Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008516.1 Hibiscus syriacus cultivar Beakdansim tig00111379_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: 131998
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:3831 original size:138 final size:138
Alignment explanation
Indices: 3583--3837 Score: 359
Period size: 138 Copynumber: 1.8 Consensus size: 138
3573 ACCTAAGTAC
* * *
3583 CGAAATGGAAATTCACAAACTCATTATGAATTCCATGGATGCACACATAGTGCCAAAAATACATA
1 CGAAATGGAAATTCACAAACTCATTATAAATACCATGGATGCACACATAGTGCCAAAAATACACA
* * * *
3648 TAGTGCTTATATAAAAATGCACCGTTATGCATTAAACAAAATCGATCAATAACTTTCATACATAA
66 TAGTACTGATACAAAAATGCACCATTATGCATTAAACAAAATCGATCAATAACTTTCATACATAA
3713 TTGTATGT
131 TTGTATGT
* * * * *
3721 CGAAATGGTAATTTACAAACTCATTATAAATACCATGGTTGCACATC-TAGTGCCTAAAGTACAC
1 CGAAATGGAAATTCACAAACTCATTATAAATACCATGGATGCACA-CATAGTGCCAAAAATACAC
* * *
3785 ATAGTACTGATACGAAAATGCACCATTATGCATTATACAAAATCGATCGATAA
65 ATAGTACTGATACAAAAATGCACCATTATGCATTAAACAAAATCGATCAATAA
3838 TTATATACAA
Statistics
Matches: 101, Mismatches: 15, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
138 100 0.99
139 1 0.01
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.28
Consensus pattern (138 bp):
CGAAATGGAAATTCACAAACTCATTATAAATACCATGGATGCACACATAGTGCCAAAAATACACA
TAGTACTGATACAAAAATGCACCATTATGCATTAAACAAAATCGATCAATAACTTTCATACATAA
TTGTATGT
Found at i:4528 original size:20 final size:19
Alignment explanation
Indices: 4484--4534 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
4474 TTTCAATTAC
4484 AGTATCGATACCTTCCCCTT
1 AGTATCGATACC-TCCCCTT
*
4504 GGTATCGATACC-CCCACATT
1 AGTATCGATACCTCCC-C-TT
4524 AGTATCGATAC
1 AGTATCGATAC
4535 TACTTGCATC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 3 0.11
19 1 0.04
20 23 0.85
ACGTcount: A:0.25, C:0.31, G:0.14, T:0.29
Consensus pattern (19 bp):
AGTATCGATACCTCCCCTT
Found at i:10022 original size:19 final size:20
Alignment explanation
Indices: 9984--10023 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
9974 CACTATTTGC
9984 ACAGTATCAATACAATTCAT
1 ACAGTATCAATACAATTCAT
* *
10004 ACAGTAT-AGTACTATTCAT
1 ACAGTATCAATACAATTCAT
10023 A
1 A
10024 AAACGTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (20 bp):
ACAGTATCAATACAATTCAT
Found at i:11220 original size:23 final size:23
Alignment explanation
Indices: 11180--11225 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
11170 TATTTTTCCA
*
11180 TTTATCTCTTTAATCATT-ATTC
1 TTTATCTCTTTAAGCATTCATTC
*
11202 TTTATCTTCTTTGAGCATTCATTC
1 TTTATC-TCTTTAAGCATTCATTC
11226 ATACTAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 6 0.30
23 10 0.50
24 4 0.20
ACGTcount: A:0.20, C:0.20, G:0.04, T:0.57
Consensus pattern (23 bp):
TTTATCTCTTTAAGCATTCATTC
Found at i:11482 original size:68 final size:68
Alignment explanation
Indices: 11425--11614 Score: 299
Period size: 68 Copynumber: 2.8 Consensus size: 68
11415 ATGCGTTTAA
* * *
11425 CCTTTCATCTAACTAGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGTCCTCAAAGGCACT
1 CCTTTCATCTAACTGGCATAATTGACACTTTTCTGTCAAATGCACAGCTAGGCCTCAAAGGCACT
11490 TAG
66 TAG
* * * *
11493 TCTTTCATCTAACTGGCATAATTGAAACTTTTCTGGCAACTGCACAGCTAGGCCTCAAAGGCACT
1 CCTTTCATCTAACTGGCATAATTGACACTTTTCTGTCAAATGCACAGCTAGGCCTCAAAGGCACT
11558 TAG
66 TAG
* *
11561 CCTTTCATCTAACTGGCATAATGGACACTTTTCTGTTAAATGCACAGCTAGGCC
1 CCTTTCATCTAACTGGCATAATTGACACTTTTCTGTCAAATGCACAGCTAGGCC
11615 ATTAATCTTT
Statistics
Matches: 109, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
68 109 1.00
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (68 bp):
CCTTTCATCTAACTGGCATAATTGACACTTTTCTGTCAAATGCACAGCTAGGCCTCAAAGGCACT
TAG
Found at i:12694 original size:55 final size:55
Alignment explanation
Indices: 11774--12675 Score: 1161
Period size: 55 Copynumber: 16.4 Consensus size: 55
11764 GATGCACCCG
* * ** * *
11774 TAGTGCATATACTG-TAGTTCATCAACTCATGATGAATTCCATGG-GTTGGACACA
1 TAGTGCATGTACGGTTA-TTCATCAACTCATGATGAATTCTGTGGATTTGCACACA
* * * * * *
11828 TCGTTCCTGTATGATTATTCATCAACTCATGATGAATTATGTGGATTTGCACACA
1 TAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATTTGCACACA
* * * * *
11883 TAGTGCATATACGGTTATTCATCAACTCATGATAAATT-TCGTTGATTTGTAAACA
1 TAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCT-GTGGATTTGCACACA
* * * * *
11938 TAGTGTATGTACGATTATTCATCAACTCATGGTGAATTCCGTGGATTTGCATACA
1 TAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATTTGCACACA
* *
11993 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATTTGTACACA
1 TAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATTTGCACACA
* * * ** *
12048 TCGTGCCTTTACAATTATTCATCAACTCATGATGAATT-TCATGGATTTGCACACA
1 TAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCT-GTGGATTTGCACACA
* * *
12103 TAGTACTTGTACGGTTATTCATCAACTCGTGATGAATTCTGTGGATTTGCACACA
1 TAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATTTGCACACA
*
12158 TAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATTTGCACACA
1 TAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATTTGCACACA
*
12213 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATTTGCACACA
1 TAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATTTGCACACA
*
12268 TAGTGCATGTACGGTTATTCATCAACTCATGATGAATTATGTGGATTTGCACACA
1 TAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATTTGCACACA
* * * *
12323 TAGTGCCTGTACGGTTATTCATCAACGT-ATGATAAATTCTATGGATTTGCACATA
1 TAGTGCATGTACGGTTATTCATCAAC-TCATGATGAATTCTGTGGATTTGCACACA
* * * *
12378 TAGTGCCTGTATGGTTATTCATCAACTCATGATGAATT-TCATGGATTTGTACACA
1 TAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCT-GTGGATTTGCACACA
* * ** * *
12433 TCGTGCCTGTATAGTTATTCATCAAGTCATGATGAATTCCGTGGATTTGCACACA
1 TAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATTTGCACACA
* *
12488 TAGTGCTTGTACGGTTATTCATCAACTCATGATGAATT-TCGTAGATTTGCACACA
1 TAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCT-GTGGATTTGCACACA
* * * *
12543 TAGTGCATATACGGTTATTCATTAACTCATGATGAATTCCGTAGATTTGCACACA
1 TAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATTTGCACACA
* * *
12598 TAGTGCATGCACGGTTATCCATCAACTCATGATGAATTCTGTAGATTTGCACACA
1 TAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATTTGCACACA
*
12653 CAGTGCATGTACGGTTATTCATC
1 TAGTGCATGTACGGTTATTCATC
12676 TACGTGGGAT
Statistics
Matches: 742, Mismatches: 94, Indels: 23
0.86 0.11 0.03
Matches are distributed among these distances:
54 35 0.05
55 705 0.95
56 2 0.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.35
Consensus pattern (55 bp):
TAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATTTGCACACA
Found at i:12727 original size:54 final size:54
Alignment explanation
Indices: 12663--12767 Score: 165
Period size: 54 Copynumber: 1.9 Consensus size: 54
12653 CAGTGCATGT
* * * *
12663 ACGGTTATTCATCTACGTGGGATGAATTCTGTGAAATGCACAATTAGTGCCGAA
1 ACGGTCATTCATCCACGTAGGATGAATTCCGTGAAATGCACAATTAGTGCCGAA
*
12717 ACGGTCATTCATCCACGTAGGATGAATTCCGTGAAATGCACACTTAGTGCC
1 ACGGTCATTCATCCACGTAGGATGAATTCCGTGAAATGCACAATTAGTGCC
12768 TATTTGGTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.28
Consensus pattern (54 bp):
ACGGTCATTCATCCACGTAGGATGAATTCCGTGAAATGCACAATTAGTGCCGAA
Found at i:16465 original size:14 final size:14
Alignment explanation
Indices: 16446--16475 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
16436 ATATATATTT
16446 AAATTATTCGAATC
1 AAATTATTCGAATC
16460 AAATTATTCGAATC
1 AAATTATTCGAATC
16474 AA
1 AA
16476 TTTTGAATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (14 bp):
AAATTATTCGAATC
Found at i:17579 original size:36 final size:36
Alignment explanation
Indices: 17539--17607 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
17529 AAATGTCAAA
*
17539 GTGTATCC-ATACACCCAGCAGTGTATCCATACATTG
1 GTGTA-CCGATACAACCAGCAGTGTATCCATACATTG
* *
17575 GTGTACCGATACAACCTGTAGTGTATCCATACA
1 GTGTACCGATACAACCAGCAGTGTATCCATACA
17608 CCTATGACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 2 0.07
36 27 0.93
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (36 bp):
GTGTACCGATACAACCAGCAGTGTATCCATACATTG
Found at i:17606 original size:20 final size:20
Alignment explanation
Indices: 17538--17607 Score: 60
Period size: 20 Copynumber: 3.7 Consensus size: 20
17528 AAAATGTCAA
* * *
17538 AGTGTATCCATACACCCAGC
1 AGTGTATCCATACAACCTGT
17558 AGTGTATCCATAC-A--T-T
1 AGTGTATCCATACAACCTGT
*
17574 GGTGTA-CCGATACAACCTGT
1 AGTGTATCC-ATACAACCTGT
17594 AGTGTATCCATACA
1 AGTGTATCCATACA
17608 CCTATGACTG
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
15 2 0.05
16 9 0.23
17 1 0.03
19 1 0.03
20 24 0.62
21 2 0.05
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (20 bp):
AGTGTATCCATACAACCTGT
Found at i:17683 original size:20 final size:20
Alignment explanation
Indices: 17658--17695 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
17648 TACATCTATG
17658 GTGTATCAATACACCCTGCA
1 GTGTATCAATACACCCTGCA
*
17678 GTGTATCCATACACCCTG
1 GTGTATCAATACACCCTG
17696 GCTGCAACGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (20 bp):
GTGTATCAATACACCCTGCA
Found at i:20442 original size:20 final size:20
Alignment explanation
Indices: 20417--20485 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
20407 ATGTCAAAGG
20417 GTATCCATACACCCTGTAGT
1 GTATCCATACACCCTGTAGT
20437 GTATCCATACA--CTG--GT
1 GTATCCATACACCCTGTAGT
*
20453 GTA-CCGATACAACCTGTAGT
1 GTATCC-ATACACCCTGTAGT
20473 GTATCCATACACC
1 GTATCCATACACC
20486 TATGAATGCT
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
15 2 0.05
16 10 0.24
18 6 0.14
20 22 0.52
21 2 0.05
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.28
Consensus pattern (20 bp):
GTATCCATACACCCTGTAGT
Found at i:27857 original size:78 final size:77
Alignment explanation
Indices: 27724--27877 Score: 227
Period size: 78 Copynumber: 2.0 Consensus size: 77
27714 CCTCCTGTGT
* * * *
27724 TATTTCTCGATGTCCCTTCTTCTTCCCTTTCATTCTCATCCTCTTTTATTATTCCTGAAACTAGG
1 TATTTCTCGATGTCCCTTCTTCTCCCCTTCCATTCTCATCCTCTTCTATTATTCCTAAAACTAGG
*
27789 GTTTTAGAATCG
66 GTTTTACAATCG
* * *
27801 TATTATCTCGATTTCCCTTCTTCTCCCCTTCCATTCTCATTCTCTTCTATTCTTCCTAAAACTAG
1 TATT-TCTCGATGTCCCTTCTTCTCCCCTTCCATTCTCATCCTCTTCTATTATTCCTAAAACTAG
27866 GGTTTTACAATC
65 GGTTTTACAATC
27878 CTATGAGTAC
Statistics
Matches: 68, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
77 4 0.06
78 64 0.94
ACGTcount: A:0.18, C:0.29, G:0.08, T:0.46
Consensus pattern (77 bp):
TATTTCTCGATGTCCCTTCTTCTCCCCTTCCATTCTCATCCTCTTCTATTATTCCTAAAACTAGG
GTTTTACAATCG
Found at i:33923 original size:3 final size:3
Alignment explanation
Indices: 33915--33969 Score: 69
Period size: 3 Copynumber: 19.0 Consensus size: 3
33905 AATTTATTTT
* * *
33915 ATA ATA ATA ATA ATA ATA AT- ATG ATA ATA ATA ATT GTA AT- ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
33961 ATA ATA ATA
1 ATA ATA ATA
33970 TATAGTCTCG
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
2 4 0.09
3 41 0.91
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:33943 original size:20 final size:20
Alignment explanation
Indices: 33914--33969 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
33904 CAATTTATTT
33914 TATAATAATAATAATAATAA
1 TATAATAATAATAATAATAA
* **
33934 TATGATAATAATAATTGTAA
1 TATAATAATAATAATAATAA
33954 TATAATAATAATAATA
1 TATAATAATAATAATA
33970 TATAGTCTCG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.38
Consensus pattern (20 bp):
TATAATAATAATAATAATAA
Found at i:34182 original size:18 final size:18
Alignment explanation
Indices: 34159--34198 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
34149 AAGTGTATTC
34159 GGCCTACTTTCAGCATTA
1 GGCCTACTTTCAGCATTA
*
34177 GGCCTACTTTTAGCATTA
1 GGCCTACTTTCAGCATTA
34195 GGCC
1 GGCC
34199 CACAACTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.33
Consensus pattern (18 bp):
GGCCTACTTTCAGCATTA
Found at i:34728 original size:2 final size:2
Alignment explanation
Indices: 34723--34753 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
34713 GGTAAAAAAA
34723 AT AT AT 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 AT AT AT A
34754 AATTCCATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35718 original size:6 final size:6
Alignment explanation
Indices: 35709--35739 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
35699 AAATATTAAA
*
35709 AATTAT AATTAT AATTAT AATCAT AATTAT A
1 AATTAT AATTAT AATTAT AATTAT AATTAT A
35740 CCTAAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (6 bp):
AATTAT
Found at i:42964 original size:2 final size:2
Alignment explanation
Indices: 42957--42996 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
42947 TTGTAAATGA
42957 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
42997 CACTCCTAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:48676 original size:45 final size:45
Alignment explanation
Indices: 48625--48722 Score: 124
Period size: 45 Copynumber: 2.2 Consensus size: 45
48615 TCGGTTTTTT
* ** * *
48625 TACCATCTAAATGCTTTCCTTCATTAACAGTGTCGTCAGCTATTG
1 TACCATCTAAATGCTTCCCTTCAGCAACAGTGTCATCAACTATTG
* * *
48670 TACCATCCAAATGCTTCCCTTCAGCAGCAGTGTCATCAATTATTG
1 TACCATCTAAATGCTTCCCTTCAGCAACAGTGTCATCAACTATTG
48715 TACCATCT
1 TACCATCT
48723 GTCGCAACCG
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.26, C:0.28, G:0.12, T:0.35
Consensus pattern (45 bp):
TACCATCTAAATGCTTCCCTTCAGCAACAGTGTCATCAACTATTG
Found at i:49117 original size:15 final size:14
Alignment explanation
Indices: 49089--49124 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
49079 CTTAAATTTG
49089 AAAAATAAAGAAAA
1 AAAAATAAAGAAAA
*
49103 AAAAATGAAGAAAA
1 AAAAATAAAGAAAA
49117 AAAAATAA
1 AAAAATAA
49125 CAATAAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.83, C:0.00, G:0.08, T:0.08
Consensus pattern (14 bp):
AAAAATAAAGAAAA
Found at i:49614 original size:16 final size:14
Alignment explanation
Indices: 49576--49615 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
49566 ATACAGAATA
49576 TATACATATATATG
1 TATACATATATATG
*
49590 TATATATATATATAG
1 TATACATATATAT-G
49605 TATAGCATATA
1 TATA-CATATA
49616 GGTAAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 12 0.55
15 5 0.23
16 5 0.23
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.42
Consensus pattern (14 bp):
TATACATATATATG
Found at i:49694 original size:22 final size:22
Alignment explanation
Indices: 49669--49741 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 22
49659 AAAAAAAAAC
49669 TAATGATAATATAAAATATATA
1 TAATGATAATATAAAATATATA
*
49691 TAATGCTAATAGTATATATATATATA
1 TAATGATAATA-TA-A-A-ATATATA
49717 TATAT-ATAAT-T-AAATATATTA
1 TA-ATGATAATATAAAATATA-TA
49738 TAAT
1 TAAT
49742 ATTTGGAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 14
0.73 0.03 0.24
Matches are distributed among these distances:
20 7 0.16
21 5 0.12
22 11 0.26
23 2 0.05
24 2 0.05
25 1 0.02
26 13 0.30
27 2 0.05
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.42
Consensus pattern (22 bp):
TAATGATAATATAAAATATATA
Found at i:51539 original size:105 final size:105
Alignment explanation
Indices: 51340--52011 Score: 1083
Period size: 105 Copynumber: 6.4 Consensus size: 105
51330 GTATTGTTCC
* ** * * * * **
51340 GGAGTCCAATATCATTCACTGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATCGTCGGTTGACA
1 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAAT-GTTTGTTGACA
** * ****
51405 GTCAGCGGCCCCTTCGTCGTGAAGTTGAACTTATACTGTCT
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
*
51446 TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAA
1 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAA
51511 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
51551 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGGAATTGAGAAATGTTTGTTGACAA
1 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAA
51616 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
51656 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGGAATTGAGAAATGTTTGTTGACAA
1 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAA
* *
51721 CCAGCGGTCCCTTCGTCGTGAAGTTGGACTTGCATTGTCT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * *
51761 GGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAA
1 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAA
51826 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
*
51866 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAA
1 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAA
51931 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
*
51971 AGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
52012 GGTAAAACCT
Statistics
Matches: 532, Mismatches: 34, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
105 487 0.92
106 45 0.08
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (105 bp):
GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
Found at i:52835 original size:6 final size:6
Alignment explanation
Indices: 52824--52877 Score: 62
Period size: 6 Copynumber: 9.7 Consensus size: 6
52814 CGTTTTTCTC
* *
52824 TTTTTG TTTTTG TTTTTG -TTTTG TTTTGG TTTTT- TTTTTG -TTCTG
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
52869 TTTTT- TTTT
1 TTTTTG TTTT
52878 CCAACTTAGG
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
5 18 0.44
6 23 0.56
ACGTcount: A:0.00, C:0.02, G:0.15, T:0.83
Consensus pattern (6 bp):
TTTTTG
Found at i:52847 original size:17 final size:16
Alignment explanation
Indices: 52824--52877 Score: 65
Period size: 16 Copynumber: 3.3 Consensus size: 16
52814 CGTTTTTCTC
52824 TTTTTGTTTTTGTTTT
1 TTTTTGTTTTTGTTTT
*
52840 TGTTTTGTTTTGGTTTT
1 T-TTTTGTTTTTGTTTT
*
52857 TTTTT-TGTTCTGTTTT
1 TTTTTGT-TTTTGTTTT
52873 TTTTT
1 TTTTT
52878 CCAACTTAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 1 0.03
16 17 0.52
17 15 0.45
ACGTcount: A:0.00, C:0.02, G:0.15, T:0.83
Consensus pattern (16 bp):
TTTTTGTTTTTGTTTT
Found at i:52856 original size:22 final size:22
Alignment explanation
Indices: 52825--52872 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
52815 GTTTTTCTCT
* *
52825 TTTTGTTTTTGTTTTTGTTTTG
1 TTTTGGTTTTGTTTTTGTTCTG
*
52847 TTTTGGTTTTTTTTTTGTTCTG
1 TTTTGGTTTTGTTTTTGTTCTG
52869 TTTT
1 TTTT
52873 TTTTTCCAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.00, C:0.02, G:0.17, T:0.81
Consensus pattern (22 bp):
TTTTGGTTTTGTTTTTGTTCTG
Found at i:63320 original size:14 final size:13
Alignment explanation
Indices: 63293--63326 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
63283 CTTAAATTTG
63293 AAAAATAAAGAAA
1 AAAAATAAAGAAA
*
63306 AAAAATGAAGAAA
1 AAAAATAAAGAAA
63319 AAAAATAA
1 AAAAATAA
63327 CAATAAATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.82, C:0.00, G:0.09, T:0.09
Consensus pattern (13 bp):
AAAAATAAAGAAA
Found at i:63817 original size:16 final size:14
Alignment explanation
Indices: 63779--63818 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
63769 ATACATAATA
63779 TATACATATATATG
1 TATACATATATATG
*
63793 TATATATATATATAG
1 TATACATATATAT-G
63808 TATAGCATATA
1 TATA-CATATA
63819 GGTAAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 12 0.55
15 5 0.23
16 5 0.23
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.42
Consensus pattern (14 bp):
TATACATATATATG
Found at i:67010 original size:192 final size:192
Alignment explanation
Indices: 66614--67151 Score: 519
Period size: 192 Copynumber: 2.8 Consensus size: 192
66604 TTGCGATCTA
* * * * * * * *
66614 GAATGTTAGTTTTATGTTTAATAAAATC-GATTGCGCCTAAAATGTTACCAGAGTTTGAGTCAAT
1 GAATGTTAATTTTATGTTTGATAAAATCAG-CTGCGCCTAAAATGCTACTAGAGTTTAAGCCGAT
* ** ** *
66678 -G-AGGCTTTCCAATTTCTCACGATAACAAAATAAATTAAAATCAAATTTGTTATGAATATCTAT
65 AGTA-G-TTTCGAATTTCTCAAAATAACAAAATAAATTAAAAT-AAAAATATTATGAATATCTAT
* ** * * * * * * **
66741 AAGAAATCAGGTCGTGCCCATTAATGTTA-----TA--GGTCACTAAGAAAATA-GATTGCGACC
127 AAGAAATTAAATTGAGCCCATGAATGTTATGGGTTATGGGTCGCTAAGAAAGTATG-TTGCAATA
66798 TG
191 TG
* * * **
66800 GAATGTTAATTTTATGTTTGATAAAA-CTGTTTGCGCCTAAAATGCTACTTGAGTTTAAGTTGAT
1 GAATGTTAATTTTATGTTTGATAAAATCAG-CTGCGCCTAAAATGCTACTAGAGTTTAAGCCGAT
* * * *
66864 AG-GGTTTTTGAATTTCTTAAAATAA-AAAATTAAGTTAAAATAAAAATATTATGAATATCTATA
65 AGTAG-TTTCGAATTTCTCAAAATAACAAAA-TAAATTAAAATAAAAATATTATGAATATCTATA
*
66927 AGAAATTAAATTGAGTCCATGAATGTTATGGGTTATGGGTCGCTAAGAAAGTATGTTGCAATATG
128 AGAAATTAAATTGAGCCCATGAATGTTATGGGTTATGGGTCGCTAAGAAAGTATGTTGCAATATG
* * *
66992 GAATGTTAATTTTATGTTTGATAAAATCAGCTGCTCCTAAAATGTTACTAGATTTTAAGCCGATA
1 GAATGTTAATTTTATGTTTGATAAAATCAGCTGCGCCTAAAATGCTACTAGAGTTTAAGCCGATA
**
67057 GTAGTTTCGAATTTCTCACGATAACAAAATAAATTAAAATAAAAATATTATGAATATCTATAAGA
66 GTAGTTTCGAATTTCTCAAAATAACAAAATAAATTAAAATAAAAATATTATGAATATCTATAAGA
** *
67122 AATTAGGTTGAGCCCGTGAATGTTATGGGT
131 AATTAAATTGAGCCCATGAATGTTATGGGT
67152 CGTTAAGAAA
Statistics
Matches: 288, Mismatches: 50, Indels: 22
0.80 0.14 0.06
Matches are distributed among these distances:
185 45 0.16
186 79 0.27
187 1 0.00
190 2 0.01
192 153 0.53
193 8 0.03
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.35
Consensus pattern (192 bp):
GAATGTTAATTTTATGTTTGATAAAATCAGCTGCGCCTAAAATGCTACTAGAGTTTAAGCCGATA
GTAGTTTCGAATTTCTCAAAATAACAAAATAAATTAAAATAAAAATATTATGAATATCTATAAGA
AATTAAATTGAGCCCATGAATGTTATGGGTTATGGGTCGCTAAGAAAGTATGTTGCAATATG
Found at i:67677 original size:73 final size:73
Alignment explanation
Indices: 67451--67780 Score: 310
Period size: 72 Copynumber: 4.5 Consensus size: 73
67441 AAAAAATTAT
* * * * * *
67451 AAATATTGATACTTAAT-CTATGTTGATCGATACTTTCAAGTATTGAAAAAGTTGAAGATAAAAC
1 AAATATCGATACTT-ATGCTGTGATGATCGATACTTTTAAGTATTGAAAAAGTTGAAGATAAGAT
67515 CGAAAGTT-
65 CGAAAGTTA
* * * * * * ** * *
67523 AAATATTGATACTCATGCAGTGATGATCAATACTTTTAATTAAT-AAAAAAATAAAAATAAGATC
1 AAATATCGATACTTATGCTGTGATGATCGATACTTTTAAGTATTGAAAAAGTTGAAGATAAGATC
67587 GAAAGTTA
66 GAAAGTTA
* *
67595 AAATATCGATACTTATGCGGTGATGATCGATACTTTTAAGTATTGAAAGAGTTGAAGATAAGATC
1 AAATATCGATACTTATGCTGTGATGATCGATACTTTTAAGTATTGAAAAAGTTGAAGATAAGATC
67660 GAAAGTTA
66 GAAAGTTA
* * * * * * *
67668 AATTATCGATATTTATGCTTTGATGATCGATGCTTTT-A-TATAGAAGAAGTTGTTGAAGATATG
1 AAATATCGATACTTATGCTGTGATGATCGATACTTTTAAGTATTGAA-AA--AGTTGAAGATAAG
*
67731 ATCGATAGTTA
63 ATCGAAAGTTA
* ** * *
67742 AAATATCGATACATATATTATGATGTTCGATACTTTTAA
1 AAATATCGATACTTATGCTGTGATGATCGATACTTTTAA
67781 ATTTATATCG
Statistics
Matches: 208, Mismatches: 43, Indels: 11
0.79 0.16 0.04
Matches are distributed among these distances:
71 29 0.14
72 73 0.35
73 55 0.26
74 50 0.24
75 1 0.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.35
Consensus pattern (73 bp):
AAATATCGATACTTATGCTGTGATGATCGATACTTTTAAGTATTGAAAAAGTTGAAGATAAGATC
GAAAGTTA
Found at i:67765 original size:144 final size:142
Alignment explanation
Indices: 67474--67780 Score: 317
Period size: 147 Copynumber: 2.1 Consensus size: 142
67464 TAATCTATGT
* *
67474 TGATCGATACTTTCAAGTATTGAAAAAGTTGAAGATAAAACCGAAAGTTAAATATTGATACTCAT
1 TGATCGATACTTTTAAGTATTGAAAAAGTTGAAGATAAAACCGAAAGTTAAATATCGATACTCAT
* *
67539 GCAGTGATGATCAATACTTTTAATTAATAAAAAAATAAAAATAAGATCGAAAGTTAAAATATCGA
66 GCAGTGATGATCAATACTTTTAATGAAGAAAAAAATAAAAATAAGATCGAAAGTTAAAATATCGA
* *
67604 TACTTATGCGGTGA
131 TACATAT--GATGA
* * * * *
67618 TGATCGATACTTTTAAGTATTGAAAGAGTTGAAGATAAGATCGAAAGTTAAATTATCGATATTTA
1 TGATCGATACTTTTAAGTATTGAAAAAGTTGAAGATAAAACCGAAAGTTAAA-TATCGATACTCA
** * * ***** * * * *
67683 TGCTTTGATGATCGATGCTTTTATATAGAAGAAGTTGTTGAAGATATGATCGATAGTTAAAATAT
65 TGCAGTGATGATCAATACTTTTA-AT-GAAGAAAAAAATAAAAATAAGATCGAAAGTTAAAATAT
*
67748 CGATACATATATTATGA
128 CGATAC--ATATGATGA
*
67765 TGTTCGATACTTTTAA
1 TGATCGATACTTTTAA
67781 ATTTATATCG
Statistics
Matches: 132, Mismatches: 26, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
144 48 0.36
145 28 0.21
146 2 0.02
147 51 0.39
149 3 0.02
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.34
Consensus pattern (142 bp):
TGATCGATACTTTTAAGTATTGAAAAAGTTGAAGATAAAACCGAAAGTTAAATATCGATACTCAT
GCAGTGATGATCAATACTTTTAATGAAGAAAAAAATAAAAATAAGATCGAAAGTTAAAATATCGA
TACATATGATGA
Found at i:69556 original size:15 final size:15
Alignment explanation
Indices: 69536--69564 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
69526 TTTAAAAATC
69536 TTTTAAATTAATTTG
1 TTTTAAATTAATTTG
69551 TTTTAAATTAATTT
1 TTTTAAATTAATTT
69565 TTTATATCGA
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:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (15 bp):
TTTTAAATTAATTTG
Found at i:75854 original size:22 final size:23
Alignment explanation
Indices: 75828--75888 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
75818 TTAGTGCAGA
**
75828 GGGAATCGATACCCCCTTGA-AG
1 GGGAATCGATACCCCCTCCACAG
* *
75850 GGGAACCGATTCCCCC-CCACAG
1 GGGAATCGATACCCCCTCCACAG
75872 GGGAATCGATACCCCCT
1 GGGAATCGATACCCCCT
75889 GAGGGTTCTG
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
21 1 0.03
22 30 0.97
ACGTcount: A:0.25, C:0.36, G:0.25, T:0.15
Consensus pattern (23 bp):
GGGAATCGATACCCCCTCCACAG
Found at i:77507 original size:18 final size:18
Alignment explanation
Indices: 77470--77507 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
77460 AGAACAACAC
* *
77470 GAGGAACAAGCACGAGCA
1 GAGGAACAAGCACAACCA
77488 GAGGAACAAGCACAACCA
1 GAGGAACAAGCACAACCA
77506 GA
1 GA
77508 TGATGTAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.47, C:0.24, G:0.29, T:0.00
Consensus pattern (18 bp):
GAGGAACAAGCACAACCA
Found at i:77985 original size:13 final size:13
Alignment explanation
Indices: 77967--77991 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
77957 GCCACGTCAC
77967 ATTGATTATGAAT
1 ATTGATTATGAAT
77980 ATTGATTATGAA
1 ATTGATTATGAA
77992 ACTAATGGCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (13 bp):
ATTGATTATGAAT
Found at i:80351 original size:20 final size:20
Alignment explanation
Indices: 80315--80415 Score: 71
Period size: 20 Copynumber: 5.1 Consensus size: 20
80305 ACTGGAATGG
* *
80315 CCTGAACCGA-CCAACCTTGT
1 CCTGAACCGAGTCAACC-TGA
80335 CC-GAACCGAGTCAACCTGA
1 CCTGAACCGAGTCAACCTGA
* **
80354 CCTGAATCGAGTCAACCCAA
1 CCTGAACCGAGTCAACCTGA
* * *
80374 CCCGAACCAATTCAACCTGA
1 CCTGAACCGAGTCAACCTGA
* * * *
80394 CCCGACCCGAGTTAAACTGA
1 CCTGAACCGAGTCAACCTGA
80414 CC
1 CC
80416 CGACCCGTTG
Statistics
Matches: 63, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
19 11 0.17
20 52 0.83
ACGTcount: A:0.31, C:0.39, G:0.16, T:0.15
Consensus pattern (20 bp):
CCTGAACCGAGTCAACCTGA
Found at i:84589 original size:22 final size:22
Alignment explanation
Indices: 84561--84608 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
84551 ACCTGAAGCG
* * *
84561 TTGACCGGTTTGACTGTTGACT
1 TTGACCGGTCTAACTGTTAACT
84583 TTGACCGGTCTAACTGTTAACT
1 TTGACCGGTCTAACTGTTAACT
84605 TTGA
1 TTGA
84609 TAAAAAAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.40
Consensus pattern (22 bp):
TTGACCGGTCTAACTGTTAACT
Found at i:86232 original size:19 final size:19
Alignment explanation
Indices: 86210--86249 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
86200 CTCTGAGCTT
*
86210 TGATATATGTTCTGATCTC
1 TGATATATGTTATGATCTC
* *
86229 TGATGTTTGTTATGATCTC
1 TGATATATGTTATGATCTC
86248 TG
1 TG
86250 CTTTGATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.17, C:0.12, G:0.20, T:0.50
Consensus pattern (19 bp):
TGATATATGTTATGATCTC
Found at i:88038 original size:5 final size:5
Alignment explanation
Indices: 88028--88056 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
88018 TGCCCTTCAA
88028 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
88057 AAACTAAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:89920 original size:17 final size:17
Alignment explanation
Indices: 89898--89954 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
89888 CATATATCCT
* *
89898 TCAAATTGAAATTGAAA
1 TCAAATTCAAATTAAAA
89915 TCAAATTCAAATTAAAA
1 TCAAATTCAAATTAAAA
* *
89932 TTAAAAT-AAATTTAAAA
1 TCAAATTCAAA-TTAAAA
89949 TTCAAA
1 -TCAAA
89955 GCAAAATTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
16 3 0.09
17 26 0.79
18 4 0.12
ACGTcount: A:0.58, C:0.07, G:0.04, T:0.32
Consensus pattern (17 bp):
TCAAATTCAAATTAAAA
Found at i:89923 original size:23 final size:22
Alignment explanation
Indices: 89897--89943 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
89887 ACATATATCC
* *
89897 TTCAAATTGAAATTGAAATCAAA
1 TTCAAATTAAAATTAAAAT-AAA
89920 TTCAAATTAAAATTAAAATAAA
1 TTCAAATTAAAATTAAAATAAA
89942 TT
1 TT
89944 TAAAATTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.34
Consensus pattern (22 bp):
TTCAAATTAAAATTAAAATAAA
Found at i:92171 original size:664 final size:665
Alignment explanation
Indices: 90891--92877 Score: 2933
Period size: 663 Copynumber: 3.0 Consensus size: 665
90881 ACTTCATATT
* * *
90891 AACTTTAAATCAATTGTCAAACTGATACAAGTTTGACACAAGTTAAAATAATAATTTGTCAAATC
1 AACTTTAAATCAATTGTCAATCTGATACAAGTTTGATACAAGTTAAAATAATAATTTGTCAAACC
* * *
90956 TGCTCTAATTCAAAATCACATTAAGACAAAGCTTAATTCAAGTCAAAATAAGGACAAATGAATGG
66 TGCTCTAATTCAATATCACATTAAGCCAAAGCTTAATTCAAGTCAAAATAAGGACAAAAGAATGG
* ** * * *
91021 TTATACATAAAAACCATTACAATCAAAATAATCGATATCCTATAACTAGCAAGTATATGACAAAA
131 TTATACAT-AAAACCATTATAATCAAAATAATATATATCCTATAAGTAGTAGGTATATGACAAAA
91086 TAAGTCAAGTTCCCAAGTAAATTACATAAAAAGTTCCATCATCACTTGGACATACTTCAATCCTT
195 TAAGTCAAGTTCCCAAGTAAATTACATAAAAAGTTCCATCATCACTTGGACATACTTCAATCCTT
* *
91151 TGATGTAGTGTAAAATTTTTGAGTGGGAGGGTTAAAAAGAAATATTCTTGACTAGCAGGT-ATCG
260 TGATGTAGTGTAAAATTTTTGAGTGAGAGGGTTAAAAAGAAATATTCTTGACTGGCA-GTCATCG
* * *
91215 TATGGATTGTTTTAGGTGGTGGCATCATCTAATGAACTATTGTAGGTGGATTAAGTGGTCTCCTT
324 TATGGATTGTTGTA-G-GGTAG-A-C--C-AATGAACTATTGTAGGTGGATTAAGTGGCCTCCTT
* * *
91280 ATAGGTAATTTGTGCCTTACTTGTTGTTCCTTGGAGTTAGCTATTGGGATGGTTGGTTACATGCA
382 ATAGGTAATTTGTGCCTTACTTGTTGTTCCTTGGAGTTGGCTGTTGGGATGGTTGGTTAGA-GCA
* * * *
91345 CATCAAGCTTGTTGTTGGTGAGTTATATGTCGCTGGTTGGATCTAACTTCATGTTGGTTTAGTCT
446 CGTCGAGCTTGTTGTTGGTGAGTTATATGTCGTTGGTTGGATCTAAGTTCATGTTGGTTTAGTCT
** * *
91410 CCTATTACCATAGATTTTTCCTTTACAAGTCCTCTTATTGTAACCAAGTTTCCCACAATTGGAGC
511 CCTATTACCACCGATTTTTCCTCTACAAGTCCTCTTATTGTAACCAAGTTTCCCACACTTGGAGC
* * * * * *
91475 AGTTTTCGAGCGAACTTTTCTTACAAAGCTTAGATCGATTGTTTCCTTCTTCAACTTCTTTCATC
576 AGTTTTCGAGCGAACTTTTCTTGCATAGCTTAGGTCGATTGTTTCCTTTTTCAGCTTATTTCATC
*
91540 CTTTTTTTAGTTAGCAAACGAAATTC
641 C-TTTTTTAGTTAGCAAAAGAAATTC
*
91566 AACTTTAAATCAATTGTCAATCTGATACAAGTTTGATACAAATTAAAATAATAATTTGTCAAACC
1 AACTTTAAATCAATTGTCAATCTGATACAAGTTTGATACAAGTTAAAATAATAATTTGTCAAACC
*
91631 TGCTCTAATTCAATATCACATTAATCCAAAGCTTAATTCAAGTCAAAATAAGGACAAAAGAATGG
66 TGCTCTAATTCAATATCACATTAAGCCAAAGCTTAATTCAAGTCAAAATAAGGACAAAAGAATGG
* *
91696 TTATACATAAAACCATTATAATTAAAATAATATATATCCTATAAGTATTAGGTATATGACAAAAT
131 TTATACATAAAACCATTATAATCAAAATAATATATATCCTATAAGTAGTAGGTATATGACAAAAT
* * *
91761 AAGTCAAGTTCCAAATTAAATTACATAAAAAGTTCCATCATCACTTGGACATACTTCAATCATTT
196 AAGTCAAGTTCCCAAGTAAATTACATAAAAAGTTCCATCATCACTTGGACATACTTCAATCCTTT
* * *
91826 GATGTAGTGTAAAAATTTTGAGTGAAAGGGTTAAAAAGAAATATTCTTGACTGGCAGTCATCGCA
261 GATGTAGTGTAAAATTTTTGAGTGAGAGGGTTAAAAAGAAATATTCTTGACTGGCAGTCATCGTA
*
91891 TGGATTGTTGTA-GGT-G-CCAATGAACTATTATAGGTGGATTAAGTGGCCTCCTTATAGGTAAT
326 TGGATTGTTGTAGGGTAGACCAATGAACTATTGTAGGTGGATTAAGTGGCCTCCTTATAGGTAAT
* * * *
91953 TTGTGCCTTAGTTGTTGTTCCTTGGAGTTGGTTGTTGAGATGGCTGGTTATGAGCACGTCGAGCT
391 TTGTGCCTTACTTGTTGTTCCTTGGAGTTGGCTGTTGGGATGGTTGGTTA-GAGCACGTCGAGCT
* *
92018 TGTTGCTGGTGAGATATATGTCGTTGGTTGGATCTAAGTTCATGTTGGTTTAGTCTCCTATTACC
455 TGTTGTTGGTGAGTTATATGTCGTTGGTTGGATCTAAGTTCATGTTGGTTTAGTCTCCTATTACC
* * * *
92083 ACCGATTTTTCCTCTACAAGTCCTCTTATTGTATCCAAGTTTTCCACACTTGGAGTAGTTTCCGA
520 ACCGATTTTTCCTCTACAAGTCCTCTTATTGTAACCAAGTTTCCCACACTTGGAGCAGTTTTCGA
* *
92148 GCGAACTTTTCTTGCATAGCTTAGGTCGATTGTTTTCTTTTTCAGTTTATTTCATCCTTTTTTAG
585 GCGAACTTTTCTTGCATAGCTTAGGTCGATTGTTTCCTTTTTCAGCTTATTTCATCCTTTTTTAG
*
92213 TTGGCAAAAGAAATTC
650 TTAGCAAAAGAAATTC
* *
92229 AACTTTAAATCAATT-T---TC----A-AA--CTGATACAAGTTAAAACAATAATTTGTCAAACC
1 AACTTTAAATCAATTGTCAATCTGATACAAGTTTGATACAAGTTAAAATAATAATTTGTCAAACC
92283 TGCTCTAATTCAATATCACATTAAGCCAAAGCTTAATTCAAGTCAAAATAAGGACAAAAGAATGG
66 TGCTCTAATTCAATATCACATTAAGCCAAAGCTTAATTCAAGTCAAAATAAGGACAAAAGAATGG
*
92348 TTATACATAAAAGCCATTATAATCAAAATAACATATATCCTATAAGTAGTAGGTATATGACAAAA
131 TTATACATAAAA-CCATTATAATCAAAATAATATATATCCTATAAGTAGTAGGTATATGACAAAA
* * *
92413 TAAGTCAAGTTCCCAAGTAAATTACACAAAAAGTTCCATAATTACTTGGACATACTTCAATCCTT
195 TAAGTCAAGTTCCCAAGTAAATTACATAAAAAGTTCCATCATCACTTGGACATACTTCAATCCTT
* * * * *
92478 TGATGTAGTATAAAATTTTTGAGTGTGAGGGTTAAAAATAAATATTATTGACTGGCAGGCATCGT
260 TGATGTAGTGTAAAATTTTTGAGTGAGAGGGTTAAAAAGAAATATTCTTGACTGGCAGTCATCGT
* *
92543 ATGGATTGTTGTAGGTGGTAGCATAATCCAATAAACTATTGTAGGTGGATTAAGTGGCATCCTTA
325 ATGGATTGTTGTA-G-GGTAG----A-CCAATGAACTATTGTAGGTGGATTAAGTGGCCTCCTTA
* * *
92608 TAGGTTATTTGAGCCTTACTTGTTGTTCCTTGGAGTTGGCTGTTGGGATGGTTGGTTACGTGCAC
383 TAGGTAATTTGTGCCTTACTTGTTGTTCCTTGGAGTTGGCTGTTGGGATGGTTGGTTA-GAGCAC
* *
92673 GTCGAGCTTGTTGTTGGAGAGTTATATGTCGTTAGTTGGATCTAAGTTCATGTTGGTTTAGTCTC
447 GTCGAGCTTGTTGTTGGTGAGTTATATGTCGTTGGTTGGATCTAAGTTCATGTTGGTTTAGTCTC
* *
92738 CTATTACCACCGATTTTTCCTCTACAGGTCCTCTTATTGTAGCCAAGTTTCCCACACTTGGAGCA
512 CTATTACCACCGATTTTTCCTCTACAAGTCCTCTTATTGTAACCAAGTTTCCCACACTTGGAGCA
* * * *
92803 GTTTTTGAGCGAACTTTTCTTGCATAGCTTAGGTCGATTATTTCATTTTTCAGCTTTTTTCATCC
577 GTTTTCGAGCGAACTTTTCTTGCATAGCTTAGGTCGATTGTTTCCTTTTTCAGCTTATTTCATCC
92868 TTTTTTAGTT
642 TTTTTTAGTT
92878 TGCCTTGCAG
Statistics
Matches: 1194, Mismatches: 105, Indels: 38
0.89 0.08 0.03
Matches are distributed among these distances:
652 106 0.09
653 178 0.15
654 2 0.00
655 1 0.00
656 3 0.00
657 1 0.00
659 2 0.00
662 1 0.00
663 319 0.27
664 263 0.22
665 2 0.00
667 1 0.00
670 1 0.00
671 3 0.00
673 2 0.00
674 179 0.15
675 130 0.11
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (665 bp):
AACTTTAAATCAATTGTCAATCTGATACAAGTTTGATACAAGTTAAAATAATAATTTGTCAAACC
TGCTCTAATTCAATATCACATTAAGCCAAAGCTTAATTCAAGTCAAAATAAGGACAAAAGAATGG
TTATACATAAAACCATTATAATCAAAATAATATATATCCTATAAGTAGTAGGTATATGACAAAAT
AAGTCAAGTTCCCAAGTAAATTACATAAAAAGTTCCATCATCACTTGGACATACTTCAATCCTTT
GATGTAGTGTAAAATTTTTGAGTGAGAGGGTTAAAAAGAAATATTCTTGACTGGCAGTCATCGTA
TGGATTGTTGTAGGGTAGACCAATGAACTATTGTAGGTGGATTAAGTGGCCTCCTTATAGGTAAT
TTGTGCCTTACTTGTTGTTCCTTGGAGTTGGCTGTTGGGATGGTTGGTTAGAGCACGTCGAGCTT
GTTGTTGGTGAGTTATATGTCGTTGGTTGGATCTAAGTTCATGTTGGTTTAGTCTCCTATTACCA
CCGATTTTTCCTCTACAAGTCCTCTTATTGTAACCAAGTTTCCCACACTTGGAGCAGTTTTCGAG
CGAACTTTTCTTGCATAGCTTAGGTCGATTGTTTCCTTTTTCAGCTTATTTCATCCTTTTTTAGT
TAGCAAAAGAAATTC
Found at i:94262 original size:17 final size:17
Alignment explanation
Indices: 94240--94304 Score: 64
Period size: 17 Copynumber: 3.9 Consensus size: 17
94230 GATTGCTTGG
*
94240 ATGGTATCTATACCCCT
1 ATGGTATCGATACCCCT
94257 ATGGTATCGATA--CC-
1 ATGGTATCGATACCCCT
*
94271 ATGGTATGGATACCCCT
1 ATGGTATCGATACCCCT
* *
94288 AGGGGTATCTATACCCC
1 A-TGGTATCGATACCCC
94305 CTGGCTACAA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
14 11 0.28
15 2 0.05
16 2 0.05
17 12 0.31
18 12 0.31
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (17 bp):
ATGGTATCGATACCCCT
Found at i:94284 original size:31 final size:32
Alignment explanation
Indices: 94240--94302 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
94230 GATTGCTTGG
* *
94240 ATGGTATCTATACCCCTA-TGGTATCGATACC
1 ATGGTATCGATACCCCTAGGGGTATCGATACC
* *
94271 ATGGTATGGATACCCCTAGGGGTATCTATACC
1 ATGGTATCGATACCCCTAGGGGTATCGATACC
94303 CCCTGGCTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
31 16 0.59
32 11 0.41
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (32 bp):
ATGGTATCGATACCCCTAGGGGTATCGATACC
Found at i:94362 original size:21 final size:21
Alignment explanation
Indices: 94336--94377 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
94326 ATTTGAATTT
94336 TATGAAGGAG-TACCGATACCC
1 TATGAAGG-GTTACCGATACCC
94357 TATGAAGGGTTACCGATACCC
1 TATGAAGGGTTACCGATACCC
94378 CCTATTGTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.21
Consensus pattern (21 bp):
TATGAAGGGTTACCGATACCC
Found at i:94435 original size:21 final size:21
Alignment explanation
Indices: 94406--94477 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
94396 TTTGAGCAGA
94406 AAAATCATCCCCAAATGGCTCC
1 AAAA-CATCCCCAAATGGCTCC
*
94428 AAAACATCCCC-AATGGAT--
1 AAAACATCCCCAAATGGCTCC
* *
94446 -ATATA-CCCCAAATGGCTCC
1 AAAACATCCCCAAATGGCTCC
94465 AAAACATCCCCAA
1 AAAACATCCCCAA
94478 TGGATATATA
Statistics
Matches: 39, Mismatches: 6, Indels: 11
0.70 0.11 0.20
Matches are distributed among these distances:
16 4 0.10
17 9 0.23
20 9 0.23
21 13 0.33
22 4 0.10
ACGTcount: A:0.40, C:0.35, G:0.08, T:0.17
Consensus pattern (21 bp):
AAAACATCCCCAAATGGCTCC
Found at i:94464 original size:37 final size:37
Alignment explanation
Indices: 94414--94488 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
94404 GAAAAATCAT
94414 CCCCAAATGGCTCCAAAACATCCCCAATGGATATATA
1 CCCCAAATGGCTCCAAAACATCCCCAATGGATATATA
94451 CCCCAAATGGCTCCAAAACATCCCCAATGGATATATA
1 CCCCAAATGGCTCCAAAACATCCCCAATGGATATATA
94488 C
1 C
94489 AACTTCAAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.37, C:0.33, G:0.11, T:0.19
Consensus pattern (37 bp):
CCCCAAATGGCTCCAAAACATCCCCAATGGATATATA
Found at i:95763 original size:22 final size:22
Alignment explanation
Indices: 95734--95789 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
95724 TTCTAAAGGT
95734 GGTA-CGGTACTGGTTGAATAG
1 GGTATCGGTACTGGTTGAATAG
95755 GGTATCGGTACTGGTTGAATAG
1 GGTATCGGTACTGGTTGAATAG
*
95777 GGTATCGATACTG
1 GGTATCGGTACTG
95790 AGTAGGGAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 4 0.12
22 29 0.88
ACGTcount: A:0.23, C:0.11, G:0.36, T:0.30
Consensus pattern (22 bp):
GGTATCGGTACTGGTTGAATAG
Found at i:96522 original size:23 final size:23
Alignment explanation
Indices: 96488--96540 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
96478 TTGGGACAAT
*
96488 TATGTGGCACTTCGGTGCAAACC
1 TATGTGGAACTTCGGTGCAAACC
*
96511 TATGTGGAACTTTGGTGCAAACC
1 TATGTGGAACTTCGGTGCAAACC
96534 TATGTGG
1 TATGTGG
96541 TCCTTCGGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (23 bp):
TATGTGGAACTTCGGTGCAAACC
Found at i:96923 original size:17 final size:16
Alignment explanation
Indices: 96901--96934 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
96891 TAAAAACAGT
96901 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
96918 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
96934 A
1 A
96935 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:97454 original size:24 final size:25
Alignment explanation
Indices: 97409--97456 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
97399 ATAAAGAACC
*
97409 AAAATAAAACTTAAATATACCATTA
1 AAAATAAAACTTAAACATACCATTA
**
97434 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAAACTTAAACATACCATT
97457 CAACCAACCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.27
Consensus pattern (25 bp):
AAAATAAAACTTAAACATACCATTA
Found at i:100811 original size:19 final size:19
Alignment explanation
Indices: 100764--100811 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
100754 AAGAAAGAGA
* *
100764 AAAGGTAAAAGTTAAAATG
1 AAAGATAAAAATTAAAATG
*
100783 AAAGAGAAAAATTAATAATG
1 AAAGATAAAAATTAA-AATG
100803 -AAGATAAAA
1 AAAGATAAAA
100812 GAAAAAGTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 20 0.83
20 4 0.17
ACGTcount: A:0.65, C:0.00, G:0.17, T:0.19
Consensus pattern (19 bp):
AAAGATAAAAATTAAAATG
Found at i:107184 original size:17 final size:16
Alignment explanation
Indices: 107162--107195 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
107152 TAAAAACAGT
107162 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
107179 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
107195 A
1 A
107196 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:107714 original size:24 final size:24
Alignment explanation
Indices: 107670--107716 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
107660 ATAAAAAACC
*
107670 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
107694 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
107717 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:115375 original size:37 final size:37
Alignment explanation
Indices: 115334--115416 Score: 123
Period size: 37 Copynumber: 2.3 Consensus size: 37
115324 TTATGAAAAA
*
115334 ATCGAATGCATTTGATGCATTGATGCAACAGCCATAC
1 ATCGAATGCATTTGATGCATCGATGCAACAGCCATAC
* * *
115371 ATCGAATGCATTTGATGCATCGATGCACCAGTCATGC
1 ATCGAATGCATTTGATGCATCGATGCAACAGCCATAC
115408 ATCG-ATGCA
1 ATCGAATGCA
115417 CTCTGGCTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
36 5 0.12
37 37 0.88
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (37 bp):
ATCGAATGCATTTGATGCATCGATGCAACAGCCATAC
Found at i:121341 original size:23 final size:23
Alignment explanation
Indices: 121267--121343 Score: 79
Period size: 23 Copynumber: 3.5 Consensus size: 23
121257 CTTAACAGTC
121267 CATCGATGCA-TCCTTGAATGTG
1 CATCGATGCACTCCTTGAATGTG
* * * *
121289 CATCGAT--ACACCATGAAGGTT
1 CATCGATGCACTCCTTGAATGTG
* *
121310 CACCAATGCACTCCTTGAATGTG
1 CATCGATGCACTCCTTGAATGTG
121333 CATCGATGCAC
1 CATCGATGCAC
121344 AAGGACATAC
Statistics
Matches: 40, Mismatches: 12, Indels: 5
0.70 0.21 0.09
Matches are distributed among these distances:
20 1 0.03
21 13 0.32
22 7 0.17
23 19 0.47
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.26
Consensus pattern (23 bp):
CATCGATGCACTCCTTGAATGTG
Found at i:124754 original size:13 final size:13
Alignment explanation
Indices: 124736--124760 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
124726 AACTAAAAAA
124736 TCTAAATTTGATT
1 TCTAAATTTGATT
124749 TCTAAATTTGAT
1 TCTAAATTTGAT
124761 ATTTTTGATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (13 bp):
TCTAAATTTGATT
Found at i:126488 original size:2 final size:2
Alignment explanation
Indices: 126481--126527 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
126471 CAGCTTAAGC
126481 TA TA TA TA TA TA T- TA TA TA TA TA TA TA -A TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
126521 TA TA TA T
1 TA TA TA T
126528 CAATTGGCTA
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:126501 original size:15 final size:14
Alignment explanation
Indices: 126481--126527 Score: 80
Period size: 13 Copynumber: 3.5 Consensus size: 14
126471 CAGCTTAAGC
126481 TATATATATATAT-
1 TATATATATATATA
126494 TATATATATATATA
1 TATATATATATATA
126508 -ATATATATATATA
1 TATATATATATATA
126521 TATATAT
1 TATATAT
126528 CAATTGGCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
13 26 0.81
14 6 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TATATATATATATA
Found at i:126679 original size:13 final size:14
Alignment explanation
Indices: 126648--126681 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
126638 GGGGGAGTAA
126648 TTTCAAAATTAATT
1 TTTCAAAATTAATT
126662 TTTCAAAATTAA-T
1 TTTCAAAATTAATT
126675 TTTCAAA
1 TTTCAAA
126682 GAAAATCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (14 bp):
TTTCAAAATTAATT
Found at i:127092 original size:64 final size:63
Alignment explanation
Indices: 127024--127182 Score: 155
Period size: 64 Copynumber: 2.5 Consensus size: 63
127014 GAATAAATTG
* **
127024 AACATCGAATACA-TTCATGCATCGATGCACATACTATGCATCGATGCACTCCGAG-T-TTTATG
1 AACATCGAATACATTTCATGCATCGATGCACA-ACCATGCATCGACACACTCCG-GCTATTT-TG
127086 AA
63 -A
* * * **
127088 AACATCGAA-AGCATTTGATGCGTCGATGCACCAGCCATGCATCGACACACTTTGGCTATTTTGA
1 AACATCGAATA-CATTTCATGCATCGATGCA-CAACCATGCATCGACACACTCCGGCTATTTTGA
*
127152 AACATCGAATGCATTTCATGCATCGATGCAC
1 AACATCGAATACATTTCATGCATCGATGCAC
127183 TCTTAGTGCA
Statistics
Matches: 78, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
63 2 0.03
64 39 0.50
65 32 0.41
66 5 0.06
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.27
Consensus pattern (63 bp):
AACATCGAATACATTTCATGCATCGATGCACAACCATGCATCGACACACTCCGGCTATTTTGA
Found at i:130015 original size:64 final size:63
Alignment explanation
Indices: 129925--130083 Score: 187
Period size: 64 Copynumber: 2.5 Consensus size: 63
129915 AATTAAATTG
* *
129925 AACATCGAATGCATTTCATGCATCGATGCACATACCATGCACCAATGCACTGAGGAT-TTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACA-ACCATGCACCAATGCACTCAGGATATTT-T-A
129989 A
63 A
* * * * * *
129990 AACATTGAATGCATTTGATG-ATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTAA
1 AACATCGAATGCATTTGATGCATCGATGCA-CAACCATGCACCAATGCACTCAGGATATTTTAA
*
130053 AACATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
130084 TCTTAGTGCA
Statistics
Matches: 81, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
63 21 0.26
64 37 0.46
65 23 0.28
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.27
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACAACCATGCACCAATGCACTCAGGATATTTTAA
Found at i:130083 original size:17 final size:19
Alignment explanation
Indices: 130055--130103 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
130045 TATTTTAAAA
130055 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
130073 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
130092 CACCGATGCACT
1 CATCGATGCACT
130104 GAGAGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:130099 original size:64 final size:63
Alignment explanation
Indices: 129925--130103 Score: 170
Period size: 64 Copynumber: 2.8 Consensus size: 63
129915 AATTAAATTG
* * *
129925 AACATCGAATGCATTTCATGCATCGATGCACATACCA-TGCACCAATGCACTGAGGATTTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCAC-T--CAGTGCACCGATGCACTCAGGATTTTATGA
129989 A
63 A
* * * *
129990 AACATTGAATGCATTTGATG-ATCGATGCAC-CAGCCATGCATCGATGCACTCTGGCTATTT-T-
1 AACATCGAATGCATTTGATGCATCGATGCACTCAG---TGCACCGATGCACTCAGGAT-TTTATG
130051 AA
62 AA
*
130053 AACATCGAATGCACTTGATGCATCGATGCACTCTTAGTGCACCGATGCACT
1 AACATCGAATGCATTTGATGCATCGATGCACTC--AGTGCACCGATGCACT
130104 GAGAGTCCAA
Statistics
Matches: 95, Mismatches: 10, Indels: 19
0.77 0.08 0.15
Matches are distributed among these distances:
60 2 0.02
63 20 0.21
64 49 0.52
65 22 0.23
67 2 0.02
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.27
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACTCAGTGCACCGATGCACTCAGGATTTTATGAA
Done.