Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002705.1 Hibiscus syriacus cultivar Beakdansim tig00005582_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 469953
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:1001 original size:21 final size:21
Alignment explanation
Indices: 975--1019 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
965 GATTTCTGGG
* *
975 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
996 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1017 CAA
1 CAA
1020 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1862 original size:30 final size:31
Alignment explanation
Indices: 1682--1850 Score: 308
Period size: 30 Copynumber: 5.5 Consensus size: 31
1672 GGGTCGAGGG
1682 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
1713 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
1744 TTACCTATGTTCTTC-GGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
1774 TTACCTATGTTCTTCGGGAC-TATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
1804 TTACCTATG-TCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
1834 TTACCTAGGTTCTTCGG
1 TTACCTATGTTCTTCGG
1851 AATCTAGGAC
Statistics
Matches: 134, Mismatches: 1, Indels: 6
0.95 0.01 0.04
Matches are distributed among these distances:
29 10 0.07
30 67 0.50
31 57 0.43
ACGTcount: A:0.18, C:0.20, G:0.22, T:0.39
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:5484 original size:21 final size:21
Alignment explanation
Indices: 5458--5502 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
5448 GATTTCTGGG
* *
5458 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
5479 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
5500 CAA
1 CAA
5503 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:5572 original size:23 final size:22
Alignment explanation
Indices: 5528--5572 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
5518 AACGCTAGAG
*
5528 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
* *
5550 GGGAATCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
5573 AAATGTTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.31, C:0.31, G:0.27, T:0.11
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:6206 original size:31 final size:31
Alignment explanation
Indices: 6168--6352 Score: 336
Period size: 31 Copynumber: 6.0 Consensus size: 31
6158 GGGTCGAGGG
6168 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
6199 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
6230 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
6261 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
6292 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
6323 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
6353 GTCCTTCGGG
Statistics
Matches: 151, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
31 150 0.99
32 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:6940 original size:4 final size:4
Alignment explanation
Indices: 6931--6962 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
6921 ACAAATCATC
6931 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
6963 AGTTTAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
CTTT
Found at i:12366 original size:19 final size:19
Alignment explanation
Indices: 12339--12376 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
12329 AACTTAAACA
*
12339 GATATTGATATAGA-CAATT
1 GATAATGAT-TAGATCAATT
12358 GATAATGATTAGATCAATT
1 GATAATGATTAGATCAATT
12377 TTTGAAGCCG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.42, C:0.05, G:0.16, T:0.37
Consensus pattern (19 bp):
GATAATGATTAGATCAATT
Found at i:15286 original size:18 final size:18
Alignment explanation
Indices: 15260--15294 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
15250 TCGAAAGGAC
*
15260 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
15278 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
15295 CCGGATGACA
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:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:16532 original size:12 final size:12
Alignment explanation
Indices: 16491--16550 Score: 54
Period size: 12 Copynumber: 5.0 Consensus size: 12
16481 CGATTTGAAT
16491 TCTGATATGATA
1 TCTGATATGATA
*
16503 -CTTGACATGGAT-
1 TC-TGATAT-GATA
*
16515 TCTGATCTGATA
1 TCTGATATGATA
16527 TCTGATATGGAT-
1 TCTGATAT-GATA
16539 TCTGATATGATA
1 TCTGATATGATA
16551 CTTGACTTGG
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
11 7 0.18
12 24 0.63
13 7 0.18
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (12 bp):
TCTGATATGATA
Found at i:16541 original size:48 final size:47
Alignment explanation
Indices: 16489--16604 Score: 162
Period size: 48 Copynumber: 2.4 Consensus size: 47
16479 TTCGATTTGA
*
16489 ATTCTGATATGATACTTGACATGGATTCTGATCTGATA-TCTGATATGG
1 ATTCTGATATGATACTTGACATGGATTCTGATCTGATACT-TGACAT-G
* * *
16537 ATTCTGATATGATACTTGACTTGGATTCTGATCTGTTACTTGACCTG
1 ATTCTGATATGATACTTGACATGGATTCTGATCTGATACTTGACATG
16584 ATTTCTGATATGATACTTGAC
1 A-TTCTGATATGATACTTGAC
16605 CTGATTTATG
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
47 2 0.03
48 59 0.95
49 1 0.02
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.41
Consensus pattern (47 bp):
ATTCTGATATGATACTTGACATGGATTCTGATCTGATACTTGACATG
Found at i:16611 original size:24 final size:24
Alignment explanation
Indices: 16489--16604 Score: 146
Period size: 24 Copynumber: 4.8 Consensus size: 24
16479 TTCGATTTGA
16489 ATTCTGATATGATACTTGACATGG
1 ATTCTGATATGATACTTGACATGG
* *
16513 ATTCTGATCTGATA-TCTGATATGG
1 ATTCTGATATGATACT-TGACATGG
*
16537 ATTCTGATATGATACTTGACTTGG
1 ATTCTGATATGATACTTGACATGG
* * *
16561 ATTCTGATCTGTTACTTGACCT-G
1 ATTCTGATATGATACTTGACATGG
16584 ATTTCTGATATGATACTTGAC
1 A-TTCTGATATGATACTTGAC
16605 CTGATTTATG
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
23 3 0.04
24 75 0.95
25 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.41
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:16627 original size:24 final size:24
Alignment explanation
Indices: 16541--16614 Score: 87
Period size: 24 Copynumber: 3.1 Consensus size: 24
16531 ATATGGATTC
* *
16541 TGATATGATACTTGACTTGGA-TTC
1 TGATATGATACTTGACCT-GATTTA
* * *
16565 TGATCTGTTACTTGACCTGATTTC
1 TGATATGATACTTGACCTGATTTA
16589 TGATATGATACTTGACCTGATTTA
1 TGATATGATACTTGACCTGATTTA
16613 TG
1 TG
16615 TTTTGATTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
23 2 0.05
24 41 0.95
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.43
Consensus pattern (24 bp):
TGATATGATACTTGACCTGATTTA
Found at i:18687 original size:18 final size:18
Alignment explanation
Indices: 18660--18699 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
18650 GACCAGTCAC
18660 GACCCAACCCGACCCGTT
1 GACCCAACCCGACCCGTT
*
18678 GACCCGACCCGACCCGTT
1 GACCCAACCCGACCCGTT
18696 GACC
1 GACC
18700 GTTGACCGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.20, C:0.50, G:0.20, T:0.10
Consensus pattern (18 bp):
GACCCAACCCGACCCGTT
Found at i:19963 original size:19 final size:19
Alignment explanation
Indices: 19936--19980 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
19926 CACTTGACCC
*
19936 GTAACTATTCGAATAATGA
1 GTAAATATTCGAATAATGA
19955 GTAAATATTCGAATAATGA
1 GTAAATATTCGAATAATGA
19974 GTAAATA
1 GTAAATA
19981 CTTGAAGAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.47, C:0.07, G:0.16, T:0.31
Consensus pattern (19 bp):
GTAAATATTCGAATAATGA
Found at i:21294 original size:24 final size:24
Alignment explanation
Indices: 21263--21378 Score: 137
Period size: 24 Copynumber: 4.8 Consensus size: 24
21253 TTTTATTTGA
*
21263 ATTCTGATCTAATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
* *
21287 ATTTTGATATGATA-TCTGACATGG
1 ATTCTGATCTGATACT-TGACATGG
*
21311 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
* *
21335 ATTCTGATCTGTTACTTGACCT-G
1 ATTCTGATCTGATACTTGACATGG
*
21358 ATTTCTGATATGATACTTGAC
1 A-TTCTGATCTGATACTTGAC
21379 CTGATTTATG
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
23 3 0.04
24 75 0.95
25 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.41
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:22945 original size:20 final size:20
Alignment explanation
Indices: 22922--22977 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
22912 TATTGGAATA
22922 TACATTCTGGAATATGCATT
1 TACATTCTGGAATATGCATT
22942 TACATTCTGGAATATGCATT
1 TACATTCTGGAATATGCATT
*
22962 TACATTCTAGAATATG
1 TACATTCTGGAATATG
22978 TAGTGTTAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (20 bp):
TACATTCTGGAATATGCATT
Found at i:34462 original size:29 final size:30
Alignment explanation
Indices: 34399--34484 Score: 86
Period size: 29 Copynumber: 2.9 Consensus size: 30
34389 TTGATTTTTT
* * *
34399 AAAAAA-TAATTTACTTAAAATATATTACC
1 AAAAAATTATTTTACATAAAATAAATTACC
**
34428 TGAAAATTATTTTACATAAAATAAATTA-C
1 AAAAAATTATTTTACATAAAATAAATTACC
* * *
34457 AAAAAATTGTTTTACGTAAAATGAATTA
1 AAAAAATTATTTTACATAAAATAAATTA
34485 TCTAAAACTG
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
29 28 0.61
30 18 0.39
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (30 bp):
AAAAAATTATTTTACATAAAATAAATTACC
Found at i:34491 original size:29 final size:27
Alignment explanation
Indices: 34408--34501 Score: 71
Period size: 29 Copynumber: 3.2 Consensus size: 27
34398 TAAAAAATAA
* *
34408 TTTACTTAAAATATATTACCTGAAAATTAT
1 TTTACATAAAATA-ATTA-CT-AAAATTGT
*
34438 TTTACATAAAATAAATTACAAAAAATTGT
1 TTTACATAAAAT-AATTAC-TAAAATTGT
* *
34467 TTTACGTAAAATGAATTATCTAAAACTGT
1 TTTACATAAAAT-AATTA-CTAAAATTGT
*
34496 ATTACA
1 TTTACA
34502 CTTTCTAAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
29 35 0.67
30 16 0.31
31 1 0.02
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.38
Consensus pattern (27 bp):
TTTACATAAAATAATTACTAAAATTGT
Found at i:34784 original size:17 final size:16
Alignment explanation
Indices: 34762--34843 Score: 76
Period size: 17 Copynumber: 5.0 Consensus size: 16
34752 ATAATACTAA
34762 ATTATTAAACATTATAT
1 ATTATTAAA-ATTATAT
*
34779 ATTATTATAA-TATAT
1 ATTATTAAAATTATAT
* * *
34794 TTTAGTAATATTAATAT
1 ATTATTAAAATT-ATAT
* *
34811 AATATTAAAAATATAAT
1 ATTATTAAAATTAT-AT
34828 ATTATTAAAATTATAT
1 ATTATTAAAATTATAT
34844 TATAATAATA
Statistics
Matches: 50, Mismatches: 12, Indels: 7
0.72 0.17 0.10
Matches are distributed among these distances:
15 11 0.22
16 6 0.12
17 33 0.66
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (16 bp):
ATTATTAAAATTATAT
Found at i:34850 original size:22 final size:22
Alignment explanation
Indices: 34772--34858 Score: 68
Period size: 22 Copynumber: 3.8 Consensus size: 22
34762 ATTATTAAAC
*
34772 ATTAT-ATATTATTATAATATAT
1 ATTATAATATTATTAAAAT-TAT
* * *
34794 TTTAGTAATATTAATATAATATTAAA
1 ATTA-TAATATT-AT-TAAAATT-AT
*
34820 AATATAATATTATTAAAATTAT
1 ATTATAATATTATTAAAATTAT
*
34842 ATTATAATAATATTAAA
1 ATTATAATATTATTAAA
34859 TATTTAATAA
Statistics
Matches: 50, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
22 19 0.38
23 7 0.14
24 7 0.14
25 10 0.20
26 7 0.14
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (22 bp):
ATTATAATATTATTAAAATTAT
Found at i:35010 original size:26 final size:24
Alignment explanation
Indices: 34954--35010 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 24
34944 GTGAAAAGTC
**
34954 AGGAAAATGTTTTACGAAAATCAA
1 AGGAAAACATTTTACGAAAATCAA
34978 ATGGGAAAACATTTTACAGAAAATACAA
1 A--GGAAAACATTTTAC-GAAAAT-CAA
35006 AGGAA
1 AGGAA
35011 CTAAGAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
24 1 0.04
26 16 0.59
27 6 0.22
28 4 0.15
ACGTcount: A:0.53, C:0.09, G:0.18, T:0.21
Consensus pattern (24 bp):
AGGAAAACATTTTACGAAAATCAA
Found at i:35080 original size:42 final size:42
Alignment explanation
Indices: 35034--35113 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
35024 TTACATTAGA
* *
35034 AAAATCAATTACAACTATCAAACA-CTGGAAAATGTTTTATGT
1 AAAATAAAGTACAACTATCAAACATC-GGAAAATGTTTTATGT
*
35076 AAAATAAAGTACATCTATCAAACATCGGAAAATGTTTT
1 AAAATAAAGTACAACTATCAAACATCGGAAAATGTTTT
35114 TCACCTATCA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
42 33 0.97
43 1 0.03
ACGTcount: A:0.46, C:0.14, G:0.10, T:0.30
Consensus pattern (42 bp):
AAAATAAAGTACAACTATCAAACATCGGAAAATGTTTTATGT
Found at i:44904 original size:20 final size:21
Alignment explanation
Indices: 44880--44949 Score: 63
Period size: 20 Copynumber: 3.3 Consensus size: 21
44870 ATATCTAGAG
44880 TTAATTAAATATATGTTTTAA
1 TTAATTAAATATATGTTTTAA
* * *
44901 -TAATCCCAAATATTTAATTTTAA
1 TTAAT--TAAATATAT-GTTTTAA
*
44924 TTAATTAAATATA-GATTTAA
1 TTAATTAAATATATGTTTTAA
44944 TTAATT
1 TTAATT
44950 TGAAATAATA
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
20 15 0.39
22 13 0.34
23 6 0.16
24 4 0.11
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (21 bp):
TTAATTAAATATATGTTTTAA
Found at i:50547 original size:65 final size:63
Alignment explanation
Indices: 50476--50635 Score: 207
Period size: 65 Copynumber: 2.5 Consensus size: 63
50466 AATTAAATTG
* *
50476 AACATCGAATGCATTTCATGCATCGATGCACATACCATGCACCGATGCA-T-TGAGGATTTTATG
1 AACATCGAATGCATTTGATGCATCGATGCACA-ACCATGCACCGATGCACTCTGACGA-TTT-TG
50539 AA
63 -A
* * *
50541 AACATCGAATGCATTTGATGCATCGATACACCAACCATGCATCGATGCACTCTGACTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCA-CAACCATGCACCGATGCACTCTGACGATTTTGA
*
50605 AACATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
50636 TCTTAGTGCA
Statistics
Matches: 85, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
63 1 0.01
64 29 0.34
65 45 0.53
66 6 0.07
67 4 0.05
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACAACCATGCACCGATGCACTCTGACGATTTTGA
Found at i:56451 original size:24 final size:24
Alignment explanation
Indices: 56423--56502 Score: 73
Period size: 24 Copynumber: 3.5 Consensus size: 24
56413 CACTTAACAA
56423 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGATGCATCCCTTTGAATG
* *
56447 TGCATCGATTCAT-CATGTTG-A--
1 TGCATCGATGCATCCCT-TTGAATG
56468 TGCATCGATGCA-CGCC-TTGAATG
1 TGCATCGATGCATC-CCTTTGAATG
*
56491 TGCATCAATGCA
1 TGCATCGATGCA
56503 CGAGGTCTTG
Statistics
Matches: 45, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
20 3 0.07
21 12 0.27
22 1 0.02
23 14 0.31
24 15 0.33
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (24 bp):
TGCATCGATGCATCCCTTTGAATG
Found at i:59278 original size:64 final size:63
Alignment explanation
Indices: 59181--59390 Score: 185
Period size: 65 Copynumber: 3.3 Consensus size: 63
59171 ATTTTTAGTG
* * * * * *
59181 TGATGCACCAATGCACCAATCCATGTATCGATGCACCATGAATTAAATTG-AACATCGAATGCAT
1 TGATGCATCGATGCA-CAA-CCATGCACCGATGCACC-TGAATTATATTGAAACATCAAATGCAT
59245 T
63 T
* * *
59246 TCATGCATCGATGCACATACCATGCACCGATGCA-TTGAGGATTTTA-TGAAAACATCAAATGCA
1 TGATGCATCGATGCACA-ACCATGCACCGATGCACCTGA--ATTATATTG-AAACATCAAATGCA
59309 TT
62 TT
* * * * *
59311 TGATGCATCGATGCACCAGCCATGCATCGATGCACTCTG-ACTATTTTGAAACATCAAATGCACT
1 TGATGCATCGATGCA-CAACCATGCACCGATGCAC-CTGAATTATATTGAAACATCAAATGCATT
59375 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
59391 TCTTAGTGCA
Statistics
Matches: 119, Mismatches: 17, Indels: 20
0.76 0.11 0.13
Matches are distributed among these distances:
62 3 0.03
63 3 0.03
64 52 0.44
65 57 0.48
66 2 0.02
67 2 0.02
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (63 bp):
TGATGCATCGATGCACAACCATGCACCGATGCACCTGAATTATATTGAAACATCAAATGCATT
Found at i:59300 original size:65 final size:63
Alignment explanation
Indices: 59231--59390 Score: 198
Period size: 65 Copynumber: 2.5 Consensus size: 63
59221 AATTAAATTG
* * *
59231 AACATCGAATGCATTTCATGCATCGATGCACATACCATGCACCGATGCA-T-TGAGGATTTTATG
1 AACATCAAATGCATTTGATGCATCGATGCACA-ACCATGCACCGATGCACTCTGACGA-TTT-TG
59294 AA
63 -A
* * *
59296 AACATCAAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGACTATTTTGA
1 AACATCAAATGCATTTGATGCATCGATGCA-CAACCATGCACCGATGCACTCTGACGATTTTGA
*
59360 AACATCAAATGCACTTGATGCATCGATGCAC
1 AACATCAAATGCATTTGATGCATCGATGCAC
59391 TCTTAGTGCA
Statistics
Matches: 85, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
63 1 0.01
64 30 0.35
65 44 0.52
66 6 0.07
67 4 0.05
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (63 bp):
AACATCAAATGCATTTGATGCATCGATGCACAACCATGCACCGATGCACTCTGACGATTTTGA
Found at i:59390 original size:17 final size:19
Alignment explanation
Indices: 59368--59410 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
59358 GAAACATCAA
*
59368 ATGCACT-TGA-TGCATCG
1 ATGCACTCTGAGTGCACCG
*
59385 ATGCACTCTTAGTGCACCG
1 ATGCACTCTGAGTGCACCG
59404 ATGCACT
1 ATGCACT
59411 AAGGGTCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 2 0.09
19 13 0.59
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (19 bp):
ATGCACTCTGAGTGCACCG
Found at i:59406 original size:64 final size:64
Alignment explanation
Indices: 59231--59410 Score: 183
Period size: 64 Copynumber: 2.8 Consensus size: 64
59221 AATTAAATTG
* * *
59231 AACATCGAATGCATTTCATGCATCGATGCACATACCA-TGCACCGATGCA-TTGAGGATTTTATG
1 AACATCAAATGCATTTGATGCATCGATGCAC-T--CAGTGCACCGATGCACTTGACGATTTTATG
59294 AA
63 AA
* *
59296 AACATCAAATGCATTTGATGCATCGATGCAC-CAGCCATGCATCGATGCACTCTGACTA-TTT-T
1 AACATCAAATGCATTTGATGCATCGATGCACTCAG---TGCACCGATGCACT-TGACGATTTTAT
59358 G-A
62 GAA
*
59360 AACATCAAATGCACTTGATGCATCGATGCACTCTTAGTGCACCGATGCACT
1 AACATCAAATGCATTTGATGCATCGATGCACTC--AGTGCACCGATGCACT
59411 AAGGGTCCAA
Statistics
Matches: 99, Mismatches: 7, Indels: 19
0.79 0.06 0.15
Matches are distributed among these distances:
61 2 0.02
64 44 0.44
65 43 0.43
66 4 0.04
67 6 0.06
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (64 bp):
AACATCAAATGCATTTGATGCATCGATGCACTCAGTGCACCGATGCACTTGACGATTTTATGAA
Found at i:68606 original size:20 final size:20
Alignment explanation
Indices: 68581--68618 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
68571 AACAAATATA
* *
68581 TAAAATATTATTTTAATTGG
1 TAAAATATAAATTTAATTGG
68601 TAAAATATAAATTTAATT
1 TAAAATATAAATTTAATT
68619 AAAAAAATAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (20 bp):
TAAAATATAAATTTAATTGG
Found at i:68670 original size:2 final size:2
Alignment explanation
Indices: 68663--68695 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
68653 TCCCTAAATT
68663 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
68696 TGTTACCTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:72398 original size:15 final size:17
Alignment explanation
Indices: 72367--72399 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
72357 GATAAGTACA
72367 TAATTATAGTATTTTAT
1 TAATTATAGTATTTTAT
72384 TAATTATA-T-TTTTAT
1 TAATTATAGTATTTTAT
72399 T
1 T
72400 TTAGAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 1 0.06
17 8 0.50
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (17 bp):
TAATTATAGTATTTTAT
Found at i:75200 original size:27 final size:28
Alignment explanation
Indices: 75140--75201 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
75130 CTATTTACTG
* *
75140 CTTTATTGTTTTTTATGGCCTTATGGGA
1 CTTTATTGTTTTCTATGGCCTCATGGGA
*
75168 CATTATT-TTTCTCTATGG-CTCATGGGA
1 CTTTATTGTTT-TCTATGGCCTCATGGGA
75195 CTTTATT
1 CTTTATT
75202 ACTTATTGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 17 0.59
28 12 0.41
ACGTcount: A:0.16, C:0.15, G:0.18, T:0.52
Consensus pattern (28 bp):
CTTTATTGTTTTCTATGGCCTCATGGGA
Found at i:104874 original size:21 final size:22
Alignment explanation
Indices: 104824--104877 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 22
104814 ACTTTTAATA
104824 AAATAAATATATATAATTTTATC
1 AAATAAATATATATAA-TTTATC
*
104847 -AA-CAATATATATAA-TTATC
1 AAATAAATATATATAATTTATC
104866 AAATAAATATAT
1 AAATAAATATAT
104878 TTTTAATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
19 5 0.19
20 2 0.07
21 18 0.67
22 2 0.07
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (22 bp):
AAATAAATATATATAATTTATC
Found at i:105273 original size:183 final size:183
Alignment explanation
Indices: 104965--105330 Score: 732
Period size: 183 Copynumber: 2.0 Consensus size: 183
104955 CTTTAGCAAA
104965 GATAGTTTAGGAATGCATCAAAGTAACGATGAAAAATTATCACAAGTACTAGATAGAGCACTACA
1 GATAGTTTAGGAATGCATCAAAGTAACGATGAAAAATTATCACAAGTACTAGATAGAGCACTACA
105030 AATTGATCAAAATTTTGTGATCAAATTAAGATACTATATATATAAAATTAGATCTTTAAAAAAAA
66 AATTGATCAAAATTTTGTGATCAAATTAAGATACTATATATATAAAATTAGATCTTTAAAAAAAA
105095 TTATTGGCACGATCACTTGAATCGATTACTTTCTAAGGTGGATTTCGTATTTT
131 TTATTGGCACGATCACTTGAATCGATTACTTTCTAAGGTGGATTTCGTATTTT
105148 GATAGTTTAGGAATGCATCAAAGTAACGATGAAAAATTATCACAAGTACTAGATAGAGCACTACA
1 GATAGTTTAGGAATGCATCAAAGTAACGATGAAAAATTATCACAAGTACTAGATAGAGCACTACA
105213 AATTGATCAAAATTTTGTGATCAAATTAAGATACTATATATATAAAATTAGATCTTTAAAAAAAA
66 AATTGATCAAAATTTTGTGATCAAATTAAGATACTATATATATAAAATTAGATCTTTAAAAAAAA
105278 TTATTGGCACGATCACTTGAATCGATTACTTTCTAAGGTGGATTTCGTATTTT
131 TTATTGGCACGATCACTTGAATCGATTACTTTCTAAGGTGGATTTCGTATTTT
105331 AAGGCCACGT
Statistics
Matches: 183, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
183 183 1.00
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.33
Consensus pattern (183 bp):
GATAGTTTAGGAATGCATCAAAGTAACGATGAAAAATTATCACAAGTACTAGATAGAGCACTACA
AATTGATCAAAATTTTGTGATCAAATTAAGATACTATATATATAAAATTAGATCTTTAAAAAAAA
TTATTGGCACGATCACTTGAATCGATTACTTTCTAAGGTGGATTTCGTATTTT
Found at i:105641 original size:20 final size:21
Alignment explanation
Indices: 105616--105667 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
105606 TTTTCCCAAT
105616 TCGCAATGCGAATAAG-TAAA
1 TCGCAATGCGAATAAGATAAA
* * **
105636 TCGCAACGTGAATTGGATAAA
1 TCGCAATGCGAATAAGATAAA
105657 TCGCAATGCGA
1 TCGCAATGCGA
105668 TACTGACTAT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATAAGATAAA
Found at i:105681 original size:20 final size:20
Alignment explanation
Indices: 105656--105749 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
105646 AATTGGATAA
*
105656 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
105676 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
105697 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
105717 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
105737 TTCGCAACGCGAT
1 ATCGCAACGCGAT
105750 TTACATAGCG
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 2 0.03
20 45 0.73
21 13 0.21
22 2 0.03
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:106327 original size:19 final size:19
Alignment explanation
Indices: 106303--106366 Score: 110
Period size: 19 Copynumber: 3.4 Consensus size: 19
106293 GCAACGAGAG
106303 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATAAA
106322 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATAAA
**
106341 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAATAAA
106360 AATCGCA
1 AATCGCA
106367 TTGCGATTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 43 1.00
ACGTcount: A:0.50, C:0.25, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAATAAA
Found at i:106413 original size:33 final size:33
Alignment explanation
Indices: 106376--106463 Score: 158
Period size: 33 Copynumber: 2.6 Consensus size: 33
106366 ATTGCGATTT
106376 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
106409 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
106442 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
106464 ATTATCTCGT
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 38 0.72
34 15 0.28
ACGTcount: A:0.11, C:0.27, G:0.23, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:106465 original size:20 final size:20
Alignment explanation
Indices: 106431--106488 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
106421 GCGATTCTCT
**
106431 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
106451 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
106471 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
106489 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:108329 original size:91 final size:90
Alignment explanation
Indices: 108164--108346 Score: 257
Period size: 91 Copynumber: 2.0 Consensus size: 90
108154 TAGATTGCTT
108164 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTATTTATTAACACTATGAAGTTAGTATTT
1 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTATTTATTAACACTATGAAGTTAGTATTT
108229 GTCTTTTTGTTTTATCTTTTGGTTGA
66 GTC-TTTTGTTTTATCTTTTGGTTGA
* *
108255 AGTAAATTTATTCGGTTGCTGCCAAT-TTGCT-AACTGTGTATTCT-TTAACACTGTGAAGTTAG
1 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC----TATT-TATTAACACTATGAAGTTAG
*
108317 TATTTGTC-TTTGTTTTGTCTTTTGGTTGA
61 TATTTGTCTTTTGTTTTATCTTTTGGTTGA
108346 A
1 A
108347 AGTTTGAAAT
Statistics
Matches: 84, Mismatches: 3, Indels: 10
0.87 0.03 0.10
Matches are distributed among these distances:
89 3 0.04
90 4 0.05
91 47 0.56
93 29 0.35
94 1 0.01
ACGTcount: A:0.23, C:0.12, G:0.17, T:0.48
Consensus pattern (90 bp):
AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTATTTATTAACACTATGAAGTTAGTATTT
GTCTTTTGTTTTATCTTTTGGTTGA
Found at i:108643 original size:41 final size:42
Alignment explanation
Indices: 108591--108766 Score: 180
Period size: 41 Copynumber: 4.2 Consensus size: 42
108581 GTCCTCCTAT
*
108591 CGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCA-
1 CGTTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCAC
* * * * * * *
108632 CGTTCAAGAGGCCACTGTCATCCCTCAAGAGTCCACTCCTAT
1 CGTTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCAC
*
108674 CG-TGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCAC
1 CGTTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCAC
* * * *
108715 CGTTCAAGAGGCCACTGTCA-TCGTTGAAGAGGT-CCCTCCCAC
1 CGTTCAAGAGGCCCCTATCATTCCTCG-AGA-GTCCCCTCCCAC
*
108757 CATTCAAGAG
1 CGTTCAAGAG
108767 CCCGATTCAC
Statistics
Matches: 110, Mismatches: 21, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
41 71 0.65
42 37 0.34
43 2 0.02
ACGTcount: A:0.22, C:0.36, G:0.20, T:0.22
Consensus pattern (42 bp):
CGTTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCAC
Found at i:108724 original size:21 final size:21
Alignment explanation
Indices: 108700--108766 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
108690 TCATTCCTCG
108700 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
108721 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
108742 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
108763 AGAG
1 AGAG
108767 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:108745 original size:83 final size:82
Alignment explanation
Indices: 108565--108736 Score: 312
Period size: 82 Copynumber: 2.1 Consensus size: 82
108555 CCCGACTCGC
108565 CTGTCATCCCTCAAGAGT-CCTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTC
1 CTGTCATCCCTCAAGAGTCCCTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTC
108629 CCACGTTCAAGAGGCCA
66 CCACGTTCAAGAGGCCA
108646 CTGTCATCCCTCAAGAGTCCACTCCTATCG-TGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCC-CTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
108710 CCCACCGTTCAAGAGGCCA
65 CCCA-CGTTCAAGAGGCCA
108729 CTGTCATC
1 CTGTCATC
108737 GTTGAAGAGG
Statistics
Matches: 88, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
81 18 0.20
82 39 0.44
83 31 0.35
ACGTcount: A:0.21, C:0.38, G:0.18, T:0.23
Consensus pattern (82 bp):
CTGTCATCCCTCAAGAGTCCCTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTC
CCACGTTCAAGAGGCCA
Found at i:110114 original size:13 final size:14
Alignment explanation
Indices: 110106--110142 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
110096 GATTGTTTAA
110106 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
*
110120 GTGATTTGTAAAAG
1 TTGATTTGTAAAAG
110134 TTGATTTGT
1 TTGATTTGT
110143 TTAATTGATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.24, T:0.46
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:110281 original size:14 final size:14
Alignment explanation
Indices: 110262--110318 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
110252 GCGAAATGAA
110262 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
110276 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
110295 AATCGCAACGAGAG
1 AATCGCAACGAGAG
110309 AATCGCAACG
1 AATCGCAACG
110319 CGAAATTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:110289 original size:33 final size:33
Alignment explanation
Indices: 110244--110333 Score: 153
Period size: 33 Copynumber: 2.7 Consensus size: 33
110234 AAAAAGTACT
*
110244 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
110277 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* *
110310 ATCGCAACGCGAAATTAAATTCGC
1 ATCGCAACGCGAAATGAAAATCGC
110334 GTTGCGATTT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.43, C:0.21, G:0.22, T:0.13
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:110303 original size:19 final size:19
Alignment explanation
Indices: 110244--110304 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
110234 AAAAAGTACT
*
110244 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
110263 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
110277 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
110296 ATCGCAACG
1 ATCGCAACG
110305 AGAGAATCGC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 10 0.29
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 19 0.54
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:110424 original size:19 final size:19
Alignment explanation
Indices: 110400--110458 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
110390 GAAATTAGCG
110400 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
110419 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
110433 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
110452 TTGCGAT
1 TTGCGAT
110459 AGTAATTTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 6 0.18
16 7 0.21
17 7 0.21
19 13 0.39
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:110458 original size:33 final size:33
Alignment explanation
Indices: 110333--110458 Score: 175
Period size: 33 Copynumber: 3.8 Consensus size: 33
110323 ATTAAATTCG
*
110333 CGTTGCGATTTTCATTTCGCATTGCAATTC-CT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
* * * **
110365 CGTTGTGATTTTCATTTCACATTGCGAAAT-TAG
1 CGTTGCGATTTTCATTTCGCATTGCG-ATTCTCT
110398 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
110431 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
110459 AGTAATTTCT
Statistics
Matches: 80, Mismatches: 11, Indels: 5
0.83 0.11 0.05
Matches are distributed among these distances:
32 25 0.31
33 55 0.69
ACGTcount: A:0.17, C:0.21, G:0.18, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:112503 original size:12 final size:12
Alignment explanation
Indices: 112486--112510 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
112476 TTTCTCGGGA
112486 CTTTTTCTTCTT
1 CTTTTTCTTCTT
112498 CTTTTTCTTCTT
1 CTTTTTCTTCTT
112510 C
1 C
112511 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:112720 original size:24 final size:24
Alignment explanation
Indices: 112686--112755 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
112676 CTGAAACATC
*
112686 ATCAAAATCCGAGTATTGACTAAT
1 ATCAAAATCCGAGTATTGACTAAG
* * *
112710 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACTAAG
* * *
112734 ATCAAATTTCGAATATTGACTA
1 ATCAAAATCCGAGTATTGACTA
112756 GTACACAATT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.29
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACTAAG
Found at i:113534 original size:20 final size:21
Alignment explanation
Indices: 113509--113560 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
113499 TTTTCCTAAT
*
113509 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
113529 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
113550 TCGCAATGCGA
1 TCGCAATGCGA
113561 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:113871 original size:20 final size:20
Alignment explanation
Indices: 113846--113892 Score: 78
Period size: 19 Copynumber: 2.4 Consensus size: 20
113836 GCAACGGGGA
*
113846 ATCGCAACGTGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
113866 ATCGC-ACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
113885 ATCGCAAC
1 ATCGCAAC
113893 TAGAAAATCG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.34, C:0.26, G:0.23, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:113900 original size:20 final size:19
Alignment explanation
Indices: 113846--113900 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
113836 GCAACGGGGA
113846 ATCGCAACGTGAAAATGGCT
1 ATCGCAAC-TGAAAATGGCT
*
113866 ATCGC-ACGCGAAAATGGCT
1 ATCGCAAC-TGAAAATGGCT
113885 ATCGCAACTAGAAAAT
1 ATCGCAACT-GAAAAT
113901 CGCAATGCGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 18 0.58
20 13 0.42
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (19 bp):
ATCGCAACTGAAAATGGCT
Found at i:113947 original size:18 final size:19
Alignment explanation
Indices: 113919--113955 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
113909 GAAATGAAAA
113919 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
113938 TCGC-TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
113956 GCGATAGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.14, C:0.22, G:0.16, T:0.49
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:114119 original size:14 final size:14
Alignment explanation
Indices: 114083--114119 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
114073 CATCAATTAA
*
114083 ACAAATCAACATTT
1 ACAAATCATCATTT
*
114097 ACAAATCATCTTTT
1 ACAAATCATCATTT
114111 ACAAATCAT
1 ACAAATCAT
114120 TAAACAATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCATCATTT
Found at i:115553 original size:41 final size:42
Alignment explanation
Indices: 115508--115588 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
115498 ATGACAGTGG
115508 CCTCTTGAACG-GT-GAGGGGGACTCTTGAGGGAGGATAGGGA
1 CCTCTTGAACGAGTGGA-GGGGACTCTTGAGGGAGGATAGGGA
* *
115549 CCTCTTGAACGATTGGAGGGGACTCTTGAGGGATGATAGG
1 CCTCTTGAACGAGTGGAGGGGACTCTTGAGGGAGGATAGG
115589 TGAGTCGGTC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
41 11 0.31
42 23 0.64
43 2 0.06
ACGTcount: A:0.22, C:0.15, G:0.41, T:0.22
Consensus pattern (42 bp):
CCTCTTGAACGAGTGGAGGGGACTCTTGAGGGAGGATAGGGA
Found at i:115995 original size:19 final size:20
Alignment explanation
Indices: 115944--116008 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
115934 ACTTAAAATT
115944 GCAACGC-GAAAATGACTATC
1 GCAACGCTG-AAATGACTATC
*
115964 GCAACGCTGAAATGGCTATC
1 GCAACGCTGAAATGACTATC
* **
115984 GCAATG-TGAAATGAAAATC
1 GCAACGCTGAAATGACTATC
116003 GCAACG
1 GCAACG
116009 ACAAAATCGC
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
19 15 0.39
20 22 0.58
21 1 0.03
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.17
Consensus pattern (20 bp):
GCAACGCTGAAATGACTATC
Found at i:116016 original size:14 final size:14
Alignment explanation
Indices: 115997--116086 Score: 90
Period size: 14 Copynumber: 5.9 Consensus size: 14
115987 ATGTGAAATG
115997 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
116011 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
116027 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
116043 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
116059 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
116075 AAAATCGCAACG
1 AAAATCGCAACG
116087 CGAAACACAA
Statistics
Matches: 64, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
14 30 0.47
16 16 0.25
18 18 0.28
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:116039 original size:32 final size:32
Alignment explanation
Indices: 115981--116091 Score: 195
Period size: 32 Copynumber: 3.4 Consensus size: 32
115971 TGAAATGGCT
*
115981 ATCGCAATGTGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
116014 ATCGCAATGCGAAATGAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAATCGCAACGACAAA
116046 ATCGCAATGCGAAATGAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAATCGCAACGACAAA
*
116078 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
116092 CACAAATTGC
Statistics
Matches: 76, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
32 61 0.80
33 15 0.20
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.13
Consensus pattern (32 bp):
ATCGCAATGCGAAATGAAATCGCAACGACAAA
Found at i:116137 original size:13 final size:14
Alignment explanation
Indices: 116121--116175 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 14
116111 TTCATTTCGT
116121 GTTGCGA-TTTGTC
1 GTTGCGATTTTGTC
*
116134 GTTGCGATTTCATTTC
1 GTTGCGATTT--TGTC
116150 GCATTGCGATTTTGTC
1 G--TTGCGATTTTGTC
116166 GTTGCGATTT
1 GTTGCGATTT
116176 CATTTCGCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
13 7 0.20
14 11 0.31
16 8 0.23
18 9 0.26
ACGTcount: A:0.11, C:0.16, G:0.25, T:0.47
Consensus pattern (14 bp):
GTTGCGATTTTGTC
Found at i:116210 original size:37 final size:32
Alignment explanation
Indices: 116103--116191 Score: 144
Period size: 32 Copynumber: 2.8 Consensus size: 32
116093 ACAAATTGCA
**
116103 TTGCGATTTTCATTTCGTGTTGCGA-TTTGTCG
1 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
116135 TTGCGATTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTCATTTCGCATTGCGATTTTGTCG
116167 TTGCGATTTCATTTCGCATTGCGAT
1 TTGCGATTTCATTTCGCATTGCGAT
116192 AGCCATTTCG
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
31 16 0.30
32 38 0.70
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.47
Consensus pattern (32 bp):
TTGCGATTTCATTTCGCATTGCGATTTTGTCG
Found at i:116226 original size:20 final size:19
Alignment explanation
Indices: 116176--116229 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
116166 GTTGCGATTT
*
116176 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
116195 CATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGC
*
116214 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
116230 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 19 0.61
20 12 0.39
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:116727 original size:18 final size:18
Alignment explanation
Indices: 116701--116745 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
116691 GTCGATCAGA
*
116701 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
116719 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
116737 TGATGGCTC
1 TGATGGCTC
116746 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:118070 original size:20 final size:20
Alignment explanation
Indices: 118047--118090 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
118037 AATGAAAATT
118047 GCAACACGAAAATGACTATC
1 GCAACACGAAAATGACTATC
* **
118067 GCAACGCGAATTTGACTATC
1 GCAACACGAAAATGACTATC
118087 GCAA
1 GCAA
118091 TGAGAGAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (20 bp):
GCAACACGAAAATGACTATC
Found at i:118368 original size:20 final size:21
Alignment explanation
Indices: 118343--118390 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
118333 TCTGAGAGAT
118343 GGAGAT-AGACGGATTTCGCC
1 GGAGATGAGACGGATTTCGCC
* *
118363 GGAGATGGGGACGGATTTCGTC
1 GGAGAT-GAGACGGATTTCGCC
118385 -GAGATG
1 GGAGATG
118391 GGTGAGAGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 7 0.29
21 5 0.21
22 12 0.50
ACGTcount: A:0.23, C:0.15, G:0.42, T:0.21
Consensus pattern (21 bp):
GGAGATGAGACGGATTTCGCC
Found at i:118390 original size:21 final size:22
Alignment explanation
Indices: 118350--118392 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
118340 GATGGAGATA
118350 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
118372 GACGGATTTCGTC-GAGATGGG
1 GACGGATTTCGCCGGAGATGGG
118393 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.19, C:0.16, G:0.44, T:0.21
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:118601 original size:20 final size:20
Alignment explanation
Indices: 118576--118614 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
118566 ATTATGTATT
118576 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
118596 AATCGCGTTGCGAAAGTCA
1 AATCGCGTTGCGAAAGTCA
118615 TTCGTTGCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.21, G:0.28, T:0.21
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:118658 original size:20 final size:20
Alignment explanation
Indices: 118633--118683 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
118623 GATTTTGTAT
118633 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
118653 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
118673 TATCGCATTGC
1 TATCGCATTGC
118684 AATTTTCCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:118658 original size:57 final size:58
Alignment explanation
Indices: 118561--118671 Score: 152
Period size: 57 Copynumber: 1.9 Consensus size: 58
118551 GAAAATCGCA
* * *
118561 TTGCGATTATGTATTAATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCATTCG
1 TTGCGATTATGTATTAATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCATTCG
* * * *
118619 TTGCGATTTTGTATT-ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCA
1 TTGCGATTATGTATTAATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCA
118672 GTATCGCATT
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
57 32 0.70
58 14 0.30
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.34
Consensus pattern (58 bp):
TTGCGATTATGTATTAATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCATTCG
Found at i:119417 original size:167 final size:167
Alignment explanation
Indices: 119140--119473 Score: 652
Period size: 167 Copynumber: 2.0 Consensus size: 167
119130 GCTCACCGGT
119140 AACGGTTGATCAAGACTTAATTGTTGTTACTAGAATGCTAGATATGGACGAAATGGGCATGCATC
1 AACGGTTGATCAAGACTTAATTGTTGTTACTAGAATGCTAGATATGGACGAAATGGGCATGCATC
119205 ACATGTATAGGGCATAAAGTTATTTGCTCCATCAAACTCATATTTAATTTTTTTAGAGAAGTCTT
66 ACATGTATAGGGCATAAAGTTATTTGCTCCATCAAACTCATATTTAATTTTTTTAGAGAAGTCTT
119270 TAATTTTATTAAAATAAAAATATTTTAAATTAAAATAA
131 TAA-TTTATTAAAATAAAAATATTTTAAATTAAAATAA
119308 AACGGTTGATCAAGAC-TAATTGTTGTTACTAGAATGCTAGATATGGACGAAATGGGCATGCATC
1 AACGGTTGATCAAGACTTAATTGTTGTTACTAGAATGCTAGATATGGACGAAATGGGCATGCATC
119372 ACATGTATAGGGCATAAAGTTATTTGCTCCATCAAACTCATATTTAATTTTTTTAGAGAAGTCTT
66 ACATGTATAGGGCATAAAGTTATTTGCTCCATCAAACTCATATTTAATTTTTTTAGAGAAGTCTT
119437 TAATTTATTAAAATAAAAATATTTTAAATTAAAATAA
131 TAATTTATTAAAATAAAAATATTTTAAATTAAAATAA
119474 GATTTACAAT
Statistics
Matches: 166, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
166 34 0.20
167 116 0.70
168 16 0.10
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (167 bp):
AACGGTTGATCAAGACTTAATTGTTGTTACTAGAATGCTAGATATGGACGAAATGGGCATGCATC
ACATGTATAGGGCATAAAGTTATTTGCTCCATCAAACTCATATTTAATTTTTTTAGAGAAGTCTT
TAATTTATTAAAATAAAAATATTTTAAATTAAAATAA
Found at i:121649 original size:7 final size:7
Alignment explanation
Indices: 121637--121701 Score: 130
Period size: 7 Copynumber: 9.3 Consensus size: 7
121627 GTTGATTAGA
121637 TCATCTT
1 TCATCTT
121644 TCATCTT
1 TCATCTT
121651 TCATCTT
1 TCATCTT
121658 TCATCTT
1 TCATCTT
121665 TCATCTT
1 TCATCTT
121672 TCATCTT
1 TCATCTT
121679 TCATCTT
1 TCATCTT
121686 TCATCTT
1 TCATCTT
121693 TCATCTT
1 TCATCTT
121700 TC
1 TC
121702 CACTGTCATT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 58 1.00
ACGTcount: A:0.14, C:0.29, G:0.00, T:0.57
Consensus pattern (7 bp):
TCATCTT
Found at i:123934 original size:58 final size:57
Alignment explanation
Indices: 123867--123983 Score: 209
Period size: 58 Copynumber: 2.0 Consensus size: 57
123857 AAATCAATAT
123867 ATGTCAAATATATATTCTATAATCCATAACTTTTTAAAAAAAAT-AATTGAATTATCTG
1 ATGTCAAATATATATTCTATAATCCATAAC-TTTTAAAAAAAATAAATTGAA-TATCTG
123925 ATGTCAAATATATATTCTATAATCCATAACTTTTAAAAAAAATAAATTGAATATCTG
1 ATGTCAAATATATATTCTATAATCCATAACTTTTAAAAAAAATAAATTGAATATCTG
123982 AT
1 AT
123984 CACAATGTAG
Statistics
Matches: 58, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
57 21 0.36
58 37 0.64
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.38
Consensus pattern (57 bp):
ATGTCAAATATATATTCTATAATCCATAACTTTTAAAAAAAATAAATTGAATATCTG
Found at i:124252 original size:25 final size:25
Alignment explanation
Indices: 124220--124271 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
124210 TTGTAAAATA
124220 ATCATTAAATTTTTAATTTATTTTC
1 ATCATTAAATTTTTAATTTATTTTC
124245 ATCATTAAATTTTTAATTTATTTTC
1 ATCATTAAATTTTTAATTTATTTTC
124270 AT
1 AT
124272 TTTAATTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.60
Consensus pattern (25 bp):
ATCATTAAATTTTTAATTTATTTTC
Found at i:125674 original size:2 final size:2
Alignment explanation
Indices: 125669--125701 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
125659 ACACACAAAC
125669 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
125702 AACGGTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:126326 original size:15 final size:16
Alignment explanation
Indices: 126297--126328 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
126287 TGTATTTAAT
126297 TTATTTAAGTATTTAC
1 TTATTTAAGTATTTAC
126313 TTATTTAA-TATTTAC
1 TTATTTAAGTATTTAC
126328 T
1 T
126329 AATATAATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.59
Consensus pattern (16 bp):
TTATTTAAGTATTTAC
Found at i:128403 original size:3 final size:3
Alignment explanation
Indices: 128388--128434 Score: 58
Period size: 3 Copynumber: 15.7 Consensus size: 3
128378 ATCTGCTCAG
* * * *
128388 GAC GAC GAT GAC GAC GAC GGC GAC GGC GAC GAT GAC GAC GAC GAC GA
1 GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GA
128435 TGGTGATGAT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.30, C:0.28, G:0.38, T:0.04
Consensus pattern (3 bp):
GAC
Found at i:138599 original size:44 final size:42
Alignment explanation
Indices: 138545--138647 Score: 118
Period size: 46 Copynumber: 2.4 Consensus size: 42
138535 GAACCCATTG
*
138545 GGGGTATCGATTCCCTCAATGAGGGAATCAGTTCCCATTCAAAA
1 GGGGTATCGATTCCCTCAAAGAGGGAATCAGTTCCCATTC--AA
* * * *
138589 GGGGAATCGATTCCCATTCAAAGGGGGAATCGGTTCCCCTTCAA
1 GGGGTATCGATTCCC--TCAAAGAGGGAATCAGTTCCCATTCAA
138633 -GGGTATCGATTCCCT
1 GGGGTATCGATTCCCT
138648 ATGCTCTATA
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
41 1 0.02
43 13 0.25
44 16 0.31
46 21 0.41
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.25
Consensus pattern (42 bp):
GGGGTATCGATTCCCTCAAAGAGGGAATCAGTTCCCATTCAA
Found at i:138645 original size:20 final size:22
Alignment explanation
Indices: 138545--138646 Score: 88
Period size: 23 Copynumber: 4.7 Consensus size: 22
138535 GAACCCATTG
* *
138545 GGGGTATCGATTCCC--TCAAT
1 GGGGAATCGATTCCCATTCAAA
138565 GAGGGAATC-AGTTCCCATTCAAAA
1 G-GGGAATCGA-TTCCCATTC-AAA
138589 GGGGAATCGATTCCCATTCAAA
1 GGGGAATCGATTCCCATTCAAA
* *
138611 GGGGGAATCGGTTCCCCTTC-AA
1 -GGGGAATCGATTCCCATTCAAA
*
138633 -GGGTATCGATTCCC
1 GGGGAATCGATTCCC
138647 TATGCTCTAT
Statistics
Matches: 69, Mismatches: 6, Indels: 14
0.78 0.07 0.16
Matches are distributed among these distances:
20 14 0.20
21 11 0.16
22 5 0.07
23 35 0.51
24 4 0.06
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (22 bp):
GGGGAATCGATTCCCATTCAAA
Found at i:138803 original size:15 final size:15
Alignment explanation
Indices: 138783--138815 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
138773 TATATTTGAA
138783 CATAAAGTTAATTTT
1 CATAAAGTTAATTTT
138798 CATAAAGTTAATTTT
1 CATAAAGTTAATTTT
138813 CAT
1 CAT
138816 TAAGAATCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.45
Consensus pattern (15 bp):
CATAAAGTTAATTTT
Found at i:140863 original size:21 final size:21
Alignment explanation
Indices: 140837--140888 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
140827 ATTGCATTTC
*
140837 GCGTTGCGATAGTTGAAAATT
1 GCGTTGCGATAGTTGAAAATA
*
140858 GCGTTGTGATAGTTGAAAATA
1 GCGTTGCGATAGTTGAAAATA
140879 GCGTTGCGAT
1 GCGTTGCGAT
140889 TTTCCATTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.27, C:0.10, G:0.31, T:0.33
Consensus pattern (21 bp):
GCGTTGCGATAGTTGAAAATA
Found at i:140904 original size:20 final size:20
Alignment explanation
Indices: 140879--140928 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
140869 GTTGAAAATA
140879 GCGTTGCGATTTTCCATTTC
1 GCGTTGCGATTTTCCATTTC
140899 GCGTTGCGATTTTCCATTTC
1 GCGTTGCGATTTTCCATTTC
140919 GCGTTGCGAT
1 GCGTTGCGAT
140929 AGTCCAAGTT
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:0.10, C:0.24, G:0.24, T:0.42
Consensus pattern (20 bp):
GCGTTGCGATTTTCCATTTC
Found at i:140934 original size:20 final size:20
Alignment explanation
Indices: 140879--140952 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
140869 GTTGAAAATA
**
140879 GCGTTGCGATTTTCCATTTC
1 GCGTTGCGATAGTCCATTTC
**
140899 GCGTTGCGATTTTCCATTTC
1 GCGTTGCGATAGTCCATTTC
*
140919 GCGTTGCGATAGTCCAAGTT-
1 GCGTTGCGATAGTCC-ATTTC
140939 GTCGTTGCGATAGT
1 G-CGTTGCGATAGT
140953 TTCCAAATTC
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
20 34 0.69
21 15 0.31
ACGTcount: A:0.14, C:0.22, G:0.26, T:0.39
Consensus pattern (20 bp):
GCGTTGCGATAGTCCATTTC
Found at i:140946 original size:21 final size:19
Alignment explanation
Indices: 140920--141014 Score: 73
Period size: 21 Copynumber: 4.6 Consensus size: 19
140910 TTCCATTTCG
*
140920 CGTTGCGATAGTCCAAGTTGT
1 CGTTGCGATAGTCCAA-AT-T
140941 CGTTGCGATAGTTTCCAAATT
1 CGTTGCGATAG--TCCAAATT
**
140962 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTC--CAAAT-T
* **
140984 CATTGCGATTTTCCAAATT
1 CGTTGCGATAGTCCAAATT
141003 CGTTGCGATAGT
1 CGTTGCGATAGT
141015 AAAAAAGATA
Statistics
Matches: 58, Mismatches: 11, Indels: 12
0.72 0.14 0.15
Matches are distributed among these distances:
19 12 0.21
20 3 0.05
21 26 0.45
22 12 0.21
23 5 0.09
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (19 bp):
CGTTGCGATAGTCCAAATT
Found at i:140970 original size:42 final size:41
Alignment explanation
Indices: 140902--141014 Score: 149
Period size: 41 Copynumber: 2.7 Consensus size: 41
140892 CCATTTCGCG
* *
140902 TTGCGATTTTCC-ATTTCGCGTTGCGATAGTCCA-AGTTGTCG
1 TTGCGATTTTCCAAATT--CGTTGCGATAGTCCACAGTTGTCA
*
140943 TTGCGATAGTTTCCAAATTCGTTGCGATAGTCTACAGTTGTCA
1 TTGCGAT--TTTCCAAATTCGTTGCGATAGTCCACAGTTGTCA
140986 TTGCGATTTTCCAAATTCGTTGCGATAGT
1 TTGCGATTTTCCAAATTCGTTGCGATAGT
141015 AAAAAAGATA
Statistics
Matches: 65, Mismatches: 3, Indels: 8
0.86 0.04 0.11
Matches are distributed among these distances:
41 29 0.45
42 14 0.22
43 19 0.29
44 3 0.05
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.39
Consensus pattern (41 bp):
TTGCGATTTTCCAAATTCGTTGCGATAGTCCACAGTTGTCA
Found at i:142094 original size:13 final size:13
Alignment explanation
Indices: 142076--142111 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
142066 TTAACTATCA
142076 CAACGAATTTTCG
1 CAACGAATTTTCG
142089 CAACGAATTTTCG
1 CAACGAATTTTCG
142102 CAACGAATTT
1 CAACGAATTT
142112 GGAAAATCGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (13 bp):
CAACGAATTTTCG
Found at i:146272 original size:2 final size:2
Alignment explanation
Indices: 146224--146258 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
146214 AATTAAATTG
146224 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
146259 GGATTAGGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:146889 original size:21 final size:21
Alignment explanation
Indices: 146829--146877 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
146819 CTTTTTATAT
*
146829 TCAAACCTCAAAC-CTTAAATC
1 TCAAACCACAAACTC-TAAATC
146850 TCAAACCACAAACTCTAAATC
1 TCAAACCACAAACTCTAAATC
146871 TCAAACC
1 TCAAACC
146878 CTAGACCATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 25 0.96
22 1 0.04
ACGTcount: A:0.45, C:0.35, G:0.00, T:0.20
Consensus pattern (21 bp):
TCAAACCACAAACTCTAAATC
Found at i:153509 original size:31 final size:31
Alignment explanation
Indices: 153468--153540 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
153458 AAAACTAATG
153468 AATTGGTCACTAACATTATTGATGTATAAAA
1 AATTGGTCACTAACATTATTGATGTATAAAA
* * * * *
153499 AATTGATCACTAACATTTTTTATTTATAACA
1 AATTGGTCACTAACATTATTGATGTATAAAA
153530 AATTGGTCACT
1 AATTGGTCACT
153541 CAACGTTAAC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (31 bp):
AATTGGTCACTAACATTATTGATGTATAAAA
Found at i:159177 original size:31 final size:30
Alignment explanation
Indices: 159137--159241 Score: 104
Period size: 31 Copynumber: 3.4 Consensus size: 30
159127 ATAAATTTTC
* * *
159137 ATAATTTTAAGGACTATTTTATAATAATTTG
1 ATAAGTTTAATGACTATTTTGTAAT-ATTTG
* * *
159168 ATAAGTTTAATTACTATGTTGTAACTGTTTG
1 ATAAGTTTAATGACTATTTTGTAA-TATTTG
159199 ATAAAGTTTAATGACTATTTTGTAATTATTTG
1 AT-AAGTTTAATGACTATTTTGTAA-TATTTG
159231 A-AGAGTTTAAT
1 ATA-AGTTTAAT
159242 AATCATTTTA
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
30 1 0.02
31 33 0.54
32 27 0.44
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.48
Consensus pattern (30 bp):
ATAAGTTTAATGACTATTTTGTAATATTTG
Found at i:159216 original size:32 final size:32
Alignment explanation
Indices: 159163--159241 Score: 99
Period size: 32 Copynumber: 2.5 Consensus size: 32
159153 TTTTATAATA
*
159163 ATTTGAT-AAGTTTAATTACTATGTTGTAACT
1 ATTTGATAAAGTTTAATGACTATGTTGTAACT
* * *
159194 GTTTGATAAAGTTTAATGACTATTTTGTAATT
1 ATTTGATAAAGTTTAATGACTATGTTGTAACT
*
159226 ATTTGA-AGAGTTTAAT
1 ATTTGATAAAGTTTAAT
159242 AATCATTTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
31 15 0.37
32 26 0.63
ACGTcount: A:0.33, C:0.04, G:0.15, T:0.48
Consensus pattern (32 bp):
ATTTGATAAAGTTTAATGACTATGTTGTAACT
Found at i:169132 original size:22 final size:22
Alignment explanation
Indices: 169094--169137 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
169084 TCTCTCGTTT
*
169094 CCTTGTTTATCTATTTCTTTTC
1 CCTTGTTTATCTATTTCATTTC
*
169116 CCTTGTTTTTC-ATTTTCATTTC
1 CCTTGTTTATCTA-TTTCATTTC
169138 TTCAATTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.09, C:0.23, G:0.05, T:0.64
Consensus pattern (22 bp):
CCTTGTTTATCTATTTCATTTC
Found at i:179661 original size:20 final size:20
Alignment explanation
Indices: 179638--179689 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
179628 CTTTTGCATG
179638 AGTATCGATACTCTTGGGCT
1 AGTATCGATACTCTTGGGCT
179658 AGTATCGATACTCTTGGGCT
1 AGTATCGATACTCTTGGGCT
179678 AGTATCGATACT
1 AGTATCGATACT
179690 TTCAGTCTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (20 bp):
AGTATCGATACTCTTGGGCT
Found at i:180669 original size:20 final size:21
Alignment explanation
Indices: 180644--180682 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
180634 AGCGGTGCTT
180644 TAAAAAA-GCCGCTATAGAAC
1 TAAAAAACGCCGCTATAGAAC
*
180664 TAAAAAACGCTGCTATAGA
1 TAAAAAACGCCGCTATAGA
180683 CCTATTCTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.49, C:0.18, G:0.15, T:0.18
Consensus pattern (21 bp):
TAAAAAACGCCGCTATAGAAC
Found at i:182487 original size:3 final size:3
Alignment explanation
Indices: 182481--182587 Score: 81
Period size: 3 Copynumber: 35.0 Consensus size: 3
182471 TTCATTTAAA
** * * * *
182481 ATT ATT ATT ATT AAA ATT ATT AGT ATT AGT ATT ATT ATT AGT ATT AGT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * *
182529 ATTT ATT A-T AAT AAT AAT AAT AAT ATT ATT ATTT ATT ATT ATT ATAT
1 A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT AT-T
182576 ATT ATT ATT ATT
1 ATT ATT ATT ATT
182588 TTAATAAATA
Statistics
Matches: 87, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
2 2 0.02
3 77 0.89
4 8 0.09
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (3 bp):
ATT
Found at i:182496 original size:15 final size:15
Alignment explanation
Indices: 182476--182520 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
182466 TTTTTTTCAT
182476 TTAAAATTATTATTA
1 TTAAAATTATTATTA
*
182491 TTAAAATTATTAGTA
1 TTAAAATTATTATTA
**
182506 TTAGTATTATTATTA
1 TTAAAATTATTATTA
182521 GTATTAGTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.53
Consensus pattern (15 bp):
TTAAAATTATTATTA
Found at i:184152 original size:23 final size:24
Alignment explanation
Indices: 184128--184172 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
184118 ATATTATATA
184128 AAATTATAAT-TTAAT-TTTATTT
1 AAATTATAATATTAATATTTATTT
*
184150 AAATTATTATATTAATATTTATT
1 AAATTATAATATTAATATTTATT
184173 AATATCGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 5 0.25
24 6 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
AAATTATAATATTAATATTTATTT
Found at i:184174 original size:23 final size:22
Alignment explanation
Indices: 184117--184174 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 22
184107 TGGTATTTTA
*
184117 AATATTATATAAAATTATAATTT
1 AATATT-TATTAAATTATAATTT
*
184140 AAT-TTTATTTAAATTATTATATT
1 AATATTTA-TTAAATTATAAT-TT
184163 AATATTTATTAA
1 AATATTTATTAA
184175 TATCGAAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
21 2 0.07
22 12 0.40
23 12 0.40
24 4 0.13
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
AATATTTATTAAATTATAATTT
Found at i:184265 original size:112 final size:112
Alignment explanation
Indices: 184035--184269 Score: 246
Period size: 112 Copynumber: 2.1 Consensus size: 112
184025 ATTTTTTTTC
* * * * *
184035 ATAAATTATTTTAATATTTATTTTTCAATATCGAGGAAAATGGCAGTCTTAATACAACTAGATGT
1 ATAAATTATTATAATATATATTTTTCAATATCGAAGAAAATGGCAGTCTTAAGACAACTAGAAGT
* * *
184100 CCTATTCTGGTATTTTAAATATTATATAAAATTATAATTTAATTTTAT
66 CCTATTCTGATATTTTAAATA-TATATAAAATTATAATTTAAATATAT
* * * *
184148 TTAAATTATTATATTA-ATATTTATT-AATATCGAAGAAAA-GAGCTGTCTTAAGACACCTAGAA
1 ATAAATTATTATAATATATATTT-TTCAATATCGAAGAAAATG-GCAGTCTTAAGACAACTAGAA
* * *
184210 GTCCTTTTCTGATATTTCTAAATA-A-ATAAACATTTTATTTATAAATATAT
64 GTCCTATTCTGATATTT-TAAATATATATAAA-ATTATAATT-TAAATATAT
184260 ATAAATTATT
1 ATAAATTATT
184270 TTTTTCTCAT
Statistics
Matches: 101, Mismatches: 16, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
110 5 0.05
111 9 0.09
112 66 0.65
113 21 0.21
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.43
Consensus pattern (112 bp):
ATAAATTATTATAATATATATTTTTCAATATCGAAGAAAATGGCAGTCTTAAGACAACTAGAAGT
CCTATTCTGATATTTTAAATATATATAAAATTATAATTTAAATATAT
Found at i:184764 original size:17 final size:18
Alignment explanation
Indices: 184742--184780 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
184732 CTTTTCAAAT
184742 TTTTTATA-TATTTAT-TA
1 TTTTTATAGT-TTTATATA
184759 TTTTTATAGTTTTATATA
1 TTTTTATAGTTTTATATA
184777 TTTT
1 TTTT
184781 CTTATTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (18 bp):
TTTTTATAGTTTTATATA
Found at i:189128 original size:2 final size:2
Alignment explanation
Indices: 189121--189226 Score: 212
Period size: 2 Copynumber: 53.0 Consensus size: 2
189111 TTATCCTTTA
189121 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
189163 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
189205 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
189227 CCTTTGTTGT
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 104 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:191988 original size:92 final size:92
Alignment explanation
Indices: 191831--192172 Score: 605
Period size: 92 Copynumber: 3.7 Consensus size: 92
191821 AAATAAGGAG
* * *
191831 GCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAAC
1 GCTCATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATATGATTTGGTATGAACCACAGAAC
191896 CAGTTATTGAATTTGGAAGAGGAATGT
66 CAGTTATTGAATTTGGAAGAGGAATGT
191923 GCTCATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATATGATTTGGTATGAACCACAGAAC
1 GCTCATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATATGATTTGGTATGAACCACAGAAC
191988 CAGTTATTGAATTTGGAAGAGGAATGT
66 CAGTTATTGAATTTGGAAGAGGAATGT
192015 GCTCATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATATGATTTGGTATGAACCACAGAAC
1 GCTCATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATATGATTTGGTATGAACCACAGAAC
192080 CAGTTATTGAATTTGGAAGAGGAATGT
66 CAGTTATTGAATTTGGAAGAGGAATGT
* * * *
192107 GC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATGATTCGGTAGGAACCCCAGAA
1 GCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATATGATTTGGTATGAACCACAGAA
192171 CC
65 CC
192173 GATCATTGGA
Statistics
Matches: 242, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
91 1 0.00
92 241 1.00
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (92 bp):
GCTCATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATATGATTTGGTATGAACCACAGAAC
CAGTTATTGAATTTGGAAGAGGAATGT
Found at i:194753 original size:22 final size:23
Alignment explanation
Indices: 194701--194754 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
194691 CTACACTCTT
** *
194701 CAAAGATGATGGATTCTCTTTTT
1 CAAAGATGACAGATTCTCTTTTC
*
194724 AAAAGATGACAGATTCTC-TTTC
1 CAAAGATGACAGATTCTCTTTTC
194746 CAAAGATGA
1 CAAAGATGA
194755 AAATTTTATG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 11 0.42
23 15 0.58
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (23 bp):
CAAAGATGACAGATTCTCTTTTC
Found at i:195513 original size:76 final size:76
Alignment explanation
Indices: 195431--195918 Score: 904
Period size: 76 Copynumber: 6.4 Consensus size: 76
195421 CTATTTCCCC
195431 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
195496 ATCCTTCGGGT
66 ATCCTTCGGGT
*
195507 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTAATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
*
195572 AAACCTTCGGGT
65 AATCCTTCGGGT
* *
195584 CATCTGTAAGTCCTCCAGTGCATGATGTCTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
195649 ATCCTTCGGGT
66 ATCCTTCGGGT
195660 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
195725 ATCCTTCGGGT
66 ATCCTTCGGGT
195736 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
195801 AATCCTTCGGGT
65 AATCCTTCGGGT
195813 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
195878 AGCCTTCGGGT
66 ATCCTTCGGGT
*
195889 CATCTGTAAGTCGTTCAGTGCATGATGTTT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTT
195919 TCAACATTTC
Statistics
Matches: 400, Mismatches: 10, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
76 252 0.63
77 148 0.37
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
ATCCTTCGGGT
Found at i:195609 original size:153 final size:152
Alignment explanation
Indices: 195431--195918 Score: 904
Period size: 153 Copynumber: 3.2 Consensus size: 152
195421 CTATTTCCCC
195431 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
195496 ATCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 ATCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
*
195561 AATGTTTTCAAAAACCTTCGGGT
131 GATGTTTTC-AAAACCTTCGGGT
* *
195584 CATCTGTAAGTCCTCCAGTGCATGATGTCTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
195649 ATCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 ATCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
*
195714 GATGTTTTCAAATCCTTCGGGT
131 GATGTTTTCAAAACCTTCGGGT
195736 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
195801 AATCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
65 AATCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
*
195866 TGATGTTTTCAAAGCCTTCGGGT
130 TGATGTTTTCAAAACCTTCGGGT
*
195889 CATCTGTAAGTCGTTCAGTGCATGATGTTT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTT
195919 TCAACATTTC
Statistics
Matches: 326, Mismatches: 8, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
152 73 0.22
153 253 0.78
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (152 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
ATCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
GATGTTTTCAAAACCTTCGGGT
Found at i:195834 original size:229 final size:229
Alignment explanation
Indices: 195431--195918 Score: 922
Period size: 229 Copynumber: 2.1 Consensus size: 229
195421 CTATTTCCCC
195431 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
195496 ATCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 ATCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
195561 AATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTCCAGTGCATGATGTCTCCAAAAAGCCTT
131 AATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTCCAGTGCATGATGTCTCCAAAAAGCCTT
*
195626 CGGGAGCTTTTTGATGTTTTCAAATCCTTCGGGT
196 CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
195660 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
195725 ATCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 ATCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
* * * *
195790 GATGTTTTCAAAATCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
131 AATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTCCAGTGCATGATGTCTCCAAAAAGCCTT
195855 CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
196 CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
*
195889 CATCTGTAAGTCGTTCAGTGCATGATGTTT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTT
195919 TCAACATTTC
Statistics
Matches: 253, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
229 253 1.00
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (229 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
ATCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
AATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTCCAGTGCATGATGTCTCCAAAAAGCCTT
CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
Found at i:196056 original size:3 final size:3
Alignment explanation
Indices: 196050--196159 Score: 116
Period size: 3 Copynumber: 36.3 Consensus size: 3
196040 TTCATTTAAA
** * * *
196050 ATT ATT ATT AAA ATT ATT A-T AGT A-T ATT ATT AGT ATT AGT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
196096 ATT ATT ATA ATA ATAT ATT ATT ATT ATT ATT ATT ATT ATT ATT AATT
1 ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT
196143 ATAT ATT ATT ATT ATT A
1 AT-T ATT ATT ATT ATT A
196160 ATAAATAATT
Statistics
Matches: 92, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
2 4 0.04
3 80 0.87
4 8 0.09
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:196093 original size:34 final size:34
Alignment explanation
Indices: 196050--196159 Score: 132
Period size: 34 Copynumber: 3.2 Consensus size: 34
196040 TTCATTTAAA
** *
196050 ATTATTATTAAAATTATTATAGT-ATATTATTAGT
1 ATTATTATTATTATTATTATAATAATA-TATTAGT
* *
196084 ATTAGTATTATTATTATTATAATAATATATTATT
1 ATTATTATTATTATTATTATAATAATATATTAGT
* *
196118 ATTATTATTATTATTATTATTAATTATATATTATT
1 ATTATTATTATTATTATTA-TAATAATATATTAGT
196153 ATTATTA
1 ATTATTA
196160 ATAAATAATT
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
34 43 0.64
35 24 0.36
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (34 bp):
ATTATTATTATTATTATTATAATAATATATTAGT
Found at i:196103 original size:37 final size:36
Alignment explanation
Indices: 196052--196156 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 36
196042 CATTTAAAAT
**
196052 TATTATTAAAATTATTATAGTATATTATTAGTATTAG
1 TATTATTATTATTATTATA-TATATTATTAGTATTAG
* * *
196089 TATTATTATTATTATAATAATATATTATTATTATTAT
1 TATTATTATTATTATTAT-ATATATTATTAGTATTAG
196126 TATTATTATTATTAATTATATATTATTATTA
1 TATTATTATTATT-ATTATATA-TATTATTA
196157 TTAATAAATA
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
37 46 0.78
38 13 0.22
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (36 bp):
TATTATTATTATTATTATATATATTATTAGTATTAG
Found at i:197718 original size:23 final size:24
Alignment explanation
Indices: 197694--197738 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
197684 ATATTATATA
197694 AAATTATAAT-TTAAT-TTTATTT
1 AAATTATAATATTAATATTTATTT
*
197716 AAATTATTATATTAATATTTATT
1 AAATTATAATATTAATATTTATT
197739 AATATCGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 5 0.25
24 6 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
AAATTATAATATTAATATTTATTT
Found at i:197740 original size:23 final size:22
Alignment explanation
Indices: 197683--197740 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 22
197673 TGGTATTTTA
*
197683 AATATTATATAAAATTATAATTT
1 AATATT-TATTAAATTATAATTT
*
197706 AAT-TTTATTTAAATTATTATATT
1 AATATTTA-TTAAATTATAAT-TT
197729 AATATTTATTAA
1 AATATTTATTAA
197741 TATCGAAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
21 2 0.07
22 12 0.40
23 12 0.40
24 4 0.13
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
AATATTTATTAAATTATAATTT
Found at i:197831 original size:112 final size:112
Alignment explanation
Indices: 197601--197835 Score: 244
Period size: 112 Copynumber: 2.1 Consensus size: 112
197591 TATTTTTTTC
* * * * * *
197601 ATAAATTATTTTAATATTTATTTTTCAATATCGAGGAAAAGGGCAGTCTTAATACAACTAGATGT
1 ATAAATTATTATAATATATATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAGACAACTAGAAGT
* * *
197666 CCTATTCTGGTATTTTAAATATTATATAAAATTATAATTTAATTTTAT
66 CCTATTCTGATATTTTAAATA-TATATAAAATTATAATTTAAATATAT
* * * *
197714 TTAAATTATTATATTA-ATATTTATT-AATATCGAAGAAAAGAGCTGTCTTAAGACACCTAGAAG
1 ATAAATTATTATAATATATATTT-TTCAATATCGAAGAAAAGAGCAGTCTTAAGACAACTAGAAG
* * * *
197777 TCCTTTTTTGATATTTCTAAATA-A-ATAAACATTTTATTTATAAATATAT
65 TCCTATTCTGATATTT-TAAATATATATAAA-ATTATAATT-TAAATATAT
197826 ATAAATTATT
1 ATAAATTATT
197836 TTTTTCTCAT
Statistics
Matches: 100, Mismatches: 18, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
110 5 0.05
111 8 0.08
112 66 0.66
113 21 0.21
ACGTcount: A:0.40, C:0.08, G:0.09, T:0.43
Consensus pattern (112 bp):
ATAAATTATTATAATATATATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAGACAACTAGAAGT
CCTATTCTGATATTTTAAATATATATAAAATTATAATTTAAATATAT
Found at i:198833 original size:26 final size:27
Alignment explanation
Indices: 198796--198846 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
198786 ATCTGGTGAT
198796 TTTAAAATTTATT-T-TTTAAAAAATA
1 TTTAAAATTTATTATATTTAAAAAATA
198821 TTTAAAATATTATTATATTTAAAAAA
1 TTTAAAAT-TTATTATATTTAAAAAA
198847 CCATAATTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 8 0.35
26 5 0.22
27 1 0.04
28 9 0.39
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
TTTAAAATTTATTATATTTAAAAAATA
Found at i:204227 original size:18 final size:18
Alignment explanation
Indices: 204204--204249 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
204194 AAATTGTCCT
*
204204 TATTATATATTTGTATAA
1 TATTATATATTTGTAAAA
*
204222 TATTATA-AATTGTAAAA
1 TATTATATATTTGTAAAA
204239 TATT-TATATTT
1 TATTATATATTT
204250 TCTTTAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 2 0.08
17 15 0.62
18 7 0.29
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (18 bp):
TATTATATATTTGTAAAA
Found at i:218328 original size:22 final size:22
Alignment explanation
Indices: 218302--218356 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
218292 CAAAGGGAAT
*
218302 CGATTCCCCTCCAAGGGGGTAC
1 CGATTCCCCTCCAAGGAGGTAC
*
218324 CGATTCCCCAT--GAGGAGGTAC
1 CGATTCCCC-TCCAAGGAGGTAC
218345 CGATT-CCCTCCA
1 CGATTCCCCTCCA
218357 CGCTCCAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
19 1 0.04
20 3 0.11
21 13 0.48
22 9 0.33
23 1 0.04
ACGTcount: A:0.20, C:0.36, G:0.24, T:0.20
Consensus pattern (22 bp):
CGATTCCCCTCCAAGGAGGTAC
Found at i:218502 original size:17 final size:16
Alignment explanation
Indices: 218476--218508 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
218466 AGCCATTGAT
218476 CAATAACAAGAATCAA
1 CAATAACAAGAATCAA
218492 CAATCAACAAGAATCAA
1 CAAT-AACAAGAATCAA
218509 GAGAGAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.61, C:0.21, G:0.06, T:0.12
Consensus pattern (16 bp):
CAATAACAAGAATCAA
Found at i:220926 original size:2 final size:2
Alignment explanation
Indices: 220919--220946 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
220909 CATCGTTAGG
220919 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
220947 GACTGAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:222380 original size:30 final size:31
Alignment explanation
Indices: 222312--222387 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 31
222302 ATGTCACTGT
* * **
222312 AGTGAACAAATCTTAATTATAACGAAACGAA
1 AGTGACCAAATCTTAACTATAAAAAAACGAA
* *
222343 AGAGACCAAATCTTAACTA-AAAAAAATGAA
1 AGTGACCAAATCTTAACTATAAAAAAACGAA
222373 AGTGACCAAATCTTA
1 AGTGACCAAATCTTA
222388 TGTTTTTTAA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 22 0.58
31 16 0.42
ACGTcount: A:0.53, C:0.14, G:0.12, T:0.21
Consensus pattern (31 bp):
AGTGACCAAATCTTAACTATAAAAAAACGAA
Found at i:223364 original size:24 final size:25
Alignment explanation
Indices: 223299--223373 Score: 82
Period size: 24 Copynumber: 3.0 Consensus size: 25
223289 GTAACAAACC
*
223299 ATACACCAAACTAACATATTATAAG
1 ATACATCAAACTAACATATTATAAG
* *
223324 TTTACAATCAAAGTAACA-ATTCATAA-
1 -ATAC-ATCAAACTAACATATT-ATAAG
223350 ATACATCAAACTAACATATTATAA
1 ATACATCAAACTAACATATTATAA
223374 TCATTCTTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
24 15 0.37
25 6 0.15
26 6 0.15
27 14 0.34
ACGTcount: A:0.52, C:0.17, G:0.03, T:0.28
Consensus pattern (25 bp):
ATACATCAAACTAACATATTATAAG
Done.