Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008805.1 Hibiscus syriacus cultivar Beakdansim tig00111958_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: 49055
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:4318 original size:19 final size:20
Alignment explanation
Indices: 4288--4331 Score: 81
Period size: 19 Copynumber: 2.2 Consensus size: 20
4278 CATGGTATCA
4288 ATACTCCCATCACGGTACCG
1 ATACTCCCATCACGGTACCG
4308 ATACT-CCATCACGGTACCG
1 ATACTCCCATCACGGTACCG
4327 ATACT
1 ATACT
4332 ATTTTTACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.27, C:0.36, G:0.14, T:0.23
Consensus pattern (20 bp):
ATACTCCCATCACGGTACCG
Found at i:4401 original size:19 final size:20
Alignment explanation
Indices: 4352--4403 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
4342 TCTGTTAACA
*
4352 ATGGTATCGATACCATCCTC
1 ATGGTATCGATACCACCCTC
* *
4372 ATAGTAACGATACC-CCCTC
1 ATGGTATCGATACCACCCTC
*
4391 TTGGTATCGATAC
1 ATGGTATCGATAC
4404 TGCTTACATA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.29
Consensus pattern (20 bp):
ATGGTATCGATACCACCCTC
Found at i:6477 original size:18 final size:19
Alignment explanation
Indices: 6454--6498 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
6444 CCGGTCTAAT
6454 CCATTGA-ATTAACCTGAC
1 CCATTGACATTAACCTGAC
* *
6472 CCATTGACTTTAACTTGAC
1 CCATTGACATTAACCTGAC
*
6491 CCGTTGAC
1 CCATTGAC
6499 TTTGAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.27, C:0.29, G:0.13, T:0.31
Consensus pattern (19 bp):
CCATTGACATTAACCTGAC
Found at i:6490 original size:19 final size:19
Alignment explanation
Indices: 6462--6501 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
6452 ATCCATTGAA
6462 TTAACCTGACCCATTGACT
1 TTAACCTGACCCATTGACT
* *
6481 TTAACTTGACCCGTTGACT
1 TTAACCTGACCCATTGACT
6500 TT
1 TT
6502 GAAAAAAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.23, C:0.28, G:0.12, T:0.38
Consensus pattern (19 bp):
TTAACCTGACCCATTGACT
Found at i:9909 original size:69 final size:69
Alignment explanation
Indices: 9772--9915 Score: 173
Period size: 69 Copynumber: 2.1 Consensus size: 69
9762 CAAGTCATCT
* * * *
9772 GAAATAATTATGATTAAGTGTTCCCGTACGAGACACTCTAACCCTTCGGGGCTCCAATACGAGTC
1 GAAATAATTATGATTAAGTGCTCCCATACGAGACACTCTAACCCTTAGGGGCTCCAATACGAGAC
9837 ACCC
66 ACCC
* * * ** *
9841 GAAATAATTATGATT-AGATGCTCTCATGCGAGACACTCTAACCTTTAGGGGCTCCCGTGCGAGA
1 GAAATAATTATGATTAAG-TGCTCCCATACGAGACACTCTAACCCTTAGGGGCTCCAATACGAGA
9905 CACCC
65 CACCC
*
9910 AAAATA
1 GAAATA
9916 TCTATCATTA
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
68 2 0.03
69 61 0.97
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (69 bp):
GAAATAATTATGATTAAGTGCTCCCATACGAGACACTCTAACCCTTAGGGGCTCCAATACGAGAC
ACCC
Found at i:15084 original size:64 final size:63
Alignment explanation
Indices: 15012--15153 Score: 171
Period size: 64 Copynumber: 2.2 Consensus size: 63
15002 AATTAAATTT
* * * *
15012 AAAAAATAAATCAAA-GAAGTAAATATTAAA-AAAATAAAATATATATATATAAAAATGTTAAAA
1 AAAAAATAAAT-AAATGAAGAAAATATTAAATAAAA-AAAATA-AAAAATAAAAAAATGTTAAAA
15075 G
63 G
**
15076 AAAAAATAAATAAATGAAGAAAATATTAAATTCAAAAAATAAAAAATAAAAAAATGTTAAAAG
1 AAAAAATAAATAAATGAAGAAAATATTAAATAAAAAAAATAAAAAATAAAAAAATGTTAAAAG
*
15139 AGAAAATAAAATAAA
1 AAAAAAT-AAATAAA
15154 ACAAAACAAA
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
63 28 0.41
64 38 0.56
65 2 0.03
ACGTcount: A:0.70, C:0.01, G:0.06, T:0.22
Consensus pattern (63 bp):
AAAAAATAAATAAATGAAGAAAATATTAAATAAAAAAAATAAAAAATAAAAAAATGTTAAAAG
Found at i:15089 original size:16 final size:16
Alignment explanation
Indices: 15070--15176 Score: 53
Period size: 15 Copynumber: 6.8 Consensus size: 16
15060 ATAAAAATGT
15070 TAAAAGAAAAAATAAA
1 TAAAAGAAAAAATAAA
* *
15086 TAAATGAAGAAAAT-AT
1 TAAAAGAA-AAAATAAA
**
15102 TAAATTCAAAAAATAAA
1 TAAA-AGAAAAAATAAA
**
15119 -AAATA-AAAAAAT-GT
1 TAAA-AGAAAAAATAAA
*
15133 TAAAAGAGAAAATAAAA
1 TAAAAGAAAAAAT-AAA
* *
15150 TAAAACAAAACA-AAA
1 TAAAAGAAAAAATAAA
*
15165 TAAAATAAAAAA
1 TAAAAGAAAAAA
15177 GTGGGAAAAT
Statistics
Matches: 69, Mismatches: 15, Indels: 15
0.70 0.15 0.15
Matches are distributed among these distances:
14 1 0.01
15 29 0.42
16 21 0.30
17 18 0.26
ACGTcount: A:0.75, C:0.03, G:0.06, T:0.17
Consensus pattern (16 bp):
TAAAAGAAAAAATAAA
Found at i:15151 original size:5 final size:5
Alignment explanation
Indices: 15141--15174 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
15131 GTTAAAAGAG
* *
15141 AAAAT AAAAT AAAAC AAAAC AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
15175 AAGTGGGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.82, C:0.06, G:0.00, T:0.12
Consensus pattern (5 bp):
AAAAT
Found at i:15212 original size:16 final size:16
Alignment explanation
Indices: 15182--15211 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
15172 AAAAAGTGGG
15182 AAAATAAAGATAAAAC
1 AAAATAAAGATAAAAC
15198 AAAAT-AAGATAAAA
1 AAAATAAAGATAAAA
15212 AAAGGGAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.77, C:0.03, G:0.07, T:0.13
Consensus pattern (16 bp):
AAAATAAAGATAAAAC
Found at i:15302 original size:18 final size:18
Alignment explanation
Indices: 15281--15323 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
15271 GTTATTTTTA
*
15281 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAAGAATT
*
15299 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
15317 AAATAAA
1 AAATAAA
15324 TAATCTAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:15934 original size:12 final size:13
Alignment explanation
Indices: 15917--15945 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
15907 AAAGATAAAA
15917 TAAAATAATAT-T
1 TAAAATAATATCT
15929 TAAAATAATATCT
1 TAAAATAATATCT
15942 TAAA
1 TAAA
15946 TCCTAATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATAATATCT
Found at i:16984 original size:123 final size:123
Alignment explanation
Indices: 16768--16994 Score: 312
Period size: 123 Copynumber: 1.8 Consensus size: 123
16758 AAATCGTAGG
** *
16768 TGGCTCCTTCGTTGTGAAGTTGACCTTTGAATTGGATATCCTTCGTTCTGAAGTTAAAATCCAAT
1 TGGCTCCTTCCCTGTGAAGTTGACCTTTGAATTGGATATCATTCGTTCTGAAGTTAAAATCCAAT
* * *
16833 CTTGTAAATTGAATCGCTTTGAGATTAATATCTTTCGCTGTCAAGTTGAAATTGTGGA
66 CTTGAAAATTGAATCGCTTCGAGATTAATATCCTTCGCTGTCAAGTTGAAATTGTGGA
* * * * *
16891 TGGCTCCTTCCCTGTGAATTTGAGCTTTGAATTGGATGTCATTCGTTGTGAAGTTGAAATCCAAT
1 TGGCTCCTTCCCTGTGAAGTTGACCTTTGAATTGGATATCATTCGTTCTGAAGTTAAAATCCAAT
* * *
16956 CTTGAAAATTGCATTGGC-TCGAGTTTAATATCCTTCGCT
66 CTTGAAAATTG-AATCGCTTCGAGATTAATATCCTTCGCT
16995 ATGAAGCTAA
Statistics
Matches: 89, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
123 85 0.96
124 4 0.04
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.39
Consensus pattern (123 bp):
TGGCTCCTTCCCTGTGAAGTTGACCTTTGAATTGGATATCATTCGTTCTGAAGTTAAAATCCAAT
CTTGAAAATTGAATCGCTTCGAGATTAATATCCTTCGCTGTCAAGTTGAAATTGTGGA
Found at i:22529 original size:25 final size:24
Alignment explanation
Indices: 22472--22529 Score: 62
Period size: 26 Copynumber: 2.3 Consensus size: 24
22462 AAATATCAAA
*
22472 TAAAAATTAAATTTAAAAAAAAAT
1 TAAAAATGAAATTTAAAAAAAAAT
* **
22496 CAAAGAATGAAATATTAAAAAAATGT
1 TAAA-AATGAAAT-TTAAAAAAAAAT
22522 TAAAAATG
1 TAAAAATG
22530 TTAAAAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
24 3 0.11
25 11 0.41
26 13 0.48
ACGTcount: A:0.66, C:0.02, G:0.07, T:0.26
Consensus pattern (24 bp):
TAAAAATGAAATTTAAAAAAAAAT
Found at i:22645 original size:37 final size:37
Alignment explanation
Indices: 22604--22676 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 37
22594 AATGTTAAAA
* *
22604 GAGAACATAAAAATAAAATAAAATAAA-ATAAAAAAGT
1 GAGAAAATAAAAATAAAACAAAA-AAAGATAAAAAAGT
*
22641 GAGAAAATAAAGATAAAACAAAAAAAGATAAAAAAG
1 GAGAAAATAAAAATAAAACAAAAAAAGATAAAAAAG
22677 GGAAATATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
36 3 0.09
37 29 0.91
ACGTcount: A:0.74, C:0.03, G:0.11, T:0.12
Consensus pattern (37 bp):
GAGAAAATAAAAATAAAACAAAAAAAGATAAAAAAGT
Found at i:22669 original size:15 final size:16
Alignment explanation
Indices: 22644--22673 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
22634 AAAAAGTGAG
22644 AAAATAAAGATAAAAC
1 AAAATAAAGATAAAAC
22660 AAAA-AAAGATAAAA
1 AAAATAAAGATAAAA
22674 AAGGGAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.80, C:0.03, G:0.07, T:0.10
Consensus pattern (16 bp):
AAAATAAAGATAAAAC
Found at i:22764 original size:18 final size:18
Alignment explanation
Indices: 22743--22785 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
22733 GTTGTTTTTA
*
22743 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAAGAATT
*
22761 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
22779 AAATAAA
1 AAATAAA
22786 TAATCTAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:25540 original size:28 final size:28
Alignment explanation
Indices: 25509--25601 Score: 81
Period size: 28 Copynumber: 3.4 Consensus size: 28
25499 TTGTAAAAGA
*
25509 ACAGAGGTGCTTGATTTTAGATTGTAGC
1 ACAGAGGTGCTAGATTTTAGATTGTAGC
25537 ACAGAGGTGCTCA-ATCCTTCTA-A---T-GC
1 ACAGAGGTGCT-AGAT--TT-TAGATTGTAGC
* *
25563 ACAGAGGTGCCAGATTTTAGATTGAAGC
1 ACAGAGGTGCTAGATTTTAGATTGTAGC
25591 ACAGAGGTGCT
1 ACAGAGGTGCT
25602 CAGTCATTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 20
0.68 0.05 0.27
Matches are distributed among these distances:
23 2 0.04
24 3 0.06
25 1 0.02
26 14 0.27
27 1 0.02
28 25 0.49
30 3 0.06
31 2 0.04
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (28 bp):
ACAGAGGTGCTAGATTTTAGATTGTAGC
Found at i:25646 original size:27 final size:28
Alignment explanation
Indices: 25528--25824 Score: 119
Period size: 27 Copynumber: 10.8 Consensus size: 28
25518 CTTGATTTTA
* *
25528 GATTGTAGCACAGAGGTGCTCAATCCT-
1 GATTGAAGCACAGAGGTGCTCAGTCCTC
** *
25555 --TCT-AATGCACAGAGGTGC-CAGATTTTA
1 GAT-TGAA-GCACAGAGGTGCTCAG-TCCTC
*
25582 GATTGAAGCACAGAGGTGCTCAGTCAT-
1 GATTGAAGCACAGAGGTGCTCAGTCCTC
* **
25609 -TTTGGCTGCACAGAGGTG-TCAGTCCTC
1 GATT-GAAGCACAGAGGTGCTCAGTCCTC
* *
25636 GATTGAAGCACAGAGGTGCTCAATCATC
1 GATTGAAGCACAGAGGTGCTCAGTCCTC
*
25664 --TTAGCTA-CACAGAGGTG-TCAGCTCC-C
1 GATT-G-AAGCACAGAGGTGCTCAG-TCCTC
** * * *
25690 GGCTGAATCACAGAGGTGCTCAGTCATTT
1 GATTGAAGCACAGAGGTGCTCAGTC-CTC
** * *
25719 TTTTTAACTGCACAGAGGTG-TCAGTTCTC
1 GATTGAA--GCACAGAGGTGCTCAGTCCTC
*
25748 GATTGAAGCACAGAGGTGCTCAATCACT-
1 GATTGAAGCACAGAGGTGCTCAGTC-CTC
* *
25776 -TTTGGCTA-CACAGAGGTG-TCAG-CTCTC
1 GATT-G-AAGCACAGAGGTGCTCAGTC-CTC
25803 GATTGAAGCACAGAGGTGCTCA
1 GATTGAAGCACAGAGGTGCTCA
25825 ATCGTTAATT
Statistics
Matches: 198, Mismatches: 41, Indels: 61
0.66 0.14 0.20
Matches are distributed among these distances:
25 4 0.02
26 35 0.18
27 77 0.39
28 50 0.25
29 17 0.09
30 5 0.03
31 10 0.05
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (28 bp):
GATTGAAGCACAGAGGTGCTCAGTCCTC
Found at i:25767 original size:112 final size:109
Alignment explanation
Indices: 25585--25824 Score: 356
Period size: 112 Copynumber: 2.2 Consensus size: 109
25575 GATTTTAGAT
**
25585 TGAAGCACAGAGGTGCTCAGTCATTTTGGCTGCACAGAGGTGTCAGTCCTCGATTGAAGCACAGA
1 TGAAGCACAGAGGTGCTCAGTCATTTTAACTGCACAGAGGTGTCAGTCCTCGATTGAAGCACAGA
*
25650 GGTGCTCAATCA-TCTTAGCTACACAGAGGTGTCAGCTCCCGGC
66 GGTGCTCAATCACTCTTAGCTACACAGAGGTGTCAGCTCCCGAC
* *
25693 TGAATCACAGAGGTGCTCAGTCATTTTTTTTAACTGCACAGAGGTGTCAGTTCTCGATTGAAGCA
1 TGAAGCACAGAGGTGCTCAGTCA----TTTTAACTGCACAGAGGTGTCAGTCCTCGATTGAAGCA
* * * *
25758 CAGAGGTGCTCAATCACTTTTGGCTACACAGAGGTGTCAGCTCTCGAT
62 CAGAGGTGCTCAATCACTCTTAGCTACACAGAGGTGTCAGCTCCCGAC
25806 TGAAGCACAGAGGTGCTCA
1 TGAAGCACAGAGGTGCTCA
25825 ATCGTTAATT
Statistics
Matches: 117, Mismatches: 10, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
108 22 0.19
112 51 0.44
113 44 0.38
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (109 bp):
TGAAGCACAGAGGTGCTCAGTCATTTTAACTGCACAGAGGTGTCAGTCCTCGATTGAAGCACAGA
GGTGCTCAATCACTCTTAGCTACACAGAGGTGTCAGCTCCCGAC
Found at i:25803 original size:55 final size:54
Alignment explanation
Indices: 25528--25827 Score: 334
Period size: 54 Copynumber: 5.5 Consensus size: 54
25518 CTTGATTTTA
* * * * * * * *
25528 GATTGTAGCACAGAGGTGCTCAATCCTTCTA-ATGCACAGAGGTGCCAGATTTTA
1 GATTGAAGCACAGAGGTGCTCAATCATTTTAGCTGCACAGAGGTGTCAG-CTCTC
* *
25582 GATTGAAGCACAGAGGTGCTCAGTCATTTTGGCTGCACAGAGGTGTCAG-TCCTC
1 GATTGAAGCACAGAGGTGCTCAATCATTTTAGCTGCACAGAGGTGTCAGCT-CTC
* * *
25636 GATTGAAGCACAGAGGTGCTCAATCATCTTAGCTACACAGAGGTGTCAGCTCCC
1 GATTGAAGCACAGAGGTGCTCAATCATTTTAGCTGCACAGAGGTGTCAGCTCTC
** * * * *
25690 GGCTGAATCACAGAGGTGCTCAGTCATTTTTTTTAACTGCACAGAGGTGTCAGTTCTC
1 GATTGAAGCACAGAGGTGCTCAATCA----TTTTAGCTGCACAGAGGTGTCAGCTCTC
* *
25748 GATTGAAGCACAGAGGTGCTCAATCACTTTTGGCTACACAGAGGTGTCAGCTCTC
1 GATTGAAGCACAGAGGTGCTCAATCA-TTTTAGCTGCACAGAGGTGTCAGCTCTC
25803 GATTGAAGCACAGAGGTGCTCAATC
1 GATTGAAGCACAGAGGTGCTCAATC
25828 GTTAATTCTA
Statistics
Matches: 207, Mismatches: 32, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
53 1 0.00
54 96 0.46
55 65 0.31
58 45 0.22
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (54 bp):
GATTGAAGCACAGAGGTGCTCAATCATTTTAGCTGCACAGAGGTGTCAGCTCTC
Found at i:26074 original size:81 final size:81
Alignment explanation
Indices: 25939--26101 Score: 272
Period size: 81 Copynumber: 2.0 Consensus size: 81
25929 GCCAGCGAGT
*
25939 TATAGAGAATGGTTCGCACATGAAATGGCTGAGCAACAAGCTCTCACAGAGGTGTAGAGCAGGAA
1 TATAGAGAATGGTTCGCACATGAAATGGCGGAGCAACAAGCTCTCACAGAGGTGTAGAGCAGGAA
* *
26004 GTTACTGAGCCAGTTG
66 GCTACCGAGCCAGTTG
* *
26020 TATAGAGAATGGTTCGCACATGAAATGGCGGATCGACAAGCTCTCACAGAGGTGTAGAGCAGGAA
1 TATAGAGAATGGTTCGCACATGAAATGGCGGAGCAACAAGCTCTCACAGAGGTGTAGAGCAGGAA
*
26085 GCTACCGATCCAGTTG
66 GCTACCGAGCCAGTTG
26101 T
1 T
26102 GCAAGAGACT
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
81 76 1.00
ACGTcount: A:0.31, C:0.18, G:0.29, T:0.21
Consensus pattern (81 bp):
TATAGAGAATGGTTCGCACATGAAATGGCGGAGCAACAAGCTCTCACAGAGGTGTAGAGCAGGAA
GCTACCGAGCCAGTTG
Found at i:33418 original size:12 final size:12
Alignment explanation
Indices: 33401--33425 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33391 CCATGAAAGG
33401 GAAACCATCCAT
1 GAAACCATCCAT
33413 GAAACCATCCAT
1 GAAACCATCCAT
33425 G
1 G
33426 GCAGTCACAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.32, G:0.12, T:0.16
Consensus pattern (12 bp):
GAAACCATCCAT
Found at i:34117 original size:3 final size:3
Alignment explanation
Indices: 34109--34170 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
34099 ATATGTAATC
34109 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
34157 ATT ATT ATT ATT AT
1 ATT ATT ATT ATT AT
34171 ATACACACAC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:35816 original size:20 final size:20
Alignment explanation
Indices: 35791--35883 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
35781 TTTTCCCAAT
*
35791 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
* **
35811 TCGCAACGCGAATTGGAAAAA
1 TCGCAATGCGAATAAG-AAAA
*
35832 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
* **
35852 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
35873 TCGCAATGCGA
1 TCGCAATGCGA
35884 TAATACAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:35836 original size:41 final size:41
Alignment explanation
Indices: 35791--35883 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
35781 TTTTCCCAAT
35791 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGAAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGAAAAA
*
35832 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGAAAAA
35873 TCGCAATGCGA
1 TCGCAATGCGA
35884 TAATACAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGAAAAA
Found at i:35919 original size:20 final size:20
Alignment explanation
Indices: 35894--35966 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
35884 TAATACAAAA
* *
35894 TCGCAACGAGATACTTACTT
1 TCGCAACGCGATACTGACTT
35914 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
*
35934 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATACTGACTT
35954 TCGCAACGCGATA
1 TCGCAACGCGATA
35967 ATACATAATC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:36182 original size:22 final size:22
Alignment explanation
Indices: 36154--36197 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
36144 CACTCTCTCA
36154 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
36176 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
36198 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:36500 original size:20 final size:20
Alignment explanation
Indices: 36441--36504 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 20
36431 GCGATTTTAG
*
36441 TTTCGCGTTGCGATTGTCAA
1 TTTCGCGTTGCGATTGTCAT
* *
36461 ATTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATTGTCAT
* *
36481 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTGTCAT
36501 TTTC
1 TTTC
36505 AGAAACTATT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.14, C:0.19, G:0.22, T:0.45
Consensus pattern (20 bp):
TTTCGCGTTGCGATTGTCAT
Found at i:37844 original size:18 final size:18
Alignment explanation
Indices: 37823--37867 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
37813 TCCACTTCGG
*
37823 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
37841 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
37859 GAGCCATCA
1 GAGCCATCA
37868 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:38375 original size:20 final size:20
Alignment explanation
Indices: 38350--38391 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
38340 TAGTTTACTT
38350 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
38370 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
38390 TC
1 TC
38392 ACAATGCGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:38404 original size:19 final size:20
Alignment explanation
Indices: 38361--38405 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
38351 CGCAACACGA
*
38361 AAATGACTATCGCAACGCGG
1 AAATGACTATCACAACGCGG
* *
38381 AAATGGCTATCACAATGC-G
1 AAATGACTATCACAACGCGG
38400 AAATGA
1 AAATGA
38406 AAATCGCAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (20 bp):
AAATGACTATCACAACGCGG
Found at i:38424 original size:14 final size:14
Alignment explanation
Indices: 38405--38462 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
38395 ATGCGAAATG
*
38405 AAAATCGCAACGAC
1 AAAATCGCAACGAA
38419 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAA
*
38435 ATGAAATCGCAACGAT
1 A--AAATCGCAACGAA
38451 AAAATCGCAACG
1 AAAATCGCAACG
38463 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAA
Found at i:38447 original size:32 final size:33
Alignment explanation
Indices: 38393--38479 Score: 149
Period size: 32 Copynumber: 2.7 Consensus size: 33
38383 ATGGCTATCA
38393 CAATGCGAAATGAAAATCGCAACGACAAAATCG
1 CAATGCGAAATGAAAATCGCAACGACAAAATCG
*
38426 CAATGCGAAATG-AAATCGCAACGATAAAATCG
1 CAATGCGAAATGAAAATCGCAACGACAAAATCG
*
38458 CAACGCGAAATGAAAATCGCAA
1 CAATGCGAAATGAAAATCGCAA
38480 TGCGATTTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
32 30 0.59
33 21 0.41
ACGTcount: A:0.48, C:0.21, G:0.18, T:0.13
Consensus pattern (33 bp):
CAATGCGAAATGAAAATCGCAACGACAAAATCG
Found at i:38515 original size:14 final size:14
Alignment explanation
Indices: 38496--38553 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
38486 TTGTGTTTCG
38496 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
38510 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
38526 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
*
38542 CGTTGAGATTTT
1 CGTTGCGATTTT
38554 TATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 22 0.59
16 4 0.11
18 11 0.30
ACGTcount: A:0.10, C:0.16, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:38530 original size:32 final size:33
Alignment explanation
Indices: 38491--38569 Score: 124
Period size: 32 Copynumber: 2.4 Consensus size: 33
38481 GCGATTTGTG
*
38491 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGAGATTTTCA
*
38523 TTTCGCGTTGCGATTTTGTCGTTGAGATTTTTA
1 TTTCGCGTTGCGATTTTGTCGTTGAGATTTTCA
*
38556 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
38570 AGCCATTTCC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
32 26 0.60
33 17 0.40
ACGTcount: A:0.11, C:0.16, G:0.24, T:0.48
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGAGATTTTCA
Found at i:38588 original size:20 final size:20
Alignment explanation
Indices: 38563--38609 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
38553 TTATTTCGCA
38563 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* *
38583 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGCCATTTCCGCG
38603 TTGCGAT
1 TTGCGAT
38610 TTTAAGTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.15, C:0.23, G:0.26, T:0.36
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:40653 original size:19 final size:19
Alignment explanation
Indices: 40631--40686 Score: 103
Period size: 19 Copynumber: 2.9 Consensus size: 19
40621 ATCGCAACGA
40631 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
40650 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
*
40669 GAAAATCGCAATGAGAAA
1 GAAAATCGCAATGCGAAA
40687 ATCGCAATGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.50, C:0.14, G:0.21, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:40686 original size:14 final size:14
Alignment explanation
Indices: 40669--40695 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40659 AATGCGAAAT
40669 GAAAATCGCAATGA
1 GAAAATCGCAATGA
40683 GAAAATCGCAATG
1 GAAAATCGCAATG
40696 CGATTTTCAT
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:0.48, C:0.15, G:0.22, T:0.15
Consensus pattern (14 bp):
GAAAATCGCAATGA
Found at i:40742 original size:20 final size:20
Alignment explanation
Indices: 40717--40754 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
40707 TCGCATTGCG
*
40717 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
40737 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
40755 TCAAATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:41785 original size:24 final size:24
Alignment explanation
Indices: 41758--41811 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
41748 GTATTCGAAA
* *
41758 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
41782 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
41806 TTTGAT
1 TTTGAT
41812 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:42021 original size:12 final size:12
Alignment explanation
Indices: 41986--42022 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
41976 ATATAATCCT
*
41986 GAAGAAGAAAAT
1 GAAGAAGAAAAA
41998 GAAGAAGAAAAA
1 GAAGAAGAAAAA
42010 GAAGAAGAAAAA
1 GAAGAAGAAAAA
42022 G
1 G
42023 TCCCCGAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.70, C:0.00, G:0.27, T:0.03
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:44357 original size:33 final size:33
Alignment explanation
Indices: 44312--44436 Score: 171
Period size: 33 Copynumber: 3.8 Consensus size: 33
44302 AAATTACTAC
44312 CGCAATGCGAAATGAAAATCGCAACGAGAGAAT
1 CGCAATGCGAAATGAAAATCGCAACGAGAGAAT
** ** *
44345 CATAATGCGAAATGAAAATCGCAACGCTA-ATTT
1 CGCAATGCGAAATGAAAATCGCAACGAGAGA-AT
* *
44378 CGCAATGCAAAATGAAAATCGCAACGAGGGAAT
1 CGCAATGCGAAATGAAAATCGCAACGAGAGAAT
44411 CGCAATGCGAAATGAAAATCGCAACG
1 CGCAATGCGAAATGAAAATCGCAACG
44437 CGAATTTAAT
Statistics
Matches: 77, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
32 1 0.01
33 75 0.97
34 1 0.01
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.15
Consensus pattern (33 bp):
CGCAATGCGAAATGAAAATCGCAACGAGAGAAT
Found at i:44391 original size:66 final size:66
Alignment explanation
Indices: 44312--44443 Score: 219
Period size: 66 Copynumber: 2.0 Consensus size: 66
44302 AAATTACTAC
* * *
44312 CGCAATGCGAAATGAAAATCGCAACGAGAGAATCATAATGCGAAATGAAAATCGCAACGCTAATT
1 CGCAATGCAAAATGAAAATCGCAACGAGAGAATCACAATGCGAAATGAAAATCGCAACGCGAATT
44377 T
66 T
* *
44378 CGCAATGCAAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAATT
1 CGCAATGCAAAATGAAAATCGCAACGAGAGAATCACAATGCGAAATGAAAATCGCAACGCGAATT
44443 T
66 T
44444 AATTTCGCGT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.43, C:0.19, G:0.21, T:0.17
Consensus pattern (66 bp):
CGCAATGCAAAATGAAAATCGCAACGAGAGAATCACAATGCGAAATGAAAATCGCAACGCGAATT
T
Found at i:44487 original size:33 final size:33
Alignment explanation
Indices: 44436--44525 Score: 144
Period size: 33 Copynumber: 2.7 Consensus size: 33
44426 AAATCGCAAC
*
44436 GCGAATTTAATTTCGCGTTGCGATTCTCTCGTT
1 GCGAATTTCATTTCGCGTTGCGATTCTCTCGTT
*
44469 GCGAGTTTCATTTCGCGTTGCGATTCTCTCGTT
1 GCGAATTTCATTTCGCGTTGCGATTCTCTCGTT
* *
44502 GCGATTTTCATTTCGCATTGCGAT
1 GCGAATTTCATTTCGCGTTGCGAT
44526 AGTACTTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.42
Consensus pattern (33 bp):
GCGAATTTCATTTCGCGTTGCGATTCTCTCGTT
Found at i:44489 original size:19 final size:18
Alignment explanation
Indices: 44440--44525 Score: 62
Period size: 14 Copynumber: 5.1 Consensus size: 18
44430 CGCAACGCGA
*
44440 ATTTAATTTCGCGTTGCG
1 ATTTCATTTCGCGTTGCG
*
44458 A-TTC---TCTCGTTGCG
1 ATTTCATTTCGCGTTGCG
44472 AGTTTCATTTCGCGTTGCG
1 A-TTTCATTTCGCGTTGCG
*
44491 A-TTC---TCTCGTTGCG
1 ATTTCATTTCGCGTTGCG
*
44505 ATTTTCATTTCGCATTGCG
1 A-TTTCATTTCGCGTTGCG
44524 AT
1 AT
44526 AGTACTTTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 20
0.67 0.08 0.26
Matches are distributed among these distances:
14 20 0.38
16 6 0.12
17 5 0.10
18 2 0.04
19 19 0.37
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.44
Consensus pattern (18 bp):
ATTTCATTTCGCGTTGCG
Found at i:44651 original size:14 final size:14
Alignment explanation
Indices: 44632--44668 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
44622 CATCAATTAA
44632 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
44646 ACAAATCACCTTTT
1 ACAAATCAACTTTT
44660 ACAAATCAA
1 ACAAATCAA
44669 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:46078 original size:21 final size:21
Alignment explanation
Indices: 46012--46078 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
46002 GTGAATCGGG
*
46012 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
46032 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
46054 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
46075 CTCT
1 CTCT
46079 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:46117 original size:41 final size:41
Alignment explanation
Indices: 46051--46129 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
46041 CGATGACAGT
* * *
46051 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAG
* * *
46092 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
46130 CAGGCGAGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.23, C:0.18, G:0.38, T:0.22
Consensus pattern (41 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAG
Found at i:48112 original size:33 final size:33
Alignment explanation
Indices: 48055--48142 Score: 142
Period size: 33 Copynumber: 2.6 Consensus size: 33
48045 ACGAGATAAT
*
48055 GAGAATCGCAACGCGGAAATGACTATCGC-ATTGA
1 GAGAATCGCAACGC-GAAATGACTATCGCGA-CGA
48089 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCGACGA
48122 GAGAATCGCAACGCGAAATGA
1 GAGAATCGCAACGCGAAATGA
48143 AAATCGCAAC
Statistics
Matches: 52, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
33 37 0.71
34 15 0.29
ACGTcount: A:0.38, C:0.22, G:0.27, T:0.14
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCGACGA
Found at i:48147 original size:19 final size:19
Alignment explanation
Indices: 48125--48194 Score: 122
Period size: 19 Copynumber: 3.7 Consensus size: 19
48115 GCGACGAGAG
48125 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
48144 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATGAA
48163 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
48182 AATCGCAATGCGA
1 AATCGCAACGCGA
48195 TTTTTGTTTC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 48 1.00
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:48149 original size:33 final size:33
Alignment explanation
Indices: 48055--48188 Score: 126
Period size: 33 Copynumber: 3.9 Consensus size: 33
48045 ACGAGATAAT
** **
48055 GAGAATCGCAACGCGGAAATGACTATCGCATTGA
1 GAGAATCGCAACGC-GAAATGAAAATCGCACCGA
**
48089 GAGAATCGCAACGCGAAATGACTATCGCGA-CGA
1 GAGAATCGCAACGCGAAATGAAAATCGC-ACCGA
48122 GAGAATCGCAACGCGAAATGAAAATCGCAACGCGAAA
1 GAGAATCGCAACGCGAAATGAAAATCGC-AC-CG--A
* *
48159 TAAAAATCGCAACGCGAAATGAAAATCGCA
1 -GAGAATCGCAACGCGAAATGAAAATCGCA
48189 ATGCGATTTT
Statistics
Matches: 88, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
33 43 0.49
34 15 0.17
35 2 0.02
37 2 0.02
38 26 0.30
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.13
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGAAAATCGCACCGA
Found at i:48226 original size:19 final size:19
Alignment explanation
Indices: 48190--48256 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
48180 AAAATCGCAA
*
48190 TGCGATTTTTGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
48209 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
48228 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
48248 TGCGATTTT
1 TGCGATTTT
48257 CATTCTCGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 28 0.70
20 12 0.30
ACGTcount: A:0.09, C:0.16, G:0.24, T:0.51
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:48837 original size:20 final size:20
Alignment explanation
Indices: 48765--48836 Score: 108
Period size: 20 Copynumber: 3.6 Consensus size: 20
48755 CGCTATGTAA
*
48765 ATCGCGTTGCGAAAGTCAGA
1 ATCGCGTTGCGAAAGTCAGT
48785 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTCAGT
* *
48805 ATCTCGTTGCGATAGTCAGT
1 ATCGCGTTGCGAAAGTCAGT
*
48825 ATCGCATTGCGA
1 ATCGCGTTGCGA
48837 TTTTTCCAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTCAGT
Found at i:48929 original size:21 final size:21
Alignment explanation
Indices: 48905--48958 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
48895 ACTGTAGACC
48905 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGATTTCCAACT
48926 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGATTTCCAACT
48947 ATCGCAACGCGA
1 ATCGCAACGCGA
48959 ATTTGCGATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.30, C:0.33, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGATTTCCAACT
Done.