Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006219.1 Hibiscus syriacus cultivar Beakdansim tig00014819_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: 80145
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:22 original size:12 final size:12
Alignment explanation
Indices: 5--48 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
1 ATCG
*
5 TGAACAGTATCA
1 TGAACAGTACCA
**
17 TGAACAACACCA
1 TGAACAGTACCA
29 TGAACAGTACCA
1 TGAACAGTACCA
41 TGAACAGT
1 TGAACAGT
49 GCTGCAGTGC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.43, C:0.23, G:0.16, T:0.18
Consensus pattern (12 bp):
TGAACAGTACCA
Found at i:2647 original size:20 final size:20
Alignment explanation
Indices: 2615--2652 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2605 GTGAATTATT
*
2615 GTTGTTGTATTTTTTTAATA
1 GTTGTTGTATTTTATTAATA
2635 GTTGTTAGT-TTTTATTAA
1 GTTGTT-GTATTTTATTAA
2653 AAATAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.21, C:0.00, G:0.16, T:0.63
Consensus pattern (20 bp):
GTTGTTGTATTTTATTAATA
Found at i:3166 original size:20 final size:20
Alignment explanation
Indices: 3143--3189 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
3133 GTTTCCAATT
3143 TCGCAACGGGAATCTGTAAA
1 TCGCAACGGGAATCTGTAAA
* *
3163 TCGCAACGTGAATTTGTAAA
1 TCGCAACGGGAATCTGTAAA
*
3183 TCACAAC
1 TCGCAAC
3190 ACATAAGTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.23
Consensus pattern (20 bp):
TCGCAACGGGAATCTGTAAA
Found at i:3207 original size:40 final size:40
Alignment explanation
Indices: 3183--3270 Score: 124
Period size: 40 Copynumber: 2.2 Consensus size: 40
3173 AATTTGTAAA
*
3183 TCACAACACATAAGTCAAATTCGCAACGCGATAGTCAAAT
1 TCACAACACAAAAGTCAAATTCGCAACGCGATAGTCAAAT
* *
3223 TCGCAACACAAAAGTCAAATTCGCAACGCGGA-ATTTCAAAT
1 TCACAACACAAAAGTCAAATTCGCAACGC-GATA-GTCAAAT
3264 TCACAAC
1 TCACAAC
3271 TGAATTTCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
40 28 0.67
41 14 0.33
ACGTcount: A:0.42, C:0.26, G:0.12, T:0.19
Consensus pattern (40 bp):
TCACAACACAAAAGTCAAATTCGCAACGCGATAGTCAAAT
Found at i:3218 original size:20 final size:20
Alignment explanation
Indices: 3194--3289 Score: 95
Period size: 20 Copynumber: 4.8 Consensus size: 20
3184 CACAACACAT
3194 AAGTCAAATTCGCAACGCGA
1 AAGTCAAATTCGCAACGCGA
* * *
3214 TAGTCAAATTCGCAACACAA
1 AAGTCAAATTCGCAACGCGA
3234 AAGTCAAATTCGCAACGCGGA
1 AAGTCAAATTCGCAACGC-GA
** * *
3255 ATTTCAAATTCACAAC-TGA
1 AAGTCAAATTCGCAACGCGA
**
3274 ATTTCAAATTCGCAAC
1 AAGTCAAATTCGCAAC
3290 TAGATTTTCG
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
19 17 0.27
20 33 0.52
21 14 0.22
ACGTcount: A:0.41, C:0.24, G:0.14, T:0.22
Consensus pattern (20 bp):
AAGTCAAATTCGCAACGCGA
Found at i:3277 original size:19 final size:20
Alignment explanation
Indices: 3237--3309 Score: 85
Period size: 19 Copynumber: 3.6 Consensus size: 20
3227 AACACAAAAG
**
3237 TCAAATTCGCAACGCGGAATT
1 TCAAATTCGCAAC-TAGAATT
*
3258 TCAAATTCACAACT-GAATT
1 TCAAATTCGCAACTAGAATT
*
3277 TCAAATTCGCAACTAGATTT
1 TCAAATTCGCAACTAGAATT
*
3297 TCGAATTCGCAAC
1 TCAAATTCGCAAC
3310 ACGAATTTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
19 18 0.39
20 16 0.35
21 12 0.26
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.29
Consensus pattern (20 bp):
TCAAATTCGCAACTAGAATT
Found at i:3316 original size:40 final size:40
Alignment explanation
Indices: 3197--3317 Score: 111
Period size: 40 Copynumber: 3.0 Consensus size: 40
3187 AACACATAAG
** * **
3197 TCAAATTCGCAACGC-GATAGTCAAATTCGCAACACAAAAG
1 TCAAATTCGCAAC-CAGATTTTCAAATTCGCAACACGAATT
* * * *
3237 TCAAATTCGCAACGCGGAATTTCAAATTCACAAC-TGAATT
1 TCAAATTCGCAAC-CAGATTTTCAAATTCGCAACACGAATT
* *
3277 TCAAATTCGCAACTAGATTTTCGAATTCGCAACACGAATT
1 TCAAATTCGCAACCAGATTTTCAAATTCGCAACACGAATT
3317 T
1 T
3318 AATTTCGTAA
Statistics
Matches: 65, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
39 15 0.23
40 36 0.55
41 14 0.22
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (40 bp):
TCAAATTCGCAACCAGATTTTCAAATTCGCAACACGAATT
Found at i:4327 original size:24 final size:24
Alignment explanation
Indices: 4276--4329 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
4266 GTATTCGAAA
*
4276 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
4300 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
4324 TTTGAT
1 TTTGAT
4330 GATGTGATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:7482 original size:24 final size:24
Alignment explanation
Indices: 7431--7483 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
7421 TTTCATATGT
* * *
7431 AATTGGAGTTTGAATTTCAATTTC
1 AATTTGAGTTTGAATTTCAATATA
*
7455 AATTTGAGTTTGAATTTTAATATA
1 AATTTGAGTTTGAATTTCAATATA
7479 AATTT
1 AATTT
7484 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.34, C:0.04, G:0.13, T:0.49
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTCAATATA
Found at i:8450 original size:18 final size:18
Alignment explanation
Indices: 8427--8462 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
8417 AAGCAAAAGG
8427 AAATCAAAATCGCAATCA
1 AAATCAAAATCGCAATCA
*
8445 AAATCAAAATCTCAATCA
1 AAATCAAAATCGCAATCA
8463 CAACCGGCTT
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:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCGCAATCA
Found at i:8691 original size:14 final size:14
Alignment explanation
Indices: 8653--8691 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
8643 ATTTACATTT
8653 TCGCAACGCG-AAA
1 TCGCAACGCGAAAA
8666 TCGCAAAC-CGAAAA
1 TCGC-AACGCGAAAA
8680 TCGCAACGCGAA
1 TCGCAACGCGAA
8692 TTTGACTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 9 0.39
14 14 0.61
ACGTcount: A:0.41, C:0.31, G:0.21, T:0.08
Consensus pattern (14 bp):
TCGCAACGCGAAAA
Found at i:8845 original size:64 final size:66
Alignment explanation
Indices: 8721--8848 Score: 224
Period size: 65 Copynumber: 2.0 Consensus size: 66
8711 ATTTACCTTT
8721 CAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATTAAACAAATCAACTTTT
1 CAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATTAAACAAATCAACTTTT
8786 A
66 A
* *
8787 CAAATCAATTAAACAAGC-AAAAAATAATTCTTATTTTCTCATC-AATTAAACAAATCAACTTT
1 CAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATTAAACAAATCAACTTT
8849 CAATGTAAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
64 19 0.32
65 23 0.38
66 18 0.30
ACGTcount: A:0.51, C:0.17, G:0.02, T:0.30
Consensus pattern (66 bp):
CAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATTAAACAAATCAACTTTT
A
Found at i:9724 original size:21 final size:20
Alignment explanation
Indices: 9675--9720 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
9665 CATATAAATC
*
9675 GGGCTCTTGAACGGCGGGCG
1 GGGCTCTTGAACGGCGGGAG
* *
9695 GGTCCTCTTGAACGGTGGGAG
1 GG-GCTCTTGAACGGCGGGAG
9716 GGGCT
1 GGGCT
9721 TCTTCGATGA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.11, C:0.22, G:0.48, T:0.20
Consensus pattern (20 bp):
GGGCTCTTGAACGGCGGGAG
Found at i:9940 original size:4 final size:4
Alignment explanation
Indices: 9919--9960 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
9909 AGGCCGCTGA
* * *
9919 AAAT AAAT TAAT ACAT AAAT AAGT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
9961 TGCCGAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:11966 original size:20 final size:19
Alignment explanation
Indices: 11943--11982 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
11933 CTTAAATTCA
11943 CAACACGAAAATGAAAATCG
1 CAACACGAAAAT-AAAATCG
* *
11963 CAACGCGAAACTAAAATCG
1 CAACACGAAAATAAAATCG
11982 C
1 C
11983 GTTGCGATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.50, C:0.25, G:0.15, T:0.10
Consensus pattern (19 bp):
CAACACGAAAATAAAATCG
Found at i:12004 original size:20 final size:20
Alignment explanation
Indices: 11979--12053 Score: 150
Period size: 20 Copynumber: 3.8 Consensus size: 20
11969 GAAACTAAAA
11979 TCGCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCATTT
11999 TCGCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCATTT
12019 TCGCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCATTT
12039 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
12054 GGTGTTGCGA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.09, C:0.20, G:0.21, T:0.49
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATTT
Found at i:12445 original size:20 final size:21
Alignment explanation
Indices: 12420--12469 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
12410 CTCTGAGAGA
12420 TGGAGAT-AGACGGATTTCGC
1 TGGAGATGAGACGGATTTCGC
*
12440 TGGAGATGGGGACGGATTTCG-
1 TGGAGAT-GAGACGGATTTCGC
12461 TCGGAGATG
1 T-GGAGATG
12470 GGGACGTATG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 7 0.27
21 2 0.08
22 17 0.65
ACGTcount: A:0.22, C:0.12, G:0.42, T:0.24
Consensus pattern (21 bp):
TGGAGATGAGACGGATTTCGC
Found at i:12456 original size:22 final size:22
Alignment explanation
Indices: 12428--12475 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
12418 GATGGAGATA
12428 GACGGATTTCG-CTGGAGATGGG
1 GACGGATTTCGTC-GGAGATGGG
12450 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
12472 GACG
1 GACG
12476 TATGTCGCCG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 24 0.96
23 1 0.04
ACGTcount: A:0.19, C:0.15, G:0.46, T:0.21
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:12619 original size:20 final size:20
Alignment explanation
Indices: 12594--12680 Score: 84
Period size: 20 Copynumber: 4.3 Consensus size: 20
12584 TGTGTTTCGC
12594 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
* * * *
12614 GTTGCGAATTTGGCTATCGC
1 GTTGCGAATTTGACTTTTGT
* * *
12634 ATTACGAATTTGACTTATGT
1 GTTGCGAATTTGACTTTTGT
* * *
12654 GTTGCGATTTTAACTTCTGT
1 GTTGCGAATTTGACTTTTGT
12674 GTTGCGA
1 GTTGCGA
12681 TTTACAAATT
Statistics
Matches: 51, Mismatches: 16, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.18, C:0.14, G:0.24, T:0.44
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTTGT
Found at i:16381 original size:16 final size:16
Alignment explanation
Indices: 16360--16391 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
16350 ATCCCATTTC
16360 ATATAGTTCACATATA
1 ATATAGTTCACATATA
16376 ATATAGTTCACATATA
1 ATATAGTTCACATATA
16392 CCTTTTTCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (16 bp):
ATATAGTTCACATATA
Found at i:19365 original size:131 final size:130
Alignment explanation
Indices: 19188--19504 Score: 340
Period size: 126 Copynumber: 2.5 Consensus size: 130
19178 GTTGTTCTTA
* * * * **
19188 AAGGTAGATCATATCTAAAAACGTTGATTCACTCCACTGCTCTTCAGGGAATGTTGAATTGGGTT
1 AAGGTATATCAGATCCAAAAACTTTGATTCACTCCACTGCTCTTCAGGGAA-GTTGAATCAGGTT
* * * * *
19253 TGATTTGCTACACTGCTCTTCAAGGAATG-TCAAATTTGAGAAAATG-GATATTCTTCGCTGCGT
65 TGATTTGCTACACTGCTCTTCAA-GAAAGATAAAATCTGAGAAAA-GAGATATGCTCCGCTGCGT
19316 TTC
128 TTC
* * * * ** *
19319 AGGGTATATCAGATTCGAAAACTTTGATTCACTCTACTATTCTTCA-GG--G-TGAATCATGTTT
1 AAGGTATATCAGATCCAAAAACTTTGATTCACTCCACTGCTCTTCAGGGAAGTTGAATCAGGTTT
* * *
19380 GATTTGCTTCACTGCTTTTCAAGAAAGATAAAATCTGAGAAAAGAGATATGCTCCGCTGTGTTTC
66 GATTTGCTACACTGCTCTTCAAGAAAGATAAAATCTGAGAAAAGAGATATGCTCCGCTGCGTTTC
* * *
19445 AAGGTATATCGGATCCAAAAACTTTTATTCGCTCCACTGCTCTTCAGGGAAGATTGAATC
1 AAGGTATATCAGATCCAAAAACTTTGATTCACTCCACTGCTCTTCAGGGAAG-TTGAATC
19505 TAAAAATTAA
Statistics
Matches: 149, Mismatches: 30, Indels: 14
0.77 0.16 0.07
Matches are distributed among these distances:
125 5 0.03
126 96 0.64
127 3 0.02
129 1 0.01
130 2 0.01
131 42 0.28
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.34
Consensus pattern (130 bp):
AAGGTATATCAGATCCAAAAACTTTGATTCACTCCACTGCTCTTCAGGGAAGTTGAATCAGGTTT
GATTTGCTACACTGCTCTTCAAGAAAGATAAAATCTGAGAAAAGAGATATGCTCCGCTGCGTTTC
Found at i:20313 original size:16 final size:17
Alignment explanation
Indices: 20279--20318 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
20269 ACGGTGGTCG
20279 AAAAGTAAAAAAAACCCC
1 AAAA-TAAAAAAAACCCC
*
20297 AAAATAAAATAAA-CCC
1 AAAATAAAAAAAACCCC
20313 AAAATA
1 AAAATA
20319 TCTTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.43
17 8 0.38
18 4 0.19
ACGTcount: A:0.70, C:0.17, G:0.03, T:0.10
Consensus pattern (17 bp):
AAAATAAAAAAAACCCC
Found at i:20540 original size:14 final size:14
Alignment explanation
Indices: 20505--20547 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
20495 TCCTTTTGAA
*
20505 TTTCTCTATTTTATTT
1 TTTCTCTA-TTT-TTC
20521 TTTCTCTATTTTTC
1 TTTCTCTATTTTTC
*
20535 TTTCTCTCTTTTT
1 TTTCTCTATTTTT
20548 TAAAAGTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 14 0.56
15 3 0.12
16 8 0.32
ACGTcount: A:0.07, C:0.19, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTCTCTATTTTTC
Found at i:20542 original size:16 final size:15
Alignment explanation
Indices: 20507--20548 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
20497 CTTTTGAATT
*
20507 TCTCTATTTTATTTTT
1 TCTCTATTTT-TTTTC
20523 TCTCTATTTTTCTTTC
1 TCTCTATTTTT-TTTC
20539 TCTCT-TTTTT
1 TCTCTATTTTT
20549 AAAAGTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 6 0.25
16 18 0.75
ACGTcount: A:0.07, C:0.19, G:0.00, T:0.74
Consensus pattern (15 bp):
TCTCTATTTTTTTTC
Found at i:21024 original size:3 final size:3
Alignment explanation
Indices: 21016--21064 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
21006 TGCTTGTAAC
21016 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
21064 A
1 A
21065 AATGGTTATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:22115 original size:5 final size:6
Alignment explanation
Indices: 22104--22128 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
22094 TTTTTTGCCC
22104 TGTTTT TGTTTT TGTTTT TGTTTT T
1 TGTTTT TGTTTT TGTTTT TGTTTT T
22129 TACTTTTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (6 bp):
TGTTTT
Found at i:24422 original size:46 final size:47
Alignment explanation
Indices: 24364--24482 Score: 154
Period size: 46 Copynumber: 2.6 Consensus size: 47
24354 GATAAAACGT
* *
24364 TACC-TAAAACATTATTTTTTTTATCGAAAATGTTAATATTAGGCGC
1 TACCTTAAAACATTATTTTTTTTATCGAAAATGTTAATATTAGACGA
**
24410 TA-CTTAAAACATTATTTTTTTTATAAAAAATGTTAATATTAGACGA
1 TACCTTAAAACATTATTTTTTTTATCGAAAATGTTAATATTAGACGA
** *
24456 TACCTT-AAATGTTATTTTTTCTATCGA
1 TACCTTAAAACATTATTTTTTTTATCGA
24483 TTTTTAAATA
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
45 1 0.02
46 58 0.94
47 3 0.05
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.45
Consensus pattern (47 bp):
TACCTTAAAACATTATTTTTTTTATCGAAAATGTTAATATTAGACGA
Found at i:25888 original size:14 final size:15
Alignment explanation
Indices: 25869--25897 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
25859 TTTGGTTTAG
25869 TAATTAT-ATTAATT
1 TAATTATAATTAATT
25883 TAATTATAATTAATT
1 TAATTATAATTAATT
25898 ATATATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TAATTATAATTAATT
Found at i:26255 original size:28 final size:28
Alignment explanation
Indices: 26222--26313 Score: 175
Period size: 28 Copynumber: 3.3 Consensus size: 28
26212 TACAAATGGC
*
26222 CAAAACCCGTTCAGCATACAATCCATTA
1 CAAAACCCGTTCAGCACACAATCCATTA
26250 CAAAACCCGTTCAGCACACAATCCATTA
1 CAAAACCCGTTCAGCACACAATCCATTA
26278 CAAAACCCGTTCAGCACACAATCCATTA
1 CAAAACCCGTTCAGCACACAATCCATTA
26306 CAAAACCC
1 CAAAACCC
26314 ACTACTAGCC
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 63 1.00
ACGTcount: A:0.40, C:0.36, G:0.07, T:0.17
Consensus pattern (28 bp):
CAAAACCCGTTCAGCACACAATCCATTA
Found at i:28544 original size:21 final size:21
Alignment explanation
Indices: 28519--28562 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
28509 TTTAAACCTG
28519 TATTTAATTTCAAATAAGAAT
1 TATTTAATTTCAAATAAGAAT
28540 TATTTAATTTCAAATAAGAAT
1 TATTTAATTTCAAATAAGAAT
28561 TA
1 TA
28563 ATTTGAGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (21 bp):
TATTTAATTTCAAATAAGAAT
Found at i:29194 original size:24 final size:23
Alignment explanation
Indices: 29140--29208 Score: 66
Period size: 24 Copynumber: 2.9 Consensus size: 23
29130 TGTCCGTTTA
*
29140 TTTATTGTTCGCGAACGTATTCTT
1 TTTA-TGTTCGCGAACATATTCTT
* * *
29164 TTAATGTTCGTGAACATTTTCATT
1 TTTATGTTCGCGAACATATTC-TT
**
29188 TTTATGTTAACGAACATATTC
1 TTTATGTTCGCGAACATATTC
29209 ATTTAATATT
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
23 14 0.40
24 21 0.60
ACGTcount: A:0.25, C:0.14, G:0.13, T:0.48
Consensus pattern (23 bp):
TTTATGTTCGCGAACATATTCTT
Found at i:30330 original size:2 final size:2
Alignment explanation
Indices: 30323--30376 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
30313 TTATTGTTGC
30323 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
30365 TA TA TA TA TA TA
1 TA TA TA TA TA TA
30377 GATTAGCCTG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31019 original size:33 final size:34
Alignment explanation
Indices: 30977--31043 Score: 127
Period size: 33 Copynumber: 2.0 Consensus size: 34
30967 AGTTGACATG
30977 TTGGAAATTTCATCTTGGTTGGTGGCC-AACTTT
1 TTGGAAATTTCATCTTGGTTGGTGGCCAAACTTT
31010 TTGGAAATTTCATCTTGGTTGGTGGCCAAACTTT
1 TTGGAAATTTCATCTTGGTTGGTGGCCAAACTTT
31044 GAACATGTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 27 0.82
34 6 0.18
ACGTcount: A:0.19, C:0.15, G:0.24, T:0.42
Consensus pattern (34 bp):
TTGGAAATTTCATCTTGGTTGGTGGCCAAACTTT
Found at i:35610 original size:21 final size:21
Alignment explanation
Indices: 35584--35626 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
35574 TTTCTGGGTT
* *
35584 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
35605 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
35626 A
1 A
35627 CGAAATGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:35727 original size:68 final size:68
Alignment explanation
Indices: 35606--35758 Score: 209
Period size: 68 Copynumber: 2.2 Consensus size: 68
35596 ACCCATTCAA
* *
35606 GGGGAACCGATACCCCTTCAACGAAATGAATTTCCAGAATGCAAGAGGGGAATCGATACCCCCA-
1 GGGGAACCGATACCCCCTCAACGAAATGAAATTCCAGAATGCAAGAGGGGAATCGATACCCCCAG
35670 GGG
66 GGG
* * * * **
35673 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTTCTTGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACG-AAATGAAATTCCAGAATGCAAGAGGGGAATCGATACCCCCA
35738 GGGG
65 GGGG
*
35742 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
35759 ATGAGAAAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
67 21 0.28
68 35 0.47
69 19 0.25
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.18
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGAAATGAAATTCCAGAATGCAAGAGGGGAATCGATACCCCCAG
GGG
Found at i:36095 original size:29 final size:29
Alignment explanation
Indices: 36061--36130 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
36051 CATATTATGA
**
36061 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
**
36090 TACATGACATGAATTCATATTGTATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
36119 TACATGACATGA
1 TACATGACATGA
36131 TTATGCAGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:36188 original size:30 final size:31
Alignment explanation
Indices: 36146--36205 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
36136 CAGAAAAGTT
*
36146 ATATGCACTATGTGATAAAGGTATGTAAATG
1 ATATGCACTATGTGATAAAGGTATGGAAATG
*
36177 ATATGC-CTATGTGTTAAAGGTATGGAAAT
1 ATATGCACTATGTGATAAAGGTATGGAAAT
36206 ACTATGTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (31 bp):
ATATGCACTATGTGATAAAGGTATGGAAATG
Found at i:36499 original size:22 final size:22
Alignment explanation
Indices: 36425--36491 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
36415 TTATGGACAT
36425 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
36447 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
36469 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
36491 A
1 A
36492 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:42537 original size:21 final size:21
Alignment explanation
Indices: 42511--42553 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
42501 TTTCTGGGTT
* *
42511 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
42532 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
42553 A
1 A
42554 CGAAATGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:42654 original size:68 final size:68
Alignment explanation
Indices: 42533--42685 Score: 218
Period size: 68 Copynumber: 2.2 Consensus size: 68
42523 ACCCATTCAA
* *
42533 GGGGAACCGATACCCCTTCAACGAAATGAATTTCCAGAATGCAAGAGGGGAATCGATACCCCCA-
1 GGGGAACCGATACCCCCTCAACGAAATGAAATTCCAGAATGCAAGAGGGGAATCGATACCCCCAG
42597 GGG
66 GGG
* * * **
42600 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTTGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACG-AAATGAAATTCCAGAATGCAAGAGGGGAATCGATACCCCCA
42665 GGGG
65 GGGG
*
42669 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
42686 ATGAGAAAAA
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
67 21 0.28
68 36 0.47
69 19 0.25
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.17
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGAAATGAAATTCCAGAATGCAAGAGGGGAATCGATACCCCCAG
GGG
Found at i:43022 original size:29 final size:29
Alignment explanation
Indices: 42988--43057 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
42978 CATATTATGA
**
42988 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
**
43017 TACATGACATGAATTCATATTGTATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
43046 TACATGACATGA
1 TACATGACATGA
43058 TTATGCAGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:43115 original size:30 final size:31
Alignment explanation
Indices: 43073--43132 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
43063 CAGAAAAGTT
*
43073 ATATGCACTATGTGATAAAGGTATGTAAATG
1 ATATGCACTATGTGATAAAGGTATGGAAATG
*
43104 ATATGC-CTATGTGTTAAAGGTATGGAAAT
1 ATATGCACTATGTGATAAAGGTATGGAAAT
43133 ACTATGTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (31 bp):
ATATGCACTATGTGATAAAGGTATGGAAATG
Found at i:43426 original size:22 final size:22
Alignment explanation
Indices: 43352--43418 Score: 125
Period size: 22 Copynumber: 3.0 Consensus size: 22
43342 TTATGGACAT
43352 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
*
43374 AATTCTACGGGCACTTCGATGC
1 AATTCTACGGGCACTTCGGTGC
43396 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
43418 A
1 A
43419 TTTATACGAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.21, C:0.27, G:0.25, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:48295 original size:31 final size:30
Alignment explanation
Indices: 48249--48337 Score: 97
Period size: 31 Copynumber: 2.8 Consensus size: 30
48239 TTCGATAATA
*
48249 TAATAATTATTTTATAGTATTTAAATAAATT
1 TAATAA-TATTTTATAATATTTAAATAAATT
* * *
48280 TATTAATAATTTTATAATCTTTTAATAAATT
1 TAATAAT-ATTTTATAATATTTAAATAAATT
*
48311 TAATAAGTATTTTATAATTTTTTAAAT
1 TAATAA-TATTTTATAA-TATTTAAAT
48338 TTTATTGAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
30 1 0.02
31 39 0.81
32 8 0.17
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (30 bp):
TAATAATATTTTATAATATTTAAATAAATT
Found at i:48306 original size:19 final size:20
Alignment explanation
Indices: 48282--48331 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
48272 AATAAATTTA
*
48282 TTAATAATTTTATAA-TCTT
1 TTAATAATTTTATAAGTATT
*
48301 TTAATAAATTTAATAAGTATT
1 TTAAT-AATTTTATAAGTATT
48322 TT-ATAATTTT
1 TTAATAATTTT
48332 TTAAATTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.38
20 11 0.42
21 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TTAATAATTTTATAAGTATT
Found at i:48327 original size:11 final size:10
Alignment explanation
Indices: 48251--48342 Score: 52
Period size: 11 Copynumber: 9.2 Consensus size: 10
48241 CGATAATATA
48251 ATAATTATTTT
1 ATAA-TATTTT
*
48262 ATAGTA-TTT
1 ATAATATTTT
*
48271 A-AATAAATTT
1 ATAAT-ATTTT
48281 ATTAATAATTTT
1 A-TAAT-ATTTT
*
48293 ATAATCTTTT
1 ATAATATTTT
*
48303 AATAA-ATTTA
1 -ATAATATTTT
48313 ATAAGTATTTT
1 ATAA-TATTTT
48324 ATAAT-TTTT
1 ATAATATTTT
48333 -TAA-ATTTT
1 ATAATATTTT
48341 AT
1 AT
48343 TGAAAAAATG
Statistics
Matches: 65, Mismatches: 7, Indels: 20
0.71 0.08 0.22
Matches are distributed among these distances:
8 9 0.14
9 14 0.22
10 14 0.22
11 19 0.29
12 9 0.14
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.55
Consensus pattern (10 bp):
ATAATATTTT
Found at i:49675 original size:30 final size:30
Alignment explanation
Indices: 49639--49741 Score: 170
Period size: 30 Copynumber: 3.4 Consensus size: 30
49629 CCCGAAGGAC
49639 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
49669 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* **
49699 CTATCCAGAGGTCATAAAGATTCTCCATAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
49729 CTATCCATAGGTC
1 CTATCCAGAGGTC
49742 CCGAAGAACC
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 69 1.00
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:49758 original size:60 final size:61
Alignment explanation
Indices: 49639--49766 Score: 168
Period size: 60 Copynumber: 2.1 Consensus size: 61
49629 CCCGAAGGAC
** * * *
49639 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGT-AA
1 CTATCCAGAGGTCATAAAGATCCTCCATAACTATCCAGAGGTCACAAAGAACCTAGGTAAA
* * * *
49699 CTATCCAGAGGTCATAAAGATTCTCCATAACTATCCATAGGTCCCGAAGAACCTAGGTAAA
1 CTATCCAGAGGTCATAAAGATCCTCCATAACTATCCAGAGGTCACAAAGAACCTAGGTAAA
49760 CTATCCA
1 CTATCCA
49767 TATGTTCCTT
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
60 49 0.84
61 9 0.16
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.23
Consensus pattern (61 bp):
CTATCCAGAGGTCATAAAGATCCTCCATAACTATCCAGAGGTCACAAAGAACCTAGGTAAA
Found at i:50431 original size:7 final size:7
Alignment explanation
Indices: 50419--50447 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
50409 ATATAGTTCA
50419 ATATCAC
1 ATATCAC
50426 ATATCAC
1 ATATCAC
50433 ATATCAC
1 ATATCAC
50440 ATAT-AC
1 ATATCAC
50446 AT
1 AT
50448 GTAATCATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.18
7 18 0.82
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.31
Consensus pattern (7 bp):
ATATCAC
Found at i:54070 original size:30 final size:30
Alignment explanation
Indices: 54034--54136 Score: 188
Period size: 30 Copynumber: 3.4 Consensus size: 30
54024 CCCGAAGGAC
54034 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
54064 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
54094 CTATCCAGAGGTCATAAAGATCCTCGATAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
54124 CTATCCATAGGTC
1 CTATCCAGAGGTC
54137 CCGAAGAACC
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 71 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:54153 original size:60 final size:61
Alignment explanation
Indices: 54034--54161 Score: 186
Period size: 60 Copynumber: 2.1 Consensus size: 61
54024 CCCGAAGGAC
* * * *
54034 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGT-AA
1 CTATCCAGAGGTCATAAAGATCCTCGATAACTATCCAGAGGTCACAAAGAACCTAGGTAAA
* * *
54094 CTATCCAGAGGTCATAAAGATCCTCGATAACTATCCATAGGTCCCGAAGAACCTAGGTAAA
1 CTATCCAGAGGTCATAAAGATCCTCGATAACTATCCAGAGGTCACAAAGAACCTAGGTAAA
54155 CTATCCA
1 CTATCCA
54162 TATGTTCCTT
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
60 51 0.85
61 9 0.15
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (61 bp):
CTATCCAGAGGTCATAAAGATCCTCGATAACTATCCAGAGGTCACAAAGAACCTAGGTAAA
Found at i:54176 original size:31 final size:31
Alignment explanation
Indices: 54122--54214 Score: 89
Period size: 31 Copynumber: 3.0 Consensus size: 31
54112 GATCCTCGAT
* *
54122 AACTATCCATAGGTCCCGAAGAACCTAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* **
54153 AACTATCCATATGTTCCTTAGAACATAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* * * *
54184 TACTGTCCATATATCTCGAA-AGACATAGGTA
1 AACTATCCATATGTCCCGAAGA-ACATAGGTA
54215 GTTCTTTGAC
Statistics
Matches: 49, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
30 1 0.02
31 48 0.98
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (31 bp):
AACTATCCATATGTCCCGAAGAACATAGGTA
Found at i:73329 original size:14 final size:14
Alignment explanation
Indices: 73310--73346 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
73300 GGAAACTCTC
*
73310 TTCTTCTTCTTTCT
1 TTCTTCTTCTTGCT
73324 TTCTTCTTCTTGCT
1 TTCTTCTTCTTGCT
73338 TTCTTCTTC
1 TTCTTCTTC
73347 CTCCGTGTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.00, C:0.30, G:0.03, T:0.68
Consensus pattern (14 bp):
TTCTTCTTCTTGCT
Found at i:73330 original size:17 final size:17
Alignment explanation
Indices: 73308--73346 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
73298 ATGGAAACTC
73308 TCTTCTTCTT-CTTTCTT
1 TCTTCTTCTTGCTTTC-T
73325 TCTTCTTCTTGCTTTCT
1 TCTTCTTCTTGCTTTCT
73342 TCTTC
1 TCTTC
73347 CTCCGTGTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.00, C:0.31, G:0.03, T:0.67
Consensus pattern (17 bp):
TCTTCTTCTTGCTTTCT
Found at i:73957 original size:64 final size:62
Alignment explanation
Indices: 73828--73966 Score: 170
Period size: 64 Copynumber: 2.2 Consensus size: 62
73818 ATATTCAATA
* * * * *
73828 TGTACCGATGCACTCTTTAAAGAAGAAACATCGAATGCATGAGTGAATCGATACACAGTTAG
1 TGTATCGATGCACTCTTGAAAGAAAAAACATCGAATGCATGAGTGAACCGATACACAGGTAG
* * * *
73890 TGTATCGATGCACTCCTTGAAATAAAAAACATCGAATGCAATGAGTGTACCGATGCATAGGTAG
1 TGTATCGATGCACT-CTTGAAAGAAAAAACATCGAATGC-ATGAGTGAACCGATACACAGGTAG
*
73954 TGTATCGTTGCAC
1 TGTATCGATGCAC
73967 ACGTTAAGGG
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
62 13 0.20
63 21 0.32
64 31 0.48
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.26
Consensus pattern (62 bp):
TGTATCGATGCACTCTTGAAAGAAAAAACATCGAATGCATGAGTGAACCGATACACAGGTAG
Found at i:74730 original size:31 final size:31
Alignment explanation
Indices: 74691--74846 Score: 192
Period size: 31 Copynumber: 5.0 Consensus size: 31
74681 AGAGTCGAGG
*
74691 GTTTACCTATGTTCTTTGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
74722 CTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
74753 GTTTACCTATGTTCTTGGGGACATATAGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
74784 GATTACCTA-GATTCTTCGGGATATATGGACT
1 GTTTACCTATG-TTCTTCGGGACATATGGACT
* *
74815 GATTACCTA-GATTCTTCAGGATC-TATGGACT
1 GTTTACCTATG-TTCTTCGGGA-CATATGGACT
74846 G
1 G
74847 GTCTTTCGGG
Statistics
Matches: 112, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
30 1 0.01
31 111 0.99
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:75557 original size:21 final size:21
Alignment explanation
Indices: 75533--75574 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
75523 TCAAAATTAT
* *
75533 TGTAGCATTGTATCGATACAC
1 TGTAGCAGTGCATCGATACAC
75554 TGTAGCAGTGCATCGATACAC
1 TGTAGCAGTGCATCGATACAC
75575 AATTTATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (21 bp):
TGTAGCAGTGCATCGATACAC
Found at i:79246 original size:15 final size:15
Alignment explanation
Indices: 79226--79257 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
79216 TAGCAGAAAC
79226 GAAAAACATTGTACT
1 GAAAAACATTGTACT
79241 GAAAAACATTGTACT
1 GAAAAACATTGTACT
79256 GA
1 GA
79258 TTTTTCCGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.12, G:0.16, T:0.25
Consensus pattern (15 bp):
GAAAAACATTGTACT
Done.