Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005882.1 Hibiscus syriacus cultivar Beakdansim tig00013814_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: 111598
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2111 original size:23 final size:22
Alignment explanation
Indices: 2072--2118 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
2062 CTTAACTATT
*
2072 ATATCTATTAATATTAGATTAA
1 ATATCTATTAATATTAGATCAA
*
2094 ATATGTATTGAATATTAGATCAA
1 ATATCTATT-AATATTAGATCAA
2117 AT
1 AT
2119 CTATCATCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.43
Consensus pattern (22 bp):
ATATCTATTAATATTAGATCAA
Found at i:12123 original size:18 final size:18
Alignment explanation
Indices: 12102--12164 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
12092 TGTCCCGAAT
12102 GACCACTATGTCTTGAAG
1 GACCACTATGTCTTGAAG
**
12120 GACCACTGATTGT-TCCAAAG
1 GACCACT-A-TGTCT-TGAAG
* *
12140 AACCACTATGTCCTGAAG
1 GACCACTATGTCTTGAAG
12158 GACCACT
1 GACCACT
12165 GATAATCCCT
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
18 19 0.56
19 3 0.09
20 12 0.35
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (18 bp):
GACCACTATGTCTTGAAG
Found at i:12807 original size:64 final size:64
Alignment explanation
Indices: 12736--12875 Score: 167
Period size: 64 Copynumber: 2.2 Consensus size: 64
12726 ATCCCTTGAC
* * *
12736 GGGTGCATCGATGTACAA-TCTATGCATCGGTACA-TAAATCTCATTCGATGTTTATATTTTAAG
1 GGGTGCATCGATGTACAACT-TATGCATCGATACACT-AATCACATTCGATGTTTATATTTTAAA
12799 G
64 G
* * * * *
12800 GGGTGCATTGATGTACTACTTGTGCATCGATACACTAATGACATTCGATGTTTTTATTTTAAAG
1 GGGTGCATCGATGTACAACTTATGCATCGATACACTAATCACATTCGATGTTTATATTTTAAAG
*
12864 GAGTGCATCGAT
1 GGGTGCATCGAT
12876 ACACCTCATG
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
64 62 0.97
65 2 0.03
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.36
Consensus pattern (64 bp):
GGGTGCATCGATGTACAACTTATGCATCGATACACTAATCACATTCGATGTTTATATTTTAAAG
Found at i:12888 original size:64 final size:64
Alignment explanation
Indices: 12777--12898 Score: 156
Period size: 64 Copynumber: 1.9 Consensus size: 64
12767 ACATAAATCT
* * * ** *
12777 CATTCGATGTTTATATTTTAAGGGGGTGCATTGATGTACTACTTGTGCATCGATACACTAATGA
1 CATTCGATGTTTATATTTTAAAGGAGTGCATCGATACACTACATGTGCATCGATACACTAATGA
* *
12841 CATTCGATGTTTTTATTTTAAAGGAGTGCATCGATACACCT-CATGTGCATTGATACAC
1 CATTCGATGTTTATATTTTAAAGGAGTGCATCGATACA-CTACATGTGCATCGATACAC
12899 CTTGAATAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
64 47 0.96
65 2 0.04
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (64 bp):
CATTCGATGTTTATATTTTAAAGGAGTGCATCGATACACTACATGTGCATCGATACACTAATGA
Found at i:17454 original size:52 final size:52
Alignment explanation
Indices: 17375--17532 Score: 273
Period size: 52 Copynumber: 3.0 Consensus size: 52
17365 ACCCACCGAA
* *
17375 AATTGCTTTGATTCTTCAACAATTGTTGGCTGGCCACCGAATTGACTTTTAAC
1 AATTG-TTTGAATCTTCAACAATTGTTGGCTGGCCACCGAATTCACTTTTAAC
17428 AATTGTTTGAATCTTCAACAATTGTTGGCTGGCCACCGAATTCACTTTTAAC
1 AATTGTTTGAATCTTCAACAATTGTTGGCTGGCCACCGAATTCACTTTTAAC
*
17480 AATTGTTTGAATCTTCAACAATCGTTGGCTGGCCACCGAATTCAC-TTTAAC
1 AATTGTTTGAATCTTCAACAATTGTTGGCTGGCCACCGAATTCACTTTTAAC
17531 AA
1 AA
17533 CCTCTCACTT
Statistics
Matches: 102, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
51 8 0.08
52 89 0.87
53 5 0.05
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (52 bp):
AATTGTTTGAATCTTCAACAATTGTTGGCTGGCCACCGAATTCACTTTTAAC
Found at i:20266 original size:16 final size:17
Alignment explanation
Indices: 20238--20272 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
20228 TATATTGCCA
20238 ACAAAATTTTACTATTC
1 ACAAAATTTTACTATTC
20255 ACAAAA-TTTACTATTC
1 ACAAAATTTTACTATTC
20271 AC
1 AC
20273 GTAAATAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.43, C:0.20, G:0.00, T:0.37
Consensus pattern (17 bp):
ACAAAATTTTACTATTC
Found at i:23895 original size:59 final size:60
Alignment explanation
Indices: 23831--23969 Score: 158
Period size: 59 Copynumber: 2.3 Consensus size: 60
23821 TAAATATGCT
* * * * *
23831 AATTTTATCCCTAAACTATGACTATCATTCTAAATTAGT-TCTCAAA-TT-TTGAATATTTC
1 AATTTTATCCC-AAACTATGACCATCATTCTAAATTGGTCCCT-AAACTTATTGAACATTCC
* *
23890 AATTTTATCCCCAAACTATGACCCTCATTTTAAATTGGTCCCTAAACTTATTGAACATTCC
1 AATTTTAT-CCCAAACTATGACCATCATTCTAAATTGGTCCCTAAACTTATTGAACATTCC
*
23951 AATTTCATCCCAAACTATG
1 AATTTTATCCCAAACTATG
23970 TGATACAAAT
Statistics
Matches: 68, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
59 34 0.50
60 18 0.26
61 16 0.24
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.39
Consensus pattern (60 bp):
AATTTTATCCCAAACTATGACCATCATTCTAAATTGGTCCCTAAACTTATTGAACATTCC
Found at i:24172 original size:29 final size:29
Alignment explanation
Indices: 24139--24237 Score: 85
Period size: 29 Copynumber: 3.3 Consensus size: 29
24129 TGAGGATCAT
24139 AGTTTAGGGATGAAATTAAAATGTTCAAA
1 AGTTTAGGGATGAAATTAAAATGTTCAAA
* * * *
24168 AGTTTAAGGACT-AATTTAAAATGAGAGTC-AT
1 AGTTTAGGGA-TGAAATTAAAAT--G-TTCAAA
* *
24199 AGTTTAGGGATGAAATTAAAATATTTAAA
1 AGTTTAGGGATGAAATTAAAATGTTCAAA
*
24228 AATTTAGGGA
1 AGTTTAGGGA
24238 CCAATATTAA
Statistics
Matches: 53, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
28 1 0.02
29 28 0.53
30 2 0.04
31 20 0.38
32 2 0.04
ACGTcount: A:0.44, C:0.03, G:0.20, T:0.32
Consensus pattern (29 bp):
AGTTTAGGGATGAAATTAAAATGTTCAAA
Found at i:24184 original size:60 final size:60
Alignment explanation
Indices: 24106--24265 Score: 200
Period size: 60 Copynumber: 2.7 Consensus size: 60
24096 GGAATCTTCA
* *
24106 AAAAGTTT-GGGACCAATTTAGAATGAG-GATCATAGTTTAGGGATGAAATTAAAATGTTC
1 AAAAGTTTAGGGACCAATTTAAAATGAGAG-TCATAGTTTAGGGATGAAATTAAAATATTC
* * *
24165 AAAAGTTTAAGGACTAATTTAAAATGAGAGTCATAGTTTAGGGATGAAATTAAAATATTT
1 AAAAGTTTAGGGACCAATTTAAAATGAGAGTCATAGTTTAGGGATGAAATTAAAATATTC
* * * *
24225 AAAAATTTAGGGACCAATATT-AAATAAGATTTATAGTTTAG
1 AAAAGTTTAGGGACCAAT-TTAAAATGAGAGTCATAGTTTAG
24266 AGACATATGA
Statistics
Matches: 87, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
59 8 0.09
60 76 0.87
61 3 0.03
ACGTcount: A:0.43, C:0.05, G:0.19, T:0.33
Consensus pattern (60 bp):
AAAAGTTTAGGGACCAATTTAAAATGAGAGTCATAGTTTAGGGATGAAATTAAAATATTC
Found at i:24218 original size:31 final size:30
Alignment explanation
Indices: 24127--24220 Score: 95
Period size: 31 Copynumber: 3.1 Consensus size: 30
24117 ACCAATTTAG
24127 AATGAGGATCATAGTTTAGGGATGAAATTAA
1 AATGAGG-TCATAGTTTAGGGATGAAATTAA
* * * *
24158 AAT--GTTCAAAAGTTTAAGGACT-AATTTAA
1 AATGAGGTC-ATAGTTTAGGGA-TGAAATTAA
24187 AATGAGAGTCATAGTTTAGGGATGAAATTAA
1 AATGAG-GTCATAGTTTAGGGATGAAATTAA
24218 AAT
1 AAT
24221 ATTTAAAAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
28 2 0.04
29 20 0.41
30 2 0.04
31 23 0.47
32 2 0.04
ACGTcount: A:0.44, C:0.04, G:0.21, T:0.31
Consensus pattern (30 bp):
AATGAGGTCATAGTTTAGGGATGAAATTAA
Found at i:28536 original size:27 final size:27
Alignment explanation
Indices: 28498--28549 Score: 88
Period size: 27 Copynumber: 1.9 Consensus size: 27
28488 CACGCATTCA
28498 ATCAATCGTGACCTT-GAAATGTCTTGG
1 ATCAATCGTGA-CTTGGAAATGTCTTGG
28525 ATCAATCGTGACTTGGAAATGTCTT
1 ATCAATCGTGACTTGGAAATGTCTT
28550 AGATACAGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 3 0.12
27 21 0.88
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (27 bp):
ATCAATCGTGACTTGGAAATGTCTTGG
Found at i:31192 original size:14 final size:14
Alignment explanation
Indices: 31173--31202 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
31163 TTTTTGATAT
31173 AACAAAACAACAAC
1 AACAAAACAACAAC
31187 AACAAAACAACAAC
1 AACAAAACAACAAC
31201 AA
1 AA
31203 AACCCTATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.73, C:0.27, G:0.00, T:0.00
Consensus pattern (14 bp):
AACAAAACAACAAC
Found at i:31195 original size:11 final size:11
Alignment explanation
Indices: 31181--31205 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
31171 ATAACAAAAC
31181 AACAACAACAA
1 AACAACAACAA
31192 AACAACAACAA
1 AACAACAACAA
31203 AAC
1 AAC
31206 CCTATTCCCA
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:0.72, C:0.28, G:0.00, T:0.00
Consensus pattern (11 bp):
AACAACAACAA
Found at i:34134 original size:20 final size:20
Alignment explanation
Indices: 34096--34155 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 20
34086 CAGAACCCCA
*
34096 GGGGGGTATCGATTCCC-CTGT
1 GGGGGG-ATCGATTCCCTC-AT
*
34117 GGGGGGAATCGGTTCCCTCAT
1 GGGGGG-ATCGATTCCCTCAT
34138 GGGGGGATCGATTCCCTC
1 GGGGGGATCGATTCCCTC
34156 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 11 0.32
21 22 0.65
22 1 0.03
ACGTcount: A:0.12, C:0.25, G:0.38, T:0.25
Consensus pattern (20 bp):
GGGGGGATCGATTCCCTCAT
Found at i:40311 original size:24 final size:23
Alignment explanation
Indices: 40265--40319 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
40255 CAACCACCTA
*
40265 TTAGAAAATGAATTTTTTAAATT
1 TTAGAAAATGAATTTTATAAATT
40288 TTAGAAAATG-ATATTTATATAATT
1 TTAGAAAATGAAT-TTTATA-AATT
*
40312 TTAAAAAA
1 TTAGAAAA
40320 GAAAATATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 2 0.07
23 15 0.54
24 11 0.39
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (23 bp):
TTAGAAAATGAATTTTATAAATT
Found at i:42439 original size:16 final size:16
Alignment explanation
Indices: 42418--42450 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
42408 TAATAAATAA
42418 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
42434 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
42450 A
1 A
42451 AATTTTTTTT
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:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:43461 original size:14 final size:14
Alignment explanation
Indices: 43444--43472 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
43434 ATAAATGACT
43444 GAACATAACCGAAC
1 GAACATAACCGAAC
43458 GAACATAACCGAAC
1 GAACATAACCGAAC
43472 G
1 G
43473 TTCATGAACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.28, G:0.17, T:0.07
Consensus pattern (14 bp):
GAACATAACCGAAC
Found at i:46077 original size:15 final size:14
Alignment explanation
Indices: 46050--46082 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
46040 ACATAATACA
46050 AGTT-AAAAAACAT
1 AGTTAAAAAAACAT
46063 AGTTAAAAAAGACAT
1 AGTTAAAAAA-ACAT
46078 AGTTA
1 AGTTA
46083 CAATACAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 5 0.28
15 9 0.50
ACGTcount: A:0.58, C:0.06, G:0.12, T:0.24
Consensus pattern (14 bp):
AGTTAAAAAAACAT
Found at i:46115 original size:22 final size:23
Alignment explanation
Indices: 46067--46115 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
46057 AAACATAGTT
46067 AAAAAAGACATAGTTACAATACA
1 AAAAAAGACATAGTTACAATACA
*
46090 AAAAAATACATAGTTA-AAGTACA
1 AAAAAAGACATAGTTACAA-TACA
46113 AAA
1 AAA
46116 TATTTTATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 2 0.08
23 22 0.92
ACGTcount: A:0.63, C:0.10, G:0.08, T:0.18
Consensus pattern (23 bp):
AAAAAAGACATAGTTACAATACA
Found at i:49728 original size:19 final size:21
Alignment explanation
Indices: 49704--49756 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
49694 AAATCACAAC
49704 GCGATTTT-AGTTTT-GCGTT
1 GCGATTTTAAGTTTTCGCGTT
*
49723 GCGATTTTCA-TTTTCGCGTT
1 GCGATTTTAAGTTTTCGCGTT
*
49743 ACGATTTTAAGTTT
1 GCGATTTTAAGTTT
49757 CAGAAACTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 12 0.41
20 14 0.48
21 3 0.10
ACGTcount: A:0.15, C:0.13, G:0.21, T:0.51
Consensus pattern (21 bp):
GCGATTTTAAGTTTTCGCGTT
Found at i:51411 original size:21 final size:21
Alignment explanation
Indices: 51356--51416 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
51346 GCCCGATTCA
*
51356 CCTGTCATCATTTAAGAGGCC
1 CCTGTCATCATTCAAGAGGCC
* * *
51377 TCT-CCTATCGTTCAAGAGGCC
1 CCTGTC-ATCATTCAAGAGGCC
51398 CCTGTCATCATTCAAGAGG
1 CCTGTCATCATTCAAGAGG
51417 TCCTTCCCAC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 1 0.03
21 29 0.94
22 1 0.03
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.28
Consensus pattern (21 bp):
CCTGTCATCATTCAAGAGGCC
Found at i:51431 original size:42 final size:42
Alignment explanation
Indices: 51356--51436 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
51346 GCCCGATTCA
* * *
51356 CCTGTCATCATTTAAGAGGCCTCTCCTATCGTTCAAGAGGCC
1 CCTGTCATCATTCAAGAGGCCTCTCCCACCGTTCAAGAGGCC
*
51398 CCTGTCATCATTCAAGAGGTCCT-TCCCACCGTTCGAGAG
1 CCTGTCATCATTCAAGAGG-CCTCTCCCACCGTTCAAGAG
51437 CCCGATTCAC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 31 0.91
43 3 0.09
ACGTcount: A:0.21, C:0.32, G:0.20, T:0.27
Consensus pattern (42 bp):
CCTGTCATCATTCAAGAGGCCTCTCCCACCGTTCAAGAGGCC
Found at i:52683 original size:13 final size:14
Alignment explanation
Indices: 52658--52690 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
52648 AAATTAATGT
52658 ATTTGTAAAAGTTG
1 ATTTGTAAAAGTTG
52672 ATTTGT-AAAGTTG
1 ATTTGTAAAAGTTG
52685 ATTTGT
1 ATTTGT
52691 CTAATTGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.30, C:0.00, G:0.21, T:0.48
Consensus pattern (14 bp):
ATTTGTAAAAGTTG
Found at i:52747 original size:64 final size:65
Alignment explanation
Indices: 52669--52821 Score: 213
Period size: 65 Copynumber: 2.4 Consensus size: 65
52659 TTTGTAAAAG
*
52669 TTGATTTGT-AAAGTTGATTTGTCT-AATTGATGAGGAAATAAGAATTA-TTTTTTGCTTGTTTA
1 TTGATTTGTAAAAGTTGATTTAT-TGAATTGATGAGGAAATAAGAATTATTTTTTTGCTTGTTTA
52731 A
65 A
* *** *
52732 TTGATTTGTAAAAGTTGATTTATTGAATTGATGAGTAAATAATTCTTATTTTTTTGCTTGTTTGA
1 TTGATTTGTAAAAGTTGATTTATTGAATTGATGAGGAAATAAGAATTATTTTTTTGCTTGTTTAA
*
52797 TTGATTTATAAAAGTTGATTTATTG
1 TTGATTTGTAAAAGTTGATTTATTG
52822 TTTTAAATTT
Statistics
Matches: 80, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
63 10 0.12
64 31 0.39
65 39 0.49
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (65 bp):
TTGATTTGTAAAAGTTGATTTATTGAATTGATGAGGAAATAAGAATTATTTTTTTGCTTGTTTAA
Found at i:52960 original size:20 final size:20
Alignment explanation
Indices: 52935--52972 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
52925 TTGCGATGGT
52935 TGCGAAAGTCAAATTCGCAA
1 TGCGAAAGTCAAATTCGCAA
52955 TGCGAAAGTCAAATTCGC
1 TGCGAAAGTCAAATTCGC
52973 GTTGTGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (20 bp):
TGCGAAAGTCAAATTCGCAA
Found at i:55549 original size:24 final size:24
Alignment explanation
Indices: 55498--55549 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
55488 ATCTGAGTAT
* ** *
55498 TGACTAAGATCAAATTCCGGGTAT
1 TGACCAAGATCAAATTCCGAATAC
*
55522 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAATTCCGAATAC
55546 TGAC
1 TGAC
55550 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (24 bp):
TGACCAAGATCAAATTCCGAATAC
Found at i:55685 original size:12 final size:12
Alignment explanation
Indices: 55668--55696 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
55658 GGGTTTTAAG
55668 ATTGTGTTTGAT
1 ATTGTGTTTGAT
55680 ATTGTGTTTGAT
1 ATTGTGTTTGAT
55692 ATTGT
1 ATTGT
55697 AAATGTGGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.24, T:0.59
Consensus pattern (12 bp):
ATTGTGTTTGAT
Found at i:56546 original size:20 final size:19
Alignment explanation
Indices: 56495--56546 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 19
56485 TACGAATTTG
56495 AAAATCGAGTTGCGAAAAC
1 AAAATCGAGTTGCGAAAAC
*
56514 AAAATTCGCGTTGCGAAAAC
1 AAAA-TCGAGTTGCGAAAAC
56534 AGAAATCGAGTTG
1 A-AAATCGAGTTG
56547 TGAATTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 4 0.14
20 22 0.76
21 3 0.10
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.19
Consensus pattern (19 bp):
AAAATCGAGTTGCGAAAAC
Found at i:56595 original size:20 final size:20
Alignment explanation
Indices: 56570--56635 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 20
56560 CAGTGTTACG
56570 AATTTGGAAATCGCGTTGCA
1 AATTTGGAAATCGCGTTGCA
*
56590 AATTTGGAAA-CTGAGTTGCGA
1 AATTTGGAAATC-GCGTTGC-A
** *
56611 AA-TTGGAGTTCGCGTTGCG
1 AATTTGGAAATCGCGTTGCA
56630 AATTTG
1 AATTTG
56636 TTGGTCATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
19 3 0.08
20 30 0.81
21 4 0.11
ACGTcount: A:0.27, C:0.12, G:0.29, T:0.32
Consensus pattern (20 bp):
AATTTGGAAATCGCGTTGCA
Found at i:60986 original size:25 final size:25
Alignment explanation
Indices: 60958--61116 Score: 93
Period size: 25 Copynumber: 6.5 Consensus size: 25
60948 TTACAAATAT
*
60958 CAATTACTAACTTAATTAATATTAC
1 CAATTAATAACTTAATTAATATTAC
*
60983 CAATTAAT-A-TTCACTTAATATTTAC
1 CAATTAATAACTT-AATTAATA-TTAC
*
61008 C-ATTAATAACATAATTAATATT-C
1 CAATTAATAACTTAATTAATATTAC
* * * *
61031 ACAATTAACAACATCATTAATAATA-
1 -CAATTAATAACTTAATTAATATTAC
* **
61056 TAA-TAATAACAAAATTAATCA--AC
1 CAATTAATAACTTAATTAAT-ATTAC
* *
61079 ATAATTAATAACGTAATTAATATTTA-
1 -CAATTAATAACTTAATTAATA-TTAC
61105 CAATTAATAACT
1 CAATTAATAACT
61117 ATTGACCATT
Statistics
Matches: 105, Mismatches: 15, Indels: 28
0.71 0.10 0.19
Matches are distributed among these distances:
22 1 0.01
23 16 0.15
24 24 0.23
25 62 0.59
26 1 0.01
27 1 0.01
ACGTcount: A:0.50, C:0.13, G:0.01, T:0.36
Consensus pattern (25 bp):
CAATTAATAACTTAATTAATATTAC
Found at i:61026 original size:12 final size:12
Alignment explanation
Indices: 61009--61100 Score: 96
Period size: 12 Copynumber: 7.6 Consensus size: 12
60999 AATATTTACC
61009 ATTAATAACATA
1 ATTAATAACATA
* *
61021 ATTAATATTCACA
1 ATTAATA-ACATA
* *
61034 ATTAACAACATC
1 ATTAATAACATA
*
61046 ATTAATAATATA
1 ATTAATAACATA
*
61058 A-TAATAACAAA
1 ATTAATAACATA
61069 ATTAATCAACATA
1 ATTAAT-AACATA
*
61082 ATTAATAACGTA
1 ATTAATAACATA
61094 ATTAATA
1 ATTAATA
61101 TTTACAATTA
Statistics
Matches: 64, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
11 9 0.14
12 35 0.55
13 20 0.31
ACGTcount: A:0.55, C:0.11, G:0.01, T:0.33
Consensus pattern (12 bp):
ATTAATAACATA
Found at i:61038 original size:13 final size:13
Alignment explanation
Indices: 60971--61038 Score: 63
Period size: 13 Copynumber: 5.5 Consensus size: 13
60961 TTACTAACTT
60971 AATTAATATT-ACC
1 AATTAATATTCA-C
60984 AATTAATATTCAC
1 AATTAATATTCAC
*
60997 --TTAATATTTAC
1 AATTAATATTCAC
* * *
61008 CATTAATA-ACAT
1 AATTAATATTCAC
61020 AATTAATATTCAC
1 AATTAATATTCAC
61033 AATTAA
1 AATTAA
61039 CAACATCATT
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
11 10 0.23
12 8 0.18
13 25 0.57
14 1 0.02
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (13 bp):
AATTAATATTCAC
Found at i:62642 original size:15 final size:15
Alignment explanation
Indices: 62624--62658 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
62614 CGAGGGTATT
62624 GTAGTCCTTCGGAAC
1 GTAGTCCTTCGGAAC
*
62639 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGAAC
62654 GTAGT
1 GTAGT
62659 GGTCTTACGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.17, C:0.23, G:0.31, T:0.29
Consensus pattern (15 bp):
GTAGTCCTTCGGAAC
Found at i:68868 original size:22 final size:22
Alignment explanation
Indices: 68842--68883 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
68832 AGTATGTCCA
*
68842 GGGGGTATCGATTCCCCCCTGG
1 GGGGGTATCGAATCCCCCCTGG
68864 GGGGGTATCGAATCCCCCCT
1 GGGGGTATCGAATCCCCCCT
68884 AAAGGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.12, C:0.33, G:0.33, T:0.21
Consensus pattern (22 bp):
GGGGGTATCGAATCCCCCCTGG
Found at i:69542 original size:15 final size:15
Alignment explanation
Indices: 69524--69558 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
69514 CGAGGGTATT
69524 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
69539 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
*
69554 ATAGT
1 GTAGT
69559 GGTCCTACGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.17, C:0.23, G:0.31, T:0.29
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:72010 original size:1 final size:1
Alignment explanation
Indices: 72006--72081 Score: 53
Period size: 1 Copynumber: 76.0 Consensus size: 1
71996 TTTTCATTTC
* * * ** * ** * *
72006 TTTTTTCTTCTTTTTTCTTTTTTTTTTTTTTTTTTTTTCATTTTTTCTTCATTTTTTATTTTCTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
72071 TTTTCTTTTTT
1 TTTTTTTTTTT
72082 CATGTATAAT
Statistics
Matches: 55, Mismatches: 20, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.04, C:0.11, G:0.00, T:0.86
Consensus pattern (1 bp):
T
Found at i:72014 original size:7 final size:7
Alignment explanation
Indices: 72002--72082 Score: 73
Period size: 7 Copynumber: 11.6 Consensus size: 7
71992 CCCCTTTTCA
72002 TTTCTTT
1 TTTCTTT
72009 TTTCTTCT
1 TTTCTT-T
*
72017 TTT-TTC
1 TTTCTTT
72023 TTT-TTT
1 TTTCTTT
72029 TTT-TTT
1 TTTCTTT
72035 TTT-TTT
1 TTTCTTT
72041 TTTCATTT
1 TTTC-TTT
72049 TTTCTTCAT
1 TTTCTT--T
72058 TTT-TTAT
1 TTTCTT-T
72065 TTTCTTT
1 TTTCTTT
72072 TTTCTTT
1 TTTCTTT
72079 TTTC
1 TTTC
72083 ATGTATAATA
Statistics
Matches: 66, Mismatches: 2, Indels: 12
0.82 0.03 0.15
Matches are distributed among these distances:
6 20 0.30
7 27 0.41
8 15 0.23
9 4 0.06
ACGTcount: A:0.04, C:0.12, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTCTTT
Found at i:72020 original size:11 final size:11
Alignment explanation
Indices: 72006--72074 Score: 65
Period size: 10 Copynumber: 6.5 Consensus size: 11
71996 TTTTCATTTC
72006 TTTTTTCTTC-
1 TTTTTTCTTCT
72016 TTTTTTCTT-T
1 TTTTTTCTTCT
72026 TTTTTT-TT-T
1 TTTTTTCTTCT
* *
72035 TTTTTTTTTCA
1 TTTTTTCTTCT
72046 TTTTTTCTTCAT
1 TTTTTTCTTC-T
*
72058 TTTTTATTTTCT
1 TTTTT-TCTTCT
72070 TTTTT
1 TTTTT
72075 CTTTTTTCAT
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
9 9 0.18
10 17 0.34
11 9 0.18
12 11 0.22
13 4 0.08
ACGTcount: A:0.04, C:0.10, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTTTCTTCT
Found at i:72050 original size:30 final size:30
Alignment explanation
Indices: 71996--72082 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 30
71986 TTGAACCCCC
* *
71996 TTTTCATTTCTTTTTTCTTCTTTTTTCTT-TT
1 TTTTTATTT-TTTTTT-TTCTTTTTTCTTCAT
*
72027 TTTTTTTTTTTTTTTTTCATTTTTTCTTCAT
1 TTTTTATTTTTTTTTTTC-TTTTTTCTTCAT
*
72058 TTTTTATTTTCTTTTTTCTTTTTTC
1 TTTTTATTTTTTTTTTTCTTTTTTC
72083 ATGTATAATA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
29 3 0.06
30 22 0.45
31 24 0.49
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.83
Consensus pattern (30 bp):
TTTTTATTTTTTTTTTTCTTTTTTCTTCAT
Found at i:72055 original size:40 final size:40
Alignment explanation
Indices: 72002--72081 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 40
71992 CCCCTTTTCA
* * *
72002 TTTCTTTTTTCTTC-TTTTTTCTTTTTTTTTTTTTTTTTT
1 TTTCTTTTTTCTTCATTTTTTATTTTCTTTTTTCTTTTTT
72041 TTTCATTTTTTCTTCATTTTTTATTTTCTTTTTTCTTTTTT
1 TTTC-TTTTTTCTTCATTTTTTATTTTCTTTTTTCTTTTTT
72082 CATGTATAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 4 0.11
40 10 0.28
41 22 0.61
ACGTcount: A:0.04, C:0.11, G:0.00, T:0.85
Consensus pattern (40 bp):
TTTCTTTTTTCTTCATTTTTTATTTTCTTTTTTCTTTTTT
Found at i:75546 original size:3 final size:3
Alignment explanation
Indices: 75538--75576 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
75528 TATTTACTAA
75538 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
75577 GCAATACAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:78077 original size:16 final size:16
Alignment explanation
Indices: 78030--78068 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
78020 TATATATATA
*
78030 CATGTACGTACGTACG
1 CATGTACGTACGTATG
78046 CATGTACGTACGTATG
1 CATGTACGTACGTATG
78062 CATGTAC
1 CATGTAC
78069 ATATGTATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (16 bp):
CATGTACGTACGTATG
Found at i:78125 original size:4 final size:4
Alignment explanation
Indices: 78118--78235 Score: 55
Period size: 4 Copynumber: 30.5 Consensus size: 4
78108 TGATACATAC
* * * * * * * *
78118 GTAT GTAT ATAT GTAG GTGT GTAG GTGT GTAG GTGT GTAC GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* * * * * *
78166 ATAT ATAT GTAT GTAT G--T GTGT GTAT GTCT GTAT GTGT GTGT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* * *
78212 ATAT G--T GTGT GTAT GTGT GTAT GT
1 GTAT GTAT GTAT GTAT GTAT GTAT GT
78236 GTGTGTGTGT
Statistics
Matches: 82, Mismatches: 28, Indels: 8
0.69 0.24 0.07
Matches are distributed among these distances:
2 4 0.05
4 78 0.95
ACGTcount: A:0.19, C:0.02, G:0.32, T:0.47
Consensus pattern (4 bp):
GTAT
Found at i:78186 original size:2 final size:2
Alignment explanation
Indices: 78181--78760 Score: 232
Period size: 2 Copynumber: 290.0 Consensus size: 2
78171 TATGTATGTA
* * * * * *
78181 TG TG TG TG TA TG TC TG TA TG TG TG TG TG TA TA TA TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
* * * * * * *
78223 TA TG TG TG TA TG TG TG TG TG TG TG TG AG TG TG CG CG CG CG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
* * * * *
78265 AG TG CG TG CG TG CG TG CG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
* * * * *
78307 T- TG TG TG TG TG TG TG CG TG CG TG CG TG CG TG TG TG TG CG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
* * * * * * * ** *
78348 CG TG TA TG TG TG TG TG TA TG TG TC TG TG CG CG TG TA CA TG CG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
* * * * * * * * * * * *
78390 CG GG TG CG GG TG CG TG TG CG GG TG CG TG GG TG CG GG TG CG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
* *
78432 TG TG TG TG TG TG CG TG TG TG TG -G TG TG TG TG CG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
* * * * * * *
78473 CG TG TC TG CG TG CG TG TG CG TG TC TG TG TG TG TG TG TG CG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
* * * *
78515 CG TG CG TG TG TG TG CG TG TG TG T- TG TG TG TC TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
* * * * * * * * *
78556 TG CG TG CG TG CG TG CG CG CG CG TG TG CG TG TG TG TG CG -G TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
* * * * * * * * *
78597 TG CG TG TG TG GG TG AG TG GG TG TG TG TG GG TG TG CG CG CG CG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
* * * * * * * * *
78639 CG TG TG TG CG CG CG CG CG CG TG TG CG CG TG TG TG CTCG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG -T-G TG TG TG
* * * * *
78683 TG AG TG CG CG TG TG TG CTCG TG TG TG TG CG TG TG TG TG TG CG TG
1 TG TG TG TG TG TG TG TG -T-G TG TG TG TG TG TG TG TG TG TG TG TG
* * * * * *
78727 TG CG TG TG CG CG TG CG TG TG CG TG CG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
78761 CGCGCGCGCG
Statistics
Matches: 429, Mismatches: 141, Indels: 16
0.73 0.24 0.03
Matches are distributed among these distances:
1 4 0.01
2 419 0.98
3 4 0.01
4 2 0.00
ACGTcount: A:0.03, C:0.13, G:0.48, T:0.36
Consensus pattern (2 bp):
TG
Found at i:78192 original size:14 final size:14
Alignment explanation
Indices: 78173--78245 Score: 60
Period size: 14 Copynumber: 5.2 Consensus size: 14
78163 TATATATATA
78173 TGTATGTATGTGTG
1 TGTATGTATGTGTG
*
78187 TGTATGTCTGTATGTG
1 TGTATGTATG--TGTG
* * *
78203 TGTGTGTATATATG
1 TGTATGTATGTGTG
*
78217 TGTGTGTA--TGTG
1 TGTATGTATGTGTG
*
78229 TGTATGTGTGTGTG
1 TGTATGTATGTGTG
78243 TGT
1 TGT
78246 GTGAGTGTGC
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
12 9 0.19
14 27 0.57
16 11 0.23
ACGTcount: A:0.12, C:0.01, G:0.36, T:0.51
Consensus pattern (14 bp):
TGTATGTATGTGTG
Found at i:78198 original size:18 final size:18
Alignment explanation
Indices: 78171--78241 Score: 101
Period size: 18 Copynumber: 4.1 Consensus size: 18
78161 TGTATATATA
78171 TATGTATGTATGTGTGTG
1 TATGTATGTATGTGTGTG
*
78189 TATGTCTGTATGTGTGTG
1 TATGTATGTATGTGTGTG
*
78207 --TGTATATATGTGTGTG
1 TATGTATGTATGTGTGTG
*
78223 TATGTGTGTATGTGTGTG
1 TATGTATGTATGTGTGTG
78241 T
1 T
78242 GTGTGTGAGT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
16 14 0.30
18 32 0.70
ACGTcount: A:0.14, C:0.01, G:0.34, T:0.51
Consensus pattern (18 bp):
TATGTATGTATGTGTGTG
Found at i:78199 original size:34 final size:34
Alignment explanation
Indices: 78150--78233 Score: 96
Period size: 34 Copynumber: 2.5 Consensus size: 34
78140 AGGTGTGTAG
* *
78150 GTGTGTACGTATGTATATATATATGTATGTATGT
1 GTGTGTATGTATGTATATATATATGTATATATGT
* * * * *
78184 GTGTGTATGTCTGTATGTGTGTGTGTATATATGT
1 GTGTGTATGTATGTATATATATATGTATATATGT
*
78218 GTGTGTATGTGTGTAT
1 GTGTGTATGTATGTAT
78234 GTGTGTGTGT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.19, C:0.02, G:0.30, T:0.49
Consensus pattern (34 bp):
GTGTGTATGTATGTATATATATATGTATATATGT
Found at i:78200 original size:22 final size:22
Alignment explanation
Indices: 78165--78233 Score: 84
Period size: 22 Copynumber: 3.1 Consensus size: 22
78155 TACGTATGTA
*
78165 TATATATATGTATGTATGTGTG
1 TATATATCTGTATGTATGTGTG
* * *
78187 TGTATGTCTGTATGTGTGTGTG
1 TATATATCTGTATGTATGTGTG
* *
78209 TATATATGTGTGTGTATGTGTG
1 TATATATCTGTATGTATGTGTG
78231 TAT
1 TAT
78234 GTGTGTGTGT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.19, C:0.01, G:0.29, T:0.51
Consensus pattern (22 bp):
TATATATCTGTATGTATGTGTG
Found at i:78234 original size:34 final size:34
Alignment explanation
Indices: 78173--78243 Score: 124
Period size: 34 Copynumber: 2.1 Consensus size: 34
78163 TATATATATA
*
78173 TGTATGTATGTGTGTGTATGTCTGTATGTGTGTG
1 TGTATATATGTGTGTGTATGTCTGTATGTGTGTG
*
78207 TGTATATATGTGTGTGTATGTGTGTATGTGTGTG
1 TGTATATATGTGTGTGTATGTCTGTATGTGTGTG
78241 TGT
1 TGT
78244 GTGTGAGTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.13, C:0.01, G:0.35, T:0.51
Consensus pattern (34 bp):
TGTATATATGTGTGTGTATGTCTGTATGTGTGTG
Found at i:78236 original size:8 final size:8
Alignment explanation
Indices: 78129--78247 Score: 76
Period size: 8 Copynumber: 14.4 Consensus size: 8
78119 TATGTATATA
*
78129 TGTAGGTG
1 TGTATGTG
*
78137 TGTAGGTG
1 TGTATGTG
*
78145 TGTAGGTG
1 TGTATGTG
* *
78153 TGTACGTA
1 TGTATGTG
* *
78161 TGTATATA
1 TGTATGTG
* *
78169 TATATGTA
1 TGTATGTG
78177 TGTATGTGTG
1 TGTA--TGTG
*
78187 TGTATGTC
1 TGTATGTG
78195 TGTATGTG
1 TGTATGTG
* *
78203 TGTGTGTA
1 TGTATGTG
*
78211 TATATGTGTG
1 TGTA--TGTG
78221 TGTATGTG
1 TGTATGTG
78229 TGTATGTG
1 TGTATGTG
*
78237 TGTGTGTG
1 TGTATGTG
78245 TGT
1 TGT
78248 GAGTGTGCGC
Statistics
Matches: 90, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
8 77 0.86
10 13 0.14
ACGTcount: A:0.16, C:0.02, G:0.35, T:0.47
Consensus pattern (8 bp):
TGTATGTG
Found at i:78791 original size:28 final size:28
Alignment explanation
Indices: 78720--78791 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 28
78710 GCGTGTGTGT
* * * *
78720 GTGCGTGTGCGTGTGCGCGTGCGTGTGC
1 GTGCGTGTGTGTGCGCGCGCGCGCGTGC
78748 GTGCGTGTGTGTGCGCGCGCGCGCGTGC
1 GTGCGTGTGTGTGCGCGCGCGCGCGTGC
78776 GTGCGTGTGTGTGCGC
1 GTGCGTGTGTGTGCGC
78792 TTGTGTTATT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.00, C:0.24, G:0.50, T:0.26
Consensus pattern (28 bp):
GTGCGTGTGTGTGCGCGCGCGCGCGTGC
Found at i:80413 original size:25 final size:25
Alignment explanation
Indices: 80385--80463 Score: 122
Period size: 25 Copynumber: 3.2 Consensus size: 25
80375 ATATTCACTT
* *
80385 AATATTCACCATTAATAACATAATA
1 AATATTCACAATTAACAACATAATA
80410 AATATTCACAATTAACAACATAATA
1 AATATTCACAATTAACAACATAATA
* *
80435 AATATTCACAATTAACAACACAATT
1 AATATTCACAATTAACAACATAATA
80460 AATA
1 AATA
80464 ATATAATTAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 50 1.00
ACGTcount: A:0.54, C:0.16, G:0.00, T:0.29
Consensus pattern (25 bp):
AATATTCACAATTAACAACATAATA
Found at i:80458 original size:12 final size:12
Alignment explanation
Indices: 80395--80539 Score: 137
Period size: 12 Copynumber: 11.8 Consensus size: 12
80385 AATATTCACC
*
80395 ATTAATAACATA
1 ATTAATAACACA
* *
80407 ATAAATATTCACA
1 ATTAATA-ACACA
* *
80420 ATTAACAACATA
1 ATTAATAACACA
* *
80432 ATAAATATTCACA
1 ATTAATA-ACACA
*
80445 ATTAACAACACA
1 ATTAATAACACA
* *
80457 ATTAATAATATA
1 ATTAATAACACA
80469 ATTAATAACACA
1 ATTAATAACACA
*
80481 ATTAATAACCCA
1 ATTAATAACACA
80493 ATTAATAACACA
1 ATTAATAACACA
*
80505 ATTAATCAACATA
1 ATTAAT-AACACA
*
80518 ATTAATATTCACA
1 ATTAATA-ACACA
80531 ATTAATAAC
1 ATTAATAAC
80540 TATTGATCAT
Statistics
Matches: 104, Mismatches: 25, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
12 67 0.64
13 37 0.36
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (12 bp):
ATTAATAACACA
Found at i:84932 original size:18 final size:15
Alignment explanation
Indices: 84892--84930 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
84882 ACCGAAAGCT
84892 GAGAAGAAGCCAGCG
1 GAGAAGAAGCCAGCG
*
84907 GAGAAGAAGCCAGCT
1 GAGAAGAAGCCAGCG
*
84922 GAGGAGAAG
1 GAGAAGAAG
84931 AAAACCGTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.41, C:0.15, G:0.41, T:0.03
Consensus pattern (15 bp):
GAGAAGAAGCCAGCG
Found at i:86134 original size:67 final size:67
Alignment explanation
Indices: 86024--86171 Score: 242
Period size: 67 Copynumber: 2.2 Consensus size: 67
86014 TTTAATGTAT
* *
86024 ACATATTAAAAACAAAGTAACAATTTAGAAATTTATTAAAGTAACAATCTACAAATACATCAAAC
1 ACATATTAAAAACAAAGTAACAATTTAAAAATTTATCAAAGTAACAATCTACAAATACATCAAAC
86089 TA
66 TA
* * * *
86091 ATATATTATAAGCAAAGTAATAATTTAAAAATTTATCAAAGTAACAATCTACAAATACATCAAAC
1 ACATATTAAAAACAAAGTAACAATTTAAAAATTTATCAAAGTAACAATCTACAAATACATCAAAC
86156 TA
66 TA
86158 ACATATTAAAAACA
1 ACATATTAAAAACA
86172 TTTTTTTTTA
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
67 72 1.00
ACGTcount: A:0.55, C:0.13, G:0.04, T:0.28
Consensus pattern (67 bp):
ACATATTAAAAACAAAGTAACAATTTAAAAATTTATCAAAGTAACAATCTACAAATACATCAAAC
TA
Found at i:86146 original size:24 final size:24
Alignment explanation
Indices: 86103--86169 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
86093 ATATTATAAG
* * **
86103 CAAAGTAATAATTTAAAAATTTAT
1 CAAAGTAACAATCTAAAAATACAT
*
86127 CAAAGTAACAATCTACAAATACAT
1 CAAAGTAACAATCTAAAAATACAT
*
86151 CAAACTAACATAT-TAAAAA
1 CAAAGTAACA-ATCTAAAAA
86170 CATTTTTTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
24 33 0.94
25 2 0.06
ACGTcount: A:0.57, C:0.13, G:0.03, T:0.27
Consensus pattern (24 bp):
CAAAGTAACAATCTAAAAATACAT
Found at i:94284 original size:26 final size:27
Alignment explanation
Indices: 94236--94307 Score: 114
Period size: 27 Copynumber: 2.8 Consensus size: 27
94226 ATTTTTTAAT
94236 ATTTTAATTTTAAAAATAATAAATAAA
1 ATTTTAATTTTAAAAATAATAAATAAA
94263 ATTTTAATTTTAAAAAT-ATAAATAAA
1 ATTTTAATTTTAAAAATAATAAATAAA
*
94289 ATGTTAA-TTTAAAAA-AATA
1 ATTTTAATTTTAAAAATAATA
94308 TTTATTATTA
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
25 11 0.26
26 15 0.35
27 17 0.40
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (27 bp):
ATTTTAATTTTAAAAATAATAAATAAA
Found at i:94678 original size:28 final size:25
Alignment explanation
Indices: 94646--94704 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 25
94636 AAGATAATTG
*
94646 ATTTTTTATTTGACATGAATAAGTCAAA
1 ATTTTTTA-TT-AAATGAATAAGTC-AA
*
94674 ATTTTTTATTAAATGGATAAGTCAA
1 ATTTTTTATTAAATGAATAAGTCAA
94699 ATTTTT
1 ATTTTT
94705 ATCTATATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 8 0.28
26 11 0.38
27 2 0.07
28 8 0.28
ACGTcount: A:0.37, C:0.05, G:0.10, T:0.47
Consensus pattern (25 bp):
ATTTTTTATTAAATGAATAAGTCAA
Found at i:96450 original size:29 final size:31
Alignment explanation
Indices: 96400--96462 Score: 103
Period size: 30 Copynumber: 2.1 Consensus size: 31
96390 TTTAGATTTG
*
96400 GTCCCTTAACTTTAGACTTTCT-ATATTTTA
1 GTCCCTTAACTTTAGACTTTCTCACATTTTA
96430 GTCCCTTAACTTTAGA-TTTCTCACATTTTA
1 GTCCCTTAACTTTAGACTTTCTCACATTTTA
96460 GTC
1 GTC
96463 ATTAATGTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 5 0.16
30 26 0.84
ACGTcount: A:0.22, C:0.22, G:0.08, T:0.48
Consensus pattern (31 bp):
GTCCCTTAACTTTAGACTTTCTCACATTTTA
Found at i:98292 original size:27 final size:28
Alignment explanation
Indices: 98234--98298 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 28
98224 TTAACTTAGA
* *
98234 GGAGAAGAAG-AAAGAAGATGAAGATTT
1 GGAGAAGAAGAAAAGAAGAGGAAGAGTT
98261 GGAGAAGAAGAAAAGACA-AGGAAGAGTT
1 GGAGAAGAAGAAAAGA-AGAGGAAGAGTT
*
98289 -GAGAAAAAGA
1 GGAGAAGAAGA
98299 GAGAGTATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 19 0.58
28 13 0.39
29 1 0.03
ACGTcount: A:0.55, C:0.02, G:0.34, T:0.09
Consensus pattern (28 bp):
GGAGAAGAAGAAAAGAAGAGGAAGAGTT
Found at i:110260 original size:174 final size:175
Alignment explanation
Indices: 109971--110431 Score: 646
Period size: 174 Copynumber: 2.6 Consensus size: 175
109961 GATCCAAATT
* * **
109971 AAAAATGTATCGATTCACAACGATAT-ACAAGTAAAACTATGACAAAACTGGTATTGAAATGATA
1 AAAAATGTATCGATCCACAACGATATAACAAGTAAAA-TATGATAAAACTGGTATCAAAATGATA
* * * *
110035 AACCGGTAAAGCGGTACCGAATATATTTAAAGTGTC-AGTACTTTAATATAAGGATCGACACTTC
65 AACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGA-TACTTTAATATAAGGATCGACACTTC
*
110099 GTTAATTTAAAAG-AGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
129 GTGAATTTAAAAGAAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
* * *
110145 AAAAATATATCGATCCACAACGATATAACATGTAAAATATGATAAAACCGGTATCAAAATGATGA
1 AAAAATGTATCGATCCACAACGATATAACAAGTAAAATATGATAAAACTGGTATCAAAATGAT-A
* * *
110210 AACCGGTAAAACGCTACTGGATATATTGCAAGTGTCGATACTTT-ATATAAGGATCGACACTTTG
65 AACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTCG
110274 TGAATTTAAAAGATAAACAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
130 TGAATTTAAAAG----A-AGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
*
110325 AAAAATGTATCGATCCACAACGATATAACAAGTAAAA-AT-ATAAAAACTGGTATGAAAATGATA
1 AAAAATGTATCGATCCACAACGATATAACAAGTAAAATATGAT-AAAACTGGTATCAAAATGATA
*
110388 AACCGGTAAAACGCTACCGGCTATATTGAAAGTGTCGATACTTT
65 AACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTT
110432 CGTAAGTACG
Statistics
Matches: 255, Mismatches: 22, Indels: 16
0.87 0.08 0.05
Matches are distributed among these distances:
174 76 0.30
175 46 0.18
176 1 0.00
178 44 0.17
179 20 0.08
180 68 0.27
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (175 bp):
AAAAATGTATCGATCCACAACGATATAACAAGTAAAATATGATAAAACTGGTATCAAAATGATAA
ACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTCGT
GAATTTAAAAGAAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
Done.