Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003512.1 Hibiscus syriacus cultivar Beakdansim tig00007423_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: 62952
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1538 original size:17 final size:18
Alignment explanation
Indices: 1506--1542 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
1496 ACTGTCACGG
1506 AATAGACGACGAGAGAGA
1 AATAGACGACGAGAGAGA
*
1524 AATAGATGA-GAGAGAGA
1 AATAGACGACGAGAGAGA
1541 AA
1 AA
1543 AGGAAACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.54, C:0.05, G:0.32, T:0.08
Consensus pattern (18 bp):
AATAGACGACGAGAGAGA
Found at i:3278 original size:17 final size:18
Alignment explanation
Indices: 3256--3289 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3246 AGCAGGTGTG
3256 AAAGATGCTAG-TGATAA
1 AAAGATGCTAGTTGATAA
*
3273 AAAGATTCTAGTTGATA
1 AAAGATGCTAGTTGATA
3290 TGTTGTTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.44, C:0.06, G:0.21, T:0.29
Consensus pattern (18 bp):
AAAGATGCTAGTTGATAA
Found at i:3576 original size:27 final size:27
Alignment explanation
Indices: 3546--3606 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
3536 ATTTTAACTT
3546 TGAAATGTCGTCCTATAATACAATTCC
1 TGAAATGTCGTCCTATAATACAATTCC
* * *
3573 TGAAATGTCGTCGTATGATCCAATTCC
1 TGAAATGTCGTCCTATAATACAATTCC
3600 TGAAATG
1 TGAAATG
3607 GTTCAGTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (27 bp):
TGAAATGTCGTCCTATAATACAATTCC
Found at i:6512 original size:27 final size:28
Alignment explanation
Indices: 6455--6512 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
6445 AGAGCTACAC
6455 AAAAAATCTGAATATCCGATTTTGGGTAA
1 AAAAAATCTGAATATCCGATTTTGGG-AA
*
6484 AAAATATCTGAA-A-CCGGATTTT-GGAA
1 AAAAAATCTGAATATCC-GATTTTGGGAA
6510 AAA
1 AAA
6513 CCGATTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 5 0.19
27 4 0.15
28 7 0.26
29 11 0.41
ACGTcount: A:0.45, C:0.10, G:0.17, T:0.28
Consensus pattern (28 bp):
AAAAAATCTGAATATCCGATTTTGGGAA
Found at i:13965 original size:20 final size:20
Alignment explanation
Indices: 13924--13969 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
13914 GACATTATAT
**
13924 TTTTAATTATTTTTCTTGTA
1 TTTTAATTATTTTTAATGTA
13944 TTTTAATTATTATTTAAT-TA
1 TTTTAATTATT-TTTAATGTA
13964 TTTTAA
1 TTTTAA
13970 GCACTTAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTTAATTATTTTTAATGTA
Found at i:14995 original size:12 final size:11
Alignment explanation
Indices: 14974--15004 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
14964 TGAATAAAAT
14974 TAATTAAATAA
1 TAATTAAATAA
14985 TAATATAAATAA
1 TAAT-TAAATAA
14997 TAATTAAA
1 TAATTAAA
15005 AATTAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
TAATTAAATAA
Found at i:15486 original size:65 final size:65
Alignment explanation
Indices: 15382--15509 Score: 177
Period size: 65 Copynumber: 2.0 Consensus size: 65
15372 TTTTGTCGTC
* *
15382 ATTTGTGGCTATTTGGTTCAACTGACCTACCTAAACACCG-TCCATATCTACACCAAGATAACAT
1 ATTTGAGGCTATTTGGTTCAACTGACCCACCTAAACACCGCT-CATATCTACACCAAGATAACAT
15446 T
65 T
* * * * *
15447 ATTTGAGGCTATTTGGTTCAGCTGACCCACCTAGACACCGCTCATATTTATACCAAGGTAACA
1 ATTTGAGGCTATTTGGTTCAACTGACCCACCTAAACACCGCTCATATCTACACCAAGATAACA
15510 CTAATCGTGC
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
65 54 0.98
66 1 0.02
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.30
Consensus pattern (65 bp):
ATTTGAGGCTATTTGGTTCAACTGACCCACCTAAACACCGCTCATATCTACACCAAGATAACATT
Found at i:15723 original size:15 final size:15
Alignment explanation
Indices: 15672--15727 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
15662 CAAATGTTAT
*
15672 GGGTACTCGGTAATC
1 GGGTACCCGGTAATC
* **
15687 GGGTATCCGGATTTTGC
1 GGGTACCCGG-TAAT-C
15704 GGGTACCCGGTAATC
1 GGGTACCCGGTAATC
15719 GGGTACCCG
1 GGGTACCCG
15728 ATACCCGGTT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
15 18 0.56
16 4 0.12
17 10 0.31
ACGTcount: A:0.16, C:0.23, G:0.36, T:0.25
Consensus pattern (15 bp):
GGGTACCCGGTAATC
Found at i:16841 original size:99 final size:100
Alignment explanation
Indices: 16729--16925 Score: 283
Period size: 99 Copynumber: 2.0 Consensus size: 100
16719 ATGTAACCGT
* *
16729 TTAAAATAAAATAAGCGCTACATATTACGTTAAACTATA-TACC-AGTTTGTTTAAA-GTATAAT
1 TTAAAATAAAATAAGCACTACATATTACGTTAAACTA-ACTACCGA-TTTGTTTAAAGGTATAAG
** *
16791 ATTAATGTAAAAAGTAAATTATTTACAACTTAACCAG
64 AACAATGTAAAAAGTAAAATATTTACAACTTAACCAG
*
16828 TTAAAATAAAATAAGCACTACCTATTACGTTAAACTAACTACCGATTTGTTTAAAGGTATAAGAA
1 TTAAAATAAAATAAGCACTACATATTACGTTAAACTAACTACCGATTTGTTTAAAGGTATAAGAA
**
16893 CAATGTAAACGGTAAAATATTTACAACTTAACC
66 CAATGTAAAAAGTAAAATATTTACAACTTAACC
16926 GTTTGAAATA
Statistics
Matches: 87, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
98 1 0.01
99 49 0.56
100 37 0.43
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.32
Consensus pattern (100 bp):
TTAAAATAAAATAAGCACTACATATTACGTTAAACTAACTACCGATTTGTTTAAAGGTATAAGAA
CAATGTAAAAAGTAAAATATTTACAACTTAACCAG
Found at i:17757 original size:108 final size:106
Alignment explanation
Indices: 17598--17925 Score: 379
Period size: 107 Copynumber: 3.1 Consensus size: 106
17588 ATATTACACC
* * * * * *
17598 TATTTTGTTATCATGAGATTTATAAGGCTCATCAGCTTAAACTTTGTTAACATTTTAGGCGGTAC
1 TATTTTATTATCGTCAGATTT-TAAGGCCCATCAGCTTAAACTTTGATAACATTTTAGGCGCTAC
*
17663 CTAATATGTTGATAATATTAATAACAAAATAAATAATTAATC-
65 CTAATATGTTGATAATATTAATAACAAAATAAGTAATTAA-CA
* * * * * *
17705 TATTTTATTATTGTCGGATTTCTAAGGGCCCATCAACTTAAACTTTGGTAACATTCTAGGCGTTA
1 TATTTTATTATCGTCAGATTT-TAA-GGCCCATCAGCTTAAACTTTGATAACATTTTAGGCGCTA
*
17770 CCTAATACGTTGATAATATTAATAACAAAATAAGTAATTAACA
64 CCTAATATGTTGATAATATTAATAACAAAATAAGTAATTAACA
* * * * * * *
17813 TATTTTGTTATCGTCAAATATTTAAGGCCCATCAGCTTAAACTCTCATAATATATTAGGTGCTAC
1 TATTTTATTATCGTCAGAT-TTTAAGGCCCATCAGCTTAAACTTTGATAACATTTTAGGCGCTAC
* * * *
17878 TTAATATGTTGATAATATTAATAAAAAAATAAGTAATTTACT
65 CTAATATGTTGATAATATTAATAACAAAATAAGTAATTAACA
17920 TATTTT
1 TATTTT
17926 CTTACCGTTT
Statistics
Matches: 187, Mismatches: 31, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
107 94 0.50
108 91 0.49
109 2 0.01
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (106 bp):
TATTTTATTATCGTCAGATTTTAAGGCCCATCAGCTTAAACTTTGATAACATTTTAGGCGCTACC
TAATATGTTGATAATATTAATAACAAAATAAGTAATTAACA
Found at i:19030 original size:31 final size:31
Alignment explanation
Indices: 18955--19047 Score: 107
Period size: 31 Copynumber: 3.0 Consensus size: 31
18945 TAAGTATGAA
* *
18955 AGTTTGATAAATTTAATAATTATTTAATAAC
1 AGTTTGATAAATTTAATGATTATTTTATAAC
* **
18986 A-ATCAATATAATTTAATGATTATTTTATAAC
1 AGTTTGATA-AATTTAATGATTATTTTATAAC
* *
19017 AGTTTGATAAATTTAATGACTATTATATAAC
1 AGTTTGATAAATTTAATGATTATTTTATAAC
19048 TTTTAGAAGT
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
30 4 0.08
31 42 0.84
32 4 0.08
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.44
Consensus pattern (31 bp):
AGTTTGATAAATTTAATGATTATTTTATAAC
Found at i:20253 original size:20 final size:20
Alignment explanation
Indices: 20230--20272 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
20220 GTTTCCAAAT
20230 TCGCAACGCGAATCTGTAAA
1 TCGCAACGCGAATCTGTAAA
* *
20250 TCGCAACGTGAATTTGTAAA
1 TCGCAACGCGAATCTGTAAA
20270 TCG
1 TCG
20273 TAACACAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGAATCTGTAAA
Found at i:20314 original size:60 final size:61
Alignment explanation
Indices: 20250--20496 Score: 240
Period size: 60 Copynumber: 4.1 Consensus size: 61
20240 AATCTGTAAA
* * *
20250 TCGCAACGTGAATTTGTAAA-TCGTAACACAAAAGTCAAATTCGCAACACAGAAGTCAAAT
1 TCGCAACGCGAATTTGTAAATTCGCAACGCAAAAGTCAAATTCGCAACACAGAAGTCAAAT
* * * * *
20310 TCGCAACGCG-A-TAGTCAAATTCGTAACGCGATAGTCAAATTCGCAACACAAAAGTCAAAT
1 TCGCAACGCGAATTTGT-AAATTCGCAACGCAAAAGTCAAATTCGCAACACAGAAGTCAAAT
* * **
20370 TCGCAATGCGAATCTGTAAA-TCGCAACGCGAATTTGT-AAA-TCGCAACACAGAAGTCAAAT
1 TCGCAACGCGAATTTGTAAATTCGCAACGC-AA-AAGTCAAATTCGCAACACAGAAGTCAAAT
* * * * *
20430 TCACAACGCTGAATTT-CAAATTCGCAACGCGAAAGTCAAATTCGCAA-AGCGGAAGTTAAAT
1 TCGCAACGC-GAATTTGTAAATTCGCAACGCAAAAGTCAAATTCGCAACA-CAGAAGTCAAAT
20491 TCGCAA
1 TCGCAA
20497 AGCGCGTTTA
Statistics
Matches: 153, Mismatches: 23, Indels: 21
0.78 0.12 0.11
Matches are distributed among these distances:
58 3 0.02
59 6 0.04
60 96 0.63
61 43 0.28
62 5 0.03
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.21
Consensus pattern (61 bp):
TCGCAACGCGAATTTGTAAATTCGCAACGCAAAAGTCAAATTCGCAACACAGAAGTCAAAT
Found at i:20470 original size:20 final size:20
Alignment explanation
Indices: 20280--20496 Score: 185
Period size: 20 Copynumber: 10.8 Consensus size: 20
20270 TCGTAACACA
*
20280 AAAGTCAAATTCGCAACAC-
1 AAAGTCAAATTCGCAACGCG
20299 AGAAGTCAAATTCGCAACGCG
1 A-AAGTCAAATTCGCAACGCG
* *
20320 ATAGTCAAATTCGTAACGCG
1 AAAGTCAAATTCGCAACGCG
* * *
20340 ATAGTCAAATTCGCAACACA
1 AAAGTCAAATTCGCAACGCG
*
20360 AAAGTCAAATTCGCAATGCG
1 AAAGTCAAATTCGCAACGCG
*
20380 AATCTGT-AAA-TCGCAACGCG
1 AA--AGTCAAATTCGCAACGCG
* *
20400 AATTTGT-AAA-TCGCAACAC-
1 AA--AGTCAAATTCGCAACGCG
*
20419 AGAAGTCAAATTCACAACGCTG
1 A-AAGTCAAATTCGCAACGC-G
**
20441 AATTTCAAATTCGCAACGCG
1 AAAGTCAAATTCGCAACGCG
*
20461 AAAGTCAAATTCGCAAAGCG
1 AAAGTCAAATTCGCAACGCG
* *
20481 GAAGTTAAATTCGCAA
1 AAAGTCAAATTCGCAA
20497 AGCGCGTTTA
Statistics
Matches: 164, Mismatches: 25, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
18 2 0.01
19 5 0.03
20 135 0.82
21 19 0.12
22 3 0.02
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (20 bp):
AAAGTCAAATTCGCAACGCG
Found at i:20710 original size:20 final size:21
Alignment explanation
Indices: 20654--20710 Score: 89
Period size: 21 Copynumber: 2.7 Consensus size: 21
20644 CTACAGCGAC
20654 ATCCGTCCCCATCTCCGACGAA
1 ATCCGT-CCCATCTCCGACGAA
20676 ATCCGTCCCATCTCCGACGAA
1 ATCCGTCCCATCTCCGACGAA
*
20697 ATCCG-CCTATCTCC
1 ATCCGTCCCATCTCC
20711 ATCTCTCATA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
20 8 0.24
21 20 0.59
22 6 0.18
ACGTcount: A:0.21, C:0.46, G:0.12, T:0.21
Consensus pattern (21 bp):
ATCCGTCCCATCTCCGACGAA
Found at i:21139 original size:20 final size:20
Alignment explanation
Indices: 21096--21140 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
21086 GTGTTGCGAT
* * * *
21096 TTTCTCGTTGCGATTTTCAT
1 TTTCACGTTGCGAATTTAAG
21116 TTTCACGTTGCGAATTTAAG
1 TTTCACGTTGCGAATTTAAG
21136 TTTCA
1 TTTCA
21141 AAAACTACTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.49
Consensus pattern (20 bp):
TTTCACGTTGCGAATTTAAG
Found at i:25008 original size:20 final size:20
Alignment explanation
Indices: 24983--25151 Score: 329
Period size: 20 Copynumber: 8.4 Consensus size: 20
24973 GCGATTTTCC
24983 TAAATCGCAATGCGAATACG
1 TAAATCGCAATGCGAATACG
25003 TAAATCGCAATGCGAATACG
1 TAAATCGCAATGCGAATACG
25023 TAAATCGCAATGCGAATACG
1 TAAATCGCAATGCGAATACG
25043 TAAATCGCAATGCGAATACG
1 TAAATCGCAATGCGAATACG
25063 TAAATCGCAATGCGAATACG
1 TAAATCGCAATGCGAATACG
25083 TAAATCGCAATGCGAATACG
1 TAAATCGCAATGCGAATACG
25103 TAAATCGCAATGCGAATACG
1 TAAATCGCAATGCGAATACG
*
25123 TAAATCGCAATACGAATACG
1 TAAATCGCAATGCGAATACG
25143 TAAATCGCA
1 TAAATCGCA
25152 TTCGCAACGC
Statistics
Matches: 148, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
20 148 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (20 bp):
TAAATCGCAATGCGAATACG
Found at i:25204 original size:20 final size:20
Alignment explanation
Indices: 25179--25228 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
25169 ACTATCGCAA
*
25179 ACTATCGCAACAAGATTTTG
1 ACTATCGCAACAAGATTCTG
*
25199 ACTATCGCAACGAGATTCTG
1 ACTATCGCAACAAGATTCTG
25219 ACTATCGCAA
1 ACTATCGCAA
25229 TACTGAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (20 bp):
ACTATCGCAACAAGATTCTG
Found at i:26079 original size:24 final size:24
Alignment explanation
Indices: 26052--26105 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
26042 GTATTCGAAA
26052 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
26076 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
26100 TTTGAT
1 TTTGAT
26106 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:28561 original size:20 final size:20
Alignment explanation
Indices: 28536--28624 Score: 101
Period size: 20 Copynumber: 4.5 Consensus size: 20
28526 CAACACGGAA
*
28536 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAA-ATAACT
*
28556 ATCGCAACACGGAAATAACT
1 ATCGCAACGCGGAAATAACT
*
28576 ATCGCAACGC-GAAATTGACT
1 ATCGCAACGCGGAAA-TAACT
* *
28596 ATCGTAATGCGGAAATAACT
1 ATCGCAACGCGGAAATAACT
28616 ATCGCAACG
1 ATCGCAACG
28625 AGAGAATCGA
Statistics
Matches: 57, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
19 4 0.07
20 46 0.81
21 7 0.12
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGGAAATAACT
Found at i:28595 original size:40 final size:40
Alignment explanation
Indices: 28536--28624 Score: 135
Period size: 40 Copynumber: 2.2 Consensus size: 40
28526 CAACACGGAA
28536 ATCGCAACGCGAATATGACTATCGCAACACGGAAATAACT
1 ATCGCAACGCGAATATGACTATCGCAACACGGAAATAACT
* **
28576 ATCGCAACGCGAA-ATTGACTATCGTAATGCGGAAATAACT
1 ATCGCAACGCGAATA-TGACTATCGCAACACGGAAATAACT
28616 ATCGCAACG
1 ATCGCAACG
28625 AGAGAATCGA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
39 1 0.02
40 44 0.98
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (40 bp):
ATCGCAACGCGAATATGACTATCGCAACACGGAAATAACT
Found at i:28653 original size:33 final size:34
Alignment explanation
Indices: 28616--28691 Score: 136
Period size: 33 Copynumber: 2.3 Consensus size: 34
28606 GGAAATAACT
28616 ATCGCAACGAGAGAATCGAAATGCG-AAATGAAA
1 ATCGCAACGAGAGAATCGAAATGCGAAAATGAAA
*
28649 ATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
1 ATCGCAACGAGAGAATCGAAATGCGAAAATGAAA
28683 ATCGCAACG
1 ATCGCAACG
28692 CGAAGCGTTG
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
33 24 0.59
34 17 0.41
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.12
Consensus pattern (34 bp):
ATCGCAACGAGAGAATCGAAATGCGAAAATGAAA
Found at i:28761 original size:33 final size:34
Alignment explanation
Indices: 28704--28772 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 34
28694 AAGCGTTGAT
*
28704 ATTCTCTCGTTGCGATTTTCATTT-CGCATTGCG
1 ATTCTCTCGTTGCGATGTTCATTTCCGCATTGCG
*
28737 ATTCTCTCGTTGCGATAGTT-ATTTCCGCGTTGCG
1 ATTCTCTCGTTGCGAT-GTTCATTTCCGCATTGCG
28771 AT
1 AT
28773 AGTCTGTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
33 20 0.62
34 12 0.38
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.43
Consensus pattern (34 bp):
ATTCTCTCGTTGCGATGTTCATTTCCGCATTGCG
Found at i:30906 original size:20 final size:20
Alignment explanation
Indices: 30883--30951 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
30873 GAAACTTAAA
30883 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
30903 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
30923 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
30943 ATCGCAACG
1 ATCGCAACG
30952 AGAGAATCGC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:31021 original size:20 final size:20
Alignment explanation
Indices: 30996--31082 Score: 140
Period size: 20 Copynumber: 4.3 Consensus size: 20
30986 GATTCTCTCG
*
30996 TTGCGATAGTCAAATTT-GCA
1 TTGCGATAGTC-ATTTTCGCA
31016 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
31036 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
31056 CTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
31076 TTGCGAT
1 TTGCGAT
31083 TTTATTGTTG
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
19 4 0.06
20 59 0.94
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:32459 original size:31 final size:31
Alignment explanation
Indices: 32421--32576 Score: 217
Period size: 31 Copynumber: 5.0 Consensus size: 31
32411 CCCGAAGGAC
* *
32421 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
32452 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
* *
32483 CAGTCCGTATGTTCCGAAGAACATAGGTAAT
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
32514 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
32545 CAGTCCATATG-TCCAGAAGAACATAGGTAAA
1 CAGTCCATATGTTCC-GAAGAACATAGGTAAA
32576 C
1 C
32577 CCTCGACCCT
Statistics
Matches: 111, Mismatches: 12, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
30 2 0.02
31 108 0.97
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:32518 original size:62 final size:62
Alignment explanation
Indices: 32421--32574 Score: 249
Period size: 62 Copynumber: 2.5 Consensus size: 62
32411 CCCGAAGGAC
* *
32421 CAGTCCATA-GATTCCGAAGAACCTAGGTAATCAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATG-TTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
*
32483 CAGTCCGTATGTTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
32545 CAGTCCATATG-TCCAGAAGAACATAGGTAA
1 CAGTCCATATGTTCC-GAAGAACATAGGTAA
32575 ACCCTCGACC
Statistics
Matches: 86, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
61 3 0.03
62 82 0.95
63 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (62 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:32780 original size:23 final size:24
Alignment explanation
Indices: 32754--32800 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
32744 ATATACTTGT
*
32754 TTTCACATATATA-TTTCATATCA
1 TTTCACATATACACTTTCATATCA
32777 TTTCACATATACACTTTCATATCA
1 TTTCACATATACACTTTCATATCA
32801 CATGCCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTCACATATACACTTTCATATCA
Found at i:33428 original size:21 final size:21
Alignment explanation
Indices: 33398--33442 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
33388 ATTCTGTCGT
* *
33398 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
33419 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
33440 TTG
1 TTG
33443 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:36299 original size:31 final size:31
Alignment explanation
Indices: 36261--36416 Score: 208
Period size: 31 Copynumber: 5.0 Consensus size: 31
36251 CCCGAAGGAC
* *
36261 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
36292 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
* * *
36323 CAGTCCGTATGTTCCGAAGAACTTAGGTAAT
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
36354 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
36385 CAGTCCATATG-TCCAGAAGAACATAGGTAAA
1 CAGTCCATATGTTCC-GAAGAACATAGGTAAA
36416 C
1 C
36417 CCTCGACCCT
Statistics
Matches: 109, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
30 2 0.02
31 106 0.97
32 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:36358 original size:62 final size:62
Alignment explanation
Indices: 36261--36414 Score: 240
Period size: 62 Copynumber: 2.5 Consensus size: 62
36251 CCCGAAGGAC
* *
36261 CAGTCCATA-GATTCCGAAGAACCTAGGTAATCAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATG-TTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
36323 CAGTCCGTATGTTCCGAAGAACTTAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
36385 CAGTCCATATG-TCCAGAAGAACATAGGTAA
1 CAGTCCATATGTTCC-GAAGAACATAGGTAA
36415 ACCCTCGACC
Statistics
Matches: 85, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
61 3 0.04
62 81 0.95
63 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (62 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:37269 original size:21 final size:21
Alignment explanation
Indices: 37239--37283 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
37229 ATTCTGTCGT
* *
37239 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
37260 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
37281 TTG
1 TTG
37284 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:39331 original size:20 final size:20
Alignment explanation
Indices: 39315--39404 Score: 101
Period size: 20 Copynumber: 4.5 Consensus size: 20
39305 TCTGAAACTT
39315 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
39335 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * **
39355 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACACGAAAATG
** *
39375 ACTATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
39394 AAAATCGCAAC
1 AAAATCGCAAC
39405 GACAGAATCG
Statistics
Matches: 61, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
19 12 0.20
20 49 0.80
ACGTcount: A:0.46, C:0.23, G:0.17, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:39766 original size:22 final size:22
Alignment explanation
Indices: 39732--39807 Score: 107
Period size: 22 Copynumber: 3.5 Consensus size: 22
39722 TGAGCGTGAA
* *
39732 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
*
39754 TGATATCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
39776 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
* *
39798 AGATGTCGTC
1 TGATTTCGTC
39808 TTAGAGAGTG
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.21, C:0.16, G:0.38, T:0.25
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:40045 original size:21 final size:21
Alignment explanation
Indices: 40021--40066 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
40011 TATTCGCATT
40021 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
40042 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
40063 GCGA
1 GCGA
40067 TAGTCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:40435 original size:60 final size:60
Alignment explanation
Indices: 40371--40501 Score: 162
Period size: 60 Copynumber: 2.2 Consensus size: 60
40361 TTTTATCCAT
* *
40371 AAACTATGAC-TATCATTCTAAATTAG-TCCTCAAAC-TTTTGAACATTTCAATTTCATTCCC
1 AAACTATGACAT-TCATTCTAAATTAGCTCC-CAAACTTTTTGAAAATTCCAATTTCA-TCCC
* * *
40431 AAACTATGACATTCATTTTAAATTGGCTCCCAAACTTTTTGAAAATTCCAATTTCATCCT
1 AAACTATGACATTCATTCTAAATTAGCTCCCAAACTTTTTGAAAATTCCAATTTCATCCC
40491 AAACTAT-ACAT
1 AAACTATGACAT
40502 ATATACTAAT
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
59 4 0.06
60 37 0.59
61 22 0.35
ACGTcount: A:0.35, C:0.22, G:0.05, T:0.37
Consensus pattern (60 bp):
AAACTATGACATTCATTCTAAATTAGCTCCCAAACTTTTTGAAAATTCCAATTTCATCCC
Found at i:40728 original size:60 final size:61
Alignment explanation
Indices: 40608--40729 Score: 151
Period size: 60 Copynumber: 2.0 Consensus size: 61
40598 TTGCATATTT
* * * * *
40608 GGATGAATTTGGAATGTTCAAAAAGTTTAGGGACTAATTTAAAAGGATGTTCATAGTTTAG
1 GGATGAAATTGAAATGTTCAAAAAGTTTAAGGACCAATTTAAAAGGAGGTTCATAGTTTAG
*
40669 GGATGAAATTGAAATGTTC-AAAA-TTTGAAGGACCAATTTAAAATGAGGGTT-ATAGTTTAG
1 GGATGAAATTGAAATGTTCAAAAAGTTT-AAGGACCAATTTAAAAGGA-GGTTCATAGTTTAG
40729 G
1 G
40730 AATATATGAT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
59 3 0.06
60 30 0.57
61 20 0.38
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.33
Consensus pattern (61 bp):
GGATGAAATTGAAATGTTCAAAAAGTTTAAGGACCAATTTAAAAGGAGGTTCATAGTTTAG
Found at i:46425 original size:33 final size:33
Alignment explanation
Indices: 46388--46461 Score: 105
Period size: 33 Copynumber: 2.2 Consensus size: 33
46378 AACACGCTGG
* *
46388 GCATCCGA-GGCCATCCGATCGAGCTATGCGAGA
1 GCATCCGAGGGCC-GCCGAGCGAGCTATGCGAGA
*
46421 GCATCCGAGGGCCGCCGAGCGAGCTATGCGAGG
1 GCATCCGAGGGCCGCCGAGCGAGCTATGCGAGA
46454 GCATCCGA
1 GCATCCGA
46462 CCGAGCGAGC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
33 33 0.89
34 4 0.11
ACGTcount: A:0.22, C:0.31, G:0.35, T:0.12
Consensus pattern (33 bp):
GCATCCGAGGGCCGCCGAGCGAGCTATGCGAGA
Found at i:46517 original size:30 final size:30
Alignment explanation
Indices: 46481--46568 Score: 117
Period size: 30 Copynumber: 3.0 Consensus size: 30
46471 CGAGCAAAGG
* *
46481 TAGGTCGCCCGGAGTGCATGGCGACCTTTA
1 TAGGTCGCCCGGAGTGCATGACGACCTATA
*
46511 TAGGTCGCCCGGAGTGCATGTCGACCTATA
1 TAGGTCGCCCGGAGTGCATGACGACCTATA
*
46541 -AAGTCGCCCGGAG-GACATGACGACCTAT
1 TAGGTCGCCCGGAGTG-CATGACGACCTAT
46569 GTGTTGGGGC
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
28 1 0.02
29 24 0.45
30 28 0.53
ACGTcount: A:0.22, C:0.27, G:0.31, T:0.20
Consensus pattern (30 bp):
TAGGTCGCCCGGAGTGCATGACGACCTATA
Found at i:59919 original size:15 final size:15
Alignment explanation
Indices: 59899--59929 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
59889 ATATTAGAGG
59899 AGTACATTTTTAATT
1 AGTACATTTTTAATT
*
59914 AGTACATTTTTCATT
1 AGTACATTTTTAATT
59929 A
1 A
59930 CTAAAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.10, G:0.06, T:0.52
Consensus pattern (15 bp):
AGTACATTTTTAATT
Done.