Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003911.1 Hibiscus syriacus cultivar Beakdansim tig00008460_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: 121441
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:7813 original size:20 final size:18
Alignment explanation
Indices: 7766--7813 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
7756 CCCTAAATTG
*
7766 AGAAAAGAAAAAAGAAAA
1 AGAAGAGAAAAAAGAAAA
*
7784 AGAGGA-AAAAAAGAATAAA
1 AGAAGAGAAAAAAG-A-AAA
7803 AGAAGAGAAAA
1 AGAAGAGAAAA
7814 TAAGGTGGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 7 0.29
18 5 0.21
19 8 0.33
20 4 0.17
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (18 bp):
AGAAGAGAAAAAAGAAAA
Found at i:8706 original size:105 final size:105
Alignment explanation
Indices: 8524--9293 Score: 1246
Period size: 105 Copynumber: 7.4 Consensus size: 105
8514 AGGTTTTACC
* * *
8524 CAGAGCCAATTTCAACTTCACAACAAAGGATATTGGACTCCAGACAACTCATGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
8589 ACGAAGGGACCGCTGGTTGTCAATAAACATTTCTTAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
8629 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
8694 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
8734 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
8799 ATGAAGGGACCGCTGGTTGTCAACAAATATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
8839 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
8904 ATGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
8944 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
9009 ACGAAGGGACCGCTGGTTGTCAATAAACATTTCTTAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
9049 CAGAGCCACTTTCAACTTCACAACGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
9114 ACGAAGGGA---C---TTGTCAATAAACATTTCTTAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
9148 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAAACAACACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * * * *
9213 ACGAAGGGACCGTTAGTTGTCAACAAACAATTTCCCAGTTC
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTT
* * * *
9254 CAGAACCAGTTTCAACTTCACAGCGGAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
9294 GGAACAATAC
Statistics
Matches: 627, Mismatches: 31, Indels: 13
0.93 0.05 0.02
Matches are distributed among these distances:
99 94 0.15
102 1 0.00
105 488 0.78
106 44 0.07
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:9809 original size:8 final size:8
Alignment explanation
Indices: 9796--9835 Score: 57
Period size: 8 Copynumber: 5.1 Consensus size: 8
9786 ATTAAACACA
9796 TATTTTAT
1 TATTTTAT
9804 TATTTTAT
1 TATTTTAT
9812 TA-TTTAT
1 TATTTTAT
9819 TA-TTTATT
1 TATTTTA-T
9827 TATTTTAT
1 TATTTTAT
9835 T
1 T
9836 TCATGTTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 11 0.37
8 15 0.50
9 4 0.13
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (8 bp):
TATTTTAT
Found at i:9819 original size:15 final size:17
Alignment explanation
Indices: 9796--9835 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
9786 ATTAAACACA
9796 TATTTTATTATTTTA-T
1 TATTTTATTATTTTATT
9812 TA-TTTATTA-TTTATT
1 TATTTTATTATTTTATT
9827 TATTTTATT
1 TATTTTATT
9836 TCATGTTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 4 0.18
15 10 0.45
16 8 0.36
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (17 bp):
TATTTTATTATTTTATT
Found at i:11187 original size:3 final size:3
Alignment explanation
Indices: 11181--11223 Score: 54
Period size: 3 Copynumber: 14.3 Consensus size: 3
11171 ACTCTTGTTT
11181 TTA TTA TTA TCTA -TA TTA TTA TTA TTA -TA TATA TTA TTA TTA T
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA T
11224 ATATATTACT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
2 4 0.11
3 27 0.75
4 5 0.14
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:11199 original size:15 final size:15
Alignment explanation
Indices: 11182--11231 Score: 84
Period size: 15 Copynumber: 3.3 Consensus size: 15
11172 CTCTTGTTTT
11182 TATTATTATCTATAT-
1 TATTATTAT-TATATA
11197 TATTATTATTATATA
1 TATTATTATTATATA
11212 TATTATTATTATATA
1 TATTATTATTATATA
11227 TATTA
1 TATTA
11232 CTAACCAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.15
15 29 0.85
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (15 bp):
TATTATTATTATATA
Found at i:11204 original size:18 final size:18
Alignment explanation
Indices: 11181--11229 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
11171 ACTCTTGTTT
*
11181 TTATTATTATCTATATTA
1 TTATTATTATATATATTA
11199 TTATTATTATATATATTA
1 TTATTATTATATATATTA
11217 TTATTA-TATATAT
1 TTATTATTATATAT
11230 TACTAACCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 7 0.23
18 23 0.77
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (18 bp):
TTATTATTATATATATTA
Found at i:11528 original size:18 final size:19
Alignment explanation
Indices: 11507--11542 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
11497 TATATATAAT
11507 TATATTT-TTTTTATTCTC
1 TATATTTCTTTTTATTCTC
*
11525 TATATTTCTTTTTGTTCT
1 TATATTTCTTTTTATTCT
11543 TACTACTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.14, C:0.11, G:0.03, T:0.72
Consensus pattern (19 bp):
TATATTTCTTTTTATTCTC
Found at i:13132 original size:37 final size:36
Alignment explanation
Indices: 13058--13133 Score: 98
Period size: 37 Copynumber: 2.1 Consensus size: 36
13048 TGGGCAATGT
* ** *
13058 TCGACTCGTGCTCGTTAAAAAATTTTGCTGCTTGAC
1 TCGACTCGTGCTCATTAAAAAAAATTGCTGCTCGAC
*
13094 TCGACTCGTGCTCATTAAAAAAAAATTGTTGCTCGAC
1 TCGACTCGTGCTCATT-AAAAAAAATTGCTGCTCGAC
13131 TCG
1 TCG
13134 TTGCTCGTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
36 15 0.44
37 19 0.56
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.33
Consensus pattern (36 bp):
TCGACTCGTGCTCATTAAAAAAAATTGCTGCTCGAC
Found at i:14414 original size:35 final size:35
Alignment explanation
Indices: 14364--14505 Score: 212
Period size: 35 Copynumber: 4.0 Consensus size: 35
14354 TGAATAAGAA
14364 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAGT
1 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAGT
* * * *
14399 GCACGGAAGGAAGCATCGACACTTTCGATTCAAGAA
1 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAG-T
*
14435 GAACGAAATGAAGCATCGGCACTTTCGATTCAAGT
1 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAGT
* *
14470 GAACGAAAGGAAGCGTCAGCACTTTCGATTCAAGT
1 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAGT
14505 G
1 G
14506 TTCATCTTTT
Statistics
Matches: 94, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
35 64 0.68
36 30 0.32
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (35 bp):
GAACGAAAGGAAGCATCGGCACTTTCGATTCAAGT
Found at i:14434 original size:71 final size:71
Alignment explanation
Indices: 14359--14503 Score: 238
Period size: 71 Copynumber: 2.0 Consensus size: 71
14349 GAAGGTGAAT
* *
14359 AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAGTGCACGGAAGGAAGCATC-GACACTT
1 AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAGTGAACGAAAGGAAGCATCAG-CACTT
14423 TCGATTC
65 TCGATTC
* *
14430 AAGAAGAACGAAATGAAGCATCGGCACTTTCGATTCAAGTGAACGAAAGGAAGCGTCAGCACTTT
1 AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAGTGAACGAAAGGAAGCATCAGCACTTT
14495 CGATTC
66 CGATTC
14501 AAG
1 AAG
14504 TGTTCATCTT
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
71 68 0.99
72 1 0.01
ACGTcount: A:0.37, C:0.20, G:0.25, T:0.19
Consensus pattern (71 bp):
AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAGTGAACGAAAGGAAGCATCAGCACTTT
CGATTC
Found at i:14771 original size:12 final size:12
Alignment explanation
Indices: 14754--14779 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
14744 CAACAGTTGT
14754 GCAATCTGTTAG
1 GCAATCTGTTAG
14766 GCAATCTGTTAG
1 GCAATCTGTTAG
14778 GC
1 GC
14780 TTATGTTAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (12 bp):
GCAATCTGTTAG
Found at i:15561 original size:9 final size:9
Alignment explanation
Indices: 15543--15573 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
15533 ACACGCACAC
*
15543 AGCAGTATG
1 AGCAGCATG
15552 AGCAGCATG
1 AGCAGCATG
15561 AGCAGCATG
1 AGCAGCATG
15570 AGCA
1 AGCA
15574 TTGTTGTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.35, C:0.19, G:0.32, T:0.13
Consensus pattern (9 bp):
AGCAGCATG
Found at i:15953 original size:35 final size:35
Alignment explanation
Indices: 15835--15974 Score: 183
Period size: 36 Copynumber: 3.9 Consensus size: 35
15825 TGAATAAGAA
* *
15835 GAACGAAAGGAAGCATCAACACTTTCGATTCAAAGT
1 GAACGGAAGGAAGCATCGACACTTTCGATTC-AAGT
* *
15871 GGACGGAAGGAAGCATCGACACTTTCGATTCAAGAA
1 GAACGGAAGGAAGCATCGACACTTTCGATTCAAG-T
**
15907 GAACGGAAGGAAGCATCGGTACTTTCGATTCAAGT
1 GAACGGAAGGAAGCATCGACACTTTCGATTCAAGT
*
15942 GAACGGAAGGAAGCGTCTG-CACTTTCGATTCAA
1 GAACGGAAGGAAGCATC-GACACTTTCGATTCAA
15975 TTGTTCATCT
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
35 32 0.35
36 60 0.65
ACGTcount: A:0.35, C:0.19, G:0.26, T:0.20
Consensus pattern (35 bp):
GAACGGAAGGAAGCATCGACACTTTCGATTCAAGT
Found at i:28362 original size:30 final size:31
Alignment explanation
Indices: 28323--28393 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
28313 ACATAATTTA
28323 TATCGCATAAACATATCA-TTTCCATACCTT
1 TATCGCATAAACATATCATTTTCCATACCTT
* * *
28353 TATCACATAAACATTTCATTTTTCATACCTT
1 TATCGCATAAACATATCATTTTCCATACCTT
28384 TATCGCATAA
1 TATCGCATAA
28394 TTCATATAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 16 0.44
31 20 0.56
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.39
Consensus pattern (31 bp):
TATCGCATAAACATATCATTTTCCATACCTT
Found at i:35208 original size:30 final size:31
Alignment explanation
Indices: 35167--35237 Score: 117
Period size: 31 Copynumber: 2.3 Consensus size: 31
35157 ACATAATTTA
*
35167 TATCGCATAAACATATCA-TTTCCATACCTT
1 TATCACATAAACATATCATTTTCCATACCTT
*
35197 TATCACATAAACATTTCATTTTCCATACCTT
1 TATCACATAAACATATCATTTTCCATACCTT
35228 TATCACATAA
1 TATCACATAA
35238 TTCATATAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
30 16 0.42
31 22 0.58
ACGTcount: A:0.35, C:0.25, G:0.01, T:0.38
Consensus pattern (31 bp):
TATCACATAAACATATCATTTTCCATACCTT
Found at i:35665 original size:21 final size:21
Alignment explanation
Indices: 35641--35683 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
35631 TCATATTCGT
*
35641 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
35662 TTGAATGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
35683 T
1 T
35684 AGCCCAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.23, G:0.28, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:44175 original size:21 final size:21
Alignment explanation
Indices: 44132--44208 Score: 109
Period size: 21 Copynumber: 3.6 Consensus size: 21
44122 AGTTTGTCCT
* * *
44132 GAAGGACCTGTGAATATGTCCC
1 GAAGGACCTATGAGT-TATCCC
*
44154 GAATGACCTATGAGTTATCCC
1 GAAGGACCTATGAGTTATCCC
44175 GAAGGACCTATGAGTTATCCC
1 GAAGGACCTATGAGTTATCCC
44196 GAAGGACCTATGA
1 GAAGGACCTATGA
44209 AATCCTCGAC
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
21 38 0.76
22 12 0.24
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.23
Consensus pattern (21 bp):
GAAGGACCTATGAGTTATCCC
Found at i:47287 original size:19 final size:19
Alignment explanation
Indices: 47246--47287 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
47236 AATAAGATGT
*
47246 TAAAAGAAAATAATAATAA
1 TAAAAGAAAATAATAAAAA
47265 TAAAAGAAAATAA-AAAAA
1 TAAAAGAAAATAATAAAAA
47283 CTAAA
1 -TAAA
47288 GAGTAAACCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (19 bp):
TAAAAGAAAATAATAAAAA
Found at i:47397 original size:20 final size:24
Alignment explanation
Indices: 47351--47401 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
47341 ATGAAACAAA
47351 AAAATAAAATGAAATTGAATTGAAT
1 AAAATAAAATGAAATTGAA-TGAAT
47376 AAAATAAAAT-AAA-TGAA-G-AT
1 AAAATAAAATGAAATTGAATGAAT
47396 AAAATA
1 AAAATA
47402 TATATACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 8 0.31
21 1 0.04
23 4 0.15
24 3 0.12
25 10 0.38
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.24
Consensus pattern (24 bp):
AAAATAAAATGAAATTGAATGAAT
Found at i:47519 original size:14 final size:14
Alignment explanation
Indices: 47496--47542 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
47486 GAAAATAAGT
* *
47496 AAATAGTATAAATA
1 AAATAATATATATA
47510 AAATAATATATAT-
1 AAATAATATATATA
*
47523 ATATATATATATATA
1 AAATA-ATATATATA
47538 AAATA
1 AAATA
47543 TAAAAATGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 4 0.15
14 19 0.70
15 4 0.15
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (14 bp):
AAATAATATATATA
Found at i:47777 original size:28 final size:28
Alignment explanation
Indices: 47710--47777 Score: 68
Period size: 28 Copynumber: 2.4 Consensus size: 28
47700 GGAAAATATA
47710 AAATATAGTA-AAAAAATAATAAATAAGT
1 AAATATA-TATAAAAAATAATAAATAAGT
* * *
47738 AAACATAGATAAAAAATAATATATATA-T
1 AAATATATATAAAAAATAATAAATA-AGT
*
47766 ATATATATATAA
1 AAATATATATAA
47778 TAGGAAAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
27 1 0.03
28 30 0.94
29 1 0.03
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.29
Consensus pattern (28 bp):
AAATATATATAAAAAATAATAAATAAGT
Found at i:47847 original size:83 final size:79
Alignment explanation
Indices: 47680--47861 Score: 183
Period size: 85 Copynumber: 2.2 Consensus size: 79
47670 ATGAAGTAAG
** * * *
47680 AATATATATATATAT-TGTTAGGAAAATATAAAATATAGTAAAAAAATAATAAATAAGTAAACAT
1 AATATATATATATATATAATAGGAAAATATAAAATATAGCAAAAAAATAAAAAAAAAGTAAACAT
47744 AGATAAAAAATAAT
66 AGATAAAAAATAAT
*
47758 ATATATATATATATATATAATAGGAAAATAATATAATATAACGCAAAAAAATAAAAAAAAAAG-A
1 A-ATATATATATATATATAATAGGAAAAT-ATAAAATAT-A-GCAAAAAAAT-AAAAAAAAAGTA
47822 GAACTATA-ATAAATAAATAA-
61 -AAC-ATAGATAAA-AAATAAT
*
47842 AATATAATTAAATATATATA
1 AATAT-A-TATATATATATA
47862 TATATATACA
Statistics
Matches: 86, Mismatches: 7, Indels: 15
0.80 0.06 0.14
Matches are distributed among these distances:
78 1 0.01
79 14 0.16
80 10 0.12
81 8 0.09
82 1 0.01
83 14 0.16
84 18 0.21
85 20 0.23
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (79 bp):
AATATATATATATATATAATAGGAAAATATAAAATATAGCAAAAAAATAAAAAAAAAGTAAACAT
AGATAAAAAATAAT
Found at i:48316 original size:17 final size:18
Alignment explanation
Indices: 48296--48336 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
48286 GAAACATCGA
48296 ATGCATTC-CATGCACCG
1 ATGCATTCACATGCACCG
*
48313 ATGCATTCTACATGCATCG
1 ATGCATTC-ACATGCACCG
48332 ATGCA
1 ATGCA
48337 CTCTGAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.38
19 13 0.62
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (18 bp):
ATGCATTCACATGCACCG
Found at i:48356 original size:65 final size:63
Alignment explanation
Indices: 48237--48446 Score: 226
Period size: 65 Copynumber: 3.2 Consensus size: 63
48227 TTATTCAAAG
* * * *
48237 TCATGCACCGATGCATCAGTACATGCATCGATGCATTAGTGAAT-TAATTGAAACATCGAATGCA
1 TCATGCACCGATGCATC--TACATGCATCGATGCACT-CTGAATAT-TTTCAAACATCGAATGCA
48301 TT
62 TT
*
48303 CCATGCACCGATGCATTCTACATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATT
1 TCATGCACCGATGCA-TCTACATGCATCGATGCACTCTGAATATTTTC-AAACATCGAATGCATT
* * * * **
48368 TGATGCATCGATGCA-CAAGCCATGCATCGATGCACTCAGGCTATTTTCAAACATCGAATGCATT
1 TCATGCACCGATGCATCTA--CATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATT
*
48432 TCATGCATCGATGCA
1 TCATGCACCGATGCA
48447 CACTTGGTGC
Statistics
Matches: 126, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
63 2 0.02
64 37 0.29
65 71 0.56
66 14 0.11
67 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (63 bp):
TCATGCACCGATGCATCTACATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATT
Found at i:54259 original size:20 final size:21
Alignment explanation
Indices: 54230--54285 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
54220 TTTGTGCTTC
*
54230 ATGCACCGATGCAT-TT-AACA
1 ATGCATCGATGCATCTTGAA-A
*
54250 ATGCATCGATGCATCCTTGAAT
1 ATGCATCGATGCAT-CTTGAAA
54272 ATGCATCGATGCAT
1 ATGCATCGATGCAT
54286 AAGACCATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.42
22 16 0.52
23 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGCATCGATGCATCTTGAAA
Found at i:55810 original size:21 final size:21
Alignment explanation
Indices: 55768--55811 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
55758 ACCCCGGGAG
*
55768 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
55789 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
55810 CT
1 CT
55812 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:56851 original size:17 final size:18
Alignment explanation
Indices: 56831--56871 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
56821 GAAACATCGA
56831 ATGCATTC-CATGCACCG
1 ATGCATTCACATGCACCG
*
56848 ATGCATTCTACATGCATCG
1 ATGCATTC-ACATGCACCG
56867 ATGCA
1 ATGCA
56872 CTCTGAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.38
19 13 0.62
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (18 bp):
ATGCATTCACATGCACCG
Found at i:56891 original size:65 final size:63
Alignment explanation
Indices: 56772--56981 Score: 226
Period size: 65 Copynumber: 3.2 Consensus size: 63
56762 TTATTCAAAG
* * * *
56772 TCATGCACCGATGCATCAGTACATGCATCGATGCATTAGTGAAT-TAATTGAAACATCGAATGCA
1 TCATGCACCGATGCATC--TACATGCATCGATGCACT-CTGAATAT-TTTCAAACATCGAATGCA
56836 TT
62 TT
*
56838 CCATGCACCGATGCATTCTACATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATT
1 TCATGCACCGATGCA-TCTACATGCATCGATGCACTCTGAATATTTTC-AAACATCGAATGCATT
* * * * **
56903 TGATGCATCGATGCA-CAAGCCATGCATCGATGCACTCAGGCTATTTTCAAACATCGAATGCATT
1 TCATGCACCGATGCATCTA--CATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATT
*
56967 TCATGCATCGATGCA
1 TCATGCACCGATGCA
56982 CACTTGGTGC
Statistics
Matches: 126, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
63 2 0.02
64 37 0.29
65 71 0.56
66 14 0.11
67 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (63 bp):
TCATGCACCGATGCATCTACATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATT
Found at i:58091 original size:37 final size:38
Alignment explanation
Indices: 58049--58134 Score: 102
Period size: 38 Copynumber: 2.3 Consensus size: 38
58039 GGATTCTATA
* *
58049 TTTAGGAGTTTAAATAATAG-TAGAACTCTATCATATT
1 TTTAGGAGTTTAAATAATAGCAAAAACTCTATCATATT
* ** * *
58086 TTTAGGAGTTTGAATCCTAGCAAAAATTCTATCTTATT
1 TTTAGGAGTTTAAATAATAGCAAAAACTCTATCATATT
58124 TTTAGGAGTTT
1 TTTAGGAGTTT
58135 GAATCCTAGT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
37 17 0.41
38 24 0.59
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.43
Consensus pattern (38 bp):
TTTAGGAGTTTAAATAATAGCAAAAACTCTATCATATT
Found at i:60562 original size:20 final size:21
Alignment explanation
Indices: 60537--60588 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
60527 TTTTCCCAAT
*
60537 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
60557 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
60578 TCGCAATGCGA
1 TCGCAATGCGA
60589 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:60602 original size:20 final size:20
Alignment explanation
Indices: 60577--60691 Score: 99
Period size: 20 Copynumber: 5.7 Consensus size: 20
60567 AATTGGGAAA
60577 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
60597 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
60618 ATCGCAATGAGATACCGACT
1 ATCGCAATGCGATACTGACT
* *
60638 TTCGCAATGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
60658 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
60678 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
60692 TTTCAAAGCG
Statistics
Matches: 75, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
19 4 0.05
20 45 0.60
21 24 0.32
22 2 0.03
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:61219 original size:20 final size:20
Alignment explanation
Indices: 61165--61223 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
61155 GCGATTCTCT
**
61165 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
61185 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
61205 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
61224 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:61414 original size:25 final size:24
Alignment explanation
Indices: 61360--61414 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
61350 TGTTTATTAT
* *
61360 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
61384 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
61410 TGTTT
1 TGTTT
61415 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:62563 original size:18 final size:18
Alignment explanation
Indices: 62542--62586 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
62532 TCTACTTTGG
*
62542 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
62560 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
62578 GAGCCATCA
1 GAGCCATCA
62587 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:63000 original size:12 final size:13
Alignment explanation
Indices: 62969--63011 Score: 52
Period size: 12 Copynumber: 3.2 Consensus size: 13
62959 ACTGCTAAAC
62969 TGTTTTTGTTAGTATT
1 TGTTTTTG-TA-T-TT
62985 TGTTTTTG-ATTT
1 TGTTTTTGTATTT
62997 TGTTTTTGTATTT
1 TGTTTTTGTATTT
63010 TG
1 TG
63012 GTTGAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 10 0.38
13 7 0.27
14 1 0.04
16 8 0.31
ACGTcount: A:0.09, C:0.00, G:0.19, T:0.72
Consensus pattern (13 bp):
TGTTTTTGTATTT
Found at i:63147 original size:19 final size:19
Alignment explanation
Indices: 63125--63192 Score: 73
Period size: 20 Copynumber: 3.5 Consensus size: 19
63115 GCTATTTTGT
**
63125 CATTGCGATTTTCATTTCG
1 CATTGCGATAGTCATTTCG
*
63144 CATTGCGATAGCCATTTCCG
1 CATTGCGATAGTCATTT-CG
*
63164 CGTTGCGATAGTCATTTTCG
1 CATTGCGATAGTCA-TTTCG
*
63184 CGTTGCGAT
1 CATTGCGAT
63193 TTTAAGTTTC
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
19 14 0.33
20 25 0.60
21 3 0.07
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.38
Consensus pattern (19 bp):
CATTGCGATAGTCATTTCG
Found at i:63171 original size:20 final size:19
Alignment explanation
Indices: 63137--63192 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
63127 TTGCGATTTT
*
63137 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
63156 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
63176 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
63193 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:65080 original size:14 final size:14
Alignment explanation
Indices: 65061--65096 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
65051 ATTGTTTAAT
65061 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
65075 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
65089 TGATTTGT
1 TGATTTGT
65097 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:65292 original size:20 final size:20
Alignment explanation
Indices: 65267--65342 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
65257 TCGCATTGCG
*
65267 ATTTTCTAGTTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
* ***
65287 ATTTTCGCGTTGCGATTTTTC
1 ATTTTCGAGTTGCGA-TAGCC
*
65308 A-TTTCGAATTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
*
65327 ATTTTCGCGTTGCGAT
1 ATTTTCGAGTTGCGAT
65343 TTCCCCGTTG
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
19 3 0.07
20 36 0.86
21 3 0.07
ACGTcount: A:0.17, C:0.20, G:0.21, T:0.42
Consensus pattern (20 bp):
ATTTTCGAGTTGCGATAGCC
Found at i:65300 original size:34 final size:34
Alignment explanation
Indices: 65255--65358 Score: 109
Period size: 40 Copynumber: 2.9 Consensus size: 34
65245 GCGATTTTCA
*
65255 TTTCGCATTGCGATTTTCTAGTTGCGATAGCCAT
1 TTTCGCGTTGCGATTTTCTAGTTGCGATAGCCAT
*
65289 TTTCGCGTTGCGATTTTTCATTTCGAATTGCGATAGCCAT
1 TTTCGCGTTGCGA-TTTTC---T--AGTTGCGATAGCCAT
* **
65329 TTTCGCGTTGCGATTTCCCCGTTGCGATAG
1 TTTCGCGTTGCGATTTTCTAGTTGCGATAG
65359 TCAAATGAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
34 21 0.36
35 5 0.09
38 1 0.02
39 4 0.07
40 27 0.47
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.40
Consensus pattern (34 bp):
TTTCGCGTTGCGATTTTCTAGTTGCGATAGCCAT
Found at i:65678 original size:20 final size:21
Alignment explanation
Indices: 65630--65681 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
65620 ATAGTCAATA
*
65630 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
* **
65651 TCGTATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
65671 TCGCATTGCGA
1 TCGCATTGCGA
65682 ATTAGGAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:66517 original size:24 final size:24
Alignment explanation
Indices: 66460--66519 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
66450 TAGTCAGTAT
*
66460 TCGAAATTTGATCTTGGTCAATAC
1 TCGAAATTTGATATTGGTCAATAC
* * *
66484 CCGGACTTTGATATTGGTCAATAC
1 TCGAAATTTGATATTGGTCAATAC
*
66508 TCGAATTTTGAT
1 TCGAAATTTGAT
66520 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (24 bp):
TCGAAATTTGATATTGGTCAATAC
Found at i:66725 original size:21 final size:21
Alignment explanation
Indices: 66659--66725 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
66649 GTGAATCGGG
*
66659 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
66679 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
66701 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
66722 CTCT
1 CTCT
66726 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:66744 original size:42 final size:42
Alignment explanation
Indices: 66659--66865 Score: 184
Period size: 42 Copynumber: 4.9 Consensus size: 42
66649 GTGAATCGGG
* * * *
66659 CTCTTGAATGGTGGGA-GGGACCTCTTCAACG-ATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGAATGACAGGGGC
*
66701 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGACAGGGGC
* * * * * * * *
66743 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGTGAC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGACAGGGGC
* *
66785 CTCTTGAACGGTGGAAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGACAGGGGC
* * * * * * *
66827 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATAACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGACAGG
66866 CGAGTCGGGC
Statistics
Matches: 130, Mismatches: 33, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
41 4 0.03
42 122 0.94
43 4 0.03
ACGTcount: A:0.24, C:0.18, G:0.36, T:0.22
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGACAGGGGC
Found at i:66804 original size:84 final size:84
Alignment explanation
Indices: 66689--66864 Score: 325
Period size: 84 Copynumber: 2.1 Consensus size: 84
66679 CCTCTTCAAC
* *
66689 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGACCTCTTGAACGGTGGAAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
66754 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
66773 GATGACAGTGACCTCTTGAACGGTGGAAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGACCTCTTGAACGGTGGAAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
66838 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
*
66857 GATAACAG
1 GATGACAG
66865 GCGAGTCGGG
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 89 1.00
ACGTcount: A:0.25, C:0.18, G:0.36, T:0.21
Consensus pattern (84 bp):
GATGACAGTGACCTCTTGAACGGTGGAAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
TAGGAGTGGACTCTTGAGG
Found at i:67258 original size:91 final size:90
Alignment explanation
Indices: 67083--67267 Score: 300
Period size: 91 Copynumber: 2.0 Consensus size: 90
67073 ATTTCAAACT
*
67083 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
67148 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
67176 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
*
67240 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
67267 T
1 T
67268 AAGCAATCTA
Statistics
Matches: 88, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
91 42 0.48
93 19 0.22
95 27 0.31
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:68984 original size:20 final size:19
Alignment explanation
Indices: 68953--69093 Score: 95
Period size: 19 Copynumber: 7.8 Consensus size: 19
68943 TCTTTTGGTT
68953 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
68972 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
68993 GAAATGACCATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
69012 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
** * *
69026 GAAATGACTATTGCGACGA
1 GAAATGAAAATCGCAACGA
*
69045 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
69059 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
69078 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
69094 TGCGATTTTG
Statistics
Matches: 95, Mismatches: 15, Indels: 24
0.71 0.11 0.18
Matches are distributed among these distances:
14 18 0.19
16 4 0.04
17 4 0.04
19 38 0.40
20 29 0.31
21 2 0.02
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:69045 original size:33 final size:33
Alignment explanation
Indices: 68978--69076 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
68968 ACGAGATAAT
68978 GAGAATCGCAACGCGGAAATGACCATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACCATCGCAACGA
* * *
69012 GAGAATCGCAACGCGAAATGACTATTGCGACGA
1 GAGAATCGCAACGCGAAATGACCATCGCAACGA
**
69045 GAGAATCGCAACGCGAAATGAAAATCGCAACG
1 GAGAATCGCAACGCGAAATGACCATCGCAACG
69077 CGAAATGAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
33 44 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.23, G:0.26, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACCATCGCAACGA
Found at i:69128 original size:19 final size:19
Alignment explanation
Indices: 69106--69160 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 19
69096 CGATTTTGGC
69106 TTCGCGTTGCGATTTTTAT
1 TTCGCGTTGCGATTTTTAT
**
69125 TTCGCGTTGCGATAGTTAT
1 TTCGCGTTGCGATTTTTAT
69144 TTCCGCGTTGCGATTTT
1 TT-CGCGTTGCGATTTT
69161 CATTCTCGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 19 0.61
20 12 0.39
ACGTcount: A:0.11, C:0.18, G:0.24, T:0.47
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTTAT
Found at i:69695 original size:20 final size:20
Alignment explanation
Indices: 69670--69722 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
69660 GCGCTATGTA
69670 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
*
69690 AATCGCGTTGCAAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
69710 TATCTCGTTGCGA
1 AATCGCGTTGCGA
69723 TTTTGTATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:69875 original size:21 final size:21
Alignment explanation
Indices: 69835--69875 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
69825 ACTGTAGACC
**
69835 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
69856 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
69876 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:77584 original size:31 final size:31
Alignment explanation
Indices: 77549--77608 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
77539 GGCTACATTC
77549 CTGTTGTTATTAACAACCGATCAAAAAGTAT
1 CTGTTGTTATTAACAACCGATCAAAAAGTAT
77580 CTGTTGTTATTAACAACCGATCAAAAAGT
1 CTGTTGTTATTAACAACCGATCAAAAAGT
77609 GTCCATTCCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (31 bp):
CTGTTGTTATTAACAACCGATCAAAAAGTAT
Found at i:80411 original size:36 final size:36
Alignment explanation
Indices: 80364--80435 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
80354 TTTAAAAAAG
* *
80364 CAGATTGCAAAAGATGAGAGTAAATCTACATCACGA
1 CAGATTACAAAAGATAAGAGTAAATCTACATCACGA
80400 CAGATTACAAAAGATAAGAGTAAATCTACATCACGA
1 CAGATTACAAAAGATAAGAGTAAATCTACATCACGA
80436 TAACATAGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.19
Consensus pattern (36 bp):
CAGATTACAAAAGATAAGAGTAAATCTACATCACGA
Found at i:92791 original size:2 final size:2
Alignment explanation
Indices: 92784--92818 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
92774 TACTATTTAT
92784 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
92819 TTAGAAAACG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:102338 original size:21 final size:21
Alignment explanation
Indices: 102312--102353 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
102302 CCATAATGGG
*
102312 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
102333 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
102354 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:102430 original size:19 final size:20
Alignment explanation
Indices: 102390--102427 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
102380 TGTTGAACAG
102390 GGGGGGAATCGGTACCCCCT
1 GGGGGGAATCGGTACCCCCT
102410 GGGGGGAATCGGTACCCC
1 GGGGGGAATCGGTACCCC
102428 TGGACATTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.16, C:0.29, G:0.42, T:0.13
Consensus pattern (20 bp):
GGGGGGAATCGGTACCCCCT
Found at i:102480 original size:20 final size:20
Alignment explanation
Indices: 102455--102532 Score: 94
Period size: 20 Copynumber: 4.2 Consensus size: 20
102445 GCTTTAGACA
*
102455 GGGGGGAATCAGTACCCCCT
1 GGGGGGAATCTGTACCCCCT
*
102475 GGGGGGTATCTGTA--CCC-
1 GGGGGGAATCTGTACCCCCT
*
102492 --GGGGTATCTGTACCCCCT
1 GGGGGGAATCTGTACCCCCT
102510 GGGGGGAATCTGTACCCCCT
1 GGGGGGAATCTGTACCCCCT
102530 GGG
1 GGG
102533 CAATCTTGAA
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
15 12 0.24
17 3 0.06
18 3 0.06
20 32 0.64
ACGTcount: A:0.14, C:0.28, G:0.37, T:0.21
Consensus pattern (20 bp):
GGGGGGAATCTGTACCCCCT
Found at i:102497 original size:15 final size:15
Alignment explanation
Indices: 102477--102506 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
102467 TACCCCCTGG
102477 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
102492 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
102507 CCTGGGGGGA
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:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:102512 original size:35 final size:35
Alignment explanation
Indices: 102457--102526 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
102447 TTTAGACAGG
*
102457 GGGGAATCAGTACCCCCTGGGGGGTATCTGTACCC
1 GGGGAATCAGTACCCCCTGGGGGGAATCTGTACCC
* *
102492 GGGGTATCTGTACCCCCTGGGGGGAATCTGTACCC
1 GGGGAATCAGTACCCCCTGGGGGGAATCTGTACCC
102527 CCTGGGCAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.16, C:0.29, G:0.34, T:0.21
Consensus pattern (35 bp):
GGGGAATCAGTACCCCCTGGGGGGAATCTGTACCC
Found at i:102869 original size:22 final size:22
Alignment explanation
Indices: 102838--102884 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
102828 AAGCTCCCCC
102838 TTTTTCATTAAGAAATTGAATT
1 TTTTTCATTAAGAAATTGAATT
*
102860 TTTTTTATTAAGAAATTGAATT
1 TTTTTCATTAAGAAATTGAATT
102882 TTT
1 TTT
102885 CAAACCAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.34, C:0.02, G:0.09, T:0.55
Consensus pattern (22 bp):
TTTTTCATTAAGAAATTGAATT
Found at i:104002 original size:19 final size:20
Alignment explanation
Indices: 103959--104006 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
103949 TCTAAATCCT
*
103959 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
103979 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
103998 TTTTCAAAA
1 TTTTCAAAA
104007 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:104911 original size:34 final size:32
Alignment explanation
Indices: 104858--104927 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
104848 ACCTTACAAC
* *
104858 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACATT
* *
104890 TCCCTAGCTTTTACACGGGCTAAGCTATAACATT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACATT
104924 TCCC
1 TCCC
104928 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 5 0.16
34 20 0.62
ACGTcount: A:0.23, C:0.30, G:0.14, T:0.33
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACATT
Found at i:105237 original size:21 final size:21
Alignment explanation
Indices: 105211--105252 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
105201 CCAGAATGGG
*
105211 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
105232 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
105253 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:105314 original size:20 final size:20
Alignment explanation
Indices: 105289--105350 Score: 124
Period size: 20 Copynumber: 3.1 Consensus size: 20
105279 TGTTGAACAG
105289 GGGGGGAATCGGTACCCCCT
1 GGGGGGAATCGGTACCCCCT
105309 GGGGGGAATCGGTACCCCCT
1 GGGGGGAATCGGTACCCCCT
105329 GGGGGGAATCGGTACCCCCT
1 GGGGGGAATCGGTACCCCCT
105349 GG
1 GG
105351 ACATTCTGTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.15, C:0.29, G:0.42, T:0.15
Consensus pattern (20 bp):
GGGGGGAATCGGTACCCCCT
Found at i:105402 original size:21 final size:21
Alignment explanation
Indices: 105376--105455 Score: 91
Period size: 21 Copynumber: 4.1 Consensus size: 21
105366 GCTTTAGACA
*
105376 GGGGGGAATCGGTACCCCCTG
1 GGGGGGAATCTGTACCCCCTG
*
105397 GGGGGGTATCTGTA--CCC--
1 GGGGGGAATCTGTACCCCCTG
*
105414 --GGGGTATCTGTACCCCCTG
1 GGGGGGAATCTGTACCCCCTG
105433 GGGGGGAATCTGTACCCCCTG
1 GGGGGGAATCTGTACCCCCTG
105454 GG
1 GG
105456 CAATCTTGAA
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
15 12 0.24
17 3 0.06
19 3 0.06
21 32 0.64
ACGTcount: A:0.12, C:0.28, G:0.40, T:0.20
Consensus pattern (21 bp):
GGGGGGAATCTGTACCCCCTG
Found at i:105417 original size:15 final size:15
Alignment explanation
Indices: 105399--105428 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
105389 ACCCCCTGGG
105399 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
105414 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
105429 CCTGGGGGGG
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:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:105434 original size:36 final size:36
Alignment explanation
Indices: 105378--105449 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
105368 TTTAGACAGG
*
105378 GGGGAATCGGTACCCCCTGGGGGGGTATCTGTACCC
1 GGGGAATCGGTACCCCCTGGGGGGGAATCTGTACCC
* *
105414 GGGGTATCTGTACCCCCTGGGGGGGAATCTGTACCC
1 GGGGAATCGGTACCCCCTGGGGGGGAATCTGTACCC
105450 CCTGGGCAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.14, C:0.28, G:0.38, T:0.21
Consensus pattern (36 bp):
GGGGAATCGGTACCCCCTGGGGGGGAATCTGTACCC
Found at i:109185 original size:14 final size:16
Alignment explanation
Indices: 109164--109199 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
109154 GAAGTTGGTG
*
109164 GTTTTTTTTGGTTTT-
1 GTTTTTTATGGTTTTA
109179 GTTTTTTATGGTTTTA
1 GTTTTTTATGGTTTTA
109195 GTTTT
1 GTTTT
109200 CACAATTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.06, C:0.00, G:0.19, T:0.75
Consensus pattern (16 bp):
GTTTTTTATGGTTTTA
Found at i:111870 original size:16 final size:17
Alignment explanation
Indices: 111849--111900 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 17
111839 AAATTAATTT
111849 AATTACT-TAACTTTCA
1 AATTACTCTAACTTTCA
111865 AATTACTCATAA-TTT--
1 AATTACTC-TAACTTTCA
*
111880 AATCACTCTAACTTTCA
1 AATTACTCTAACTTTCA
111897 AATT
1 AATT
111901 TAAATATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 3 0.10
15 10 0.34
16 7 0.24
17 6 0.21
18 3 0.10
ACGTcount: A:0.38, C:0.19, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTACTCTAACTTTCA
Found at i:119620 original size:10 final size:10
Alignment explanation
Indices: 119607--119652 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
119597 AAATATAAAA
119607 AAAAAATAAG
1 AAAAAATAAG
119617 AAAAAATAATG
1 AAAAAATAA-G
*
119628 TAAAAA-AAG
1 AAAAAATAAG
119637 AAAAAAATAA-
1 -AAAAAATAAG
119647 AAAAAA
1 AAAAAA
119653 AAAAACCAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
9 7 0.23
10 16 0.52
11 8 0.26
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.11
Consensus pattern (10 bp):
AAAAAATAAG
Found at i:119655 original size:13 final size:13
Alignment explanation
Indices: 119594--119656 Score: 56
Period size: 13 Copynumber: 4.5 Consensus size: 13
119584 AAATTATAAT
*
119594 AAAAAATATAAAA
1 AAAAAATAAAAAA
119607 AAAAAATAAGAAAA
1 AAAAAATAA-AAAA
119621 AATAATGTAA-AAAAAGA
1 AA-AA---AATAAAAA-A
119638 AAAAAATAAAAAA
1 AAAAAATAAAAAA
119651 AAAAAA
1 AAAAAA
119657 ACCAAAACCA
Statistics
Matches: 42, Mismatches: 1, Indels: 14
0.74 0.02 0.25
Matches are distributed among these distances:
13 17 0.40
14 11 0.26
15 2 0.05
16 5 0.12
17 5 0.12
18 2 0.05
ACGTcount: A:0.84, C:0.00, G:0.05, T:0.11
Consensus pattern (13 bp):
AAAAAATAAAAAA
Done.