Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002587.1 Hibiscus syriacus cultivar Beakdansim tig00005234_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: 72027
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:371 original size:21 final size:21
Alignment explanation
Indices: 347--433 Score: 72
Period size: 21 Copynumber: 4.1 Consensus size: 21
337 CTGGTTACAG
*
347 CAGTCCATCATCCCCTGGGTA
1 CAGTCCATCATCACCTGGGTA
* *
368 CAGTCC-TACTTCGCCTGGGTA
1 CAGTCCAT-CATCACCTGGGTA
* *
389 CAGCCCCACCA-CACCTGGGTA
1 CAG-TCCATCATCACCTGGGTA
*
410 CAGTCC-TACCTCACCTGGGTA
1 CAGTCCAT-CATCACCTGGGTA
431 CAG
1 CAG
434 CCCCCACACT
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
20 4 0.08
21 45 0.87
22 3 0.06
ACGTcount: A:0.20, C:0.39, G:0.21, T:0.21
Consensus pattern (21 bp):
CAGTCCATCATCACCTGGGTA
Found at i:549 original size:21 final size:21
Alignment explanation
Indices: 513--664 Score: 143
Period size: 21 Copynumber: 7.2 Consensus size: 21
503 CACTTATTCT
* * * *
513 CCAACCTCACCGAGCTACATC
1 CCAACTTCACCTAGCTATAGC
*
534 CCTACTTCACCTAGCTATAGTC
1 CCAACTTCACCTAGCTATAG-C
*
556 CC-ACTTCACCTAGCTACAGC
1 CCAACTTCACCTAGCTATAGC
*
576 CCTACTTCACCTAGCTATAGC
1 CCAACTTCACCTAGCTATAGC
597 CCAACTTCACC-AGCATATAGC
1 CCAACTTCACCTAGC-TATAGC
618 CCAACTTCACCT-GCATATAGTC
1 CCAACTTCACCTAGC-TATAG-C
* *
640 CC-ACTTCTCC-ATCATATAGC
1 CCAACTTCACCTAGC-TATAGC
660 CCAAC
1 CCAAC
665 GTCTCCATCA
Statistics
Matches: 114, Mismatches: 10, Indels: 14
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.08
21 99 0.87
22 6 0.05
ACGTcount: A:0.27, C:0.41, G:0.09, T:0.24
Consensus pattern (21 bp):
CCAACTTCACCTAGCTATAGC
Found at i:579 original size:42 final size:41
Alignment explanation
Indices: 519--646 Score: 170
Period size: 42 Copynumber: 3.0 Consensus size: 41
509 TTCTCCAACC
*
519 TCACCGAGCTACATCCCTACTTCACCTAGCTATAGTCCCACT
1 TCACC-AGCTACAGCCCTACTTCACCTAGCTATAGTCCCACT
561 TCACCTAGCTACAGCCCTACTTCACCTAGCTATAG-CCCAACT
1 TCACC-AGCTACAGCCCTACTTCACCTAGCTATAGTCCC-ACT
* *
603 TCACCAGCATATAGCCCAACTTCACCT-GCATATAGTCCCACT
1 TCACCAGC-TACAGCCCTACTTCACCTAGC-TATAGTCCCACT
645 TC
1 TC
647 TCCATCATAT
Statistics
Matches: 78, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
41 8 0.10
42 67 0.86
43 3 0.04
ACGTcount: A:0.26, C:0.40, G:0.09, T:0.25
Consensus pattern (41 bp):
TCACCAGCTACAGCCCTACTTCACCTAGCTATAGTCCCACT
Found at i:646 original size:63 final size:61
Alignment explanation
Indices: 519--754 Score: 145
Period size: 63 Copynumber: 3.7 Consensus size: 61
509 TTCTCCAACC
* * *
519 TCACCGAGCTACATCCCTACTTCACCTAGC-TATAGTCCCACTTCACCTAGCTACAGCCCTACT
1 TCACC-AGCTATAGCCCAACTTCACC-AGCATATAG-CCCACTTCACCTAGCTACAGCCCTACT
*
582 TCACCTAGCTATAGCCCAACTTCACCAGCATATAGCCCAACTTCACCT-GCATATAGTCCC-ACT
1 TCACC-AGCTATAGCCCAACTTCACCAGCATATAGCCC-ACTTCACCTAGC-TACAG-CCCTACT
* * * * * * * * ** * *
645 TCTCCATCATATAGCCCAACGTCTCCATCATACAGCCCGACATCTCCTTCCTACAGCCCAACC
1 TCACCAGC-TATAGCCCAACTTCACCAGCATATAGCCC-ACTTCACCTAGCTACAGCCCTACT
** * * * * *
708 TCACCCTCCTATAGCCCTACATCTCCATCTTATAGCCCCACTTCACC
1 TCA-CCAGCTATAGCCCAACTTCACCAGCATATAG-CCCACTTCACC
755 GGCTTATAGC
Statistics
Matches: 138, Mismatches: 26, Indels: 18
0.76 0.14 0.10
Matches are distributed among these distances:
62 13 0.09
63 115 0.83
64 10 0.07
ACGTcount: A:0.25, C:0.42, G:0.08, T:0.25
Consensus pattern (61 bp):
TCACCAGCTATAGCCCAACTTCACCAGCATATAGCCCACTTCACCTAGCTACAGCCCTACT
Found at i:656 original size:42 final size:41
Alignment explanation
Indices: 537--776 Score: 155
Period size: 42 Copynumber: 5.7 Consensus size: 41
527 CTACATCCCT
* * * *
537 ACTTCACCTAGCTATAGTCCC-ACTTCACCTAGC-TACAGCCCT
1 ACTTCACCT-GCTATAG-CCCAACTTCTCC-ATCATATAGCCCA
* *
579 ACTTCACCTAGCTATAGCCCAACTTCACCAGCATATAGCCCA
1 ACTTCACCT-GCTATAGCCCAACTTCTCCATCATATAGCCCA
621 ACTTCACCTGCATATAGTCCC-ACTTCTCCATCATATAGCCCA
1 ACTTCACCTGC-TATAG-CCCAACTTCTCCATCATATAGCCCA
* * * * * * * *
663 ACGTCTCCAT-CATACAGCCCGACATCTCCTTCCTACAGCCCA
1 ACTTCACC-TGC-TATAGCCCAACTTCTCCATCATATAGCCCA
* * * * * *
705 ACCTCACCCTCCTATAGCCCTACATCTCCATCTTATAGCCCC
1 ACTTCA-CCTGCTATAGCCCAACTTCTCCATCATATAGCCCA
* * *
747 ACTTCACCGGCTTATAGCCCCAGTTCTCCA
1 ACTTCACCTGC-TATAGCCCAACTTCTCCA
777 GGCTATAGCC
Statistics
Matches: 164, Mismatches: 25, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
41 14 0.09
42 143 0.87
43 7 0.04
ACGTcount: A:0.25, C:0.42, G:0.09, T:0.25
Consensus pattern (41 bp):
ACTTCACCTGCTATAGCCCAACTTCTCCATCATATAGCCCA
Found at i:669 original size:21 final size:21
Alignment explanation
Indices: 591--751 Score: 128
Period size: 21 Copynumber: 7.7 Consensus size: 21
581 TTCACCTAGC
* *
591 TATAGCCCAACTTCACCAGCA
1 TATAGCCCAACTTCTCCATCA
*
612 TATAGCCCAACTTCACC-TGCA
1 TATAGCCCAACTTCTCCAT-CA
633 TATAGTCCC-ACTTCTCCATCA
1 TATAG-CCCAACTTCTCCATCA
*
654 TATAGCCCAACGTCTCCATCA
1 TATAGCCCAACTTCTCCATCA
* * * * *
675 TACAGCCCGACATCTCCTTCC
1 TATAGCCCAACTTCTCCATCA
* * * * *
696 TACAGCCCAACCTCACCCTCC
1 TATAGCCCAACTTCTCCATCA
* * *
717 TATAGCCCTACATCTCCATCT
1 TATAGCCCAACTTCTCCATCA
*
738 TATAGCCCCACTTC
1 TATAGCCCAACTTC
752 ACCGGCTTAT
Statistics
Matches: 116, Mismatches: 20, Indels: 8
0.81 0.14 0.06
Matches are distributed among these distances:
20 3 0.03
21 109 0.94
22 4 0.03
ACGTcount: A:0.25, C:0.42, G:0.07, T:0.25
Consensus pattern (21 bp):
TATAGCCCAACTTCTCCATCA
Found at i:760 original size:21 final size:22
Alignment explanation
Indices: 736--787 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
726 ACATCTCCAT
736 CTTATAGCCCCACTTCACC-GG
1 CTTATAGCCCCACTTCACCAGG
* *
757 CTTATAGCCCCAGTTCTCCAGG
1 CTTATAGCCCCACTTCACCAGG
779 C-TATAGCCC
1 CTTATAGCCC
788 TACCTCTCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 25 0.89
22 3 0.11
ACGTcount: A:0.19, C:0.40, G:0.15, T:0.25
Consensus pattern (22 bp):
CTTATAGCCCCACTTCACCAGG
Found at i:795 original size:21 final size:20
Alignment explanation
Indices: 716--839 Score: 70
Period size: 21 Copynumber: 6.0 Consensus size: 20
706 CCTCACCCTC
*
716 CTATAGCCCTACATCTCCAT
1 CTATAGCCCTACATCTCCAG
* * * *
736 CTTATAGCCCCACTTCACCGG
1 C-TATAGCCCTACATCTCCAG
* **
757 CTTATAGCCCCAGTTCTCCAGG
1 C-TATAGCCCTACATCTCCA-G
*
779 CTATAGCCCTACCTCTCCAAG
1 CTATAGCCCTACATCTCC-AG
* * *
800 TTATAGTCCC-ACATCACCTAC
1 CTATAG-CCCTACATCTCC-AG
*
821 CTATAGCCCTACCTCTCCA
1 CTATAGCCCTACATCTCCA
840 AGTTACAATC
Statistics
Matches: 80, Mismatches: 19, Indels: 10
0.73 0.17 0.09
Matches are distributed among these distances:
20 5 0.06
21 69 0.86
22 6 0.08
ACGTcount: A:0.23, C:0.41, G:0.10, T:0.27
Consensus pattern (20 bp):
CTATAGCCCTACATCTCCAG
Found at i:838 original size:63 final size:63
Alignment explanation
Indices: 716--839 Score: 149
Period size: 63 Copynumber: 2.0 Consensus size: 63
706 CCTCACCCTC
* * * * **
716 CTATAGCCCTACATCTCCATCTTATAGCCCCACTTCACCGGCTTATAGCCCCAGTTCTCCAGG
1 CTATAGCCCTACATCTCCAACTTATAGCCCCACATCACCGACCTATAGCCCCACCTCTCCAGG
* * * * *
779 CTATAGCCCTACCTCTCCAAGTTATAGTCCCACATCACCTACCTATAGCCCTACCTCTCCA
1 CTATAGCCCTACATCTCCAACTTATAGCCCCACATCACCGACCTATAGCCCCACCTCTCCA
840 AGTTACAATC
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
63 50 1.00
ACGTcount: A:0.23, C:0.41, G:0.10, T:0.27
Consensus pattern (63 bp):
CTATAGCCCTACATCTCCAACTTATAGCCCCACATCACCGACCTATAGCCCCACCTCTCCAGG
Found at i:6831 original size:37 final size:37
Alignment explanation
Indices: 6781--6851 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
6771 TATCGAGCTC
*
6781 TCGACAATTATGCAAAGCCTGTTAATCAGTTGTTGTT
1 TCGACAATTATGCAAAGCCTGTTAATAAGTTGTTGTT
6818 TCGACAATTATGCAAAGCCTGTTAATAAGTTGTT
1 TCGACAATTATGCAAAGCCTGTTAATAAGTTGTT
6852 TCATCAATCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (37 bp):
TCGACAATTATGCAAAGCCTGTTAATAAGTTGTTGTT
Found at i:13824 original size:44 final size:44
Alignment explanation
Indices: 13761--13849 Score: 160
Period size: 44 Copynumber: 2.0 Consensus size: 44
13751 CTATGACAAT
*
13761 GTATAGTCCTACAGACACAATTACTTAAACTCATATCATTTTTA
1 GTATAGTCCTACAGACACAATTACTTAAACCCATATCATTTTTA
*
13805 GTATAGTCCTACAGACACAATTACTTAAACCCATATCGTTTTTA
1 GTATAGTCCTACAGACACAATTACTTAAACCCATATCATTTTTA
13849 G
1 G
13850 CACTAAGGTG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (44 bp):
GTATAGTCCTACAGACACAATTACTTAAACCCATATCATTTTTA
Found at i:15996 original size:47 final size:47
Alignment explanation
Indices: 15927--16018 Score: 166
Period size: 47 Copynumber: 2.0 Consensus size: 47
15917 TTCTCAACCA
*
15927 ACATAATTATATGAGTAATGGATGTTAATGTTGGAGATAAAAAAGCG
1 ACATAATTATATGAGCAATGGATGTTAATGTTGGAGATAAAAAAGCG
*
15974 ACATAATTATATGAGCAATGGATGTTGATGTTGGAGATAAAAAAG
1 ACATAATTATATGAGCAATGGATGTTAATGTTGGAGATAAAAAAG
16019 AAACTTCATT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.42, C:0.04, G:0.24, T:0.29
Consensus pattern (47 bp):
ACATAATTATATGAGCAATGGATGTTAATGTTGGAGATAAAAAAGCG
Found at i:18556 original size:35 final size:35
Alignment explanation
Indices: 18510--18579 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
18500 AAAACAATTC
*
18510 TCAATTTCATTCTAAACCTCAAATTCCAAAATAAT
1 TCAATTACATTCTAAACCTCAAATTCCAAAATAAT
18545 TCAATTACATTCTAAACCTCAAATTCCAAAATAAT
1 TCAATTACATTCTAAACCTCAAATTCCAAAATAAT
18580 CAAAATAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.44, C:0.23, G:0.00, T:0.33
Consensus pattern (35 bp):
TCAATTACATTCTAAACCTCAAATTCCAAAATAAT
Found at i:28549 original size:260 final size:260
Alignment explanation
Indices: 28087--28607 Score: 943
Period size: 260 Copynumber: 2.0 Consensus size: 260
28077 AGGGGGCCAC
*
28087 CAAAATCATCAAGAAGTCATCTTTTGTTGCTACATTAATGCACCGAATTCGGTGCAATTAATGTG
1 CAAAATCATCAAGAAGTCATCTTTTGCTGCTACATTAATGCACCGAATTCGGTGCAATTAATGTG
*
28152 TGTTGAAATTTTGAGATGGCTAAATTACATTTTAGTCATTACACTTTAGGGTATTTTCAAAGATT
66 TGTTGAAATTTTGAGATGGCTAAATTACATTTTAATCATTACACTTTAGGGTATTTTCAAAGATT
*
28217 AGTCCCTGAGCTTCAACTATAAATACCCTAGCTCATTTAGCTTCAAAATCATCCCAAAATCATTT
131 AGTCCCTAAGCTTCAACTATAAATACCCTAGCTCATTTAGCTTCAAAATCATCCCAAAATCATTT
* *
28282 CTTTCTCCTAATACTAGAGAGTTTTATTGTGAGTAGTGAGTGTTTTGTAAACACCTGTAATTTTT
196 CTTTCTCCCAATACTAGAGAGCTTTATTGTGAGTAGTGAGTGTTTTGTAAACACCTGTAATTTTT
*
28347 CAAAATCATCAAGAAGTCATCTTTTGCTGCTATATTAATGCACCGAATTCGGTGCAATTAATGTG
1 CAAAATCATCAAGAAGTCATCTTTTGCTGCTACATTAATGCACCGAATTCGGTGCAATTAATGTG
**
28412 TGTTGAAATTTTGAGATGGCTAAATTACATTTTAATCATTGTACTTTAGGGTATTTTCAAAGATT
66 TGTTGAAATTTTGAGATGGCTAAATTACATTTTAATCATTACACTTTAGGGTATTTTCAAAGATT
*
28477 AGTCCCTAAGTTTCAACTATAAATACCCTAGCTCATTTAGCTTCAAAATCATCCCAAAATCATTT
131 AGTCCCTAAGCTTCAACTATAAATACCCTAGCTCATTTAGCTTCAAAATCATCCCAAAATCATTT
* *
28542 TTTTCTCCCAATACTAGAGAGCTTTCTTGTGAGTAGTGAGTGTTTTGTAAACACCTGTAATTTTT
196 CTTTCTCCCAATACTAGAGAGCTTTATTGTGAGTAGTGAGTGTTTTGTAAACACCTGTAATTTTT
28607 C
1 C
28608 TCTCTTAGTA
Statistics
Matches: 250, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
260 250 1.00
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (260 bp):
CAAAATCATCAAGAAGTCATCTTTTGCTGCTACATTAATGCACCGAATTCGGTGCAATTAATGTG
TGTTGAAATTTTGAGATGGCTAAATTACATTTTAATCATTACACTTTAGGGTATTTTCAAAGATT
AGTCCCTAAGCTTCAACTATAAATACCCTAGCTCATTTAGCTTCAAAATCATCCCAAAATCATTT
CTTTCTCCCAATACTAGAGAGCTTTATTGTGAGTAGTGAGTGTTTTGTAAACACCTGTAATTTTT
Found at i:46136 original size:3 final size:3
Alignment explanation
Indices: 46128--46160 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
46118 TTTTATTCAC
46128 TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
46161 TAATTACAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:46147 original size:14 final size:14
Alignment explanation
Indices: 46128--46156 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
46118 TTTTATTCAC
46128 TATTATTATTATTA
1 TATTATTATTATTA
46142 TATTATTATTATTA
1 TATTATTATTATTA
46156 T
1 T
46157 TATTTAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TATTATTATTATTA
Found at i:53091 original size:11 final size:11
Alignment explanation
Indices: 53039--53102 Score: 53
Period size: 11 Copynumber: 5.8 Consensus size: 11
53029 CTCATATATT
53039 AGAAGAAAAAA
1 AGAAGAAAAAA
53050 AG--GAAAAAA
1 AGAAGAAAAAA
53059 AGAA-ATAAAAA
1 AGAAGA-AAAAA
** *
53070 CTATGAAAAAA
1 AGAAGAAAAAA
53081 AGAAAAGAAAAAA
1 AG--AAGAAAAAA
53094 AGAAGAAAA
1 AGAAGAAAA
53103 TAAATTGAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
9 9 0.22
10 1 0.02
11 20 0.49
12 1 0.02
13 10 0.24
ACGTcount: A:0.78, C:0.02, G:0.16, T:0.05
Consensus pattern (11 bp):
AGAAGAAAAAA
Found at i:55473 original size:42 final size:41
Alignment explanation
Indices: 55402--55514 Score: 109
Period size: 42 Copynumber: 2.7 Consensus size: 41
55392 TCTTGATTTG
* * * * * *
55402 TAAATCCTTCGGGTCATCAATAAGTCTTTCTAGCATGATGTT
1 TAAATCCTTCGGGTCATTAGTAAGCCTTTCGAGCAAGATG-A
* *
55444 TAAATCCTTTGGGTCATTTGTAAGCCTTTCGAGCAAGATGA
1 TAAATCCTTCGGGTCATTAGTAAGCCTTTCGAGCAAGATGA
* * *
55485 TAAGTCCTTCGGGCCATTCGTAAGACCTTT
1 TAAATCCTTCGGGTCATTAGTAAG-CCTTT
55515 GGGCAGAATG
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
41 20 0.34
42 38 0.66
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.35
Consensus pattern (41 bp):
TAAATCCTTCGGGTCATTAGTAAGCCTTTCGAGCAAGATGA
Found at i:55919 original size:18 final size:18
Alignment explanation
Indices: 55896--55932 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
55886 CTGTAAGCCT
55896 TTCGAGCAAGATGATAAG
1 TTCGAGCAAGATGATAAG
55914 TTCGAGCAAGATGATAAG
1 TTCGAGCAAGATGATAAG
55932 T
1 T
55933 CCTTCGGGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.11, G:0.27, T:0.24
Consensus pattern (18 bp):
TTCGAGCAAGATGATAAG
Found at i:57869 original size:2 final size:2
Alignment explanation
Indices: 57862--57887 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
57852 AGTCACATGA
57862 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
57888 GAAAGGATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62249 original size:21 final size:21
Alignment explanation
Indices: 62224--62271 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
62214 CCTAATATTG
62224 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
62245 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
*
62266 TAATGT
1 CAATGT
62272 TTGAAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTGCAA
Found at i:63103 original size:12 final size:12
Alignment explanation
Indices: 63086--63111 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
63076 TCCGGTCCAC
63086 ATGTTCTTTGGA
1 ATGTTCTTTGGA
63098 ATGTTCTTTGGA
1 ATGTTCTTTGGA
63110 AT
1 AT
63112 CAGCCTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.19, C:0.08, G:0.23, T:0.50
Consensus pattern (12 bp):
ATGTTCTTTGGA
Found at i:65010 original size:2 final size:2
Alignment explanation
Indices: 65003--65039 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
64993 AATTAATCGA
65003 AT AT AT 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 AT AT AT A
65040 ATAGTTGGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:67344 original size:14 final size:14
Alignment explanation
Indices: 67322--67355 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
67312 CATTTTATTT
*
67322 ATCATGCAATTCCC
1 ATCAAGCAATTCCC
67336 ATCAAGCAATTCCC
1 ATCAAGCAATTCCC
67350 ATCAAG
1 ATCAAG
67356 ATTGAGTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.35, C:0.32, G:0.09, T:0.24
Consensus pattern (14 bp):
ATCAAGCAATTCCC
Done.