Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A08
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: 123748673
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5630000 characters in sequence are not A, C, G, or T
File 11 of 373
Found at i:3226505 original size:48 final size:52
Alignment explanation
Indices: 3226435--3226533 Score: 118
Period size: 52 Copynumber: 2.0 Consensus size: 52
3226425 AATAATTATT
3226435 ATTTTAAATTATACAAATTCATA-AACT-A-T-AATCATATTAGTTATAATA
1 ATTTTAAATTATACAAATTCATATAACTAATTAAATCATATTAGTTATAATA
* * **
3226483 ATTTTAAATTTTATTAAA-TCATATATTTAATTAAATCATATTAGTTATAAT
1 ATTTTAAATTATA-CAAATTCATATAACTAATTAAATCATATTAGTTATAAT
3226534 CATATATTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
48 17 0.40
49 5 0.12
50 1 0.02
51 1 0.02
52 18 0.43
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.46
Consensus pattern (52 bp):
ATTTTAAATTATACAAATTCATATAACTAATTAAATCATATTAGTTATAATA
Found at i:3226515 original size:17 final size:17
Alignment explanation
Indices: 3226490--3226523 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3226480 ATAATTTTAA
*
3226490 ATTTTATTAAATCATAT
1 ATTTAATTAAATCATAT
3226507 ATTTAATTAAATCATAT
1 ATTTAATTAAATCATAT
3226524 TAGTTATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTAATTAAATCATAT
Found at i:3226540 original size:17 final size:16
Alignment explanation
Indices: 3226495--3226542 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
3226485 TTTAAATTTT
3226495 ATTAAATCATATATTTA
1 ATTAAATCATATA-TTA
3226512 ATTAAATC--ATATTA
1 ATTAAATCATATATTA
*
3226526 GTTATAATCATATATTA
1 ATTA-AATCATATATTA
3226543 TGATTTGAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 6 0.22
15 7 0.26
17 14 0.52
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (16 bp):
ATTAAATCATATATTA
Found at i:3226597 original size:54 final size:54
Alignment explanation
Indices: 3226539--3226717 Score: 128
Period size: 54 Copynumber: 3.1 Consensus size: 54
3226529 ATAATCATAT
3226539 ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
1 ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
* * * * * * * *
3226593 ATTATATATTTTAATTATATT-ATATTTAATAATAATTATGTTATTTTA-TATTTTACAGTAACA
1 ATTAT-GA-TTTGAGTAAATTCATA--TAAGAAT-ATTA-ATTA-TTAAGAATTTT--A-T----
*
3226656 TAT
52 TAA
*
3226659 ATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
1 ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
3226713 ATTAT
1 ATTAT
3226718 ATATTTTAAT
Statistics
Matches: 90, Mismatches: 19, Indels: 32
0.64 0.13 0.23
Matches are distributed among these distances:
54 12 0.13
55 4 0.04
56 9 0.10
57 6 0.07
58 5 0.06
59 9 0.10
60 6 0.07
61 9 0.10
62 5 0.06
63 6 0.07
64 9 0.10
65 3 0.03
66 7 0.08
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (54 bp):
ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
Found at i:3226600 original size:61 final size:61
Alignment explanation
Indices: 3226535--3226722 Score: 183
Period size: 61 Copynumber: 3.1 Consensus size: 61
3226525 AGTTATAATC
3226535 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
* * * * * * * * *
3226596 ATATATTTTAATTAT-ATTATATTTA-ATAATAATTATGTTATT-TT-A-TATTTTA-CAGTAA-
1 ATATATTATGATT-TGAGTAAATTCATATAAGAA-TAT-TAATTATTAAGAATTTTATTA--AAT
*
3226654 C
61 T
*
3226655 ATATATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
3226716 ATATATT
1 ATATATT
3226723 TTAATTAAAA
Statistics
Matches: 94, Mismatches: 21, Indels: 24
0.68 0.15 0.17
Matches are distributed among these distances:
58 6 0.06
59 28 0.30
60 18 0.19
61 36 0.38
62 6 0.06
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (61 bp):
ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
Found at i:3226614 original size:18 final size:17
Alignment explanation
Indices: 3226583--3226617 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3226573 ATTATTAAGA
3226583 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
*
3226600 ATTTTAATTATATTATAT
1 ATTTT-ATTAAATTATAT
3226618 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:3226663 original size:120 final size:120
Alignment explanation
Indices: 3226534--3226754 Score: 415
Period size: 120 Copynumber: 1.8 Consensus size: 120
3226524 TAGTTATAAT
3226534 CATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATA
1 CATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATA
* *
3226599 TATTTTAATTATATTATATTTAATAATAATTATGTTATTTTATATTTTACAGTAA
66 TATTTTAATTAAAATATATTTAATAATAATTATGTTATTTTATATTTTACAGTAA
*
3226654 CATATATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATA
1 CATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATA
3226719 TATTTTAATTAAAATATATTTAATAATAATTATGTT
66 TATTTTAATTAAAATATATTTAATAATAATTATGTT
3226755 TAAATATGAT
Statistics
Matches: 98, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 98 1.00
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (120 bp):
CATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATA
TATTTTAATTAAAATATATTTAATAATAATTATGTTATTTTATATTTTACAGTAA
Found at i:3226731 original size:18 final size:17
Alignment explanation
Indices: 3226703--3226737 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3226693 ATTATTAAGA
*
3226703 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
3226720 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
3226738 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:3226749 original size:54 final size:54
Alignment explanation
Indices: 3226566--3226751 Score: 149
Period size: 54 Copynumber: 3.2 Consensus size: 54
3226556 TTCATATAAG
* *
3226566 AATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTATATTATATTT
1 AATAATAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAATTATATTT
** * * *
3226620 AATAATAATTATGTTATTTTATATTTTACAGTAACA-TATATTATGGTTTGAGTAAATTCATATA
1 AATAATAATTA--TTA--AGA-ATTTT--ATTAA-ATTATA-TAT--TTTAATTAAATT-ATAT-
**
3226684 AG
53 TT
* *
3226686 AATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTT
1 AATAATAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAATTATATTT
3226740 AATAATAATTAT
1 AATAATAATTAT
3226752 GTTTAAATAT
Statistics
Matches: 99, Mismatches: 19, Indels: 28
0.68 0.13 0.19
Matches are distributed among these distances:
54 21 0.21
55 4 0.04
56 12 0.12
58 5 0.05
59 13 0.13
61 13 0.13
62 5 0.05
64 12 0.12
65 4 0.04
66 10 0.10
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.50
Consensus pattern (54 bp):
AATAATAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAATTATATTT
Found at i:3226858 original size:144 final size:147
Alignment explanation
Indices: 3226691--3226962 Score: 487
Period size: 144 Copynumber: 1.9 Consensus size: 147
3226681 ATAAGAATAT
*
3226691 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
3226756 AAATATGATTAAATTATTTATTATTGAT-AT-TAATCTTATTAAAATTTAAATAA-AATAATTTA
66 AAATATGATTAAATTATTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAATTTA
3226818 CCAAAACAAATTTCTGC
131 CCAAAACAAATTTCTGC
3226835 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
*
3226900 AAATATGATTAAATTATTTATTTTTGATAATAAATAATCTTATTAAAATTTAAATAACAATAA
66 AAATATGATTAAATTATTTATTATTGATAAT--ATAATCTTATTAAAATTTAAATAACAATAA
3226963 CAATAATCAT
Statistics
Matches: 121, Mismatches: 2, Indels: 5
0.95 0.02 0.04
Matches are distributed among these distances:
144 91 0.75
145 2 0.02
148 23 0.19
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (147 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAATTTA
CCAAAACAAATTTCTGC
Found at i:3226875 original size:18 final size:17
Alignment explanation
Indices: 3226847--3226881 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3226837 ATTATTAAGA
*
3226847 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
3226864 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
3226882 TAAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:3227092 original size:44 final size:45
Alignment explanation
Indices: 3227043--3227137 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 45
3227033 TTACACCTCT
* *
3227043 ATTACATTCAACCAAACA-CAGTTTTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
** *
3227087 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
3227132 ATTACA
1 ATTACA
3227138 CCTTTAATCC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (45 bp):
ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
Found at i:3227158 original size:21 final size:21
Alignment explanation
Indices: 3227129--3227171 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
3227119 ACACCTCTAT
* *
3227129 TCCATTACACCTTTAATCCAA
1 TCCAATACACCTCTAATCCAA
3227150 TCCAATACACCTCTAATCCAA
1 TCCAATACACCTCTAATCCAA
3227171 T
1 T
3227172 ACAGCGAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.30
Consensus pattern (21 bp):
TCCAATACACCTCTAATCCAA
Found at i:3228182 original size:89 final size:88
Alignment explanation
Indices: 3228088--3228686 Score: 303
Period size: 90 Copynumber: 6.8 Consensus size: 88
3228078 TCATACCCAG
* * * * * *
3228088 TTGAGTCTGGTGTTGTAATAATATTTTTTATTTTATGGAATAATCATAATAATTGTTATTAATTT
1 TTGAGTCTGGTATTGCAATAATATTTTTTATTTTTTGAAATAATTATAATAATTGTTATTTATTT
* * *
3228153 TATTTCATTATCCAACATTTGGAC
66 CATTTCATTAT-GAGCATTTGGAC
* ** * * *** * *
3228177 TTGAGTTTGGTGCTACAATAATTTATTTTTATTTTCCAAAATAATTATAATAATAGCTATTTATT
1 TTGAGTCTGGTATTGCAATAATAT-TTTTTATTTTTTGAAATAATTATAATAATTGTTATTTATT
*
3228242 TCATTTCATTATGAGGCATTT-GAGT
65 TCATTTCATTATGA-GCATTTGGA-C
*
3228267 TTGAGTCTGGTATTGCAATAA-ATTTTTTTATTTTTTGGAATAATTATAATAATTGATTTATTTC
1 TTGAGTCTGGTATTGCAATAATA-TTTTTTATTTTTTGAAATAATTATAATAATTG--TTATTT-
* * *
3228331 ATTCCATTTCATTTTTGGGCATTTAGG-C
62 ATTTCATTTCA-TTATGAGCATTT-GGAC
* * * *
3228359 TT--GTTTGGTATTGTAATAATATTTTTTATTTTTTGAAATAATTATAATATTTTTTTATTTATT
1 TTGAGTCTGGTATTGCAATAATATTTTTTATTTTTTGAAATAATTATAATA-ATTGTTATTTATT
* * * * *
3228422 TTATTTCATTTCTAAG-GTATT-GAG
65 TCATTTCA-TTATGAGCAT-TTGGAC
* * **
3228446 TGTG-GGCTGGTGTTG---TAATGA-TTTTT-TTTTCAG-AATAATTATAATAATT-TCTATTTA
1 T-TGAGTCTGGTATTGCAATAAT-ATTTTTTATTTTTTGAAATAATTATAATAATTGT-TATTTA
* * * *
3228503 TTTTATTTCATTTCTGGGCCATTTGGGC
63 TTTCATTTCA-TTATGAG-CATTTGGAC
* * ** * * * * *
3228531 TTGAGTTTGGTGTTATAAT-ATTTTTTTATATTTTTTTGGAATACTTATAATAGTTGCTATTTAT
1 TTGAGTCTGGTATTGCAATAATATTTTT-TA-TTTTTTGAAATAATTATAATAATTGTTATTTAT
* * *
3228595 TTCATTTTATTTTCAAAGCATTTAGG--
64 TTCATTTCATTAT--GAGCATTT-GGAC
* *
3228621 TTCGAGTC------TGCAATAATATTTTTTTATTTTTCGAAATAATTATAATAATT-TTATTTTT
1 TT-GAGTCTGGTATTGCAATAATA-TTTTTTATTTTTTGAAATAATTATAATAATTGTTATTTAT
3228679 TTCATTTC
64 TTCATTTC
3228687 GTTCTTGAGT
Statistics
Matches: 393, Mismatches: 80, Indels: 79
0.71 0.14 0.14
Matches are distributed among these distances:
82 1 0.00
83 24 0.06
84 30 0.08
85 40 0.10
86 14 0.04
87 14 0.04
88 19 0.05
89 62 0.16
90 118 0.30
91 45 0.11
92 21 0.05
93 4 0.01
94 1 0.00
ACGTcount: A:0.27, C:0.07, G:0.13, T:0.53
Consensus pattern (88 bp):
TTGAGTCTGGTATTGCAATAATATTTTTTATTTTTTGAAATAATTATAATAATTGTTATTTATTT
CATTTCATTATGAGCATTTGGAC
Found at i:3229591 original size:32 final size:32
Alignment explanation
Indices: 3229555--3229619 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
3229545 ATATTAGGGT
3229555 TCTCACTTGCACAGTTGTGAATTATAGTGCAC
1 TCTCACTTGCACAGTTGTGAATTATAGTGCAC
3229587 TCTCACTTGCACAGTTGTGAATTATAGTGCAC
1 TCTCACTTGCACAGTTGTGAATTATAGTGCAC
3229619 T
1 T
3229620 TACATAAATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (32 bp):
TCTCACTTGCACAGTTGTGAATTATAGTGCAC
Found at i:3235494 original size:44 final size:44
Alignment explanation
Indices: 3235424--3235552 Score: 201
Period size: 44 Copynumber: 3.0 Consensus size: 44
3235414 AATCCCTGTG
* *
3235424 ACTAGAACTCATAG-TTGTATGGAGGGTGAACACCCTTGGCCAA
1 ACTAGAACTCACAGATTGTATGTAGGGTGAACACCCTTGGCCAA
*
3235467 ACTAGAACTCAGAGATTGTATGTAGGGTGAACACCCTTGGCCAA
1 ACTAGAACTCACAGATTGTATGTAGGGTGAACACCCTTGGCCAA
*
3235511 ACTAGAACTCACAGATTGTATGTAAGGTGAAC-CCC-TGGCCAA
1 ACTAGAACTCACAGATTGTATGTAGGGTGAACACCCTTGGCCAA
3235553 TGAGTCAACA
Statistics
Matches: 81, Mismatches: 4, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
42 7 0.09
43 16 0.20
44 58 0.72
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.22
Consensus pattern (44 bp):
ACTAGAACTCACAGATTGTATGTAGGGTGAACACCCTTGGCCAA
Found at i:3245014 original size:11 final size:11
Alignment explanation
Indices: 3245000--3245033 Score: 50
Period size: 11 Copynumber: 2.9 Consensus size: 11
3244990 AAGATTTTTA
3245000 TTTTTATTAAT
1 TTTTTATTAAT
3245011 TTTTTATTAAT
1 TTTTTATTAAT
3245022 TTATTTAATTAA
1 TT-TTT-ATTAA
3245034 ATCATCTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 13 0.62
12 3 0.14
13 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTTTATTAAT
Found at i:3248849 original size:17 final size:17
Alignment explanation
Indices: 3248829--3248862 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3248819 TAAGACTCGG
3248829 GAAAGAA-AAAGAAATAA
1 GAAAGAACAAA-AAATAA
3248846 GAAAGAACAAAAAATAA
1 GAAAGAACAAAAAATAA
3248863 ATCTTATGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.76, C:0.03, G:0.15, T:0.06
Consensus pattern (17 bp):
GAAAGAACAAAAAATAA
Found at i:3252482 original size:113 final size:113
Alignment explanation
Indices: 3252284--3252505 Score: 417
Period size: 113 Copynumber: 2.0 Consensus size: 113
3252274 CTGGTTATAG
*
3252284 CAGTTAAGAACGTCCTAACCACCAATTCTTCCTTTAGCAGTTGGTTCCGGTACGACCTGCAAACC
1 CAGTTAAGAACGTCCTAACCACCAATTCTTCCTTTAGCAGCTGGTTCCGGTACGACCTGCAAACC
3252349 AACATTTACCGATTATCTAACCGAGATAAACGTATTCCCGATTCGTAT
66 AACATTTACCGATTATCTAACCGAGATAAACGTATTCCCGATTCGTAT
*
3252397 CAGTTAAGAACGTCCTAACCACCAATTCTTCCTTTAGCAGCTGGTTCCGGTACGACCTGTAAACC
1 CAGTTAAGAACGTCCTAACCACCAATTCTTCCTTTAGCAGCTGGTTCCGGTACGACCTGCAAACC
*
3252462 AACCTTTACCGATTATCTAACCGAGATAAACGTATTCCCGATTC
66 AACATTTACCGATTATCTAACCGAGATAAACGTATTCCCGATTC
3252506 AAGTTCCCGG
Statistics
Matches: 106, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
113 106 1.00
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (113 bp):
CAGTTAAGAACGTCCTAACCACCAATTCTTCCTTTAGCAGCTGGTTCCGGTACGACCTGCAAACC
AACATTTACCGATTATCTAACCGAGATAAACGTATTCCCGATTCGTAT
Found at i:3253162 original size:5 final size:5
Alignment explanation
Indices: 3253152--3253176 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3253142 AACCTAAATT
3253152 AATAA AATAA AATAA AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA
3253177 TAAAACAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:3253191 original size:23 final size:23
Alignment explanation
Indices: 3253146--3253194 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
3253136 TAGCTTAACC
* * *
3253146 TAAATTAATAAAATAAAATAAAA
1 TAAAATAATAAAACAAAACAAAA
*
3253169 TAAAATAATAAAACAAGACAAAA
1 TAAAATAATAAAACAAAACAAAA
3253192 TAA
1 TAA
3253195 TATATTCCTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.20
Consensus pattern (23 bp):
TAAAATAATAAAACAAAACAAAA
Found at i:3253816 original size:12 final size:12
Alignment explanation
Indices: 3253799--3253824 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3253789 TATTTATTTA
3253799 TTCTCTTTTTTT
1 TTCTCTTTTTTT
3253811 TTCTCTTTTTTT
1 TTCTCTTTTTTT
3253823 TT
1 TT
3253825 GTGTAAAGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (12 bp):
TTCTCTTTTTTT
Found at i:3259407 original size:23 final size:25
Alignment explanation
Indices: 3259374--3259419 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
3259364 CTAATCACTA
*
3259374 TTATTATATAT-TA-ATGTATATTT
1 TTATTACATATATATATGTATATTT
3259397 TTATTACATATATATATGTATAT
1 TTATTACATATATATATGTATAT
3259420 GTATATGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
24 2 0.10
25 8 0.40
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (25 bp):
TTATTACATATATATATGTATATTT
Found at i:3259424 original size:12 final size:12
Alignment explanation
Indices: 3259404--3259435 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
3259394 TTTTTATTAC
3259404 ATATATATATGT
1 ATATATATATGT
*
3259416 ATATGTATATGT
1 ATATATATATGT
3259428 ATATATAT
1 ATATATAT
3259436 TTATACATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (12 bp):
ATATATATATGT
Found at i:3259524 original size:147 final size:147
Alignment explanation
Indices: 3259361--3259648 Score: 372
Period size: 147 Copynumber: 2.0 Consensus size: 147
3259351 TAATATTATT
*
3259361 AATCTAATCACTATTATTA-TA-TATTAATGTATATTTTTA-T-TACATATATATATGTA-TATG
1 AATCTAATCACTATTATTATTATTATT-AT-TATA-TATTAGTGTACAT-TATATAT-TAGTATG
* ** **
3259421 TATATGTATATATATTTATACATAAGTATTATTTTTTAATTACTTTATTTTAGTATTTTTATTAT
61 TATATGTATATATATTTATACAT-AGTAGTATTTTTTAATTACTTTATTTTAACATCATTATTAT
3259486 A-TATATTAGCTTTTTGTATTTC
125 ATTATATTAGCTTTTTGTATTTC
* * * *
3259508 AATCTAATCACTATTATTATTATTATTATTATATATTAGTGTATATTTTTTATTATGTATGTATG
1 AATCTAATCACTATTATTATTATTATTATTATATATTAGTGTACATTATATATTA-GTATGTATA
3259573 TGTATATATATTTATACATAGTAGTATTTTTTAATTACTTTATTTTAACATCATTATTATATTAT
65 TGTATATATATTTATACATAGTAGTATTTTTTAATTACTTTATTTTAACATCATTATTATATTAT
*
3259638 ATTTGCTTTTT
130 ATTAGCTTTTT
3259649 TTTGTATTTC
Statistics
Matches: 123, Mismatches: 11, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
146 6 0.05
147 66 0.54
148 47 0.38
149 4 0.03
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.56
Consensus pattern (147 bp):
AATCTAATCACTATTATTATTATTATTATTATATATTAGTGTACATTATATATTAGTATGTATAT
GTATATATATTTATACATAGTAGTATTTTTTAATTACTTTATTTTAACATCATTATTATATTATA
TTAGCTTTTTGTATTTC
Found at i:3259554 original size:26 final size:27
Alignment explanation
Indices: 3259525--3259585 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 27
3259515 TCACTATTAT
3259525 TATTATTATTATTATATAT-TA-GTGTA
1 TATTATT-TTATTATATATGTATGTGTA
*
3259551 TATT-TTTTATTATGTATGTATGTGTA
1 TATTATTTTATTATATATGTATGTGTA
3259577 TATATATTT
1 TAT-TATTT
3259586 ATACATAGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
24 10 0.33
25 4 0.13
26 12 0.40
27 1 0.03
28 3 0.10
ACGTcount: A:0.30, C:0.00, G:0.10, T:0.61
Consensus pattern (27 bp):
TATTATTTTATTATATATGTATGTGTA
Found at i:3259680 original size:148 final size:148
Alignment explanation
Indices: 3259417--3259687 Score: 352
Period size: 148 Copynumber: 1.8 Consensus size: 148
3259407 TATATATGTA
* ** **
3259417 TATGTATATGTATATATATTTATACATAAGTATTATTTTTTAATTACTTTATTTTAGTATTTTTA
1 TATGTATATGTATATATATTTATACATAAGTAGTATTTTTTAATTACTTTATTTTAACATCATTA
* * * *
3259482 TTATATATATTAGCTTTTTGTATTTCAATCTAATCACTATTATTATTATTATTATTATATATTAG
66 TTATATATATTAGCTTTTTGTATTTCAATCTAATCACTACTAGTACTATTATCATTATATATTAG
3259547 TGTATATTTTTTATTATG
131 TGTATATTTTTTATTATG
*
3259565 TATGTATGTGTATATATATTTATACAT-AGTAGTATTTTTTAATTACTTTATTTTAACATCATTA
1 TATGTATATGTATATATATTTATACATAAGTAGTATTTTTTAATTACTTTATTTTAACATCATTA
* * * *
3259629 TTATATTATATTTGCTTTTTTTTGTATTTC-AT-T-ATTATTGCTAGTACTATTATCATTAT
66 TTATA-TATATTAGC---TTTTTGTATTTCAATCTAATCACTACTAGTACTATTATCATTAT
3259688 CATCATTATT
Statistics
Matches: 105, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
147 37 0.35
148 53 0.50
149 1 0.01
150 2 0.02
151 12 0.11
ACGTcount: A:0.30, C:0.06, G:0.07, T:0.58
Consensus pattern (148 bp):
TATGTATATGTATATATATTTATACATAAGTAGTATTTTTTAATTACTTTATTTTAACATCATTA
TTATATATATTAGCTTTTTGTATTTCAATCTAATCACTACTAGTACTATTATCATTATATATTAG
TGTATATTTTTTATTATG
Found at i:3270993 original size:23 final size:23
Alignment explanation
Indices: 3270923--3270993 Score: 54
Period size: 23 Copynumber: 3.0 Consensus size: 23
3270913 TATTATGCCT
3270923 AAAAAAAA-GAATCAAGATGAAA
1 AAAAAAAAGGAATCAAGATGAAA
* * ** ** *
3270945 ACCAGAAAAGGGTGTCTTGATTAAA
1 A--AAAAAAAGGAATCAAGATGAAA
3270970 AAAAAAAAGGAATCAAGATGAAA
1 AAAAAAAAGGAATCAAGATGAAA
3270993 A
1 A
3270994 CCCGAAAAGG
Statistics
Matches: 32, Mismatches: 14, Indels: 5
0.63 0.27 0.10
Matches are distributed among these distances:
22 1 0.03
23 16 0.50
24 5 0.16
25 10 0.31
ACGTcount: A:0.61, C:0.07, G:0.18, T:0.14
Consensus pattern (23 bp):
AAAAAAAAGGAATCAAGATGAAA
Found at i:3271039 original size:46 final size:46
Alignment explanation
Indices: 3270924--3271097 Score: 219
Period size: 46 Copynumber: 3.8 Consensus size: 46
3270914 ATTATGCCTA
* * * *
3270924 AAAAAAAGAATCAAGATGAAAACCAGAAAAGGGTGTCTTGATTAAAAA
1 AAAAAAGGAATCAAGATGAAAACCCGAAAAGGGCGTCTTGA-T-AAAC
3270972 AAAAAAGGAATCAAGATGAAAACCCGAAAAGGGCGTCTTGATAAAC
1 AAAAAAGGAATCAAGATGAAAACCCGAAAAGGGCGTCTTGATAAAC
* * *
3271018 AAAAAAGGAATCAAGATGAAAACCTGAAAAAGACGTCTTGATAAAC
1 AAAAAAGGAATCAAGATGAAAACCCGAAAAGGGCGTCTTGATAAAC
* * *
3271064 --AAAAGG-GTTAGGATGAAAACCCGAAAAGGGCGTC
1 AAAAAAGGAATCAAGATGAAAACCCGAAAAGGGCGTC
3271098 CCAGTGAAGT
Statistics
Matches: 113, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
43 22 0.19
44 6 0.05
46 46 0.41
47 1 0.01
48 38 0.34
ACGTcount: A:0.51, C:0.13, G:0.22, T:0.14
Consensus pattern (46 bp):
AAAAAAGGAATCAAGATGAAAACCCGAAAAGGGCGTCTTGATAAAC
Found at i:3271946 original size:75 final size:76
Alignment explanation
Indices: 3271859--3272281 Score: 449
Period size: 78 Copynumber: 5.5 Consensus size: 76
3271849 TTTATTTATG
* * *
3271859 TTTTTCAAAAATCAACTCATGTTGCGAGAGGTGAGTTGAGCCCCGGGTCACACG-TCGAGATATT
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCT-GAGGTATT
3271923 TTCAATTTCT-T
65 TTCAATTTCTGT
*** * *
3271934 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAATCACGCACTGAGGTATTT
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTT
*
3271999 TCAATTTATGT
66 TCAATTTCTGT
**** *
3272010 TTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCGGGTCACACGCTGAGGTATTT
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTT
* * *
3272075 TTAGTCTCTGT
66 TCAATTTCTGT
* *
3272086 TTTTTCAAAAAAATCAACTCATATAGCGAGAAGTGAGTTGAGCCTCGGGTCACACGCTGAGGTAT
1 TTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTAT
* *
3272151 TTTTAGTTT-T-T
64 TTTCAATTTCTGT
* * *
3272162 ATTTTTCAAATCAATCAATTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACACACTGAGGTA
1 -TTTTTCAAA--AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTA
* * *
3272227 TTTTTAATTTTTTAAT
63 TTTTCAA-TTTCT-GT
* * * * * *
3272243 TTTTTTAAAAATTAACTCATAATCCGAAAGATGAGTTGA
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
3272282 ACGTCAGTTT
Statistics
Matches: 293, Mismatches: 44, Indels: 19
0.82 0.12 0.05
Matches are distributed among these distances:
75 66 0.23
76 67 0.23
77 61 0.21
78 89 0.30
79 1 0.00
80 8 0.03
81 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (76 bp):
TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTT
TCAATTTCTGT
Found at i:3272115 original size:78 final size:75
Alignment explanation
Indices: 3271845--3272239 Score: 451
Period size: 77 Copynumber: 5.2 Consensus size: 75
3271835 GATATCCTGA
* *
3271845 TATTTTT-ATTTATGTTTTTC--AAAAATCAACTCATGTTGCGAGAGGTGAGTTGAGCCCCGGGT
1 TATTTTTAATTT-T-TTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
*
3271907 CACACG-TCGAGA
64 CACACGCT-GAGG
* ***
3271919 TATTTTCAATTTCTTTTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAAT
1 TATTTTTAA-TT-TTTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
* *
3271982 CACGCACTGAGG
64 CACACGCTGAGG
* * * *
3271994 TATTTTCAATTTATGTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCGGGTC
1 TATTTTTAATTTTTTTTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
3272059 ACACGCTGAGG
65 ACACGCTGAGG
* * *
3272070 TATTTTTAGTCTCTGTTTTTTCAAAAAAATCAACTCATATAGCGAGAAGTGAGTTGAGCCTCGGG
1 TATTTTTAAT-T-T-TTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
3272135 TCACACGCTGAGG
63 TCACACGCTGAGG
* ** * *
3272148 TATTTTTAGTTTTTATTTTTCAAATCAATCAATTCATATTGCGAGAGGTGAGTTGAGCCTCAGGT
1 TATTTTTA-ATTTT-TTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
*
3272213 CACACACTGAGG
64 CACACGCTGAGG
3272225 TATTTTTAATTTTTT
1 TATTTTTAATTTTTT
3272240 AATTTTTTTA
Statistics
Matches: 276, Mismatches: 33, Indels: 23
0.83 0.10 0.07
Matches are distributed among these distances:
73 6 0.02
74 8 0.03
75 62 0.22
76 65 0.24
77 66 0.24
78 63 0.23
79 6 0.02
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (75 bp):
TATTTTTAATTTTTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
CACGCTGAGG
Found at i:3272204 original size:77 final size:73
Alignment explanation
Indices: 3271845--3272239 Score: 441
Period size: 75 Copynumber: 5.2 Consensus size: 73
3271835 GATATCCTGA
* * *
3271845 TATTTTTATTTATGTTTTTCAAAAATCAACTCATGTTGCGAGAGGTGAGTTGAGCCCCGGGTCAC
1 TATTTTTATTT-TTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
*
3271910 ACG-TCGAGA
65 ACGCT-GAGG
* ***
3271919 TATTTTCAATTTCTTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAATCA
1 TATTTT-TATTT-TTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
* *
3271984 CGCACTGAGG
64 CACGCTGAGG
* * * * *
3271994 TATTTTCAATTTATGTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCGGGTC
1 TATTTTTATTTTTTTTTTC---AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
3272059 ACACGCTGAGG
63 ACACGCTGAGG
* * *
3272070 TATTTTTAGTCTCTGTTTTTTCAAAAAAATCAACTCATATAGCGAGAAGTGAGTTGAGCCTCGGG
1 TATTTTTA-T-T-TTTTTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
3272135 TCACACGCTGAGG
61 TCACACGCTGAGG
* *
3272148 TATTTTTAGTTTTTATTTTTCAAATCAATCAATTCATATTGCGAGAGGTGAGTTGAGCCTCAGGT
1 TATTTTTA-TTTTT-TTTTTCAAA--AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
*
3272213 CACACACTGAGG
62 CACACGCTGAGG
*
3272225 TATTTTTAATTTTTT
1 TATTTTTATTTTTTT
3272240 AATTTTTTTA
Statistics
Matches: 274, Mismatches: 36, Indels: 21
0.83 0.11 0.06
Matches are distributed among these distances:
73 6 0.02
74 9 0.03
75 66 0.24
76 62 0.23
77 61 0.22
78 64 0.23
79 6 0.02
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (73 bp):
TATTTTTATTTTTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACA
CGCTGAGG
Found at i:3272253 original size:155 final size:149
Alignment explanation
Indices: 3271845--3272263 Score: 455
Period size: 155 Copynumber: 2.7 Consensus size: 149
3271835 GATATCCTGA
* * * *
3271845 TATTTTTATTTATGTTTTTCAAAAATCAACTCATGTTGCGAGAGGTGAGTTGAGCCCCGGGTCAC
1 TATTTTTATTTTTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
* * * * * * *
3271910 ACGTCGAGATATTTTCAA-TTTCTTTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
66 ACCT-GAGGTATTTTTAATTTTTTTTTTTTAAAAAATCAACTCATATAGCGAGAAGTGAGTTGAG
*
3271974 CCTCAAATCACGCACTGAGG
130 CCTCAAATCACACACTGAGG
* * * *
3271994 TATTTTCA-ATTTATGTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCGGGT
1 TATTTTTATTTTTATTTTTC---AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
* * **
3272058 CACACGCTGAGGTATTTTTAGTCTCTGTTTTTTCAAAAAAATCAACTCATATAGCGAGAAGTGAG
63 CACAC-CTGAGGTATTTTTAAT-T-TTTTTTTTTTAAAAAATCAACTCATATAGCGAGAAGTGAG
*** *
3272123 TTGAGCCTCGGGTCACACGCTGAGG
125 TTGAGCCTCAAATCACACACTGAGG
* *
3272148 TATTTTTAGTTTTTATTTTTCAAATCAATCAATTCATATTGCGAGAGGTGAGTTGAGCCTCAGGT
1 TATTTTTA-TTTTTATTTTTCAAA--AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT
* *
3272213 CACACACTGAGGTATTTTTAATTTTTTAATTTTTTTAAAAATTAACTCATA
63 CACAC-CTGAGGTATTTTTAATTTTTT--TTTTTTAAAAAATCAACTCATA
3272264 ATCCGAAAGA
Statistics
Matches: 220, Mismatches: 37, Indels: 20
0.79 0.13 0.07
Matches are distributed among these distances:
148 7 0.03
149 7 0.03
151 54 0.25
152 1 0.00
153 7 0.03
154 61 0.28
155 74 0.34
156 9 0.04
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (149 bp):
TATTTTTATTTTTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
ACCTGAGGTATTTTTAATTTTTTTTTTTTAAAAAATCAACTCATATAGCGAGAAGTGAGTTGAGC
CTCAAATCACACACTGAGG
Found at i:3272466 original size:19 final size:19
Alignment explanation
Indices: 3272417--3272466 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
3272407 CTTATCTCCA
*
3272417 TGAAGTTGTAGCAGAACCC
1 TGAAGTTGTAGTAGAACCC
3272436 TGAAGTTGTAGTAGAACCC
1 TGAAGTTGTAGTAGAACCC
3272455 TGAAGTTGTAGT
1 TGAAGTTGTAGT
3272467 GGAGCGGACC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (19 bp):
TGAAGTTGTAGTAGAACCC
Found at i:3274000 original size:23 final size:25
Alignment explanation
Indices: 3273969--3274021 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 25
3273959 ATTTAATCAC
*
3273969 TATTATTATTATATAT-TAT-TGTA
1 TATTATTATTACATATGTATATGTA
*
3273992 TATTTTTATTACATATGTATATGTA
1 TATTATTATTACATATGTATATGTA
3274017 T-TTAT
1 TATTAT
3274022 ACATAAGTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 14 0.56
24 6 0.24
25 5 0.20
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.60
Consensus pattern (25 bp):
TATTATTATTACATATGTATATGTA
Found at i:3274026 original size:20 final size:19
Alignment explanation
Indices: 3273988--3274038 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
3273978 TATATATTAT
3273988 TGTATATTTTTATTACATA
1 TGTATATTTTTATTACATA
3274007 TGTATATGTATTTA-TACATA
1 TGTATAT-T-TTTATTACATA
*
3274027 AGTATTATTTTT
1 TGTA-TATTTTT
3274039 TAATTACTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
19 10 0.36
20 11 0.39
21 7 0.25
ACGTcount: A:0.31, C:0.04, G:0.08, T:0.57
Consensus pattern (19 bp):
TGTATATTTTTATTACATA
Found at i:3274040 original size:20 final size:21
Alignment explanation
Indices: 3273994--3274045 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
3273984 TTATTGTATA
*
3273994 TTTTTATTACATATGTATATG
1 TTTTTATTACATAAGTATATG
*
3274015 TATTTA-TACATAAGTATTAT-
1 TTTTTATTACATAAGTA-TATG
3274035 TTTTTAATTAC
1 TTTTT-ATTAC
3274046 TTTATTTTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 13 0.52
21 9 0.36
22 3 0.12
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.56
Consensus pattern (21 bp):
TTTTTATTACATAAGTATATG
Found at i:3275825 original size:21 final size:20
Alignment explanation
Indices: 3275796--3275835 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
3275786 TTTCCTTTAA
*
3275796 ACATATTCTTATATTATATT
1 ACATATTCTTATAATATATT
3275816 ACATAATTCTTATAATATAT
1 ACAT-ATTCTTATAATATAT
3275836 CTTTTAAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (20 bp):
ACATATTCTTATAATATATT
Found at i:3276518 original size:15 final size:15
Alignment explanation
Indices: 3276498--3276528 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3276488 TACTTGATTA
3276498 TTAGTCCATCATTTT
1 TTAGTCCATCATTTT
*
3276513 TTAGTCCATTATTTT
1 TTAGTCCATCATTTT
3276528 T
1 T
3276529 GTATCTTGTT
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:0.19, C:0.16, G:0.06, T:0.58
Consensus pattern (15 bp):
TTAGTCCATCATTTT
Found at i:3277073 original size:132 final size:133
Alignment explanation
Indices: 3276869--3277206 Score: 371
Period size: 132 Copynumber: 2.6 Consensus size: 133
3276859 ATTATTCATT
* * * * *
3276869 TAAAAATTCTTTAAAACGGAGACGAGATTTGATATTTGGCAAATTCGCGGAATCGTGCCCTAACG
1 TAAAAATCCTTTAAAACGAAGACGAGATTCGATATTTGACAAATTCACGGAATCGTGCCCTAACG
* * *
3276934 TGTTGGGTTGCAATTTCGCATTTGCTCAAAATGATCGAATATCCCTCCAAAATTTCATTCATGTC
66 TGCTGGGTTGCAATTTCGCATTTGCTCAAAATAATCGAATATCCCTCCAAAATCTCATTCATGTC
3276999 TTC
131 TTC
* *
3277002 TAAAAATCCTTTAAAACGAAGGCGATG-TTCGATATTTGAC-AATTCACTGAATCGTGCCCTAAC
1 TAAAAATCCTTTAAAACGAAGACGA-GATTCGATATTTGACAAATTCACGGAATCGTGCCCTAAC
* * * * ** * *
3277065 GTGCTGGGTTGCAATTTCTCGTTTGCTCAAAGTAATCGAATGTCCCTTTAGAATCTCGTTCATGT
65 GTGCTGGGTTGCAATTTCGCATTTGCTCAAAATAATCGAATATCCCTCCAAAATCTCATTCATGT
3277130 CTTC
130 CTTC
* ** * * * * * * *
3277134 TAAAAA-CTCTTTAAAACAAAGAAAATACTCGATGTTTGGCAATTTGA--GAATCGTGCCCTATC
1 TAAAAATC-CTTTAAAACGAAGACGAGATTCGATATTTGACAAATTCACGGAATCGTGCCCTAAC
3277196 GTGCTGGGTTG
65 GTGCTGGGTTG
3277207 TGATTCCCCG
Statistics
Matches: 172, Mismatches: 29, Indels: 10
0.82 0.14 0.05
Matches are distributed among these distances:
131 26 0.15
132 108 0.63
133 37 0.22
134 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.33
Consensus pattern (133 bp):
TAAAAATCCTTTAAAACGAAGACGAGATTCGATATTTGACAAATTCACGGAATCGTGCCCTAACG
TGCTGGGTTGCAATTTCGCATTTGCTCAAAATAATCGAATATCCCTCCAAAATCTCATTCATGTC
TTC
Found at i:3284032 original size:5 final size:5
Alignment explanation
Indices: 3284022--3284051 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
3284012 AACCTAAATT
*
3284022 AATAA AATAA AATAA AATAA AACAA AATAA
1 AATAA AATAA AATAA AATAA AATAA AATAA
3284052 TATATTCCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (5 bp):
AATAA
Found at i:3287699 original size:4 final size:4
Alignment explanation
Indices: 3287690--3287714 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3287680 TAAATTTAAA
3287690 AATT AATT AATT AATT AATT AATT A
1 AATT AATT AATT AATT AATT AATT A
3287715 GACCCAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:3289792 original size:26 final size:26
Alignment explanation
Indices: 3289763--3289870 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
3289753 TGGTACAAAT
*
3289763 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
*
3289789 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
*
3289815 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
* *
3289841 TGATAATGGTTTAGGTAAATATTCTA
1 TGATAATGGGTTAGGTAAATATTCCA
3289867 TGAT
1 TGAT
3289871 GGGCATTTCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.33, C:0.06, G:0.23, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATATTCCA
Found at i:3289825 original size:52 final size:52
Alignment explanation
Indices: 3289763--3289870 Score: 198
Period size: 52 Copynumber: 2.1 Consensus size: 52
3289753 TGGTACAAAT
3289763 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
* *
3289815 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGTTTAGGTAAATATTCTA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
3289867 TGAT
1 TGAT
3289871 GGGCATTTCA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.33, C:0.06, G:0.23, T:0.37
Consensus pattern (52 bp):
TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
Found at i:3291563 original size:54 final size:54
Alignment explanation
Indices: 3291478--3291617 Score: 219
Period size: 54 Copynumber: 2.6 Consensus size: 54
3291468 GGAAGCGTCT
* * *
3291478 TGGTGGCTATGCCACAATTATCTAATTTGGTGGCTCTGCCACATATATCTGTCC
1 TGGTGGCTATGCCACAATTATTTGATCTGGTGGCTCTGCCACATATATCTGTCC
*
3291532 TGGTGGCTATGCCACAATTATTTGATCTGGTGGCTCTGCCACATATATCTGTTC
1 TGGTGGCTATGCCACAATTATTTGATCTGGTGGCTCTGCCACATATATCTGTCC
*
3291586 TGGTGGCTCTGCCACAA-TATTTGTATCTGGTG
1 TGGTGGCTATGCCACAATTATTTG-ATCTGGTG
3291618 ACTTCGTCAC
Statistics
Matches: 80, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
53 6 0.08
54 74 0.93
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.36
Consensus pattern (54 bp):
TGGTGGCTATGCCACAATTATTTGATCTGGTGGCTCTGCCACATATATCTGTCC
Found at i:3291614 original size:27 final size:27
Alignment explanation
Indices: 3291478--3291635 Score: 155
Period size: 27 Copynumber: 5.9 Consensus size: 27
3291468 GGAAGCGTCT
* * *
3291478 TGGTGGCTATGCCACAATTATCT-AATT
1 TGGTGGCTCTGCCACAA-TATCTGTATC
*
3291505 TGGTGGCTCTGCCACATATATCTGT-CC
1 TGGTGGCTCTGCCACA-ATATCTGTATC
* *
3291532 TGGTGGCTATGCCACAATTATTTG-ATC
1 TGGTGGCTCTGCCACAA-TATCTGTATC
3291559 TGGTGGCTCTGCCACATATATCTGT-TC
1 TGGTGGCTCTGCCACA-ATATCTGTATC
*
3291586 TGGTGGCTCTGCCACAATATTTGTATC
1 TGGTGGCTCTGCCACAATATCTGTATC
* *
3291613 TGGTGACT-TCGTCACAATATCTG
1 TGGTGGCTCT-GCCACAATATCTG
3291636 GCAGCCTCGC
Statistics
Matches: 110, Mismatches: 13, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
26 9 0.08
27 99 0.90
28 2 0.02
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.36
Consensus pattern (27 bp):
TGGTGGCTCTGCCACAATATCTGTATC
Found at i:3293288 original size:31 final size:28
Alignment explanation
Indices: 3293221--3293277 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
3293211 TTACTTAAAA
3293221 AAATTTATTGGTTGTGTAGTTTTTTTTT
1 AAATTTATTGGTTGTGTAGTTTTTTTTT
3293249 AAATTTATTGGTTGTGTAGTTTTTTTTT
1 AAATTTATTGGTTGTGTAGTTTTTTTTT
3293277 A
1 A
3293278 CTTTCATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.19, C:0.00, G:0.18, T:0.63
Consensus pattern (28 bp):
AAATTTATTGGTTGTGTAGTTTTTTTTT
Found at i:3296763 original size:14 final size:13
Alignment explanation
Indices: 3296744--3296777 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
3296734 CTTCAATCTT
3296744 TTTTTTCAAATTTA
1 TTTTTT-AAATTTA
3296758 TTTTTTAAATTTA
1 TTTTTTAAATTTA
3296771 TATTTTT
1 T-TTTTT
3296778 GTCCAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTTTAAATTTA
Found at i:3296796 original size:20 final size:20
Alignment explanation
Indices: 3296771--3296817 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
3296761 TTTAAATTTA
3296771 TATTTTTGTCCAAATTTTCT
1 TATTTTTGTCCAAATTTTCT
*
3296791 TATTTTTGTCTAAATTTTCT
1 TATTTTTGTCCAAATTTTCT
3296811 TATTTTT
1 TATTTTT
3296818 TGAGCAGACC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.19, C:0.11, G:0.04, T:0.66
Consensus pattern (20 bp):
TATTTTTGTCCAAATTTTCT
Found at i:3307271 original size:48 final size:48
Alignment explanation
Indices: 3307212--3307307 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
3307202 CCATTGTGTC
3307212 GTCATCCCTCTCCCTTGCCATTAGATTTTCTATTTCCTTTGTAAGCTT
1 GTCATCCCTCTCCCTTGCCATTAGATTTTCTATTTCCTTTGTAAGCTT
3307260 GTCATCCCTCTCCCTTGCCATTAGATTTTCTATTTCCTTTGTAAGCTT
1 GTCATCCCTCTCCCTTGCCATTAGATTTTCTATTTCCTTTGTAAGCTT
3307308 ACTCTTTAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.15, C:0.29, G:0.10, T:0.46
Consensus pattern (48 bp):
GTCATCCCTCTCCCTTGCCATTAGATTTTCTATTTCCTTTGTAAGCTT
Found at i:3313943 original size:13 final size:13
Alignment explanation
Indices: 3313925--3313956 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
3313915 AAGTTTAGTT
3313925 TTAATTAATGATG
1 TTAATTAATGATG
3313938 TTAATTAATGATG
1 TTAATTAATGATG
3313951 TTAATT
1 TTAATT
3313957 TGTCAGGTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (13 bp):
TTAATTAATGATG
Found at i:3316309 original size:15 final size:15
Alignment explanation
Indices: 3316291--3316322 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
3316281 TATTATAAAT
3316291 TTATTATTTATATAA
1 TTATTATTTATATAA
3316306 TTATTATTTATATAA
1 TTATTATTTATATAA
3316321 TT
1 TT
3316323 TTTTTTCACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTATTATTTATATAA
Found at i:3316805 original size:14 final size:16
Alignment explanation
Indices: 3316776--3316817 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
3316766 CATATTGTTT
*
3316776 TTTTTGAATTTTTTATA
1 TTTTTGAATTTTATA-A
3316793 TTTTT-AATTTTATAA
1 TTTTTGAATTTTATAA
3316808 TTTTTGAATT
1 TTTTTGAATT
3316818 ATTTGTTGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 6 0.26
16 12 0.52
17 5 0.22
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (16 bp):
TTTTTGAATTTTATAA
Found at i:3322957 original size:20 final size:20
Alignment explanation
Indices: 3322932--3322981 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
3322922 AAGACATGAC
3322932 ACACGCCCGTGTAGAGGGCA
1 ACACGCCCGTGTAGAGGGCA
3322952 ACACGCCCGTGTAGAGGGCA
1 ACACGCCCGTGTAGAGGGCA
3322972 ACACGCCCGT
1 ACACGCCCGT
3322982 CTGGCCATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.10
Consensus pattern (20 bp):
ACACGCCCGTGTAGAGGGCA
Found at i:3324793 original size:46 final size:45
Alignment explanation
Indices: 3324726--3324900 Score: 190
Period size: 46 Copynumber: 3.8 Consensus size: 45
3324716 TGTAACCCGC
*
3324726 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGC-TTAGCAT
* *
3324772 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--GCTTAGCAT
* *** * * * *
3324818 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTTGGACATTTGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGGC-TTAGCAT
*
3324865 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
3324901 ATGCTCAACC
Statistics
Matches: 106, Mismatches: 18, Indels: 10
0.79 0.13 0.07
Matches are distributed among these distances:
45 1 0.01
46 70 0.66
47 33 0.31
48 2 0.02
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCTTAGCAT
Found at i:3324849 original size:93 final size:93
Alignment explanation
Indices: 3324734--3324904 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
3324724 GCCCATAAGT
* *
3324734 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
3324799 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
* * *
3324827 GAACTCGGACTCAACTCAACGAGTTTGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
3324892 CGAGTTCGGATGC
66 CGAGCTCGGATGC
3324905 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:3326624 original size:46 final size:45
Alignment explanation
Indices: 3326490--3326709 Score: 153
Period size: 46 Copynumber: 4.8 Consensus size: 45
3326480 GCATATCTGT
*
3326490 GCCGATGCCATGTCCCAGACATGGTCTTACACTAACACATC-TCAT-A-
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCAC-TCGTC-TGAG
** *
3326536 GCTAATGCATGTCCCAGACATGTCTTACACTGGCTTA-T-GTCTCGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGC--ACTCGTCT-GAG
* * *
3326582 GCCGATGCATGTCCTAGACATGTCTTACACTAGCACTCGTCTCAAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCACTCGTCT-GAG
* * * * * * * *
3326628 GCCGATGTCATGTCTCAGGCACGGTCTTACACTGGCTCTCATAATGTG
1 GCCGATG-CATGTCCCAGACA-TGTCTTACACTAGCACTCGT-CTGAG
* *
3326676 GCTGATGCATGTCCCAGTCATGTCTTACACTAGC
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGC
3326710 TCACACAAGT
Statistics
Matches: 137, Mismatches: 26, Indels: 22
0.74 0.14 0.12
Matches are distributed among these distances:
43 1 0.01
44 15 0.11
45 16 0.12
46 61 0.45
47 21 0.15
48 22 0.16
49 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (45 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGCACTCGTCTGAG
Found at i:3326656 original size:94 final size:92
Alignment explanation
Indices: 3326490--3326714 Score: 226
Period size: 94 Copynumber: 2.4 Consensus size: 92
3326480 GCATATCTGT
*
3326490 GCCGATGCCATGTCCCAGACATGGTCTTACACTA--ACACATCTCATAGCTAATGCATGTCCCAG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCACACATCTCATAGCCAATGCATGTCCCAG
* **
3326553 ACATGTCTTACACTGGCT-T-ATGTCTCGAG
64 ACAGGTCTTACACTGGCTCTCAT-AAT-GAG
* * * * *
3326582 GCCGATGCATGTCCTAGACATGTCTTACACTAGCACTCGTCTCA-ATGCCGATGTCATGTCTCAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCACACATCTCATA-GCCAATG-CATGTCCCAG
* *
3326646 GCACGGTCTTACACTGGCTCTCATAATGTG
64 ACA-GGTCTTACACTGGCTCTCATAATGAG
* * *
3326676 GCTGATGCATGTCCCAGTCATGTCTTACACTAGCTCACA
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCACACA
3326715 CAAGTGACCC
Statistics
Matches: 109, Mismatches: 17, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
90 11 0.10
91 14 0.13
92 20 0.18
93 11 0.10
94 49 0.45
95 2 0.02
96 2 0.02
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (92 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGCACACATCTCATAGCCAATGCATGTCCCAGAC
AGGTCTTACACTGGCTCTCATAATGAG
Found at i:3329458 original size:67 final size:67
Alignment explanation
Indices: 3329341--3329524 Score: 217
Period size: 67 Copynumber: 2.7 Consensus size: 67
3329331 GTGGGCTGTA
* * *
3329341 ATAGGGTATAATGTGTAAGACTATAGCTCGATTATGACAACACAGAGAGTTTGCCAAGACT-TTA
1 ATAGGGTATAATGTGTAAGACCATAGCTCGATTATGACAACATAGAGAGTTCGCCAAGA-TGTTA
3329405 AAC
65 AAC
* * * * **
3329408 ATGGGGTATAATGTGTAAGACCATAGGTCGATTATGACAACATAGGGAGTTCGTCTGGATGTTAA
1 ATAGGGTATAATGTGTAAGACCATAGCTCGATTATGACAACATAGAGAGTTCGCCAAGATGTTAA
*
3329473 AT
66 AC
* * * * *
3329475 ATAAGGTATAACGTGTAAGACCATAGCTCGACTATGACAGCATATAGAGT
1 ATAGGGTATAATGTGTAAGACCATAGCTCGATTATGACAACATAGAGAGT
3329525 CCACAAAGAC
Statistics
Matches: 98, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
66 1 0.01
67 97 0.99
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (67 bp):
ATAGGGTATAATGTGTAAGACCATAGCTCGATTATGACAACATAGAGAGTTCGCCAAGATGTTAA
AC
Found at i:3332684 original size:23 final size:23
Alignment explanation
Indices: 3332658--3332716 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
3332648 TACAGAACGT
*
3332658 GCCACAAAGGCATCACGGAATAC
1 GCCACAAAGGCATCACAGAATAC
* * *
3332681 GCCACAAAGGCATTATAGAATAT
1 GCCACAAAGGCATCACAGAATAC
*
3332704 GCCATAAAGGCAT
1 GCCACAAAGGCAT
3332717 AAAAAAGTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.41, C:0.24, G:0.20, T:0.15
Consensus pattern (23 bp):
GCCACAAAGGCATCACAGAATAC
Found at i:3336474 original size:15 final size:16
Alignment explanation
Indices: 3336454--3336493 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
3336444 GTCTTAAGAA
3336454 AAAAATAAATA-AAAT
1 AAAAATAAATAGAAAT
*
3336469 AAAAATAAAAAGAAAT
1 AAAAATAAATAGAAAT
3336485 -AAAATAAAT
1 AAAAATAAAT
3336494 GGACTCAGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 18 0.82
16 4 0.18
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (16 bp):
AAAAATAAATAGAAAT
Found at i:3338121 original size:18 final size:18
Alignment explanation
Indices: 3338098--3338132 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3338088 GTAATAAAGG
*
3338098 AATAATAATCATACTTAT
1 AATAATAATAATACTTAT
3338116 AATAATAATAATACTTA
1 AATAATAATAATACTTA
3338133 ATAACAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (18 bp):
AATAATAATAATACTTAT
Found at i:3338201 original size:18 final size:18
Alignment explanation
Indices: 3338178--3338212 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3338168 TAATGAAGAA
*
3338178 AAATAATTAAAAATAAAT
1 AAATAAATAAAAATAAAT
*
3338196 AAATAAATAAATATAAA
1 AAATAAATAAAAATAAA
3338213 GGGTAAAAGG
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:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AAATAAATAAAAATAAAT
Found at i:3345683 original size:35 final size:35
Alignment explanation
Indices: 3345617--3345711 Score: 111
Period size: 35 Copynumber: 2.7 Consensus size: 35
3345607 ATTTGTTAAT
3345617 ATTCTGATTCGCATGTTAATCATGCTATTATTCTG
1 ATTCTGATTCGCATGTTAATCATGCTATTATTCTG
* * * *
3345652 ATTTTGATTTGCATGTTAATCATG-TCGTTATTTTG
1 ATTCTGATTCGCATGTTAATCATGCT-ATTATTCTG
* * *
3345687 ATTCTGATTCTCAAGTTAAGCATGC
1 ATTCTGATTCGCATGTTAATCATGC
3345712 CACTGTATTA
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
34 1 0.02
35 48 0.98
ACGTcount: A:0.23, C:0.15, G:0.16, T:0.46
Consensus pattern (35 bp):
ATTCTGATTCGCATGTTAATCATGCTATTATTCTG
Found at i:3359552 original size:12 final size:11
Alignment explanation
Indices: 3359514--3359562 Score: 66
Period size: 11 Copynumber: 4.5 Consensus size: 11
3359504 TATATATAAA
3359514 TTTTATTATA-
1 TTTTATTATAT
*
3359524 TGTTA-TATAT
1 TTTTATTATAT
3359534 TTTTATTATAT
1 TTTTATTATAT
3359545 TATTTATTATAT
1 T-TTTATTATAT
3359557 TTTTAT
1 TTTTAT
3359563 ATGTAAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
9 4 0.12
10 8 0.24
11 11 0.32
12 11 0.32
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (11 bp):
TTTTATTATAT
Found at i:3359552 original size:18 final size:19
Alignment explanation
Indices: 3359514--3359552 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
3359504 TATATATAAA
3359514 TTTTATTATATGTTATATAT
1 TTTTATTATA-GTTATATAT
*
3359534 TTTTATTATA-TTATTTAT
1 TTTTATTATAGTTATATAT
3359552 T
1 T
3359553 ATATTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
20 10 0.56
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (19 bp):
TTTTATTATAGTTATATAT
Found at i:3359574 original size:40 final size:42
Alignment explanation
Indices: 3359519--3359598 Score: 103
Period size: 40 Copynumber: 1.9 Consensus size: 42
3359509 ATAAATTTTA
* *
3359519 TTATATGTTATATATTT-TT-ATTA-TATTATTTATTATATTT
1 TTATATGTAAAATATTTGTTAATTATTATTA-TTATTATATTT
3359559 TTATATGTAAAATATTTGTTACATTATTATTATTATTATA
1 TTATATGTAAAATATTTGTTA-ATTATTATTATTATTATA
3359599 CTACATATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
40 15 0.44
41 2 0.06
43 12 0.35
44 5 0.15
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.61
Consensus pattern (42 bp):
TTATATGTAAAATATTTGTTAATTATTATTATTATTATATTT
Found at i:3371555 original size:49 final size:47
Alignment explanation
Indices: 3371260--3371834 Score: 891
Period size: 47 Copynumber: 12.1 Consensus size: 47
3371250 GAAATGATAG
*
3371260 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGAGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
3371307 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * *
3371354 TAGGGCCGAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
3371401 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
3371448 TAAGG-CGAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
3371494 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
*
3371543 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
3371592 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
*
3371641 TAAGGCCTAATGTCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
3371688 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
3371735 TAAGGCCTAATGGCCGATGTGATGAATGTGGAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
* * * * * * * *
3371784 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
3371831 TAAG
1 TAAG
3371835 TCCCGAAGGG
Statistics
Matches: 496, Mismatches: 27, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
46 43 0.09
47 272 0.55
49 181 0.36
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.29
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:3372010 original size:38 final size:37
Alignment explanation
Indices: 3371953--3372031 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 37
3371943 CTGAGCTCTA
* * *
3371953 AAGACCCGATGACTACGTGTGG-GAATTTTTGTCCGGGT
1 AAGACCCAATAACTACGTGTGGAG-A-TTATGTCCGGGT
*
3371991 AAGACCCAATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCAATAACTACGTGTGGAGATTATGTCCGGGT
3372028 AAGA
1 AAGA
3372032 TTTCGTAGTA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
37 15 0.42
38 20 0.56
39 1 0.03
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.27
Consensus pattern (37 bp):
AAGACCCAATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:3377932 original size:15 final size:17
Alignment explanation
Indices: 3377899--3377935 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
3377889 GGGTCAAGAT
*
3377899 AAAAATATCAAAAGTCA
1 AAAAATATCAAAAGACA
3377916 AAAAATAT-AAAA-ACA
1 AAAAATATCAAAAGACA
3377931 AAAAA
1 AAAAA
3377936 ATGACTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 7 0.37
16 4 0.21
17 8 0.42
ACGTcount: A:0.76, C:0.08, G:0.03, T:0.14
Consensus pattern (17 bp):
AAAAATATCAAAAGACA
Found at i:3379087 original size:43 final size:43
Alignment explanation
Indices: 3379020--3379427 Score: 230
Period size: 43 Copynumber: 9.6 Consensus size: 43
3379010 CAAAAGTTGA
* * * * *
3379020 CGGCATTTTTTAGAAAAAACGCCGCTAAAGACCACGATCTTTAG
1 CGGCGTTTTTTA-TAAAAGCGCCGCTAAAGACCAGGACCTTTAG
*
3379064 CGGCGTTTTTTATAAACGCGCCGCTAAAGACCAGGACCTTTAG
1 CGGCGTTTTTTATAAAAGCGCCGCTAAAGACCAGGACCTTTAG
* * * *
3379107 CGGTG-CTCTTA-AAAAACGCCGCTAAAGACCAGGACCTTTAG
1 CGGCGTTTTTTATAAAAGCGCCGCTAAAGACCAGGACCTTTAG
* * * ** ** *
3379148 CGGCATTTTTTATAAAAGCGCCGCTAATGTTCTTGG-TGTATAG
1 CGGCGTTTTTTATAAAAGCGCCGCTAAAG-ACCAGGACCTTTAG
*
3379191 CGGCGTTTTTTATAAAAGCGCCGCT--A-A--A-GATCTTTAG
1 CGGCGTTTTTTATAAAAGCGCCGCTAAAGACCAGGACCTTTAG
* * * * * *
3379228 CGGCG-CTTTTATAAAAAACGCCGCTATACACCAAGAACTTTAG
1 CGGCGTTTTTTAT-AAAAGCGCCGCTAAAGACCAGGACCTTTAG
* ** * * * * *
3379271 CGGCG-CTTTTATAAAAAAAGCCGCTACAGGTCCTGG-TCTTTGG
1 CGGCGTTTTTTAT-AAAAGCGCCGCTA-AAGACCAGGACCTTTAG
* * * * *
3379314 CGGCGTTTTGTACAAAAGCGCCGCTATAGACCAAGAACTTTAG
1 CGGCGTTTTTTATAAAAGCGCCGCTAAAGACCAGGACCTTTAG
** * * * * * *
3379357 C-GCGCTTTAATAAAAAAACGCCGCTATAGACCAAGAACATTAG
1 CGGCG-TTTTTTATAAAAGCGCCGCTAAAGACCAGGACCTTTAG
* *
3379400 CGGCGCTTTTTTAAAAAAACGCCGCTAA
1 CGGCG-TTTTTTATAAAAGCGCCGCTAA
3379428 TTTGCCCAGT
Statistics
Matches: 287, Mismatches: 61, Indels: 32
0.76 0.16 0.08
Matches are distributed among these distances:
36 7 0.02
37 21 0.07
39 1 0.00
40 1 0.00
41 31 0.11
42 16 0.06
43 166 0.58
44 44 0.15
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (43 bp):
CGGCGTTTTTTATAAAAGCGCCGCTAAAGACCAGGACCTTTAG
Found at i:3379317 original size:123 final size:125
Alignment explanation
Indices: 3379057--3379428 Score: 380
Period size: 123 Copynumber: 2.9 Consensus size: 125
3379047 AAGACCACGA
* * * * *
3379057 TCTTTAGCGGCGTTTTTTATAAACGCGCCGCTAAAGACCAGGACCTTTAGCGGTGC-TCT-TAAA
1 TCTTTAGCGGCGTTTTTTATAAAAGCGCCGCT--A-A-CAAGAACTTTAGCGGCGCTTTTATAAA
* * * * ** * *
3379120 AAACGCCGCTAAAGACCAGGACCTTTAGCGGC-ATTTTTTATAAAAGCGCCGCTAATGTTCTTGG
62 AAACGCCGCTATAGACCAAGAACTTTAGCGGCGCTTTTTTA-AAAAAAGCCGCTAATGGTCCTGG
* * *
3379184 TGTATAGCGGCGTTTTTTATAAAAGCGCCGCT-A-AAGATCTTTAGCGGCGCTTTTATAAAAAAC
1 TCTTTAGCGGCGTTTTTTATAAAAGCGCCGCTAACAAGAACTTTAGCGGCGCTTTTATAAAAAAC
* *
3379247 GCCGCTATACACCAAGAACTTTAGCGGCGCTTTTATAAAAAAAGCCGCTACA-GGTCCTGG
66 GCCGCTATAGACCAAGAACTTTAGCGGCGCTTTTTTAAAAAAAGCCGCTA-ATGGTCCTGG
* * * *
3379307 TCTTTGGCGGCGTTTTGTACAAAAGCGCCGCTATAGACCAAGAACTTTAGC-GCGCTTTAATAAA
1 TCTTTAGCGGCGTTTTTTATAAAAGCGCCGC--TA-A-CAAGAACTTTAGCGGCGCTTTTAT-AA
*
3379371 AAAACGCCGCTATAGACCAAGAACATTAGCGGCGCTTTTTTAAAAAAACGCCGCTAAT
61 AAAACGCCGCTATAGACCAAGAACTTTAGCGGCGCTTTTTTAAAAAAA-GCCGCTAAT
3379429 TTGCCCAGTT
Statistics
Matches: 205, Mismatches: 27, Indels: 23
0.80 0.11 0.09
Matches are distributed among these distances:
121 14 0.07
122 2 0.01
123 76 0.37
124 7 0.03
125 1 0.00
127 30 0.15
128 9 0.04
129 59 0.29
130 7 0.03
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.27
Consensus pattern (125 bp):
TCTTTAGCGGCGTTTTTTATAAAAGCGCCGCTAACAAGAACTTTAGCGGCGCTTTTATAAAAAAC
GCCGCTATAGACCAAGAACTTTAGCGGCGCTTTTTTAAAAAAAGCCGCTAATGGTCCTGG
Found at i:3379746 original size:21 final size:21
Alignment explanation
Indices: 3379722--3379766 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
3379712 TCCTGTTCTG
3379722 CTCCGCCTCCCTCGCTGCTGC
1 CTCCGCCTCCCTCGCTGCTGC
3379743 CTCCGCCTCCCTCGCTGCTGC
1 CTCCGCCTCCCTCGCTGCTGC
3379764 CTC
1 CTC
3379767 TGCTCTAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.00, C:0.58, G:0.18, T:0.24
Consensus pattern (21 bp):
CTCCGCCTCCCTCGCTGCTGC
Found at i:3380356 original size:18 final size:18
Alignment explanation
Indices: 3380324--3380361 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
3380314 TACAATATAG
3380324 TAGTAAAAATATTATTTAA
1 TAGTAAAAATATTA-TTAA
*
3380343 TAGTAAAAA-GTTATTAA
1 TAGTAAAAATATTATTAA
3380360 TA
1 TA
3380362 CTTGATAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 3 0.17
19 9 0.50
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (18 bp):
TAGTAAAAATATTATTAA
Found at i:3385932 original size:29 final size:28
Alignment explanation
Indices: 3385896--3385973 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
3385886 TCATGAGATT
3385896 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
3385926 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
3385953 TGGCACTAAGTGTGCGTGGTT
1 -GGCACTAAGTGTGCG-GGTT
3385974 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.29
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:3386191 original size:174 final size:174
Alignment explanation
Indices: 3385926--3386253 Score: 611
Period size: 174 Copynumber: 1.9 Consensus size: 174
3385916 AAATTGTACA
3385926 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGTGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGTGGTTGATTATTAAGCACTATG
* *
3385991 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACCTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACCTTACCGAGTCAA
3386056 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
* *
3386100 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGTGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGTGGTTGATTATTAAGCACTATG
*
3386165 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACCTTACCGAGTCAA
3386230 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
3386254 ACCTTGAGTT
Statistics
Matches: 149, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
174 149 1.00
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGTGGTTGATTATTAAGCACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACCTTACCGAGTCAA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:3389291 original size:21 final size:21
Alignment explanation
Indices: 3389267--3389306 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3389257 AAATTAATTC
*
3389267 ATACTTAAGTTGAATCAAATA
1 ATACTTAAGTTGAACCAAATA
3389288 ATACTTAAGTTGAACCAAA
1 ATACTTAAGTTGAACCAAA
3389307 ATATAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.30
Consensus pattern (21 bp):
ATACTTAAGTTGAACCAAATA
Found at i:3391788 original size:133 final size:133
Alignment explanation
Indices: 3391255--3391771 Score: 1018
Period size: 133 Copynumber: 3.9 Consensus size: 133
3391245 GAATTCAACA
3391255 ATATAAAACGTGAGCAACAAGACAGCAATAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
1 ATATAAAACGTGAGCAACAAGACAGCAATAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
3391320 TAAGTTGGATAGAAACATGAAAACAGACCAAAAGAACATCTAAATAACCAAAATATAACAATTTT
66 TAAGTTGGATAGAAACATGAAAACAGACCAAAAGAACATCTAAATAACCAAAATATAACAATTTT
3391385 ATT
131 ATT
3391388 ATATAAAACGTGAGCAACAAGACAGCAATAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
1 ATATAAAACGTGAGCAACAAGACAGCAATAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
3391453 TAAGTTGGATAGAAACATGAAAACAGACCAAAAGAACATCTAAATAACCAAAATATAACAATTTT
66 TAAGTTGGATAGAAACATGAAAACAGACCAAAAGAACATCTAAATAACCAAAATATAACAATTTT
3391518 ATT
131 ATT
3391521 ATATAAAACGTGAGCAACAAGACAGCAATAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
1 ATATAAAACGTGAGCAACAAGACAGCAATAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
3391586 TAAGTTGGATAGAAACATGAAAACAGACCAAAAGAACATCTAAATAACCAAAATATAACAATTTT
66 TAAGTTGGATAGAAACATGAAAACAGACCAAAAGAACATCTAAATAACCAAAATATAACAATTTT
3391651 ATT
131 ATT
*
3391654 ATATAAAACGTAAGCAACAAGACAGCAATAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
1 ATATAAAACGTGAGCAACAAGACAGCAATAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
3391719 TAAGTTGGATAGAAACATG-AAACAGACCAAAAGAACATCTAAATAACCAAAAT
66 TAAGTTGGATAGAAACATGAAAACAGACCAAAAGAACATCTAAATAACCAAAAT
3391772 GGAATCACCA
Statistics
Matches: 383, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
132 34 0.09
133 349 0.91
ACGTcount: A:0.51, C:0.18, G:0.10, T:0.20
Consensus pattern (133 bp):
ATATAAAACGTGAGCAACAAGACAGCAATAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
TAAGTTGGATAGAAACATGAAAACAGACCAAAAGAACATCTAAATAACCAAAATATAACAATTTT
ATT
Found at i:3396142 original size:41 final size:40
Alignment explanation
Indices: 3395770--3396142 Score: 476
Period size: 41 Copynumber: 9.1 Consensus size: 40
3395760 GTTCTATGAC
*
3395770 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCT-GT
* *
3395811 TTTTAGCGGCGTTTTATCGAAAGCGCCGCTAATGCTCTAGT
1 TTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCT-GT
* *
3395852 TTTTAGCGGCGTTTTACCGAAAGCGGCGCTAATGCTCTGTT
1 TTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCTG-T
3395893 TTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCT-GT
3395934 TTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCTGT
1 TTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCTGT
* * *
3395974 GTTTTAGCGGCATTTTACCCGAAGCGCCGCTAATGATCTGGT
1 -TTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCT-GT
* *
3396016 TTTTAGCGGCGTTTTACCTAAAGCGCCGCTAATGATCTGT
1 TTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCTGT
* *** * **
3396056 TTTTAGAGGCGTTTTAGTAAAAAACGCCGCTGTTGCTCTGT
1 TTTTAGCGGCGTTTTA-CCCAAAGCGCCGCTAATGCTCTGT
* ** * *
3396097 TTTTAGCGGCGTTTTTCTTAAAACGCCGCTATTGCTCTGT
1 TTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCTGT
3396137 ATTTTA
1 -TTTTA
3396143 AAATTTTTGC
Statistics
Matches: 299, Mismatches: 27, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
40 40 0.13
41 256 0.86
42 3 0.01
ACGTcount: A:0.19, C:0.23, G:0.24, T:0.35
Consensus pattern (40 bp):
TTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCTGT
Found at i:3396617 original size:23 final size:22
Alignment explanation
Indices: 3396591--3396634 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
3396581 CAATAACAGC
*
3396591 ATGCAGATAAACTGTAGGTAAAA
1 ATGCAGACAAACTGTA-GTAAAA
*
3396614 ATGCAGACACACTGTAGTAAA
1 ATGCAGACAAACTGTAGTAAA
3396635 GATGTGATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.45, C:0.14, G:0.20, T:0.20
Consensus pattern (22 bp):
ATGCAGACAAACTGTAGTAAAA
Found at i:3400169 original size:27 final size:27
Alignment explanation
Indices: 3400139--3400532 Score: 468
Period size: 27 Copynumber: 14.6 Consensus size: 27
3400129 TTAGTTTACC
*
3400139 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTA
* * *
3400166 AAATTACTAAAATACCCTTAGTTTATA
1 AAATTACCAAAATACCCCTAGTTTGTA
*
3400193 AAATCACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTA
* ** * **
3400220 AGATTACCAAAATACCTTTGGTTTACA
1 AAATTACCAAAATACCCCTAGTTTGTA
* *
3400247 AAATTACCAAAATACCCTTGGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTA
* ** * *
3400274 AAATTACTAAAATACCATTGGTTTATA
1 AAATTACCAAAATACCCCTAGTTTGTA
* *
3400301 AAATCACCAAAATACCCCTAATTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTA
* **
3400328 AAATTACCAAAATACCCTTAGTTTACA
1 AAATTACCAAAATACCCCTAGTTTGTA
3400355 AAATTACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTA
* * * *
3400382 AAATTACTAAAATACCCTTGGTTTAT-
1 AAATTACCAAAATACCCCTAGTTTGTA
*
3400408 AAATTACCAAAATACCCCTAATTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTA
*
3400435 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTA
*
3400462 AAATTATCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTA
*
3400489 AAATTACCAAAATACCCCT-GATTTGTG
1 AAATTACCAAAATACCCCTAG-TTTGTA
**
3400516 AAATTACTGAAATACCC
1 AAATTACCAAAATACCC
3400533 TCGACCTGTA
Statistics
Matches: 311, Mismatches: 54, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
26 22 0.07
27 289 0.93
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTAGTTTGTA
Found at i:3400204 original size:54 final size:54
Alignment explanation
Indices: 3400139--3400532 Score: 547
Period size: 54 Copynumber: 7.3 Consensus size: 54
3400129 TTAGTTTACC
* * *
3400139 AAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCTTAGTTTATA
1 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTGGTTTATA
* * * *
3400193 AAATCACCAAAATACCCCTAGTTTGTAAGATTACCAAAATACCTTTGGTTTACA
1 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTGGTTTATA
* * * *
3400247 AAATTACCAAAATACCCTTGGTTTGTAAAATTACTAAAATACCATTGGTTTATA
1 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTGGTTTATA
* * * *
3400301 AAATCACCAAAATACCCCTAATTTGTAAAATTACCAAAATACCCTTAGTTTACA
1 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTGGTTTATA
*
3400355 AAATTACCAAAATACCCCTAGTTTGTAAAATTACTAAAATACCCTTGGTTTAT-
1 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTGGTTTATA
* * *
3400408 AAATTACCAAAATACCCCTAATTTGTAAAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTGGTTTATA
* * * * *
3400462 AAATTATCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGATTTGTG
1 AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTGGTTTATA
**
3400516 AAATTACTGAAATACCC
1 AAATTACCAAAATACCC
3400533 TCGACCTGTA
Statistics
Matches: 301, Mismatches: 38, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
53 49 0.16
54 252 0.84
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (54 bp):
AAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTGGTTTATA
Found at i:3400543 original size:81 final size:80
Alignment explanation
Indices: 3400139--3400591 Score: 419
Period size: 81 Copynumber: 5.6 Consensus size: 80
3400129 TTAGTTTACC
* * * *
3400139 AAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATA-CCCTTAGTTTATAAAATCACCAA
1 AAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCTGA-TTTGTAAAATTACCAA
*
3400203 AATACCCCTAGTTTGTA
65 AATACCCCGA-TTTGTA
* ** ** * * *
3400220 AGATTACCAAAATACCTTTGGTTTACAAAATTACCAAAATACCCTTGGTTTGTAAAATTACTAAA
1 AAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCTGATTTGTAAAATTACCAAA
** * *
3400285 ATACCATTGGTTTATA
66 ATACC-CCGATTTGTA
* ** * **
3400301 AAATCACCAAAATACCCCTAATTTGTAAAATTACCAAAATA-CCCTTAGTTTACAAAATTACCAA
1 AAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCTGA-TTTGTAAAATTACCAA
*
3400365 AATACCCCTAGTTTGTA
65 AATACCCCGA-TTTGTA
* * * *
3400382 AAATTACTAAAATACCCTTGGTTTAT-AAATTACCAAAATACCCCTAATTTGTAAAATTACCAAA
1 AAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCTGATTTGTAAAATTACCAAA
*
3400446 ATACCCCTGGTTTGTA
66 ATACCCC-GATTTGTA
* * * **
3400462 AAATTATCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGATTTGTGAAATTACTGAA
1 AAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCTGATTTGTAAAATTACCAAA
**
3400527 ATACCCTCGACCTGTA
66 ATACCC-CGATTTGTA
*** ** * *
3400543 AAATTATTGAAATA-CCCTCGACTTGTAAAATTACCAAAGTACCCTTGAT
1 AAATTACCAAAATACCCCT-GGTTTGTAAAATTACCAAAATACCCCTGAT
3400592 CTACAGAATT
Statistics
Matches: 297, Mismatches: 66, Indels: 18
0.78 0.17 0.05
Matches are distributed among these distances:
80 70 0.24
81 223 0.75
82 4 0.01
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (80 bp):
AAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCTGATTTGTAAAATTACCAAA
ATACCCCGATTTGTA
Found at i:3400585 original size:27 final size:27
Alignment explanation
Indices: 3400139--3400587 Score: 344
Period size: 27 Copynumber: 16.7 Consensus size: 27
3400129 TTAGTTTACC
*
3400139 AAATTACCAAAATACCC-CTGGTTTGTA
1 AAATTACCAAAATACCCTC-GATTTGTA
* * *
3400166 AAATTACTAAAATACCCT-TAGTTTATA
1 AAATTACCAAAATACCCTCGA-TTTGTA
* *
3400193 AAATCACCAAAATACCC-CTAGTTTGTA
1 AAATTACCAAAATACCCTCGA-TTTGTA
* * * * **
3400220 AGATTACCAAAATACCTTTGGTTTACA
1 AAATTACCAAAATACCCTCGATTTGTA
* *
3400247 AAATTACCAAAATACCCTTGGTTTGTA
1 AAATTACCAAAATACCCTCGATTTGTA
* * * * *
3400274 AAATTACTAAAATACCATTGGTTTATA
1 AAATTACCAAAATACCCTCGATTTGTA
* *
3400301 AAATCACCAAAATACCC-CTAATTTGTA
1 AAATTACCAAAATACCCTC-GATTTGTA
* **
3400328 AAATTACCAAAATACCCT-TAGTTTACA
1 AAATTACCAAAATACCCTCGA-TTTGTA
*
3400355 AAATTACCAAAATACCC-CTAGTTTGTA
1 AAATTACCAAAATACCCTCGA-TTTGTA
* * * *
3400382 AAATTACTAAAATACCCTTGGTTTAT-
1 AAATTACCAAAATACCCTCGATTTGTA
*
3400408 AAATTACCAAAATACCC-CTAATTTGTA
1 AAATTACCAAAATACCCTC-GATTTGTA
*
3400435 AAATTACCAAAATACCC-CTGGTTTGTA
1 AAATTACCAAAATACCCTC-GATTTGTA
* *
3400462 AAATTATCAAAATACCC-CTAGTTTGTA
1 AAATTACCAAAATACCCTCGA-TTTGTA
*
3400489 AAATTACCAAAATACCC-CTGATTTGTG
1 AAATTACCAAAATACCCTC-GATTTGTA
** **
3400516 AAATTACTGAAATACCCTCGACCTGTA
1 AAATTACCAAAATACCCTCGATTTGTA
*** *
3400543 AAATTATTGAAATACCCTCGACTTGTA
1 AAATTACCAAAATACCCTCGATTTGTA
*
3400570 AAATTACCAAAGTACCCT
1 AAATTACCAAAATACCCT
3400588 TGATCTACAG
Statistics
Matches: 344, Mismatches: 64, Indels: 28
0.79 0.15 0.06
Matches are distributed among these distances:
26 21 0.06
27 321 0.93
28 2 0.01
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (27 bp):
AAATTACCAAAATACCCTCGATTTGTA
Found at i:3400639 original size:27 final size:27
Alignment explanation
Indices: 3400222--3400640 Score: 118
Period size: 27 Copynumber: 15.6 Consensus size: 27
3400212 AGTTTGTAAG
* * * *
3400222 ATTACCAAAATACCTTTGGTTTACAAA
1 ATTACCGAAATACCCTCGATTTACAAA
* * * **
3400249 ATTACCAAAATACCCTTGGTTTGTAAA
1 ATTACCGAAATACCCTCGATTTACAAA
** * * * *
3400276 ATTACTAAAATACCATTGGTTTATAAA
1 ATTACCGAAATACCCTCGATTTACAAA
* * * **
3400303 ATCACCAAAATACCC-CTAATTTGTAAA
1 ATTACCGAAATACCCTC-GATTTACAAA
* *
3400330 ATTACCAAAATACCCT-TAGTTTACAAA
1 ATTACCGAAATACCCTCGA-TTTACAAA
* * **
3400357 ATTACCAAAATACCC-CTAGTTTGTAAA
1 ATTACCGAAATACCCTCGA-TTTACAAA
** * * *
3400384 ATTACTAAAATACCCTTGGTTTA-TAA
1 ATTACCGAAATACCCTCGATTTACAAA
* * **
3400410 ATTACCAAAATACCC-CTAATTTGTAAA
1 ATTACCGAAATACCCTC-GATTTACAAA
* * **
3400437 ATTACCAAAATACCC-CTGGTTTGTAAA
1 ATTACCGAAATACCCTC-GATTTACAAA
* * * **
3400464 ATTATCAAAATACCC-CTAGTTTGTAAA
1 ATTACCGAAATACCCTCGA-TTTACAAA
* ***
3400491 ATTACCAAAATACCC-CTGATTTGTGAA
1 ATTACCGAAATACCCTC-GATTTACAAA
* ** **
3400518 ATTACTGAAATACCCTCGACCTGTAAA
1 ATTACCGAAATACCCTCGATTTACAAA
** * **
3400545 ATTATTGAAATACCCTCGACTTGTAAA
1 ATTACCGAAATACCCTCGATTTACAAA
* * *
3400572 ATTACC-AAAGTACCCTTGATCTACAGA
1 ATTACCGAAA-TACCCTCGATTTACAAA
***
3400599 ATTACCGTTTTACCCTCGATTTACAAA
1 ATTACCGAAATACCCTCGATTTACAAA
*
3400626 ATTACCGGAATACCC
1 ATTACCGAAATACCC
3400641 CTGTAGGGTA
Statistics
Matches: 317, Mismatches: 63, Indels: 24
0.78 0.16 0.06
Matches are distributed among these distances:
26 23 0.07
27 292 0.92
28 2 0.01
ACGTcount: A:0.39, C:0.21, G:0.08, T:0.31
Consensus pattern (27 bp):
ATTACCGAAATACCCTCGATTTACAAA
Found at i:3400655 original size:27 final size:27
Alignment explanation
Indices: 3400625--3400706 Score: 130
Period size: 27 Copynumber: 3.1 Consensus size: 27
3400615 CGATTTACAA
*
3400625 AATTACCGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
3400652 AATTACCGAAATACCTCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
3400679 AATTACCGAAATACCCCTATA-GGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
3400705 AA
1 AA
3400707 CTGTAAGTAA
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
26 7 0.14
27 44 0.86
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:3402806 original size:16 final size:16
Alignment explanation
Indices: 3402787--3402832 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
3402777 GCAAAATTTT
*
3402787 AAAAAACTAAAAGATA
1 AAAAAACTAAAAAATA
3402803 AAAAAA-TATAAAAATA
1 AAAAAACTA-AAAAATA
*
3402819 TAAAAAC-AAAAAAT
1 AAAAAACTAAAAAAT
3402833 GATCTAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 8 0.31
16 18 0.69
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.15
Consensus pattern (16 bp):
AAAAAACTAAAAAATA
Found at i:3403031 original size:281 final size:281
Alignment explanation
Indices: 3402524--3403038 Score: 843
Period size: 281 Copynumber: 1.8 Consensus size: 281
3402514 TAAAAAACAT
* *
3402524 AAAATATAAAATATAAAAACAAAAAATGATCTAATTGGAGAATCGAAACTAAATCCACAACTTAC
1 AAAATATAAAATATAAAAACAAAAAATGATCTAATTAGAGAATAGAAACTAAATCCACAACTTAC
* * *
3402589 AAATAGTACGAGACTAATAGCATAATTTAATCTTACCAATTTAATTGCTAATGTTTATGCAAGTA
66 AAATAGTACGAGACTAATAGCATAATTTAATCTAACAAATTTAACTGCTAATGTTTATGCAAGTA
* *
3402654 CTAGAATTTCAAATTAAAAAAGTAGAATAATTAAAATTGATCAAATAAAACTGAAAGGACTAAAT
131 CTAGAATTTCAAATTAAAAAAGGAGAATAATTAAAATTGATCAAATAAAACTAAAAGGACTAAAT
* * *
3402719 CCACAACTTATGTACAGTACAAAGGTTAATAAAAAAAATGACTTCTTACCTTATTCCAGCAAAAT
196 CCACAACTTATGAACAGTAAAAAGATTAATAAAAAAAATGACTTCTTACCTTATTCCAGCAAAAT
3402784 TTTAAAAAACTAAAAGATAAA
261 TTTAAAAAACTAAAAGATAAA
*
3402805 AAAATATAAAAATATAAAAACAAAAAATGATCTAATTAGAGAATAGGAACTAAATCCACAAC-TA
1 AAAATAT-AAAATATAAAAACAAAAAATGATCTAATTAGAGAATAGAAACTAAATCCACAACTTA
* * *
3402869 CATATAGTACGAGACTAATAGCATAATTTAATCTAATAAATTTAACTGCTATTGTTTATGCAAGT
65 CAAATAGTACGAGACTAATAGCATAATTTAATCTAACAAATTTAACTGCTAATGTTTATGCAAGT
* * * *
3402934 ACTATAATTTCAAATTAAAAAAGGAGAATAATTGAAATTGATTAGATAAAACTAAAAGGACTAAA
130 ACTAGAATTTCAAATTAAAAAAGGAGAATAATTAAAATTGATCAAATAAAACTAAAAGGACTAAA
*
3402999 TCCACAACTTATGAATAGTAAAAAGATTAATAAAAAAAAT
195 TCCACAACTTATGAACAGTAAAAAGATTAATAAAAAAAAT
3403039 TCAATCGTAT
Statistics
Matches: 214, Mismatches: 19, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
281 163 0.76
282 51 0.24
ACGTcount: A:0.51, C:0.11, G:0.10, T:0.27
Consensus pattern (281 bp):
AAAATATAAAATATAAAAACAAAAAATGATCTAATTAGAGAATAGAAACTAAATCCACAACTTAC
AAATAGTACGAGACTAATAGCATAATTTAATCTAACAAATTTAACTGCTAATGTTTATGCAAGTA
CTAGAATTTCAAATTAAAAAAGGAGAATAATTAAAATTGATCAAATAAAACTAAAAGGACTAAAT
CCACAACTTATGAACAGTAAAAAGATTAATAAAAAAAATGACTTCTTACCTTATTCCAGCAAAAT
TTTAAAAAACTAAAAGATAAA
Found at i:3403431 original size:19 final size:19
Alignment explanation
Indices: 3403407--3403487 Score: 135
Period size: 19 Copynumber: 4.2 Consensus size: 19
3403397 AATCTTTAAG
3403407 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
3403426 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
3403445 GATATGCAGTCTTAGATAT
1 GATATGCAATCTTAGATAT
3403464 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
3403485 GAT
1 GAT
3403488 CTTGTAATCT
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
19 49 0.84
21 9 0.16
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:3409937 original size:44 final size:44
Alignment explanation
Indices: 3409885--3410592 Score: 559
Period size: 44 Copynumber: 16.1 Consensus size: 44
3409875 CAAGATTTGG
*
3409885 CATCCCTGTTTTTATAGGGAACAGATCGAAGATAGCAGATCTGA
1 CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGA
* * *** ** *
3409929 CA-CTCCTGTGCTTACAACAAAGCAGATCGAAGATTTCAG--CATGG
1 CATC-CCTGTGTTTATAGGGAA-CAGATCGAAGATAGCAGATC-TGA
* * *
3409973 CATCCCTGTGTTTATAGGGAACA-AGTTGAAGATAGCAGATTTGG
1 CATCCCTGTGTTTATAGGGAACAGA-TCGAAGATAGCAGATCTGA
* * * *
3410017 CACCCCTATATTTATAGGGAACAAATCGAAGATAGCAGATCTGA
1 CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGA
* * * * ** * *
3410061 CA-CTCCTATGCTTACAGCGAAGCAGATCGAAGATTTCAG-TATGG
1 CATC-CCTGTGTTTATAGGGAA-CAGATCGAAGATAGCAGATCTGA
* * *
3410105 CATCCCTGTGTTTATAGGGAACA-AGTTGAAGATAGCAGATTTGG
1 CATCCCTGTGTTTATAGGGAACAGA-TCGAAGATAGCAGATCTGA
*
3410149 CATCCCTGTGTTTATAGGGAACATATCGAAGATAGCAGATCTGA
1 CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGA
* * * ** *
3410193 CA-CTCCTGTGCTTACAGCGAAGCAGATCGAAGATTTCAG--CATGG
1 CATC-CCTGTGTTTATAGGGAA-CAGATCGAAGATAGCAGATC-TGA
* * * * *
3410237 CATCCCTATGTTTATAGGGAACA-AGTTGAAAATAGCAGATTTGG
1 CATCCCTGTGTTTATAGGGAACAGA-TCGAAGATAGCAGATCTGA
* *
3410281 CATCCCTGTGTTTATAGGGAACAAATCGAAGATAACAGATCTGA
1 CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGA
* * * ** *
3410325 CATTCCTGTGATTATAGCGAAGCAGATCGAAGATTTCAG--CATGG
1 CATCCCTGTGTTTATAGGGAA-CAGATCGAAGATAGCAGATC-TGA
* * *
3410369 CATCCCTGTGTTTATAGGGAACA-AGTTGAAGATAGCAGATTTGG
1 CATCCCTGTGTTTATAGGGAACAGA-TCGAAGATAGCAGATCTGA
*
3410413 CATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGA
1 CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGA
* * * ** ** *
3410457 CATTCCTATGCTTATAGTAAAGCAGATCGAAGATTTCAG-TATGA
1 CATCCCTGTGTTTATAGGGAA-CAGATCGAAGATAGCAGATCTGA
* * *
3410501 CATCCTTGTGTTTATAGGGAACA-AGTTGAAGATAGCAGATTTGGA
1 CATCCCTGTGTTTATAGGGAACAGA-TCGAAGATAGCAGATCT-GA
* * *
3410546 -ATCCCTGTATTTATAGGGAACAAATCGAAGATAACAGATCTGA
1 CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGA
3410589 CATC
1 CATC
3410593 TCCATTTCGA
Statistics
Matches: 523, Mismatches: 107, Indels: 68
0.75 0.15 0.10
Matches are distributed among these distances:
42 5 0.01
43 67 0.13
44 370 0.71
45 81 0.15
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (44 bp):
CATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGA
Found at i:3410114 original size:132 final size:132
Alignment explanation
Indices: 3409877--3410595 Score: 1186
Period size: 132 Copynumber: 5.4 Consensus size: 132
3409867 CAAAGAAACA
* *
3409877 AGATTTGGCATCCCTGTTTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACACTCCTGTGCTT
* *
3409942 ACAACAAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
3410007 GC
131 GC
* * * *
3410009 AGATTTGGCACCCCTATATTTATAGGGAACAAATCGAAGATAGCAGATCTGACACTCCTATGCTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACACTCCTGTGCTT
*
3410074 ACAGCGAAGCAGATCGAAGATTTCAGTATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
3410139 GC
131 GC
*
3410141 AGATTTGGCATCCCTGTGTTTATAGGGAACATATCGAAGATAGCAGATCTGACACTCCTGTGCTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACACTCCTGTGCTT
* *
3410206 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTATGTTTATAGGGAACAAGTTGAAAATA
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
3410271 GC
131 GC
* * *
3410273 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAACAGATCTGACATTCCTGTGATT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACACTCCTGTGCTT
*
3410338 ATAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
3410403 GC
131 GC
* *
3410405 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTATGCTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACACTCCTGTGCTT
* ** * * *
3410470 ATAGTAAAGCAGATCGAAGATTTCAGTATGACATCCTTGTGTTTATAGGGAACAAGTTGAAGATA
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
3410535 GC
131 GC
* * *
3410537 AGATTTGGAATCCCTGTATTTATAGGGAACAAATCGAAGATAACAGATCTGACATCTCC
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACA-CTCC
3410596 ATTTCGACGG
Statistics
Matches: 551, Mismatches: 35, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
132 548 0.99
133 3 0.01
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (132 bp):
AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACACTCCTGTGCTT
ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
GC
Found at i:3411187 original size:19 final size:19
Alignment explanation
Indices: 3411163--3411241 Score: 126
Period size: 19 Copynumber: 4.2 Consensus size: 19
3411153 AATCTTTAAG
3411163 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
3411182 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
3411201 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
3411218 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
3411239 GAT
1 GAT
3411242 CTTGTAATCT
Statistics
Matches: 56, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
17 17 0.30
19 30 0.54
21 9 0.16
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:3411193 original size:36 final size:36
Alignment explanation
Indices: 3411153--3411240 Score: 119
Period size: 36 Copynumber: 2.4 Consensus size: 36
3411143 ATGGAAATAT
3411153 AATCTTTAAGGATATG-CAATCTTAGATATGATATGC
1 AATCTTTAA-GATATGACAATCTTAGATATGATATGC
3411189 AATC-TT-AGATATGATACAATCTTAGATATGATATGC
1 AATCTTTAAGATATG--ACAATCTTAGATATGATATGC
*
3411225 AATCTTGAAGATATGA
1 AATCTTTAAGATATGA
3411241 TCTTGTAATC
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
33 6 0.13
34 1 0.02
35 2 0.04
36 29 0.63
37 1 0.02
38 7 0.15
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (36 bp):
AATCTTTAAGATATGACAATCTTAGATATGATATGC
Found at i:3414287 original size:12 final size:12
Alignment explanation
Indices: 3414270--3414309 Score: 71
Period size: 12 Copynumber: 3.3 Consensus size: 12
3414260 CATACACGCG
*
3414270 CGTGTGCCAGGC
1 CGTGTGCTAGGC
3414282 CGTGTGCTAGGC
1 CGTGTGCTAGGC
3414294 CGTGTGCTAGGC
1 CGTGTGCTAGGC
3414306 CGTG
1 CGTG
3414310 CCAAACCTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.07, C:0.28, G:0.42, T:0.23
Consensus pattern (12 bp):
CGTGTGCTAGGC
Found at i:3424722 original size:44 final size:44
Alignment explanation
Indices: 3424658--3424899 Score: 342
Period size: 44 Copynumber: 5.5 Consensus size: 44
3424648 AGAAATACAT
* * * *
3424658 AGCAGATCTAAGAGGTCAGATTTGGCGTCTCTGTATTGATAGAG
1 AGCAGATCGAAGATGACAGATTTGGCGTCTCTGTATTGACAGAG
* *
3424702 AGCAGATCAAAGATGACAGATTTGGCATCTCTGTATTGACAGAG
1 AGCAGATCGAAGATGACAGATTTGGCGTCTCTGTATTGACAGAG
* *
3424746 GGCAGATTGAAGATGACAGATTTGGCGTCTCTGTATTGACAGAG
1 AGCAGATCGAAGATGACAGATTTGGCGTCTCTGTATTGACAGAG
* *
3424790 AGCAGATCGAAGATAACAGATTTGGCATCTCTGTATTGACAGAG
1 AGCAGATCGAAGATGACAGATTTGGCGTCTCTGTATTGACAGAG
*
3424834 AGCAGATCGAAGAT-AGCAGATTTGACGTCTCTGTATTGACAGAG
1 AGCAGATCGAAGATGA-CAGATTTGGCGTCTCTGTATTGACAGAG
* * *
3424878 GGCAGGTCAAAGATGACAGATT
1 AGCAGATCGAAGATGACAGATT
3424900 CGGTTTCTCC
Statistics
Matches: 178, Mismatches: 18, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
43 1 0.01
44 176 0.99
45 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (44 bp):
AGCAGATCGAAGATGACAGATTTGGCGTCTCTGTATTGACAGAG
Found at i:3424947 original size:132 final size:132
Alignment explanation
Indices: 3424674--3424993 Score: 346
Period size: 132 Copynumber: 2.4 Consensus size: 132
3424664 TCTAAGAGGT
* * * *
3424674 CAGATTTGGCGTCTCTGTATTGATAGAGAGCAGATCAAAGAT-GACAGATTTGGCATCTCTGTAT
1 CAGACTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAG-CAGATTTGACATCTCTGTAT
** * * *
3424738 TGACAGAGGGCAGATTGAAGATGACAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGA
65 TGACAGAGGGCAGATCAAAGATGACAGATTCGGCGTCTCCGTATTGACAGAGAGCAGATCAAAGA
3424803 TAA
130 TAA
* * *
3424806 CAGATTTGGCATCTCTGTATTGACAGAGAGCAGATCGAAGATAGCAGATTTGACGTCTCTGTATT
1 CAGACTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAGCAGATTTGACATCTCTGTATT
* ** * *
3424871 GACAGAGGGCAGGTCAAAGATGACAGATTCGGTTTCTCCGTATTAGGCA-AGGAGTAGATCAAAG
66 GACAGAGGGCAGATCAAAGATGACAGATTCGGCGTCTCCGTATT-GACAGA-GAGCAGATCAAAG
**
3424935 ATTT
129 ATAA
* * *
3424939 CAG-CTTGGCGT-TCCTG-AGTTTG-CAGGGAGCAGGTTGAAGATAGCAGATTTGACAT
1 CAGACTTGGCGTCT-CTGTA--TTGACAGAGAGCAGATCGAAGATAGCAGATTTGACAT
3424994 TCCTGAGTTA
Statistics
Matches: 159, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
131 2 0.01
132 134 0.84
133 23 0.14
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.27
Consensus pattern (132 bp):
CAGACTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAGCAGATTTGACATCTCTGTATT
GACAGAGGGCAGATCAAAGATGACAGATTCGGCGTCTCCGTATTGACAGAGAGCAGATCAAAGAT
AA
Found at i:3426491 original size:14 final size:13
Alignment explanation
Indices: 3426457--3426506 Score: 59
Period size: 12 Copynumber: 3.9 Consensus size: 13
3426447 GTACAAATTG
3426457 TATATATATTATTT
1 TATATATATTA-TT
*
3426471 TTTATATATTATT
1 TATATATATTATT
*
3426484 TAT-CATATTATT
1 TATATATATTATT
3426496 TATAT-TATTAT
1 TATATATATTAT
3426507 ACATTTTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
12 17 0.55
13 4 0.13
14 10 0.32
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (13 bp):
TATATATATTATT
Found at i:3426501 original size:21 final size:21
Alignment explanation
Indices: 3426475--3426520 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
3426465 TTATTTTTTA
3426475 TATATTATT-TATCATATTATT
1 TATATTATTATA-CATATTATT
*
3426496 TATATTATTATACATTTTATT
1 TATATTATTATACATATTATT
3426517 TATA
1 TATA
3426521 AATTTTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (21 bp):
TATATTATTATACATATTATT
Found at i:3426551 original size:19 final size:19
Alignment explanation
Indices: 3426516--3426552 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3426506 TACATTTTAT
*
3426516 TTATAAATTTTATTATATG
1 TTATAAATTTTACTATATG
*
3426535 TTATAAATTTTCCTATAT
1 TTATAAATTTTACTATAT
3426553 ATATATTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (19 bp):
TTATAAATTTTACTATATG
Found at i:3427171 original size:71 final size:67
Alignment explanation
Indices: 3427057--3427212 Score: 199
Period size: 71 Copynumber: 2.3 Consensus size: 67
3427047 GTTATTTTAA
* * * *
3427057 GTTATATTTGCATAAAATATTGTTATATATTATGTAATTTATATTGTTAT-ATTCATTGTTTTCT
1 GTTATATTTGCATGAAATATTATTATATATTATGTAATCTATATCGTTATGA-TCATTGTTTTCT
3427121 AT-
65 ATG
3427123 GTTATATTTTGCATGAAATATTATTATGTATGCATTATGTAATCTATATCGTTATGATCATTGTT
1 GTTATA-TTTGCATGAAATATTATTA--TAT--ATTATGTAATCTATATCGTTATGATCATTGTT
3427188 TTCTATG
61 TTCTATG
*
3427195 GTTATATATGCATGAAAT
1 GTTATATTTGCATGAAAT
3427213 GATGATGCAT
Statistics
Matches: 78, Mismatches: 5, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
66 6 0.08
67 17 0.22
69 3 0.04
71 45 0.58
72 7 0.09
ACGTcount: A:0.30, C:0.06, G:0.12, T:0.51
Consensus pattern (67 bp):
GTTATATTTGCATGAAATATTATTATATATTATGTAATCTATATCGTTATGATCATTGTTTTCTA
TG
Found at i:3445268 original size:23 final size:23
Alignment explanation
Indices: 3445238--3445309 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 23
3445228 AGATCTAAGA
3445238 TGACAGATTTGGCGTCTCTGTAT
1 TGACAGATTTGGCGTCTCTGTAT
* * *
3445261 TGACAGA--TGGCAG-ATC-GAAGA
1 TGACAGATTTGGC-GTCTCTGTA-T
3445282 TGACAGATTTGGCGTCTCTGTAT
1 TGACAGATTTGGCGTCTCTGTAT
3445305 TGACA
1 TGACA
3445310 AAGGGCAGAT
Statistics
Matches: 37, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
20 2 0.05
21 13 0.35
22 2 0.05
23 18 0.49
24 2 0.05
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.31
Consensus pattern (23 bp):
TGACAGATTTGGCGTCTCTGTAT
Found at i:3445789 original size:44 final size:44
Alignment explanation
Indices: 3445021--3445774 Score: 1030
Period size: 44 Copynumber: 17.1 Consensus size: 44
3445011 TCACCGATAG
*
3445021 CAGATTTGGCGTCTCTGTATTGATAGAGAGCAGATCGAAGATGA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATGA
* *
3445065 CAGATTTGGCGCCTCTGTATTGACAGAGAGCAAATCGAAGATGA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATGA
* * * *
3445109 TAGATTTCGCGTTTCTGTATTGACAGAGAGCAGATCAAAGATGA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATGA
* *
3445153 CAAATTTGGCGTCTCTGTATTGACAGTGAGCAGATCGAAGATGA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATGA
* * * * *
3445197 CAAATTCGGTGTCTCTATATTGACAGAGAGCAGATCTAAGATGA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATGA
3445241 CAGATTTGGCGTCTCTGTATTGACAGATG-GCAGATCGAAGATGA
1 CAGATTTGGCGTCTCTGTATTGACAGA-GAGCAGATCGAAGATGA
* * * * *
3445285 CAGATTTGGCGTCTCTGTATTGACAAAGGGCAGATTGAAAATAA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATGA
** *
3445329 CAGATTTAACGTCTCTATATTGACAGAGAGCAGATCGAAGAT-A
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATGA
* *
3445372 GCAGATTTGACGTCTCTGTATTGACAGAGATCAGATCGAAGAT-A
1 -CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATGA
**
3445416 GCAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATTAAAGATGA
1 -CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATGA
* *
3445461 CAGATTTGGCGTTTCTGTATTGACAGTGAGCAGATCGAAGATGA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATGA
* * * * *
3445505 CAGATTTGACATCTCTGTATTGACAGAGAGCAGATCTAAGAGGT
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATGA
* *
3445549 CAGATTTGGCGTCTCTGTATTGATAGAGAGCAGATCAAAGATGA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATGA
** * *
3445593 CAGATTTGGTATCTCTGTATTGACAGAGGGCAGATTGAAGATGA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATGA
*
3445637 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATGA
* *
3445681 CAGATTTGGCATCTCTGTATTGACAGAGAGCAGATCGAAGGT-A
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATGA
* * * *
3445724 GCAGATTTGACGTCTCTGTATTGACAGAGGGCAGGTCAAAGATGA
1 -CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATGA
3445769 CAGATT
1 CAGATT
3445775 CAGTTTCTCC
Statistics
Matches: 625, Mismatches: 79, Indels: 12
0.87 0.11 0.02
Matches are distributed among these distances:
43 3 0.00
44 619 0.99
45 3 0.00
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (44 bp):
CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATGA
Found at i:3447390 original size:21 final size:21
Alignment explanation
Indices: 3447341--3447394 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
3447331 TATATATATT
3447341 ATTTT-TTATATATTATTTATC
1 ATTTTATT-TATATTATTTATC
**
3447362 ATAATATTTATATTA-TTATAC
1 ATTTTATTTATATTATTTAT-C
3447383 ATTTTATTTATA
1 ATTTTATTTATA
3447395 AATTTTATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
20 4 0.15
21 21 0.78
22 2 0.07
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (21 bp):
ATTTTATTTATATTATTTATC
Found at i:3448032 original size:71 final size:69
Alignment explanation
Indices: 3447918--3448073 Score: 203
Period size: 71 Copynumber: 2.3 Consensus size: 69
3447908 GTTATTTTAA
* * *
3447918 GTTATATTTGCAT-AAA-ATATTGTTATATATTATGTAATTTATATTGTTAT-ATTCATTGTTTT
1 GTTATATTTGCATGAAATATATTATTATATATTATGTAATCTATATCGTTATGA-TCATTGTTTT
3447980 CTAT-
65 CTATG
*
3447984 GTTATATTTTGCATGAAATATTATTATGTATGTATTATGTAATCTATATCGTTATGATCATTGTT
1 GTTATA-TTTGCATGAAATA-TATTAT-TATATATTATGTAATCTATATCGTTATGATCATTGTT
3448049 TTCTATG
63 TTCTATG
*
3448056 GTTATATCTGCATGAAAT
1 GTTATATTTGCATGAAAT
3448074 GATGATGCAT
Statistics
Matches: 78, Mismatches: 5, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
66 6 0.08
67 7 0.09
68 3 0.04
69 1 0.01
70 5 0.06
71 49 0.63
72 7 0.09
ACGTcount: A:0.29, C:0.06, G:0.12, T:0.52
Consensus pattern (69 bp):
GTTATATTTGCATGAAATATATTATTATATATTATGTAATCTATATCGTTATGATCATTGTTTTC
TATG
Found at i:3457038 original size:5 final size:5
Alignment explanation
Indices: 3457028--3457065 Score: 69
Period size: 5 Copynumber: 7.8 Consensus size: 5
3457018 TTTGTGTGTT
3457028 TTTTA TTTTA TTTTA -TTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
3457066 TCACAAATTG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:3457048 original size:14 final size:15
Alignment explanation
Indices: 3457028--3457065 Score: 69
Period size: 14 Copynumber: 2.6 Consensus size: 15
3457018 TTTGTGTGTT
3457028 TTTTATTTTATTTTA
1 TTTTATTTTATTTTA
3457043 -TTTATTTTATTTTA
1 TTTTATTTTATTTTA
3457057 TTTTATTTT
1 TTTTATTTT
3457066 TCACAAATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTATTTTATTTTA
Found at i:3457052 original size:19 final size:19
Alignment explanation
Indices: 3457028--3457064 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
3457018 TTTGTGTGTT
3457028 TTTTATTTTATTTTATTTA
1 TTTTATTTTATTTTATTTA
3457047 TTTTATTTTATTTTATTT
1 TTTTATTTTATTTTATTT
3457065 TTCACAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTATTTTATTTTATTTA
Found at i:3468843 original size:17 final size:19
Alignment explanation
Indices: 3468821--3468863 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
3468811 ATGGAAATAT
3468821 AATCTT-CA-ATGATATGC
1 AATCTTACATATGATATGC
*
3468838 AATCTTAGATATGATATGC
1 AATCTTACATATGATATGC
3468857 AATCTTA
1 AATCTTA
3468864 GAAGATATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.26
18 1 0.04
19 16 0.70
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (19 bp):
AATCTTACATATGATATGC
Found at i:3468853 original size:19 final size:19
Alignment explanation
Indices: 3468829--3468865 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
3468819 ATAATCTTCA
3468829 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
3468848 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
3468866 AGATATGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:3468891 original size:22 final size:22
Alignment explanation
Indices: 3468829--3468888 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 22
3468819 ATAATCTTCA
3468829 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
3468848 ATGATATGCAATCTTAGAAGAT
1 ATGATATGCAATCTTAGAAGAT
* *
3468870 ATGATTTTGTAATCTTAGA
1 ATGA-TATGCAATCTTAGA
3468889 GATTTAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.43
22 8 0.23
23 12 0.34
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.38
Consensus pattern (22 bp):
ATGATATGCAATCTTAGAAGAT
Found at i:3469894 original size:22 final size:22
Alignment explanation
Indices: 3469869--3469921 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
3469859 TAGACATATA
*
3469869 AATACATATAAAAAACA-AATGT
1 AATA-ATATAAAAAAAATAATGT
3469891 AATAATATAAAAAAAATAATGT
1 AATAATATAAAAAAAATAATGT
*
3469913 AGTAATATA
1 AATAATATA
3469922 TATATATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 11 0.39
22 17 0.61
ACGTcount: A:0.64, C:0.04, G:0.06, T:0.26
Consensus pattern (22 bp):
AATAATATAAAAAAAATAATGT
Found at i:3495873 original size:89 final size:87
Alignment explanation
Indices: 3495744--3495905 Score: 191
Period size: 89 Copynumber: 1.8 Consensus size: 87
3495734 ATTCAACGGA
* * * * *
3495744 GAGCAGATCGAAGACATAGTAGATCTAACCTTCGGATGTTTTCACATCGAAGTAGATCCAAGAAG
1 GAGCAGATCGAAGACATAGCAGATCTAACATTCCGATGTTTACAC-T-GAAGCAGATCCAAGAAG
3495809 ATTTGGCATCCTTGCATTTACAAG
64 ATTTGGCATCCTTGCATTTACAAG
* ** * * *
3495833 GAGCAGATCGAAGACATAGCAGATTTGGCATTCACG-TGTTTACGCTGAAGCAGATCTAAGATGA
1 GAGCAGATCGAAGACATAGCAGATCTAACATTC-CGATGTTTACACTGAAGCAGATCCAAGAAGA
3495897 TTTGGCATC
65 TTTGGCATC
3495906 TCTGTACTGT
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
87 24 0.39
88 1 0.02
89 35 0.57
90 1 0.02
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (87 bp):
GAGCAGATCGAAGACATAGCAGATCTAACATTCCGATGTTTACACTGAAGCAGATCCAAGAAGAT
TTGGCATCCTTGCATTTACAAG
Found at i:3495981 original size:220 final size:220
Alignment explanation
Indices: 3495408--3495996 Score: 937
Period size: 219 Copynumber: 2.7 Consensus size: 220
3495398 CAGGCTAAAG
* * * **
3495408 CATAGCAGATTTGACCTTCAGGTGTTTACGCTGAAGCGGATCCAAGATGATTTAACATCTCTGTA
1 CATAGCAGATTTGACCTTCACGTGTTTACGCTGAAGCAGATCTAAGATGATTTGGCATCTCTGTA
* * *
3495473 TTGTCAGAGAACAAATTGAAGAAATAGATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAG
66 CTGTCAGAGAACAAATCGAAGAAATAGATTTGGCATCTCCATATTCAACGGAGAGCAGATCGAAG
* * *
3495538 ACATAGCAGATCTAACCTTTGGATGTCTTCACATCGAAGTAGATCCAAGATGATTTGGCATCCTT
131 ACATAGTAGATCTAACCTTCGGATGTCTTCACATCGAAGTAGATCCAAGAAGATTTGGCATCCTT
** *
3495603 GGGTTGATAAGGAGCAGATCGAAGA
196 GCATTGACAAGGAGCAGATCGAAGA
* *
3495628 CATAGCAGATTTGACCTTCACATGTTTA-GCTGAAGTAGATCTAAGATGATTTGGCATCTCTGTA
1 CATAGCAGATTTGACCTTCACGTGTTTACGCTGAAGCAGATCTAAGATGATTTGGCATCTCTGTA
*
3495692 CTGTCAGAGAACAAATCGAAGAAATAGATTTAGCATCTCCATATTCAACGGAGAGCAGATCGAAG
66 CTGTCAGAGAACAAATCGAAGAAATAGATTTGGCATCTCCATATTCAACGGAGAGCAGATCGAAG
*
3495757 ACATAGTAGATCTAACCTTCGGATGTTTTCACATCGAAGTAGATCCAAGAAGATTTGGCATCCTT
131 ACATAGTAGATCTAACCTTCGGATGTCTTCACATCGAAGTAGATCCAAGAAGATTTGGCATCCTT
*
3495822 GCATTTACAAGGAGCAGATCGAAGA
196 GCATTGACAAGGAGCAGATCGAAGA
* *
3495847 CATAGCAGATTTGGCATTCACGTGTTTACGCTGAAGCAGATCTAAGATGATTTGGCATCTCTGTA
1 CATAGCAGATTTGACCTTCACGTGTTTACGCTGAAGCAGATCTAAGATGATTTGGCATCTCTGTA
* * *
3495912 CTGTCAGAGAACAAATCGAAGAAATAGATTTGGCATCTCCATTTTCAACGGAGAGCGGATTGAAG
66 CTGTCAGAGAACAAATCGAAGAAATAGATTTGGCATCTCCATATTCAACGGAGAGCAGATCGAAG
* *
3495977 ACATAATAGATCTGACCTTC
131 ACATAGTAGATCTAACCTTC
3495997 ATTGAAGCAG
Statistics
Matches: 339, Mismatches: 29, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
219 199 0.59
220 140 0.41
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.27
Consensus pattern (220 bp):
CATAGCAGATTTGACCTTCACGTGTTTACGCTGAAGCAGATCTAAGATGATTTGGCATCTCTGTA
CTGTCAGAGAACAAATCGAAGAAATAGATTTGGCATCTCCATATTCAACGGAGAGCAGATCGAAG
ACATAGTAGATCTAACCTTCGGATGTCTTCACATCGAAGTAGATCCAAGAAGATTTGGCATCCTT
GCATTGACAAGGAGCAGATCGAAGA
Found at i:3496075 original size:78 final size:78
Alignment explanation
Indices: 3495959--3496309 Score: 553
Period size: 78 Copynumber: 4.5 Consensus size: 78
3495949 TCCATTTTCA
* * * *
3495959 ACGGAGAGCGGATTGAAGACATAATAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGC
1 ACGGGGAGCAGATCGAAGACATAACAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGC
3496024 ATCTCTGTATTAG
66 ATCTCTGTATTAG
*
3496037 ACGGGGAGCAGATCGAAGACACAACAGAT-TGGACCTTCATTGAAGCAGATCCAAGATGATTTGG
1 ACGGGGAGCAGATCGAAGACATAACAGATCT-GACCTTCATTGAAGCAGATCCAAGATGATTTGG
** *
3496101 CATCTCCATATTCG
65 CATCTCTGTATTAG
* *
3496115 ACGGAGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGC
1 ACGGGGAGCAGATCGAAGACATAACAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGC
3496180 ATCTCTGTATTAG
66 ATCTCTGTATTAG
* *
3496193 ACGGGGAGCAGATCGAAGACACAACAGAT-TGGACCTTTATTGAAGCAGATCCAAGATGATTTGG
1 ACGGGGAGCAGATCGAAGACATAACAGATCT-GACCTTCATTGAAGCAGATCCAAGATGATTTGG
3496257 CATCTCTGTATTAG
65 CATCTCTGTATTAG
*
3496271 ACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCA
1 ACGGGGAGCAGATCGAAGACATAACAGATCTGACCTTCA
3496310 CGTGTTTACG
Statistics
Matches: 248, Mismatches: 21, Indels: 8
0.90 0.08 0.03
Matches are distributed among these distances:
77 2 0.01
78 244 0.98
79 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.23
Consensus pattern (78 bp):
ACGGGGAGCAGATCGAAGACATAACAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGC
ATCTCTGTATTAG
Found at i:3496154 original size:156 final size:156
Alignment explanation
Indices: 3495938--3496309 Score: 645
Period size: 156 Copynumber: 2.4 Consensus size: 156
3495928 CGAAGAAATA
* * * * **
3495938 GATTTGGCATCTCCATTTTCAACGGAGAGCGGATTGAAGACATAATAGATCTGACCTTCATTGAA
1 GATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAA
3496003 GCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAACAGATTG
66 GCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAACAGATTG
3496068 GACCTTCATTGAAGCAGATCCAAGAT
131 GACCTTCATTGAAGCAGATCCAAGAT
3496094 GATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAA
1 GATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAA
3496159 GCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAACAGATTG
66 GCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAACAGATTG
*
3496224 GACCTTTATTGAAGCAGATCCAAGAT
131 GACCTTCATTGAAGCAGATCCAAGAT
** * *
3496250 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCA
1 GATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAGACATAGCAGATCTGACCTTCA
3496310 CGTGTTTACG
Statistics
Matches: 205, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
156 205 1.00
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.24
Consensus pattern (156 bp):
GATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAA
GCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAACAGATTG
GACCTTCATTGAAGCAGATCCAAGAT
Found at i:3496355 original size:443 final size:442
Alignment explanation
Indices: 3495792--3496656 Score: 1333
Period size: 443 Copynumber: 2.0 Consensus size: 442
3495782 TTTTCACATC
* *
3495792 GAAGTAGATCCAAGAAGATTTGGCATCCTTGCATTTACAAGGAGCAGATCGAAGACATAGCAGAT
1 GAAGCAGATCCAAGAAGATTTGGCATCCTTGCATTGACAAGGAGCAGATCGAAGACATAGCAGAT
* *
3495857 TTGGCATTCACGTGTTTACGCTGAAGCAGATCTAAGATGATTTGGCATCTCTGTACTGTCAGAGA
66 CTGACATTCACGTGTTTACGCTGAAGCAGATCTAAGATGATTTGGCATCTCTGTACTGTCAGAGA
* * ** * * *
3495922 ACAAATCGAAGAAATAGATTTGGCATCTCCATTTTCAACGGAGAGCGGATTGAAGACATAATAGA
131 ACAAATCGAAGAAACAGATTTGGCATCTCCATATTCAACAAAGAGCAGATCGAAGACATAACAGA
* *
3495987 TCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCG
196 TCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTATATTAGACGGGAAGCAGATCG
*
3496052 AAGACACAACAGAT-TGGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCCATATTCGA
261 AAGACACAACAGATCT-GACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCCATATTAGA
* * * *
3496116 C-GGAGAGCAGATCGAAGACATAGCAGATCT-GACCTTCATTGAAGCAGATCCAAGATGATTTGG
325 CAGG-GAGCAGATCAAAGACATAACAGAT-TGGACCTTCATTGAAACAGATCCAAGATAATTTGG
3496179 CATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAACAGATTGGACCTTTATT
388 CATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAACAGATTGGACCTTTATT
* * **
3496234 GAAGCAGATCCAAGATGATTTGGCAT-CTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAG
1 GAAGCAGATCCAAGAAGATTTGGCATCCT-TGCATT-GACAAGGAGCAGATCGAAGACATAGCAG
* * * *
3496298 ATCTGACCTTCACGTGTTTACGTTGAAGTAGATCTAAGATGATTTGGCATTTCTGTACTGTCAGA
64 ATCTGACATTCACGTGTTTACGCTGAAGCAGATCTAAGATGATTTGGCATCTCTGTACTGTCAGA
* *
3496363 GAACAAATCGAAGAAACAGATTTGGCATCTCCATATTCGACAAAGAGCAGATCGAAGACATAGCA
129 GAACAAATCGAAGAAACAGATTTGGCATCTCCATATTCAACAAAGAGCAGATCGAAGACATAACA
*
3496428 GATCTGACCTTCATTGAAGCAGATCCAAGTTGATTTGGCATCTCTATATTAGACGGGAAGCAGAT
194 GATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTATATTAGACGGGAAGCAGAT
* * * **
3496493 TGAAGACACAGCATATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAG
259 CGAAGACACAACAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCCATATTAG
*
3496558 ACAGGGAGTAGATCAAAGACATAACAGATTGGACCTTCATTGAAACAGATCCAAGATAATTTGGC
324 ACAGGGAGCAGATCAAAGACATAACAGATTGGACCTTCATTGAAACAGATCCAAGATAATTTGGC
*
3496623 ATCTCTGTATTAGATGGGGAGCAGATCGAAGACA
389 ATCTCTGTATTAGACGGGGAGCAGATCGAAGACA
3496657 TAGTAGATCT
Statistics
Matches: 382, Mismatches: 36, Indels: 9
0.89 0.08 0.02
Matches are distributed among these distances:
441 2 0.01
442 30 0.08
443 347 0.91
444 3 0.01
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.25
Consensus pattern (442 bp):
GAAGCAGATCCAAGAAGATTTGGCATCCTTGCATTGACAAGGAGCAGATCGAAGACATAGCAGAT
CTGACATTCACGTGTTTACGCTGAAGCAGATCTAAGATGATTTGGCATCTCTGTACTGTCAGAGA
ACAAATCGAAGAAACAGATTTGGCATCTCCATATTCAACAAAGAGCAGATCGAAGACATAACAGA
TCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTATATTAGACGGGAAGCAGATCG
AAGACACAACAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCCATATTAGAC
AGGGAGCAGATCAAAGACATAACAGATTGGACCTTCATTGAAACAGATCCAAGATAATTTGGCAT
CTCTGTATTAGACGGGGAGCAGATCGAAGACACAACAGATTGGACCTTTATT
Found at i:3496449 original size:365 final size:368
Alignment explanation
Indices: 3496016--3496791 Score: 1103
Period size: 365 Copynumber: 2.1 Consensus size: 368
3496006 GATCCAAGAT
** ***
3496016 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAACAGATTGGACCTTCATTGAA
1 GATTTGGCATCTCCATATTAGACAAAGAGCAGATCGAAGACACAACAGATTGGACCTTCATTGAA
* *
3496081 GCAGATCCAAGATGATTTGGCATCTCCATATTCGAC-GGAGAGCAGATCGAAGACATAGCAGATC
66 GCAGATCCAAGATGATTTGGCATCTCCATATTAGACGGGA-AGCAGATCGAAGACACAGCAGATC
* *
3496145 TGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAA
130 TGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACAGGGAGCAGATCAAA
* * *
3496210 GACACAACAGATTGGACCTTTATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGG
195 GACACAACAGATTGGACCTTCATTGAAACAGATCCAAGATAATTTGGCATCTCTGTATTAGACGG
* * * * *
3496275 GGAGCAGATCGAAGACATAGCAGATCTGACCTTCACGTGTTTACGTTGAAGTAGATCTAAGAT-G
260 GGAGCAGATCGAAGACATAGCAGATCTGACCTTCACATGTTTACATCGAAGCAGATCCAAGATAG
* *
3496339 ATTTGGCATTTCTGTACT-GTCAGAGAACAAATCGAAGA-AACA
325 ATTTGGCATCTCTGTACTAGACAGAGAACAAATCGAAGATAACA
* * *
3496381 GATTTGGCATCTCCATATTCGACAAAGAGCAGATCGAAGACATAGCAGATCT-GACCTTCATTGA
1 GATTTGGCATCTCCATATTAGACAAAGAGCAGATCGAAGACACAACAGAT-TGGACCTTCATTGA
* * * *
3496445 AGCAGATCCAAGTTGATTTGGCATCTCTATATTAGACGGGAAGCAGATTGAAGACACAGCATATC
65 AGCAGATCCAAGATGATTTGGCATCTCCATATTAGACGGGAAGCAGATCGAAGACACAGCAGATC
*
3496510 TGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACAGGGAGTAGATCAAA
130 TGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACAGGGAGCAGATCAAA
* *
3496575 GACATAACAGATTGGACCTTCATTGAAACAGATCCAAGATAATTTGGCATCTCTGTATTAGATGG
195 GACACAACAGATTGGACCTTCATTGAAACAGATCCAAGATAATTTGGCATCTCTGTATTAGACGG
* *
3496640 GGAGCAGATCGAAGACATAGTAGATCTGACCTTCATATGTTTACATCGAAGCAGATCCAAGATGA
260 GGAGCAGATCGAAGACATAGCAGATCTGACCTTCACATGTTTACATCGAAGCAGATCCAAGAT--
* * * * *
3496705 CAGATTTGGCATCTCTGTATTAGACAGGGAGCAAATCGGAGATAATA
323 -AGATTTGGCATCTCTGTACTAGACAGAGAACAAATCGAAGATAACA
** * * *
3496752 GATTTGGCATCTCTGTATTAGACGAGGAGCAGATTGAAGA
1 GATTTGGCATCTCCATATTAGACAAAGAGCAGATCGAAGA
3496792 AGAAGATTTG
Statistics
Matches: 361, Mismatches: 42, Indels: 10
0.87 0.10 0.02
Matches are distributed among these distances:
365 287 0.80
366 4 0.01
369 17 0.05
370 16 0.04
371 37 0.10
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.26
Consensus pattern (368 bp):
GATTTGGCATCTCCATATTAGACAAAGAGCAGATCGAAGACACAACAGATTGGACCTTCATTGAA
GCAGATCCAAGATGATTTGGCATCTCCATATTAGACGGGAAGCAGATCGAAGACACAGCAGATCT
GACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACAGGGAGCAGATCAAAG
ACACAACAGATTGGACCTTCATTGAAACAGATCCAAGATAATTTGGCATCTCTGTATTAGACGGG
GAGCAGATCGAAGACATAGCAGATCTGACCTTCACATGTTTACATCGAAGCAGATCCAAGATAGA
TTTGGCATCTCTGTACTAGACAGAGAACAAATCGAAGATAACA
Found at i:3496511 original size:78 final size:78
Alignment explanation
Indices: 3496381--3496675 Score: 380
Period size: 78 Copynumber: 3.8 Consensus size: 78
3496371 CGAAGAAACA
* * **
3496381 GATTTGGCATCTCCATATTCGAC-AAAGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGA
1 GATTTGGCATCTCTATATTAGACGGGA-AGCAGATCGAAGACATAGCAGATCTGACCTTCATTGA
*
3496445 AGCAGATCCAAGTT
65 AGCAGATCCAAGAT
* * *
3496459 GATTTGGCATCTCTATATTAGACGGGAAGCAGATTGAAGACACAGCATATCTGACCTTCATTGAA
1 GATTTGGCATCTCTATATTAGACGGGAAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAA
3496524 GCAGATCCAAGAT
66 GCAGATCCAAGAT
* * * *
3496537 GATTTGGCATCTCTGTATTAGACAGGG-AGTAGATCAAAGACATAACAGAT-TGGACCTTCATTG
1 GATTTGGCATCTCTATATTAGAC-GGGAAGCAGATCGAAGACATAGCAGATCT-GACCTTCATTG
*
3496600 AAACAGATCCAAGAT
64 AAGCAGATCCAAGAT
* * * * *
3496615 AATTTGGCATCTCTGTATTAGATGGGGAGCAGATCGAAGACATAGTAGATCTGACCTTCAT
1 GATTTGGCATCTCTATATTAGACGGGAAGCAGATCGAAGACATAGCAGATCTGACCTTCAT
3496676 ATGTTTACAT
Statistics
Matches: 190, Mismatches: 22, Indels: 10
0.86 0.10 0.05
Matches are distributed among these distances:
77 4 0.02
78 181 0.95
79 5 0.03
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (78 bp):
GATTTGGCATCTCTATATTAGACGGGAAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAA
GCAGATCCAAGAT
Found at i:3496770 original size:45 final size:44
Alignment explanation
Indices: 3496689--3496882 Score: 246
Period size: 45 Copynumber: 4.3 Consensus size: 44
3496679 TTTACATCGA
* * *
3496689 AGCAGATCCAAGATGACAGATTTGGCATCTCTGTATTAGACAGGG
1 AGCAGATCGAAGAT-AAAGATTTGGCATCTCTGTATTAGACGGGG
* * *
3496734 AGCAAATCGGAGATAATAGATTTGGCATCTCTGTATTAGACGAGG
1 AGCAGATCGAAGATAA-AGATTTGGCATCTCTGTATTAGACGGGG
* * *
3496779 AGCAGATTGAAGA-AGAAGATTTGGCGTCTCTGTATTATACGGGG
1 AGCAGATCGAAGATA-AAGATTTGGCATCTCTGTATTAGACGGGG
*
3496823 AGCAGATCGAAGATAACAGATTTGGCGTCTCTGTATTAGACGGGG
1 AGCAGATCGAAGATAA-AGATTTGGCATCTCTGTATTAGACGGGG
*
3496868 AGCAGATCAAAGATA
1 AGCAGATCGAAGATA
3496883 GCATATATCG
Statistics
Matches: 130, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
44 40 0.31
45 90 0.69
ACGTcount: A:0.32, C:0.14, G:0.28, T:0.25
Consensus pattern (44 bp):
AGCAGATCGAAGATAAAGATTTGGCATCTCTGTATTAGACGGGG
Found at i:3496824 original size:89 final size:89
Alignment explanation
Indices: 3496706--3496874 Score: 266
Period size: 89 Copynumber: 1.9 Consensus size: 89
3496696 CCAAGATGAC
* *
3496706 AGATTTGGCATCTCTGTATTAGACAGGGAGCAAATCGGAGATAATAGATTTGGCATCTCTGTATT
1 AGATTTGGCATCTCTGTATTAGACAGGGAGCAAATCGAAGATAACAGATTTGGCATCTCTGTATT
3496771 AGACGAGGAGCAGATTGAAGAAGA
66 AGACGAGGAGCAGATTGAAGAAGA
* * * * *
3496795 AGATTTGGCGTCTCTGTATTATACGGGGAGCAGATCGAAGATAACAGATTTGGCGTCTCTGTATT
1 AGATTTGGCATCTCTGTATTAGACAGGGAGCAAATCGAAGATAACAGATTTGGCATCTCTGTATT
*
3496860 AGACGGGGAGCAGAT
66 AGACGAGGAGCAGAT
3496875 CAAAGATAGC
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
89 72 1.00
ACGTcount: A:0.30, C:0.14, G:0.30, T:0.27
Consensus pattern (89 bp):
AGATTTGGCATCTCTGTATTAGACAGGGAGCAAATCGAAGATAACAGATTTGGCATCTCTGTATT
AGACGAGGAGCAGATTGAAGAAGA
Done.