Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015595.1 Corchorus olitorius cultivar O-4 contig15628, 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: 11654
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Found at i:2068 original size:10 final size:11
Alignment explanation
Indices: 2051--2082 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
2041 CTTTAGTTTG
2051 CATTTTCTTTT
1 CATTTTCTTTT
2062 C-TTTTC-TTT
1 CATTTTCTTTT
2071 CATTTTCTTTT
1 CATTTTCTTTT
2082 C
1 C
2083 CTTCCTTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
9 4 0.21
10 10 0.53
11 5 0.26
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (11 bp):
CATTTTCTTTT
Found at i:6025 original size:32 final size:32
Alignment explanation
Indices: 5971--6034 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
5961 AACCTATGCA
* * * *
5971 CATGCAAGATGAATTAACTAAAATCTAGGTGC
1 CATGCAAGATAAATCAACTAAAACCTAAGTGC
*
6003 CATGCAAGATAAATCAAGTAAAACCTAAGTGC
1 CATGCAAGATAAATCAACTAAAACCTAAGTGC
6035 TAAAAATGAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.22
Consensus pattern (32 bp):
CATGCAAGATAAATCAACTAAAACCTAAGTGC
Found at i:6389 original size:26 final size:26
Alignment explanation
Indices: 6307--6391 Score: 100
Period size: 26 Copynumber: 3.3 Consensus size: 26
6297 TCTTTCAAAC
* *
6307 AATTCCTGATAAACCATCTTTCGATT
1 AATTTCTGATAAACCGTCTTTCGATT
* *
6333 AATCTCTGATAAATCGTCTTTCGATCT
1 AATTTCTGATAAACCGTCTTTCGAT-T
* *
6360 -ATTTCTGACAAACCGTCTTCCGATT
1 AATTTCTGATAAACCGTCTTTCGATT
6385 AATTTCT
1 AATTTCT
6392 TTAGAAAATC
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
25 1 0.02
26 47 0.96
27 1 0.02
ACGTcount: A:0.27, C:0.24, G:0.09, T:0.40
Consensus pattern (26 bp):
AATTTCTGATAAACCGTCTTTCGATT
Found at i:6448 original size:50 final size:49
Alignment explanation
Indices: 6389--7163 Score: 440
Period size: 50 Copynumber: 15.4 Consensus size: 49
6379 CCGATTAATT
* *
6389 TCTTTAGAAAATCGTCTTCCGCTCATCTTTCGAGCTATCTTCCAATTCAA
1 TCTTTA-AAAATCGTCTTCCGCTCATCTTTCGAACTGTCTTCCAATTCAA
* * * *
6439 TCTTTAGAAAATCGTCTTCTGATCAACTTTCGAACTGTCTTCCAA-TCCA
1 TCTTTA-AAAATCGTCTTCCGCTCATCTTTCGAACTGTCTTCCAATTCAA
* * *
6488 T-TTTCAAAAGGA-CTGTCTCCCACTCATACTATT--TA-T-T-TTCCAA-TCAA
1 TCTTT-AAAA--ATC-GTCTTCCGCTCAT-CT-TTCGAACTGTCTTCCAATTCAA
* * * * *
6535 AC-TTAAAAGGATCATCTTCTGCTCATCCCTT-GAACTGTCTTCCAATTCAT
1 TCTTTAAAA--ATCGTCTTCCGCTCAT-CTTTCGAACTGTCTTCCAATTCAA
* * *
6585 TCTTTAGAAAATCGTCTTCCGATCAACTTTCGAACTGTCTTCCAATCCAA
1 TCTTTA-AAAATCGTCTTCCGCTCATCTTTCGAACTGTCTTCCAATTCAA
* * * * *
6635 TCTTAAAAGGAAATTGTCTTCTGTTTATCTTTCGAACTGTCTTCCAATTCAA
1 TCTT-TAA--AAATCGTCTTCCGCTCATCTTTCGAACTGTCTTCCAATTCAA
* *
6687 TC-TTAAAAGGACCGTCTTCCGCTCATCATTT-AAACTGTCTTCCAATTCAA
1 TCTTTAAAA--ATCGTCTTCCGCTCATC-TTTCGAACTGTCTTCCAATTCAA
* *
6737 TC-TTAAAAGGACCGTCTTCCGATCATCTTTCGAACTGTCTTCCAATTCAA
1 TCTTTAAAA--ATCGTCTTCCGCTCATCTTTCGAACTGTCTTCCAATTCAA
* * * * * *
6787 TCTTTAAAGGACCGTCTTTCGCTTATCCTTCAAACTGTCTTCCAATTCAATAA
1 TCTTTAAA-AATCGTCTTCCGCTCATCTTTCGAACTGTCTTCCAATTC---AA
** * * * *
6840 CTCTTTGAACGACCGTCTTCTGCTTATCTTTCGAACTGTCTTCCAATTGAA
1 -TCTTT-AAAAATCGTCTTCCGCTCATCTTTCGAACTGTCTTCCAATTCAA
* * * *
6891 TCTTTAAAGGATCTTCTTCCGCTTATCTTT-TAGACTGTCTTCCAATTCAA
1 TCTTTAAA-AATCGTCTTCCGCTCATCTTTCGA-ACTGTCTTCCAATTCAA
** * * *
6941 TCTTTAGAGGACCGTCTTCCGATCATCTTTCGAACTGACTTCCAATTCAA
1 TCTTTA-AAAATCGTCTTCCGCTCATCTTTCGAACTGTCTTCCAATTCAA
* * * ** *
6991 T-TTTAAGAGGACCATCTTCCTATCAACTTCTTT-GAATTGTCTTCCAATTCAA
1 TCTTTAA-A-AATCGTCTTCCGCTC-A--TCTTTCGAACTGTCTTCCAATTCAA
* * * * * *
7043 TCCTGAAAGGATCGTCTTCCGCAT-ATCCTTCGATCTGTCTTCCAATTCAT
1 TCTTTAAA-AATCGTCTTCCGC-TCATCTTTCGAACTGTCTTCCAATTCAA
* * ** *
7093 TC-TTAAGAGGACCGTCTTCCAATCGACTTCTTT-GAACTGTCTTCCAATTCAT
1 TCTTTAA-A-AATCGTCTTCCGCTC-A--TCTTTCGAACTGTCTTCCAATTCAA
*
7145 TC-TTAAGAAATTGTCTTCC
1 TCTTTAA-AAATCGTCTTCC
7164 AATCGTCTAT
Statistics
Matches: 583, Mismatches: 95, Indels: 93
0.76 0.12 0.12
Matches are distributed among these distances:
45 2 0.00
46 18 0.03
47 13 0.02
48 11 0.02
49 34 0.06
50 321 0.55
51 30 0.05
52 98 0.17
53 15 0.03
54 39 0.07
55 2 0.00
ACGTcount: A:0.25, C:0.26, G:0.11, T:0.38
Consensus pattern (49 bp):
TCTTTAAAAATCGTCTTCCGCTCATCTTTCGAACTGTCTTCCAATTCAA
Found at i:6704 original size:27 final size:26
Alignment explanation
Indices: 6673--6804 Score: 98
Period size: 27 Copynumber: 5.2 Consensus size: 26
6663 CTTTCGAACT
6673 GTCTTCCAATTCAATCTTAAAAGGACC
1 GTCTTCCAATTCAATCTT-AAAGGACC
** * *
6700 GTCTTCC-GCTC-ATCATTTAA--ACT
1 GTCTTCCAATTCAATC-TTAAAGGACC
6723 GTCTTCCAATTCAATCTTAAAAGGACC
1 GTCTTCCAATTCAATCTT-AAAGGACC
* ** * *
6750 GTCTTCCGA-TC-ATCTT-TCGAACT
1 GTCTTCCAATTCAATCTTAAAGGACC
6773 GTCTTCCAATTCAATCTTTAAAGGACC
1 GTCTTCCAATTCAATC-TTAAAGGACC
6800 GTCTT
1 GTCTT
6805 TCGCTTATCC
Statistics
Matches: 77, Mismatches: 18, Indels: 20
0.67 0.16 0.17
Matches are distributed among these distances:
23 20 0.26
24 6 0.08
25 18 0.23
26 8 0.10
27 25 0.32
ACGTcount: A:0.27, C:0.27, G:0.11, T:0.35
Consensus pattern (26 bp):
GTCTTCCAATTCAATCTTAAAGGACC
Found at i:6959 original size:27 final size:27
Alignment explanation
Indices: 6877--7010 Score: 79
Period size: 27 Copynumber: 5.3 Consensus size: 27
6867 CTTTCGAACT
* * *
6877 GTCTTCCAATTGAATCTTTAAAGGATC
1 GTCTTCCAATTCAATCTTTAGAGGACC
* ** * *
6904 TTCTTCCGCTT--ATCTTT-TA-GACT
1 GTCTTCCAATTCAATCTTTAGAGGACC
6927 GTCTTCCAATTCAATCTTTAGAGGACC
1 GTCTTCCAATTCAATCTTTAGAGGACC
* * *
6954 GTCTTCCGA-TC-ATCTTTCGA--ACT
1 GTCTTCCAATTCAATCTTTAGAGGACC
*
6977 GACTTCCAATTCAAT-TTTAAGAGGACC
1 GTCTTCCAATTCAATCTTT-AGAGGACC
*
7004 ATCTTCC
1 GTCTTCC
7011 TATCAACTTC
Statistics
Matches: 78, Mismatches: 20, Indels: 18
0.67 0.17 0.16
Matches are distributed among these distances:
23 19 0.24
24 6 0.08
25 24 0.31
26 3 0.04
27 26 0.33
ACGTcount: A:0.24, C:0.25, G:0.13, T:0.38
Consensus pattern (27 bp):
GTCTTCCAATTCAATCTTTAGAGGACC
Found at i:7134 original size:204 final size:199
Alignment explanation
Indices: 6426--7150 Score: 629
Period size: 204 Copynumber: 3.6 Consensus size: 199
6416 TTTCGAGCTA
* * * * *
6426 TCTTCCAATTCAATCTTTAGAAA--ATCGTCTTCTGATCAACTTTCGAACTGTCTTCCAA-TCCA
1 TCTTCCAATTCAATC-CT-GAAAGGATCGTCTTCTGCTTATCTTTCGAACTGTCTTCCAATTCAA
* * * * * * *
6488 TTTTCAAAAGGACTGTCTCCCACTCATACTATT-TA-T-T-TTCCAA-TCAAACTTAAAAGGATC
64 TCTT--AAAGGACCGTCTTCCGCTCAT-CT-TTAAACTGTCTTCCAATTCAATCTTAAAAGGACC
* * * * * * * * * *
6548 ATCTTCTGCTCATCCCTT-GAACTGTCTTCCAATTCATTCTTTAGAA-AATCGTCTTCCGATCAA
125 GTCTTCCGATCAT-CTTTCGAACTGACTTCCAATTCAATCTTTA-AAGGACCATCTTCCTATCAA
*
6611 CTT-TCGAACTG
188 CTTCTTGAACTG
* * * * *
6622 TCTTCCAATCCAATCTTAAAAGGAAATTGTCTTCTGTTTATCTTTCGAACTGTCTTCCAATTCAA
1 TCTTCCAATTCAATCCTGAAAGG--ATCGTCTTCTGCTTATCTTTCGAACTGTCTTCCAATTCAA
6687 TCTTAAAAGGACCGTCTTCCGCTCATCATTTAAACTGTCTTCCAATTCAATCTTAAAAGGACCGT
64 TCTT-AAAGGACCGTCTTCCGCTCATC-TTTAAACTGTCTTCCAATTCAATCTTAAAAGGACCGT
* *
6752 CTTCCGATCATCTTTCGAACTGTCTTCCAATTCAATCTTTAAAGGACCGTCTTTCGCTTATC--C
127 CTTCCGATCATCTTTCGAACTGACTTCCAATTCAATCTTTAAAGGACCATC-TTC-C-TATCAAC
*
6815 TTC--AAACTG
189 TTCTTGAACTG
* *
6824 TCTTCCAATTCAATAACTCTTTG-AACGACCGTCTTCTGCTTATCTTTCGAACTGTCTTCCAATT
1 TCTTCCAATTCAAT--C-C--TGAAAGGATCGTCTTCTGCTTATCTTTCGAACTGTCTTCCAATT
* * * * * * *
6888 GAATCTTTAAAGGATCTTCTTCCGCTTATCTTTTAGACTGTCTTCCAATTCAATCTTTAGAGGAC
61 CAATC-TTAAAGGACCGTCTTCCGCTCATC-TTTAAACTGTCTTCCAATTCAATCTTAAAAGGAC
6953 CGTCTTCCGATCATCTTTCGAACTGACTTCCAATTCAAT-TTTAAGAGGACCATCTTCCTATCAA
124 CGTCTTCCGATCATCTTTCGAACTGACTTCCAATTCAATCTTTAA-AGGACCATCTTCCTATCAA
*
7017 CTTCTTTGAATTG
188 CTTC-TTGAACTG
* * * * *
7030 TCTTCCAATTCAATCCTGAAAGGATCGTCTTCCGCATATCCTTCGATCTGTCTTCCAATTCATTC
1 TCTTCCAATTCAATCCTGAAAGGATCGTCTTCTGCTTATCTTTCGAACTGTCTTCCAATTCAATC
** * *
7095 TTAAGAGGACCGTCTTCCAATCGACTTCTTTGAACTGTCTTCCAATTCATTCTTAA
66 TTAA-AGGACCGTCTTCCGCTC-A--TCTTTAAACTGTCTTCCAATTCAATCTTAA
7151 GAAATTGTCT
Statistics
Matches: 436, Mismatches: 59, Indels: 60
0.79 0.11 0.11
Matches are distributed among these distances:
194 3 0.01
195 2 0.00
196 14 0.03
197 3 0.01
198 52 0.12
199 7 0.02
200 1 0.00
201 21 0.05
202 123 0.28
203 20 0.05
204 161 0.37
205 7 0.02
206 21 0.05
207 1 0.00
ACGTcount: A:0.25, C:0.26, G:0.11, T:0.38
Consensus pattern (199 bp):
TCTTCCAATTCAATCCTGAAAGGATCGTCTTCTGCTTATCTTTCGAACTGTCTTCCAATTCAATC
TTAAAGGACCGTCTTCCGCTCATCTTTAAACTGTCTTCCAATTCAATCTTAAAAGGACCGTCTTC
CGATCATCTTTCGAACTGACTTCCAATTCAATCTTTAAAGGACCATCTTCCTATCAACTTCTTGA
ACTG
Found at i:7438 original size:40 final size:39
Alignment explanation
Indices: 7317--7446 Score: 111
Period size: 40 Copynumber: 3.3 Consensus size: 39
7307 CAAATCCTAA
* *
7317 TTCTGAAAATC-TTCTTGAAAAATCGTCTTCCAATTGAC
1 TTCTGAAAATCTTTTTTGAAAAATCGTCTTCCGATTGAC
* * ** * * * * * *
7355 TTTTGAATATCTAAATATGATAAACCTTCTTCTGGTT-AGC
1 TTCTGAAAATCT-TTTTTGAAAAATCGTCTTCCGATTGA-C
7395 TTCTGAAAATCTTTTTTGAAATAATCGTCTTCCGATTGAC
1 TTCTGAAAATCTTTTTTGAAA-AATCGTCTTCCGATTGAC
7435 TTCTGAAAATCT
1 TTCTGAAAATCT
7447 ATTTCTGATA
Statistics
Matches: 65, Mismatches: 22, Indels: 8
0.68 0.23 0.08
Matches are distributed among these distances:
38 9 0.14
39 6 0.09
40 49 0.75
41 1 0.02
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.41
Consensus pattern (39 bp):
TTCTGAAAATCTTTTTTGAAAAATCGTCTTCCGATTGAC
Found at i:7456 original size:80 final size:78
Alignment explanation
Indices: 7317--7465 Score: 217
Period size: 80 Copynumber: 1.9 Consensus size: 78
7307 CAAATCCTAA
* *
7317 TTCTGAAAATCTTCTTGAAAAATCGTCTTCCAATTGACTTTTGAATATCTAAATATGATAAACCT
1 TTCTGAAAATCTTCTTGAAAAATCGTCTTCCAATTGACTTCTGAAAATCTAAATATGATAAACCT
7382 TCTTCTGGTTAGC
66 TCTTCTGGTTAGC
* * ** *
7395 TTCTGAAAATCTTTTTTGAAATAATCGTCTTCCGATTGACTTCTGAAAATCTATTTCTGATAAAC
1 TTCTGAAAATC-TTCTTGAAA-AATCGTCTTCCAATTGACTTCTGAAAATCTAAATATGATAAAC
7460 CTTCTT
64 CTTCTT
7466 TCGGCATAAC
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
78 11 0.18
79 8 0.13
80 43 0.69
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.42
Consensus pattern (78 bp):
TTCTGAAAATCTTCTTGAAAAATCGTCTTCCAATTGACTTCTGAAAATCTAAATATGATAAACCT
TCTTCTGGTTAGC
Found at i:7743 original size:66 final size:65
Alignment explanation
Indices: 7478--8112 Score: 216
Period size: 67 Copynumber: 9.5 Consensus size: 65
7468 GGCATAACTC
** * * * * *
7478 TTAACAAGATCATCTTCTTATTAACTTCTGAAGA-TCATTTTTAAGTAATCATCTTCCGATCAAT
1 TTAACAAGATCATCTTCCGATCAACTTCTGAAAACTC-TTTCT-AGCAAACATCTTCCGATCAAT
*
7542 CTC
64 -TT
* * * * * * *
7545 TAAACAAGATCATCTTCCGATC-ACTTTCT-AAAATTTCTCTCTAGTAAACAGCCTTCTGGTCAA
1 TTAACAAGATCATCTTCCGATCAAC-TTCTGAAAA-CTCTTTCTAGCAAACA-TCTTCCGATCAA
7608 TTT
63 TTT
* * * * * ** * *
7611 CTAAACAAGATCGTCTTCCGATCAACTTCTGTAAA-TCTCTCCGAG-AAATTGTCTT-CTAGTGT
1 -TTAACAAGATCATCTTCCGATCAACTTCTGAAAACTCT-TTCTAGCAAA-CATCTTCCGA-T-C
7673 AATTT
61 AATTT
* * * * *
7678 TTAACAAGATCATCTTCTGATCAACTTCTTAAAACTCTTTCTTGGAAACCATCTTCCGATGAATT
1 TTAACAAGATCATCTTCCGATCAACTTCTGAAAACTCTTTCTAGCAAA-CATCTTCCGATCAATT
7743 T
65 T
** * * * *
7744 CTTAATGAGATCA-CTTTCCAATCAACTTCTGAAAATTCTTTCTAGCAAACGTCTTCCGGTCAAT
1 -TTAACAAGATCATC-TTCCGATCAACTTCTGAAAACTCTTTCTAGCAAACATCTTCCGATCAAT
*
7808 CTA
64 -TT
* * ** * * * * * *
7811 TGAACAAGGTCATCTTCCGATCAACTTCTGAAATTTCTATCTGAGGAACCTTCTT-CTAGCCAAT
1 TTAACAAGATCATCTTCCGATCAACTTCTGAAAACTCTTTCT-AGCAAACATCTTCCGA-TCAAT
7875 TT
64 TT
* * * * * * * * *
7877 CTAAATAAGATCGTCTTCCAATCGATTTCTGAAAACTCTTTCTAAGAAAACCGTCTT-CTAGT-A
1 -TTAACAAGATCATCTTCCGATCAACTTCTGAAAACTCTTTCT-AGCAAA-CATCTTCCGA-TCA
7940 TATTT
62 -ATTT
** * * * * * * *
7945 CTTAATGAGATCGTCTTCCAATCAACTTCTAAAAACACTTTCTTGGAAACAATCTTTCGATGC-A
1 -TTAACAAGATCATCTTCCGATCAACTTCTGAAAACTCTTTCTAGCAAAC-ATCTTCCGAT-CAA
8009 TTT
63 TTT
** * * * * * * *
8012 CTTAATTAGATC-GCTTTCCAAACAACTTCTGAAAATTCCTTCTAGCAAACCGTCTT-CAAGTCA
1 -TTAACAAGATCATC-TTCCGATCAACTTCTGAAAACTCTTTCTAGCAAA-CATCTTCCGA-TCA
*
8075 ATCTA
62 AT-TT
* * *
8080 TGAACAAGATCGTCTTCTGATCAACTTCTGAAA
1 TTAACAAGATCATCTTCCGATCAACTTCTGAAA
8113 TTTCTATCTA
Statistics
Matches: 428, Mismatches: 107, Indels: 66
0.71 0.18 0.11
Matches are distributed among these distances:
66 113 0.26
67 251 0.59
68 64 0.15
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.36
Consensus pattern (65 bp):
TTAACAAGATCATCTTCCGATCAACTTCTGAAAACTCTTTCTAGCAAACATCTTCCGATCAATTT
Found at i:7768 original size:67 final size:67
Alignment explanation
Indices: 7606--8319 Score: 406
Period size: 67 Copynumber: 10.7 Consensus size: 67
7596 CCTTCTGGTC
* * * * * * ** *
7606 AATTTCTAAACAAGATCGTCTTCCGATCAACTTCTGTAAA-TCTCTC-CGAGAAATTGTCTT-CT
1 AATTTCTTAATAAGATCGTCTTCCAATCAACTTCTGAAAACTCTTTCTAG-GAAACCGTCTTCCG
7668 AGTG
65 A-TG
* * ** * * *
7672 TAATTT-TTAACAAGATCATCTTCTGATCAACTTCTTAAAACTCTTTCTTGGAAACCATCTTCCG
1 -AATTTCTTAATAAGATCGTCTTCCAATCAACTTCTGAAAACTCTTTCTAGGAAACCGTCTTCCG
7736 ATG
65 ATG
* * * *
7739 AATTTCTTAATGAGATC-ACTTTCCAATCAACTTCTGAAAATTCTTTCTAGCAAA-CGTCTTCCG
1 AATTTCTTAATAAGATCGTC-TTCCAATCAACTTCTGAAAACTCTTTCTAGGAAACCGTCTTCCG
* *
7802 GTC
65 ATG
* * * * * * * ** * * *
7805 AATCTATGAACAAGGTCATCTTCCGATCAACTTCTGAAATTTCTATCTGAGG-AACCTTCTT-CT
1 AATTTCTTAATAAGATCGTCTTCCAATCAACTTCTGAAAACTCTTTCT-AGGAAACCGTCTTCCG
7868 A-G
65 ATG
* * * *
7870 CCAATTTCTAAATAAGATCGTCTTCCAATCGATTTCTGAAAACTCTTTCTAAGAAAACCGTCTT-
1 --AATTTCTTAATAAGATCGTCTTCCAATCAACTTCTGAAAACTCTTTCT-AGGAAACCGTCTTC
*
7934 CTA-G
63 CGATG
* * * * ** *
7938 TATATTTCTTAATGAGATCGTCTTCCAATCAACTTCTAAAAACACTTTCTTGGAAACAATCTTTC
1 -A-ATTTCTTAATAAGATCGTCTTCCAATCAACTTCTGAAAACTCTTTCTAGGAAACCGTCTTCC
8003 GATG
64 GATG
* * * * * * *
8007 CATTTCTTAATTAGATCG-CTTTCCAAACAACTTCTGAAAATTCCTTCTAGCAAACCGTCTT-CA
1 AATTTCTTAATAAGATCGTC-TTCCAATCAACTTCTGAAAACTCTTTCTAGGAAACCGTCTTCCG
*
8070 AGTC
65 A-TG
* * * * ** ** * * **
8074 AATCTATGAACAAGATCGTCTTCTGATCAACTTCTGAAATTTCTATCTAAGG-AACCTTCTTTTG
1 AATTTCTTAATAAGATCGTCTTCCAATCAACTTCTGAAAACTCTTTCT-AGGAAACCGTCTTCCG
*
8138 -GG
65 ATG
* * * * * *
8140 CAATTTCTAAATAAGATCGTCTTCCAATCGATTTCTAAAAACTCTTTCTAAGAAAACTGTCTTCC
1 -AATTTCTTAATAAGATCGTCTTCCAATCAACTTCTGAAAACTCTTTCT-AGGAAACCGTCTTCC
8205 -A-G
64 GATG
* * * * *
8207 TA-TTCTTAATGAGATCGTCTTCCAATCAACTTCTAAAAACTCTTTCTTGGAAATCGTCTTCCGA
1 AATTTCTTAATAAGATCGTCTTCCAATCAACTTCTGAAAACTCTTTCTAGGAAACCGTCTTCCGA
8271 TG
66 TG
* * * * *
8273 TATTTCTTAATGAGATAGTTTTCCAATCAACTTCT--AAACGCTTTCTA
1 AATTTCTTAATAAGATCGTCTTCCAATCAACTTCTGAAAACTCTTTCTA
8320 AAAAACCATC
Statistics
Matches: 496, Mismatches: 126, Indels: 52
0.74 0.19 0.08
Matches are distributed among these distances:
64 11 0.02
65 52 0.10
66 90 0.18
67 274 0.55
68 68 0.14
69 1 0.00
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (67 bp):
AATTTCTTAATAAGATCGTCTTCCAATCAACTTCTGAAAACTCTTTCTAGGAAACCGTCTTCCGA
TG
Found at i:7868 original size:200 final size:200
Alignment explanation
Indices: 7476--7978 Score: 461
Period size: 200 Copynumber: 2.5 Consensus size: 200
7466 TCGGCATAAC
* * * * * * *
7476 TCTTAACAAGATCATCTTCTTATTAACTTCTGAAGA-TCATTT-TTAAGTAATCATCTTCCGATC
1 TCTTAACAAGATCATCTTCTAATCAACTTCTGAAAACTC-TTTCTT-GGAAACCATCTTCCGATG
* * ** * * *
7539 AATCTCTAAACAAGATCATCTTCCGATC-ACTTTCTAAAATTTCTCTCTAGTAAACAGCCTTCTG
64 AATTTCTTAATGAGATCATCTTCCAATCAAC-TTCTAAAATTTCTCTCTAGCAAACAGCCTTCCG
* * * * *
7603 GTCAATTTCTAAACAAGATCGTCTTCCGATCAACTTCTGTAAATCTCTCCGAGAAATTGTCTTCT
128 GTCAATCTATAAACAAGATCATCTTCCGATCAACTTCTGTAAATCTATCCGAGAAACTGTCTTCT
**
7668 AGTGTAATT
193 AG-CCAATT
* *
7677 T-TTAACAAGATCATCTTCTGATCAACTTCTTAAAACTCTTTCTTGGAAACCATCTTCCGATGAA
1 TCTTAACAAGATCATCTTCTAATCAACTTCTGAAAACTCTTTCTTGGAAACCATCTTCCGATGAA
* *
7741 TTTCTTAATGAGATCA-CTTTCCAATCAACTTCTGAAAA-TTCTTTCTAGCAAAC-GTCTTCCGG
66 TTTCTTAATGAGATCATC-TTCCAATCAACTTCT-AAAATTTCTCTCTAGCAAACAGCCTTCCGG
* * * *
7803 TCAATCTATGAACAAGGTCATCTTCCGATCAACTTCTG-AAATTTCTATCTGAGGAACCT-TCTT
129 TCAATCTATAAACAAGATCATCTTCCGATCAACTTCTGTAAA--TCTATCCGA-GAAACTGTCTT
7866 CTAGCCAATT
191 CTAGCCAATT
* * * * * * * * * *
7876 TCTAAATAAGATCGTCTTCCAATCGATTTCTGAAAACTCTTTCTAAGAAAACCGTCTT-CTA-GT
1 TCTTAACAAGATCATCTTCTAATCAACTTCTGAAAACTCTTTCT-TGGAAACCATCTTCCGATG-
*
7939 ATATTTCTTAATGAGATCGTCTTCCAATCAACTTCTAAAA
64 A-ATTTCTTAATGAGATCATCTTCCAATCAACTTCTAAAA
7979 ACACTTTCTT
Statistics
Matches: 248, Mismatches: 41, Indels: 27
0.78 0.13 0.09
Matches are distributed among these distances:
198 3 0.01
199 47 0.19
200 141 0.57
201 56 0.23
202 1 0.00
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.36
Consensus pattern (200 bp):
TCTTAACAAGATCATCTTCTAATCAACTTCTGAAAACTCTTTCTTGGAAACCATCTTCCGATGAA
TTTCTTAATGAGATCATCTTCCAATCAACTTCTAAAATTTCTCTCTAGCAAACAGCCTTCCGGTC
AATCTATAAACAAGATCATCTTCCGATCAACTTCTGTAAATCTATCCGAGAAACTGTCTTCTAGC
CAATT
Found at i:8146 original size:134 final size:133
Alignment explanation
Indices: 7537--8240 Score: 462
Period size: 133 Copynumber: 5.3 Consensus size: 133
7527 CATCTTCCGA
* * * * * * *** *
7537 TCAATCTCTAAACAAGATCATCTTCCGATC-ACTTTCTAAAATTTCTCTCTAGTAAACAGCCTTC
1 TCAATCTATGAACAAGATCGTCTTCCGATCAAC-TTCTGAAATTTCTATCTAG-GAACCTTCTTT
* * * * * * **
7601 TGGTCAATTTCTAAACAAGATCGTCTTCCGATCAACTTCTGTAAA-TCTCTCCGAG-AAATTGTC
64 TGGGCAATTTCTAAATAAGATCGTCTTCCAATCAACTTCTGAAAATTCT-TTCTAGCAAACCGTC
*
7664 TTCTAG
128 TTCAAG
* * * * * * ** * * * *
7670 TGTAAT-TTTTAACAAGATCATCTTCTGATCAACTTCTTAAAACTCTTTCTTGGAAACCATCTTC
1 T-CAATCTATGAACAAGATCGTCTTCCGATCAACTTCTGAAATTTCTATCTAGG-AACCTTCTTT
* * * * *
7734 CGATG-AATTTCTTAATGAGATC-ACTTTCCAATCAACTTCTGAAAATTCTTTCTAGCAAA-CGT
64 TG-GGCAATTTCTAAATAAGATCGTC-TTCCAATCAACTTCTGAAAATTCTTTCTAGCAAACCGT
**
7796 CTTCCGG
127 CTTCAAG
* * *
7803 TCAATCTATGAACAAGGTCATCTTCCGATCAACTTCTGAAATTTCTATCTGAGGAACCTTCTTCT
1 TCAATCTATGAACAAGATCGTCTTCCGATCAACTTCTGAAATTTCTATCT-AGGAACCTTCTTTT
* * * * * *
7868 AGCCAATTTCTAAATAAGATCGTCTTCCAATCGATTTCTGAAAACTCTTTCTAAGAAAACCGTCT
65 GGGCAATTTCTAAATAAGATCGTCTTCCAATCAACTTCTGAAAATTCTTTCT-AGCAAACCGTCT
*
7933 TCTAG
129 TCAAG
* * * ** * * *** * * **
7938 T-ATATTTCTTAATGAGATCGTCTTCCAATCAACTTCTAAAAACACTTTCTTGGAAACAATCTTT
1 TCA-ATCTATGAACAAGATCGTCTTCCGATCAACTTCTGAAATTTCTATCTAGG-AACCTTCTTT
* * * * * *
8002 CGATGC-ATTTCTTAATTAGATCG-CTTTCCAAACAACTTCTGAAAATTCCTTCTAGCAAACCGT
64 TG-GGCAATTTCTAAATAAGATCGTC-TTCCAATCAACTTCTGAAAATTCTTTCTAGCAAACCGT
8065 CTTCAAG
127 CTTCAAG
*
8072 TCAATCTATGAACAAGATCGTCTTCTGATCAACTTCTGAAATTTCTATCTAAGGAACCTTCTTTT
1 TCAATCTATGAACAAGATCGTCTTCCGATCAACTTCTGAAATTTCTATCT-AGGAACCTTCTTTT
* * * * * *
8137 GGGCAATTTCTAAATAAGATCGTCTTCCAATCGATTTCTAAAAACTCTTTCTAAGAAAACTGTCT
65 GGGCAATTTCTAAATAAGATCGTCTTCCAATCAACTTCTGAAAATTCTTTCT-AGCAAACCGTCT
*
8202 TCCAG
129 TCAAG
* ** *
8207 T-ATTCT-T-AATGAGATCGTCTTCCAATCAACTTCT
1 TCAATCTATGAACAAGATCGTCTTCCGATCAACTTCT
8241 AAAAACTCTT
Statistics
Matches: 435, Mismatches: 114, Indels: 45
0.73 0.19 0.08
Matches are distributed among these distances:
132 27 0.06
133 176 0.40
134 124 0.29
135 107 0.25
136 1 0.00
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (133 bp):
TCAATCTATGAACAAGATCGTCTTCCGATCAACTTCTGAAATTTCTATCTAGGAACCTTCTTTTG
GGCAATTTCTAAATAAGATCGTCTTCCAATCAACTTCTGAAAATTCTTTCTAGCAAACCGTCTTC
AAG
Found at i:8157 original size:269 final size:266
Alignment explanation
Indices: 7537--8307 Score: 980
Period size: 266 Copynumber: 2.9 Consensus size: 266
7527 CATCTTCCGA
* * * * * ***
7537 TCAATCTCTAAACAAGATCATCTTCCGATC-ACTTTCTAAAATTTCTCTCT-AGTAAACAGCCTT
1 TCAATCTATGAACAAGATCATCTTCCGATCAAC-TTCTGAAATTTCTATCTAAG-GAACCTTCTT
* * * * * * * * ** *
7600 CTGGTCAATTTCTAAACAAGATCGTCTTCCGATCAACTTCTGTAAA-TCTCTCCGAG-AAATTGT
64 CTAGCCAATTTCTAAATAAGATCGTCTTCCAATCGATTTCTGAAAACTCTTTCTAAGAAAACTGT
** * ** *
7663 CTTCTAGTGTAATTT-TTAACAAGATCATCTTCTGATCAACTTCTTAAAACTCTTTCTTGGAAAC
129 CTTCTAGT-T-ATTTCTTAATGAGATCGTCTTCCAATCAACTTCTAAAAACTCTTTCTTGGAAA-
* *
7727 CATCTTCCGATGAATTTCTTAATGAGATCACTTTCCAATCAACTTCTGAAAATTCTTTCTAGCAA
191 CATCTTCCGATGAATTTCTTAATGAGATCGCTTTCCAATCAACTTCTGAAAATTCCTTCTAGCAA
**
7792 ACGTCTTCCGG
256 ACGTCTTCAAG
* *
7803 TCAATCTATGAACAAGGTCATCTTCCGATCAACTTCTGAAATTTCTATCTGAGGAACCTTCTTCT
1 TCAATCTATGAACAAGATCATCTTCCGATCAACTTCTGAAATTTCTATCTAAGGAACCTTCTTCT
*
7868 AGCCAATTTCTAAATAAGATCGTCTTCCAATCGATTTCTGAAAACTCTTTCTAAGAAAACCGTCT
66 AGCCAATTTCTAAATAAGATCGTCTTCCAATCGATTTCTGAAAACTCTTTCTAAGAAAACTGTCT
*
7933 TCTAGTATATTTCTTAATGAGATCGTCTTCCAATCAACTTCTAAAAACACTTTCTTGGAAACAAT
131 TCTAGT-TATTTCTTAATGAGATCGTCTTCCAATCAACTTCTAAAAACTCTTTCTTGGAAAC-AT
* * * *
7998 CTTTCGATGCATTTCTTAATTAGATCGCTTTCCAAACAACTTCTGAAAATTCCTTCTAGCAAACC
194 CTTCCGATGAATTTCTTAATGAGATCGCTTTCCAATCAACTTCTGAAAATTCCTTCTAGCAAA-C
8063 GTCTTCAAG
258 GTCTTCAAG
* * *
8072 TCAATCTATGAACAAGATCGTCTTCTGATCAACTTCTGAAATTTCTATCTAAGGAACCTTCTTTT
1 TCAATCTATGAACAAGATCATCTTCCGATCAACTTCTGAAATTTCTATCTAAGGAACCTTCTTCT
* * *
8137 GGGCAATTTCTAAATAAGATCGTCTTCCAATCGATTTCTAAAAACTCTTTCTAAGAAAACTGTCT
66 AGCCAATTTCTAAATAAGATCGTCTTCCAATCGATTTCTGAAAACTCTTTCTAAGAAAACTGTCT
* *
8202 TCCAG-TA-TTCTTAATGAGATCGTCTTCCAATCAACTTCTAAAAACTCTTTCTTGGAAATCGTC
131 TCTAGTTATTTCTTAATGAGATCGTCTTCCAATCAACTTCTAAAAACTCTTTCTTGGAAA-CATC
* * *
8265 TTCCGATGTATTTCTTAATGAGATAGTTTTCCAATCAACTTCT
195 TTCCGATGAATTTCTTAATGAGATCGCTTTCCAATCAACTTCT
8308 AAACGCTTTC
Statistics
Matches: 442, Mismatches: 55, Indels: 16
0.86 0.11 0.03
Matches are distributed among these distances:
266 176 0.40
267 19 0.04
268 114 0.26
269 133 0.30
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (266 bp):
TCAATCTATGAACAAGATCATCTTCCGATCAACTTCTGAAATTTCTATCTAAGGAACCTTCTTCT
AGCCAATTTCTAAATAAGATCGTCTTCCAATCGATTTCTGAAAACTCTTTCTAAGAAAACTGTCT
TCTAGTTATTTCTTAATGAGATCGTCTTCCAATCAACTTCTAAAAACTCTTTCTTGGAAACATCT
TCCGATGAATTTCTTAATGAGATCGCTTTCCAATCAACTTCTGAAAATTCCTTCTAGCAAACGTC
TTCAAG
Found at i:11279 original size:2 final size:2
Alignment explanation
Indices: 11267--11314 Score: 78
Period size: 2 Copynumber: 23.5 Consensus size: 2
11257 TCAGTATGCA
*
11267 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11310 AT AT A
1 AT AT A
11315 AAAACAACAT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 41 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Done.