Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold228
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: 4123243
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
File 18 of 27
Found at i:2643344 original size:51 final size:53
Alignment explanation
Indices: 2643281--2643399 Score: 154
Period size: 52 Copynumber: 2.3 Consensus size: 53
2643271 TTATTTTTTA
*
2643281 GGGGATACTCCAACCCT-AG-TTTTACTTCCAAAACATCAATTTTCCACAATC
1 GGGGATACTCCAACCCTCAGTTTTTACTTCCAAAACACCAATTTTCCACAATC
* * ** * *
2643332 GGGGATACTCCAA-CCTCGGTTTTTATTTTTAAAACACCGATTTTCCATAATC
1 GGGGATACTCCAACCCTCAGTTTTTACTTCCAAAACACCAATTTTCCACAATC
2643384 GGGGATACTCCAACCC
1 GGGGATACTCCAACCC
2643400 CATTAATTCT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
50 3 0.05
51 14 0.24
52 39 0.67
53 2 0.03
ACGTcount: A:0.29, C:0.28, G:0.13, T:0.30
Consensus pattern (53 bp):
GGGGATACTCCAACCCTCAGTTTTTACTTCCAAAACACCAATTTTCCACAATC
Found at i:2643349 original size:79 final size:78
Alignment explanation
Indices: 2642984--2643346 Score: 363
Period size: 79 Copynumber: 4.6 Consensus size: 78
2642974 TCATTGATGT
* * * * * * *
2642984 TTTTATTTCTAAAATACCGATTTTCCACCATCGAGGATACTCCAACCCCGTTATTTCTGAGGGGA
1 TTTTATTTCCAAAACATCGATTTTCCACAATCGGGGATACTCCAACCCCGTTATTTTTAAGGGGA
2643049 TACTCCAACTCCGA
66 TACTCCAAC-CCGA
* * * * * * *
2643063 TTTTATTTCTAAAACA-CTGATTTTTCACCATCAGGGATACTCCAATCCCGTTATTTTCAAAGGG
1 TTTTATTTCCAAAACATC-GATTTTCCACAATCGGGGATACTCCAACCCCGTTATTTTTAAGGGG
2643127 ATACTCCAACCTCGA
65 ATACTCCAACC-CGA
* * * ** *
2643142 TTTTATTTCCAAAACATTGATTTTTCACAATCGGGGATACTCTAACCCCCGTTA--TTTCCGGCA
1 TTTTATTTCCAAAACATCGATTTTCCACAATCGGGGATACTCCAA-CCCCGTTATTTTTAAGG-G
*
2643205 GATACTTCAATCCCGA
64 GATACTCCAA-CCCGA
* ** * * * *
2643221 TTTTATTTTCAAAACATCGATTTTCCACAATCAAGAATACTCTAACCTCGTTATTTTTTAGGGGA
1 TTTTATTTCCAAAACATCGATTTTCCACAATCGGGGATACTCCAACCCCGTTATTTTTAAGGGGA
*
2643286 TACTCCAACCCTA
66 TACTCCAACCCGA
* *
2643299 GTTTTACTTCCAAAACATCAATTTTCCACAATCGGGGATACTCCAACC
1 -TTTTATTTCCAAAACATCGATTTTCCACAATCGGGGATACTCCAACC
2643347 TCGGTTTTTA
Statistics
Matches: 235, Mismatches: 40, Indels: 18
0.80 0.14 0.06
Matches are distributed among these distances:
78 16 0.07
79 205 0.87
80 14 0.06
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.34
Consensus pattern (78 bp):
TTTTATTTCCAAAACATCGATTTTCCACAATCGGGGATACTCCAACCCCGTTATTTTTAAGGGGA
TACTCCAACCCGA
Found at i:2643552 original size:127 final size:128
Alignment explanation
Indices: 2643222--2643571 Score: 321
Period size: 131 Copynumber: 2.7 Consensus size: 128
2643212 CAATCCCGAT
* * * * * * * * ***
2643222 TTTATTTTCAAAACATCGATTTTCCACAATC-AAGAATACTCTAACCTCGTTATTTTTTAGGGGA
1 TTTATTTTTAAAACACCAATTTTCCACAATCGGAG-ATACTCCAACCCCATTAATTCCAAGGGGA
* *
2643286 TACTCCAACCCTAGTTTTACTTCCAAAACATCAATTTTCCACAATCGGGGATACTCCAACCTCGG
65 TACTCCAACCC-AGTTTTATTTCCAAAACATCAATTTTCCACAATCAGGGATACTCCAACCTC-G
*
2643351 TT
128 -C
* * * *** *
2643353 TTTATTTTTAAAACACCGATTTTCCATAATCGGGGATACTCCAACCCCATTAATTCTGCGAGGAT
1 TTTATTTTTAAAACACCAATTTTCCACAATCGGAGATACTCCAACCCCATTAATTCCAAGGGGAT
* ** *
2643418 ACTCCAACCTCAGTTTTATTTCCAAAACA-CTGATTTTTTACAATCAGGGATGCTCCAACC-C-C
66 ACTCCAACC-CAGTTTTATTTCCAAAACATC-AATTTTCCACAATCAGGGATACTCCAACCTCGC
* * * * *
2643480 TTTATTTTTAGAACACCAATTTTTCACAATCGGAGATACTTCGACCCCATTATTTCCAAGGGGAT
1 TTTATTTTTAAAACACCAATTTTCCACAATCGGAGATACTCCAACCCCATTAATTCCAAGGGGAT
* *
2643545 ACTCCAACCCCATTTTTATCTCCAAAA
66 ACTCCAA-CCCAGTTTTATTTCCAAAA
2643572 TAGTAAATGT
Statistics
Matches: 181, Mismatches: 34, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
127 75 0.41
128 2 0.01
130 2 0.01
131 100 0.55
132 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (128 bp):
TTTATTTTTAAAACACCAATTTTCCACAATCGGAGATACTCCAACCCCATTAATTCCAAGGGGAT
ACTCCAACCCAGTTTTATTTCCAAAACATCAATTTTCCACAATCAGGGATACTCCAACCTCGC
Found at i:2646530 original size:25 final size:27
Alignment explanation
Indices: 2646495--2646547 Score: 74
Period size: 25 Copynumber: 2.0 Consensus size: 27
2646485 AATTTTTTAT
*
2646495 AAAAAAGTTATA-AT-TTAAAAATAAA
1 AAAAAAATTATATATATTAAAAATAAA
*
2646520 AAAAAAATTATATATATTAAAATTAAA
1 AAAAAAATTATATATATTAAAAATAAA
2646547 A
1 A
2646548 TTTTAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 11 0.46
26 2 0.08
27 11 0.46
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (27 bp):
AAAAAAATTATATATATTAAAAATAAA
Found at i:2646533 original size:27 final size:26
Alignment explanation
Indices: 2646495--2646547 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
2646485 AATTTTTTAT
2646495 AAAAAAGTTATA-ATTTAAAAATAAAA
1 AAAAAAGTTATATA-TTAAAAATAAAA
* *
2646521 AAAAAATTATATATATTAAAATTAAAA
1 AAAAAAGT-TATATATTAAAAATAAAA
2646548 TTTTAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 7 0.30
27 15 0.65
28 1 0.04
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (26 bp):
AAAAAAGTTATATATTAAAAATAAAA
Found at i:2646925 original size:53 final size:53
Alignment explanation
Indices: 2646838--2646953 Score: 130
Period size: 53 Copynumber: 2.2 Consensus size: 53
2646828 TTTAAGATGC
* * *
2646838 TATATATTTATATAAATATTGATACGTTTAATTATTTATATTATA-TATATT-TT
1 TATATATTTATATAAATAATAATAC-TTTAATTATTT-TATTATATTATATTATA
* *
2646891 TATATATTTATATAATTAAATAATA-TTTATATTATTTTTTTATATTATATTATA
1 TATATATTTATATAAAT-AATAATACTTTA-ATTATTTTATTATATTATATTATA
2646945 TATATATTT
1 TATATATTT
2646954 TTTTTATATT
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
52 10 0.19
53 29 0.54
54 15 0.28
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.59
Consensus pattern (53 bp):
TATATATTTATATAAATAATAATACTTTAATTATTTTATTATATTATATTATA
Found at i:2647989 original size:2 final size:2
Alignment explanation
Indices: 2647982--2648013 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2647972 AAAAGTCTAA
2647982 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
2648014 TGTACATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2648831 original size:20 final size:20
Alignment explanation
Indices: 2648798--2648837 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2648788 TATTTTTATT
2648798 TAAATTTAATTATAAAAATA
1 TAAATTTAATTATAAAAATA
2648818 TAAATATTAA-TATAAAAATA
1 TAAAT-TTAATTATAAAAATA
2648838 ATTTTGGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAATTTAATTATAAAAATA
Found at i:2648852 original size:34 final size:34
Alignment explanation
Indices: 2648814--2648880 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
2648804 TAATTATAAA
*
2648814 AATATAAATATTAATA-TAAAAATAATTTTGGATT
1 AATATAAA-AATAATATTAAAAATAATTTTGGATT
*
2648848 AATATAAAAATAATATTAATAATAATTTTGGAT
1 AATATAAAAATAATATTAAAAATAATTTTGGAT
2648881 AAATTTTTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 6 0.20
34 24 0.80
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (34 bp):
AATATAAAAATAATATTAAAAATAATTTTGGATT
Found at i:2649372 original size:20 final size:20
Alignment explanation
Indices: 2649347--2649386 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2649337 TTTTTAAATT
2649347 TTTTATA-TAAAACTAATTAA
1 TTTTATACTAAAA-TAATTAA
*
2649367 TTTTATACTAATATAATTAA
1 TTTTATACTAAAATAATTAA
2649387 ATCTCTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTTATACTAAAATAATTAA
Found at i:2650023 original size:75 final size:75
Alignment explanation
Indices: 2649934--2650085 Score: 223
Period size: 75 Copynumber: 2.0 Consensus size: 75
2649924 ACTTTGGCAT
* * *
2649934 ATAATCCTTTGGTGGCTTAATTGATCGAATTTATTTGTCTTATTAAGGGAGCAAATCATAGATGA
1 ATAATCCTTTGGTGGCTTAATTGATCAAATTTATTTGTCCTATTAAGGGAGCAAATCATAGACGA
*
2649999 ATTATTCTTG
66 ATTATGCTTG
* * * * *
2650009 ATAATCTTTTGGTGGCTTAATTTATCAAATTTATTTGTCCTATTGAGGGGGCAAATCATGGACGA
1 ATAATCCTTTGGTGGCTTAATTGATCAAATTTATTTGTCCTATTAAGGGAGCAAATCATAGACGA
2650074 ATTATGCTTG
66 ATTATGCTTG
2650084 AT
1 AT
2650086 TAAGCCCTTA
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
75 68 1.00
ACGTcount: A:0.28, C:0.11, G:0.20, T:0.41
Consensus pattern (75 bp):
ATAATCCTTTGGTGGCTTAATTGATCAAATTTATTTGTCCTATTAAGGGAGCAAATCATAGACGA
ATTATGCTTG
Found at i:2651331 original size:18 final size:17
Alignment explanation
Indices: 2651308--2651351 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
2651298 CAAAAAATGT
2651308 TTTCTTTCCTTTTTTTTC
1 TTTCTTT-CTTTTTTTTC
*
2651326 TTTCTTTCTTTTTTTTT
1 TTTCTTTCTTTTTTTTC
*
2651343 TTTTTTTCT
1 TTTCTTTCT
2651352 CATTTATTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 17 0.71
18 7 0.29
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTCTTTCTTTTTTTTC
Found at i:2651333 original size:22 final size:21
Alignment explanation
Indices: 2651308--2651351 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2651298 CAAAAAATGT
2651308 TTTCTTTCCTTTTTTTTCTTTC
1 TTTCTTT-CTTTTTTTTCTTTC
* *
2651330 TTTCTTTTTTTTTTTTTTTTC
1 TTTCTTTCTTTTTTTTCTTTC
2651351 T
1 T
2651352 CATTTATTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (21 bp):
TTTCTTTCTTTTTTTTCTTTC
Found at i:2651825 original size:23 final size:24
Alignment explanation
Indices: 2651799--2651846 Score: 89
Period size: 23 Copynumber: 2.0 Consensus size: 24
2651789 AATAAAAGTA
2651799 TGTATTTAGTTAATTATAT-TTTT
1 TGTATTTAGTTAATTATATGTTTT
2651822 TGTATTTAGTTAATTATATGTTTT
1 TGTATTTAGTTAATTATATGTTTT
2651846 T
1 T
2651847 TAATATTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 19 0.79
24 5 0.21
ACGTcount: A:0.25, C:0.00, G:0.10, T:0.65
Consensus pattern (24 bp):
TGTATTTAGTTAATTATATGTTTT
Found at i:2653627 original size:2 final size:2
Alignment explanation
Indices: 2653620--2653649 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2653610 GATGGAGGGA
2653620 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2653650 TAACAGGTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2653772 original size:21 final size:22
Alignment explanation
Indices: 2653729--2653772 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
2653719 AATAAATAAA
* * *
2653729 ATTACTTTCATATTTTTATTTT
1 ATTACTTTAATATTTTAAATTT
2653751 ATTA-TTTAATATTTTAAATTT
1 ATTACTTTAATATTTTAAATTT
2653772 A
1 A
2653773 ATTTTTTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.64
Consensus pattern (22 bp):
ATTACTTTAATATTTTAAATTT
Found at i:2653996 original size:25 final size:26
Alignment explanation
Indices: 2653942--2654002 Score: 63
Period size: 25 Copynumber: 2.3 Consensus size: 26
2653932 TATTACGAAT
* *
2653942 TAAAAAATATAATTTATTGATAAATT
1 TAAAAAATATAATTAATTGATAAATA
*
2653968 TAAAAAAT-TAATTAATT-TTATAATA
1 TAAAAAATATAATTAATTGATA-AATA
2653993 TAAAATAATA
1 TAAAA-AATA
2654003 AAATAGAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
24 2 0.07
25 16 0.55
26 11 0.38
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (26 bp):
TAAAAAATATAATTAATTGATAAATA
Found at i:2654202 original size:28 final size:28
Alignment explanation
Indices: 2654170--2654238 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 28
2654160 TAATATAATA
* *
2654170 TAAAATATAAATATAATAATTAATTTTT
1 TAAAATATAAATATAATAAATAATATTT
2654198 TAAAAT-T--ATATAA-AAATAATATTT
1 TAAAATATAAATATAATAAATAATATTT
2654222 T-AAATA-AAATTATAATA
1 TAAAATATAAA-TATAATA
2654239 TAAAATAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
23 4 0.12
24 10 0.29
25 7 0.21
26 5 0.15
27 2 0.06
28 6 0.18
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (28 bp):
TAAAATATAAATATAATAAATAATATTT
Found at i:2654256 original size:30 final size:28
Alignment explanation
Indices: 2654198--2654257 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 28
2654188 ATTAATTTTT
**
2654198 TAAAATTATATAAAAATAATATTTTAAA
1 TAAAATTATATAAAAATAATATCATAAA
2654226 TAAAATTATAATATAAAATAAT-TACATAAA
1 TAAAATTAT-ATA-AAAATAATAT-CATAAA
2654256 TA
1 TA
2654258 TAATAATGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 9 0.33
29 4 0.15
30 14 0.52
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (28 bp):
TAAAATTATATAAAAATAATATCATAAA
Found at i:2654523 original size:23 final size:21
Alignment explanation
Indices: 2654504--2654563 Score: 70
Period size: 20 Copynumber: 2.8 Consensus size: 21
2654494 ATAATTTTAA
2654504 TAAATATTTATTTTTTATTTT
1 TAAATATTTATTTTTTATTTT
*
2654525 TTAA-A-TTATTATTTTATTTT
1 TAAATATTTATT-TTTTATTTT
2654545 TAAATATTTTATATTTTTA
1 TAAATA-TTTAT-TTTTTA
2654564 ATACATATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
19 5 0.16
20 13 0.41
21 4 0.12
23 9 0.28
24 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TAAATATTTATTTTTTATTTT
Found at i:2654544 original size:19 final size:18
Alignment explanation
Indices: 2654511--2654564 Score: 74
Period size: 19 Copynumber: 2.9 Consensus size: 18
2654501 TAATAAATAT
2654511 TTATTTTTTATTTTTTAAA
1 TTATTTTTTA-TTTTTAAA
2654530 TTATTATTTTATTTTTAAA
1 TTATT-TTTTATTTTTAAA
*
2654549 -TATTTTATATTTTTAA
1 TTATTTTTTATTTTTAA
2654565 TACATATGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
17 11 0.33
18 4 0.12
19 13 0.39
20 5 0.15
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTATTTTTTATTTTTAAA
Found at i:2654552 original size:15 final size:16
Alignment explanation
Indices: 2654534--2654566 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2654524 TTTAAATTAT
2654534 TATTTTAT-TTTTAAA
1 TATTTTATATTTTAAA
*
2654549 TATTTTATATTTTTAA
1 TATTTTATATTTTAAA
2654565 TA
1 TA
2654567 CATATGTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TATTTTATATTTTAAA
Found at i:2657087 original size:2 final size:2
Alignment explanation
Indices: 2657080--2657118 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
2657070 AACTCTAGAC
2657080 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CTA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
2657119 ACTCACTGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2659953 original size:13 final size:13
Alignment explanation
Indices: 2659935--2659960 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2659925 TACACAAGTA
2659935 TTTATTTATTTAT
1 TTTATTTATTTAT
2659948 TTTATTTATTTAT
1 TTTATTTATTTAT
2659961 CCAAGTAAAA
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTATTTATTTAT
Found at i:2660409 original size:4 final size:4
Alignment explanation
Indices: 2660392--2660427 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
2660382 ACATTTGGGC
* *
2660392 TCTT TATT TATT TCTT TCTT TCTT TCTT TCTT TCTT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT
2660428 ATTATTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (4 bp):
TCTT
Found at i:2660434 original size:3 final size:3
Alignment explanation
Indices: 2660426--2660460 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2660416 TCTTTCTTTC
2660426 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2660461 GGGTTTTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2661234 original size:15 final size:15
Alignment explanation
Indices: 2661214--2661250 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
2661204 AAAGGAGAAG
*
2661214 AATGTTAATTAAGCT
1 AATGTTAATTAAGAT
2661229 AATGTTAATTAAGAT
1 AATGTTAATTAAGAT
2661244 AAT-TTAA
1 AATGTTAA
2661251 ATAATTAGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.46, C:0.03, G:0.11, T:0.41
Consensus pattern (15 bp):
AATGTTAATTAAGAT
Found at i:2662076 original size:2 final size:2
Alignment explanation
Indices: 2662071--2662111 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
2662061 AACACACACT
* *
2662071 TA TA TA TG TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2662112 TGTTTACTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2662473 original size:12 final size:11
Alignment explanation
Indices: 2662420--2662475 Score: 55
Period size: 10 Copynumber: 5.3 Consensus size: 11
2662410 TAATTGGTGC
2662420 ATATATT-TAT
1 ATATATTATAT
* *
2662430 ATATTTTATGTT
1 ATATATTAT-AT
*
2662442 ATATATTATGT
1 ATATATTATAT
2662453 -TATATTATAT
1 ATATATTATAT
2662463 ATATA-TATAT
1 ATATATTATAT
2662473 ATA
1 ATA
2662476 GTTACAGTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
10 23 0.61
11 6 0.16
12 9 0.24
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (11 bp):
ATATATTATAT
Found at i:2663638 original size:33 final size:33
Alignment explanation
Indices: 2663595--2663659 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
2663585 TGTGTTTACG
* *
2663595 AGTTAAATAATTTATTTAATTTAATTTTTATTA
1 AGTTAAATAATTTATTTAATTAAATTTATATTA
* *
2663628 AGTTATATAATTTATTTAGTTAAATTTATATT
1 AGTTAAATAATTTATTTAATTAAATTTATATT
2663660 GAATCAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (33 bp):
AGTTAAATAATTTATTTAATTAAATTTATATTA
Found at i:2664450 original size:22 final size:22
Alignment explanation
Indices: 2664403--2664452 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
2664393 TATATTGAAG
* *
2664403 ACTATGAGTTAAGGTGAATGCT
1 ACTATGAGTTAACGTAAATGCT
*
2664425 ACTATGAGTTACCGTAAATAGC-
1 ACTATGAGTTAACGTAAAT-GCT
2664447 ACTATG
1 ACTATG
2664453 TCCTTTCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 22 0.92
23 2 0.08
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (22 bp):
ACTATGAGTTAACGTAAATGCT
Found at i:2667017 original size:20 final size:21
Alignment explanation
Indices: 2666974--2667022 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
2666964 TAATAGTGAA
* * *
2666974 TAATAGTAAAATTAAATATCG
1 TAATAATAAAATAAAATATAG
2666995 TAATAATAAAATAAAAT-TAG
1 TAATAATAAAATAAAATATAG
2667015 TAATAATA
1 TAATAATA
2667023 TATGTATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (21 bp):
TAATAATAAAATAAAATATAG
Found at i:2667971 original size:17 final size:16
Alignment explanation
Indices: 2667945--2668012 Score: 57
Period size: 17 Copynumber: 4.1 Consensus size: 16
2667935 TTTATATATT
*
2667945 ATATTAAATATTAATAA
1 ATATTTAATATTAA-AA
*
2667962 ATATTTAATA-TAAAT
1 ATATTTAATATTAAAA
* *
2667977 ATATTTATTTTTAAAA
1 ATATTTAATATTAAAA
2667993 TATATTTAATTATTTAAAA
1 -ATATTTAA-TA-TTAAAA
2668012 A
1 A
2668013 AATTATATTT
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
15 9 0.22
16 7 0.17
17 16 0.40
18 2 0.05
19 6 0.15
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATATTTAATATTAAAA
Found at i:2667997 original size:19 final size:19
Alignment explanation
Indices: 2667973--2668011 Score: 64
Period size: 17 Copynumber: 2.2 Consensus size: 19
2667963 TATTTAATAT
2667973 AAATATATTT-ATT-TTTA
1 AAATATATTTAATTATTTA
2667990 AAATATATTTAATTATTTA
1 AAATATATTTAATTATTTA
2668009 AAA
1 AAA
2668012 AAATTATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 10 0.50
18 3 0.15
19 7 0.35
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AAATATATTTAATTATTTA
Found at i:2668013 original size:21 final size:20
Alignment explanation
Indices: 2667963--2668026 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 20
2667953 TATTAATAAA
2667963 TATTTAATATAAATATATTTAT
1 TATTTAA-A-AAATATATTTAT
2667985 T-TTT--AAAATATATTTAAT
1 TATTTAAAAAATATATTT-AT
2668003 TATTTAAAAAAATTATATTT-T
1 TATTT-AAAAAA-TATATTTAT
2668024 TAT
1 TAT
2668027 ATTTATATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 13
0.73 0.00 0.27
Matches are distributed among these distances:
17 10 0.28
18 4 0.11
19 3 0.08
21 7 0.19
22 5 0.14
23 7 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TATTTAAAAAATATATTTAT
Found at i:2670048 original size:10 final size:10
Alignment explanation
Indices: 2670033--2670071 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
2670023 TATGTAAATT
2670033 ATATATATAA
1 ATATATATAA
2670043 ATATATATAA
1 ATATATATAA
2670053 AT-TAT-TAA
1 ATATATATAA
2670061 ATATATA-AA
1 ATATATATAA
2670070 AT
1 AT
2670072 CTTAAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 5 0.19
9 10 0.37
10 12 0.44
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
ATATATATAA
Found at i:2670064 original size:16 final size:16
Alignment explanation
Indices: 2670035--2670080 Score: 56
Period size: 18 Copynumber: 2.7 Consensus size: 16
2670025 TGTAAATTAT
2670035 ATATATAAATATATATAA
1 ATAT-TAAATATATA-AA
2670053 ATTATTAAATATATAAA
1 A-TATTAAATATATAAA
*
2670070 ATCTTAAATAT
1 ATATTAAATAT
2670081 TAATATGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 9 0.35
17 3 0.12
18 11 0.42
19 3 0.12
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATTAAATATATAAA
Found at i:2670539 original size:20 final size:20
Alignment explanation
Indices: 2670518--2670625 Score: 73
Period size: 20 Copynumber: 5.3 Consensus size: 20
2670508 AATTTTTATT
* *
2670518 TTTTATTATAGTTATATATT
1 TTTTATTATATTTATATATA
*
2670538 TTAATGTATTATAATTATATTTAATA
1 TT--T-TATTAT-ATT-TATAT-ATA
*
2670564 TTTTA-TATATTTATATAAA
1 TTTTATTATATTTATATATA
*
2670583 TTTTAATATATTTATATAATA
1 TTTTATTATATTTATAT-ATA
2670604 TTTTATT-TA--TATA-ATA
1 TTTTATTATATTTATATATA
2670620 TTTTAT
1 TTTTAT
2670626 ATTATTTTTG
Statistics
Matches: 73, Mismatches: 7, Indels: 20
0.73 0.07 0.20
Matches are distributed among these distances:
16 9 0.12
18 4 0.05
19 7 0.10
20 19 0.26
21 11 0.15
22 4 0.05
23 8 0.11
24 3 0.04
25 4 0.05
26 4 0.05
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TTTTATTATATTTATATATA
Found at i:2670562 original size:10 final size:9
Alignment explanation
Indices: 2670531--2670624 Score: 59
Period size: 10 Copynumber: 10.0 Consensus size: 9
2670521 TATTATAGTT
2670531 ATATATTTTA
1 ATATA-TTTA
*
2670541 ATGTATTATA
1 ATATATT-TA
2670551 ATTATATTTA
1 A-TATATTTA
2670561 ATAT-TTT-
1 ATATATTTA
2670568 ATATATTTA
1 ATATATTTA
*
2670577 TATAAATTTTA
1 -ATATA-TTTA
2670588 ATATATTTA
1 ATATATTTA
*
2670597 TATAATATTTT
1 -AT-ATATTTA
* *
2670608 ATTTATATA
1 ATATATTTA
2670617 ATAT-TTTA
1 ATATATTTA
2670625 TATTATTTTT
Statistics
Matches: 66, Mismatches: 10, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
7 4 0.06
8 9 0.14
9 16 0.24
10 22 0.33
11 15 0.23
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (9 bp):
ATATATTTA
Found at i:2670574 original size:16 final size:16
Alignment explanation
Indices: 2670553--2670632 Score: 61
Period size: 16 Copynumber: 4.4 Consensus size: 16
2670543 GTATTATAAT
2670553 TATATTTAATATTTTA
1 TATATTTAATATTTTA
2670569 TATATTTATATAAATTTTAA
1 TATATTTA-AT--ATTTT-A
2670589 TATATTTATATAATATTTTA
1 TATA--T-T-TAATATTTTA
* *
2670609 TTTATATAATATTTTA
1 TATATTTAATATTTTA
2670625 TATTATTT
1 TA-TATTT
2670633 TTGATACGAC
Statistics
Matches: 51, Mismatches: 4, Indels: 17
0.71 0.06 0.24
Matches are distributed among these distances:
16 19 0.37
17 6 0.12
18 1 0.02
19 5 0.10
20 9 0.18
21 5 0.10
22 1 0.02
23 3 0.06
24 2 0.04
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TATATTTAATATTTTA
Found at i:2670631 original size:10 final size:10
Alignment explanation
Indices: 2670513--2670633 Score: 50
Period size: 10 Copynumber: 12.7 Consensus size: 10
2670503 TAGGTAATTT
*
2670513 TTATTTTTTA
1 TTATTTTATA
*
2670523 TTATAGTTATA
1 TTAT-TTTATA
2670534 -TATTTTA-A
1 TTATTTTATA
*
2670542 TGTATTATA-A
1 T-TATTTTATA
2670552 TTATATTTA-A
1 TTAT-TTTATA
2670562 -TATTTTATA
1 TTATTTTATA
2670571 -TA-TTTATA
1 TTATTTTATA
*
2670579 TAAATTTTA-A
1 T-TATTTTATA
2670589 TATATTTATATA
1 T-TATTT-TATA
*
2670601 ATATTTTAT-
1 TTATTTTATA
2670610 TTA---TATA
1 TTATTTTATA
*
2670617 ATATTTTATA
1 TTATTTTATA
2670627 TTATTTT
1 TTATTTT
2670634 TGATACGACG
Statistics
Matches: 86, Mismatches: 11, Indels: 28
0.69 0.09 0.22
Matches are distributed among these distances:
6 3 0.03
7 2 0.02
8 11 0.13
9 14 0.16
10 40 0.47
11 15 0.17
12 1 0.01
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (10 bp):
TTATTTTATA
Found at i:2670633 original size:47 final size:45
Alignment explanation
Indices: 2670507--2670633 Score: 116
Period size: 47 Copynumber: 2.7 Consensus size: 45
2670497 GGACGTTAGG
* * * *
2670507 TAATTTTTATTTTTTATTATAGTTATA-TATTTTAATGTATTATAA
1 TAATATTTATATTTTA-TATATTTATATTATTTTAATATATTATAA
* *
2670552 TTATATTTAATATTTTATATATTTATATAAATTTTAATATATT-TATA
1 TAATATTT-ATATTTTATATATTTATAT-TATTTTAATATATTATA-A
2670599 TAATATTT-TATTTATATAATATTTTATATTATTTT
1 TAATATTTATATTT-TAT-ATA-TTTATATTATTTT
2670634 TGATACGACG
Statistics
Matches: 67, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
45 20 0.30
46 12 0.18
47 28 0.42
48 7 0.10
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (45 bp):
TAATATTTATATTTTATATATTTATATTATTTTAATATATTATAA
Found at i:2671005 original size:13 final size:14
Alignment explanation
Indices: 2670979--2671015 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
2670969 AAATAGATAG
2670979 ATAATTTAAATTAA
1 ATAATTTAAATTAA
2670993 ATAATTT-AATTAA
1 ATAATTTAAATTAA
*
2671006 A-AAATTAAAT
1 ATAATTTAAAT
2671016 ATCATATAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
12 4 0.19
13 10 0.48
14 7 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAATTTAAATTAA
Found at i:2671687 original size:20 final size:20
Alignment explanation
Indices: 2671662--2671713 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
2671652 TAGAAATTTT
*
2671662 TTTAATTTGAATTATTTTAA
1 TTTAATTTAAATTATTTTAA
*
2671682 TTTAATTTAAATTATTTTTTA
1 TTTAATTTAAATTA-TTTTAA
2671703 TTTGAATTTAA
1 TTT-AATTTAA
2671714 TTAAAATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 13 0.46
21 8 0.29
22 7 0.25
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (20 bp):
TTTAATTTAAATTATTTTAA
Found at i:2678245 original size:133 final size:133
Alignment explanation
Indices: 2677846--2678245 Score: 570
Period size: 133 Copynumber: 3.0 Consensus size: 133
2677836 TTATATGTAA
* * * * **
2677846 GGCTCTTTGTACATGTAAAATACGCATAAAAACAATAACATACATAGTATTTAAAAATTTTAGAA
1 GGCTCTCTGTATATGTAAAACACGCATAAAAATAATAACATATGTAGTATTTAAAAATTTTAGAA
* * * *
2677911 AGTGTGAAGAAATGTATGTTTAAGTAGGATAGAATTAAATCATTTGTAATCGTTACATCAAGTTT
66 AGTGCGAAGAAATGTATGTTTAGGTAGGATAGAATTAAATCATTTGTAATCGTTACATCAAGCTC
2677976 ATG
131 ATG
* * *
2677979 AGCTCTCTGTATACGTAAAACACGCATAAAAATAATAACATATGTAGTATTTAAAAATTTTGGAA
1 GGCTCTCTGTATATGTAAAACACGCATAAAAATAATAACATATGTAGTATTTAAAAATTTTAGAA
*
2678044 AGTGCGAAGAAATGTATGTTTAGGTAGGATAGAATTAAATCATTTGTAATCGTTACATTAAGCTC
66 AGTGCGAAGAAATGTATGTTTAGGTAGGATAGAATTAAATCATTTGTAATCGTTACATCAAGCTC
2678109 ATG
131 ATG
* *
2678112 GGCTCTCTGTATATGTAAAACACGTATAAAAATAATAACATATGTAGTGTTTAAAAATTTT-GAA
1 GGCTCTCTGTATATGTAAAACACGCATAAAAATAATAACATATGTAGTATTTAAAAATTTTAGAA
* * * * * *
2678176 GAGTGCG-AGAAAATATATGTTTAGGTAGAATAGAATCAAATAATTTGTTATCCTTACATCAAGC
66 -AGTGCGAAG-AAATGTATGTTTAGGTAGGATAGAATTAAATCATTTGTAATCGTTACATCAAGC
2678240 TCATG
129 TCATG
2678245 G
1 G
2678246 TTTTGTCTTT
Statistics
Matches: 240, Mismatches: 25, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
132 5 0.02
133 235 0.98
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (133 bp):
GGCTCTCTGTATATGTAAAACACGCATAAAAATAATAACATATGTAGTATTTAAAAATTTTAGAA
AGTGCGAAGAAATGTATGTTTAGGTAGGATAGAATTAAATCATTTGTAATCGTTACATCAAGCTC
ATG
Found at i:2679531 original size:30 final size:29
Alignment explanation
Indices: 2679458--2679562 Score: 111
Period size: 30 Copynumber: 3.5 Consensus size: 29
2679448 CAATTTTAAG
* * *
2679458 AAACAATCCGTCAATAAAAGTGAGCTGCAA
1 AAACAATCCGTCAGT-AAAGTGAGGTTCAA
*
2679488 ATACAATCCGTCAGTAAACGTGAGGTTCAA
1 AAACAATCCGTCAGTAAA-GTGAGGTTCAA
** *
2679518 AAACAATCCGTCAGTGTAGCTGCGGTTCAA
1 AAACAATCCGTCAGTAAAG-TGAGGTTCAA
*
2679548 AAACATTCCGTCAGT
1 AAACAATCCGTCAGT
2679563 GTACCTGGGG
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
29 4 0.06
30 60 0.94
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (29 bp):
AAACAATCCGTCAGTAAAGTGAGGTTCAA
Found at i:2679563 original size:30 final size:30
Alignment explanation
Indices: 2679485--2679577 Score: 114
Period size: 30 Copynumber: 3.1 Consensus size: 30
2679475 AAGTGAGCTG
* ** * *
2679485 CAAATACAATCCGTCAGTAAACGTGAGGTT
1 CAAAAACAATCCGTCAGTGTACCTGCGGTT
*
2679515 CAAAAACAATCCGTCAGTGTAGCTGCGGTT
1 CAAAAACAATCCGTCAGTGTACCTGCGGTT
* *
2679545 CAAAAACATTCCGTCAGTGTACCTGGGGTT
1 CAAAAACAATCCGTCAGTGTACCTGCGGTT
2679575 CAA
1 CAA
2679578 GCAAATTCCT
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 54 1.00
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.24
Consensus pattern (30 bp):
CAAAAACAATCCGTCAGTGTACCTGCGGTT
Found at i:2683348 original size:33 final size:33
Alignment explanation
Indices: 2683257--2683341 Score: 109
Period size: 33 Copynumber: 2.6 Consensus size: 33
2683247 CCAAAGCACG
* *
2683257 CGAGGTTCAAGAAAAATCCTCCAAGGTCGGCGA
1 CGAGGTTCAACAAAAATCCTCCAAGGTAGGCGA
* *
2683290 CGAGGTTCAACAAAAAACCTCCAAGGTAGGGGA
1 CGAGGTTCAACAAAAATCCTCCAAGGTAGGCGA
*
2683323 CTAGGTTCAA-AAACAATCC
1 CGAGGTTCAACAAA-AATCC
2683342 GTCAAGGCAC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
32 3 0.07
33 42 0.93
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.15
Consensus pattern (33 bp):
CGAGGTTCAACAAAAATCCTCCAAGGTAGGCGA
Found at i:2683362 original size:30 final size:30
Alignment explanation
Indices: 2683328--2683401 Score: 130
Period size: 30 Copynumber: 2.5 Consensus size: 30
2683318 GGGGACTAGG
* *
2683328 TTCAAAAACAATCCGTCAAGGCACATGACC
1 TTCAAAAACAATCCATCAAGACACATGACC
2683358 TTCAAAAACAATCCATCAAGACACATGACC
1 TTCAAAAACAATCCATCAAGACACATGACC
2683388 TTCAAAAACAATCC
1 TTCAAAAACAATCC
2683402 TTCTTTTAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.45, C:0.30, G:0.08, T:0.18
Consensus pattern (30 bp):
TTCAAAAACAATCCATCAAGACACATGACC
Found at i:2684584 original size:17 final size:17
Alignment explanation
Indices: 2684544--2684592 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
2684534 TAAGATGAAG
* *
2684544 AAAAA-TAATAAAATAA
1 AAAAATTAATTAATTAA
2684560 AAATAATTAATTAATTAA
1 AAA-AATTAATTAATTAA
2684578 AAAAATTAATTAATT
1 AAAAATTAATTAATT
2684593 TTGCATGTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 3 0.10
17 14 0.48
18 12 0.41
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAAATTAATTAATTAA
Found at i:2685764 original size:6 final size:5
Alignment explanation
Indices: 2685741--2685774 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
2685731 AAATGTTAAA
* *
2685741 AAAAG AAAAG AAAAG AAAAG GAAAG AAAGG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
2685775 CTTAAGAGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:2687415 original size:30 final size:31
Alignment explanation
Indices: 2687381--2687693 Score: 344
Period size: 30 Copynumber: 10.5 Consensus size: 31
2687371 GTTCCCGATG
*
2687381 AATTCAACAAG-CTTCGACGGGCTCCAGACA
1 AATTCAACAAGCCTTCAACGGGCTCCAGACA
*
2687411 AATTCAA-AAGCCTTCAAGGGGCTCCAGACA
1 AATTCAACAAGCCTTCAACGGGCTCCAGACA
* *
2687441 AATTCAAC-AGCCTCCAAGGGGCTCCAGACA
1 AATTCAACAAGCCTTCAACGGGCTCCAGACA
* *
2687471 AATTCAAC-ACCCTTTAA-GGTGCTCCAGACA
1 AATTCAACAAGCCTTCAACGG-GCTCCAGACA
* * *
2687501 AATTCAAC-ACCCTTCAAGGGGCTCCAAACA
1 AATTCAACAAGCCTTCAACGGGCTCCAGACA
* *
2687531 AGTTCAAC-ACCCTTCAACGGGCTCCAGACA
1 AATTCAACAAGCCTTCAACGGGCTCCAGACA
* * *
2687561 AATTCAAC-AGCCTCCAACGTGCTCCAGAGA
1 AATTCAACAAGCCTTCAACGGGCTCCAGACA
* *
2687591 ATTTCAA-AAGCCTTCAAGGGGCTCCAGACA
1 AATTCAACAAGCCTTCAACGGGCTCCAGACA
* * *
2687621 AATTCAAC-AGCCTCCAACGTGCTCCAGAGA
1 AATTCAACAAGCCTTCAACGGGCTCCAGACA
* *
2687651 ATTTCAA-AAGCCTTCAAGGGGCTCCAGACA
1 AATTCAACAAGCCTTCAACGGGCTCCAGACA
2687681 AATTCAAC-AGCCT
1 AATTCAACAAGCCT
2687694 CGACCAGTAT
Statistics
Matches: 243, Mismatches: 32, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
29 5 0.02
30 236 0.97
31 2 0.01
ACGTcount: A:0.34, C:0.31, G:0.17, T:0.18
Consensus pattern (31 bp):
AATTCAACAAGCCTTCAACGGGCTCCAGACA
Found at i:2687474 original size:60 final size:60
Alignment explanation
Indices: 2687397--2687694 Score: 425
Period size: 60 Copynumber: 5.0 Consensus size: 60
2687387 ACAAGCTTCG
2687397 ACGGGCTCCAGACAAATTCAAAAGCCTTCAAGGGGCTCCAGACAAATTCAACAGCCTCCA
1 ACGGGCTCCAGACAAATTCAAAAGCCTTCAAGGGGCTCCAGACAAATTCAACAGCCTCCA
* * * * * * *
2687457 AGGGGCTCCAGACAAATTCAACACCCTTTAAGGTGCTCCAGACAAATTCAACACCCTTCA
1 ACGGGCTCCAGACAAATTCAAAAGCCTTCAAGGGGCTCCAGACAAATTCAACAGCCTCCA
* * * * * *
2687517 AGGGGCTCCAAACAAGTTCAACACCCTTCAACGGGCTCCAGACAAATTCAACAGCCTCCA
1 ACGGGCTCCAGACAAATTCAAAAGCCTTCAAGGGGCTCCAGACAAATTCAACAGCCTCCA
* * *
2687577 ACGTGCTCCAGAGAATTTCAAAAGCCTTCAAGGGGCTCCAGACAAATTCAACAGCCTCCA
1 ACGGGCTCCAGACAAATTCAAAAGCCTTCAAGGGGCTCCAGACAAATTCAACAGCCTCCA
* * *
2687637 ACGTGCTCCAGAGAATTTCAAAAGCCTTCAAGGGGCTCCAGACAAATTCAACAGCCTC
1 ACGGGCTCCAGACAAATTCAAAAGCCTTCAAGGGGCTCCAGACAAATTCAACAGCCTC
2687695 GACCAGTATG
Statistics
Matches: 216, Mismatches: 22, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 216 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (60 bp):
ACGGGCTCCAGACAAATTCAAAAGCCTTCAAGGGGCTCCAGACAAATTCAACAGCCTCCA
Found at i:2687507 original size:90 final size:90
Alignment explanation
Indices: 2687401--2687693 Score: 415
Period size: 90 Copynumber: 3.3 Consensus size: 90
2687391 GCTTCGACGG
*
2687401 GCTCCAGACAAATTCAAAAGCCTTCAAGGGGCTCCAGACAAATTCAACAGCCTCCAAGGGGCTCC
1 GCTCCAGACAAATTCAAAAGCCTTCAAGGGGCTCCAGACAAATTCAACAGCCTCCAACGGGCTCC
* *
2687466 AGACAAATTCAACACCCTTTAAGGT
66 AGACAAATTCAACAGCCTTCAAGGT
* * * * * *
2687491 GCTCCAGACAAATTCAACACCCTTCAAGGGGCTCCAAACAAGTTCAACACCCTTCAACGGGCTCC
1 GCTCCAGACAAATTCAAAAGCCTTCAAGGGGCTCCAGACAAATTCAACAGCCTCCAACGGGCTCC
* *
2687556 AGACAAATTCAACAGCCTCCAACGT
66 AGACAAATTCAACAGCCTTCAAGGT
* * *
2687581 GCTCCAGAGAATTTCAAAAGCCTTCAAGGGGCTCCAGACAAATTCAACAGCCTCCAACGTGCTCC
1 GCTCCAGACAAATTCAAAAGCCTTCAAGGGGCTCCAGACAAATTCAACAGCCTCCAACGGGCTCC
* * * *
2687646 AGAGAATTTCAAAAGCCTTCAAGGG
66 AGACAAATTCAACAGCCTTCAAGGT
*
2687671 GCTCCAGACAAATTCAACAGCCT
1 GCTCCAGACAAATTCAAAAGCCT
2687694 CGACCAGTAT
Statistics
Matches: 174, Mismatches: 29, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
90 174 1.00
ACGTcount: A:0.34, C:0.31, G:0.17, T:0.18
Consensus pattern (90 bp):
GCTCCAGACAAATTCAAAAGCCTTCAAGGGGCTCCAGACAAATTCAACAGCCTCCAACGGGCTCC
AGACAAATTCAACAGCCTTCAAGGT
Found at i:2696016 original size:18 final size:18
Alignment explanation
Indices: 2695961--2696017 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
2695951 ATTTAATTTT
*
2695961 TAAAACATTAATTTAATA
1 TAAAATATTAATTTAATA
*
2695979 -AAAATAATAATTATAATA
1 TAAAATATTAATT-TAATA
* *
2695997 TAAATTATTAATTTATTA
1 TAAAATATTAATTTAATA
2696015 TAA
1 TAA
2696018 TTTTTTAACT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
17 10 0.31
18 12 0.38
19 10 0.31
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAAATATTAATTTAATA
Found at i:2696682 original size:39 final size:39
Alignment explanation
Indices: 2696639--2696714 Score: 100
Period size: 38 Copynumber: 1.9 Consensus size: 39
2696629 TTATAACAAT
* *
2696639 TTTTTATCGTTATATATATTATTTAAAATAAAA-ATATTA
1 TTTTTATCGTTA-AAATATAATTTAAAATAAAATATATTA
**
2696678 TTTTTATTTTTAAAATATAATTTAAAATAAAATATAT
1 TTTTTATCGTTAAAATATAATTTAAAATAAAATATAT
2696715 AAAATAAGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 18 0.56
39 14 0.44
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (39 bp):
TTTTTATCGTTAAAATATAATTTAAAATAAAATATATTA
Found at i:2698069 original size:20 final size:19
Alignment explanation
Indices: 2698044--2698155 Score: 77
Period size: 20 Copynumber: 5.7 Consensus size: 19
2698034 TGTAAAATTA
2698044 TTAATTAATCAATTTATCTT
1 TTAATTAAT-AATTTATCTT
2698064 TTAATTAAATAATTTA-CTTT
1 TTAATT-AATAATTTATC-TT
* *
2698084 TTAACTTAAT-AGTTAT-AT
1 TTAA-TTAATAATTTATCTT
**
2698102 AAAATTAATTAATTTATCTT
1 TTAATTAA-TAATTTATCTT
*
2698122 ATAATTAAATAATTTATCTT
1 TTAATT-AATAATTTATCTT
* *
2698142 ATACTTAAATAATT
1 TTAATT-AATAATT
2698156 ATTTATGTAT
Statistics
Matches: 76, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
17 4 0.05
18 4 0.05
19 10 0.13
20 51 0.67
21 7 0.09
ACGTcount: A:0.42, C:0.06, G:0.01, T:0.51
Consensus pattern (19 bp):
TTAATTAATAATTTATCTT
Found at i:2698134 original size:24 final size:22
Alignment explanation
Indices: 2698107--2698161 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 22
2698097 TATATAAAAT
2698107 TAATTAATTTATCTTATAATTA
1 TAATTAATTTATCTTATAATTA
*
2698129 -AA-TAATTTATCTTATACTTAAA
1 TAATTAATTTATCTTATAATT--A
2698151 TAATT-ATTTAT
1 TAATTAATTTAT
2698162 GTATGTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 16 0.57
21 2 0.07
22 1 0.04
23 8 0.29
24 1 0.04
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (22 bp):
TAATTAATTTATCTTATAATTA
Found at i:2703195 original size:16 final size:16
Alignment explanation
Indices: 2703176--2703211 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2703166 CTTTTTTGAG
* *
2703176 TTTATATTATTTTAGA
1 TTTAAATTATTTCAGA
2703192 TTTAAATTATTTCAGA
1 TTTAAATTATTTCAGA
2703208 TTTA
1 TTTA
2703212 GATCAATTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.58
Consensus pattern (16 bp):
TTTAAATTATTTCAGA
Found at i:2704803 original size:16 final size:15
Alignment explanation
Indices: 2704782--2704857 Score: 62
Period size: 16 Copynumber: 4.7 Consensus size: 15
2704772 TCAGTCTCGA
*
2704782 GTTCGGGTTCTTTCGG
1 GTTCGAGTT-TTTCGG
*
2704798 GTTCGGGTTTTCTCGG
1 GTTCGAGTTTT-TCGG
* *
2704814 GTTCGAGTTGTCTCGA
1 GTTCGAGTT-TTTCGG
*
2704830 GTTCGAGTTATTTCAG
1 GTTCGAGTT-TTTCGG
2704846 GTTCGAGATTTT
1 GTTCGAG-TTTT
2704858 GACTTTTTGG
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
15 2 0.04
16 45 0.90
17 3 0.06
ACGTcount: A:0.09, C:0.16, G:0.32, T:0.43
Consensus pattern (15 bp):
GTTCGAGTTTTTCGG
Found at i:2705302 original size:58 final size:58
Alignment explanation
Indices: 2705240--2705657 Score: 189
Period size: 58 Copynumber: 7.3 Consensus size: 58
2705230 CTAAGATGTG
* * * * **
2705240 TGAAATTATATGAAAGTCCCTAGATCATGAAAAATTACTTGCATGACATCAAAATACA
1 TGAAATTATATAAAAGTTCCTAGATCATGAAAAATCACCTAAATGACATCAAAATACA
* ** * * *
2705298 TGAAATTACACCAAAGTTCCTAGATCATGAGAAATCACCTAAATGATATCAAAATTCA
1 TGAAATTATATAAAAGTTCCTAGATCATGAAAAATCACCTAAATGACATCAAAATACA
* * * * *
2705356 TAAAATTTGTATAAAAGTTCCTAGATCATGAAAAATGACCTAAATGAC-CCAACATACA
1 TGAAA-TTATATAAAAGTTCCTAGATCATGAAAAATCACCTAAATGACATCAAAATACA
* ** ** * ** * *
2705414 TGGAATT-TGCATAAAAG-TCCCGGATCAAT-AAAAATGTCCTAAACGACCCCAACATATA
1 TGAAATTAT--ATAAAAGTTCCTAGATC-ATGAAAAATCACCTAAATGACATCAAAATACA
* * * * * * * *
2705472 TGAATTTGTATAAAAG-TCTTTAGATCATG-------ACTTAATTGACCTTAAAAATATA
1 TGAAATTATATAAAAGTTC-CTAGATCATGAAAAATCACCTAAATGA-CATCAAAATACA
* * * * * * * *
2705524 TGGAATTACATAAAAG-TCTTTAGATCATGGAAAATGATCTAAATGACAACAAAATTCA
1 TGAAATTATATAAAAGTTC-CTAGATCATGAAAAATCACCTAAATGACATCAAAATACA
** ** ** * *
2705582 T-AAGATTGCATCTAAGCCCCTAGATCATGAAAAATAACCTAAATGACATCAAAATATA
1 TGAA-ATTATATAAAAGTTCCTAGATCATGAAAAATCACCTAAATGACATCAAAATACA
*
2705640 TGAAATTTGTATAAAAGT
1 TGAAA-TTATATAAAAGT
2705658 CCATAGGACC
Statistics
Matches: 270, Mismatches: 70, Indels: 39
0.71 0.18 0.10
Matches are distributed among these distances:
51 6 0.02
52 33 0.12
56 1 0.00
57 37 0.14
58 139 0.51
59 54 0.20
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (58 bp):
TGAAATTATATAAAAGTTCCTAGATCATGAAAAATCACCTAAATGACATCAAAATACA
Found at i:2705455 original size:57 final size:57
Alignment explanation
Indices: 2705359--2705489 Score: 167
Period size: 57 Copynumber: 2.3 Consensus size: 57
2705349 AAATTCATAA
* *
2705359 AATTTGTATAAAAGTTCCTAGATCATGAAAAATGACCTAAATGA-CCCAACATACATGG
1 AATTTGTATAAAAG-TCCCAGATCATGAAAAATGACCTAAACGACCCCAACATACAT-G
* * * *
2705417 AATTTGCATAAAAGTCCCGGATCAAT-AAAAATGTCCTAAACGACCCCAACATATATG
1 AATTTGTATAAAAGTCCCAGATC-ATGAAAAATGACCTAAACGACCCCAACATACATG
2705474 AATTTGTATAAAAGTC
1 AATTTGTATAAAAGTC
2705490 TTTAGATCAT
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
57 38 0.59
58 26 0.41
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.26
Consensus pattern (57 bp):
AATTTGTATAAAAGTCCCAGATCATGAAAAATGACCTAAACGACCCCAACATACATG
Found at i:2706461 original size:24 final size:24
Alignment explanation
Indices: 2706429--2706507 Score: 122
Period size: 24 Copynumber: 3.3 Consensus size: 24
2706419 CTTAGCCCAA
2706429 ATCATTACCTAAGCATGACTTAGG
1 ATCATTACCTAAGCATGACTTAGG
* * *
2706453 ATCATTACCTAAACATCATTTAGG
1 ATCATTACCTAAGCATGACTTAGG
*
2706477 ATCATTACCTAAGCATGACTTAAG
1 ATCATTACCTAAGCATGACTTAGG
2706501 ATCATTA
1 ATCATTA
2706508 AGCTCTCATA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.32
Consensus pattern (24 bp):
ATCATTACCTAAGCATGACTTAGG
Found at i:2707967 original size:22 final size:22
Alignment explanation
Indices: 2707920--2707967 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
2707910 TTATTTTTTC
* *
2707920 TTTATTTTATTTTATTAGATTG
1 TTTAGTTTATTTTATTAAATTG
*
2707942 TTTAGTTTA-TTTATTATAATTT
1 TTTAGTTTATTTTATTA-AATTG
2707964 TTTA
1 TTTA
2707968 AGGGTTGCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (22 bp):
TTTAGTTTATTTTATTAAATTG
Found at i:2709211 original size:23 final size:23
Alignment explanation
Indices: 2709185--2709228 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
2709175 AATTAATTTT
*
2709185 ATTG-ATAATATATTATTAATAAA
1 ATTGTATAATA-ATTATAAATAAA
2709208 ATTGTATAATAATTATAAATA
1 ATTGTATAATAATTATAAATA
2709229 TTTTTTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (23 bp):
ATTGTATAATAATTATAAATAAA
Found at i:2710070 original size:51 final size:51
Alignment explanation
Indices: 2709964--2710132 Score: 304
Period size: 51 Copynumber: 3.3 Consensus size: 51
2709954 ATGCAGGTTA
* *
2709964 GGTTGAAAAATAAAATATGATATTGT-AAATACATATTTAAATGGAGGTGG
1 GGTTGAAAAATAAAATATGATATTGTAAAAGACATATTTAAATAGAGGTGG
*
2710014 GGTTGAAAAATAAAATTTGATATTGTAAAAGACATATTTAAATAGAGGTGG
1 GGTTGAAAAATAAAATATGATATTGTAAAAGACATATTTAAATAGAGGTGG
2710065 GGTTGAAAAATAAAATATGATATTGTAAAAGACATATTTAAATAGAGGTGG
1 GGTTGAAAAATAAAATATGATATTGTAAAAGACATATTTAAATAGAGGTGG
2710116 GGTTGAAAAATAAAATA
1 GGTTGAAAAATAAAATA
2710133 CATACGGAGA
Statistics
Matches: 114, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
50 25 0.22
51 89 0.78
ACGTcount: A:0.47, C:0.02, G:0.21, T:0.30
Consensus pattern (51 bp):
GGTTGAAAAATAAAATATGATATTGTAAAAGACATATTTAAATAGAGGTGG
Found at i:2710514 original size:30 final size:31
Alignment explanation
Indices: 2710472--2710530 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
2710462 AAAATTATAT
* *
2710472 AAAAATAATAATAAATAAAATTAAATGTGCC
1 AAAAATAATAATAAACAAAACTAAATGTGCC
2710503 AAAAA-AATAATAAACAAAACTAAATGTG
1 AAAAATAATAATAAACAAAACTAAATGTG
2710531 TTAAAACTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.64, C:0.07, G:0.07, T:0.22
Consensus pattern (31 bp):
AAAAATAATAATAAACAAAACTAAATGTGCC
Found at i:2712300 original size:33 final size:33
Alignment explanation
Indices: 2712176--2712293 Score: 193
Period size: 33 Copynumber: 3.6 Consensus size: 33
2712166 CCAAAGCACG
*
2712176 CGAGGTTCAAGAAAAATCCTCCAAGGTAGGCGA
1 CGAGGTTCAACAAAAATCCTCCAAGGTAGGCGA
2712209 CGAGGTTCAACAAAAATCCTCCAAGGTAGGCGA
1 CGAGGTTCAACAAAAATCCTCCAAGGTAGGCGA
*
2712242 CGAGGTTCAACAAAAATCCTCCAAGGTAGGGGA
1 CGAGGTTCAACAAAAATCCTCCAAGGTAGGCGA
*
2712275 CTAGGTTCAA-AAACAATCC
1 CGAGGTTCAACAAA-AATCC
2712294 GTCAAGGCAC
Statistics
Matches: 81, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
32 3 0.04
33 78 0.96
ACGTcount: A:0.37, C:0.23, G:0.24, T:0.16
Consensus pattern (33 bp):
CGAGGTTCAACAAAAATCCTCCAAGGTAGGCGA
Found at i:2712314 original size:30 final size:30
Alignment explanation
Indices: 2712280--2712353 Score: 130
Period size: 30 Copynumber: 2.5 Consensus size: 30
2712270 GGGGACTAGG
* *
2712280 TTCAAAAACAATCCGTCAAGGCACATGACC
1 TTCAAAAACAATCCATCAAGACACATGACC
2712310 TTCAAAAACAATCCATCAAGACACATGACC
1 TTCAAAAACAATCCATCAAGACACATGACC
2712340 TTCAAAAACAATCC
1 TTCAAAAACAATCC
2712354 TTCTTTTAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.45, C:0.30, G:0.08, T:0.18
Consensus pattern (30 bp):
TTCAAAAACAATCCATCAAGACACATGACC
Found at i:2713496 original size:16 final size:17
Alignment explanation
Indices: 2713468--2713500 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
2713458 TAATAAAATA
2713468 AAAATAATTAATTAATT
1 AAAATAATTAATTAATT
2713485 AAAA-AATTAATTAATT
1 AAAATAATTAATTAATT
2713501 TTGCTCGTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAAATAATTAATTAATT
Found at i:2715918 original size:16 final size:16
Alignment explanation
Indices: 2715899--2715934 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2715889 AAAAAGCAAA
2715899 AAAAAAAAAAAAAAAG
1 AAAAAAAAAAAAAAAG
* *
2715915 AAAAAGAAAAGAAAAG
1 AAAAAAAAAAAAAAAG
2715931 AAAA
1 AAAA
2715935 CTTAAGAGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAAAG
Found at i:2717444 original size:36 final size:36
Alignment explanation
Indices: 2717397--2717561 Score: 287
Period size: 36 Copynumber: 4.6 Consensus size: 36
2717387 GGCAGAGATC
*
2717397 GGCTCCAGACAAAATCAACAGGCGTCT-ACTTCAATG
1 GGCTCCAGACAAAATCAACAGTCGT-TGACTTCAATG
*
2717433 GGCTCCAGACAAAATCAACAGTCGTCGACTTCAATG
1 GGCTCCAGACAAAATCAACAGTCGTTGACTTCAATG
2717469 GGCTCCAGACAAAATCAACAGTCGTTGACTTCAATG
1 GGCTCCAGACAAAATCAACAGTCGTTGACTTCAATG
2717505 GGCTCCAGACAAAATCAACAGTCGTTGACTTCAATG
1 GGCTCCAGACAAAATCAACAGTCGTTGACTTCAATG
*
2717541 GGCTCCAGACAAATTCAACAG
1 GGCTCCAGACAAAATCAACAG
2717562 GCTTCAACCT
Statistics
Matches: 124, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
36 124 1.00
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (36 bp):
GGCTCCAGACAAAATCAACAGTCGTTGACTTCAATG
Found at i:2718548 original size:4 final size:4
Alignment explanation
Indices: 2718535--2718584 Score: 57
Period size: 4 Copynumber: 12.8 Consensus size: 4
2718525 TGGAAAAAAA
* * * *
2718535 AAAG AGAG AAAG AAAG AAAG AAAG AAAG AAAG -GAG AAAT AAGG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
2718582 AAA
1 AAA
2718585 AAAAAGAAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
3 2 0.05
4 35 0.95
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02
Consensus pattern (4 bp):
AAAG
Found at i:2718570 original size:27 final size:27
Alignment explanation
Indices: 2718527--2718605 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
2718517 TTAGATTTTG
*
2718527 GAAAAAAAAAAGAGAGAAAGAAAGAAA
1 GAAAAAAGAAAGAGAGAAAGAAAGAAA
* *
2718554 GAAAGAAAGAAAG-GAGAAATAAGGAAA
1 GAAA-AAAGAAAGAGAGAAAGAAAGAAA
* *
2718581 GAAAAAAAAGAAAAAGAAAAAGAAA
1 G--AAAAAAGAAAGAGAGAAAGAAA
2718606 AAGTGATTTG
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
27 17 0.41
28 14 0.34
29 10 0.24
ACGTcount: A:0.76, C:0.00, G:0.23, T:0.01
Consensus pattern (27 bp):
GAAAAAAGAAAGAGAGAAAGAAAGAAA
Found at i:2718571 original size:23 final size:23
Alignment explanation
Indices: 2718545--2718607 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 23
2718535 AAAGAGAGAA
* *
2718545 AGAAAGAAAGAAAGAAAGAAAGG
1 AGAAAGAAAGAAAGAAAAAAAAG
* *
2718568 AGAAATAAGGAAAGAAAAAAAAG
1 AGAAAGAAAGAAAGAAAAAAAAG
*
2718591 AAAAAG-AA-AAAGAAAAA
1 AGAAAGAAAGAAAGAAAAA
2718608 GTGATTTGAG
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
21 9 0.27
22 1 0.03
23 23 0.70
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (23 bp):
AGAAAGAAAGAAAGAAAAAAAAG
Found at i:2721623 original size:16 final size:17
Alignment explanation
Indices: 2721598--2721704 Score: 102
Period size: 16 Copynumber: 6.6 Consensus size: 17
2721588 CAACTCGAAT
*
2721598 CCGAACTGACCCT-AAC
1 CCGAAATGACCCTGAAC
*
2721614 CCGAAATGACCC-GAAT
1 CCGAAATGACCCTGAAC
*
2721630 CC-AGAAT-AACCTGAAC
1 CCGA-AATGACCCTGAAC
*
2721646 TCGAAATGA-CCTGAAC
1 CCGAAATGACCCTGAAC
* *
2721662 TCGAAATGA-CCTGAAT
1 CCGAAATGACCCTGAAC
2721678 CCGAAATGACCC-GAAC
1 CCGAAATGACCCTGAAC
2721694 CCGAAATGACC
1 CCGAAATGACC
2721705 AGAATAATTA
Statistics
Matches: 77, Mismatches: 8, Indels: 12
0.79 0.08 0.12
Matches are distributed among these distances:
15 4 0.05
16 69 0.90
17 4 0.05
ACGTcount: A:0.37, C:0.32, G:0.17, T:0.14
Consensus pattern (17 bp):
CCGAAATGACCCTGAAC
Found at i:2721699 original size:32 final size:32
Alignment explanation
Indices: 2721614--2721709 Score: 115
Period size: 32 Copynumber: 3.0 Consensus size: 32
2721604 TGACCCTAAC
* *
2721614 CCGAAATGACCCGAATCC-AGAATAACCTGAA-
1 CCGAAATGACCCGAACCCGA-AATGACCTGAAT
* *
2721645 CTCGAAATGACCTGAACTCGAAATGACCTGAAT
1 C-CGAAATGACCCGAACCCGAAATGACCTGAAT
*
2721678 CCGAAATGACCCGAACCCGAAATGACCAGAAT
1 CCGAAATGACCCGAACCCGAAATGACCTGAAT
2721710 AATTAACCCG
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
31 1 0.02
32 52 0.95
33 2 0.04
ACGTcount: A:0.40, C:0.28, G:0.18, T:0.15
Consensus pattern (32 bp):
CCGAAATGACCCGAACCCGAAATGACCTGAAT
Found at i:2722792 original size:32 final size:32
Alignment explanation
Indices: 2722756--2722867 Score: 102
Period size: 32 Copynumber: 3.5 Consensus size: 32
2722746 TAAACCCGAT
**
2722756 TGACCCGAACCTGAAACAACCCGAACCCAAAA
1 TGACCCGAACCTGAAATGACCCGAACCCAAAA
* * * *
2722788 TGACCCGAA-CTCGAAATGACCCAAATCTAAAG
1 TGACCCGAACCT-GAAATGACCCGAACCCAAAA
** *
2722820 TGACCTAAACAC-AAAATGACCCGAACCCAAAA
1 TGACCCGAAC-CTGAAATGACCCGAACCCAAAA
*
2722852 TGATCCGAACCTGAAA
1 TGACCCGAACCTGAAA
2722868 ATAACCCAAA
Statistics
Matches: 59, Mismatches: 17, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
31 3 0.05
32 55 0.93
34 1 0.02
ACGTcount: A:0.44, C:0.31, G:0.13, T:0.12
Consensus pattern (32 bp):
TGACCCGAACCTGAAATGACCCGAACCCAAAA
Found at i:2722793 original size:16 final size:16
Alignment explanation
Indices: 2722774--2722862 Score: 88
Period size: 16 Copynumber: 5.6 Consensus size: 16
2722764 ACCTGAAACA
2722774 ACCCGAACCCAAAATG
1 ACCCGAACCCAAAATG
* *
2722790 ACCCGAACTCGAAATG
1 ACCCGAACCCAAAATG
* * * *
2722806 ACCCAAATCTAAAGTG
1 ACCCGAACCCAAAATG
** *
2722822 ACCTAAACACAAAATG
1 ACCCGAACCCAAAATG
2722838 ACCCGAACCCAAAATG
1 ACCCGAACCCAAAATG
*
2722854 ATCCGAACC
1 ACCCGAACC
2722863 TGAAAATAAC
Statistics
Matches: 56, Mismatches: 17, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 56 1.00
ACGTcount: A:0.44, C:0.33, G:0.12, T:0.11
Consensus pattern (16 bp):
ACCCGAACCCAAAATG
Found at i:2725692 original size:13 final size:13
Alignment explanation
Indices: 2725657--2725695 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
2725647 TCCCTACAAA
*
2725657 TTAAAATCAT-TT
1 TTAAAATTATCTT
2725669 TTAACAATTATCTT
1 TTAA-AATTATCTT
2725683 TTAAAATTATCTT
1 TTAAAATTATCTT
2725696 AAAAAAGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 4 0.17
13 14 0.58
14 6 0.25
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.51
Consensus pattern (13 bp):
TTAAAATTATCTT
Found at i:2726695 original size:2 final size:2
Alignment explanation
Indices: 2726688--2726720 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2726678 AGCAAACTAA
2726688 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
2726721 AACTTTACCA
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:2736096 original size:14 final size:14
Alignment explanation
Indices: 2736064--2736149 Score: 52
Period size: 14 Copynumber: 6.0 Consensus size: 14
2736054 TAAATTCTTT
2736064 TTTAATTAAAATT-A
1 TTTAA-TAAAATTAA
*
2736078 CTTAATAAAATTAA
1 TTTAATAAAATTAA
**
2736092 TTTAA-ATAGTTTAA
1 TTTAATA-AAATTAA
* *
2736106 TTTATTAATAATAAAAA
1 TTTAATAA-AAT--TAA
*
2736123 TTTAATAATA-TAA
1 TTTAATAAAATTAA
2736136 TTTAATAAAATTAA
1 TTTAATAAAATTAA
2736150 ATATTTATAA
Statistics
Matches: 53, Mismatches: 12, Indels: 14
0.67 0.15 0.18
Matches are distributed among these distances:
13 19 0.36
14 22 0.42
15 2 0.04
16 1 0.02
17 9 0.17
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (14 bp):
TTTAATAAAATTAA
Found at i:2736139 original size:13 final size:14
Alignment explanation
Indices: 2736110--2736143 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
2736100 GTTTAATTTA
2736110 TTAATAATAAAAAT
1 TTAATAATAAAAAT
*
2736124 TTAATAAT-ATAAT
1 TTAATAATAAAAAT
2736137 TTAATAA
1 TTAATAA
2736144 AATTAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TTAATAATAAAAAT
Found at i:2736139 original size:30 final size:29
Alignment explanation
Indices: 2736103--2736160 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
2736093 TTAAATAGTT
*
2736103 TAATTTATTAATAA-TAAAAATTTAATAATA
1 TAATTTAATAA-AATTAAAAATTT-ATAATA
*
2736133 TAATTTAATAAAATTAAATATTTATAAT
1 TAATTTAATAAAATTAAAAATTTATAAT
2736161 CTATATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
TAATTTAATAAAATTAAAAATTTATAATA
Found at i:2736173 original size:26 final size:24
Alignment explanation
Indices: 2736114--2736175 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
2736104 AATTTATTAA
* *
2736114 TAATAAAAATTTAATAATATAATT
1 TAATAAAAATTAAATAATATAATC
*
2736138 TAAT-AAAATTAAATATTTATAATC
1 TAATAAAAATTAAATA-ATATAATC
2736162 TATATAAAAATTAA
1 TA-ATAAAAATTAA
2736176 TCTTAATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 10 0.31
24 12 0.38
25 2 0.06
26 8 0.25
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (24 bp):
TAATAAAAATTAAATAATATAATC
Found at i:2736546 original size:20 final size:20
Alignment explanation
Indices: 2736521--2736586 Score: 66
Period size: 20 Copynumber: 3.3 Consensus size: 20
2736511 AATATAAAAA
2736521 TAATTTATTTATTTAAAATT
1 TAATTTATTTATTTAAAATT
* *
2736541 TAATTTATTGAATTAAAA--
1 TAATTTATTTATTTAAAATT
2736559 -AATTTATTTTTATTTAAAATAT
1 TAATTTA--TTTATTTAAAAT-T
2736581 TAATTT
1 TAATTT
2736587 TATATTAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
17 6 0.17
19 9 0.25
20 16 0.44
23 5 0.14
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
TAATTTATTTATTTAAAATT
Found at i:2736577 original size:17 final size:17
Alignment explanation
Indices: 2736528--2736601 Score: 58
Period size: 18 Copynumber: 3.9 Consensus size: 17
2736518 AAATAATTTA
2736528 TTTATTTAAAATTTAATT
1 TTTATTTAAAATTT-ATT
*
2736546 TATTGAATTAAAAAATTTATT
1 T-TT--ATT-TAAAATTTATT
*
2736567 TTTATTTAAAATATTAAT
1 TTTATTTAAAAT-TTATT
*
2736585 TTTATATTAATATTTAT
1 TTTAT-TTAAAATTTAT
2736602 ATATTTTATT
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
17 5 0.11
18 16 0.36
19 8 0.18
20 2 0.04
21 7 0.16
22 7 0.16
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (17 bp):
TTTATTTAAAATTTATT
Found at i:2736594 original size:19 final size:19
Alignment explanation
Indices: 2736557--2736632 Score: 59
Period size: 19 Copynumber: 3.9 Consensus size: 19
2736547 ATTGAATTAA
*
2736557 AAAAT-TTATTTTTAT-TT
1 AAAATATTAATTTTATATT
2736574 AAAATATTAATTTTATATT
1 AAAATATTAATTTTATATT
* *
2736593 AATATTTATATATTTTATTATT
1 AAAATAT-TA-ATTTTA-TATT
*
2736615 AAAA-ATAAATATTTATAT
1 AAAATATTAAT-TTTATAT
2736633 CAATTAAATA
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
17 5 0.11
18 9 0.19
19 12 0.26
20 7 0.15
21 7 0.15
22 7 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
AAAATATTAATTTTATATT
Found at i:2737325 original size:55 final size:56
Alignment explanation
Indices: 2737266--2737394 Score: 138
Period size: 55 Copynumber: 2.3 Consensus size: 56
2737256 ATCAAGTTTT
* * *
2737266 AAAAAATTTACATTAACAAATTAAAA-TATTAATTATTA-TATTTTTTAA-AAAATAA
1 AAAAAATTTA-ATTAAAAAATAAAAAGGATTAATTATTATTA-TTTTTAATAAAATAA
* **
2737321 AAAAAATTTAATTAAAAAATAAAAAGGGTTTTTTATTATTATTTTTAATAAAATAAA
1 AAAAAATTTAATTAAAAAATAAAAAGGATTAATTATTATTATTTTTAATAAAAT-AA
2737378 AAATAATATTTAATTAA
1 AAA-AA-ATTTAATTAA
2737395 GTTTAAAAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
54 13 0.21
55 25 0.40
56 7 0.11
57 5 0.08
58 2 0.03
59 10 0.16
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (56 bp):
AAAAAATTTAATTAAAAAATAAAAAGGATTAATTATTATTATTTTTAATAAAATAA
Found at i:2737328 original size:132 final size:128
Alignment explanation
Indices: 2737192--2737513 Score: 330
Period size: 132 Copynumber: 2.4 Consensus size: 128
2737182 TAAATTAATT
*
2737192 AAATTTAAAAATATTAATAAATAATAATATATTAATTATTA-TTTT-T-AATAAAAAATAATAGT
1 AAATTTAAAAA-A--AATAAA-AAGAAT-TATTAATTATTATTTTTATAAATAAAAAATAATAGT
* *
2737254 TAATCAAGTTTTAAAAAATTTACATTAACAAATTAAAATATTAATTATTATATTTTT-TAAAAAA
61 TAATCAAG-TTTAAAAAA-TTACATTAAAAAATTAAAATATTAATTATTATGTTTTTAT-AAAAA
2737318 TAAAAA
123 TAAAAA
** * * *
2737324 AAATTTAATTAAAAAATAAAAAGGGTTTTTTATTATTATTTTTAATAAAATAAAAAATAATATTT
1 AAATTTAA--AAAAAATAAAAAGAATTATTAATTATTATTTTT-AT-AAATAAAAAATAATAGTT
*
2737389 AATTAAGTTTAAAAAATTACATTAAAAAATTAAAATATTAATTATTATGTTTTTATAAAAATAAA
62 AATCAAGTTTAAAAAATTACATTAAAAAATTAAAATATTAATTATTATGTTTTTATAAAAATAAA
2737454 AA
127 AA
* * * **
2737456 AAATTAAAATAAAAAATAAAAA-AGATTTTTTATTACAATTTTTATTAAAATAAAAAAT
1 AAATT-TAA-AAAAAATAAAAAGA-ATTATTAATTATTATTTTTA-T-AAATAAAAAAT
2737514 TTATATTAAC
Statistics
Matches: 165, Mismatches: 14, Indels: 22
0.82 0.07 0.11
Matches are distributed among these distances:
129 10 0.06
130 7 0.04
131 7 0.04
132 103 0.62
133 13 0.08
134 25 0.15
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (128 bp):
AAATTTAAAAAAAATAAAAAGAATTATTAATTATTATTTTTATAAATAAAAAATAATAGTTAATC
AAGTTTAAAAAATTACATTAAAAAATTAAAATATTAATTATTATGTTTTTATAAAAATAAAAA
Found at i:2737459 original size:54 final size:53
Alignment explanation
Indices: 2737399--2737549 Score: 158
Period size: 54 Copynumber: 2.8 Consensus size: 53
2737389 AATTAAGTTT
*
2737399 AAAAAATTACATTAAAAAATTAAAATATTAATTATTATGTTTTTATAAAAATAA
1 AAAAAATTAAATTAAAAAATTAAAATATTAATTATTATGTTTTTATAAAAAT-A
* * * ** ** *
2737453 AAAAAATTAAAATAAAAAATAAAAAAGATTTTTTATTACAATTTTTATTAAAATA
1 AAAAAATTAAATTAAAAAAT-TAAAATATTAATTATTA-TGTTTTTATAAAAATA
* * * *
2737508 AAAAATTTATATTAACAAATTAAAGTATTAATTATTATGTTT
1 AAAAAATTAAATTAAAAAATTAAAATATTAATTATTATGTTT
2737550 AAAAAATCAC
Statistics
Matches: 75, Mismatches: 20, Indels: 5
0.75 0.20 0.05
Matches are distributed among these distances:
53 3 0.04
54 30 0.40
55 30 0.40
56 12 0.16
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.40
Consensus pattern (53 bp):
AAAAAATTAAATTAAAAAATTAAAATATTAATTATTATGTTTTTATAAAAATA
Found at i:2737556 original size:132 final size:132
Alignment explanation
Indices: 2737238--2737513 Score: 401
Period size: 132 Copynumber: 2.1 Consensus size: 132
2737228 TATTATTTTT
* * *
2737238 AATAAAAAATAATAGTTAATCAAGTTTTAAAAAATTTACATTAACAAATTAAAATATTAATTATT
1 AATAAAAAATAATATTTAATCAAG-ATTAAAAAA-TTACATTAAAAAATTAAAATATTAATTATT
* * * * **
2737303 ATATTTTTTAAAAAATAAAAAAAATTTAATTAAAAAATAAAAAGGGTTTTTTATTATTATTTTTA
64 ATATTTTTTAAAAAATAAAAAAAATTAAAATAAAAAATAAAAAAGATTTTTTATTACAATTTTTA
2737368 ATAA
129 ATAA
* *
2737372 AATAAAAAATAATATTTAATTAAGTTTAAAAAATTACATTAAAAAATTAAAATATTAATTATTAT
1 AATAAAAAATAATATTTAATCAAGATTAAAAAATTACATTAAAAAATTAAAATATTAATTATTAT
* *
2737437 -GTTTTTATAAAAATAAAAAAAATTAAAATAAAAAATAAAAAAGATTTTTTATTACAATTTTTAT
66 ATTTTTTA-AAAAATAAAAAAAATTAAAATAAAAAATAAAAAAGATTTTTTATTACAATTTTTAA
2737501 TAA
130 TAA
2737504 AATAAAAAAT
1 AATAAAAAAT
2737514 TTATATTAAC
Statistics
Matches: 130, Mismatches: 11, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
131 6 0.05
132 93 0.72
133 9 0.07
134 22 0.17
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.39
Consensus pattern (132 bp):
AATAAAAAATAATATTTAATCAAGATTAAAAAATTACATTAAAAAATTAAAATATTAATTATTAT
ATTTTTTAAAAAATAAAAAAAATTAAAATAAAAAATAAAAAAGATTTTTTATTACAATTTTTAAT
AA
Found at i:2741416 original size:20 final size:19
Alignment explanation
Indices: 2741391--2741450 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 19
2741381 GTTGGGCCAA
2741391 ATGTATCGATACAATATAGG
1 ATGTATCGATACAATATA-G
* *
2741411 ATGTATCGATACATTCTAG
1 ATGTATCGATACAATATAG
2741430 ACTTGTATCGATACATATATA
1 A--TGTATCGATACA-ATATA
2741451 TATATGTGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 2 0.06
20 16 0.48
21 12 0.36
22 3 0.09
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (19 bp):
ATGTATCGATACAATATAG
Found at i:2742495 original size:21 final size:21
Alignment explanation
Indices: 2742470--2742510 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2742460 ATCAGAGATA
*
2742470 GATGCAAACATCCCCTGAATT
1 GATGCAAACATCCCATGAATT
2742491 GATGCAAACATCCCATGAAT
1 GATGCAAACATCCCATGAAT
2742511 GTCGGTAGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.27, G:0.15, T:0.22
Consensus pattern (21 bp):
GATGCAAACATCCCATGAATT
Found at i:2744443 original size:14 final size:14
Alignment explanation
Indices: 2744424--2744451 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2744414 TAATTGTGCA
2744424 AAATCTATCCTTGT
1 AAATCTATCCTTGT
2744438 AAATCTATCCTTGT
1 AAATCTATCCTTGT
2744452 CAAGAGATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.21, G:0.07, T:0.43
Consensus pattern (14 bp):
AAATCTATCCTTGT
Found at i:2746138 original size:14 final size:14
Alignment explanation
Indices: 2746119--2746148 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2746109 GGTAGAGTTA
2746119 AATTCATCAAAAAC
1 AATTCATCAAAAAC
2746133 AATTCATCAAAAAC
1 AATTCATCAAAAAC
2746147 AA
1 AA
2746149 CATGTATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (14 bp):
AATTCATCAAAAAC
Found at i:2748360 original size:3 final size:3
Alignment explanation
Indices: 2748352--2748385 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2748342 TAACCTCTTG
2748352 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
2748386 CTTGGAGTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:2750114 original size:21 final size:21
Alignment explanation
Indices: 2750080--2750134 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
2750070 GCCAATAACT
* *
2750080 TGTATCAATGCATT-CACATAA
1 TGTATCGATACATTGCA-ATAA
2750101 TGTATCGATACATTGCAATAA
1 TGTATCGATACATTGCAATAA
2750122 -GTATCGATACATT
1 TGTATCGATACATT
2750135 TTCATGTGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
20 13 0.42
21 16 0.52
22 2 0.06
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (21 bp):
TGTATCGATACATTGCAATAA
Found at i:2751278 original size:71 final size:73
Alignment explanation
Indices: 2751079--2751290 Score: 197
Period size: 71 Copynumber: 2.9 Consensus size: 73
2751069 AAAACATTCT
* *
2751079 TAAAAATTTAAAGTTC-TATCAT--CAAATTAAAAAAATAAATCATAAATTTTTATAAATAAAAT
1 TAAAAATTTAAA-CTCATATCATACCAAA-T-AAAAAATAAAT-ATAAATTTTTACAAATAAAA-
*
2751141 TAAATTACACCAT
61 TAAATTACACCAC
* * *
2751154 TAAAAATTTAAACTCATATCATACCTAATAAAAAACACAAT-TAAATTTTTACAAATCCAAATAA
1 TAAAAATTTAAACTCATATCATACCAAATAAAAAATA-AATATAAATTTTTACAAAT-AAAATAA
*
2751218 ATTATACC-C
64 ATTACACCAC
* * *
2751227 TAAAAATTTAGAC-C-TAT-ATATTCAAATAAAAAATAAATATAAACTTTTACAAATAGAAATAA
1 TAAAAATTTAAACTCATATCATA-CCAAATAAAAAATAAATATAAATTTTTACAAATA-AAATAA
2751289 AT
64 AT
2751291 AATAACTCTA
Statistics
Matches: 116, Mismatches: 13, Indels: 20
0.78 0.09 0.13
Matches are distributed among these distances:
70 6 0.05
71 36 0.31
72 1 0.01
73 12 0.10
74 26 0.22
75 28 0.24
76 4 0.03
77 3 0.03
ACGTcount: A:0.55, C:0.12, G:0.01, T:0.32
Consensus pattern (73 bp):
TAAAAATTTAAACTCATATCATACCAAATAAAAAATAAATATAAATTTTTACAAATAAAATAAAT
TACACCAC
Found at i:2754642 original size:29 final size:29
Alignment explanation
Indices: 2754595--2754664 Score: 115
Period size: 29 Copynumber: 2.4 Consensus size: 29
2754585 ATTTGGTGAA
2754595 ATGCATGAAATGAACATTACGTAAAATGC
1 ATGCATGAAATGAACATTACGTAAAATGC
*
2754624 ATGCATGAAATGCAA-ATTACGTGAAATGC
1 ATGCATGAAATG-AACATTACGTAAAATGC
2754653 ATGCATGAAATG
1 ATGCATGAAATG
2754665 TAATGCATGA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 37 0.95
30 2 0.05
ACGTcount: A:0.43, C:0.13, G:0.20, T:0.24
Consensus pattern (29 bp):
ATGCATGAAATGAACATTACGTAAAATGC
Found at i:2754650 original size:16 final size:15
Alignment explanation
Indices: 2754627--2754723 Score: 62
Period size: 14 Copynumber: 6.7 Consensus size: 15
2754617 AAAATGCATG
2754627 CATGAAATGCAAATTA
1 CATGAAATGCAAA-TA
* *
2754643 CGTGAAATGC--ATG
1 CATGAAATGCAAATA
* *
2754656 CATGAAATG-TAATG
1 CATGAAATGCAAATA
2754670 CATGAAATGCAAATTA
1 CATGAAATGCAAA-TA
* *
2754686 CGTGAAATGC--ATG
1 CATGAAATGCAAATA
* *
2754699 CATGAAATG-TAATG
1 CATGAAATGCAAATA
2754713 CATGAAATGCA
1 CATGAAATGCA
2754724 TAAAAATATG
Statistics
Matches: 65, Mismatches: 9, Indels: 15
0.73 0.10 0.17
Matches are distributed among these distances:
13 18 0.28
14 26 0.40
15 2 0.03
16 19 0.29
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25
Consensus pattern (15 bp):
CATGAAATGCAAATA
Found at i:2754671 original size:18 final size:18
Alignment explanation
Indices: 2754648--2754716 Score: 66
Period size: 18 Copynumber: 3.4 Consensus size: 18
2754638 AATTACGTGA
2754648 AATGCATGCATGAAATGT
1 AATGCATGCATGAAATGT
*
2754666 AATGCATGAAATGCAAATTACGT
1 AATGCATG-CATG-AAA-T--GT
2754689 GAAATGCATGCATGAAATGT
1 --AATGCATGCATGAAATGT
2754709 AATGCATG
1 AATGCATG
2754717 AAATGCATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
18 16 0.38
19 3 0.07
20 5 0.12
21 1 0.02
22 1 0.02
23 5 0.12
24 3 0.07
25 8 0.19
ACGTcount: A:0.41, C:0.12, G:0.22, T:0.26
Consensus pattern (18 bp):
AATGCATGCATGAAATGT
Found at i:2754672 original size:14 final size:14
Alignment explanation
Indices: 2754653--2754721 Score: 77
Period size: 14 Copynumber: 4.9 Consensus size: 14
2754643 CGTGAAATGC
2754653 ATGCATGAAATGTA
1 ATGCATGAAATGTA
*
2754667 ATGCATGAAATGCAA
1 ATGCATGAAATG-TA
* * *
2754682 ATTACGTGAAATG-C
1 A-TGCATGAAATGTA
2754696 ATGCATGAAATGTA
1 ATGCATGAAATGTA
2754710 ATGCATGAAATG
1 ATGCATGAAATG
2754722 CATAAAAATA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
13 9 0.20
14 25 0.56
15 2 0.04
16 9 0.20
ACGTcount: A:0.42, C:0.10, G:0.22, T:0.26
Consensus pattern (14 bp):
ATGCATGAAATGTA
Found at i:2754673 original size:43 final size:43
Alignment explanation
Indices: 2754624--2754723 Score: 200
Period size: 43 Copynumber: 2.3 Consensus size: 43
2754614 CGTAAAATGC
2754624 ATGCATGAAATGCAAATTACGTGAAATGCATGCATGAAATGTA
1 ATGCATGAAATGCAAATTACGTGAAATGCATGCATGAAATGTA
2754667 ATGCATGAAATGCAAATTACGTGAAATGCATGCATGAAATGTA
1 ATGCATGAAATGCAAATTACGTGAAATGCATGCATGAAATGTA
2754710 ATGCATGAAATGCA
1 ATGCATGAAATGCA
2754724 TAAAAATATG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25
Consensus pattern (43 bp):
ATGCATGAAATGCAAATTACGTGAAATGCATGCATGAAATGTA
Found at i:2754795 original size:15 final size:15
Alignment explanation
Indices: 2754770--2754841 Score: 62
Period size: 15 Copynumber: 4.7 Consensus size: 15
2754760 TAATTTGGGT
2754770 TTTTTTCTTTATTTAC
1 TTTTTT-TTTATTTAC
*
2754786 TTTTTTTTTA-TTATT
1 TTTTTTTTTATTTA-C
2754801 TTTATTTTTTATATATAC
1 TTT-TTTTTTAT-T-TAC
2754819 --TTTTTTTATTTA-
1 TTTTTTTTTATTTAC
2754831 TTTTTTTTTAT
1 TTTTTTTTTAT
2754842 AAATGTTAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
13 2 0.04
14 13 0.28
15 15 0.32
16 14 0.30
18 1 0.02
19 2 0.04
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTTTTTATTTAC
Found at i:2754799 original size:18 final size:18
Alignment explanation
Indices: 2754769--2754825 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 18
2754759 CTAATTTGGG
*
2754769 TTTTTTTCT-TTATTTAC
1 TTTTTTTTTATTATTTAC
2754786 TTTTTTTTTATTATTT--
1 TTTTTTTTTATTATTTAC
* *
2754802 TTATTTTTTA-TATATAC
1 TTTTTTTTTATTATTTAC
2754819 TTTTTTT
1 TTTTTTT
2754826 ATTTATTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
15 4 0.12
16 9 0.27
17 14 0.42
18 6 0.18
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTTTTTTATTATTTAC
Found at i:2755412 original size:42 final size:42
Alignment explanation
Indices: 2755366--2756007 Score: 482
Period size: 42 Copynumber: 15.4 Consensus size: 42
2755356 AGTGAAAATG
* *
2755366 TCTCCAAGGTCAAAGCCGACAGGCAGACTTGAGGTAAGGAAA
1 TCTCCAAGGTCAAAGCCGACAGGCAGACTTGAGATGAGGAAA
* * * **
2755408 TCTCC-AGGTCAAAGCCGACAGGCAAACTTGAGGTAAGTCAA
1 TCTCCAAGGTCAAAGCCGACAGGCAGACTTGAGATGAGGAAA
* * * *
2755449 TCTTC-AGGTCAAAGTCGACAGGCAAAC-TGAG-GGTAGGAAA
1 TCTCCAAGGTCAAAGCCGACAGGCAGACTTGAGATG-AGGAAA
* * * * *
2755489 GTCTCCAAGGTCAAAGCCGATAAGCAGACTTTAGATGAGGCAG
1 -TCTCCAAGGTCAAAGCCGACAGGCAGACTTGAGATGAGGAAA
* * * *
2755532 TCTCTAAGGTCAAAGCCGACAGGCAGACTTTAGATGAGGCAG
1 TCTCCAAGGTCAAAGCCGACAGGCAGACTTGAGATGAGGAAA
* *
2755574 TCTCCAAGGTCAAAGCCGACAGACAGAC-TGAG-GGTAGGAAA
1 TCTCCAAGGTCAAAGCCGACAGGCAGACTTGAGATG-AGGAAA
*** * * * * *
2755615 GTCTCTGGGGTCAAAGCTGACAGGCAAACTTTAGATGAGGCAG
1 -TCTCCAAGGTCAAAGCCGACAGGCAGACTTGAGATGAGGAAA
* * * * * * *
2755658 TCTCTAGGGTCAAAGCCGATAGGCAGACTTTAGATAAGGTAG
1 TCTCCAAGGTCAAAGCCGACAGGCAGACTTGAGATGAGGAAA
* * *
2755700 TCTCCAAGGTCAAAGCCGACAGGTAGAC-TGAG-GGTAGAAAA
1 TCTCCAAGGTCAAAGCCGACAGGCAGACTTGAGATG-AGGAAA
* * * * * *
2755741 GTCTCCAAGATCAAAGCCGATAGGTAAACTTTAGATGAGGTAA
1 -TCTCCAAGGTCAAAGCCGACAGGCAGACTTGAGATGAGGAAA
* * * *
2755784 TCTCCAAGGTCAAAGCCGACAAGCAGACTTTAGATGAGGCAG
1 TCTCCAAGGTCAAAGCCGACAGGCAGACTTGAGATGAGGAAA
* *
2755826 TCTCCAAGGTCAAAGCCGACAGGCAGAC-TGAG-GGTAGAAAA
1 TCTCCAAGGTCAAAGCCGACAGGCAGACTTGAGATG-AGGAAA
* * * * * *
2755867 TCTCCAGGGTCAAAGCCGACAGGAAAACTTTAGATGAGGTAG
1 TCTCCAAGGTCAAAGCCGACAGGCAGACTTGAGATGAGGAAA
* * * * *
2755909 TCTCTAGGGTCAAAACTGATAGGCAGAC-TGAGA-GTAGGAAA
1 TCTCCAAGGTCAAAGCCGACAGGCAGACTTGAGATG-AGGAAA
* * * * *
2755950 GTCTTCAGGGTCAAAACCGACAGGCAGAC-TGTAGATGAGGCAG
1 -TCTCCAAGGTCAAAGCCGACAGGCAGACTTG-AGATGAGGAAA
*
2755993 TCTCCAAGGTTAAAG
1 TCTCCAAGGTCAAAG
2756008 TCGATAGGTA
Statistics
Matches: 480, Mismatches: 100, Indels: 40
0.77 0.16 0.06
Matches are distributed among these distances:
40 11 0.02
41 114 0.24
42 322 0.67
43 29 0.06
44 4 0.01
ACGTcount: A:0.34, C:0.20, G:0.28, T:0.18
Consensus pattern (42 bp):
TCTCCAAGGTCAAAGCCGACAGGCAGACTTGAGATGAGGAAA
Found at i:2755612 original size:126 final size:126
Alignment explanation
Indices: 2755365--2755980 Score: 729
Period size: 126 Copynumber: 4.9 Consensus size: 126
2755355 AAGTGAAAAT
* * * * * * *
2755365 GTCTCCAAGGTCAAAGCCGACAGGCAGACTTGAGGTAAGGAAATCTC-CAGGTCAAAGCCGACAG
1 GTCTCCAAGGTCAAAGCCGACAGGCAAACTTTAGATGAGGCAGTCTCTAAGGTCAAAGCCGACAG
* * * * * * * * *
2755429 GCAAACTTGAGGTAAGTCAATCTTC-AGGTCAAAGTCGACAGGCAAACTGAGGGTAGGAAA
66 GCAGACTTTAGATGAGGCAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAGGGTAGGAAA
* * *
2755489 GTCTCCAAGGTCAAAGCCGATAAGCAGACTTTAGATGAGGCAGTCTCTAAGGTCAAAGCCGACAG
1 GTCTCCAAGGTCAAAGCCGACAGGCAAACTTTAGATGAGGCAGTCTCTAAGGTCAAAGCCGACAG
*
2755554 GCAGACTTTAGATGAGGCAGTCTCCAAGGTCAAAGCCGACAGACAGACTGAGGGTAGGAAA
66 GCAGACTTTAGATGAGGCAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAGGGTAGGAAA
*** * * *
2755615 GTCTCTGGGGTCAAAGCTGACAGGCAAACTTTAGATGAGGCAGTCTCTAGGGTCAAAGCCGATAG
1 GTCTCCAAGGTCAAAGCCGACAGGCAAACTTTAGATGAGGCAGTCTCTAAGGTCAAAGCCGACAG
* * * *
2755680 GCAGACTTTAGATAAGGTAGTCTCCAAGGTCAAAGCCGACAGGTAGACTGAGGGTAGAAAA
66 GCAGACTTTAGATGAGGCAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAGGGTAGGAAA
* * * * * * *
2755741 GTCTCCAAGATCAAAGCCGATAGGTAAACTTTAGATGAGGTAATCTCCAAGGTCAAAGCCGACAA
1 GTCTCCAAGGTCAAAGCCGACAGGCAAACTTTAGATGAGGCAGTCTCTAAGGTCAAAGCCGACAG
2755806 GCAGACTTTAGATGAGGCAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAGGGTA-GAAA
66 GCAGACTTTAGATGAGGCAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAGGGTAGGAAA
* * * * * * * *
2755866 ATCTCCAGGGTCAAAGCCGACAGGAAAACTTTAGATGAGGTAGTCTCTAGGGTCAAAACTGATAG
1 GTCTCCAAGGTCAAAGCCGACAGGCAAACTTTAGATGAGGCAGTCTCTAAGGTCAAAGCCGACAG
* * * * *
2755931 GCAGAC-TGAGA-GTAGGAAAGTCTTCAGGGTCAAAACCGACAGGCAGACTG
66 GCAGACTTTAGATG-AGG-CAGTCTCCAAGGTCAAAGCCGACAGGCAGACTG
2755981 TAGATGAGGC
Statistics
Matches: 422, Mismatches: 66, Indels: 7
0.85 0.13 0.01
Matches are distributed among these distances:
123 1 0.00
124 47 0.11
125 125 0.30
126 249 0.59
ACGTcount: A:0.34, C:0.20, G:0.28, T:0.18
Consensus pattern (126 bp):
GTCTCCAAGGTCAAAGCCGACAGGCAAACTTTAGATGAGGCAGTCTCTAAGGTCAAAGCCGACAG
GCAGACTTTAGATGAGGCAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAGGGTAGGAAA
Found at i:2773559 original size:20 final size:20
Alignment explanation
Indices: 2773495--2773569 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
2773485 AAAAAGACAG
* *
2773495 AATGTATCGATACACTGAAG
1 AATGTATCGATACATTGAAA
* *
2773515 AATGTATC-ATTACATTCATA
1 AATGTATCGA-TACATTGAAA
* *
2773535 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTGAAA
*
2773555 AATGTATCAATACAT
1 AATGTATCGATACAT
2773570 ATGGGTAAAA
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
19 1 0.02
20 40 0.95
21 1 0.02
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTGAAA
Found at i:2774064 original size:45 final size:46
Alignment explanation
Indices: 2773943--2774064 Score: 147
Period size: 49 Copynumber: 2.6 Consensus size: 46
2773933 ATGAGAGGAT
*
2773943 TGCCAATGTGCCAATTCAAGGCCAGCGACATTGGGCTAAGGGAAAAG
1 TGCCAATGTGCTAATTCAAGGCCAGCGACATTGGGCTAA-GGAAAAG
* * *
2773990 TGGACCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTAA-TAAAGG
1 T-G-CCAATGTGCTAATTCAAGGCCAGCGACATTGGGCTAAGGAAAAG
* * *
2774037 TGCCAATATGCTAATTCAATGCTAGCGA
1 TGCCAATGTGCTAATTCAAGGCCAGCGA
2774065 TGTTAGACAG
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
45 22 0.34
46 1 0.02
47 6 0.09
48 1 0.02
49 35 0.54
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.21
Consensus pattern (46 bp):
TGCCAATGTGCTAATTCAAGGCCAGCGACATTGGGCTAAGGAAAAG
Found at i:2774215 original size:28 final size:28
Alignment explanation
Indices: 2774133--2774503 Score: 483
Period size: 28 Copynumber: 13.0 Consensus size: 28
2774123 AAAAAAGAAT
*
2774133 GGTGCCACTAACTTGTGTGGGCTTTGAAAAG
1 GGTGCCACTGAC-T-TGTGGGCTTTG-AAAG
* *
2774164 AGTTGCCACCGACTTGTGTGGGCTTTGAAAG
1 -GGTGCCACTGAC-T-TGTGGGCTTTGAAAG
* *
2774195 GGTGCCACTAACTTATGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
2774223 GATGCCACTGACTCGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
*
2774251 GGTGCCACTGACTCGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
*
2774279 GGTGCCACTGACTCGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
2774307 GGTGCCACTGA-TTCGTGGGCTTTGAAAG
1 GGTGCCACTGACTT-GTGGGCTTTGAAAG
* *
2774335 GGTGCCACTGACTCGTGGGCTTTGGAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
*
2774363 GGTGCCACTCACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * * *
2774391 AGTGCCACTCATTTGTGGGATTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
** *
2774419 AATGCCACTAACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
*
2774447 GGTGCCACTGACTTATGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
*
2774475 GGTGCCACTGACTTGTAGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
2774503 G
1 G
2774504 ATGAACGTTC
Statistics
Matches: 306, Mismatches: 31, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
27 1 0.00
28 267 0.87
29 2 0.01
30 9 0.03
31 4 0.01
32 23 0.08
ACGTcount: A:0.21, C:0.19, G:0.33, T:0.28
Consensus pattern (28 bp):
GGTGCCACTGACTTGTGGGCTTTGAAAG
Found at i:2775734 original size:1 final size:1
Alignment explanation
Indices: 2775730--2775781 Score: 50
Period size: 1 Copynumber: 52.0 Consensus size: 1
2775720 TTTTTCTTGG
* * * * * *
2775730 TTTTTTTGTTTTTTTATTTTTTTATTTTTTTATTTTTGTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2775782 GTGCAAAGAA
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.06, C:0.00, G:0.06, T:0.88
Consensus pattern (1 bp):
T
Found at i:2775751 original size:16 final size:17
Alignment explanation
Indices: 2775730--2775778 Score: 73
Period size: 16 Copynumber: 2.9 Consensus size: 17
2775720 TTTTTCTTGG
2775730 TTTTTTTGTTTTTTTA-
1 TTTTTTTGTTTTTTTAT
*
2775746 TTTTTTTATTTTTTTAT
1 TTTTTTTGTTTTTTTAT
2775763 TTTTGTTTGTTTTTTT
1 TTTT-TTTGTTTTTTT
2775779 TTTGTGCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 15 0.52
17 4 0.14
18 10 0.34
ACGTcount: A:0.06, C:0.00, G:0.06, T:0.88
Consensus pattern (17 bp):
TTTTTTTGTTTTTTTAT
Found at i:2775781 original size:16 final size:15
Alignment explanation
Indices: 2775730--2775783 Score: 65
Period size: 15 Copynumber: 3.6 Consensus size: 15
2775720 TTTTTCTTGG
2775730 TTTTTTTGTTTTTTT
1 TTTTTTTGTTTTTTT
*
2775745 ATTTTTTT-ATTTTTT
1 -TTTTTTTGTTTTTTT
* *
2775760 TATTTTTGTTTGTTT
1 TTTTTTTGTTTTTTT
2775775 TTTTTTTGT
1 TTTTTTTGT
2775784 GCAAAGAACG
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
14 6 0.19
15 19 0.59
16 7 0.22
ACGTcount: A:0.06, C:0.00, G:0.07, T:0.87
Consensus pattern (15 bp):
TTTTTTTGTTTTTTT
Found at i:2789770 original size:20 final size:20
Alignment explanation
Indices: 2789745--2789821 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
2789735 GTAAAAAGAT
2789745 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
*
2789765 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
* *
2789785 TA-CATGTATCGATATATTGA
1 -AGAATGTATCGATACATTGA
*
2789805 AAAATGTATCGATACAT
1 AGAATGTATCGATACAT
2789822 CTGGGTAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
19 1 0.02
20 47 0.96
21 1 0.02
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:2790486 original size:16 final size:16
Alignment explanation
Indices: 2790465--2790496 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2790455 AGCTTCATTG
2790465 CATTCTTCATTGCTGC
1 CATTCTTCATTGCTGC
2790481 CATTCTTCATTGCTGC
1 CATTCTTCATTGCTGC
2790497 AGTTTGCAGC
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:0.12, C:0.31, G:0.12, T:0.44
Consensus pattern (16 bp):
CATTCTTCATTGCTGC
Found at i:2790734 original size:16 final size:16
Alignment explanation
Indices: 2790713--2790767 Score: 71
Period size: 16 Copynumber: 3.6 Consensus size: 16
2790703 AATGCATGTA
*
2790713 TGAAATGCAAATTACG
1 TGAAATGCAAATCACG
2790729 TGAAATGC-AATGCAC-
1 TGAAATGCAAAT-CACG
2790744 -GAAATGCAAATCACG
1 TGAAATGCAAATCACG
2790759 TGAAATGCA
1 TGAAATGCA
2790768 TGCATGAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
14 10 0.29
15 6 0.18
16 18 0.53
ACGTcount: A:0.44, C:0.16, G:0.20, T:0.20
Consensus pattern (16 bp):
TGAAATGCAAATCACG
Found at i:2790749 original size:14 final size:14
Alignment explanation
Indices: 2790730--2790785 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
2790720 CAAATTACGT
2790730 GAAATGCAATGCAC
1 GAAATGCAATGCAC
2790744 GAAATGCAAAT-CAC
1 GAAATGC-AATGCAC
*
2790758 GTGAAATGC-ATGCAT
1 --GAAATGCAATGCAC
*
2790773 GAAATGTAATGCA
1 GAAATGCAATGCA
2790786 TGCATGAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
13 6 0.17
14 17 0.49
15 5 0.14
16 7 0.20
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.20
Consensus pattern (14 bp):
GAAATGCAATGCAC
Found at i:2790750 original size:30 final size:29
Alignment explanation
Indices: 2790679--2790778 Score: 139
Period size: 29 Copynumber: 3.4 Consensus size: 29
2790669 TGGTGAAGAA
*
2790679 ATGCATGAAATG-AACATTACGTAAAATGC
1 ATGCATGAAATGCAA-ATTACGTGAAATGC
*
2790708 ATGTATGAAATGCAAATTACGTGAAATGC
1 ATGCATGAAATGCAAATTACGTGAAATGC
* *
2790737 AATGCACGAAATGCAAATCACGTGAAATGC
1 -ATGCATGAAATGCAAATTACGTGAAATGC
2790767 ATGCATGAAATG
1 ATGCATGAAATG
2790779 TAATGCATGC
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
29 35 0.56
30 28 0.44
ACGTcount: A:0.43, C:0.14, G:0.20, T:0.23
Consensus pattern (29 bp):
ATGCATGAAATGCAAATTACGTGAAATGC
Found at i:2790861 original size:3 final size:3
Alignment explanation
Indices: 2790855--2790883 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2790845 TTTACTTTTT
2790855 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2790884 TATATATACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Done.