Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010996.1 Corchorus capsularis cultivar CVL-1 contig11017, 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: 77226
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:24652 original size:17 final size:18
Alignment explanation
Indices: 24630--24664 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
24620 ATATGAATTT
*
24630 ATAATGATGAG-AATTGA
1 ATAATGATCAGAAATTGA
24647 ATAATGATCAGAAATTGA
1 ATAATGATCAGAAATTGA
24665 TAAGGGTGCA
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:0.49, C:0.03, G:0.20, T:0.29
Consensus pattern (18 bp):
ATAATGATCAGAAATTGA
Found at i:24667 original size:17 final size:16
Alignment explanation
Indices: 24624--24667 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
24614 AAAATTATAT
* *
24624 GAATTTATAATGATGA
1 GAATTGATAATGATCA
24640 GAATTGAATAATGATCA
1 GAATTG-ATAATGATCA
24657 GAAATTGATAA
1 G-AATTGATAA
24668 GGGTGCATGC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 5 0.21
17 14 0.58
18 5 0.21
ACGTcount: A:0.48, C:0.02, G:0.18, T:0.32
Consensus pattern (16 bp):
GAATTGATAATGATCA
Found at i:24776 original size:43 final size:43
Alignment explanation
Indices: 24715--24801 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 43
24705 ATATGATGCA
* *
24715 AGCCATCAAGCACGTTATAATATCCAAAAGCAATGCATAGCAC
1 AGCCATCAAGCACATTATAATATCCAAAAGCAATGCATAACAC
*
24758 AGCCATCAAGCACATTATAATATCCAAAAGCAATGTATAACAC
1 AGCCATCAAGCACATTATAATATCCAAAAGCAATGCATAACAC
24801 A
1 A
24802 TTGTAACCCG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.45, C:0.24, G:0.11, T:0.20
Consensus pattern (43 bp):
AGCCATCAAGCACATTATAATATCCAAAAGCAATGCATAACAC
Found at i:24796 original size:20 final size:20
Alignment explanation
Indices: 24730--24797 Score: 57
Period size: 20 Copynumber: 3.2 Consensus size: 20
24720 TCAAGCACGT
24730 TATAATATCCAAAAGCAATG
1 TATAATATCCAAAAGCAATG
* * * *
24750 CATAGCACAGCCATCAAGCACAT-
1 TATA--ATATCCA-AAAGCA-ATG
24773 TATAATATCCAAAAGCAATG
1 TATAATATCCAAAAGCAATG
24793 TATAA
1 TATAA
24798 CACATTGTAA
Statistics
Matches: 35, Mismatches: 8, Indels: 10
0.66 0.15 0.19
Matches are distributed among these distances:
19 2 0.06
20 13 0.37
21 5 0.14
22 5 0.14
23 8 0.23
24 2 0.06
ACGTcount: A:0.47, C:0.21, G:0.10, T:0.22
Consensus pattern (20 bp):
TATAATATCCAAAAGCAATG
Found at i:26430 original size:32 final size:32
Alignment explanation
Indices: 26389--26453 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
26379 ACATTACCAT
*
26389 ATTCTTATCTCATCCAATTGACCTATATTTCA
1 ATTCTTATCTCATCCAATTAACCTATATTTCA
26421 ATTCTTATCTCATCCAATTAACCTATATTTCA
1 ATTCTTATCTCATCCAATTAACCTATATTTCA
26453 A
1 A
26454 AAATCTTAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.25, G:0.02, T:0.43
Consensus pattern (32 bp):
ATTCTTATCTCATCCAATTAACCTATATTTCA
Found at i:35886 original size:3 final size:3
Alignment explanation
Indices: 35880--35908 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
35870 TATATAATAA
35880 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
35909 ATATATATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:46691 original size:174 final size:174
Alignment explanation
Indices: 46401--46740 Score: 572
Period size: 174 Copynumber: 2.0 Consensus size: 174
46391 ATATGCTGAT
* *
46401 TGTTTTCCCCCATCCTACTCCCACTTTCCCAAGATGCCTTACATTTTTTCATTTCTTTTAATCTG
1 TGTTTTCCCCCATCCCACTCCCACTTTCCCAAGATGCCCTACATTTTTTCATTTCTTTTAATCTG
*
46466 TTAACCATAACTTCATAAGACTTTTTACGATTCGGGAAATAAGGATCCTCAAACCCAACTAATTG
66 TTAACCATAACTTCATAAGACTTTTTACGATTCGGGAAATAAGGATCCTCAAACCCAACAAATTG
*
46531 ACCAGTAAAATGCATTTGACAATGCTGAGAACTCAATTCGGGAC
131 ACCAGCAAAATGCATTTGACAATGCTGAGAACTCAATTCGGGAC
* * * *
46575 TGTTTTCCCCCATCCCACTCTCACTTTTCCAAGCTGCCCTACGTTTTTTCATTTCTTTTAATCTG
1 TGTTTTCCCCCATCCCACTCCCACTTTCCCAAGATGCCCTACATTTTTTCATTTCTTTTAATCTG
* *
46640 TTAACCCTAGCTTCATAAGACTTTTTACGATTCGGGAAATAAGGATCCTCAAACCCAACAAATTG
66 TTAACCATAACTTCATAAGACTTTTTACGATTCGGGAAATAAGGATCCTCAAACCCAACAAATTG
* *
46705 ACCAGCAAGATGCATTTGACAATGTTGAGAACTCAA
131 ACCAGCAAAATGCATTTGACAATGCTGAGAACTCAA
46741 CTCAGGAACA
Statistics
Matches: 154, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
174 154 1.00
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (174 bp):
TGTTTTCCCCCATCCCACTCCCACTTTCCCAAGATGCCCTACATTTTTTCATTTCTTTTAATCTG
TTAACCATAACTTCATAAGACTTTTTACGATTCGGGAAATAAGGATCCTCAAACCCAACAAATTG
ACCAGCAAAATGCATTTGACAATGCTGAGAACTCAATTCGGGAC
Found at i:55406 original size:50 final size:49
Alignment explanation
Indices: 55299--55875 Score: 640
Period size: 50 Copynumber: 11.6 Consensus size: 49
55289 AGAGAAAACT
* * * *
55299 GGACCTTCTGACCGGGAAGGGGCATTTTGGGAAACAAAGAAAGAAA-ACT
1 GGACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAACAAAGAAACA-G
* *
55348 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAACAAACAAAGAATACAG
1 GGACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAACAAAGAA-ACAG
* * * *
55398 GGACCTTCCGACCGGGAAGGGGCATTTTGGGTAACAAATAAACAAAACAG
1 GGACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAACAAA-GAAACAG
* * *
55448 GGACCTTCCGACCGGGAAGGGGCA-TTTTGCAATAAACAAATAAAGAAAACAA
1 GGACCTTCCGACCGGGAAGGGGCATTTTTG---GAAACAAACAAAG-AAACAG
** * * * *
55500 GGACCTTCCGACCAAGAATGGGCATTTTTGG-AATAAATAAAGAAACTG
1 GGACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAACAAAGAAACAG
* ** * * *
55548 TGACCTTCCGACTAGGAAGGGGCATTTTGGGAAACAAAGAAAGAAAACTG
1 GGACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAACAAAG-AAACAG
* * * *
55598 GGACCTTCCAACCGGGAGGGGGCAATTTTGGAAACAAACAAAGGAAACAA
1 GGACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAACAAA-GAAACAG
* **
55648 GGACCTTCCGACCAGGAAGGGGCA-TTTTGGTAAACAATTAAAGAAAACAG
1 GGACCTTCCGACCGGGAAGGGGCATTTTTGG-AAACAAACAAAG-AAACAG
*
55698 GGACCTTTCGACCGGGAAGGGGCATTTTTGGAAACAAACAAAGTAAACAG
1 GGACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAACAAAG-AAACAG
55748 GGACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAACAAAGGAAACAG
1 GGACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAACAAA-GAAACAG
** * * * *
55798 GGACCTTCCGACTAGGAAGGAGCATTTTGGGAAACAAATAAAAGAAATAG
1 GGACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAA-CAAAGAAACAG
*
55848 GGACCTTCCAACCGGGAAGGGGCATTTT
1 GGACCTTCCGACCGGGAAGGGGCATTTT
55876 GGTAATAAGA
Statistics
Matches: 449, Mismatches: 63, Indels: 31
0.83 0.12 0.06
Matches are distributed among these distances:
48 30 0.07
49 70 0.16
50 294 0.65
51 14 0.03
52 36 0.08
53 5 0.01
ACGTcount: A:0.38, C:0.18, G:0.27, T:0.17
Consensus pattern (49 bp):
GGACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAACAAAGAAACAG
Found at i:55578 original size:150 final size:148
Alignment explanation
Indices: 55291--55877 Score: 750
Period size: 150 Copynumber: 3.9 Consensus size: 148
55281 AAATGTGAAG
* * * *
55291 AGAAAAC-TGGACCTTCTGACCGGGAAGGGGCATTTTGGGAAACAAAGAAAGAAAAC-TGGACCT
1 AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTT-GGAAACAAACAAAGAAAACAAGGACCT
* *
55354 TCCAACCAGGAAGGGGCATTTTTGGAAACAAACAAAGAATACAGGGACCTTCCGACCGGGAAGGG
65 TCCGACCAGGAAGGGGCATTTTTGGAAACAAATAAAGAA-ACAGGGACCTTCCGACCGGGAAGGG
* *
55419 GCATTTTGGGTAACAAATAA
129 GCATTTTGGGAAACAAACAA
* * *
55439 ACAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGCAATAAACAAATAAAGAAAACAAGGAC
1 AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTG---GAAACAAACAAAGAAAACAAGGAC
* * * * * **
55504 CTTCCGACCAAGAATGGGCATTTTTGG-AATAAATAAAGAAACTGTGACCTTCCGACTAGGAAGG
63 CTTCCGACCAGGAAGGGGCATTTTTGGAAACAAATAAAGAAACAGGGACCTTCCGACCGGGAAGG
*
55568 GGCATTTTGGGAAACAAAGAA
128 GGCATTTTGGGAAACAAACAA
* * * *
55589 AGAAAACTGGGACCTTCCAACCGGGAGGGGGCAATTTTGGAAACAAACAAAGGAAACAAGGACCT
1 AGAAAACAGGGACCTTCCGACCGGGAAGGGGC-ATTTTGGAAACAAACAAAGAAAACAAGGACCT
* *
55654 TCCGACCAGGAAGGGGCA-TTTTGGTAAACAATTAAAGAAAACAGGGACCTTTCGACCGGGAAGG
65 TCCGACCAGGAAGGGGCATTTTTGG-AAACAAATAAAG-AAACAGGGACCTTCCGACCGGGAAGG
*
55718 GGCATTTTTGGAAACAAACAA
128 GGCATTTTGGGAAACAAACAA
* * *
55739 AGTAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTTGGAAACAAACAAAGGAAACAGGGACCT
1 AGAAAACAGGGACCTTCCGACCGGGAAGGGGCA-TTTTGGAAACAAACAAAGAAAACAAGGACCT
* * * * *
55804 TCCGACTAGGAAGGAGCATTTTGGGAAACAAATAAAAGAAATAGGGACCTTCCAACCGGGAAGGG
65 TCCGACCAGGAAGGGGCATTTTTGGAAACAAAT-AAAGAAACAGGGACCTTCCGACCGGGAAGGG
55869 GCATTTTGG
129 GCATTTTGG
55878 TAATAAGAAA
Statistics
Matches: 379, Mismatches: 48, Indels: 22
0.84 0.11 0.05
Matches are distributed among these distances:
147 6 0.02
148 46 0.12
149 37 0.10
150 220 0.58
151 42 0.11
152 28 0.07
ACGTcount: A:0.38, C:0.18, G:0.27, T:0.17
Consensus pattern (148 bp):
AGAAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGAAACAAACAAAGAAAACAAGGACCTT
CCGACCAGGAAGGGGCATTTTTGGAAACAAATAAAGAAACAGGGACCTTCCGACCGGGAAGGGGC
ATTTTGGGAAACAAACAA
Found at i:55877 original size:200 final size:198
Alignment explanation
Indices: 55291--55880 Score: 751
Period size: 200 Copynumber: 3.0 Consensus size: 198
55281 AAATGTGAAG
* * * *
55291 AGAAAAC-TGGACC-TTCTGACCGGGAAGGGGCATTTTGGGAAACAAAGAAAGAAAACTGGACCT
1 AGAAAACAAGGACCTTTC-GACCGGGAAGGGGCATTTTTGGAAACAAACAAAG-AAACGGGACCT
*
55354 TCCAACCAGGAAGGGGCATTTTTGGAAACAAACAAA-GAATACAGGGACCTTCCGACCGGGAAGG
64 TCCGACCAGGAAGGGGCATTTTTGGAAACAAACAAAGGAA-ACAGGGACCTTCCGACCGGGAAGG
* *
55418 GGCATTTTGGGTAACAAATAAACA-AAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGCAATA
128 GGCATTTTGGGAAACAAATAAA-AGAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTG--GTA
55482 AACAAATAA
190 AACAAATAA
* ** * * * *
55491 AGAAAACAAGGACCTTCCGACCAAGAATGGGCATTTTTGG-AATAAATAAAGAAACTGTGACCTT
1 AGAAAACAAGGACCTTTCGACCGGGAAGGGGCATTTTTGGAAACAAACAAAGAAAC-GGGACCTT
* * * * * * *
55555 CCGACTAGGAAGGGGCATTTTGGGAAACAAAGAAAGAAAACTGGGACCTTCCAACCGGGAGGGGG
65 CCGACCAGGAAGGGGCATTTTTGGAAACAAACAAAGGAAACAGGGACCTTCCGACCGGGAAGGGG
* * * *
55620 CAATTTT-GGAAACAAACAAAGGAAACAAGGACCTTCCGACCAGGAAGGGGCATTTTGGTAAACA
130 C-ATTTTGGGAAACAAATAAAAGAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGTAAACA
*
55684 ATTAA
194 AATAA
*
55689 AGAAAACAGGGACCTTTCGACCGGGAAGGGGCATTTTTGGAAACAAACAAAGTAAACAGGGACCT
1 AGAAAACAAGGACCTTTCGACCGGGAAGGGGCATTTTTGGAAACAAACAAAG-AAAC-GGGACCT
* ** *
55754 TCCGACCGGGAAGGGGCATTTTTGGAAACAAACAAAGGAAACAGGGACCTTCCGACTAGGAAGGA
64 TCCGACCAGGAAGGGGCATTTTTGGAAACAAACAAAGGAAACAGGGACCTTCCGACCGGGAAGGG
* *
55819 GCATTTTGGGAAACAAATAAAAGAAATAGGGACCTTCCAACCGGGAAGGGGCATTTTGGTAA
129 GCATTTTGGGAAACAAATAAAAGAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGTAA
55881 TAAGAAAAGT
Statistics
Matches: 330, Mismatches: 51, Indels: 18
0.83 0.13 0.05
Matches are distributed among these distances:
198 45 0.14
199 18 0.05
200 235 0.71
201 30 0.09
202 2 0.01
ACGTcount: A:0.38, C:0.18, G:0.27, T:0.17
Consensus pattern (198 bp):
AGAAAACAAGGACCTTTCGACCGGGAAGGGGCATTTTTGGAAACAAACAAAGAAACGGGACCTTC
CGACCAGGAAGGGGCATTTTTGGAAACAAACAAAGGAAACAGGGACCTTCCGACCGGGAAGGGGC
ATTTTGGGAAACAAATAAAAGAAACAGGGACCTTCCGACCGGGAAGGGGCATTTTGGTAAACAAA
TAA
Found at i:55944 original size:40 final size:41
Alignment explanation
Indices: 55884--56001 Score: 157
Period size: 40 Copynumber: 2.9 Consensus size: 41
55874 TTGGTAATAA
* * * *
55884 GAAAAGTAAACTACACCTTCCGGTGAGGAAGGACAAAACAG
1 GAAATGTAAACAACACCTTCCGGTGGGGAAGGGCAAAACAG
*
55925 G-AATGTAAACAACACCTTCCGGTGGGGAAGGGCAAAACGG
1 GAAATGTAAACAACACCTTCCGGTGGGGAAGGGCAAAACAG
* * *
55965 GAAATCTAAACAACAGCTTCCTGTGGGGAAGGGCAAA
1 GAAATGTAAACAACACCTTCCGGTGGGGAAGGGCAAA
56002 CTGGGAAATG
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
40 35 0.51
41 33 0.49
ACGTcount: A:0.39, C:0.19, G:0.28, T:0.14
Consensus pattern (41 bp):
GAAATGTAAACAACACCTTCCGGTGGGGAAGGGCAAAACAG
Found at i:56066 original size:40 final size:39
Alignment explanation
Indices: 56020--56355 Score: 250
Period size: 39 Copynumber: 8.3 Consensus size: 39
56010 TGTAGACTTA
56020 GGCAAACTGGGAAAAGTAAACAACACCTTCCGATGGGAAG
1 GGCAAACTGGG-AAAGTAAACAACACCTTCCGATGGGAAG
** *** * *
56060 TACAAAC-AAAAATGAGTAAACAACACCTTCGGTTGGGGAAG
1 GGCAAACTGGGAA--AGTAAACAACACCTTCCGAT-GGGAAG
** *
56101 GGCAAAC-AAGAATGTAAACAACACCTTCCGACTGGGAAG
1 GGCAAACTGGGAAAGTAAACAACACCTTCCGA-TGGGAAG
* **
56140 GGCAGACAT--GAGTGTAAACAACACCTTCCGATGAGGAAG
1 GGCAAAC-TGGGAAAGTAAACAACACCTTCCGATG-GGAAG
* *
56179 GGCAAACTGGGAAACTAAACAACACCTTCCGATGGGGATG
1 GGCAAACTGGGAAAGTAAACAACACCTTCCGAT-GGGAAG
* * *
56219 GGCAAATTGGGAAACGTAGACTTAGACAACAACTTCCGTTGGGGAAG
1 GGCAAACTGGGAAA-GT--A---A-ACAACACCTTCCGAT-GGGAAG
** * * *
56266 GGCAAACTGAAAAACCTAAACAACACATTCCGGTGAGGAAG
1 GGCAAACTGGGAAA-GTAAACAACACCTTCCGATG-GGAAG
*
56307 GGCAAACTGGG-AACTAAACAACACCTTCCGACTGGGAAG
1 GGCAAACTGGGAAAGTAAACAACACCTTCCGA-TGGGAAG
56346 GGCAAACTGG
1 GGCAAACTGG
56356 AATAAGACAA
Statistics
Matches: 241, Mismatches: 36, Indels: 39
0.76 0.11 0.12
Matches are distributed among these distances:
38 5 0.02
39 91 0.38
40 66 0.27
41 43 0.18
42 1 0.00
43 1 0.00
45 1 0.00
46 1 0.00
47 32 0.13
ACGTcount: A:0.38, C:0.21, G:0.26, T:0.15
Consensus pattern (39 bp):
GGCAAACTGGGAAAGTAAACAACACCTTCCGATGGGAAG
Found at i:56202 original size:79 final size:80
Alignment explanation
Indices: 56020--56214 Score: 234
Period size: 79 Copynumber: 2.5 Consensus size: 80
56010 TGTAGACTTA
*
56020 GGCAAACTGGGAAAAGTAAACAACACCTTCCGATGGGAAGTACAAACAAAAATGAGTAAACAACA
1 GGCAAACTGGG-AAAGTAAACAACACCTTCCGATGGGAAGGACAAACAAAAATGAGTAAACAACA
* * *
56085 CCTTCGGTTGGGGAAG
65 CCTTCCGATGAGGAAG
** * * * ** *
56101 GGCAAAC-AAGAATGTAAACAACACCTTCCGACTGGGAAGGGCAGAC-ATGA-GTGTAAACAACA
1 GGCAAACTGGGAAAGTAAACAACACCTTCCGA-TGGGAAGGACAAACAAAAATGAGTAAACAACA
56163 CCTTCCGATGAGGAAG
65 CCTTCCGATGAGGAAG
*
56179 GGCAAACTGGGAAACTAAACAACACCTTCCGATGGG
1 GGCAAACTGGGAAAGTAAACAACACCTTCCGATGGG
56215 GATGGGCAAA
Statistics
Matches: 96, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
78 35 0.36
79 42 0.44
80 12 0.12
81 7 0.07
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.14
Consensus pattern (80 bp):
GGCAAACTGGGAAAGTAAACAACACCTTCCGATGGGAAGGACAAACAAAAATGAGTAAACAACAC
CTTCCGATGAGGAAG
Found at i:56382 original size:127 final size:128
Alignment explanation
Indices: 56154--56397 Score: 316
Period size: 127 Copynumber: 1.9 Consensus size: 128
56144 GACATGAGTG
* *
56154 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAACTAAACAACACCTTCCGATGGGGATG
1 TAAACAACACATTCCGATGAGGAAGGGCAAACTGGGAAACTAAACAACACCTTCCGATGGGGAAG
* * * * * * ***
56219 GGCAAATTGGGAAACGTAGACTTAGACAACAACTTCCGTTGGGGAAGGGCAAACTGAAAAACC
66 GGCAAACTGGGAAAAGTACAATGAAACAACAACTTCCGACCGGGAAGGGCAAACTGAAAAACC
*
56282 TAAACAACACATTCCGGTGAGGAAGGGCAAACTGGG-AACTAAACAACACCTTCCGACT-GGGAA
1 TAAACAACACATTCCGATGAGGAAGGGCAAACTGGGAAACTAAACAACACCTTCCGA-TGGGGAA
*
56345 GGGCAAACT-GGAATAAG-ACAATGAAAGCAACACCTTCCGACCGGGAAGGGCAA
65 GGGCAAACTGGGAA-AAGTACAATGAAA-CAACAACTTCCGACCGGGAAGGGCAA
56398 TTTGGGAAAA
Statistics
Matches: 100, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
126 9 0.09
127 56 0.56
128 35 0.35
ACGTcount: A:0.38, C:0.22, G:0.26, T:0.14
Consensus pattern (128 bp):
TAAACAACACATTCCGATGAGGAAGGGCAAACTGGGAAACTAAACAACACCTTCCGATGGGGAAG
GGCAAACTGGGAAAAGTACAATGAAACAACAACTTCCGACCGGGAAGGGCAAACTGAAAAACC
Found at i:57047 original size:51 final size:50
Alignment explanation
Indices: 56968--57324 Score: 206
Period size: 51 Copynumber: 7.0 Consensus size: 50
56958 TCATTAGAAG
* * *
56968 ACAAATCAATCAAAATTGAATCTTTTAGTTCAAAGATTTCATTTTTATTT
1 ACAAATTAATCAAAATTTAATCTCTTAGTTCAAAGATTTCATTTTTATTT
* * **
57018 ACGAATTAATCTAAAATTTAATCTCTTAGTCCAAAGATTTCACCTTTATTT
1 ACAAATTAATC-AAAATTTAATCTCTTAGTTCAAAGATTTCATTTTTATTT
* * * *
57069 ACAAATTGATCAAAAGTTTAATCTCTTAGTTCAAAGGTCTCATTTTTA-TC
1 ACAAATTAATCAAAA-TTTAATCTCTTAGTTCAAAGATTTCATTTTTATTT
* * ** * * ** * *
57119 ACAAATTACTTAAAGGTCAAT-TTTTA-ACCTAAAGATCTCACTTTTATTT
1 ACAAATTAATCAAAATTTAATCTCTTAGTTC-AAAGATTTCATTTTTATTT
* * *
57168 ACAAATTAATCATTAATCAAAAGTTTAATCAT-TTGGTTCAAAGATCTCATTTTTATTA
1 AC-----AA--ATTAATCAAAA-TTTAATC-TCTTAGTTCAAAGATTTCATTTTTATTT
* * * * * *
57226 ACAAATTAATCACAAGTTCAATCAT-TTAATTCATAGATCTCA-TTTTATTC
1 ACAAATTAATCA-AAATTTAATC-TCTTAGTTCAAAGATTTCATTTTTATTT
* * * * *
57276 A-AAAGTTAGTCAAAATTCAATCTTTTAGATTTAAAGATTTCATCTTTAT
1 ACAAA-TTAATCAAAATTTAATCTCTTAG-TTCAAAGATTTCATTTTTAT
57325 AACCAAATTT
Statistics
Matches: 237, Mismatches: 50, Indels: 39
0.73 0.15 0.12
Matches are distributed among these distances:
47 1 0.00
48 19 0.08
49 22 0.09
50 49 0.21
51 105 0.44
52 2 0.01
53 2 0.01
54 2 0.01
56 8 0.03
57 4 0.02
58 21 0.09
59 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (50 bp):
ACAAATTAATCAAAATTTAATCTCTTAGTTCAAAGATTTCATTTTTATTT
Found at i:57340 original size:51 final size:49
Alignment explanation
Indices: 57183--57345 Score: 134
Period size: 51 Copynumber: 3.2 Consensus size: 49
57173 TTAATCATTA
* ** *
57183 ATCAAAAGTTTAATCATTTGGTTCAAAGATCTCATTTTTATTAA-CAAATTA
1 ATCAAAA-TTCAATCATTTAATTCAAAGATCTCA-TTTTA-TAACCAAATTT
* * * * *
57234 ATCACAAGTTCAATCATTTAATTCATAGATCTCATTTTAT-TCAAAAGTT
1 ATCA-AAATTCAATCATTTAATTCAAAGATCTCATTTTATAACCAAATTT
* * *
57283 AGTCAAAATTCAATCTTTTAGATTTAAAGATTTCATCTTTATAACCAAATTT
1 A-TCAAAATTCAATCATTTA-ATTCAAAGATCTCAT-TTTATAACCAAATTT
57335 ATC-AAATTCAA
1 ATCAAAATTCAA
57346 AGTGAAAATC
Statistics
Matches: 89, Mismatches: 17, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
49 19 0.21
50 28 0.31
51 33 0.37
52 9 0.10
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.40
Consensus pattern (49 bp):
ATCAAAATTCAATCATTTAATTCAAAGATCTCATTTTATAACCAAATTT
Found at i:70467 original size:183 final size:183
Alignment explanation
Indices: 70117--70593 Score: 622
Period size: 183 Copynumber: 2.6 Consensus size: 183
70107 TTATGATTAG
* * *
70117 TAAAGTTACGTGCGTTGCACATGCGTTAATAACTTAGAAAACATAAAAATTAAAATAATAAATAT
1 TAAAGCTACATGCGTTGCACATGCGTTAATAACTTAAAAAACATAAAAATTAAAATAATAAATAT
* *
70182 AATAAATAGTAGATTAATTTGTAATATATAACATGAAGTATTGAGTTTTATAATCATATATATAA
66 AATAAATAGTATATTAATTTGTAATATATAACAT-AAATATTGAGTTTTATAATCATATATATAA
* *
70247 TAAAAAATTCCAAATCTAAATGGAATAAG-T-AT-ATAATAAATAATATATACT
130 TAAAAAATACCAAATCCAAATGGAATAAGATAATAATAATAAATAATATATACT
* * * * *
70298 TAAAGCTACATGCGTTGCACATGGGTTAGTAACGTACAAAATATATAAAAAATAAAATAATAAAT
1 TAAAGCTACATGCGTTGCACATGCGTTAATAACTTA-AAAA-ACATAAAAATTAAAATAATAAAT
*
70363 ATAATAAATTGTATATTAATTTGTAATATATAACATAAATATTGAGTTTTATAATCATATATATA
64 ATAATAAATAGTATATTAATTTGTAATATATAACATAAATATTGAGTTTTATAATC--ATATATA
70428 TAATAAGAAAA-ACCAAATCCAAAT-GAATAAGTATATAATAAATAATAAATAATATATACT
127 TAATAA-AAAATACCAAATCCAAATGGAATAAG---ATAAT-AATAATAAATAATATATACT
* * * * * * *
70488 TAAAGCTACTTGCATTGCACGTGCGTCAATAACTTATAAAACATGAAAATTAAATTAATAAATAT
1 TAAAGCTACATGCGTTGCACATGCGTTAATAACTTAAAAAACATAAAAATTAAAATAATAAATAT
* * *
70553 AATAAATGGTATATTAATTTGTAAAATATAACATGAATATT
66 AATAAATAGTATATTAATTTGTAATATATAACATAAATATT
70594 TTTTTAATAG
Statistics
Matches: 256, Mismatches: 28, Indels: 17
0.85 0.09 0.06
Matches are distributed among these distances:
181 31 0.12
182 22 0.09
183 62 0.24
184 24 0.09
185 4 0.02
187 1 0.00
188 61 0.24
189 3 0.01
190 48 0.19
ACGTcount: A:0.49, C:0.08, G:0.09, T:0.33
Consensus pattern (183 bp):
TAAAGCTACATGCGTTGCACATGCGTTAATAACTTAAAAAACATAAAAATTAAAATAATAAATAT
AATAAATAGTATATTAATTTGTAATATATAACATAAATATTGAGTTTTATAATCATATATATAAT
AAAAAATACCAAATCCAAATGGAATAAGATAATAATAATAAATAATATATACT
Found at i:75011 original size:15 final size:15
Alignment explanation
Indices: 74993--75064 Score: 55
Period size: 15 Copynumber: 5.1 Consensus size: 15
74983 AAAATATATG
74993 TTTTAAAGGATTTAT
1 TTTTAAAGGATTTAT
*
75008 TTTTGAAGGA--TA-
1 TTTTAAAGGATTTAT
* *
75020 -TTT-AAGAATGTACT
1 TTTTAAAGGATTTA-T
75034 TTTTAAAGGATTTAT
1 TTTTAAAGGATTTAT
* *
75049 TTTTGAAGGATATAT
1 TTTTAAAGGATTTAT
75064 T
1 T
75065 ATGATGATAT
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
10 4 0.09
11 3 0.07
12 2 0.04
13 2 0.04
15 27 0.60
16 7 0.16
ACGTcount: A:0.33, C:0.01, G:0.17, T:0.49
Consensus pattern (15 bp):
TTTTAAAGGATTTAT
Found at i:75038 original size:41 final size:41
Alignment explanation
Indices: 74969--75061 Score: 143
Period size: 41 Copynumber: 2.3 Consensus size: 41
74959 TCCTCCATTG
*
74969 TTGAAGAATATTTAAAAATATATGTTTTAAAGGATTTATTT
1 TTGAAGGATATTTAAAAATATATGTTTTAAAGGATTTATTT
* *
75010 TTGAAGGATATTTAAGAATGTACT-TTTTAAAGGATTTATTT
1 TTGAAGGATATTTAAAAATATA-TGTTTTAAAGGATTTATTT
75051 TTGAAGGATAT
1 TTGAAGGATAT
75062 ATTATGATGA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
41 47 0.98
42 1 0.02
ACGTcount: A:0.38, C:0.01, G:0.16, T:0.45
Consensus pattern (41 bp):
TTGAAGGATATTTAAAAATATATGTTTTAAAGGATTTATTT
Found at i:76980 original size:4 final size:4
Alignment explanation
Indices: 76971--77001 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
76961 TCACAAGGAT
76971 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
77002 TATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Done.