Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005974.1 Hibiscus syriacus cultivar Beakdansim tig00014043_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: 75117
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:1661 original size:18 final size:18
Alignment explanation
Indices: 1638--1673 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1628 AAGCAAAAGG
*
1638 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
1656 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
1674 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:2245 original size:66 final size:65
Alignment explanation
Indices: 2163--2338 Score: 257
Period size: 66 Copynumber: 2.6 Consensus size: 65
2153 AATTTAAAAC
2163 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTATTATTTACACATCAAATT
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTATTATTTACACATC-AATT
2228 A
65 A
* *
2229 AACAAATCAACTTTTACAAATCAATTAAACAAGC-AAAAAATAATTATTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTATTATTTACACATCAATTA
2293 AACAAATCAACTTTCAATGTA-AAATTCAATTAAACAAGCAAAAAAA
1 AACAAATCAAC-TT---T-TACAAA-TCAATTAAACAAGCAAAAAAA
2339 GTGTACACCG
Statistics
Matches: 101, Mismatches: 2, Indels: 10
0.89 0.02 0.09
Matches are distributed among these distances:
64 16 0.16
65 25 0.25
66 34 0.34
68 4 0.04
69 16 0.16
70 6 0.06
ACGTcount: A:0.54, C:0.16, G:0.02, T:0.28
Consensus pattern (65 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTATTATTTACACATCAATTA
Found at i:3705 original size:21 final size:21
Alignment explanation
Indices: 3681--3756 Score: 82
Period size: 21 Copynumber: 3.6 Consensus size: 21
3671 GCGGGCGGGA
*
3681 CCTCTTGAACGATGACAGGGG
1 CCTCTTGAACGATGAGAGGGG
* *
3702 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAACGATGAGAGGGG
* * *
3723 CTTCTTCG-ATGGTGAGAGGGG
1 CCTCTT-GAACGATGAGAGGGG
3744 CCTCTTGAACGAT
1 CCTCTTGAACGAT
3757 AGGAGACGAC
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
20 1 0.02
21 42 0.95
22 1 0.02
ACGTcount: A:0.18, C:0.21, G:0.37, T:0.24
Consensus pattern (21 bp):
CCTCTTGAACGATGAGAGGGG
Found at i:4206 original size:63 final size:63
Alignment explanation
Indices: 4112--4233 Score: 138
Period size: 63 Copynumber: 1.9 Consensus size: 63
4102 ACTATGTAGC
* * * *
4112 GCACCATTGTCATCGCGTAAAAAATCCACCTCACCACG-TAAAGACCGAACCTCATCACGCCAT
1 GCACCATTATCATCACGTAAAAAATCCACCTCACCACGCAAAACACCG-ACCTCATCACGCCAT
* ** * **
4175 GCACCATTATCTTCACGTAAAGTATCGACCTCATGACGCAAAACACCGACCTCATCACG
1 GCACCATTATCATCACGTAAAAAATCCACCTCACCACGCAAAACACCGACCTCATCACG
4234 TAACTCCCTA
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
63 41 0.85
64 7 0.15
ACGTcount: A:0.33, C:0.35, G:0.13, T:0.19
Consensus pattern (63 bp):
GCACCATTATCATCACGTAAAAAATCCACCTCACCACGCAAAACACCGACCTCATCACGCCAT
Found at i:6675 original size:40 final size:40
Alignment explanation
Indices: 6495--6760 Score: 240
Period size: 40 Copynumber: 6.7 Consensus size: 40
6485 TTGTTCCGCA
*
6495 TTGCGAATTTGACTT-TCGCGTTGCGAATTTGACT-TCCGCG
1 TTGCGAATTTGACTTCT-GTGTTGCGAATTTGACTAT-CGCG
* * *
6535 TTGCGAATTTGACTTCCGCGTTGCGAATTTGACTATCTCG
1 TTGCGAATTTGACTTCTGTGTTGCGAATTTGACTATCGCG
** *
6575 TTATGAATTTGACTTCTGTGTTGCGAATTTGACTATCTCG
1 TTGCGAATTTGACTTCTGTGTTGCGAATTTGACTATCGCG
**
6615 TTATGAATTTGACTTCTGTGTTGCGAATTTGGA-TATCGCG
1 TTGCGAATTTGACTTCTGTGTTGCGAATTT-GACTATCGCG
* * *
6655 TTGCGAATTTGACTTATGTGTTGCG-ATTT-ACAAATTCGTG
1 TTGCGAATTTGACTTCTGTGTTGCGAATTTGAC-TA-TCGCG
* * ** * *
6695 TTACGAATTTGACTATC-GCGTTGTAAATTTGACGT-TTGTG
1 TTGCGAATTTGACT-TCTGTGTTGCGAATTTGAC-TATCGCG
**
6735 TTGTAAATTTGACTTCTGTGTTGCGA
1 TTGCGAATTTGACTTCTGTGTTGCGA
6761 TTTACAAATT
Statistics
Matches: 190, Mismatches: 26, Indels: 20
0.81 0.11 0.08
Matches are distributed among these distances:
37 1 0.01
39 7 0.04
40 172 0.91
41 8 0.04
42 2 0.01
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.42
Consensus pattern (40 bp):
TTGCGAATTTGACTTCTGTGTTGCGAATTTGACTATCGCG
Found at i:6754 original size:20 final size:20
Alignment explanation
Indices: 6495--6760 Score: 210
Period size: 20 Copynumber: 13.3 Consensus size: 20
6485 TTGTTCCGCA
6495 TTGCGAATTTGACTT-TCGCG
1 TTGCGAATTTGACTTCT-GCG
*
6515 TTGCGAATTTGACTTCCGCG
1 TTGCGAATTTGACTTCTGCG
*
6535 TTGCGAATTTGACTTCCGCG
1 TTGCGAATTTGACTTCTGCG
6555 TTGCGAATTTGACTATCT-CG
1 TTGCGAATTTGACT-TCTGCG
** *
6575 TTATGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTCTGCG
6595 TTGCGAATTTGACTATCT-CG
1 TTGCGAATTTGACT-TCTGCG
** *
6615 TTATGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTCTGCG
6635 TTGCGAATTTGGA-TATC-GCG
1 TTGCGAATTT-GACT-TCTGCG
* *
6655 TTGCGAATTTGACTTATGTG
1 TTGCGAATTTGACTTCTGCG
*
6675 TTGCG-ATTT-ACAAATTC-GTG
1 TTGCGAATTTGAC---TTCTGCG
*
6695 TTACGAATTTGACTATC-GCG
1 TTGCGAATTTGACT-TCTGCG
** *
6715 TTGTAAATTTGACGTT-TGTG
1 TTGCGAATTTGAC-TTCTGCG
** *
6735 TTGTAAATTTGACTTCTGTG
1 TTGCGAATTTGACTTCTGCG
6755 TTGCGA
1 TTGCGA
6761 TTTACAAATT
Statistics
Matches: 203, Mismatches: 25, Indels: 36
0.77 0.09 0.14
Matches are distributed among these distances:
18 2 0.01
19 16 0.08
20 167 0.82
21 16 0.08
22 2 0.01
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.42
Consensus pattern (20 bp):
TTGCGAATTTGACTTCTGCG
Found at i:6778 original size:40 final size:40
Alignment explanation
Indices: 6531--6786 Score: 159
Period size: 40 Copynumber: 6.4 Consensus size: 40
6521 ATTTGACTTC
* * * *
6531 CGCGTTGCGAATTTGACTTCCGCGTTGCGAATTTGAC-TA-T
1 CGCGTTGTGAATTTGACTTCTGTGTTGCG-ATTT-ACAAATT
* * *
6571 CTCGTTATGAATTTGACTTCTGTGTTGCGAATTTGAC-TA-T
1 CGCGTTGTGAATTTGACTTCTGTGTTGCG-ATTT-ACAAATT
* * ** *
6611 CTCGTTATGAATTTGACTTCTGTGTTGCGAATTTGGATA-T
1 CGCGTTGTGAATTTGACTTCTGTGTTGCG-ATTTACAAATT
* *
6651 CGCGTTGCGAATTTGACTTATGTGTTGCGATTTACAAATT
1 CGCGTTGTGAATTTGACTTCTGTGTTGCGATTTACAAATT
* ** * ** *
6691 CGTGTTACGAATTTGACTATC-GCGTTGTAAATTTGAC--GTT
1 CGCGTTGTGAATTTGACT-TCTGTGTTG-CGATTT-ACAAATT
* * *
6731 TGTGTTGTAAATTTGACTTCTGTGTTGCGATTTACAAATT
1 CGCGTTGTGAATTTGACTTCTGTGTTGCGATTTACAAATT
*
6771 CGCGTTGTGAAATTGA
1 CGCGTTGTGAATTTGA
6787 AAACTGGGTT
Statistics
Matches: 175, Mismatches: 33, Indels: 16
0.78 0.15 0.07
Matches are distributed among these distances:
38 2 0.01
39 12 0.07
40 154 0.88
41 5 0.03
42 2 0.01
ACGTcount: A:0.21, C:0.15, G:0.23, T:0.41
Consensus pattern (40 bp):
CGCGTTGTGAATTTGACTTCTGTGTTGCGATTTACAAATT
Found at i:6812 original size:80 final size:80
Alignment explanation
Indices: 6660--6812 Score: 184
Period size: 80 Copynumber: 1.9 Consensus size: 80
6650 TCGCGTTGCG
* * ** *
6660 AATTTGACTTATGTGTTGCGATTTACAAATTCGTGTTACGAATTTGACTATCGCGTTGTAAATTT
1 AATTTGACTTATGTGTTGCGATTTACAAATTCGCGTTACGAAATTGAAAATCGCGTTGGAAATTT
*
6725 GACGTTTGTGTTGTA
66 GAAGTTTGTGTTGTA
* ** *
6740 AATTTGACTTCTGTGTTGCGATTTACAAATTCGCGTTGTGAAATTGAAAA-CTGGGTTGCGAAA-
1 AATTTGACTTATGTGTTGCGATTTACAAATTCGCGTTACGAAATTGAAAATC-GCGTTG-GAAAT
6803 TTGAAGTTTG
64 TTGAAGTTTG
6813 CATTGCGAAT
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
79 1 0.02
80 57 0.93
81 3 0.05
ACGTcount: A:0.25, C:0.11, G:0.23, T:0.41
Consensus pattern (80 bp):
AATTTGACTTATGTGTTGCGATTTACAAATTCGCGTTACGAAATTGAAAATCGCGTTGGAAATTT
GAAGTTTGTGTTGTA
Found at i:7277 original size:24 final size:24
Alignment explanation
Indices: 7247--7295 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
7237 ATTAAACTTG
7247 CTACTCTTTTAATCTCATCTGTTA
1 CTACTCTTTTAATCTCATCTGTTA
7271 CTACTCTTTTAATCTCATCTGTTA
1 CTACTCTTTTAATCTCATCTGTTA
7295 C
1 C
7296 AAGTTGTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.27, G:0.04, T:0.49
Consensus pattern (24 bp):
CTACTCTTTTAATCTCATCTGTTA
Found at i:28209 original size:24 final size:21
Alignment explanation
Indices: 28167--28210 Score: 52
Period size: 24 Copynumber: 2.0 Consensus size: 21
28157 AAATACTATT
*
28167 AATATTTTATGTTATGCTGAA
1 AATATTTTATGTTAAGCTGAA
28188 AATATTATTATAGTTTAAGCTGA
1 AATATT-TTAT-G-TTAAGCTGA
28211 TAGAACATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 6 0.32
22 4 0.21
23 1 0.05
24 8 0.42
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.45
Consensus pattern (21 bp):
AATATTTTATGTTAAGCTGAA
Found at i:28364 original size:74 final size:77
Alignment explanation
Indices: 28276--28602 Score: 202
Period size: 77 Copynumber: 4.3 Consensus size: 77
28266 GAATATATAT
* * *
28276 ATAAAATAAGGTTGC-ACCTAAAAATTTCATGGTTCAATAAGAA-A-CATATAATCTGGAATGTT
1 ATAAAATAAGGTTGCGACC-AAAAATGTCATAGTTCAATAAGAATAGCATACAATCTGGAATGTT
28338 AATATTTTTATTA
65 AATATTTTTATTA
* * * * * ** *
28351 ATAAAAT-TGGTTGCGTCCAAGAATGTCATATTTCATTAAGAATTAGGTTACAATTTGGAATGTT
1 ATAAAATAAGGTTGCGACCAAAAATGTCATAGTTCAATAAGAA-TAGCATACAATCTGGAATGTT
28415 AATATTTTTATTA
65 AATATTTTTATTA
* * ** * * * * ** *** *
28428 ATAAAAT-ATGCTGCGTTCAAGAATGTCAT-GATTTACTAAGAAAAAGGTTGTGATCTGAAATGT
1 ATAAAATAAGGTTGCGACCAAAAATGTCATAG-TTCAATAAG-AATAGCATACAATCTGGAATGT
28491 TAATATTTTTATTA
64 TAATATTTTTATTA
* * * * * * * * * * * *
28505 ATAAAATGA-GTTACGCCCAAGAATGTCATGGTTCATTAATAAATAGGATGCGATATGGAATATT
1 ATAAAATAAGGTTGCGACCAAAAATGTCATAGTTCAATAA-GAATAGCATACAATCTGGAATGTT
28569 AATATTTTTATTA
65 AATATTTTTATTA
* *
28582 ATAAAATGA-GTTGCGCCCAAA
1 ATAAAATAAGGTTGCGACCAAA
28603 TGTCAATGAT
Statistics
Matches: 204, Mismatches: 39, Indels: 16
0.79 0.15 0.06
Matches are distributed among these distances:
74 25 0.12
75 9 0.04
76 1 0.00
77 165 0.81
78 4 0.02
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (77 bp):
ATAAAATAAGGTTGCGACCAAAAATGTCATAGTTCAATAAGAATAGCATACAATCTGGAATGTTA
ATATTTTTATTA
Found at i:28417 original size:77 final size:77
Alignment explanation
Indices: 28329--28665 Score: 353
Period size: 77 Copynumber: 4.4 Consensus size: 77
28319 ACATATAATC
*
28329 TGGAATGTTAATATTTTTATTAATAAAATTG-GTTGCGTCCAAGAATGTCATATTTCATTAAGAA
1 TGGAATGTTAATATTTTTATTAATAAAA-TGAGTTGCGCCCAAGAATGTCATATTTCATTAAGAA
* * * *
28393 TTAGGTTACAATT
65 ATAGGTTGCGATA
* ** *
28406 TGGAATGTTAATATTTTTATTAATAAAAT-ATGCTGCGTTCAAGAATGTCATGATTT-ACTAAGA
1 TGGAATGTTAATATTTTTATTAATAAAATGA-GTTGCGCCCAAGAATGTCAT-ATTTCATTAAGA
* * *
28469 AAAAGGTTGTGATC
64 AATAGGTTGCGATA
* * ** *
28483 TGAAATGTTAATATTTTTATTAATAAAATGAGTTACGCCCAAGAATGTCATGGTTCATTAATAAA
1 TGGAATGTTAATATTTTTATTAATAAAATGAGTTGCGCCCAAGAATGTCATATTTCATTAAGAAA
*
28548 TAGGATGCGATA
66 TAGGTTGCGATA
* * * *
28560 TGGAATATTAATATTTTTATTAATAAAATGAGTTGCGCCC-A-AATGTCA-ATGATCACTAATAA
1 TGGAATGTTAATATTTTTATTAATAAAATGAGTTGCGCCCAAGAATGTCATAT-TTCATTAAGAA
* *
28622 ATAAGTTGTGATA
65 ATAGGTTGCGATA
* *
28635 TGGAAATGTTAATAATTTTATAAATAAAATG
1 TGG-AATGTTAATATTTTTATTAATAAAATG
28666 GACTGCACAC
Statistics
Matches: 218, Mismatches: 35, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
75 29 0.13
76 28 0.13
77 156 0.72
78 5 0.02
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.38
Consensus pattern (77 bp):
TGGAATGTTAATATTTTTATTAATAAAATGAGTTGCGCCCAAGAATGTCATATTTCATTAAGAAA
TAGGTTGCGATA
Found at i:28502 original size:154 final size:153
Alignment explanation
Indices: 28326--28664 Score: 409
Period size: 154 Copynumber: 2.2 Consensus size: 153
28316 GAAACATATA
* * * *
28326 ATCTGGAATGTTAATATTTTTATTAATAAAATTG-GTTGCGTCCAAGAATGTCATATTTCATTAA
1 ATCTGAAATGTTAATATTTTTATTAATAAAATTGAGTTACGCCCAAGAATGTCATAGTTCATTAA
* * * * *
28390 GAATTAGGTTACAATTTGGAATGTTAATATTTTTATTAATAAAAT-ATGCTGCGTTCAAGAATGT
66 GAAATAGGATACAATATGGAATATTAATATTTTTATTAATAAAATGA-GCTGCG-CCAA-AATGT
*
28454 C-ATGATTTACTAAGAAA-AAGGTTGTG
128 CAATGA-TCACTAAGAAATAA-GTTGTG
*
28480 ATCTGAAATGTTAATATTTTTATTAATAAAA-TGAGTTACGCCCAAGAATGTCATGGTTCATTAA
1 ATCTGAAATGTTAATATTTTTATTAATAAAATTGAGTTACGCCCAAGAATGTCATAGTTCATTAA
* * * * *
28544 TAAATAGGATGCGATATGGAATATTAATATTTTTATTAATAAAATGAGTTGCGCCCAAATGTCAA
66 GAAATAGGATACAATATGGAATATTAATATTTTTATTAATAAAATGAGCTGCGCCAAAATGTCAA
*
28609 TGATCACTAATAAATAAGTTGTG
131 TGATCACTAAGAAATAAGTTGTG
* * *
28632 ATATGGAAATGTTAATAATTTTATAAATAAAAT
1 ATCT-GAAATGTTAATATTTTTATTAATAAAAT
28665 GGACTGCACA
Statistics
Matches: 159, Mismatches: 20, Indels: 12
0.83 0.10 0.06
Matches are distributed among these distances:
152 24 0.15
153 35 0.22
154 99 0.62
155 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.38
Consensus pattern (153 bp):
ATCTGAAATGTTAATATTTTTATTAATAAAATTGAGTTACGCCCAAGAATGTCATAGTTCATTAA
GAAATAGGATACAATATGGAATATTAATATTTTTATTAATAAAATGAGCTGCGCCAAAATGTCAA
TGATCACTAAGAAATAAGTTGTG
Found at i:28711 original size:154 final size:153
Alignment explanation
Indices: 28406--28740 Score: 346
Period size: 153 Copynumber: 2.2 Consensus size: 153
28396 GGTTACAATT
* *
28406 TGGAATGTTAATATTTTTATTAATAAAATATGCTGCGTTCAAGAATGTCATGATTTACTAAGAAA
1 TGGAATGTTAATATTTTTATTAATAAAATATGCTGCGTCCAAGAATGTCATGATTCACTAAGAAA
* * * * *
28471 AAGGTTGTGATCTGAAATGTTAATATTTTTATTAATAAAATGAGTTACGCCCAAGAATGTCATGG
66 AAGGTTGTGATATGAAATGTTAATAATTTTATAAATAAAATGAG-TACGCCCAAGAATATCATGA
** * *
28536 TTCATTAATAAATAGGATGCGATA
130 TTCACAAAAAAATAAGATGCGATA
* * * *
28560 TGGAATATTAATATTTTTATTAATAAAATGA-GTTGCG-CCCA-AATGTCAATGA-TCACTAATA
1 TGGAATGTTAATATTTTTATTAATAAAAT-ATGCTGCGTCCAAGAATGTC-ATGATTCACTAAGA
28621 AATAA-GTTGTGATATGGAAATGTTAATAATTTTATAAATAAAATG-G-ACTGCACACAAGAATA
64 AA-AAGGTTGTGATAT-GAAATGTTAATAATTTTATAAATAAAATGAGTAC-GC-C-CAAGAATA
* * *
28683 TTATGATTCACAAAGAAAATAAGTTGCGATC
124 TCATGATTCACAAA-AAAATAAGATGCGATA
*
28714 TGAAATGTTAAT-TTTTCTATT-ATAAAA
1 TGGAATGTTAATATTTT-TATTAATAAAA
28741 AATTCGAAAG
Statistics
Matches: 152, Mismatches: 20, Indels: 19
0.80 0.10 0.10
Matches are distributed among these distances:
150 2 0.01
151 2 0.01
152 26 0.17
153 62 0.41
154 59 0.39
155 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.36
Consensus pattern (153 bp):
TGGAATGTTAATATTTTTATTAATAAAATATGCTGCGTCCAAGAATGTCATGATTCACTAAGAAA
AAGGTTGTGATATGAAATGTTAATAATTTTATAAATAAAATGAGTACGCCCAAGAATATCATGAT
TCACAAAAAAATAAGATGCGATA
Found at i:28887 original size:123 final size:123
Alignment explanation
Indices: 28740--28962 Score: 356
Period size: 123 Copynumber: 1.8 Consensus size: 123
28730 CTATTATAAA
* *
28740 AAATTCGAAAGTAAGTATACTTTTTCAAAAGTATCTATAATTTTGAATTTAAAAAAAATGAAAAA
1 AAATTCGAAAGTAAGAATACTTTTTCAAAAGTATCGATAATTTTGAATTTAAAAAAAATGAAAAA
28805 TGATATTTTAAATTTCAAAGTTAAAAGTATCGATACTTTGCAGTCTTTTCATTTTTTT
66 TGATATTTTAAATTTCAAAGTTAAAAGTATCGATACTTTGCAGTCTTTTCATTTTTTT
* * * * *
28863 AAATTCGAAAGTATGAATATTTTTTCAAAAGTATCGATACTTTTGAATTTATAAAAAATGTAAAA
1 AAATTCGAAAGTAAGAATACTTTTTCAAAAGTATCGATAATTTTGAATTTAAAAAAAATGAAAAA
* * *
28928 TGATATTTTAACTTTCGAATTTAAAAGTATCGATA
66 TGATATTTTAAATTTCAAAGTTAAAAGTATCGATA
28963 TTTTTGTAAA
Statistics
Matches: 90, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
123 90 1.00
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.40
Consensus pattern (123 bp):
AAATTCGAAAGTAAGAATACTTTTTCAAAAGTATCGATAATTTTGAATTTAAAAAAAATGAAAAA
TGATATTTTAAATTTCAAAGTTAAAAGTATCGATACTTTGCAGTCTTTTCATTTTTTT
Found at i:29046 original size:19 final size:19
Alignment explanation
Indices: 29022--29058 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
29012 CTTTAAATTT
29022 GAAAGTA-TCGATACTTTCA
1 GAAAGTATTC-ATACTTTCA
29041 GAAAGTATTCATACTTTC
1 GAAAGTATTCATACTTTC
29059 GAATTTTTTA
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:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (19 bp):
GAAAGTATTCATACTTTCA
Found at i:29195 original size:77 final size:77
Alignment explanation
Indices: 29064--29356 Score: 340
Period size: 77 Copynumber: 3.8 Consensus size: 77
29054 CTTTCGAATT
* * *
29064 TTTTA-TAATAGAAAA-ATTAACATTACAGATCGCAAC-TAACTTTCTTAGTGAACCATAACATT
1 TTTTATTAATA-AAAATATTAACATTCCAGATCGCAACAT-A-TTTCTCAGTGAACCATGACATT
* *
29126 CTTGTGTGCAACCCA
63 CTTGAGCGCAACCCA
* * * * * *
29141 TTTTATTTATAAAAATATTAACATTCCAAATCGCAACCTATTTATTAGTGAACCATGACATTATT
1 TTTTATTAATAAAAATATTAACATTCCAGATCGCAACATATTTCTCAGTGAACCATGACATTCTT
29206 GAGCGCAACCCA
66 GAGCGCAACCCA
* * *
29218 TTTTATTAATAAAAATATTAACATTCTAGATCGTAACATATTTCTCAGTGAATCATGACATTCTT
1 TTTTATTAATAAAAATATTAACATTCCAGATCGCAACATATTTCTCAGTGAACCATGACATTCTT
* ***
29283 GGGCGCAAGTTA
66 GAGCGCAACCCA
* * * *
29295 TTTTATTAATAAAAATAGTAAAATTCTAGATCGCAACATGTTTCTCAGTGAACCATGACATT
1 TTTTATTAATAAAAATATTAACATTCCAGATCGCAACATATTTCTCAGTGAACCATGACATT
29357 TTCAGCTTTT
Statistics
Matches: 187, Mismatches: 26, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
77 162 0.87
78 24 0.13
79 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (77 bp):
TTTTATTAATAAAAATATTAACATTCCAGATCGCAACATATTTCTCAGTGAACCATGACATTCTT
GAGCGCAACCCA
Found at i:30618 original size:21 final size:25
Alignment explanation
Indices: 30594--30650 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 25
30584 TTTGTGTTTG
30594 ATTTAAAACTTA-AAA-A-TTATC-
1 ATTTAAAACTTAGAAATATTTATCA
*
30615 ATTTAAAACTTAGAAATATTTTTCA
1 ATTTAAAACTTAGAAATATTTATCA
30640 ATTTAAAACTT
1 ATTTAAAACTT
30651 CAATATTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 12 0.39
22 3 0.10
23 1 0.03
24 4 0.13
25 11 0.35
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.42
Consensus pattern (25 bp):
ATTTAAAACTTAGAAATATTTATCA
Found at i:32217 original size:21 final size:21
Alignment explanation
Indices: 32188--32229 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
32178 GTTCACCCCA
*
32188 TCAATGCTAAAACACTTTAGT
1 TCAACGCTAAAACACTTTAGT
**
32209 TCAACGCTAAGGCACTTTAGT
1 TCAACGCTAAAACACTTTAGT
32230 GTATTAGTGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.31
Consensus pattern (21 bp):
TCAACGCTAAAACACTTTAGT
Found at i:32985 original size:41 final size:41
Alignment explanation
Indices: 32913--33002 Score: 126
Period size: 41 Copynumber: 2.2 Consensus size: 41
32903 ATATTTTAAA
* * * * *
32913 CATCTCGAATGGTGAACCCACTAATATTCCAAAGTGAAATT
1 CATCCCGAAAGGTGAACACACTAATAATCCAAAGTAAAATT
*
32954 CATCCCGAAAGGTGAATACACTAATAATCCAAAGTAAAATT
1 CATCCCGAAAGGTGAACACACTAATAATCCAAAGTAAAATT
32995 CATCCCGA
1 CATCCCGA
33003 GTGGTAAATC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.40, C:0.23, G:0.13, T:0.23
Consensus pattern (41 bp):
CATCCCGAAAGGTGAACACACTAATAATCCAAAGTAAAATT
Found at i:34095 original size:21 final size:21
Alignment explanation
Indices: 34070--34117 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
34060 CCTAATATTG
34070 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
34091 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
*
34112 TAATGT
1 CAATGT
34118 TTGAAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTGCAA
Found at i:38752 original size:21 final size:21
Alignment explanation
Indices: 38727--38774 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
38717 CCTAATATTG
38727 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
38748 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
*
38769 TAATGT
1 CAATGT
38775 TTGAAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTGCAA
Found at i:39284 original size:41 final size:41
Alignment explanation
Indices: 39239--39405 Score: 145
Period size: 41 Copynumber: 4.1 Consensus size: 41
39229 AGTCTGTCTT
* * *
39239 GAAGGGAGGAGGCAGTGATAATCCAAAGTGAAATTAATCCC
1 GAAGGGAGAAGCCAGTAATAATCCAAAGTGAAATTAATCCC
* * * * *
39280 GAAGGGTGAATCCATTAATATTCTAAAGTGAAATTAATCCC
1 GAAGGGAGAAGCCAGTAATAATCCAAAGTGAAATTAATCCC
* * * * * * *
39321 GAAGGGTGAATCCACTAATAATTCGAAGTGAAATTCATCCT
1 GAAGGGAGAAGCCAGTAATAATCCAAAGTGAAATTAATCCC
* * * * * *
39362 GAATGGTGAACCCATTAATATTCCAAAGTGAAATTTATCCC
1 GAAGGGAGAAGCCAGTAATAATCCAAAGTGAAATTAATCCC
39403 GAA
1 GAA
39406 TGGTAAATCC
Statistics
Matches: 103, Mismatches: 23, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 103 1.00
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.25
Consensus pattern (41 bp):
GAAGGGAGAAGCCAGTAATAATCCAAAGTGAAATTAATCCC
Found at i:39297 original size:22 final size:22
Alignment explanation
Indices: 39271--39339 Score: 56
Period size: 22 Copynumber: 3.3 Consensus size: 22
39261 CCAAAGTGAA
39271 ATTAATCCCGAAGGGTGAATCC
1 ATTAATCCCGAAGGGTGAATCC
** * *
39293 ATTAATATTCTAA-AGTGAA---
1 ATTAAT-CCCGAAGGGTGAATCC
39312 ATTAATCCCGAAGGGTGAATCC
1 ATTAATCCCGAAGGGTGAATCC
*
39334 ACTAAT
1 ATTAAT
39340 AATTCGAAGT
Statistics
Matches: 33, Mismatches: 9, Indels: 10
0.63 0.17 0.19
Matches are distributed among these distances:
18 3 0.09
19 11 0.33
22 16 0.48
23 3 0.09
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (22 bp):
ATTAATCCCGAAGGGTGAATCC
Found at i:39329 original size:19 final size:19
Alignment explanation
Indices: 39266--39330 Score: 51
Period size: 19 Copynumber: 3.3 Consensus size: 19
39256 ATAATCCAAA
39266 GTGAAATTAATCCCGAAGG
1 GTGAAATTAATCCCGAAGG
** * *
39285 GTGAATCCATTAATATTCTAA-A
1 GTGAA---ATTAAT-CCCGAAGG
39307 GTGAAATTAATCCCGAAGG
1 GTGAAATTAATCCCGAAGG
39326 GTGAA
1 GTGAA
39331 TCCACTAATA
Statistics
Matches: 33, Mismatches: 8, Indels: 10
0.65 0.16 0.20
Matches are distributed among these distances:
18 3 0.09
19 16 0.48
22 11 0.33
23 3 0.09
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.26
Consensus pattern (19 bp):
GTGAAATTAATCCCGAAGG
Found at i:39370 original size:82 final size:82
Alignment explanation
Indices: 39264--39420 Score: 242
Period size: 82 Copynumber: 1.9 Consensus size: 82
39254 TGATAATCCA
* * *
39264 AAGTGAAATTAATCCCGAAGGGTGAATCCATTAATATTCTAAAGTGAAATTAATCCCGAAGGGTG
1 AAGTGAAATTAATCCCGAAGGGTGAACCCATTAATATTCCAAAGTGAAATTAATCCCGAAGGGTA
39329 AATCCACTAATAATTCG
66 AATCCACTAATAATTCG
* * * * *
39346 AAGTGAAATTCATCCTGAATGGTGAACCCATTAATATTCCAAAGTGAAATTTATCCCGAATGGTA
1 AAGTGAAATTAATCCCGAAGGGTGAACCCATTAATATTCCAAAGTGAAATTAATCCCGAAGGGTA
39411 AATCCACTAA
66 AATCCACTAA
39421 ACTTCCTCGA
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
82 67 1.00
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (82 bp):
AAGTGAAATTAATCCCGAAGGGTGAACCCATTAATATTCCAAAGTGAAATTAATCCCGAAGGGTA
AATCCACTAATAATTCG
Found at i:39407 original size:41 final size:41
Alignment explanation
Indices: 39260--39416 Score: 208
Period size: 41 Copynumber: 3.8 Consensus size: 41
39250 GCAGTGATAA
39260 TCCAAAGTGAAATTAATCCCGAAGGGTGAATCCATTAATAT
1 TCCAAAGTGAAATTAATCCCGAAGGGTGAATCCATTAATAT
* *
39301 TCTAAAGTGAAATTAATCCCGAAGGGTGAATCCACTAATAAT
1 TCCAAAGTGAAATTAATCCCGAAGGGTGAATCCATTAAT-AT
* * * * *
39343 T-CGAAGTGAAATTCATCCTGAATGGTGAACCCATTAATAT
1 TCCAAAGTGAAATTAATCCCGAAGGGTGAATCCATTAATAT
* * *
39383 TCCAAAGTGAAATTTATCCCGAATGGTAAATCCA
1 TCCAAAGTGAAATTAATCCCGAAGGGTGAATCCA
39417 CTAAACTTCC
Statistics
Matches: 100, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
40 3 0.03
41 94 0.94
42 3 0.03
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (41 bp):
TCCAAAGTGAAATTAATCCCGAAGGGTGAATCCATTAATAT
Found at i:48555 original size:20 final size:20
Alignment explanation
Indices: 48526--48574 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
48516 CATACCCTTG
* *
48526 GTATCGATACTGGC-CTTACA
1 GTATCTATACTCGCTCTT-CA
*
48546 GTATCTATACTCTCTCTTCA
1 GTATCTATACTCGCTCTTCA
48566 GTATCTATA
1 GTATCTATA
48575 TCCTACCCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 22 0.88
21 3 0.12
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.39
Consensus pattern (20 bp):
GTATCTATACTCGCTCTTCA
Found at i:58455 original size:23 final size:24
Alignment explanation
Indices: 58424--58491 Score: 72
Period size: 23 Copynumber: 3.0 Consensus size: 24
58414 CAGCTCGTAT
*
58424 AAATACACCGAAGTGCCACGTA-A-
1 AAATGCACCGAAGTGCCA-GTATAG
* *
58447 AATTGCACCTAAGTG-CAGTATAG
1 AAATGCACCGAAGTGCCAGTATAG
58470 AAATGCACCGAAGTGCCA-TATA
1 AAATGCACCGAAGTGCCAGTATA
58492 AGATGTCCCT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
21 3 0.08
22 3 0.08
23 29 0.78
24 2 0.05
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.19
Consensus pattern (24 bp):
AAATGCACCGAAGTGCCAGTATAG
Found at i:62205 original size:11 final size:12
Alignment explanation
Indices: 62189--62221 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
62179 TAATGGGAAA
62189 ATTTGAAAAC-T
1 ATTTGAAAACAT
62200 ATTTGAAAACAAT
1 ATTTGAAAAC-AT
62213 ATTTGAAAA
1 ATTTGAAAA
62222 TTCATAATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.50
13 10 0.50
ACGTcount: A:0.52, C:0.06, G:0.09, T:0.33
Consensus pattern (12 bp):
ATTTGAAAACAT
Found at i:69121 original size:18 final size:19
Alignment explanation
Indices: 69079--69127 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
69069 ACTCAGTTTC
69079 CAAATTCGCAACACATAAGT
1 CAAATTCGCAACACA-AAGT
* *
69099 CAAATTTGCAACAC-AATT
1 CAAATTCGCAACACAAAGT
69117 CAAATTCGCAA
1 CAAATTCGCAA
69128 AGCGCATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 13 0.50
20 13 0.50
ACGTcount: A:0.45, C:0.24, G:0.08, T:0.22
Consensus pattern (19 bp):
CAAATTCGCAACACAAAGT
Found at i:69145 original size:19 final size:20
Alignment explanation
Indices: 69121--69161 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
69111 ACAATTCAAA
*
69121 TTCGCAAAGCGCA-TTTATT
1 TTCGCAAAGCGAATTTTATT
*
69140 TTCGCAACGCGAATTTTATT
1 TTCGCAAAGCGAATTTTATT
69160 TT
1 TT
69162 TGAATTCGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (20 bp):
TTCGCAAAGCGAATTTTATT
Found at i:69895 original size:419 final size:420
Alignment explanation
Indices: 69116--69939 Score: 1434
Period size: 419 Copynumber: 2.0 Consensus size: 420
69106 GCAACACAAT
* *
69116 TCAAATTCGCAAAGCGCATTTATTTTCGCAACGCGAATTTTATTTTTGAATTCGAAACACAATAT
1 TCAAATTCGCAAAGCACATTTATTTTCGCAACGCGAATTTTATTTTCGAATTCGAAACACAATAT
* *
69181 TTATTTCGCAACACAAATATAAATAGTATAATCGTAAATCATAACCTAAAACCCTAAATCACAAC
66 TTATTTCGCAACACAAATATAAACAATATAATCGTAAATCATAACCTAAAACCCTAAATCACAAC
* * *
69246 TCAGTCTCATCTTCATCTCTTACTCTCTACGGCGACATCCGTCCCCATCTCCGACGAAATCCATC
131 TCAGTCCCATCTCCATCTCTCACTCTCTACGGCGACATCCGTCCCCATCTCCGACGAAATCCATC
* * * *
69311 CCCATCTCTGGTGAAATCCATTTATCTTCATCTCTCAGAGCCACCCTCACAACCATTCATGGTCA
196 CCCATCTCCGGCGAAATCCATCTATCTTCATCTCTCAGAGCCACCCTCACAACCATTCACGGTCA
69376 GAAATGGAAAATCAACCACCGAGGGTTAGTTTTTTAATTATTTTTATTTTGAAATTTTTGTATTA
261 GAAATGGAAAATCAACCACCGAGGGTTAGTTTTTTAATTATTTTTATTTTGAAATTTTTGTATTA
*
69441 TTATTAGATTTTTCATGCTTAAATTGATGATAAATTTACTGGTAATTTCAGTAATAGATTAACCA
326 TTATTAGATTTTTCATACTTAAATTGATGATAAATTTACTGGTAATTTCAGTAATAGATTAACCA
69506 TTTCACTTAGATTGCGAATTTGGACAGAAG
391 TTTCACTTAGATTGCGAATTTGGACAGAAG
*
69536 TCAAATTCGCAAAGCACGTTTATTTTCGCAACGCGAATTTTATTTTCGAATTCGAAACACAATAT
1 TCAAATTCGCAAAGCACATTTATTTTCGCAACGCGAATTTTATTTTCGAATTCGAAACACAATAT
* *
69601 TTATTTCGC-ACACAAATATATACAATATAATCGTAAATTATAACCTAAAACCCTAAATCACAAC
66 TTATTTCGCAACACAAATATAAACAATATAATCGTAAATCATAACCTAAAACCCTAAATCACAAC
* * *
69665 TCAGTCCCATCTCCATCTCTCACTCTCTACGGCGACATCCGTCCCCATCTCCGATGAAATTCGTC
131 TCAGTCCCATCTCCATCTCTCACTCTCTACGGCGACATCCGTCCCCATCTCCGACGAAATCCATC
** *
69730 CTTATCTCCGGCGAAATCCGTCTATCTTCATCTCTCAGAGCCACCCTCACAACCATTCACGGTCA
196 CCCATCTCCGGCGAAATCCATCTATCTTCATCTCTCAGAGCCACCCTCACAACCATTCACGGTCA
*
69795 GAAATGGAAAATCAACCACTGAGGGTTAGTTTTTTAATTATTTTTATTTTGAAATTTTTGTATTA
261 GAAATGGAAAATCAACCACCGAGGGTTAGTTTTTTAATTATTTTTATTTTGAAATTTTTGTATTA
*
69860 TTATTAGATTTTTCATATTTAAATTGATGATAAATTTACTGGTAATTTCAGTAATAGATTAACCA
326 TTATTAGATTTTTCATACTTAAATTGATGATAAATTTACTGGTAATTTCAGTAATAGATTAACCA
69925 TTTCACTTAGATTGC
391 TTTCACTTAGATTGC
69940 TTAGTAAATT
Statistics
Matches: 381, Mismatches: 23, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
419 310 0.81
420 71 0.19
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.35
Consensus pattern (420 bp):
TCAAATTCGCAAAGCACATTTATTTTCGCAACGCGAATTTTATTTTCGAATTCGAAACACAATAT
TTATTTCGCAACACAAATATAAACAATATAATCGTAAATCATAACCTAAAACCCTAAATCACAAC
TCAGTCCCATCTCCATCTCTCACTCTCTACGGCGACATCCGTCCCCATCTCCGACGAAATCCATC
CCCATCTCCGGCGAAATCCATCTATCTTCATCTCTCAGAGCCACCCTCACAACCATTCACGGTCA
GAAATGGAAAATCAACCACCGAGGGTTAGTTTTTTAATTATTTTTATTTTGAAATTTTTGTATTA
TTATTAGATTTTTCATACTTAAATTGATGATAAATTTACTGGTAATTTCAGTAATAGATTAACCA
TTTCACTTAGATTGCGAATTTGGACAGAAG
Found at i:72201 original size:21 final size:20
Alignment explanation
Indices: 72161--72257 Score: 94
Period size: 20 Copynumber: 4.8 Consensus size: 20
72151 AGCACCTGTC
72161 ATCGTTCAAGAGG-CCTCCT
1 ATCGTTCAAGAGGCCCTCCT
72180 ATCGTTCAAGAGGCCTCTCCT
1 ATCGTTCAAGAGGCC-CTCCT
* *
72201 ATCATTCAAGA-GCCACT-AT
1 ATCGTTCAAGAGGCC-CTCCT
* *
72220 CATCCTTCAAGAGGCCCCTCCC
1 -ATCGTTCAAGAGG-CCCTCCT
72242 A-CGTTCAAGAGGCCCT
1 ATCGTTCAAGAGGCCCT
72258 GGTCCTCCCA
Statistics
Matches: 65, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
19 18 0.28
20 26 0.40
21 19 0.29
22 2 0.03
ACGTcount: A:0.24, C:0.35, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGTTCAAGAGGCCCTCCT
Found at i:73734 original size:75 final size:76
Alignment explanation
Indices: 73599--73740 Score: 216
Period size: 75 Copynumber: 1.9 Consensus size: 76
73589 GAAATGATGT
73599 ATTTGTAAAGTTGATTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTGATT
1 ATTTGTAAAGTTGATTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTGATT
73664 TGAAAAAGTTG
66 TGAAAAAGTTG
* * ***
73675 ATTTGTAAAG-TGATTTGTTTAATTGATGTGTAAAT-ATTCTTATTTTTTGCTTGTTTAATTGAT
1 ATTTGTAAAGTTGA-TTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTGAT
73738 TTG
65 TTG
73741 TAAAGTTAAT
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
75 31 0.52
76 29 0.48
ACGTcount: A:0.29, C:0.02, G:0.18, T:0.51
Consensus pattern (76 bp):
ATTTGTAAAGTTGATTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTGATT
TGAAAAAGTTG
Found at i:73867 original size:20 final size:19
Alignment explanation
Indices: 73812--73879 Score: 73
Period size: 20 Copynumber: 3.5 Consensus size: 19
73802 AAGGTACACT
*
73812 TTCGCAACGCGAAGTCAAA
1 TTCGCAACGCAAAGTCAAA
*** *
73831 TTCGCGTTGCGATAGTCAAA
1 TTCGCAACGC-AAAGTCAAA
73851 TTCGCAACGCAAAAGTCAAA
1 TTCGCAACGC-AAAGTCAAA
73871 TTCGCAACG
1 TTCGCAACG
73880 TGAAGCCAAA
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
19 7 0.18
20 31 0.82
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.21
Consensus pattern (19 bp):
TTCGCAACGCAAAGTCAAA
Found at i:73890 original size:39 final size:39
Alignment explanation
Indices: 73812--73914 Score: 91
Period size: 39 Copynumber: 2.6 Consensus size: 39
73802 AAGGTACACT
* *** *
73812 TTCGCAACGCGAAGTCAAATTCGCGTTGCGATAGTCAAA
1 TTCGCAACGCAAAGTCAAATTCGCAACGCGATAGCCAAA
*
73851 TTCGCAACGCAAAAGTCAAATTCGCAACGTGA-AGCCAAA
1 TTCGCAACGC-AAAGTCAAATTCGCAACGCGATAGCCAAA
* * * *
73890 TTTGTAATGCGAAAGTCAACTTCGC
1 TTCGCAACGC-AAAGTCAAATTCGC
73915 GTTGCGATTT
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
39 36 0.69
40 16 0.31
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.22
Consensus pattern (39 bp):
TTCGCAACGCAAAGTCAAATTCGCAACGCGATAGCCAAA
Found at i:74196 original size:17 final size:18
Alignment explanation
Indices: 74174--74207 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
74164 AAGCCGGTTG
*
74174 TGATTGGGA-TTTGATTT
1 TGATTGCGATTTTGATTT
74191 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
74208 CCTTTTGCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.18, C:0.03, G:0.26, T:0.53
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Done.