Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002842.1 Hibiscus syriacus cultivar Beakdansim tig00005852_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: 65746
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1229 original size:19 final size:18
Alignment explanation
Indices: 1205--1242 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1195 TATATGTATA
1205 TATTTAATTATATT-TAATT
1 TATTT-ATT-TATTATAATT
1224 TATTTATTTATTATAATT
1 TATTTATTTATTATAATT
1242 T
1 T
1243 TTTCATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.22
18 9 0.50
19 5 0.28
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATTTATTATAATT
Found at i:1242 original size:10 final size:9
Alignment explanation
Indices: 1205--1242 Score: 51
Period size: 10 Copynumber: 4.1 Consensus size: 9
1195 TATATGTATA
1205 TATTTAATT
1 TATTTAATT
1214 ATATTTAATT
1 -TATTTAATT
1224 TATTT-ATT
1 TATTTAATT
1232 TATTATAATT
1 TATT-TAATT
1242 T
1 T
1243 TTTCATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 7 0.27
9 6 0.23
10 13 0.50
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
TATTTAATT
Found at i:1368 original size:2 final size:2
Alignment explanation
Indices: 1361--1387 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1351 TTCCTAACGT
1361 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1388 TTTACTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1491 original size:65 final size:66
Alignment explanation
Indices: 1368--1492 Score: 150
Period size: 67 Copynumber: 1.9 Consensus size: 66
1358 CGTTATATAT
*
1368 ATATATATATATATATATATTTTACTTTATTTTATTTTATATTTCTATGATTACTATTTTTTAGT
1 ATATATATATATATATATATTTTACTTTATTTTATATTATATTTCTAT-ATTACTATTTTTTAGT
1433 TA
65 TA
* * *
1435 ATATATATGTATATTTAT-TTTTA-TTTATATATTATATTAT-TTTACTAT-TTAGTATTTT
1 ATATATATATATATATATATTTTACTTTAT-T-TTATATTATATTT-CTATATTACTATTTT
1493 ATTATATACA
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
65 14 0.27
66 9 0.18
67 28 0.55
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.62
Consensus pattern (66 bp):
ATATATATATATATATATATTTTACTTTATTTTATATTATATTTCTATATTACTATTTTTTAGTT
A
Found at i:1682 original size:20 final size:19
Alignment explanation
Indices: 1655--1709 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 19
1645 TTTTATCTTC
*
1655 ATTTATTTTATTTTATTCA
1 ATTTATTTTATTTTATCCA
1674 ATTTCATTTT-TTTTCATCCA
1 ATTT-ATTTTATTTT-ATCCA
1694 A-TTATTTTATGTTTAT
1 ATTTATTTTAT-TTTAT
1710 ATTGATTCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
18 5 0.16
19 13 0.42
20 13 0.42
ACGTcount: A:0.24, C:0.09, G:0.02, T:0.65
Consensus pattern (19 bp):
ATTTATTTTATTTTATCCA
Found at i:2555 original size:27 final size:27
Alignment explanation
Indices: 2519--2570 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
2509 AGAGGGCTAC
*
2519 TTATTCATAATATTTAACTATTATACT
1 TTATTAATAATATTTAACTATTATACT
2546 TTATTAATAATATTTAACTATTATA
1 TTATTAATAATATTTAACTATTATA
2571 ATATTGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (27 bp):
TTATTAATAATATTTAACTATTATACT
Found at i:2573 original size:16 final size:16
Alignment explanation
Indices: 2520--2575 Score: 50
Period size: 16 Copynumber: 3.8 Consensus size: 16
2510 GAGGGCTACT
2520 TATTCATAATATTTAAC
1 TATT-ATAATATTTAAC
*
2537 TATTAT-A-CTTT-A-
1 TATTATAATATTTAAC
*
2549 T-TAATAATATTTAAC
1 TATTATAATATTTAAC
2564 TATTATAATATT
1 TATTATAATATT
2576 GATTTTACAA
Statistics
Matches: 30, Mismatches: 4, Indels: 11
0.67 0.09 0.24
Matches are distributed among these distances:
11 3 0.10
12 2 0.07
13 4 0.13
14 4 0.13
15 2 0.07
16 11 0.37
17 4 0.13
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (16 bp):
TATTATAATATTTAAC
Found at i:7034 original size:50 final size:51
Alignment explanation
Indices: 6935--7091 Score: 185
Period size: 50 Copynumber: 3.1 Consensus size: 51
6925 GTCAAGGTTG
* * *
6935 GGTTAGAGAAGATGAACAGAGAGAAGATGAAGAGGCTCGGTTTGGGTTTGA
1 GGTTAGAGAAGATGAACAGAGAGAAAATGAAGAGGCTAGGTTAGGGTTTGA
*
6986 GGTTAGAGAAGATGAACAAAGA-AAAATGAAGAGGCTAGGTTAGGGTTTG-
1 GGTTAGAGAAGATGAACAGAGAGAAAATGAAGAGGCTAGGTTAGGGTTTGA
* * * * *
7035 GGATTAGAGAAGATAAATAGAGATAGAAAGTGAAGAGACTTGGTTAGGGTTT-A
1 GG-TTAGAGAAGATGAACAGAG--AGAAAATGAAGAGGCTAGGTTAGGGTTTGA
7088 GGTT
1 GGTT
7092 TGGCCCACGT
Statistics
Matches: 91, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
49 2 0.02
50 40 0.44
51 21 0.23
52 3 0.03
53 25 0.27
ACGTcount: A:0.38, C:0.04, G:0.36, T:0.23
Consensus pattern (51 bp):
GGTTAGAGAAGATGAACAGAGAGAAAATGAAGAGGCTAGGTTAGGGTTTGA
Found at i:7360 original size:25 final size:25
Alignment explanation
Indices: 7327--7397 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 25
7317 TCAAATTTTC
7327 AATTAATATATATTTTATATTAATA
1 AATTAATATATATTTTATATTAATA
* * *
7352 AATTAATATAGT-TTATATACTAATG
1 AATTAATATA-TATTTTATATTAATA
*
7377 AACTATATATATATTTTATAT
1 AATTA-ATATATATTTTATAT
7398 ATACTAATGA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
25 25 0.68
26 12 0.32
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (25 bp):
AATTAATATATATTTTATATTAATA
Found at i:7401 original size:30 final size:30
Alignment explanation
Indices: 7357--7476 Score: 154
Period size: 31 Copynumber: 4.0 Consensus size: 30
7347 TAATAAATTA
7357 ATATAG-TT-TATATACTAATGAACTATAT
1 ATATAGTTTATATATACTAATGAACTATAT
*
7385 ATATATTTTATATATACTAATGAACTTATAAT
1 ATATAGTTTATATATACTAATGAAC-TAT-AT
* * *
7417 ATATAGTTTATATATACCAATAAATTATAT
1 ATATAGTTTATATATACTAATGAACTATAT
*
7447 AATATAGTTTATTTATACTAATGAACTATA
1 -ATATAGTTTATATATACTAATGAACTATA
7477 GTTTATTAAT
Statistics
Matches: 78, Mismatches: 9, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
28 5 0.06
29 2 0.03
30 17 0.22
31 31 0.40
32 23 0.29
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (30 bp):
ATATAGTTTATATATACTAATGAACTATAT
Found at i:7469 original size:63 final size:60
Alignment explanation
Indices: 7357--7473 Score: 162
Period size: 63 Copynumber: 1.9 Consensus size: 60
7347 TAATAAATTA
* * *
7357 ATATAGTTTATATACTAATGAACTATATATATATTTTATATATACTAATGAACTTATAAT
1 ATATAGTTTATATACCAATAAACTATATATATAGTTTATATATACTAATGAACTTATAAT
* *
7417 ATATAGTTTATATATACCAATAAATTATATAATATAGTTTATTTATACTAATGAACT
1 ATATAG-TT-TATATACCAATAAACTATAT-ATATAGTTTATATATACTAATGAACT
7474 ATAGTTTATT
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
60 6 0.12
61 2 0.04
62 17 0.35
63 24 0.49
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (60 bp):
ATATAGTTTATATACCAATAAACTATATATATAGTTTATATATACTAATGAACTTATAAT
Found at i:7561 original size:2 final size:2
Alignment explanation
Indices: 7551--7589 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
7541 ATACAAAAAC
7551 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7590 AATAACCATA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:7670 original size:15 final size:15
Alignment explanation
Indices: 7627--7674 Score: 60
Period size: 15 Copynumber: 3.0 Consensus size: 15
7617 ATAGTTTTTG
*
7627 TATTAATAAACTATG
1 TATTAATAAACTATA
7642 TAGTGTATATAAACTATA
1 TA-T-TA-ATAAACTATA
7660 TATTAATAAACTATA
1 TATTAATAAACTATA
7675 AACTATATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
15 12 0.41
16 3 0.10
17 3 0.10
18 11 0.38
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.40
Consensus pattern (15 bp):
TATTAATAAACTATA
Found at i:7736 original size:31 final size:30
Alignment explanation
Indices: 7701--7840 Score: 101
Period size: 31 Copynumber: 4.7 Consensus size: 30
7691 TTAATAAACC
7701 ATAGTTTATATATAGTATATATAGTTTATAT
1 ATAGTTTATATATA-TATATATAGTTTATAT
* * * *
7732 ATAGTTCATATATACACTACATAGTTTATAC
1 ATAGTTTATATATATA-TATATAGTTTATAT
* * * **
7763 A-A-TGTATA-AAATATAAATA-TAAACTAT
1 ATAGTTTATATATATATATATAGTTTA-TAT
* *
7790 ATAGTTATATATATTTATATATACTTTATAT
1 ATAGTT-TATATATATATATATAGTTTATAT
*
7821 ATA-TATATATATATATATAT
1 ATAGTTTATATATATATATAT
7841 TAATAAACCA
Statistics
Matches: 82, Mismatches: 20, Indels: 16
0.69 0.17 0.14
Matches are distributed among these distances:
26 2 0.02
27 8 0.10
28 4 0.05
29 19 0.23
30 7 0.09
31 40 0.49
32 2 0.02
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (30 bp):
ATAGTTTATATATATATATATAGTTTATAT
Found at i:7743 original size:13 final size:11
Alignment explanation
Indices: 7701--7745 Score: 67
Period size: 11 Copynumber: 4.3 Consensus size: 11
7691 TTAATAAACC
7701 ATAGTTTATAT
1 ATAGTTTATAT
7712 ATAG--TATAT
1 ATAGTTTATAT
7721 ATAGTTTATAT
1 ATAGTTTATAT
*
7732 ATAGTTCATAT
1 ATAGTTTATAT
7743 ATA
1 ATA
7746 CACTACATAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 9 0.29
11 22 0.71
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (11 bp):
ATAGTTTATAT
Found at i:7743 original size:20 final size:20
Alignment explanation
Indices: 7678--7736 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
7668 AACTATAAAC
*
7678 TATATAGTTTATAT-TAATA
1 TATATAGTTTATATATAGTA
* *
7697 AACCATAGTTTATATATAGTA
1 TA-TATAGTTTATATATAGTA
7718 TATATAGTTTATATATAGT
1 TATATAGTTTATATATAGT
7737 TCATATATAC
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
19 1 0.03
20 27 0.82
21 5 0.15
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (20 bp):
TATATAGTTTATATATAGTA
Found at i:7800 original size:2 final size:2
Alignment explanation
Indices: 7773--7840 Score: 66
Period size: 2 Copynumber: 33.0 Consensus size: 2
7763 AATGTATAAA
* * *
7773 AT AT AA AT AT AA ACT AT AT AGT -T AT AT AT AT TT AT AT AT ACT
1 AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT A-T
*
7815 TT 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
7841 TAATAAACCA
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
1 1 0.02
2 50 0.93
3 3 0.06
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:7838 original size:27 final size:27
Alignment explanation
Indices: 7773--7839 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
7763 AATGTATAAA
* *
7773 ATATAAATATAAACTATATAGTTATAT
1 ATATATATATATACTATATAGTTATAT
* *
7800 ATATTTATATATACTTTATA-TATATAT
1 ATATATATATATACTATATAGT-TATAT
7827 ATATATATATATA
1 ATATATATATATA
7840 TTAATAAACC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
26 1 0.03
27 33 0.97
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (27 bp):
ATATATATATATACTATATAGTTATAT
Found at i:7916 original size:252 final size:253
Alignment explanation
Indices: 7551--8097 Score: 889
Period size: 252 Copynumber: 2.2 Consensus size: 253
7541 ATACAAAAAC
*
7551 TATATTATATA-TATATATATATATATATATATATATATAAATAACCATATAAAATGTAGTTTAT
1 TATATTATATACTTTATATATATATATATATATATATATAAATAACCATATAAAATGTAGTTTAT
*
7615 ATATAGTTTTTGTATTAATAAACTATGTAGTGTATATAAACTATATATTAATAAACTATAAACTA
66 ATATAGTTTTTGTATTAATAAACTATGTAGTGTATATAAACTATATATTAATAAACTATAAAATA
7680 TATAGTTTATATTAATAAACC-ATAGTTTATATATAG-TAT-ATATAGTTTATATATAGTTCATA
131 TATAGTTTATATTAATAAACCAATAGTTTATATATAGATATAATATAGTTTATATATAGTTCATA
*
7742 TATACACTACATAGTT-TATACAATGTATAAAATATAAATATAAACTATATAGTTATATATAT
196 TATACACT--AT--TTATATACAATATATAAAATATAAATATAAACTATATAGTT-TATATAT
*
7804 T-TA-TATATACTTTATATATATATATATATATATATATTAATAAACCATAT-AAATGTAGTTTA
1 TATATTATATACTTTATATATATATATATATATATATATAAAT-AACCATATAAAATGTAGTTTA
7866 TATAT-GTTTTTGTATTAATAAACTATGTAGTGTATATATAACTATATATTAATAAACTATAAAA
65 TATATAGTTTTTGTATTAATAAACTATGTAGTGTATATA-AACTATATATTAATAAACTATAAAA
7930 TATATAGTTTATATTAATAAACCATATAGTTTATATATAGTATATAATATAGTTTATATATAGTT
129 TATATAGTTTATATTAATAAACCA-ATAGTTTATATATAG-ATATAATATAGTTTATATATAGTT
*
7995 CATATATACACTATTTATATACAATATATAAATTATAAATATAAACTATATAGTTTATATAT
192 CATATATACACTATTTATATACAATATATAAAATATAAATATAAACTATATAGTTTATATAT
8057 TATATTAATATACTTTATATATATATATATATA-ATATATAA
1 TATATT-ATATACTTTATATATATATATATATATATATATAA
8098 TTGTTTTAAT
Statistics
Matches: 276, Mismatches: 6, Indels: 22
0.91 0.02 0.07
Matches are distributed among these distances:
251 39 0.14
252 95 0.34
253 19 0.07
254 53 0.19
255 10 0.04
256 29 0.11
257 31 0.11
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.44
Consensus pattern (253 bp):
TATATTATATACTTTATATATATATATATATATATATATAAATAACCATATAAAATGTAGTTTAT
ATATAGTTTTTGTATTAATAAACTATGTAGTGTATATAAACTATATATTAATAAACTATAAAATA
TATAGTTTATATTAATAAACCAATAGTTTATATATAGATATAATATAGTTTATATATAGTTCATA
TATACACTATTTATATACAATATATAAAATATAAATATAAACTATATAGTTTATATAT
Found at i:7968 original size:2 final size:2
Alignment explanation
Indices: 7961--8096 Score: 63
Period size: 2 Copynumber: 68.0 Consensus size: 2
7951 CCATATAGTT
*
7961 TA TA TA TA GTA TA TA -A TA TA GTT TA TA TA TA GT- TCA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA -TA T-A TA TA TA
* * * * * *
8003 CA CTA TT TA TA TA CA -A TA TA TA AA T- TA TA AA TA TA AA CTA TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* *
8045 TA GTT TA TA TA T- TA TA T- TA -A TA TA CTT TA TA TA TA TA TA TA
1 TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
8086 TA TA -A TA TA TA
1 TA TA TA TA TA TA
8097 ATTGTTTTAA
Statistics
Matches: 101, Mismatches: 17, Indels: 32
0.67 0.11 0.21
Matches are distributed among these distances:
1 8 0.08
2 84 0.83
3 9 0.09
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:7969 original size:11 final size:11
Alignment explanation
Indices: 7953--8002 Score: 73
Period size: 11 Copynumber: 4.5 Consensus size: 11
7943 TTAATAAACC
7953 ATATAGTTTAT
1 ATATAGTTTAT
*
7964 ATATAGTATAT
1 ATATAGTTTAT
7975 AATATAGTTTAT
1 -ATATAGTTTAT
*
7987 ATATAGTTCAT
1 ATATAGTTTAT
7998 ATATA
1 ATATA
8003 CACTATTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
11 25 0.71
12 10 0.29
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (11 bp):
ATATAGTTTAT
Found at i:8052 original size:22 final size:22
Alignment explanation
Indices: 7883--8053 Score: 70
Period size: 22 Copynumber: 7.9 Consensus size: 22
7873 TTTTGTATTA
* *
7883 ATAAACTATGTAGTGTAT--AT
1 ATAAACTATATAGTTTATAAAT
*
7903 AT-AACTATATA-TTAATAAACT
1 ATAAACTATATAGTTTATAAA-T
* *
7924 ATAAAATATATAGTTTAT-ATT
1 ATAAACTATATAGTTTATAAAT
* *
7945 AATAAACCATATAGTTTATATAT
1 -ATAAACTATATAGTTTATAAAT
* *
7968 AGTATA-TAATATAGTTTATATAT
1 A-TAAACT-ATATAGTTTATAAAT
** *** **
7991 AGTTCA-TATATACACTATTTAT
1 A-TAAACTATATAGTTTATAAAT
**
8013 ATACAA-TATATAAATTATAAAT
1 ATA-AACTATATAGTTTATAAAT
8035 ATAAACTATATAGTTTATA
1 ATAAACTATATAGTTTATA
8054 TATTATATTA
Statistics
Matches: 114, Mismatches: 26, Indels: 20
0.71 0.16 0.12
Matches are distributed among these distances:
18 3 0.03
19 8 0.07
20 3 0.03
21 7 0.06
22 65 0.57
23 28 0.25
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (22 bp):
ATAAACTATATAGTTTATAAAT
Found at i:8067 original size:22 final size:23
Alignment explanation
Indices: 8042--8084 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
8032 AATATAAACT
*
8042 ATATAGTTTATATAT-TATATTA
1 ATATACTTTATATATATATATTA
8064 ATATACTTTATATATATATAT
1 ATATACTTTATATATATATAT
8085 ATATAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (23 bp):
ATATACTTTATATATATATATTA
Found at i:8093 original size:11 final size:11
Alignment explanation
Indices: 7898--8096 Score: 55
Period size: 11 Copynumber: 18.4 Consensus size: 11
7888 CTATGTAGTG
7898 TATATATAACTA
1 TATATATAA-TA
7910 TATAT-TAATA
1 TATATATAATA
7920 -A-ACTATAA-A
1 TATA-TATAATA
* *
7929 -ATATATAGTT
1 TATATATAATA
7939 TATAT-TAATA
1 TATATATAATA
* * * *
7949 AACCATATAGTT
1 TA-TATATAATA
*
7961 TATATATAGTA
1 TATATATAATA
* *
7972 TATAATATAGTT
1 TAT-ATATAATA
*
7984 TATATATAGT-
1 TATATATAATA
7994 TCATATATACACTA
1 T-ATATATA-A-TA
*
8008 TTTATATACA-A
1 TATATATA-ATA
8019 TATATA-AATTA
1 TATATATAA-TA
*
8030 TAAATATAA-A
1 TATATATAATA
* * *
8040 -CTATATAGTT
1 TATATATAATA
*
8050 TATATATTATA
1 TATATATAATA
* *
8061 T-TAATATACTT
1 TAT-ATATAATA
8072 TATATAT-ATA
1 TATATATAATA
8082 TATATATAATA
1 TATATATAATA
8093 TATA
1 TATA
8097 ATTGTTTTAA
Statistics
Matches: 138, Mismatches: 29, Indels: 41
0.66 0.14 0.20
Matches are distributed among these distances:
8 1 0.01
9 14 0.10
10 22 0.16
11 69 0.50
12 22 0.16
13 9 0.07
14 1 0.01
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (11 bp):
TATATATAATA
Found at i:12065 original size:12 final size:12
Alignment explanation
Indices: 12049--12117 Score: 75
Period size: 12 Copynumber: 5.5 Consensus size: 12
12039 TTAAATTTAT
12049 TATTATTATTAA
1 TATTATTATTAA
*
12061 AATTATTATTAA
1 TATTATTATTAA
*
12073 TAGTATTATTAA
1 TATTATTATTAA
* *
12085 TATTAATAATATA
1 TATTATTATTA-A
12098 TATTATTTATTAAA
1 TATTA-TTATT-AA
12112 TATTAT
1 TATTAT
12118 AAGCCCAAGA
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
12 29 0.63
13 7 0.15
14 9 0.20
15 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (12 bp):
TATTATTATTAA
Found at i:27936 original size:60 final size:60
Alignment explanation
Indices: 27863--27977 Score: 196
Period size: 60 Copynumber: 1.9 Consensus size: 60
27853 TAGAAATGTA
27863 TTACTTTGAATCCTAAACTACTGGAAACACTAAACAA-GATCAAATAGATGAGTTACTAAC
1 TTACTTTGAATCCTAAACTACT-GAAACACTAAACAATGATCAAATAGATGAGTTACTAAC
* *
27923 TTACTTTGAATCCTAAGCTACTGAAACACTAGACAATGATCAAATAGATGAGTTA
1 TTACTTTGAATCCTAAACTACTGAAACACTAAACAATGATCAAATAGATGAGTTA
27978 TTGACTTGCT
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
59 13 0.25
60 39 0.75
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28
Consensus pattern (60 bp):
TTACTTTGAATCCTAAACTACTGAAACACTAAACAATGATCAAATAGATGAGTTACTAAC
Found at i:29882 original size:20 final size:20
Alignment explanation
Indices: 29857--29910 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
29847 AGTTTGAAGG
29857 TAAGTAAACACAATTACACA
1 TAAGTAAACACAATTACACA
29877 TAAGTAAACACAATTACACA
1 TAAGTAAACACAATTACACA
29897 TAAGTAAACACAAT
1 TAAGTAAACACAAT
29911 ATATAAATAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.56, C:0.19, G:0.06, T:0.20
Consensus pattern (20 bp):
TAAGTAAACACAATTACACA
Found at i:34388 original size:60 final size:60
Alignment explanation
Indices: 34294--34459 Score: 192
Period size: 60 Copynumber: 2.8 Consensus size: 60
34284 TATATATATT
* *
34294 TAGTTTG-GGATAAAATTGAAATGTTCAAAAAGTTTGGGGACCAATTGAGAAT-AAAGGTCA
1 TAGTTTGAGGATGAAATTGAAATGTTC-AAAAGTTTGGGGACTAATTGAGAATGAAA-GTCA
* * * * * *
34354 TAGTTTGAGGATGAAATTGAAATGTTCCAAAGTTTGAGGACTAATTTAGATTGATAGTCG
1 TAGTTTGAGGATGAAATTGAAATGTTCAAAAGTTTGGGGACTAATTGAGAATGAAAGTCA
* ** *
34414 TAGTTTAAGGATGAAATTGAAACATTTAAAAGTTTGGGGACTAATT
1 TAGTTTGAGGATGAAATTGAAATGTTCAAAAGTTTGGGGACTAATT
34460 TAAAATGGGG
Statistics
Matches: 90, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
60 70 0.78
61 20 0.22
ACGTcount: A:0.37, C:0.06, G:0.24, T:0.33
Consensus pattern (60 bp):
TAGTTTGAGGATGAAATTGAAATGTTCAAAAGTTTGGGGACTAATTGAGAATGAAAGTCA
Found at i:37178 original size:17 final size:18
Alignment explanation
Indices: 37158--37196 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
37148 GATACAAAGC
37158 AAAC-GAATTTACATT-AG
1 AAACTGAATTTA-ATTGAG
37175 AAACTGAATTTAATTGAG
1 AAACTGAATTTAATTGAG
37193 AAAC
1 AAAC
37197 CAACTTGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.49, C:0.10, G:0.13, T:0.28
Consensus pattern (18 bp):
AAACTGAATTTAATTGAG
Found at i:43740 original size:38 final size:38
Alignment explanation
Indices: 43682--43794 Score: 147
Period size: 38 Copynumber: 3.0 Consensus size: 38
43672 CTTCTAAAAG
* * *
43682 AGTCATTAAACAAGTTTGTTCATGAACATAAACGAACA
1 AGTCAATAAACGAGCTTGTTCATGAACATAAACGAACA
*
43720 GGTCAATTAAA-GAGCTTGTTCATGAACATAAACGAACA
1 AGTCAA-TAAACGAGCTTGTTCATGAACATAAACGAACA
* * *
43758 AGTCGATAAACGAGTTTGTTCGTGAACATAAACGAAC
1 AGTCAATAAACGAGCTTGTTCATGAACATAAACGAAC
43795 CAAACACTCC
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
37 4 0.06
38 57 0.88
39 4 0.06
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.25
Consensus pattern (38 bp):
AGTCAATAAACGAGCTTGTTCATGAACATAAACGAACA
Found at i:46945 original size:29 final size:29
Alignment explanation
Indices: 46911--46969 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
46901 CCTAAATTAA
*
46911 TTTGATCTCATTCCTTACATCAATTTAGT
1 TTTGATCTCATTCCTTACATCAATATAGT
* *
46940 TTTGATGTCATTGCTTACATCAATATAGT
1 TTTGATCTCATTCCTTACATCAATATAGT
46969 T
1 T
46970 AGGTGAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.47
Consensus pattern (29 bp):
TTTGATCTCATTCCTTACATCAATATAGT
Found at i:48826 original size:29 final size:29
Alignment explanation
Indices: 48791--48848 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
48781 ACCTAAATTA
48791 ATTTGATCTCATTGCTTACATCAATTTAG
1 ATTTGATCTCATTGCTTACATCAATTTAG
*
48820 ATTTGATGTCATTGCTTACATCAATTTAG
1 ATTTGATCTCATTGCTTACATCAATTTAG
48849 TTAGGTGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.45
Consensus pattern (29 bp):
ATTTGATCTCATTGCTTACATCAATTTAG
Found at i:50708 original size:29 final size:29
Alignment explanation
Indices: 50674--50732 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
50664 CCTAAATTAA
50674 TTTGATCTCATTGCTTACATCAATTTAGT
1 TTTGATCTCATTGCTTACATCAATTTAGT
*
50703 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATCTCATTGCTTACATCAATTTAGT
50732 T
1 T
50733 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.15, G:0.12, T:0.49
Consensus pattern (29 bp):
TTTGATCTCATTGCTTACATCAATTTAGT
Found at i:55866 original size:29 final size:29
Alignment explanation
Indices: 55793--55852 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
55783 ATTTTCACCT
*
55793 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTAATGTAAGCAATGACATCAA
55822 AACTAAATTAATGTAAGCAATGACATCAA
1 AACTAAATTAATGTAAGCAATGACATCAA
55851 AA
1 AA
55853 TAATTTAGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.52, C:0.13, G:0.12, T:0.23
Consensus pattern (29 bp):
AACTAAATTAATGTAAGCAATGACATCAA
Found at i:62723 original size:20 final size:20
Alignment explanation
Indices: 62698--62755 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
62688 TTCCCATTAA
62698 AGTGCATCGGTGCATTCTAC
1 AGTGCATCGGTGCATTCTAC
62718 AGTGCATCGGTGCATTCTAC
1 AGTGCATCGGTGCATTCTAC
*
62738 AGTGCATCGATGCATTCT
1 AGTGCATCGGTGCATTCT
62756 TTAATAGGTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.31
Consensus pattern (20 bp):
AGTGCATCGGTGCATTCTAC
Done.