Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024126.1 Corchorus olitorius cultivar O-4 contig24159, 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: 98232
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:228 original size:27 final size:25
Alignment explanation
Indices: 207--261 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
197 TATAACTTCT
*
207 TTTATAATTATTTTTTAAATAATTTA
1 TTTA-AATTATATTTTAAATAATTTA
*
233 TTTAATTTATATTTTAAAT-ATTTCA
1 TTTAAATTATATTTTAAATAATTT-A
258 TTTA
1 TTTA
262 TTTTGATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (25 bp):
TTTAAATTATATTTTAAATAATTTA
Found at i:248 original size:25 final size:25
Alignment explanation
Indices: 214--270 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
204 TCTTTTATAA
*
214 TTATTTTTTAAATAATTT-ATTTAAT
1 TTATATTTTAAAT-ATTTCATTTAAT
*
239 TTATATTTTAAATATTTCATTTATT
1 TTATATTTTAAATATTTCATTTAAT
264 TTGATAT
1 TT-ATAT
271 AAAAATCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 4 0.14
25 20 0.71
26 4 0.14
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (25 bp):
TTATATTTTAAATATTTCATTTAAT
Found at i:2034 original size:19 final size:18
Alignment explanation
Indices: 1996--2043 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
1986 AAAAAGAGAA
1996 AAAAAGGAAAAGGAAAAAG
1 AAAAA-GAAAAGGAAAAAG
* *
2015 AAATAGAAAAGGGAAGAAG
1 AAAAAGAAAA-GGAAAAAG
2034 AAAAAGAAAA
1 AAAAAGAAAA
2044 ATAGAAAGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 5 0.20
19 20 0.80
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (18 bp):
AAAAAGAAAAGGAAAAAG
Found at i:2065 original size:27 final size:27
Alignment explanation
Indices: 1985--2071 Score: 65
Period size: 27 Copynumber: 3.2 Consensus size: 27
1975 GGCCCAGCGG
* *
1985 GAAAAAGAGAAA-AAAAGGAAAAGGAAAA
1 GAAAAATAGAAAGGAAAGG-AAA-GAAAA
* *
2013 -AGAAATAGAAAAGGGAA-G-AAGAAAAA
1 GAAAAATAG-AAAGGAAAGGAAAG-AAAA
2039 GAAAAATAGAAAGGAAAGGAAAGAAAA
1 GAAAAATAGAAAGGAAAGGAAAGAAAA
2066 TGAAAA
1 -GAAAA
2072 GGGAAAAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
25 1 0.02
26 13 0.28
27 18 0.39
28 12 0.26
29 2 0.04
ACGTcount: A:0.71, C:0.00, G:0.25, T:0.03
Consensus pattern (27 bp):
GAAAAATAGAAAGGAAAGGAAAGAAAA
Found at i:2093 original size:17 final size:17
Alignment explanation
Indices: 2054--2106 Score: 54
Period size: 17 Copynumber: 3.0 Consensus size: 17
2044 ATAGAAAGGA
*
2054 AAGGAAAGAAAATGAAA-
1 AAGGAAA-AAAAAGAAAT
*
2071 AGGGAAAAAAAAGAAAT
1 AAGGAAAAAAAAGAAAT
2088 AAGGAAAATAAAGAGAAAT
1 AAGGAAAA-AAA-AGAAAT
2107 TTGGAAATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 8 0.27
17 13 0.43
18 3 0.10
19 6 0.20
ACGTcount: A:0.70, C:0.00, G:0.23, T:0.08
Consensus pattern (17 bp):
AAGGAAAAAAAAGAAAT
Found at i:2106 original size:19 final size:19
Alignment explanation
Indices: 2073--2119 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
2063 AAATGAAAAG
2073 GGAAAA-AAA-AGAAATAA
1 GGAAAATAAAGAGAAATAA
**
2090 GGAAAATAAAGAGAAATTT
1 GGAAAATAAAGAGAAATAA
2109 GG-AAATAAAGA
1 GGAAAATAAAGA
2120 ATTGGCTCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 6 0.23
18 12 0.46
19 8 0.31
ACGTcount: A:0.66, C:0.00, G:0.21, T:0.13
Consensus pattern (19 bp):
GGAAAATAAAGAGAAATAA
Found at i:6754 original size:21 final size:22
Alignment explanation
Indices: 6727--6774 Score: 89
Period size: 21 Copynumber: 2.2 Consensus size: 22
6717 AACTCCACTC
6727 CACTTTCACTGCTCATGAACTG
1 CACTTTCACTGCTCATGAACTG
6749 -ACTTTCACTGCTCATGAACTG
1 CACTTTCACTGCTCATGAACTG
6770 CACTT
1 CACTT
6775 GAAGAATGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.23, C:0.31, G:0.12, T:0.33
Consensus pattern (22 bp):
CACTTTCACTGCTCATGAACTG
Found at i:11008 original size:28 final size:28
Alignment explanation
Indices: 10939--11041 Score: 80
Period size: 31 Copynumber: 3.5 Consensus size: 28
10929 TTAGTAATGT
*
10939 TACCAAATTGAACCAATTTTGAAAGGTTTGA
1 TACCAAATTG-AGCAA--TTGAAAGGTTTGA
** *
10970 TACTGATTTGAGCAATTGAAAGGTTTGA
1 TACCAAATTGAGCAATTGAAAGGTTTGA
* * * *
10998 TACCAAATTGAACATTTCACCAAAGGTTTGG
1 TACCAAATTGAGCAATT---GAAAGGTTTGA
11029 TACCAAATTGAGC
1 TACCAAATTGAGC
11042 TTTTGGCCTT
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
28 25 0.44
30 4 0.07
31 28 0.49
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (28 bp):
TACCAAATTGAGCAATTGAAAGGTTTGA
Found at i:20521 original size:15 final size:16
Alignment explanation
Indices: 20496--20542 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
20486 CAAATTAGCA
20496 AAAAGCAAATTAAATAG
1 AAAAGC-AATTAAATAG
*
20513 -GAAGCAATTAAAATAG
1 AAAAGCAATT-AAATAG
20529 AAAAGCAA-TAAATA
1 AAAAGCAATTAAATA
20543 TAAACATCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 9 0.35
16 11 0.42
17 6 0.23
ACGTcount: A:0.64, C:0.06, G:0.13, T:0.17
Consensus pattern (16 bp):
AAAAGCAATTAAATAG
Found at i:24190 original size:14 final size:15
Alignment explanation
Indices: 24171--24199 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
24161 TCTAGTTCTT
24171 CAAAAT-ATTCTACA
1 CAAAATAATTCTACA
24185 CAAAATAATTCTACA
1 CAAAATAATTCTACA
24200 TAATAAAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
CAAAATAATTCTACA
Found at i:24815 original size:30 final size:30
Alignment explanation
Indices: 24758--24818 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
24748 CAATTCTTTC
* **
24758 TTCTTGAAATAATTCTTCAGTGGTCTTCAA
1 TTCTTGAAATAATTCTTCAATAATCTTCAA
24788 TTCTTGAAATAA-TCTTCAATAAATCTTCAA
1 TTCTTGAAATAATTCTTCAAT-AATCTTCAA
24818 T
1 T
24819 CACGAACTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 7 0.26
30 20 0.74
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (30 bp):
TTCTTGAAATAATTCTTCAATAATCTTCAA
Found at i:37619 original size:38 final size:39
Alignment explanation
Indices: 37523--37632 Score: 170
Period size: 39 Copynumber: 2.9 Consensus size: 39
37513 GGTTGTGCAT
*
37523 AGTGGACCCGTACCTCAGGGGGTTAAACTGATGGTAAAG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAAG
* *
37562 AGTGGACCCATACCACAGGGGGTTAAACTGTTGGT-AAG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAAG
*
37600 AGTGGACCCGTGCCTCAGGGGGTT-AACTGTTGG
1 AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGG
37633 CTAGACTCGA
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
37 9 0.14
38 24 0.37
39 32 0.49
ACGTcount: A:0.25, C:0.19, G:0.35, T:0.22
Consensus pattern (39 bp):
AGTGGACCCGTACCTCAGGGGGTTAAACTGTTGGTAAAG
Found at i:44851 original size:7 final size:7
Alignment explanation
Indices: 44835--44864 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
44825 TTCATACTTA
44835 TTTTAAT
1 TTTTAAT
*
44842 TTTCAAT
1 TTTTAAT
44849 TTTTAAT
1 TTTTAAT
44856 TTTTAAT
1 TTTTAAT
44863 TT
1 TT
44865 CTAACTTGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (7 bp):
TTTTAAT
Found at i:45552 original size:19 final size:19
Alignment explanation
Indices: 45530--45576 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 19
45520 TTAATAATTG
45530 TAAATTTGGTTAACATTAA
1 TAAATTTGGTTAACATTAA
45549 TAAA--T-G-TAACATTAA
1 TAAATTTGGTTAACATTAA
45564 TAAATTTGGTTAA
1 TAAATTTGGTTAA
45577 TATTGTTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
15 13 0.54
16 1 0.04
17 2 0.08
18 1 0.04
19 7 0.29
ACGTcount: A:0.45, C:0.04, G:0.11, T:0.40
Consensus pattern (19 bp):
TAAATTTGGTTAACATTAA
Found at i:46425 original size:27 final size:28
Alignment explanation
Indices: 46357--46431 Score: 82
Period size: 27 Copynumber: 2.6 Consensus size: 28
46347 ATTGGCATTA
46357 GGCATTTTGGTCATTTTCAAAAATCTAGG
1 GGCATTTTGGTCATTTT-AAAAATCTAGG
* * *
46386 GGCATTTTAGTCATTTGT-ATATTC-AGG
1 GGCATTTTGGTCATTT-TAAAAATCTAGG
46413 GGCATTTTGGTCACTTTTA
1 GGCATTTTGGTCA-TTTTA
46432 GTCCACGCTT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
27 16 0.41
28 7 0.18
29 15 0.38
30 1 0.03
ACGTcount: A:0.23, C:0.13, G:0.21, T:0.43
Consensus pattern (28 bp):
GGCATTTTGGTCATTTTAAAAATCTAGG
Found at i:57694 original size:2 final size:2
Alignment explanation
Indices: 57606--57683 Score: 61
Period size: 2 Copynumber: 40.0 Consensus size: 2
57596 TTTAACTTTG
* * * * *
57606 AT AT AT AT AT AT AT AT AT AT -T AT CT AT AT AT AT TT TT TT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
57647 AG A- AT AA AT AT AT AT AT AT AT AT AT AC AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
57684 GGTGTATATA
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
1 2 0.03
2 61 0.97
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59611 original size:43 final size:43
Alignment explanation
Indices: 59550--59650 Score: 166
Period size: 43 Copynumber: 2.3 Consensus size: 43
59540 TAGGAACAGC
* * *
59550 AACAAAGTTAGGAATGACTTTTACCTCATTCCAAAAGTTTAGG
1 AACAATGTTTGGAATGACTTTTACCTCATTCCAAAACTTTAGG
*
59593 AACAATGTTTGGAATGACTTTTATCTCATTCCAAAACTTTAGG
1 AACAATGTTTGGAATGACTTTTACCTCATTCCAAAACTTTAGG
59636 AACAATGTTTGGAAT
1 AACAATGTTTGGAAT
59651 AATTACTTCG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.34
Consensus pattern (43 bp):
AACAATGTTTGGAATGACTTTTACCTCATTCCAAAACTTTAGG
Found at i:60745 original size:151 final size:151
Alignment explanation
Indices: 60471--60917 Score: 732
Period size: 151 Copynumber: 3.0 Consensus size: 151
60461 GGAAAAACAG
* *
60471 AAGCAAATATAACAATTCCAGCCAAAACAAGGCCATATCAGCAAGCAAAGCTACTAGATACACAA
1 AAGCAAATATAACAATTCCAGCCAAAACAAGGCCATATCAACAAGCAAAGCTACTACATACACAA
* * *
60536 GTCAGAAAAGAAAGGTTCAAAGCAGACCCAAATTAATAATTCATCTACTACTTAACACCAAGCTG
66 GACAAAAAAGAAAGATTCAAAGCAGACCCAAATTAATAATTCATCTACTACTTAACACCAAGCTG
60601 GACAAAGAAAAACTATATTAT
131 GACAAAGAAAAACTATATTAT
* *
60622 AAGCAAATATAACAATTTCAGCCAAAACAAGGCCATATCAACAAGCAAAGCTACTACATACACAT
1 AAGCAAATATAACAATTCCAGCCAAAACAAGGCCATATCAACAAGCAAAGCTACTACATACACAA
* * * *
60687 GACAAAAAAGAAAGATTCAACGCAGACCCGAATTAATAATTCACCGACTACTTAACACCAAGCTG
66 GACAAAAAAGAAAGATTCAAAGCAGACCCAAATTAATAATTCATCTACTACTTAACACCAAGCTG
*
60752 GATAAAGAAAAACTATATTAT
131 GACAAAGAAAAACTATATTAT
60773 AAGCAAATATAACAATTCCAGCCAAAACAAGGCCATATCAACAAGCAAAGCTACTACATACACAA
1 AAGCAAATATAACAATTCCAGCCAAAACAAGGCCATATCAACAAGCAAAGCTACTACATACACAA
* * * *
60838 GACAAAATAGAAAGATTCAAAGCAGACCCAAATTAATAATTTATTTACTACCTAACACCAAGCTG
66 GACAAAAAAGAAAGATTCAAAGCAGACCCAAATTAATAATTCATCTACTACTTAACACCAAGCTG
* *
60903 CACAATGAAAAACTA
131 GACAAAGAAAAACTA
60918 CATGAATGAT
Statistics
Matches: 271, Mismatches: 25, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
151 271 1.00
ACGTcount: A:0.49, C:0.22, G:0.11, T:0.18
Consensus pattern (151 bp):
AAGCAAATATAACAATTCCAGCCAAAACAAGGCCATATCAACAAGCAAAGCTACTACATACACAA
GACAAAAAAGAAAGATTCAAAGCAGACCCAAATTAATAATTCATCTACTACTTAACACCAAGCTG
GACAAAGAAAAACTATATTAT
Found at i:63301 original size:108 final size:109
Alignment explanation
Indices: 63146--63362 Score: 384
Period size: 108 Copynumber: 2.0 Consensus size: 109
63136 ACATTTCCAC
63146 ATGCAAAACCATAATTCATAAACATAAATTGAAAATTTCCTTAATTTATATAATTAATTATAAGT
1 ATGCAAAACCATAATTCATAAACATAAATTGAAAATTTCCTTAATTTATATAATTAATTATAAGT
63211 CCAAATTAAAACAAAGCAGGCTTACCAACAAGCTGCTACATTTAA
66 CCAAATTAAAACAAA-CAGGCTTACCAACAAGCTGCTACATTTAA
63256 ATGCAAAACCAT-ATTCATAAACATAAATT-AAAATTTCCTTAATTTATATAATTAATTATAAGT
1 ATGCAAAACCATAATTCATAAACATAAATTGAAAATTTCCTTAATTTATATAATTAATTATAAGT
** *
63319 CCAAATTAAAACTCATAGGCTTACCAACAAGCTGCTACATTTAA
66 CCAAATTAAAACAAACAGGCTTACCAACAAGCTGCTACATTTAA
63363 TAGGCATCTT
Statistics
Matches: 104, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
107 28 0.27
108 47 0.45
109 17 0.16
110 12 0.12
ACGTcount: A:0.46, C:0.17, G:0.06, T:0.31
Consensus pattern (109 bp):
ATGCAAAACCATAATTCATAAACATAAATTGAAAATTTCCTTAATTTATATAATTAATTATAAGT
CCAAATTAAAACAAACAGGCTTACCAACAAGCTGCTACATTTAA
Found at i:67586 original size:21 final size:21
Alignment explanation
Indices: 67560--67609 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
67550 CAAAAAAGCA
67560 AGAAAATGATGATATTTTAGG
1 AGAAAATGATGATATTTTAGG
67581 AGAAAATGATGATATTTTAGG
1 AGAAAATGATGATATTTTAGG
67602 AGAAAATG
1 AGAAAATG
67610 TTCTCCCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.30
Consensus pattern (21 bp):
AGAAAATGATGATATTTTAGG
Found at i:69306 original size:114 final size:113
Alignment explanation
Indices: 68924--69470 Score: 579
Period size: 114 Copynumber: 4.8 Consensus size: 113
68914 GCAGTTCGAA
* * * * *
68924 TCCAAAACGCCACTATATAGGGGCGTTTCA-AGCTAAAAACGCCACCATGTTTAAATTTTTT-C-
1 TCCAAAACGCCACTATAT-GGGGCGTTT-ATGGATAAAAACGCCACTATATAT-AATTTTTTCCA
* * * *
68986 TAGAAA-ATGAAATTTGGTAAAAATAAACACTAAAATTAGTGGCATTTTTTTT
63 TAGAAATAT-AAATTTGGTAAAAATAAAGACTAAAATTAGTGAC-GTTTCTTT
* * * * * *
69038 TCCAAAATGCCACTATATGGGGTGTTTAAGGATAAAAACACCACCATATATAATTTTTT-CTTAG
1 TCCAAAACGCCACTATATGGGGCGTTTATGGATAAAAACGCCACTATATATAATTTTTTCCATAG
* * * *
69102 AAATATAATTTTGGTATAAATAATTAAAGACTAAAACTAGTGGCGTTTCTAT
66 AAATATAAATTTGG--TAAA-AA-TAAAGACTAAAATTAGTGACGTTTCTTT
* * * * *
69154 TCAAAGAACTCCACTATATGGGGGCGTTTATGGGTAAAAACGCCACTATATATATTTTTTTCCAC
1 TCCAA-AACGCCACTATAT-GGGGCGTTTATGGATAAAAACGCCACTATATATAATTTTTTCCAT
* * *
69219 AGTAATGTAAATTTAGTAAAAATAAAGACTAAAATTAGTGACGTTTCTTT
64 AGAAATATAAATTTGGTAAAAATAAAGACTAAAATTAGTGACGTTTCTTT
* * * *
69269 TCCAAAACGCCACTATATGGGGGCGTTTATGGATAAAAACACAATTGTATATAATATTTTTCC-T
1 TCCAAAACGCCACTATAT-GGGGCGTTTATGGATAAAAACGCCACTATATATAAT-TTTTTCCAT
* * *
69333 AAAAATATAAATATAGTAAAAATAAAGACTAAAATTAGT-AGCGTTTCTTT
64 AGAAATATAAATTTGGTAAAAATAAAGACTAAAATTAGTGA-CGTTTCTTT
* *
69383 TCCAAAATGCCACTATATGGGGCGTTTATGGATAAAAACGCCACTTTATATAATTTTTTCC-TAG
1 TCCAAAACGCCACTATATGGGGCGTTTATGGATAAAAACGCCACTATATATAATTTTTTCCATAG
*
69447 AAATATAAATTTGGTAAATATAAA
66 AAATATAAATTTGGTAAAAATAAA
69471 TAAATTCAGT
Statistics
Matches: 368, Mismatches: 53, Indels: 26
0.82 0.12 0.06
Matches are distributed among these distances:
112 40 0.11
113 71 0.19
114 123 0.33
115 40 0.11
116 13 0.04
117 33 0.09
118 35 0.10
119 13 0.04
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (113 bp):
TCCAAAACGCCACTATATGGGGCGTTTATGGATAAAAACGCCACTATATATAATTTTTTCCATAG
AAATATAAATTTGGTAAAAATAAAGACTAAAATTAGTGACGTTTCTTT
Found at i:70426 original size:11 final size:13
Alignment explanation
Indices: 70400--70432 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
70390 TAATGTCGGG
70400 TTAATAAAATATT
1 TTAATAAAATATT
70413 TTAA-AAAATATT
1 TTAATAAAATATT
70425 TATAATAA
1 T-TAATAA
70433 TTTATAGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 9 0.50
13 7 0.39
14 2 0.11
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
TTAATAAAATATT
Found at i:81149 original size:2 final size:2
Alignment explanation
Indices: 81142--81208 Score: 74
Period size: 2 Copynumber: 35.5 Consensus size: 2
81132 GAGTAATAAT
81142 TA TA TA TA TA TA TA TA TA GTA -A TA -A T- 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 TA TA TA TA
81182 TA GTA -A TA -A T- TA TA TA TA TA TA TA TA T
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA T
81209 TTATTGGTTA
Statistics
Matches: 57, Mismatches: 0, Indels: 16
0.78 0.00 0.22
Matches are distributed among these distances:
1 6 0.11
2 47 0.82
3 4 0.07
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:81163 original size:26 final size:26
Alignment explanation
Indices: 81133--81208 Score: 138
Period size: 24 Copynumber: 3.0 Consensus size: 26
81123 CATCTATAGG
81133 AGTAATAATTATATATATATATATAT
1 AGTAATAATTATATATATATATATAT
81159 AGTAATAA-T-TATATATATATATAT
1 AGTAATAATTATATATATATATATAT
81183 AGTAATAATTATATATATATATATAT
1 AGTAATAATTATATATATATATATAT
81209 TTATTGGTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
24 23 0.48
25 2 0.04
26 23 0.48
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (26 bp):
AGTAATAATTATATATATATATATAT
Found at i:82562 original size:27 final size:28
Alignment explanation
Indices: 82531--82601 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 28
82521 TATGTGCATT
* **
82531 AAACATCAAAGAAATTTGATGAAAA-AA
1 AAACATCAAAGAAATTTAACCAAAAGAA
82558 AAACATCAAAGAAATTTAACCAAAAGAA
1 AAACATCAAAGAAATTTAACCAAAAGAA
* *
82586 AAGCATCAAAGTAATT
1 AAACATCAAAGAAATT
82602 AATTATCCAA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
27 22 0.58
28 16 0.42
ACGTcount: A:0.61, C:0.11, G:0.10, T:0.18
Consensus pattern (28 bp):
AAACATCAAAGAAATTTAACCAAAAGAA
Found at i:87118 original size:10 final size:11
Alignment explanation
Indices: 87081--87120 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
87071 GAAGTTCGTG
87081 TTTGAAGACTA
1 TTTGAAGACTA
87092 TTTGAAGA-TAA
1 TTTGAAGACT-A
87103 TTTGAAGACT-
1 TTTGAAGACTA
87113 TTTGAAGA
1 TTTGAAGA
87121 ATTATTTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 9 0.33
11 17 0.63
12 1 0.04
ACGTcount: A:0.38, C:0.05, G:0.20, T:0.38
Consensus pattern (11 bp):
TTTGAAGACTA
Found at i:87132 original size:22 final size:22
Alignment explanation
Indices: 87085--87132 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
87075 TTCGTGTTTG
*
87085 AAGACTATTTGAAGATAATTTG
1 AAGACTATTTGAAGATAATTTC
*
87107 AAGACT-TTTGAAGAATTATTTC
1 AAGACTATTTGAAG-ATAATTTC
87129 AAGA
1 AAGA
87133 GCAAGAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.35
Consensus pattern (22 bp):
AAGACTATTTGAAGATAATTTC
Found at i:88924 original size:21 final size:21
Alignment explanation
Indices: 88876--88924 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
88866 AGTAACAATA
*
88876 AAATAAA-TAAGCAAGAAAAT
1 AAATAAATTAAGCAACAAAAT
*
88896 -AATAAAATTAAGCAACAAGAT
1 AAAT-AAATTAAGCAACAAAAT
88917 AAATAAAT
1 AAATAAAT
88925 ACTCCAATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
19 3 0.12
20 3 0.12
21 15 0.62
22 3 0.12
ACGTcount: A:0.67, C:0.06, G:0.08, T:0.18
Consensus pattern (21 bp):
AAATAAATTAAGCAACAAAAT
Found at i:91050 original size:20 final size:20
Alignment explanation
Indices: 91025--91062 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
91015 GTTTGGTAAA
91025 GTGAGTTTT-TCGGTAAAATG
1 GTGAGTTTTGT-GGTAAAATG
91045 GTGAGTTTTGTGGTAAAA
1 GTGAGTTTTGTGGTAAAA
91063 GAGGTGCTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.26, C:0.03, G:0.32, T:0.39
Consensus pattern (20 bp):
GTGAGTTTTGTGGTAAAATG
Found at i:91984 original size:27 final size:27
Alignment explanation
Indices: 91935--91987 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
91925 CACTGGACAA
*
91935 CCATGATTCCCGCTGCTGGCATACCAG
1 CCATGATTCCCGCTGCTGACATACCAG
91962 CCATGATTCCCGCTG-TCGACATACCA
1 CCATGATTCCCGCTGCT-GACATACCA
91988 ACTCTGCCGC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.04
27 23 0.96
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.23
Consensus pattern (27 bp):
CCATGATTCCCGCTGCTGACATACCAG
Found at i:92543 original size:26 final size:28
Alignment explanation
Indices: 92491--92545 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
92481 GAGGAAAAGA
* *
92491 GATGTGTTGGGCCTCTTTTTGTGTATGT
1 GATGTATTGGGCCTCTTTTTGTATATGT
92519 GATGTATTGGG-CTCTTTTT-TATATGT
1 GATGTATTGGGCCTCTTTTTGTATATGT
92545 G
1 G
92546 TGTGATGTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 7 0.28
27 8 0.32
28 10 0.40
ACGTcount: A:0.11, C:0.09, G:0.29, T:0.51
Consensus pattern (28 bp):
GATGTATTGGGCCTCTTTTTGTATATGT
Found at i:92552 original size:30 final size:28
Alignment explanation
Indices: 92491--92553 Score: 72
Period size: 30 Copynumber: 2.2 Consensus size: 28
92481 GAGGAAAAGA
* *
92491 GATGTGTTGGGCCTCTTTTTGTGTATGT
1 GATGTATTGGGCCTCTTTTTATGTATGT
* *
92519 GATGTATTGGGCTCTTTTTTATATGTGTGT
1 GATGTATTGGGC-CTCTTTT-TATGTATGT
92549 GATGT
1 GATGT
92554 GTTAATGACC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 11 0.38
29 6 0.21
30 12 0.41
ACGTcount: A:0.11, C:0.08, G:0.30, T:0.51
Consensus pattern (28 bp):
GATGTATTGGGCCTCTTTTTATGTATGT
Found at i:94504 original size:22 final size:21
Alignment explanation
Indices: 94452--94505 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
94442 TGCTTCTTGA
94452 AATAATTCTTC-AATGATCTTC
1 AATAA-TCTTCAAATGATCTTC
*
94473 -A-AATCTTCAAATTATCTTC
1 AATAATCTTCAAATGATCTTC
94492 AATAAGTCTTCAAA
1 AATAA-TCTTCAAA
94506 CACGAGCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (21 bp):
AATAATCTTCAAATGATCTTC
Found at i:95332 original size:18 final size:18
Alignment explanation
Indices: 95297--95331 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
95287 CTCCTCTATC
*
95297 ATGAAAACACTTCTTTTT
1 ATGAAAACAATTCTTTTT
95315 ATGAAAACAATT-TTTTT
1 ATGAAAACAATTCTTTTT
95332 TTTGTAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (18 bp):
ATGAAAACAATTCTTTTT
Found at i:95629 original size:8 final size:8
Alignment explanation
Indices: 95618--95688 Score: 142
Period size: 8 Copynumber: 8.9 Consensus size: 8
95608 GAAAAATCAA
95618 AAATTTTG
1 AAATTTTG
95626 AAATTTTG
1 AAATTTTG
95634 AAATTTTG
1 AAATTTTG
95642 AAATTTTG
1 AAATTTTG
95650 AAATTTTG
1 AAATTTTG
95658 AAATTTTG
1 AAATTTTG
95666 AAATTTTG
1 AAATTTTG
95674 AAATTTTG
1 AAATTTTG
95682 AAATTTT
1 AAATTTT
95689 ATTTCAAAAT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 63 1.00
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (8 bp):
AAATTTTG
Done.