Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004992.1 Hibiscus syriacus cultivar Beakdansim tig00011205_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: 75249
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:2346 original size:16 final size:15
Alignment explanation
Indices: 2325--2367 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
2315 AGATAAAAAT
2325 AAATAAAACAAAGTA
1 AAATAAAACAAAGTA
*
2340 GAAATAAAACGAAGTA
1 -AAATAAAACAAAGTA
2356 AAA-AAAATCAAA
1 AAATAAAA-CAAA
2368 ACAAAAATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 4 0.17
15 6 0.25
16 14 0.58
ACGTcount: A:0.72, C:0.07, G:0.09, T:0.12
Consensus pattern (15 bp):
AAATAAAACAAAGTA
Found at i:2554 original size:2 final size:2
Alignment explanation
Indices: 2547--2591 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
2537 TATGTAAATA
2547 AT AT AT AT AT AT AT AT AT AT -T 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
2588 AT AT
1 AT AT
2592 GCGCATAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2864 original size:15 final size:16
Alignment explanation
Indices: 2844--2873 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2834 CAGAAAAAAA
2844 TAAAATGTT-GAAATT
1 TAAAATGTTAGAAATT
2859 TAAAATGTTAGAAAT
1 TAAAATGTTAGAAAT
2874 AAATAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (16 bp):
TAAAATGTTAGAAATT
Found at i:3033 original size:40 final size:41
Alignment explanation
Indices: 2989--3066 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 41
2979 AAGTCAATAT
* *
2989 GTTAGTATGAACAATAAAAT-AAAAGTTAGAATGTTAGTAA
1 GTTAGTACGAACAACAAAATAAAAAGTTAGAATGTTAGTAA
* *
3029 GTTAGTACGGACAACAAAATAAAAAGTTTGAATGTTAG
1 GTTAGTACGAACAACAAAATAAAAAGTTAGAATGTTAG
3067 CGGTTAGTGG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
40 17 0.52
41 16 0.48
ACGTcount: A:0.47, C:0.05, G:0.19, T:0.28
Consensus pattern (41 bp):
GTTAGTACGAACAACAAAATAAAAAGTTAGAATGTTAGTAA
Found at i:3340 original size:99 final size:98
Alignment explanation
Indices: 3170--3351 Score: 265
Period size: 99 Copynumber: 1.8 Consensus size: 98
3160 TATAAAAACA
* * * * *
3170 AAATAAATAAAAAAAGGTTTGTATTTAGCAAAGTCCGAACCATAATAATGTGGATTTTACCCCGG
1 AAATAAATAAAAAAAAGTTAGTAGTTAGCAAAGTCCGAACAATAATAATGTGGATCTTACCCCGG
*
3235 ATCGGGTCACCGCAAGGTTGAATCGAATAATGC
66 ATCGGGTCACCACAAGGTTGAATCGAATAATGC
* * * *
3268 AAATAAATATAAAAAAAGTTAGTGGTTAGCATAGTCCGAACAATAATAATGTGGGTCTTACCTCG
1 AAATAAATA-AAAAAAAGTTAGTAGTTAGCAAAGTCCGAACAATAATAATGTGGATCTTACCCCG
3333 GATCGGGTCACCACAAGGT
65 GATCGGGTCACCACAAGGT
3352 CGAGTAATAT
Statistics
Matches: 73, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
98 9 0.12
99 64 0.88
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (98 bp):
AAATAAATAAAAAAAAGTTAGTAGTTAGCAAAGTCCGAACAATAATAATGTGGATCTTACCCCGG
ATCGGGTCACCACAAGGTTGAATCGAATAATGC
Found at i:4452 original size:16 final size:16
Alignment explanation
Indices: 4431--4474 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 16
4421 ATTACAAGAG
4431 AAAATGATAAAAATAA
1 AAAATGATAAAAATAA
*
4447 AAAATG-TTAAAATAA
1 AAAATGATAAAAATAA
4462 AAAATGA-AAAAAT
1 AAAATGATAAAAAT
4475 GTTAATTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 19 0.76
16 6 0.24
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (16 bp):
AAAATGATAAAAATAA
Found at i:5516 original size:7 final size:6
Alignment explanation
Indices: 5497--5564 Score: 59
Period size: 6 Copynumber: 11.0 Consensus size: 6
5487 TCTTGGACCC
* *
5497 TAAAAA TTAAAA TAATAAA TAAAAA TAGAAAA -AAAAA -AAAAA AAAGAAA
1 TAAAAA TAAAAA TAA-AAA TAAAAA TA-AAAA TAAAAA TAAAAA TAA-AAA
*
5546 TAAATAA TATAAA TAAAAA
1 TAAA-AA TAAAAA TAAAAA
5565 CTATATAATA
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
5 9 0.17
6 23 0.44
7 20 0.38
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (6 bp):
TAAAAA
Found at i:5521 original size:13 final size:12
Alignment explanation
Indices: 5497--5564 Score: 59
Period size: 13 Copynumber: 5.5 Consensus size: 12
5487 TCTTGGACCC
*
5497 TAAAAATTAAAA
1 TAAAAATAAAAA
5509 TAATAAATAAAAA
1 TAA-AAATAAAAA
5522 TAGAAAA-AAAAA
1 TA-AAAATAAAAA
*
5534 -AAAAAAAAGAAA
1 TAAAAATAA-AAA
*
5546 TAAATAATATAAA
1 TAAA-AATAAAAA
5559 TAAAAA
1 TAAAAA
5565 CTATATAATA
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
10 4 0.09
11 3 0.06
12 13 0.28
13 23 0.49
14 4 0.09
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (12 bp):
TAAAAATAAAAA
Found at i:5593 original size:17 final size:17
Alignment explanation
Indices: 5552--5587 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
5542 GAAATAAATA
5552 ATATAA-AT-AAAAACT
1 ATATAATATAAAAAACT
5567 ATATAATATAAAAAACT
1 ATATAATATAAAAAACT
5584 ATAT
1 ATAT
5588 TGTATATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.32
16 2 0.11
17 11 0.58
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.31
Consensus pattern (17 bp):
ATATAATATAAAAAACT
Found at i:5663 original size:35 final size:34
Alignment explanation
Indices: 5622--5780 Score: 164
Period size: 37 Copynumber: 4.5 Consensus size: 34
5612 TTCCAAATTA
5622 TATATTATATATATTTTTTCAAACA-TTTT-AAAAC
1 TATA-TATATATATTTTTTCAAA-AGTTTTCAAAAC
* *
5656 TAT-TATTATATATATTTTCAAAAATGGTTTCAAAAAC
1 TATATA-TATATATTTTTTC-AAAA-GTTTTC-AAAAC
*
5693 TATATAT-TATATATTTTCAAAATGTTTTCAAACAC
1 TATATATATATATTTTTTCAAAA-GTTTTCAAA-AC
5728 TATATATTATATATTTTTTCAAAATGTTTTCAAAAC
1 TATATA-TATATATTTTTTCAAAA-GTTTTCAAAAC
5764 TATATAGTATATATTTT
1 TATATA-TATATATTTT
5781 CAAAAATTGA
Statistics
Matches: 110, Mismatches: 5, Indels: 18
0.83 0.04 0.14
Matches are distributed among these distances:
32 2 0.02
33 13 0.12
34 9 0.08
35 21 0.19
36 30 0.27
37 33 0.30
38 2 0.02
ACGTcount: A:0.40, C:0.08, G:0.03, T:0.48
Consensus pattern (34 bp):
TATATATATATATTTTTTCAAAAGTTTTCAAAAC
Found at i:5743 original size:71 final size:68
Alignment explanation
Indices: 5578--5785 Score: 210
Period size: 71 Copynumber: 2.9 Consensus size: 68
5568 TATAATATAA
* * *
5578 AAAACTATAT-TGTATATATTTTCGAAAAAATGTTTTCCAAATTA-TATATTATATATATTTTTT
1 AAAACTATATATATATATATTTTC--AAAAATGTTTT-CAAA-AACTATA-TAT-TATATATTTT
5641 CAAACATTTT
60 CAAA-ATTTT
*
5651 AAAACTAT-TATTATATATATTTTCAAAAATGGTTTCAAAAACTATATATTATATATTTTCAAAA
1 AAAACTATATA-TATATATATTTTCAAAAATGTTTTCAAAAACTATATATTATATATTTTCAAAA
5715 TGTTTT
65 --TTTT
* *
5721 CAAACACTATATATTATATATTTTTTC-AAAATGTTTTC-AAAACTATATAGTATATATTTTCAA
1 -AAA-ACTATATA-TATATATATTTTCAAAAATGTTTTCAAAAACTATATATTATATATTTTCAA
5784 AA
63 AA
5786 ATTGATTTTT
Statistics
Matches: 120, Mismatches: 7, Indels: 18
0.83 0.05 0.12
Matches are distributed among these distances:
68 1 0.01
69 13 0.11
70 8 0.07
71 37 0.31
72 26 0.22
73 23 0.19
74 12 0.10
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.46
Consensus pattern (68 bp):
AAAACTATATATATATATATTTTCAAAAATGTTTTCAAAAACTATATATTATATATTTTCAAAAT
TTT
Found at i:7387 original size:22 final size:23
Alignment explanation
Indices: 7341--7397 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
7331 TGTAAGGGAT
*
7341 GTATCGATACC-TGTTGAGAGTG
1 GTATCGATACCTTGATGAGAGTG
7363 GTATCGATACCTTGATG-GA-TGG
1 GTATCGATACCTTGATGAGAGT-G
*
7385 GTATCGGTACCTT
1 GTATCGATACCTT
7398 AGGGGGTATC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 1 0.03
22 26 0.84
23 4 0.13
ACGTcount: A:0.21, C:0.16, G:0.30, T:0.33
Consensus pattern (23 bp):
GTATCGATACCTTGATGAGAGTG
Found at i:7549 original size:20 final size:21
Alignment explanation
Indices: 7507--7559 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
7497 TACATGCGTC
7507 GGTATCGATACCCTGAGGGGT
1 GGTATCGATACCCTGAGGGGT
* *
7528 GGTATCGGTACCCTTA-GGGT
1 GGTATCGATACCCTGAGGGGT
*
7548 GGTACCGATACC
1 GGTATCGATACC
7560 TCTAAGTATG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.19, C:0.23, G:0.34, T:0.25
Consensus pattern (21 bp):
GGTATCGATACCCTGAGGGGT
Found at i:7910 original size:21 final size:21
Alignment explanation
Indices: 7869--7918 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
7859 GTGTTATGAA
*
7869 AATATGAACCTTGAATAAGTG
1 AATATGAACCTTGAACAAGTG
*
7890 AATATGAA-CTTCGAACCAGTG
1 AATATGAACCTT-GAACAAGTG
*
7911 AATGTGAA
1 AATATGAA
7919 TATACTCTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 3 0.12
21 22 0.88
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.26
Consensus pattern (21 bp):
AATATGAACCTTGAACAAGTG
Found at i:14794 original size:21 final size:22
Alignment explanation
Indices: 14770--14819 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
14760 GTGTTATGAA
14770 AATATGAACCTT-GAACAAGTG
1 AATATGAACCTTCGAACAAGTG
* *
14791 AATATG-ATCTTCGAACCAGTG
1 AATATGAACCTTCGAACAAGTG
*
14812 AATGTGAA
1 AATATGAA
14820 TATACTCTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 4 0.17
21 19 0.79
22 1 0.04
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (22 bp):
AATATGAACCTTCGAACAAGTG
Found at i:15025 original size:23 final size:23
Alignment explanation
Indices: 14995--15069 Score: 107
Period size: 23 Copynumber: 3.3 Consensus size: 23
14985 CTGGGACAAA
14995 TATGTGGCACTTTGGTGCAACCC
1 TATGTGGCACTTTGGTGCAACCC
**
15018 TATGTGGCACTTCAGTGCAACCC
1 TATGTGGCACTTTGGTGCAACCC
* *
15041 TATGTGGTACTTTGGTGCAA-AC
1 TATGTGGCACTTTGGTGCAACCC
15063 TATGTGG
1 TATGTGG
15070 TCCTTCGGGA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
22 8 0.17
23 38 0.83
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.32
Consensus pattern (23 bp):
TATGTGGCACTTTGGTGCAACCC
Found at i:15109 original size:22 final size:22
Alignment explanation
Indices: 14991--15109 Score: 93
Period size: 23 Copynumber: 5.4 Consensus size: 22
14981 TCCTCTGGGA
*
14991 CAAA-TATGTGGCACTTTGGTG
1 CAAACTATGTGGCACTTCGGTG
* *
15012 CAACCCTATGTGGCACTTCAGTG
1 CAA-ACTATGTGGCACTTCGGTG
* * *
15035 CAACCCTATGTGGTACTTTGGTG
1 CAA-ACTATGTGGCACTTCGGTG
15058 CAAACTATGTGGTC-CTTCGG-G
1 CAAACTATGTGG-CACTTCGGTG
*
15079 -ACAATTATGTGGCACTTCGGTG
1 CA-AACTATGTGGCACTTCGGTG
* *
15101 TAAATTATG
1 CAAACTATG
15110 AGTTGTGGTG
Statistics
Matches: 81, Mismatches: 10, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
20 2 0.02
21 19 0.23
22 21 0.26
23 39 0.48
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (22 bp):
CAAACTATGTGGCACTTCGGTG
Found at i:16393 original size:201 final size:201
Alignment explanation
Indices: 15732--16389 Score: 863
Period size: 201 Copynumber: 3.3 Consensus size: 201
15722 GGGTGTTACA
* ** *
15732 GCTACAATGCGGTTGATACACCCTCGAGCTGAATGGAATCAAACTCAAAAGTGGTCATTGAGAGA
1 GCTACAATGCGGTTGATACACCCTCGAGTTGAATGGAATCAAACTCAAAAGTCTTCATTGATAGA
* * *
15797 TAACCCTTATCGCATTGAGCTATGCTGTGAATTTGGATGGGATATAGTTCCTTATTGCTAAATCG
66 TAACCCTTATCGCCTTGAGCTATGCTGTGAATTTGGCTGGGATATAGTTCCTTTTTGCTAAATCG
* * *
15862 CATCCAAACCGGGTCA-TCTTCTGGACTTAAAGACCTCAGTTTAAACTTCAACCGAAAAGTAGTT
131 CATCCAACCCGGGT-ATTCTTCTAGACTTAAAGACCTCAGTTTAAACTTCAACCGGAAAGTAGTT
**
15926 CCTCTTT
195 CCTCGCT
* * *
15933 GCTACAATGCGGTTGATACACCCTCAAGATT-AATGGAATCGAACTCGAAAGTCTTCATTGATAG
1 GCTACAATGCGGTTGATACACCCTCGAG-TTGAATGGAATCAAACTCAAAAGTCTTCATTGATAG
* * *
15997 ATATCCTTTATCGCCTTGAGCTATGCTGTGAATTTGGCTGGGATATAGTTCATTGTTT-CTAAAT
65 ATAACCCTTATCGCCTTGAGCTATGCTGTGAATTTGGCTGGGATATAGTTCCTT-TTTGCTAAAT
* * * * * *
16061 CGCATCCAACCCGGGTCTTTTTTTCGACTTAAATACCTCAGTTTAAACTTCACCCGGAAAGTAGT
129 CGCATCCAACCCGGGTATTCTTCTAGACTTAAAGACCTCAGTTTAAACTTCAACCGGAAAGTAGT
*
16126 TCCTTGCT
194 TCCTCGCT
* * * ** **
16134 GCTACAATGCAGTTGATACACCATCGAGTTGAATGGAATCAAATTTGAAAGTCTTTGTTGATAGA
1 GCTACAATGCGGTTGATACACCCTCGAGTTGAATGGAATCAAACTCAAAAGTCTTCATTGATAGA
* * **
16199 TAACCCTTATCTCCTTGAGCTATGCTGTGAATTTAGCTGAAATATAGTTCCTTTTTGCTAAATCG
66 TAACCCTTATCGCCTTGAGCTATGCTGTGAATTTGGCTGGGATATAGTTCCTTTTTGCTAAATCG
* ** * *
16264 CAGCCAACCCAAGTATTCTTCTAGACTTAAAGACCTCAATTTAAACTTCAACAGGAAAGTAGTTC
131 CATCCAACCCGGGTATTCTTCTAGACTTAAAGACCTCAGTTTAAACTTCAACCGGAAAGTAGTTC
*
16329 ATCGCT
196 CTCGCT
* * *
16335 ACTACAATACGGTTGATACACCCTCGAGTTGAATGGAATCGAACTCAAAAGTCTT
1 GCTACAATGCGGTTGATACACCCTCGAGTTGAATGGAATCAAACTCAAAAGTCTT
16390 TGTTAACAGA
Statistics
Matches: 392, Mismatches: 60, Indels: 10
0.85 0.13 0.02
Matches are distributed among these distances:
200 5 0.01
201 384 0.98
202 3 0.01
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.31
Consensus pattern (201 bp):
GCTACAATGCGGTTGATACACCCTCGAGTTGAATGGAATCAAACTCAAAAGTCTTCATTGATAGA
TAACCCTTATCGCCTTGAGCTATGCTGTGAATTTGGCTGGGATATAGTTCCTTTTTGCTAAATCG
CATCCAACCCGGGTATTCTTCTAGACTTAAAGACCTCAGTTTAAACTTCAACCGGAAAGTAGTTC
CTCGCT
Found at i:20766 original size:12 final size:12
Alignment explanation
Indices: 20749--20779 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
20739 TGAGATAAAT
20749 ATAATAATCAAA
1 ATAATAATCAAA
*
20761 ATAATAATGAAA
1 ATAATAATCAAA
20773 ATAATAA
1 ATAATAA
20780 GTCCTACCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (12 bp):
ATAATAATCAAA
Found at i:22199 original size:54 final size:54
Alignment explanation
Indices: 22156--22548 Score: 563
Period size: 54 Copynumber: 7.3 Consensus size: 54
22146 TTCCTTGTTT
* * * *
22156 TGCAC-CTATAGTGCCAAAATGGTTATTCATCCACGTTGGATGAATTCCGTGAAA
1 TGCACACT-TAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * * *
22210 TGCACACTTAGTGCCGAGACGGTTATTCATCTATATAGGATGAATTCCGTGAAG
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * **
22264 TGCACAATTAGTGTCGAAACAATTATTCATCCACATAGGATGAATTCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* *
22318 TGCACACTTAGTGCCGAAATGGTTATTCATCCACATATGATGAATTCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
** *
22372 TGCACACTTAGTTTCGAAACGGTTATTCATCCACATAGGATGAATTCCATGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* *
22426 TGCACACTTAGTGCCGAAACGGTTATTTATCCACATAGGATGAATTCCATGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* **
22480 TGCACACTTAGTGCTGAAACAATTATTCATCCACATAGGATGAATTCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
*
22534 TGTACACTTAGTGCC
1 TGCACACTTAGTGCC
22549 TATTTGATAA
Statistics
Matches: 301, Mismatches: 37, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
54 299 0.99
55 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (54 bp):
TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
Found at i:22914 original size:22 final size:22
Alignment explanation
Indices: 22872--22942 Score: 71
Period size: 22 Copynumber: 3.5 Consensus size: 22
22862 TAGTCCCTCA
*
22872 GTATCGATA--ACCATACCATG
1 GTATCGATACTACCATACTATG
*
22892 GTATCGATACTACCATTCTATG
1 GTATCGATACTACCATACTATG
* *
22914 GTACCGATACT---ATGCTATG
1 GTATCGATACTACCATACTATG
22933 GTATCGATAC
1 GTATCGATAC
22943 CATTTTTGTA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
19 16 0.36
20 9 0.20
22 19 0.43
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.31
Consensus pattern (22 bp):
GTATCGATACTACCATACTATG
Found at i:32143 original size:3 final size:3
Alignment explanation
Indices: 32137--32196 Score: 70
Period size: 3 Copynumber: 20.7 Consensus size: 3
32127 TTTATTATTC
* * *
32137 AAT AAT AAT GAT AAT AAT AAT ATT AAT AA- AAT AAT AAT ATT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
32184 AAT ATT AA- AAT AA
1 AAT AAT AAT AAT AA
32197 AATGGGGAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
2 4 0.09
3 43 0.91
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:32171 original size:17 final size:18
Alignment explanation
Indices: 32137--32187 Score: 77
Period size: 17 Copynumber: 2.9 Consensus size: 18
32127 TTTATTATTC
* *
32137 AATAATAATGATAATAAT
1 AATATTAATAATAATAAT
32155 AATATTAATAA-AATAAT
1 AATATTAATAATAATAAT
32172 AATATTAATAATAATA
1 AATATTAATAATAATA
32188 TTAAAATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 17 0.57
18 13 0.43
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (18 bp):
AATATTAATAATAATAAT
Found at i:32180 original size:26 final size:26
Alignment explanation
Indices: 32140--32196 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
32130 ATTATTCAAT
* *
32140 AATAATGATAATAATAATATTAATAA
1 AATAATAATAATAATAATAATAATAA
* *
32166 AATAATAATATTAATAATAATATTAA
1 AATAATAATAATAATAATAATAATAA
32192 AATAA
1 AATAA
32197 AATGGGGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (26 bp):
AATAATAATAATAATAATAATAATAA
Found at i:32537 original size:123 final size:122
Alignment explanation
Indices: 32315--32738 Score: 575
Period size: 123 Copynumber: 3.5 Consensus size: 122
32305 TTGATTCTGA
* * * * *
32315 TCTATCTCCTTCTGCGAT-GAATCGATCAAAAGGTTGAATAAGTTCTTTAGATTGTGAACTTTTT
1 TCTATCTCCTTCTGCGATAGAATCGAGCAAAAGGTTGAACAAGTTCTTTAGACTATGAACTTCTT
* * *
32379 CTTCCTCTTCAGATGAGTTTATCTTATTACGAACTCCT-TCTGGAAAT-TTTAATGCTAC
66 CTTCCTCTTCAGATGAGTTT-TCTTATTACGAACT-CTATCTGGAAATGGTT-CTGCTGC
* *
32437 TCTATTTCCTTCTGCGATAGAATCGAGCAAAAGATTGAACAAGTTCTTTAGACTATGAACTTCTT
1 TCTATCTCCTTCTGCGATAGAATCGAGCAAAAGGTTGAACAAGTTCTTTAGACTATGAACTTCTT
* * *
32502 CTTCCTCTTCAGATGAGTTCTTCTTATTACAAACTCTGTCTGGAAATGGTTCTGTTGC
66 CTTCCTCTTCAGATGAGTT-TTCTTATTACGAACTCTATCTGGAAATGGTTCTGCTGC
* * *
32560 TCTATCTCCTTCTGTGATAGAATCGAGCAAAAGGTTAAACAAGTTCTTCAGACTATGAACTTCTT
1 TCTATCTCCTTCTGCGATAGAATCGAGCAAAAGGTTGAACAAGTTCTTTAGACTATGAACTTCTT
* * *
32625 CTTCCTCTTCAGATGAGTTTTTCTTATTATGAACTCTATGTGGAAATGGTTCTGCTGG
66 CTTCCTCTTCAGATGAG-TTTTCTTATTACGAACTCTATCTGGAAATGGTTCTGCTGC
* * * *
32683 TCTATCTCCTTTTGTGATTGAATAGAGCAAAAGGTTGAACAAGTTCTTTAGACTAT
1 TCTATCTCCTTCTGCGATAGAATCGAGCAAAAGGTTGAACAAGTTCTTTAGACTAT
32739 AAATGTTGAG
Statistics
Matches: 269, Mismatches: 28, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
122 19 0.07
123 245 0.91
124 5 0.02
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.39
Consensus pattern (122 bp):
TCTATCTCCTTCTGCGATAGAATCGAGCAAAAGGTTGAACAAGTTCTTTAGACTATGAACTTCTT
CTTCCTCTTCAGATGAGTTTTCTTATTACGAACTCTATCTGGAAATGGTTCTGCTGC
Found at i:40896 original size:91 final size:88
Alignment explanation
Indices: 40744--40922 Score: 331
Period size: 91 Copynumber: 2.0 Consensus size: 88
40734 AGATTGGTCA
40744 AACCTAATTCTCTCTAAGTGTCCAATCGTTCCTTGTCTAAAGGTTTTGTAAAGATATCCGCTAAT
1 AACCTAATTCTCTCTAAGTGTCCAATCGTTCCTTGTCTAAAGGTTTTGTAAAGATATCCGCTAAT
40809 TGGTGCAAAGTATCAACAAATTC
66 TGGTGCAAAGTATCAACAAATTC
40832 AACCTAATTCTCTCCTAAGTGTCCAAAATCGTTCCTTGTCTAAAGGTTTTGTAAAGATATCCGCT
1 AACCTAATTCTCT-CTAAGTGTCC--AATCGTTCCTTGTCTAAAGGTTTTGTAAAGATATCCGCT
40897 AATTGGTGCAAAGTATCAACAAATTC
63 AATTGGTGCAAAGTATCAACAAATTC
40923 TAGAAACATC
Statistics
Matches: 88, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
88 13 0.15
89 10 0.11
91 65 0.74
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.34
Consensus pattern (88 bp):
AACCTAATTCTCTCTAAGTGTCCAATCGTTCCTTGTCTAAAGGTTTTGTAAAGATATCCGCTAAT
TGGTGCAAAGTATCAACAAATTC
Found at i:46454 original size:123 final size:123
Alignment explanation
Indices: 46238--46662 Score: 660
Period size: 123 Copynumber: 3.5 Consensus size: 123
46228 GTTTTCAACA
*
46238 ATGAACTTCTTCTTCCTCTTCAGATGA--T-TTCTTATTACGAACTCTGTCTGGAAATGGTTCTG
1 ATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCTGTCTGGAAATGGTTATG
*
46300 TTGCTCTATCTCCTTATGCGATAGAATCGAGCAAAAGATTGAACAAGTTCTTCAGACT
66 TTTCTCTATCTCCTTATGCGATAGAATCGAGCAAAAGATTGAACAAGTTCTTCAGACT
* *
46358 ATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTTTGTCTGGAAATGGTTTTG
1 ATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCTGTCTGGAAATGGTTATG
* * *
46423 TTTCTCTATCTCCTTTTGCGATAAAATCGAGCAAAAGGTTGAACAAGTTCTTCAGACT
66 TTTCTCTATCTCCTTATGCGATAGAATCGAGCAAAAGATTGAACAAGTTCTTCAGACT
* * *
46481 ATGAACTTCTTCTTCCTCTTAAGATAAGTTCTTCTTATTATGAACTCTGTCTGGAAATGGTTATG
1 ATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCTGTCTGGAAATGGTTATG
* * * *
46546 CTGT-TCTATCTCCTTCTACGATAGAATCGAGCAAAAGTTTGAACAAGTTCTTCAGACT
66 -TTTCTCTATCTCCTTATGCGATAGAATCGAGCAAAAGATTGAACAAGTTCTTCAGACT
* * *
46604 ATTAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCTATCTGGCAATG
1 ATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCTGTCTGGAAATG
46663 TTGATCTCTT
Statistics
Matches: 279, Mismatches: 22, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
120 27 0.10
122 1 0.00
123 249 0.89
124 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (123 bp):
ATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCTGTCTGGAAATGGTTATG
TTTCTCTATCTCCTTATGCGATAGAATCGAGCAAAAGATTGAACAAGTTCTTCAGACT
Found at i:49073 original size:19 final size:20
Alignment explanation
Indices: 49045--49102 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
49035 CAACTTATTC
* *
49045 TCTTTCTTTTC-TGTATTTT
1 TCTTTTTTTTCTTCTATTTT
*
49064 TCTTTTTTTTCTTCTTTTTT
1 TCTTTTTTTTCTTCTATTTT
49084 TCTTTTCTTTT-TTCTATTT
1 TCTTTT-TTTTCTTCTATTT
49103 GAAACTTATC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 10 0.30
20 19 0.58
21 4 0.12
ACGTcount: A:0.03, C:0.16, G:0.02, T:0.79
Consensus pattern (20 bp):
TCTTTTTTTTCTTCTATTTT
Found at i:49084 original size:13 final size:13
Alignment explanation
Indices: 49061--49096 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
49051 TTTTCTGTAT
49061 TTTTCTTTTTTT-
1 TTTTCTTTTTTTC
*
49073 TCTTCTTTTTTTC
1 TTTTCTTTTTTTC
49086 TTTTCTTTTTT
1 TTTTCTTTTTT
49097 CTATTTGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTCTTTTTTTC
Found at i:51415 original size:26 final size:26
Alignment explanation
Indices: 51386--51440 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
51376 GTTTGAAACA
* *
51386 AAATGTAAATGCAAAGATGCAAATGC
1 AAATGCAAATACAAAGATGCAAATGC
**
51412 AAATGCAAATACAAAGATGTGAATGC
1 AAATGCAAATACAAAGATGCAAATGC
51438 AAA
1 AAA
51441 ATAAAAATAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.53, C:0.11, G:0.18, T:0.18
Consensus pattern (26 bp):
AAATGCAAATACAAAGATGCAAATGC
Found at i:51479 original size:26 final size:25
Alignment explanation
Indices: 51433--51481 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
51423 CAAAGATGTG
*
51433 AATGCAAAATAAAAATACAAATGAA
1 AATGAAAAATAAAAATACAAATGAA
*
51458 AATGAAAATATAAAAATGCAAATG
1 AATGAAAA-ATAAAAATACAAATG
51482 CAAACATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.65, C:0.06, G:0.10, T:0.18
Consensus pattern (25 bp):
AATGAAAAATAAAAATACAAATGAA
Found at i:51480 original size:20 final size:19
Alignment explanation
Indices: 51433--51520 Score: 61
Period size: 20 Copynumber: 4.5 Consensus size: 19
51423 CAAAGATGTG
*
51433 AATGCAAAAT-AAAAATACA
1 AATGC-AAATGAAAAATAAA
*
51452 AATGAAAATGAAAATATAAA
1 AATGCAAATGAAAA-ATAAA
*
51472 AATGCAAATGCAAACATAAA
1 AATGCAAATG-AAAAATAAA
* * * * *
51492 AGTACGAATGCAAAATGAA
1 AATGCAAATGAAAAATAAA
*
51511 AATACAAATG
1 AATGCAAATG
51521 CAACGAAGGA
Statistics
Matches: 54, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
18 4 0.07
19 22 0.41
20 25 0.46
21 3 0.06
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.17
Consensus pattern (19 bp):
AATGCAAATGAAAAATAAA
Found at i:51522 original size:19 final size:19
Alignment explanation
Indices: 51470--51523 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
51460 TGAAAATATA
*
51470 AAAATGCAAATGCAAACAT
1 AAAATACAAATGCAAACAT
*
51489 AAAAGTACGAATGCAAA-AT
1 AAAA-TACAAATGCAAACAT
51508 GAAAATACAAATGCAA
1 -AAAATACAAATGCAA
51524 CGAAGGAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.59, C:0.13, G:0.13, T:0.15
Consensus pattern (19 bp):
AAAATACAAATGCAAACAT
Found at i:55230 original size:23 final size:22
Alignment explanation
Indices: 55191--55234 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
55181 CTGTGGGTTG
*
55191 CTTGTTGTTGGTTTTGTATTTTT
1 CTTGTTGTTGGTATTGT-TTTTT
55214 CTTGTTG-TGTGTATTGTTTTT
1 CTTGTTGTTG-GTATTGTTTTT
55235 CTCTCCATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.05, C:0.05, G:0.23, T:0.68
Consensus pattern (22 bp):
CTTGTTGTTGGTATTGTTTTTT
Found at i:55728 original size:3 final size:3
Alignment explanation
Indices: 55722--55787 Score: 61
Period size: 3 Copynumber: 23.7 Consensus size: 3
55712 TTTATTATTC
* *
55722 AAT AAT AAT GAT AAT AAT AAT -AT AAT -AT AAT ATT AAT AA- AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
55767 -AT TAT AAT AAT ATT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
55788 AATGGGAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
2 10 0.20
3 41 0.80
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:55748 original size:11 final size:11
Alignment explanation
Indices: 55722--55779 Score: 64
Period size: 11 Copynumber: 5.0 Consensus size: 11
55712 TTTATTATTC
55722 AATAATAATGAT
1 AATAATAAT-AT
55734 AATAATAATAT
1 AATAATAATAT
55745 AAT-ATAATATT
1 AATAATAATA-T
55756 AATAAAATAATAT
1 AAT--AATAATAT
*
55769 TATAATAATAT
1 AATAATAATAT
55780 TAAAATAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
10 6 0.15
11 17 0.41
12 9 0.22
13 3 0.07
14 6 0.15
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (11 bp):
AATAATAATAT
Found at i:55758 original size:22 final size:23
Alignment explanation
Indices: 55722--55787 Score: 75
Period size: 22 Copynumber: 2.9 Consensus size: 23
55712 TTTATTATTC
55722 AATAATAATGA-TAATAATAATAT
1 AATAATAAT-ATTAATAATAATAT
55745 AAT-ATAATATTAATAAAATAATAT
1 AATAATAATATTAAT--AATAATAT
*
55769 TATAATAATATTAA-AATAA
1 AATAATAATATTAATAATAA
55788 AATGGGAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
21 1 0.03
22 14 0.37
23 3 0.08
24 10 0.26
25 10 0.26
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
AATAATAATATTAATAATAATAT
Found at i:55760 original size:19 final size:19
Alignment explanation
Indices: 55722--55778 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
55712 TTTATTATTC
*
55722 AATAATAATGATAATAATAA
1 AATAAT-ATAATAATAATAA
* *
55742 TATAATATAATATTAATAA
1 AATAATATAATAATAATAA
*
55761 AATAATATTATAATAATA
1 AATAATATAATAATAATA
55779 TTAAAATAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
19 26 0.84
20 5 0.16
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (19 bp):
AATAATATAATAATAATAA
Found at i:55780 original size:11 final size:11
Alignment explanation
Indices: 55723--55787 Score: 60
Period size: 11 Copynumber: 5.6 Consensus size: 11
55713 TTATTATTCA
*
55723 ATAATAATGATA
1 ATAATAAT-ATT
*
55735 ATAATAATATA
1 ATAATAATATT
55746 AT-ATAATATT
1 ATAATAATATT
55756 AATAAAATAATATT
1 -AT--AATAATATT
55770 ATAATAATATT
1 ATAATAATATT
*
55781 AAAATAA
1 ATAATAA
55788 AATGGGAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
10 7 0.15
11 22 0.47
12 8 0.17
13 2 0.04
14 8 0.17
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (11 bp):
ATAATAATATT
Found at i:55786 original size:19 final size:18
Alignment explanation
Indices: 55732--55786 Score: 51
Period size: 19 Copynumber: 3.1 Consensus size: 18
55722 AATAATAATG
55732 ATAATAATAATAT--AAT
1 ATAATAATAATATAAAAT
* *
55748 ATAATATTAATAAAATAAT
1 ATAATAATAATATAA-AAT
*
55767 ATTATAATAATATTAAAAT
1 ATAATAATAATA-TAAAAT
55786 A
1 A
55787 AAATGGGAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
16 11 0.37
19 17 0.57
20 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAATAATAATATAAAAT
Found at i:63639 original size:2 final size:2
Alignment explanation
Indices: 63632--63659 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
63622 CAGTTCACTC
63632 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
63660 TCCCCCACTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:63969 original size:15 final size:16
Alignment explanation
Indices: 63944--63973 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
63934 AAGTTAACGC
63944 CGTTAAACTTTGACGG
1 CGTTAAACTTTGACGG
63960 CGTT-AACTTTGACG
1 CGTTAAACTTTGACG
63974 TGTGAGTGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.33
Consensus pattern (16 bp):
CGTTAAACTTTGACGG
Found at i:65776 original size:15 final size:15
Alignment explanation
Indices: 65752--65786 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
65742 ATGATCCAAT
* *
65752 TCTTTTAGCTGAATC
1 TCTTTCAGCTAAATC
65767 TCTTTCAGCTAAATC
1 TCTTTCAGCTAAATC
65782 TCTTT
1 TCTTT
65787 ACATATTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.20, C:0.23, G:0.09, T:0.49
Consensus pattern (15 bp):
TCTTTCAGCTAAATC
Found at i:72050 original size:21 final size:21
Alignment explanation
Indices: 72024--72063 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
72014 TTCTATTTTA
*
72024 TTTATTTAATTGAGAATTAAG
1 TTTATTTAATTGACAATTAAG
*
72045 TTTATTTATTTGACAATTA
1 TTTATTTAATTGACAATTA
72064 CGATGCTTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.53
Consensus pattern (21 bp):
TTTATTTAATTGACAATTAAG
Found at i:74722 original size:3 final size:3
Alignment explanation
Indices: 74714--74772 Score: 93
Period size: 3 Copynumber: 19.3 Consensus size: 3
74704 TCCCGACACC
74714 ATT ATT ATT ATT ATT ATT ATT ATT -TT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
74761 AATGT ATT ATT A
1 -AT-T ATT ATT A
74773 ATGGGTTTTC
Statistics
Matches: 53, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.04
3 46 0.87
4 4 0.08
5 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:74745 original size:23 final size:23
Alignment explanation
Indices: 74715--74760 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
74705 CCCGACACCA
74715 TTATTATTATTATTATTATTATT
1 TTATTATTATTATTATTATTATT
74738 TTATTATTATTATTATTATTATT
1 TTATTATTATTATTATTATTATT
74761 AATGTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (23 bp):
TTATTATTATTATTATTATTATT
Found at i:74768 original size:23 final size:23
Alignment explanation
Indices: 74717--74772 Score: 87
Period size: 23 Copynumber: 2.4 Consensus size: 23
74707 CGACACCATT
*
74717 ATTATTATTATTATTATTATTTT
1 ATTATTATTATTATTATTATTTA
74740 ATTATTATTATTATTATTA-TTA
1 ATTATTATTATTATTATTATTTA
74762 ATGTATTATTA
1 AT-TATTATTA
74773 ATGGGTTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 4 0.13
23 27 0.87
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (23 bp):
ATTATTATTATTATTATTATTTA
Done.