Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008134.1 Hibiscus syriacus cultivar Beakdansim tig00110689_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: 61509
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Found at i:1373 original size:7 final size:7
Alignment explanation
Indices: 1363--1388 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1353 GTATTTTCTT
1363 TTTTTTC
1 TTTTTTC
1370 TTTTTTC
1 TTTTTTC
1377 TTTTTTC
1 TTTTTTC
1384 TTTTT
1 TTTTT
1389 GAATTAATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:3903 original size:2 final size:2
Alignment explanation
Indices: 3896--3925 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3886 ATTTAAAAAC
3896 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
3926 TTAATTTCGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9842 original size:15 final size:15
Alignment explanation
Indices: 9802--9843 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
9792 AGGGTAAGTT
*
9802 TAAAT-TTATAAAGA
1 TAAATATTAAAAAGA
*
9816 TTAATAATTAAAAAGA
1 TAAAT-ATTAAAAAGA
9832 TAAATATTAAAA
1 TAAATATTAAAA
9844 TAATTCATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 4 0.17
15 7 0.30
16 12 0.52
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (15 bp):
TAAATATTAAAAAGA
Found at i:11176 original size:16 final size:16
Alignment explanation
Indices: 11157--11221 Score: 85
Period size: 16 Copynumber: 4.1 Consensus size: 16
11147 CTTTCAGATC
* *
11157 GGTTAATTTCAGTTTG
1 GGTTAATTTCGGTTCG
**
11173 GGTTGCTTTCGGTTCG
1 GGTTAATTTCGGTTCG
11189 GGTTAATTTCGGTTCG
1 GGTTAATTTCGGTTCG
*
11205 GTTTAATTTCGGTTCG
1 GGTTAATTTCGGTTCG
11221 G
1 G
11222 ATGCTTTGGT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 42 1.00
ACGTcount: A:0.11, C:0.12, G:0.31, T:0.46
Consensus pattern (16 bp):
GGTTAATTTCGGTTCG
Found at i:13988 original size:25 final size:25
Alignment explanation
Indices: 13841--13982 Score: 252
Period size: 25 Copynumber: 5.8 Consensus size: 25
13831 TGGAAGGGGA
13841 TTAGGG-TTGAAACCCTAAATTGAT
1 TTAGGGTTTGAAACCCTAAATTGAT
13865 TTA-GGTTTGAAACCCTAAATTGAT
1 TTAGGGTTTGAAACCCTAAATTGAT
*
13889 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAATTGAT
*
13914 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAATTGAT
13939 TTAGGGTTTGAAACCCTAAATTGAT
1 TTAGGGTTTGAAACCCTAAATTGAT
13964 TTAGGGTTTGAAACCCTAA
1 TTAGGGTTTGAAACCCTAA
13983 TCTGATGGGT
Statistics
Matches: 114, Mismatches: 2, Indels: 3
0.96 0.02 0.03
Matches are distributed among these distances:
23 2 0.02
24 24 0.21
25 88 0.77
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAAATTGAT
Found at i:14124 original size:3 final size:3
Alignment explanation
Indices: 14116--14173 Score: 77
Period size: 3 Copynumber: 19.7 Consensus size: 3
14106 TGCAAAATTG
14116 TAA TAA TAAA TAA TAA TAA -AA TAA T-A TAA TATA TAA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA
14161 TAA TAA TAA -AA TA
1 TAA TAA TAA TAA TA
14174 CGGAAAAAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
2 6 0.12
3 38 0.76
4 6 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:14145 original size:23 final size:24
Alignment explanation
Indices: 14118--14165 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
14108 CAAAATTGTA
14118 ATAATAAATAATAATAA-AATAAT
1 ATAATAAATAATAATAATAATAAT
*
14141 ATAATATATAATAATAATAATAAT
1 ATAATAAATAATAATAATAATAAT
14165 A
1 A
14166 ATAAAATACG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (24 bp):
ATAATAAATAATAATAATAATAAT
Found at i:14534 original size:87 final size:87
Alignment explanation
Indices: 14374--14751 Score: 524
Period size: 87 Copynumber: 4.3 Consensus size: 87
14364 CGTCTAAGGG
* * * * * * * * * *
14374 TGACATGGCTCCTACGTGATGAGGAAATCTGGTCATTTTAGGGATGATAACTCGGTTCCTACGTA
1 TGACACGGCTCTTACGTGATGAAGAGATCTGGCCATCTAAAGG-TGATAACACGGTTCCTACGTG
*
14439 ATGAGGACGACTGGTTATCAGGT
65 ATGAGGACGGCTGGTTATCAGGT
*
14462 TGACACGGCTCTTACGTGATGAAGAGATCTGGCCATCTAAAGGTGATAACACGGTTCCTACATGA
1 TGACACGGCTCTTACGTGATGAAGAGATCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
14527 TGAGGACGGCTGGTTATCAGGT
66 TGAGGACGGCTGGTTATCAGGT
14549 TGACACGGCTCTTACGTGATGAAGAGATCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
1 TGACACGGCTCTTACGTGATGAAGAGATCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
14614 TGAGGACGGCTGGTTATCAGGT
66 TGAGGACGGCTGGTTATCAGGT
*
14636 TGACACGGCTCTTACGTGATG-AGAGATCTGGCCATCTAAAGGTGAGGTGATAACTCGGTTCCTA
1 TGACACGGCTCTTACGTGATGAAGAGATCTGGCCATCT-AA----AGGTGATAACACGGTTCCTA
* *
14700 CGTGATAAGGACGGCTGGTTATCCTAATGT
61 CGTGATGAGGACGGCTGGTTAT-C--AGGT
*
14730 TGACACGGCTCCTACGTGATGA
1 TGACACGGCTCTTACGTGATGA
14752 GGAAGTCTGG
Statistics
Matches: 264, Mismatches: 17, Indels: 11
0.90 0.06 0.04
Matches are distributed among these distances:
86 16 0.06
87 149 0.56
88 35 0.13
91 40 0.15
92 1 0.00
94 23 0.09
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (87 bp):
TGACACGGCTCTTACGTGATGAAGAGATCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
TGAGGACGGCTGGTTATCAGGT
Found at i:14569 original size:41 final size:41
Alignment explanation
Indices: 14433--14658 Score: 177
Period size: 41 Copynumber: 5.3 Consensus size: 41
14423 ACTCGGTTCC
* *
14433 TACGTAATGAGGACGACTGGTTATCAGGTTGACACGGCTCT
1 TACGTGATGAGGACGGCTGGTTATCAGGTTGACACGGCTCT
* * ** * * *
14474 TACGTGATGAAGA-GATCTGGCCATCTAAAGGTGATAACACGGTTCC
1 TACGTGATGAGGACG-GCTGGTTATC---AGGT--TGACACGGCTCT
*
14520 TACATGATGAGGACGGCTGGTTATCAGGTTGACACGGCTCT
1 TACGTGATGAGGACGGCTGGTTATCAGGTTGACACGGCTCT
* * ** * * *
14561 TACGTGATGAAGA-GATCTGGCCATCTAAAGGTGATAACACGGTTCC
1 TACGTGATGAGGACG-GCTGGTTATC---AGGT--TGACACGGCTCT
14607 TACGTGATGAGGACGGCTGGTTATCAGGTTGACACGGCTCT
1 TACGTGATGAGGACGGCTGGTTATCAGGTTGACACGGCTCT
14648 TACGTGATGAG
1 TACGTGATGAG
14659 AGATCTGGCC
Statistics
Matches: 140, Mismatches: 31, Indels: 28
0.70 0.16 0.14
Matches are distributed among these distances:
40 2 0.01
41 65 0.46
43 8 0.06
44 8 0.06
46 55 0.39
47 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.26
Consensus pattern (41 bp):
TACGTGATGAGGACGGCTGGTTATCAGGTTGACACGGCTCT
Found at i:27387 original size:15 final size:16
Alignment explanation
Indices: 27369--27402 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
27359 TATGAACATC
*
27369 AAATAAATTAACAA-A
1 AAATAAAATAACAATA
27384 AAATAAAATAACAATA
1 AAATAAAATAACAATA
27400 AAA
1 AAA
27403 ATAATTTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (16 bp):
AAATAAAATAACAATA
Found at i:29187 original size:25 final size:25
Alignment explanation
Indices: 28989--29181 Score: 352
Period size: 25 Copynumber: 7.8 Consensus size: 25
28979 TGGAAGGGGA
28989 TTAGGG-TTGAAACCCTAAATTGAT
1 TTAGGGTTTGAAACCCTAAATTGAT
29013 TTAGGGTTTGAAACCCTAAATTGAT
1 TTAGGGTTTGAAACCCTAAATTGAT
*
29038 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAATTGAT
29063 TTAGGGTTTGAAACCCTAAATTGAT
1 TTAGGGTTTGAAACCCTAAATTGAT
*
29088 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAATTGAT
*
29113 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAATTGAT
29138 TTAGGGTTTGAAACCCTAAATTGAT
1 TTAGGGTTTGAAACCCTAAATTGAT
29163 TTAGGGTTTGAAACCCTAA
1 TTAGGGTTTGAAACCCTAA
29182 TCTGATGGGT
Statistics
Matches: 164, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
24 6 0.04
25 158 0.96
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAAATTGAT
Found at i:29325 original size:3 final size:3
Alignment explanation
Indices: 29317--29380 Score: 89
Period size: 3 Copynumber: 22.0 Consensus size: 3
29307 GCAAAAATTG
*
29317 TAA TAA TAAA TAA TAA TAA -AA TAA TAA T-A TAA TGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
29361 TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA
29381 CGGAAAAAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
2 6 0.11
3 46 0.84
4 3 0.05
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:32701 original size:20 final size:20
Alignment explanation
Indices: 32668--32707 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
32658 ATTGTTCATG
*
32668 TTTGAACTTTAATCAAGTTA
1 TTTGAACTTCAATCAAGTTA
* *
32688 TTTGAGCTTCAATCGAGTTA
1 TTTGAACTTCAATCAAGTTA
32708 AATTTGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.42
Consensus pattern (20 bp):
TTTGAACTTCAATCAAGTTA
Found at i:35244 original size:23 final size:23
Alignment explanation
Indices: 35198--35245 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
35188 GAACATGTGC
*
35198 ATGAACACGTTCGCGAACATTAA
1 ATGAACACGTTCGCGAACAATAA
* * *
35221 ATGAACATGTTCGTGAATAATAA
1 ATGAACACGTTCGCGAACAATAA
35244 AT
1 AT
35246 AAACGAACAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.27
Consensus pattern (23 bp):
ATGAACACGTTCGCGAACAATAA
Found at i:43742 original size:84 final size:84
Alignment explanation
Indices: 43599--44114 Score: 395
Period size: 84 Copynumber: 6.1 Consensus size: 84
43589 GCTCAGCTTG
* * * * ** * * *
43599 TTTCTTACTTCAACAGCCTTCTTCAT-GTTTTCTTCAGCAATCTTAGTTTGCTCCGCTGCTTCAG
1 TTTCTTTCTTCAACAGCCTTCTTCTTAG-TTTCTTTAGCAACCTTCCTCTGCTTCTCTGCTTCAG
*
43663 CCATCTCTAAATCAGCATGT
65 CCATCTCTAAATCAGCACGT
* * * *
43683 TTTCTTTCTTCAACGGCCTTCTTCTTAGTTTCTTTAGCTACCCTCCTCTGCTTCTCTGCTTTAGC
1 TTTCTTTCTTCAACAGCCTTCTTCTTAGTTTCTTTAGCAACCTTCCTCTGCTTCTCTGCTTCAGC
* * *
43748 CATCTCTGAATCGGCACAT
66 CATCTCTAAATCAGCACGT
* * * * * *
43767 TTCCTTTCATCAACAGCCTTTTTCTTAGTTTCTTCT-GCAATCTTCCTTTGCTCCTCTGCCTT-A
1 TTTCTTTCTTCAACAGCCTTCTTCTTAGTTTCTT-TAGCAACCTTCCTCTGCTTCTCTG-CTTCA
**
43830 GCCATCTC-AAACTCAGCTTGT
64 GCCATCTCTAAA-TCAGCACGT
* * * * * * * *
43851 TTTCTTACTTCAAAAGCATTTTTCAT-GTTTTCTTCAGCAATCTTCCTTTG-TTCTGCTGCTTCA
1 TTTCTTTCTTCAACAGCCTTCTTCTTAG-TTTCTTTAGCAACCTTCCTCTGCTTCT-CTGCTTCA
43914 GCCATCTCTAAATCAGCACGT
64 GCCATCTCTAAATCAGCACGT
* * * * *
43935 TTTCCTTCTTCAGCAGCCTTCTTCTTAGTTTCTTTAGCAACCTTCCTCTGTTTCTCCGCTTTAGC
1 TTTCTTTCTTCAACAGCCTTCTTCTTAGTTTCTTTAGCAACCTTCCTCTGCTTCTCTGCTTCAGC
** * *
44000 CATCTCCGAATCAACACAT
66 CATCTCTAAATCAGCACGT
* * * * ** * *
44019 TTTCTATCGTCAACAGCCTGT-TTCTTAGTTT-TTTCTGCAATCTTCCTCAAC-TCCCTTGCTTT
1 TTTCTTTCTTCAACAGCCT-TCTTCTTAGTTTCTTT-AGCAACCTTCCTCTGCTTCTC-TGCTTC
* * *
44081 AGCCATTTCTAAAT-TGACAAGT
63 AGCCATCTCTAAATCAG-CACGT
44103 TTTCTTTCTTCA
1 TTTCTTTCTTCA
44115 CCTGCCTTTT
Statistics
Matches: 340, Mismatches: 77, Indels: 30
0.76 0.17 0.07
Matches are distributed among these distances:
83 15 0.04
84 311 0.91
85 14 0.04
ACGTcount: A:0.17, C:0.30, G:0.10, T:0.43
Consensus pattern (84 bp):
TTTCTTTCTTCAACAGCCTTCTTCTTAGTTTCTTTAGCAACCTTCCTCTGCTTCTCTGCTTCAGC
CATCTCTAAATCAGCACGT
Found at i:44086 original size:252 final size:251
Alignment explanation
Indices: 43536--44065 Score: 801
Period size: 252 Copynumber: 2.1 Consensus size: 251
43526 CTTCAACAGC
* * *
43536 TTTCTTAGTTTCTTCTGCAATCCTCTTTTGCTCCTCTGCCTTAGCCATTGCAAGCTCAGCTTGTT
1 TTTCTTAGTTTCTTCTGCAATCTTCCTTTGCTCCTCTGCCTTAGCCATTGCAAACTCAGCTTGTT
* * *
43601 TCTTACTTCAACAGCCTTCTTCATGTTTTCTTCAGCAATCTTAGTTTGCTCCGCTGCTTCAGCCA
66 TCTTACTTCAAAAGCATTCTTCATGTTTTCTTCAGCAATCTTACTTTGCTCCGCTGCTTCAGCCA
* * * *
43666 TCTCTAAATCAGCATGTTTTCTTTCTTCAACGGCCTTCTTCTTAGTTTCTTTAGCTACCCTCCTC
131 TCTCTAAATCAGCACGTTTTCCTTCTTCAACAGCCTTCTTCTTAGTTTCTTTAGCAACCCTCCTC
* * ** * *
43731 TGCTTCTCTGCTTTAGCCATCTCTGAATCGGCACATTTCCTTTCATCAACAGCCTT
196 TGCTTCTCCGCTTTAGCCATCTCCGAATCAACACATTTCCTATCATCAACAGCCTG
43787 TTTCTTAGTTTCTTCTGCAATCTTCCTTTGCTCCTCTGCCTTAGCCATCT-CAAACTCAGCTTGT
1 TTTCTTAGTTTCTTCTGCAATCTTCCTTTGCTCCTCTGCCTTAGCCAT-TGCAAACTCAGCTTG-
* * * *
43851 TTTCTTACTTCAAAAGCATTTTTCATGTTTTCTTCAGCAATCTTCCTTTGTTCTGCTGCTTCAGC
64 TTTCTTACTTCAAAAGCATTCTTCATGTTTTCTTCAGCAATCTTACTTTGCTCCGCTGCTTCAGC
* *
43916 CATCTCTAAATCAGCACGTTTTCCTTCTTCAGCAGCCTTCTTCTTAGTTTCTTTAGCAACCTTCC
129 CATCTCTAAATCAGCACGTTTTCCTTCTTCAACAGCCTTCTTCTTAGTTTCTTTAGCAACCCTCC
* * *
43981 TCTGTTTCTCCGCTTTAGCCATCTCCGAATCAACACATTTTCTATCGTCAACAGCCTG
194 TCTGCTTCTCCGCTTTAGCCATCTCCGAATCAACACATTTCCTATCATCAACAGCCTG
*
44039 TTTCTTAGTTTTTTCTGCAATCTTCCT
1 TTTCTTAGTTTCTTCTGCAATCTTCCT
44066 CAACTCCCTT
Statistics
Matches: 251, Mismatches: 26, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
251 58 0.23
252 193 0.77
ACGTcount: A:0.16, C:0.30, G:0.11, T:0.43
Consensus pattern (251 bp):
TTTCTTAGTTTCTTCTGCAATCTTCCTTTGCTCCTCTGCCTTAGCCATTGCAAACTCAGCTTGTT
TCTTACTTCAAAAGCATTCTTCATGTTTTCTTCAGCAATCTTACTTTGCTCCGCTGCTTCAGCCA
TCTCTAAATCAGCACGTTTTCCTTCTTCAACAGCCTTCTTCTTAGTTTCTTTAGCAACCCTCCTC
TGCTTCTCCGCTTTAGCCATCTCCGAATCAACACATTTCCTATCATCAACAGCCTG
Found at i:45850 original size:38 final size:39
Alignment explanation
Indices: 45799--45875 Score: 120
Period size: 38 Copynumber: 2.0 Consensus size: 39
45789 GATATGGCAA
45799 TGACATAAAATTAGTAAGCTG-TTTTTTATATAACCATC
1 TGACATAAAATTAGTAAGCTGTTTTTTTATATAACCATC
* *
45837 TGACATTAAATTAGTAAGTTGTTTTTTTTATATAACCAT
1 TGACATAAAATTAGTAAGCTG-TTTTTTTATATAACCAT
45876 GTGAAGTCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 19 0.54
40 16 0.46
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.44
Consensus pattern (39 bp):
TGACATAAAATTAGTAAGCTGTTTTTTTATATAACCATC
Found at i:48977 original size:28 final size:28
Alignment explanation
Indices: 48946--49007 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 28
48936 TGACGATATC
48946 CTTCCGAGTAAGGATCAAACGACGCCGT
1 CTTCCGAGTAAGGATCAAACGACGCCGT
48974 CTTCCGAGTAAGGATCAAACGACGCCGT
1 CTTCCGAGTAAGGATCAAACGACGCCGT
49002 C-TCCGA
1 CTTCCGA
49008 AGCTCCATTC
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 5 0.15
28 29 0.85
ACGTcount: A:0.27, C:0.31, G:0.24, T:0.18
Consensus pattern (28 bp):
CTTCCGAGTAAGGATCAAACGACGCCGT
Found at i:50379 original size:17 final size:18
Alignment explanation
Indices: 50359--50397 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
50349 TAAATTTAAA
*
50359 TATAA-TTAAAATATATT
1 TATAATTTAAAATAAATT
50376 TATAATTTTAAAATAAATT
1 TATAA-TTTAAAATAAATT
50395 TAT
1 TAT
50398 GAAATTCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
19 14 0.74
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TATAATTTAAAATAAATT
Found at i:50819 original size:22 final size:23
Alignment explanation
Indices: 50762--50824 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 23
50752 GATATTTAGT
*
50762 TATATATTCATGAACATGTTCTG
1 TATATATTCATGAATATGTTCTG
** *
50785 --TACGTTCGTGAATATGTT-TG
1 TATATATTCATGAATATGTTCTG
50805 TATATATTCATGAATATGTT
1 TATATATTCATGAATATGTT
50825 AATTTGTAAG
Statistics
Matches: 31, Mismatches: 7, Indels: 5
0.72 0.16 0.12
Matches are distributed among these distances:
20 2 0.06
21 14 0.45
22 15 0.48
ACGTcount: A:0.29, C:0.10, G:0.16, T:0.46
Consensus pattern (23 bp):
TATATATTCATGAATATGTTCTG
Found at i:52183 original size:18 final size:18
Alignment explanation
Indices: 52150--52184 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
52140 TGAAGAAGAA
**
52150 CAAGATGTGATTCCTCCG
1 CAAGATGTGAACCCTCCG
52168 CAAGATGTGAACCCTCC
1 CAAGATGTGAACCCTCC
52185 ATAGGATATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (18 bp):
CAAGATGTGAACCCTCCG
Found at i:61206 original size:30 final size:31
Alignment explanation
Indices: 61137--61203 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
61127 TATTTTTTAT
* *
61137 AAAAAATTAAACAAGCCCTCAAACTTTCTAA
1 AAAAAATCAAACAAGCCCTCAAACTTACTAA
* *
61168 AAAAAATCAAACAAGCCCTCAAACTTAGTCA
1 AAAAAATCAAACAAGCCCTCAAACTTACTAA
61199 AAAAA
1 AAAAA
61204 TCAGTAAACC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.55, C:0.22, G:0.04, T:0.18
Consensus pattern (31 bp):
AAAAAATCAAACAAGCCCTCAAACTTACTAA
Done.