Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006227.1 Hibiscus syriacus cultivar Beakdansim tig00014842_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: 68145
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:6300 original size:24 final size:24
Alignment explanation
Indices: 6268--6313 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
6258 AGTTGATCGC
6268 TTCAAACAGTTAAAATGAGATAAA
1 TTCAAACAGTTAAAATGAGATAAA
6292 TTCAAACAGTTAAAATGAGATA
1 TTCAAACAGTTAAAATGAGATA
6314 GACAAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.52, C:0.09, G:0.13, T:0.26
Consensus pattern (24 bp):
TTCAAACAGTTAAAATGAGATAAA
Found at i:13557 original size:6 final size:6
Alignment explanation
Indices: 13546--13571 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
13536 TTTTTAACTA
13546 TTCGGT TTCGGT TTCGGT TTCGGT TT
1 TTCGGT TTCGGT TTCGGT TTCGGT TT
13572 AAATATTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.31, T:0.54
Consensus pattern (6 bp):
TTCGGT
Found at i:19357 original size:21 final size:21
Alignment explanation
Indices: 19308--19346 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
19298 ATTATTTATT
19308 ATAT-ATATTTAATGATTTGG
1 ATATGATATTTAATGATTTGG
*
19328 ATTTGATATTTAATGATTT
1 ATATGATATTTAATGATTT
19347 AGTAATGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.54
Consensus pattern (21 bp):
ATATGATATTTAATGATTTGG
Found at i:19361 original size:16 final size:16
Alignment explanation
Indices: 19340--19371 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
19330 TTGATATTTA
19340 ATGATTTAGTAATGAT
1 ATGATTTAGTAATGAT
*
19356 ATGATTTAGTTATGAT
1 ATGATTTAGTAATGAT
19372 TACTGTAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (16 bp):
ATGATTTAGTAATGAT
Found at i:20918 original size:19 final size:19
Alignment explanation
Indices: 20890--20940 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
20880 AATACAATAG
*
20890 GGGTATCGATACCCAGGGA
1 GGGTACCGATACCCAGGGA
20909 GGGTACCGATACCCAGGGA
1 GGGTACCGATACCCAGGGA
20928 GGGTACCGATACC
1 GGGTACCGATACC
20941 TCAGTCGAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.25, C:0.25, G:0.35, T:0.14
Consensus pattern (19 bp):
GGGTACCGATACCCAGGGA
Found at i:22552 original size:24 final size:24
Alignment explanation
Indices: 22525--22616 Score: 114
Period size: 24 Copynumber: 3.8 Consensus size: 24
22515 TTTAAATATT
*
22525 TAATCATTATTAAATAATTATTAG
1 TAATCATTATTAAATCATTATTAG
* *
22549 TAATCGTTATTAAATCATGATTAG
1 TAATCATTATTAAATCATTATTAG
* *
22573 TAATTATTA-TAAGTTCATTATTAG
1 TAATCATTATTAA-ATCATTATTAG
*
22597 TAATCATTACTAAATCATTA
1 TAATCATTATTAAATCATTA
22617 GTATCAAATC
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
23 3 0.05
24 51 0.89
25 3 0.05
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.45
Consensus pattern (24 bp):
TAATCATTATTAAATCATTATTAG
Found at i:22637 original size:21 final size:22
Alignment explanation
Indices: 22607--22651 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
22597 TAATCATTAC
*
22607 TAAATCATTAGT-ATCAAATCAT
1 TAAATCATTAATAAT-AAATCAT
22629 TAAAT-ATTAATAATAAATCAT
1 TAAATCATTAATAATAAATCAT
22650 TA
1 TA
22652 TTAGGAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.51, C:0.09, G:0.02, T:0.38
Consensus pattern (22 bp):
TAAATCATTAATAATAAATCAT
Found at i:22650 original size:59 final size:60
Alignment explanation
Indices: 22587--22717 Score: 219
Period size: 60 Copynumber: 2.2 Consensus size: 60
22577 TATTATAAGT
*
22587 TCATTATTAGTAATCATTACTAAATCATT-AGTATCAAATCATTAAATATTAATAATAAA
1 TCATTATTAGTAATCATTACTAAATCATTAAATATCAAATCATTAAATATTAATAATAAA
*
22646 TCATTATTAGGAATCATTACTAAATCATTAAATATCAAATCATTAAATATTAATAATAAA
1 TCATTATTAGTAATCATTACTAAATCATTAAATATCAAATCATTAAATATTAATAATAAA
* *
22706 TAATTAGTAGTA
1 TCATTATTAGTA
22718 TCGGTACTAT
Statistics
Matches: 66, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
59 28 0.42
60 38 0.58
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.38
Consensus pattern (60 bp):
TCATTATTAGTAATCATTACTAAATCATTAAATATCAAATCATTAAATATTAATAATAAA
Found at i:22673 original size:11 final size:11
Alignment explanation
Indices: 22598--22676 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
22588 CATTATTAGT
*
22598 AATCATTACTA
1 AATCATTAATA
22609 AATCATTAGTATCA
1 AATCATTA--AT-A
22623 AATCATTAA-A
1 AATCATTAATA
* * *
22633 TATTAATAATA
1 AATCATTAATA
*
22644 AATCATTATTA
1 AATCATTAATA
*
22655 GGAATCATTACTA
1 --AATCATTAATA
22668 AATCATTAA
1 AATCATTAA
22677 ATATCAAATC
Statistics
Matches: 52, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
10 7 0.13
11 24 0.46
12 1 0.02
13 11 0.21
14 9 0.17
ACGTcount: A:0.48, C:0.11, G:0.04, T:0.37
Consensus pattern (11 bp):
AATCATTAATA
Found at i:22682 original size:21 final size:21
Alignment explanation
Indices: 22622--22683 Score: 54
Period size: 24 Copynumber: 2.8 Consensus size: 21
22612 CATTAGTATC
*
22622 AAATCATTAAATATTAATAAT
1 AAATCATTAAATATCAATAAT
* *
22643 AAATCATTATTAGGA-ATCATTACT
1 AAATCATTA--A--ATATCAATAAT
22667 AAATCATTAAATATCAA
1 AAATCATTAAATATCAA
22684 ATCATTAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
20 1 0.03
21 13 0.41
22 1 0.03
23 1 0.03
24 15 0.47
25 1 0.03
ACGTcount: A:0.52, C:0.10, G:0.03, T:0.35
Consensus pattern (21 bp):
AAATCATTAAATATCAATAAT
Found at i:22687 original size:15 final size:15
Alignment explanation
Indices: 22667--22695 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
22657 AATCATTACT
22667 AAATCATTAAATATC
1 AAATCATTAAATATC
22682 AAATCATTAAATAT
1 AAATCATTAAATAT
22696 TAATAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (15 bp):
AAATCATTAAATATC
Found at i:23485 original size:14 final size:14
Alignment explanation
Indices: 23466--23496 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
23456 CTCGACAAAG
23466 CAAAACTCTATAAT
1 CAAAACTCTATAAT
23480 CAAAACTCTATAAT
1 CAAAACTCTATAAT
23494 CAA
1 CAA
23497 TGAACTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (14 bp):
CAAAACTCTATAAT
Found at i:25392 original size:35 final size:36
Alignment explanation
Indices: 25315--25394 Score: 128
Period size: 36 Copynumber: 2.2 Consensus size: 36
25305 CATAATTTTT
25315 ATATAACTTAAACTAATAAACTATTATTTTATTATA
1 ATATAACTTAAACTAATAAACTATTATTTTATTATA
*
25351 ATATAACTTAAACTAATTAACTAATT-TTTT-TTATA
1 ATATAACTTAAACTAATAAACT-ATTATTTTATTATA
25386 ATATAACTT
1 ATATAACTT
25395 CAACAAACAA
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
35 14 0.33
36 25 0.60
37 3 0.07
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.46
Consensus pattern (36 bp):
ATATAACTTAAACTAATAAACTATTATTTTATTATA
Found at i:28016 original size:2 final size:2
Alignment explanation
Indices: 28009--28033 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
27999 GTTTTCCCTA
28009 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
28034 ACTTTCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28327 original size:21 final size:21
Alignment explanation
Indices: 28297--28351 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
28287 ATTATTACTA
*
28297 TCGCAATGCGATTTT-CCAATT
1 TCGCATTGCGATTTTCCCAA-T
*
28318 TCGCGTTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
28339 TCGCATTGCGATT
1 TCGCATTGCGATT
28352 AAGTAAATCA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 26 0.87
22 4 0.13
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:28404 original size:20 final size:20
Alignment explanation
Indices: 28379--28513 Score: 103
Period size: 20 Copynumber: 6.7 Consensus size: 20
28369 AATTTGGAAA
28379 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
28399 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
28420 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
28440 TTCGCAACGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* **
28460 TTCGCAATTAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * * *
28480 TTCGCAACGAGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
28500 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
28514 TTTCAAAGCG
Statistics
Matches: 91, Mismatches: 19, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
19 4 0.04
20 61 0.67
21 24 0.26
22 2 0.02
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:28421 original size:41 final size:41
Alignment explanation
Indices: 28376--28513 Score: 181
Period size: 41 Copynumber: 3.4 Consensus size: 41
28366 GCGAATTTGG
*
28376 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAATGCGATACTGACTTTCGCAACGCGATAATAC
*
28417 AAAATCGCAATGCGATACTGACTTTCGCAACGCGATACTTAC
1 AAAATCGCAATGCGATACTGACTTTCGCAACGCGATA-ATAC
** ** *
28459 --TTTCGCAATTAGATACTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAATGCGATACTGACTTTCGCAACGCGATAATAC
*
28498 ATAATCGCAATGCGAT
1 AAAATCGCAATGCGAT
28514 TTTCAAAGCG
Statistics
Matches: 82, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
39 3 0.04
40 30 0.37
41 46 0.56
42 3 0.04
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.25
Consensus pattern (41 bp):
AAAATCGCAATGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:28706 original size:22 final size:22
Alignment explanation
Indices: 28680--28723 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
28670 CACTCTCTCA
*
28680 CCCATTTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
28702 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
28724 TATCTCCATC
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:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:28998 original size:20 final size:20
Alignment explanation
Indices: 28973--29020 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
28963 TTATTCTCTC
28973 GTTGCGATAATCAAATTCGT
1 GTTGCGATAATCAAATTCGT
** **
28993 GTTGCGATTGTCATTTTCGT
1 GTTGCGATAATCAAATTCGT
29013 GTTGCGAT
1 GTTGCGAT
29021 TTTCATTTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.19, C:0.15, G:0.25, T:0.42
Consensus pattern (20 bp):
GTTGCGATAATCAAATTCGT
Found at i:29021 original size:20 final size:20
Alignment explanation
Indices: 28988--29030 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
28978 GATAATCAAA
28988 TTCGTGTTGCGATTGTCATT
1 TTCGTGTTGCGATTGTCATT
*
29008 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTGTCATT
29028 TTC
1 TTC
29031 AGAAACTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.09, C:0.16, G:0.21, T:0.53
Consensus pattern (20 bp):
TTCGTGTTGCGATTGTCATT
Found at i:29221 original size:25 final size:26
Alignment explanation
Indices: 29167--29221 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 26
29157 TGTTTATTAT
* *
29167 TGTTTTTGGTATATCTTCACAGCGTA
1 TGTTTTTGGTATATCTTAACAGAGTA
**
29193 -GTTTTTGGTATATC-TAACTTAGTA
1 TGTTTTTGGTATATCTTAACAGAGTA
29217 TGTTT
1 TGTTT
29222 ATTGTTTTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
24 6 0.25
25 18 0.75
ACGTcount: A:0.20, C:0.11, G:0.18, T:0.51
Consensus pattern (26 bp):
TGTTTTTGGTATATCTTAACAGAGTA
Found at i:30371 original size:18 final size:18
Alignment explanation
Indices: 30350--30397 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
30340 TCCACTTCGG
30350 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
30368 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
30386 GAGCCATCACCT
1 GAGCCATCACCT
30398 AATCGACCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:30986 original size:19 final size:20
Alignment explanation
Indices: 30932--30977 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
30922 TAGTTTACTT
* *
30932 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
30952 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
30972 TCGCAA
1 TCGCAA
30978 TGTGAAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:31019 original size:33 final size:33
Alignment explanation
Indices: 30971--31062 Score: 157
Period size: 33 Copynumber: 2.8 Consensus size: 33
30961 GGAAATGGCT
30971 ATCGCAATGTGAAATGAAAATCGCAACGACAAG
1 ATCGCAATGTGAAATGAAAATCGCAACGACAAG
**
31004 ATCGCAATGCAAAATGAAAATCGCAACGACAAG
1 ATCGCAATGTGAAATGAAAATCGCAACGACAAG
*
31037 ATCGCAACGTGAAATGAAAATCGCAA
1 ATCGCAATGTGAAATGAAAATCGCAA
31063 TAGCCATTTC
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.14
Consensus pattern (33 bp):
ATCGCAATGTGAAATGAAAATCGCAACGACAAG
Found at i:31087 original size:20 final size:20
Alignment explanation
Indices: 31062--31142 Score: 144
Period size: 20 Copynumber: 4.0 Consensus size: 20
31052 GAAAATCGCA
31062 ATAGCCATTTCCGCGTTGCG
1 ATAGCCATTTCCGCGTTGCG
31082 ATAGCCATTTCCGCGTTGCG
1 ATAGCCATTTCCGCGTTGCG
31102 ATAGCCATTTCCGCGTTGCG
1 ATAGCCATTTCCGCGTTGCG
* *
31122 ATAGTCATTTTCGCGTTGCG
1 ATAGCCATTTCCGCGTTGCG
31142 A
1 A
31143 AAGTATGTTT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 59 1.00
ACGTcount: A:0.16, C:0.27, G:0.25, T:0.32
Consensus pattern (20 bp):
ATAGCCATTTCCGCGTTGCG
Found at i:31153 original size:20 final size:19
Alignment explanation
Indices: 31068--31167 Score: 74
Period size: 20 Copynumber: 5.1 Consensus size: 19
31058 CGCAATAGCC
* * *
31068 ATTTCCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGAAAG-T
* * *
31088 ATTTCCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGAAAG-T
* *
31108 ATTTCCGCGTTGCGATAGT
1 ATTTTCGCGTTGCGAAAGT
31127 CATTTTCGCGTTGCGAAAGT
1 -ATTTTCGCGTTGCGAAAGT
* *
31147 ATGTTTCGTGTTACGAAAGT
1 AT-TTTCGCGTTGCGAAAGT
31167 A
1 A
31168 AACTATTCTT
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
19 2 0.03
20 71 0.97
ACGTcount: A:0.19, C:0.22, G:0.25, T:0.34
Consensus pattern (19 bp):
ATTTTCGCGTTGCGAAAGT
Found at i:31562 original size:21 final size:20
Alignment explanation
Indices: 31510--31565 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
31500 GACTCACCTG
*
31510 TCATCCCTCAAGAGTCCCCT
1 TCATCCCTCAAGAGGCCCCT
* **
31530 CCAATCGTTCAAGAGGCCCCT
1 TC-ATCCCTCAAGAGGCCCCT
31551 ATCATCCCTCAAGAG
1 -TCATCCCTCAAGAG
31566 TCTCCCCCCA
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
20 1 0.04
21 25 0.93
22 1 0.04
ACGTcount: A:0.25, C:0.39, G:0.14, T:0.21
Consensus pattern (20 bp):
TCATCCCTCAAGAGGCCCCT
Found at i:31581 original size:42 final size:42
Alignment explanation
Indices: 31510--31589 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
31500 GACTCACCTG
*
31510 TCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCCCTA
*
31552 TCATCCCTCAAGAGTCTCCC-CCCACCGTTCAAGAGGCC
1 TCATCCCTCAAGAGTC-CCCTCCAACCGTTCAAGAGGCC
31590 ACTGTCATTG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
42 32 0.91
43 3 0.09
ACGTcount: A:0.23, C:0.42, G:0.15, T:0.20
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCCCTA
Found at i:33205 original size:19 final size:19
Alignment explanation
Indices: 33181--33264 Score: 133
Period size: 19 Copynumber: 4.7 Consensus size: 19
33171 GCAATGAGAG
33181 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
33200 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
33219 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
33238 AATCGCAA--CG--A-GAA
1 AATCGCAATGCGAAATGAA
33252 AATCGCAATGCGA
1 AATCGCAATGCGA
33265 TTTTCATTTC
Statistics
Matches: 62, Mismatches: 0, Indels: 8
0.89 0.00 0.11
Matches are distributed among these distances:
14 11 0.18
15 1 0.02
16 2 0.03
17 2 0.03
19 46 0.74
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:33258 original size:33 final size:33
Alignment explanation
Indices: 33168--33264 Score: 131
Period size: 38 Copynumber: 2.8 Consensus size: 33
33158 GAAACTGACT
* *
33168 ATCGCAATGAGAGAATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAAAATCGCAATGCGAAATGAAA
33201 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAAATCGCAATGCGAAATGAAA
33239 ATCGCAACGAGAAAATCGCAATGCGA
1 ATCGCAACGAGAAAATCGCAATGCGA
33265 TTTTCATTTC
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
33 23 0.40
34 1 0.02
35 1 0.02
36 2 0.04
37 1 0.02
38 29 0.51
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAACGAGAAAATCGCAATGCGAAATGAAA
Found at i:33308 original size:20 final size:20
Alignment explanation
Indices: 33283--33338 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
33273 TCGCGTTGCG
*
33283 ATTTTCTCGTTGCGATAGTC
1 ATTTTCGCGTTGCGATAGTC
33303 ATTTTCGCGTTGCGATAGTC
1 ATTTTCGCGTTGCGATAGTC
33323 ATTTTCGCGTTGCGAT
1 ATTTTCGCGTTGCGAT
33339 TTCCCCATTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.14, C:0.20, G:0.23, T:0.43
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGTC
Found at i:33706 original size:20 final size:20
Alignment explanation
Indices: 33681--33743 Score: 108
Period size: 20 Copynumber: 3.1 Consensus size: 20
33671 ATTCTGTATT
*
33681 ATCTCGTTGCGATAGTCAGA
1 ATCTCGTTGCGAAAGTCAGA
33701 ATCTCGTTGCGAAAGTCAGA
1 ATCTCGTTGCGAAAGTCAGA
*
33721 ATCGCGTTGCGAAAGTCAGA
1 ATCTCGTTGCGAAAGTCAGA
33741 ATC
1 ATC
33744 ACGATTTTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (20 bp):
ATCTCGTTGCGAAAGTCAGA
Found at i:34455 original size:24 final size:24
Alignment explanation
Indices: 34428--34481 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
34418 GTATTCGAAA
*
34428 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
34452 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
34476 TTTGAT
1 TTTGAT
34482 GATGTTTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:34673 original size:12 final size:12
Alignment explanation
Indices: 34656--34680 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34646 ATATAATCCT
34656 GAAGAAGAAAAA
1 GAAGAAGAAAAA
34668 GAAGAAGAAAAA
1 GAAGAAGAAAAA
34680 G
1 G
34681 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:36995 original size:20 final size:20
Alignment explanation
Indices: 36928--37000 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
36918 GACATTCATT
*
36928 TGACTATCGCAACACGGAAA
1 TGACTATCGCAAAACGGAAA
* **
36948 TGACGT-TCGCAATCATC-TTAA
1 TGAC-TATCGCAA--AACGGAAA
*
36969 TGTCTATCGCAAAACGGAAA
1 TGACTATCGCAAAACGGAAA
36989 TGACTATCGCAA
1 TGACTATCGCAA
37001 TGCGAAATAA
Statistics
Matches: 39, Mismatches: 9, Indels: 10
0.67 0.16 0.17
Matches are distributed among these distances:
19 2 0.05
20 24 0.62
21 12 0.31
22 1 0.03
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (20 bp):
TGACTATCGCAAAACGGAAA
Found at i:37016 original size:19 final size:19
Alignment explanation
Indices: 36994--37123 Score: 83
Period size: 19 Copynumber: 7.6 Consensus size: 19
36984 GGAAATGACT
*
36994 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATGAAA
*
37013 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
37027 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
37046 ATCGCAACGCG--A-G--A
1 ATCGCAATGCGAAATGAAA
37060 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* **
37079 ATCGTAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
*
37093 ATCGCAAAGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
37112 ATCGCAACGCGA
1 ATCGCAATGCGA
37124 TTTTAGTTTC
Statistics
Matches: 84, Mismatches: 12, Indels: 30
0.67 0.10 0.24
Matches are distributed among these distances:
14 28 0.33
15 2 0.02
16 6 0.07
17 6 0.07
18 2 0.02
19 40 0.48
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:37036 original size:33 final size:33
Alignment explanation
Indices: 36994--37120 Score: 209
Period size: 33 Copynumber: 3.8 Consensus size: 33
36984 GGAAATGACT
*
36994 ATCGCAATGCGAAATAAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
37027 ATCGCAATGCGAAATGAAAATCGCAACGCGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
37060 ATCGCAATGCGAAATGAAAATCGTAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
37093 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
37121 CGATTTTAGT
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 87 1.00
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:37142 original size:19 final size:19
Alignment explanation
Indices: 37120--37195 Score: 83
Period size: 19 Copynumber: 4.3 Consensus size: 19
37110 AAATCGCAAC
37120 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCA-TTTCGCGTT
*
37139 GCGA-TTT--TGTCG--TT
1 GCGATTTTCATTTCGCGTT
37153 GCGATTTTCATTTCGCGTT
1 GCGATTTTCATTTCGCGTT
*
37172 GCGATTTTCATTTCGCATT
1 GCGATTTTCATTTCGCGTT
37191 GCGAT
1 GCGAT
37196 AGTCATTTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
14 6 0.12
15 3 0.06
16 4 0.08
17 4 0.08
18 3 0.06
19 29 0.59
ACGTcount: A:0.12, C:0.18, G:0.24, T:0.46
Consensus pattern (19 bp):
GCGATTTTCATTTCGCGTT
Found at i:37201 original size:19 final size:19
Alignment explanation
Indices: 37160--37203 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
37150 GTTGCGATTT
* **
37160 TCATTTCGCGTTGCGATTT
1 TCATTTCGCATTGCGATAG
37179 TCATTTCGCATTGCGATAG
1 TCATTTCGCATTGCGATAG
37198 TCATTT
1 TCATTT
37204 TTGCCTTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.45
Consensus pattern (19 bp):
TCATTTCGCATTGCGATAG
Found at i:37321 original size:14 final size:14
Alignment explanation
Indices: 37302--37338 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
37292 CATCAATTAA
37302 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
37316 ACAAATCATCTTTT
1 ACAAATCAACTTTT
37330 ACAAATCAA
1 ACAAATCAA
37339 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:40124 original size:363 final size:363
Alignment explanation
Indices: 39454--40192 Score: 1388
Period size: 363 Copynumber: 2.0 Consensus size: 363
39444 TCTCACGTAG
* *
39454 AGCGACAACCTCAACACGTAAAGTAGACACCTCCACACGCCATGCACTATCGTTATCGCGTAGAG
1 AGCGGCAACCTCAACACGTAAAGTAGACACCTCCACACGCCATGCACCATCGTTATCGCGTAGAG
*
39519 TACCGATCTCCTCACGCAAGGCATTGACCTCATCACGTAACTCCCTTGACTCATCCCGTGGAGGT
66 TACCGATCTCCTCACGCAAGGCATTGACCTCATCACATAACTCCCTTGACTCATCCCGTGGAGGT
39584 GGAGAACAGGGAGATAGAAGTCGTGGCATCTTTGTCGGTCGCCTATCATGAGGTGATGGTGGAGA
131 GGAGAACAGGGAGATAGAAGTCGTGGCATCTTTGTCGGTCGCCTATCATGAGGTGATGGTGGAGA
39649 TGAGGCTCGATGATGTAACGGGATAGGTGATGGCTCTCGTTGTAGAGGTGTATAGTCGGGTCGAT
196 TGAGGCTCGATGATGTAACGGGATAGGTGATGGCTCTCGTTGTAGAGGTGTATAGTCGGGTCGAT
*
39714 CAGGTGATGGCTTTGGGTGAGGTGATGGCTCTCGAAGTGGAGAAAATGGAGGCTGCTCATCGTTC
261 CAGGTGATGGCTCTGGGTGAGGTGATGGCTCTCGAAGTGGAGAAAATGGAGGCTGCTCATCGTTC
* *
39779 GTGCCATCAAAAAAATGCTGACTAGCTTGCCACTAATC
326 GTGCCATCAAAAAAACGCTGACTAGCTTGCCAATAATC
39817 AGCGGCAACCTCAACACGTAAAGTAGACACCTCCACACGCCATGCACCATCGTTATCGCGTAGAG
1 AGCGGCAACCTCAACACGTAAAGTAGACACCTCCACACGCCATGCACCATCGTTATCGCGTAGAG
39882 TACCGATCTCCTCACGCAAGGCATTGACCTCATCACATAACTCCCTTGACTCATCCCGTGGAGGT
66 TACCGATCTCCTCACGCAAGGCATTGACCTCATCACATAACTCCCTTGACTCATCCCGTGGAGGT
39947 GGAGAACAGGGAGATAGAAGTCGTGGCATCTTTGTCGGTCGCCTATCATGAGGTGATGGTGGAGA
131 GGAGAACAGGGAGATAGAAGTCGTGGCATCTTTGTCGGTCGCCTATCATGAGGTGATGGTGGAGA
*
40012 TGAGGCTCGATGATGTGACGGGATAGGTGATGGCTCTCGTTGTAGAGGTGTATAGTCGGGTCGAT
196 TGAGGCTCGATGATGTAACGGGATAGGTGATGGCTCTCGTTGTAGAGGTGTATAGTCGGGTCGAT
*
40077 CAGGTGATGGCTCTGGGTGAGGTGATGGCTCTCGAAGTGGAGAAAATGGAGGCTGCTCATTGTTC
261 CAGGTGATGGCTCTGGGTGAGGTGATGGCTCTCGAAGTGGAGAAAATGGAGGCTGCTCATCGTTC
40142 GTGCCATCAAAAAAACGCTGACTAGCTTGCCAATAATC
326 GTGCCATCAAAAAAACGCTGACTAGCTTGCCAATAATC
* *
40180 AGTGGCAAGCTCA
1 AGCGGCAACCTCA
40193 GCCTCCGTGA
Statistics
Matches: 366, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
363 366 1.00
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.24
Consensus pattern (363 bp):
AGCGGCAACCTCAACACGTAAAGTAGACACCTCCACACGCCATGCACCATCGTTATCGCGTAGAG
TACCGATCTCCTCACGCAAGGCATTGACCTCATCACATAACTCCCTTGACTCATCCCGTGGAGGT
GGAGAACAGGGAGATAGAAGTCGTGGCATCTTTGTCGGTCGCCTATCATGAGGTGATGGTGGAGA
TGAGGCTCGATGATGTAACGGGATAGGTGATGGCTCTCGTTGTAGAGGTGTATAGTCGGGTCGAT
CAGGTGATGGCTCTGGGTGAGGTGATGGCTCTCGAAGTGGAGAAAATGGAGGCTGCTCATCGTTC
GTGCCATCAAAAAAACGCTGACTAGCTTGCCAATAATC
Found at i:41379 original size:20 final size:20
Alignment explanation
Indices: 41354--41394 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
41344 TTGGTTGAAC
41354 TGAAAATCGCAACGAGAGAA
1 TGAAAATCGCAACGAGAGAA
41374 TGAAAATCGCAACGAGAGAA
1 TGAAAATCGCAACGAGAGAA
41394 T
1 T
41395 CGCAACGCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.49, C:0.15, G:0.24, T:0.12
Consensus pattern (20 bp):
TGAAAATCGCAACGAGAGAA
Found at i:41467 original size:33 final size:34
Alignment explanation
Indices: 41419--41545 Score: 168
Period size: 34 Copynumber: 3.8 Consensus size: 34
41409 AAAATCGCAA
** **
41419 TGCGATTTTGGTTT-CGCGTTGTTATTATCTCGT
1 TGCGATTTTCATTTCCGCGTTGCGATTATCTCGT
* *
41452 TGCGATTTTCATTT-CGCGTTGCGATTCTCTCAT
1 TGCGATTTTCATTTCCGCGTTGCGATTATCTCGT
41485 TGCGATTTTCATTTCCGCGTTGCGATTATCTCGT
1 TGCGATTTTCATTTCCGCGTTGCGATTATCTCGT
**
41519 TGCGATAGTCATTTCCGCGTTGCGATT
1 TGCGATTTTCATTTCCGCGTTGCGATT
41546 TTCATTCTCG
Statistics
Matches: 83, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 41 0.49
34 42 0.51
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.45
Consensus pattern (34 bp):
TGCGATTTTCATTTCCGCGTTGCGATTATCTCGT
Found at i:41509 original size:20 final size:19
Alignment explanation
Indices: 41449--41551 Score: 73
Period size: 20 Copynumber: 5.8 Consensus size: 19
41439 GTTATTATCT
41449 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
41468 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
*
41482 CATTGCGATTTTCATTTCCG
1 CGTTGCGATTTTCATTT-CG
*
41502 CGTTGCGA--TT-A--TCT
1 CGTTGCGATTTTCATTTCG
**
41516 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTT-CG
41536 CGTTGCGATTTTCATT
1 CGTTGCGATTTTCATT
41552 CTCGAAACTA
Statistics
Matches: 63, Mismatches: 9, Indels: 23
0.66 0.09 0.24
Matches are distributed among these distances:
14 18 0.29
15 1 0.02
16 4 0.06
17 5 0.08
18 2 0.03
19 10 0.16
20 23 0.37
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:42123 original size:20 final size:20
Alignment explanation
Indices: 42096--42186 Score: 110
Period size: 20 Copynumber: 4.5 Consensus size: 20
42086 CGATAGTCAG
42096 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * *
42116 ATTTGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGT
*
42136 AATTCGCATTGCGATTTACTT
1 -ATTCGCATTGCGATTTACGT
* * *
42157 AATCGCGTTGCGATTAACGT
1 ATTCGCATTGCGATTTACGT
42177 ATTCGCATTG
1 ATTCGCATTG
42187 TGAATTATGA
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
20 41 0.71
21 17 0.29
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.41
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:42230 original size:20 final size:20
Alignment explanation
Indices: 42073--42232 Score: 87
Period size: 20 Copynumber: 7.9 Consensus size: 20
42063 ATGACGCTAT
42073 GTAAATCGCATTGCGA-TA-
1 GTAAATCGCATTGCGATTAC
*
42091 GTCAGATTCGCATTGCGATTTAC
1 GT-A-AATCGCATTGCGA-TTAC
* * *
42114 GT-ATTTGCATTGCGATTTTC
1 GTAAATCGCATTGCGA-TTAC
* *
42134 CTAATTCGCATTGCGATTTAC
1 GTAAATCGCATTGCGA-TTAC
* *
42155 -TTAATCGCGTTGCGATTAAC
1 GTAAATCGCATTGCGATT-AC
* * *
42175 GT-ATTCGCATTGTGAATTAT
1 GTAAATCGCATTGCG-ATTAC
* ** *
42195 GAAAATCGCAACGCGAATAC
1 GTAAATCGCATTGCGATTAC
42215 GTAAATCGCATTGCGATT
1 GTAAATCGCATTGCGATT
42233 TTTTATTATC
Statistics
Matches: 108, Mismatches: 24, Indels: 18
0.72 0.16 0.12
Matches are distributed among these distances:
18 2 0.02
19 3 0.03
20 71 0.66
21 28 0.26
22 2 0.02
23 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (20 bp):
GTAAATCGCATTGCGATTAC
Found at i:42244 original size:21 final size:21
Alignment explanation
Indices: 42219--42295 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 21
42209 GAATACGTAA
* *
42219 ATCGCATTGCGATTTTTTATT
1 ATCGCATTGCGATTTTTCAGT
* **
42240 ATCGCGTTGCGA-TAGTCAGT
1 ATCGCATTGCGATTTTTCAGT
* *
42260 ATCGCATTGCGATTTTCCA-A
1 ATCGCATTGCGATTTTTCAGT
42280 ATTCGCATTGCGATTT
1 A-TCGCATTGCGATTT
42296 ACTTATTCAC
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
20 16 0.36
21 28 0.64
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.40
Consensus pattern (21 bp):
ATCGCATTGCGATTTTTCAGT
Found at i:42334 original size:21 final size:21
Alignment explanation
Indices: 42308--42375 Score: 111
Period size: 21 Copynumber: 3.2 Consensus size: 21
42298 TTATTCACAT
42308 TGCGAATTGGGAAAATCGCAA
1 TGCGAATTGGGAAAATCGCAA
42329 TGCGAATTGGGAAAATCGCAA
1 TGCGAATTGGGAAAATCGCAA
*
42350 TGCGAAATT-GGAAAATCGCAT
1 TGCG-AATTGGGAAAATCGCAA
42371 TGCGA
1 TGCGA
42376 TAGTAATAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
20 1 0.02
21 40 0.89
22 4 0.09
ACGTcount: A:0.37, C:0.15, G:0.28, T:0.21
Consensus pattern (21 bp):
TGCGAATTGGGAAAATCGCAA
Found at i:42403 original size:41 final size:41
Alignment explanation
Indices: 42305--42404 Score: 105
Period size: 42 Copynumber: 2.4 Consensus size: 41
42295 TACTTATTCA
*
42305 CATTGCGAATTGGGAAAATCGCAATGCGAATTGGGAAAATCG
1 CATTGCGAATT-GGAAAATCGCAATGCGAATTAGGAAAATCG
* * *
42347 CAATGCGAAATTGGAAAATCGCATTGCG-A-TAGTAATAATCG
1 CATTGCG-AATTGGAAAATCGCAATGCGAATTAGGAA-AATCG
*
42388 CGTTGCGAATCTGGAAA
1 CATTGCGAAT-TGGAAA
42405 CTGATTTGCG
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
40 7 0.14
41 17 0.35
42 21 0.43
43 4 0.08
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.23
Consensus pattern (41 bp):
CATTGCGAATTGGAAAATCGCAATGCGAATTAGGAAAATCG
Found at i:48197 original size:10 final size:10
Alignment explanation
Indices: 48182--48208 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
48172 TTATCCAGAG
48182 TCTTCTTTCT
1 TCTTCTTTCT
48192 TCTTCTTTCT
1 TCTTCTTTCT
48202 TCTTCTT
1 TCTTCTT
48209 CCTCCTCCCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (10 bp):
TCTTCTTTCT
Found at i:58541 original size:11 final size:11
Alignment explanation
Indices: 58525--58608 Score: 57
Period size: 11 Copynumber: 7.5 Consensus size: 11
58515 TTATGACAAT
58525 AATTTGTAATA
1 AATTTGTAATA
*
58536 AATTTGAAATA
1 AATTTGTAATA
** *
58547 AAAATAT-ATA
1 AATTTGTAATA
*
58557 AATGTG-AGTATA
1 AATTTGTA--ATA
58569 AATTTGTAATA
1 AATTTGTAATA
*
58580 AATTATGACAAT-
1 AATT-TG-TAATA
58592 AATTTGTAATA
1 AATTTGTAATA
58603 AATTTG
1 AATTTG
58609 AAAATAAAAA
Statistics
Matches: 55, Mismatches: 11, Indels: 14
0.69 0.14 0.17
Matches are distributed among these distances:
10 9 0.16
11 28 0.51
12 14 0.25
13 4 0.07
ACGTcount: A:0.49, C:0.01, G:0.11, T:0.39
Consensus pattern (11 bp):
AATTTGTAATA
Found at i:58581 original size:23 final size:22
Alignment explanation
Indices: 58569--58615 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
58559 TGTGAGTATA
58569 AATTTGTAATAAATTATGACAAT
1 AATTTGTAATAAA-TATGACAAT
* *
58592 AATTTGTAATAAATTTGAAAAT
1 AATTTGTAATAAATATGACAAT
58614 AA
1 AA
58616 AAATAAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (22 bp):
AATTTGTAATAAATATGACAAT
Found at i:60054 original size:36 final size:36
Alignment explanation
Indices: 60013--60081 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
60003 AAACGGGGAT
* *
60013 GGGAAAAATCGTTTATGCTAAACGGGGACGGGGGGG
1 GGGAAAAACCATTTATGCTAAACGGGGACGGGGGGG
60049 GGGAAAAACCATTTATGCTAAACGGGGACGGGG
1 GGGAAAAACCATTTATGCTAAACGGGGACGGGG
60082 ACGGGTTTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.30, C:0.13, G:0.41, T:0.16
Consensus pattern (36 bp):
GGGAAAAACCATTTATGCTAAACGGGGACGGGGGGG
Found at i:60190 original size:2 final size:2
Alignment explanation
Indices: 60180--60231 Score: 65
Period size: 2 Copynumber: 27.5 Consensus size: 2
60170 AAATTAAAAA
* *
60180 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT TT A- AT TT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
60219 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
60232 CCAGTCCCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
1 3 0.07
2 40 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61886 original size:18 final size:18
Alignment explanation
Indices: 61830--61888 Score: 50
Period size: 18 Copynumber: 3.1 Consensus size: 18
61820 CCAATCTAAG
*
61830 AACAAATTATAAAAAAAAC
1 AACAAATT-TAAAATAAAC
61849 TAACTAAA--TAAAACTAAAAC
1 -AAC-AAATTTAAAA-T-AAAC
61869 AACAAATTTAAAATAAAC
1 AACAAATTTAAAATAAAC
61887 AA
1 AA
61889 TAAGCATGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
18 14 0.42
19 4 0.12
20 12 0.36
21 3 0.09
ACGTcount: A:0.69, C:0.12, G:0.00, T:0.19
Consensus pattern (18 bp):
AACAAATTTAAAATAAAC
Found at i:63846 original size:15 final size:15
Alignment explanation
Indices: 63826--63870 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
63816 TTTATCTCTA
*
63826 AATATATATAAATTT
1 AATATATATAAATAT
*
63841 AATATATATATATAT
1 AATATATATAAATAT
* *
63856 AATATCTCTAAATAT
1 AATATATATAAATAT
63871 CTTGATTTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (15 bp):
AATATATATAAATAT
Done.