Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001375.1 Hibiscus syriacus cultivar Beakdansim tig00002687_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: 71592
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3177 original size:28 final size:28
Alignment explanation
Indices: 3133--3217 Score: 143
Period size: 28 Copynumber: 3.0 Consensus size: 28
3123 CTCTCCATGT
* *
3133 ACATTATGTTGTCGAGCCAGTGATTGAA
1 ACATTGTGTTGTCGAGCCAGTGCTTGAA
*
3161 ACATTGTGTTGTTGAGCCAGTGCTTGAA
1 ACATTGTGTTGTCGAGCCAGTGCTTGAA
3189 ACATTGTGTTGTCGAGCCAGTGCTTGAA
1 ACATTGTGTTGTCGAGCCAGTGCTTGAA
3217 A
1 A
3218 GCAATAGCGG
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 53 1.00
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (28 bp):
ACATTGTGTTGTCGAGCCAGTGCTTGAA
Found at i:5624 original size:16 final size:16
Alignment explanation
Indices: 5579--5627 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
5569 TGAGTAATTG
*
5579 GAATTTTAGGAGTTGA
1 GAATTTTAGGATTTGA
5595 -AA-TTTAGGGATTTGA
1 GAATTTTA-GGATTTGA
*
5610 GAATTTTAGGTTTTGA
1 GAATTTTAGGATTTGA
5626 GA
1 GA
5628 TCATAATAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
14 4 0.14
15 9 0.32
16 11 0.39
17 4 0.14
ACGTcount: A:0.31, C:0.00, G:0.29, T:0.41
Consensus pattern (16 bp):
GAATTTTAGGATTTGA
Found at i:6309 original size:13 final size:13
Alignment explanation
Indices: 6280--6320 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
6270 ACCATTTGAG
*
6280 AGAAAGAGAGAAGA
1 AGAAAGA-AGAAAA
6294 AGAAAGAAGAAAA
1 AGAAAGAAGAAAA
*
6307 AGAAAAAAGAAAA
1 AGAAAGAAGAAAA
6320 A
1 A
6321 ATAAGTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 18 0.72
14 7 0.28
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AGAAAGAAGAAAA
Found at i:18395 original size:2 final size:2
Alignment explanation
Indices: 18388--18457 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
18378 CCAGGTTTGA
18388 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
18430 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
18458 TAACAGTAGG
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:19864 original size:14 final size:15
Alignment explanation
Indices: 19845--19875 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
19835 ATTATAAAAC
19845 AATAAAATAT-TTAA
1 AATAAAATATATTAA
19859 AATAAAATATATTAA
1 AATAAAATATATTAA
19874 AA
1 AA
19876 AAATCAATCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AATAAAATATATTAA
Found at i:19876 original size:16 final size:16
Alignment explanation
Indices: 19832--19876 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 16
19822 AAAAATATCA
*
19832 AAAAT-TATAAAACAAT
1 AAAATATATTAAA-AAT
19848 AAAATAT-TT-AAAAT
1 AAAATATATTAAAAAT
19862 AAAATATATTAAAAA
1 AAAATATATTAAAAA
19877 AATCAATCGA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
14 10 0.40
15 4 0.16
16 10 0.40
17 1 0.04
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATATATTAAAAAT
Found at i:20095 original size:5 final size:5
Alignment explanation
Indices: 20085--20112 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
20075 ATGCAACTTA
20085 TATTT TATTT TATTT TATTT TATTT TAT
1 TATTT TATTT TATTT TATTT TATTT TAT
20113 CTAAACCTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TATTT
Found at i:23760 original size:20 final size:21
Alignment explanation
Indices: 23698--23760 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
23688 CCCTCGAGGA
* *
23698 AAAGGATCGATCCCTTTACCA
1 AAAGGATCAATCCCTTTACCT
**
23719 AAAGGATCAATCCCTTCCCCT
1 AAAGGATCAATCCCTTTACCT
* *
23740 AAATGATCAA-CCCTTTTCCT
1 AAAGGATCAATCCCTTTACCT
23760 A
1 A
23761 TAACGCTTGA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
20 9 0.26
21 26 0.74
ACGTcount: A:0.32, C:0.32, G:0.10, T:0.27
Consensus pattern (21 bp):
AAAGGATCAATCCCTTTACCT
Found at i:26218 original size:21 final size:21
Alignment explanation
Indices: 26152--26218 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 21
26142 ATTCTTAAGA
* *
26152 AAAATATTCGATCTCTTTACC
1 AAAATAATCGATCCCTTTACC
** * * * **
26173 AAAAGGATCGACCCCATGAGG
1 AAAATAATCGATCCCTTTACC
26194 AAAATAATCGATCCCTTTACC
1 AAAATAATCGATCCCTTTACC
26215 AAAA
1 AAAA
26219 GGATTGATTC
Statistics
Matches: 30, Mismatches: 16, Indels: 0
0.65 0.35 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.40, C:0.24, G:0.12, T:0.24
Consensus pattern (21 bp):
AAAATAATCGATCCCTTTACC
Found at i:27113 original size:18 final size:19
Alignment explanation
Indices: 27092--27132 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
27082 TTTTTAGACT
*
27092 AAGTCAAT-GGCTAGGTTA
1 AAGTCAATAGGCTAGGTCA
*
27110 AAGTCAATAGTCTAGGTCA
1 AAGTCAATAGGCTAGGTCA
27129 AAGT
1 AAGT
27133 TAACGATTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (19 bp):
AAGTCAATAGGCTAGGTCA
Found at i:31246 original size:24 final size:23
Alignment explanation
Indices: 31216--31262 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 23
31206 TCAACAAAGC
31216 AGGAATAAAATATATTAAATTGAA
1 AGGAATAAAATATATT-AATTGAA
31240 AGGAATAAAATATATTAATTGAA
1 AGGAATAAAATATATTAATTGAA
31263 GAAAATCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.57, C:0.00, G:0.13, T:0.30
Consensus pattern (23 bp):
AGGAATAAAATATATTAATTGAA
Found at i:31314 original size:5 final size:5
Alignment explanation
Indices: 31304--31333 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
31294 TTCACATTAC
31304 TAAAA TAAAA TAAAAA TAAAA TAAAA TAAA
1 TAAAA TAAAA T-AAAA TAAAA TAAAA TAAA
31334 GAGTAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:31321 original size:11 final size:10
Alignment explanation
Indices: 31304--31333 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
31294 TTCACATTAC
31304 TAAAATAAAA
1 TAAAATAAAA
31314 TAAAAATAAAA
1 T-AAAATAAAA
31325 TAAAATAAA
1 TAAAATAAA
31334 GAGTAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (10 bp):
TAAAATAAAA
Found at i:32588 original size:3 final size:3
Alignment explanation
Indices: 32582--32622 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
32572 TATTATTATT
* *
32582 TAA TAA TAA TAA T-A TAA TGA TAA TAA T-A TAA TAA TGA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
32623 GGGGTAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 4 0.12
3 28 0.88
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:32599 original size:14 final size:14
Alignment explanation
Indices: 32582--32622 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
32572 TATTATTATT
32582 TAATAATAATAATA
1 TAATAATAATAATA
*
32596 TAATGATAATAATA
1 TAATAATAATAATA
*
32610 TAATAATGATAAT
1 TAATAATAATAAT
32623 GGGGTAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.37
Consensus pattern (14 bp):
TAATAATAATAATA
Found at i:32604 original size:17 final size:17
Alignment explanation
Indices: 32584--32622 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
32574 TTATTATTTA
32584 ATAATAATA-ATATAATG
1 ATAATAATATA-ATAATG
32601 ATAATAATATAATAATG
1 ATAATAATATAATAATG
32618 ATAAT
1 ATAAT
32623 GGGGTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 20 0.95
18 1 0.05
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (17 bp):
ATAATAATATAATAATG
Found at i:33466 original size:176 final size:176
Alignment explanation
Indices: 32924--33849 Score: 1415
Period size: 177 Copynumber: 5.2 Consensus size: 176
32914 TCAAGTGAGA
*
32924 TAAAAT-TTATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGTCCGTAGGATTTACAAATC
1 TAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGG-CCGTAGGATTTACAAATC
* * * * *
32988 AAAAAACCCCCAAAGGCTTAGTTTCTTAGTTATCAAGGAACCCATTTGTTAGGCTTAACTTCCTT
65 AAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTT
*
33053 TAACAACTCTTTTGAGATAATTAGTAAACCCCTGAAGGCTTGGTTTC
130 TAACAGCTCTTTTGAGATAATTAGTAAACCCCTGAAGGCTTGGTTTC
* *
33100 TAAAATCTCATTTGAAAACATCTTGCACTGAAGGTCTTATGGATGGCCTGTAGGACTTACAAATC
1 TAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCC-GTAGGATTTACAAATC
* * *
33165 AAGAAACCCCCGAAGGCTTGGTTTTTTAGTTGTCAAGGAACCTCTTTGTTAGGCTTAGCTTCCTT
65 AAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTT
* *
33230 TAACAGCTCTTTTGAGATAATTAGTAAACCCATAAAGGCTTGGTTTC
130 TAACAGCTCTTTTGAGATAATTAGTAAACCCCTGAAGGCTTGGTTTC
* * * *
33277 TAAAATATCATTTGGAAACATCCTGCATTTAAGGTCTTATGGATGGCTCGTAGGATTTACAAATC
1 TAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGC-CGTAGGATTTACAAATC
* * *
33342 AAGAAACCCCTGAAGGCTT-GTTTCTTAATTGTCAATGAACCCCTTTGTTAGGCTTAGCTTCCTT
65 AAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTT
* * * *
33406 TAACAGCTTTTTTTAGATAATTAGTAAACCCCCGAAGTCTTGGTTTC
130 TAACAGCTCTTTTGAGATAATTAGTAAACCCCTGAAGGCTTGGTTTC
* *
33453 TAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCGTAGGACTTATAAATCA
1 TAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCGTAGGATTTACAAATCA
*
33518 AGAAACCCCCGAAGGCTTGGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTTT
66 AGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTTT
* ** *
33583 TACAATTCTTTTGAGATAATTAGTAAACCCCTGAAGACTTGGTTTC
131 AACAGCTCTTTTGAGATAATTAGTAAACCCCTGAAGGCTTGGTTTC
*
33629 TAAAATCTCATTTGAAAACATCCTGCACTAAAGGTCTTATGGATGGCCCGTAGGATTTACAAATC
1 TAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGG-CCGTAGGATTTACAAATC
* * * *
33694 AAGAAACCCCCAAAGGCTTAGTTTATTAGTTGTCAAGTAACCCTTTTGTTAGGCTTAGCTTCCTT
65 AAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTT
* * *
33759 TAACGGCTCTTTTGAGATAATTAGTAAACCCCCGAAAGCTTGGTTTC
130 TAACAGCTCTTTTGAGATAATTAGTAAACCCCTGAAGGCTTGGTTTC
* * *
33806 TAAAATCTCATTTGGAAACATCCTACACTAAAGGTCTTATGGAT
1 TAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGAT
33850 TGCCCGAAGG
Statistics
Matches: 681, Mismatches: 64, Indels: 9
0.90 0.08 0.01
Matches are distributed among these distances:
175 33 0.05
176 261 0.38
177 386 0.57
178 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (176 bp):
TAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCGTAGGATTTACAAATCA
AGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTGTTAGGCTTAGCTTCCTTT
AACAGCTCTTTTGAGATAATTAGTAAACCCCTGAAGGCTTGGTTTC
Found at i:33917 original size:42 final size:42
Alignment explanation
Indices: 33866--33947 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
33856 AAGGTCTTAT
* * *
33866 CATCTTGCTCAAAAGGCTTACAGATGACCCGAAGGCTTTAAA
1 CATCATGCTCAAAAGACTTACAGATGACCCGAAGGATTTAAA
* *
33908 CATCATGCTCGAAAGACTTACTGATGACCCGAAGGATTTA
1 CATCATGCTCAAAAGACTTACAGATGACCCGAAGGATTTA
33948 CAAATTCGGG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (42 bp):
CATCATGCTCAAAAGACTTACAGATGACCCGAAGGATTTAAA
Found at i:35508 original size:41 final size:41
Alignment explanation
Indices: 35419--35511 Score: 102
Period size: 41 Copynumber: 2.2 Consensus size: 41
35409 TTGATATGAG
*
35419 CTTTCAAAATGCCCCACATGGATCATTTCTGTCTAAAATGGA
1 CTTTCAAAATGCCCCACAT-GATCATTTCTGTCTAAAATAGA
* *
35461 CCTTCAAAATGCCCCA-AT-ATTCTATTTCTGGT-TTAAATAGA
1 CTTTCAAAATGCCCCACATGA-TC-ATTTCT-GTCTAAAATAGA
35502 CTTTCAAAAT
1 CTTTCAAAAT
35512 ATCCCAACCT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
39 1 0.02
40 2 0.05
41 24 0.55
42 17 0.39
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.34
Consensus pattern (41 bp):
CTTTCAAAATGCCCCACATGATCATTTCTGTCTAAAATAGA
Found at i:35659 original size:52 final size:52
Alignment explanation
Indices: 35521--35716 Score: 279
Period size: 52 Copynumber: 3.8 Consensus size: 52
35511 TATCCCAACC
* * * * *
35521 TTTTCATGCTGGTGTGAGCTTTCAAGATGCCCCACATGGATTACTTTTGTCTT
1 TTTTCATGCTGATGTGAGCCTTCAAGATACCCCACATGGATTACTTCTATC-T
* *
35574 TTTTCATGCTGATGTGAGCCTTCAAAATGCCCCACATGGATTACTTCTATCT
1 TTTTCATGCTGATGTGAGCCTTCAAGATACCCCACATGGATTACTTCTATCT
* *
35626 TTTTCATGTTGATGTGAGCATTCAAGATACCCCACATGGATTACTTCTATC-
1 TTTTCATGCTGATGTGAGCCTTCAAGATACCCCACATGGATTACTTCTATCT
*
35677 TTTTCATGTTGATGTGAGCCTTCAAGATA-CCCACATGGAT
1 TTTTCATGCTGATGTGAGCCTTCAAGATACCCCACATGGAT
35717 AATATGGACC
Statistics
Matches: 133, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
50 11 0.08
51 28 0.21
52 48 0.36
53 46 0.35
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (52 bp):
TTTTCATGCTGATGTGAGCCTTCAAGATACCCCACATGGATTACTTCTATCT
Found at i:37204 original size:20 final size:18
Alignment explanation
Indices: 37181--37313 Score: 91
Period size: 17 Copynumber: 7.3 Consensus size: 18
37171 CTTGATTCAA
37181 TTTCTTTGTTCTTATTTTCT
1 TTTCTTT-TTCTT-TTTTCT
*
37201 TTTCTATTTTCTCTTTTCTT
1 TTTCT-TTTTCTTTTTTC-T
37221 TTTCTTTTTTTCTTTTTTCT
1 TTTC--TTTTTCTTTTTTCT
37241 TTT-TTTATT-TTTTTT-T
1 TTTCTTT-TTCTTTTTTCT
*
37257 ATTT-TTTTTATTTTTTCT
1 -TTTCTTTTTCTTTTTTCT
* *
37275 TCT-TTTTTCTTCTTT-T
1 TTTCTTTTTCTTTTTTCT
*
37291 TTTCTTTTT-TTTCTTTTT
1 TTTCTTTTTCTTT-TTTCT
37309 TTTCT
1 TTTCT
37314 GATGGATGAG
Statistics
Matches: 95, Mismatches: 7, Indels: 24
0.75 0.06 0.19
Matches are distributed among these distances:
16 8 0.08
17 41 0.43
18 9 0.09
19 5 0.05
20 18 0.19
21 13 0.14
22 1 0.01
ACGTcount: A:0.04, C:0.13, G:0.01, T:0.83
Consensus pattern (18 bp):
TTTCTTTTTCTTTTTTCT
Found at i:37210 original size:7 final size:6
Alignment explanation
Indices: 37181--37308 Score: 72
Period size: 6 Copynumber: 20.5 Consensus size: 6
37171 CTTGATTCAA
37181 TTTCTT TGTTCTT ATTT-TCT TTTCTAT TTTCTCT TTTCTT TTTCTTTT
1 TTTCTT T-TTCTT -TTTCT-T TTTCT-T TTTCT-T TTTCTT TTTC--TT
* * *
37229 TTTCTTT TTTCTT TTT-TT ATTTTTT TTTATT TTT-TT TAT-TT TTTCTT
1 TTTC-TT TTTCTT TTTCTT -TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
37276 CTTT-TT TCTTCTT TTT-TT CTTT-TT TTTCTT TTT
1 -TTTCTT T-TTCTT TTTCTT -TTTCTT TTTCTT TTT
37309 TTTCTGATGG
Statistics
Matches: 103, Mismatches: 5, Indels: 28
0.76 0.04 0.21
Matches are distributed among these distances:
5 16 0.16
6 44 0.43
7 36 0.35
8 7 0.07
ACGTcount: A:0.04, C:0.12, G:0.01, T:0.83
Consensus pattern (6 bp):
TTTCTT
Found at i:37219 original size:19 final size:20
Alignment explanation
Indices: 37195--37309 Score: 80
Period size: 20 Copynumber: 5.8 Consensus size: 20
37185 TTTGTTCTTA
37195 TTTTCTTTTC-TATTTTCTC
1 TTTTCTTTTCTTATTTTCTC
* *
37214 TTTTCTTTTTCTTTTTTTCTT
1 TTTTC-TTTTCTTATTTTCTC
*
37235 TTTTCTTTTTTTATTTT-T-
1 TTTTCTTTTCTTATTTTCTC
* * *
37253 TTTTATTTTTTTTATTTTTTC
1 TTTT-CTTTTCTTATTTTCTC
* *
37274 TTCTT-TTTTCTTCTTTTTTTC
1 TT-TTCTTTTCTT-ATTTTCTC
37295 TTTT-TTTTCTT-TTTT
1 TTTTCTTTTCTTATTTT
37310 TTCTGATGGA
Statistics
Matches: 82, Mismatches: 7, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
18 8 0.10
19 18 0.22
20 31 0.38
21 23 0.28
22 2 0.02
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.84
Consensus pattern (20 bp):
TTTTCTTTTCTTATTTTCTC
Found at i:37229 original size:1 final size:1
Alignment explanation
Indices: 37214--37311 Score: 79
Period size: 1 Copynumber: 98.0 Consensus size: 1
37204 CTATTTTCTC
* * * * * * * * *
37214 TTTTCTTTTTCTTTTTTTCTTTTTTCTTTTTTTATTTTTTTTTATTTTTTTTATTTTTTCTTCTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * *
37279 TTTTCTTCTTTTTTTCTTTTTTTTCTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
37312 CTGATGGATG
Statistics
Matches: 71, Mismatches: 26, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 71 1.00
ACGTcount: A:0.03, C:0.10, G:0.00, T:0.87
Consensus pattern (1 bp):
T
Found at i:37232 original size:8 final size:8
Alignment explanation
Indices: 37219--37310 Score: 93
Period size: 8 Copynumber: 11.6 Consensus size: 8
37209 TTCTCTTTTC
37219 TTTTTCTT
1 TTTTTCTT
37227 TTTTTC-T
1 TTTTTCTT
37234 TTTTTCTT
1 TTTTTCTT
*
37242 TTTTTATT
1 TTTTTCTT
37250 TTTTT-TT
1 TTTTTCTT
*
37257 ATTTT-TT
1 TTTTTCTT
*
37264 TTATT-TT
1 TTTTTCTT
*
37271 TTCTTCTTT
1 TTTTTC-TT
37280 TTTCTTCTT
1 TTT-TTCTT
37289 TTTTTCTTT
1 TTTTTC-TT
37298 TTTTTCTT
1 TTTTTCTT
37306 TTTTT
1 TTTTT
37311 TCTGATGGAT
Statistics
Matches: 73, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
7 24 0.33
8 29 0.40
9 17 0.23
10 3 0.04
ACGTcount: A:0.03, C:0.10, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTCTT
Found at i:37240 original size:28 final size:26
Alignment explanation
Indices: 37195--37313 Score: 116
Period size: 28 Copynumber: 4.4 Consensus size: 26
37185 TTTGTTCTTA
* *
37195 TTTTCTTTTCTATTTTCTCTTTTCTTT
1 TTTTTTTTTCTTTTTTCTCTTTT-TTT
*
37222 TTCTTTTTTTCTTTTTTCT-TTTTTTA
1 TT-TTTTTTTCTTTTTTCTCTTTTTTT
* * *
37248 TTTTTTTTTATTTTTTTTATTTTTTCT
1 TTTTTTTTTCTTTTTTCTCTTTTTT-T
37275 TCTTTTTTCTTCTTTTTT-TCTTTTTTT
1 T-TTTTTT-TTCTTTTTTCTCTTTTTTT
37302 TCTTTTTTTTCT
1 T-TTTTTTTTCT
37314 GATGGATGAG
Statistics
Matches: 79, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
25 14 0.18
26 14 0.18
27 16 0.20
28 27 0.34
29 8 0.10
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (26 bp):
TTTTTTTTTCTTTTTTCTCTTTTTTT
Found at i:37246 original size:10 final size:10
Alignment explanation
Indices: 37207--37311 Score: 96
Period size: 10 Copynumber: 10.5 Consensus size: 10
37197 TTCTTTTCTA
*
37207 TTTTCTCTTT
1 TTTTTTCTTT
37217 TCTTTTTC--T
1 T-TTTTTCTTT
37226 TTTTTTCTTT
1 TTTTTTCTTT
37236 TTTCTTT-TTT
1 TTT-TTTCTTT
37246 TATTTTT-TTT
1 T-TTTTTCTTT
37256 TATTTTT-TTT
1 T-TTTTTCTTT
*
37266 ATTTTTTCTTC
1 -TTTTTTCTTT
37277 TTTTTTCTTCT
1 TTTTTTCTT-T
37288 TTTTTTC-TT
1 TTTTTTCTTT
37297 TTTTTTCTTT
1 TTTTTTCTTT
37307 TTTTT
1 TTTTT
37312 CTGATGGATG
Statistics
Matches: 83, Mismatches: 3, Indels: 18
0.80 0.03 0.17
Matches are distributed among these distances:
8 6 0.07
9 10 0.12
10 47 0.57
11 20 0.24
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:37309 original size:7 final size:7
Alignment explanation
Indices: 37181--37300 Score: 92
Period size: 7 Copynumber: 17.4 Consensus size: 7
37171 CTTGATTCAA
37181 TTTCTTT
1 TTTCTTT
*
37188 GTTCTTAT
1 TTTCTT-T
37196 TTTC--T
1 TTTCTTT
*
37201 TTTCTAT
1 TTTCTTT
*
37208 TTTCTCT
1 TTTCTTT
37215 TTTC-TT
1 TTTCTTT
37221 TTTCTTTT
1 TTTC-TTT
37229 TTTCTTT
1 TTTCTTT
37236 TTTCTTT
1 TTTCTTT
37243 TTT-TATT
1 TTTCT-TT
37250 TTT-TTT
1 TTTCTTT
37256 TATT-TTT
1 T-TTCTTT
*
37263 TTTATTT
1 TTTCTTT
*
37270 TTTCTTC
1 TTTCTTT
37277 TTT-TTT
1 TTTCTTT
*
37283 CTTCTTTT
1 TTTC-TTT
37291 TTTCTTT
1 TTTCTTT
37298 TTT
1 TTT
37301 TTCTTTTTTT
Statistics
Matches: 94, Mismatches: 9, Indels: 20
0.76 0.07 0.16
Matches are distributed among these distances:
5 5 0.05
6 15 0.16
7 58 0.62
8 16 0.17
ACGTcount: A:0.04, C:0.12, G:0.01, T:0.82
Consensus pattern (7 bp):
TTTCTTT
Found at i:37310 original size:19 final size:19
Alignment explanation
Indices: 37181--37311 Score: 105
Period size: 19 Copynumber: 7.1 Consensus size: 19
37171 CTTGATTCAA
* * *
37181 TTTCTTTGTTCTTATTTTCT
1 TTTCTTT-TTTTTCTTTTTT
* *
37201 TTTCTATTTTCTCTTTTCTT
1 TTTCTTTTTTTTCTTTT-TT
37221 TTTC-TTTTTTTC---TTT
1 TTTCTTTTTTTTCTTTTTT
*
37236 TTTC-TTTTTTTATTTTTT
1 TTTCTTTTTTTTCTTTTTT
* *
37254 TTTATTTTTTTTATTTTTT
1 TTTCTTTTTTTTCTTTTTT
*
37273 CTTC--TTTTTTCTTCTTTT
1 TTTCTTTTTTTTCTT-TTTT
37291 TTTCTTTTTTTTCTTTTTT
1 TTTCTTTTTTTTCTTTTTT
37310 TT
1 TT
37312 CTGATGGATG
Statistics
Matches: 90, Mismatches: 13, Indels: 17
0.75 0.11 0.14
Matches are distributed among these distances:
15 13 0.14
16 1 0.01
17 8 0.09
18 13 0.14
19 35 0.39
20 20 0.22
ACGTcount: A:0.04, C:0.12, G:0.01, T:0.83
Consensus pattern (19 bp):
TTTCTTTTTTTTCTTTTTT
Found at i:39767 original size:42 final size:42
Alignment explanation
Indices: 39708--39797 Score: 162
Period size: 42 Copynumber: 2.1 Consensus size: 42
39698 TCTGATTTTC
39708 TTTTTGCCATTATCTTGAAAACCTTGTGAATGTTCGTATAGA
1 TTTTTGCCATTATCTTGAAAACCTTGTGAATGTTCGTATAGA
* *
39750 TTTTTGTCATTATCTTGAAAACCTTGTGAATGTTTGTATAGA
1 TTTTTGCCATTATCTTGAAAACCTTGTGAATGTTCGTATAGA
39792 TTTTTG
1 TTTTTG
39798 ATTTGATTCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.24, C:0.11, G:0.17, T:0.48
Consensus pattern (42 bp):
TTTTTGCCATTATCTTGAAAACCTTGTGAATGTTCGTATAGA
Found at i:44056 original size:13 final size:15
Alignment explanation
Indices: 44038--44069 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
44028 AAAGAGTAAT
44038 AATTAAAG-TATT-A
1 AATTAAAGATATTGA
44051 AATTAAAGATATTGA
1 AATTAAAGATATTGA
44066 AATT
1 AATT
44070 TAAATGGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 4 0.24
15 5 0.29
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (15 bp):
AATTAAAGATATTGA
Found at i:45353 original size:3 final size:3
Alignment explanation
Indices: 45347--45415 Score: 101
Period size: 3 Copynumber: 24.3 Consensus size: 3
45337 TATTATTATT
45347 TAA TAA TAA TAA TAA TAA TAA -AA -AA TAA TAA TAA TAA TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
45392 TAA TAA T-A TAA TAA TAA TGA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
45416 GGGGCAAAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
2 8 0.13
3 53 0.87
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:45373 original size:22 final size:23
Alignment explanation
Indices: 45348--45414 Score: 102
Period size: 22 Copynumber: 3.0 Consensus size: 23
45338 ATTATTATTT
45348 AATAATAATAATAATAATA-AAA
1 AATAATAATAATAATAATATAAA
*
45370 AATAATAATAATAATAATATAAT
1 AATAATAATAATAATAATATAAA
45393 AATAAT-ATAATAATAATGATAA
1 AATAATAATAATAATAAT-ATAA
45415 TGGGGCAAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
22 30 0.71
23 12 0.29
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.31
Consensus pattern (23 bp):
AATAATAATAATAATAATATAAA
Found at i:45381 original size:25 final size:27
Alignment explanation
Indices: 45347--45415 Score: 101
Period size: 25 Copynumber: 2.7 Consensus size: 27
45337 TATTATTATT
45347 TAATAATAATAATAATAATAA-AA-AA
1 TAATAATAATAATAATAATAATAATAA
45372 TAATAATAATAATAAT-ATAATAATAA
1 TAATAATAATAATAATAATAATAATAA
*
45398 T-ATAATAATAATGATAAT
1 TAATAATAATAATAATAAT
45416 GGGGCAAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
24 4 0.10
25 31 0.77
26 5 0.12
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (27 bp):
TAATAATAATAATAATAATAATAATAA
Found at i:49497 original size:15 final size:16
Alignment explanation
Indices: 49477--49508 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
49467 GGTACCCATA
49477 TTAAATAAAA-AAAAT
1 TTAAATAAAATAAAAT
49492 TTAAATAAAATAAAAT
1 TTAAATAAAATAAAAT
49508 T
1 T
49509 AAAAAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
TTAAATAAAATAAAAT
Found at i:49510 original size:15 final size:14
Alignment explanation
Indices: 49476--49511 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 14
49466 AGGTACCCAT
49476 ATTAAATAAAAAAA
1 ATTAAATAAAAAAA
49490 ATTTAAATAAAATAAA
1 A-TTAAATAAAA-AAA
49506 ATTAAA
1 ATTAAA
49512 AAATTTAGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 1 0.05
15 15 0.75
16 4 0.20
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
ATTAAATAAAAAAA
Found at i:61407 original size:13 final size:13
Alignment explanation
Indices: 61385--61418 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
61375 AGGGGGATTA
*
61385 ATTTTCAAAATTG
1 ATTTTCAAAAATG
61398 A-TTTCAAAAATG
1 ATTTTCAAAAATG
61410 ATTTTCAAA
1 ATTTTCAAA
61419 GAAAATCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (13 bp):
ATTTTCAAAAATG
Found at i:61564 original size:17 final size:18
Alignment explanation
Indices: 61523--61565 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
61513 ATGAATTTTA
*
61523 AAATTTTATATTCAATTT
1 AAATTATATATTCAATTT
*
61541 AACATTATATATTCGA-TT
1 AA-ATTATATATTCAATTT
61559 AAATTAT
1 AAATTAT
61566 TTGAATATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 5 0.23
18 6 0.27
19 11 0.50
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (18 bp):
AAATTATATATTCAATTT
Found at i:61866 original size:20 final size:20
Alignment explanation
Indices: 61841--61893 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
61831 TGTAATTTAG
*
61841 GTACCGATACGCTCTTGAGT
1 GTACCGATACACTCTTGAGT
61861 GTACCGATACACTCTTGAGT
1 GTACCGATACACTCTTGAGT
61881 GTACCGATACACT
1 GTACCGATACACT
61894 AGGTCAACCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (20 bp):
GTACCGATACACTCTTGAGT
Found at i:66153 original size:17 final size:17
Alignment explanation
Indices: 66131--66169 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
66121 TATAACTCCT
66131 TTCTTCCTTTTACTTTC
1 TTCTTCCTTTTACTTTC
66148 TTCTTCCTTTTACTTTC
1 TTCTTCCTTTTACTTTC
66165 TTCTT
1 TTCTT
66170 TCTCTTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.05, C:0.28, G:0.00, T:0.67
Consensus pattern (17 bp):
TTCTTCCTTTTACTTTC
Found at i:66808 original size:17 final size:17
Alignment explanation
Indices: 66786--66824 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
66776 TTAAAAGAGA
66786 AAGAAGAAAGTAAAAGG
1 AAGAAGAAAGTAAAAGG
66803 AAGAAGAAAGTAAAAGG
1 AAGAAGAAAGTAAAAGG
66820 AAGAA
1 AAGAA
66825 AGGAGTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.28, T:0.05
Consensus pattern (17 bp):
AAGAAGAAAGTAAAAGG
Done.