Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005929.1 Hibiscus syriacus cultivar Beakdansim tig00013919_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: 93793
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:7820 original size:15 final size:15
Alignment explanation
Indices: 7796--7858 Score: 60
Period size: 15 Copynumber: 4.3 Consensus size: 15
7786 TATATTTAAT
7796 ATTTTATTTTTGATG
1 ATTTTATTTTTGATG
7811 ATTTT-TTTTTG-TG
1 ATTTTATTTTTGATG
*
7824 AACTTTT-TTTTTGGTG
1 -A-TTTTATTTTTGATG
**
7840 AACTTATTTTTGATG
1 ATTTTATTTTTGATG
7855 ATTT
1 ATTT
7859 GATATGGTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
13 2 0.05
14 9 0.23
15 26 0.67
16 2 0.05
ACGTcount: A:0.17, C:0.03, G:0.14, T:0.65
Consensus pattern (15 bp):
ATTTTATTTTTGATG
Found at i:7831 original size:16 final size:16
Alignment explanation
Indices: 7812--7850 Score: 62
Period size: 15 Copynumber: 2.4 Consensus size: 16
7802 TTTTTGATGA
7812 TTTTTTTTT-GTGAAC
1 TTTTTTTTTGGTGAAC
7827 TTTTTTTTTGGTGAAC
1 TTTTTTTTTGGTGAAC
7843 TTATTTTT
1 TT-TTTTT
7851 GATGATTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 9 0.41
16 8 0.36
17 5 0.23
ACGTcount: A:0.13, C:0.05, G:0.13, T:0.69
Consensus pattern (16 bp):
TTTTTTTTTGGTGAAC
Found at i:8804 original size:31 final size:31
Alignment explanation
Indices: 8766--8824 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
8756 ACTACATTTT
8766 AATTAAATAAAAACAAAAGAGACCAAATCTA
1 AATTAAATAAAAACAAAAGAGACCAAATCTA
* * *
8797 AATTAAATAAAAACTAAAGCGATCAAAT
1 AATTAAATAAAAACAAAAGAGACCAAAT
8825 ATTATGTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.63, C:0.12, G:0.07, T:0.19
Consensus pattern (31 bp):
AATTAAATAAAAACAAAAGAGACCAAATCTA
Found at i:9581 original size:31 final size:31
Alignment explanation
Indices: 9536--9610 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
9526 AACATGCTAC
* *
9536 GCATTATCTGAATGCGAA-CCTGACATACTGT
1 GCATTACCTGAATGC-AATCCTAACATACTGT
* *
9567 GCATTACCTTAATGCAATCCTAACATGCTGT
1 GCATTACCTGAATGCAATCCTAACATACTGT
*
9598 GCATTATCTGAAT
1 GCATTACCTGAAT
9611 ACACCCTGAC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
30 2 0.05
31 35 0.95
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (31 bp):
GCATTACCTGAATGCAATCCTAACATACTGT
Found at i:12066 original size:30 final size:31
Alignment explanation
Indices: 12032--12096 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 31
12022 TTTAACTGAA
12032 TTTAAAGGTCAAATTTA-TATTT-ATCTAAAG
1 TTTAAAGGTCAAA-TTAGTATTTCATCTAAAG
* **
12062 TTTAAGGGTTGAATTAGTATTTCATCTAAAG
1 TTTAAAGGTCAAATTAGTATTTCATCTAAAG
12093 TTTA
1 TTTA
12097 TAGTAAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 3 0.10
30 15 0.50
31 12 0.40
ACGTcount: A:0.35, C:0.06, G:0.14, T:0.45
Consensus pattern (31 bp):
TTTAAAGGTCAAATTAGTATTTCATCTAAAG
Found at i:12123 original size:26 final size:27
Alignment explanation
Indices: 12094--12144 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
12084 CATCTAAAGT
*
12094 TTATAGT-AAAATATTTTCTATTTTCA
1 TTATAGTAAAAATATTTTCAATTTTCA
**
12120 TTATTTTAAAAATATTTTCAATTTT
1 TTATAGTAAAAATATTTTCAATTTT
12145 AGTTTTTCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 5 0.24
27 16 0.76
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.57
Consensus pattern (27 bp):
TTATAGTAAAAATATTTTCAATTTTCA
Found at i:13824 original size:33 final size:33
Alignment explanation
Indices: 13786--13870 Score: 91
Period size: 33 Copynumber: 2.6 Consensus size: 33
13776 TGACTAAATA
* * *
13786 ATTTGTTACAATTTTTTATTATGA-AAGAATATT
1 ATTTGTTACAAATTTTTATAATGAGAA-AATAAT
* *
13819 ATTTGTCACAAATTTTTATAATGAGAAATTAAT
1 ATTTGTTACAAATTTTTATAATGAGAAAATAAT
* *
13852 ATTTGTTATAAATTGTTAT
1 ATTTGTTACAAATTTTTAT
13871 TTTGATTAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
33 41 0.95
34 2 0.05
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (33 bp):
ATTTGTTACAAATTTTTATAATGAGAAAATAAT
Found at i:14102 original size:11 final size:11
Alignment explanation
Indices: 14077--14119 Score: 61
Period size: 11 Copynumber: 3.8 Consensus size: 11
14067 ATGTGTGGCC
14077 ATATATATTATT
1 ATATATA-TATT
14089 ATATCATA-ATT
1 ATAT-ATATATT
14100 ATATATATATT
1 ATATATATATT
14111 ATATATATA
1 ATATATATA
14120 CGTATAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 3 0.10
11 19 0.66
12 4 0.14
13 3 0.10
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (11 bp):
ATATATATATT
Found at i:14965 original size:23 final size:23
Alignment explanation
Indices: 14939--14987 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
14929 ATCAGTAAAA
14939 ATAATAATAGTAGAAAATAAGAG
1 ATAATAATAGTAGAAAATAAGAG
*
14962 ATAATAATAGTATAAAATAAGAG
1 ATAATAATAGTAGAAAATAAGAG
14985 ATA
1 ATA
14988 GGAAAGAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.61, C:0.00, G:0.14, T:0.24
Consensus pattern (23 bp):
ATAATAATAGTAGAAAATAAGAG
Found at i:15523 original size:15 final size:15
Alignment explanation
Indices: 15505--15536 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
15495 ATACTAATAG
*
15505 TGACAAAATTAATTT
1 TGACAAAATTAAATT
15520 TGACAAAATTAAATT
1 TGACAAAATTAAATT
15535 TG
1 TG
15537 TCATAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (15 bp):
TGACAAAATTAAATT
Found at i:19002 original size:42 final size:42
Alignment explanation
Indices: 18955--19041 Score: 174
Period size: 42 Copynumber: 2.1 Consensus size: 42
18945 TACAAGTAGA
18955 AAATCTAAAAGAACAATAAGAAACAAAATACAATCAAATAGC
1 AAATCTAAAAGAACAATAAGAAACAAAATACAATCAAATAGC
18997 AAATCTAAAAGAACAATAAGAAACAAAATACAATCAAATAGC
1 AAATCTAAAAGAACAATAAGAAACAAAATACAATCAAATAGC
19039 AAA
1 AAA
19042 GCCTGGCTAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.66, C:0.14, G:0.07, T:0.14
Consensus pattern (42 bp):
AAATCTAAAAGAACAATAAGAAACAAAATACAATCAAATAGC
Found at i:20662 original size:22 final size:23
Alignment explanation
Indices: 20614--20667 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 23
20604 AATTATCTTT
20614 AATTTTT-GGATTTAATTCAAAC
1 AATTTTTAGGATTTAATTCAAAC
*
20636 AATTTTTAGGATTTATCTTC-AAC
1 AATTTTTAGGATTTA-ATTCAAAC
20659 -ATTTTTAGG
1 AATTTTTAGG
20668 GCTTGTAGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 16 0.55
23 10 0.34
24 3 0.10
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.48
Consensus pattern (23 bp):
AATTTTTAGGATTTAATTCAAAC
Found at i:27372 original size:27 final size:26
Alignment explanation
Indices: 27303--27373 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 26
27293 TAAAAATTGA
*
27303 CAAAGAGGAGAAAAGAGAATTAAAAT
1 CAAAGAGAAGAAAAGAGAATTAAAAT
* *
27329 C-ATGCGTAAGGAAAAGAGAATTAGAAAT
1 CAAAGAG-AA-GAAAAGAGAATTA-AAAT
*
27357 CAAAGAGAAGAGAAGAG
1 CAAAGAGAAGAAAAGAG
27374 GAAGAAAAGT
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
25 3 0.09
26 2 0.06
27 20 0.57
28 7 0.20
29 3 0.09
ACGTcount: A:0.56, C:0.06, G:0.27, T:0.11
Consensus pattern (26 bp):
CAAAGAGAAGAAAAGAGAATTAAAAT
Found at i:33922 original size:12 final size:12
Alignment explanation
Indices: 33905--33929 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33895 AGATTTAGAG
33905 TGGTTCAACTTC
1 TGGTTCAACTTC
33917 TGGTTCAACTTC
1 TGGTTCAACTTC
33929 T
1 T
33930 CAACGAAGTC
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:0.16, C:0.24, G:0.16, T:0.44
Consensus pattern (12 bp):
TGGTTCAACTTC
Found at i:39627 original size:19 final size:19
Alignment explanation
Indices: 39603--39642 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
39593 GGCTAGAAAT
*
39603 CATCCCTAACTGATATAAA
1 CATCCCTAACGGATATAAA
*
39622 CATCCCTAACGGCTATAAA
1 CATCCCTAACGGATATAAA
39641 CA
1 CA
39643 GACACAACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.40, C:0.30, G:0.07, T:0.23
Consensus pattern (19 bp):
CATCCCTAACGGATATAAA
Found at i:44439 original size:127 final size:127
Alignment explanation
Indices: 44213--44598 Score: 763
Period size: 127 Copynumber: 3.0 Consensus size: 127
44203 CCAGATTCGA
*
44213 GCAGTGATGTCTGCAAGGTGTTTGTACACTCATTATCAACGAAAATACAAAGAAAATACTTAAAT
1 GCAGTGATGTCTGCAAGGTGTTTGTACACTTATTATCAACGAAAATACAAAGAAAATACTTAAAT
44278 TAAATGACAGCTACAACAGAAGTTACTAACATGTTCACCAACAATCATTTTATCCATTCCTT
66 TAAATGACAGCTACAACAGAAGTTACTAACATGTTCACCAACAATCATTTTATCCATTCCTT
44340 GCAGTGATGTCTGCAAGGTGTTTGTACACTTATTATCAACGAAAATACAAAGAAAATACTTAAAT
1 GCAGTGATGTCTGCAAGGTGTTTGTACACTTATTATCAACGAAAATACAAAGAAAATACTTAAAT
44405 TAAATGACAGCTACAACAGAAGTTACTAACATGTTCACCAACAATCATTTTATCCATTCCTT
66 TAAATGACAGCTACAACAGAAGTTACTAACATGTTCACCAACAATCATTTTATCCATTCCTT
44467 GCAGTGATGTCTGCAAGGTGTTTGTACACTTATTATCAACGAAAATACAAAGAAAATACTTAAAT
1 GCAGTGATGTCTGCAAGGTGTTTGTACACTTATTATCAACGAAAATACAAAGAAAATACTTAAAT
44532 TAAATGACAGCTACAACAGAAGTTACTAACATGTTCACCAACAATCATTTTATCCATTCCTT
66 TAAATGACAGCTACAACAGAAGTTACTAACATGTTCACCAACAATCATTTTATCCATTCCTT
44594 GCAGT
1 GCAGT
44599 TGCTTTTCGC
Statistics
Matches: 258, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
127 258 1.00
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (127 bp):
GCAGTGATGTCTGCAAGGTGTTTGTACACTTATTATCAACGAAAATACAAAGAAAATACTTAAAT
TAAATGACAGCTACAACAGAAGTTACTAACATGTTCACCAACAATCATTTTATCCATTCCTT
Found at i:49488 original size:4 final size:4
Alignment explanation
Indices: 49479--49530 Score: 65
Period size: 4 Copynumber: 13.5 Consensus size: 4
49469 TCATTCTAAA
*
49479 ATTT ATTT ATTT ATTT ATTTT ATTT ATTT A--T ATTT A-TT ATTT AATT
1 ATTT ATTT ATTT ATTT A-TTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
49525 ATTT AT
1 ATTT AT
49531 ATTTGTTTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 2 0.05
3 3 0.07
4 33 0.79
5 4 0.10
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (4 bp):
ATTT
Found at i:49531 original size:21 final size:23
Alignment explanation
Indices: 49486--49534 Score: 75
Period size: 21 Copynumber: 2.2 Consensus size: 23
49476 AAAATTTATT
*
49486 TATTTATTTATTTTATTTATTTA
1 TATTTATTTATTTTAATTATTTA
49509 TATTTA-TTA-TTTAATTATTTA
1 TATTTATTTATTTTAATTATTTA
49530 TATTT
1 TATTT
49535 GTTTTAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 16 0.64
22 3 0.12
23 6 0.24
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (23 bp):
TATTTATTTATTTTAATTATTTA
Found at i:49533 original size:17 final size:17
Alignment explanation
Indices: 49481--49533 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 17
49471 ATTCTAAAAT
*
49481 TTATTTATTTATTTATT
1 TTATTTATTTATTTATA
49498 TTATTTATTTATATT-TA
1 TTATTTATTTAT-TTATA
*
49515 TTATTTAATTATTTATA
1 TTATTTATTTATTTATA
49532 TT
1 TT
49534 TGTTTTAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 2 0.06
17 28 0.88
18 2 0.06
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TTATTTATTTATTTATA
Found at i:49545 original size:21 final size:21
Alignment explanation
Indices: 49481--49553 Score: 59
Period size: 21 Copynumber: 3.7 Consensus size: 21
49471 ATTCTAAAAT
*
49481 TTATTTATTTATTTATT-TT-AT
1 TTATTTA--TATTTATTATTAAA
*
49502 TTATTTATATTTATTATTTAA
1 TTATTTATATTTATTATTAAA
*
49523 TTATTTATATTTGTT-TTAAA
1 TTATTTATATTTATTATTAAA
49543 --ATTT-TATTTAT
1 TTATTTATATTTAT
49554 GTTAATCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
17 6 0.13
18 4 0.09
19 8 0.17
20 6 0.13
21 22 0.48
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.70
Consensus pattern (21 bp):
TTATTTATATTTATTATTAAA
Found at i:49551 original size:44 final size:49
Alignment explanation
Indices: 49501--49590 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 49
49491 ATTTATTTTA
*
49501 TTTATTTATATTTAT-TA-TTTA-ATTATT-TATATTTGT-TTTAAAAT
1 TTTATTTATATTAATCTATTTTATATTATTATATATTTGTGTTTAAAAT
*
49545 TTTATTTATGTTAATCTATTTTATATTATTAATATATTTGTGTTTA
1 TTTATTTATATTAATCTATTTTATATTATT-ATATATTTGTGTTTA
49591 TTTTTTAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
44 13 0.34
45 2 0.05
46 4 0.11
47 6 0.16
49 9 0.24
50 4 0.11
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.64
Consensus pattern (49 bp):
TTTATTTATATTAATCTATTTTATATTATTATATATTTGTGTTTAAAAT
Found at i:51521 original size:30 final size:30
Alignment explanation
Indices: 51487--51549 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
51477 TTTAAAAGAT
51487 TAATTTTTTCCGAATAATTTAGAACACTTA
1 TAATTTTTTCCGAATAATTTAGAACACTTA
51517 TAATTTTTTCCGAATAATTTAGAACACTTA
1 TAATTTTTTCCGAATAATTTAGAACACTTA
51547 TAA
1 TAA
51550 AGTAATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.43
Consensus pattern (30 bp):
TAATTTTTTCCGAATAATTTAGAACACTTA
Found at i:54061 original size:37 final size:37
Alignment explanation
Indices: 54019--54120 Score: 161
Period size: 37 Copynumber: 2.8 Consensus size: 37
54009 TAGGTAATCA
*
54019 GTCCATATGTCCCGAAGAACATAGGTAATCTATACCT
1 GTCCATATGTCCCGAAGAACATAGGTAATCTATAACT
*
54056 GTCCATATGTCCCGAAGAACATAGGTAATCTGTAACT
1 GTCCATATGTCCCGAAGAACATAGGTAATCTATAACT
*
54093 GTCCATATGTTCC-ACAGAACATAGGTAA
1 GTCCATATGTCCCGA-AGAACATAGGTAA
54121 CCCTCGACTC
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
36 1 0.02
37 60 0.98
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (37 bp):
GTCCATATGTCCCGAAGAACATAGGTAATCTATAACT
Found at i:57561 original size:24 final size:25
Alignment explanation
Indices: 57511--57573 Score: 92
Period size: 24 Copynumber: 2.6 Consensus size: 25
57501 GTGTATATTT
*
57511 AACTATTTTCAATCCTCTTTAAAAA
1 AACTATTTTCAATCCTCATTAAAAA
*
57536 AACTATTTTCAGTCCT-ATTAAAAA
1 AACTATTTTCAATCCTCATTAAAAA
*
57560 AATTATTTTCAATC
1 AACTATTTTCAATC
57574 ATCAAATTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 19 0.56
25 15 0.44
ACGTcount: A:0.40, C:0.17, G:0.02, T:0.41
Consensus pattern (25 bp):
AACTATTTTCAATCCTCATTAAAAA
Found at i:61562 original size:16 final size:16
Alignment explanation
Indices: 61541--61574 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
61531 TATCGTCGAC
61541 CAAATTTTACTATGCA
1 CAAATTTTACTATGCA
*
61557 CAAATTTTACTATTCA
1 CAAATTTTACTATGCA
61573 CA
1 CA
61575 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.38, C:0.21, G:0.03, T:0.38
Consensus pattern (16 bp):
CAAATTTTACTATGCA
Found at i:69698 original size:2 final size:2
Alignment explanation
Indices: 69691--69717 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
69681 TAATTTAAAC
69691 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
69718 TACCGGATCG
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:70136 original size:2 final size:2
Alignment explanation
Indices: 70129--70158 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
70119 GATAATGTAA
70129 AT AT 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 AT AT
70159 GCAGATCTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:79605 original size:19 final size:19
Alignment explanation
Indices: 79581--79617 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
79571 TATTGGAATA
*
79581 TGCATTCTAGAATATGCAG
1 TGCATTCTAGAACATGCAG
79600 TGCATTCTAGAACATGCA
1 TGCATTCTAGAACATGCA
79618 CTGTTAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (19 bp):
TGCATTCTAGAACATGCAG
Found at i:79889 original size:31 final size:31
Alignment explanation
Indices: 79828--79889 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
79818 TGGTATCAAA
****
79828 GATTAATATTGGAATTAATATTGGGTAAAAT
1 GATTAATATTGGAATTAATAAAAAGTAAAAT
79859 GATTAATATTGGAATTAATTAAAAAG-AAAAT
1 GATTAATATTGGAATTAA-TAAAAAGTAAAAT
79890 AGTGGGTGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
31 23 0.88
32 3 0.12
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.35
Consensus pattern (31 bp):
GATTAATATTGGAATTAATAAAAAGTAAAAT
Found at i:81736 original size:2 final size:2
Alignment explanation
Indices: 81729--81795 Score: 125
Period size: 2 Copynumber: 33.5 Consensus size: 2
81719 AAAAGAAATA
*
81729 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
81771 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
81796 AGAGTAGTAT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:82939 original size:33 final size:35
Alignment explanation
Indices: 82855--82946 Score: 107
Period size: 34 Copynumber: 2.6 Consensus size: 35
82845 AAAATTAAAA
*
82855 TTTAAAATTATATACTATATATGTTTTAAAAAAATATT
1 TTTAAAATTATATA-TATATA--TTTTAAAAAAATAGT
* * *
82893 TTTAAAATCATATA-ATATATTTTCAAATAAT-GT
1 TTTAAAATTATATATATATATTTTAAAAAAATAGT
82926 TTTAAAATTATATATATATAT
1 TTTAAAATTATATATATATAT
82947 ATATATACTT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
33 14 0.29
34 16 0.33
36 5 0.10
38 13 0.27
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (35 bp):
TTTAAAATTATATATATATATTTTAAAAAAATAGT
Found at i:82969 original size:43 final size:43
Alignment explanation
Indices: 82902--82990 Score: 119
Period size: 43 Copynumber: 2.1 Consensus size: 43
82892 TTTTAAAATC
* * *
82902 ATATAATATATTTTCAAATAATGTTTT-AAAATTATATA-TAT
1 ATATAATATACTTTCAAAAAATGTTTTCAAAATCATATACTAT
82943 ATATATATATACTTTCTAAAAAATGTTTTCAAAATCATATACTAT
1 ATATA-ATATACTTTC-AAAAAATGTTTTCAAAATCATATACTAT
82988 ATA
1 ATA
82991 GTTTCCAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
41 5 0.12
42 9 0.22
43 11 0.27
44 10 0.24
45 6 0.15
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.45
Consensus pattern (43 bp):
ATATAATATACTTTCAAAAAATGTTTTCAAAATCATATACTAT
Found at i:82980 original size:77 final size:76
Alignment explanation
Indices: 82883--83025 Score: 200
Period size: 77 Copynumber: 1.9 Consensus size: 76
82873 ATATGTTTTA
* *
82883 AAAAAATATTTTTAAAATCATATA-ATATATTTTCAAATAATGTTTT-AAAATTATATATATATA
1 AAAAAATATTTTCAAAATCATATACATATAGTTTCAAA-AATGTTTTAAAAATTATAT-TATA-A
82946 TATATATACTTTCT
63 TATATATACTTTCT
* *
82960 AAAAAATGTTTTCAAAATCATATACTATATAGTTTCCAAAATGTTTTAAAAATTATATTATAATA
1 AAAAAATATTTTCAAAATCATATAC-ATATAGTTTCAAAAATGTTTTAAAAATTATATTATAATA
83025 T
65 T
83026 TTTTCAAAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
77 26 0.44
78 12 0.20
79 21 0.36
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (76 bp):
AAAAAATATTTTCAAAATCATATACATATAGTTTCAAAAATGTTTTAAAAATTATATTATAATAT
ATATACTTTCT
Found at i:83002 original size:35 final size:31
Alignment explanation
Indices: 82941--83100 Score: 113
Period size: 35 Copynumber: 4.7 Consensus size: 31
82931 AATTATATAT
*
82941 ATATATATATATACTTTCTAAAAAATGTTTTCAAA
1 ATATATATATATA-TTTC---AAAATGTTTTAAAA
82976 ATCATATACTATATAGTTTCCAAAATGTTTTAAAA
1 AT-ATATA-TATATA-TTT-CAAAATGTTTTAAAA
* *
83011 ATTATATTATAATATTTTTCAAAATGTTTTTTTAAA
1 A-TATA-TAT-ATATATTTCAAAATG--TTTTAAAA
* * *
83047 TTATATATATATATTTCAAAATATTTTTTAAA
1 ATATATATATATATTTCAAAAT-GTTTTAAAA
* *
83079 CTATATATATATGTTTTCAAAA
1 ATATATATATAT-ATTTCAAAA
83101 ACTATATATA
Statistics
Matches: 106, Mismatches: 9, Indels: 22
0.77 0.07 0.16
Matches are distributed among these distances:
32 19 0.18
33 21 0.20
34 10 0.09
35 27 0.25
36 19 0.18
37 9 0.08
38 1 0.01
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.47
Consensus pattern (31 bp):
ATATATATATATATTTCAAAATGTTTTAAAA
Found at i:83039 original size:34 final size:34
Alignment explanation
Indices: 82962--83100 Score: 117
Period size: 35 Copynumber: 4.1 Consensus size: 34
82952 TACTTTCTAA
* * *
82962 AAAATGTTTTCAAAATCATATACT-ATATAGTTTCC
1 AAAATGTTTTAAAAATTATATA-TAATATA-TTTTC
82997 AAAATGTTTTAAAAATTATATTATAATAT-TTTTC
1 AAAATGTTTTAAAAATTATA-TATAATATATTTTC
**
83031 AAAATGTTTTTTTAAATTATATAT-ATATA-TTTC
1 AAAATG-TTTTAAAAATTATATATAATATATTTTC
* ** * *
83064 AAAATATTTTTTAAACTATATAT-ATATGTTTTC
1 AAAATGTTTTAAAAATTATATATAATATATTTTC
83097 AAAA
1 AAAA
83101 ACTATATATA
Statistics
Matches: 91, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
32 20 0.22
33 21 0.23
34 13 0.14
35 31 0.34
36 6 0.07
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.47
Consensus pattern (34 bp):
AAAATGTTTTAAAAATTATATATAATATATTTTC
Found at i:83107 original size:53 final size:53
Alignment explanation
Indices: 83052--83155 Score: 142
Period size: 55 Copynumber: 2.0 Consensus size: 53
83042 TTAAATTATA
*
83052 TATATATATTT-CAAAA-TATTTTTTAAACTATATA-TATATGTTTTCAAAAAC
1 TATATATATTTCCAAAACTATTTTTTAAACTATATATTATAT-ATTTCAAAAAC
*
83103 TATATATATTTCCAAAAGCTTTTTTTTTAAACTATATATTATATATTTCAAAA
1 TATATATATTTCCAAAA-C-TATTTTTTAAACTATATATTATATATTTCAAAA
83156 GCCATTAGCA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
51 11 0.24
52 5 0.11
55 25 0.54
56 5 0.11
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48
Consensus pattern (53 bp):
TATATATATTTCCAAAACTATTTTTTAAACTATATATTATATATTTCAAAAAC
Found at i:84309 original size:10 final size:9
Alignment explanation
Indices: 84288--84345 Score: 53
Period size: 9 Copynumber: 6.1 Consensus size: 9
84278 AAGAAATAAC
84288 AAAATAATA
1 AAAATAATA
84297 AAAATATATA
1 AAAATA-ATA
**
84307 AAAATTAGGA
1 AAAA-TAATA
84317 AATAATAATA
1 AA-AATAATA
*
84327 ATAATAATA
1 AAAATAATA
*
84336 ATAATAATA
1 AAAATAATA
84345 A
1 A
84346 TTTGTATTCT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
9 23 0.56
10 14 0.34
11 4 0.10
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (9 bp):
AAAATAATA
Found at i:84325 original size:3 final size:3
Alignment explanation
Indices: 84317--84346 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
84307 AAAATTAGGA
84317 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
84347 TTGTATTCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:85814 original size:84 final size:84
Alignment explanation
Indices: 85696--86230 Score: 661
Period size: 84 Copynumber: 6.4 Consensus size: 84
85686 TCCTGTTAGT
* * * * ** *
85696 AGATAGCTCTTCTCGCCTTGAGCTATGCTTCAAATAATGCACCTTTGAGTTGAGTGTAATCGAAC
1 AGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAAC
* *
85761 TCGAATGTCTTTTATTGGC
66 TCGAAGGTCTTTTGTTGGC
* * * * *
85780 AGATAACCCTTCTAGCCTTGAGCTAAGCTACAAATGATGTGCCTTTGAGCTGAATGTAATCGAAC
1 AGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAAC
* *
85845 TCGAAGG---TTTGCTGAC
66 TCGAAGGTCTTTTGTTGGC
* * *
85861 AGATAGCCTTTCTCGCCTTGAGATATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAAC
1 AGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAAC
*
85926 TCGAAGGTCTTTTGTTGGT
66 TCGAAGGTCTTTTGTTGGC
*
85945 AGATAGCCCTTCTTACCTTGAGCTATGCTGC-AA--ATGTGCCTTTGAGCTGAGTGTAATCGAAC
1 AGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAAC
* *
86007 TCGAAGGTCTTTTCTTAGC
66 TCGAAGGTCTTTTGTTGGC
* * * * *
86026 AGATAGCCCTTCTTGCCTTGA-CATTTGTTGCAAATGATGTGCCTTTGAGCTGTGCGTAGTCGAA
1 AGATAGCCCTTCTTGCCTTGAGC-TATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
*
86090 CTTGAAGGTCTTTTGTTGGC
65 CTCGAAGGTCTTTTGTTGGC
* * * * * *
86110 AAATAGCCCTTCTTTCCGTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCAAAC
1 AGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAAC
86175 TCGAAGGTCTTTTGTTGGC
66 TCGAAGGTCTTTTGTTGGC
* * * *
86194 AAATATCCCTTCTTGCCTTGAGCTATGTTGCACATGA
1 AGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGA
86231 ACACGATATC
Statistics
Matches: 390, Mismatches: 53, Indels: 16
0.85 0.12 0.03
Matches are distributed among these distances:
80 1 0.00
81 142 0.36
82 2 0.01
83 2 0.01
84 242 0.62
85 1 0.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.34
Consensus pattern (84 bp):
AGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAAC
TCGAAGGTCTTTTGTTGGC
Found at i:85938 original size:165 final size:165
Alignment explanation
Indices: 85696--86182 Score: 615
Period size: 165 Copynumber: 2.9 Consensus size: 165
85686 TCCTGTTAGT
* * * ** *
85696 AGATAG-CTCTTCTCGCCTTGAGCTATGCTTCAAATAATGCACCTTTGAGTTGAGTGTAATCGAA
1 AGATAGCCT-TTCTCGCCTTGAGATATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
* * * * *
85760 CTCGAATGTCTTTTATTGGCAGATAACCCTTCTAGCCTTGAGCTAAGCTACAAATGATGTGCCTT
65 CTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTA-CCTTGAGCTATGCTGCAAATGATGTGCCTT
*
85825 TGAGCTGAATGTAATCGAACTCGAAGGTTTGCTGA-C
129 TGAGCTGAGTGTAATCGAACTCGAAGGTTTGCTGAGC
85861 AGATAGCCTTTCTCGCCTTGAGATATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAAC
1 AGATAGCCTTTCTCGCCTTGAGATATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAAC
*
85926 TCGAAGGTCTTTTGTTGGTAGATAGCCCTTCTTACCTTGAGCTATGCTGC-AA--ATGTGCCTTT
66 TCGAAGGTCTTTTGTTGGCAGATAGCCCTTC-TACCTTGAGCTATGCTGCAAATGATGTGCCTTT
* *
85988 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTTCTTAGC
130 GAGCTGAGTGTAATCGAACTCGAAGG--TTTGCTGAGC
* * * * * * * *
86026 AGATAGCCCTTCTTGCCTTGACATTTGTTGCAAATGATGTGCCTTTGAGCTGTGCGTAGTCGAAC
1 AGATAGCCTTTCTCGCCTTGAGATATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAAC
* * * *
86091 TTGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTTCCGTGAGCTATGCTGCAAATGATGTGCCTTT
66 TCGAAGGTCTTTTGTTGGCAGATAGCCCTTC-TACCTTGAGCTATGCTGCAAATGATGTGCCTTT
* * *
86156 GAGCTGAGCGTAGTCAAACTCGAAGGT
130 GAGCTGAGTGTAATCGAACTCGAAGGT
86183 CTTTTGTTGG
Statistics
Matches: 283, Mismatches: 31, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
162 35 0.12
164 8 0.03
165 200 0.71
166 7 0.02
168 33 0.12
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (165 bp):
AGATAGCCTTTCTCGCCTTGAGATATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAAC
TCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTACCTTGAGCTATGCTGCAAATGATGTGCCTTTG
AGCTGAGTGTAATCGAACTCGAAGGTTTGCTGAGC
Found at i:89960 original size:20 final size:21
Alignment explanation
Indices: 89921--89959 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
89911 TGCAAATGAT
89921 AAAAATAAAATGAAAGAAAAC
1 AAAAATAAAATGAAAGAAAAC
89942 AAAAA-AAAATG-AAGAAAA
1 AAAAATAAAATGAAAGAAAA
89960 AAGTTAGTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 6 0.33
21 5 0.28
ACGTcount: A:0.79, C:0.03, G:0.10, T:0.08
Consensus pattern (21 bp):
AAAAATAAAATGAAAGAAAAC
Found at i:91206 original size:24 final size:25
Alignment explanation
Indices: 91179--91227 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
91169 CAAGATAAAT
91179 AAATAAAAA-TAAAGAAAATGTTAA
1 AAATAAAAATTAAAGAAAATGTTAA
*
91203 AAATAAAAATTTAAGAAAATGTTAA
1 AAATAAAAATTAAAGAAAATGTTAA
91228 TTTCTAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 9 0.39
25 14 0.61
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.24
Consensus pattern (25 bp):
AAATAAAAATTAAAGAAAATGTTAA
Found at i:91273 original size:3 final size:3
Alignment explanation
Indices: 91265--91297 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
91255 ATAAATTAGG
91265 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
91298 TTTATTCTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Done.