Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016759.1 Corchorus olitorius cultivar O-4 contig16792, 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: 25196
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:2992 original size:47 final size:46
Alignment explanation
Indices: 2939--3997 Score: 1042
Period size: 47 Copynumber: 22.6 Consensus size: 46
2929 GTAAACAGTA
*
2939 ATTAGTTTAATTCTAGGTAATTAAACTAAAGAGTAAAAGAAGAAGAG
1 ATTAGTTTAATTCTGGGTAATTAAACT-AAGAGTAAAAGAAGAAGAG
** *
2986 GGTAGTTAAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGAG
1 ATTAGTTTAATTCTGGGTAATTAAACT-AAGAGTAAAAGAAGAAGAG
** * *
3033 GGTAGTTTAATTCTGGGTAATTAAACTAAAAAGAGCAAGAA-AAGAAGAA
1 ATTAGTTTAATTCTGGGTAATTAAACT---AAGAGTAA-AAGAAGAAGAG
* * *
3082 AATAGTTTAATTATTGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAG
1 ATTAGTTTAATTCTGGGTAATTAAACT-AAGAGTAAAAGAAGAAG-----AG
* * * * *
3134 AGGCTAGTTTAGTTCTTGGTAATTAAATTAAAAAGT--AAGAAGAA-A-
1 A--TTAGTTTAATTCTGGGTAATTAAACT-AAGAGTAAAAGAAGAAGAG
* * * *
3179 A-GAGTTTAATTCCGGGTAATTAAACTAAAAAGTAAGAGAAGAAG-G
1 ATTAGTTTAATTCTGGGTAATTAAACT-AAGAGTAAAAGAAGAAGAG
* *** * * *
3224 AAATAGTTTAATTCCAAGTAATTAAACTAAAAAGTAAGAGAAGAAGAA
1 -ATTAGTTTAATTCTGGGTAATTAAACT-AAGAGTAAAAGAAGAAGAG
** * *
3272 AAGAATTTAATTC-GGGTAATTAAACTAAAGAGCAAGAA-AAGAAGA-
1 ATTAGTTTAATTCTGGGTAATTAAACT-AAGAGTAA-AAGAAGAAGAG
* * * *
3317 ATACAGTTTAATTCGGGGTAATTAAACTAAAGAGCAAGAA-AAGAAGAA
1 AT-TAGTTTAATTCTGGGTAATTAAACT-AAGAGTAA-AAGAAGAAGAG
** * *
3365 AACAGTTTAATTCTGGGAAATTAAACTAAGTAGCAAAAGAAGAAGAG
1 ATTAGTTTAATTCTGGGTAATTAAACTAAG-AGTAAAAGAAGAAGAG
* * * * *
3412 GTTAGTTTAATTTTGGGTAATTAAACTAAACAGTGAAAAAAAGGAGTA-
1 ATTAGTTTAATTCTGGGTAATTAAACT-AAGAGT-AAAAGAAGAAG-AG
3460 ATTAGTTTAATTCTGGGTAATTAAACTAAGTAGTAAAAGAA-AACGAG
1 ATTAGTTTAATTCTGGGTAATTAAACTAAG-AGTAAAAGAAGAA-GAG
** *
3507 ATTAGTTTAATTCCAGGTAAGTAAACT-A-AGTAAAAGGAAG-AGAG
1 ATTAGTTTAATTCTGGGTAATTAAACTAAGAGTAAAA-GAAGAAGAG
* * *
3551 ATGAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAATAAGAG
1 ATTAGTTTAATTCTGGGTAATTAAACTAAG-AGTAAAAGAAGAAGAG
* * ** *
3598 GTTAGTTTGATTCCAGGTAATTAAACT-A-AGTAAAAGGAGAAGAG
1 ATTAGTTTAATTCTGGGTAATTAAACTAAGAGTAAAAGAAGAAGAG
3642 ATTAGTTTAATTCTGGGTAATTAAACTAAGTAGTAAAAGAAGAAGAG
1 ATTAGTTTAATTCTGGGTAATTAAACTAAG-AGTAAAAGAAGAAGAG
*
3689 ATTAGTTTAATTCTGGGTAATTAAACTAAGTAGTAAAAGAAGAAGAA
1 ATTAGTTTAATTCTGGGTAATTAAACTAAG-AGTAAAAGAAGAAGAG
*
3736 ATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAG
1 ATTAGTTTAATTCTGGGTAATTAAACTAAG-AGTAAAAGAAGAAGAG
*
3783 ATTAGTTTAATTCTGGGTAATTAAACTAAGTAGT--AAGAAGAAGAA
1 ATTAGTTTAATTCTGGGTAATTAAACTAAG-AGTAAAAGAAGAAGAG
*
3828 ATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAG
1 ATTAGTTTAATTCTGGGTAATTAAACTAAG-AGTAAAAGAAGAAGAG
* *
3875 ATTAGTTTAATTCTAGGTAGTTAAACTAAGTAGTAAAAGAAGAAGAG
1 ATTAGTTTAATTCTGGGTAATTAAACTAAG-AGTAAAAGAAGAAGAG
* *
3922 ATTAGCTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAG
1 ATTAGTTTAATTCTGGGTAATTAAACTAAG-AGTAAAAGAAGAAGAG
***
3969 ATTAGTTTAATTCCAAGTAATTAAACTAA
1 ATTAGTTTAATTCTGGGTAATTAAACTAA
3998 AGAAGAGGTT
Statistics
Matches: 884, Mismatches: 87, Indels: 82
0.84 0.08 0.08
Matches are distributed among these distances:
42 27 0.03
44 78 0.09
45 51 0.06
46 50 0.06
47 559 0.63
48 40 0.05
49 39 0.04
50 2 0.00
52 10 0.01
54 28 0.03
ACGTcount: A:0.47, C:0.06, G:0.20, T:0.27
Consensus pattern (46 bp):
ATTAGTTTAATTCTGGGTAATTAAACTAAGAGTAAAAGAAGAAGAG
Found at i:3583 original size:186 final size:185
Alignment explanation
Indices: 2886--3998 Score: 1057
Period size: 186 Copynumber: 5.9 Consensus size: 185
2876 TAAACAGAGG
* *
2886 TTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAGGAGTAAACAGTAATTAGTTTAATT
1 TTAGTTTAATTCTGGGTAATTAAACTAAGTAGT--AA-AA-GA--AAAGAG--ATTAGTTTAATT
* ** * *
2951 CTAGGTAATTAAACTAAAG-AGTAAAAGAAGAAG-AGGGTAGTTAAATTCTGGGTAATTAAACTA
58 CTAGGTAATTAAACT-AAGTAG-AAAGGAAGAAGAAATG-AGTTTAATTCTAGGTAATTAAACT-
** ** *
3014 AAG-AGTAAAAGAAGAAGAGGGTAGTTTAATTCTGGGTAATTAAACTAAAAAG-AGCAAGAAAAG
119 AAGTAGTAAAAGAAGAAGAGATTAGTTTAATTCCAGGTAATTAAACTAAAAAGTA--AA-AGAAG
3077 AAGAAA
181 AAG-AA
* * * * *
3083 ATAGTTTAATTATTGGTAATTAAACTAAAG-AGTAAAAGAAGAAGTAAACAGAGGCTAGTTTAGT
1 TTAGTTTAATTCTGGGTAATTAAACT-AAGTAGTAAAAGAA-AAG-----AGA--TTAGTTTAAT
* * * * ** *
3147 TCTTGGTAATTAAA-T---TAAAAAGTAAGAAGAAAAGAGTTTAATTCCGGGTAATTAAACTAAA
57 TCTAGGTAATTAAACTAAGTAGAAAGGAAGAAGAAATGAGTTTAATTCTAGGTAATTAAACTAAG
* * * * *
3208 AAGTAAGAGAAGAAG-GAAATAGTTTAATTCCAAGTAATTAAACTAAAAAGTAAGAGAAGAAGAA
122 TAGTAAAAGAAGAAGAG-ATTAGTTTAATTCCAGGTAATTAAACTAAAAAGTAAAAGAAGAAGAA
* * * *
3272 -AAGAATTTAATTC-GGGTAATTAAACTAA--AG-AGCAAGAAAAGAAGAATACAGTTTAATTCG
1 TTAG--TTTAATTCTGGGTAATTAAACTAAGTAGTA-AAAGAAAAG-AG-AT-TAGTTTAATTCT
* * * ** * *
3332 GGGTAATTAAACTAAAG-AGCAAGAAAAGAAGAAAACAGTTTAATTCTGGGAAATTAAACTAAGT
60 AGGTAATTAAACT-AAGTAGAAAG-GAAGAAGAAATGAGTTTAATTCTAGGTAATTAAACTAAGT
* * *** * * *
3396 AGCAAAAGAAGAAGAGGTTAGTTTAATTTTGGGTAATTAAACTAAACAGTGAAAAAAAGGAGTAA
123 AGTAAAAGAAGAAGAGATTAGTTTAATTCCAGGTAATTAAACTAAAAAGT-AAAAGAAGAAG-AA
*
3461 TTAGTTTAATTCTGGGTAATTAAACTAAGTAGTAAAAGAAAACGAGATTAGTTTAATTCCAGGTA
1 TTAGTTTAATTCTGGGTAATTAAACTAAGTAGTAAAAGAAAA-GAGATTAGTTTAATTCTAGGTA
* *
3526 AGTAAACTAAGTA-AAAGGAAG-AGAGATGAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAA
65 ATTAAACTAAGTAGAAAGGAAGAAGAAATGAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAA
* * * *
3589 GAATAAGAGGTTAGTTTGATTCCAGGTAATTAAACT---AAGTAAAAGGAGAAGAGA
130 GAAGAAGAGATTAGTTTAATTCCAGGTAATTAAACTAAAAAGTAAAAGAAGAAGA-A
*
3643 TTAGTTTAATTCTGGGTAATTAAACTAAGTAGTAAAAGAAGAAGAGATTAGTTTAATTCTGGGTA
1 TTAGTTTAATTCTGGGTAATTAAACTAAGTAGTAAAAGAA-AAGAGATTAGTTTAATTCTAGGTA
* *
3708 ATTAAACTAAGTAGTAAAAGAAGAAGAAATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAA
65 ATTAAACTAAGTAG-AAAGGAAGAAGAAATGAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAA
** **
3773 AGAAGAAGAGATTAGTTTAATTCTGGGTAATTAAACTAAGTAGT--AAGAAGAAGAAA
129 AGAAGAAGAGATTAGTTTAATTCCAGGTAATTAAACTAAAAAGTAAAAGAAGAAG-AA
*
3829 TTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAGATTAGTTTAATTCTAGGTA
1 TTAGTTTAATTCTGGGTAATTAAACTAAGTAGTAAAAGAA-AAGAGATTAGTTTAATTCTAGGTA
* * * * *
3894 GTTAAACTAAGTAGTAAAAGAAGAAGAGATTAGCTTAATTCTAGGTAATTAAACTAAGTAGTAAA
65 ATTAAACTAAGTAG-AAAGGAAGAAGAAATGAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAA
*
3959 AGAAGAAGAGATTAGTTTAATTCCAAGTAATTAAACTAAA
129 AGAAGAAGAGATTAGTTTAATTCCAGGTAATTAAACTAAA
3999 GAAGAGGTTA
Statistics
Matches: 773, Mismatches: 99, Indels: 99
0.80 0.10 0.10
Matches are distributed among these distances:
181 1 0.00
182 102 0.13
183 7 0.01
184 7 0.01
185 71 0.09
186 245 0.32
187 84 0.11
188 30 0.04
189 53 0.07
190 18 0.02
191 16 0.02
192 76 0.10
193 6 0.01
194 2 0.00
195 3 0.00
196 1 0.00
197 49 0.06
198 2 0.00
ACGTcount: A:0.47, C:0.06, G:0.20, T:0.27
Consensus pattern (185 bp):
TTAGTTTAATTCTGGGTAATTAAACTAAGTAGTAAAAGAAAAGAGATTAGTTTAATTCTAGGTAA
TTAAACTAAGTAGAAAGGAAGAAGAAATGAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAG
AAGAAGAGATTAGTTTAATTCCAGGTAATTAAACTAAAAAGTAAAAGAAGAAGAA
Found at i:4001 original size:36 final size:36
Alignment explanation
Indices: 3961--4033 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
3951 GTAGTAAAAG
* *
3961 AAGAAGAGATTAGTTTAATTCCAAGTAATTAAACTA
1 AAGAAGAGATTAGTTCAATTCCAAGAAATTAAACTA
* * *
3997 AAGAAGAGGTTAGTTCAATTCTAGGAAATTAAACTA
1 AAGAAGAGATTAGTTCAATTCCAAGAAATTAAACTA
4033 A
1 A
4034 GTAGCAAATG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.47, C:0.08, G:0.16, T:0.29
Consensus pattern (36 bp):
AAGAAGAGATTAGTTCAATTCCAAGAAATTAAACTA
Found at i:6607 original size:22 final size:21
Alignment explanation
Indices: 6577--6722 Score: 80
Period size: 22 Copynumber: 6.6 Consensus size: 21
6567 GGGCGTGACA
* *
6577 TTGACAACCGCACCGTGAAAAT
1 TTGATAACC-CACTGTGAAAAT
* *
6599 TTGATAACCTCATTATG-AAAT
1 TTGATAACC-CACTGTGAAAAT
*
6620 TTCGATAACCTATCTGTGAAAAT
1 TT-GATAACCCA-CTGTGAAAAT
* *
6643 TTGATAACCTCATTATG-AAAT
1 TTGATAACC-CACTGTGAAAAT
* * *
6664 TTCGATAACCTCCCTATGCAAAT
1 TT-GATAACC-CACTGTGAAAAT
* * *
6687 TTGATAACGACTCTGTGAAATT
1 TTGATAAC-CCACTGTGAAAAT
6709 TTGATAACCACACT
1 TTGATAACC-CACT
6723 AATCAATTTG
Statistics
Matches: 96, Mismatches: 20, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
21 13 0.14
22 70 0.73
23 13 0.14
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.32
Consensus pattern (21 bp):
TTGATAACCCACTGTGAAAAT
Found at i:6654 original size:44 final size:44
Alignment explanation
Indices: 6591--6694 Score: 172
Period size: 44 Copynumber: 2.4 Consensus size: 44
6581 CAACCGCACC
*
6591 GTGAAAATTTGATAACCTCATTATGAAATTTCGATAACCTATCT
1 GTGAAAATTTGATAACCTCATTATGAAATTTCGATAACCTACCT
*
6635 GTGAAAATTTGATAACCTCATTATGAAATTTCGATAACCTCCCT
1 GTGAAAATTTGATAACCTCATTATGAAATTTCGATAACCTACCT
* *
6679 ATGCAAATTTGATAAC
1 GTGAAAATTTGATAAC
6695 GACTCTGTGA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 56 1.00
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.35
Consensus pattern (44 bp):
GTGAAAATTTGATAACCTCATTATGAAATTTCGATAACCTACCT
Found at i:6702 original size:66 final size:65
Alignment explanation
Indices: 6595--6740 Score: 172
Period size: 66 Copynumber: 2.2 Consensus size: 65
6585 CGCACCGTGA
* *
6595 AAATTTGATAACCTCATTATGAAATTTCGATAACCTATCTGTGAAAATTTGATAACCTCATTATG
1 AAATTTGATAACCTCACTATGAAATTTCGATAACCGATCTGTGAAAATTTGATAACCTCATTATG
* * *
6660 AAATTTCGATAACCTCCCTATGCAAATTT-GATAA-CGACTCTGTGAAATTTTGATAACCACACT
1 AAATTT-GATAACCTCACTATG-AAATTTCGATAACCGA-TCTGTGAAAATTTGATAACCTCA-T
*
6723 AAT-
62 TATG
*
6726 CAATTTGATAACCTC
1 AAATTTGATAACCTC
6741 TTAGTGTGAA
Statistics
Matches: 70, Mismatches: 7, Indels: 8
0.82 0.08 0.09
Matches are distributed among these distances:
65 17 0.24
66 44 0.63
67 9 0.13
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.34
Consensus pattern (65 bp):
AAATTTGATAACCTCACTATGAAATTTCGATAACCGATCTGTGAAAATTTGATAACCTCATTATG
Found at i:6706 original size:44 final size:43
Alignment explanation
Indices: 6592--6717 Score: 155
Period size: 44 Copynumber: 2.9 Consensus size: 43
6582 AACCGCACCG
* *
6592 TGAAAATTTGATAACCTCATTATGAAATTTCGATAACCTATCTG
1 TGAAAATTTGATAACCTCA-TATGAAATTTCGATAACCTACCTA
*
6636 TGAAAATTTGATAACCTCATTATGAAATTTCGATAACCTCCCTA
1 TGAAAATTTGATAACCTCA-TATGAAATTTCGATAACCTACCTA
* * *
6680 TGCAAATTTGATAACGACTC-TGTGAAATTTTGATAACC
1 TGAAAATTTGATAAC--CTCATATGAAATTTCGATAACC
6718 ACACTAATCA
Statistics
Matches: 74, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
44 71 0.96
46 3 0.04
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (43 bp):
TGAAAATTTGATAACCTCATATGAAATTTCGATAACCTACCTA
Found at i:6753 original size:66 final size:65
Alignment explanation
Indices: 6595--6759 Score: 160
Period size: 66 Copynumber: 2.5 Consensus size: 65
6585 CGCACCGTGA
* * *
6595 AAATTTGATAACCTCATTA--TGAAATTTCGATAACCTATCTGTGAAAATTTGATAACCTCATTA
1 AAATTTGATAACCTC-TTATGTGAAATTT-GATAACCGATCTGTGAAAATTTGATAACCACATAA
6658 TG
64 TG
* * *
6660 AAATTTCGATAACCTCCCTATG-CAAATTTGATAA-CGACTCTGTGAAATTTTGATAACCACACT
1 AAATTT-GATAACCT-CTTATGTGAAATTTGATAACCGA-TCTGTGAAAATTTGATAACCACA-T
6723 AAT-
62 AATG
*
6726 CAATTTGATAACCTCTTAGTGTGAAATTTTGATA
1 AAATTTGATAACCTCTTA-TGTGAAA-TTTGATA
6760 TGATACTTAT
Statistics
Matches: 82, Mismatches: 9, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
64 3 0.04
65 18 0.22
66 44 0.54
67 17 0.21
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.36
Consensus pattern (65 bp):
AAATTTGATAACCTCTTATGTGAAATTTGATAACCGATCTGTGAAAATTTGATAACCACATAATG
Found at i:7025 original size:22 final size:22
Alignment explanation
Indices: 7000--7052 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
6990 CTACAAATAT
* *
7000 TTTTCATAACCTCCCTATAAAA
1 TTTTGATAACCTCCCTAGAAAA
* * *
7022 TTTTGTTAACCTCTCTAGGAAA
1 TTTTGATAACCTCCCTAGAAAA
7044 TTTTGATAA
1 TTTTGATAA
7053 GCAGACATTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.32, C:0.19, G:0.08, T:0.42
Consensus pattern (22 bp):
TTTTGATAACCTCCCTAGAAAA
Found at i:7107 original size:22 final size:22
Alignment explanation
Indices: 7079--7206 Score: 73
Period size: 22 Copynumber: 5.8 Consensus size: 22
7069 TTACCCTCCC
7079 TATGAAATTTTGTTAACCTTCT
1 TATGAAATTTTGTTAACCTTCT
* * *
7101 TATGAAATTTT-TATAGCCATAT
1 TATGAAATTTTGT-TAACCTTCT
*
7123 TAT-AAATTTTCGATAACCTT-T
1 TATGAAATTTT-GTTAACCTTCT
* * * *
7144 GAATGCAATTTTGTTAACCTCCC
1 -TATGAAATTTTGTTAACCTTCT
* * * *
7167 TAAGAAATTTTGCTAACTATTTT
1 TATGAAATTTTGTTAAC-CTTCT
* *
7190 TATAAAATTTTGATAAC
1 TATGAAATTTTGTTAAC
7207 TACTACACTA
Statistics
Matches: 77, Mismatches: 22, Indels: 13
0.69 0.20 0.12
Matches are distributed among these distances:
21 9 0.12
22 47 0.61
23 21 0.27
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.45
Consensus pattern (22 bp):
TATGAAATTTTGTTAACCTTCT
Found at i:8245 original size:21 final size:21
Alignment explanation
Indices: 8211--8258 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
8201 AAAACAAAAG
* *
8211 AAAAAATTAGAAATTTTCAACA
1 AAAAAAATAGAAATCTTC-ACA
8233 AAAAAAATA-AAATCTTCACA
1 AAAAAAATAGAAATCTTCACA
*
8253 AGAAAA
1 AAAAAA
8259 GAGATGAGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 8 0.35
21 7 0.30
22 8 0.35
ACGTcount: A:0.65, C:0.10, G:0.04, T:0.21
Consensus pattern (21 bp):
AAAAAAATAGAAATCTTCACA
Found at i:22580 original size:18 final size:18
Alignment explanation
Indices: 22557--22596 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
22547 GCCCAAAGCG
*
22557 TGGCATCGTGTGCTCTTA
1 TGGCATCGTGCGCTCTTA
*
22575 TGGCATTGTGCGCTCTTA
1 TGGCATCGTGCGCTCTTA
22593 TGGC
1 TGGC
22597 GTTATGTGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.10, C:0.23, G:0.30, T:0.38
Consensus pattern (18 bp):
TGGCATCGTGCGCTCTTA
Found at i:22607 original size:18 final size:18
Alignment explanation
Indices: 22565--22608 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
22555 CGTGGCATCG
*
22565 TGTGCTCTTATGGCATTG
1 TGTGCTCTTATGGCATTA
* *
22583 TGCGCTCTTATGGCGTTA
1 TGTGCTCTTATGGCATTA
22601 TGTGCTCT
1 TGTGCTCT
22609 CCGCTTTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.09, C:0.20, G:0.27, T:0.43
Consensus pattern (18 bp):
TGTGCTCTTATGGCATTA
Found at i:23173 original size:59 final size:59
Alignment explanation
Indices: 23101--23214 Score: 219
Period size: 59 Copynumber: 1.9 Consensus size: 59
23091 GAATGGATAG
23101 CGTGCGACCGAGGGATGCTCGATCGTTCTTAATGCTCGTGTGGGGGATGCCCACTACGC
1 CGTGCGACCGAGGGATGCTCGATCGTTCTTAATGCTCGTGTGGGGGATGCCCACTACGC
*
23160 CGTGCGACCGAGGGATGCTCGATCGTTCTTATTGCTCGTGTGGGGGATGCCCACT
1 CGTGCGACCGAGGGATGCTCGATCGTTCTTAATGCTCGTGTGGGGGATGCCCACT
23215 CGGTCGTACG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 54 1.00
ACGTcount: A:0.14, C:0.26, G:0.34, T:0.25
Consensus pattern (59 bp):
CGTGCGACCGAGGGATGCTCGATCGTTCTTAATGCTCGTGTGGGGGATGCCCACTACGC
Found at i:23227 original size:59 final size:59
Alignment explanation
Indices: 23105--23229 Score: 207
Period size: 59 Copynumber: 2.1 Consensus size: 59
23095 GGATAGCGTG
*
23105 CGACCGAGGGATGCTCGATCGTTCTTAATGCTCGTGTGGGGGATGCCCACTACGCCGTG
1 CGACCGAGGGATGCTCGATCGTTCTTAATGCTCGTGTGGGGGATGCCCACTACGCCGTA
* *
23164 CGACCGAGGGATGCTCGATCGTTCTTATTGCTCGTGTGGGGGATGCCCACT-CGGTCGTA
1 CGACCGAGGGATGCTCGATCGTTCTTAATGCTCGTGTGGGGGATGCCCACTAC-GCCGTA
23223 CGACCGA
1 CGACCGA
23230 ATACGAAGCA
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
58 1 0.02
59 61 0.98
ACGTcount: A:0.15, C:0.27, G:0.34, T:0.24
Consensus pattern (59 bp):
CGACCGAGGGATGCTCGATCGTTCTTAATGCTCGTGTGGGGGATGCCCACTACGCCGTA
Done.