Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001072.1 Hibiscus syriacus cultivar Beakdansim tig00002122_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: 82625
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1099 original size:14 final size:14
Alignment explanation
Indices: 1082--1126 Score: 51
Period size: 11 Copynumber: 3.3 Consensus size: 14
1072 TACAAATATA
1082 ATAATACTCAAAAT
1 ATAATACTCAAAAT
1096 ATAATA--C-AAAT
1 ATAATACTCAAAAT
1107 ATAATACTCATAAAAT
1 ATAATACTC--AAAAT
1123 ATAA
1 ATAA
1127 AACAACACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
11 10 0.38
12 1 0.04
13 1 0.04
14 6 0.23
16 8 0.31
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.29
Consensus pattern (14 bp):
ATAATACTCAAAAT
Found at i:1116 original size:25 final size:26
Alignment explanation
Indices: 1082--1131 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
1072 TACAAATATA
*
1082 ATAATACTC-AAAATATAATACAAAT
1 ATAATACTCAAAAATATAAAACAAAT
1107 ATAATACTCATAAAATATAAAACAA
1 ATAATACTCA-AAAATATAAAACAA
1132 CACATAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 9 0.41
27 13 0.59
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.26
Consensus pattern (26 bp):
ATAATACTCAAAAATATAAAACAAAT
Found at i:16477 original size:29 final size:29
Alignment explanation
Indices: 16396--16483 Score: 74
Period size: 29 Copynumber: 3.0 Consensus size: 29
16386 ATAAGTTCTC
* *
16396 TTGATTATAGATA-TTATTTTATTAATTTTT
1 TTGATTATAGAAAGTTA-TTTAAT-ATTTTT
**
16426 TT-ATTATTA-AAAGTTATAAAATATTTTT
1 TTGATTA-TAGAAAGTTATTTAATATTTTT
* *
16454 TTGATTATAGAGAGTTATTTAATAATTTT
1 TTGATTATAGAAAGTTATTTAATATTTTT
16483 T
1 T
16484 AATTAAATGA
Statistics
Matches: 46, Mismatches: 8, Indels: 9
0.73 0.13 0.14
Matches are distributed among these distances:
28 10 0.22
29 29 0.63
30 7 0.15
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (29 bp):
TTGATTATAGAAAGTTATTTAATATTTTT
Found at i:17288 original size:39 final size:39
Alignment explanation
Indices: 17234--17314 Score: 153
Period size: 39 Copynumber: 2.1 Consensus size: 39
17224 GTTGTTCATG
*
17234 TTCGTTCAGTTAAAGTTAAATAACAAACATAAAGATACA
1 TTCGTTCAGTTAAAGTTAAATAACAAACATAAACATACA
17273 TTCGTTCAGTTAAAGTTAAATAACAAACATAAACATACA
1 TTCGTTCAGTTAAAGTTAAATAACAAACATAAACATACA
17312 TTC
1 TTC
17315 ATTTGTGTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.47, C:0.15, G:0.09, T:0.30
Consensus pattern (39 bp):
TTCGTTCAGTTAAAGTTAAATAACAAACATAAACATACA
Found at i:19532 original size:24 final size:23
Alignment explanation
Indices: 19495--19541 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
19485 TTTTCTCTTT
*
19495 ATATTTAATTTTATACTCTTAAA
1 ATATTTAAATTTATACTCTTAAA
*
19518 ATATTATAAATTTATATTCTTAAA
1 ATATT-TAAATTTATACTCTTAAA
19542 TTTTTAATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (23 bp):
ATATTTAAATTTATACTCTTAAA
Found at i:22347 original size:24 final size:24
Alignment explanation
Indices: 22310--22363 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
22300 AAAAGAACTG
* *
22310 AATAAATGAACTTATGATTGAGTC
1 AATAAACGAACTTATGATCGAGTC
*
22334 AATAAACGAGCTTATGATCGAGTC
1 AATAAACGAACTTATGATCGAGTC
22358 AATAAA
1 AATAAA
22364 TGAATTTGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.28
Consensus pattern (24 bp):
AATAAACGAACTTATGATCGAGTC
Found at i:22595 original size:19 final size:19
Alignment explanation
Indices: 22571--22612 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
22561 AACTTTATAT
22571 AAAATATAAAAA-CAAAATA
1 AAAATA-AAAAATCAAAATA
*
22590 AAAATAAAAAATCAACATA
1 AAAATAAAAAATCAAAATA
22609 AAAA
1 AAAA
22613 CAAGATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (19 bp):
AAAATAAAAAATCAAAATA
Found at i:28833 original size:21 final size:20
Alignment explanation
Indices: 28747--28904 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
28737 AAATGACCAA
**
28747 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
28766 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
28786 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
28806 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
28827 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
28848 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
28868 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
28889 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
28905 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:28933 original size:20 final size:20
Alignment explanation
Indices: 28871--29064 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
28861 CGATTTTCCA
* ** *
28871 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
28891 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
28911 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
28931 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
28951 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
28971 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
28991 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
29011 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
29031 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
29052 AAATCGCAACGCG
1 AAATCGCAACGCG
29065 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:28955 original size:60 final size:60
Alignment explanation
Indices: 28871--29064 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
28861 CGATTTTCCA
* ** * *
28871 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
28931 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
28991 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
29052 AAATCGCAACGCG
1 AAATCGCAACGCG
29065 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:29485 original size:33 final size:33
Alignment explanation
Indices: 29446--29516 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
29436 TTCACTTAGA
*
29446 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
29479 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
29512 TTTCA
1 TTTCA
29517 AGTTAATATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:29621 original size:21 final size:20
Alignment explanation
Indices: 29595--29702 Score: 86
Period size: 21 Copynumber: 5.7 Consensus size: 20
29585 TGCAGAAGAG
29595 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* ***
29616 TCGCAACGAGAGAATGATTG
1 TCGCAACGAGAAAATGAAAA
29636 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
*
29657 TCACAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
29671 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
*
29690 TCGCAACGCGAAA
1 TCGCAACGAGAAA
29703 CCAAAATCGC
Statistics
Matches: 69, Mismatches: 11, Indels: 15
0.73 0.12 0.16
Matches are distributed among these distances:
14 10 0.14
16 2 0.03
17 2 0.03
19 12 0.17
20 18 0.26
21 25 0.36
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:29652 original size:41 final size:41
Alignment explanation
Indices: 29594--29671 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
29584 TTGCAGAAGA
* *
29594 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGATT
1 GTCGCAACGAGAGAAATGAAAATCACAACGAGAGAATGATT
29635 GTCGCAACGAGAGAAATGAAAATCACAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAATCACAACGAGAGAAT
29672 CGCAACGCGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.46, C:0.15, G:0.24, T:0.14
Consensus pattern (41 bp):
GTCGCAACGAGAGAAATGAAAATCACAACGAGAGAATGATT
Found at i:29693 original size:19 final size:19
Alignment explanation
Indices: 29669--29713 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
29659 ACAACGAGAG
**
29669 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAACCAA
29688 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
29707 AATCGCA
1 AATCGCA
29714 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.47, C:0.27, G:0.18, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:29731 original size:19 final size:19
Alignment explanation
Indices: 29709--29814 Score: 106
Period size: 19 Copynumber: 6.1 Consensus size: 19
29699 GAAACCAAAA
*
29709 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
29728 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
29742 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
29761 TCGCGTTGCGA--TT-A--
1 TCGCGTTGCGATTTTCATT
* *
29775 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
29794 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
29813 TC
1 TC
29815 AACCAAAAGA
Statistics
Matches: 70, Mismatches: 7, Indels: 20
0.72 0.07 0.21
Matches are distributed among these distances:
14 20 0.29
16 5 0.07
17 6 0.09
19 39 0.56
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:29750 original size:14 final size:14
Alignment explanation
Indices: 29731--29787 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
29721 TTTCATTTCG
29731 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
29745 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
*
29764 CGTTGCGATTATCT
1 CGTTGCGATTCTCT
29778 CGTTGCGATT
1 CGTTGCGATT
29788 GTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 3 0.09
17 2 0.06
19 10 0.29
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:29756 original size:33 final size:33
Alignment explanation
Indices: 29714--29806 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
29704 CAAAATCGCA
*
29714 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTATCTCG
29747 TTGCGATTTTCATTTCGCGTTGCGATTATCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTATCTCG
*
29780 TTGCGATTGTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
29807 TTCATTTCAA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.11, C:0.22, G:0.23, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTATCTCG
Found at i:31669 original size:93 final size:93
Alignment explanation
Indices: 31510--32160 Score: 1249
Period size: 93 Copynumber: 7.1 Consensus size: 93
31500 TAGATTGCTT
*
31510 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
31575 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
31603 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
31668 -TTGTCTTTG-TTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
31694 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
31759 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
31787 AGTAAATTTGTTCGGTTGCTGCCAATTATGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
31852 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
31880 AGTAAA-TTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
31944 TTTGTCTTTG-TTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
31971 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
32036 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
32064 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
32129 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
32156 AGTAA
1 AGTAA
32161 TGCAATCCAT
Statistics
Matches: 551, Mismatches: 3, Indels: 9
0.98 0.01 0.02
Matches are distributed among these distances:
91 105 0.19
92 159 0.29
93 287 0.52
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:31821 original size:184 final size:186
Alignment explanation
Indices: 31510--32160 Score: 1249
Period size: 184 Copynumber: 3.5 Consensus size: 186
31500 TAGATTGCTT
*
31510 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
31575 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
31640 GTGTATTCTTTAACACTGTGAAATAGTA-TTGTCTTTG-TTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
31694 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
31759 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTATGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
31824 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
31880 AGTAAA-TTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
31944 TTTGTCTTTG-TTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
32008 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
32064 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
32129 TTTGTCTTTGTTTTGTCTTTTGGTTG-AAGTAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAA
32161 TGCAATCCAT
Statistics
Matches: 460, Mismatches: 3, Indels: 7
0.98 0.01 0.01
Matches are distributed among these distances:
184 271 0.59
185 151 0.33
186 38 0.08
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:32004 original size:277 final size:277
Alignment explanation
Indices: 31510--32160 Score: 1261
Period size: 277 Copynumber: 2.4 Consensus size: 277
31500 TAGATTGCTT
*
31510 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
31575 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
31640 GTGTATTCTTTAACACTGTGAAATAGTATTGTCTTTGTTTGTCTTTTGGTTGAAAGTAAATTTGT
131 GTGTATTCTTTAACACTGTGAAATAGTATTGTCTTTGTTTGTCTTTTGGTTGAAAGTAAATTTGT
31705 TCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGT
196 TCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGT
31770 TTTGTCTTTTGGTTGAA
261 TTTGTCTTTTGGTTGAA
*
31787 AGTAAATTTGTTCGGTTGCTGCCAATTATGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
31852 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAA-TTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
31916 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTGTCTTTTGGTTGAAAGTAAATTTG
131 GTGTATTCTTTAACACTGTGAAATAGTA-TTGTCTTTGTTTGTCTTTTGGTTGAAAGTAAATTTG
31981 TTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTG
195 TTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTG
32046 TTTTGTCTTTTGGTTGAA
260 TTTTGTCTTTTGGTTGAA
32064 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
32129 TTTGTCTTTGTTTTGTCTTTTGGTTG-AAGTAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAA
32161 TGCAATCCAT
Statistics
Matches: 370, Mismatches: 3, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
276 64 0.17
277 306 0.83
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (277 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTGTCTTTGTTTGTCTTTTGGTTGAAAGTAAATTTGT
TCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGT
TTTGTCTTTTGGTTGAA
Found at i:32248 original size:19 final size:19
Alignment explanation
Indices: 32208--32336 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
32198 TAGTTTACTT
* *
32208 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
32228 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
32247 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
32266 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
32280 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
32299 TCGCAA--CG--A-TAAAA
1 TCGCAACGCGAAACCAAAA
32313 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
32332 TCGCA
1 TCGCA
32337 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.47, C:0.28, G:0.16, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:32287 original size:33 final size:33
Alignment explanation
Indices: 32242--32336 Score: 154
Period size: 33 Copynumber: 2.9 Consensus size: 33
32232 AACGCGAAAC
**
32242 CAAAATCGCAACGCGAAATGAAAATCGCAACGA
1 CAAAATCGCAACGCGAAACCAAAATCGCAACGA
*
32275 CAGAATCGCAACGCGAAACCAAAATCGCAACGA
1 CAAAATCGCAACGCGAAACCAAAATCGCAACGA
*
32308 TAAAATCGCAACGCGAAACCAAAATCGCA
1 CAAAATCGCAACGCGAAACCAAAATCGCA
32337 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.27, G:0.17, T:0.08
Consensus pattern (33 bp):
CAAAATCGCAACGCGAAACCAAAATCGCAACGA
Found at i:32334 original size:52 final size:54
Alignment explanation
Indices: 32208--32336 Score: 146
Period size: 52 Copynumber: 2.4 Consensus size: 54
32198 TAGTTTACTT
*
32208 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAA
1 TCGCAAC-CGAAAC-CAAAATCGCAACGCGAAACCAAAATCGCAAC-CG-AATGAAAA
*
32266 TCGCAA-CG--A-CAGAATCGCAACGCGAAACCAAAATCGCAA-CG-AT-AAAA
1 TCGCAACCGAAACCAAAATCGCAACGCGAAACCAAAATCGCAACCGAATGAAAA
32313 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAAC-CGAAACCAAAATCGCA
32337 TTGCGATTTT
Statistics
Matches: 63, Mismatches: 3, Indels: 16
0.77 0.04 0.20
Matches are distributed among these distances:
47 10 0.16
48 2 0.03
49 2 0.03
50 2 0.03
51 1 0.02
52 37 0.59
54 1 0.02
56 2 0.03
58 6 0.10
ACGTcount: A:0.47, C:0.28, G:0.16, T:0.09
Consensus pattern (54 bp):
TCGCAACCGAAACCAAAATCGCAACGCGAAACCAAAATCGCAACCGAATGAAAA
Found at i:32354 original size:19 final size:19
Alignment explanation
Indices: 32332--32465 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
32322 GAAACCAAAA
*
32332 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
32351 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
32367 T--CGTTGCGA-TTTCATT
1 TCGCGTTGCGATTTTCATT
* *
32383 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
32399 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
32416 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
32435 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
32455 TCGTGTTGCGA
1 TCGCGTTGCGA
32466 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 19
0.77 0.08 0.15
Matches are distributed among these distances:
14 15 0.16
15 3 0.03
16 11 0.12
17 8 0.08
18 7 0.07
19 39 0.41
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:32373 original size:14 final size:14
Alignment explanation
Indices: 32354--32409 Score: 67
Period size: 14 Copynumber: 3.7 Consensus size: 14
32344 TTTCATTTCG
32354 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
32368 CGTTGCGATTTCATTT
1 CGTTGCGA-TTC-TTT
*
32384 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
32400 CGTTGCGATT
1 CGTTGCGATT
32410 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 16 0.43
15 3 0.08
16 9 0.24
17 3 0.08
18 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.45
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:32418 original size:33 final size:33
Alignment explanation
Indices: 32337--32428 Score: 159
Period size: 32 Copynumber: 2.8 Consensus size: 33
32327 CAAAATCGCA
*
32337 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
32370 TTGCGA-TTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
32402 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
32429 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.11, C:0.21, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:34404 original size:14 final size:14
Alignment explanation
Indices: 34385--34420 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
34375 ATTGTTTAAT
34385 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
34399 TGATTTGTATAAGT
1 TGATTTGTAAAAGA
34413 TGATTTGT
1 TGATTTGT
34421 GTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:34549 original size:19 final size:18
Alignment explanation
Indices: 34527--34623 Score: 112
Period size: 19 Copynumber: 5.4 Consensus size: 18
34517 AAAAATGACT
34527 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAAT-AAA
*
34546 ATCGCAATGCGAAATGAA
1 ATCGCAATGCGAAATAAA
*
34564 ATCGCAA--CGAGAT--A
1 ATCGCAATGCGAAATAAA
34578 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAAT-AAA
34597 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAAT-AAA
34617 ATCGCAA
1 ATCGCAA
34624 CGAGAGAATC
Statistics
Matches: 69, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
14 8 0.12
16 10 0.14
18 9 0.13
19 26 0.38
20 16 0.23
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (18 bp):
ATCGCAATGCGAAATAAA
Found at i:34603 original size:51 final size:53
Alignment explanation
Indices: 34527--34641 Score: 198
Period size: 51 Copynumber: 2.2 Consensus size: 53
34517 AAAAATGACT
*
34527 ATCGCAATGCGAAATAAAAATCGCAATGC-GAAATG-AAATCGCAACGAGATA
1 ATCGCAATGCGAAATAAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
*
34578 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATAAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
34631 ATCGCAATGCG
1 ATCGCAATGCG
34642 TTTATAATTT
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
51 28 0.47
52 6 0.10
53 26 0.43
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGAAATAAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:34694 original size:19 final size:19
Alignment explanation
Indices: 34670--34853 Score: 227
Period size: 19 Copynumber: 10.4 Consensus size: 19
34660 GATTCTCTCG
34670 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
34689 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
34708 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
34722 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
34741 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
34760 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
34779 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
34793 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
34813 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
*
34827 TTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
34846 TTGCGATT
1 TTGCGATT
34854 CTCTCGTTGC
Statistics
Matches: 143, Mismatches: 6, Indels: 32
0.79 0.03 0.18
Matches are distributed among these distances:
14 23 0.16
16 16 0.11
17 13 0.09
18 3 0.02
19 76 0.53
20 12 0.08
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:34705 original size:52 final size:52
Alignment explanation
Indices: 34648--34853 Score: 276
Period size: 52 Copynumber: 3.9 Consensus size: 52
34638 TGCGTTTATA
34648 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
34700 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* * * * *
34752 ATTTCGCATTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
* *
34804 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTCATTTCGCATTGCGATT
1 ATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTCATTTCGCATTGCGATT
34854 CTCTCGTTGC
Statistics
Matches: 135, Mismatches: 11, Indels: 15
0.84 0.07 0.09
Matches are distributed among these distances:
50 9 0.07
51 5 0.04
52 86 0.64
53 23 0.17
54 5 0.04
55 6 0.04
56 1 0.01
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:34748 original size:71 final size:72
Alignment explanation
Indices: 34670--34886 Score: 347
Period size: 71 Copynumber: 3.1 Consensus size: 72
34660 GATTCTCTCG
34670 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
34735 TT-CGCA
66 TTCCGCA
34741 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
34806 TTCCGCA
66 TTCCGCA
* * *
34813 TTGCGATTTTCA--T-G--TTGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTGTAAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
**
34873 TTCCGTG
66 TTCCGCA
34880 TTGCGAT
1 TTGCGAT
34887 AGTCAAATGC
Statistics
Matches: 140, Mismatches: 5, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
67 55 0.39
69 1 0.01
70 1 0.01
71 67 0.48
72 16 0.11
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (72 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
TTCCGCA
Found at i:34875 original size:33 final size:33
Alignment explanation
Indices: 34689--34867 Score: 261
Period size: 33 Copynumber: 5.2 Consensus size: 33
34679 TCATTTCGCA
34689 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
34722 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
34758 CATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
34793 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
34827 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
34860 TTGCGATT
1 TTGCGATT
34868 GTAATTTCCG
Statistics
Matches: 132, Mismatches: 6, Indels: 16
0.86 0.04 0.10
Matches are distributed among these distances:
32 1 0.01
33 62 0.47
34 29 0.22
35 8 0.06
36 7 0.05
38 25 0.19
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:37094 original size:12 final size:12
Alignment explanation
Indices: 37077--37101 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
37067 TCTTCGGTGA
37077 CTTTTTCTTCTT
1 CTTTTTCTTCTT
37089 CTTTTTCTTCTT
1 CTTTTTCTTCTT
37101 C
1 C
37102 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:38030 original size:20 final size:20
Alignment explanation
Indices: 38002--38231 Score: 228
Period size: 20 Copynumber: 11.5 Consensus size: 20
37992 AAATTTCAGT
* * *
38002 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
38022 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
38042 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
38062 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
38082 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
38102 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
38122 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
38142 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
38162 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
38182 GTTACGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
38202 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
38222 GTTGCGATTT
1 GTTGCGATTT
38232 TGGAAAATCG
Statistics
Matches: 180, Mismatches: 28, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
20 179 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:38248 original size:21 final size:21
Alignment explanation
Indices: 38218--38300 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
38208 ATTTTCATAT
*
38218 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
38239 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
38260 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
38281 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
38301 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:38291 original size:42 final size:43
Alignment explanation
Indices: 38198--38296 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
38188 ATTTATGTGT
* *
38198 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
38239 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
38281 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
38297 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:43412 original size:22 final size:23
Alignment explanation
Indices: 43378--43422 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
43368 AATTAATTTT
* *
43378 ATTTTAGAGAATAAGTTTTTAAA
1 ATTTTAGAGAATAAATTTGTAAA
43401 ATTTTA-AGAATAAATTTGTAAA
1 ATTTTAGAGAATAAATTTGTAAA
43423 GCTTTCAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (23 bp):
ATTTTAGAGAATAAATTTGTAAA
Found at i:47331 original size:30 final size:30
Alignment explanation
Indices: 47290--47346 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
47280 TGCTCAATGG
*
47290 AGATGCAATCCTTCGTCAACCCCTTAATCA
1 AGATGCAATCCTCCGTCAACCCCTTAATCA
*
47320 AGATTCAATCCTCCGTCAACCCCTTAA
1 AGATGCAATCCTCCGTCAACCCCTTAA
47347 GCCATTAACC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.30, C:0.35, G:0.09, T:0.26
Consensus pattern (30 bp):
AGATGCAATCCTCCGTCAACCCCTTAATCA
Found at i:48755 original size:392 final size:390
Alignment explanation
Indices: 48005--48788 Score: 1415
Period size: 392 Copynumber: 2.0 Consensus size: 390
47995 TTTTTACACA
* *
48005 AATAGAAATAACTAGTTTTATTATAAAAAATAAAATATTTAAAATTAATTACAATAAATTTTTAC
1 AATAGAAATAACCAGTTTTATTATAAAAAATAAAATATTTAAAATTAATTACAATAAAATTTTAC
*
48070 AATTATAATCGTGAATTAGACATATAATTAAGACATTTTCTTATAATCATTACAAAACAATTACC
66 AATTATAATCGTGAATTAGACACATAATTAAGACATTTTCTTATAATCATTACAAAACAATTACC
48135 TCTTTGATCAATAAATGATTATACAAGGAAAAGGCTACAAAGACGTCCAAAAAATTCGAACAAAA
131 TCTTTGATCAATAAATGATTATACAAGGAAAAGGCTACAAAGACGTCCAAAAAATTCGAACAAAA
* * * *
48200 ATATATATACGAACAAATCTGATTACATTTGAAAATGAACCACACATAGATGAAACAATTGAAAG
196 ATATATATACGAAAAAATCTAATTACATTTAAAAATGAACCACACAGAGATGAAACAATTGAAAG
* *
48265 ACTACTGACAATCGCAAATCAGAGTCGAACAATGTGAAACAATTATCTCCGAATACAAATCGCGT
261 ACTACTGACAATCGCAAATCAGAGTCGAACAACGTAAAACAATTATCTCCGAATACAAATCGCGT
* *
48330 ATCTAAATCTAATCCGAGAGTCTAAAGCAAAGAAGATCTACAGGATAACAAATAAGCGTCATCCG
326 ATCTAAATCTAACCCGAGAGTCTAAAACAAAGAAGATCTACAGGATAACAAATAAGCGTCATCCG
48395 AATAGAAATAACCAGTTTTATTATAAAAAAAATAAAATATTTAAAATTAATTACAATAAAATTTT
1 AATAGAAATAACCAGTTTTATTAT--AAAAAATAAAATATTTAAAATTAATTACAATAAAATTTT
48460 ACAATTATAATCGTGAATTAGACACATAATTAAGACATTTTCTTATAATCATTACAAAACAATTA
64 ACAATTATAATCGTGAATTAGACACATAATTAAGACATTTTCTTATAATCATTACAAAACAATTA
48525 CCTCTTTGATCAATAAATGATTATACAAGGAAAAGGCTACAAAGACGTCCAAAAAATTCGAACAA
129 CCTCTTTGATCAATAAATGATTATACAAGGAAAAGGCTACAAAGACGTCCAAAAAATTCGAACAA
48590 AAATATATATACGAAAAAATCTAATTACATTTAAAAATGAACCACACAGAGATGAAACAATTGAA
194 AAATATATATACGAAAAAATCTAATTACATTTAAAAATGAACCACACAGAGATGAAACAATTGAA
* *
48655 AGACTATTGACAATCGCAAATCAGAGTCGAACAACGTAAAACAATTATCTCCGAATACAAATTGC
259 AGACTACTGACAATCGCAAATCAGAGTCGAACAACGTAAAACAATTATCTCCGAATACAAATCGC
* *
48720 GTATCTAAATCTAACCCGAGAGTCTAAAACAAAGAAGATCTACAGGATTACAAATAAGCGTCGTC
324 GTATCTAAATCTAACCCGAGAGTCTAAAACAAAGAAGATCTACAGGATAACAAATAAGCGTCATC
48785 CG
389 CG
48787 AA
1 AA
48789 CATAAATCCC
Statistics
Matches: 377, Mismatches: 15, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
390 23 0.06
392 354 0.94
ACGTcount: A:0.47, C:0.15, G:0.11, T:0.26
Consensus pattern (390 bp):
AATAGAAATAACCAGTTTTATTATAAAAAATAAAATATTTAAAATTAATTACAATAAAATTTTAC
AATTATAATCGTGAATTAGACACATAATTAAGACATTTTCTTATAATCATTACAAAACAATTACC
TCTTTGATCAATAAATGATTATACAAGGAAAAGGCTACAAAGACGTCCAAAAAATTCGAACAAAA
ATATATATACGAAAAAATCTAATTACATTTAAAAATGAACCACACAGAGATGAAACAATTGAAAG
ACTACTGACAATCGCAAATCAGAGTCGAACAACGTAAAACAATTATCTCCGAATACAAATCGCGT
ATCTAAATCTAACCCGAGAGTCTAAAACAAAGAAGATCTACAGGATAACAAATAAGCGTCATCCG
Found at i:51582 original size:35 final size:37
Alignment explanation
Indices: 51536--51611 Score: 129
Period size: 35 Copynumber: 2.1 Consensus size: 37
51526 AACAGACAAG
51536 AAAGTAAAACGAGATCAACG-AAAAAAAATCACACA-
1 AAAGTAAAACGAGATCAACGTAAAAAAAATCACACAC
*
51571 AAAGTAAAACGAGATCAACGTAAAAAAAATCATACAC
1 AAAGTAAAACGAGATCAACGTAAAAAAAATCACACAC
51608 AAAG
1 AAAG
51612 AGACGATATT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
35 20 0.53
36 14 0.37
37 4 0.11
ACGTcount: A:0.62, C:0.16, G:0.12, T:0.11
Consensus pattern (37 bp):
AAAGTAAAACGAGATCAACGTAAAAAAAATCACACAC
Found at i:54968 original size:17 final size:17
Alignment explanation
Indices: 54946--54979 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
54936 TGACTACAAG
54946 ATAATATTTATTAATTA
1 ATAATATTTATTAATTA
*
54963 ATAATATTTTTTAATTA
1 ATAATATTTATTAATTA
54980 TTGACAATGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATAATATTTATTAATTA
Found at i:55982 original size:17 final size:16
Alignment explanation
Indices: 55958--55999 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
55948 AAATTTTAAA
55958 ACATAAAAATAA-ATT
1 ACATAAAAATAACATT
55973 ATCAATAAAAA-AACATT
1 A-C-ATAAAAATAACATT
55990 ACATAAAAAT
1 ACATAAAAAT
56000 TTAAAAAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
15 8 0.35
16 4 0.17
17 11 0.48
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.24
Consensus pattern (16 bp):
ACATAAAAATAACATT
Found at i:58136 original size:19 final size:19
Alignment explanation
Indices: 58097--58151 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 19
58087 ATTCATAAGA
* *
58097 TATAAACATTTTTAT-TTT
1 TATAAAAATATTTATATTT
58115 TATAAAAATATTTATATTT
1 TATAAAAATATTTATATTT
*
58134 TAT-GAAATA-TTATATTT
1 TATAAAAATATTTATATTT
58151 T
1 T
58152 TATATATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
17 9 0.27
18 18 0.55
19 6 0.18
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (19 bp):
TATAAAAATATTTATATTT
Found at i:61047 original size:60 final size:61
Alignment explanation
Indices: 60925--61063 Score: 147
Period size: 60 Copynumber: 2.3 Consensus size: 61
60915 GAGAAAATGA
* * * ***
60925 ATAGTCGAGTGACCATTTTTGTAACTTTTAATAATCAGAGGACCCAACAAAGCAGTGCCCT
1 ATAGTCGAGAGACCATTTTTGTAACTTTTAATAATAAGAGGACCCAACAAAACAACACCCT
* * *
60986 ATAGTCGGGAGACCA-TTTTGTAACTTTTAATAATTAAG-GGACTCAACAAAACAACATCCT
1 ATAGTCGAGAGACCATTTTTGTAACTTTTAATAA-TAAGAGGACCCAACAAAACAACACCCT
* * *
61046 ATAATTGAGTGACCATTT
1 ATAGTCGAGAGACCATTT
61064 ATGTCCTTTA
Statistics
Matches: 63, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
60 45 0.71
61 18 0.29
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (61 bp):
ATAGTCGAGAGACCATTTTTGTAACTTTTAATAATAAGAGGACCCAACAAAACAACACCCT
Found at i:68011 original size:59 final size:59
Alignment explanation
Indices: 67939--68056 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
67929 TCATTAAACG
67939 ATTTTACTAGTAAAAGAGAGTGTTGTTCTTTTTAAGGTTATGGGTTCTAGCATCTGCGT
1 ATTTTACTAGTAAAAGAGAGTGTTGTTCTTTTTAAGGTTATGGGTTCTAGCATCTGCGT
67998 ATTTTACTAGTAAAAGAGAGTGTTGTTCTTTTTAAGGTTATGGGTTCTAGCATCTGCGT
1 ATTTTACTAGTAAAAGAGAGTGTTGTTCTTTTTAAGGTTATGGGTTCTAGCATCTGCGT
68057 CTGTGGAGTG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.24, C:0.10, G:0.24, T:0.42
Consensus pattern (59 bp):
ATTTTACTAGTAAAAGAGAGTGTTGTTCTTTTTAAGGTTATGGGTTCTAGCATCTGCGT
Found at i:74988 original size:64 final size:63
Alignment explanation
Indices: 74915--75075 Score: 184
Period size: 64 Copynumber: 2.5 Consensus size: 63
74905 TAATGAAGGT
* **
74915 ATGCATCGATGCACTACTTGTGCATCGGTGCA-TAAAATGCATTCGAT-GTTTTATTATTAATGG
1 ATGCATCGATGCACTACTTGTGCATCGATGCACT-AAATGCATTCGATCGTTTTATT-TTAA-AA
74978 G
63 G
* * * *
74979 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATCTTTTTATTTTAAAAG
1 ATGCATCGATGCACT-ACTTGTGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAG
*
75042 AGTGCATCGATGCACTACCTGTGCATCGATGCAC
1 A-TGCATCGATGCACTACTTGTGCATCGATGCAC
75076 CTTCAAACAA
Statistics
Matches: 82, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
63 3 0.04
64 70 0.85
65 9 0.11
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAG
Found at i:78851 original size:18 final size:17
Alignment explanation
Indices: 78823--78856 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
78813 TATACTTAAA
78823 TTAATTTGATTAAAATT
1 TTAATTTGATTAAAATT
*
78840 TTAATCTTGATTTAAAT
1 TTAAT-TTGATTAAAAT
78857 CATACGAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (17 bp):
TTAATTTGATTAAAATT
Found at i:81764 original size:7 final size:7
Alignment explanation
Indices: 81754--81787 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
81744 TTATCTCATT
81754 CCTAAAC
1 CCTAAAC
81761 CCTAAAC
1 CCTAAAC
81768 CCTAAAC
1 CCTAAAC
81775 CCTAAAC
1 CCTAAAC
*
81782 ACTAAA
1 CCTAAA
81788 ACACTAATCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.47, C:0.38, G:0.00, T:0.15
Consensus pattern (7 bp):
CCTAAAC
Done.