Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2741
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: 43045
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.31
Found at i:365 original size:20 final size:20
Alignment explanation
Indices: 337--379 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
327 AACATATAAA
* *
337 AAAACTTATAATTATTTTTT
1 AAAACTTATAATGAATTTTT
* *
357 AAAATTTATTATGAATTTTT
1 AAAACTTATAATGAATTTTT
377 AAA
1 AAA
380 GTCAGAACAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (20 bp):
AAAACTTATAATGAATTTTT
Found at i:1312 original size:45 final size:45
Alignment explanation
Indices: 1248--1414 Score: 177
Period size: 45 Copynumber: 3.7 Consensus size: 45
1238 AACCCGCCCC
*
1248 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGCGTTCGCATCCA
*
1293 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC-G--G-C--GTTCGCATCCA
* * *
1341 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGC-ATCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGCGTTCGCATCCA
*
1384 TAGGTGAACTC-GACTCAACTCAACGA-TTCGG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1415 ATGCTCAACC
Statistics
Matches: 103, Mismatches: 9, Indels: 23
0.76 0.07 0.17
Matches are distributed among these distances:
40 1 0.01
41 3 0.03
42 6 0.06
43 17 0.17
44 7 0.07
45 30 0.29
46 2 0.02
47 26 0.25
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (45 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGCGTTCGCATCCA
Found at i:1364 original size:92 final size:89
Alignment explanation
Indices: 1253--1418 Score: 278
Period size: 92 Copynumber: 1.8 Consensus size: 89
1243 GCCCCTAAGT
*
1253 GAACTCGGACTCAACTCAACGAGCTCGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGCTCGGC-ATCGCATCCATAAGTGAACTC-GACTCAACTCAAC
1318 GAGTTCGGATGCCTAGTTACATCTCAC
64 GA-TTCGGATGCCTAGTTACATCTCAC
* *
1345 GAACTCGGACTCAACTCAACGAGTTCGGCATCGCATCCATAGGTGAACTCGACTCAACTCAACGA
1 GAACTCGGACTCAACTCAACGAGCTCGGCATCGCATCCATAAGTGAACTCGACTCAACTCAACGA
1410 TTCGGATGC
66 TTCGGATGC
1419 TCAACCATCC
Statistics
Matches: 71, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
89 9 0.13
90 15 0.21
91 19 0.27
92 28 0.39
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (89 bp):
GAACTCGGACTCAACTCAACGAGCTCGGCATCGCATCCATAAGTGAACTCGACTCAACTCAACGA
TTCGGATGCCTAGTTACATCTCAC
Found at i:6632 original size:27 final size:28
Alignment explanation
Indices: 6548--6645 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
6538 CATGAGATTG
* * * *
6548 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
6577 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
6605 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
6632 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
6646 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:6656 original size:27 final size:27
Alignment explanation
Indices: 6576--6658 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
6566 TAAATTGTAC
* *
6576 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
6604 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
6631 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
6658 A
1 A
6659 TTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:6659 original size:29 final size:27
Alignment explanation
Indices: 6548--6659 Score: 98
Period size: 28 Copynumber: 4.0 Consensus size: 27
6538 CATGAGATTG
** * *
6548 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGC-GACTT-AATTATATA
* *
6577 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
6605 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
*
6632 GCACTGAGTGTGCGGACTTAATATATAT
1 GCACTAAGTGTGC-GACTTAAT-TATAT
6660 TTTTGAATCA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 23 0.32
28 28 0.39
29 21 0.29
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Found at i:9748 original size:40 final size:40
Alignment explanation
Indices: 9658--9861 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
9648 TCGAATGATG
* *
9658 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATA
* *
9698 TCTGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-A
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA
* *
9737 TTCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
*
9777 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
* * **
9817 ACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATA
9857 TCCGG
1 TCCGG
9862 TTAAATTCCG
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
39 37 0.26
40 96 0.68
41 8 0.06
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
Found at i:9797 original size:79 final size:81
Alignment explanation
Indices: 9658--9840 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
9648 TCGAATGATG
* * *
9658 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCTGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATT
9722 TGTGCGAGTTACTA-A
66 TGTGCGAGTTACTATA
* * **
9737 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACTAAATCCGGACTAAGAT-CCGAAGGCA
9799 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGTTACTATA
* *
9817 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
9841 TGAACGAGTA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 59 0.66
80 30 0.33
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGTTACTATA
Found at i:9864 original size:79 final size:79
Alignment explanation
Indices: 9711--9875 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
9701 GGACTAAGAT
* **
9711 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
*
9776 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
9790 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
* *
9853 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
9869 CCGAAGG
1 CCGAAGG
9876 TACGTGATTC
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 49 0.65
80 24 0.32
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:16977 original size:39 final size:40
Alignment explanation
Indices: 16882--17065 Score: 191
Period size: 40 Copynumber: 4.7 Consensus size: 40
16872 TCGAATGATG
* *
16882 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
*
16921 AT-CGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
16961 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
17000 TCCGGGTTAAGTCCCGAAGGCATTTGTGTGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* * * *
17039 AACCGGGCTATGTCCCAAAGGCCTTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
17066 AACGAGTAGC
Statistics
Matches: 122, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
39 59 0.48
40 63 0.52
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:17020 original size:79 final size:79
Alignment explanation
Indices: 16882--17060 Score: 204
Period size: 79 Copynumber: 2.3 Consensus size: 79
16872 TCGAATGATG
* *
16882 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATATCGGACTAAGATCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCTTGGTGCTAAGTGACTAAATCGGACTAAGATCCGAAGGCATTTG
16947 TGCGAGTTACTAAT
66 TGCGAGTTACTAAT
* * **
16961 TCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGC-TTGGTGCTAAGTGACTAAAT-CGGACTAAGAT-CCGAAGGCAT
*
17023 TTGTGTGAGTTACT-AT
63 TTGTGCGAGTTACTAAT
* * *
17039 AACCGGGCTATGTCCCAAAGGC
1 -TCCGGGCTAAGTCCCGAAGGC
17061 CTTTGAACGA
Statistics
Matches: 85, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
78 21 0.25
79 56 0.66
80 8 0.09
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (79 bp):
TCCGGGCTAAGTCCCGAAGGCTTGGTGCTAAGTGACTAAATCGGACTAAGATCCGAAGGCATTTG
TGCGAGTTACTAAT
Found at i:17087 original size:79 final size:79
Alignment explanation
Indices: 16934--17088 Score: 181
Period size: 79 Copynumber: 2.0 Consensus size: 79
16924 GGACTAAGAT
* * **
16934 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCAAAGGCATTGGAACGAGTTACTAA
16999 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
* * * *
17013 CCGAAGGCATTTGTGTGAGTTACT-ATAACCGGGCTATGTCCCAAAGGCCTTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCAAAGGCATTGGAACGAGTTA-C
*
17076 TATATCC-GGTTAA
63 TAAATCCGGGTTAA
17089 ATTTCGAAGG
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
78 2 0.03
79 40 0.62
80 22 0.34
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCAAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAGTC
Found at i:24354 original size:27 final size:28
Alignment explanation
Indices: 24270--24367 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
24260 CATGAGATTG
* * * *
24270 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
24299 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
24327 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
24354 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
24368 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:24378 original size:27 final size:27
Alignment explanation
Indices: 24298--24380 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
24288 TAAATTGTAC
* *
24298 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
24326 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
24353 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
24380 A
1 A
24381 TTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:24381 original size:29 final size:27
Alignment explanation
Indices: 24270--24381 Score: 98
Period size: 28 Copynumber: 4.0 Consensus size: 27
24260 CATGAGATTG
** * *
24270 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGC-GACTT-AATTATATA
* *
24299 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
24327 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
*
24354 GCACTGAGTGTGCGGACTTAATATATAT
1 GCACTAAGTGTGC-GACTTAAT-TATAT
24382 TTTTGAATCA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 23 0.32
28 28 0.39
29 21 0.29
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Found at i:29925 original size:93 final size:93
Alignment explanation
Indices: 29818--29988 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
29808 GCCCCTAAGT
* *
29818 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
29883 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* *
29911 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
29976 CGAGTTCGGATGC
66 CGAGTTCGGATGC
29989 TCAACCATCC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:29985 original size:46 final size:46
Alignment explanation
Indices: 29813--29985 Score: 217
Period size: 46 Copynumber: 3.7 Consensus size: 46
29803 AACCCGCCCC
* * * *
29813 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
* *
29859 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCATCCA
* *
29907 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
29952 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
29986 TGCTCAACCA
Statistics
Matches: 108, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 61 0.56
47 29 0.27
48 2 0.02
49 2 0.02
50 4 0.04
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
Found at i:30440 original size:30 final size:30
Alignment explanation
Indices: 30406--30465 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
30396 ATTTAATACG
30406 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
30436 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
30466 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:31459 original size:50 final size:50
Alignment explanation
Indices: 31281--31498 Score: 204
Period size: 50 Copynumber: 4.3 Consensus size: 50
31271 TATTACAGTC
* * * * *
31281 CAGGCTACTACGTGTACCAGATTGTTAGGTCGCATGTGTAGTACTAGGTT
1 CAGGCTACTATGTGTACCAGATTGTTAGGTCACGTGTGTAGTACTAAGTG
** * * * * *
31331 CAGGCTACTATGCATACCCGATAGCTTCGATCACGTGTGTAGTACTAAGTA
1 CAGGCTACTATGTGTACCAGATTG-TTAGGTCACGTGTGTAGTACTAAGTG
* * * * *
31382 CAGGCTACTACGTGTATTC-GATGGTTAGGTCATGTGTGTAGTACTAATTG
1 CAGGCTACTATGTGTA-CCAGATTGTTAGGTCACGTGTGTAGTACTAAGTG
* ** * *
31432 CAGGCTACTATATGTACCAGATTGTTAGGTTGCATGTGTAGTACAAAGTG
1 CAGGCTACTATGTGTACCAGATTGTTAGGTCACGTGTGTAGTACTAAGTG
*
31482 CAGGCTAGTATGTGTAC
1 CAGGCTACTATGTGTAC
31499 TAGAGAGCTT
Statistics
Matches: 132, Mismatches: 33, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
49 1 0.01
50 93 0.70
51 37 0.28
52 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (50 bp):
CAGGCTACTATGTGTACCAGATTGTTAGGTCACGTGTGTAGTACTAAGTG
Found at i:38348 original size:50 final size:50
Alignment explanation
Indices: 38267--38665 Score: 406
Period size: 50 Copynumber: 7.9 Consensus size: 50
38257 TAAGACAGTT
* *
38267 TTAGGTCATGTGTGTAGTATTAAGTGCAGGCTACTACGTGTACCAGATTG
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTG
* * * * * * * **
38317 TTAGGTCGCATGTGTAGTACTAATTGAAGGCTACTATGGGTACCCGATACC
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGAT-TG
* * * *
38368 TTCGATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATTC-GATGG
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CCAGATTG
*
38418 TAAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTG
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTG
* * * * * ** *
38468 TTAGGTCGCATGTGTGGTACTAAGTGCAAGCTACTATGCATACTC-GATAG
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTAC-CAGATTG
* * * *** *
38518 CTTCGATCACGTGTGTAGTACTAAGTGGAGGCTACTACGTGTATTTGATAG
1 -TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTG
* *
38569 TTAGGTCATGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCTGATTG
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTG
* * * * *
38619 TTAGGTCACATGTGTAGTACTAAGTGTAGGCTAGTATGCGTACCAGA
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGA
38666 GAGCTTCAAT
Statistics
Matches: 281, Mismatches: 62, Indels: 12
0.79 0.17 0.03
Matches are distributed among these distances:
49 1 0.00
50 204 0.73
51 75 0.27
52 1 0.00
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (50 bp):
TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTG
Found at i:38401 original size:101 final size:99
Alignment explanation
Indices: 38221--38665 Score: 422
Period size: 101 Copynumber: 4.4 Consensus size: 99
38211 GTTGCTGAAA
* * * * *** * *
38221 CACATGTGTCGTACTATGTGCAGGCTACTATGTGTTTAAGACAGTTTTAGGTCATGTGTGTAGTA
1 CACATGTGTAGTACTAAGTGAAGGCTACTACGTGTACCAGATAG--TTAGGTCACGTGTGTAGTA
*
38286 TTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGT
64 CTAAGTGCAGGCTACTACGTGTACC-GATTGTTAGGT
* * * * * * * *
38323 CGCATGTGTAGTACTAATTGAAGGCTACTATGGGTACCCGATACCTTCGATCACGTGTGTAGTAC
1 CACATGTGTAGTACTAAGTGAAGGCTACTACGTGTACCAGATA-GTTAGGTCACGTGTGTAGTAC
* * *
38388 TAAGTGCAGGCTACTACGTGTATTCGATGGTAAGGT
65 TAAGTGCAGGCTACTACGTGTA-CCGATTGTTAGGT
* * * * * *
38424 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGTCGCATGTGTGGTACT
1 CACATGTGTAGTACTAAGTGAAGGCTACTACGTGTACCAGATAGTTAGGTCACGTGTGTAGTACT
* * ** * * *
38489 AAGTGCAAGCTACTATGCATACTCGATAGCTTCGAT
66 AAGTGCAGGCTACTACGTGTAC-CGATTG-TTAGGT
* * *** *
38525 CACGTGTGTAGTACTAAGTGGAGGCTACTACGTGTATTTGATAGTTAGGTCATGTGTGTAGTACT
1 CACATGTGTAGTACTAAGTGAAGGCTACTACGTGTACCAGATAGTTAGGTCACGTGTGTAGTACT
38590 AAGTGCAGGCTACTACGTGTACCTGATTGTTAGGT
66 AAGTGCAGGCTACTACGTGTACC-GATTGTTAGGT
* * * *
38625 CACATGTGTAGTACTAAGTGTAGGCTAGTATGCGTACCAGA
1 CACATGTGTAGTACTAAGTGAAGGCTACTACGTGTACCAGA
38666 GAGCTTCAAT
Statistics
Matches: 272, Mismatches: 66, Indels: 12
0.78 0.19 0.03
Matches are distributed among these distances:
100 76 0.28
101 163 0.60
102 33 0.12
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (99 bp):
CACATGTGTAGTACTAAGTGAAGGCTACTACGTGTACCAGATAGTTAGGTCACGTGTGTAGTACT
AAGTGCAGGCTACTACGTGTACCGATTGTTAGGT
Found at i:38671 original size:151 final size:150
Alignment explanation
Indices: 38225--38672 Score: 630
Period size: 151 Copynumber: 3.0 Consensus size: 150
38215 CTGAAACACA
* * * * * *
38225 TGTGTCGTACTATGTGCAGGCTACTATGTGT-TTAAGACAGTTTTAGGTCATGTGTGTAGTATTA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATT-CGATAG--TTAGGTCATGTGTGTAGTACTA
*
38289 AGTGCAGGCTACTACGTGTACCAGATTGTTAGGTCGCATGTGTAGTACTAATTGAAGGCTACTAT
63 AGTGCAGGCTACTACGTGTACCAGATTGTTAGGTCGCATGTGTAGTACTAAGTGAAGGCTACTAT
* *
38354 GGGTACCCGATACCTTCGATCACG
128 GCGTA-CCGATAGCTTCGATCACG
* * *
38378 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATTCGATGGTAAGGTCACGTGTGTAGTACTAAGT
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATTCGATAGTTAGGTCATGTGTGTAGTACTAAGT
*
38443 GCAGGCTACTACGTGTACCAGATTGTTAGGTCGCATGTGTGGTACTAAGTGCAA-GCTACTATGC
66 GCAGGCTACTACGTGTACCAGATTGTTAGGTCGCATGTGTAGTACTAAGTG-AAGGCTACTATGC
*
38507 ATACTCGATAGCTTCGATCACG
130 GTAC-CGATAGCTTCGATCACG
* *
38529 TGTGTAGTACTAAGTGGAGGCTACTACGTGTATTTGATAGTTAGGTCATGTGTGTAGTACTAAGT
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATTCGATAGTTAGGTCATGTGTGTAGTACTAAGT
* * * *
38594 GCAGGCTACTACGTGTACCTGATTGTTAGGTCACATGTGTAGTACTAAGTGTAGGCTAGTATGCG
66 GCAGGCTACTACGTGTACCAGATTGTTAGGTCGCATGTGTAGTACTAAGTGAAGGCTACTATGCG
*
38659 TACCAGAGAGCTTC
131 TACC-GATAGCTTC
38673 AATTACAAGG
Statistics
Matches: 264, Mismatches: 26, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
150 3 0.01
151 226 0.86
152 2 0.01
153 31 0.12
154 2 0.01
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (150 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTATTCGATAGTTAGGTCATGTGTGTAGTACTAAGT
GCAGGCTACTACGTGTACCAGATTGTTAGGTCGCATGTGTAGTACTAAGTGAAGGCTACTATGCG
TACCGATAGCTTCGATCACG
Found at i:41644 original size:20 final size:20
Alignment explanation
Indices: 41609--41778 Score: 81
Period size: 20 Copynumber: 8.8 Consensus size: 20
41599 TAGTATTTGA
* *
41609 CACAAAGCCATGAGTAGCGG
1 CACAAAGCCTTCAGTAGCGG
* *
41629 CACGAAGCCTTCAGTAGTGG
1 CACAAAGCCTTCAGTAGCGG
*
41649 CACAAAG-C--C--TAG-GT
1 CACAAAGCCTTCAGTAGCGG
* *
41663 C-CAAAGCCATCAGTAGTGG
1 CACAAAGCCTTCAGTAGCGG
* * *
41682 CACAAAGCCATCAATTA-TGG
1 CACAAAGCCTTC-AGTAGCGG
* * *
41702 TA-ACAAGCCATCAATAGCGG
1 CACA-AAGCCTTCAGTAGCGG
* * *
41722 CACAAAGCCATCAATAGTGG
1 CACAAAGCCTTCAGTAGCGG
*
41742 CACAAAGCCATCTA-TAGCGG
1 CACAAAGCCTTC-AGTAGCGG
*
41762 CACAAAGCCATCAGTAG
1 CACAAAGCCTTCAGTAG
41779 GTCCACAATC
Statistics
Matches: 123, Mismatches: 14, Indels: 26
0.75 0.09 0.16
Matches are distributed among these distances:
13 5 0.04
14 3 0.02
15 3 0.02
16 1 0.01
17 1 0.01
18 3 0.02
19 8 0.07
20 94 0.76
21 5 0.04
ACGTcount: A:0.36, C:0.26, G:0.22, T:0.15
Consensus pattern (20 bp):
CACAAAGCCTTCAGTAGCGG
Found at i:41724 original size:40 final size:40
Alignment explanation
Indices: 41664--41774 Score: 154
Period size: 40 Copynumber: 2.8 Consensus size: 40
41654 AGCCTAGGTC
* *
41664 CAAAGCCATCAGTAGTGGCACAAAGCCATCAATTA-TGGTAA
1 CAAAGCCATCAATAGCGGCACAAAGCCATCAA-TAGTGG-AA
*
41705 C-AAGCCATCAATAGCGGCACAAAGCCATCAATAGTGGCA
1 CAAAGCCATCAATAGCGGCACAAAGCCATCAATAGTGGAA
*
41744 CAAAGCCATCTATAGCGGCACAAAGCCATCA
1 CAAAGCCATCAATAGCGGCACAAAGCCATCA
41775 GTAGGTCCAC
Statistics
Matches: 64, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
39 4 0.06
40 59 0.92
41 1 0.02
ACGTcount: A:0.39, C:0.27, G:0.19, T:0.15
Consensus pattern (40 bp):
CAAAGCCATCAATAGCGGCACAAAGCCATCAATAGTGGAA
Found at i:41785 original size:20 final size:20
Alignment explanation
Indices: 41664--41786 Score: 105
Period size: 20 Copynumber: 6.2 Consensus size: 20
41654 AGCCTAGGTC
*
41664 CAAAGCCATCAGTA-GTGGCA
1 CAAAGCCATCAATAGGT-GCA
*
41684 CAAAGCCATCAATTATGGT-AA
1 CAAAGCCATCAA-TA-GGTGCA
41705 C-AAGCCATCAATAGCG-GCA
1 CAAAGCCATCAATAG-GTGCA
41724 CAAAGCCATCAATA-GTGGCA
1 CAAAGCCATCAATAGGT-GCA
*
41744 CAAAGCCATCTATAGCG-GCA
1 CAAAGCCATCAATAG-GTGCA
* *
41764 CAAAGCCATCAGTAGGTCCA
1 CAAAGCCATCAATAGGTGCA
41784 CAA
1 CAA
41787 TCGTCTTGTG
Statistics
Matches: 85, Mismatches: 7, Indels: 22
0.75 0.06 0.19
Matches are distributed among these distances:
18 2 0.02
19 6 0.07
20 70 0.82
21 4 0.05
22 1 0.01
23 2 0.02
ACGTcount: A:0.38, C:0.27, G:0.20, T:0.15
Consensus pattern (20 bp):
CAAAGCCATCAATAGGTGCA
Found at i:41786 original size:40 final size:38
Alignment explanation
Indices: 41658--41786 Score: 145
Period size: 40 Copynumber: 3.3 Consensus size: 38
41648 GCACAAAGCC
*
41658 TAGGTC-CAAAGCCATCAGTAGTGGCACAAAGCCATCAA
1 TAGGTCACAAAGCCATCA-TAGCGGCACAAAGCCATCAA
*
41696 TTATGGTAAC-AAGCCATCAATAGCGGCACAAAGCCATCAA
1 -TA-GGTCACAAAGCCATC-ATAGCGGCACAAAGCCATCAA
* *
41736 TAGTGGCACAAAGCCATCTATAGCGGCACAAAGCCATCAG
1 TAG-GTCACAAAGCCATC-ATAGCGGCACAAAGCCATCAA
41776 TAGGTCCACAA
1 TAGGT-CACAA
41787 TCGTCTTGTG
Statistics
Matches: 77, Mismatches: 7, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
38 1 0.01
39 8 0.10
40 66 0.86
41 2 0.03
ACGTcount: A:0.37, C:0.26, G:0.20, T:0.16
Consensus pattern (38 bp):
TAGGTCACAAAGCCATCATAGCGGCACAAAGCCATCAA
Done.