Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold125
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: 3608436
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 25 characters in sequence are not A, C, G, or T
File 16 of 18
Found at i:2913688 original size:2 final size:2
Alignment explanation
Indices: 2913681--2913730 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
2913671 AGTGTATAAG
2913681 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
2913723 AT AT AT AT
1 AT AT AT AT
2913731 GGGCTTGTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2913959 original size:3 final size:3
Alignment explanation
Indices: 2913951--2913977 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2913941 ACTCAAGTTC
2913951 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
2913978 TGAGATTTTA
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2916534 original size:2 final size:2
Alignment explanation
Indices: 2916527--2916560 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2916517 ATGTATTTCT
2916527 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
2916561 TATATATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:2916565 original size:2 final size:2
Alignment explanation
Indices: 2916560--2916588 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2916550 ACACACACAC
2916560 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2916589 AACAGTTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2922259 original size:2 final size:2
Alignment explanation
Indices: 2922243--2922288 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
2922233 AGCAAATAAG
* * * *
2922243 TA TA TA TG TA CA TA TA TA TA TA TA TG TA TA TA TA TA TA TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2922285 TA TA
1 TA TA
2922289 CGAGTATACA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2922287 original size:16 final size:16
Alignment explanation
Indices: 2922243--2922288 Score: 74
Period size: 16 Copynumber: 2.8 Consensus size: 16
2922233 AGCAAATAAG
2922243 TATATATGTACATATATA
1 TATATATGT--ATATATA
2922261 TATATATGTATATATA
1 TATATATGTATATATA
2922277 TATATATGTATA
1 TATATATGTATA
2922289 CGAGTATACA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 19 0.68
18 9 0.32
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (16 bp):
TATATATGTATATATA
Found at i:2929395 original size:127 final size:125
Alignment explanation
Indices: 2929170--2929420 Score: 394
Period size: 127 Copynumber: 2.0 Consensus size: 125
2929160 TAATAATAAT
* * *
2929170 TCTCCAACTAGGAATAAAAGCCTTCAATTTGTCTTTCATCCACAAGTAAGAAAGTCGAGGATTTC
1 TCTCCAACTAGGAATAAAAGACTTCAATTTGTCTTGCATCCACAAGTAAGAAAGTCAAGGATTTC
2929235 GCATTTTAACAATTTCAGGGCATCTCATCAACAAACAATTCCAGGGACGCCAATGAATTCC
66 GCATTTTAACAATTTCAGGGCATCTCATCAACAAACAATTCCA-GGACGCCAATGAATTCC
* * *
2929296 TCTCCAACTAGGAATCAAAGACTTCAATTTGTCTTCGCATCCCCATGTAAGAAAGTCAAGGATTT
1 TCTCCAACTAGGAATAAAAGACTTCAATTTGTCTT-GCATCCACAAGTAAGAAAGTCAAGGATTT
* * * *
2929361 CTCATTTTAACAATTTCAGGGCTTCTTATCAACAAACAATTCCAGGACGCTAATGAATTC
65 CGCATTTTAACAATTTCAGGGCATCTCATCAACAAACAATTCCAGGACGCCAATGAATTC
2929421 TCCGCTTGCA
Statistics
Matches: 114, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
126 48 0.42
127 66 0.58
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (125 bp):
TCTCCAACTAGGAATAAAAGACTTCAATTTGTCTTGCATCCACAAGTAAGAAAGTCAAGGATTTC
GCATTTTAACAATTTCAGGGCATCTCATCAACAAACAATTCCAGGACGCCAATGAATTCC
Found at i:2930520 original size:2 final size:2
Alignment explanation
Indices: 2930513--2930540 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2930503 AAAATTTAAA
2930513 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
2930541 GAAAGATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2933945 original size:2 final size:2
Alignment explanation
Indices: 2933938--2933972 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
2933928 GAACGTAGCC
* *
2933938 GA GA GA GA GA GA GA GA GA GA CA GA AA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
2933973 GTACTGAGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.51, C:0.03, G:0.46, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2937456 original size:27 final size:24
Alignment explanation
Indices: 2937396--2937474 Score: 74
Period size: 30 Copynumber: 3.1 Consensus size: 24
2937386 TCATCGTACG
2937396 TAAAATAATTAATTATATAAAATA
1 TAAAATAATTAATTATATAAAATA
2937420 TAATATAATAATTAAATATTATATAAAATA
1 T-A-A-AATAATT--A-ATTATATAAAATA
2937450 TAAAATAA-T--TTATATAATAATA
1 TAAAATAATTAATTATATAA-AATA
2937472 TAA
1 TAA
2937475 GTTTTTTTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 16
0.75 0.00 0.25
Matches are distributed among these distances:
21 8 0.17
22 7 0.15
24 1 0.02
25 1 0.02
26 2 0.04
27 12 0.25
28 1 0.02
29 2 0.04
30 14 0.29
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
TAAAATAATTAATTATATAAAATA
Found at i:2942347 original size:38 final size:38
Alignment explanation
Indices: 2942296--2942373 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
2942286 TCGTGCTTAC
2942296 TGTACTTCTAAGCTTTTTGTTTGTTCTACTTGTTCTCT
1 TGTACTTCTAAGCTTTTTGTTTGTTCTACTTGTTCTCT
2942334 TGTACTTCTAAGCTTTTTGTTTGTTCTACTTGTTCTCT
1 TGTACTTCTAAGCTTTTTGTTTGTTCTACTTGTTCTCT
2942372 TG
1 TG
2942374 CTTTGGTGGC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.10, C:0.18, G:0.14, T:0.58
Consensus pattern (38 bp):
TGTACTTCTAAGCTTTTTGTTTGTTCTACTTGTTCTCT
Found at i:2950907 original size:18 final size:18
Alignment explanation
Indices: 2950882--2950933 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
2950872 ATTTAAATAA
2950882 AAAT-ATTAATTTTGTT-
1 AAATAATTAATTTTGTTC
2950898 AAATTAATTAATTTAT-TTC
1 AAA-TAATTAATTT-TGTTC
*
2950917 AAATAATAAATTTTGTT
1 AAATAATTAATTTTGTT
2950934 TAAAAATGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
16 3 0.10
17 2 0.07
18 21 0.70
19 4 0.13
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (18 bp):
AAATAATTAATTTTGTTC
Found at i:2953948 original size:32 final size:30
Alignment explanation
Indices: 2953904--2953971 Score: 82
Period size: 32 Copynumber: 2.2 Consensus size: 30
2953894 CATATTCAAT
* *
2953904 ATATTTTTAAATATATATAATTTTTTTAAA
1 ATATTTTTAAATAAAAATAATTTTTTTAAA
*
2953934 ATATTTTTAAAAATAAAAATATTTTTTTTAAA
1 ATATTTTT--AAATAAAAATAATTTTTTTAAA
*
2953966 AAATTT
1 ATATTT
2953972 AACATATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 8 0.25
32 24 0.75
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (30 bp):
ATATTTTTAAATAAAAATAATTTTTTTAAA
Found at i:2955224 original size:2 final size:2
Alignment explanation
Indices: 2955219--2955271 Score: 70
Period size: 2 Copynumber: 26.5 Consensus size: 2
2955209 TATGTGTGTG
* * * *
2955219 TA TA TA TA TA TA TA TA TG TA TA AA TA TA TG CA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2955261 TA TA TA TA TA T
1 TA TA TA TA TA T
2955272 GTGCAGATTC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2959294 original size:18 final size:18
Alignment explanation
Indices: 2959267--2959326 Score: 56
Period size: 18 Copynumber: 3.6 Consensus size: 18
2959257 ATATAATAAT
*
2959267 TTTATTTAAAATATTATA
1 TTTATATAAAATATTATA
* *
2959285 TTTATATAAATTATAATA
1 TTTATATAAAATATTATA
*
2959303 TTT-TA-ATAAT-TTATA
1 TTTATATAAAATATTATA
2959318 -TTATATAAA
1 TTTATATAAA
2959327 TTTTAATATA
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
14 2 0.06
15 6 0.18
16 5 0.15
17 2 0.06
18 18 0.55
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTATATAAAATATTATA
Found at i:2959322 original size:32 final size:34
Alignment explanation
Indices: 2959269--2959340 Score: 105
Period size: 32 Copynumber: 2.2 Consensus size: 34
2959259 ATAATAATTT
2959269 TATTTAAAATATTATATTTATATAAATTATAATA
1 TATTTAAAATATTATATTTATATAAATTATAATA
*
2959303 T-TTTAATAAT-TTATA-TTATATAAATTTTAATA
1 TATTTAA-AATATTATATTTATATAAATTATAATA
2959335 TATTTA
1 TATTTA
2959341 TATATTCATA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
32 17 0.49
33 14 0.40
34 4 0.11
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (34 bp):
TATTTAAAATATTATATTTATATAAATTATAATA
Found at i:2959324 original size:25 final size:25
Alignment explanation
Indices: 2959281--2959343 Score: 67
Period size: 25 Copynumber: 2.4 Consensus size: 25
2959271 TTTAAAATAT
*
2959281 TATATTTATATAAATTATAATATTTT-A
1 TATATTTATAT-TA-TATAA-ATTTTAA
2959308 -ATAATTTATATTATATAAATTTTAA
1 TAT-ATTTATATTATATAAATTTTAA
2959333 TATATTTATAT
1 TATATTTATAT
2959344 ATTCATATCA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
24 5 0.16
25 14 0.44
26 5 0.16
27 8 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TATATTTATATTATATAAATTTTAA
Found at i:2961680 original size:73 final size:75
Alignment explanation
Indices: 2961563--2961701 Score: 212
Period size: 73 Copynumber: 1.9 Consensus size: 75
2961553 AACCCCCTTT
*
2961563 TTTTTTGCCATTTAAATGGGCTATGACATAACCCCAATTATTAAGC-AAATTACTTGGGCAAAGC
1 TTTTTTGCCATTTAAATGGGCTATGACACAACCCCAATTATTAAGCGAAATTACTTGGGCAAAGC
2961627 TGCCCATCCC
66 TGCCCATCCC
* * *
2961637 TTTTTT-CCATTTAAATGGGCTTAT-ATACAACCCCAATTATTAAGCGAATTTACTTGGGCTAAG
1 TTTTTTGCCATTTAAATGGGC-TATGACACAACCCCAATTATTAAGCGAAATTACTTGGGCAAAG
2961700 CT
65 CT
2961702 TGCTCTGGGC
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
73 33 0.56
74 26 0.44
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (75 bp):
TTTTTTGCCATTTAAATGGGCTATGACACAACCCCAATTATTAAGCGAAATTACTTGGGCAAAGC
TGCCCATCCC
Found at i:2965911 original size:20 final size:18
Alignment explanation
Indices: 2965871--2965910 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2965861 ATGACTAAAC
*
2965871 ATAAT-TAAAAAAATATT
1 ATAATATAAAAAAAAATT
2965888 ATAATATAAAAAAAAATT
1 ATAATATAAAAAAAAATT
2965906 A-AATA
1 ATAATA
2965911 AAATAAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
ATAATATAAAAAAAAATT
Found at i:2972605 original size:15 final size:16
Alignment explanation
Indices: 2972585--2972614 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2972575 TTTAAATTAT
2972585 AAAAT-AAATTTTTAA
1 AAAATAAAATTTTTAA
2972600 AAAATAAAATTTTTA
1 AAAATAAAATTTTTA
2972615 TTATTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AAAATAAAATTTTTAA
Found at i:2973353 original size:15 final size:14
Alignment explanation
Indices: 2973321--2973359 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
2973311 ATATCTATTA
2973321 AATTTATTAAAAAT
1 AATTTATTAAAAAT
2973335 -ATTTATATAAAAAT
1 AATTTAT-TAAAAAT
2973349 AATTTTATTAA
1 AA-TTTATTAA
2973360 TTAATACGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 6 0.27
14 7 0.32
15 4 0.18
16 5 0.23
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
AATTTATTAAAAAT
Found at i:2973563 original size:12 final size:13
Alignment explanation
Indices: 2973516--2973561 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
2973506 CTATTTACTG
*
2973516 ATATTAAAATCAA
1 ATATTAAAATAAA
*
2973529 ATATTAAAACAAA
1 ATATTAAAATAAA
*
2973542 A-AATAAAATAAA
1 ATATTAAAATAAA
2973554 ATATTAAA
1 ATATTAAA
2973562 TATTTAATTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
12 10 0.37
13 17 0.63
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (13 bp):
ATATTAAAATAAA
Found at i:2974070 original size:20 final size:20
Alignment explanation
Indices: 2974041--2974103 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 20
2974031 TTAATTTGAG
*
2974041 AATTTAAAAAATT-AATTATA
1 AATTTTAAAAATTAAATT-TA
*
2974061 AATTTTAAAATTTAAATTTA
1 AATTTTAAAAATTAAATTTA
* *
2974081 AATCTTAATTAATTAAA-TTA
1 AATTTTAA-AAATTAAATTTA
2974101 AAT
1 AAT
2974104 ATCAGATATA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 26 0.72
21 10 0.28
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
AATTTTAAAAATTAAATTTA
Found at i:2976371 original size:17 final size:16
Alignment explanation
Indices: 2976339--2976381 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
2976329 TACAAATCAA
2976339 TTTAAAATTATCTTTT
1 TTTAAAATTATCTTTT
*
2976355 TTTATAAATTA-ATTTT
1 TTTA-AAATTATCTTTT
*
2976371 TTAAAAATTAT
1 TTTAAAATTAT
2976382 ATATTAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 6 0.26
16 11 0.48
17 6 0.26
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTAAAATTATCTTTT
Found at i:2978898 original size:5 final size:5
Alignment explanation
Indices: 2978888--2978926 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
2978878 AGCACCTTCC
* *
2978888 TTTCT TTTCT TTTCT TTTCT TTTTT TTTTT TTTCCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT-CT TTT
2978927 TATTTTTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 27 0.87
6 4 0.13
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (5 bp):
TTTCT
Found at i:2978927 original size:15 final size:15
Alignment explanation
Indices: 2978891--2978933 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
2978881 ACCTTCCTTT
*
2978891 CTTTTCTTTTCTTTTC
1 CTTTT-TTTTTTTTTC
*
2978907 TTTTTTTTTTTTTTC
1 CTTTTTTTTTTTTTC
2978922 CTTTTTATTTTT
1 CTTTTT-TTTTT
2978934 CAATGATGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (15 bp):
CTTTTTTTTTTTTTC
Found at i:2980796 original size:16 final size:16
Alignment explanation
Indices: 2980734--2980801 Score: 73
Period size: 17 Copynumber: 4.0 Consensus size: 16
2980724 TTAATTTTAT
2980734 TAAAATATTATAAAAGAAA
1 TAAAA-ATTA-AAAA-AAA
2980753 TAAAAATTAAAAATAAA
1 TAAAAATTAAAAA-AAA
**
2980770 TAAATTTTAAAAAAAA
1 TAAAAATTAAAAAAAA
*
2980786 TAAAAAGTAAAAAAAA
1 TAAAAATTAAAAAAAA
2980802 AGTTTTCATG
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
16 16 0.37
17 18 0.42
18 4 0.09
19 5 0.12
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (16 bp):
TAAAAATTAAAAAAAA
Found at i:2981674 original size:15 final size:15
Alignment explanation
Indices: 2981654--2981695 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
2981644 AAGGAAATAA
* *
2981654 AAAATTATATATTTT
1 AAAATTATAAAATTT
2981669 AAAATT-TAAAATTT
1 AAAATTATAAAATTT
*
2981683 AAAATTATTAAAT
1 AAAATTATAAAAT
2981696 ATTATTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AAAATTATAAAATTT
Found at i:2982748 original size:2 final size:2
Alignment explanation
Indices: 2982741--2982771 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2982731 CACTTTATCA
2982741 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
2982772 ATGATTGGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:2985405 original size:17 final size:17
Alignment explanation
Indices: 2985347--2985407 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
2985337 TTAATTATCA
*
2985347 ATATTGATTAAATATTATT
1 ATATT-ATTATAT-TTATT
* * **
2985366 TTATTATTATTTTTAAA
1 ATATTATTATATTTATT
*
2985383 AAATTATTATATTTATT
1 ATATTATTATATTTATT
2985400 ATATTATT
1 ATATTATT
2985408 TTTATAATTT
Statistics
Matches: 31, Mismatches: 11, Indels: 2
0.70 0.25 0.05
Matches are distributed among these distances:
17 22 0.71
18 5 0.16
19 4 0.13
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (17 bp):
ATATTATTATATTTATT
Found at i:2991790 original size:11 final size:11
Alignment explanation
Indices: 2991761--2991791 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
2991751 GAAAGAACTT
2991761 AAAAAAAA-AA
1 AAAAAAAAGAA
2991771 AAAAAAAAGAA
1 AAAAAAAAGAA
2991782 AAAAAAAAGA
1 AAAAAAAAGA
2991792 GAGAAGGAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.40
11 12 0.60
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:2991796 original size:15 final size:15
Alignment explanation
Indices: 2991761--2991789 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2991751 GAAAGAACTT
2991761 AAAA-AAAAAAAAAA
1 AAAAGAAAAAAAAAA
2991775 AAAAGAAAAAAAAAA
1 AAAAGAAAAAAAAAA
2991790 GAGAGAAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAAAAAAA
Found at i:2992745 original size:21 final size:19
Alignment explanation
Indices: 2992699--2992768 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 19
2992689 TTTTTTGTAT
*
2992699 ATAAGTAATTTTTTAATTAAA
1 ATAA-TAATTTTTTAA-AAAA
2992720 ATAATTAATTTTTTAAAAAA
1 ATAA-TAATTTTTTAAAAAA
2992740 ATTAATAAGTTTTTTTATAAAAA
1 A-TAATAA--TTTTTTA-AAAAA
2992763 A-AATAA
1 ATAATAA
2992769 ATTTAAATAT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
20 7 0.16
21 23 0.53
22 7 0.16
23 6 0.14
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (19 bp):
ATAATAATTTTTTAAAAAA
Found at i:2992850 original size:11 final size:11
Alignment explanation
Indices: 2992824--2992860 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
2992814 TATAAAAATT
*
2992824 ATTTAATATTTT
1 ATTTAA-ATTTA
2992836 ATTTAAATTTA
1 ATTTAAATTTA
2992847 ATTTAAATTTA
1 ATTTAAATTTA
2992858 ATT
1 ATT
2992861 CGAGTTACTC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 18 0.75
12 6 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
ATTTAAATTTA
Found at i:2995138 original size:24 final size:21
Alignment explanation
Indices: 2995109--2995173 Score: 67
Period size: 24 Copynumber: 2.8 Consensus size: 21
2995099 AAATTGTTTT
2995109 TTATTTATTTTAATATTTAAATA
1 TTATTTATTTTAA-ATTT-AATA
*
2995132 TATATTTAATTTAAATATTAATA
1 T-TATTTATTTTAAAT-TTAATA
2995155 TTATTTGATATTTAAATTT
1 TTATTT-AT-TTTAAATTT
2995174 GTTAAATACA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
22 5 0.14
23 11 0.31
24 20 0.56
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
TTATTTATTTTAAATTTAATA
Found at i:2995215 original size:29 final size:27
Alignment explanation
Indices: 2995169--2995223 Score: 65
Period size: 29 Copynumber: 2.0 Consensus size: 27
2995159 TTGATATTTA
*
2995169 AATTTGTTAAATACATAAATTATTAAATT
1 AATTTGTTAAAAACATAAA--ATTAAATT
* *
2995198 AATTTTTTAAAAATATAAAATTAAAT
1 AATTTGTTAAAAACATAAAATTAAAT
2995224 AATAAATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 7 0.30
29 16 0.70
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (27 bp):
AATTTGTTAAAAACATAAAATTAAATT
Found at i:2995234 original size:13 final size:13
Alignment explanation
Indices: 2995208--2995244 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
2995198 AATTTTTTAA
*
2995208 AAAT-ATAAAATT
1 AAATAATAAATTT
2995220 AAATAATAAATTT
1 AAATAATAAATTT
2995233 AAATAA-AAATTT
1 AAATAATAAATTT
2995245 GTGATATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
AAATAATAAATTT
Found at i:3006840 original size:27 final size:27
Alignment explanation
Indices: 3006810--3006865 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
3006800 CATGGGTTCC
*
3006810 AGGTTACAAGTTATTATGTATTTGTCT
1 AGGTTACAAGTTAATATGTATTTGTCT
*
3006837 AGGTTACAAGTTAATCTGTATTTGTCT
1 AGGTTACAAGTTAATATGTATTTGTCT
3006864 AG
1 AG
3006866 AAAATATTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.27, C:0.09, G:0.20, T:0.45
Consensus pattern (27 bp):
AGGTTACAAGTTAATATGTATTTGTCT
Found at i:3010931 original size:22 final size:22
Alignment explanation
Indices: 3010891--3010937 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 22
3010881 TAAATTTATA
3010891 TATTAAAATAAATAATTATATTT
1 TATTAAAATAAATAATTAT-TTT
3010914 TATTAAGAAT-AA-AATTATTTT
1 TATTAA-AATAAATAATTATTTT
3010935 TAT
1 TAT
3010938 ATATTTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 6 0.26
22 6 0.26
23 8 0.35
24 3 0.13
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TATTAAAATAAATAATTATTTT
Found at i:3010942 original size:25 final size:25
Alignment explanation
Indices: 3010885--3010942 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 25
3010875 AATATATAAA
3010885 TTTATATATTAAAATAAATAATTAT
1 TTTATATATTAAAATAAATAATTAT
*
3010910 ATT-T-TATTAAGAAT-AA-AATTATT
1 TTTATATATTAA-AATAAATAATTA-T
3010933 TTTATATATT
1 TTTATATATT
3010943 TTTAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
22 5 0.19
23 11 0.41
24 5 0.19
25 6 0.22
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TTTATATATTAAAATAAATAATTAT
Found at i:3011582 original size:14 final size:14
Alignment explanation
Indices: 3011545--3011585 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
3011535 TTTTACTTGT
3011545 TTTATTTTTAAATA
1 TTTATTTTTAAATA
3011559 -TTATTTTTTAAATA
1 TTTA-TTTTTAAATA
*
3011573 TTTATATTTAAAT
1 TTTATTTTTAAAT
3011586 TTAAATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 3 0.12
14 18 0.75
15 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTATTTTTAAATA
Found at i:3011727 original size:2 final size:2
Alignment explanation
Indices: 3011720--3011764 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
3011710 TAATTTCTTC
3011720 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3011762 TA T
1 TA T
3011765 GCAGATTTTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3012619 original size:21 final size:21
Alignment explanation
Indices: 3012589--3012628 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3012579 AGGTACAACC
*
3012589 AGAACCAAGAGGAGTTCGAAG
1 AGAACCAAGAAGAGTTCGAAG
*
3012610 AGAACGAAGAAGAGTTCGA
1 AGAACCAAGAAGAGTTCGA
3012629 GCCCTGATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.12, G:0.33, T:0.10
Consensus pattern (21 bp):
AGAACCAAGAAGAGTTCGAAG
Found at i:3019674 original size:27 final size:27
Alignment explanation
Indices: 3019635--3019687 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
3019625 TTGTACCGTC
* * *
3019635 AATTTTAACATTTAATTTGAAATAGTA
1 AATTATAAAATTTAATTTAAAATAGTA
3019662 AATTATAAAATTTAATTTAAAATAGT
1 AATTATAAAATTTAATTTAAAATAGT
3019688 GAAGGTTGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (27 bp):
AATTATAAAATTTAATTTAAAATAGTA
Found at i:3023086 original size:27 final size:27
Alignment explanation
Indices: 3023047--3023099 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
3023037 CTGTGCCGTC
* *
3023047 AATTTTGACATTCAATTTGAAATAGTA
1 AATTATGAAATTCAATTTGAAATAGTA
3023074 AATTATGAAATTCAATTTGAAATAGT
1 AATTATGAAATTCAATTTGAAATAGT
3023100 GAAGGTTGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (27 bp):
AATTATGAAATTCAATTTGAAATAGTA
Found at i:3023096 original size:12 final size:12
Alignment explanation
Indices: 3023045--3023096 Score: 50
Period size: 12 Copynumber: 4.0 Consensus size: 12
3023035 AACTGTGCCG
*
3023045 TCAATTTTGACAT
1 TCAA-TTTGAAAT
3023058 TCAATTTGAAAT
1 TCAATTTGAAAT
*
3023070 AGTAAATTATGAAAT
1 --TCAATT-TGAAAT
3023085 TCAATTTGAAAT
1 TCAATTTGAAAT
3023097 AGTGAAGGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
12 13 0.39
13 9 0.27
14 5 0.15
15 6 0.18
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.40
Consensus pattern (12 bp):
TCAATTTGAAAT
Found at i:3028232 original size:28 final size:28
Alignment explanation
Indices: 3028171--3028252 Score: 105
Period size: 28 Copynumber: 2.9 Consensus size: 28
3028161 TTTTGGAGAT
*
3028171 AATAACGGGGTTGGAGTGTTCCCTCG--GA
1 AATAACGGGGTTGGAGT-AT-CCTCGATGA
*
3028199 AGTAACGGGGTTGGAGTATCCTCGATGA
1 AATAACGGGGTTGGAGTATCCTCGATGA
*
3028227 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGGGGTTGGAGTATCCTCGAT
3028253 TGTGAAAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
26 5 0.10
27 1 0.02
28 42 0.88
ACGTcount: A:0.26, C:0.16, G:0.33, T:0.26
Consensus pattern (28 bp):
AATAACGGGGTTGGAGTATCCTCGATGA
Found at i:3028296 original size:52 final size:51
Alignment explanation
Indices: 3028235--3028671 Score: 471
Period size: 52 Copynumber: 8.4 Consensus size: 51
3028225 GAAATAACGA
* * *
3028235 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTAGT-GTTTTGGAAATAAAATCGG
* ** * * *
3028287 TGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATT-GTGAAAAATTAGTGTTTTGGAAATAAAATCGG
* * * *
3028339 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGA
1 GGTTGGAGTATCCCCGATTGT-GAAAAATTAGTGTTTTGGAAATAAAATCGG
** * * * *
3028391 GGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-GTGAAAAATTAGTGTTTTGGAAATAAAATCGG
* * *
3028443 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTGT-GAAAAATTAGTGTTTTGGAAATAAAATCGG
* * * * *
3028495 GGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTGGAAATAAAATCGG
* *
3028546 GGTTGGAGTATCCCCGATTGTGAAAATTTGGTGTTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTAGTG--TTTTGGAAATAAAATCGG
* * * * *
3028599 AGTCGGAGTATCCCCGATTAT-AGAAAATTAGTGTCTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGA-AAAATTAGTGTTTTGGAAATAAAATCGG
* *
3028650 AGTTGGAATATCCCCGATTGTG
1 GGTTGGAGTATCCCCGATTGTG
3028672 GAGAATTGAG
Statistics
Matches: 320, Mismatches: 57, Indels: 16
0.81 0.15 0.04
Matches are distributed among these distances:
51 84 0.26
52 183 0.57
53 53 0.17
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTGGAAATAAAATCGG
Found at i:3028384 original size:104 final size:103
Alignment explanation
Indices: 3028235--3028673 Score: 553
Period size: 104 Copynumber: 4.2 Consensus size: 103
3028225 GAAATAACGA
* * * * *
3028235 GGTTGGAGTATCCTCGATTGT-GAAAAATTGGTATTTTTGGAAATAAAATCGGTGTTGGAGTATC
1 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGT-GTTTTAGAAATAAAACCGG-GTTGGAGTATC
*
3028299 CCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAATCGG
64 CCCGATTAAAGGAAAATTAGTGTTTTGAAAATAAAATCGG
*
3028339 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGAGGTTGGAGTATCC
1 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGAAATAAAACCG-GGTTGGAGTATCC
* *
3028404 CCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAACCGG
65 CCGATTAAAGGAAAATTAGTGTTTTGAAAATAAAATCGG
*
3028443 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCGGGGTTGGAGTATCC
1 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGAAATAAAACC-GGGTTGGAGTATCC
* * * * * * *
3028508 CCGATT-ATGAAAAATCAATATTTTGGAAATAAAGTCGG
65 CCGATTAAAGGAAAATTAGTGTTTTGAAAATAAAATCGG
* * * * *
3028546 GGTTGGAGTATCCCCGATTGT-GAAAATTTGGTGTTTTTTGGAAATAAAATCGGAGTCGGAGTAT
1 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTG--TTTTAGAAATAAAACCGG-GTTGGAGTAT
* *
3028610 CCCCGATTATA-GAAAATTAGTGTCTTGAAAATAAAATCGG
63 CCCCGATTAAAGGAAAATTAGTGTTTTGAAAATAAAATCGG
* *
3028650 AGTTGGAATATCCCCGATTGTGGA
1 GGTTGGAGTATCCCCGATTGTGGA
3028674 GAATTGAGAA
Statistics
Matches: 294, Mismatches: 33, Indels: 15
0.86 0.10 0.04
Matches are distributed among these distances:
102 10 0.03
103 46 0.16
104 224 0.76
105 14 0.05
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (103 bp):
GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGAAATAAAACCGGGTTGGAGTATCCC
CGATTAAAGGAAAATTAGTGTTTTGAAAATAAAATCGG
Found at i:3028429 original size:156 final size:153
Alignment explanation
Indices: 3028232--3028673 Score: 523
Period size: 156 Copynumber: 2.8 Consensus size: 153
3028222 GATGAAATAA
* * *
3028232 CGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGTGTTGGAGTA
1 CGAGGTTGGAGTATCCCCGATTG-G-AAAATTGGT-GTTTTGGAAATAAAATCGGAGTTGGAGTA
*
3028297 TCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAATCGGGGTTGGAGTATCCCCGATTGTGG
63 TCCCCGATTAAAGGAAAATTAGTGTTTTGAAAATAAAATCGGGGTTGGAGTATCCCCGATTGTGG
* * * *
3028362 AAAAATTAGTGTTTTAGCAATAAAAC
128 AAAAATCAATATTTTAGAAATAAAAC
* * *
3028388 CGAGGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAACCGGGGTTGGAGTA
1 CGAGGTTGGAGTATCCCCGATT---GGAAAATTGGTGTTTTGGAAATAAAATCGGAGTTGGAGTA
** * * *
3028453 TCCCCGATT-GTGGAAAAATTAGTGTTTT-AGCAATAAAACCGGGGTTGGAGTATCCCCGATTAT
63 TCCCCGATTAAAGG-AAAATTAGTGTTTTGA-AAATAAAATCGGGGTTGGAGTATCCCCGATTGT
* **
3028516 -GAAAAATCAATATTTTGGAAATAAAGT
126 GGAAAAATCAATATTTTAGAAATAAAAC
* *
3028543 CGGGGTTGGAGTATCCCCGATTGTGAAAATTTGGTGTTTTTTGGAAATAAAATCGGAGTCGGAGT
1 CGAGGTTGGAGTATCCCCGATTG-GAAAA-TTGGTG--TTTTGGAAATAAAATCGGAGTTGGAGT
* * * *
3028608 ATCCCCGATTATA-GAAAATTAGTGTCTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTGTG
62 ATCCCCGATTAAAGGAAAATTAGTGTTTTGAAAATAAAATCGGGGTTGGAGTATCCCCGATTGTG
3028672 GA
127 GA
3028674 GAATTGAGAA
Statistics
Matches: 243, Mismatches: 31, Indels: 24
0.82 0.10 0.08
Matches are distributed among these distances:
152 1 0.00
153 5 0.02
154 6 0.02
155 85 0.35
156 135 0.56
157 9 0.04
158 1 0.00
159 1 0.00
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (153 bp):
CGAGGTTGGAGTATCCCCGATTGGAAAATTGGTGTTTTGGAAATAAAATCGGAGTTGGAGTATCC
CCGATTAAAGGAAAATTAGTGTTTTGAAAATAAAATCGGGGTTGGAGTATCCCCGATTGTGGAAA
AATCAATATTTTAGAAATAAAAC
Found at i:3031052 original size:13 final size:13
Alignment explanation
Indices: 3031034--3031059 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3031024 ACAAAGATCC
3031034 ATGTATCGATACA
1 ATGTATCGATACA
3031047 ATGTATCGATACA
1 ATGTATCGATACA
3031060 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3031055 original size:33 final size:33
Alignment explanation
Indices: 3031013--3031079 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3031003 AAAATTTCCA
***
3031013 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
3031046 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
3031079 A
1 A
3031080 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:3031123 original size:19 final size:18
Alignment explanation
Indices: 3031099--3031166 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
3031089 CAGTAGCTAA
3031099 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
3031118 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
3031133 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
3031150 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
3031167 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:3031139 original size:13 final size:13
Alignment explanation
Indices: 3031121--3031145 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3031111 ACAATACTTA
3031121 TGTATCGATACAT
1 TGTATCGATACAT
3031134 TGTATCGATACA
1 TGTATCGATACA
3031146 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3031143 original size:32 final size:32
Alignment explanation
Indices: 3031102--3031164 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
3031092 TAGCTAATTA
*
3031102 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
3031134 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
3031165 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:3040471 original size:24 final size:25
Alignment explanation
Indices: 3040444--3040500 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
3040434 TAAAAATAAA
*
3040444 ATAAAATTATAATATT-TAAATTTT
1 ATAAAATTAAAATATTATAAATTTT
** *
3040468 ATAATTTTAAAATATTACTCAATTTT
1 ATAAAATTAAAATATTA-TAAATTTT
3040494 ATAAAAT
1 ATAAAAT
3040501 CTTTTAAATT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
24 13 0.52
26 12 0.48
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (25 bp):
ATAAAATTAAAATATTATAAATTTT
Found at i:3041741 original size:17 final size:17
Alignment explanation
Indices: 3041708--3041755 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
3041698 GTAGAGGATA
*
3041708 TTAAT-TTTTATAA-AT
1 TTAATATTTTAAAATAT
3041723 TTAATATTTTAAAATAT
1 TTAATATTTTAAAATAT
*
3041740 TTATTATTTTATAAAT
1 TTAATATTTTA-AAAT
3041756 TTACTAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 5 0.18
16 7 0.25
17 12 0.43
18 4 0.14
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTAATATTTTAAAATAT
Found at i:3041808 original size:21 final size:20
Alignment explanation
Indices: 3041775--3041822 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
3041765 AATAAATAAA
3041775 AATTTAATTTTTA-ATAATAT
1 AATTTAATTTTTATA-AATAT
3041795 -ATTTAATATATTTATAAATAT
1 AATTTAAT-T-TTTATAAATAT
3041816 AATTTAA
1 AATTTAA
3041823 AATTGTATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
19 7 0.29
20 1 0.04
21 9 0.38
22 7 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
AATTTAATTTTTATAAATAT
Found at i:3045718 original size:73 final size:72
Alignment explanation
Indices: 3045641--3045776 Score: 254
Period size: 73 Copynumber: 1.9 Consensus size: 72
3045631 TCATTTATTA
3045641 AATTTAATATAATATATTAATTTTATTAATTATTTTTTAAATTATATTTTAATTCTTTTTAATAG
1 AATTTAATATAATATATTAATTTTATTAATTATTTTTTAAATTATATTTTAATT-TTTTTAATAG
3045706 AATCATTG
65 AATCATTG
*
3045714 AATTTAATATAATATATTAATTTTATTAATTATTTTTTAAATTATGTTTTAATTTTTTTAATA
1 AATTTAATATAATATATTAATTTTATTAATTATTTTTTAAATTATATTTTAATTTTTTTAATA
3045777 AAATTTTAAC
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
72 9 0.15
73 53 0.85
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.58
Consensus pattern (72 bp):
AATTTAATATAATATATTAATTTTATTAATTATTTTTTAAATTATATTTTAATTTTTTTAATAGA
ATCATTG
Found at i:3045869 original size:17 final size:17
Alignment explanation
Indices: 3045812--3045871 Score: 50
Period size: 21 Copynumber: 3.4 Consensus size: 17
3045802 AATATAATAA
* *
3045812 TAAAAATTATTATTAAT
1 TAAAAATTTTTATAAAT
*
3045829 T-AATATTTTTATTTAATAT
1 TAAAAATTTTTA--TAA-AT
3045848 ATAAAAATTTTTATAAAT
1 -TAAAAATTTTTATAAAT
3045866 TAAAAA
1 TAAAAA
3045872 ATTATATATA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
16 8 0.24
17 7 0.21
18 4 0.12
19 5 0.15
20 1 0.03
21 9 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TAAAAATTTTTATAAAT
Found at i:3046401 original size:30 final size:34
Alignment explanation
Indices: 3046367--3046430 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
3046357 ATATATATTT
*
3046367 TATATAT-TTTTTAA-A-ATTTATTT-TAAAATA
1 TATATATAATTTTAATATATTTATTTATAAAATA
3046397 TATATATAATTTTAATTATATTTATTTATAAAAT
1 TATATATAATTTTAA-TATATTTATTTATAAAAT
3046431 TTTTACATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
30 7 0.25
31 6 0.21
33 1 0.04
34 8 0.29
35 6 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (34 bp):
TATATATAATTTTAATATATTTATTTATAAAATA
Found at i:3046431 original size:18 final size:17
Alignment explanation
Indices: 3046382--3046431 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 17
3046372 ATTTTTTAAA
3046382 ATTTATTTTAAAATATAT
1 ATTTATTTTAAAAT-TAT
*
3046400 ATATAATTTT--AATTAT
1 AT-TTATTTTAAAATTAT
3046416 ATTTATTTATAAAATT
1 ATTTATTT-TAAAATT
3046432 TTTACATTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
15 5 0.19
16 6 0.23
17 3 0.12
18 6 0.23
19 6 0.23
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTATTTTAAAATTAT
Found at i:3064120 original size:3 final size:3
Alignment explanation
Indices: 3064063--3064101 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
3064053 ACAGTAACAT
3064063 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3064102 CTATCAAGCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3064514 original size:2 final size:2
Alignment explanation
Indices: 3064507--3064544 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3064497 CTAAAACCCC
3064507 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3064545 TTTTTTCTGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3065602 original size:43 final size:43
Alignment explanation
Indices: 3065541--3065626 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
3065531 TTATTAATCA
3065541 AAATTTCATGATGATTCTAAATCAAAGGTGTTTTGTATATAAT
1 AAATTTCATGATGATTCTAAATCAAAGGTGTTTTGTATATAAT
3065584 AAATTTCATGATGATTCTAAATCAAAGGTGTTTTGTATATAAT
1 AAATTTCATGATGATTCTAAATCAAAGGTGTTTTGTATATAAT
3065627 TTCTGGGTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42
Consensus pattern (43 bp):
AAATTTCATGATGATTCTAAATCAAAGGTGTTTTGTATATAAT
Found at i:3066786 original size:18 final size:18
Alignment explanation
Indices: 3066763--3066797 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3066753 TAAATTAAAT
3066763 TGATATTTAA-TTAATTAA
1 TGATA-TTAATTTAATTAA
3066781 TGATATTAATTTAATTA
1 TGATATTAATTTAATTA
3066798 GGTACCTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (18 bp):
TGATATTAATTTAATTAA
Found at i:3069327 original size:2 final size:2
Alignment explanation
Indices: 3069320--3069352 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3069310 CTAGTTTTAT
3069320 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3069353 AGTTCTGGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3071183 original size:4 final size:4
Alignment explanation
Indices: 3071174--3071216 Score: 59
Period size: 4 Copynumber: 10.8 Consensus size: 4
3071164 TTTATAAATT
* * *
3071174 TATA TATA TATA TATA TATA TATA TATT TATA TCTA TTTA TAT
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TAT
3071217 CTATCTGAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (4 bp):
TATA
Found at i:3071185 original size:6 final size:6
Alignment explanation
Indices: 3071174--3071216 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
3071164 TTTATAAATT
* * *
3071174 TATATA TATATA TATATA TATATA TATTTA TATCTA TTTATA T
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA T
3071217 CTATCTGAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (6 bp):
TATATA
Found at i:3071220 original size:10 final size:10
Alignment explanation
Indices: 3071166--3071216 Score: 61
Period size: 10 Copynumber: 5.3 Consensus size: 10
3071156 ACTCTCTTTT
*
3071166 TATAAATTTA
1 TATATATTTA
3071176 TATATA--TA
1 TATATATTTA
*
3071184 TATATATATA
1 TATATATTTA
3071194 TATATATTTA
1 TATATATTTA
*
3071204 TATCTATTTA
1 TATATATTTA
3071214 TAT
1 TAT
3071217 CTATCTGAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
8 8 0.22
10 28 0.78
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (10 bp):
TATATATTTA
Found at i:3077805 original size:2 final size:2
Alignment explanation
Indices: 3077798--3077843 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
3077788 AGCTACTATG
3077798 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3077840 TA TA
1 TA TA
3077844 GTAGTGATGG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3081637 original size:18 final size:17
Alignment explanation
Indices: 3081619--3081666 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 17
3081609 TATATACATA
3081619 ATAATATAAATTTTAAT
1 ATAATATAAATTTTAAT
3081636 A-AATATATAA-TTT-AT
1 ATAATATA-AATTTTAAT
*
3081651 ATTATATAAATTTTAA
1 ATAATATAAATTTTAA
3081667 AATACTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
15 5 0.19
16 17 0.65
17 4 0.15
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATAATATAAATTTTAAT
Found at i:3081927 original size:13 final size:14
Alignment explanation
Indices: 3081904--3081969 Score: 57
Period size: 13 Copynumber: 4.7 Consensus size: 14
3081894 AAATTCGATT
3081904 TTTATAAAATAAAA
1 TTTATAAAATAAAA
3081918 TTTA-AAAATAAAA
1 TTTATAAAATAAAA
3081931 TTT-TAAATATATTAAA
1 TTTATAAA-ATA--AAA
* *
3081947 TTAATAAAA-AACA
1 TTTATAAAATAAAA
*
3081960 TTTTTAAAAT
1 TTTATAAAAT
3081970 TATTAAAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
13 24 0.57
14 7 0.17
15 1 0.02
16 6 0.14
17 4 0.10
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (14 bp):
TTTATAAAATAAAA
Found at i:3081935 original size:14 final size:14
Alignment explanation
Indices: 3081903--3081937 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
3081893 AAAATTCGAT
3081903 TTTTATAAAATAAAA
1 TTTTA-AAAATAAAA
3081918 -TTTAAAAATAAAA
1 TTTTAAAAATAAAA
3081931 TTTTAAA
1 TTTTAAA
3081938 TATATTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TTTTAAAAATAAAA
Found at i:3082604 original size:2 final size:2
Alignment explanation
Indices: 3082597--3082629 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3082587 TGAAATCAGA
3082597 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3082630 AAGGATGAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3083705 original size:18 final size:19
Alignment explanation
Indices: 3083667--3083710 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
3083657 TTTAAAAATA
*
3083667 AATATAAATAATTTTATTTT
1 AATA-AAATAATATTATTTT
3083687 AATAAAATAATATTA-TTT
1 AATAAAATAATATTATTTT
3083705 AATAAA
1 AATAAA
3083711 TAAATAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.39
19 10 0.43
20 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AATAAAATAATATTATTTT
Found at i:3083716 original size:18 final size:19
Alignment explanation
Indices: 3083670--3083716 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
3083660 AAAAATAAAT
*
3083670 ATAAAT-AATTTTATTTTA
1 ATAAATAAATATTATTTTA
3083688 ATAAA-ATAATATTA-TTTA
1 ATAAATA-AATATTATTTTA
3083706 ATAAATAAATA
1 ATAAATAAATA
3083717 AAATATAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 18 0.72
19 7 0.28
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATAAATAAATATTATTTTA
Found at i:3083721 original size:23 final size:22
Alignment explanation
Indices: 3083649--3083722 Score: 64
Period size: 22 Copynumber: 3.4 Consensus size: 22
3083639 ATTAATTTAT
3083649 TAAAA-ATTTTTAA-AAATAAA
1 TAAAATATTTTTAATAAATAAA
* * *
3083669 TATAAATAATTTTATTTTAATAAA
1 TA-AAATATTTTTA-ATAAATAAA
*
3083693 -ATAATATTATTTAATAAATAAA
1 TAAAATATT-TTTAATAAATAAA
3083715 TAAAATAT
1 TAAAATAT
3083723 AAATTTATAC
Statistics
Matches: 40, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
20 2 0.05
21 3 0.08
22 18 0.45
23 11 0.28
24 6 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAAATATTTTTAATAAATAAA
Found at i:3084021 original size:2 final size:2
Alignment explanation
Indices: 3084014--3084050 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3084004 GTCCCATCAC
3084014 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3084051 AAGGCTGCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3084455 original size:18 final size:19
Alignment explanation
Indices: 3084432--3084475 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
3084422 AATAAAATAC
3084432 ATAAAAATTTT-ATATAAT
1 ATAAAAATTTTAATATAAT
3084450 AT-AAAATTTTAATATAAT
1 ATAAAAATTTTAATATAAT
*
3084468 AAAAAAAT
1 ATAAAAAT
3084476 AATATAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 8 0.35
18 10 0.43
19 5 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
ATAAAAATTTTAATATAAT
Found at i:3084457 original size:17 final size:17
Alignment explanation
Indices: 3084432--3084472 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
3084422 AATAAAATAC
3084432 ATAAAAATTTT-ATATA
1 ATAAAAATTTTAATATA
3084448 ATATAAAATTTTAATATA
1 ATA-AAAATTTTAATATA
3084466 ATAAAAA
1 ATAAAAA
3084473 AATAATATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.13
17 12 0.52
18 8 0.35
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATAAAAATTTTAATATA
Found at i:3084495 original size:11 final size:11
Alignment explanation
Indices: 3084460--3084503 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
3084450 ATAAAATTTT
3084460 AATATAATAAA
1 AATATAATAAA
* *
3084471 AAAATAATATA
1 AATATAATAAA
*
3084482 AATACAATAAA
1 AATATAATAAA
3084493 AATATACATAA
1 AATATA-ATAA
3084504 GTGGATCTGA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
11 22 0.85
12 4 0.15
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (11 bp):
AATATAATAAA
Found at i:3087233 original size:2 final size:2
Alignment explanation
Indices: 3087228--3087256 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3087218 GGGGGAGGGG
3087228 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
3087257 CTCCAGATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3087399 original size:2 final size:2
Alignment explanation
Indices: 3087392--3087417 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3087382 CCCCTCACCA
3087392 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
3087418 GCAAAATTTA
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:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3089042 original size:31 final size:32
Alignment explanation
Indices: 3089000--3089069 Score: 106
Period size: 31 Copynumber: 2.2 Consensus size: 32
3088990 AATATTTTTA
*
3089000 TATTTTGAATTTAATAGTATTAGGGA-AATGT
1 TATTTTGAATTTAATAGTATTAGGAAGAATGT
*
3089031 TATTTTTAATTTAATAGTATTAGGAATGAATGT
1 TATTTTGAATTTAATAGTATTAGGAA-GAATGT
3089064 TATTTT
1 TATTTT
3089070 CAAAATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 24 0.69
33 11 0.31
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (32 bp):
TATTTTGAATTTAATAGTATTAGGAAGAATGT
Found at i:3091493 original size:18 final size:18
Alignment explanation
Indices: 3091452--3091500 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
3091442 TAAAATGAAA
*
3091452 TTTATATTTTTAATAATT
1 TTTATATTTATAATAATT
* * *
3091470 TATATATTTATGATATTT
1 TTTATATTTATAATAATT
3091488 TTTATA-TTATAAT
1 TTTATATTTATAAT
3091501 TATATTTAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
17 6 0.24
18 19 0.76
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTATATTTATAATAATT
Found at i:3091534 original size:27 final size:27
Alignment explanation
Indices: 3091505--3091557 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
3091495 TATAATTATA
*
3091505 TTTAAAATAGTATATATTTTATATAAAT
1 TTTAAAATAGTA-ATAATTTATATAAAT
* *
3091533 TTTAATATATTAATAATTTATATAA
1 TTTAAAATAGTAATAATTTATATAA
3091558 TATAAATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 12 0.55
28 10 0.45
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (27 bp):
TTTAAAATAGTAATAATTTATATAAAT
Found at i:3091565 original size:32 final size:33
Alignment explanation
Indices: 3091525--3091593 Score: 104
Period size: 32 Copynumber: 2.1 Consensus size: 33
3091515 TATATATTTT
3091525 ATATAAATTTTAATATATTAATAAT-TTATATA
1 ATATAAATTTTAATATATTAATAATATTATATA
* * *
3091557 ATATAAATTTTAATATATTTATATTATTATATC
1 ATATAAATTTTAATATATTAATAATATTATATA
3091590 ATAT
1 ATAT
3091594 CATAATATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 23 0.70
33 10 0.30
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (33 bp):
ATATAAATTTTAATATATTAATAATATTATATA
Found at i:3091628 original size:22 final size:24
Alignment explanation
Indices: 3091595--3091652 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
3091585 ATATCATATC
*
3091595 ATAATATATTTT-TATTACATTTT
1 ATAATATTTTTTCTATTACATTTT
*
3091618 A-AATATTTTTTCCTATTATATTTT
1 ATAATATTTTTT-CTATTACATTTT
*
3091642 ATAAAATTTTT
1 ATAATATTTTT
3091653 ACGTCTAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 9 0.31
23 1 0.03
24 11 0.38
25 8 0.28
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.60
Consensus pattern (24 bp):
ATAATATTTTTTCTATTACATTTT
Found at i:3093637 original size:22 final size:22
Alignment explanation
Indices: 3093597--3093638 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3093587 AAGATGATGA
**
3093597 ATTAATTATTTTACGAAAATTT
1 ATTAATTATTTTAAAAAAATTT
*
3093619 ATTAATTTTTTTAAAAAAAT
1 ATTAATTATTTTAAAAAAAT
3093639 AAAAATCAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (22 bp):
ATTAATTATTTTAAAAAAATTT
Found at i:3095603 original size:22 final size:20
Alignment explanation
Indices: 3095573--3095614 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
3095563 TTTTATTTAA
3095573 TTTAATTTATTAAATTTAAAAT
1 TTTAATTTATT--ATTTAAAAT
*
3095595 TTTATTTTATTATTTAAAAT
1 TTTAATTTATTATTTAAAAT
3095615 ATAAAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
22 10 0.53
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTAATTTATTATTTAAAAT
Found at i:3095937 original size:19 final size:19
Alignment explanation
Indices: 3095899--3095938 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
3095889 AATTTATGAA
*
3095899 TATCAATAAATTATTTATT
1 TATCAATAAATTATTAATT
3095918 TATCAATAATATT-TTAATT
1 TATCAATAA-ATTATTAATT
3095937 TA
1 TA
3095939 AATAAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 16 0.84
20 3 0.16
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (19 bp):
TATCAATAAATTATTAATT
Found at i:3096236 original size:17 final size:18
Alignment explanation
Indices: 3096202--3096258 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 18
3096192 ATTTTAATAT
*
3096202 TTATATTATT-ATTATTA
1 TTATAATATTAATTATTA
3096219 TTATAATATTAATT-TTA
1 TTATAATATTAATTATTA
* *
3096236 -TATTATATTTAATTATTT
1 TTATAATA-TTAATTATTA
3096254 TTATA
1 TTATA
3096259 TTAAATTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
16 6 0.19
17 18 0.56
18 5 0.16
19 3 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTATAATATTAATTATTA
Found at i:3096255 original size:21 final size:21
Alignment explanation
Indices: 3096198--3096268 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
3096188 ATAAATTTTA
*
3096198 ATATTTATATTATTATTATTATT
1 ATATTTA-ATTATTTTTA-TATT
* *
3096221 ATA-AT-ATTAATTTTATATT
1 ATATTTAATTATTTTTATATT
3096240 ATATTTAATTATTTTTATATT
1 ATATTTAATTATTTTTATATT
*
3096261 AAATTTAA
1 ATATTTAA
3096269 AATTATTAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
19 7 0.17
20 9 0.22
21 20 0.50
22 1 0.03
23 3 0.08
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
ATATTTAATTATTTTTATATT
Found at i:3097765 original size:24 final size:24
Alignment explanation
Indices: 3097721--3097767 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3097711 AGCACCCGTA
* *
3097721 GTGCTGTTGTTGGCTGCGCTGCTT
1 GTGCTGGTGCTGGCTGCGCTGCTT
3097745 GTGCTGGTGCTGG-TGCTGCTGCT
1 GTGCTGGTGCTGGCTGC-GCTGCT
3097768 GTTGTTGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.00, C:0.21, G:0.40, T:0.38
Consensus pattern (24 bp):
GTGCTGGTGCTGGCTGCGCTGCTT
Found at i:3110296 original size:2 final size:2
Alignment explanation
Indices: 3110289--3110317 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3110279 GAAGATGATT
3110289 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3110318 ATTATTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3112346 original size:53 final size:53
Alignment explanation
Indices: 3112280--3112385 Score: 158
Period size: 53 Copynumber: 2.0 Consensus size: 53
3112270 TGTGGAAGTG
*
3112280 ATGGTCTTGGAAGTATGCTTCACTTTTTCCCCTCATCCTCTTCTGGCAATGTA
1 ATGGTCTTGGAAGTATGCGTCACTTTTTCCCCTCATCCTCTTCTGGCAATGTA
* * * * *
3112333 ATGGTCTTTGAAGTGTGCGTCGCTTTTTTCCTTCATCCTCTTCTGGCAATGTA
1 ATGGTCTTGGAAGTATGCGTCACTTTTTCCCCTCATCCTCTTCTGGCAATGTA
3112386 GATTCCGTAC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.15, C:0.25, G:0.19, T:0.42
Consensus pattern (53 bp):
ATGGTCTTGGAAGTATGCGTCACTTTTTCCCCTCATCCTCTTCTGGCAATGTA
Found at i:3113017 original size:223 final size:221
Alignment explanation
Indices: 3112632--3113056 Score: 739
Period size: 223 Copynumber: 1.9 Consensus size: 221
3112622 TTTGAGCAAT
3112632 GAAACAAGTGCATGTATGAAATCTTACAAATATGTAATACTCAGTGGCTCACATTTCCATCCATT
1 GAAACAAGTGCATGTATGAAATCTTACAAATATGTAATACTCAGTGGCTCACATTTCCATCCATT
3112697 GCAGCACTAACACCAGACCAGCTAAGTGAATCATTAAACAAGACATAACCCTTGAAAGCAGCATT
66 GCAGCACTAACACCAGACCAGCTAAGTGAATCATTAAACAAGACATAACCCTTGAAAGCAGCATT
*
3112762 TACAAGTATTTTTGCCCTCGCGGAACCTTTATAAAATGACTTAAAACCCTCAGTTCT-TTTT-TT
131 TACAAGTATTTTTGCCCCCGCGGAACCTTTAT-AAATGACTTAAAACCCTCAGTTCTCTTTTGTT
3112825 TTTTTTTTGGGGGGGGGGGGGGGGAGG
195 TTTTTTTTGGGGGGGGGGGGGGGGAGG
* * *
3112852 GAAACAAGTGGATTTATGAAATCTTACAAATATGTAATACTCAGTGGCTCACATTTGCATCCATT
1 GAAACAAGTGCATGTATGAAATCTTACAAATATGTAATACTCAGTGGCTCACATTTCCATCCATT
*
3112917 GCAGCACTAAGAACACCAGACCAGCTAAGTGAATCATTAAACAAGACATAACCCTTGAAATCAGC
66 GCAGCACT---AACACCAGACCAGCTAAGTGAATCATTAAACAAGACATAACCCTTGAAAGCAGC
3112982 ATTTACAA-TATTTTTGCCCCCCGCGGAACCTTTATAAATGACTTAAAACCCTCAGTTCTCTTTT
128 ATTTACAAGTATTTTTG-CCCCCGCGGAACCTTTATAAATGACTTAAAACCCTCAGTTCTCTTTT
3113046 GTTTTTTTTTT
192 GTTTTTTTTTT
3113057 TTTTTGGGGG
Statistics
Matches: 194, Mismatches: 5, Indels: 8
0.94 0.02 0.04
Matches are distributed among these distances:
220 70 0.36
222 32 0.16
223 82 0.42
224 10 0.05
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (221 bp):
GAAACAAGTGCATGTATGAAATCTTACAAATATGTAATACTCAGTGGCTCACATTTCCATCCATT
GCAGCACTAACACCAGACCAGCTAAGTGAATCATTAAACAAGACATAACCCTTGAAAGCAGCATT
TACAAGTATTTTTGCCCCCGCGGAACCTTTATAAATGACTTAAAACCCTCAGTTCTCTTTTGTTT
TTTTTTTGGGGGGGGGGGGGGGGAGG
Found at i:3116197 original size:2 final size:2
Alignment explanation
Indices: 3116190--3116220 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3116180 ATCACAAAAG
3116190 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3116221 GAATCTACAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3119180 original size:31 final size:31
Alignment explanation
Indices: 3119145--3119205 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
3119135 TTGCAAAAAG
*
3119145 AAGAAACAAGAAACCGATGTAGAAAAATTAC
1 AAGAAACAAGAAACCAATGTAGAAAAATTAC
* *
3119176 AAGAAATAAGAAACCAATGTAGAAGAATTA
1 AAGAAACAAGAAACCAATGTAGAAAAATTA
3119206 GACCAATTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.59, C:0.10, G:0.16, T:0.15
Consensus pattern (31 bp):
AAGAAACAAGAAACCAATGTAGAAAAATTAC
Found at i:3119746 original size:6 final size:6
Alignment explanation
Indices: 3119731--3119773 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
3119721 ACCCTTAGGC
* *
3119731 AAAA-A AAAAGA AAAAGA AAAAGA AAATAGA AGAAGA AGAAGA A
1 AAAAGA AAAAGA AAAAGA AAAAGA AAA-AGA AAAAGA AAAAGA A
3119774 CTCACATTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
5 4 0.11
6 26 0.74
7 5 0.14
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (6 bp):
AAAAGA
Found at i:3119761 original size:19 final size:18
Alignment explanation
Indices: 3119731--3119773 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
3119721 ACCCTTAGGC
3119731 AAAA-AAAAAGAAAAAGA
1 AAAAGAAAAAGAAAAAGA
*
3119748 AAAAGAAAATAGAAGAAGA
1 AAAAGAAAA-AGAAAAAGA
*
3119767 AGAAGAA
1 AAAAGAA
3119774 CTCACATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 4 0.18
18 4 0.18
19 14 0.64
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (18 bp):
AAAAGAAAAAGAAAAAGA
Found at i:3120751 original size:12 final size:12
Alignment explanation
Indices: 3120734--3120769 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
3120724 TGTTGTAATG
3120734 TATTTTATATAA
1 TATTTTATATAA
3120746 TATTTTA-AT--
1 TATTTTATATAA
3120755 TATTTTATATAA
1 TATTTTATATAA
3120767 TAT
1 TAT
3120770 AATTTTACCT
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
9 7 0.33
10 2 0.10
11 2 0.10
12 10 0.48
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TATTTTATATAA
Found at i:3120760 original size:21 final size:22
Alignment explanation
Indices: 3120729--3120769 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
3120719 TTTTATGTTG
3120729 TAATGTATTTTATATAATATTT
1 TAATGTATTTTATATAATATTT
3120751 TAAT-TATTTTATATAATAT
1 TAATGTATTTTATATAATAT
3120770 AATTTTACCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
TAATGTATTTTATATAATATTT
Found at i:3134313 original size:27 final size:26
Alignment explanation
Indices: 3134246--3134324 Score: 76
Period size: 26 Copynumber: 3.1 Consensus size: 26
3134236 ATACATAGTT
3134246 TTAAATA-A-ATTAAAAAGTTTTAATTA
1 TTAAATATATATTAAAAA-TTTTAA-TA
* * *
3134272 TTTATTTTATA-TAAAAATTTTAATA
1 TTAAATATATATTAAAAATTTTAATA
3134297 GTTAAATATATATTAAAAA-TTTAATA
1 -TTAAATATATATTAAAAATTTTAATA
3134323 TT
1 TT
3134325 TTTAATTAAC
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
25 4 0.09
26 25 0.58
27 13 0.30
28 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (26 bp):
TTAAATATATATTAAAAATTTTAATA
Found at i:3138065 original size:2 final size:2
Alignment explanation
Indices: 3138058--3138097 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3138048 ATGATTTCAA
3138058 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3138098 TTTGATTGCC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3139360 original size:9 final size:9
Alignment explanation
Indices: 3139348--3139372 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3139338 GTGTTGTTGC
3139348 TGCTGCTCG
1 TGCTGCTCG
3139357 TGCTGCTCG
1 TGCTGCTCG
3139366 TGCTGCT
1 TGCTGCT
3139373 GTTGGGACTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.32, G:0.32, T:0.36
Consensus pattern (9 bp):
TGCTGCTCG
Found at i:3140791 original size:7 final size:7
Alignment explanation
Indices: 3140779--3140803 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3140769 TAATAATAAA
3140779 ATTAATT
1 ATTAATT
3140786 ATTAATT
1 ATTAATT
3140793 ATTAATT
1 ATTAATT
3140800 ATTA
1 ATTA
3140804 TATTTAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
ATTAATT
Found at i:3141821 original size:21 final size:21
Alignment explanation
Indices: 3141772--3141821 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
3141762 ATCAACTATT
3141772 TATTATAAAAATAATTAATAAA
1 TATT-TAAAAATAATTAATAAA
* *
3141794 T-TATTAAAAATAATTATTTAA
1 TAT-TTAAAAATAATTAATAAA
3141815 TATTTAA
1 TATTTAA
3141822 TTATTATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TATTTAAAAATAATTAATAAA
Found at i:3141833 original size:18 final size:18
Alignment explanation
Indices: 3141806--3141840 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3141796 ATTAAAAATA
* *
3141806 ATTATTTAATATTTAATT
1 ATTATATAATATATAATT
3141824 ATTATATAATATATAAT
1 ATTATATAATATATAAT
3141841 AAATAATTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTATATAATATATAATT
Found at i:3143316 original size:21 final size:21
Alignment explanation
Indices: 3143272--3143316 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3143262 TTAATAAAAT
*
3143272 ATTAAATTTTTAAATTTAATA
1 ATTAAATTTTTAAATTCAATA
*
3143293 ATTAAATATTTTGAATTCAA-A
1 ATTAAAT-TTTTAAATTCAATA
3143314 ATT
1 ATT
3143317 TATGGACTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
ATTAAATTTTTAAATTCAATA
Found at i:3143515 original size:40 final size:39
Alignment explanation
Indices: 3143444--3143530 Score: 106
Period size: 40 Copynumber: 2.2 Consensus size: 39
3143434 TTTAAATAAA
* *
3143444 TTAATTTAAATTATTATTTATTAATAAAATTTATTTAAT-T
1 TTAATTTAAAATATTAATTATTAAT-AAATTT-TTTAATAT
3143484 TTAATTATAAAATATATAATTATTAAT-AATTTTTTAATAT
1 TTAATT-TAAAATAT-TAATTATTAATAAATTTTTTAATAT
3143524 TTAATTT
1 TTAATTT
3143531 TATTAAATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
39 7 0.17
40 18 0.43
41 7 0.17
42 10 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (39 bp):
TTAATTTAAAATATTAATTATTAATAAATTTTTTAATAT
Found at i:3146128 original size:12 final size:12
Alignment explanation
Indices: 3146077--3146130 Score: 63
Period size: 12 Copynumber: 4.5 Consensus size: 12
3146067 GCGGGTGTAC
3146077 TGGTGGCTTAGT
1 TGGTGGCTTAGT
* * *
3146089 CGGGGGCTGAGT
1 TGGTGGCTTAGT
* *
3146101 TGGAGGCTTGGT
1 TGGTGGCTTAGT
3146113 TGGTGGCTTAGT
1 TGGTGGCTTAGT
3146125 TGGTGG
1 TGGTGG
3146131 GTGAACTGGT
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.07, C:0.09, G:0.50, T:0.33
Consensus pattern (12 bp):
TGGTGGCTTAGT
Found at i:3146140 original size:24 final size:24
Alignment explanation
Indices: 3146113--3146332 Score: 131
Period size: 24 Copynumber: 9.2 Consensus size: 24
3146103 GAGGCTTGGT
* *
3146113 TGGTGGCTTAGTTGGTGGGTGAAC
1 TGGTGGCTTGGGTGGTGGGTGAAC
* * * *
3146137 TGGTGGCTTGGGAGGAGCGT-AAG
1 TGGTGGCTTGGGTGGTGGGTGAAC
* * *
3146160 TCGGTGGCTTGGTTGGTGGCTGCAC
1 T-GGTGGCTTGGGTGGTGGGTGAAC
* *
3146185 TGGTGGCTTGGGTGGCGGATGAAC
1 TGGTGGCTTGGGTGGTGGGTGAAC
* * *
3146209 TGGTGGCTTGGGTGGAGCGT-AAGT
1 TGGTGGCTTGGGTGGTGGGTGAA-C
* * * *
3146233 TGGCGGCTTGGTTGGTGGCTGCAC
1 TGGTGGCTTGGGTGGTGGGTGAAC
* * * * *
3146257 TGGGGGCTTGGGGGGAGCGT-AAGT
1 TGGTGGCTTGGGTGGTGGGTGAA-C
* *
3146281 TGGGGGCTTGGGTGGAGGGTGAAC
1 TGGTGGCTTGGGTGGTGGGTGAAC
* * * *
3146305 TGGGGGTTTGGGTGGTGGATAAAC
1 TGGTGGCTTGGGTGGTGGGTGAAC
3146329 TGGT
1 TGGT
3146333 AGAGGAGTCG
Statistics
Matches: 146, Mismatches: 44, Indels: 12
0.72 0.22 0.06
Matches are distributed among these distances:
23 6 0.04
24 135 0.92
25 5 0.03
ACGTcount: A:0.11, C:0.11, G:0.50, T:0.27
Consensus pattern (24 bp):
TGGTGGCTTGGGTGGTGGGTGAAC
Found at i:3146145 original size:36 final size:36
Alignment explanation
Indices: 3146077--3146147 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
3146067 GCGGGTGTAC
**
3146077 TGGTGGCTTAGTCGGGGGCTGAGTTGGAGGCTTGGT
1 TGGTGGCTTAGTCGGGGGCTGAACTGGAGGCTTGGT
* *
3146113 TGGTGGCTTAGTTGGTGGG-TGAACTGGTGGCTTGG
1 TGGTGGCTTAGTCGG-GGGCTGAACTGGAGGCTTGG
3146148 GAGGAGCGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 27 0.90
37 3 0.10
ACGTcount: A:0.08, C:0.10, G:0.49, T:0.32
Consensus pattern (36 bp):
TGGTGGCTTAGTCGGGGGCTGAACTGGAGGCTTGGT
Found at i:3146162 original size:72 final size:72
Alignment explanation
Indices: 3146086--3146265 Score: 211
Period size: 72 Copynumber: 2.5 Consensus size: 72
3146076 CTGGTGGCTT
** * * *
3146086 AGTCGGGGGC-TGAGTTGGAGGCTTG-GTTGGTGGCTTAGTTGGTGGGTGAACTGGTGGCTTGGG
1 AGTCGGGGGCTTG-GTTGGAGGC-TGCACTGGTGGCTTAGGTGGCGGATGAACTGGTGGCTTGGG
3146149 AGGAGCGTA
64 AGGAGCGTA
* * * *
3146158 AGTCGGTGGCTTGGTTGGTGGCTGCACTGGTGGCTTGGGTGGCGGATGAACTGGTGGCTTGGGTG
1 AGTCGGGGGCTTGGTTGGAGGCTGCACTGGTGGCTTAGGTGGCGGATGAACTGGTGGCTTGGGAG
3146223 GAGCGTA
66 GAGCGTA
* * * *
3146230 AGTTGGCGGCTTGGTTGGTGGCTGCACTGGGGGCTT
1 AGTCGGGGGCTTGGTTGGAGGCTGCACTGGTGGCTT
3146266 GGGGGGAGCG
Statistics
Matches: 94, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
71 2 0.02
72 90 0.96
73 2 0.02
ACGTcount: A:0.10, C:0.13, G:0.49, T:0.28
Consensus pattern (72 bp):
AGTCGGGGGCTTGGTTGGAGGCTGCACTGGTGGCTTAGGTGGCGGATGAACTGGTGGCTTGGGAG
GAGCGTA
Found at i:3146241 original size:48 final size:48
Alignment explanation
Indices: 3146189--3146319 Score: 172
Period size: 48 Copynumber: 2.7 Consensus size: 48
3146179 CTGCACTGGT
* *
3146189 GGCTTGGGTGGCGGATGAACTGGTGGCTTGGGTGGAGCGTAAGTTGGC
1 GGCTTGGGTGGAGGATGAACTGGGGGCTTGGGTGGAGCGTAAGTTGGC
* * * * * *
3146237 GGCTTGGTTGGTGGCTGCACTGGGGGCTTGGGGGGAGCGTAAGTTGGG
1 GGCTTGGGTGGAGGATGAACTGGGGGCTTGGGTGGAGCGTAAGTTGGC
* *
3146285 GGCTTGGGTGGAGGGTGAACTGGGGGTTTGGGTGG
1 GGCTTGGGTGGAGGATGAACTGGGGGCTTGGGTGG
3146320 TGGATAAACT
Statistics
Matches: 70, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 70 1.00
ACGTcount: A:0.10, C:0.11, G:0.54, T:0.25
Consensus pattern (48 bp):
GGCTTGGGTGGAGGATGAACTGGGGGCTTGGGTGGAGCGTAAGTTGGC
Found at i:3146266 original size:72 final size:72
Alignment explanation
Indices: 3146132--3146268 Score: 238
Period size: 72 Copynumber: 1.9 Consensus size: 72
3146122 AGTTGGTGGG
* *
3146132 TGAACTGGTGGCTTGGGAGGAGCGTAAGTCGGTGGCTTGGTTGGTGGCTGCACTGGTGGCTTGGG
1 TGAACTGGTGGCTTGGGAGGAGCGTAAGTCGGCGGCTTGGTTGGTGGCTGCACTGGGGGCTTGGG
3146197 TGGCGGA
66 TGGCGGA
* *
3146204 TGAACTGGTGGCTTGGGTGGAGCGTAAGTTGGCGGCTTGGTTGGTGGCTGCACTGGGGGCTTGGG
1 TGAACTGGTGGCTTGGGAGGAGCGTAAGTCGGCGGCTTGGTTGGTGGCTGCACTGGGGGCTTGGG
3146269 GGGAGCGTAA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 61 1.00
ACGTcount: A:0.10, C:0.14, G:0.49, T:0.27
Consensus pattern (72 bp):
TGAACTGGTGGCTTGGGAGGAGCGTAAGTCGGCGGCTTGGTTGGTGGCTGCACTGGGGGCTTGGG
TGGCGGA
Found at i:3146289 original size:72 final size:72
Alignment explanation
Indices: 3146132--3146297 Score: 219
Period size: 72 Copynumber: 2.3 Consensus size: 72
3146122 AGTTGGTGGG
* * * *
3146132 TGAACTGGTGGCTTGGGAGGAGCGTAAGTCGGTGGCTTGGTTGGTGGCTGCACTGGTGGCTTGGG
1 TGAACTGGGGGCTTGGGTGGAGCGTAAGTCGGCGGCTTGGTTGGTGGCTGCACTGGGGGCTTGGG
* *
3146197 TGGCGGA
66 GGGAGGA
* *
3146204 TGAACTGGTGGCTTGGGTGGAGCGTAAGTTGGCGGCTTGGTTGGTGGCTGCACTGGGGGCTTGGG
1 TGAACTGGGGGCTTGGGTGGAGCGTAAGTCGGCGGCTTGGTTGGTGGCTGCACTGGGGGCTTGGG
3146269 GGGAGCG-
66 GGGAG-GA
*
3146276 T-AAGTTGGGGGCTTGGGTGGAG
1 TGAA-CTGGGGGCTTGGGTGGAG
3146298 GGTGAACTGG
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
71 2 0.02
72 81 0.96
73 1 0.01
ACGTcount: A:0.11, C:0.13, G:0.51, T:0.26
Consensus pattern (72 bp):
TGAACTGGGGGCTTGGGTGGAGCGTAAGTCGGCGGCTTGGTTGGTGGCTGCACTGGGGGCTTGGG
GGGAGGA
Found at i:3149689 original size:14 final size:14
Alignment explanation
Indices: 3149667--3149697 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3149657 TCATGGCCCG
3149667 TTTTCTTTTCTTTT
1 TTTTCTTTTCTTTT
*
3149681 TTTTTTTTTCTTTT
1 TTTTCTTTTCTTTT
3149695 TTT
1 TTT
3149698 CCTCCTTTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (14 bp):
TTTTCTTTTCTTTT
Done.