Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold457
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: 607290
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 2 of 3
Found at i:260757 original size:31 final size:31
Alignment explanation
Indices: 260722--260782 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
260712 TTGATTATTT
* *
260722 GTTATAAAGGAAGAAACTGAAAATATTGAAA
1 GTTATAAAGGAAGAAACTAAAAACATTGAAA
260753 GTTATAAAGGAAGAAACTAAAAACATTGAA
1 GTTATAAAGGAAGAAACTAAAAACATTGAA
260783 GAATATTGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.56, C:0.05, G:0.18, T:0.21
Consensus pattern (31 bp):
GTTATAAAGGAAGAAACTAAAAACATTGAAA
Found at i:261403 original size:21 final size:21
Alignment explanation
Indices: 261370--261410 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
261360 CTAAGTAAAA
261370 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
261391 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
261411 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:261475 original size:20 final size:20
Alignment explanation
Indices: 261450--261520 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
261440 ACCCTGAAAA
261450 GTATCGATACACATATAAAT
1 GTATCGATACACATATAAAT
* **
261470 GTATCGATACAAAT-TGCAT
1 GTATCGATACACATATAAAT
*
261489 AGTATCGATACACA-AAAATAT
1 -GTATCGATACACATATAA-AT
261510 GTATCGATACA
1 GTATCGATACA
261521 AGACATTGGC
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
19 3 0.07
20 36 0.88
21 2 0.05
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (20 bp):
GTATCGATACACATATAAAT
Found at i:261570 original size:53 final size:53
Alignment explanation
Indices: 261490--261626 Score: 229
Period size: 53 Copynumber: 2.6 Consensus size: 53
261480 AAATTGCATA
*
261490 GTATCGATACACAAAAATATGTATCGATACAAGACATTGGCAGTAGCCAAATTT
1 GTATCGATACAC-AAAATATGTATCGATACAAGACATTGGCAGTACCCAAATTT
* * *
261544 GTATCGATACACACAATATGTATCGATACAGGTCATTGGCAGTACCCAAATTT
1 GTATCGATACACAAAATATGTATCGATACAAGACATTGGCAGTACCCAAATTT
261597 GTATCGATACACAAAATATGTATCGATACA
1 GTATCGATACACAAAATATGTATCGATACA
261627 TTGGAAGTAG
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
53 66 0.85
54 12 0.15
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (53 bp):
GTATCGATACACAAAATATGTATCGATACAAGACATTGGCAGTACCCAAATTT
Found at i:261804 original size:20 final size:20
Alignment explanation
Indices: 261779--261817 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
261769 AGATACAATT
261779 AGTGAATGTATCGATACATA
1 AGTGAATGTATCGATACATA
261799 AGTGAATGTATCGATACAT
1 AGTGAATGTATCGATACAT
261818 GTCTAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (20 bp):
AGTGAATGTATCGATACATA
Found at i:262147 original size:21 final size:21
Alignment explanation
Indices: 262100--262157 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
262090 AAAAATTATC
*
262100 CAAATGTATCGATACATTTGT
1 CAAATGTATCGATACATTTGA
**
262121 GGAATGTATCGATACATTCT-A
1 CAAATGTATCGATACATT-TGA
262142 CAAATGTATCGATACA
1 CAAATGTATCGATACA
262158 GGGTCCCAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 30 0.97
22 1 0.03
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (21 bp):
CAAATGTATCGATACATTTGA
Found at i:262217 original size:19 final size:19
Alignment explanation
Indices: 262193--262260 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
262183 AATTCAACAA
262193 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
262212 TTTGTATCGAT--ATAA--
1 TTTGTATCGATACATAAGT
262227 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
262244 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
262261 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 9 0.21
15 4 0.09
17 4 0.09
19 26 0.60
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:262231 original size:32 final size:32
Alignment explanation
Indices: 262195--262255 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
262185 TTCAACAATT
*
262195 TGTATCGATACATAAGTTTTGTATCGATATAA
1 TGTATCGATACATAAGTATTGTATCGATATAA
262227 TGTATCGATACATAAGTATTGTATCGATA
1 TGTATCGATACATAAGTATTGTATCGATA
262256 CATAATTAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATATAA
Found at i:262318 original size:13 final size:13
Alignment explanation
Indices: 262300--262326 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
262290 CATTTTTCTG
262300 TGTATCGATACAT
1 TGTATCGATACAT
262313 TGTATCGATACAT
1 TGTATCGATACAT
262326 T
1 T
262327 TGGAAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:262854 original size:12 final size:12
Alignment explanation
Indices: 262837--262865 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
262827 ATCCTTTAGC
262837 AAAAAAAAC-CA
1 AAAAAAAACACA
262848 AAAAAAAACACA
1 AAAAAAAACACA
262860 AAAAAA
1 AAAAAA
262866 CACTATTCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAACACA
Found at i:264849 original size:28 final size:27
Alignment explanation
Indices: 264779--264854 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 27
264769 TTTCTTCACA
264779 ATCGGGGATACTCCAACCCCGTTAATC
1 ATCGGGGATACTCCAACCCCGTTAATC
*
264806 ATCGGGGATACTCCAACCCCGTT-ATT
1 ATCGGGGATACTCCAACCCCGTTAATC
*
264832 TTCGAGGGGATACTCCAACCCCG
1 ATC--GGGGATACTCCAACCCCG
264855 GCTTTATTCC
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
26 4 0.09
27 23 0.51
28 18 0.40
ACGTcount: A:0.24, C:0.33, G:0.21, T:0.22
Consensus pattern (27 bp):
ATCGGGGATACTCCAACCCCGTTAATC
Found at i:266062 original size:51 final size:51
Alignment explanation
Indices: 265985--266098 Score: 158
Period size: 51 Copynumber: 2.2 Consensus size: 51
265975 GTTGCGACAG
* *
265985 ATACATTCTGGATTTTTGACCCAAATGTATCGATACATTATTCATTGTATCA
1 ATACATTCTGGA-TTTTGACCCAAATGTATCGACACATTATTCAATGTATCA
* *
266037 ATACATTCTAGG-TTTTGACCCAAATGTATTGACACATTCTTCAATGTATCA
1 ATACATTCT-GGATTTTGACCCAAATGTATCGACACATTATTCAATGTATCA
*
266088 ATACATGCTGG
1 ATACATTCTGG
266099 CAATTTTACA
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
50 2 0.04
51 43 0.77
52 9 0.16
53 2 0.04
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (51 bp):
ATACATTCTGGATTTTGACCCAAATGTATCGACACATTATTCAATGTATCA
Found at i:268540 original size:97 final size:97
Alignment explanation
Indices: 268438--268624 Score: 268
Period size: 97 Copynumber: 1.9 Consensus size: 97
268428 CTCTTTCGAG
* * * * *
268438 GAGATACTCTAACCCCGTTTTTAAACTCGTCAAGATTTAAGTCTTATTTTTACTTAAGTTATCAA
1 GAGATACTCTAACCCCATTTTTAAACTCGTCAAGATTTAAATATTATTTTTACTCAAATTAT-AA
268503 T-ATCAGGGATACTCTAACCCCATTTTTTTGAA
65 TCATCAGGGATACTCTAACCCCATTTTTTTGAA
* * * *
268535 GAGATACTCTAACCCTATTTTTAAACTTGTCAAGATTTAAATATTATTTTTTCTCAAATTATTAT
1 GAGATACTCTAACCCCATTTTTAAACTCGTCAAGATTTAAATATTATTTTTACTCAAATTATAAT
*
268600 CATCGGGGATACTCTAACCCCATTT
66 CATCAGGGATACTCTAACCCCATTT
268625 CTCCGAGGGA
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
96 2 0.03
97 77 0.97
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.40
Consensus pattern (97 bp):
GAGATACTCTAACCCCATTTTTAAACTCGTCAAGATTTAAATATTATTTTTACTCAAATTATAAT
CATCAGGGATACTCTAACCCCATTTTTTTGAA
Found at i:268653 original size:97 final size:96
Alignment explanation
Indices: 268451--268653 Score: 212
Period size: 97 Copynumber: 2.1 Consensus size: 96
268441 ATACTCTAAC
* * * *
268451 CCCGTTTTTAAACTCGTCAAGATTTAAGTCTTATTTTTACTTAAGTTATCAATATCAGGGATACT
1 CCCGTTTTTAAACTCGTCAAGATTTAAATATTATTTTTACTCAAATTATCAATATCAGGGATACT
* ** * *
268516 CTAACCCCATTTTTTTGAAGAGATACTCTAA
66 CTAACCCCATTTCTCCGAAGAGACACTCCAA
* * * * *
268547 CCCTATTTTTAAACTTGTCAAGATTTAAATATTATTTTTTCTCAAATTAT-TATCATCGGGGATA
1 CCC-GTTTTTAAACTCGTCAAGATTTAAATATTATTTTTACTCAAATTATCAAT-ATCAGGGATA
* *
268611 CTCTAACCCCATTTCTCCG-AGGGAACACTCCAT
64 CTCTAACCCCATTTCTCCGAAGAG-ACACTCCAA
268644 CCTCGTTTTT
1 CC-CGTTTTT
268654 CACTAAAAAT
Statistics
Matches: 86, Mismatches: 17, Indels: 7
0.78 0.15 0.06
Matches are distributed among these distances:
96 8 0.09
97 77 0.90
98 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.40
Consensus pattern (96 bp):
CCCGTTTTTAAACTCGTCAAGATTTAAATATTATTTTTACTCAAATTATCAATATCAGGGATACT
CTAACCCCATTTCTCCGAAGAGACACTCCAA
Found at i:268876 original size:30 final size:30
Alignment explanation
Indices: 268840--268900 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
268830 TTAGCTAGGA
268840 TGAATTCTCTTCATGAAATATTGTATGCTT
1 TGAATTCTCTTCATGAAATATTGTATGCTT
268870 TGAATTCTCTTCATGAAATATTGTATGCTT
1 TGAATTCTCTTCATGAAATATTGTATGCTT
268900 T
1 T
268901 CATCGTCTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (30 bp):
TGAATTCTCTTCATGAAATATTGTATGCTT
Found at i:270442 original size:11 final size:12
Alignment explanation
Indices: 270420--270456 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
270410 TTTTTTAATT
270420 ATATAATTATATA
1 ATAT-ATTATATA
270433 ATAT-TTATAT-
1 ATATATTATATA
270443 ATATATTATATA
1 ATATATTATATA
270455 AT
1 AT
270457 TTATATCATA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
10 4 0.18
11 12 0.55
12 2 0.09
13 4 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
ATATATTATATA
Found at i:270503 original size:28 final size:29
Alignment explanation
Indices: 270449--270505 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
270439 ATATATATAT
*
270449 TATATAATTTATATCATATAAAAATTAAA
1 TATATAATATATATCATATAAAAATTAAA
* *
270478 TATATAATAT-TATGATATAAAGATTAAA
1 TATATAATATATATCATATAAAAATTAAA
270506 AATAAATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 16 0.64
29 9 0.36
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (29 bp):
TATATAATATATATCATATAAAAATTAAA
Found at i:271800 original size:7 final size:6
Alignment explanation
Indices: 271772--271805 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
271762 AATATCGATT
271772 TTTTAA TTTTAA TTTTAA TTTTAA TTTTTAA TTT
1 TTTTAA TTTTAA TTTTAA TTTTAA -TTTTAA TTT
271806 ATCTATATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTTAA
Found at i:272996 original size:79 final size:77
Alignment explanation
Indices: 272851--273061 Score: 217
Period size: 79 Copynumber: 2.7 Consensus size: 77
272841 TATTTTGGAG
* * * * ** *
272851 ATAATAACGGGGTTGGAGTATCCTCTTGAAAATAACAGGGTTGGAGTATCCTCGGTTGTGAAAAA
1 ATAA-AACCGGGTTGGAGTATCCCCTTGGAAATAACAGGGTTGGAGTATCCCCAATTATGAAAAA
* *
272916 TCGATGA-TTAGGAA
65 TCAAT-ATTTA-AAA
* * *
272930 ATAAAATCGGGATTGGAGTATCCCCTTGGAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAA
1 ATAAAACCGGG-TTGGAGTATCCCCTTGGAAATAACAGGGTTGGAGTATCCCCAATTATGAAAAA
272995 TCAATATTTTAAAA
65 TCAATA-TTTAAAA
* * **
273009 ATAAAGCCGAGGTTGGAGTATCCCCTCGGAGGTAACAGGGTTGGAGTATCCCC
1 ATAAAACCG-GGTTGGAGTATCCCCTTGGAAATAACAGGGTTGGAGTATCCCC
273062 GATGAAATAA
Statistics
Matches: 110, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
78 6 0.05
79 99 0.90
80 5 0.05
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.26
Consensus pattern (77 bp):
ATAAAACCGGGTTGGAGTATCCCCTTGGAAATAACAGGGTTGGAGTATCCCCAATTATGAAAAAT
CAATATTTAAAA
Found at i:273189 original size:51 final size:51
Alignment explanation
Indices: 273081--273191 Score: 125
Period size: 51 Copynumber: 2.2 Consensus size: 51
273071 ACGAGGTTGA
* * * *
273081 AGTATCCTCGATTGTGAAAAACTAGTGTTTTGGAAATAAAATCGGAGTTGG
1 AGTATCCCCGATTGTGAAAAACTAGTGTTTTAGAAATAAAACCGGAGTTCG
* * * * *
273132 AATATCCCCGATTGTGGAGAATTGGTGTTTTAGAAATAAAACCGG-GATTCG
1 AGTATCCCCGATTGTGAAAAACTAGTGTTTTAGAAATAAAACCGGAG-TTCG
273183 AGTATCCCC
1 AGTATCCCC
273192 TCGAGAATAA
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
50 1 0.02
51 48 0.98
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (51 bp):
AGTATCCCCGATTGTGAAAAACTAGTGTTTTAGAAATAAAACCGGAGTTCG
Found at i:273299 original size:27 final size:27
Alignment explanation
Indices: 273255--273323 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
273245 AATAAAACCG
*
273255 GGGGTTGGAGCATCCCCTCAAAAATAAC
1 GGGGTTGGAGTAT-CCCTCAAAAATAAC
* ** *
273283 GGGGTTGGAGTATCCCTGATGATTAAC
1 GGGGTTGGAGTATCCCTCAAAAATAAC
273310 GGGGTTGGAGTATC
1 GGGGTTGGAGTATC
273324 TCCAATTGTG
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 24 0.67
28 12 0.33
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (27 bp):
GGGGTTGGAGTATCCCTCAAAAATAAC
Found at i:273348 original size:237 final size:238
Alignment explanation
Indices: 272927--273430 Score: 640
Period size: 237 Copynumber: 2.1 Consensus size: 238
272917 CGATGATTAG
* * * *
272927 GAAATAAAATCGGGATTGGAGTATCCCCTTGGAAATAACGGGGTTGGAGTATCCCCAATTATGAG
1 GAAATAAAACCGGGATTGGAGTATCCCCTCGGAAATAACGAGGTTGGAGTATCCCCAATTATGAA
* * ** **
272992 AAATCAATATTTTAAAAATAAAGCCGAGGTTGGAGTATCCCCTCGGAGGTAACAGGGTTGGAGTA
66 AAATCAATATTTTAAAAATAAAACCGAGGTTGGAGCATCCCCTCAAAAATAACAGGGTTGGAGTA
*
273057 TCCCCGATGAAATAACGAGGTTGAAGTATCCTCGATTGTGAAAAACTAGTG-TTTTGGAAATAAA
131 TCCCCGATGAAATAACGAGGTTGAAGTATCCTCAATTGTGAAAAACTAGTGTTTTTGGAAATAAA
** *
273121 ATCGGAGTTGGAATATCCCCGATT-GTGGAGAATTGGTGTTTT
196 ATCGGAGTTGGAATATCCCCGATTAAAGGAAAATTGGTGTTTT
* * * *
273163 AGAAATAAAACCGGGATTCGAGTATCCCCTC-GAGAATAATGAGGTTGGAGTATCTCCGATTATG
1 -GAAATAAAACCGGGATTGGAGTATCCCCTCGGA-AATAACGAGGTTGGAGTATCCCCAATTATG
** * * * *
273227 AAAAATTGATGTTTTAGAAATAAAACCGGGGGTTGGAGCATCCCCTCAAAAATAACGGGGTTGGA
64 AAAAATCAATATTTTAAAAATAAAACC-GAGGTTGGAGCATCCCCTCAAAAATAACAGGGTTGGA
* * * * * *
273292 GTATCCCTGATG-ATTAACGGGGTTGGAGTAT-CTCCAATTGTGAAAAATTGGTGTTTTTGGAAA
128 GTATCCCCGATGAAATAACGAGGTTGAAGTATCCT-CAATTGTGAAAAACTAGTGTTTTTGGAAA
*
273355 TAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTT
192 TAAAATCGGAGTTGGAATATCCCCGATTAAAGGAAAATTGGTGTTTT
*
273402 GAAAATAAAACCGGGGTTGGAGTATCCCC
1 G-AAATAAAACCGGGATTGGAGTATCCCC
273431 GATTGTGAAA
Statistics
Matches: 228, Mismatches: 33, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
236 4 0.02
237 106 0.46
238 78 0.34
239 40 0.18
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.27
Consensus pattern (238 bp):
GAAATAAAACCGGGATTGGAGTATCCCCTCGGAAATAACGAGGTTGGAGTATCCCCAATTATGAA
AAATCAATATTTTAAAAATAAAACCGAGGTTGGAGCATCCCCTCAAAAATAACAGGGTTGGAGTA
TCCCCGATGAAATAACGAGGTTGAAGTATCCTCAATTGTGAAAAACTAGTGTTTTTGGAAATAAA
ATCGGAGTTGGAATATCCCCGATTAAAGGAAAATTGGTGTTTT
Found at i:273468 original size:51 final size:50
Alignment explanation
Indices: 273309--273495 Score: 232
Period size: 52 Copynumber: 3.7 Consensus size: 50
273299 TGATGATTAA
* * *
273309 CGGGGTTGGAGTATCTCCAATTGTGAAAAATTGGTGTTTTTGGAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGGTG-TTTT-GAAATAAAAT
* * * *
273361 CGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATT-ATGAAAAATTGGTGTTTTG-AAATAAAAT
* *
273413 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTAGAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTT-GAAATAAAAT
*
273464 CGGGGTTAGAGTAT-CCCGATTATGAAAAATTG
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTG
273496 AGAAACTTAA
Statistics
Matches: 116, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
50 16 0.14
51 36 0.31
52 53 0.46
53 11 0.09
ACGTcount: A:0.33, C:0.10, G:0.26, T:0.30
Consensus pattern (50 bp):
CGGGGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGAAATAAAAT
Found at i:275927 original size:19 final size:21
Alignment explanation
Indices: 275903--275954 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
275893 AGCGATACAC
*
275903 TGTATCGATACA-TTACT-TA
1 TGTATCGATACATTTACTGAA
275922 TGTATCGATACATTTACTGAA
1 TGTATCGATACATTTACTGAA
275943 TGTATCGATACA
1 TGTATCGATACA
275955 AATTATTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 12 0.40
20 5 0.17
21 13 0.43
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTTACTGAA
Found at i:277723 original size:15 final size:15
Alignment explanation
Indices: 277705--277787 Score: 78
Period size: 16 Copynumber: 5.3 Consensus size: 15
277695 TATTTAATTT
*
277705 TTTAATTATTTTAGG
1 TTTAATTATTTTAGA
*
277720 TTTAATTATTTTATA
1 TTTAATTATTTTAGA
277735 TTTGAATTATTTTA-A
1 TTT-AATTATTTTAGA
277750 TTTTAATTTATTTTAGA
1 -TTTAA-TTATTTTAGA
* * *
277767 TCTAAATAATTTTAAA
1 T-TTAATTATTTTAGA
277783 TTTAA
1 TTTAA
277788 ATTAATTAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
15 22 0.39
16 31 0.54
17 4 0.07
ACGTcount: A:0.35, C:0.01, G:0.05, T:0.59
Consensus pattern (15 bp):
TTTAATTATTTTAGA
Found at i:277728 original size:31 final size:31
Alignment explanation
Indices: 277688--277762 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
277678 TATATTAGAT
* * *
277688 TTTACATTATTTAATTTTTTAATTATTTTAGG
1 TTTA-ATTATTTAATATTTGAATTATTTTAAG
* *
277720 TTTAATTATTTTATATTTGAATTATTTTAAT
1 TTTAATTATTTAATATTTGAATTATTTTAAG
277751 TTTAATTTATTT
1 TTTAA-TTATTT
277763 TAGATCTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 27 0.73
32 10 0.27
ACGTcount: A:0.29, C:0.01, G:0.04, T:0.65
Consensus pattern (31 bp):
TTTAATTATTTAATATTTGAATTATTTTAAG
Found at i:277744 original size:16 final size:16
Alignment explanation
Indices: 277664--277764 Score: 84
Period size: 16 Copynumber: 6.4 Consensus size: 16
277654 AAGAAAGATC
277664 ATTTTA-ATTTTAGA-T
1 ATTTTATATTTTA-ATT
* *
277679 ATATTAGATTTTACATT
1 ATTTTATATTTTA-ATT
* *
277696 ATTTAATTTTTTAATT
1 ATTTTATATTTTAATT
**
277712 ATTTTA-GGTTTAATT
1 ATTTTATATTTTAATT
*
277727 ATTTTATATTTGAATT
1 ATTTTATATTTTAATT
277743 ATTTTA-ATTTTAATTT
1 ATTTTATATTTTAA-TT
277759 ATTTTA
1 ATTTTA
277765 GATCTAAATA
Statistics
Matches: 69, Mismatches: 13, Indels: 7
0.78 0.15 0.08
Matches are distributed among these distances:
15 24 0.35
16 35 0.51
17 10 0.14
ACGTcount: A:0.32, C:0.01, G:0.05, T:0.62
Consensus pattern (16 bp):
ATTTTATATTTTAATT
Found at i:277880 original size:16 final size:15
Alignment explanation
Indices: 277854--277892 Score: 62
Period size: 16 Copynumber: 2.6 Consensus size: 15
277844 AAGATTATTA
277854 AATTTAATTATTTTG
1 AATTTAATTATTTTG
277869 AATTTGAATTATTTTG
1 AATTT-AATTATTTTG
277885 AA-TTAATT
1 AATTTAATT
277893 GTTGAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 4 0.17
15 7 0.30
16 12 0.52
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (15 bp):
AATTTAATTATTTTG
Found at i:278761 original size:35 final size:34
Alignment explanation
Indices: 278681--278764 Score: 89
Period size: 35 Copynumber: 2.4 Consensus size: 34
278671 CTTTAAATTT
278681 ATTTTTATATTAATTTTAAAATTTAAAATATATCA
1 ATTTTT-TATTAATTTTAAAATTTAAAATATATCA
** **
278716 ATTAAATTATTAATTTTAAAATTTAATCTTAATAT-A
1 ATT-TTTTATTAATTTTAAAATTTAA-AAT-ATATCA
278752 ATTTTTTATTAAT
1 ATTTTTTATTAAT
278765 AAAATCGTGA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
35 30 0.75
36 6 0.15
37 4 0.10
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (34 bp):
ATTTTTTATTAATTTTAAAATTTAAAATATATCA
Found at i:287161 original size:27 final size:27
Alignment explanation
Indices: 287085--287213 Score: 77
Period size: 27 Copynumber: 4.7 Consensus size: 27
287075 GAAAGCTTTA
**
287085 AAATTTTTAATTAAATCTTTTAACTAGTG
1 AAATTTTTAATTAAA-CTTTTATGTA-TG
* **
287114 -AATATTTAAATTAAAAATTTATGTATG
1 AAAT-TTTTAATTAAACTTTTATGTATG
**
287141 AAATTTTTAATTAAACTTTTACATAT-
1 AAATTTTTAATTAAACTTTTATGTATG
* * *
287167 AGATTTTTTAGTTAAATTTTTACATGTA-G
1 A-AATTTTTAATTAAACTTTT--ATGTATG
*
287196 -AAGTTTTAATTAAACTTT
1 AAATTTTTAATTAAACTTT
287214 CGCATGTGGA
Statistics
Matches: 75, Mismatches: 19, Indels: 14
0.69 0.18 0.13
Matches are distributed among these distances:
26 1 0.01
27 49 0.65
28 12 0.16
29 13 0.17
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.49
Consensus pattern (27 bp):
AAATTTTTAATTAAACTTTTATGTATG
Found at i:287219 original size:27 final size:26
Alignment explanation
Indices: 287145--287228 Score: 87
Period size: 27 Copynumber: 3.2 Consensus size: 26
287135 TGTATGAAAT
* *
287145 TTTTAATTAAACTTTTACATATAGATT
1 TTTTAATTAAACTTTTACATGTAGA-A
* *
287172 TTTTAGTTAAATTTTTACATGTAGAA
1 TTTTAATTAAACTTTTACATGTAGAA
** *
287198 GTTTTAATTAAACTTTCGCATGTGGAA
1 -TTTTAATTAAACTTTTACATGTAGAA
287225 TTTT
1 TTTT
287229 CGATCTTACT
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
26 4 0.09
27 43 0.91
ACGTcount: A:0.32, C:0.07, G:0.11, T:0.50
Consensus pattern (26 bp):
TTTTAATTAAACTTTTACATGTAGAA
Found at i:287384 original size:28 final size:27
Alignment explanation
Indices: 287320--287384 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
287310 TTACACCTTA
287320 GAAATTTTAATTGAACTTGTACATATG
1 GAAATTTTAATTGAACTTGTACATATG
* * *
287347 GAACTTTTAATTAGACCTTTTACATAT-
1 GAAATTTTAATT-GAACTTGTACATATG
287374 GAAATTCTTAA
1 GAAATT-TTAA
287385 ACTTTCTTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 16 0.50
28 16 0.50
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.42
Consensus pattern (27 bp):
GAAATTTTAATTGAACTTGTACATATG
Found at i:288885 original size:17 final size:17
Alignment explanation
Indices: 288843--288891 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
288833 TATTCTAAAA
*
288843 ATAAAA-AATTCTT-AG
1 ATAAAATAATTTTTAAG
*
288858 A-AAATTAATTTTTAAG
1 ATAAAATAATTTTTAAG
288874 ATAAAATAATTTTCTAAG
1 ATAAAATAATTTT-TAAG
288892 TCAAGTATAG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
14 3 0.11
15 7 0.26
16 3 0.11
17 10 0.37
18 4 0.15
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.39
Consensus pattern (17 bp):
ATAAAATAATTTTTAAG
Found at i:292317 original size:2 final size:2
Alignment explanation
Indices: 292312--292349 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
292302 TGTGTGTGTG
292312 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
292350 CTTAAAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:293172 original size:16 final size:16
Alignment explanation
Indices: 293153--293186 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
293143 TTCAAAAAAA
293153 AAATTATAAGAAAAGT
1 AAATTATAAGAAAAGT
* *
293169 AAATTATTATAAAAGT
1 AAATTATAAGAAAAGT
293185 AA
1 AA
293187 GTTGCGACAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.29
Consensus pattern (16 bp):
AAATTATAAGAAAAGT
Found at i:293210 original size:61 final size:61
Alignment explanation
Indices: 293102--293217 Score: 139
Period size: 61 Copynumber: 1.9 Consensus size: 61
293092 AGATTGTAAT
* *
293102 GAAAATAAATGATTATAAAAGTAAATTAGGAGAAAATAATTTTCAAAAAA-AAAATTATAA
1 GAAAATAAATGATTATAAAAGTAAATTAGGACAAAATAATTTGCAAAAAATAAAATTATAA
* * *
293162 GAAAAGTAAATTATTATAAAAGTAAGTT-GCGACAAAATGGA-TTGCAAAAAATAAAA
1 GAAAA-TAAATGATTATAAAAGTAAATTAG-GACAAAAT-AATTTGCAAAAAATAAAA
293218 GTAAATTGTA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
60 6 0.13
61 36 0.77
62 5 0.11
ACGTcount: A:0.59, C:0.03, G:0.13, T:0.25
Consensus pattern (61 bp):
GAAAATAAATGATTATAAAAGTAAATTAGGACAAAATAATTTGCAAAAAATAAAATTATAA
Found at i:293537 original size:15 final size:15
Alignment explanation
Indices: 293517--293571 Score: 76
Period size: 15 Copynumber: 3.6 Consensus size: 15
293507 TGCTATTACA
293517 AAAATAAATTGTAAT
1 AAAATAAATTGTAAT
*
293532 AAAATAAATTG-AGAG
1 AAAATAAATTGTA-AT
293547 AAAATAAATTGTAAT
1 AAAATAAATTGTAAT
293562 AAAAGTAAAT
1 AAAA-TAAAT
293572 ATTTGATCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
14 1 0.03
15 28 0.80
16 6 0.17
ACGTcount: A:0.62, C:0.00, G:0.11, T:0.27
Consensus pattern (15 bp):
AAAATAAATTGTAAT
Found at i:295247 original size:37 final size:36
Alignment explanation
Indices: 295197--295278 Score: 137
Period size: 37 Copynumber: 2.2 Consensus size: 36
295187 ATTTATGTAG
*
295197 CATCCAGTAGCTCTTAACCAACCAAACTAATGTCCAA
1 CATCCA-TAGCTCTTAACCAACAAAACTAATGTCCAA
295234 CATCCATCAGCTCTTAACCAACAAAACTAATGTCCAA
1 CATCCAT-AGCTCTTAACCAACAAAACTAATGTCCAA
295271 CATCCATA
1 CATCCATA
295279 ATGATACTCA
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
36 2 0.05
37 41 0.95
ACGTcount: A:0.39, C:0.33, G:0.06, T:0.22
Consensus pattern (36 bp):
CATCCATAGCTCTTAACCAACAAAACTAATGTCCAA
Found at i:295677 original size:21 final size:22
Alignment explanation
Indices: 295652--295694 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
295642 CTTGATGAAG
295652 ATTAT-TTTTTTTAGCTTAAGT
1 ATTATCTTTTTTTAGCTTAAGT
295673 ATTATCTTTTTTTAGCTTAAGT
1 ATTATCTTTTTTTAGCTTAAGT
295695 TACTTTCACT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.23, C:0.07, G:0.09, T:0.60
Consensus pattern (22 bp):
ATTATCTTTTTTTAGCTTAAGT
Found at i:303544 original size:18 final size:20
Alignment explanation
Indices: 303521--303559 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
303511 CCTGTTTATT
303521 TTTTTCTTT-TTTAT-TGCA
1 TTTTTCTTTCTTTATATGCA
303539 TTTTTCTTTCTTTATATGCA
1 TTTTTCTTTCTTTATATGCA
303559 T
1 T
303560 ACGGAATGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.47
19 5 0.26
20 5 0.26
ACGTcount: A:0.13, C:0.13, G:0.05, T:0.69
Consensus pattern (20 bp):
TTTTTCTTTCTTTATATGCA
Found at i:318806 original size:84 final size:84
Alignment explanation
Indices: 318673--318833 Score: 223
Period size: 84 Copynumber: 1.9 Consensus size: 84
318663 CATCAACCTT
* * * *
318673 CTTGAATTGTTGGTTCGTATGGTTTTATCTTGGCCAACTCATTTCTAACTCATTGACACGTATGG
1 CTTGAATTGTTGGTTCGCATGGTTTTATCCTAGCCAACTCATTTCTAACTCATTGACACGTATAG
318738 GTTCATCTCGGTCAACTCG
66 GTTCATCTCGGTCAACTCG
* * * * *
318757 CTTGACTTGTTGGTTCGCATGGTTTTGTCCTAGCCAATTCTTTTCTAACTCATTGACTCGTATAG
1 CTTGAATTGTTGGTTCGCATGGTTTTATCCTAGCCAACTCATTTCTAACTCATTGACACGTATAG
* *
318822 TTTTATCTCGGT
66 GTTCATCTCGGT
318834 TAAATGTCCT
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
84 66 1.00
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.42
Consensus pattern (84 bp):
CTTGAATTGTTGGTTCGCATGGTTTTATCCTAGCCAACTCATTTCTAACTCATTGACACGTATAG
GTTCATCTCGGTCAACTCG
Found at i:318854 original size:84 final size:84
Alignment explanation
Indices: 318682--318855 Score: 190
Period size: 84 Copynumber: 2.1 Consensus size: 84
318672 TCTTGAATTG
* * * *
318682 TTGGTTCGTATGGTTTTATCTTGGCCAACTCATTTCTAACTCATTGACACGTATGGGTTCATCTC
1 TTGGTTCGCATGGTTTTATCCTAGCCAACTCATTTCTAACTCATTGACACGTATAGGTTCATCTC
* * *
318747 GGTCAACTCGCTTGACTTG
66 GGTAAACTCGCTAGACTTA
* * * * * *
318766 TTGGTTCGCATGGTTTTGTCCTAGCCAATTCTTTTCTAACTCATTGACTCGTATAGTTTTATCTC
1 TTGGTTCGCATGGTTTTATCCTAGCCAACTCATTTCTAACTCATTGACACGTATAGGTTCATCTC
*
318831 GGTTAAATGTC-CTAG-CTTA
66 GG-TAAA-CTCGCTAGACTTA
318850 TTGGTT
1 TTGGTT
318856 TTTGTGGTTT
Statistics
Matches: 74, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
84 66 0.89
85 6 0.08
86 2 0.03
ACGTcount: A:0.18, C:0.21, G:0.19, T:0.43
Consensus pattern (84 bp):
TTGGTTCGCATGGTTTTATCCTAGCCAACTCATTTCTAACTCATTGACACGTATAGGTTCATCTC
GGTAAACTCGCTAGACTTA
Found at i:319006 original size:84 final size:83
Alignment explanation
Indices: 318918--319457 Score: 421
Period size: 84 Copynumber: 6.5 Consensus size: 83
318908 TTTTATCTTT
* * **
318918 ATCAACTCTCCTTACTTGTTGGCTCGTATGGTTTTGTCCCAGCTAACCCCTTTCTAACTTATTGA
1 ATCAACTCTCCTAACTTGTTGGTTCGTATGGTTTCATCCC-GCTAACCCCTTTCTAACTTATTGA
318983 CTCATATGGTTTCATCCCA
65 CTCATATGGTTTCATCCCA
* * *
319002 ATCAACTCTCCTAACTTGTTAGTTCGTATGGTTTCATCCTCGCTAACTCCC-TTATAACTTATTA
1 ATCAACTCTCCTAACTTGTTGGTTCGTATGGTTTCATCC-CGCTAAC-CCCTTTCTAACTTATTG
*
319066 ACTCATATGGTTTCATCCCG
64 ACTCATATGGTTTCATCCCA
* * * * * *
319086 ATCAACTCTTCTGACTTGTTGGTTCGGATGGTTTCATCTCGGCTAACTCCTTTCTAACTTGTTGA
1 ATCAACTCTCCTAACTTGTTGGTTCGTATGGTTTCATC-CCGCTAACCCCTTTCTAACTTATTGA
319151 CTCATATGGTTTCATCCCA
65 CTCATATGGTTTCATCCCA
* * * * * * ** * ** * *
319170 GTTAATTGTCCTGACTTATTGGTTTTTATGGTTTCAT--C-TTAACCAAATTTTGTCTATCTTGT
1 ATCAACTCTCCTAACTTGTTGGTTCGTATGGTTTCATCCCGCTAACC---CCTT-TCTAACTTAT
* * * * *
319232 TTACTTATATAGCTTCATCCTA
62 TGACTCATATGGTTTCATCCCA
* * * * * * * * * **
319254 GTCAACT-TTCTCAAATTTTTAGTTCGAATGGTTTCATCCCAGCCAACACCTTTCTAACTTGTCA
1 ATCAACTCTCCT-AACTTGTTGGTTCGTATGGTTTCATCCC-GCTAACCCCTTTCTAACTTATTG
319318 ACTCATATGGTTTCATCCCA
64 ACTCATATGGTTTCATCCCA
* * ** * * *
319338 ATCAACTCTTCTAACTCGTTGACTCATATGGTTTCATCCCGGTCAA-CCC-TTCTAACTCATTGA
1 ATCAACTCTCCTAACTTGTTGGTTCGTATGGTTTCATCCCGCT-AACCCCTTTCTAACTTATTGA
* *
319401 CTCATATGGTTTTATCTCA
65 CTCATATGGTTTCATCCCA
* * *
319420 ATCAACTCTCTTAACTTATTAGG-TCATATGGTTTCATC
1 ATCAACTCTCCTAACTTGTT-GGTTCGTATGGTTTCATC
319458 TCGGCCAATT
Statistics
Matches: 357, Mismatches: 83, Indels: 34
0.75 0.18 0.07
Matches are distributed among these distances:
80 4 0.01
82 58 0.16
83 11 0.03
84 269 0.75
85 11 0.03
86 1 0.00
88 3 0.01
ACGTcount: A:0.22, C:0.25, G:0.12, T:0.41
Consensus pattern (83 bp):
ATCAACTCTCCTAACTTGTTGGTTCGTATGGTTTCATCCCGCTAACCCCTTTCTAACTTATTGAC
TCATATGGTTTCATCCCA
Found at i:319032 original size:41 final size:41
Alignment explanation
Indices: 318987--319123 Score: 134
Period size: 41 Copynumber: 3.3 Consensus size: 41
318977 TATTGACTCA
*
318987 TATGGTTTCATCCCAATCAACTCTCCTAACTTGTTAGTTCG
1 TATGGTTTCATCCCGATCAACTCTCCTAACTTGTTAGTTCG
* * ** *
319028 TATGGTTTCATCCTCGCT-AACTC-CCTTATAACTTATTAACTCA
1 TATGGTTTCATCC-CGATCAACTCTCC---TAACTTGTTAGTTCG
* * *
319071 TATGGTTTCATCCCGATCAACTCTTCTGACTTGTTGGTTCG
1 TATGGTTTCATCCCGATCAACTCTCCTAACTTGTTAGTTCG
*
319112 GATGGTTTCATC
1 TATGGTTTCATC
319124 TCGGCTAACT
Statistics
Matches: 75, Mismatches: 15, Indels: 12
0.74 0.15 0.12
Matches are distributed among these distances:
40 2 0.03
41 38 0.51
42 5 0.07
43 29 0.39
44 1 0.01
ACGTcount: A:0.20, C:0.26, G:0.14, T:0.40
Consensus pattern (41 bp):
TATGGTTTCATCCCGATCAACTCTCCTAACTTGTTAGTTCG
Found at i:319075 original size:43 final size:42
Alignment explanation
Indices: 318931--319168 Score: 182
Period size: 43 Copynumber: 5.6 Consensus size: 42
318921 AACTCTCCTT
* * **
318931 ACTTGTTGGCTCGTATGGTTTTGTCCCAGCTAAC-CCCTTTCTA
1 ACTTGTTGACTCATATGGTTTCATCCC-GCTAACTCCC-TTCTA
* ** *
318974 ACTTATTGACTCATATGGTTTCATCCCAATCAACT--CTCCTA
1 ACTTGTTGACTCATATGGTTTCATCCCGCT-AACTCCCTTCTA
* * *
319015 ACTTGTT-AGTTCGTATGGTTTCATCCTCGCTAACTCCCTTATA
1 ACTTGTTGA-CTCATATGGTTTCATCC-CGCTAACTCCCTTCTA
* * * *
319058 ACTTATTAACTCATATGGTTTCATCCCGATCAACT--CTTCTG
1 ACTTGTTGACTCATATGGTTTCATCCCGCT-AACTCCCTTCTA
** ** * *
319099 ACTTGTTGGTTCGGATGGTTTCATCTCGGCTAACTCCTTTCTA
1 ACTTGTTGACTCATATGGTTTCATC-CCGCTAACTCCCTTCTA
319142 ACTTGTTGACTCATATGGTTTCATCCC
1 ACTTGTTGACTCATATGGTTTCATCCC
319169 AGTTAATTGT
Statistics
Matches: 148, Mismatches: 36, Indels: 23
0.71 0.17 0.11
Matches are distributed among these distances:
40 1 0.01
41 56 0.38
42 11 0.07
43 79 0.53
44 1 0.01
ACGTcount: A:0.19, C:0.26, G:0.14, T:0.40
Consensus pattern (42 bp):
ACTTGTTGACTCATATGGTTTCATCCCGCTAACTCCCTTCTA
Found at i:319140 original size:168 final size:166
Alignment explanation
Indices: 318918--319496 Score: 474
Period size: 168 Copynumber: 3.5 Consensus size: 166
318908 TTTTATCTTT
* * * ** * * *
318918 ATCAACTCTCCTTACTTGTTGGCTCGTATGGTTTTGTCCCAGCTAACCCCTTTCTAACTTATTGA
1 ATCAACTCTTCTAACTTGTTGGTTCGTATGGTTTCATCCCAGCCAACTCCTTTCTAACTTGTTGA
*
318983 CTCATATGGTTTCATCCCAATCAACTCTCCTAACTTGTTAGTTCGTATGGTTTCATCCTCGCTAA
66 CTCATATGGTTTCATCCCAATCAACTCTCCTAACTTGTT-GTTCATATGGTTTCATCCTCGCTAA
* *
319048 CTCCCTTATAACTTATTAACTCATATGGTTTCATCCCG
130 -TCCCTTCTAACTTATTAACTCATATGGTTTCATCCCA
* * * * *
319086 ATCAACTCTTCTGACTTGTTGGTTCGGATGGTTTCATCTCGGCTAACTCCTTTCTAACTTGTTGA
1 ATCAACTCTTCTAACTTGTTGGTTCGTATGGTTTCATCCCAGCCAACTCCTTTCTAACTTGTTGA
* * * * * * ** * *
319151 CTCATATGGTTTCATCCCAGTTAATTGTCCTGACTTATTGGTTTTTATGGTTTCATCTTAAC-CA
66 CTCATATGGTTTCATCCCAATCAACTCTCCTAACTTGTT-GTTCATATGGTTTCATCCT--CGCT
** * * * * * * *
319215 AAT-TTTGTCTATCTTGTTTACTTATATAGCTTCATCCTA
128 AATCCCT-TCTAACTTATTAACTCATATGGTTTCATCCCA
* * * * * * **
319254 GTCAACT-TTCTCAAATTTTTAGTTCGAATGGTTTCATCCCAGCCAACACCTTTCTAACTTGTCA
1 ATCAACTCTTCT-AACTTGTTGGTTCGTATGGTTTCATCCCAGCCAACTCCTTTCTAACTTGTTG
* * * *
319318 ACTCATATGGTTTCATCCCAATCAACTCTTCTAACTCGTTGACTCATATGGTTTCATCC-CGGTC
65 ACTCATATGGTTTCATCCCAATCAACTCTCCTAACTTGTTG-TTCATATGGTTTCATCCTCGCT-
* * * *
319382 AA-CCCTTCTAACTCATTGACTCATATGGTTTTATCTCA
128 AATCCCTTCTAACTTATTAACTCATATGGTTTCATCCCA
* * * * *
319420 ATCAACTC-TCTTAACTTATTAGG-TCATATGGTTTCATCTCGGCCAA-TTCTACTT-TAACTTG
1 ATCAACTCTTC-TAACTTGTT-GGTTCGTATGGTTTCATCCCAGCCAACTCCT--TTCTAACTTG
319481 TTGACTCATATGGTTT
62 TTGACTCATATGGTTT
319497 AGTTCTGGTC
Statistics
Matches: 316, Mismatches: 82, Indels: 28
0.74 0.19 0.07
Matches are distributed among these distances:
165 3 0.01
166 76 0.24
167 13 0.04
168 220 0.70
169 3 0.01
170 1 0.00
ACGTcount: A:0.22, C:0.25, G:0.12, T:0.41
Consensus pattern (166 bp):
ATCAACTCTTCTAACTTGTTGGTTCGTATGGTTTCATCCCAGCCAACTCCTTTCTAACTTGTTGA
CTCATATGGTTTCATCCCAATCAACTCTCCTAACTTGTTGTTCATATGGTTTCATCCTCGCTAAT
CCCTTCTAACTTATTAACTCATATGGTTTCATCCCA
Found at i:319330 original size:43 final size:41
Alignment explanation
Indices: 319281--319412 Score: 174
Period size: 41 Copynumber: 3.2 Consensus size: 41
319271 TTTAGTTCGA
* * **
319281 ATGGTTTCATCCCAGCCAACACCTTTCTAACTTGTCAACTCAT
1 ATGGTTTCATCCCAGTCAAC-CC-TTCTAACTCGTTGACTCAT
* *
319324 ATGGTTTCATCCCAATCAACTCTTCTAACTCGTTGACTCAT
1 ATGGTTTCATCCCAGTCAACCCTTCTAACTCGTTGACTCAT
* *
319365 ATGGTTTCATCCCGGTCAACCCTTCTAACTCATTGACTCAT
1 ATGGTTTCATCCCAGTCAACCCTTCTAACTCGTTGACTCAT
319406 ATGGTTT
1 ATGGTTT
319413 TATCTCAATC
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
41 60 0.76
42 1 0.01
43 18 0.23
ACGTcount: A:0.23, C:0.30, G:0.11, T:0.36
Consensus pattern (41 bp):
ATGGTTTCATCCCAGTCAACCCTTCTAACTCGTTGACTCAT
Found at i:319459 original size:41 final size:41
Alignment explanation
Indices: 319318--319457 Score: 176
Period size: 41 Copynumber: 3.4 Consensus size: 41
319308 TAACTTGTCA
*
319318 ACTCATATGGTTTCATCCCAATCAACTCTTCTAACTCGTTG
1 ACTCATATGGTTTCATCCCAATCAACTCTTCTAACTCATTG
** *
319359 ACTCATATGGTTTCATCCCGGTCAACCCTTCTAACTCATTG
1 ACTCATATGGTTTCATCCCAATCAACTCTTCTAACTCATTG
* * *
319400 ACTCATATGGTTTTATCTCAATCAACTC-TCTTAACTTATT-
1 ACTCATATGGTTTCATCCCAATCAACTCTTC-TAACTCATTG
*
319440 AGGTCATATGGTTTCATC
1 A-CTCATATGGTTTCATC
319458 TCGGCCAATT
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
40 3 0.04
41 82 0.96
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (41 bp):
ACTCATATGGTTTCATCCCAATCAACTCTTCTAACTCATTG
Found at i:319509 original size:84 final size:84
Alignment explanation
Indices: 319421--319580 Score: 198
Period size: 84 Copynumber: 1.9 Consensus size: 84
319411 TTTATCTCAA
* *
319421 TCAACTCTCTTAACTTATTAGGTCATATGGTTTCAT-CTCGGCCAA-TTCTACTTTAACTTGTTG
1 TCAACTCTCTTAACTTATTAGGTCATATAGTTTCATCCT-AGCCAATTTCT-CTTTAACTTGTTG
*
319484 ACTCATATGGTTTAGTTCTGG
64 ACCCATATGGTTTAGTTCTGG
* * * * * *
319505 TCAACTCTCTTGATTTATTAGTTCGTATAGTTTTATCCTAGCCAATTTCTTTTTAACTTGTTGAC
1 TCAACTCTCTTAACTTATTAGGTCATATAGTTTCATCCTAGCCAATTTCTCTTTAACTTGTTGAC
*
319570 CCGTATGGTTT
66 CCATATGGTTT
319581 CATCCCGGTC
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
84 58 0.91
85 6 0.09
ACGTcount: A:0.21, C:0.19, G:0.14, T:0.46
Consensus pattern (84 bp):
TCAACTCTCTTAACTTATTAGGTCATATAGTTTCATCCTAGCCAATTTCTCTTTAACTTGTTGAC
CCATATGGTTTAGTTCTGG
Found at i:319896 original size:84 final size:84
Alignment explanation
Indices: 319724--319973 Score: 213
Period size: 84 Copynumber: 3.0 Consensus size: 84
319714 GTTCTGCCCT
** * ** *
319724 ATCAAGTCTCTTAACTTGTTGGTTTGTATGGTTTCATCTTAGCCAACTCTTTTCTAACATGTTGA
1 ATCAAGTCTCTTAACTTGTTGGTTCATATGATTTCATCCCAGCCAACTCTTTTCCAACATGTTGA
*
319789 CTTATATGGCTTTGTCTCA
66 CTTAGATGGCTTTGTCTCA
* *
319808 ATCAAGTCTCTTGAA-TTGTTGGTTCATATGATTTCATCCCGGCCAACTCTTTTCCAACTTGTTG
1 ATCAAGTCTCTT-AACTTGTTGGTTCATATGATTTCATCCCAGCCAACTCTTTTCCAACATGTTG
* *
319872 ACTTGGATGGTCTTAT-T-TCG
65 ACTTAGATGG-CTT-TGTCTCA
* * ** * * * * * * *
319892 ATCAACTCTCCTAACTTGTTTTTTCGTATCG-TTTCATCCTAACCAACTCCTTTCTAACTTATTG
1 ATCAAGTCTCTTAACTTGTTGGTTCATAT-GATTTCATCCCAGCCAACTCTTTTCCAACATGTTG
*
319956 ACTT-GAATGGTTTTGTCT
65 ACTTAG-ATGGCTTTGTCT
319974 TTGTTAACTC
Statistics
Matches: 135, Mismatches: 23, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
82 1 0.01
83 6 0.04
84 120 0.89
85 7 0.05
86 1 0.01
ACGTcount: A:0.20, C:0.22, G:0.14, T:0.44
Consensus pattern (84 bp):
ATCAAGTCTCTTAACTTGTTGGTTCATATGATTTCATCCCAGCCAACTCTTTTCCAACATGTTGA
CTTAGATGGCTTTGTCTCA
Found at i:320010 original size:84 final size:84
Alignment explanation
Indices: 319922--320100 Score: 186
Period size: 84 Copynumber: 2.1 Consensus size: 84
319912 TTTTCGTATC
* ** * * *
319922 GTTTCATCCTAA-CCAACTCCTTTCTAACTTATT-GACTTGAATGGTTTTGTCTTTGTTAA-CTC
1 GTTTCATCCTAAGCCAACT--TTCCTAACTTATTAG-CTTGAATGGTTTCATCCTGGCTAACCTC
* *
319984 TTTTAACTCATTGACTCATATG
63 TTTTAACTCATTAACTCATATA
* * *
320006 GTTTCATCC-AAGTCAACTTTCCTAACTTATTAGTTTGTATGGTTTCATCCTGGCTAACTCTCTT
1 GTTTCATCCTAAGCCAACTTTCCTAACTTATTAGCTTGAATGGTTTCATCCTGGCTAAC-CTCTT
*
320070 TTAACTCGTTAACTCATATA
65 TTAACTCATTAACTCATATA
320090 GTTTCATCCTA
1 GTTTCATCCTA
320101 GTCAACTCTC
Statistics
Matches: 78, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
82 29 0.37
83 3 0.04
84 45 0.58
85 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.11, T:0.44
Consensus pattern (84 bp):
GTTTCATCCTAAGCCAACTTTCCTAACTTATTAGCTTGAATGGTTTCATCCTGGCTAACCTCTTT
TAACTCATTAACTCATATA
Found at i:320148 original size:41 final size:41
Alignment explanation
Indices: 320103--320209 Score: 115
Period size: 43 Copynumber: 2.6 Consensus size: 41
320093 TCATCCTAGT
*
320103 CAACTCTCTTGACTTGTTGGTTCGTATGGTTTCATCTCAAC
1 CAACTCTCTTGACTTGTTGGTTCATATGGTTTCATCTCAAC
* *** * **
320144 CAACTCTTTTGTAACTTGTTAACTCATATGGTTTCATCTTAGT
1 CAACTCTCTTG--ACTTGTTGGTTCATATGGTTTCATCTCAAC
*
320187 CTACTCTCTTGACTTGTTGGTTC
1 CAACTCTCTTGACTTGTTGGTTC
320210 CAGCCAACTC
Statistics
Matches: 51, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
41 19 0.37
43 32 0.63
ACGTcount: A:0.18, C:0.22, G:0.15, T:0.45
Consensus pattern (41 bp):
CAACTCTCTTGACTTGTTGGTTCATATGGTTTCATCTCAAC
Found at i:320193 original size:43 final size:43
Alignment explanation
Indices: 319997--320193 Score: 138
Period size: 43 Copynumber: 4.7 Consensus size: 43
319987 TAACTCATTG
* ** *
319997 ACTCATATGGTTTCATCCAAGTCAA--CTTTCCTAACTTATTA
1 ACTCATATGGTTTCATCCTAGTCAACTCTTTTGTAACTTGTTA
** ** * *
320038 GTTTGTATGGTTTCATCCT-GGCTAACTCTCTTT-TAACTCGTTA
1 ACTCATATGGTTTCATCCTAGTC-AACTCT-TTTGTAACTTGTTA
* * *
320081 ACTCATATAGTTTCATCCTAGTCAACTCTCTTG--ACTTGTTG
1 ACTCATATGGTTTCATCCTAGTCAACTCTTTTGTAACTTGTTA
** * **
320122 GTTCGTATGGTTTCAT-CTCAACCAACTCTTTTGTAACTTGTTA
1 ACTCATATGGTTTCATCCT-AGTCAACTCTTTTGTAACTTGTTA
* *
320165 ACTCATATGGTTTCATCTTAGTCTACTCT
1 ACTCATATGGTTTCATCCTAGTCAACTCT
320194 CTTGACTTGT
Statistics
Matches: 113, Mismatches: 33, Indels: 18
0.69 0.20 0.11
Matches are distributed among these distances:
40 4 0.04
41 45 0.40
42 2 0.02
43 57 0.50
44 5 0.04
ACGTcount: A:0.22, C:0.23, G:0.12, T:0.43
Consensus pattern (43 bp):
ACTCATATGGTTTCATCCTAGTCAACTCTTTTGTAACTTGTTA
Found at i:320195 original size:84 final size:84
Alignment explanation
Indices: 319981--320209 Score: 282
Period size: 84 Copynumber: 2.7 Consensus size: 84
319971 TCTTTGTTAA
* * * * * * * * *
319981 CTCTTTTAACTCATTGACTCATATGGTTTCATCCAAGTCAACTTTCCTAACTTATTAGTTTGTAT
1 CTCTTTTAACTCGTTAACTCATATGGTTTCATCCTAGTCAACTCTCTTGACTTGTTGGTTCGTAT
** *
320046 GGTTTCATCCTGGCTAACT
66 GGTTTCATCCTAACCAACT
*
320065 CTCTTTTAACTCGTTAACTCATATAGTTTCATCCTAGTCAACTCTCTTGACTTGTTGGTTCGTAT
1 CTCTTTTAACTCGTTAACTCATATGGTTTCATCCTAGTCAACTCTCTTGACTTGTTGGTTCGTAT
320130 GGTTTCAT-CTCAACCAACT
66 GGTTTCATCCT-AACCAACT
* * *
320149 CT-TTTGTAACTTGTTAACTCATATGGTTTCATCTTAGTCTACTCTCTTGACTTGTTGGTTC
1 CTCTTT-TAACTCGTTAACTCATATGGTTTCATCCTAGTCAACTCTCTTGACTTGTTGGTTC
320210 CAGCCAACTC
Statistics
Matches: 126, Mismatches: 17, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
83 5 0.04
84 121 0.96
ACGTcount: A:0.21, C:0.23, G:0.13, T:0.44
Consensus pattern (84 bp):
CTCTTTTAACTCGTTAACTCATATGGTTTCATCCTAGTCAACTCTCTTGACTTGTTGGTTCGTAT
GGTTTCATCCTAACCAACT
Found at i:320221 original size:70 final size:70
Alignment explanation
Indices: 320143--320279 Score: 193
Period size: 70 Copynumber: 2.0 Consensus size: 70
320133 TTCATCTCAA
* * * * *
320143 CCAACTCTTTTGTAACTTGTTAACTCATATGGTTTCATCTTAGTCTACTCTCTTGACTTGTTGGT
1 CCAACTCTTTTGTAACTTGTTAACTCATATAGTTTCATCTCAGTCAACTCTCCTGACTTGTTAGT
320208 TCCAG
66 TCCAG
* * * *
320213 CCAACTCTTTTGTAACTTGTTGACTCCTATAGTTTTATCTCGGTCAACTCTCCTGACTTGTTAGT
1 CCAACTCTTTTGTAACTTGTTAACTCATATAGTTTCATCTCAGTCAACTCTCCTGACTTGTTAGT
320278 TC
66 TC
320280 ATATGGTTTT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
70 58 1.00
ACGTcount: A:0.18, C:0.24, G:0.14, T:0.44
Consensus pattern (70 bp):
CCAACTCTTTTGTAACTTGTTAACTCATATAGTTTCATCTCAGTCAACTCTCCTGACTTGTTAGT
TCCAG
Found at i:320631 original size:41 final size:41
Alignment explanation
Indices: 320225--320727 Score: 206
Period size: 41 Copynumber: 12.2 Consensus size: 41
320215 AACTCTTTTG
** * * * *
320225 TAACTTGTTGACTCCTATAGTTTTATCTCGGTCAACTCTCC
1 TAACTTGTTGACTTGTATGGTTTCATCTTGGTCAACTCTTC
* * * * * *
320266 TGACTTGTT-AGTTCATATGGTTTTATCCTGGCCAACTTCTTTC
1 TAACTTGTTGACTT-GTATGGTTTCATCTTGGTCAAC-TC-TTC
* * * * * *
320309 TAACTCGTTGACTCGTATGGTTTCGT-TCTAGTTAACCCTTC
1 TAACTTGTTGACTTGTATGGTTTCATCT-TGGTCAACTCTTC
* ** ** * * *
320350 TAACTCGTTGACTAATATGGTTTTGTCCTAGTCAACCCTTC
1 TAACTTGTTGACTTGTATGGTTTCATCTTGGTCAACTCTTC
* ** * * * ** ** *
320391 AAACTCATTGACTCGTATAGTTTTATCCCGACCAATTCTTC
1 TAACTTGTTGACTTGTATGGTTTCATCTTGGTCAACTCTTC
* * *
320432 TAACTTGTTGACTCGTATGGTTTCAACTTGGTCAATTCTTC
1 TAACTTGTTGACTTGTATGGTTTCATCTTGGTCAACTCTTC
* * * *
320473 TAACTTGTTGACTCGCATAGTTTCGT-TTGGGTCAACTC-TC
1 TAACTTGTTGACTTGTATGGTTTCATCTT-GGTCAACTCTTC
** ** * ** *
320513 TCAACTTACTGGTTTGTATGATTTTGTCTTGGCCAACTCTTC
1 T-AACTTGTTGACTTGTATGGTTTCATCTTGGTCAACTCTTC
* * * **
320555 TAACTTGTTAACATGTATGGTTTCACCTTATTCAACTCTTC
1 TAACTTGTTGACTTGTATGGTTTCATCTTGGTCAACTCTTC
* * *
320596 TAACTTGCTGACTTATATGGTTTCATCTCGGTCAAC-CTTC
1 TAACTTGTTGACTTGTATGGTTTCATCTTGGTCAACTCTTC
* *** *** * ** * * *
320636 TTGACACATTGACTCAAATAGTTTTGTCCTAGTCAACTTTTC
1 -TAACTTGTTGACTTGTATGGTTTCATCTTGGTCAACTCTTC
* * ** *
320678 TAACTTGTTGTCTTGTATGGTTTTATCCCGATCAACTCTTC
1 TAACTTGTTGACTTGTATGGTTTCATCTTGGTCAACTCTTC
320719 TAACTTGTT
1 TAACTTGTT
320728 AACAGGTATT
Statistics
Matches: 338, Mismatches: 112, Indels: 24
0.71 0.24 0.05
Matches are distributed among these distances:
40 11 0.03
41 291 0.86
42 11 0.03
43 23 0.07
44 2 0.01
ACGTcount: A:0.20, C:0.23, G:0.15, T:0.42
Consensus pattern (41 bp):
TAACTTGTTGACTTGTATGGTTTCATCTTGGTCAACTCTTC
Found at i:321329 original size:21 final size:19
Alignment explanation
Indices: 321291--321331 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
321281 TTCATTTTTC
*
321291 ATTTTTTGAAATTTTCAAG
1 ATTTTTTGAAAGTTTCAAG
321310 ATTTTTCTGTAAAGTTTCAAG
1 ATTTTT-TG-AAAGTTTCAAG
321331 A
1 A
321332 ATTGATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 2 0.11
21 11 0.58
ACGTcount: A:0.32, C:0.07, G:0.12, T:0.49
Consensus pattern (19 bp):
ATTTTTTGAAAGTTTCAAG
Found at i:323738 original size:28 final size:28
Alignment explanation
Indices: 323698--323870 Score: 166
Period size: 28 Copynumber: 6.0 Consensus size: 28
323688 TTTAGGGTAA
* *
323698 AAGTCAATGGCATCTTTTCAAAGTCCAC
1 AAGTCAGTGGCATCTTTTCAAAGCCCAC
*
323726 AAGTCAGTGGCATCCTTTCAAAGCCCAC
1 AAGTCAGTGGCATCTTTTCAAAGCCCAC
* * * *
323754 AAGTTAGTGGCACCTTTTCAAAGCCTAT
1 AAGTCAGTGGCATCTTTTCAAAGCCCAC
* * * *
323782 AAGTCAATGGCACCTTTTCAAAACCCAT
1 AAGTCAGTGGCATCTTTTCAAAGCCCAC
* * *
323810 AACTCAGTGGCATCCTTTCAAAACCCACAC
1 AAGTCAGTGGCATCTTTTC-AAAGCC-CAC
* *
323840 AAGTCGGTGGCAACTTTCTCTAAAGCCCAC
1 AAGTCAGTGGCATCTTT-TC-AAAGCCCAC
323870 A
1 A
323871 CAAGTTGGTG
Statistics
Matches: 118, Mismatches: 24, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
28 87 0.74
29 5 0.04
30 19 0.16
31 7 0.06
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.25
Consensus pattern (28 bp):
AAGTCAGTGGCATCTTTTCAAAGCCCAC
Found at i:338045 original size:21 final size:21
Alignment explanation
Indices: 338021--338073 Score: 83
Period size: 20 Copynumber: 2.6 Consensus size: 21
338011 TTCTATGATT
338021 TGTATCGATACAAGTAA-TGAA
1 TGTATCGATACAA-TAATTGAA
338042 TGTATCGATAC-ATAATTGAA
1 TGTATCGATACAATAATTGAA
338062 TGTATCGATACA
1 TGTATCGATACA
338074 TGCCTAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 3 0.10
20 16 0.53
21 11 0.37
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (21 bp):
TGTATCGATACAATAATTGAA
Found at i:338170 original size:22 final size:20
Alignment explanation
Indices: 338139--338198 Score: 84
Period size: 22 Copynumber: 2.9 Consensus size: 20
338129 ATGCATTAGC
338139 CAATGTATCGATACATGCTT
1 CAATGTATCGATACATGCTT
*
338159 ACAATTGTATCGATACATTCTT
1 -CAA-TGTATCGATACATGCTT
*
338181 CAACGTATCGATACATGC
1 CAATGTATCGATACATGC
338199 AGGCAAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 13 0.37
21 6 0.17
22 16 0.46
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33
Consensus pattern (20 bp):
CAATGTATCGATACATGCTT
Found at i:342401 original size:3 final size:3
Alignment explanation
Indices: 342393--342448 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
342383 CAATATGGAT
342393 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
342441 TTA TTA TT
1 TTA TTA TT
342449 GATGATTACC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:343602 original size:20 final size:20
Alignment explanation
Indices: 343561--343612 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
343551 TCGATACAAA
* *
343561 GTATCGATACAT-GTTTATT
1 GTATCGATACATGGATAATT
343580 GTATCGATACATGGATAATT
1 GTATCGATACATGGATAATT
343600 GTATCGATACATG
1 GTATCGATACATG
343613 AAACTGGCAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (20 bp):
GTATCGATACATGGATAATT
Found at i:343701 original size:33 final size:33
Alignment explanation
Indices: 343642--343706 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
343632 TACCATTATT
*
343642 TGTATCGATACATGGCACATTTTATCGATACAA
1 TGTATCGATACATGGCACATTGTATCGATACAA
**
343675 TGTATCGATACATGATTA-ATTGTATCGATACA
1 TGTATCGATACATG-GCACATTGTATCGATACA
343707 TTGCTTGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Consensus pattern (33 bp):
TGTATCGATACATGGCACATTGTATCGATACAA
Found at i:345316 original size:3 final size:3
Alignment explanation
Indices: 345302--345347 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
345292 CATCAAAGAC
* *
345302 GAT GAA GAT GAT GAT GAT GAT GAT GAC GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
345348 GTGACTCGGA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.35, C:0.02, G:0.35, T:0.28
Consensus pattern (3 bp):
GAT
Found at i:349677 original size:21 final size:22
Alignment explanation
Indices: 349653--349702 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
349643 ATCGAATCTT
* *
349653 CTTCAAATTTCTT-ATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
349674 CTTCAAAATACTTCATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
349696 --TCAAAAT
1 CTTCAAAAT
349703 CATCAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 7 0.27
21 11 0.42
22 8 0.31
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (22 bp):
CTTCAAAATACTTCATTTTTCA
Found at i:351945 original size:19 final size:20
Alignment explanation
Indices: 351921--351968 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
351911 TCGATACAAA
**
351921 GTATCGATACATGTTC-ATT
1 GTATCGATACATGGACAATT
351940 GTATCGATACATGGACAATT
1 GTATCGATACATGGACAATT
351960 GTATCGATA
1 GTATCGATA
351969 ATGAAACTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (20 bp):
GTATCGATACATGGACAATT
Found at i:352038 original size:33 final size:32
Alignment explanation
Indices: 352001--352065 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
351991 TACCATTGTT
352001 TGTATCGATACATG-GCACATTGTATCGATACAA
1 TGTATCGATACATGAG-A-ATTGTATCGATACAA
352034 TGTATCGATACATGATGAATTGTATCGATACA
1 TGTATCGATACATGA-GAATTGTATCGATACA
352066 TTGCTTCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 28 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.32
Consensus pattern (32 bp):
TGTATCGATACATGAGAATTGTATCGATACAA
Found at i:352039 original size:13 final size:13
Alignment explanation
Indices: 352021--352045 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
352011 CATGGCACAT
352021 TGTATCGATACAA
1 TGTATCGATACAA
352034 TGTATCGATACA
1 TGTATCGATACA
352046 TGATGAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:353889 original size:80 final size:80
Alignment explanation
Indices: 353756--353916 Score: 295
Period size: 80 Copynumber: 2.0 Consensus size: 80
353746 GATTGGTTAT
353756 TATTTTATCTTATGGCAACTAGACCCAATAAAATGTTTAATGCATGCCTATGTTCTAGATATCAA
1 TATTTTATCTTATGGCAACTAGACCCAATAAAATGTTTAATGCATGCCTATGTTCTAGATATCAA
353821 TCTTCACTAAAAGAG
66 TCTTCACTAAAAGAG
* * *
353836 TATTTTATCTTATGGCAAGTAGACCCAATAAAATGTTTAATGTATGCCTATGTTTTAGATATCAA
1 TATTTTATCTTATGGCAACTAGACCCAATAAAATGTTTAATGCATGCCTATGTTCTAGATATCAA
353901 TCTTCACTAAAAGAG
66 TCTTCACTAAAAGAG
353916 T
1 T
353917 CATATTTAGT
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 78 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.37
Consensus pattern (80 bp):
TATTTTATCTTATGGCAACTAGACCCAATAAAATGTTTAATGCATGCCTATGTTCTAGATATCAA
TCTTCACTAAAAGAG
Found at i:357370 original size:20 final size:21
Alignment explanation
Indices: 357323--357378 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
357313 ATTTTTGTTC
357323 AAATGTATTGATACATTTCTT
1 AAATGTATTGATACATTTCTT
357344 AAATGTATTGATACATTTCTT
1 AAATGTATTGATACATTTCTT
*
357365 -AATGTATCGATACA
1 AAATGTATTGATACA
357379 AGGTCCCAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 13 0.38
21 21 0.62
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.43
Consensus pattern (21 bp):
AAATGTATTGATACATTTCTT
Found at i:357541 original size:50 final size:51
Alignment explanation
Indices: 357416--357549 Score: 216
Period size: 50 Copynumber: 2.6 Consensus size: 51
357406 TTTTATTGTT
* * *
357416 TGTATCGATACATTATTCATTGTATCAATACATTATGGGTTTTTACCCAGA
1 TGTATCGATACATTATTCATTGTATCGATACATTATGGGATTTTACCCAAA
*
357467 TGTATCGATACATTCTTCATTGTATCGATACATTAT-GGATTTTACCCAAA
1 TGTATCGATACATTATTCATTGTATCGATACATTATGGGATTTTACCCAAA
*
357517 TGTATCGATACATTATTCAATGTATCGATACAT
1 TGTATCGATACATTATTCATTGTATCGATACAT
357550 GCAGGCAAAT
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
50 43 0.56
51 34 0.44
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (51 bp):
TGTATCGATACATTATTCATTGTATCGATACATTATGGGATTTTACCCAAA
Found at i:357810 original size:31 final size:31
Alignment explanation
Indices: 357775--357841 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 31
357765 GTACTCATCT
*
357775 CCAGCCACCCTACTCTGTTCCTGAGCTTTGA
1 CCAGCCACCCTACTCTGTTCCTGAGCTCTGA
*
357806 CCAG----CCTACTTTGTTCCTGAGCTCTGA
1 CCAGCCACCCTACTCTGTTCCTGAGCTCTGA
357833 CCAGCCACC
1 CCAGCCACC
357842 ATGGCATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
27 25 0.83
31 5 0.17
ACGTcount: A:0.16, C:0.40, G:0.16, T:0.27
Consensus pattern (31 bp):
CCAGCCACCCTACTCTGTTCCTGAGCTCTGA
Found at i:357821 original size:27 final size:27
Alignment explanation
Indices: 357783--357838 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
357773 CTCCAGCCAC
*
357783 CCTACTCTGTTCCTGAGCTTTGACCAG
1 CCTACTCTGTTCCTGAGCTCTGACCAG
*
357810 CCTACTTTGTTCCTGAGCTCTGACCAG
1 CCTACTCTGTTCCTGAGCTCTGACCAG
357837 CC
1 CC
357839 ACCATGGCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.14, C:0.36, G:0.18, T:0.32
Consensus pattern (27 bp):
CCTACTCTGTTCCTGAGCTCTGACCAG
Found at i:366166 original size:34 final size:34
Alignment explanation
Indices: 366128--366194 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
366118 TTAATAATAC
366128 AAAGCTAAGCTTGTTGTTAAATAATATAAATAAA
1 AAAGCTAAGCTTGTTGTTAAATAATATAAATAAA
366162 AAAGCTAAGCTTGTTGTTAAATAATATAAATAA
1 AAAGCTAAGCTTGTTGTTAAATAATATAAATAA
366195 CAAATGTAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.49, C:0.06, G:0.12, T:0.33
Consensus pattern (34 bp):
AAAGCTAAGCTTGTTGTTAAATAATATAAATAAA
Found at i:371526 original size:22 final size:21
Alignment explanation
Indices: 371490--371533 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 21
371480 ATCAAATATT
371490 TATAATTTA-TTTTTTAAAAA
1 TATAATTTATTTTTTTAAAAA
371510 TATAATATTAATTTTTTTAAAAA
1 TATAAT-TT-ATTTTTTTAAAAA
371533 T
1 T
371534 TTCATCCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.29
21 2 0.10
22 1 0.05
23 12 0.57
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TATAATTTATTTTTTTAAAAA
Found at i:372068 original size:19 final size:19
Alignment explanation
Indices: 372030--372068 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
372020 ATATTTTTAT
*
372030 AAATTATAATTATATTTAA
1 AAATTATAATTATATATAA
372049 AAATTATATATT-TATATAA
1 AAATTATA-ATTATATATAA
372068 A
1 A
372069 TTTTAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AAATTATAATTATATATAA
Found at i:372148 original size:17 final size:17
Alignment explanation
Indices: 372122--372158 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
372112 TAATCTAATT
*
372122 TTTTATATTATATTATA
1 TTTTAAATTATATTATA
*
372139 TTTTAAATTATATTTTA
1 TTTTAAATTATATTATA
372156 TTT
1 TTT
372159 ATTTATATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTAAATTATATTATA
Found at i:379702 original size:16 final size:15
Alignment explanation
Indices: 379683--379748 Score: 53
Period size: 16 Copynumber: 4.1 Consensus size: 15
379673 ATAATTAAAA
379683 ATATATATAAA-TAT
1 ATATATATAAATTAT
* *
379697 ATATATTTTAAATTTT
1 ATATA-TATAAATTAT
379713 ATATAATATAAATTAT
1 ATAT-ATATAAATTAT
*
379729 CAATATATCATAATTTAT
1 --ATATAT-ATAAATTAT
379747 AT
1 AT
379749 TAATTATAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
14 5 0.12
15 5 0.12
16 16 0.39
17 3 0.07
18 12 0.29
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
ATATATATAAATTAT
Found at i:381072 original size:5 final size:5
Alignment explanation
Indices: 381062--381088 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
381052 TCTCATTGCA
381062 CAAGG CAAGG CAAGG CAAGG CAAGG CA
1 CAAGG CAAGG CAAGG CAAGG CAAGG CA
381089 TCCAAGTACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.22, G:0.37, T:0.00
Consensus pattern (5 bp):
CAAGG
Found at i:381796 original size:2 final size:2
Alignment explanation
Indices: 381789--381831 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
381779 CCTTTCACCC
* *
381789 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AC 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
381831 A
1 A
381832 ACAATATTCC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:382382 original size:19 final size:19
Alignment explanation
Indices: 382360--382425 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 19
382350 CTTTTTTATA
382360 TAAAAAAATCAATTTTTCT
1 TAAAAAAATCAATTTTTCT
* ***
382379 TAAAAAAAAT-TATCCCTCT
1 T-AAAAAAATCAATTTTTCT
382398 TAAAAATAGATCAATTTTT-T
1 TAAAAA-A-ATCAATTTTTCT
382418 TAAAAAAA
1 TAAAAAAA
382426 ATCGATCTCT
Statistics
Matches: 35, Mismatches: 8, Indels: 9
0.67 0.15 0.17
Matches are distributed among these distances:
18 6 0.17
19 9 0.26
20 17 0.49
21 3 0.09
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.36
Consensus pattern (19 bp):
TAAAAAAATCAATTTTTCT
Found at i:382413 original size:40 final size:39
Alignment explanation
Indices: 382360--382448 Score: 119
Period size: 40 Copynumber: 2.3 Consensus size: 39
382350 CTTTTTTATA
* *
382360 TAAAAA-AATCAATTTTTCTTAAAAAAAAT-TATCCCTCT
1 TAAAAATAATCAATTTTT-TTAAAAAAAATCGATCCCTAT
*
382398 TAAAAATAGATCAATTTTTTTAAAAAAAATCGATCTCTAT
1 TAAAAATA-ATCAATTTTTTTAAAAAAAATCGATCCCTAT
382438 TAAAAATAATC
1 TAAAAATAATC
382449 GCTTTCTTGA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
38 6 0.13
39 15 0.33
40 24 0.53
ACGTcount: A:0.49, C:0.12, G:0.02, T:0.36
Consensus pattern (39 bp):
TAAAAATAATCAATTTTTTTAAAAAAAATCGATCCCTAT
Found at i:383169 original size:47 final size:48
Alignment explanation
Indices: 383111--383202 Score: 134
Period size: 47 Copynumber: 1.9 Consensus size: 48
383101 TTTAAATTCA
383111 ATTTCAAATATT-TCTTCGGACTCCCCT-TTTATTAAAATAAATAATCG
1 ATTTCAAATATTCT-TTCGGACTCCCCTATTTATTAAAATAAATAATCG
* * *
383158 ATTTCAAATATTCTTTCTGCCTCTCCTATTTATTAAAATAAATAA
1 ATTTCAAATATTCTTTCGGACTCCCCTATTTATTAAAATAAATAA
383203 ATAAATAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
47 22 0.55
48 18 0.45
ACGTcount: A:0.35, C:0.18, G:0.04, T:0.42
Consensus pattern (48 bp):
ATTTCAAATATTCTTTCGGACTCCCCTATTTATTAAAATAAATAATCG
Found at i:384240 original size:24 final size:23
Alignment explanation
Indices: 384195--384253 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 23
384185 TTCATACATG
*
384195 ATATAATAAATAAATAAAAAATA
1 ATATAATAAAAAAATAAAAAATA
*
384218 ATATAATAGAAAAAATAATAAATA
1 ATATAATA-AAAAAATAAAAAATA
384242 ATA-AGATAAAAA
1 ATATA-ATAAAAA
384254 TGTATAAATG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 13 0.41
24 19 0.59
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (23 bp):
ATATAATAAAAAAATAAAAAATA
Found at i:384262 original size:22 final size:19
Alignment explanation
Indices: 384197--384254 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 19
384187 CATACATGAT
*
384197 ATAATAAATAA-ATAAAAA
1 ATAATAAATAATAGAAAAA
384215 ATAAT--ATAATAGAAAAA
1 ATAATAAATAATAGAAAAA
384232 ATAATAAATAATAAGATAAAA
1 ATAATAAATAAT-AGA-AAAA
384253 AT
1 AT
384255 GTATAAATGT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
16 4 0.12
17 11 0.32
18 5 0.15
19 5 0.15
20 3 0.09
21 6 0.18
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.24
Consensus pattern (19 bp):
ATAATAAATAATAGAAAAA
Found at i:387118 original size:18 final size:18
Alignment explanation
Indices: 387095--387144 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
387085 ATAAAAACTG
387095 AATTTTTTAATATTTTAA
1 AATTTTTTAATATTTTAA
* *
387113 AA-TTTTTAAAAATTTAA
1 AATTTTTTAATATTTTAA
*
387130 ATATTTTTAAATATT
1 A-ATTTTTTAATATT
387145 AGATAAAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
17 14 0.56
18 3 0.12
19 8 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AATTTTTTAATATTTTAA
Found at i:387141 original size:10 final size:10
Alignment explanation
Indices: 387096--387144 Score: 52
Period size: 9 Copynumber: 5.3 Consensus size: 10
387086 TAAAAACTGA
*
387096 ATTTTTTAAT
1 ATTTTTAAAT
387106 A-TTTTAAA-
1 ATTTTTAAAT
387114 ATTTTTAAA-
1 ATTTTTAAAT
*
387123 A-ATTTAAAT
1 ATTTTTAAAT
387132 ATTTTTAAAT
1 ATTTTTAAAT
387142 ATT
1 ATT
387145 AGATAAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
8 7 0.21
9 15 0.45
10 11 0.33
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
ATTTTTAAAT
Found at i:387197 original size:13 final size:13
Alignment explanation
Indices: 387181--387206 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
387171 AAAATTAAAA
387181 AATTTTATAAATT
1 AATTTTATAAATT
387194 AATTTTATAAATT
1 AATTTTATAAATT
387207 TAATATATTT
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AATTTTATAAATT
Found at i:387231 original size:19 final size:18
Alignment explanation
Indices: 387195--387241 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
387185 TTATAAATTA
387195 ATTTTATAAATTTAATAT
1 ATTTTATAAATTTAATAT
387213 ATTTTATTAAATATT-ATAT
1 ATTTTA-TAAAT-TTAATAT
*
387232 AATTTA-AAAT
1 ATTTTATAAAT
387242 AAATAACATA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 4 0.15
18 6 0.23
19 14 0.54
20 2 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTTATAAATTTAATAT
Found at i:387568 original size:2 final size:2
Alignment explanation
Indices: 387561--387604 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
387551 GATTAGGAGA
387561 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
387603 AT
1 AT
387605 GGTTATAGTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:388579 original size:2 final size:2
Alignment explanation
Indices: 388568--388601 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
388558 AGCTGTAATC
*
388568 TA TA -A TA TA TA TA TA TA TA TA TA TA TA AA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
388602 CAAAATTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:388719 original size:17 final size:17
Alignment explanation
Indices: 388697--388732 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
388687 AGGAATCATA
388697 TAGGCAGAGGGAAGAGT
1 TAGGCAGAGGGAAGAGT
388714 TAGGCAGAGGGAAGAGT
1 TAGGCAGAGGGAAGAGT
388731 TA
1 TA
388733 AATTAGTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.06, G:0.44, T:0.14
Consensus pattern (17 bp):
TAGGCAGAGGGAAGAGT
Found at i:391534 original size:27 final size:28
Alignment explanation
Indices: 391486--391546 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
391476 CCCATGGCCA
391486 TTTCTTTATGTTATTATTCTTTT-TCTAT
1 TTTCTTTATGTTATTATTCTTTTCT-TAT
*
391514 TTTCTTTAT-TTCTT-TTCCTTTTCTTAT
1 TTTCTTTATGTTATTATT-CTTTTCTTAT
391541 TTTCTT
1 TTTCTT
391547 CTTGAATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 2 0.07
27 18 0.60
28 10 0.33
ACGTcount: A:0.10, C:0.15, G:0.02, T:0.74
Consensus pattern (28 bp):
TTTCTTTATGTTATTATTCTTTTCTTAT
Found at i:394037 original size:27 final size:27
Alignment explanation
Indices: 393976--394046 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
393966 AAACAAGCCT
* *
393976 CCATATTTGACAAATACAAAGGAAACCA
1 CCATTTTTGACAAACACAAA-GAAACCA
394004 CCATTTTTGACAAACACAAA-ATAACCA
1 CCATTTTTGACAAACACAAAGA-AACCA
*
394031 CCATTTTTTACAAACA
1 CCATTTTTGACAAACA
394047 AATGGGTGGC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 1 0.03
27 20 0.51
28 18 0.46
ACGTcount: A:0.46, C:0.24, G:0.06, T:0.24
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAGAAACCA
Found at i:395968 original size:21 final size:22
Alignment explanation
Indices: 395930--395975 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
395920 ATCTGTTGAA
* **
395930 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
395951 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
395973 ACT
1 ACT
395976 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:398614 original size:27 final size:27
Alignment explanation
Indices: 398549--398619 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
398539 AAACAAGCCT
* *
398549 CCATATTTGACAAATACAAAGGAAACCA
1 CCATTTTTGACAAACACAAA-GAAACCA
*
398577 CCATTTTTGACAAACACAAA-ATAACTA
1 CCATTTTTGACAAACACAAAGA-AACCA
398604 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
398620 AATGGGTGGC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 1 0.03
27 20 0.51
28 18 0.46
ACGTcount: A:0.46, C:0.23, G:0.07, T:0.24
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAGAAACCA
Found at i:400444 original size:23 final size:24
Alignment explanation
Indices: 400395--400445 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
400385 AAATTTGAAA
* *
400395 TAAATTTATTAATATATTTTTAAT
1 TAAATTAATTAATATACTTTTAAT
*
400419 TAAATTAATTAAT-TACTTTTATT
1 TAAATTAATTAATATACTTTTAAT
400442 TAAA
1 TAAA
400446 AATTTAATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 12 0.50
24 12 0.50
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (24 bp):
TAAATTAATTAATATACTTTTAAT
Found at i:404348 original size:2 final size:2
Alignment explanation
Indices: 404341--404369 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
404331 TTACAGTTCT
404341 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 T
404370 TTTATAAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:407437 original size:34 final size:34
Alignment explanation
Indices: 407399--407567 Score: 257
Period size: 34 Copynumber: 5.0 Consensus size: 34
407389 TAGGTGAAGC
407399 ATGTTAGGTGTGTTAGGTAATGTATTTGGTGAGA
1 ATGTTAGGTGTGTTAGGTAATGTATTTGGTGAGA
* *
407433 ATGTTATGTGTGTTAGGTGATGTATTTGGTGAGA
1 ATGTTAGGTGTGTTAGGTAATGTATTTGGTGAGA
*
407467 ATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGA
1 ATGTTAGGTGTGTTAGGTAATGTATTTGGTGAGA
* * *
407501 ATATTAGATGTGTTAGGTAATGTATTTGGTGAAA
1 ATGTTAGGTGTGTTAGGTAATGTATTTGGTGAGA
* * *
407535 ATATTAGGTGTGTTAGGTAATGTGTTAGGTGAG
1 ATGTTAGGTGTGTTAGGTAATGTATTTGGTGAG
407568 TAAGATATTT
Statistics
Matches: 124, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 124 1.00
ACGTcount: A:0.24, C:0.00, G:0.34, T:0.41
Consensus pattern (34 bp):
ATGTTAGGTGTGTTAGGTAATGTATTTGGTGAGA
Found at i:412318 original size:34 final size:34
Alignment explanation
Indices: 412283--412414 Score: 201
Period size: 34 Copynumber: 3.9 Consensus size: 34
412273 GTGAAGCATG
* *
412283 TTAGGTGTGTTAGGTGATGTATTTGGTGAGAATG
1 TTAGGTGTGTTAGGTAATGTATTTGGTGAGAATA
*
412317 TTAGGTGTGTTAGGTGATGTATTTGGTGAGAATA
1 TTAGGTGTGTTAGGTAATGTATTTGGTGAGAATA
* *
412351 TTAGATGTGTTAGGTAATGTATTTGGTGAAAATA
1 TTAGGTGTGTTAGGTAATGTATTTGGTGAGAATA
* *
412385 TTAGGTGTGTTAGGTAATGTGTTAGGTGAG
1 TTAGGTGTGTTAGGTAATGTATTTGGTGAG
412415 TAAGGTATTT
Statistics
Matches: 90, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 90 1.00
ACGTcount: A:0.24, C:0.00, G:0.35, T:0.41
Consensus pattern (34 bp):
TTAGGTGTGTTAGGTAATGTATTTGGTGAGAATA
Found at i:412903 original size:2 final size:2
Alignment explanation
Indices: 412898--412935 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
412888 TATGTGTGTT
412898 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
412936 ATGAAAGTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:413148 original size:6 final size:6
Alignment explanation
Indices: 413120--413180 Score: 50
Period size: 6 Copynumber: 10.0 Consensus size: 6
413110 TAATTATTTG
* * * * *
413120 AATAGA AATAGA AATATA AATATA AATATA ATTTATA TATATA TATATA
1 AATATA AATATA AATATA AATATA AATATA A-ATATA AATATA AATATA
* *
413169 TATATA TATATA
1 AATATA AATATA
413181 TCAGCATCTA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
6 46 0.92
7 4 0.08
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.39
Consensus pattern (6 bp):
AATATA
Found at i:413160 original size:2 final size:2
Alignment explanation
Indices: 413133--413181 Score: 64
Period size: 2 Copynumber: 25.0 Consensus size: 2
413123 AGAAATAGAA
* * *
413133 AT AT AA AT AT AA AT AT A- AT TT 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
413174 AT AT AT AT
1 AT AT AT AT
413182 CAGCATCTAC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:414457 original size:26 final size:26
Alignment explanation
Indices: 414428--414481 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
414418 TCTTCATGAT
*
414428 GAAAAATAAAAGTGGGATACAATGGA
1 GAAAAATAAAAGTGGGATACAATAGA
* *
414454 GAAAAATGAAAGTGGGATATAATAGA
1 GAAAAATAAAAGTGGGATACAATAGA
414480 GA
1 GA
414482 TAGCTAGGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.54, C:0.02, G:0.28, T:0.17
Consensus pattern (26 bp):
GAAAAATAAAAGTGGGATACAATAGA
Found at i:416038 original size:15 final size:15
Alignment explanation
Indices: 416018--416062 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
416008 ATTTTTAAAT
*
416018 AAACTTTTTCAACTC
1 AAACTTTTTCAACTA
* *
416033 AAACTTTTTTAAGTA
1 AAACTTTTTCAACTA
416048 AAACTTTTTTCAACT
1 AAAC-TTTTTCAACT
416063 TCAATACTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
15 16 0.67
16 8 0.33
ACGTcount: A:0.36, C:0.18, G:0.02, T:0.44
Consensus pattern (15 bp):
AAACTTTTTCAACTA
Found at i:419667 original size:21 final size:18
Alignment explanation
Indices: 419642--419686 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 18
419632 TTTCTACAAA
419642 AAAAAAGCTAGAGAAAAAGAGG
1 AAAAAA-CTA-AGAAAAA-A-G
419664 AAAAAACTAAGAAAAAAG
1 AAAAAACTAAGAAAAAAG
419682 AAAAA
1 AAAAA
419687 TAAAGAAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.26
19 1 0.04
20 7 0.30
21 3 0.13
22 6 0.26
ACGTcount: A:0.73, C:0.04, G:0.18, T:0.04
Consensus pattern (18 bp):
AAAAAACTAAGAAAAAAG
Found at i:421607 original size:3 final size:3
Alignment explanation
Indices: 421599--421633 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
421589 CCATGCTTCT
421599 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
421634 TCATGCAATA
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:421743 original size:23 final size:23
Alignment explanation
Indices: 421702--421746 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
421692 TAATGCATTT
*
421702 ATAAATATCAATTATATATTTTC
1 ATAAATATCAAATATATATTTTC
421725 ATAAATATCAAGATA-ATATTTT
1 ATAAATATCAA-ATATATATTTT
421747 GTGTTAGGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (23 bp):
ATAAATATCAAATATATATTTTC
Found at i:430789 original size:20 final size:20
Alignment explanation
Indices: 430764--430813 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
430754 TTCCCAGATG
430764 TATCGATACAATGATAAATA
1 TATCGATACAATGATAAATA
* * * *
430784 TATCGATACACTTATTAATG
1 TATCGATACAATGATAAATA
430804 TATCGATACA
1 TATCGATACA
430814 TTACCTTGGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.34
Consensus pattern (20 bp):
TATCGATACAATGATAAATA
Found at i:431632 original size:61 final size:61
Alignment explanation
Indices: 431537--431673 Score: 186
Period size: 61 Copynumber: 2.2 Consensus size: 61
431527 AAAGATGATG
* * * *
431537 AAGATGA-AAAGAGTGATAAAGGTGCCAATATGCTGATTCAGGACCAGTGATATTGGGCTTA
1 AAGATGAGAAA-AATGATAAAGGCGCCAATATGCTGATTCAAGACCAGTGATATTGGGCATA
* *
431598 AAGATGAGAAAAATGATAAGGGCGCCAATATGCTGATTCAAGCCCAGTGATATTGGGCATA
1 AAGATGAGAAAAATGATAAAGGCGCCAATATGCTGATTCAAGACCAGTGATATTGGGCATA
* *
431659 AAGATGCGAAGAATG
1 AAGATGAGAAAAATG
431674 CCAATGTGCT
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
61 64 0.96
62 3 0.04
ACGTcount: A:0.38, C:0.12, G:0.28, T:0.22
Consensus pattern (61 bp):
AAGATGAGAAAAATGATAAAGGCGCCAATATGCTGATTCAAGACCAGTGATATTGGGCATA
Found at i:431833 original size:52 final size:53
Alignment explanation
Indices: 431729--431920 Score: 158
Period size: 52 Copynumber: 3.7 Consensus size: 53
431719 GAAGAATGCT
* * * * ** *
431729 AATGTACTGATTCAAAGCCAGCAACATTGGGCTT--AGTAATGTTAAAGATGCC
1 AATGTACTGATTCAAGGCCAGCGACATTGGACTTAAAG-AAAGAAAAAGGTGCC
* * * *
431781 AATATACTGATTCAAGGCCAGCGATATTTGG-CTTAAAG-ATGACAAAGGTGCC
1 AATGTACTGATTCAAGGCCAGCGACA-TTGGACTTAAAGAAAGAAAAAGGTGCC
* * * * *
431833 AATGTGCTGATTCTAGGCTAGCGACATTGGACTTGAAGAAAGAAAAAGGTGCT
1 AATGTACTGATTCAAGGCCAGCGACATTGGACTTAAAGAAAGAAAAAGGTGCC
* * * *
431886 AATGTACTAATTCAAGGCCAACAACATTGGGCTTA
1 AATGTACTGATTCAAGGCCAGCGACATTGGACTTA
431921 GAAGTAAATG
Statistics
Matches: 111, Mismatches: 24, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
51 4 0.04
52 63 0.57
53 42 0.38
54 2 0.02
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.26
Consensus pattern (53 bp):
AATGTACTGATTCAAGGCCAGCGACATTGGACTTAAAGAAAGAAAAAGGTGCC
Found at i:431887 original size:157 final size:157
Alignment explanation
Indices: 431621--431921 Score: 412
Period size: 157 Copynumber: 1.9 Consensus size: 157
431611 TGATAAGGGC
* * *
431621 GCCAATATGCTGATTCAAGCCCAGTGATATTGGGCATAAAGATGCGAAGAATGCCAATGTGCTTG
1 GCCAATATACTGATTCAAGCCCAGCGATATTGGGCATAAAGATGCAAAGAATGCCAATGTGCTTG
* * * * *
431686 ATTTATGGCTAGTGACATTAGACTTGAAGATGAGAAGAATGCTAATGTACTGATTCAAAGCCAGC
66 ATTTATGGCTAGCGACATTAGACTTGAAGATAAGAAAAATGCTAATGTACTAATTCAAAGCCAAC
431751 AACATTGGGCTTAGTAATGTTAAAGAT
131 AACATTGGGCTTAGTAATGTTAAAGAT
* * * *
431778 GCCAATATACTGATTCAAGGCCAGCGATATTTGGCTTAAAGATGACAAAG-GTGCCAATGTGC-T
1 GCCAATATACTGATTCAAGCCCAGCGATATTGGGCATAAAGATG-CAAAGAATGCCAATGTGCTT
* *
431841 GATTCTA-GGCTAGCGACATTGGACTTGAAGA-AAGAAAAAGGTGCTAATGTACTAATTCAAGGC
65 GATT-TATGGCTAGCGACATTAGACTTGAAGATAAGAAAAA--TGCTAATGTACTAATTCAAAGC
431904 CAACAACATTGGGCTTAG
127 CAACAACATTGGGCTTAG
431922 AAGTAAATGC
Statistics
Matches: 126, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
155 6 0.05
156 27 0.21
157 89 0.71
158 4 0.03
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (157 bp):
GCCAATATACTGATTCAAGCCCAGCGATATTGGGCATAAAGATGCAAAGAATGCCAATGTGCTTG
ATTTATGGCTAGCGACATTAGACTTGAAGATAAGAAAAATGCTAATGTACTAATTCAAAGCCAAC
AACATTGGGCTTAGTAATGTTAAAGAT
Found at i:431995 original size:31 final size:31
Alignment explanation
Indices: 431929--432029 Score: 85
Period size: 31 Copynumber: 3.2 Consensus size: 31
431919 TAGAAGTAAA
* * * * *
431929 TGCCACCGACTTATGTGGGCTTTTGAGAGGGT
1 TGCCACCAACCTATATGGGCTTTAGA-AAGGT
*
431961 TGCCACCAACCTATATGGGTTTTAGAAAGGT
1 TGCCACCAACCTATATGGGCTTTAGAAAGGT
* * * * * *
431992 TGCCATCGACTTTTGTGGGCTTTAGAAGGGT
1 TGCCACCAACCTATATGGGCTTTAGAAAGGT
432023 TGCCACC
1 TGCCACC
432030 GACTTGTGTA
Statistics
Matches: 55, Mismatches: 14, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
31 34 0.62
32 21 0.38
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.31
Consensus pattern (31 bp):
TGCCACCAACCTATATGGGCTTTAGAAAGGT
Found at i:432082 original size:28 final size:27
Alignment explanation
Indices: 432004--432238 Score: 218
Period size: 28 Copynumber: 8.2 Consensus size: 27
431994 CCATCGACTT
*
432004 TTGTGGGCTTTAGAAGGGTTGCCACCGAC
1 TTGTGGGCTTTAGAA-GG-TGCCACTGAC
*
432033 TTGTGTAGGCTTTAGAAGGGTGCCACCGAC
1 TTGTG--GGCTTTAGAA-GGTGCCACTGAC
* *
432063 TTGTGAGCTTTGAGAAGGTGCCACTAAC
1 TTGTGGGCTTT-AGAAGGTGCCACTGAC
* * *
432091 TTGTGGGCTTTTGAAGGGTTACCACCGAC
1 TTGTGGGCTTTAGAA-GG-TGCCACTGAC
* *
432120 TTGTAGGCTTTAAGAAGATGCCACTGAC
1 TTGTGGGCTTT-AGAAGGTGCCACTGAC
* *
432148 TTGTGGGCTTTGAAAAGGGTGGCACTGAC
1 TTGTGGGCTTT-AGAA-GGTGCCACTGAC
*
432177 TTGTGGGCTTTCGAAGAGTGCCACTGAC
1 TTGTGGGCTTTAGAAG-GTGCCACTGAC
* *
432205 TTGTGGGCTTTAAAAGGGTGACACTGAC
1 TTGTGGGCTTTAGAA-GGTGCCACTGAC
*
432233 TCGTGG
1 TTGTGG
432239 ACTTAAAAGG
Statistics
Matches: 172, Mismatches: 25, Indels: 19
0.80 0.12 0.09
Matches are distributed among these distances:
27 4 0.02
28 88 0.51
29 49 0.28
30 18 0.10
31 13 0.08
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (27 bp):
TTGTGGGCTTTAGAAGGTGCCACTGAC
Found at i:432130 original size:57 final size:55
Alignment explanation
Indices: 432004--432238 Score: 238
Period size: 57 Copynumber: 4.1 Consensus size: 55
431994 CCATCGACTT
* *
432004 TTGTGGGCTTTAGAAGGGTTGCCACCGACTTGTGTAGGCTTTAGAAGGGTGCCACCGAC
1 TTGTGGGCTTTAGAA-GG-TGCCACTGACTTGTG--GGCTTTTGAAGGGTGCCACCGAC
* * *
432063 TTGTGAGCTTTGAGAAGGTGCCACTAACTTGTGGGCTTTTGAAGGGTTACCACCGAC
1 TTGTGGGCTTT-AGAAGGTGCCACTGACTTGTGGGCTTTTGAAGGG-TGCCACCGAC
* * * *
432120 TTGTAGGCTTTAAGAAGATGCCACTGACTTGTGGGC-TTTGAAAAGGGTGGCACTGAC
1 TTGTGGGCTTT-AGAAGGTGCCACTGACTTGTGGGCTTTTG--AAGGGTGCCACCGAC
* ** * *
432177 TTGTGGGCTTTCGAAGAGTGCCACTGACTTGTGGGCTTTAAAAGGGTGACACTGAC
1 TTGTGGGCTTTAGAAG-GTGCCACTGACTTGTGGGCTTTTGAAGGGTGCCACCGAC
*
432233 TCGTGG
1 TTGTGG
432239 ACTTAAAAGG
Statistics
Matches: 150, Mismatches: 20, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
56 39 0.26
57 75 0.50
58 20 0.13
59 12 0.08
60 4 0.03
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (55 bp):
TTGTGGGCTTTAGAAGGTGCCACTGACTTGTGGGCTTTTGAAGGGTGCCACCGAC
Found at i:432230 original size:85 final size:86
Alignment explanation
Indices: 432004--432252 Score: 292
Period size: 85 Copynumber: 2.9 Consensus size: 86
431994 CCATCGACTT
* * *
432004 TTGTGGGCTTTAGAAGGGTTGCCACCGACTTGTGTAGGCTTTAGAAGGGTGCCACCGACTTGTGA
1 TTGTGGGCTTTAGAAGGGTTGCCACCGACTTGTG--GGCTTTAAAAGGGTGCCACTGACTTGTGG
*
432069 GCTTTGAGAA-GGTGCCACTAAC
64 GCTTTGAAAAGGGTGCCACTAAC
* * * *
432091 TTGTGGGCTTTTGAAGGGTTACCACCGACTTGTAGGCTTTAAGAA-GATGCCACTGACTTGTGGG
1 TTGTGGGCTTTAGAAGGGTTGCCACCGACTTGTGGGCTTTAA-AAGGGTGCCACTGACTTGTGGG
* *
432155 CTTTGAAAAGGGTGGCACTGAC
65 CTTTGAAAAGGGTGCCACTAAC
* * * * * *
432177 TTGTGGGCTTTCGAAGAG-TGCCACTGACTTGTGGGCTTTAAAAGGGTGACACTGACTCGTGGAC
1 TTGTGGGCTTTAGAAGGGTTGCCACCGACTTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGC
432241 -TT-AAAAGGGTGC
66 TTTGAAAAGGGTGC
432253 ATAGAGTAGT
Statistics
Matches: 139, Mismatches: 20, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
83 9 0.06
84 4 0.03
85 67 0.48
86 28 0.20
87 31 0.22
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (86 bp):
TTGTGGGCTTTAGAAGGGTTGCCACCGACTTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGC
TTTGAAAAGGGTGCCACTAAC
Found at i:433785 original size:14 final size:14
Alignment explanation
Indices: 433768--433794 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
433758 TCTTTTTCTT
433768 TTTTTTTGTTTTTA
1 TTTTTTTGTTTTTA
433782 TTTTTTTGTTTTT
1 TTTTTTTGTTTTT
433795 TTTATGAAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.04, C:0.00, G:0.07, T:0.89
Consensus pattern (14 bp):
TTTTTTTGTTTTTA
Found at i:433798 original size:17 final size:16
Alignment explanation
Indices: 433753--433799 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
433743 TTTCATACCC
* *
433753 TTTTTTCTTTTTCTTT
1 TTTTTTGTTTTTATTT
433769 TTTTTTGTTTTTATTT
1 TTTTTTGTTTTTATTT
*
433785 TTTTGTTTTTTTTAT
1 TTTT-TTGTTTTTAT
433800 GAAGGACGCC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 18 0.67
17 9 0.33
ACGTcount: A:0.04, C:0.04, G:0.04, T:0.87
Consensus pattern (16 bp):
TTTTTTGTTTTTATTT
Found at i:436721 original size:26 final size:30
Alignment explanation
Indices: 436687--436762 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 30
436677 TCCACTTTTC
* *
436687 TTCCTTGTTGCTTTG-CTT-T-TTTGCTG-
1 TTCCATGTTGCTTTGTCTTATCATTGCTGT
*
436713 TTCCATGTTACTTTGTCTTAATCATTGCTGT
1 TTCCATGTTGCTTTGTCTT-ATCATTGCTGT
436744 TTCCATGTTGCTTTGTCTT
1 TTCCATGTTGCTTTGTCTT
436763 CCACCTTCTT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
26 13 0.32
27 3 0.07
29 1 0.02
30 6 0.15
31 18 0.44
ACGTcount: A:0.08, C:0.20, G:0.16, T:0.57
Consensus pattern (30 bp):
TTCCATGTTGCTTTGTCTTATCATTGCTGT
Found at i:436967 original size:15 final size:15
Alignment explanation
Indices: 436937--436991 Score: 78
Period size: 15 Copynumber: 3.8 Consensus size: 15
436927 ATCAACTTTC
436937 ATGC-ATGAAA-ACA
1 ATGCAATGAAATACA
436950 ATGCAATGAAATACA
1 ATGCAATGAAATACA
*
436965 ATGCAATGAAATGCA
1 ATGCAATGAAATACA
*
436980 ATGAAATGAAAT
1 ATGCAATGAAAT
436992 GTTTTTGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.11
14 6 0.16
15 28 0.74
ACGTcount: A:0.53, C:0.11, G:0.16, T:0.20
Consensus pattern (15 bp):
ATGCAATGAAATACA
Done.