Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002425.1 Hibiscus syriacus cultivar Beakdansim tig00004962_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: 81161
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:3550 original size:2 final size:2
Alignment explanation
Indices: 3543--3607 Score: 80
Period size: 2 Copynumber: 33.0 Consensus size: 2
3533 CCTATAAAAC
* * *
3543 TA TA TA TA TA TA TA TA TA GCA -A CA TA CA -A TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
3584 TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
3608 CACACATAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
1 2 0.04
2 54 0.95
3 1 0.02
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.43
Consensus pattern (2 bp):
TA
Found at i:6068 original size:183 final size:184
Alignment explanation
Indices: 5868--6412 Score: 742
Period size: 182 Copynumber: 3.0 Consensus size: 184
5858 TGATCCATAG
* * * * * *
5868 CAATATAACATGTAAAAATATGACAAAACCGGTCTCAAAATGACCAAACCGGTAAAGCGTTATCG
1 CAATATAACAGGTAAAAATATGATAAAATCGATCTCAAAATGACAAAACCGGTAAAGCGTTACCG
*
5933 GATATGTTGAAAAGTTTCGATATTTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGC
66 GATATGTTGAAAAGTTTCGATACTTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGC
* * * ** *
5998 AATCATAGAGTTTATAAAGTGTCGATA-TTTAAAAAAAATGTATCAACACTTAA
131 AGTAATAGCGCCTATAAAGTGTCGATACTTTAAAAAAAATGTATCGACACTTAA
** * *
6051 CAATATAACAGGTAAAAATATGATAAAATTAATATCAAAATGACAAAACCGGTAAAGCGTCACCG
1 CAATATAACAGGTAAAAATATGATAAAATCGATCTCAAAATGACAAAACCGGTAAAGCGTTACCG
* * * *
6116 AATATGTT-AATAGTGTT-GATACTTTATTATAAGTATCGACACTTTTAGAATTT-AAAGATAAG
66 GATATGTTGAAAAGT-TTCGATACTTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAAAAG
* * * *
6178 CAGTAATAGCGCCTAAAAAGAGTCGATATTTTAAAAAAAATGTATTGACACTTAA
130 CAGTAATAGCGCCTATAAAGTGTCGATACTTTAAAAAAAATGTATCGACACTTAA
* *
6233 CAATATAACAGGTAAAAATATGATAAAATCGATCTCAAAATGACAAAACCGGTAAAGTGCTACCG
1 CAATATAACAGGTAAAAATATGATAAAATCGATCTCAAAATGACAAAACCGGTAAAGCGTTACCG
* * * * **
6298 GATATGTTG-AAAGTGTCAAAACTTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAATT
66 GATATGTTGAAAAGTTTCGATACTTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGC
6362 AGTAATAGCGCCTATAAAGTGTCGATACTTT-AAAAAAATGTATCGACACTT
131 AGTAATAGCGCCTATAAAGTGTCGATACTTTAAAAAAAATGTATCGACACTT
6413 GGGTTATTGT
Statistics
Matches: 314, Mismatches: 43, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
181 30 0.10
182 185 0.59
183 99 0.32
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.29
Consensus pattern (184 bp):
CAATATAACAGGTAAAAATATGATAAAATCGATCTCAAAATGACAAAACCGGTAAAGCGTTACCG
GATATGTTGAAAAGTTTCGATACTTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGC
AGTAATAGCGCCTATAAAGTGTCGATACTTTAAAAAAAATGTATCGACACTTAA
Found at i:7550 original size:66 final size:65
Alignment explanation
Indices: 7462--7585 Score: 178
Period size: 65 Copynumber: 1.9 Consensus size: 65
7452 CCATTCAACA
7462 GGTACCGATACCCTCTCAAACGAGAAAAATTACAGAATG-CATAAGGGTACCGATACCCCCCAGT
1 GGTACCGATACCCTCTCAAAC--GAAAAATTACAGAATGCCATAAGGGTACCGATACCCCCCAGT
7526 TG
64 TG
* ** * *
7528 GGTACCGATACCCTTTTGAACGAAAAATTACATAATGCCATGAGGGTACCGATACCCC
1 GGTACCGATACCCTCTCAAACGAAAAATTACAGAATGCCATAAGGGTACCGATACCCC
7586 GAAAAGGAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
64 15 0.29
65 19 0.37
66 18 0.35
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (65 bp):
GGTACCGATACCCTCTCAAACGAAAAATTACAGAATGCCATAAGGGTACCGATACCCCCCAGTTG
Found at i:8225 original size:23 final size:23
Alignment explanation
Indices: 8199--8266 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
8189 CACTACAGTA
*
8199 CAATTCTACGCGGCATTTCGGTG
1 CAATTCTACGCGGCACTTCGGTG
*
8222 CAATTCTACGCGGTACTTCGGTG
1 CAATTCTACGCGGCACTTCGGTG
* *
8245 CAATTCTACGTGGTACTTCGGT
1 CAATTCTACGCGGCACTTCGGT
8267 ACATTTATAC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.32
Consensus pattern (23 bp):
CAATTCTACGCGGCACTTCGGTG
Found at i:8277 original size:23 final size:23
Alignment explanation
Indices: 8196--8277 Score: 83
Period size: 23 Copynumber: 3.6 Consensus size: 23
8186 TGGCACTACA
* * *
8196 GTACAATTCTACGCGGCATTTCG
1 GTACAATTATACGCGGTACTTCG
* *
8219 GTGCAATTCTACGCGGTACTTCG
1 GTACAATTATACGCGGTACTTCG
* * *
8242 GTGCAATTCTACGTGGTACTTCG
1 GTACAATTATACGCGGTACTTCG
*
8265 GTACATTTATACG
1 GTACAATTATACG
8278 AGTTGTGGTG
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (23 bp):
GTACAATTATACGCGGTACTTCG
Found at i:8382 original size:23 final size:23
Alignment explanation
Indices: 8356--8451 Score: 174
Period size: 23 Copynumber: 4.2 Consensus size: 23
8346 AGTCTGAGTA
8356 TAAACCAGAGTCTATAGAGTCTT
1 TAAACCAGAGTCTATAGAGTCTT
*
8379 TAAATCAGAGTCTATAGAGTCTT
1 TAAACCAGAGTCTATAGAGTCTT
*
8402 TAAAACAGAGTCTATAGAGTCTT
1 TAAACCAGAGTCTATAGAGTCTT
8425 TAAACCAGAGTCTATAGAGTCTT
1 TAAACCAGAGTCTATAGAGTCTT
8448 TAAA
1 TAAA
8452 TTGAGACTAA
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 70 1.00
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.31
Consensus pattern (23 bp):
TAAACCAGAGTCTATAGAGTCTT
Found at i:8487 original size:9 final size:9
Alignment explanation
Indices: 8473--8520 Score: 73
Period size: 9 Copynumber: 5.4 Consensus size: 9
8463 CATAAACCTT
8473 ACATTACTC
1 ACATTACTC
8482 ACATTACTC
1 ACATTACTC
8491 ACATTACTC
1 ACATTACTC
8500 ACA--ACCTC
1 ACATTA-CTC
8508 ACATTACTC
1 ACATTACTC
8517 ACAT
1 ACAT
8521 ACGAGCTATG
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
7 1 0.03
8 6 0.17
9 28 0.78
10 1 0.03
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.29
Consensus pattern (9 bp):
ACATTACTC
Found at i:14755 original size:23 final size:23
Alignment explanation
Indices: 14711--14755 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
14701 CATCTTATAT
*
14711 GACACTACGGTGAAATTCTACGC
1 GACACTACGGTGAAATTATACGC
* * *
14734 GACACTTCGGTGCATTTATACG
1 GACACTACGGTGAAATTATACG
14756 AGCTGTGGTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (23 bp):
GACACTACGGTGAAATTATACGC
Found at i:18448 original size:2 final size:2
Alignment explanation
Indices: 18441--18480 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
18431 TTCACATGCC
18441 AT 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 AT
18481 TTATGATATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20315 original size:20 final size:19
Alignment explanation
Indices: 20277--20315 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
20267 ATATTTATGT
* *
20277 AAATATTATTTTTTAATTA
1 AAATAATATTTTATAATTA
20296 AAATAATATTTATATAATTA
1 AAATAATATTT-TATAATTA
20316 TTATTTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AAATAATATTTTATAATTA
Found at i:20487 original size:17 final size:17
Alignment explanation
Indices: 20465--20518 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
20455 AATGTTAATA
20465 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * *
20482 TTTAAATTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
20499 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
20516 TTT
1 TTT
20519 TTATAATGTA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:22137 original size:21 final size:21
Alignment explanation
Indices: 22104--22260 Score: 208
Period size: 21 Copynumber: 7.5 Consensus size: 21
22094 TATGCCATCT
*
22104 CCGCAGAGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
*
22125 CCGTAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
*
22146 TCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
*
22167 CCACAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
* *
22188 TCTCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
* *
22209 CCGTAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCGAGC
* *
22230 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCGAGC
22251 CCGCAGGGTT
1 CCGCAGGGTT
22261 TTATACCATA
Statistics
Matches: 120, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
20 2 0.02
21 117 0.98
22 1 0.01
ACGTcount: A:0.20, C:0.31, G:0.26, T:0.23
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCGAGC
Found at i:22832 original size:34 final size:34
Alignment explanation
Indices: 22782--22879 Score: 133
Period size: 34 Copynumber: 2.9 Consensus size: 34
22772 AAATGTTTTT
*
22782 AAAATACAAATTATATTATTCAAAATTTAAAATA
1 AAAATAAAAATTATATTATTCAAAATTTAAAATA
* * *
22816 AAAATAAAAATAATATTATTCAAAATTTAAATTT
1 AAAATAAAAATTATATTATTCAAAATTTAAAATA
* * *
22850 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCAAAATTTAA
22880 CATTAAATTT
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 56 1.00
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCAAAATTTAAAATA
Found at i:24070 original size:128 final size:128
Alignment explanation
Indices: 23780--24278 Score: 930
Period size: 128 Copynumber: 3.9 Consensus size: 128
23770 TTACATGATT
23780 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
23845 TGACAAAATAATGGAAGGCGTG-CCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
23907 TACTGATATATCTACTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
23972 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
24035 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
24100 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
24163 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT-
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* * *
24227 TGACAAAATAATGGAAGGCGCGCCCTCGGGAATGCGCCTTCATATGAATAGT
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
24279 ACTCCGTGTA
Statistics
Matches: 363, Mismatches: 8, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
127 133 0.37
128 230 0.63
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:24233 original size:255 final size:255
Alignment explanation
Indices: 23780--24278 Score: 928
Period size: 255 Copynumber: 2.0 Consensus size: 255
23770 TTACATGATT
23780 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
23845 TGACAAAATAATGGAAGGCGTGCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAC
66 TGACAAAATAATGGAAGGCGCGCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTAC
23910 TGATATATCTACTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
131 TGATATATCTACTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
*
23975 CAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
196 CAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATATGAATAGTGAAATAATAGG
24035 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
24100 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTA
66 TGACAAAATAATGGAAGGCGCG-CCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTA
*
24165 CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT-TG
130 CTGATATATCTACTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
* *
24229 ACAAAATAATGGAAGGCGCGCCCTCGGGAATGCGCCTTCATATGAATAGT
195 ACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATATGAATAGT
24279 ACTCCGTGTA
Statistics
Matches: 237, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
255 135 0.57
256 102 0.43
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (255 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACAAAATAATGGAAGGCGCGCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTAC
TGATATATCTACTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
CAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATATGAATAGTGAAATAATAGG
Found at i:24841 original size:18 final size:18
Alignment explanation
Indices: 24818--24852 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
24808 CTAGGAGATT
24818 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
24836 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
24853 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:24987 original size:2 final size:2
Alignment explanation
Indices: 24980--25037 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
24970 CAAATTAGAT
24980 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25022 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
25038 AATAATAGAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25141 original size:2 final size:2
Alignment explanation
Indices: 25134--25237 Score: 201
Period size: 2 Copynumber: 52.5 Consensus size: 2
25124 AATCTTGAGG
25134 AT AT 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 AT AT
25176 AT AT 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 AT AT
25218 AT AT -T AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
25238 GACATGAATG
Statistics
Matches: 101, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 100 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26033 original size:149 final size:149
Alignment explanation
Indices: 25859--26173 Score: 533
Period size: 149 Copynumber: 2.1 Consensus size: 149
25849 GAGTCGAGGG
* **
25859 TCTACGCGGTCCTTCGGGATATATATATATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
25924 A-TATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
66 ACT-TGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGAACATCATT
*
25988 ATATGGCACTACGGTGCAAT
130 ATATGGCACTACGGTACAAT
* *
26008 TCTACGCGGTCTTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
26073 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGAACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGAACATCATTA
26138 TATGGCACTACGGTACAAT
131 TATGGCACTACGGTACAAT
*
26157 TCTACGCGGTACTTCGG
1 TCTACGCGGTCCTTCGG
26174 TGCAATTATA
Statistics
Matches: 155, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
149 154 0.99
150 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGAACATCATTA
TATGGCACTACGGTACAAT
Found at i:31469 original size:15 final size:15
Alignment explanation
Indices: 31449--31477 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
31439 CACCTGAAGA
31449 GTAACTTCTATTAGT
1 GTAACTTCTATTAGT
31464 GTAACTTCTATTAG
1 GTAACTTCTATTAG
31478 GATTACGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.45
Consensus pattern (15 bp):
GTAACTTCTATTAGT
Found at i:33473 original size:31 final size:31
Alignment explanation
Indices: 33435--33561 Score: 200
Period size: 31 Copynumber: 4.1 Consensus size: 31
33425 GAGTCAAGGG
*
33435 TTACCTATGTTCTTCGAGACATATGGACAGA
1 TTACCTATGTTCTTCGGGACATATGGACAGA
*
33466 TTACCTATGTTCTTCGGGACATATGGACATA
1 TTACCTATGTTCTTCGGGACATATGGACAGA
* *
33497 TTACCTATGTTCTTCGGGATATATAGACAGA
1 TTACCTATGTTCTTCGGGACATATGGACAGA
* *
33528 TTACCTATGTTCTTCGGGATATATGGATAGA
1 TTACCTATGTTCTTCGGGACATATGGACAGA
33559 TTA
1 TTA
33562 TTATACGAGC
Statistics
Matches: 89, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 89 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.36
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACAGA
Found at i:37366 original size:31 final size:31
Alignment explanation
Indices: 37328--37516 Score: 306
Period size: 31 Copynumber: 6.1 Consensus size: 31
37318 GAGTCGAGGG
37328 TTACCTATGTTCTTCGGGACATATGGACAAA
1 TTACCTATGTTCTTCGGGACATATGGACAAA
37359 TTACCTATGTTCTTCGGGACATATGGACAAA
1 TTACCTATGTTCTTCGGGACATATGGACAAA
* *
37390 TTACCTATGTTCTTCTGGACATATGGATAAA
1 TTACCTATGTTCTTCGGGACATATGGACAAA
*
37421 TTACCTATGTTCTTCGGGACATATGGACATA
1 TTACCTATGTTCTTCGGGACATATGGACAAA
* *
37452 TTACTTATGTTCTTCGGGACATATGGACATA
1 TTACCTATGTTCTTCGGGACATATGGACAAA
* * *
37483 TTACCTATGTTCTTCGAGACATATGAACAGA
1 TTACCTATGTTCTTCGGGACATATGGACAAA
37514 TTA
1 TTA
37517 TTATACGAGC
Statistics
Matches: 148, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 148 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACAAA
Found at i:38627 original size:160 final size:161
Alignment explanation
Indices: 38393--38744 Score: 480
Period size: 160 Copynumber: 2.2 Consensus size: 161
38383 TCATTATTTG
* * ** ** * *
38393 TTTCAATTCCTCATTCATTTTAAGTTCA---TTTTTTACCAAATTCAAACCACATGCTCCTAAAC
1 TTTCAATTCATCATTTATTTTAAGTTCATTTTTTTTTATTAAATTTGAGCTACATGCTCCTAAAC
* * *
38455 TATAGTAGAATACATGTGTACTTTCAATTCCTCTTTTTGATAACAAGTTTTTTAATTTTCAATTT
66 CATAGTAGAATACATGTGTACTTTCAATTCCTCTTTTTAATAACAAATTTTTTAATTTTCAATTT
* *
38520 AGTCCTTCAAATTTTCATAATTTCCTTATT-
131 AGTCCTTCAAATTTTCATAATCTCCTTGTTC
38550 TCTTCAATTCATCATTTATTTTAAG-TCATTTTTTTTTATTAAATTTGAGCTACATGCTCCTAAA
1 T-TTCAATTCATCATTTATTTTAAGTTCATTTTTTTTTATTAAATTTGAGCTACATGCTCCTAAA
* *
38614 CCATAGTAGAATACATGTGTACTTTCAATTCCTCTTTTTAATAATAAATTTTTTACTTTTCAATT
65 CCATAGTAGAATACATGTGTACTTTCAATTCCTCTTTTTAATAACAAATTTTTTAATTTTCAATT
* *
38679 TAGTCCTTTAATTTTTCATAATCTCCTTGTTC
130 TAGTCCTTCAAATTTTCATAATCTCCTTGTTC
** *
38711 TTTCAATTTGTGATTTATTTTAAGTTCATTTTTT
1 TTTCAATTCATCATTTATTTTAAGTTCATTTTTT
38745 ACCAAATTTG
Statistics
Matches: 169, Mismatches: 20, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
157 4 0.02
158 21 0.12
160 134 0.79
161 10 0.06
ACGTcount: A:0.28, C:0.17, G:0.06, T:0.49
Consensus pattern (161 bp):
TTTCAATTCATCATTTATTTTAAGTTCATTTTTTTTTATTAAATTTGAGCTACATGCTCCTAAAC
CATAGTAGAATACATGTGTACTTTCAATTCCTCTTTTTAATAACAAATTTTTTAATTTTCAATTT
AGTCCTTCAAATTTTCATAATCTCCTTGTTC
Found at i:50519 original size:10 final size:10
Alignment explanation
Indices: 50504--50531 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
50494 CCAAGTAAGC
50504 CTGTTAACTA
1 CTGTTAACTA
50514 CTGTTAACTA
1 CTGTTAACTA
50524 CTGTTAAC
1 CTGTTAAC
50532 AGGCCACGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.39
Consensus pattern (10 bp):
CTGTTAACTA
Found at i:61662 original size:18 final size:18
Alignment explanation
Indices: 61615--61696 Score: 74
Period size: 18 Copynumber: 4.4 Consensus size: 18
61605 ACCGAACTGG
*
61615 GTTGACCTGACCCAAACC
1 GTTGACCTGACCCGAACC
*
61633 AGTTTTACCTGACCCGAACC
1 -G-TTGACCTGACCCGAACC
* *
61653 GTTGACCTGATCCGAAACT
1 GTTGACCTGACCCG-AACC
** *
61672 GTTGACCTGATTCGAACT
1 GTTGACCTGACCCGAACC
61690 GTTGACC
1 GTTGACC
61697 AGTCAGACCA
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
18 22 0.40
19 18 0.33
20 15 0.27
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (18 bp):
GTTGACCTGACCCGAACC
Found at i:61677 original size:19 final size:18
Alignment explanation
Indices: 61639--61696 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
61629 AACCAGTTTT
* *
61639 ACCTGACCCGAACCGTTG
1 ACCTGATCCGAACTGTTG
61657 ACCTGATCCGAAACTGTTG
1 ACCTGATCCG-AACTGTTG
*
61676 ACCTGATTCGAACTGTTG
1 ACCTGATCCGAACTGTTG
61694 ACC
1 ACC
61697 AGTCAGACCA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
18 20 0.56
19 16 0.44
ACGTcount: A:0.24, C:0.31, G:0.21, T:0.24
Consensus pattern (18 bp):
ACCTGATCCGAACTGTTG
Found at i:62400 original size:18 final size:18
Alignment explanation
Indices: 62363--62400 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
62353 TTTTAAGATT
*
62363 TTATATTCGATTTAAATA
1 TTATATTCGATTCAAATA
*
62381 TTATATTCGATTCAATTA
1 TTATATTCGATTCAAATA
62399 TT
1 TT
62401 CGAATATCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.34, C:0.08, G:0.05, T:0.53
Consensus pattern (18 bp):
TTATATTCGATTCAAATA
Found at i:64224 original size:79 final size:81
Alignment explanation
Indices: 64106--64273 Score: 252
Period size: 79 Copynumber: 2.1 Consensus size: 81
64096 TTTAGGAAAA
* *
64106 TATTTTAAATATTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTGTT-AGTATTTC
1 TATTTTAAATA-TATATTTTATCTTTATTTTAGATATTTTAGTTTAAATA-GTGTTAAGTATTTC
64170 AATTAGGATTTAAGATAT
64 AATTAGGATTTAAGATAT
* * *
64188 TATTTTAAATA-GTATTTTAT-TTTATTTTAGATATTTTAGTTTAAATAGTTTTAAGTATTTTAA
1 TATTTTAAATATATATTTTATCTTTATTTTAGATATTTTAGTTTAAATAGTGTTAAGTATTTCAA
64251 TTAGGATTTAAGATAT
66 TTAGGATTTAAGATAT
64267 TATTTTA
1 TATTTTA
64274 CGAATTATAT
Statistics
Matches: 80, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
78 4 0.05
79 57 0.71
80 8 0.10
82 11 0.14
ACGTcount: A:0.32, C:0.01, G:0.11, T:0.55
Consensus pattern (81 bp):
TATTTTAAATATATATTTTATCTTTATTTTAGATATTTTAGTTTAAATAGTGTTAAGTATTTCAA
TTAGGATTTAAGATAT
Found at i:70472 original size:13 final size:13
Alignment explanation
Indices: 70454--70494 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
70444 TCAATGATGC
70454 TAAATGAGCGTCA
1 TAAATGAGCGTCA
*
70467 TAAATGCGCGTCA
1 TAAATGAGCGTCA
*
70480 TAAATGTGCGTCA
1 TAAATGAGCGTCA
70493 TA
1 TA
70495 GATTTATGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (13 bp):
TAAATGAGCGTCA
Found at i:70821 original size:15 final size:15
Alignment explanation
Indices: 70801--70829 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
70791 TTTATCCCAA
70801 TTTATTTATTTTTTG
1 TTTATTTATTTTTTG
70816 TTTATTTATTTTTT
1 TTTATTTATTTTTT
70830 ATCTCATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.83
Consensus pattern (15 bp):
TTTATTTATTTTTTG
Found at i:72401 original size:21 final size:21
Alignment explanation
Indices: 72377--72423 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
72367 AATTTCACAA
*
72377 GAAAAGTTGGTTACATCCAAG
1 GAAAAGCTGGTTACATCCAAG
* *
72398 GAAAAGCTGGTTGCATCCCAG
1 GAAAAGCTGGTTACATCCAAG
72419 GAAAA
1 GAAAA
72424 ATTCCAAAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.38, C:0.17, G:0.26, T:0.19
Consensus pattern (21 bp):
GAAAAGCTGGTTACATCCAAG
Found at i:73223 original size:135 final size:134
Alignment explanation
Indices: 72992--73234 Score: 346
Period size: 135 Copynumber: 1.8 Consensus size: 134
72982 TATCACCTTT
** *
72992 AGATGGCCAGAACTCTTCATCGTGTATGAGCCGTGTCATCACCTGACCAGATATCCTCATTATGT
1 AGATGGCCAGAACTCTTCATCACGTATGAGCAGTGTCATCACCTGACCAGATATCCTCATTATGT
* * *
73057 AGGAGTCGTGTCAATCCTTGATAACCAGAACTCTTTATCACGTGTCAGCCGTGTTATCACCCTTC
66 AGGAGTCGTGTCAACCCTTGACAACCAGAACTCTTCATCACGTGTCAGCCGTGTTATCACCCTTC
73122 CTAA
131 CTAA
* *
73126 AGATGGCCAAGAACTCTTCATCACGTATGAGCAGTGTCATC-CCTTGACTAGATCTCCTCATTAT
1 AGATGGCC-AGAACTCTTCATCACGTATGAGCAGTGTCATCACC-TGACCAGATATCCTCATTAT
* * *
73190 GTAGGAGTCTTGTC-ACCCTTAGACGACCCGAACTCTTCATCACGT
64 GTAGGAGTCGTGTCAACCCTT-GACAACCAGAACTCTTCATCACGT
73235 ATGAGAAGTG
Statistics
Matches: 95, Mismatches: 11, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
134 15 0.16
135 80 0.84
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.29
Consensus pattern (134 bp):
AGATGGCCAGAACTCTTCATCACGTATGAGCAGTGTCATCACCTGACCAGATATCCTCATTATGT
AGGAGTCGTGTCAACCCTTGACAACCAGAACTCTTCATCACGTGTCAGCCGTGTTATCACCCTTC
CTAA
Found at i:75090 original size:5 final size:5
Alignment explanation
Indices: 75068--75108 Score: 64
Period size: 5 Copynumber: 8.2 Consensus size: 5
75058 CGCGTTTCAC
* *
75068 TTTTA TTTTG TTTCA TTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
75109 CTTTGAGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:75107 original size:15 final size:15
Alignment explanation
Indices: 75062--75108 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
75052 TTTTATCGCG
*
75062 TTTCACTTTTATTTTG
1 TTTCA-TTTTATTTTA
75078 TTTCATTTTATTTTA
1 TTTCATTTTATTTTA
*
75093 TTTTATTTTATTTTA
1 TTTCATTTTATTTTA
75108 T
1 T
75109 CTTTGAGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
15 24 0.83
16 5 0.17
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.74
Consensus pattern (15 bp):
TTTCATTTTATTTTA
Found at i:78739 original size:28 final size:28
Alignment explanation
Indices: 78707--78761 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
78697 TTCCGTTTAC
* *
78707 ATTATATT-GTCGAGTCAGTTCTTGAAAT
1 ATTATATTGGT-GAGTCAATGCTTGAAAT
*
78735 ATTATGTTGGTGAGTCAATGCTTGAAA
1 ATTATATTGGTGAGTCAATGCTTGAAA
78762 GCAATGACGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 21 0.91
29 2 0.09
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.40
Consensus pattern (28 bp):
ATTATATTGGTGAGTCAATGCTTGAAAT
Found at i:79961 original size:21 final size:21
Alignment explanation
Indices: 79935--79993 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
79925 ATTTACCGTG
79935 ATTGCGGCCGTCGCGGGCGCT
1 ATTGCGGCCGTCGCGGGCGCT
* *
79956 ATTGCGGTCGTCGCGGACGCT
1 ATTGCGGCCGTCGCGGGCGCT
79977 ATTGCGGCCGTCGCGGG
1 ATTGCGGCCGTCGCGGG
79994 TAACTCGGAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.07, C:0.31, G:0.42, T:0.20
Consensus pattern (21 bp):
ATTGCGGCCGTCGCGGGCGCT
Done.