Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 26 of 204
Found at i:9513180 original size:3 final size:3
Alignment explanation
Indices: 9513165--9513215 Score: 77
Period size: 3 Copynumber: 17.3 Consensus size: 3
9513155 CCACTCATCT
* *
9513165 TAA TAA -AA AAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
9513212 TAA T
1 TAA T
9513216 TTTCTCACAT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:9514522 original size:25 final size:23
Alignment explanation
Indices: 9514478--9514538 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
9514468 ATTTTGATTT
*
9514478 ATTTAATAATATAATATCATTATA
1 ATTTAATTATATAATATCA-TATA
9514502 ATTTAATTATCATAA-ATTCATATA
1 ATTTAATTAT-ATAATA-TCATATA
*
9514526 ATATAAATTATAT
1 AT-TTAATTATAT
9514539 TTAAATATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 18 0.56
25 14 0.44
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTAATTATATAATATCATATA
Found at i:9514541 original size:35 final size:35
Alignment explanation
Indices: 9514486--9514565 Score: 103
Period size: 35 Copynumber: 2.3 Consensus size: 35
9514476 TTATTTAATA
* *
9514486 ATATAATAT-CATTATAATTTAATTATCATAAATT
1 ATATAATATAAATTATAATTTAAATATCATAAATT
*
9514520 CATATAATATAAATTAT-ATTTAAATATCATTAATT
1 -ATATAATATAAATTATAATTTAAATATCATAAATT
9514555 ATATAAT-TAAA
1 ATATAATATAAA
9514566 CAAATAAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
33 4 0.10
34 7 0.17
35 25 0.61
36 5 0.12
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (35 bp):
ATATAATATAAATTATAATTTAAATATCATAAATT
Found at i:9516340 original size:23 final size:23
Alignment explanation
Indices: 9516313--9516381 Score: 111
Period size: 23 Copynumber: 3.0 Consensus size: 23
9516303 AAAAATGAAA
9516313 CCAAAATTGAAATAACCCTAAAT
1 CCAAAATTGAAATAACCCTAAAT
9516336 CCAAAATTGAAATAACCCTAAAT
1 CCAAAATTGAAATAACCCTAAAT
* * *
9516359 TCAAAATTAAAATAACCCAAAAT
1 CCAAAATTGAAATAACCCTAAAT
9516382 AACCTTACAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.55, C:0.20, G:0.03, T:0.22
Consensus pattern (23 bp):
CCAAAATTGAAATAACCCTAAAT
Found at i:9516937 original size:31 final size:30
Alignment explanation
Indices: 9516902--9516962 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
9516892 CCAGTGATTA
* *
9516902 TTTTGACACTTTTTTATAATGTT-AGTGACTG
1 TTTTGACA-TTTTTCA-AAAGTTGAGTGACTG
*
9516933 TTTTGTCATTTTTCAAAAGTTGAGTGACTG
1 TTTTGACATTTTTCAAAAGTTGAGTGACTG
9516963 AAATAAAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
29 5 0.19
30 14 0.54
31 7 0.27
ACGTcount: A:0.23, C:0.10, G:0.18, T:0.49
Consensus pattern (30 bp):
TTTTGACATTTTTCAAAAGTTGAGTGACTG
Found at i:9526225 original size:3 final size:3
Alignment explanation
Indices: 9526217--9526274 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
9526207 TTTGTAGGCT
9526217 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
9526265 TTA TTA TTA T
1 TTA TTA TTA T
9526275 ATATATATGA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:9527605 original size:11 final size:11
Alignment explanation
Indices: 9527589--9527636 Score: 60
Period size: 11 Copynumber: 4.3 Consensus size: 11
9527579 ATTTTTTAAC
9527589 TTTAAAATACT
1 TTTAAAATACT
9527600 TTTAAAATACTT
1 TTTAAAATAC-T
* **
9527612 TTTTAAATTTT
1 TTTAAAATACT
9527623 TTTAAAATACT
1 TTTAAAATACT
9527634 TTT
1 TTT
9527637 TTTAATTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
11 22 0.73
12 8 0.27
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (11 bp):
TTTAAAATACT
Found at i:9527625 original size:23 final size:23
Alignment explanation
Indices: 9527599--9527650 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
9527589 TTTAAAATAC
9527599 TTTTAAAATACTTTTTTAAATTT
1 TTTTAAAATACTTTTTTAAATTT
*
9527622 TTTTAAAATACTTTTTTTAATTT
1 TTTTAAAATACTTTTTTAAATTT
9527645 TTTTAA
1 TTTTAA
9527651 TTTTAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (23 bp):
TTTTAAAATACTTTTTTAAATTT
Found at i:9527681 original size:40 final size:43
Alignment explanation
Indices: 9527610--9527704 Score: 133
Period size: 40 Copynumber: 2.3 Consensus size: 43
9527600 TTTAAAATAC
* * *
9527610 TTTTTTAAATTTTTTTAAAATACTTTTTTTAA-TTT-TTTTAA
1 TTTTTAAAATATTTTAAAAATACTTTTTTTAATTTTATTTTAA
9527651 -TTTTAAAATATTTTAAAAATACTTTTTTTAATTTTTATTTTAA
1 TTTTTAAAATATTTTAAAAATACTTTTTTTAA-TTTTATTTTAA
9527694 TTTTTAAAATA
1 TTTTTAAAATA
9527705 AATTTTTAGT
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
40 28 0.60
42 3 0.06
43 6 0.13
44 10 0.21
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (43 bp):
TTTTTAAAATATTTTAAAAATACTTTTTTTAATTTTATTTTAA
Found at i:9536549 original size:12 final size:12
Alignment explanation
Indices: 9536532--9536556 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9536522 AAAAATGACG
9536532 AGAGGAATTTGT
1 AGAGGAATTTGT
9536544 AGAGGAATTTGT
1 AGAGGAATTTGT
9536556 A
1 A
9536557 CCTAGGAGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (12 bp):
AGAGGAATTTGT
Found at i:9537762 original size:13 final size:13
Alignment explanation
Indices: 9537720--9537762 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
9537710 TTGCTTTTGG
9537720 AAAGTGC-TGTGA
1 AAAGTGCTTGTGA
9537732 AAATGTGCTTGTGA
1 AAA-GTGCTTGTGA
* *
9537746 AAAGTGTTTTTGA
1 AAAGTGCTTGTGA
9537759 AAAG
1 AAAG
9537763 CTTGGTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 3 0.11
13 16 0.59
14 8 0.30
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.33
Consensus pattern (13 bp):
AAAGTGCTTGTGA
Found at i:9541678 original size:3 final size:3
Alignment explanation
Indices: 9541670--9541765 Score: 126
Period size: 3 Copynumber: 32.3 Consensus size: 3
9541660 GTAAATGATC
*
9541670 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
9541718 ATA AT- ATA GCTA ATTA AT- TTA ATA ATA ATA ATA ATA ATA ATA A-A
1 ATA ATA ATA -ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
9541762 ATA A
1 ATA A
9541766 CGGGACTAAA
Statistics
Matches: 82, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
2 5 0.06
3 72 0.88
4 5 0.06
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:9542477 original size:13 final size:13
Alignment explanation
Indices: 9542459--9542483 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9542449 TTTAATGTAA
9542459 AAAAATAAAAAAT
1 AAAAATAAAAAAT
9542472 AAAAATAAAAAA
1 AAAAATAAAAAA
9542484 GGAACTACAA
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:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:9548967 original size:32 final size:32
Alignment explanation
Indices: 9548926--9549020 Score: 163
Period size: 32 Copynumber: 3.0 Consensus size: 32
9548916 TGTCCAGTAT
*
9548926 TGTTTTTAGCTTTTGAATTGAGATTCCATCAC
1 TGTTTTTAGCTTATGAATTGAGATTCCATCAC
9548958 TGTTTTTAGCTTATGAATTGAGATTCCATCAC
1 TGTTTTTAGCTTATGAATTGAGATTCCATCAC
* *
9548990 TGTTTTTAGCTTCTGAATTGAGTTTCCATCA
1 TGTTTTTAGCTTATGAATTGAGATTCCATCA
9549021 ATCTATTTTA
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 60 1.00
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.46
Consensus pattern (32 bp):
TGTTTTTAGCTTATGAATTGAGATTCCATCAC
Found at i:9550425 original size:301 final size:292
Alignment explanation
Indices: 9549888--9550746 Score: 899
Period size: 301 Copynumber: 2.9 Consensus size: 292
9549878 TTGTTATGGG
* * * *
9549888 TTCAAATCTCAGCATATACATATTTTTATTAGTTTTTT-AGTGAAAAGAGTGAAATACCCTTAAA
1 TTCAAATCTCA-CATATACATATTTTTATTAGTTTTTTAAGTGAAAAGACTAAAATACTCTCAAA
* * * * * *
9549952 TAATATTACTTATTTTAATTACAAAATGACATTCTCGTAATTTTCTAACCGAGTTGTTACTCGGT
65 TAATATTACTTATTTTAATTACGAAAGGGCATTCTCGTACTTCT-TAACCGAGTTGTGACTCGGT
* * * *
9550017 TGAGGATGACACCGACTCAATAAAACAG-TTAAATAATAGCAAGTATAGATATACAACTGATAAA
129 TGAGGGTGACACCGACTCAA-ACAAGAGCTTAAATAATAG-AAGTA-AGATATACAACTGATGAA
* * * *
9550081 TGTAGTAAAGTGTGCATAATAAAATTAAAATGTATAAAAATATAAAAAAAAAAGTTGTAGTTGAA
191 GGTAATAAAGTGTGCATAATAAAATTAAAATGTATAAAAATATATAATAAAAAGTT-TAGTTGAA
* *
9550146 TGGTAAATTAAAGGTTTAACTAAAGTAATTGGTGTAAA
255 TGATAAATTAAAGGTTTAACTAAAGCAATTGGTGTAAA
* *
9550184 TTCAAATCTCACTAAATTCATATTTTTA-TAGTTTTTTAAAGTGAAAAGACTAAAATACTCTCAA
1 TTCAAATCTCAC-ATATACATATTTTTATTAGTTTTTT-AAGTGAAAAGACTAAAATACTCTCAA
*
9550248 ATAATATTACTTATTTTAATTACGAAAGGGCATTCTCGTGACTTCTTAACCAAGTTGATGACTCG
64 ATAATATTACTTATTTTAATTACGAAAGGGCATTCTCGT-ACTTCTTAACCGAGTTG-TGACTCG
** *
9550313 GTTGAGGGTGACAATGACTCAACCAAGAGCTTAATTATAGTATAGAAGTAGAGATATACAA-TCG
127 GTTGAGGGTGACACCGACTCAAACAAGAGCTTAA--ATA--ATAGAAGTA-AGATATACAACT-G
** * *
9550377 ATGAAGGTAATAAAGTGTGCATAATAAAATTAAAATGTATAAAAATATATTTTTTAAAACTTTAG
186 ATGAAGGTAATAAAGTGTGCATAATAAAATTAAAATGTATAAAAATATA-TAATAAAAAGTTTAG
* * * **
9550442 TTGAATGATAAATTAAAGGTTTTATTAATGCAATTGGTGTGGA
250 TTGAATGATAAATTAAAGGTTTAACTAAAGCAATTGGTGTAAA
* * * * *
9550485 TTCAAACTTTGC-CATATGCATATATTTATTGGTTTTTTAAGTGAAAAGACTAAAATGCTCTCAA
1 TTCAAA-TCT-CACATATACATATTTTTATTAGTTTTTTAAGTGAAAAGACTAAAATACTCTCAA
* * *
9550549 ATAATATTACTTATTTTAATTAAATATTATGAAAGGGCATTCTCATAACTTCTTAATCGAGTTTG
64 ATAATATTACTTA--TT--TT--A-ATTACGAAAGGGCATTCTCGT-ACTTCTTAACCGAG-TT-
* * * * * *
9550614 GTGACCCGATTAAGGGTGACACCAATTCAATCAAGAGCTTAAATAATA-ATA-TAA-ATATACAA
119 GTGACTCGGTTGAGGGTGACACCGACTCAAACAAGAGCTTAAATAATAGA-AGTAAGATATACAA
* * * *
9550676 CTAATGGAGGTAATAAATTGTACATAATAAAATTAAAATGTATAAAAATAT-TAATAAAAAGTTT
183 CTGATGAAGGTAATAAAGTGTGCATAATAAAATTAAAATGTATAAAAATATATAATAAAAAG-TT
9550740 TAGTTGA
247 TAGTTGA
9550747 CAGAAGTTTT
Statistics
Matches: 473, Mismatches: 63, Indels: 49
0.81 0.11 0.08
Matches are distributed among these distances:
295 10 0.02
296 24 0.05
297 71 0.15
298 33 0.07
300 10 0.02
301 166 0.35
302 74 0.16
303 5 0.01
304 3 0.01
305 6 0.01
307 4 0.01
308 31 0.07
309 35 0.07
310 1 0.00
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.34
Consensus pattern (292 bp):
TTCAAATCTCACATATACATATTTTTATTAGTTTTTTAAGTGAAAAGACTAAAATACTCTCAAAT
AATATTACTTATTTTAATTACGAAAGGGCATTCTCGTACTTCTTAACCGAGTTGTGACTCGGTTG
AGGGTGACACCGACTCAAACAAGAGCTTAAATAATAGAAGTAAGATATACAACTGATGAAGGTAA
TAAAGTGTGCATAATAAAATTAAAATGTATAAAAATATATAATAAAAAGTTTAGTTGAATGATAA
ATTAAAGGTTTAACTAAAGCAATTGGTGTAAA
Found at i:9552334 original size:41 final size:41
Alignment explanation
Indices: 9552232--9552337 Score: 176
Period size: 41 Copynumber: 2.6 Consensus size: 41
9552222 ACTGGCAATT
* * *
9552232 AGCCTGCTAGACGTAAAGTCCGAAATATTTCACCGGCGTCA
1 AGCCTGCTAGACGTAAAGTCTGAAACATTTCACCGGCATCA
*
9552273 AGCCTGCTAGACGTATAGTCTGAAACATTTCACCGGCATCA
1 AGCCTGCTAGACGTAAAGTCTGAAACATTTCACCGGCATCA
9552314 AGCCTGCTAGACGTAAAGTCTGAA
1 AGCCTGCTAGACGTAAAGTCTGAA
9552338 TTATCTCATT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (41 bp):
AGCCTGCTAGACGTAAAGTCTGAAACATTTCACCGGCATCA
Found at i:9556352 original size:22 final size:23
Alignment explanation
Indices: 9556325--9556403 Score: 92
Period size: 22 Copynumber: 3.4 Consensus size: 23
9556315 CACTAATGAA
9556325 CAGAGAGCACTGAAGTGCTATA-
1 CAGAGAGCACTGAAGTGCTATAT
*
9556347 CAGAGAGCACAGATA-TGCTA-AT
1 CAGAGAGCACTGA-AGTGCTATAT
*
9556369 CAGAGAGCACTGACGTGCTAGTAAT
1 CAGAGAGCACTGAAGTGCTA-T-AT
9556394 CAGAGAGCAC
1 CAGAGAGCAC
9556404 CAACGTCCTA
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
21 1 0.02
22 34 0.71
23 1 0.02
25 12 0.25
ACGTcount: A:0.37, C:0.20, G:0.27, T:0.16
Consensus pattern (23 bp):
CAGAGAGCACTGAAGTGCTATAT
Found at i:9556422 original size:25 final size:25
Alignment explanation
Indices: 9556369--9556422 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
9556359 ATATGCTAAT
** * * *
9556369 CAGAGAGCACTGACGTGCTAGTAAT
1 CAGAGAGCACCAACGTCCTAATAAA
9556394 CAGAGAGCACCAACGTCCTAATAAA
1 CAGAGAGCACCAACGTCCTAATAAA
9556419 CAGA
1 CAGA
9556423 TAGCGAGCTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (25 bp):
CAGAGAGCACCAACGTCCTAATAAA
Found at i:9595998 original size:57 final size:56
Alignment explanation
Indices: 9595894--9596071 Score: 233
Period size: 50 Copynumber: 3.2 Consensus size: 56
9595884 ACTTTTGATT
* *
9595894 AGTGACAAGTGATAAGTGGTAGCTTTAGCTGCACTTATCTGATCAGTGACAAGTGACA
1 AGTGATAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAGTGACAAGTGA-A
*
9595952 AGTGATAAGTGATAAGTGGCAGCTTAGCTACACTTATCTGATCAGTGACAAGTG--
1 AGTGATAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACAAGTGAA
* *
9596006 A-TG---AGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGATAAGAGATA
1 AGTGATAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACAAGTGA-A
*
9596059 AATGATAAGTGAT
1 AGTGATAAGTGAT
9596072 TCCGTGTAAG
Statistics
Matches: 107, Mismatches: 6, Indels: 15
0.84 0.05 0.12
Matches are distributed among these distances:
50 44 0.41
53 3 0.03
54 3 0.03
57 36 0.34
58 21 0.20
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (56 bp):
AGTGATAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACAAGTGAA
Found at i:9600309 original size:60 final size:60
Alignment explanation
Indices: 9600243--9600357 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 60
9600233 TTTTTTGAAA
* * * * * *
9600243 TTTTTAGAATTAT-AATTAAATTGTCAAATTTTATAAATATTGAGGGTTAAATTTATTAAT
1 TTTTTAGAATT-TGAACTAAAATGACAAATTTTATAAACATTAAGAGTTAAATTTATTAAT
9600303 TTTTTAGAATTTGAACTAAAATGACAAATTTTATAAACATTAAGAGTTAAATTTA
1 TTTTTAGAATTTGAACTAAAATGACAAATTTTATAAACATTAAGAGTTAAATTTA
9600358 AAATCAAATT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
59 1 0.02
60 47 0.98
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (60 bp):
TTTTTAGAATTTGAACTAAAATGACAAATTTTATAAACATTAAGAGTTAAATTTATTAAT
Found at i:9618294 original size:81 final size:81
Alignment explanation
Indices: 9618115--9618294 Score: 283
Period size: 81 Copynumber: 2.2 Consensus size: 81
9618105 GGGACGAAAT
**
9618115 TTTTTAGGGGGTCGGAATTAAATTATAATTTTTACGATTGTAAAAATATAATTATTAAAGGATTA
1 TTTTTAGGGGGTCAAAATTAAATTATAATTTTTACGATTGTAAAAATATAATTATTAAAGGATTA
9618180 AATAAAAAATTTATCA
66 AATAAAAAATTTATCA
*
9618196 TTTTT-GGGCGG-CTAAAATTAAATTATAATTTTTACGATTGTAAAAATATAATTATTAAATGAT
1 TTTTTAGGG-GGTC-AAAATTAAATTATAATTTTTACGATTGTAAAAATATAATTATTAAAGGAT
* *
9618259 TAAATCAAAATTTTATCA
64 TAAATAAAAAATTTATCA
9618277 TTTTTAGGGGGTCAAAAT
1 TTTTTAGGGGGTCAAAAT
9618295 GTAATTTTAC
Statistics
Matches: 90, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
80 4 0.04
81 82 0.91
82 4 0.04
ACGTcount: A:0.41, C:0.05, G:0.13, T:0.41
Consensus pattern (81 bp):
TTTTTAGGGGGTCAAAATTAAATTATAATTTTTACGATTGTAAAAATATAATTATTAAAGGATTA
AATAAAAAATTTATCA
Found at i:9619952 original size:2 final size:2
Alignment explanation
Indices: 9619945--9619969 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9619935 CACAAAATGT
9619945 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
9619970 TGCTATGCGT
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:9623547 original size:4 final size:4
Alignment explanation
Indices: 9623538--9623649 Score: 224
Period size: 4 Copynumber: 28.0 Consensus size: 4
9623528 TAGAAATCTT
9623538 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
9623586 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
9623634 ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC
9623650 TCTTTACCAT
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 108 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:9625852 original size:45 final size:45
Alignment explanation
Indices: 9625788--9625881 Score: 152
Period size: 45 Copynumber: 2.1 Consensus size: 45
9625778 AACAGATACT
* *
9625788 CGGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTC
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
* *
9625833 CGGTGGAATCAGCACATAGCAACCACCTTACTAATTAATGATGTT
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
9625878 CGGT
1 CGGT
9625882 TCACATAGTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
Found at i:9625945 original size:51 final size:51
Alignment explanation
Indices: 9625883--9626021 Score: 185
Period size: 49 Copynumber: 2.8 Consensus size: 51
9625873 ATGTTCGGTT
* *
9625883 CACATAGTAGCCTGCACATAGTACTATACATGTGACCATTACCATCCGATA
1 CACATAGTAGCCTGCACATAGTACTATACACGTGACCATAACCATCCGATA
* * * *
9625934 CACGTAGTAGCCTGCACATAGTAC--TACACGTGATCGA-AACTATCCGGTA
1 CACATAGTAGCCTGCACATAGTACTATACACGTGA-CCATAACCATCCGATA
*
9625983 CACATAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 CACATAGTAGCCTGCACATAGTACTATACACGTGACCAT
9626022 CACTTTCACT
Statistics
Matches: 75, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
49 40 0.53
50 4 0.05
51 31 0.41
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (51 bp):
CACATAGTAGCCTGCACATAGTACTATACACGTGACCATAACCATCCGATA
Found at i:9633755 original size:43 final size:42
Alignment explanation
Indices: 9633698--9633847 Score: 171
Period size: 42 Copynumber: 3.5 Consensus size: 42
9633688 AATGCCAACA
*
9633698 TCCCAGACGTGGTCTTACATGTAATCAAATAACGATGCCACTG
1 TCCCAGACGTGGTCTTACACGTAATCAAAT-ACGATGCCACTG
* * *
9633741 TCCCAGACAG-GGTCTTACACGTAATCATATACGATGGCAATG
1 TCCCAGAC-GTGGTCTTACACGTAATCAAATACGATGCCACTG
* *
9633783 TCCCAGACATGATCTTACACGTAAATCTCAAATA-GATGCCAAC-G
1 TCCCAGACGTGGTCTTACACGT-AA--TCAAATACGATGCC-ACTG
9633827 TCCCAGACGTGGTCTTACACG
1 TCCCAGACGTGGTCTTACACG
9633848 ATATCACATA
Statistics
Matches: 90, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
42 29 0.32
43 28 0.31
44 26 0.29
45 7 0.08
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.24
Consensus pattern (42 bp):
TCCCAGACGTGGTCTTACACGTAATCAAATACGATGCCACTG
Found at i:9633788 original size:42 final size:42
Alignment explanation
Indices: 9633689--9633847 Score: 178
Period size: 43 Copynumber: 3.7 Consensus size: 42
9633679 AGCTTGTACA
** *
9633689 ATGCCAACATCCCAGACGTGGTCTTACATGTAATCAAATAACG
1 ATGCCAATGTCCCAGACGTGGTCTTACACGTAATCAAAT-ACG
* *
9633732 ATGCCACTGTCCCAGACAG-GGTCTTACACGTAATCATATACG
1 ATGCCAATGTCCCAGAC-GTGGTCTTACACGTAATCAAATACG
* * *
9633774 ATGGCAATGTCCCAGACATGATCTTACACGTAAATCTCAAATA-G
1 ATGCCAATGTCCCAGACGTGGTCTTACACGT-AA--TCAAATACG
*
9633818 ATGCCAACGTCCCAGACGTGGTCTTACACG
1 ATGCCAATGTCCCAGACGTGGTCTTACACG
9633848 ATATCACATA
Statistics
Matches: 97, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
42 29 0.30
43 34 0.35
44 28 0.29
45 6 0.06
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.23
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACGTGGTCTTACACGTAATCAAATACG
Found at i:9634940 original size:13 final size:13
Alignment explanation
Indices: 9634922--9634946 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9634912 ACAAACGATA
9634922 AAATTTTCACACG
1 AAATTTTCACACG
9634935 AAATTTTCACAC
1 AAATTTTCACAC
9634947 ATTTTAATTC
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:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:9635407 original size:22 final size:22
Alignment explanation
Indices: 9635379--9635453 Score: 105
Period size: 22 Copynumber: 3.4 Consensus size: 22
9635369 AAATTAATAG
9635379 AGTACGTTAGCCATGAGAGCTT
1 AGTACGTTAGCCATGAGAGCTT
* *
9635401 AGTACGTTAGCCATGAGGGTTT
1 AGTACGTTAGCCATGAGAGCTT
* **
9635423 AGTTCGTTAAACATGAGAGCTT
1 AGTACGTTAGCCATGAGAGCTT
9635445 AGTACGTTA
1 AGTACGTTA
9635454 AACAAGATAC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.31
Consensus pattern (22 bp):
AGTACGTTAGCCATGAGAGCTT
Found at i:9637570 original size:25 final size:25
Alignment explanation
Indices: 9637482--9637571 Score: 126
Period size: 25 Copynumber: 3.6 Consensus size: 25
9637472 ACAAGCTATA
* *
9637482 AACGGGAAGCTCCTTCGAGCTGAAT
1 AACGGGAAGCTCATGCGAGCTGAAT
* *
9637507 AACGGGAAGCTCTTGCGAGCTGTAT
1 AACGGGAAGCTCATGCGAGCTGAAT
*
9637532 AACAGGAAGCTCATGCGAGCTGAAT
1 AACGGGAAGCTCATGCGAGCTGAAT
*
9637557 AACGGGAAGTTCATG
1 AACGGGAAGCTCATG
9637572 TGAGAAAATT
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 57 1.00
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (25 bp):
AACGGGAAGCTCATGCGAGCTGAAT
Found at i:9640132 original size:25 final size:25
Alignment explanation
Indices: 9640058--9640402 Score: 272
Period size: 25 Copynumber: 14.6 Consensus size: 25
9640048 ATTATTCAGC
* *
9640058 AAATTGGACAGCAAT-AATATGCTCA
1 AAATTGGACAGC-ATCAATATACTTA
* *
9640083 AAA-TGGACAGCAT---TATACATC
1 AAATTGGACAGCATCAATATACTTA
*
9640104 AAATTAGACAGCATCAATATACTTA
1 AAATTGGACAGCATCAATATACTTA
*
9640129 AAATCGGACAGCAT---TATACATTA
1 AAATTGGACAGCATCAATATAC-TTA
* * *
9640152 AAAATGGACAGCATCAATACACTCA
1 AAATTGGACAGCATCAATATACTTA
* *
9640177 AAATTCGATAGCAT---TATACATTA
1 AAATTGGACAGCATCAATATAC-TTA
* *
9640200 AAA-TGGGCAGCATCAATATACTCA
1 AAATTGGACAGCATCAATATACTTA
* *
9640224 AAATTGGACAGCATCAATACACTCA
1 AAATTGGACAGCATCAATATACTTA
*
9640249 AAATTGAACAGCAT---TATACATTA
1 AAATTGGACAGCATCAATATAC-TTA
* *
9640272 AAA-TGGGCAGCATCAATATAATTA
1 AAATTGGACAGCATCAATATACTTA
9640296 AAATTGGACAGCAT---TATACATTA
1 AAATTGGACAGCATCAATATAC-TTA
* *
9640319 AAA-TGGACAGCATCAATACACTCA
1 AAATTGGACAGCATCAATATACTTA
9640343 AAATTGGACAGCAT---TATACATTA
1 AAATTGGACAGCATCAATATAC-TTA
*
9640366 AAA-TGGACAGCATCAATATACTCA
1 AAATTGGACAGCATCAATATACTTA
9640390 AAA-TGGACAGCAT
1 AAATTGGACAGCAT
9640403 TATACATCAA
Statistics
Matches: 256, Mismatches: 37, Indels: 55
0.74 0.11 0.16
Matches are distributed among these distances:
21 7 0.03
22 65 0.25
23 38 0.15
24 39 0.15
25 103 0.40
26 4 0.02
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.24
Consensus pattern (25 bp):
AAATTGGACAGCATCAATATACTTA
Found at i:9640223 original size:47 final size:46
Alignment explanation
Indices: 9640062--9640237 Score: 210
Period size: 47 Copynumber: 3.7 Consensus size: 46
9640052 TTCAGCAAAT
* * * *
9640062 TGGACAGCAAT-AATATGCTCAAAATGGACAGCATTATACATCAAAT
1 TGGACAGC-ATCAATATACTCAAAATCGACAGCATTATACATTAAAA
* *
9640108 TAGACAGCATCAATATACTTAAAATCGGACAGCATTATACATTAAAAA
1 TGGACAGCATCAATATACTCAAAATC-GACAGCATTATACATT-AAAA
* *
9640156 TGGACAGCATCAATACACTCAAAATTCGATAGCATTATACATTAAAA
1 TGGACAGCATCAATATACTCAAAA-TCGACAGCATTATACATTAAAA
* *
9640203 TGGGCAGCATCAATATACTCAAAATTGGACAGCAT
1 TGGACAGCATCAATATACTCAAAA-TCGACAGCAT
9640238 CAATACACTC
Statistics
Matches: 112, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
45 2 0.02
46 19 0.17
47 50 0.45
48 39 0.35
49 2 0.02
ACGTcount: A:0.44, C:0.18, G:0.14, T:0.24
Consensus pattern (46 bp):
TGGACAGCATCAATATACTCAAAATCGACAGCATTATACATTAAAA
Found at i:9640239 original size:72 final size:70
Alignment explanation
Indices: 9640062--9640409 Score: 333
Period size: 72 Copynumber: 4.9 Consensus size: 70
9640052 TTCAGCAAAT
* * * *
9640062 TGGACAGCAATAATATGCTCAAAATGGACAGCAT-TATACA-TC-AAATTAGACAGCATCAATAT
1 TGGACAGC-ATAATATACTTAAAATGGACAGCATCAATACACTCAAAATTGGACAGCAT---TAT
9640124 AC-TTAAAA
62 ACATTAAAA
* *
9640132 TCGGACAGCAT--TATACATTAAAAATGGACAGCATCAATACACTCAAAATTCGATAGCATTATA
1 T-GGACAGCATAATATAC-TT-AAAATGGACAGCATCAATACACTCAAAATTGGACAGCATTATA
9640195 CATTAAAA
63 CATTAAAA
* * *
9640203 TGGGCAGCATCAATATACTCAAAATTGGACAGCATCAATACACTCAAAATTGAACAGCATTATAC
1 TGGACAGCAT-AATATACTTAAAA-TGGACAGCATCAATACACTCAAAATTGGACAGCATTATAC
9640268 ATTAAAA
64 ATTAAAA
* * * * *
9640275 TGGGCAGCATCAATATAATTAAAATTGGACAGCAT-TATACA-TTAAAA-TGGACAGCATCAATA
1 TGGACAGCAT-AATATACTTAAAA-TGGACAGCATCAATACACTCAAAATTGGACAGCAT-TATA
*
9640337 CACTCAAAA
63 CA-TTAAAA
*
9640346 TTGGACAGCAT--TATACATTAAAATGGACAGCATCAATATACTCAAAA-TGGACAGCATTATAC
1 -TGGACAGCATAATATAC-TTAAAATGGACAGCATCAATACACTCAAAATTGGACAGCATTATAC
9640408 AT
64 AT
9640410 CAAATTATAA
Statistics
Matches: 238, Mismatches: 23, Indels: 35
0.80 0.08 0.12
Matches are distributed among these distances:
68 4 0.02
69 25 0.11
70 55 0.23
71 48 0.20
72 89 0.37
73 17 0.07
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.25
Consensus pattern (70 bp):
TGGACAGCATAATATACTTAAAATGGACAGCATCAATACACTCAAAATTGGACAGCATTATACAT
TAAAA
Found at i:9640267 original size:47 final size:47
Alignment explanation
Indices: 9640082--9640409 Score: 309
Period size: 47 Copynumber: 7.0 Consensus size: 47
9640072 TAATATGCTC
* *
9640082 AAAATGGACAGCAT-TATACA-TC-AAATTAGACAGCATCAATATAC-TT
1 AAAATGGACAGCATCAATACACTCAAAATTGGACAGCAT---TATACATT
* * * * *
9640128 AAAATCGGACAGCAT-TATACA-TTAAAAATGGACAGCATCAATACACTC
1 AAAAT-GGACAGCATCAATACACTCAAAATTGGACAGCAT-TATACA-TT
* * * * * *
9640176 AAAATTCGATAGCAT-TATACA-TTAAAA-TGGGCAGCATCAATATAC-TC
1 AAAA-TGGACAGCATCAATACACTCAAAATTGGACAGCAT---TATACATT
*
9640223 AAAATTGGACAGCATCAATACACTCAAAATTGAACAGCATTATACATT
1 AAAA-TGGACAGCATCAATACACTCAAAATTGGACAGCATTATACATT
* * * *
9640271 AAAATGGGCAGCATCAATATAATTAAAATTGGACAGCATTATACATT
1 AAAATGGACAGCATCAATACACTCAAAATTGGACAGCATTATACATT
9640318 AAAATGGACAGCATCAATACACTCAAAATTGGACAGCATTATACATT
1 AAAATGGACAGCATCAATACACTCAAAATTGGACAGCATTATACATT
*
9640365 AAAATGGACAGCATCAATATACTCAAAA-TGGACAGCATTATACAT
1 AAAATGGACAGCATCAATACACTCAAAATTGGACAGCATTATACAT
9640410 CAAATTATAA
Statistics
Matches: 243, Mismatches: 28, Indels: 22
0.83 0.10 0.08
Matches are distributed among these distances:
46 26 0.11
47 153 0.63
48 46 0.19
49 10 0.04
50 8 0.03
ACGTcount: A:0.45, C:0.18, G:0.12, T:0.25
Consensus pattern (47 bp):
AAAATGGACAGCATCAATACACTCAAAATTGGACAGCATTATACATT
Found at i:9641384 original size:28 final size:27
Alignment explanation
Indices: 9641352--9641450 Score: 103
Period size: 28 Copynumber: 3.6 Consensus size: 27
9641342 TTAATAAGTA
*
9641352 CGCACACTTAGTGCTTAATAATCAAACT
1 CGCACACTTAGTGCTT-ATAATTAAACT
* *
9641380 CGCACACTTAGTGCTT-TACCCTTATACT
1 CGCACACTTAGTGCTTATA--ATTAAACT
*
9641408 CGAACACTTAGTGCATT-TCAATTAAACT
1 CGCACACTTAGTGC-TTAT-AATTAAACT
9641436 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
9641451 AATCTCATTA
Statistics
Matches: 60, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
26 2 0.03
27 1 0.02
28 53 0.88
29 3 0.05
30 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.31
Consensus pattern (27 bp):
CGCACACTTAGTGCTTATAATTAAACT
Found at i:9651672 original size:33 final size:32
Alignment explanation
Indices: 9651537--9651675 Score: 93
Period size: 33 Copynumber: 4.2 Consensus size: 32
9651527 AGACCATATC
9651537 CCATAGCTGGAC-TATGGCATTCTGATGATAAGA
1 CCATAGCTGG-CTTATGGCATTCTGATG-TAAGA
* * * *
9651570 CCATAACTAGG-TTATGGCACTATGAACGTAAGA
1 CCATAGCT-GGCTTATGGCATTCTG-ATGTAAGA
* * * * * * *
9651603 TCATGGTTGGATTATGACAGTGTTTATATGTAAGA
1 CCATAGCTGGCTTATGGCA-T-TCT-GATGTAAGA
9651638 CCATAGCTGGCTTATGGCATTCTGATGATAAGA
1 CCATAGCTGGCTTATGGCATTCTGATG-TAAGA
9651671 CCATA
1 CCATA
9651676 ACACAGTTAT
Statistics
Matches: 78, Mismatches: 20, Indels: 16
0.68 0.18 0.14
Matches are distributed among these distances:
32 5 0.06
33 45 0.58
34 5 0.06
35 23 0.29
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (32 bp):
CCATAGCTGGCTTATGGCATTCTGATGTAAGA
Found at i:9651723 original size:24 final size:24
Alignment explanation
Indices: 9651695--9651745 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
9651685 TGGCACTACG
9651695 AATGT-AAAGAATGAATTGACGAAA
1 AATGTAAAAG-ATGAATTGACGAAA
*
9651719 AATGTAAAAGATGAATTGACGACA
1 AATGTAAAAGATGAATTGACGAAA
9651743 AAT
1 AAT
9651746 TACCCAAGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 21 0.84
25 4 0.16
ACGTcount: A:0.53, C:0.06, G:0.20, T:0.22
Consensus pattern (24 bp):
AATGTAAAAGATGAATTGACGAAA
Found at i:9655551 original size:6 final size:6
Alignment explanation
Indices: 9655517--9655550 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
9655507 ACCTCATAGG
*
9655517 TTTTTA TTTTTA TTTTTA TTTTTA TTTTCA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT
9655551 CTTAACAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTTA
Found at i:9659939 original size:57 final size:59
Alignment explanation
Indices: 9659828--9659975 Score: 203
Period size: 57 Copynumber: 2.5 Consensus size: 59
9659818 AATTGACGGT
*
9659828 AAAAAGGATCTAGCCCGGACGGCTGATCCTATCCTGATATAGCCCTCCCGAAGAATATGTGTG
1 AAAAA-GATCTAGCCCGGACGGGTGATCC-AT-CTGATATAGCCCTCCCGAAGAATATGTG-G
9659891 AAAAAGATCTAGCCCGGACGGGTGAT-C-T-TGATATAGCCCTCCCGAAGAATATGTGG
1 AAAAAGATCTAGCCCGGACGGGTGATCCATCTGATATAGCCCTCCCGAAGAATATGTGG
* *
9659947 AAAATAGATTTAGCCCGGACGGGTAATCC
1 AAAA-AGATCTAGCCCGGACGGGTGATCC
9659976 GAATTAGGGT
Statistics
Matches: 80, Mismatches: 3, Indels: 9
0.87 0.03 0.10
Matches are distributed among these distances:
56 5 0.06
57 47 0.59
58 1 0.01
59 1 0.01
61 1 0.01
62 20 0.25
63 5 0.06
ACGTcount: A:0.30, C:0.23, G:0.25, T:0.22
Consensus pattern (59 bp):
AAAAAGATCTAGCCCGGACGGGTGATCCATCTGATATAGCCCTCCCGAAGAATATGTGG
Found at i:9660206 original size:67 final size:67
Alignment explanation
Indices: 9660098--9660228 Score: 226
Period size: 67 Copynumber: 2.0 Consensus size: 67
9660088 TTTATATTAC
*
9660098 AGGGGATTTAGCCTGGACTGGTAATCCCACTGTAAGAAATGAGATTAGCGGGAGTGTGCTCTCTT
1 AGGGGATTTAGCCTGGACTGGTAATCCCACTGTAAGAAATGAGATTAGCGAGAGTGTGCTCTCTT
9660163 AA
66 AA
* * *
9660165 AGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGAGAGTGTGCTCTCT
1 AGGGGATTTAGCCTGGACTGGTAATCCCACTGTAAGAAATGAGATTAGCGAGAGTGTGCTCTCT
9660229 GAATTGGAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 60 1.00
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (67 bp):
AGGGGATTTAGCCTGGACTGGTAATCCCACTGTAAGAAATGAGATTAGCGAGAGTGTGCTCTCTT
AA
Found at i:9660950 original size:2 final size:2
Alignment explanation
Indices: 9660945--9660977 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
9660935 TTCTAAAATC
9660945 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 T
9660978 TTAGGATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9668029 original size:21 final size:20
Alignment explanation
Indices: 9667984--9668030 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 20
9667974 AGTTAATTAA
9667984 TTTAATTAAT--TTT-AATT
1 TTTAATTAATCATTTAAATT
9668001 TTTAATTAATCATTTAAATT
1 TTTAATTAATCATTTAAATT
*
9668021 ATTTGATTAA
1 -TTTAATTAA
9668031 AAAATAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 10 0.40
19 3 0.12
20 4 0.16
21 8 0.32
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (20 bp):
TTTAATTAATCATTTAAATT
Found at i:9675026 original size:46 final size:46
Alignment explanation
Indices: 9674976--9675124 Score: 262
Period size: 46 Copynumber: 3.2 Consensus size: 46
9674966 AGTGATAAGT
9674976 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGTTAGCTTTA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGTTAGCTTTA
9675022 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGTTAGCTTTA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGTTAGCTTTA
* *
9675068 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGTTAGCTTTA
* *
9675114 TCTACATTTAT
1 GCTACACTTAT
9675125 GTAACACCCC
Statistics
Matches: 99, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 99 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (46 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGTTAGCTTTA
Found at i:9675829 original size:46 final size:46
Alignment explanation
Indices: 9675726--9676061 Score: 491
Period size: 46 Copynumber: 7.6 Consensus size: 46
9675716 TACGTATGAT
*
9675726 CACTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
9675769 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
*
9675815 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTGAGGCTAC
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
* *
9675861 CACTTATCACTTTTTCACTTGATCGGATAAGTGTAGCTGAGGCTAC
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
* *
9675907 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
*
9675953 CACTTATCACTTTGTCACTTGATCAGATAA--GTA--T-A-G----
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
*
9675989 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
* *
9676035 CACTTATCACTTTATCTCTTGATCAGA
1 CACTTATCACTTTTTCACTTGATCAGA
9676062 AGTACTCAAA
Statistics
Matches: 270, Mismatches: 10, Indels: 23
0.89 0.03 0.08
Matches are distributed among these distances:
36 29 0.11
38 3 0.01
40 2 0.01
41 2 0.01
42 2 0.01
43 10 0.04
44 7 0.03
45 21 0.08
46 194 0.72
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
Found at i:9675994 original size:36 final size:36
Alignment explanation
Indices: 9675953--9676025 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
9675943 CTAAAGCTAC
9675953 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
* *
9675989 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
9676025 C
1 C
9676026 TAAAGCTACC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.37
Consensus pattern (36 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
Found at i:9676001 original size:82 final size:82
Alignment explanation
Indices: 9675907--9676061 Score: 283
Period size: 82 Copynumber: 1.9 Consensus size: 82
9675897 CTGAGGCTAC
*
9675907 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCACT
9675972 TGATCAGATAAGTATAG
66 TGATCAGATAAGTATAG
* *
9675989 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCTCT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCACT
9676054 TGATCAGA
66 TGATCAGA
9676062 AGTACTCAAA
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 70 1.00
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (82 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCACT
TGATCAGATAAGTATAG
Found at i:9678550 original size:46 final size:46
Alignment explanation
Indices: 9678483--9678604 Score: 212
Period size: 46 Copynumber: 2.7 Consensus size: 46
9678473 GGCTGTTACA
*
9678483 ACTTATCTGATCAAGTGACAAAATGATAAGTGGTAGCCTTAGCTAC
1 ACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTAC
9678529 ACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTAC
1 ACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTAC
*
9678575 ACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 ACTTATCTGATCAAGTGACAAAGTGATAAGTG
9678605 ATCATACGTA
Statistics
Matches: 74, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
44 12 0.16
45 5 0.07
46 57 0.77
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (46 bp):
ACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTAC
Found at i:9685524 original size:17 final size:16
Alignment explanation
Indices: 9685493--9685531 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
9685483 AATTTTTATT
*
9685493 TTTATTTTTATTTTAC
1 TTTATTTTTACTTTAC
*
9685509 TTTATTTGTTACTTTAT
1 TTTATTT-TTACTTTAC
9685526 TTTATT
1 TTTATT
9685532 ATACTATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.18, C:0.05, G:0.03, T:0.74
Consensus pattern (16 bp):
TTTATTTTTACTTTAC
Found at i:9710085 original size:19 final size:19
Alignment explanation
Indices: 9710061--9710097 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
9710051 TTATTTTTTA
9710061 TTTTTTATTTTTAAAATAC
1 TTTTTTATTTTTAAAATAC
9710080 TTTTTTATTTTTAAAATA
1 TTTTTTATTTTTAAAATA
9710098 AATTTTTGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTTTATTTTTAAAATAC
Found at i:9710103 original size:20 final size:19
Alignment explanation
Indices: 9710060--9710104 Score: 72
Period size: 19 Copynumber: 2.3 Consensus size: 19
9710050 TTTATTTTTT
9710060 ATTTTTTATTTTTAAAATA
1 ATTTTTTATTTTTAAAATA
*
9710079 CTTTTTTATTTTTAAAATAA
1 ATTTTTTATTTTTAAAAT-A
9710099 ATTTTT
1 ATTTTT
9710105 GGTGTTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTTTTTATTTTTAAAATA
Found at i:9711589 original size:46 final size:46
Alignment explanation
Indices: 9711514--9712188 Score: 867
Period size: 46 Copynumber: 15.6 Consensus size: 46
9711504 TACGTATGAT
* * *
9711514 CACTTATCAC-TTGTC-CCTGATCAGATAAGTATAGCTAAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
9711558 CACTTATCACTTTGTCACTTGATCAGGTAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
9711604 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
9711650 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
9711696 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
9711742 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAACGCTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
9711788 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
9711834 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGTTAAAGCTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* * *
9711880 CACTTATCACTTTGTCATTTGATCAGATAAGTGTAGCTAACGCTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
9711926 CACTTATCACTTTGTCACTTGATCAGATAA--GTA--T--A---A-
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
9711962 CACTTATCACTTTGTCACTTGATCAGATAA--GTA--T--A---A-
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
9711998 CACTTATCACTTTTTCACTTGATCAGATAA--GTA--T--AG----
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
9712034 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
9712080 CACTTATCATTTTGTCTCTTGATCAGATAA--GT-G-T--AG----
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
9712116 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
9712162 CACTTATCACTTTATCTCTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
9712189 AGTACTCAAA
Statistics
Matches: 583, Mismatches: 25, Indels: 44
0.89 0.04 0.07
Matches are distributed among these distances:
36 127 0.22
37 1 0.00
38 5 0.01
39 1 0.00
40 4 0.01
42 6 0.01
43 1 0.00
44 15 0.03
45 5 0.01
46 418 0.72
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:9711963 original size:36 final size:36
Alignment explanation
Indices: 9711923--9712147 Score: 288
Period size: 36 Copynumber: 6.0 Consensus size: 36
9711913 TAGCTAACGC
9711923 TAACACTTATCACTTTGTCACTTGATCAGATAAGTA
1 TAACACTTATCACTTTGTCACTTGATCAGATAAGTA
9711959 TAACACTTATCACTTTGTCACTTGATCAGATAAGTA
1 TAACACTTATCACTTTGTCACTTGATCAGATAAGTA
*
9711995 TAACACTTATCACTTTTTCACTTGATCAGATAAGTA
1 TAACACTTATCACTTTGTCACTTGATCAGATAAGTA
* *
9712031 TAGCACTTATCACTTTTTCACTTGATCAGATAAGTGTA
1 TAACACTTATCACTTTGTCACTTGATCAGATAA--GTA
* * *
9712069 GCTAAAGCTACCACTTATCATTTTGTCTCTTGATCAGATAAGTG
1 --T--A---A-CACTTATCACTTTGTCACTTGATCAGATAAGTA
* *
9712113 TAGCACTTATCACTTTTTCACTTGATCAGATAAGT
1 TAACACTTATCACTTTGTCACTTGATCAGATAAGT
9712148 GTAGCTAAAG
Statistics
Matches: 168, Mismatches: 11, Indels: 20
0.84 0.06 0.10
Matches are distributed among these distances:
36 132 0.79
38 3 0.02
40 2 0.01
42 2 0.01
44 2 0.01
46 27 0.16
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.38
Consensus pattern (36 bp):
TAACACTTATCACTTTGTCACTTGATCAGATAAGTA
Found at i:9711970 original size:82 final size:82
Alignment explanation
Indices: 9711877--9712188 Score: 428
Period size: 82 Copynumber: 3.9 Consensus size: 82
9711867 TAGTTAAAGC
* *
9711877 TAACACTTATCACTTTGTCATTTGATCAGATAAGTGTAGCTAACGCTAACACTTATCACTTTGTC
1 TAACACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAACACTTATCACTTTGTC
9711942 ACTTGATCAGATAAGTA
66 ACTTGATCAGATAAGTA
*
9711959 TAACACTTATCACTTTGTCACTTGATCAGAT-A----AG-T--A--TAACACTTATCACTTTTTC
1 TAACACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAACACTTATCACTTTGTC
9712014 ACTTGATCAGATAAGTA
66 ACTTGATCAGATAAGTA
* * * *
9712031 TAGCACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCATTTTGTC
1 TAACACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAACACTTATCACTTTGTC
* *
9712096 TCTTGATCAGATAAGTG
66 ACTTGATCAGATAAGTA
* * * *
9712113 TAGCACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATC
1 TAACACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAACACTTATCACTTTGTC
*
9712178 TCTTGATCAGA
66 ACTTGATCAGA
9712189 AGTACTCAAA
Statistics
Matches: 208, Mismatches: 12, Indels: 20
0.87 0.05 0.08
Matches are distributed among these distances:
72 64 0.31
73 1 0.00
76 1 0.00
77 4 0.02
78 1 0.00
80 1 0.00
81 1 0.00
82 135 0.65
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.37
Consensus pattern (82 bp):
TAACACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAACACTTATCACTTTGTC
ACTTGATCAGATAAGTA
Found at i:9732284 original size:18 final size:17
Alignment explanation
Indices: 9732258--9732296 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
9732248 ATTTTCCTTC
9732258 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
9732275 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
9732293 CACA
1 CACA
9732297 ATTTATACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:9735460 original size:22 final size:22
Alignment explanation
Indices: 9735432--9735504 Score: 110
Period size: 22 Copynumber: 3.3 Consensus size: 22
9735422 CCAGCATCAG
*
9735432 TCTCATGTTTCACGTACTAAGC
1 TCTCATGTTTAACGTACTAAGC
9735454 TCTCATGTTTAACGTACTAAGC
1 TCTCATGTTTAACGTACTAAGC
* *
9735476 TCTCATGTTTAACGAACTAAAC
1 TCTCATGTTTAACGTACTAAGC
*
9735498 CCTCATG
1 TCTCATG
9735505 GCTAACGCCT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.27, C:0.26, G:0.12, T:0.34
Consensus pattern (22 bp):
TCTCATGTTTAACGTACTAAGC
Found at i:9741052 original size:21 final size:21
Alignment explanation
Indices: 9741006--9741052 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
9740996 ATTTACAACT
*
9741006 TTATTTTTAGAAATTTAATCC
1 TTATTTTTAGAAATTTAATCA
* *
9741027 CTATTTCTTAGACATTTAAT-A
1 TTATTT-TTAGAAATTTAATCA
9741048 TTATT
1 TTATT
9741053 AAATTACATT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.32, C:0.11, G:0.04, T:0.53
Consensus pattern (21 bp):
TTATTTTTAGAAATTTAATCA
Found at i:9745554 original size:10 final size:10
Alignment explanation
Indices: 9745534--9745596 Score: 56
Period size: 11 Copynumber: 6.1 Consensus size: 10
9745524 TGACCATGTT
9745534 AATTGATAAAA
1 AATT-ATAAAA
9745545 AATTATAAAA
1 AATTATAAAA
* *
9745555 ATTTAT-GAA
1 AATTATAAAA
9745564 AATTATTAAAA
1 AATTA-TAAAA
* *
9745575 AAATACTAAAT
1 AATTA-TAAAA
9745586 AATTATAAAA
1 AATTATAAAA
9745596 A
1 A
9745597 TAATTAAAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
9 6 0.15
10 17 0.41
11 18 0.44
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (10 bp):
AATTATAAAA
Found at i:9745578 original size:31 final size:31
Alignment explanation
Indices: 9745540--9745606 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
9745530 TGTTAATTGA
* * *
9745540 TAAAAAATTA-TAAA-AATTTATGAAAATTAT
1 TAAAAAAATACTAAATAA-TTATAAAAATAAT
9745570 TAAAAAAATACTAAATAATTATAAAAATAAT
1 TAAAAAAATACTAAATAATTATAAAAATAAT
9745601 TAAAAA
1 TAAAAA
9745607 GTGGTCTCGG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 9 0.28
31 21 0.66
32 2 0.06
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (31 bp):
TAAAAAAATACTAAATAATTATAAAAATAAT
Found at i:9745767 original size:19 final size:18
Alignment explanation
Indices: 9745745--9745816 Score: 65
Period size: 19 Copynumber: 3.7 Consensus size: 18
9745735 AAAGTTGTTG
9745745 AAATTTATAAAAAAATGTA
1 AAATTTATAAAAAAAT-TA
*
9745764 AAATATT-TAAAATATATTTA
1 AAAT-TTATAAAA-A-AATTA
9745784 AAATTTTATAAAAAATATTA
1 AAA-TTTATAAAAAA-ATTA
*
9745804 AAAATTATAAAAA
1 AAATTTATAAAAA
9745817 CATATACTTC
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
19 19 0.43
20 17 0.39
21 8 0.18
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (18 bp):
AAATTTATAAAAAAATTA
Found at i:9745771 original size:21 final size:20
Alignment explanation
Indices: 9745747--9745816 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
9745737 AGTTGTTGAA
9745747 ATTTATAAAAAAATGTAAAAT
1 ATTTATAAAAAAAT-TAAAAT
* *
9745768 ATTTA-AAATATATTTAAAAT
1 ATTTATAAA-AAAATTAAAAT
9745788 -TTTATAAAAAATATTAAAA-
1 ATTTATAAAAAA-ATTAAAAT
9745807 A-TTATAAAAA
1 ATTTATAAAAA
9745817 CATATACTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
19 15 0.37
20 18 0.44
21 8 0.20
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (20 bp):
ATTTATAAAAAAATTAAAAT
Found at i:9745816 original size:20 final size:20
Alignment explanation
Indices: 9745749--9745821 Score: 62
Period size: 21 Copynumber: 3.7 Consensus size: 20
9745739 TTGTTGAAAT
*
9745749 TTATAAAAAAAT-GTAAAATA
1 TTATAAAAAAATATTAAAA-A
* *
9745769 TT-T-AAAATATATTTAAAA
1 TTATAAAAAAATATTAAAAA
*
9745787 TTTTATAAAAAATATTAAAAA
1 TTATA-AAAAAATATTAAAAA
*
9745808 TTATAAAAACATAT
1 TTATAAAAAAATAT
9745822 ACTTCATTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
18 9 0.21
19 6 0.14
20 10 0.24
21 17 0.40
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (20 bp):
TTATAAAAAAATATTAAAAA
Found at i:9759341 original size:125 final size:124
Alignment explanation
Indices: 9759113--9759391 Score: 441
Period size: 125 Copynumber: 2.2 Consensus size: 124
9759103 GCCCATGTTT
9759113 ACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTAAGCAAATAGTA
1 ACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTAAGCAAATAGTA
* * * *
9759178 TAAAATCGCTTCTAGCAGGATGATGTTTGATAATAATTTGGGAAATCGTGGCCTCGTGG
66 TAAAATCGCTTCTAGCAGGATGATATTTGAGAAGAATTTGGGAAATCGTGCCCTCGTGG
* * *
9759237 ACGCGCTTTTGCTACGGTAGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGT
1 ACGCGCTTTTGCTACAGTAGGTCCT-GAAAAAATAATTTCGAGTTGACGTTTCTAAGCAAATAGT
* *
9759302 ATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGTGCCCTCGTGG
65 ATAAAATCGCTTCTAGCAGGATGATATTTGAGAAGAATTTGGGAAATCGTGCCCTCGTGG
* * *
9759362 ACCCGCTTTTGCTACAATAAGTCCTGAAAA
1 ACGCGCTTTTGCTACAGTAGGTCCTGAAAA
9759392 TTGAGAGAGG
Statistics
Matches: 140, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
124 28 0.20
125 112 0.80
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.30
Consensus pattern (124 bp):
ACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTAAGCAAATAGTA
TAAAATCGCTTCTAGCAGGATGATATTTGAGAAGAATTTGGGAAATCGTGCCCTCGTGG
Found at i:9763968 original size:45 final size:45
Alignment explanation
Indices: 9763904--9763993 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
9763894 GTTATGCCCT
**
9763904 TGAGCTATATGGCATCAATTTCATCACCCTTTTTTCTTTCCTACC
1 TGAGCTATATGGCATCAATTTCATCACCCCCTTTTCTTTCCTACC
9763949 TGAGCTATATGGCATCAATTTCATCACCCCCTTTTCTTTCCTACC
1 TGAGCTATATGGCATCAATTTCATCACCCCCTTTTCTTTCCTACC
9763994 ATCAAAGAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.20, C:0.31, G:0.09, T:0.40
Consensus pattern (45 bp):
TGAGCTATATGGCATCAATTTCATCACCCCCTTTTCTTTCCTACC
Found at i:9767104 original size:34 final size:35
Alignment explanation
Indices: 9767049--9767115 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
9767039 TAAACATCAG
*
9767049 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
9767084 AAAACATTTTCCTG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
9767116 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:9770004 original size:21 final size:21
Alignment explanation
Indices: 9769970--9770010 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
9769960 AGAAGAAGAA
*
9769970 CCCAAGAAGTCTAATATCAAG
1 CCCAAGAAGTCTAAGATCAAG
9769991 CCCAAGAAAG-CTAAGATCAA
1 CCCAAG-AAGTCTAAGATCAA
9770011 CTAGTACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.46, C:0.24, G:0.15, T:0.15
Consensus pattern (21 bp):
CCCAAGAAGTCTAAGATCAAG
Found at i:9773686 original size:22 final size:21
Alignment explanation
Indices: 9773653--9773693 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
9773643 TTTTCGTTTA
*
9773653 AATCTTTTAAAATTTTAAATT
1 AATCTTTTAAAATTATAAATT
9773674 AATCTTTTAAAAATTATAAA
1 AATCTTTT-AAAATTATAAA
9773694 GATATAGACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (21 bp):
AATCTTTTAAAATTATAAATT
Found at i:9779743 original size:10 final size:11
Alignment explanation
Indices: 9779712--9779744 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
9779702 CGACCCACCC
9779712 ATATTAATGTTT
1 ATATTAAT-TTT
9779724 ATATTAATTTT
1 ATATTAATTTT
9779735 ATA-TAATTTT
1 ATATTAATTTT
9779745 TAAATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 7 0.33
11 6 0.29
12 8 0.38
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (11 bp):
ATATTAATTTT
Found at i:9781712 original size:49 final size:49
Alignment explanation
Indices: 9781553--9781715 Score: 240
Period size: 49 Copynumber: 3.4 Consensus size: 49
9781543 TGTTAAGCCA
* *
9781553 TGTG-GGGGCACAC-GGTGTGTGTGATTACACGGGTAAATCAGGTAGGT
1 TGTGTGGGGCACACAGGCGTGTGTGATTACATGGGTAAATCAGGTAGGT
* *
9781600 TGTGTGGGGCACACGGGCGTGTGTGATTACATGGGTAAATCAGGTAGGC
1 TGTGTGGGGCACACAGGCGTGTGTGATTACATGGGTAAATCAGGTAGGT
* * *
9781649 CGTGTGGGGCACACAGGCGTATGAGATTACATGGGTAAATCAGGTAGGT
1 TGTGTGGGGCACACAGGCGTGTGTGATTACATGGGTAAATCAGGTAGGT
*
9781698 TGTGTAGGGCACACAGGC
1 TGTGTGGGGCACACAGGC
9781716 AAATCAGGTA
Statistics
Matches: 104, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
47 4 0.04
48 9 0.09
49 91 0.88
ACGTcount: A:0.23, C:0.15, G:0.39, T:0.23
Consensus pattern (49 bp):
TGTGTGGGGCACACAGGCGTGTGTGATTACATGGGTAAATCAGGTAGGT
Found at i:9782072 original size:18 final size:18
Alignment explanation
Indices: 9782051--9782103 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
9782041 TCTATTCTAA
9782051 TATGATATATGATTCGAC
1 TATGATATATGATTCGAC
9782069 TATG-TGATATG--T--A-
1 TATGAT-ATATGATTCGAC
9782082 TATGATATATGATTCGAC
1 TATGATATATGATTCGAC
9782100 TATG
1 TATG
9782104 TGATATGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 14
0.67 0.00 0.33
Matches are distributed among these distances:
13 9 0.32
14 2 0.07
15 1 0.04
16 1 0.04
17 2 0.07
18 13 0.46
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.42
Consensus pattern (18 bp):
TATGATATATGATTCGAC
Found at i:9782088 original size:31 final size:31
Alignment explanation
Indices: 9782050--9782113 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
9782040 ATCTATTCTA
9782050 ATATGATATATGATTCGACTATGTGATATGT
1 ATATGATATATGATTCGACTATGTGATATGT
9782081 ATATGATATATGATTCGACTATGTGATATGT
1 ATATGATATATGATTCGACTATGTGATATGT
9782112 AT
1 AT
9782114 GTATGTTGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.33, C:0.06, G:0.19, T:0.42
Consensus pattern (31 bp):
ATATGATATATGATTCGACTATGTGATATGT
Found at i:9782109 original size:18 final size:18
Alignment explanation
Indices: 9782057--9782110 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
9782047 CTAATATGAT
9782057 ATATGATTCGACTATGTG
1 ATATGATTCGACTATGTG
9782075 ATATG--T--A-TATGAT-
1 ATATGATTCGACTATG-TG
9782088 ATATGATTCGACTATGTG
1 ATATGATTCGACTATGTG
9782106 ATATG
1 ATATG
9782111 TATGTATGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 14
0.67 0.00 0.33
Matches are distributed among these distances:
13 9 0.31
14 2 0.07
15 1 0.03
16 1 0.03
17 2 0.07
18 14 0.48
ACGTcount: A:0.31, C:0.07, G:0.20, T:0.41
Consensus pattern (18 bp):
ATATGATTCGACTATGTG
Found at i:9787012 original size:5 final size:5
Alignment explanation
Indices: 9787002--9787027 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
9786992 TGAGCATTCG
9787002 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
9787028 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:9788068 original size:9 final size:9
Alignment explanation
Indices: 9788054--9788090 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
9788044 TATAGTTTGA
9788054 TATTCGAAT
1 TATTCGAAT
9788063 TATTCGAAT
1 TATTCGAAT
*
9788072 TATTCGAGT
1 TATTCGAAT
9788081 TATTCGAAT
1 TATTCGAAT
9788090 T
1 T
9788091 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:9788161 original size:9 final size:9
Alignment explanation
Indices: 9788144--9788174 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
9788134 TCGAGTTGAT
9788144 TCGAATAAC
1 TCGAATAAC
*
9788153 TCGATTAAC
1 TCGAATAAC
9788162 TCGAATAAC
1 TCGAATAAC
9788171 TCGA
1 TCGA
9788175 TTTGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:9788910 original size:25 final size:25
Alignment explanation
Indices: 9788882--9788930 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
9788872 GGTTTGCAGC
9788882 TCGTAAGAACTTACCG-ATTCTCAGT
1 TCGTAAGAACTTACCGTATT-TCAGT
* *
9788907 TCGTATGAGCTTACCGTATTTCAG
1 TCGTAAGAACTTACCGTATTTCAG
9788931 CTCGGAGGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 18 0.86
26 3 0.14
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.35
Consensus pattern (25 bp):
TCGTAAGAACTTACCGTATTTCAGT
Found at i:9803873 original size:27 final size:27
Alignment explanation
Indices: 9803825--9803889 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
9803815 AAAAATAACT
*
9803825 AAAATATTAT-AATTTTTTTATTTATC
1 AAAATATTATAAATTTTTTTATTTACC
9803851 AAAATATTATAAATTTTTTTATTTACC
1 AAAATATTATAAATTTTTTTATTTACC
9803878 AAAATA-TATAAA
1 AAAATATTATAAA
9803890 AACAAAACAA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
26 16 0.43
27 21 0.57
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (27 bp):
AAAATATTATAAATTTTTTTATTTACC
Found at i:9804568 original size:23 final size:23
Alignment explanation
Indices: 9804542--9804613 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 23
9804532 ACTCTATTTT
9804542 AATTTAATAAACTATTCTCATCA
1 AATTTAATAAACTATTCTCATCA
*
9804565 AATTACTTAATAACTCTATT-T--T--
1 AA-T--TTAATAA-ACTATTCTCATCA
9804587 AATTTAATAAACTATTCTCATCA
1 AATTTAATAAACTATTCTCATCA
9804610 AATT
1 AATT
9804614 ACCAAAATAG
Statistics
Matches: 38, Mismatches: 2, Indels: 18
0.66 0.03 0.31
Matches are distributed among these distances:
18 5 0.13
19 8 0.21
21 2 0.05
22 2 0.05
23 6 0.16
24 2 0.05
26 8 0.21
27 5 0.13
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.43
Consensus pattern (23 bp):
AATTTAATAAACTATTCTCATCA
Found at i:9804586 original size:45 final size:44
Alignment explanation
Indices: 9804528--9804615 Score: 167
Period size: 45 Copynumber: 2.0 Consensus size: 44
9804518 TCTAATTAAG
9804528 TAATACTCTATTTTAATTTAATAAACTATTCTCATCAAATTACT
1 TAATACTCTATTTTAATTTAATAAACTATTCTCATCAAATTACT
9804572 TAATAACTCTATTTTAATTTAATAAACTATTCTCATCAAATTAC
1 TAAT-ACTCTATTTTAATTTAATAAACTATTCTCATCAAATTAC
9804616 CAAAATAGAG
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 4 0.09
45 39 0.91
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (44 bp):
TAATACTCTATTTTAATTTAATAAACTATTCTCATCAAATTACT
Found at i:9804660 original size:18 final size:18
Alignment explanation
Indices: 9804624--9804661 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
9804614 ACCAAAATAG
*
9804624 AGTTTATTAAATGAGAAT
1 AGTTTATTAAATGAAAAT
*
9804642 AGTTTATTAAATTAAAAT
1 AGTTTATTAAATGAAAAT
9804660 AG
1 AG
9804662 AGTTATTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.39
Consensus pattern (18 bp):
AGTTTATTAAATGAAAAT
Found at i:9807659 original size:18 final size:18
Alignment explanation
Indices: 9807624--9807662 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
9807614 ATTACTTTTT
* **
9807624 AAAAATATTTTTGGGATA
1 AAAAATACTTTTAAGATA
9807642 AAAAATACTTTTAAGATA
1 AAAAATACTTTTAAGATA
9807660 AAA
1 AAA
9807663 GTATTCCTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.54, C:0.03, G:0.10, T:0.33
Consensus pattern (18 bp):
AAAAATACTTTTAAGATA
Found at i:9807942 original size:14 final size:14
Alignment explanation
Indices: 9807909--9807948 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
9807899 TCCAAGTCAC
9807909 ATAAAA-AAGTTAAA
1 ATAAAATAAG-TAAA
9807923 AT-AAATAAGTAAA
1 ATAAAATAAGTAAA
9807936 ATAAAATAA-TAAA
1 ATAAAATAAGTAAA
9807949 TCAAAGATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (14 bp):
ATAAAATAAGTAAA
Found at i:9808162 original size:26 final size:27
Alignment explanation
Indices: 9808133--9808185 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
9808123 AAACTCTTCT
* *
9808133 AAAAGAAACTCA-AGAGAAATTCTTAA
1 AAAAAAAACTCAGAGAGAAATTATTAA
9808159 AAAAAAAACTCAGAGAGAAATTATTAA
1 AAAAAAAACTCAGAGAGAAATTATTAA
9808186 CTCAAAAGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 11 0.46
27 13 0.54
ACGTcount: A:0.60, C:0.09, G:0.11, T:0.19
Consensus pattern (27 bp):
AAAAAAAACTCAGAGAGAAATTATTAA
Found at i:9809455 original size:52 final size:52
Alignment explanation
Indices: 9809347--9809477 Score: 142
Period size: 53 Copynumber: 2.6 Consensus size: 52
9809337 CTTTTAAAAT
* * * *** *
9809347 TTTAAAAAAATTGGATGTTGGGACACTGACGTCCGACATCTTTATACCAGTT
1 TTTAAAAAAATTGGATATTGGGACACTGACGGCCGACACCCCAATACCAGTA
*
9809399 TTTAAAAAAATTGGGATATTGGGACACTGATGGCCGACACCCCAATACCAG-A
1 TTTAAAAAAATT-GGATATTGGGACACTGACGGCCGACACCCCAATACCAGTA
* *
9809451 TTTAAAAAAA-T-AATGTTGGGACACTGA
1 TTTAAAAAAATTGGATATTGGGACACTGA
9809478 TAGTCGGCAT
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
49 14 0.21
51 1 0.01
52 22 0.32
53 31 0.46
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (52 bp):
TTTAAAAAAATTGGATATTGGGACACTGACGGCCGACACCCCAATACCAGTA
Found at i:9809995 original size:90 final size:90
Alignment explanation
Indices: 9809840--9810042 Score: 243
Period size: 90 Copynumber: 2.3 Consensus size: 90
9809830 ACTACAATTC
* * * **
9809840 AAAATGTTGGTATTATTTTTGTATCTGTAAATCAATTTTAGTCCGTATTATTTGTTGGTTGAATT
1 AAAATGTTGGTATTATTTTTGTATCTATAAATAAATTTTAGTCCATATTATTTGTTGGTAAAATT
* *
9809905 TTATATTTTCGAATATCAGTTTTGT
66 TTATATTTTAGAATATCAATTTTGT
9809930 AAAATGGTT-GTATTATTTTTAG-ATCTATAAA-AATATTTTAGTCCATATTATTTGTTGGTAAA
1 AAAAT-GTTGGTATTATTTTT-GTATCTATAAATAA-ATTTTAGTCCATATTATTTGTTGGTAAA
* *
9809992 ATTTTATATTTTAGTATATCAATTTTCT
63 ATTTTATATTTTAGAATATCAATTTTGT
* * *
9810020 AAGATGTTCGTATT-TTCTTGTAT
1 AAAATGTTGGTATTATTTTTGTAT
9810043 ATGTAAAAAA
Statistics
Matches: 97, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
88 1 0.01
89 10 0.10
90 82 0.85
91 4 0.04
ACGTcount: A:0.29, C:0.06, G:0.13, T:0.52
Consensus pattern (90 bp):
AAAATGTTGGTATTATTTTTGTATCTATAAATAAATTTTAGTCCATATTATTTGTTGGTAAAATT
TTATATTTTAGAATATCAATTTTGT
Found at i:9811998 original size:15 final size:17
Alignment explanation
Indices: 9811978--9812009 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
9811968 CTTTTTTTAA
9811978 TTAAA-TTAT-ATTATT
1 TTAAATTTATAATTATT
9811993 TTAAATTTATAATTATT
1 TTAAATTTATAATTATT
9812010 CTTTTATACT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 4 0.27
17 6 0.40
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTAAATTTATAATTATT
Found at i:9812124 original size:14 final size:15
Alignment explanation
Indices: 9812093--9812128 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
9812083 ATTTTTTAAA
*
9812093 TTAAATTCTATTCTT
1 TTAAATTCTATTCAT
9812108 TTAAATT-TATTCAT
1 TTAAATTCTATTCAT
9812122 TTAAATT
1 TTAAATT
9812129 ATTTTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.58
Consensus pattern (15 bp):
TTAAATTCTATTCAT
Found at i:9812360 original size:17 final size:18
Alignment explanation
Indices: 9812338--9812373 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
9812328 CTTTTTTATC
9812338 TTTAC-ATACAAAATTGA
1 TTTACAATACAAAATTGA
9812355 TTTACAGATACAAAATTGA
1 TTTACA-ATACAAAATTGA
9812374 ATCACATAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
19 12 0.71
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.33
Consensus pattern (18 bp):
TTTACAATACAAAATTGA
Found at i:9814468 original size:16 final size:16
Alignment explanation
Indices: 9814431--9814470 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
9814421 TAAATAAAAT
* *
9814431 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
9814447 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
9814463 TAAAATTA
1 TAAAATTA
9814471 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:9814555 original size:9 final size:9
Alignment explanation
Indices: 9814543--9814586 Score: 65
Period size: 9 Copynumber: 5.1 Consensus size: 9
9814533 TTTATCAAAT
9814543 TATTAATTG
1 TATTAATTG
9814552 TATTAATTG
1 TATTAATTG
9814561 --TTAATTG
1 TATTAATTG
*
9814568 TATTAATTA
1 TATTAATTG
9814577 TATTAATTG
1 TATTAATTG
9814586 T
1 T
9814587 TGTAACAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 7 0.23
9 24 0.77
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:9814559 original size:16 final size:16
Alignment explanation
Indices: 9814540--9814577 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
9814530 AAATTTATCA
9814540 AATTATTAATTGTATT
1 AATTATTAATTGTATT
*
9814556 AATTGTTAATTGTATT
1 AATTATTAATTGTATT
9814572 AATTAT
1 AATTAT
9814578 ATTAATTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (16 bp):
AATTATTAATTGTATT
Found at i:9815648 original size:18 final size:17
Alignment explanation
Indices: 9815625--9815665 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
9815615 TACAGTGAAT
9815625 AAAAATATATTAGAAGTA
1 AAAAATATATTA-AAGTA
* *
9815643 AAAAATCTATTACAGTA
1 AAAAATATATTAAAGTA
9815660 AAAAAT
1 AAAAAT
9815666 CTATGAGGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.61, C:0.05, G:0.07, T:0.27
Consensus pattern (17 bp):
AAAAATATATTAAAGTA
Found at i:9815659 original size:17 final size:17
Alignment explanation
Indices: 9815607--9815669 Score: 72
Period size: 17 Copynumber: 3.5 Consensus size: 17
9815597 GAAATTAATG
9815607 AAATCTATTACAGTGAATAA
1 AAATCTATTACAGT--A-AA
* *
9815627 AAATATATTAGAAGTAAA
1 AAATCTATTA-CAGTAAA
9815645 AAATCTATTACAGTAAA
1 AAATCTATTACAGTAAA
9815662 AAATCTAT
1 AAATCTAT
9815670 GAGGACTGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
17 14 0.37
18 11 0.29
19 1 0.03
20 9 0.24
21 3 0.08
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.30
Consensus pattern (17 bp):
AAATCTATTACAGTAAA
Found at i:9817098 original size:30 final size:29
Alignment explanation
Indices: 9817036--9817106 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 29
9817026 TACTAATAAC
9817036 TTAAACAT-AAAAATAAATATATATATTT
1 TTAAACATAAAAAATAAATATATATATTT
9817064 TTAAACATAAAAAACTTAAACTAT-TATA-TT
1 TTAAACATAAAAAA--TAAA-TATATATATTT
*
9817094 TTAAAAATAAAAA
1 TTAAACATAAAAA
9817107 TATATATTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
28 8 0.21
29 5 0.13
30 14 0.37
31 8 0.21
32 3 0.08
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (29 bp):
TTAAACATAAAAAATAAATATATATATTT
Found at i:9819376 original size:126 final size:126
Alignment explanation
Indices: 9819151--9819693 Score: 865
Period size: 126 Copynumber: 4.3 Consensus size: 126
9819141 CCAAACATGT
*
9819151 GCCACTGTAGCAAAAGTGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCAT-CA
1 GCCACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATAC-
* *
9819215 TGCTTAAAGTGTTTTTGACACTATTTGCTCAGAAACGTCTACTCAAAATTATTTTTTCAAGA
65 TGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAAGA
* *
9819277 GCCACTGTAGCAAAAGCGCGTCTACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATATT
1 GCCACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATACT
9819342 GCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTC-AGAA
66 GCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAAG-A
* * *
9819403 GCTACTGTAGCAAAAGCGCGTCCACGTGGGAGATTCTTTCAGTACTTCTGCTGACAAAGCATCCT
1 GCCACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATACT
* * *
9819468 GCTTAAAACGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGGAATTATTTTTTCAGGA
66 GCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAAGA
* * * * *
9819529 GCCACTGTAGCAAAAGCGCATCCACGTGGGAGCTTCTTTTAGTACTTCTGTTGACAAATCATCCT
1 GCCACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATACT
* * *
9819594 GCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACATCTACTTGAAATTATTTTTTCAGGA
66 GCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAAGA
* *
9819655 GCTACTGTAGCAAAAGCGCGTCCATGTGGGAGCTTCTTT
1 GCCACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTT
9819694 AAATTAACAA
Statistics
Matches: 388, Mismatches: 26, Indels: 6
0.92 0.06 0.01
Matches are distributed among these distances:
125 2 0.01
126 385 0.99
127 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (126 bp):
GCCACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTCTGCTGACAAAGCATACT
GCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTACTCGAAATTATTTTTTCAAGA
Found at i:9819853 original size:96 final size:97
Alignment explanation
Indices: 9819722--9819929 Score: 260
Period size: 96 Copynumber: 2.2 Consensus size: 97
9819712 ATTAACCATA
* * *
9819722 AACCCCAAACCTTAATTTATTTGAGTTTTTACTTAAAAACCCTAAACACTAACCCCTAATCAAAT
1 AACCCTAAACCCTAATTTATTTGAGTTTTTACTTAAAAACCCTAAACACTAAACCCTAATCAAAT
* *
9819787 TTTATAAA-AA-ATTATAATTAATTTACTCAATT
66 TTT-TAAATAATATT-TAATTAAATTACTCAAGT
* * * * * * **
9819819 AATCCTGAACCCTAATTTATTTGA-TTTTTCCTTAAAAACCCTTAACTCTAAACCCTTATCTGAT
1 AACCCTAAACCCTAATTTATTTGAGTTTTTACTTAAAAACCCTAAACACTAAACCCTAATCAAAT
9819883 TTTTAAATAATATTTAATTAAATTACTCAAGT
66 TTTTAAATAATATTTAATTAAATTACTCAAGT
9819915 AACCCTAAACCCTAA
1 AACCCTAAACCCTAA
9819930 ATCCTAATTT
Statistics
Matches: 94, Mismatches: 15, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
95 4 0.04
96 67 0.71
97 23 0.24
ACGTcount: A:0.39, C:0.21, G:0.03, T:0.37
Consensus pattern (97 bp):
AACCCTAAACCCTAATTTATTTGAGTTTTTACTTAAAAACCCTAAACACTAAACCCTAATCAAAT
TTTTAAATAATATTTAATTAAATTACTCAAGT
Found at i:9828860 original size:10 final size:10
Alignment explanation
Indices: 9828829--9828927 Score: 73
Period size: 10 Copynumber: 10.0 Consensus size: 10
9828819 TATTTAAAAA
9828829 ATTAAATATT
1 ATTAAATATT
9828839 A-TAAATAGTT
1 ATTAAATA-TT
9828849 ATTAAATATT
1 ATTAAATATT
9828859 ATTAAAATATT
1 ATT-AAATATT
9828870 -TTAAA-ATT
1 ATTAAATATT
* *
9828878 ATTAAAAATC
1 ATTAAATATT
* *
9828888 ATAAAAGATT
1 ATTAAATATT
9828898 ATTTAAA-ATT
1 A-TTAAATATT
*
9828908 -TGTAAAAATT
1 AT-TAAATATT
*
9828918 ATTGAATATT
1 ATTAAATATT
9828928 GTGAAATCTA
Statistics
Matches: 73, Mismatches: 7, Indels: 18
0.74 0.07 0.18
Matches are distributed among these distances:
8 4 0.05
9 18 0.25
10 33 0.45
11 18 0.25
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.43
Consensus pattern (10 bp):
ATTAAATATT
Found at i:9828884 original size:9 final size:9
Alignment explanation
Indices: 9828805--9828920 Score: 58
Period size: 10 Copynumber: 12.0 Consensus size: 9
9828795 AAAAATGTAA
*
9828805 AAAAATATT
1 AAAATTATT
*
9828814 TAAATTATTT
1 AAAATTA-TT
*
9828824 AAAA-AATT
1 AAAATTATT
9828832 AAATATTA-T
1 AAA-ATTATT
9828841 AAATAGTTATT
1 AAA-A-TTATT
9828852 AAATATTATT
1 AAA-ATTATT
*
9828862 AAAATATTTT
1 AAAAT-TATT
9828872 AAAATTATT
1 AAAATTATT
* *
9828881 AAAAATCATA
1 -AAAATTATT
9828891 AAAGATTATTT
1 AAA-ATTA-TT
9828902 AAAATT-TGT
1 AAAATTAT-T
9828911 AAAAATTATT
1 -AAAATTATT
9828921 GAATATTGTG
Statistics
Matches: 84, Mismatches: 11, Indels: 23
0.71 0.09 0.19
Matches are distributed among these distances:
8 6 0.07
9 22 0.26
10 45 0.54
11 11 0.13
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (9 bp):
AAAATTATT
Found at i:9829226 original size:20 final size:20
Alignment explanation
Indices: 9829187--9829236 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
9829177 AATAATTTGT
9829187 TAATTATTTATATTTTTTTAA
1 TAATTATTTATA-TTTTTTAA
9829208 TAATTATTTATGA-TTTTTAA
1 TAATTATTTAT-ATTTTTTAA
9829228 TAATT-TTTA
1 TAATTATTTA
9829237 AAAAATTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.14
20 12 0.43
21 11 0.39
22 1 0.04
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
TAATTATTTATATTTTTTAA
Found at i:9829235 original size:10 final size:10
Alignment explanation
Indices: 9829201--9829262 Score: 51
Period size: 10 Copynumber: 6.5 Consensus size: 10
9829191 TATTTATATT
9829201 TTTTTAATAA
1 TTTTTAATAA
*
9829211 TTATTT-ATGA
1 TT-TTTAATAA
9829221 TTTTTAATAA
1 TTTTTAATAA
9829231 TTTTTAA-AA
1 TTTTTAATAA
**
9829240 -AATT-ATAA
1 TTTTTAATAA
*
9829248 CTTTTAATAA
1 TTTTTAATAA
9829258 TTTTT
1 TTTTT
9829263 TTACAATTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
7 1 0.03
8 4 0.10
9 7 0.17
10 25 0.62
11 3 0.08
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:9829274 original size:20 final size:20
Alignment explanation
Indices: 9829249--9829305 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
9829239 AAATTATAAC
*
9829249 TTTTAATAATTTTTTTACAA
1 TTTTAATAATTTTTTAACAA
9829269 TTTTAA-AATATTTTTAACAA
1 TTTTAATAAT-TTTTTAACAA
* *
9829289 TATTTGATAATTATTTA
1 T-TTTAATAATTTTTTA
9829306 CATATTTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 3 0.10
20 16 0.52
21 9 0.29
22 3 0.10
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTTAATAATTTTTTAACAA
Found at i:9829318 original size:35 final size:34
Alignment explanation
Indices: 9829277--9829346 Score: 88
Period size: 34 Copynumber: 2.0 Consensus size: 34
9829267 AATTTTAAAA
*
9829277 TATTTTTAACAATATTTGATA-ATTATTTACATATT
1 TATTTTTAACAAT-TTTGATATATT-TTTAAATATT
* *
9829312 TATTTTTTACAATTTTTATATATTTTTAAATATT
1 TATTTTTAACAATTTTGATATATTTTTAAATATT
9829346 T
1 T
9829347 TACGATTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
34 16 0.52
35 15 0.48
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.60
Consensus pattern (34 bp):
TATTTTTAACAATTTTGATATATTTTTAAATATT
Found at i:9829337 original size:20 final size:20
Alignment explanation
Indices: 9829259--9829338 Score: 55
Period size: 20 Copynumber: 4.2 Consensus size: 20
9829249 TTTTAATAAT
* *
9829259 TTTTTTACAATTTTAAAATA
1 TTTTTTACAATTTTTATATA
* *
9829279 TTTTTAACAATATTTGATA-A
1 TTTTTTACAAT-TTTTATATA
* *
9829299 TTATTTAC-A----TATTTA
1 TTTTTTACAATTTTTATATA
9829314 TTTTTTACAATTTTTATATA
1 TTTTTTACAATTTTTATATA
9829334 TTTTT
1 TTTTT
9829339 AAATATTTTA
Statistics
Matches: 44, Mismatches: 9, Indels: 14
0.66 0.13 0.21
Matches are distributed among these distances:
14 2 0.05
15 8 0.18
16 1 0.02
19 1 0.02
20 27 0.61
21 5 0.11
ACGTcount: A:0.34, C:0.05, G:0.01, T:0.60
Consensus pattern (20 bp):
TTTTTTACAATTTTTATATA
Found at i:9831445 original size:24 final size:25
Alignment explanation
Indices: 9831403--9831449 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
9831393 GGCCTTGAGT
9831403 CGGTGTTATCTATCAGGCTTTGTAC
1 CGGTGTTATCTATCAGGCTTTGTAC
* *
9831428 CGGTG-TATTTATCGGGCTTTGT
1 CGGTGTTATCTATCAGGCTTTGT
9831450 GCCTAGCAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.13, C:0.17, G:0.28, T:0.43
Consensus pattern (25 bp):
CGGTGTTATCTATCAGGCTTTGTAC
Found at i:9831555 original size:25 final size:25
Alignment explanation
Indices: 9831508--9831567 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
9831498 GGCTTTGTGT
** *
9831508 TGGTGTTATCTATCAGGCCTTGAGC
1 TGGTGTTATCTATCAAACATTGAGC
* *
9831533 TGGTGTTGTCTATCAAACATTGAGT
1 TGGTGTTATCTATCAAACATTGAGC
9831558 TGGTGATTAT
1 TGGTG-TTAT
9831568 TTAGCAAGTA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
25 25 0.89
26 3 0.11
ACGTcount: A:0.20, C:0.13, G:0.27, T:0.40
Consensus pattern (25 bp):
TGGTGTTATCTATCAAACATTGAGC
Found at i:9838999 original size:18 final size:19
Alignment explanation
Indices: 9838967--9839004 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
9838957 TTTATATTCT
9838967 TTGAGAGTGAATAC-TAAA
1 TTGAGAGTGAATACTTAAA
**
9838985 TTGAGAGTGTTTACTTAAA
1 TTGAGAGTGAATACTTAAA
9839004 T
1 T
9839005 ACCTATTGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.37, C:0.05, G:0.21, T:0.37
Consensus pattern (19 bp):
TTGAGAGTGAATACTTAAA
Found at i:9848915 original size:12 final size:12
Alignment explanation
Indices: 9848900--9848931 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
9848890 AACTAAGTTG
9848900 TAAATATTTTTA
1 TAAATATTTTTA
9848912 TAAATATTTTTA
1 TAAATATTTTTA
9848924 TAAATATT
1 TAAATATT
9848932 ACGGAGTGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
TAAATATTTTTA
Found at i:9851293 original size:108 final size:107
Alignment explanation
Indices: 9850992--9851538 Score: 766
Period size: 108 Copynumber: 5.1 Consensus size: 107
9850982 GATTAAGATA
* * *
9850992 TAAAATGATATTTGGCTATTTGGTCCG-ACG-GGAAATCGAGACCCAATACATTAGGGCACGTTT
1 TAAAAGGATATTTGGCTATTTGGT-CGAACGAGGAAATCGAAACCCAACACATTAGGGCACGTTT
9851055 TCTCGAATTTCCAAACGCAAAACA---CCTTATTTTGAAAATT
65 TCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAAATT
* * * * *
9851095 TAAAAGGATATTCGGCTATTTGGTCGAACGAGGTAATCGAAACCCAGCACATTAGGGCATGTTTC
1 TAAAAGGATATTTGGCTATTTGGTCGAACGAGGAAATCGAAACCCAACACATTAGGGCACGTTTT
*
9851160 CTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTT
66 CTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAAATT
* *
9851202 TAAAAGGATATTTAGCTATTTGGTCGAACGAGAAAGATCGAAACCCAACACATTAGGGCACGTTT
1 TAAAAGGATATTTGGCTATTTGGTCGAACGAGGAA-ATCGAAACCCAACACATTAGGGCACGTTT
** *
9851267 TCTTAAATTTCCAAACGCAAAACATTGCTTTATTTTGAAAATT
65 TCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAAATT
* * * *
9851310 TAAAAGGATATTCGGCTATTTGGTCGAACGAGGTAATCGAAACCCAGCACATTAGGGCACGTTTC
1 TAAAAGGATATTTGGCTATTTGGTCGAACGAGGAAATCGAAACCCAACACATTAGGGCACGTTTT
* *
9851375 CTCGAATTTCCAAACGCAAAACATTGCTTTATTTTGAAATTT
66 CTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAAATT
* *
9851417 TAAAAGGATATTTAGCTATTTGGTCGAACGA-GAATGATCGAAACCCAACACATTAGGGCACATT
1 TAAAAGGATATTTGGCTATTTGGTCGAACGAGGAA--ATCGAAACCCAACACATTAGGGCACGTT
9851481 TTCTCGAACTTT-CAAACGCAAAACATTGCCTTATTTTTGAAAAATT
64 TTCTCGAA-TTTCCAAACGCAAAACATTGCCTTA-TTTTG-AAAATT
**
9851527 TTTAAGGATATT
1 TAAAAGGATATT
9851539 AATATGCATA
Statistics
Matches: 394, Mismatches: 39, Indels: 15
0.88 0.09 0.03
Matches are distributed among these distances:
102 2 0.01
103 25 0.06
104 51 0.13
106 2 0.01
107 142 0.36
108 149 0.38
109 8 0.02
110 15 0.04
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (107 bp):
TAAAAGGATATTTGGCTATTTGGTCGAACGAGGAAATCGAAACCCAACACATTAGGGCACGTTTT
CTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAAATT
Found at i:9851409 original size:215 final size:215
Alignment explanation
Indices: 9850992--9851538 Score: 874
Period size: 215 Copynumber: 2.6 Consensus size: 215
9850982 GATTAAGATA
* * * * *
9850992 TAAAATGATATTTGGCTATTTGGTCCG-ACG-GGAA-ATCGAGACCCAATACATTAGGGCACGTT
1 TAAAAGGATATTTAGCTATTTGGT-CGAACGAGAAAGATCGAAACCCAACACATTAGGGCACGTT
*
9851054 TTCTCGAATTTCCAAACGCAAAACA---CCTTATTTTGAAAATTTAAAAGGATATTCGGCTATTT
65 TTCTCAAATTTCCAAACGCAAAACATTGCCTTATTTTGAAAATTTAAAAGGATATTCGGCTATTT
*
9851116 GGTCGAACGAGGTAATCGAAACCCAGCACATTAGGGCATGTTTCCTCGAATTTCCAAACGCAAAA
130 GGTCGAACGAGGTAATCGAAACCCAGCACATTAGGGCACGTTTCCTCGAATTTCCAAACGCAAAA
9851181 CATTGCCTTATTTTGAAATTT
195 CATTGCCTTATTTTGAAATTT
9851202 TAAAAGGATATTTAGCTATTTGGTCGAACGAGAAAGATCGAAACCCAACACATTAGGGCACGTTT
1 TAAAAGGATATTTAGCTATTTGGTCGAACGAGAAAGATCGAAACCCAACACATTAGGGCACGTTT
* *
9851267 TCTTAAATTTCCAAACGCAAAACATTGCTTTATTTTGAAAATTTAAAAGGATATTCGGCTATTTG
66 TCTCAAATTTCCAAACGCAAAACATTGCCTTATTTTGAAAATTTAAAAGGATATTCGGCTATTTG
9851332 GTCGAACGAGGTAATCGAAACCCAGCACATTAGGGCACGTTTCCTCGAATTTCCAAACGCAAAAC
131 GTCGAACGAGGTAATCGAAACCCAGCACATTAGGGCACGTTTCCTCGAATTTCCAAACGCAAAAC
*
9851397 ATTGCTTTATTTTGAAATTT
196 ATTGCCTTATTTTGAAATTT
* *
9851417 TAAAAGGATATTTAGCTATTTGGTCGAACGAGAATGATCGAAACCCAACACATTAGGGCACATTT
1 TAAAAGGATATTTAGCTATTTGGTCGAACGAGAAAGATCGAAACCCAACACATTAGGGCACGTTT
* **
9851482 TCTCGAACTTT-CAAACGCAAAACATTGCCTTATTTTTGAAAAATTTTTAAGGATATT
66 TCTC-AAATTTCCAAACGCAAAACATTGCCTTA-TTTTG-AAAATTTAAAAGGATATT
9851539 AATATGCATA
Statistics
Matches: 311, Mismatches: 17, Indels: 11
0.92 0.05 0.03
Matches are distributed among these distances:
209 2 0.01
210 25 0.08
211 3 0.01
212 49 0.16
215 206 0.66
216 10 0.03
217 16 0.05
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (215 bp):
TAAAAGGATATTTAGCTATTTGGTCGAACGAGAAAGATCGAAACCCAACACATTAGGGCACGTTT
TCTCAAATTTCCAAACGCAAAACATTGCCTTATTTTGAAAATTTAAAAGGATATTCGGCTATTTG
GTCGAACGAGGTAATCGAAACCCAGCACATTAGGGCACGTTTCCTCGAATTTCCAAACGCAAAAC
ATTGCCTTATTTTGAAATTT
Found at i:9851937 original size:3 final size:3
Alignment explanation
Indices: 9851929--9851979 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
9851919 AAAATAAACA
*
9851929 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
9851977 AAT
1 AAT
9851980 GATGATGATG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:9851980 original size:6 final size:6
Alignment explanation
Indices: 9851933--9852021 Score: 63
Period size: 6 Copynumber: 15.0 Consensus size: 6
9851923 TAAACAAATA
* * * * * *
9851933 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATG ATAATG
1 ATAATG ATAATG ATAATG ATAATG ATAATG ATAATG ATAATG ATAATG
* * * * * *
9851981 ATGATG ATGATG ATGATG ATGATG ATGATG ATGATG -TAATG
1 ATAATG ATAATG ATAATG ATAATG ATAATG ATAATG ATAATG
9852022 TGATAACAAT
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
5 4 0.05
6 76 0.95
ACGTcount: A:0.49, C:0.00, G:0.17, T:0.34
Consensus pattern (6 bp):
ATAATG
Found at i:9851984 original size:3 final size:3
Alignment explanation
Indices: 9851972--9852016 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
9851962 AATAATAATA
*
9851972 ATG ATA ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
9852017 TAATGTGATA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.36, C:0.00, G:0.31, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:9853379 original size:37 final size:38
Alignment explanation
Indices: 9853314--9853393 Score: 117
Period size: 37 Copynumber: 2.1 Consensus size: 38
9853304 TGTCAATTTA
* *
9853314 TTACTTCGGATTTATTCGATGAGGCACTAGGTGGCAAC
1 TTACTTCGGATTTAATCGATGAGACACTAGGTGGCAAC
* *
9853352 TTACTTCGG-TTTAATCGATGAGACACTAGGTGTCAAT
1 TTACTTCGGATTTAATCGATGAGACACTAGGTGGCAAC
9853389 TTACT
1 TTACT
9853394 ACTTCAAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
37 29 0.76
38 9 0.24
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (38 bp):
TTACTTCGGATTTAATCGATGAGACACTAGGTGGCAAC
Found at i:9855795 original size:40 final size:40
Alignment explanation
Indices: 9855701--9855801 Score: 116
Period size: 40 Copynumber: 2.5 Consensus size: 40
9855691 TGGCGTTTGG
*
9855701 ACAAAAAAGCGCCGCTAAAAATCGAGCATTAGCGACGCTTT
1 ACAAAAAA-CGCCGCTAAAAATCGAACATTAGCGACGCTTT
* *
9855742 ACATAAAAA-GCCGCTAAAAAT-GAACATTAGCGGCGTTTTT
1 ACA-AAAAACGCCGCTAAAAATCGAACATTAGCGACG-CTTT
* *
9855782 CCAAAAAACGCCGCAAAAAA
1 ACAAAAAACGCCGCTAAAAA
9855802 CCTAAGCCGA
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
39 17 0.33
40 27 0.52
41 3 0.06
42 5 0.10
ACGTcount: A:0.44, C:0.23, G:0.17, T:0.17
Consensus pattern (40 bp):
ACAAAAAACGCCGCTAAAAATCGAACATTAGCGACGCTTT
Found at i:9856296 original size:14 final size:15
Alignment explanation
Indices: 9856268--9856297 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
9856258 AAGGTTTATA
9856268 GATTATGGAATTAGG
1 GATTATGGAATTAGG
9856283 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
9856297 G
1 G
9856298 GTTCTAGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:9856454 original size:21 final size:21
Alignment explanation
Indices: 9856430--9856485 Score: 53
Period size: 20 Copynumber: 2.7 Consensus size: 21
9856420 AAATATGGTT
*
9856430 TAGGGGTTAAGGGTTGGGGGA
1 TAGGGGTTAAGGGTTCGGGGA
*
9856451 TA-GGGTT-AGGGATTCGGGGT
1 TAGGGGTTAAGGG-TTCGGGGA
* *
9856471 TAGTGGTTAGGGGTT
1 TAGGGGTTAAGGGTT
9856486 TAGGGTTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
19 4 0.14
20 13 0.46
21 8 0.29
22 3 0.11
ACGTcount: A:0.16, C:0.02, G:0.52, T:0.30
Consensus pattern (21 bp):
TAGGGGTTAAGGGTTCGGGGA
Found at i:9856480 original size:7 final size:7
Alignment explanation
Indices: 9856429--9856490 Score: 54
Period size: 7 Copynumber: 8.9 Consensus size: 7
9856419 TAAATATGGT
9856429 TTAGGGG
1 TTAGGGG
*
9856436 TTAAGGG
1 TTAGGGG
*
9856443 TTGGGGG
1 TTAGGGG
*
9856450 ATA-GGG
1 TTAGGGG
*
9856456 TTAGGGA
1 TTAGGGG
*
9856463 TTCGGGG
1 TTAGGGG
*
9856470 TTAGTGG
1 TTAGGGG
9856477 TTAGGGG
1 TTAGGGG
9856484 TTTAGGG
1 -TTAGGG
9856491 TTTATGTTTT
Statistics
Matches: 41, Mismatches: 12, Indels: 3
0.73 0.21 0.05
Matches are distributed among these distances:
6 5 0.12
7 30 0.73
8 6 0.15
ACGTcount: A:0.16, C:0.02, G:0.52, T:0.31
Consensus pattern (7 bp):
TTAGGGG
Found at i:9860979 original size:87 final size:87
Alignment explanation
Indices: 9860879--9861039 Score: 207
Period size: 87 Copynumber: 1.9 Consensus size: 87
9860869 GTGTTTGTTA
* * * * *
9860879 AAAAGCGCCGCTAAGAGTCAT-CTTTATTGTGGCATTTTGTTGTAGAAGAGTCGCTAAAAGTCAT
1 AAAAGCGCCGCTAAAAATCATGCTCTATAGTGGCATTTT-TAGTAGAAGAGTCGCTAAAAGTCAT
* *
9860943 TGTCTTTAGCCACATTTTTTGAG
65 GGTCTATAGCCACATTTTTTGAG
* * * *
9860966 AAAAGCGCCGCTAAAAATTATGGTCTATAGTGGCATTTTTAGTAGAAGCGTCGCTAAAGGTCATG
1 AAAAGCGCCGCTAAAAATCATGCTCTATAGTGGCATTTTTAGTAGAAGAGTCGCTAAAAGTCATG
9861031 GTCTATAGC
66 GTCTATAGC
9861040 GACGTTTGTA
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
87 48 0.77
88 14 0.23
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (87 bp):
AAAAGCGCCGCTAAAAATCATGCTCTATAGTGGCATTTTTAGTAGAAGAGTCGCTAAAAGTCATG
GTCTATAGCCACATTTTTTGAG
Found at i:9861066 original size:87 final size:88
Alignment explanation
Indices: 9860907--9861079 Score: 197
Period size: 87 Copynumber: 2.0 Consensus size: 88
9860897 CATCTTTATT
* * * * * * *
9860907 GTGGCATTTTGTTGTAGAAGAGTCGCTAAAAGTCATTGTCTTTAGCCACATTTTTTGAGAAAAGC
1 GTGGCATTTTGTAGTAGAAGAGTCGCTAAAAGTCATGGTCTATAGCCACAGTTTGTAAAAAAAGC
*
9860972 GCCGCTAAAAATTATGGTCTATA
66 GCCGCTAAAAATTATGATCTATA
* * *
9860995 GTGGCATTTT-TAGTAGAAGCGTCGCTAAAGGTCATGGTCTATAGCGAC-GTTTGTAAAAAAAGG
1 GTGGCATTTTGTAGTAGAAGAGTCGCTAAAAGTCATGGTCTATAGCCACAGTTTGTAAAAAAA-G
* * *
9861058 TGCTGCTAAAGATTATGATCTA
65 CGCCGCTAAAAATTATGATCTA
9861080 GCGTTTGTGA
Statistics
Matches: 70, Mismatches: 14, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
86 9 0.13
87 51 0.73
88 10 0.14
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (88 bp):
GTGGCATTTTGTAGTAGAAGAGTCGCTAAAAGTCATGGTCTATAGCCACAGTTTGTAAAAAAAGC
GCCGCTAAAAATTATGATCTATA
Found at i:9863790 original size:93 final size:93
Alignment explanation
Indices: 9863631--9863810 Score: 324
Period size: 93 Copynumber: 1.9 Consensus size: 93
9863621 CCACAAAAAA
*
9863631 TACAAGATAGCTTAAGTACTTATGACACTTACATGTACAAGTTTAAATATTATTAGATGGATATG
1 TACAAGATAGCTTAAGTACTTATGACACTTACATGTACAAGTTTAAATATTATTACATGGATATG
9863696 ATATTTAGACTACTAATACATTAAGCAT
66 ATATTTAGACTACTAATACATTAAGCAT
* * *
9863724 TACAAGATAGGTTAAGTACTTATGACGCTTACATGTACAAGTTTAATTATTATTACATGGATATG
1 TACAAGATAGCTTAAGTACTTATGACACTTACATGTACAAGTTTAAATATTATTACATGGATATG
9863789 ATATTTAGACTACTAATACATT
66 ATATTTAGACTACTAATACATT
9863811 GAGAAAGCAA
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 83 1.00
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (93 bp):
TACAAGATAGCTTAAGTACTTATGACACTTACATGTACAAGTTTAAATATTATTACATGGATATG
ATATTTAGACTACTAATACATTAAGCAT
Found at i:9865372 original size:2 final size:2
Alignment explanation
Indices: 9865332--9865363 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
9865322 AACGCATTTT
*
9865332 GA GA GA GA GA GA GA GA GA GA GA AA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
9865364 CGGGAGAGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Done.