Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005848.1 Hibiscus syriacus cultivar Beakdansim tig00013723_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: 58786
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:4818 original size:54 final size:54
Alignment explanation
Indices: 4662--4911 Score: 352
Period size: 54 Copynumber: 4.7 Consensus size: 54
4652 TTTTCAAAAC
* * * *
4662 ATTAT-AAGTTCTTTGGGGTGCACACGTAGTGCCGATACGGTCGTTCATAAACTT
1 ATTATGAA-TTCTGTGGGTTGCACACATAGTGTCGATACGGTCGTTCATAAACTT
4716 ATTATGAATTCTGTGGGTTG--CACATAGTG-CTGATACGGTCGTTCATAAACTT
1 ATTATGAATTCTGTGGGTTGCACACATAGTGTC-GATACGGTCGTTCATAAACTT
*
4768 ATTATGAATT-TCGTGGGTTGCACACATAGTGTCGATATGGTCGTTCATAAACTT
1 ATTATGAATTCT-GTGGGTTGCACACATAGTGTCGATACGGTCGTTCATAAACTT
* *
4822 ATTATGAATT-TCATGGGTTGCACACATAGTGTCGATATGGTCGTTCAT-AACTT
1 ATTATGAATTCT-GTGGGTTGCACACATAGTGTCGATACGGTCGTTCATAAACTT
4875 ATTATGAATTCTGTGGGTTGCACACATAGTGTCGATA
1 ATTATGAATTCTGTGGGTTGCACACATAGTGTCGATA
4912 GTACACATAG
Statistics
Matches: 183, Mismatches: 6, Indels: 15
0.90 0.03 0.07
Matches are distributed among these distances:
51 2 0.01
52 47 0.26
53 39 0.21
54 92 0.50
55 3 0.02
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.36
Consensus pattern (54 bp):
ATTATGAATTCTGTGGGTTGCACACATAGTGTCGATACGGTCGTTCATAAACTT
Found at i:14876 original size:54 final size:54
Alignment explanation
Indices: 14818--15252 Score: 505
Period size: 54 Copynumber: 8.2 Consensus size: 54
14808 GGTGCACATG
*
14818 TAGTGCCGATACGATCGTTCATAAACTTATTATGAATTCAGTGGGTTGCACACA
1 TAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCAGTGGGTTGCACACA
* * *
14872 TAGTGTCGATACGGTCATTCATAAACTTGTTATGAATTTC-GTGGGTTGCACACA
1 TAGTGCCGATACGGTCGTTCATAAACTTATTATGAA-TTCAGTGGGTTGCACACA
* * * **
14926 TAGTGCCGAAAC-GCCGTTCATAAACATATTATGAATTTTGTGGGTTGCACACA
1 TAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCAGTGGGTTGCACACA
* * * *
14979 TAGTGCTGATACGGTCGTTCATAAACTTATTCTGAATTCTGTGGGTTGCACGCA
1 TAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCAGTGGGTTGCACACA
**
15033 TAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTTTGTGGGTT-------
1 TAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCAGTGGGTTGCACACA
* * * * * *
15080 TAGTGCTGATACGATCATTTATAAACTTATTATAAATT-ATGTGGGTTGCATACA
1 TAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCA-GTGGGTTGCACACA
* * * *
15134 TAGTGTCGATACGGTCATTCATAAACTTATTATGAATTCCGTGGGATGCACACA
1 TAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCAGTGGGTTGCACACA
* *
15188 TAGTGTCGATACGGTCGTTCATAAACTTATTATGAATT-ATGTGGGCTGCACACA
1 TAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCA-GTGGGTTGCACACA
* *
15242 TATTGTCGATA
1 TAGTGCCGATA
15253 GTACACATAT
Statistics
Matches: 329, Mismatches: 39, Indels: 26
0.84 0.10 0.07
Matches are distributed among these distances:
47 40 0.12
52 2 0.01
53 43 0.13
54 241 0.73
55 3 0.01
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (54 bp):
TAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTCAGTGGGTTGCACACA
Found at i:15104 original size:47 final size:47
Alignment explanation
Indices: 15033--15171 Score: 134
Period size: 47 Copynumber: 2.8 Consensus size: 47
15023 GTTGCACGCA
* * * *
15033 TAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTTTGTGGGTT
1 TAGTGCCGATACGATCATTCATAAACTTATTATAAATTATGTGGGTT
* *
15080 TAGTGCTGATACGATCATTTATAAACTTATTATAAATTATGTGGGTTGCAT
1 TAGTGCCGATACGATCATTCATAAACTTATTATAAATTATGTGGG-T---T
* * *
15131 ACATAGTGTCGATACGGTCATTCATAAACTTATTATGAATT
1 ---TAGTGCCGATACGATCATTCATAAACTTATTATAAATT
15172 CCGTGGGATG
Statistics
Matches: 74, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
47 39 0.53
48 1 0.01
51 1 0.01
54 33 0.45
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (47 bp):
TAGTGCCGATACGATCATTCATAAACTTATTATAAATTATGTGGGTT
Found at i:15178 original size:155 final size:154
Alignment explanation
Indices: 14818--15232 Score: 544
Period size: 155 Copynumber: 2.6 Consensus size: 154
14808 GGTGCACATG
*
14818 TAGTGCCGATACGATCGTTCATAAACTTATTATGAATTCAGTGGGTTGCACACATAGTGTCGATA
1 TAGTG-CGATACGGTCGTTCATAAACTTATTATGAATTCAGTGGGTTGCACACATAGTGTCGATA
* * * *
14883 CGGTCATTCATAAACTTGTTATGAATTTCGTGGGTTGCACACATAGTGCCGAAACGCCGTTCATA
65 CGGTCGTTCATAAACTTATTATGAATTTTGTGGGTT------ATAGTGCCGAAACGCCATTCATA
* *
14948 AACATATTATGAATTTTGTGGGTTGCACACA
124 AACATATTATAAATTATGTGGGTTGCACACA
* * * *
14979 TAGTGCTGATACGGTCGTTCATAAACTTATTCTGAATTCTGTGGGTTGCACGCATAGTGCCGATA
1 TAGTGC-GATACGGTCGTTCATAAACTTATTATGAATTCAGTGGGTTGCACACATAGTGTCGATA
* * * * *
15044 CGGTCGTTCATAAACTTATTATGAATTTTGTGGGTT-TAGTGCTGATACGATCATTTATAAACTT
65 CGGTCGTTCATAAACTTATTATGAATTTTGTGGGTTATAGTGCCGAAACG-CCATTCATAAACAT
*
15108 ATTATAAATTATGTGGGTTGCATACA
129 ATTATAAATTATGTGGGTTGCACACA
* * *
15134 TAGTGTCGATACGGTCATTCATAAACTTATTATGAATTCCGTGGGATGCACACATAGTGTCGATA
1 TAGTG-CGATACGGTCGTTCATAAACTTATTATGAATTCAGTGGGTTGCACACATAGTGTCGATA
*
15199 CGGTCGTTCATAAACTTATTATGAATTATGTGGG
65 CGGTCGTTCATAAACTTATTATGAATTTTGTGGG
15233 CTGCACACAT
Statistics
Matches: 227, Mismatches: 24, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
154 11 0.05
155 123 0.54
156 1 0.00
160 1 0.00
161 91 0.40
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (154 bp):
TAGTGCGATACGGTCGTTCATAAACTTATTATGAATTCAGTGGGTTGCACACATAGTGTCGATAC
GGTCGTTCATAAACTTATTATGAATTTTGTGGGTTATAGTGCCGAAACGCCATTCATAAACATAT
TATAAATTATGTGGGTTGCACACA
Found at i:15591 original size:20 final size:21
Alignment explanation
Indices: 15566--15620 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
15556 TGACATATTA
*
15566 GTATCGGTAC-CCCT-CATATG
1 GTATCGATACTCCCTAC-TATG
15586 GTATCGATACTTCCCTACTATG
1 GTATCGATAC-TCCCTACTATG
15608 GTATCGATACTCC
1 GTATCGATACTCC
15621 TTTCAGTATC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
20 9 0.29
21 3 0.10
22 18 0.58
23 1 0.03
ACGTcount: A:0.22, C:0.29, G:0.16, T:0.33
Consensus pattern (21 bp):
GTATCGATACTCCCTACTATG
Found at i:18207 original size:3 final size:3
Alignment explanation
Indices: 18199--18253 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
18189 ATTGTCCAAT
18199 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
18247 ATA ATA A
1 ATA ATA A
18254 AAAAGAAGTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:18431 original size:31 final size:33
Alignment explanation
Indices: 18359--18434 Score: 93
Period size: 31 Copynumber: 2.4 Consensus size: 33
18349 TAACGGAAGT
* *
18359 TAACGTTAGAGAGACTTAAATCAAACGGGCTGA
1 TAACGTTAGAGAGACTTAAATCAAACGGACTAA
* * *
18392 TAATGTTAG-G-GCCTTAAATCAAACGGATTAA
1 TAACGTTAGAGAGACTTAAATCAAACGGACTAA
18423 TAACGTTAGAGA
1 TAACGTTAGAGA
18435 TTATTTACTC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
31 25 0.71
32 2 0.06
33 8 0.23
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.25
Consensus pattern (33 bp):
TAACGTTAGAGAGACTTAAATCAAACGGACTAA
Found at i:22160 original size:17 final size:17
Alignment explanation
Indices: 22138--22171 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
22128 TATTAAAAGT
22138 ATAAAATGATCACCCAA
1 ATAAAATGATCACCCAA
*
22155 ATAAAATGATCATCCAA
1 ATAAAATGATCACCCAA
22172 CTATTCATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.21, G:0.06, T:0.21
Consensus pattern (17 bp):
ATAAAATGATCACCCAA
Found at i:23069 original size:85 final size:82
Alignment explanation
Indices: 22979--23168 Score: 245
Period size: 85 Copynumber: 2.3 Consensus size: 82
22969 TATGATGTGC
* * * *
22979 ATTTATGACACACATTTATGATGCGCATTGAGCATCAATGAAGCCCCCGTCATAAATGAAGATGA
1 ATTTATGACACGCATGTATGAT-CACATTGAGCATCAATGAAGCCCCCATCATAAATGAAGATGA
23044 CACACATTTGTGTGTCATAA
65 CACACA-TT-TGTGTCATAA
* * ** * **
23064 ATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGAAGTTCCCATCATAAATGAAGATGA
1 ATTTATGACACGCATGTATGA-TCACATTGAGCATCAATGAAGCCCCCATCATAAATGAAGATGA
23129 CACACATTTGTGTCATAA
65 CACACATTTGTGTCATAA
23147 ATTTATGACACGCATGTATGAT
1 ATTTATGACACGCATGTATGAT
23169 TTACATTGCG
Statistics
Matches: 93, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
82 1 0.01
83 31 0.33
84 2 0.02
85 58 0.62
86 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Consensus pattern (82 bp):
ATTTATGACACGCATGTATGATCACATTGAGCATCAATGAAGCCCCCATCATAAATGAAGATGAC
ACACATTTGTGTCATAA
Found at i:23173 original size:83 final size:85
Alignment explanation
Indices: 23028--23229 Score: 293
Period size: 83 Copynumber: 2.4 Consensus size: 85
23018 GAAGCCCCCG
23028 TCATAAATGAAGATGACACACATTTGTGTGTCATAAATTTATGACACGCATGTATGACTTACATT
1 TCATAAATGAAGATGACACACATTTGTGTGTCATAAATTTATGACACGCATGTATGACTTACATT
*
23093 GCGTGTCATTGAAGTTCCCA
66 GCGTGTAATTGAAGTTCCCA
*
23113 TCATAAATGAAGATGACACACA-TT-TGTGTCATAAATTTATGACACGCATGTATGATTTACATT
1 TCATAAATGAAGATGACACACATTTGTGTGTCATAAATTTATGACACGCATGTATGACTTACATT
** * *
23176 GCGTGTAATTGAAGCACGCG
66 GCGTGTAATTGAAGTTCCCA
** *
23196 TCATTAAAAAAAG-TGACACACATTCGTGTGTCAT
1 TCA-TAAATGAAGATGACACACATTTGTGTGTCAT
23230 GATTGTATTT
Statistics
Matches: 105, Mismatches: 9, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
83 65 0.62
84 10 0.10
85 30 0.29
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Consensus pattern (85 bp):
TCATAAATGAAGATGACACACATTTGTGTGTCATAAATTTATGACACGCATGTATGACTTACATT
GCGTGTAATTGAAGTTCCCA
Found at i:23254 original size:2 final size:2
Alignment explanation
Indices: 23247--23271 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
23237 TTTCATAAAT
23247 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
23272 TGTAGATTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24579 original size:15 final size:15
Alignment explanation
Indices: 24556--24588 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
24546 CGTAGGACTC
24556 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
24571 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
24586 CTA
1 CTA
24589 TTATACCCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.30, C:0.33, G:0.21, T:0.15
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:24720 original size:29 final size:29
Alignment explanation
Indices: 24673--24782 Score: 177
Period size: 29 Copynumber: 3.8 Consensus size: 29
24663 TTTTATATGT
* *
24673 TCATGTA-CTCATGTGATTTCTCTTGTGT
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
24701 TCATGTAGCTCATGTCATTTATCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
24730 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
24759 TCATGTAGCTCATGTCATGTTCTC
1 TCATGTAGCTCATGTCAT-TTCTC
24783 ATATCACATA
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
28 7 0.09
29 64 0.84
30 5 0.07
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.45
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:24778 original size:14 final size:14
Alignment explanation
Indices: 24701--24778 Score: 57
Period size: 14 Copynumber: 5.4 Consensus size: 14
24691 TCTCTTGTGT
24701 TCATGTAGCTCATG
1 TCATGTAGCTCATG
* * **
24715 TCATTTATCTTGTG
1 TCATGTAGCTCATG
24729 ATCATGTAGCTCATG
1 -TCATGTAGCTCATG
* ** **
24744 TCATTTCTCTTGTG
1 TCATGTAGCTCATG
24758 ATCATGTAGCTCATG
1 -TCATGTAGCTCATG
24773 TCATGT
1 TCATGT
24779 TCTCATATCA
Statistics
Matches: 44, Mismatches: 18, Indels: 4
0.67 0.27 0.06
Matches are distributed among these distances:
14 25 0.57
15 19 0.43
ACGTcount: A:0.19, C:0.19, G:0.18, T:0.44
Consensus pattern (14 bp):
TCATGTAGCTCATG
Found at i:25352 original size:64 final size:64
Alignment explanation
Indices: 25246--25384 Score: 190
Period size: 64 Copynumber: 2.2 Consensus size: 64
25236 TGAAGGTATA
* * * *
25246 CATCGATGCACTACTGATGCATCGGTGCATAAAATACTTTCGATGTTGT-ATTATTACTGGGATG
1 CATCGATGCACTACTGATGCATCGATGCACAAAATACATTCGATGTT-TCATTATTAATGGGATG
* * * *
25310 CATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTTTCATTATTAATGGGATG
1 CATCGATGCACTACTGATGCATCGATGCACAAAATACATTCGATGTTTCATTATTAATGGGATG
25374 CATCGATGCAC
1 CATCGATGCAC
25385 GAATTGCATT
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
63 1 0.02
64 65 0.98
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (64 bp):
CATCGATGCACTACTGATGCATCGATGCACAAAATACATTCGATGTTTCATTATTAATGGGATG
Found at i:25421 original size:45 final size:45
Alignment explanation
Indices: 25326--25429 Score: 149
Period size: 45 Copynumber: 2.3 Consensus size: 45
25316 TGCACTACTT
* *
25326 ATGCATCGATGCACGAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACGAATTGCATTCGATGTTTCATTATTAAAGAG
*
25371 ATGCATCGATGCACGAATTGCATTCGATGTATTTATT-TTAAA-AG
1 ATGCATCGATGCACGAATTGCATTCGATGT-TTCATTATTAAAGAG
25415 AGTGCATCGATGCAC
1 A-TGCATCGATGCAC
25430 TTCTTGTGCA
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
44 2 0.04
45 47 0.87
46 5 0.09
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (45 bp):
ATGCATCGATGCACGAATTGCATTCGATGTTTCATTATTAAAGAG
Found at i:29658 original size:29 final size:29
Alignment explanation
Indices: 29615--29724 Score: 186
Period size: 29 Copynumber: 3.8 Consensus size: 29
29605 TTTTATATGT
29615 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
29643 TCATGTAGATCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
29672 TCTTGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
29701 TCATGTAGCTCATGTCATGTTCTC
1 TCATGTAGCTCATGTCAT-TTCTC
29725 ATATCACATA
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
28 7 0.09
29 64 0.84
30 5 0.07
ACGTcount: A:0.17, C:0.21, G:0.16, T:0.45
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:30294 original size:64 final size:64
Alignment explanation
Indices: 30185--30355 Score: 245
Period size: 64 Copynumber: 2.7 Consensus size: 64
30175 TAATGAAGGT
* * * * ** * * *
30185 ATGCATCGATGCATTACTGATGCATCGGTACATAAAATGCTTTCGATGTTGT-ATTATTACTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTT-TCATTATTAATGGG
30249 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTTTCATTATTAATGGG
30313 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATT
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATT
30356 TAATGCATTT
Statistics
Matches: 97, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
63 1 0.01
64 96 0.99
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTTTCATTATTAATGGG
Found at i:30382 original size:64 final size:64
Alignment explanation
Indices: 30185--30405 Score: 198
Period size: 64 Copynumber: 3.5 Consensus size: 64
30175 TAATGAAGGT
* * * * ** * * * ** *
30185 ATGCATCGATGCATTACTGATGCATCGGTACATAAAATGCTTTCGATGTTGT-ATTATTACTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCAATGTT-TCATTATTAAAGAG
* * *
30249 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCAATGTTTCATTATTAAAGAG
*
30313 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTTAATGCATTT-ATT-TTAAA-A
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCAATG--TTTCATTATTAAAGA
30375 G
64 G
* * * *
30376 AGTGCATCGATGTACTTCCTGTGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
30406 ACATCTTCAA
Statistics
Matches: 136, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
63 3 0.02
64 127 0.93
65 3 0.02
66 3 0.02
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCAATGTTTCATTATTAAAGAG
Found at i:30951 original size:3 final size:3
Alignment explanation
Indices: 30943--30971 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
30933 TCTTGTACAT
30943 GAA GAA GAA GAA GAA GAA GAA GAA -AA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
30972 TATCTCTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:32378 original size:25 final size:25
Alignment explanation
Indices: 32348--32424 Score: 64
Period size: 25 Copynumber: 3.0 Consensus size: 25
32338 TTGTGGTGTC
32348 CTTTCTCCTTTCCCCTCTTCCTTTT
1 CTTTCTCCTTTCCCCTCTTCCTTTT
** * ** ** *
32373 CTTTCTTTTTTTCGGTCTTCGGTGT
1 CTTTCTCCTTTCCCCTCTTCCTTTT
*
32398 CTCTTCTCCTTTCTCCTCTTCCTTTT
1 CT-TTCTCCTTTCCCCTCTTCCTTTT
32424 C
1 C
32425 AACAAGTTCT
Statistics
Matches: 34, Mismatches: 17, Indels: 1
0.65 0.33 0.02
Matches are distributed among these distances:
25 19 0.56
26 15 0.44
ACGTcount: A:0.00, C:0.36, G:0.06, T:0.57
Consensus pattern (25 bp):
CTTTCTCCTTTCCCCTCTTCCTTTT
Found at i:39050 original size:75 final size:76
Alignment explanation
Indices: 38956--39150 Score: 200
Period size: 75 Copynumber: 2.6 Consensus size: 76
38946 CATAAATAAA
* * * *
38956 GTCAAATATCAAGAGTCAAACCACAATATTAAGAT-TAGAACAGTAAAATCCATAAACAAACCAC
1 GTCAAATTTCAAGACTCAAACCAAAATATTAAGATCTAGAACAATAAAATCCATAAACAAACCAC
39020 AATATTAAAAT
66 AATATTAAAAT
* * * * ** * *
39031 GTCAAATTTCAAGATTCAAACTAAAATATTAA-CTCTAGAATAATAAAATCCATAATGAAATCAT
1 GTCAAATTTCAAGACTCAAACCAAAATATTAAGATCTAGAACAATAAAATCCATAAACAAACCAC
*
39095 AATATTAAAGT
66 AATATTAAAAT
* * * *
39106 ATTAAATCTT-AAGACTCAAACCATAATATTAAG-TCTAGAAAAATA
1 GTCAAAT-TTCAAGACTCAAACCAAAATATTAAGATCTAGAACAATA
39151 TTAAACACAA
Statistics
Matches: 99, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
74 1 0.01
75 96 0.97
76 2 0.02
ACGTcount: A:0.52, C:0.14, G:0.07, T:0.27
Consensus pattern (76 bp):
GTCAAATTTCAAGACTCAAACCAAAATATTAAGATCTAGAACAATAAAATCCATAAACAAACCAC
AATATTAAAAT
Found at i:41089 original size:22 final size:22
Alignment explanation
Indices: 41060--41111 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
41050 CACAAAGTCC
*
41060 GATAAAAAATTGATCCGGATCAT
1 GATAAAAAATTGATCCGAATC-T
41083 -ATAAAAAATTGATCCGAATCT
1 GATAAAAAATTGATCCGAATCT
41104 GATAAAAA
1 GATAAAAA
41112 TTAATCTGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 1 0.04
22 26 0.96
ACGTcount: A:0.50, C:0.12, G:0.13, T:0.25
Consensus pattern (22 bp):
GATAAAAAATTGATCCGAATCT
Found at i:42286 original size:37 final size:36
Alignment explanation
Indices: 42211--42286 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
42201 TTTTTATATT
*
42211 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
42247 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
42284 TTT
1 TTT
42287 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:42469 original size:20 final size:20
Alignment explanation
Indices: 42432--42469 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
42422 ATCCTATTCC
* *
42432 CTGGTAATCTTTTGTTCCCA
1 CTGGTAATCTTATATTCCCA
42452 CTGGTAATCTTATATTCC
1 CTGGTAATCTTATATTCC
42470 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.24, G:0.13, T:0.45
Consensus pattern (20 bp):
CTGGTAATCTTATATTCCCA
Found at i:47560 original size:35 final size:35
Alignment explanation
Indices: 47507--47578 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
47497 CCTATTTTAG
*
47507 TGCCACTTAATGTGTAGTGTCAGTTAGTTTGTTTC
1 TGCCACTTAATGTATAGTGTCAGTTAGTTTGTTTC
*
47542 TGCCACTTAGTGTATAGTGTCAGTTAGTTTGTTTC
1 TGCCACTTAATGTATAGTGTCAGTTAGTTTGTTTC
47577 TG
1 TG
47579 AGAGTCTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.17, C:0.14, G:0.24, T:0.46
Consensus pattern (35 bp):
TGCCACTTAATGTATAGTGTCAGTTAGTTTGTTTC
Found at i:50129 original size:2 final size:2
Alignment explanation
Indices: 50122--50156 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
50112 ATTATATCAT
50122 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
50157 TAATGATTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:53415 original size:64 final size:65
Alignment explanation
Indices: 53300--53424 Score: 200
Period size: 64 Copynumber: 1.9 Consensus size: 65
53290 GAATGCATTT
* *
53300 CATGTATCGATGCACTCAGGGTTTTATGAAAACATCGAATGTATTTGATGCATCGATGCACCAGC
1 CATGTATCGATGCACTCAGGCTTTTATGAAAACATCGAATGCATTTGATGCATCGATGCACCAGC
*
53365 CATGTATCGATGCACTCAGGCTATTT-TG-AAACATCGAATGCATTTTATGCATCGATGCAC
1 CATGTATCGATGCACTCAGGCT-TTTATGAAAACATCGAATGCATTTGATGCATCGATGCAC
53425 ACTTAATGCA
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
64 30 0.54
65 23 0.41
66 3 0.05
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (65 bp):
CATGTATCGATGCACTCAGGCTTTTATGAAAACATCGAATGCATTTGATGCATCGATGCACCAGC
Done.