Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023697.1 Corchorus olitorius cultivar O-4 contig23730, 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: 85212
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1140 original size:31 final size:29
Alignment explanation
Indices: 1070--1149 Score: 88
Period size: 31 Copynumber: 2.7 Consensus size: 29
1060 CTCACTTTTG
* * **
1070 AAACGTAAGGGATTAATTTGTTTAAAAAA
1 AAACATAAGGGATTATTTTGTCCAAAAAA
*
1099 AAACAAAAGGGATTATTTTGTCCCAAAAGAA
1 AAACATAAGGGATTATTTTGT-CCAAAA-AA
*
1130 AAACATAAGGGATTTTTTTG
1 AAACATAAGGGATTATTTTG
1150 GATATTTAGC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 18 0.43
30 4 0.10
31 20 0.48
ACGTcount: A:0.45, C:0.07, G:0.17, T:0.30
Consensus pattern (29 bp):
AAACATAAGGGATTATTTTGTCCAAAAAA
Found at i:4040 original size:27 final size:27
Alignment explanation
Indices: 4000--4053 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
3990 GGAATATTCT
4000 TTCTGCCAACAAAAACGTTGTTTATAA
1 TTCTGCCAACAAAAACGTTGTTTATAA
4027 TTCTGGCCAA-AAAAACGTTGTTTATAA
1 TTCT-GCCAACAAAAACGTTGTTTATAA
4054 AGGCAAAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 21 0.81
28 5 0.19
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (27 bp):
TTCTGCCAACAAAAACGTTGTTTATAA
Found at i:7974 original size:87 final size:87
Alignment explanation
Indices: 7595--7966 Score: 564
Period size: 87 Copynumber: 4.3 Consensus size: 87
7585 TGAGAAGTTC
* * * * * *
7595 ACTCCAAGGAGACTAGAGTTCAGGCAAAGAGTGCTTGTTGGGAACAGAAATGCTGATAGCTCAAA
1 ACTCCAAGGAGACTAAAGTTCAAGCCAAGAGTTCTTGTTGGCAACAGAAATGCTGATAGCCCAAA
* *
7660 TGGCAAAGGCGATGATGATCAT
66 TGGCAAAGGTGACGATGATCAT
* * * *
7682 ACTCCAAGGAGGCTAAAGTTCAAGCCAAGGGTTCTTGTTGGCAACAGAATTGCTGATAGTCCAAA
1 ACTCCAAGGAGACTAAAGTTCAAGCCAAGAGTTCTTGTTGGCAACAGAAATGCTGATAGCCCAAA
* *
7747 TGGCAAAGGTGGCAATGATCAT
66 TGGCAAAGGTGACGATGATCAT
* * *
7769 ACTCCAAGGAGACTAAAGTTCAAGCCAAGGGTTATTGTTGGCAACAGAAATGCTGGTAGCCCAAA
1 ACTCCAAGGAGACTAAAGTTCAAGCCAAGAGTTCTTGTTGGCAACAGAAATGCTGATAGCCCAAA
7834 TGGCAAAGGTGACGATGATCAT
66 TGGCAAAGGTGACGATGATCAT
7856 ACTCCAAGGAGACTAAAGTTCAAGCCAAGAGTTCTTGTTGGCAACAGAAATGCTGATAGCCCAAA
1 ACTCCAAGGAGACTAAAGTTCAAGCCAAGAGTTCTTGTTGGCAACAGAAATGCTGATAGCCCAAA
*
7921 TGGCAAAAGTGACGATGATCAT
66 TGGCAAAGGTGACGATGATCAT
* *
7943 ACTCCAAGGAGACTTACGTTCAAG
1 ACTCCAAGGAGACTAAAGTTCAAG
7967 AGAAGAGTGA
Statistics
Matches: 258, Mismatches: 27, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 258 1.00
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (87 bp):
ACTCCAAGGAGACTAAAGTTCAAGCCAAGAGTTCTTGTTGGCAACAGAAATGCTGATAGCCCAAA
TGGCAAAGGTGACGATGATCAT
Found at i:13017 original size:276 final size:272
Alignment explanation
Indices: 12524--13046 Score: 796
Period size: 276 Copynumber: 1.9 Consensus size: 272
12514 TATTTAATGT
* *
12524 TCAAAACTATTCCCTAAGGAGACACATGTCGACCCTTTAACCCTAGCCCTGCATGTGCAGTCTGC
1 TCAAAACTATTCCCTAAGGAGACACATGTCAACCCTTTAACCCTAACCCTGCATGTGCAGTCTGC
* * * *
12589 TAAATTTCACTAATGGTGGATAAGATAATTTTCCTTAAAAAATATACACTAAAAAGATACATGTC
66 TAAACTTCACTAAAGGTGGATAAAATAATTTTCCTTAAAAAATATACACTAAAAAGACACATGTC
* * *
12654 AATCCTTTAACCCCGTTTGTACAATCTAATAGTAACCTACACTAATAGTGGATGTGATGATTTTA
131 AAACCTTTAACCCCGTTTGTACAATCTAATAGTAAACTACACTAATAGTGGATGTGATAATTTTA
* *
12719 CTTTTTGTAATAACCATAAACACTTTTAGGTTTAATTTAAGTAACAATATTATGGCTTTTTACTT
196 CTTTTCGTAATAACCATAAACACTTTTAAG--T--TTTAAGTAACAATATTATGGCTTTTTACTT
12784 AATTAATGTTCAAAAA
257 AATTAATGTTCAAAAA
** *
12800 TCAAAACTATTCCCTAAGG-GTACATGTGTCAACCCTTTAACCGTAACCCTGCATGTGCAGTCTG
1 TCAAAACTATTCCCTAAGGAG-ACACATGTCAACCCTTTAACCCTAACCCTGCATGTGCAGTCTG
* *
12864 CTAAACTTCACTAAAGGTGGATAAAATATTTTTCCTTAAAAAATATACACTAAAAAGACATATGT
65 CTAAACTTCACTAAAGGTGGATAAAATAATTTTCCTTAAAAAATATACACTAAAAAGACACATGT
* * * * *
12929 CAAACTTTTAACCCTGTTTGTATAATCTAATAGTAAACTACATTGATAGTGGATGTGATAATTTT
130 CAAACCTTTAACCCCGTTTGTACAATCTAATAGTAAACTACACTAATAGTGGATGTGATAATTTT
*
12994 ACTTTTCGTAATAACCATAAACACTTTTAAGTTTTAAGTAACATTATTATGGC
195 ACTTTTCGTAATAACCATAAACACTTTTAAGTTTTAAGTAACAATATTATGGC
13047 AAAACTTTAG
Statistics
Matches: 224, Mismatches: 22, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
272 20 0.09
274 1 0.00
275 1 0.00
276 202 0.90
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.34
Consensus pattern (272 bp):
TCAAAACTATTCCCTAAGGAGACACATGTCAACCCTTTAACCCTAACCCTGCATGTGCAGTCTGC
TAAACTTCACTAAAGGTGGATAAAATAATTTTCCTTAAAAAATATACACTAAAAAGACACATGTC
AAACCTTTAACCCCGTTTGTACAATCTAATAGTAAACTACACTAATAGTGGATGTGATAATTTTA
CTTTTCGTAATAACCATAAACACTTTTAAGTTTTAAGTAACAATATTATGGCTTTTTACTTAATT
AATGTTCAAAAA
Found at i:19410 original size:204 final size:204
Alignment explanation
Indices: 18844--19453 Score: 1069
Period size: 204 Copynumber: 3.0 Consensus size: 204
18834 GCTTAATAAC
*
18844 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTCATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
* *
18909 GATACAACACATTATTATTATATATA-A-AACTATACCCAAAAAAAAAGTAGTTGAACATTAGTG
66 GATACAACACATTACTATTATATATATAGAACTATA-CC-AAAAAAAATTAGTTGAACATTAGTG
18972 GTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAA
129 GTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAA
*
19037 GATCCAATTTA
194 GATCCGATTTA
*
19048 TTTATAAATGGTGAATG-CTATTAATTTTTTAAGTC------TACTAACAAAGTTGTAGTGAATA
1 TTTATCAATGGTGAATGTC-ATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATA
19106 AGATACAACACATTACTATTATATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGG
65 AGATACAACACATTACTATTATATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGG
*
19171 TTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAATAGATATTAAAG
130 TTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAG
19236 ATCCGATTTA
195 ATCCGATTTA
19246 TTTATCAATGGTGAATGTCATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTCATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
19311 GATACAACACATTACTATTATATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGGT
66 GATACAACACATTACTATTATATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGGT
19376 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT-AAGA
131 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGA
19440 TCCGATTTA
196 TCCGATTTA
19449 TTTAT
1 TTTAT
19454 TTTTAAGGAA
Statistics
Matches: 388, Mismatches: 8, Indels: 21
0.93 0.02 0.05
Matches are distributed among these distances:
198 179 0.46
199 4 0.01
200 7 0.02
203 18 0.05
204 180 0.46
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (204 bp):
TTTATCAATGGTGAATGTCATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
GATACAACACATTACTATTATATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGGT
TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGA
TCCGATTTA
Found at i:19879 original size:6 final size:6
Alignment explanation
Indices: 19868--19914 Score: 76
Period size: 6 Copynumber: 7.5 Consensus size: 6
19858 CTTCTATAAT
19868 ATATAG ATATAG ATATAG ATATAG ATATAG ATATATAG ATATAG ATA
1 ATATAG ATATAG ATATAG ATATAG ATATAG --ATATAG ATATAG ATA
19915 CTTCATCTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
6 33 0.85
8 6 0.15
ACGTcount: A:0.51, C:0.00, G:0.15, T:0.34
Consensus pattern (6 bp):
ATATAG
Found at i:19891 original size:18 final size:19
Alignment explanation
Indices: 19868--19914 Score: 78
Period size: 20 Copynumber: 2.5 Consensus size: 19
19858 CTTCTATAAT
19868 ATATAGATATAG-ATATAG
1 ATATAGATATAGAATATAG
19886 ATATAGATATAGATATATAG
1 ATATAGATATAGA-ATATAG
19906 ATATAGATA
1 ATATAGATA
19915 CTTCATCTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 12 0.44
20 15 0.56
ACGTcount: A:0.51, C:0.00, G:0.15, T:0.34
Consensus pattern (19 bp):
ATATAGATATAGAATATAG
Found at i:19903 original size:14 final size:14
Alignment explanation
Indices: 19874--19914 Score: 68
Period size: 14 Copynumber: 3.1 Consensus size: 14
19864 TAATATATAG
19874 ATATAGATATAG--
1 ATATAGATATAGAT
19886 ATATAGATATAGAT
1 ATATAGATATAGAT
19900 ATATAGATATAGAT
1 ATATAGATATAGAT
19914 A
1 A
19915 CTTCATCTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 12 0.44
14 15 0.56
ACGTcount: A:0.51, C:0.00, G:0.15, T:0.34
Consensus pattern (14 bp):
ATATAGATATAGAT
Found at i:22974 original size:7 final size:7
Alignment explanation
Indices: 22957--22998 Score: 77
Period size: 7 Copynumber: 6.1 Consensus size: 7
22947 CTGACTCATT
22957 ATGAT-A
1 ATGATGA
22963 ATGATGA
1 ATGATGA
22970 ATGATGA
1 ATGATGA
22977 ATGATGA
1 ATGATGA
22984 ATGATGA
1 ATGATGA
22991 ATGATGA
1 ATGATGA
22998 A
1 A
22999 ATATTATGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 5 0.14
7 30 0.86
ACGTcount: A:0.45, C:0.00, G:0.26, T:0.29
Consensus pattern (7 bp):
ATGATGA
Found at i:26391 original size:125 final size:127
Alignment explanation
Indices: 26159--26415 Score: 387
Period size: 125 Copynumber: 2.0 Consensus size: 127
26149 ATTTAAGAAA
* *
26159 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGTTAAAAATAAAA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGAAAAATGGTAAAAAT---A
*
26224 TATGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAA
63 TA-GTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAA
26289 G
127 G
*
26290 TATATTTAAATAATTCTAATATATATATAAGTTTTTTAATTAAAATAGAAAAATGGTAAAAAT-T
1 TATATTTAAAAAATTCT-A-ATATATATAAGTTTTTTAATTAAAATAGAAAAATGGTAAAAATAT
*
26354 A-TA-AA-GATATTAGATTTAATTAAATAAAATTAGAGTTTTTAGTTGAGTAAAACTATAAAAG
64 AGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
26415 T
1 T
26416 TTAAACAATG
Statistics
Matches: 119, Mismatches: 5, Indels: 10
0.89 0.04 0.07
Matches are distributed among these distances:
125 55 0.46
126 2 0.02
127 2 0.02
129 2 0.02
131 16 0.13
132 1 0.01
133 41 0.34
ACGTcount: A:0.49, C:0.02, G:0.10, T:0.39
Consensus pattern (127 bp):
TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGAAAAATGGTAAAAATATAG
TATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
Found at i:30283 original size:19 final size:20
Alignment explanation
Indices: 30233--30283 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
30223 TGTGGTGTTC
30233 TTAATAA-TAATTATTCAAT
1 TTAATAATTAATTATTCAAT
**
30252 AAAATAATT-ATTATTC-AT
1 TTAATAATTAATTATTCAAT
30270 TTAATAATTAATTA
1 TTAATAATTAATTA
30284 ATTTCAGTCC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 9 0.35
19 16 0.62
20 1 0.04
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (20 bp):
TTAATAATTAATTATTCAAT
Found at i:44326 original size:17 final size:18
Alignment explanation
Indices: 44296--44329 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
44286 TTTTTAAAGC
*
44296 TTTTTTTATATAATTTTA
1 TTTTATTATATAATTTTA
44314 TTTTATTAT-TAATTTT
1 TTTTATTATATAATTTT
44330 TTATTTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTATTATATAATTTTA
Found at i:45044 original size:32 final size:32
Alignment explanation
Indices: 44989--45086 Score: 126
Period size: 32 Copynumber: 3.1 Consensus size: 32
44979 AGCCCGAACT
*
44989 CGAACCCGAAT-AACCTGACCCAAAATTGACC
1 CGAACCCGAATCAACCTGACCCAAAATTAACC
* *
45020 CGAACCCGAATCAATCTGACCCAAATTTAACC
1 CGAACCCGAATCAACCTGACCCAAAATTAACC
* * * *
45052 CAAACCCGAATCAACCTGACTCAAATTTAAAC
1 CGAACCCGAATCAACCTGACCCAAAATTAACC
45084 CGA
1 CGA
45087 CCTGACTCAA
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
31 11 0.19
32 47 0.81
ACGTcount: A:0.40, C:0.34, G:0.10, T:0.16
Consensus pattern (32 bp):
CGAACCCGAATCAACCTGACCCAAAATTAACC
Found at i:45303 original size:31 final size:31
Alignment explanation
Indices: 45204--45303 Score: 96
Period size: 31 Copynumber: 3.3 Consensus size: 31
45194 AACCTAAATT
* *
45204 GTCCCTATACTATTGAAAAAAGATCATTTTA
1 GTCCCTCTACTATTGAAAAAAGATCAATTTA
* * ***
45235 GTCCCTCAATTA-TGAAATCTG-TCAATTTA
1 GTCCCTCTACTATTGAAAAAAGATCAATTTA
** *
45264 GTTACTCTACTATTGAAAAGAGATCAATTTA
1 GTCCCTCTACTATTGAAAAAAGATCAATTTA
45295 GTCCCTCTA
1 GTCCCTCTA
45304 TATAACAGGA
Statistics
Matches: 51, Mismatches: 16, Indels: 4
0.72 0.23 0.06
Matches are distributed among these distances:
29 15 0.29
30 12 0.24
31 24 0.47
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (31 bp):
GTCCCTCTACTATTGAAAAAAGATCAATTTA
Found at i:60443 original size:70 final size:71
Alignment explanation
Indices: 60361--60497 Score: 258
Period size: 70 Copynumber: 1.9 Consensus size: 71
60351 TTTGCATAAA
60361 AGTCTCTTTTTCCATGCTGAGATGTGTGTATGAATGTGCATGTTTGAT-AAATATTGATGTCATT
1 AGTCTCTTTTTCCATGCTGAGATGTGTGTATGAATGTGCATGTTTGATAAAATATTGATGTCATT
60425 TTGCAT
66 TTGCAT
*
60431 AGTCTCTTTTTCCATGCTGAGATGTGTGTATGAATGTGCATGTTTGATAAAATATTGATGTCTTT
1 AGTCTCTTTTTCCATGCTGAGATGTGTGTATGAATGTGCATGTTTGATAAAATATTGATGTCATT
60496 TT
66 TT
60498 AGTTGTTATT
Statistics
Matches: 65, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
70 48 0.74
71 17 0.26
ACGTcount: A:0.23, C:0.11, G:0.21, T:0.45
Consensus pattern (71 bp):
AGTCTCTTTTTCCATGCTGAGATGTGTGTATGAATGTGCATGTTTGATAAAATATTGATGTCATT
TTGCAT
Found at i:62636 original size:12 final size:11
Alignment explanation
Indices: 62621--62650 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
62611 TCTTTTAAGA
62621 TTTTTTTTTTG
1 TTTTTTTTTTG
62632 TTTTTTTTTTG
1 TTTTTTTTTTG
62643 TTTTTTTT
1 TTTTTTTT
62651 GGGGTGCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:74373 original size:21 final size:19
Alignment explanation
Indices: 74348--74389 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
74338 TTGCCCCTTG
*
74348 TTCAT-ATTTCTTAA-AAC
1 TTCATCATTTTTTAACAAC
74365 TCTCATCATTTTTTAACAAC
1 T-TCATCATTTTTTAACAAC
74385 TTCAT
1 TTCAT
74390 TTCCTAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 1 0.05
18 4 0.19
19 12 0.57
20 4 0.19
ACGTcount: A:0.31, C:0.21, G:0.00, T:0.48
Consensus pattern (19 bp):
TTCATCATTTTTTAACAAC
Found at i:74380 original size:19 final size:18
Alignment explanation
Indices: 74348--74403 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 18
74338 TTGCCCCTTG
74348 TTCATATTTCTTAA-AAC
1 TTCATATTTCTTAACAAC
*
74365 TCTCATCATTTTTTAACAAC
1 T-TCAT-ATTTCTTAACAAC
*
74385 TTC--ATTTCCTAACAAC
1 TTCATATTTCTTAACAAC
74401 TTC
1 TTC
74404 TTCAAACTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
16 14 0.42
17 1 0.03
18 4 0.12
19 10 0.30
20 4 0.12
ACGTcount: A:0.30, C:0.25, G:0.00, T:0.45
Consensus pattern (18 bp):
TTCATATTTCTTAACAAC
Found at i:74663 original size:33 final size:31
Alignment explanation
Indices: 74573--74674 Score: 134
Period size: 32 Copynumber: 3.2 Consensus size: 31
74563 CCGCCCTGGG
74573 GGGCGGCAAGCCATGGCAATGCCGC-CCTAGCT
1 GGGCGGCAAGCCATGGC-ATGCCGCACC-AGCT
* *
74605 GGGCGGCAAGCCCGTGGCATGCCGCACCAGCC
1 GGGCGGCAAG-CCATGGCATGCCGCACCAGCT
74637 GGGCGGCAACGCCATGGACATGCCGCACCAGCT
1 GGGCGGCAA-GCCATGG-CATGCCGCACCAGCT
74670 GGGCG
1 GGGCG
74675 ACATGCCCAT
Statistics
Matches: 62, Mismatches: 4, Indels: 7
0.85 0.05 0.10
Matches are distributed among these distances:
32 34 0.55
33 28 0.45
ACGTcount: A:0.18, C:0.36, G:0.37, T:0.09
Consensus pattern (31 bp):
GGGCGGCAAGCCATGGCATGCCGCACCAGCT
Found at i:75244 original size:14 final size:13
Alignment explanation
Indices: 75221--75259 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
75211 AGTTTGTTAC
75221 AATTTGTTTTATT
1 AATTTGTTTTATT
75234 AATTTGATTTTATT
1 AATTTG-TTTTATT
*
75248 AGATTAGTTTTA
1 A-ATTTGTTTTA
75260 GGGTTAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 6 0.26
14 13 0.57
15 4 0.17
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (13 bp):
AATTTGTTTTATT
Found at i:76862 original size:22 final size:22
Alignment explanation
Indices: 76853--76928 Score: 86
Period size: 23 Copynumber: 3.4 Consensus size: 22
76843 GAAAAGGAAA
76853 AAAAAGAAAAGAAAAGAAAAAG
1 AAAAAGAAAAGAAAAGAAAAAG
76875 AAAAAGAAAAAGAAAA-ATTAGAAAG
1 AAAAAG-AAAAGAAAAGA--A-AAAG
*
76900 GAAAAG-AAAGAAAAGAAAAAG
1 AAAAAGAAAAGAAAAGAAAAAG
76921 -AAAAGAAA
1 AAAAAGAAA
76929 TAAGGAAAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 13
0.77 0.02 0.21
Matches are distributed among these distances:
20 5 0.11
21 6 0.13
22 8 0.17
23 17 0.36
24 2 0.04
25 9 0.19
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (22 bp):
AAAAAGAAAAGAAAAGAAAAAG
Found at i:76864 original size:5 final size:5
Alignment explanation
Indices: 76843--76928 Score: 79
Period size: 5 Copynumber: 16.8 Consensus size: 5
76833 GGGAAAAAGG
76843 GAAAA GGAAAA -AAAA GAAAA GAAAA GAAAAA GAAAAA GAAAAA GAAAA
1 GAAAA -GAAAA GAAAA GAAAA GAAAA G-AAAA G-AAAA G-AAAA GAAAA
** *
76891 -ATTA GAAAG GAAAA G-AAA GAAAA GAAAAA GAAAA GAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA G-AAAA GAAAA GAAA
76929 TAAGGAAAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
4 10 0.14
5 32 0.46
6 27 0.39
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (5 bp):
GAAAA
Found at i:82221 original size:18 final size:18
Alignment explanation
Indices: 82198--82251 Score: 99
Period size: 18 Copynumber: 3.0 Consensus size: 18
82188 TAAATACATG
*
82198 ATTTCTTTTACTTTTTAT
1 ATTTCTTTTACTTATTAT
82216 ATTTCTTTTACTTATTAT
1 ATTTCTTTTACTTATTAT
82234 ATTTCTTTTACTTATTAT
1 ATTTCTTTTACTTATTAT
82252 GTTTTGTTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.69
Consensus pattern (18 bp):
ATTTCTTTTACTTATTAT
Found at i:84754 original size:19 final size:19
Alignment explanation
Indices: 84732--84788 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
84722 ATAAATGAAT
84732 ACATTAATAAATAATAATA
1 ACATTAATAAATAATAATA
*
84751 ACATTAAT-AATAAATACT-
1 ACATTAATAAAT-AATAATA
*
84769 ACGACTAATAAATAATAATA
1 AC-ATTAATAAATAATAATA
84789 CCACCTGATG
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
18 5 0.16
19 23 0.74
20 3 0.10
ACGTcount: A:0.60, C:0.09, G:0.02, T:0.30
Consensus pattern (19 bp):
ACATTAATAAATAATAATA
Done.