Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000998.1 Hibiscus syriacus cultivar Beakdansim tig00001998_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: 86064
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:2079 original size:11 final size:11
Alignment explanation
Indices: 2063--2088 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2053 TTATATGACT
2063 ATATAATAATA
1 ATATAATAATA
2074 ATATAATAATA
1 ATATAATAATA
2085 ATAT
1 ATAT
2089 TTAAATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
ATATAATAATA
Found at i:3481 original size:3 final size:3
Alignment explanation
Indices: 3475--3532 Score: 75
Period size: 3 Copynumber: 19.3 Consensus size: 3
3465 TAATATTTAT
*
3475 TAA TAA TAA -AA TAA T-A TTA 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
3521 TATA TAAA TAA T
1 TA-A T-AA TAA T
3533 TTAAATAAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 8
0.85 0.02 0.14
Matches are distributed among these distances:
2 4 0.08
3 41 0.82
4 4 0.08
5 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3926 original size:118 final size:116
Alignment explanation
Indices: 3674--3943 Score: 364
Period size: 118 Copynumber: 2.3 Consensus size: 116
3664 TAAATTCTTC
* * *
3674 TCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCCGCTGGGGATGATGTTGACCTATTTCCT
1 TCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCCGCTGGAGATGATGCTGAACTATTTCCT
* *
3739 TATGTGATAGAGTCATTCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACT
66 TATGTGATAGAATCATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACT
* * * *
3790 TCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CTCTGGAAAAGCTGATGCT-AATTTT
1 TC-T-TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCCGCTGG---AGATGATGCTGAACTAT
* * *
3853 TCTCCTTCTGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGACCT
61 T-TCCTTATGTGATAGAATCATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACT
3910 TCTTTCTTCAGATGAGTTCTTCTCATTATGAACT
1 TCTTTCTTCAGATGAGTTCTTCTCATTATGAACT
3944 CTACCTGGCA
Statistics
Matches: 136, Mismatches: 12, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
116 2 0.01
117 6 0.04
118 64 0.47
119 5 0.04
120 59 0.43
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (116 bp):
TCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCCGCTGGAGATGATGCTGAACTATTTCCT
TATGTGATAGAATCATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACT
Found at i:4116 original size:109 final size:113
Alignment explanation
Indices: 3876--4358 Score: 601
Period size: 109 Copynumber: 4.4 Consensus size: 113
3866 TAGAATTATG
** *
3876 CAAAAGGTTGAACAAGCTCTTCTCATTGTG-AC--CTTC-T--TTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
3935 TTATGAACTCTACCTGGCAATGTTGAT-CATCAAATGATGAATTCAAA
66 TTATGAACTCTACCTGGCAAAGTTGATCCATCAAATGATGAATTCAAA
3982 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTT-TTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * * * *
4046 TTATGAACT-TTCTCTGG-AAAGCTGATCCATCAAGTGATGGATT-GAG
66 TTATGAACTCTAC-CTGGCAAAGTTGATCCATCAAATGATGAATTCAAA
* * **
4092 TAAAA-GTTGAACAAATTCTTCTCATTATGAATTTCTTCTT-CTTC-AGATGATGAGTTCTTCTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA-GATGAGTTCTTCTC
*
4154 ATTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAA
65 ATTATGAACTCTACCTGGCAAAGTTGATCCATCAAATGATGAATTCAAA
4203 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * * * *
4268 TTATGAACT-TTCTCTGGAAAAGTTGATCCATCAAGTGATGGATT-GAG
66 TTATGAACTCTAC-CTGGCAAAGTTGATCCATCAAATGATGAATTCAAA
*
4315 TAAAAGGTTGAA-AAA-TCTTCTCATTATGAA-TTCTTCTT-CTTCTT
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTT
4359 ATTATGAACT
Statistics
Matches: 327, Mismatches: 33, Indels: 32
0.83 0.08 0.08
Matches are distributed among these distances:
106 27 0.08
107 3 0.01
108 18 0.06
109 65 0.20
110 54 0.17
111 41 0.13
112 63 0.19
113 55 0.17
114 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (113 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTCTACCTGGCAAAGTTGATCCATCAAATGATGAATTCAAA
Found at i:4232 original size:221 final size:220
Alignment explanation
Indices: 3920--4356 Score: 808
Period size: 221 Copynumber: 2.0 Consensus size: 220
3910 TCTTTCTTCA
3920 GATGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTGATCATCAAATGATGAATTCAAACAA
1 GATGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTGATCATCAAATGATGAATTCAAACAA
3985 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTT-TTCTCATTA
66 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
4049 TGAACTTTCTCTGG-AAAGCTGATCCATCAAGTGATGGATTGAGTAAAA-GTTGAACAAATTCTT
131 TGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTGAGTAAAAGGTTGAA-AAA-TCTT
4112 CTCATTATGAATTTCTTCTTCTTCAGAT
194 CTCATTATGAA-TTCTTCTTCTTCAGAT
4140 GATGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAACA
1 GATGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTGAT-CATCAAATGATGAATTCAAACA
4205 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
65 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
4270 ATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGGATTGAGTAAAAGGTTGAAAAATCTTC
130 ATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTGAGTAAAAGGTTGAAAAATCTTC
4335 TCATTATGAATTCTTCTTCTTC
195 TCATTATGAATTCTTCTTCTTC
4357 TTATTATGAA
Statistics
Matches: 212, Mismatches: 1, Indels: 7
0.96 0.00 0.03
Matches are distributed among these distances:
220 42 0.20
221 90 0.42
222 38 0.18
223 36 0.17
224 6 0.03
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.38
Consensus pattern (220 bp):
GATGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTGATCATCAAATGATGAATTCAAACAA
AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
TGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTGAGTAAAAGGTTGAAAAATCTTCT
CATTATGAATTCTTCTTCTTCAGAT
Found at i:5169 original size:114 final size:114
Alignment explanation
Indices: 5006--5343 Score: 568
Period size: 114 Copynumber: 3.0 Consensus size: 114
4996 GATCATGCAG
* * * * * * * * *
5006 TTCATCTTTTAATTCCAATGATTGGTTCTGTGGTTCTTACCGAACCAGATCAGATGACTCAAAGA
1 TTCATCTTTTAAATCTAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
*
5071 AAACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
*
5120 TTCATCTTTCAAATCTAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTTAAATCTAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
5185 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
5234 TTCATCTTTTAAATCTAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTTAAATCTAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
*
5299 ACACTTCCAGAAGATGTTATTGGGTCTTCTTATTTCTACTATGAG
66 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAG
5344 AACGTAGCAC
Statistics
Matches: 211, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 211 1.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.36
Consensus pattern (114 bp):
TTCATCTTTTAAATCTAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
Found at i:5661 original size:19 final size:19
Alignment explanation
Indices: 5637--5708 Score: 67
Period size: 19 Copynumber: 3.7 Consensus size: 19
5627 AAAATAAAAG
*
5637 AATAAATTGAATTTTAGAA
1 AATAAATTGAATTTCAGAA
*
5656 AATAAATTGAATCTCA-AA
1 AATAAATTGAATTTCAGAA
* *
5674 GA-AAATTGAATTTAGAGAA
1 AATAAATTGAATTT-CAGAA
5693 AATAAACTTAGAATTT
1 AATAAA-TT-GAATTT
5709 ATTAATAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
17 10 0.24
18 4 0.10
19 17 0.40
20 3 0.07
21 2 0.05
22 6 0.14
ACGTcount: A:0.53, C:0.04, G:0.11, T:0.32
Consensus pattern (19 bp):
AATAAATTGAATTTCAGAA
Found at i:6051 original size:10 final size:10
Alignment explanation
Indices: 6038--6118 Score: 66
Period size: 10 Copynumber: 8.4 Consensus size: 10
6028 TCTTGACCCC
6038 TCTTTTTTCT
1 TCTTTTTTCT
6048 TC--TTTTC-
1 TCTTTTTTCT
6055 T-TTTTTT-T
1 TCTTTTTTCT
6063 TC-TTTTTCTT
1 TCTTTTTTC-T
*
6073 TCTTTTTTCC
1 TCTTTTTTCT
6083 TCATTTTTTTCT
1 TC--TTTTTTCT
*
6095 TTTTTTTTCT
1 TCTTTTTTCT
*
6105 TCTTTTTTTT
1 TCTTTTTTCT
6115 TCTT
1 TCTT
6119 CAAGCATAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 18
0.71 0.06 0.22
Matches are distributed among these distances:
7 1 0.02
8 15 0.26
10 27 0.47
11 6 0.11
12 8 0.14
ACGTcount: A:0.01, C:0.17, G:0.00, T:0.81
Consensus pattern (10 bp):
TCTTTTTTCT
Found at i:6077 original size:35 final size:36
Alignment explanation
Indices: 6038--6120 Score: 111
Period size: 35 Copynumber: 2.4 Consensus size: 36
6028 TCTTGACCCC
6038 TCTTTTTTCTTC-TTTTCTTT-TTTTTTCTTT-TTCTT
1 TCTTTTTTCTTCATTTT-TTTCTTTTTT-TTTCTTCTT
*
6073 TCTTTTTTCCTCATTTTTTTCTTTTTTTTTCTTCTT
1 TCTTTTTTCTTCATTTTTTTCTTTTTTTTTCTTCTT
6109 T-TTTTTTCTTCA
1 TCTTTTTTCTTCA
6121 AGCATAATAT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
35 27 0.63
36 16 0.37
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (36 bp):
TCTTTTTTCTTCATTTTTTTCTTTTTTTTTCTTCTT
Found at i:6095 original size:23 final size:22
Alignment explanation
Indices: 6065--6114 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
6055 TTTTTTTTTC
6065 TTTTTCTTTCTTTTTTCCTCATT
1 TTTTTCTTT-TTTTTTCCTCATT
* *
6088 TTTTTCTTTTTTTTTCTTCTTT
1 TTTTTCTTTTTTTTTCCTCATT
6110 TTTTT
1 TTTTT
6115 TCTTCAAGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 16 0.64
23 9 0.36
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (22 bp):
TTTTTCTTTTTTTTTCCTCATT
Found at i:17473 original size:21 final size:21
Alignment explanation
Indices: 17448--17504 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 21
17438 ATATTGAAAA
17448 ATAAATA-AATATT-AAAATAT
1 ATAAATATAAT-TTAAAAATAT
*
17468 GATAAAAATAATTTAAAAATAT
1 -ATAAATATAATTTAAAAATAT
*
17490 ATAAATTATTATTTA
1 ATAAA-TATAATTTA
17505 TTATATATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 13 0.43
22 17 0.57
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
ATAAATATAATTTAAAAATAT
Found at i:18919 original size:18 final size:18
Alignment explanation
Indices: 18892--18927 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
18882 GTTTTAGGGT
18892 TTCCTAATGGGTTTGGGC
1 TTCCTAATGGGTTTGGGC
*
18910 TTCCTGATGGGTTTGGGC
1 TTCCTAATGGGTTTGGGC
18928 CAGTTGGGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.08, C:0.17, G:0.36, T:0.39
Consensus pattern (18 bp):
TTCCTAATGGGTTTGGGC
Found at i:18995 original size:3 final size:3
Alignment explanation
Indices: 18987--19047 Score: 54
Period size: 3 Copynumber: 20.7 Consensus size: 3
18977 TAATATTTAT
* * * * *
18987 TAA TAA TAA -AA TAA TAA TAA TTA TTA TTA TTA TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
19034 TAA T-A TAAA TAA TA
1 TAA TAA T-AA TAA TA
19048 TTTAAATGAA
Statistics
Matches: 53, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
2 4 0.08
3 47 0.89
4 2 0.04
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:20597 original size:28 final size:28
Alignment explanation
Indices: 20537--20622 Score: 79
Period size: 28 Copynumber: 3.1 Consensus size: 28
20527 AAATTTTAAC
* ***
20537 ATAAAAAATATATATTTTTAAATAAAAAAA
1 ATAAAAAA-A-ATATTTTTAAATTAAGTTA
20567 ATAAAAAAAATATTTTTAAATTAAGTTA
1 ATAAAAAAAATATTTTTAAATTAAGTTA
* *
20595 AT-AATAAAATATATTT-AA-TAAGTTA
1 ATAAAAAAAATATTTTTAAATTAAGTTA
20620 ATA
1 ATA
20623 TAATTTTTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
25 9 0.18
26 2 0.04
27 12 0.24
28 17 0.35
29 1 0.02
30 8 0.16
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (28 bp):
ATAAAAAAAATATTTTTAAATTAAGTTA
Found at i:20612 original size:22 final size:22
Alignment explanation
Indices: 20587--20653 Score: 52
Period size: 22 Copynumber: 3.0 Consensus size: 22
20577 TATTTTTAAA
20587 TTAAGTTAATAATAAAATATAT
1 TTAAGTTAATAATAAAATATAT
* *
20609 TTAA--TAAGTTAATATAAT-TTT
1 TTAAGTTAA--TAATAAAATATAT
20630 TTAAGTTAATATATATAAA-ATAT
1 TTAAGTTAATA-ATA-AAATATAT
20653 T
1 T
20654 ATGAATTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 13
0.67 0.08 0.25
Matches are distributed among these distances:
20 3 0.09
21 8 0.24
22 15 0.44
23 8 0.24
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.46
Consensus pattern (22 bp):
TTAAGTTAATAATAAAATATAT
Found at i:20626 original size:27 final size:27
Alignment explanation
Indices: 20573--20622 Score: 77
Period size: 25 Copynumber: 1.9 Consensus size: 27
20563 AAAAATAAAA
*
20573 AAAATATTTTTAAATTAAGTTAATAAT
1 AAAATATATTTAAATTAAGTTAATAAT
20600 AAAATATATTT-AA-TAAGTTAATA
1 AAAATATATTTAAATTAAGTTAATA
20623 TAATTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 10 0.45
26 2 0.09
27 10 0.45
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (27 bp):
AAAATATATTTAAATTAAGTTAATAAT
Found at i:36061 original size:27 final size:28
Alignment explanation
Indices: 36028--36118 Score: 101
Period size: 32 Copynumber: 3.1 Consensus size: 28
36018 CTGAGGTAAC
*
36028 AATTTAAATAAAATAAAATATATTTTTA
1 AATTAAAATAAAATAAAATATATTTTTA
* * *
36056 TATTAAAATAGTAATAAAATATTTTTAAATTA
1 AATTAAAATA-AAATAAAATATATTT---TTA
36088 AATTAATAATAAAATAAAATATATTTTTA
1 AATTAA-AATAAAATAAAATATATTTTTA
36117 AA
1 AA
36119 GATATATAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
28 8 0.16
29 18 0.35
32 21 0.41
33 4 0.08
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (28 bp):
AATTAAAATAAAATAAAATATATTTTTA
Found at i:42753 original size:14 final size:14
Alignment explanation
Indices: 42734--42760 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
42724 TTCGTGAACG
42734 TTCAGTTATGTTCA
1 TTCAGTTATGTTCA
42748 TTCAGTTATGTTC
1 TTCAGTTATGTTC
42761 GTTTATGTTT
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:0.19, C:0.15, G:0.15, T:0.52
Consensus pattern (14 bp):
TTCAGTTATGTTCA
Found at i:42766 original size:24 final size:24
Alignment explanation
Indices: 42739--42807 Score: 102
Period size: 24 Copynumber: 2.9 Consensus size: 24
42729 GAACGTTCAG
42739 TTATGTTCATTCAGTTATGTTCGT
1 TTATGTTCATTCAGTTATGTTCGT
** *
42763 TTATGTTTGTTCGGTTATGTTCGT
1 TTATGTTCATTCAGTTATGTTCGT
*
42787 TTATGTTCATTCATTTATGTT
1 TTATGTTCATTCAGTTATGTT
42808 TAAGCCAATC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.14, C:0.10, G:0.17, T:0.58
Consensus pattern (24 bp):
TTATGTTCATTCAGTTATGTTCGT
Found at i:43423 original size:16 final size:16
Alignment explanation
Indices: 43404--43464 Score: 95
Period size: 16 Copynumber: 3.8 Consensus size: 16
43394 CCAATGTTTA
43404 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
43420 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
*
43436 TGTTCGTTTATGTTTG
1 TGTTCGTTTATGTTCG
*
43452 TATTCGTTTATGT
1 TGTTCGTTTATGT
43465 CCGTTTATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.10, C:0.10, G:0.21, T:0.59
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:43563 original size:16 final size:16
Alignment explanation
Indices: 43538--43570 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
43528 AAAAACATTT
*
43538 TGTTCGTTTATGTTCG
1 TGTTCCTTTATGTTCG
43554 TGTTCCTTTATGTTCG
1 TGTTCCTTTATGTTCG
43570 T
1 T
43571 TTATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.15, G:0.21, T:0.58
Consensus pattern (16 bp):
TGTTCCTTTATGTTCG
Found at i:43888 original size:37 final size:37
Alignment explanation
Indices: 43838--43914 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
43828 CTTTAAGTTA
*
43838 CCAATTTCTGATCTTTCAGCTGTTAACTCCCATTAAC
1 CCAATTTCTGATCTTTCAGATGTTAACTCCCATTAAC
*
43875 CCAATTTCTGATCTTTCGGATGTTAACTCCCATTAAC
1 CCAATTTCTGATCTTTCAGATGTTAACTCCCATTAAC
43912 CCA
1 CCA
43915 GCAACATCGC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.30, G:0.09, T:0.36
Consensus pattern (37 bp):
CCAATTTCTGATCTTTCAGATGTTAACTCCCATTAAC
Found at i:43967 original size:10 final size:11
Alignment explanation
Indices: 43947--43971 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
43937 AGTGTCAAGA
43947 TTTCTTTTTTT
1 TTTCTTTTTTT
43958 TTTCTTTTTTT
1 TTTCTTTTTTT
43969 TTT
1 TTT
43972 TTGATAGGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:63398 original size:23 final size:23
Alignment explanation
Indices: 63355--63399 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
63345 TTTTGTGTTG
* **
63355 AATCATTCAACATTATTTTATTA
1 AATCAATCAACATTAAATTATTA
63378 AATCAATCAACATTAAATTATT
1 AATCAATCAACATTAAATTATT
63400 CAGAGATAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.42
Consensus pattern (23 bp):
AATCAATCAACATTAAATTATTA
Found at i:68241 original size:45 final size:45
Alignment explanation
Indices: 68186--68406 Score: 372
Period size: 45 Copynumber: 4.9 Consensus size: 45
68176 AATTTCTTAT
*
68186 CAATATACTTACCATTTATCCCATAAGCCCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
68231 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
*
68276 CAATATACATACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
* *
68321 CAATATACTTGCCATTTATCCCATAAGCTCGTAAACTTATTTTAC
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
* * *
68366 CAATATATTTACCA-TTATTCCATGAGCTCGTAAGCTTATTT
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTT
68407 GTATGATTAT
Statistics
Matches: 166, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
44 24 0.14
45 142 0.86
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (45 bp):
CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
Found at i:68630 original size:61 final size:61
Alignment explanation
Indices: 68529--68644 Score: 187
Period size: 61 Copynumber: 1.9 Consensus size: 61
68519 CTAAATCTGC
* * *
68529 ACTAAACTTACGCCATAGTGCTAATCCGGATATGACACATAAGGTCGTGTCCACCACCTAT
1 ACTAAACTTACGCCATAGTGCTAATCCGAACATGACACATAAGGTCGTATCCACCACCTAT
* *
68590 ACTAAACTTACGCTATAGTGCTAATCCGAACATGATACATAAGGTCGTATCCACC
1 ACTAAACTTACGCCATAGTGCTAATCCGAACATGACACATAAGGTCGTATCCACC
68645 TTCCCGCACT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 50 1.00
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.25
Consensus pattern (61 bp):
ACTAAACTTACGCCATAGTGCTAATCCGAACATGACACATAAGGTCGTATCCACCACCTAT
Found at i:74605 original size:2 final size:2
Alignment explanation
Indices: 74598--74623 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
74588 ATATGAAGAA
74598 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
74624 TATTGTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:74882 original size:13 final size:13
Alignment explanation
Indices: 74866--74890 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
74856 TCTGGACTTA
74866 TTTTATTGGTTAC
1 TTTTATTGGTTAC
74879 TTTTATTGGTTA
1 TTTTATTGGTTA
74891 AAATTTATTT
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:0.16, C:0.04, G:0.16, T:0.64
Consensus pattern (13 bp):
TTTTATTGGTTAC
Found at i:77078 original size:21 final size:23
Alignment explanation
Indices: 77039--77080 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
77029 CTATTTATTT
77039 TATTTATTCGTTTTATTTTTTAC
1 TATTTATTCGTTTTATTTTTTAC
*
77062 TATTT-TT-GTTTTGTTTTTT
1 TATTTATTCGTTTTATTTTTT
77081 TTTTGTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 2 0.11
23 5 0.28
ACGTcount: A:0.12, C:0.05, G:0.07, T:0.76
Consensus pattern (23 bp):
TATTTATTCGTTTTATTTTTTAC
Found at i:77082 original size:25 final size:26
Alignment explanation
Indices: 77048--77098 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
77038 TTATTTATTC
77048 GTTTTATTTTTTACTATT-TTTGTTTT
1 GTTTTATTTTTT-CTATTATTTGTTTT
*
77074 GTTTT-TTTTTTGTATTATTTGTTTT
1 GTTTTATTTTTTCTATTATTTGTTTT
77099 CTTAACATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 4 0.17
25 14 0.61
26 5 0.22
ACGTcount: A:0.10, C:0.02, G:0.10, T:0.78
Consensus pattern (26 bp):
GTTTTATTTTTTCTATTATTTGTTTT
Found at i:77166 original size:6 final size:6
Alignment explanation
Indices: 77155--77258 Score: 83
Period size: 6 Copynumber: 17.5 Consensus size: 6
77145 TTCTTTCTAT
* *
77155 TTTTTA TTTTTA TTTTTA TTTTTA -TTTTA --TTTA TCTTTA TCTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
* * * *
77200 TTTTTTA TTTTTTTA TATTTA -TTTTA TTTTTTA TATTTA -TTTTA TTCTTG
1 -TTTTTA --TTTTTA TTTTTA TTTTTA -TTTTTA TTTTTA TTTTTA TTTTTA
77250 TTTTTA TTT
1 TTTTTA TTT
77259 ATTTATTTAT
Statistics
Matches: 82, Mismatches: 9, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
4 4 0.05
5 13 0.16
6 48 0.59
7 10 0.12
8 7 0.09
ACGTcount: A:0.17, C:0.03, G:0.01, T:0.79
Consensus pattern (6 bp):
TTTTTA
Found at i:77168 original size:56 final size:53
Alignment explanation
Indices: 77106--77286 Score: 141
Period size: 56 Copynumber: 3.5 Consensus size: 53
77096 TTTCTTAACA
77106 TTTTATTATTATATATATATATATTTACTATTATTTTCTTTCTTTCTATTTTTTAT
1 TTTTATTATTATATATATATATATTTACT-TTATTTTCTTT-TTT-TATTTTTTAT
* * * * *
77162 TTTTATTTTTATTTTTAT-TTTATTTATCTTTATCTTT-ATTTTTTATTTTTTTAT
1 TTTTATTATTATATATATATATATTTA-CTTTAT-TTTCTTTTTTTA-TTTTTTAT
* * *
77216 ATTTATT-TTAT-T-T-TTTATATTTA-TTT-TATTCTTGTTTTTATTTATTTA-
1 TTTTATTATTATATATATATATATTTACTTTATTTTCTT-TTTTTATTT-TTTAT
77264 -TTTATTA-TATATATATATATATT
1 TTTTATTATTATATATATATATATT
77287 ATTACTTTCT
Statistics
Matches: 104, Mismatches: 10, Indels: 28
0.73 0.07 0.20
Matches are distributed among these distances:
47 11 0.11
48 6 0.06
49 14 0.13
50 8 0.08
51 8 0.08
52 1 0.01
53 6 0.06
54 17 0.16
55 13 0.12
56 20 0.19
ACGTcount: A:0.23, C:0.04, G:0.01, T:0.72
Consensus pattern (53 bp):
TTTTATTATTATATATATATATATTTACTTTATTTTCTTTTTTTATTTTTTAT
Found at i:77193 original size:21 final size:20
Alignment explanation
Indices: 77157--77368 Score: 125
Period size: 21 Copynumber: 10.2 Consensus size: 20
77147 CTTTCTATTT
77157 TTTATTTTTATTTTTATTTTTA
1 TTTA-TTTTATTTTTA-TTTTA
*
77179 TTT-TATTTATCTTTATCTTTA
1 TTTAT-TTTATTTTTAT-TTTA
*
77200 -TT-TTTTATTTTT-TTATA
1 TTTATTTTATTTTTATTTTA
77217 TTTATTTTATTTTTTATATTTA
1 TTTATTTTA-TTTTTAT-TTTA
*
77239 TTTTATTCTTGTTTTTA-TTTA
1 -TTTATT-TTATTTTTATTTTA
* *
77260 TTTA-TTTATTATATATATATA
1 TTTATTTTATT-TTTAT-TTTA
*
77281 TATATTATTACTTTCTTCATTTTA
1 TTTATT-TTA-TTT-TT-ATTTTA
* *
77305 TTTATTTTCTTTTTATCCTTA
1 TTTATTTTATTTTTAT-TTTA
* *
77326 TTTTTATTTATTTTTATTTTC
1 TTTAT-TTTATTTTTATTTTA
77347 TTTATCTTTA-TTTTA-TTTA
1 TTTAT-TTTATTTTTATTTTA
77366 TTT
1 TTT
77369 TTGTACTTTT
Statistics
Matches: 150, Mismatches: 21, Indels: 41
0.71 0.10 0.19
Matches are distributed among these distances:
17 3 0.02
18 7 0.05
19 23 0.15
20 21 0.14
21 43 0.29
22 20 0.13
23 18 0.12
24 13 0.09
25 2 0.01
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTATTTTATTTTTATTTTA
Found at i:77240 original size:4 final size:4
Alignment explanation
Indices: 77196--77269 Score: 50
Period size: 4 Copynumber: 18.5 Consensus size: 4
77186 TATCTTTATC
* *
77196 TTTA TTT- TTTA TTT- TTT- TATA TTTA TTTTA TTTT TTATA TTTA TTTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TT-TA TTTA -TTTA
77244 TTCT- TGTT- TTTA TTTA TTTA TTTA TT
1 TT-TA T-TTA TTTA TTTA TTTA TTTA TT
77270 ATATATATAT
Statistics
Matches: 58, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
3 10 0.17
4 35 0.60
5 13 0.22
ACGTcount: A:0.19, C:0.01, G:0.01, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:77387 original size:10 final size:10
Alignment explanation
Indices: 77300--77387 Score: 56
Period size: 10 Copynumber: 8.3 Consensus size: 10
77290 ACTTTCTTCA
*
77300 TTTTATTTATT
1 TTTT-TTTATC
77311 TTCTTTTTATCC
1 TT-TTTTTAT-C
77323 TTATTTTTAT-
1 TT-TTTTTATC
77333 TTATTTTTAT-
1 TT-TTTTTATC
*
77343 TTTCTTTATC
1 TTTTTTTATC
77353 TTTATTTTAT-
1 TTT-TTTTATC
*
77363 TTATTTTTGTAC
1 TT-TTTTTAT-C
77375 TTTTTTTATC
1 TTTTTTTATC
77385 TTT
1 TTT
77388 ACCTTATCGT
Statistics
Matches: 64, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
9 6 0.09
10 26 0.41
11 19 0.30
12 13 0.20
ACGTcount: A:0.15, C:0.08, G:0.01, T:0.76
Consensus pattern (10 bp):
TTTTTTTATC
Found at i:77448 original size:5 final size:5
Alignment explanation
Indices: 77440--77490 Score: 54
Period size: 5 Copynumber: 10.6 Consensus size: 5
77430 TCTCATTTTC
* *
77440 TTTAT TTTAT TTGTTT TTTAT TTTA- ATTAT TTTA- TTTAT TTTA- TTTAT
1 TTTAT TTTAT TT-TAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
77488 TTT
1 TTT
77491 CATTACTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
4 11 0.29
5 23 0.61
6 4 0.11
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (5 bp):
TTTAT
Found at i:79594 original size:16 final size:16
Alignment explanation
Indices: 79573--79622 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
79563 CGTCCTATGT
79573 TATAAT-TATATGATTA
1 TATAATGTATAT-ATTA
79589 TATAATGTATATATTA
1 TATAATGTATATATTA
*
79605 TAT-ATATATATA-TA
1 TATAATGTATATATTA
79619 TATA
1 TATA
79623 TCATTTACAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
14 5 0.16
15 8 0.26
16 13 0.42
17 5 0.16
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (16 bp):
TATAATGTATATATTA
Found at i:79601 original size:2 final size:2
Alignment explanation
Indices: 79587--79623 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
79577 ATTATATGAT
*
79587 TA TA TA -A TG TA TA TA T- 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 TA T
79624 CATTTACATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:80636 original size:15 final size:15
Alignment explanation
Indices: 80619--80652 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
80609 GTTATTATTA
80619 TTTATTTATTGTTTAT
1 TTTA-TTATTGTTTAT
*
80635 TTTATTATTTTTTAT
1 TTTATTATTGTTTAT
80650 TTT
1 TTT
80653 TATCAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (15 bp):
TTTATTATTGTTTAT
Found at i:80851 original size:27 final size:28
Alignment explanation
Indices: 80813--80866 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
80803 TATTTATTCG
80813 TTTTATTTTTTTACTATT-TTTGTTTTT
1 TTTTATTTTTTTACTATTATTTGTTTTT
* **
80840 TTTTGTTTTTTTTGTATTATTTGTTTT
1 TTTTATTTTTTTACTATTATTTGTTTT
80867 CCTAACATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 15 0.65
28 8 0.35
ACGTcount: A:0.09, C:0.02, G:0.07, T:0.81
Consensus pattern (28 bp):
TTTTATTTTTTTACTATTATTTGTTTTT
Found at i:80925 original size:6 final size:6
Alignment explanation
Indices: 80914--81127 Score: 86
Period size: 6 Copynumber: 34.8 Consensus size: 6
80904 TTTCTTCTAT
* *
80914 TTTTTA TTTTTA TTTATTT TATTTTA -TTTTA TTTTTA TCTTTA TTTTT-
1 TTTTTA TTTTTA TTT-TTA T-TTTTA TTTTTA TTTTTA TTTTTA TTTTTA
* * * * *
80962 TATTT- CTTTTA TATTTA -TTTTA -TTTTA TATTTA -TTTTA TTTTTG
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
* * * * *
81006 TTTTTA TTTATTTA TTTATCA TATATA TTATTA CTTTCTTCA TTTTATT
1 TTTTTA -TT-TTTA TTT-TTA TTTTTA TTTTTA -TTT-TT-A TTTT-TA
* * * *
81055 TATTTTC TTTTTA TCTTTA TTTTTA TTTCTT- TTATTT- TCTTTA TCTTTA
1 T-TTTTA TTTTTA TTTTTA TTTTTA TTT-TTA TT-TTTA TTTTTA TTTTTA
*
81104 -TTTTA TTTATTT TTTTTA CTTTTT
1 TTTTTA TTT-TTA TTTTTA -TTTTT
81128 TATCTTTACT
Statistics
Matches: 157, Mismatches: 31, Indels: 39
0.69 0.14 0.17
Matches are distributed among these distances:
5 32 0.20
6 77 0.49
7 32 0.20
8 15 0.10
9 1 0.01
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (6 bp):
TTTTTA
Found at i:80933 original size:15 final size:15
Alignment explanation
Indices: 80916--81141 Score: 117
Period size: 16 Copynumber: 14.3 Consensus size: 15
80906 TCTTCTATTT
*
80916 TTTATTTT-TATTTA
1 TTTATTTTATTTTTA
*
80930 TTTTATTTTATTTTATT
1 -TTTATTTTATTTT-TA
80947 TTTATCTTTATTTTTTA
1 TTTAT-TTTA-TTTTTA
* *
80964 TTTCTTTTATATTTA
1 TTTATTTTATTTTTA
*
80979 TTTTATTTTATATTTA
1 -TTTATTTTATTTTTA
*
80995 TTTTATTTTTGTTTTTA
1 -TTTA-TTTTATTTTTA
81012 TTTA-TTTATTTATCATA
1 TTTATTTTATTT-T--TA
*
81029 TATATTATTACTTTCTTCA
1 TTTATT-TTA-TTT-TT-A
*
81048 TTT-TATTTATTTTCTT
1 TTTAT-TTTATTTT-TA
81064 TTTATCTTTATTTTTA
1 TTTAT-TTTATTTTTA
* *
81080 TTTCTTTTA-TTTTC
1 TTTATTTTATTTTTA
81094 TTTATCTTTA-TTTTA
1 TTTAT-TTTATTTTTA
81109 TTTA-TTT-TTTTTA
1 TTTATTTTATTTTTA
* *
81122 CTT-TTTTATCTTTA
1 TTTATTTTATTTTTA
81136 CTTTAT
1 -TTTAT
81142 CGTTTCTTTT
Statistics
Matches: 167, Mismatches: 22, Indels: 43
0.72 0.09 0.19
Matches are distributed among these distances:
13 13 0.08
14 19 0.11
15 32 0.19
16 45 0.27
17 37 0.22
18 10 0.06
19 7 0.04
20 4 0.02
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTATTTTATTTTTA
Found at i:80934 original size:5 final size:5
Alignment explanation
Indices: 80915--81219 Score: 120
Period size: 5 Copynumber: 59.8 Consensus size: 5
80905 TTCTTCTATT
*
80915 TTTTA TTTT- TATTTA TTTTA TTTTA TTTTA TTTTTA TCTTTA TTTTT
1 TTTTA TTTTA T-TTTA TTTTA TTTTA TTTTA -TTTTA T-TTTA TTTTA
* *
80962 TATTTC TTTTA TATTTA TTTTA TTTTA TATTTA TTTTA TTTT- TGTTTT
1 T-TTTA TTTTA T-TTTA TTTTA TTTTA T-TTTA TTTTA TTTTA T-TTTA
* * * *
81010 TATTTA -TTTA TTTATCA TATATA TTATTA CTTT- CTTCA TTTTA -TTTA
1 T-TTTA TTTTA TTT-T-A T-TTTA TT-TTA TTTTA TTTTA TTTTA TTTTA
* * *
81057 TTTTCT TTTTA TCTTTA TTTT- TATTTC TTTTA TTTT- CTTTA TCTTTA
1 TTTT-A TTTTA T-TTTA TTTTA T-TTTA TTTTA TTTTA TTTTA T-TTTA
* * *
81104 TTTTA -TTTA TTTT- TTTTA -CTT- TTTTA TCTTTA CTTTA TCGTTTC
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T-TTTA TTTTA T--TTTA
* * * * * * *
81148 TTTTC TCTTTA TCTTTT TGTTTT TTTTA TCTCA TTTT- CTTTA TTTCA
1 TTTTA T-TTTA T-TTTA T-TTTA TTTTA TTTTA TTTTA TTTTA TTTTA
81195 -TTTA TTTT- TTTTA -TTTA -TTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
81220 CATTACCTTT
Statistics
Matches: 233, Mismatches: 33, Indels: 68
0.70 0.10 0.20
Matches are distributed among these distances:
4 47 0.20
5 110 0.47
6 68 0.29
7 7 0.03
8 1 0.00
ACGTcount: A:0.17, C:0.08, G:0.01, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:80961 original size:56 final size:57
Alignment explanation
Indices: 80897--81141 Score: 180
Period size: 62 Copynumber: 4.1 Consensus size: 57
80887 ATATTTACTA
* *
80897 TTATTTTTTTCTTCTATTT-TTTATTTTTATTTATTTTATTTTATTTTATTTTTATCT
1 TTATTTATTTATT-TATTTATTTATTTTTATTTATTTTATTTTATTTTATTTTTATCT
* * * * *
80954 TTATTT-TTTATTTCTTT-TATATTTAT-TTTATTTTATATTTATTTTATTTTTGTTT
1 TTATTTATTTATTTATTTATTTATTTTTATTTATTTTAT-TTTATTTTATTTTTATCT
* * *
81009 TTATTTATTTATTTATCATATATATTATTACTTTCTTCATTTTA-TTTATTTTCTTTTTATCT
1 TTATTTATTTATTTAT--T-TAT-TTATT--TTTATTTATTTTATTTTATTTTATTTTTATCT
* * *
81071 TTATTTTTATTTCTTTTATTTTCTTTATCTTTATTT-TATTTATTTT-TTTTACTTTTTTATCT
1 TTA--TTTATTT-ATTTA-TTTATTTATTTTTATTTAT-TTTATTTTATTTTA--TTTTTATCT
81133 TTACTTTAT
1 TTA-TTTAT
81142 CGTTTCTTTT
Statistics
Matches: 150, Mismatches: 20, Indels: 32
0.74 0.10 0.16
Matches are distributed among these distances:
54 10 0.07
55 33 0.22
56 13 0.09
57 6 0.04
58 1 0.01
59 2 0.01
60 14 0.09
61 12 0.08
62 34 0.23
63 4 0.03
64 16 0.11
65 4 0.03
66 1 0.01
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (57 bp):
TTATTTATTTATTTATTTATTTATTTTTATTTATTTTATTTTATTTTATTTTTATCT
Found at i:80972 original size:38 final size:36
Alignment explanation
Indices: 80916--81210 Score: 180
Period size: 36 Copynumber: 7.9 Consensus size: 36
80906 TCTTCTATTT
*
80916 TTTATTTTTATTTATTTTATTTTATTTTATTTTTATC
1 TTTATTTTTATTTCTTTTATTTT-TTTTATTTTTATC
*
80953 TTTATTTTTTATTTCTTTTATATTTATTTTA-TTTTATA
1 TTTA-TTTTTATTTCTTTTAT-TTT-TTTTATTTTTATC
* *
80991 TTTA-TTTTATTT-TTGTTTTTATTTATTTATTTATCATATA
1 TTTATTTTTATTTCTT-TTATT-TTT-TTTATTT-T--TATC
* * *
81031 TATTATTACTTT-CTTCATTTTATTTATTTTCTTTTTATC
1 T-TTATT--TTTATTTC-TTTTATTTTTTTTATTTTTATC
* *
81070 TTTATTTTTATTTCTTTTATTTTCTTTATCTTTAT-
1 TTTATTTTTATTTCTTTTATTTTTTTTATTTTTATC
* * *
81105 TTTA--TTTATTTTTTTTA-CTTTTTTATCTTTA-C
1 TTTATTTTTATTTCTTTTATTTTTTTTATTTTTATC
*
81137 TTTATCGTTTCT-TTTCTCTTTATCTTTTTGTTTTTTTTATC
1 TTTAT--TTT-TATTTCT-TTTAT-TTTTT-TTATTTTTATC
*
81178 TCATT-TTCTTTATTTCATTTATTTTTTTTATTT
1 T--TTATT-TTTATTTCTTTTATTTTTTTTATTT
81211 ATTTATTTTC
Statistics
Matches: 205, Mismatches: 22, Indels: 61
0.71 0.08 0.21
Matches are distributed among these distances:
32 16 0.08
33 12 0.06
35 8 0.04
36 43 0.21
37 14 0.07
38 36 0.18
39 22 0.11
40 19 0.09
41 12 0.06
42 8 0.04
43 6 0.03
44 7 0.03
45 2 0.01
ACGTcount: A:0.17, C:0.08, G:0.01, T:0.75
Consensus pattern (36 bp):
TTTATTTTTATTTCTTTTATTTTTTTTATTTTTATC
Found at i:81151 original size:23 final size:23
Alignment explanation
Indices: 81125--81178 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
81115 TTTTTTACTT
81125 TTTTATCTTTA-CTTTATCGTTTC
1 TTTTATCTTTATCTTT-TCGTTTC
* * *
81148 TTTTCTCTTTATCTTTTTGTTTT
1 TTTTATCTTTATCTTTTCGTTTC
81171 TTTTATCT
1 TTTTATCT
81179 CATTTTCTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 22 0.85
24 4 0.15
ACGTcount: A:0.09, C:0.15, G:0.04, T:0.72
Consensus pattern (23 bp):
TTTTATCTTTATCTTTTCGTTTC
Found at i:83044 original size:2 final size:2
Alignment explanation
Indices: 83027--83060 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
83017 TTTTATTTTA
83027 AT AT A- AT AT A- 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
83061 GGTTCAGGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:84940 original size:154 final size:154
Alignment explanation
Indices: 84660--84973 Score: 493
Period size: 154 Copynumber: 2.0 Consensus size: 154
84650 CTCCCGAAGG
* *
84660 CTAAATTAACGAAAATACTTTACACATCTAAATTATTCGAAATGATTATATTATATGACAAAGTT
1 CTAAATTAACGAAAATACTTTACACATCTAAATTATTCGAAATGACTACATTATATGACAAAGTT
* * *
84725 GAACTGAATAGAAGTATTGTACGTATCCAAATTGTTGAAACGATCAAATTACTCTGGAAACTCCG
66 GAACTGAATAGAAGTATTATACATATCCAAATTATTGAAACGATCAAATTACTCTGGAAACTCCG
84790 AAATGACAAGGATAAACTTGAATA
131 AAATGACAAGGATAAACTTGAATA
* * *
84814 CTAAATTAGCGAAAGTACTTTACACATCTGAATTATTCGAAATGACTACATTATATGACAAAGTT
1 CTAAATTAACGAAAATACTTTACACATCTAAATTATTCGAAATGACTACATTATATGACAAAGTT
* *** *
84879 GAACTGAATGGAAGTATTATACATATTTGAATTATTGAAACGATCGAATTACTCTGGAAACTCCG
66 GAACTGAATAGAAGTATTATACATATCCAAATTATTGAAACGATCAAATTACTCTGGAAACTCCG
**
84944 AAATGACCGGGATAAACTTGAATA
131 AAATGACAAGGATAAACTTGAATA
84968 CTAAAT
1 CTAAAT
84974 GACCTAAGTA
Statistics
Matches: 145, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
154 145 1.00
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (154 bp):
CTAAATTAACGAAAATACTTTACACATCTAAATTATTCGAAATGACTACATTATATGACAAAGTT
GAACTGAATAGAAGTATTATACATATCCAAATTATTGAAACGATCAAATTACTCTGGAAACTCCG
AAATGACAAGGATAAACTTGAATA
Done.