Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014240.1 Kokia drynarioides strain JFW-HI SEQ_129273, 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: 412615
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 62 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:4481 original size:21 final size:21
Alignment explanation
Indices: 4454--4509 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
4444 GATACCTGAT
4454 AAAAGGTATCGATACATTTTG
1 AAAAGGTATCGATACATTTTG
* *
4475 ACAAGGTATCGATACTTTTTG
1 AAAAGGTATCGATACATTTTG
4496 AAAAGGTATCGATA
1 AAAAGGTATCGATA
4510 TTTTGTGTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.32
Consensus pattern (21 bp):
AAAAGGTATCGATACATTTTG
Found at i:4902 original size:33 final size:32
Alignment explanation
Indices: 4855--4920 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 32
4845 TGAATAGATT
*
4855 GCTCCCCCTAATAAAAGA-CATTTTGAATTTAA
1 GCTCCCCCTAATAAAA-ATCATTTTCAATTTAA
*
4887 GCTCCCTCTATATAAAAATCATTTTCAATTTAA
1 GCTCCCCCTA-ATAAAAATCATTTTCAATTTAA
4920 G
1 G
4921 GCATAAAGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
32 10 0.33
33 20 0.67
ACGTcount: A:0.36, C:0.21, G:0.08, T:0.35
Consensus pattern (32 bp):
GCTCCCCCTAATAAAAATCATTTTCAATTTAA
Found at i:7443 original size:21 final size:20
Alignment explanation
Indices: 7413--7451 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
7403 GATACCTAAT
*
7413 AAAAGGTATCGATACTTTTTG
1 AAAAGATATCGATA-TTTTTG
7434 AAAAGATATCGATATTTT
1 AAAAGATATCGATATTTT
7452 GTGTCATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (20 bp):
AAAAGATATCGATATTTTTG
Found at i:17515 original size:105 final size:105
Alignment explanation
Indices: 17333--17563 Score: 435
Period size: 105 Copynumber: 2.2 Consensus size: 105
17323 AGTCCTCGAC
*
17333 AGCTCGTGTGAGCAGCATCTTGAGTCGGGAAATGAGTAAAGAATCCAAGAACGGATTACAAGCCC
1 AGCTCGTGTGAGCAGCATCGTGAGTCGGGAAATGAGTAAAGAATCCAAGAACGGATTACAAGCCC
17398 TACGATGGCTGAGATTTATGCATAAGTGCATATTATCTAT
66 TACGATGGCTGAGATTTATGCATAAGTGCATATTATCTAT
*
17438 AGCTCGTGTGAGCAGCATCGTGAGTCGGGAAATGAGTAAAGAATCCAAGAATGGATTACAAGCCC
1 AGCTCGTGTGAGCAGCATCGTGAGTCGGGAAATGAGTAAAGAATCCAAGAACGGATTACAAGCCC
17503 TACGATGGCTGAGATTTATGCATAAGTGCATATTATCTAT
66 TACGATGGCTGAGATTTATGCATAAGTGCATATTATCTAT
*
17543 AGCTCATGTGAGCAGCATCGT
1 AGCTCGTGTGAGCAGCATCGT
17564 TAGGGAATAA
Statistics
Matches: 123, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 123 1.00
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.26
Consensus pattern (105 bp):
AGCTCGTGTGAGCAGCATCGTGAGTCGGGAAATGAGTAAAGAATCCAAGAACGGATTACAAGCCC
TACGATGGCTGAGATTTATGCATAAGTGCATATTATCTAT
Found at i:17741 original size:194 final size:195
Alignment explanation
Indices: 17438--17846 Score: 483
Period size: 194 Copynumber: 2.1 Consensus size: 195
17428 TATTATCTAT
*
17438 AGCTCGTGTGAGCAGCATCGTGAGTCGGGAAATGAGTAAAGAATCCAAGAATGGATTACAAGCCC
1 AGCTCGTGTGAGCAGCATCGTGAGTCGGGAAAAGAGTAAAGAATCCAAGAATGGATTACAAGCCC
* * * * *
17503 TACGATGGCTGAGATTTATGCATAAGTGCATATTATCTATAGCTCATGTGAGCAGCATCGT-TAG
66 TACGATGGCTGAGACTTATGCATAAGTGCATATCACCTATAGCTCATGTGAGCAGCATCATCAAG
* * * *
17567 -GG-AATAATTATATG-CACAGATACCGTA-TCGATGGCTGAGGTACCGCATATGTTGCGAGTCC
131 AGGCAATTA-TATA-GACAAACATA--GTACT-GATGACTGAGGTACCGCATATGTTGCGAGTCC
17628 TCGAC
191 TCGAC
* * * * * *
17633 AGCTCGTGTGAGTAGCATCGTGAGT-TGGAAAAGAG-ATATGAATCCTAGAATGGATTATAGGCC
1 AGCTCGTGTGAGCAGCATCGTGAGTCGGGAAAAGAGTA-AAGAATCCAAGAATGGATTACAAGCC
* * * * *
17696 CTGCGATGGTTGGGACTTATGCATAAGTGCATA-CACCTGATAGCTCGTGTGAGCATCATCATCA
65 CTACGATGGCTGAGACTTATGCATAAGTGCATATCACCT-ATAGCTCATGTGAGCAGCATCATCA
* * *
17760 AGAGGCAGTTATATAGACAAACATAGTACTGATGATTGGGGTACCGCATATGTTGCGAGTCCTCG
129 AGAGGCAATTATATAGACAAACATAGTACTGATGACTGAGGTACCGCATATGTTGCGAGTCCTCG
17825 AC
194 AC
17827 AGCTCGTGTGAGCAGCATCG
1 AGCTCGTGTGAGCAGCATCG
17847 AGTACTAGTA
Statistics
Matches: 182, Mismatches: 25, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
193 4 0.02
194 135 0.74
195 28 0.15
196 12 0.07
197 3 0.02
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.26
Consensus pattern (195 bp):
AGCTCGTGTGAGCAGCATCGTGAGTCGGGAAAAGAGTAAAGAATCCAAGAATGGATTACAAGCCC
TACGATGGCTGAGACTTATGCATAAGTGCATATCACCTATAGCTCATGTGAGCAGCATCATCAAG
AGGCAATTATATAGACAAACATAGTACTGATGACTGAGGTACCGCATATGTTGCGAGTCCTCGAC
Found at i:36729 original size:7 final size:7
Alignment explanation
Indices: 36711--36752 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 7
36701 ATAAAAAGAA
36711 AGAAAA-
1 AGAAAAG
36717 AGAAAAG
1 AGAAAAG
36724 AGAAAAG
1 AGAAAAG
36731 AGAAAAG
1 AGAAAAG
*
36738 AAAAGAAG
1 AGAA-AAG
36746 A-AAAAG
1 AGAAAAG
36752 A
1 A
36753 TTTTATTGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
6 10 0.30
7 19 0.58
8 4 0.12
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (7 bp):
AGAAAAG
Found at i:37687 original size:23 final size:23
Alignment explanation
Indices: 37660--37703 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
37650 TAGCCTAGAG
37660 ATAGTATATTCCGATGTATTCGT
1 ATAGTATATTCCGATGTATTCGT
* *
37683 ATAGTGTATTCTGATGTATTC
1 ATAGTATATTCCGATGTATTC
37704 ATTAACTTCT
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:0.25, C:0.11, G:0.18, T:0.45
Consensus pattern (23 bp):
ATAGTATATTCCGATGTATTCGT
Found at i:49463 original size:8 final size:9
Alignment explanation
Indices: 49442--49479 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
49432 AATAACAGCA
49442 AAAAACAAC
1 AAAAACAAC
49451 AAAAACAAC
1 AAAAACAAC
*
49460 AAAAATAAC
1 AAAAACAAC
49469 AATAAA-AAC
1 AA-AAACAAC
49478 AA
1 AA
49480 CATCGAAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
9 24 0.89
10 3 0.11
ACGTcount: A:0.79, C:0.16, G:0.00, T:0.05
Consensus pattern (9 bp):
AAAAACAAC
Found at i:49469 original size:21 final size:20
Alignment explanation
Indices: 49441--49481 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
49431 AAATAACAGC
49441 AAAAAACAACAAAAACAACA
1 AAAAAACAACAAAAACAACA
*
49461 AAAATAACAATAAAAACAACA
1 AAAA-AACAACAAAAACAACA
49482 TCGAAACAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.78, C:0.17, G:0.00, T:0.05
Consensus pattern (20 bp):
AAAAAACAACAAAAACAACA
Found at i:55520 original size:24 final size:24
Alignment explanation
Indices: 55488--55536 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
55478 AATGATTATG
55488 ATAACCAATCCTGCTAACACTTGT
1 ATAACCAATCCTGCTAACACTTGT
55512 ATAACCAATCCTGCTAACACTTGT
1 ATAACCAATCCTGCTAACACTTGT
55536 A
1 A
55537 GAAAGTAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.29, G:0.08, T:0.29
Consensus pattern (24 bp):
ATAACCAATCCTGCTAACACTTGT
Found at i:56982 original size:20 final size:20
Alignment explanation
Indices: 56941--56981 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
56931 TGATTTAGAT
56941 AATTCTAAAAATATATTTAA
1 AATTCTAAAAATATATTTAA
*
56961 AATTTTAAAAAT-TATTTAA
1 AATTCTAAAAATATATTTAA
56980 AA
1 AA
56982 AATACTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
AATTCTAAAAATATATTTAA
Found at i:61306 original size:17 final size:17
Alignment explanation
Indices: 61273--61333 Score: 86
Period size: 17 Copynumber: 3.5 Consensus size: 17
61263 CATTAATTTA
*
61273 CAATGACAAATGGAAATG
1 CAATGAC-AATGAAAATG
*
61291 CAATGATAATGAAAATG
1 CAATGACAATGAAAATG
*
61308 CAATGACAATTAAAATG
1 CAATGACAATGAAAATG
61325 CAATGACAA
1 CAATGACAA
61334 AAGAAATGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
17 33 0.85
18 6 0.15
ACGTcount: A:0.52, C:0.11, G:0.16, T:0.20
Consensus pattern (17 bp):
CAATGACAATGAAAATG
Found at i:61340 original size:17 final size:17
Alignment explanation
Indices: 61273--61341 Score: 61
Period size: 17 Copynumber: 4.0 Consensus size: 17
61263 CATTAATTTA
*
61273 CAATGACAAATGGAAATG
1 CAATGACAAA-AGAAATG
* *
61291 CAATGA-TAATGAAAATG
1 CAATGACAAAAG-AAATG
*
61308 CAATGACAATTA-AAATG
1 CAATGACAA-AAGAAATG
61325 CAATGACAAAAGAAATG
1 CAATGACAAAAGAAATG
61342 TAGTGACAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
16 2 0.05
17 32 0.78
18 7 0.17
ACGTcount: A:0.54, C:0.10, G:0.17, T:0.19
Consensus pattern (17 bp):
CAATGACAAAAGAAATG
Found at i:61341 original size:34 final size:34
Alignment explanation
Indices: 61286--61355 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 34
61276 TGACAAATGG
* *
61286 AAATGCAATGATAATGAAAATGCAATGACAATTA
1 AAATGCAATGAAAAAGAAAATGCAATGACAATTA
* *
61320 AAATGCAATGACAAAAG-AAATGTAGTGACAATTA
1 AAATGCAATGA-AAAAGAAAATGCAATGACAATTA
61354 AA
1 AA
61356 TTACAGCTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 28 0.90
35 3 0.10
ACGTcount: A:0.54, C:0.09, G:0.16, T:0.21
Consensus pattern (34 bp):
AAATGCAATGAAAAAGAAAATGCAATGACAATTA
Found at i:67340 original size:18 final size:18
Alignment explanation
Indices: 67317--67399 Score: 57
Period size: 18 Copynumber: 4.5 Consensus size: 18
67307 TTTGGTTTAC
67317 TTGGTTTAGGGTTTAGGT
1 TTGGTTTAGGGTTTAGGT
**
67335 TTGGTTTA--AATTAGGT
1 TTGGTTTAGGGTTTAGGT
*
67351 TTAAGTTTAGGGTTATTAGG-
1 TT-GGTTTAGGG-T-TTAGGT
67371 TTGGTTTA-GGTTTAATGGT
1 TTGGTTTAGGGTTT-A-GGT
67390 TTGGGTTTAG
1 TT-GGTTTAG
67400 AGGGTTTGGG
Statistics
Matches: 49, Mismatches: 6, Indels: 17
0.68 0.08 0.24
Matches are distributed among these distances:
16 10 0.20
17 7 0.14
18 12 0.24
19 7 0.14
20 8 0.16
21 5 0.10
ACGTcount: A:0.18, C:0.00, G:0.33, T:0.49
Consensus pattern (18 bp):
TTGGTTTAGGGTTTAGGT
Found at i:75263 original size:69 final size:68
Alignment explanation
Indices: 75152--75376 Score: 299
Period size: 69 Copynumber: 3.2 Consensus size: 68
75142 ACAGACTGCC
** *
75152 TTCTGACT-TAAGACCATGGTTGGACCATGGCAGTGTATATAGATGTAAGACCATAACTAGGCTA
1 TTCTGA-TGTAAGACCATGGTTGGACCAT-GCAGTGTATATAGATGTAAGACCATAGTTGGGCTA
75216 TGGCA
64 TGGCA
75221 TTCTGATGTAAGACCATGGTTGGACCATAGCAGTGTATATAGATGTAAGACCATAGTTGGGCTAT
1 TTCTGATGTAAGACCATGGTTGGACCAT-GCAGTGTATATAGATGTAAGACCATAGTTGGGCTAT
75286 GGCA
65 GGCA
* * * * * *
75290 TTTTGATGTAAGACCATTGTTGGACTATGATAGTATATATATATGTAAGACCATAGTTGGGCTAT
1 TTCTGATGTAAGACCATGGTTGGACCATG-CAGTGTATATAGATGTAAGACCATAGTTGGGCTAT
*
75355 GACA
65 GGCA
*
75359 ATCTGATGTTAAGACCAT
1 TTCTGATG-TAAGACCAT
75377 AACCCGGTTA
Statistics
Matches: 140, Mismatches: 13, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
68 2 0.01
69 129 0.92
70 9 0.06
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (68 bp):
TTCTGATGTAAGACCATGGTTGGACCATGCAGTGTATATAGATGTAAGACCATAGTTGGGCTATG
GCA
Found at i:75356 original size:37 final size:35
Alignment explanation
Indices: 75187--75356 Score: 113
Period size: 37 Copynumber: 4.9 Consensus size: 35
75177 CATGGCAGTG
* ** *
75187 TATATAGATGTAAGACCATAACTAGGCTATG-GCA
1 TATATATATGTAAGACCATAGTTGGGCTATGAGCA
* * * * *
75221 T-TCT-GATGTAAGACCATGGTTGGACCAT-AGCA
1 TATATATATGTAAGACCATAGTTGGGCTATGAGCA
*
75253 GTGTATATAGATGTAAGACCATAGTTGGGCTATG-GCA
1 ---TATATATATGTAAGACCATAGTTGGGCTATGAGCA
* * *
75290 T-T-T-TGATGTAAGACCATTGTTGGACTATGATAGTA
1 TATATAT-ATGTAAGACCATAGTTGGGCTATG--AGCA
75325 TATATATATGTAAGACCATAGTTGGGCTATGA
1 TATATATATGTAAGACCATAGTTGGGCTATGA
75357 CAATCTGATG
Statistics
Matches: 105, Mismatches: 17, Indels: 27
0.70 0.11 0.18
Matches are distributed among these distances:
32 44 0.42
33 3 0.03
34 2 0.02
35 5 0.05
36 3 0.03
37 47 0.45
38 1 0.01
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (35 bp):
TATATATATGTAAGACCATAGTTGGGCTATGAGCA
Found at i:76747 original size:48 final size:48
Alignment explanation
Indices: 76695--76786 Score: 184
Period size: 48 Copynumber: 1.9 Consensus size: 48
76685 ATGATATGTG
76695 ATATGAGTATTGATTCTTTCTTGGAAAATGTATTGATGAGTATGCCTT
1 ATATGAGTATTGATTCTTTCTTGGAAAATGTATTGATGAGTATGCCTT
76743 ATATGAGTATTGATTCTTTCTTGGAAAATGTATTGATGAGTATG
1 ATATGAGTATTGATTCTTTCTTGGAAAATGTATTGATGAGTATG
76787 TCTTGGGTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.28, C:0.07, G:0.22, T:0.43
Consensus pattern (48 bp):
ATATGAGTATTGATTCTTTCTTGGAAAATGTATTGATGAGTATGCCTT
Found at i:80050 original size:14 final size:14
Alignment explanation
Indices: 80023--80057 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
80013 GTAAATATAA
80023 TTTTTTCTTCTTTT
1 TTTTTTCTTCTTTT
80037 TTCTTTTC-TCTTTT
1 TT-TTTTCTTCTTTT
80051 TTTTTTC
1 TTTTTTC
80058 AAGTGACTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 5 0.25
14 10 0.50
15 5 0.25
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTTCTTCTTTT
Found at i:81115 original size:12 final size:12
Alignment explanation
Indices: 81100--81135 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
81090 CTTCTCTTTA
81100 TTCTCTTCTTCC
1 TTCTCTTCTTCC
81112 TTCTCTTCTT-C
1 TTCTCTTCTTCC
81123 TTC-CTT-TTCC
1 TTCTCTTCTTCC
81133 TTC
1 TTC
81136 AGCTGATCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 2 0.09
10 7 0.30
11 4 0.17
12 10 0.43
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (12 bp):
TTCTCTTCTTCC
Found at i:88356 original size:14 final size:14
Alignment explanation
Indices: 88337--88370 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
88327 ATCACCGATT
*
88337 TCAGCTCGAAATTA
1 TCAGCTCAAAATTA
88351 TCAGCTCAAAATTA
1 TCAGCTCAAAATTA
*
88365 CCAGCT
1 TCAGCT
88371 TGAATAGACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.35, C:0.26, G:0.12, T:0.26
Consensus pattern (14 bp):
TCAGCTCAAAATTA
Found at i:89032 original size:13 final size:14
Alignment explanation
Indices: 89014--89043 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
89004 GTCAATGCAA
89014 TCAGA-GTTAAATG
1 TCAGAGGTTAAATG
89027 TCAGAGGTTAAATG
1 TCAGAGGTTAAATG
89041 TCA
1 TCA
89044 ATGTACTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (14 bp):
TCAGAGGTTAAATG
Found at i:97747 original size:28 final size:28
Alignment explanation
Indices: 97711--97767 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
97701 TTATGCTTGG
97711 TTTAAATTCTTGTTATTTTATCTCTTTT
1 TTTAAATTCTTGTTATTTTATCTCTTTT
97739 TTTAAATTCTTGTTATTTTATCTCTTTT
1 TTTAAATTCTTGTTATTTTATCTCTTTT
97767 T
1 T
97768 GTGCACTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.18, C:0.11, G:0.04, T:0.68
Consensus pattern (28 bp):
TTTAAATTCTTGTTATTTTATCTCTTTT
Found at i:98858 original size:22 final size:23
Alignment explanation
Indices: 98816--98859 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
98806 AATTTGATTT
*
98816 ACTTTTAATTGCACTGACAATTA
1 ACTTTTAATTACACTGACAATTA
*
98839 ACTTTT-ATTACATTGACAATT
1 ACTTTTAATTACACTGACAATT
98860 TTAACTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.34, C:0.16, G:0.07, T:0.43
Consensus pattern (23 bp):
ACTTTTAATTACACTGACAATTA
Found at i:100086 original size:39 final size:39
Alignment explanation
Indices: 100032--100109 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
100022 TGGCGGCAAA
100032 GATAAATTTTTTTTCTCTTAACTCTACAAAGAGTTTTTT
1 GATAAATTTTTTTTCTCTTAACTCTACAAAGAGTTTTTT
100071 GATAAATTTTTTTTCTCTTAACTCTACAAAGAGTTTTTT
1 GATAAATTTTTTTTCTCTTAACTCTACAAAGAGTTTTTT
100110 TTTTTTTTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.28, C:0.13, G:0.08, T:0.51
Consensus pattern (39 bp):
GATAAATTTTTTTTCTCTTAACTCTACAAAGAGTTTTTT
Found at i:101867 original size:21 final size:21
Alignment explanation
Indices: 101841--101891 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
101831 GTACATTGCC
* *
101841 CAAAACCTCGAATAAAAAGCT
1 CAAAACCCCGAATAAAAAACT
101862 CAAAACCCCGAATAAAAAACT
1 CAAAACCCCGAATAAAAAACT
101883 CAAAACCCC
1 CAAAACCCC
101892 AAAAAGCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.53, C:0.31, G:0.06, T:0.10
Consensus pattern (21 bp):
CAAAACCCCGAATAAAAAACT
Found at i:114399 original size:18 final size:18
Alignment explanation
Indices: 114376--114414 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
114366 TATCTCAGCA
114376 AGAAGTTCACTAAATGCG
1 AGAAGTTCACTAAATGCG
114394 AGAAGTTCACTAAATGCG
1 AGAAGTTCACTAAATGCG
114412 AGA
1 AGA
114415 TAAGATATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.41, C:0.15, G:0.23, T:0.21
Consensus pattern (18 bp):
AGAAGTTCACTAAATGCG
Found at i:116529 original size:46 final size:46
Alignment explanation
Indices: 116461--116561 Score: 168
Period size: 46 Copynumber: 2.2 Consensus size: 46
116451 AAAAACACAA
116461 AAAAAAAAAGTTTGAGTTGAAAACCTGAAAGGGCGA-CTCAAACTAG
1 AAAAAAAAAGTTTGAGTTGAAAACCTGAAAGGG-GAGCTCAAACTAG
* *
116507 GAAAAAAAAGTTTGAGTTGAAAACCTGAAAGGGTAGCTCAAACTAG
1 AAAAAAAAAGTTTGAGTTGAAAACCTGAAAGGGGAGCTCAAACTAG
116553 AAAAAAAAA
1 AAAAAAAAA
116562 AAAGGGAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
45 1 0.02
46 50 0.98
ACGTcount: A:0.51, C:0.11, G:0.21, T:0.17
Consensus pattern (46 bp):
AAAAAAAAAGTTTGAGTTGAAAACCTGAAAGGGGAGCTCAAACTAG
Found at i:118769 original size:12 final size:12
Alignment explanation
Indices: 118746--118799 Score: 74
Period size: 12 Copynumber: 4.3 Consensus size: 12
118736 GCAAACATTT
118746 TTTTCTTCTTTTC
1 TTTTC-TCTTTTC
118759 TTTTCTCTTTTC
1 TTTTCTCTTTTC
118771 TTTTCTC-TTTC
1 TTTTCTCTTTTC
118782 TTTTTCTCATTTTC
1 -TTTTCTC-TTTTC
118796 TTTT
1 TTTT
118800 TTCAAGTGAC
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
11 4 0.11
12 21 0.55
13 9 0.24
14 4 0.11
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTCTCTTTTC
Found at i:118786 original size:24 final size:23
Alignment explanation
Indices: 118741--118799 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 23
118731 TTATAGCAAA
*
118741 CATTTTTTTCTTCTTTTCTTTTCT
1 CATTTTCTT-TTCTTTTCTTTTCT
118765 C-TTTTCTTTTCTCTTTCTTTTTCT
1 CATTTTCTTTTCT-TTTC-TTTTCT
118789 CATTTTCTTTT
1 CATTTTCTTTT
118800 TTCAAGTGAC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
22 4 0.13
23 10 0.32
24 8 0.26
25 9 0.29
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.75
Consensus pattern (23 bp):
CATTTTCTTTTCTTTTCTTTTCT
Found at i:120725 original size:144 final size:145
Alignment explanation
Indices: 120461--120753 Score: 473
Period size: 144 Copynumber: 2.0 Consensus size: 145
120451 TGTCTTCAAG
* *
120461 TTTT-TGAGGCTGTTTTGCTGTAGCATTTGTGGCGACAAAGTGATCTGATTTTGTTGTCGCAATA
1 TTTTGTGAGGCTATTTTGCTGTAGCATTTGTGGCGACAAAGTGATCTGATTCTGTTGTCGCAATA
**
120525 TTTTGTTTAACCTCTTCAGCTGCAGTTTACTTTTCAGATTGTGCTGACATCTTTCCATTGTTGAG
66 TTTTGTTTAACCTCTTCAGCTGCAGTTTACTTTTCAGATTACGCTGACATCTTTCCATTGTTGAG
*
120590 ATTTGAATTAT-TTT
131 ATTTGAATTATCTTC
* * * **
120604 TTTTGTGAGGCTATTTTGCTGTAGCATTTGTGGTGGCAAAGTGATCTGATTCTGTTGTTGTGATA
1 TTTTGTGAGGCTATTTTGCTGTAGCATTTGTGGCGACAAAGTGATCTGATTCTGTTGTCGCAATA
*
120669 TTTTGTTTAACCTCTTCAGCTGCAGTTTGCTTTTCAGATTACGCTGACATCTTTCCATTGTTGAG
66 TTTTGTTTAACCTCTTCAGCTGCAGTTTACTTTTCAGATTACGCTGACATCTTTCCATTGTTGAG
120734 ATTTGAATTATCTTC
131 ATTTGAATTATCTTC
120749 TTTTG
1 TTTTG
120754 CTGTAGCATC
Statistics
Matches: 137, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
143 4 0.03
144 126 0.92
145 7 0.05
ACGTcount: A:0.18, C:0.15, G:0.21, T:0.46
Consensus pattern (145 bp):
TTTTGTGAGGCTATTTTGCTGTAGCATTTGTGGCGACAAAGTGATCTGATTCTGTTGTCGCAATA
TTTTGTTTAACCTCTTCAGCTGCAGTTTACTTTTCAGATTACGCTGACATCTTTCCATTGTTGAG
ATTTGAATTATCTTC
Found at i:124025 original size:42 final size:42
Alignment explanation
Indices: 123928--124350 Score: 359
Period size: 42 Copynumber: 10.4 Consensus size: 42
123918 TTACATCATC
* * *
123928 CCATCCAATCTTTTACCCCAACCATG-GGGCAGATTGAAG---
1 CCATCCAATCTCTTACCCTAA-CAAGAGGGCAGATTGAAGACA
* * * *
123967 CCATCTAATCTTTTACCCTAACAAGAGGGTAGATTAAAGACA
1 CCATCCAATCTCTTACCCTAACAAGAGGGCAGATTGAAGACA
*
124009 CCATCCAATCTCTTACCCCAACAATG-GGGCAGATTGAAG---
1 CCATCCAATCTCTTACCCTAACAA-GAGGGCAGATTGAAGACA
*
124048 CCATCCAATCTCTTTCCCTAACAAGAGGGCAGATTGAAGACA
1 CCATCCAATCTCTTACCCTAACAAGAGGGCAGATTGAAGACA
** * * * *
124090 TTAGT-CAATCTCTTACCCCAACCATAGGGTAGATTGAAG---
1 CCA-TCCAATCTCTTACCCTAACAAGAGGGCAGATTGAAGACA
* * * *
124129 TCATCCAATCTTTTACCCAAACAAGTGGGCAGATTGAAGACA
1 CCATCCAATCTCTTACCCTAACAAGAGGGCAGATTGAAGACA
* * *
124171 CCATCCAATCTCTTTCCCTAACCATG-GGGCATATTGAAG---
1 CCATCCAATCTCTTACCCTAA-CAAGAGGGCAGATTGAAGACA
* * *
124210 CCATCCAATCTTTTACCCTAACAAGAGGGCAAATTGAAGATA
1 CCATCCAATCTCTTACCCTAACAAGAGGGCAGATTGAAGACA
* * *
124252 CCATCCAATCTCTTACCCCAACCATG-GGGCATATTGAAGACA
1 CCATCCAATCTCTTACCCTAA-CAAGAGGGCAGATTGAAGACA
*
124294 CCATCCAATCT-TTAACCTAATCCAA-AGGGCAGATTG-A-A-A
1 CCATCCAATCTCTTACCCTAA--CAAGAGGGCAGATTGAAGACA
*
124333 TCATCCAATCTCTTACCC
1 CCATCCAATCTCTTACCC
124351 CTAATTTAGA
Statistics
Matches: 314, Mismatches: 47, Indels: 45
0.77 0.12 0.11
Matches are distributed among these distances:
38 8 0.03
39 137 0.44
40 6 0.02
41 8 0.03
42 147 0.47
43 8 0.03
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.24
Consensus pattern (42 bp):
CCATCCAATCTCTTACCCTAACAAGAGGGCAGATTGAAGACA
Found at i:124027 original size:81 final size:81
Alignment explanation
Indices: 123928--124351 Score: 556
Period size: 81 Copynumber: 5.2 Consensus size: 81
123918 TTACATCATC
* *
123928 CCATCCAATCTTTTACCCCAACCATGGGGCAGATTGAAGCCATCTAATCTTTTACCCTAACAAGA
1 CCATCCAATCTCTTACCCCAACCATGGGGCAGATTGAAGCCATCCAATCTTTTACCCTAACAAGA
* *
123993 GGGTAGATTAAAGACA
66 GGGCAGATTGAAGACA
*
124009 CCATCCAATCTCTTACCCCAACAATGGGGCAGATTGAAGCCATCCAATCTCTTT-CCCTAACAAG
1 CCATCCAATCTCTTACCCCAACCATGGGGCAGATTGAAGCCATCCAATCT-TTTACCCTAACAAG
124073 AGGGCAGATTGAAGACA
65 AGGGCAGATTGAAGACA
** * * * *
124090 TTAGT-CAATCTCTTACCCCAACCATAGGGTAGATTGAAGTCATCCAATCTTTTACCCAAACAAG
1 CCA-TCCAATCTCTTACCCCAACCATGGGGCAGATTGAAGCCATCCAATCTTTTACCCTAACAAG
*
124154 TGGGCAGATTGAAGACA
65 AGGGCAGATTGAAGACA
* * *
124171 CCATCCAATCTCTTTCCCTAACCATGGGGCATATTGAAGCCATCCAATCTTTTACCCTAACAAGA
1 CCATCCAATCTCTTACCCCAACCATGGGGCAGATTGAAGCCATCCAATCTTTTACCCTAACAAGA
* *
124236 GGGCAAATTGAAGATA
66 GGGCAGATTGAAGACA
* *
124252 CCATCCAATCTCTTACCCCAACCATGGGGCATATTGAAGACACCATCCAATC-TTTAACCTAATC
1 CCATCCAATCTCTTACCCCAACCATGGGGCAGATTGAAG---CCATCCAATCTTTTACCCTAA--
124316 CAA-AGGGCAGATTG-A-A-A
61 CAAGAGGGCAGATTGAAGACA
*
124333 TCATCCAATCTCTTACCCC
1 CCATCCAATCTCTTACCCC
124352 TAATTTAGAG
Statistics
Matches: 304, Mismatches: 30, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
80 4 0.01
81 262 0.86
82 5 0.02
83 10 0.03
84 20 0.07
85 3 0.01
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.24
Consensus pattern (81 bp):
CCATCCAATCTCTTACCCCAACCATGGGGCAGATTGAAGCCATCCAATCTTTTACCCTAACAAGA
GGGCAGATTGAAGACA
Found at i:125700 original size:52 final size:52
Alignment explanation
Indices: 125625--125857 Score: 349
Period size: 52 Copynumber: 4.5 Consensus size: 52
125615 GAAAAGGTTA
* * *
125625 GATGACTATGTGTCATCGGGAGTATATGAATCCTTTACGAATTTTAAGGTCC
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGGTCC
*
125677 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATCAGGTCC
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGGTCC
* * * *
125729 GATGATTATGTGTCATCGTGAGTACATGAATACTTTACGGATTATAAGGTCT
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGGTCC
* * * *
125781 GATAACTATGTGTCATCGTGAGTGTATGAATCCTTTACGGATTATGAGGTTC
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGGTCC
*
125833 GATGACTATGTGTTATCGTGAGTAT
1 GATGACTATGTGTCATCGTGAGTAT
125858 TAAAAGAAAT
Statistics
Matches: 161, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 161 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (52 bp):
GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGGTCC
Found at i:126511 original size:21 final size:21
Alignment explanation
Indices: 126485--126539 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
126475 CTGTACATGT
126485 TTGTATCGGTAGATAGAATAC
1 TTGTATCGGTAGATAGAATAC
126506 TTGTATCGGTAGATAGAATAC
1 TTGTATCGGTAGATAGAATAC
*
126527 TTGTATCGATAGA
1 TTGTATCGGTAGA
126540 AGTTGCAGGG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.33, C:0.09, G:0.24, T:0.35
Consensus pattern (21 bp):
TTGTATCGGTAGATAGAATAC
Found at i:133054 original size:52 final size:52
Alignment explanation
Indices: 132912--133148 Score: 361
Period size: 52 Copynumber: 4.6 Consensus size: 52
132902 GTAAATGAAA
* * *
132912 AGGTTCGATGACTATGTGTCATCGTGAATATATGAATCCTTTATGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
132964 AGGTCCGGTGAC--TGTGTCATCGTGAGTATATGAATCCTTTATGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
133014 AGGTCCGATGACTATGTGTCATCGTGAGTGTATGAATCCTTTACGGATTATA
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
133066 AGGTCCGATGACTATGTGTCATCGTGAGTGTATGAATCCTTTACAGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
133118 AGGTCCGATGACTATGTGTTATCATGAGTAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTAT
133149 TAAAAGAAAT
Statistics
Matches: 171, Mismatches: 12, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
50 48 0.28
52 123 0.72
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:137273 original size:32 final size:32
Alignment explanation
Indices: 137232--137294 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
137222 AGTCTCATGG
137232 TGTAGCTCGTGAACTTGACGATATATCCATAA
1 TGTAGCTCGTGAACTTGACGATATATCCATAA
* *
137264 TGTAGCTCGTGAACTTGATGATATATTCATA
1 TGTAGCTCGTGAACTTGACGATATATCCATA
137295 GAAAACTTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (32 bp):
TGTAGCTCGTGAACTTGACGATATATCCATAA
Found at i:142829 original size:21 final size:21
Alignment explanation
Indices: 142804--142865 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
142794 TATCGTTGCA
142804 TTTATTCTTTATTATCTAAAT
1 TTTATTCTTTATTATCTAAAT
* *
142825 TTTA---TTTGTCA-CTAAAT
1 TTTATTCTTTATTATCTAAAT
142842 TTTATTCTTTATTATCTAAAT
1 TTTATTCTTTATTATCTAAAT
142863 TTT
1 TTT
142866 TTTTTTCTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
17 10 0.30
18 5 0.15
20 5 0.15
21 13 0.39
ACGTcount: A:0.27, C:0.10, G:0.02, T:0.61
Consensus pattern (21 bp):
TTTATTCTTTATTATCTAAAT
Found at i:144677 original size:17 final size:18
Alignment explanation
Indices: 144657--144690 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
144647 CGACTGTAAC
144657 ACACTGAG-TTAGTTTTT
1 ACACTGAGTTTAGTTTTT
*
144674 ACACTTAGTTTAGTTTT
1 ACACTGAGTTTAGTTTT
144691 CATGCATATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.50
Consensus pattern (18 bp):
ACACTGAGTTTAGTTTTT
Found at i:155404 original size:56 final size:56
Alignment explanation
Indices: 155335--155450 Score: 198
Period size: 56 Copynumber: 2.1 Consensus size: 56
155325 CCTAGGCTTT
*
155335 CAAAGGTTGATGTATTTAATCCACAAGATGTTTTGCAACTAAATAGAAATCAATCA
1 CAAAGGTTGATGTATTTAATCCAAAAGATGTTTTGCAACTAAATAGAAATCAATCA
*
155391 CAAA-GTTGAATGTATTTAATCCAAAAGATGTTTTTCAACTAAATAGAAATCAATCA
1 CAAAGGTTG-ATGTATTTAATCCAAAAGATGTTTTGCAACTAAATAGAAATCAATCA
155447 CAAA
1 CAAA
155451 TTGGTAGTAA
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
55 4 0.07
56 53 0.93
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (56 bp):
CAAAGGTTGATGTATTTAATCCAAAAGATGTTTTGCAACTAAATAGAAATCAATCA
Found at i:159671 original size:266 final size:268
Alignment explanation
Indices: 159193--159720 Score: 916
Period size: 266 Copynumber: 2.0 Consensus size: 268
159183 CTCTTGAGTC
* *
159193 TAAATTCATAGTCTGTATCGTCAAATTCGAACTTGAGAGCTTGTTTTAGCTATTTACAAGTTATT
1 TAAATTCATAGTCTGTATCGTCAAATTCAAACTTGAGAGCCTGTTTTAGCTATTTACAAGTTATT
* * *
159258 GTACTCAGTAATTTTTAAGAAAAATGAATAAGGGATTTGACTCGTGTTATTCTGTGTTTAAGTGA
66 GTAC-CA-TAATTTCTAAGAAAAATGAATAAGAGATTTGACTCGTGTTATTCTATGTTTAAGTGA
* * *
159323 TAACGATTCTGAGGTCGATGAGTTACCTCCTTTACCTGTGCAGATTGCCCCTGCACAAGGTCCAA
129 TAACGATTCTGAGGTCGATGAGTTACCTCCTTCACCTGTACAGACTGCCCCTGCACAAGGTCCAA
*
159388 TAATTAGACATGAGTATTCGTTATTCAATTTAGTGTTGTGTTTAGTATGTGACTTAGTGATAGAT
194 TAATTAGACATGAGTATTCGTTATTCAATTTAGTGTTGTGTTTAGTATGTGACTTAGCGATAGAT
159453 TTGACTCGTG
259 TTGACTCGTG
159463 TAAATTCATAGTCTGTATCGTCAAATTCAAACTTGAGAGCCTGTTTTAGCTATTTACAAGTTATT
1 TAAATTCATAGTCTGTATCGTCAAATTCAAACTTGAGAGCCTGTTTTAGCTATTTACAAGTTATT
*
159528 GTA-C-TAATTTCTAATAAAAATGAATAAGAGATTTGACTCGTGTTATTCTATGTTTAAGTGATA
66 GTACCATAATTTCTAAGAAAAATGAATAAGAGATTTGACTCGTGTTATTCTATGTTTAAGTGATA
159591 ACGATTCTGAGGTCGATGAGTTACCTCCTTCACCTGTACAGACTGCCCCTGCACAAGGTCCAATA
131 ACGATTCTGAGGTCGATGAGTTACCTCCTTCACCTGTACAGACTGCCCCTGCACAAGGTCCAATA
* *
159656 GTTAGACATGAGTATTCGTTATTCGATTTAGTGTTGTGTTTAGTATGTGACTTAGCGATAGATTT
196 ATTAGACATGAGTATTCGTTATTCAATTTAGTGTTGTGTTTAGTATGTGACTTAGCGATAGATTT
159721 AATGTAAAAT
Statistics
Matches: 246, Mismatches: 12, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
266 179 0.73
268 1 0.00
270 66 0.27
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.38
Consensus pattern (268 bp):
TAAATTCATAGTCTGTATCGTCAAATTCAAACTTGAGAGCCTGTTTTAGCTATTTACAAGTTATT
GTACCATAATTTCTAAGAAAAATGAATAAGAGATTTGACTCGTGTTATTCTATGTTTAAGTGATA
ACGATTCTGAGGTCGATGAGTTACCTCCTTCACCTGTACAGACTGCCCCTGCACAAGGTCCAATA
ATTAGACATGAGTATTCGTTATTCAATTTAGTGTTGTGTTTAGTATGTGACTTAGCGATAGATTT
GACTCGTG
Found at i:159873 original size:29 final size:29
Alignment explanation
Indices: 159823--159886 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
159813 CCTGCTTAAG
* *
159823 GTGTGTCTTGGTCTGTGCTACATAATGTT
1 GTGTGTCTTGATCTATGCTACATAATGTT
* * **
159852 GTGTGTCTTTATCTATGTTACATTCTGTT
1 GTGTGTCTTGATCTATGCTACATAATGTT
159881 GTGTGT
1 GTGTGT
159887 TAATGCTCTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.12, C:0.12, G:0.25, T:0.50
Consensus pattern (29 bp):
GTGTGTCTTGATCTATGCTACATAATGTT
Found at i:160269 original size:5 final size:5
Alignment explanation
Indices: 160227--160268 Score: 50
Period size: 5 Copynumber: 8.6 Consensus size: 5
160217 TGAAAGCATA
* * *
160227 AAAAT AAAA- AGATT AAAAT AAAAT AAAAT AAAAT AAAGT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
160269 GATGAGTTGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
4 2 0.06
5 29 0.94
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:160821 original size:15 final size:15
Alignment explanation
Indices: 160801--160830 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
160791 AACCCTAGTG
*
160801 CTAAAGGTCTTATTT
1 CTAAAGGTCCTATTT
160816 CTAAAGGTCCTATTT
1 CTAAAGGTCCTATTT
160831 ATAGCTTTAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (15 bp):
CTAAAGGTCCTATTT
Found at i:172549 original size:19 final size:20
Alignment explanation
Indices: 172507--172550 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
172497 AACTCGAAGG
172507 CCCAATTTGTGAACCCAATA
1 CCCAATTTGTGAACCCAATA
* *
172527 CCCAATTTGT-AATCCACTA
1 CCCAATTTGTGAACCCAATA
172546 CCCAA
1 CCCAA
172551 CCCAAATCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.34, C:0.34, G:0.07, T:0.25
Consensus pattern (20 bp):
CCCAATTTGTGAACCCAATA
Found at i:179090 original size:12 final size:12
Alignment explanation
Indices: 179055--179090 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
179045 AACTAGATGA
179055 ATATATACATAC
1 ATATATACATAC
*
179067 ATACATACATAC
1 ATATATACATAC
*
179079 ATATATATATAC
1 ATATATACATAC
179091 CAATTAACTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (12 bp):
ATATATACATAC
Found at i:179984 original size:37 final size:37
Alignment explanation
Indices: 179938--180008 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
179928 ATTGACATCT
* *
179938 AGTGTCTCATCGA-TTAAACTAAAGTATAATGGCACCC
1 AGTGCCTCAT-GAGTTAAACCAAAGTATAATGGCACCC
* *
179975 AGTGCCTCATTAGTTAAACCGAAGTATAATGGCA
1 AGTGCCTCATGAGTTAAACCAAAGTATAATGGCA
180009 GTCAATTCCT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 1 0.03
37 28 0.97
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (37 bp):
AGTGCCTCATGAGTTAAACCAAAGTATAATGGCACCC
Found at i:180170 original size:18 final size:18
Alignment explanation
Indices: 180135--180182 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
180125 TATCCAACCA
*
180135 ATATCTCAATTATATATAT
1 ATAT-TCAATAATATATAT
*
180154 ATATTCAATAATGTATAT
1 ATATTCAATAATATATAT
*
180172 TTATTCAATAA
1 ATATTCAATAA
180183 AATAATAGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 22 0.85
19 4 0.15
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (18 bp):
ATATTCAATAATATATAT
Found at i:181452 original size:24 final size:24
Alignment explanation
Indices: 181420--181465 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
181410 CATTACAGAT
*
181420 TATTTCAAATATAAATATTTTTTA
1 TATTCCAAATATAAATATTTTTTA
*
181444 TATTCCAAATATGAATATTTTT
1 TATTCCAAATATAAATATTTTT
181466 ACTGAATGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (24 bp):
TATTCCAAATATAAATATTTTTTA
Found at i:184913 original size:20 final size:20
Alignment explanation
Indices: 184888--184925 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
184878 AATTCTACCA
*
184888 ATACCAATTCATGTCAATTC
1 ATACCAATTCAAGTCAATTC
184908 ATACCAATTCAAGTCAAT
1 ATACCAATTCAAGTCAAT
184926 AAAACCTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.24, G:0.05, T:0.32
Consensus pattern (20 bp):
ATACCAATTCAAGTCAATTC
Found at i:186568 original size:24 final size:24
Alignment explanation
Indices: 186541--186670 Score: 127
Period size: 24 Copynumber: 5.4 Consensus size: 24
186531 GAGAACGTAT
**
186541 GTTTATGCTCGCCTGTCACTATAC
1 GTTTATGCTCGCCAATCACTATAC
** *
186565 GTTTATGCTCTTC-AGCTACTATAC
1 GTTTATGCTCGCCAATC-ACTATAC
*
186589 GTTTATGCTCACCAATCACTATAC
1 GTTTATGCTCGCCAATCACTATAC
* *
186613 GTTTATGCTCGTCAACCACTATAC
1 GTTTATGCTCGCCAATCACTATAC
* *** *
186637 GTTTTTGCTCATTAACCACTATAC
1 GTTTATGCTCGCCAATCACTATAC
186661 GTTTATGCTC
1 GTTTATGCTC
186671 ATATATTTGG
Statistics
Matches: 90, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
23 1 0.01
24 87 0.97
25 2 0.02
ACGTcount: A:0.22, C:0.27, G:0.12, T:0.38
Consensus pattern (24 bp):
GTTTATGCTCGCCAATCACTATAC
Found at i:186612 original size:48 final size:48
Alignment explanation
Indices: 186541--186670 Score: 170
Period size: 48 Copynumber: 2.7 Consensus size: 48
186531 GAGAACGTAT
* ** * * *
186541 GTTTATGCTCGCCTGTCACTATACGTTTATGCTCTTCAGCTACTATAC
1 GTTTATGCTCACCAATCACTATACGTTTATGCTCGTCAACCACTATAC
186589 GTTTATGCTCACCAATCACTATACGTTTATGCTCGTCAACCACTATAC
1 GTTTATGCTCACCAATCACTATACGTTTATGCTCGTCAACCACTATAC
* ** *
186637 GTTTTTGCTCATTAACCACTATACGTTTATGCTC
1 GTTTATGCTCACCAATCACTATACGTTTATGCTC
186671 ATATATTTGG
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 72 1.00
ACGTcount: A:0.22, C:0.27, G:0.12, T:0.38
Consensus pattern (48 bp):
GTTTATGCTCACCAATCACTATACGTTTATGCTCGTCAACCACTATAC
Found at i:186671 original size:24 final size:24
Alignment explanation
Indices: 186557--186672 Score: 160
Period size: 24 Copynumber: 4.8 Consensus size: 24
186547 GCTCGCCTGT
* *
186557 CACTATACGTTTATGCTCTTCAGC
1 CACTATACGTTTATGCTCATCAAC
* * *
186581 TACTATACGTTTATGCTCACCAAT
1 CACTATACGTTTATGCTCATCAAC
*
186605 CACTATACGTTTATGCTCGTCAAC
1 CACTATACGTTTATGCTCATCAAC
* *
186629 CACTATACGTTTTTGCTCATTAAC
1 CACTATACGTTTATGCTCATCAAC
186653 CACTATACGTTTATGCTCAT
1 CACTATACGTTTATGCTCAT
186673 ATATTTGGTA
Statistics
Matches: 79, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 79 1.00
ACGTcount: A:0.25, C:0.27, G:0.10, T:0.38
Consensus pattern (24 bp):
CACTATACGTTTATGCTCATCAAC
Found at i:193259 original size:24 final size:24
Alignment explanation
Indices: 193201--193262 Score: 90
Period size: 23 Copynumber: 2.6 Consensus size: 24
193191 GTTAGAGAAC
* * *
193201 ATATGTTTATGCTTGTCAGTCACT
1 ATATGTTTATGCTCGCCAGCCACT
193225 ATA-GTTTATGCTCGCCAGCCACT
1 ATATGTTTATGCTCGCCAGCCACT
193248 ATATGTTTATGCTCG
1 ATATGTTTATGCTCG
193263 TATATTTGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 20 0.59
24 14 0.41
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.40
Consensus pattern (24 bp):
ATATGTTTATGCTCGCCAGCCACT
Found at i:194250 original size:42 final size:42
Alignment explanation
Indices: 194181--194294 Score: 129
Period size: 42 Copynumber: 2.7 Consensus size: 42
194171 GAAGTTGTCG
* ** * *
194181 TGAATGTTGCAATATTAAAATTCAATGTCACGACATTGGAAT
1 TGAATGTTGCAACATTGGAATTGAATGTCACGACATGGGAAT
** *
194223 TGAATGTTGCAACATTGGAATTGAATGTCGTGACATGGGGAT
1 TGAATGTTGCAACATTGGAATTGAATGTCACGACATGGGAAT
* *
194265 TGAATGATGCAACATTGGAATCTGAGTGTC
1 TGAATGTTGCAACATTGGAAT-TGAATGTC
194295 GCGTTATTGA
Statistics
Matches: 61, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
42 54 0.89
43 7 0.11
ACGTcount: A:0.32, C:0.11, G:0.25, T:0.32
Consensus pattern (42 bp):
TGAATGTTGCAACATTGGAATTGAATGTCACGACATGGGAAT
Found at i:194258 original size:21 final size:21
Alignment explanation
Indices: 194199--194297 Score: 92
Period size: 21 Copynumber: 4.7 Consensus size: 21
194189 GCAATATTAA
* *
194199 AATTCAATGTCACGACATTGG
1 AATTGAATGTCGCGACATTGG
* *
194220 AATTGAATGTTGCAACATTGG
1 AATTGAATGTCGCGACATTGG
* *
194241 AATTGAATGTCGTGACATGGG
1 AATTGAATGTCGCGACATTGG
* *
194262 GATTGAATGAT-GCAACATTGG
1 AATTGAATG-TCGCGACATTGG
*
194283 AATCTGAGTGTCGCG
1 AAT-TGAATGTCGCG
194298 TTATTGAAGA
Statistics
Matches: 60, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
21 52 0.87
22 8 0.13
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.29
Consensus pattern (21 bp):
AATTGAATGTCGCGACATTGG
Found at i:195482 original size:57 final size:57
Alignment explanation
Indices: 195410--195535 Score: 164
Period size: 57 Copynumber: 2.2 Consensus size: 57
195400 TTATAAGCAA
* * *
195410 AATTCATCTCAAATATCATATTATATCATCAAT-TCATAATATCATACCAATTTCACAT
1 AATTCATTTC-AATATCATATTATATCATCAATCT-ATAAGATCATACCAATTTCACAC
* * * *
195468 AGTTCATTTCAATATCATATTTTATTATCAATCTATAAGATCATACCCATTTCACAC
1 AATTCATTTCAATATCATATTATATCATCAATCTATAAGATCATACCAATTTCACAC
195525 AATTCATTTCA
1 AATTCATTTCA
195536 TTGTTATATC
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
57 50 0.85
58 9 0.15
ACGTcount: A:0.38, C:0.21, G:0.02, T:0.40
Consensus pattern (57 bp):
AATTCATTTCAATATCATATTATATCATCAATCTATAAGATCATACCAATTTCACAC
Found at i:202269 original size:37 final size:37
Alignment explanation
Indices: 202222--202319 Score: 126
Period size: 38 Copynumber: 2.6 Consensus size: 37
202212 ATTTTCGGAA
202222 TGCACCCAAGACTGTCGCTGCATAAATATTCTTCAATT
1 TGCACCCAAGACTGTCGCTGCATAAATATTCTTCAA-T
* * *
202260 TGCA-TCAAGAACTATCGCTGCATAATTATTCTTCAAT
1 TGCACCCAAG-ACTGTCGCTGCATAAATATTCTTCAAT
* *
202297 TGCACCCAAGAATGTCGTTGCAT
1 TGCACCCAAGACTGTCGCTGCAT
202320 GAACATGTAC
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
37 19 0.37
38 32 0.63
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (37 bp):
TGCACCCAAGACTGTCGCTGCATAAATATTCTTCAAT
Found at i:202344 original size:26 final size:26
Alignment explanation
Indices: 202305--202365 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 26
202295 ATTGCACCCA
*
202305 AGAA-TGTCGTTGCATGAACATGTAC
1 AGAATTGTCGCTGCATGAACATGTAC
* *
202330 AGAATTGTCGCTGCATGAACGTGTCC
1 AGAATTGTCGCTGCATGAACATGTAC
202356 AGAATTGTCG
1 AGAATTGTCG
202366 TCGCATTTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
25 4 0.12
26 28 0.88
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (26 bp):
AGAATTGTCGCTGCATGAACATGTAC
Found at i:206039 original size:26 final size:26
Alignment explanation
Indices: 205995--206061 Score: 107
Period size: 26 Copynumber: 2.6 Consensus size: 26
205985 TACAAGTTGA
205995 TAAAAAAAAAATTTACTTGTAAAAGT
1 TAAAAAAAAAATTTACTTGTAAAAGT
* * *
206021 TTAAAAAAAATTTTGCTTGTAAAAGT
1 TAAAAAAAAAATTTACTTGTAAAAGT
206047 TAAAAAAAAAATTTA
1 TAAAAAAAAAATTTA
206062 GACCTCTTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.57, C:0.03, G:0.07, T:0.33
Consensus pattern (26 bp):
TAAAAAAAAAATTTACTTGTAAAAGT
Found at i:206072 original size:29 final size:28
Alignment explanation
Indices: 205899--206079 Score: 83
Period size: 29 Copynumber: 6.4 Consensus size: 28
205889 GGCAAAATAA
*
205899 TAAACGTTGAAAAAAAAAA-TTAGATCTCT
1 TAAAAGTT-AAAAAAAAAATTTAGA-CTCT
*** * * *
205928 TAAAAGTTGGTAAAAATATTTGAGGCCCT
1 TAAAAGTTAAAAAAAAAATTT-AGACTCT
*** *
205957 TAAAAACAAAAAAAAAAATTGAGA-TCCT
1 TAAAAGTTAAAAAAAAAATTTAGACT-CT
*
205985 TACAAGTTGATAAAAAAAAAATTT--ACT-T
1 TAAAAG-T--TAAAAAAAAAATTTAGACTCT
* *
206013 GTAAAAGTT-TAAAAAAAATTTTG-CT-T
1 -TAAAAGTTAAAAAAAAAATTTAGACTCT
206039 GTAAAAGTTAAAAAAAAAATTTAGACCTCT
1 -TAAAAGTTAAAAAAAAAATTTAGA-CTCT
206069 TAAAAG-TAAAA
1 TAAAAGTTAAAA
206080 CATAAAACAA
Statistics
Matches: 112, Mismatches: 26, Indels: 29
0.67 0.16 0.17
Matches are distributed among these distances:
25 11 0.10
26 13 0.12
27 12 0.11
28 21 0.19
29 39 0.35
30 4 0.04
31 12 0.11
ACGTcount: A:0.52, C:0.08, G:0.11, T:0.28
Consensus pattern (28 bp):
TAAAAGTTAAAAAAAAAATTTAGACTCT
Found at i:209746 original size:21 final size:21
Alignment explanation
Indices: 209707--209762 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
209697 TATTTTATAA
* * * *
209707 TATTAAATAATAAAATATTTT
1 TATTAATTAATATACTATTAT
* *
209728 TATTATTTATTATACTATTAT
1 TATTAATTAATATACTATTAT
209749 TATTAATTAATATA
1 TATTAATTAATATA
209763 TCATTTGAAA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (21 bp):
TATTAATTAATATACTATTAT
Found at i:216027 original size:14 final size:14
Alignment explanation
Indices: 215997--216026 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
215987 CATATGTTTC
215997 TTTACTTACTGTAT
1 TTTACTTACTGTAT
216011 TTTA-TTACTGTAT
1 TTTACTTACTGTAT
216024 TTT
1 TTT
216027 TGAGAGATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.20, C:0.10, G:0.07, T:0.63
Consensus pattern (14 bp):
TTTACTTACTGTAT
Found at i:222856 original size:158 final size:158
Alignment explanation
Indices: 222568--222869 Score: 419
Period size: 158 Copynumber: 1.9 Consensus size: 158
222558 GATTTACGTG
* * * *
222568 TTATATGGGTGCTGGTCTTAGACGTCCTACCGATGGCTGAGATCTGGCATATGTTGCAGATACTC
1 TTATATGGGTGCTAGTCTTAGAAGTCCTACCGATGGCTGAGATCTGGCATATGTTACAGATACCC
* * * * *
222633 CACAGCTCGTGTGAGCAGCATCGTGTAGCTTAACATCTCGACCCACAGCTTCTGTGTGCAAACCC
66 CACAACTCGTGTGAGCAACATCGTGCAGCTTAACATCTCGACCCACAACTTCTGTGAGCAAACCC
222698 ACTGCACAGCTCGTGTAAGCTTTACATC
131 ACTGCACAGCTCGTGTAAGCTTTACATC
* * ** *
222726 TTATATGGGTGCTAGTCTTAGAAGTTCTACCGATGGCTGAGAT-TCGGTATATGTTATGGATTCC
1 TTATATGGGTGCTAGTCTTAGAAGTCCTACCGATGGCTGAGATCT-GGCATATGTTACAGATACC
*
222790 CCACAACTCGTGTGAGCAACATCGTGCAGCTTAACATCTCGACCCACAAC-TCATGTGAGCAGAC
65 CCACAACTCGTGTGAGCAACATCGTGCAGCTTAACATCTCGACCCACAACTTC-TGTGAGCAAAC
* *
222854 CCATTTCACAGCTCGT
129 CCACTGCACAGCTCGT
222870 CTGAGCACTA
Statistics
Matches: 125, Mismatches: 17, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
157 3 0.02
158 122 0.98
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.28
Consensus pattern (158 bp):
TTATATGGGTGCTAGTCTTAGAAGTCCTACCGATGGCTGAGATCTGGCATATGTTACAGATACCC
CACAACTCGTGTGAGCAACATCGTGCAGCTTAACATCTCGACCCACAACTTCTGTGAGCAAACCC
ACTGCACAGCTCGTGTAAGCTTTACATC
Found at i:228976 original size:6 final size:6
Alignment explanation
Indices: 228960--228993 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
228950 AAATTGAATT
* *
228960 AAAAAG GAAAAG AAAAAG AAAAAG AGAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
228994 TTTGGCTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:230080 original size:131 final size:131
Alignment explanation
Indices: 229839--230108 Score: 387
Period size: 131 Copynumber: 2.1 Consensus size: 131
229829 ATTTCGGGAT
* * *
229839 TTACATGTTATATGGGTGCTGGTCTTAGATGTCCTACTGATGGCTGAGATCTGACATATGTTACG
1 TTACATGTTATATGGGTGCTAGTCTTAGATGTCCTACCGATGGCTGAGATCCGACATATGTTACG
* * * ** * *
229904 GATTCTCCACAGCTCGTGCGAGCAGCATTGTGTAGCTTAATATCTCGACCCACAGCTCGTGTGAG
66 GATTCCCCACAGCTCGTGCGAGCAACATCGTACAGCTTAACATCTCAACCCACAGCTCGTGTGAG
229969 A
131 A
* * **
229970 TTACGTGTTATATGGGTGCTAGTCTTAGATGTTCTACCGATGGCTGAGATCCGGTATATGTTACG
1 TTACATGTTATATGGGTGCTAGTCTTAGATGTCCTACCGATGGCTGAGATCCGACATATGTTACG
*
230035 GATTCCCCACAGCTCGTGTGAGCAACATCGTACAGCTTAACATCTCAACCCACAGCTCGTGTGAG
66 GATTCCCCACAGCTCGTGCGAGCAACATCGTACAGCTTAACATCTCAACCCACAGCTCGTGTGAG
230100 CA
131 -A
*
230102 CTACATG
1 TTACATG
230109 ATACAGAAAA
Statistics
Matches: 121, Mismatches: 17, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
131 115 0.95
132 6 0.05
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.30
Consensus pattern (131 bp):
TTACATGTTATATGGGTGCTAGTCTTAGATGTCCTACCGATGGCTGAGATCCGACATATGTTACG
GATTCCCCACAGCTCGTGCGAGCAACATCGTACAGCTTAACATCTCAACCCACAGCTCGTGTGAG
A
Found at i:242054 original size:12 final size:12
Alignment explanation
Indices: 242037--242062 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
242027 AATTTGTTTG
242037 TTGTTTTAATAT
1 TTGTTTTAATAT
242049 TTGTTTTAATAT
1 TTGTTTTAATAT
242061 TT
1 TT
242063 TTAAGTATTT
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:0.00, G:0.08, T:0.69
Consensus pattern (12 bp):
TTGTTTTAATAT
Found at i:254401 original size:15 final size:15
Alignment explanation
Indices: 254363--254407 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
254353 AGTAAGTATG
*
254363 TGTACTTTAGTTAAT
1 TGTACTTTAGTTACT
*
254378 TGTATTTTAGTTACT
1 TGTACTTTAGTTACT
*
254393 TTTACTTTAG-TACT
1 TGTACTTTAGTTACT
254407 T
1 T
254408 CAGTAAAACT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
14 5 0.19
15 21 0.81
ACGTcount: A:0.22, C:0.09, G:0.11, T:0.58
Consensus pattern (15 bp):
TGTACTTTAGTTACT
Found at i:255959 original size:15 final size:15
Alignment explanation
Indices: 255930--255971 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
255920 GGTAGTGGGG
255930 ATTTG-TTTTATTTTT
1 ATTTGATTTTA-TTTT
255945 ATTTGATTTTATTTT
1 ATTTGATTTTATTTT
255960 A-TT-ATTTTATTT
1 ATTTGATTTTATTT
255972 GAAATTATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 9 0.35
14 2 0.08
15 10 0.38
16 5 0.19
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.76
Consensus pattern (15 bp):
ATTTGATTTTATTTT
Found at i:259409 original size:33 final size:33
Alignment explanation
Indices: 259372--259454 Score: 139
Period size: 33 Copynumber: 2.5 Consensus size: 33
259362 ATGTTCATAA
259372 AAATATGATATTCTGATCTAGTAAATATTATGG
1 AAATATGATATTCTGATCTAGTAAATATTATGG
* *
259405 AAATATGATATTTTGATCTAGTAAATATTTTGG
1 AAATATGATATTCTGATCTAGTAAATATTATGG
*
259438 AAATATCATATTCTGAT
1 AAATATGATATTCTGAT
259455 TTGAGTCTGT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.42
Consensus pattern (33 bp):
AAATATGATATTCTGATCTAGTAAATATTATGG
Found at i:261261 original size:69 final size:69
Alignment explanation
Indices: 261145--261297 Score: 261
Period size: 69 Copynumber: 2.2 Consensus size: 69
261135 GATACGCGAA
* *
261145 TCTCTAACACACCAACACTAGACTTATAGAGTCGAAACATATCCCATAAGTGAAGCATATAACCA
1 TCTCCAACACACCAACACTAGACTCATAGAGTCGAAACATATCCCATAAGTGAAGCATATAACCA
261210 ACAC
66 ACAC
* **
261214 TCTCCAACACACCAACACTGGACTCATAGAGTCGAAACATATCCCATAAGTGAAGCATATAGTCA
1 TCTCCAACACACCAACACTAGACTCATAGAGTCGAAACATATCCCATAAGTGAAGCATATAACCA
261279 ACAC
66 ACAC
261283 TCTCCAACACACCAA
1 TCTCCAACACACCAA
261298 ACATATCCCG
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 79 1.00
ACGTcount: A:0.41, C:0.30, G:0.10, T:0.19
Consensus pattern (69 bp):
TCTCCAACACACCAACACTAGACTCATAGAGTCGAAACATATCCCATAAGTGAAGCATATAACCA
ACAC
Found at i:262245 original size:24 final size:23
Alignment explanation
Indices: 262217--262269 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
262207 TACAAATGAT
*
262217 TAAAAAGATTGAATAAATAAAAAA
1 TAAAAAGATTAAAT-AATAAAAAA
* **
262241 TAAAAGGATTAAATTTTAAAAAA
1 TAAAAAGATTAAATAATAAAAAA
262264 TAAAAA
1 TAAAAA
262270 TAAAAATATT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 12 0.50
24 12 0.50
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.25
Consensus pattern (23 bp):
TAAAAAGATTAAATAATAAAAAA
Found at i:262273 original size:29 final size:29
Alignment explanation
Indices: 262231--262343 Score: 133
Period size: 29 Copynumber: 3.8 Consensus size: 29
262221 AAGATTGAAT
*
262231 AAATAAAAAATAAAAGGATTAAATTTTAAA
1 AAAT-AAAAATAAAAAGATTAAATTTTAAA
*
262261 AAATAAAAATAAAAATATTAAATTTTAAA
1 AAATAAAAATAAAAAGATTAAATTTTAAA
*
262290 AAAT-AAAAT-AAAAGAACTAAATTTATAAA
1 AAATAAAAATAAAAAG-ATTAAATTT-TAAA
262319 TAAA-ATAAAATAAAAAGATTAAATT
1 -AAATA-AAAATAAAAAGATTAAATT
262344 AAAAAAAAGA
Statistics
Matches: 72, Mismatches: 5, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
27 4 0.06
28 13 0.18
29 31 0.43
30 7 0.10
31 12 0.17
32 5 0.07
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.27
Consensus pattern (29 bp):
AAATAAAAATAAAAAGATTAAATTTTAAA
Found at i:264149 original size:100 final size:99
Alignment explanation
Indices: 264029--264360 Score: 342
Period size: 100 Copynumber: 3.4 Consensus size: 99
264019 TTGAAGCTTC
*
264029 ACTCCATTCCACTGTAACCTCAGGGACATTGAGATTTGCTTTGTTGTTGTAATCTGACCTACTGT
1 ACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTGCTTTGTTGTT-TAATCTGACCTACTGT
* *
264094 AACCCTAGAGGTATAGGATTTGGTGTTGTAATTTT
65 AACCCAAGAGGTATAGGATTTGGTGTTGTAACTTT
* * ** * *
264129 ACTCCATTCCATTGTAACCTCAGGGAGATTGAGATCTG-TTACTTGCTTTAATCCG-CTTCACTG
1 ACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTGCTTTGTTG-TTTAATCTGACCT-ACTG
* * * ** * *
264192 CAACTTCAAGAAG-ATAGGATTTGAAGCT-TCACTTT
64 TAAC-CCAAGAGGTATAGGATTTGGTGTTGTAACTTT
* * *
264227 ATTCCA--CC-C-GTGACCTCAGGGACATTGAGATCTGCTTTGTCAT-TTTAATCTGACCCACTG
1 ACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTGCTTTGT--TGTTTAATCTGACCTACTG
*
264287 TAACCTCAAG-GGTATAGGATTAGGTGTTGTAACTTT
64 TAACC-CAAGAGGTATAGGATTTGGTGTTGTAACTTT
*
264323 ACTCCATTCCACTGTAACCTCAGGGAGATTGAGATCTG
1 ACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTG
264361 TTACTTACTT
Statistics
Matches: 182, Mismatches: 36, Indels: 28
0.74 0.15 0.11
Matches are distributed among these distances:
94 24 0.13
95 33 0.18
96 14 0.08
97 1 0.01
98 14 0.08
99 31 0.17
100 65 0.36
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (99 bp):
ACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTGCTTTGTTGTTTAATCTGACCTACTGTA
ACCCAAGAGGTATAGGATTTGGTGTTGTAACTTT
Found at i:264329 original size:194 final size:193
Alignment explanation
Indices: 263952--264437 Score: 733
Period size: 194 Copynumber: 2.5 Consensus size: 193
263942 TCACAATATC
* * * *
263952 ACCTCAGAGAGATTGAGATCTGCTACTTGTTTTAATCCGATTCACTGCAACTTCAAGAAGATAGG
1 ACCTCAGGGAGATTGAGATCTGTTACTTGCTTTAATCCGCTTCACTGCAACTTCAAGAAGATAGG
* * **
264017 ATTTGAAGCTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATTTGCTTTGTTGTTGTAAT
66 ATTTGAAGCTTCACTCCATTCCACCGTAACCTCAGGGACATTGAGATCTGCTTTGTCATTGTAAT
* * * * *
264082 CTGACCTACTGTAACCCTAGAGGTATAGGATTTGGTGTTGTAATTTTACTCCATTCCATTGTA
131 CTGACCCACTGTAACCCAAGAGGTATAGGATTAGGTGTTGTAACTTTACTCCATTCCACTGTA
264145 ACCTCAGGGAGATTGAGATCTGTTACTTGCTTTAATCCGCTTCACTGCAACTTCAAGAAGATAGG
1 ACCTCAGGGAGATTGAGATCTGTTACTTGCTTTAATCCGCTTCACTGCAACTTCAAGAAGATAGG
** * *
264210 ATTTGAAGCTTCACTTTATTCCACCCGTGACCTCAGGGACATTGAGATCTGCTTTGTCATTTTAA
66 ATTTGAAGCTTCACTCCATTCCA-CCGTAACCTCAGGGACATTGAGATCTGCTTTGTCATTGTAA
264275 TCTGACCCACTGTAACCTCAAG-GGTATAGGATTAGGTGTTGTAACTTTACTCCATTCCACTGTA
130 TCTGACCCACTGTAACC-CAAGAGGTATAGGATTAGGTGTTGTAACTTTACTCCATTCCACTGTA
* * *
264339 ACCTCAGGGAGATTGAGATCTGTTACTTACTTTAATCTGCTTCACTGCAACTTCAGGAAGATAGG
1 ACCTCAGGGAGATTGAGATCTGTTACTTGCTTTAATCCGCTTCACTGCAACTTCAAGAAGATAGG
* *
264404 ATTTGAAGCTTTACTCCA-TCCTACTGTAACCTCA
66 ATTTGAAGCTTCACTCCATTCC-ACCGTAACCTCA
264438 TGGGTATATG
Statistics
Matches: 265, Mismatches: 25, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
193 94 0.35
194 168 0.63
195 3 0.01
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.34
Consensus pattern (193 bp):
ACCTCAGGGAGATTGAGATCTGTTACTTGCTTTAATCCGCTTCACTGCAACTTCAAGAAGATAGG
ATTTGAAGCTTCACTCCATTCCACCGTAACCTCAGGGACATTGAGATCTGCTTTGTCATTGTAAT
CTGACCCACTGTAACCCAAGAGGTATAGGATTAGGTGTTGTAACTTTACTCCATTCCACTGTA
Found at i:275183 original size:29 final size:29
Alignment explanation
Indices: 275118--275185 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
275108 AAAGATTGAA
275118 TAAATAAAAACAAAACAAAATGATTAAATT
1 TAAA-AAAAACAAAACAAAATGATTAAATT
** * *
275148 TTTAAAAAATAAAATAAAA-GAATTAAATT
1 TAAAAAAAACAAAACAAAATG-ATTAAATT
275177 TAAAAAAAA
1 TAAAAAAAA
275186 AAAGGACTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
28 1 0.03
29 28 0.90
30 2 0.06
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.25
Consensus pattern (29 bp):
TAAAAAAAACAAAACAAAATGATTAAATT
Found at i:275188 original size:22 final size:22
Alignment explanation
Indices: 275158--275229 Score: 99
Period size: 22 Copynumber: 3.3 Consensus size: 22
275148 TTTAAAAAAT
* *
275158 AAAATAAAAGAATTAAATTTAA
1 AAAAAAAAAGGATTAAATTTAA
*
275180 AAAAAAAAAGGACTAAATTTAA
1 AAAAAAAAAGGATTAAATTTAA
* *
275202 AGAATAAAAGGATTAAATTTAA
1 AAAAAAAAAGGATTAAATTTAA
275224 AAAAAA
1 AAAAAA
275230 CATAATAAAG
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.68, C:0.01, G:0.08, T:0.22
Consensus pattern (22 bp):
AAAAAAAAAGGATTAAATTTAA
Found at i:276701 original size:23 final size:23
Alignment explanation
Indices: 276673--276782 Score: 166
Period size: 23 Copynumber: 4.8 Consensus size: 23
276663 CATTATTATT
276673 ACATTAATATTTAAGCACAAATC
1 ACATTAATATTTAAGCACAAATC
* *
276696 AAATTAATATTTAAGCATAAATC
1 ACATTAATATTTAAGCACAAATC
*
276719 ACATTAATATTTGAGCACAAATC
1 ACATTAATATTTAAGCACAAATC
* *
276742 ATATTAATATTTAAGCATAAATC
1 ACATTAATATTTAAGCACAAATC
*
276765 GCATTAATATTTAAGCAC
1 ACATTAATATTTAAGCAC
276783 TTACACTCGG
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 76 1.00
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.34
Consensus pattern (23 bp):
ACATTAATATTTAAGCACAAATC
Found at i:276723 original size:46 final size:46
Alignment explanation
Indices: 276673--276782 Score: 193
Period size: 46 Copynumber: 2.4 Consensus size: 46
276663 CATTATTATT
276673 ACATTAATATTTAAGCACAAATCAAATTAATATTTAAGCATAAATC
1 ACATTAATATTTAAGCACAAATCAAATTAATATTTAAGCATAAATC
* *
276719 ACATTAATATTTGAGCACAAATCATATTAATATTTAAGCATAAATC
1 ACATTAATATTTAAGCACAAATCAAATTAATATTTAAGCATAAATC
*
276765 GCATTAATATTTAAGCAC
1 ACATTAATATTTAAGCAC
276783 TTACACTCGG
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 60 1.00
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.34
Consensus pattern (46 bp):
ACATTAATATTTAAGCACAAATCAAATTAATATTTAAGCATAAATC
Found at i:277611 original size:19 final size:19
Alignment explanation
Indices: 277587--277629 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
277577 GTTTCTCTTG
277587 GTTTTTATTGGTATTTAAC
1 GTTTTTATTGGTATTTAAC
*
277606 GTTTTTATTGGTATTTAAG
1 GTTTTTATTGGTATTTAAC
277625 GTTTT
1 GTTTT
277630 AAGGTTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.19, C:0.02, G:0.19, T:0.60
Consensus pattern (19 bp):
GTTTTTATTGGTATTTAAC
Found at i:292899 original size:21 final size:21
Alignment explanation
Indices: 292875--292917 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
292865 CATTCAGGAT
292875 TGTCGTCGCATCCAACAGCTG
1 TGTCGTCGCATCCAACAGCTG
292896 TGTCGTCGCATCCAACAGCTG
1 TGTCGTCGCATCCAACAGCTG
292917 T
1 T
292918 TTGGATAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.33, G:0.23, T:0.26
Consensus pattern (21 bp):
TGTCGTCGCATCCAACAGCTG
Found at i:300102 original size:2 final size:2
Alignment explanation
Indices: 300095--300128 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
300085 ATCCCTTATT
*
300095 CA CA CA CA CA CA CA CA CA TA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
300129 TACATATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.47, G:0.00, T:0.03
Consensus pattern (2 bp):
CA
Found at i:302973 original size:13 final size:13
Alignment explanation
Indices: 302955--302980 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
302945 GCATCTGTTG
302955 AGTTAGCTCTCTT
1 AGTTAGCTCTCTT
302968 AGTTAGCTCTCTT
1 AGTTAGCTCTCTT
302981 CGTCTTGCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.15, T:0.46
Consensus pattern (13 bp):
AGTTAGCTCTCTT
Found at i:306081 original size:24 final size:24
Alignment explanation
Indices: 306054--306113 Score: 95
Period size: 24 Copynumber: 2.5 Consensus size: 24
306044 TTCGCTTCAA
*
306054 AAGCTCGTTTATTGGCTTGTTTAT
1 AAGCTCGTTTATTGACTTGTTTAT
306078 AAGCTCGTTTATTGACTTGTTTAT
1 AAGCTCGTTTATTGACTTGTTTAT
*
306102 AA-CTCATTTATT
1 AAGCTCGTTTATT
306114 TATTATTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
23 9 0.26
24 25 0.74
ACGTcount: A:0.22, C:0.13, G:0.15, T:0.50
Consensus pattern (24 bp):
AAGCTCGTTTATTGACTTGTTTAT
Found at i:308192 original size:35 final size:35
Alignment explanation
Indices: 308112--308188 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 35
308102 TCTTATTAGT
* **
308112 ATATGATTAAATTGAAAATAAAATTTAAATATTTC
1 ATATCATTAAATTGAAAATAAAATTTAAATATTAA
* *
308147 ATATTATTAAATT-AGAATAATAATTTAAAT-TTAA
1 ATATCATTAAATTGAAAATAA-AATTTAAATATTAA
308181 ATATCATT
1 ATATCATT
308189 TAAAATTAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
34 15 0.42
35 21 0.58
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.43
Consensus pattern (35 bp):
ATATCATTAAATTGAAAATAAAATTTAAATATTAA
Found at i:308689 original size:9 final size:9
Alignment explanation
Indices: 308675--308699 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
308665 CATAATATCT
308675 CATATTCTA
1 CATATTCTA
308684 CATATTCTA
1 CATATTCTA
308693 CATATTC
1 CATATTC
308700 AATCTTGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.44
Consensus pattern (9 bp):
CATATTCTA
Found at i:316969 original size:15 final size:17
Alignment explanation
Indices: 316934--316971 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
316924 AATATCGGAT
*
316934 AAAACTTAAACCACATC
1 AAAATTTAAACCACATC
316951 AAAATTTAAA-CAC-TC
1 AAAATTTAAACCACATC
316966 AAAATT
1 AAAATT
316972 ATCAATATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 8 0.40
16 3 0.15
17 9 0.45
ACGTcount: A:0.55, C:0.21, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAATTTAAACCACATC
Found at i:319979 original size:7 final size:7
Alignment explanation
Indices: 319967--319998 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
319957 GATAAAAAAA
319967 TAAAGAT
1 TAAAGAT
319974 TAAAGAT
1 TAAAGAT
319981 TAAAGAT
1 TAAAGAT
319988 TAAAGAT
1 TAAAGAT
319995 TAAA
1 TAAA
319999 TTTATTATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.28
Consensus pattern (7 bp):
TAAAGAT
Found at i:321091 original size:8 final size:9
Alignment explanation
Indices: 321057--321090 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
321047 AGAAAAATAA
*
321057 AAAAAAACA
1 AAAAAAACT
321066 AAGAAAAACT
1 AA-AAAAACT
321076 AAAAAAACT
1 AAAAAAACT
321085 AAAAAA
1 AAAAAA
321091 CGAAACATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.82, C:0.09, G:0.03, T:0.06
Consensus pattern (9 bp):
AAAAAAACT
Found at i:321515 original size:16 final size:17
Alignment explanation
Indices: 321476--321515 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
321466 ACAAAGGTAG
321476 ATAAAAATTAGAAAAAA
1 ATAAAAATTAGAAAAAA
* *
321493 ATCAAAA-TATAAAAAA
1 ATAAAAATTAGAAAAAA
321509 ATAAAAA
1 ATAAAAA
321516 CTAAATATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.17
Consensus pattern (17 bp):
ATAAAAATTAGAAAAAA
Found at i:323811 original size:18 final size:19
Alignment explanation
Indices: 323790--323825 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
323780 ATTAATGATG
323790 ATAATAATATTA-AATATT
1 ATAATAATATTATAATATT
323808 ATAATAATATTATAATAT
1 ATAATAATATTATAATAT
323826 GAGATAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATAATAATATTATAATATT
Found at i:323832 original size:18 final size:18
Alignment explanation
Indices: 323787--323827 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
323777 AAAATTAATG
323787 ATGATAATAATATTAAAT
1 ATGATAATAATATTAAAT
*
323805 ATTATAATAATATTATAAT
1 ATGATAATAATATTA-AAT
323824 ATGA
1 ATGA
323828 GATAAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (18 bp):
ATGATAATAATATTAAAT
Found at i:323832 original size:21 final size:20
Alignment explanation
Indices: 323784--323832 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
323774 TGTAAAATTA
323784 ATGATGATAATAATATTAAAT
1 ATGA-GATAATAATATTAAAT
*
323805 AT--TATAATAATATTATAAT
1 ATGAGATAATAATATTA-AAT
323824 ATGAGATAA
1 ATGAGATAA
323833 AAAATAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
18 12 0.52
19 5 0.22
21 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (20 bp):
ATGAGATAATAATATTAAAT
Found at i:328224 original size:21 final size:21
Alignment explanation
Indices: 328200--328242 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
328190 AACAACTGTA
328200 AAACAACA-ATAAAACAACACC
1 AAACAACATA-AAAACAACACC
328221 AAACAACATAAAAACAACACC
1 AAACAACATAAAAACAACACC
328242 A
1 A
328243 TGCCACACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.67, C:0.28, G:0.00, T:0.05
Consensus pattern (21 bp):
AAACAACATAAAAACAACACC
Found at i:328539 original size:14 final size:14
Alignment explanation
Indices: 328520--328558 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
328510 TTATTCGGAC
328520 TTTATTTTTTTAAA
1 TTTATTTTTTTAAA
*
328534 TTTA-TTTTTTGAA
1 TTTATTTTTTTAAA
*
328547 TTTATATTTTTA
1 TTTATTTTTTTA
328559 TCTAAATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (14 bp):
TTTATTTTTTTAAA
Found at i:342438 original size:13 final size:13
Alignment explanation
Indices: 342420--342444 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
342410 ACTAAGTGCG
342420 AAAAAAATAAAAT
1 AAAAAAATAAAAT
342433 AAAAAAATAAAA
1 AAAAAAATAAAA
342445 ACTTAGTGTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAAATAAAAT
Found at i:342528 original size:21 final size:21
Alignment explanation
Indices: 342504--342550 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
342494 CTTCCGTTCC
*
342504 TCCTTGCG-TTGCTTCTTCTTG
1 TCCTTGCGCTT-CCTCTTCTTG
*
342525 TCCTTGCGCTTCCTCTTTTTG
1 TCCTTGCGCTTCCTCTTCTTG
342546 TCCTT
1 TCCTT
342551 CGAACCAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.00, C:0.32, G:0.15, T:0.53
Consensus pattern (21 bp):
TCCTTGCGCTTCCTCTTCTTG
Found at i:343935 original size:15 final size:15
Alignment explanation
Indices: 343915--343943 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
343905 ATGATTGTTA
343915 TTATAACTCCCTTGT
1 TTATAACTCCCTTGT
343930 TTATAACTCCCTTG
1 TTATAACTCCCTTG
343944 ATGTGAGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.28, G:0.07, T:0.45
Consensus pattern (15 bp):
TTATAACTCCCTTGT
Found at i:344735 original size:22 final size:22
Alignment explanation
Indices: 344707--344758 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
344697 AAATTGCATT
344707 GACAATGGAATCCTAATGCGTC
1 GACAATGGAATCCTAATGCGTC
344729 GACAATGGAATCCTAATGCGTC
1 GACAATGGAATCCTAATGCGTC
344751 GACAATGG
1 GACAATGG
344759 TGTTTATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.21
Consensus pattern (22 bp):
GACAATGGAATCCTAATGCGTC
Found at i:348326 original size:15 final size:14
Alignment explanation
Indices: 348307--348394 Score: 54
Period size: 15 Copynumber: 6.0 Consensus size: 14
348297 TAATTCATAT
348307 TTTAATAATAATTA
1 TTTAATAATAATTA
*
348321 TATTAAAAAT-ATTA
1 T-TTAATAATAATTA
* *
348335 TTAAATTATATATTA
1 TTTAATAATA-ATTA
* *
348350 TTTTATTAA-ATTGTA
1 -TTTAATAATAAT-TA
348365 TTTAATAATAATTA
1 TTTAATAATAATTA
*
348379 TGTTAAAATATAATTA
1 T-TTAATA-ATAATTA
348395 AATGATTTAT
Statistics
Matches: 55, Mismatches: 11, Indels: 14
0.69 0.14 0.17
Matches are distributed among these distances:
13 5 0.09
14 17 0.31
15 21 0.38
16 12 0.22
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (14 bp):
TTTAATAATAATTA
Found at i:348445 original size:58 final size:58
Alignment explanation
Indices: 348284--348450 Score: 212
Period size: 58 Copynumber: 2.9 Consensus size: 58
348274 ATATTATATA
* * * *
348284 TTATGATTTTTACT-AATTCATATTTTAATAATAATTATATTAAAAATATTATTAAATTAT
1 TTATTATTTTTATTAAATT-ATA-TTTAATAATAATTATATT-AAAATATAATTAAATGAT
* * *
348344 ATATTA-TTTTATTAAATTGTATTTAATAATAATTATGTTAAAATATAATTAAATGAT
1 TTATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATGAT
* *
348401 TTATTATTTTTATTAAATTATATTTAATAATAATTTTATTAAAATTTAAT
1 TTATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAAT
348451 AACAATAATC
Statistics
Matches: 93, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
57 21 0.23
58 56 0.60
59 8 0.09
60 8 0.09
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (58 bp):
TTATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATGAT
Found at i:353338 original size:2 final size:2
Alignment explanation
Indices: 353325--353355 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
353315 CATTCTGAAT
*
353325 AC AC AC AG AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
353356 TATCCAATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.45, G:0.03, T:0.00
Consensus pattern (2 bp):
AC
Found at i:357796 original size:24 final size:25
Alignment explanation
Indices: 357760--357808 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
357750 GATGAAGAAG
*
357760 AAAAAGAAGAGAAAA-AAATGAAAT
1 AAAAAGAAAAGAAAAGAAATGAAAT
*
357784 AAAAAGAAAAGAAAAGAAATTAAAT
1 AAAAAGAAAAGAAAAGAAATGAAAT
357809 TGAAGGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (25 bp):
AAAAAGAAAAGAAAAGAAATGAAAT
Found at i:359276 original size:29 final size:30
Alignment explanation
Indices: 359230--359387 Score: 139
Period size: 29 Copynumber: 5.3 Consensus size: 30
359220 TTTGACCCCC
* * *
359230 AAACTTTTCAAAAATTATGTTTTGACCCTT
1 AAACTTTTCCAAAATTATATTTTAACCCTT
359260 AAA-TTTTCCAAAATTATATTTTAACACC-T
1 AAACTTTTCCAAAATTATATTTTAAC-CCTT
* * **
359289 AAACTTTT-CACAATTCA-AATTTGGCCCTT
1 AAACTTTTCCAAAATT-ATATTTTAACCCTT
* *
359318 AAAC-TTTCAAAAAAAAATATATTTTAACCCTT
1 AAACTTTTC---CAAAATTATATTTTAACCCTT
359350 AAA-TTTTCCAAAAATTATATTTTAACCCTT
1 AAACTTTTCC-AAAATTATATTTTAACCCTT
359380 AAACTTTT
1 AAACTTTT
359388 AAAAAATTCA
Statistics
Matches: 101, Mismatches: 15, Indels: 23
0.73 0.11 0.17
Matches are distributed among these distances:
28 5 0.05
29 39 0.39
30 32 0.32
31 5 0.05
32 20 0.20
ACGTcount: A:0.39, C:0.18, G:0.03, T:0.41
Consensus pattern (30 bp):
AAACTTTTCCAAAATTATATTTTAACCCTT
Found at i:359334 original size:91 final size:93
Alignment explanation
Indices: 359239--359422 Score: 259
Period size: 90 Copynumber: 2.0 Consensus size: 93
359229 CAAACTTTTC
* * * * *
359239 AAAAATTATGTTTTGACCCTTAAATTTTCC-AAAATTATATTTTAACACC-TAAACTTTT-CACA
1 AAAAAATATATTTTAACCCTTAAATTTTCCAAAAATTATATTTTAAC-CCTTAAACTTTTAAAAA
* *
359301 ATTCAAATTTGGCCCTTAAACTTT-CAAA
65 ATTCAAATTTAGCCCCTAAACTTTGCAAA
359329 AAAAAATATATTTTAACCCTTAAATTTTCCAAAAATTATATTTTAACCCTTAAACTTTTAAAAAA
1 AAAAAATATATTTTAACCCTTAAATTTTCCAAAAATTATATTTTAACCCTTAAACTTTTAAAAAA
*
359394 TTCAAATTTAGCCCCTGAACTTTGCAAA
66 TTCAAATTTAGCCCCTAAACTTTGCAAA
359422 A
1 A
359423 TTTAATTTTT
Statistics
Matches: 82, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
90 29 0.35
91 25 0.30
92 23 0.28
93 5 0.06
ACGTcount: A:0.41, C:0.18, G:0.04, T:0.38
Consensus pattern (93 bp):
AAAAAATATATTTTAACCCTTAAATTTTCCAAAAATTATATTTTAACCCTTAAACTTTTAAAAAA
TTCAAATTTAGCCCCTAAACTTTGCAAA
Found at i:359391 original size:29 final size:30
Alignment explanation
Indices: 359230--359395 Score: 155
Period size: 30 Copynumber: 5.5 Consensus size: 30
359220 TTTGACCCCC
* *
359230 AAACTTTTCAAAAATTATGTTTTGACCCTT
1 AAACTTTTCAAAAATTATATTTTAACCCTT
*
359260 AAA-TTTTCCAAAATTATATTTTAACACC-T
1 AAACTTTTCAAAAATTATATTTTAAC-CCTT
* * **
359289 AAACTTTTC-ACAATTCA-AATTTGGCCCTT
1 AAACTTTTCAAAAATT-ATATTTTAACCCTT
*
359318 AAAC-TTTCAAAAAAAAATATATTTTAACCCTT
1 AAACTTTTC---AAAAATTATATTTTAACCCTT
359350 AAA-TTTTCCAAAAATTATATTTTAACCCTT
1 AAACTTTT-CAAAAATTATATTTTAACCCTT
*
359380 AAACTTTTAAAAAATT
1 AAACTTTTCAAAAATT
359396 CAAATTTAGC
Statistics
Matches: 110, Mismatches: 14, Indels: 24
0.74 0.09 0.16
Matches are distributed among these distances:
28 6 0.05
29 38 0.35
30 41 0.37
31 5 0.05
32 19 0.17
33 1 0.01
ACGTcount: A:0.41, C:0.17, G:0.02, T:0.40
Consensus pattern (30 bp):
AAACTTTTCAAAAATTATATTTTAACCCTT
Found at i:363775 original size:4 final size:4
Alignment explanation
Indices: 363766--363792 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
363756 AAAAGAGGAA
363766 AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAA
363793 AAGAAAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:364768 original size:12 final size:11
Alignment explanation
Indices: 364749--364797 Score: 55
Period size: 13 Copynumber: 4.2 Consensus size: 11
364739 GAGTGAAAAT
364749 AAGAGAAAAGAA
1 AAGA-AAAAGAA
364761 AAGGGAAAAAGAA
1 AA--GAAAAAGAA
364774 AA-AAAAAGAAA
1 AAGAAAAAG-AA
364785 AAGAAAAAGAA
1 AAGAAAAAGAA
364796 AA
1 AA
364798 ATGAGAGGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
10 6 0.18
11 8 0.24
12 8 0.24
13 9 0.27
14 2 0.06
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (11 bp):
AAGAAAAAGAA
Found at i:364776 original size:6 final size:6
Alignment explanation
Indices: 364749--364798 Score: 59
Period size: 6 Copynumber: 8.3 Consensus size: 6
364739 GAGTGAAAAT
*
364749 AAGAGAA AAGAAA AGGGAAA AAG-AA AA-AAA AAGAAA AAGAAA AAGAAA
1 AAGA-AA AAGAAA A-AGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
364797 AA
1 AA
364799 TGAGAGGTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
5 8 0.21
6 21 0.55
7 9 0.24
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:364784 original size:16 final size:17
Alignment explanation
Indices: 364749--364797 Score: 64
Period size: 16 Copynumber: 2.8 Consensus size: 17
364739 GAGTGAAAAT
364749 AAGAGAAAAGAAAAGGGAAA
1 AAGA-AAAAGAAAA--GAAA
364769 AAGAAAAA-AAAAGAAA
1 AAGAAAAAGAAAAGAAA
364785 AAGAAAAAGAAAA
1 AAGAAAAAGAAAA
364798 ATGAGAGGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
16 12 0.43
17 4 0.14
18 4 0.14
19 4 0.14
20 4 0.14
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (17 bp):
AAGAAAAAGAAAAGAAA
Found at i:364792 original size:23 final size:22
Alignment explanation
Indices: 364754--364798 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
364744 AAAATAAGAG
*
364754 AAAAGAAAAGGGAAAAAGAAAAA
1 AAAAGAAAA-AGAAAAAGAAAAA
364777 AAAAGAAAAAGAAAAAGAAAAA
1 AAAAGAAAAAGAAAAAGAAAAA
364799 TGAGAGGTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (22 bp):
AAAAGAAAAAGAAAAAGAAAAA
Found at i:365828 original size:49 final size:49
Alignment explanation
Indices: 365652--365939 Score: 210
Period size: 49 Copynumber: 5.9 Consensus size: 49
365642 ACGAGATGGA
** * * * *
365652 AAAGATTGAAGTCGCAACAGCGAATCTTGTACCATAG-GAATGAGAA-GG
1 AAAGATTGAAGTCGCAATGGTGAATCTTATACCCTAGAG-ATGTGAAGGG
* * * * *
365700 AAGAGATTAAATTCACAATGGTGAATCTTATACCTTAGAGATGTGATGGG
1 AA-AGATTGAAGTCGCAATGGTGAATCTTATACCCTAGAGATGTGAAGGG
* * **** * * *
365750 AAAGGTTGAAGCCGCAATAACAAACCTTATACCTTAGTGATGTGAAGGG
1 AAAGATTGAAGTCGCAATGGTGAATCTTATACCCTAGAGATGTGAAGGG
* * *
365799 AAAGATTGAAGTCGCAACGGTGAATCTTATACCCTAAAGATG-AAGAGGG
1 AAAGATTGAAGTCGCAATGGTGAATCTTATACCCTAGAGATGTGA-AGGG
* * * * * *
365848 AAAGGTGGAAGCCACAATGGTGAACCTTGTACCCTAGAGATGTGAAGGG
1 AAAGATTGAAGTCGCAATGGTGAATCTTATACCCTAGAGATGTGAAGGG
*
365897 AAAGATTGAAGCTCTG--ATGATGAATCTTATACCCT-GAAGATGT
1 AAAGATTGAAG-TC-GCAATGGTGAATCTTATACCCTAG-AGATGT
365940 AAAGAAGTAA
Statistics
Matches: 182, Mismatches: 50, Indels: 15
0.74 0.20 0.06
Matches are distributed among these distances:
48 4 0.02
49 171 0.94
50 7 0.04
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.23
Consensus pattern (49 bp):
AAAGATTGAAGTCGCAATGGTGAATCTTATACCCTAGAGATGTGAAGGG
Found at i:365874 original size:98 final size:98
Alignment explanation
Indices: 365719--365938 Score: 257
Period size: 98 Copynumber: 2.2 Consensus size: 98
365709 AATTCACAAT
* * * * * *
365719 GGTGAATCTTATACCTTAGAGATGTGATGGGAAAGGTTGAAGCCGCAATAACAAACCTTATACCT
1 GGTGAATCTTATACCCTAAAGATGAGATGGGAAAGGTGGAAGCCACAATAACAAACCTTATACCC
*
365784 TAGTGATGTGAAGGGAAAGATTGAAG-TC-GCAAC
66 TAGAGATGTGAAGGGAAAGATTGAAGCTCTG--AC
**** *
365817 GGTGAATCTTATACCCTAAAGATGAAGA-GGGAAAGGTGGAAGCCACAATGGTGAACCTTGTACC
1 GGTGAATCTTATACCCTAAAGATG-AGATGGGAAAGGTGGAAGCCACAATAACAAACCTTATACC
*
365881 CTAGAGATGTGAAGGGAAAGATTGAAGCTCTGAT
65 CTAGAGATGTGAAGGGAAAGATTGAAGCTCTGAC
* *
365915 GATGAATCTTATACCCTGAAGATG
1 GGTGAATCTTATACCCTAAAGATG
365939 TAAAGAAGTA
Statistics
Matches: 104, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
98 99 0.95
99 4 0.04
100 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.24
Consensus pattern (98 bp):
GGTGAATCTTATACCCTAAAGATGAGATGGGAAAGGTGGAAGCCACAATAACAAACCTTATACCC
TAGAGATGTGAAGGGAAAGATTGAAGCTCTGAC
Found at i:366225 original size:42 final size:42
Alignment explanation
Indices: 366163--366266 Score: 136
Period size: 42 Copynumber: 2.5 Consensus size: 42
366153 GAAGTTACAT
* * *
366163 CATCATCCAATCTTTCACCCCGACCATAAGGCAGATTGAAGA
1 CATCATCCAATCTTTTACCCCGACCACAAGGCAGATTAAAGA
* ** * *
366205 CATCATTCAATCTTTTACCCCGACCACGGGGCATATTAAAGC
1 CATCATCCAATCTTTTACCCCGACCACAAGGCAGATTAAAGA
366247 CATCATCCAATCTTTTACCC
1 CATCATCCAATCTTTTACCC
366267 TTAAGTCAAG
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.30, C:0.33, G:0.12, T:0.26
Consensus pattern (42 bp):
CATCATCCAATCTTTTACCCCGACCACAAGGCAGATTAAAGA
Found at i:366295 original size:46 final size:46
Alignment explanation
Indices: 366232--366382 Score: 212
Period size: 46 Copynumber: 3.3 Consensus size: 46
366222 CCCCGACCAC
* * * *
366232 GGGGCATATTAAAGCCATCATCCAATCTTTTACCCTTAAGTCAAGA
1 GGGGCAAATTGAAGCCATCATCCAATCTTTTACCCCTAAGTTAAGA
*
366278 GGGGCAGATTGAAGCCATCATCCAATCTTTTACCCCTAAGTTAAGA
1 GGGGCAAATTGAAGCCATCATCCAATCTTTTACCCCTAAGTTAAGA
* ** *
366324 AGGATAAATTGAAGCCATAATCCAATCTTTTACCCCTAAGTTAAGA
1 GGGGCAAATTGAAGCCATCATCCAATCTTTTACCCCTAAGTTAAGA
*
366370 GGGGTAAATTGAA
1 GGGGCAAATTGAA
366383 ACTATTATCT
Statistics
Matches: 94, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 94 1.00
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (46 bp):
GGGGCAAATTGAAGCCATCATCCAATCTTTTACCCCTAAGTTAAGA
Found at i:366535 original size:75 final size:75
Alignment explanation
Indices: 366427--366573 Score: 249
Period size: 75 Copynumber: 2.0 Consensus size: 75
366417 CAATTCAGTG
* *
366427 GAGCTTAATGTGAGTGAAACTTCAAACTCCATCTTCCTGATGAGATACAGAGAAGTGAGTCAAAA
1 GAGCTCAATGTGAGTGAAACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGAGTCAAAA
366492 CAATGAAACA
66 CAATGAAACA
* *
366502 GAGCTCAATGTGAGTGAAACTTCAAACCCCATCTTCCTGATGAGATACAGATAAGTGGGTCAAAA
1 GAGCTCAATGTGAGTGAAACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGAGTCAAAA
*
366567 TAATGAA
66 CAATGAA
366574 GCGGTCATCT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 67 1.00
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.23
Consensus pattern (75 bp):
GAGCTCAATGTGAGTGAAACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGAGTCAAAA
CAATGAAACA
Found at i:366614 original size:48 final size:48
Alignment explanation
Indices: 366531--366623 Score: 123
Period size: 48 Copynumber: 1.9 Consensus size: 48
366521 CTTCAAACCC
* * * *** *
366531 CATCTTCCTGATGAGATACAGATAAGTGGGTCAAAATAATGAAGCGGT
1 CATCTTCCTAATGAGATAAAGAGAAGTGAACCAAAACAATGAAGCGGT
366579 CATCTTCCTAATGAGATAAAGAGAAGTGAACCAAAACAATGAAGC
1 CATCTTCCTAATGAGATAAAGAGAAGTGAACCAAAACAATGAAGC
366624 AGAGCTCAAC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 38 1.00
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.22
Consensus pattern (48 bp):
CATCTTCCTAATGAGATAAAGAGAAGTGAACCAAAACAATGAAGCGGT
Found at i:366860 original size:122 final size:124
Alignment explanation
Indices: 366658--366899 Score: 328
Period size: 122 Copynumber: 2.0 Consensus size: 124
366648 AGTAGAGTAA
* * * * * * *
366658 AGTGAAACTTCAAACCCCTATCTTCCTGATGAGATACAGAGAAGTGGATCGAAACAATGAAGAGG
1 AGTGAAACTTCAAACCCCTATCTTCCTGATGAGATACAAAAAAATAGATCAAAAAAATGAAGAGA
*
366723 TCATCTTCCTAATGAGATACAGAGAAATGAATCAAAACAATGAAGT-GAAGCTCAATGTG
66 TCATCTTCCTAATGAGATACAGAGAAAGGAATCAAAACAATGAAGTAG-AGCTCAATGTG
* * *
366782 AGTGAAACTTCAAACTCC-ATCTTCCTGAT-AGATACAAAAAAATAGATTAAAAAAATGAAGCGA
1 AGTGAAACTTCAAACCCCTATCTTCCTGATGAGATACAAAAAAATAGATCAAAAAAATGAAGAGA
* * *
366845 TCATCTTCTTGATGAGATACAGAGAAAGGGATCAAAACAATGAAGTAGAGCTCAA
66 TCATCTTCCTAATGAGATACAGAGAAAGGAATCAAAACAATGAAGTAGAGCTCAA
366900 CATCCTTAAG
Statistics
Matches: 103, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
122 74 0.72
123 12 0.12
124 17 0.17
ACGTcount: A:0.43, C:0.16, G:0.19, T:0.22
Consensus pattern (124 bp):
AGTGAAACTTCAAACCCCTATCTTCCTGATGAGATACAAAAAAATAGATCAAAAAAATGAAGAGA
TCATCTTCCTAATGAGATACAGAGAAAGGAATCAAAACAATGAAGTAGAGCTCAATGTG
Found at i:366887 original size:48 final size:48
Alignment explanation
Indices: 366799--367033 Score: 119
Period size: 48 Copynumber: 4.9 Consensus size: 48
366789 CTTCAAACTC
* * * ** * *
366799 CATCTTCCTGAT-AGATACAAAAAAATAGATTAAAAAAATGAAGCGAT
1 CATCTTCTTGATGAGATACAGAGAAAGGGATCAAAACAATGAAGCGAT
*
366846 CATCTTCTTGATGAGATACAGAGAAAGGGATCAAAACAATGAAGTAGAGCT
1 CATCTTCTTGATGAGATACAGAGAAAGGGATCAAAACAATGAAG-CGA--T
* * * * * * * * * *
366897 CAACATCCTT-A--AGATTACAGTAGAGTAGAG-T-GAAAC-TTCAAACCAA
1 CATC-TTCTTGATGAGA-TACAG-AGA-AAGGGATCAAAACAATGAAGCGAT
* *
366943 CATCTTCTTGATGAGATATAGA-AAAGTGGATCAAAACAATGTAGCGAT
1 CATCTTCTTGATGAGATACAGAGAAAG-GGATCAAAACAATGAAGCGAT
* * *
366991 CATCTTCCTGATGAGATACAGAG-AAGTGAACCAAAACAATGAA
1 CATCTTCTTGATGAGATACAGAGAAAG-GGATCAAAACAATGAA
367034 ACGAAGCTCA
Statistics
Matches: 136, Mismatches: 36, Indels: 31
0.67 0.18 0.15
Matches are distributed among these distances:
44 2 0.01
45 6 0.04
46 6 0.04
47 19 0.14
48 70 0.51
49 8 0.06
50 9 0.07
51 9 0.07
52 7 0.05
ACGTcount: A:0.44, C:0.15, G:0.18, T:0.23
Consensus pattern (48 bp):
CATCTTCTTGATGAGATACAGAGAAAGGGATCAAAACAATGAAGCGAT
Found at i:366932 original size:267 final size:266
Alignment explanation
Indices: 366456--367158 Score: 991
Period size: 267 Copynumber: 2.6 Consensus size: 266
366446 CTTCAAACTC
* *
366456 CATCTTCCTGATGAGATACAGAGAAGTGAGTCAAAACAATGAAACAGAGCTCAATGTGAGTGAAA
1 CATCTTCCTGATGAGATACAGAGAAGTGAATCAAAACAATGAAAGA-AGCTCAATGTGAGTGAAA
*
366521 CTTCAAACCCCATCTTCCTGATGAGATACAGATAAGTGGGTCAAAATAATGAAGCGGTCATCTTC
65 CTTCAAA-CCCATCTTCCTGATGAGATACAGAAAAGTGGGTCAAAATAATGAAGCGGTCATCTTC
* * * * *
366586 CTAATGAGATAAAGAGAAGTGAACCAAAACAATGAAGCAGAGCTCAACATCCCTGAAGTTACAGT
129 TTGATGAGATACAGAGAAGTGGATCAAAACAATGAAGCAGAGCTCAACATCCCTGAAGTTACAGT
* * *
366651 AGAGTAAAGTGAAACTTCAAACC-CCTATCTTCCTGATGAGATACAGAGAAGTGGATCGAAACAA
194 AGAGTAAAGTGAAACTTCAAACCAAC-ATCTTCCTGATGAGATACAGAAAAGTGGATCAAAACAA
*
366715 TGAAGAGGT
258 TGAAGAGAT
* * *
366724 CATCTTCCTAATGAGATACAGAGAAATGAATCAAAACAATGAAGTGAAGCTCAATGTGAGTGAAA
1 CATCTTCCTGATGAGATACAGAGAAGTGAATCAAAACAATGAA-AGAAGCTCAATGTGAGTGAAA
* * * * * * *
366789 CTTCAAACTCCATCTTCCTGAT-AGATACAAAAAAATAGATTAAAAAAATGAAGCGATCATCTTC
65 CTTCAAAC-CCATCTTCCTGATGAGATACAGAAAAGTGGGTCAAAATAATGAAGCGGTCATCTTC
* *
366853 TTGATGAGATACAGAGAAAG-GGATCAAAACAATGAAGTAGAGCTCAACAT-CCTTAAGATTACA
129 TTGATGAGATACAGAG-AAGTGGATCAAAACAATGAAGCAGAGCTCAACATCCCTGAAG-TTACA
* * *
366916 GTAGAGTAGAGTGAAACTTCAAACCAACATCTTCTTGATGAGATATAGAAAAGTGGATCAAAACA
192 GTAGAGTAAAGTGAAACTTCAAACCAACATCTTCCTGATGAGATACAGAAAAGTGGATCAAAACA
* *
366981 ATGTAGCGAT
257 ATGAAGAGAT
* *
366991 CATCTTCCTGATGAGATACAGAGAAGTGAACCAAAACAATGAAACGAAGCTCAATGTGAGCGAAA
1 CATCTTCCTGATGAGATACAGAGAAGTGAATCAAAACAATGAAA-GAAGCTCAATGTGAGTGAAA
* *
367056 CTTCAAACCACATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAATAATGAAGCGGTTATCTTC
65 CTTCAAACC-CATCTTCCTGATGAGATACAGAAAAGTGGGTCAAAATAATGAAGCGGTCATCTTC
*
367121 TTGATGAGATACAGAGAAGTGGATCAAAATAATGAAGC
129 TTGATGAGATACAGAGAAGTGGATCAAAACAATGAAGC
367159 GGTCATCTTC
Statistics
Matches: 381, Mismatches: 45, Indels: 18
0.86 0.10 0.04
Matches are distributed among these distances:
266 7 0.02
267 226 0.59
268 147 0.39
269 1 0.00
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (266 bp):
CATCTTCCTGATGAGATACAGAGAAGTGAATCAAAACAATGAAAGAAGCTCAATGTGAGTGAAAC
TTCAAACCCATCTTCCTGATGAGATACAGAAAAGTGGGTCAAAATAATGAAGCGGTCATCTTCTT
GATGAGATACAGAGAAGTGGATCAAAACAATGAAGCAGAGCTCAACATCCCTGAAGTTACAGTAG
AGTAAAGTGAAACTTCAAACCAACATCTTCCTGATGAGATACAGAAAAGTGGATCAAAACAATGA
AGAGAT
Done.