Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003904.1 Hibiscus syriacus cultivar Beakdansim tig00008440_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: 85949
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:210 original size:21 final size:21
Alignment explanation
Indices: 184--225 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
174 AATATAAATT
* *
184 GTGTATCGATGTACTGCTACA
1 GTGTATCGATGCAATGCTACA
205 GTGTATCGATGCAATGCTACA
1 GTGTATCGATGCAATGCTACA
226 ATACTGCTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (21 bp):
GTGTATCGATGCAATGCTACA
Found at i:700 original size:17 final size:19
Alignment explanation
Indices: 678--715 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
668 CTTCTTTCTT
678 ATCATT-AT-CCTATTATC
1 ATCATTAATACCTATTATC
*
695 ATCATTAATACCTTTTATC
1 ATCATTAATACCTATTATC
714 AT
1 AT
716 ATAATCATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 2 0.11
19 10 0.56
ACGTcount: A:0.32, C:0.21, G:0.00, T:0.47
Consensus pattern (19 bp):
ATCATTAATACCTATTATC
Found at i:1079 original size:31 final size:31
Alignment explanation
Indices: 1043--1105 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
1033 GGACCTATGT
1043 AACTGTCCATATGTTCCGAAGAACATAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
* *
1074 AACTGTCCATATGTTTCGTAGAACATAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
1105 A
1 A
1106 CCTTCGACTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGAAGAACATAGGTA
Found at i:4573 original size:2 final size:2
Alignment explanation
Indices: 4566--4609 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
4556 TCTTTCCATT
4566 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4608 TA
1 TA
4610 GATTTGAATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4747 original size:2 final size:2
Alignment explanation
Indices: 4740--4787 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
4730 TCAATTTGTG
4740 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4781 TA TA TA T
1 TA TA TA T
4788 GAACTTAAGG
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5537 original size:21 final size:21
Alignment explanation
Indices: 5488--5537 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
5478 ATATGGTACC
*
5488 GATACCTCACATTTGGGTATT
1 GATACCTTACATTTGGGTATT
*
5509 GATACCTTACCTTTGGGTATT
1 GATACCTTACATTTGGGTATT
5530 GATACCTT
1 GATACCTT
5538 TTAAATAGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40
Consensus pattern (21 bp):
GATACCTTACATTTGGGTATT
Found at i:8281 original size:14 final size:14
Alignment explanation
Indices: 8262--8294 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
8252 TATTTATGTT
8262 TATATTATATATAG
1 TATATTATATATAG
*
8276 TATATTTTATATAG
1 TATATTATATATAG
8290 TATAT
1 TATAT
8295 GGTTCAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
TATATTATATATAG
Found at i:9545 original size:30 final size:30
Alignment explanation
Indices: 9511--9572 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
9501 ATTTGTTTTT
9511 TTAATTTAATTGCTTAACATTAATTTTACA
1 TTAATTTAATTGCTTAACATTAATTTTACA
*
9541 TTAATTTTATTGCTTAACATTAATTTTACA
1 TTAATTTAATTGCTTAACATTAATTTTACA
9571 TT
1 TT
9573 TTTATGCTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.34, C:0.10, G:0.03, T:0.53
Consensus pattern (30 bp):
TTAATTTAATTGCTTAACATTAATTTTACA
Found at i:11516 original size:15 final size:15
Alignment explanation
Indices: 11496--11524 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
11486 TCTAAATTTT
11496 TTTTTGAGTTCAAGC
1 TTTTTGAGTTCAAGC
11511 TTTTTGAGTTCAAG
1 TTTTTGAGTTCAAG
11525 TTTCAATATT
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:0.10, G:0.21, T:0.48
Consensus pattern (15 bp):
TTTTTGAGTTCAAGC
Found at i:12573 original size:7 final size:6
Alignment explanation
Indices: 12554--12596 Score: 59
Period size: 6 Copynumber: 6.8 Consensus size: 6
12544 TAATATTATA
*
12554 TAAAAT TAAATT TAAAATT TAAATT TAAATT TAAATT TCAAAT
1 TAAATT TAAATT T-AAATT TAAATT TAAATT TAAATT T-AAAT
12597 AAAAGAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
6 24 0.71
7 10 0.29
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (6 bp):
TAAATT
Found at i:14586 original size:19 final size:21
Alignment explanation
Indices: 14543--14590 Score: 64
Period size: 19 Copynumber: 2.3 Consensus size: 21
14533 TAATAACCTT
14543 ATAAATATTTATAATTAAATTAA
1 ATAAA-ATTTATAATTAAA-TAA
14566 ATAAAATTTA-AATTAAA-AA
1 ATAAAATTTATAATTAAATAA
14585 ATAAAA
1 ATAAAA
14591 GTAAATAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.32
21 7 0.28
22 5 0.20
23 5 0.20
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
ATAAAATTTATAATTAAATAA
Found at i:15435 original size:16 final size:16
Alignment explanation
Indices: 15414--15446 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
15404 TAATAAATAA
15414 ATGAACATAAACGAAC
1 ATGAACATAAACGAAC
15430 ATGAACATAAACGAAC
1 ATGAACATAAACGAAC
15446 A
1 A
15447 ATTTTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.18, G:0.12, T:0.12
Consensus pattern (16 bp):
ATGAACATAAACGAAC
Found at i:15536 original size:16 final size:16
Alignment explanation
Indices: 15515--15563 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
15505 AATAAATAAA
**
15515 ACGAACATAAACGCGC
1 ACGAACATAAACGAAC
15531 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
15547 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
15563 A
1 A
15564 TAAACGTTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.53, C:0.27, G:0.14, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:15544 original size:10 final size:10
Alignment explanation
Indices: 15531--15569 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
15521 ATAAACGCGC
15531 ACGAACATAA
1 ACGAACATAA
15541 ACGAAC----
1 ACGAACATAA
15547 ACGAACATAA
1 ACGAACATAA
15557 ACGAACATAA
1 ACGAACATAA
15567 ACG
1 ACG
15570 TTGGAGACCC
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
6 6 0.24
10 19 0.76
ACGTcount: A:0.56, C:0.23, G:0.13, T:0.08
Consensus pattern (10 bp):
ACGAACATAA
Found at i:16643 original size:14 final size:14
Alignment explanation
Indices: 16626--16652 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
16616 AATGAACATA
16626 AACGAACATAACCG
1 AACGAACATAACCG
16640 AACGAACATAACC
1 AACGAACATAACC
16653 TTACGTTCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.30, G:0.11, T:0.07
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:18050 original size:14 final size:14
Alignment explanation
Indices: 18031--18096 Score: 55
Period size: 14 Copynumber: 4.8 Consensus size: 14
18021 CAGGGTTAGG
18031 TTTAAGATTTATGA
1 TTTAAGATTTATGA
18045 TTTAAGATTTA-GA
1 TTTAAGATTTATGA
**
18058 GTTT-AGGGTTATGA
1 -TTTAAGATTTATGA
* * *
18072 TTTAGGATTTAAGG
1 TTTAAGATTTATGA
*
18086 TTTAAAATTTA
1 TTTAAGATTTA
18097 AGGTTTAGAA
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
13 10 0.25
14 30 0.75
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (14 bp):
TTTAAGATTTATGA
Found at i:18056 original size:27 final size:27
Alignment explanation
Indices: 18026--18096 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
18016 ATTTCCAGGG
18026 TTAGGTTTAAGATTTATGATTTAAGAT
1 TTAGGTTTAAGATTTATGATTTAAGAT
** *
18053 TTAGAGTTT-AGGGTTATGATTTAGGAT
1 TTAG-GTTTAAGATTTATGATTTAAGAT
*
18080 TTAAGGTTTAAAATTTA
1 TT-AGGTTTAAGATTTA
18097 AGGTTTAGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
27 25 0.71
28 10 0.29
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.46
Consensus pattern (27 bp):
TTAGGTTTAAGATTTATGATTTAAGAT
Found at i:18064 original size:34 final size:34
Alignment explanation
Indices: 18026--18103 Score: 93
Period size: 34 Copynumber: 2.3 Consensus size: 34
18016 ATTTCCAGGG
* * *
18026 TTAGGTTTAAGATTTATGATTTAAGATTTAGAGT
1 TTAGGTTTAAGATTTAGGATTTAAGATTTAAAAT
* * *
18060 TTAGGGTTATGATTTAGGATTTAAGGTTTAAAAT
1 TTAGGTTTAAGATTTAGGATTTAAGATTTAAAAT
18094 TTAAGGTTTA
1 TT-AGGTTTA
18104 GAATTTAAGG
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
34 30 0.83
35 6 0.17
ACGTcount: A:0.32, C:0.00, G:0.22, T:0.46
Consensus pattern (34 bp):
TTAGGTTTAAGATTTAGGATTTAAGATTTAAAAT
Found at i:18082 original size:20 final size:20
Alignment explanation
Indices: 18050--18087 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
18040 TATGATTTAA
*
18050 GATTTAGAGTTTAGGGTTAT
1 GATTTAGAGTTTAAGGTTAT
18070 GATTTAG-GATTTAAGGTT
1 GATTTAGAG-TTTAAGGTT
18088 TAAAATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.06
20 15 0.94
ACGTcount: A:0.26, C:0.00, G:0.29, T:0.45
Consensus pattern (20 bp):
GATTTAGAGTTTAAGGTTAT
Found at i:18097 original size:14 final size:14
Alignment explanation
Indices: 18078--18114 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
18068 ATGATTTAGG
18078 ATTTAAGGTTTAAA
1 ATTTAAGGTTTAAA
*
18092 ATTTAAGGTTTAGA
1 ATTTAAGGTTTAAA
18106 ATTTAAGGT
1 ATTTAAGGT
18115 AGAGGTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.43
Consensus pattern (14 bp):
ATTTAAGGTTTAAA
Found at i:20105 original size:53 final size:53
Alignment explanation
Indices: 20025--20127 Score: 181
Period size: 53 Copynumber: 1.9 Consensus size: 53
20015 GTTCTTTCGA
20025 CACTATGTGTCCATCCATGATATTCATAATGAGTTTGTGAATTACCATTTTGG
1 CACTATGTGTCCATCCATGATATTCATAATGAGTTTGTGAATTACCATTTTGG
*
20078 CACTATGTGTGCATCCATGGA-ATTCATAATGAGTTTGTGAATTACCATTT
1 CACTATGTGTCCATCCAT-GATATTCATAATGAGTTTGTGAATTACCATTT
20128 CGATACTTAG
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
53 46 0.96
54 2 0.04
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (53 bp):
CACTATGTGTCCATCCATGATATTCATAATGAGTTTGTGAATTACCATTTTGG
Found at i:26296 original size:3 final size:3
Alignment explanation
Indices: 26278--26370 Score: 159
Period size: 3 Copynumber: 30.7 Consensus size: 3
26268 TATATATATT
*
26278 TAA TATA TAT TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
26324 TAA TAA TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
26371 TGAATAAAAA
Statistics
Matches: 85, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
3 82 0.96
4 3 0.04
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:26959 original size:113 final size:112
Alignment explanation
Indices: 26688--27357 Score: 1094
Period size: 113 Copynumber: 5.9 Consensus size: 112
26678 AGTATCAAAC
** *
26688 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * * **
26753 ATGAAC-TTCTCTGGAAAAGTTGATCCATTAAGTGATGGATT-TGACA
66 ATGAACTTTCTCTGGAAAAGCTGATCC-TCAAATGATGGATTCAGGTA
*
26799 AAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * * *
26864 ATGAACCTTCTCTGGCAAAA-ATAATCCATCAAGTGATGAATTCAGGTA
66 ATGAACTTTCTCTGG-AAAAGCTGATCC-TCAAATGATGGATTCAGGTA
26912 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
26977 ATGAACTTTCTCTGGAAAAGCTGATCTCTCAAATGATGGATTCAGGTA
66 ATGAACTTTCTCTGGAAAAGCTGATC-CTCAAATGATGGATTCAGGTA
27025 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
27090 ATGAACTTTCTCTGGAAAAGCTGATCTCTCAAATGATGGATTCAGGTA
66 ATGAACTTTCTCTGGAAAAGCTGATC-CTCAAATGATGGATTCAGGTA
27138 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
27203 ATGAACTTTCTCTGGAAAAGCTGATCCCTCAAATGATGGATTCAGGTA
66 ATGAACTTTCTCTGGAAAAGCTGAT-CCTCAAATGATGGATTCAGGTA
27251 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
27316 ATGAACTTTCTCTGGAAAAGCTAATCTTTCAAATGATAGATT
66 ATGAACTTTCTCTGGAAAAGCTGATC-CTCAAATGATGGATT
27358 TGAATCTTTG
Statistics
Matches: 532, Mismatches: 20, Indels: 12
0.94 0.04 0.02
Matches are distributed among these distances:
111 67 0.13
112 31 0.06
113 432 0.81
114 2 0.00
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.38
Consensus pattern (112 bp):
AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTCTCTGGAAAAGCTGATCCTCAAATGATGGATTCAGGTA
Found at i:28168 original size:82 final size:82
Alignment explanation
Indices: 27884--28592 Score: 1249
Period size: 82 Copynumber: 8.6 Consensus size: 82
27874 TGCACTTCTT
* * * *
27884 CAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAA
** *
27949 TGCTTGATTCTGTCCAAT
66 TAATTG-TTCTGTCCAAC
*
27967 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATTGGCAAATTCATCTTCTAAACTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAA
** *
28032 TGCTTGATTCTGTCCAAT
66 TAATTG-TTCTGTCCAAC
28050 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAA
28115 TAATTGTTCTGTCCAAC
66 TAATTGTTCTGTCCAAC
28132 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAA
28197 TAATTGTTCTGTCCAAC
66 TAATTGTTCTGTCCAAC
28214 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAA
*
28279 TGATTGTTCTGTCCAAC
66 TAATTGTTCTGTCCAAC
28296 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAA
28361 TAA-TGTTCTGTCCAAC
66 TAATTGTTCTGTCCAAC
28377 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAA
* *
28442 TGATTGTTTTGTCCAAC
66 TAATTGTTCTGTCCAAC
28459 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAA
28524 TAATTGTTCTGTCCAAC
66 TAATTGTTCTGTCCAAC
**
28541 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCAT
28593 TTGTTCTATT
Statistics
Matches: 608, Mismatches: 17, Indels: 3
0.97 0.03 0.00
Matches are distributed among these distances:
81 80 0.13
82 382 0.63
83 146 0.24
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.28
Consensus pattern (82 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAA
TAATTGTTCTGTCCAAC
Found at i:28442 original size:245 final size:246
Alignment explanation
Indices: 27884--28592 Score: 1267
Period size: 245 Copynumber: 2.9 Consensus size: 246
27874 TGCACTTCTT
* * * *
27884 CAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAA
* * *
27949 TGCTTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATTGGCAAA
66 TGATTG-TTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAA
* *
28014 TTCATCTTCTAAACTCAATGCTTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCA
130 TTCATCTTCTAAACTCAATGATTG-TTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCA
28079 GAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATAATTGTTCTGTCCAAC
194 GAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATAATTGTTCTGTCCAAC
28132 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAA
*
28197 TAATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAAT
66 TGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAAT
28262 TCATCTTCTAAACTCAATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGA
131 TCATCTTCTAAACTCAATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGA
28327 AGATGCTATTGGCAAATTCATCTTCTAAACTCAATAA-TGTTCTGTCCAAC
196 AGATGCTATTGGCAAATTCATCTTCTAAACTCAATAATTGTTCTGTCCAAC
28377 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAA
*
28442 TGATTGTTTTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAAT
66 TGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAAT
*
28507 TCATCTTCTAAACTCAATAATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGA
131 TCATCTTCTAAACTCAATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGA
**
28572 AGATGCTATTAACAAATTCAT
196 AGATGCTATTGGCAAATTCAT
28593 TTGTTCTATT
Statistics
Matches: 446, Mismatches: 15, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
245 224 0.50
246 78 0.17
247 79 0.18
248 65 0.15
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.28
Consensus pattern (246 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAA
TGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAAT
TCATCTTCTAAACTCAATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGA
AGATGCTATTGGCAAATTCATCTTCTAAACTCAATAATTGTTCTGTCCAAC
Found at i:28481 original size:327 final size:330
Alignment explanation
Indices: 27884--28592 Score: 1280
Period size: 327 Copynumber: 2.2 Consensus size: 330
27874 TGCACTTCTT
* *
27884 CAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAACTCAA
* * *
27949 TGCTTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATTGGCAAA
66 TGATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAA
** *
28014 TTCATCTTCTAAACTCAATGCTTGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCA
131 TTCATCTTCTAAACTCAATGAATGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCA
28079 GAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATAATTGTTCTGTCCAACCAGATCAGATAA
196 GAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATAATTGTTCTGTCCAACCAGATCAGATAA
28144 CTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATAATTGTTCTGT
261 CTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATAATTGTTCTGT
28209 CCAAC
326 CCAAC
* *
28214 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAACTCAA
28279 TGATTG-TTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAA
66 TGATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAA
28343 TTCATCTTCTAAACTCAAT-AATG-TTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCA
131 TTCATCTTCTAAACTCAATGAATGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCA
* *
28406 GAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGATTGTTTTGTCCAACCAGATCAGATAA
196 GAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATAATTGTTCTGTCCAACCAGATCAGATAA
28471 CTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATAATTGTTCTGT
261 CTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATAATTGTTCTGT
28536 CCAAC
326 CCAAC
*
28541 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCAT
28593 TTGTTCTATT
Statistics
Matches: 365, Mismatches: 14, Indels: 3
0.96 0.04 0.01
Matches are distributed among these distances:
327 222 0.61
328 2 0.01
329 75 0.21
330 66 0.18
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.28
Consensus pattern (330 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAACTCAA
TGATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAA
TTCATCTTCTAAACTCAATGAATGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCA
GAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATAATTGTTCTGTCCAACCAGATCAGATAA
CTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATAATTGTTCTGT
CCAAC
Found at i:40427 original size:25 final size:24
Alignment explanation
Indices: 40375--40444 Score: 63
Period size: 25 Copynumber: 2.9 Consensus size: 24
40365 ACTTGCAAAT
* *
40375 AAAATAAAACATATAAATATTATG
1 AAAATAAAACATATAAAAATTATA
* *
40399 AAAATAATAATATATAAAAATTTTA
1 AAAATAA-AACATATAAAAATTATA
*
40424 AAAAGAAAGA-AT-TAAAAATTA
1 AAAATAAA-ACATATAAAAATTA
40445 AATATATGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
23 8 0.21
24 10 0.26
25 20 0.53
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (24 bp):
AAAATAAAACATATAAAAATTATA
Found at i:42590 original size:11 final size:11
Alignment explanation
Indices: 42567--42598 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
42557 TGTAATTAAT
42567 TATTTATATATA
1 TATTTA-ATATA
42579 TATTTAATATA
1 TATTTAATATA
42590 TATTTAATA
1 TATTTAATA
42599 ATAATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTTAATATA
Found at i:42602 original size:3 final size:3
Alignment explanation
Indices: 42594--42682 Score: 160
Period size: 3 Copynumber: 29.7 Consensus size: 3
42584 AATATATATT
*
42594 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
42642 TAA TAA TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
42683 TGGATAAAAA
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 82 1.00
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:44618 original size:25 final size:25
Alignment explanation
Indices: 44590--44648 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
44580 TTTAACGAAT
* *
44590 ATTTAATTTAGAATATTTAAATAAG
1 ATTTAATTTAGAATAATTAAATAAC
* *
44615 ATTTATTTTGGAATAATTAAATAAC
1 ATTTAATTTAGAATAATTAAATAAC
44640 ATTTCAATT
1 ATTT-AATT
44649 AATTTGGAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 25 0.89
26 3 0.11
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (25 bp):
ATTTAATTTAGAATAATTAAATAAC
Found at i:45490 original size:60 final size:59
Alignment explanation
Indices: 45389--45517 Score: 136
Period size: 60 Copynumber: 2.2 Consensus size: 59
45379 AATCTTATCT
* * * **
45389 CTAAATTATGACTATCATTCTAAATTAGTCCTCAAACTTTTGAATATTTTAATTTCACCC
1 CTAAATTATAACTATCATTCTAAATTAGTCCCCAAACTTTTGAACATTCCAATTTCA-CC
* * *
45449 CTAAATTATAAC-ATTCATTCTAAA-TGGTCCCCAAATTTTTTGACCATTCCAATTTCACC
1 CTAAATTATAACTA-TCATTCTAAATTAGTCCCCAAA-CTTTTGAACATTCCAATTTCACC
*
45508 CTAAACTATA
1 CTAAATTATA
45518 TGCATATACT
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
59 21 0.36
60 37 0.64
ACGTcount: A:0.34, C:0.22, G:0.05, T:0.39
Consensus pattern (59 bp):
CTAAATTATAACTATCATTCTAAATTAGTCCCCAAACTTTTGAACATTCCAATTTCACC
Found at i:45851 original size:2 final size:2
Alignment explanation
Indices: 45844--45883 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
45834 AACTCATTTA
45844 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
45884 TTTAAATATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47011 original size:21 final size:21
Alignment explanation
Indices: 46987--47049 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
46977 ATTAGATGCG
46987 AATATCTGCTAATTACTACGA
1 AATATCTGCTAATTACTACGA
* *
47008 AATA-CT-C--ATTAGATGCG-
1 AATATCTGCTAATTA-CTACGA
47025 AATATCTGCTAATTACTACGA
1 AATATCTGCTAATTACTACGA
47046 AATA
1 AATA
47050 CTCACCTCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
17 8 0.25
18 5 0.16
19 2 0.06
20 5 0.16
21 12 0.38
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (21 bp):
AATATCTGCTAATTACTACGA
Found at i:47025 original size:38 final size:38
Alignment explanation
Indices: 46974--47053 Score: 160
Period size: 38 Copynumber: 2.1 Consensus size: 38
46964 GCAACACAAG
46974 CTCATTAGATGCGAATATCTGCTAATTACTACGAAATA
1 CTCATTAGATGCGAATATCTGCTAATTACTACGAAATA
47012 CTCATTAGATGCGAATATCTGCTAATTACTACGAAATA
1 CTCATTAGATGCGAATATCTGCTAATTACTACGAAATA
47050 CTCA
1 CTCA
47054 CCTCATGCGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.31
Consensus pattern (38 bp):
CTCATTAGATGCGAATATCTGCTAATTACTACGAAATA
Found at i:47062 original size:38 final size:38
Alignment explanation
Indices: 46982--47062 Score: 128
Period size: 38 Copynumber: 2.1 Consensus size: 38
46972 AGCTCATTAG
* *
46982 ATGCGAATATCTGCTAATTACTACGAAATACTCATTAG
1 ATGCGAATATCTGCTAATTACTACGAAATACTCACTAC
47020 ATGCGAATATCTGCTAATTACTACGAAATACTCACCT-C
1 ATGCGAATATCTGCTAATTACTACGAAATACTCA-CTAC
47058 ATGCG
1 ATGCG
47063 TACATATAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
38 39 0.98
39 1 0.03
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.30
Consensus pattern (38 bp):
ATGCGAATATCTGCTAATTACTACGAAATACTCACTAC
Found at i:47145 original size:2 final size:2
Alignment explanation
Indices: 47140--47169 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
47130 TTATATACGC
47140 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
47170 GAGATGTGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47403 original size:24 final size:24
Alignment explanation
Indices: 47376--47430 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
47366 CGTTCATTTA
*
47376 CGTTCGTGAACGTTCGGTTATGTT
1 CGTTCATGAACGTTCGGTTATGTT
* **
47400 CGTTTATGTTCGTTCGGTTATGTT
1 CGTTCATGAACGTTCGGTTATGTT
*
47424 CATTCAT
1 CGTTCAT
47431 TTATATTTAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.13, C:0.16, G:0.24, T:0.47
Consensus pattern (24 bp):
CGTTCATGAACGTTCGGTTATGTT
Found at i:48538 original size:10 final size:10
Alignment explanation
Indices: 48523--48565 Score: 59
Period size: 10 Copynumber: 4.1 Consensus size: 10
48513 TTTATGTTCG
48523 TGTTCGTTTA
1 TGTTCGTTTA
*
48533 TGTTCGTGTTTG
1 TGTTC--GTTTA
48545 TGTTCGTTTA
1 TGTTCGTTTA
48555 TGTTCGTTTA
1 TGTTCGTTTA
48565 T
1 T
48566 TTATTAAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 20 0.69
12 9 0.31
ACGTcount: A:0.07, C:0.09, G:0.23, T:0.60
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:48542 original size:22 final size:22
Alignment explanation
Indices: 48517--48561 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
48507 CCAATGTTTA
48517 TGTTCGTGTTCGTTTATGTTCG
1 TGTTCGTGTTCGTTTATGTTCG
*
48539 TGTTTGTGTTCGTTTATGTTCG
1 TGTTCGTGTTCGTTTATGTTCG
48561 T
1 T
48562 TTATTTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.04, C:0.11, G:0.27, T:0.58
Consensus pattern (22 bp):
TGTTCGTGTTCGTTTATGTTCG
Found at i:48558 original size:16 final size:16
Alignment explanation
Indices: 48512--48542 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
48502 GGTCTCCAAT
48512 GTTTATGTTCGTGTTC
1 GTTTATGTTCGTGTTC
48528 GTTTATGTTCGTGTT
1 GTTTATGTTCGTGTT
48543 TGTGTTCGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.10, G:0.26, T:0.58
Consensus pattern (16 bp):
GTTTATGTTCGTGTTC
Found at i:48956 original size:10 final size:10
Alignment explanation
Indices: 48941--48965 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
48931 AGAATCTAAG
48941 AAACTAAGGA
1 AAACTAAGGA
48951 AAACTAAGGA
1 AAACTAAGGA
48961 AAACT
1 AAACT
48966 TGCTTATAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.12, G:0.16, T:0.12
Consensus pattern (10 bp):
AAACTAAGGA
Found at i:50455 original size:30 final size:30
Alignment explanation
Indices: 50418--50485 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 30
50408 TGAAGGTTTA
*
50418 TTTTTTTTGTTTATTCTCTTTCTTCTTT-CTC
1 TTTTTTTCGTTTATTCTCTTT-TT-TTTCCTC
* *
50449 TTTTTTTCTTTTTTTCTCTTTTTTTTCCTC
1 TTTTTTTCGTTTATTCTCTTTTTTTTCCTC
50479 TTTTTTT
1 TTTTTTT
50486 TTCTCTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 3 0.09
30 12 0.36
31 18 0.55
ACGTcount: A:0.01, C:0.18, G:0.01, T:0.79
Consensus pattern (30 bp):
TTTTTTTCGTTTATTCTCTTTTTTTTCCTC
Found at i:50462 original size:10 final size:10
Alignment explanation
Indices: 50443--50495 Score: 61
Period size: 10 Copynumber: 5.1 Consensus size: 10
50433 CTCTTTCTTC
*
50443 TTTCTCTTTT
1 TTTCTTTTTT
50453 TTTCTTTTTT
1 TTTCTTTTTT
*
50463 TCTCTTTTTT
1 TTTCTTTTTT
50473 TTCCTCTTTTTT
1 TT--TCTTTTTT
*
50485 TTTCTCTTTT
1 TTTCTTTTTT
50495 T
1 T
50496 CTCTCTCTCT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
10 27 0.73
12 10 0.27
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:50474 original size:12 final size:12
Alignment explanation
Indices: 50457--50495 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
50447 TCTTTTTTTC
50457 TTTTTTTCTCTT
1 TTTTTTTCTCTT
*
50469 TTTTTTCCTCTT
1 TTTTTTTCTCTT
50481 TTTTTTTCTCTT
1 TTTTTTTCTCTT
50493 TTT
1 TTT
50496 CTCTCTCTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTTTCTCTT
Found at i:50500 original size:10 final size:10
Alignment explanation
Indices: 50445--50511 Score: 53
Period size: 10 Copynumber: 6.3 Consensus size: 10
50435 CTTTCTTCTT
*
50445 TCTCTTTTTT
1 TCTCTTTTTC
*
50455 TCTTTTTTTC
1 TCTCTTTTTC
*
50465 TCTTTTTTTTCC
1 TC-TCTTTTT-C
* *
50477 TCTTTTTTTT
1 TCTCTTTTTC
50487 TCTCTTTTTC
1 TCTCTTTTTC
50497 TCTCTCTCTTTC
1 TCTCT-T-TTTC
50509 TCT
1 TCT
50512 TTTAATAACT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
10 23 0.48
11 15 0.31
12 10 0.21
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (10 bp):
TCTCTTTTTC
Found at i:50502 original size:12 final size:12
Alignment explanation
Indices: 50432--50511 Score: 64
Period size: 12 Copynumber: 7.1 Consensus size: 12
50422 TTTTGTTTAT
*
50432 TCTCTTTCTTCTT
1 TCTCTTT-TTCTC
50445 TCTCTTTTT-T-
1 TCTCTTTTTCTC
50455 TCT-TTTTT-TC
1 TCTCTTTTTCTC
*
50465 TCT-TTTTTTTC
1 TCTCTTTTTCTC
* *
50476 -CTCTTTTTTTT
1 TCTCTTTTTCTC
50487 TCTCTTTTTCTC
1 TCTCTTTTTCTC
*
50499 TCTCTCTTTCTC
1 TCTCTTTTTCTC
50511 T
1 T
50512 TTTAATAACT
Statistics
Matches: 59, Mismatches: 4, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
9 6 0.10
10 13 0.22
11 10 0.17
12 23 0.39
13 7 0.12
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TCTCTTTTTCTC
Found at i:50503 original size:24 final size:24
Alignment explanation
Indices: 50457--50507 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 24
50447 TCTTTTTTTC
*
50457 TTTTTTTCTCTTTTTTTTCCTCTT
1 TTTTTTTCTCTTTTTTCTCCTCTT
50481 TTTTTTTCTCTTTTTCTCTCTCTCTT
1 TTTTTTTCTCTTTTT-TCTC-CTCTT
50507 T
1 T
50508 CTCTTTTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 15 0.62
25 3 0.12
26 6 0.25
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (24 bp):
TTTTTTTCTCTTTTTTCTCCTCTT
Found at i:50512 original size:32 final size:30
Alignment explanation
Indices: 50418--50514 Score: 97
Period size: 32 Copynumber: 3.1 Consensus size: 30
50408 TGAAGGTTTA
* *
50418 TTTTTTTTGTTTATTCTCTTTCTTCTTTCTCT
1 TTTTTTTTCTTTTTTCTC-TTC-TCTTTCTCT
* * *
50450 TTTTTTCT-TTTTTTCTCTTTTTTTTCCTCT
1 TTTTTTTTCTTTTTTCTCTTCTCTTT-CTCT
50480 TTTTTTTTCTCTTTTTCTCTCTCTCTTTCTCT
1 TTTTTTTTCT-TTTTTCTCT-TCTCTTTCTCT
50512 TTT
1 TTT
50515 AATAACTTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
29 4 0.07
30 13 0.24
31 9 0.17
32 23 0.43
33 5 0.09
ACGTcount: A:0.01, C:0.22, G:0.01, T:0.76
Consensus pattern (30 bp):
TTTTTTTTCTTTTTTCTCTTCTCTTTCTCT
Found at i:50958 original size:20 final size:20
Alignment explanation
Indices: 50933--50971 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
50923 TAATCATCAT
50933 GCTCGAAAGACTTACTGATG
1 GCTCGAAAGACTTACTGATG
* *
50953 GCTCGAATGACTTTCTGAT
1 GCTCGAAAGACTTACTGAT
50972 TTTGGAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.31
Consensus pattern (20 bp):
GCTCGAAAGACTTACTGATG
Found at i:51062 original size:257 final size:257
Alignment explanation
Indices: 50601--51114 Score: 759
Period size: 257 Copynumber: 2.0 Consensus size: 257
50591 TTGCCCAAAA
* *
50601 GTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACATATGACCAAAGGATTT
1 GTCTTATAGATGGCCCGAAGGACTCATCATCTTGCTCAAAAGACTGACATATGACCAAAGGATTT
*
50666 AATCATCATGCTCGAAAGGCTTACTGATGGCCCGAAGGACTTACCGATTTTGGAAATAGTTTAAT
66 AATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCGATTTTGGAAATAGTTTAAT
* * * * *
50731 GGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAATTTTAATTTTTTGAAAATACTAAAT
131 GCGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTAATTTTCTAAAAACACTAAAT
50796 GAGAAACTTTGGAAATCGCTTTCTCATTTAT-TGAAAATCACGTGAAAACATCCTACCCGAAG
196 GAGAAACTTTGGAAATCGCTTTCTCATTT-TCTGAAAATCACGTGAAAACATCCTACCCGAAG
* * *
50858 GTCTTATAGATGGGCCGAATGACTCATCATCTTGCTCAAAAGCCTGAC-TGGA-GACCTGAAA-G
1 GTCTTATAGATGGCCCGAAGGACTCATCATCTTGCTCAAAAGACTGACAT--ATGACC--AAAGG
* * * *
50920 ATTTAATCATCATGCTCGAAAGACTTACTGATGGCTCGAATGACTTTCTGATTTTGGAAATAGTT
62 ATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCGATTTTGGAAATAGTT
* * * *
50985 TACT-CGTAAGAACCTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTAAAAACATT
127 TAATGCGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTAATTTTCTAAAAACACT
* *
51049 AAATGATAAACTTTGGAAATCGCTTTCTCATTTTCTGAAAATCACGTGAAAACATCCTGCCCGAA
192 AAATGAGAAACTTTGGAAATCGCTTTCTCATTTTCTGAAAATCACGTGAAAACATCCTACCCGAA
51114 G
257 G
51115 TAGGGGTGTT
Statistics
Matches: 231, Mismatches: 21, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
256 2 0.01
257 161 0.70
258 65 0.28
259 3 0.01
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Consensus pattern (257 bp):
GTCTTATAGATGGCCCGAAGGACTCATCATCTTGCTCAAAAGACTGACATATGACCAAAGGATTT
AATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCGATTTTGGAAATAGTTTAAT
GCGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTAATTTTCTAAAAACACTAAAT
GAGAAACTTTGGAAATCGCTTTCTCATTTTCTGAAAATCACGTGAAAACATCCTACCCGAAG
Found at i:51769 original size:42 final size:40
Alignment explanation
Indices: 51669--51773 Score: 120
Period size: 42 Copynumber: 2.5 Consensus size: 40
51659 ATCTGAAGGT
* * *
51669 CTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
1 CTTACAGATGGCCCGAATGA-TTATCATCATGCTCGAAAGA
** *
51710 CTTACAGATTACTCGAATGATTAAATCATCATGCTCGAAAGA
1 CTTACAGATGGCCCGAATGATT--ATCATCATGCTCGAAAGA
*
51752 CTTACTGATGGCCCGAATGATT
1 CTTACAGATGGCCCGAATGATT
51774 TACCAATTTT
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
40 2 0.04
41 15 0.29
42 35 0.67
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (40 bp):
CTTACAGATGGCCCGAATGATTATCATCATGCTCGAAAGA
Found at i:52021 original size:42 final size:41
Alignment explanation
Indices: 51931--52025 Score: 118
Period size: 42 Copynumber: 2.3 Consensus size: 41
51921 TTATAGATGG
* *
51931 CCCGAAGGACTTATAATCTTGCTCGAAAGACTTACAAATGA
1 CCCGAAGGACTTATAATCATGCTCGAAAGACTTACAAATAA
* * * **
51972 CCAGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATAA
1 CCCGAAGGACTT-ATAATCATGCTCGAAAGACTTACAAATAA
52014 CCCGAAGGACTT
1 CCCGAAGGACTT
52026 GTCAATTTTG
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
41 10 0.23
42 34 0.77
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (41 bp):
CCCGAAGGACTTATAATCATGCTCGAAAGACTTACAAATAA
Found at i:52195 original size:258 final size:257
Alignment explanation
Indices: 51663--52403 Score: 1032
Period size: 258 Copynumber: 2.9 Consensus size: 257
51653 CCCCTAATCT
* * * *
51663 GAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTACAGATTACTCGAAT
1 GAAGGTCTTACAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTACAAATGAC-CGAAG
* * *
51728 GATTAAATCATCATGCTCGAAAGACTTACTGATGGCCCGAATGATTTACCAATTTTGAAAATAGT
65 GATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGAAAATAGT
*
51793 TTACTAGGTAAGAAAC--T-----TCACTTTCTTACTTTTCAAAAATTTCATTTTATGAAAATAG
130 TTACTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTATGAAAATAC
* * * * * *
51851 TAAATGATAAACTTTGTAAATCGATTTCTCATTTTTTGAAAATCATGTGAAAACATCTTGCCC
195 TAAATGAGAAACTTTGGAAATCGCTTTTTCATTTTTTGAAAATCATGTGAAAACATCCTACCC
* *
51914 GAAGGTCTTATAGATGGCCCGAAGGACTTATAATCTTGCTCGAAAGACTTACAAATGACCAGAAG
1 GAAGGTCTTACAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTACAAATGACC-GAAG
** **
51979 GATTTAATCATCATGCTCGAAAGACTTACTGATAACCCGAAGGACTTGTCAATTTTGAAAATAGT
65 GATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGAAAATAGT
* *
52044 TTACTTGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTTTGAAAATAC
130 TTACTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTATGAAAATAC
* *
52109 TAAATGAGAAACTTTGGAAATCGCTTTTTCATTTTTTGAAAATTATGTGAAAATATCCTACCC
195 TAAATGAGAAACTTTGGAAATCGCTTTTTCATTTTTTGAAAATCATGTGAAAACATCCTACCC
* * * *
52172 GAAGGTTTTACGGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGACTAACAAATGACCCGAAG
1 GAAGGTCTTACAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTACAAATGA-CCGAAG
* *
52237 GATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCGATTATGAAAATAGT
65 GATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGAAAATAGT
* * * * *
52302 TTAATGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTAAAAAATTTCATTTTCTGAAAA-AC
130 TTACTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTATGAAAATAC
* *
52366 ATTAAATGAGAAACTTTAGAAATCACTTTCTT-ATTTTT
195 --TAAATGAGAAACTTTGGAAATCGCTTT-TTCATTTTT
52404 CAAAATAACT
Statistics
Matches: 437, Mismatches: 41, Indels: 16
0.88 0.08 0.03
Matches are distributed among these distances:
250 1 0.00
251 132 0.30
253 1 0.00
257 2 0.00
258 266 0.61
259 33 0.08
260 2 0.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (257 bp):
GAAGGTCTTACAGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTACAAATGACCGAAGG
ATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGAAAATAGTT
TACTAGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCATTTTATGAAAATACT
AAATGAGAAACTTTGGAAATCGCTTTTTCATTTTTTGAAAATCATGTGAAAACATCCTACCC
Found at i:52254 original size:42 final size:41
Alignment explanation
Indices: 52189--52284 Score: 120
Period size: 42 Copynumber: 2.3 Consensus size: 41
52179 TTACGGATGG
*
52189 CCCGAAGGACTTATCATCTTGCTCAAAAGACTAACAAATGA
1 CCCGAAGGACTTATCATCATGCTCAAAAGACTAACAAATGA
* * * ** *
52230 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
1 CCCGAAGGACTT-ATCATCATGCTCAAAAGACTAACAAATGA
52272 CCCGAAGGACTTA
1 CCCGAAGGACTTA
52285 CCGATTATGA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
41 12 0.26
42 34 0.74
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (41 bp):
CCCGAAGGACTTATCATCATGCTCAAAAGACTAACAAATGA
Found at i:54057 original size:2 final size:2
Alignment explanation
Indices: 54050--54086 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
54040 AACTTTATTG
54050 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
54087 CGCCTTTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:55123 original size:13 final size:13
Alignment explanation
Indices: 55097--55134 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
55087 ATTAAAGCAG
55097 TGCAAATG-AAAA
1 TGCAAATGCAAAA
* *
55109 TGTATATGCAAAA
1 TGCAAATGCAAAA
55122 TGCAAATGCAAAA
1 TGCAAATGCAAAA
55135 GGTGTTAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.53, C:0.11, G:0.16, T:0.21
Consensus pattern (13 bp):
TGCAAATGCAAAA
Found at i:56217 original size:19 final size:19
Alignment explanation
Indices: 56193--56236 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
56183 TTTTATGTAA
56193 ATATATAT-TATATCATATT
1 ATATATATATATATC-TATT
*
56212 ATATATGTATATATCTATT
1 ATATATATATATATCTATT
*
56231 AAATAT
1 ATATAT
56237 TTCTTAACCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (19 bp):
ATATATATATATATCTATT
Found at i:57060 original size:19 final size:19
Alignment explanation
Indices: 57006--57054 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
56996 ATGACGACTC
*
57006 CAATTCAAAATTTTTAAAT
1 CAATTCAAAATTTTCAAAT
57025 CAATTCAAAATTTTCAAAT
1 CAATTCAAAATTTTCAAAT
*
57044 TAATTCAAAAT
1 CAATTCAAAAT
57055 CGTCAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (19 bp):
CAATTCAAAATTTTCAAAT
Found at i:57668 original size:22 final size:22
Alignment explanation
Indices: 57623--57668 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
57613 AATCAAATTC
*
57623 ATTTAAATCAAATATTAATTGA
1 ATTTAAATCAAATATAAATTGA
*
57645 ATTTTAATCAAAT-TAAATTCGA
1 ATTTAAATCAAATATAAATT-GA
57667 AT
1 AT
57669 AGATTGCTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (22 bp):
ATTTAAATCAAATATAAATTGA
Found at i:62997 original size:5 final size:5
Alignment explanation
Indices: 62987--63019 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
62977 CTCAGGCAGC
62987 AATTA AATTA AATTA AATTA AATTA AATTA AAT
1 AATTA AATTA AATTA AATTA AATTA AATTA AAT
63020 GGTGTAGGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
AATTA
Found at i:65150 original size:17 final size:15
Alignment explanation
Indices: 65128--65169 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
65118 TATGAGATAA
65128 AAAATAATATTATTAT
1 AAAATAATATTATT-T
65144 GAAAAT-ATAATTATTT
1 -AAAATAAT-ATTATTT
65160 AAAATAATAT
1 AAAATAATAT
65170 AACTTTAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 7 0.30
16 5 0.22
17 11 0.48
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (15 bp):
AAAATAATATTATTT
Found at i:65389 original size:22 final size:22
Alignment explanation
Indices: 65361--65403 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
65351 GTTAGATAAT
65361 ATTTATAAATTAATATTAAAAC
1 ATTTATAAATTAATATTAAAAC
65383 ATTTATAAATTAATATTAAAA
1 ATTTATAAATTAATATTAAAA
65404 TTAATATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
ATTTATAAATTAATATTAAAAC
Found at i:65406 original size:12 final size:13
Alignment explanation
Indices: 65357--65411 Score: 57
Period size: 12 Copynumber: 4.5 Consensus size: 13
65347 AAAAGTTAGA
65357 TAATATTTATAAAT
1 TAATA-TTATAAAT
65371 TAATATTA-AAA-
1 TAATATTATAAAT
*
65382 -CAT-TTATAAAT
1 TAATATTATAAAT
65393 TAATATTA-AAAT
1 TAATATTATAAAT
65405 TAATATT
1 TAATATT
65412 TTTTAATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
9 3 0.09
10 5 0.14
12 16 0.46
13 6 0.17
14 5 0.14
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (13 bp):
TAATATTATAAAT
Found at i:65422 original size:2 final size:2
Alignment explanation
Indices: 65417--65481 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
65407 ATATTTTTTA
65417 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
65459 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
65482 AGTATAATTT
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:69949 original size:20 final size:21
Alignment explanation
Indices: 69924--69965 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
69914 CCCTGCAACC
69924 AAATCAACCCAAATA-AAAAA
1 AAATCAACCCAAATATAAAAA
**
69944 AAATCAATTCAAATATAAAAA
1 AAATCAACCCAAATATAAAAA
69965 A
1 A
69966 TATATAACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.69, C:0.14, G:0.00, T:0.17
Consensus pattern (21 bp):
AAATCAACCCAAATATAAAAA
Found at i:71069 original size:37 final size:37
Alignment explanation
Indices: 71014--71125 Score: 197
Period size: 37 Copynumber: 3.0 Consensus size: 37
71004 AACATAACGT
* *
71014 TAGAGTTTTATTAGGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
*
71051 TAGAGTTTTACTATGATTCAAACTCCTAAAAATATGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
71088 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
71125 T
1 T
71126 TCATAAGTAT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 71 1.00
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.34
Consensus pattern (37 bp):
TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
Found at i:71488 original size:3 final size:3
Alignment explanation
Indices: 71482--71534 Score: 58
Period size: 3 Copynumber: 18.3 Consensus size: 3
71472 TTTTTCTTAC
*
71482 TAT TAT TAT TA- TAT ATAC T-T TAT TAT TAT TAT TAT TAT TAT TA-
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
71525 TAT TTT TAT T
1 TAT TAT TAT T
71535 TTGTTTTATC
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
2 5 0.12
3 35 0.83
4 2 0.05
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:71533 original size:23 final size:25
Alignment explanation
Indices: 71482--71534 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 25
71472 TTTTTCTTAC
*
71482 TATTATTATTATATATACTTTATTAT
1 TATTATTATTATATATA-TATATTAT
*
71508 TATTATTATTAT-TAT-TATATTTT
1 TATTATTATTATATATATATATTAT
71531 TATT
1 TATT
71535 TTGTTTTATC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 10 0.40
25 3 0.12
26 12 0.48
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (25 bp):
TATTATTATTATATATATATATTAT
Found at i:71533 original size:26 final size:28
Alignment explanation
Indices: 71472--71534 Score: 85
Period size: 29 Copynumber: 2.3 Consensus size: 28
71462 TTTTATATTT
*
71472 TTTTTCTTACTATTATTATTATATATAC
1 TTTTTATTACTATTATTATTATATATAC
*
71500 TTTATTATTATTATTATTATTAT-TATA-
1 TTT-TTATTACTATTATTATTATATATAC
71527 TTTTTATT
1 TTTTTATT
71535 TTGTTTTATC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 5 0.16
27 3 0.09
28 7 0.22
29 17 0.53
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (28 bp):
TTTTTATTACTATTATTATTATATATAC
Found at i:71724 original size:2 final size:2
Alignment explanation
Indices: 71679--71715 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
71669 TACGTATGAT
71679 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
71716 TTCATATATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:72044 original size:22 final size:23
Alignment explanation
Indices: 72018--72064 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
72008 ATTATTATCA
* *
72018 TTATTATTCTTTTTAT-TTCATT
1 TTATTATTCTTATCATATTCATT
*
72040 TTATTTTTCTTATCATATTCATT
1 TTATTATTCTTATCATATTCATT
72063 TT
1 TT
72065 TATCTCTACT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.19, C:0.11, G:0.00, T:0.70
Consensus pattern (23 bp):
TTATTATTCTTATCATATTCATT
Found at i:75931 original size:17 final size:19
Alignment explanation
Indices: 75903--75951 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
75893 TATTTTAAAT
75903 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
75921 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
75940 CACCGATGCACT
1 CATCGATGCACT
75952 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:81721 original size:24 final size:24
Alignment explanation
Indices: 81694--81773 Score: 73
Period size: 24 Copynumber: 3.5 Consensus size: 24
81684 TTGTGCTTCA
81694 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGATGCATCCCTTTGAATG
* *
81718 TGCATCGATTCAT-CATGTTG-A--
1 TGCATCGATGCATCCCT-TTGAATG
*
81739 TGCACCGATGCA-CGCC-TTGAATG
1 TGCATCGATGCATC-CCTTTGAATG
81762 TGCATCGATGCA
1 TGCATCGATGCA
81774 CAAGGTCATG
Statistics
Matches: 44, Mismatches: 6, Indels: 13
0.70 0.10 0.21
Matches are distributed among these distances:
20 3 0.07
21 11 0.25
22 1 0.02
23 14 0.32
24 15 0.34
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.30
Consensus pattern (24 bp):
TGCATCGATGCATCCCTTTGAATG
Found at i:83895 original size:2 final size:2
Alignment explanation
Indices: 83888--83917 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
83878 CAGCTTAAGC
83888 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
83918 CAATTGGCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:84013 original size:16 final size:16
Alignment explanation
Indices: 83989--84029 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
83979 AAAGGGGGAG
*
83989 AAGTGTTAAGTGTTAA
1 AAGTTTTAAGTGTTAA
84005 AAGTTTTAAGTGTTAA
1 AAGTTTTAAGTGTTAA
84021 AAGTTTTAA
1 AAGTTTTAA
84030 AGGGGAGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.20, T:0.41
Consensus pattern (16 bp):
AAGTTTTAAGTGTTAA
Found at i:84542 original size:46 final size:45
Alignment explanation
Indices: 84486--84591 Score: 115
Period size: 45 Copynumber: 2.3 Consensus size: 45
84476 TGCACATACC
* * * *
84486 ATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCATTTG
1 ATGCATCGATGCACTCAGGATATTT-T-AAAACATCGAATGAACTTG
* * *
84532 ATGCATCGATGCACTCTGGCTATTTTAAATCATCGAATGAACTTG
1 ATGCATCGATGCACTCAGGATATTTTAAAACATCGAATGAACTTG
*
84577 ATGCATCGGTGCACT
1 ATGCATCGATGCACT
84592 AAGAGTGCAC
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
45 30 0.59
46 18 0.35
47 3 0.06
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (45 bp):
ATGCATCGATGCACTCAGGATATTTTAAAACATCGAATGAACTTG
Done.