Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005667.1 Hibiscus syriacus cultivar Beakdansim tig00013256_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: 107325
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:2662 original size:23 final size:23
Alignment explanation
Indices: 2636--2695 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
2626 AATCTTATAT
2636 GGCACTTCGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
* *
2659 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCAATTCTACGC
*
2682 GGCACTTTGGTGCA
1 GGCACTTCGGTGCA
2696 TTTATGAGCT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.18, C:0.27, G:0.28, T:0.27
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:4090 original size:27 final size:27
Alignment explanation
Indices: 4040--4091 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
4030 ATGAAAAACG
* * *
4040 ACACAAACAAAATAAATAAGTTAGTGT
1 ACACAAACAAAAAAAAGAAATTAGTGT
*
4067 ACACAAGCAAAAAAAAGAAATTAGT
1 ACACAAACAAAAAAAAGAAATTAGT
4092 TAGTACTGGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.60, C:0.12, G:0.12, T:0.17
Consensus pattern (27 bp):
ACACAAACAAAAAAAAGAAATTAGTGT
Found at i:6400 original size:122 final size:123
Alignment explanation
Indices: 6241--6467 Score: 352
Period size: 122 Copynumber: 1.9 Consensus size: 123
6231 TAATTGTTAG
* * *
6241 AAAAATTAAAGGTTAACAGAGTTCGAACCATAATAATGTAGATCATACTCCGGATCAGGTCACCA
1 AAAAATTAAAGGTTAACAGAGTCCGAACCATAATAATGCAGATCATACCCCGGATCAGGTCACCA
*
6306 CAA-AGCCGAATCAAATATTA-AAATAATAAATAAATAAATGTTATAATGCAATAAAAT
66 CAAGA-CCGAATCAAATAATAGAAATAATAAATAAATAAATGTTATAATGCAATAAAAT
* *
6363 AAAAATTAATA-GTTAACAGAGTCCGAACCATAATAATGCGGATCATACCCCGGATCGGGTCACC
1 AAAAATTAA-AGGTTAACAGAGTCCGAACCATAATAATGCAGATCATACCCCGGATCAGGTCACC
*
6427 ACAAGACCGAATCGAATAATAGAAATAATAAATAAATAAAT
65 ACAAGACCGAATCAAATAATAGAAATAATAAATAAATAAAT
6468 AAAGGTTAGA
Statistics
Matches: 95, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
122 74 0.78
123 21 0.22
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.22
Consensus pattern (123 bp):
AAAAATTAAAGGTTAACAGAGTCCGAACCATAATAATGCAGATCATACCCCGGATCAGGTCACCA
CAAGACCGAATCAAATAATAGAAATAATAAATAAATAAATGTTATAATGCAATAAAAT
Found at i:6520 original size:122 final size:122
Alignment explanation
Indices: 6241--6493 Score: 321
Period size: 122 Copynumber: 2.0 Consensus size: 122
6231 TAATTGTTAG
* * * *
6241 AAAAATTAA-AGGTTAACAGAGTTCGAACCATAATAATGTAGATCATACTCCGGATCAGGTCACC
1 AAAAATTAATA-GTTAACAGAGTACGAACCAAAATAATGCAGATCATACCCCGGATCAGGTCACC
* *
6305 ACAAAGCCGAATCAAATATTAAAATAATAAATAAATAAATGTTATAATGCAATAAAAT
65 ACAAAGCCGAATCAAATAATAAAATAATAAATAAATAAATGTTAGAATGCAATAAAAT
* * * *
6363 AAAAATTAATAGTTAACAGAGTCCGAACCATAATAATGCGGATCATACCCCGGATCGGGTCACCA
1 AAAAATTAATAGTTAACAGAGTACGAACCAAAATAATGCAGATCATACCCCGGATCAGGTCACCA
* *
6428 C-AAGACCGAATCGAATAATAGAAATAATAAATAAATAAATAAAGGTTAGAGTGCAATAAAAT
66 CAAAG-CCGAATCAAATAATA-AAATAATAAATAAATAAAT----GTTAGAATGCAATAAAAT
6490 AAAA
1 AAAA
6494 GTTAGTGATT
Statistics
Matches: 115, Mismatches: 9, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
121 3 0.03
122 72 0.63
123 20 0.17
127 20 0.17
ACGTcount: A:0.49, C:0.15, G:0.14, T:0.22
Consensus pattern (122 bp):
AAAAATTAATAGTTAACAGAGTACGAACCAAAATAATGCAGATCATACCCCGGATCAGGTCACCA
CAAAGCCGAATCAAATAATAAAATAATAAATAAATAAATGTTAGAATGCAATAAAAT
Found at i:6543 original size:29 final size:29
Alignment explanation
Indices: 6481--6544 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
6471 GGTTAGAGTG
*
6481 CAATAAAATAAAAGTTAGTGATTAATATA
1 CAATAAAATAAAAGTTAGTGATTAAAATA
*
6510 CAATAAAATAAAATTTAGT-AGTTAGAAATA
1 CAATAAAATAAAAGTTAGTGA-TTA-AAATA
6540 -AATAA
1 CAATAA
6545 CATAGCAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 1 0.03
29 26 0.84
30 4 0.13
ACGTcount: A:0.58, C:0.03, G:0.09, T:0.30
Consensus pattern (29 bp):
CAATAAAATAAAAGTTAGTGATTAAAATA
Found at i:14295 original size:20 final size:21
Alignment explanation
Indices: 14258--14296 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
14248 TTTGAGTAGA
14258 AAAATATCCCCAAACGGCTCC
1 AAAATATCCCCAAACGGCTCC
14279 AAAATATCCCC-AACGGCT
1 AAAATATCCCCAAACGGCT
14297 ATATATGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.38, C:0.36, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATATCCCCAAACGGCTCC
Found at i:20497 original size:14 final size:14
Alignment explanation
Indices: 20478--20524 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 14
20468 CAACGGGTTG
*
20478 ACTCAGACGAGTTA
1 ACTCAGATGAGTTA
*
20492 ACTCAGATGAGTTG
1 ACTCAGATGAGTTA
*
20506 ACTCAGATGGGTTA
1 ACTCAGATGAGTTA
20520 ACTCA
1 ACTCA
20525 TACCGAGTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (14 bp):
ACTCAGATGAGTTA
Found at i:20566 original size:15 final size:15
Alignment explanation
Indices: 20526--20568 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
20516 GTTAACTCAT
*
20526 ACCGAGTTGACTTGG
1 ACCGAGTTGACTCGG
*
20541 ACGGA-TTGACTCGG
1 ACCGAGTTGACTCGG
20555 ACCGAGTTGACTCG
1 ACCGAGTTGACTCG
20569 ATGACTGGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.21, C:0.23, G:0.33, T:0.23
Consensus pattern (15 bp):
ACCGAGTTGACTCGG
Found at i:21140 original size:23 final size:23
Alignment explanation
Indices: 21110--21175 Score: 105
Period size: 23 Copynumber: 2.9 Consensus size: 23
21100 CTGAATGATT
21110 CAGTGCTGACTGATTCAGCAAAA
1 CAGTGCTGACTGATTCAGCAAAA
21133 CAGTGCTGACTGATTCAGCAAAA
1 CAGTGCTGACTGATTCAGCAAAA
* * *
21156 CAATGCTAAATGATTCAGCA
1 CAGTGCTGACTGATTCAGCA
21176 CAGAAGTATA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (23 bp):
CAGTGCTGACTGATTCAGCAAAA
Found at i:29654 original size:13 final size:13
Alignment explanation
Indices: 29636--29662 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
29626 CGTGAGTTCT
29636 GCCGCCGGCCACC
1 GCCGCCGGCCACC
29649 GCCGCCGGCCACC
1 GCCGCCGGCCACC
29662 G
1 G
29663 TCTTCGGTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.59, G:0.33, T:0.00
Consensus pattern (13 bp):
GCCGCCGGCCACC
Found at i:30461 original size:3 final size:3
Alignment explanation
Indices: 30453--30537 Score: 145
Period size: 3 Copynumber: 28.7 Consensus size: 3
30443 TTAATATATT
*
30453 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA AAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
30500 TAA TAA TAA TAA TAA TAT TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
30538 TGGATAAAAA
Statistics
Matches: 77, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
2 2 0.03
3 75 0.97
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:31049 original size:113 final size:113
Alignment explanation
Indices: 30832--31843 Score: 1418
Period size: 113 Copynumber: 8.9 Consensus size: 113
30822 AATATCAAAC
**
30832 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* ** * * * **
30897 CATGAACTTTCTCTGGCAATGTTGATCCATCAAATGATGAATTTAAACA
66 -ATGAACTCTAACTGGAAATGATGATCCATCAAATGATGAATTCAAGTA
* *
30946 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* ** * * **
31011 ATGAACTTTCTCTGGCAATGATGATCCATCAAATGATGAATTTAAACA
66 ATGAACTCTAACTGGAAATGATGATCCATCAAATGATGAATTCAAGTA
* ** *
31059 AAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTTATTCTTCAGATAAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * *
31124 ATGAACTCGACCTGGCAATGCTGATCCAT-AGAATGATGAATTCAAGTGA
66 ATGAACTCTAACTGGAAATGATGATCCATCA-AATGATGAATTCAAGT-A
*
31173 AAA-GTTGAACAAATTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAAATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
31236 ATGAACTCTAACTGGTAATGATGATCCATCAAATGATGAATTTAAGCA
66 ATGAACTCTAACTGGAAATGATGATCCATCAAATGATGAATTCAAGTA
* *
31284 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *** * * *
31349 ATGAACTTTCTTTGGAAATGCTGATCCATCGAATGATGAATTCAGGTA
66 ATGAACTCTAACTGGAAATGATGATCCATCAAATGATGAATTCAAGTA
31397 AAAGGTTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAGG-TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * *
31462 TATGAACTCGAACTGGAAAAGATGATCCACCAAATGATGGATTCAGGTA
65 TATGAACTCTAACTGGAAATGATGATCCATCAAATGATGAATTCAAGTA
31511 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * * *
31576 ATGAACTCGAACTGGAAAAGATGATCCACCAAATGATGGATTCAGGTA
66 ATGAACTCTAACTGGAAATGATGATCCATCAAATGATGAATTCAAGTA
31624 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * * *
31689 ATGAACTCGAACTGGAAAAGATGATCCACCAAATGATGGATTCAGGTA
66 ATGAACTCTAACTGGAAATGATGATCCATCAAATGATGAATTCAAGTA
*
31737 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * * *
31802 ATGAACTCGAACTGGAAAAGCTGATCCTTCAAATGATAAATT
66 ATGAACTCTAACTGGAAATGATGATCCATCAAATGATGAATT
31844 TGAATCTTTG
Statistics
Matches: 838, Mismatches: 54, Indels: 13
0.93 0.06 0.01
Matches are distributed among these distances:
111 4 0.00
112 96 0.11
113 569 0.68
114 169 0.20
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.36
Consensus pattern (113 bp):
AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTCTAACTGGAAATGATGATCCATCAAATGATGAATTCAAGTA
Found at i:32587 original size:83 final size:83
Alignment explanation
Indices: 32486--32952 Score: 812
Period size: 83 Copynumber: 5.6 Consensus size: 83
32476 CTTACCAAAA
* *
32486 CAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
*
32551 TGATTGATTCTGTCCAAC
66 TGATTGGTTCTGTCCAAC
*
32569 CAGATCAGATAACTCAAAGAAAACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
*
32634 TGATTGGTTATG-CCAAAC
66 TGATTGGTTCTGTCC-AAC
* *
32652 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
32717 TGATTGGTTCTGTCCAAC
66 TGATTGGTTCTGTCCAAC
32735 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
32800 TGATTGGTTCTGTCCAAC
66 TGATTGGTTCTGTCCAAC
32818 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
*
32883 TGATTGGTTTTG-CCAAAC
66 TGATTGGTTCTGTCC-AAC
* *
32901 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCAT
32953 TTGTTCCATT
Statistics
Matches: 367, Mismatches: 14, Indels: 6
0.95 0.04 0.02
Matches are distributed among these distances:
82 4 0.01
83 361 0.98
84 2 0.01
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.27
Consensus pattern (83 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAA
TGATTGGTTCTGTCCAAC
Found at i:33698 original size:16 final size:17
Alignment explanation
Indices: 33660--33704 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
33650 AATATAAAAG
*
33660 AATAAATTGAATTTCAAA
1 AATAAATTGAATCTC-AA
33678 AATAAATTGAATCTC-A
1 AATAAATTGAATCTCAA
33694 AATAAATTGAA
1 AATAAATTGAA
33705 CTTGAAATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 12 0.46
18 14 0.54
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.31
Consensus pattern (17 bp):
AATAAATTGAATCTCAA
Found at i:34042 original size:6 final size:6
Alignment explanation
Indices: 34031--34101 Score: 96
Period size: 6 Copynumber: 12.2 Consensus size: 6
34021 ACCTTGACCC
34031 TCTTTT TCTTTT TCTTTT TCTTTT T-TTTT TCTTTT T-TTCTT T-TTTT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT
34077 TCTTTTT TCTTTT T-TTTT TCTTTT T
1 TC-TTTT TCTTTT TCTTTT TCTTTT T
34102 TCAAGCATAA
Statistics
Matches: 60, Mismatches: 0, Indels: 10
0.86 0.00 0.14
Matches are distributed among these distances:
5 15 0.25
6 39 0.65
7 6 0.10
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (6 bp):
TCTTTT
Found at i:34043 original size:1 final size:1
Alignment explanation
Indices: 34033--34102 Score: 68
Period size: 1 Copynumber: 70.0 Consensus size: 1
34023 CTTGACCCTC
* * * * * * * *
34033 TTTTTCTTTTTCTTTTTCTTTTTTTTTTCTTTTTTTCTTTTTTTTCTTTTTTCTTTTTTTTTTCT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
34098 TTTTT
1 TTTTT
34103 CAAGCATAAT
Statistics
Matches: 53, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (1 bp):
T
Found at i:34054 original size:17 final size:17
Alignment explanation
Indices: 34031--34101 Score: 108
Period size: 17 Copynumber: 4.1 Consensus size: 17
34021 ACCTTGACCC
34031 TCTTTTTCTTTTTCTTTT
1 TCTTTTT-TTTTTCTTTT
34049 TCTTTTTTTTTTCTTTT
1 TCTTTTTTTTTTCTTTT
34066 T-TTCTTTTTTTTCTTTTT
1 TCTT-TTTTTTTTC-TTTT
34084 TCTTTTTTTTTTCTTTT
1 TCTTTTTTTTTTCTTTT
34101 T
1 T
34102 TCAAGCATAA
Statistics
Matches: 50, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.04
17 25 0.50
18 21 0.42
19 2 0.04
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (17 bp):
TCTTTTTTTTTTCTTTT
Found at i:34102 original size:18 final size:18
Alignment explanation
Indices: 34031--34103 Score: 114
Period size: 18 Copynumber: 4.1 Consensus size: 18
34021 ACCTTGACCC
34031 TCTTTTTCTTTTTC-TTTT
1 TCTTTTT-TTTTTCTTTTT
34049 TCTTTTTTTTTTCTTTTT
1 TCTTTTTTTTTTCTTTTT
*
34067 T-TCTTTTTTTTCTTTTT
1 TCTTTTTTTTTTCTTTTT
34084 TCTTTTTTTTTTCTTTTT
1 TCTTTTTTTTTTCTTTTT
34102 TC
1 TC
34104 AAGCATAATA
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
17 22 0.43
18 29 0.57
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (18 bp):
TCTTTTTTTTTTCTTTTT
Found at i:44730 original size:13 final size:15
Alignment explanation
Indices: 44708--44744 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
44698 TTGACATAAA
44708 AAAT-AAATAC-TG-
1 AAATAAAATACTTGC
44720 AAATAAAATACTTGC
1 AAATAAAATACTTGC
44735 AAATAAAATA
1 AAATAAAATA
44745 AAACATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.18
13 6 0.27
14 2 0.09
15 10 0.45
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.24
Consensus pattern (15 bp):
AAATAAAATACTTGC
Found at i:44783 original size:18 final size:17
Alignment explanation
Indices: 44735--44785 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
44725 AAATACTTGC
*
44735 AAATAAAATAAAACATAT
1 AAAT-AAATAAAAAATAT
*
44753 AAAT-ATTATAAAAATAAT
1 AAATAAATA-AAAAAT-AT
44771 AAATAAATAAAAAAT
1 AAATAAATAAAAAAT
44786 TTGAAAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
16 3 0.11
17 5 0.19
18 16 0.59
19 3 0.11
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (17 bp):
AAATAAATAAAAAATAT
Found at i:46968 original size:3 final size:3
Alignment explanation
Indices: 46960--47056 Score: 169
Period size: 3 Copynumber: 32.7 Consensus size: 3
46950 TTAATATATT
*
46960 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA AAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
47007 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
47055 TA
1 TA
47057 TGGATAAAAA
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
2 2 0.02
3 87 0.98
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:57570 original size:45 final size:42
Alignment explanation
Indices: 57431--57655 Score: 213
Period size: 41 Copynumber: 5.2 Consensus size: 42
57421 AGAACAAAAC
* * *
57431 ACGCCGCAATAGGTGAAGAGATATAGCGGCGTTTTTTGAACAA
1 ACGCCGCAAAAGGTCAAGATATATAGCGGCG-TTTTTGAACAA
* * * *
57474 ACGCCGCAAAAGGTCGATATCTATAGCGGTGTTTTT-AACAA
1 ACGCCGCAAAAGGTCAAGATATATAGCGGCGTTTTTGAACAA
*
57515 ACACCGCAAAAGGTCAAGATATATAGCGGCGTTTTCTAGATACAA
1 ACGCCGCAAAAGGTCAAGATATATAGCGGCGTTTT-T-GA-ACAA
* * *
57560 ACGCCGCAAAAGATCTAA-ATCTATAGCGGCGTTTTTTAACAA
1 ACGCCGCAAAAGGTC-AAGATATATAGCGGCGTTTTTGAACAA
* * * *
57602 ACGACGTAAAAGGTC-AGGTATATAGCGGTGTTTTTTGGATACAA
1 ACGCCGCAAAAGGTCAAGATATATAGCGGCG-TTTTT-GA-ACAA
*
57646 ACGTCGCAAA
1 ACGCCGCAAA
57656 TATCTAATTT
Statistics
Matches: 148, Mismatches: 25, Indels: 17
0.78 0.13 0.09
Matches are distributed among these distances:
40 1 0.01
41 45 0.30
42 27 0.18
43 26 0.18
44 14 0.09
45 33 0.22
46 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (42 bp):
ACGCCGCAAAAGGTCAAGATATATAGCGGCGTTTTTGAACAA
Found at i:57582 original size:86 final size:87
Alignment explanation
Indices: 57434--57655 Score: 274
Period size: 86 Copynumber: 2.6 Consensus size: 87
57424 ACAAAACACG
* * * * * *
57434 CCGCAATAGGTGAAGAGATATAGCGGCGTTTTTTGA-ACAAACGCCGCAAAAGGTCGATATCTAT
1 CCGCAAAAGGTCAAGATATATAGCGGCGTTTTTAGATACAAACGCCGCAAAAGATCGAAATCTAT
*
57498 AGCGGTG-TTTTTAACAAAC-A
66 AGCGGCGTTTTTTAACAAACGA
*
57518 CCGCAAAAGGTCAAGATATATAGCGGCGTTTTCTAGATACAAACGCCGCAAAAGATCTAAATCTA
1 CCGCAAAAGGTCAAGATATATAGCGGCGTTTT-TAGATACAAACGCCGCAAAAGATCGAAATCTA
57583 TAGCGGCGTTTTTTAACAAACGA
65 TAGCGGCGTTTTTTAACAAACGA
* * * * *
57606 -CGTAAAAGGTC-AGGTATATAGCGGTGTTTTTTGGATACAAACGTCGCAAA
1 CCGCAAAAGGTCAAGATATATAGCGGCG-TTTTTAGATACAAACGCCGCAAA
57656 TATCTAATTT
Statistics
Matches: 120, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
84 29 0.24
85 3 0.03
86 61 0.51
87 26 0.22
88 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (87 bp):
CCGCAAAAGGTCAAGATATATAGCGGCGTTTTTAGATACAAACGCCGCAAAAGATCGAAATCTAT
AGCGGCGTTTTTTAACAAACGA
Found at i:66071 original size:41 final size:41
Alignment explanation
Indices: 65965--66157 Score: 124
Period size: 41 Copynumber: 4.6 Consensus size: 41
65955 GACAATCGCT
* * * *
65965 GCGTTTATAATAAAAACGCCGCTAATGTACATGACTATTGGG
1 GCGTTT-TAAAAAAAACGCCACTAAAGTACATGACTATTGCG
* * *
66007 GCCTTTATTACAAAAAAATGCCACTAAAGTATATGACTATTGCG
1 G-CGTT-TTA-AAAAAAACGCCACTAAAGTACATGACTATTGCG
* * *
66051 GCGTTTTAACAAAAACGCCACTAAAGTACGA-GTCTATAGCG
1 GCGTTTTAAAAAAAACGCCACTAAAGTAC-ATGACTATTGCG
* ** * *
66092 ACGTTTGCATAAAAATGCCACTAAAGTA-A-GAGTCT-TTCGCG
1 GCGTTTTAAAAAAAACGCCACTAAAGTACATGA--CTATT-GCG
* * *
66133 GCGTTTTCATACAAACGCCACTAAA
1 GCGTTTTAAAAAAAACGCCACTAAA
66158 CATTTTGATT
Statistics
Matches: 120, Mismatches: 24, Indels: 15
0.75 0.15 0.09
Matches are distributed among these distances:
39 2 0.02
40 1 0.01
41 75 0.62
42 5 0.04
43 8 0.07
44 29 0.24
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (41 bp):
GCGTTTTAAAAAAAACGCCACTAAAGTACATGACTATTGCG
Found at i:66363 original size:40 final size:40
Alignment explanation
Indices: 66268--66396 Score: 127
Period size: 40 Copynumber: 3.1 Consensus size: 40
66258 CGTTTGTGTT
* * *
66268 TAAAAACACCGCTAAAGTACGAGTCTATAGCGACACTTTTTA
1 TAAAAAAACCACTAAAGTACGAGTATATAGCG--ACTTTTTA
* *
66310 TAAAAAAACCACTAAAGTACGAGTATATATCGACTTTGTA
1 TAAAAAAACCACTAAAGTACGAGTATATAGCGACTTTTTA
* * *
66350 TAAAAATGA-CACTAACA-TATGAGTATATAGCGGCGTTTTTA
1 TAAAAA-AACCACTAA-AGTACGAGTATATAGCGAC-TTTTTA
66391 TAAAAA
1 TAAAAA
66397 CTCCGCTAAG
Statistics
Matches: 74, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
40 33 0.45
41 13 0.18
42 28 0.38
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.28
Consensus pattern (40 bp):
TAAAAAAACCACTAAAGTACGAGTATATAGCGACTTTTTA
Found at i:66471 original size:82 final size:82
Alignment explanation
Indices: 66385--66538 Score: 197
Period size: 82 Copynumber: 1.9 Consensus size: 82
66375 TATAGCGGCG
* * *
66385 TTTTTATAAAAACT-CCGCTAAGGTACA-ACTATGTT-GCGGCGTTTGTTGAAAAATGCCACTAT
1 TTTTTATAAAAA-TGCCGCTAAAGTA-ATACTAT-TTAACGGCGTTTGTTGAAAAACGCCACTAT
66447 AGATGAACCTTATTGCAGCA
63 AGATGAACCTTATTGCAGCA
* * * *
66467 TTTTTATATAAATGCCGCTAAAGTAATACTCTTTAACGGTGTTTGTTGAGAAACGCCACTATAGA
1 TTTTTATAAAAATGCCGCTAAAGTAATACTATTTAACGGCGTTTGTTGAAAAACGCCACTATAGA
66532 TGAACCT
66 TGAACCT
66539 ATTACTTCGT
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
81 4 0.06
82 58 0.94
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Consensus pattern (82 bp):
TTTTTATAAAAATGCCGCTAAAGTAATACTATTTAACGGCGTTTGTTGAAAAACGCCACTATAGA
TGAACCTTATTGCAGCA
Found at i:68216 original size:48 final size:48
Alignment explanation
Indices: 68146--68247 Score: 152
Period size: 48 Copynumber: 2.1 Consensus size: 48
68136 AAATTCAGTA
* *
68146 TTCAG-TAATACTTAAGCTCAACTCGGCTCACTAAGCAAGTGGGATGT
1 TTCAGTTAATACTCAAGCTCAACTCGGCCCACTAAGCAAGTGGGATGT
* * *
68193 TTCAGTTATTACTCAAGCTCAACTCGGCCCACTAGGCATGTGGGATGT
1 TTCAGTTAATACTCAAGCTCAACTCGGCCCACTAAGCAAGTGGGATGT
68241 TTCAGTT
1 TTCAGTT
68248 TTCTAATTTG
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 5 0.10
48 44 0.90
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (48 bp):
TTCAGTTAATACTCAAGCTCAACTCGGCCCACTAAGCAAGTGGGATGT
Found at i:72400 original size:3 final size:3
Alignment explanation
Indices: 72392--72418 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
72382 CTAAATCCCC
72392 CAA CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA
72419 AACCCAATTC
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:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:77135 original size:2 final size:2
Alignment explanation
Indices: 77128--77166 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
77118 GATTTCCTTT
77128 TA 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 TA T
77167 TGTATTCGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:77644 original size:3 final size:3
Alignment explanation
Indices: 77636--77771 Score: 272
Period size: 3 Copynumber: 45.3 Consensus size: 3
77626 TTTGGGTTTG
77636 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
77684 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
77732 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
77772 GTAAGGCGAT
Statistics
Matches: 133, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 133 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:78414 original size:3 final size:3
Alignment explanation
Indices: 78408--78448 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
78398 TTTTAAAATA
*
78408 AAT AAT AAT AAT AAT AAT CAT -AT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
78449 GTAAGGTGGT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:78947 original size:114 final size:115
Alignment explanation
Indices: 78714--78967 Score: 336
Period size: 114 Copynumber: 2.2 Consensus size: 115
78704 GCTAATGCTA
* * * *
78714 ATCCAACTCTTTATATGATGG-AT-GAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTT
1 ATCCACCTCATTATATGATGGAATCGAACCAAGGTTGAACAAG-T-TTCTCATTATAAACTTCTT
* * *
78777 CTCCATCATCGGATGAGTTCTTCTTATTATGAACTCTCCATTGGAAATATTG
64 CTCCATCATCGGATGAGTTCTTCTCATTATGAACTATCAATTGGAAATATTG
*
78829 ATCCACCTCATTCTATGATGGAATCGAACCAAGGTTGAACAAG-TTCTCATTATAAACTTCTTCT
1 ATCCACCTCATTATATGATGGAATCGAACCAAGGTTGAACAAGTTTCTCATTATAAACTTCTTCT
* * *
78893 CCCTCGTCGGATGAGTTCTTCTCATTATGAACTATCAATTGGAAATGTAT-
66 CCATCATCGGATGAGTTCTTCTCATTATGAACTATCAATTGGAAATAT-TG
* *
78943 ATCCACCTCCTTATGTGATGGAATC
1 ATCCACCTCATTATATGATGGAATC
78968 AGACAAAGTG
Statistics
Matches: 122, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
114 84 0.69
115 19 0.16
116 2 0.02
117 17 0.14
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (115 bp):
ATCCACCTCATTATATGATGGAATCGAACCAAGGTTGAACAAGTTTCTCATTATAAACTTCTTCT
CCATCATCGGATGAGTTCTTCTCATTATGAACTATCAATTGGAAATATTG
Found at i:79229 original size:117 final size:118
Alignment explanation
Indices: 79044--79264 Score: 302
Period size: 117 Copynumber: 1.9 Consensus size: 118
79034 ACTCTTTATG
* * * * * *
79044 TGATGGAATCGAGCTAAGGTTGAATAAGTTCTTCTCATTACGAACTTCTTCTCCCTTTTCTGATG
1 TGATGGAATCGAACCAAGGTTGAACAAGTTATTCTCATTACGAACTTCTTCTCCCTTTTCAGACG
* *
79109 AGTTCTTCTTATTATGAA-CTCTCCACTGAAAATGTTGATCCACCTTCTTTTA
66 AGTTCTTCTCATTATGAACCCCTCCACTGAAAATGTTGATCCACCTTCTTTTA
* * *
79161 TGATGGAATCGAACCAAGGTTGAACAAGTTATTCTCATTATGAATTTCTTCT-CTTTCTTCAGAC
1 TGATGGAATCGAACCAAGGTTGAACAAGTTATTCTCATTACGAACTTCTTCTCCCTT-TTCAGAC
* *
79225 GAGTTCTTCTCATTATGAACCCCTCCATTGGAAATGTTGA
65 GAGTTCTTCTCATTATGAACCCCTCCACTGAAAATGTTGA
79265 ATGGTTTATC
Statistics
Matches: 89, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
116 3 0.03
117 69 0.78
118 17 0.19
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.38
Consensus pattern (118 bp):
TGATGGAATCGAACCAAGGTTGAACAAGTTATTCTCATTACGAACTTCTTCTCCCTTTTCAGACG
AGTTCTTCTCATTATGAACCCCTCCACTGAAAATGTTGATCCACCTTCTTTTA
Found at i:82414 original size:20 final size:20
Alignment explanation
Indices: 82373--82415 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
82363 GCAATCAGTG
*
82373 AATTTATTGCTCAAGTAGTA
1 AATTTATTGCTCAAGTAATA
82393 AATTTATTGCTC-AGATAATA
1 AATTTATTGCTCAAG-TAATA
82413 AAT
1 AAT
82416 GTCTCTTTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.40
Consensus pattern (20 bp):
AATTTATTGCTCAAGTAATA
Found at i:85625 original size:23 final size:23
Alignment explanation
Indices: 85546--85621 Score: 116
Period size: 23 Copynumber: 3.3 Consensus size: 23
85536 CTCGTATAAA
*
85546 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTACCACGTAGAAT
85569 TGCACCGAAGTACCACGTAGAAT
1 TGCACCGAAGTACCACGTAGAAT
* * *
85592 TGCACCGTAGTACCGCGTATAAT
1 TGCACCGAAGTACCACGTAGAAT
85615 TGCACCG
1 TGCACCG
85622 TAGTGCCATA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.29, C:0.28, G:0.24, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTACCACGTAGAAT
Found at i:86633 original size:21 final size:21
Alignment explanation
Indices: 86601--86641 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
86591 TGTTTGTTTA
86601 ATTGAGAGTGCATCGATGCAC
1 ATTGAGAGTGCATCGATGCAC
86622 ATTGA-AGATGCATCGATGCA
1 ATTGAGAG-TGCATCGATGCA
86642 TATAACCCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.24
Consensus pattern (21 bp):
ATTGAGAGTGCATCGATGCAC
Found at i:95753 original size:2 final size:2
Alignment explanation
Indices: 95748--95777 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
95738 TTTTTTCGTG
95748 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
95778 TCTAAAATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:96233 original size:3 final size:3
Alignment explanation
Indices: 96227--96270 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
96217 ATATTTTTAA
96227 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
96271 GTAAGGTGGT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:98882 original size:119 final size:120
Alignment explanation
Indices: 98712--98944 Score: 274
Period size: 119 Copynumber: 1.9 Consensus size: 120
98702 TAGTTGAGTG
* * * * * * ** **
98712 ATCATTTTGTAACTTTTAATAGTAGGAGAATTCAACAAAGCAACACTCTATAGTTGAGGGATTAT
1 ATCATTTTGTAAATTTTAATAGTACGAGAACTCAACAAAGCAACACACTATAATCGAGCAACCAT
* * *
98777 TTTGTAACTTTTAATAG-CCAGGAACTCAACAAAGTGAA-ATCCTATAGTTAGATA
66 TTTATAACTTTTAATAGTCAAAGAACTCAACAAAGT-AAGATCCTATAGTTAGATA
** *
98831 ATCATTTTGTAAATTTTAATAGT-CGATGAACTCAACGTAGCAACGCACTATAATCGAGCAACCA
1 ATCATTTTGTAAATTTTAATAGTACGA-GAACTCAACAAAGCAACACACTATAATCGAGCAACCA
*
98895 TTTTATAACTTTTAATAGTTAAAGAACTCAACAAAGTAAGATCCTATAGT
65 TTTTATAACTTTTAATAGTCAAAGAACTCAACAAAGTAAGATCCTATAGT
98945 CAAGGAACCA
Statistics
Matches: 94, Mismatches: 17, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
118 2 0.02
119 67 0.71
120 25 0.27
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (120 bp):
ATCATTTTGTAAATTTTAATAGTACGAGAACTCAACAAAGCAACACACTATAATCGAGCAACCAT
TTTATAACTTTTAATAGTCAAAGAACTCAACAAAGTAAGATCCTATAGTTAGATA
Found at i:98922 original size:60 final size:59
Alignment explanation
Indices: 98833--98977 Score: 148
Period size: 60 Copynumber: 2.4 Consensus size: 59
98823 GTTAGATAAT
* * ** * ** *
98833 CATTTTGTAAATTTTAATAGTCGATGAACTCAACGTAGCAACG-CACTATAATCGAGCAAC
1 CATTTTATAACTTTTAATAGTTAAAGAACTCAACAAAGCAA-GAC-CTATAATCAAGCAAC
* * *
98893 CATTTTATAACTTTTAATAGTTAAAGAACTCAACAAAGTAAGATCCTATAGTCAAGGAAC
1 CATTTTATAACTTTTAATAGTTAAAGAACTCAACAAAGCAAGA-CCTATAATCAAGCAAC
*
98953 CATTTTATAACTTTTAATAATTAAA
1 CATTTTATAACTTTTAATAGTTAAA
98978 AGATTTAAGA
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
59 1 0.01
60 69 0.97
61 1 0.01
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (59 bp):
CATTTTATAACTTTTAATAGTTAAAGAACTCAACAAAGCAAGACCTATAATCAAGCAAC
Found at i:99912 original size:73 final size:75
Alignment explanation
Indices: 99791--99971 Score: 269
Period size: 73 Copynumber: 2.4 Consensus size: 75
99781 CTTAACCGGT
* ** * *
99791 TAAAATAAAATAGGTGCTATGTATTATGTTAAACTACCTACTGGTTTGTTTGAAGGTTACTAATA
1 TAAAATAAAATAGGCGCTACCTATTATGTTAAAATACCTACTGGTTTGTTTAAAGGTTACTAATA
99856 ATGTAAACGG
66 ATGTAAACGG
* *
99866 TAAAAT-AAATAGGCGCTA-CTATTACGTTAAAATACTTACAT-GTTTGTTTAAAGGTTACTAAT
1 TAAAATAAAATAGGCGCTACCTATTATGTTAAAATACCTAC-TGGTTTGTTTAAAGGTTACTAAT
99928 AATGTAAACGG
65 AATGTAAACGG
99939 TAAAATAAAATAGGCGCTACCTATTATGTTAAA
1 TAAAATAAAATAGGCGCTACCTATTATGTTAAA
99972 TAAGCTCTAC
Statistics
Matches: 96, Mismatches: 7, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
73 54 0.56
74 24 0.25
75 18 0.19
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.34
Consensus pattern (75 bp):
TAAAATAAAATAGGCGCTACCTATTATGTTAAAATACCTACTGGTTTGTTTAAAGGTTACTAATA
ATGTAAACGG
Found at i:99981 original size:23 final size:23
Alignment explanation
Indices: 99946--100017 Score: 108
Period size: 23 Copynumber: 3.1 Consensus size: 23
99936 CGGTAAAATA
*
99946 AAATAGGCGCTACCTATTATGTT
1 AAATAAGCGCTACCTATTATGTT
*
99969 AAATAAGCTCTACCTATTATGTT
1 AAATAAGCGCTACCTATTATGTT
**
99992 AAATAAGCGCTATTTATTATGTT
1 AAATAAGCGCTACCTATTATGTT
100015 AAA
1 AAA
100018 CTAGCCACCG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (23 bp):
AAATAAGCGCTACCTATTATGTT
Found at i:100082 original size:72 final size:74
Alignment explanation
Indices: 99992--100164 Score: 244
Period size: 75 Copynumber: 2.4 Consensus size: 74
99982 CTATTATGTT
* * * * *
99992 AAATAAGCGCTATTTATTATGTTAAACTAGCC-ACCGGTTTGTTTAAATG-T-TAATAATGTAAA
1 AAATAGGCGCTATCTATTACGTTAAAATA-CCTACCGGTTTGTTTAAAGGTTATAATAATGTAAA
100054 CGGTAAAATA
65 CGGTAAAATA
*
100064 AAATAGGCGCTACCTATTACGTTAAAATACCTACCGGTTTGTTTAAAGGTTACTAATAATGTAAA
1 AAATAGGCGCTATCTATTACGTTAAAATACCTACCGGTTTGTTTAAAGGTTA-TAATAATGTAAA
100129 CGGTAAAATA
65 CGGTAAAATA
*
100139 AAATAGACGCTATCTATTACGTTAAA
1 AAATAGGCGCTATCTATTACGTTAAA
100165 TAGACGCTAC
Statistics
Matches: 89, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
71 2 0.02
72 40 0.45
73 1 0.01
75 46 0.52
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.32
Consensus pattern (74 bp):
AAATAGGCGCTATCTATTACGTTAAAATACCTACCGGTTTGTTTAAAGGTTATAATAATGTAAAC
GGTAAAATA
Found at i:100142 original size:193 final size:192
Alignment explanation
Indices: 99806--100258 Score: 617
Period size: 193 Copynumber: 2.3 Consensus size: 192
99796 TAAAATAGGT
* * *
99806 GCTATGTATTATGTTAAACTA-CCTACTGGTTTGTTTGAAGGTTACTAATAATGTAAACGGTAAA
1 GCTATATATTATGTTAAACTAGCC-ACCGGTTTGTTTAAAGG-T--TAATAATGTAAACGGTAAA
* *
99870 AT-AAATAGGCGCTACTATTACGTTAAAATACTTACATGTTTGTTTAAAGGTTACTAATAATGTA
62 ATAAAATAGGCGCTACTATTACGTTAAAATACCTACAGGTTTGTTTAAAGGTTACTAATAATGTA
* * * *
99934 AACGGTAAAATAAAATAGGCGCTACCTATTATGTTAAATA-AGCTCTACCTATTATGTTAAATAA
127 AACGGTAAAATAAAATAGACGCTACCTATTACGTTAAATAGA-CGCTACCTATTACGTTAAATAA
99998 GC
191 GC
* *
100000 GCTATTTATTATGTTAAACTAGCCACCGGTTTGTTTAAATGTTAATAATGTAAACGGTAAAATAA
1 GCTATATATTATGTTAAACTAGCCACCGGTTTGTTTAAAGGTTAATAATGTAAACGGTAAAATAA
*
100065 AATAGGCGCTACCTATTACGTTAAAATACCTACCGGTTTGTTTAAAGGTTACTAATAATGTAAAC
66 AATAGGCGCTA-CTATTACGTTAAAATACCTACAGGTTTGTTTAAAGGTTACTAATAATGTAAAC
*
100130 GGTAAAATAAAATAGACGCTATCTATTACGTTAAATAGACGCTACCTATTACGTTAAATAAGC
130 GGTAAAATAAAATAGACGCTACCTATTACGTTAAATAGACGCTACCTATTACGTTAAATAAGC
** * * * * *
100193 GCTGCATATTACGCTAAACTAGCTACCAGTTTG-TTAAAGGTTAACGATTATGTAAACGGTAAAA
1 GCTATATATTATGTTAAACTAGCCACCGGTTTGTTTAAAGGTT-A--ATAATGTAAACGGTAAAA
100257 TA
63 TA
100259 TATACAACTT
Statistics
Matches: 231, Mismatches: 21, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
191 21 0.09
192 20 0.09
193 134 0.58
194 35 0.15
195 21 0.09
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (192 bp):
GCTATATATTATGTTAAACTAGCCACCGGTTTGTTTAAAGGTTAATAATGTAAACGGTAAAATAA
AATAGGCGCTACTATTACGTTAAAATACCTACAGGTTTGTTTAAAGGTTACTAATAATGTAAACG
GTAAAATAAAATAGACGCTACCTATTACGTTAAATAGACGCTACCTATTACGTTAAATAAGC
Found at i:100195 original size:23 final size:23
Alignment explanation
Indices: 100139--100189 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
100129 CGGTAAAATA
*
100139 AAATAGACGCTATCTATTACGTT
1 AAATAGACGCTACCTATTACGTT
100162 AAATAGACGCTACCTATTACGTT
1 AAATAGACGCTACCTATTACGTT
100185 AAATA
1 AAATA
100190 AGCGCTGCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (23 bp):
AAATAGACGCTACCTATTACGTT
Found at i:100202 original size:23 final size:23
Alignment explanation
Indices: 100139--100210 Score: 85
Period size: 23 Copynumber: 3.1 Consensus size: 23
100129 CGGTAAAATA
100139 AAATAGACGCTATC-TATTACGTT
1 AAATAGACGCTA-CATATTACGTT
*
100162 AAATAGACGCTACCTATTACGTT
1 AAATAGACGCTACATATTACGTT
* *
100185 AAATA-AGCGCTGCATATTACGCT
1 AAATAGA-CGCTACATATTACGTT
100208 AAA
1 AAA
100211 CTAGCTACCA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
22 2 0.05
23 42 0.95
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (23 bp):
AAATAGACGCTACATATTACGTT
Found at i:101930 original size:35 final size:36
Alignment explanation
Indices: 101841--101944 Score: 126
Period size: 35 Copynumber: 2.9 Consensus size: 36
101831 AATAATATTC
101841 TTTTGAATATTTCAAATTAAAAGATATCTATTATCT
1 TTTTGAATATTTCAAATTAAAAGATATCTATTATCT
* * *
101877 ATTT-AAT-TTTGAATATTAAAATATAAT-TA-TATCT
1 TTTTGAATATTTCAA-ATTAAAAGAT-ATCTATTATCT
*
101911 TTTTGAATATTTCAAATTAAAAAATATCTATTAT
1 TTTTGAATATTTCAAATTAAAAGATATCTATTAT
101945 GTCTTTTAAG
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
34 15 0.27
35 28 0.50
36 13 0.23
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (36 bp):
TTTTGAATATTTCAAATTAAAAGATATCTATTATCT
Found at i:102945 original size:16 final size:15
Alignment explanation
Indices: 102926--102968 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
102916 TTATGAGGTG
102926 AAAATATTATTATTGT
1 AAAATATTATTATT-T
*
102942 AAAAAATTAATTATTT
1 AAAATATT-ATTATTT
*
102958 AAAATAATATT
1 AAAATATTATT
102969 TAATTTTGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 3 0.13
16 14 0.61
17 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (15 bp):
AAAATATTATTATTT
Found at i:105165 original size:20 final size:20
Alignment explanation
Indices: 105124--105193 Score: 54
Period size: 20 Copynumber: 3.5 Consensus size: 20
105114 ACAATTTTTG
* * *
105124 GTATCGATAC-CAAGTGTGA
1 GTATCTATACTCAAGGGTTA
105143 GTATCTATACTCAAGGGTTA
1 GTATCTATACTCAAGGGTTA
*
105163 GTAT-TGATACTAAAGGGCTTA
1 GTATCT-ATACTCAAGGG-TTA
* *
105184 ATATCAATAC
1 GTATCTATAC
105194 CCTTATTTGA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
19 10 0.24
20 21 0.51
21 10 0.24
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.31
Consensus pattern (20 bp):
GTATCTATACTCAAGGGTTA
Found at i:107272 original size:22 final size:21
Alignment explanation
Indices: 107234--107289 Score: 103
Period size: 22 Copynumber: 2.6 Consensus size: 21
107224 CTCGGAGGGA
107234 ACCGATTCCCCCCAGGGGGGT
1 ACCGATTCCCCCCAGGGGGGT
107255 ACCGATTCCCTCCCAGGGGGGT
1 ACCGATTCCC-CCCAGGGGGGT
107277 ACCGATTCCCCCC
1 ACCGATTCCCCCC
107290 TTGTATAACG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 13 0.38
22 21 0.62
ACGTcount: A:0.14, C:0.43, G:0.27, T:0.16
Consensus pattern (21 bp):
ACCGATTCCCCCCAGGGGGGT
Done.