Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022547.1 Corchorus olitorius cultivar O-4 contig22580, 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: 40674
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Found at i:7161 original size:14 final size:14
Alignment explanation
Indices: 7142--7180 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 14
7132 TATGATAATT
7142 ATATTTTAGCATAC
1 ATATTTTAGCATAC
7156 ATATTTTTTTAGCATAC
1 ATA---TTTTAGCATAC
7173 ATATTTTA
1 ATATTTTA
7181 TCTTATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 8 0.36
17 14 0.64
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.51
Consensus pattern (14 bp):
ATATTTTAGCATAC
Found at i:7167 original size:17 final size:17
Alignment explanation
Indices: 7145--7179 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
7135 GATAATTATA
7145 TTTTAGCATACATATTT
1 TTTTAGCATACATATTT
7162 TTTTAGCATACATATTT
1 TTTTAGCATACATATTT
7179 T
1 T
7180 ATCTTATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.06, T:0.54
Consensus pattern (17 bp):
TTTTAGCATACATATTT
Found at i:10765 original size:11 final size:11
Alignment explanation
Indices: 10749--10783 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
10739 TTAACAGCGC
10749 AACAAAAACAA
1 AACAAAAACAA
*
10760 AACAAAAACGA
1 AACAAAAACAA
10771 AACAAAAACAA
1 AACAAAAACAA
10782 AA
1 AA
10784 AATAGAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.80, C:0.17, G:0.03, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:16745 original size:12 final size:13
Alignment explanation
Indices: 16711--16752 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 13
16701 GATCTTGTTG
*
16711 GTTT-TGTTTTGT
1 GTTTGTGTTGTGT
16723 -TTTGTGTTGTGT
1 GTTTGTGTTGTGT
16735 GTTTGTG-TGTGT
1 GTTTGTGTTGTGT
16747 GTTTGT
1 GTTTGT
16753 TTTCTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
11 3 0.11
12 18 0.67
13 6 0.22
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (13 bp):
GTTTGTGTTGTGT
Found at i:18044 original size:48 final size:46
Alignment explanation
Indices: 17966--18073 Score: 144
Period size: 48 Copynumber: 2.3 Consensus size: 46
17956 AAGGAACAAT
**
17966 AAAAAGTAAAAGATCAATTTTATCTTAAAAATTGAGAAAAAGTGCAAGG
1 AAAAA-TAAAAGATCAATTTTATCGGAAAAATTGAGAAAAAGTGC-A-G
* *
18015 AAAAATAAAAGATCAATTTTGTGGGAAAAATTGAGAAAAAGTGCAG
1 AAAAATAAAAGATCAATTTTATCGGAAAAATTGAGAAAAAGTGCAG
*
18061 AAAAGTAAAAGAT
1 AAAAATAAAAGAT
18074 TGCTTTGAGT
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
46 13 0.24
47 1 0.02
48 35 0.65
49 5 0.09
ACGTcount: A:0.55, C:0.05, G:0.19, T:0.22
Consensus pattern (46 bp):
AAAAATAAAAGATCAATTTTATCGGAAAAATTGAGAAAAAGTGCAG
Found at i:19368 original size:9 final size:9
Alignment explanation
Indices: 19348--19385 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
19338 TTAATTCATT
19348 TAATTTCC-
1 TAATTTCCA
19356 TAATTTCCA
1 TAATTTCCA
*
19365 TAATTTCCC
1 TAATTTCCA
19374 TAATTTCCA
1 TAATTTCCA
19383 TAA
1 TAA
19386 GTAATTTGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 8 0.30
9 19 0.70
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.45
Consensus pattern (9 bp):
TAATTTCCA
Found at i:19377 original size:18 final size:17
Alignment explanation
Indices: 19348--19385 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 17
19338 TTAATTCATT
19348 TAATTTCCTAATTTCCA
1 TAATTTCCTAATTTCCA
19365 TAATTTCCCTAATTTCCA
1 TAATTT-CCTAATTTCCA
19383 TAA
1 TAA
19386 GTAATTTGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.45
Consensus pattern (17 bp):
TAATTTCCTAATTTCCA
Found at i:22162 original size:24 final size:24
Alignment explanation
Indices: 22135--22200 Score: 87
Period size: 24 Copynumber: 2.8 Consensus size: 24
22125 CACATTTTGT
* *
22135 GTTTGGGCTTTAGTTTTTGCTTAG
1 GTTTGGGCTTTAGTTTTTGATAAG
*
22159 GTTTGGGCCTTAGTTTTTGATAAG
1 GTTTGGGCTTTAGTTTTTGATAAG
* *
22183 ATTTGGGGTTTAGTTTTT
1 GTTTGGGCTTTAGTTTTT
22201 AGTTATAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.12, C:0.06, G:0.29, T:0.53
Consensus pattern (24 bp):
GTTTGGGCTTTAGTTTTTGATAAG
Found at i:22223 original size:25 final size:24
Alignment explanation
Indices: 22136--22223 Score: 81
Period size: 24 Copynumber: 3.6 Consensus size: 24
22126 ACATTTTGTG
* * * *
22136 TTTGGGCTTTAGTTTTTGCTTAGG
1 TTTGGGCCTTAGTTTTTGATAAGA
22160 TTTGGGCCTTAGTTTTTGATAAGA
1 TTTGGGCCTTAGTTTTTGATAAGA
**
22184 TTTGGGGTTTAGTTTTTAGTTATAA-A
1 TTTGGGCCTTAGTTTTT-G--ATAAGA
22210 TTTGGGCCTT-GTTT
1 TTTGGGCCTTAGTTT
22224 GTTACATTTA
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
24 35 0.66
25 5 0.09
26 9 0.17
27 4 0.08
ACGTcount: A:0.15, C:0.07, G:0.26, T:0.52
Consensus pattern (24 bp):
TTTGGGCCTTAGTTTTTGATAAGA
Found at i:22826 original size:15 final size:16
Alignment explanation
Indices: 22800--22830 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
22790 CTTTTAGTTT
22800 TCAAAGATAAAAAAAA
1 TCAAAGATAAAAAAAA
22816 TCAAA-ATAAAAAAAA
1 TCAAAGATAAAAAAAA
22831 ATGAGTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.77, C:0.06, G:0.03, T:0.13
Consensus pattern (16 bp):
TCAAAGATAAAAAAAA
Found at i:22986 original size:42 final size:41
Alignment explanation
Indices: 22912--22997 Score: 136
Period size: 42 Copynumber: 2.1 Consensus size: 41
22902 CAAAATAAAA
*
22912 AAGAAGTTTTCCAAATTTTCAATTTAGAGAAAGATACCATC
1 AAGAAGTTTTCCAAATTTTCAATTTAGAGAAAGACACCATC
* *
22953 AAGAAGTTTTCCAAAGTTTTCAATTTAGGGAAAGACCCCATC
1 AAGAAGTTTTCCAAA-TTTTCAATTTAGAGAAAGACACCATC
22995 AAG
1 AAG
22998 TTTTCAAAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 15 0.37
42 26 0.63
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (41 bp):
AAGAAGTTTTCCAAATTTTCAATTTAGAGAAAGACACCATC
Found at i:23028 original size:23 final size:22
Alignment explanation
Indices: 22993--23038 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 22
22983 AAAGACCCCA
22993 TCAAGTTTTCAAAGTATTCAAT
1 TCAAGTTTTCAAAGTATTCAAT
*
23015 TCAAGTTTTTCAAAGTTTTCAAT
1 TCAAG-TTTTCAAAGTATTCAAT
23038 T
1 T
23039 TAGTGAAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.46
Consensus pattern (22 bp):
TCAAGTTTTCAAAGTATTCAAT
Found at i:23072 original size:39 final size:40
Alignment explanation
Indices: 23018--23096 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 40
23008 ATTCAATTCA
*
23018 AGTTTTTCAAAG-TTTTCAA-TTTAGTGAAAGATCCCATCC
1 AGTTTTTCAAAGTTTTTCAACTTAAG-GAAAGATCCCATCC
*
23057 AGTTTTTTAAAGTTTTTTCAACTTAAGGAAAGATCCCATC
1 AGTTTTTCAAAG-TTTTTCAACTTAAGGAAAGATCCCATC
23097 AAAGTTTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 11 0.31
41 20 0.57
42 4 0.11
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (40 bp):
AGTTTTTCAAAGTTTTTCAACTTAAGGAAAGATCCCATCC
Found at i:23098 original size:102 final size:101
Alignment explanation
Indices: 22915--23104 Score: 240
Period size: 102 Copynumber: 1.9 Consensus size: 101
22905 AATAAAAAAG
*
22915 AAGTTTTCCAAATTTTCAATTTAGAGAAAGATACCATCAAGAAGTTTTCCAAAGTTTTCAATTTA
1 AAGTTTTCCAAATTTTCAATTTAGAGAAAGATACCATC-A-AAGTTTTCCAAAGTTTTCAACTTA
*
22980 GGGAAAGACCCCATC-AAGTTTTCAAAGTATTCAATTC
64 AGGAAAGACCCCATCAAAGTTTTCAAAGTATTCAATTC
* * * * **
23017 AAGTTTTTCAAAGTTTTCAATTTAGTGAAAGATCCCATC-CAGTTTTTTAAAGTTTTTTCAACTT
1 AAGTTTTCCAAA-TTTTCAATTTAGAGAAAGATACCATCAAAGTTTTCCAAAG--TTTTCAACTT
*
23081 AAGGAAAGATCCCATCAAAGTTTT
63 AAGGAAAGACCCCATCAAAGTTTT
23105 AAAATTGAGT
Statistics
Matches: 75, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
100 10 0.13
102 34 0.45
103 31 0.41
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (101 bp):
AAGTTTTCCAAATTTTCAATTTAGAGAAAGATACCATCAAAGTTTTCCAAAGTTTTCAACTTAAG
GAAAGACCCCATCAAAGTTTTCAAAGTATTCAATTC
Found at i:27185 original size:2 final size:2
Alignment explanation
Indices: 27178--27204 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
27168 AGCAACATCT
27178 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
27205 TGACATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31393 original size:2 final size:2
Alignment explanation
Indices: 31386--31415 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
31376 GATCTCTTTC
31386 AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
31416 GTAATTATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:32294 original size:83 final size:83
Alignment explanation
Indices: 32193--32432 Score: 453
Period size: 83 Copynumber: 2.9 Consensus size: 83
32183 AGGCTTTTAT
***
32193 TGTTAAAGTATTAAGAATGTAAAATTTTGACATTTTATATCTATAGTTATGCAACACATGTTCAA
1 TGTTAAAGTATTAAGAATGTAGTTTTTTGACATTTTATATCTATAGTTATGCAACACATGTTCAA
32258 TTTTATATCTATCGTTAA
66 TTTTATATCTATCGTTAA
32276 TGTTAAAGTATTAAGAATGTAGTTTTTTGACATTTTATATCTATAGTTATGCAACACATGTTCAA
1 TGTTAAAGTATTAAGAATGTAGTTTTTTGACATTTTATATCTATAGTTATGCAACACATGTTCAA
32341 TTTTATATCTATCGTTAA
66 TTTTATATCTATCGTTAA
32359 TGTTAAAGTATTAAGAATGTAGTTTTTTGACATTTTATATCTATAGTTATGCAACACATGTTCAA
1 TGTTAAAGTATTAAGAATGTAGTTTTTTGACATTTTATATCTATAGTTATGCAACACATGTTCAA
32424 TTTTATATC
66 TTTTATATC
32433 ACTTAAGTCA
Statistics
Matches: 154, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 154 1.00
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.45
Consensus pattern (83 bp):
TGTTAAAGTATTAAGAATGTAGTTTTTTGACATTTTATATCTATAGTTATGCAACACATGTTCAA
TTTTATATCTATCGTTAA
Found at i:33407 original size:39 final size:40
Alignment explanation
Indices: 33351--33431 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
33341 TTTAATTCCT
33351 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
33391 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
33430 AT
1 AT
33432 TCTTAGGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:33459 original size:24 final size:25
Alignment explanation
Indices: 33422--33468 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
33412 AATACTTACA
33422 TTAATTAAATTC-TTAGGTATTTTT
1 TTAATTAAATTCTTTAGGTATTTTT
33446 TTAATTCAAA-TCTTTAGGTATTT
1 TTAATT-AAATTCTTTAGGTATTT
33469 GTGCAAATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (25 bp):
TTAATTAAATTCTTTAGGTATTTTT
Found at i:33941 original size:201 final size:204
Alignment explanation
Indices: 33547--33950 Score: 681
Period size: 201 Copynumber: 2.0 Consensus size: 204
33537 TTAATAATAA
33547 ATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTCGACATTGATCTAATTTAATTT
1 ATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTCGACATTGATCTAATTTAATTT
* **
33612 AATAAATCAACCACTAATGTTCAACTAATTTTTTTTTGGTATAGTTCTATATATATAATAGTAAT
66 AATAAATCAACCACTAATGTTCAACTAATCTTTTTTTGGTATAGTTCTATATATATAATAACAAT
*
33677 GTGTTGTATCTTATTCACTACAACTTTGTTAGTAATTTTAAACTTAAAAAATTAATAACATTCAC
131 GTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAAACTTAAAAAATTAATAACATTCAC
*
33742 CATTGATAT
196 CATCGATAT
* * *
33751 ATAAATCGGATCTTTAATATCTTTTATAATTTTGGAATTTTTTTTGACATTGATCTAATTTAATT
1 ATAAATCGGATC-TTAATATCTTTTATAATTTTGAAATTTTGTTCGACATTGATCTAATTTAATT
33816 TAATAAATCAACCACTAATGTTCAACT-A-CTTTTTTTGGTATAGTT-T-TATATATAATAACAA
65 TAATAAATCAACCACTAATGTTCAACTAATCTTTTTTTGGTATAGTTCTATATATATAATAACAA
*
33877 TGTGTTGTATCTTATTCACTGCAACTTTGTTAGTAATCTTAAACTTAAAAAATTAATAACATTCA
130 TGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAAACTTAAAAAATTAATAACATTCA
*
33942 TCATCGATA
195 CCATCGATA
33951 AAGTTATTAA
Statistics
Matches: 189, Mismatches: 10, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
201 83 0.44
202 1 0.01
203 16 0.08
204 13 0.07
205 76 0.40
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.45
Consensus pattern (204 bp):
ATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTCGACATTGATCTAATTTAATTT
AATAAATCAACCACTAATGTTCAACTAATCTTTTTTTGGTATAGTTCTATATATATAATAACAAT
GTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAAACTTAAAAAATTAATAACATTCAC
CATCGATAT
Found at i:34518 original size:35 final size:36
Alignment explanation
Indices: 34472--34540 Score: 113
Period size: 35 Copynumber: 1.9 Consensus size: 36
34462 GAGATTTTGG
* *
34472 AGAAATATGATAATCAAAATTACAAAA-ATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAGATGTAATA
34507 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAGATGTAA
34541 GGTTAATGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 25 0.81
36 6 0.19
ACGTcount: A:0.59, C:0.09, G:0.10, T:0.22
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATCACAAAAGATGTAATA
Found at i:35906 original size:56 final size:57
Alignment explanation
Indices: 35812--35923 Score: 172
Period size: 56 Copynumber: 2.0 Consensus size: 57
35802 ATAGCATCAT
*
35812 GCCTCGGTCCTAAAACGTCTTTTTTAGGCATCTAATAAAAAACATGTCACTCGATAA
1 GCCTCGGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAACATGTCACTCGATAA
* * * *
35869 GCCTTGGTCCGAAAACGTC-TTTTTATGCATCTAATAAAGAACATGTCACTTGATA
1 GCCTCGGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAACATGTCACTCGATA
35924 TCTAATTAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
56 33 0.66
57 17 0.34
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.31
Consensus pattern (57 bp):
GCCTCGGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAACATGTCACTCGATAA
Found at i:38390 original size:22 final size:22
Alignment explanation
Indices: 38364--38442 Score: 74
Period size: 22 Copynumber: 3.6 Consensus size: 22
38354 AATTTATATT
38364 AAATTTTGATAATCACACCATA
1 AAATTTTGATAATCACACCATA
*
38386 AAA-TTT--TAATGACATCCATA
1 AAATTTTGATAATCACA-CCATA
* *
38406 TGAAATTTTGATAATCACACTATG
1 --AAATTTTGATAATCACACCATA
*
38430 AAATTCTGATAAT
1 AAATTTTGATAAT
38443 GATATCTAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
19 7 0.15
20 5 0.11
21 3 0.07
22 18 0.39
23 3 0.07
24 3 0.07
25 7 0.15
ACGTcount: A:0.43, C:0.14, G:0.08, T:0.35
Consensus pattern (22 bp):
AAATTTTGATAATCACACCATA
Found at i:38604 original size:22 final size:22
Alignment explanation
Indices: 38579--38639 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
38569 ATAACGAAAC
* *
38579 TATGAAAATTTAATAAGCTGCT
1 TATGAAAATTTGATAAGCTCCT
* *
38601 TATGAAATTTTGATAACCTCCT
1 TATGAAAATTTGATAAGCTCCT
*
38623 CATG-AAATTTGATAAGC
1 TATGAAAATTTGATAAGC
38640 ACACTATGAT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 11 0.34
22 21 0.66
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (22 bp):
TATGAAAATTTGATAAGCTCCT
Found at i:38648 original size:21 final size:20
Alignment explanation
Indices: 38601--38653 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
38591 ATAAGCTGCT
*
38601 TATGAAATTTTGATAACCTCC
1 TATGAAA-TTTGATAACCACC
*
38622 TCATGAAATTTGATAAGCACAC
1 T-ATGAAATTTGATAACCAC-C
*
38644 TATGATATTT
1 TATGAAATTT
38654 TAATAACCTC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 19 0.70
22 8 0.30
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (20 bp):
TATGAAATTTGATAACCACC
Found at i:38765 original size:22 final size:21
Alignment explanation
Indices: 38734--38812 Score: 68
Period size: 22 Copynumber: 3.6 Consensus size: 21
38724 GATCACTATC
*
38734 AAATTGTGATAACCTCATTATA
1 AAATTTTGATAACCTC-TTATA
* * *
38756 AAATTTTGATAAAGCTTTCTGTA
1 AAATTTTGAT-AACCTCT-TATA
* *
38779 AAATTTTGATAACCCTCTTTTG
1 AAATTTTGATAA-CCTCTTATA
38801 AAATTTTGATAA
1 AAATTTTGATAA
38813 TCTCGTCATG
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
22 26 0.57
23 20 0.43
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.42
Consensus pattern (21 bp):
AAATTTTGATAACCTCTTATA
Found at i:38824 original size:22 final size:22
Alignment explanation
Indices: 38799--38855 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
38789 AACCCTCTTT
* *
38799 TGAAATTTTGATAATCTCGTCA
1 TGAAATTTTGATAATCACCTCA
*
38821 TGAAATTTCGATAATCACCTCA
1 TGAAATTTTGATAATCACCTCA
38843 TGAAATTTTGATA
1 TGAAATTTTGATA
38856 GCTACCCTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (22 bp):
TGAAATTTTGATAATCACCTCA
Found at i:38867 original size:22 final size:21
Alignment explanation
Indices: 38820--38938 Score: 80
Period size: 22 Copynumber: 5.4 Consensus size: 21
38810 TAATCTCGTC
* *
38820 ATGAAATTTCGATA-ATCACCT
1 ATGAAATTTTGATAGCTC-CCT
38841 CATGAAATTTTGATAGCTACCCT
1 -ATGAAATTTTGATAGCT-CCCT
* *
38864 ATGAAATTTTTATAACCTCCCT
1 ATGAAATTTTGAT-AGCTCCCT
* *
38886 ATGAATTTTTGATAGCATCCTT
1 ATGAAATTTTGATAGC-TCCCT
* * *
38908 A-CAGAATTTTGTTAATCTCCCT
1 ATGA-AATTTTGAT-AGCTCCCT
38930 ATGAAATTT
1 ATGAAATTT
38939 CGAAAACCAT
Statistics
Matches: 76, Mismatches: 14, Indels: 14
0.73 0.13 0.13
Matches are distributed among these distances:
21 3 0.04
22 62 0.82
23 10 0.13
24 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.10, T:0.39
Consensus pattern (21 bp):
ATGAAATTTTGATAGCTCCCT
Found at i:38953 original size:22 final size:22
Alignment explanation
Indices: 38928--39013 Score: 64
Period size: 22 Copynumber: 3.9 Consensus size: 22
38918 GTTAATCTCC
*
38928 CTATGAAATTTCGAAAACCATA
1 CTATGAAATTTCGAAAACCACA
* * * *
38950 CTATTAAATTTTGACAACTACA
1 CTATGAAATTTCGAAAACCACA
* * * *
38972 CTATGAAATTACGATAACCTCC
1 CTATGAAATTTCGAAAACCACA
* * *
38994 CTATGTAATTTTGATAACCA
1 CTATGAAATTTCGAAAACCA
39014 AATTATCAAT
Statistics
Matches: 48, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.33
Consensus pattern (22 bp):
CTATGAAATTTCGAAAACCACA
Found at i:39098 original size:22 final size:22
Alignment explanation
Indices: 39073--39132 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
39063 CCCTCTTAAA
*
39073 AACCATACTATAAAATCTTGAT
1 AACCACACTATAAAATCTTGAT
* *
39095 AACCACACTATCAAATTTTGAT
1 AACCACACTATAAAATCTTGAT
* *
39117 AATCACACAATAAAAT
1 AACCACACTATAAAAT
39133 TTAAATCGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.48, C:0.20, G:0.03, T:0.28
Consensus pattern (22 bp):
AACCACACTATAAAATCTTGAT
Found at i:39768 original size:13 final size:13
Alignment explanation
Indices: 39750--39783 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
39740 TGAATTGAAC
*
39750 AATTTTATAATTA
1 AATTTTATAATAA
*
39763 AATTTTAAAATAA
1 AATTTTATAATAA
39776 AATTTTAT
1 AATTTTAT
39784 TAAATTAGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AATTTTATAATAA
Done.