Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011403.1 Corchorus olitorius cultivar O-4 contig11436, 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: 68561
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:644 original size:27 final size:28
Alignment explanation
Indices: 589--644 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
579 CTCATTTTTG
*
589 AAACGTAAGGGATTAATTTGTCCCAAAA
1 AAACATAAGGGATTAATTTGTCCCAAAA
* *
617 AAACATAAGGGGTTATTTTGTCCCAAAA
1 AAACATAAGGGATTAATTTGTCCCAAAA
645 GCAAAACATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (28 bp):
AAACATAAGGGATTAATTTGTCCCAAAA
Found at i:1526 original size:21 final size:21
Alignment explanation
Indices: 1496--1537 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1486 TATACGCATT
*
1496 TGCGATGGACAAA-AGCTAATC
1 TGCGACGGACAAACA-CTAATC
1517 TGCGACGGACAAACACTAATC
1 TGCGACGGACAAACACTAATC
1538 AATGACGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.17
Consensus pattern (21 bp):
TGCGACGGACAAACACTAATC
Found at i:3071 original size:64 final size:64
Alignment explanation
Indices: 2932--3108 Score: 210
Period size: 64 Copynumber: 2.8 Consensus size: 64
2922 TCCGGTGCAT
* * * * * * *
2932 TTCTTAAAAAGATCGTCCTCCGATCAACTTCTGAAACCTGTTCGAGAAACTATCTTCTGGTGTAC
1 TTCTTAACAAGATCGTCTTCCGATCAACTTCTGAAA-ATTTTTGAGAAACCATCTTCTGGCGTAC
* *
2997 TTTTTAACAAGATCATCTTCCGATCAACTTCTGAAAATTTTTGAGAAACCATCTTCTGGCGTAC
1 TTCTTAACAAGATCGTCTTCCGATCAACTTCTGAAAATTTTTGAGAAACCATCTTCTGGCGTAC
* * * * * *
3061 TTCTTGACAAGATCGCCTTCCGTTCAACTTCGGAAAACTCTTGAGAAA
1 TTCTTAACAAGATCGTCTTCCGATCAACTTCTGAAAATTTTTGAGAAA
3109 AGATCGTCTT
Statistics
Matches: 95, Mismatches: 17, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
64 63 0.66
65 32 0.34
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.33
Consensus pattern (64 bp):
TTCTTAACAAGATCGTCTTCCGATCAACTTCTGAAAATTTTTGAGAAACCATCTTCTGGCGTAC
Found at i:3114 original size:39 final size:39
Alignment explanation
Indices: 3069--3147 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
3059 ACTTCTTGAC
* *
3069 AAGATCGCCTTCCGTTCAACTTCGGAAAACTCTTGAGAA
1 AAGATCGCCTTCCGATCAACTTCAGAAAACTCTTGAGAA
*
3108 AAGATCGTCTTCCGATCAACTTCAGAAAACTCTTGAGAA
1 AAGATCGCCTTCCGATCAACTTCAGAAAACTCTTGAGAA
3147 A
1 A
3148 CCATCTTCTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.25
Consensus pattern (39 bp):
AAGATCGCCTTCCGATCAACTTCAGAAAACTCTTGAGAA
Found at i:3181 original size:64 final size:64
Alignment explanation
Indices: 3108--3315 Score: 317
Period size: 64 Copynumber: 3.2 Consensus size: 64
3098 CTCTTGAGAA
* *
3108 AAGATCGTCTTCCGATCAACTTCAGAAAACTCTTGAGAAACCATCTTCTGGTGTACTTCTTGAC
1 AAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACTTCTTGAC
*
3172 AAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAATCATCTTCTGGTGTACTTCTTGAC
1 AAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACTTCTTGAC
* * * * * * *
3236 GAGATCATCTTCCGATCATCTTCTGAATATTGTTGAGAAACCATCTTCTGGTGTACTTTTTAAC
1 AAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACTTCTTGAC
*
3300 AAGATTGTCTTCCGAT
1 AAGATCGTCTTCCGAT
3316 GTATTCCTTA
Statistics
Matches: 130, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
64 130 1.00
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.35
Consensus pattern (64 bp):
AAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACTTCTTGAC
Found at i:3184 original size:103 final size:103
Alignment explanation
Indices: 3005--3211 Score: 333
Period size: 103 Copynumber: 2.0 Consensus size: 103
2995 ACTTTTTAAC
* * *
3005 AAGATCATCTTCCGATCAACTTCTGAAAATTTTTGAGAAACCATCTTCTGGCGTACTTCTTGACA
1 AAGATCATCTTCCGATCAACTTCAGAAAACTCTTGAGAAACCATCTTCTGGCGTACTTCTTGACA
*
3070 AGATCGCCTTCCGTTCAACTTCGGAAAACTCTTGAGAA
66 AGATCGCCTTCCGATCAACTTCGGAAAACTCTTGAGAA
* *
3108 AAGATCGTCTTCCGATCAACTTCAGAAAACTCTTGAGAAACCATCTTCTGGTGTACTTCTTGACA
1 AAGATCATCTTCCGATCAACTTCAGAAAACTCTTGAGAAACCATCTTCTGGCGTACTTCTTGACA
* * *
3173 AGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAA
66 AGATCGCCTTCCGATCAACTTCGGAAAACTCTTGAGAA
3211 A
1 A
3212 TCATCTTCTG
Statistics
Matches: 95, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
103 95 1.00
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (103 bp):
AAGATCATCTTCCGATCAACTTCAGAAAACTCTTGAGAAACCATCTTCTGGCGTACTTCTTGACA
AGATCGCCTTCCGATCAACTTCGGAAAACTCTTGAGAA
Found at i:3219 original size:167 final size:168
Alignment explanation
Indices: 2938--3241 Score: 484
Period size: 167 Copynumber: 1.8 Consensus size: 168
2928 GCATTTCTTA
* * * * *
2938 AAAAGATCGTCCTCCGATCAACTTCTGAAACCTGTTCGAGAAACTATCTTCTGGTGTACTTTTTA
1 AAAAGATCGTCCTCCGATCAACTTCAGAAAACTCTTCGAGAAACCATCTTCTGGTGTACTTCTTA
* *
3003 ACAAGATCATCTTCCGATCAACTTCTGAAAATTTTTGAGAAACCATCTTCTGGCGTACTTCTTGA
66 ACAAGATCATCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGCGTACTTCTTGA
3068 CAAGATCGCCTTCCGTTCAACTTCGGAAAACTCTTGAG
131 CAAGATCGCCTTCCGTTCAACTTCGGAAAACTCTTGAG
* *
3106 AAAAGATCGTCTTCCGATCAACTTCAGAAAACTCTT-GAGAAACCATCTTCTGGTGTACTTCTTG
1 AAAAGATCGTCCTCCGATCAACTTCAGAAAACTCTTCGAGAAACCATCTTCTGGTGTACTTCTTA
* * *
3170 ACAAGATCGTCTTCCGATCAACTTCTGAAAACTGTTGAGAAATCATCTTCTGGTGTACTTCTTGA
66 ACAAGATCATCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGCGTACTTCTTGA
*
3235 CGAGATC
131 CAAGATC
3242 ATCTTCCGAT
Statistics
Matches: 123, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
167 91 0.74
168 32 0.26
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (168 bp):
AAAAGATCGTCCTCCGATCAACTTCAGAAAACTCTTCGAGAAACCATCTTCTGGTGTACTTCTTA
ACAAGATCATCTTCCGATCAACTTCTGAAAACTGTTGAGAAACCATCTTCTGGCGTACTTCTTGA
CAAGATCGCCTTCCGTTCAACTTCGGAAAACTCTTGAG
Found at i:3391 original size:67 final size:66
Alignment explanation
Indices: 3306--3445 Score: 253
Period size: 67 Copynumber: 2.1 Consensus size: 66
3296 TAACAAGATT
*
3306 GTCTTCCGATGTATTCCTTAATGAGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAA
1 GTCTTCCAATGTATTCCTTAATGAGATTGTCTTCCAATCAACATTTG-AAATTCTTTCTAGCAAA
3371 CC
65 CC
3373 GTCTTCCAATGTATTCCTTAATGAGATTGTCTTCCAATCAACATTTGAAATTCTTTCTAGCAAAC
1 GTCTTCCAATGTATTCCTTAATGAGATTGTCTTCCAATCAACATTTGAAATTCTTTCTAGCAAAC
3438 C
66 C
*
3439 GTATTCC
1 GTCTTCC
3446 GGTGTACTTC
Statistics
Matches: 71, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
66 25 0.35
67 46 0.65
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.38
Consensus pattern (66 bp):
GTCTTCCAATGTATTCCTTAATGAGATTGTCTTCCAATCAACATTTGAAATTCTTTCTAGCAAAC
C
Found at i:5701 original size:15 final size:14
Alignment explanation
Indices: 5666--5705 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
5656 ACTCAAAATC
5666 TTTTTGAAAACCTA
1 TTTTTGAAAACCTA
* *
5680 TTTTTGAAAGCCTT
1 TTTTTGAAAACCTA
5694 TTTCTTGAAAAC
1 TTT-TTGAAAAC
5706 AATTTTCTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 15 0.68
15 7 0.32
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.45
Consensus pattern (14 bp):
TTTTTGAAAACCTA
Found at i:7472 original size:31 final size:29
Alignment explanation
Indices: 7430--7535 Score: 86
Period size: 31 Copynumber: 3.5 Consensus size: 29
7420 TCCGTCAAAA
* *
7430 TTAGGCCCAATTTGGTGCCTCCCGAATAGGT
1 TTAGGCTCAATTTGGTG-CTCACGAA-AGGT
* *
7461 TTAGGCTCAATTTGGTGCTGAGGAAAGGT
1 TTAGGCTCAATTTGGTGCTCACGAAAGGT
* * * **
7490 TTAGGCTCAAATTGAGCAGATCGTGAAAGGT
1 TTAGGCTCAATTTG-G-TGCTCACGAAAGGT
*
7521 TTAGGCCCAATTTGG
1 TTAGGCTCAATTTGG
7536 ATATTTAGCC
Statistics
Matches: 61, Mismatches: 12, Indels: 5
0.78 0.15 0.06
Matches are distributed among these distances:
29 17 0.28
30 7 0.11
31 37 0.61
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (29 bp):
TTAGGCTCAATTTGGTGCTCACGAAAGGT
Found at i:8477 original size:46 final size:45
Alignment explanation
Indices: 8426--8518 Score: 118
Period size: 46 Copynumber: 2.0 Consensus size: 45
8416 ATGCATGAAC
* *
8426 ATATATACAAAGGA-ATGAATAATGCATGACA-GATGTATGAACATAT
1 ATATATACAAA-GACATGAACAATGCATGA-AGGATGTACG-ACATAT
*
8472 ATATATACAAAGACATGGACAATGCATGAAGGATGTACGACATAT
1 ATATATACAAAGACATGAACAATGCATGAAGGATGTACGACATAT
8517 AT
1 AT
8519 CAATGGATAT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
45 11 0.26
46 31 0.74
ACGTcount: A:0.46, C:0.11, G:0.18, T:0.25
Consensus pattern (45 bp):
ATATATACAAAGACATGAACAATGCATGAAGGATGTACGACATAT
Found at i:18972 original size:7 final size:7
Alignment explanation
Indices: 18960--18998 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
18950 TTCCTACTTA
18960 TTTTAAT
1 TTTTAAT
18967 TTTTAAT
1 TTTTAAT
*
18974 TTTTAAGA
1 TTTTAA-T
*
18982 TTTTACT
1 TTTTAAT
18989 TTTTAAT
1 TTTTAAT
18996 TTT
1 TTT
18999 CTGACTTGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 22 0.81
8 5 0.19
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (7 bp):
TTTTAAT
Found at i:25436 original size:33 final size:33
Alignment explanation
Indices: 25399--25465 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
25389 TCAAGCTTCA
25399 TGGGTGCACGATCAAGTTCATCCATGGTGATCT
1 TGGGTGCACGATCAAGTTCATCCATGGTGATCT
25432 TGGGTGCACGATCAAGTTCATCCATGGTGATCT
1 TGGGTGCACGATCAAGTTCATCCATGGTGATCT
25465 T
1 T
25466 ATCAAAAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.31
Consensus pattern (33 bp):
TGGGTGCACGATCAAGTTCATCCATGGTGATCT
Found at i:37969 original size:18 final size:18
Alignment explanation
Indices: 37946--37984 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
37936 GATGGCGTGG
* *
37946 ATTGCCATTCCTAATGCC
1 ATTGCCACTCCCAATGCC
*
37964 ATTGCCACTCCCATTGCC
1 ATTGCCACTCCCAATGCC
37982 ATT
1 ATT
37985 CTCGACATGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.36, G:0.10, T:0.33
Consensus pattern (18 bp):
ATTGCCACTCCCAATGCC
Found at i:38555 original size:16 final size:15
Alignment explanation
Indices: 38523--38560 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
38513 AGACCTTGCA
38523 AAAAAG-AGGAAAAT
1 AAAAAGAAGGAAAAT
*
38537 AAAAAGAAGTAAAAGT
1 AAAAAGAAGGAAAA-T
38553 AAAAAGAA
1 AAAAAGAA
38561 AACCTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.29
15 6 0.29
16 9 0.43
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (15 bp):
AAAAAGAAGGAAAAT
Found at i:39163 original size:31 final size:31
Alignment explanation
Indices: 39098--39263 Score: 170
Period size: 31 Copynumber: 5.4 Consensus size: 31
39088 TCCTTTTGTG
** **
39098 CACGTGGCATGCCATGTGTCACTTTTTGAAA
1 CACGTGGCATGCCACATGTCACTTTTTGGTA
* *
39129 CACATGGCATGCCACATGTCACTTTTGGGTA
1 CACGTGGCATGCCACATGTCACTTTTTGGTA
* * **
39160 CACATGGCGTGATACATGTCACTTTTTGGTA
1 CACGTGGCATGCCACATGTCACTTTTTGGTA
* ** *
39191 CACGTGGCGTGCCTGATGTCGCTTTTTGGTA
1 CACGTGGCATGCCACATGTCACTTTTTGGTA
* * **
39222 CACGTGGCGTGCTACATGTTGCTTTTTGGTA
1 CACGTGGCATGCCACATGTCACTTTTTGGTA
39253 CACGTGGCATG
1 CACGTGGCATG
39264 TCACGTCGGA
Statistics
Matches: 114, Mismatches: 21, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 114 1.00
ACGTcount: A:0.18, C:0.22, G:0.27, T:0.33
Consensus pattern (31 bp):
CACGTGGCATGCCACATGTCACTTTTTGGTA
Found at i:39185 original size:62 final size:62
Alignment explanation
Indices: 39114--39263 Score: 192
Period size: 62 Copynumber: 2.4 Consensus size: 62
39104 GCATGCCATG
** *
39114 TGTCACTTTTTGAAACACATGGCATGCCACATGTCACTTTTGGGTACACATGGCGTGATACA
1 TGTCACTTTTTGGTACACGTGGCATGCCACATGTCACTTTTGGGTACACATGGCGTGATACA
* ** * * * *
39176 TGTCACTTTTTGGTACACGTGGCGTGCCTGATGTCGCTTTTTGGTACACGTGGCGTGCTACA
1 TGTCACTTTTTGGTACACGTGGCATGCCACATGTCACTTTTGGGTACACATGGCGTGATACA
**
39238 TGTTGCTTTTTGGTACACGTGGCATG
1 TGTCACTTTTTGGTACACGTGGCATG
39264 TCACGTCGGA
Statistics
Matches: 75, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
62 75 1.00
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.35
Consensus pattern (62 bp):
TGTCACTTTTTGGTACACGTGGCATGCCACATGTCACTTTTGGGTACACATGGCGTGATACA
Found at i:45210 original size:19 final size:18
Alignment explanation
Indices: 45166--45210 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
45156 TAGATAATTG
45166 TTTATTCACTGTTTTGAT
1 TTTATTCACTGTTTTGAT
* *
45184 TTTAATTCAGTGTTTTCTAT
1 TTT-ATTCACTGTTTT-GAT
45204 TTTATTC
1 TTTATTC
45211 TCAAAATTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 3 0.13
19 15 0.65
20 5 0.22
ACGTcount: A:0.18, C:0.11, G:0.09, T:0.62
Consensus pattern (18 bp):
TTTATTCACTGTTTTGAT
Found at i:49039 original size:21 final size:20
Alignment explanation
Indices: 48969--49044 Score: 59
Period size: 21 Copynumber: 3.8 Consensus size: 20
48959 CTAAGACACA
*
48969 AAATTAAACATGCAAACAAG
1 AAATTAAATATGCAAACAAG
* *
48989 AAAATTAAATCT--AAACATG
1 -AAATTAAATATGCAAACAAG
*
49008 CAATCCT-AATATGCAAACAAG
1 AAAT--TAAATATGCAAACAAG
49029 AAATTCAAATATGCAA
1 AAATT-AAATATGCAA
49045 GATAGATAGA
Statistics
Matches: 42, Mismatches: 7, Indels: 12
0.69 0.11 0.20
Matches are distributed among these distances:
18 3 0.07
19 11 0.26
20 1 0.02
21 27 0.64
ACGTcount: A:0.55, C:0.16, G:0.08, T:0.21
Consensus pattern (20 bp):
AAATTAAATATGCAAACAAG
Found at i:56171 original size:18 final size:18
Alignment explanation
Indices: 56148--56184 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
56138 GTACTTGCAC
56148 CAGAGTTCAAATGCGTTA
1 CAGAGTTCAAATGCGTTA
56166 CAGAGTTCAAATGCGTTA
1 CAGAGTTCAAATGCGTTA
56184 C
1 C
56185 CTGTGTTCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (18 bp):
CAGAGTTCAAATGCGTTA
Found at i:59088 original size:21 final size:21
Alignment explanation
Indices: 59021--59093 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 21
59011 AGACACAAAA
* *
59021 TTAAACATGCAAACAAGAAAA
1 TTAAATATGCAAACAAGAAAT
* * *
59042 TTAAATCT--AAACATGCAAT
1 TTAAATATGCAAACAAGAAAT
*
59061 CCT-AATATGCAAACAAGAAAT
1 -TTAAATATGCAAACAAGAAAT
59082 TTAAATATGCAA
1 TTAAATATGCAA
59094 GATAGATAGA
Statistics
Matches: 38, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
19 12 0.32
20 2 0.05
21 24 0.63
ACGTcount: A:0.53, C:0.15, G:0.08, T:0.23
Consensus pattern (21 bp):
TTAAATATGCAAACAAGAAAT
Found at i:64797 original size:16 final size:16
Alignment explanation
Indices: 64776--64806 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
64766 CGAATTTTAG
*
64776 TAAATAATTATTATTT
1 TAAATAATAATTATTT
64792 TAAATAATAATTATT
1 TAAATAATAATTATT
64807 ATATATCCTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TAAATAATAATTATTT
Found at i:65812 original size:21 final size:21
Alignment explanation
Indices: 65786--65848 Score: 126
Period size: 21 Copynumber: 3.0 Consensus size: 21
65776 GCATCTTAGG
65786 CAACTCCGATGAGCTTGAAAC
1 CAACTCCGATGAGCTTGAAAC
65807 CAACTCCGATGAGCTTGAAAC
1 CAACTCCGATGAGCTTGAAAC
65828 CAACTCCGATGAGCTTGAAAC
1 CAACTCCGATGAGCTTGAAAC
65849 TTCTTTGTGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.33, C:0.29, G:0.19, T:0.19
Consensus pattern (21 bp):
CAACTCCGATGAGCTTGAAAC
Found at i:67706 original size:33 final size:32
Alignment explanation
Indices: 67669--67766 Score: 124
Period size: 33 Copynumber: 3.0 Consensus size: 32
67659 AGAATTTGTT
67669 TCATCACAAACAACACCTAAAATAGATTTAGA
1 TCATCACAAACAACACCTAAAATAGATTTAGA
* * *
67701 GTCATCACAAACAACACTTAAATTAGGTTTAGTA
1 -TCATCACAAACAACACCTAAAATAGATTTAG-A
* * *
67735 TCATCGCAAACAACATCTAAAACAGATTTAGA
1 TCATCACAAACAACACCTAAAATAGATTTAGA
67767 ATTACTCTTT
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
32 1 0.02
33 53 0.96
34 1 0.02
ACGTcount: A:0.46, C:0.20, G:0.09, T:0.24
Consensus pattern (32 bp):
TCATCACAAACAACACCTAAAATAGATTTAGA
Done.