Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2037
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: 122848
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:6197 original size:79 final size:81
Alignment explanation
Indices: 6061--6245 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
6051 TTGAATGATG
*
6061 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
6125 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
6140 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
6202 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
6220 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
6246 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:6259 original size:40 final size:40
Alignment explanation
Indices: 6062--6245 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
6052 TGAATGATGT
* * * *
6062 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
6102 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
6142 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
6180 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
6221 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
6246 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:6267 original size:79 final size:79
Alignment explanation
Indices: 6114--6278 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
6104 GGACTAAGAT
* **
6114 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
6179 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
6193 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
6256 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
6272 CCGAAGG
1 CCGAAGG
6279 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.64
80 25 0.33
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:12154 original size:20 final size:20
Alignment explanation
Indices: 12129--12179 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
12119 TTGAAGTGTC
*
12129 ACACGCCTGTGTGACTTGGG
1 ACACGCCCGTGTGACTTGGG
12149 ACACGCCCGTGTGACTTGGG
1 ACACGCCCGTGTGACTTGGG
*
12169 ACATGCCCGTG
1 ACACGCCCGTG
12180 CAATCACCCC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.16, C:0.29, G:0.33, T:0.22
Consensus pattern (20 bp):
ACACGCCCGTGTGACTTGGG
Found at i:18494 original size:47 final size:45
Alignment explanation
Indices: 18423--18546 Score: 137
Period size: 46 Copynumber: 2.7 Consensus size: 45
18413 ATGGTTGAGT
* * *
18423 TCCGAACTCGTTGAGTTGATTCCGAGTTCGTGA-GATG-TAACTAGGC
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCGTGAGGATGCGAAC---GC
*
18469 ATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTGATGGATGCGAACGC
1 -TCCGAGCTCGTTGAGTTGAGTCCGAGTTC-GTGA-GGATGCGAACGC
18517 -CCGAGCTCGTTGAGTTGAGTCCGAGTTCGT
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCGT
18547 TTATGGGTGG
Statistics
Matches: 68, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
45 1 0.01
46 28 0.41
47 27 0.40
48 5 0.07
50 4 0.06
51 3 0.04
ACGTcount: A:0.19, C:0.22, G:0.31, T:0.28
Consensus pattern (45 bp):
TCCGAGCTCGTTGAGTTGAGTCCGAGTTCGTGAGGATGCGAACGC
Found at i:31691 original size:34 final size:34
Alignment explanation
Indices: 31653--31721 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
31643 ATATGTTAGA
*
31653 AAGGGATATGATGTTTATCTTGCGTATGTGTTGG
1 AAGGGATATGATGCTTATCTTGCGTATGTGTTGG
31687 AAGGGATATGATGCTTATCTTGCGTATGTGTTGG
1 AAGGGATATGATGCTTATCTTGCGTATGTGTTGG
31721 A
1 A
31722 TACTAAAGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.22, C:0.07, G:0.32, T:0.39
Consensus pattern (34 bp):
AAGGGATATGATGCTTATCTTGCGTATGTGTTGG
Found at i:36943 original size:39 final size:39
Alignment explanation
Indices: 36842--36980 Score: 122
Period size: 39 Copynumber: 3.6 Consensus size: 39
36832 CAAAAAATCT
* * * * * *
36842 TATTCAGTATAATAAGTGGGTAATGCTCGTTTGAGTAAG
1 TATTCAGTAGAATCAGTAGATATTGCTCGTTTGAGCAAG
* * * * *
36881 CATTCAGTATAATCAGTGGATATTTCTCGCTTGAGCAAG
1 TATTCAGTAGAATCAGTAGATATTGCTCGTTTGAGCAAG
* * *
36920 TATTCAGTAGAATTAGTATATATTGCTCATTTGAGC-AG
1 TATTCAGTAGAATCAGTAGATATTGCTCGTTTGAGCAAG
*
36958 T-TT-AGTAGAATCAGTAGACATTG
1 TATTCAGTAGAATCAGTAGATATTG
36981 AACATTCAGT
Statistics
Matches: 82, Mismatches: 18, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
36 17 0.21
37 2 0.02
38 3 0.04
39 60 0.73
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.36
Consensus pattern (39 bp):
TATTCAGTAGAATCAGTAGATATTGCTCGTTTGAGCAAG
Found at i:39463 original size:19 final size:19
Alignment explanation
Indices: 39436--39478 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
39426 AGATTTTCGG
* *
39436 GTGTCCGGTAATATTCTGA
1 GTGTTCGGTAATATTCCGA
*
39455 GTGTTCGGTACTATTCCGA
1 GTGTTCGGTAATATTCCGA
39474 GTGTT
1 GTGTT
39479 GAACAGGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.16, C:0.16, G:0.28, T:0.40
Consensus pattern (19 bp):
GTGTTCGGTAATATTCCGA
Found at i:42371 original size:27 final size:27
Alignment explanation
Indices: 42354--42406 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
42344 TTTAGTATGT
*
42354 TTGGCACACTATATCACTTTCCCATAA
1 TTGGCACACTATATCACTTTACCATAA
*
42381 TTGGCACACTTTATCACTTTACCATA
1 TTGGCACACTATATCACTTTACCATA
42407 GTTCAACTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.28, C:0.28, G:0.08, T:0.36
Consensus pattern (27 bp):
TTGGCACACTATATCACTTTACCATAA
Found at i:42541 original size:31 final size:31
Alignment explanation
Indices: 42499--42642 Score: 189
Period size: 31 Copynumber: 4.6 Consensus size: 31
42489 TCACTTGTAA
* **
42499 CCGAAGCTACCACTATTCTTTGATCAGGTAG
1 CCGAAGCTACCACTTTTCACTGATCAGGTAG
* * *
42530 CTGGAGCTACCACTTTTCACTAATCAGGTAG
1 CCGAAGCTACCACTTTTCACTGATCAGGTAG
* * *
42561 CTGAAGCTACTACTTTTCACTGATTAGGTAG
1 CCGAAGCTACCACTTTTCACTGATCAGGTAG
* *
42592 CCGAAGTTACCACTTTTCACTGGTCAGGTAG
1 CCGAAGCTACCACTTTTCACTGATCAGGTAG
42623 CCGAAGCTACCACTTTTCAC
1 CCGAAGCTACCACTTTTCAC
42643 ATTGTACACA
Statistics
Matches: 97, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 97 1.00
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (31 bp):
CCGAAGCTACCACTTTTCACTGATCAGGTAG
Found at i:42723 original size:31 final size:32
Alignment explanation
Indices: 42635--42745 Score: 138
Period size: 32 Copynumber: 3.5 Consensus size: 32
42625 GAAGCTACCA
*
42635 CTTTTCACA-TTGTACACACAAGGCGTACATTTC
1 CTTTTCA-AGTTGTACACACAA-GTGTACATTTC
*
42668 CTTTTCAAG-TGTACACACAAAGTGTACGTTTC
1 CTTTTCAAGTTGTACACAC-AAGTGTACATTTC
*
42700 CTTTTTAAGTTGTACACAC-AGTGTACATTTC
1 CTTTTCAAGTTGTACACACAAGTGTACATTTC
*
42731 CTTTTCCAGTTGTAC
1 CTTTTCAAGTTGTAC
42746 CTTTGAGGTA
Statistics
Matches: 69, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
31 24 0.35
32 27 0.39
33 18 0.26
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (32 bp):
CTTTTCAAGTTGTACACACAAGTGTACATTTC
Found at i:44406 original size:11 final size:11
Alignment explanation
Indices: 44390--44442 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
44380 TATACTGAAT
44390 AAATAATAATA
1 AAATAATAATA
44401 AAATAATAAT-
1 AAATAATAATA
* *
44411 AAATATCTCATTA
1 AAATA-AT-AATA
*
44424 AAATATTAATA
1 AAATAATAATA
44435 AAATAATA
1 AAATAATA
44443 TTTATCTAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
10 5 0.15
11 21 0.62
12 3 0.09
13 5 0.15
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATAATAATA
Found at i:44449 original size:31 final size:33
Alignment explanation
Indices: 44390--44455 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 33
44380 TATACTGAAT
*
44390 AAATAATAATAAAATAATAATAAATATCTCATTA
1 AAATAATAATAAAATAATAAT-AATATCTAATTA
* *
44424 AAATATTAATAAAATAAT-AT-TTATCTAATTA
1 AAATAATAATAAAATAATAATAATATCTAATTA
44455 A
1 A
44456 CTAATTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
31 10 0.34
33 2 0.07
34 17 0.59
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (33 bp):
AAATAATAATAAAATAATAATAATATCTAATTA
Found at i:45916 original size:29 final size:29
Alignment explanation
Indices: 45874--45933 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
45864 ACCCTGAGAT
45874 GGCTGAGAAAGAACAATTTCATAGTGCAA
1 GGCTGAGAAAGAACAATTTCATAGTGCAA
45903 GGCTGAGAAAGAACAATTTCATAGTGCAA
1 GGCTGAGAAAGAACAATTTCATAGTGCAA
45932 GG
1 GG
45934 TCGAGTAAAT
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:0.40, C:0.13, G:0.27, T:0.20
Consensus pattern (29 bp):
GGCTGAGAAAGAACAATTTCATAGTGCAA
Found at i:49720 original size:49 final size:49
Alignment explanation
Indices: 49648--49879 Score: 259
Period size: 49 Copynumber: 4.7 Consensus size: 49
49638 TTAGTACGCA
*
49648 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCTGGTACACG
* * ** * *
49697 TAGTAGCCTACACTTAGTACTACACACGTGACCTAACCATTTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGCGACC-AATTATCTGGTACACG
** ** * *
49747 TAGTAGCCTGCACTTAGTACTACACACATGATTGAAGTTATCGGGTAC-GG
1 TAGTAGCCTGCACTTAGTACTACACACGCGA-CCAA-TTATCTGGTACACG
* * *
49797 ATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCTAGTACATG
1 -TAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCTGGTACACG
* *
49847 TAGTAGCCTGCACTTAGTACTACATACGTGACC
1 TAGTAGCCTGCACTTAGTACTACACACGCGACC
49880 TAACAATAGA
Statistics
Matches: 150, Mismatches: 28, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
49 69 0.46
50 47 0.31
51 34 0.23
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCTGGTACACG
Found at i:49821 original size:101 final size:98
Alignment explanation
Indices: 49639--49870 Score: 261
Period size: 101 Copynumber: 2.3 Consensus size: 98
49629 TAAAGCTATT
* * ** *
49639 TAGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCTGGTACACGTAGTAGC
1 TAGTACACGTAGTAGCCTGCACTTAGTACTACACACACGACCAATTATCGGGTACACGTAGTAGC
*
49704 CTACACTTAGTACTACACACGTGACCTAACCAT-
66 CTACACTTAGTACTACACACGCGACC-AACCATC
* * ** *
49737 TTGATACACGTAGTAGCCTGCACTTAGTACTACACACATGATTGAAGTTATCGGGTAC-GGATAG
1 TAG-TACACGTAGTAGCCTGCACTTAGTACTACACACACGA-CCAA-TTATCGGGTACACG-TAG
* * **
49801 TAGCCTGCACTTAGTACTACACATGCGACCAATTATC
62 TAGCCTACACTTAGTACTACACACGCGACCAACCATC
*
49838 TAGTACATGTAGTAGCCTGCACTTAGTACTACA
1 TAGTACACGTAGTAGCCTGCACTTAGTACTACA
49871 TACGTGACCT
Statistics
Matches: 112, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
98 2 0.02
99 32 0.29
100 36 0.32
101 42 0.38
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (98 bp):
TAGTACACGTAGTAGCCTGCACTTAGTACTACACACACGACCAATTATCGGGTACACGTAGTAGC
CTACACTTAGTACTACACACGCGACCAACCATC
Found at i:51251 original size:16 final size:16
Alignment explanation
Indices: 51227--51277 Score: 75
Period size: 16 Copynumber: 3.2 Consensus size: 16
51217 GTAGATCGGC
* *
51227 AAATCCCGAAAAGCCG
1 AAATGCCGAAAAGCTG
*
51243 AAATGCCGAAAAGGTG
1 AAATGCCGAAAAGCTG
51259 AAATGCCGAAAAGCTG
1 AAATGCCGAAAAGCTG
51275 AAA
1 AAA
51278 GTTTGGCTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.47, C:0.20, G:0.24, T:0.10
Consensus pattern (16 bp):
AAATGCCGAAAAGCTG
Found at i:51602 original size:28 final size:29
Alignment explanation
Indices: 51488--51612 Score: 164
Period size: 29 Copynumber: 4.3 Consensus size: 29
51478 GAAAGCATGT
51488 ATATGAATGTGATTTGGGCCT-GATGGGCC
1 ATATGAATGTGATTTGGGCCTAG-TGGGCC
* *
51517 ATATGAATGTGATTTTGGCCTATTGGGCC
1 ATATGAATGTGATTTGGGCCTAGTGGGCC
* *
51546 ATACGAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAGTGGGCC
* *
51575 ATATGAATGAGA-TTGGGCCTAGTAGGCC
1 ATATGAATGTGATTTGGGCCTAGTGGGCC
*
51603 ATATGCATGT
1 ATATGAATGT
51613 ATGTAGACTT
Statistics
Matches: 84, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
28 22 0.26
29 62 0.74
ACGTcount: A:0.24, C:0.14, G:0.30, T:0.31
Consensus pattern (29 bp):
ATATGAATGTGATTTGGGCCTAGTGGGCC
Found at i:54402 original size:21 final size:21
Alignment explanation
Indices: 54376--54419 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
54366 TTTGGCTAAA
54376 ATTAAG-GAGATAAGGATGAGG
1 ATTAAGTGAGAT-AGGATGAGG
* *
54397 ATTAAGTGTGATATGATGAGG
1 ATTAAGTGAGATAGGATGAGG
54418 AT
1 AT
54420 AAAAATTAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.39, C:0.00, G:0.34, T:0.27
Consensus pattern (21 bp):
ATTAAGTGAGATAGGATGAGG
Found at i:55326 original size:28 final size:29
Alignment explanation
Indices: 55212--55336 Score: 153
Period size: 29 Copynumber: 4.3 Consensus size: 29
55202 GAAAACATGT
*
55212 ATATGAATGTGATTTGGGCCTAATGCGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
* * *
55241 ATATGAATGTGATTTAGGCCTATTGAGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
* *
55270 ATACGAATGTGATTTGGGCCTAATAGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
* * *
55299 ATATAAATGAGA-TTGGGCCTAGTGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
*
55327 ATATGCATGT
1 ATATGAATGT
55337 ATGTAGACTT
Statistics
Matches: 80, Mismatches: 16, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
28 21 0.26
29 59 0.74
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.30
Consensus pattern (29 bp):
ATATGAATGTGATTTGGGCCTAATGGGCC
Found at i:68841 original size:20 final size:20
Alignment explanation
Indices: 68818--68859 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
68808 TTTTTGAAAG
68818 AATATAATACTTTTAAAGCA
1 AATATAATACTTTTAAAGCA
68838 AATATAATACTTTTAAAGCA
1 AATATAATACTTTTAAAGCA
68858 AA
1 AA
68860 CTTTCTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.52, C:0.10, G:0.05, T:0.33
Consensus pattern (20 bp):
AATATAATACTTTTAAAGCA
Found at i:76045 original size:20 final size:20
Alignment explanation
Indices: 76012--76051 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
76002 AACATTTTGG
76012 TTTTATTCCATTTTG-TTCC
1 TTTTATTCCATTTTGATTCC
*
76031 TTTTAATTCCGTTTTGATTCC
1 TTTT-ATTCCATTTTGATTCC
76052 GATTTAACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 10 0.56
21 4 0.22
ACGTcount: A:0.12, C:0.20, G:0.07, T:0.60
Consensus pattern (20 bp):
TTTTATTCCATTTTGATTCC
Found at i:88801 original size:45 final size:45
Alignment explanation
Indices: 88732--89099 Score: 201
Period size: 45 Copynumber: 8.1 Consensus size: 45
88722 AGAAGATACG
* *
88732 GTGGAGTAGGTTGAA-ATTA-CAAGTCGTATCTCCCTGAAGTTGCA
1 GTGGAGCAGGTTGAAGA-TAGCAAGTCTTATCTCCCTGAAGTTGCA
* * * * *
88776 GTGGAGCAGGCTGAAGATAGCAAGTCTTATTTCCCTGGATTTGTA
1 GTGGAGCAGGTTGAAGATAGCAAGTCTTATCTCCCTGAAGTTGCA
* * *
88821 GTGGAACAGATTGAAGCTATAAATTGC-AGATCTTATCTCTCTGAAGTTGCA
1 GTGGAGCAGGTTGAAG--AT--A--GCAAG-TCTTATCTCCCTGAAGTTGCA
* * * *
88872 GTAGAGCA-GATCAA-A-A-TAAGTCTTATCTCCCTGAAGTTGCA
1 GTGGAGCAGGTTGAAGATAGCAAGTCTTATCTCCCTGAAGTTGCA
* *
88913 GTAGAGCAGGTTGAAGATAGCAAGTCTTATTTCCCT-AGAGTTGCA
1 GTGGAGCAGGTTGAAGATAGCAAGTCTTATCTCCCTGA-AGTTGCA
* * * *
88958 GTGGAACAGATTGAAGCTATAAATTG-TAGATCTTATCTCTCTGAAGTTGCA
1 GTGGAGCAGGTTGAAG--AT--A--GCAAG-TCTTATCTCCCTGAAGTTGCA
* *
89009 GTAGAGCA--TATCAA-A-A-CAAGTCTTATCTCCCTGAAGTTGCA
1 GTGGAGCAGGT-TGAAGATAGCAAGTCTTATCTCCCTGAAGTTGCA
** * * * *
89050 ACGGAGC-GGACTAAAGATAACAAGTCTTAT-TCCCCTGGAGTTGCA
1 GTGGAGCAGG-TTGAAGATAGCAAGTCTTATCT-CCCTGAAGTTGCA
89095 GTGGA
1 GTGGA
89100 ATAGATTGAA
Statistics
Matches: 247, Mismatches: 45, Indels: 63
0.70 0.13 0.18
Matches are distributed among these distances:
41 52 0.21
42 11 0.04
43 2 0.01
44 21 0.09
45 93 0.38
47 6 0.02
49 3 0.01
50 10 0.04
51 48 0.19
52 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (45 bp):
GTGGAGCAGGTTGAAGATAGCAAGTCTTATCTCCCTGAAGTTGCA
Found at i:88908 original size:41 final size:42
Alignment explanation
Indices: 88851--89049 Score: 154
Period size: 41 Copynumber: 4.5 Consensus size: 42
88841 AAATTGCAGA
* *
88851 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCAAAA-TAAG
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCAAAAGCAAG
* *
88892 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGGTTGAAGATAGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCA-GATCAA-A-AGCAAG
* * * *
88937 TCTTATTTCCCT-AGAGTTGCAGTGGAACAGATTGAAGCTATAAATTG-TAG
1 TCTTATCTCCCTGA-AGTTGCAGTAGAGCAGA-T----C-A-AAA--GCAAG
* *
88987 ATCTTATCTCTCTGAAGTTGCAGTAGAGCATATCAAAA-CAAG
1 -TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCAAAAGCAAG
89029 TCTTATCTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCA
89050 ACGGAGCGGA
Statistics
Matches: 124, Mismatches: 17, Indels: 34
0.71 0.10 0.19
Matches are distributed among these distances:
41 48 0.39
42 6 0.05
43 1 0.01
44 6 0.05
45 29 0.23
46 1 0.01
49 1 0.01
50 5 0.04
51 26 0.21
52 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.31
Consensus pattern (42 bp):
TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCAAAAGCAAG
Found at i:88922 original size:137 final size:137
Alignment explanation
Indices: 88750--89154 Score: 605
Period size: 137 Copynumber: 3.0 Consensus size: 137
88740 GGTTGAAATT
*
88750 ACAAGTCGTATCTCCCTGAAGTTGCAGTGGAGCAGGCTGAAGATAGCAAGTCTTATTTCCCTGGA
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCTGAAGATAGCAAGTCTTATTTCCCTGGA
* * *
88815 TTTGTAGTGGAACAGATTGAAGCTATAAATTGCAGATCTTATCTCTCTGAAGTTGCAGTAGAGCA
66 GTTGCAGTGGAACAGATTGAAGCTATAAATTGTAGATCTTATCTCTCTGAAGTTGCAGTAGAGCA
88880 GATCAAA
131 GATCAAA
* * * *
88887 ATAAGTCTTATCTCCCTGAAGTTGCAGTAGAGCAGGTTGAAGATAGCAAGTCTTATTTCCCTAGA
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCTGAAGATAGCAAGTCTTATTTCCCTGGA
88952 GTTGCAGTGGAACAGATTGAAGCTATAAATTGTAGATCTTATCTCTCTGAAGTTGCAGTAGAGCA
66 GTTGCAGTGGAACAGATTGAAGCTATAAATTGTAGATCTTATCTCTCTGAAGTTGCAGTAGAGCA
*
89017 TATCAAA
131 GATCAAA
** * * *
89024 ACAAGTCTTATCTCCCTGAAGTTGCAACGGAGC-GGACTAAAGATAACAAGTCTTATTCCCCTGG
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGG-CTGAAGATAGCAAGTCTTATTTCCCTGG
* * ** * * *
89088 AGTTGCAGTGGAATAGATTGAATCTATAAATCATAGATCTTATCTCTCTGGAGTTGTAATAGAGC
65 AGTTGCAGTGGAACAGATTGAAGCTATAAATTGTAGATCTTATCTCTCTGAAGTTGCAGTAGAGC
89153 AG
130 AG
89155 TTGTAGTGGA
Statistics
Matches: 241, Mismatches: 26, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
136 2 0.01
137 239 0.99
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.29
Consensus pattern (137 bp):
ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCTGAAGATAGCAAGTCTTATTTCCCTGGA
GTTGCAGTGGAACAGATTGAAGCTATAAATTGTAGATCTTATCTCTCTGAAGTTGCAGTAGAGCA
GATCAAA
Found at i:90072 original size:9 final size:9
Alignment explanation
Indices: 90058--90082 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
90048 GCCACCGCCT
90058 TACGTGCCC
1 TACGTGCCC
90067 TACGTGCCC
1 TACGTGCCC
90076 TACGTGC
1 TACGTGC
90083 TGGATGTGAT
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:0.12, C:0.40, G:0.24, T:0.24
Consensus pattern (9 bp):
TACGTGCCC
Found at i:95734 original size:20 final size:20
Alignment explanation
Indices: 95709--95762 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
95699 AACAGGGGTT
95709 ACACGCCCGTGTGGCTTAGG
1 ACACGCCCGTGTGGCTTAGG
*
95729 ACACGCCCGTGTGGCTTGGG
1 ACACGCCCGTGTGGCTTAGG
95749 ACACGCCCGTGTGG
1 ACACGCCCGTGTGG
95763 GTAGGCCGTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.13, C:0.31, G:0.37, T:0.19
Consensus pattern (20 bp):
ACACGCCCGTGTGGCTTAGG
Found at i:96301 original size:15 final size:17
Alignment explanation
Indices: 96283--96314 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
96273 TAGTATAAAT
96283 TACCAAA-TCA-ATTCA
1 TACCAAACTCACATTCA
96298 TACCAAACTCACATTCA
1 TACCAAACTCACATTCA
96315 CAAGTATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.25
Consensus pattern (17 bp):
TACCAAACTCACATTCA
Found at i:102768 original size:15 final size:15
Alignment explanation
Indices: 102737--102803 Score: 68
Period size: 15 Copynumber: 4.6 Consensus size: 15
102727 CCATTTATTC
*
102737 AAAACTAAAAAAT-T
1 AAAATTAAAAAATAT
102751 AAAATTAAAAAATAT
1 AAAATTAAAAAATAT
102766 AAAGA-TAAAAAATAT
1 AAA-ATTAAAAAATAT
* **
102781 TAAATTAAAGTATA-
1 AAAATTAAAAAATAT
102795 AAAATTAAA
1 AAAATTAAA
102804 TCTATATAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
14 21 0.47
15 23 0.51
16 1 0.02
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.25
Consensus pattern (15 bp):
AAAATTAAAAAATAT
Found at i:102776 original size:22 final size:22
Alignment explanation
Indices: 102751--102803 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
102741 CTAAAAAATT
102751 AAAATTAAAAAATATAAAG-ATA
1 AAAATTAAAAAAT-TAAAGTATA
* **
102773 AAAAATATTAAATTAAAGTATA
1 AAAATTAAAAAATTAAAGTATA
102795 AAAATTAAA
1 AAAATTAAA
102804 TCTATATAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (22 bp):
AAAATTAAAAAATTAAAGTATA
Found at i:103268 original size:26 final size:26
Alignment explanation
Indices: 103232--103282 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
103222 TTACAAGTAA
*
103232 AATTATCAAAATATTCTTATTTATAG
1 AATTATCAAAATATCCTTATTTATAG
103258 AATTATCAAAATATCCTTATTTATA
1 AATTATCAAAATATCCTTATTTATA
103283 TTAATTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (26 bp):
AATTATCAAAATATCCTTATTTATAG
Found at i:103878 original size:22 final size:21
Alignment explanation
Indices: 103853--103895 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
103843 CAATTTCTTA
103853 AAAT-TTAATTATAAAATTATAT
1 AAATGTTAA-TATAAAA-TATAT
103875 AAATGTTAATATAAAATATAT
1 AAATGTTAATATAAAATATAT
103896 TTTTAAATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
AAATGTTAATATAAAATATAT
Found at i:111269 original size:44 final size:44
Alignment explanation
Indices: 111206--111297 Score: 159
Period size: 44 Copynumber: 2.1 Consensus size: 44
111196 GTAAGCATTC
111206 ATGTAAATATATTTCTAATATAGG-TATAAGTGAATTTTGCATGA
1 ATGTAAATATATTTCTAATAT-GGATATAAGTGAATTTTGCATGA
*
111250 ATGTAAATATATTTCTAATATGGATATGAGTGAATTTTGCATGA
1 ATGTAAATATATTTCTAATATGGATATAAGTGAATTTTGCATGA
111294 ATGT
1 ATGT
111298 GTATTTATGT
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
43 2 0.04
44 44 0.96
ACGTcount: A:0.37, C:0.04, G:0.17, T:0.41
Consensus pattern (44 bp):
ATGTAAATATATTTCTAATATGGATATAAGTGAATTTTGCATGA
Found at i:112730 original size:48 final size:48
Alignment explanation
Indices: 112666--112772 Score: 160
Period size: 48 Copynumber: 2.2 Consensus size: 48
112656 GTGGACGAAG
* * *
112666 CCACCAAATTTGCAGACAAGCTGCTAAAACATGTAGCTTGTGGATAAA
1 CCACCAAATTTGCAGACAAACTACTAAAACATGTAGCTTATGGATAAA
* * *
112714 CCACCAAATTTTCAGACAAACTACTAAAGCATGTAGGTTATGGATAAA
1 CCACCAAATTTGCAGACAAACTACTAAAACATGTAGCTTATGGATAAA
112762 CCACCAAATTT
1 CCACCAAATTT
112773 ATAAATTAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 53 1.00
ACGTcount: A:0.39, C:0.21, G:0.15, T:0.24
Consensus pattern (48 bp):
CCACCAAATTTGCAGACAAACTACTAAAACATGTAGCTTATGGATAAA
Found at i:114208 original size:40 final size:40
Alignment explanation
Indices: 114146--114363 Score: 239
Period size: 40 Copynumber: 5.5 Consensus size: 40
114136 AAACCAAGTA
* * * *
114146 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
** * *
114185 CCTTCGGGACTTAGCCCGGATATAGTAGTTCGCAAAAATT
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
114225 CCTTCGGGACTTAGCTCGGATATAGTAACTCCCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
114265 CCTTCGGCACTTAGCCCGGA-ATTAGTAACTCGCA-ACAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACA-AATG
* * *
114305 CCTTCGGGACTTAGCCTGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
114345 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
114364 TTATCATCCG
Statistics
Matches: 152, Mismatches: 22, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
39 15 0.10
40 136 0.89
41 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:121483 original size:40 final size:39
Alignment explanation
Indices: 121400--121616 Score: 298
Period size: 40 Copynumber: 5.5 Consensus size: 39
121390 AAACCAAGTA
* * *
121400 CCTTCGGGATTTA-ACCGGATATAGCTACTCGCTC-AATG
1 CCTTCGGGACTTAGCCCGGATATAG-TACTCGCACAAATG
*
121438 CCTTCGGGACTTAGCCCGGATATAGTAGTTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTA-CTCGCACAAATG
121478 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGT-ACTCGCACAAATG
121518 CCTTCGGGACTTAGCCCGGA-ATTAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGT-ACTCGCACAAATG
*
121558 CCTTCGGGACTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGT-ACTCGCACAAATG
121598 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
121617 TTATCATCCG
Statistics
Matches: 167, Mismatches: 7, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
38 14 0.08
39 16 0.10
40 136 0.81
41 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.24
Consensus pattern (39 bp):
CCTTCGGGACTTAGCCCGGATATAGTACTCGCACAAATG
Done.