Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004257.1 Hibiscus syriacus cultivar Beakdansim tig00009328_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: 100695
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:11520 original size:19 final size:20
Alignment explanation
Indices: 11481--11520 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
11471 CGATAGAGTG
* *
11481 CTACCTAAAATGTTATTTTT
1 CTACCAAAAATGTTATATTT
11501 CTACCAAAAATGTTA-ATTT
1 CTACCAAAAATGTTATATTT
11520 C
1 C
11521 GCTACCTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.35, C:0.17, G:0.05, T:0.42
Consensus pattern (20 bp):
CTACCAAAAATGTTATATTT
Found at i:11540 original size:21 final size:20
Alignment explanation
Indices: 11480--11533 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
11470 CCGATAGAGT
*
11480 GCTACCTAAAATGTTATTTT
1 GCTACCTAAAATGTTATTTC
* *
11500 TCTACCAAAAATGTTAATTTC
1 GCTACCTAAAATGTT-ATTTC
11521 GCTACCTAAAATG
1 GCTACCTAAAATG
11534 AATATTTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 13 0.46
21 15 0.54
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (20 bp):
GCTACCTAAAATGTTATTTC
Found at i:11624 original size:45 final size:46
Alignment explanation
Indices: 11544--11631 Score: 142
Period size: 45 Copynumber: 1.9 Consensus size: 46
11534 AATATTTTTT
*
11544 ATATTAAAATTTCTGGTAGAAAAAAATAATATTTTAGGTAGCGTCCA
1 ATATTAAAATTTCCGGTA-AAAAAAATAATATTTTAGGTAGCGTCCA
*
11591 ATATTAATATTTCCGGT-AAAAAAATAATATTTTAGGTAGCG
1 ATATTAAAATTTCCGGTAAAAAAAATAATATTTTAGGTAGCG
11632 CTCTACCGGA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
45 24 0.62
47 15 0.38
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (46 bp):
ATATTAAAATTTCCGGTAAAAAAAATAATATTTTAGGTAGCGTCCA
Found at i:14973 original size:2 final size:2
Alignment explanation
Indices: 14968--14999 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
14958 GGATAAATAA
14968 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
15000 CTAAAATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16239 original size:23 final size:23
Alignment explanation
Indices: 16209--16252 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
16199 CTAATTCAGT
16209 TCAACACCCAGAACCCAAAACAA
1 TCAACACCCAGAACCCAAAACAA
16232 TCAACACCCAGAACCCAAAAC
1 TCAACACCCAGAACCCAAAAC
16253 TAAAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.50, C:0.41, G:0.05, T:0.05
Consensus pattern (23 bp):
TCAACACCCAGAACCCAAAACAA
Found at i:20389 original size:14 final size:15
Alignment explanation
Indices: 20363--20397 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
20353 TTCTCCTCTG
20363 GTTCGACTAACAACA
1 GTTCGACTAACAACA
20378 GTTCGA-TAACAACA
1 GTTCGACTAACAACA
20392 GTTCGA
1 GTTCGA
20398 GTAGTCTTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (15 bp):
GTTCGACTAACAACA
Found at i:24379 original size:2 final size:2
Alignment explanation
Indices: 24372--24409 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
24362 AAGAGAACTA
24372 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
24410 GGAGGTGGGG
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:28341 original size:2 final size:2
Alignment explanation
Indices: 28334--28377 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
28324 GATCTTGCCT
28334 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
28376 TA
1 TA
28378 AGAAAGAGAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:34790 original size:32 final size:32
Alignment explanation
Indices: 34749--34812 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
34739 AGATAACCTT
34749 TTTTGCTCTTATGGATGATGATTAGTTGATTG
1 TTTTGCTCTTATGGATGATGATTAGTTGATTG
34781 TTTTGCTCTTATGGATGATGATTAGTTGATTG
1 TTTTGCTCTTATGGATGATGATTAGTTGATTG
34813 ACTGATACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.19, C:0.06, G:0.25, T:0.50
Consensus pattern (32 bp):
TTTTGCTCTTATGGATGATGATTAGTTGATTG
Found at i:40890 original size:2 final size:2
Alignment explanation
Indices: 40885--40914 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
40875 ATATGTATTC
40885 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
40915 GCATACGTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45829 original size:174 final size:175
Alignment explanation
Indices: 45531--45879 Score: 533
Period size: 174 Copynumber: 2.0 Consensus size: 175
45521 TGAAGCTCTA
* ** * *
45531 ATTCGACGATGCAATGCCTCACTAGAATCCGTAGAAGTTAAATCCGGTCAAAGCATTCACCGATT
1 ATTCGACGATGCAATGCATCACTAGAATCCGTAGAAGCAAAATCAGATCAAAGCATTCACCGATT
* * *
45596 TACAAGTAAGGAAATCATCAAACAAAATAGGATCCAACACATTTCCTCTGAAACAGTGAAAGAAC
66 TACAAGTAAAGAAATCATCAAACAAAATAAGATCCAAAACATTTCCTCTGAAACAGTGAAAGAAC
45661 CAGATATCAAGAAATCAAAAGAAAC-AAAGCAGATTTAAGAAATC
131 CAGATATCAAGAAATCAAAAGAAACAAAAGCAGATTTAAGAAATC
*
45705 ATTCGACGATGTAATGCATCACTAGAATCCGTAGAAGCAAAATCAGATCAAAGCATTCACCGATT
1 ATTCGACGATGCAATGCATCACTAGAATCCGTAGAAGCAAAATCAGATCAAAGCATTCACCGATT
*
45770 TACGAGTAAAGAAATCATCAAACAAAATAAGATCCAAAACA-TTCGCTCT-AAAGCAGTGAAAGA
66 TACAAGTAAAGAAATCATCAAACAAAATAAGATCCAAAACATTTC-CTCTGAAA-CAGTGAAAGA
* * **
45833 ATCAGATATCATGAAATCTCAAGAAACAAAAGCAGATTTAAGAAATC
129 ACCAGATATCAAGAAATCAAAAGAAACAAAAGCAGATTTAAGAAATC
45880 GGGAACAGCA
Statistics
Matches: 158, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
173 6 0.04
174 133 0.84
175 19 0.12
ACGTcount: A:0.45, C:0.19, G:0.15, T:0.20
Consensus pattern (175 bp):
ATTCGACGATGCAATGCATCACTAGAATCCGTAGAAGCAAAATCAGATCAAAGCATTCACCGATT
TACAAGTAAAGAAATCATCAAACAAAATAAGATCCAAAACATTTCCTCTGAAACAGTGAAAGAAC
CAGATATCAAGAAATCAAAAGAAACAAAAGCAGATTTAAGAAATC
Found at i:50512 original size:27 final size:27
Alignment explanation
Indices: 50474--50530 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
50464 CAATATCTAA
* *
50474 TTTATTAAAAAATATT-TTAAATTGAAT
1 TTTATAAAAAAATATTGTTAAAAT-AAT
50501 TTTATAAAAAAATATTGTTAAAATAAT
1 TTTATAAAAAAATATTGTTAAAATAAT
50528 TTT
1 TTT
50531 TTAATTTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 21 0.78
28 6 0.22
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (27 bp):
TTTATAAAAAAATATTGTTAAAATAAT
Found at i:51653 original size:2 final size:2
Alignment explanation
Indices: 51646--51670 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
51636 TACTCATTCT
51646 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
51671 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:51675 original size:2 final size:2
Alignment explanation
Indices: 51670--51706 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
51660 TCTCTCTCTC
51670 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
51707 CCTTCCGTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:56408 original size:23 final size:23
Alignment explanation
Indices: 56375--56418 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
56365 GAGTCGAGGG
56375 TCTACGCGGTCCTTCGGGACAAT
1 TCTACGCGGTCCTTCGGGACAAT
*
56398 TCTACGTGGTCCTTCGGGACA
1 TCTACGCGGTCCTTCGGGACA
56419 CATATGTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.16, C:0.30, G:0.27, T:0.27
Consensus pattern (23 bp):
TCTACGCGGTCCTTCGGGACAAT
Found at i:56717 original size:6 final size:6
Alignment explanation
Indices: 56699--56984 Score: 458
Period size: 6 Copynumber: 48.2 Consensus size: 6
56689 AAATATATTA
*
56699 TATGTG ATATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTA
1 TATGTG -TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
56748 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
56796 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
* *
56844 TATGTG TACGTG TACGTG TATGTG TATGTG TA--TG TATGTG TA--TG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
* *
56888 TATGTG TATGTG TATGTG TATGTG TATGTG TA--TG TATATG TATGTA
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
56934 TATGTGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
1 TA--TGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
56984 T
1 T
56985 GACATGTTAT
Statistics
Matches: 264, Mismatches: 7, Indels: 17
0.92 0.02 0.06
Matches are distributed among these distances:
4 12 0.05
6 241 0.91
7 6 0.02
8 5 0.02
ACGTcount: A:0.18, C:0.01, G:0.32, T:0.49
Consensus pattern (6 bp):
TATGTG
Found at i:60131 original size:6 final size:6
Alignment explanation
Indices: 60120--60168 Score: 89
Period size: 6 Copynumber: 8.2 Consensus size: 6
60110 GACACGTATT
*
60120 ACCACG ACCACG ACCACG ACCACG ACCTCG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
60168 A
1 A
60169 GCCGAGCCGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.33, C:0.49, G:0.16, T:0.02
Consensus pattern (6 bp):
ACCACG
Found at i:60176 original size:5 final size:5
Alignment explanation
Indices: 60166--60229 Score: 92
Period size: 5 Copynumber: 12.8 Consensus size: 5
60156 ACCACGACCA
* * *
60166 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGTGC CGTGC CGTGC CGAGC
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC
*
60216 CGAGC CGAGA CGAG
1 CGAGC CGAGC CGAG
60230 ACGGACGGAC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 56 1.00
ACGTcount: A:0.17, C:0.38, G:0.41, T:0.05
Consensus pattern (5 bp):
CGAGC
Found at i:65873 original size:27 final size:27
Alignment explanation
Indices: 65842--65898 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
65832 TTAACAGCTT
65842 GTCTCCTCTGTACAAAGCTGTAAATCA
1 GTCTCCTCTGTACAAAGCTGTAAATCA
65869 GTCTCCTCTGTACAAAGCTGTAAATCA
1 GTCTCCTCTGTACAAAGCTGTAAATCA
65896 GTC
1 GTC
65899 CAGGTACATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (27 bp):
GTCTCCTCTGTACAAAGCTGTAAATCA
Found at i:71831 original size:169 final size:166
Alignment explanation
Indices: 71510--71843 Score: 634
Period size: 165 Copynumber: 2.0 Consensus size: 166
71500 TGCTGCTCCC
71510 CTCCGTTATCACCCACCCCTCTACTCCATCTTCTTTTTGTCTTCTACTTTTCTTATTATACTTCA
1 CTCCGTTATCACCCACCCCTCTACTCCATCTTCTTTTTGTCTTCTACTTTTCTTATTATACTTCA
71575 AATACTGTCTATCAAATTATTGAGTAATCTCGTTGATAAAAAGAATTATTATATAATCATTTTGA
66 AATA---TCTATCAAATTATTGAGTAATCTCGTTGATAAAAAGAATTATTATATAATCATTTTGA
71640 ATTATTAAAAGTAATTTATATATATATATTTGTGTATAT
128 ATTATTAAAAGTAATTTATATATATATATTTGTGTATAT
71679 CTCCGTTATCACCCACCCCTCTACTCCATCTTCTTTTTGTCTTCTACTTTTCTTATTATACTTCA
1 CTCCGTTATCACCCACCCCTCTACTCCATCTTCTTTTTGTCTTCTACTTTTCTTATTATACTTCA
71744 AATA-CTATCAAATTATTGAGTAATCTCGTTGATAAAAAGAATTATTATATAATCATTTTGAATT
66 AATATCTATCAAATTATTGAGTAATCTCGTTGATAAAAAGAATTATTATATAATCATTTTGAATT
71808 ATTAAAAGTAATTTATATATATATATTTGTGTATAT
131 ATTAAAAGTAATTTATATATATATATTTGTGTATAT
71844 TTATATTTAT
Statistics
Matches: 165, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
165 96 0.58
169 69 0.42
ACGTcount: A:0.31, C:0.17, G:0.07, T:0.45
Consensus pattern (166 bp):
CTCCGTTATCACCCACCCCTCTACTCCATCTTCTTTTTGTCTTCTACTTTTCTTATTATACTTCA
AATATCTATCAAATTATTGAGTAATCTCGTTGATAAAAAGAATTATTATATAATCATTTTGAATT
ATTAAAAGTAATTTATATATATATATTTGTGTATAT
Found at i:73515 original size:2 final size:2
Alignment explanation
Indices: 73508--73568 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
73498 TTGACTAGGG
73508 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
73550 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
73569 GGAATAAATT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:74747 original size:22 final size:22
Alignment explanation
Indices: 74719--74764 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
74709 ATATTTATAA
*
74719 TTTTTTCATGTGTACGTAATAT
1 TTTTTTCATGTGTACGTAAGAT
*
74741 TTTTTTCATTTGTACGTAAGAT
1 TTTTTTCATGTGTACGTAAGAT
74763 TT
1 TT
74765 GTAATGATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.22, C:0.09, G:0.13, T:0.57
Consensus pattern (22 bp):
TTTTTTCATGTGTACGTAAGAT
Found at i:79178 original size:3 final size:3
Alignment explanation
Indices: 79170--79196 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
79160 GGGAATAAAA
79170 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
79197 TGATGTCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:82449 original size:20 final size:22
Alignment explanation
Indices: 82424--82465 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
82414 TATACTTTAT
82424 ATTT-AAAA-TAATTATAAAAA
1 ATTTAAAAATTAATTATAAAAA
82444 ATTTAAAAATTTAATTATAAAA
1 ATTTAAAAA-TTAATTATAAAA
82466 TGTAATGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
21 4 0.21
23 11 0.58
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
ATTTAAAAATTAATTATAAAAA
Found at i:83243 original size:2 final size:2
Alignment explanation
Indices: 83236--83263 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
83226 TTAAAGAACA
83236 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
83264 TCCTAGGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:90741 original size:21 final size:21
Alignment explanation
Indices: 90711--90759 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
90701 TAATTTTCAA
*
90711 ACATTATTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
90732 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
90753 ACATTGT
1 ACATTGT
90760 AATATTAGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.43
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:91023 original size:26 final size:26
Alignment explanation
Indices: 90994--91050 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
90984 ACACGCCTAC
90994 ATCTTGTGCCTTAGTGCTACACAACA
1 ATCTTGTGCCTTAGTGCTACACAACA
91020 ATCTTGTGCCTTAGTGCTACACAACA
1 ATCTTGTGCCTTAGTGCTACACAACA
*
91046 TTCTT
1 ATCTT
91051 CACAATAGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.25, C:0.26, G:0.14, T:0.35
Consensus pattern (26 bp):
ATCTTGTGCCTTAGTGCTACACAACA
Found at i:96699 original size:34 final size:34
Alignment explanation
Indices: 96659--96739 Score: 83
Period size: 34 Copynumber: 2.4 Consensus size: 34
96649 ACATAGTCTC
96659 GTTCGTTCATTTACGTTC-GTGAACGTTCGGTTAT
1 GTTCGTTCATTTACGTTCAGT-AACGTTCGGTTAT
* * * * * *
96693 GTTCGTTTATATGCGTTCAGTTATGTTCGTTTAT
1 GTTCGTTCATTTACGTTCAGTAACGTTCGGTTAT
*
96727 GTGCGTTCATTTA
1 GTTCGTTCATTTA
96740 TGTTTAACAT
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
34 34 0.94
35 2 0.06
ACGTcount: A:0.15, C:0.15, G:0.22, T:0.48
Consensus pattern (34 bp):
GTTCGTTCATTTACGTTCAGTAACGTTCGGTTAT
Found at i:96709 original size:24 final size:24
Alignment explanation
Indices: 96682--96743 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
96672 CGTTCGTGAA
*
96682 CGTTCGGTTATGTTCGTTTATATG
1 CGTTCAGTTATGTTCGTTTATATG
*
96706 CGTTCAGTTATGTTCGTTTATGTG
1 CGTTCAGTTATGTTCGTTTATATG
*
96730 CGTTCATTTATGTT
1 CGTTCAGTTATGTT
96744 TAACATAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.13, C:0.13, G:0.23, T:0.52
Consensus pattern (24 bp):
CGTTCAGTTATGTTCGTTTATATG
Found at i:100590 original size:16 final size:15
Alignment explanation
Indices: 100553--100596 Score: 63
Period size: 16 Copynumber: 2.9 Consensus size: 15
100543 GGGTCTCCAA
100553 CTTTATGTTCG-GTT
1 CTTTATGTTCGTGTT
*
100567 CATTATGTTCGTGTT
1 CTTTATGTTCGTGTT
100582 CGTTTATGTTCGTGT
1 C-TTTATGTTCGTGT
100597 ATTTATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 10 0.38
15 4 0.15
16 12 0.46
ACGTcount: A:0.09, C:0.14, G:0.23, T:0.55
Consensus pattern (15 bp):
CTTTATGTTCGTGTT
Done.