Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007971.1 Hibiscus syriacus cultivar Beakdansim tig00110408_pilon, whole genome shotgun sequence
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: 346037
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:213441 original size:22 final size:22
Alignment explanation
Indices: 213416--213457 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
213406 TTCTGGTATT
*
213416 GGATT-AAATGGTAATTATGGAA
1 GGATTGAAAGGGT-ATTATGGAA
213438 GGATTGAAAGGGTATTATGG
1 GGATTGAAAGGGTATTATGG
213458 TAATTTTAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.36, C:0.00, G:0.33, T:0.31
Consensus pattern (22 bp):
GGATTGAAAGGGTATTATGGAA
Found at i:215074 original size:32 final size:30
Alignment explanation
Indices: 215033--215122 Score: 126
Period size: 32 Copynumber: 2.9 Consensus size: 30
215023 GAGTCGAGGG
215033 TTACCTATGTCATTCGGGACATATGGACATGA
1 TTACCTATGTC-TTCGGGACATATGGACA-GA
*
215065 TTACCTATGTCCTTCGGGACATATGGACAGG
1 TTACCTATGT-CTTCGGGACATATGGACAGA
*
215096 TTACCTATGTTCTTGGGGACATATGGA
1 TTACCTATG-TCTTCGGGACATATGGA
215123 TAGGTCTTTC
Statistics
Matches: 54, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
31 25 0.46
32 28 0.52
33 1 0.02
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.32
Consensus pattern (30 bp):
TTACCTATGTCTTCGGGACATATGGACAGA
Found at i:215103 original size:31 final size:31
Alignment explanation
Indices: 215031--215127 Score: 140
Period size: 31 Copynumber: 3.1 Consensus size: 31
215021 AAGAGTCGAG
*
215031 GGTTACCTATGTCATTCGGGACATATGGACA
1 GGTTACCTATGTCCTTCGGGACATATGGACA
*
215062 TGATTACCTATGTCCTTCGGGACATATGGACA
1 -GGTTACCTATGTCCTTCGGGACATATGGACA
* * *
215094 GGTTACCTATGTTCTTGGGGACATATGGATA
1 GGTTACCTATGTCCTTCGGGACATATGGACA
215125 GGT
1 GGT
215128 CTTTCGGGGC
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
31 30 0.51
32 29 0.49
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.32
Consensus pattern (31 bp):
GGTTACCTATGTCCTTCGGGACATATGGACA
Found at i:215136 original size:23 final size:23
Alignment explanation
Indices: 215110--215163 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
215100 CTATGTTCTT
* *
215110 GGGGACATATGGATAGGTCTTTC
1 GGGGACATATGCATAGGTCCTTC
*
215133 GGGG-CACATGCATAGGTCCTTC
1 GGGGACATATGCATAGGTCCTTC
215155 -GGGACATAT
1 GGGGACATAT
215164 TTCACATGCC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 3 0.12
22 19 0.73
23 4 0.15
ACGTcount: A:0.22, C:0.19, G:0.33, T:0.26
Consensus pattern (23 bp):
GGGGACATATGCATAGGTCCTTC
Found at i:222817 original size:55 final size:56
Alignment explanation
Indices: 222733--222847 Score: 187
Period size: 55 Copynumber: 2.1 Consensus size: 56
222723 TGTCACTTGT
222733 AAATAGGAATGAACCGAAAGGTGATGATGGATATAATCATA-CTCTGAAAATATTA
1 AAATAGGAATGAACCGAAAGGTGATGATGGATATAATCATACCTCTGAAAATATTA
** *
222788 AAATAGGAATGAACCGAAAGGTTTTGATGGATATAATTATACTCTCTGAAAATATTA
1 AAATAGGAATGAACCGAAAGGTGATGATGGATATAATCATAC-CTCTGAAAATATTA
222845 AAA
1 AAA
222848 CTAAATTGTC
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
55 38 0.69
57 17 0.31
ACGTcount: A:0.45, C:0.09, G:0.18, T:0.28
Consensus pattern (56 bp):
AAATAGGAATGAACCGAAAGGTGATGATGGATATAATCATACCTCTGAAAATATTA
Found at i:224957 original size:59 final size:59
Alignment explanation
Indices: 224867--225005 Score: 142
Period size: 59 Copynumber: 2.4 Consensus size: 59
224857 GATTTTTCCA
* * * * **
224867 ACTATTAAAATTTATAAAATACACTCTGACTATA-GAGTATAGT-TTTGATGAGTCTTTCG
1 ACTATTAAAAGTTATAAAATACACTCCGACTATAGGA-CAT-GTCTTTGATGAGACCCTCG
* *
224926 ACTATTAAAAGTTATAAAATGATC-C-CCGACTATAGGACATTTCTTTGTTGAGACCCTCG
1 ACTATTAAAAGTTATAAAAT-A-CACTCCGACTATAGGACATGTCTTTGATGAGACCCTCG
224985 ACTATTAAAAGTTATAAAATA
1 ACTATTAAAAGTTATAAAATA
225006 ATCACTTAAC
Statistics
Matches: 68, Mismatches: 8, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
58 2 0.03
59 61 0.90
60 4 0.06
61 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.35
Consensus pattern (59 bp):
ACTATTAAAAGTTATAAAATACACTCCGACTATAGGACATGTCTTTGATGAGACCCTCG
Found at i:235514 original size:20 final size:20
Alignment explanation
Indices: 235485--235522 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
235475 CCCCTTCAAA
*
235485 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
235505 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
235523 TGCACCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.26, G:0.37, T:0.24
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:239331 original size:22 final size:21
Alignment explanation
Indices: 239289--239328 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
239279 GAGTTTGTTT
*
239289 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
239310 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
239329 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:242307 original size:20 final size:21
Alignment explanation
Indices: 242271--242309 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
242261 GGGATTTCAA
242271 GCAAGGAGTATCAATATTGCT
1 GCAAGGAGTATCAATATTGCT
*
242292 GCAAGG-GTATCGATATTG
1 GCAAGGAGTATCAATATTG
242310 TCCCTTCAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.31, C:0.13, G:0.28, T:0.28
Consensus pattern (21 bp):
GCAAGGAGTATCAATATTGCT
Found at i:244919 original size:16 final size:16
Alignment explanation
Indices: 244898--244928 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
244888 AGCAATCAAC
*
244898 AAAAAAATGCATATAT
1 AAAAAAATACATATAT
244914 AAAAAAATACATATA
1 AAAAAAATACATATA
244929 AATCAATATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.06, G:0.03, T:0.23
Consensus pattern (16 bp):
AAAAAAATACATATAT
Found at i:247025 original size:21 final size:20
Alignment explanation
Indices: 246985--247047 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 20
246975 TTCTATAATG
*
246985 AATGGTCAAATT-AAAGAATT
1 AATGGTCAATTTGAAA-AATT
247005 AATAGGTCAATTTGAAAAATT
1 AAT-GGTCAATTTGAAAAATT
*
247026 GAAT-GACTAATTTGAAAAATT
1 -AATGGTC-AATTTGAAAAATT
247047 A
1 A
247048 GTGAGCATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
20 6 0.16
21 25 0.68
22 6 0.16
ACGTcount: A:0.49, C:0.05, G:0.14, T:0.32
Consensus pattern (20 bp):
AATGGTCAATTTGAAAAATT
Found at i:257069 original size:43 final size:43
Alignment explanation
Indices: 257013--257262 Score: 430
Period size: 43 Copynumber: 5.8 Consensus size: 43
257003 AGGTCTTATA
* * *
257013 CTTGCACATAGCAAA-AGAGCCTGGGGAAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAGGGA-CCTGGGGGAACTGTAAGGCTTACC
*
257056 CTTGCACACAGCAAAGGAACCTGGGGGAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACC
257099 CTTGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACC
257142 CTTGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACC
* *
257185 CTTGCACACAGTAAAGGGACCTGGGGGAAATGTAAGGCTTACC
1 CTTGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACC
257228 CTTGCACACAGCAAAGGGACCTGGGGGAACTGTAA
1 CTTGCACACAGCAAAGGGACCTGGGGGAACTGTAA
257263 CGGTAATTAA
Statistics
Matches: 197, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
43 196 0.99
44 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.29, T:0.17
Consensus pattern (43 bp):
CTTGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACC
Found at i:260177 original size:22 final size:23
Alignment explanation
Indices: 260145--260193 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
260135 CCACATTCTA
260145 CAAATATTTAC-CAAACTAACACC
1 CAAATATTTACACAAAC-AACACC
*
260168 CAAAT-TTTACATAAACAACACC
1 CAAATATTTACACAAACAACACC
260190 CAAA
1 CAAA
260194 CAGAAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.51, C:0.29, G:0.00, T:0.20
Consensus pattern (23 bp):
CAAATATTTACACAAACAACACC
Found at i:262135 original size:43 final size:44
Alignment explanation
Indices: 262084--262375 Score: 422
Period size: 43 Copynumber: 6.8 Consensus size: 44
262074 AGGTCTTATA
*
262084 CTTGCACATAGCAAAAGAG-CCTGGGGAAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAAGAGACCTGGGGAAACTGTAAGGCTTACC
* *
262127 CTTGCACATAGCAAAGGA-ACCT-GGGAAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAAGAGACCTGGGGAAACTGTAAGGCTTACC
* *
262169 CTTGCACACAGCAAAGGA-ACCTGGGGGAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAAGAGACCTGGGGAAACTGTAAGGCTTACC
* *
262212 CTTGCACACAGC-AAAGGGACCTGGGGGAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAAGAGACCTGGGGAAACTGTAAGGCTTACC
*
262255 CTTGCACACAGC-AAAGGGACCTGGGGAAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAAGAGACCTGGGGAAACTGTAAGGCTTACC
262298 CTTGCACACAGCAAAA-AGACCTGGGGGAAA-TGTAAGGCTTACC
1 CTTGCACACAGCAAAAGAGACCT-GGGGAAACTGTAAGGCTTACC
* *
262341 CTTGCACACAG-AAAAGGGACCTGGGGGAACTGTAA
1 CTTGCACACAGCAAAAGAGACCTGGGGAAACTGTAA
262376 CGATAATTAA
Statistics
Matches: 233, Mismatches: 9, Indels: 14
0.91 0.04 0.05
Matches are distributed among these distances:
42 54 0.23
43 169 0.73
44 10 0.04
ACGTcount: A:0.32, C:0.24, G:0.27, T:0.17
Consensus pattern (44 bp):
CTTGCACACAGCAAAAGAGACCTGGGGAAACTGTAAGGCTTACC
Found at i:262322 original size:129 final size:128
Alignment explanation
Indices: 262066--262375 Score: 471
Period size: 129 Copynumber: 2.4 Consensus size: 128
262056 GAGCATGCAA
** * * *
262066 AAATGATAAGGTCTTATACTTGCACATAGCAAA-AGAGCCTGGGGAAACTGTAAGGCTTACCCTT
1 AAATG-TAAGG-CTTACCCTTGCACACAGCAAAGGGA-CCTGGGGGAACTGTAAGGCTTACCCTT
* *
262130 GCACATAGCAAAGGAACCTGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGG
63 GCACACAGCAAAGGAACCTGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAAGAACCTGGGG
262195 G
128 G
*
262196 AACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACCCTTGCA
1 AAATGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACCCTTGCA
*
262261 CACAGCAAAGGGACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAA-AGACCTGGGGG
66 CACAGCAAAGGAACCT-GGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAAGA-ACCTGGGGG
*
262325 AAATGTAAGGCTTACCCTTGCACACAGAAAAGGGACCTGGGGGAACTGTAA
1 AAATGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAACTGTAA
262376 CGATAATTAA
Statistics
Matches: 166, Mismatches: 11, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
128 62 0.37
129 100 0.60
130 4 0.02
ACGTcount: A:0.33, C:0.23, G:0.27, T:0.18
Consensus pattern (128 bp):
AAATGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACCCTTGCA
CACAGCAAAGGAACCTGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAAGAACCTGGGGG
Found at i:266098 original size:9 final size:9
Alignment explanation
Indices: 266084--266118 Score: 70
Period size: 9 Copynumber: 3.9 Consensus size: 9
266074 GATAAAACAC
266084 TATTTATTT
1 TATTTATTT
266093 TATTTATTT
1 TATTTATTT
266102 TATTTATTT
1 TATTTATTT
266111 TATTTATT
1 TATTTATT
266119 GAGTTCTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (9 bp):
TATTTATTT
Found at i:269937 original size:23 final size:24
Alignment explanation
Indices: 269905--269957 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
269895 AAGTTTTACA
* *
269905 TCAAGTTTTTCATTAGGTTTTCTT
1 TCAATTTTTTCATTAGGTGTTCTT
* *
269929 T-AATTTTTTCTTTTGGTGTTCTT
1 TCAATTTTTTCATTAGGTGTTCTT
269952 TCAATT
1 TCAATT
269958 ATGAGCAACT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 19 0.79
24 5 0.21
ACGTcount: A:0.15, C:0.11, G:0.11, T:0.62
Consensus pattern (24 bp):
TCAATTTTTTCATTAGGTGTTCTT
Found at i:270407 original size:955 final size:940
Alignment explanation
Indices: 268629--270518 Score: 3168
Period size: 955 Copynumber: 2.0 Consensus size: 940
268619 GGAAAAATCA
* *
268629 GAATTCAAGAAGTTGGCAAGACCAGAAGAGGTTTTCGCATAAGGCGTGGGCACGGCTTATTCATC
1 GAATTCAAGAAGTTGGCAAGACCAGAAGAGGTTTTCGCATAAGGCGTAGGCACGACTTATTCATC
*
268694 TTGAGCTATCACAGAAGAAGTCTTCAGTTAAGGCGTGGGAGCGCCTTACCAGTATGTACAACCCT
66 TTGAGCTATCACAGAAGAAGTCTTCAGTTAAGGCGTGGGAGCGCCTTACCAGTATATACAACCCT
* *
268759 AAATTAGGGTTACGAATTTAAAAGGAAAAAAGTTTAATTACGGCTGGAAGACTCTTTTGAATTAT
131 AAATTAGGATTACGAATTTAAAAGGAAAAAAGTTTAATGACGGCTGGAAGACTCTTTTGAATTAT
*
268824 TCTTATCTTTAGAAAAGGATGAGGGCATTTAAACCCCTATTTTTGTGGGATTTTCTTTAAGAGAA
196 TCTTATCTTTAGAAAAGGACGAGGGCATTTAAACCCCTATTTTTGTGGGATTTTCTTTAAGAGAA
* * * * *
268889 ATTTCCTTATTTAGAATAGGAAAATCCTTATAAAAGGGGAGCTAGGGGTTTCATAGGAGGCATAA
261 ATTTCCTTATCTAGAATAGGAAAATACTTATAAAAGAGGAGCTAGGGCTTTCATAAGAGGCATAA
*
268954 GTTTTACATCAAGTTTTCTTTAAGTTTTTCTTTTGGTGTTCTTTCAATTATGAGCAGCTAAATAC
326 GTTTTACATCAAGTTTTCTTTAAGTTTTTCTTTTGGTGTTCTTTCAATTATGAGCAACTAAATAC
* * * * *
269019 TTTTGTTCCAACTGGAGGAAAATTGAAGTTTTGGTTCTTCAAGGATTGTGAGATCTAAATAATTT
391 TTTTCTTCCAACTAGAGGAAAATTGAAGTTTTGGTTCATCAAGAATTATGAGATCTAAATAATTT
* *
269084 TCATTGTTCTTTTACTTCTTTTCTATTTATATATCTTCTGTTTTTATTAAGAATTATTATCTTGA
456 TCATTGTTCCTTTACTTCTTTGCTATTTATATATCTTCTGTTTTTATTAAGAATTATTATCTTGA
* * *
269149 TTGATTGTGCAAAGGGCCCGTTGTTCAATTGTCAGGTTGATAAGTTGTCATTTAGAACTTTAAAT
521 TTGATTGTGCAAAGGGCCCGTTGTTCAATTATCAGGTTGATAAATTGCCATTTAGAACTTTAAAT
269214 ATGTAATTGTTTAAACGTTCTAATATTAGTGGTAAAGTAACATAGTTGATTTTGATTATATTATG
586 ATGTAATTGTTTAAACGTTCTAATATTAGTGGTAAAGTAACATAGTTGATTTTGATTATATTATG
* *
269279 AAGGTATGTAACCTAGTCTAAATGAATCGAGCTTGTGTATTCGTTGGCTAGAATTGGTGGTCCCT
651 AAGATATATAACCTAGTCTAAATGAATCGAGCTTGTGTATTCGTTGGCTAGAATTGGTGGTCCCT
*
269344 CTACTGGTTAAAGTTGTTGGTGGATTAAATCCTAAGAGCTTGTCTAGGGTTGTTCATTAACAAGG
716 CTACTGGTTAAAGTTGTTGGTGGATTAAATCCTAAGAACTTGTCTAGGGTTGTTCATTAACAAGG
* * *
269409 GAAATAATCAAAGAGCTTCTCTTGATTATCGAGAAATTAAGGAGAGACATGTTGTTAGAGCTTCT
781 GAAATAATCAAAGAGCTTCTCTTGATTATCAAGAAACTAAGGAGAGACAAGTTGTTAGAGCTTCT
269474 CAATAACCATAACCAATTTAGTGAAAAGTAGAAGATTATATCATTACATCTATGATCAATTCTCT
846 CAATAACCATAACCAATTTAGTGAAAAGTAGAAGATTATATCATTACATCTATGATCAATTCTCT
* *
269539 GAACCAATTTTGAAATTATACCTTTAGTCG
911 GAACAAATTCTGAAATTATACCTTTAGTCG
* *
269569 GAATTCAAGAAGTTGGCAAGACCAGAAGAGGTTTTTGCATAAGGCTTAGGCACGACTTATTCATC
1 GAATTCAAGAAGTTGGCAAGACCAGAAGAGGTTTTCGCATAAGGCGTAGGCACGACTTATTCATC
* * * *
269634 TTGAGCTATCGCAGAAGAAGTCTTCAGTTAAGGCGTGGGCGTGCCTTACCAGTCTATACAACCCT
66 TTGAGCTATCACAGAAGAAGTCTTCAGTTAAGGCGTGGGAGCGCCTTACCAGTATATACAACCCT
* *
269699 AAATTAGGATTATGAATTTACAAGGGAAAAAGAGTTTAATGACGGCTGGAAGACTCTTTTGAATT
131 AAATTAGGATTACGAATTTA-AAAGGAAAAA-AGTTTAATGACGGCTGGAAGACTCTTTTGAATT
*
269764 ATTCTTATCTTTAGAAAATGACGAGGGCATTTAAAACCCCTATTTTTGTGGGATTTTCTTTAAGA
194 ATTCTTATCTTTAGAAAAGGACGAGGGCATTT-AAACCCCTATTTTTGTGGGATTTTCTTTAAGA
269829 GAAATTTCCTTATCTAGAATAGGAAAATACTTATAAAAGAGGAGCTAGGGCTTTCATAAGAGGCA
258 GAAATTTCCTTATCTAGAATAGGAAAATACTTATAAAAGAGGAGCTAGGGCTTTCATAAGAGGCA
*
269894 TAAGTTTTACATCAAGTTTTTCATTAGGTTTTCTTTAATTTTTTCTTTTGGTGTTCTTTCAATTA
323 TAAGTTTT--A-C-A-----TCA--A-GTTTTCTTTAAGTTTTTCTTTTGGTGTTCTTTCAATTA
269959 TGAGCAACTAAATACTTTTCTTCCAACTAGAGGAAAATTGAAGTTTTGGTTCATCAAGAATTATG
376 TGAGCAACTAAATACTTTTCTTCCAACTAGAGGAAAATTGAAGTTTTGGTTCATCAAGAATTATG
* *
270024 AGATCTAATTAATTTTGATTGTTCCTTTACTTCTTTGCTATTTATATATCTTCTGTTTTTATTAA
441 AGATCTAAATAATTTTCATTGTTCCTTTACTTCTTTGCTATTTATATATCTTCTGTTTTTATTAA
*
270089 GAATTATTGTCTTGATTGATTGTGCAAAGGGCCCGTTGTTCAATTATCAGGTTGATAAATTGCCA
506 GAATTATTATCTTGATTGATTGTGCAAAGGGCCCGTTGTTCAATTATCAGGTTGATAAATTGCCA
* *
270154 TTTAGAACTTTAAATCTGTAGTTGTTTAAACGTTCTAATATTAGTGGTAAAGTAACATAGTTGAT
571 TTTAGAACTTTAAATATGTAATTGTTTAAACGTTCTAATATTAGTGGTAAAGTAACATAGTTGAT
* *
270219 TTTGATTATGTTATGAAGATATATAACCTAGTCTAAATGAATTGAGCTTGTGTATTCGTTGGCTA
636 TTTGATTATATTATGAAGATATATAACCTAGTCTAAATGAATCGAGCTTGTGTATTCGTTGGCTA
* * *
270284 GAATTGGTGGTCCCTCTAGTGGTTAATGTTGTTGGTGGATTAAATCTTAAGAACTTGTCTAGGGT
701 GAATTGGTGGTCCCTCTACTGGTTAAAGTTGTTGGTGGATTAAATCCTAAGAACTTGTCTAGGGT
*
270349 TGTTCATTAACGAGGGAAATAATCAAAGAGCTTCTCTTGATTATCAAGAAACTAAGGAGAGACAA
766 TGTTCATTAACAAGGGAAATAATCAAAGAGCTTCTCTTGATTATCAAGAAACTAAGGAGAGACAA
* *
270414 GTTGTTAGAGCTTCTCAATAACCATAACCAATTTAGTGAAAAGTAGAAGATTTTATCATTGCATC
831 GTTGTTAGAGCTTCTCAATAACCATAACCAATTTAGTGAAAAGTAGAAGATTATATCATTACATC
270479 TATGATCAATTCTCTGAACAAATTCTGAAATTATACCTTT
896 TATGATCAATTCTCTGAACAAATTCTGAAATTATACCTTT
270519 CGTTGGATAT
Statistics
Matches: 882, Mismatches: 53, Indels: 15
0.93 0.06 0.02
Matches are distributed among these distances:
940 139 0.16
941 9 0.01
942 62 0.07
943 100 0.11
945 1 0.00
946 1 0.00
947 1 0.00
952 3 0.00
954 1 0.00
955 565 0.64
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (940 bp):
GAATTCAAGAAGTTGGCAAGACCAGAAGAGGTTTTCGCATAAGGCGTAGGCACGACTTATTCATC
TTGAGCTATCACAGAAGAAGTCTTCAGTTAAGGCGTGGGAGCGCCTTACCAGTATATACAACCCT
AAATTAGGATTACGAATTTAAAAGGAAAAAAGTTTAATGACGGCTGGAAGACTCTTTTGAATTAT
TCTTATCTTTAGAAAAGGACGAGGGCATTTAAACCCCTATTTTTGTGGGATTTTCTTTAAGAGAA
ATTTCCTTATCTAGAATAGGAAAATACTTATAAAAGAGGAGCTAGGGCTTTCATAAGAGGCATAA
GTTTTACATCAAGTTTTCTTTAAGTTTTTCTTTTGGTGTTCTTTCAATTATGAGCAACTAAATAC
TTTTCTTCCAACTAGAGGAAAATTGAAGTTTTGGTTCATCAAGAATTATGAGATCTAAATAATTT
TCATTGTTCCTTTACTTCTTTGCTATTTATATATCTTCTGTTTTTATTAAGAATTATTATCTTGA
TTGATTGTGCAAAGGGCCCGTTGTTCAATTATCAGGTTGATAAATTGCCATTTAGAACTTTAAAT
ATGTAATTGTTTAAACGTTCTAATATTAGTGGTAAAGTAACATAGTTGATTTTGATTATATTATG
AAGATATATAACCTAGTCTAAATGAATCGAGCTTGTGTATTCGTTGGCTAGAATTGGTGGTCCCT
CTACTGGTTAAAGTTGTTGGTGGATTAAATCCTAAGAACTTGTCTAGGGTTGTTCATTAACAAGG
GAAATAATCAAAGAGCTTCTCTTGATTATCAAGAAACTAAGGAGAGACAAGTTGTTAGAGCTTCT
CAATAACCATAACCAATTTAGTGAAAAGTAGAAGATTATATCATTACATCTATGATCAATTCTCT
GAACAAATTCTGAAATTATACCTTTAGTCG
Found at i:273612 original size:18 final size:18
Alignment explanation
Indices: 273574--273614 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
273564 ATTTTTGTTC
* *
273574 TTTTTATTTTTTATTTTA
1 TTTTTATTTTTTACTTGA
*
273592 TTTTTATTTTTTCCTTGA
1 TTTTTATTTTTTACTTGA
273610 TTTTT
1 TTTTT
273615 CGGAGTACAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.12, C:0.05, G:0.02, T:0.80
Consensus pattern (18 bp):
TTTTTATTTTTTACTTGA
Found at i:275951 original size:11 final size:11
Alignment explanation
Indices: 275914--275956 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
275904 ATAAGAGGCA
275914 TAAGTTTTACAT
1 TAAGTTTT-CAT
*
275926 CAAGTTTTTCAT
1 TAAG-TTTTCAT
*
275938 TAAGTTTTCTT
1 TAAGTTTTCAT
275949 TAAGTTTT
1 TAAGTTTT
275957 TGTTTTGGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
11 14 0.52
12 9 0.33
13 4 0.15
ACGTcount: A:0.26, C:0.09, G:0.09, T:0.56
Consensus pattern (11 bp):
TAAGTTTTCAT
Found at i:275957 original size:12 final size:12
Alignment explanation
Indices: 275914--275957 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
275904 ATAAGAGGCA
*
275914 TAAGTTTTACAT
1 TAAGTTTTTCAT
*
275926 CAAGTTTTTCAT
1 TAAGTTTTTCAT
*
275938 TAAG-TTTTCTT
1 TAAGTTTTTCAT
275949 TAAGTTTTT
1 TAAGTTTTT
275958 GTTTTGGTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 10 0.37
12 17 0.63
ACGTcount: A:0.25, C:0.09, G:0.09, T:0.57
Consensus pattern (12 bp):
TAAGTTTTTCAT
Found at i:277166 original size:18 final size:18
Alignment explanation
Indices: 277143--277178 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
277133 GAAAATACCC
277143 TGCACCAGTCTTTTAGAT
1 TGCACCAGTCTTTTAGAT
*
277161 TGCACCATTCTTTTAGAT
1 TGCACCAGTCTTTTAGAT
277179 GTTTTGGCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.42
Consensus pattern (18 bp):
TGCACCAGTCTTTTAGAT
Found at i:282053 original size:7 final size:7
Alignment explanation
Indices: 282037--282075 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
282027 TATGATAAGA
*
282037 TTTAGGG
1 TTTAGAG
282044 TTTAGAG
1 TTTAGAG
*
282051 TTTAGGG
1 TTTAGAG
282058 TTTAGAG
1 TTTAGAG
282065 TTTAGAG
1 TTTAGAG
282072 TTTA
1 TTTA
282076 TGTGATATGA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (7 bp):
TTTAGAG
Found at i:282056 original size:14 final size:14
Alignment explanation
Indices: 282037--282174 Score: 72
Period size: 14 Copynumber: 9.9 Consensus size: 14
282027 TATGATAAGA
282037 TTTAGGGTTTAGAG
1 TTTAGGGTTTAGAG
282051 TTTAGGGTTTAGAG
1 TTTAGGGTTTAGAG
* *
282065 TTTAGAGTTTA-TG
1 TTTAGGGTTTAGAG
* * *
282078 TGATATGATTTA-AGG
1 T-TTAGGGTTTAGA-G
282093 TTTAGGGTTTAGAG
1 TTTAGGGTTTAGAG
* *
282107 TTTA-TGTAATAG-G
1 TTTAGGGT-TTAGAG
*
282120 ATTTAAGGTTTAGAG
1 -TTTAGGGTTTAGAG
* *
282135 TCTAGTGTTTATG-G
1 TTTAGGGTTTA-GAG
*
282149 TTTAAGGTTTAG-G
1 TTTAGGGTTTAGAG
*
282162 TATTAAGGTTTAG
1 T-TTAGGGTTTAG
282175 GATTTAGAGT
Statistics
Matches: 95, Mismatches: 20, Indels: 18
0.71 0.15 0.14
Matches are distributed among these distances:
13 8 0.08
14 80 0.84
15 7 0.07
ACGTcount: A:0.25, C:0.01, G:0.29, T:0.45
Consensus pattern (14 bp):
TTTAGGGTTTAGAG
Found at i:282067 original size:21 final size:21
Alignment explanation
Indices: 282037--282110 Score: 73
Period size: 21 Copynumber: 3.5 Consensus size: 21
282027 TATGATAAGA
*
282037 TTTAGGGTTTAGAGTTTAGGG
1 TTTAGAGTTTAGAGTTTAGGG
*
282058 TTTAGAGTTTAGAGTTTA-TG
1 TTTAGAGTTTAGAGTTTAGGG
*
282078 TGATATGA-TTTA-AGGTTTAGGG
1 T-TTA-GAGTTTAGA-GTTTAGGG
282100 TTTAGAGTTTA
1 TTTAGAGTTTA
282111 TGTAATAGGA
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
20 5 0.12
21 34 0.79
22 4 0.09
ACGTcount: A:0.24, C:0.00, G:0.30, T:0.46
Consensus pattern (21 bp):
TTTAGAGTTTAGAGTTTAGGG
Found at i:282103 original size:35 final size:35
Alignment explanation
Indices: 282051--282147 Score: 140
Period size: 35 Copynumber: 2.8 Consensus size: 35
282041 GGGTTTAGAG
* * *
282051 TTTAGGGTTTAGAGTTTAGAGTTTATGTGATATGA
1 TTTAAGGTTTAGAGTTTAGAGTTTATGTAATAGGA
*
282086 TTTAAGGTTTAGGGTTTAGAGTTTATGTAATAGGA
1 TTTAAGGTTTAGAGTTTAGAGTTTATGTAATAGGA
* *
282121 TTTAAGGTTTAGAGTCTAGTGTTTATG
1 TTTAAGGTTTAGAGTTTAGAGTTTATG
282148 GTTTAAGGTT
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 55 1.00
ACGTcount: A:0.26, C:0.01, G:0.28, T:0.45
Consensus pattern (35 bp):
TTTAAGGTTTAGAGTTTAGAGTTTATGTAATAGGA
Found at i:282145 original size:21 final size:21
Alignment explanation
Indices: 282116--282174 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
282106 GTTTATGTAA
282116 TAGGATTTAAGGTTTAGA-GTC
1 TAGG-TTTAAGGTTTAGAGGTC
* *
282137 TAGTGTTTATGGTTTA-AGGTT
1 TAG-GTTTAAGGTTTAGAGGTC
282158 TAGGTATTAAGGTTTAG
1 TAGGT-TTAAGGTTTAG
282175 GATTTAGAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
20 3 0.10
21 27 0.87
22 1 0.03
ACGTcount: A:0.25, C:0.02, G:0.29, T:0.44
Consensus pattern (21 bp):
TAGGTTTAAGGTTTAGAGGTC
Found at i:282180 original size:21 final size:21
Alignment explanation
Indices: 282121--282181 Score: 56
Period size: 21 Copynumber: 2.9 Consensus size: 21
282111 TGTAATAGGA
*
282121 TTTAAGGTTTA-GAGTCTAGTG
1 TTTAAGGTTTAGGA-TTTAGTG
*
282142 TTTATGGTTTAAGG-TTTAG-G
1 TTTAAGGTTT-AGGATTTAGTG
282162 TATTAAGGTTTAGGATTTAG
1 T-TTAAGGTTTAGGATTTAG
282182 AGTTCAGAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
20 5 0.15
21 26 0.79
22 1 0.03
23 1 0.03
ACGTcount: A:0.25, C:0.02, G:0.28, T:0.46
Consensus pattern (21 bp):
TTTAAGGTTTAGGATTTAGTG
Found at i:282269 original size:58 final size:59
Alignment explanation
Indices: 282169--282297 Score: 208
Period size: 58 Copynumber: 2.2 Consensus size: 59
282159 AGGTATTAAG
* *
282169 GTTTAGGATTTAGAGTTCAGAAGTTTTAGACTTTATGTGATATGATTTAAGGTTTATA-
1 GTTTAGGGTTTAGAGTTCAGAAGTTTTAGACTTTACGTGATATGATTTAAGGTTTATAT
*
282227 GTTTTAGGGTTTAGAGTTCA-AAGTTTTAGAGTTTACGTGATATGATTTAAGGTTTATAT
1 G-TTTAGGGTTTAGAGTTCAGAAGTTTTAGACTTTACGTGATATGATTTAAGGTTTATAT
282286 GTTTAGGGTTTA
1 GTTTAGGGTTTA
282298 TATGTTAGGG
Statistics
Matches: 66, Mismatches: 3, Indels: 4
0.90 0.04 0.05
Matches are distributed among these distances:
58 48 0.73
59 18 0.27
ACGTcount: A:0.27, C:0.03, G:0.24, T:0.46
Consensus pattern (59 bp):
GTTTAGGGTTTAGAGTTCAGAAGTTTTAGACTTTACGTGATATGATTTAAGGTTTATAT
Found at i:282310 original size:15 final size:15
Alignment explanation
Indices: 282266--282307 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
282256 AGTTTACGTG
*
282266 ATATGATTTAAGGTTT
1 ATATG-TTTAGGGTTT
282282 ATATGTTTAGGGTTT
1 ATATGTTTAGGGTTT
282297 ATATG-TTAGGG
1 ATATGTTTAGGG
282308 GTTAGGGGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 6 0.24
15 14 0.56
16 5 0.20
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (15 bp):
ATATGTTTAGGGTTT
Found at i:284229 original size:11 final size:11
Alignment explanation
Indices: 284213--284313 Score: 69
Period size: 11 Copynumber: 8.9 Consensus size: 11
284203 TAACCCATCC
284213 TCGAGCTT-AA
1 TCGAGCTTGAA
284223 GTCGAGCTTGAA
1 -TCGAGCTTGAA
**
284235 TCGAGCTCACAA
1 TCGAGCT-TGAA
*
284247 TCGAGTTTGAA
1 TCGAGCTTGAA
**
284258 TCGAGCTCACAA
1 TCGAGCT-TGAA
*
284270 TCGAGCCTGAA
1 TCGAGCTTGAA
**
284281 TCGAGCTCAAAA
1 TCGAGCT-TGAA
*
284293 TCGAGCTTCAA
1 TCGAGCTTGAA
*
284304 TTGAGCTTGA
1 TCGAGCTTGA
284314 GTCTTGAGCT
Statistics
Matches: 68, Mismatches: 18, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
11 41 0.60
12 27 0.40
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (11 bp):
TCGAGCTTGAA
Found at i:284250 original size:12 final size:12
Alignment explanation
Indices: 284233--284299 Score: 66
Period size: 12 Copynumber: 5.8 Consensus size: 12
284223 GTCGAGCTTG
284233 AATCGAGCTCAC
1 AATCGAGCTCAC
***
284245 AATCGAG-TTTG
1 AATCGAGCTCAC
284256 AATCGAGCTCAC
1 AATCGAGCTCAC
**
284268 AATCGAGC-CTG
1 AATCGAGCTCAC
*
284279 AATCGAGCTCAA
1 AATCGAGCTCAC
284291 AATCGAGCT
1 AATCGAGCT
284300 TCAATTGAGC
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
11 17 0.40
12 26 0.60
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (12 bp):
AATCGAGCTCAC
Found at i:284256 original size:23 final size:23
Alignment explanation
Indices: 284224--284310 Score: 129
Period size: 23 Copynumber: 3.8 Consensus size: 23
284214 CGAGCTTAAG
284224 TCGAGCTTGAATCGAGCTCACAA
1 TCGAGCTTGAATCGAGCTCACAA
*
284247 TCGAGTTTGAATCGAGCTCACAA
1 TCGAGCTTGAATCGAGCTCACAA
* *
284270 TCGAGCCTGAATCGAGCTCAAAA
1 TCGAGCTTGAATCGAGCTCACAA
* *
284293 TCGAGCTTCAATTGAGCT
1 TCGAGCTTGAATCGAGCT
284311 TGAGTCTTGA
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (23 bp):
TCGAGCTTGAATCGAGCTCACAA
Found at i:287373 original size:7 final size:7
Alignment explanation
Indices: 287361--287387 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
287351 ATCTCTTAAA
287361 TTTCAGT
1 TTTCAGT
287368 TTTCAGT
1 TTTCAGT
287375 TTTCAGT
1 TTTCAGT
287382 TTTCAG
1 TTTCAG
287388 ATTATTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.56
Consensus pattern (7 bp):
TTTCAGT
Found at i:287532 original size:16 final size:18
Alignment explanation
Indices: 287496--287532 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
287486 TCACATAAAT
*
287496 ATTACAAAAATGAAGTTA
1 ATTACAAAAATGAAATTA
287514 ATTAC-AAAA-GAAATTA
1 ATTACAAAAATGAAATTA
287530 ATT
1 ATT
287533 TGATTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 9 0.50
17 4 0.22
18 5 0.28
ACGTcount: A:0.57, C:0.05, G:0.08, T:0.30
Consensus pattern (18 bp):
ATTACAAAAATGAAATTA
Found at i:293096 original size:12 final size:12
Alignment explanation
Indices: 293081--293126 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
293071 CGGTTTTTTT
*
293081 ACCGGATAAAAA
1 ACCGGTTAAAAA
293093 ACCGGTTTGAAAAAA
1 ACCGG-TT--AAAAA
293108 ACCGGTTAAAAA
1 ACCGGTTAAAAA
293120 ACCGGTT
1 ACCGGTT
293127 TTTATCCGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 17 0.57
13 1 0.03
14 2 0.07
15 10 0.33
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:293108 original size:15 final size:13
Alignment explanation
Indices: 293087--293127 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
293077 TTTTACCGGA
293087 TAAAAAACCGGTT
1 TAAAAAACCGGTT
293100 TGAAAAAAACCGG-T
1 T--AAAAAACCGGTT
293114 TAAAAAACCGGTT
1 TAAAAAACCGGTT
293127 T
1 T
293128 TTATCCGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 3 0.12
14 2 0.08
15 10 0.40
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:295441 original size:21 final size:21
Alignment explanation
Indices: 295417--295456 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
295407 TTTATTTTAT
295417 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
295438 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
295457 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:295504 original size:33 final size:33
Alignment explanation
Indices: 295451--295549 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
295441 TTTGTTTCAA
295451 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
295483 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
295516 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
295549 T
1 T
295550 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:295578 original size:13 final size:13
Alignment explanation
Indices: 295535--295589 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
295525 TTGGAAGTAT
295535 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
295548 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
295562 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
295575 TTAAGTATTTGAA
1 TTAAGTATTTCAA
295588 TT
1 TT
295590 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:296010 original size:15 final size:15
Alignment explanation
Indices: 295985--296023 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
295975 ATCTGGAATA
*
295985 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
296000 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
296015 TTAAAACCG
1 TTAAAACCG
296024 AAACCGGTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:296140 original size:15 final size:17
Alignment explanation
Indices: 296114--296145 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
296104 TTCTATGGGA
296114 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
296130 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
296146 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:298564 original size:21 final size:21
Alignment explanation
Indices: 298538--298584 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
298528 ATTAAAATAT
*
298538 TTTTATAAATTTTAT-TTAAAA
1 TTTTAT-AATTTAATATTAAAA
*
298559 TTTTATAATTTAATATTAAAG
1 TTTTATAATTTAATATTAAAA
298580 TTTTA
1 TTTTA
298585 CTTGTTAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
TTTTATAATTTAATATTAAAA
Found at i:302895 original size:4 final size:4
Alignment explanation
Indices: 302879--302909 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
302869 CATCATAAAA
*
302879 AAAG AAAG GAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
302910 TGATCATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:303998 original size:17 final size:17
Alignment explanation
Indices: 303976--304009 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
303966 TATAATAAAC
303976 TTATGATAATTAAATTA
1 TTATGATAATTAAATTA
303993 TTATGATAATTAAATTA
1 TTATGATAATTAAATTA
304010 ATATAATTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (17 bp):
TTATGATAATTAAATTA
Found at i:304044 original size:51 final size:50
Alignment explanation
Indices: 303986--304083 Score: 153
Period size: 51 Copynumber: 1.9 Consensus size: 50
303976 TTATGATAAT
*
303986 TAAATTATTATGATAATTAAATTAATATAATTA-CTTTTTGAAATTTTATCA
1 TAAATTATTATGATAATCAAATTAATAT-ATTATCTTTTTG-AATTTTATCA
*
304037 TAAATTATTATGATAATCAAATTAATATATTATTTTTTTGAATTTTA
1 TAAATTATTATGATAATCAAATTAATATATTATCTTTTTGAATTTTA
304084 GTTTTATATT
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
50 11 0.25
51 33 0.75
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (50 bp):
TAAATTATTATGATAATCAAATTAATATATTATCTTTTTGAATTTTATCA
Found at i:304931 original size:20 final size:20
Alignment explanation
Indices: 304908--304951 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
304898 AATATCAAGT
*
304908 AGAAGCAAGCAATATAAAAC
1 AGAAGCAAACAATATAAAAC
304928 AGAAGCAAACAATATAAAAC
1 AGAAGCAAACAATATAAAAC
304948 AGAA
1 AGAA
304952 TAAAGCAGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.64, C:0.14, G:0.14, T:0.09
Consensus pattern (20 bp):
AGAAGCAAACAATATAAAAC
Found at i:307341 original size:51 final size:49
Alignment explanation
Indices: 307302--307481 Score: 186
Period size: 51 Copynumber: 3.6 Consensus size: 49
307292 TTTATATTAA
*
307302 TAAATTAATATATAGTTTATATATACTATATAGTTTATATATGCTAATGAAC
1 TAAA-TAATATATAGTTTATATATACTATATAGTTTATAT-T-TTAATGAAC
* **
307354 T--AT-ATATATAGTTGTATATACCATACTATATAGGTTATATACTAATGAAC
1 TAAATAATATATAGTT-TATAT---ATACTATATAGTTTATATTTTAATGAAC
* *
307404 TATATATTATATAGTTTATATATACTATATAGTTTATATATATTAATGAAC
1 TAAATAATATATAGTTTATATATACTATATAGTTTATAT-T-TTAATGAAC
* *
307455 TATATATTATATAGTTTATATATACTA
1 TAAATAATATATAGTTTATATATACTA
307482 ATGAACTATA
Statistics
Matches: 113, Mismatches: 6, Indels: 19
0.82 0.04 0.14
Matches are distributed among these distances:
48 10 0.09
49 23 0.20
50 11 0.10
51 35 0.31
52 25 0.22
53 9 0.08
ACGTcount: A:0.41, C:0.06, G:0.07, T:0.46
Consensus pattern (49 bp):
TAAATAATATATAGTTTATATATACTATATAGTTTATATTTTAATGAAC
Found at i:307459 original size:33 final size:33
Alignment explanation
Indices: 307422--307609 Score: 236
Period size: 33 Copynumber: 5.5 Consensus size: 33
307412 ATATAGTTTA
* *
307422 TATATACTATATAGTTTATATATATTAATGAAC
1 TATATAATATATAGTTTATATATACTAATGAAC
*
307455 TATATATTATATAGTTTATATATACTAATGAAC
1 TATATAATATATAGTTTATATATACTAATGAAC
307488 TATATAATATATAGTTTATATATACTAATGAAC
1 TATATAATATATAGTTTATATATACTAATGAAC
* *
307521 TATATATAATGTATAGTTTATATATA-TCATAT-AGTC
1 --TATATAATATATAGTTTATATATACT-A-ATGA-AC
*
307557 TATATATATCATATAGTTTATATATACTAATAAAC
1 TATATA-AT-ATATAGTTTATATATACTAATGAAC
*
307592 TATATAATGTATAGTTTA
1 TATATAATATATAGTTTA
307610 GGGTTTAGGA
Statistics
Matches: 138, Mismatches: 8, Indels: 18
0.84 0.05 0.11
Matches are distributed among these distances:
33 72 0.52
34 9 0.07
35 36 0.26
36 20 0.14
37 1 0.01
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (33 bp):
TATATAATATATAGTTTATATATACTAATGAAC
Found at i:307491 original size:26 final size:27
Alignment explanation
Indices: 307328--307528 Score: 86
Period size: 33 Copynumber: 7.2 Consensus size: 27
307318 TTATATATAC
*
307328 TATATAGTTTATATATGCTAATGAACTA
1 TATATAGTTTATATATACTAATGAAC-A
* *
307356 TATATA-TAGTTGTATATAC-CAT--AC-
1 TATATAGT--TTATATATACTAATGAACA
*
307380 TATATAG-GT-TATATACTAATGAAC-
1 TATATAGTTTATATATACTAATGAACA
*
307404 TATATA--TTATATAGT-TTATAT-ATAC-
1 TATATAGTTTATATA-TACTA-ATGA-ACA
*
307429 TATATAGTTTATATATATTAATGAACTATATA
1 TATATAGTTTATATATACTAATGAAC-----A
307461 TTATATAGTTTATATATACTAATGAACTATATAA
1 -TATATAGTTTATATATACTAATGAAC------A
307495 TATATAGTTTATATATACTAATGAACTA
1 TATATAGTTTATATATACTAATGAAC-A
307523 TATATA
1 TATATA
307529 ATGTATAGTT
Statistics
Matches: 137, Mismatches: 14, Indels: 44
0.70 0.07 0.23
Matches are distributed among these distances:
21 7 0.05
22 3 0.02
23 1 0.01
24 21 0.15
25 11 0.08
26 7 0.05
27 12 0.09
28 15 0.11
29 8 0.06
33 51 0.37
34 1 0.01
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.44
Consensus pattern (27 bp):
TATATAGTTTATATATACTAATGAACA
Found at i:307661 original size:7 final size:6
Alignment explanation
Indices: 307646--307759 Score: 61
Period size: 7 Copynumber: 17.7 Consensus size: 6
307636 GTATGTAAAT
* *
307646 TATACTA TATAGTA TATATA GTTTATA TATATA -ATATA TAGTATA TAAATA
1 TATA-TA TATA-TA TATATA -TATATA TATATA TATATA TA-TATA TATATA
* * * * *
307697 TAAACTA TAGTATG TAGTATA TAAATA TAAACTA TA-ATT TATATA TATAGTA
1 TATA-TA TA-TATA TA-TATA TATATA TATA-TA TATATA TATATA TATA-TA
307749 TATACTA TATA
1 TATA-TA TATA
307760 AATAGTGTAT
Statistics
Matches: 88, Mismatches: 11, Indels: 16
0.77 0.10 0.14
Matches are distributed among these distances:
5 8 0.09
6 29 0.33
7 50 0.57
8 1 0.01
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (6 bp):
TATATA
Found at i:307676 original size:20 final size:20
Alignment explanation
Indices: 307646--307772 Score: 95
Period size: 20 Copynumber: 6.3 Consensus size: 20
307636 GTATGTAAAT
307646 TATACTATATAGT-ATATATAG
1 TATA-TATATA-TAATATATAG
*
307667 TTTATATATATAATATATAG
1 TATATATATATAATATATAG
*
307687 TATATAAATATAA-ACTATAG
1 TATATATATATAATA-TATAG
* * *
307707 TATGTAGTATATAAATATAAAC
1 TATATA-TATAT-AATATATAG
*
307729 TATA-ATTTAT-ATATATAG
1 TATATATATATAATATATAG
307747 TATATACTATATAA-ATAGT-G
1 TATATA-TATATAATATA-TAG
307767 TATATA
1 TATATA
307773 GCTTACTGAT
Statistics
Matches: 85, Mismatches: 12, Indels: 19
0.73 0.10 0.16
Matches are distributed among these distances:
18 10 0.12
19 3 0.04
20 53 0.62
21 10 0.12
22 8 0.09
23 1 0.01
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (20 bp):
TATATATATATAATATATAG
Found at i:307816 original size:20 final size:20
Alignment explanation
Indices: 307791--307842 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
307781 ATAAACTATA
307791 TATATAGTTCATATGTAAAC
1 TATATAGTTCATATGTAAAC
*
307811 TATATAGTTTATATGTAAAC
1 TATATAGTTCATATGTAAAC
307831 --TATAGTTCATAT
1 TATATAGTTCATAT
307843 ATATAGTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 11 0.37
20 19 0.63
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (20 bp):
TATATAGTTCATATGTAAAC
Found at i:307846 original size:31 final size:33
Alignment explanation
Indices: 307826--307959 Score: 109
Period size: 33 Copynumber: 4.2 Consensus size: 33
307816 AGTTTATATG
307826 TAAACTATAGTTCATATATATAGTATATAAATA
1 TAAACTATAGTTCATATATATAGTATATAAATA
* *
307859 TAAACTATAGTTTATATAAATAGTATA-AAATA
1 TAAACTATAGTTCATATATATAGTATATAAATA
* * * *
307891 TAGTA-TGTAGTTTATATAAATATA-AATATAAATA
1 TA-AACTATAGTTCATAT--ATATAGTATATAAATA
** * *
307925 TAAA-TATAAAT-ATAAATATA-AATATAAATA
1 TAAACTATAGTTCATATATATAGTATATAAATA
307955 TAAAC
1 TAAAC
307960 CCTAAACCAT
Statistics
Matches: 85, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
30 19 0.22
32 21 0.25
33 34 0.40
34 11 0.13
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.37
Consensus pattern (33 bp):
TAAACTATAGTTCATATATATAGTATATAAATA
Found at i:307852 original size:18 final size:17
Alignment explanation
Indices: 307787--307852 Score: 51
Period size: 18 Copynumber: 3.6 Consensus size: 17
307777 ACTGATAAAC
307787 TATATATATAGTTCATA
1 TATATATATAGTTCATA
* *
307804 TGTAAACTATATAGTTTATA
1 --TATA-TATATAGTTCATA
* *
307824 TGTAAACTATAGTTCATA
1 TATATA-TATAGTTCATA
307842 TATATAGTATA
1 TATATA-TATA
307853 TAAATATAAA
Statistics
Matches: 36, Mismatches: 9, Indels: 5
0.72 0.18 0.10
Matches are distributed among these distances:
17 1 0.03
18 20 0.56
19 3 0.08
20 12 0.33
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (17 bp):
TATATATATAGTTCATA
Found at i:307854 original size:20 final size:19
Alignment explanation
Indices: 307787--307854 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 19
307777 ACTGATAAAC
*
307787 TATATATATAGTTCATATG
1 TATATATATAGTTCATATA
*
307806 TAAACTATATAGTT--TATA
1 TATA-TATATAGTTCATATA
* *
307824 TGTAAACTATAGTTCATATA
1 TATATA-TATAGTTCATATA
307844 TATAGTATATA
1 TATA-TATATA
307855 AATATAAACT
Statistics
Matches: 37, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
17 1 0.03
18 12 0.32
19 3 0.08
20 20 0.54
21 1 0.03
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (19 bp):
TATATATATAGTTCATATA
Found at i:307902 original size:32 final size:33
Alignment explanation
Indices: 307826--307932 Score: 123
Period size: 33 Copynumber: 3.3 Consensus size: 33
307816 AGTTTATATG
* *
307826 TAAACTATAGTTCATATATATAGTATATAAATA
1 TAAACTATAGTTTATATAAATAGTATATAAATA
307859 TAAACTATAGTTTATATAAATAGTATA-AAATA
1 TAAACTATAGTTTATATAAATAGTATATAAATA
* *
307891 TAGTA-TGTAGTTTATATAAATA-TAAATATAAATA
1 TA-AACTATAGTTTATATAAATAGT--ATATAAATA
307925 TAAA-TATA
1 TAAACTATA
307933 AATATAAATA
Statistics
Matches: 64, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
31 1 0.02
32 23 0.36
33 33 0.52
34 7 0.11
ACGTcount: A:0.51, C:0.03, G:0.07, T:0.39
Consensus pattern (33 bp):
TAAACTATAGTTTATATAAATAGTATATAAATA
Found at i:307915 original size:6 final size:6
Alignment explanation
Indices: 307904--307958 Score: 110
Period size: 6 Copynumber: 9.2 Consensus size: 6
307894 TATGTAGTTT
307904 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
307952 ATATAA A
1 ATATAA A
307959 CCCTAAACCA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
ATATAA
Found at i:308001 original size:20 final size:20
Alignment explanation
Indices: 307978--308292 Score: 114
Period size: 20 Copynumber: 15.4 Consensus size: 20
307968 ATATATACTC
307978 TATATATAAACTATATAATT
1 TATATATAAACTATATAATT
*
307998 TATATTAATCAACTATATAATT
1 TATA-T-ATAAACTATATAATT
* * *
308020 TATACA-ATA-TATATTATT
1 TATATATAAACTATATAATT
* *
308038 TATA-ATTATAC-ATA-ATATA
1 TATATA-TAAACTATATA-ATT
* * * *
308057 TAAATATAAATTGTATAGTT
1 TATATATAAACTATATAATT
*
308077 TATATATAATTCATATATAA-T
1 TATATATAA-AC-TATATAATT
* *
308098 T-TATATAAACTATGTAGTT
1 TATATATAAACTATATAATT
* ** *
308117 TCTATAT-AGTTCA-ATAGTT
1 TATATATAAACT-ATATAATT
* * *
308136 CATAAATAAACTATATAGTAT
1 TATATATAAACTATATAAT-T
* * *
308157 TATACTTTATACTTTATACATAATA
1 TATA-TATAAAC--TAT--ATAATT
*
308182 TATATATAAACTATATAGTT
1 TATATATAAACTATATAATT
*
308202 TATATATATAA-TACATATAGTT
1 TATATATA-AACT--ATATAATT
308224 TATATATAATAC-ATATAATT
1 TATATATAA-ACTATATAATT
* *
308244 TATATATAAACTCTATAGTT
1 TATATATAAACTATATAATT
* *
308264 TATATTATATA-TATATATATA
1 TATA-TATAAACTATATA-ATT
308285 TATATATA
1 TATATATA
308293 TATATATATA
Statistics
Matches: 219, Mismatches: 46, Indels: 60
0.67 0.14 0.18
Matches are distributed among these distances:
17 1 0.00
18 17 0.08
19 32 0.15
20 85 0.39
21 21 0.10
22 47 0.21
24 8 0.04
25 4 0.02
26 4 0.02
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (20 bp):
TATATATAAACTATATAATT
Found at i:308095 original size:22 final size:22
Alignment explanation
Indices: 308070--308309 Score: 86
Period size: 22 Copynumber: 11.3 Consensus size: 22
308060 ATATAAATTG
308070 TATAGTTTATATATAATTCATA
1 TATAGTTTATATATAATTCATA
*
308092 TATAATTTATATA-AA--C-TA
1 TATAGTTTATATATAATTCATA
* * *
308110 TGTAGTTTCTATATAGTTC--A
1 TATAGTTTATATATAATTCATA
* * *
308130 -ATAGTTCATAAATAA-AC-TA
1 TATAGTTTATATATAATTCATA
* *
308149 TATAGTATTATACTTTATACTTTATA
1 TATAGT-TTATA---TATAATTCATA
* * * *
308175 CATAATATATATATAA-AC-TA
1 TATAGTTTATATATAATTCATA
* *
308195 TATAGTTTATATATATAAT-ACA
1 TATAGTTTATATATA-ATTCATA
*
308217 TATAGTTTATATATAATACATA
1 TATAGTTTATATATAATTCATA
* *
308239 TA-A-TTTATATATAA-AC-TC
1 TATAGTTTATATATAATTCATA
308257 TATAGTTTATATTATATATAT-ATA
1 TATAGTTTATA-TATA-AT-TCATA
*
308281 TATA-TATATATATATATAT-ATA
1 TATAGTTTATATATA-AT-TCATA
308303 TATAGTT
1 TATAGTT
308310 GTTTTAATTT
Statistics
Matches: 160, Mismatches: 35, Indels: 45
0.67 0.15 0.19
Matches are distributed among these distances:
18 16 0.10
19 16 0.10
20 37 0.23
21 14 0.09
22 53 0.33
23 6 0.04
24 8 0.05
25 4 0.03
26 6 0.04
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (22 bp):
TATAGTTTATATATAATTCATA
Found at i:308102 original size:9 final size:10
Alignment explanation
Indices: 308026--308105 Score: 51
Period size: 9 Copynumber: 7.8 Consensus size: 10
308016 AATTTATACA
308026 ATATAT-ATT
1 ATATATAATT
*
308035 ATTTATAATT
1 ATATATAATT
*
308045 ATACATAATAT
1 ATATATAAT-T
308056 ATAAATATAAATT
1 AT--ATAT-AATT
*
308069 GTATAGT--TT
1 ATATA-TAATT
308078 ATATATAATT
1 ATATATAATT
308088 CATATATAATT
1 -ATATATAATT
308099 -TATATAA
1 ATATATAA
308106 ACTATGTAGT
Statistics
Matches: 56, Mismatches: 6, Indels: 18
0.70 0.08 0.22
Matches are distributed among these distances:
8 1 0.02
9 18 0.32
10 12 0.21
11 16 0.29
12 1 0.02
13 5 0.09
14 3 0.05
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (10 bp):
ATATATAATT
Found at i:308186 original size:2 final size:2
Alignment explanation
Indices: 308179--308306 Score: 102
Period size: 2 Copynumber: 63.5 Consensus size: 2
308169 TTTATACATA
* * *
308179 AT AT AT AT AT AA ACT AT AT AGT TT AT AT AT AT A- AT AC AT AT AGT
1 AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T
* * * * * *
308223 TT AT AT AT A- AT AC AT AT A- AT TT AT AT AT AA ACT CT AT AGT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT
308265 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
308306 A
1 A
308307 GTTGTTTTAA
Statistics
Matches: 99, Mismatches: 18, Indels: 18
0.73 0.13 0.13
Matches are distributed among these distances:
1 4 0.04
2 91 0.92
3 4 0.04
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:308248 original size:9 final size:9
Alignment explanation
Indices: 308203--308306 Score: 68
Period size: 9 Copynumber: 11.0 Consensus size: 9
308193 TATATAGTTT
308203 ATATATATA
1 ATATATATA
*
308212 ATACATATA
1 ATATATATA
*
308221 GTTTATATATA
1 --ATATATATA
*
308232 ATACATATA
1 ATATATATA
308241 ATTTATATATA
1 A--TATATATA
*
308252 A-ACTCTATA
1 ATA-TATATA
* * *
308261 GTTTATATT
1 ATATATATA
308270 ATATATAT-
1 ATATATATA
308278 ATATATATA
1 ATATATATA
308287 TATATATATA
1 -ATATATATA
308297 TATATATATA
1 -ATATATATA
308307 GTTGTTTTAA
Statistics
Matches: 74, Mismatches: 13, Indels: 15
0.73 0.13 0.15
Matches are distributed among these distances:
8 9 0.12
9 31 0.42
10 19 0.26
11 15 0.20
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (9 bp):
ATATATATA
Found at i:308921 original size:217 final size:217
Alignment explanation
Indices: 308460--309138 Score: 1116
Period size: 217 Copynumber: 3.1 Consensus size: 217
308450 TTGTTTAATA
**
308460 TTTT-TTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGCACCTGAAATTGAT
1 TTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGCATATGAAATTGAT
* *
308524 CTATACTTATTACTTATTTCTATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATCTAGT
66 CCATACTTATTACTTATTTCTATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGT
* * * *
308589 A-TTTTTTTTTATTAATTTCAACATCATAATTTCAAATTATTTCGATTGGATCCCTCATCAATGT
131 ACTTTTTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGT
* *
308653 GTGTTGTTTAATATATTTAATT
196 GTGTTGTTTAATTTATTTAAAT
* * *
308675 TTTTATTTGTAATTTCATATTTATTCAATTTATTCCTCCAAATTTTATTTGCATATGAAATTGAC
1 TTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGCATATGAAATTGAT
* *
308740 CCATACTTATTACTTATTTATATTTTTAAATTGACCCATAACTTTTTAAATGGGTATAATTTAGT
66 CCATACTTATTACTTATTTCTATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGT
308805 ACTTTTTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGT
131 ACTTTTTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGT
308870 GTGTTGTTTAATTTATTTAAAT
196 GTGTTGTTTAATTTATTTAAAT
308892 TTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGCATATGAAATTGAT
1 TTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGCATATGAAATTGAT
* * * * *
308957 CCATAGTTATTACTTAATTCTATTTTTTAATTGGCCCATAACTTTTTAAATCGGTATAATTCAGT
66 CCATACTTATTACTTATTTCTATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGT
* *
309022 AC--TTTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCGATTTGATCCCTCGTCATTGT
131 ACTTTTTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGT
309085 GTGTTGTTTAATTTATTTAAAT
196 GTGTTGTTTAATTTATTTAAAT
309107 TTTTATTTGTAATTTCATATTT-TGTCAATTTA
1 TTTTATTTGTAATTTCATATTTGT-TCAATTTA
309139 ATTCTTAAAT
Statistics
Matches: 434, Mismatches: 27, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
214 1 0.00
215 115 0.26
216 117 0.27
217 201 0.46
ACGTcount: A:0.29, C:0.13, G:0.08, T:0.50
Consensus pattern (217 bp):
TTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGCATATGAAATTGAT
CCATACTTATTACTTATTTCTATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGT
ACTTTTTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGT
GTGTTGTTTAATTTATTTAAAT
Found at i:309277 original size:433 final size:429
Alignment explanation
Indices: 308460--309277 Score: 942
Period size: 433 Copynumber: 1.9 Consensus size: 429
308450 TTGTTTAATA
*
308460 TTTTTTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGCACCTGAAATTGATC
1 TTTTTTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGCACATGAAATTGATC
* * *
308525 TATACTTATTACTTATTTCTATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATCTAGTA
66 CATACTTATTACTTAATTCTATTTTTAAATTGGCCCATAACTTTTTAAATCGGTATAATCTAGTA
* * * *
308590 TTTTTTTTTATTAATTTCAACATCATAATTTCAAATTATTTCGATTGGATCCCTCATCAATGTGT
131 TCTTTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCGATTGGATCCCTCATCAATGTGT
*
308655 GTTGTTTAATATATTTAATTTTTTATTTGTAATTTCATATTTATTCAATTTATTCCTCCAAATTT
196 GTTGTTTAATATATTTAAATTTTTATTTGTAATTTCATATTTATTCAATTTATTCCTCCAAATTT
* * * * * * *
308720 TATTTGCATATGAAATTGACCCATACTTATTACTTATTTATATTTTTAAATTGACCCATAACTTT
261 TATTTGCATA-GAAATTGAACCATACTTATTAATTATTAATATATTTAAATTAAACCATAACATT
** ** * ******* * * * * *
308785 TTAAATGGGTATAATTTAGTACTTTTTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCG
325 ACAAATGGCAATAAGTTAG-ACGAAAGACGAAATAATTTCAACA-CAAAAATAAAAATTATTTCG
308850 ATTTGATCCCTCATCAATGTGTGTTGTTTAATTTATTTAAAT
388 ATTTGATCCCTCATCAATGTGTGTTGTTTAATTTATTTAAAT
*
308892 TTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGCATATGAAATTGAT
1 TTTT-TTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGCACATGAAATTGAT
* *
308957 CCATAGTTATTACTTAATTCTATTTTTTAATTGGCCCATAACTTTTTAAATCGGTATAAT-TCAG
65 CCATACTTATTACTTAATTCTATTTTTAAATTGGCCCATAACTTTTTAAATCGGTATAATCT-AG
* * *
309021 TA-CTTTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCGATTTGATCCCTCGTCATTGT
129 TATCTTTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCGATTGGATCCCTCATCAATGT
* *
309085 GTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTT-TGTCAATTTAATT-CT-TAA
194 GTGTTGTTTAATATATTTAAATTTTTATTTGTAATTTCATATTTAT-TCAATTT-ATTCCTCCAA
* * * *
309147 ATTTGTATTTTTCATA-AAATTGAACTATGA-TTATTTATATTCTTAATA-ATTT-ACTCTAAAC
257 ATTT-TA-TTTGCATAGAAATTGAACCAT-ACTTA-TTA-ATTATTAATATATTTAAAT-TAAAC
* *
309208 CATATACAATTACAAATTGCAATTCAACGTTCG-CGAAAGACGAAAATAA-TT-AATC-CAAAAA
316 CATA-AC-ATTACAAATGGCAA-T-AA-GTTAGACGAAAGACG-AAATAATTTCAA-CACAAAAA
309269 TAAAAATTA
374 TAAAAATTA
309278 ACCCGATTTG
Statistics
Matches: 322, Mismatches: 47, Indels: 33
0.80 0.12 0.08
Matches are distributed among these distances:
431 22 0.07
432 127 0.39
433 148 0.46
434 10 0.03
435 6 0.02
436 6 0.02
437 3 0.01
ACGTcount: A:0.31, C:0.13, G:0.08, T:0.48
Consensus pattern (429 bp):
TTTTTTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGCACATGAAATTGATC
CATACTTATTACTTAATTCTATTTTTAAATTGGCCCATAACTTTTTAAATCGGTATAATCTAGTA
TCTTTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCGATTGGATCCCTCATCAATGTGT
GTTGTTTAATATATTTAAATTTTTATTTGTAATTTCATATTTATTCAATTTATTCCTCCAAATTT
TATTTGCATAGAAATTGAACCATACTTATTAATTATTAATATATTTAAATTAAACCATAACATTA
CAAATGGCAATAAGTTAGACGAAAGACGAAATAATTTCAACACAAAAATAAAAATTATTTCGATT
TGATCCCTCATCAATGTGTGTTGTTTAATTTATTTAAAT
Found at i:314031 original size:19 final size:19
Alignment explanation
Indices: 314007--314044 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
313997 AACTAGTCCA
314007 AAATCAACATTTCAATATT
1 AAATCAACATTTCAATATT
* *
314026 AAATCAATATTTTAATATT
1 AAATCAACATTTCAATATT
314045 CGATTCCAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATCAACATTTCAATATT
Found at i:315610 original size:23 final size:23
Alignment explanation
Indices: 315577--315629 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
315567 TCCCGAAGGA
315577 CCACATAGGTTTGCACCAAAGTG
1 CCACATAGGTTTGCACCAAAGTG
* * *
315600 CCACATGGGTTTGCATCGAAGTG
1 CCACATAGGTTTGCACCAAAGTG
315623 CCACATA
1 CCACATA
315630 TTTGTCACGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.23
Consensus pattern (23 bp):
CCACATAGGTTTGCACCAAAGTG
Found at i:315647 original size:21 final size:21
Alignment explanation
Indices: 315623--315671 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
315613 CATCGAAGTG
*
315623 CCACATATTTGT-CACGGAGGA
1 CCACATATTTGTCCA-GAAGGA
315644 CCACATATTTGTCCAGAAGGA
1 CCACATATTTGTCCAGAAGGA
315665 CCACATA
1 CCACATA
315672 AGACCATCGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (21 bp):
CCACATATTTGTCCAGAAGGA
Found at i:316300 original size:53 final size:51
Alignment explanation
Indices: 316218--316357 Score: 176
Period size: 53 Copynumber: 2.7 Consensus size: 51
316208 GATACTTCAC
* * *
316218 TTCAAGAGTATTGATACCTCCTCATGGTACCGATACCAAAATAGCATTCGA
1 TTCAAGGGTATCGATACCTCCTCAAGGTACCGATACCAAAATAGCATTCGA
* *
316269 TGTTCAAGGGTATCGATACCTCCTCAAGGTACCGATACCAATATGGCATTCGA
1 --TTCAAGGGTATCGATACCTCCTCAAGGTACCGATACCAAAATAGCATTCGA
*
316322 TTC-AGGGTATCGATACCATCCTTC-AGGTATCGATAC
1 TTCAAGGGTATCGATACC-TCC-TCAAGGTACCGATAC
316358 TACCCCTTAC
Statistics
Matches: 79, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
50 14 0.18
51 17 0.22
52 2 0.03
53 46 0.58
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (51 bp):
TTCAAGGGTATCGATACCTCCTCAAGGTACCGATACCAAAATAGCATTCGA
Found at i:316365 original size:21 final size:21
Alignment explanation
Indices: 316322--316404 Score: 55
Period size: 21 Copynumber: 4.0 Consensus size: 21
316312 TGGCATTCGA
* *
316322 TTCAGGGTATCGATACCA-TCC
1 TTCA-GGTATCGATACTACCCC
316343 TTCAGGTATCGATACTACCCC
1 TTCAGGTATCGATACTACCCC
* **
316364 TTACA-TTATCGATACCT-CTTC
1 TT-CAGGTATCGATA-CTACCCC
**
316385 AACAGGTATCGATACTACCC
1 TTCAGGTATCGATACTACCC
316405 TTACAAAATA
Statistics
Matches: 47, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
20 16 0.34
21 27 0.57
22 4 0.09
ACGTcount: A:0.27, C:0.30, G:0.13, T:0.30
Consensus pattern (21 bp):
TTCAGGTATCGATACTACCCC
Found at i:322600 original size:21 final size:21
Alignment explanation
Indices: 322574--322622 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
322564 CACCGAAGTG
322574 CCACATATTTGTCCTAG-AGGA
1 CCACATATTTGTCC-AGAAGGA
*
322595 CCACATATTTGTCCCGAAGGA
1 CCACATATTTGTCCAGAAGGA
322616 CCACATA
1 CCACATA
322623 ACACCCTCGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 1 0.04
21 25 0.96
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (21 bp):
CCACATATTTGTCCAGAAGGA
Found at i:323235 original size:53 final size:54
Alignment explanation
Indices: 323132--323271 Score: 160
Period size: 53 Copynumber: 2.6 Consensus size: 54
323122 ATTTCCCTTT
* *
323132 AAGGGTATCGATACCTCCTCATGGTACCGATACCAAAATAACATTCGATG-TTC
1 AAGGGTATCGATACCTCCTCAAGGTATCGATACCAAAATAACATTCGATGTTTC
* * ** ** *
323185 AAGGGTATCGATACCTCCTCAAGGTATCGATATCGATCTGGCATTTGATGTTTC
1 AAGGGTATCGATACCTCCTCAAGGTATCGATACCAAAATAACATTCGATGTTTC
323239 AA-GGTATCGATACCATCCT-ATAGGTATCGATAC
1 AAGGGTATCGATACC-TCCTCA-AGGTATCGATAC
323272 TGCCCCTTAT
Statistics
Matches: 74, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
53 54 0.73
54 20 0.27
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.29
Consensus pattern (54 bp):
AAGGGTATCGATACCTCCTCAAGGTATCGATACCAAAATAACATTCGATGTTTC
Found at i:330603 original size:10 final size:10
Alignment explanation
Indices: 330590--330643 Score: 54
Period size: 10 Copynumber: 5.2 Consensus size: 10
330580 TATTTTTTTC
330590 AAAACAAAAAA
1 AAAAC-AAAAA
330601 AAAACAAAAA
1 AAAACAAAAA
*
330611 AAAGGCAAAAA
1 AAA-ACAAAAA
**
330622 AAGGCAAAAA
1 AAAACAAAAA
*
330632 AAAATAAAAA
1 AAAACAAAAA
330642 AA
1 AA
330644 TAAAAAAGCC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
10 24 0.65
11 13 0.35
ACGTcount: A:0.83, C:0.07, G:0.07, T:0.02
Consensus pattern (10 bp):
AAAACAAAAA
Found at i:330606 original size:11 final size:11
Alignment explanation
Indices: 330590--330623 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
330580 TATTTTTTTC
330590 AAAACAAAAAA
1 AAAACAAAAAA
330601 AAAACAAAAAA
1 AAAACAAAAAA
**
330612 AAGGCAAAAAA
1 AAAACAAAAAA
330623 A
1 A
330624 GGCAAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.85, C:0.09, G:0.06, T:0.00
Consensus pattern (11 bp):
AAAACAAAAAA
Found at i:330631 original size:11 final size:11
Alignment explanation
Indices: 330594--330634 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
330584 TTTTTCAAAA
**
330594 CAAAAAAAAAA
1 CAAAAAAAAGG
330605 CAAAAAAAAGG
1 CAAAAAAAAGG
330616 C-AAAAAAAGG
1 CAAAAAAAAGG
330626 CAAAAAAAA
1 CAAAAAAAA
330635 ATAAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
10 10 0.37
11 17 0.63
ACGTcount: A:0.80, C:0.10, G:0.10, T:0.00
Consensus pattern (11 bp):
CAAAAAAAAGG
Found at i:338923 original size:13 final size:14
Alignment explanation
Indices: 338905--338936 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
338895 TTAACATTCA
338905 AGTTTTTTT-TTTT
1 AGTTTTTTTATTTT
338918 AGTTTTTTTATTTT
1 AGTTTTTTTATTTT
338932 A-TTTT
1 AGTTTT
338937 GTAATTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.81
Consensus pattern (14 bp):
AGTTTTTTTATTTT
Found at i:339251 original size:19 final size:19
Alignment explanation
Indices: 339224--339271 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
339214 TAACTTTTTT
339224 TTTTATCTTTCATTATTAA-
1 TTTTATCTTTCATT-TTAAC
*
339243 TTTTCTCTTTCATTTTAAC
1 TTTTATCTTTCATTTTAAC
*
339262 TTTTACCTTT
1 TTTTATCTTT
339272 TCTCTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.19, C:0.17, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTATCTTTCATTTTAAC
Done.