Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003299.1 Hibiscus syriacus cultivar Beakdansim tig00006939_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: 55428
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.34
Found at i:601 original size:100 final size:100
Alignment explanation
Indices: 284--757 Score: 466
Period size: 100 Copynumber: 4.7 Consensus size: 100
274 AATATGCCTC
* * *
284 TAAAAAAATCGGTAGGTAGTTTAACGTAATAAGTAGCTCCTA-TTTATTTTAACCGGTTAAGTTG
1 TAAACAAATCGATAGGTAGTTTAACGTAATAAGTAGCACCTATTTTATTTTAACCGGTTAAGTTG
* * *
348 AAAATAGTTTACCGTTT--A-TAATATTATACTTT
66 TAAATATTTTACCGTTTACATTAATATTATACCTT
* * * *** * * *
380 TAAACAAA-CCAGTAGTTAGTTTAACGTAATAGGTAGCGTATATTTTATTGTAACCGATTATGTT
1 TAAACAAATCGA-TAGGTAGTTTAACGTAATAAGTAGCACCTATTTTATTTTAACCGGTTAAGTT
444 GTAAATA--TTACCGTTTACATTAA-ATTATACCTT
65 GTAAATATTTTACCGTTTACATTAATATTATACCTT
* * *
477 TAAAACAAATCGATAGGTAGTTTAACGAAATATGTAGCACCTATTTTATTTTAATCGGTTAAGTT
1 T-AAACAAATCGATAGGTAGTTTAACGTAATAAGTAGCACCTATTTTATTTTAACCGGTTAAGTT
*
542 GTAAATATTTTACCGTTTACATTATTATTATACCTT
65 GTAAATATTTTACCGTTTACATTAATATTATACCTT
* * **
578 TAAAGAAATCGATAGCTAGTTTAACGTAATAAGTAGTGCCTATTTTATTTTAA-CGGTTAAAGTT
1 TAAACAAATCGATAGGTAGTTTAACGTAATAAGTAGCACCTATTTTATTTTAACCGGTT-AAGTT
* ***
642 ATAAATATATGTATATATTTTAATTTACATTAATATTTATACCTT
65 GT-AA-ATAT-T-T-TA---CCGTTTACATTAATA-TTATACCTT
* * * * *
687 TAAACAAA-CTGATAGTTATTTTAACGTAATAGGTAACACCTA-TTTATTTTAACCTGTTAAGTT
1 TAAACAAATC-GATAGGTAGTTTAACGTAATAAGTAGCACCTATTTTATTTTAACCGGTTAAGTT
750 GTAAATAT
65 GTAAATAT
758 AGGTATCGAT
Statistics
Matches: 311, Mismatches: 45, Indels: 34
0.80 0.12 0.09
Matches are distributed among these distances:
95 10 0.03
96 32 0.10
97 35 0.11
98 59 0.19
99 7 0.02
100 67 0.22
101 13 0.04
102 4 0.01
103 1 0.00
104 1 0.00
105 2 0.01
106 4 0.01
107 2 0.01
108 28 0.09
109 46 0.15
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.41
Consensus pattern (100 bp):
TAAACAAATCGATAGGTAGTTTAACGTAATAAGTAGCACCTATTTTATTTTAACCGGTTAAGTTG
TAAATATTTTACCGTTTACATTAATATTATACCTT
Found at i:649 original size:198 final size:193
Alignment explanation
Indices: 284--649 Score: 475
Period size: 198 Copynumber: 1.9 Consensus size: 193
274 AATATGCCTC
* * *
284 TAAAAAAATCGGTAGGTAGTTTAACGTAATAAGTAGCTCCTATTTATTTTAACCGGTTAAGTTGA
1 TAAAAAAATCGATAGGTAGTTTAACGAAATAAGTAGCACCTATTTATTTTAACCGGTTAAGTTGA
* * *
349 AAATAGTTTACCGTTTATAATATTATACTTTTAAACAAACCAGTAGTTAGTTTAACGTAATAGGT
66 AAATAGTTTACCGTTTATAATATTATACCTTTAAACAAACCAGTAGCTAGTTTAACGTAATAAGT
* * *
414 AGCGTATATTTTATTGTAACCGATTATGTTGTAAATATTACCGTTTACATTAAATTATACCTT
131 AGCGCATATTTTATTGTAACCGATTAAGTTATAAATATTACCGTTTACATTAAATTATACCTT
* *
477 TAAAACAAATCGATAGGTAGTTTAACGAAATATGTAGCACCTATTTTATTTTAATCGGTTAAGTT
1 TAAAA-AAATCGATAGGTAGTTTAACGAAATAAGTAGCACCTA-TTTATTTTAACCGGTTAAGTT
* * * * *
542 GTAAATATTTTACCGTTTACATTATTATTATACCTTTAAAGAAATC-GATAGCTAGTTTAACGTA
64 GAAAATAGTTTACCGTTT--A-TAATATTATACCTTTAAACAAACCAG-TAGCTAGTTTAACGTA
* * * *
606 ATAAGTAGTGCCTATTTTATTTTAA-CGGTTAAAGTTATAAATAT
125 ATAAGTAGCGCATATTTTATTGTAACCGATT-AAGTTATAAATAT
650 ATGTATATAT
Statistics
Matches: 146, Mismatches: 20, Indels: 9
0.83 0.11 0.05
Matches are distributed among these distances:
193 5 0.03
194 33 0.23
195 36 0.25
197 6 0.04
198 66 0.45
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.40
Consensus pattern (193 bp):
TAAAAAAATCGATAGGTAGTTTAACGAAATAAGTAGCACCTATTTATTTTAACCGGTTAAGTTGA
AAATAGTTTACCGTTTATAATATTATACCTTTAAACAAACCAGTAGCTAGTTTAACGTAATAAGT
AGCGCATATTTTATTGTAACCGATTAAGTTATAAATATTACCGTTTACATTAAATTATACCTT
Found at i:710 original size:109 final size:107
Alignment explanation
Indices: 557--763 Score: 265
Period size: 109 Copynumber: 1.9 Consensus size: 107
547 TATTTTACCG
* * ***
557 TTTACATTATTATTATACCTTTAAAGAAATCGATAGCTAGTTTAACGTAATAAGTAGTGCCTATT
1 TTTACATTAATATTATACCTTTAAACAAATCGATAGCTAGTTTAACGTAATAAGTAACACCTA-T
*
622 TTATTTTAA-CGGTTAAAGTTATAAATATATGTATATATTTTAA
65 TTATTTTAACCGGTT-AAGTTATAAATATAGGTATATATTTTAA
* * *
665 TTTACATTAATATTTATACCTTTAAACAAA-CTGATAGTTATTTTAACGTAATAGGTAACACCTA
1 TTTACATTAATA-TTATACCTTTAAACAAATC-GATAGCTAGTTTAACGTAATAAGTAACACCTA
* *
729 TTTATTTTAACCTGTTAAGTTGTAAATATAGGTAT
64 TTTATTTTAACCGGTTAAGTTATAAATATAGGTAT
764 CGATACATAC
Statistics
Matches: 85, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
108 39 0.46
109 46 0.54
ACGTcount: A:0.37, C:0.10, G:0.11, T:0.43
Consensus pattern (107 bp):
TTTACATTAATATTATACCTTTAAACAAATCGATAGCTAGTTTAACGTAATAAGTAACACCTATT
TATTTTAACCGGTTAAGTTATAAATATAGGTATATATTTTAA
Found at i:16782 original size:18 final size:18
Alignment explanation
Indices: 16759--16818 Score: 86
Period size: 18 Copynumber: 3.3 Consensus size: 18
16749 TGATTGCATC
16759 AGAAGACCTTGGTTGAGA
1 AGAAGACCTTGGTTGAGA
16777 AGAAGACCTTGGTTGAGA
1 AGAAGACCTTGGTTGAGA
* *
16795 AGATGAACTTGGTTG-GTA
1 AGAAGACCTTGGTTGAG-A
16813 AGAAGA
1 AGAAGA
16819 TTTTTCTTGA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
17 1 0.03
18 37 0.97
ACGTcount: A:0.35, C:0.08, G:0.33, T:0.23
Consensus pattern (18 bp):
AGAAGACCTTGGTTGAGA
Found at i:17162 original size:21 final size:21
Alignment explanation
Indices: 17136--17178 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
17126 AACAATTATA
*
17136 ACTAGTTGAATAAGTATCGAT
1 ACTAGTTGAATAAGGATCGAT
* *
17157 ACTAGTTGTATGAGGATCGAT
1 ACTAGTTGAATAAGGATCGAT
17178 A
1 A
17179 TTTTTTAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.09, G:0.23, T:0.33
Consensus pattern (21 bp):
ACTAGTTGAATAAGGATCGAT
Found at i:18199 original size:439 final size:439
Alignment explanation
Indices: 17295--18277 Score: 1492
Period size: 436 Copynumber: 2.2 Consensus size: 439
17285 TTACATTCTA
* * * * **
17295 ACCGGTTTGTTTATATGGTTAACAATAATGTAAATGGTAAAATATTTACAACCTAATCAATTAAT
1 ACCGGTTTGTTTATAGGGTTAATAATAATGTAAACGGTAAAATATTTACAACCTAACCGGTTAAT
* *
17360 TGGTTTAATATCATTACTTGTTATGA-AAGTATCGATACTTTTTTTCCAGTATGGTCTCTCAAAC
66 AGGTTTAATATCAATACTTGTTATGACAA-TATCGATACTTTTTTTCCAGTATGGTCTCTCAAAC
* *
17424 ATTTTGTATAAAAAGGTATCGATAGACATAGATAAAGTATTGGTCTTGTTTATTTCGAAACAAGA
130 ATTTTGCATAAAAAGGTATCGATACACATAGATAAAGTATTGGTCTTGTTTATTTCGAAACAAGA
* *
17489 TATGCAATAACTTCAACGTCAAAGTATTGATACTTGGTATGACAATATCGATACTTTTTGTTTCC
195 TATGCAACAACTTCAACGTCAAAGTATTGATACTTGGTATGACAATACCGATAC-TTTTGTTTCC
* *
17554 AATATGCTCTCTCAAACAATTTGCATGAAAACGTATCGATACACATATATGAAGTATCGATCTTT
259 AATATGCTCTCTCAAACAATTTGCATGAAAACGTATCGATACACATATATAAAGTATCAATCTTT
* ** * **
17619 ACAAACAACCTATTGCATTAAACTATATATGGATATTCTAATAATGTAAATGGTAAAATATTTAC
324 ACAAACAACCTATTACATTAAACTATATATCAATATTATAATAATGTAAACAGTAAAATATTTAC
* *
17684 AACCTAACCGGTTAAAACAATTTAGGTGCAACTTATTAGTTTAAACTTGCT
389 AACCTAACCAGTTAAAACAATTTAGGTGCAACCTATTAGTTTAAACTTGCT
*
17735 ACCGGTTTTTTTATAGGGTTAATAATAATGTAAACGGTAAAATATTTACAACCTAACCGGTTAAT
1 ACCGGTTTGTTTATAGGGTTAATAATAATGTAAACGGTAAAATATTTACAACCTAACCGGTTAAT
17800 AGGTTTAATATCAATACTTGTTATGACAATATC-A-ACATTTTTTTCCAGTATGGTCTCTCAAAC
66 AGGTTTAATATCAATACTTGTTATGACAATATCGATAC-TTTTTTTCCAGTATGGTCTCTCAAAC
* *
17863 ATTTTGCATGAAAAGTTATCGATACACATAGATAAAGTATCT-GTCTTGTTTATTTCGAAACAAG
130 ATTTTGCATAAAAAGGTATCGATACACATAGATAAAGTAT-TGGTCTTGTTTATTTCGAAACAAG
* * * *
17927 ATATGCCACAGCTTCAACGTCAAAGTATTGATACTTTGTATGACAGTACCGATAC-TTTGTTTCC
194 ATATGCAACAACTTCAACGTCAAAGTATTGATACTTGGTATGACAATACCGATACTTTTGTTTCC
* * * *
17991 AGTATGTTCTCTCAAACAATTTGCATGAAAATGTATCTATACACATATATAAAGTATCAATCTTT
259 AATATGCTCTCTCAAACAATTTGCATGAAAACGTATCGATACACATATATAAAGTATCAATCTTT
** *
18056 ACAAACAACCTATTATGTTAAACTATATA-CAATATTATAATAATGTAAACAGTAAAATATTTTC
324 ACAAACAACCTATTACATTAAACTATATATCAATATTATAATAATGTAAACAGTAAAATATTTAC
18120 AACCTAACCAGTTAAAACAATTTAGGTGCAACCTATTAGTTTAAACTTGCT
389 AACCTAACCAGTTAAAACAATTTAGGTGCAACCTATTAGTTTAAACTTGCT
* * *
18171 ACCGGTTTGTTTATAGGGTTAATAATAATATAAACGATAAAATATTTACAACCTAACCGGTTAAA
1 ACCGGTTTGTTTATAGGGTTAATAATAATGTAAACGGTAAAATATTTACAACCTAACCGGTTAAT
* * ** *
18236 ATGTTTAACATTGATACTTGTTATGACATTATCGATACTTTT
66 AGGTTTAATATCAATACTTGTTATGACAATATCGATACTTTT
18278 AACACAATCA
Statistics
Matches: 493, Mismatches: 45, Indels: 13
0.89 0.08 0.02
Matches are distributed among these distances:
436 167 0.34
437 99 0.20
438 4 0.01
439 134 0.27
440 87 0.18
441 2 0.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (439 bp):
ACCGGTTTGTTTATAGGGTTAATAATAATGTAAACGGTAAAATATTTACAACCTAACCGGTTAAT
AGGTTTAATATCAATACTTGTTATGACAATATCGATACTTTTTTTCCAGTATGGTCTCTCAAACA
TTTTGCATAAAAAGGTATCGATACACATAGATAAAGTATTGGTCTTGTTTATTTCGAAACAAGAT
ATGCAACAACTTCAACGTCAAAGTATTGATACTTGGTATGACAATACCGATACTTTTGTTTCCAA
TATGCTCTCTCAAACAATTTGCATGAAAACGTATCGATACACATATATAAAGTATCAATCTTTAC
AAACAACCTATTACATTAAACTATATATCAATATTATAATAATGTAAACAGTAAAATATTTACAA
CCTAACCAGTTAAAACAATTTAGGTGCAACCTATTAGTTTAAACTTGCT
Found at i:19384 original size:231 final size:230
Alignment explanation
Indices: 18957--19459 Score: 625
Period size: 231 Copynumber: 2.2 Consensus size: 230
18947 ATGATATTTC
* * * *
18957 AACCGGTTAAGTTGTACATATTTTATTATTGACCTTATTAATATACCTATAAACAAATCGGTAAA
1 AACCGGTTAAGTTGTA-ATATTTTACTGTT-ACATTATTAATATACCTATAAACAAAACGGTAAA
* * **
19022 AAGTTTAAAGTAATAGGTTGCGCCTAAATTGCTTTAACCGGTTAAATCGCCAGTATTTTATTGTT
64 AAGTTTAAAGTAATAGGTTGCGCCTAAATTGCTTTAACCGGTTAAATCGCCAATATTATACCGTT
* ** * * *
19087 TACATTATGATTCTACCGGTTAGGTTCAAACAATATTACCATCTATATTATCATTATACTGGTAG
129 TACATTATGATTATACCAATTAGGCTCAAACAATATTACCATCTACATTATCATTATACCGGTAG
*
19152 AAACTTTAATGTAACAGGTTAAACCTATTGT-TTTTT
194 AAACTTTAATGCAACAGGTTAAACCTATTGTATTTTT
* *
19188 AACCGGTTAAGGTGTATATATTTTACTGTGTACATTATTAATATACCTATAAACAAAACGGTAAG
1 AACCGGTTAAGTTGTA-ATATTTTACTGT-TACATTATTAATATACCTATAAACAAAACGGTAAA
* * * ** * *
19253 AAGTTTAAAGTAATAGGTTGCGCCTAAATTGTTTTAATCGTTTATGTTGTCAATATTATACCGTT
64 AAGTTTAAAGTAATAGGTTGCGCCTAAATTGCTTTAACCGGTTAAATCGCCAATATTATACCGTT
* * * * *
19318 TACATTATGATTATACCAATTAGGCTGAAA-ATATTTTATCGTTTACATTATTC-TTATACCGGT
129 TACATTATGATTATACCAATTAGGCTCAAACA-ATATTACCATCTACATTA-TCATTATACCGGT
**
19381 AGAAACTTTAATGCAACAGGTTGCACCTATTGTATTTTT
192 AGAAACTTTAATGCAACAGGTTAAACCTATTGTATTTTT
*
19420 AACCGGTTAAGTTGTAATTATTTTACCGTTTACATTATTA
1 AACCGGTTAAGTTGTAA-TATTTTACTG-TTACATTATTA
19460 TCAATGATTA
Statistics
Matches: 232, Mismatches: 34, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
230 1 0.00
231 188 0.81
232 42 0.18
233 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.40
Consensus pattern (230 bp):
AACCGGTTAAGTTGTAATATTTTACTGTTACATTATTAATATACCTATAAACAAAACGGTAAAAA
GTTTAAAGTAATAGGTTGCGCCTAAATTGCTTTAACCGGTTAAATCGCCAATATTATACCGTTTA
CATTATGATTATACCAATTAGGCTCAAACAATATTACCATCTACATTATCATTATACCGGTAGAA
ACTTTAATGCAACAGGTTAAACCTATTGTATTTTT
Found at i:20116 original size:142 final size:141
Alignment explanation
Indices: 19812--20299 Score: 541
Period size: 142 Copynumber: 3.4 Consensus size: 141
19802 TTGTAGTGTA
* * * * *
19812 ATAA-AAGTATCGATACGTAGACATTTTAGATATTGCATATATTGTTTCGAAATTATATATATAT
1 ATAACAAGTATCAATACTTTGACATTTCAGATATTGCATATCTTGTTTC-AAA--ATATATATAT
* * * * * * *
19876 CGATACTTTATATATGTGTATTGATAAATTTTGCGTACAAAATGTTTGAGAAGCATACTGGAATA
63 CGATACTTTATATA--TATATCGATACATTTTACATGCAAATTGTTTGAGAAGCATACTGGAATA
* **
19941 AAAGTATCAATTTGGGC
126 AAAGTATCGA-TACGGC
* * * *
19958 ATCACAAGTATCAATACTTTTACATTTCAGATACTGCATATCTTGTTTCAAAATCATATATATCA
1 ATAACAAGTATCAATACTTTGACATTTCAGATATTGCATATCTTGTTTCAAAAT-ATATATATCG
* *
20023 ATACATTATATATATATCAATACATTTT-CATGCAAATTGTTTGAGAAGCATACTGGGAA-AAAA
65 ATACTTTATATATATATCGATACATTTTACATGCAAATTGTTTGAGAAGCATACT-GGAATAAAA
20086 GTATCGATACAGGC
129 GTATCGATAC-GGC
* * *
20100 ATAACAAGTATCAATACTTTGACATTTAAGATATTCCATATCTTGTTTCGAAATTATATATATCG
1 ATAACAAGTATCAATACTTTGACATTTCAGATATTGCATATCTTGTTTC-AAAATATATATATCG
*
20165 ATACTTTATATATATGTATCGATACATTTTACATGCAAATTGTTTGAGAAGCATAGTGGAATAAA
65 ATACTTTATATATA--TATCGATACATTTTACATGCAAATTGTTTGAGAAGCATACTGGAATAAA
*
20230 AGTATCGATACGATC
128 AGTATCGATACG-GC
* * * * * * *
20245 ATAACTAGTAACGATACATTGACATTTCAGATATTGCAAATGTTGTTTCGAAATA
1 ATAACAAGTATCAATACTTTGACATTTCAGATATTGCATATCTTGTTTCAAAATA
20300 AGCAATATCG
Statistics
Matches: 291, Mismatches: 41, Indels: 22
0.82 0.12 0.06
Matches are distributed among these distances:
141 1 0.00
142 102 0.35
143 20 0.07
144 24 0.08
145 101 0.35
146 6 0.02
147 37 0.13
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (141 bp):
ATAACAAGTATCAATACTTTGACATTTCAGATATTGCATATCTTGTTTCAAAATATATATATCGA
TACTTTATATATATATCGATACATTTTACATGCAAATTGTTTGAGAAGCATACTGGAATAAAAGT
ATCGATACGGC
Found at i:20267 original size:145 final size:144
Alignment explanation
Indices: 19812--20333 Score: 606
Period size: 145 Copynumber: 3.6 Consensus size: 144
19802 TTGTAGTGTA
* * * * *
19812 ATAA-AAGTATCGATACGTAGACATTTTAGATATTGCATATATTGTTTCGAAATTATATATATAT
1 ATAACAAGTATCAATACTTTGACATTTCAGATATTGCATATCTTGTTTCGAAA-T-TATATATAT
* * * * * *
19876 CGATACTTTATATATGTGTATTGATAAATTTTGCGTACAAAATGTTTGAGAAGCATACTGGAATA
64 CGATACTTTATATATATGTATCGATACATTTT-CATGCAAATTGTTTGAGAAGCATACTGGAATA
* ** *
19941 AAAGTATCAATTTGGGC
128 AAAGTATCGATACGAGC
* * * * * *
19958 ATCACAAGTATCAATACTTTTACATTTCAGATACTGCATATCTTGTTTCAAAATCATATATATCA
1 ATAACAAGTATCAATACTTTGACATTTCAGATATTGCATATCTTGTTTCGAAATTATATATATCG
* *
20023 ATACATTATATATA--TATCAATACATTTTCATGCAAATTGTTTGAGAAGCATACTGGGAA-AAA
66 ATACTTTATATATATGTATCGATACATTTTCATGCAAATTGTTTGAGAAGCATACT-GGAATAAA
20085 AGTATCGATAC-AGGC
130 AGTATCGATACGA-GC
* *
20100 ATAACAAGTATCAATACTTTGACATTTAAGATATTCCATATCTTGTTTCGAAATTATATATATCG
1 ATAACAAGTATCAATACTTTGACATTTCAGATATTGCATATCTTGTTTCGAAATTATATATATCG
*
20165 ATACTTTATATATATGTATCGATACATTTTACATGCAAATTGTTTGAGAAGCATAGTGGAATAAA
66 ATACTTTATATATATGTATCGATACATTTT-CATGCAAATTGTTTGAGAAGCATACTGGAATAAA
*
20230 AGTATCGATACGATC
130 AGTATCGATACGAGC
* * * * * * * *
20245 ATAACTAGTAACGATACATTGACATTTCAGATATTGCAAATGTTGTTTCGAAATAAGCA-ATATC
1 ATAACAAGTATCAATACTTTGACATTTCAGATATTGCATATCTTGTTTCGAAATTA-TATATATC
* *
20309 GATACTTGATCTATATGTATCGATA
65 GATACTTTATATATATGTATCGATA
20334 TTGTTCATAC
Statistics
Matches: 320, Mismatches: 47, Indels: 19
0.83 0.12 0.05
Matches are distributed among these distances:
142 106 0.33
143 15 0.05
144 17 0.05
145 136 0.43
146 6 0.02
147 40 0.12
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (144 bp):
ATAACAAGTATCAATACTTTGACATTTCAGATATTGCATATCTTGTTTCGAAATTATATATATCG
ATACTTTATATATATGTATCGATACATTTTCATGCAAATTGTTTGAGAAGCATACTGGAATAAAA
GTATCGATACGAGC
Found at i:26080 original size:59 final size:58
Alignment explanation
Indices: 25984--26104 Score: 156
Period size: 59 Copynumber: 2.1 Consensus size: 58
25974 AATAGATGGA
* *
25984 TAAGTGTCCTATCGAAGCTTCCTAGTCGCAATGAAAAGGCAAACTCGATAATATGGCTC
1 TAAGTGTCCTATCGAAGCTTCCTAGTC-CAATAAAAAGGAAAACTCGATAATATGGCTC
* *
26043 TAAGTGTCCTATCGAA-CTCTCTTAGT-CAAGTTAAAAAGTAAAACTCGATAATATGGCTC
1 TAAGTGTCCTATCGAAGCT-TCCTAGTCCAA--TAAAAAGGAAAACTCGATAATATGGCTC
26102 TAA
1 TAA
26105 CCAACCCTCC
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
57 3 0.05
58 2 0.04
59 50 0.91
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (58 bp):
TAAGTGTCCTATCGAAGCTTCCTAGTCCAATAAAAAGGAAAACTCGATAATATGGCTC
Found at i:36228 original size:19 final size:19
Alignment explanation
Indices: 36204--36243 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
36194 GTGTTTTAAG
36204 TGTGTTTTAAAATGATAAA
1 TGTGTTTTAAAATGATAAA
36223 TGTGTTTTAAAATGATAAA
1 TGTGTTTTAAAATGATAAA
36242 TG
1 TG
36244 GGAGAAGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.42
Consensus pattern (19 bp):
TGTGTTTTAAAATGATAAA
Found at i:37902 original size:21 final size:22
Alignment explanation
Indices: 37876--37916 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
37866 TTCAGGATTA
* *
37876 TAAATTGAATT-AGCTGAATTT
1 TAAATTCAATTGAACTGAATTT
37897 TAAATTCAATTGAACTGAAT
1 TAAATTCAATTGAACTGAAT
37917 GGGGTATTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.39
Consensus pattern (22 bp):
TAAATTCAATTGAACTGAATTT
Found at i:39624 original size:23 final size:23
Alignment explanation
Indices: 39570--39625 Score: 60
Period size: 28 Copynumber: 2.3 Consensus size: 23
39560 CAACGGTCAA
39570 CGGCTCAGTCGGCTTGGCTTGGCT
1 CGGCTCAGTCGGCTTGGC-TGGCT
39594 CAAAGGCTCAGTTCGGCTTGG-TGGCT
1 C---GGCTCAG-TCGGCTTGGCTGGCT
39620 CGGCTC
1 CGGCTC
39626 GGTGGCTCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
23 5 0.18
24 1 0.04
26 6 0.21
27 7 0.25
28 9 0.32
ACGTcount: A:0.09, C:0.29, G:0.36, T:0.27
Consensus pattern (23 bp):
CGGCTCAGTCGGCTTGGCTGGCT
Found at i:51767 original size:20 final size:20
Alignment explanation
Indices: 51744--51791 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
51734 ATAGTTGTAC
*
51744 ATCAGTACTGATACT-TATGT
1 ATCAATACTGATA-TATATGT
*
51764 ATCAATACTTATATATATGT
1 ATCAATACTGATATATATGT
*
51784 ATCGATAC
1 ATCAATAC
51792 CTACCGATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 1 0.04
20 23 0.96
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (20 bp):
ATCAATACTGATATATATGT
Found at i:52226 original size:15 final size:14
Alignment explanation
Indices: 52207--52262 Score: 60
Period size: 15 Copynumber: 3.8 Consensus size: 14
52197 AGAAGAAAAA
52207 TTTATATAAAAATT
1 TTTATATAAAAATT
*
52221 ATTTATTATAATAATT
1 -TTTA-TATAAAAATT
52237 TTTATA-AATATAATT
1 TTTATATAA-A-AATT
52252 TTTATATAAAA
1 TTTATATAAAA
52263 TGTTTATTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
13 2 0.06
14 3 0.09
15 19 0.54
16 11 0.31
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTATATAAAAATT
Found at i:52252 original size:28 final size:27
Alignment explanation
Indices: 52205--52257 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
52195 TAAGAAGAAA
*
52205 AATTTATATAAAAATTATTTATTATAAT
1 AATTTATATAAAAATAATTT-TTATAAT
* *
52233 AATTTTTATAAATATAATTTTTATA
1 AATTTATATAAAAATAATTTTTATA
52258 TAAAATGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 5 0.23
28 17 0.77
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
AATTTATATAAAAATAATTTTTATAAT
Found at i:52554 original size:12 final size:11
Alignment explanation
Indices: 52531--52570 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
52521 TAATAAATAA
52531 TTATTATTAAAT
1 TTATT-TTAAAT
52543 TTATTTTAAAAT
1 TTATTTT-AAAT
*
52555 TTAATTTAAAT
1 TTATTTTAAAT
52566 TTATT
1 TTATT
52571 ATATAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TTATTTTAAAT
Found at i:53376 original size:17 final size:17
Alignment explanation
Indices: 53356--53401 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 17
53346 TTCATATTAT
53356 ATTATATATAAATAAAA
1 ATTATATATAAATAAAA
*
53373 ATTATAT-T-TATAAAA
1 ATTATATATAAATAAAA
* *
53388 AATATATAAAAATA
1 ATTATATATAAATA
53402 TAAGTTTGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
15 12 0.52
16 1 0.04
17 10 0.43
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
ATTATATATAAATAAAA
Found at i:53826 original size:4 final size:4
Alignment explanation
Indices: 53817--53843 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
53807 ATTTCATTGC
53817 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
53844 GTTCATTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:54379 original size:25 final size:25
Alignment explanation
Indices: 54349--54398 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
54339 CTATAAAAGA
*
54349 TTTTAA-TATGATCACTTATTTATTT
1 TTTTAATTA-GATCACTTAATTATTT
*
54374 TTTTAATTAGATCATTTAATTATTT
1 TTTTAATTAGATCACTTAATTATTT
54399 CAATGATATC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 20 0.91
26 2 0.09
ACGTcount: A:0.30, C:0.06, G:0.04, T:0.60
Consensus pattern (25 bp):
TTTTAATTAGATCACTTAATTATTT
Done.