
2985306 TGTTGCGAA
1 TGTTGCGAA
2985315 TTTAAAAATC
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
58 15 0.27
59 10 0.18
60 31 0.55
ACGTcount: A:0.35, C:0.09, G:0.24, T:0.31
Consensus pattern (58 bp):
TGTTGCGAAAACAAAAGTTGTTGTGAAATTAAAAATCGTGTTGCGAATAAGGAAATCG
Found at i:2985423 original size:20 final size:21
Alignment explanation
Indices: 2985400--2985448 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
2985390 TGGAGTTCGT
2985400 GTTGCGAATTTA-AAAATCGC
1 GTTGCGAATTTAGAAAATCGC
2985420 GTTGCGAATTTAGAAAATCGC
1 GTTGCGAATTTAGAAAATCGC
2985441 GTTGCGAA
1 GTTGCGAA
2985449 AAAGAAATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (21 bp):
GTTGCGAATTTAGAAAATCGC
Found at i:2985497 original size:20 final size:19
Alignment explanation
Indices: 2985460--2985508 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
2985450 AAGAAATTCA
2985460 AGTTGCGAATTTCAAAACT
1 AGTTGCGAATTTCAAAACT
**
2985479 GAGTTGCGAATTTGTAAACT
1 -AGTTGCGAATTTCAAAACT
2985499 ATGTTGCGAA
1 A-GTTGCGAA
2985509 ATTGGAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.33
Consensus pattern (19 bp):
AGTTGCGAATTTCAAAACT
Found at i:2988684 original size:17 final size:18
Alignment explanation
Indices: 2988650--2988682 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
2988640 TTTTATTTGT
2988650 AATTTATTTAAGTATTTA
1 AATTTATTTAAGTATTTA
2988668 AATTT-TTTAA-TATTT
1 AATTTATTTAAGTATTT
2988683 TATTTAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
AATTTATTTAAGTATTTA
Found at i:2994516 original size:27 final size:26
Alignment explanation
Indices: 2994469--2994535 Score: 62
Period size: 27 Copynumber: 2.5 Consensus size: 26
2994459 TAACTTTTCA
* * * *
2994469 AAATATATATTTCTATCTTAATTTACT
1 AAATATATA-TTATAACTTAAATAACT
*
2994496 AAATATATATTATAACTTTAAATAATT
1 AAATATATATTATAAC-TTAAATAACT
*
2994523 AAATATATTTTAT
1 AAATATATATTAT
2994536 TCTTACCTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
26 5 0.15
27 28 0.85
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (26 bp):
AAATATATATTATAACTTAAATAACT
Found at i:2994611 original size:26 final size:27
Alignment explanation
Indices: 2994582--2994675 Score: 85
Period size: 26 Copynumber: 3.6 Consensus size: 27
2994572 ATTTTAAAAT
2994582 TAAAAT-TATTTAAATTAAGTTTATAA
1 TAAAATATATTTAAATTAAGTTTATAA
2994608 TAAAATATATTT-AA-TAAGTTAATATAA
1 TAAAATATATTTAAATTAAGTT--TATAA
* *
2994635 -AAAATATTTTTAAAGTTAA-TATAT-A
1 TAAAATATATTTAAA-TTAAGTTTATAA
*
2994660 TAAAATAT-TATAAATT
1 TAAAATATATTTAAATT
2994676 TATATTTAAT
Statistics
Matches: 58, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
24 2 0.03
25 12 0.21
26 28 0.48
27 12 0.21
28 1 0.02
29 3 0.05
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (27 bp):
TAAAATATATTTAAATTAAGTTTATAA
Found at i:2994641 original size:24 final size:24
Alignment explanation
Indices: 2994583--2994668 Score: 75
Period size: 24 Copynumber: 3.4 Consensus size: 24
2994573 TTTTAAAATT
* *
2994583 AAAATTATTTAAATTAAGTTTATAATA
1 AAAAATATTT-AA-TAAGTTAAT-ATA
*
2994610 AAATATATTTAATAAGTTAATATA
1 AAAAATATTTAATAAGTTAATATA
*
2994634 AAAAATATTT-TTAAAGTTAATATA
1 AAAAATATTTAAT-AAGTTAATATA
2994658 TATAAAATATT
1 -A-AAAATATT
2994669 ATAAATTTAT
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
23 1 0.02
24 23 0.45
25 9 0.18
26 10 0.20
27 8 0.16
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (24 bp):
AAAAATATTTAATAAGTTAATATA
Found at i:2995029 original size:23 final size:23
Alignment explanation
Indices: 2994974--2995036 Score: 65
Period size: 23 Copynumber: 2.6 Consensus size: 23
2994964 TAAAAACAAT
2994974 AAATAATATTATTTATCATAAAAATTA
1 AAATAAT-TTATTT-T--TAAAAATTA
*
2995001 ATATAA-TTATTTTTAAAATATTA
1 AAATAATTTATTTTTAAAA-ATTA
2995024 AAATAATTTATTT
1 AAATAATTTATTT
2995037 ATTATTAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
22 5 0.16
23 9 0.28
24 7 0.22
25 6 0.19
27 5 0.16
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
AAATAATTTATTTTTAAAAATTA
Found at i:2995138 original size:31 final size:31
Alignment explanation
Indices: 2995060--2995178 Score: 86
Period size: 31 Copynumber: 3.7 Consensus size: 31
2995050 TTATTCATAA
2995060 TTTATTAT-ATATTATTATAATA-AATATATAATAT
1 TTTATTATAATATTA--ATAATATAAT-TAT--TAT
* *
2995094 CTTA-TATATTATT-ATAATATAATTGATTAT
1 TTTATTATAATATTAATAATATAATT-ATTAT
*
2995124 TTTATTATAATATTAAAAATATAA-TATTAT
1 TTTATTATAATATTAATAATATAATTATTAT
* *
2995154 ATTATTAGAAATATTAATAAATATA
1 TTTATTA-TAATATTAAT-AATATA
2995179 TTTTAAATAT
Statistics
Matches: 70, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
30 17 0.24
31 24 0.34
32 19 0.27
33 3 0.04
34 7 0.10
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.50
Consensus pattern (31 bp):
TTTATTATAATATTAATAATATAATTATTAT
Found at i:2995146 original size:32 final size:32
Alignment explanation
Indices: 2995099--2995178 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 32
2995089 AATATCTTAT
* * *
2995099 ATATTATTATAATATAATTGATTATTTTATTA-TA
1 ATATTAATA-AATATAA-T-ATTATATTATTAGAA
2995133 ATATTAA-AAATATAATATTATATTATTAGAA
1 ATATTAATAAATATAATATTATATTATTAGAA
2995164 ATATTAATAAATATA
1 ATATTAATAAATATA
2995179 TTTTAAATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
30 11 0.27
31 9 0.22
32 14 0.34
33 1 0.02
34 6 0.15
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (32 bp):
ATATTAATAAATATAATATTATATTATTAGAA
Found at i:2995154 original size:22 final size:23
Alignment explanation
Indices: 2995126--2995172 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
2995116 TTGATTATTT
2995126 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
2995148 TATTATATTATTAGAAATATTAA
1 TATTATAATATTAAAAATATTAA
2995171 TA
1 TA
2995173 AATATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:2995177 original size:22 final size:22
Alignment explanation
Indices: 2995134--2995177 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2995124 TTTATTATAA
*
2995134 TATTAAAAATATAATATTATAT
1 TATTAAAAATATAATATAATAT
*
2995156 TATTAGAAATATTAATA-AATAT
1 TATTAAAAATA-TAATATAATAT
2995178 ATTTTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TATTAAAAATATAATATAATAT
Found at i:2996118 original size:2 final size:2
Alignment explanation
Indices: 2996113--2996164 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
2996103 TTTATGCATA
2996113 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
2996155 AT AT AT AT AT
1 AT AT AT AT AT
2996165 CTTGTTTTAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2996385 original size:2 final size:2
Alignment explanation
Indices: 2996380--2996415 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2996370 GAAATTACTA
2996380 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
2996416 TCAATATCAA
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:2996932 original size:33 final size:33
Alignment explanation
Indices: 2996885--2996951 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
2996875 CATTTTTGAA
*
2996885 ATAAATAAAATTTCACAATTTAT-TTTTGAAATT
1 ATAAATAAAATTTCA-AATTTATATTTTAAAATT
* *
2996918 ATAAATATATTTTCAAATTTATATTTTAAAATT
1 ATAAATAAAATTTCAAATTTATATTTTAAAATT
2996951 A
1 A
2996952 GTAATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 7 0.23
33 23 0.77
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.48
Consensus pattern (33 bp):
ATAAATAAAATTTCAAATTTATATTTTAAAATT
Found at i:3009722 original size:10 final size:10
Alignment explanation
Indices: 3009704--3009755 Score: 51
Period size: 9 Copynumber: 5.6 Consensus size: 10
3009694 TTTTTTTTTC
3009704 TTTTC-TCAT
1 TTTTCTTCAT
3009713 TTTTCTTCAT
1 TTTTCTTCAT
3009723 TTTTCTT--T
1 TTTTCTTCAT
*
3009731 CTTTTGTTCA-
1 -TTTTCTTCAT
3009741 TTTT-TTCAT
1 TTTTCTTCAT
3009750 TTTTCT
1 TTTTCT
3009756 CTTTCTTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
8 5 0.14
9 19 0.53
10 12 0.33
ACGTcount: A:0.08, C:0.17, G:0.02, T:0.73
Consensus pattern (10 bp):
TTTTCTTCAT
Found at i:3009726 original size:19 final size:19
Alignment explanation
Indices: 3009704--3009755 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
3009694 TTTTTTTTTC
3009704 TTTTCTCATTTTTCTTCAT
1 TTTTCTCATTTTTCTTCAT
* *
3009723 TTTTCT-TTCTTTTGTTCAT
1 TTTTCTCAT-TTTTCTTCAT
3009742 TTTT-TCATTTTTCT
1 TTTTCTCATTTTTCT
3009756 CTTTCTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
18 7 0.26
19 20 0.74
ACGTcount: A:0.08, C:0.17, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTTCTCATTTTTCTTCAT
Found at i:3009741 original size:29 final size:27
Alignment explanation
Indices: 3009688--3009795 Score: 94
Period size: 28 Copynumber: 3.7 Consensus size: 27
3009678 TGAACCCTCC
* *
3009688 TTTCAATTTTTTTTTCTTTTCTCATTTT
1 TTTC-ATTTTTCTTTCTTTTTTCATTTT
3009716 TCTTCATTTTTCTTTCTTTTGTTCA-TTT
1 T-TTCATTTTTCTTTCTTTT-TTCATTTT
3009744 TTTCATTTTTCTCTTTCTTTTTTCTATTTATTT
1 TTTCA-TTTT-TCTTTCTTTTTTC-A--T-TTT
3009777 TTTC-TCTTTTCTTTCTTTT
1 TTTCAT-TTTTCTTTCTTTT
3009796 CTATTCTTTG
Statistics
Matches: 68, Mismatches: 2, Indels: 17
0.78 0.02 0.20
Matches are distributed among these distances:
27 4 0.06
28 26 0.38
29 17 0.25
31 11 0.16
32 3 0.04
33 7 0.10
ACGTcount: A:0.07, C:0.17, G:0.01, T:0.75
Consensus pattern (27 bp):
TTTCATTTTTCTTTCTTTTTTCATTTT
Found at i:3014462 original size:17 final size:17
Alignment explanation
Indices: 3014440--3014474 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3014430 AATTGGAGTC
3014440 TCCATCAACCTTTGGGT
1 TCCATCAACCTTTGGGT
3014457 TCCATCAACCTTTGGGT
1 TCCATCAACCTTTGGGT
3014474 T
1 T
3014475 AGGTAGATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.29, G:0.17, T:0.37
Consensus pattern (17 bp):
TCCATCAACCTTTGGGT
Found at i:3020431 original size:7 final size:7
Alignment explanation
Indices: 3020419--3020443 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3020409 GTACATGCCA
3020419 ACAATTT
1 ACAATTT
3020426 ACAATTT
1 ACAATTT
3020433 ACAATTT
1 ACAATTT
3020440 ACAA
1 ACAA
3020444 GAAACCTACA
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:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (7 bp):
ACAATTT
Found at i:3020810 original size:21 final size:21
Alignment explanation
Indices: 3020786--3020856 Score: 74
Period size: 21 Copynumber: 3.3 Consensus size: 21
3020776 CACCACAGAT
3020786 CACATAATT-TCACTGAAGTG-C
1 CACATAATTGTCA-TGAAG-GAC
3020807 CACATAATTGTCATGAAGGAC
1 CACATAATTGTCATGAAGGAC
* *
3020828 CACATAGTTTTGTCCTGAAGGAC
1 CACATA--ATTGTCATGAAGGAC
3020851 CACATA
1 CACATA
3020857 GTTTTGTCCC
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
20 1 0.02
21 21 0.48
22 3 0.07
23 19 0.43
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.27
Consensus pattern (21 bp):
CACATAATTGTCATGAAGGAC
Found at i:3020846 original size:23 final size:23
Alignment explanation
Indices: 3020814--3020880 Score: 98
Period size: 23 Copynumber: 2.9 Consensus size: 23
3020804 TGCCACATAA
*
3020814 TTGTCATGAAGGACCACATAGTT
1 TTGTCCTGAAGGACCACATAGTT
3020837 TTGTCCTGAAGGACCACATAGTT
1 TTGTCCTGAAGGACCACATAGTT
** *
3020860 TTGTCCCAAAGGACCATATAG
1 TTGTCCTGAAGGACCACATAG
3020881 AACCCTCAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (23 bp):
TTGTCCTGAAGGACCACATAGTT
Found at i:3025672 original size:17 final size:17
Alignment explanation
Indices: 3025652--3025690 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
3025642 GTCGGGTAGT
3025652 GGGTCGAGTCAATTTTC
1 GGGTCGAGTCAATTTTC
* *
3025669 GGGT-GCGTCAATTTTT
1 GGGTCGAGTCAATTTTC
3025685 GGGTCG
1 GGGTCG
3025691 GTGACTATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.13, C:0.15, G:0.36, T:0.36
Consensus pattern (17 bp):
GGGTCGAGTCAATTTTC
Found at i:3026105 original size:32 final size:32
Alignment explanation
Indices: 3026069--3026130 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
3026059 TTAATTTGCT
*
3026069 TTTCGGTTCGAGTTAAATTCAATTCGGGTTAC
1 TTTCGGTTCGAGTTAAATTCAATTCAGGTTAC
* *
3026101 TTTCGGTTCGGGTTAATTTCAATTCAGGTT
1 TTTCGGTTCGAGTTAAATTCAATTCAGGTT
3026131 TTTTTTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.19, C:0.15, G:0.23, T:0.44
Consensus pattern (32 bp):
TTTCGGTTCGAGTTAAATTCAATTCAGGTTAC
Found at i:3026130 original size:16 final size:16
Alignment explanation
Indices: 3026075--3026130 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 16
3026065 TGCTTTTCGG
* *
3026075 TTCGAGTTAAATTCAA
1 TTCGGGTTAATTTCAA
* **
3026091 TTCGGGTTACTTTCGG
1 TTCGGGTTAATTTCAA
3026107 TTCGGGTTAATTTCAA
1 TTCGGGTTAATTTCAA
*
3026123 TTCAGGTT
1 TTCGGGTT
3026131 TTTTTTTATT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.21, C:0.14, G:0.21, T:0.43
Consensus pattern (16 bp):
TTCGGGTTAATTTCAA
Found at i:3033085 original size:19 final size:20
Alignment explanation
Indices: 3033052--3033090 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
3033042 AAATATTATA
3033052 TATATATATAATATA-AATT
1 TATATATATAATATATAATT
3033071 TATATATA-AACTATATAATT
1 TATATATATAA-TATATAATT
3033091 ACTATAAGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 2 0.11
19 12 0.67
20 4 0.22
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (20 bp):
TATATATATAATATATAATT
Found at i:3033159 original size:15 final size:15
Alignment explanation
Indices: 3033100--3033172 Score: 55
Period size: 15 Copynumber: 5.1 Consensus size: 15
3033090 TACTATAAGC
3033100 TATATATATAAATTA
1 TATATATATAAATTA
* * * *
3033115 TGTGTATATGAA--C
1 TATATATATAAATTA
*
3033128 TATATATATAAA--C
1 TATATATATAAATTA
*
3033141 TATATATGTAAATTA
1 TATATATATAAATTA
*
3033156 TATATGTATAAATTA
1 TATATATATAAATTA
3033171 TA
1 TA
3033173 AAAAGTATAT
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
13 21 0.47
15 24 0.53
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.44
Consensus pattern (15 bp):
TATATATATAAATTA
Found at i:3033341 original size:19 final size:19
Alignment explanation
Indices: 3033306--3033359 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
3033296 TTGGGAAATT
*
3033306 TTGAGAATATAGA--GAAA
1 TTGAGAATTTAGAGGGAAA
3033323 TTGAGAATTTAGAGGGAAA
1 TTGAGAATTTAGAGGGAAA
*
3033342 TTG-GAAACTTAGAGGGAA
1 TTGAG-AATTTAGAGGGAA
3033360 TATAAAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 12 0.38
18 1 0.03
19 19 0.59
ACGTcount: A:0.44, C:0.02, G:0.30, T:0.24
Consensus pattern (19 bp):
TTGAGAATTTAGAGGGAAA
Found at i:3033576 original size:2 final size:2
Alignment explanation
Indices: 3033569--3033736 Score: 50
Period size: 2 Copynumber: 86.0 Consensus size: 2
3033559 ACTTTTAATT
* * * * *
3033569 TA TA TA TA TA TA TA TA TA TA TA TG TA TG TG TG TA TG 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
* * * * * *
3033611 AA CTA TA CA TA TA TA AA CTA TA TA -A AA TA TA TA GTT TA TA AA
1 TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA
* * * *
3033653 T- TA TA -A TT TA TA T- TA -A CA TA GTA TA TA TA TG TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* * *
3033692 -A CTA -A TA TA -A GTA -A TC CA TA GA TA -A 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
3033731 TA TA TA
1 TA TA TA
3033737 GTTTATAGAA
Statistics
Matches: 120, Mismatches: 30, Indels: 32
0.66 0.16 0.18
Matches are distributed among these distances:
1 10 0.08
2 103 0.86
3 7 0.06
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (2 bp):
TA
Found at i:3033902 original size:2 final size:2
Alignment explanation
Indices: 3033891--3033929 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
3033881 ATAAACTATG
3033891 TA TA -A 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
3033930 ACCTATAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3034036 original size:7 final size:7
Alignment explanation
Indices: 3034026--3034085 Score: 50
Period size: 7 Copynumber: 8.6 Consensus size: 7
3034016 TAGTTTATAG
3034026 AAACCTT
1 AAACCTT
*
3034033 AAACCCT
1 AAACCTT
3034040 AAA-CTCT
1 AAACCT-T
*
3034047 AAACTTT
1 AAACCTT
* *
3034054 AAATCAT
1 AAACCTT
* *
3034061 AATCCCT
1 AAACCTT
3034068 AAACCTT
1 AAACCTT
3034075 AAACCTT
1 AAACCTT
3034082 AAAC
1 AAAC
3034086 TATGTACATA
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
6 1 0.03
7 38 0.95
8 1 0.03
ACGTcount: A:0.45, C:0.28, G:0.00, T:0.27
Consensus pattern (7 bp):
AAACCTT
Found at i:3034055 original size:21 final size:21
Alignment explanation
Indices: 3034026--3034086 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
3034016 TAGTTTATAG
*
3034026 AAACCTTAAACCCTAAACTCT
1 AAACCTTAAACCATAAACTCT
* * * *
3034047 AAACTTTAAATCATAATCCCT
1 AAACCTTAAACCATAAACTCT
*
3034068 AAACCTTAAACCTTAAACT
1 AAACCTTAAACCATAAACT
3034087 ATGTACATAT
Statistics
Matches: 30, Mismatches: 10, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.44, C:0.28, G:0.00, T:0.28
Consensus pattern (21 bp):
AAACCTTAAACCATAAACTCT
Found at i:3034259 original size:35 final size:36
Alignment explanation
Indices: 3034191--3034349 Score: 102
Period size: 37 Copynumber: 4.5 Consensus size: 36
3034181 ACAATAGTTA
*
3034191 ATATATATAACCTATAGTATATGTATACATATAAACT
1 ATATATATAACCTATAGTACATGTATA-ATATAAACT
* * *
3034228 ATATATGTAACTTATAGTACATGTAT-GTATAAACT
1 ATATATATAACCTATAGTACATGTATAATATAAACT
* *
3034263 ATGTATAGT-A--TATAGTTATAT-TATATATATATATA-T
1 ATATATA-TAACCTATAG-TACATGTATA-ATATA-A-ACT
* * * *
3034299 ATATATATAATCTAT-TTATATGT-T-ATATAAACA
1 ATATATATAACCTATAGTACATGTATAATATAAACT
*
3034332 ATATATGTAACCTATAGT
1 ATATATATAACCTATAGT
3034350 TTATAAACAA
Statistics
Matches: 96, Mismatches: 14, Indels: 27
0.70 0.10 0.20
Matches are distributed among these distances:
32 1 0.01
33 22 0.23
34 10 0.10
35 19 0.20
36 16 0.17
37 25 0.26
38 3 0.03
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.43
Consensus pattern (36 bp):
ATATATATAACCTATAGTACATGTATAATATAAACT
Found at i:3034289 original size:2 final size:2
Alignment explanation
Indices: 3034266--3034307 Score: 52
Period size: 2 Copynumber: 21.0 Consensus size: 2
3034256 ATAAACTATG
3034266 TA TA GTA TA TA GT- TA TA 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 TA TA TA TA TA TA TA TA
3034308 ATCTATTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
1 2 0.06
2 31 0.86
3 3 0.08
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3035463 original size:32 final size:32
Alignment explanation
Indices: 3035427--3035494 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
3035417 TTAGGTCCTT
* *
3035427 AACAAG-TCGGATCATTTACAGGTCAGGTTAAA
1 AACAAGTTAGGATCA-TAACAGGTCAGGTTAAA
* *
3035459 AACAAGTTAGGTTCATAACAGGTCAGGTTGAA
1 AACAAGTTAGGATCATAACAGGTCAGGTTAAA
3035491 AACA
1 AACA
3035495 GACCGAGTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 25 0.81
33 6 0.19
ACGTcount: A:0.40, C:0.15, G:0.22, T:0.24
Consensus pattern (32 bp):
AACAAGTTAGGATCATAACAGGTCAGGTTAAA
Found at i:3035486 original size:16 final size:16
Alignment explanation
Indices: 3035444--3035495 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
3035434 CGGATCATTT
3035444 ACAGGTCAGGTTAAAA
1 ACAGGTCAGGTTAAAA
* * * *
3035460 ACAAGTTAGGTTCATA
1 ACAGGTCAGGTTAAAA
*
3035476 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTAAAA
3035492 ACAG
1 ACAG
3035496 ACCGAGTAAT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.40, C:0.13, G:0.25, T:0.21
Consensus pattern (16 bp):
ACAGGTCAGGTTAAAA
Found at i:3043905 original size:27 final size:27
Alignment explanation
Indices: 3043872--3043937 Score: 123
Period size: 27 Copynumber: 2.4 Consensus size: 27
3043862 AAAATGCAAT
*
3043872 TACATTGTAATATTAGAAACAAAAACA
1 TACATTGAAATATTAGAAACAAAAACA
3043899 TACATTGAAATATTAGAAACAAAAACA
1 TACATTGAAATATTAGAAACAAAAACA
3043926 TACATTGAAATA
1 TACATTGAAATA
3043938 GAAAATGCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.56, C:0.11, G:0.08, T:0.26
Consensus pattern (27 bp):
TACATTGAAATATTAGAAACAAAAACA
Found at i:3044785 original size:32 final size:33
Alignment explanation
Indices: 3044715--3044785 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 33
3044705 TTATAATCAA
* *
3044715 AAAATAATATTTATTATAAATTGTTATTTTGAT
1 AAAATAATATTTATCATAAATTGTTATTTTGAC
* * * *
3044748 TAAATAA-ATTTGTCATAATTTTTTATTTTGAC
1 AAAATAATATTTATCATAAATTGTTATTTTGAC
3044780 AAAATA
1 AAAATA
3044786 TTATGACGAA
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
32 25 0.81
33 6 0.19
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (33 bp):
AAAATAATATTTATCATAAATTGTTATTTTGAC
Found at i:3044982 original size:197 final size:197
Alignment explanation
Indices: 3044647--3045029 Score: 529
Period size: 197 Copynumber: 1.9 Consensus size: 197
3044637 CTTTTTACCA
* *
3044647 TGACTAAATAACTTTGTTACAATTTGTTATTGCGAAAGAATATTATTTGTCACAATTTTTATAAT
1 TGACTAAATAACTTTGTTACAATTTGTTATCGCGAAAGAATATTACTTGTCACAATTTTTATAAT
* *
3044712 CAAAAAATAATATTTATTATAAATTGTTATTTTGATTAAATAAATTTGTCATAATTTTTTATTTT
66 CAAAAAATAATATTTATTATAAATTATTATTTTGATTAAATAAATTTGTCAGAATTTTTTATTTT
* * *
3044777 GACAAAATATTATGACGAAATAAATTTAACATAACTTTTTACTTTGACTAAATTTAACGTGTTAT
131 GACAAAATATTATGACAAAATAAACTTAACATAAATTTTTACTTTGACTAAATTTAACGTGTTAT
3044842 TG
196 TG
* * * * *
3044844 TGACTAAATCATTTTGTTCCAATTTGTTATCGTGAAAGAATATTACTTGTCACAATTTTTTATGA
1 TGACTAAATAACTTTGTTACAATTTGTTATCGCGAAAGAATATTACTTGTCACAA-TTTTTATAA
* * * * *
3044909 TGAGAGATTAATATTTGTTATAAATTATT-TTTTGAATTAAATGAAA-TTGTCAGAA-TTTTTAT
65 TCAAAAAATAATATTTATTATAAATTATTATTTTG-ATTAAAT-AAATTTGTCAGAATTTTTTAT
* ** *
3044971 TTTGACAAAATATTGTGACAAAATAAACTTGGCATAAATTTTTATTTTGACTAAATTTA
128 TTTGACAAAATATTATGACAAAATAAACTTAACATAAATTTTTACTTTGACTAAATTTA
3045030 CTATGTTACT
Statistics
Matches: 162, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
197 113 0.70
198 46 0.28
199 3 0.02
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.45
Consensus pattern (197 bp):
TGACTAAATAACTTTGTTACAATTTGTTATCGCGAAAGAATATTACTTGTCACAATTTTTATAAT
CAAAAAATAATATTTATTATAAATTATTATTTTGATTAAATAAATTTGTCAGAATTTTTTATTTT
GACAAAATATTATGACAAAATAAACTTAACATAAATTTTTACTTTGACTAAATTTAACGTGTTAT
TG
Found at i:3048585 original size:445 final size:448
Alignment explanation
Indices: 3047602--3048674 Score: 1649
Period size: 446 Copynumber: 2.4 Consensus size: 448
3047592 TATAATGGAC
* *
3047602 TGTAAATTTACCTATTACTTTAAAGTAATCCGTTTCGAAGTTTTAAGAATAGATATTTCTCATAC
1 TGTAAATTTACCTATTACTTTAAAGTAATCCGTTTCGAAGTTTTAAGAATCGATACTTCTCATAC
* *
3047667 GTGTATCAATACATTATAGGCGCAATTATGGAAATCGGTTTTGTCAATTTTGAACATGTTATGTT
66 GTGTATCGATACTTTATAGGCGCAATTATGGAAATCGGTTTTGTCAATTTTGAACATGTTATGTT
* * *
3047732 ATTTATATTTAATCGATACAATCACCGTTACTGAAGTATCGATAATTTTGTTGAAGGTTTCGATA
131 ATTTATATTTAATCGATACAATTACCATTACTGAAGTATCGATACTTTTGTTGAAGGTTTCGATA
* *
3047797 CTTTCGACACGTTTCGTTTTTTTGTAAACCCGTATGTTTTTACTTGTTTTGTCATATTGAAACCA
196 CTTTCGACACGTTTCGTTTTTTTGTAAACCCGTATCTTTTTACCTGTTTTGTCATATTGAAACCA
* * * * **
3047862 GTTTTTATCAATTTTCAACTTGTTATATTGTTACGTATCGATACATGTGTATTATGTATTGATAC
261 GATTTTATCAATTTTCAACCTGTTATATTGTCACGTATCGATACATGTGTATTAGGTATCAATAC
* * *
3047927 TTTTTGCGTGCATCTAGTTTGAGAAGTATACTGGACAAAAAGTATCGATACATATAAAACAAGTA
326 TTTTTGCGTGCATCTAGTTTGAGAAGCATACTAGACAAAAAGTATCGATACATATAAAACAAATA
* * *
3047992 TCGATACTTTATGTTAACATATTTTGTCATTAAATCGGTATATTTTCACCGCTTAAAT
391 TCGATACTTTATGTTAACATATTTTGTCATTAAACCAGTATATTTTCACCACTTAAAT
*
3048050 TGTAAATTTACCTATTACTTTAAAGTAATCCGTTTCGAAGTTTTAAGAATCGATACTTATCATAC
1 TGTAAATTTACCTATTACTTTAAAGTAATCCGTTTCGAAGTTTTAAGAATCGATACTTCTCATAC
*
3048115 GTGTATCGATACTTTATAGGCGCAATTATGGAAATCGATTTTGTC-ATTTTGAATC-TGTTATGT
66 GTGTATCGATACTTTATAGGCGCAATTATGGAAATCGGTTTTGTCAATTTTGAA-CATGTTATGT
* *
3048178 TATTTATATTTAATCGATACCATTACCATTACTGAAGTATCAATACTTTTGTTGAAGGTATT-GA
130 TATTTATATTTAATCGATACAATTACCATTACTGAAGTATCGATACTTTTGTTGAAGGT-TTCGA
* * *
3048242 TACTTTCGAGATGTTTCGTTTTTTTGTAAACCGGTATCTTTTTACCTGTTTTGTCATATTGAAAC
194 TACTTTCGACACGTTTCGTTTTTTTGTAAACCCGTATCTTTTTACCTGTTTTGTCATATTGAAAC
*
3048307 C-GATTTTATCAATTTTCAACCTGTTATATTGTCATGTATCGATACATGTGTATTAGGTATCAAT
259 CAGATTTTATCAATTTTCAACCTGTTATATTGTCACGTATCGATACATGTGTATTAGGTATCAAT
* * *
3048371 A-TTTTCTGTGTGCATCTAGTTTGGGAAGCATACTAGATAAAAAGTATCGATACATATACAAA-A
324 ACTTTT-TGCGTGCATCTAGTTTGAGAAGCATACTAGACAAAAAGTATCGATACATATA-AAACA
* *
3048434 AATATCGATAC-TTATGTTAACATATTTTGTCATTAAACCAGTATATTTTTACCACTTACAT
387 AATATCGATACTTTATGTTAACATATTTTGTCATTAAACCAGTATATTTTCACCACTTAAAT
*
3048495 TGTAAATTTACCTATTACTTTAAAGTAATCCGTTTCGAAGTTTTAAGAATCGATACTTCTTATAC
1 TGTAAATTTACCTATTACTTTAAAGTAATCCGTTTCGAAGTTTTAAGAATCGATACTTCTCATAC
* * * *
3048560 GTGTATCGATACTTTATACGCGCAATT-TTGAAAACTGGTTTTGTCAATTTTGAACATGTTAAGT
66 GTGTATCGATACTTTATAGGCGCAATTATGGAAATC-GGTTTTGTCAATTTTGAACATGTTATGT
* * * * *
3048624 TATTTATATATAATCTATACTATTACCCTTACTTAAGTATCGATACTTTTG
130 TATTTATATTTAATCGATACAATTACCATTACTGAAGTATCGATACTTTTG
3048675 AGACGTTTCG
Statistics
Matches: 571, Mismatches: 47, Indels: 16
0.90 0.07 0.03
Matches are distributed among these distances:
444 6 0.01
445 147 0.26
446 175 0.31
447 136 0.24
448 107 0.19
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (448 bp):
TGTAAATTTACCTATTACTTTAAAGTAATCCGTTTCGAAGTTTTAAGAATCGATACTTCTCATAC
GTGTATCGATACTTTATAGGCGCAATTATGGAAATCGGTTTTGTCAATTTTGAACATGTTATGTT
ATTTATATTTAATCGATACAATTACCATTACTGAAGTATCGATACTTTTGTTGAAGGTTTCGATA
CTTTCGACACGTTTCGTTTTTTTGTAAACCCGTATCTTTTTACCTGTTTTGTCATATTGAAACCA
GATTTTATCAATTTTCAACCTGTTATATTGTCACGTATCGATACATGTGTATTAGGTATCAATAC
TTTTTGCGTGCATCTAGTTTGAGAAGCATACTAGACAAAAAGTATCGATACATATAAAACAAATA
TCGATACTTTATGTTAACATATTTTGTCATTAAACCAGTATATTTTCACCACTTAAAT
Found at i:3048882 original size:19 final size:20
Alignment explanation
Indices: 3048849--3048892 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
3048839 ATCTGTTATA
*
3048849 TTTAATCGATTTTGTCAAGT
1 TTTAATCGATTTTGTCAAAT
*
3048869 TTTAATCG-TTTTGTTAAAT
1 TTTAATCGATTTTGTCAAAT
3048888 TTTAA
1 TTTAA
3048893 CTGATTTAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.27, C:0.07, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTAATCGATTTTGTCAAAT
Found at i:3050278 original size:6 final size:6
Alignment explanation
Indices: 3050267--3050349 Score: 76
Period size: 6 Copynumber: 13.7 Consensus size: 6
3050257 AGTGGAGCCG
* * * * *
3050267 AAATTA AAATTA AAATTC AAACTC AAATTA AAATTA AAATTG AAATTG
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
* * * *
3050315 AAACTC AAATTA AAATTG AAATTGA AAATGA AAAT
1 AAATTA AAATTA AAATTA AAATT-A AAATTA AAAT
3050350 GAAATTCTGT
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
6 60 0.94
7 4 0.06
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.29
Consensus pattern (6 bp):
AAATTA
Found at i:3050332 original size:24 final size:24
Alignment explanation
Indices: 3050266--3050341 Score: 98
Period size: 24 Copynumber: 3.2 Consensus size: 24
3050256 TAGTGGAGCC
* * *
3050266 GAAATTAAAATTAAAATTCAAACT
1 GAAACTAAAATTAAAATTGAAATT
* *
3050290 CAAATTAAAATTAAAATTGAAATT
1 GAAACTAAAATTAAAATTGAAATT
*
3050314 GAAACTCAAATTAAAATTGAAATT
1 GAAACTAAAATTAAAATTGAAATT
3050338 GAAA
1 GAAA
3050342 ATGAAAATGA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.58, C:0.07, G:0.07, T:0.29
Consensus pattern (24 bp):
GAAACTAAAATTAAAATTGAAATT
Found at i:3050347 original size:30 final size:30
Alignment explanation
Indices: 3050267--3050347 Score: 119
Period size: 30 Copynumber: 2.7 Consensus size: 30
3050257 AGTGGAGCCG
*
3050267 AAATTAAAATT-AAAATTCAAACTCAAATTA
1 AAATTAAAATTGAAAA-TGAAACTCAAATTA
*
3050297 AAATTAAAATTGAAATTGAAACTCAAATTA
1 AAATTAAAATTGAAAATGAAACTCAAATTA
*
3050327 AAATTGAAATTGAAAATGAAA
1 AAATTAAAATTGAAAATGAAA
3050348 ATGAAATTCT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
30 43 0.93
31 3 0.07
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.28
Consensus pattern (30 bp):
AAATTAAAATTGAAAATGAAACTCAAATTA
Found at i:3050370 original size:6 final size:6
Alignment explanation
Indices: 3050266--3050377 Score: 75
Period size: 6 Copynumber: 18.7 Consensus size: 6
3050256 TAGTGGAGCC
* * * * * * *
3050266 GAAATT AAAATT AAAATT CAAACT CAAATT AAAATT AAAATT GAAATT
1 GAAATT GAAATT GAAATT GAAATT GAAATT GAAATT GAAATT GAAATT
* * * * * *
3050314 GAAACT CAAATT AAAATT GAAATT GAAAAT GAAAAT GAAATTCT G-TA-T
1 GAAATT GAAATT GAAATT GAAATT GAAATT GAAATT GAAA-T-T GAAATT
3050362 GAAATT GAAATT GAAA
1 GAAATT GAAATT GAAA
3050378 AGTGCATAAA
Statistics
Matches: 87, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
4 2 0.02
5 1 0.01
6 81 0.93
7 1 0.01
8 2 0.02
ACGTcount: A:0.55, C:0.05, G:0.10, T:0.29
Consensus pattern (6 bp):
GAAATT
Found at i:3052408 original size:2 final size:2
Alignment explanation
Indices: 3052401--3052466 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
3052391 GAATCTGGAG
3052401 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
3052443 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
3052467 CCTTCCACAT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3053706 original size:199 final size:200
Alignment explanation
Indices: 3053251--3054073 Score: 1175
Period size: 199 Copynumber: 4.1 Consensus size: 200
3053241 TCAGTGTTTT
* * * **
3053251 CATATTGGAAAAAAAGTATCGATACACATACAAAAAATATCGATACTTTGTGTTTAATTATTTTG
1 CATACTGGACAAAAAGTATCGATACACATACAAAAAGTATCGATACTTTGTGTTTACGTATTTTG
**
3053316 TCATTAAAATGGTATATTTTTACCGCTTACATTGTAAATTTACCTATTACTTTATACTAATCGGT
66 TCATTAAACCGGTATATTTTTACCGCTTACATTGTAAATTTACCTATTACTTTATACTAATCGGT
* * * * * *
3053381 TTCGAAGTTTTAAGAATCGATACTTCTCATAAGTATATCGATACTTTCTACGTTCATCTAGTTTG
131 TTCAAAGTTTTAAGAATCGATACTTCTCATACGTGTATCAATACTTTCTGCGTGCATCTAGTTTG
3053446 GAAAG
196 GAAAG
3053451 CATACTGGACAAAAAGTATCGATACACATACAAAAAGTATCGATACTTTGTGTTTACGTATTTTG
1 CATACTGGACAAAAAGTATCGATACACATACAAAAAGTATCGATACTTTGTGTTTACGTATTTTG
* ** *
3053516 TCATTAGATGGGTATATTTTTACCGCTTACATTGTAAATTTACCTATTACCTTATACTAATCGGT
66 TCATTAAACCGGTATATTTTTACCGCTTACATTGTAAATTTACCTATTACTTTATACTAATCGGT
* * * *
3053581 TTCAAAGTTTTAAGAATTGAT-CTTCTCATTCGTGTATCGATACTTTCTGCATGCATCTAGTTTG
131 TTCAAAGTTTTAAGAATCGATACTTCTCATACGTGTATCAATACTTTCTGCGTGCATCTAGTTTG
3053645 GAAAG
196 GAAAG
* *
3053650 CATGCTGGACAAAAAGTATCAATACACATACAAAAAGTATCGATACTTTGTGTTTACGTATTTTG
1 CATACTGGACAAAAAGTATCGATACACATACAAAAAGTATCGATACTTTGTGTTTACGTATTTTG
* * *
3053715 TTATTAAACCGGTAAATTTTTATCGCTTACATTGTAAATTTACCTATTACTTTATACTAATCGGT
66 TCATTAAACCGGTATATTTTTACCGCTTACATTGTAAATTTACCTATTACTTTATACTAATCGGT
* * * * * * *
3053780 TTCGAAGTTTCAAGAATCGATATTTTTCATACATGTATCAATACTTTATGCGTGCATCTCGTTTG
131 TTCAAAGTTTTAAGAATCGATACTTCTCATACGTGTATCAATACTTTCTGCGTGCATCTAGTTT-
*
3053845 GGATA-
195 GGAAAG
* ** *
3053850 CATACTGGA-AAAAAGTATCGATACAAATACAAAAAGTATATATACTTTGTGTTTACGTATCTTG
1 CATACTGGACAAAAAGTATCGATACACATACAAAAAGTATCGATACTTTGTGTTTACGTATTTTG
** * * *
3053914 TCATTAAACCATTATATTTCTACTGCTTACATTTTAAATTTACCTATTACTTTATACTAATCGGT
66 TCATTAAACCGGTATATTTTTACCGCTTACATTGTAAATTTACCTATTACTTTATACTAATCGGT
* * *
3053979 TTCAAAGTTTTAAGAATCGATACTTCTCATACGTGTATCAATACTTTTTGTGTGCATCTAATTTG
131 TTCAAAGTTTTAAGAATCGATACTTCTCATACGTGTATCAATACTTTCTGCGTGCATCTAGTTTG
3054044 GAAAG
196 GAAAG
* * *
3054049 CATATTGAAAAAAAAGTATCGATAC
1 CATACTGGACAAAAAGTATCGATAC
3054074 TTTATGTTTA
Statistics
Matches: 555, Mismatches: 64, Indels: 8
0.89 0.10 0.01
Matches are distributed among these distances:
198 4 0.01
199 350 0.63
200 197 0.35
201 4 0.01
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (200 bp):
CATACTGGACAAAAAGTATCGATACACATACAAAAAGTATCGATACTTTGTGTTTACGTATTTTG
TCATTAAACCGGTATATTTTTACCGCTTACATTGTAAATTTACCTATTACTTTATACTAATCGGT
TTCAAAGTTTTAAGAATCGATACTTCTCATACGTGTATCAATACTTTCTGCGTGCATCTAGTTTG
GAAAG
Found at i:3054007 original size:399 final size:398
Alignment explanation
Indices: 3053256--3054790 Score: 1640
Period size: 399 Copynumber: 3.9 Consensus size: 398
3053246 GTTTTCATAT
* * * **
3053256 TGGAAAAAAAGTATCGATACACATACAAAAAATATCGATACTTTGTGTTTAATTATTTTGTCATT
1 TGGACAAAAAGTATCGATACACATACAAAAAGTATCGATACTTTATGTTTACGTATTTTGTCATT
** *
3053321 AAAATGGTATATTTTTACCGCTTACATTGTAAATTTACCTATTACTTTATACTAATCGGTTTCGA
66 AAACCGGTATATTTTTACCGCTAACATTGTAAATTTACCTATTACTTTATACTAATCGGTTTCGA
* * * * * *
3053386 AGTTTTAAGAATCGATACTTCTCATA-AGTATATCGATACTTTCTACGTTCATCTAGTTT-GGAA
131 AGTTTTAAGAATCGATACTTTTCATACA-TGTATCGATACTTTATGCGTGCATCTAGTTTGGGAT
* *
3053449 AGCATACTGGACAAAAAGTATCGATACACATACAAAAAGTATCGATACTTTGTGTTTACGTATTT
195 AGCATACTGGACAAAAAGTATCGATACACATACAAAAAGTATCGATACTTTATGTTTACGTATCT
* *** *
3053514 TGTCATTAGATGGGTATATTTTTACCGCTTACATTGTAAATTTACCTATTACCTTATACTAATCG
260 TGTCATTAAACCAGTATATTTTTACCGCTTACATTGTAAATTTACCTATTACTTTATACTAATCG
** * * **
3053579 GTTTCAAAGTTTTAAGAATTGAT-CTTCTCATTCGTGTATCGATACTTTCTGCATGCATCTAGTT
325 GTTTCAAAGTTTTAAGAATCAATACTTCTCATACGTGTATCAATACTTTCTGTGTGCATCTA-TT
3053643 TGGAAAGCATGC
389 TGG-AAGCAT-C
* * *
3053655 TGGACAAAAAGTATCAATACACATACAAAAAGTATCGATACTTTGTGTTTACGTATTTTGTTATT
1 TGGACAAAAAGTATCGATACACATACAAAAAGTATCGATACTTTATGTTTACGTATTTTGTCATT
* * *
3053720 AAACCGGTAAATTTTTATCGCTTACATTGTAAATTTACCTATTACTTTATACTAATCGGTTTCGA
66 AAACCGGTATATTTTTACCGCTAACATTGTAAATTTACCTATTACTTTATACTAATCGGTTTCGA
* * * *
3053785 AGTTTCAAGAATCGATATTTTTCATACATGTATCAATACTTTATGCGTGCATCTCGTTTGGGATA
131 AGTTTTAAGAATCGATACTTTTCATACATGTATCGATACTTTATGCGTGCATCTAGTTTGGGATA
* ** *
3053850 -CATACTGGA-AAAAAGTATCGATACAAATACAAAAAGTATATATACTTTGTGTTTACGTATCTT
196 GCATACTGGACAAAAAGTATCGATACACATACAAAAAGTATCGATACTTTATGTTTACGTATCTT
* * * *
3053913 GTCATTAAACCATTATATTTCTACTGCTTACATTTTAAATTTACCTATTACTTTATACTAATCGG
261 GTCATTAAACCAGTATATTTTTACCGCTTACATTGTAAATTTACCTATTACTTTATACTAATCGG
* *
3053978 TTTCAAAGTTTTAAGAATCGATACTTCTCATACGTGTATCAATACTTTTTGTGTGCATCTAATTT
326 TTTCAAAGTTTTAAGAATCAATACTTCTCATACGTGTATCAATACTTTCTGTGTGCATCT-ATTT
3054043 GGAA--A--
390 GGAAGCATC
* *
3054048 --G-C----A-TAT---T-GA-A-A-AAAAAGTATCGATACTTTATGTTTATGTATTTTGTCATT
1 TGGACAAAAAGTATCGATACACATACAAAAAGTATCGATACTTTATGTTTACGTATTTTGTCATT
* * * * * * * *
3054098 AAACAGGTATATATTTACCACCAACATTGTAAATTTTCCTATTACCTTAAATTAATCGGTTTCGA
66 AAACCGGTATATTTTTACCGCTAACATTGTAAATTTACCTATTACTTTATACTAATCGGTTTCGA
* * * *
3054163 AGTTTTAAGAATCGATACTTTTCATATATGTATCGATACTTTATTGTGTGAATCTCGTTTGGGAT
131 AGTTTTAAGAATCGATACTTTTCATACATGTATCGATACTTTA-TGCGTGCATCTAGTTTGGGAT
3054228 -GC--A-T--AC--------T-G------A-ACAAAAAGTATCGATACTTTATGTTTACGTATCT
195 AGCATACTGGACAAAAAGTATCGATACACATACAAAAAGTATCGATACTTTATGTTTACGTATCT
* * *
3054271 TGTCATTAAATCAGTATATTTTTATCGCTTACATTGTAAATTTACCTATTACTTTACACTAATCG
260 TGTCATTAAACCAGTATATTTTTACCGCTTACATTGTAAATTTACCTATTACTTTATACTAATCG
* * * *
3054336 GTTTCAAA-TTTTCAAGAATCAATACTTTTCATATGTGTATCGATACTTTATTGTGTGCATCTCA
325 GTTTCAAAGTTTT-AAGAATCAATACTTCTCATACGTGTATCAATACTTT-CTGTGTGCATCT-A
*
3054400 TTTGGGATGCATAC
387 TTT-GGAAGCAT-C
* *
3054414 TGGACAAAAAGTATCGATACAAATACAAAAAGTATCGATACTTTATGTTTACGTATCTTGTCATT
1 TGGACAAAAAGTATCGATACACATACAAAAAGTATCGATACTTTATGTTTACGTATTTTGTCATT
** * * * *
3054479 AAACCAATATATTTTTACCGCTAACATTGTAAATTTACCTATTACCTTCA-AGTAATCAGTTTCA
66 AAACCGGTATATTTTTACCGCTAACATTGTAAATTTACCTATTA-CTTTATACTAATCGGTTTCG
* * * * *** * *
3054543 AAGTTTTAAGAATCGATATTTTTCATACTTTTATCGATACTTTCTTTTTACTTACTTAAGTTTGG
130 AAGTTTTAAGAATCGATACTTTTCATACATGTATCGATACTTTATGCGTGCAT-C-T-AGTTTGG
* * * *
3054608 GA-AGCGTATTGGATAAAAAGTATCGATACACATACAAAAAGTATCGATACTTTATGTTAACGTA
192 GATAGCATACTGGACAAAAAGTATCGATACACATACAAAAAGTATCGATACTTTATGTTTACGTA
* * ** * * **
3054672 TTTTATCA-TAAACTGGTATCTTTTTTACCGCTAACATTGTAAATTTACCTATTACTTTATGTTA
257 TCTTGTCATTAAACCAGTAT-ATTTTTACCGCTTACATTGTAAATTTACCTATTACTTTATACTA
* * * * **
3054736 ATCAGTTTCGAAGTTTTAAAAATCAATACTTTTCATAAATGTATCAATACTTTCT
321 ATCGGTTTCAAAGTTTTAAGAATCAATACTTCTCATACGTGTATCAATACTTTCT
3054791 TTTTACTTCT
Statistics
Matches: 956, Mismatches: 122, Indels: 112
0.80 0.10 0.09
Matches are distributed among these distances:
358 4 0.00
359 129 0.13
360 17 0.02
361 3 0.00
363 1 0.00
366 1 0.00
367 1 0.00
368 1 0.00
369 1 0.00
373 1 0.00
374 4 0.00
376 1 0.00
377 2 0.00
378 130 0.14
379 22 0.02
380 6 0.01
381 126 0.13
382 5 0.01
383 10 0.01
385 4 0.00
386 2 0.00
388 1 0.00
390 1 0.00
391 1 0.00
396 2 0.00
397 1 0.00
398 129 0.13
399 214 0.22
400 6 0.01
403 10 0.01
404 116 0.12
405 4 0.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.40
Consensus pattern (398 bp):
TGGACAAAAAGTATCGATACACATACAAAAAGTATCGATACTTTATGTTTACGTATTTTGTCATT
AAACCGGTATATTTTTACCGCTAACATTGTAAATTTACCTATTACTTTATACTAATCGGTTTCGA
AGTTTTAAGAATCGATACTTTTCATACATGTATCGATACTTTATGCGTGCATCTAGTTTGGGATA
GCATACTGGACAAAAAGTATCGATACACATACAAAAAGTATCGATACTTTATGTTTACGTATCTT
GTCATTAAACCAGTATATTTTTACCGCTTACATTGTAAATTTACCTATTACTTTATACTAATCGG
TTTCAAAGTTTTAAGAATCAATACTTCTCATACGTGTATCAATACTTTCTGTGTGCATCTATTTG
GAAGCATC
Found at i:3054180 original size:179 final size:178
Alignment explanation
Indices: 3053878--3054433 Score: 747
Period size: 180 Copynumber: 3.1 Consensus size: 178
3053868 CGATACAAAT
** * * *
3053878 ACAAAAAGTATATATACTTTGTGTTTACGTATCTTGTCATTAAACCATTATATTTCTACTGCTTA
1 ACAAAAAGTATCGATACTTTATGTTTACGTATCTTGTCATTAAACCAGTATATTT-TACCGCTTA
* * *
3053943 CATTTTAAATTTACCTATTACTTTATACTAATCGGTTTCAAAGTTTTAAGAATCGATACTTCTCA
65 CATTGTAAATTTACCTATTACTTTAAACTAATCGGTTTC-AAGTTTTAAGAATCGATACTTTTCA
* * * * * *
3054008 TACGTGTATCAATACTTT-TTGTGTGCATCTAATTTGGAAAGCATATTGA
129 TATGTGTATCGATACTTTATTGTGTGCATCTCATTTGGGATGCATACTGA
* * * * **
3054057 AAAAAAAGTATCGATACTTTATGTTTATGTATTTTGTCATTAAA-CAGGTATATATTTACCACCA
1 ACAAAAAGTATCGATACTTTATGTTTACGTATCTTGTCATTAAACCA-GTATAT-TTTACCGCTT
* * *
3054121 ACATTGTAAATTTTCCTATTACCTTAAATTAATCGGTTTCGAAGTTTTAAGAATCGATACTTTTC
64 ACATTGTAAATTTACCTATTACTTTAAACTAATCGGTTTC-AAGTTTTAAGAATCGATACTTTTC
* * *
3054186 ATATATGTATCGATACTTTATTGTGTGAATCTCGTTTGGGATGCATACTGA
128 ATATGTGTATCGATACTTTATTGTGTGCATCTCATTTGGGATGCATACTGA
* *
3054237 ACAAAAAGTATCGATACTTTATGTTTACGTATCTTGTCATTAAATCAGTATATTTTTATCGCTTA
1 ACAAAAAGTATCGATACTTTATGTTTACGTATCTTGTCATTAAACCAGTATA-TTTTACCGCTTA
* * *
3054302 CATTGTAAATTTACCTATTACTTTACACTAATCGGTTTCAAATTTTCAAGAATCAATACTTTTCA
65 CATTGTAAATTTACCTATTACTTTAAACTAATCGGTTTCAAGTTTT-AAGAATCGATACTTTTCA
*
3054367 TATGTGTATCGATACTTTATTGTGTGCATCTCATTTGGGATGCATACTGG
129 TATGTGTATCGATACTTTATTGTGTGCATCTCATTTGGGATGCATACTGA
3054417 ACAAAAAGTATCGATAC
1 ACAAAAAGTATCGATAC
3054434 AAATACAAAA
Statistics
Matches: 327, Mismatches: 44, Indels: 11
0.86 0.12 0.03
Matches are distributed among these distances:
178 2 0.01
179 127 0.39
180 195 0.60
181 3 0.01
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (178 bp):
ACAAAAAGTATCGATACTTTATGTTTACGTATCTTGTCATTAAACCAGTATATTTTACCGCTTAC
ATTGTAAATTTACCTATTACTTTAAACTAATCGGTTTCAAGTTTTAAGAATCGATACTTTTCATA
TGTGTATCGATACTTTATTGTGTGCATCTCATTTGGGATGCATACTGA
Found at i:3054699 original size:203 final size:198
Alignment explanation
Indices: 3054237--3054827 Score: 747
Period size: 203 Copynumber: 2.9 Consensus size: 198
3054227 TGCATACTGA
* *
3054237 ACAAAAAGTATCGATACTTTATGTTTACGTATCTTGTCATTAAA-TCAGTATATTTTTATCGCTT
1 ACAAAAAGTATCGATACTTTATGTTTACGTATCTTGTCATTAAACT-AGTATATTTTTACCGCTA
* *
3054301 ACATTGTAAATTTACCTATTACTTTACACTAATCGGTTTCAAA-TTTTCAAGAATCAATACTTTT
65 ACATTGTAAATTTACCTATTACTTTA-AGTAATCAGTTTCAAAGTTTT-AAGAATCAATACTTTT
* * * * * *
3054365 CATATGTGTATCGATACTTTATTGTGTGCATCTCATTTGGGATGCATACTGGACAAAAAGTATCG
128 CATAT-TGTATCGATACTTTCTT-TTTACTTCTAATTTGGGAAGCATACTGGACAAAAAGTATCG
3054430 ATACAAAT
191 ATACAAAT
* *
3054438 ACAAAAAGTATCGATACTTTATGTTTACGTATCTTGTCATTAAACCAATATATTTTTACCGCTAA
1 ACAAAAAGTATCGATACTTTATGTTTACGTATCTTGTCATTAAACTAGTATATTTTTACCGCTAA
* * *
3054503 CATTGTAAATTTACCTATTACCTTCAAGTAATCAGTTTCAAAGTTTTAAGAATCGATATTTTTCA
66 CATTGTAAATTTACCTATTA-CTTTAAGTAATCAGTTTCAAAGTTTTAAGAATCAATACTTTTCA
* * * *
3054568 TACTTTTATCGATACTTTCTTTTTACTTACTTAAGTTTGGGAAGCGTATTGGATAAAAAGTATCG
130 TA-TTGTATCGATACTTTCTTTTTACTT-C-TAA-TTTGGGAAGCATACTGGACAAAAAGTATCG
*
3054633 ATACACAT
191 ATACAAAT
* * * * *
3054641 ACAAAAAGTATCGATACTTTATGTTAACGTATTTTATCA-TAAACTGGTATCTTTTTTACCGCTA
1 ACAAAAAGTATCGATACTTTATGTTTACGTATCTTGTCATTAAACTAGTAT-ATTTTTACCGCTA
* * *
3054705 ACATTGTAAATTTACCTATTACTTTATGTTAATCAGTTTCGAAGTTTTAAAAATCAATACTTTTC
65 ACATTGTAAATTTACCTATTACTTTAAG-TAATCAGTTTCAAAGTTTTAAGAATCAATACTTTTC
* * * * *
3054770 ATAAATGTATCAATACTTTCTTTTTACTTCTAGTTTGGGGAGCATACTAGACAAAAAG
129 AT-ATTGTATCGATACTTTCTTTTTACTTCTAATTTGGGAAGCATACTGGACAAAAAG
3054828 GATGGAAACT
Statistics
Matches: 338, Mismatches: 42, Indels: 21
0.84 0.10 0.05
Matches are distributed among these distances:
200 24 0.07
201 130 0.38
202 25 0.07
203 158 0.47
204 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (198 bp):
ACAAAAAGTATCGATACTTTATGTTTACGTATCTTGTCATTAAACTAGTATATTTTTACCGCTAA
CATTGTAAATTTACCTATTACTTTAAGTAATCAGTTTCAAAGTTTTAAGAATCAATACTTTTCAT
ATTGTATCGATACTTTCTTTTTACTTCTAATTTGGGAAGCATACTGGACAAAAAGTATCGATACA
AAT
Found at i:3055633 original size:19 final size:19
Alignment explanation
Indices: 3055609--3055657 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
3055599 TTACATTCAC
3055609 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
3055628 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
3055647 ATACAAAATTA
1 ATACAAAATTA
3055658 ACCCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:3056865 original size:180 final size:181
Alignment explanation
Indices: 3056552--3057206 Score: 989
Period size: 180 Copynumber: 3.6 Consensus size: 181
3056542 GATACAAATA
* * *
3056552 AAAAATGTATCGATCCATAGCAATAGAACAGGTAAAAATATGACAAAA-CTGGTATCGAAATGAC
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCT-GTCTCGAAATGAC
* *
3056616 AAAACTGGTAAAGCGCTACCAGATATGTTGAAAGTGTCGATACTTTAGTATAAGTATCGACACTT
65 -AAACCGGTAAAGCGCTACCAGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTT
* *
3056681 TTGGAATTTAAAAGAGAAGCAATAATAGCGCCTATAAAGTGTCGATACTTTAT
129 TTGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTATCGATACTTTAT
*
3056734 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAAACCTGTCTCGAAATGAC-
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCTGTCTCGAAATGACA
* *
3056798 AACCGGTAAAGTGCTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTT
66 AACCGGTAAAGCGCTACCAGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTT
*
3056863 GGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTTTCGATACTTTAT
131 GGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTATCGATACTTTAT
* * ** * * *
3056914 AAAAATATATCAATGTATAACAATATAACATGTAAAAATATGACAAAATCGGTCTC-AAATTGAC
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCTGTCTCGAAA-TGAC
* *
3056978 AAAACTGGTAAAGCGCTACCAGATATGTTGAAAGTGTCGATACATTAATATAAGTATCGACACTT
65 -AAACCGGTAAAGCGCTACCAGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTT
* * *
3057043 TTAGAATTTAAAAGAAAAGCAGTAATAACGCCTATAAAGTATCGATACTTTAT
129 TTGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTATCGATACTTTAT
* *
3057096 ---AATGTATCGATCCATAACAATATAATAGGTAAAAATATGACAAAACCAGTCTCGAAATGACA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCTGTCTCGAAATGAC-
*
3057158 AAACCGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATACTTTAATA
65 AAACCGGTAAAGCGCTACCAGATATGTTGAAAGTGTCGATACTTTAATA
3057207 AGTACACGTA
Statistics
Matches: 431, Mismatches: 37, Indels: 13
0.90 0.08 0.03
Matches are distributed among these distances:
179 99 0.23
180 165 0.38
182 165 0.38
183 2 0.00
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (181 bp):
AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCTGTCTCGAAATGACA
AACCGGTAAAGCGCTACCAGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTTT
GGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTATCGATACTTTAT
Found at i:3057065 original size:182 final size:182
Alignment explanation
Indices: 3056552--3057206 Score: 1016
Period size: 182 Copynumber: 3.6 Consensus size: 182
3056542 GATACAAATA
* * * *
3056552 AAAAATGTATCGATCCATAGCAATAGAACAGGTAAAAATATGACAAAACTGGTATCGAAATGACA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACA
* *
3056617 AAACTGGTAAAGCGCTACCAGATATGTTGAAAGTGTCGATACTTTAGTATAAGTATCGACACTTT
66 AAACCGGTAAAGCGCTACCAGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTT
* *
3056682 TGGAATTTAAAAGAGAAGCAATAATAGCGCCTATAAAGTGTCGATACTTTAT
131 TGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTATCGATACTTTAT
* *
3056734 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAAACCTGTCTCGAAATGAC-
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACA
* *
3056798 -AACCGGTAAAGTGCTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTT
66 AAACCGGTAAAGCGCTACCAGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTT
*
3056862 TGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTTTCGATACTTTAT
131 TGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTATCGATACTTTAT
* * ** * *
3056914 AAAAATATATCAATGTATAACAATATAACATGTAAAAATATGACAAAATCGGTCTC-AAATTGAC
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAA-TGAC
* *
3056978 AAAACTGGTAAAGCGCTACCAGATATGTTGAAAGTGTCGATACATTAATATAAGTATCGACACTT
65 AAAACCGGTAAAGCGCTACCAGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTT
* * *
3057043 TTAGAATTTAAAAGAAAAGCAGTAATAACGCCTATAAAGTATCGATACTTTAT
130 TTGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTATCGATACTTTAT
* *
3057096 ---AATGTATCGATCCATAACAATATAATAGGTAAAAATATGACAAAACCAGTCTCGAAATGACA
1 AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACA
*
3057158 AAACCGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATACTTTAATA
66 AAACCGGTAAAGCGCTACCAGATATGTTGAAAGTGTCGATACTTTAATA
3057207 AGTACACGTA
Statistics
Matches: 430, Mismatches: 39, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
179 99 0.23
180 165 0.38
182 166 0.39
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (182 bp):
AAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACA
AAACCGGTAAAGCGCTACCAGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTT
TGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTATCGATACTTTAT
Found at i:3059200 original size:22 final size:23
Alignment explanation
Indices: 3059150--3059204 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
3059140 GTTTTCTTTT
*
3059150 TTTTA-TATATAAAATGATAGTA
1 TTTTATTATATAAAATGATAGAA
*
3059172 TAGTTATTATATAAAATGATA-AA
1 T-TTTATTATATAAAATGATAGAA
3059195 TTTTATTATA
1 TTTTATTATA
3059205 AATGCAGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 9 0.32
23 5 0.18
24 14 0.50
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47
Consensus pattern (23 bp):
TTTTATTATATAAAATGATAGAA
Found at i:3059512 original size:15 final size:15
Alignment explanation
Indices: 3059492--3059522 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3059482 GGTTGTAGGT
*
3059492 GGGATGACGGTCAGG
1 GGGATGACGGTAAGG
3059507 GGGATGACGGTAAGG
1 GGGATGACGGTAAGG
3059522 G
1 G
3059523 AAAACATAGT
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:0.23, C:0.10, G:0.55, T:0.13
Consensus pattern (15 bp):
GGGATGACGGTAAGG
Found at i:3059901 original size:18 final size:18
Alignment explanation
Indices: 3059878--3059916 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
3059868 GAAAAAATAT
*
3059878 GAAGAATAAAAGATGGAG
1 GAAGAAGAAAAGATGGAG
3059896 GAAGAAGAAAAGATGGAG
1 GAAGAAGAAAAGATGGAG
3059914 GAA
1 GAA
3059917 ATGAGGAGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.36, T:0.08
Consensus pattern (18 bp):
GAAGAAGAAAAGATGGAG
Found at i:3061428 original size:21 final size:21
Alignment explanation
Indices: 3061389--3061428 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3061379 ATAATTTCTT
*
3061389 TAAAATTATTTTTTGTAAAAC
1 TAAAATTATTTCTTGTAAAAC
3061410 TAAAATGTATTTCTT-TAAA
1 TAAAAT-TATTTCTTGTAAA
3061429 TAATATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (21 bp):
TAAAATTATTTCTTGTAAAAC
Found at i:3061435 original size:15 final size:15
Alignment explanation
Indices: 3061417--3061453 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
3061407 AACTAAAATG
*
3061417 TATTTCTTTAAATAA
1 TATTTATTTAAATAA
*
3061432 TATTTATTTAAATCA
1 TATTTATTTAAATAA
3061447 TATTTAT
1 TATTTAT
3061454 AGGCATAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (15 bp):
TATTTATTTAAATAA
Found at i:3068824 original size:48 final size:45
Alignment explanation
Indices: 3068762--3069034 Score: 300
Period size: 45 Copynumber: 6.0 Consensus size: 45
3068752 AATGAATGAA
*
3068762 CAAAATAATAATGCATATGGGTGCATTATCGACATGAAATGATGC
1 CAAAATAATAATGCATATGGGTGCATTATCGACATGAAAGGATGC
* *
3068807 CAAAATAATAATAATGCATACGGGTGCATTATCGTCATGAAAGGATGC
1 C--AA-AATAATAATGCATATGGGTGCATTATCGACATGAAAGGATGC
* *
3068855 CAAAATAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGC
1 CAAAATAATAATGCATATGGGTGCATTATCGACATGAAAGGATGC
3068900 CAAAATAATAATGCATATGGGTGCATTATC-AGCATGAAAGGATGC
1 CAAAATAATAATGCATATGGGTGCATTATCGA-CATGAAAGGATGC
** * * * *
3068945 CATAGTTGA-AATGCATATGGGTGCATTATCAACATAAAAGTATGC
1 CA-AAATAATAATGCATATGGGTGCATTATCGACATGAAAGGATGC
* * ** ** *
3068990 TATAATTGAA-AATGCATAACGGTGCATTATAAACATGAATGGATG
1 CA-AAAT-AATAATGCATATGGGTGCATTATCGACATGAAAGGATG
3069035 TTATTAATGA
Statistics
Matches: 199, Mismatches: 22, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
45 121 0.61
46 36 0.18
47 2 0.01
48 40 0.20
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27
Consensus pattern (45 bp):
CAAAATAATAATGCATATGGGTGCATTATCGACATGAAAGGATGC
Found at i:3079849 original size:20 final size:20
Alignment explanation
Indices: 3079777--3079845 Score: 104
Period size: 20 Copynumber: 3.5 Consensus size: 20
3079767 TTTCCCACAA
3079777 ATTTGTAAAACCTTC-AGGTC
1 ATTTGTAAAACCTTCGA-GTC
*
3079797 ATTTGTAAAACCTTCGGGTC
1 ATTTGTAAAACCTTCGAGTC
*
3079817 ATTTGTAAAGCCTTCGAGTC
1 ATTTGTAAAACCTTCGAGTC
3079837 ATTTGTAAA
1 ATTTGTAAA
3079846 GCCTATAAGT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.36
Consensus pattern (20 bp):
ATTTGTAAAACCTTCGAGTC
Found at i:3080198 original size:47 final size:47
Alignment explanation
Indices: 3080145--3080401 Score: 390
Period size: 47 Copynumber: 5.5 Consensus size: 47
3080135 ACAAATTCCC
* *
3080145 CCTTCACAAAAGAGTAGTGAAGAAAATCATTTGCAAGTCATCTTTAG
1 CCTTCACAAAAGAGTAGTGAAGCAAATCATTTGCAAGTCATCTTCAG
* * * *
3080192 CCTTCACAGAAGAGTAGTGCAGTAAATCATTTGTAAGTCATCTTCAG
1 CCTTCACAAAAGAGTAGTGAAGCAAATCATTTGCAAGTCATCTTCAG
*
3080239 CTTTCACAAAAGAGTAGTGAAGCAAATCATTTGCAAGTCATCTTCAG
1 CCTTCACAAAAGAGTAGTGAAGCAAATCATTTGCAAGTCATCTTCAG
*
3080286 CCTTCACAAAAGAGTAGTGAAGCAAATCATTTTCAAGTCATCTTCAG
1 CCTTCACAAAAGAGTAGTGAAGCAAATCATTTGCAAGTCATCTTCAG
* * *
3080333 CCTTCACAGAAGATTAGTGAAGCAAATCATTTTCAAGTCATCTTCAG
1 CCTTCACAAAAGAGTAGTGAAGCAAATCATTTGCAAGTCATCTTCAG
*
3080380 CCTTCA-ATGAAGAGTAGTGAAG
1 CCTTCACA-AAAGAGTAGTGAAG
3080402 TAATGCAAAT
Statistics
Matches: 194, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
46 1 0.01
47 193 0.99
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (47 bp):
CCTTCACAAAAGAGTAGTGAAGCAAATCATTTGCAAGTCATCTTCAG
Found at i:3080619 original size:5 final size:5
Alignment explanation
Indices: 3080609--3080661 Score: 76
Period size: 5 Copynumber: 11.2 Consensus size: 5
3080599 GTCTGAGTGT
*
3080609 TATTA TATTA TATTA TATTA TATTA TATTA TA-TA TATAA TATTA T-TT-
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
3080656 TATTA T
1 TATTA T
3080662 TACAAATAGA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
3 1 0.02
4 8 0.19
5 34 0.79
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:3086071 original size:15 final size:15
Alignment explanation
Indices: 3085993--3086073 Score: 65
Period size: 15 Copynumber: 5.5 Consensus size: 15
3085983 TATTTTATAG
*
3085993 GTGAATATGTTATAT
1 GTGAATATGTTCTAT
* * *
3086008 GTGAAAATATTCTAC
1 GTGAATATGTTCTAT
* *
3086023 ATGAAAATG-TCTAT
1 GTGAATATGTTCTAT
* * *
3086037 GTTAATATGTGCTAA
1 GTGAATATGTTCTAT
3086052 GTGAATATGTTCTAT
1 GTGAATATGTTCTAT
*
3086067 TTGAATA
1 GTGAATA
3086074 AACAATACTT
Statistics
Matches: 49, Mismatches: 16, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
14 10 0.20
15 39 0.80
ACGTcount: A:0.36, C:0.06, G:0.17, T:0.41
Consensus pattern (15 bp):
GTGAATATGTTCTAT
Found at i:3086220 original size:24 final size:24
Alignment explanation
Indices: 3086187--3086256 Score: 97
Period size: 24 Copynumber: 3.0 Consensus size: 24
3086177 TCTACGCAAA
*
3086187 CCTTCGGGACAAATTATATGTGGT
1 CCTTCGGGACAAATTCTATGTGGT
* * *
3086211 CCTTCTGGACAAATTCTACGCGGT
1 CCTTCGGGACAAATTCTATGTGGT
3086235 CCTTCGGGACAAA-TCTATGTGG
1 CCTTCGGGACAAATTCTATGTGG
3086257 CACTTCAGTG
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 7 0.18
24 32 0.82
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.30
Consensus pattern (24 bp):
CCTTCGGGACAAATTCTATGTGGT
Found at i:3086275 original size:24 final size:24
Alignment explanation
Indices: 3086244--3086306 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 24
3086234 TCCTTCGGGA
3086244 CAAA-TCTATGTGGCACTTCAGTG
1 CAAATTCTATGTGGCACTTCAGTG
* *
3086267 CATATTCTATGTGGCACTTCGGTG
1 CAAATTCTATGTGGCACTTCAGTG
* *
3086291 CAAATTTTACGTGGCA
1 CAAATTCTATGTGGCA
3086307 GTGGTGACAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 3 0.09
24 31 0.91
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (24 bp):
CAAATTCTATGTGGCACTTCAGTG
Found at i:3088993 original size:20 final size:20
Alignment explanation
Indices: 3088970--3089009 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3088960 GATTTGGTCT
3088970 GAGTTGACTCAAACCGATTC
1 GAGTTGACTCAAACCGATTC
**
3088990 GAGTTGACTTGAACCGATTC
1 GAGTTGACTCAAACCGATTC
3089010 TAGAAAGATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.28
Consensus pattern (20 bp):
GAGTTGACTCAAACCGATTC
Found at i:3091289 original size:82 final size:82
Alignment explanation
Indices: 3091094--3091500 Score: 493
Period size: 82 Copynumber: 5.0 Consensus size: 82
3091084 AATCATTTAG
* ** ** * * * * * *
3091094 TCTTTTACCCAAAGCCATTTAGTCTTTTATCTAAATTGCATAATTGACACCTTTCTGCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACTCATTTCTGTCAAATGC
**
3091159 ACAGTTAGG-CATTAAA
66 ACAACTAGGCCATTAAA
* * * * *
3091175 TCTTTAACTCAAAGGCATTTAGCCTTTTATCTAACTGGCATGATTGACTCATTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACTCATTTCTGTCAAATGC
*
3091240 ACATCTAGGCCATTAAA
66 ACAACTAGGCCATTAAA
* *
3091257 TCTTTTACTCAAATGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACTCATTTCTGTCAAATGC
3091322 ACAACTTA-GCCATT-AA
66 ACAAC-TAGGCCATTAAA
* *
3091338 TCTTTTACTCAAAGGTAATTAATCTTTCATCTAACTGGCATAATTGACAT-ATTTCTGTCAAATG
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGAC-TCATTTCTGTCAAATG
3091402 CACAACTAGGCCATTAAA
65 CACAACTAGGCCATTAAA
* * * *
3091420 GT-TTTTACTCAAATGTATTTAACCTTTCATTTAACTAGCATAATTGA-TACCTTTCTGTCAAAT
1 -TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACT-CATTTCTGTCAAAT
3091483 GCACAACTAGGCCATTAA
64 GCACAACTAGGCCATTAA
3091501 GCTTTTATTT
Statistics
Matches: 288, Mismatches: 30, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
80 3 0.01
81 135 0.47
82 147 0.51
83 3 0.01
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (82 bp):
TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACTCATTTCTGTCAAATGC
ACAACTAGGCCATTAAA
Found at i:3091304 original size:163 final size:162
Alignment explanation
Indices: 3091117--3091505 Score: 532
Period size: 163 Copynumber: 2.4 Consensus size: 162
3091107 GCCATTTAGT
* * * * * *
3091117 CTTTTATCTAAATTGCATAATTGACACCTTTCTGCCAAATGCACAGTTAGGCATTAAATCTTTAA
1 CTTTCATCTAACTAGCATAATTGACACCTTTCTGTCAAATGCACACTTAGCCATT-AATCTTTAA
* * * * *
3091182 CTCAAAGGCATTTAGCCTTTTATCTAACTGGCATGATTGAC-TCATTTCTGTCAAATGCACATCT
65 CTCAAAGGCAATTAACCTTTCATCTAACTGGCATAATTGACAT-ATTTCTGTCAAATGCACAACT
3091246 AGGCCATTAAA-TCTTTTACTCAAATGTATTTAAC
129 AGGCCATTAAAGT-TTTTACTCAAATGTATTTAAC
* * *
3091280 CTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAACTTAGCCATTAATCTTTTA
1 CTTTCATCTAACTAGCATAATTGACACCTTTCTGTCAAATGCAC-ACTTAGCCATTAATCTTTAA
* *
3091345 CTCAAAGGTAATTAATCTTTCATCTAACTGGCATAATTGACATATTTCTGTCAAATGCACAACTA
65 CTCAAAGGCAATTAACCTTTCATCTAACTGGCATAATTGACATATTTCTGTCAAATGCACAACTA
3091410 GGCCATTAAAGTTTTTACTCAAATGTATTTAAC
130 GGCCATTAAAGTTTTTACTCAAATGTATTTAAC
* * *
3091443 CTTTCATTTAACTAGCATAATTGATACCTTTCTGTCAAATGCACAAC-TAGGCCATTAAGCTTT
1 CTTTCATCTAACTAGCATAATTGACACCTTTCTGTCAAATGCAC-ACTTA-GCCATTAATCTTT
3091506 TATTTTAGAA
Statistics
Matches: 202, Mismatches: 20, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
162 2 0.01
163 189 0.94
164 11 0.05
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.37
Consensus pattern (162 bp):
CTTTCATCTAACTAGCATAATTGACACCTTTCTGTCAAATGCACACTTAGCCATTAATCTTTAAC
TCAAAGGCAATTAACCTTTCATCTAACTGGCATAATTGACATATTTCTGTCAAATGCACAACTAG
GCCATTAAAGTTTTTACTCAAATGTATTTAAC
Found at i:3093980 original size:82 final size:82
Alignment explanation
Indices: 3093806--3094193 Score: 485
Period size: 81 Copynumber: 4.7 Consensus size: 82
3093796 AGCATTTTGT
* ** * *
3093806 CTTTCATCTAACTTGCATAATTGACACCTTTCTACCAAATGCACAGCTAGG-CATTAAATCTTTA
1 CTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATACACAGCTAGGCCATTAAATCTTTT
* *
3093870 ACTCAAAGGCATTTAGC
66 ACTCAAAGGTATTTAAC
* * * * * * *
3093887 CTTTTATCTAACTGGCATGATTGATATCTTTCTGTCAAATACACAGCTAGCCCGTTAAATCGTTT
1 CTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATACACAGCTAGGCCATTAAATCTTTT
*
3093952 ACTCAAAGGTATTTCAC
66 ACTCAAAGGTATTTAAC
* * *
3093969 CTTTCATCTAACTGACATAATTGACACATTTCTGTCAAATAAACAGCTAGGCCATT-AATCTTTT
1 CTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATACACAGCTAGGCCATTAAATCTTTT
3094033 ACTCAAAGGTATTTAAC
66 ACTCAAAGGTATTTAAC
* * * *
3094050 CTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCACATCTAGGCCATTATATCTTTT
1 CTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATACACAGCTAGGCCATTAAATCTTTT
3094115 ACTCAAAGGTATTTAGTATTTAAC
66 ACTCAAA-G------GTATTTAAC
3094139 CTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAA-AGCACAGCTAGGCCAT
1 CTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATA-CACAGCTAGGCCAT
3094194 CAATATTTTA
Statistics
Matches: 261, Mismatches: 36, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
81 115 0.44
82 85 0.33
83 1 0.00
89 60 0.23
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.35
Consensus pattern (82 bp):
CTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATACACAGCTAGGCCATTAAATCTTTT
ACTCAAAGGTATTTAAC
Found at i:3093993 original size:163 final size:163
Alignment explanation
Indices: 3093806--3094190 Score: 477
Period size: 163 Copynumber: 2.3 Consensus size: 163
3093796 AGCATTTTGT
**
3093806 CTTTCATCTAACTTGCATAATTGACACCTTTCTACCAAATGCACAGCTAGGCATTAAATCTTTAA
1 CTTTCATCTAAC-TGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCATT-AATCTTTAA
* * * * * *
3093871 CTCAAAGGCATTTAGCCTTTTATCTAACTGGCATGATTGATATCTTTCTGTCAAATACACAGCTA
64 CTCAAAGGCATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATACACAGCTA
* *
3093936 GCCCGTTAAATCGTTTACTCAAA-G-GTATTTCAC
129 GCCCATTAAATCGTTTACTCAAAGGTGTATTTAAC
* ** *
3093969 CTTTCATCTAACTGACATAATTGACACATTTCTGTCAAATAAACAGCTAGGCCATTAATCTTTTA
1 CTTTCATCTAACTG-CATAATTGACACCTTTCTGTCAAATGCACAGCTAGG-CATTAATCTTTAA
* * *
3094034 CTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCACATCTA
64 CTCAAAGGCATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATACACAGCTA
* * *
3094099 GGCCATTATATCTTTTACTCAAAGGTATTTAGTATTTAAC
129 GCCCATTAAATCGTTTACTCAAAGG----T-GTATTTAAC
*
3094139 CTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAAAGCACAGCTAGGC
1 CTTTCATCTAACT-GCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGC
3094191 CATCAATATT
Statistics
Matches: 188, Mismatches: 24, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
162 2 0.01
163 126 0.67
164 5 0.03
169 1 0.01
170 53 0.28
171 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.35
Consensus pattern (163 bp):
CTTTCATCTAACTGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCATTAATCTTTAACT
CAAAGGCATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATACACAGCTAGC
CCATTAAATCGTTTACTCAAAGGTGTATTTAAC
Found at i:3094386 original size:55 final size:54
Alignment explanation
Indices: 3094270--3094443 Score: 190
Period size: 55 Copynumber: 3.2 Consensus size: 54
3094260 TCATTATAAA
* * * * * *
3094270 TTCTATAG-TTTGCACCCGTAGTGCCAATACGATAATCCA-CAACTTACTATGAAT
1 TTCT-TAGTTTTGCACACATAGTGCCCATACGAAAATTCATAAACTTA-TATGAAT
*
3094324 TTCTTAGTTTTGCACATATAGTGCCCATACGAAAATTCATAAACTTATAATGAAT
1 TTCTTAGTTTTGCACACATAGTGCCCATACGAAAATTCATAAACTTAT-ATGAAT
* * * *
3094379 TTCTTAGTTTTGCACACACAGTGTCCATATGGAAATTCATAAACTTATTATGAAT
1 TTCTTAGTTTTGCACACATAGTGCCCATACGAAAATTCATAAACTTA-TATGAAT
*
3094434 TACTTAGTTT
1 TTCTTAGTTT
3094444 GCATACACAA
Statistics
Matches: 103, Mismatches: 13, Indels: 7
0.84 0.11 0.06
Matches are distributed among these distances:
53 3 0.03
54 30 0.29
55 69 0.67
56 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (54 bp):
TTCTTAGTTTTGCACACATAGTGCCCATACGAAAATTCATAAACTTATATGAAT
Found at i:3094949 original size:20 final size:21
Alignment explanation
Indices: 3094921--3094963 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
3094911 GTCACCCGAA
*
3094921 TTTCTAAAAACCATTTAATAT
1 TTTCTAAAAACCATTTAAAAT
* *
3094942 TTTC-AAAAGCGATTTAAAAT
1 TTTCTAAAAACCATTTAAAAT
3094962 TT
1 TT
3094964 ATTTTCCTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.42
Consensus pattern (21 bp):
TTTCTAAAAACCATTTAAAAT
Found at i:3095645 original size:44 final size:44
Alignment explanation
Indices: 3095551--3095636 Score: 111
Period size: 44 Copynumber: 2.0 Consensus size: 44
3095541 TACATATCCA
* *
3095551 ATATTTTACCATATACTTACCATTTATTCCATAAGCTCGTAAAC
1 ATATTTTACCACATACTTACCATTTATTCCATAAGCTCATAAAC
** *
3095595 ATATTTTACCAACATACTTGTCA-TTATTCTATAAGCTCATAA
1 ATATTTTACC-ACATACTTACCATTTATTCCATAAGCTCATAA
3095637 GTTTATTTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
44 27 0.75
45 9 0.25
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.40
Consensus pattern (44 bp):
ATATTTTACCACATACTTACCATTTATTCCATAAGCTCATAAAC
Found at i:3095790 original size:40 final size:41
Alignment explanation
Indices: 3095717--3095799 Score: 114
Period size: 40 Copynumber: 2.0 Consensus size: 41
3095707 ATATAGGAGT
* *
3095717 TAATTATTGCACAGTAGTGCTGAGGTCGAGCTTTGCTCACC
1 TAATTATTGCACAGTAGTGCTGAGGTCGAGCTTTACCCACC
* * *
3095758 TAATTA-TGCACCGTAGTGCTGAGGTTGGGCTTTACCCACC
1 TAATTATTGCACAGTAGTGCTGAGGTCGAGCTTTACCCACC
3095798 TA
1 TA
3095800 GTATACCATA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 31 0.84
41 6 0.16
ACGTcount: A:0.22, C:0.23, G:0.24, T:0.31
Consensus pattern (41 bp):
TAATTATTGCACAGTAGTGCTGAGGTCGAGCTTTACCCACC
Found at i:3096221 original size:7 final size:7
Alignment explanation
Indices: 3096211--3096291 Score: 69
Period size: 7 Copynumber: 11.9 Consensus size: 7
3096201 TTTTCTATTT
*
3096211 TTTCTTC
1 TTTCTTA
*
3096218 TTTCTTC
1 TTTCTTA
3096225 TTTCTTA
1 TTTCTTA
*
3096232 TTTCTTC
1 TTTCTTA
3096239 TTTCTTA
1 TTTCTTA
3096246 TTTCTTA
1 TTTCTTA
*
3096253 TTTATATA
1 TTTCT-TA
* *
3096261 TTTTTTC
1 TTTCTTA
3096268 TTT-TT-
1 TTTCTTA
*
3096273 TTTATTA
1 TTTCTTA
3096280 TTTCTT-
1 TTTCTTA
3096286 TTTCTT
1 TTTCTT
3096292 TTCTTCTTTT
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
5 3 0.05
6 10 0.16
7 45 0.70
8 6 0.09
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTCTTA
Found at i:3096230 original size:14 final size:14
Alignment explanation
Indices: 3096211--3096291 Score: 78
Period size: 14 Copynumber: 5.9 Consensus size: 14
3096201 TTTTCTATTT
*
3096211 TTTCTTCTTTCTTC
1 TTTCTTATTTCTTC
3096225 TTTCTTATTTCTTC
1 TTTCTTATTTCTTC
*
3096239 TTTCTTATTTCTTA
1 TTTCTTATTTCTTC
* *
3096253 TTTATATATTTTTTC
1 TTTCT-TATTTCTTC
* *
3096268 TTT-TT-TTTATTA
1 TTTCTTATTTCTTC
3096280 TTTCTT-TTTCTT
1 TTTCTTATTTCTT
3096292 TTCTTCTTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
12 8 0.14
13 8 0.14
14 31 0.54
15 10 0.18
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTCTTATTTCTTC
Found at i:3096236 original size:21 final size:19
Alignment explanation
Indices: 3096209--3096316 Score: 85
Period size: 21 Copynumber: 5.4 Consensus size: 19
3096199 TTTTTTCTAT
3096209 TTTTTCTTCTTTCTTCTTTC
1 TTTTTCTTCTTTCTT-TTTC
3096229 TTATTTCTTCTTTCTTATTTC
1 TT-TTTCTTCTTTCTT-TTTC
* * *
3096250 TTATTTATATATTT-TTTCTTT
1 TT-TTTCT-TCTTTCTTT-TTC
* *
3096271 TTTTTATTATTTCTTTTTC
1 TTTTTCTTCTTTCTTTTTC
3096290 -TTTTCTTCTTTTCTTTTTC
1 TTTTTCTTC-TTTCTTTTTC
*
3096309 TGTTTCTT
1 TTTTTCTT
3096317 TTTTTCTATT
Statistics
Matches: 74, Mismatches: 8, Indels: 12
0.79 0.09 0.13
Matches are distributed among these distances:
18 6 0.08
19 17 0.23
20 17 0.23
21 30 0.41
22 4 0.05
ACGTcount: A:0.07, C:0.16, G:0.01, T:0.76
Consensus pattern (19 bp):
TTTTTCTTCTTTCTTTTTC
Found at i:3096298 original size:14 final size:13
Alignment explanation
Indices: 3096208--3096320 Score: 72
Period size: 14 Copynumber: 8.5 Consensus size: 13
3096198 TTTTTTTCTA
3096208 TTTTTTCTTCTTTC
1 TTTTTTCTT-TTTC
*
3096222 TTCTTTCTTATTTC
1 TTTTTTCTT-TTTC
*
3096236 TTCTTTCTTATTTC
1 TTTTTTCTT-TTTC
*
3096250 TTATTTATATATTTT-
1 TT-TTT-TCT-TTTTC
* *
3096265 TTCTTT-TTTTTA
1 TTTTTTCTTTTTC
*
3096277 TTATTTCTTTTTC
1 TTTTTTCTTTTTC
3096290 TTTTCTTC-TTTTC
1 TTTT-TTCTTTTTC
*
3096303 -TTTTTCTGTTTC
1 TTTTTTCTTTTTC
3096315 TTTTTT
1 TTTTTT
3096321 TCTATTTTTT
Statistics
Matches: 82, Mismatches: 9, Indels: 17
0.76 0.08 0.16
Matches are distributed among these distances:
11 7 0.09
12 13 0.16
13 19 0.23
14 33 0.40
15 4 0.05
16 5 0.06
17 1 0.01
ACGTcount: A:0.07, C:0.15, G:0.01, T:0.77
Consensus pattern (13 bp):
TTTTTTCTTTTTC
Found at i:3096314 original size:25 final size:24
Alignment explanation
Indices: 3096264--3096331 Score: 68
Period size: 25 Copynumber: 2.9 Consensus size: 24
3096254 TTATATATTT
* * *
3096264 TTTCTTTT-TTTTA-TTATTTCTT
1 TTTCTTTTCTTCTATTTTTTTCTG
*
3096286 TTTCTTTTCTTCTTTTCTTTTTCTG
1 TTTCTTTTCTTCTATT-TTTTTCTG
*
3096311 TTTCTTTTTTTCTATTTTTTT
1 TTTCTTTTCTTCTATTTTTTT
3096332 AGCTCATATG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
22 8 0.22
23 3 0.08
24 6 0.16
25 20 0.54
ACGTcount: A:0.04, C:0.13, G:0.01, T:0.81
Consensus pattern (24 bp):
TTTCTTTTCTTCTATTTTTTTCTG
Found at i:3096321 original size:14 final size:14
Alignment explanation
Indices: 3096198--3096328 Score: 65
Period size: 16 Copynumber: 8.9 Consensus size: 14
3096188 GCATCTCTCA
3096198 TTTTTTTCTATTTT-
1 TTTTTTTCT-TTTTC
3096212 TTCTTCTTTCTTCTTTC
1 TT-TT-TTTCTT-TTTC
*
3096229 -TTATTTCTTCTTTC
1 TTTTTTTCTT-TTTC
* * *
3096243 TTATTTCTTATTTATA
1 TT-TTT-TTCTTTTTC
*
3096259 TATTTTTTCTTTTTT
1 T-TTTTTTCTTTTTC
3096274 TTATTATTTCTTTTTC
1 TT-TT-TTTCTTTTTC
*
3096290 TTTTCTTC-TTTTC
1 TTTTTTTCTTTTTC
*
3096303 --TTTTTCTGTTTC
1 TTTTTTTCTTTTTC
3096315 TTTTTTTCTATTTT
1 TTTTTTTCT-TTTT
3096329 TTTAGCTCAT
Statistics
Matches: 90, Mismatches: 13, Indels: 27
0.69 0.10 0.21
Matches are distributed among these distances:
11 5 0.06
12 4 0.04
13 5 0.06
14 24 0.27
15 19 0.21
16 28 0.31
17 5 0.06
ACGTcount: A:0.08, C:0.15, G:0.01, T:0.77
Consensus pattern (14 bp):
TTTTTTTCTTTTTC
Found at i:3098101 original size:19 final size:19
Alignment explanation
Indices: 3098079--3098127 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
3098069 TATTAATGGT
3098079 GTAAAAAAAATAAAAAAAG
1 GTAAAAAAAATAAAAAAAG
* *
3098098 GTAAAAGAAAT-TAAAAAG
1 GTAAAAAAAATAAAAAAAG
3098116 G-AAAAAAAATAA
1 GTAAAAAAAATAA
3098128 TGTGTACATA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 8 0.32
18 7 0.28
19 10 0.40
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (19 bp):
GTAAAAAAAATAAAAAAAG
Found at i:3098318 original size:40 final size:41
Alignment explanation
Indices: 3098262--3098354 Score: 100
Period size: 40 Copynumber: 2.3 Consensus size: 41
3098252 AAAATATAAT
* *
3098262 ATATATAAATAAATAAAAACA-AAAATAGAATATTAAGAAA
1 ATATATATATATATAAAAACATAAAATAGAATATTAAGAAA
*** * *
3098302 ATATATATATATATAAACGTATAAAATATAATATTACGAAA
1 ATATATATATATATAAAAACATAAAATAGAATATTAAGAAA
*
3098343 A-AAATATATATA
1 ATATATATATATA
3098355 CATAGTAAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
40 26 0.59
41 18 0.41
ACGTcount: A:0.63, C:0.03, G:0.04, T:0.29
Consensus pattern (41 bp):
ATATATATATATATAAAAACATAAAATAGAATATTAAGAAA
Found at i:3098330 original size:19 final size:20
Alignment explanation
Indices: 3098306--3098354 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
3098296 AAGAAAATAT
* *
3098306 ATATATATATAAACGTATAAA
1 ATATATATAT-AACGAAAAAA
*
3098327 ATATA-ATATTACGAAAAAA
1 ATATATATATAACGAAAAAA
3098346 ATATATATA
1 ATATATATA
3098355 CATAGTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 12 0.50
20 7 0.29
21 5 0.21
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (20 bp):
ATATATATATAACGAAAAAA
Found at i:3098396 original size:2 final size:2
Alignment explanation
Indices: 3098384--3098498 Score: 64
Period size: 2 Copynumber: 60.0 Consensus size: 2
3098374 TTAATACATC
* * *
3098384 TA TA CA TA TA TA TA TA TA TA TA CA TA -A TGA TA TA -A GA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA
* * * * * * *
3098425 TA TA -A TA AA AA TA -A TA TA -A TA TA AA TA AA AA AA GA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
3098463 TA GTA AA TA -A 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
3098499 GGAGACAAAA
Statistics
Matches: 91, Mismatches: 13, Indels: 18
0.75 0.11 0.15
Matches are distributed among these distances:
1 7 0.08
2 80 0.88
3 4 0.04
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (2 bp):
TA
Found at i:3098441 original size:25 final size:24
Alignment explanation
Indices: 3098389--3098464 Score: 68
Period size: 25 Copynumber: 3.2 Consensus size: 24
3098379 ACATCTATAC
* * *
3098389 ATATATATATATAT-ATACATAATG
1 ATATAAATATATATAATA-AAAATA
3098413 ATATAAGATATATATAATAAAAATA
1 ATATAA-ATATATATAATAAAAATA
* *
3098438 ATAT-AATATAAATAA-AAAAAGA
1 ATATAAATATATATAATAAAAATA
3098460 ATATA
1 ATATA
3098465 GTAAATAATA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
22 10 0.23
23 9 0.20
24 6 0.14
25 16 0.36
26 3 0.07
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.33
Consensus pattern (24 bp):
ATATAAATATATATAATAAAAATA
Found at i:3099648 original size:84 final size:83
Alignment explanation
Indices: 3099492--3099717 Score: 226
Period size: 84 Copynumber: 2.7 Consensus size: 83
3099482 TGTGATTGAG
* * * * * * *
3099492 GTGTCATCGAGCTGAATGGAATCGAACTCGACA-AT-TTTCGTTGATAGATAGCCCTTTTTGCCT
1 GTGTCCTCGAGCTGAACGTAATCGAACTCGA-AGGTCTTT-GATGATAGATAACCCTTCTTGCCT
*
3099555 TGAGCTATGCTG-TAATT-T
64 TGAGCTATGCTGCAAATTAT
* * *
3099573 GATTTACCTCTGAGTTGAATGTAATCGAACTCGAAGGTCTTTGATGATAGATAACCCTTCTTGCC
1 G-TGT-CCTC-GAGCTGAACGTAATCGAACTCGAAGGTCTTTGATGATAGATAACCCTTCTTGCC
*
3099638 TTGAGTTATGCTGCAAATTAT
63 TTGAGCTATGCTGCAAATTAT
* * * * *
3099659 GTGTCTTCGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTAATAGATAACCCTTCTT
1 GTGTCCTCGAGCTGAACGTAATCGAACTCGAAGGTCTTTGATGATAGATAACCCTTCTT
3099718 TGAGTTGGAT
Statistics
Matches: 120, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
81 1 0.01
82 2 0.02
83 49 0.41
84 57 0.47
85 9 0.08
86 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (83 bp):
GTGTCCTCGAGCTGAACGTAATCGAACTCGAAGGTCTTTGATGATAGATAACCCTTCTTGCCTTG
AGCTATGCTGCAAATTAT
Found at i:3100085 original size:110 final size:109
Alignment explanation
Indices: 3099949--3100147 Score: 283
Period size: 110 Copynumber: 1.8 Consensus size: 109
3099939 AACTGGGAAA
* * *
3099949 TTGTTTGTTGACAGCCAGCCGCCCCTTCACTGTA-AAGTTGAGCTTGTGTTGTCTCGATTTCAAT
1 TTGTTTGTTGACAACCAGCCGCCCCTT-ACT-TAGAAGTTGAGCTTGTGTTGTCTCGAGTCCAAT
*
3100013 ATCCTTCGCTGTGAAGTTGAAATTGAATCTGAATGAAACTGAAAAG
64 ATCCCTCGCTGTGAAGTTGAAATTGAATCTGAATGAAACTGAAAAG
* * * * *
3100059 TTGTTTGTTGACAATCAGTCGCCCCTTAGTTATGAATTTGAGCTTGTGTTGTCTTGAGTCCAATA
1 TTGTTTGTTGACAACCAGCCGCCCCTTACTTA-GAAGTTGAGCTTGTGTTGTCTCGAGTCCAATA
3100124 TCCCTCGCTGTGAAGTTGAAATTG
65 TCCCTCGCTGTGAAGTTGAAATTG
3100148 GCTCTAAAAC
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
108 2 0.03
109 2 0.03
110 74 0.95
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (109 bp):
TTGTTTGTTGACAACCAGCCGCCCCTTACTTAGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATAT
CCCTCGCTGTGAAGTTGAAATTGAATCTGAATGAAACTGAAAAG
Found at i:3100960 original size:67 final size:69
Alignment explanation
Indices: 3100816--3100963 Score: 176
Period size: 67 Copynumber: 2.2 Consensus size: 69
3100806 GGAAACAATC
* * * *
3100816 TCAAAGATATCTGTTGTTTCATGAAAAACGATCTCAAGGGATATCAAATTTTGTTTTAAAGGAAA
1 TCAAAGAT-TTTGTTGTTTCAAGAAAAACGATCTCAAGGGAGATCAAAATTTGTTTTAAAGGAAA
3100881 TAAAT
65 TAAAT
** * * *
3100886 TTGAAGATTTTG-TGTTTCAAGAGAAACTATCTCAAGGGAGA-CAAAATTTGTTTT-AGGAGAAA
1 TCAAAGATTTTGTTGTTTCAAGAAAAACGATCTCAAGGGAGATCAAAATTTGTTTTAAAG-GAAA
3100948 TAAAT
65 TAAAT
3100953 TCAAAGATTTT
1 TCAAAGATTTT
3100964 ATTTCAAGGG
Statistics
Matches: 66, Mismatches: 11, Indels: 5
0.80 0.13 0.06
Matches are distributed among these distances:
66 2 0.03
67 30 0.45
68 25 0.38
69 3 0.05
70 6 0.09
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (69 bp):
TCAAAGATTTTGTTGTTTCAAGAAAAACGATCTCAAGGGAGATCAAAATTTGTTTTAAAGGAAAT
AAAT
Found at i:3101958 original size:32 final size:32
Alignment explanation
Indices: 3101917--3102028 Score: 113
Period size: 32 Copynumber: 3.5 Consensus size: 32
3101907 TTTGCATCAG
* * *
3101917 GATGTTGAAT-TCCTAAAGATGCCCCAATATTC
1 GATGTTGAATCT-CAAAAAATGCCCCAACATTC
*
3101949 GATGTTGAATCTCAAAAAATGCCCCAACATTT
1 GATGTTGAATCTCAAAAAATGCCCCAACATTC
* *
3101981 GATGTT-ATATCT-AAAAAATGTCCCAACATTT
1 GATGTTGA-ATCTCAAAAAATGCCCCAACATTC
*
3102012 GATGTTAAATCTTCAAA
1 GATGTTGAATC-TCAAA
3102029 GATGCCCTCA
Statistics
Matches: 70, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
31 28 0.40
32 38 0.54
33 4 0.06
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.32
Consensus pattern (32 bp):
GATGTTGAATCTCAAAAAATGCCCCAACATTC
Found at i:3102000 original size:31 final size:31
Alignment explanation
Indices: 3101935--3102028 Score: 118
Period size: 31 Copynumber: 2.9 Consensus size: 31
3101925 ATTCCTAAAG
* *
3101935 ATGCCCCAATATTCGATGTTGAATCTCAAAAA
1 ATGCCCCAACATTTGATGTT-AATCTCAAAAA
3101967 ATGCCCCAACATTTGATGTTATATCT-AAAAA
1 ATGCCCCAACATTTGATGTTA-ATCTCAAAAA
*
3101998 ATGTCCCAACATTTGATGTTAAATCTTCAAA
1 ATGCCCCAACATTTGATGTT-AATC-TCAAA
3102029 GATGCCCTCA
Statistics
Matches: 55, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
31 28 0.51
32 24 0.44
33 3 0.05
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.32
Consensus pattern (31 bp):
ATGCCCCAACATTTGATGTTAATCTCAAAAA
Found at i:3110146 original size:10 final size:9
Alignment explanation
Indices: 3110126--3110190 Score: 51
Period size: 10 Copynumber: 6.6 Consensus size: 9
3110116 ATTATGCTTG
3110126 AAGAAAAAA
1 AAGAAAAAA
3110135 AAGAATAAAA
1 AAGAA-AAAA
3110145 AAGAAAAGAA
1 AAGAAAA-AA
3110155 AA-AAAGGAAA
1 AAGAAA--AAA
*
3110165 AGGAAAAAGAAA
1 A--AGAAA-AAA
3110177 AAGAAAAAA
1 AAGAAAAAA
3110186 AAGAA
1 AAGAA
3110191 TATAATAATA
Statistics
Matches: 48, Mismatches: 1, Indels: 14
0.76 0.02 0.22
Matches are distributed among these distances:
9 18 0.38
10 20 0.42
11 1 0.02
12 6 0.12
13 3 0.06
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.02
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:3110157 original size:6 final size:6
Alignment explanation
Indices: 3110142--3110184 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
3110132 AAAAAGAATA
* *
3110142 AAAAAG AAAAGAA AAAAAGG AAAAGG AAAAAG AAAAAG AAAAA
1 AAAAAG AAAA-AG AAAAA-G AAAAAG AAAAAG AAAAAG AAAAA
3110185 AAAGAATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
6 22 0.71
7 9 0.29
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:3110157 original size:13 final size:13
Alignment explanation
Indices: 3110141--3110186 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
3110131 AAAAAAGAAT
3110141 AAAAAAGAAAAGA
1 AAAAAAGAAAAGA
3110154 AAAAAAGGAAAAG-
1 AAAAAA-GAAAAGA
*
3110167 GAAAAAGAAAAAGA
1 AAAAAAG-AAAAGA
3110181 AAAAAA
1 AAAAAA
3110187 AGAATATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
12 1 0.04
13 16 0.57
14 11 0.39
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAGA
Found at i:3111360 original size:122 final size:123
Alignment explanation
Indices: 3111096--3111425 Score: 583
Period size: 122 Copynumber: 2.7 Consensus size: 123
3111086 TCGATGGATC
*
3111096 AACATTGCAAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATG
1 AACATTGCCAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATG
*
3111161 AGAAGAACTTGTTCAACCTTTCGCTTGATTCTATCACAGAAGAAGATAAATCAACATA
66 AGAAGAACTTGTTCAACCTTTCACTTGATTCTATCACAGAAGAAGATAAATCAACATA
* *
3111219 AACATTGCCAGGAATAGTTCATAATGAGAAGAACTCATCTAAAGAGGAAGAAGAAGTTCATAATG
1 AACATTGCCAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATG
* *
3111284 AGAAGAACTT-TTCAACCTTTCACTTGATTCTATCACAGAAGGAGATAGATCAACA-A
66 AGAAGAACTTGTTCAACCTTTCACTTGATTCTATCACAGAAGAAGATAAATCAACATA
3111340 TAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAAT
1 -AACATTGCCAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAAT
3111405 GAGAAGAACTTGTTCAACCTT
65 GAGAAGAACTTGTTCAACCTT
3111426 AGATTGATTT
Statistics
Matches: 197, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
121 1 0.01
122 115 0.58
123 81 0.41
ACGTcount: A:0.42, C:0.15, G:0.20, T:0.24
Consensus pattern (123 bp):
AACATTGCCAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATG
AGAAGAACTTGTTCAACCTTTCACTTGATTCTATCACAGAAGAAGATAAATCAACATA
Found at i:3111664 original size:134 final size:136
Alignment explanation
Indices: 3111341--3111698 Score: 433
Period size: 134 Copynumber: 2.6 Consensus size: 136
3111331 GATCAACAAT
*
3111341 AACATTGCCAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATG
1 AACATTTCCA-GAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATG
* *
3111406 AGAAGAACTTGTTCAACCTTAGATTGATTTAGCATCTACGAAAATGAATACAAGAAGAATCTCAC
65 TGAAGAACTTGTTCAACCTTAGATTGATTTA-CATCTAC-AAAATGAATACAACAAGAATCTCAC
3111471 TTGAGGATC
128 TTGAGGATC
* * *
3111480 AACATTTTCAGAGGAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATG
1 AACATTTCCAGAAG-AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATG
* * * ** *
3111545 TGAAGAACTTGTTTAACCTT-G-TCTTATTT-CATC-AC-ATATGAAGTTGAATCAA-CATCTC-
65 TGAAGAACTTGTTCAACCTTAGAT-TGATTTACATCTACAAAATGAA-TACAA-CAAGAATCTCA
*
3111603 TTTCGAGGATC
127 CTT-GAGGATC
* * *
3111614 AGCATTTCCAGATAGAGTTCATAATAAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATC
1 AACATTTCCAGA-AGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATG
*
3111679 TGAAGAACTTATTCAACCTT
65 TGAAGAACTTGTTCAACCTT
3111699 TTGCTCAACT
Statistics
Matches: 192, Mismatches: 21, Indels: 17
0.83 0.09 0.07
Matches are distributed among these distances:
133 8 0.04
134 90 0.47
135 5 0.03
136 4 0.02
137 1 0.01
138 9 0.05
139 75 0.39
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (136 bp):
AACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGT
GAAGAACTTGTTCAACCTTAGATTGATTTACATCTACAAAATGAATACAACAAGAATCTCACTTG
AGGATC
Found at i:3112059 original size:27 final size:27
Alignment explanation
Indices: 3111978--3112062 Score: 73
Period size: 27 Copynumber: 3.1 Consensus size: 27
3111968 CAAATGCAGT
*
3111978 AGCCCCTCCACCACAAAAAATTCCAGC
1 AGCCCCTCCACCACAAAAAATTCCAAC
* ** ** *
3112005 AGGCCCTCCACGTTTCAATTAACT-CAAC
1 AGCCCCTCCAC--CACAAAAAATTCCAAC
*
3112033 AGCCCCTCCACCACAACAAATTCCAAC
1 AGCCCCTCCACCACAAAAAATTCCAAC
3112060 AGC
1 AGC
3112063 TTCCACCAAC
Statistics
Matches: 42, Mismatches: 13, Indels: 6
0.69 0.21 0.10
Matches are distributed among these distances:
26 6 0.14
27 17 0.40
28 13 0.31
29 6 0.14
ACGTcount: A:0.34, C:0.42, G:0.08, T:0.15
Consensus pattern (27 bp):
AGCCCCTCCACCACAAAAAATTCCAAC
Found at i:3120297 original size:21 final size:21
Alignment explanation
Indices: 3120273--3120323 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
3120263 TAACATCTCT
3120273 AAGTATTGAGAAATACACCTA
1 AAGTATTGAGAAATACACCTA
3120294 AAGTATTGAGAAATACACCTA
1 AAGTATTGAGAAATACACCTA
*
3120315 AAGTGTTGA
1 AAGTATTGA
3120324 AAAGTTTCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.25
Consensus pattern (21 bp):
AAGTATTGAGAAATACACCTA
Found at i:3121530 original size:40 final size:40
Alignment explanation
Indices: 3121486--3121566 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
3121476 TCAGATGCTT
3121486 ACAAAATTTCTCCCAATGGAGTGTAGCAATGGTATATGTG
1 ACAAAATTTCTCCCAATGGAGTGTAGCAATGGTATATGTG
3121526 ACAAAATTTCTCCCAATGGAGTGTAGCAATGGTATATGTG
1 ACAAAATTTCTCCCAATGGAGTGTAGCAATGGTATATGTG
3121566 A
1 A
3121567 TATAGTATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (40 bp):
ACAAAATTTCTCCCAATGGAGTGTAGCAATGGTATATGTG
Found at i:3121828 original size:12 final size:13
Alignment explanation
Indices: 3121804--3121837 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
3121794 ATTTTTTTAG
3121804 AGGAATGAAGAAA
1 AGGAATGAAGAAA
3121817 AGGAAT-AAGAAA
1 AGGAATGAAGAAA
*
3121829 ATGAATGAA
1 AGGAATGAA
3121838 AATATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.62, C:0.00, G:0.26, T:0.12
Consensus pattern (13 bp):
AGGAATGAAGAAA
Found at i:3153304 original size:15 final size:15
Alignment explanation
Indices: 3153260--3153309 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
3153250 ATCCACTTCG
*
3153260 CATATAACACTTTCCA
1 CATATAACACATT-CA
* *
3153276 CGTAGAACACATTCA
1 CATATAACACATTCA
*
3153291 CATATAACATATTCA
1 CATATAACACATTCA
3153306 CATA
1 CATA
3153310 CTAATACAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
15 18 0.64
16 10 0.36
ACGTcount: A:0.42, C:0.26, G:0.04, T:0.28
Consensus pattern (15 bp):
CATATAACACATTCA
Found at i:3156145 original size:4 final size:4
Alignment explanation
Indices: 3156136--3156162 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3156126 AACAAAGATG
3156136 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
3156163 ACTCAACACA
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:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:3158080 original size:130 final size:130
Alignment explanation
Indices: 3157911--3158175 Score: 363
Period size: 130 Copynumber: 2.0 Consensus size: 130
3157901 ATCTTTATGG
* *
3157911 AGGG-TGATAACACGGTTCCTACGCGATGAGGATGGCTGGTTATCT-AGGGGTGACATAGCTCCT
1 AGGGATGATAACACGGTTCCTACGCGATGAGGATGACTGGTTATCTGA-GGGTGACACAGCTCCT
* * * * *
3157974 ACGTAATGAAGAGGTCTGGTAGGGGATTACACGATTCTTATATGATGAGGATGAAAAGCCATATT
65 ACATAATGAAGAGGTCTGGTAGGGGATGACACGATTCCTACACGATGAGGATGAAAAGCCATATT
3158039 T
130 T
* * *
3158040 AGGGATGATAACATGGTTCCTACGTGATGAGGATGACTGGTTATCTGAGGTTGACACAGCTCCTA
1 AGGGATGATAACACGGTTCCTACGCGATGAGGATGACTGGTTATCTGAGGGTGACACAGCTCCTA
* * *** *
3158105 CATAATGAGGAGGTTTGGTAGGGGATGACACGATTCCTACACGATGAGGATGACTGGCCATCTTT
66 CATAATGAAGAGGTCTGGTAGGGGATGACACGATTCCTACACGATGAGGATGAAAAGCCATATTT
3158170 AGGGAT
1 AGGGAT
3158176 TTATTTCAGG
Statistics
Matches: 118, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
129 4 0.03
130 113 0.96
131 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.31, T:0.27
Consensus pattern (130 bp):
AGGGATGATAACACGGTTCCTACGCGATGAGGATGACTGGTTATCTGAGGGTGACACAGCTCCTA
CATAATGAAGAGGTCTGGTAGGGGATGACACGATTCCTACACGATGAGGATGAAAAGCCATATTT
Found at i:3158363 original size:66 final size:66
Alignment explanation
Indices: 3158198--3158395 Score: 188
Period size: 66 Copynumber: 3.0 Consensus size: 66
3158188 AAACAGAATG
* ** * * **
3158198 AAAGAT-GGTGCTTTAAGAGAAGTTGTCTCAAGATAGACAAAATTTGTTTCAATGGAAATGATCT
1 AAAGATAGGTGTTTTAAGAGAAGTTGTCTCAAGGGAGACAAAACTTGTTTCAAGGGAAACAATCT
3158262 C
66 C
* * * * * *
3158263 AAAGATGGGTGTTTCAATAGAAACTT-TCTTAAGGGAGACAAAACTTGTTTCACGGGAAACAATC
1 AAAGATAGGTGTTTTAAGAG-AAGTTGTCTCAAGGGAGACAAAACTTGTTTCAAGGGAAACAATC
3158327 TC
65 TC
* * * *
3158329 AAATG-TAGGTGTTTTAGGAGAAGTTGTCTCAAGGGAGACAAATA-TTTTTTTAAGAGAAACAAT
1 AAA-GATAGGTGTTTTAAGAGAAGTTGTCTCAAGGGAGACAAA-ACTTGTTTCAAGGGAAACAAT
3158392 CTC
64 CTC
3158395 A
1 A
3158396 GAGGTTGTGT
Statistics
Matches: 106, Mismatches: 22, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
65 10 0.09
66 90 0.85
67 6 0.06
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.30
Consensus pattern (66 bp):
AAAGATAGGTGTTTTAAGAGAAGTTGTCTCAAGGGAGACAAAACTTGTTTCAAGGGAAACAATCT
C
Found at i:3162924 original size:3 final size:3
Alignment explanation
Indices: 3162916--3162975 Score: 75
Period size: 3 Copynumber: 19.3 Consensus size: 3
3162906 TTTTTCTTAA
** *
3162916 ATT ATT ATT AAA ATT ATT ATT ATT ATTT ATT ATT ATT ATT AAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT
3162962 ATT ATTT ATT ATT A
1 ATT A-TT ATT ATT A
3162976 ATTACAAGCC
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
3 43 0.88
4 6 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:3162956 original size:25 final size:25
Alignment explanation
Indices: 3162917--3162976 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
3162907 TTTTCTTAAA
*
3162917 TTATTATTAAAATTATTATTATTAT
1 TTATTATTAAAATTAATATTATTAT
**
3162942 TTATTATTATTATTAATATTATTAT
1 TTATTATTAAAATTAATATTATTAT
3162967 TTATTATTAA
1 TTATTATTAA
3162977 TTACAAGCCC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
TTATTATTAAAATTAATATTATTAT
Done.