Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000406.1 Hibiscus syriacus cultivar Beakdansim tig00000748_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: 62271
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:3199 original size:34 final size:34
Alignment explanation
Indices: 3101--3200 Score: 155
Period size: 34 Copynumber: 2.9 Consensus size: 34
3091 TTAACTTGAA
* *
3101 TTTAATGTTAAATTTCGAATACTATAATTTATAT
1 TTTAATTTTAAATTTCGAATACTATAATTTGTAT
* * *
3135 TTTAAATTTAAATTTCGAATAATATTATTTGTAT
1 TTTAATTTTAAATTTCGAATACTATAATTTGTAT
3169 TTTAATTTTAAATTTCGAATACTATAATTTGT
1 TTTAATTTTAAATTTCGAATACTATAATTTGT
3201 TAAAAACATT
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 58 1.00
ACGTcount: A:0.37, C:0.05, G:0.06, T:0.52
Consensus pattern (34 bp):
TTTAATTTTAAATTTCGAATACTATAATTTGTAT
Found at i:3756 original size:21 final size:21
Alignment explanation
Indices: 3705--3777 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
3695 ATATGGTATA
* *
3705 AACCCTGCGGTCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
3726 -AGCCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
3747 AACCCTGCGGGCTAGGAATGT
1 AACCCTGCGGGCTAGGAATGT
*
3768 AACCTTGCGG
1 AACCCTGCGG
3778 AGATGACATA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
20 4 0.09
21 37 0.82
22 4 0.09
ACGTcount: A:0.21, C:0.25, G:0.34, T:0.21
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:5604 original size:32 final size:29
Alignment explanation
Indices: 5532--5610 Score: 104
Period size: 30 Copynumber: 2.6 Consensus size: 29
5522 TTAATAAATT
*
5532 TAAATAAATAATAATTATAAATTATTTTAA
1 TAAA-AAATAATAATTATAAATTATATTAA
*
5562 TAAAAAATAATATTTATATAATTATATTAA
1 TAAAAAATAATAATTATA-AATTATATTAA
5592 TATAAAATATAATAATTAT
1 TA-AAAA-ATAATAATTAT
5611 TTAAAAAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
29 13 0.30
30 16 0.37
31 4 0.09
32 10 0.23
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (29 bp):
TAAAAAATAATAATTATAAATTATATTAA
Found at i:6108 original size:15 final size:15
Alignment explanation
Indices: 6088--6117 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
6078 AAAATCAATC
6088 AATCAAACATTCATT
1 AATCAAACATTCATT
6103 AATCAAACATTCATT
1 AATCAAACATTCATT
6118 GGTCACTCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (15 bp):
AATCAAACATTCATT
Found at i:7491 original size:6 final size:6
Alignment explanation
Indices: 7436--7490 Score: 101
Period size: 6 Copynumber: 9.2 Consensus size: 6
7426 ATTAATCTTC
7436 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
7484 TGTAAA T
1 TTTAAA T
7491 GGAGGAGACA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:17329 original size:23 final size:23
Alignment explanation
Indices: 17299--17348 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
17289 GCTAAAAATT
17299 TTGGGATATTTTGTTTGCTTGAG
1 TTGGGATATTTTGTTTGCTTGAG
17322 TTGGGATATTTTGTTTGCTTGAG
1 TTGGGATATTTTGTTTGCTTGAG
17345 TTGG
1 TTGG
17349 AGAAAGAGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.12, C:0.04, G:0.32, T:0.52
Consensus pattern (23 bp):
TTGGGATATTTTGTTTGCTTGAG
Found at i:17704 original size:2 final size:2
Alignment explanation
Indices: 17697--17745 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
17687 ATCATGCTAT
17697 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17739 TA TA TA T
1 TA TA TA T
17746 TAGGTATGAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:22217 original size:3 final size:3
Alignment explanation
Indices: 22209--22275 Score: 102
Period size: 3 Copynumber: 23.0 Consensus size: 3
22199 ACATGTATTA
* *
22209 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AGT TA- AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
22255 AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT
22276 TAAAATTAGA
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
2 3 0.05
3 55 0.95
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:22747 original size:129 final size:129
Alignment explanation
Indices: 22614--22988 Score: 662
Period size: 129 Copynumber: 2.9 Consensus size: 129
22604 AAAGGTGATA
* * * *
22614 ACACGGTTCCTACGTGATGAGGACG-GCTGGTCGGGGAATGACACGGCTCATACGTGATGAAGAG
1 ACACGGCTCCTACGTGATAAGGA-GATCTGGTCAGGGAATGACACGGCTCATACGTGATGAAGAG
22678 TTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTG
65 TTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTG
*
22743 ACACGGCTCCTACGTGATAAGGAGATCTGGTCTGGGAATGACACGGCTCATACGTGATGAAGAGT
1 ACACGGCTCCTACGTGATAAGGAGATCTGGTCAGGGAATGACACGGCTCATACGTGATGAAGAGT
*
22808 TCTGGCCATCTTAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTG
66 TCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTG
*
22872 ACACGGCTCCTACGTGATAAGGAGATCTGGCCAGGGAATGACACGGCTCATACGTGATGAAGAGT
1 ACACGGCTCCTACGTGATAAGGAGATCTGGTCAGGGAATGACACGGCTCATACGTGATGAAGAGT
*
22937 TCTGGCCAGCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGT
66 TCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGT
22989 CGGGGAATGA
Statistics
Matches: 236, Mismatches: 9, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
128 1 0.00
129 235 1.00
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (129 bp):
ACACGGCTCCTACGTGATAAGGAGATCTGGTCAGGGAATGACACGGCTCATACGTGATGAAGAGT
TCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTG
Found at i:22815 original size:215 final size:211
Alignment explanation
Indices: 22436--23156 Score: 802
Period size: 215 Copynumber: 3.4 Consensus size: 211
22426 TTGGTTGTTG
* * *
22436 GGGACGACACTGCTCATACGTGATGAAGAGTTCGGGTCGTCTAAGGG-TGACACGGTTCCTACGT
1 GGGATGACACGGCTCATACGTGATGAAGAGTTCTGG-C-TCTAAGGGATGACACGGTTCCTACGT
* * *
22500 GATGAGGAGATTTGGTCAACTGTGGTTGACACGGCTCCTACGTGATGAA-GAGATCTGGCCAGGG
64 GATGAGGAGATCTGGTCAACTATGGTTGACACGGCTCCTACGTGAT-AAGGAGATCTGGTCAGGG
*
22564 AATGACACGGCTCATACGTGATGAAGAGTTCTGGCCAGCTAAAGGTGATAACACGGTTCCTACGT
128 AATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGT
*
22629 GATGAGGACGGCTGGTC-G
193 GATGAGGACGGCTGGTCTA
*
22647 GGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTA
1 GGG-ATGACACGGCTCATACGTGATGAAGAGTTCTGG-C-TCT-AAGG-GATGACACGGTTCCTA
* * * *
22712 CGTGATGAGGACG-GCTGGTTATCTATGGTTGACACGGCTCCTACGTGATAAGGAGATCTGGTCT
61 CGTGATGAGGA-GATCTGGTCAACTATGGTTGACACGGCTCCTACGTGATAAGGAGATCTGGTCA
*
22776 GGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTTAAGGTGATAACACGGTTCCTA
125 GGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTA
22841 CGTGATGAGGACGGCTGGTTATCTA
190 CGTGATGAGGACGGCTGG---TCTA
* * * * * *
22866 TGGTTGACACGGCTCCTACGTGAT-AAGGAGATCTGGC-C--AGGGAATGACACGGCTCATACGT
1 GGGATGACACGGCTCATACGTGATGAA-GAGTTCTGGCTCTAAGGG-ATGACACGGTTCCTACGT
* * * * * * * * * *
22927 GATGAAGAGTTCTGGCCAGCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACG-GCTGGTCG
64 GATGAGGAGATCTGGTCAACT-ATGGT--TGACACGGCTCCTACGTGATAAGGA-GATCTGGTCA
22991 GGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTA
125 GGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTA
23056 CGTGATGAGGACGGCTGGTTATCTA
190 CGTGATGAGGACGGCTGG---TCTA
* * * * * *
23081 TGGTTGACACGGCTCCTACGTGAT-AAGGAGATCTGG-TCT--GGGAATGACACGGCTCATACGT
1 GGGATGACACGGCTCATACGTGATGAA-GAGTTCTGGCTCTAAGGG-ATGACACGGTTCCTACGT
* *
23142 GATGAAGAGTTCTGG
64 GATGAGGAGATCTGG
23157 CCATCTTAAG
Statistics
Matches: 456, Mismatches: 35, Indels: 34
0.87 0.07 0.06
Matches are distributed among these distances:
211 5 0.01
212 66 0.14
213 8 0.02
214 3 0.01
215 338 0.74
216 2 0.00
217 3 0.01
218 29 0.06
219 2 0.00
ACGTcount: A:0.25, C:0.20, G:0.32, T:0.24
Consensus pattern (211 bp):
GGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCTCTAAGGGATGACACGGTTCCTACGTGA
TGAGGAGATCTGGTCAACTATGGTTGACACGGCTCCTACGTGATAAGGAGATCTGGTCAGGGAAT
GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGAT
GAGGACGGCTGGTCTA
Found at i:23074 original size:86 final size:86
Alignment explanation
Indices: 22528--23074 Score: 552
Period size: 86 Copynumber: 6.4 Consensus size: 86
22518 ACTGTGGTTG
* * * *
22528 ACACGGCTCCTACGTGATGAAGA-GATCTGGCCAGGGAATGACACGGCTCATACGTGATGAAGAG
1 ACACGGTTCCTACGTGATGAGGACG-GCTGGTCAGGGAATGACACGGCTCATACGTGATGAAGAG
*
22592 TTCTGGCCAGCTAAAGGTGATA
65 TTCTGGCCATCTAAAGGTGATA
*
22614 ACACGGTTCCTACGTGATGAGGACGGCTGGTCGGGGAATGACACGGCTCATACGTGATGAAGAGT
1 ACACGGTTCCTACGTGATGAGGACGGCTGGTCAGGGAATGACACGGCTCATACGTGATGAAGAGT
22679 TCTGGCCATCTAAAGGTGATA
66 TCTGGCCATCTAAAGGTGATA
* * *
22700 ACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGG-TTGACACGGCTCCTACGTGAT-AA
1 ACACGGTTCCTACGTGATGAGGACGGCTGG---TC-AGGGAATGACACGGCTCATACGTGATGAA
* *
22763 GGAGATCTGG---TCT---GG-GAATG
62 -GAGTTCTGGCCATCTAAAGGTG-ATA
* * * * * * *
22783 ACACGGCTCATACGTGATGAAGA-GTTCTGGCCATCTTAAGGTG-ATAACACGGTTCCTACGTGA
1 ACACGGTTCCTACGTGATGAGGACG-GCTGG---TC---AGG-GAATGACACGGCTCATACGTGA
* * ** * *
22846 TGAGGACG-GCTGGTTATCT-ATGGT--TG
58 TGAAGA-GTTCTGGCCATCTAAAGGTGATA
* * * *
22872 ACACGGCTCCTACGTGATAAGGA-GATCTGGCCAGGGAATGACACGGCTCATACGTGATGAAGAG
1 ACACGGTTCCTACGTGATGAGGACG-GCTGGTCAGGGAATGACACGGCTCATACGTGATGAAGAG
*
22936 TTCTGGCCAGCTAAAGGTGATA
65 TTCTGGCCATCTAAAGGTGATA
*
22958 ACACGGTTCCTACGTGATGAGGACGGCTGGTCGGGGAATGACACGGCTCATACGTGATGAAGAGT
1 ACACGGTTCCTACGTGATGAGGACGGCTGGTCAGGGAATGACACGGCTCATACGTGATGAAGAGT
23023 TCTGGCCATCTAAAGGTGATA
66 TCTGGCCATCTAAAGGTGATA
23044 ACACGGTTCCTACGTGATGAGGACGGCTGGT
1 ACACGGTTCCTACGTGATGAGGACGGCTGGT
23075 TATCTATGGT
Statistics
Matches: 390, Mismatches: 46, Indels: 50
0.80 0.09 0.10
Matches are distributed among these distances:
82 4 0.01
83 63 0.16
84 4 0.01
85 2 0.01
86 247 0.63
87 4 0.01
88 2 0.01
89 60 0.15
90 2 0.01
91 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.23
Consensus pattern (86 bp):
ACACGGTTCCTACGTGATGAGGACGGCTGGTCAGGGAATGACACGGCTCATACGTGATGAAGAGT
TCTGGCCATCTAAAGGTGATA
Found at i:23091 original size:129 final size:129
Alignment explanation
Indices: 22958--23273 Score: 505
Period size: 129 Copynumber: 2.5 Consensus size: 129
22948 AAAGGTGATA
* *
22958 ACACGGTTCCTACGTGATGAGGACG-GCTGGTCGGGGAATGACACGGCTCATACGTGATGAAGAG
1 ACACGGCTCCTACGTGATAAGGA-GAGCTGGTCGGGGAATGACACGGCTCATACGTGATGAAGAG
23022 TTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTG
65 TTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTG
* *
23087 ACACGGCTCCTACGTGATAAGGAGATCTGGTCTGGGAATGACACGGCTCATACGTGATGAAGAGT
1 ACACGGCTCCTACGTGATAAGGAGAGCTGGTCGGGGAATGACACGGCTCATACGTGATGAAGAGT
*
23152 TCTGGCCATCTTAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTG
66 TCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTG
* * * *
23216 ACACGGCTCCTACGTGATAAGGAGA--TGGTCTGGGG-ATGATACGGTTCCTACATGATGA
1 ACACGGCTCCTACGTGATAAGGAGAGCTGGTC-GGGGAATGACACGGCTCATACGTGATGA
23274 GGACGGCTGG
Statistics
Matches: 175, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
127 24 0.14
128 4 0.02
129 147 0.84
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.25
Consensus pattern (129 bp):
ACACGGCTCCTACGTGATAAGGAGAGCTGGTCGGGGAATGACACGGCTCATACGTGATGAAGAGT
TCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTG
Found at i:23112 original size:344 final size:344
Alignment explanation
Indices: 22441--23241 Score: 1459
Period size: 344 Copynumber: 2.3 Consensus size: 344
22431 TGTTGGGGAC
* * * * *
22441 GACACTGCTCATACGTGATGAAGAGTTCGGGTCGTC-TAAGG-G-TGACACGGTTCCTACGTGAT
1 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTTAAGGTGATAACACGGTTCCTACGTGAT
** * * *
22503 GAGGA-GATTTGGTCAACTGTGGTTGACACGGCTCCTACGTGATGAA-GAGATCTGGCCAGGGAA
66 GAGGACG-GCTGGTTATCTATGGTTGACACGGCTCCTACGTGAT-AAGGAGATCTGGCCAGGGAA
22566 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCAGCTAAAGGTGATAACACGGTTCCTACGTGA
129 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCAGCTAAAGGTGATAACACGGTTCCTACGTGA
22631 TGAGGACGGCTGGTCGGGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGT
194 TGAGGACGGCTGGTCGGGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGT
22696 GATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACGTGAT
259 GATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACGTGAT
22761 AAGGAGATCTGGTCTGGGAAT
324 AAGGAGATCTGGTCTGGGAAT
22782 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTTAAGGTGATAACACGGTTCCTACGTGAT
1 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTTAAGGTGATAACACGGTTCCTACGTGAT
22847 GAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATAAGGAGATCTGGCCAGGGAATG
66 GAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATAAGGAGATCTGGCCAGGGAATG
22912 ACACGGCTCATACGTGATGAAGAGTTCTGGCCAGCTAAAGGTGATAACACGGTTCCTACGTGATG
131 ACACGGCTCATACGTGATGAAGAGTTCTGGCCAGCTAAAGGTGATAACACGGTTCCTACGTGATG
22977 AGGACGGCTGGTCGGGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGA
196 AGGACGGCTGGTCGGGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGA
23042 TAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATAA
261 TAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATAA
23107 GGAGATCTGGTCTGGGAAT
326 GGAGATCTGGTCTGGGAAT
23126 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTTAAGGTGATAACACGGTTCCTACGTGAT
1 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTTAAGGTGATAACACGGTTCCTACGTGAT
23191 GAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATAAGGAGAT
66 GAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATAAGGAGAT
23242 GGTCTGGGGA
Statistics
Matches: 445, Mismatches: 10, Indels: 7
0.96 0.02 0.02
Matches are distributed among these distances:
341 32 0.07
342 5 0.01
343 3 0.01
344 404 0.91
345 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (344 bp):
GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTTAAGGTGATAACACGGTTCCTACGTGAT
GAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATAAGGAGATCTGGCCAGGGAATG
ACACGGCTCATACGTGATGAAGAGTTCTGGCCAGCTAAAGGTGATAACACGGTTCCTACGTGATG
AGGACGGCTGGTCGGGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGA
TAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATAA
GGAGATCTGGTCTGGGAAT
Found at i:23157 original size:215 final size:214
Alignment explanation
Indices: 22528--23203 Score: 897
Period size: 215 Copynumber: 3.1 Consensus size: 214
22518 ACTGTGGTTG
* * *
22528 ACACGGCTCCTACGTGATGAAGAGATCTGGCCAGGGAATGACACGGCTCATACGTGATGAAGAGT
1 ACACGGCTCCTACGTGATGAGGAGAGCTGGTCAGGGAATGACACGGCTCATACGTGATGAAGAGT
* ** *
22593 TCTGGCCAGCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGG---TC-GGGGAATG
66 TCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGG-TTG
* * * * *
22654 ACACGGCTCATACGTGATGAA-GAGTTCTGGCCATCTAAAGGTG-ATAACACGGTTCCTACGTGA
130 ACACGGCTCCTACGTGAT-AAGGAGATCTGG---TCT---GG-GAATGACACGGCTCATACGTGA
* * ** * *
22717 TGAGGACG-GCTGGTTATCTATGGT--TG
187 TGAAGA-GTTCTGGCCATCTAAGGTGATA
* * *
22743 ACACGGCTCCTACGTGATAAGGAGATCTGGTCTGGGAATGACACGGCTCATACGTGATGAAGAGT
1 ACACGGCTCCTACGTGATGAGGAGAGCTGGTCAGGGAATGACACGGCTCATACGTGATGAAGAGT
*
22808 TCTGGCCATCTTAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGA
66 TCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGA
* *
22873 CACGGCTCCTACGTGATAAGGAGATCTGGCCAGGGAATGACACGGCTCATACGTGATGAAGAGTT
131 CACGGCTCCTACGTGATAAGGAGATCTGGTCTGGGAATGACACGGCTCATACGTGATGAAGAGTT
*
22938 CTGGCCAGCTAAAGGTGATA
196 CTGGCCATCT-AAGGTGATA
* *
22958 ACACGGTTCCTACGTGATGAGGACG-GCTGGTCGGGGAATGACACGGCTCATACGTGATGAAGAG
1 ACACGGCTCCTACGTGATGAGGA-GAGCTGGTCAGGGAATGACACGGCTCATACGTGATGAAGAG
23022 TTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTG
65 TTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTG
23087 ACACGGCTCCTACGTGATAAGGAGATCTGGTCTGGGAATGACACGGCTCATACGTGATGAAGAGT
130 ACACGGCTCCTACGTGATAAGGAGATCTGGTCTGGGAATGACACGGCTCATACGTGATGAAGAGT
23152 TCTGGCCATCTTAAGGTGATA
195 TCTGGCCATC-TAAGGTGATA
*
23173 ACACGGTTCCTACGTGATGAGGACG-GCTGGT
1 ACACGGCTCCTACGTGATGAGGA-GAGCTGGT
23204 TATCTATGGT
Statistics
Matches: 418, Mismatches: 31, Indels: 24
0.88 0.07 0.05
Matches are distributed among these distances:
211 2 0.00
212 31 0.07
213 4 0.01
215 346 0.83
216 2 0.00
217 2 0.00
218 29 0.07
219 2 0.00
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (214 bp):
ACACGGCTCCTACGTGATGAGGAGAGCTGGTCAGGGAATGACACGGCTCATACGTGATGAAGAGT
TCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGA
CACGGCTCCTACGTGATAAGGAGATCTGGTCTGGGAATGACACGGCTCATACGTGATGAAGAGTT
CTGGCCATCTAAGGTGATA
Found at i:23678 original size:35 final size:36
Alignment explanation
Indices: 23631--23713 Score: 100
Period size: 35 Copynumber: 2.3 Consensus size: 36
23621 ACAAAATTCA
**
23631 TTTCAAGAGAAAC-GATCTCAAAGAT-GTTTATTTTG
1 TTTCAAGAGAAACAGAT-TCAAAGATGGTAAATTTTG
*
23666 TTTCAAGGGAAACAGATTCAAAGATGGTAAATTTTG
1 TTTCAAGAGAAACAGATTCAAAGATGGTAAATTTTG
23702 TTTCCAA-AGAAA
1 TTT-CAAGAGAAA
23714 TAAACTCAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
35 20 0.49
36 18 0.44
37 3 0.07
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.33
Consensus pattern (36 bp):
TTTCAAGAGAAACAGATTCAAAGATGGTAAATTTTG
Found at i:23801 original size:28 final size:28
Alignment explanation
Indices: 23756--23819 Score: 101
Period size: 28 Copynumber: 2.2 Consensus size: 28
23746 GAGAGACACA
*
23756 ATTTTGTTTCAAAGGAAACAAACTCAAAG
1 ATTTT-TTTCAAAAGAAACAAACTCAAAG
*
23785 ATTTTTTTCAAAAGAAACAATCTCAAAG
1 ATTTTTTTCAAAAGAAACAAACTCAAAG
23813 ATTTTTT
1 ATTTTTT
23820 CACAAAATTG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
28 28 0.85
29 5 0.15
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.36
Consensus pattern (28 bp):
ATTTTTTTCAAAAGAAACAAACTCAAAG
Found at i:23817 original size:88 final size:89
Alignment explanation
Indices: 23696--23891 Score: 247
Period size: 88 Copynumber: 2.2 Consensus size: 89
23686 AAGATGGTAA
* * * **
23696 ATTTTGTTTCCAAAGAAATAAACTCAAAGATTTTTCTCA-AAGACTGTCTC-GAGAGACACAATT
1 ATTTT-TTTCAAAAGAAACAAACTCAAAGATTTTT-TCACAAAACTGTCTCAGAGAGACA-AAAC
23759 TTGTTTCAAAGGAAACA-A-ACTCAAAG
63 TTGTTTCAAAGGAAA-ATAGACTCAAAG
* *
23785 ATTTTTTTCAAAAGAAACAATCTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTT
1 ATTTTTTTCAAAAGAAACAAACTCAAAGATTTTTTCACAAAACTGTCTC-AGAGAGACAAAACTT
*
23850 GTTTCAAAGTAAAATAGACTCAAAG
65 GTTTCAAAGGAAAATAGACTCAAAG
23875 ATTTTTTTCAAAAGAAA
1 ATTTTTTTCAAAAGAAA
23892 TTGTCTTTAA
Statistics
Matches: 94, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
87 3 0.03
88 36 0.38
89 22 0.23
90 33 0.35
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.31
Consensus pattern (89 bp):
ATTTTTTTCAAAAGAAACAAACTCAAAGATTTTTTCACAAAACTGTCTCAGAGAGACAAAACTTG
TTTCAAAGGAAAATAGACTCAAAG
Found at i:24209 original size:66 final size:67
Alignment explanation
Indices: 24092--24336 Score: 270
Period size: 66 Copynumber: 3.7 Consensus size: 67
24082 ACTCAAAGAT
* * ** * *
24092 TTTCAAAATG-AACATATTCAAAGA--TTTGCTTCAAAAGAAACGGTCTCAAGAGATACAAAATT
1 TTTCAAAA-GAAACAAATTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGACAAAATT
24154 CAT-
65 -ATG
* * * *
24157 TTT-AAGAGAAACAGATTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTT
1 TTTCAAAAGAAACAAATTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGACAAAATTA
24221 TG
66 TG
* *
24223 TTTCAAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAAAAATT
1 TTTCAAAAGAAACAAATTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAG-ACAAAATT
*
24288 TTG
65 ATG
* * *
24291 TTTCCAAAGAAACAAACTCAAAGA-TTTT-TTTCAAAAGAAACAATCT
1 TTTCAAAAGAAACAAATTCAAAGATTTTTGTTTCAAAAGAAACTATCT
24337 CAAAGATTTT
Statistics
Matches: 158, Mismatches: 16, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
63 1 0.01
64 16 0.10
65 4 0.03
66 52 0.33
67 52 0.33
68 33 0.21
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.30
Consensus pattern (67 bp):
TTTCAAAAGAAACAAATTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGACAAAATTA
TG
Found at i:24257 original size:67 final size:68
Alignment explanation
Indices: 24163--24336 Score: 273
Period size: 67 Copynumber: 2.6 Consensus size: 68
24153 TCATTTTAAG
* * * *
24163 AGAAACAGATTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAG-ACAAAATTTTGTTTC
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAAAAATTTTGTTTC
24227 AAA
66 AAA
24230 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAAAAATTTTGTTTC
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAAAAATTTTGTTTC
*
24295 CAA
66 AAA
*
24298 AGAAACAAACTCAAAGA-TTTT-TTTCAAAAGAAACAATCT
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAACTATCT
24337 CAAAGATTTT
Statistics
Matches: 100, Mismatches: 6, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
66 17 0.17
67 50 0.50
68 33 0.33
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.30
Consensus pattern (68 bp):
AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAAAAATTTTGTTTC
AAA
Found at i:24275 original size:29 final size:30
Alignment explanation
Indices: 24218--24352 Score: 123
Period size: 28 Copynumber: 4.3 Consensus size: 30
24208 AGAGACAAAA
24218 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
* * * *
24248 TTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAAAAA
1 TTTTGTTTCAAAAGAAACAAAC-TCA-A-AG-----AT
*
24286 TTTTGTTTCCAAAGAAACAAACTCAAAGA-
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
*
24315 TTTT-TTTCAAAAGAAACAATCTCAAAGAT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
24344 TTTT-TTTCA
1 TTTTGTTTCA
24353 CAAAATTGTC
Statistics
Matches: 86, Mismatches: 10, Indels: 19
0.75 0.09 0.17
Matches are distributed among these distances:
28 22 0.26
29 13 0.15
30 21 0.24
31 2 0.02
32 1 0.01
33 2 0.02
35 2 0.02
36 1 0.01
37 2 0.02
38 20 0.23
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.33
Consensus pattern (30 bp):
TTTTGTTTCAAAAGAAACAAACTCAAAGAT
Found at i:24588 original size:27 final size:28
Alignment explanation
Indices: 24448--24608 Score: 204
Period size: 29 Copynumber: 5.8 Consensus size: 28
24438 AAATAAATAG
* *
24448 ACTCAAAGA-TTT-TTCAAAAGAAAC-G
1 ACTCAAAGATTTTATTCAAAAGGAACAA
24473 ACTCAAAGATATTTATTCAAAAGGAACAA
1 ACTCAAAGAT-TTTATTCAAAAGGAACAA
*
24502 ACTCCAAGATTTTTATTCAAAAGGAACAA
1 ACTCAAAGA-TTTTATTCAAAAGGAACAA
*
24531 ACTCCAAGATTTTTATTCAAAAGGAACAA
1 ACTCAAAGA-TTTTATTCAAAAGGAACAA
* *
24560 ACTCAAAGATTTT-TTCAAGAGGAAAAA
1 ACTCAAAGATTTTATTCAAAAGGAACAA
*
24587 ACTCAAAGATTTTTTTCAAAAG
1 ACTCAAAGATTTTATTCAAAAG
24609 AAATTGTCTT
Statistics
Matches: 123, Mismatches: 7, Indels: 9
0.88 0.05 0.06
Matches are distributed among these distances:
25 9 0.07
27 28 0.23
28 22 0.18
29 63 0.51
30 1 0.01
ACGTcount: A:0.47, C:0.15, G:0.11, T:0.27
Consensus pattern (28 bp):
ACTCAAAGATTTTATTCAAAAGGAACAA
Found at i:24611 original size:27 final size:27
Alignment explanation
Indices: 24433--24611 Score: 166
Period size: 29 Copynumber: 6.4 Consensus size: 27
24423 CAAAACTTTG
* *
24433 TTTCAAAATAAATAGACTCAAAGA--TT
1 TTTCAAAAGAAA-AAACTCAAAGATTTT
**
24459 TTTCAAAAGAAACGACTCAAAGATATTT
1 TTTCAAAAGAAAAAACTCAAAGAT-TTT
* * *
24487 ATTCAAAAGGAACAAACTCCAAGATTTT
1 TTTCAAAA-GAAAAAACTCAAAGATTTT
* *
24515 TATTCAAAAGGAACAAACTCCAAGATTTT
1 T-TTCAAAA-GAAAAAACTCAAAGATTTT
*
24544 TATTCAAAAGGAACAAACTCAAAGA-TTT
1 T-TTCAAAA-GAAAAAACTCAAAGATTTT
*
24572 TTTCAAGAGGAAAAAACTCAAAGATTTT
1 TTTCAA-AAGAAAAAACTCAAAGATTTT
24600 TTTCAAAAGAAA
1 TTTCAAAAGAAA
24612 TTGTCTTTAA
Statistics
Matches: 134, Mismatches: 12, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
25 10 0.07
26 11 0.08
27 24 0.18
28 26 0.19
29 63 0.47
ACGTcount: A:0.48, C:0.14, G:0.11, T:0.27
Consensus pattern (27 bp):
TTTCAAAAGAAAAAACTCAAAGATTTT
Found at i:24934 original size:36 final size:36
Alignment explanation
Indices: 24850--24953 Score: 115
Period size: 36 Copynumber: 3.0 Consensus size: 36
24840 GAGAAAATGA
* * *
24850 TGTCTCAAGCGAGACGAAATTTG-CTTTA-AGATAC
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAC
* ** *
24884 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAC
*
24920 TGTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAA
24954 ACGATCTCAA
Statistics
Matches: 57, Mismatches: 11, Indels: 3
0.80 0.15 0.04
Matches are distributed among these distances:
34 19 0.33
35 10 0.18
36 28 0.49
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAC
Found at i:24981 original size:36 final size:36
Alignment explanation
Indices: 24851--24969 Score: 111
Period size: 36 Copynumber: 3.4 Consensus size: 36
24841 AGAAAATGAT
* * * *
24851 GTCTCAAGCGAGACGAAATTTG-CTTTA-AG-ATAC
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
* **
24884 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATT
1 -GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
* *
24921 GTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAAAC
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
24956 GATCTCAAGTGAGA
1 G-TCTCAAGTGAGA
24970 TCAACTTTGT
Statistics
Matches: 68, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
34 19 0.28
35 11 0.16
36 37 0.54
37 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.29
Consensus pattern (36 bp):
GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
Found at i:25108 original size:105 final size:102
Alignment explanation
Indices: 24921--25158 Score: 270
Period size: 105 Copynumber: 2.3 Consensus size: 102
24911 TAGAGAAATT
*
24921 GTCTCAAGCGAGAC-AAAGTTTGTTTTTGAGA-AAACGATCTCAAGTGAGATCAACTTTGTTTAA
1 GTCTCAAGCGAGACGAAA-TTTG-TTTTGAAATAAACGATCTCAAGTGAGATCAACTTTGTTTAA
* *
24984 TGCGAAACAAATTCGAAATTT-TGATCTCAAAGGGAAAAG
64 TGCGAAACAAATTCAAAATTTGT-ATCTCAAAGGAAAAAG
* *
25023 GTCTCAAGCGAGACGAAATTTGTTTTGAAATAAACAAGAATCT-AAGGTGAGATTAATTTTGTAT
1 GTCTCAAGCGAGACGAAATTTGTTTTGAAATAAAC--G-ATCTCAA-GTGAGATCAACTTTGT-T
* * * *
25087 TTA-GTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
61 TAATGCGAAACAAATTCAAAATTTGTATCTCAAAGGAAAAAG
* *
25128 GTCTCAAGCGAGACGCAATTTGTTTTAAAAT
1 GTCTCAAGCGAGACGAAATTTGTTTTGAAAT
25159 TTTCAAAATT
Statistics
Matches: 117, Mismatches: 11, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
101 7 0.06
102 22 0.19
103 3 0.03
104 3 0.03
105 78 0.67
106 4 0.03
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (102 bp):
GTCTCAAGCGAGACGAAATTTGTTTTGAAATAAACGATCTCAAGTGAGATCAACTTTGTTTAATG
CGAAACAAATTCAAAATTTGTATCTCAAAGGAAAAAG
Found at i:25257 original size:36 final size:37
Alignment explanation
Indices: 25173--25281 Score: 114
Period size: 38 Copynumber: 2.9 Consensus size: 37
25163 AAAATTTGTG
*
25173 GAAAAATGTCTCAAGCGAGACATAATTTG-TTTTAGA
1 GAAAAATGTCTCAAGCGAGACAAAATTTGTTTTTAGA
* *
25209 GAGAAAGTTGTCTCAAGCGAGATAAAATTTGTTTTTA-A
1 GA-AAA-ATGTCTCAAGCGAGACAAAATTTGTTTTTAGA
* * * *
25247 GAAAACTGTCTCTAGTGAGACGAAACTTTGTTTTT
1 GAAAAATGTCTCAAGCGAGAC-AAAATTTGTTTTT
25282 TTAATAAGAT
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
36 14 0.23
37 18 0.30
38 24 0.39
39 5 0.08
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.34
Consensus pattern (37 bp):
GAAAAATGTCTCAAGCGAGACAAAATTTGTTTTTAGA
Found at i:25658 original size:12 final size:14
Alignment explanation
Indices: 25609--25662 Score: 76
Period size: 14 Copynumber: 3.9 Consensus size: 14
25599 TTTATGTATC
25609 ATGTATGTATGTGT
1 ATGTATGTATGTGT
25623 ATGTATGTATGTATGT
1 ATGTATGTATG--TGT
25639 ATGTATGTATGTGT
1 ATGTATGTATGTGT
25653 -TG-ATGTATGT
1 ATGTATGTATGT
25663 TTTTCTCGAG
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
12 8 0.21
13 2 0.05
14 14 0.37
16 14 0.37
ACGTcount: A:0.22, C:0.00, G:0.28, T:0.50
Consensus pattern (14 bp):
ATGTATGTATGTGT
Found at i:25662 original size:4 final size:4
Alignment explanation
Indices: 25609--25650 Score: 70
Period size: 4 Copynumber: 11.0 Consensus size: 4
25599 TTTATGTATC
25609 ATGT ATGT ATG- -TGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
25651 GTTGATGTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
4 34 0.94
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:26847 original size:13 final size:12
Alignment explanation
Indices: 26831--26881 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
26821 TCTTTGTCCT
26831 CTTTTGTTCTTTG
1 CTTTT-TTCTTTG
26844 C-TTTTTCTTTG
1 CTTTTTTCTTTG
*
26855 ATTTTTTGCTTTG
1 CTTTTTT-CTTTG
* *
26868 ATTTTCTCTTTG
1 CTTTTTTCTTTG
26880 CT
1 CT
26882 CTTTGTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
11 7 0.21
12 14 0.42
13 12 0.36
ACGTcount: A:0.04, C:0.16, G:0.12, T:0.69
Consensus pattern (12 bp):
CTTTTTTCTTTG
Found at i:26909 original size:31 final size:32
Alignment explanation
Indices: 26849--26911 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
26839 CTTTGCTTTT
**
26849 TCTTTGATTTTTTGCTTTGATTTTCTCTTTGC
1 TCTTTGATTTTTTGCTTTGATTTGATCTTTGC
* *
26881 TCTTTG-TTTTTTTCTTTGGTTTGATCTTTGC
1 TCTTTGATTTTTTGCTTTGATTTGATCTTTGC
26912 ACTCTGCGTC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
31 21 0.78
32 6 0.22
ACGTcount: A:0.05, C:0.14, G:0.14, T:0.67
Consensus pattern (32 bp):
TCTTTGATTTTTTGCTTTGATTTGATCTTTGC
Found at i:28183 original size:14 final size:13
Alignment explanation
Indices: 28138--28181 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
28128 GCATAAAAAT
*
28138 AAAATACAGATGC
1 AAAATGCAGATGC
28151 AAAATGCAAAGATGC
1 AAAATGC--AGATGC
28166 -AAATGCAGATGC
1 AAAATGCAGATGC
28178 AAAA
1 AAAA
28182 ATATTGATCC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 6 0.22
13 9 0.33
14 6 0.22
15 6 0.22
ACGTcount: A:0.55, C:0.14, G:0.18, T:0.14
Consensus pattern (13 bp):
AAAATGCAGATGC
Found at i:28669 original size:211 final size:210
Alignment explanation
Indices: 28305--28720 Score: 564
Period size: 211 Copynumber: 2.0 Consensus size: 210
28295 AGTAGATCGA
* * * *
28305 TGCTTCGTCTCGGATCTTCGTCCTTGAAAATAATGCCCCTCAATGATCTGTAATCTGACACCATT
1 TGCTTCGTCTCGGATCTTCGTACTTGAAAACAATGCCCCTCAATGATCTGTAAACTAACACCATT
* * * * *
28370 AATGCCCCGGCGGTGCTGAAGTCAGTGCGTCGCTCCTTGATGGATAGCGATGAAATAATTGTAGA
66 AATACCCCGGCGATGCTGAAGTCAGTGCGTCACTCCCTGATGGATAACGATGAAATAATTGTAGA
* *
28435 TGAGAATCTACTGTTGGATTACT-CTTCGGGATCAATGGATTATCATATCAGTCTCGAATGATGC
131 TGAGAATCTACTGCTGGATTACTCCTT--AGATCAATGGATTATCATATCAGTCTCGAATGATGC
28499 ACGATCTTCGAGCTCAC
194 ACGATCTTCGAGCTCAC
* * * * * * *
28516 TGCTTCGTCTCGGATCTTTGTACTTGGAACCGATGCCCCTCTATGCTCTGTAAACTAACTCCATT
1 TGCTTCGTCTCGGATCTTCGTACTTGAAAACAATGCCCCTCAATGATCTGTAAACTAACACCATT
* * ** * * * *
28581 AATACCTCGGCTATGCTGAAGTTTGTGCTTCACTCCCTGATGGTTAACGATGGAATAATTGTGGA
66 AATACCCCGGCGATGCTGAAGTCAGTGCGTCACTCCCTGATGGATAACGATGAAATAATTGTAGA
*
28646 TGAGAATCTACTGCTGGATTACTCCTTAGATCAGTGGATTATCATATCAGTCTCGAATGATGCAC
131 TGAGAATCTACTGCTGGATTACTCCTTAGATCAATGGATTATCATATCAGTCTCGAATGATGCAC
28711 GATCTTCGAG
196 GATCTTCGAG
28721 AAAATCTCAT
Statistics
Matches: 177, Mismatches: 27, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
210 46 0.26
211 128 0.72
212 3 0.02
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.32
Consensus pattern (210 bp):
TGCTTCGTCTCGGATCTTCGTACTTGAAAACAATGCCCCTCAATGATCTGTAAACTAACACCATT
AATACCCCGGCGATGCTGAAGTCAGTGCGTCACTCCCTGATGGATAACGATGAAATAATTGTAGA
TGAGAATCTACTGCTGGATTACTCCTTAGATCAATGGATTATCATATCAGTCTCGAATGATGCAC
GATCTTCGAGCTCAC
Found at i:28955 original size:31 final size:32
Alignment explanation
Indices: 28899--28960 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
28889 TGACAAAATG
28899 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
28931 ACACAAACAAAAGAGAA-AAATAAGTTAGTA
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTA
28961 CATGTAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.61, C:0.10, G:0.15, T:0.15
Consensus pattern (32 bp):
ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
Found at i:32523 original size:3 final size:3
Alignment explanation
Indices: 32515--32587 Score: 114
Period size: 3 Copynumber: 25.0 Consensus size: 3
32505 ACATGTATTA
* *
32515 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AGT TA- AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
32561 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
32588 TAAAATTAGA
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
2 3 0.05
3 61 0.95
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:32782 original size:27 final size:27
Alignment explanation
Indices: 32744--32802 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
32734 CAAGCCTTGA
32744 CAACTTTATATTCGGTTCCGGAATTTC
1 CAACTTTATATTCGGTTCCGGAATTTC
32771 CAACTTTATATTCGGTTCCGGAATTTC
1 CAACTTTATATTCGGTTCCGGAATTTC
32798 CAACT
1 CAACT
32803 ACGTCTATTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.39
Consensus pattern (27 bp):
CAACTTTATATTCGGTTCCGGAATTTC
Found at i:36172 original size:15 final size:15
Alignment explanation
Indices: 36147--36181 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
36137 ATAATTACAC
*
36147 ATTTA-ACATTTATT
1 ATTTATACATTTAAT
36161 ATTTATACATTTAAT
1 ATTTATACATTTAAT
36176 ATTTAT
1 ATTTAT
36182 TAAACCAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTTATACATTTAAT
Found at i:43634 original size:41 final size:39
Alignment explanation
Indices: 43589--43677 Score: 133
Period size: 41 Copynumber: 2.2 Consensus size: 39
43579 GATCTCAACT
43589 TCGCAACGATAATATGTAGATAGCAACGCGATTTTCCAAAA
1 TCGCAACG--AATATGTAGATAGCAACGCGATTTTCCAAAA
*
43630 TCGCAAACCGAATATGTAGATCGCAACGCGATTTTCCAAAA
1 TCGC-AA-CGAATATGTAGATAGCAACGCGATTTTCCAAAA
43671 TCGCAAC
1 TCGCAAC
43678 ACAGAAGTTA
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
39 1 0.02
40 2 0.04
41 38 0.84
42 2 0.04
43 2 0.04
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (39 bp):
TCGCAACGAATATGTAGATAGCAACGCGATTTTCCAAAA
Found at i:43675 original size:21 final size:21
Alignment explanation
Indices: 43611--43677 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
43601 TATGTAGATA
43611 GCAACGCGATTTTCCAAAATC
1 GCAACGCGATTTTCCAAAATC
* * ** *
43632 GCAAAC-CGAATAT-GTAGATC
1 GC-AACGCGATTTTCCAAAATC
43652 GCAACGCGATTTTCCAAAATC
1 GCAACGCGATTTTCCAAAATC
43673 GCAAC
1 GCAAC
43678 ACAGAAGTTA
Statistics
Matches: 33, Mismatches: 10, Indels: 6
0.67 0.20 0.12
Matches are distributed among these distances:
19 3 0.09
20 11 0.33
21 16 0.48
22 3 0.09
ACGTcount: A:0.36, C:0.27, G:0.16, T:0.21
Consensus pattern (21 bp):
GCAACGCGATTTTCCAAAATC
Found at i:43713 original size:21 final size:21
Alignment explanation
Indices: 43666--43717 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
43656 CGCGATTTTC
*
43666 CAAAATCGCAACACAGAAGTT
1 CAAATTCGCAACACAGAAGTT
* *
43687 -AAATTCGCAACACGGAATTT
1 CAAATTCGCAACACAGAAGTT
43707 CAAATTCGCAA
1 CAAATTCGCAA
43718 AGCGAATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.44, C:0.23, G:0.13, T:0.19
Consensus pattern (21 bp):
CAAATTCGCAACACAGAAGTT
Found at i:43817 original size:20 final size:20
Alignment explanation
Indices: 43750--43819 Score: 56
Period size: 20 Copynumber: 3.5 Consensus size: 20
43740 CAAGTTTCCT
* *
43750 TTTCGCAACAAGATTTTCTAA
1 TTTCGCAACACGAATTT-TAA
* *
43771 -ATCGCAACTCG-ATTTTCAAA
1 TTTCGCAACACGAATTTT--AA
43791 TTT-GCAACACGAATTTTAA
1 TTTCGCAACACGAATTTTAA
43810 TTTCGCAACA
1 TTTCGCAACA
43820 ACTTTTATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 11
0.69 0.11 0.20
Matches are distributed among these distances:
18 1 0.03
19 8 0.21
20 23 0.61
21 6 0.16
ACGTcount: A:0.34, C:0.21, G:0.10, T:0.34
Consensus pattern (20 bp):
TTTCGCAACACGAATTTTAA
Found at i:43997 original size:16 final size:16
Alignment explanation
Indices: 43976--44014 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
43966 TCCCCATCTC
*
43976 AATTTTTTTTTTACAT
1 AATTTTTTTTCTACAT
* *
43992 AATTTTATTTCTATAT
1 AATTTTTTTTCTACAT
44008 AATTTTT
1 AATTTTT
44015 CAATGATTTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (16 bp):
AATTTTTTTTCTACAT
Found at i:44778 original size:23 final size:24
Alignment explanation
Indices: 44727--44803 Score: 129
Period size: 24 Copynumber: 3.2 Consensus size: 24
44717 GTATTCGAAA
44727 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
44751 TTTGATCTTGGTCAATACCC-GAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
44774 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
44798 TTTGAT
1 TTTGAT
44804 GATGTTTCAT
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
23 22 0.44
24 28 0.56
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.39
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:47451 original size:20 final size:20
Alignment explanation
Indices: 47380--47447 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
47370 ATGTACACTT
*
47380 TCGCAATGCAAAAGTCAAAA
1 TCGCAATGCGAAAGTCAAAA
* * *
47400 TTGCAATGCGAAAATCAAAC
1 TCGCAATGCGAAAGTCAAAA
* *
47420 TCGCAACGTGAAAGTCAAAA
1 TCGCAATGCGAAAGTCAAAA
47440 TCGCAATG
1 TCGCAATG
47448 TGAATTTGAC
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.44, C:0.21, G:0.18, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAAAGTCAAAA
Found at i:47538 original size:16 final size:16
Alignment explanation
Indices: 47517--47552 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
47507 TGCAGAGTGA
* *
47517 AATTAAACAACAAATC
1 AATTAAACAAAAAAAC
47533 AATTAAACAAAAAAAC
1 AATTAAACAAAAAAAC
47549 AATT
1 AATT
47553 CTTATTTACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.67, C:0.14, G:0.00, T:0.19
Consensus pattern (16 bp):
AATTAAACAAAAAAAC
Found at i:47690 original size:20 final size:20
Alignment explanation
Indices: 47667--47711 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
47657 AAATCGCAAC
* *
47667 GCGAATTTGACTTTCGCGTT
1 GCGAATTTGAATTTCACGTT
*
47687 GCGATTTTGAATTTCACGTT
1 GCGAATTTGAATTTCACGTT
47707 GCGAA
1 GCGAA
47712 AGTGTACCTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (20 bp):
GCGAATTTGAATTTCACGTT
Found at i:49216 original size:21 final size:20
Alignment explanation
Indices: 49190--49304 Score: 88
Period size: 21 Copynumber: 5.5 Consensus size: 20
49180 GTGAATCGGG
*
49190 CTCTTGAACGGTGGGAGGAAC
1 CTCTTGAACGGTGGGAGG-GC
* **
49211 CTCTTGAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAG-GGC
49232 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGGTGGGA-GGGC
**
49253 CTCTTGAA-GGATGATAGTGGC
1 CTCTTGAACGG-TGGGAG-GGC
* * *
49274 CTCTTGAACGATAGGAAAGGC
1 CTCTTGAACGGT-GGGAGGGC
49295 CTCTTGAACG
1 CTCTTGAACG
49305 ATGACAGGTG
Statistics
Matches: 75, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
20 3 0.04
21 67 0.89
22 5 0.07
ACGTcount: A:0.23, C:0.20, G:0.34, T:0.23
Consensus pattern (20 bp):
CTCTTGAACGGTGGGAGGGC
Found at i:49249 original size:42 final size:42
Alignment explanation
Indices: 49190--49311 Score: 158
Period size: 42 Copynumber: 2.9 Consensus size: 42
49180 GTGAATCGGG
49190 CTCTTGAACGGTGGGAGGAACCTCTTGAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGAACCTCTTGAACGATGACAGTGGC
** * *
49232 CTCTTGAACGGTGGGAGGGGCCTCTTGAAGGATGATAGTGGC
1 CTCTTGAACGGTGGGAGGAACCTCTTGAACGATGACAGTGGC
* *
49274 CTCTTGAACGATAGGA--AAGGCCTCTTGAACGATGACAG
1 CTCTTGAACGGTGGGAGGAA--CCTCTTGAACGATGACAG
49312 GTGAATCGGG
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
42 68 1.00
ACGTcount: A:0.25, C:0.20, G:0.34, T:0.22
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGAACCTCTTGAACGATGACAGTGGC
Found at i:49679 original size:21 final size:21
Alignment explanation
Indices: 49653--49696 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
49643 TTTGTCATCG
49653 CGTAAA-ACCTCTACCTCACCA
1 CGTAAAGACC-CTACCTCACCA
* *
49674 CGTAAAGACCGTACCTCATCA
1 CGTAAAGACCCTACCTCACCA
49695 CG
1 CG
49697 CCATGCACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.32, C:0.39, G:0.11, T:0.18
Consensus pattern (21 bp):
CGTAAAGACCCTACCTCACCA
Found at i:49737 original size:21 final size:21
Alignment explanation
Indices: 49713--49758 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
49703 ACAATTGTCG
* * *
49713 TCACGTAAAGTACTGACCTCC
1 TCACGCAAAGCACTGACCTCA
*
49734 TCACGCAAAGCATTGACCTCA
1 TCACGCAAAGCACTGACCTCA
49755 TCAC
1 TCAC
49759 TTAACTCCCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.35, G:0.13, T:0.22
Consensus pattern (21 bp):
TCACGCAAAGCACTGACCTCA
Found at i:52049 original size:19 final size:20
Alignment explanation
Indices: 52010--52052 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
52000 GTTTTGAATT
*
52010 CGAAAATAAAATTCGCGTTG
1 CGAAAATAAAATGCGCGTTG
*
52030 CGAAAAT-AAATGCGCTTTG
1 CGAAAATAAAATGCGCGTTG
52049 CGAA
1 CGAA
52053 TTTGACTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (20 bp):
CGAAAATAAAATGCGCGTTG
Found at i:52106 original size:20 final size:20
Alignment explanation
Indices: 52062--52106 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
52052 ATTTGACTTC
*
52062 TGTTGTGATTTACAAATTCG
1 TGTTGCGATTTACAAATTCG
* **
52082 CGTTGCGATTTACCTATTCG
1 TGTTGCGATTTACAAATTCG
52102 TGTTG
1 TGTTG
52107 TGAATTTGGA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.18, C:0.16, G:0.22, T:0.44
Consensus pattern (20 bp):
TGTTGCGATTTACAAATTCG
Found at i:57926 original size:23 final size:23
Alignment explanation
Indices: 57900--57943 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
57890 TGTGTACAAG
57900 TTAGCCACCAAATATGAAATTCA
1 TTAGCCACCAAATATGAAATTCA
57923 TTAGCCACCAAATATGAAATT
1 TTAGCCACCAAATATGAAATT
57944 TACATGTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.27
Consensus pattern (23 bp):
TTAGCCACCAAATATGAAATTCA
Done.