Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006136.1 Hibiscus syriacus cultivar Beakdansim tig00014554_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: 137434
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:2316 original size:7 final size:7
Alignment explanation
Indices: 2304--2329 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2294 AAACTAAGGA
2304 TGGCATT
1 TGGCATT
2311 TGGCATT
1 TGGCATT
2318 TGGCATT
1 TGGCATT
2325 TGGCA
1 TGGCA
2330 ATGACAATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.15, G:0.31, T:0.38
Consensus pattern (7 bp):
TGGCATT
Found at i:14122 original size:23 final size:23
Alignment explanation
Indices: 14092--14138 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
14082 CTTTGGCTCC
14092 AAACAAAATCTGAATCTGGTTCG
1 AAACAAAATCTGAATCTGGTTCG
*
14115 AAACAAAATCTGGATCTGGTTCG
1 AAACAAAATCTGAATCTGGTTCG
14138 A
1 A
14139 GTGTTTTGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (23 bp):
AAACAAAATCTGAATCTGGTTCG
Found at i:15516 original size:8 final size:9
Alignment explanation
Indices: 15498--15528 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
15488 TATATTAAGA
15498 TTTTTATTT
1 TTTTTATTT
15507 TTTTTATTTT
1 TTTTTA-TTT
15517 TTTTTATTT
1 TTTTTATTT
15526 TTT
1 TTT
15529 GCAATTTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTTATTT
Found at i:15517 original size:10 final size:10
Alignment explanation
Indices: 15498--15528 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
15488 TATATTAAGA
15498 TTTTTA-TTT
1 TTTTTATTTT
15507 TTTTTATTTT
1 TTTTTATTTT
15517 TTTTTATTTT
1 TTTTTATTTT
15527 TT
1 TT
15529 GCAATTTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.29
10 15 0.71
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (10 bp):
TTTTTATTTT
Found at i:15536 original size:19 final size:19
Alignment explanation
Indices: 15498--15536 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
15488 TATATTAAGA
** *
15498 TTTTTATTTTTTTTATTTT
1 TTTTTATTTTTTGCAATTT
15517 TTTTTATTTTTTGCAATTT
1 TTTTTATTTTTTGCAATTT
15536 T
1 T
15537 CATAGGCAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.13, C:0.03, G:0.03, T:0.82
Consensus pattern (19 bp):
TTTTTATTTTTTGCAATTT
Found at i:41993 original size:12 final size:12
Alignment explanation
Indices: 41976--42006 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
41966 GAGATTAAAC
41976 ATTAAGCAAATT
1 ATTAAGCAAATT
41988 ATTAAGCAAATT
1 ATTAAGCAAATT
42000 ATGTAAG
1 AT-TAAG
42007 ATGAAAGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.78
13 4 0.22
ACGTcount: A:0.48, C:0.06, G:0.13, T:0.32
Consensus pattern (12 bp):
ATTAAGCAAATT
Found at i:43343 original size:7 final size:7
Alignment explanation
Indices: 43330--43361 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
43320 ATAACATTGA
43330 AATTATT
1 AATTATT
*
43337 CATTATT
1 AATTATT
43344 AATTATT
1 AATTATT
43351 AATTATT
1 AATTATT
43358 AATT
1 AATT
43362 GGAGTGATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (7 bp):
AATTATT
Found at i:44421 original size:31 final size:30
Alignment explanation
Indices: 44378--44445 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
44368 CATAAGGGAA
* *
44378 TACCTTGGGGCCTTAGAGCCCACCAAGAGTG
1 TACCTTGAGGCCTCAGAGCCCACCAA-AGTG
* *
44409 TACCTTGAGGCCTCAGAGCCTACCCAAGTG
1 TACCTTGAGGCCTCAGAGCCCACCAAAGTG
44439 TCACCTT
1 T-ACCTT
44446 AAGTCCGTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 5 0.16
31 27 0.84
ACGTcount: A:0.22, C:0.32, G:0.24, T:0.22
Consensus pattern (30 bp):
TACCTTGAGGCCTCAGAGCCCACCAAAGTG
Found at i:45546 original size:27 final size:28
Alignment explanation
Indices: 45493--45555 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 28
45483 CAGGGATTGG
* *
45493 GGGTATTTTAGGTTATTTCACACTTCAA
1 GGGTATTTTAGGTCATTTCACAATTCAA
* *
45521 GGGTATTTT-GGTCATTTTATAATTCAA
1 GGGTATTTTAGGTCATTTCACAATTCAA
45548 GGGTATTT
1 GGGTATTT
45556 CTTTCATTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 22 0.71
28 9 0.29
ACGTcount: A:0.24, C:0.10, G:0.21, T:0.46
Consensus pattern (28 bp):
GGGTATTTTAGGTCATTTCACAATTCAA
Found at i:51118 original size:23 final size:23
Alignment explanation
Indices: 51069--51118 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
51059 GGTTCAAGTA
*
51069 CAAACTCGAATTTGAGCTTGAAC
1 CAAACTCGAATTTGAGCTTCAAC
* * *
51092 CAAACTTGAATTTGAGTTTCAAT
1 CAAACTCGAATTTGAGCTTCAAC
51115 CAAA
1 CAAA
51119 TTAAGTCTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (23 bp):
CAAACTCGAATTTGAGCTTCAAC
Found at i:51187 original size:26 final size:26
Alignment explanation
Indices: 51158--51207 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
51148 TTTTTCAAGC
* *
51158 TCGAGTCAAACTTCTAATTTTTAATT
1 TCGAGTAAAACTTCAAATTTTTAATT
*
51184 TCGAGTAAAACTTGAAATTTTTAA
1 TCGAGTAAAACTTCAAATTTTTAA
51208 GTTCACGAGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (26 bp):
TCGAGTAAAACTTCAAATTTTTAATT
Found at i:55651 original size:6 final size:6
Alignment explanation
Indices: 55637--55693 Score: 62
Period size: 6 Copynumber: 9.5 Consensus size: 6
55627 ATAGAAAAAT
* * * *
55637 AAATAA AAATGA AAAGAC AAATAA AAATAA AAATAA AAA-AA TAAAAAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA -AAATAA
55685 AAATAA AAA
1 AAATAA AAA
55694 ATAATAGTAG
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
5 2 0.05
6 38 0.90
7 2 0.05
ACGTcount: A:0.82, C:0.02, G:0.04, T:0.12
Consensus pattern (6 bp):
AAATAA
Found at i:55668 original size:24 final size:24
Alignment explanation
Indices: 55631--55693 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
55621 TATTAGATAG
* * *
55631 AAAAATAAATAAAAATGAAAAGAC
1 AAAAAAAAATAAAAATAAAAAAAC
* *
55655 AAATAAAAATAAAAATAAAAAAAT
1 AAAAAAAAATAAAAATAAAAAAAC
55679 AAAAAAAAATAAAAA
1 AAAAAAAAATAAAAA
55694 ATAATAGTAG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.83, C:0.02, G:0.03, T:0.13
Consensus pattern (24 bp):
AAAAAAAAATAAAAATAAAAAAAC
Found at i:55686 original size:18 final size:18
Alignment explanation
Indices: 55631--55694 Score: 65
Period size: 18 Copynumber: 3.2 Consensus size: 18
55621 TATTAGATAG
*
55631 AAAAATAAATAAAAATGAAA
1 AAAAATAAAAAAAAAT--AA
55651 AGACAAATAAAAATAAAAATAA
1 A-A-AAAT-AAAA-AAAAATAA
55673 AAAAATAAAAAAAAATAA
1 AAAAATAAAAAAAAATAA
55691 AAAA
1 AAAA
55695 TAATAGTAGT
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
18 12 0.31
19 4 0.10
20 5 0.13
21 2 0.05
22 7 0.18
23 3 0.08
24 6 0.15
ACGTcount: A:0.83, C:0.02, G:0.03, T:0.12
Consensus pattern (18 bp):
AAAAATAAAAAAAAATAA
Found at i:55886 original size:20 final size:20
Alignment explanation
Indices: 55861--55929 Score: 61
Period size: 20 Copynumber: 3.3 Consensus size: 20
55851 AATAAAATGG
55861 AAAAAATATGAAATAAAAAT
1 AAAAAATATGAAATAAAAAT
*
55881 AAAAAATACT--AATAATAATT
1 AAAAAATA-TGAAATAA-AAAT
*
55901 AAAAAAACATGATAATAAATAAT
1 -AAAAAATATGA-AATAAA-AAT
55924 AAAAAA
1 AAAAAA
55930 AAAAAAGAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
19 5 0.13
20 12 0.31
21 8 0.21
22 7 0.18
23 7 0.18
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.22
Consensus pattern (20 bp):
AAAAAATATGAAATAAAAAT
Found at i:57024 original size:13 final size:14
Alignment explanation
Indices: 57008--57037 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
56998 TAAAAACATA
57008 AAAAGAAAAT-AAT
1 AAAAGAAAATGAAT
57021 AAAAGAAAATGAAT
1 AAAAGAAAATGAAT
57035 AAA
1 AAA
57038 TAATAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (14 bp):
AAAAGAAAATGAAT
Found at i:57044 original size:3 final size:3
Alignment explanation
Indices: 57015--57063 Score: 57
Period size: 3 Copynumber: 16.3 Consensus size: 3
57005 ATAAAAAGAA
*
57015 AAT AAT AA- AAG AA- AAT GAAT AAAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT -AAT -AAT AAT AAT AAT AAT AAT AAT AAT
57060 AAT A
1 AAT A
57064 TAAATTATAT
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
2 4 0.10
3 32 0.76
4 6 0.14
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:57082 original size:9 final size:8
Alignment explanation
Indices: 57032--57081 Score: 50
Period size: 9 Copynumber: 6.1 Consensus size: 8
57022 AAAGAAAATG
57032 AATAA-AT
1 AATAATAT
57039 AATAATAAT
1 AATAAT-AT
57048 AATAATAAT
1 AATAAT-AT
57057 AATAATAT
1 AATAATAT
*
57065 AAATTATAT
1 -AATAATAT
57074 AAT-ATAT
1 AATAATAT
57081 A
1 A
57082 TTTTCTTCAA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
7 10 0.26
8 5 0.13
9 24 0.62
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
AATAATAT
Found at i:57126 original size:32 final size:31
Alignment explanation
Indices: 57105--57218 Score: 88
Period size: 33 Copynumber: 3.5 Consensus size: 31
57095 TATTTTTTTG
*
57105 AACTATATATTATATTTAAAAAAGTTTTCAA
1 AACTATATATTATATTCAAAAAAGTTTTCAA
*
57136 AACTATATATTATATAGTTTTC-AAAATGTTTT-AA
1 AACTATATA-T-TATA---TTCAAAAAAGTTTTCAA
* * * *
57170 AAATATTATATAAGTTTTCAAAAAATGTTTTTAA
1 AACTA-TATATTA-TATTCAAAAAA-GTTTTCAA
57204 AACTATATATTATAT
1 AACTATATATTATAT
57219 AATTTTTTTC
Statistics
Matches: 64, Mismatches: 9, Indels: 19
0.70 0.10 0.21
Matches are distributed among these distances:
31 12 0.19
32 7 0.11
33 16 0.25
34 14 0.22
35 13 0.20
36 2 0.03
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (31 bp):
AACTATATATTATATTCAAAAAAGTTTTCAA
Found at i:57180 original size:68 final size:68
Alignment explanation
Indices: 57105--57296 Score: 215
Period size: 66 Copynumber: 2.9 Consensus size: 68
57095 TATTTTTTTG
*
57105 AACTATATAT-TATATTTAAAAAAGTTTTCAAAACTATATATTATATA-GTTTTCAAAATGTTTT
1 AACTATATATATATATTTAAAAAAGTTTTCAAAACTATATATTATATATATTTTCAAAATGTTTT
57168 AAA
66 AAA
* *
57171 AA-TAT-TATATA-AGTTTTCAAAAAATGTTTTTAAAACTATATATTATATAATTTTTTTCAAAA
1 AACTATATATATATA--TTT-AAAAAA-GTTTTCAAAACTATATATTATAT-A-TATTTTC-AAA
57233 ATGTTTTAAA
59 ATGTTTTAAA
*
57243 AACTATATA-ATATA--T--AAATGTTTTCAAAACTATATATTATATATATTTTCAAAA
1 AACTATATATATATATTTAAAAAAGTTTTCAAAACTATATATTATATATATTTTCAAAA
57297 ACCATATAAT
Statistics
Matches: 109, Mismatches: 5, Indels: 27
0.77 0.04 0.19
Matches are distributed among these distances:
63 4 0.04
64 10 0.09
65 6 0.06
66 27 0.25
67 9 0.08
68 22 0.20
69 1 0.01
70 1 0.01
71 5 0.05
72 15 0.14
73 6 0.06
74 3 0.03
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.45
Consensus pattern (68 bp):
AACTATATATATATATTTAAAAAAGTTTTCAAAACTATATATTATATATATTTTCAAAATGTTTT
AAA
Found at i:57239 original size:39 final size:37
Alignment explanation
Indices: 57122--57271 Score: 161
Period size: 39 Copynumber: 4.1 Consensus size: 37
57112 TATTATATTT
* *
57122 AAAAAAGTTTTCAAAACTATATATTATAT-AGTTTTC
1 AAAAATGTTTTTAAAACTATATATTATATAAGTTTTC
57158 -AAAATG-TTTT-AAA--A-ATATTATATAAGTTTTC
1 AAAAATGTTTTTAAAACTATATATTATATAAGTTTTC
*
57189 AAAAAATGTTTTTAAAACTATATATTATATAATTTTTTTC
1 -AAAAATGTTTTTAAAACTATATATTATATAA--GTTTTC
* *
57229 AAAAATGTTTTAAAAACTATATAATATATAAATGTTTTC
1 AAAAATGTTTTTAAAACTATATATTATAT-AA-GTTTTC
57268 AAAA
1 AAAA
57272 CTATATATTA
Statistics
Matches: 97, Mismatches: 6, Indels: 19
0.80 0.05 0.16
Matches are distributed among these distances:
30 9 0.09
31 8 0.08
33 9 0.09
34 7 0.07
35 8 0.08
37 1 0.01
38 11 0.11
39 37 0.38
40 7 0.07
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.43
Consensus pattern (37 bp):
AAAAATGTTTTTAAAACTATATATTATATAAGTTTTC
Found at i:57283 original size:25 final size:27
Alignment explanation
Indices: 57231--57309 Score: 99
Period size: 27 Copynumber: 3.0 Consensus size: 27
57221 TTTTTTTCAA
*
57231 AAATGTTTTAAAAACTATATAATATAT
1 AAATGTTTTCAAAACTATATAATATAT
57258 AAATGTTTTCAAAACTATAT-AT-TAT
1 AAATGTTTTCAAAACTATATAATATAT
* * *
57283 ATATATTTTCAAAAACCATATAATATA
1 AAATGTTTTC-AAAACTATATAATATA
57310 CAAACTTTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
25 11 0.24
26 11 0.24
27 21 0.47
28 2 0.04
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.41
Consensus pattern (27 bp):
AAATGTTTTCAAAACTATATAATATAT
Found at i:57304 original size:26 final size:26
Alignment explanation
Indices: 57231--57323 Score: 84
Period size: 26 Copynumber: 3.6 Consensus size: 26
57221 TTTTTTTCAA
*
57231 AAATGTTTT-AAAAACTATATAATATAT
1 AAATATTTTCAAAAACTATAT-AT-TAT
*
57258 AAATGTTTTC-AAAACTATATATTAT
1 AAATATTTTCAAAAACTATATATTAT
* * *
57283 ATATATTTTCAAAAACCATATAATAT
1 AAATATTTTCAAAAACTATATATTAT
*
57309 ACAA-ACTTTCAAAAA
1 A-AATATTTTCAAAAA
57324 TCGTTTTCTG
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
25 11 0.19
26 26 0.46
27 20 0.35
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.38
Consensus pattern (26 bp):
AAATATTTTCAAAAACTATATATTAT
Found at i:57424 original size:15 final size:15
Alignment explanation
Indices: 57390--57436 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
57380 TACTATATAC
* *
57390 ATATATATATATAT-
1 ATATATATAAAAATA
57404 ATATATAATAAAAA-A
1 ATATAT-ATAAAAATA
57419 ATATATATAAAAATA
1 ATATATATAAAAATA
57434 ATA
1 ATA
57437 AAATAACTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
14 13 0.46
15 15 0.54
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
ATATATATAAAAATA
Found at i:57424 original size:19 final size:20
Alignment explanation
Indices: 57398--57441 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
57388 ACATATATAT
*
57398 ATATATATATATAATAAAAAA
1 ATATATATA-AAAATAAAAAA
*
57419 ATATATATAAAAATAATAAA
1 ATATATATAAAAATAAAAAA
57439 ATA
1 ATA
57442 ACTTCGGACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
ATATATATAAAAATAAAAAA
Found at i:57426 original size:23 final size:23
Alignment explanation
Indices: 57396--57439 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
57386 ATACATATAT
* *
57396 ATATATATATATATAATAAAAAA
1 ATATATATAAAAATAATAAAAAA
57419 ATATATATAAAAATAATAAAA
1 ATATATATAAAAATAATAAAA
57440 TAACTTCGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (23 bp):
ATATATATAAAAATAATAAAAAA
Found at i:59049 original size:33 final size:34
Alignment explanation
Indices: 58974--59038 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
58964 CAAAACTAAC
*
58974 CAAAATACATTAACAAAAAGTCCAACAAATTTAA
1 CAAAATAAATTAACAAAAAGTCCAACAAATTTAA
59008 CAAAATAAATTAA-AATAAA-TCCAACCAAATT
1 CAAAATAAATTAACAA-AAAGTCCAA-CAAATT
59039 AATGAAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 7 0.25
34 21 0.75
ACGTcount: A:0.60, C:0.17, G:0.02, T:0.22
Consensus pattern (34 bp):
CAAAATAAATTAACAAAAAGTCCAACAAATTTAA
Found at i:61367 original size:17 final size:18
Alignment explanation
Indices: 61347--61389 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
61337 ATTAATTAAA
61347 TAAAATATTAAA-AAATT
1 TAAAATATTAAATAAATT
61364 T-AAATACTTAAATAAATT
1 TAAAATA-TTAAATAAATT
*
61382 AAAAATAT
1 TAAAATAT
61390 AATATTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
16 5 0.23
17 6 0.27
18 6 0.27
19 5 0.23
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (18 bp):
TAAAATATTAAATAAATT
Found at i:61376 original size:24 final size:22
Alignment explanation
Indices: 61349--61412 Score: 60
Period size: 22 Copynumber: 2.8 Consensus size: 22
61339 TAATTAAATA
*
61349 AAATATTAAAAAATTTAAATACTT
1 AAATATTAAAAAATAT-AATA-TT
61373 AAATAAATT-AAAAATATAATATT
1 AAAT--ATTAAAAAATATAATATT
61396 AAATA-TAATAAAATATA
1 AAATATTAA-AAAATATA
61413 CCTTAAACAG
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
20 1 0.03
21 2 0.06
22 8 0.23
23 6 0.17
24 8 0.23
25 7 0.20
26 3 0.09
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (22 bp):
AAATATTAAAAAATATAATATT
Found at i:61387 original size:25 final size:23
Alignment explanation
Indices: 61366--61412 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 23
61356 AAAAAATTTA
61366 AATACTTAAATA-AATTAAAAATAT
1 AATA-TTAAATATAA-TAAAAATAT
61390 AATATTAAATATAAT-AAAATAT
1 AATATTAAATATAATAAAAATAT
61412 A
1 A
61413 CCTTAAACAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.36
23 8 0.36
24 6 0.27
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (23 bp):
AATATTAAATATAATAAAAATAT
Found at i:65328 original size:3 final size:3
Alignment explanation
Indices: 65320--65345 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
65310 GAATTGGGTT
65320 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
65346 ATATTGTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:66773 original size:35 final size:35
Alignment explanation
Indices: 66723--66861 Score: 170
Period size: 35 Copynumber: 3.9 Consensus size: 35
66713 TGAATAAGAA
* **
66723 GAACGGAAAGAAGCATTGGCACTTTCGATTCAAGT
1 GAACGGAAGGAAGCATCAGCACTTTCGATTCAAGT
* * *
66758 GAACAGAAGGAAGCATCATCACTTTCGATTCAAGAA
1 GAACGGAAGGAAGCATCAGCACTTTCGATTCAAG-T
* * *
66794 GAACGAAAGGAAGCATCGGCATTTTCGATTCAAGT
1 GAACGGAAGGAAGCATCAGCACTTTCGATTCAAGT
* *
66829 GAACGGGAGGAAGCATAAGCACTTTCGATTCAA
1 GAACGGAAGGAAGCATCAGCACTTTCGATTCAA
66862 TTGTTCATAT
Statistics
Matches: 86, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
35 57 0.66
36 29 0.34
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.21
Consensus pattern (35 bp):
GAACGGAAGGAAGCATCAGCACTTTCGATTCAAGT
Found at i:66797 original size:71 final size:71
Alignment explanation
Indices: 66718--66861 Score: 218
Period size: 71 Copynumber: 2.0 Consensus size: 71
66708 GAAGGTGAAT
* * *
66718 AAGAAGAACGGAAA-GAAGCATTGGCACTTTCGATTCAAGTGAACAGAAGGAAGCATCATCACTT
1 AAGAAGAAC-GAAAGGAAGCATCGGCACTTTCGATTCAAGTGAACAGAAGGAAGCATAAGCACTT
66782 TCGATTC
65 TCGATTC
* * *
66789 AAGAAGAACGAAAGGAAGCATCGGCATTTTCGATTCAAGTGAACGGGAGGAAGCATAAGCACTTT
1 AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAGTGAACAGAAGGAAGCATAAGCACTTT
66854 CGATTC
66 CGATTC
66860 AA
1 AA
66862 TTGTTCATAT
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
70 4 0.06
71 62 0.94
ACGTcount: A:0.38, C:0.17, G:0.24, T:0.20
Consensus pattern (71 bp):
AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAGTGAACAGAAGGAAGCATAAGCACTTT
CGATTC
Found at i:68565 original size:17 final size:18
Alignment explanation
Indices: 68532--68565 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
68522 TTTACTGTCA
68532 TTTTGTTGTCTTAATTTC
1 TTTTGTTGTCTTAATTTC
*
68550 TTTTGTT-TCTTTATTT
1 TTTTGTTGTCTTAATTT
68566 ATTGATTTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.09, C:0.09, G:0.09, T:0.74
Consensus pattern (18 bp):
TTTTGTTGTCTTAATTTC
Found at i:69402 original size:10 final size:10
Alignment explanation
Indices: 69387--69444 Score: 53
Period size: 10 Copynumber: 5.5 Consensus size: 10
69377 TTACATTCTT
69387 TTTTATTGAA
1 TTTTATTGAA
69397 TTTTATTGAA
1 TTTTATTGAA
***
69407 TTTTAATTCTTT
1 TTTT-ATT-GAA
*
69419 TTTTATTGCAT
1 TTTTATTG-AA
69430 TTTTATTGAA
1 TTTTATTGAA
69440 TTTTA
1 TTTTA
69445 ATTATATGAG
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
10 20 0.51
11 15 0.38
12 4 0.10
ACGTcount: A:0.24, C:0.03, G:0.07, T:0.66
Consensus pattern (10 bp):
TTTTATTGAA
Found at i:69434 original size:33 final size:31
Alignment explanation
Indices: 69376--69447 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 31
69366 ATTTTTTAGC
69376 TTTACATTCTTTTTTATTGAATTTTATTGAAT
1 TTTA-ATTCTTTTTTATTGAATTTTATTGAAT
*
69408 TTTAATTCTTTTTTTATTGCATTTTTATTGAAT
1 TTTAATTC-TTTTTTATTG-AATTTTATTGAAT
69441 TTTAATT
1 TTTAATT
69448 ATATGAGTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
31 4 0.11
32 14 0.38
33 19 0.51
ACGTcount: A:0.24, C:0.06, G:0.06, T:0.65
Consensus pattern (31 bp):
TTTAATTCTTTTTTATTGAATTTTATTGAAT
Found at i:71349 original size:8 final size:8
Alignment explanation
Indices: 70903--71345 Score: 607
Period size: 8 Copynumber: 55.4 Consensus size: 8
70893 TGATCTTAGA
70903 GTATGTAT
1 GTATGTAT
70911 GTATGTAT
1 GTATGTAT
70919 GTATGTAT
1 GTATGTAT
70927 GTATGTAT
1 GTATGTAT
70935 GTATGTAT
1 GTATGTAT
70943 GTATGTAT
1 GTATGTAT
70951 GTATGTAT
1 GTATGTAT
70959 GTATGTAT
1 GTATGTAT
* *
70967 GCACGTAT
1 GTATGTAT
* *
70975 GCACGTAT
1 GTATGTAT
* *
70983 GCACGTAT
1 GTATGTAT
* *
70991 GCACGTAT
1 GTATGTAT
* *
70999 GCACGTAT
1 GTATGTAT
* *
71007 GCACGTAT
1 GTATGTAT
*
71015 GTATGTAC
1 GTATGTAT
* *
71023 GTACGTAC
1 GTATGTAT
* * *
71031 GCACGTAC
1 GTATGTAT
* *
71039 GTACGTAC
1 GTATGTAT
* * *
71047 GCACGTAC
1 GTATGTAT
* *
71055 GTACGTAC
1 GTATGTAT
** *
71063 GTGCGTAC
1 GTATGTAT
71071 GTATGTAT
1 GTATGTAT
71079 GTATGTAT
1 GTATGTAT
71087 GTATGTAT
1 GTATGTAT
71095 GTATGTAT
1 GTATGTAT
71103 GTATGTAT
1 GTATGTAT
*
71111 ATATGTAT
1 GTATGTAT
71119 GTATGTAT
1 GTATGTAT
71127 GTATGTAT
1 GTATGTAT
71135 GTATGTAT
1 GTATGTAT
71143 GTATGTAT
1 GTATGTAT
71151 GTATGTAT
1 GTATGTAT
71159 GTATGTAT
1 GTATGTAT
71167 GTATGTAT
1 GTATGTAT
71175 GTATGTAT
1 GTATGTAT
71183 GTATGTAT
1 GTATGTAT
71191 GTATGTAT
1 GTATGTAT
71199 GTATGTAT
1 GTATGTAT
71207 GTATGTAT
1 GTATGTAT
71215 GTATGTAT
1 GTATGTAT
71223 GTATGTAT
1 GTATGTAT
71231 GTATGTAT
1 GTATGTAT
71239 GTATGTAT
1 GTATGTAT
71247 GTATGTAT
1 GTATGTAT
71255 GTATGTAT
1 GTATGTAT
71263 GTATGTAT
1 GTATGTAT
71271 GTATGTAT
1 GTATGTAT
71279 GTATGTAT
1 GTATGTAT
71287 GTATGTAT
1 GTATGTAT
71295 GTATGTAT
1 GTATGTAT
71303 GTATGTAT
1 GTATGTAT
71311 GTATGTAT
1 GTATGTAT
71319 GTATGTAT
1 GTATGTAT
*
71327 GTACGTAT
1 GTATGTAT
*
71335 GTACGTAT
1 GTATGTAT
71343 GTA
1 GTA
71346 CGTACGTAAG
Statistics
Matches: 418, Mismatches: 17, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 418 1.00
ACGTcount: A:0.25, C:0.07, G:0.25, T:0.43
Consensus pattern (8 bp):
GTATGTAT
Found at i:75937 original size:64 final size:64
Alignment explanation
Indices: 75853--76126 Score: 233
Period size: 64 Copynumber: 4.3 Consensus size: 64
75843 CATTCATAAG
**
75853 TGCATCGATGCATTCC-TTTAA-AAGAAGAACATCGAATGCCTTTGATGCATCGATGCAT-AGCT
1 TGCATCGATGCA-TCCTTTTAATAAGAAGAACATCGAATGCAATT-ATGCATCGATGCATAAG-T
75915 AA
63 AA
* * * * *
75917 TGCATCGATGCATCCTTTTAA-AATAATAACATCGAATGCAATCAATGCATCGATGCATAAGGAG
1 TGCATCGATGCATCCTTTTAATAAGAAGAACATCGAATGCAAT-TATGCATCGATGCATAAGTAA
* ** * * *
75981 TGCATCAATGCATCCCATTAATAA-TAGAACATCAAATGAAATTAGTGCATCGATGCATAAGGT-
1 TGCATCGATGCATCCTTTTAATAAGAAGAACATCGAATGCAATTA-TGCATCGATGCATAA-GTA
76044 A
64 A
* * * *
76045 TGCATCGATGCAT-CTCATTAATAAGGA-AACATCGAATGCATTTTATGCA-CTGATGCACAAGT
1 TGCATCGATGCATCCT-TTTAATAAGAAGAACATCGAATGCA-ATTATGCATC-GATGCATAAGT
*
76107 AG
63 AA
76109 TGCATCGATGCATACCTT
1 TGCATCGATGCAT-CCTT
76127 CATTGAAAGA
Statistics
Matches: 171, Mismatches: 26, Indels: 25
0.77 0.12 0.11
Matches are distributed among these distances:
63 8 0.05
64 152 0.89
65 9 0.05
66 2 0.01
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (64 bp):
TGCATCGATGCATCCTTTTAATAAGAAGAACATCGAATGCAATTATGCATCGATGCATAAGTAA
Found at i:76815 original size:31 final size:31
Alignment explanation
Indices: 76777--76844 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
76767 GTCGAGGGTT
*
76777 TACCTATGTTAAAAGGAACATATGGATAGTA
1 TACCTATGTTAAAAGGAACATATGGACAGTA
** *
76808 TACCTATGTTCTAAGGAATATATGGACAGTA
1 TACCTATGTTAAAAGGAACATATGGACAGTA
76839 TACCTA
1 TACCTA
76845 GGTTTTTTGG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (31 bp):
TACCTATGTTAAAAGGAACATATGGACAGTA
Found at i:81566 original size:21 final size:21
Alignment explanation
Indices: 81540--81579 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
81530 CAGAACCCCA
*
81540 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
81561 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
81580 TCAAAGGGGG
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:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:81608 original size:19 final size:20
Alignment explanation
Indices: 81562--81621 Score: 68
Period size: 19 Copynumber: 2.9 Consensus size: 20
81552 TTCCCCTGTG
81562 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TC-AA
81585 GGGGGAATCGGTTCCCTC-A
1 GGGGGAATCGGTTCCCTCAA
* *
81604 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
81622 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 17 0.49
21 2 0.06
22 3 0.09
23 13 0.37
ACGTcount: A:0.17, C:0.27, G:0.35, T:0.22
Consensus pattern (20 bp):
GGGGGAATCGGTTCCCTCAA
Found at i:85467 original size:22 final size:21
Alignment explanation
Indices: 85425--85464 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
85415 GAGTTTGTTT
*
85425 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
85446 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
85465 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:89896 original size:64 final size:61
Alignment explanation
Indices: 89812--90085 Score: 210
Period size: 64 Copynumber: 4.3 Consensus size: 61
89802 CATTCATAAG
**
89812 TGCATCGATGCATTCCTTTAAAAGAAGAACATCGAATGCCTTTGATGCATCGATGCAT-AGCTAA
1 TGCATCGATGCA-TCCTTTAAAA-AAGAACATCGAATGCAATT-ATGCATCGATGCATAAG-TAA
* * * *
89876 TGCATCGATGCATCCTTTTAAAATAATAACATCGAATGCAATCAATGCATCGATGCATAAGGAG
1 TGCATCGATGCATCC-TTTAAAA-AAGAACATCGAATGCAAT-TATGCATCGATGCATAAGTAA
* * * * *
89940 TGCATCAATGCATCCCATTAATAATAGAACATCAAATGAAATTAGTGCATCGATGCATAAGGT-A
1 TGCATCGATGCAT-CCTTTAA-AAAAGAACATCGAATGCAATTA-TGCATCGATGCATAA-GTAA
* * * * * * * * *
90004 TGCATCGATGCATTTCATTAATAAGGAAACATCGAAAGCATTTTATGCACCGATGCACAAGTAG
1 TGCATCGATGCA-TCCTTTAAAAAAG-AACATCGAATGCA-ATTATGCATCGATGCATAAGTAA
*
90068 TGCATCGGTGCATACCTT
1 TGCATCGATGCAT-CCTT
90086 CATTGAAAGA
Statistics
Matches: 167, Mismatches: 31, Indels: 24
0.75 0.14 0.11
Matches are distributed among these distances:
63 9 0.05
64 147 0.88
65 11 0.07
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.27
Consensus pattern (61 bp):
TGCATCGATGCATCCTTTAAAAAAGAACATCGAATGCAATTATGCATCGATGCATAAGTAA
Found at i:90775 original size:31 final size:31
Alignment explanation
Indices: 90737--90804 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
90727 GTCGAGGGTT
*
90737 TACCTATGTTAAAAGGAACATATGGATAGTA
1 TACCTATGTTAAAAGGAACATATGGACAGTA
** *
90768 TACCTATGTTCTAAGGAATATATGGACAGTA
1 TACCTATGTTAAAAGGAACATATGGACAGTA
90799 TACCTA
1 TACCTA
90805 GGTTTTTTGG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (31 bp):
TACCTATGTTAAAAGGAACATATGGACAGTA
Found at i:94269 original size:64 final size:64
Alignment explanation
Indices: 94185--94458 Score: 249
Period size: 64 Copynumber: 4.3 Consensus size: 64
94175 CATTCATAAG
**
94185 TGCATCGATGCATTCC-TTTAA-AAGAAGAACATCGAATGCCTTTGATGCATCGATGCAT-AGCT
1 TGCATCGATGCA-TCCTTTTAATAAGAAGAACATCGAATGCAATT-ATGCATCGATGCATAAG-T
94247 AA
63 AA
* * * * *
94249 TGCATCGATGCATCCTTTTAA-AATAATAACATCGAATGCAATCAATGCATCGATGCATAAGGAG
1 TGCATCGATGCATCCTTTTAATAAGAAGAACATCGAATGCAAT-TATGCATCGATGCATAAGTAA
* ** * * *
94313 TGCATCAATGCATCCCATTAATAA-TAGAACATCAAATGAAATTAGTGCATCGATGCATAAGGT-
1 TGCATCGATGCATCCTTTTAATAAGAAGAACATCGAATGCAATTA-TGCATCGATGCATAA-GTA
94376 A
64 A
* * * *
94377 TGCATCGATGCAT-CTCATTAATAAGAA-AACATCGAATGCATTTTATGCACCGATGCACAAGTA
1 TGCATCGATGCATCCT-TTTAATAAGAAGAACATCGAATGCA-ATTATGCATCGATGCATAAGTA
*
94440 G
64 A
94441 TGCATCGATGCATACCTT
1 TGCATCGATGCAT-CCTT
94459 CATTGAAAGA
Statistics
Matches: 171, Mismatches: 27, Indels: 23
0.77 0.12 0.10
Matches are distributed among these distances:
63 7 0.04
64 153 0.89
65 9 0.05
66 2 0.01
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (64 bp):
TGCATCGATGCATCCTTTTAATAAGAAGAACATCGAATGCAATTATGCATCGATGCATAAGTAA
Found at i:94325 original size:128 final size:128
Alignment explanation
Indices: 94183--94458 Score: 310
Period size: 128 Copynumber: 2.2 Consensus size: 128
94173 CACATTCATA
* * ** *
94183 AGTGCATCGATGCATTCCTTTAA-AAGAAGAACATCGAATG-CCTTTGATGCATCGATGCAT-AG
1 AGTGCATCGATGCATACCTTTAATAA-AAGAACATCAAATGAAATTAG-TGCATCGATGCATAAG
* * * *
94245 CTAATGCATCGATGCATC-CTTTTAA-AATAATAACATCGAATGCAATCAATGCATCGATGCATA
64 CT-ATGCATCGATGCATCTC-ATTAATAAGAA-AACATCGAATGCAATCAATGCACCGATGCACA
94308 AGG
126 AGG
* * * * *
94311 AGTGCATCAATGCATCCCATTAATAATAGAACATCAAATGAAATTAGTGCATCGATGCATAAGGT
1 AGTGCATCGATGCATACCTTTAATAAAAGAACATCAAATGAAATTAGTGCATCGATGCATAAGCT
* ** *
94376 ATGCATCGATGCATCTCATTAATAAGAAAACATCGAATGCATTTTATGCACCGATGCACAAGT
66 ATGCATCGATGCATCTCATTAATAAGAAAACATCGAATGCAATCAATGCACCGATGCACAAGG
94439 AGTGCATCGATGCATACCTT
1 AGTGCATCGATGCATACCTT
94459 CATTGAAAGA
Statistics
Matches: 123, Mismatches: 20, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
128 110 0.89
129 13 0.11
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (128 bp):
AGTGCATCGATGCATACCTTTAATAAAAGAACATCAAATGAAATTAGTGCATCGATGCATAAGCT
ATGCATCGATGCATCTCATTAATAAGAAAACATCGAATGCAATCAATGCACCGATGCACAAGG
Found at i:95148 original size:31 final size:31
Alignment explanation
Indices: 95110--95177 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
95100 GTCGAGGGTT
*
95110 TACCTATGTTAAAAGGAACATATGGATAATA
1 TACCTATGTTAAAAGGAACATATGGACAATA
** * *
95141 TACCTATGTTCTAAGGAATATATGGACAGTA
1 TACCTATGTTAAAAGGAACATATGGACAATA
95172 TACCTA
1 TACCTA
95178 GGTTTTTTGG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (31 bp):
TACCTATGTTAAAAGGAACATATGGACAATA
Found at i:98934 original size:22 final size:23
Alignment explanation
Indices: 98895--98943 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
98885 ACCTTTAGAG
*
98895 TGAAATGAAATAACTA-TTTTCA
1 TGAAAAGAAATAACTATTTTTCA
* *
98917 TGAAAAGAATTAATTATTTTTCA
1 TGAAAAGAAATAACTATTTTTCA
98940 TGAA
1 TGAA
98944 TAGTCATGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (23 bp):
TGAAAAGAAATAACTATTTTTCA
Found at i:103628 original size:2 final size:2
Alignment explanation
Indices: 103623--103691 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
103613 ATCTTAATTA
103623 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
103665 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
103692 AAGACATTTA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:104752 original size:2 final size:2
Alignment explanation
Indices: 104745--104809 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
104735 GTAAATACGA
104745 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
104787 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
104810 CTTTATAAAC
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:105621 original size:8 final size:8
Alignment explanation
Indices: 105608--105645 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
105598 TTCCTCTCAA
105608 CTCTTCTT
1 CTCTTCTT
105616 CTCTTCTT
1 CTCTTCTT
105624 CTCTTCTT
1 CTCTTCTT
105632 CATC-TCTT
1 C-TCTTCTT
*
105640 CACTTC
1 CTCTTC
105646 CTCACACTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
7 1 0.04
8 24 0.89
9 2 0.07
ACGTcount: A:0.05, C:0.39, G:0.00, T:0.55
Consensus pattern (8 bp):
CTCTTCTT
Found at i:107838 original size:111 final size:111
Alignment explanation
Indices: 107504--107905 Score: 628
Period size: 111 Copynumber: 3.6 Consensus size: 111
107494 GGGAAGATTA
* * *
107504 AATCAGGGTAGACTTGTTCCGCTGTCACTCGGGGAATATCAAATCTTGAAAGAGATGGATCTGTT
1 AATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAAAGAGGGATCTGTT
* *
107569 CCGCTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
66 CCACTTTCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
* * *
107615 AATCAGGGTAGACTTGTTCTGCTGTCACTCAGGGAATATCAAATCTTG--AAAGAGAGATCTATT
1 AATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAAAGAGGGATCTGTT
** * *
107678 CTGCTTTTTCTAAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
66 CCACTTTCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
* * *
107724 AATCAGAGTAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGAAAAAGAGGGATCTGTT
1 AATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAAAGAGGGATCTGTT
*
107789 TCACTTTCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
66 CCACTTTCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
* *
107835 AATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTTAAAAAGAGTGATCTGTT
1 AATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAAAGAGGGATCTGTT
107900 CCACTT
66 CCACTT
107906 CTTCTGAATG
Statistics
Matches: 262, Mismatches: 27, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
109 97 0.37
111 165 0.63
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (111 bp):
AATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAAAGAGGGATCTGTT
CCACTTTCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTCATTG
Found at i:108348 original size:17 final size:17
Alignment explanation
Indices: 108326--108364 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
108316 TTGGACCCAC
108326 CCTCTTCTTCAGGTTCA
1 CCTCTTCTTCAGGTTCA
108343 CCTCTTCTTCAGGTTCA
1 CCTCTTCTTCAGGTTCA
108360 CCTCT
1 CCTCT
108365 CTAAATACGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.10, C:0.38, G:0.10, T:0.41
Consensus pattern (17 bp):
CCTCTTCTTCAGGTTCA
Found at i:116266 original size:2 final size:2
Alignment explanation
Indices: 116259--116283 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
116249 GTAAATATGA
116259 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
116284 CTTTATAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:118055 original size:4 final size:4
Alignment explanation
Indices: 118046--118070 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
118036 TTGCTTCGAA
118046 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
118071 CATGCACAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:118650 original size:3 final size:3
Alignment explanation
Indices: 118631--118680 Score: 75
Period size: 3 Copynumber: 17.0 Consensus size: 3
118621 ACCTGTAAAA
* *
118631 AAT AAT TAT ATT AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
118678 AAT
1 AAT
118681 CAGGACGAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:118666 original size:17 final size:17
Alignment explanation
Indices: 118644--118678 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
118634 AATTATATTA
118644 ATAATAATAATAATAAT
1 ATAATAATAATAATAAT
118661 ATAATAATAATAATAAT
1 ATAATAATAATAATAAT
118678 A
1 A
118679 ATCAGGACGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATAATAATAATAATAAT
Found at i:123242 original size:45 final size:45
Alignment explanation
Indices: 123188--123280 Score: 150
Period size: 45 Copynumber: 2.1 Consensus size: 45
123178 GTTGAAGGAG
*
123188 CACGCATGGGACCAAGGGCATTATCAACACGCATTGAAGAAGCAT
1 CACGCATGGGACCAAGAGCATTATCAACACGCATTGAAGAAGCAT
* * *
123233 CACGTATGGGACCATGAGCATTATCAACACGCATTGAAGGAGCAT
1 CACGCATGGGACCAAGAGCATTATCAACACGCATTGAAGAAGCAT
123278 CAC
1 CAC
123281 ATGGGTTGTT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.34, C:0.25, G:0.24, T:0.17
Consensus pattern (45 bp):
CACGCATGGGACCAAGAGCATTATCAACACGCATTGAAGAAGCAT
Found at i:123346 original size:15 final size:15
Alignment explanation
Indices: 123315--123364 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
123305 CATCGGTTGA
*
123315 TGGAGCAGGTTATGG
1 TGGAGCAGGTCATGG
123330 TGGAGCAGGTGCA-GG
1 TGGAGCAGGT-CATGG
*
123345 TGGAGCATGCTC-TGG
1 TGGAGCA-GGTCATGG
123360 TGGAG
1 TGGAG
123365 TATGTGATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
15 27 0.90
16 3 0.10
ACGTcount: A:0.18, C:0.12, G:0.48, T:0.22
Consensus pattern (15 bp):
TGGAGCAGGTCATGG
Found at i:128521 original size:41 final size:41
Alignment explanation
Indices: 128464--128542 Score: 140
Period size: 41 Copynumber: 1.9 Consensus size: 41
128454 GTTTTTCGGC
128464 CTTACTGCAATGAATCCATCTGTGAAAACCAAGATTTTGGG
1 CTTACTGCAATGAATCCATCTGTGAAAACCAAGATTTTGGG
* *
128505 CTTACTGCAATGAATCCATCTGTGAGAATCAAGATTTT
1 CTTACTGCAATGAATCCATCTGTGAAAACCAAGATTTT
128543 AGAGCAGATC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Consensus pattern (41 bp):
CTTACTGCAATGAATCCATCTGTGAAAACCAAGATTTTGGG
Found at i:133159 original size:19 final size:20
Alignment explanation
Indices: 133135--133185 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
133125 GATTCAATCA
* *
133135 GTATCGATATCAAAGGG-GG
1 GTATCGATACCAAAGGGAAG
*
133154 GTATCGATACCGAAGGGAAG
1 GTATCGATACCAAAGGGAAG
133174 GTATCGATACCA
1 GTATCGATACCA
133186 TTTCAAAACA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.33, C:0.16, G:0.31, T:0.20
Consensus pattern (20 bp):
GTATCGATACCAAAGGGAAG
Found at i:133786 original size:47 final size:47
Alignment explanation
Indices: 133661--133898 Score: 358
Period size: 47 Copynumber: 5.1 Consensus size: 47
133651 TAAATCGAAT
133661 CCATAAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
1 CCATAAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
* * * *
133708 CCAT-AA-TTAAATGCATGAAAAT-ATGGATTAAGGTATAAAAGGATG
1 CCATAAACTAAAATGCATG-AAATGATGCATTAAGGCATGAAAGGATG
* * *
133753 TCATAAACTAAAATGCACGAAAGGATGCATTAAGGCATGAAAGGATG
1 CCATAAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
* *
133800 TCAT-AATTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
1 CCATAAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
133846 CCATAAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
1 CCATAAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
133893 CCATAA
1 CCATAA
133899 TTTAAATATA
Statistics
Matches: 170, Mismatches: 16, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
45 33 0.19
46 53 0.31
47 84 0.49
ACGTcount: A:0.45, C:0.11, G:0.21, T:0.23
Consensus pattern (47 bp):
CCATAAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATG
Found at i:133796 original size:20 final size:20
Alignment explanation
Indices: 133771--133893 Score: 93
Period size: 20 Copynumber: 5.5 Consensus size: 20
133761 TAAAATGCAC
133771 GAAAGGATGCATTAAGGCAT
1 GAAAGGATGCATTAAGGCAT
*
133791 GAAAGGATGTCATAATTAAAATGCAT
1 GAAAGGATG-C---ATT--AAGGCAT
*
133817 GAAATGATGCATTAAGGCAT
1 GAAAGGATGCATTAAGGCAT
*
133837 GAAAGGATGCCATAAACTAAAATGCAT
1 GAAAGGATG-CAT----T--AAGGCAT
*
133864 GAAATGATGCATTAAGGCAT
1 GAAAGGATGCATTAAGGCAT
133884 GAAAGGATGC
1 GAAAGGATGC
133894 CATAATTTAA
Statistics
Matches: 82, Mismatches: 8, Indels: 26
0.71 0.07 0.22
Matches are distributed among these distances:
20 38 0.46
21 4 0.05
22 4 0.05
24 3 0.04
25 2 0.02
26 17 0.21
27 14 0.17
ACGTcount: A:0.43, C:0.11, G:0.24, T:0.22
Consensus pattern (20 bp):
GAAAGGATGCATTAAGGCAT
Found at i:133861 original size:93 final size:92
Alignment explanation
Indices: 133661--133905 Score: 393
Period size: 93 Copynumber: 2.6 Consensus size: 92
133651 TAAATCGAAT
133661 CCATAAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAATTAAATGCATGA
1 CCATAAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAATTAAATGCATGA
* *
133726 AAATATGGATTAAGGTATAAAAGGATG
66 AAATATGCATTAAGGCATAAAAGGATG
* * * *
133753 TCATAAACTAAAATGCACGAAAGGATGCATTAAGGCATGAAAGGATGTCATAATTAAAATGCATG
1 CCATAAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAATT-AAATGCATG
*
133818 -AAATGATGCATTAAGGCATGAAAGGATG
65 AAAAT-ATGCATTAAGGCATAAAAGGATG
133846 CCATAAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAATTTAAAT
1 CCATAAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAA-TTAAAT
133906 ATATATAAAT
Statistics
Matches: 139, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
92 55 0.40
93 82 0.59
94 2 0.01
ACGTcount: A:0.45, C:0.11, G:0.20, T:0.24
Consensus pattern (92 bp):
CCATAAACTAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGCCATAATTAAATGCATGA
AAATATGCATTAAGGCATAAAAGGATG
Done.