Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012464.1 Corchorus olitorius cultivar O-4 contig12497, 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: 99241
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:11658 original size:29 final size:29
Alignment explanation
Indices: 11626--11713 Score: 158
Period size: 29 Copynumber: 3.0 Consensus size: 29
11616 TAACACTACG
*
11626 ATAACCATGAGATACGTACATGACTAATT
1 ATAACCATGAGATACGTACATAACTAATT
11655 ATAACCATGAGATACGTACATAACTAATT
1 ATAACCATGAGATACGTACATAACTAATT
*
11684 ATAACCATGAGATACGTACATAACTTATT
1 ATAACCATGAGATACGTACATAACTAATT
11713 A
1 A
11714 CTTTAAACTA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 57 1.00
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.28
Consensus pattern (29 bp):
ATAACCATGAGATACGTACATAACTAATT
Found at i:13760 original size:59 final size:60
Alignment explanation
Indices: 13689--13819 Score: 237
Period size: 60 Copynumber: 2.2 Consensus size: 60
13679 GTTGAGAAGT
*
13689 TGACACATGTCAA-TTTTTCAATTAATTGAATTTTAAATATTTCAATCTAAGTCCCAAGA
1 TGACACATGTCAATTTTTTCAATTAATTGAATTTTAAATATTTCAATCTAAGTCCCAAAA
13748 TGACACATGTCAATTTTTTCAATTAATTGAATTTTAAATATTTCAATCTAAGTCCCAAAA
1 TGACACATGTCAATTTTTTCAATTAATTGAATTTTAAATATTTCAATCTAAGTCCCAAAA
*
13808 TGACACTTGTCA
1 TGACACATGTCA
13820 CCCTTTTGGA
Statistics
Matches: 69, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
59 13 0.19
60 56 0.81
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (60 bp):
TGACACATGTCAATTTTTTCAATTAATTGAATTTTAAATATTTCAATCTAAGTCCCAAAA
Found at i:18950 original size:13 final size:13
Alignment explanation
Indices: 18932--18956 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18922 GAAAAATATC
18932 AAAAATAAAAAAT
1 AAAAATAAAAAAT
18945 AAAAATAAAAAA
1 AAAAATAAAAAA
18957 ATTTTCGACC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:19994 original size:49 final size:50
Alignment explanation
Indices: 19937--20045 Score: 184
Period size: 49 Copynumber: 2.2 Consensus size: 50
19927 TAAAGATGCA
19937 TTTATCAATTTCGCCTTTTGTCCTTAATTGAACAACATACAAAGTC-AAT
1 TTTATCAATTTCGCCTTTTGTCCTTAATTGAACAACATACAAAGTCGAAT
* *
19986 TTTATCAATTTCGCTTTTTGTCCTTAATTGAACAACATACAAAGTCGTAT
1 TTTATCAATTTCGCCTTTTGTCCTTAATTGAACAACATACAAAGTCGAAT
20036 TTTATTCAAT
1 TTTA-TCAAT
20046 AGAGATCAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
49 45 0.80
50 6 0.11
51 5 0.09
ACGTcount: A:0.31, C:0.18, G:0.08, T:0.42
Consensus pattern (50 bp):
TTTATCAATTTCGCCTTTTGTCCTTAATTGAACAACATACAAAGTCGAAT
Found at i:22166 original size:19 final size:19
Alignment explanation
Indices: 22133--22169 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
22123 GCATGATGTC
22133 GGGATAAAGAAAAGGAAAA
1 GGGATAAAGAAAAGGAAAA
22152 GGGA-AAAGAACAAGGAAA
1 GGGATAAAGAA-AAGGAAA
22170 GAAAACGCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.62, C:0.03, G:0.32, T:0.03
Consensus pattern (19 bp):
GGGATAAAGAAAAGGAAAA
Found at i:23189 original size:23 final size:22
Alignment explanation
Indices: 23156--23199 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
23146 CTTACCCTAA
23156 ATTGAAAACTTTGAAAAACTTGG
1 ATTGAAAACTTTG-AAAACTTGG
*
23179 ATTGAATACTTTGAAAACTTG
1 ATTGAAAACTTTGAAAACTTG
23200 ATGGGATCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (22 bp):
ATTGAAAACTTTGAAAACTTGG
Found at i:24480 original size:18 final size:18
Alignment explanation
Indices: 24457--24492 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
24447 ATAAGTTTAG
24457 CAAATTTTTTCTATATTA
1 CAAATTTTTTCTATATTA
24475 CAAATTTTTTCTATATTA
1 CAAATTTTTTCTATATTA
24493 TAGGAAACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.00, T:0.56
Consensus pattern (18 bp):
CAAATTTTTTCTATATTA
Found at i:25586 original size:60 final size:58
Alignment explanation
Indices: 25522--25654 Score: 171
Period size: 60 Copynumber: 2.3 Consensus size: 58
25512 AATTTTATTC
* *
25522 ACTTTAAGCTAAAAGGATCTAACTTTCTACATATTATGAATG-AAA-ATCTAATTTCTTTAT
1 ACTTTAAGCTAAAAGGATATAACTTTCTACATATTATG-A-GCAAAGACCT-ATTT-TTTAT
* *
25582 ACTTTAAGCCAAAAGGATATAATTTTCTACATATTATGAGCAAAGACCTATTTTTTAT
1 ACTTTAAGCTAAAAGGATATAACTTTCTACATATTATGAGCAAAGACCTATTTTTTAT
*
25640 ACTTAAAGCTAAAAG
1 ACTTTAAGCTAAAAG
25655 ATTACATATT
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
58 19 0.29
59 8 0.12
60 38 0.58
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.37
Consensus pattern (58 bp):
ACTTTAAGCTAAAAGGATATAACTTTCTACATATTATGAGCAAAGACCTATTTTTTAT
Found at i:31487 original size:21 final size:21
Alignment explanation
Indices: 31463--31526 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
31453 CCTTAGGCAA
31463 CTCCAATGAGCTTGAAACCTT
1 CTCCAATGAGCTTGAAACCTT
*
31484 CTCCAATGAGCTTGAAACTTT
1 CTCCAATGAGCTTGAAACCTT
31505 CTCCAATGAGCTTGAAA-CTT
1 CTCCAATGAGCTTGAAACCTT
31525 CT
1 CT
31527 TTGTGTGAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
20 4 0.10
21 37 0.90
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (21 bp):
CTCCAATGAGCTTGAAACCTT
Found at i:33480 original size:25 final size:24
Alignment explanation
Indices: 33449--33502 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
33439 CTTGAAAATT
33449 TGAAAAACTTTGATGGATGAGATG-GA
1 TGAAAAAC-TTGAT-GAT-AGATGAGA
33475 TGAAAAACTTGATGATAGATGAGA
1 TGAAAAACTTGATGATAGATGAGA
33499 TGAA
1 TGAA
33503 TAGAAGGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
23 5 0.19
24 9 0.33
25 5 0.19
26 8 0.30
ACGTcount: A:0.43, C:0.04, G:0.28, T:0.26
Consensus pattern (24 bp):
TGAAAAACTTGATGATAGATGAGA
Found at i:33490 original size:28 final size:26
Alignment explanation
Indices: 33449--33500 Score: 77
Period size: 28 Copynumber: 1.9 Consensus size: 26
33439 CTTGAAAATT
*
33449 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAACTTTGATAGATGAGATGGA
33475 TGAAAAACTTGATGATAGATGAGATG
1 TGAAAAACTT--TGATAGATGAGATG
33501 AATAGAAGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 10 0.43
28 13 0.57
ACGTcount: A:0.40, C:0.04, G:0.29, T:0.27
Consensus pattern (26 bp):
TGAAAAACTTTGATAGATGAGATGGA
Found at i:34391 original size:21 final size:21
Alignment explanation
Indices: 34367--34413 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
34357 CCTTAGGCAA
34367 CTCCAATGAGCTTGAAACCTT
1 CTCCAATGAGCTTGAAACCTT
*
34388 CTCCAATGAGCTTGAAACTTT
1 CTCCAATGAGCTTGAAACCTT
34409 CTCCA
1 CTCCA
34414 TGATCTCCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.28, C:0.30, G:0.13, T:0.30
Consensus pattern (21 bp):
CTCCAATGAGCTTGAAACCTT
Found at i:37924 original size:10 final size:10
Alignment explanation
Indices: 37913--37950 Score: 67
Period size: 10 Copynumber: 3.7 Consensus size: 10
37903 AAGGTTATAT
37913 AAAAAAATATA
1 AAAAAAAT-TA
37924 AAAAAAATTA
1 AAAAAAATTA
37934 AAAAAAATTA
1 AAAAAAATTA
37944 AAAAAAA
1 AAAAAAA
37951 AATTTCGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 19 0.70
11 8 0.30
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (10 bp):
AAAAAAATTA
Found at i:37928 original size:12 final size:12
Alignment explanation
Indices: 37908--37953 Score: 53
Period size: 11 Copynumber: 4.1 Consensus size: 12
37898 ACCTCAAGGT
*
37908 TATATAAAAAAA
1 TATAAAAAAAAA
37920 TAT-AAAAAAAA
1 TATAAAAAAAAA
*
37931 T-TAAAAAAAAT
1 TATAAAAAAAAA
37942 TA-AAAAAAAAA
1 TATAAAAAAAAA
37953 T
1 T
37954 TTCGATTAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
10 1 0.03
11 25 0.86
12 3 0.10
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (12 bp):
TATAAAAAAAAA
Found at i:37948 original size:22 final size:21
Alignment explanation
Indices: 37913--37954 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
37903 AAGGTTATAT
*
37913 AAAAAAATATAAAAAAAATTA
1 AAAAAAATAAAAAAAAAATTA
37934 AAAAAAATTAAAAAAAAAATT
1 AAAAAAA-TAAAAAAAAAATT
37955 TCGATTAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (21 bp):
AAAAAAATAAAAAAAAAATTA
Found at i:37954 original size:12 final size:11
Alignment explanation
Indices: 37913--37951 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
37903 AAGGTTATAT
37913 AAAAAAA-TATA
1 AAAAAAATTA-A
37924 AAAAAAATT-A
1 AAAAAAATTAA
37934 AAAAAAATTAA
1 AAAAAAATTAA
37945 AAAAAAA
1 AAAAAAA
37952 ATTTCGATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.38
11 15 0.58
12 1 0.04
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAAAATTAA
Found at i:42405 original size:181 final size:181
Alignment explanation
Indices: 42089--42434 Score: 482
Period size: 181 Copynumber: 1.9 Consensus size: 181
42079 TGCCTACTTT
* * *
42089 GGTGATATCTATAAAGCATGTGCTAAATCTGGTTTTGGGAAGTATTATATGCATAATGGATTTTT
1 GGTGATATCTATAAAGCATGTGCTAAATCTAGATTTGGGAAGTATTATATGCATAATGGATTTTC
* * * **
42154 GTTTAAAGAATCTAGATTATGTATTCCTTCTTGTTCTTTGCGTGATGTGCTTACGAGGGAATTGC
66 CTTTAAAGAATCTAGATTATGTATTCCTTCTTGTTCTTTGCGAGATGTGCTTACGAGAGAATCAC
*
42219 ATGAAGGGGGTTTAATGGGTCATTTTGGTATTGATAGAAGTCATTTTGGTC
131 ATGAAGGGGGCTTAATGGGTCATTTTGGTATTGATAGAAGTCATTTTGGTC
* * * **
42270 GGTGATATCTTTAAGGCATGTGCTAATTCTAGATTTGGGAAGTATTACT-TGCATTCTGGATTTT
1 GGTGATATCTATAAAGCATGTGCTAAATCTAGATTTGGGAAGTATTA-TATGCATAATGGATTTT
* **
42334 CCTTTAAAGAATCTAGACTT-TGTATTCCTTCTTGTTCTTTGCGAGATGT-TTTGTTGAGAGAAT
65 CCTTTAAAGAATCTAGA-TTATGTATTCCTTCTTGTTCTTTGCGAGATGTGCTT-ACGAGAGAAT
*
42397 CACATGAAGGGGGCTTAATGGGTCATTTTGGTGTTGAT
128 CACATGAAGGGGGCTTAATGGGTCATTTTGGTATTGAT
42435 TGAACATATG
Statistics
Matches: 144, Mismatches: 18, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
180 2 0.01
181 139 0.97
182 3 0.02
ACGTcount: A:0.24, C:0.11, G:0.25, T:0.41
Consensus pattern (181 bp):
GGTGATATCTATAAAGCATGTGCTAAATCTAGATTTGGGAAGTATTATATGCATAATGGATTTTC
CTTTAAAGAATCTAGATTATGTATTCCTTCTTGTTCTTTGCGAGATGTGCTTACGAGAGAATCAC
ATGAAGGGGGCTTAATGGGTCATTTTGGTATTGATAGAAGTCATTTTGGTC
Found at i:61142 original size:50 final size:50
Alignment explanation
Indices: 61082--61207 Score: 225
Period size: 50 Copynumber: 2.5 Consensus size: 50
61072 CGATCAACCT
*
61082 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTCCCGCTTATC
*
61132 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGATCGTCTCCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTCCCGCTTATC
*
61182 CTTTGAATTGTCTTCCAATTCAATCT
1 CTTTGAACTGTCTTCCAATTCAATCT
61208 GGATGTCTAA
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 73 1.00
ACGTcount: A:0.24, C:0.27, G:0.11, T:0.38
Consensus pattern (50 bp):
CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTCCCGCTTATC
Found at i:61422 original size:64 final size:64
Alignment explanation
Indices: 61280--61594 Score: 425
Period size: 64 Copynumber: 4.9 Consensus size: 64
61270 GCCTCTTTTA
* *
61280 ACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTTGCGAAACCATCTTCTGGTGTACTTCTTA
1 ACAAGATCGTCTTCCGATCAACTTCTGAAAACTC-TTGAGAAACCATCTTCTGGTGTACTTCTTG
** * * *
61345 ACAAGATAATCTTCCGATCAACTTCTGAAAACTCTTAAGAAACCATCTTCTGGTGTAATTTTTG
1 ACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACTTCTTG
* * * *
61409 ACAAGATCGTCTTCCGATCATCTTCTCAAAACTCTTGAGAAACCATATTCTGATGTACTTCTTG
1 ACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACTTCTTG
* * *
61473 ACAAGATCGTCTTCCGATCATCTTCTGAAAA-TTTTGGAGAAACCATCTTCTGGCGTACTTCTTG
1 ACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTT-GAGAAACCATCTTCTGGTGTACTTCTTG
* * * * * *
61537 ACAAGGTTGTCTTCCGATCAGCATCTGGAAACTGTTGAGAAACCATCTTCTGGTGTAC
1 ACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTAC
61595 ATCTCAATGA
Statistics
Matches: 220, Mismatches: 28, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
63 3 0.01
64 182 0.83
65 35 0.16
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (64 bp):
ACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACTTCTTG
Found at i:61611 original size:64 final size:64
Alignment explanation
Indices: 61256--61689 Score: 419
Period size: 64 Copynumber: 6.7 Consensus size: 64
61246 ATTTCTAAAT
* *
61256 AACCATCTTCCGGTGCCT-CTT-TTAACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTTGC
1 AACCATCTTCTGGTG--TACTTCTTAACAAGATCGTCTTCCGATCAACTTCTGAAAACTC-TTGA
61319 GA
63 GA
** *
61321 AACCATCTTCTGGTGTACTTCTTAACAAGATAATCTTCCGATCAACTTCTGAAAACTCTTAAGA
1 AACCATCTTCTGGTGTACTTCTTAACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGA
* * * * *
61385 AACCATCTTCTGGTGTAATTTTTGACAAGATCGTCTTCCGATCATCTTCTCAAAACTCTTGAGA
1 AACCATCTTCTGGTGTACTTCTTAACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGA
* * * * *
61449 AACCATATTCTGATGTACTTCTTGACAAGATCGTCTTCCGATCATCTTCTGAAAA-TTTTGGAGA
1 AACCATCTTCTGGTGTACTTCTTAACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTT-GAGA
* * * * * * * *
61513 AACCATCTTCTGGCGTACTTCTTGACAAGGTTGTCTTCCGATCAGCATCTGGAAACTGTTGAGA
1 AACCATCTTCTGGTGTACTTCTTAACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGA
* * ** * * *
61577 AACCATCTTCTGGTGTACATCTCAATGAGATTGTCTTCCAATCAACATT-TGAAAATTCCCTCT-
1 AACCATCTTCTGGTGTACTTCTTAACAAGATCGTCTTCCGATCAAC-TTCTGAAAA--CTCT-TG
61640 AGCA
62 AG-A
* * * ** * *
61644 AACCGTCTTCTGGTGTACTCCTAAATGAGATTGTCTTCCAATCAAC
1 AACCATCTTCTGGTGTACTTCTTAACAAGATCGTCTTCCGATCAAC
61690 CATTTGAAAA
Statistics
Matches: 315, Mismatches: 45, Indels: 16
0.84 0.12 0.04
Matches are distributed among these distances:
63 4 0.01
64 210 0.67
65 53 0.17
66 4 0.01
67 44 0.14
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.33
Consensus pattern (64 bp):
AACCATCTTCTGGTGTACTTCTTAACAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGA
Found at i:61736 original size:68 final size:67
Alignment explanation
Indices: 61576--61736 Score: 232
Period size: 67 Copynumber: 2.4 Consensus size: 67
61566 AACTGTTGAG
* * * *
61576 AAACCATCTTCTGGTGTACATCTCAATGAGATTGTCTTCCAATCAACATTTGAAAATTCCCTCTA
1 AAACCGTCTTCTGGTGTACTTCTAAATGAGATTGTCTTCCAATCAACATTTGAAAATTCCCTATA
61641 GC
66 GC
* **
61643 AAACCGTCTTCTGGTGTACTCCTAAATGAGATTGTCTTCCAATCAACCATTTGAAAATTCTTTAT
1 AAACCGTCTTCTGGTGTACTTCTAAATGAGATTGTCTTCCAATCAA-CATTTGAAAATTCCCTAT
61708 AGC
65 AGC
* *
61711 AAACCGTCTTCCGGTGTATTTCTAAA
1 AAACCGTCTTCTGGTGTACTTCTAAA
61737 AAAATCCTCT
Statistics
Matches: 83, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
67 42 0.51
68 41 0.49
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (67 bp):
AAACCGTCTTCTGGTGTACTTCTAAATGAGATTGTCTTCCAATCAACATTTGAAAATTCCCTATA
GC
Found at i:66201 original size:13 final size:14
Alignment explanation
Indices: 66183--66217 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
66173 AAACCTTATT
66183 TTGAAAAC-TTTTC
1 TTGAAAACATTTTC
66196 TTGAAAACAATTTTC
1 TTGAAAAC-ATTTTC
66211 TTGAAAA
1 TTGAAAA
66218 ATGTCTCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 8 0.40
15 12 0.60
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (14 bp):
TTGAAAACATTTTC
Found at i:67428 original size:42 final size:42
Alignment explanation
Indices: 67382--67477 Score: 124
Period size: 42 Copynumber: 2.3 Consensus size: 42
67372 CAACCTATGC
* *
67382 ATGAACATATATCCAAAGGA-ATGAATAATGCATGATGGATAT
1 ATGAACATATATCCAAA-GACATGAACAATGCATGAAGGATAT
* * *
67424 ATGAACATATATACAAAGACATGGACAATGCATGAAGGATGT
1 ATGAACATATATCCAAAGACATGAACAATGCATGAAGGATAT
67466 ATG-ACATATATC
1 ATGAACATATATC
67478 AATGGATAGG
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
41 10 0.21
42 37 0.79
ACGTcount: A:0.45, C:0.11, G:0.19, T:0.25
Consensus pattern (42 bp):
ATGAACATATATCCAAAGACATGAACAATGCATGAAGGATAT
Found at i:72449 original size:27 final size:28
Alignment explanation
Indices: 72401--72472 Score: 76
Period size: 27 Copynumber: 2.6 Consensus size: 28
72391 TCTCCATTAT
* * *
72401 GGCCCAAAA-GCAAATCCTAAGCTAAAA
1 GGCCTAAAATGCAAGTCCAAAGCTAAAA
* *
72428 GGTCT-GAATGCAAGTCCAAAGCTAAAA
1 GGCCTAAAATGCAAGTCCAAAGCTAAAA
*
72455 TGCCTAAAATGCAAGTCC
1 GGCCTAAAATGCAAGTCC
72473 GAAGTCAACC
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
26 2 0.06
27 22 0.63
28 11 0.31
ACGTcount: A:0.42, C:0.24, G:0.18, T:0.17
Consensus pattern (28 bp):
GGCCTAAAATGCAAGTCCAAAGCTAAAA
Found at i:72761 original size:27 final size:26
Alignment explanation
Indices: 72731--72827 Score: 108
Period size: 26 Copynumber: 3.7 Consensus size: 26
72721 AAAAAAAGAG
* *
72731 CAAAACGCCCCTGAATGTGAAAATGAC
1 CAAAATGCCCCTG-GTGTGAAAATGAC
*
72758 CAAAATGCCCTTGGTGTGCAAAA-GAC
1 CAAAATGCCCCTGGTGTG-AAAATGAC
*
72784 CAAAATGCCCCTGGTGTAAAAATGAC
1 CAAAATGCCCCTGGTGTGAAAATGAC
**
72810 TGAAATGCCCCTGG-GTGA
1 CAAAATGCCCCTGGTGTGA
72828 CCCTAATGCC
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
25 7 0.12
26 38 0.63
27 15 0.25
ACGTcount: A:0.35, C:0.24, G:0.23, T:0.19
Consensus pattern (26 bp):
CAAAATGCCCCTGGTGTGAAAATGAC
Found at i:73794 original size:7 final size:7
Alignment explanation
Indices: 73782--73815 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
73772 TAATATCAAG
73782 TTAAAAA
1 TTAAAAA
73789 TTAAAAA
1 TTAAAAA
**
73796 TTGGAAA
1 TTAAAAA
73803 TTAAAAA
1 TTAAAAA
73810 TTAAAA
1 TTAAAA
73816 TAAGTAGGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (7 bp):
TTAAAAA
Found at i:81856 original size:33 final size:33
Alignment explanation
Indices: 81819--81908 Score: 135
Period size: 33 Copynumber: 2.7 Consensus size: 33
81809 GATTGTTTTA
* *
81819 TCATCACAAACAACACTTAAAACAGATTTAGTT
1 TCATCACAAACAACACTCAAAACAGATTTAGTG
* *
81852 TCATCACCAACAACACTCAAAGCAGATTTAGTG
1 TCATCACAAACAACACTCAAAACAGATTTAGTG
*
81885 TCATCGCAAACAACACTCAAAACA
1 TCATCACAAACAACACTCAAAACA
81909 AATTGAGACT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.44, C:0.27, G:0.08, T:0.21
Consensus pattern (33 bp):
TCATCACAAACAACACTCAAAACAGATTTAGTG
Found at i:86776 original size:15 final size:16
Alignment explanation
Indices: 86756--86785 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
86746 GAAAAAAAAT
86756 ATTAATTT-ATTTAAA
1 ATTAATTTAATTTAAA
86771 ATTAATTTAATTTAA
1 ATTAATTTAATTTAA
86786 CCAGAAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTAATTTAATTTAAA
Found at i:87333 original size:13 final size:13
Alignment explanation
Indices: 87315--87340 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
87305 ATCATTAATT
87315 GGAATTAAAATCC
1 GGAATTAAAATCC
87328 GGAATTAAAATCC
1 GGAATTAAAATCC
87341 CAATTAATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.23
Consensus pattern (13 bp):
GGAATTAAAATCC
Found at i:88516 original size:22 final size:22
Alignment explanation
Indices: 88465--88516 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 22
88455 CTGCTTTCTG
**
88465 ATTAATTGTTTTCTTTAATTTT
1 ATTAATTGTTTTCTTTAATAAT
* *
88487 CTTGATTGTTTTC-TTAGATAAT
1 ATTAATTGTTTTCTTTA-ATAAT
88509 ATTAATTG
1 ATTAATTG
88517 CTAGATTGGT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
21 3 0.13
22 20 0.87
ACGTcount: A:0.25, C:0.06, G:0.10, T:0.60
Consensus pattern (22 bp):
ATTAATTGTTTTCTTTAATAAT
Found at i:89818 original size:21 final size:21
Alignment explanation
Indices: 89793--89901 Score: 128
Period size: 21 Copynumber: 5.2 Consensus size: 21
89783 ATATGAGAAA
* *
89793 GAAAATTCAGTTGAAGGAGTT
1 GAAAATCCAGTTGATGGAGTT
* **
89814 GAAAATCCAGTAGATGGTTTT
1 GAAAATCCAGTTGATGGAGTT
89835 GAAAATCCAGTTGATGGAGTT
1 GAAAATCCAGTTGATGGAGTT
* * *
89856 GAAAATTCAGTAGATGGTGTT
1 GAAAATCCAGTTGATGGAGTT
* *
89877 GAAAATCCAGTTGAAGAAGTT
1 GAAAATCCAGTTGATGGAGTT
89898 GAAA
1 GAAA
89902 TGCCTGGAAA
Statistics
Matches: 72, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 72 1.00
ACGTcount: A:0.38, C:0.07, G:0.27, T:0.28
Consensus pattern (21 bp):
GAAAATCCAGTTGATGGAGTT
Found at i:89916 original size:42 final size:42
Alignment explanation
Indices: 89793--89901 Score: 173
Period size: 42 Copynumber: 2.6 Consensus size: 42
89783 ATATGAGAAA
* *
89793 GAAAATTCAGTTGAAGGAGTTGAAAATCCAGTAGATGGTTTT
1 GAAAATCCAGTTGAAGGAGTTGAAAATCCAGTAGATGGTGTT
* *
89835 GAAAATCCAGTTGATGGAGTTGAAAATTCAGTAGATGGTGTT
1 GAAAATCCAGTTGAAGGAGTTGAAAATCCAGTAGATGGTGTT
*
89877 GAAAATCCAGTTGAAGAAGTTGAAA
1 GAAAATCCAGTTGAAGGAGTTGAAA
89902 TGCCTGGAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 61 1.00
ACGTcount: A:0.38, C:0.07, G:0.27, T:0.28
Consensus pattern (42 bp):
GAAAATCCAGTTGAAGGAGTTGAAAATCCAGTAGATGGTGTT
Found at i:97611 original size:54 final size:54
Alignment explanation
Indices: 97529--97638 Score: 220
Period size: 54 Copynumber: 2.0 Consensus size: 54
97519 TATCTACAAT
97529 TGCATTGAATCCAAGGAGGATCATGAAGATATAAGATGCGCCAAAGACTTATCA
1 TGCATTGAATCCAAGGAGGATCATGAAGATATAAGATGCGCCAAAGACTTATCA
97583 TGCATTGAATCCAAGGAGGATCATGAAGATATAAGATGCGCCAAAGACTTATCA
1 TGCATTGAATCCAAGGAGGATCATGAAGATATAAGATGCGCCAAAGACTTATCA
97637 TG
1 TG
97639 GACTTGAAGA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (54 bp):
TGCATTGAATCCAAGGAGGATCATGAAGATATAAGATGCGCCAAAGACTTATCA
Found at i:99117 original size:21 final size:21
Alignment explanation
Indices: 99091--99131 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
99081 TTGAAGCCCT
99091 ATTGGAGAC-AAGTGGTACTAA
1 ATTGGA-ACTAAGTGGTACTAA
*
99112 ATTGGATCTAAGTGGTACTA
1 ATTGGAACTAAGTGGTACTA
99132 GGGTTTTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29
Consensus pattern (21 bp):
ATTGGAACTAAGTGGTACTAA
Done.