Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005949.1 Hibiscus syriacus cultivar Beakdansim tig00013970_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: 67210
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:81 original size:40 final size:40
Alignment explanation
Indices: 31--110 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
21 TAATGATAAA
*
31 TGCTTTGCTATTTGAAACTGTGGCCAACAAGTTACATGCT
1 TGCTTTGCTATTTGAAACTGTAGCCAACAAGTTACATGCT
71 TGCTTTGCTATTTGAAACTGTAGCCAACAAGTTACATGCT
1 TGCTTTGCTATTTGAAACTGTAGCCAACAAGTTACATGCT
111 CTTAAAACTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (40 bp):
TGCTTTGCTATTTGAAACTGTAGCCAACAAGTTACATGCT
Found at i:3189 original size:2 final size:2
Alignment explanation
Indices: 3178--3242 Score: 95
Period size: 2 Copynumber: 35.0 Consensus size: 2
3168 TTACCCTTTA
3178 AT AT AT -T AT AT AT AT AT AT -T AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3217 AT AT AT -T AT AT AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3243 TACTAATGTA
Statistics
Matches: 58, Mismatches: 0, Indels: 10
0.85 0.00 0.15
Matches are distributed among these distances:
1 5 0.09
2 53 0.91
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3194 original size:11 final size:10
Alignment explanation
Indices: 3178--3242 Score: 95
Period size: 9 Copynumber: 7.0 Consensus size: 10
3168 TTACCCTTTA
3178 ATATAT-TAT
1 ATATATATAT
3187 ATATATATAT
1 ATATATATAT
3197 -TATATATAT
1 ATATATATAT
3206 ATAT-TATAT
1 ATATATATAT
3215 ATATATAT-T
1 ATATATATAT
3224 ATATATA-AT
1 ATATATATAT
3233 ATATATATAT
1 ATATATATAT
3243 TACTAATGTA
Statistics
Matches: 51, Mismatches: 0, Indels: 9
0.85 0.00 0.15
Matches are distributed among these distances:
9 40 0.78
10 11 0.22
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
ATATATATAT
Found at i:3196 original size:13 final size:13
Alignment explanation
Indices: 3178--3242 Score: 116
Period size: 13 Copynumber: 5.2 Consensus size: 13
3168 TTACCCTTTA
3178 ATATATTATATAT
1 ATATATTATATAT
3191 ATATATTATATAT
1 ATATATTATATAT
3204 ATATATTATATAT
1 ATATATTATATAT
3217 ATATATTATATAT
1 ATATATTATATAT
3230 A-ATA-TATATAT
1 ATATATTATATAT
3241 AT
1 AT
3243 TACTAATGTA
Statistics
Matches: 51, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
11 8 0.16
12 3 0.06
13 40 0.78
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATATATTATATAT
Found at i:7496 original size:2 final size:2
Alignment explanation
Indices: 7485--7528 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
7475 TATACCCAAA
7485 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7526 AT A
1 AT A
7529 CAATAAGTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8888 original size:36 final size:36
Alignment explanation
Indices: 8858--8925 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
8848 GTTTTTCTTG
8858 AAACAAATTTTATCTCGCTTGAGATAGTTTTATTAA
1 AAACAAATTTTATCTCGCTTGAGATAGTTTTATTAA
* *
8894 AAACAAATTTTGTCTCGCTTGAGACA-TTTTAT
1 AAACAAATTTTATCTCGCTTGAGATAGTTTTAT
8926 CTCGGAATAC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 6 0.20
36 24 0.80
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.41
Consensus pattern (36 bp):
AAACAAATTTTATCTCGCTTGAGATAGTTTTATTAA
Found at i:9179 original size:67 final size:70
Alignment explanation
Indices: 9066--9196 Score: 178
Period size: 67 Copynumber: 1.9 Consensus size: 70
9056 AAAATTTACT
* * * * *
9066 ATCTTTGAGATCGTTTCTCTTGAAACAAATCTTATTTTTCTTGAGACATTTTCTCATGAAACAAT
1 ATCTTTGAGATCATTTCCCTTGAAACAAATCTTATGTCTCTTGAGACAGTTTCTCATGAAACAAT
9131 AAATC
66 AAATC
* *
9136 ATCTTTGAG-TCATTTCCCTTGAAACGAAT-TT-TGTCTCTTGAGACAGTTTCTCTTGAAACAA
1 ATCTTTGAGATCATTTCCCTTGAAACAAATCTTATGTCTCTTGAGACAGTTTCTCATGAAACAA
9197 ATCTTTGAGT
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
67 26 0.48
68 2 0.04
69 17 0.31
70 9 0.17
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.40
Consensus pattern (70 bp):
ATCTTTGAGATCATTTCCCTTGAAACAAATCTTATGTCTCTTGAGACAGTTTCTCATGAAACAAT
AAATC
Found at i:9193 original size:34 final size:35
Alignment explanation
Indices: 9070--9203 Score: 107
Period size: 34 Copynumber: 3.9 Consensus size: 35
9060 TTTACTATCT
* *
9070 TTGAGATC-GTTTCTCTTGAAACAAATCTTATTTTTC
1 TTGAGA-CAGTTTCTCTTGAAACAAATCTT-TGTCTC
* * ** **
9106 TTGAGACATTTTCTCATGAAAC-AATAAATCATCT-
1 TTGAGACAGTTTCTCTTGAAACAAAT-CTTTGTCTC
* * *
9140 TTGAGTCA-TTTCCCTTGAAACGAAT-TTTGTCTC
1 TTGAGACAGTTTCTCTTGAAACAAATCTTTGTCTC
9173 TTGAGACAGTTTCTCTTGAAACAAATCTTTG
1 TTGAGACAGTTTCTCTTGAAACAAATCTTTG
9204 AGTCTGTTCC
Statistics
Matches: 76, Mismatches: 16, Indels: 13
0.72 0.15 0.12
Matches are distributed among these distances:
32 4 0.05
33 18 0.24
34 25 0.33
35 10 0.13
36 19 0.25
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (35 bp):
TTGAGACAGTTTCTCTTGAAACAAATCTTTGTCTC
Found at i:10003 original size:131 final size:134
Alignment explanation
Indices: 9767--10109 Score: 362
Period size: 131 Copynumber: 2.6 Consensus size: 134
9757 AAACCATTAT
* * * *
9767 TCCTAAAGATGGCCTGCCGTCCTCATCACGTAGGAATCGTGTCATCCCCCGACCAGATCTTCTCA
1 TCCTAAAGATGGCCTGCCGTCATCATCACGTAGGAACCGTGCCATCCCCCGACCAGACCTTCTCA
*
9832 TCACGTAGGAGCCACGTCAACCCTAGATAACATGTCGTCCTCATCACGTAGGAA-CTGTGTTATC
66 TCACGTAAGAGCCACGTCAACCCTAGATAACATGTCGTCCTCATCACGTAGGAATC-GTGTTATC
9896 AC-CC
130 ACACC
* *
9900 TCCTAAAGATGGCCTGCCGTCATCATCGC-TAGGAACCGTGCCA-CCCCCGACTAGACC-TCTTC
1 TCCTAAAGATGGCCTGCCGTCATCATCACGTAGGAACCGTGCCATCCCCCGACCAGACCTTC-TC
** *
9962 ATCACGTAAGAGCCGTGTC-ACCCATAGATAACCA-GTCGTCCTCATCGCGTAGGAATCGTGTTA
65 ATCACGTAAGAGCCACGTCAACCC-TAGATAA-CATGTCGTCCTCATCACGTAGGAATCGTGTTA
* **
10025 TCGCATT
128 TCACACC
* * * * * * * * *
10032 TCCTAAAGATGGCCAGAAC-TCTTCATCAAGTATG-ACCAATGTCATCCCCCGACCAGATCTCCT
1 TCCTAAAGATGGCCTG-CCGTCATCATCACGTAGGAACC-GTGCCATCCCCCGACCAGACCTTCT
*
10095 CATCACGTAGGAGCC
64 CATCACGTAAGAGCC
10110 GAGTCACCCT
Statistics
Matches: 175, Mismatches: 25, Indels: 19
0.80 0.11 0.09
Matches are distributed among these distances:
130 6 0.03
131 66 0.38
132 40 0.23
133 35 0.20
134 27 0.15
135 1 0.01
ACGTcount: A:0.25, C:0.33, G:0.19, T:0.23
Consensus pattern (134 bp):
TCCTAAAGATGGCCTGCCGTCATCATCACGTAGGAACCGTGCCATCCCCCGACCAGACCTTCTCA
TCACGTAAGAGCCACGTCAACCCTAGATAACATGTCGTCCTCATCACGTAGGAATCGTGTTATCA
CACC
Found at i:10348 original size:21 final size:21
Alignment explanation
Indices: 10306--10349 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
10296 TCTACAAAAA
* *
10306 TATTATATTTATTATTATTAT
1 TATTATATTTATAATTAATAT
10327 TATTATATTTA-AATTACATAT
1 TATTATATTTATAATTA-ATAT
10348 TA
1 TA
10350 CATTTTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
TATTATATTTATAATTAATAT
Found at i:11574 original size:7 final size:8
Alignment explanation
Indices: 11561--11588 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
11551 TTGATTCATT
11561 TTTTTTTA
1 TTTTTTTA
11569 TTTTTTTA
1 TTTTTTTA
11577 TTTTTTTA
1 TTTTTTTA
11585 TTTT
1 TTTT
11589 ACGATTCTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTTTA
Found at i:11818 original size:21 final size:21
Alignment explanation
Indices: 11773--11823 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
11763 ATTTTTATTT
*
11773 TATTTCATTACATACACATGC
1 TATTTCATTACATACACATAC
11794 TATTTCATATAC-T-CACATAC
1 TATTTCAT-TACATACACATAC
11814 ATATTT-ATTA
1 -TATTTCATTA
11824 AATTTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 2 0.07
20 8 0.30
21 14 0.52
22 3 0.11
ACGTcount: A:0.35, C:0.20, G:0.02, T:0.43
Consensus pattern (21 bp):
TATTTCATTACATACACATAC
Found at i:12148 original size:21 final size:21
Alignment explanation
Indices: 12103--12153 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
12093 ATTTTTATTT
*
12103 TATTTCATTACATACACATGC
1 TATTTCATTACATACACATAC
12124 TATTTCATATAC-T-CACATAC
1 TATTTCAT-TACATACACATAC
12144 ATATTT-ATTA
1 -TATTTCATTA
12154 AATTTGTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 2 0.07
20 8 0.30
21 14 0.52
22 3 0.11
ACGTcount: A:0.35, C:0.20, G:0.02, T:0.43
Consensus pattern (21 bp):
TATTTCATTACATACACATAC
Found at i:12166 original size:330 final size:330
Alignment explanation
Indices: 11588--12192 Score: 1192
Period size: 330 Copynumber: 1.8 Consensus size: 330
11578 TTTTTTATTT
11588 TACGATTCTGATATTGTGTTCTTAATTTATGCAGTTTAGTCACTTGTTTTTAAAGCTTATTAATC
1 TACGATTCTGATATTGTGTTCTTAATTTATGCAGTTTAGTCACTTGTTTTTAAAGCTTATTAATC
11653 TTATGTTATTTGCATTATAGTATGCCATGTTTGCATGATTACATATTAACCCATGTTATAATATT
66 TTATGTTATTTGCATTATAGTATGCCATGTTTGCATGATTACATATTAACCCATGTTATAATATT
*
11718 CATGTACATATTCTGCTTCAAATGTATTGGTGTGTGTCTTAATTTATTTTTATTTTATTTCATTA
131 CATGTACATATTCTGCTTCAAATGTATTGGTGCGTGTCTTAATTTATTTTTATTTTATTTCATTA
*
11783 CATACACATGCTATTTCATATACTCACATACATATTTATTAAATTTTTTTTTTACCTTTTATGTT
196 CATACACATGCTATTTCATATACTCACATACATATTTATTAAATTTGTTTTTTACCTTTTATGTT
11848 CATATATATATATATTACTAATGTATATTCCATTTTATTCAATTTGATTTATTTTAATTTGTAAA
261 CATATATATATATATTACTAATGTATATTCCATTTTATTCAATTTGATTTATTTTAATTTGTAAA
11913 ATATC
326 ATATC
11918 TACGATTCTGATATTGTGTTCTTAATTTATGCAGTTTAGTCACTTGTTTTTAAAGCTTATTAATC
1 TACGATTCTGATATTGTGTTCTTAATTTATGCAGTTTAGTCACTTGTTTTTAAAGCTTATTAATC
11983 TTATGTTATTTGCATTATAGTATGCCATGTTTGCATGATTACATATTAACCCATGTTATAATATT
66 TTATGTTATTTGCATTATAGTATGCCATGTTTGCATGATTACATATTAACCCATGTTATAATATT
12048 CATGTACATATTCTGCTTCAAATGTATTGGTGCGTGTCTTAATTTATTTTTATTTTATTTCATTA
131 CATGTACATATTCTGCTTCAAATGTATTGGTGCGTGTCTTAATTTATTTTTATTTTATTTCATTA
12113 CATACACATGCTATTTCATATACTCACATACATATTTATTAAATTTGTTTTTTACCTTTTATGTT
196 CATACACATGCTATTTCATATACTCACATACATATTTATTAAATTTGTTTTTTACCTTTTATGTT
12178 CATATATATATATAT
261 CATATATATATATAT
12193 ATATATATAT
Statistics
Matches: 273, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
330 273 1.00
ACGTcount: A:0.28, C:0.13, G:0.10, T:0.50
Consensus pattern (330 bp):
TACGATTCTGATATTGTGTTCTTAATTTATGCAGTTTAGTCACTTGTTTTTAAAGCTTATTAATC
TTATGTTATTTGCATTATAGTATGCCATGTTTGCATGATTACATATTAACCCATGTTATAATATT
CATGTACATATTCTGCTTCAAATGTATTGGTGCGTGTCTTAATTTATTTTTATTTTATTTCATTA
CATACACATGCTATTTCATATACTCACATACATATTTATTAAATTTGTTTTTTACCTTTTATGTT
CATATATATATATATTACTAATGTATATTCCATTTTATTCAATTTGATTTATTTTAATTTGTAAA
ATATC
Found at i:12184 original size:2 final size:2
Alignment explanation
Indices: 12179--12216 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
12169 TTTTATGTTC
12179 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12217 TACTAATGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23282 original size:15 final size:16
Alignment explanation
Indices: 23250--23290 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
23240 ATATTATAAG
23250 TAAATAT-AATATATT
1 TAAATATAAATATATT
*
23265 TAAATATAAATTTA-T
1 TAAATATAAATATATT
23280 TAAAGTATAAA
1 TAAA-TATAAA
23291 AGTATAGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (16 bp):
TAAATATAAATATATT
Found at i:25115 original size:19 final size:20
Alignment explanation
Indices: 25077--25115 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
25067 ATATATATAT
* *
25077 TTAAATAAACTCGAACAATA
1 TTAAATAAAATCGAAAAATA
25097 TTAAA-AAAATCGAAAAATA
1 TTAAATAAAATCGAAAAATA
25116 ATATAAAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.62, C:0.10, G:0.05, T:0.23
Consensus pattern (20 bp):
TTAAATAAAATCGAAAAATA
Found at i:28005 original size:48 final size:48
Alignment explanation
Indices: 27866--28008 Score: 157
Period size: 48 Copynumber: 3.0 Consensus size: 48
27856 CAGAACTCCG
* * * * * *
27866 AGCACCTCCTCCCGGAAGACAAGAATCTGACAACACAAGTAAAGGTTT
1 AGCACCTTCTCCCGGAACACAAGAATCCGAAAACACAACTAAAGGTCT
*
27914 AGCA-CTTCCTCCCGGGACACAAGAATCC-AATAACACAACTAAAGGTCT
1 AGCACCTT-CTCCCGGAACACAAGAATCCGAA-AACACAACTAAAGGTCT
* *
27962 AGCACCTTCTCCTGGAACACAAGAATCCGAAAACTCGAA-TAAAGGTC
1 AGCACCTTCTCCCGGAACACAAGAATCCGAAAACAC-AACTAAAGGTC
28009 CAGGCGTACG
Statistics
Matches: 80, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
47 3 0.04
48 70 0.88
49 7 0.09
ACGTcount: A:0.38, C:0.29, G:0.17, T:0.17
Consensus pattern (48 bp):
AGCACCTTCTCCCGGAACACAAGAATCCGAAAACACAACTAAAGGTCT
Found at i:29187 original size:14 final size:14
Alignment explanation
Indices: 29153--29185 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
29143 AAACCCTAAC
*
29153 TTAGGGTTTATAAT
1 TTAGGGTTTATAAG
29167 TTAGGGTTT-TAAG
1 TTAGGGTTTATAAG
29180 TTAGGG
1 TTAGGG
29186 GTATGATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.24, C:0.00, G:0.30, T:0.45
Consensus pattern (14 bp):
TTAGGGTTTATAAG
Found at i:43102 original size:16 final size:16
Alignment explanation
Indices: 43078--43128 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
43068 GGTCTCCAAC
*
43078 GTTTATGTTCGTTTAT
1 GTTTGTGTTCGTTTAT
*
43094 GTTTGTGTTCATTTAT
1 GTTTGTGTTCGTTTAT
* *
43110 GTTCGCGTTCGTTTAT
1 GTTTGTGTTCGTTTAT
43126 GTT
1 GTT
43129 CGTTTATTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.10, C:0.10, G:0.22, T:0.59
Consensus pattern (16 bp):
GTTTGTGTTCGTTTAT
Found at i:43129 original size:16 final size:16
Alignment explanation
Indices: 43084--43130 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
43074 CAACGTTTAT
* *
43084 GTTCGTTTATGTTTGT
1 GTTCGTTTATGTTCGC
*
43100 GTTCATTTATGTTCGC
1 GTTCGTTTATGTTCGC
43116 GTTCGTTTATGTTCG
1 GTTCGTTTATGTTCG
43131 TTTATTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.09, C:0.13, G:0.23, T:0.55
Consensus pattern (16 bp):
GTTCGTTTATGTTCGC
Found at i:47474 original size:28 final size:28
Alignment explanation
Indices: 47404--47467 Score: 128
Period size: 28 Copynumber: 2.3 Consensus size: 28
47394 CCACATAATA
47404 GTTGCCACCTTAATTTGTATTGTAAGCT
1 GTTGCCACCTTAATTTGTATTGTAAGCT
47432 GTTGCCACCTTAATTTGTATTGTAAGCT
1 GTTGCCACCTTAATTTGTATTGTAAGCT
47460 GTTGCCAC
1 GTTGCCAC
47468 TTCAATTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.41
Consensus pattern (28 bp):
GTTGCCACCTTAATTTGTATTGTAAGCT
Found at i:49514 original size:7 final size:7
Alignment explanation
Indices: 49502--49613 Score: 224
Period size: 7 Copynumber: 16.0 Consensus size: 7
49492 TAAAAAAGAA
49502 TACGCCT
1 TACGCCT
49509 TACGCCT
1 TACGCCT
49516 TACGCCT
1 TACGCCT
49523 TACGCCT
1 TACGCCT
49530 TACGCCT
1 TACGCCT
49537 TACGCCT
1 TACGCCT
49544 TACGCCT
1 TACGCCT
49551 TACGCCT
1 TACGCCT
49558 TACGCCT
1 TACGCCT
49565 TACGCCT
1 TACGCCT
49572 TACGCCT
1 TACGCCT
49579 TACGCCT
1 TACGCCT
49586 TACGCCT
1 TACGCCT
49593 TACGCCT
1 TACGCCT
49600 TACGCCT
1 TACGCCT
49607 TACGCCT
1 TACGCCT
49614 AAGCTCTAGG
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 105 1.00
ACGTcount: A:0.14, C:0.43, G:0.14, T:0.29
Consensus pattern (7 bp):
TACGCCT
Found at i:50599 original size:19 final size:19
Alignment explanation
Indices: 50575--50612 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
50565 CCGCACATGG
50575 TCCAATTTTTGTAAGGGCC
1 TCCAATTTTTGTAAGGGCC
50594 TCCAATTTTTGTAAGGGCC
1 TCCAATTTTTGTAAGGGCC
50613 AATTTTTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (19 bp):
TCCAATTTTTGTAAGGGCC
Found at i:50616 original size:16 final size:17
Alignment explanation
Indices: 50576--50619 Score: 63
Period size: 19 Copynumber: 2.5 Consensus size: 17
50566 CGCACATGGT
50576 CCAATTTTTGTAAGGGCC
1 CCAATTTTTGTAAGGG-C
50594 TCCAATTTTTGTAAGGG-
1 -CCAATTTTTGTAAGGGC
50611 CCAATTTTT
1 CCAATTTTT
50620 TCTATAGTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.36
19 16 0.64
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41
Consensus pattern (17 bp):
CCAATTTTTGTAAGGGC
Found at i:52373 original size:21 final size:20
Alignment explanation
Indices: 52348--52400 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
52338 ATTTTCTTTA
* *
52348 TTATTTATTATTTTTATTGTT
1 TTATTTATT-TTATTATTATT
52369 TTATTTAATTTTATTATTATT
1 TTATTT-ATTTTATTATTATT
*
52390 TAATTTATTTT
1 TTATTTATTTT
52401 GCAATTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.18
21 20 0.71
22 3 0.11
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.74
Consensus pattern (20 bp):
TTATTTATTTTATTATTATT
Found at i:56893 original size:36 final size:36
Alignment explanation
Indices: 56835--56916 Score: 103
Period size: 36 Copynumber: 2.3 Consensus size: 36
56825 TAACATTTCC
* *
56835 AAACAAATTTTGTCTCAATTGAGACATTTTTGC-TAA
1 AAACAAATTTTGCCTCAATTGAGACAATTTT-CTTAA
* **
56871 AAATAAATTTTGCCTCGCTTGAGACAATTTTCTTAA
1 AAACAAATTTTGCCTCAATTGAGACAATTTTCTTAA
56907 AAACAAATTT
1 AAACAAATTT
56917 CGTCTCACTG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
35 1 0.03
36 38 0.97
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.38
Consensus pattern (36 bp):
AAACAAATTTTGCCTCAATTGAGACAATTTTCTTAA
Found at i:57049 original size:39 final size:39
Alignment explanation
Indices: 56973--57429 Score: 668
Period size: 39 Copynumber: 11.8 Consensus size: 39
56963 TTGATTAACT
* * *
56973 TTGAGATTGTTTCTCTC-AAA-ACAA-ATTTTATCTCGC
1 TTGAGATAGTTTCCCTCGAAACAAAAGATTTTATCTCGC
*
57009 TTGAGATAATTTCCCTCGAAACAAAAGATTTTATCTCGC
1 TTGAGATAGTTTCCCTCGAAACAAAAGATTTTATCTCGC
* *
57048 TTGAGATAGTTTCCCTCGAAACATAAGATTTTGTCTCGC
1 TTGAGATAGTTTCCCTCGAAACAAAAGATTTTATCTCGC
* * *
57087 TTGAGATAGTTTCCCTCGAAGCAAAATATTTTGTCTCGC
1 TTGAGATAGTTTCCCTCGAAACAAAAGATTTTATCTCGC
*
57126 TTGAGATAGTTTCCCTCGAAGCAAAAGATTTTATCTCGC
1 TTGAGATAGTTTCCCTCGAAACAAAAGATTTTATCTCGC
57165 TTGAGATAGTTTCCCTCGAAACAAAAGATTTTATCTCGC
1 TTGAGATAGTTTCCCTCGAAACAAAAGATTTTATCTCGC
*
57204 TTGAGATAGTTTCCCTCGTAACAAAAGATTTTATCTCGC
1 TTGAGATAGTTTCCCTCGAAACAAAAGATTTTATCTCGC
* * *
57243 TTGAGATAGTTTCCCTCGAAACAGAAGATTTTGTATCGC
1 TTGAGATAGTTTCCCTCGAAACAAAAGATTTTATCTCGC
* * ***
57282 TTGAGATAGTTTCTCTCGAAACAGAAGATTTTGGATCGC
1 TTGAGATAGTTTCCCTCGAAACAAAAGATTTTATCTCGC
* *
57321 TTGAGATAGTTTCCCTTGAAACAAAAGATTTTATATCGC
1 TTGAGATAGTTTCCCTCGAAACAAAAGATTTTATCTCGC
* *
57360 TTGAGATATTTTTCCTCGAAACAAAAGATTTTATCTCGC
1 TTGAGATAGTTTCCCTCGAAACAAAAGATTTTATCTCGC
* *
57399 TTGAGATAGTTTCCCTTGAAACAAAAAATTT
1 TTGAGATAGTTTCCCTCGAAACAAAAGATTT
57430 AAAGAAACTA
Statistics
Matches: 385, Mismatches: 33, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
36 14 0.04
37 3 0.01
38 3 0.01
39 365 0.95
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (39 bp):
TTGAGATAGTTTCCCTCGAAACAAAAGATTTTATCTCGC
Found at i:59051 original size:21 final size:20
Alignment explanation
Indices: 59027--59066 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
59017 TTTGTTATTT
* *
59027 TTATTCTTTTATTTAATTTTA
1 TTATTATTTAATTT-ATTTTA
59048 TTATTATTTAATTTATTTT
1 TTATTATTTAATTTATTTT
59067 GCAATTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (20 bp):
TTATTATTTAATTTATTTTA
Found at i:60969 original size:31 final size:31
Alignment explanation
Indices: 60934--60994 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
60924 CAATTACGTC
60934 GGGACCATATTACAAACAGACTAAATGTTGA
1 GGGACCATATTACAAACAGACTAAATGTTGA
* *
60965 GGGACTATATTACAAACGGACTAAATGTTG
1 GGGACCATATTACAAACAGACTAAATGTTG
60995 GAGGATTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (31 bp):
GGGACCATATTACAAACAGACTAAATGTTGA
Found at i:62211 original size:20 final size:19
Alignment explanation
Indices: 62186--62239 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
62176 GCGAAATAAA
62186 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATC-CCAG
** *
62206 AATCGCAAATCAGTTCCCAG
1 AATCGCAACGC-GATCCCAG
62226 AATCGCAACGCGAT
1 AATCGCAACGCGAT
62240 TATGAATAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAACGCGATCCCAG
Found at i:62252 original size:21 final size:21
Alignment explanation
Indices: 62226--62341 Score: 64
Period size: 20 Copynumber: 5.6 Consensus size: 21
62216 CAGTTCCCAG
*
62226 AATCGCAACGCGATTATGAAT
1 AATCGCAACGCGAATATGAAT
*
62247 AATCGCAATGC-AATA-GTACA-
1 AATCGCAACGCGAATATG-A-AT
** * * **
62267 AATTCGCATTGCGATTTTCCAT
1 AA-TCGCAACGCGAATATGAAT
*
62289 AATCGCAATGCGAATATGAA-
1 AATCGCAACGCGAATATGAAT
*
62309 AATCGCAACGCGAACAT--AT
1 AATCGCAACGCGAATATGAAT
62328 AAATCGCAACGCGA
1 -AATCGCAACGCGA
62342 TTCTGACTAT
Statistics
Matches: 73, Mismatches: 14, Indels: 17
0.70 0.13 0.16
Matches are distributed among these distances:
18 1 0.01
19 1 0.01
20 34 0.47
21 33 0.45
22 4 0.05
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (21 bp):
AATCGCAACGCGAATATGAAT
Found at i:62314 original size:20 final size:20
Alignment explanation
Indices: 62289--62566 Score: 116
Period size: 20 Copynumber: 13.7 Consensus size: 20
62279 GATTTTCCAT
*
62289 AATCGCAATGCGAATATGAA
1 AATCGCAACGCGAATATGAA
*
62309 AATCGCAACGCGAACAT-ATA
1 AATCGCAACGCGAATATGA-A
* * *
62329 AATCGCAACGCGATTCTGAC
1 AATCGCAACGCGAATATGAA
* * * * **
62349 TATCGCAATGAGTATCCGTAA
1 AATCGCAACGCGAATATG-AA
* ** *
62370 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATATGAA
*
62390 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATATG-AA
* * *
62411 AATAGCAACGCGTATATCCGTA
1 AATCGCAACGCGAATAT--GAA
* * *
62433 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATATGAA
* * *
62453 AATCGCAACGCGTATCTGTA
1 AATCGCAACGCGAATATGAA
* * *
62473 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATATGAA
* * *
62493 AATCGTAATGCG--TATCCATA
1 AATCGCAACGCGAATAT-GA-A
62513 AATCGCAACGAC-AATATGTAA
1 AATCGCAACG-CGAATATG-AA
* ** *
62534 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATATGAA
62554 AATCGCAACGCGA
1 AATCGCAACGCGA
62567 TTTTTAAAGC
Statistics
Matches: 193, Mismatches: 50, Indels: 30
0.71 0.18 0.11
Matches are distributed among these distances:
18 2 0.01
19 1 0.01
20 125 0.65
21 46 0.24
22 18 0.09
23 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAATATGAA
Found at i:62485 original size:40 final size:41
Alignment explanation
Indices: 62350--62563 Score: 297
Period size: 40 Copynumber: 5.2 Consensus size: 41
62340 GATTCTGACT
* * *
62350 ATCGCAATGAGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
62391 ATCGCAACGACAATACGTAAAATAGCAACGCGTATATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCG--TATCCGTAA
*
62434 ATCGCAACGAGAATACGT-AAATCGCAACGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* * *
62474 ATCGCAACGAGAATACGT-AAATCGTAATGCGTATCCATAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
62514 ATCGCAACGACAATATGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
62555 ATCGCAACG
1 ATCGCAACG
62564 CGATTTTTAA
Statistics
Matches: 153, Mismatches: 17, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
40 60 0.39
41 55 0.36
42 12 0.08
43 26 0.17
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.20
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:63134 original size:20 final size:20
Alignment explanation
Indices: 63105--63195 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
63095 TTCTAAACTT
* *
63105 AAAATTGCAACATGAAAATG
1 AAAATCGCAACACGAAAATG
63125 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** *
63145 ACTATTGCAACGA-GAGAAATG
1 AAAATCGCAAC-ACGA-AAATG
*
63166 AAAATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
63185 AAAATCGCAAC
1 AAAATCGCAAC
63196 GAGATAATCG
Statistics
Matches: 59, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
19 16 0.27
20 28 0.47
21 15 0.25
ACGTcount: A:0.51, C:0.18, G:0.18, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:63184 original size:19 final size:19
Alignment explanation
Indices: 63120--63196 Score: 82
Period size: 19 Copynumber: 3.9 Consensus size: 19
63110 TGCAACATGA
*
63120 AAATGAAAATCGCAACACG
1 AAATGAAAATCGCAACGCG
** * *
63139 AAAATGACTATTGCAACGAGAG
1 -AAATGAAAATCGCAAC--GCG
63161 AAATGAAAATCGCAACGCG
1 AAATGAAAATCGCAACGCG
63180 AAATGAAAATCGCAACG
1 AAATGAAAATCGCAACG
63197 AGATAATCGC
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
19 19 0.41
20 13 0.28
21 13 0.28
22 1 0.02
ACGTcount: A:0.49, C:0.18, G:0.19, T:0.13
Consensus pattern (19 bp):
AAATGAAAATCGCAACGCG
Found at i:63184 original size:40 final size:40
Alignment explanation
Indices: 63105--63199 Score: 122
Period size: 40 Copynumber: 2.4 Consensus size: 40
63095 TTCTAAACTT
63105 AAAATTGCAAC-ATGAAAATGAAAATCGCAACACGAAAATG
1 AAAATTGCAACGA-GAAAATGAAAATCGCAACACGAAAATG
** *
63145 ACTATTGCAACGAGAGAAATGAAAATCGCAACGCG-AAATG
1 AAAATTGCAACGAGA-AAATGAAAATCGCAACACGAAAATG
*
63185 AAAATCGCAACGAGA
1 AAAATTGCAACGAGA
63200 TAATCGCAAC
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
40 28 0.60
41 19 0.40
ACGTcount: A:0.51, C:0.17, G:0.19, T:0.14
Consensus pattern (40 bp):
AAAATTGCAACGAGAAAATGAAAATCGCAACACGAAAATG
Found at i:63268 original size:33 final size:33
Alignment explanation
Indices: 63226--63320 Score: 145
Period size: 33 Copynumber: 2.8 Consensus size: 33
63216 CCAAAATCGT
63226 ATTGCGATTTTCATTTCGCGTTGCGATTCTCTC
1 ATTGCGATTTTCATTTCGCGTTGCGATTCTCTC
63259 ATTGCGATTTTCATTTCGCGTTGCGATTCTCTC
1 ATTGCGATTTTCATTTCGCGTTGCGATTCTCTC
* ** *
63292 GTTGCGATAGTCATTTCCGTGTTGCGATT
1 ATTGCGATTTTCATTT-CGCGTTGCGATT
63321 TTCATTCTCT
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 46 0.81
34 11 0.19
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.44
Consensus pattern (33 bp):
ATTGCGATTTTCATTTCGCGTTGCGATTCTCTC
Found at i:63325 original size:20 final size:21
Alignment explanation
Indices: 63285--63348 Score: 80
Period size: 20 Copynumber: 3.1 Consensus size: 21
63275 CGCGTTGCGA
**
63285 TTCTCTCGTTGCGATAGTCAT
1 TTCTCTCGTTGCGATTTTCAT
63306 TTC-CGT-GTTGCGATTTTCA-
1 TTCTC-TCGTTGCGATTTTCAT
63325 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
63346 TTC
1 TTC
63349 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
19 4 0.11
20 26 0.70
21 7 0.19
ACGTcount: A:0.11, C:0.23, G:0.17, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:65341 original size:21 final size:21
Alignment explanation
Indices: 65317--65383 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
65307 TCATTCATCG
65317 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
65338 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
65359 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
65380 AGAG
1 AGAG
65384 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:65341 original size:42 final size:42
Alignment explanation
Indices: 65290--65383 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 42
65280 CCACTCCTAT
* *
65290 CGTTGAAGAGGCCCCTATCATTCATCG-AGA-GTCCCCTCCCAC
1 CGTTCAAGAGGCCACTATCA-TCATCGAAGAGGT-CCCTCCCAC
* * *
65332 CGTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCAC
1 CGTTCAAGAGGCCACTATCATCATCGAAGAGGTCCCTCCCAC
*
65374 CATTCAAGAG
1 CGTTCAAGAG
65384 CCCGATTCAC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
41 4 0.09
42 38 0.86
43 2 0.05
ACGTcount: A:0.23, C:0.34, G:0.21, T:0.21
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATCATCGAAGAGGTCCCTCCCAC
Done.