Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002287.1 Hibiscus syriacus cultivar Beakdansim tig00004652_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: 74101
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:1484 original size:195 final size:195
Alignment explanation
Indices: 1116--1785 Score: 822
Period size: 195 Copynumber: 3.4 Consensus size: 195
1106 CTACCTAAAT
* * *
1116 AGTGTCGATACATTTATAAAAAGTAGCGATCCCAAAAATATCGAAACCCATAATTATAATGTAAT
1 AGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAAT
* * * * * *
1181 AGGTAAATTTACAATGTAACCAATA-TAATTTACCGGTTTATGAGAAAATAGGTCTAC--AATGT
66 ATGTAAATTTACAATGTAACCAGTAGAAATTTACTGTTTTATGAAAAAATAGGTCTACATAATGT
* *
1243 ATCGACACTTGTGGAACTTGTGTCGATACTTGTTGTTCATAATGAATGCCCAAAAGGTGCACGCA
131 ATCGACACTTGTGG-ACTTGTGTCGATACTT-TT-TCCAGAATGAATGCCCAAAAGGTGCACGCA
1308 TAA
193 TAA
*
1311 AGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATTGAAACTC-ATAATTATAATGTAA
1 AGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAAC-CGATAATTATAATGTAA
*
1375 TATGTAAATTTACAATGTAACCTGTAGAAATTTACATGTTTTATGAAAAAATAGGTCTACATAAT
65 TATGTAAATTTACAATGTAACCAGTAGAAATTTAC-TGTTTTATGAAAAAATAGGTCTACATAAT
* *
1440 GTATCGACACTTGTGGACTTGTGTCGATAC-TTTTCCAGAATGAATG-TCAAACGGGGTGCACGC
129 GTATCGACACTTGTGGACTTGTGTCGATACTTTTTCCAGAATGAATGCCCAAA--AGGTGCACGC
1503 AT-A
192 ATAA
* * *
1506 AGTGTCGATACATTTATTAAAAGTATCCATCCCAAAAACATCGAAACCGATAATTACAATGTAAT
1 AGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAAT
* ** * *
1571 ATGTAAATTTACAATGT-ACCCGATAGAAAGATACTGGTTTTATGATAAAATAGTTCTACATAAT
66 ATGTAAATTTACAATGTAACCAG-TAGAAATTTACT-GTTTTATGAAAAAATAGGTCTACATAAT
* ** * * * *
1635 GTATCGACACTTTTTAAGTTTGTGCCGATACTTTTTTTCCAGAATGAATGCCCAACGAGGTGCAT
129 GTATCGACACTTGTGGA-CTTGTGTCGATAC--TTTTTCCAGAATGAATGCCCAA-AAGGTGCAC
1700 GCATAA
190 GCATAA
** * *
1706 AGTGTCGATACATTTA-AAATTGTATTGATCCC-AAAATATCGAAACCGATAATTATAATGTAAT
1 AGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAAT
*
1769 A-GATAAATTTGCAATGT
66 ATG-TAAATTTACAATGT
1786 TACCGGTATA
Statistics
Matches: 417, Mismatches: 40, Indels: 33
0.85 0.08 0.07
Matches are distributed among these distances:
194 10 0.02
195 219 0.53
196 32 0.08
197 23 0.06
198 57 0.14
199 56 0.13
200 20 0.05
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (195 bp):
AGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAAT
ATGTAAATTTACAATGTAACCAGTAGAAATTTACTGTTTTATGAAAAAATAGGTCTACATAATGT
ATCGACACTTGTGGACTTGTGTCGATACTTTTTCCAGAATGAATGCCCAAAAGGTGCACGCATAA
Found at i:18983 original size:3 final size:3
Alignment explanation
Indices: 18975--19015 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
18965 CTTTCTTTCT
18975 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
19016 ATGTCCCTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:24937 original size:35 final size:35
Alignment explanation
Indices: 24873--24972 Score: 110
Period size: 35 Copynumber: 2.7 Consensus size: 35
24863 TTTCGTCCTA
* *
24873 CTAGGATTCAAACTCTCAAAAATAAGATAGAATTCTG
1 CTAGGATTC-AACTC-CTAAAATAGGATAGAATTCTG
*
24910 CTAGGATTCAACTCCTAAAATAGGATAGAATTTTG
1 CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
** *
24945 CTATGTTTTAAACTCCTAAAGATAGGAT
1 CTA-GGATTCAACTCCTAAA-ATAGGAT
24973 CCACAAGCAC
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
35 21 0.38
36 18 0.33
37 16 0.29
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (35 bp):
CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
Found at i:25556 original size:17 final size:16
Alignment explanation
Indices: 25524--25557 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
25514 TTTACTCATT
*
25524 TATTTATCTATTTTTA
1 TATTTATCTATATTTA
25540 TATTTATCCTATATTTA
1 TATTTAT-CTATATTTA
25557 T
1 T
25558 GTTTTTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTTATCTATATTTA
Found at i:27696 original size:18 final size:18
Alignment explanation
Indices: 27673--27712 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
27663 TTCCTTCAAG
27673 TCTGGATTCACATCCACT
1 TCTGGATTCACATCCACT
27691 TCTGGATTCACATCCACT
1 TCTGGATTCACATCCACT
27709 TCTG
1 TCTG
27713 AAAGACTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.20, C:0.33, G:0.12, T:0.35
Consensus pattern (18 bp):
TCTGGATTCACATCCACT
Found at i:29460 original size:8 final size:8
Alignment explanation
Indices: 29449--29492 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
29439 CAAAAAAGGC
29449 AAAAAGAA
1 AAAAAGAA
29457 AAAAAG-A
1 AAAAAGAA
29464 AAAAAGAA
1 AAAAAGAA
* *
29472 AAGAAGCA
1 AAAAAGAA
*
29480 AAAAAGGA
1 AAAAAGAA
29488 AAAAA
1 AAAAA
29493 CAAGAACAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
7 7 0.23
8 24 0.77
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:29460 original size:15 final size:14
Alignment explanation
Indices: 29440--29506 Score: 55
Period size: 16 Copynumber: 4.5 Consensus size: 14
29430 CAATCAGAAC
29440 AAAAAAGGCAAAAAG
1 AAAAAA-GCAAAAAG
*
29455 AAAAAAAGAAAAAAG
1 -AAAAAAGCAAAAAG
29470 AAAAGAAGCAAAAAAGG
1 AAAA-AAGC-AAAAA-G
* *
29487 AAAAAA-CAAGAAC
1 AAAAAAGCAAAAAG
29500 AAAAAAG
1 AAAAAAG
29507 AAAGAACAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
13 6 0.14
14 8 0.19
15 11 0.26
16 13 0.30
17 5 0.12
ACGTcount: A:0.78, C:0.06, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAAAGCAAAAAG
Found at i:29461 original size:16 final size:15
Alignment explanation
Indices: 29440--29505 Score: 62
Period size: 15 Copynumber: 4.4 Consensus size: 15
29430 CAATCAGAAC
*
29440 AAAAAAGGCAAAAAG
1 AAAAAAAGCAAAAAG
*
29455 AAAAAAAGAAAAAAG
1 AAAAAAAGCAAAAAG
*
29470 AAAAGAAGCAAAAAAG
1 AAAAAAAGC-AAAAAG
* * *
29486 GAAAAAA-CAAGAAC
1 AAAAAAAGCAAAAAG
29500 AAAAAA
1 AAAAAA
29506 GAAAGAACAA
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
14 9 0.22
15 21 0.51
16 11 0.27
ACGTcount: A:0.79, C:0.06, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAAAAAGCAAAAAG
Found at i:30163 original size:22 final size:22
Alignment explanation
Indices: 30136--30184 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
30126 CCATCAATCT
30136 TTTGAGCATCAAATACCAAACC
1 TTTGAGCATCAAATACCAAACC
*
30158 TTTGAGCATCAAATGCCAAACC
1 TTTGAGCATCAAATACCAAACC
30180 TTTGA
1 TTTGA
30185 CCAAACACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (22 bp):
TTTGAGCATCAAATACCAAACC
Found at i:30604 original size:18 final size:18
Alignment explanation
Indices: 30581--30616 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
30571 TCAACATCAA
*
30581 ATATTGGGGCATTTTTGG
1 ATATTGGGGCATCTTTGG
30599 ATATTGGGGCATCTTTGG
1 ATATTGGGGCATCTTTGG
30617 GGATTCAACA
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:0.17, C:0.08, G:0.33, T:0.42
Consensus pattern (18 bp):
ATATTGGGGCATCTTTGG
Found at i:31148 original size:36 final size:36
Alignment explanation
Indices: 31098--31343 Score: 217
Period size: 36 Copynumber: 7.0 Consensus size: 36
31088 ACTAGAAGAG
31098 TTTTGTCCCTCTTGAGACAATTTCCCTTGAAACAAA
1 TTTTGTCCCTCTTGAGACAATTTCCCTTGAAACAAA
* * *
31134 TTTTGTCTCC-CTTGAGATAGTTTCTCTTGAAACATAA
1 TTTTGTC-CCTCTTGAGACAATTTCCCTTGAAACA-AA
* * * *
31171 -------AC-ATTGA-AAACATTTCCCTTGAAATAAA
1 TTTTGTCCCTCTTGAGACA-ATTTCCCTTGAAACAAA
* *
31199 TTTTCGTCTCTCTTGAGATAATTTCCCTTGAAACAAAA
1 TTTT-GTCCCTCTTGAGACAATTTCCCTTGAAAC-AAA
* * *
31237 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAA
1 TTTTGTCCCTCTTGAGACAATTTCCCTTGAAACAAA
* * *
31273 TTTTGTCTCTCTTGAGACATTTTCCCTTGAAATAAA
1 TTTTGTCCCTCTTGAGACAATTTCCCTTGAAACAAA
* *
31309 TTTTGTCTCTCTTGAGACAGTTTCCCTT-AAACAAA
1 TTTTGTCCCTCTTGAGACAATTTCCCTTGAAACAAA
31344 ATATTTAAAT
Statistics
Matches: 177, Mismatches: 19, Indels: 29
0.79 0.08 0.13
Matches are distributed among these distances:
28 4 0.02
29 17 0.10
35 6 0.03
36 94 0.53
37 47 0.27
38 9 0.05
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.39
Consensus pattern (36 bp):
TTTTGTCCCTCTTGAGACAATTTCCCTTGAAACAAA
Found at i:31245 original size:37 final size:36
Alignment explanation
Indices: 31182--31336 Score: 247
Period size: 36 Copynumber: 4.2 Consensus size: 36
31172 CATTGAAAAC
*
31182 ATTTCCCTTGAAATAAATTTTCGTCTCTCTTGAGATA
1 ATTTCCCTTGAAATAAATTTT-GTCTCTCTTGAGACA
*
31219 ATTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACA
1 ATTTCCCTTGAAA-TAAATTTTGTCTCTCTTGAGACA
*
31256 GTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACA
1 ATTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACA
*
31292 TTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACA
1 ATTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACA
*
31328 GTTTCCCTT
1 ATTTCCCTT
31337 AAACAAAATA
Statistics
Matches: 111, Mismatches: 6, Indels: 3
0.93 0.05 0.03
Matches are distributed among these distances:
36 65 0.59
37 39 0.35
38 7 0.06
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.43
Consensus pattern (36 bp):
ATTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACA
Found at i:31449 original size:173 final size:175
Alignment explanation
Indices: 31098--31479 Score: 482
Period size: 173 Copynumber: 2.2 Consensus size: 175
31088 ACTAGAAGAG
* * *
31098 TTTTGTCCCTCTTGAGACAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATAGTTTCTCTTG
1 TTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTG
* * * *
31163 AAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTCGTCTCTCTTGAGATAATTTCCCTT
66 AAACATAAACATTGAAAACATTTCCCTTGAAACAAATTTTCGTCCCCCTTGAGACAATTTCCCTT
*
31228 GAAACAAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAA
131 GAAACAAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * *
31273 TTTTGTCTCTCTTGAGACATTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTT-
1 TTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTG
* * ** * * * **
31337 AAACA-AAATATTTAAATATGTTTTCTTTGAAACAAA-TTTCGTCCCCCTTGAGACAGTTTCTTT
66 AAACATAAACATTGAAA-ACATTTCCCTTGAAACAAATTTTCGTCCCCCTTGAGACAATTTCCCT
* * * *
31400 TGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
130 TGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * * *
31446 TTTTGTCTCCCTTGAGACAGTTACTCTTGAAACA
1 TTTTGTCTCTCTTGAGACAATTTCCCTTGAAACA
31480 CAAAATCTTC
Statistics
Matches: 177, Mismatches: 29, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
173 100 0.56
174 19 0.11
175 58 0.33
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (175 bp):
TTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTG
AAACATAAACATTGAAAACATTTCCCTTGAAACAAATTTTCGTCCCCCTTGAGACAATTTCCCTT
GAAACAAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:31460 original size:36 final size:36
Alignment explanation
Indices: 31358--31479 Score: 165
Period size: 36 Copynumber: 3.4 Consensus size: 36
31348 TTAAATATGT
* *
31358 TTTCT-TTGAAACAAATTTCGTCCCCCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAG
* * * *
31393 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAAC-AAATTTTGTCTCCCTTGAGACAG
31430 TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAG
*
31466 TTACTCTTGAAACA
1 TTTCTCTTGAAACA
31480 CAAAATCTTC
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
35 5 0.07
36 40 0.53
37 30 0.40
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAG
Found at i:32383 original size:105 final size:104
Alignment explanation
Indices: 32151--33544 Score: 1393
Period size: 105 Copynumber: 13.3 Consensus size: 104
32141 GCCATCCGCG
* * *
32151 ATTTCAACTCCAC-GACGGAGGATATTGTGGCACTCGAGACAACGCAAGTTCAACTTCACAACGA
1 ATTTCAACTTCACAG-CGAAGGATA-T-TGG-ACTCGAGACAACACAAGTTCAACTTCAC-ACGA
* *
32215 AGGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
61 AGGGACGGCTGCTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
* * *
32260 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCAC-ACGAAGGG
* *
32325 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
65 ACGGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* **
32365 ATTTCAACTTCACAACGAAGGATATTGGACTTC-AGACAATGCAAGTTCAACTTCACGACGAAGG
1 ATTTCAACTTCACAGCGAAGGATATTGGAC-TCGAGACAACACAAGTTCAACTTCAC-ACGAAGG
* *
32429 GACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
64 GACGGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* * **
32470 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCAC-ACGAAGGG
* *
32535 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
65 ACGGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* *
32575 ATTTCAACTTCACAGCGAATGATATTGAACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCAC-ACGAAGGG
* * * * * *
32640 ACGGCTGGTTGTCAATAATAATTTCCCAGTTTCAGGGCCA
65 ACGGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* * * * *
32680 ATTTCAACTTCACAGTGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCACAGCGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACA-CGAAGGG
* * * *
32745 GCGGCTGAC-TGT---CGACAA----GCAATTTCGGAGCCA
65 ACGGCTG-CTTGTCAACAACAACTTCCCAATTTCAGAGCCA
*
32778 ATCTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAGCGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACA-CGAAGGG
* * * *
32843 ACGGCTGATTGTCAACAAACAATTTCCCAGTTTCAGGGCCA
65 ACGGCTGCTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
* * * *
32884 ATTTCAACTTCACAGCGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCACAGCGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACA-CGAAGGG
* * * *
32949 GCGGCTGAC-TGT---CGACAA----GCAATTTCGGAGCCA
65 ACGGCTG-CTTGTCAACAACAACTTCCCAATTTCAGAGCCA
*
32982 ATCTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAGCGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACA-CGAAGGG
* * * *
33047 ACGGCTGGTTGTCAACAAACAATTTCCCAATTCCAGAGCCG
65 ACGGCTGCTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
* * * *
33088 ATTTCAACTCCAC-GACGGAGGATATCGTGCTACCCGAGACAACACAAGTTCAACTTCACAACGA
1 ATTTCAACTTCACAG-CGAAGGATAT--TG-GACTCGAGACAACACAAGTTCAACTTCAC-ACGA
* * ** * ** *
33152 AGGGACGGCTGGTTGTCAACGAATAACTTTTCAGTTTCA-TCCGCG
61 AGGGACGGCTGCTTGTCAAC-AACAACTTCCCAATTTCAGAGC-CA
* * * *
33197 ATTTCAACTCCAC-GACGGAGGATATCGTGCCACTCGATACAACACAAGTTCAACTTCACAACGA
1 ATTTCAACTTCACAG-CGAAGGATAT--TG-GACTCGAGACAACACAAGTTCAACTTCAC-ACGA
* ** * *
33261 AGGGACGGCTGGTTGTCAACAAACATTTTTCAAATTTCAGAGCCA
61 AGGGACGGCTGCTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
**
33306 ATTTCAACTTCGTAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCAC-ACGAAGGG
* * * * *
33371 ACGGCTGATTGTCAACAA-GA-TT-TC--GTTCAGAGTCA
65 ACGGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* * * * * *
33406 ATTTCATCTTCACAGCGAAGGATATTAGACTCGAGATAGCACAAGCTCAACTTCACAGCAAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACA-CGAAGGG
* * * * * *
33471 GCGACTGAC-TGTCAACAAACAATTTCCCAGTTCCAGAACCA
65 ACGGCTG-CTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
* *
33512 ATTTCAACTTCACATCGGAGGATATTGGACTCG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCG
33545 GAACAATATT
Statistics
Matches: 1106, Mismatches: 139, Indels: 83
0.83 0.10 0.06
Matches are distributed among these distances:
98 159 0.14
99 1 0.00
100 76 0.07
101 4 0.00
102 16 0.01
103 5 0.00
104 4 0.00
105 383 0.35
106 249 0.23
107 5 0.00
108 4 0.00
109 197 0.18
110 3 0.00
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.22
Consensus pattern (104 bp):
ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACACGAAGGGA
CGGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
Found at i:34064 original size:35 final size:37
Alignment explanation
Indices: 34009--34079 Score: 110
Period size: 35 Copynumber: 2.0 Consensus size: 37
33999 GTCCTACTAA
34009 GATTCAAACTCTCAAAAATAGGATAGAATTCTGCTAG
1 GATTCAAACTCTCAAAAATAGGATAGAATTCTGCTAG
* *
34046 GATTC-AACTC-CTAAAATAGGATAGAATTTTGCTA
1 GATTCAAACTCTCAAAAATAGGATAGAATTCTGCTA
34080 TGTTTTAAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 22 0.69
36 5 0.16
37 5 0.16
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.30
Consensus pattern (37 bp):
GATTCAAACTCTCAAAAATAGGATAGAATTCTGCTAG
Found at i:34672 original size:21 final size:19
Alignment explanation
Indices: 34648--34688 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
34638 GCTTTTACTT
34648 TTTATATATTTTACTCATTTA
1 TTTATATATTTTA-T-ATTTA
*
34669 TTTATCTATTTTATATTTA
1 TTTATATATTTTATATTTA
34688 T
1 T
34689 CCTATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 1 0.05
21 12 0.63
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTATATATTTTATATTTA
Found at i:38141 original size:20 final size:19
Alignment explanation
Indices: 38116--38181 Score: 60
Period size: 21 Copynumber: 3.2 Consensus size: 19
38106 AAAGTATTAT
38116 TTAAAATATTATTTTTTTA
1 TTAAAATATTATTTTTTTA
* *
38135 TTGAAAATGTTAATTTTGTTA
1 TT-AAAATATT-ATTTTTTTA
*
38156 CTTAAAATAAATATTTTTTATA
1 -TTAAAAT-ATTATTTTTT-TA
38178 TTAA
1 TTAA
38182 TATTTTCGGT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
19 2 0.05
20 7 0.19
21 23 0.62
22 5 0.14
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (19 bp):
TTAAAATATTATTTTTTTA
Found at i:40738 original size:45 final size:47
Alignment explanation
Indices: 40671--40761 Score: 159
Period size: 47 Copynumber: 2.0 Consensus size: 47
40661 GCAATTCGTG
*
40671 TGTATGTGTCTGTTCTT-TTTTTTTC-TTTCTAAGTATGCATTTATT
1 TGTATGTGTCTGTTCTTGTTTTTTTCTTTTCTAAGTATGCAGTTATT
40716 TGTATGTGTCTGTTCTTGTTTTTTTCTTTTCTAAGTATGCAGTTAT
1 TGTATGTGTCTGTTCTTGTTTTTTTCTTTTCTAAGTATGCAGTTAT
40762 AATCATCGTG
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
45 17 0.40
46 8 0.19
47 18 0.42
ACGTcount: A:0.13, C:0.11, G:0.15, T:0.60
Consensus pattern (47 bp):
TGTATGTGTCTGTTCTTGTTTTTTTCTTTTCTAAGTATGCAGTTATT
Found at i:43605 original size:16 final size:16
Alignment explanation
Indices: 43584--43625 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
43574 CTTTGTTATT
43584 TATTATATTTTCAAAA
1 TATTATATTTTCAAAA
* * *
43600 TATTATGTATTCATAA
1 TATTATATTTTCAAAA
43616 TA-TATATTTT
1 TATTATATTTT
43626 ATTAACTTTT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (16 bp):
TATTATATTTTCAAAA
Found at i:56637 original size:135 final size:136
Alignment explanation
Indices: 56466--57078 Score: 890
Period size: 135 Copynumber: 4.6 Consensus size: 136
56456 AGGTGAACCA
56466 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAG-AGTTCATAAT
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAAT
** *
56530 GAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGTATTTCAAATCAGTGATGCCTCGCTTGAG
66 GAGAAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGATGCCTCGCTTGAG
*
56595 GG-TTCA
131 GGATT-G
* * *
56601 ACATTTCCAGTGAAGAGTTCATAATGAGAAGAACTCATCCGACAGAAGGAGAAGAAGTTCATAAT
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAAT
* * * ** *
56666 GAGAATAGCTTATTCGATCTATCACTCGATTC-CGGTATTTCGAATCAGTGA--CCTCACTTGAG
66 GAGAAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGATGCCTCGCTTGAG
56728 GGATTG
131 GGATTG
*
56734 ACATTTCCAATGGAGAATTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAAT
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAAT
* * * *
56799 GAGAAGAGCTTGTTCGACCTATCATTCGATTCATGACA-TTCGAATCAGTGATACCTCGCTTAAG
66 GAGAAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGATGCCTCGCTTGAG
56863 GGATTG
131 GGATTG
* *
56869 ACATTTCCAATTGAGAG-T--T-ATGAGAAGAACTCATCCGACAGAGGGATAAGAAGTTCATAAT
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAAT
* * *
56930 GAGAAGATCTTGTTCGACCTATCACTCGATTCACGACATTTTGAATCAGTGACGCCTCGC-TGAG
66 GAGAAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGATGCCTCGCTTGAG
56994 GGATTG
131 GGATTG
* * *
57000 ACATTTCTAATGGAGAGTTCATAATGAGAAGAATTCATCCAACA-AGGGAGAAGAAGTTCATAAT
1 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAAT
*
57064 GAGAAGAACTTGTTC
66 GAGAAGAGCTTGTTC
57079 AACTTCAGAC
Statistics
Matches: 430, Mismatches: 38, Indels: 21
0.88 0.08 0.04
Matches are distributed among these distances:
131 100 0.23
132 20 0.05
133 114 0.27
134 39 0.09
135 118 0.27
136 39 0.09
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (136 bp):
ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAAT
GAGAAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTCGAATCAGTGATGCCTCGCTTGAG
GGATTG
Found at i:58256 original size:2 final size:2
Alignment explanation
Indices: 58249--58279 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
58239 AGTCATGTTA
58249 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
58280 AAACATTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:58971 original size:14 final size:15
Alignment explanation
Indices: 58943--58973 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
58933 CTTTAAGGAT
58943 TAAATATTATTATTA
1 TAAATATTATTATTA
58958 TAAATATT-TTATTA
1 TAAATATTATTATTA
58972 TA
1 TA
58974 TTTCTTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TAAATATTATTATTA
Found at i:69064 original size:43 final size:44
Alignment explanation
Indices: 68967--69069 Score: 129
Period size: 43 Copynumber: 2.4 Consensus size: 44
68957 CTTGCATAAC
* * * *
68967 TTGTCAACTTGCCAACCAAGGATGAATTATCCCATGTGCTCACG
1 TTGTCAACTTGCCAACCAAAGATGAATTATCACATGTGCACAAG
* *
69011 TTGTCCACTTGCTAACCAAAGAT-AATTATCACATGTGCACAAG
1 TTGTCAACTTGCCAACCAAAGATGAATTATCACATGTGCACAAG
69054 TTAG-CAACTTGCCAAC
1 TT-GTCAACTTGCCAAC
69070 TTGTCAACTT
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
43 29 0.58
44 21 0.42
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (44 bp):
TTGTCAACTTGCCAACCAAAGATGAATTATCACATGTGCACAAG
Found at i:70711 original size:18 final size:19
Alignment explanation
Indices: 70676--70712 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
70666 CCGTTAAACA
70676 GGGGAGAATCGTACCCCCT
1 GGGGAGAATCGTACCCCCT
70695 GGGG-GAATCTGTACCCCC
1 GGGGAGAATC-GTACCCCC
70713 CAGACATTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.19, C:0.32, G:0.32, T:0.16
Consensus pattern (19 bp):
GGGGAGAATCGTACCCCCT
Found at i:72470 original size:22 final size:22
Alignment explanation
Indices: 72445--72498 Score: 108
Period size: 22 Copynumber: 2.5 Consensus size: 22
72435 ACTGAGGTAG
72445 GTATCGGTACCATAGAAGGGAA
1 GTATCGGTACCATAGAAGGGAA
72467 GTATCGGTACCATAGAAGGGAA
1 GTATCGGTACCATAGAAGGGAA
72489 GTATCGGTAC
1 GTATCGGTAC
72499 TAGGTGTAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.33, C:0.15, G:0.31, T:0.20
Consensus pattern (22 bp):
GTATCGGTACCATAGAAGGGAA
Found at i:73062 original size:23 final size:23
Alignment explanation
Indices: 73018--73067 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
73008 ATAATTCTTT
** *
73018 GTGGTCCTTCGAGATGATTCTAC
1 GTGGTCCTTCGAGACAAATCTAC
* *
73041 GTGGTTCTTCGAGACAAATCTAT
1 GTGGTCCTTCGAGACAAATCTAC
73064 GTGG
1 GTGG
73068 CACTACGGTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.20, C:0.18, G:0.28, T:0.34
Consensus pattern (23 bp):
GTGGTCCTTCGAGACAAATCTAC
Found at i:73115 original size:25 final size:24
Alignment explanation
Indices: 73034--73123 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
73024 CTTCGAGATG
**
73034 ATTCTACGTGGTTCTTCGAG-ACAA
1 ATTCTACGTGGCACTTCG-GTACAA
* * *
73058 A-TCTATGTGGCACTACGGTACAT
1 ATTCTACGTGGCACTTCGGTACAA
*
73081 ATTCTACGTGGCACTTCGGTGCAAA
1 ATTCTACGTGGCACTTCGGTAC-AA
*
73106 ATTCTACGTGGCATTTCG
1 ATTCTACGTGGCACTTCG
73124 ACTGTAATTA
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
22 1 0.02
23 16 0.30
24 18 0.34
25 18 0.34
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.32
Consensus pattern (24 bp):
ATTCTACGTGGCACTTCGGTACAA
Done.