Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003599.1 Hibiscus syriacus cultivar Beakdansim tig00007612_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: 60068
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:1033 original size:2 final size:2
Alignment explanation
Indices: 1020--1917 Score: 799
Period size: 2 Copynumber: 451.0 Consensus size: 2
1010 CAGACAAACA
*
1020 AC AC AG AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* * * * *
1062 AC AC GC AC AC AC GC AC AC AC GC AC AC AC AC GC AC AC AC GC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* * * * * * * * ** ** *
1104 GC AC GC AC GC AC GC AC GC GC GC AC GC AC GT AC GT GC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* * * * * * * *
1146 AC AC AC AC AC AC AC TC AC AT AC AC AC AT AC AC TC TC TC TC TC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* * * * * ** * * *
1188 TC TC TC AC AC AC AC AC AC AC GC GC AC GT AC GC AC GC AC GC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* * * * *
1230 GC -C TAC GC AC AC AC AC AC AC AC AC AC TC TC AC AT AC AC -C AC
1 AC AC -AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* * * * * * * *
1271 TC TC TC TC AC AC AC AC AC AC AC AC GC AGC AC GC AC AC GC AC GC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A-C AC AC AC AC AC AC AC
* * * * * * * *
1314 AC GC AC GC AC GC AC GC AC AC AC GC AC GC AC -C AC GC AC AC GC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1355 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* * * * * * *
1397 AC AC TC AC AT AC AC AT AC AC AC AT AC AC AC ATC AC TC TC AC AT
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A-C AC AC AC AC AC
* * * * * *
1440 AC AC AC AT AC AC AC TGC AC AC AT AC AC AC AT AC AC AT GC AC AC
1 AC AC AC AC AC AC AC -AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* *
1483 AT AC AC AC AC AC AC AC -C AC AC AC AC AC GC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
*
1524 -C AC AC AC AC AC AC AC AC AC AC AC AC AC AC -C TC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1564 AC AC AC A- AC AC AC AC AC AC -C AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1604 AC AC AC -C AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* *
1645 AC AC AC GC AC AC AC CC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* *
1687 AC AC AC AT AC AC AC AC AC AC AC AC AC AT AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* *
1729 AC AC AC AC AC AC AC AC AC AT AC AC AC AT AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
*
1771 AC AC AC AC AC -C AC AC AC AC AC AC AC AC AC AC AC AC AC CC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* * * * * * *
1812 AC AC AC TC TC AC AT AC AC AC AT AC AC TAC AC TC TC AC AT AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC -AC AC AC AC AC AC AC AC
* * * * * *
1855 AT AT AC AC AC AT GC AC AC AT AC AC AC AC AC AT AC AC AC TAC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC -AC AC
* * *
1898 AC AT AC AT AC AC AC AT AC AC
1 AC AC AC AC AC AC AC AC AC AC
1918 TACATACATA
Statistics
Matches: 726, Mismatches: 154, Indels: 32
0.80 0.17 0.04
Matches are distributed among these distances:
1 10 0.01
2 706 0.97
3 10 0.01
ACGTcount: A:0.42, C:0.47, G:0.05, T:0.06
Consensus pattern (2 bp):
AC
Found at i:1925 original size:4 final size:4
Alignment explanation
Indices: 1847--1941 Score: 66
Period size: 4 Copynumber: 23.2 Consensus size: 4
1837 CTACACTCTC
* * * * * * * *
1847 ACAT ACAC ATAT ACAC ACAT GCAC ACAT ACAC ACAC ACAT ACAC AC-T
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* *
1894 ACAC ACAT ACAT ACAC ACAT ACACT ACAT ACAT ACATT CACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACA-T ACAT ACAT ACA-T -ACAT ACAT A
1942 TATGATACAT
Statistics
Matches: 69, Mismatches: 18, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
3 2 0.03
4 58 0.84
5 6 0.09
6 3 0.04
ACGTcount: A:0.47, C:0.34, G:0.01, T:0.18
Consensus pattern (4 bp):
ACAT
Found at i:3014 original size:28 final size:28
Alignment explanation
Indices: 2976--3040 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
2966 TTTTTTTTTT
*
2976 TCTTGAGACAAATCTTTGAGTAT-GTTTC
1 TCTTGAAACAAATCTTTGAGT-TGGTTTC
*
3004 TTTTGAAACAAATCTTTGAGTTGGTTTC
1 TCTTGAAACAAATCTTTGAGTTGGTTTC
3032 TCTTGAAAC
1 TCTTGAAAC
3041 CATAATTCCT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 1 0.03
28 32 0.97
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.43
Consensus pattern (28 bp):
TCTTGAAACAAATCTTTGAGTTGGTTTC
Found at i:3435 original size:3 final size:3
Alignment explanation
Indices: 3427--3458 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
3417 GTCTTTTCCC
*
3427 TAT TAT TAT TAT TAT TAT TAT TAT TAT AAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3459 ATTTTACATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:4845 original size:29 final size:30
Alignment explanation
Indices: 4799--4965 Score: 80
Period size: 29 Copynumber: 5.7 Consensus size: 30
4789 TTATTTGTAA
*
4799 TTACTGTTTTAGTCCTTTTAG-TTACTGTTT
1 TTACTGTTTTAGTCCTTTAAGATTA-TGTTT
4829 TTACTG-TTTA-TCCCTTTAAGATTATGTTT
1 TTACTGTTTTAGT-CCTTTAAGATTATGTTT
* * * * *
4858 TT-GT-TATTTAGTTC-TTAAGTTTCTATTT
1 TTACTGT-TTTAGTCCTTTAAGATTATGTTT
* *
4886 TTACTGTTTTGGCCCTTTAA-ATTTATGTTT
1 TTACTGTTTTAGTCCTTTAAGA-TTATGTTT
* * ** * * *
4916 ATGCCATTTTAGTTCTTTAAG-TTTTGGTT
1 TTACTGTTTTAGTCCTTTAAGATTATGTTT
* * *
4945 TTGCTATTTTGGTCCTTTAAG
1 TTACTGTTTTAGTCCTTTAAG
4966 TTGTTGTTTT
Statistics
Matches: 101, Mismatches: 26, Indels: 21
0.68 0.18 0.14
Matches are distributed among these distances:
28 15 0.15
29 52 0.51
30 34 0.34
ACGTcount: A:0.17, C:0.12, G:0.14, T:0.57
Consensus pattern (30 bp):
TTACTGTTTTAGTCCTTTAAGATTATGTTT
Found at i:4903 original size:58 final size:60
Alignment explanation
Indices: 4826--4965 Score: 148
Period size: 59 Copynumber: 2.4 Consensus size: 60
4816 TTAGTTACTG
* **
4826 TTTTTACTGTTTAT--CCCTTTAAGA-TTATGTTTTTGTTA-TTTAGTTC-TTAAGTTTCTA
1 TTTTTACTGTTT-TGGCCCTTTAAGATTTATGTTTATGCCATTTTAGTTCTTTAAGTTT-TA
*
4883 TTTTTACTGTTTTGGCCCTTTAA-ATTTATGTTTATGCCATTTTAGTTCTTTAAGTTTTG
1 TTTTTACTGTTTTGGCCCTTTAAGATTTATGTTTATGCCATTTTAGTTCTTTAAGTTTTA
* * * *
4942 GTTTTGCTATTTTGGTCCTTTAAG
1 TTTTTACTGTTTTGGCCCTTTAAG
4966 TTGTTGTTTT
Statistics
Matches: 69, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
56 1 0.01
57 13 0.19
58 19 0.28
59 28 0.41
60 8 0.12
ACGTcount: A:0.17, C:0.11, G:0.14, T:0.58
Consensus pattern (60 bp):
TTTTTACTGTTTTGGCCCTTTAAGATTTATGTTTATGCCATTTTAGTTCTTTAAGTTTTA
Found at i:4966 original size:29 final size:28
Alignment explanation
Indices: 4892--4991 Score: 101
Period size: 30 Copynumber: 3.4 Consensus size: 28
4882 ATTTTTACTG
* * *
4892 TTTTGGCCCTTTAAATTTATGTTTATGCCA
1 TTTTGGTCCTTTAAGTTT-TGTTT-TGCTA
* *
4922 TTTTAGTTCTTTAAGTTTTGGTTTTGCTA
1 TTTTGGTCCTTTAAGTTTT-GTTTTGCTA
*
4951 TTTTGGTCCTTTAAGTTGTTGTTTTTCTCA
1 TTTTGGTCCTTTAAGTT-TTGTTTTGCT-A
4981 TTTTGGTCCTT
1 TTTTGGTCCTT
4992 GTAACTTTAA
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
29 27 0.46
30 32 0.54
ACGTcount: A:0.13, C:0.13, G:0.16, T:0.58
Consensus pattern (28 bp):
TTTTGGTCCTTTAAGTTTTGTTTTGCTA
Found at i:10019 original size:19 final size:20
Alignment explanation
Indices: 9949--10020 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
9939 TGTTGGAGCC
* *
9949 AAAGTATCAAAACT-TTAGGG
1 AAAGTATCGAAACTCTT-GAG
* *
9969 AAAGTTTTGAAACTCTTGAG
1 AAAGTATCGAAACTCTTGAG
* *
9989 ATAGTTTCGAAACTCTTGA-
1 AAAGTATCGAAACTCTTGAG
10008 AAAGTATCGAAAC
1 AAAGTATCGAAAC
10021 CTTTTGGGAA
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
19 11 0.26
20 30 0.70
21 2 0.05
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.29
Consensus pattern (20 bp):
AAAGTATCGAAACTCTTGAG
Found at i:12200 original size:21 final size:20
Alignment explanation
Indices: 12176--12308 Score: 74
Period size: 20 Copynumber: 6.5 Consensus size: 20
12166 TAGTTACCAG
12176 AATCGCAACGCGATTATGAA
1 AATCGCAACGCGATTATGAA
*
12196 GAATCGCAATGCGA-TA-GTACA
1 -AATCGCAACGCGATTATG-A-A
* ** * * *
12217 AATTCACATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTAT-GAA
*
12239 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGATTATGAA
**
12259 AATCGCAACGCGAACAT-ATA
1 AATCGCAACGCGATTATGA-A
* *
12279 AATCGCAACGCGATTCTGAC
1 AATCGCAACGCGATTATGAA
*
12299 TATCGCAACG
1 AATCGCAACG
12309 AGTATCCGTA
Statistics
Matches: 85, Mismatches: 19, Indels: 17
0.70 0.16 0.14
Matches are distributed among these distances:
19 2 0.02
20 46 0.54
21 33 0.39
22 3 0.04
23 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
AATCGCAACGCGATTATGAA
Found at i:12264 original size:20 final size:20
Alignment explanation
Indices: 12239--12732 Score: 258
Period size: 20 Copynumber: 24.5 Consensus size: 20
12229 GATTTTCCAG
* *
12239 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGTA
* **
12259 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAATACGTA
*
12279 AATCGCAACGCG-ATTC-TGA
1 AATCGCAACGCGAATACGT-A
* * * *
12298 CTATCGCAACGAGTATCCGTAA
1 -AATCGCAACGCGAATACGT-A
* *
12320 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
*
12340 AATTGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACGT-A
* *
12361 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
*
12381 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
* **
12401 AATCGCAACGCGTATTTGTA
1 AATCGCAACGCGAATACGTA
*
12421 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
* * *
12441 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
12461 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACGT-A
* *
12482 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
12502 AATCGCAACGCG-AT-CGATA
1 AATCGCAACGCGAATACG-TA
* * *
12521 ATTCGCAACGCGATCTCCGGT-
1 AATCGCAACGCGA-ATAC-GTA
** * *
12542 -ATCGCAAATC-AGTTTC-TA
1 AATCGCAACGCGA-ATACGTA
* *
12560 GATTCGCAACGCG-ATTC-TGA
1 -AATCGCAACGCGAATACGT-A
* ** * * **
12580 CTATCGCATTGCGATTTCCCA
1 -AATCGCAACGCGAATACGTA
*** * * *
12601 AATTCGCGTTGCGATTTTCCTA
1 AA-TCGCAACGCGA-ATACGTA
* *
12623 AATCGCAATGCGATTACGTA
1 AATCGCAACGCGAATACGTA
*
12643 AATCGCAATGCGAATACGTA
1 AATCGCAACGCGAATACGTA
*
12663 AATCGCAATGCGAATACGTA
1 AATCGCAACGCGAATACGTA
* *
12683 AATCGCAATGCGCATACGTA
1 AATCGCAACGCGAATACGTA
*
12703 AATCGCAATGCGAAT-CTGTA
1 AATCGCAACGCGAATAC-GTA
12723 AATCGCAACG
1 AATCGCAACG
12733 AGATTCTGAC
Statistics
Matches: 381, Mismatches: 68, Indels: 50
0.76 0.14 0.10
Matches are distributed among these distances:
17 1 0.00
18 3 0.01
19 25 0.07
20 262 0.69
21 77 0.20
22 12 0.03
23 1 0.00
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.22
Consensus pattern (20 bp):
AATCGCAACGCGAATACGTA
Found at i:12331 original size:41 final size:41
Alignment explanation
Indices: 12300--12511 Score: 338
Period size: 41 Copynumber: 5.2 Consensus size: 41
12290 GATTCTGACT
* *
12300 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
12341 ATTGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
**
12382 ATCGCAACGAGAATACGT-AAATCGCAACGCGTATTTGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
12422 ATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
12462 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
12503 ATCGCAACG
1 ATCGCAACG
12512 CGATCGATAA
Statistics
Matches: 157, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
40 74 0.47
41 83 0.53
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:12415 original size:40 final size:40
Alignment explanation
Indices: 12239--12532 Score: 326
Period size: 40 Copynumber: 7.3 Consensus size: 40
12229 GATTTTCCAG
* ** * * * **
12239 AATCGCAACGCGAATATGAAAATCGCAACGCGAACATATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
* * * *
12279 AATCGCAACGCG-ATTC-TGACTATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGTATCCGT-A-AATCGCAACGAGAATACGT-A
* *
12320 AATCGCAACGCGTATCCGTAAATTGCAACGACAATACGTAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGT-A
12361 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
**
12401 AATCGCAACGCGTATTTGTAAATCGCAACGAGAATACGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
* *
12441 AATCGCAATGCGTATCCGTAAATCGCAACGACAATACGTAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGT-A
*
12482 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AT-CGATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACG-TA
*
12521 ATTCGCAACGCG
1 AATCGCAACGCG
12533 ATCTCCGGTA
Statistics
Matches: 219, Mismatches: 28, Indels: 15
0.84 0.11 0.06
Matches are distributed among these distances:
39 17 0.08
40 101 0.46
41 96 0.44
42 4 0.02
43 1 0.00
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (40 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
Found at i:12628 original size:21 final size:21
Alignment explanation
Indices: 12582--12637 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
12572 GATTCTGACT
12582 ATCGCATTGCGA-TTTCCCAA
1 ATCGCATTGCGATTTTCCCAA
* *
12602 ATTCGCGTTGCGATTTTCCTAA
1 A-TCGCATTGCGATTTTCCCAA
*
12624 ATCGCAATGCGATT
1 ATCGCATTGCGATT
12638 ACGTAAATCG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 1 0.03
21 21 0.70
22 8 0.27
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (21 bp):
ATCGCATTGCGATTTTCCCAA
Found at i:13618 original size:24 final size:24
Alignment explanation
Indices: 13591--13644 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
13581 GTATTCGAAA
13591 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
13615 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
13639 TTTGAT
1 TTTGAT
13645 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:16275 original size:33 final size:33
Alignment explanation
Indices: 16238--16317 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
16228 GCGAATTTAG
* * *
16238 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
16271 TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
16304 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
16318 AGTCATTTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.46
Consensus pattern (33 bp):
TTTCGCATTGCGATTCTCTCGTTGCGATTTTCA
Found at i:16283 original size:19 final size:19
Alignment explanation
Indices: 16259--16317 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
16249 GATTTTGTCG
16259 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
16278 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
16292 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
16311 TTGCGAT
1 TTGCGAT
16318 AGTCATTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 6 0.18
16 7 0.21
17 7 0.21
19 13 0.39
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:16325 original size:19 final size:17
Alignment explanation
Indices: 16267--16317 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
16257 CGTTGCGATT
16267 TTCATTTCGCATTGCGA
1 TTCATTTCGCATTGCGA
*
16284 TTC-TCTCG--TTGCGA
1 TTCATTTCGCATTGCGA
16298 TTTTCATTTCGCATTGCGA
1 --TTCATTTCGCATTGCGA
16317 T
1 T
16318 AGTCATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 10
0.69 0.05 0.26
Matches are distributed among these distances:
14 6 0.22
16 7 0.26
17 8 0.30
19 6 0.22
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.45
Consensus pattern (17 bp):
TTCATTTCGCATTGCGA
Found at i:16443 original size:14 final size:15
Alignment explanation
Indices: 16424--16461 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
16414 CATCAATTAA
16424 ACAAATCAA-CTTTT
1 ACAAATCAATCTTTT
16438 ACAAAT-AATCTTTT
1 ACAAATCAATCTTTT
16452 ACAAATCAAT
1 ACAAATCAAT
16462 TAAACAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.09
14 17 0.77
15 3 0.14
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.34
Consensus pattern (15 bp):
ACAAATCAATCTTTT
Found at i:17875 original size:21 final size:21
Alignment explanation
Indices: 17809--17875 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
17799 GTGAATCGGT
*
17809 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
17829 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
17851 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
17872 CTCT
1 CTCT
17876 CGAGGAATTA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:18368 original size:19 final size:17
Alignment explanation
Indices: 18352--18451 Score: 89
Period size: 19 Copynumber: 5.7 Consensus size: 17
18342 AAAAATGACT
18352 ATCGCAACGCGAAATGA
1 ATCGCAACGCGAAATGA
*
18369 ATCACAACGCGAAATGAAA
1 ATCGCAACGCGAAATG--A
18388 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATG--A
* *
18407 ACCGCAA--CGAGA-GA
1 ATCGCAACGCGAAATGA
*
18421 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATG--A
18440 ATCGCAACGCGA
1 ATCGCAACGCGA
18452 TTATAGTTTA
Statistics
Matches: 69, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
14 7 0.10
16 5 0.07
17 20 0.29
19 37 0.54
ACGTcount: A:0.45, C:0.23, G:0.22, T:0.10
Consensus pattern (17 bp):
ATCGCAACGCGAAATGA
Found at i:18470 original size:19 final size:19
Alignment explanation
Indices: 18448--18491 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
18438 AAATCGCAAC
18448 GCGATTATAGTTTAGCGTT
1 GCGATTATAGTTTAGCGTT
* * *
18467 GCGATTTTGGTTTCGCGTT
1 GCGATTATAGTTTAGCGTT
18486 GCGATT
1 GCGATT
18492 TTGTCGTTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.30, T:0.43
Consensus pattern (19 bp):
GCGATTATAGTTTAGCGTT
Found at i:18505 original size:33 final size:33
Alignment explanation
Indices: 18463--18558 Score: 147
Period size: 33 Copynumber: 2.9 Consensus size: 33
18453 TATAGTTTAG
** * *
18463 CGTTGCGATTTTGGTTTCGCGTTGCGATTTTGT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
18496 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
*
18529 CGTTACGATTTTCATTTCGCGTTGCGATTC
1 CGTTGCGATTTTCATTTCGCGTTGCGATTC
18559 ATTTCGCGTT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.09, C:0.21, G:0.24, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:18556 original size:19 final size:19
Alignment explanation
Indices: 18462--18611 Score: 90
Period size: 19 Copynumber: 8.4 Consensus size: 19
18452 TTATAGTTTA
**
18462 GCGTTGCGATTTTGGTTTC
1 GCGTTGCGATTTTCATTTC
*
18481 GCGTTGCGA-TTT--TGT-
1 GCGTTGCGATTTTCATTTC
18496 -CGTTGCGATTTTCATTTC
1 GCGTTGCGATTTTCATTTC
18514 GCGTTGCGA--TTC---TC
1 GCGTTGCGATTTTCATTTC
* *
18528 TCGTTACGATTTTCATTTC
1 GCGTTGCGATTTTCATTTC
18547 GCGTTGCGA--TTCATTTC
1 GCGTTGCGATTTTCATTTC
* **
18564 GCGTTGAGATAGTCATTTTTC
1 GCGTTGCGATTTTCA--TTTC
* *
18585 ACGTTGCGATTTTAAGTTTC
1 GCGTTGCGATTTTCA-TTTC
*
18605 GTGTTGC
1 GCGTTGC
18612 AAAAGTAAAC
Statistics
Matches: 101, Mismatches: 16, Indels: 27
0.70 0.11 0.19
Matches are distributed among these distances:
14 17 0.17
15 3 0.03
16 5 0.05
17 21 0.21
18 3 0.03
19 29 0.29
20 9 0.09
21 14 0.14
ACGTcount: A:0.12, C:0.19, G:0.24, T:0.45
Consensus pattern (19 bp):
GCGTTGCGATTTTCATTTC
Found at i:18915 original size:92 final size:94
Alignment explanation
Indices: 18665--19038 Score: 610
Period size: 94 Copynumber: 4.0 Consensus size: 94
18655 ATTGCATTAA
* * *
18665 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGTTTAAC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
18730 AGAATTGGCAGCAACCGAACAAATTTACT
66 AGAATTGGCAGCAACCGAACAAATTTACT
18759 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
18824 AGAATTGGCAGCAACCGAACAAATTTACT
66 AGAATTGGCAGCAACCGAACAAATTTACT
* *
18853 TTCAACC-TAA-ACACAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
*
18916 AGAATTGGCAGCAACCGAATAAATTTAC-
66 AGAATTGGCAGCAACCGAACAAATTTACT
* * * *
18944 TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTTACATTGTTAAAGAATAAACAATTTAG
1 TTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAG
* *
19009 CAGTATTGGCAGCAACCGAATAAATTTACT
65 CAGAATTGGCAGCAACCGAACAAATTTACT
19039 AAGCAATCTA
Statistics
Matches: 263, Mismatches: 13, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
91 7 0.03
92 81 0.31
93 8 0.03
94 167 0.63
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (94 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
AGAATTGGCAGCAACCGAACAAATTTACT
Found at i:18995 original size:186 final size:186
Alignment explanation
Indices: 18681--19038 Score: 610
Period size: 186 Copynumber: 1.9 Consensus size: 186
18671 CAAAAGACAA
*
18681 AACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGTTTAACAGAATTGGCAGCAACC
1 AACAAAGACAAATACTAACTTCACAGTATTAAAGAATACACAGTTTAACAGAATTGGCAGCAACC
18746 GAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAA
66 GAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAA
* *
18811 TACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCTAAACAC
131 TAAACAATTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCTAAACAC
* *
18867 AACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACC
1 AACAAAGACAAATACTAACTTCACAGTATTAAAGAATACACAGTTTAACAGAATTGGCAGCAACC
* * *
18932 GAATAAATTTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTTACATTGTTAAAGA
66 GAACAAATTTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGA
* *
18996 ATAAACAATTTAGCAGTATTGGCAGCAACCGAATAAATTTACT
130 ATAAACAATTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
19039 AAGCAATCTA
Statistics
Matches: 161, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
185 19 0.12
186 142 0.88
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (186 bp):
AACAAAGACAAATACTAACTTCACAGTATTAAAGAATACACAGTTTAACAGAATTGGCAGCAACC
GAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAA
TAAACAATTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCTAAACAC
Found at i:20777 original size:19 final size:19
Alignment explanation
Indices: 20722--20792 Score: 88
Period size: 20 Copynumber: 3.6 Consensus size: 19
20712 TGAAATGAAA
*
20722 ATCGCAACGAGAGAATGACT
1 ATCGCAACGCGA-AATGACT
20742 ATCGCAACGCGGAAATGACT
1 ATCGCAACGC-GAAATGACT
**
20762 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
*
20781 ATCGCAATGCGA
1 ATCGCAACGCGA
20793 TTTTGGTTTC
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
19 18 0.39
20 26 0.57
21 2 0.04
ACGTcount: A:0.39, C:0.23, G:0.24, T:0.14
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:20840 original size:33 final size:33
Alignment explanation
Indices: 20803--20867 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
20793 TTTTGGTTTC
*
20803 GCGTTGCGATTATCTCGTTGTAATTTTCATTTA
1 GCGTTGCGATTATCTCGTTGCAATTTTCATTTA
* *
20836 GCGTTGCGATTCTCTCGTTGCGATTTTCATTT
1 GCGTTGCGATTATCTCGTTGCAATTTTCATTT
20868 CTCTCGTTGC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.14, C:0.18, G:0.20, T:0.48
Consensus pattern (33 bp):
GCGTTGCGATTATCTCGTTGCAATTTTCATTTA
Found at i:20871 original size:21 final size:21
Alignment explanation
Indices: 20845--20908 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
20835 AGCGTTGCGA
20845 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
**
20866 TTCTCTCGTTGCGATAGTCAT
1 TTCTCTCGTTGCGATTTTCAT
20887 TT-TCGT-GTTGCGATTTTCAT
1 TTCTC-TCGTTGCGATTTTCAT
20907 TT
1 TT
20909 TCATGTTGTG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 16 0.42
21 22 0.58
ACGTcount: A:0.11, C:0.20, G:0.17, T:0.52
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:20921 original size:20 final size:19
Alignment explanation
Indices: 20852--20923 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 19
20842 CGATTCTCTC
20852 GTTGCGATTTTCATTTCTCT
1 GTTGCGATTTTCATTT-TCT
**
20872 CGTTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTC-T
20893 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTC-T
*
20913 GTTGTGATTTT
1 GTTGCGATTTT
20924 AAGTTTAGAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
20 29 0.66
21 15 0.34
ACGTcount: A:0.12, C:0.15, G:0.19, T:0.53
Consensus pattern (19 bp):
GTTGCGATTTTCATTTTCT
Found at i:21517 original size:21 final size:21
Alignment explanation
Indices: 21480--21573 Score: 124
Period size: 21 Copynumber: 4.6 Consensus size: 21
21470 GCTTTAAAAA
21480 ATGCGTTGCGA-TTTACGGAT
1 ATGCGTTGCGATTTTACGGAT
*
21500 ATGCGTTGCGATTTTACGTAT
1 ATGCGTTGCGATTTTACGGAT
21521 -TGTCGTTGCGA-TTTACGGAT
1 ATG-CGTTGCGATTTTACGGAT
*
21541 ACGCGTTGCGATTTTACGGAT
1 ATGCGTTGCGATTTTACGGAT
21562 ACT-CGTTGCGAT
1 A-TGCGTTGCGAT
21574 AGTCAGAATC
Statistics
Matches: 65, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
20 29 0.45
21 36 0.55
ACGTcount: A:0.18, C:0.17, G:0.28, T:0.37
Consensus pattern (21 bp):
ATGCGTTGCGATTTTACGGAT
Found at i:21540 original size:41 final size:41
Alignment explanation
Indices: 21483--21573 Score: 146
Period size: 41 Copynumber: 2.2 Consensus size: 41
21473 TTAAAAAATG
* * **
21483 CGTTGCGATTTACGGATATGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACT
21524 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACT
21565 CGTTGCGAT
1 CGTTGCGAT
21574 AGTCAGAATC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACT
Found at i:21587 original size:41 final size:41
Alignment explanation
Indices: 21483--21595 Score: 122
Period size: 41 Copynumber: 2.8 Consensus size: 41
21473 TTAAAAAATG
* * * * **
21483 CGTTGCGATTTACGGATATGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTCACGAATACGCGTTGCGATTTTACGGATACT
* *
21524 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTCACGAATACGCGTTGCGATTTTACGGATACT
21565 CGTTGCGATAGTCA-GAAT-CGCGTTGCGATTT
1 CGTTGCGAT--TCACGAATACGCGTTGCGATTT
21596 ATATGTTCGC
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
41 59 0.92
42 3 0.05
43 2 0.03
ACGTcount: A:0.19, C:0.18, G:0.27, T:0.36
Consensus pattern (41 bp):
CGTTGCGATTCACGAATACGCGTTGCGATTTTACGGATACT
Found at i:21733 original size:20 final size:19
Alignment explanation
Indices: 21684--21737 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
21674 ATTCTTCATA
21684 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
21703 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
21724 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
21738 TTTATTTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:26611 original size:14 final size:14
Alignment explanation
Indices: 26592--26643 Score: 95
Period size: 14 Copynumber: 3.6 Consensus size: 14
26582 TCATGTGCAT
26592 CATGCTCTGCAACA
1 CATGCTCTGCAACA
26606 CATGCTCTGCAACA
1 CATGCTCTGCAACA
26620 CATGCTCTGCAACA
1 CATGCTCTGCAACA
26634 CATGCATCTG
1 CATGC-TCTG
26644 GAGTAGCCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
14 33 0.89
15 4 0.11
ACGTcount: A:0.27, C:0.35, G:0.15, T:0.23
Consensus pattern (14 bp):
CATGCTCTGCAACA
Found at i:28607 original size:208 final size:208
Alignment explanation
Indices: 28238--28660 Score: 659
Period size: 208 Copynumber: 2.0 Consensus size: 208
28228 CCTTTAGAAG
*
28238 AAAACATCGACCGTAGAAGCGTTGTTCCAAGTATAAGGTTACAGCAAACAACATGCCCAACAAAA
1 AAAAC-TCGAACGTAGAAGCGTTGTTCCAAGTATAAGGTTACAGCAAACAACATGCCCAACAAAA
*
28303 GAAGAAGAACAAGAAGTGTCAAACATACTGAGTCAACTAGTTTAACGTGCCATGTCAGCATTCCA
65 GAAGAAGAACAAGAAGAGTCAAACATACTGAGTCAACTAGTTTAACGTGCCATGTCAGCATTCCA
* * * *
28368 TTATTGCAGTAACGACTATTAACGATGAGTGACTGATTTGTTTTAAATTAATAACGTTAGTGACC
130 TTATTGCAGTAACAACTATTAACGATGAGTGACTGATTTGTTATAAATCAATAACATTAGTGACC
28433 AATTTGTTACTTTT
195 AATTTGTTACTTTT
* * * *
28447 AAAACTCGAACGTAGAAGCGTTGTTCCAAGTATAAGGTTGCATCAAAGAACATGCCCAACATAAG
1 AAAACTCGAACGTAGAAGCGTTGTTCCAAGTATAAGGTTACAGCAAACAACATGCCCAACAAAAG
** * * *
28512 AAGAAGAAGGAGAAGAGTCAAACATA-TCGAGTCAGCTGGTTTAACGTGCCATGTCAGCATTCCG
66 AAGAAGAACAAGAAGAGTCAAACATACT-GAGTCAACTAGTTTAACGTGCCATGTCAGCATTCCA
* *
28576 TTATTGCAGTAACAACTATTAACGGTGAGTGACTGATTTGTTATAAATCGATAACATTAGTGACC
130 TTATTGCAGTAACAACTATTAACGATGAGTGACTGATTTGTTATAAATCAATAACATTAGTGACC
28641 AATTTGTTACTTTT
195 AATTTGTTACTTTT
*
28655 GAAACT
1 AAAACT
28661 TCAGTGAAAA
Statistics
Matches: 195, Mismatches: 18, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
207 1 0.01
208 189 0.97
209 5 0.03
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.27
Consensus pattern (208 bp):
AAAACTCGAACGTAGAAGCGTTGTTCCAAGTATAAGGTTACAGCAAACAACATGCCCAACAAAAG
AAGAAGAACAAGAAGAGTCAAACATACTGAGTCAACTAGTTTAACGTGCCATGTCAGCATTCCAT
TATTGCAGTAACAACTATTAACGATGAGTGACTGATTTGTTATAAATCAATAACATTAGTGACCA
ATTTGTTACTTTT
Found at i:29446 original size:2 final size:2
Alignment explanation
Indices: 29439--29508 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
29429 TTGATAAGAA
29439 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29481 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29509 TGGTTTAGCT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31604 original size:171 final size:171
Alignment explanation
Indices: 31288--31815 Score: 788
Period size: 171 Copynumber: 3.1 Consensus size: 171
31278 TATAGTTCAT
* *
31288 GACTGTCAACATCATAACTTCAACATAATTTAGTGAGGCATGCAGATAAAATCTGACAAAAAAGA
1 GACTGCCAACATCATAACTTCAACATAATTTAGTGAGGCATGCAGATAAAATCTGAC-AAAAAGG
* * * * * * * * *
31353 AAAGACTCATTCTAAGAGAATCGTTTTTCCTTTTCTCAGAGAATCTTTGGCATGTCATAGTGTCT
65 AAAGGCTCGTTCCAAGGGAAACGCTTTTCCTTTTCTCAAAGAATCTCTGCCATGTCATAGTGTCT
* *
31418 CATCCCATAAAACATAAATTGGGTTGACGAGAATAGTTCCCC
130 CATCCCATCAAACATAAATTGGGTTGACGGGAATAGTTCCCC
* *
31460 AACTGCCAACATCATAACTTCAACATAATTTAGTGAGGCATACAGATAAAATCTGACAAAAAGGA
1 GACTGCCAACATCATAACTTCAACATAATTTAGTGAGGCATGCAGATAAAATCTGACAAAAAGGA
* * * *
31525 AAGGCTCGTTCCAAGGGAAACACTTTTCTTTTTCTCAAAGAATCTCTGTCAAGTCATAGTGTCTC
66 AAGGCTCGTTCCAAGGGAAACGCTTTTCCTTTTCTCAAAGAATCTCTGCCATGTCATAGTGTCTC
*
31590 ATCCCATCAAACATAAATTGGGTTGAAGGGAATAGTTCCCC
131 ATCCCATCAAACATAAATTGGGTTGACGGGAATAGTTCCCC
* * *
31631 GACTACCAACATCATAACTTCAACATAATTTAGTGAGGCATGCAGGTAAAATTTGACAAAAAGGA
1 GACTGCCAACATCATAACTTCAACATAATTTAGTGAGGCATGCAGATAAAATCTGACAAAAAGGA
* *
31696 AAGGCTCGTTCC-AGGGAAGCGCTTTTCCTTTTCTCAAAGAATCTCTGCCATGTCATAGTATCTC
66 AAGGCTCGTTCCAAGGGAAACGCTTTTCCTTTTCTCAAAGAATCTCTGCCATGTCATAGTGTCTC
* *
31760 ATCCCATCAAACATAAATTGGGTTGACGGGAATAATTCCCT
131 ATCCCATCAAACATAAATTGGGTTGACGGGAATAGTTCCCC
*
31801 GACTGCCAAGATCAT
1 GACTGCCAACATCAT
31816 TTCTTCTTTT
Statistics
Matches: 321, Mismatches: 35, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
170 97 0.30
171 170 0.53
172 54 0.17
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.28
Consensus pattern (171 bp):
GACTGCCAACATCATAACTTCAACATAATTTAGTGAGGCATGCAGATAAAATCTGACAAAAAGGA
AAGGCTCGTTCCAAGGGAAACGCTTTTCCTTTTCTCAAAGAATCTCTGCCATGTCATAGTGTCTC
ATCCCATCAAACATAAATTGGGTTGACGGGAATAGTTCCCC
Found at i:32946 original size:23 final size:23
Alignment explanation
Indices: 32920--33018 Score: 67
Period size: 23 Copynumber: 4.3 Consensus size: 23
32910 CACTGAAGTT
*
32920 CCACATATAAATGTCTCGAAGGA
1 CCACATATAAATGTCCCGAAGGA
* *
32943 CCACACAGT-ATTGTCCCGAAGGA
1 CCACATA-TAAATGTCCCGAAGGA
** * *
32966 CTGCGTAGAAATGTCCCGAAGGA
1 CCACATATAAATGTCCCGAAGGA
* * *
32989 CCACGTA-AAATTATCCCGGAGGA
1 CCACATATAAA-TGTCCCGAAGGA
*
33012 CCGCATA
1 CCACATA
33019 GAACCCTCAA
Statistics
Matches: 58, Mismatches: 15, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
22 3 0.05
23 54 0.93
24 1 0.02
ACGTcount: A:0.33, C:0.26, G:0.22, T:0.18
Consensus pattern (23 bp):
CCACATATAAATGTCCCGAAGGA
Found at i:33006 original size:46 final size:46
Alignment explanation
Indices: 32923--33021 Score: 108
Period size: 46 Copynumber: 2.2 Consensus size: 46
32913 TGAAGTTCCA
* * ** * *
32923 CATATAAATGTCTCGAAGGACCACACAGTATTGTCCCGAAGGACTG
1 CATAGAAATGTCCCGAAGGACCACACAAAATTATCCCGAAGGACCG
* ** *
32969 CGTAGAAATGTCCCGAAGGACCACGTAAAATTATCCCGGAGGACCG
1 CATAGAAATGTCCCGAAGGACCACACAAAATTATCCCGAAGGACCG
33015 CATAGAA
1 CATAGAA
33022 CCCTCAACTC
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.34, C:0.24, G:0.23, T:0.18
Consensus pattern (46 bp):
CATAGAAATGTCCCGAAGGACCACACAAAATTATCCCGAAGGACCG
Found at i:35721 original size:20 final size:20
Alignment explanation
Indices: 35696--35733 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
35686 CCCCCTTTGA
*
35696 AGGGGAACCGATTCCCCCAC
1 AGGGGAACCGATACCCCCAC
*
35716 AGGGGAATCGATACCCCC
1 AGGGGAACCGATACCCCC
35734 TGGGGTTCTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.37, G:0.26, T:0.11
Consensus pattern (20 bp):
AGGGGAACCGATACCCCCAC
Found at i:42837 original size:24 final size:24
Alignment explanation
Indices: 42810--42861 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
42800 TAGCTCGTAC
* *
42810 AAATTACACCGAAGTACCGCATAG
1 AAATTACACCGAAATACCACATAG
* * *
42834 AAATTTCACTGAAATACCACATAT
1 AAATTACACCGAAATACCACATAG
42858 AAAT
1 AAAT
42862 ATCCCGAATG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.46, C:0.21, G:0.10, T:0.23
Consensus pattern (24 bp):
AAATTACACCGAAATACCACATAG
Found at i:42879 original size:23 final size:23
Alignment explanation
Indices: 42849--42951 Score: 107
Period size: 23 Copynumber: 4.5 Consensus size: 23
42839 TCACTGAAAT
* *
42849 ACCACATATAAATATCCCGAATG
1 ACCACATAGAAATATCCCGAAGG
* * *
42872 ACCACATAGTATTGTCCCGAAGG
1 ACCACATAGAAATATCCCGAAGG
* * *
42895 ACCACGTAGAAATGTCCCGAATG
1 ACCACATAGAAATATCCCGAAGG
* *
42918 ACCACGTAGAATTATCCCGAAGG
1 ACCACATAGAAATATCCCGAAGG
*
42941 ACCGCATAGAA
1 ACCACATAGAA
42952 CCCTCGACTC
Statistics
Matches: 66, Mismatches: 14, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
23 66 1.00
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.18
Consensus pattern (23 bp):
ACCACATAGAAATATCCCGAAGG
Found at i:42913 original size:46 final size:46
Alignment explanation
Indices: 42849--42951 Score: 143
Period size: 46 Copynumber: 2.2 Consensus size: 46
42839 TCACTGAAAT
* * *
42849 ACCACATATAAATATCCCGAATGACCACATAGTATTGTCCCGAAGG
1 ACCACATAGAAATATCCCGAATGACCACATAGAATTATCCCGAAGG
* * *
42895 ACCACGTAGAAATGTCCCGAATGACCACGTAGAATTATCCCGAAGG
1 ACCACATAGAAATATCCCGAATGACCACATAGAATTATCCCGAAGG
*
42941 ACCGCATAGAA
1 ACCACATAGAA
42952 CCCTCGACTC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.18
Consensus pattern (46 bp):
ACCACATAGAAATATCCCGAATGACCACATAGAATTATCCCGAAGG
Found at i:43107 original size:14 final size:14
Alignment explanation
Indices: 43088--43122 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
43078 ATACAACCCC
43088 ATCACATAGCTTAT
1 ATCACATAGCTTAT
43102 ATCACATAGCTTAT
1 ATCACATAGCTTAT
43116 ATCACAT
1 ATCACAT
43123 GTTCATATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.34
Consensus pattern (14 bp):
ATCACATAGCTTAT
Found at i:45113 original size:101 final size:102
Alignment explanation
Indices: 44952--45204 Score: 271
Period size: 101 Copynumber: 2.5 Consensus size: 102
44942 TGGCAACATC
* * * * * * *
44952 CCTTCTAGTTCAATGGGAAGACATTCATCTGCCAATTTATTTGACATAAATATGGAGATGCATTC
1 CCTTCAAGTTTAAGGGGAAGGCATTCATCTGCCAACTTATTCGACCTAAATATGGAGATGCATTC
* * **
45017 GACACAACAATCT-GTTCAATAAC-CATATGATATTATG
66 GACACAACAAT-TAATTCAA-AACGCATATGACACGATG
* * * *
45054 CCTTCAAGTTCT-AGGGG-AGGCATTCATTTGCCAACTTCTTCGACCTCAATATGGAGATGCCTT
1 CCTTCAAGTT-TAAGGGGAAGGCATTCATCTGCCAACTTATTCGACCTAAATATGGAGATGCATT
* *
45117 TGACACAACAGTTAATTCAAAACGCATATGACACGATG
65 CGACACAACAATTAATTCAAAACGCATATGACACGATG
* * *
45155 CCTTCAAGTTTAAGGGGAATGCATTCATCTGCGAACTTGTTCGACCTAAA
1 CCTTCAAGTTTAAGGGGAAGGCATTCATCTGCCAACTTATTCGACCTAAA
45205 CATCAGAATC
Statistics
Matches: 124, Mismatches: 22, Indels: 10
0.79 0.14 0.06
Matches are distributed among these distances:
100 5 0.04
101 79 0.64
102 40 0.32
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.30
Consensus pattern (102 bp):
CCTTCAAGTTTAAGGGGAAGGCATTCATCTGCCAACTTATTCGACCTAAATATGGAGATGCATTC
GACACAACAATTAATTCAAAACGCATATGACACGATG
Found at i:51223 original size:16 final size:16
Alignment explanation
Indices: 51202--51237 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
51192 TTCGAGTAAA
51202 ATGTACTATCAATAAT
1 ATGTACTATCAATAAT
*
51218 ATGTACTATCAATGAT
1 ATGTACTATCAATAAT
51234 ATGT
1 ATGT
51238 GGGAGAGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (16 bp):
ATGTACTATCAATAAT
Found at i:54841 original size:18 final size:18
Alignment explanation
Indices: 54804--54866 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
54794 TGGAATTATT
* *
54804 ATAATA-TTTTAAAATTA
1 ATAATATTTTTATAATAA
54821 ATAATATTTTTATAATAA
1 ATAATATTTTTATAATAA
*
54839 ATAATATTAATTATATATTAA
1 ATAATATT--TT-TATAATAA
54860 ATAATAT
1 ATAATAT
54867 AATTAATCAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
17 6 0.15
18 17 0.44
20 2 0.05
21 14 0.36
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
ATAATATTTTTATAATAA
Found at i:54855 original size:21 final size:21
Alignment explanation
Indices: 54820--54871 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
54810 TTTTAAAATT
54820 AATAATATT--TT-TATAATA
1 AATAATATTAATTATATAATA
*
54838 AATAATATTAATTATATATTA
1 AATAATATTAATTATATAATA
54859 AATAATA-TAATTA
1 AATAATATTAATTA
54872 ATCATTTTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 9 0.30
20 8 0.27
21 13 0.43
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AATAATATTAATTATATAATA
Found at i:56511 original size:23 final size:23
Alignment explanation
Indices: 56463--56512 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
56453 TGAAGTTTGA
* *
56463 ATAAATTGAATTAAATGTTATGG
1 ATAAATTGAATTAAATGTGAAGG
56486 ATAAATTGAA-TAAATGTGAAGTG
1 ATAAATTGAATTAAATGTGAAG-G
56509 ATAA
1 ATAA
56513 GTTGGTTGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.48, C:0.00, G:0.18, T:0.34
Consensus pattern (23 bp):
ATAAATTGAATTAAATGTGAAGG
Found at i:56630 original size:14 final size:14
Alignment explanation
Indices: 56611--56641 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
56601 TAACACGTGG
56611 GTTTTAATGTATAT
1 GTTTTAATGTATAT
56625 GTTTTAATGTATAT
1 GTTTTAATGTATAT
56639 GTT
1 GTT
56642 AAGGATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.16, T:0.58
Consensus pattern (14 bp):
GTTTTAATGTATAT
Found at i:56789 original size:33 final size:34
Alignment explanation
Indices: 56724--56791 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
56714 ATAAGTTGAA
56724 TTTAATGTTAAATTTTGAATACTATAATTTGTAT
1 TTTAATGTTAAATTTTGAATACTATAATTTGTAT
* *
56758 TTTAATTTTAATTTTTGAATACTATAA-TTGTAT
1 TTTAATGTTAAATTTTGAATACTATAATTTGTAT
56791 T
1 T
56792 ATAAAAACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 7 0.22
34 25 0.78
ACGTcount: A:0.34, C:0.03, G:0.07, T:0.56
Consensus pattern (34 bp):
TTTAATGTTAAATTTTGAATACTATAATTTGTAT
Found at i:57326 original size:21 final size:21
Alignment explanation
Indices: 57302--57361 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 21
57292 ATAAAACCCT
*
57302 GCGGGCTAGGCATGTAACCTG
1 GCGGGCTAGGCATGTAACCTA
* *
57323 GCGGGCTAGGCAT-AAAACTA
1 GCGGGCTAGGCATGTAACCTA
*
57343 GCGGGCTAGGAATGTAACC
1 GCGGGCTAGGCATGTAACC
57362 CTACAAGATA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 16 0.50
21 16 0.50
ACGTcount: A:0.27, C:0.22, G:0.35, T:0.17
Consensus pattern (21 bp):
GCGGGCTAGGCATGTAACCTA
Found at i:59024 original size:17 final size:17
Alignment explanation
Indices: 58984--59025 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
58974 TTCATGGATA
58984 AATT-TAAATTAAAAAT
1 AATTATAAATTAAAAAT
* * *
59000 AATAATAAATTAACATT
1 AATTATAAATTAAAAAT
59017 AATTATAAA
1 AATTATAAA
59026 AAAAATATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (17 bp):
AATTATAAATTAAAAAT
Found at i:59236 original size:30 final size:31
Alignment explanation
Indices: 59155--59243 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 31
59145 GTAATAAATT
*
59155 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAA-AAATAAT-ATTATAT-AATATTATATTAA
59189 TAAAAAATAATATT-TAT-ATAATTATATTAA
1 TAAAAAATAATATTATATAAT-ATTATATTAA
*
59219 TATAAAATAATGATTATATTAATAT
1 TAAAAAATAAT-ATTATA-TAATAT
59244 AAAATATAAC
Statistics
Matches: 48, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
29 2 0.04
30 19 0.40
31 6 0.12
32 5 0.10
33 10 0.21
34 6 0.12
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (31 bp):
TAAAAAATAATATTATATAATATTATATTAA
Found at i:59258 original size:24 final size:22
Alignment explanation
Indices: 59208--59258 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 22
59198 ATATTTATAT
*
59208 AATTATATTAATATAAAATAAT
1 AATTATATTAATATAAAATAAC
*
59230 GATTATATTAATATAAAATATAAC
1 AATTATATTAATAT-AAA-ATAAC
59254 AATTA
1 AATTA
59259 ATAAAAATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 13 0.54
23 3 0.12
24 8 0.33
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (22 bp):
AATTATATTAATATAAAATAAC
Found at i:59462 original size:59 final size:60
Alignment explanation
Indices: 59366--59512 Score: 163
Period size: 59 Copynumber: 2.5 Consensus size: 60
59356 CAATTAATGA
* * * ** *
59366 AAAGTGCGTCCCCGGGGATGTGCCTTACCCTTATGGCATCTGACTCAGCA-AAATCCC-GT
1 AAAGTGCGTCCCCGAGGATGCGCCTTTCCCGCATGGCATCCGACTCAGCATAAA-CCCAGT
* * *
59425 GAAGTGCGTCCCCAAGGATGCGCCTTTCCCGCGTGGCATCCGACTCAGCATAAACCCAGGT
1 AAAGTGCGTCCCCGAGGATGCGCCTTTCCCGCATGGCATCCGACTCAGCATAAACCCA-GT
* *
59486 AAAGCGCGTCCCCGAGGATGCACCTTT
1 AAAGTGCGTCCCCGAGGATGCGCCTTT
59513 GTGCCACCTC
Statistics
Matches: 72, Mismatches: 13, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
59 44 0.61
60 3 0.04
61 25 0.35
ACGTcount: A:0.22, C:0.33, G:0.25, T:0.20
Consensus pattern (60 bp):
AAAGTGCGTCCCCGAGGATGCGCCTTTCCCGCATGGCATCCGACTCAGCATAAACCCAGT
Found at i:59512 original size:61 final size:59
Alignment explanation
Indices: 59399--59512 Score: 149
Period size: 61 Copynumber: 1.9 Consensus size: 59
59389 CTTACCCTTA
* * * *
59399 TGGCATCTGACTCAGCAAAATCCCGTGAAGTGCGTCCCCAAGGATGCGCCTTTCCCGCG
1 TGGCATCCGACTCAGCAAAATCCCGTAAAGCGCGTCCCCAAGGATGCACCTTTCCCGCG
*
59458 TGGCATCCGACTCAGCATAAA-CCCAGGTAAAGCGCGTCCCCGAGGATGCACCTTT
1 TGGCATCCGACTCAGCA-AAATCCC--GTAAAGCGCGTCCCCAAGGATGCACCTTT
59513 GTGCCACCTC
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
59 19 0.40
60 3 0.06
61 25 0.53
ACGTcount: A:0.23, C:0.33, G:0.25, T:0.19
Consensus pattern (59 bp):
TGGCATCCGACTCAGCAAAATCCCGTAAAGCGCGTCCCCAAGGATGCACCTTTCCCGCG
Done.