Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005184.1 Hibiscus syriacus cultivar Beakdansim tig00011706_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: 75271
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Found at i:7218 original size:20 final size:20
Alignment explanation
Indices: 7183--7220 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
7173 AGCCATTTCA
*
7183 GTATCGATATCAAGGGGTGG
1 GTATCGATACCAAGGGGTGG
*
7203 GTATCGATACCTAGGGGT
1 GTATCGATACCAAGGGGT
7221 CAATACCAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.13, G:0.37, T:0.26
Consensus pattern (20 bp):
GTATCGATACCAAGGGGTGG
Found at i:8521 original size:36 final size:36
Alignment explanation
Indices: 8433--8824 Score: 343
Period size: 35 Copynumber: 10.8 Consensus size: 36
8423 TCAAATATAG
* *
8433 TTTTGGAAAATATATAATATATAGTTTTTTGAAAACTTAT
1 TTTT-GAAAACATATAATATATAGTTTTTT-AAAAC--AA
* * *
8473 TTTTAAAAAAAACATATAATATATAGTTTTTTAAAGCAG
1 TTTT---GAAAACATATAATATATAGTTTTTTAAAACAA
* *
8512 TTTTGAAAACATATATTATATAG-TTTTTAAAATAA
1 TTTTGAAAACATATAATATATAGTTTTTTAAAACAA
** *
8547 TTTTGAAAATGTATAATATATAGTTTTTTAAAATAA
1 TTTTGAAAACATATAATATATAGTTTTTTAAAACAA
* *
8583 TTTTGAAAACGTATAATA-A-AG-TTTTTAAAATAA
1 TTTTGAAAACATATAATATATAGTTTTTTAAAACAA
* *
8616 TTTTGAAAACGTATAATATATAG-TTTTTAAAATAA
1 TTTTGAAAACATATAATATATAGTTTTTTAAAACAA
* * *
8651 TTTTGAAAACGTATAATATATAGTGTTTTAAAACCGA
1 TTTTGAAAACATATAATATATAGTTTTTTAAAA-CAA
* * ***
8688 TTTTGAAAACATATAGTATATGGTTTTTTGAAAATGG
1 TTTTGAAAACATATAATATATAGTTTTTT-AAAACAA
* *
8725 TTTTGAAAACGTATAATATATA-TTTTTTAAAAACGAT
1 TTTTGAAAACATATAATATATAGTTTTTT-AAAAC-AA
* *
8762 TTTTGAGAACATATAA-ATA-A-TTTTTGAAAACATA
1 TTTTGAAAACATATAATATATAGTTTTTTAAAACA-A
* *
8796 TTTTTGAAAATATAGTATTATATAGTTTT
1 -TTTTGAAAACATA-TAATATATAGTTTT
8825 GGTTATTATA
Statistics
Matches: 300, Mismatches: 37, Indels: 31
0.82 0.10 0.08
Matches are distributed among these distances:
33 31 0.10
34 8 0.03
35 84 0.28
36 69 0.23
37 63 0.21
38 5 0.02
39 9 0.03
40 4 0.01
41 4 0.01
42 23 0.08
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.43
Consensus pattern (36 bp):
TTTTGAAAACATATAATATATAGTTTTTTAAAACAA
Found at i:8620 original size:104 final size:106
Alignment explanation
Indices: 8433--8756 Score: 382
Period size: 104 Copynumber: 3.0 Consensus size: 106
8423 TCAAATATAG
* * *
8433 TTTTGGAAAATATATAATATATAGTTTTTTGAAAACTTATTTTTAAAAAAAACATATAATATATA
1 TTTT-GAAAATGTATAATATATAGTTTTTT-AAAAC-TAATTTT---GAAAACATATAATA-A-A
** * *
8498 GTTTTTTAAAGCAGTTTTGAAAACATATATTATATAGTTTTTAAAATAA
58 GTTTTTTAAAATAGTTTTGAAAACGTATAATATATAGTTTTTAAAATAA
*
8547 TTTTGAAAATGTATAATATATAGTTTTTTAAAA-TAATTTTGAAAACGTATAATAAAG-TTTTTA
1 TTTTGAAAATGTATAATATATAGTTTTTTAAAACTAATTTTGAAAACATATAATAAAGTTTTTTA
*
8610 AAATAATTTTGAAAACGTATAATATATAGTTTTTAAAATAA
66 AAATAGTTTTGAAAACGTATAATATATAGTTTTTAAAATAA
* * ** **
8651 TTTTGAAAACGTATAATATATAGTGTTTTAAAACCGATTTTGAAAACATATAGTATATGGTTTTT
1 TTTTGAAAATGTATAATATATAGTTTTTTAAAACTAATTTTGAAAACATATA--ATAAAGTTTTT
* *
8716 TGAAAATGGTTTTGAAAACGTATAATATATATTTTTTAAAA
64 T-AAAATAGTTTTGAAAACGTATAATATATAGTTTTTAAAA
8757 ACGATTTTTG
Statistics
Matches: 186, Mismatches: 19, Indels: 15
0.85 0.09 0.07
Matches are distributed among these distances:
104 73 0.39
105 17 0.09
106 1 0.01
107 16 0.09
108 5 0.03
109 36 0.19
110 6 0.03
112 4 0.02
113 24 0.13
114 4 0.02
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.43
Consensus pattern (106 bp):
TTTTGAAAATGTATAATATATAGTTTTTTAAAACTAATTTTGAAAACATATAATAAAGTTTTTTA
AAATAGTTTTGAAAACGTATAATATATAGTTTTTAAAATAA
Found at i:11060 original size:34 final size:34
Alignment explanation
Indices: 11019--11117 Score: 162
Period size: 34 Copynumber: 2.9 Consensus size: 34
11009 CCGCCCCGAT
* *
11019 TATATATAATATTTTTTTTATTTTTTATATTAATTA
1 TATATATAATA--TTTTATATATTTTATATTAATTA
11055 TATATATAATATTTTATATATTTTATATTAATTA
1 TATATATAATATTTTATATATTTTATATTAATTA
11089 TATATATAATATTTTATATATTTTATATT
1 TATATATAATATTTTATATATTTTATATT
11118 TTATTATTTT
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
34 50 0.82
36 11 0.18
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (34 bp):
TATATATAATATTTTATATATTTTATATTAATTA
Found at i:11080 original size:25 final size:25
Alignment explanation
Indices: 11037--11127 Score: 80
Period size: 25 Copynumber: 3.6 Consensus size: 25
11027 ATATTTTTTT
*
11037 TATTTTTTATATTAATTATATATATAA
1 TATTTTATATATT--TTATATATATAA
*
11064 TATTTTATATATTTTATAT-TA-AT
1 TATTTTATATATTTTATATATATAA
* * *
11087 TATATATATAATATTTTATATATTTTA
1 TAT-TTTAT-ATATTTTATATATATAA
11114 TATTTTAT-TATTTT
1 TATTTTATATATTTT
11128 TTAATGAAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
23 4 0.08
24 12 0.23
25 17 0.32
26 5 0.09
27 15 0.28
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (25 bp):
TATTTTATATATTTTATATATATAA
Found at i:11128 original size:16 final size:16
Alignment explanation
Indices: 11018--11127 Score: 96
Period size: 16 Copynumber: 6.7 Consensus size: 16
11008 TCCGCCCCGA
** *
11018 TTATATATAATATTTT
1 TTATATATTTTATATT
* *
11034 TTTTATTTTTTATATT
1 TTATATATTTTATATT
* *
11050 AATTATATATATAATATT
1 --TTATATATTTTATATT
11068 TTATATATTTTATATT
1 TTATATATTTTATATT
* *
11084 AATTATATATATAATATT
1 --TTATATATTTTATATT
11102 TTATATATTTTATATT
1 TTATATATTTTATATT
11118 TTAT-TATTTT
1 TTATATATTTT
11128 TTAATGAAAA
Statistics
Matches: 75, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
15 6 0.08
16 43 0.57
18 26 0.35
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATATATTTTATATT
Found at i:19108 original size:3 final size:3
Alignment explanation
Indices: 19100--19132 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
19090 TTCCAGAGTT
*
19100 TTC TTC TTC TTC TTC TTC TTT TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
19133 CTTAATACGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TTC
Found at i:20755 original size:32 final size:32
Alignment explanation
Indices: 20714--20806 Score: 120
Period size: 32 Copynumber: 3.0 Consensus size: 32
20704 GAGTTGAGGG
20714 TTACCTATGTCTTTCGGGACATATGGATAGGA
1 TTACCTATGTCTTTCGGGACATATGGATAGGA
* * *
20746 TTACCTATGTCCTTCGGGACATATAGACA--A
1 TTACCTATGTCTTTCGGGACATATGGATAGGA
*
20776 TTACCTATGT-TCTTCGGAACATATGGATAGG
1 TTACCTATGTCT-TTCGGGACATATGGATAGG
20807 TCATTCGGGA
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
30 25 0.49
32 26 0.51
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (32 bp):
TTACCTATGTCTTTCGGGACATATGGATAGGA
Found at i:22674 original size:22 final size:22
Alignment explanation
Indices: 22646--22692 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
22636 CCACCAGATC
22646 GAAACGTATCTTGAAGAGGAGG
1 GAAACGTATCTTGAAGAGGAGG
*
22668 GAAACGTATCTTGAGGAGGAGG
1 GAAACGTATCTTGAAGAGGAGG
22690 GAA
1 GAA
22693 TACCTTTGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.36, C:0.09, G:0.38, T:0.17
Consensus pattern (22 bp):
GAAACGTATCTTGAAGAGGAGG
Found at i:23812 original size:59 final size:58
Alignment explanation
Indices: 23713--24177 Score: 294
Period size: 59 Copynumber: 7.9 Consensus size: 58
23703 ACATTCTATA
* * * * * *
23713 GGAAATTCATACAATTAGTATAATTTCCTTATAATATTAGCACTTTTAGTGCTCTATCT
1 GGAAA-TCATATACTTAGTATGATTTCCTTATCATTTTAGCACATTTAGTGCTCTATCT
* * *** *
23772 GGAATATCATATACTTAATATGATTTCCTTCTCATTTTAGCACACGAAGTGCCCTAT-T
1 GGAA-ATCATATACTTAGTATGATTTCCTTATCATTTTAGCACATTTAGTGCTCTATCT
** * * * * ** * *
23830 CAAAAATC-CATACATTAGTATGATTTCTTTACCATTTTAGCATATGAAATGCTCTATGT
1 -GGAAATCATATAC-TTAGTATGATTTCCTTATCATTTTAGCACATTTAGTGCTCTATCT
* * * * * *
23889 GAAAATCCATA-CCATTAGTATGATTTCCTTATCCTTGTAGCACCTTTAGTGCTTTATCT
1 GGAAAT-CATATAC-TTAGTATGATTTCCTTATCATTTTAGCACATTTAGTGCTCTATCT
* * * * * * *
23948 -GAGAATCCATACACTCAGTATGATTCCCTTACCATTTTAGCACATATAATGCCCTATCT
1 GGA-AAT-CATATACTTAGTATGATTTCCTTATCATTTTAGCACATTTAGTGCTCTATCT
* * * * * * *
24007 AGAAATCCATATA-TTCAATATGATTTCCTTATCATTTTATCACACTTAGTGATCCATAT
1 GGAAAT-CATATACTT-AGTATGATTTCCTTATCATTTTAGCACATTTAGTGCTCTATCT
* * * * * *
24066 GGAAATTCATACACTTAGTATGATTTACTTATCATTTTAGCACACTCAGAT-CTCCATAT
1 GGAAA-TCATATACTTAGTATGATTTCCTTATCATTTTAGCACATTTAG-TGCTCTATCT
* ** *
24125 GGAAATTCATACACTCGGTATGATTTCCTTATCATTTTTAGCACATATAGTGC
1 GGAAA-TCATATACTTAGTATGATTTCCTTATCA-TTTTAGCACATTTAGTGC
24178 CATTTGGTAA
Statistics
Matches: 316, Mismatches: 75, Indels: 29
0.75 0.18 0.07
Matches are distributed among these distances:
57 4 0.01
58 46 0.15
59 244 0.77
60 22 0.07
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (58 bp):
GGAAATCATATACTTAGTATGATTTCCTTATCATTTTAGCACATTTAGTGCTCTATCT
Found at i:26935 original size:35 final size:35
Alignment explanation
Indices: 26867--27068 Score: 237
Period size: 35 Copynumber: 5.8 Consensus size: 35
26857 TTATTTTTAA
* *
26867 AAAACATATAATATGTAGTTTTTTAAAACAATTTTG
1 AAAACATATAATATATAG-TTTTTAAAATAATTTTG
* * *
26903 AAAACATATAGTGTATATTTTTTAAAATAATTTTG
1 AAAACATATAATATATAGTTTTTAAAATAATTTTG
** ***
26938 AAAATGTATAATATATAGTTTTTAAAACGTTTTTG
1 AAAACATATAATATATAGTTTTTAAAATAATTTTG
* *
26973 AAAACATATAGTATATAGTGTTTTATAATAATTTTG
1 AAAACATATAATATATAGT-TTTTAAAATAATTTTG
*
27009 AAAACGTATAATA-A-AGTTTTTAAAATAATTTTG
1 AAAACATATAATATATAGTTTTTAAAATAATTTTG
* *
27042 AAAACGTATAATGTATAGTTTTTAAAA
1 AAAACATATAATATATAGTTTTTAAAA
27069 AACGGCTTCG
Statistics
Matches: 139, Mismatches: 24, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
33 27 0.19
34 4 0.03
35 71 0.51
36 37 0.27
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.43
Consensus pattern (35 bp):
AAAACATATAATATATAGTTTTTAAAATAATTTTG
Found at i:26948 original size:71 final size:69
Alignment explanation
Indices: 26867--27068 Score: 253
Period size: 71 Copynumber: 2.9 Consensus size: 69
26857 TTATTTTTAA
*
26867 AAAACATATAATATGTAGTTTTTTAAAACAATTTTGAAAACATATAGTGTATATTTTTTAAAATA
1 AAAACGTATAATAT-TAG-TTTTTAAAACAATTTTGAAAACATATAGTGTATATTTTTTAAAATA
26932 ATTTTG
64 ATTTTG
* ** * * *
26938 AAAATGTATAATATATAGTTTTTAAAACGTTTTTGAAAACATATAGTATATAGTGTTTTATAATA
1 AAAACGTATAATAT-TAGTTTTTAAAACAATTTTGAAAACATATAGTGTATA-TTTTTTAAAATA
27003 ATTTTG
64 ATTTTG
* * * * *
27009 AAAACGTATAATA-AAGTTTTTAAAATAATTTTGAAAACGTATAATGTATAGTTTTTAAAA
1 AAAACGTATAATATTAGTTTTTAAAACAATTTTGAAAACATATAGTGTATATTTTTTAAAA
27069 AACGGCTTCG
Statistics
Matches: 111, Mismatches: 19, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
68 7 0.06
69 30 0.27
70 31 0.28
71 43 0.39
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.43
Consensus pattern (69 bp):
AAAACGTATAATATTAGTTTTTAAAACAATTTTGAAAACATATAGTGTATATTTTTTAAAATAAT
TTTG
Found at i:30607 original size:94 final size:96
Alignment explanation
Indices: 30468--30646 Score: 265
Period size: 94 Copynumber: 1.9 Consensus size: 96
30458 CCTGGTATCG
* * *
30468 ATACTTCTATACTGTGGTACCGATACTCCCTTTCAGTATCAATACCATTTCTACATTCTG-GATC
1 ATACTTCTATACTATGGTACCGATACTCCATTTCAGTATCAATACCATTTCTACATTCTGTAATC
*
30532 CATGGTATCGATA-CTTCTCTCCCAGTACCA
66 AATGGTATCGATACCTTCTCTCCCAGTACCA
** *
30562 ATACTTCTATACTATGGTACCGATACTCCATTAT-AGTATTGATACCATTTCTGCATTCTGTAAT
1 ATACTTCTATACTATGGTACCGATACTCCATT-TCAGTATCAATACCATTTCTACATTCTGTAAT
30626 CAATGGTATCGATACCTTCTC
65 CAATGGTATCGATACCTTCTC
30647 CATAGTATCG
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
94 53 0.71
95 16 0.21
96 6 0.08
ACGTcount: A:0.26, C:0.26, G:0.12, T:0.37
Consensus pattern (96 bp):
ATACTTCTATACTATGGTACCGATACTCCATTTCAGTATCAATACCATTTCTACATTCTGTAATC
AATGGTATCGATACCTTCTCTCCCAGTACCA
Found at i:35268 original size:13 final size:13
Alignment explanation
Indices: 35228--35277 Score: 68
Period size: 13 Copynumber: 3.9 Consensus size: 13
35218 CTAAAAACAA
35228 AAATAAAATGAAAT
1 AAATAAAAT-AAAT
35242 AAAT--AATAAAT
1 AAATAAAATAAAT
*
35253 AAATAAAATAACT
1 AAATAAAATAAAT
35266 AAATAAAATAAA
1 AAATAAAATAAA
35278 CAAAACTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
11 8 0.25
12 3 0.09
13 17 0.53
14 4 0.12
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (13 bp):
AAATAAAATAAAT
Found at i:35335 original size:22 final size:22
Alignment explanation
Indices: 35307--35350 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
35297 ATTTTCAAAA
*
35307 ATATGTTTTCAAAAATTATTTT
1 ATATGTTCTCAAAAATTATTTT
*
35329 ATATGTTCTCAAAAATTGTTTT
1 ATATGTTCTCAAAAATTATTTT
35351 TAAAAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (22 bp):
ATATGTTCTCAAAAATTATTTT
Found at i:35378 original size:37 final size:36
Alignment explanation
Indices: 35279--35775 Score: 313
Period size: 36 Copynumber: 13.8 Consensus size: 36
35269 TAAAATAAAC
* * * *
35279 AAAACTATATAATACTATATTTTCAAAAATATG-TTTTC
1 AAAAATATATATTA-TATGTTTTC-AAAAT-TGTTTTTA
* *
35317 AAAAAT-TATTTTATATGTTCTCAAAAATTGTTTTTA
1 AAAAATATATATTATATGTTTTC-AAAATTGTTTTTA
* ** *
35353 AAAAATATATATTATACGTTTTCAAAACCGTTTTCA
1 AAAAATATATATTATATGTTTTCAAAATTGTTTTTA
* *
35389 AAAAACCATATACTATATGTTTTCAAAATCAT-TTTTTA
1 AAAAA-TATATATTATATGTTTTCAAAAT--TGTTTTTA
* * *
35427 AAAACTATATATTATATATTTTCAAAATT-ATTTTA
1 AAAAATATATATTATATGTTTTCAAAATTGTTTTTA
* * * * *
35462 TAAACT-T-TATTATACGTTTTAAAAATT-ATTTTA
1 AAAAATATATATTATATGTTTTCAAAATTGTTTTTA
** **
35495 AAAAACTATATATTATATGTTTTTTAAACCG-TTTTA
1 AAAAA-TATATATTATATGTTTTCAAAATTGTTTTTA
** * * * *
35531 AAAGCTATATATTAAACGTTTTCAATATT-ATTTTA
1 AAAAATATATATTATATGTTTTCAAAATTGTTTTTA
* * *
35566 AAAACT-T-TATTATACGTTTTCAAAATT-ATTTTA
1 AAAAATATATATTATATGTTTTCAAAATTGTTTTTA
* *
35599 AAAAACTATATACTATATGTTTTCAAAATCG-TTTTA
1 AAAAA-TATATATTATATGTTTTCAAAATTGTTTTTA
* * *
35635 AAAACTATATATTATACGTTTTCAAAATT-ATTTT-
1 AAAAATATATATTATATGTTTTCAAAATTGTTTTTA
* * * * *
35669 AAAAATAATATAGTATATATATTCAAAACTATTTTTA
1 AAAAAT-ATATATTATATGTTTTCAAAATTGTTTTTA
* * **
35706 AAAAACTATATATTATATGTTTATTAAAAATAAGTTTCCA
1 AAAAA-TATATATTATATG-TT-TTCAAAAT-TGTTTTTA
* *
35746 AAAACTATATATTATATATTTTCCAAAATT
1 AAAAATATATATTATATGTTTT-CAAAATT
35776 ATATTTGAAA
Statistics
Matches: 362, Mismatches: 74, Indels: 47
0.75 0.15 0.10
Matches are distributed among these distances:
33 54 0.15
34 9 0.02
35 85 0.23
36 91 0.25
37 74 0.20
38 23 0.06
39 18 0.05
40 8 0.02
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.45
Consensus pattern (36 bp):
AAAAATATATATTATATGTTTTCAAAATTGTTTTTA
Found at i:35541 original size:35 final size:35
Alignment explanation
Indices: 35348--35761 Score: 354
Period size: 35 Copynumber: 11.6 Consensus size: 35
35338 CAAAAATTGT
* * *
35348 TTTTAAAAAATATATATTATACGTTTTCAAAACCG
1 TTTTAAAAACTATATATTATACGTTTTCAAAATCA
* * *
35383 TTTTCAAAAAACCATATACTATATGTTTTCAAAATCA
1 TTTT--AAAAACTATATATTATACGTTTTCAAAATCA
** *
35420 TTTTTTAAAAACTATATATTATATATTTTCAAAATTA
1 --TTTTAAAAACTATATATTATACGTTTTCAAAATCA
* * *
35457 TTTTATAAACT-T-TATTATACGTTTTAAAAATTA
1 TTTTAAAAACTATATATTATACGTTTTCAAAATCA
* ** * *
35490 TTTTAAAAAACTATATATTATATGTTTTTTAAACCG
1 TTTT-AAAAACTATATATTATACGTTTTCAAAATCA
* * * *
35526 TTTTAAAAGCTATATATTAAACGTTTTCAATATTA
1 TTTTAAAAACTATATATTATACGTTTTCAAAATCA
*
35561 TTTTAAAAACT-T-TATTATACGTTTTCAAAATTA
1 TTTTAAAAACTATATATTATACGTTTTCAAAATCA
* * *
35594 TTTTAAAAAACTATATACTATATGTTTTCAAAATCG
1 TTTT-AAAAACTATATATTATACGTTTTCAAAATCA
*
35630 TTTTAAAAACTATATATTATACGTTTTCAAAATTA
1 TTTTAAAAACTATATATTATACGTTTTCAAAATCA
* ** *
35665 TTTTAAAAA-TAATATAGTATATATATTCAAAA-CTA
1 TTTTAAAAACT-ATATATTATACGTTTTCAAAATC-A
* * *
35700 TTTTTAAAAAACTATATATTATATGTTTATTAAAAATAA
1 -TTTT-AAAAACTATATATTATACG-TT-TTCAAAATCA
*
35739 GTTTCCAAAAACTATATATTATA
1 -TTT-TAAAAACTATATATTATA
35762 TATTTTCCAA
Statistics
Matches: 307, Mismatches: 53, Indels: 34
0.78 0.13 0.09
Matches are distributed among these distances:
33 45 0.15
34 16 0.05
35 102 0.33
36 44 0.14
37 67 0.22
38 2 0.01
39 31 0.10
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.45
Consensus pattern (35 bp):
TTTTAAAAACTATATATTATACGTTTTCAAAATCA
Found at i:35561 original size:104 final size:103
Alignment explanation
Indices: 35362--35793 Score: 445
Period size: 104 Copynumber: 4.1 Consensus size: 103
35352 AAAAAATATA
** * **
35362 TATTATACGTTTTCAAAACCGTTTTCAAAAAACCATATACTATATGTTTTCAAAATCATTTTTTA
1 TATTATACGTTTTCAAAACTATTTT-AAAAAACTATATACTATATGTTTTCAAAA-C-CGTTTTA
**
35427 AAAACTATATATTATATATTTTCAAAATTATTTTATAAACTT
63 AAAACTATATATTATACGTTTTCAAAATTATTTTA-AAACTT
* * * **
35469 TATTATACGTTTTAAAAATTATTTTAAAAAACTATATATTATATGTTTTTTAAACCGTTTTAAAA
1 TATTATACGTTTTCAAAACTATTTTAAAAAACTATATACTATATGTTTTCAAAACCGTTTTAAAA
* * *
35534 GCTATATATTAAACGTTTTCAATATTATTTTAAAAACTT
66 ACTATATATTATACGTTTTCAAAATTATTTT-AAAACTT
* *
35573 TATTATACGTTTTCAAAATTATTTTAAAAAACTATATACTATATGTTTTCAAAATCGTTTTAAAA
1 TATTATACGTTTTCAAAACTATTTTAAAAAACTATATACTATATGTTTTCAAAACCGTTTTAAAA
*
35638 ACTATATATTATACGTTTTCAAAATTATTTTAAAAATAAT
66 ACTATATATTATACGTTTTCAAAATTATTTTAAAACT--T
* ** * * * **
35678 ATAGTATATATATTCAAAACTATTTTTAAAAAACTATATATTATATGTTTATTAAAAATAAGTTT
1 -TATTATACGTTTTCAAAACTA-TTTTAAAAAACTATATACTATATG-TT-TTCAAAA-CCGTTT
* ** *
35743 CCAAAAACTATATATTATATATTTTCCAAAATTATATTTGAAA--T
61 -TAAAAACTATATATTATACGTTTT-CAAAATTAT-TTTAAAACTT
35787 TATTATA
1 TATTATA
35794 TATACTATGC
Statistics
Matches: 276, Mismatches: 38, Indels: 21
0.82 0.11 0.06
Matches are distributed among these distances:
103 5 0.02
104 128 0.46
105 3 0.01
106 41 0.15
107 44 0.16
108 8 0.03
109 7 0.03
110 4 0.01
111 21 0.08
112 9 0.03
113 6 0.02
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (103 bp):
TATTATACGTTTTCAAAACTATTTTAAAAAACTATATACTATATGTTTTCAAAACCGTTTTAAAA
ACTATATATTATACGTTTTCAAAATTATTTTAAAACTT
Found at i:35716 original size:70 final size:68
Alignment explanation
Indices: 35360--35716 Score: 204
Period size: 69 Copynumber: 5.1 Consensus size: 68
35350 TTAAAAAATA
*** * * *
35360 TATATTATACGTTTTCAAAACCGTTTTCAAAAAACCATATACTATATGTTTTCAAAATCATTTTT
1 TATATTATACGTTTTCAAAATTATTTT-AAAAAA-CATATACTATATATATTCAAAAT-A-GTTT
35425 TAAAAAC
62 TAAAAAC
** * * * ** * *
35432 TATATATTATATATTTTCAAAATTATTTT-ATAAAC-TTTATTATACGTTTTAAAAATTA-TTTT
1 --TATATTATACGTTTTCAAAATTATTTTAAAAAACATATACTATATATATTCAAAA-TAGTTTT
35494 AAAAAAC
63 -AAAAAC
* ** *** * * * ** * *
35501 TATATATTATATGTTTTTTAAACCGTTTT-AAAAGCTATATATTAAACGTTTTCAATATTA-TTT
1 --TATATTATACGTTTTCAAAATTATTTTAAAAAAC-ATATACTATATATATTCAA-AATAGTTT
35564 TAAAAAC
62 TAAAAAC
* * * *
35571 TTTATTATACGTTTTCAAAATTATTTTAAAAAACTATATACTATATGTTTTCAAAATCGTTTTAA
1 TATATTATACGTTTTCAAAATTATTTTAAAAAAC-ATATACTATATATATTCAAAATAGTTTTAA
35636 AAAC
65 AAAC
* *
35640 TATATATTATACGTTTTCAAAATTATTTTAAAAATA-ATATAGTATATATATTCAAAACTATTTT
1 --TATATTATACGTTTTCAAAATTATTTTAAAAA-ACATATACTATATATATTCAAAA-TAGTTT
35704 TAAAAAAC
62 T-AAAAAC
35712 TATAT
1 TATAT
35717 ATTATATGTT
Statistics
Matches: 230, Mismatches: 41, Indels: 28
0.77 0.14 0.09
Matches are distributed among these distances:
68 26 0.11
69 65 0.28
70 46 0.20
71 59 0.26
72 12 0.05
74 22 0.10
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (68 bp):
TATATTATACGTTTTCAAAATTATTTTAAAAAACATATACTATATATATTCAAAATAGTTTTAAA
AAC
Found at i:43676 original size:21 final size:21
Alignment explanation
Indices: 43651--43692 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
43641 ATATATTAAT
43651 GAAGAAAATTCGAATTCTAAA
1 GAAGAAAATTCGAATTCTAAA
43672 GAAGAAAATTCGAATTCTAAA
1 GAAGAAAATTCGAATTCTAAA
43693 AAATTTCAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.10, G:0.14, T:0.24
Consensus pattern (21 bp):
GAAGAAAATTCGAATTCTAAA
Found at i:49102 original size:37 final size:36
Alignment explanation
Indices: 49027--49102 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
49017 TTTTTATATT
*
49027 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
49063 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
49100 TTT
1 TTT
49103 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:51459 original size:33 final size:35
Alignment explanation
Indices: 51388--51462 Score: 109
Period size: 35 Copynumber: 2.2 Consensus size: 35
51378 AAAATACTTT
*
51388 AATTTAGGGTTTAAAATGTAATTAAAGTATTTTGG
1 AATTTTGGGTTTAAAATGTAATTAAAGTATTTTGG
* *
51423 AATTTTGGGTTTAGAATGTAA-T-AAGTGTTTTGG
1 AATTTTGGGTTTAAAATGTAATTAAAGTATTTTGG
51456 AATTTTG
1 AATTTTG
51463 AACATGAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
33 17 0.46
34 1 0.03
35 19 0.51
ACGTcount: A:0.32, C:0.00, G:0.23, T:0.45
Consensus pattern (35 bp):
AATTTTGGGTTTAAAATGTAATTAAAGTATTTTGG
Found at i:53189 original size:64 final size:64
Alignment explanation
Indices: 53116--53237 Score: 174
Period size: 64 Copynumber: 1.9 Consensus size: 64
53106 GCATAAATCC
* *
53116 CATTTGATGTTTGTATTTT-AAGCAGGTGCATCGATGCACTACTTGTGCATCGATACACTGATGG
1 CATTCGATGTTTGTATTTTAAAGCA-GTGCATCGATGCACTACATGTGCATCGATACACTGATGG
* * * *
53180 CATTCGATGTTTTTATTTTAAAGGAGTGCATCGATGCATTTCATGTGCATCGATACAC
1 CATTCGATGTTTGTATTTTAAAGCAGTGCATCGATGCACTACATGTGCATCGATACAC
53238 CTTGAACAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
64 47 0.92
65 4 0.08
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37
Consensus pattern (64 bp):
CATTCGATGTTTGTATTTTAAAGCAGTGCATCGATGCACTACATGTGCATCGATACACTGATGG
Found at i:55036 original size:12 final size:12
Alignment explanation
Indices: 55019--55043 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55009 TTCAGGTTGA
55019 CTTCTACCTCTT
1 CTTCTACCTCTT
55031 CTTCTACCTCTT
1 CTTCTACCTCTT
55043 C
1 C
55044 CTCTTTGAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.44, G:0.00, T:0.48
Consensus pattern (12 bp):
CTTCTACCTCTT
Found at i:57444 original size:21 final size:21
Alignment explanation
Indices: 57416--57465 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
57406 TTCTAAATCT
57416 ATAT-AGTAATACATTGATAC
1 ATATCAGTAATACATTGATAC
57436 ATATCAGTAATACATTGATAC
1 ATATCAGTAATACATTGATAC
57457 ATATCAGTA
1 ATATCAGTA
57466 TACTAATGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 4 0.14
21 25 0.86
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (21 bp):
ATATCAGTAATACATTGATAC
Found at i:57694 original size:64 final size:64
Alignment explanation
Indices: 57621--57741 Score: 154
Period size: 64 Copynumber: 1.9 Consensus size: 64
57611 GCATAAATTC
* *
57621 CATTTGATGTTTGTATTTT-AAGCAGGTACATCGATGCACTACTTGTGCATCGATACAATGATGG
1 CATTCGATGTTTGTATTTTAAAGCA-GTACATCGATGCACTACATGTGCATCGATACAATGATGG
* * * * * *
57685 CATTCGATGTTTTTATTTTAAAGGAGTGCATTGATGCATTTCATGTGCATCGATACA
1 CATTCGATGTTTGTATTTTAAAGCAGTACATCGATGCACTACATGTGCATCGATACA
57742 CCTTGAACAA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
64 44 0.92
65 4 0.08
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (64 bp):
CATTCGATGTTTGTATTTTAAAGCAGTACATCGATGCACTACATGTGCATCGATACAATGATGG
Found at i:61939 original size:64 final size:64
Alignment explanation
Indices: 61871--61992 Score: 174
Period size: 64 Copynumber: 1.9 Consensus size: 64
61861 GTATAAATCT
* *
61871 CATTCGATGTTTGTATTTT-AAGCAGGTGCATCGATACACTACTTGTGCATCGATACACTGATGG
1 CATTCGATGTTTGTATTTTAAAGCA-GTACATCGATACACTACATGTGCATCGATACACTGATGG
* * * *
61935 CATTCGATGTTTTTATTTTAAAGGAGTACATCGATGCACTTCATGTGCATCGATACAC
1 CATTCGATGTTTGTATTTTAAAGCAGTACATCGATACACTACATGTGCATCGATACAC
61993 CTTGAACAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
64 47 0.92
65 4 0.08
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (64 bp):
CATTCGATGTTTGTATTTTAAAGCAGTACATCGATACACTACATGTGCATCGATACACTGATGG
Found at i:70259 original size:18 final size:18
Alignment explanation
Indices: 70236--70271 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
70226 CAAGAAAAAC
70236 GCAAAGGAACCGTGAAAG
1 GCAAAGGAACCGTGAAAG
70254 GCAAAGGAACCGTGAAAG
1 GCAAAGGAACCGTGAAAG
70272 TGAAGCTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.17, G:0.33, T:0.06
Consensus pattern (18 bp):
GCAAAGGAACCGTGAAAG
Found at i:74594 original size:22 final size:23
Alignment explanation
Indices: 74547--74594 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
74537 ATTTTTTTTT
*
74547 TATTTTTTTCTTAATTTATTAAA
1 TATTTTTTTCTTAATTTAATAAA
* *
74570 TATTTTTTT-TTATTTTAATATA
1 TATTTTTTTCTTAATTTAATAAA
74592 TAT
1 TAT
74595 ATATTTATCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (23 bp):
TATTTTTTTCTTAATTTAATAAA
Found at i:74737 original size:25 final size:25
Alignment explanation
Indices: 74681--74735 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 25
74671 TAATTTAATA
74681 TAAAAATATATTTTACTCTTATTATT
1 TAAAAATATATTTTA-TCTTATTATT
74707 T-AAAATATAATTTT-TCTTATT-TT
1 TAAAAATAT-ATTTTATCTTATTATT
74730 TAAAAA
1 TAAAAA
74736 ATTAGATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
23 3 0.11
24 11 0.41
25 7 0.26
26 6 0.22
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (25 bp):
TAAAAATATATTTTATCTTATTATT
Found at i:75024 original size:27 final size:28
Alignment explanation
Indices: 74964--75027 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
74954 TTTTTACATT
* *
74964 AAAATAAAAAATATTTAATAAATTAATAC
1 AAAAT-AAAAATATTTAATAAATAAAAAC
*
74993 AAAATAAAAATATTTAATAAGTAAAAAC
1 AAAATAAAAATATTTAATAAATAAAAAC
75021 -AAATAAA
1 AAAATAAA
75028 GAGATAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
27 7 0.22
28 20 0.62
29 5 0.16
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.27
Consensus pattern (28 bp):
AAAATAAAAATATTTAATAAATAAAAAC
Done.