Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A10
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: 110302803
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1825971 characters in sequence are not A, C, G, or T
File 7 of 343
Found at i:2417624 original size:25 final size:26
Alignment explanation
Indices: 2417584--2417632 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
2417574 TGCATTGCAA
*
2417584 CAAAGAACCAGTAGCAGA-AAATTGAT
1 CAAAGAACCAGCAGCA-ACAAATTGAT
2417610 CAAAG-ACCAGCAGCAACAAATTG
1 CAAAGAACCAGCAGCAACAAATTG
2417633 TATAATTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 1 0.05
25 15 0.71
26 5 0.24
ACGTcount: A:0.49, C:0.20, G:0.18, T:0.12
Consensus pattern (26 bp):
CAAAGAACCAGCAGCAACAAATTGAT
Found at i:2437301 original size:30 final size:30
Alignment explanation
Indices: 2437266--2437329 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
2437256 CATATTGAAT
* *
2437266 TTTGGTGATAAAAAAAATAAAATTGAACAA
1 TTTGGTAATAAAAAAAATAAAATTAAACAA
** *
2437296 TTTGGTAATAAAAATGATAAAATTAAATAA
1 TTTGGTAATAAAAAAAATAAAATTAAACAA
2437326 TTTG
1 TTTG
2437330 ACGATAAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.53, C:0.02, G:0.12, T:0.33
Consensus pattern (30 bp):
TTTGGTAATAAAAAAAATAAAATTAAACAA
Found at i:2438818 original size:16 final size:14
Alignment explanation
Indices: 2438797--2438834 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
2438787 TAAAATAATT
2438797 TTTTTAAATTTAAATA
1 TTTTTAAATTT--ATA
2438813 TTTTTAAATTTATA
1 TTTTTAAATTTATA
2438827 TTTTTAAA
1 TTTTTAAA
2438835 AAATTTATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 11 0.50
16 11 0.50
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TTTTTAAATTTATA
Found at i:2438860 original size:33 final size:31
Alignment explanation
Indices: 2438780--2438860 Score: 76
Period size: 33 Copynumber: 2.5 Consensus size: 31
2438770 TCTCTCAATA
**
2438780 AAAATTTTAAAATA-ATTTTTTTAAATTTA-
1 AAAATTTTAAAATATATTTTTAAAAATTTAT
* *
2438809 AATATTTTTAAATTTATATTTTTAAAAAATTTAT
1 AA-AATTTTAAA-ATATATTTTT-AAAAATTTAT
2438843 AAACATTTTAAAATATAT
1 AAA-ATTTTAAAATATAT
2438861 AAAGAAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
29 2 0.05
30 8 0.20
31 2 0.05
32 6 0.15
33 13 0.32
34 9 0.22
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (31 bp):
AAAATTTTAAAATATATTTTTAAAAATTTAT
Found at i:2440407 original size:11 final size:11
Alignment explanation
Indices: 2440391--2440423 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
2440381 TATTGTTGTG
2440391 TCTGGTTTTAA
1 TCTGGTTTTAA
2440402 TCTGGTTTTAA
1 TCTGGTTTTAA
2440413 TCTGGTTTTAA
1 TCTGGTTTTAA
2440424 CTTAGGTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.18, C:0.09, G:0.18, T:0.55
Consensus pattern (11 bp):
TCTGGTTTTAA
Found at i:2442043 original size:4 final size:4
Alignment explanation
Indices: 2442034--2442059 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2442024 TATTGCAGAA
2442034 ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT AT
2442060 CAACATAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:2444744 original size:19 final size:19
Alignment explanation
Indices: 2444720--2444756 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2444710 AATATGTATG
*
2444720 AAATTAAAATGAACAAAAT
1 AAATTAAAATAAACAAAAT
*
2444739 AAATTAAATTAAACAAAA
1 AAATTAAAATAAACAAAA
2444757 CAAAATTTAA
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:0.70, C:0.05, G:0.03, T:0.22
Consensus pattern (19 bp):
AAATTAAAATAAACAAAAT
Found at i:2445423 original size:11 final size:11
Alignment explanation
Indices: 2445409--2445451 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
2445399 CGCAAATGCC
*
2445409 AACAAAATAGT
1 AACAAAATAAT
*
2445420 AACAATATAAT
1 AACAAAATAAT
*
2445431 AGCAAAATAAT
1 AACAAAATAAT
2445442 AACAAAATAA
1 AACAAAATAA
2445452 CAGGAAAATG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.67, C:0.09, G:0.05, T:0.19
Consensus pattern (11 bp):
AACAAAATAAT
Found at i:2445439 original size:22 final size:22
Alignment explanation
Indices: 2445411--2445460 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
2445401 CAAATGCCAA
* * *
2445411 CAAAATAGTAACAATATAATAG
1 CAAAATAATAACAAAATAACAG
2445433 CAAAATAATAACAAAATAACAG
1 CAAAATAATAACAAAATAACAG
*
2445455 GAAAAT
1 CAAAAT
2445461 GGCAGCAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.64, C:0.10, G:0.08, T:0.18
Consensus pattern (22 bp):
CAAAATAATAACAAAATAACAG
Found at i:2446104 original size:22 final size:22
Alignment explanation
Indices: 2446064--2446119 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
2446054 TTAAAAAATA
*
2446064 TAAATTTAAA-AGTTTTAT-AT
1 TAAATTTAAATAATTTTATAAT
*
2446084 TCAAATTTATATAATTTTATAAT
1 T-AAATTTAAATAATTTTATAAT
2446107 TAAATTTAAATAA
1 TAAATTTAAATAA
2446120 AATAATATGT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 1 0.03
21 8 0.27
22 18 0.60
23 3 0.10
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
TAAATTTAAATAATTTTATAAT
Found at i:2453292 original size:21 final size:22
Alignment explanation
Indices: 2453268--2453310 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2453258 CGGGAAACCA
2453268 AATT-AAAATTTT-AATTTAATT
1 AATTAAAAATTTTCAA-TTAATT
2453289 AATTAAAAATTTTCAATTAATT
1 AATTAAAAATTTTCAATTAATT
2453311 TACTTGTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.20
22 14 0.70
23 2 0.10
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
AATTAAAAATTTTCAATTAATT
Found at i:2454941 original size:17 final size:19
Alignment explanation
Indices: 2454921--2454964 Score: 58
Period size: 17 Copynumber: 2.4 Consensus size: 19
2454911 ACAGATGTAA
2454921 AAAAAATTATAGAAA-A-T
1 AAAAAATTATAGAAATATT
2454938 -AAAAATATATAGAAATATT
1 AAAAAAT-TATAGAAATATT
2454957 AAAAAATT
1 AAAAAATT
2454965 TAAATTCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 6 0.26
17 8 0.35
18 1 0.04
19 2 0.09
20 6 0.26
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (19 bp):
AAAAAATTATAGAAATATT
Found at i:2455830 original size:26 final size:27
Alignment explanation
Indices: 2455779--2455831 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
2455769 AAAAAAGTCA
*
2455779 TAAATATTTATCACCTTTTTGAATTTT
1 TAAATATTTATCACCTTTTTAAATTTT
**
2455806 TAAATATTT-TCATTTTTTTAAATTTT
1 TAAATATTTATCACCTTTTTAAATTTT
2455832 AATAATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.30, C:0.08, G:0.02, T:0.60
Consensus pattern (27 bp):
TAAATATTTATCACCTTTTTAAATTTT
Found at i:2457073 original size:15 final size:17
Alignment explanation
Indices: 2457044--2457086 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
2457034 TTTAACCTTT
2457044 TAAAAGTTATAAAAAT-A
1 TAAAA-TTATAAAAATAA
*
2457061 T-AAATTATTAAAATAA
1 TAAAATTATAAAAATAA
2457077 TAAAATTATA
1 TAAAATTATA
2457087 TTTTTACTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 9 0.41
16 5 0.23
17 8 0.36
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (17 bp):
TAAAATTATAAAAATAA
Found at i:2458190 original size:31 final size:30
Alignment explanation
Indices: 2458114--2458190 Score: 75
Period size: 31 Copynumber: 2.5 Consensus size: 30
2458104 TTCAAAAATA
2458114 TTGAAGGATCTAATTAAAAATTTTAAAACTT
1 TTGAAGGA-CTAATTAAAAATTTTAAAACTT
* * **
2458145 TTGAATGG-CTTAATTAGACATTTTAAATTTT
1 TTGAA-GGAC-TAATTAAAAATTTTAAAACTT
2458176 TTGAAGGGACTAATT
1 TTGAA-GGACTAATT
2458191 CAGATTTTCA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
30 1 0.03
31 34 0.89
32 3 0.08
ACGTcount: A:0.38, C:0.06, G:0.14, T:0.42
Consensus pattern (30 bp):
TTGAAGGACTAATTAAAAATTTTAAAACTT
Found at i:2460372 original size:35 final size:37
Alignment explanation
Indices: 2460303--2460378 Score: 102
Period size: 35 Copynumber: 2.1 Consensus size: 37
2460293 AAACAATAAA
*
2460303 AATACAATATTAAAATATATATATATAATGTATACAT
1 AATACAATATTAAAATATATATATATAATATATACAT
* **
2460340 AATATAATATTAAAATAT-T-TATATGGTATATACAT
1 AATACAATATTAAAATATATATATATAATATATACAT
2460375 AATA
1 AATA
2460379 ATGTAAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 17 0.49
36 1 0.03
37 17 0.49
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (37 bp):
AATACAATATTAAAATATATATATATAATATATACAT
Found at i:2460981 original size:40 final size:39
Alignment explanation
Indices: 2460870--2461024 Score: 238
Period size: 40 Copynumber: 3.9 Consensus size: 39
2460860 TTGATTCCAC
* * *
2460870 TCCCCCATGCTACTTTGTTTTATTATTAATTAAAACTAC
1 TCCCCCATACTATTTTGTTTTATTATTAATTAAAACTAT
*
2460909 TCCTCCATACTATTTTGTTTTATTATTAATTAAAACTAT
1 TCCCCCATACTATTTTGTTTTATTATTAATTAAAACTAT
*
2460948 TCCCCCGTACTATTTTGTTTTTATTATTAATTAAAACTAT
1 TCCCCCATACTATTTTG-TTTTATTATTAATTAAAACTAT
*
2460988 TCCCTCATACTATTTTGTTTTTATTATTAATTAAAAC
1 TCCCCCATACTATTTTG-TTTTATTATTAATTAAAAC
2461025 CATACTTTAT
Statistics
Matches: 107, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
39 50 0.47
40 57 0.53
ACGTcount: A:0.29, C:0.18, G:0.04, T:0.49
Consensus pattern (39 bp):
TCCCCCATACTATTTTGTTTTATTATTAATTAAAACTAT
Found at i:2461514 original size:22 final size:23
Alignment explanation
Indices: 2461466--2461522 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
2461456 AACCCCCTCT
**
2461466 AATACAATCTCTTCTGTCCCCAA
1 AATACAATCGATTCTGTCCCCAA
*
2461489 AATACAATCGATTCT-TCCTCAA
1 AATACAATCGATTCTGTCCCCAA
*
2461511 AATACCATCGAT
1 AATACAATCGAT
2461523 CCCCCCCTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 17 0.57
23 13 0.43
ACGTcount: A:0.35, C:0.30, G:0.05, T:0.30
Consensus pattern (23 bp):
AATACAATCGATTCTGTCCCCAA
Found at i:2476412 original size:41 final size:41
Alignment explanation
Indices: 2476366--2476454 Score: 160
Period size: 41 Copynumber: 2.2 Consensus size: 41
2476356 TATTGATGAA
2476366 AAAATATGGGTCAATAATTAATAACGATTCACCTAAAAACT
1 AAAATATGGGTCAATAATTAATAACGATTCACCTAAAAACT
* *
2476407 AAAATATGGGTCAATAATTAATAACGATTCACCTGAAGACT
1 AAAATATGGGTCAATAATTAATAACGATTCACCTAAAAACT
2476448 AAAATAT
1 AAAATAT
2476455 AGAAATGATC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.48, C:0.13, G:0.11, T:0.27
Consensus pattern (41 bp):
AAAATATGGGTCAATAATTAATAACGATTCACCTAAAAACT
Found at i:2477108 original size:18 final size:20
Alignment explanation
Indices: 2477073--2477110 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
2477063 AGTCCACTAT
*
2477073 TTTTATTTTAGAATATTTAA
1 TTTTATTTTAGAAAATTTAA
2477093 TTTT-TTTTA-AAAATTTAA
1 TTTTATTTTAGAAAATTTAA
2477111 GTCCAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 5 0.29
20 4 0.24
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (20 bp):
TTTTATTTTAGAAAATTTAA
Found at i:2479994 original size:22 final size:23
Alignment explanation
Indices: 2479969--2480028 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 23
2479959 TATAAGAATC
2479969 AAATTA-AACATTGAAAAAAA-TT
1 AAATTACAA-ATTGAAAAAAACTT
2479991 AAA-TACTAAATTGAAAAAAACTT
1 AAATTAC-AAATTGAAAAAAACTT
*
2480014 AAA-TACAAAATGAAA
1 AAATTACAAATTGAAA
2480029 CATTGAAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
21 2 0.06
22 22 0.65
23 10 0.29
ACGTcount: A:0.65, C:0.07, G:0.05, T:0.23
Consensus pattern (23 bp):
AAATTACAAATTGAAAAAAACTT
Found at i:2480015 original size:23 final size:21
Alignment explanation
Indices: 2479978--2480028 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 21
2479968 CAAATTAAAC
2479978 ATTGAAAAAAATTAAATACTAA
1 ATTGAAAAAAATTAAATAC-AA
2480000 ATTGAAAAAAACTTAAATACAA
1 ATTGAAAAAAA-TTAAATACAA
*
2480022 AATGAAA
1 ATTGAAA
2480029 CATTGAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 19 0.70
23 8 0.30
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (21 bp):
ATTGAAAAAAATTAAATACAA
Found at i:2481177 original size:154 final size:154
Alignment explanation
Indices: 2480975--2481594 Score: 889
Period size: 154 Copynumber: 4.0 Consensus size: 154
2480965 ATATGTTTGA
* * * * *
2480975 TGTGTGAATTACATTTGTTTTTATTAAGCTTCTTGTAAACGAGTCTTGTTTTGTTATAATTCAGT
1 TGTGAGAATTACATTTATTTTGATTAAGCTTCTTATAAACGAGTCTTGTTTTTTTATAATTCAGT
*
2481040 TTACGATTCGTTTTTTCGCTTTGGTGATTTGGTAGATTGGCTGGTTTTTGGAATGTGAATTTAGT
66 TTACGATTCGTTTTTTCGCTTTGGTGATTTGGTAGATTGGCTGGTTTTTGAAATGTGAATTTAGT
2481105 GTTTTGTGTTGATTTTCAGTGAGT
131 GTTTTGTGTTGATTTTCAGTGAGT
*
2481129 TGTGAGAATTACATTTATTTTGATTAAGCTTCTTATAAACGAGGCTTGTTTTTTTATAATTCAGT
1 TGTGAGAATTACATTTATTTTGATTAAGCTTCTTATAAACGAGTCTTGTTTTTTTATAATTCAGT
* *
2481194 TTACGATTCGTTTTTTCGCTTTGGTGATTTGGTAGATTGGCTGGTTTTCGGAA--TG--TTTAGT
66 TTACGATTCGTTTTTTCGCTTTGGTGATTTGGTAGATTGGCTGGTTTTTGAAATGTGAATTTAGT
2481255 GTTTTGTGTTGATTTTCAGTGAGT
131 GTTTTGTGTTGATTTTCAGTGAGT
*
2481279 TGTGAGAATTACATTTATTTTGATTAAGCTTCTTATAAATGAGTCTTG-TTTTTTATAATTCAGT
1 TGTGAGAATTACATTTATTTTGATTAAGCTTCTTATAAACGAGTCTTGTTTTTTTATAATTCAGT
*
2481343 TTACGATTCGTTTTTTCGCTTTGGTGATTTGGTCGATTGGCTGGTTTTTGAAATGTGAATTTAGT
66 TTACGATTCGTTTTTTCGCTTTGGTGATTTGGTAGATTGGCTGGTTTTTGAAATGTGAATTTAGT
* * * *
2481408 GTTTTGTATTGATGTT-AGTGGGC
131 GTTTTGTGTTGATTTTCAGTGAGT
**
2481431 TGTGAGAATTACATTTCATTTTGATTAAGCTTCTTATAAACGTTTCTTGTTTTTTTATAATTCAG
1 TGTGAGAATTACATTT-ATTTTGATTAAGCTTCTTATAAACGAGTCTTGTTTTTTTATAATTCAG
* * * * * *
2481496 TTTAGGATTCAATTTTTT-GCTTTGGTTTG-TTTGGTCGATTGGCTGTTTTTTTTAAACGTGAAT
65 TTTACGATTC-GTTTTTTCGCTTTGG--TGATTTGGTAGATTGGCTG-GTTTTTGAAATGTGAAT
* * *
2481559 TGAGTGTTTCGTGTTG-TTGTTTAGTGAGT
126 TTAGTGTTTTGTGTTGATT-TTCAGTGAGT
2481588 TGTGAGA
1 TGTGAGA
2481595 TTGAGTCAAA
Statistics
Matches: 424, Mismatches: 30, Indels: 21
0.89 0.06 0.04
Matches are distributed among these distances:
149 66 0.16
150 76 0.18
151 2 0.00
152 23 0.05
153 49 0.12
154 142 0.33
155 23 0.05
156 31 0.07
157 12 0.03
ACGTcount: A:0.19, C:0.08, G:0.22, T:0.50
Consensus pattern (154 bp):
TGTGAGAATTACATTTATTTTGATTAAGCTTCTTATAAACGAGTCTTGTTTTTTTATAATTCAGT
TTACGATTCGTTTTTTCGCTTTGGTGATTTGGTAGATTGGCTGGTTTTTGAAATGTGAATTTAGT
GTTTTGTGTTGATTTTCAGTGAGT
Found at i:2486259 original size:18 final size:18
Alignment explanation
Indices: 2486213--2486263 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
2486203 TCATCTTAAC
*
2486213 TTATTTTTAT-TGTT-TG
1 TTATTTTTATATATTATG
*
2486229 TAATATTTT-TATATTATG
1 TTAT-TTTTATATATTATG
2486247 TTATTTTTATATATTAT
1 TTATTTTTATATATTAT
2486264 ATAATTTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 4 0.14
17 11 0.39
18 13 0.46
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (18 bp):
TTATTTTTATATATTATG
Found at i:2511678 original size:20 final size:20
Alignment explanation
Indices: 2511642--2511688 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
2511632 GAATCGAATT
*
2511642 TATAAAT-AATTTTTTATAC
1 TATAAATAAATCTTTTATAC
2511661 TATAAATAAATCTTTTATAC
1 TATAAATAAATCTTTTATAC
2511681 -ATAAATAA
1 TATAAATAA
2511689 TGAAAATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (20 bp):
TATAAATAAATCTTTTATAC
Found at i:2517383 original size:32 final size:32
Alignment explanation
Indices: 2517306--2517383 Score: 79
Period size: 32 Copynumber: 2.5 Consensus size: 32
2517296 AAATATGTTG
* *
2517306 TTAGT-CTCTGTA-TTTTGATAGAATTTGAGAT
1 TTAGTCCT-TGTACTTTTGATAGAATATGAAAT
* * * *
2517337 TTAATCTTTATACTTTTTATAGAATATGAAAT
1 TTAGTCCTTGTACTTTTGATAGAATATGAAAT
2517369 TTAGTCCTTGTACTT
1 TTAGTCCTTGTACTT
2517384 AAAACGTTGA
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
31 7 0.19
32 29 0.81
ACGTcount: A:0.28, C:0.09, G:0.13, T:0.50
Consensus pattern (32 bp):
TTAGTCCTTGTACTTTTGATAGAATATGAAAT
Found at i:2519496 original size:17 final size:17
Alignment explanation
Indices: 2519446--2519497 Score: 50
Period size: 20 Copynumber: 2.9 Consensus size: 17
2519436 ATATATAAAA
* *
2519446 TATAAATTTTAAATATT
1 TATAAAATTTAATTATT
*
2519463 TTTAAGTAATATTAATTATT
1 TATAA--AAT-TTAATTATT
2519483 TATAAAATTTAATTA
1 TATAAAATTTAATTA
2519498 AAATATATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
17 11 0.39
18 3 0.11
19 2 0.07
20 12 0.43
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (17 bp):
TATAAAATTTAATTATT
Found at i:2523860 original size:11 final size:11
Alignment explanation
Indices: 2523844--2523868 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2523834 ACATTTATGA
2523844 TTTTCTCTTTT
1 TTTTCTCTTTT
2523855 TTTTCTCTTTT
1 TTTTCTCTTTT
2523866 TTT
1 TTT
2523869 GTAATAGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTCTCTTTT
Found at i:2529113 original size:75 final size:75
Alignment explanation
Indices: 2529003--2529252 Score: 430
Period size: 75 Copynumber: 3.3 Consensus size: 75
2528993 CATTGTTGTA
* *
2529003 CTCATTGTTACCATTGTAATAGTTGTTGTTG-TTCTGGTTTTCCTTAGTACTCCATCCTTTCTCA
1 CTCATTGTTACCATTGTAATAGTTGTTG-CGATTCTGGTTTTCCTTAGTACTCCACCCTTTCTCA
*
2529067 GTGAACATGGC
65 GTGAACAAGGC
*
2529078 CTCATTGTTACCGTTGTAATAGTTGTTGCGATTCTGGTTTTCCTTAGTACTCCACCCTTTCTCAG
1 CTCATTGTTACCATTGTAATAGTTGTTGCGATTCTGGTTTTCCTTAGTACTCCACCCTTTCTCAG
2529143 TGAACAAGGC
66 TGAACAAGGC
* *
2529153 CTCATTGTTACCATTGTAATAGTTGTTGCTATTCTGGTTTTCCTTGGTACTCCACCCTTTCTCAG
1 CTCATTGTTACCATTGTAATAGTTGTTGCGATTCTGGTTTTCCTTAGTACTCCACCCTTTCTCAG
2529218 TGAACAAGGC
66 TGAACAAGGC
2529228 CTCATTGTTACCATTGTAATAGTTG
1 CTCATTGTTACCATTGTAATAGTTG
2529253 ACATTGTAGT
Statistics
Matches: 167, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
74 1 0.01
75 166 0.99
ACGTcount: A:0.19, C:0.22, G:0.18, T:0.41
Consensus pattern (75 bp):
CTCATTGTTACCATTGTAATAGTTGTTGCGATTCTGGTTTTCCTTAGTACTCCACCCTTTCTCAG
TGAACAAGGC
Found at i:2534951 original size:26 final size:24
Alignment explanation
Indices: 2534921--2534970 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
2534911 AAATAAAAAA
*
2534921 ATTTAAAAATATAATAAATCAAATAT
1 ATTTAAAAACATAA-AAA-CAAATAT
2534947 ATTTAAAAACATAAAAACAAATAT
1 ATTTAAAAACATAAAAACAAATAT
2534971 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (24 bp):
ATTTAAAAACATAAAAACAAATAT
Found at i:2537772 original size:3 final size:3
Alignment explanation
Indices: 2537764--2537790 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2537754 GAGAGAGATG
2537764 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
2537791 AAGGTCTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2551921 original size:23 final size:23
Alignment explanation
Indices: 2551895--2551947 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
2551885 ATAAGTGCCA
2551895 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
2551918 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
2551941 CACTGAT
1 CACTGAT
2551948 CAATAACACT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:2552047 original size:8 final size:8
Alignment explanation
Indices: 2552034--2552062 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
2552024 ACCCGGGACT
2552034 CACTGTAA
1 CACTGTAA
2552042 CACTGTAA
1 CACTGTAA
2552050 CACTGTAA
1 CACTGTAA
2552058 CACTG
1 CACTG
2552063 GTCTCTAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (8 bp):
CACTGTAA
Found at i:2552193 original size:18 final size:17
Alignment explanation
Indices: 2552167--2552205 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
2552157 ATTTTCCTTC
2552167 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
2552184 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
2552202 CACA
1 CACA
2552206 ATTTATACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:2562787 original size:21 final size:21
Alignment explanation
Indices: 2562763--2562815 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
2562753 TATGGACTCT
2562763 TTTTATTATATTATTT-ATAAA
1 TTTTATTA-ATTATTTAATAAA
* *
2562784 TTTTTTTAATTATTTAATATA
1 TTTTATTAATTATTTAATAAA
*
2562805 TTTTAGTAATT
1 TTTTATTAATT
2562816 TTTCTATGTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 7 0.26
21 20 0.74
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTTATTAATTATTTAATAAA
Found at i:2565341 original size:16 final size:16
Alignment explanation
Indices: 2565316--2565347 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2565306 TTTTTATTGC
2565316 TAAAAACTTAAAATTT
1 TAAAAACTTAAAATTT
*
2565332 TAAAACCTTAAAATTT
1 TAAAAACTTAAAATTT
2565348 CGACAAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAAAACTTAAAATTT
Found at i:2576250 original size:29 final size:30
Alignment explanation
Indices: 2576190--2576250 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
2576180 TCAACTCTTT
* *
2576190 TTTTTTAAAAGGCTGATAGTCAAATTTGAA
1 TTTTTTAAAAGACTGATAGTCAAAATTGAA
*
2576220 TTTTTTAAAAGATTGA-AGATCAAAATT-AA
1 TTTTTTAAAAGACTGATAG-TCAAAATTGAA
2576249 TT
1 TT
2576251 AAAAAAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.41, C:0.05, G:0.13, T:0.41
Consensus pattern (30 bp):
TTTTTTAAAAGACTGATAGTCAAAATTGAA
Found at i:2586361 original size:28 final size:28
Alignment explanation
Indices: 2586321--2586380 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
2586311 GTCATTATCA
2586321 ACCCCATAAGTTATAAAACCCTTCCTAT
1 ACCCCATAAGTTATAAAACCCTTCCTAT
* * **
2586349 ACCCCATAAGTTATTAGACTTTTCCTAT
1 ACCCCATAAGTTATAAAACCCTTCCTAT
2586377 ACCC
1 ACCC
2586381 ATTAATATGG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.32, G:0.05, T:0.32
Consensus pattern (28 bp):
ACCCCATAAGTTATAAAACCCTTCCTAT
Found at i:2600150 original size:17 final size:17
Alignment explanation
Indices: 2600128--2600161 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2600118 AACCGCTTCA
2600128 TTTGAACAAATCACATT
1 TTTGAACAAATCACATT
2600145 TTTGAACAAATCACATT
1 TTTGAACAAATCACATT
2600162 AATAAAAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (17 bp):
TTTGAACAAATCACATT
Found at i:2602259 original size:13 final size:13
Alignment explanation
Indices: 2602241--2602268 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2602231 ATTTAAATCT
2602241 TAATGCAAAACAA
1 TAATGCAAAACAA
2602254 TAATGCAAAACAA
1 TAATGCAAAACAA
2602267 TA
1 TA
2602269 TTCGTTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.61, C:0.14, G:0.07, T:0.18
Consensus pattern (13 bp):
TAATGCAAAACAA
Found at i:2604719 original size:11 final size:10
Alignment explanation
Indices: 2604703--2604744 Score: 57
Period size: 11 Copynumber: 4.0 Consensus size: 10
2604693 TTTTTCTCAC
2604703 AAAATTAAATA
1 AAAATTAAA-A
2604714 AAAATTATAAA
1 AAAATTA-AAA
*
2604725 AAAATTGAAA
1 AAAATTAAAA
2604735 AAAATTAAAA
1 AAAATTAAAA
2604745 TTAGTATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 12 0.43
11 14 0.50
12 2 0.07
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (10 bp):
AAAATTAAAA
Found at i:2604725 original size:9 final size:9
Alignment explanation
Indices: 2604711--2604835 Score: 55
Period size: 9 Copynumber: 13.7 Consensus size: 9
2604701 ACAAAATTAA
2604711 ATAAAAATT
1 ATAAAAATT
2604720 ATAAAAAAATT
1 AT--AAAAATT
2604731 GA-AAAAA--
1 -ATAAAAATT
*
2604738 ATTAAAATT
1 ATAAAAATT
*
2604747 AGTATAAACTT
1 A-TA-AAAATT
*
2604758 ATTAAAATT
1 ATAAAAATT
*
2604767 ATAAAAAAT
1 ATAAAAATT
*
2604776 ATAAATATT
1 ATAAAAATT
2604785 AT-AAAATCT
1 ATAAAAAT-T
*
2604794 A-ATAAATCT
1 ATAAAAAT-T
*
2604803 A-ATAAATT
1 ATAAAAATT
*
2604811 GTAAAAATAT
1 ATAAAAAT-T
*
2604821 ATAAAAATA
1 ATAAAAATT
2604830 ATAAAA
1 ATAAAA
2604836 CTTGTTTAAA
Statistics
Matches: 89, Mismatches: 15, Indels: 24
0.70 0.12 0.19
Matches are distributed among these distances:
6 1 0.01
7 4 0.04
8 5 0.06
9 55 0.62
10 10 0.11
11 13 0.15
12 1 0.01
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (9 bp):
ATAAAAATT
Found at i:2604800 original size:19 final size:19
Alignment explanation
Indices: 2604776--2604826 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 19
2604766 TATAAAAAAT
2604776 ATAAATATTATAAAATCTA
1 ATAAATATTATAAAATCTA
* * * *
2604795 ATAAATCTAATAAATTGTA
1 ATAAATATTATAAAATCTA
2604814 A-AAATA-TATAAAA
1 ATAAATATTATAAAA
2604827 ATAATAAAAC
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
17 5 0.20
18 4 0.16
19 16 0.64
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (19 bp):
ATAAATATTATAAAATCTA
Found at i:2605106 original size:32 final size:32
Alignment explanation
Indices: 2605039--2605110 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 32
2605029 AATTTTTTAT
*
2605039 TTTTTTAATATTTTTATCAAATCAAAATTAAA
1 TTTTTAAATATTTTTATCAAATCAAAATTAAA
* ** *
2605071 TTTTGTAAATATTTTTAT-ATATCTTAATTAGA
1 TTTT-TAAATATTTTTATCAAATCAAAATTAAA
2605103 TTTTTAAA
1 TTTTTAAA
2605111 CTTCTATAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
31 4 0.12
32 18 0.53
33 12 0.35
ACGTcount: A:0.39, C:0.04, G:0.03, T:0.54
Consensus pattern (32 bp):
TTTTTAAATATTTTTATCAAATCAAAATTAAA
Found at i:2606964 original size:30 final size:28
Alignment explanation
Indices: 2606929--2607010 Score: 85
Period size: 29 Copynumber: 2.8 Consensus size: 28
2606919 ATAATTTATG
2606929 AAATTTTAAATTAATAATAAAATTAT-ATTTT
1 AAATTTTAAA--AATAATAAAATT-TGA-TTT
*
2606960 AATTTTTTAAAAATAATAAAATTTGATTT
1 AA-ATTTTAAAAATAATAAAATTTGATTT
*
2606989 AAATTTTAAAAAAATATAAAAT
1 AAATTTTAAAAATA-ATAAAAT
2607011 ATAAAATATT
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
28 10 0.22
29 13 0.29
30 13 0.29
31 2 0.04
32 7 0.16
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (28 bp):
AAATTTTAAAAATAATAAAATTTGATTT
Found at i:2607023 original size:8 final size:7
Alignment explanation
Indices: 2606999--2607033 Score: 52
Period size: 7 Copynumber: 4.7 Consensus size: 7
2606989 AAATTTTAAA
2606999 AAAATAT
1 AAAATAT
2607006 AAAATAT
1 AAAATAT
2607013 AAAATATT
1 AAAATA-T
2607021 AAAATAAT
1 AAAAT-AT
2607029 AAAAT
1 AAAAT
2607034 TATATATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 13 0.50
8 12 0.46
9 1 0.04
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
AAAATAT
Found at i:2607023 original size:25 final size:24
Alignment explanation
Indices: 2606989--2607037 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
2606979 AATTTGATTT
*
2606989 AAATTTTAAAAAAATATAAAATATA
1 AAATATTAAAAAAATA-AAAATATA
* *
2607014 AAATATTAAAATAATAAAATTATA
1 AAATATTAAAAAAATAAAAATATA
2607038 TATATAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (24 bp):
AAATATTAAAAAAATAAAAATATA
Found at i:2607030 original size:16 final size:14
Alignment explanation
Indices: 2606999--2607033 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 14
2606989 AAATTTTAAA
2606999 AAAATATAAAATAT
1 AAAATATAAAATAT
2607013 AAAATATTAAAATAAT
1 AAAATA-TAAAAT-AT
2607029 AAAAT
1 AAAAT
2607034 TATATATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.32
15 6 0.32
16 7 0.37
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
AAAATATAAAATAT
Found at i:2610134 original size:19 final size:18
Alignment explanation
Indices: 2610106--2610141 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2610096 ATGCTTCACA
2610106 TTAAATCTAAACTAACAT
1 TTAAATCTAAACTAACAT
*
2610124 TTAACATCTAACCTAACA
1 TTAA-ATCTAAACTAACA
2610142 ATCAAATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (18 bp):
TTAAATCTAAACTAACAT
Found at i:2613956 original size:3 final size:3
Alignment explanation
Indices: 2613948--2613976 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2613938 ATCACATGTT
2613948 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2613977 TGGATGTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2614096 original size:73 final size:73
Alignment explanation
Indices: 2613977--2614162 Score: 363
Period size: 73 Copynumber: 2.5 Consensus size: 73
2613967 TATTATTATT
*
2613977 TGGATGTAATGATGTAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
2614042 ATTTTAAG
66 ATTTTAAG
2614050 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
2614115 ATTTTAAG
66 ATTTTAAG
2614123 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT
1 TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTT
2614163 GTCAAGTTGT
Statistics
Matches: 112, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 112 1.00
ACGTcount: A:0.28, C:0.06, G:0.25, T:0.41
Consensus pattern (73 bp):
TGGATGTAATGATGAAACTTAGTTGTATTCCAACTAAGTTTGTTAGTGGTAGTAGGTGGTGATTT
ATTTTAAG
Found at i:2637898 original size:5 final size:5
Alignment explanation
Indices: 2637888--2637913 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
2637878 AAAATTTTTA
2637888 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
2637914 TCATATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:2642089 original size:25 final size:29
Alignment explanation
Indices: 2642040--2642111 Score: 86
Period size: 25 Copynumber: 2.7 Consensus size: 29
2642030 TGTTGAGTTG
2642040 TATTTATTTTAATATTATTTAAATAAAAA
1 TATTTATTTTAATATTATTTAAATAAAAA
2642069 TATTT-TTTTAAT-TT-TTT-AAT--AAA
1 TATTTATTTTAATATTATTTAAATAAAAA
*
2642092 TATCTATTTTAATATT-TTTA
1 TATTTATTTTAATATTATTTA
2642112 GTAATTTTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
23 7 0.18
24 7 0.18
25 8 0.21
26 3 0.08
27 2 0.05
28 7 0.18
29 5 0.13
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (29 bp):
TATTTATTTTAATATTATTTAAATAAAAA
Found at i:2642101 original size:26 final size:28
Alignment explanation
Indices: 2642040--2642111 Score: 75
Period size: 24 Copynumber: 2.7 Consensus size: 28
2642030 TGTTGAGTTG
2642040 TATTTATTTTAATATTATTTAAATAAAAA
1 TATTT-TTTTAATATTATTTAAATAAAAA
2642069 TATTTTTTTAAT-TT-TTT-AAT--AAA
1 TATTTTTTTAATATTATTTAAATAAAAA
*
2642092 TATCTATTTTAATATT-TTTA
1 TAT-TTTTTTAATATTATTTA
2642112 GTAATTTTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
23 6 0.15
24 8 0.21
25 8 0.21
26 3 0.08
27 2 0.05
28 7 0.18
29 5 0.13
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (28 bp):
TATTTTTTTAATATTATTTAAATAAAAA
Found at i:2649369 original size:14 final size:14
Alignment explanation
Indices: 2649330--2649371 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
2649320 CAATTTTTTA
2649330 GTTTAGGGTTTGA-
1 GTTTAGGGTTTGAG
*
2649343 GTTTAAGGTTTTGAG
1 GTTT-AGGGTTTGAG
2649358 GTTTAGGGTTTGAG
1 GTTTAGGGTTTGAG
2649372 ATTCTGGGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 17 0.68
15 4 0.16
ACGTcount: A:0.17, C:0.00, G:0.38, T:0.45
Consensus pattern (14 bp):
GTTTAGGGTTTGAG
Found at i:2649694 original size:20 final size:20
Alignment explanation
Indices: 2649649--2649696 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
2649639 AAATTCTATT
*
2649649 TGTATTTTATAATAATTAAT
1 TGTATTTTATAATAATTAAA
*
2649669 TCTATTTT-TAATAATTTAAA
1 TGTATTTTATAATAA-TTAAA
2649689 TGTATTTT
1 TGTATTTT
2649697 CTTTAAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.58
Consensus pattern (20 bp):
TGTATTTTATAATAATTAAA
Found at i:2650721 original size:31 final size:33
Alignment explanation
Indices: 2650659--2650721 Score: 76
Period size: 34 Copynumber: 1.9 Consensus size: 33
2650649 TACTATAAAA
* *
2650659 ATTTATTATTAAACATTTATAAATTTTAATATAT
1 ATTTATTATTAAACA-TTATAAATATAAATATAT
*
2650693 ATTTATTATTAAA-A-TATGAATATAAATAT
1 ATTTATTATTAAACATTATAAATATAAATAT
2650722 TTTCAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
31 12 0.46
33 1 0.04
34 13 0.50
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (33 bp):
ATTTATTATTAAACATTATAAATATAAATATAT
Found at i:2650755 original size:12 final size:11
Alignment explanation
Indices: 2650696--2650820 Score: 55
Period size: 11 Copynumber: 11.2 Consensus size: 11
2650686 AATATATATT
2650696 TATTATTAAAA
1 TATTATTAAAA
* *
2650707 TATGAATATAAA
1 TATTATTA-AAA
2650719 TATT-TTCAAAA
1 TATTATT-AAAA
2650730 -ATATATTAAGAA
1 TAT-TATTAA-AA
2650742 TATTATTTAAAA
1 TATTA-TTAAAA
* *
2650754 TA-TAATAATAT
1 TATTATTAA-AA
* *
2650765 TATTTTTAAATTT
1 TATTATTAAA--A
2650778 TATTATTAAAA
1 TATTATTAAAA
** *
2650789 TAAAATTATAA
1 TATTATTAAAA
2650800 TATTA--AAAA
1 TATTATTAAAA
2650809 -ATTATTAAAA
1 TATTATTAAAA
2650819 TA
1 TA
2650821 ATAGATTATA
Statistics
Matches: 84, Mismatches: 16, Indels: 28
0.66 0.12 0.22
Matches are distributed among these distances:
8 4 0.05
9 3 0.04
10 9 0.11
11 31 0.37
12 21 0.25
13 16 0.19
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.44
Consensus pattern (11 bp):
TATTATTAAAA
Found at i:2650768 original size:23 final size:22
Alignment explanation
Indices: 2650696--2650774 Score: 70
Period size: 23 Copynumber: 3.5 Consensus size: 22
2650686 AATATATATT
*
2650696 TATTATTAAAATATGAAT-ATAAA
1 TATTTTTAAAATAT-AATAAT-AA
* * *
2650719 TATTTTCAAAAATATATTAAGAA
1 TATTTT-TAAAATATAATAATAA
*
2650742 TATTATTTAAAATATAATAATAT
1 TATT-TTTAAAATATAATAATAA
2650765 TATTTTTAAA
1 TATTTTTAAA
2650775 TTTTATTATT
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
22 6 0.13
23 29 0.64
24 10 0.22
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (22 bp):
TATTTTTAAAATATAATAATAA
Found at i:2650813 original size:30 final size:32
Alignment explanation
Indices: 2650779--2650838 Score: 97
Period size: 30 Copynumber: 1.9 Consensus size: 32
2650769 TTTAAATTTT
2650779 ATTATTAAAATAA-A-ATTATAATATTAAAAA
1 ATTATTAAAATAATAGATTATAATATTAAAAA
*
2650809 ATTATTAAAATAATAGATTATATTATTAAA
1 ATTATTAAAATAATAGATTATAATATTAAA
2650839 TATAAATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 13 0.48
31 1 0.04
32 13 0.48
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (32 bp):
ATTATTAAAATAATAGATTATAATATTAAAAA
Found at i:2652733 original size:17 final size:18
Alignment explanation
Indices: 2652703--2652736 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2652693 ATTTAAATTG
2652703 CGGTCGCGGTCGCGTTTT
1 CGGTCGCGGTCGCGTTTT
2652721 CGGTCGC-GTCGCGTTT
1 CGGTCGCGGTCGCGTTT
2652737 GTCGCGGACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.00, C:0.29, G:0.38, T:0.32
Consensus pattern (18 bp):
CGGTCGCGGTCGCGTTTT
Found at i:2653892 original size:16 final size:16
Alignment explanation
Indices: 2653871--2653905 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
2653861 ATTTCAAGTC
2653871 TTACAGCCTATTAATT
1 TTACAGCCTATTAATT
2653887 TTACAGCCTATTAATT
1 TTACAGCCTATTAATT
2653903 TTA
1 TTA
2653906 GTCAAAGTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.17, G:0.06, T:0.46
Consensus pattern (16 bp):
TTACAGCCTATTAATT
Found at i:2655621 original size:12 final size:12
Alignment explanation
Indices: 2655604--2655628 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2655594 TCTTTCACGT
2655604 TCTGTATATCTA
1 TCTGTATATCTA
2655616 TCTGTATATCTA
1 TCTGTATATCTA
2655628 T
1 T
2655629 TAAGGAGATA
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:0.24, C:0.16, G:0.08, T:0.52
Consensus pattern (12 bp):
TCTGTATATCTA
Found at i:2662859 original size:12 final size:12
Alignment explanation
Indices: 2662844--2662869 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2662834 GCAAACATTA
2662844 ATGACCAAATTT
1 ATGACCAAATTT
2662856 ATGACCAAATTT
1 ATGACCAAATTT
2662868 AT
1 AT
2662870 AATTAATCCT
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:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (12 bp):
ATGACCAAATTT
Found at i:2663085 original size:17 final size:17
Alignment explanation
Indices: 2663065--2663104 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
2663055 AAAAAATCCT
2663065 AAAATTAAAATAATTTA
1 AAAATTAAAATAATTTA
* *
2663082 AAAATTAAATTTATTTA
1 AAAATTAAAATAATTTA
2663099 ATAAAT
1 A-AAAT
2663105 ATACTTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AAAATTAAAATAATTTA
Found at i:2664637 original size:13 final size:13
Alignment explanation
Indices: 2664621--2664651 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2664611 CCTTCTCCTT
2664621 CCCTTTCCCCTAC
1 CCCTTTCCCCTAC
*
2664634 CCCTTTCCCTTAC
1 CCCTTTCCCCTAC
2664647 CCCTT
1 CCCTT
2664652 CCCTTTCCCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.06, C:0.58, G:0.00, T:0.35
Consensus pattern (13 bp):
CCCTTTCCCCTAC
Found at i:2664637 original size:31 final size:31
Alignment explanation
Indices: 2664602--2664660 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
2664592 CCATTCTTCT
*
2664602 CCCCTTTCCCCTT-CTCCTTCCCTTTCCCCTA
1 CCCCTTT-CCCTTACCCCTTCCCTTTCCCCTA
2664633 CCCCTTTCCCTTACCCCTTCCCTTTCCC
1 CCCCTTTCCCTTACCCCTTCCCTTTCCC
2664661 GTTTTGAAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 5 0.19
31 21 0.81
ACGTcount: A:0.03, C:0.59, G:0.00, T:0.37
Consensus pattern (31 bp):
CCCCTTTCCCTTACCCCTTCCCTTTCCCCTA
Found at i:2664653 original size:12 final size:12
Alignment explanation
Indices: 2664603--2664656 Score: 56
Period size: 12 Copynumber: 4.4 Consensus size: 12
2664593 CATTCTTCTC
*
2664603 CCCTTTCCCCTT
1 CCCTTACCCCTT
*
2664615 CTCCTT-CCCTTT
1 C-CCTTACCCCTT
*
2664627 CCCCTACCCCTTT
1 CCCTTACCCC-TT
2664640 CCCTTACCCCTT
1 CCCTTACCCCTT
2664652 CCCTT
1 CCCTT
2664657 TCCCGTTTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
11 3 0.09
12 17 0.49
13 15 0.43
ACGTcount: A:0.04, C:0.57, G:0.00, T:0.39
Consensus pattern (12 bp):
CCCTTACCCCTT
Found at i:2664657 original size:18 final size:18
Alignment explanation
Indices: 2664603--2664660 Score: 73
Period size: 18 Copynumber: 3.2 Consensus size: 18
2664593 CATTCTTCTC
2664603 CCCTTTCCCCTTCTCC-TT
1 CCCTTTCCCCTTC-CCTTT
*
2664621 CCCTTTCCCCTACCCCTTT
1 CCCTTTCCCCT-TCCCTTT
*
2664640 CCCTTACCCCTTCCCTTT
1 CCCTTTCCCCTTCCCTTT
2664658 CCC
1 CCC
2664661 GTTTTGAAGC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
18 22 0.63
19 13 0.37
ACGTcount: A:0.03, C:0.59, G:0.00, T:0.38
Consensus pattern (18 bp):
CCCTTTCCCCTTCCCTTT
Found at i:2670301 original size:12 final size:13
Alignment explanation
Indices: 2670284--2670320 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
2670274 GAACCGGACA
2670284 CGAACCGAA-CTC
1 CGAACCGAAGCTC
2670296 CGAACC-AAGCTC
1 CGAACCGAAGCTC
*
2670308 CGAACCGTAGCTC
1 CGAACCGAAGCTC
2670321 TGATGCCACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
11 2 0.09
12 15 0.68
13 5 0.23
ACGTcount: A:0.30, C:0.41, G:0.19, T:0.11
Consensus pattern (13 bp):
CGAACCGAAGCTC
Found at i:2673283 original size:3 final size:3
Alignment explanation
Indices: 2673275--2673308 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
2673265 TGTTTTTCTT
*
2673275 TTA TTA TTA TTA TTA TTA TTA TT- TTG TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2673309 TAATGTATGT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:2674614 original size:16 final size:15
Alignment explanation
Indices: 2674595--2674634 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
2674585 AATTTTCAAT
2674595 AAATAAAAAATATATA
1 AAATAAAAAATAT-TA
*
2674611 AAATAATTAAATATTA
1 AAATAA-AAAATATTA
2674627 AAATAAAA
1 AAATAAAA
2674635 TGATATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 1 0.05
16 14 0.67
17 6 0.29
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
AAATAAAAAATATTA
Found at i:2674824 original size:28 final size:28
Alignment explanation
Indices: 2674793--2674849 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
2674783 AACCCGGCCC
*
2674793 ATTATTACCTCTGCATCAAATTAAGATT
1 ATTATCACCTCTGCATCAAATTAAGATT
2674821 ATTATCACCTCTGCATCAAATTAAGATT
1 ATTATCACCTCTGCATCAAATTAAGATT
2674849 A
1 A
2674850 GGACTATGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37
Consensus pattern (28 bp):
ATTATCACCTCTGCATCAAATTAAGATT
Found at i:2678655 original size:23 final size:23
Alignment explanation
Indices: 2678621--2678666 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
2678611 ACTAGGAGTC
*
2678621 AGTTTTATTATTAAAAATTGGTT
1 AGTTTTACTATTAAAAATTGGTT
2678644 AGTTTTACTATTAAAAATTGGTT
1 AGTTTTACTATTAAAAATTGGTT
2678667 CTCATACACC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.02, G:0.13, T:0.50
Consensus pattern (23 bp):
AGTTTTACTATTAAAAATTGGTT
Found at i:2680695 original size:18 final size:20
Alignment explanation
Indices: 2680658--2680700 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
2680648 GATTGGAAAA
2680658 TGAAATATACTTGTTTTGGTT
1 TGAAATATACTTGTTTTGG-T
2680679 TGAAATA-A-TTG-TTTGGT
1 TGAAATATACTTGTTTTGGT
2680696 TGAAA
1 TGAAA
2680701 ATTTTTAGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 6 0.27
18 5 0.23
19 3 0.14
20 1 0.05
21 7 0.32
ACGTcount: A:0.30, C:0.02, G:0.21, T:0.47
Consensus pattern (20 bp):
TGAAATATACTTGTTTTGGT
Found at i:2680702 original size:18 final size:20
Alignment explanation
Indices: 2680658--2680702 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 20
2680648 GATTGGAAAA
*
2680658 TGAAATATACTTGTTTTGGTT
1 TGAAA-ATAATTGTTTTGGTT
2680679 TG-AAATAATTG-TTTGG-T
1 TGAAAATAATTGTTTTGGTT
2680696 TGAAAAT
1 TGAAAAT
2680703 TTTTAGGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
17 3 0.14
18 9 0.41
19 6 0.27
20 2 0.09
21 2 0.09
ACGTcount: A:0.31, C:0.02, G:0.20, T:0.47
Consensus pattern (20 bp):
TGAAAATAATTGTTTTGGTT
Found at i:2680960 original size:20 final size:20
Alignment explanation
Indices: 2680935--2680986 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
2680925 CAGCTGCAGG
* * *
2680935 ACACGGGCATGTTCTAGGCC
1 ACACGGGCATGTCCCAAGCC
*
2680955 ACACGGGCGTGTCCCAAGCC
1 ACACGGGCATGTCCCAAGCC
2680975 ACACGGGCATGT
1 ACACGGGCATGT
2680987 GCCCCTATCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.21, C:0.33, G:0.31, T:0.15
Consensus pattern (20 bp):
ACACGGGCATGTCCCAAGCC
Found at i:2681820 original size:28 final size:29
Alignment explanation
Indices: 2681767--2681834 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 29
2681757 TTTTATTTTA
2681767 TTATTAAAATTTAAATATTAAATAAT-TGT
1 TTATTAAAA-TTAAATATTAAATAATATGT
*
2681796 TTATTAAAATTAAA-ATTAATTTAATGATGT
1 TTATTAAAATTAAATATTAA-ATAAT-ATGT
2681826 TT-TTAAAAT
1 TTATTAAAAT
2681835 CATTCAGTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
27 5 0.14
28 9 0.26
29 16 0.46
30 5 0.14
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (29 bp):
TTATTAAAATTAAATATTAAATAATATGT
Found at i:2684162 original size:26 final size:26
Alignment explanation
Indices: 2684124--2684185 Score: 115
Period size: 26 Copynumber: 2.3 Consensus size: 26
2684114 GTAACTTATA
2684124 ATTATTATAAATATGATTATAATTAAT
1 ATTA-TATAAATATGATTATAATTAAT
2684151 ATTATATAAATATGATTATAATTAAT
1 ATTATATAAATATGATTATAATTAAT
2684177 ATTATATAA
1 ATTATATAA
2684186 TTTTAAAATC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 31 0.89
27 4 0.11
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (26 bp):
ATTATATAAATATGATTATAATTAAT
Found at i:2684184 original size:14 final size:14
Alignment explanation
Indices: 2684141--2684187 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
2684131 TAAATATGAT
2684141 TATAATTAATATTA
1 TATAATTAATATTA
*
2684155 TAT-A--AATATGA
1 TATAATTAATATTA
2684166 TTATAATTAATATTA
1 -TATAATTAATATTA
2684181 TATAATT
1 TATAATT
2684188 TTAAAATCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
11 6 0.22
12 3 0.11
13 2 0.07
14 10 0.37
15 6 0.22
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (14 bp):
TATAATTAATATTA
Found at i:2688347 original size:23 final size:23
Alignment explanation
Indices: 2688321--2688364 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
2688311 AATATTAGTA
2688321 AGTAAAG-AAAAAGGAATAATAAT
1 AGTAAAGTAAAAA-GAATAATAAT
* *
2688344 AGTATAGTAAAAATAATAATA
1 AGTAAAGTAAAAAGAATAATA
2688365 TGTTAATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 13 0.72
24 5 0.28
ACGTcount: A:0.64, C:0.00, G:0.14, T:0.23
Consensus pattern (23 bp):
AGTAAAGTAAAAAGAATAATAAT
Found at i:2690590 original size:122 final size:122
Alignment explanation
Indices: 2690366--2690593 Score: 269
Period size: 122 Copynumber: 1.9 Consensus size: 122
2690356 AGGTTAAAAC
* * * * *
2690366 GTTTTGTTAGTCCCTGTACTTAGACAAACTTTAAAATTTAGTTCCTGTAACATCATTAGTATTTT
1 GTTTTGTTAGTCCCTGTACTTAGACAAAATTGAAAATGTAGATCCTGTAACATCAGTAGTATTTT
* * * * *
2690431 CTGCCAAATTTTGCCATGAGATGTTAATTACACTGCCTCATTTCATATTGCATAAAT
66 CTACCAAAATTTACCATGACATCTTAATTACACTGCCTCATTTCATATTGCATAAAT
* * * *
2690488 GTTTTTTTAGTCCTTGTACTTGGACAAAATTGAAAATGTA-ATCCATGTAACATTAGTAGTATTT
1 GTTTTGTTAGTCCCTGTACTTAGACAAAATTGAAAATGTAGATCC-TGTAACATCAGTAGTATTT
* * * * *
2690552 TCTACCAAAATTTATCGTGACATCTTGATTAGATTGCCTCAT
65 TCTACCAAAATTTACCATGACATCTTAATTACACTGCCTCAT
2690594 ATAACATTAG
Statistics
Matches: 86, Mismatches: 19, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
121 3 0.03
122 83 0.97
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41
Consensus pattern (122 bp):
GTTTTGTTAGTCCCTGTACTTAGACAAAATTGAAAATGTAGATCCTGTAACATCAGTAGTATTTT
CTACCAAAATTTACCATGACATCTTAATTACACTGCCTCATTTCATATTGCATAAAT
Found at i:2692471 original size:59 final size:59
Alignment explanation
Indices: 2692379--2692496 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
2692369 ATTTCAACTG
2692379 CACTCATTCTAATGGCAAAGATCATGGTAATATTAATTAGTTTTGCTAAAGGCACTCGT
1 CACTCATTCTAATGGCAAAGATCATGGTAATATTAATTAGTTTTGCTAAAGGCACTCGT
2692438 CACTCATTCTAATGGCAAAGATCATGGTAATATTAATTAGTTTTGCTAAAGGCACTCGT
1 CACTCATTCTAATGGCAAAGATCATGGTAATATTAATTAGTTTTGCTAAAGGCACTCGT
2692497 TTTGGTTACC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (59 bp):
CACTCATTCTAATGGCAAAGATCATGGTAATATTAATTAGTTTTGCTAAAGGCACTCGT
Found at i:2703431 original size:28 final size:28
Alignment explanation
Indices: 2703399--2703455 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
2703389 ATATATGTTG
2703399 AATCAGTGAATTAATTGAGGTATTTACC
1 AATCAGTGAATTAATTGAGGTATTTACC
2703427 AATCAGTGAATTAATTGAGGTATTTACC
1 AATCAGTGAATTAATTGAGGTATTTACC
2703455 A
1 A
2703456 TTAACTTCTT
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:0.37, C:0.11, G:0.18, T:0.35
Consensus pattern (28 bp):
AATCAGTGAATTAATTGAGGTATTTACC
Found at i:2710033 original size:19 final size:19
Alignment explanation
Indices: 2710009--2710050 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
2709999 AAAAATAAAA
2710009 TAAAGGTAAGGTTAAGTAC
1 TAAAGGTAAGGTTAAGTAC
2710028 TAAAGGTAAGGTTAAGTAC
1 TAAAGGTAAGGTTAAGTAC
2710047 TAAA
1 TAAA
2710051 TATATATCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.45, C:0.05, G:0.24, T:0.26
Consensus pattern (19 bp):
TAAAGGTAAGGTTAAGTAC
Found at i:2725973 original size:18 final size:18
Alignment explanation
Indices: 2725946--2726038 Score: 123
Period size: 18 Copynumber: 5.2 Consensus size: 18
2725936 TACGACCGTT
2725946 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
* * *
2725964 TACGGCACTATTTATGTA
1 TACGGTACTATTCACGTA
*
2725982 TACGGTACTATTTACGTA
1 TACGGTACTATTCACGTA
* *
2726000 TACGGCACTATTAACGTA
1 TACGGTACTATTCACGTA
*
2726018 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
2726036 TAC
1 TAC
2726039 AGTAGTTGGG
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 65 1.00
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.34
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:2725993 original size:36 final size:36
Alignment explanation
Indices: 2725946--2726038 Score: 150
Period size: 36 Copynumber: 2.6 Consensus size: 36
2725936 TACGACCGTT
* *
2725946 TACGGTACTATTCACGTATACGGCACTATTTATGTA
1 TACGGTACTATTCACGTATACGGCACTATTAACGTA
*
2725982 TACGGTACTATTTACGTATACGGCACTATTAACGTA
1 TACGGTACTATTCACGTATACGGCACTATTAACGTA
*
2726018 TACGGTACTGTTCACGTATAC
1 TACGGTACTATTCACGTATAC
2726039 AGTAGTTGGG
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 52 1.00
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.34
Consensus pattern (36 bp):
TACGGTACTATTCACGTATACGGCACTATTAACGTA
Found at i:2734235 original size:27 final size:27
Alignment explanation
Indices: 2734205--2734256 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
2734195 ATGACTTGTT
2734205 TTCAAAAGAAATTGATGAAAATACTTA
1 TTCAAAAGAAATTGATGAAAATACTTA
2734232 TTCAAAAGAAATTGATGAAAATACT
1 TTCAAAAGAAATTGATGAAAATACT
2734257 CATCTTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.52, C:0.08, G:0.12, T:0.29
Consensus pattern (27 bp):
TTCAAAAGAAATTGATGAAAATACTTA
Found at i:2734392 original size:23 final size:24
Alignment explanation
Indices: 2734362--2734407 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 24
2734352 TTTAAATTTG
2734362 TAAAAATTAATATAATAT-TATTA
1 TAAAAATTAATATAATATGTATTA
2734385 TAAAAATTAATATAATATGTATT
1 TAAAAATTAATATAATATGTATT
2734408 TCATTGGGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
TAAAAATTAATATAATATGTATTA
Found at i:2734398 original size:12 final size:12
Alignment explanation
Indices: 2734362--2734399 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
2734352 TTTAAATTTG
2734362 TAAAAATTAATA
1 TAAAAATTAATA
* *
2734374 T-AATATTATTA
1 TAAAAATTAATA
2734385 TAAAAATTAATA
1 TAAAAATTAATA
2734397 TAA
1 TAA
2734400 TATGTATTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
TAAAAATTAATA
Found at i:2742753 original size:32 final size:33
Alignment explanation
Indices: 2742686--2742757 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
2742676 ATTGTAGAAA
* * *
2742686 AAACTTTAAATCAAACATTTGAATAAAAATTTT
1 AAACTTTAAATCAAACAATAGAATAAAAATATT
2742719 AAACTTTAAATCAAACAAATAGAA-AAAAA-ATT
1 AAACTTTAAATCAAAC-AATAGAATAAAAATATT
2742751 AAACTTT
1 AAACTTT
2742758 TTAGAGAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
32 9 0.26
33 21 0.60
34 5 0.14
ACGTcount: A:0.57, C:0.10, G:0.03, T:0.31
Consensus pattern (33 bp):
AAACTTTAAATCAAACAATAGAATAAAAATATT
Found at i:2753229 original size:20 final size:20
Alignment explanation
Indices: 2753204--2753243 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2753194 TCTGATCTGA
2753204 TCCTTTATTATCCCATAAAC
1 TCCTTTATTATCCCATAAAC
2753224 TCCTTTATTATCCCATAAAC
1 TCCTTTATTATCCCATAAAC
2753244 AAGTGGTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.40
Consensus pattern (20 bp):
TCCTTTATTATCCCATAAAC
Found at i:2766448 original size:212 final size:199
Alignment explanation
Indices: 2766118--2766734 Score: 781
Period size: 212 Copynumber: 3.0 Consensus size: 199
2766108 TTAATTTTAA
* * * * *
2766118 TGAGTGAGTGGATAATTC-TTCAATTTTCAATCATCTCATGTTTTAAAATTGTTTATTGGATGCA
1 TGAGTGAGTGGATAATTCTTTTATTTTTAAATCATCTCATGCTTTAAAATTGTTTACTGGATGCA
* * *
2766182 TGAGTCCACTTCACAGTCATTTTTTTATTTGTTAGCCTGTACATTGGATCTGTTGCAGGTTGGAT
66 --AGTCAACTTCACATTCATTTTTTTATTTGTTAGCCTGTACATTGTATCTGTTGCAGGTTGGAT
* *
2766247 GATTTTGATTTTGATTCAGCCCTGAATAAAGGAGAGAAGACTAGTAAGAAAAACCAGGAAAGTAA
129 GATTTTGATTTTGATTCAGCCCTAAATAAAGGAGAGAAGACTAGTAAGAAAAACCAGGAAAGCAA
2766312 AGACGC
194 AGACGC
* ** *
2766318 TGAGTGAGTGGATTATTCTTTTATTTTTCAGTTATCTCATGTACAATCTTTTGCTTTGAAATTGT
1 TGAGTGAGTGGATAATTCTTTTATTTTT-A---A----A--T-C-ATCTCATGCTTTAAAATTGT
*
2766383 TTACTGGACATGCAAGTCAACTTCACATTCA-TTTTTTATTTGTTAGCCTGTATATTGTATCTGT
54 TTACTGG--ATGCAAGTCAACTTCACATTCATTTTTTTATTTGTTAGCCTGTACATTGTATCTGT
*
2766447 TGCAGGTTGGATGATTTTGATTTTGATTCAACCCTAAATAAAGGAGAGAAGACTAGTAAGAAAAA
117 TGCAGGTTGGATGATTTTGATTTTGATTCAGCCCTAAATAAAGGAGAGAAGACTAGTAAGAAAAA
** * *
2766512 TAAGGAATGCAAAGCCGC
182 CCAGGAAAGCAAAGACGC
*
2766530 TGAGTGAGTGGATAATTCTTTTATTTTTAAATCATCTCATGCTTTAAAATTGTTTGCTGGATGCA
1 TGAGTGAGTGGATAATTCTTTTATTTTTAAATCATCTCATGCTTTAAAATTGTTTACTGGATGC-
* *
2766595 TAAGTCAACTTAACATTCATTTTTTTTAATTTATTAGCCTGTACATTGTATCTGTTGCAGGTTGG
65 -AAGTCAACTTCACATTCA-TTTTTTT-ATTTGTTAGCCTGTACATTGTATCTGTTGCAGGTTGG
** *
2766660 ATGATTTTGATTTTGATTC-GACCCTAAATATTGGAGAGAAGACTAGTAAGAAAAACCAGGAAGG
127 ATGATTTTGATTTTGATTCAG-CCCTAAATAAAGGAGAGAAGACTAGTAAGAAAAACCAGGAAAG
*
2766724 CAAAGCCGC
191 CAAAGACGC
2766733 TG
1 TG
2766735 CTTCTGAGAG
Statistics
Matches: 362, Mismatches: 34, Indels: 39
0.83 0.08 0.09
Matches are distributed among these distances:
198 4 0.01
200 57 0.16
201 8 0.02
202 7 0.02
203 103 0.28
204 1 0.00
205 1 0.00
208 1 0.00
209 1 0.00
211 2 0.01
212 135 0.37
213 37 0.10
215 5 0.01
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37
Consensus pattern (199 bp):
TGAGTGAGTGGATAATTCTTTTATTTTTAAATCATCTCATGCTTTAAAATTGTTTACTGGATGCA
AGTCAACTTCACATTCATTTTTTTATTTGTTAGCCTGTACATTGTATCTGTTGCAGGTTGGATGA
TTTTGATTTTGATTCAGCCCTAAATAAAGGAGAGAAGACTAGTAAGAAAAACCAGGAAAGCAAAG
ACGC
Found at i:2766698 original size:203 final size:199
Alignment explanation
Indices: 2766369--2766734 Score: 572
Period size: 203 Copynumber: 1.8 Consensus size: 199
2766359 TACAATCTTT
* * *
2766369 TGCTTTGAAATTGTTTACTGGACATGCAAGTCAACTTCACATTCATTTTTTATTTGTTAGCCTGT
1 TGCTTTAAAATTGTTTACTGGACAT-CAAGTCAACTTAACATTCATTTTTTATTTATTAGCCTGT
*
2766434 ATATTGTATCTGTTGCAGGTTGGATGATTTTGATTTTGATTCAACCCTAAATAAAGGAGAGAAGA
65 ACATTGTATCTGTTGCAGGTTGGATGATTTTGATTTTGATTCAACCCTAAATAAAGGAGAGAAGA
* *
2766499 CTAGTAAGAAAAATAAGGAATGCAAAGCCGCTGAGTGAGTGGATAATTCTTTTATTTTTAAATCA
130 CTAGTAAGAAAAACAAGGAAGGCAAAGCCGCTGAGTGAGTGGATAATTCTTTTATTTTTAAATCA
2766564 TCTCA
195 TCTCA
*
2766569 TGCTTTAAAATTGTTTGCTGGATGCAT-AAGTCAACTTAACATTCATTTTTTTTAATTTATTAGC
1 TGCTTTAAAATTGTTTACTGGA--CATCAAGTCAACTTAACATTCA--TTTTTT-ATTTATTAGC
* **
2766633 CTGTACATTGTATCTGTTGCAGGTTGGATGATTTTGATTTTGATTCGACCCTAAATATTGGAGAG
61 CTGTACATTGTATCTGTTGCAGGTTGGATGATTTTGATTTTGATTCAACCCTAAATAAAGGAGAG
*
2766698 AAGACTAGTAAGAAAAACCAGGAAGGCAAAGCCGCTG
126 AAGACTAGTAAGAAAAACAAGGAAGGCAAAGCCGCTG
2766735 CTTCTGAGAG
Statistics
Matches: 150, Mismatches: 11, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
200 37 0.25
202 9 0.06
203 104 0.69
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (199 bp):
TGCTTTAAAATTGTTTACTGGACATCAAGTCAACTTAACATTCATTTTTTATTTATTAGCCTGTA
CATTGTATCTGTTGCAGGTTGGATGATTTTGATTTTGATTCAACCCTAAATAAAGGAGAGAAGAC
TAGTAAGAAAAACAAGGAAGGCAAAGCCGCTGAGTGAGTGGATAATTCTTTTATTTTTAAATCAT
CTCA
Found at i:2771420 original size:15 final size:15
Alignment explanation
Indices: 2771402--2771431 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2771392 CTCTCTGCCC
2771402 TTCTCCTCCACCTCT
1 TTCTCCTCCACCTCT
*
2771417 TTCTCCTCCCCCTCT
1 TTCTCCTCCACCTCT
2771432 CTCAGTCAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.03, C:0.57, G:0.00, T:0.40
Consensus pattern (15 bp):
TTCTCCTCCACCTCT
Found at i:2772564 original size:23 final size:24
Alignment explanation
Indices: 2772519--2772566 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
2772509 AAATAATTTA
*
2772519 TTTTTAGAAATTTAAAATTTATAT
1 TTTTTAGAAATTTAAAATATATAT
2772543 TTTTTA-AAATTTAAAGAATATATA
1 TTTTTAGAAATTT-AA-AATATATA
2772567 AAGAAAGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 6 0.29
24 8 0.38
25 7 0.33
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (24 bp):
TTTTTAGAAATTTAAAATATATAT
Found at i:2776196 original size:4 final size:4
Alignment explanation
Indices: 2776179--2776209 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
2776169 CAATGACAAG
*
2776179 ATAC ATAT ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
2776210 AAACCCTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.19, G:0.00, T:0.29
Consensus pattern (4 bp):
ATAC
Found at i:2785067 original size:5 final size:5
Alignment explanation
Indices: 2785057--2785082 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
2785047 TTGCTATGAT
2785057 TTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA T
2785083 ATATGTTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:2786353 original size:44 final size:44
Alignment explanation
Indices: 2786290--2786375 Score: 154
Period size: 44 Copynumber: 2.0 Consensus size: 44
2786280 TGATTGAATT
* *
2786290 GAATTGACTCGAATAAAAAATATTTGAGTTAGTCAAGTTGACAA
1 GAATTGACTCGAATAAAAAATATATGAGTTAATCAAGTTGACAA
2786334 GAATTGACTCGAATAAAAAATATATGAGTTAATCAAGTTGAC
1 GAATTGACTCGAATAAAAAATATATGAGTTAATCAAGTTGAC
2786376 GAGTTTTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.44, C:0.09, G:0.17, T:0.29
Consensus pattern (44 bp):
GAATTGACTCGAATAAAAAATATATGAGTTAATCAAGTTGACAA
Found at i:2786755 original size:20 final size:20
Alignment explanation
Indices: 2786723--2786775 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
2786713 AACCTTTATT
2786723 TTTTA-AAATTTTTATAAAAA
1 TTTTAGAAA-TTTTATAAAAA
*
2786743 TTTTAGAAATTTTATAAATA
1 TTTTAGAAATTTTATAAAAA
*
2786763 TTTT-GAAAATTTA
1 TTTTAGAAATTTTA
2786776 AGGTTATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 8 0.27
20 19 0.63
21 3 0.10
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (20 bp):
TTTTAGAAATTTTATAAAAA
Found at i:2786759 original size:45 final size:45
Alignment explanation
Indices: 2786672--2786759 Score: 117
Period size: 46 Copynumber: 2.0 Consensus size: 45
2786662 TTTATCATTT
* * *
2786672 TTTATTTTTTTAATTTTTTAAAGATTTTTAGAATTTTATATAACC
1 TTTATTTTTTAAATTTTTTAAAGAATTTTAGAAATTTATATAACC
2786717 TTTATTTTTTAAAATTTTTATAAA-AATTTTAGAAATTT-TATAA
1 TTTATTTTTT-AAATTTTT-TAAAGAATTTTAGAAATTTATATAA
2786760 ATATTTTGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
45 15 0.39
46 19 0.50
47 4 0.11
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.58
Consensus pattern (45 bp):
TTTATTTTTTAAATTTTTTAAAGAATTTTAGAAATTTATATAACC
Found at i:2793859 original size:12 final size:12
Alignment explanation
Indices: 2793842--2793866 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2793832 AATTTCTATA
2793842 TATATATATATT
1 TATATATATATT
2793854 TATATATATATT
1 TATATATATATT
2793866 T
1 T
2793867 TAAATGTCAT
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TATATATATATT
Found at i:2799989 original size:16 final size:16
Alignment explanation
Indices: 2799968--2800002 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2799958 AAAATTCAAA
*
2799968 ATATTTATAAAAATTT
1 ATATTTATAAAAAATT
*
2799984 ATATTTTTAAAAAATT
1 ATATTTATAAAAAATT
2800000 ATA
1 ATA
2800003 ATATTTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATATTTATAAAAAATT
Found at i:2800008 original size:19 final size:19
Alignment explanation
Indices: 2799957--2800017 Score: 65
Period size: 20 Copynumber: 3.3 Consensus size: 19
2799947 AATAAGGTTC
* *
2799957 AAAAATTCAAAATATTTAT-
1 AAAAATT-ATAATATTTTTA
2799976 AAAAATT-T-ATATTTTTA
1 AAAAATTATAATATTTTTA
2799993 AAAAATTATAATATTTTTTA
1 AAAAATTATAATA-TTTTTA
2800013 AAAAA
1 AAAAA
2800018 ATTAAAGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
16 7 0.19
17 7 0.19
18 1 0.03
19 10 0.28
20 11 0.31
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
AAAAATTATAATATTTTTA
Found at i:2805818 original size:55 final size:55
Alignment explanation
Indices: 2805757--2805866 Score: 168
Period size: 55 Copynumber: 2.0 Consensus size: 55
2805747 TGATATGTCT
* * *
2805757 GGTAATGCCTCGTAACCCTATTTCGGA-GACGGTTTGGGGTTAAAAGGGTGTTACA
1 GGTAATGCCTCGTAACCCTATTTC-AACGACGATTTGCGGTTAAAAGGGTGTTACA
*
2805812 GGTAATGCCTCGTAACCCTATTTCAACGACGATTTGCGGTTAAAGGGGTGTTACA
1 GGTAATGCCTCGTAACCCTATTTCAACGACGATTTGCGGTTAAAAGGGTGTTACA
2805867 ATATTCTGGA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
54 1 0.02
55 49 0.98
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (55 bp):
GGTAATGCCTCGTAACCCTATTTCAACGACGATTTGCGGTTAAAAGGGTGTTACA
Found at i:2807438 original size:6 final size:6
Alignment explanation
Indices: 2807427--2807453 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2807417 AGCAATAGTT
2807427 TGAATG TGAATG TGAATG TGAATG TGA
1 TGAATG TGAATG TGAATG TGAATG TGA
2807454 GGTGAAGTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (6 bp):
TGAATG
Found at i:2808949 original size:63 final size:63
Alignment explanation
Indices: 2808809--2809257 Score: 376
Period size: 63 Copynumber: 7.1 Consensus size: 63
2808799 AAACCGGGCT
* * * * *
2808809 ACACCGAAAAGCA-ATACAAAC-AAAGACCACTGTTGTCTTC-AATGAGAAAGCAATGAAACCCT
1 ACACCCAAAAGCATA-ACAAACGAAA-ACCACTGTTGTCTGCAAATAAAAAAG-AGT-AAACCCT
2808871 AA
62 AA
* * *
2808873 ACACCCAAAAGCATAACAAACGAAAGCCACTGTTGTATGCAAATAAAAAAGAGTAAACCCCAA
1 ACACCCAAAAGCATAACAAACGAAAACCACTGTTGTCTGCAAATAAAAAAGAGTAAACCCTAA
* * * * * * * *
2808936 ACACTCAAAAGCATTACAAAC-AAATACCAGTATTGTCTTC-AATGAGAAAGAAATGAAACCCTA
1 ACACCCAAAAGCATAACAAACGAAA-ACCACTGTTGTCTGCAAATAAAAAAG-AGT-AAACCCTA
2808999 A
63 A
* * * *
2809000 ACACCCAAAGGAATAACAAACGAAAACCACTGTTGTCTGCAAATAAAAAAGAGTAAGCCCCAA
1 ACACCCAAAAGCATAACAAACGAAAACCACTGTTGTCTGCAAATAAAAAAGAGTAAACCCTAA
* * * * * * * *
2809063 ACACTCAAAAGCATTACAAAC-AAAGACCAGTATTGTCTTC-AATTAGAAAGCAATGAAACCCTA
1 ACACCCAAAAGCATAACAAACGAAA-ACCACTGTTGTCTGCAAATAAAAAAG-AGT-AAACCCTA
2809126 A
63 A
* * * * *
2809127 ACACCCAAAGGAATAACAAACGAAAACCACTGTTGTCTGCAAACAAAAAGGAGTAAAGCCTAA
1 ACACCCAAAAGCATAACAAACGAAAACCACTGTTGTCTGCAAATAAAAAAGAGTAAACCCTAA
* * * * * *
2809190 ACACCCAAAAGCATTACAAACAAAAACCAC-GTTGATCAGC-AATGAAAAAGCAATCAACCCTAA
1 ACACCCAAAAGCATAACAAACGAAAACCACTGTTG-TCTGCAAATAAAAAAG-AGTAAACCCTAA
2809253 ACACC
1 ACACC
2809258 AATTGAGTTA
Statistics
Matches: 303, Mismatches: 67, Indels: 31
0.76 0.17 0.08
Matches are distributed among these distances:
62 33 0.11
63 129 0.43
64 109 0.36
65 32 0.11
ACGTcount: A:0.49, C:0.24, G:0.12, T:0.15
Consensus pattern (63 bp):
ACACCCAAAAGCATAACAAACGAAAACCACTGTTGTCTGCAAATAAAAAAGAGTAAACCCTAA
Found at i:2809041 original size:127 final size:127
Alignment explanation
Indices: 2808815--2809257 Score: 658
Period size: 127 Copynumber: 3.5 Consensus size: 127
2808805 GGCTACACCG
* * *
2808815 AAAAGCAATACAAACAAAGACCACTGTTGTCTTCAATGAGAAAGCAATGAAACCCTAAACACCCA
1 AAAAGCATTACAAACAAAGACCAGTATTGTCTTCAATGAGAAAGCAATGAAACCCTAAACACCCA
* * * *
2808880 AAAGCATAACAAACGAAAGCCACTGTTGTATGCAAATAAAAAAGAGTAAACCCCAAACACTC
66 AAGGAATAACAAACGAAAACCACTGTTGTCTGCAAATAAAAAAGAGTAAACCCCAAACACTC
* *
2808942 AAAAGCATTACAAACAAATACCAGTATTGTCTTCAATGAGAAAGAAATGAAACCCTAAACACCCA
1 AAAAGCATTACAAACAAAGACCAGTATTGTCTTCAATGAGAAAGCAATGAAACCCTAAACACCCA
*
2809007 AAGGAATAACAAACGAAAACCACTGTTGTCTGCAAATAAAAAAGAGTAAGCCCCAAACACTC
66 AAGGAATAACAAACGAAAACCACTGTTGTCTGCAAATAAAAAAGAGTAAACCCCAAACACTC
*
2809069 AAAAGCATTACAAACAAAGACCAGTATTGTCTTCAATTAGAAAGCAATGAAACCCTAAACACCCA
1 AAAAGCATTACAAACAAAGACCAGTATTGTCTTCAATGAGAAAGCAATGAAACCCTAAACACCCA
* * * * *
2809134 AAGGAATAACAAACGAAAACCACTGTTGTCTGCAAACAAAAAGGAGTAAAGCCTAAACACCC
66 AAGGAATAACAAACGAAAACCACTGTTGTCTGCAAATAAAAAAGAGTAAACCCCAAACACTC
* ** * *
2809196 AAAAGCATTACAAACAAAAACCACG--TTGATCAGCAATGAAAAAGCAAT-CAACCCTAAACACC
1 AAAAGCATTACAAACAAAGACCA-GTATTG-TCTTCAATGAGAAAGCAATGAAACCCTAAACACC
2809258 AATTGAGTTA
Statistics
Matches: 289, Mismatches: 25, Indels: 5
0.91 0.08 0.02
Matches are distributed among these distances:
126 16 0.06
127 272 0.94
128 1 0.00
ACGTcount: A:0.49, C:0.23, G:0.12, T:0.15
Consensus pattern (127 bp):
AAAAGCATTACAAACAAAGACCAGTATTGTCTTCAATGAGAAAGCAATGAAACCCTAAACACCCA
AAGGAATAACAAACGAAAACCACTGTTGTCTGCAAATAAAAAAGAGTAAACCCCAAACACTC
Found at i:2809614 original size:10 final size:10
Alignment explanation
Indices: 2809601--2809679 Score: 53
Period size: 10 Copynumber: 8.2 Consensus size: 10
2809591 TTTTTAAGAC
2809601 TTATTAAAAA
1 TTATTAAAAA
2809611 TTA-TAAAAA
1 TTATTAAAAA
* *
2809620 -TATTTGAACA
1 TTA-TTAAAAA
2809630 -TATTAAAAA
1 TTATTAAAAA
2809639 TT-TGT-AAAA
1 TTAT-TAAAAA
2809648 TTATTAAAAA
1 TTATTAAAAA
* *
2809658 ATAATAAAAA
1 TTATTAAAAA
2809668 TT-TTAAACAA
1 TTATTAAA-AA
2809678 TT
1 TT
2809680 GTGAAAATCA
Statistics
Matches: 54, Mismatches: 8, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
8 2 0.04
9 23 0.43
10 29 0.54
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (10 bp):
TTATTAAAAA
Found at i:2809652 original size:19 final size:19
Alignment explanation
Indices: 2809607--2809760 Score: 67
Period size: 19 Copynumber: 8.2 Consensus size: 19
2809597 AGACTTATTA
*
2809607 AAAATTATAAAAATATTTG-
1 AAAATTATTAAAA-ATTTGT
*
2809626 AACA-TATTAAAAATTTGT
1 AAAATTATTAAAAATTTGT
* **
2809644 AAAATTATTAAAAAATAAT
1 AAAATTATTAAAAATTTGT
2809663 AAAAATT-TTAAACAA-TTGT
1 -AAAATTATTAAA-AATTTGT
* *
2809682 GAAAATCATTTAAAAAATT-T
1 -AAAATTA-TTAAAAATTTGT
*
2809702 -AAATTGATTAAAAA-ATGT
1 AAAATT-ATTAAAAATTTGT
** *
2809720 AAGAATTATTTGAAATTTAT
1 AA-AATTATTAAAAATTTGT
2809740 AAGAATT-TT-AAAATTT-T
1 AA-AATTATTAAAAATTTGT
2809757 AAAA
1 AAAA
2809761 AATTATAATA
Statistics
Matches: 106, Mismatches: 17, Indels: 27
0.71 0.11 0.18
Matches are distributed among these distances:
16 2 0.02
17 9 0.08
18 28 0.26
19 36 0.34
20 24 0.23
21 7 0.07
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37
Consensus pattern (19 bp):
AAAATTATTAAAAATTTGT
Found at i:2809652 original size:29 final size:28
Alignment explanation
Indices: 2809602--2809674 Score: 83
Period size: 29 Copynumber: 2.6 Consensus size: 28
2809592 TTTTAAGACT
* ** *
2809602 TATTAAAAATTATAAAAATATTTGAACA
1 TATTAAAAATTTTAAAAATATTAAAAAA
*
2809630 TATTAAAAATTTGTAAAATTATTAAAAAA
1 TATTAAAAATTT-TAAAAATATTAAAAAA
*
2809659 TAATAAAAATTTTAAA
1 TATTAAAAATTTTAAA
2809675 CAATTGTGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 15 0.39
29 23 0.61
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (28 bp):
TATTAAAAATTTTAAAAATATTAAAAAA
Found at i:2809674 original size:9 final size:9
Alignment explanation
Indices: 2809604--2809761 Score: 54
Period size: 9 Copynumber: 16.8 Consensus size: 9
2809594 TTAAGACTTA
2809604 TTAAAAATT
1 TTAAAAATT
*
2809613 ATAAAAATAT
1 TTAAAAAT-T
* * *
2809623 TTGAACATA
1 TTAAAAATT
2809632 TTAAAAATT
1 TTAAAAATT
2809641 TGT-AAAATT
1 T-TAAAAATT
*
2809650 ATTAAAAAATA
1 -TT-AAAAATT
*
2809661 ATAAAAATT
1 TTAAAAATT
2809670 TTAAACAATT
1 TTAAA-AATT
* *
2809680 GTGAAAATCAT
1 TTAAAAAT--T
*
2809691 TTAAAAAAT
1 TTAAAAATT
2809700 TT--AAATT
1 TTAAAAATT
*
2809707 GATTAAAAAAT
1 --TTAAAAATT
* *
2809718 GTAAGAATT
1 TTAAAAATT
**
2809727 ATTTGAAATT
1 -TTAAAAATT
*
2809737 TATAAGAATT
1 T-TAAAAATT
2809747 TT-AAAATT
1 TTAAAAATT
2809755 TTAAAAA
1 TTAAAAA
2809762 ATTATAATAT
Statistics
Matches: 104, Mismatches: 30, Indels: 30
0.63 0.18 0.18
Matches are distributed among these distances:
7 4 0.04
8 7 0.07
9 51 0.49
10 27 0.26
11 15 0.14
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37
Consensus pattern (9 bp):
TTAAAAATT
Found at i:2811029 original size:9 final size:9
Alignment explanation
Indices: 2811017--2811069 Score: 52
Period size: 9 Copynumber: 5.6 Consensus size: 9
2811007 TTTTAATACC
2811017 TTTTATTAT
1 TTTTATTAT
2811026 TTTTATTAT
1 TTTTATTAT
*
2811035 TTTATATGAT
1 TTT-TATTAT
*
2811045 TTTATGATTTT
1 TTT-T-ATTAT
*
2811056 TTTTTTTAT
1 TTTTATTAT
2811065 TTTTA
1 TTTTA
2811070 CCCATGTGGT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
9 19 0.53
10 11 0.31
11 6 0.17
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75
Consensus pattern (9 bp):
TTTTATTAT
Found at i:2813379 original size:7 final size:7
Alignment explanation
Indices: 2813369--2813464 Score: 51
Period size: 7 Copynumber: 13.9 Consensus size: 7
2813359 AGGTTTATAG
2813369 TTTAAGA
1 TTTAAGA
2813376 TTTAAGA
1 TTTAAGA
2813383 TTTAA-A
1 TTTAAGA
*
2813389 TTTTAGA
1 TTTAAGA
2813396 GTTTAAG-
1 -TTTAAGA
* *
2813403 TTTAGGTT
1 TTTAAG-A
*
2813411 TTTAACA
1 TTTAAGA
2813418 -TT-AGA
1 TTTAAGA
*
2813423 GTTTAGGA
1 -TTTAAGA
2813431 TTTATAG-
1 TTTA-AGA
2813438 TTTAAGA
1 TTTAAGA
2813445 TTTAAG-
1 TTTAAGA
*
2813451 TTTTAGA
1 TTTAAGA
2813458 GTTTAAG
1 -TTTAAG
2813465 TTGAGATTTT
Statistics
Matches: 67, Mismatches: 11, Indels: 21
0.68 0.11 0.21
Matches are distributed among these distances:
5 2 0.03
6 19 0.28
7 29 0.43
8 17 0.25
ACGTcount: A:0.33, C:0.01, G:0.18, T:0.48
Consensus pattern (7 bp):
TTTAAGA
Found at i:2813379 original size:14 final size:13
Alignment explanation
Indices: 2813357--2813466 Score: 73
Period size: 14 Copynumber: 8.0 Consensus size: 13
2813347 TTATTTCGTG
*
2813357 TAAGGTTTATAGTT
1 TAAGATTTA-AGTT
2813371 TAAGATTTAAGATT
1 TAAGATTTAAG-TT
2813385 TAA-ATTTTAGAGTT
1 TAAGA-TTTA-AGTT
*
2813399 TAAG-TTTAGGTTTT
1 TAAGATTTAAG--TT
*
2813413 TAACA-TTAGAGTT
1 TAAGATTTA-AGTT
*
2813426 TAGGATTTATAGTT
1 TAAGATTTA-AGTT
2813440 TAAGATTTAAGTT
1 TAAGATTTAAGTT
*
2813453 TTAGAGTTTAAGTT
1 TAAGA-TTTAAGTT
2813467 GAGATTTTTA
Statistics
Matches: 77, Mismatches: 9, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
12 1 0.01
13 20 0.26
14 53 0.69
15 3 0.04
ACGTcount: A:0.33, C:0.01, G:0.18, T:0.48
Consensus pattern (13 bp):
TAAGATTTAAGTT
Found at i:2813413 original size:21 final size:20
Alignment explanation
Indices: 2813389--2813466 Score: 77
Period size: 21 Copynumber: 3.8 Consensus size: 20
2813379 AAGATTTAAA
2813389 TTTTAGAGTTTAAGTTTAGG
1 TTTTAGAGTTTAAGTTTAGG
**
2813409 TTTTTA-ACATTAGAGTTTAGG
1 -TTTTAGAGTTTA-AGTTTAGG
* * *
2813430 ATTTATAGTTTAAGATTTAAG
1 TTTTAGAGTTTAAG-TTTAGG
2813451 TTTTAGAGTTTAAGTT
1 TTTTAGAGTTTAAGTT
2813467 GAGATTTTTA
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
20 12 0.26
21 34 0.74
ACGTcount: A:0.29, C:0.01, G:0.19, T:0.50
Consensus pattern (20 bp):
TTTTAGAGTTTAAGTTTAGG
Found at i:2819655 original size:31 final size:31
Alignment explanation
Indices: 2819620--2819682 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
2819610 ACAACTCGAC
* *
2819620 TTTTTAAAAAAAATTAATAGTTAAATTTAAT
1 TTTTTAAAAAAAATTAAGAGTAAAATTTAAT
***
2819651 TTTTTTTTAAAAATTAAGAGTAAAATTTAAT
1 TTTTTAAAAAAAATTAAGAGTAAAATTTAAT
2819682 T
1 T
2819683 AAAAAATAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (31 bp):
TTTTTAAAAAAAATTAAGAGTAAAATTTAAT
Found at i:2823169 original size:17 final size:17
Alignment explanation
Indices: 2823149--2823215 Score: 52
Period size: 17 Copynumber: 4.1 Consensus size: 17
2823139 CAATAAATAA
2823149 AAATATATAAAAATATT
1 AAATATATAAAAATATT
*
2823166 AAATAT-T-AAAATAAT
1 AAATATATAAAAATATT
* *
2823181 ATAATATA-AATAATTTT
1 A-AATATATAAAAATATT
*
2823198 AAA-AAATCAAAAATATT
1 AAATATAT-AAAAATATT
2823215 A
1 A
2823216 TAGGAGGGTT
Statistics
Matches: 38, Mismatches: 7, Indels: 10
0.69 0.13 0.18
Matches are distributed among these distances:
15 10 0.26
16 8 0.21
17 20 0.53
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (17 bp):
AAATATATAAAAATATT
Found at i:2823186 original size:16 final size:15
Alignment explanation
Indices: 2823143--2823190 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
2823133 AAATTTCAAT
*
2823143 AAATAAAAATATATAA
1 AAATAATAA-ATATAA
* *
2823159 AAATATTAAATATTA
1 AAATAATAAATATAA
2823174 AAATAATATAATATAA
1 AAATAATA-AATATAA
2823190 A
1 A
2823191 TAATTTTAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 12 0.46
16 14 0.54
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AAATAATAAATATAA
Found at i:2827723 original size:12 final size:12
Alignment explanation
Indices: 2827706--2827734 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
2827696 CAGTGCTTGT
2827706 TTGTTTGTTTGC
1 TTGTTTGTTTGC
2827718 TTGTTTGTTTGC
1 TTGTTTGTTTGC
2827730 TTGTT
1 TTGTT
2827735 CTCATTCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.07, G:0.24, T:0.69
Consensus pattern (12 bp):
TTGTTTGTTTGC
Done.