Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008955.1 Hibiscus syriacus cultivar Beakdansim tig00112285_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: 4658001
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 23
Found at i:2362979 original size:16 final size:17
Alignment explanation
Indices: 2362952--2362987 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
2362942 GATATGAGAA
2362952 AAATTCAATTTAAATTT
1 AAATTCAATTTAAATTT
*
2362969 AAATT-AATTTAATTTT
1 AAATTCAATTTAAATTT
2362985 AAA
1 AAA
2362988 ATAACGTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATTCAATTTAAATTT
Found at i:2365781 original size:24 final size:23
Alignment explanation
Indices: 2365754--2365804 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
2365744 GCATGCATAA
2365754 TTAATA-TCATTTTAAT-ATAATTAT
1 TTAATACT-ATTTT-ATCATAA-TAT
2365778 TTAATACTATTTTATCATAATAT
1 TTAATACTATTTTATCATAATAT
2365801 TTAA
1 TTAA
2365805 AACATAAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
23 9 0.36
24 15 0.60
25 1 0.04
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (23 bp):
TTAATACTATTTTATCATAATAT
Found at i:2366036 original size:16 final size:16
Alignment explanation
Indices: 2366018--2366062 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 16
2366008 TGATATTAAT
2366018 AAATTTAGATAAAATTA
1 AAATTTA-ATAAAATTA
2366035 AAATTTAATAAAACATTAA
1 AAATTTAAT-AAA-ATT-A
2366054 AAATTTAAT
1 AAATTTAAT
2366063 TTTATTATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 2 0.08
17 10 0.40
18 3 0.12
19 10 0.40
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (16 bp):
AAATTTAATAAAATTA
Found at i:2366058 original size:19 final size:17
Alignment explanation
Indices: 2366012--2366062 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 17
2366002 AAAGAGTGAT
2366012 ATTAATAAATTTAGATAAA
1 ATTAA-AAATTTA-ATAAA
2366031 ATT-AAAATTTAATAAAA
1 ATTAAAAATTTAAT-AAA
2366048 CATTAAAAATTTAAT
1 -ATTAAAAATTTAAT
2366063 TTTATTATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
16 2 0.07
17 10 0.34
18 4 0.14
19 13 0.45
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (17 bp):
ATTAAAAATTTAATAAA
Found at i:2371686 original size:55 final size:53
Alignment explanation
Indices: 2371571--2371710 Score: 151
Period size: 53 Copynumber: 2.6 Consensus size: 53
2371561 ATTTTATTTT
* * *
2371571 AAAAATATTTATTAATATAAAAATATCATATTCGTATTATATTCAATAAAATTTAAA
1 AAAAATA-TAATTAATA-AAATATATCATATTCATATTATATT-AATAAAATTT-AA
* *
2371628 AAAAATTGTAATTAATAAAATATAT-ATATTCATATTATATT-TTCAAAATTTAA
1 AAAAA-TATAATTAATAAAATATATCATATTCATATTATATTAAT-AAAATTTAA
2371681 GAAAAATATAATTAATAAAATAT-TCATATT
1 -AAAAATATAATTAATAAAATATATCATATT
2371711 TTTAATGTAA
Statistics
Matches: 73, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
52 1 0.01
53 24 0.33
54 12 0.16
55 15 0.21
56 7 0.10
57 13 0.18
58 1 0.01
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (53 bp):
AAAAATATAATTAATAAAATATATCATATTCATATTATATTAATAAAATTTAA
Found at i:2372086 original size:10 final size:10
Alignment explanation
Indices: 2372054--2372097 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
2372044 ATAAATCTAT
2372054 TAAATAAAAA
1 TAAATAAAAA
** *
2372064 TAAAT-CTAT
1 TAAATAAAAA
2372073 TAAATAAAAA
1 TAAATAAAAA
2372083 TAAATAAAAA
1 TAAATAAAAA
2372093 TAAAT
1 TAAAT
2372098 TTAGTCCCCT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
9 6 0.22
10 21 0.78
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (10 bp):
TAAATAAAAA
Found at i:2372090 original size:23 final size:19
Alignment explanation
Indices: 2372040--2372087 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
2372030 CTTATTAGAG
2372040 AAAAATAAATCTATTAAAT
1 AAAAATAAATCTATTAAAT
2372059 AAAAATAAATCTATTAAAT
1 AAAAATAAATCTATTAAAT
2372078 AAAAATAAAT
1 AAAAATAAAT
2372088 AAAAATAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAAATAAATCTATTAAAT
Found at i:2387034 original size:23 final size:24
Alignment explanation
Indices: 2386994--2387046 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
2386984 CCACTAGGGG
*
2386994 CTATGAAATTTGTCCCGAATGACCA
1 CTATGAAA-TTGTCCCGAAAGACCA
2387019 CTATGAAA-TGTCCCGAAAGACCA
1 CTATGAAATTGTCCCGAAAGACCA
2387042 CTATG
1 CTATG
2387047 TCCCGAAGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 19 0.70
25 8 0.30
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.25
Consensus pattern (24 bp):
CTATGAAATTGTCCCGAAAGACCA
Found at i:2387049 original size:18 final size:18
Alignment explanation
Indices: 2387026--2387061 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2387016 CCACTATGAA
2387026 ATGTCCCGAAAGACCACT
1 ATGTCCCGAAAGACCACT
*
2387044 ATGTCCCGAAGGACCACT
1 ATGTCCCGAAAGACCACT
2387062 GTAAATCCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.33, G:0.19, T:0.17
Consensus pattern (18 bp):
ATGTCCCGAAAGACCACT
Found at i:2387461 original size:2 final size:2
Alignment explanation
Indices: 2387454--2387493 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2387444 GCTTATGTAA
2387454 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
2387494 CACTTATATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2389399 original size:19 final size:20
Alignment explanation
Indices: 2389377--2389414 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
2389367 TTCTCTCATC
*
2389377 TCTTCTTCATTCTT-TCTTA
1 TCTTCTTCACTCTTCTCTTA
2389396 TCTTCTTCACTCTTCTCTT
1 TCTTCTTCACTCTTCTCTT
2389415 CTTCCAAACG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.08, C:0.32, G:0.00, T:0.61
Consensus pattern (20 bp):
TCTTCTTCACTCTTCTCTTA
Found at i:2390410 original size:21 final size:21
Alignment explanation
Indices: 2390384--2390468 Score: 134
Period size: 21 Copynumber: 4.0 Consensus size: 21
2390374 AGTCGAGGGT
*
2390384 TTCATAGGTCATTCGGGACAA
1 TTCATAGGTCCTTCGGGACAA
2390405 TTCATAGGTCCTTCGGGACAA
1 TTCATAGGTCCTTCGGGACAA
*
2390426 CTCATAGGTCCTTCGGGACATA
1 TTCATAGGTCCTTCGGGACA-A
*
2390448 TTCACAGGTCCTTCGGGACAA
1 TTCATAGGTCCTTCGGGACAA
2390469 ATTTCATATG
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
21 40 0.68
22 19 0.32
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.27
Consensus pattern (21 bp):
TTCATAGGTCCTTCGGGACAA
Found at i:2390444 original size:42 final size:43
Alignment explanation
Indices: 2390385--2390468 Score: 143
Period size: 43 Copynumber: 2.0 Consensus size: 43
2390375 GTCGAGGGTT
*
2390385 TCATAGGTCATTCGGGACA-ATTCATAGGTCCTTCGGGACAAC
1 TCATAGGTCATTCGGGACATATTCACAGGTCCTTCGGGACAAC
*
2390427 TCATAGGTCCTTCGGGACATATTCACAGGTCCTTCGGGACAA
1 TCATAGGTCATTCGGGACATATTCACAGGTCCTTCGGGACAA
2390469 ATTTCATATG
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
42 18 0.46
43 21 0.54
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.26
Consensus pattern (43 bp):
TCATAGGTCATTCGGGACATATTCACAGGTCCTTCGGGACAAC
Found at i:2391084 original size:23 final size:24
Alignment explanation
Indices: 2391042--2391088 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
2391032 GTGTAATCGA
2391042 TAATGTAGCAGGTTACTGTTCACG
1 TAATGTAGCAGGTTACTGTTCACG
*
2391066 TAATGTAGCA-GTTATTGTTCACG
1 TAATGTAGCAGGTTACTGTTCACG
2391089 CACTATTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (24 bp):
TAATGTAGCAGGTTACTGTTCACG
Found at i:2393814 original size:60 final size:60
Alignment explanation
Indices: 2393689--2393814 Score: 157
Period size: 60 Copynumber: 2.1 Consensus size: 60
2393679 ATGGTACCTC
** * *
2393689 GACTATAGGGTGTTGCTTTGTTTTGTCTCTCGACTATTAAAAGTTACAAAATGATCTTCT
1 GACTATAGGGTGTTGCTTTGTTGAGTCTCTCAACCATTAAAAGTTACAAAATGATCTTCT
* * *
2393749 AACTATAGGGTGTTGTTTTGTTGAGTCATC-CAACCATTAAAAGTTACAAAATGGTCATT-T
1 GACTATAGGGTGTTGCTTTGTTGAGTC-TCTCAACCATTAAAAGTTACAAAATGATC-TTCT
2393809 GACTAT
1 GACTAT
2393815 TCATATGTTG
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
60 52 0.93
61 4 0.07
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (60 bp):
GACTATAGGGTGTTGCTTTGTTGAGTCTCTCAACCATTAAAAGTTACAAAATGATCTTCT
Found at i:2401502 original size:17 final size:17
Alignment explanation
Indices: 2401464--2401496 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2401454 CGCAGGGGGC
2401464 GCGCCTTACCCCACGTA
1 GCGCCTTACCCCACGTA
*
2401481 GCGCCTTATCCCACGT
1 GCGCCTTACCCCACGT
2401497 GACGCCAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.45, G:0.18, T:0.21
Consensus pattern (17 bp):
GCGCCTTACCCCACGTA
Found at i:2403142 original size:30 final size:30
Alignment explanation
Indices: 2403055--2403144 Score: 144
Period size: 30 Copynumber: 3.0 Consensus size: 30
2403045 CACAGTCCAG
* * *
2403055 GACTTAGTTCCATCACCACCGATCAAAGTA
1 GACTTAGTTCCATCACCGCCAATCAAATTA
2403085 GACTTAGTTCCATCACCGCCAATCAAATTA
1 GACTTAGTTCCATCACCGCCAATCAAATTA
*
2403115 GACTTAGATCCATCACCGCCAATCAAATTA
1 GACTTAGTTCCATCACCGCCAATCAAATTA
2403145 AATTCTCCCC
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 56 1.00
ACGTcount: A:0.34, C:0.30, G:0.11, T:0.24
Consensus pattern (30 bp):
GACTTAGTTCCATCACCGCCAATCAAATTA
Found at i:2408063 original size:148 final size:147
Alignment explanation
Indices: 2407791--2408087 Score: 477
Period size: 148 Copynumber: 2.0 Consensus size: 147
2407781 ATGAGATGAA
* * * * *
2407791 TACCGGCTATCAATTTTATTTCGTTTTAATACGTTAACTTTCATTTTTTTAAATCATATCTACTG
1 TACCAGCTATCAATTTTATTTCGTTATAATACGTAAACTTTCATTTTTTTAAATCATACCTAATG
* * *
2407856 CTTACTTTTTATTTTATTTTAGTATCTATCGTTAAAAACTTAACGACATAACTAACGTGGAGATC
66 CTTACTTTTTATTTCATTTTAGTATCAACCGTTAAAAACTTAACGACATAACTAACGTGGAGATC
2407921 TTTAATTTTTTAATTTT
131 TTTAATTTTTTAATTTT
*
2407938 TACCAGCTATCAATTTTATTTCGTTATAATACGTAAACTTTTATTTTTTTAAAATCATACCTAAT
1 TACCAGCTATCAATTTTATTTCGTTATAATACGTAAACTTTCATTTTTTT-AAATCATACCTAAT
* * *
2408003 GTTTACTTTTTATTTCATTTTAGTATCAACCGTTAAAAACTTAACGACATAGCTAACGTGGATAT
65 GCTTACTTTTTATTTCATTTTAGTATCAACCGTTAAAAACTTAACGACATAACTAACGTGGAGAT
2408068 CTTTAATTTTTTAATTTT
130 CTTTAATTTTTTAATTTT
2408086 TA
1 TA
2408088 AATCATTGTT
Statistics
Matches: 137, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
147 46 0.34
148 91 0.66
ACGTcount: A:0.30, C:0.14, G:0.08, T:0.48
Consensus pattern (147 bp):
TACCAGCTATCAATTTTATTTCGTTATAATACGTAAACTTTCATTTTTTTAAATCATACCTAATG
CTTACTTTTTATTTCATTTTAGTATCAACCGTTAAAAACTTAACGACATAACTAACGTGGAGATC
TTTAATTTTTTAATTTT
Found at i:2409721 original size:8 final size:8
Alignment explanation
Indices: 2409708--2409767 Score: 66
Period size: 8 Copynumber: 7.2 Consensus size: 8
2409698 TAATTGCCCG
2409708 AACTCTCA
1 AACTCTCA
2409716 AACTCTCTTA
1 AACTCTC--A
*
2409726 AATTCTCA
1 AACTCTCA
*
2409734 AACTCTCT
1 AACTCTCA
*
2409742 AACTTTCA
1 AACTCTCA
2409750 AACTCTCA
1 AACTCTCA
*
2409758 AATTCTCA
1 AACTCTCA
2409766 AA
1 AA
2409768 ATGACTCATA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
8 36 0.84
10 7 0.16
ACGTcount: A:0.37, C:0.30, G:0.00, T:0.33
Consensus pattern (8 bp):
AACTCTCA
Found at i:2409766 original size:16 final size:17
Alignment explanation
Indices: 2409711--2409767 Score: 82
Period size: 16 Copynumber: 3.4 Consensus size: 17
2409701 TTGCCCGAAC
2409711 TCTCAAACTCTCTTAAAT
1 TCTCAAACTCTC-TAAAT
*
2409729 TCTCAAACTCTCTAACT
1 TCTCAAACTCTCTAAAT
2409746 T-TCAAACTCTC-AAAT
1 TCTCAAACTCTCTAAAT
2409761 TCTCAAA
1 TCTCAAA
2409768 ATGACTCATA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
15 4 0.11
16 15 0.42
17 5 0.14
18 12 0.33
ACGTcount: A:0.35, C:0.30, G:0.00, T:0.35
Consensus pattern (17 bp):
TCTCAAACTCTCTAAAT
Found at i:2410383 original size:58 final size:60
Alignment explanation
Indices: 2410273--2410397 Score: 191
Period size: 58 Copynumber: 2.1 Consensus size: 60
2410263 TTCTTTGATG
* * *
2410273 TCAATATGGATATGCCTTCTAGTTTCATGGGGAGACATTCATTTGCTAGCTTCTTCGACC
1 TCAATATGGATATGCCTTCCAATTTCATGGGAAGACATTCATTTGCTAGCTTCTTCGACC
* *
2410333 TCAATATGGATATGTCTTCCAATTT-A-GGGAAGACATTTATTTGCTAGCTTCTTCGACC
1 TCAATATGGATATGCCTTCCAATTTCATGGGAAGACATTCATTTGCTAGCTTCTTCGACC
2410391 TCAATAT
1 TCAATAT
2410398 AGAGATGCAT
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
58 37 0.62
59 1 0.02
60 22 0.37
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.38
Consensus pattern (60 bp):
TCAATATGGATATGCCTTCCAATTTCATGGGAAGACATTCATTTGCTAGCTTCTTCGACC
Found at i:2412842 original size:17 final size:18
Alignment explanation
Indices: 2412812--2412845 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
2412802 ATAAAGATAA
2412812 AATAAATGAAAATATTAG
1 AATAAATGAAAATATTAG
2412830 AATAAAT-AAAATATTA
1 AATAAATGAAAATATTA
2412846 TCAACATTAT
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:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (18 bp):
AATAAATGAAAATATTAG
Found at i:2414459 original size:2 final size:2
Alignment explanation
Indices: 2414447--2414487 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
2414437 CACCCATTTA
2414447 AT AT A- 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
2414488 GTTATTTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2415533 original size:10 final size:11
Alignment explanation
Indices: 2415515--2415579 Score: 53
Period size: 13 Copynumber: 5.7 Consensus size: 11
2415505 TTTACAATTA
2415515 AATAA-AAAAT
1 AATAATAAAAT
2415525 AAT-ATAAAAT
1 AATAATAAAAT
2415535 AATGTAATAAAAT
1 AA--TAATAAAAT
*
2415548 AATAATAAATTT
1 AATAATAAA-AT
* *
2415560 ATTAAATAAAAA
1 AAT-AATAAAAT
2415572 AATAATAA
1 AATAATAA
2415580 TATACCTTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
9 1 0.02
10 10 0.23
11 12 0.27
12 6 0.14
13 15 0.34
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (11 bp):
AATAATAAAAT
Found at i:2415557 original size:23 final size:24
Alignment explanation
Indices: 2415510--2415579 Score: 72
Period size: 24 Copynumber: 2.9 Consensus size: 24
2415500 ATAAGTTTAC
*
2415510 AATTAAATAAAA-AATAATATAAAAT
1 AATTAAATAAAATAAT-A-ATAAATT
2415535 AATGT-AATAAAATAATAATAAATT
1 AAT-TAAATAAAATAATAATAAATT
* *
2415559 TATTAAATAAAAAAATAATAA
1 AATTAAATAAAATAATAATAA
2415580 TATACCTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
23 1 0.03
24 23 0.59
25 11 0.28
26 4 0.10
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.30
Consensus pattern (24 bp):
AATTAAATAAAATAATAATAAATT
Found at i:2422954 original size:80 final size:80
Alignment explanation
Indices: 2422821--2422981 Score: 313
Period size: 80 Copynumber: 2.0 Consensus size: 80
2422811 ATGAAGTACC
*
2422821 AGCAAATGTGGCATAAACTGACCCTCCATTACACATGTATGAAGCTGATTATGATGCAATGTACG
1 AGCAAATGTGGCATAAACTGACCCTCCATCACACATGTATGAAGCTGATTATGATGCAATGTACG
2422886 GGCCAGAATTTACGG
66 GGCCAGAATTTACGG
2422901 AGCAAATGTGGCATAAACTGACCCTCCATCACACATGTATGAAGCTGATTATGATGCAATGTACG
1 AGCAAATGTGGCATAAACTGACCCTCCATCACACATGTATGAAGCTGATTATGATGCAATGTACG
2422966 GGCCAGAATTTACGG
66 GGCCAGAATTTACGG
2422981 A
1 A
2422982 TATGCCTCAT
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 80 1.00
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.24
Consensus pattern (80 bp):
AGCAAATGTGGCATAAACTGACCCTCCATCACACATGTATGAAGCTGATTATGATGCAATGTACG
GGCCAGAATTTACGG
Found at i:2425220 original size:35 final size:34
Alignment explanation
Indices: 2425135--2425221 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
2425125 AAAATAATTT
*
2425135 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
* *
2425169 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--G-TATTAAATGG
2425207 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
2425222 ACTGAAATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 4 0.09
38 11 0.24
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:2430134 original size:23 final size:23
Alignment explanation
Indices: 2430104--2430189 Score: 72
Period size: 23 Copynumber: 3.8 Consensus size: 23
2430094 ACCCAACGGA
*
2430104 TGCATCGGTGCACATTCAAGGAG
1 TGCATCGATGCACATTCAAGGAG
* *
2430127 TGCATCGGTGCATC-TTC-ATGA-
1 TGCATCGATGCA-CATTCAAGGAG
*
2430148 TGTATCGATGCACATTCAAAGG-G
1 TGCATCGATGCACATTC-AAGGAG
*
2430171 ATGCATCGATGCACTTTCA
1 -TGCATCGATGCACATTCA
2430190 TAGTGTATCG
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
20 1 0.02
21 13 0.25
22 3 0.06
23 18 0.35
24 16 0.31
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (23 bp):
TGCATCGATGCACATTCAAGGAG
Found at i:2430165 original size:21 final size:21
Alignment explanation
Indices: 2430141--2430204 Score: 58
Period size: 24 Copynumber: 2.9 Consensus size: 21
2430131 TCGGTGCATC
2430141 TTCATGATGTATCGATGCACA
1 TTCATGATGTATCGATGCACA
* * *
2430162 TTCAAAGGGATGCATCGATGCACT
1 TTC--A-TGATGTATCGATGCACA
2430186 TTCAT-AGTGTATCGATGCA
1 TTCATGA-TGTATCGATGCA
2430205 TTAAGCACAA
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
20 1 0.03
21 14 0.41
22 1 0.03
23 1 0.03
24 17 0.50
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (21 bp):
TTCATGATGTATCGATGCACA
Found at i:2430190 original size:45 final size:44
Alignment explanation
Indices: 2430102--2430204 Score: 122
Period size: 45 Copynumber: 2.3 Consensus size: 44
2430092 AAACCCAACG
* * *
2430102 GATGCATCGGTGCACATTCAAGGAGTGCATCGGTGCATCTTCAT
1 GATGTATCGATGCACATTCAAGGAGTGCATCGATGCATCTTCAT
2430146 GATGTATCGATGCACATTCAAAGG-GATGCATCGATGCA-CTTTCAT
1 GATGTATCGATGCACATTC-AAGGAG-TGCATCGATGCATC-TTCAT
2430191 -AGTGTATCGATGCA
1 GA-TGTATCGATGCA
2430205 TTAAGCACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
44 20 0.38
45 32 0.62
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.28
Consensus pattern (44 bp):
GATGTATCGATGCACATTCAAGGAGTGCATCGATGCATCTTCAT
Found at i:2434056 original size:22 final size:21
Alignment explanation
Indices: 2434014--2434053 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2434004 GAGATTATTT
*
2434014 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTAAAATA
2434035 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
2434054 ATAGTTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Found at i:2446443 original size:16 final size:16
Alignment explanation
Indices: 2446424--2446461 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
2446414 ATAATGAGCT
*
2446424 ATTACCCACTCGCACC
1 ATTACCCACTCACACC
2446440 ATTACCCACTCACACC
1 ATTACCCACTCACACC
2446456 ATTACC
1 ATTACC
2446462 GGATGGAGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.29, C:0.47, G:0.03, T:0.21
Consensus pattern (16 bp):
ATTACCCACTCACACC
Found at i:2449367 original size:21 final size:21
Alignment explanation
Indices: 2449328--2449372 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
2449318 TAACTTTTTA
*
2449328 TTTTCTCTTTCATCCTTAACAT
1 TTTTCTATTTCATCCTTAAC-T
*
2449350 TTTTCTATTTCAT-TTTAACT
1 TTTTCTATTTCATCCTTAACT
2449370 TTT
1 TTT
2449373 ACTTTTTCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.19
21 5 0.24
22 12 0.57
ACGTcount: A:0.18, C:0.20, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTTCTATTTCATCCTTAACT
Found at i:2450336 original size:24 final size:24
Alignment explanation
Indices: 2450309--2450361 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
2450299 TGACCCGACT
*
2450309 CCTGATCAGCACCGTTCTGAGACA
1 CCTGATCAGCACCGTTCTGACACA
* *
2450333 CCTGATCCGCACCGTTCTGACACC
1 CCTGATCAGCACCGTTCTGACACA
2450357 CCTGA
1 CCTGA
2450362 ATATCCGCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.21, C:0.40, G:0.19, T:0.21
Consensus pattern (24 bp):
CCTGATCAGCACCGTTCTGACACA
Found at i:2460732 original size:6 final size:6
Alignment explanation
Indices: 2460721--2460746 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2460711 AGCTGGATAA
2460721 CTGCCC CTGCCC CTGCCC CTGCCC CT
1 CTGCCC CTGCCC CTGCCC CTGCCC CT
2460747 TCCACTTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.65, G:0.15, T:0.19
Consensus pattern (6 bp):
CTGCCC
Found at i:2468281 original size:21 final size:22
Alignment explanation
Indices: 2468257--2468301 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
2468247 AAAATATATA
*
2468257 ATATA-AATAGTTTTTGAAGAT
1 ATATAGAATAGTTTTTGAAAAT
*
2468278 ATATAGTATAGTTTTTGAAAAT
1 ATATAGAATAGTTTTTGAAAAT
2468300 AT
1 AT
2468302 TTTTGAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.44
Consensus pattern (22 bp):
ATATAGAATAGTTTTTGAAAAT
Found at i:2468361 original size:38 final size:36
Alignment explanation
Indices: 2468276--2468372 Score: 115
Period size: 38 Copynumber: 2.6 Consensus size: 36
2468266 GTTTTTGAAG
* * *
2468276 ATATATAGTATAGTTTTTGAAAATATTTTTGAAAAC
1 ATATATAATATAGTTTTTGAAAAAATGTTTGAAAAC
*
2468312 ATATA-ATATATAGTTTTTAAAAAAAGGTGTTTGAAAAC
1 ATATATA-ATATAGTTTTTGAAAAAA--TGTTTGAAAAC
*
2468350 GTATATAATATAGTTTTTGAAAA
1 ATATATAATATAGTTTTTGAAAA
2468373 CATATTATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
35 1 0.02
36 20 0.39
38 29 0.57
39 1 0.02
ACGTcount: A:0.44, C:0.02, G:0.12, T:0.41
Consensus pattern (36 bp):
ATATATAATATAGTTTTTGAAAAAATGTTTGAAAAC
Found at i:2470229 original size:16 final size:16
Alignment explanation
Indices: 2470208--2470239 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2470198 AATAAATAAG
2470208 CGAACATAAACGAACA
1 CGAACATAAACGAACA
2470224 CGAACATAAACGAACA
1 CGAACATAAACGAACA
2470240 AAATTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.25, G:0.12, T:0.06
Consensus pattern (16 bp):
CGAACATAAACGAACA
Found at i:2470320 original size:10 final size:10
Alignment explanation
Indices: 2470305--2470379 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
2470295 CATTTAATAA
2470305 ATAAACGAAC
1 ATAAACGAAC
2470315 ATAAACGAAC
1 ATAAACGAAC
*
2470325 ----ACAAAC
1 ATAAACGAAC
2470331 ATAAACGAAC
1 ATAAACGAAC
** *
2470341 ACGAAC-ATAA
1 ATAAACGA-AC
2470351 ATGAACACGAAC
1 AT-AA-ACGAAC
2470363 ATAAACGAAC
1 ATAAACGAAC
2470373 ATAAACG
1 ATAAACG
2470380 TTGGAGACCC
Statistics
Matches: 49, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
6 5 0.10
9 1 0.02
10 34 0.69
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.59, C:0.21, G:0.11, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:2470333 original size:16 final size:16
Alignment explanation
Indices: 2470312--2470378 Score: 98
Period size: 16 Copynumber: 4.2 Consensus size: 16
2470302 TAAATAAACG
2470312 AACATAAACGAACACA
1 AACATAAACGAACACA
*
2470328 AACATAAACGAACACG
1 AACATAAACGAACACA
* *
2470344 AACATAAATGAACACG
1 AACATAAACGAACACA
*
2470360 AACATAAACGAACATA
1 AACATAAACGAACACA
2470376 AAC
1 AAC
2470379 GTTGGAGACC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.60, C:0.22, G:0.09, T:0.09
Consensus pattern (16 bp):
AACATAAACGAACACA
Found at i:2470345 original size:32 final size:32
Alignment explanation
Indices: 2470309--2470373 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
2470299 TAATAAATAA
2470309 ACGAACATAAACGAACACAAACATAAACGAAC
1 ACGAACATAAACGAACACAAACATAAACGAAC
* *
2470341 ACGAACATAAATGAACACGAACATAAACGAAC
1 ACGAACATAAACGAACACAAACATAAACGAAC
2470373 A
1 A
2470374 TAAACGTTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.58, C:0.23, G:0.11, T:0.08
Consensus pattern (32 bp):
ACGAACATAAACGAACACAAACATAAACGAAC
Found at i:2471952 original size:24 final size:24
Alignment explanation
Indices: 2471891--2471952 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
2471881 TATTAGGTTA
*
2471891 AACATAAATGAACGCACATAAACG
1 AACATAACTGAACGCACATAAACG
* *
2471915 AACATAACTAAACGCATATAAACG
1 AACATAACTGAACGCACATAAACG
*
2471939 AACATAACCGAACG
1 AACATAACTGAACG
2471953 TTCACGAACG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.53, C:0.23, G:0.11, T:0.13
Consensus pattern (24 bp):
AACATAACTGAACGCACATAAACG
Found at i:2480312 original size:3 final size:3
Alignment explanation
Indices: 2480304--2480355 Score: 68
Period size: 3 Copynumber: 16.7 Consensus size: 3
2480294 AGTGTAAAGT
*
2480304 TAA TAA TAA TAA TAA TAA TAGT TAA TAA TAA TTAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA -TAA TAA TAA TAA TAA
*
2480351 AAA TA
1 TAA TA
2480356 TAAAATATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
3 38 0.88
4 5 0.12
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2480331 original size:10 final size:10
Alignment explanation
Indices: 2480307--2480350 Score: 65
Period size: 10 Copynumber: 4.6 Consensus size: 10
2480297 GTAAAGTTAA
2480307 TAATAATAA-
1 TAATAATAAT
*
2480316 TAATAATAGT
1 TAATAATAAT
2480326 TAATAATAAT
1 TAATAATAAT
2480336 TAATAATAA-
1 TAATAATAAT
2480345 TAATAA
1 TAATAA
2480351 AAATATAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
9 14 0.44
10 18 0.56
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (10 bp):
TAATAATAAT
Found at i:2480331 original size:13 final size:12
Alignment explanation
Indices: 2480304--2480355 Score: 68
Period size: 13 Copynumber: 4.2 Consensus size: 12
2480294 AGTGTAAAGT
2480304 TAATAATAATAA
1 TAATAATAATAA
*
2480316 TAATAATAGTTAA
1 TAATAATA-ATAA
2480329 TAATAATTAATAA
1 TAATAA-TAATAA
*
2480342 TAATAATAAAAA
1 TAATAATAATAA
2480354 TA
1 TA
2480356 TAAAATATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
12 15 0.43
13 18 0.51
14 2 0.06
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (12 bp):
TAATAATAATAA
Found at i:2480577 original size:43 final size:40
Alignment explanation
Indices: 2480523--2480627 Score: 113
Period size: 40 Copynumber: 2.5 Consensus size: 40
2480513 GACGACACTG
* *
2480523 CTCATACGTGATGAAGAGTTC-GGATCGTCTAAGGGTGACACGG
1 CTCATACGTGATGAAGAGTTCTGG-TCG---AAGGATGACACGA
* * **
2480566 TTCATACGTGATGAGGAAATCTGGTCGAAGGATGACACGA
1 CTCATACGTGATGAAGAGTTCTGGTCGAAGGATGACACGA
2480606 CTCATACGTGATGAAGAGTTCT
1 CTCATACGTGATGAAGAGTTCT
2480628 TGGCCATCTT
Statistics
Matches: 51, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
40 29 0.57
43 20 0.39
44 2 0.04
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.25
Consensus pattern (40 bp):
CTCATACGTGATGAAGAGTTCTGGTCGAAGGATGACACGA
Found at i:2480858 original size:130 final size:134
Alignment explanation
Indices: 2480550--2480858 Score: 355
Period size: 135 Copynumber: 2.3 Consensus size: 134
2480540 GTTCGGATCG
** *
2480550 TCTAAGGGTGACACGGTTCATACGTGATGAGGAAATCTGGTC-GAAGGATGACACGACTCATACG
1 TCTAAGGGTGACACGACTCCTACGTGATGAGGAAATCTGGTCAGAAGGATGACACGACTCATACG
* *
2480614 TGATGAAGAGTTCTTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGACGGC
66 TGATGAAGAGTTCTTGGCCATCTTTA-GAA-GGTGATAACTCAGTTCCTACGCAATGAGGACGGC
2480679 TGGTTA
129 TGGTTA
* * * * *
2480685 TTTAAGGGTGACACGACTCCTACGTGATGAGGATATCTAGTCAG-GGGATGACACTG-CTCCTAC
1 TCTAAGGGTGACACGACTCCTACGTGATGAGGAAATCTGGTCAGAAGGATGACAC-GACTCATAC
* *
2480748 GTGATGAAGAGTTCTTGGCCAT-TTTA-TA-GTGATAACAT-AGTTCCTACGTAATGAGGACGGC
65 GTGATGAAGAGTTCTTGGCCATCTTTAGAAGGTGATAAC-TCAGTTCCTACGCAATGAGGACGGC
2480809 TGGTTA
129 TGGTTA
* * ** * *
2480815 TCTAATGTTGACGTTG-CTCCTACGTGATGAGGAGATCCGGTCAG
1 TCTAAGGGTGAC-ACGACTCCTACGTGATGAGGAAATCTGGTCAG
2480859 CTGATGTTGA
Statistics
Matches: 150, Mismatches: 20, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
130 68 0.45
131 2 0.01
132 1 0.01
134 4 0.03
135 73 0.49
136 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (134 bp):
TCTAAGGGTGACACGACTCCTACGTGATGAGGAAATCTGGTCAGAAGGATGACACGACTCATACG
TGATGAAGAGTTCTTGGCCATCTTTAGAAGGTGATAACTCAGTTCCTACGCAATGAGGACGGCTG
GTTA
Found at i:2481829 original size:8 final size:8
Alignment explanation
Indices: 2481807--2481867 Score: 63
Period size: 8 Copynumber: 7.5 Consensus size: 8
2481797 TCCTTTATTT
2481807 ATTTTTTC
1 ATTTTTTC
*
2481815 TTCTTTTTC
1 AT-TTTTTC
2481824 A-TTTTTC
1 ATTTTTTC
2481831 ATTTTTTC
1 ATTTTTTC
2481839 ATTTCCTTT-
1 ATTT--TTTC
*
2481848 TTTTTTTC
1 ATTTTTTC
2481856 ATTTTTTC
1 ATTTTTTC
2481864 ATTT
1 ATTT
2481868 CCCTTTTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
7 10 0.23
8 22 0.50
9 9 0.20
10 3 0.07
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.75
Consensus pattern (8 bp):
ATTTTTTC
Found at i:2481843 original size:13 final size:13
Alignment explanation
Indices: 2481827--2481868 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
2481817 CTTTTTCATT
2481827 TTTCATTTTTTCA
1 TTTCATTTTTTCA
* *
2481840 TTTCCTTTTTT-T
1 TTTCATTTTTTCA
2481852 TTTCATTTTTTCA
1 TTTCATTTTTTCA
2481865 TTTC
1 TTTC
2481869 CCTTTTTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
12 10 0.42
13 14 0.58
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTCATTTTTTCA
Found at i:2481874 original size:24 final size:25
Alignment explanation
Indices: 2481825--2481883 Score: 102
Period size: 25 Copynumber: 2.4 Consensus size: 25
2481815 TTCTTTTTCA
*
2481825 TTTTTCATTTTTTCATTTCCTTTTT
1 TTTTTCATTTTTTCATTTCCTCTTT
2481850 TTTTTCATTTTTTCATTTCC-CTTT
1 TTTTTCATTTTTTCATTTCCTCTTT
2481874 TTTTTCATTT
1 TTTTTCATTT
2481884 CCCTTTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 13 0.39
25 20 0.61
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (25 bp):
TTTTTCATTTTTTCATTTCCTCTTT
Found at i:2481895 original size:17 final size:16
Alignment explanation
Indices: 2481857--2481894 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
2481847 TTTTTTTTCA
2481857 TTTTTTCATTTCCCTT
1 TTTTTTCATTTCCCTT
2481873 TTTTTTCATTTCCCTT
1 TTTTTTCATTTCCCTT
2481889 TTTTTT
1 TTTTTT
2481895 TTTTTTAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTTCATTTCCCTT
Found at i:2491925 original size:13 final size:13
Alignment explanation
Indices: 2491907--2491931 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2491897 TTCTACACTC
2491907 AAAATAAATAAAT
1 AAAATAAATAAAT
2491920 AAAATAAATAAA
1 AAAATAAATAAA
2491932 AAGGTTAGAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:2495186 original size:3 final size:3
Alignment explanation
Indices: 2495178--2495219 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
2495168 AGTGTAAAGT
* *
2495178 TAA TAA TAA TAA TAA TAA TAGT TAA TAA TAA TAA TAA AAA TA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TA
2495220 TAAAATATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 32 0.94
4 2 0.06
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2495203 original size:22 final size:22
Alignment explanation
Indices: 2495175--2495219 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
2495165 AAAAGTGTAA
*
2495175 AGTTAATAATAATAATAATAAT
1 AGTTAATAATAATAATAAAAAT
2495197 AGTTAATAATAATAATAAAAAT
1 AGTTAATAATAATAATAAAAAT
2495219 A
1 A
2495220 TAAAATATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (22 bp):
AGTTAATAATAATAATAAAAAT
Found at i:2496216 original size:19 final size:19
Alignment explanation
Indices: 2496200--2496240 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
2496190 AATTTCCGAT
2496200 GGATTACATGTTTTCCGTC
1 GGATTACATGTTTTCCGTC
*
2496219 GGATTACATGTTTTCCATC
1 GGATTACATGTTTTCCGTC
2496238 GGA
1 GGA
2496241 AATTTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.39
Consensus pattern (19 bp):
GGATTACATGTTTTCCGTC
Found at i:2496397 original size:17 final size:17
Alignment explanation
Indices: 2496375--2496432 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
2496365 ACCAAAAATT
2496375 AATAATAATATAATTAA
1 AATAATAATATAATTAA
*
2496392 AATAATTATATTAATTAA
1 AATAATAATA-TAATTAA
* *
2496410 AA-AATTAGATAA-TAA
1 AATAATAATATAATTAA
2496425 TAATAATA
1 -AATAATA
2496433 CTAACAAGTC
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
15 3 0.09
16 5 0.14
17 18 0.51
18 9 0.26
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (17 bp):
AATAATAATATAATTAA
Found at i:2496404 original size:14 final size:15
Alignment explanation
Indices: 2496371--2496431 Score: 51
Period size: 14 Copynumber: 4.2 Consensus size: 15
2496361 AAAGACCAAA
2496371 AATTAATAATAATAT
1 AATTAATAATAATAT
2496386 AATTAA-AATAAT-T
1 AATTAATAATAATAT
*
2496399 ATATTAAT--TAA-AA
1 A-ATTAATAATAATAT
2496412 AATTAGATAATAATAAT
1 AATTA-ATAATAAT-AT
2496429 AAT
1 AAT
2496432 ACTAACAAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
12 4 0.11
13 8 0.22
14 11 0.31
15 9 0.25
17 4 0.11
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (15 bp):
AATTAATAATAATAT
Found at i:2496432 original size:9 final size:10
Alignment explanation
Indices: 2496374--2496432 Score: 51
Period size: 9 Copynumber: 6.5 Consensus size: 10
2496364 GACCAAAAAT
2496374 TAATAA-TAA
1 TAATAATTAA
2496383 T-ATAATTAA
1 TAATAATTAA
2496392 -AATAATT-A
1 TAATAATTAA
*
2496400 TATTAATTAA
1 TAATAATTAA
2496410 -AA-AATTAGA
1 TAATAATTA-A
2496419 TAATAA-TAA
1 TAATAATTAA
2496428 TAATA
1 TAATA
2496433 CTAACAAGTC
Statistics
Matches: 41, Mismatches: 2, Indels: 14
0.72 0.04 0.25
Matches are distributed among these distances:
8 10 0.24
9 24 0.59
10 5 0.12
11 2 0.05
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (10 bp):
TAATAATTAA
Found at i:2497072 original size:30 final size:31
Alignment explanation
Indices: 2497033--2497104 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
2497023 TAGTGAATCT
*
2497033 GTCAGAAATTTGTGACCG-ATCCACATA-TCC
1 GTCACAAATTTGTGA-CGTATCCACATATTCC
* *
2497063 GTCACAAATTTGTGATGTGTCCACATATTCC
1 GTCACAAATTTGTGACGTATCCACATATTCC
*
2497094 ATCACAAATTT
1 GTCACAAATTT
2497105 AAAAAATTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 1 0.03
30 22 0.61
31 13 0.36
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.32
Consensus pattern (31 bp):
GTCACAAATTTGTGACGTATCCACATATTCC
Found at i:2497639 original size:75 final size:75
Alignment explanation
Indices: 2497548--2497697 Score: 300
Period size: 75 Copynumber: 2.0 Consensus size: 75
2497538 ACGGTTTCGA
2497548 TACCATATCCTATAGTAGTACCGATACCATGATCATGGTACCAATACTACTCCTTTGGTTTTGAC
1 TACCATATCCTATAGTAGTACCGATACCATGATCATGGTACCAATACTACTCCTTTGGTTTTGAC
2497613 TCCAAGATTT
66 TCCAAGATTT
2497623 TACCATATCCTATAGTAGTACCGATACCATGATCATGGTACCAATACTACTCCTTTGGTTTTGAC
1 TACCATATCCTATAGTAGTACCGATACCATGATCATGGTACCAATACTACTCCTTTGGTTTTGAC
2497688 TCCAAGATTT
66 TCCAAGATTT
2497698 AACAGAATGC
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 75 1.00
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (75 bp):
TACCATATCCTATAGTAGTACCGATACCATGATCATGGTACCAATACTACTCCTTTGGTTTTGAC
TCCAAGATTT
Found at i:2497719 original size:75 final size:75
Alignment explanation
Indices: 2497559--2497724 Score: 255
Period size: 75 Copynumber: 2.2 Consensus size: 75
2497549 ACCATATCCT
2497559 ATAGTAGTACCGATACCATGATCATGGTACCAATACTACTCCTTTGGTTTTGACTCCAAGATTTT
1 ATAGTAGTACCGATACCATGATCATGGTACCAATACTACTCCTTTGGTTTTGACTCCAAGATTTT
* * **
2497624 ACCATATCCT
66 AACAAATCAA
2497634 ATAGTAGTACCGATACCATGATCATGGTACCAATACTACTCCTTTGGTTTTGACTCCAAGA-TTT
1 ATAGTAGTACCGATACCATGATCATGGTACCAATACTACTCCTTTGGTTTTGACTCCAAGATTTT
2497698 AACAGAATGCAA
66 AACA-AAT-CAA
*
2497710 ATA-TGGTACCGATAC
1 ATAGTAGTACCGATAC
2497725 TACTCTTTAT
Statistics
Matches: 84, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
74 6 0.07
75 74 0.88
76 4 0.05
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (75 bp):
ATAGTAGTACCGATACCATGATCATGGTACCAATACTACTCCTTTGGTTTTGACTCCAAGATTTT
AACAAATCAA
Found at i:2500005 original size:113 final size:113
Alignment explanation
Indices: 2499866--2500096 Score: 349
Period size: 113 Copynumber: 2.0 Consensus size: 113
2499856 ATGTAGTTAT
* * * * *
2499866 TTTTTTATTTCCGACAGAATGGTTA-TTCTTTCACAAATTAGATTGGTATATTTTAATTAAAGTT
1 TTTTTAATTTCCGACAGAATGATTATTTC-ATCACAAATTAAATTGGTATATTTTAATTAAAATT
* * *
2499930 GAACAAAACTTT-TGATGGAATCATTGTCCCGTCATAAATTAAATTGATA
65 GAACAAAA-TTTCCGACGGAATCATTGTCCCGTCATAAATTAAATTAATA
*
2499979 TTTTTAATTTCCGACGGAATGATTATTTCATCACAAATTAAATTGGTATATTTTAATTAAAATTG
1 TTTTTAATTTCCGACAGAATGATTATTTCATCACAAATTAAATTGGTATATTTTAATTAAAATTG
2500044 AACAAAATTTCCGACGGAATCATTGTCCCGTCATAAATTAAATTAATA
66 AACAAAATTTCCGACGGAATCATTGTCCCGTCATAAATTAAATTAATA
2500092 TTTTT
1 TTTTT
2500097 TTTATTTAAA
Statistics
Matches: 107, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
112 3 0.03
113 101 0.94
114 3 0.03
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (113 bp):
TTTTTAATTTCCGACAGAATGATTATTTCATCACAAATTAAATTGGTATATTTTAATTAAAATTG
AACAAAATTTCCGACGGAATCATTGTCCCGTCATAAATTAAATTAATA
Found at i:2504786 original size:25 final size:25
Alignment explanation
Indices: 2504707--2504805 Score: 94
Period size: 25 Copynumber: 3.8 Consensus size: 25
2504697 GTAGCTGAAC
2504707 TTTATTTTATTTATAATATTATTTA
1 TTTATTTTATTTATAATATTATTTA
* ** * *
2504732 TTTATTTTGTCAAGGAATA-TATATA
1 TTTATTTTATTTA-TAATATTATTTA
2504757 TTTTATTTTATTTATAATATTATTTA
1 -TTTATTTTATTTATAATATTATTTA
2504783 TTTATTCTTTATATTAT-ATATTA
1 TTTA-T-TTTAT-TTATAATATTA
2504806 GATAAAATTT
Statistics
Matches: 58, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
25 23 0.40
26 20 0.34
27 11 0.19
28 4 0.07
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (25 bp):
TTTATTTTATTTATAATATTATTTA
Found at i:2504793 original size:11 final size:12
Alignment explanation
Indices: 2504755--2504804 Score: 52
Period size: 11 Copynumber: 4.3 Consensus size: 12
2504745 GGAATATATA
2504755 TATTT-TATT-T
1 TATTTATATTAT
*
2504765 TATTTATAATAT
1 TATTTATATTAT
2504777 TATTTAT-TTAT
1 TATTTATATTAT
*
2504788 TCTTTATATTAT
1 TATTTATATTAT
2504800 ATATT
1 -TATT
2504805 AGATAAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
10 5 0.16
11 12 0.38
12 12 0.38
13 3 0.09
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (12 bp):
TATTTATATTAT
Found at i:2508375 original size:3 final size:3
Alignment explanation
Indices: 2508367--2508392 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2508357 TTTTATTCTA
2508367 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
2508393 GTCATGACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2510203 original size:2 final size:2
Alignment explanation
Indices: 2510196--2510220 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2510186 GCTTAGGATC
2510196 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
2510221 AATGTGTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2515756 original size:58 final size:58
Alignment explanation
Indices: 2515666--2515779 Score: 167
Period size: 58 Copynumber: 2.0 Consensus size: 58
2515656 GACATTTCCG
* * * *
2515666 GCGTATATTGACATTGAGATACTATATTCAGTAATATCAAACCAGCTGCGTGTAACCA
1 GCGTATATTGACATTCAGATACTAGACTCAGTAATATCAAACCAGCTGCATGTAACCA
*
2515724 GCGTATATT-AGCATTCAGATATTAGACTCAGTAATATCAAACCAGCTGCATGTAAC
1 GCGTATATTGA-CATTCAGATACTAGACTCAGTAATATCAAACCAGCTGCATGTAAC
2515780 AAATCAGGAG
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
57 1 0.02
58 49 0.98
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (58 bp):
GCGTATATTGACATTCAGATACTAGACTCAGTAATATCAAACCAGCTGCATGTAACCA
Found at i:2515905 original size:36 final size:36
Alignment explanation
Indices: 2515858--2515926 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
2515848 TTGAATTTGC
* * *
2515858 AACAATGTAGGTAGATTGAGTTGCTTAAGGATTTCA
1 AACAATGTAGGTAAATGGAGTTGCTCAAGGATTTCA
2515894 AACAATGTAGGTAAATGGAGTTGCTCAAGGATT
1 AACAATGTAGGTAAATGGAGTTGCTCAAGGATT
2515927 ATAATCGTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.35, C:0.09, G:0.26, T:0.30
Consensus pattern (36 bp):
AACAATGTAGGTAAATGGAGTTGCTCAAGGATTTCA
Found at i:2519122 original size:18 final size:18
Alignment explanation
Indices: 2519099--2519137 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
2519089 CCAAGCAAAT
2519099 GGGAGGAGTCTCACTGAA
1 GGGAGGAGTCTCACTGAA
2519117 GGGAGGAGTCTCACTGAA
1 GGGAGGAGTCTCACTGAA
2519135 GGG
1 GGG
2519138 TGAAGAGGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.26, C:0.15, G:0.44, T:0.15
Consensus pattern (18 bp):
GGGAGGAGTCTCACTGAA
Found at i:2525600 original size:29 final size:28
Alignment explanation
Indices: 2525465--2525693 Score: 110
Period size: 29 Copynumber: 8.0 Consensus size: 28
2525455 TGTAAATAAA
* ** * *
2525465 GTAATATTTATATTTTTATTTAATTAAT
1 GTAATATTTATATTTTAAAATATTTATT
* *
2525493 GTGATATATTTAT-TTTAATAAAATATTAAAT
1 GT-A-ATATTTATATTT--TAAAATATTTATT
* *
2525524 GCT-ATATTTATAATTTAAAAACATTT-TAT
1 G-TAATATTTAT-ATTTTAAAATATTTAT-T
* *
2525553 ATAATATTTATATTTTAAAATGTTTATT
1 GTAATATTTATATTTTAAAATATTTATT
* *
2525581 GTGATGTTTATATTTCTAAAATATTTATT
1 GTAATATTTATATTT-TAAAATATTTATT
* * *
2525610 TTAATATTTATGTTTTTAAAATATTTAAT
1 GTAATATTTAT-ATTTTAAAATATTTATT
* * **
2525639 CTGATATTTA-ATTTTTTAAT-TTTA-T
1 GTAATATTTATATTTTAAAATATTTATT
* *
2525664 ATATTATTATAATATTTTAACAATATTTAT
1 GTAATATT-T-ATATTTTAA-AATATTTAT
2525694 AAATATCGTA
Statistics
Matches: 151, Mismatches: 32, Indels: 33
0.70 0.15 0.15
Matches are distributed among these distances:
25 6 0.04
26 5 0.03
27 8 0.05
28 32 0.21
29 72 0.48
30 15 0.10
31 12 0.08
32 1 0.01
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.55
Consensus pattern (28 bp):
GTAATATTTATATTTTAAAATATTTATT
Found at i:2525889 original size:12 final size:12
Alignment explanation
Indices: 2525872--2525919 Score: 62
Period size: 12 Copynumber: 4.0 Consensus size: 12
2525862 TTATAATCAT
2525872 ATAAAAATATAA
1 ATAAAAATATAA
* *
2525884 ATAAAAACATATG
1 ATAAAAATATA-A
2525897 ATAAAAATATAA
1 ATAAAAATATAA
2525909 ATAAAAA-ATAA
1 ATAAAAATATAA
2525920 TATTATTGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
11 4 0.13
12 17 0.55
13 10 0.32
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (12 bp):
ATAAAAATATAA
Found at i:2525915 original size:13 final size:13
Alignment explanation
Indices: 2525874--2525918 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
2525864 ATAATCATAT
2525874 AAAAATATAAATA
1 AAAAATATAAATA
*
2525887 AAAACATAT-GAT-
1 AAAA-ATATAAATA
2525899 AAAAATATAAATA
1 AAAAATATAAATA
2525912 AAAAATA
1 AAAAATA
2525919 ATATTATTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
11 4 0.15
12 6 0.22
13 13 0.48
14 4 0.15
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (13 bp):
AAAAATATAAATA
Found at i:2528877 original size:53 final size:53
Alignment explanation
Indices: 2528797--2528902 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
2528787 AAACCTGCAA
2528797 CAGAGTTATGAACTTCCGGCCACTGTTAGTGAGCAGACAGTATTCTGGATGTT
1 CAGAGTTATGAACTTCCGGCCACTGTTAGTGAGCAGACAGTATTCTGGATGTT
2528850 CAGAGTTATGAACTTCCGGCCACTGTTAGTGAGCAGACAGTATTCTGGATGTT
1 CAGAGTTATGAACTTCCGGCCACTGTTAGTGAGCAGACAGTATTCTGGATGTT
2528903 GCCCAGCAAC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (53 bp):
CAGAGTTATGAACTTCCGGCCACTGTTAGTGAGCAGACAGTATTCTGGATGTT
Found at i:2532952 original size:2 final size:2
Alignment explanation
Indices: 2532895--2532942 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
2532885 ATATTCATTC
2532895 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
2532937 AT AT AT
1 AT AT AT
2532943 TAACATATAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2533535 original size:31 final size:32
Alignment explanation
Indices: 2533499--2533559 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
2533489 CATGGTCACA
*
2533499 TCACATAGT-TCTTTATCTCAT-TTCATATAGT
1 TCACATA-TATCTTTATCTCATATGCATATAGT
*
2533530 TCACATATATCTTTTTCTCATATGCATATA
1 TCACATATATCTTTATCTCATATGCATATA
2533560 ACATATTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 1 0.04
31 18 0.69
32 7 0.27
ACGTcount: A:0.28, C:0.20, G:0.05, T:0.48
Consensus pattern (32 bp):
TCACATATATCTTTATCTCATATGCATATAGT
Found at i:2533660 original size:22 final size:22
Alignment explanation
Indices: 2533635--2533681 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
2533625 ATCTCATAGA
2533635 TCACTATCATACAATACATATC
1 TCACTATCATACAATACATATC
2533657 TCACTATCATACAATACATATC
1 TCACTATCATACAATACATATC
2533679 TCA
1 TCA
2533682 TAACATGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.40, C:0.28, G:0.00, T:0.32
Consensus pattern (22 bp):
TCACTATCATACAATACATATC
Found at i:2535530 original size:23 final size:20
Alignment explanation
Indices: 2535493--2535535 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 20
2535483 ATTTTATTAT
2535493 TAATATAATATAAAATAAAA
1 TAATATAATATAAAATAAAA
2535513 TAATAATAATGATCAAAATAAAA
1 TAAT-ATAAT-AT-AAAATAAAA
2535536 GAAATTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 5 0.25
22 2 0.10
23 9 0.45
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (20 bp):
TAATATAATATAAAATAAAA
Found at i:2538301 original size:20 final size:20
Alignment explanation
Indices: 2538278--2538337 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
2538268 TTTTACAATA
2538278 GTTTAATTATTTTAGTTATT
1 GTTTAATTATTTTAGTTATT
*
2538298 GTTTAAATATATTTTA-ATA-T
1 GTTT-AAT-TATTTTAGTTATT
2538318 GTTTAATTATTATT-GTTATT
1 GTTTAATTATT-TTAGTTATT
2538338 TTATTTTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
18 4 0.12
19 7 0.21
20 10 0.30
21 5 0.15
22 7 0.21
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (20 bp):
GTTTAATTATTTTAGTTATT
Found at i:2538388 original size:27 final size:26
Alignment explanation
Indices: 2538340--2538406 Score: 73
Period size: 28 Copynumber: 2.5 Consensus size: 26
2538330 TTGTTATTTT
* *
2538340 ATTTTTATTAATATATATTATTTGATTA
1 ATTTTTA-AAATATATAATATTT-ATTA
*
2538368 ATTTTATAAAATA-ATAATATTTATTT
1 ATTTT-TAAAATATATAATATTTATTA
2538394 ATTTTTAAAATAT
1 ATTTTTAAAATAT
2538407 TAAGAAAAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
25 7 0.21
26 8 0.24
27 8 0.24
28 9 0.26
29 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (26 bp):
ATTTTTAAAATATATAATATTTATTA
Found at i:2538487 original size:2 final size:2
Alignment explanation
Indices: 2538480--2538516 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2538470 ATTATGCTAA
2538480 AT AT AT AT AT AT AT AT AT AT AT AT AT A- 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
2538517 TATTAATTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2538789 original size:137 final size:135
Alignment explanation
Indices: 2538382--2538796 Score: 367
Period size: 137 Copynumber: 3.0 Consensus size: 135
2538372 TATAAAATAA
*
2538382 TAATATTTATTTATTTTTAAAATATTAAGAAAAGGGCAGTCTTAAAACAACTAGATTTCCTATTC
1 TAATATTTA-TT-TTTTTAAAATATTAAGAAAAGGGCAGTCTT-AAACAACTAGATGTCCTATTC
* * *
2538447 TGGTATTTTAAAGAAT-AATAAATATTATGCTAAATATATATATATATATATATATATATAATAT
63 TGGTATTTTAAA-AATAAAT-AA-A-TAT-CT---TATTTATATAAATA-ATATATAT-TAATAC
**
2538511 ATATATTATTAATTATGTTT
118 AT-T-TTATTAAAAATGTTT
** * * *
2538531 TAATATTTATTTATTTTTCAATATTAAG-AAAGGGCAGTTTTAACACAACTGGATGTTC-AGTTC
1 TAATATTTATTT-TTTTAAAATATTAAGAAAAGGGCAGTCTTAA-ACAACTAGATGTCCTA-TTC
** * * *
2538594 TAATATTTT-TAAATAAATAAATATCCTATCTT-TATAAATAATATATATTAAT-CTATTTTTTT
63 TGGTATTTTAAAAATAAATAAATATCTTAT-TTATATAAATAATATATATTAATAC-ATTTTATT
2538656 AGAAAAATGTTT
126 --AAAAATGTTT
* * *
2538668 TAATATTTATTTTTTTAAAATATTAAGAAAATGACAGTCTTAAAGCAACTAGATGTCCTATTTTG
1 TAATATTTATTTTTTTAAAATATTAAGAAAAGGGCAGTCTTAAA-CAACTAGATGTCCTATTCTG
* * * *
2538733 GTATTTTAAAAATAAATAGATATCTTATTTATA-AAATAATAAAAATTAATACATTTTCTTAAAA
65 GTATTTTAAAAATAAATAAATATCTTATTTATATAAATAATATATATTAATACATTTTATTAAAA
2538797 GTTATACTAA
Statistics
Matches: 220, Mismatches: 32, Indels: 42
0.75 0.11 0.14
Matches are distributed among these distances:
135 8 0.04
136 15 0.07
137 82 0.37
138 29 0.13
139 10 0.05
140 1 0.00
142 1 0.00
143 3 0.01
144 1 0.00
145 5 0.02
146 7 0.03
147 34 0.15
148 15 0.07
149 9 0.04
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (135 bp):
TAATATTTATTTTTTTAAAATATTAAGAAAAGGGCAGTCTTAAACAACTAGATGTCCTATTCTGG
TATTTTAAAAATAAATAAATATCTTATTTATATAAATAATATATATTAATACATTTTATTAAAAA
TGTTT
Found at i:2539328 original size:26 final size:27
Alignment explanation
Indices: 2539272--2539329 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
2539262 TAATTTGTTC
*
2539272 TTTTCAAAAAATTTATATATACTTATTA
1 TTTTCAAAAAATTTATATATAC-TATAA
* * *
2539300 TTTTCATAATATTTATATGTA-TATAA
1 TTTTCAAAAAATTTATATATACTATAA
2539326 TTTT
1 TTTT
2539330 TTATTTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 8 0.31
28 18 0.69
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (27 bp):
TTTTCAAAAAATTTATATATACTATAA
Found at i:2541002 original size:26 final size:25
Alignment explanation
Indices: 2540955--2541008 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 25
2540945 TTTTGCATTT
*
2540955 TTTTCATTTTTACGTTTGTATTTATA
1 TTTTCATTTTTACATTTGTATTT-TA
*
2540981 TTTTCATTTTTGCATTAT-TATTTTA
1 TTTTCATTTTTACATT-TGTATTTTA
2541006 TTT
1 TTT
2541009 CAAACTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 5 0.20
26 19 0.76
27 1 0.04
ACGTcount: A:0.19, C:0.07, G:0.06, T:0.69
Consensus pattern (25 bp):
TTTTCATTTTTACATTTGTATTTTA
Found at i:2543403 original size:72 final size:72
Alignment explanation
Indices: 2543286--2543420 Score: 225
Period size: 72 Copynumber: 1.9 Consensus size: 72
2543276 ATATAATAAA
*
2543286 GCTTGAGTTATCCCCCTAAAGCAATTGGTTAATAGCCCTGGCTTTATGGATAATATTCAGCTAGT
1 GCTTGAGTTATCCCCCTAAAGCAATTGGTTAATAGCCCCGGCTTTATGGATAATATTCAGCTAGT
2543351 TTGTTAT
66 TTGTTAT
* ** *
2543358 GCTTGAGTTGTCCCTTTAAAGCAATTGGTTAATTGCCCCGGCTTTATGGATAATATTCAGCTA
1 GCTTGAGTTATCCCCCTAAAGCAATTGGTTAATAGCCCCGGCTTTATGGATAATATTCAGCTA
2543421 ACCTATTATA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 58 1.00
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (72 bp):
GCTTGAGTTATCCCCCTAAAGCAATTGGTTAATAGCCCCGGCTTTATGGATAATATTCAGCTAGT
TTGTTAT
Found at i:2547433 original size:22 final size:22
Alignment explanation
Indices: 2547405--2547458 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
2547395 TCTACATTCC
2547405 TCAAAGATGATAGATTATCTCT
1 TCAAAGATGATAGATTATCTCT
* *
2547427 TCAAAGATGATAGATTCTCTTT
1 TCAAAGATGATAGATTATCTCT
*
2547449 TCGAAGATGA
1 TCAAAGATGA
2547459 AAGTTTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (22 bp):
TCAAAGATGATAGATTATCTCT
Found at i:2548199 original size:222 final size:224
Alignment explanation
Indices: 2547813--2548353 Score: 935
Period size: 222 Copynumber: 2.4 Consensus size: 224
2547803 GATTTAAATC
* *
2547813 CATCACTCGATGGATCAACATTGCCAGGTAGAGTTCGTAATGAGAAGAACTCATCTGAAGAAGAA
1 CATCACTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
2547878 AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATTCATCACTCGATGGATTA
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATTCATCACTAGATGGATTA
* *
2547943 GCATTGCCAGTTAGACTTCATAATGAGAAGAACTCATCTGAAG-A-AGAAGAAGTTCATAATGAG
131 GCATTGCCAGGTAGACTTCATAATGAGAAGAACTCATATGAAGAAGAGAAGAAGTTCATAATGAG
2548006 AAGAACTTGTTCAACCTTTTGCTCGAATT
196 AAGAACTTGTTCAACCTTTTGCTCGAATT
* * *
2548035 CATCACTCGATCGATCATCATTGCCTGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCACTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
2548100 AGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTTCTCAAATTCATCACTAGATGGATTA
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATTCATCACTAGATGGATTA
*
2548165 GCATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATATGAAGAAGGAGAAGAAGTTCATAATGA
131 GCATTGCCAGGTAGACTTCATAATGAGAAGAACTCATATGAAGAA-GAGAAGAAGTTCATAATGA
2548230 GAAGAACTTGTTCAACCTTTTGCTCGAATT
195 GAAGAACTTGTTCAACCTTTTGCTCGAATT
2548260 CATCACTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG-
1 CATCACTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
2548324 AGAAGAAGTTCATAATGAGAAGAGCTTGTT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTT
2548354 TGACCTTAGC
Statistics
Matches: 299, Mismatches: 17, Indels: 4
0.93 0.05 0.01
Matches are distributed among these distances:
222 161 0.54
223 1 0.00
224 28 0.09
225 109 0.36
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.27
Consensus pattern (224 bp):
CATCACTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATTCATCACTAGATGGATTA
GCATTGCCAGGTAGACTTCATAATGAGAAGAACTCATATGAAGAAGAGAAGAAGTTCATAATGAG
AAGAACTTGTTCAACCTTTTGCTCGAATT
Found at i:2548360 original size:112 final size:112
Alignment explanation
Indices: 2547808--2548353 Score: 873
Period size: 113 Copynumber: 4.9 Consensus size: 112
2547798 GAAAAGATTT
* *
2547808 AAATCCATCACTCGATGGATCAACATTGCCAGGTAGAGTTCGTAATGAGAAGAACTCATCTGAAG
1 AAATTCATCACTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAG
* *
2547873 AAGAAAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
66 AAG-GAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
* * * *
2547921 AAATTCATCACTCGATGGATTAGCATTGCCAGTTAGACTTCATAATGAGAAGAACTCATCTGAAG
1 AAATTCATCACTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAG
2547986 -A--AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
66 AAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
* * * *
2548030 GAATTCATCACTCGATCGATCATCATTGCCTGGTAGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATTCATCACTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAG
* *
2548095 AAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTTCTC
66 AAGG-AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
* * * *
2548143 AAATTCATCACTAGATGGATTAGCATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATATGAAG
1 AAATTCATCACTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAG
2548208 AAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
66 AAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
*
2548255 GAATTCATCACTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATTCATCACTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAG
*
2548320 AAGGAGAAGAAGTTCATAATGAGAAGAGCTTGTT
66 AAGGAGAAGAAGTTCATAATGAGAAGAACTTGTT
2548354 TGACCTTAGC
Statistics
Matches: 398, Mismatches: 31, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
109 100 0.25
110 1 0.00
112 135 0.34
113 162 0.41
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (112 bp):
AAATTCATCACTCGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTC
Found at i:2548769 original size:28 final size:26
Alignment explanation
Indices: 2548715--2548777 Score: 90
Period size: 28 Copynumber: 2.3 Consensus size: 26
2548705 TTATTTTTAT
*
2548715 TATTATTATAATTGTTATAATAATAA
1 TATTATTATAATTATTATAATAATAA
*
2548741 TATTATTATATTTTATTATTAATAATAA
1 TATTATTATA-ATTATTA-TAATAATAA
2548769 TATTATTAT
1 TATTATTAT
2548778 TACATATTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
26 10 0.30
27 5 0.15
28 18 0.55
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (26 bp):
TATTATTATAATTATTATAATAATAA
Found at i:2548785 original size:28 final size:28
Alignment explanation
Indices: 2548732--2548786 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
2548722 ATAATTGTTA
**
2548732 TAATAATAATATTATTATATTTTATTAT
1 TAATAATAATATTATTATATCATATTAT
2548760 TAATAATAATATTATTAT-TACATATTA
1 TAATAATAATATTATTATAT-CATATTA
2548787 CAGGCCCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 1 0.04
28 23 0.96
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (28 bp):
TAATAATAATATTATTATATCATATTAT
Found at i:2550072 original size:25 final size:25
Alignment explanation
Indices: 2550014--2550075 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
2550004 AGTCCCTAAA
* * *
2550014 TTAATTATAAATTAGGTAATTAATT
1 TTAATAATTAATTAGGTAATTAATG
2550039 TTAATAATTAATTAGGTAA-TATATG
1 TTAATAATTAATTAGGTAATTA-ATG
2550064 TT-ATAAATTAAT
1 TTAAT-AATTAAT
2550076 CATTAAGTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
24 4 0.12
25 28 0.88
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (25 bp):
TTAATAATTAATTAGGTAATTAATG
Found at i:2550151 original size:9 final size:9
Alignment explanation
Indices: 2550134--2550207 Score: 57
Period size: 8 Copynumber: 8.1 Consensus size: 9
2550124 TTTACTATAG
2550134 TTTAATTAT
1 TTTAATTAT
*
2550143 TTTAGTTATT
1 TTTAATTA-T
2550153 GTTTAAATATAT
1 -TTT-AAT-TAT
2550165 TTTAA-TAT
1 TTTAATTAT
2550173 GTTTAA-TAT
1 -TTTAATTAT
2550182 TTTAATTAT
1 TTTAATTAT
*
2550191 TAT-ATTAT
1 TTTAATTAT
2550199 TTT-ATTAT
1 TTTAATTAT
2550207 T
1 T
2550208 AATATATTAT
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
8 21 0.38
9 20 0.36
10 3 0.05
11 6 0.11
12 3 0.05
13 2 0.04
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (9 bp):
TTTAATTAT
Found at i:2550156 original size:20 final size:19
Alignment explanation
Indices: 2550123--2550207 Score: 63
Period size: 17 Copynumber: 4.5 Consensus size: 19
2550113 TTACCACTTT
* *
2550123 TTTTACTATAGTTTAATTA
1 TTTTATTATTGTTTAATTA
2550142 TTTTAGTTATTGTTTAAATATA
1 TTTTA-TTATTGTTT-AAT-TA
*
2550164 TTTTAATA-TGTTTAA-TA
1 TTTTATTATTGTTTAATTA
*
2550181 TTTTA--ATT-ATTATATTA
1 TTTTATTATTGTTTA-ATTA
2550198 TTTTATTATT
1 TTTTATTATT
2550208 AATATATTAT
Statistics
Matches: 54, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
15 4 0.07
16 2 0.04
17 14 0.26
19 10 0.19
20 12 0.22
21 5 0.09
22 7 0.13
ACGTcount: A:0.32, C:0.01, G:0.05, T:0.62
Consensus pattern (19 bp):
TTTTATTATTGTTTAATTA
Found at i:2550195 original size:31 final size:31
Alignment explanation
Indices: 2550160--2550229 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 31
2550150 ATTGTTTAAA
*
2550160 TATATTTTAATATGT-TTAATATTTTAATTAT
1 TATATTTTAATAT-TATTAATATATTAATTAT
* *
2550191 TATATTATT-TTATTATTAATATATTATTTAT
1 TATATT-TTAATATTATTAATATATTAATTAT
2550222 TA-ATTTTA
1 TATATTTTA
2550230 TAAAATAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
29 2 0.06
30 4 0.12
31 25 0.76
32 2 0.06
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (31 bp):
TATATTTTAATATTATTAATATATTAATTAT
Found at i:2550213 original size:19 final size:18
Alignment explanation
Indices: 2550186--2550223 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
2550176 TAATATTTTA
*
2550186 ATTATTATATTATTTTATT
1 ATTAATATATTA-TTTATT
2550205 ATTAATATATTATTTATT
1 ATTAATATATTATTTATT
2550223 A
1 A
2550224 ATTTTATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
ATTAATATATTATTTATT
Found at i:2550996 original size:3 final size:3
Alignment explanation
Indices: 2550981--2551025 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
2550971 AGGTTACGAC
* * *
2550981 AAT AAT TAT AAT AAT AAT AAT AAT ACAT ATT ATT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AA
2551026 AAGAAAAAGG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:2551248 original size:45 final size:45
Alignment explanation
Indices: 2551182--2551769 Score: 982
Period size: 45 Copynumber: 13.1 Consensus size: 45
2551172 AAGGTCTTAT
* * * *
2551182 CATCTTGCACTGTAGGTCTTACAGATGACCCGGAGGCTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAA
*
2551227 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAA
* *
2551272 CATCATGCACTGAAGGGTTTATAGATGACCCGAAGGCTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAA
* * *
2551317 CATCATGCACTGAAGGGCTTACAAATAACCCGAAGGTTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAA
*
2551362 CATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAA
* *
2551407 CATCATGCACTGAAGGGATTACATATGACCCGAAGGCTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAA
2551452 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAA
* * *
2551497 CATCATGCACTGAAGGGCTTAAAGATGACCTGAAGGCTTTAAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAA
2551542 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAA
*
2551587 CATCATGCACTGAAGGGCTTACATATGACCCGAAGGCTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAA
*
2551632 CATCATGCACTGAAGGGCTTACAGATGACCCGAATGCTTTG-AAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAA
*
2551676 CATCATGCACTGAAGGGCTTACAGATGACCCGAATGCTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAA
*
2551721 CATCATGCACTGAA-GGCTTACAGATGACCCGAAGGTTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAA
2551765 CATCA
1 CATCA
2551770 AAAAGCTCCC
Statistics
Matches: 509, Mismatches: 33, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
44 77 0.15
45 432 0.85
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.22
Consensus pattern (45 bp):
CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAA
Found at i:2552530 original size:22 final size:22
Alignment explanation
Indices: 2552488--2552532 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2552478 TTTGAAAAAA
* **
2552488 GAATCTATCATTTTTGGAGAGT
1 GAATCTATCATCTTTAAAGAGT
2552510 GAATCTATCATCTTTAAAGAGT
1 GAATCTATCATCTTTAAAGAGT
2552532 G
1 G
2552533 TAGATGTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (22 bp):
GAATCTATCATCTTTAAAGAGT
Found at i:2553160 original size:54 final size:54
Alignment explanation
Indices: 2553090--2553291 Score: 282
Period size: 54 Copynumber: 3.7 Consensus size: 54
2553080 AAATATCTGG
* *
2553090 CAACACATTCATCATTTCCTGTTGCTTCTGCTCAGATGTTCGTAAAACATTTGA
1 CAACACATTCATCATTTCATGTGGCTTCTGCTCAGATGTTCGTAAAACATTTGA
* * *
2553144 CAACACATTCATCATTTCATGTGGTTTATGCAT-AGATGTTTGTAAAACATTTGA
1 CAACACATTCATCATTTCATGTGGCTTCTGC-TCAGATGTTCGTAAAACATTTGA
* * *
2553198 CAACACATTCATCATTTCCTGTGTCTTCTG-TACAGATGTTCGTAATACATTTGA
1 CAACACATTCATCATTTCATGTGGCTTCTGCT-CAGATGTTCGTAAAACATTTGA
* *
2553252 CAACACATTCATCATTTCATGTGGCTTCTACACAGATGTT
1 CAACACATTCATCATTTCATGTGGCTTCTGCTCAGATGTT
2553292 TGCCATGAAG
Statistics
Matches: 129, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
52 1 0.01
54 127 0.98
55 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (54 bp):
CAACACATTCATCATTTCATGTGGCTTCTGCTCAGATGTTCGTAAAACATTTGA
Found at i:2553267 original size:108 final size:108
Alignment explanation
Indices: 2553090--2553293 Score: 331
Period size: 108 Copynumber: 1.9 Consensus size: 108
2553080 AAATATCTGG
2553090 CAACACATTCATCATTTCCTGTTGCTTCTGCTCAGATGTTCGTAAAACATTTGACAACACATTCA
1 CAACACATTCATCATTTCCTGTTGCTTCTGCTCAGATGTTCGTAAAACATTTGACAACACATTCA
* * *
2553155 TCATTTCATGTGGTTTATGCATAGATGTTTGTAAAACATTTGA
66 TCATTTCATGTGGCTTATACACAGATGTTTGTAAAACATTTGA
*
2553198 CAACACATTCATCATTTCCTG-TGTCTTCTG-TACAGATGTTCGTAATACATTTGACAACACATT
1 CAACACATTCATCATTTCCTGTTG-CTTCTGCT-CAGATGTTCGTAAAACATTTGACAACACATT
*
2553261 CATCATTTCATGTGGCTTCTACACAGATGTTTG
64 CATCATTTCATGTGGCTTATACACAGATGTTTG
2553294 CCATGAAGCT
Statistics
Matches: 89, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
107 3 0.03
108 86 0.97
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (108 bp):
CAACACATTCATCATTTCCTGTTGCTTCTGCTCAGATGTTCGTAAAACATTTGACAACACATTCA
TCATTTCATGTGGCTTATACACAGATGTTTGTAAAACATTTGA
Found at i:2554281 original size:75 final size:75
Alignment explanation
Indices: 2554155--2554324 Score: 216
Period size: 75 Copynumber: 2.3 Consensus size: 75
2554145 GATGATAGTC
* * * * * *
2554155 TTCAGCATGACCCAACATTTGCTAATACAAACGTTCAAAATGAGTTAATATTTC-AATTTCTGAT
1 TTCAGCATGCCCCATCATTTACTAATACAAACATTCAAAATGAGTCAATATTCCTAA-TTCTGAT
2554219 TGAAATGGGCT
65 TGAAATGGGCT
* * * * * *
2554230 TTTAGCATGCCCCATCATTTACTGATGCAAACATTTAAAATGTGTCAATATTCCTGATTCTGATT
1 TTCAGCATGCCCCATCATTTACTAATACAAACATTCAAAATGAGTCAATATTCCTAATTCTGATT
2554295 GAAATGGGCT
66 GAAATGGGCT
2554305 TTCAGCATGCCCCATCATTT
1 TTCAGCATGCCCCATCATTT
2554325 GTTTCTTGCT
Statistics
Matches: 81, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
75 80 0.99
76 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.35
Consensus pattern (75 bp):
TTCAGCATGCCCCATCATTTACTAATACAAACATTCAAAATGAGTCAATATTCCTAATTCTGATT
GAAATGGGCT
Found at i:2556676 original size:72 final size:72
Alignment explanation
Indices: 2556595--2556729 Score: 216
Period size: 72 Copynumber: 1.9 Consensus size: 72
2556585 ATATATAAGT
* *
2556595 TAGCTGAATATTATCCATAAAGCCAGGGCTATTAACCAATTGCTTTAGGGGGATAATTCAAGCAT
1 TAGCTGAATATTATCCATAAAGCCAGGGCTATTAACCAATTGCTTTAAGGGGATAACTCAAGCAT
2556660 AACAGAC
66 AACAGAC
* * * *
2556667 TAGCTGAATATTATCCATAAAGTCGGGGCTATTAACCTATTGTTTTAAGGGGATAACTCAAGC
1 TAGCTGAATATTATCCATAAAGCCAGGGCTATTAACCAATTGCTTTAAGGGGATAACTCAAGC
2556730 TTTATTGTGT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 57 1.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (72 bp):
TAGCTGAATATTATCCATAAAGCCAGGGCTATTAACCAATTGCTTTAAGGGGATAACTCAAGCAT
AACAGAC
Found at i:2559226 original size:8 final size:7
Alignment explanation
Indices: 2559198--2559238 Score: 50
Period size: 6 Copynumber: 6.0 Consensus size: 7
2559188 ATAAAAATAC
2559198 AAATGCA
1 AAATGCA
*
2559205 AAAT-AA
1 AAATGCA
2559211 AAATGCA
1 AAATGCA
2559218 AAGATGCA
1 AA-ATGCA
2559226 AAATGC-
1 AAATGCA
2559232 AAATGCA
1 AAATGCA
2559239 TGTATGAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
6 11 0.38
7 11 0.38
8 7 0.24
ACGTcount: A:0.59, C:0.12, G:0.15, T:0.15
Consensus pattern (7 bp):
AAATGCA
Found at i:2559238 original size:13 final size:13
Alignment explanation
Indices: 2559191--2559234 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
2559181 AGAAAACATA
2559191 AAAATACAAATGC
1 AAAATACAAATGC
*
2559204 AAAATAAAAATGC
1 AAAATACAAATGC
*
2559217 AAAGATGCAAAATGC
1 AAA-ATAC-AAATGC
2559232 AAA
1 AAA
2559235 TGCATGTATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 15 0.58
14 2 0.08
15 9 0.35
ACGTcount: A:0.64, C:0.11, G:0.11, T:0.14
Consensus pattern (13 bp):
AAAATACAAATGC
Found at i:2560984 original size:46 final size:46
Alignment explanation
Indices: 2560917--2561004 Score: 133
Period size: 46 Copynumber: 1.9 Consensus size: 46
2560907 AGGTATAAGT
* * *
2560917 CCTAACCTCATGCTTTCTAGTTTCATGCTTTGTTTGGAAAAATTAA
1 CCTAACCTCATGATTTCTAGTTCCATGCTTTGTTTAGAAAAATTAA
2560963 CCTAA-CTGCATGATTTCTAGTTCCATGCTTTGTTTAGAAAAA
1 CCTAACCT-CATGATTTCTAGTTCCATGCTTTGTTTAGAAAAA
2561005 AATATGAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
45 2 0.05
46 36 0.95
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (46 bp):
CCTAACCTCATGATTTCTAGTTCCATGCTTTGTTTAGAAAAATTAA
Found at i:2562162 original size:2 final size:2
Alignment explanation
Indices: 2562157--2562196 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
2562147 TAAAACTAAG
*
2562157 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2562197 AGCAGGATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2562358 original size:4 final size:4
Alignment explanation
Indices: 2562349--2562375 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2562339 TAGTGAATAA
2562349 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
2562376 ATACTATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:2563246 original size:3 final size:3
Alignment explanation
Indices: 2563240--2563287 Score: 69
Period size: 3 Copynumber: 15.7 Consensus size: 3
2563230 ATAATTTATA
* *
2563240 AAT AAT AAT AAT AAT AAT AAT AAT ACAT ATT ATT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT
2563286 AA
1 AA
2563288 AAGAAAAAGG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:2568291 original size:2 final size:2
Alignment explanation
Indices: 2568284--2568341 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
2568274 TGTTTGTGTA
2568284 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
2568326 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
2568342 GTGTGTGTGT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2568346 original size:2 final size:2
Alignment explanation
Indices: 2568341--2568366 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2568331 TATATATATA
2568341 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
2568367 AACATGGAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:2570705 original size:3 final size:3
Alignment explanation
Indices: 2570692--2570757 Score: 96
Period size: 3 Copynumber: 21.7 Consensus size: 3
2570682 TTTTTATCCA
* *
2570692 TAT TTT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
2570740 TAT TAT TAA TAT ATAT TA
1 TAT TAT TAT TAT -TAT TA
2570758 AATAAATATA
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
3 53 0.95
4 3 0.05
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:2570773 original size:12 final size:13
Alignment explanation
Indices: 2570750--2570781 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
2570740 TATTATTAAT
2570750 ATATATTAAATAA
1 ATATATTAAATAA
2570763 ATATA-TAAATAA
1 ATATATTAAATAA
2570775 ATA-ATTA
1 ATATATTA
2570782 CAGACCAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 1 0.06
12 12 0.67
13 5 0.28
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATATATTAAATAA
Found at i:2572938 original size:18 final size:17
Alignment explanation
Indices: 2572915--2572965 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
2572905 TTCTTTTCAA
2572915 ATTTTTTATTTATTTATT
1 ATTTTTTATTTATTTA-T
*
2572933 ATTTTTATAATT-TTTAT
1 ATTTTT-TATTTATTTAT
*
2572950 ATGTTTTATTTTATTT
1 ATTTTTTA-TTTATTT
2572966 GCAAGTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
16 2 0.07
17 8 0.30
18 13 0.48
19 4 0.15
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.75
Consensus pattern (17 bp):
ATTTTTTATTTATTTAT
Found at i:2572987 original size:13 final size:15
Alignment explanation
Indices: 2572956--2572992 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
2572946 TTATATGTTT
2572956 TATTTTATTTGCAAG
1 TATTTTATTTGCAAG
2572971 TATTTTATTT-C-AG
1 TATTTTATTTGCAAG
2572984 TA-TTTATTT
1 TATTTTATTT
2572993 TTCTGTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.32
13 4 0.18
14 1 0.05
15 10 0.45
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.62
Consensus pattern (15 bp):
TATTTTATTTGCAAG
Found at i:2580060 original size:10 final size:10
Alignment explanation
Indices: 2580045--2580077 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
2580035 GCAATCATTC
2580045 TTTACATTTT
1 TTTACATTTT
2580055 TTTACA-TTT
1 TTTACATTTT
*
2580064 TTTACATTTA
1 TTTACATTTT
2580074 TTTA
1 TTTA
2580078 TTTCATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTACATTTT
Found at i:2580067 original size:19 final size:19
Alignment explanation
Indices: 2580040--2580077 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2580030 AGATGGCAAT
*
2580040 CATTCTTTACATTTTTTTA
1 CATTCTTTACATTTATTTA
*
2580059 CATTTTTTACATTTATTTA
1 CATTCTTTACATTTATTTA
2580078 TTTCATAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.13, G:0.00, T:0.63
Consensus pattern (19 bp):
CATTCTTTACATTTATTTA
Found at i:2583631 original size:16 final size:16
Alignment explanation
Indices: 2583610--2583699 Score: 112
Period size: 15 Copynumber: 5.6 Consensus size: 16
2583600 TGCTTGAAGA
2583610 AAAAAGAAAAAAAAAG
1 AAAAAGAAAAAAAAAG
2583626 AAAAAGAAAAAAAAA-
1 AAAAAGAAAAAAAAAG
*
2583641 AAAAAAAAAAAAAAAG
1 AAAAAGAAAAAAAAAG
*
2583657 -AAAAGAAAAAAATAG
1 AAAAAGAAAAAAAAAG
*
2583672 AAAATGAAAAAAAGAGAAG
1 AAAAAG-AAAAAA-A-AAG
2583691 AAAAAGAAA
1 AAAAAGAAA
2583700 GGGGGTCAAG
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
15 27 0.43
16 19 0.30
17 6 0.10
18 4 0.06
19 7 0.11
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (16 bp):
AAAAAGAAAAAAAAAG
Found at i:2583645 original size:31 final size:32
Alignment explanation
Indices: 2583609--2583699 Score: 114
Period size: 31 Copynumber: 2.8 Consensus size: 32
2583599 ATGCTTGAAG
2583609 AAAAAAGAAAAAAAAAGAAAAAGAAAAAAA-A
1 AAAAAAGAAAAAAAAAGAAAAAGAAAAAAATA
*
2583640 AAAAAAAAAAAAAAAAG-AAAAGAAAAAAATA
1 AAAAAAGAAAAAAAAAGAAAAAGAAAAAAATA
* *
2583671 GAAAATGAAAAAAAGAGAAGAAAAAGAAA
1 AAAAAAG-AAAAAA-A-AAGAAAAAGAAA
2583700 GGGGGTCAAG
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
30 12 0.24
31 21 0.41
32 6 0.12
33 1 0.02
34 3 0.06
35 8 0.16
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (32 bp):
AAAAAAGAAAAAAAAAGAAAAAGAAAAAAATA
Found at i:2583684 original size:1 final size:1
Alignment explanation
Indices: 2583609--2583668 Score: 75
Period size: 1 Copynumber: 60.0 Consensus size: 1
2583599 ATGCTTGAAG
* * * * *
2583609 AAAAAAGAAAAAAAAAGAAAAAGAAAAAAAAAAAAAAAAAAAAAAAAGAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2583669 TAGAAAATGA
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (1 bp):
A
Found at i:2583698 original size:25 final size:22
Alignment explanation
Indices: 2583609--2583699 Score: 85
Period size: 23 Copynumber: 3.9 Consensus size: 22
2583599 ATGCTTGAAG
*
2583609 AAAAAAGAAAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAGAAAAA
2583631 GAAAAAAAAAAAAAAAA-AAAAA
1 -AAAAAAAAAAAAAAAAGAAAAA
*
2583653 AAAGAAAAGAAAAAAATAGAAAATGA
1 AAA-AAAA-AAAAAAAAAGAAAA--A
* *
2583679 AAAAAAGAGAAGAAAAAGAAA
1 AAAAAA-AAAAAAAAAAGAAA
2583700 GGGGGTCAAG
Statistics
Matches: 57, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
21 3 0.05
22 9 0.16
23 23 0.40
24 4 0.07
25 13 0.23
26 5 0.09
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (22 bp):
AAAAAAAAAAAAAAAAGAAAAA
Found at i:2583700 original size:15 final size:14
Alignment explanation
Indices: 2583606--2583700 Score: 94
Period size: 14 Copynumber: 6.9 Consensus size: 14
2583596 ATTATGCTTG
2583606 AAGAAAAAAGAA-AA
1 AAGAAAAAA-AAGAA
2583620 AA-AAAGAAAAAGAA
1 AAGAAA-AAAAAGAA
2583634 AA-AAAAAAAA-AA
1 AAGAAAAAAAAGAA
2583646 AA-AAAAAAAAGAA
1 AAGAAAAAAAAGAA
2583659 AAGAAAAAAATAGAA
1 AAGAAAAAAA-AGAA
*
2583674 AATG-AAAAAAAGAG
1 AA-GAAAAAAAAGAA
2583688 AAGAAAAAGAAAG
1 AAGAAAAA-AAAG
2583701 GGGGTCAAGG
Statistics
Matches: 72, Mismatches: 1, Indels: 15
0.82 0.01 0.17
Matches are distributed among these distances:
12 12 0.17
13 15 0.21
14 28 0.39
15 16 0.22
16 1 0.01
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (14 bp):
AAGAAAAAAAAGAA
Done.