Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 19 of 226
Found at i:8650732 original size:22 final size:22
Alignment explanation
Indices: 8650707--8650751 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
8650697 TAGGTTTTAT
* *
8650707 TGTTTTTAGGGTTTATTGTTTG
1 TGTTTTTAGGGTCTATGGTTTG
8650729 TGTTTTTAGGGTCTATGGTTTG
1 TGTTTTTAGGGTCTATGGTTTG
8650751 T
1 T
8650752 AGGTTTTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.09, C:0.02, G:0.29, T:0.60
Consensus pattern (22 bp):
TGTTTTTAGGGTCTATGGTTTG
Found at i:8654899 original size:6 final size:6
Alignment explanation
Indices: 8654885--8654920 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
8654875 AGATGGGAGA
*
8654885 GAATGG GAATTG GAATTG GAATTG GAATTG GAATTG
1 GAATTG GAATTG GAATTG GAATTG GAATTG GAATTG
8654921 AAAGAAGTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.31
Consensus pattern (6 bp):
GAATTG
Found at i:8655567 original size:25 final size:24
Alignment explanation
Indices: 8655535--8655581 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
8655525 TTTAAATTTT
8655535 ATATTAATATTAAATAAATATAATC
1 ATATTAATATTAAATAAA-ATAATC
*
8655560 ATATTAATCTTAAATAAAATAA
1 ATATTAATATTAAATAAAATAA
8655582 AATCCCCTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (24 bp):
ATATTAATATTAAATAAAATAATC
Found at i:8662244 original size:222 final size:222
Alignment explanation
Indices: 8661858--8662274 Score: 762
Period size: 222 Copynumber: 1.9 Consensus size: 222
8661848 ACGCGAAGAA
* *
8661858 TGTACCAGGACGTTTTTGGGCAGAAGCAATGAGGACGGCTGCATTTGTAATCAATAGGCTTTCTC
1 TGTACCAGGACATTTTTGGGCAGAAGCAATGAGGACGGCTGCATTTGTAATCAATAGGCTTCCTC
* *
8661923 AACAAAGGTTATGTTTTATTTCACCTTTTGAAAAATTTTGCAACATGAAACCTTCAATTAGTTAT
66 AACAAAGGTTATGTTTTATTTCACCTTTTGAAAAATTATGCAACATAAAACCTTCAATTAGTTAT
*
8661988 TTCAGAGTTTTCGGATATGTTTGCTATGTATTTGTACCTGATTATTTACGTAGCAAAATAGACAA
131 TTCAGAGTTTTCGGATATGTTTGCTATGTATTTGTACCTGATCATTTACGTAGCAAAATAGACAA
8662053 AAATTATGCAACGTGAAACCTTCATAG
196 AAATTATGCAACGTGAAACCTTCATAG
8662080 TGTACCAGGACATTTTTGGGCAGAAGCAATGAGGACGGCTGCATTTGTAATCAATAGGCTTCCTC
1 TGTACCAGGACATTTTTGGGCAGAAGCAATGAGGACGGCTGCATTTGTAATCAATAGGCTTCCTC
*
8662145 AACAAAGGTTATGTTTTATTTCACCTTTTGAAAAATTATGCAACATAAAACCTTCAGTTAGTTAT
66 AACAAAGGTTATGTTTTATTTCACCTTTTGAAAAATTATGCAACATAAAACCTTCAATTAGTTAT
* *
8662210 TTTAGAGTTTTCGGATATGTTTGCTATGTATTTGTGCCTGATCATTTACGTAGCAAAATAGACAA
131 TTCAGAGTTTTCGGATATGTTTGCTATGTATTTGTACCTGATCATTTACGTAGCAAAATAGACAA
8662275 TAAGGTTGTT
Statistics
Matches: 187, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
222 187 1.00
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (222 bp):
TGTACCAGGACATTTTTGGGCAGAAGCAATGAGGACGGCTGCATTTGTAATCAATAGGCTTCCTC
AACAAAGGTTATGTTTTATTTCACCTTTTGAAAAATTATGCAACATAAAACCTTCAATTAGTTAT
TTCAGAGTTTTCGGATATGTTTGCTATGTATTTGTACCTGATCATTTACGTAGCAAAATAGACAA
AAATTATGCAACGTGAAACCTTCATAG
Found at i:8671226 original size:27 final size:28
Alignment explanation
Indices: 8671195--8671247 Score: 90
Period size: 27 Copynumber: 1.9 Consensus size: 28
8671185 AACTAAATAT
*
8671195 ATGATGTTTTATACTAT-CTAATTTTAC
1 ATGATGTTTTATACCATACTAATTTTAC
8671222 ATGATGTTTTATACCATACTAATTTT
1 ATGATGTTTTATACCATACTAATTTT
8671248 TAAAATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 16 0.67
28 8 0.33
ACGTcount: A:0.30, C:0.11, G:0.08, T:0.51
Consensus pattern (28 bp):
ATGATGTTTTATACCATACTAATTTTAC
Found at i:8678742 original size:16 final size:16
Alignment explanation
Indices: 8678716--8678754 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
8678706 AATATATATT
8678716 TATTATAAAT-ATTGAAA
1 TATT-TAAATAATT-AAA
8678733 TATTTAAATAATTAAA
1 TATTTAAATAATTAAA
8678749 TATTTA
1 TATTTA
8678755 TTACAAATCG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (16 bp):
TATTTAAATAATTAAA
Found at i:8685348 original size:23 final size:24
Alignment explanation
Indices: 8685318--8685362 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
8685308 AGAGACTACT
8685318 GTTATCTA-TTCTAAGTTGTTTAA
1 GTTATCTATTTCTAAGTTGTTTAA
8685341 GTTATCTATTTCTAAGTTGTTT
1 GTTATCTATTTCTAAGTTGTTT
8685363 GAATCATGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.22, C:0.09, G:0.13, T:0.56
Consensus pattern (24 bp):
GTTATCTATTTCTAAGTTGTTTAA
Found at i:8685985 original size:190 final size:190
Alignment explanation
Indices: 8685656--8686029 Score: 658
Period size: 190 Copynumber: 2.0 Consensus size: 190
8685646 ACAAGATCTC
* *
8685656 TAAAGAAATATCTGAAATAAAAATTAGATAGGATATTTCTTTAATTTCATTTATGTGAAGGGCTT
1 TAAAGAAATATCTGAAATAAAAATTAGATAGAATATTGCTTTAATTTCATTTATGTGAAGGGCTT
*
8685721 CTACCAACATTTTGCTTTATCTCTATTTCTCTCATTTTTCTTTAGGTTATATAAGGGCATTGATA
66 CTACCAACATTTTGCTTTATCTCTATTTCTCTCATTTTTCTTAAGGTTATATAAGGGCATTGATA
* *
8685786 CTGTCTGGTTTCTTTTGTCATAAGAGGGGGATCTAAGCTTATTGTACAGGGATTTTGAAA
131 CTATCTGGTTTCTTTTGTCATAAGAGCGGGATCTAAGCTTATTGTACAGGGATTTTGAAA
* **
8685846 TAAAGAAATATCTGAAATAAAAATTAGATAGAATATTGCTTTAGTTTCATTTATGTGAAGGTTTT
1 TAAAGAAATATCTGAAATAAAAATTAGATAGAATATTGCTTTAATTTCATTTATGTGAAGGGCTT
* *
8685911 TTACCAACATTTTGCTTTATCTCTATTTCTCTCATTTTTCTTAAGGTTATATACGGGCATTGATA
66 CTACCAACATTTTGCTTTATCTCTATTTCTCTCATTTTTCTTAAGGTTATATAAGGGCATTGATA
8685976 CTATCTGGTTTCTTTTGTCATAAGAGCGGGATCTAAGCTTATTGTACAGGGATT
131 CTATCTGGTTTCTTTTGTCATAAGAGCGGGATCTAAGCTTATTGTACAGGGATT
8686030 CTGAGATGAC
Statistics
Matches: 174, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
190 174 1.00
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (190 bp):
TAAAGAAATATCTGAAATAAAAATTAGATAGAATATTGCTTTAATTTCATTTATGTGAAGGGCTT
CTACCAACATTTTGCTTTATCTCTATTTCTCTCATTTTTCTTAAGGTTATATAAGGGCATTGATA
CTATCTGGTTTCTTTTGTCATAAGAGCGGGATCTAAGCTTATTGTACAGGGATTTTGAAA
Found at i:8687186 original size:103 final size:103
Alignment explanation
Indices: 8686991--8687194 Score: 349
Period size: 103 Copynumber: 2.0 Consensus size: 103
8686981 ACTTTGTAAG
* * *
8686991 AGTCATATGCATTTCTTTTAAAATCTCGAGGTTGACCGAGCAATATAACTCTGGTTATACACGAA
1 AGTCATATGCATTTCTTTTAAAATCTCAAAGTTGACAGAGCAATATAACTCTGGTTATACACGAA
8687056 GAAAAAGAGACAAAAAGGAAAAAAAAAAGAATCTTAAT
66 GAAAAAGAGACAAAAAGGAAAAAAAAAAGAATCTTAAT
8687094 AGTCATATGCATTTCTTTTAAAATCTCAAAGTTGACAGAGCAATATAACTCTGGTTATACAC-AG
1 AGTCATATGCATTTCTTTTAAAATCTCAAAGTTGACAGAGCAATATAACTCTGGTTATACACGA-
8687158 AGAAAAAGAGA-AAAAAGGAAAAAGAAAAAGAATCTTA
65 AGAAAAAGAGACAAAAAGGAAAAA-AAAAAGAATCTTA
8687195 TGCCAAGCTG
Statistics
Matches: 96, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
102 13 0.14
103 83 0.86
ACGTcount: A:0.47, C:0.13, G:0.16, T:0.24
Consensus pattern (103 bp):
AGTCATATGCATTTCTTTTAAAATCTCAAAGTTGACAGAGCAATATAACTCTGGTTATACACGAA
GAAAAAGAGACAAAAAGGAAAAAAAAAAGAATCTTAAT
Found at i:8688543 original size:190 final size:189
Alignment explanation
Indices: 8688182--8688569 Score: 758
Period size: 190 Copynumber: 2.0 Consensus size: 189
8688172 GCACTTGGAC
8688182 CTTGTAATGGGACAAGACAAATTTGTTTCAACAAACAGGGATGGGCATTTTCTTAATGTTTCTAC
1 CTTGT-ATGGGACAAGACAAATTTGTTTCAACAAACAGGGATGGGCATTTTCTTAATGTTTCTAC
8688247 TACATGAATGTCATCATATTTACTCTTACAACCTAATGCTCCTGTTTCTGTTCCACTTTTAGCAT
65 TACATGAATGTCATCATATTTACTCTTACAACCTAATGCTCCTGTTTCTGTTCCACTTTTAGCAT
8688312 GCAAGTAATTCATTTGTCTTTTTTATCACATTCAACCTGGTCGTTATCATACATCTTTCA
130 GCAAGTAATTCATTTGTCTTTTTTATCACATTCAACCTGGTCGTTATCATACATCTTTCA
8688372 CTTGTATGGGACAAGACAAATTTGTTTCAACAAACAGGGATGGGCATTTTCTTAATGTTTCTACT
1 CTTGTATGGGACAAGACAAATTTGTTTCAACAAACAGGGATGGGCATTTTCTTAATGTTTCTACT
8688437 ACATGAATGTCATCATATTTACTACTTACAACCTAATGCTCCTGTTTCTGTTCCACTTTTAGCAT
66 ACATGAATGTCATCATATTTACT-CTTACAACCTAATGCTCCTGTTTCTGTTCCACTTTTAGCAT
8688502 GCAAGTAATTCATTTGTCTTTTTTATCACATTCAACCTGGTCGTTATCATACATCTTTCA
130 GCAAGTAATTCATTTGTCTTTTTTATCACATTCAACCTGGTCGTTATCATACATCTTTCA
8688562 CTTGTATG
1 CTTGTATG
8688570 AGGTTGACAT
Statistics
Matches: 197, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
189 83 0.42
190 114 0.58
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (189 bp):
CTTGTATGGGACAAGACAAATTTGTTTCAACAAACAGGGATGGGCATTTTCTTAATGTTTCTACT
ACATGAATGTCATCATATTTACTCTTACAACCTAATGCTCCTGTTTCTGTTCCACTTTTAGCATG
CAAGTAATTCATTTGTCTTTTTTATCACATTCAACCTGGTCGTTATCATACATCTTTCA
Found at i:8697578 original size:63 final size:63
Alignment explanation
Indices: 8697475--8697607 Score: 212
Period size: 63 Copynumber: 2.1 Consensus size: 63
8697465 GTTATCTCCG
* * *
8697475 GTTTCTGCTCATCCCTAATCTGGTCTGTCTCAAGTTCAATGGTAAGTGCCCACATTCTAGACA
1 GTTTCTGCTCACCCCTAATCTGGTCTGTCTCAAGTACAATGGTAAGCGCCCACATTCTAGACA
* * *
8697538 GTTTCTGCTCACCCCTGATCTGGTCTGTCTCAAGTACAATGGTAAGCGGCCACATTCTGGACA
1 GTTTCTGCTCACCCCTAATCTGGTCTGTCTCAAGTACAATGGTAAGCGCCCACATTCTAGACA
8697601 GTTTCTG
1 GTTTCTG
8697608 TGAAGAGGAT
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.32
Consensus pattern (63 bp):
GTTTCTGCTCACCCCTAATCTGGTCTGTCTCAAGTACAATGGTAAGCGCCCACATTCTAGACA
Found at i:8724118 original size:12 final size:12
Alignment explanation
Indices: 8724101--8724126 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
8724091 CATAAATTCA
8724101 AAAAAAAAAAAG
1 AAAAAAAAAAAG
8724113 AAAAAAAAAAAG
1 AAAAAAAAAAAG
8724125 AA
1 AA
8724127 GAAGAGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:8724123 original size:18 final size:20
Alignment explanation
Indices: 8724100--8724137 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
8724090 ACATAAATTC
8724100 AAAAAA-AA-AAAAGAAAAA
1 AAAAAAGAAGAAAAGAAAAA
*
8724118 AAAAAAGAAGAAGAGAAAAA
1 AAAAAAGAAGAAAAGAAAAA
8724138 CTAGTTATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 2 0.12
20 9 0.53
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (20 bp):
AAAAAAGAAGAAAAGAAAAA
Found at i:8724137 original size:15 final size:15
Alignment explanation
Indices: 8724100--8724129 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
8724090 ACATAAATTC
8724100 AAAAAAAAAAAAGAA
1 AAAAAAAAAAAAGAA
*
8724115 AAAAAAAAAGAAGAA
1 AAAAAAAAAAAAGAA
8724130 GAGAAAAACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAGAA
Found at i:8726339 original size:29 final size:30
Alignment explanation
Indices: 8726271--8726354 Score: 97
Period size: 29 Copynumber: 2.9 Consensus size: 30
8726261 TGATAATTAT
*
8726271 ATTAATAATTTAT-TA-AAATTTA-ATC-AA
1 ATTAATAATTTATGTATAAAATTACA-CAAA
*
8726298 ATTAATATTTTATGTATAAAATTACACAAA
1 ATTAATAATTTATGTATAAAATTACACAAA
*
8726328 ATTAA-AATTTATGTATAATATTACACA
1 ATTAATAATTTATGTATAAAATTACACA
8726355 TTGAACAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
27 12 0.24
28 2 0.04
29 27 0.55
30 8 0.16
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (30 bp):
ATTAATAATTTATGTATAAAATTACACAAA
Found at i:8731435 original size:18 final size:17
Alignment explanation
Indices: 8731408--8731441 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
8731398 ATCCTTTTTA
8731408 TATTTTTTAAAATTATT
1 TATTTTTTAAAATTATT
*
8731425 TATTGTTTTAAAGTTAT
1 TATT-TTTTAAAATTAT
8731442 GTGTTAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (17 bp):
TATTTTTTAAAATTATT
Found at i:8734898 original size:14 final size:14
Alignment explanation
Indices: 8734879--8734907 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
8734869 GACCCTTGAA
8734879 TGGGTGACATATCT
1 TGGGTGACATATCT
8734893 TGGGTGACATATCT
1 TGGGTGACATATCT
8734907 T
1 T
8734908 TTACTTACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.14, G:0.28, T:0.38
Consensus pattern (14 bp):
TGGGTGACATATCT
Found at i:8758255 original size:7 final size:7
Alignment explanation
Indices: 8758243--8758267 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
8758233 CTGACTTTAG
8758243 GTCTTTT
1 GTCTTTT
8758250 GTCTTTT
1 GTCTTTT
8758257 GTCTTTT
1 GTCTTTT
8758264 GTCT
1 GTCT
8758268 GATTTTCTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.16, G:0.16, T:0.68
Consensus pattern (7 bp):
GTCTTTT
Found at i:8758715 original size:22 final size:23
Alignment explanation
Indices: 8758690--8758745 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 23
8758680 TAAAATTTCA
8758690 AATATATATATTTTTTATAT-TT
1 AATATATATATTTTTTATATGTT
*
8758712 AATA-A-ATATTTTTTGTATGTT
1 AATATATATATTTTTTATATGTT
*
8758733 AATCTTATATATT
1 AAT-ATATATATT
8758746 AAATCATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
20 12 0.43
21 6 0.21
22 4 0.14
23 1 0.04
24 5 0.18
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.59
Consensus pattern (23 bp):
AATATATATATTTTTTATATGTT
Found at i:8759492 original size:18 final size:18
Alignment explanation
Indices: 8759460--8759497 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
8759450 AGTGGTAGAG
*
8759460 TATTGTGAATTAAGAGCAT
1 TATTGTGAATAAAGAG-AT
8759479 TATTG-GAATAAAGAGAT
1 TATTGTGAATAAAGAGAT
8759496 TA
1 TA
8759498 GATGAGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 9 0.50
19 5 0.28
ACGTcount: A:0.42, C:0.03, G:0.21, T:0.34
Consensus pattern (18 bp):
TATTGTGAATAAAGAGAT
Found at i:8774241 original size:26 final size:26
Alignment explanation
Indices: 8774204--8774253 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
8774194 ATTTTTTTCA
* * *
8774204 TCAATTTGGGTACTCGAATTAAAGGG
1 TCAATTTAGGTAATCAAATTAAAGGG
8774230 TCAATTTAGGTAATCAAATTAAAG
1 TCAATTTAGGTAATCAAATTAAAG
8774254 TTTAGGTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.32
Consensus pattern (26 bp):
TCAATTTAGGTAATCAAATTAAAGGG
Found at i:8776075 original size:26 final size:26
Alignment explanation
Indices: 8776037--8776090 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
8776027 TTAGTTTCAA
** * *
8776037 ATTTTGTTGTATATGTACATACTTAC
1 ATTTTGTCATATATATACATACGTAC
8776063 ATTTTGTCATATATATACATACGTAC
1 ATTTTGTCATATATATACATACGTAC
8776089 AT
1 AT
8776091 ATTATTTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.31, C:0.13, G:0.09, T:0.46
Consensus pattern (26 bp):
ATTTTGTCATATATATACATACGTAC
Found at i:8776148 original size:20 final size:19
Alignment explanation
Indices: 8776109--8776153 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
8776099 AATTTATTTG
*
8776109 TATATA-TATTTTTATACT
1 TATATATTATTTATATACT
8776127 TATATATTATTTATATACCT
1 TATATATTATTTATATA-CT
8776147 TATATAT
1 TATATAT
8776154 ATACATATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 6 0.25
19 9 0.38
20 9 0.38
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATATTATTTATATACT
Found at i:8776598 original size:23 final size:24
Alignment explanation
Indices: 8776572--8776616 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
8776562 ATTACTCGCG
8776572 TTATT-TTTATGCCAT-CATATTCA
1 TTATTGTTT-TGCCATACATATTCA
*
8776595 TTATTGTTTTGCTATACATATT
1 TTATTGTTTTGCCATACATATT
8776617 TTACCATACA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.24, C:0.13, G:0.07, T:0.56
Consensus pattern (24 bp):
TTATTGTTTTGCCATACATATTCA
Found at i:8776975 original size:107 final size:107
Alignment explanation
Indices: 8776636--8777053 Score: 648
Period size: 107 Copynumber: 4.0 Consensus size: 107
8776626 ATCAAAAGAA
* * * *
8776636 AAGATTTTCTAAATAAGACAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGTCCTAACGTGCTA
1 AAGATTTTCTAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTG
8776701 GGTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCATTTT
66 GGTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCATTTT
* * * *
8776743 AAGATTTTTTAAATAGGGAAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGTTG
1 AAGATTTTCTAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTG
* *
8776808 GGTTTC-A-AT-T-GTTCGACCAAATAGCCAAATATCCTTTT
66 GGTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCATTTT
** *
8776846 AAGATTTTCTAAATAAGGCAATATTTTGTATTTGGAAATTCAAGAAAACGTGCCCTAACGTGCTG
1 AAGATTTTCTAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTG
*
8776911 GGTTTCGATTTCTCGTTCGACCAAATTGCCAAATATCATTTT
66 GGTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCATTTT
* *
8776953 AAGATTTTTTAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTG-CCTAACGCGCTG
1 AAGATTTTCTAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTG
*
8777017 GGTTTCGATTTCTCGTTCGACTAAATAGCCAAATATC
66 GGTTTCGATTTCTCGTTCGACCAAATAGCCAAATATC
8777054 CTCTTAAAAC
Statistics
Matches: 280, Mismatches: 27, Indels: 9
0.89 0.09 0.03
Matches are distributed among these distances:
103 91 0.32
104 2 0.01
105 2 0.01
106 48 0.17
107 137 0.49
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34
Consensus pattern (107 bp):
AAGATTTTCTAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGCTG
GGTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCATTTT
Found at i:8776998 original size:210 final size:213
Alignment explanation
Indices: 8776636--8777060 Score: 678
Period size: 210 Copynumber: 2.0 Consensus size: 213
8776626 ATCAAAAGAA
* * * *
8776636 AAGATTTTCTAAATAAGACAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGTCCTAACGTGCTA
1 AAGATTTTCTAAATAAGACAATATTTTGCATTTGGAAATTCAAGAAAACGTGCCCTAACGTGCTA
*
8776701 GGTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCATTTTAAGATTTTTTAAATAGGGAAATA
66 GGTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCATTTTAAGATTTTTTAAATAAGGAAATA
* *
8776766 TTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGTTGGGTTTC-A-AT-T-GTTCGACCA
131 TTTTGCGTTTGGAAATTCGAGAAAACGTG-CCTAACGCGCTGGGTTTCGATATCTCGTTCGACCA
*
8776827 AATAGCCAAATATCCTTTT
195 AATAGCCAAATATCCTCTT
* * *
8776846 AAGATTTTCTAAATAAGGCAATATTTTGTATTTGGAAATTCAAGAAAACGTGCCCTAACGTGCTG
1 AAGATTTTCTAAATAAGACAATATTTTGCATTTGGAAATTCAAGAAAACGTGCCCTAACGTGCTA
* *
8776911 GGTTTCGATTTCTCGTTCGACCAAATTGCCAAATATCATTTTAAGATTTTTTAAATAAGGCAATA
66 GGTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCATTTTAAGATTTTTTAAATAAGGAAATA
* *
8776976 TTTTGCGTTTGGAAATTCGAGAAAACGTGCCTAACGCGCTGGGTTTCGATTTCTCGTTCGACTAA
131 TTTTGCGTTTGGAAATTCGAGAAAACGTGCCTAACGCGCTGGGTTTCGATATCTCGTTCGACCAA
8777041 ATAGCCAAATATCCTCTT
196 ATAGCCAAATATCCTCTT
8777059 AA
1 AA
8777061 AACTTCAAAG
Statistics
Matches: 196, Mismatches: 15, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
209 16 0.08
210 150 0.77
211 1 0.01
212 1 0.01
213 28 0.14
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (213 bp):
AAGATTTTCTAAATAAGACAATATTTTGCATTTGGAAATTCAAGAAAACGTGCCCTAACGTGCTA
GGTTTCGATTTCTCGTTCGACCAAATAGCCAAATATCATTTTAAGATTTTTTAAATAAGGAAATA
TTTTGCGTTTGGAAATTCGAGAAAACGTGCCTAACGCGCTGGGTTTCGATATCTCGTTCGACCAA
ATAGCCAAATATCCTCTT
Found at i:8783771 original size:2 final size:2
Alignment explanation
Indices: 8783764--8783797 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
8783754 GAAGATTTTC
8783764 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
8783798 NNNNNNNNNN
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8784242 original size:4 final size:4
Alignment explanation
Indices: 8784233--8784257 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
8784223 TTAAACACGA
8784233 GTAT GTAT GTAT GTAT GTAT GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT G
8784258 CATGCATACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (4 bp):
GTAT
Found at i:8790146 original size:20 final size:20
Alignment explanation
Indices: 8790112--8790153 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
8790102 TAACTATTAA
** *
8790112 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
8790132 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
8790152 AT
1 AT
8790154 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:8792990 original size:2 final size:2
Alignment explanation
Indices: 8792983--8793019 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
8792973 TAATATTTAG
8792983 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
8793020 GTGGAAAGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:8801933 original size:14 final size:14
Alignment explanation
Indices: 8801914--8801940 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
8801904 ATCAAGAAGG
8801914 AAAAGAAAAAAAAA
1 AAAAGAAAAAAAAA
8801928 AAAAGAAAAAAAA
1 AAAAGAAAAAAAA
8801941 GAAGTGCGTT
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:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAAAAA
Found at i:8805895 original size:6 final size:7
Alignment explanation
Indices: 8805877--8805904 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
8805867 GAAAGAAATG
8805877 CTTTTTT
1 CTTTTTT
8805884 CTTTTTT
1 CTTTTTT
8805891 CTTTTTT
1 CTTTTTT
8805898 CTTTTTT
1 CTTTTTT
8805905 TACTATCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
CTTTTTT
Found at i:8807726 original size:34 final size:35
Alignment explanation
Indices: 8807688--8807758 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 35
8807678 AACCCAGATG
**
8807688 TTATTAAATTTTATATT-ATTTTTAA-TTTATTAAT
1 TTATT-AATTTTATATTAAGATTTAATTTTATTAAT
*
8807722 TTATTAATTTTTTATTAAGATTTAATTTTATTAAT
1 TTATTAATTTTATATTAAGATTTAATTTTATTAAT
8807757 TT
1 TT
8807759 TATTTTATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 10 0.31
34 11 0.34
35 11 0.34
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (35 bp):
TTATTAATTTTATATTAAGATTTAATTTTATTAAT
Found at i:8815239 original size:20 final size:19
Alignment explanation
Indices: 8815203--8815247 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
8815193 TAAAAACAAT
* *
8815203 TATTTTATTAAATAAATTA
1 TATTTTATAAAAAAAATTA
*
8815222 TATTATTATAAAAAAAATTC
1 TATT-TTATAAAAAAAATTA
8815242 TATTTT
1 TATTTT
8815248 TCTATAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTTTATAAAAAAAATTA
Found at i:8818798 original size:8 final size:8
Alignment explanation
Indices: 8818785--8818809 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
8818775 AAAAAAAATC
8818785 ATATATAA
1 ATATATAA
8818793 ATATATAA
1 ATATATAA
8818801 ATATATAA
1 ATATATAA
8818809 A
1 A
8818810 AGTATTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
ATATATAA
Found at i:8835539 original size:7 final size:7
Alignment explanation
Indices: 8835527--8835555 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
8835517 AAAGGGGATT
8835527 AGAAGAG
1 AGAAGAG
8835534 AGAAGAG
1 AGAAGAG
8835541 AGAAGAG
1 AGAAGAG
8835548 AGAAGAG
1 AGAAGAG
8835555 A
1 A
8835556 TGATGGAAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (7 bp):
AGAAGAG
Found at i:8844244 original size:13 final size:13
Alignment explanation
Indices: 8844226--8844252 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
8844216 TTATAATTTA
8844226 GCTTCCCAAAACC
1 GCTTCCCAAAACC
8844239 GCTTCCCAAAACC
1 GCTTCCCAAAACC
8844252 G
1 G
8844253 ACAGACGAGA
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:0.44, G:0.11, T:0.15
Consensus pattern (13 bp):
GCTTCCCAAAACC
Found at i:8845218 original size:32 final size:31
Alignment explanation
Indices: 8845182--8845290 Score: 91
Period size: 32 Copynumber: 3.5 Consensus size: 31
8845172 CTAAATATAA
*
8845182 AAAATTTAATAAATTTAACTCTCAATATTTAC
1 AAAATTTAATAAATTT-AGTCTCAATATTTAC
* * * * *
8845214 AAAATAT-ATCATTTTAGT-TCAGATTATTAAA
1 AAAATTTAATAAATTTAGTCTCA-A-TATTTAC
*
8845245 AAAATTCAATAAATTTAGTCCTCAATATTTAC
1 AAAATTTAATAAATTTAGT-CTCAATATTTAC
8845277 AAAA--TAATAAATTT
1 AAAATTTAATAAATTT
8845291 TGATTTTTAA
Statistics
Matches: 59, Mismatches: 13, Indels: 12
0.70 0.15 0.14
Matches are distributed among these distances:
29 3 0.05
30 12 0.20
31 16 0.27
32 24 0.41
33 1 0.02
34 3 0.05
ACGTcount: A:0.48, C:0.10, G:0.03, T:0.39
Consensus pattern (31 bp):
AAAATTTAATAAATTTAGTCTCAATATTTAC
Found at i:8847511 original size:19 final size:20
Alignment explanation
Indices: 8847484--8847525 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
8847474 AATATAAACC
*
8847484 ATATTTTTTTTA-TTTTAAA
1 ATATATTTTTTATTTTTAAA
8847503 ATATATTTTTTATTTTTAAA
1 ATATATTTTTTATTTTTAAA
8847523 ATA
1 ATA
8847526 CACTACATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
ATATATTTTTTATTTTTAAA
Found at i:8847513 original size:20 final size:19
Alignment explanation
Indices: 8847488--8847525 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
8847478 TAAACCATAT
8847488 TTTTTTTA-TTTTAAAATA
1 TTTTTTTATTTTTAAAATA
8847506 TATTTTTTATTTTTAAAATA
1 T-TTTTTTATTTTTAAAATA
8847526 CACTACATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 1 0.06
19 7 0.39
20 10 0.56
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTTTTTATTTTTAAAATA
Found at i:8859120 original size:14 final size:14
Alignment explanation
Indices: 8859101--8859134 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
8859091 TCATCATTTA
8859101 CCTATAACCAAAAC
1 CCTATAACCAAAAC
*
8859115 CCTATAACTAAAAC
1 CCTATAACCAAAAC
8859129 CC-ATAA
1 CCTATAA
8859135 ACCCATACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18
Consensus pattern (14 bp):
CCTATAACCAAAAC
Found at i:8866512 original size:16 final size:17
Alignment explanation
Indices: 8866486--8866520 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
8866476 TATATATTTT
*
8866486 ATTTGTTTTCAGATAAA
1 ATTTGTTTTCAAATAAA
8866503 ATTT-TTTTCAAATAAA
1 ATTTGTTTTCAAATAAA
8866519 AT
1 AT
8866521 ATTAATCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.49
Consensus pattern (17 bp):
ATTTGTTTTCAAATAAA
Found at i:8873098 original size:34 final size:34
Alignment explanation
Indices: 8873048--8873130 Score: 94
Period size: 34 Copynumber: 2.4 Consensus size: 34
8873038 CAAACATTTC
* * *
8873048 AACAATTGATTCAAAAGAAATAATATTTTAACAT
1 AACAATCGATTTAAAAGAAATAATATTCTAACAT
* * * *
8873082 AATAATCGATTTAAAAGGAGTAATATTCTAATAT
1 AACAATCGATTTAAAAGAAATAATATTCTAACAT
*
8873116 GACAATCGATTTAAA
1 AACAATCGATTTAAA
8873131 CATAAAAACA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.49, C:0.08, G:0.10, T:0.33
Consensus pattern (34 bp):
AACAATCGATTTAAAAGAAATAATATTCTAACAT
Found at i:8876311 original size:25 final size:27
Alignment explanation
Indices: 8876254--8876315 Score: 83
Period size: 25 Copynumber: 2.3 Consensus size: 27
8876244 GTGAGATTGT
*
8876254 AATAATTTAATTAATTTTCAAGTAATAC
1 AATAATTT-ATTAATATTCAAGTAATAC
*
8876282 AATAATTTATTAA-ATTGAAG-AATAC
1 AATAATTTATTAATATTCAAGTAATAC
8876307 AATAATTTA
1 AATAATTTA
8876316 GTTGTTAAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
25 14 0.44
26 5 0.16
27 5 0.16
28 8 0.25
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (27 bp):
AATAATTTATTAATATTCAAGTAATAC
Found at i:8876547 original size:3 final size:3
Alignment explanation
Indices: 8876539--8876571 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
8876529 TTTGTTATTT
*
8876539 TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
8876572 AGTTATTAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:8881359 original size:22 final size:22
Alignment explanation
Indices: 8881334--8881409 Score: 116
Period size: 22 Copynumber: 3.5 Consensus size: 22
8881324 TTTGTTAATT
*
8881334 AGCTCTCATGTTTCACGTACTA
1 AGCTCTCATGTTTAACGTACTA
8881356 AGCTCTCATGTTTAACGTACTA
1 AGCTCTCATGTTTAACGTACTA
*
8881378 AGCTCTCATGTTTAACGAACTA
1 AGCTCTCATGTTTAACGTACTA
* *
8881400 AACCCTCATG
1 AGCTCTCATG
8881410 GCTAACGTGC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (22 bp):
AGCTCTCATGTTTAACGTACTA
Found at i:8887449 original size:19 final size:19
Alignment explanation
Indices: 8887425--8887463 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
8887415 TCAATGAGGT
8887425 TATTGTTTTAATGCACTGG
1 TATTGTTTTAATGCACTGG
8887444 TATTGTTTTAATGCACTGG
1 TATTGTTTTAATGCACTGG
8887463 T
1 T
8887464 TCGAGCCAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.10, G:0.21, T:0.49
Consensus pattern (19 bp):
TATTGTTTTAATGCACTGG
Found at i:8905543 original size:2 final size:2
Alignment explanation
Indices: 8905531--8905563 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
8905521 ATAGTTATCT
*
8905531 TA TA CA 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
8905564 GCATATACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:8917089 original size:17 final size:18
Alignment explanation
Indices: 8917060--8917099 Score: 73
Period size: 17 Copynumber: 2.3 Consensus size: 18
8917050 AAAAAATATT
8917060 ATTTTTCACATTTTCATA
1 ATTTTTCACATTTTCATA
8917078 ATTTTTCA-ATTTTCATA
1 ATTTTTCACATTTTCATA
8917095 ATTTT
1 ATTTT
8917100 CTTAGATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.28, C:0.12, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTTTCACATTTTCATA
Found at i:8919480 original size:17 final size:19
Alignment explanation
Indices: 8919460--8919497 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
8919450 TTAAAACTTT
*
8919460 TAAAAGA-AATTAT-TTTA
1 TAAAAGATAAATATATTTA
8919477 TAAAAGATAAATATATTTA
1 TAAAAGATAAATATATTTA
8919496 TA
1 TA
8919498 TATTTAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 5 0.28
19 6 0.33
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (19 bp):
TAAAAGATAAATATATTTA
Found at i:8938608 original size:9 final size:9
Alignment explanation
Indices: 8938594--8938618 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
8938584 GGAACATTCT
8938594 GCCCAATTG
1 GCCCAATTG
8938603 GCCCAATTG
1 GCCCAATTG
8938612 GCCCAAT
1 GCCCAAT
8938619 AGGCTGGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.36, G:0.20, T:0.20
Consensus pattern (9 bp):
GCCCAATTG
Found at i:8941554 original size:15 final size:16
Alignment explanation
Indices: 8941522--8941556 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
8941512 CGAAAACCGT
8941522 CTTTGCCTTTGCCTTC
1 CTTTGCCTTTGCCTTC
*
8941538 CTTTGCC-TTGTCTTC
1 CTTTGCCTTTGCCTTC
8941553 CTTT
1 CTTT
8941557 ACTTTTACTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.00, C:0.34, G:0.11, T:0.54
Consensus pattern (16 bp):
CTTTGCCTTTGCCTTC
Found at i:8961301 original size:13 final size:13
Alignment explanation
Indices: 8961271--8961301 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
8961261 GAAATAATTT
*
8961271 ATTAAATTAATAA
1 ATTATATTAATAA
8961284 ATTATATTAATAA
1 ATTATATTAATAA
8961297 ATTAT
1 ATTAT
8961302 TATATCACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
ATTATATTAATAA
Found at i:8961833 original size:27 final size:27
Alignment explanation
Indices: 8961799--8961868 Score: 106
Period size: 27 Copynumber: 2.6 Consensus size: 27
8961789 AAAAATAAAA
* *
8961799 ATTTACCAAAATACTA-CAAGTTTTTTT
1 ATTTACCAAAATA-TATAAACTTTTTTT
8961826 ATTTACCAAAATATATAAACTTTTTTT
1 ATTTACCAAAATATATAAACTTTTTTT
8961853 ATTTACCAAAATATAT
1 ATTTACCAAAATATAT
8961869 CAAAAAAAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
26 2 0.05
27 38 0.95
ACGTcount: A:0.41, C:0.13, G:0.01, T:0.44
Consensus pattern (27 bp):
ATTTACCAAAATATATAAACTTTTTTT
Found at i:8961976 original size:27 final size:27
Alignment explanation
Indices: 8961946--8962012 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
8961936 CGCCAATGGT
8961946 ATTGGCGGCACCAAAGGTGCCAAAACC
1 ATTGGCGGCACCAAAGGTGCCAAAACC
* **
8961973 ATTGGCGGCACCAACGGTGCCAATGCC
1 ATTGGCGGCACCAAAGGTGCCAAAACC
8962000 ATTGGCGGCACCA
1 ATTGGCGGCACCA
8962013 GTTGGTGTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.27, C:0.31, G:0.28, T:0.13
Consensus pattern (27 bp):
ATTGGCGGCACCAAAGGTGCCAAAACC
Found at i:8962066 original size:4 final size:4
Alignment explanation
Indices: 8962057--8962180 Score: 87
Period size: 4 Copynumber: 30.2 Consensus size: 4
8962047 GAAGGAGAGG
* * *
8962057 GAAA GAAA GAAA GGAGAG GAAA GAAA GAAA GAAA GAAA GAAA GGGGAG
1 GAAA GAAA GAAA -GA-AA GAAA GAAA GAAA GAAA GAAA GAAA --GAAA
*
8962105 GAAA GAAA GAAAA GGAAA G-GA GAAGA GAAA -AAA GGAAA GAAA G-AA
1 GAAA GAAA G-AAA -GAAA GAAA GAA-A GAAA GAAA -GAAA GAAA GAAA
* *
8962150 G-AA GAAA -AAA GAAA GAAG GAAG GAAA GAAA G
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA G
8962181 GGAAAGGAGA
Statistics
Matches: 98, Mismatches: 10, Indels: 24
0.74 0.08 0.18
Matches are distributed among these distances:
3 14 0.14
4 63 0.64
5 17 0.17
6 4 0.04
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:8962072 original size:19 final size:18
Alignment explanation
Indices: 8962048--8962203 Score: 97
Period size: 17 Copynumber: 9.1 Consensus size: 18
8962038 TGGGGGGCAG
8962048 AAGGAGAGGGAAAGAAAGA
1 AAGGAGA-GGAAAGAAAGA
8962067 AAGGAGAGGAAAGAAAG-
1 AAGGAGAGGAAAGAAAGA
8962084 -A--A-A-GAAAGAAAGA
1 AAGGAGAGGAAAGAAAGA
*
8962097 AAGGGGAGGAAAGAAAGAA
1 AAGGAGAGGAAAGAAAG-A
*
8962116 AAGGAAAGG--AGAAGAGA
1 AAGGAGAGGAAAGAA-AGA
*
8962133 AA--AAAGGAAAGAAAG-
1 AAGGAGAGGAAAGAAAGA
* **
8962148 AAGAAGAAAAAAGAAAG-
1 AAGGAGAGGAAAGAAAGA
8962165 AAGGA-AGGAAAGAAAGGGA
1 AAGGAGAGGAAAGAAA--GA
8962184 AAGGAGAAGAGAAA-AAAGA
1 AAGGAG-AG-GAAAGAAAGA
8962203 A
1 A
8962204 GAAGAAGAAG
Statistics
Matches: 110, Mismatches: 9, Indels: 36
0.71 0.06 0.23
Matches are distributed among these distances:
12 9 0.08
13 1 0.01
14 2 0.02
15 7 0.06
16 11 0.10
17 26 0.24
18 22 0.20
19 23 0.21
21 5 0.05
22 4 0.04
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (18 bp):
AAGGAGAGGAAAGAAAGA
Found at i:8962085 original size:22 final size:22
Alignment explanation
Indices: 8962058--8962203 Score: 94
Period size: 22 Copynumber: 6.6 Consensus size: 22
8962048 AAGGAGAGGG
*
8962058 AAAGAAAGAAAGGAGAGGAAA-G
1 AAAGAAAGAAA-GAAAGGAAAGG
8962080 AAAGAAAGAAAGAAA-GAAAGGG
1 AAAGAAAGAAAGAAAGGAAA-GG
* *
8962102 GAGGAAAGAAAGAAAAGGAAAGG
1 AAAGAAAGAAAG-AAAGGAAAGG
8962125 --AGAAGAGAAA-AAAGGAAA-G
1 AAAGAA-AGAAAGAAAGGAAAGG
8962144 AAAGAAGAAGAAA-AAA-GAAA-G
1 AAAG-A-AAGAAAGAAAGGAAAGG
* *
8962165 AAGGAAGGAAAGAAAGGGAAAGG
1 AAAGAAAGAAAGAAA-GGAAAGG
*
8962188 AGAAGAGAAAAAAGAA
1 A-AAGA-AAGAAAGAA
8962204 GAAGAAGAAG
Statistics
Matches: 100, Mismatches: 9, Indels: 27
0.74 0.07 0.20
Matches are distributed among these distances:
19 6 0.06
20 16 0.16
21 16 0.16
22 40 0.40
23 8 0.08
24 7 0.07
25 7 0.07
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (22 bp):
AAAGAAAGAAAGAAAGGAAAGG
Found at i:8962093 original size:30 final size:30
Alignment explanation
Indices: 8962057--8962179 Score: 126
Period size: 30 Copynumber: 4.0 Consensus size: 30
8962047 GAAGGAGAGG
8962057 GAAAGAAAGAAAGGAGAGGAAAGAAAG-AAA
1 GAAAGAAAGAAA-GAGAGGAAAGAAAGAAAA
*
8962087 GAAAGAAAGAAAGGGGAGGAAAGAAAGAAAA
1 GAAAGAAAGAAA-GAGAGGAAAGAAAGAAAA
* *
8962118 GGAAAGGAGAAGAGAAAAAAGGAAAGAAAGAAGAA
1 -GAAA-GA-AAGA-AAGAGAGGAAAGAAAGAA-AA
*
8962153 GAAA-AAAGAAAGA-AGGAAGGAAAGAAA
1 GAAAGAAAGAAAGAGAGGAAAGAAAGAAA
8962180 GGGAAAGGAG
Statistics
Matches: 81, Mismatches: 6, Indels: 14
0.80 0.06 0.14
Matches are distributed among these distances:
28 1 0.01
29 12 0.15
30 29 0.36
31 7 0.09
32 5 0.06
33 2 0.02
34 21 0.26
35 4 0.05
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (30 bp):
GAAAGAAAGAAAGAGAGGAAAGAAAGAAAA
Found at i:8962123 original size:44 final size:45
Alignment explanation
Indices: 8962059--8962228 Score: 124
Period size: 44 Copynumber: 3.8 Consensus size: 45
8962049 AGGAGAGGGA
* * **
8962059 AAGAAAGAAAGGAGAGGAAAGAAAGAAAGAAA-GAAAGAAAGGGG
1 AAGAAAGAAAGAAAAGGAAAGAAAGAAAGAAAGGAAAGAAAGAAG
* *
8962103 AGGAAAGAAAGAAAAGGAAAGGAGAAGAGAAAAAAGGAAAGAAAGAAG
1 AAGAAAGAAAGAAAAGGAAA-GA-AAGA-AAGAAAGGAAAGAAAGAAG
* * *
8962151 AAGAAA-AAAG-AAA-GAAGGAAGGAAAGAAAGGGAAAG-GAGAAG
1 AAGAAAGAAAGAAAAGGAAAGAAAGAAAGAAA-GGAAAGAAAGAAG
*
8962193 -AGAAA-AAAGAAGAA-G-AAGAAGAGGGAAGAAAGGAAA
1 AAGAAAGAAAGAA-AAGGAAAGAA-A-GAAAGAAAGGAAA
8962229 AAAAAGGGAA
Statistics
Matches: 103, Mismatches: 14, Indels: 19
0.76 0.10 0.14
Matches are distributed among these distances:
41 9 0.09
42 15 0.15
43 17 0.17
44 26 0.25
45 5 0.05
46 7 0.07
47 9 0.09
48 15 0.15
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (45 bp):
AAGAAAGAAAGAAAAGGAAAGAAAGAAAGAAAGGAAAGAAAGAAG
Found at i:8962176 original size:63 final size:65
Alignment explanation
Indices: 8962073--8962227 Score: 200
Period size: 63 Copynumber: 2.5 Consensus size: 65
8962063 AAGAAAGGAG
*
8962073 AGGAAAGAAAG-A-AAGAAAGAAAGAAAGGGGAGGAAAGAAAGAAAAGGAAAGGAGAAGAGAAAA
1 AGGAAAGAAAGAAGAAGAAAGAAAGAAA-GGAAGGAAAGAAAGAAAAGGAAAGGAGAAGAGAAAA
8962136 A
65 A
* *
8962137 AGGAAAGAAAGAAGAAGAAA-AAAGAAA-GAAGGAAGGAAAGAAAGGGAAAGGAGAAGAGAAAAA
1 AGGAAAGAAAGAAGAAGAAAGAAAGAAAGGAAGGAAAGAAAGAAAAGGAAAGGAGAAGAGAAAAA
* *
8962200 A-G-AAG-AAGAAGAAG-AGGGAAGAAAGGAA
1 AGGAAAGAAAGAAGAAGAAAGAAAGAAAGGAA
8962228 AAAAAAGGGA
Statistics
Matches: 82, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
59 1 0.01
60 15 0.18
61 6 0.07
62 1 0.01
63 34 0.41
64 11 0.13
65 8 0.10
66 6 0.07
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (65 bp):
AGGAAAGAAAGAAGAAGAAAGAAAGAAAGGAAGGAAAGAAAGAAAAGGAAAGGAGAAGAGAAAAA
Found at i:8962210 original size:81 final size:82
Alignment explanation
Indices: 8962056--8962215 Score: 198
Period size: 81 Copynumber: 1.9 Consensus size: 82
8962046 AGAAGGAGAG
* ** *
8962056 GGAAAGAAAGAAAGGAGAGGAAAGAAAGAAAGAAAGAAAGAAAGGGGAGGAAAGAAAGAAAAGGA
1 GGAAAGAAAGAAAGAAGAAAAAAGAAAGAAAGAAAGAAAGAAAGGGAAGGAAAGAAAGAAAAGGA
*
8962121 AAGGAGAAGAGAAAAAA
66 AAGAAGAAGAGAAAAAA
* *
8962138 GGAAAGAAAG-AAGAAGAAAAAAGAAAGAAGGAAGGAAAGAAAGGGAAAGGAGAAGAGAA-AAAA
1 GGAAAGAAAGAAAGAAGAAAAAAGAAAGAAAGAAAGAAAGAAAGGG-AAGGA-AAGA-AAGAAAA
*
8962201 GAAGAAGAAGAAGAG
63 GGA-AAGAAGAAGAG
8962216 GGAAGAAAGG
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
81 30 0.45
82 14 0.21
83 10 0.15
84 12 0.18
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (82 bp):
GGAAAGAAAGAAAGAAGAAAAAAGAAAGAAAGAAAGAAAGAAAGGGAAGGAAAGAAAGAAAAGGA
AAGAAGAAGAGAAAAAA
Found at i:8962569 original size:13 final size:13
Alignment explanation
Indices: 8962551--8962575 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8962541 GAAAATAAAT
8962551 AAATGCGAAAAAG
1 AAATGCGAAAAAG
8962564 AAATGCGAAAAA
1 AAATGCGAAAAA
8962576 TGTACATGAA
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:0.64, C:0.08, G:0.20, T:0.08
Consensus pattern (13 bp):
AAATGCGAAAAAG
Found at i:8968180 original size:26 final size:26
Alignment explanation
Indices: 8968131--8968183 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
8968121 ACACACTAAA
* *
8968131 ATTATTAATTTTATACTACGAATAAT
1 ATTATTAATTTTACACTACAAATAAT
8968157 ATTATTAATTTTACACT-CAAAATAAT
1 ATTATTAATTTTACACTAC-AAATAAT
8968183 A
1 A
8968184 CACACTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 1 0.04
26 23 0.96
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.43
Consensus pattern (26 bp):
ATTATTAATTTTACACTACAAATAAT
Found at i:8968373 original size:3 final size:3
Alignment explanation
Indices: 8968365--8968393 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
8968355 TCTTCATACT
8968365 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
8968394 TAATAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:8968398 original size:3 final size:3
Alignment explanation
Indices: 8968392--8968422 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
8968382 CAACAACAAC
8968392 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
8968423 CTTTTATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:8968678 original size:27 final size:27
Alignment explanation
Indices: 8968640--8968715 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
8968630 ATAATACGAG
8968640 TGGTGCCGCCAATGGCATTGGCACCAT
1 TGGTGCCGCCAATGGCATTGGCACCAT
** *
8968667 TGGTGCCGCCAATGGTTTTGGCACCTT
1 TGGTGCCGCCAATGGCATTGGCACCAT
**
8968694 TGGTGCCGCCAATACCATTGGC
1 TGGTGCCGCCAATGGCATTGGC
8968716 GTGACCAGTG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (27 bp):
TGGTGCCGCCAATGGCATTGGCACCAT
Found at i:8968792 original size:19 final size:18
Alignment explanation
Indices: 8968757--8968796 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
8968747 TTTTTTATCA
**
8968757 GGTTTTTTTTTTAATTTT
1 GGTTTTTTTGATAATTTT
8968775 GGTTTTTTTGATATATTTT
1 GGTTTTTTTGATA-ATTTT
8968794 GGT
1 GGT
8968797 AAATAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.12, C:0.00, G:0.17, T:0.70
Consensus pattern (18 bp):
GGTTTTTTTGATAATTTT
Found at i:8968848 original size:29 final size:28
Alignment explanation
Indices: 8968785--8968857 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 28
8968775 GGTTTTTTTG
**
8968785 ATATATTTTGGTAAATAAAAAAAAGTTT
1 ATATATTTTGGTAAATAAAAAAAAACTT
8968813 ATATATTTTGGTAAATAAAAAAAAACTT
1 ATATATTTTGGTAAATAAAAAAAAACTT
* *
8968841 GTAGTATTTTGATAAAT
1 ATA-TATTTTGGTAAAT
8968858 TTTTATTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 28 0.70
29 12 0.30
ACGTcount: A:0.48, C:0.01, G:0.11, T:0.40
Consensus pattern (28 bp):
ATATATTTTGGTAAATAAAAAAAAACTT
Found at i:8982966 original size:20 final size:20
Alignment explanation
Indices: 8982927--8982966 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
8982917 AATATTTTCT
* *
8982927 AGTAAATCATTTTACTGAAA
1 AGTAAAACATTTTACCGAAA
*
8982947 AGTAAAACATTTTCCCGAAA
1 AGTAAAACATTTTACCGAAA
8982967 TCATTTTACG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.15, G:0.10, T:0.30
Consensus pattern (20 bp):
AGTAAAACATTTTACCGAAA
Found at i:8986668 original size:23 final size:22
Alignment explanation
Indices: 8986641--8986689 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 22
8986631 ACTTTAGTCC
8986641 TTAGT-TTTGAATTGATTGTAAAT
1 TTAGTCTTTGAA-TG-TTGTAAAT
*
8986664 TTAGTCCTTTGAATGTTGTAATT
1 TTAGT-CTTTGAATGTTGTAAAT
8986687 TTA
1 TTA
8986690 ATGCGATTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 15 0.65
24 2 0.09
25 6 0.26
ACGTcount: A:0.27, C:0.04, G:0.16, T:0.53
Consensus pattern (22 bp):
TTAGTCTTTGAATGTTGTAAAT
Found at i:8992869 original size:31 final size:31
Alignment explanation
Indices: 8992831--8992893 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
8992821 AACACAATTT
8992831 ATAATTATTACCAATCACATACCATACATAC
1 ATAATTATTACCAATCACATACCATACATAC
8992862 ATAATTATTACCAATCACATACCATACATAC
1 ATAATTATTACCAATCACATACCATACATAC
8992893 A
1 A
8992894 ATCAAAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.29
Consensus pattern (31 bp):
ATAATTATTACCAATCACATACCATACATAC
Found at i:8994675 original size:57 final size:57
Alignment explanation
Indices: 8994597--8994709 Score: 174
Period size: 57 Copynumber: 2.0 Consensus size: 57
8994587 GGATGATCCT
*
8994597 ATCTTGATATACCCCTCCCGAAGAATATGTGTGAAAA-AGATCTAGCCCGGACGGGTG
1 ATCTTGATATACCCCTCCCGAAGAATATGAG-GAAAATAGATCTAGCCCGGACGGGTG
* * *
8994654 ATCTTGATATAGCCCTCCCGAAGAATATGAGGAAAATGGATTTAGCCCGGACGGGT
1 ATCTTGATATACCCCTCCCGAAGAATATGAGGAAAATAGATCTAGCCCGGACGGGT
8994710 AATCCGAATT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
56 5 0.10
57 46 0.90
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.23
Consensus pattern (57 bp):
ATCTTGATATACCCCTCCCGAAGAATATGAGGAAAATAGATCTAGCCCGGACGGGTG
Found at i:8995989 original size:18 final size:17
Alignment explanation
Indices: 8995956--8995992 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
8995946 GAGTTAAGAT
8995956 ATAATTTTATCATTTTA
1 ATAATTTTATCATTTTA
*
8995973 ATAATTTATATCCTTTTA
1 ATAATTT-TATCATTTTA
8995991 AT
1 AT
8995993 TTTTAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.57
Consensus pattern (17 bp):
ATAATTTTATCATTTTA
Found at i:8996072 original size:16 final size:16
Alignment explanation
Indices: 8996053--8996084 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
8996043 TTTTATCATA
8996053 TATAAATTTAAAATTT
1 TATAAATTTAAAATTT
*
8996069 TATAAATTTTAAATTT
1 TATAAATTTAAAATTT
8996085 CTCATTTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATAAATTTAAAATTT
Found at i:8996926 original size:132 final size:133
Alignment explanation
Indices: 8996689--8996972 Score: 426
Period size: 132 Copynumber: 2.1 Consensus size: 133
8996679 TATTTAGTGC
* * * *
8996689 CCCACAAGTTGTATTGATCTTAAGCCTTTTTTCGACCAAAACCACCTCTTATTCTCACATCTATC
1 CCCACAAGTTGTATTTATCTTAAGCCTTTTCTCCACCAAAACCACCTCCTATTCTCACATCTATC
8996754 CACCTACGTAAACTTTTTCTACACTGCCTATATATTTAGTGCCCTATGTGTCCTTAACCTAC-AT
66 CACCTACGTAAACTTTTTCTACACTGCCTATATATTTAGTGCCCTATGTGTCCTTAACCTACAAT
8996818 ACA
131 ACA
* * *
8996821 CCCACAAGTTGTATTTATCTTAAGCCTTTTCTCCATCAAAACCACTTCCTATTCTCACATCTATT
1 CCCACAAGTTGTATTTATCTTAAGCCTTTTCTCCACCAAAACCACCTCCTATTCTCACATCTATC
* * * * *
8996886 CACCTACGTAAATTTTTTCTACATTTCTTCTATATTTAGTGCCCTATGTGTCCTTAACCTACAAT
66 CACCTACGTAAACTTTTTCTACACTGCCTATATATTTAGTGCCCTATGTGTCCTTAACCTACAAT
8996951 ACA
131 ACA
* * *
8996954 CCTAGACGTTGTATTTATC
1 CCCACAAGTTGTATTTATC
8996973 GGATCACGTT
Statistics
Matches: 136, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
132 115 0.85
133 21 0.15
ACGTcount: A:0.26, C:0.28, G:0.08, T:0.38
Consensus pattern (133 bp):
CCCACAAGTTGTATTTATCTTAAGCCTTTTCTCCACCAAAACCACCTCCTATTCTCACATCTATC
CACCTACGTAAACTTTTTCTACACTGCCTATATATTTAGTGCCCTATGTGTCCTTAACCTACAAT
ACA
Found at i:9004473 original size:27 final size:27
Alignment explanation
Indices: 9004436--9004506 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
9004426 ATGATGGGCC
*
9004436 TGCCACAGGCGGCACCAAAGGTGCC-T
1 TGCCACAGGCGGCACCAAAGCTGCCAT
* *
9004462 GTGGCAGAGGCGGCACCAAAGCTGCCAT
1 -TGCCACAGGCGGCACCAAAGCTGCCAT
9004490 TGCCACAGGCGGCACCA
1 TGCCACAGGCGGCACCA
9004507 CTTCAGTTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
27 37 0.97
28 1 0.03
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.10
Consensus pattern (27 bp):
TGCCACAGGCGGCACCAAAGCTGCCAT
Found at i:9004551 original size:3 final size:3
Alignment explanation
Indices: 9004538--9004571 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
9004528 CAGTCCAGCT
*
9004538 GAA GGA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
9004572 GTGGTGCCGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:9004973 original size:39 final size:40
Alignment explanation
Indices: 9004827--9004973 Score: 96
Period size: 39 Copynumber: 3.8 Consensus size: 40
9004817 AAAAAACTAA
* *
9004827 TATTATTATTATGGTTAGTTATTAGGATTAGTAAAAACCCT
1 TATTATTATTGTAGTTAGTTATTAGGATTAGT-AAAACCCT
* * *** *
9004868 AATTATTATTTTAGTTAGTATGATT--G-TTAGTTTTTA-CAT
1 TATTATTATTGTAGTTAGT-T-ATTAGGATTAG-TAAAACCCT
***
9004907 TA-TATTA--GT-GTTAGTTATTATTTTTAGTAAAACCCT
1 TATTATTATTGTAGTTAGTTATTAGGATTAGTAAAACCCT
9004943 TATTATTATTGT-GTTAGTTATTAGGATTAGT
1 TATTATTATTGTAGTTAGTTATTAGGATTAGT
9004974 GGTTAAACGT
Statistics
Matches: 79, Mismatches: 17, Indels: 22
0.67 0.14 0.19
Matches are distributed among these distances:
33 3 0.04
34 1 0.01
35 8 0.10
36 9 0.11
37 5 0.06
38 5 0.06
39 21 0.27
40 5 0.06
41 18 0.23
42 1 0.01
43 3 0.04
ACGTcount: A:0.30, C:0.05, G:0.14, T:0.51
Consensus pattern (40 bp):
TATTATTATTGTAGTTAGTTATTAGGATTAGTAAAACCCT
Found at i:9008985 original size:157 final size:153
Alignment explanation
Indices: 9008478--9009242 Score: 1042
Period size: 157 Copynumber: 4.9 Consensus size: 153
9008468 TGCAACTTCA
** * * * *
9008478 AAATAAATTTAGTAAAAAACCATTATTTCGGCCCTTTGTTCATATTTTTTCCCGGATTTTATTAC
1 AAATAAATTTAAAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCGAATTTTATTAC
* *
9008543 TTT-AAAAAATATACTATTTTTTAATTTTATTATTTTACATTATTTTAGTAAATTATGTTTGAAA
66 TTTAAAAAAATATACTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAA
9008607 TGTATTAATTTA-T-TGTTTTTT
131 TGTATTAATTTAGTGTGTTTTTT
* *
9008628 AAATAAATTTAAAAAAAAACCCTTATTTCGTCCCTTTGTTCGTATTTTTTTTGCCGGATTTTATT
1 AAATAAATTTAAAAAAAAACCCTTATTTCGGCCCTTTGTTCGTA-TTTTTTT-CCGAATTTTATT
*
9008693 ACTTTAAAAAAATATATTCTACTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTT
64 ACTTTAAAAAAATATA--CTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTT
9008758 GAAATGTATTAATTTAGTGTGTTTTTT
127 GAAATGTATTAATTTAGTGTGTTTTTT
* * *
9008785 AAATAAATTTCAAAAAATAACCCTTATTTCGACCATTTGTTCGTATTTTTTTCCTGAATTTTATT
1 AAATAAATTT-AAAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCC-GAATTTTATT
*
9008850 ACTTTTAAAAAAATATACTATTTTCTAATTTTATTATTTTATATTATTTTAGTACATTATGTTTG
64 AC-TTTAAAAAAATATACTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTG
9008915 AAATGTATTAATTTAGTGTGTGTTTTT
128 AAATGTATTAATTTAGTGTGT-TTTTT
* * *
9008942 AAATAAATTTAAAAAAATAACCCTTATTTAGGCCCTTTGTTCGTATTTTTTCCCCAAATTTTATT
1 AAATAAATTTAAAAAAA-AACCCTTATTTCGGCCCTTTGTTCGTATTTTTT-TCCGAATTTTATT
* * *
9009007 ACTTTCAATAAAAAAGATATTATTTTCGT-ATTTTATTATTTTAGATTATTTTAGTACATTATGT
64 ACTTT--A-AAAAAATATACTATTTTC-TAATTTTATTATTTTACATTATTTTAGTACATTATGT
*
9009071 TTGAAATGTATTAATTTAGTGTGTGTTTT
125 TTGAAATGTATTAATTTAGTGTGTTTTTT
** **
9009100 AAATAAATTTAGTAAAAAACCCTTATTTCGG-CC-TTGTTCGTATTTTTTTACCGAAGCCTTATT
1 AAATAAATTTAAAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTT-CCGAA-TTTTATT
* * * *
9009163 -GTTTCAAAAAATATATTATTTTCGT-ATTTTATTATTTTACGTTATTTTAGTACATTATGTTTG
64 ACTTTAAAAAAATATACTATTTTC-TAATTTTATTATTTTACATTATTTTAGTACATTATGTTTG
*
9009226 AAATGCATTAATTTAGT
128 AAATGTATTAATTTAGT
9009243 AAAAAACTCT
Statistics
Matches: 558, Mismatches: 38, Indels: 36
0.88 0.06 0.06
Matches are distributed among these distances:
150 39 0.07
151 6 0.01
152 88 0.16
153 10 0.02
155 82 0.15
156 86 0.15
157 105 0.19
158 67 0.12
159 74 0.13
160 1 0.00
ACGTcount: A:0.32, C:0.10, G:0.09, T:0.50
Consensus pattern (153 bp):
AAATAAATTTAAAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCGAATTTTATTAC
TTTAAAAAAATATACTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAA
TGTATTAATTTAGTGTGTTTTTT
Found at i:9009197 original size:16 final size:18
Alignment explanation
Indices: 9009176--9009211 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
9009166 TCAAAAAATA
9009176 TATTATTTT-CG-TATTT
1 TATTATTTTACGTTATTT
9009192 TATTATTTTACGTTATTT
1 TATTATTTTACGTTATTT
9009210 TA
1 TA
9009212 GTACATTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
17 2 0.11
18 7 0.39
ACGTcount: A:0.22, C:0.06, G:0.06, T:0.67
Consensus pattern (18 bp):
TATTATTTTACGTTATTT
Found at i:9009539 original size:26 final size:27
Alignment explanation
Indices: 9009485--9009539 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
9009475 GGGTTTTTTC
* * * *
9009485 ATGCTAAATAAATTTCATAAAATATAT
1 ATGCTAAATAAATATAATAAAACACAT
9009512 ATGCTAAATAAA-ATAATAAAACACAT
1 ATGCTAAATAAATATAATAAAACACAT
9009538 AT
1 AT
9009540 AATGTACATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 12 0.50
27 12 0.50
ACGTcount: A:0.56, C:0.09, G:0.04, T:0.31
Consensus pattern (27 bp):
ATGCTAAATAAATATAATAAAACACAT
Found at i:9009596 original size:20 final size:20
Alignment explanation
Indices: 9009567--9009605 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
9009557 TTTTTTACAC
*
9009567 AAATATTACAAAAAAAATTT
1 AAATAATACAAAAAAAATTT
*
9009587 AAATAATACAAAAAGAATT
1 AAATAATACAAAAAAAATT
9009606 ACCTTTACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.26
Consensus pattern (20 bp):
AAATAATACAAAAAAAATTT
Found at i:9009666 original size:5 final size:5
Alignment explanation
Indices: 9009656--9009717 Score: 63
Period size: 5 Copynumber: 12.4 Consensus size: 5
9009646 CTTCTTCTTC
* * *
9009656 TCCTT TCCTT TCCTT TCTTT TTCTT T-CTT CTCCTT TCCTT TCCTT TTCTT
1 TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT -TCCTT TCCTT TCCTT TCCTT
* *
9009706 TCTTT TTCTT TC
1 TCCTT TCCTT TC
9009718 TTCTCCTTCT
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
4 3 0.07
5 40 0.87
6 3 0.07
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (5 bp):
TCCTT
Found at i:9009694 original size:25 final size:25
Alignment explanation
Indices: 9009661--9009737 Score: 95
Period size: 25 Copynumber: 3.2 Consensus size: 25
9009651 TCTTCTCCTT
9009661 TCCTTTCCTTTCTTTTTCTTTCTTC
1 TCCTTTCCTTTCTTTTTCTTTCTTC
* *
9009686 TCCTTTCCTTTCCTTTTCTTTCTTT
1 TCCTTTCCTTTCTTTTTCTTTCTTC
* **
9009711 TTCTTT-C-TTCTCCTTCTTTCTTC
1 TCCTTTCCTTTCTTTTTCTTTCTTC
9009734 TCCT
1 TCCT
9009738 CCAGCCGAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
23 15 0.34
24 1 0.02
25 28 0.64
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (25 bp):
TCCTTTCCTTTCTTTTTCTTTCTTC
Found at i:9009707 original size:35 final size:36
Alignment explanation
Indices: 9009645--9009727 Score: 141
Period size: 35 Copynumber: 2.3 Consensus size: 36
9009635 CTTCCCTCCC
*
9009645 TCTTCTTCTTCTCCTTTCCTTTCCTTTCTTTTTCTT
1 TCTTCTCCTTCTCCTTTCCTTTCCTTTCTTTTTCTT
*
9009681 TCTTCTCCTT-TCCTTTCCTTTTCTTTCTTTTTCTT
1 TCTTCTCCTTCTCCTTTCCTTTCCTTTCTTTTTCTT
9009716 TCTTCTCCTTCT
1 TCTTCTCCTTCT
9009728 TTCTTCTCCT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
35 34 0.77
36 10 0.23
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (36 bp):
TCTTCTCCTTCTCCTTTCCTTTCCTTTCTTTTTCTT
Found at i:9016335 original size:15 final size:16
Alignment explanation
Indices: 9016315--9016344 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9016305 AGAAATGGGA
9016315 AATTT-AATTAGAAAG
1 AATTTAAATTAGAAAG
9016330 AATTTAAATTAGAAA
1 AATTTAAATTAGAAA
9016345 AGTTTTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (16 bp):
AATTTAAATTAGAAAG
Found at i:9017936 original size:26 final size:27
Alignment explanation
Indices: 9017906--9017959 Score: 85
Period size: 26 Copynumber: 2.0 Consensus size: 27
9017896 ATCCAACTTA
9017906 TTAGTAA-TTATTTTATAAAAAAA-ATT
1 TTAGTAAGTT-TTTTATAAAAAAATATT
9017932 TTAGTAAGTTTTTTATAAAAAAATATT
1 TTAGTAAGTTTTTTATAAAAAAATATT
9017959 T
1 T
9017960 CAAAGAATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 20 0.77
27 6 0.23
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (27 bp):
TTAGTAAGTTTTTTATAAAAAAATATT
Found at i:9021674 original size:66 final size:66
Alignment explanation
Indices: 9021568--9021707 Score: 253
Period size: 66 Copynumber: 2.1 Consensus size: 66
9021558 ACACTTTACC
* *
9021568 AATATCCAAATATGAAAATCAGGTGTAAAACCAAAACTATCCCATAATGGGTTATTGAAAATTAT
1 AATATCCAAATATGAAAATCAGCTGTAAAACCAAAACTATCCAATAATGGGTTATTGAAAATTAT
9021633 G
66 G
*
9021634 AATATCTAAATATGAAAATCAGCTGTAAAACCAAAACTATCCAATAATGGGTTATTGAAAATTAT
1 AATATCCAAATATGAAAATCAGCTGTAAAACCAAAACTATCCAATAATGGGTTATTGAAAATTAT
9021699 G
66 G
9021700 AATATCCA
1 AATATCCA
9021708 TGTATTTCGG
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 70 1.00
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.28
Consensus pattern (66 bp):
AATATCCAAATATGAAAATCAGCTGTAAAACCAAAACTATCCAATAATGGGTTATTGAAAATTAT
G
Found at i:9022830 original size:35 final size:34
Alignment explanation
Indices: 9022771--9022864 Score: 93
Period size: 33 Copynumber: 2.8 Consensus size: 34
9022761 TGAATTGACG
* * * *
9022771 GATAAGACCATGGTTGGACCATGGCAATGTTTAAAT
1 GATAAGACCATAGCTGGGCTATGGCAAT-TTT-AAT
9022807 G-TAAGACCATAGCTGGGCTATGGC-ATTTTAAT
1 GATAAGACCATAGCTGGGCTATGGCAATTTTAAT
* * *
9022839 GAAAAGACCATAACTGGGTTATGGCA
1 GATAAGACCATAGCTGGGCTATGGCA
9022865 CCTTGAACGT
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
32 4 0.08
33 23 0.47
34 2 0.04
35 19 0.39
36 1 0.02
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.27
Consensus pattern (34 bp):
GATAAGACCATAGCTGGGCTATGGCAATTTTAAT
Found at i:9022879 original size:33 final size:32
Alignment explanation
Indices: 9022807--9022882 Score: 80
Period size: 33 Copynumber: 2.3 Consensus size: 32
9022797 ATGTTTAAAT
* * * *
9022807 GTAAGACCATAGCTGGGCTATGGCATTTTAAT
1 GTAAGACCATAACTGGGCTATGGCACTTGAAC
* *
9022839 GAAAAGACCATAACTGGGTTATGGCACCTTGAAC
1 G-TAAGACCATAACTGGGCTATGGCA-CTTGAAC
9022873 GTAAGACCAT
1 GTAAGACCAT
9022883 GGTTGGACCA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
32 1 0.03
33 29 0.83
34 5 0.14
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (32 bp):
GTAAGACCATAACTGGGCTATGGCACTTGAAC
Found at i:9022983 original size:33 final size:32
Alignment explanation
Indices: 9022911--9022987 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 32
9022901 TAGATACATG
* * **
9022911 TGTAAGACCATAGTTGGGATATGGCATTCTGA
1 TGTAAGACCATAATTGGGATATGGCATACAAA
*
9022943 TGATAAGACCATAATTGGGTTATGGCACTACAAA
1 TG-TAAGACCATAATTGGGATATGGCA-TACAAA
9022977 TGTAAGACCAT
1 TGTAAGACCAT
9022988 GGCAGGGCCA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
32 2 0.05
33 31 0.82
34 5 0.13
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (32 bp):
TGTAAGACCATAATTGGGATATGGCATACAAA
Found at i:9022999 original size:105 final size:105
Alignment explanation
Indices: 9022806--9022999 Score: 264
Period size: 105 Copynumber: 1.8 Consensus size: 105
9022796 AATGTTTAAA
* * **
9022806 TGTAAGACCATAGCTGGGCTATGGCATTTTAATGAAAAGACCATAACTGGGTTATGGCACCTTGA
1 TGTAAGACCATAGCTGGGATATGGCATTCTAATGAAAAGACCATAACTGGGTTATGGCACCTCAA
**
9022871 ACGTAAGACCATGGTTGGACCATGACAGTATAGATACATG
66 ACGTAAGACCATGGCAGGACCATGACAGTATAGATACATG
* * * *
9022911 TGTAAGACCATAGTTGGGATATGGCATTCTGATGATAAGACCATAATTGGGTTATGGCA-CTACA
1 TGTAAGACCATAGCTGGGATATGGCATTCTAATGAAAAGACCATAACTGGGTTATGGCACCT-CA
* *
9022975 AATGTAAGACCATGGCAGGGCCATG
65 AACGTAAGACCATGGCAGGACCATG
9023000 GCAATGCATG
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
104 2 0.03
105 74 0.97
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (105 bp):
TGTAAGACCATAGCTGGGATATGGCATTCTAATGAAAAGACCATAACTGGGTTATGGCACCTCAA
ACGTAAGACCATGGCAGGACCATGACAGTATAGATACATG
Found at i:9030080 original size:12 final size:11
Alignment explanation
Indices: 9030049--9030087 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
9030039 ATATTTTTTG
9030049 TTTTAAAATAT
1 TTTTAAAATAT
9030060 TTTTAAAATACT
1 TTTTAAAATA-T
* *
9030072 TTTTTAAATTT
1 TTTTAAAATAT
9030083 TTTTA
1 TTTTA
9030088 TTTTAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 15 0.62
12 9 0.38
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:9033527 original size:3 final size:3
Alignment explanation
Indices: 9033502--9033559 Score: 75
Period size: 3 Copynumber: 19.3 Consensus size: 3
9033492 GTTATCTTTG
*
9033502 TTA TTA -TA TTA TATA TTA CTA TTA TTA TTA -TA TTA CTTA TTA TTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
9033547 TTA TTA TTA TTA T
1 TTA TTA TTA TTA T
9033560 AATAATATAT
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
2 4 0.08
3 39 0.80
4 6 0.12
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:9033545 original size:27 final size:24
Alignment explanation
Indices: 9033502--9033556 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
9033492 GTTATCTTTG
9033502 TTATTATATTATATATTACTATTA
1 TTATTATATTATATATTACTATTA
*
9033526 TTATTATATTACT-TATTATTATTA
1 TTATTATATTA-TATATTACTATTA
9033550 TTATTAT
1 TTATTAT
9033557 TATAATAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 28 0.97
25 1 0.03
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (24 bp):
TTATTATATTATATATTACTATTA
Found at i:9033572 original size:24 final size:25
Alignment explanation
Indices: 9033502--9033569 Score: 75
Period size: 27 Copynumber: 2.7 Consensus size: 25
9033492 GTTATCTTTG
* *
9033502 TTATTAT-ATTATATATTACTATTA
1 TTATTATAATAATATATTATTATTA
* *
9033526 TTATTATATTACTTATTATTATTATTA
1 TTATTATAATA-ATA-TATTATTATTA
9033553 TTATTATAATAATATAT
1 TTATTATAATAATATAT
9033570 ATTTATGCGC
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
24 7 0.20
25 4 0.11
26 4 0.11
27 20 0.57
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (25 bp):
TTATTATAATAATATATTATTATTA
Found at i:9033623 original size:30 final size:28
Alignment explanation
Indices: 9033589--9033668 Score: 85
Period size: 32 Copynumber: 2.8 Consensus size: 28
9033579 CATATGTATC
9033589 TTATTTTATATATATATATTTTATTTTATT
1 TTATTTTATATATATATATTTT-TTTTA-T
9033619 TTATTTTTATAATATATATACTATTTTTTTAT
1 TTA-TTTTAT-ATATATATA-T-TTTTTTTAT
9033651 TT-TTTTAT-TAT-TATATTT
1 TTATTTTATATATATATATTT
9033669 ATGCATATAT
Statistics
Matches: 46, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
25 2 0.04
26 1 0.02
27 4 0.09
28 3 0.07
30 9 0.20
31 6 0.13
32 12 0.26
33 6 0.13
34 3 0.07
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.70
Consensus pattern (28 bp):
TTATTTTATATATATATATTTTTTTTAT
Found at i:9033635 original size:36 final size:36
Alignment explanation
Indices: 9033596--9033665 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
9033586 ATCTTATTTT
* *
9033596 ATATATATA-TATTTTATT-TTATTTTATTTTTATA
1 ATATATATACTATTTTTTTATTATTTTATTATTATA
*
9033630 ATATATATACTATTTTTTTATTTTTTTATTATTATA
1 ATATATATACTATTTTTTTATTATTTTATTATTATA
9033666 TTTATGCATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
34 9 0.29
35 8 0.26
36 14 0.45
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.67
Consensus pattern (36 bp):
ATATATATACTATTTTTTTATTATTTTATTATTATA
Found at i:9056159 original size:18 final size:18
Alignment explanation
Indices: 9056124--9056159 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
9056114 CTCTTGACAA
*
9056124 GCAAAACAAGTTAAATTC
1 GCAAAACAAGTCAAATTC
*
9056142 GCAAAACAAGTCATATTC
1 GCAAAACAAGTCAAATTC
9056160 TGATTATAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.47, C:0.19, G:0.11, T:0.22
Consensus pattern (18 bp):
GCAAAACAAGTCAAATTC
Found at i:9056176 original size:17 final size:17
Alignment explanation
Indices: 9056150--9056184 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
9056140 TCGCAAAACA
*
9056150 AGTCATATTCTGATTAT
1 AGTCAGATTCTGATTAT
9056167 AGTCAGATTCTGATTAT
1 AGTCAGATTCTGATTAT
9056184 A
1 A
9056185 CGACTCGTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.43
Consensus pattern (17 bp):
AGTCAGATTCTGATTAT
Found at i:9063457 original size:12 final size:13
Alignment explanation
Indices: 9063433--9063465 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
9063423 AATTTAATCA
9063433 TAATATATAATAT
1 TAATATATAATAT
9063446 TAATAT-TAATAT
1 TAATATATAATAT
*
9063458 TAAAATAT
1 TAATATAT
9063466 TGTTTTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TAATATATAATAT
Found at i:9073809 original size:24 final size:24
Alignment explanation
Indices: 9073754--9073829 Score: 73
Period size: 24 Copynumber: 3.1 Consensus size: 24
9073744 CCGGGATTAA
* *
9073754 TAACGGGAAGCTCACAAAGAGC-CT
1 TAACGGGAAGCT-TCGAAGAGCACT
* * * *
9073778 ATATCGGGTAGCTTTGAAGAGTACT
1 -TAACGGGAAGCTTCGAAGAGCACT
9073803 TAACGGGAAGCTTCGAAGAGCACT
1 TAACGGGAAGCTTCGAAGAGCACT
9073827 TAA
1 TAA
9073830 GTCAGAAAGC
Statistics
Matches: 40, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
24 28 0.70
25 12 0.30
ACGTcount: A:0.34, C:0.18, G:0.26, T:0.21
Consensus pattern (24 bp):
TAACGGGAAGCTTCGAAGAGCACT
Found at i:9074586 original size:19 final size:20
Alignment explanation
Indices: 9074555--9074598 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
9074545 AACTCAATAA
* *
9074555 TTCCATGAAATTTCAGAATT
1 TTCCATGAAATTTAACAATT
9074575 TTCCAT-AAATTTAACAATT
1 TTCCATGAAATTTAACAATT
9074594 TTCCA
1 TTCCA
9074599 AATTAATCCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.36, C:0.18, G:0.05, T:0.41
Consensus pattern (20 bp):
TTCCATGAAATTTAACAATT
Found at i:9088074 original size:78 final size:78
Alignment explanation
Indices: 9087992--9088201 Score: 249
Period size: 81 Copynumber: 2.7 Consensus size: 78
9087982 TGCCTTCTCG
** *
9087992 GGAGATGCATGTAATGAGGTTGATGATGGCACCGTTGGAGGAGGATGCATTTTCTGTTTTGATGG
1 GGAGATGCATGTAATGAGGTTGATGATGGCATTGTTGGAGGAGGATGCATTCTCTGTTTTGATGG
* **
9088057 AACTGCTGGTGTA
66 AACCGCTGGCATA
* * * * **
9088070 GGAGATGCATGGAATGAGGTTGGTTATGGCATTATTGGAGGAGGATGCACCGAACTCTGTTTTGA
1 GGAGATGCATGTAATGAGGTTGATGATGGCATTGTTGGAGGAGGATGCA---TTCTCTGTTTTGA
*
9088135 TGGAACCGCTGGCATG
63 TGGAACCGCTGGCATA
* * *
9088151 GGAAATGCATGTAATGAGGTCGATGATGGCATTGTTAGAGGAGGATGCATT
1 GGAGATGCATGTAATGAGGTTGATGATGGCATTGTTGGAGGAGGATGCATT
9088202 GAGATCTCTG
Statistics
Matches: 107, Mismatches: 22, Indels: 6
0.79 0.16 0.04
Matches are distributed among these distances:
78 43 0.40
81 64 0.60
ACGTcount: A:0.24, C:0.11, G:0.36, T:0.29
Consensus pattern (78 bp):
GGAGATGCATGTAATGAGGTTGATGATGGCATTGTTGGAGGAGGATGCATTCTCTGTTTTGATGG
AACCGCTGGCATA
Found at i:9090180 original size:231 final size:230
Alignment explanation
Indices: 9089777--9090466 Score: 1101
Period size: 231 Copynumber: 3.0 Consensus size: 230
9089767 AAATTTGCTG
* * *
9089777 GGAGGGGAGTTGCATGTGGGGTGGTTGGTGATGGCTTTTTTGGGTAAGGATGCACTAAACTCTGT
1 GGAGGGGAGTTGCATGTGGGGTGGTTGGTGATGGC-ATTTTGGGGAAGGATGCACTAAGCTCTGT
* *
9089842 ATGGGTGGAGATGCTGGAATAGGCGGCAACAACATGGCTCTTGGTGCTGGTAGTGTAGGAGGTAA
65 ATGGGTGGACATGCTGGAATAGGCGGCAACAGCATGGCTCTTGGTGCTGGTAGTGTAGGAGGTAA
* * *
9089907 AATTAAATTTGATGAATGTATCATTATCTGATCGCATGGTTTTGCAGTTTCATCGTTTTGATCAC
130 AATTAAATTTGATGAAGGTATCATTAACTTATCGCATGGTTTTGCAGTTTCATCGTTTTGATCAC
*
9089972 TTTTGCGGATTACTTGTTGCTGCTCAATTGTTTCTA
195 TTTTGCGGTTTACTTGTTGCTGCTCAATTGTTTCTA
* * *
9090008 GGAGGGGAGTTGCATGTGGGGTGGTTGATGATGGCATTTTCGGGGAAGGATGCAATAAGCTCTCT
1 GGAGGGGAGTTGCATGTGGGGTGGTTGGTGATGGCATTTT-GGGGAAGGATGCACTAAGCTCTGT
*
9090073 ATGGGTGGACATGCTGGAATAGGCGACAACAGCATGGCTCTTGGTGCTGGTAGTGTAGGAGGTAA
65 ATGGGTGGACATGCTGGAATAGGCGGCAACAGCATGGCTCTTGGTGCTGGTAGTGTAGGAGGTAA
* *
9090138 AATTAAATTTGATGAAGGTAGCATTAACTTATCGCATGGTTTTGCAGTTTCATCGTTTTGATCAT
130 AATTAAATTTGATGAAGGTATCATTAACTTATCGCATGGTTTTGCAGTTTCATCGTTTTGATCAC
* *
9090203 TTTTGCGGTTTACTTGTCGCTGCTCAATTGTTTCTG
195 TTTTGCGGTTTACTTGTTGCTGCTCAATTGTTTCTA
* * *
9090239 GGAGGAGAGTTGCATGTAGGGTGGTTGGTGATGGCATTATTGGGGAAGGGTGCACTAAGCTCTGT
1 GGAGGGGAGTTGCATGTGGGGTGGTTGGTGATGGCATT-TTGGGGAAGGATGCACTAAGCTCTGT
* * * *
9090304 ATGGGTGGACATTCTGAAATAGGCGGCAACAGCATGGCTCCTGGTGCTGGTAGTGTAGAAGGTAA
65 ATGGGTGGACATGCTGGAATAGGCGGCAACAGCATGGCTCTTGGTGCTGGTAGTGTAGGAGGTAA
* * * *
9090369 AATTAAATTTGATGAAGGTATTATTGACTTATCGCATGGTTCTGCAGTTTCATCGGTTTGATCAC
130 AATTAAATTTGATGAAGGTATCATTAACTTATCGCATGGTTTTGCAGTTTCATCGTTTTGATCAC
9090434 TTTTGCGGTTTACTTGTTGCTGCTCAATTGTTT
195 TTTTGCGGTTTACTTGTTGCTGCTCAATTGTTT
9090467 TTGCTGCTTT
Statistics
Matches: 422, Mismatches: 35, Indels: 4
0.92 0.08 0.01
Matches are distributed among these distances:
230 4 0.01
231 416 0.99
232 2 0.00
ACGTcount: A:0.22, C:0.13, G:0.31, T:0.34
Consensus pattern (230 bp):
GGAGGGGAGTTGCATGTGGGGTGGTTGGTGATGGCATTTTGGGGAAGGATGCACTAAGCTCTGTA
TGGGTGGACATGCTGGAATAGGCGGCAACAGCATGGCTCTTGGTGCTGGTAGTGTAGGAGGTAAA
ATTAAATTTGATGAAGGTATCATTAACTTATCGCATGGTTTTGCAGTTTCATCGTTTTGATCACT
TTTGCGGTTTACTTGTTGCTGCTCAATTGTTTCTA
Found at i:9093198 original size:25 final size:26
Alignment explanation
Indices: 9093152--9093202 Score: 95
Period size: 25 Copynumber: 2.0 Consensus size: 26
9093142 ATTATATTTT
9093152 AGTAAGAATATAAAAAATTATTATAA
1 AGTAAGAATATAAAAAATTATTATAA
9093178 AGTAAGAATAT-AAAAATTATTATAA
1 AGTAAGAATATAAAAAATTATTATAA
9093203 CTTGTTGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 14 0.56
26 11 0.44
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.31
Consensus pattern (26 bp):
AGTAAGAATATAAAAAATTATTATAA
Found at i:9093266 original size:24 final size:24
Alignment explanation
Indices: 9093232--9093277 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
9093222 CATATGAAAT
* *
9093232 ATAAATTTTAAATATTTTTAAACA
1 ATAAATATTAAATATTTATAAACA
*
9093256 ATAAATATTAATTATTTATAAA
1 ATAAATATTAAATATTTATAAA
9093278 ATTTAATTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
ATAAATATTAAATATTTATAAACA
Found at i:9094216 original size:3 final size:3
Alignment explanation
Indices: 9094199--9094298 Score: 116
Period size: 3 Copynumber: 33.7 Consensus size: 3
9094189 TATACATAAA
* * * **
9094199 TAT TA- TAT ATAT TAT TAT TAT AAT TAT TAAC CAT TAT TAT GGT T-T
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT
9094244 TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
9094291 TAT TAT TA
1 TAT TAT TA
9094299 AATAAAGTAA
Statistics
Matches: 83, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
2 6 0.07
3 73 0.88
4 4 0.05
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:9094428 original size:10 final size:10
Alignment explanation
Indices: 9094413--9094437 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
9094403 TATAAGATAT
9094413 TTATTAGTTA
1 TTATTAGTTA
9094423 TTATTAGTTA
1 TTATTAGTTA
9094433 TTATT
1 TTATT
9094438 TATTATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (10 bp):
TTATTAGTTA
Found at i:9095786 original size:41 final size:41
Alignment explanation
Indices: 9095740--9095844 Score: 105
Period size: 38 Copynumber: 2.6 Consensus size: 41
9095730 TCGACCTCGA
9095740 GTCGATGAGACACTGGGTGTCACTATA-TTTCTTCGGATAGTT
1 GTCGATGAGACACTGGGTGTCACTATACTTTCTTCGGAT--TT
** *
9095782 -TCGATGAGGTACT-GG-GT-ACTA-ACTTTCTTCGGCTTT
1 GTCGATGAGACACTGGGTGTCACTATACTTTCTTCGGATTT
*
9095818 GCCGATGAGACACTGGGTGTCAACTAT
1 GTCGATGAGACACTGGGTGTC-ACTAT
9095845 TGCTTCGAAC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
36 2 0.04
37 11 0.22
38 16 0.32
39 4 0.08
40 2 0.04
41 15 0.30
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (41 bp):
GTCGATGAGACACTGGGTGTCACTATACTTTCTTCGGATTT
Found at i:9097180 original size:18 final size:18
Alignment explanation
Indices: 9097157--9097197 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
9097147 TTTTTAAAAT
9097157 ATTTTTTTGTAATTTTT-A
1 ATTTTTTT-TAATTTTTAA
*
9097175 ATTTTTTTTATTTTTTAA
1 ATTTTTTTTAATTTTTAA
9097193 ATTTT
1 ATTTT
9097198 GTTGCTGTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (18 bp):
ATTTTTTTTAATTTTTAA
Found at i:9097181 original size:17 final size:18
Alignment explanation
Indices: 9097159--9097197 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
9097149 TTTAAAATAT
9097159 TTTTTTGTAATTTTT-AA
1 TTTTTTGTAATTTTTAAA
* *
9097176 TTTTTTTTATTTTTTAAA
1 TTTTTTGTAATTTTTAAA
9097194 TTTT
1 TTTT
9097198 GTTGCTGTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.77
Consensus pattern (18 bp):
TTTTTTGTAATTTTTAAA
Found at i:9102388 original size:25 final size:25
Alignment explanation
Indices: 9102333--9102405 Score: 71
Period size: 24 Copynumber: 3.0 Consensus size: 25
9102323 CTCTCAAGCA
* *
9102333 CTATAACGGAAAGCTCAT--TGAGC
1 CTATAACGGGAAGCTCATAAAGAGC
*
9102356 CTTGTAACGGGAAGCTCATAAAGAGC
1 C-TATAACGGGAAGCTCATAAAGAGC
* *
9102382 CTATAACGGGTAGCTC-CAAAGAGC
1 CTATAACGGGAAGCTCATAAAGAGC
9102406 AATTAATGGG
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
23 1 0.02
24 22 0.54
25 13 0.32
26 5 0.12
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.19
Consensus pattern (25 bp):
CTATAACGGGAAGCTCATAAAGAGC
Found at i:9102416 original size:24 final size:24
Alignment explanation
Indices: 9102389--9102435 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
9102379 AGCCTATAAC
9102389 GGGTAGCTCCAAAGAGCAATTAAT
1 GGGTAGCTCCAAAGAGCAATTAAT
**
9102413 GGGTAGCTCTTAAGAGCAATTAA
1 GGGTAGCTCCAAAGAGCAATTAA
9102436 CGGGAAGCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.23
Consensus pattern (24 bp):
GGGTAGCTCCAAAGAGCAATTAAT
Found at i:9102515 original size:24 final size:25
Alignment explanation
Indices: 9102488--9102544 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 25
9102478 CACTAACGAA
9102488 AAGCTCAC-AAAGCC-TATAATCGGG
1 AAGCTCACAAAAGCCATATAA-CGGG
9102512 AAGCTCACGAAAAGCCATATAACGGG
1 AAGCTCAC-AAAAGCCATATAACGGG
*
9102538 ACGCTCA
1 AAGCTCA
9102545 TAAGAGCTGC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 8 0.28
26 16 0.55
27 5 0.17
ACGTcount: A:0.39, C:0.26, G:0.21, T:0.14
Consensus pattern (25 bp):
AAGCTCACAAAAGCCATATAACGGG
Found at i:9104929 original size:21 final size:22
Alignment explanation
Indices: 9104879--9104929 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
9104869 TCAACTTTTA
* *
9104879 AATGATTTTTATAATTTTTATTT
1 AATG-TTTTTATAAATTTTATAT
9104902 AAT-TTTTTATAAATTTTA-AT
1 AATGTTTTTATAAATTTTATAT
9104922 AATGTTTT
1 AATGTTTT
9104930 AAAAAATTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 4 0.16
21 18 0.72
23 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (22 bp):
AATGTTTTTATAAATTTTATAT
Found at i:9104962 original size:16 final size:17
Alignment explanation
Indices: 9104918--9104966 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
9104908 TTATAAATTT
9104918 TAATAATGTTTTAAAAAA
1 TAATAA-GTTTTAAAAAA
* * *
9104936 TTACAATTTTTAAAAAA
1 TAATAAGTTTTAAAAAA
9104953 -AATAAGTTTTAAAA
1 TAATAAGTTTTAAAA
9104967 GTTTTAAAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
16 11 0.44
17 10 0.40
18 4 0.16
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (17 bp):
TAATAAGTTTTAAAAAA
Found at i:9115165 original size:24 final size:24
Alignment explanation
Indices: 9115129--9115223 Score: 108
Period size: 23 Copynumber: 4.0 Consensus size: 24
9115119 TCTACCATGT
*
9115129 TTGGACAGC-TTTTATACACCAAA
1 TTGGACAGCATTATATACACCAAA
*
9115152 TTGGACAGCATT-TTTACACCAAAA
1 TTGGACAGCATTATATACACC-AAA
*
9115176 TTGGACAGCA-TATAGACACCAAA
1 TTGGACAGCATTATATACACCAAA
*
9115199 TTGGGCAGCATATATATAC-CCAAA
1 TTGGACAGCAT-TATATACACCAAA
9115223 T
1 T
9115224 ATATATACCA
Statistics
Matches: 62, Mismatches: 5, Indels: 9
0.82 0.07 0.12
Matches are distributed among these distances:
23 29 0.47
24 27 0.44
25 6 0.10
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
TTGGACAGCATTATATACACCAAA
Found at i:9115183 original size:47 final size:47
Alignment explanation
Indices: 9115129--9115358 Score: 196
Period size: 47 Copynumber: 5.1 Consensus size: 47
9115119 TCTACCATGT
* * * *
9115129 TTGGACAGCTTTTATACACCAAATTGGACAGCATTTTTACACCAAAA
1 TTGGACAGCATATATACACCAAATTGGACAGCATATATACACCAAAA
* * * *
9115176 TTGGACAGCATATAGACACCAAATTGGGCAGCATATATATACCCAAA
1 TTGGACAGCATATATACACCAAATTGGACAGCATATATACACCAAAA
* * *
9115223 -T-------ATATAT--ACCAAATTGGACAGCATTTTTACACTAAAA
1 TTGGACAGCATATATACACCAAATTGGACAGCATATATACACCAAAA
* * * *
9115260 TTGGATAGCATATAGACACCAAATTGGGCAGCATATATATACC-AAA
1 TTGGACAGCATATATACACCAAATTGGACAGCATATATACACCAAAA
* * * *
9115306 TTGGACAGCATTTTTACACCCAAATTGGACAGCATATAGACACC-GAA
1 TTGGACAGCATATATACA-CCAAATTGGACAGCATATATACACCAAAA
9115353 TTGGAC
1 TTGGAC
9115359 TTGAATCGAA
Statistics
Matches: 143, Mismatches: 29, Indels: 22
0.74 0.15 0.11
Matches are distributed among these distances:
37 24 0.17
38 1 0.01
39 5 0.03
45 5 0.03
46 18 0.13
47 90 0.63
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.26
Consensus pattern (47 bp):
TTGGACAGCATATATACACCAAATTGGACAGCATATATACACCAAAA
Done.