Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012246.1 Corchorus olitorius cultivar O-4 contig12279, 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: 10910
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:1948 original size:71 final size:71
Alignment explanation
Indices: 1808--2499 Score: 668
Period size: 71 Copynumber: 9.7 Consensus size: 71
1798 CTCTATCAAA
* * * * * * **
1808 GACCGCCCTGGGTCAAC-TGAAATAAATTGAAGAACGACCACCCTCGATC-ATTCCAAACTGGAC
1 GACCGCCCTGGGTCAACTTGAAATAAACTGAAGAAAGACCACCCTAGGTCAACT-GAAA-TAAAC
*
1871 TGAAGAAC
64 TGAAGAAT
*
1879 GACCACCCTGGGTCAACTTGAAATAAACTGAAAGAAAGACCACCCT-GGTCAACTGAAATAAACT
1 GACCGCCCTGGGTCAACTTGAAATAAACTG-AAGAAAGACCACCCTAGGTCAACTGAAATAAACT
*
1943 TAAGAAT
65 GAAGAAT
* * *
1950 GATCGCCCTGGATCAACTTGAAA-ACAACTGAAGAAAGACCGA-CCTGGGTCAACTGAAATAAAC
1 GACCGCCCTGGGTCAACTTGAAATA-AACTGAAGAAAGACC-ACCCTAGGTCAACTGAAATAAAC
*
2013 TGAAGAAA
64 TGAAGAAT
* * * * * * * * *
2021 GACCGCCCTGGGTCAAC-TAAAACAAACTGAAGAACGACAAACCTTGATCATTCTGACATAAACT
1 GACCGCCCTGGGTCAACTTGAAATAAACTGAAGAAAGACCACCCTAGGTCA-ACTGAAATAAACT
*
2085 GAAGAAAA
65 GAAG-AAT
* * *
2093 GACCACCCTGGGTCAA-TTGAAATAAACTGAAGAAAGACCGCCCTAGGTCAACTGAAATAAACTT
1 GACCGCCCTGGGTCAACTTGAAATAAACTGAAGAAAGACCACCCTAGGTCAACTGAAATAAACTG
2157 AAGAAT
66 AAGAAT
* * * * * *
2163 GACCGCCTTGGATCAACTTGAAA-ACAACTAAAGAAAGACCACCATGGGTCAACTGAAATAAATT
1 GACCGCCCTGGGTCAACTTGAAATA-AACTGAAGAAAGACCACCCTAGGTCAACTGAAATAAACT
*
2227 GAAGAAA
65 GAAGAAT
* * * * * * **
2234 GACCGCGCTGGGTCAAC-TGAAATAAACTGAAGAACGACCACCCTCA-ATCATTCCGAACTGGAC
1 GACCGCCCTGGGTCAACTTGAAATAAACTGAAGAAAGACCACCCT-AGGTCA-ACTGAAATAAAC
*
2297 TGAAGAAC
64 TGAAGAAT
* * *
2305 GACCACCCTGGGTCAACTTGAAATAAACTGAAAGAGAGACCACCCTGGGTCAACTGAAATAAACT
1 GACCGCCCTGGGTCAACTTGAAATAAACTG-AAGAAAGACCACCCTAGGTCAACTGAAATAAACT
*
2370 TAAGAAT
65 GAAGAAT
* * * * *
2377 GATCTCCCTGGATCAACTTGAAA-ACAACTAAAGAAAGACCGCCCTAGGTCAACTGAAATAAACT
1 GACCGCCCTGGGTCAACTTGAAATA-AACTGAAGAAAGACCACCCTAGGTCAACTGAAATAAACT
*
2441 GAGGAAT
65 GAAGAAT
* * * * *
2448 GATCGCCCAGGATCAACTTGAAAAAAACTGAAGAAAGACCGCCCTAGGTCAA
1 GACCGCCCTGGGTCAACTTGAAATAAACTGAAGAAAGACCACCCTAGGTCAA
2500 TATGAAACTA
Statistics
Matches: 513, Mismatches: 87, Indels: 42
0.80 0.14 0.07
Matches are distributed among these distances:
69 1 0.00
70 79 0.15
71 291 0.57
72 110 0.21
73 32 0.06
ACGTcount: A:0.41, C:0.23, G:0.19, T:0.17
Consensus pattern (71 bp):
GACCGCCCTGGGTCAACTTGAAATAAACTGAAGAAAGACCACCCTAGGTCAACTGAAATAAACTG
AAGAAT
Found at i:1966 original size:35 final size:35
Alignment explanation
Indices: 1805--2499 Score: 608
Period size: 35 Copynumber: 19.5 Consensus size: 35
1795 TAGCTCTATC
*
1805 AAAGACCGCCCTGGGTCAACTGAAATAAATTGAAG
1 AAAGACCGCCCTGGGTCAACTGAAATAAACTGAAG
* * * * * * **
1840 AACGACCACCCTCGATC-ATTCCAAACTGGACTGAAG
1 AAAGACCGCCCTGGGTCAACT-GAAA-TAAACTGAAG
* *
1876 AACGACCACCCTGGGTCAACTTGAAATAAACTGAAAG
1 AAAGACCGCCCTGGGTCAAC-TGAAATAAACTG-AAG
* *
1913 AAAGACCACCCT-GGTCAACTGAAATAAACTTAAG
1 AAAGACCGCCCTGGGTCAACTGAAATAAACTGAAG
* * *
1947 AATGATCGCCCTGGATCAACTTGAAA-ACAACTGAAG
1 AAAGACCGCCCTGGGTCAAC-TGAAATA-AACTGAAG
*
1983 AAAGACCGACCTGGGTCAACTGAAATAAACTGAAG
1 AAAGACCGCCCTGGGTCAACTGAAATAAACTGAAG
* *
2018 AAAGACCGCCCTGGGTCAACTAAAACAAACTGAAG
1 AAAGACCGCCCTGGGTCAACTGAAATAAACTGAAG
* *** * * * *
2053 AACGACAAACCTTGATCATTCTGACATAAACTGAAG
1 AAAGACCGCCCTGGGTCA-ACTGAAATAAACTGAAG
* *
2089 AAAAGACCACCCTGGGTCAATTGAAATAAACTGAAG
1 -AAAGACCGCCCTGGGTCAACTGAAATAAACTGAAG
* *
2125 AAAGACCGCCCTAGGTCAACTGAAATAAACTTAAG
1 AAAGACCGCCCTGGGTCAACTGAAATAAACTGAAG
* * * *
2160 AATGACCGCCTTGGATCAACTTGAAA-ACAACTAAAG
1 AAAGACCGCCCTGGGTCAAC-TGAAATA-AACTGAAG
* * *
2196 AAAGACCACCATGGGTCAACTGAAATAAATTGAAG
1 AAAGACCGCCCTGGGTCAACTGAAATAAACTGAAG
*
2231 AAAGACCGCGCTGGGTCAACTGAAATAAACTGAAG
1 AAAGACCGCCCTGGGTCAACTGAAATAAACTGAAG
* * *** * * * **
2266 AACGACCACCCTCAATCATTCCGAACTGGACTGAAG
1 AAAGACCGCCCTGGGTCA-ACTGAAATAAACTGAAG
* *
2302 AACGACCACCCTGGGTCAACTTGAAATAAACTGAAAG
1 AAAGACCGCCCTGGGTCAAC-TGAAATAAACTG-AAG
* * *
2339 AGAGACCACCCTGGGTCAACTGAAATAAACTTAAG
1 AAAGACCGCCCTGGGTCAACTGAAATAAACTGAAG
* * * * *
2374 AATGATCTCCCTGGATCAACTTGAAA-ACAACTAAAG
1 AAAGACCGCCCTGGGTCAAC-TGAAATA-AACTGAAG
* *
2410 AAAGACCGCCCTAGGTCAACTGAAATAAACTGAGG
1 AAAGACCGCCCTGGGTCAACTGAAATAAACTGAAG
* * * * *
2445 AATGATCGCCCAGGATCAACTTGAAAAAAACTGAAG
1 AAAGACCGCCCTGGGTCAAC-TGAAATAAACTGAAG
*
2481 AAAGACCGCCCTAGGTCAA
1 AAAGACCGCCCTGGGTCAA
2500 TATGAAACTA
Statistics
Matches: 526, Mismatches: 113, Indels: 41
0.77 0.17 0.06
Matches are distributed among these distances:
34 14 0.03
35 239 0.45
36 220 0.42
37 52 0.10
38 1 0.00
ACGTcount: A:0.41, C:0.23, G:0.19, T:0.17
Consensus pattern (35 bp):
AAAGACCGCCCTGGGTCAACTGAAATAAACTGAAG
Found at i:2177 original size:213 final size:212
Alignment explanation
Indices: 1805--2492 Score: 990
Period size: 213 Copynumber: 3.2 Consensus size: 212
1795 TAGCTCTATC
* * *
1805 AAAGACCGCCCTGGGTCAACTGAAATAAATTGAAGAACGACCACCCTCGATCATTCCAAACTGGA
1 AAAGACCGCCCTGGGTCAACTAAAATAAACTGAAGAACGACCACCCTCGATCATT-CGAACTGGA
1870 CTGAAGAACGACCACCCTGGGTCAACTTGAAATAAACTGAAAGAAAGACCACCCTGGTCAACTGA
65 CTGAAGAACGACCACCCTGGGTCAACTTGAAATAAACTGAAAGAAAGACCACCCTGGTCAACTGA
*
1935 AATAAACTTAAGAATGATCGCCCTGGATCAACTTGAAAACAACTGAAGAAAGACCGACCTGGGTC
130 AATAAACTTAAGAATGATCGCCCTGGATCAACTTGAAAACAACTAAAGAAAGACCGACCTGGGTC
2000 AACTGAAATAAACTGAAG
195 AACTGAAATAAACTGAAG
* * * * **
2018 AAAGACCGCCCTGGGTCAACTAAAACAAACTGAAGAACGACAAACCTTGATCATTCTG-ACATAA
1 AAAGACCGCCCTGGGTCAACTAAAATAAACTGAAGAACGACCACCCTCGATCATTC-GAAC-TGG
* *
2082 ACTGAAGAAAAGACCACCCTGGGTCAA-TTGAAATAAACTG-AAGAAAGACCGCCCTAGGTCAAC
64 ACTGAAG-AACGACCACCCTGGGTCAACTTGAAATAAACTGAAAGAAAGACCACCCT-GGTCAAC
* *
2145 TGAAATAAACTTAAGAATGACCGCCTTGGATCAACTTGAAAACAACTAAAGAAAGACC-ACCATG
127 TGAAATAAACTTAAGAATGATCGCCCTGGATCAACTTGAAAACAACTAAAGAAAGACCGACC-TG
*
2209 GGTCAACTGAAATAAATTGAAG
191 GGTCAACTGAAATAAACTGAAG
* * *
2231 AAAGACCGCGCTGGGTCAACTGAAATAAACTGAAGAACGACCACCCTCAATCATTCCGAACTGGA
1 AAAGACCGCCCTGGGTCAACTAAAATAAACTGAAGAACGACCACCCTCGATCATT-CGAACTGGA
*
2296 CTGAAGAACGACCACCCTGGGTCAACTTGAAATAAACTGAAAGAGAGACCACCCTGGGTCAACTG
65 CTGAAGAACGACCACCCTGGGTCAACTTGAAATAAACTGAAAGAAAGACCACCCT-GGTCAACTG
* * *
2361 AAATAAACTTAAGAATGATCTCCCTGGATCAACTTGAAAACAACTAAAGAAAGACCGCCCTAGGT
129 AAATAAACTTAAGAATGATCGCCCTGGATCAACTTGAAAACAACTAAAGAAAGACCGACCTGGGT
*
2426 CAACTGAAATAAACTGAGG
194 CAACTGAAATAAACTGAAG
* * * * * *
2445 AATGATCGCCCAGGATCAACTTGAAAA-AAACTGAAGAAAGACCGCCCT
1 AAAGACCGCCCTGGGTCAAC-T-AAAATAAACTGAAGAACGACCACCCT
2493 AGGTCAATAT
Statistics
Matches: 420, Mismatches: 43, Indels: 22
0.87 0.09 0.05
Matches are distributed among these distances:
212 38 0.09
213 225 0.54
214 132 0.31
215 22 0.05
216 3 0.01
ACGTcount: A:0.41, C:0.23, G:0.19, T:0.17
Consensus pattern (212 bp):
AAAGACCGCCCTGGGTCAACTAAAATAAACTGAAGAACGACCACCCTCGATCATTCGAACTGGAC
TGAAGAACGACCACCCTGGGTCAACTTGAAATAAACTGAAAGAAAGACCACCCTGGTCAACTGAA
ATAAACTTAAGAATGATCGCCCTGGATCAACTTGAAAACAACTAAAGAAAGACCGACCTGGGTCA
ACTGAAATAAACTGAAG
Found at i:3704 original size:25 final size:25
Alignment explanation
Indices: 3676--3724 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
3666 CACCCTAAAG
3676 CTTTATCTTTTCTT-TTTCCCTTTTA
1 CTTTATCTTTT-TTATTTCCCTTTTA
* *
3701 CTTTTTCTTTTTTATTTCTCTTTT
1 CTTTATCTTTTTTATTTCCCTTTT
3725 TTCTTCTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 2 0.10
25 19 0.90
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.73
Consensus pattern (25 bp):
CTTTATCTTTTTTATTTCCCTTTTA
Found at i:3724 original size:12 final size:10
Alignment explanation
Indices: 3702--3751 Score: 55
Period size: 12 Copynumber: 4.5 Consensus size: 10
3692 TCCCTTTTAC
3702 TTTTTCTTTT
1 TTTTTCTTTT
3712 TTATTTCTCTTT
1 TT-TTTCT-TTT
3724 TTTCTTCTTTT
1 TTT-TTCTTTT
3735 TTTTTCTCTTCT
1 TTTTTCT-TT-T
3747 TTTTT
1 TTTTT
3752 TATTTTACTT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
10 6 0.17
11 14 0.40
12 15 0.43
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:3739 original size:13 final size:13
Alignment explanation
Indices: 3705--3752 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
3695 CTTTTACTTT
3705 TTCTTTTTTATTTC
1 TTCTTTTTT-TTTC
*
3719 -TCTTTTTTCTTC
1 TTCTTTTTTTTTC
*
3731 TT-TTTTTTTCTC
1 TTCTTTTTTTTTC
3743 TTCTTTTTTT
1 TTCTTTTTTT
3753 ATTTTACTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 13 0.45
13 16 0.55
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (13 bp):
TTCTTTTTTTTTC
Found at i:3739 original size:15 final size:15
Alignment explanation
Indices: 3721--3762 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
3711 TTTATTTCTC
3721 TTTTTTCTTCTTTTT
1 TTTTTTCTTCTTTTT
*
3736 TTTTCTCTTCTTTTT
1 TTTTTTCTTCTTTTT
3751 TTATTTTACTTC
1 TT-TTTT-CTTC
3763 ACCATGCACC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 16 0.70
16 3 0.13
17 4 0.17
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTTCTTCTTTTT
Found at i:3757 original size:22 final size:21
Alignment explanation
Indices: 3701--3758 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 21
3691 TTCCCTTTTA
3701 CTTTTTCTTTTTTATTTCTCTT
1 CTTTTT-TTTTTTATTTCTCTT
*
3723 -TTTTCTTCTTTTTTTTTCTCTT
1 CTTTT-TT-TTTTTATTTCTCTT
3745 CTTTTTTTATTTTA
1 CTTTTTTT-TTTTA
3759 CTTCACCATG
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
21 6 0.20
22 20 0.67
23 4 0.13
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (21 bp):
CTTTTTTTTTTTATTTCTCTT
Found at i:3853 original size:22 final size:22
Alignment explanation
Indices: 3815--3862 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
3805 CTAAAAACCT
3815 TTTTGAGAAAAACATTT-TTCC
1 TTTTGAGAAAAACATTTCTTCC
*
3836 TTTTGA-AAAAATCAATTTCTTCT
1 TTTTGAGAAAAA-C-ATTTCTTCC
3859 TTTT
1 TTTT
3863 CGAACAATCC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 5 0.22
21 7 0.30
22 4 0.17
23 7 0.30
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.50
Consensus pattern (22 bp):
TTTTGAGAAAAACATTTCTTCC
Found at i:5639 original size:42 final size:41
Alignment explanation
Indices: 5592--5692 Score: 121
Period size: 42 Copynumber: 2.4 Consensus size: 41
5582 ATGTAGTAAT
*
5592 GAATGGATAATGCATGACCTACGCATGAACATATATACAAA
1 GAATGGATAATGCATGACCGACGCATGAACATATATACAAA
* ** * *
5633 GGAATGGATAATGCCTGATGGATGTATGAACATATATACAAA
1 -GAATGGATAATGCATGACCGACGCATGAACATATATACAAA
*
5675 GACATGGACAATGCATGA
1 GA-ATGGATAATGCATGA
5693 AGGATGTATG
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
41 2 0.04
42 48 0.96
ACGTcount: A:0.42, C:0.14, G:0.22, T:0.23
Consensus pattern (41 bp):
GAATGGATAATGCATGACCGACGCATGAACATATATACAAA
Found at i:5698 original size:42 final size:42
Alignment explanation
Indices: 5616--5710 Score: 131
Period size: 42 Copynumber: 2.3 Consensus size: 42
5606 TGACCTACGC
* * *
5616 ATGAACATATATACAAAGGAATGGATAATGCCTGATGGATGT
1 ATGAACATATATACAAAGGAATGGACAATGCATGAAGGATGT
5658 ATGAACATATATACAAA-GACATGGACAATGCATGAAGGATGT
1 ATGAACATATATACAAAGGA-ATGGACAATGCATGAAGGATGT
*
5700 ATG-GCATATAT
1 ATGAACATATAT
5711 CAATGGATAT
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
41 9 0.19
42 39 0.81
ACGTcount: A:0.42, C:0.11, G:0.22, T:0.25
Consensus pattern (42 bp):
ATGAACATATATACAAAGGAATGGACAATGCATGAAGGATGT
Found at i:6709 original size:4 final size:4
Alignment explanation
Indices: 6700--6766 Score: 50
Period size: 4 Copynumber: 17.5 Consensus size: 4
6690 TACATAATAG
* ** * * *
6700 TAAA TAAA TAGA T-AA TAGC TAAA TTAA TAAA TAAA TAGA TAAA T-AG
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
*
6746 TAAA TAAA T-AA TAGA TAAA TA
1 TAAA TAAA TAAA TAAA TAAA TA
6767 GCTATAATAA
Statistics
Matches: 46, Mismatches: 14, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
3 7 0.15
4 39 0.85
ACGTcount: A:0.63, C:0.01, G:0.07, T:0.28
Consensus pattern (4 bp):
TAAA
Found at i:6734 original size:12 final size:12
Alignment explanation
Indices: 6695--6766 Score: 62
Period size: 11 Copynumber: 6.0 Consensus size: 12
6685 AGAAATACAT
6695 AATAG-TAAATA
1 AATAGATAAATA
6706 AATAGATAATAGCTA
1 AATAGATAA-A--TA
6721 AATTA-ATAAATA
1 AA-TAGATAAATA
6733 AATAGATAAAT-
1 AATAGATAAATA
* *
6744 AGTAAATAAAT-
1 AATAGATAAATA
6755 AATAGATAAATA
1 AATAGATAAATA
6767 GCTATAATAA
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
11 25 0.50
12 13 0.26
13 1 0.02
14 1 0.02
15 8 0.16
16 2 0.04
ACGTcount: A:0.62, C:0.01, G:0.08, T:0.28
Consensus pattern (12 bp):
AATAGATAAATA
Found at i:6766 original size:15 final size:15
Alignment explanation
Indices: 6687--6766 Score: 67
Period size: 15 Copynumber: 5.3 Consensus size: 15
6677 TAGGTAAAAG
*
6687 AAATACATAATAG-T
1 AAATAAATAATAGAT
6701 AAATAAATAGATA-AT
1 AAATAAATA-ATAGAT
** *
6716 AGCTAAATTAATAAAT
1 AAATAAA-TAATAGAT
*
6732 AAATAGATAAATAG-T
1 AAATAAAT-AATAGAT
6747 AAATAAATAATAGAT
1 AAATAAATAATAGAT
6762 AAATA
1 AAATA
6767 GCTATAATAA
Statistics
Matches: 52, Mismatches: 8, Indels: 11
0.73 0.11 0.15
Matches are distributed among these distances:
14 13 0.25
15 27 0.52
16 12 0.23
ACGTcount: A:0.62, C:0.03, G:0.07, T:0.28
Consensus pattern (15 bp):
AAATAAATAATAGAT
Found at i:6781 original size:27 final size:26
Alignment explanation
Indices: 6701--6779 Score: 96
Period size: 27 Copynumber: 3.1 Consensus size: 26
6691 ACATAATAGT
6701 AAATAAATAGAT-AATAGCTAAATTAA
1 AAATAAATAGATAAATAGCTAAA-TAA
6727 TAAATAAATAGATAAATAG-TAAAT--
1 -AAATAAATAGATAAATAGCTAAATAA
6751 AAAT-AATAGATAAATAGCTATAATAA
1 AAATAAATAGATAAATAGCTA-AATAA
6777 AAA
1 AAA
6780 ATCTTTTTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 11
0.81 0.00 0.19
Matches are distributed among these distances:
22 13 0.28
23 6 0.13
24 3 0.06
26 4 0.09
27 16 0.34
28 5 0.11
ACGTcount: A:0.63, C:0.03, G:0.08, T:0.27
Consensus pattern (26 bp):
AAATAAATAGATAAATAGCTAAATAA
Found at i:9274 original size:41 final size:41
Alignment explanation
Indices: 9214--9463 Score: 294
Period size: 41 Copynumber: 6.1 Consensus size: 41
9204 ATCAAGAATG
* * * * *
9214 AAATCGAACTAGTTGAAAGATAAT-AACCTCAATCAAGGAGC
1 AAATCGAACCAATTAAAAGAT-ATCAACATCAATCAAGGGGC
* * * *
9255 AAATTGAA-CAGATTAAAAGATCTTAACATCAATCAGGGGGC
1 AAATCGAACCA-ATTAAAAGATATCAACATCAATCAAGGGGC
* *
9296 AAATCGAATCAATTAAAAGATATCAACATCAATC-AGGGGTT
1 AAATCGAACCAATTAAAAGATATCAACATCAATCAAGGGG-C
*
9337 AAATCGAACCAATTAAAAGATATCAACATCAATC-AGGGGTT
1 AAATCGAACCAATTAAAAGATATCAACATCAATCAAGGGG-C
9378 AAATCGAACCAATTAAAAGATATCAACATCAATC-AGGGAGC
1 AAATCGAACCAATTAAAAGATATCAACATCAATCAAGGG-GC
* *
9419 AAATCGAACCAATTAAAGGATATCAACATCAATCAAAGGGC
1 AAATCGAACCAATTAAAAGATATCAACATCAATCAAGGGGC
9460 AAAT
1 AAAT
9464 TGAAGAAGAA
Statistics
Matches: 186, Mismatches: 17, Indels: 12
0.87 0.08 0.06
Matches are distributed among these distances:
40 6 0.03
41 174 0.94
42 6 0.03
ACGTcount: A:0.47, C:0.17, G:0.16, T:0.20
Consensus pattern (41 bp):
AAATCGAACCAATTAAAAGATATCAACATCAATCAAGGGGC
Found at i:10653 original size:12 final size:12
Alignment explanation
Indices: 10636--10662 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
10626 TCTTTTATGC
10636 CTAAAATGACAA
1 CTAAAATGACAA
10648 CTAAAATGACAA
1 CTAAAATGACAA
10660 CTA
1 CTA
10663 TCTTAAGTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.19, G:0.07, T:0.19
Consensus pattern (12 bp):
CTAAAATGACAA
Done.