Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002650.1 Hibiscus syriacus cultivar Beakdansim tig00005416_pilon, 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: 65787
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:3752 original size:16 final size:16
Alignment explanation
Indices: 3710--3760 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
3700 AATTCAAATC
3710 GAAATTAATTTG-A-T
1 GAAATTAATTTGAACT
** *
3724 GAAAACAACTTGAACT
1 GAAATTAATTTGAACT
*
3740 GAAATTAATTTGAACC
1 GAAATTAATTTGAACT
3756 GAAAT
1 GAAAT
3761 CAACTCGAAT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
14 9 0.32
15 1 0.04
16 18 0.64
ACGTcount: A:0.47, C:0.10, G:0.14, T:0.29
Consensus pattern (16 bp):
GAAATTAATTTGAACT
Found at i:3775 original size:32 final size:31
Alignment explanation
Indices: 3710--3791 Score: 85
Period size: 32 Copynumber: 2.6 Consensus size: 31
3700 AATTCAAATC
* *
3710 GAAATTAATTTG-ATGAAAACAACTTGAACT
1 GAAATTAATTTGAACGAAAACAACTCGAACT
* *
3740 GAAATTAATTTGAACCGAAATCAACTCGAATT
1 GAAATTAATTTGAA-CGAAAACAACTCGAACT
* *
3772 GAAAGTAATCTGAATCGAAA
1 GAAATTAATTTGAA-CGAAA
3792 GTAACCCAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 12 0.28
31 1 0.02
32 30 0.70
ACGTcount: A:0.46, C:0.12, G:0.15, T:0.27
Consensus pattern (31 bp):
GAAATTAATTTGAACGAAAACAACTCGAACT
Found at i:12088 original size:20 final size:20
Alignment explanation
Indices: 12036--12081 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
12026 GTTGGAAACT
12036 AAGTTTCAAAACTTTGATGA
1 AAGTTTCAAAACTTTGATGA
12056 AAGTTTCAAAACTATTGA-GA
1 AAGTTTCAAAACT-TTGATGA
12076 AAGTTT
1 AAGTTT
12082 TGAAACTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 21 0.84
21 4 0.16
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (20 bp):
AAGTTTCAAAACTTTGATGA
Found at i:13923 original size:53 final size:53
Alignment explanation
Indices: 13851--13960 Score: 184
Period size: 53 Copynumber: 2.1 Consensus size: 53
13841 GTTGCACCTA
*
13851 AGTGTCGAAATGGTAATTCAAAAACTCATTATGAATTCCATGGATGCACACAT
1 AGTGTCGAAATGGTAATTCAAAAACTCATTATGAATACCATGGATGCACACAT
* * *
13904 AGTGTCGAAATGGTCATTCATAAACTCATTATGAATACCATGGGTGCACACAT
1 AGTGTCGAAATGGTAATTCAAAAACTCATTATGAATACCATGGATGCACACAT
13957 AGTG
1 AGTG
13961 CCAAAAGTAC
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.28
Consensus pattern (53 bp):
AGTGTCGAAATGGTAATTCAAAAACTCATTATGAATACCATGGATGCACACAT
Found at i:22045 original size:20 final size:20
Alignment explanation
Indices: 22020--22065 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
22010 TTGGAACCCT
22020 AAGTTTTGAAACT-TTGATGA
1 AAGTTTTGAAACTCTTGA-GA
22040 AAGTTTTGAAACTCTTGAGA
1 AAGTTTTGAAACTCTTGAGA
22060 AAGTTT
1 AAGTTT
22066 CAAAAATTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 21 0.84
21 4 0.16
ACGTcount: A:0.35, C:0.07, G:0.20, T:0.39
Consensus pattern (20 bp):
AAGTTTTGAAACTCTTGAGA
Found at i:24831 original size:182 final size:182
Alignment explanation
Indices: 24494--25157 Score: 917
Period size: 182 Copynumber: 3.6 Consensus size: 182
24484 TTGTCGGTAC
* * * ** *
24494 GTATCGATACTATTA-AAATATATATCAATACATAATTATATATCAGGTAAAAATATGAAAAAAC
1 GTATCGATACT-TTATAAAAATATATCGATACATAA-CATATAAAAGGTAAAAATATGACAAAAC
* * * *
24558 CGATTT-AATATGACAAAACCGGTAAAGCGCTACC-GAATATGTTGAAAGTATCGATTCCAATGA
64 CGGTTTCATTATGACAAAACCGGTAAAGCGCTACCAG-ATATGTTGAAAGTATCGATTCCATTCA
*
24621 AATAAGTATCGAAACTTTTGGAATTTAAAAGAAAAGCAGTAATAGCACCTATAAA
128 AATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGCAGTAATAGCACCTATAAA
* * * *
24676 GTATCGATACTTTATAAACATGTATCGATACATAACGATATAAAAAGTAAAAATATGATAAAACC
1 GTATCGATACTTTATAAAAATATATCGATACATAAC-ATATAAAAGGTAAAAATATGACAAAACC
* *
24741 GGTTTCATAATGACAAAACCGGTAAAGCGCTACCAGATATGTTGAAAGTATCGATTCCATTTAAA
65 GGTTTCATTATGACAAAACCGGTAAAGCGCTACCAGATATGTTGAAAGTATCGATTCCATTCAAA
24806 TAAGTATCGACAC-TTTGGAATTTAAAAGAAAAGCAGTAATAGCACCTATAAA
130 TAAGTATCGACACTTTTGGAATTTAAAAGAAAAGCAGTAATAGCACCTATAAA
** * *
24858 GTATTAATACTTTATAAAAATGTATTGATACATAACAATATAAAAGGTAAAAATATGACAAAATC
1 GTATCGATACTTTATAAAAATATATCGATACATAAC-ATATAAAAGGTAAAAATATGACAAAA-C
* * * *
24923 AGG-TTCATTATGACAAAACTGGTAAAGAGCTACCAGATATGTTGAAAATATCGATTCCATTCAA
64 CGGTTTCATTATGACAAAACCGGTAAAGCGCTACCAGATATGTTGAAAGTATCGATTCCATTCAA
* * ** *
24987 ATAAATATCGACACTTTTGGAATTAAAAAGAAAAAAAGTAATAGCTCCTATAAA
129 ATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGCAGTAATAGCACCTATAAA
*
25041 GTATCGATACTTTATAAAAATATATCGATACATAACACTATAACAGGTAAAAATATGACAAAACC
1 GTATCGATACTTTATAAAAATATATCGATACATAACA-TATAAAAGGTAAAAATATGACAAAACC
* *
25106 GGTTTCATTATGACAAAACCGGTAAAACGCTACCGGATATGTT-AAATGTATC
65 GGTTTCATTATGACAAAACCGGTAAAGCGCTACCAGATATGTTGAAA-GTATC
25158 AATACTATAA
Statistics
Matches: 430, Mismatches: 43, Indels: 17
0.88 0.09 0.03
Matches are distributed among these distances:
181 3 0.01
182 227 0.53
183 199 0.46
184 1 0.00
ACGTcount: A:0.45, C:0.13, G:0.14, T:0.28
Consensus pattern (182 bp):
GTATCGATACTTTATAAAAATATATCGATACATAACATATAAAAGGTAAAAATATGACAAAACCG
GTTTCATTATGACAAAACCGGTAAAGCGCTACCAGATATGTTGAAAGTATCGATTCCATTCAAAT
AAGTATCGACACTTTTGGAATTTAAAAGAAAAGCAGTAATAGCACCTATAAA
Found at i:34648 original size:200 final size:199
Alignment explanation
Indices: 34295--35225 Score: 1317
Period size: 200 Copynumber: 4.7 Consensus size: 199
34285 TGAAGTATAT
* *
34295 ATCCCAAAAACATCGAAATCGATAATTATAAAGTAATAGGTAAATTTAAAATGTAACCGATAAAA
1 ATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGTAAATTTACAATGTAA-CGATAAAA
* * * * *
34360 ATATACTGGTTTAATGAGAGAATAGGTAAACATAATGTATCGACATTTTTTTAAATTGTATCGAT
65 ATATAATGGTTTAATGAGAGAATAGGTAAACATAATGTATCGATACTTTTTAAAATTGTGTCGAT
* * * * * **
34425 ACTTTTTGCCCATAATTAATGCCCAATGAGGTGCACACATAAAGTGTCGATAAATTTATTGCAAG
130 ACTTTTTGTCCAGAATGAATGCCCAACGAGGTGCACACATAAAGTGTCGATACATTTATTATAAG
34490 TATCG
195 TATCG
* *
34495 ATCCTAAAAACATCAAAACCGATAATTATAAAGTAATAGGTAAATTTACAATGTAATCGATAAAA
1 ATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGTAAATTTACAATGTAA-CGATAAAA
*
34560 ATATAATGGTTTAATGAGAGAATAGGTAAACATAATGTATCGATACTTTTTAAAAATGTGTCGAT
65 ATATAATGGTTTAATGAGAGAATAGGTAAACATAATGTATCGATACTTTTTAAAATTGTGTCGAT
* * *
34625 ACTTTTTGTCCAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATGTATTGTAAG
130 ACTTTTTGTCCAGAATGAATGCCCAACGAGGTGCACACATAAAGTGTCGATACATTTATTATAAG
* *
34690 TTTTG
195 TATCG
* *
34695 ATCCCAAAAATATCGAAACCGATAATTATAAAGTAATAGGTAAATTTACAATGTAACTAGTAAAA
1 ATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGTAAATTTACAATGTAACGA-TAAAA
* * *
34760 ATATAACGGTTTAATGAGAGAATAGGTAAACATAATGTATCGATACTTTTTAAAATTGTGCCTAT
65 ATATAATGGTTTAATGAGAGAATAGGTAAACATAATGTATCGATACTTTTTAAAATTGTGTCGAT
* ** *
34825 ACGTTTTGTCCAGAATGAATGCCCAACGAGGTGCATGCATAAAGTGTCAATACATTTATTATAAG
130 ACTTTTTGTCCAGAATGAATGCCCAACGAGGTGCACACATAAAGTGTCGATACATTTATTATAAG
34890 TATCG
195 TATCG
* ** * *
34895 ATCCCAAAAATATCGAAACAAATAATTATAAAGTAATAGGTAAATTTAAAATGTAACCAGTAAAA
1 ATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGTAAATTTACAATGTAACGA-TAAAA
*
34960 ATAT-ATCGGTTTAATGAGAGAATAGGTAAACATATTGTATCGATACTTTTTAAAATTGTGTCGA
65 ATATAAT-GGTTTAATGAGAGAATAGGTAAACATAATGTATCGATACTTTTTAAAATTGTGTCGA
* *
35024 TACATTTTGTCCAGAATGAATGCCCAATGAGGTGCACACATAAAGTGTCGATACATTTATTATAA
129 TACTTTTTGTCCAGAATGAATGCCCAACGAGGTGCACACATAAAGTGTCGATACATTTATTATAA
*
35089 GTATTG
194 GTATCG
* * * * * *
35095 ATTCCAAAAACATCAAAATCGATAATTATACAGTAATAGGTTAATTAACAATGTAACCGATAAAA
1 ATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGTAAATTTACAATGTAA-CGATAAAA
* * * * * *
35160 ATAT-ATCGATTTTATGAGAGAATAGGTAAACATAATGTATCGACAATTTTTAAAATTATATCGA
65 ATATAAT-GGTTTAATGAGAGAATAGGTAAACATAATGTATCGATACTTTTTAAAATTGTGTCGA
35224 TA
129 TA
35226 TGTTTTTTAA
Statistics
Matches: 660, Mismatches: 68, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
199 3 0.00
200 655 0.99
201 2 0.00
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.31
Consensus pattern (199 bp):
ATCCCAAAAACATCGAAACCGATAATTATAAAGTAATAGGTAAATTTACAATGTAACGATAAAAA
TATAATGGTTTAATGAGAGAATAGGTAAACATAATGTATCGATACTTTTTAAAATTGTGTCGATA
CTTTTTGTCCAGAATGAATGCCCAACGAGGTGCACACATAAAGTGTCGATACATTTATTATAAGT
ATCG
Found at i:36674 original size:12 final size:12
Alignment explanation
Indices: 36657--36690 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
36647 CAAGCACTCA
*
36657 ATGAAGAAGACG
1 ATGAAGAAGAAG
*
36669 ATGAAGATGAAG
1 ATGAAGAAGAAG
36681 ATGAAGAAGA
1 ATGAAGAAGA
36691 TGATCCAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.53, C:0.03, G:0.32, T:0.12
Consensus pattern (12 bp):
ATGAAGAAGAAG
Found at i:38143 original size:12 final size:12
Alignment explanation
Indices: 38126--38192 Score: 71
Period size: 12 Copynumber: 5.6 Consensus size: 12
38116 GGCTCCACTA
38126 TAAATTTGAGTT
1 TAAATTTGAGTT
* *
38138 TAAATTTAAATT
1 TAAATTTGAGTT
38150 TAAATTTGAGTT
1 TAAATTTGAGTT
* * *
38162 TGAATTTAAATT
1 TAAATTTGAGTT
*
38174 TCAATTTGAGTT
1 TAAATTTGAGTT
*
38186 TGAATTT
1 TAAATTT
38193 CAATATAAAT
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 44 1.00
ACGTcount: A:0.36, C:0.01, G:0.12, T:0.51
Consensus pattern (12 bp):
TAAATTTGAGTT
Found at i:38147 original size:6 final size:6
Alignment explanation
Indices: 38126--38204 Score: 59
Period size: 6 Copynumber: 13.2 Consensus size: 6
38116 GGCTCCACTA
* * * * *
38126 TAAATT TGAGTT TAAATT TAAATT TAAATT TGAGTT TGAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
* * * * * *
38174 TCAATT TGAGTT TGAATT TCAATA TAAATT T
1 TAAATT TAAATT TAAATT TAAATT TAAATT T
38205 CAGCTCCACT
Statistics
Matches: 57, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
6 57 1.00
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.49
Consensus pattern (6 bp):
TAAATT
Found at i:38154 original size:24 final size:24
Alignment explanation
Indices: 38126--38204 Score: 122
Period size: 24 Copynumber: 3.3 Consensus size: 24
38116 GGCTCCACTA
*
38126 TAAATTTGAGTTTAAATTTAAATT
1 TAAATTTGAGTTTGAATTTAAATT
38150 TAAATTTGAGTTTGAATTTAAATT
1 TAAATTTGAGTTTGAATTTAAATT
* * *
38174 TCAATTTGAGTTTGAATTTCAATA
1 TAAATTTGAGTTTGAATTTAAATT
38198 TAAATTT
1 TAAATTT
38205 CAGCTCCACT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.49
Consensus pattern (24 bp):
TAAATTTGAGTTTGAATTTAAATT
Found at i:38181 original size:18 final size:18
Alignment explanation
Indices: 38140--38196 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 18
38130 TTTGAGTTTA
* *
38140 AATTTAAATTTAAATTTG
1 AATTTGAATTTAAATTTC
*
38158 AGTTTGAATTTAAATTTC
1 AATTTGAATTTAAATTTC
* *
38176 AATTTGAGTTTGAATTTC
1 AATTTGAATTTAAATTTC
38194 AAT
1 AAT
38197 ATAAATTTCA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.37, C:0.04, G:0.11, T:0.49
Consensus pattern (18 bp):
AATTTGAATTTAAATTTC
Found at i:40685 original size:38 final size:38
Alignment explanation
Indices: 40645--41011 Score: 265
Period size: 38 Copynumber: 9.9 Consensus size: 38
40635 TTTTTTATTT
40645 ATATATATATTATATAG-TTTGAAATCA-TTTTG-AAA
1 ATATATATATTATATAGTTTTGAAATCATTTTTGAAAA
* * *
40680 AT-TATATAATATATGGCTTTTTTTAAAT-A-TTTTG-AAA
1 ATATATATATTATATAG---TTTTGAAATCATTTTTGAAAA
*
40717 ATATATA-A-TATATAGTTTTTGAAAACATTTTTG--AA
1 ATATATATATTATATAG-TTTTGAAATCATTTTTGAAAA
* * * *
40752 A-ATACATATTATATTGTTTTGAAAAC-TTTTTTAAAA
1 ATATATATATTATATAGTTTTGAAATCATTTTTGAAAA
* * *
40788 ATATATATAATATATAGTTTTTAAAAAACATTTTTGAAAA
1 ATATATATATTATATAG-TTTT-GAAATCATTTTTGAAAA
* **
40828 ACATATATATTATATAGTTTTGAAA--ATTAGTTTCTAAA
1 ATATATATATTATATAGTTTTGAAATCATT--TTTGAAAA
* *
40866 A-ATATATATTAAATAGTTTTGGAAATTAGTTTTT--AAA
1 ATATATATATTATATAGTTTT-GAAATCA-TTTTTGAAAA
*
40903 ATATATATATTATATAGTTTTGAAATTTAGTTTTT-AAAA
1 ATATATATATTATATAGTTTTGAAA-TCA-TTTTTGAAAA
* *
40942 ATATATATATTATATAGTTTTGAAAATTATTTTT--TAA
1 ATATATATATTATATAGTTTTG-AAATCATTTTTGAAAA
* *
40979 A-ATATATATTATATGGTTTTGAAAATTATTTTT
1 ATATATATATTATATAGTTTTG-AAATCATTTTT
41012 TTAAAACATA
Statistics
Matches: 284, Mismatches: 23, Indels: 49
0.80 0.06 0.14
Matches are distributed among these distances:
34 29 0.10
35 17 0.06
36 54 0.19
37 53 0.19
38 61 0.21
39 40 0.14
40 28 0.10
41 2 0.01
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (38 bp):
ATATATATATTATATAGTTTTGAAATCATTTTTGAAAA
Found at i:40722 original size:36 final size:35
Alignment explanation
Indices: 40647--41010 Score: 222
Period size: 36 Copynumber: 9.9 Consensus size: 35
40637 TTTTATTTAT
*
40647 ATATATATTATATAG--TTTG-AAATCATTTTGAAA
1 ATATATAATATATAGTTTTTGAAAAT-ATTTTGAAA
* **
40680 ATTATATAATATATGGCTTTTTTTAAATATTTTGAAA
1 A-TATATAATATATAG-TTTTTGAAAATATTTTGAAA
*
40717 ATATATAATATATAGTTTTTGAAAACATTTTTGAAA
1 ATATATAATATATAGTTTTTGAAAATA-TTTTGAAA
* * * * *
40753 ATACATATTATATTG-TTTTGAAAACTTTTTTAAAAA
1 ATATATAATATATAGTTTTTGAAAA-TATTTT-GAAA
* *
40789 TATATATAATATATAGTTTTTAAAAAACATTTTTGAAAAA
1 -ATATATAATATATAGTTTTT-GAAAATA-TTTTG--AAA
* *
40829 CATATATATTATATAG-TTTTGAAAATTAGTTTCTAAAA
1 -ATATATAATATATAGTTTTTGAAAA-TA-TTT-TGAAA
* * * * *
40867 ATATATATTAAATAGTTTTGGAAATTAGTTTTTAAA
1 ATATATAATATATAGTTTTTGAAAATA-TTTTGAAA
* *
40903 ATATATATATTATATAG-TTTTGAAATTTAGTTTTTAAAA
1 ATATATA-A-TATATAGTTTTTGAAA-ATA--TTTTGAAA
*
40942 ATATATATATTATATAG-TTTTGAAAATTATTTTTTAAA
1 ATATATA-A-TATATAGTTTTTGAAAA-TA-TTTTGAAA
* *
40980 ATATATATTATAT-GGTTTTGAAAATTATTTT
1 ATATATAATATATAGTTTTTGAAAA-TATTTT
41011 TTTAAAACAT
Statistics
Matches: 270, Mismatches: 38, Indels: 44
0.77 0.11 0.12
Matches are distributed among these distances:
33 1 0.00
34 12 0.04
35 27 0.10
36 64 0.24
37 52 0.19
38 46 0.17
39 50 0.19
40 18 0.07
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (35 bp):
ATATATAATATATAGTTTTTGAAAATATTTTGAAA
Found at i:40882 original size:37 final size:38
Alignment explanation
Indices: 40645--41034 Score: 339
Period size: 37 Copynumber: 10.5 Consensus size: 38
40635 TTTTTTATTT
* *
40645 ATATATATATTATATAG-TTTG-AAATCA-TTTTGAAA
1 ATATATATATTATATAGTTTTGAAAATTAGTTTTTAAA
* * ** *
40680 AT-TATATAATATATGGCTTTTTTTAAA-TA-TTTTGAAA
1 ATATATATATTATATAG--TTTTGAAAATTAGTTTTTAAA
* *
40717 ATATATA-A-TATATAGTTTTTGAAAA-CA-TTTTTGAA
1 ATATATATATTATATAG-TTTTGAAAATTAGTTTTTAAA
* * *
40752 A-ATACATATTATATTGTTTTGAAAACTT--TTTTAAAA
1 ATATATATATTATATAGTTTTGAAAA-TTAGTTTTTAAA
* * * *
40788 ATATATATAATATATAGTTTTTAAAA-AACATTTTTGAAAA
1 ATATATATATTATATAGTTTTGAAAATTA-GTTTTT--AAA
* *
40828 ACATATATATTATATAGTTTTGAAAATTAGTTTCTAAA
1 ATATATATATTATATAGTTTTGAAAATTAGTTTTTAAA
* *
40866 A-ATATATATTAAATAGTTTTGGAAATTAGTTTTTAAA
1 ATATATATATTATATAGTTTTGAAAATTAGTTTTTAAA
*
40903 ATATATATATTATATAGTTTTGAAATTTAGTTTTTAAAA
1 ATATATATATTATATAGTTTTGAAAATTAGTTTTT-AAA
*
40942 ATATATATATTATATAGTTTTGAAAATTA-TTTTTTAA
1 ATATATATATTATATAGTTTTGAAAATTAGTTTTTAAA
* * *
40979 A-ATATATATTATATGGTTTTGAAAATTATTTTTTTAA
1 ATATATATATTATATAGTTTTGAAAATTAGTTTTTAAA
* *
41016 A-ACATATATTGTATAGTTT
1 ATATATATATTATATAGTTT
41035 AAAAAAATGT
Statistics
Matches: 297, Mismatches: 39, Indels: 36
0.80 0.10 0.10
Matches are distributed among these distances:
34 16 0.05
35 28 0.09
36 45 0.15
37 96 0.32
38 50 0.17
39 31 0.10
40 30 0.10
41 1 0.00
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (38 bp):
ATATATATATTATATAGTTTTGAAAATTAGTTTTTAAA
Found at i:40925 original size:75 final size:73
Alignment explanation
Indices: 40731--41034 Score: 317
Period size: 75 Copynumber: 4.1 Consensus size: 73
40721 ATAATATATA
* * * * * *
40731 GTTTTTGAAAACATTTTTGAAAATACATATTATATTGTTTTGAAAACT--TTTTTAAAAATATAT
1 GTTTTGGAAAATATTTTTAAAAATATATATTATATAGTTTTGAAAATTAGTTTTTAAAAATATAT
40794 ATAATATATA
66 AT--TATATA
** * *
40804 GTTTTTAAAAAACATTTTTGAAAAACATATATATTATATAGTTTTGAAAATTAGTTTCTAAAAAT
1 G-TTTTGGAAAATATTTTT--AAAA-ATATATATTATATAGTTTTGAAAATTAGTTTTTAAAAAT
*
40869 ATATATTAAATA
62 ATATATTATATA
* *
40881 GTTTTGGAAATTAGTTTTTAAAATATATATATTATATAGTTTTGAAATTTAGTTTTTAAAAATAT
1 GTTTTGGAAAATA-TTTTTAAAA-ATATATATTATATAGTTTTGAAAATTAGTTTTT-AAAA-AT
40946 ATATATTATATA
62 ATATATTATATA
* * * * *
40958 GTTTT-GAAAATTATTTTTTAAAATATATATTATATGGTTTTGAAAATTATTTTTTTAAAACATA
1 GTTTTGGAAAA-TATTTTTAAAAATATATATTATATAGTTTTGAAAATTAGTTTTTAAAAATATA
*
41022 TATTGTATA
65 TATTATATA
41031 GTTT
1 GTTT
41035 AAAAAAATGT
Statistics
Matches: 197, Mismatches: 24, Indels: 20
0.82 0.10 0.08
Matches are distributed among these distances:
73 17 0.09
74 18 0.09
75 65 0.33
76 27 0.14
77 54 0.27
79 16 0.08
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.48
Consensus pattern (73 bp):
GTTTTGGAAAATATTTTTAAAAATATATATTATATAGTTTTGAAAATTAGTTTTTAAAAATATAT
ATTATATA
Found at i:41059 original size:4 final size:4
Alignment explanation
Indices: 41050--41105 Score: 69
Period size: 4 Copynumber: 13.8 Consensus size: 4
41040 AATGTTTTTA
* *
41050 ATTT ATTT ATTT ATCT ATTT ATTT ATTTT ATCTC ATTT A-TT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT A-TTT AT-TT ATTT ATTT ATTT ATTT
41099 ATTT ATT
1 ATTT ATT
41106 ACTGTTTGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
3 3 0.07
4 35 0.78
5 7 0.16
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (4 bp):
ATTT
Found at i:41074 original size:25 final size:24
Alignment explanation
Indices: 41046--41105 Score: 77
Period size: 25 Copynumber: 2.5 Consensus size: 24
41036 AAAAAATGTT
*
41046 TTTAATTTATTTATTTATCTATTTA
1 TTTAATTTATTCATTTAT-TATTTA
*
41071 TTTATTTTATCTCATTTATTATTTA
1 TTTAATTTAT-TCATTTATTATTTA
41096 TTT-ATTTATT
1 TTTAATTTATT
41106 ACTGTTTGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
23 1 0.03
24 5 0.16
25 18 0.58
26 7 0.23
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (24 bp):
TTTAATTTATTCATTTATTATTTA
Found at i:41282 original size:16 final size:15
Alignment explanation
Indices: 41261--41290 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
41251 GTCGGCCGGT
41261 ATCCCGGGACTGACCC
1 ATCCCGGGA-TGACCC
41277 ATCCCGGGATGACC
1 ATCCCGGGATGACC
41291 GGTCACACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.20, C:0.40, G:0.27, T:0.13
Consensus pattern (15 bp):
ATCCCGGGATGACCC
Found at i:42194 original size:2 final size:2
Alignment explanation
Indices: 42189--42214 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
42179 TTCTATTATC
42189 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
42215 GTGTGTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43617 original size:14 final size:16
Alignment explanation
Indices: 43598--43630 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
43588 AGAGGTGACA
43598 ATCGGGT-C-ATTCAG
1 ATCGGGTGCGATTCAG
43612 ATCGGGTGCGATTCAG
1 ATCGGGTGCGATTCAG
43628 ATC
1 ATC
43631 ATTTTGGGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 1 0.06
16 9 0.53
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.27
Consensus pattern (16 bp):
ATCGGGTGCGATTCAG
Found at i:44441 original size:16 final size:16
Alignment explanation
Indices: 44370--44452 Score: 55
Period size: 16 Copynumber: 5.3 Consensus size: 16
44360 ACTAAATTCG
44370 GGTTGCTTTCGGTTCA
1 GGTTGCTTTCGGTTCA
* **
44386 AGTT--TTTCGGTTTG
1 GGTTGCTTTCGGTTCA
* * *
44400 GGCTGTTTTCCGTTC-
1 GGTTGCTTTCGGTTCA
**
44415 GAGTTAATTTCGGTTCA
1 G-GTTGCTTTCGGTTCA
*
44432 GGTTGCTTTCGATTCA
1 GGTTGCTTTCGGTTCA
44448 GGTTG
1 GGTTG
44453 GTTTTAGGTC
Statistics
Matches: 49, Mismatches: 14, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
14 10 0.20
15 1 0.02
16 37 0.76
17 1 0.02
ACGTcount: A:0.10, C:0.16, G:0.29, T:0.46
Consensus pattern (16 bp):
GGTTGCTTTCGGTTCA
Found at i:48948 original size:29 final size:29
Alignment explanation
Indices: 48892--49082 Score: 106
Period size: 29 Copynumber: 6.6 Consensus size: 29
48882 ACCGGTTGAG
* *
48892 ATTTTGGTAATTATTTGGGAAATG-GTGCT
1 ATTTTGGTAATTATTT-TGAAAAGAGTGCT
*
48921 ATTCTGGTAATTATTTTGAAAAGAGTGCT
1 ATTTTGGTAATTATTTTGAAAAGAGTGCT
* * * * *
48950 ATTTTTGT-ATTTTTTTTATAAAAAGGTAAC-
1 ATTTTGGTAATTATTTTGA-AAAGA-GT-GCT
* ** *
48980 AATTTCATAAATT-TTTT-AAAAGAGTGAT
1 ATTTTGGT-AATTATTTTGAAAAGAGTGCT
* * * *
49008 ATTGTAGTAATTATTTTGAAAATAATGCT
1 ATTTTGGTAATTATTTTGAAAAGAGTGCT
* *
49037 ATTTTGGTAATTAATTTCAAAATG-GTGCT
1 ATTTTGGTAATTATTTTGAAAA-GAGTGCT
* *
49066 ATTTTCGTAATTTTTTT
1 ATTTTGGTAATTATTTT
49083 TAAATGTTAA
Statistics
Matches: 121, Mismatches: 31, Indels: 20
0.70 0.18 0.12
Matches are distributed among these distances:
27 4 0.03
28 23 0.19
29 78 0.64
30 8 0.07
31 5 0.04
32 3 0.02
ACGTcount: A:0.32, C:0.05, G:0.16, T:0.48
Consensus pattern (29 bp):
ATTTTGGTAATTATTTTGAAAAGAGTGCT
Found at i:50217 original size:117 final size:117
Alignment explanation
Indices: 50012--50298 Score: 454
Period size: 117 Copynumber: 2.5 Consensus size: 117
50002 GTATTTCAGA
*
50012 CTCCTTTGTTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCA-GTGGGTGTATGGTTCTGGGGAA
1 CTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGGAA
*
50076 CCTACACATTGTAGTGATTGGAGTGACTGGATTG-GGAATTTATTA-TCGAAGG
66 CCTACACATTGTAGTGATTGGAGTGACTGGA-TGAGGAAGTTATTACT-GAAGG
50128 CTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGGAA
1 CTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGGAA
*
50193 CCTACACATTGTAGTGATTGGAGTGACTGGATGAGGAAGTTATTACTGCAGG
66 CCTACACATTGTAGTGATTGGAGTGACTGGATGAGGAAGTTATTACTGAAGG
** * * * *
50245 CTCCTCGGCTTTGTGCTTAGGGTAAGTCCTTAGTGGTGTGTAGGTGGGTGTATG
1 CTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATG
50299 TTTTGGGAAA
Statistics
Matches: 159, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
116 43 0.27
117 115 0.72
118 1 0.01
ACGTcount: A:0.17, C:0.15, G:0.34, T:0.34
Consensus pattern (117 bp):
CTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGGAA
CCTACACATTGTAGTGATTGGAGTGACTGGATGAGGAAGTTATTACTGAAGG
Found at i:50334 original size:117 final size:117
Alignment explanation
Indices: 50021--50335 Score: 325
Period size: 117 Copynumber: 2.7 Consensus size: 117
50011 ACTCCTTTGT
* * *
50021 TGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCA-GTGGGTGTATGGTTCTGGGGAACCTACACAT
1 TGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGAAACATACACAA
* ** ** * **
50085 TGTAGTGATTGGAGTGACTGGATTGGGAATTTATTATCGAAGGCTCCTTTGC
66 AGTAGAAATCAGAGTGACTGGATTGGGAAGTTATTATCGAAGGCTCCTCGGC
* * *
50137 TGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGGAACCTACACAT
1 TGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGAAACATACACAA
* ** ** *
50202 TGTAGTGATTGGAGTGACTGGA-TGAGGAAGTTATTA-CTGCAGGCTCCTCGGC
66 AGTAGAAATCAGAGTGACTGGATTG-GGAAGTTATTATC-GAAGGCTCCTCGGC
* * * * * *
50254 TTTGTGCTTAGGGTAAGTCCTTAGTGGTGTGTAGGTGGGTGTAT-GTTTTGGGAAA-ATATACAA
1 TGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGAAACATACAC-A
50317 AAGATAGAAATCAGAGTGA
65 AAG-TAGAAATCAGAGTGA
50336 TTGAATGGAA
Statistics
Matches: 176, Mismatches: 18, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
115 4 0.02
116 47 0.27
117 125 0.71
ACGTcount: A:0.22, C:0.13, G:0.33, T:0.32
Consensus pattern (117 bp):
TGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGAAACATACACAA
AGTAGAAATCAGAGTGACTGGATTGGGAAGTTATTATCGAAGGCTCCTCGGC
Found at i:56486 original size:29 final size:29
Alignment explanation
Indices: 56352--56540 Score: 118
Period size: 29 Copynumber: 6.6 Consensus size: 29
56342 CGTTGACCGG
* * *
56352 GTGATATTTTGGTAATTATTTAGGAAATA
1 GTGATATTTTGGTAATTATTTTGAAAAGA
* *
56381 GT-ACTATTCTGGTAATTATTTTGAAAAGG
1 GTGA-TATTTTGGTAATTATTTTGAAAAGA
* * * *
56410 GTGTTATTTTTGTAATT-TTTTTAAAAAA
1 GTGATATTTTGGTAATTATTTTGAAAAGA
* * * * **
56438 GTGACAATTTCGTAA-AATTTTTCAAAGA
1 GTGATATTTTGGTAATTATTTTGAAAAGA
*
56466 GTGATATTTTAGTAATTATTTTGAAAATG-
1 GTGATATTTTGGTAATTATTTTGAAAA-GA
* * * *
56495 TTGCTATTTTGGTAATTAATTTCAAAATG-
1 GTGATATTTTGGTAATTATTTTGAAAA-GA
* *
56524 GTGTTATTTTCGTAATT
1 GTGATATTTTGGTAATT
56541 TAAAAAATGT
Statistics
Matches: 123, Mismatches: 32, Indels: 10
0.75 0.19 0.06
Matches are distributed among these distances:
28 41 0.33
29 81 0.66
30 1 0.01
ACGTcount: A:0.32, C:0.04, G:0.16, T:0.47
Consensus pattern (29 bp):
GTGATATTTTGGTAATTATTTTGAAAAGA
Found at i:57684 original size:117 final size:117
Alignment explanation
Indices: 57478--57886 Score: 694
Period size: 117 Copynumber: 3.5 Consensus size: 117
57468 GAAAGTATTT
* * * *
57478 CAGGCTCCTTTGTTGTGTGCTTAGGGTAAGTCCTTACTGGTGTGTAAGTGGGTGTATGGTTCTGG
1 CAGGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGG
*
57543 GGAACCTACACATTGTAGTGATTGGAGTGACTGGAAGGGGAAGTTATTATCG
66 GGAACCTACACATTGTAGTGATTGGAGTGACTGGATGGGGAAGTTATTATCG
57595 CAGGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGG
1 CAGGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGG
57660 GGAACCTACACATTGTAGTGATTGGAGTGACTGGATGGGGAAGTTATTATCG
66 GGAACCTACACATTGTAGTGATTGGAGTGACTGGATGGGGAAGTTATTATCG
* *
57712 CAGGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGTAGGTGGGTGTATGGTTTTGG
1 CAGGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGG
57777 GGAACCTACACATTGTAGTGATTGGAGTGACTGGATGGGGAAGTTATTA-CTG
66 GGAACCTACACATTGTAGTGATTGGAGTGACTGGATGGGGAAGTTATTATC-G
** * * *
57829 CAGGCTCCTCGGCTTTGTGCTTAGGGTAAGTCCTTACTGGTGTGCAGGTAGGTGTATG
1 CAGGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATG
57887 TTTCAGGAAA
Statistics
Matches: 278, Mismatches: 13, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
116 1 0.00
117 277 1.00
ACGTcount: A:0.18, C:0.15, G:0.35, T:0.33
Consensus pattern (117 bp):
CAGGCTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGG
GGAACCTACACATTGTAGTGATTGGAGTGACTGGATGGGGAAGTTATTATCG
Found at i:59257 original size:24 final size:23
Alignment explanation
Indices: 59229--59285 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
59219 AACACAAAAT
59229 GAACACGTTCAAGAACATATAAAC
1 GAACACGTTCAAGAACAT-TAAAC
* ***
59253 GAACACATTTGCGAACATTAAAC
1 GAACACGTTCAAGAACATTAAAC
*
59276 GAACATGTTC
1 GAACACGTTC
59286 GTGAACAATA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
23 12 0.46
24 14 0.54
ACGTcount: A:0.44, C:0.21, G:0.14, T:0.21
Consensus pattern (23 bp):
GAACACGTTCAAGAACATTAAAC
Done.