Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008835.1 Hibiscus syriacus cultivar Beakdansim tig00112034_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: 40002
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:294 original size:109 final size:114
Alignment explanation
Indices: 1--776 Score: 546
Period size: 123 Copynumber: 6.7 Consensus size: 114
*
1 CATTT-CGGAAGAGTTCATAATGAGAAGAACTCATCT--GAA-GAATGAAGAAGTTCATAATAAG
1 CATTTCCGGAAGAGTTCATAATGAGAAGAACTCATCTGAGAAGGAA-GAAGAAGTTCATAATGAG
* * * *
62 -ATAA-TTGTTCAACATTTTACTCGAATTC-ATC-ACTAGAT-GA--ATCAT
65 AAGAACTTGTTCAACCTTTTGCTCG-ATTCAATCAAATAGATAGATCA-CAT
* * *
107 CATTGCCAGAGAA-AGTTC--AATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAAAATG
1 CATTTCC-G-GAAGAGTTCATAATGAGAAGAACTCATCTG-AGAAGGAAGAAGAAGTTCATAATG
* * *
169 AGAAGAACTTG-TCAACCTTTTGCTTGAATTC-ATC-ACTCGAT-GATCA-A-
63 AGAAGAACTTGTTCAACCTTTTGCTCG-ATTCAATCAAATAGATAGATCACAT
*
216 CATTTCCGGAAGAGTTCATAATGAGAAGAACTCATCTGAGAAGGAAGAACAAGTTCATAATGAGA
1 CATTTCCGGAAGAGTTCATAATGAGAAGAACTCATCTGAGAAGGAAGAAGAAGTTCATAATGAGA
*
281 AGAA-TTGTTCAACCTTTTGCTCGATTCTATCAAGAAATAGATAGATCAGCAT
66 AGAACTTGTTCAACCTTTTGCTCGATTCAATC---AAATAGATAGATCA-CAT
* * * *
333 CAAAATTT-CAGAAGTGTTCATAATGA-AA-AACTCTTCTGAG-AGGAATAAGAAG-TCATAATG
1 C---ATTTCCGGAAGAGTTCATAATGAGAAGAACTCATCTGAGAAGGAAGAAGAAGTTCATAATG
* *
393 AGAAGAATTTGTTCAACCTTTTTGCTCGATTCAATCAAAGAAAGAGATAGATCATCAT
63 AGAAGAACTTGTTCAACC-TTTTGCTCGATTCAATC----AAATAGATAGATCA-CAT
* * *
451 CAAAATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGA-AGAGGAATAAGAAGTTCATAAT
1 C---ATTTCCGGAAGAGTTCATAATGAGAAGAACTCATCTGAGA-AGGAAGAAGAAGTTCATAAT
* * * *
515 GAGAAGAACTTGTTCAACCTTTTG-TATGACTCTATCACAGAAGGAGATAGATCAGCAT
62 GAGAAGAACTTGTTCAACCTTTTGCT-CGATTCAAT--CA-AA-TAGATAGATCA-CAT
* * *
573 CAACTTTTCCAGAGAA-AGTTCATAATGAGAAGAACTTATCTGA-AGATGAAGTAGAAGTTCATA
1 C-A--TTTCC-G-GAAGAGTTCATAATGAGAAGAACTCATCTGAGA-AGGAAGAAGAAGTTCATA
* * *
636 ATGAGAAGAGC-TGTTCAACCTTTGTATGACTCTA-TC-A-CAGAAGGAGATAGATCAACAT
60 ATGAGAAGAACTTGTTCAACC-TT-T-TG-CTCGATTCAATCA-AA-TAGATAGATC-ACAT
* * *
694 CAACATTTCCAGAAGTGTTCATAATGA-AAGAA-TCATCTGA-AGAGGAAGAAGAAATTCATAAT
1 ---CATTTCCGGAAGAGTTCATAATGAGAAGAACTCATCTGAGA-AGGAAGAAGAAGTTCATAAT
*
756 GAGAATAACTTGTTCAACCTT
62 GAGAAGAACTTGTTCAACCTT
777 GCTTTAATTC
Statistics
Matches: 567, Mismatches: 47, Indels: 100
0.79 0.07 0.14
Matches are distributed among these distances:
106 21 0.04
107 4 0.01
108 19 0.03
109 74 0.13
110 53 0.09
111 3 0.01
112 1 0.00
113 5 0.01
114 5 0.01
115 15 0.03
116 21 0.04
117 28 0.05
118 64 0.11
119 51 0.09
120 20 0.04
121 37 0.07
122 53 0.09
123 80 0.14
124 7 0.01
125 4 0.01
126 1 0.00
127 1 0.00
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (114 bp):
CATTTCCGGAAGAGTTCATAATGAGAAGAACTCATCTGAGAAGGAAGAAGAAGTTCATAATGAGA
AGAACTTGTTCAACCTTTTGCTCGATTCAATCAAATAGATAGATCACAT
Found at i:536 original size:123 final size:123
Alignment explanation
Indices: 211--776 Score: 707
Period size: 123 Copynumber: 4.7 Consensus size: 123
201 TCACTCGATG
* * * *
211 ATCAACATTTCCGGAAGAGTTCATAATGAGAAGAACTCATCTG-AGAAGGAAGAACAAGTTCATA
1 ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAG-AGGAATAAGAAGTTCATA
* *
275 ATGAGAAGAA-TTGTTCAACC-TTTTGCTCGATTCTATC-AAGAAATAGATAGATCAGC
65 ATGAGAAGAACTTGTTCAACCTTTTTGCTCGACTCTATCAAAGAAAGAGATAGATCAGC
* *
331 ATCAAAATTT-CAGAAGTGTTCATAATGA-AA-AACTCTTCTG-AGAGGAATAAGAAG-TCATAA
1 ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAGGAATAAGAAGTTCATAA
* * * *
391 TGAGAAGAATTTGTTCAACCTTTTTGCTCGATTCAATCAAAGAAAGAGATAGATCATC
66 TGAGAAGAACTTGTTCAACCTTTTTGCTCGACTCTATCAAAGAAAGAGATAGATCAGC
*
449 ATCAAAATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAGGAATAAGAAGTTCATAA
1 ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAGGAATAAGAAGTTCATAA
* * *
514 TGAGAAGAACTTGTTCAACC-TTTTG-TATGACTCTATCACAGAAGGAGATAGATCAGC
66 TGAGAAGAACTTGTTCAACCTTTTTGCT-CGACTCTATCAAAGAAAGAGATAGATCAGC
* ** * *
571 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGATGAAGT-AGAAGTTCAT
1 ATCAACATTTCCAGA-AGTGTTCATAATGAGAAGAACTCATCTGAAGAGGAA-TAAGAAGTTCAT
* * * * * *
635 AATGAGAAGAGC-TGTTCAACCTTTGT-AT-GACTCTATCACAGAAGGAGATAGATCAAC
64 AATGAGAAGAACTTGTTCAACCTTTTTGCTCGACTCTATCAAAGAAAGAGATAGATCAGC
* *
692 ATCAACATTTCCAGAAGTGTTCATAATGA-AAGAA-TCATCTGAAGAGGAAGAAGAAATTCATAA
1 ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAGGAATAAGAAGTTCATAA
*
755 TGAGAATAACTTGTTCAACCTT
66 TGAGAAGAACTTGTTCAACCTT
777 GCTTTAATTC
Statistics
Matches: 396, Mismatches: 35, Indels: 31
0.86 0.08 0.07
Matches are distributed among these distances:
115 15 0.04
116 20 0.05
117 27 0.07
118 61 0.15
119 50 0.13
120 23 0.06
121 52 0.13
122 65 0.16
123 82 0.21
124 1 0.00
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.27
Consensus pattern (123 bp):
ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAGGAATAAGAAGTTCATAA
TGAGAAGAACTTGTTCAACCTTTTTGCTCGACTCTATCAAAGAAAGAGATAGATCAGC
Found at i:1008 original size:19 final size:19
Alignment explanation
Indices: 954--1010 Score: 59
Period size: 17 Copynumber: 3.2 Consensus size: 19
944 ATTCCCAGTG
954 GAAGAGTTCATAAT-AGAA
1 GAAGAGTTCATAATAAGAA
* *
972 GAACTAG-TCCT-A-AAGAA
1 GAA-GAGTTCATAATAAGAA
989 GAAGAGTTCATAATAAGAA
1 GAAGAGTTCATAATAAGAA
1008 GAA
1 GAA
1011 TTTGTTCAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 9
0.70 0.09 0.21
Matches are distributed among these distances:
16 2 0.07
17 11 0.37
18 7 0.23
19 10 0.33
ACGTcount: A:0.51, C:0.09, G:0.21, T:0.19
Consensus pattern (19 bp):
GAAGAGTTCATAATAAGAA
Found at i:1229 original size:21 final size:21
Alignment explanation
Indices: 1199--1280 Score: 94
Period size: 21 Copynumber: 4.0 Consensus size: 21
1189 TTAATTTTAT
*
1199 AGGCCCAGATCTAGAACCCGG
1 AGGCCCAGATCCAGAACCCGG
* * * *
1220 AGGCCTAGATCTAGAACCTGA
1 AGGCCCAGATCCAGAACCCGG
*
1241 AGGCCCAGATCCAAAACCCGG
1 AGGCCCAGATCCAGAACCCGG
*
1262 AAGCCCAGATCCAG-ACCCG
1 AGGCCCAGATCCAGAACCCG
1281 ACCCAACACC
Statistics
Matches: 51, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
20 5 0.10
21 46 0.90
ACGTcount: A:0.32, C:0.34, G:0.24, T:0.10
Consensus pattern (21 bp):
AGGCCCAGATCCAGAACCCGG
Found at i:3542 original size:2 final size:2
Alignment explanation
Indices: 3535--3559 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3525 AAAATAAAGG
3535 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
3560 TTTCTTAAAA
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:7117 original size:41 final size:42
Alignment explanation
Indices: 7070--7162 Score: 134
Period size: 42 Copynumber: 2.2 Consensus size: 42
7060 CTTACAAATT
* *
7070 ACCCGAAGGTTTTAATCATCATGCTC-AAAGACTTACTGATG
1 ACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATG
* *
7111 ACCCGAAGGATTTAGGCATCATTCTCGAAAGACTTACTGATG
1 ACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATG
*
7153 GCCCGAAGGA
1 ACCCGAAGGA
7163 CTTATAAATC
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 22 0.48
42 24 0.52
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.25
Consensus pattern (42 bp):
ACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATG
Found at i:7575 original size:215 final size:215
Alignment explanation
Indices: 7084--8134 Score: 1594
Period size: 215 Copynumber: 4.9 Consensus size: 215
7074 GAAGGTTTTA
* * * * *
7084 ATCATCATGCTC-AAAGACTTACTGATGACCCGAAGGATTTAGGCATCATTCTCGAAAGACTTAC
1 ATCATCTTGCTCTAAAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTAC
* *
7148 TGATGGCCCGAAGGACTTATAAATCGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTC
66 TGATGGCCCGAAGGACTTATAAATCGTGAAATTTTGAAAATCGCCTTCTTCGTTTTAAAAAATTC
* *
7213 CATCTTCTTAAAACACCATTTTTTTCATTTTCAAATTCATGTGAAAACATCCTACTCGAAGGTTT
131 CATCTTCTTAAAACATCA-TTTTTTCATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTTT
*
7278 TATGGATGGCCCAAAGGACTT
195 TATGGATGGCCCGAAGGACTT
* *
7299 ATCATCTTGCTCTAAAGGCTTACAGATGACCCGAATGATTTAAGCATTATGCTCGAAAGACTTAC
1 ATCATCTTGCTCTAAAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTAC
*
7364 TGATGGCCCGAAGGACTTATAAATCGTGAAATTTTGAAAATTGCCTTCTTCGTTTTAAAAAATTC
66 TGATGGCCCGAAGGACTTATAAATCGTGAAATTTTGAAAATCGCCTTCTTCGTTTTAAAAAATTC
* *
7429 CATCTTCTTAAAACATCATTTTTTCATTTTCAAATTCATGTGAAAATATCATACCCGAAGGTTTT
131 CATCTTCTTAAAACATCATTTTTTCATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTTTT
*
7494 ATGGATGGTCCGAAGGACTT
196 ATGGATGGCCCGAAGGACTT
* *
7514 ATCATCTTGCTCTAAAGGCTTACAGATGACACGAAGGATTTAAGCATCATGCTCAAAAGACTTAC
1 ATCATCTTGCTCTAAAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTAC
* *
7579 TGATGGCCCGAAGGACTTATAAATCGTGAAATTTTGAAAATCACATTCTTCGTTTTAAAAAATTC
66 TGATGGCCCGAAGGACTTATAAATCGTGAAATTTTGAAAATCGCCTTCTTCGTTTTAAAAAATTC
**
7644 CATCTTCTTAAAACATCA--TTTT--TTTTCATTTTCATGTGAAAACATCCTACCCGAAGGTTTT
131 CATCTTCTTAAAACATCATTTTTTCATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTTTT
7705 ATGGATGGCCCGAAGGACTT
196 ATGGATGGCCCGAAGGACTT
** *
7725 ATCATCTTTATCTAAAGGCTTACAGATGACCCGAAGGATTTAAACATCATGCTCGAAAGACTTAC
1 ATCATCTTGCTCTAAAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTAC
* * *
7790 TGATGGCCCGAAGGACTTATAAATCGTGAAATTTTAAAAATCGTCTTCTTCATTTTCAAAAAA-T
66 TGATGGCCCGAAGGACTTATAAATCGTGAAATTTTGAAAATCGCCTTCTTCGTTTT-AAAAAATT
* *
7854 CCATCTTCTTAAAACATCATTTTTTTCA--TT----TTCATGTGAAAACATCCTACCC-AAGCTC
130 CCATCTTCTTAAAACATCA-TTTTTTCATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTT
*
7912 TTATGGATGGCCCGAAGGACTC
194 TTATGGATGGCCCGAAGGACTT
7934 ATCATCTTGCTCTTAAAGGCTTACAGATGACCCGAA-GATTTAAGCATCATGCTCGAAAGACTTA
1 ATCATCTTGCTC-TAAAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTA
** * * * *
7998 CTGATGGCCCGAAGGACTTATAAATTATGAAATTTTGAAAATC-ACAT-TTCGTTTTCAAGAATT
65 CTGATGGCCCGAAGGACTTATAAATCGTGAAATTTTGAAAATCGCCTTCTTCGTTTTAAAAAATT
* * *
8061 CCATCTTCTTAAAACTTCATTTTTTCATTTTCAAATTCATATGAAAACATCATACCCGAAGGTTT
130 CCATCTTCTTAAAACATCATTTTTTCATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTTT
8126 TATGGATGG
195 TATGGATGG
8135 ATTTGCTTTA
Statistics
Matches: 763, Mismatches: 57, Indels: 34
0.89 0.07 0.04
Matches are distributed among these distances:
206 12 0.02
207 26 0.03
208 4 0.01
209 102 0.13
210 45 0.06
211 185 0.24
212 26 0.03
213 18 0.02
214 6 0.01
215 214 0.28
216 125 0.16
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (215 bp):
ATCATCTTGCTCTAAAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTAC
TGATGGCCCGAAGGACTTATAAATCGTGAAATTTTGAAAATCGCCTTCTTCGTTTTAAAAAATTC
CATCTTCTTAAAACATCATTTTTTCATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTTTT
ATGGATGGCCCGAAGGACTT
Found at i:7870 original size:426 final size:420
Alignment explanation
Indices: 7084--8134 Score: 1567
Period size: 426 Copynumber: 2.5 Consensus size: 420
7074 GAAGGTTTTA
* * * * *
7084 ATCATCATGCTC-AAAGACTTACTGATGACCCGAAGGATTTAGGCATCATTCTCGAAAGACTTAC
1 ATCATCTTGCTCTAAAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTAC
*
7148 TGATGGCCCGAAGGACTTATAAATCGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTC
66 TGATGGCCCGAAGGACTTATAAATCGTGAAATTTTGAAAATCACATTCTTCGTTTTCAAAAATTC
* *
7213 CATCTTCTTAAAACACCA-TTTTTTTCATTTTCAAATTCATGTGAAAACATCCTACTCGAAGGTT
131 CATCTTCTTAAAACATCATTTTTTTTCA--TT----TTCATGTGAAAACATCCTACCCGAAGGTT
* *
7277 TTATGGATGGCCCAAAGGACTTATCATCTTGCTCTAAAGGCTTACAGATGACCCGAATGATTTAA
190 TTATGGATGGCCCAAAGGACTTATCATCTTGATCTAAAGGCTTACAGATGACCCGAAGGATTTAA
* * * *
7342 GCATTATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATCGTGAAATTTTGAAAATTG
255 ACATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATCGTGAAATTTTAAAAATCG
*
7407 CCTTCTTCGTTTTAAAAAATTCCATCTTCTTAAAACATCA-TTTTTTCATTTTCAAATTCATGTG
320 CCTTCTTCATTTTAAAAAATTCCATCTTCTTAAAACATCATTTTTTTCA--TT----TTCATGTG
* * * * *
7471 AAAATATCATACCCGAAGGTTTTATGGATGGTCCGAAGGACTT
379 AAAACATCATACCC-AAGCTCTTATGGATGGCCCGAAGGACTC
* *
7514 ATCATCTTGCTCTAAAGGCTTACAGATGACACGAAGGATTTAAGCATCATGCTCAAAAGACTTAC
1 ATCATCTTGCTCTAAAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTAC
*
7579 TGATGGCCCGAAGGACTTATAAATCGTGAAATTTTGAAAATCACATTCTTCGTTTTAAAAAATTC
66 TGATGGCCCGAAGGACTTATAAATCGTGAAATTTTGAAAATCACATTCTTCGTTTTCAAAAATTC
7644 CATCTTCTTAAAACATCATTTTTTTTCATTTTCATGTGAAAACATCCTACCCGAAGGTTTTATGG
131 CATCTTCTTAAAACATCATTTTTTTTCATTTTCATGTGAAAACATCCTACCCGAAGGTTTTATGG
* *
7709 ATGGCCCGAAGGACTTATCATCTTTATCTAAAGGCTTACAGATGACCCGAAGGATTTAAACATCA
196 ATGGCCCAAAGGACTTATCATCTTGATCTAAAGGCTTACAGATGACCCGAAGGATTTAAACATCA
*
7774 TGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATCGTGAAATTTTAAAAATCGTCTTCT
261 TGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATCGTGAAATTTTAAAAATCGCCTTCT
*
7839 TCATTTTCAAAAAA-TCCATCTTCTTAAAACATCATTTTTTTCATTTTCATGTGAAAACATCCTA
326 TCATTTT-AAAAAATTCCATCTTCTTAAAACATCATTTTTTTCATTTTCATGTGAAAACATCATA
7903 CCCAAGCTCTTATGGATGGCCCGAAGGACTC
390 CCCAAGCTCTTATGGATGGCCCGAAGGACTC
7934 ATCATCTTGCTCTTAAAGGCTTACAGATGACCCGAA-GATTTAAGCATCATGCTCGAAAGACTTA
1 ATCATCTTGCTC-TAAAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTA
** *
7998 CTGATGGCCCGAAGGACTTATAAATTATGAAATTTTGAAAATCACA-T-TTCGTTTTCAAGAATT
65 CTGATGGCCCGAAGGACTTATAAATCGTGAAATTTTGAAAATCACATTCTTCGTTTTCAAAAATT
* ** * *
8061 CCATCTTCTTAAAACTTCATTTTTTCATTTTCAAATTCATATGAAAACATCATACCCGAAGGTTT
130 CCATCTTCTTAAAACATCA--TTTT--TTTTCATTTTCATGTGAAAACATCCTACCCGAAGGTTT
8126 TATGGATGG
191 TATGGATGG
8135 ATTTGCTTTA
Statistics
Matches: 574, Mismatches: 38, Indels: 26
0.90 0.06 0.04
Matches are distributed among these distances:
418 32 0.06
419 1 0.00
420 111 0.19
421 42 0.07
422 43 0.07
425 2 0.00
426 181 0.32
427 14 0.02
430 13 0.02
431 126 0.22
432 9 0.02
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (420 bp):
ATCATCTTGCTCTAAAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTAC
TGATGGCCCGAAGGACTTATAAATCGTGAAATTTTGAAAATCACATTCTTCGTTTTCAAAAATTC
CATCTTCTTAAAACATCATTTTTTTTCATTTTCATGTGAAAACATCCTACCCGAAGGTTTTATGG
ATGGCCCAAAGGACTTATCATCTTGATCTAAAGGCTTACAGATGACCCGAAGGATTTAAACATCA
TGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATCGTGAAATTTTAAAAATCGCCTTCT
TCATTTTAAAAAATTCCATCTTCTTAAAACATCATTTTTTTCATTTTCATGTGAAAACATCATAC
CCAAGCTCTTATGGATGGCCCGAAGGACTC
Found at i:8176 original size:34 final size:34
Alignment explanation
Indices: 8138--8343 Score: 261
Period size: 35 Copynumber: 5.9 Consensus size: 34
8128 TGGATGGATT
*
8138 TGCTTTACTACTCTTCGGTGAAGGCTTAAGATGG
1 TGCTTCACTACTCTTCGGTGAAGGCTTAAGATGG
* *
8172 TGCTTCACTACTCCTCTGTGAAGGCTTAAGATGG
1 TGCTTCACTACTCTTCGGTGAAGGCTTAAGATGG
* *
8206 TGCTTCACTACTCTTCTGTGAAGGCTTAAGATGAT
1 TGCTTCACTACTCTTCGGTGAAGGCTTAAGATG-G
* *
8241 TGCTTCACTATTCTTCGGTGAAGGCTTAAGATGAT
1 TGCTTCACTACTCTTCGGTGAAGGCTTAAGATG-G
* *
8276 TGCTTCACTTCTCTCCGGTGAAGGCTTAAGATGG
1 TGCTTCACTACTCTTCGGTGAAGGCTTAAGATGG
* *
8310 TTTGATTCACT-CATCTTTGGTGAAGGCTTAAGAT
1 --TGCTTCACTAC-TCTTCGGTGAAGGCTTAAGAT
8344 TGACTTGCCC
Statistics
Matches: 154, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
34 63 0.41
35 64 0.42
36 27 0.18
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (34 bp):
TGCTTCACTACTCTTCGGTGAAGGCTTAAGATGG
Found at i:8256 original size:35 final size:34
Alignment explanation
Indices: 8137--8343 Score: 263
Period size: 34 Copynumber: 6.0 Consensus size: 34
8127 ATGGATGGAT
*
8137 TTGCTTTACTACTCTTCGGTGAAGGCTTAAGATG
1 TTGCTTCACTACTCTTCGGTGAAGGCTTAAGATG
* * *
8171 GTGCTTCACTACTCCTCTGTGAAGGCTTAAGATG
1 TTGCTTCACTACTCTTCGGTGAAGGCTTAAGATG
* *
8205 GTGCTTCACTACTCTTCTGTGAAGGCTTAAGATG
1 TTGCTTCACTACTCTTCGGTGAAGGCTTAAGATG
*
8239 ATTGCTTCACTATTCTTCGGTGAAGGCTTAAGATG
1 -TTGCTTCACTACTCTTCGGTGAAGGCTTAAGATG
* *
8274 ATTGCTTCACTTCTCTCCGGTGAAGGCTTAAGATGG
1 -TTGCTTCACTACTCTTCGGTGAAGGCTTAAGAT-G
* *
8310 TTTGATTCACT-CATCTTTGGTGAAGGCTTAAGAT
1 -TTGCTTCACTAC-TCTTCGGTGAAGGCTTAAGAT
8344 TGACTTGCCC
Statistics
Matches: 155, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
34 63 0.41
35 63 0.41
36 29 0.19
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (34 bp):
TTGCTTCACTACTCTTCGGTGAAGGCTTAAGATG
Found at i:8345 original size:103 final size:103
Alignment explanation
Indices: 8137--8343 Score: 285
Period size: 103 Copynumber: 2.0 Consensus size: 103
8127 ATGGATGGAT
* *
8137 TTGCTTTACTACTCTTCGGTGAAGGCTTAAGATGGTGCTTCACTACTCCTCTGTGAAGGCTTAAG
1 TTGCTTCACTACTCTTCGGTGAAGGCTTAAGATGGTGCTTCACTACTCCTCGGTGAAGGCTTAAG
*
8202 ATGGTGCTTCACTACTCTTCTGTGAAGGCTTAAGATGA
66 ATGGTGATTCACTACTCTTCTGTGAAGGCTTAAGATGA
* * *
8240 TTGCTTCACTATTCTTCGGTGAAGGCTTAAGATGATTGCTTCACTTCT-CTCCGGTGAAGGCTTA
1 TTGCTTCACTACTCTTCGGTGAAGGCTTAAGATG-GTGCTTCACTACTCCT-CGGTGAAGGCTTA
8304 AGATGGTTTGATTCACT-CATCTT-TGGTGAAGGCTTAAGAT
64 AGATGG--TGATTCACTAC-TCTTCT-GTGAAGGCTTAAGAT
8344 TGACTTGCCC
Statistics
Matches: 92, Mismatches: 6, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
103 34 0.37
104 29 0.32
105 2 0.02
106 27 0.29
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (103 bp):
TTGCTTCACTACTCTTCGGTGAAGGCTTAAGATGGTGCTTCACTACTCCTCGGTGAAGGCTTAAG
ATGGTGATTCACTACTCTTCTGTGAAGGCTTAAGATGA
Found at i:13103 original size:54 final size:55
Alignment explanation
Indices: 12994--13121 Score: 215
Period size: 54 Copynumber: 2.3 Consensus size: 55
12984 CTTCAAACTC
* *
12994 CATTCATTGGATGGCCTTCTTCATGAATCGTTCTTCAATCAGGTTCAAATTTCTT
1 CATTCATTTGATGTCCTTCTTCATGAATCGTTCTTCAATCAGGTTCAAATTTCTT
13049 CATTCATTTGATGTCCTTCTTCATGAATCG-TCTTCAATCAGGTTCAAATTTCTT
1 CATTCATTTGATGTCCTTCTTCATGAATCGTTCTTCAATCAGGTTCAAATTTCTT
13103 CATTC-TTTGGATGTCCTTC
1 CATTCATTT-GATGTCCTTC
13122 CTGAATCATT
Statistics
Matches: 70, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
53 3 0.04
54 39 0.56
55 28 0.40
ACGTcount: A:0.20, C:0.23, G:0.13, T:0.44
Consensus pattern (55 bp):
CATTCATTTGATGTCCTTCTTCATGAATCGTTCTTCAATCAGGTTCAAATTTCTT
Found at i:14118 original size:25 final size:23
Alignment explanation
Indices: 14068--14144 Score: 68
Period size: 25 Copynumber: 3.2 Consensus size: 23
14058 AAGTATTTTC
* *
14068 TTTCAAAATTTTATTACTTATAAT
1 TTTCATAATTTTATTA-TTATTAT
14092 TTTCATAATATTTATTATATATTAT
1 TTTCATAAT-TTTATTAT-TATTAT
*
14117 TTTTATTAATGTTT-TTATT-TTAT
1 TTTCA-TAAT-TTTATTATTATTAT
14140 TTTCA
1 TTTCA
14145 AGTATTAAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
23 8 0.18
24 10 0.22
25 20 0.44
26 7 0.16
ACGTcount: A:0.31, C:0.05, G:0.01, T:0.62
Consensus pattern (23 bp):
TTTCATAATTTTATTATTATTAT
Found at i:24777 original size:17 final size:17
Alignment explanation
Indices: 24755--24793 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
24745 ATATTATGCT
24755 TGAAAAAAAAATG-AAAA
1 TGAAAAAAAAA-GAAAAA
*
24772 TGAAAAAGAAAGAAAAA
1 TGAAAAAAAAAGAAAAA
24789 TGAAA
1 TGAAA
24794 TGAAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.10
Consensus pattern (17 bp):
TGAAAAAAAAAGAAAAA
Found at i:24801 original size:23 final size:23
Alignment explanation
Indices: 24756--24800 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
24746 TATTATGCTT
24756 GAAAAAAAAATGAAAATGAAAAA
1 GAAAAAAAAATGAAAATGAAAAA
*
24779 GAAAGAAAAATG-AAATGAAAAA
1 GAAAAAAAAATGAAAATGAAAAA
24801 AATATAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.09
Consensus pattern (23 bp):
GAAAAAAAAATGAAAATGAAAAA
Found at i:25191 original size:18 final size:18
Alignment explanation
Indices: 25168--25202 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
25158 TTATCTTATT
25168 GAAATTCAATTTATTTTC
1 GAAATTCAATTTATTTTC
*
25186 GAAATTTAATTTATTTT
1 GAAATTCAATTTATTTT
25203 TTCACATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.54
Consensus pattern (18 bp):
GAAATTCAATTTATTTTC
Found at i:26819 original size:122 final size:122
Alignment explanation
Indices: 26601--27128 Score: 749
Period size: 122 Copynumber: 4.3 Consensus size: 122
26591 CACTCGATAG
* * *
26601 ATCAACATTTCCGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCTTCTGAAG-AGGAAGAAGAAGTTCATA
* * * *
26666 ATGAGAAGAATTTGTTCAACCTTTTGCTCGATTCTATCAAATAAAGAGATAAATCAGC
65 ATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCAAAGAAAGAGATAGATCAGC
* *
26724 ATCAAAATTTCCAGAAGTGTTCATAATGAGAAGAACTCTTCTGAAGATGAAGAAGAAGTTCATAA
1 ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCTTCTGAAGAGGAAGAAGAAGTTCATAA
* *
26789 TGAGAAGAATTTGTTCAACCTTTTGCTCGATTCTATCAAAGAAAGAGATAGATCAGC
66 TGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCAAAGAAAGAGATAGATCAGC
* * *
26846 ATCAAAATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAGGAAGTTCATAA
1 ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCTTCTGAAGAGGAAGAAGAAGTTCATAA
* * *
26911 TGAGAAGAACTTGTTCAACCTTTTG-TATGACTCTATCACAGAAGGAGATAGATCAGC
66 TGAGAAGAACTTGTTCAACCTTTTGCT-CGACTCTATCAAAGAAAGAGATAGATCAGC
* ** *
26968 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACT-TATCTGAAGATGAAGAAGAAGTTCAT
1 ATCAACATTTCCAGA-AGTGTTCATAATGAGAAGAACTCT-TCTGAAGAGGAAGAAGAAGTTCAT
* * * * *
27032 AATGAGAAGAGCTTGTTCAACC-TTTGAAT-GACTCTATCATAGAAGGAAATAGATCAGC
64 AATGAGAAGAACTTGTTCAACCTTTTG-CTCGACTCTATCAAAGAAAGAGATAGATCAGC
27090 ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCT
1 ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCT
27129 GTAGACACCC
Statistics
Matches: 371, Mismatches: 28, Indels: 13
0.90 0.07 0.03
Matches are distributed among these distances:
121 21 0.06
122 244 0.66
123 105 0.28
124 1 0.00
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.27
Consensus pattern (122 bp):
ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCTTCTGAAGAGGAAGAAGAAGTTCATAA
TGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCAAAGAAAGAGATAGATCAGC
Found at i:26927 original size:244 final size:240
Alignment explanation
Indices: 26376--27127 Score: 886
Period size: 244 Copynumber: 3.2 Consensus size: 240
26366 CACTCGATGG
* * *
26376 ATCAGCATTTCCGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAATAAGAAGTTCATA
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
* * * *
26441 ATAAGAATAATTTGTTCAACCTTTTGCTCGAATTC-ATC-ACT---AGATGAAT---CATC--AT
66 ATGAGAAGAATTTGTTCAACCTTTTGCTCG-ATTCTATCAAATAAGAGATAAATCAGCATCAAAT
* * * *
26496 TGCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAA
130 TTCCAGAGAAAGTTCATAATGAGAAGAACTCTTCTGAAG-ATGAAGAAGAAGTTCATAATGAGAA
* * *
26561 GAACTTGTTCAACCTTTTTCTTGAATTC-ATC------ACTCGAT-AG-
194 GAACTTGTTCAACCTTTTGC-TG-ATTCTATCAAGAAGAATAGATCAGC
*
26601 ATCAACATTTCCGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
26666 ATGAGAAGAATTTGTTCAACCTTTTGCTCGATTCTATCAAATAAAGAGATAAATCAGCATCAAAA
66 ATGAGAAGAATTTGTTCAACCTTTTGCTCGATTCTATCAAAT-AAGAGATAAATCAGCATC-AAA
**
26731 TTTCCAGA-AGTGTTCATAATGAGAAGAACTCTTCTGAAGATGAAGAAGAAGTTCATAATGAGAA
129 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCTTCTGAAGATGAAGAAGAAGTTCATAATGAGAA
*
26795 GAATTTGTTCAACCTTTTGCTCGATTCTATCAAAGAAAGAGATAGATCAGC
194 GAACTTGTTCAACCTTTTGCT-GATTCTATC-AAG-AAGA-ATAGATCAGC
* * *
26846 ATCAAAATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAGGAAGTTCATA
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
* * * * * *
26910 ATGAGAAGAACTTGTTCAACCTTTTG-TATGACTCTATCACAGAAGGAGATAGATCAGCATCAAC
66 ATGAGAAGAATTTGTTCAACCTTTTGCT-CGATTCTATCAAATAA-GAGATAAATCAGCATCAA-
*
26974 TTTTCCAGAGAAAGTTCATAATGAGAAGAACT-TATCTGAAGATGAAGAAGAAGTTCATAATGAG
128 ATTTCCAGAGAAAGTTCATAATGAGAAGAACTCT-TCTGAAGATGAAGAAGAAGTTCATAATGAG
* * *
27038 AAGAGCTTGTTCAACC-TTTGAATGACTCTATCATAGAAGGAAATAGATCAGC
192 AAGAACTTGTTCAACCTTTTG-CTGATTCTATCA-AGAA-G-AATAGATCAGC
*
27090 ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTC
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTC
27128 TGTAGACACC
Statistics
Matches: 459, Mismatches: 34, Indels: 49
0.85 0.06 0.09
Matches are distributed among these distances:
224 4 0.01
225 94 0.20
226 2 0.00
230 7 0.02
233 9 0.02
234 46 0.10
235 27 0.06
236 8 0.02
242 1 0.00
243 12 0.03
244 140 0.31
245 109 0.24
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (240 bp):
ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
ATGAGAAGAATTTGTTCAACCTTTTGCTCGATTCTATCAAATAAGAGATAAATCAGCATCAAATT
TCCAGAGAAAGTTCATAATGAGAAGAACTCTTCTGAAGATGAAGAAGAAGTTCATAATGAGAAGA
ACTTGTTCAACCTTTTGCTGATTCTATCAAGAAGAATAGATCAGC
Found at i:27191 original size:3 final size:3
Alignment explanation
Indices: 27169--27215 Score: 51
Period size: 3 Copynumber: 15.3 Consensus size: 3
27159 ATATTAAAAA
* *
27169 TAT TAAT TA- TAT TGT TAT TAT TAT TAT TAT TAT TAA TATT TAT TAT
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT
27215 T
1 T
27216 TTACATTTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
2 2 0.05
3 30 0.81
4 5 0.14
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:28751 original size:4 final size:4
Alignment explanation
Indices: 28742--28767 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
28732 TTTTAACTTG
28742 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
28768 TTTTTTTGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Done.