Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold8
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: 6381039
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 22487 characters in sequence are not A, C, G, or T
File 7 of 33
Found at i:884372 original size:3 final size:3
Alignment explanation
Indices: 884364--884396 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
884354 CCATAAAACT
*
884364 AAG AAG AAG AAG TAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
884397 CATAAAACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.33, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:886254 original size:51 final size:53
Alignment explanation
Indices: 886158--886259 Score: 131
Period size: 55 Copynumber: 1.9 Consensus size: 53
886148 ATAAATATCT
886158 TAAAATTTATATAATATTAATTATTAATATATTAAAATAAATATAAATATAAAAA
1 TAAAATTTATATAATATTAATTATTAATATA-TAAAATAAATAT-AATATAAAAA
* *
886213 TAAAATATTATA-AATATTATTTA-TAATATA-AAAAT-ACTATAATATAA
1 TAAAAT-TTATATAATATTAATTATTAATATATAAAATAAATATAATATAA
886260 TATGAGTATT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
50 7 0.16
51 4 0.09
52 5 0.11
54 7 0.16
55 16 0.36
56 5 0.11
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (53 bp):
TAAAATTTATATAATATTAATTATTAATATATAAAATAAATATAATATAAAAA
Found at i:886478 original size:17 final size:16
Alignment explanation
Indices: 886456--886488 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
886446 AATTTTTTAC
886456 TTTAAAAAAGTTTAAAA
1 TTTAAAAAA-TTTAAAA
886473 TTTAAAAAATTTAAAA
1 TTTAAAAAATTTAAAA
886489 GTTGTAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
TTTAAAAAATTTAAAA
Found at i:886547 original size:19 final size:18
Alignment explanation
Indices: 886523--886567 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
886513 TTGTTTTTTG
886523 ATAAATACCATACAAATTT
1 ATAAATACCATA-AAATTT
* *
886542 ATAAATATCTTAAAATTT
1 ATAAATACCATAAAATTT
886560 ATATAATA
1 ATA-AATA
886568 TTAATTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAAATACCATAAAATTT
Found at i:886594 original size:14 final size:14
Alignment explanation
Indices: 886577--886616 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
886567 ATTAATTATT
886577 AATATATTAAAATA
1 AATATATTAAAATA
886591 AATATA--AAAATA
1 AATATATTAAAATA
886603 AA-ATATTATAAATA
1 AATATATTA-AAATA
886617 TTATTTATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
11 3 0.13
12 8 0.35
13 1 0.04
14 11 0.48
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AATATATTAAAATA
Found at i:886630 original size:21 final size:20
Alignment explanation
Indices: 886604--886642 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
886594 ATAAAAATAA
*
886604 AATATTATAAATATTATTTAT
1 AATATTA-AAATAGTATTTAT
886625 AATATTAAAATAGTATTT
1 AATATTAAAATAGTATTT
886643 GAATTATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
AATATTAAAATAGTATTTAT
Found at i:886918 original size:19 final size:18
Alignment explanation
Indices: 886894--886938 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
886884 TTGTTTTTTG
886894 ATAAATACCATACAAATTT
1 ATAAATACCATA-AAATTT
* *
886913 ATAAATATCTTAAAATTT
1 ATAAATACCATAAAATTT
886931 ATATAATA
1 ATA-AATA
886939 TTAATTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAAATACCATAAAATTT
Found at i:886934 original size:371 final size:371
Alignment explanation
Indices: 886250--887171 Score: 1634
Period size: 371 Copynumber: 2.5 Consensus size: 371
886240 ATAAAAATAC
* * *
886250 TATAATATAATATGAGTATTTGAATTATTGAAATTTTATGTTGTCCTAAGATACCACTATTTTTC
1 TATAATATAAAAT-AGTATTTGAATTATTGAAATTTTATGTTGTCCTAAGGTACTACTATTTTTC
*
886315 TGTTATTTATAGCCACAGTCAGTTTCAACCTACAAAAACCAAGCCCATCATAGTCACAGGCACAA
65 TGTTATTTATAGCCACAGTCAGTTTCAGCCTACAAAAACCAAGCCCATCATAGTCACAGGCACAA
* *
886380 AAGACCTAAGAATCTGTGCCCCATCCTCACTCTACCCAAGTCCAAAAAAATCTTGAGACCAAAAT
130 AAGGCCTGAGAATCTGTGCCCCATCCTCACTCTACCCAAGTCCAAAAAAATCTTGAGACCAAAAT
*
886445 TAATTTTTTACTTTAAAAAAGTTTAAAATTTAAAAAATTTAAAAGTTGTAAATGATCGAAATTTT
195 TAATTTTTTACTTTAAAAAAGTTTAAAAATTAAAAAATTTAAAAGTTGTAAATGATCGAAATTTT
886510 TATTTGTTTTTTGATAAATACCATACAAATTTATAAATATCTTAAAATTTATATAATATTAATTA
260 TATTTGTTTTTTGATAAATACCATACAAATTTATAAATATCTTAAAATTTATATAATATTAATTA
886575 TTAATATATTAAAATAAATATAAAAATAAAATATTATAAATATTATT
325 TTAATATATTAAAATAAATATAAAAATAAAATATTATAAATATTATT
886622 TATAATATTAAAATAGTATTTGAATTATTGAAATTTTATGTTGTCCTAAGGTACTACTATTTTTC
1 TATAATA-TAAAATAGTATTTGAATTATTGAAATTTTATGTTGTCCTAAGGTACTACTATTTTTC
886687 TGTTATTTATAGCCACAGTCAGTTTCAGCCTACAAAAACCAAGCCCATCATAGTCACAGGCACAA
65 TGTTATTTATAGCCACAGTCAGTTTCAGCCTACAAAAACCAAGCCCATCATAGTCACAGGCACAA
* * **
886752 AAGGCCTGAGAATATGTGTCCCATCCTCACTCTACCCAAGTCCAAAAAAATCTTGAGGTCAAAA-
130 AAGGCCTGAGAATCTGTGCCCCATCCTCACTCTACCCAAGTCCAAAAAAATCTTGAGACCAAAAT
886816 TAATTTTTTACTTTAAAAAAGTTTAAAAATTAAAAAATTTAAAAGTTGTAAATGATCGAAATTTT
195 TAATTTTTTACTTTAAAAAAGTTTAAAAATTAAAAAATTTAAAAGTTGTAAATGATCGAAATTTT
886881 TATTTGTTTTTTGATAAATACCATACAAATTTATAAATATCTTAAAATTTATATAATATTAATTA
260 TATTTGTTTTTTGATAAATACCATACAAATTTATAAATATCTTAAAATTTATATAATATTAATTA
886946 TTAATATATTAAAATAAATATAAAAATAAAATATTATAAATATTATT
325 TTAATATATTAAAATAAATATAAAAATAAAATATTATAAATATTATT
* * *
886993 TATAATATAAATATAGTATTTAAATTATTGAAATTTTATATTGTCTTAAGGTA-TCACTATTTTT
1 TATAATATAAA-ATAGTATTTGAATTATTGAAATTTTATGTTGTCCTAAGGTACT-ACTATTTTT
* * *
887057 CTGTTATTTATAGCTACAGTCAATTTCAGCCTACAAAAATCAAGCCCATCATAGTCACAGGCAC-
64 CTGTTATTTATAGCCACAGTCAGTTTCAGCCTACAAAAACCAAGCCCATCATAGTCACAGGCACA
887121 AAAGGCCTGAGAATCTGTGCCCCATCCTCACTCTACCCAAGTCCAAAAAAA
129 AAAGGCCTGAGAATCTGTGCCCCATCCTCACTCTACCCAAGTCCAAAAAAA
887172 CTAACGCACA
Statistics
Matches: 528, Mismatches: 19, Indels: 8
0.95 0.03 0.01
Matches are distributed among these distances:
370 54 0.10
371 291 0.55
372 178 0.34
373 5 0.01
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (371 bp):
TATAATATAAAATAGTATTTGAATTATTGAAATTTTATGTTGTCCTAAGGTACTACTATTTTTCT
GTTATTTATAGCCACAGTCAGTTTCAGCCTACAAAAACCAAGCCCATCATAGTCACAGGCACAAA
AGGCCTGAGAATCTGTGCCCCATCCTCACTCTACCCAAGTCCAAAAAAATCTTGAGACCAAAATT
AATTTTTTACTTTAAAAAAGTTTAAAAATTAAAAAATTTAAAAGTTGTAAATGATCGAAATTTTT
ATTTGTTTTTTGATAAATACCATACAAATTTATAAATATCTTAAAATTTATATAATATTAATTAT
TAATATATTAAAATAAATATAAAAATAAAATATTATAAATATTATT
Found at i:886965 original size:14 final size:14
Alignment explanation
Indices: 886948--886987 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
886938 ATTAATTATT
886948 AATATATTAAAATA
1 AATATATTAAAATA
886962 AATATA--AAAATA
1 AATATATTAAAATA
886974 AA-ATATTATAAATA
1 AATATATTA-AAATA
886988 TTATTTATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
11 3 0.13
12 8 0.35
13 1 0.04
14 11 0.48
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AATATATTAAAATA
Found at i:887577 original size:32 final size:32
Alignment explanation
Indices: 887521--887595 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
887511 TATTTAAAAT
**
887521 ATTATA-TATATAAATTTTTTTATATTAAT-A
1 ATTATATTATATAAATTTTGATATATTAATGA
* *
887551 ATTAATATTATATAAATTTTGATATATTTATGT
1 ATT-ATATTATATAAATTTTGATATATTAATGA
887584 ATTATATTATAT
1 ATTATATTATAT
887596 TATATTTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
30 3 0.08
31 3 0.08
32 29 0.76
33 3 0.08
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (32 bp):
ATTATATTATATAAATTTTGATATATTAATGA
Found at i:887917 original size:31 final size:30
Alignment explanation
Indices: 887880--887962 Score: 80
Period size: 31 Copynumber: 2.8 Consensus size: 30
887870 AATATTAAAA
887880 TAATATTTTTTAAAATTTAATTATAAAATAT
1 TAATATTTTTTAAAA-TTAATTATAAAATAT
* * **
887911 TAATATTAATTTAAAATTAATTTTTTAATAT
1 TAATATT-TTTTAAAATTAATTATAAAATAT
**
887942 TTTTATTTTTT-AAA-TAATTAT
1 TAATATTTTTTAAAATTAATTAT
887963 TTAAATCAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
28 6 0.14
29 3 0.07
30 3 0.07
31 24 0.56
32 7 0.16
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (30 bp):
TAATATTTTTTAAAATTAATTATAAAATAT
Found at i:888475 original size:19 final size:19
Alignment explanation
Indices: 888453--888495 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
888443 TAATTTAATA
* *
888453 ATTTTTTTTTAAAATTTAT
1 ATTTTTTTTAAAAAATTAT
*
888472 A-TTTATTTAAAAAATTAT
1 ATTTTTTTTAAAAAATTAT
888490 ATTTTT
1 ATTTTT
888496 ATATTCATAT
Statistics
Matches: 19, Mismatches: 4, Indels: 2
0.76 0.16 0.08
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTTTTTTTAAAAAATTAT
Found at i:888931 original size:22 final size:21
Alignment explanation
Indices: 888906--888974 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 21
888896 TTTTATATAG
888906 TATAATTATATTTAAAATATTA
1 TATAATTATATTTAAAAT-TTA
* * *
888928 TATATTTTTATATAAAATTTA
1 TATAATTATATTTAAAATTTA
888949 -ATATATTAATAATTT-AAA-TTA
1 TATA-ATT-AT-ATTTAAAATTTA
888970 TATAA
1 TATAA
888975 ATTTTAATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
20 3 0.08
21 9 0.24
22 22 0.59
23 3 0.08
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TATAATTATATTTAAAATTTA
Found at i:888980 original size:16 final size:16
Alignment explanation
Indices: 888935--888981 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
888925 TTATATATTT
888935 TTATATAAAATTT-AA
1 TTATATAAAATTTAAA
888950 -TATATTAATAATTTAAA
1 TTATA-TAA-AATTTAAA
*
888967 TTATATAAATTTTAA
1 TTATATAAAATTTAA
888982 TTTTTTTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
14 4 0.15
15 3 0.11
16 11 0.41
17 5 0.19
18 4 0.15
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TTATATAAAATTTAAA
Found at i:889006 original size:11 final size:11
Alignment explanation
Indices: 888987--889053 Score: 57
Period size: 11 Copynumber: 6.0 Consensus size: 11
888977 TTTAATTTTT
*
888987 TTATTTTTATA
1 TTATATTTATA
888998 TTATATTTAT-
1 TTATATTTATA
889008 TATATATTT-TAA
1 T-TATATTTAT-A
*
889020 TTATTTTTTATA
1 TTA-TATTTATA
889032 TTATATTTATA
1 TTATATTTATA
**
889043 TCGTATTTATA
1 TTATATTTATA
889054 ATGATACGGC
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
10 2 0.04
11 34 0.74
12 9 0.20
13 1 0.02
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (11 bp):
TTATATTTATA
Found at i:889040 original size:22 final size:24
Alignment explanation
Indices: 888991--889052 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 24
888981 ATTTTTTTAT
888991 TTTTATATTATATTTATTATA-TA
1 TTTTATATTATATTTATTATATTA
889014 TTTTA-ATTAT-TTT-TTATATTA
1 TTTTATATTATATTTATTATATTA
**
889035 TATTTATATCGTATTTAT
1 T-TTTATATTATATTTAT
889053 AATGATACGG
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
20 5 0.16
21 6 0.19
22 9 0.28
23 8 0.25
24 3 0.09
25 1 0.03
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (24 bp):
TTTTATATTATATTTATTATATTA
Found at i:889050 original size:34 final size:35
Alignment explanation
Indices: 888990--889055 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
888980 AATTTTTTTA
888990 TTTTTATATTATATTTATTATATATTT-TAATTAT
1 TTTTTATATTATATTTATTATATATTTATAATTAT
*
889024 TTTTTATATTATATTTA-TATCGTATTTATAAT
1 TTTTTATATTATATTTATTAT-ATATTTATAAT
889056 GATACGGCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 3 0.10
34 22 0.76
35 4 0.14
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (35 bp):
TTTTTATATTATATTTATTATATATTTATAATTAT
Found at i:889918 original size:13 final size:13
Alignment explanation
Indices: 889900--889963 Score: 60
Period size: 13 Copynumber: 4.9 Consensus size: 13
889890 TTGATTAATT
*
889900 ATAATAAATATTA
1 ATAATAAATATAA
889913 ATAATAAATATAA
1 ATAATAAATATAA
*
889926 ATAATAAA-AAAA
1 ATAATAAATATAA
*
889938 AT-TTAAATTATATA
1 ATAATAAA-TATA-A
*
889952 ATAATAATTATA
1 ATAATAAATATA
889964 TTATCACGTT
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
11 4 0.10
12 5 0.12
13 22 0.54
14 7 0.17
15 3 0.07
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
ATAATAAATATAA
Found at i:891272 original size:25 final size:25
Alignment explanation
Indices: 891222--891280 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
891212 TCAACCATAT
891222 TATTTTTTAATTTTAAAAAATATTA
1 TATTTTTTAATTTTAAAAAATATTA
* **
891247 TATTTATTTAATTTTTAGTAAT-TTA
1 TATTT-TTTAATTTTAAAAAATATTA
891272 TATTTTTTA
1 TATTTTTTA
891281 TTAAGTTCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.13
25 13 0.43
26 13 0.43
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.63
Consensus pattern (25 bp):
TATTTTTTAATTTTAAAAAATATTA
Found at i:892297 original size:2 final size:2
Alignment explanation
Indices: 892290--892321 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
892280 AACGTTGCTC
892290 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
892322 AGGAAGGTGC
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):
TA
Found at i:894963 original size:21 final size:21
Alignment explanation
Indices: 894924--894963 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
894914 TAGATATATA
* * *
894924 AATATAAAAATATATTTAAAC
1 AATAAAAAAATAAAATTAAAC
894945 AATAAAAAAATAAAATTAA
1 AATAAAAAAATAAAATTAA
894964 TTATTATATC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (21 bp):
AATAAAAAAATAAAATTAAAC
Found at i:895466 original size:2 final size:2
Alignment explanation
Indices: 895459--895484 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
895449 AGAACAATCC
895459 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
895485 GTTACATAAA
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:901510 original size:9 final size:9
Alignment explanation
Indices: 901496--901520 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
901486 TGACAATTGA
901496 AAAAAAAAG
1 AAAAAAAAG
901505 AAAAAAAAG
1 AAAAAAAAG
901514 AAAAAAA
1 AAAAAAA
901521 GAATTGTTAA
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:902331 original size:2 final size:2
Alignment explanation
Indices: 902324--902358 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
902314 GGAACAGAAT
902324 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
902359 GTTTCAGATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:906182 original size:3 final size:3
Alignment explanation
Indices: 906176--906228 Score: 61
Period size: 3 Copynumber: 17.7 Consensus size: 3
906166 TGATGATGAT
* * * * *
906176 GAG GAG GAG GAG GAG GAG GAA GAA GAG GAG GTG GAG GCG GAG GAG GAA
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
906224 GAG GA
1 GAG GA
906229 AGATTTGGGA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.36, C:0.02, G:0.60, T:0.02
Consensus pattern (3 bp):
GAG
Found at i:908153 original size:1 final size:1
Alignment explanation
Indices: 908147--908172 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
908137 GAACCAATAC
908147 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
908173 TCACAAAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:910506 original size:26 final size:26
Alignment explanation
Indices: 910464--910514 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
910454 ATGACCTTCA
*
910464 AATAATCTACACAAAATGATAAATTT
1 AATAATCTACAAAAAATGATAAATTT
*
910490 AATAATCTA-AAATAAATTATAAATT
1 AATAATCTACAAA-AAATGATAAATT
910515 ACTCTCTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 2 0.09
26 20 0.91
ACGTcount: A:0.57, C:0.08, G:0.02, T:0.33
Consensus pattern (26 bp):
AATAATCTACAAAAAATGATAAATTT
Found at i:916511 original size:48 final size:48
Alignment explanation
Indices: 916412--916524 Score: 115
Period size: 48 Copynumber: 2.4 Consensus size: 48
916402 GTAAAATTTA
* * * * *
916412 TTTATTAATATTATGATTAAATTAAATGATTTATATATTTATGTTATT
1 TTTATTAATATTATAATTAAATTAAATAATTTATATATTTATATAAAT
*
916460 TTTATT-ATATTATAAATTATATTAAA-AATATTATATATTTATATAAAT
1 TTTATTAATATTAT-AATTAAATTAAATAAT-TTATATATTTATATAAAT
* *
916508 TTTA-AAATATTTTAATT
1 TTTATTAATATTATAATT
916525 TTATATTATA
Statistics
Matches: 54, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
47 13 0.24
48 41 0.76
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (48 bp):
TTTATTAATATTATAATTAAATTAAATAATTTATATATTTATATAAAT
Found at i:916538 original size:27 final size:27
Alignment explanation
Indices: 916475--916574 Score: 80
Period size: 27 Copynumber: 3.7 Consensus size: 27
916465 TATATTATAA
* *
916475 ATTATATTAAAAATATTAT-ATATTTAT
1 ATTATATTTAAAATATTTTAAT-TTTAT
*
916502 A-TAAATTTTAAAATATTTTAATTTTAT
1 ATTATA-TTTAAAATATTTTAATTTTAT
* * * *
916529 ATTATATTTATATTATTTTTA-TATAT
1 ATTATATTTAAAATATTTTAATTTTAT
* *
916555 ATTATATTTTAATTATTTTA
1 ATTATATTTAAAATATTTTA
916575 TAATATATTC
Statistics
Matches: 59, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
26 24 0.41
27 30 0.51
28 5 0.08
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (27 bp):
ATTATATTTAAAATATTTTAATTTTAT
Found at i:916539 original size:38 final size:37
Alignment explanation
Indices: 916493--916576 Score: 100
Period size: 37 Copynumber: 2.3 Consensus size: 37
916483 AAAAATATTA
*
916493 TATATTTATATAAATTTTAAAATATTTTA-ATTTTATAT
1 TATATTTATAT-AATTTTAAAATATATTATATTTTA-AT
* * *
916531 TATATTTATATTATTTTTATATATATTATATTTTAAT
1 TATATTTATATAATTTTAAAATATATTATATTTTAAT
916568 TAT-TTTATA
1 TATATTTATA
916577 ATATATTCAT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
36 6 0.15
37 18 0.44
38 17 0.41
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (37 bp):
TATATTTATATAATTTTAAAATATATTATATTTTAAT
Found at i:916540 original size:11 final size:11
Alignment explanation
Indices: 916524--916576 Score: 56
Period size: 11 Copynumber: 5.0 Consensus size: 11
916514 ATATTTTAAT
916524 TTTATATTATA
1 TTTATATTATA
*
916535 TTTATATTATT
1 TTTATATTATA
916546 TTTATA-TATA
1 TTTATATTATA
*
916556 -TTATATTTTA
1 TTTATATTATA
* *
916566 ATTATTTTATA
1 TTTATATTATA
916577 ATATATTCAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
9 5 0.14
10 6 0.17
11 24 0.69
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TTTATATTATA
Found at i:916550 original size:17 final size:16
Alignment explanation
Indices: 916514--916565 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 16
916504 AAATTTTAAA
916514 ATATTTTA-AT-T-TT
1 ATATTTTATATATATT
* *
916527 ATATTATATTTATATT
1 ATATTTTATATATATT
916543 AT-TTTTATATATATT
1 ATATTTTATATATATT
916558 ATATTTTA
1 ATATTTTA
916566 ATTATTTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
13 7 0.23
14 1 0.03
15 14 0.45
16 9 0.29
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATATTTTATATATATT
Found at i:916561 original size:26 final size:26
Alignment explanation
Indices: 916526--916583 Score: 84
Period size: 26 Copynumber: 2.2 Consensus size: 26
916516 ATTTTAATTT
916526 TATATTATA-TTTATATTATTTT-TATA
1 TATATTATATTTTA-ATTATTTTATA-A
916552 TATATTATATTTTAATTATTTTATAA
1 TATATTATATTTTAATTATTTTATAA
916578 TATATT
1 TATATT
916584 CATACATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
26 24 0.80
27 6 0.20
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (26 bp):
TATATTATATTTTAATTATTTTATAA
Found at i:917305 original size:21 final size:23
Alignment explanation
Indices: 917260--917307 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
917250 TTTATATTTA
*
917260 ATATATTAATAATATATAAATTT
1 ATATATTAATAATATATAAAATT
*
917283 ATATATTATTAATA-A-AAAATT
1 ATATATTAATAATATATAAAATT
917304 ATAT
1 ATAT
917308 CACCTCGAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 9 0.39
22 1 0.04
23 13 0.57
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
ATATATTAATAATATATAAAATT
Found at i:917307 original size:31 final size:31
Alignment explanation
Indices: 917242--917307 Score: 73
Period size: 31 Copynumber: 2.1 Consensus size: 31
917232 AAAAATATAC
* *
917242 ATATAAAGTTTATATTTAATATATTAATAAT
1 ATATAAAGTTTATATTTAATATATAAAAAAT
*
917273 ATATAAA-TTTATATATTATTA-ATAAAAAATT
1 ATATAAAGTTTATAT-TTAATATATAAAAAA-T
917304 ATAT
1 ATAT
917308 CACCTCGAGC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
30 13 0.43
31 17 0.57
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (31 bp):
ATATAAAGTTTATATTTAATATATAAAAAAT
Found at i:917621 original size:14 final size:15
Alignment explanation
Indices: 917570--917621 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
917560 ATGTTTTTGG
*
917570 TATATATTAAATATA
1 TATATACTAAATATA
* *
917585 TTTATACTAAAATCATT
1 TATATACT-AAAT-ATA
917602 TATATACT-AATATA
1 TATATACTAAATATA
917616 TATATA
1 TATATA
917622 TTTTATATGT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
14 8 0.27
15 9 0.30
16 4 0.13
17 9 0.30
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (15 bp):
TATATACTAAATATA
Found at i:917626 original size:23 final size:23
Alignment explanation
Indices: 917600--917659 Score: 75
Period size: 25 Copynumber: 2.5 Consensus size: 23
917590 ACTAAAATCA
917600 TTTATATACTAATATATATATAT
1 TTTATATACTAATATATATATAT
**
917623 TTTATATGTGTATATATATATATAT
1 TTTATAT-ACTA-ATATATATATAT
*
917648 TCTATATACTAA
1 TTTATATACTAA
917660 AAAATTTTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
23 8 0.27
24 4 0.13
25 18 0.60
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.52
Consensus pattern (23 bp):
TTTATATACTAATATATATATAT
Found at i:917861 original size:19 final size:19
Alignment explanation
Indices: 917821--917863 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
917811 CTGTTATTTT
*
917821 TAAATTTAATGATAATATA
1 TAAATTTAATGATAATAAA
*
917840 TAAATTTATAT-ATTATAAA
1 TAAATTTA-ATGATAATAAA
917859 TAAAT
1 TAAAT
917864 AAAATATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (19 bp):
TAAATTTAATGATAATAAA
Found at i:919215 original size:2 final size:2
Alignment explanation
Indices: 919195--919241 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
919185 AAAGTTAGCA
* *
919195 AT AT AT A- AT AC AT AC 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
919236 AT AT AT
1 AT AT AT
919242 GAGATTTAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:922717 original size:28 final size:28
Alignment explanation
Indices: 922672--922726 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
922662 ATTACTAGTT
* **
922672 TTGAGTATTTTGGGAGTTCAATGAAAAC
1 TTGAGTATTTAGCAAGTTCAATGAAAAC
*
922700 TTGAGTATTTAGCAAGTTCAATTAAAA
1 TTGAGTATTTAGCAAGTTCAATGAAAA
922727 TTTTGGATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.36, C:0.07, G:0.20, T:0.36
Consensus pattern (28 bp):
TTGAGTATTTAGCAAGTTCAATGAAAAC
Found at i:923998 original size:193 final size:193
Alignment explanation
Indices: 923646--923998 Score: 417
Period size: 193 Copynumber: 1.8 Consensus size: 193
923636 TTGATTGTAG
* *
923646 TTATAAATTTTCAATTTGCATTCTGCACCCTATAGCAAAATTATTTAAGTTTATAAGTGGAAGAG
1 TTATAAATTTTCAATTTGCATTCTGCACCCTATACCAAAATTATTCAAGTTTATAAGTGGAAGAG
* * * * *
923711 CCCAATTTTAGTTACAAATTTTCAATTTGCATGTTAGACCTCGATGCCAATATTATTACAAATGT
66 CCCAATTTTAGTTACAAAATTTCAATTTGCATGTTAGACATCAATACCAATATTAATACAAATGT
* * **
923776 TATAAGTGGGAGATCTTAGGTGCAGTGAGGGCTTGCGATCACGTGGCCCTCATCCAATTTTAA
131 TATAAGTGGGAGAGCCTACATGCAGTGAGGGCTTGCGATCACGTGGCCCTCATCCAATTTTAA
** * *
923839 TTATAAATTTTTTATTTGCATTTTGCACCCTAATACCAATATTATTGCCAA-TGTTATAAGT-G-
1 TTATAAATTTTCAATTTGCATTCTGCACCCT-ATACCAAAATTATT--CAAGT-TTATAAGTGGA
* ** * * * * *
923901 A-AGCCCGATTTTAGTTGTAAAATTTCAATTTGCATTTTATACATTAATACCAATGTTAATGCAA
62 AGAGCCCAATTTTAGTTACAAAATTTCAATTTGCATGTTAGACATCAATACCAATATTAATACAA
* *
923965 ATGTTATACGTGGGAGAGCCTACATGTAGTGAGG
127 ATGTTATAAGTGGGAGAGCCTACATGCAGTGAGG
923999 CCAGCATTTG
Statistics
Matches: 131, Mismatches: 25, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
193 106 0.81
194 13 0.10
195 2 0.02
196 10 0.08
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (193 bp):
TTATAAATTTTCAATTTGCATTCTGCACCCTATACCAAAATTATTCAAGTTTATAAGTGGAAGAG
CCCAATTTTAGTTACAAAATTTCAATTTGCATGTTAGACATCAATACCAATATTAATACAAATGT
TATAAGTGGGAGAGCCTACATGCAGTGAGGGCTTGCGATCACGTGGCCCTCATCCAATTTTAA
Found at i:925878 original size:34 final size:34
Alignment explanation
Indices: 925832--926049 Score: 282
Period size: 34 Copynumber: 6.5 Consensus size: 34
925822 GTAAAAACCA
*
925832 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
925866 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
925900 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
925934 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
925967 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * *
926001 CCATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
926034 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
926050 TCTCCCACTT
Statistics
Matches: 162, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
33 45 0.28
34 115 0.71
35 2 0.01
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:925946 original size:68 final size:67
Alignment explanation
Indices: 925830--926049 Score: 323
Period size: 67 Copynumber: 3.3 Consensus size: 67
925820 TGGTAAAAAC
* * *
925830 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
925895 AT
66 AT
* * *
925897 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
925962 AAT
65 AAT
* * * * * *
925965 CTCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACTAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
926030 AT
66 AT
926032 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
926050 TCTCCCACTT
Statistics
Matches: 136, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
67 75 0.55
68 61 0.45
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:930142 original size:19 final size:19
Alignment explanation
Indices: 930115--930177 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
930105 TCACGTGTAC
* *
930115 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
930134 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
**
930153 AGTACCTATATACGTGAAT
1 AGTACCCGTATACGTGAAT
930172 AGTACC
1 AGTACC
930178 TCGACAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:930529 original size:34 final size:34
Alignment explanation
Indices: 930483--930698 Score: 278
Period size: 34 Copynumber: 6.4 Consensus size: 34
930473 GTAAAAACCA
*
930483 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
930517 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
930551 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
930585 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
930618 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * *
930652 CCATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
930685 CCATTTAATCAACA
1 CCATTTAATCAACA
930699 CCTTTGGGGT
Statistics
Matches: 160, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
33 43 0.27
34 115 0.72
35 2 0.01
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:930597 original size:68 final size:67
Alignment explanation
Indices: 930481--930698 Score: 319
Period size: 67 Copynumber: 3.2 Consensus size: 67
930471 TGGTAAAAAC
* * *
930481 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
930546 AT
66 AT
* * *
930548 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
930613 AAT
65 AAT
* * * * * *
930616 CTCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACTAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
930681 AT
66 AT
930683 CACCATTTAATCAACA
1 CACCATTTAATCAACA
930699 CCTTTGGGGT
Statistics
Matches: 134, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
67 73 0.54
68 61 0.46
ACGTcount: A:0.40, C:0.28, G:0.08, T:0.24
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:931928 original size:20 final size:20
Alignment explanation
Indices: 931883--931928 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 20
931873 TGTAGAAAGA
931883 TGTAGAACGTGTAAGATATTT
1 TGTA-AACGTGTAAGATATTT
931904 T-TAAACGTGTATAGAT-TTT
1 TGTAAACGTGTA-AGATATTT
931923 TGTAAA
1 TGTAAA
931929 TATAAATTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
19 12 0.52
20 10 0.43
21 1 0.04
ACGTcount: A:0.35, C:0.04, G:0.20, T:0.41
Consensus pattern (20 bp):
TGTAAACGTGTAAGATATTT
Found at i:933218 original size:47 final size:47
Alignment explanation
Indices: 933149--933245 Score: 194
Period size: 47 Copynumber: 2.1 Consensus size: 47
933139 ATAATTTGAG
933149 TTGGCTCATTATTATTCTCTATTTTAATCGATAAGGAAGAATAGTTT
1 TTGGCTCATTATTATTCTCTATTTTAATCGATAAGGAAGAATAGTTT
933196 TTGGCTCATTATTATTCTCTATTTTAATCGATAAGGAAGAATAGTTT
1 TTGGCTCATTATTATTCTCTATTTTAATCGATAAGGAAGAATAGTTT
933243 TTG
1 TTG
933246 TTCACAATCT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.29, C:0.10, G:0.15, T:0.45
Consensus pattern (47 bp):
TTGGCTCATTATTATTCTCTATTTTAATCGATAAGGAAGAATAGTTT
Found at i:935276 original size:166 final size:166
Alignment explanation
Indices: 934993--935298 Score: 450
Period size: 166 Copynumber: 1.8 Consensus size: 166
934983 TTGAGCTAAG
* * *
934993 CATGATCGGATGCTTATTGAAACTGATATTTTGAGTTACAAAACTCGGAATATCAATCCCGTAGT
1 CATGATCAGATGCTTATAGAAACTGATATTTTGAGTTACAAAACTCGAAATATCAATCCCGTAGT
* * * * *
935058 CTACATAATTTAGAGATTTATCGGTTAGGTTTGGGAGTTAATTACGTGCAAAGAGGTACGAACTT
66 CTACATAATTTAGAGATTCATCGATTAAGTTTGGGAGTTAAGTACATGCAAAGAGGTACGAACTT
*
935123 TCTTGCGACCTCTGTGGTCTATATAATATCAATGAA
131 TCTCGCGACCTCTGTGGTCTATATAATATCAATGAA
** *
935159 CATGATCAGATGCTTATAGAAACTGATATTTTGAGTTACAAAACTCGAAATATCAATTTCGTGGT
1 CATGATCAGATGCTTATAGAAACTGATATTTTGAGTTACAAAACTCGAAATATCAATCCCGTAGT
* * * ** *
935224 TTACATAATTTAGAGATTCGTTGATTAAGTTTGGGAGTTGGGTACATGCAAAGAGGTATGAACTT
66 CTACATAATTTAGAGATTCATCGATTAAGTTTGGGAGTTAAGTACATGCAAAGAGGTACGAACTT
935289 TCTCGCGACC
131 TCTCGCGACC
935299 CCGAAATCGA
Statistics
Matches: 122, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
166 122 1.00
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.34
Consensus pattern (166 bp):
CATGATCAGATGCTTATAGAAACTGATATTTTGAGTTACAAAACTCGAAATATCAATCCCGTAGT
CTACATAATTTAGAGATTCATCGATTAAGTTTGGGAGTTAAGTACATGCAAAGAGGTACGAACTT
TCTCGCGACCTCTGTGGTCTATATAATATCAATGAA
Found at i:937387 original size:74 final size:73
Alignment explanation
Indices: 937262--937409 Score: 251
Period size: 74 Copynumber: 2.0 Consensus size: 73
937252 CTCAAAATGC
*
937262 ATGAATATGGGCTGTCAGATGATGAAAATGAAACATAGCATTCTAATCACACAAATAGCACCAAA
1 ATGAATATGGGCTGTCAGATGACGAAAATGAAACATAGCATTCTAATCACACAAATAGCACCAAA
937327 ACATCGTA
66 ACATCGTA
* * *
937335 ATGATATATGGGCTGTTAGATGACGAAGATGAAACATGGCATTCTAATCACACAAATAGCACCAA
1 ATGA-ATATGGGCTGTCAGATGACGAAAATGAAACATAGCATTCTAATCACACAAATAGCACCAA
937400 AACATCGTA
65 AACATCGTA
937409 A
1 A
937410 CAATCCTAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
73 4 0.06
74 66 0.94
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.22
Consensus pattern (73 bp):
ATGAATATGGGCTGTCAGATGACGAAAATGAAACATAGCATTCTAATCACACAAATAGCACCAAA
ACATCGTA
Found at i:938376 original size:20 final size:20
Alignment explanation
Indices: 938351--938402 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
938341 CAGTTTAGGC
*
938351 ATGTATCGATACATTCACTT
1 ATGTATCGATACATTCACTA
*
938371 ATGTATTGATACATTCACTA
1 ATGTATCGATACATTCACTA
938391 ATTGTATCGATA
1 A-TGTATCGATA
938403 TAAATTGTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 19 0.68
21 9 0.32
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTCACTA
Found at i:940339 original size:25 final size:25
Alignment explanation
Indices: 940305--940354 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
940295 GCAATGACAC
940305 AGCTAGTGAGGTTCTAACCGAGGCG
1 AGCTAGTGAGGTTCTAACCGAGGCG
940330 AGCTAGTGAGGTTCTAACCGAGGCG
1 AGCTAGTGAGGTTCTAACCGAGGCG
940355 CATCTATTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.20, G:0.36, T:0.20
Consensus pattern (25 bp):
AGCTAGTGAGGTTCTAACCGAGGCG
Found at i:942634 original size:19 final size:21
Alignment explanation
Indices: 942590--942634 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 21
942580 TTATATAATA
942590 CATATTAATTATATATTTTTAT
1 CATATTAA-TATATATTTTTAT
942612 -ATATTAA-ATA-ATTTTTAT
1 CATATTAATATATATTTTTAT
942630 CATAT
1 CATAT
942635 AAAGAATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 8 0.36
19 7 0.32
21 7 0.32
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (21 bp):
CATATTAATATATATTTTTAT
Found at i:944395 original size:44 final size:44
Alignment explanation
Indices: 944332--944419 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
944322 TGGCACACCC
944332 CATCAATTTTAGTTAAATCATTTAAATAGGTTGGTTGAAGATAT
1 CATCAATTTTAGTTAAATCATTTAAATAGGTTGGTTGAAGATAT
944376 CATCAATTTTAGTTAAATCATTTAAATAGGTTGGTTGAAGATAT
1 CATCAATTTTAGTTAAATCATTTAAATAGGTTGGTTGAAGATAT
944420 TACTGTATTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.41
Consensus pattern (44 bp):
CATCAATTTTAGTTAAATCATTTAAATAGGTTGGTTGAAGATAT
Found at i:944646 original size:23 final size:22
Alignment explanation
Indices: 944594--944660 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 22
944584 GATTTTGATT
*
944594 TGAATTTCAAAATTTT-ATATC-
1 TGAATTTAAAAATTTTAAT-TCA
* *
944615 TGAAATTTATAATTTTTAAATTCA
1 TG-AATTTAAAAATTTT-AATTCA
944639 TGAATTTAAAAATTTTAATTCA
1 TGAATTTAAAAATTTTAATTCA
944661 GATAATTAAG
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
21 2 0.05
22 17 0.46
23 14 0.38
24 4 0.11
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (22 bp):
TGAATTTAAAAATTTTAATTCA
Found at i:946115 original size:48 final size:48
Alignment explanation
Indices: 946044--946181 Score: 249
Period size: 48 Copynumber: 2.9 Consensus size: 48
946034 CTATTTCACG
* *
946044 TGACTTTTTAACGGTATTAAGTTGATTGTTGATGGAATAAAATTCTGA
1 TGACTTTTTAACAGTGTTAAGTTGATTGTTGATGGAATAAAATTCTGA
946092 TGACTTTTTAACAGTGTTAAGTTGATTGTTGATGGAATAAAATTCTGA
1 TGACTTTTTAACAGTGTTAAGTTGATTGTTGATGGAATAAAATTCTGA
*
946140 TAACTTTTTAACAGTGTTAAGTTGATTGTTGATGGAATAAAA
1 TGACTTTTTAACAGTGTTAAGTTGATTGTTGATGGAATAAAA
946182 GTACATGAGA
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
48 87 1.00
ACGTcount: A:0.33, C:0.06, G:0.20, T:0.41
Consensus pattern (48 bp):
TGACTTTTTAACAGTGTTAAGTTGATTGTTGATGGAATAAAATTCTGA
Found at i:948858 original size:51 final size:51
Alignment explanation
Indices: 948782--948884 Score: 179
Period size: 51 Copynumber: 2.0 Consensus size: 51
948772 GACATAAAAG
*
948782 GACCACATAAAACTATTTTAAATTTACAACGAATCAGGCTTTTATTGGTGA
1 GACCACATAAAACTATTTTAAATTTACAACAAATCAGGCTTTTATTGGTGA
* *
948833 GACCACATAAAACTATTTTAAATTTATAACAAATTAGGCTTTTATTGGTGA
1 GACCACATAAAACTATTTTAAATTTACAACAAATCAGGCTTTTATTGGTGA
948884 G
1 G
948885 GTGTGCCAGG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.35
Consensus pattern (51 bp):
GACCACATAAAACTATTTTAAATTTACAACAAATCAGGCTTTTATTGGTGA
Found at i:950296 original size:77 final size:77
Alignment explanation
Indices: 950161--950315 Score: 276
Period size: 77 Copynumber: 2.0 Consensus size: 77
950151 CATGTTGAAA
*
950161 TATCTGTTTTTGCCAACATGTCATTCATGATATTCCTTCCATTTCTTGTTTTCTAATTACATTAC
1 TATCTGTTTTTGCCAACATGTCATTCATGATATTCCTTCCATTTCTTGTTTTCCAATTACATTAC
950226 CCCAAGCTTTAC
66 CCCAAGCTTTAC
*
950238 TATCTGTTTTTGCCAACATGTCATTCATGATATTCCTTCTATTTCTT-TTTGTCCAATTACATTA
1 TATCTGTTTTTGCCAACATGTCATTCATGATATTCCTTCCATTTCTTGTTT-TCCAATTACATTA
950302 CCCCAAGCTTTAC
65 CCCCAAGCTTTAC
950315 T
1 T
950316 TCGCTATTTC
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
76 3 0.04
77 72 0.96
ACGTcount: A:0.22, C:0.25, G:0.08, T:0.46
Consensus pattern (77 bp):
TATCTGTTTTTGCCAACATGTCATTCATGATATTCCTTCCATTTCTTGTTTTCCAATTACATTAC
CCCAAGCTTTAC
Found at i:950548 original size:27 final size:22
Alignment explanation
Indices: 950490--950534 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
950480 ATATTATGGG
950490 ATGCTTTAAAATATAAAATAAC
1 ATGCTTTAAAATATAAAATAAC
950512 ATGCTTTAAAATATAAAATAAC
1 ATGCTTTAAAATATAAAATAAC
950534 A
1 A
950535 ACTCTCAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.56, C:0.09, G:0.04, T:0.31
Consensus pattern (22 bp):
ATGCTTTAAAATATAAAATAAC
Found at i:950609 original size:77 final size:77
Alignment explanation
Indices: 950512--950663 Score: 270
Period size: 77 Copynumber: 2.0 Consensus size: 77
950502 ATAAAATAAC
950512 ATGCTTTAAAATATAAAATAACAACTCTCAATTTAAATAATTAAACTATTATT-GATGAGGTGCA
1 ATGCTTTAAAATATAAAATAACAACTCTCAATTTAAATAATTAAACTATTATTGGA-GAGGTGCA
950576 CCAAATCCATGGG
65 CCAAATCCATGGG
* *
950589 ATGCTTTAAAATATAAAATAACAACTCTCAATTTAAATAATTAAACTATTATTGGAGGGGTGCGC
1 ATGCTTTAAAATATAAAATAACAACTCTCAATTTAAATAATTAAACTATTATTGGAGAGGTGCAC
950654 CAAATCCATG
66 CAAATCCATG
950664 CAGTAGTGCA
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
77 70 0.97
78 2 0.03
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.31
Consensus pattern (77 bp):
ATGCTTTAAAATATAAAATAACAACTCTCAATTTAAATAATTAAACTATTATTGGAGAGGTGCAC
CAAATCCATGGG
Found at i:953157 original size:13 final size:13
Alignment explanation
Indices: 953141--953175 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
953131 AAGAAATCAA
*
953141 AAAAATCAAAAAG
1 AAAAATAAAAAAG
*
953154 AAAAATAAAAAAT
1 AAAAATAAAAAAG
953167 AAAAATAAA
1 AAAAATAAA
953176 TAAATAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.83, C:0.03, G:0.03, T:0.11
Consensus pattern (13 bp):
AAAAATAAAAAAG
Found at i:953165 original size:8 final size:8
Alignment explanation
Indices: 953105--953198 Score: 50
Period size: 8 Copynumber: 11.1 Consensus size: 8
953095 AAGACATTTT
953105 AAAAAATA
1 AAAAAATA
*
953113 AAAATTATTA
1 AAAA--AATA
953123 AAAAAA-A
1 AAAAAATA
*
953130 CAAGAAATCA
1 -AAAAAAT-A
953140 AAAAAATCA
1 AAAAAAT-A
953149 AAAAGAA-A
1 AAAA-AATA
953157 AATAAAA-A
1 AA-AAAATA
953165 ATAAAAATA
1 A-AAAAATA
*
953174 AATAAATA
1 AAAAAATA
*
953182 AATAAATA
1 AAAAAATA
*
953190 AATAAATA
1 AAAAAATA
953198 A
1 A
953199 TACAAATAAT
Statistics
Matches: 72, Mismatches: 5, Indels: 18
0.76 0.05 0.19
Matches are distributed among these distances:
7 1 0.01
8 44 0.61
9 17 0.24
10 10 0.14
ACGTcount: A:0.78, C:0.03, G:0.02, T:0.17
Consensus pattern (8 bp):
AAAAAATA
Found at i:953178 original size:4 final size:4
Alignment explanation
Indices: 953156--953198 Score: 65
Period size: 4 Copynumber: 11.5 Consensus size: 4
953146 TCAAAAAGAA
953156 AAAT AAA- AAAT -AA- AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
953199 TACAAATAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
3 7 0.19
4 29 0.81
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:953331 original size:6 final size:6
Alignment explanation
Indices: 953320--953347 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
953310 AATTGAAAAC
953320 CCAAAT CCAAAT CCAAAT CCAAAT CCAA
1 CCAAAT CCAAAT CCAAAT CCAAAT CCAA
953348 TTATTTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.36, G:0.00, T:0.14
Consensus pattern (6 bp):
CCAAAT
Found at i:954251 original size:39 final size:39
Alignment explanation
Indices: 954143--954254 Score: 100
Period size: 39 Copynumber: 2.8 Consensus size: 39
954133 CAATGCATTT
* * * * *
954143 TATTAGTGCAAATGCTATATATACGAGTAACTACCTACCTTA
1 TATTATTGCAAATGCTATATTTACAAGTAA--A-TTACCCTA
* * * * *
954185 TATT-TTGTAAATGCAACAGTTATAAGTAAATTACCCTA
1 TATTATTGCAAATGCTATATTTACAAGTAAATTACCCTA
954223 TATTATTGCAAATGCTATATTTACAAGTAAAT
1 TATTATTGCAAATGCTATATTTACAAGTAAAT
954255 AAATATATAA
Statistics
Matches: 54, Mismatches: 15, Indels: 5
0.73 0.20 0.07
Matches are distributed among these distances:
38 10 0.19
39 23 0.43
41 17 0.31
42 4 0.07
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (39 bp):
TATTATTGCAAATGCTATATTTACAAGTAAATTACCCTA
Found at i:954649 original size:2 final size:2
Alignment explanation
Indices: 954642--954671 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
954632 GAAAATATCA
*
954642 AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
954672 GCACACACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:954781 original size:22 final size:23
Alignment explanation
Indices: 954743--954787 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
954733 ATAATATAAA
954743 AAATAAATAATTATTTTA-AATT
1 AAATAAATAATTATTTTATAATT
*
954765 AAATAAAATGATT-TTTTATAATT
1 AAAT-AAATAATTATTTTATAATT
954788 TTATATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
AAATAAATAATTATTTTATAATT
Found at i:957138 original size:76 final size:76
Alignment explanation
Indices: 957012--957163 Score: 304
Period size: 76 Copynumber: 2.0 Consensus size: 76
957002 GGTTGATGAA
957012 TTTACGACCTTGTGATCAGAGCGTGATTAACCTCTTCAATAGGTGAAACCTTGTGAACCCCATTG
1 TTTACGACCTTGTGATCAGAGCGTGATTAACCTCTTCAATAGGTGAAACCTTGTGAACCCCATTG
957077 GAGTACTAGAG
66 GAGTACTAGAG
957088 TTTACGACCTTGTGATCAGAGCGTGATTAACCTCTTCAATAGGTGAAACCTTGTGAACCCCATTG
1 TTTACGACCTTGTGATCAGAGCGTGATTAACCTCTTCAATAGGTGAAACCTTGTGAACCCCATTG
957153 GAGTACTAGAG
66 GAGTACTAGAG
957164 GATCGTTCTC
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (76 bp):
TTTACGACCTTGTGATCAGAGCGTGATTAACCTCTTCAATAGGTGAAACCTTGTGAACCCCATTG
GAGTACTAGAG
Found at i:959287 original size:16 final size:17
Alignment explanation
Indices: 959266--959298 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
959256 TTGATAGATA
959266 TTAAAAAATTA-ATTTT
1 TTAAAAAATTATATTTT
959282 TTAAAAAATTATATTTT
1 TTAAAAAATTATATTTT
959299 AAATTTTACC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTAAAAAATTATATTTT
Found at i:959327 original size:53 final size:53
Alignment explanation
Indices: 959270--959373 Score: 190
Period size: 53 Copynumber: 2.0 Consensus size: 53
959260 TAGATATTAA
959270 AAAATTAATTTTTTAAAAAATTATATTTTAAATTTTACCACGAAATCACTTAG
1 AAAATTAATTTTTTAAAAAATTATATTTTAAATTTTACCACGAAATCACTTAG
* *
959323 AAAATTAATTTTTTTAAAAATTATGTTTTAAATTTTACCACGAAATCACTT
1 AAAATTAATTTTTTAAAAAATTATATTTTAAATTTTACCACGAAATCACTT
959374 TTAACCATAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.43
Consensus pattern (53 bp):
AAAATTAATTTTTTAAAAAATTATATTTTAAATTTTACCACGAAATCACTTAG
Found at i:959559 original size:52 final size:52
Alignment explanation
Indices: 959481--959585 Score: 192
Period size: 52 Copynumber: 2.0 Consensus size: 52
959471 TTTATTGGTG
*
959481 GGATTTGACAAGACCATGCTTTGGTGTAACACCTCAAGAACCCCAATAGCAA
1 GGATTTGACAAGACCATGCTATGGTGTAACACCTCAAGAACCCCAATAGCAA
*
959533 GGATTTGACAAGACCATGCTATGGTGTAACACCTCAAGAACTCCAATAGCAA
1 GGATTTGACAAGACCATGCTATGGTGTAACACCTCAAGAACCCCAATAGCAA
959585 G
1 G
959586 CTACTATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (52 bp):
GGATTTGACAAGACCATGCTATGGTGTAACACCTCAAGAACCCCAATAGCAA
Found at i:960626 original size:14 final size:14
Alignment explanation
Indices: 960607--960634 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
960597 TATATTAGTA
960607 TTTTCTATTCTATT
1 TTTTCTATTCTATT
960621 TTTTCTATTCTATT
1 TTTTCTATTCTATT
960635 AGTATTAGAT
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:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTCTATTCTATT
Found at i:960642 original size:6 final size:6
Alignment explanation
Indices: 960631--960681 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
960621 TTTTCTATTC
* *
960631 TATTAG TATTAG -ATTAG TATTA- TATT-C TATTGG TATTAG -ATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
960675 TATTAG T
1 TATTAG T
960682 TAGTAATCTC
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
5 18 0.46
6 21 0.54
ACGTcount: A:0.31, C:0.02, G:0.16, T:0.51
Consensus pattern (6 bp):
TATTAG
Found at i:960656 original size:27 final size:27
Alignment explanation
Indices: 960626--960679 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
960616 CTATTTTTTC
960626 TATTCTATTAGTATTAGATTAGTATTA
1 TATTCTATTAGTATTAGATTAGTATTA
*
960653 TATTCTATTGGTATTAGATTAGTATTA
1 TATTCTATTAGTATTAGATTAGTATTA
960680 GTTAGTAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.31, C:0.04, G:0.13, T:0.52
Consensus pattern (27 bp):
TATTCTATTAGTATTAGATTAGTATTA
Found at i:962889 original size:51 final size:51
Alignment explanation
Indices: 962813--962915 Score: 179
Period size: 51 Copynumber: 2.0 Consensus size: 51
962803 GACATAAAAG
*
962813 GACCACATAAAACTATTTTAAATTTACAACGAATCAGGCTTTTATTGGTGA
1 GACCACATAAAACTATTTTAAATTTACAACAAATCAGGCTTTTATTGGTGA
* *
962864 GACCACATAAAACTATTTTAAATTTATAACAAATTAGGCTTTTATTGGTGA
1 GACCACATAAAACTATTTTAAATTTACAACAAATCAGGCTTTTATTGGTGA
962915 G
1 G
962916 GTGTGCCAGG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.35
Consensus pattern (51 bp):
GACCACATAAAACTATTTTAAATTTACAACAAATCAGGCTTTTATTGGTGA
Found at i:964326 original size:77 final size:77
Alignment explanation
Indices: 964191--964345 Score: 276
Period size: 77 Copynumber: 2.0 Consensus size: 77
964181 CATGTTGAAA
*
964191 TATCTGTTTTTGCCAACATGTCATTCATGATATTCCTTCCATTTCTTGTTTTCTAATTACATTAC
1 TATCTGTTTTTGCCAACATGTCATTCATGATATTCCTTCCATTTCTTGTTTTCCAATTACATTAC
964256 CCCAAGCTTTAC
66 CCCAAGCTTTAC
*
964268 TATCTGTTTTTGCCAACATGTCATTCATGATATTCCTTCTATTTCTT-TTTGTCCAATTACATTA
1 TATCTGTTTTTGCCAACATGTCATTCATGATATTCCTTCCATTTCTTGTTT-TCCAATTACATTA
964332 CCCCAAGCTTTAC
65 CCCCAAGCTTTAC
964345 T
1 T
964346 TCGCTATTTC
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
76 3 0.04
77 72 0.96
ACGTcount: A:0.22, C:0.25, G:0.08, T:0.46
Consensus pattern (77 bp):
TATCTGTTTTTGCCAACATGTCATTCATGATATTCCTTCCATTTCTTGTTTTCCAATTACATTAC
CCCAAGCTTTAC
Found at i:964578 original size:27 final size:22
Alignment explanation
Indices: 964520--964564 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
964510 ATATTATGGG
964520 ATGCTTTAAAATATAAAATAAC
1 ATGCTTTAAAATATAAAATAAC
964542 ATGCTTTAAAATATAAAATAAC
1 ATGCTTTAAAATATAAAATAAC
964564 A
1 A
964565 ACTCTCAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.56, C:0.09, G:0.04, T:0.31
Consensus pattern (22 bp):
ATGCTTTAAAATATAAAATAAC
Found at i:964639 original size:77 final size:77
Alignment explanation
Indices: 964542--964693 Score: 270
Period size: 77 Copynumber: 2.0 Consensus size: 77
964532 ATAAAATAAC
964542 ATGCTTTAAAATATAAAATAACAACTCTCAATTTAAATAATTAAACTATTATT-GATGAGGTGCA
1 ATGCTTTAAAATATAAAATAACAACTCTCAATTTAAATAATTAAACTATTATTGGA-GAGGTGCA
964606 CCAAATCCATGGG
65 CCAAATCCATGGG
* *
964619 ATGCTTTAAAATATAAAATAACAACTCTCAATTTAAATAATTAAACTATTATTGGAGGGGTGCGC
1 ATGCTTTAAAATATAAAATAACAACTCTCAATTTAAATAATTAAACTATTATTGGAGAGGTGCAC
964684 CAAATCCATG
66 CAAATCCATG
964694 CAGTAGTGCA
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
77 70 0.97
78 2 0.03
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.31
Consensus pattern (77 bp):
ATGCTTTAAAATATAAAATAACAACTCTCAATTTAAATAATTAAACTATTATTGGAGAGGTGCAC
CAAATCCATGGG
Found at i:965812 original size:2 final size:2
Alignment explanation
Indices: 965807--965831 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
965797 TTATCTTATG
965807 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 A
965832 CCGAAATAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:967194 original size:13 final size:13
Alignment explanation
Indices: 967178--967212 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
967168 AAGAAATCAA
*
967178 AAAAATCAAAAAG
1 AAAAATAAAAAAG
*
967191 AAAAATAAAAAAT
1 AAAAATAAAAAAG
967204 AAAAATAAA
1 AAAAATAAA
967213 TAAATAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.83, C:0.03, G:0.03, T:0.11
Consensus pattern (13 bp):
AAAAATAAAAAAG
Found at i:967202 original size:8 final size:8
Alignment explanation
Indices: 967142--967235 Score: 50
Period size: 8 Copynumber: 11.1 Consensus size: 8
967132 AAGACATTTT
967142 AAAAAATA
1 AAAAAATA
*
967150 AAAATTATTA
1 AAAA--AATA
967160 AAAAAA-A
1 AAAAAATA
*
967167 CAAGAAATCA
1 -AAAAAAT-A
967177 AAAAAATCA
1 AAAAAAT-A
967186 AAAAGAA-A
1 AAAA-AATA
967194 AATAAAA-A
1 AA-AAAATA
967202 ATAAAAATA
1 A-AAAAATA
*
967211 AATAAATA
1 AAAAAATA
*
967219 AATAAATA
1 AAAAAATA
*
967227 AATAAATA
1 AAAAAATA
967235 A
1 A
967236 TACAAATAAT
Statistics
Matches: 72, Mismatches: 5, Indels: 18
0.76 0.05 0.19
Matches are distributed among these distances:
7 1 0.01
8 44 0.61
9 17 0.24
10 10 0.14
ACGTcount: A:0.78, C:0.03, G:0.02, T:0.17
Consensus pattern (8 bp):
AAAAAATA
Found at i:967215 original size:4 final size:4
Alignment explanation
Indices: 967193--967235 Score: 65
Period size: 4 Copynumber: 11.5 Consensus size: 4
967183 TCAAAAAGAA
967193 AAAT AAA- AAAT -AA- AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
967236 TACAAATAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
3 7 0.19
4 29 0.81
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:967502 original size:2 final size:2
Alignment explanation
Indices: 967495--967519 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
967485 AACATCCATT
967495 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 T
967520 GTAGATCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:970639 original size:22 final size:23
Alignment explanation
Indices: 970588--970646 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 23
970578 AGCACCCTTC
*
970588 AAAATTTTATA-T-ATGAAATTT
1 AAAATTTTAAATTCATGAAATTT
*
970609 ATAATTTTTAAATTCATG-AATTT
1 A-AAATTTTAAATTCATGAAATTT
*
970632 AAAATTTTTAATTCA
1 AAAATTTTAAATTCA
970647 GATAATTAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
21 1 0.03
22 20 0.65
23 7 0.23
24 3 0.10
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (23 bp):
AAAATTTTAAATTCATGAAATTT
Found at i:970653 original size:23 final size:23
Alignment explanation
Indices: 970604--970646 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
970594 TTATATATGA
*
970604 AATTTATAATTTTTAAATTCATG
1 AATTTAAAATTTTTAAATTCATG
970627 AATTTAAAATTTTT-AATTCA
1 AATTTAAAATTTTTAAATTCA
970647 GATAATTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (23 bp):
AATTTAAAATTTTTAAATTCATG
Found at i:970655 original size:22 final size:23
Alignment explanation
Indices: 970600--970660 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
970590 AATTTTATAT
*
970600 ATGAAATTTATAATTTTTAAATTC
1 ATGAAA-TTAAAATTTTTAAATTC
*
970624 ATGAATTTAAAATTTTT-AATTC
1 ATGAAATTAAAATTTTTAAATTC
*
970646 A-GATAATTAAGATTT
1 ATGA-AATTAAAATTT
970661 GGATTTAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 2 0.06
22 15 0.47
23 10 0.31
24 5 0.16
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.48
Consensus pattern (23 bp):
ATGAAATTAAAATTTTTAAATTC
Found at i:971861 original size:39 final size:39
Alignment explanation
Indices: 971753--971864 Score: 100
Period size: 39 Copynumber: 2.8 Consensus size: 39
971743 CAATGCATTT
* * * * *
971753 TATTAGTGCAAATGCTATATATACGAGTAACTACCTACCTTA
1 TATTATTGCAAATGCTATATTTACAAGTAA--A-TTACCCTA
* * * * *
971795 TATT-TTGTAAATGCAACAGTTATAAGTAAATTACCCTA
1 TATTATTGCAAATGCTATATTTACAAGTAAATTACCCTA
971833 TATTATTGCAAATGCTATATTTACAAGTAAAT
1 TATTATTGCAAATGCTATATTTACAAGTAAAT
971865 AAATATATAA
Statistics
Matches: 54, Mismatches: 15, Indels: 5
0.73 0.20 0.07
Matches are distributed among these distances:
38 10 0.19
39 23 0.43
41 17 0.31
42 4 0.07
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (39 bp):
TATTATTGCAAATGCTATATTTACAAGTAAATTACCCTA
Found at i:972389 original size:22 final size:23
Alignment explanation
Indices: 972351--972395 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
972341 ATAATATAAA
972351 AAATAAATAATTATTTTA-AATT
1 AAATAAATAATTATTTTATAATT
*
972373 AAATAAAATGATT-TTTTATAATT
1 AAAT-AAATAATTATTTTATAATT
972396 TTATATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
AAATAAATAATTATTTTATAATT
Found at i:976821 original size:16 final size:17
Alignment explanation
Indices: 976800--976832 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
976790 TTGATAGATA
976800 TTAAAAAATTA-ATTTT
1 TTAAAAAATTATATTTT
976816 TTAAAAAATTATATTTT
1 TTAAAAAATTATATTTT
976833 AAATTTTACC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTAAAAAATTATATTTT
Found at i:976861 original size:53 final size:53
Alignment explanation
Indices: 976804--976907 Score: 190
Period size: 53 Copynumber: 2.0 Consensus size: 53
976794 TAGATATTAA
976804 AAAATTAATTTTTTAAAAAATTATATTTTAAATTTTACCACGAAATCACTTAG
1 AAAATTAATTTTTTAAAAAATTATATTTTAAATTTTACCACGAAATCACTTAG
* *
976857 AAAATTAATTTTTTTAAAAATTATGTTTTAAATTTTACCACGAAATCACTT
1 AAAATTAATTTTTTAAAAAATTATATTTTAAATTTTACCACGAAATCACTT
976908 TTAACCATAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.43
Consensus pattern (53 bp):
AAAATTAATTTTTTAAAAAATTATATTTTAAATTTTACCACGAAATCACTTAG
Found at i:977093 original size:52 final size:52
Alignment explanation
Indices: 977015--977119 Score: 192
Period size: 52 Copynumber: 2.0 Consensus size: 52
977005 TTTATTGGTG
*
977015 GGATTTGACAAGACCATGCTTTGGTGTAACACCTCAAGAACCCCAATAGCAA
1 GGATTTGACAAGACCATGCTATGGTGTAACACCTCAAGAACCCCAATAGCAA
*
977067 GGATTTGACAAGACCATGCTATGGTGTAACACCTCAAGAACTCCAATAGCAA
1 GGATTTGACAAGACCATGCTATGGTGTAACACCTCAAGAACCCCAATAGCAA
977119 G
1 G
977120 CTACTATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (52 bp):
GGATTTGACAAGACCATGCTATGGTGTAACACCTCAAGAACCCCAATAGCAA
Found at i:978158 original size:14 final size:14
Alignment explanation
Indices: 978139--978166 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
978129 TATATTAGTA
978139 TTTTCTATTCTATT
1 TTTTCTATTCTATT
978153 TTTTCTATTCTATT
1 TTTTCTATTCTATT
978167 AGTATTAGAT
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:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTCTATTCTATT
Found at i:978174 original size:6 final size:6
Alignment explanation
Indices: 978163--978213 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
978153 TTTTCTATTC
* *
978163 TATTAG TATTAG -ATTAG TATTA- TATT-C TATTGG TATTAG -ATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
978207 TATTAG T
1 TATTAG T
978214 TAGTAATCTC
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
5 18 0.46
6 21 0.54
ACGTcount: A:0.31, C:0.02, G:0.16, T:0.51
Consensus pattern (6 bp):
TATTAG
Found at i:978188 original size:27 final size:27
Alignment explanation
Indices: 978158--978211 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
978148 CTATTTTTTC
978158 TATTCTATTAGTATTAGATTAGTATTA
1 TATTCTATTAGTATTAGATTAGTATTA
*
978185 TATTCTATTGGTATTAGATTAGTATTA
1 TATTCTATTAGTATTAGATTAGTATTA
978212 GTTAGTAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.31, C:0.04, G:0.13, T:0.52
Consensus pattern (27 bp):
TATTCTATTAGTATTAGATTAGTATTA
Found at i:980505 original size:51 final size:51
Alignment explanation
Indices: 980429--980531 Score: 179
Period size: 51 Copynumber: 2.0 Consensus size: 51
980419 GACATAAAAG
*
980429 GACCACATAAAACTATTTTAAATTTACAACGAATCAGGCTTTTATTGGTGA
1 GACCACATAAAACTATTTTAAATTTACAACAAATCAGGCTTTTATTGGTGA
* *
980480 GACCACATAAAACTATTTTAAATTTATAACAAATTAGGCTTTTATTGGTGA
1 GACCACATAAAACTATTTTAAATTTACAACAAATCAGGCTTTTATTGGTGA
980531 G
1 G
980532 GTGTGCCAGG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.35
Consensus pattern (51 bp):
GACCACATAAAACTATTTTAAATTTACAACAAATCAGGCTTTTATTGGTGA
Found at i:981939 original size:77 final size:77
Alignment explanation
Indices: 981804--981958 Score: 276
Period size: 77 Copynumber: 2.0 Consensus size: 77
981794 CATGTTGAAA
*
981804 TATCTGTTTTTGCCAACATGTCATTCATGATATTCCTTCCATTTCTTGTTTTCTAATTACATTAC
1 TATCTGTTTTTGCCAACATGTCATTCATGATATTCCTTCCATTTCTTGTTTTCCAATTACATTAC
981869 CCCAAGCTTTAC
66 CCCAAGCTTTAC
*
981881 TATCTGTTTTTGCCAACATGTCATTCATGATATTCCTTCTATTTCTT-TTTGTCCAATTACATTA
1 TATCTGTTTTTGCCAACATGTCATTCATGATATTCCTTCCATTTCTTGTTT-TCCAATTACATTA
981945 CCCCAAGCTTTAC
65 CCCCAAGCTTTAC
981958 T
1 T
981959 TCGCTATTTC
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
76 3 0.04
77 72 0.96
ACGTcount: A:0.22, C:0.25, G:0.08, T:0.46
Consensus pattern (77 bp):
TATCTGTTTTTGCCAACATGTCATTCATGATATTCCTTCCATTTCTTGTTTTCCAATTACATTAC
CCCAAGCTTTAC
Found at i:982191 original size:27 final size:22
Alignment explanation
Indices: 982133--982177 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
982123 ATATTATGGG
982133 ATGCTTTAAAATATAAAATAAC
1 ATGCTTTAAAATATAAAATAAC
982155 ATGCTTTAAAATATAAAATAAC
1 ATGCTTTAAAATATAAAATAAC
982177 A
1 A
982178 ACTCTCAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.56, C:0.09, G:0.04, T:0.31
Consensus pattern (22 bp):
ATGCTTTAAAATATAAAATAAC
Found at i:982252 original size:77 final size:77
Alignment explanation
Indices: 982155--982306 Score: 270
Period size: 77 Copynumber: 2.0 Consensus size: 77
982145 ATAAAATAAC
982155 ATGCTTTAAAATATAAAATAACAACTCTCAATTTAAATAATTAAACTATTATT-GATGAGGTGCA
1 ATGCTTTAAAATATAAAATAACAACTCTCAATTTAAATAATTAAACTATTATTGGA-GAGGTGCA
982219 CCAAATCCATGGG
65 CCAAATCCATGGG
* *
982232 ATGCTTTAAAATATAAAATAACAACTCTCAATTTAAATAATTAAACTATTATTGGAGGGGTGCGC
1 ATGCTTTAAAATATAAAATAACAACTCTCAATTTAAATAATTAAACTATTATTGGAGAGGTGCAC
982297 CAAATCCATG
66 CAAATCCATG
982307 CAGTAGTGCA
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
77 70 0.97
78 2 0.03
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.31
Consensus pattern (77 bp):
ATGCTTTAAAATATAAAATAACAACTCTCAATTTAAATAATTAAACTATTATTGGAGAGGTGCAC
CAAATCCATGGG
Found at i:984810 original size:13 final size:13
Alignment explanation
Indices: 984794--984828 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
984784 AAGAAATCAA
*
984794 AAAAATCAAAAAG
1 AAAAATAAAAAAG
*
984807 AAAAATAAAAAAT
1 AAAAATAAAAAAG
984820 AAAAATAAA
1 AAAAATAAA
984829 TAAATAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.83, C:0.03, G:0.03, T:0.11
Consensus pattern (13 bp):
AAAAATAAAAAAG
Found at i:984818 original size:8 final size:8
Alignment explanation
Indices: 984758--984851 Score: 50
Period size: 8 Copynumber: 11.1 Consensus size: 8
984748 AAGACATTTT
984758 AAAAAATA
1 AAAAAATA
*
984766 AAAATTATTA
1 AAAA--AATA
984776 AAAAAA-A
1 AAAAAATA
*
984783 CAAGAAATCA
1 -AAAAAAT-A
984793 AAAAAATCA
1 AAAAAAT-A
984802 AAAAGAA-A
1 AAAA-AATA
984810 AATAAAA-A
1 AA-AAAATA
984818 ATAAAAATA
1 A-AAAAATA
*
984827 AATAAATA
1 AAAAAATA
*
984835 AATAAATA
1 AAAAAATA
*
984843 AATAAATA
1 AAAAAATA
984851 A
1 A
984852 TACAAATAAT
Statistics
Matches: 72, Mismatches: 5, Indels: 18
0.76 0.05 0.19
Matches are distributed among these distances:
7 1 0.01
8 44 0.61
9 17 0.24
10 10 0.14
ACGTcount: A:0.78, C:0.03, G:0.02, T:0.17
Consensus pattern (8 bp):
AAAAAATA
Found at i:984831 original size:4 final size:4
Alignment explanation
Indices: 984809--984851 Score: 65
Period size: 4 Copynumber: 11.5 Consensus size: 4
984799 TCAAAAAGAA
984809 AAAT AAA- AAAT -AA- AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
984852 TACAAATAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
3 7 0.19
4 29 0.81
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:985119 original size:2 final size:2
Alignment explanation
Indices: 985112--985136 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
985102 AACATCCATT
985112 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 T
985137 GTAGATCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:988256 original size:22 final size:23
Alignment explanation
Indices: 988205--988263 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 23
988195 AGCACCCTTC
*
988205 AAAATTTTATA-T-ATGAAATTT
1 AAAATTTTAAATTCATGAAATTT
*
988226 ATAATTTTTAAATTCATG-AATTT
1 A-AAATTTTAAATTCATGAAATTT
*
988249 AAAATTTTTAATTCA
1 AAAATTTTAAATTCA
988264 GATAATTAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
21 1 0.03
22 20 0.65
23 7 0.23
24 3 0.10
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (23 bp):
AAAATTTTAAATTCATGAAATTT
Found at i:988270 original size:23 final size:23
Alignment explanation
Indices: 988221--988263 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
988211 TTATATATGA
*
988221 AATTTATAATTTTTAAATTCATG
1 AATTTAAAATTTTTAAATTCATG
988244 AATTTAAAATTTTT-AATTCA
1 AATTTAAAATTTTTAAATTCA
988264 GATAATTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (23 bp):
AATTTAAAATTTTTAAATTCATG
Found at i:988272 original size:22 final size:23
Alignment explanation
Indices: 988217--988277 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
988207 AATTTTATAT
*
988217 ATGAAATTTATAATTTTTAAATTC
1 ATGAAA-TTAAAATTTTTAAATTC
*
988241 ATGAATTTAAAATTTTT-AATTC
1 ATGAAATTAAAATTTTTAAATTC
*
988263 A-GATAATTAAGATTT
1 ATGA-AATTAAAATTT
988278 GGATTTAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 2 0.06
22 15 0.47
23 10 0.31
24 5 0.16
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.48
Consensus pattern (23 bp):
ATGAAATTAAAATTTTTAAATTC
Found at i:989478 original size:39 final size:39
Alignment explanation
Indices: 989370--989481 Score: 100
Period size: 39 Copynumber: 2.8 Consensus size: 39
989360 CAATGCATTT
* * * * *
989370 TATTAGTGCAAATGCTATATATACGAGTAACTACCTACCTTA
1 TATTATTGCAAATGCTATATTTACAAGTAA--A-TTACCCTA
* * * * *
989412 TATT-TTGTAAATGCAACAGTTATAAGTAAATTACCCTA
1 TATTATTGCAAATGCTATATTTACAAGTAAATTACCCTA
989450 TATTATTGCAAATGCTATATTTACAAGTAAAT
1 TATTATTGCAAATGCTATATTTACAAGTAAAT
989482 AAATATATAA
Statistics
Matches: 54, Mismatches: 15, Indels: 5
0.73 0.20 0.07
Matches are distributed among these distances:
38 10 0.19
39 23 0.43
41 17 0.31
42 4 0.07
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (39 bp):
TATTATTGCAAATGCTATATTTACAAGTAAATTACCCTA
Found at i:990007 original size:22 final size:23
Alignment explanation
Indices: 989969--990013 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
989959 ATAATATAAA
989969 AAATAAATAATTATTTTA-AATT
1 AAATAAATAATTATTTTATAATT
*
989991 AAATAAAATGATT-TTTTATAATT
1 AAAT-AAATAATTATTTTATAATT
990014 TTATATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
AAATAAATAATTATTTTATAATT
Found at i:994439 original size:16 final size:17
Alignment explanation
Indices: 994418--994450 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
994408 TTGATAGATA
994418 TTAAAAAATTA-ATTTT
1 TTAAAAAATTATATTTT
994434 TTAAAAAATTATATTTT
1 TTAAAAAATTATATTTT
994451 AAATTTTACC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTAAAAAATTATATTTT
Found at i:994479 original size:53 final size:53
Alignment explanation
Indices: 994422--994525 Score: 190
Period size: 53 Copynumber: 2.0 Consensus size: 53
994412 TAGATATTAA
994422 AAAATTAATTTTTTAAAAAATTATATTTTAAATTTTACCACGAAATCACTTAG
1 AAAATTAATTTTTTAAAAAATTATATTTTAAATTTTACCACGAAATCACTTAG
* *
994475 AAAATTAATTTTTTTAAAAATTATGTTTTAAATTTTACCACGAAATCACTT
1 AAAATTAATTTTTTAAAAAATTATATTTTAAATTTTACCACGAAATCACTT
994526 TTAACCATAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.43
Consensus pattern (53 bp):
AAAATTAATTTTTTAAAAAATTATATTTTAAATTTTACCACGAAATCACTTAG
Found at i:994711 original size:52 final size:52
Alignment explanation
Indices: 994633--994737 Score: 192
Period size: 52 Copynumber: 2.0 Consensus size: 52
994623 TTTATTGGTG
*
994633 GGATTTGACAAGACCATGCTTTGGTGTAACACCTCAAGAACCCCAATAGCAA
1 GGATTTGACAAGACCATGCTATGGTGTAACACCTCAAGAACCCCAATAGCAA
*
994685 GGATTTGACAAGACCATGCTATGGTGTAACACCTCAAGAACTCCAATAGCAA
1 GGATTTGACAAGACCATGCTATGGTGTAACACCTCAAGAACCCCAATAGCAA
994737 G
1 G
994738 CTACTATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (52 bp):
GGATTTGACAAGACCATGCTATGGTGTAACACCTCAAGAACCCCAATAGCAA
Found at i:995777 original size:14 final size:14
Alignment explanation
Indices: 995758--995785 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
995748 TATATTAGTA
995758 TTTTCTATTCTATT
1 TTTTCTATTCTATT
995772 TTTTCTATTCTATT
1 TTTTCTATTCTATT
995786 AGTATTAGAT
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:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTCTATTCTATT
Found at i:995793 original size:6 final size:6
Alignment explanation
Indices: 995782--995832 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
995772 TTTTCTATTC
* *
995782 TATTAG TATTAG -ATTAG TATTA- TATT-C TATTGG TATTAG -ATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
995826 TATTAG T
1 TATTAG T
995833 TAGTAATCTC
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
5 18 0.46
6 21 0.54
ACGTcount: A:0.31, C:0.02, G:0.16, T:0.51
Consensus pattern (6 bp):
TATTAG
Found at i:995807 original size:27 final size:27
Alignment explanation
Indices: 995777--995830 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
995767 CTATTTTTTC
995777 TATTCTATTAGTATTAGATTAGTATTA
1 TATTCTATTAGTATTAGATTAGTATTA
*
995804 TATTCTATTGGTATTAGATTAGTATTA
1 TATTCTATTAGTATTAGATTAGTATTA
995831 GTTAGTAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.31, C:0.04, G:0.13, T:0.52
Consensus pattern (27 bp):
TATTCTATTAGTATTAGATTAGTATTA
Found at i:998121 original size:51 final size:51
Alignment explanation
Indices: 998045--998147 Score: 179
Period size: 51 Copynumber: 2.0 Consensus size: 51
998035 GACATAAAAG
*
998045 GACCACATAAAACTATTTTAAATTTACAACGAATCAGGCTTTTATTGGTGA
1 GACCACATAAAACTATTTTAAATTTACAACAAATCAGGCTTTTATTGGTGA
* *
998096 GACCACATAAAACTATTTTAAATTTATAACAAATTAGGCTTTTATTGGTGA
1 GACCACATAAAACTATTTTAAATTTACAACAAATCAGGCTTTTATTGGTGA
998147 G
1 G
998148 GTGTGCCAGG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.35
Consensus pattern (51 bp):
GACCACATAAAACTATTTTAAATTTACAACAAATCAGGCTTTTATTGGTGA
Found at i:999549 original size:77 final size:77
Alignment explanation
Indices: 999414--999568 Score: 276
Period size: 77 Copynumber: 2.0 Consensus size: 77
999404 CATGTTGAAA
*
999414 TATCTGTTTTTGCCAACATGTCATTCATGATATTCCTTCCATTTCTTGTTTTCTAATTACATTAC
1 TATCTGTTTTTGCCAACATGTCATTCATGATATTCCTTCCATTTCTTGTTTTCCAATTACATTAC
999479 CCCAAGCTTTAC
66 CCCAAGCTTTAC
*
999491 TATCTGTTTTTGCCAACATGTCATTCATGATATTCCTTCTATTTCTT-TTTGTCCAATTACATTA
1 TATCTGTTTTTGCCAACATGTCATTCATGATATTCCTTCCATTTCTTGTTT-TCCAATTACATTA
999555 CCCCAAGCTTTAC
65 CCCCAAGCTTTAC
999568 T
1 T
999569 TCGCTATTTC
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
76 3 0.04
77 72 0.96
ACGTcount: A:0.22, C:0.25, G:0.08, T:0.46
Consensus pattern (77 bp):
TATCTGTTTTTGCCAACATGTCATTCATGATATTCCTTCCATTTCTTGTTTTCCAATTACATTAC
CCCAAGCTTTAC
Found at i:999801 original size:27 final size:22
Alignment explanation
Indices: 999743--999787 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
999733 ATATTATGGG
999743 ATGCTTTAAAATATAAAATAAC
1 ATGCTTTAAAATATAAAATAAC
999765 ATGCTTTAAAATATAAAATAAC
1 ATGCTTTAAAATATAAAATAAC
999787 A
1 A
999788 ACTCTCAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.56, C:0.09, G:0.04, T:0.31
Consensus pattern (22 bp):
ATGCTTTAAAATATAAAATAAC
Found at i:999862 original size:77 final size:77
Alignment explanation
Indices: 999765--999916 Score: 270
Period size: 77 Copynumber: 2.0 Consensus size: 77
999755 ATAAAATAAC
999765 ATGCTTTAAAATATAAAATAACAACTCTCAATTTAAATAATTAAACTATTATT-GATGAGGTGCA
1 ATGCTTTAAAATATAAAATAACAACTCTCAATTTAAATAATTAAACTATTATTGGA-GAGGTGCA
999829 CCAAATCCATGGG
65 CCAAATCCATGGG
* *
999842 ATGCTTTAAAATATAAAATAACAACTCTCAATTTAAATAATTAAACTATTATTGGAGGGGTGCGC
1 ATGCTTTAAAATATAAAATAACAACTCTCAATTTAAATAATTAAACTATTATTGGAGAGGTGCAC
999907 CAAATCCATG
66 CAAATCCATG
999917 CAGTAGTGCA
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
77 70 0.97
78 2 0.03
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.31
Consensus pattern (77 bp):
ATGCTTTAAAATATAAAATAACAACTCTCAATTTAAATAATTAAACTATTATTGGAGAGGTGCAC
CAAATCCATGGG
Found at i:1002413 original size:13 final size:13
Alignment explanation
Indices: 1002397--1002431 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1002387 AAGAAATCAA
*
1002397 AAAAATCAAAAAG
1 AAAAATAAAAAAG
*
1002410 AAAAATAAAAAAT
1 AAAAATAAAAAAG
1002423 AAAAATAAA
1 AAAAATAAA
1002432 TAAATAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.83, C:0.03, G:0.03, T:0.11
Consensus pattern (13 bp):
AAAAATAAAAAAG
Found at i:1002421 original size:8 final size:8
Alignment explanation
Indices: 1002361--1002454 Score: 50
Period size: 8 Copynumber: 11.1 Consensus size: 8
1002351 AAGACATTTT
1002361 AAAAAATA
1 AAAAAATA
*
1002369 AAAATTATTA
1 AAAA--AATA
1002379 AAAAAA-A
1 AAAAAATA
*
1002386 CAAGAAATCA
1 -AAAAAAT-A
1002396 AAAAAATCA
1 AAAAAAT-A
1002405 AAAAGAA-A
1 AAAA-AATA
1002413 AATAAAA-A
1 AA-AAAATA
1002421 ATAAAAATA
1 A-AAAAATA
*
1002430 AATAAATA
1 AAAAAATA
*
1002438 AATAAATA
1 AAAAAATA
*
1002446 AATAAATA
1 AAAAAATA
1002454 A
1 A
1002455 TACAAATAAT
Statistics
Matches: 72, Mismatches: 5, Indels: 18
0.76 0.05 0.19
Matches are distributed among these distances:
7 1 0.01
8 44 0.61
9 17 0.24
10 10 0.14
ACGTcount: A:0.78, C:0.03, G:0.02, T:0.17
Consensus pattern (8 bp):
AAAAAATA
Found at i:1002434 original size:4 final size:4
Alignment explanation
Indices: 1002412--1002454 Score: 65
Period size: 4 Copynumber: 11.5 Consensus size: 4
1002402 TCAAAAAGAA
1002412 AAAT AAA- AAAT -AA- AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1002455 TACAAATAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
3 7 0.19
4 29 0.81
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (4 bp):
AAAT
Done.