Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005919.1 Hibiscus syriacus cultivar Beakdansim tig00013897_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: 110942
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Found at i:3680 original size:109 final size:109
Alignment explanation
Indices: 3488--3702 Score: 367
Period size: 109 Copynumber: 2.0 Consensus size: 109
3478 GCATAGTTTA
*
3488 CCCAGAATTAAAACAAAGAAAGGGCGTCGACCTTGTCGGGAGTGAAACATTTATTTAGAAATAAT
1 CCCAGAATTAAAACAAAGAAAGGGCGTCGACCTTGTCAGGAGTGAAACATTTATTTAGAAATAAT
3553 GAAGCAGACAATTAAAATTGAAGAAGAAGATTACATTTCACTTT
66 GAAGCAGACAATTAAAATTGAAGAAGAAGATTACATTTCACTTT
* * *
3597 CCCAGAATTAAAACGAAGAAAGGGCGTCGATCTTGTCAGGAGTGAATCATTTATTTAGAAATAAT
1 CCCAGAATTAAAACAAAGAAAGGGCGTCGACCTTGTCAGGAGTGAAACATTTATTTAGAAATAAT
* * *
3662 GCAGCAGGCAATTGAAATTGAAGAAGAAGATTACATTTCAC
66 GAAGCAGACAATTAAAATTGAAGAAGAAGATTACATTTCAC
3703 CGTCCCAAAT
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
109 99 1.00
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (109 bp):
CCCAGAATTAAAACAAAGAAAGGGCGTCGACCTTGTCAGGAGTGAAACATTTATTTAGAAATAAT
GAAGCAGACAATTAAAATTGAAGAAGAAGATTACATTTCACTTT
Found at i:6137 original size:24 final size:24
Alignment explanation
Indices: 6039--6138 Score: 92
Period size: 24 Copynumber: 4.2 Consensus size: 24
6029 GATATTAGAA
* * *
6039 ATCAAAATAGAATTCAGATAAAAT
1 ATCAAAACAGAATCCAGATAAGAT
* * * *
6063 ATCAGAATAGAATCCAGATCAGAA
1 ATCAAAACAGAATCCAGATAAGAT
* * *
6087 ATCAAAACAGAATCCAGGTCAGGT
1 ATCAAAACAGAATCCAGATAAGAT
* *
6111 ATCAAAACAGAATTCAAATAAGAT
1 ATCAAAACAGAATCCAGATAAGAT
6135 ATCA
1 ATCA
6139 GATAAAATAT
Statistics
Matches: 61, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 61 1.00
ACGTcount: A:0.52, C:0.15, G:0.13, T:0.20
Consensus pattern (24 bp):
ATCAAAACAGAATCCAGATAAGAT
Found at i:10556 original size:24 final size:24
Alignment explanation
Indices: 10529--10609 Score: 72
Period size: 24 Copynumber: 3.4 Consensus size: 24
10519 GATATTAGAA
* *
10529 ATCAAAATAGAATTCAGATCAGAT
1 ATCAAAACAGAATCCAGATCAGAT
* *
10553 ATCAGAACAGAATCCAGATCAGAA
1 ATCAAAACAGAATCCAGATCAGAT
** * * *
10577 ATCGGAACATAATCCAGGTCAGGT
1 ATCAAAACAGAATCCAGATCAGAT
*
10601 ATCAGAACA
1 ATCAAAACA
10610 AAATTCAAAT
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.46, C:0.19, G:0.17, T:0.19
Consensus pattern (24 bp):
ATCAAAACAGAATCCAGATCAGAT
Found at i:11881 original size:20 final size:20
Alignment explanation
Indices: 11856--11901 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
11846 GATTCTTTCG
11856 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
11876 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
11896 TTGCGA
1 TTGCGA
11902 AAGTAAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.35
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:12072 original size:18 final size:18
Alignment explanation
Indices: 12049--12098 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
12039 TTTACTAAGC
12049 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
12067 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
12085 AATCTAAGTGAAAT
1 AATCTAAGTGAAAT
12099 TACGAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (18 bp):
AATCTAAGTGAAATGGTT
Found at i:13848 original size:20 final size:20
Alignment explanation
Indices: 13825--13951 Score: 132
Period size: 20 Copynumber: 6.5 Consensus size: 20
13815 TCTGAAACTT
13825 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
13845 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
13865 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * * **
13885 ACTATCGTAACGCGAATTTG
1 AAAATCGCAACACGAAAATG
** **
13905 ACTATCGCAATGCG-AAATG
1 AAAATCGCAACACGAAAATG
* *
13924 AAAATCGCAACGCGAAACT-
1 AAAATCGCAACACGAAAATG
13943 AAAATCGCA
1 AAAATCGCA
13952 TTGCGATTCT
Statistics
Matches: 92, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
19 23 0.25
20 69 0.75
ACGTcount: A:0.47, C:0.21, G:0.17, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:14552 original size:20 final size:20
Alignment explanation
Indices: 14522--14677 Score: 125
Period size: 20 Copynumber: 7.7 Consensus size: 20
14512 GTGCTTTGAA
14522 AATCGCATTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
* *
14542 CATCGCGTTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
* * *
14562 AATCTCGTTGCGATAGTTAG
1 AATCGCATTGCGATAGTCAG
*
14582 AATCGCATTGCGATAGTCAT
1 AATCGCATTGCGATAGTCAG
** *
14602 AATTACATTGCGATAGTCGGAA
1 AATCGCATTGCGATAGTC--AG
** * * *
14624 AATCGCAACGCGA-ATTTGGAA
1 AATCGCATTGCGATA-GT-CAG
*
14645 AATCGCAATGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
*
14665 AATCGCGTTGCGA
1 AATCGCATTGCGA
14678 ATCTGGAAAC
Statistics
Matches: 107, Mismatches: 24, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
20 79 0.74
21 16 0.15
22 12 0.11
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (20 bp):
AATCGCATTGCGATAGTCAG
Found at i:14678 original size:41 final size:40
Alignment explanation
Indices: 14633--14720 Score: 99
Period size: 40 Copynumber: 2.2 Consensus size: 40
14623 AAATCGCAAC
*
14633 GCGAATTTGGAAAATCGCA-ATGCGATAGTCAGA-ATCGCGTT
1 GCGAATTTGGAAAAT-G-ATATGCGATA-CCAGAGATCGCGTT
* * *
14674 GCGAATCTGGAAACTGATTTGCGATACCAGAGATCGCGTT
1 GCGAATTTGGAAAATGATATGCGATACCAGAGATCGCGTT
14714 GCGAATT
1 GCGAATT
14721 ATCGATCGCA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
39 5 0.12
40 22 0.55
41 13 0.32
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (40 bp):
GCGAATTTGGAAAATGATATGCGATACCAGAGATCGCGTT
Found at i:17967 original size:28 final size:28
Alignment explanation
Indices: 17936--17997 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
17926 TTGAATTTAT
* *
17936 TTATAATATATATATATATAT-ATTTAAA
1 TTATAA-ATAGATAAATATATCATTTAAA
*
17964 TTATTAAATGGATAAATATATCATTTAAA
1 TTA-TAAATAGATAAATATATCATTTAAA
17993 TTATA
1 TTATA
17998 TTATTTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 16 0.55
29 13 0.45
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (28 bp):
TTATAAATAGATAAATATATCATTTAAA
Found at i:18427 original size:28 final size:28
Alignment explanation
Indices: 18396--18457 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
18386 TTGAATTTAT
* *
18396 TTATAATATATATATATATAT-ATTTAAA
1 TTATAA-ATAGATAAATATATCATTTAAA
*
18424 TTATTAAATGGATAAATATATCATTTAAA
1 TTA-TAAATAGATAAATATATCATTTAAA
18453 TTATA
1 TTATA
18458 TTATTTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 16 0.55
29 13 0.45
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (28 bp):
TTATAAATAGATAAATATATCATTTAAA
Found at i:18809 original size:459 final size:460
Alignment explanation
Indices: 17872--19160 Score: 2420
Period size: 459 Copynumber: 2.8 Consensus size: 460
17862 TATTATAAAA
17872 TATATTTTTATTATAGTTTAAATTTATATAATTCATATGTAATAATAATTTCTTTTGAATTTATT
1 TATATTTTTATTATAGTTTAAATTTATATAATTCATATGTAATAATAATTTCTTTTGAATTTATT
17937 TATAATATATATATATATATATTTAAATTATTAAATGGATAAATATATCATTTAAATTATATTAT
66 TATAATATATATATATATATATTTAAATTATTAAATGGATAAATATATCATTTAAATTATATTAT
18002 TTTAAATTTTAAATGAGTAATTGTAGTTGAATTGAAATAATTAAACACTCCATCTGTTATGAAAT
131 TTTAAATTTTAAATGAGTAATTGTAGTTGAATTGAAATAATTAAACACTCCATCTGTTATGAAAT
*
18067 GGAATTAATGAGAGATACCATATCTTCTAGTTTAATAAATTCAGTTTAATTTATAAGAACTAATG
196 GGAATTAATGAGAGATACCATATCTTCTAGTTTAATAAATTCAGTTTAATTTATAAGCACTAATG
18132 TGTTTTTTTAATATTCTTTTTGTCGAAACAAATATTTAAATTATTATTTTGTAATAATATTATAT
261 TGTTTTTTTAATATTCTTTTTGTCGAAACAAATATTTAAATTATTATTTTGTAATAATATTATAT
* *
18197 CTACAAGTTAAAAAATATTGATAATTTATTTTTTTTAATTTATTTTAATTACTTAAAAGTAAATA
326 CTACATGTTAAAAAATATTGATAATATATTTTTTTTAATTTATTTTAATTACTTAAAAGTAAATA
18262 AAATTCATGATTTATATATTAAAATATTAATTGTGAGTTATTATAAAATATATTTTTTATTTGTA
391 AAATTCATGATTTATATATTAAAATATTAATTGTGAGTTATTATAAAATATATTTTTTATTTGTA
18327 TTTTT
456 TTTTT
18332 TATATTTTTATTATAGTTTAAATTTATATAATTCATATGTAATAATAATTTCTTTTGAATTTATT
1 TATATTTTTATTATAGTTTAAATTTATATAATTCATATGTAATAATAATTTCTTTTGAATTTATT
18397 TATAATATATATATATATATATTTAAATTATTAAATGGATAAATATATCATTTAAATTATATTAT
66 TATAATATATATATATATATATTTAAATTATTAAATGGATAAATATATCATTTAAATTATATTAT
18462 TTTAAATTTTAAATGAGTAATTGTAGTTGAATTGAAATAATTAAACACTCCATCTGTTATG-AAT
131 TTTAAATTTTAAATGAGTAATTGTAGTTGAATTGAAATAATTAAACACTCCATCTGTTATGAAAT
18526 GGAATTAATGAGAGATACCATATCTTCTAGTTTAATAAATTCAGTTTAATTTATAAGCACTAATG
196 GGAATTAATGAGAGATACCATATCTTCTAGTTTAATAAATTCAGTTTAATTTATAAGCACTAATG
18591 TG-TTTTTTAATATTCTTTTTGTCGAAACAAATATTTAAATTATTATTTTGTAATAATATTATAT
261 TGTTTTTTTAATATTCTTTTTGTCGAAACAAATATTTAAATTATTATTTTGTAATAATATTATAT
18655 CTACATGTTAAAAAATATTGATAATATATTTTTTTGTAATTTATTTTAATTACTTAAAAGTAAAT
326 CTACATGTTAAAAAATATTGATAATATATTTTTTT-TAATTTATTTTAATTACTTAAAAGTAAAT
18720 AAAATTCATGATTTATATATTAAAATATTAATTGTGAGTTATTATAAAATATATTTTTTATTTGT
390 AAAATTCATGATTTATATATTAAAATATTAATTGTGAGTTATTATAAAATATATTTTTTATTTGT
*
18785 TTTTTT
455 ATTTTT
18791 TATATTTTTATTATAGTTTAAATTTATATAATTCATATGTAATAATAATTTCTTTTGAATTTATA
1 TATATTTTTATTATAGTTTAAATTTATATAATTCATATGTAATAATAATTTCTTTTGAATTTAT-
*
18856 TATAATATATATATATATATTTATTTATTTATTTAAATTATTAAAAGGATAAATATATCATTTAA
65 T-T-ATA-ATATATATATA--TA--TA--TATTTAAATTATTAAATGGATAAATATATCATTTAA
18921 ATTATATTATTTTAAATTTTAAATGAGTAATTGTAGTTGAATTGAAATAATTAAACACTCCATCT
121 ATTATATTATTTTAAATTTTAAATGAGTAATTGTAGTTGAATTGAAATAATTAAACACTCCATCT
18986 GTTATGAAATGGAATTAATGAGAGATACCATATCTTCTAGTTTAATAAATTCAGTTTAATTTATA
186 GTTATGAAATGGAATTAATGAGAGATACCATATCTTCTAGTTTAATAAATTCAGTTTAATTTATA
19051 AGCACTAATGTGTTTTTTTAATATTCTTTTTGTCGAAACAAATATTTAAATTATTATTTTGTAAT
251 AGCACTAATGTGTTTTTTTAATATTCTTTTTGTCGAAACAAATATTTAAATTATTATTTTGTAAT
19116 AATATTATATCTACATGTTAAAAAATATTGATAATATATTTTTTT
316 AATATTATATCTACATGTTAAAAAATATTGATAATATATTTTTTT
19161 AATAAAATAT
Statistics
Matches: 811, Mismatches: 5, Indels: 15
0.98 0.01 0.02
Matches are distributed among these distances:
458 95 0.12
459 232 0.29
460 192 0.24
461 1 0.00
462 3 0.00
463 11 0.01
465 2 0.00
467 2 0.00
469 106 0.13
470 70 0.09
471 97 0.12
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (460 bp):
TATATTTTTATTATAGTTTAAATTTATATAATTCATATGTAATAATAATTTCTTTTGAATTTATT
TATAATATATATATATATATATTTAAATTATTAAATGGATAAATATATCATTTAAATTATATTAT
TTTAAATTTTAAATGAGTAATTGTAGTTGAATTGAAATAATTAAACACTCCATCTGTTATGAAAT
GGAATTAATGAGAGATACCATATCTTCTAGTTTAATAAATTCAGTTTAATTTATAAGCACTAATG
TGTTTTTTTAATATTCTTTTTGTCGAAACAAATATTTAAATTATTATTTTGTAATAATATTATAT
CTACATGTTAAAAAATATTGATAATATATTTTTTTTAATTTATTTTAATTACTTAAAAGTAAATA
AAATTCATGATTTATATATTAAAATATTAATTGTGAGTTATTATAAAATATATTTTTTATTTGTA
TTTTT
Found at i:27516 original size:10 final size:10
Alignment explanation
Indices: 27496--27564 Score: 54
Period size: 10 Copynumber: 7.1 Consensus size: 10
27486 TAAGAGCTAA
27496 AAAAAAGAAAG
1 AAAAAA-AAAG
27507 AAAAAAAAAG
1 AAAAAAAAAG
*
27517 AAGAAAAAAG
1 AAAAAAAAAG
** *
27527 -AAGGAAAAT
1 AAAAAAAAAG
* *
27536 TACAAAAAAG
1 AAAAAAAAAG
27546 --AAAAAAAG
1 AAAAAAAAAG
27554 AAAAAAAAAG
1 AAAAAAAAAG
27564 A
1 A
27565 TGAGAGATAC
Statistics
Matches: 45, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
8 7 0.16
9 5 0.11
10 27 0.60
11 6 0.13
ACGTcount: A:0.81, C:0.01, G:0.14, T:0.03
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:28424 original size:31 final size:30
Alignment explanation
Indices: 28389--28453 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
28379 AAATGGATTT
* *
28389 AGTTTAATGACCAAATTATAAGAATTTGTAA
1 AGTTTAATGACCAAAGTATAA-AATTTGAAA
** *
28420 AGTTTGGTGACCAAAGTATAAACTTTGAAA
1 AGTTTAATGACCAAAGTATAAAATTTGAAA
28450 AGTT
1 AGTT
28454 CAGGGATCAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 11 0.38
31 18 0.62
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.34
Consensus pattern (30 bp):
AGTTTAATGACCAAAGTATAAAATTTGAAA
Found at i:29705 original size:20 final size:20
Alignment explanation
Indices: 29680--29727 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
29670 TATGAAATTG
29680 TGATTTGTACAGATCGTGGT
1 TGATTTGTACAGATCGTGGT
29700 TGATTTGTACAGATCGTGGT
1 TGATTTGTACAGATCGTGGT
29720 TGATTTGT
1 TGATTTGT
29728 GACTAAGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.19, C:0.08, G:0.29, T:0.44
Consensus pattern (20 bp):
TGATTTGTACAGATCGTGGT
Found at i:30721 original size:30 final size:30
Alignment explanation
Indices: 30685--30775 Score: 130
Period size: 30 Copynumber: 3.0 Consensus size: 30
30675 TTGAGTTCTA
30685 AGTAATGTTCATGGGCTTATAAAAGATATC
1 AGTAATGTTCATGGGCTTATAAAAGATATC
*
30715 AGTAATGTTCGTGGGCTTATAAAAGATATC
1 AGTAATGTTCATGGGCTTATAAAAGATATC
* * *
30745 AGT-ATCGTACATGGGCCTACAAAAGATATC
1 AGTAAT-GTTCATGGGCTTATAAAAGATATC
30775 A
1 A
30776 AAAGTATACA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
29 2 0.04
30 53 0.96
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (30 bp):
AGTAATGTTCATGGGCTTATAAAAGATATC
Found at i:30976 original size:6 final size:6
Alignment explanation
Indices: 30965--31035 Score: 56
Period size: 6 Copynumber: 11.8 Consensus size: 6
30955 AAATGGGTTC
* * * *
30965 ATGATA ATGATA GA-GATC ATGATA ATGATA TTGATG TTGATA ATGATA
1 ATGATA ATGATA -ATGATA ATGATA ATGATA ATGATA ATGATA ATGATA
* *
31013 GA-GATC ATGATA ATGATA TTGAT
1 -ATGATA ATGATA ATGATA ATGAT
31036 GTTGAGAATG
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
5 2 0.04
6 48 0.92
7 2 0.04
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.35
Consensus pattern (6 bp):
ATGATA
Found at i:30986 original size:18 final size:18
Alignment explanation
Indices: 30963--31057 Score: 109
Period size: 18 Copynumber: 5.3 Consensus size: 18
30953 TTAAATGGGT
30963 TCATGATAATGATAGAGA
1 TCATGATAATGATAGAGA
**
30981 TCATGATAATGATATTGA
1 TCATGATAATGATAGAGA
**
30999 TGTTGATAATGATAGAGA
1 TCATGATAATGATAGAGA
**
31017 TCATGATAATGATATTGA
1 TCATGATAATGATAGAGA
** *
31035 TGTTGAGAATGATAGAGA
1 TCATGATAATGATAGAGA
31053 TCATG
1 TCATG
31058 TTAACGATAT
Statistics
Matches: 60, Mismatches: 17, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 60 1.00
ACGTcount: A:0.39, C:0.04, G:0.23, T:0.34
Consensus pattern (18 bp):
TCATGATAATGATAGAGA
Found at i:31013 original size:36 final size:36
Alignment explanation
Indices: 30966--31082 Score: 207
Period size: 36 Copynumber: 3.2 Consensus size: 36
30956 AATGGGTTCA
30966 TGATAATGATAGAGATCATGATAATGATATTGATGT
1 TGATAATGATAGAGATCATGATAATGATATTGATGT
31002 TGATAATGATAGAGATCATGATAATGATATTGATGT
1 TGATAATGATAGAGATCATGATAATGATATTGATGT
* * *
31038 TGAGAATGATAGAGATCATGTTAACGATATTGATGT
1 TGATAATGATAGAGATCATGATAATGATATTGATGT
31074 TGATAATGA
1 TGATAATGA
31083 AGGTATTTAT
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 77 1.00
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.35
Consensus pattern (36 bp):
TGATAATGATAGAGATCATGATAATGATATTGATGT
Found at i:33930 original size:157 final size:157
Alignment explanation
Indices: 33352--33905 Score: 686
Period size: 157 Copynumber: 3.5 Consensus size: 157
33342 CCTAATTTCA
* * * * * **
33352 TTATTTCTTCAATTCCTCCTTCATTTTAAATCCA-TTTTTATGAAATTTGAACCACATGCTCCTA
1 TTATTTCTTCAATTCATCATTTATTTTGAAT-TATTTTTTACCAAATTTGAACCACATGCTCCTA
*
33416 AACCATAGTAGAATACATGTTTACTTTCAATTCCTCTTTTTGATAAC-AAGTTTTTATTTTTCAA
65 AACCATAGTAGAATACATGTTTACTTTCAATTCCTCTTTTTGATAACAAAATTTTTATTTTTCAA
*
33480 TTTAGTCCTTCAATTTTTCACAATCTCC
130 TTTAGTCCTTCAATTTTTCATAATCTCC
* * * **
33508 TTATTTCTTCAATTCACCATTTATTTTAAGTATGTTTTTTTTTACCAAATTTGAGTCACATGCTC
1 TTATTTCTTCAATTCATCATTTATTTT--G-A-ATTATTTTTTACCAAATTTGAACCACATGCTC
* *
33573 CTAAACCATAGTAGAATACATGTGTGCTTTCAATTCCTCTTTTTGATAACAAAATTTTTATTTTT
62 CTAAACCATAGTAGAATACATGTTTACTTTCAATTCCTCTTTTTGATAACAAAATTTTTATTTTT
*
33638 CAATTTAGTCCTTCAATTTTTCATAATCTTC
127 CAATTTAGTCCTTCAATTTTTCATAATCTCC
* * * **
33669 TTATTTCTTCAATTCATCATTTATTTT-AAGTTAGTTTTCACCAACTTTGAGGCACATGCTCCTA
1 TTATTTCTTCAATTCATCATTTATTTTGAA-TTATTTTTTACCAAATTTGAACCACATGCTCCTA
* * * *
33733 AACCTTAGTAGAATACATGTTTAC-TACAAATTCATCTTTTTGATAACAAATTTTTTATTTTTCA
65 AACCATAGTAGAATACATGTTTACTTTC-AATTCCTCTTTTTGATAACAAAATTTTTATTTTTCA
33797 ATTTAGT-CTTCAATTTTTCATAATCTCC
129 ATTTAGTCCTTCAATTTTTCATAATCTCC
* * * * * *
33825 TTATTACTTCAATTTATGATTTATTTTGAATCTATTTTTTACAAAATTCGAACCACATGCTCATA
1 TTATTTCTTCAATTCATCATTTATTTTGAAT-TATTTTTTACCAAATTTGAACCACATGCTCCTA
* * *
33890 TACCATAATTGAATAC
65 AACCATAGTAGAATAC
33906 CTATGTAACT
Statistics
Matches: 342, Mismatches: 46, Indels: 19
0.84 0.11 0.05
Matches are distributed among these distances:
156 70 0.20
157 131 0.38
159 1 0.00
160 72 0.21
161 68 0.20
ACGTcount: A:0.29, C:0.18, G:0.07, T:0.46
Consensus pattern (157 bp):
TTATTTCTTCAATTCATCATTTATTTTGAATTATTTTTTACCAAATTTGAACCACATGCTCCTAA
ACCATAGTAGAATACATGTTTACTTTCAATTCCTCTTTTTGATAACAAAATTTTTATTTTTCAAT
TTAGTCCTTCAATTTTTCATAATCTCC
Found at i:34740 original size:23 final size:23
Alignment explanation
Indices: 34714--34764 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
34704 GTTTGCGAAT
*
34714 ATGTTCATTTA-ACGTTCGTCAAC
1 ATGTTCATTTATACATTCGTC-AC
* *
34737 ATGTTCGTTTATATATTCGTCAC
1 ATGTTCATTTATACATTCGTCAC
34760 ATGTT
1 ATGTT
34765 TTAACGACCG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.24, C:0.18, G:0.14, T:0.45
Consensus pattern (23 bp):
ATGTTCATTTATACATTCGTCAC
Found at i:36345 original size:28 final size:28
Alignment explanation
Indices: 36314--36370 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
36304 AAGATTTCAA
36314 TGCCATCTTTCCTTTTAGATTTAGTCTT
1 TGCCATCTTTCCTTTTAGATTTAGTCTT
36342 TGCCATCTTTCCTTTTAGATTTAGTCTT
1 TGCCATCTTTCCTTTTAGATTTAGTCTT
36370 T
1 T
36371 CTTTTTTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.14, C:0.21, G:0.11, T:0.54
Consensus pattern (28 bp):
TGCCATCTTTCCTTTTAGATTTAGTCTT
Found at i:37223 original size:2 final size:2
Alignment explanation
Indices: 37216--37246 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
37206 TTAAACCATA
*
37216 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
37247 AACTACTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:38166 original size:43 final size:43
Alignment explanation
Indices: 38109--38195 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 43
38099 AACCTTTATA
*
38109 TAACATTATTGAAATATTCCATAATCAAAATTAAATCATACTT
1 TAACATTATGGAAATATTCCATAATCAAAATTAAATCATACTT
* *
38152 TAACTTTATGGAAATATTCGATAATCAAAATTAAATCATACTT
1 TAACATTATGGAAATATTCCATAATCAAAATTAAATCATACTT
38195 T
1 T
38196 GAATATAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.38
Consensus pattern (43 bp):
TAACATTATGGAAATATTCCATAATCAAAATTAAATCATACTT
Found at i:39988 original size:8 final size:8
Alignment explanation
Indices: 39977--40005 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
39967 TATGGGGGAG
39977 GTAGGGTA
1 GTAGGGTA
39985 GTAGGGTA
1 GTAGGGTA
39993 GTAGGGTA
1 GTAGGGTA
40001 GTAGG
1 GTAGG
40006 ATGCCCCCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.52, T:0.24
Consensus pattern (8 bp):
GTAGGGTA
Found at i:42858 original size:35 final size:35
Alignment explanation
Indices: 42818--42888 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
42808 TTACAAACGT
42818 TATTTATTTAGTGCCCAGACTATCAATTATGTTAA
1 TATTTATTTAGTGCCCAGACTATCAATTATGTTAA
42853 TATTTATTTAGTGCCCAGACTATCAATTATGTTAA
1 TATTTATTTAGTGCCCAGACTATCAATTATGTTAA
42888 T
1 T
42889 TTCTTCTGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.44
Consensus pattern (35 bp):
TATTTATTTAGTGCCCAGACTATCAATTATGTTAA
Found at i:44385 original size:23 final size:23
Alignment explanation
Indices: 44330--44426 Score: 77
Period size: 23 Copynumber: 4.1 Consensus size: 23
44320 TTTAAATGAA
* * *
44330 AAACGAACACAAATGAACGAACAT
1 AAACTAACAC-AATAAATGAACAT
* * *
44354 AAGCAAACACTATAAATGAACAT
1 AAACTAACACAATAAATGAACAT
* * * *
44377 AAACTAACACAAATGAACGAGCGT
1 AAACTAACAC-AATAAATGAACAT
*
44401 AAACGAACACAATAAATGAACAT
1 AAACTAACACAATAAATGAACAT
44424 AAA
1 AAA
44427 TAGCACTAGA
Statistics
Matches: 55, Mismatches: 17, Indels: 3
0.73 0.23 0.04
Matches are distributed among these distances:
23 30 0.55
24 25 0.45
ACGTcount: A:0.58, C:0.19, G:0.11, T:0.12
Consensus pattern (23 bp):
AAACTAACACAATAAATGAACAT
Found at i:44389 original size:47 final size:47
Alignment explanation
Indices: 44330--44426 Score: 140
Period size: 47 Copynumber: 2.1 Consensus size: 47
44320 TTTAAATGAA
* *
44330 AAACGAACACAAATGAACGAACATAAGCAAACACTATAAATGAACAT
1 AAACGAACACAAATGAACGAACATAAACAAACACAATAAATGAACAT
* * * *
44377 AAACTAACACAAATGAACGAGCGTAAACGAACACAATAAATGAACAT
1 AAACGAACACAAATGAACGAACATAAACAAACACAATAAATGAACAT
44424 AAA
1 AAA
44427 TAGCACTAGA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.58, C:0.19, G:0.11, T:0.12
Consensus pattern (47 bp):
AAACGAACACAAATGAACGAACATAAACAAACACAATAAATGAACAT
Found at i:44692 original size:24 final size:24
Alignment explanation
Indices: 44660--44751 Score: 88
Period size: 24 Copynumber: 4.0 Consensus size: 24
44650 AGATTAGGCT
*
44660 AAACATAAATGAACGAACATAAAC
1 AAACATAAATAAACGAACATAAAC
*
44684 AAACATAAACAAACGAA-AGTAAAC
1 AAACATAAATAAACGAACA-TAAAC
*
44708 GAAC----ATAAACGAACATAAAC
1 AAACATAAATAAACGAACATAAAC
*
44728 AAACGA-AAGTAAACGAACATAAAC
1 AAAC-ATAAATAAACGAACATAAAC
44752 GAACCAACAT
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
20 16 0.29
21 1 0.02
23 1 0.02
24 38 0.68
ACGTcount: A:0.63, C:0.17, G:0.10, T:0.10
Consensus pattern (24 bp):
AAACATAAATAAACGAACATAAAC
Found at i:44741 original size:10 final size:10
Alignment explanation
Indices: 44671--44755 Score: 71
Period size: 10 Copynumber: 7.7 Consensus size: 10
44661 AACATAAATG
44671 AACGAACATA
1 AACGAACATA
*
44681 AACAAACATA
1 AACGAACATA
*
44691 AACAAACGAAAGTA
1 AACGAAC---A-TA
44705 AACGAACATA
1 AACGAACATA
44715 AACGAACATA
1 AACGAACATA
*
44725 AACAAACGAAAGTA
1 AACGAAC---A-TA
44739 AACGAACATA
1 AACGAACATA
44749 AACGAAC
1 AACGAAC
44756 CAACATATTA
Statistics
Matches: 63, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
10 43 0.68
11 2 0.03
13 2 0.03
14 16 0.25
ACGTcount: A:0.62, C:0.19, G:0.11, T:0.08
Consensus pattern (10 bp):
AACGAACATA
Found at i:44752 original size:34 final size:34
Alignment explanation
Indices: 44671--44755 Score: 161
Period size: 34 Copynumber: 2.5 Consensus size: 34
44661 AACATAAATG
*
44671 AACGAACATAAACAAACATAAACAAACGAAAGTA
1 AACGAACATAAACGAACATAAACAAACGAAAGTA
44705 AACGAACATAAACGAACATAAACAAACGAAAGTA
1 AACGAACATAAACGAACATAAACAAACGAAAGTA
44739 AACGAACATAAACGAAC
1 AACGAACATAAACGAAC
44756 CAACATATTA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.62, C:0.19, G:0.11, T:0.08
Consensus pattern (34 bp):
AACGAACATAAACGAACATAAACAAACGAAAGTA
Found at i:51490 original size:31 final size:31
Alignment explanation
Indices: 51454--51513 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
51444 AACTTAAAAG
* *
51454 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
51485 AGTTTTACAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
51514 CATACAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:52024 original size:20 final size:20
Alignment explanation
Indices: 51976--52037 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 20
51966 AACTTAAATC
*
51976 AAAATAATTAAAATAA-ATAT
1 AAAATAATT-TAATAATATAT
51996 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAATATAT
52014 AAAATAATTT-AT-ATGATAT
1 AAAATAATTTAATAAT-ATAT
52033 AAAAT
1 AAAAT
52038 TAAATATCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 5 0.14
18 13 0.35
19 11 0.30
20 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAATAATTTAATAATATAT
Found at i:62842 original size:37 final size:37
Alignment explanation
Indices: 62799--62871 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
62789 GCCAACTTTA
62799 TCACTTAGTTTATTGCTCTCACTGTTGTTTCAACTTC
1 TCACTTAGTTTATTGCTCTCACTGTTGTTTCAACTTC
*
62836 TCACTTAGTTTATTGCTCTCGCTGTTGTTTCAACTT
1 TCACTTAGTTTATTGCTCTCACTGTTGTTTCAACTT
62872 TATTCATGTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.15, C:0.23, G:0.12, T:0.49
Consensus pattern (37 bp):
TCACTTAGTTTATTGCTCTCACTGTTGTTTCAACTTC
Found at i:62855 original size:18 final size:18
Alignment explanation
Indices: 62799--62855 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 18
62789 GCCAACTTTA
62799 TCACTTAGTTTATTGCTC
1 TCACTTAGTTTATTGCTC
* *
62817 TCACTGTTGTTTCA--ACTTC
1 TCACT-TAGTTT-ATTGC-TC
62836 TCACTTAGTTTATTGCTC
1 TCACTTAGTTTATTGCTC
62854 TC
1 TC
62856 GCTGTTGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
17 1 0.03
18 15 0.50
19 13 0.43
20 1 0.03
ACGTcount: A:0.16, C:0.25, G:0.11, T:0.49
Consensus pattern (18 bp):
TCACTTAGTTTATTGCTC
Found at i:64507 original size:26 final size:26
Alignment explanation
Indices: 64478--64528 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
64468 ATTTTTTAAT
64478 GAAAAATAATGAGTTTAAAACATAAC
1 GAAAAATAATGAGTTTAAAACATAAC
64504 GAAAAATAATGAGTTTAAAACATAA
1 GAAAAATAATGAGTTTAAAACATAA
64529 TGAATATTCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.59, C:0.06, G:0.12, T:0.24
Consensus pattern (26 bp):
GAAAAATAATGAGTTTAAAACATAAC
Found at i:69870 original size:31 final size:31
Alignment explanation
Indices: 69835--69909 Score: 116
Period size: 31 Copynumber: 2.4 Consensus size: 31
69825 TCAAAAAACA
69835 TAAGATATAGTCACTTTCATTTTTATTTAAT
1 TAAGATATAGTCACTTTCATTTTTATTTAAT
*
69866 TAAGATAT-GATCATTTTCATTTTTATTTAAT
1 TAAGATATAG-TCACTTTCATTTTTATTTAAT
*
69897 TAAGATGTAGTCA
1 TAAGATATAGTCA
69910 TCATAGGTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
30 1 0.03
31 38 0.95
32 1 0.03
ACGTcount: A:0.33, C:0.08, G:0.09, T:0.49
Consensus pattern (31 bp):
TAAGATATAGTCACTTTCATTTTTATTTAAT
Found at i:70060 original size:27 final size:27
Alignment explanation
Indices: 70030--70092 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
70020 AAATTTTAAC
*
70030 ATAAAATATTTTTAAATGAAAATAAAA
1 ATAAAATATTTTAAAATGAAAATAAAA
* * ** *
70057 ATAAAAGATTTTAAAATTAAGTTAATA
1 ATAAAATATTTTAAAATGAAAATAAAA
70084 ATAAAATAT
1 ATAAAATAT
70093 ATTCAATAAG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (27 bp):
ATAAAATATTTTAAAATGAAAATAAAA
Found at i:73570 original size:29 final size:29
Alignment explanation
Indices: 73528--73637 Score: 114
Period size: 29 Copynumber: 3.8 Consensus size: 29
73518 TCCTGGATGG
*
73528 AGATATAATCTCATGCAGAATCAACACGA
1 AGATATAATCTCATGCAGAATCAAGACGA
* **
73557 AGATATAATCTCATGCATAATCAAGGTGA
1 AGATATAATCTCATGCAGAATCAAGACGA
* *
73586 GGATATAATCTCATGCA-ATATCAGGACGA
1 AGATATAATCTCATGCAGA-ATCAAGACGA
* * * *
73615 GGTTATAATCTCGTGTAGAATCA
1 AGATATAATCTCATGCAGAATCA
73638 TAAATGCATC
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
28 1 0.01
29 66 0.97
30 1 0.01
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.26
Consensus pattern (29 bp):
AGATATAATCTCATGCAGAATCAAGACGA
Found at i:74234 original size:13 final size:13
Alignment explanation
Indices: 74216--74240 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
74206 GAATAAAAGA
74216 GTCAAAGTCAATG
1 GTCAAAGTCAATG
74229 GTCAAAGTCAAT
1 GTCAAAGTCAAT
74241 ATTTAACGGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (13 bp):
GTCAAAGTCAATG
Found at i:76270 original size:19 final size:19
Alignment explanation
Indices: 76246--76282 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
76236 TTTAAAATAA
76246 TTTAATAAT-TTATTATTAC
1 TTTAATAATATT-TTATTAC
76265 TTTAATAATATTTTATTA
1 TTTAATAATATTTTATTA
76283 TTAATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTAATAATATTTTATTAC
Found at i:77073 original size:22 final size:23
Alignment explanation
Indices: 77039--77089 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
77029 CAACGGACAA
77039 CAAAGAAAGGTAACCGCTTCAGAG
1 CAAA-AAAGGTAACCGCTTCAGAG
* *
77063 CAAAAAA-GTAACTGCTTTAGAG
1 CAAAAAAGGTAACCGCTTCAGAG
77085 CAAAA
1 CAAAA
77090 GGCTTGTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 18 0.72
23 3 0.12
24 4 0.16
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.16
Consensus pattern (23 bp):
CAAAAAAGGTAACCGCTTCAGAG
Found at i:78853 original size:18 final size:18
Alignment explanation
Indices: 78830--78869 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
78820 TGCCGGTTTC
* *
78830 GGCGACATGTCTATGCCG
1 GGCGACATGGCCATGCCG
78848 GGCGACATGGCCATGCCG
1 GGCGACATGGCCATGCCG
78866 GGCG
1 GGCG
78870 TGTGGTCGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.15, C:0.30, G:0.40, T:0.15
Consensus pattern (18 bp):
GGCGACATGGCCATGCCG
Found at i:79285 original size:60 final size:60
Alignment explanation
Indices: 79173--79286 Score: 133
Period size: 60 Copynumber: 1.9 Consensus size: 60
79163 ATTTGGTCCT
* ** * * *
79173 TAAACTTTTAATGATTCTGATTTCATTCTTAAACTATAACTTTTATTTTAAATTATTCTC
1 TAAACTTTTAATGATTCTAATTTCATTCTTAAACTATAACCCTCACTCTAAATTATTCTC
*
79233 TAAACTTTTAGAT-ATTCTAATTTCA-TCTATAAATTATAACCCTCACTCTAAATT
1 TAAACTTTTA-ATGATTCTAATTTCATTCT-TAAACTATAACCCTCACTCTAAATT
79287 GATCTATACA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
59 3 0.07
60 40 0.89
61 2 0.04
ACGTcount: A:0.34, C:0.16, G:0.03, T:0.47
Consensus pattern (60 bp):
TAAACTTTTAATGATTCTAATTTCATTCTTAAACTATAACCCTCACTCTAAATTATTCTC
Found at i:83181 original size:13 final size:13
Alignment explanation
Indices: 83155--83198 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
83145 CATAATTATT
*
83155 TAAAAA-ATTAAA
1 TAAAAATATTTAA
83167 TAAAAATATTTAA
1 TAAAAATATTTAA
83180 TAAAAATATTTAA
1 TAAAAATATTTAA
83193 TAAAAA
1 TAAAAA
83199 AATAATTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
12 6 0.20
13 24 0.80
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TAAAAATATTTAA
Found at i:89290 original size:22 final size:22
Alignment explanation
Indices: 89255--89297 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
89245 CATAATTATT
89255 TAAAAAATTAAATAAA-AATAC
1 TAAAAAATTAAATAAACAATAC
*
89276 TAAAAATATTTAATAAACAATA
1 TAAAAA-ATTAAATAAACAATA
89298 ATTTTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 9 0.47
23 4 0.21
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (22 bp):
TAAAAAATTAAATAAACAATAC
Found at i:89721 original size:24 final size:25
Alignment explanation
Indices: 89689--89735 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
89679 CTATTCTTTC
89689 ACTTCAATCAAGC-TCGAATTTTAG
1 ACTTCAATCAAGCTTCGAATTTTAG
* *
89713 ACTTCAATCGAGCTTCTAATTTT
1 ACTTCAATCAAGCTTCGAATTTT
89736 TTTTGAGTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (25 bp):
ACTTCAATCAAGCTTCGAATTTTAG
Found at i:90985 original size:2 final size:2
Alignment explanation
Indices: 90978--91022 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
90968 AATTCTAAGC
90978 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
91020 AT A
1 AT A
91023 ATTTAATGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:94168 original size:103 final size:103
Alignment explanation
Indices: 93839--94160 Score: 563
Period size: 103 Copynumber: 3.1 Consensus size: 103
93829 AGTCGAGGGT
*
93839 ATATGTGGTCCTTCGGGACATATATGTATTCTTTGGAATATGTGTGAAGTCTGGTGAGACACATA
1 ATATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA
* *
93904 CTTGATCATTGGCATATGTATATGATTCTTAAGGAATG
66 CTTGATCCTTAGCATATGTATATGATTCTTAAGGAATG
93942 ATATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA
1 ATATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA
94007 CTTGATCCTTAGCATATGTATATGATTCTTAAGGAATG
66 CTTGATCCTTAGCATATGTATATGATTCTTAAGGAATG
* *
94045 ATATGTGGCCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTTTGGTGAGACACATA
1 ATATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA
* * * *
94110 CTTGATCCCTAGTATATGTATATGAATCTTGAGGAATG
66 CTTGATCCTTAGCATATGTATATGATTCTTAAGGAATG
94148 ATATGTGGTCCTT
1 ATATGTGGTCCTT
94161 ATGGACATTA
Statistics
Matches: 209, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 209 1.00
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.36
Consensus pattern (103 bp):
ATATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA
CTTGATCCTTAGCATATGTATATGATTCTTAAGGAATG
Found at i:94210 original size:23 final size:23
Alignment explanation
Indices: 94177--94234 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
94167 ATTATTATAT
94177 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* * *
94200 GGCACTGCGGTGCAATTCTATGT
1 GGCACTACGGTGCAATTCTACGC
*
94223 GGCACTTCGGTG
1 GGCACTACGGTG
94235 TATTTATATG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.17, C:0.26, G:0.31, T:0.26
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:94244 original size:23 final size:23
Alignment explanation
Indices: 94167--94244 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 23
94157 CCTTATGGAC
* *
94167 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTGCGGTGCA
* * *
94191 ATTCTACGCGGCACTGCGGTGCA
1 ATTATATGTGGCACTGCGGTGCA
* * *
94214 ATTCTATGTGGCACTTCGGTGTA
1 ATTATATGTGGCACTGCGGTGCA
*
94237 TTTATATG
1 ATTATATG
94245 AGCTGTGGTG
Statistics
Matches: 43, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
23 40 0.93
24 3 0.07
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (23 bp):
ATTATATGTGGCACTGCGGTGCA
Found at i:97465 original size:21 final size:21
Alignment explanation
Indices: 97439--97482 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
97429 ATTTATGGGA
* *
97439 AAGGGGAATCGGTACCCATTC
1 AAGGGGAACCGATACCCATTC
*
97460 AAGGGGAACCGATACCCCTTC
1 AAGGGGAACCGATACCCATTC
97481 AA
1 AA
97483 ACGAACAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.27, G:0.25, T:0.16
Consensus pattern (21 bp):
AAGGGGAACCGATACCCATTC
Found at i:99197 original size:103 final size:103
Alignment explanation
Indices: 99018--99339 Score: 581
Period size: 103 Copynumber: 3.1 Consensus size: 103
99008 AGTCGAGGGT
*
99018 ATATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA
1 ATATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA
* *
99083 CTTAACCCTTGGCATATGTATATGATTCTTAAGGAATG
66 CTTGATCCTTGGCATATGTATATGATTCTTAAGGAATG
*
99121 ATATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA
1 ATATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA
99186 CTTGATCCTTGGCATATGTATATGATTCTTAAGGAATG
66 CTTGATCCTTGGCATATGTATATGATTCTTAAGGAATG
*
99224 ATATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACACA
1 ATATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA
* *
99289 CTTGATCCTTAGTATATGTATATGATTCTTAAGGAATG
66 CTTGATCCTTGGCATATGTATATGATTCTTAAGGAATG
99327 ATATGTGGTCCTT
1 ATATGTGGTCCTT
99340 ATGGACATTA
Statistics
Matches: 211, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 211 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (103 bp):
ATATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA
CTTGATCCTTGGCATATGTATATGATTCTTAAGGAATG
Found at i:99389 original size:23 final size:23
Alignment explanation
Indices: 99356--99412 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
99346 ATTATTATAT
99356 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* * * *
99379 GGCACTGCGGTGTAATTCTATGT
1 GGCACTACGGTGCAATTCTACGC
*
99402 GGCACTTCGGT
1 GGCACTACGGT
99413 TCATTTATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.18, C:0.25, G:0.30, T:0.28
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:102639 original size:20 final size:20
Alignment explanation
Indices: 102614--102656 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
102604 TGATTCTGGG
* *
102614 CAAGGGGAATCGGTACCATT
1 CAAGGGGAACCGATACCATT
*
102634 CAAGGGGAACCGATACCCTT
1 CAAGGGGAACCGATACCATT
102654 CAA
1 CAA
102657 ACGAACAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.26, G:0.26, T:0.16
Consensus pattern (20 bp):
CAAGGGGAACCGATACCATT
Found at i:104361 original size:103 final size:102
Alignment explanation
Indices: 104182--104503 Score: 581
Period size: 103 Copynumber: 3.1 Consensus size: 102
104172 AGTCGAGGGT
*
104182 ATATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA
1 ATATGTGGTCCTTC-GGGCATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA
104247 CTTGATCCTTGGCATATGTATATGATTCTTAAGGAATG
65 CTTGATCCTTGGCATATGTATATGATTCTTAAGGAATG
104285 ATATGTGGTCCTTCGGGCTATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA
1 ATATGTGGTCCTTCGGGC-ATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA
104350 CTTGATCCTTGGCATATGTATATGATTCTTAAGGAATG
65 CTTGATCCTTGGCATATGTATATGATTCTTAAGGAATG
104388 ATATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA
1 ATATGTGGTCCTTCGGG-CATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA
* * *
104453 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATG
65 CTTGATCCTTGGCATATGTATATGATTCTTAAGGAATG
104491 ATATGTGGTCCTT
1 ATATGTGGTCCTT
104504 ATGGACATTA
Statistics
Matches: 213, Mismatches: 4, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
102 3 0.01
103 209 0.98
104 1 0.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.37
Consensus pattern (102 bp):
ATATGTGGTCCTTCGGGCATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATG
Found at i:104579 original size:23 final size:23
Alignment explanation
Indices: 104519--104571 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
104509 CATTATTATA
104519 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* * * *
104542 CGGTACTGCGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTACG
104565 TGGCACT
1 TGGCACT
104572 TCGATGCATT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.19, C:0.25, G:0.28, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:107548 original size:25 final size:24
Alignment explanation
Indices: 107514--107566 Score: 88
Period size: 25 Copynumber: 2.2 Consensus size: 24
107504 TGGAGACATT
*
107514 TATAATGTAAAATGTTATTATAAAA
1 TATAATGTAAAATATTA-TATAAAA
107539 TATAATGTAAAATATTATATAAAA
1 TATAATGTAAAATATTATATAAAA
107563 TATA
1 TATA
107567 TAAAATTATG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 11 0.41
25 16 0.59
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.40
Consensus pattern (24 bp):
TATAATGTAAAATATTATATAAAA
Found at i:107551 original size:12 final size:12
Alignment explanation
Indices: 107532--107566 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
107522 AAAATGTTAT
107532 TATAAAATATAA
1 TATAAAATATAA
* *
107544 TGTAAAATATTA
1 TATAAAATATAA
107556 TATAAAATATA
1 TATAAAATATA
107567 TAAAATTATG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (12 bp):
TATAAAATATAA
Found at i:108733 original size:29 final size:30
Alignment explanation
Indices: 108633--108852 Score: 347
Period size: 30 Copynumber: 7.4 Consensus size: 30
108623 CCCGAAGGAC
108633 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
108663 TTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
108693 CTATCCAGAGGTCATAAAGATCCTC-GTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
108722 CTATCCATAGGTCATAAAGATCCTCGATAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
108752 ATATCCAAAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
108782 CTATCCAGAGGTCAT-AAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
108811 CTATCCAGAGGTC-TAAAAATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
108840 CTGTCCATAGGTC
1 CTATCCAGAGGTC
108853 CCGAAGAACC
Statistics
Matches: 176, Mismatches: 12, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
28 1 0.01
29 79 0.45
30 96 0.55
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:108877 original size:89 final size:89
Alignment explanation
Indices: 108633--108839 Score: 346
Period size: 89 Copynumber: 2.3 Consensus size: 89
108623 CCCGAAGGAC
* *
108633 CTATCCAGAGGTCATAAAGATCCTCGGTAATTATCCAGAGGTCATAAAGATCCTCGGTAACTATC
1 CTATCCAGAGGTCATAAAGATCCTCGGTAAATATCCAAAGGTCATAAAGATCCTCGGTAACTATC
108698 CAGAGGTCATAAAGATCCTCGTAA
66 CAGAGGTCATAAAGATCCTCGTAA
* *
108722 CTATCCATAGGTCATAAAGATCCTCGATAAATATCCAAAGGTCATAAAGATCCTCGGTAACTATC
1 CTATCCAGAGGTCATAAAGATCCTCGGTAAATATCCAAAGGTCATAAAGATCCTCGGTAACTATC
108787 CAGAGGTCAT-AAGATCCTCGGTAA
66 CAGAGGTCATAAAGATCCTC-GTAA
*
108811 CTATCCAGAGGTC-TAAAAATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
108840 CTGTCCATAG
Statistics
Matches: 110, Mismatches: 7, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
88 23 0.21
89 87 0.79
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.25
Consensus pattern (89 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAAATATCCAAAGGTCATAAAGATCCTCGGTAACTATC
CAGAGGTCATAAAGATCCTCGTAA
Done.