Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022722.1 Corchorus olitorius cultivar O-4 contig22755, 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: 103326
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1998 original size:85 final size:85
Alignment explanation
Indices: 1908--2077 Score: 313
Period size: 85 Copynumber: 2.0 Consensus size: 85
1898 AAATTAAAAT
*
1908 GGTAAAAATAAAATAGTTATAATAATATTGAATTTAATTAAATAAAAATATATTTTTTAGTAGAA
1 GGTAAAAATAAAATAGTTATAATAATATTGAATTTAATTAAATAAAAATAGATTTTTTAGTAGAA
*
1973 TAATTGTAAAAGTTTATTTC
66 TAACTGTAAAAGTTTATTTC
*
1993 GGTAAAAATAAAATATTTATAATAATATTGAATTTAATTAAATAAAAATAGATTTTTTAGTAGAA
1 GGTAAAAATAAAATAGTTATAATAATATTGAATTTAATTAAATAAAAATAGATTTTTTAGTAGAA
2058 TAACTGTAAAAGTTTATTTC
66 TAACTGTAAAAGTTTATTTC
2078 TAAAAAAATT
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
85 82 1.00
ACGTcount: A:0.48, C:0.02, G:0.09, T:0.41
Consensus pattern (85 bp):
GGTAAAAATAAAATAGTTATAATAATATTGAATTTAATTAAATAAAAATAGATTTTTTAGTAGAA
TAACTGTAAAAGTTTATTTC
Found at i:2112 original size:14 final size:13
Alignment explanation
Indices: 2093--2131 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
2083 AAATTGTAAA
2093 ATTTAAAAAATTT
1 ATTTAAAAAATTT
* *
2106 CATTTAAGAAATAT
1 -ATTTAAAAAATTT
2120 ATTTAAAAAATT
1 ATTTAAAAAATT
2132 CTAATATATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (13 bp):
ATTTAAAAAATTT
Found at i:2254 original size:132 final size:123
Alignment explanation
Indices: 2118--2371 Score: 391
Period size: 132 Copynumber: 2.0 Consensus size: 123
2108 TTTAAGAAAT
2118 ATATTTAAAAAATTCTAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGTAAAAATAAAAT
1 ATATTTAAAAAATTCTAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGTAAAAAT----T
* *
2183 AGGTATAAGGTTATTAGATTTAATTAAATAAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAA
62 A--TA-AA-GATATTAGATTTAATTAAAT-AAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
2248 GC
122 GC
*
2250 ATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATTATAA
1 ATATTTAAAAAATTCTAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGTAAAAATTATAA
*
2315 AGATATTAGATTTAATTAAATAAAATTAGAGTTTTTAGTTGAGTAAAACTATAAAAG
66 AGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
2372 TTTAAACAAT
Statistics
Matches: 118, Mismatches: 4, Indels: 9
0.90 0.03 0.07
Matches are distributed among these distances:
123 34 0.29
124 19 0.16
125 2 0.02
126 2 0.02
128 2 0.02
132 59 0.50
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.37
Consensus pattern (123 bp):
ATATTTAAAAAATTCTAATATATATAAGTTTTTTAAATAAAATAGTAAAATGGTAAAAATTATAA
AGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGC
Found at i:5995 original size:49 final size:47
Alignment explanation
Indices: 5920--6059 Score: 167
Period size: 49 Copynumber: 2.9 Consensus size: 47
5910 CAAGCAATCC
* **
5920 TTTACTTTTACTGCACTTTTTCTCAATTTTTACTACAAAATTGAACT
1 TTTAATTTTACTGCACTTTTTCTCAATTTTTAAGACAAAATTGAACT
*
5967 TTTAATTTTACTTGCATCTTTTTCTCAATTTTTAAGACAAAATTGATCT
1 TTTAATTTTAC-TGCA-CTTTTTCTCAATTTTTAAGACAAAATTGAACT
** *
6016 TTTAATTTT-CATCGCACTTTTTAACAATTTTT-TGACAAAATTGA
1 TTTAATTTTAC-T-GCACTTTTTCTCAATTTTTAAGACAAAATTGA
6060 TTGGCACGCT
Statistics
Matches: 82, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
47 21 0.26
48 20 0.24
49 41 0.50
ACGTcount: A:0.29, C:0.16, G:0.06, T:0.49
Consensus pattern (47 bp):
TTTAATTTTACTGCACTTTTTCTCAATTTTTAAGACAAAATTGAACT
Found at i:6613 original size:18 final size:18
Alignment explanation
Indices: 6590--6695 Score: 158
Period size: 18 Copynumber: 5.9 Consensus size: 18
6580 CAACAACAAA
**
6590 TCGCACCGCACCAAGTAT
1 TCGCACCGCACCAAGTGG
*
6608 TCGCACCGCACCAAATGG
1 TCGCACCGCACCAAGTGG
*
6626 TCGCACCACACCAAGTGG
1 TCGCACCGCACCAAGTGG
6644 TCGCACCGCACCAAGTGG
1 TCGCACCGCACCAAGTGG
* *
6662 TTGCACCGCACCCAGTGG
1 TCGCACCGCACCAAGTGG
6680 TCGCACCGCACCAAGT
1 TCGCACCGCACCAAGT
6696 TGCCACACTT
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 78 1.00
ACGTcount: A:0.25, C:0.40, G:0.23, T:0.13
Consensus pattern (18 bp):
TCGCACCGCACCAAGTGG
Found at i:7949 original size:15 final size:15
Alignment explanation
Indices: 7929--8026 Score: 96
Period size: 15 Copynumber: 6.5 Consensus size: 15
7919 GGAGGAAGAT
7929 GATGGCACCAAAATC
1 GATGGCACCAAAATC
7944 GATGGCACCAAAA-C
1 GATGGCACCAAAATC
*
7958 TGATGGCACCAACATC
1 -GATGGCACCAAAATC
* *
7974 GACGACACCGAAAAT-
1 GATGGCACC-AAAATC
7989 GATGGCACCAAAA-C
1 GATGGCACCAAAATC
*
8003 TGATGGCACCGAAGAT-
1 -GATGGCACC-AAAATC
8019 GATGGCAC
1 GATGGCAC
8027 TGAAAGTGTT
Statistics
Matches: 69, Mismatches: 7, Indels: 14
0.77 0.08 0.16
Matches are distributed among these distances:
14 5 0.07
15 56 0.81
16 8 0.12
ACGTcount: A:0.38, C:0.27, G:0.23, T:0.12
Consensus pattern (15 bp):
GATGGCACCAAAATC
Found at i:7962 original size:30 final size:30
Alignment explanation
Indices: 7927--8026 Score: 132
Period size: 30 Copynumber: 3.3 Consensus size: 30
7917 ATGGAGGAAG
7927 ATGATGGCACCAAAATCGATGGCACC-AAA
1 ATGATGGCACCAAAATCGATGGCACCGAAA
* * *
7956 ACTGATGGCACCAACATCGACGACACCGAAA
1 A-TGATGGCACCAAAATCGATGGCACCGAAA
*
7987 ATGATGGCACCAAAA-CTGATGGCACCGAAG
1 ATGATGGCACCAAAATC-GATGGCACCGAAA
8017 ATGATGGCAC
1 ATGATGGCAC
8027 TGAAAGTGTT
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
29 2 0.03
30 55 0.90
31 4 0.07
ACGTcount: A:0.38, C:0.26, G:0.23, T:0.13
Consensus pattern (30 bp):
ATGATGGCACCAAAATCGATGGCACCGAAA
Found at i:10724 original size:49 final size:47
Alignment explanation
Indices: 10663--10788 Score: 157
Period size: 49 Copynumber: 2.6 Consensus size: 47
10653 CTTTTACTGT
*
10663 ACTTTTTCTCAATTTTTACTACAAAATTGAACTTTTAATTTT-ACTTGC
1 ACTTTTTCTCAATTTTTA-TACAAAATTGAACTTTTAATTTTCA-TCGC
* *
10711 ATCTTTTTCTCAATTTTTAAGACAAAATTGATCTTTTAATTTTCATCGC
1 A-CTTTTTCTCAATTTTT-ATACAAAATTGAACTTTTAATTTTCATCGC
*
10760 ACTTTTTATCAATTTTT-TGACAAAATTGA
1 ACTTTTTCTCAATTTTTAT-ACAAAATTGA
10789 TTGACACGCT
Statistics
Matches: 69, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
47 10 0.14
48 16 0.23
49 41 0.59
50 2 0.03
ACGTcount: A:0.30, C:0.15, G:0.06, T:0.49
Consensus pattern (47 bp):
ACTTTTTCTCAATTTTTATACAAAATTGAACTTTTAATTTTCATCGC
Found at i:15853 original size:30 final size:31
Alignment explanation
Indices: 15801--15862 Score: 99
Period size: 30 Copynumber: 2.0 Consensus size: 31
15791 TCACTTTTTG
* *
15801 TGAATCAAACTCAATTTTGAAACCACGATCA
1 TGAATCAAACTCAATCTTGAAACCAAGATCA
15832 TGAATCAAACTCAA-CTTGAAACCAAGATCA
1 TGAATCAAACTCAATCTTGAAACCAAGATCA
15862 T
1 T
15863 CAAGTTTCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 15 0.52
31 14 0.48
ACGTcount: A:0.44, C:0.23, G:0.10, T:0.24
Consensus pattern (31 bp):
TGAATCAAACTCAATCTTGAAACCAAGATCA
Found at i:29794 original size:109 final size:109
Alignment explanation
Indices: 29603--29928 Score: 584
Period size: 109 Copynumber: 3.0 Consensus size: 109
29593 TAGTCATTTT
29603 GGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTGTTTGGTATGTGTGCTT
1 GGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTGTTTGGTATGTGTGCTT
29668 ATTTAATAGGTTCAATTGAATAAACACCACAATTAATAATAATA
66 ATTTAATAGGTTCAATTGAATAAACACCACAATTAATAATAATA
*
29712 GGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTATATTGTTTGGTATGTGTGCTT
1 GGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTGTTTGGTATGTGTGCTT
* *
29777 ATTTTATAGGTTCAATTGAATAAACAACACAATTAATAATAATA
66 ATTTAATAGGTTCAATTGAATAAACACCACAATTAATAATAATA
* *
29821 GGTGCTTGTATTGTTCTTTAAATCCAATAGTTCATTGCATTTTGTATTGTTTGGTATGTGTGCTT
1 GGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTGTTTGGTATGTGTGCTT
29886 ATTTAATAGGTTCAATTGAATAAAC-CACACAA-TAATAATAATA
66 ATTTAATAGGTTCAATTGAATAAACAC-CACAATTAATAATAATA
29929 TATATATAAT
Statistics
Matches: 208, Mismatches: 8, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
108 11 0.05
109 197 0.95
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.43
Consensus pattern (109 bp):
GGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTGTTTGGTATGTGTGCTT
ATTTAATAGGTTCAATTGAATAAACACCACAATTAATAATAATA
Found at i:31627 original size:26 final size:26
Alignment explanation
Indices: 31595--31694 Score: 191
Period size: 26 Copynumber: 3.8 Consensus size: 26
31585 ACTGTACAAA
31595 TTGAATTTTTATAAATAAAATAAAAT
1 TTGAATTTTTATAAATAAAATAAAAT
31621 TTGAATTTTTATAAATAAAATAAAAT
1 TTGAATTTTTATAAATAAAATAAAAT
31647 TTGAATTTTTATAAATAAAATAAAAT
1 TTGAATTTTTATAAATAAAATAAAAT
*
31673 TTGAATTTTTCTAAATAAAATA
1 TTGAATTTTTATAAATAAAATA
31695 TTTTAATAAT
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
26 73 1.00
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.43
Consensus pattern (26 bp):
TTGAATTTTTATAAATAAAATAAAAT
Found at i:32808 original size:351 final size:352
Alignment explanation
Indices: 32150--32844 Score: 950
Period size: 351 Copynumber: 2.0 Consensus size: 352
32140 AAGTCAGATA
* ** * *
32150 TCTTGAAGTCTAAATCTGATATTCTTAAACCCAATTTGCTAATATGGAAGTCCAAAGAAGGAGTT
1 TCTTGAAATCTAAATCTGATATTCTTAAACCCAATTCACTAATATGGAAGCCCAAAGAAGGAGTC
* * *
32215 CAAGACCAATTAGTAATTATGATGTAGTGATGATTCAACCCTGATGCAGCAATGTTAAATCATAT
66 CAAGACCAATCAGTAATTATGATGCAGTAATGATTCAACCCTGATGCAGCAATGTTAAATCATAT
* * * * *
32280 TCAAAGGAGGACTTCAACAACATCAGTTTTGGAAGAAAATTCATAACTTTTGATCCAGATCTCAG
131 TCAAAAGAGGACTTCAACAACAGCAGTTTTGGAAGAAAATTCATAACTTTTAATCCAAAACTCAG
* * * *
32345 AAAAATGCAAATGAGATACCGTTGTAAAAAGAATTCCAGGATCTACAACTTTTATGTTTACTTTG
196 AAAAATGCAAATGAGATACCGTTGGAAAAAGAATTCCAAGATCTACAACTTTTATGTTTACTCTC
* * * * *
32410 AAACCTAATTCTGCAGTTTCGGTGGACGATTTTGCCCTTGAAATTTCTAGATAGAATTGATCTTC
261 AAACCTAATTCTGCAGTTTCAGTGGACGATTTTACCCTTGAAATTTCTAGACAAAATTAATCTTC
*
32475 TCCTAAACCGATTTGGAGAGCCAAATG
326 TCCTAAACCGACTTGGAGAGCCAAATG
* * * *
32502 TCTTGAAATCTAAATTTGATATTCTTAGATCCAATTCATTAATATGGAAGCCCAAAGAAGGAGTC
1 TCTTGAAATCTAAATCTGATATTCTTAAACCCAATTCACTAATATGGAAGCCCAAAGAAGGAGTC
* * ** * *
32567 CAAGTCCAATCAGTAATTATGATGCAGTAATGGTTCAACCCTGATGCATTATTGTTAAATCTTAT
66 CAAGACCAATCAGTAATTATGATGCAGTAATGATTCAACCCTGATGCAGCAATGTTAAATCATAT
* **
32632 TCAAAAGAGGACTTC-ACAAGAGCAGTTTTGGAAGAAAATTCATAACTTTTAATTTAAAACTCAG
131 TCAAAAGAGGACTTCAACAACAGCAGTTTTGGAAGAAAATTCATAACTTTTAATCCAAAACTCAG
* *
32696 AAAAATGCAAATGGGATACCGTTGGAAAGATG-ATTCCAAGATCTACAACTTTTATGTTTAC-CT
196 AAAAATGCAAATGAGATACCGTTGGAAA-AAGAATTCCAAGATCTACAACTTTTATGTTTACTCT
* *
32759 CAAGA-CTCAATTCTGCAGTTGT-AGTGGATGATTTTACCCTTGAAATTTCTGGACAAAATTAAT
260 CAA-ACCT-AATTCTGCAGTT-TCAGTGGACGATTTTACCCTTGAAATTTCTAGACAAAATTAAT
*
32822 CTTCTCCTAAACCTACTTGGAGA
322 CTTCTCCTAAACCGACTTGGAGA
32845 ATGTTTTGGA
Statistics
Matches: 298, Mismatches: 41, Indels: 9
0.86 0.12 0.03
Matches are distributed among these distances:
350 5 0.02
351 164 0.55
352 129 0.43
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Consensus pattern (352 bp):
TCTTGAAATCTAAATCTGATATTCTTAAACCCAATTCACTAATATGGAAGCCCAAAGAAGGAGTC
CAAGACCAATCAGTAATTATGATGCAGTAATGATTCAACCCTGATGCAGCAATGTTAAATCATAT
TCAAAAGAGGACTTCAACAACAGCAGTTTTGGAAGAAAATTCATAACTTTTAATCCAAAACTCAG
AAAAATGCAAATGAGATACCGTTGGAAAAAGAATTCCAAGATCTACAACTTTTATGTTTACTCTC
AAACCTAATTCTGCAGTTTCAGTGGACGATTTTACCCTTGAAATTTCTAGACAAAATTAATCTTC
TCCTAAACCGACTTGGAGAGCCAAATG
Found at i:34400 original size:31 final size:31
Alignment explanation
Indices: 34362--34423 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
34352 TATGTTAGAC
*
34362 AAATAAGGATATAATAGGTATTTCAAAAGTT
1 AAATAAGGATATAATAGGCATTTCAAAAGTT
*
34393 AAATAAGGATATAATAGGCGTTTCAAAAGTT
1 AAATAAGGATATAATAGGCATTTCAAAAGTT
34424 TTACAAAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.47, C:0.05, G:0.18, T:0.31
Consensus pattern (31 bp):
AAATAAGGATATAATAGGCATTTCAAAAGTT
Found at i:38224 original size:23 final size:23
Alignment explanation
Indices: 38198--38241 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
38188 TATTTTATTG
* *
38198 TAAAATCTTTTTATTTTTTTAAC
1 TAAAAGCTTTTTATTATTTTAAC
38221 TAAAAGCTTTTTATTATTTTA
1 TAAAAGCTTTTTATTATTTTA
38242 TAATTATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.59
Consensus pattern (23 bp):
TAAAAGCTTTTTATTATTTTAAC
Found at i:41181 original size:29 final size:29
Alignment explanation
Indices: 41148--41207 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
41138 CAAGTTTATA
41148 AGAAGCTAATTAAGATGATCATATGATGC
1 AGAAGCTAATTAAGATGATCATATGATGC
41177 AGAAGCTAATTAAGATGATCATATGATGC
1 AGAAGCTAATTAAGATGATCATATGATGC
41206 AG
1 AG
41208 GGACGGCCGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.42, C:0.10, G:0.22, T:0.27
Consensus pattern (29 bp):
AGAAGCTAATTAAGATGATCATATGATGC
Found at i:42561 original size:17 final size:18
Alignment explanation
Indices: 42529--42563 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
42519 TCATATACTT
*
42529 CAATTTCTTTGATTATTA
1 CAATTTCTTAGATTATTA
42547 CAATTT-TTAGATTATTA
1 CAATTTCTTAGATTATTA
42564 TTATTACATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.31, C:0.09, G:0.06, T:0.54
Consensus pattern (18 bp):
CAATTTCTTAGATTATTA
Found at i:56408 original size:13 final size:13
Alignment explanation
Indices: 56390--56415 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
56380 ATGAAATAAA
56390 TTAGTCAATGGTT
1 TTAGTCAATGGTT
56403 TTAGTCAATGGTT
1 TTAGTCAATGGTT
56416 CATGGTTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (13 bp):
TTAGTCAATGGTT
Found at i:57014 original size:55 final size:52
Alignment explanation
Indices: 56914--57116 Score: 329
Period size: 51 Copynumber: 3.9 Consensus size: 52
56904 CATTTTCATA
*
56914 TTACATATATACAGAATGGGATTTGCAATTTGGC-ATATATATATAATATAT
1 TTACATATATACAGAATGTGATTTGCAATTTGGCTATATATATATAATATAT
*
56965 TTACATATATATAGAATGTGATTTGCAATTTGGCATATATATATATATAATATAT
1 TTACATATATACAGAATGTGATTTGCAATTTGGC---TATATATATATAATATAT
57020 TTACATATATACAGAATGTGATTTGCAATTTGGCT-TATATATATAATATAT
1 TTACATATATACAGAATGTGATTTGCAATTTGGCTATATATATATAATATAT
*
57071 TTACATATATACAGAATGTGATTTGCAATTTGACTTATATATATAT
1 TTACATATATACAGAATGTGATTTGCAATTTGGC-TATATATATAT
57117 CTGAAGTTTA
Statistics
Matches: 142, Mismatches: 4, Indels: 10
0.91 0.03 0.06
Matches are distributed among these distances:
51 81 0.57
52 2 0.01
53 9 0.06
55 50 0.35
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.42
Consensus pattern (52 bp):
TTACATATATACAGAATGTGATTTGCAATTTGGCTATATATATATAATATAT
Found at i:57037 original size:106 final size:106
Alignment explanation
Indices: 56914--57116 Score: 361
Period size: 106 Copynumber: 1.9 Consensus size: 106
56904 CATTTTCATA
*
56914 TTACATATATACAGAATGGGATTTGCAATTTGGCATATATATATAATATATTTACATATATATAG
1 TTACATATATACAGAATGGGATTTGCAATTTGGCATATATATATAATATATTTACATATATACAG
*
56979 AATGTGATTTGCAATTTGGCATATATATATATATAATATAT
66 AATGTGATTTGCAATTTGACATATATATATATATAATATAT
* *
57020 TTACATATATACAGAATGTGATTTGCAATTTGGCTTATATATATAATATATTTACATATATACAG
1 TTACATATATACAGAATGGGATTTGCAATTTGGCATATATATATAATATATTTACATATATACAG
*
57085 AATGTGATTTGCAATTTGACTTATATATATAT
66 AATGTGATTTGCAATTTGACATATATATATAT
57117 CTGAAGTTTA
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
106 92 1.00
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.42
Consensus pattern (106 bp):
TTACATATATACAGAATGGGATTTGCAATTTGGCATATATATATAATATATTTACATATATACAG
AATGTGATTTGCAATTTGACATATATATATATATAATATAT
Found at i:59920 original size:13 final size:13
Alignment explanation
Indices: 59857--60050 Score: 116
Period size: 13 Copynumber: 15.4 Consensus size: 13
59847 TGTTTGTAGT
59857 TTCTGAAATCA-A
1 TTCTGAAATCAGA
59869 TATCTGAAATC-GAA
1 T-TCTGAAATCAG-A
59883 TTCTGAAATCAGA
1 TTCTGAAATCAGA
* **
59896 GTCTGATTTCAGA
1 TTCTGAAATCAGA
59909 TTCTGAAATCAG-
1 TTCTGAAATCAGA
* ** *
59921 -TATGATTTCAGT
1 TTCTGAAATCAGA
*
59933 TTCTGAAATCAGT
1 TTCTGAAATCAGA
***
59946 TTCTGTTTTCAGA
1 TTCTGAAATCAGA
59959 TTCTGAAATCAG-
1 TTCTGAAATCAGA
** *
59971 -TCTGATTTCAGT
1 TTCTGAAATCAGA
*
59983 TTCTGAAATCAGT
1 TTCTGAAATCAGA
***
59996 TTCTGTTTTCAGA
1 TTCTGAAATCAGA
60009 TTCTGAAATCAG-
1 TTCTGAAATCAGA
** *
60021 -TCTGATTTCAGT
1 TTCTGAAATCAGA
*
60033 TTCTGAAATCAGT
1 TTCTGAAATCAGA
60046 TTCTG
1 TTCTG
60051 TTTTCAGTTC
Statistics
Matches: 138, Mismatches: 34, Indels: 19
0.72 0.18 0.10
Matches are distributed among these distances:
11 26 0.19
12 1 0.01
13 108 0.78
14 3 0.02
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.41
Consensus pattern (13 bp):
TTCTGAAATCAGA
Found at i:59931 original size:24 final size:24
Alignment explanation
Indices: 59882--60045 Score: 220
Period size: 24 Copynumber: 6.6 Consensus size: 24
59872 CTGAAATCGA
59882 ATTCTGAAATCAGAGTCTGATTTCAG
1 ATTCTGAAATC--AGTCTGATTTCAG
*
59908 ATTCTGAAATCAGTATGATTTCAG
1 ATTCTGAAATCAGTCTGATTTCAG
* *
59932 TTTCTGAAATCAGTTTCTGTTTTCAG
1 ATTCTGAAATCAG--TCTGATTTCAG
59958 ATTCTGAAATCAGTCTGATTTCAG
1 ATTCTGAAATCAGTCTGATTTCAG
* *
59982 TTTCTGAAATCAGTTTCTGTTTTCAG
1 ATTCTGAAATCAG--TCTGATTTCAG
60008 ATTCTGAAATCAGTCTGATTTCAG
1 ATTCTGAAATCAGTCTGATTTCAG
*
60032 TTTCTGAAATCAGT
1 ATTCTGAAATCAGT
60046 TTCTGTTTTC
Statistics
Matches: 123, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
24 69 0.56
26 54 0.44
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.41
Consensus pattern (24 bp):
ATTCTGAAATCAGTCTGATTTCAG
Found at i:59943 original size:50 final size:50
Alignment explanation
Indices: 59883--60061 Score: 315
Period size: 50 Copynumber: 3.6 Consensus size: 50
59873 TGAAATCGAA
** * *
59883 TTCTGAAATCAGAGTCTGATTTCAGATTCTGAAATCAGTATGATTTCAGT
1 TTCTGAAATCAGTTTCTGTTTTCAGATTCTGAAATCAGTCTGATTTCAGT
59933 TTCTGAAATCAGTTTCTGTTTTCAGATTCTGAAATCAGTCTGATTTCAGT
1 TTCTGAAATCAGTTTCTGTTTTCAGATTCTGAAATCAGTCTGATTTCAGT
59983 TTCTGAAATCAGTTTCTGTTTTCAGATTCTGAAATCAGTCTGATTTCAGT
1 TTCTGAAATCAGTTTCTGTTTTCAGATTCTGAAATCAGTCTGATTTCAGT
60033 TTCTGAAATCAGTTTCTGTTTTCAG-TTCT
1 TTCTGAAATCAGTTTCTGTTTTCAGATTCT
60062 ATTTCCATTT
Statistics
Matches: 125, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
49 4 0.03
50 121 0.97
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.44
Consensus pattern (50 bp):
TTCTGAAATCAGTTTCTGTTTTCAGATTCTGAAATCAGTCTGATTTCAGT
Found at i:60050 original size:37 final size:38
Alignment explanation
Indices: 59928--60050 Score: 117
Period size: 37 Copynumber: 3.3 Consensus size: 38
59918 CAGTATGATT
* *
59928 TCAGTTTCTGAAATCAGTTTCTGTTTTCAGATTCTGAAA
1 TCAGTTTCTGAAATCAG-TTCTGATTTCAGTTTCTGAAA
** ** ***
59967 TCAG--TCTGATTTCAGTTTCTGAAATCAGTTTCTGTTT
1 TCAGTTTCTGAAATCAG-TTCTGATTTCAGTTTCTGAAA
*
60004 TCAGATTCTGAAATCAG-TCTGATTTCAGTTTCTGAAA
1 TCAGTTTCTGAAATCAGTTCTGATTTCAGTTTCTGAAA
60041 TCAGTTTCTG
1 TCAGTTTCTG
60051 TTTTCAGTTC
Statistics
Matches: 65, Mismatches: 17, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
37 52 0.80
39 13 0.20
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (38 bp):
TCAGTTTCTGAAATCAGTTCTGATTTCAGTTTCTGAAA
Found at i:60988 original size:9 final size:9
Alignment explanation
Indices: 60974--60998 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
60964 GATTGAAACC
60974 GACCCGACA
1 GACCCGACA
60983 GACCCGACA
1 GACCCGACA
60992 GACCCGA
1 GACCCGA
60999 AACCGACCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.44, G:0.24, T:0.00
Consensus pattern (9 bp):
GACCCGACA
Found at i:62109 original size:88 final size:88
Alignment explanation
Indices: 61960--62137 Score: 311
Period size: 88 Copynumber: 2.0 Consensus size: 88
61950 TTTTCCAGAG
* * *
61960 CCATCCTACAAGCCTCTTTGTCAAAGTATTCAGAATTCCGGTGCCATGCTTTTTCGATTCCATCT
1 CCATCCTACAAGCCTCTTCGTCAAAGTATTCAGAATCCCAGTGCCATGCTTTTTCGATTCCATCT
62025 CCTTCTAAGGTAGCTTAACTCTA
66 CCTTCTAAGGTAGCTTAACTCTA
* *
62048 CCATCCTACAAGCCTCTTCGTCAAAGTATTCGGAATCCCAGTGCCATGTTTTTTCGATTCCATCT
1 CCATCCTACAAGCCTCTTCGTCAAAGTATTCAGAATCCCAGTGCCATGCTTTTTCGATTCCATCT
62113 CCTTCTAAGGTAGCTTAACTCTA
66 CCTTCTAAGGTAGCTTAACTCTA
62136 CC
1 CC
62138 TTGGTTTCAT
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
88 85 1.00
ACGTcount: A:0.22, C:0.30, G:0.13, T:0.34
Consensus pattern (88 bp):
CCATCCTACAAGCCTCTTCGTCAAAGTATTCAGAATCCCAGTGCCATGCTTTTTCGATTCCATCT
CCTTCTAAGGTAGCTTAACTCTA
Found at i:62813 original size:6 final size:6
Alignment explanation
Indices: 62804--62842 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
62794 CCCGAAATTA
*
62804 CCCGAG CCCGA- CCCGAG CCCGAT CCCGA- CCCGAG CCCGA
1 CCCGAG CCCGAG CCCGAG CCCGAG CCCGAG CCCGAG CCCGA
62843 AATAATTTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
5 10 0.33
6 20 0.67
ACGTcount: A:0.18, C:0.54, G:0.26, T:0.03
Consensus pattern (6 bp):
CCCGAG
Found at i:62819 original size:11 final size:12
Alignment explanation
Indices: 62804--62842 Score: 55
Period size: 11 Copynumber: 3.4 Consensus size: 12
62794 CCCGAAATTA
62804 CCCGAGCCCGA-
1 CCCGAGCCCGAG
*
62815 CCCGAGCCCGAT
1 CCCGAGCCCGAG
62827 CCCGA-CCCGAG
1 CCCGAGCCCGAG
62838 CCCGA
1 CCCGA
62843 AATAATTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 21 0.81
12 5 0.19
ACGTcount: A:0.18, C:0.54, G:0.26, T:0.03
Consensus pattern (12 bp):
CCCGAGCCCGAG
Found at i:62830 original size:17 final size:17
Alignment explanation
Indices: 62804--62842 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
62794 CCCGAAATTA
62804 CCCGAGCCCGACCCGAG
1 CCCGAGCCCGACCCGAG
*
62821 CCCGATCCCGACCCGAG
1 CCCGAGCCCGACCCGAG
62838 CCCGA
1 CCCGA
62843 AATAATTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.18, C:0.54, G:0.26, T:0.03
Consensus pattern (17 bp):
CCCGAGCCCGACCCGAG
Found at i:63052 original size:2 final size:2
Alignment explanation
Indices: 63020--63044 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
63010 AAACTACTAA
63020 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 A
63045 CTTATATAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:63315 original size:19 final size:19
Alignment explanation
Indices: 63291--63347 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 19
63281 TTTTAATTTG
63291 TTTAATTTAAGACTTTCAT
1 TTTAATTTAAGACTTTCAT
*
63310 TTTAA-TT---A-TTT--G
1 TTTAATTTAAGACTTTCAT
63322 TTTAATTTAAGACTTTCAT
1 TTTAATTTAAGACTTTCAT
63341 TTTAATT
1 TTTAATT
63348 ATTTCATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 14
0.64 0.04 0.31
Matches are distributed among these distances:
12 5 0.17
13 2 0.07
14 3 0.10
15 1 0.03
16 1 0.03
17 3 0.10
18 2 0.07
19 12 0.41
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.58
Consensus pattern (19 bp):
TTTAATTTAAGACTTTCAT
Found at i:63324 original size:31 final size:31
Alignment explanation
Indices: 63286--63351 Score: 132
Period size: 31 Copynumber: 2.1 Consensus size: 31
63276 TCAGCTTTTA
63286 ATTTGTTTAATTTAAGACTTTCATTTTAATT
1 ATTTGTTTAATTTAAGACTTTCATTTTAATT
63317 ATTTGTTTAATTTAAGACTTTCATTTTAATT
1 ATTTGTTTAATTTAAGACTTTCATTTTAATT
63348 ATTT
1 ATTT
63352 CATTTTCATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.59
Consensus pattern (31 bp):
ATTTGTTTAATTTAAGACTTTCATTTTAATT
Found at i:63665 original size:13 final size:12
Alignment explanation
Indices: 63623--63675 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 12
63613 TCAATCTTTA
63623 TATATATATATAT
1 TATAT-TATATAT
* *
63636 TGATAATA-ATGT
1 T-ATATTATATAT
63648 TATATTATATTAT
1 TATATTATA-TAT
63661 TATATTATATAT
1 TATATTATATAT
63673 TAT
1 TAT
63676 CAATAAACTT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
11 5 0.15
12 11 0.33
13 14 0.42
14 3 0.09
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (12 bp):
TATATTATATAT
Found at i:63822 original size:17 final size:17
Alignment explanation
Indices: 63802--63836 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
63792 TCGAAATCAA
*
63802 ACCCGAGCCCGAATCCG
1 ACCCGAGCCCGAACCCG
*
63819 ACCCGAGTCCGAACCCG
1 ACCCGAGCCCGAACCCG
63836 A
1 A
63837 ACCCTACCCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.46, G:0.23, T:0.06
Consensus pattern (17 bp):
ACCCGAGCCCGAACCCG
Found at i:63830 original size:23 final size:23
Alignment explanation
Indices: 63804--63860 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
63794 GAAATCAAAC
* * *
63804 CCGAGCCCGAATCCGACCCGAGT
1 CCGAACCCGAACCCGACCCGAGA
*
63827 CCGAACCCGAACCCTACCCGAGA
1 CCGAACCCGAACCCGACCCGAGA
63850 CCGAACCCGAA
1 CCGAACCCGAA
63861 AATACTCGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.28, C:0.46, G:0.21, T:0.05
Consensus pattern (23 bp):
CCGAACCCGAACCCGACCCGAGA
Found at i:63872 original size:16 final size:16
Alignment explanation
Indices: 63850--63940 Score: 107
Period size: 16 Copynumber: 5.7 Consensus size: 16
63840 CTACCCGAGA
63850 CCGAACCCGAAAATAC
1 CCGAACCCGAAAATAC
*
63866 TCGAACCCGACATAAT--
1 CCGAACCCGA-A-AATAC
*
63882 CCGAGCCCGAAAATAC
1 CCGAACCCGAAAATAC
63898 CCGAACCCGAAAATAC
1 CCGAACCCGAAAATAC
*
63914 CCGAACTCGAAAA-ATC
1 CCGAACCCGAAAATA-C
63930 CCGAACCCGAA
1 CCGAACCCGAA
63941 CCCGCCCGAG
Statistics
Matches: 64, Mismatches: 6, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
14 3 0.05
15 2 0.03
16 55 0.86
17 1 0.02
18 3 0.05
ACGTcount: A:0.41, C:0.36, G:0.14, T:0.09
Consensus pattern (16 bp):
CCGAACCCGAAAATAC
Found at i:77337 original size:20 final size:20
Alignment explanation
Indices: 77300--77338 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
77290 TACTATTATT
77300 TTTTGAATTTAATATTTTAC
1 TTTTGAATTTAATATTTTAC
*
77320 TTTT-AATTTCAATTTTTTA
1 TTTTGAATTT-AATATTTTA
77339 AATGTCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTGAATTTAATATTTTAC
Found at i:77604 original size:66 final size:66
Alignment explanation
Indices: 77498--77674 Score: 205
Period size: 66 Copynumber: 2.7 Consensus size: 66
77488 TCTTGTCTCT
* * * * *
77498 GTGTGGTTATCAAAATTTCATAAGATGGTTATTATAATTTCAT-GAGGAGGTTATCAAAATTCCA
1 GTGTGGTTACCAAAATTTCATAAGATAGTTATCAAAATTTCATGGA-AAGGTTATCAAAATTCCA
77562 TA
65 TA
* * *
77564 GTGTGATTACCAAAATTTCATATGGA-AGTTATCAAAATTTCATGGAAAGGTTATCAAAATTTCA
1 GTGTGGTTACCAAAATTTCATA-AGATAGTTATCAAAATTTCATGGAAAGGTTATCAAAATTCCA
77628 TA
65 TA
* **
77630 GTGTGGTTACCAAAATTTCATAGGATCAGGTTATTGAAATTTCAT
1 GTGTGGTTACCAAAATTTCATAAGAT-A-GTTATCAAAATTTCAT
77675 AGTGTGGTTA
Statistics
Matches: 95, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
65 3 0.03
66 73 0.77
67 5 0.05
68 14 0.15
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.37
Consensus pattern (66 bp):
GTGTGGTTACCAAAATTTCATAAGATAGTTATCAAAATTTCATGGAAAGGTTATCAAAATTCCAT
A
Found at i:77622 original size:44 final size:44
Alignment explanation
Indices: 77498--77708 Score: 187
Period size: 44 Copynumber: 4.8 Consensus size: 44
77488 TCTTGTCTCT
* * *
77498 GTGTGGTTATCAAAATTTCATA-AGATGGTTATTATAATTTCATGA
1 GTGTGGTTATCAAAATTTCATAGA-AAGGTTATCAAAATTTCAT-A
* * *** * *
77543 G-GAGGTTATCAAAATTCCATAGTGTGATTACCAAAATTTCATA
1 GTGTGGTTATCAAAATTTCATAGAAAGGTTATCAAAATTTCATA
*
77586 -TG-GAAGTTATCAAAATTTCATGGAAAGGTTATCAAAATTTCATA
1 GTGTG--GTTATCAAAATTTCATAGAAAGGTTATCAAAATTTCATA
* * **
77630 GTGTGGTTACCAAAATTTCATAGGATCAGGTTATTGAAATTTCATA
1 GTGTGGTTATCAAAATTTCATA-GA-AAGGTTATCAAAATTTCATA
* *
77676 GTGTGGTTATCACAATTTTATAGAAAGGTTATC
1 GTGTGGTTATCAAAATTTCATAGAAAGGTTATC
77709 CAAGAGATTA
Statistics
Matches: 133, Mismatches: 25, Indels: 17
0.76 0.14 0.10
Matches are distributed among these distances:
42 1 0.01
43 2 0.02
44 86 0.65
45 7 0.05
46 37 0.28
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (44 bp):
GTGTGGTTATCAAAATTTCATAGAAAGGTTATCAAAATTTCATA
Found at i:77698 original size:22 final size:22
Alignment explanation
Indices: 77498--77698 Score: 160
Period size: 22 Copynumber: 9.0 Consensus size: 22
77488 TCTTGTCTCT
77498 GTGTGGTTATCAAAATTTCATAA
1 GTGTGGTTATCAAAATTTCAT-A
* * *
77521 G-ATGGTTATTATAATTTCATGA
1 GTGTGGTTATCAAAATTTCAT-A
* *
77543 G-GAGGTTATCAAAATTCCATA
1 GTGTGGTTATCAAAATTTCATA
* *
77564 GTGTGATTACCAAAATTTCATA
1 GTGTGGTTATCAAAATTTCATA
*
77586 -TG-GAAGTTATCAAAATTTCATG
1 GTGTG--GTTATCAAAATTTCATA
***
77608 GAAAGGTTATCAAAATTTCATA
1 GTGTGGTTATCAAAATTTCATA
*
77630 GTGTGGTTACCAAAATTTCATA
1 GTGTGGTTATCAAAATTTCATA
**
77652 G-GATCAGGTTATTGAAATTTCATA
1 GTG-T--GGTTATCAAAATTTCATA
* *
77676 GTGTGGTTATCACAATTTTATA
1 GTGTGGTTATCAAAATTTCATA
77698 G
1 G
77699 AAAGGTTATC
Statistics
Matches: 139, Mismatches: 30, Indels: 19
0.74 0.16 0.10
Matches are distributed among these distances:
20 1 0.01
21 5 0.04
22 113 0.81
23 1 0.01
24 18 0.13
25 1 0.01
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (22 bp):
GTGTGGTTATCAAAATTTCATA
Found at i:77741 original size:22 final size:22
Alignment explanation
Indices: 77711--77863 Score: 91
Period size: 22 Copynumber: 7.0 Consensus size: 22
77701 AGGTTATCCA
* * *
77711 AGAGATTATCAAAATGTCATAC
1 AGAGGTTATCAAAATTTCATAG
*
77733 CGAGGTTAT-AAGAATTTCATAG
1 AGAGGTTATCAA-AATTTCATAG
* * *
77755 TGTGGTTAACAAAATTTCATA-
1 AGAGGTTATCAAAATTTCATAG
*
77776 AGAAGGTTA-CTAATATTTCATAG
1 AG-AGGTTATC-AAAATTTCATAG
*
77799 GGAGGTTATCAAAATTTCATA-
1 AGAGGTTATCAAAATTTCATAG
* * *
77820 ATGTGGTTATTAAAACTTTTA-AG
1 A-GAGGTTATCAAAA-TTTCATAG
* * *
77843 TGTGGTTGTCAAAATTTCATA
1 AGAGGTTATCAAAATTTCATA
77864 TCAAGGTTTT
Statistics
Matches: 101, Mismatches: 20, Indels: 20
0.72 0.14 0.14
Matches are distributed among these distances:
21 8 0.08
22 85 0.84
23 8 0.08
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.36
Consensus pattern (22 bp):
AGAGGTTATCAAAATTTCATAG
Found at i:77775 original size:44 final size:43
Alignment explanation
Indices: 77716--77863 Score: 147
Period size: 44 Copynumber: 3.4 Consensus size: 43
77706 ATCCAAGAGA
* *
77716 TTATCAAAATGTCATACCGAGGTTA-TAAGAATTTCATAGTGTGG
1 TTATCAAAATTTCATA-AGAGGTTACTAA-AATTTCATAGTGTGG
* * * *
77760 TTAACAAAATTTCATAAGAAGGTTACTAATATTTCATAGGGAGG
1 TTATCAAAATTTCATAAG-AGGTTACTAAAATTTCATAGTGTGG
* * *
77804 TTATCAAAATTTCATAATGTGGTTATTAAAACTTTTA-AGTGTGG
1 TTATCAAAATTTCATAA-GAGGTTACTAAAA-TTTCATAGTGTGG
*
77848 TTGTCAAAATTTCATA
1 TTATCAAAATTTCATA
77864 TCAAGGTTTT
Statistics
Matches: 86, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
43 1 0.01
44 77 0.90
45 8 0.09
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.37
Consensus pattern (43 bp):
TTATCAAAATTTCATAAGAGGTTACTAAAATTTCATAGTGTGG
Found at i:77976 original size:22 final size:22
Alignment explanation
Indices: 77907--78178 Score: 143
Period size: 22 Copynumber: 12.5 Consensus size: 22
77897 TAAAAGTCTT
* *
77907 AATTTCATA-AG-GAGTACCAA
1 AATTTCATAGAGTGATTATCAA
*
77927 AATTTGATAGAAG-G-TTATC-A
1 AATTTCATAG-AGTGATTATCAA
*
77947 AATCTCATAGAGTGATTATCAA
1 AATTTCATAGAGTGATTATCAA
77969 AATTTCATAGAGATTGGATTATCAA
1 AATTTCATAGAG--T-GATTATCAA
*
77994 AATTT-ATAG-GAAGATTATCAA
1 AATTTCATAGAG-TGATTATCAA
* *
78015 AATTTCATAGTGTTG-GTATCAA
1 AATTTCATAGAG-TGATTATCAA
* * * *
78037 AATTTCAAAGCGAGGTTATCAA
1 AATTTCATAGAGTGATTATCAA
* *
78059 AATTACATA-A-TGAAAATATCAA
1 AATTTCATAGAGTG--ATTATCAA
* * * *
78081 AATTTCATAGAGGGGTCAACAA
1 AATTTCATAGAGTGATTATCAA
* * *
78103 AATTTTATAGAGAGGTTATCAA
1 AATTTCATAGAGTGATTATCAA
* * * *
78125 AATTTGATAAAGAGGTTATCAA
1 AATTTCATAGAGTGATTATCAA
* * *
78147 ATTTTCA-AAATGTGATTACCAA
1 AATTTCATAGA-GTGATTATCAA
78169 AATTTCATAG
1 AATTTCATAG
78179 TGGTATTTCG
Statistics
Matches: 195, Mismatches: 40, Indels: 31
0.73 0.15 0.12
Matches are distributed among these distances:
19 2 0.01
20 19 0.10
21 26 0.13
22 123 0.63
23 5 0.03
24 6 0.03
25 14 0.07
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.32
Consensus pattern (22 bp):
AATTTCATAGAGTGATTATCAA
Found at i:78145 original size:66 final size:65
Alignment explanation
Indices: 77924--78153 Score: 209
Period size: 66 Copynumber: 3.5 Consensus size: 65
77914 TAAGGAGTAC
* * *
77924 CAAAATTTGATAGA-AGGTTATC-AAATCTCATAGAGTGATTATCAAAATTTCATAGAGATTGGA
1 CAAAATTTGATAAAGAGGTTATCAAAATTTCATAGAGTG-GTATCAAAATTTCATAGAGA--GG-
77987 TTAT
62 TTAT
* * *
77991 CAAAATTT-ATAGGAAGA--TTATCAAAATTTCATAGTGTTGGTATCAAAATTTCAAAGCGAGGT
1 CAAAATTTGATA--AAGAGGTTATCAAAATTTCATAGAG-TGGTATCAAAATTTCATAGAGAGGT
78053 TAT
63 TAT
** * *** * * *
78056 CAAAATTACATAATGAAAATATCAAAATTTCATAGAGGGGTCAACAAAATTTTATAGAGAGGTTA
1 CAAAATTTGATAAAGAGGTTATCAAAATTTCATAGAGTGGT-ATCAAAATTTCATAGAGAGGTTA
78121 T
65 T
*
78122 CAAAATTTGATAAAGAGGTTATCAAATTTTCA
1 CAAAATTTGATAAAGAGGTTATCAAAATTTCA
78154 AAATGTGATT
Statistics
Matches: 132, Mismatches: 22, Indels: 19
0.76 0.13 0.11
Matches are distributed among these distances:
64 3 0.02
65 14 0.11
66 70 0.53
67 13 0.10
68 29 0.22
69 3 0.02
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.33
Consensus pattern (65 bp):
CAAAATTTGATAAAGAGGTTATCAAAATTTCATAGAGTGGTATCAAAATTTCATAGAGAGGTTAT
Found at i:78306 original size:22 final size:22
Alignment explanation
Indices: 78278--78706 Score: 101
Period size: 22 Copynumber: 19.7 Consensus size: 22
78268 TCAGGGAGGA
78278 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
* * *
78300 TATCAAAATTTCAGAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
* *
78322 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* * * **
78343 AGATCAAAATTTAATAGGAAAAT
1 -TATCAAAATTTCATATGAAGGT
* *
78366 TAACAAGATTTCATAATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
** * * *
78388 TATCAAAAAATCATAGGGAGGA
1 TATCAAAATTTCATATGAAGGT
*
78410 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * * *
78426 TATCAAGATTTCATAAGGAGAT
1 TATCAAAATTTCATATGAAGGT
* * * *
78448 TATCAAACTTTTATAGGGAGGTT
1 TATCAAAATTTCATATGAAGG-T
* *
78471 TATCAAAATTTTATA-GCGAGGT
1 TATCAAAATTTCATATG-AAGGT
* * *
78493 TATCACAATTTCATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
* *
78515 TATCAAAATTGCAGAGTGTAA--T
1 TATCAAAATTTCATA-TG-AAGGT
*
78537 TA-CTAACAA-TTCATATGGAGGT
1 TATC-AA-AATTTCATATGAAGGT
* * * *
78559 TTTTAAATTTTCATA--ACGTGAT
1 TATCAAAATTTCATATGAAG-G-T
* *
78581 TATCAATATATCATATGGAA-GT
1 TATCAAAATTTCATAT-GAAGGT
* ** *
78603 TATCAACATCTT-ATAGTGTTGAT
1 TATCAAAAT-TTCATA-TGAAGGT
78626 TATCAAAATTTCAT-TCGGAA-GT
1 TATCAAAATTTCATAT--GAAGGT
78648 TATCAAAATTTCATAGTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
78670 CT-TCAAAATTCCTTAGGGAGGT
1 -TATCAAAATTTCATATGAAGGT
*
78692 TAACAAAATTTCATA
1 TATCAAAATTTCATA
78707 AGAAAGTGAA
Statistics
Matches: 293, Mismatches: 75, Indels: 78
0.66 0.17 0.17
Matches are distributed among these distances:
16 8 0.03
17 2 0.01
18 2 0.01
20 4 0.01
21 16 0.05
22 216 0.74
23 42 0.14
24 2 0.01
25 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:78349 original size:44 final size:42
Alignment explanation
Indices: 78259--78354 Score: 113
Period size: 44 Copynumber: 2.2 Consensus size: 42
78249 CTATTGAGTA
* *
78259 ATCAAAATTTCAGGGAGGATATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCAGAGAGGATATCAAAATTTCATATGAAGGTG
* * *
78301 ATCAAAATTTCAGAAGAGGGTTATCAAAATTTCATA-GTATGTAG
1 ATCAAAATTTCAG-AGA-GGATATCAAAATTTCATATGAAGGT-G
78345 ATCAAAATTT
1 ATCAAAATTT
78355 AATAGGAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
42 13 0.28
43 6 0.13
44 27 0.59
ACGTcount: A:0.42, C:0.09, G:0.17, T:0.32
Consensus pattern (42 bp):
ATCAAAATTTCAGAGAGGATATCAAAATTTCATATGAAGGTG
Found at i:78415 original size:66 final size:66
Alignment explanation
Indices: 78270--78420 Score: 162
Period size: 66 Copynumber: 2.3 Consensus size: 66
78260 TCAAAATTTC
* * ** * **
78270 AGGGAGGATATCAAAATTTCATATGAAGGTTATCAAAATTTCAGAAGAGGGTTATCAAAATTTCA
1 AGGGAGGATATCAAAATTTAATAGGAAAATTAACAAAATTTCAGAAGAGGGTTATCAAAAAATCA
78335 T
66 T
* * * * *
78336 A-GTATGTAGATCAAAATTTAATAGGAAAATTAACAAGATTTCATAATGA-GGTTATCAAAAAAT
1 AGGGA-GGATATCAAAATTTAATAGGAAAATTAACAAAATTTCAGAA-GAGGGTTATCAAAAAAT
78399 CAT
64 CAT
78402 AGGGAGGATATCAAAATTT
1 AGGGAGGATATCAAAATTT
78421 GTAGTTATCA
Statistics
Matches: 67, Mismatches: 15, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
65 2 0.03
66 61 0.91
67 4 0.06
ACGTcount: A:0.44, C:0.08, G:0.18, T:0.30
Consensus pattern (66 bp):
AGGGAGGATATCAAAATTTAATAGGAAAATTAACAAAATTTCAGAAGAGGGTTATCAAAAAATCA
T
Found at i:78664 original size:45 final size:45
Alignment explanation
Indices: 78577--78665 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 45
78567 TTTCATAACG
* *
78577 TGATTATCAATATATCATATGGAAGTTATCAACATCTTATAGTGT
1 TGATTATCAAAATATCATATGGAAGTTATCAAAATCTTATAGTGT
*
78622 TGATTATCAAAATTTCAT-TCGGAAGTTATCAAAAT-TTCATAGTG
1 TGATTATCAAAATATCATAT-GGAAGTTATCAAAATCTT-ATAGTG
78666 AGGTCTTCAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
44 3 0.08
45 36 0.92
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.39
Consensus pattern (45 bp):
TGATTATCAAAATATCATATGGAAGTTATCAAAATCTTATAGTGT
Found at i:78923 original size:2 final size:2
Alignment explanation
Indices: 78916--78949 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
78906 TTAAAACTAG
78916 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
78950 CTAATTGGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:83800 original size:32 final size:32
Alignment explanation
Indices: 83759--83823 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
83749 CAAAATGGAT
* *
83759 CCGAACCCGAATTAACTTGACCCAAATTTAAC
1 CCGAACCCGAATCAACCTGACCCAAATTTAAC
*
83791 CCGAACCCGAATCAACCTGATCCAAATTTAAC
1 CCGAACCCGAATCAACCTGACCCAAATTTAAC
83823 C
1 C
83824 TGAGCTGACT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.34, G:0.09, T:0.20
Consensus pattern (32 bp):
CCGAACCCGAATCAACCTGACCCAAATTTAAC
Found at i:84192 original size:31 final size:31
Alignment explanation
Indices: 84155--84340 Score: 169
Period size: 31 Copynumber: 6.1 Consensus size: 31
84145 ACAGTGTCCT
* * *
84155 ACGTGGCATGCCACGTGTATCAAAAAGCGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
* ** * * *
84186 ATGTGGCACGTTACGTGTACAAAAAAGCGAA
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
* * *
84217 ACGTGACACACCACATGTACCAAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
* * *
84248 ATGTGGCACGCCACATGTACCAAAAAATGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
* *
84279 ACGTGTCACGCCATGTGTACCAAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
* * * *
84310 ACATGGCATGCCTCGTGCA-CAAAAAG-GAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
84339 AC
1 AC
84341 ATGCCACGTG
Statistics
Matches: 124, Mismatches: 31, Indels: 2
0.79 0.20 0.01
Matches are distributed among these distances:
29 5 0.04
30 7 0.06
31 112 0.90
ACGTcount: A:0.37, C:0.25, G:0.22, T:0.16
Consensus pattern (31 bp):
ACGTGGCACGCCACGTGTACCAAAAAGTGAC
Found at i:101130 original size:22 final size:23
Alignment explanation
Indices: 101105--101149 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
101095 ACAAAATATT
101105 AGTAGC-CCATTTCAAAAAAAAA
1 AGTAGCACCATTTCAAAAAAAAA
101127 AGTAGCAGTCCATTTCAAAAAAA
1 AGTAGCA--CCATTTCAAAAAAA
101150 GATAGAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 6 0.30
25 14 0.70
ACGTcount: A:0.51, C:0.18, G:0.11, T:0.20
Consensus pattern (23 bp):
AGTAGCACCATTTCAAAAAAAAA
Found at i:101408 original size:5 final size:5
Alignment explanation
Indices: 101390--101424 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
101380 TCTCCCATTC
*
101390 CCCCC CCCCGT CCCCT CCCCT CCCCT CCCCT CCCC
1 CCCCT CCCC-T CCCCT CCCCT CCCCT CCCCT CCCC
101425 ACTTCTTTCG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
5 24 0.86
6 4 0.14
ACGTcount: A:0.00, C:0.83, G:0.03, T:0.14
Consensus pattern (5 bp):
CCCCT
Done.