Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008316.1 Hibiscus syriacus cultivar Beakdansim tig00111013_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: 2380696
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 12
Found at i:1328456 original size:33 final size:33
Alignment explanation
Indices: 1328398--1328490 Score: 132
Period size: 33 Copynumber: 2.8 Consensus size: 33
1328388 CGAGAATGAA
**
1328398 AATCGCAACGCGGAAATGACTATCGCAACGAGAG
1 AATCGCAACGC-GAAATGAAAATCGCAACGAGAG
*
1328432 AATCGCAACGCGAAATGAAAATCGCAACGAGAT
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
**
1328465 AATCGCAACGCGAAACCAAAATCGCA
1 AATCGCAACGCGAAATGAAAATCGCA
1328491 TTGCGATTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 43 0.80
34 11 0.20
ACGTcount: A:0.43, C:0.25, G:0.22, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:1328508 original size:19 final size:19
Alignment explanation
Indices: 1328486--1328598 Score: 137
Period size: 20 Copynumber: 6.1 Consensus size: 19
1328476 GAAACCAAAA
*
1328486 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1328505 TCGCGTTGCGATTCTC--T
1 TCGCGTTGCGATTTTCATT
1328522 T---GTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1328538 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
1328557 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
1328577 CTCGCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1328597 TC
1 TC
1328599 AACCAAAAGA
Statistics
Matches: 80, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
14 11 0.14
16 2 0.03
17 2 0.03
19 30 0.38
20 34 0.43
21 1 0.01
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1328533 original size:33 final size:34
Alignment explanation
Indices: 1328491--1328590 Score: 123
Period size: 33 Copynumber: 2.8 Consensus size: 34
1328481 CAAAATCGCA
1328491 TTGCGATTTTCATTTCGCGTTGCGATTC-TCTT-G
1 TTGCGATTTTCATTTCGCGTTGCGATTCAT-TTCG
1328524 TTGCGATTTTCATTTCGCGTTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTTCGCGTTGCGAT--TCATTT---CG
1328563 TTGCGATTTTCATTCTCGCGTTGCGATT
1 TTGCGATTTTCATT-TCGCGTTGCGATT
1328591 TTCATTTCAA
Statistics
Matches: 59, Mismatches: 0, Indels: 11
0.84 0.00 0.16
Matches are distributed among these distances:
33 26 0.44
35 4 0.07
36 1 0.02
38 1 0.02
39 15 0.25
40 12 0.20
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.45
Consensus pattern (34 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCATTTCG
Found at i:1330477 original size:94 final size:94
Alignment explanation
Indices: 1330285--1330656 Score: 619
Period size: 94 Copynumber: 4.0 Consensus size: 94
1330275 TAGATTGCTT
* *
1330285 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1330346 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
*
1330375 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGCGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1330440 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
**
1330469 AGTAAATTTGCTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1330534 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * *
1330563 AGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTATGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1330628 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1330657 CTAATGCATT
Statistics
Matches: 267, Mismatches: 10, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
90 35 0.13
92 3 0.01
93 22 0.08
94 207 0.78
ACGTcount: A:0.21, C:0.13, G:0.19, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1330798 original size:19 final size:19
Alignment explanation
Indices: 1330748--1330818 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
1330738 GTCTTTTGGT
*
1330748 TGAAATGAAAAGCGCAACG
1 TGAAATGAAAATCGCAACG
*
1330767 AGAGAATGAAAATCGCAACG
1 TGA-AATGAAAATCGCAACG
*
1330787 TGAAACGAAAATCGCAACG
1 TGAAATGAAAATCGCAACG
*
1330806 CGAAATGAAAATC
1 TGAAATGAAAATC
1330819 AATCGCGTTG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
19 28 0.62
20 17 0.38
ACGTcount: A:0.49, C:0.17, G:0.23, T:0.11
Consensus pattern (19 bp):
TGAAATGAAAATCGCAACG
Found at i:1330881 original size:33 final size:34
Alignment explanation
Indices: 1330824--1330888 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
1330814 AAATCAATCG
** *
1330824 CGTTGCGATTTTTGGTTTCGCGTTGCGATTTTGT
1 CGTTGCGATTTTTCATTTCGCGTTGAGATTTTGT
1330858 CGTTGCGA-TTTTCATTTCGCGTTGAGATTTT
1 CGTTGCGATTTTTCATTTCGCGTTGAGATTTT
1330889 CATTTCGCGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 20 0.71
34 8 0.29
ACGTcount: A:0.09, C:0.15, G:0.26, T:0.49
Consensus pattern (34 bp):
CGTTGCGATTTTTCATTTCGCGTTGAGATTTTGT
Found at i:1330910 original size:19 final size:19
Alignment explanation
Indices: 1330821--1330928 Score: 91
Period size: 19 Copynumber: 5.8 Consensus size: 19
1330811 TGAAAATCAA
**
1330821 TCGCGTTGCGATTTTTGGTT
1 TCGCGTTGCGA-TTTTCATT
*
1330841 TCGCGTTGCGA-TTT--TG
1 TCGCGTTGCGATTTTCATT
1330857 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1330874 TCGCGTTGAGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1330893 TCGCGTTGCGATAGTCATTTT
1 TCGCGTTGCGATTTTCA--TT
*
1330914 TCACGTTGCGATTTT
1 TCGCGTTGCGATTTT
1330929 AAGTTCCATT
Statistics
Matches: 72, Mismatches: 9, Indels: 13
0.77 0.10 0.14
Matches are distributed among these distances:
14 8 0.11
15 3 0.04
16 2 0.03
17 2 0.03
18 3 0.04
19 29 0.40
20 11 0.15
21 14 0.19
ACGTcount: A:0.11, C:0.18, G:0.24, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1331397 original size:21 final size:21
Alignment explanation
Indices: 1331373--1331439 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1331363 TCATTCCTCG
1331373 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1331394 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1331415 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
1331436 AGAG
1 AGAG
1331440 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1331397 original size:42 final size:42
Alignment explanation
Indices: 1331321--1331439 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
1331311 GACTCGTCTG
* * * * * * *
1331321 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
1331363 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
1331405 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
1331440 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:1332808 original size:14 final size:14
Alignment explanation
Indices: 1332788--1332824 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
1332778 GATTGTTTAA
1332788 TTGATTTGTAAAA-
1 TTGATTTGTAAAAG
1332801 TATGATTTGTAAAAG
1 T-TGATTTGTAAAAG
1332816 TTGATTTGT
1 TTGATTTGT
1332825 TTAATTGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.05
14 20 0.91
15 1 0.05
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:1332977 original size:33 final size:33
Alignment explanation
Indices: 1332931--1333015 Score: 109
Period size: 33 Copynumber: 2.5 Consensus size: 33
1332921 AAAAATGACT
* *
1332931 ATCGCAA-TGCGAAATAAAAATCGCAACGAGAGA
1 ATCGCAACT-CGAAATAAAAATCGCAACGACAAA
*
1332964 ATCGCAACTCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACTCGAAATAAAAATCGCAACGACAAA
*
1332997 ATCGCAACGCGAAACTAAA
1 ATCGCAACTCGAAA-TAAA
1333016 TTCGCGTTGC
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
33 41 0.91
34 4 0.09
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAACTCGAAATAAAAATCGCAACGACAAA
Found at i:1333038 original size:19 final size:19
Alignment explanation
Indices: 1333016--1333166 Score: 89
Period size: 19 Copynumber: 8.7 Consensus size: 19
1333006 CGAAACTAAA
1333016 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1333035 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
1333050 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1333068 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
1333083 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
1333101 TTCGCGTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* * *
1333116 -TCTCTTTACGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* **
1333134 TTCGCATTGCGATAGTCAT
1 TTCGCGTTGCGATTTTCAT
1333153 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
1333167 AGACATTAAG
Statistics
Matches: 97, Mismatches: 19, Indels: 31
0.66 0.13 0.21
Matches are distributed among these distances:
14 25 0.26
16 9 0.09
17 9 0.09
19 44 0.45
20 10 0.10
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1333062 original size:33 final size:33
Alignment explanation
Indices: 1333020--1333146 Score: 209
Period size: 33 Copynumber: 3.8 Consensus size: 33
1333010 ACTAAATTCG
* *
1333020 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1333053 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
1333086 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
* *
1333119 CTTTACGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1333147 AGTCATTTCC
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 88 1.00
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:1333165 original size:20 final size:20
Alignment explanation
Indices: 1333130--1333212 Score: 64
Period size: 20 Copynumber: 4.2 Consensus size: 20
1333120 TTTACGATTT
*
1333130 TCATTT-CGCATTGCGATAG
1 TCATTTCCGCGTTGCGATAG
1333149 TCATTTCCGCGTTGCGATAG
1 TCATTTCCGCGTTGCGATAG
* ** *
1333169 ACA-TTAAGATGATTGCGA-ACG
1 TCATTTCCG-CG-TTGCGATA-G
*
1333190 TCATTTCCGTGTTGCGATAG
1 TCATTTCCGCGTTGCGATAG
1333210 TCA
1 TCA
1333213 AATGAATGCC
Statistics
Matches: 50, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
19 9 0.18
20 26 0.52
21 12 0.24
22 3 0.06
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (20 bp):
TCATTTCCGCGTTGCGATAG
Found at i:1335716 original size:24 final size:24
Alignment explanation
Indices: 1335689--1335735 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
1335679 ATCATTAAAA
1335689 TCCGAGTATTGACCAAGATCAAAG
1 TCCGAGTATTGACCAAGATCAAAG
*
1335713 TCCGGGTATTGACCAAGATCAAA
1 TCCGAGTATTGACCAAGATCAAA
1335736 TTTGGAATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (24 bp):
TCCGAGTATTGACCAAGATCAAAG
Found at i:1336635 original size:21 final size:21
Alignment explanation
Indices: 1336569--1336706 Score: 163
Period size: 21 Copynumber: 6.7 Consensus size: 21
1336559 GCGATTTACT
* *
1336569 AAATCGCAATGCG-ATTACGT
1 AAATCGCAATGCGAATTAGGA
* * * *
1336589 AAATCGTAATGCG-GTTACGT
1 AAATCGCAATGCGAATTAGGA
*
1336609 AAATCGCAATGCGAATTAGAA
1 AAATCGCAATGCGAATTAGGA
1336630 AAATCGCAATGCGAATTAGGA
1 AAATCGCAATGCGAATTAGGA
*
1336651 AAATCGCAACGCGAATTAGGA
1 AAATCGCAATGCGAATTAGGA
* * *
1336672 AAATCGCAACGCGAATTTGGG
1 AAATCGCAATGCGAATTAGGA
1336693 AAATCGCAATGCGA
1 AAATCGCAATGCGA
1336707 TAGTCAGAAT
Statistics
Matches: 105, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
20 30 0.29
21 75 0.71
ACGTcount: A:0.39, C:0.17, G:0.23, T:0.20
Consensus pattern (21 bp):
AAATCGCAATGCGAATTAGGA
Found at i:1337040 original size:2 final size:2
Alignment explanation
Indices: 1337033--1337065 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1337023 AATCCCCGAC
1337033 AT 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 AT A
1337066 AAATTAACTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1338865 original size:30 final size:30
Alignment explanation
Indices: 1338831--1338890 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
1338821 CATTATTATG
1338831 TTTTAAATACTTATTTTAATTAAAAAAATA
1 TTTTAAATACTTATTTTAATTAAAAAAATA
* * *
1338861 TTTTAGATATTTATTTTAATTAAAATAATA
1 TTTTAAATACTTATTTTAATTAAAAAAATA
1338891 ACTTTAAGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (30 bp):
TTTTAAATACTTATTTTAATTAAAAAAATA
Found at i:1341009 original size:19 final size:19
Alignment explanation
Indices: 1340968--1341009 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
1340958 AAACTGTTTG
* *
1340968 ATATGTATATAAAGTATAA
1 ATATGTACATAAAGTACAA
1340987 ATATGTACATAAA-TACAA
1 ATATGTACATAAAGTACAA
1341005 CATAT
1 -ATAT
1341010 TCACACATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.33
Consensus pattern (19 bp):
ATATGTACATAAAGTACAA
Found at i:1341479 original size:59 final size:61
Alignment explanation
Indices: 1341401--1341520 Score: 154
Period size: 64 Copynumber: 2.0 Consensus size: 61
1341391 TATGTTTGAA
* *
1341401 TCATTTTAAGTTAATGTTATTTTGG-GGA-CAGATCGCTTTGAGTTCACATTATTTTTTGT
1 TCATTTTAAGTTAAGGTTATTTTGGAGGATCAGATCGCTTTGAATTCACATTATTTTTTGT
* * *
1341460 TCATTTTAAGTTCAGGTTATTTTGGATACTGATCGGATCGCTTTGAATTCACATTATTTTT
1 TCATTTTAAGTTAAGGTTATTTTGG--A-GGATCAGATCGCTTTGAATTCACATTATTTTT
1341521 GGGTTCAGTT
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
59 23 0.45
63 2 0.04
64 26 0.51
ACGTcount: A:0.23, C:0.12, G:0.17, T:0.48
Consensus pattern (61 bp):
TCATTTTAAGTTAAGGTTATTTTGGAGGATCAGATCGCTTTGAATTCACATTATTTTTTGT
Found at i:1344412 original size:3 final size:3
Alignment explanation
Indices: 1344404--1344451 Score: 51
Period size: 3 Copynumber: 15.3 Consensus size: 3
1344394 TATATATATT
* * *
1344404 TAA TAA TAAA TAA TAA TAA TAA TATA TTA TAT TAA TAA TAA TTA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
1344451 T
1 T
1344452 TATTATTATG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
3 32 0.86
4 5 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:1344442 original size:22 final size:22
Alignment explanation
Indices: 1344414--1344459 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1344404 TAATAATAAA
1344414 TAATAATAATAATATATTA-TAT
1 TAATAATAATAATA-ATTATTAT
*
1344436 TAATAATAATTATAATTATTAT
1 TAATAATAATAATAATTATTAT
1344458 TA
1 TA
1344460 TGAAAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TAATAATAATAATAATTATTAT
Found at i:1344453 original size:16 final size:16
Alignment explanation
Indices: 1344398--1344453 Score: 62
Period size: 16 Copynumber: 3.5 Consensus size: 16
1344388 AATATATATA
*
1344398 TATATTTAATAATAAAT
1 TATAATTAATAAT-AAT
*
1344415 AATAA-TAATAATATAT
1 TATAATTAATAATA-AT
1344431 TAT-ATTAATAATAAT
1 TATAATTAATAATAAT
1344446 TATAATTA
1 TATAATTA
1344454 TTATTATGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
15 7 0.21
16 23 0.70
17 3 0.09
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TATAATTAATAATAAT
Found at i:1344734 original size:76 final size:76
Alignment explanation
Indices: 1344608--1345218 Score: 1096
Period size: 76 Copynumber: 8.0 Consensus size: 76
1344598 GGTCTTATGA
* * * * *
1344608 ATGACCCCGAGGGTTTAAAAACATCAAAAAGCTCCCGAAGGTTTTTTGGAAACATCATGCACTGC
1 ATGACCCTGAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1344673 AGGACTTACAG
66 AGGACTTACAG
* *
1344684 ATGACCCTGAGGATTTGAAAACATCAAAAAGCTCCCAAAGGCTTTTTGGAAACATCATGCACTGC
1 ATGACCCTGAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
* *
1344749 AGGACTTTCGG
66 AGGACTTACAG
*
1344760 ATGACCCTGAGGGTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCTGAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1344825 AGGACTTACAG
66 AGGACTTACAG
*
1344836 ATGACCCTGAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGC
1 ATGACCCTGAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1344901 AGGACTTACAG
66 AGGACTTACAG
*
1344912 ATGACCTTGAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCTGAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
*
1344977 AGGACTTATAG
66 AGGACTTACAG
*
1344988 ATGACCCTGAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGC
1 ATGACCCTGAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1345053 AGGACTTACAG
66 AGGACTTACAG
1345064 ATGACCCTGAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCTGAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1345129 AGGACTTACAG
66 AGGACTTACAG
1345140 ATGACCCTGAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCTGAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1345205 AGGACTTACAG
66 AGGACTTACAG
1345216 ATG
1 ATG
1345219 TGGGAAATAG
Statistics
Matches: 514, Mismatches: 21, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 514 1.00
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (76 bp):
ATGACCCTGAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
AGGACTTACAG
Found at i:1346109 original size:22 final size:22
Alignment explanation
Indices: 1346084--1346138 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
1346074 CAGAAGGCTT
1346084 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
1346106 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
1346128 TCATCTTTGAA
1 TCATCTTTGAA
1346139 GAGTGTAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:1346622 original size:54 final size:54
Alignment explanation
Indices: 1346489--1346656 Score: 255
Period size: 55 Copynumber: 3.1 Consensus size: 54
1346479 AGAATAGCAG
* *** **
1346489 GTTCGTAAAACATTTGACAGTGCATTCATCCTTTCCTGTGGCTTCTGCTCATGAT
1 GTTCATAAAACATTTGACAACACATTCATCCTTTTTTGTGGCTTCTGCTCA-GAT
*
1346544 GTTCATAAAATATTTGACAACACATTCATCCTTTTTTGTGGCTTCTGCTCAGAT
1 GTTCATAAAACATTTGACAACACATTCATCCTTTTTTGTGGCTTCTGCTCAGAT
1346598 GTTCATAAAACATTTGACAACACATTCATCCTTTTTTTGTGGCTTCTGCTCAGAT
1 GTTCATAAAACATTTGACAACACATTCATCC-TTTTTTGTGGCTTCTGCTCAGAT
1346653 GTTC
1 GTTC
1346657 TCAATCATTG
Statistics
Matches: 104, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
54 33 0.32
55 71 0.68
ACGTcount: A:0.23, C:0.22, G:0.15, T:0.40
Consensus pattern (54 bp):
GTTCATAAAACATTTGACAACACATTCATCCTTTTTTGTGGCTTCTGCTCAGAT
Found at i:1349055 original size:114 final size:113
Alignment explanation
Indices: 1348779--1349232 Score: 656
Period size: 114 Copynumber: 4.0 Consensus size: 113
1348769 GATCATGCAG
* * * * * * * *
1348779 TTCACCTTTCAATTCCAATGATCGGTTCTGGGATTCCTACCGAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGATTTTGGG-TTCATACCAAATCAAATCAGATAACTCAAAGA
* * * *
1348844 ACACTTCCAGAAGATGCTATTGGGTCTCATTATTTCTACTATGAGCAAAA
65 ACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAGC-AAA
*
1348894 TTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAAATCAGATAGCTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGATTTTGG-GTTCATACCAAATCAAATCAGATAACTCAAAGA
*
1348959 ACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAACAAA
65 ACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAGCAAA
*
1349008 TTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCAAATCAGATAGCTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGATTTTGG-GTTCATACCAAATCAAATCAGATAACTCAAAGA
1349073 ACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAGCAAA
65 ACACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAGCAAA
* * *
1349122 TTCATCTTTCAAATCCAATGATTGATTTTGGTTTCATACCAAACCAGATCAGATAACTCAAAGAA
1 TTCATCTTTCAAATCCAATGATTGATTTTGGGTTCATACCAAATCAAATCAGATAACTCAAAGAA
* * * * * *
1349187 CACTTCCAGAATATACTATTGGGTCTTCTTATTTCTACTATGAGCA
66 CACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAGCA
1349233 CATGGCACTT
Statistics
Matches: 313, Mismatches: 25, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
113 70 0.22
114 147 0.47
115 95 0.30
116 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.32
Consensus pattern (113 bp):
TTCATCTTTCAAATCCAATGATTGATTTTGGGTTCATACCAAATCAAATCAGATAACTCAAAGAA
CACTTCCAGAAGATGCTATTGAGCCTCCTTATTTCTACCATGAGCAAA
Found at i:1351719 original size:2 final size:2
Alignment explanation
Indices: 1351712--1351747 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1351702 ACAACAAAGG
1351712 AT AT AT 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 AT AT AT
1351748 TAAAGGATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1353995 original size:14 final size:15
Alignment explanation
Indices: 1353978--1354018 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
1353968 TAAAAGTATG
1353978 AATGCAAAAATG-AA
1 AATGCAAAAATGCAA
*
1353992 AATGCAAAGATGCAA
1 AATGCAAAAATGCAA
1354007 AATG--AAAATGCA
1 AATGCAAAAATGCA
1354019 TATATGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 7 0.29
14 11 0.46
15 6 0.25
ACGTcount: A:0.59, C:0.10, G:0.17, T:0.15
Consensus pattern (15 bp):
AATGCAAAAATGCAA
Found at i:1354004 original size:8 final size:7
Alignment explanation
Indices: 1353978--1354018 Score: 50
Period size: 6 Copynumber: 5.9 Consensus size: 7
1353968 TAAAAGTATG
1353978 AATGCAAA
1 AATGC-AA
1353986 AATG-AA
1 AATGCAA
1353992 AATGCAA
1 AATGCAA
1353999 AGATGCAA
1 A-ATGCAA
1354007 AATG-AA
1 AATGCAA
1354013 AATGCA
1 AATGCA
1354019 TATATGAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
6 12 0.40
7 7 0.23
8 11 0.37
ACGTcount: A:0.59, C:0.10, G:0.17, T:0.15
Consensus pattern (7 bp):
AATGCAA
Found at i:1358815 original size:16 final size:16
Alignment explanation
Indices: 1358757--1358825 Score: 64
Period size: 16 Copynumber: 4.8 Consensus size: 16
1358747 ATGTAATTTG
1358757 TAATATA-TATA-T-A
1 TAATATATTATATTAA
1358770 TATATATATT-TATTAA
1 TA-ATATATTATATTAA
*
1358786 TAA-ATA--ATAATAA
1 TAATATATTATATTAA
1358799 TAATATATTATATTAA
1 TAATATATTATATTAA
1358815 TAATA-ATTATA
1 TAATATATTATA
1358826 ATTATTATTA
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
13 10 0.22
14 13 0.28
15 9 0.20
16 14 0.30
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TAATATATTATATTAA
Found at i:1358817 original size:19 final size:22
Alignment explanation
Indices: 1358790--1358835 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1358780 TATTAATAAA
*
1358790 TAATAATAATAATATATTA-TAT
1 TAATAATAATTATA-ATTATTAT
1358812 TAATAATAATTATAATTATTAT
1 TAATAATAATTATAATTATTAT
1358834 TA
1 TA
1358836 TGAAAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TAATAATAATTATAATTATTAT
Found at i:1365261 original size:20 final size:21
Alignment explanation
Indices: 1365236--1365328 Score: 91
Period size: 21 Copynumber: 4.5 Consensus size: 21
1365226 TTTTCCCAAT
*
1365236 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1365256 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
1365277 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* * **
1365297 TTGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1365318 TCGCAATGCGA
1 TCGCAATGCGA
1365329 TACTGACTAT
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.46
21 30 0.54
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1365281 original size:41 final size:41
Alignment explanation
Indices: 1365236--1365328 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
1365226 TTTTCCCAAT
1365236 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
*
1365277 TCGCAATGCGAATAAGTAAATTGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1365318 TCGCAATGCGA
1 TCGCAATGCGA
1365329 TACTGACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:1365363 original size:21 final size:20
Alignment explanation
Indices: 1365314--1365364 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1365304 GCGAATTGGG
* *
1365314 AAAATCGCAATGCGATACTG
1 AAAATCGCAATGCGATAATA
**
1365334 ACTATCGCAATGCGATAATAA
1 AAAATCGCAATGCGATAAT-A
1365355 AAAATCGCAA
1 AAAATCGCAA
1365365 CGAGATACTT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.45, C:0.20, G:0.16, T:0.20
Consensus pattern (20 bp):
AAAATCGCAATGCGATAATA
Found at i:1365940 original size:19 final size:19
Alignment explanation
Indices: 1365902--1365968 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
1365892 TTCGAGAATG
1365902 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
1365922 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
1365941 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
1365960 AAAATCGCA
1 AAAATCGCA
1365969 TTGCGATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 30 0.73
20 11 0.27
ACGTcount: A:0.48, C:0.25, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:1365986 original size:19 final size:19
Alignment explanation
Indices: 1365964--1366148 Score: 165
Period size: 19 Copynumber: 10.1 Consensus size: 19
1365954 GAAACCAAAA
*
1365964 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1365983 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1366002 TTGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
1366021 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
1366041 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
1366057 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
1366074 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
1366088 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
1366107 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
1366127 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1366147 TC
1 TC
1366149 AACCAAAAGA
Statistics
Matches: 136, Mismatches: 17, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
14 20 0.15
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 58 0.43
20 49 0.36
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1366041 original size:39 final size:38
Alignment explanation
Indices: 1365964--1366148 Score: 165
Period size: 33 Copynumber: 5.1 Consensus size: 38
1365954 GAAACCAAAA
*
1365964 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* *
1366002 TTGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
* * **
1366041 TCGCGTTGCGATTGTC---T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* **
1366074 TCGCGTTGCGA--TTC---TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* *
1366107 TCCGCGTTGCGATTCTCATTATCTCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT-TCGCGTTGCGATTTTCATT
1366147 TC
1 TC
1366149 AACCAAAAGA
Statistics
Matches: 122, Mismatches: 15, Indels: 19
0.78 0.10 0.12
Matches are distributed among these distances:
31 3 0.02
33 38 0.31
34 10 0.08
35 1 0.01
36 3 0.02
38 20 0.16
39 29 0.24
40 18 0.15
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:1366125 original size:20 final size:20
Alignment explanation
Indices: 1366091--1366148 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
1366081 GCGATTCTCT
**
1366091 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
1366111 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
1366131 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
1366149 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:1368210 original size:42 final size:42
Alignment explanation
Indices: 1368150--1368272 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
1368140 GCCCGACTCG
* * *
1368150 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
1368192 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
1368234 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
1368273 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:1368230 original size:21 final size:21
Alignment explanation
Indices: 1368206--1368272 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1368196 TCATTCCTCG
1368206 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1368227 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1368248 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
1368269 AGAG
1 AGAG
1368273 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1369650 original size:14 final size:14
Alignment explanation
Indices: 1369631--1369666 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1369621 ATTGTTTAAT
1369631 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1369645 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1369659 TGATTTGT
1 TGATTTGT
1369667 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1369867 original size:19 final size:19
Alignment explanation
Indices: 1369845--1369995 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 19
1369835 CGAAATTAAA
1369845 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1369864 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
1369879 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
1369897 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
1369911 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1369930 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
1369945 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
1369963 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
1369982 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
1369996 GGACATTAAG
Statistics
Matches: 95, Mismatches: 21, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
14 28 0.29
16 6 0.06
17 6 0.06
19 45 0.47
20 10 0.11
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1369891 original size:33 final size:32
Alignment explanation
Indices: 1369849--1369975 Score: 193
Period size: 33 Copynumber: 3.9 Consensus size: 32
1369839 ATTAAATTCG
1369849 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
1369882 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
1369915 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
1369948 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1369976 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.03
33 80 0.93
35 3 0.03
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:1369938 original size:66 final size:66
Alignment explanation
Indices: 1369842--1369974 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
1369832 AGGCGAAATT
*
1369842 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1369907 G
66 G
*
1369908 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1369973 G
66 G
1369974 A
1 A
1369975 TAGTAATTTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:1372261 original size:12 final size:12
Alignment explanation
Indices: 1372244--1372268 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1372234 TCTTCGGGGA
1372244 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1372256 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1372268 C
1 C
1372269 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1372480 original size:24 final size:23
Alignment explanation
Indices: 1372442--1372495 Score: 81
Period size: 24 Copynumber: 2.3 Consensus size: 23
1372432 CTGAAACATC
* *
1372442 ATCAAATCCGTGTATTGACCAAT
1 ATCAAATCCGGGTATTGACCAAG
1372465 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAA-TCCGGGTATTGACCAAG
1372489 ATCAAAT
1 ATCAAAT
1372496 TTCGAATACT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 7 0.25
24 21 0.75
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (23 bp):
ATCAAATCCGGGTATTGACCAAG
Found at i:1373577 original size:20 final size:20
Alignment explanation
Indices: 1373552--1373596 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
1373542 ATTCATTTGA
1373552 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
1373572 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
1373592 TTATC
1 CTATC
1373597 ATAACGAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.20
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:1373602 original size:20 final size:20
Alignment explanation
Indices: 1373552--1373609 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
1373542 ATTCATTTGA
*
1373552 CTATCGCAACGCGAAAATGG
1 CTATCACAACGCGAAAATGG
*
1373572 CTATCGCAACGCGAAAATGG
1 CTATCACAACGCGAAAATGG
* * *
1373592 TTATCATAACGAGAAAAT
1 CTATCACAACGCGAAAAT
1373610 CGCAATGCGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.19
Consensus pattern (20 bp):
CTATCACAACGCGAAAATGG
Found at i:1373652 original size:14 final size:16
Alignment explanation
Indices: 1373632--1373705 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
1373622 TGAAAATCGC
1373632 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
1373647 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
1373664 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
1373683 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
1373699 -TTGCGAT
1 ATTGCGAT
1373706 AGCCATTTCG
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 18 0.33
16 3 0.06
17 3 0.06
19 30 0.56
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:1373669 original size:19 final size:19
Alignment explanation
Indices: 1373628--1373695 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
1373618 GAAATGAAAA
1373628 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
1373644 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1373661 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1373680 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
1373696 TCGTTGCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
17 3 0.06
19 30 0.64
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1375749 original size:20 final size:19
Alignment explanation
Indices: 1375714--1375780 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
1375704 GAAACTTAAA
1375714 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
1375733 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
1375753 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
1375772 ATCGCAACG
1 ATCGCAACG
1375781 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:1375788 original size:14 final size:14
Alignment explanation
Indices: 1375769--1375826 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1375759 ATGCGAAATG
1375769 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1375783 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
1375799 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1375815 AAAATCGCAACG
1 AAAATCGCAACG
1375827 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1375811 original size:32 final size:33
Alignment explanation
Indices: 1375753--1375831 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
1375743 GGAAATGGCT
*
1375753 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1375786 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1375818 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
1375832 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:1375879 original size:14 final size:14
Alignment explanation
Indices: 1375854--1375916 Score: 74
Period size: 14 Copynumber: 4.3 Consensus size: 14
1375844 TGCGATTTTT
1375854 ATTTCG-CGTTGCG
1 ATTTCGTCGTTGCG
1375867 ATTTCGTCGTTGCG
1 ATTTCGTCGTTGCG
1375881 ATTTCGTTTCGCTTTGCG
1 ATTTCG--TCG--TTGCG
*
1375899 ATTTTGTCGTTGCG
1 ATTTCGTCGTTGCG
1375913 ATTT
1 ATTT
1375917 TCATTTCGCA
Statistics
Matches: 44, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
13 6 0.14
14 22 0.50
16 6 0.14
18 10 0.23
ACGTcount: A:0.08, C:0.19, G:0.25, T:0.48
Consensus pattern (14 bp):
ATTTCGTCGTTGCG
Found at i:1375898 original size:32 final size:33
Alignment explanation
Indices: 1375843--1375933 Score: 130
Period size: 32 Copynumber: 2.8 Consensus size: 33
1375833 ACAAATCGCA
* *
1375843 TTGCGATTTTTATTTCGCGTTGCGATTTCGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTCGTCG
* * *
1375876 TTGCGA-TTTCGTTTCGCTTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTCGTCG
1375908 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
1375934 AGCCATTTCC
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
32 28 0.55
33 23 0.45
ACGTcount: A:0.10, C:0.19, G:0.23, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTCGTCG
Found at i:1375899 original size:18 final size:17
Alignment explanation
Indices: 1375855--1375933 Score: 62
Period size: 14 Copynumber: 4.8 Consensus size: 17
1375845 GCGATTTTTA
1375855 TTTCGCGTTGCGATTTCG
1 TTTCGC-TTGCGATTTCG
1375873 --TCG-TTGCGATTTCG
1 TTTCGCTTGCGATTTCG
1375887 TTTCGCTTTGCGATTT--
1 TTTCGC-TTGCGATTTCG
* *
1375903 TGTCG-TTGCGATTTTCA
1 TTTCGCTTGCGA-TTTCG
1375920 TTTCGCATTGCGAT
1 TTTCGC-TTGCGAT
1375934 AGCCATTTCC
Statistics
Matches: 50, Mismatches: 2, Indels: 18
0.71 0.03 0.26
Matches are distributed among these distances:
14 17 0.34
15 3 0.06
16 10 0.20
17 4 0.08
18 10 0.20
19 6 0.12
ACGTcount: A:0.09, C:0.20, G:0.24, T:0.47
Consensus pattern (17 bp):
TTTCGCTTGCGATTTCG
Found at i:1375952 original size:20 final size:19
Alignment explanation
Indices: 1375918--1375972 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
1375908 TTGCGATTTT
*
1375918 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1375937 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
1375957 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
1375973 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1376471 original size:18 final size:18
Alignment explanation
Indices: 1376445--1376489 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1376435 GTCGATCAGA
*
1376445 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
1376463 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
1376481 TGATGGCTC
1 TGATGGCTC
1376490 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:1377833 original size:20 final size:20
Alignment explanation
Indices: 1377808--1377845 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1377798 AATAGTTTCT
1377808 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
1377828 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
1377846 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:1378134 original size:22 final size:22
Alignment explanation
Indices: 1378109--1378152 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1378099 GATTTAGATA
1378109 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1378131 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
1378153 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:1378365 original size:20 final size:20
Alignment explanation
Indices: 1378340--1378433 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
1378330 GATTATGTAT
1378340 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1378360 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
1378380 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
1378401 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1378421 TATCGCATTGCGA
1 TATCGCGTTGCGA
1378434 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:1378434 original size:20 final size:20
Alignment explanation
Indices: 1378320--1378434 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
1378310 CGCTTTGAAA
*
1378320 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
1378341 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
1378361 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
1378381 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
1378402 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
1378422 ATCGCATTGCGAT
1 ATCGCATTGCGAT
1378435 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:1378452 original size:21 final size:21
Alignment explanation
Indices: 1378423--1378515 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
1378413 ATAGTCAGTA
1378423 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
1378444 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
1378464 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
1378485 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
1378505 TCGCATTGCGA
1 TCGCATTGCGA
1378516 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:1378453 original size:41 final size:41
Alignment explanation
Indices: 1378362--1378496 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
1378352 AAAGTCAGTA
* * * ** *
1378362 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
1378402 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
1378444 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
1378485 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1378497 TTACTTATTC
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 3 0.04
41 74 0.94
42 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:1378497 original size:41 final size:41
Alignment explanation
Indices: 1378423--1378515 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
1378413 ATAGTCAGTA
1378423 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1378464 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1378505 TCGCATTGCGA
1 TCGCATTGCGA
1378516 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:1381029 original size:35 final size:35
Alignment explanation
Indices: 1380971--1381047 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 35
1380961 AATTCATGTT
*
1380971 CAAAATTCTAAAACACTTCAATTACATTCTAAACTC
1 CAAATTTCTAAAACACTTCAATTACATTCTAAAC-C
* *
1381007 CAAATTTC-AAAATACTTTAATTACATTCTAAACC
1 CAAATTTCTAAAACACTTCAATTACATTCTAAACC
1381041 CTAAATT
1 C-AAATT
1381048 AAAGTATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
34 2 0.05
35 28 0.76
36 7 0.19
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.34
Consensus pattern (35 bp):
CAAATTTCTAAAACACTTCAATTACATTCTAAACC
Found at i:1381103 original size:35 final size:35
Alignment explanation
Indices: 1381043--1381120 Score: 104
Period size: 35 Copynumber: 2.2 Consensus size: 35
1381033 TCTAAACCCT
* *
1381043 AAATTAAAGTATTTTAGAATATAGGGTTTAAAAT-
1 AAATTGAATTATTTTAGAATATAGGGTTTAAAATG
* *
1381077 ATAATTGAATTATTTTAGAATTTAGGGTTTAGAATG
1 A-AATTGAATTATTTTAGAATATAGGGTTTAAAATG
1381113 AAATTGAA
1 AAATTGAA
1381121 GAATGTGTTG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
34 1 0.03
35 36 0.95
36 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.17, T:0.40
Consensus pattern (35 bp):
AAATTGAATTATTTTAGAATATAGGGTTTAAAATG
Found at i:1382477 original size:41 final size:41
Alignment explanation
Indices: 1382432--1382570 Score: 183
Period size: 41 Copynumber: 3.4 Consensus size: 41
1382422 AACTTATTCT
*
1382432 TAACTTAAAACCCTAAATTAATAACCCTAAGCCTTAAGCTC
1 TAACTTAAAACCCTCAATTAATAACCCTAAGCCTTAAGCTC
* * *
1382473 TAACTTAAAACCCTCAATTAATAACCCAAATCCTT--GCTTT
1 TAACTTAAAACCCTCAATTAATAACCCTAAGCCTTAAGC-TC
*
1382513 TAACTTAAAACCCTCAATTAATAACCCTAAGCCTTAAACTC
1 TAACTTAAAACCCTCAATTAATAACCCTAAGCCTTAAGCTC
* * *
1382554 TAAATCAAAACTCTCAA
1 TAACTTAAAACCCTCAA
1382571 ATCAGGATTT
Statistics
Matches: 84, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
39 2 0.02
40 34 0.40
41 47 0.56
42 1 0.01
ACGTcount: A:0.42, C:0.27, G:0.03, T:0.28
Consensus pattern (41 bp):
TAACTTAAAACCCTCAATTAATAACCCTAAGCCTTAAGCTC
Found at i:1382527 original size:40 final size:40
Alignment explanation
Indices: 1382431--1382548 Score: 166
Period size: 40 Copynumber: 2.9 Consensus size: 40
1382421 TAACTTATTC
* *
1382431 TTAACTTAAAACCCTAAATTAATAACCCTAAGCCTTAAGCT
1 TTAACTTAAAACCCTCAATTAATAACCCAAAGCCTT-AGCT
* *
1382472 CTAACTTAAAACCCTCAATTAATAACCCAAATCCTT-GCTT
1 TTAACTTAAAACCCTCAATTAATAACCCAAAGCCTTAGC-T
*
1382512 TTAACTTAAAACCCTCAATTAATAACCCTAAGCCTTA
1 TTAACTTAAAACCCTCAATTAATAACCCAAAGCCTTA
1382549 AACTCTAAAT
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
39 2 0.03
40 34 0.50
41 32 0.47
ACGTcount: A:0.40, C:0.27, G:0.03, T:0.30
Consensus pattern (40 bp):
TTAACTTAAAACCCTCAATTAATAACCCAAAGCCTTAGCT
Found at i:1382537 original size:21 final size:21
Alignment explanation
Indices: 1382473--1382537 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1382463 CCTTAAGCTC
1382473 TAACTTAAAACCCTCAATTAA
1 TAACTTAAAACCCTCAATTAA
** * * *
1382494 TAACCCAAATCCTTGC--TT-T
1 TAACTTAAAACCCT-CAATTAA
1382513 TAACTTAAAACCCTCAATTAA
1 TAACTTAAAACCCTCAATTAA
1382534 TAAC
1 TAAC
1382538 CCTAAGCCTT
Statistics
Matches: 30, Mismatches: 10, Indels: 8
0.62 0.21 0.17
Matches are distributed among these distances:
18 1 0.03
19 10 0.33
20 4 0.13
21 14 0.47
22 1 0.03
ACGTcount: A:0.42, C:0.26, G:0.02, T:0.31
Consensus pattern (21 bp):
TAACTTAAAACCCTCAATTAA
Found at i:1388109 original size:20 final size:18
Alignment explanation
Indices: 1388066--1388111 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
1388056 ATCATTTAAA
1388066 TAATT-AAATAATATAAT
1 TAATTAAAATAATATAAT
1388083 TAA-TAAAATAATAATAAT
1 TAATTAAAATAAT-ATAAT
1388101 TAAATTAAAAT
1 T-AATTAAAAT
1388112 TCACTCATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 1 0.04
17 10 0.40
18 6 0.24
19 2 0.08
20 6 0.24
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TAATTAAAATAATATAAT
Found at i:1391436 original size:32 final size:31
Alignment explanation
Indices: 1391397--1391458 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 31
1391387 TATTTTTTGA
*
1391397 TTTATTTA-AATTTAATTTGAGTATAATATTTT
1 TTTATTTATAATTTAATCTGA-TATAA-ATTTT
*
1391429 TTTATTTATCATTTAATCTGATATAAATTT
1 TTTATTTATAATTTAATCTGATATAAATTT
1391459 AGAAAACTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 4 0.15
32 13 0.48
33 10 0.37
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (31 bp):
TTTATTTATAATTTAATCTGATATAAATTTT
Found at i:1400519 original size:2 final size:2
Alignment explanation
Indices: 1400512--1400537 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1400502 AGCCTTTTGT
1400512 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1400538 ATTGAACCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1401471 original size:29 final size:29
Alignment explanation
Indices: 1401429--1401517 Score: 83
Period size: 29 Copynumber: 3.1 Consensus size: 29
1401419 GTCTTGTTTT
1401429 AAATTAATCACTAAACCTTTGATTATTTC
1 AAATTAATCACTAAACCTTTGATTATTTC
* * * *
1401458 AAATTCATCCCTAAA-CTATGAATCA-TTC
1 AAATTAATCACTAAACCTTTG-ATTATTTC
* * *
1401486 TAAATTAATCTCTAAACTTTTGAATATTTC
1 -AAATTAATCACTAAACCTTTGATTATTTC
1401516 AA
1 AA
1401518 CATCGTCCCC
Statistics
Matches: 46, Mismatches: 10, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
28 7 0.15
29 33 0.72
30 6 0.13
ACGTcount: A:0.39, C:0.18, G:0.03, T:0.39
Consensus pattern (29 bp):
AAATTAATCACTAAACCTTTGATTATTTC
Found at i:1405976 original size:24 final size:25
Alignment explanation
Indices: 1405948--1406002 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
1405938 CACGCTGGGT
*
1405948 ATCCGAGGC-CATCCAACCGAGGGC
1 ATCCGAGGCGCATCCAACCGAGGCC
**
1405972 ATCCGA-GCGCATCTGACCGAGGCC
1 ATCCGAGGCGCATCCAACCGAGGCC
1405996 ATCCGAG
1 ATCCGAG
1406003 CGAGCTATGC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 2 0.08
24 24 0.92
ACGTcount: A:0.24, C:0.36, G:0.29, T:0.11
Consensus pattern (25 bp):
ATCCGAGGCGCATCCAACCGAGGCC
Found at i:1406096 original size:22 final size:22
Alignment explanation
Indices: 1406067--1406123 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
1406057 TTGTCCTGTG
1406067 CCCTGCTCCCCGCTACATGCTC
1 CCCTGCTCCCCGCTACATGCTC
* * * *
1406089 GCCTGCTCCCCACTGCCTGCTC
1 CCCTGCTCCCCGCTACATGCTC
1406111 CCGCTGCTCCCCG
1 CC-CTGCTCCCCG
1406124 ATGCTCCATG
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 19 0.68
23 9 0.32
ACGTcount: A:0.05, C:0.56, G:0.18, T:0.21
Consensus pattern (22 bp):
CCCTGCTCCCCGCTACATGCTC
Found at i:1406479 original size:17 final size:18
Alignment explanation
Indices: 1406457--1406494 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
1406447 TTATTAGTTT
1406457 GTTAGTTTAGGG-TTAGG
1 GTTAGTTTAGGGTTTAGG
1406474 GTTAGTTTAGGGTTTAGG
1 GTTAGTTTAGGGTTTAGG
1406492 GTT
1 GTT
1406495 TAGGGTTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.16, C:0.00, G:0.39, T:0.45
Consensus pattern (18 bp):
GTTAGTTTAGGGTTTAGG
Found at i:1406490 original size:7 final size:7
Alignment explanation
Indices: 1406461--1406504 Score: 60
Period size: 7 Copynumber: 6.9 Consensus size: 7
1406451 TAGTTTGTTA
1406461 GTTTAGG
1 GTTTAGG
1406468 G-TTAGG
1 GTTTAGG
1406474 G-TTA--
1 GTTTAGG
1406478 GTTTAGG
1 GTTTAGG
1406485 GTTTAGG
1 GTTTAGG
1406492 GTTTAGG
1 GTTTAGG
1406499 GTTTAG
1 GTTTAG
1406505 TTTGTTACTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
4 1 0.03
5 3 0.09
6 9 0.26
7 21 0.62
ACGTcount: A:0.16, C:0.00, G:0.41, T:0.43
Consensus pattern (7 bp):
GTTTAGG
Found at i:1408396 original size:11 final size:11
Alignment explanation
Indices: 1408375--1408470 Score: 102
Period size: 11 Copynumber: 8.0 Consensus size: 11
1408365 CACCATTAAA
1408375 TATTAAAATCAT
1 TATT-AAATCAT
1408387 TATTAAATCAT
1 TATTAAATCAT
*
1408398 TATTATAATGAT
1 TATTA-AATCAT
1408410 TATTACTAAATCAT
1 TA-T--TAAATCAT
1408424 TATTAAATCAT
1 TATTAAATCAT
1408435 TATTAAATCAT
1 TATTAAATCAT
1408446 AATATTAAAATCAT
1 --TATT-AAATCAT
*
1408460 TACTAAATCAT
1 TATTAAATCAT
1408471 CAAATCATTA
Statistics
Matches: 74, Mismatches: 3, Indels: 15
0.80 0.03 0.16
Matches are distributed among these distances:
11 38 0.51
12 14 0.19
13 6 0.08
14 14 0.19
15 2 0.03
ACGTcount: A:0.47, C:0.09, G:0.01, T:0.43
Consensus pattern (11 bp):
TATTAAATCAT
Found at i:1408491 original size:8 final size:9
Alignment explanation
Indices: 1408449--1408644 Score: 102
Period size: 8 Copynumber: 22.3 Consensus size: 9
1408439 AAATCATAAT
1408449 ATTAAAATC
1 ATTAAAATC
1408458 ATTACTAAATC
1 ATTA--AAATC
*
1408469 A-TCAAATC
1 ATTAAAATC
1408477 ATT-AAAT-
1 ATTAAAATC
1408484 ATTAAAATC
1 ATTAAAATC
1408493 ATTACTAAATC
1 ATTA--AAATC
*
1408504 -TTCAAATC
1 ATTAAAATC
1408512 A-T--AAT-
1 ATTAAAATC
1408517 ATTAAAATC
1 ATTAAAATC
1408526 ATTACTAAATC
1 ATTA--AAATC
*
1408537 A-TCAAATC
1 ATTAAAATC
1408545 ATT-AAAT-
1 ATTAAAATC
*
1408552 ATTAAAATA
1 ATTAAAATC
1408561 ATTACTAAATC
1 ATTA--AAATC
*
1408572 A-TCAAATC
1 ATTAAAATC
1408580 ATT-AAAT-
1 ATTAAAATC
1408587 ATTAAAATC
1 ATTAAAATC
*
1408596 ATGACTAAATC
1 ATTA--AAATC
*
1408607 A-TCAAATC
1 ATTAAAATC
1408615 ATT-AAAT-
1 ATTAAAATC
1408622 ATTAAAATC
1 ATTAAAATC
1408631 ATTATTAAATC
1 ATTA--AAATC
1408642 ATT
1 ATT
1408645 TTTATGGTTA
Statistics
Matches: 150, Mismatches: 8, Indels: 56
0.70 0.04 0.26
Matches are distributed among these distances:
5 1 0.01
6 4 0.03
7 12 0.08
8 65 0.43
9 27 0.18
10 5 0.03
11 36 0.24
ACGTcount: A:0.51, C:0.13, G:0.01, T:0.35
Consensus pattern (9 bp):
ATTAAAATC
Found at i:1408492 original size:35 final size:35
Alignment explanation
Indices: 1408368--1408643 Score: 355
Period size: 35 Copynumber: 7.9 Consensus size: 35
1408358 AATAGCGCAC
* * *
1408368 CATTAAATATTAAAATCATTATTAAATCATTATTAT
1 CATTAAATATTAAAATCATTACTAAATCATCA-AAT
* * * * *
1408404 -AATGATTATTACTAAATCATTATTAAATCATTATTAAAT
1 CATTAAATATTA--AAATCATTACTAAATC---ATCAAAT
1408443 CA-T-AATATTAAAATCATTACTAAATCATCAAAT
1 CATTAAATATTAAAATCATTACTAAATCATCAAAT
*
1408476 CATTAAATATTAAAATCATTACTAAATCTTCAAAT
1 CATTAAATATTAAAATCATTACTAAATCATCAAAT
1408511 CA-T-AATATTAAAATCATTACTAAATCATCAAAT
1 CATTAAATATTAAAATCATTACTAAATCATCAAAT
*
1408544 CATTAAATATTAAAATAATTACTAAATCATCAAAT
1 CATTAAATATTAAAATCATTACTAAATCATCAAAT
*
1408579 CATTAAATATTAAAATCATGACTAAATCATCAAAT
1 CATTAAATATTAAAATCATTACTAAATCATCAAAT
*
1408614 CATTAAATATTAAAATCATTATTAAATCAT
1 CATTAAATATTAAAATCATTACTAAATCAT
1408644 TTTTATGGTT
Statistics
Matches: 216, Mismatches: 14, Indels: 21
0.86 0.06 0.08
Matches are distributed among these distances:
33 39 0.18
34 3 0.01
35 129 0.60
36 15 0.07
37 16 0.07
38 6 0.03
39 3 0.01
40 5 0.02
ACGTcount: A:0.50, C:0.12, G:0.01, T:0.37
Consensus pattern (35 bp):
CATTAAATATTAAAATCATTACTAAATCATCAAAT
Found at i:1408534 original size:68 final size:68
Alignment explanation
Indices: 1408439--1408643 Score: 356
Period size: 68 Copynumber: 3.0 Consensus size: 68
1408429 AATCATTATT
1408439 AAATCATAATATTAAAATCATTACTAAATCATCAAATCATTAAATATTAAAATCATTACTAAATC
1 AAATCATAATATTAAAATCATTACTAAATCATCAAATCATTAAATATTAAAATCATTACTAAATC
*
1408504 TTC
66 ATC
*
1408507 AAATCATAATATTAAAATCATTACTAAATCATCAAATCATTAAATATTAAAATAATTACTAAATC
1 AAATCATAATATTAAAATCATTACTAAATCATCAAATCATTAAATATTAAAATCATTACTAAATC
1408572 ATC
66 ATC
* *
1408575 AAATCATTAAATATTAAAATCATGACTAAATCATCAAATCATTAAATATTAAAATCATTATTAAA
1 AAATCA-T-AATATTAAAATCATTACTAAATCATCAAATCATTAAATATTAAAATCATTACTAAA
1408640 TCAT
64 TCAT
1408644 TTTTATGGTT
Statistics
Matches: 130, Mismatches: 5, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
68 72 0.55
69 1 0.01
70 57 0.44
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (68 bp):
AAATCATAATATTAAAATCATTACTAAATCATCAAATCATTAAATATTAAAATCATTACTAAATC
ATC
Found at i:1408537 original size:11 final size:11
Alignment explanation
Indices: 1408411--1408538 Score: 82
Period size: 11 Copynumber: 12.2 Consensus size: 11
1408401 TATAATGATT
1408411 ATTACTAAATC
1 ATTACTAAATC
*
1408422 ATTATTAAATC
1 ATTACTAAATC
*
1408433 ATTATTAAATC
1 ATTACTAAATC
*
1408444 ATAATATTAAAATC
1 AT--TACT-AAATC
1408458 ATTACTAAATC
1 ATTACTAAATC
1408469 A-T-C-AAATC
1 ATTACTAAATC
1408477 A-T--TAAAT-
1 ATTACTAAATC
1408484 ATTA--AAATC
1 ATTACTAAATC
1408493 ATTACTAAATC
1 ATTACTAAATC
1408504 -TT-C-AAATC
1 ATTACTAAATC
*
1408512 ATAATATTAAAATC
1 AT--TACT-AAATC
1408526 ATTACTAAATC
1 ATTACTAAATC
1408537 AT
1 AT
1408539 CAAATCATTA
Statistics
Matches: 98, Mismatches: 4, Indels: 30
0.74 0.03 0.23
Matches are distributed among these distances:
7 1 0.01
8 21 0.21
9 7 0.07
10 3 0.03
11 42 0.43
12 6 0.06
13 4 0.04
14 14 0.14
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (11 bp):
ATTACTAAATC
Found at i:1408914 original size:49 final size:49
Alignment explanation
Indices: 1408851--1409172 Score: 472
Period size: 49 Copynumber: 6.6 Consensus size: 49
1408841 ATTACTAATA
*
1408851 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTTATT
1 ATTACT-AATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
*
1408901 ATTACTAATCATTACTACCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
*
1408950 ATTGCTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
* *
1408999 ATTACTAATCATTATTACCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
1409048 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
* * * *
1409097 ATTACTAATCATTACTA-AATAATTATTATAATTTTAA-ATATAAATTCATT
1 ATTACTAATCATTACTATCA-AATCATTA-AATATTAATA-ATAATTTCATT
* * *
1409147 ATTA--AATCATGATTAGCAAATCATTA
1 ATTACTAATCATTACTATCAAATCATTA
1409173 CTAAATCAAA
Statistics
Matches: 251, Mismatches: 17, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
48 17 0.07
49 207 0.82
50 27 0.11
ACGTcount: A:0.45, C:0.11, G:0.01, T:0.43
Consensus pattern (49 bp):
ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
Found at i:1409007 original size:18 final size:17
Alignment explanation
Indices: 1408980--1409105 Score: 50
Period size: 18 Copynumber: 7.6 Consensus size: 17
1408970 AATCATTAAA
*
1408980 TATTAATAATAATTTCAT
1 TATTACTAATAA-TTCAT
1408998 TATTAC---TAA-TCAT
1 TATTACTAATAATTCAT
* * * *
1409011 TATTACCAAATCATTAAA
1 TATTA-CTAATAATTCAT
*
1409029 TATTAATAATAATTTCAT
1 TATTACTAATAA-TTCAT
* *
1409047 TATTACTAATCATT-AC
1 TATTACTAATAATTCAT
* * * *
1409063 TA-T-CAAATCATTAAA
1 TATTACTAATAATTCAT
*
1409078 TATTAATAATAATTTCAT
1 TATTACTAATAA-TTCAT
1409096 TATTACTAAT
1 TATTACTAAT
1409106 CATTACTAAA
Statistics
Matches: 78, Mismatches: 20, Indels: 20
0.66 0.17 0.17
Matches are distributed among these distances:
13 9 0.12
14 9 0.12
15 7 0.09
16 4 0.05
17 12 0.15
18 37 0.47
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (17 bp):
TATTACTAATAATTCAT
Found at i:1409012 original size:13 final size:14
Alignment explanation
Indices: 1408994--1409026 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1408984 AATAATAATT
*
1408994 TCATTATTA-CTAA
1 TCATTATTACCAAA
1409007 TCATTATTACCAAA
1 TCATTATTACCAAA
1409021 TCATTA
1 TCATTA
1409027 AATATTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.39, C:0.18, G:0.00, T:0.42
Consensus pattern (14 bp):
TCATTATTACCAAA
Found at i:1412050 original size:13 final size:14
Alignment explanation
Indices: 1412015--1412041 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1412005 TACAAATAAA
1412015 AAAAAAATTAGATT
1 AAAAAAATTAGATT
1412029 AAAAAAATTAGAT
1 AAAAAAATTAGAT
1412042 AAGATAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (14 bp):
AAAAAAATTAGATT
Found at i:1412297 original size:34 final size:33
Alignment explanation
Indices: 1412215--1412297 Score: 91
Period size: 34 Copynumber: 2.5 Consensus size: 33
1412205 TAAATATTTT
*
1412215 TAAACACAATATTTTT-TTAAACTAGAATAAAT
1 TAAACACAATATTTTTATTAAACTAGAATAAAA
* *
1412247 TAAACA-AATTAATTTTATATAATCTA-ATATAAAA
1 TAAACACAA-TATTTTTAT-TAAACTAGA-ATAAAA
1412281 TAAACACAATATTTTTA
1 TAAACACAATATTTTTA
1412298 AACACAATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
31 2 0.05
32 12 0.29
33 2 0.05
34 24 0.57
35 2 0.05
ACGTcount: A:0.52, C:0.08, G:0.01, T:0.39
Consensus pattern (33 bp):
TAAACACAATATTTTTATTAAACTAGAATAAAA
Found at i:1412299 original size:15 final size:16
Alignment explanation
Indices: 1412281--1412316 Score: 65
Period size: 15 Copynumber: 2.3 Consensus size: 16
1412271 TAATATAAAA
1412281 TAAACACAATA-TTTT
1 TAAACACAATATTTTT
1412296 TAAACACAATATTTTT
1 TAAACACAATATTTTT
1412312 TAAAC
1 TAAAC
1412317 GGGAATACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (16 bp):
TAAACACAATATTTTT
Found at i:1412329 original size:80 final size:81
Alignment explanation
Indices: 1412207--1412359 Score: 263
Period size: 80 Copynumber: 1.9 Consensus size: 81
1412197 AACAACACTA
*
1412207 AATATTTTTAAACACAATATTTTTTTAAACTAGAATAAATTAAACAAATTAATTTTATATAATCT
1 AATATTTTTAAACACAATATTTTTTTAAACGAGAATAAATTAAACAAATTAATTTTATATAATCT
1412272 AATATAAAATAAACAC
66 AATATAAAATAAACAC
* * *
1412288 AATATTTTTAAACACAATA-TTTTTTAAACGGGAATACATTAAACAAATTAATTTTATATACTCT
1 AATATTTTTAAACACAATATTTTTTTAAACGAGAATAAATTAAACAAATTAATTTTATATAATCT
1412352 AATATAAA
66 AATATAAA
1412360 CTAACTAACT
Statistics
Matches: 68, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
80 49 0.72
81 19 0.28
ACGTcount: A:0.50, C:0.09, G:0.03, T:0.39
Consensus pattern (81 bp):
AATATTTTTAAACACAATATTTTTTTAAACGAGAATAAATTAAACAAATTAATTTTATATAATCT
AATATAAAATAAACAC
Found at i:1412835 original size:28 final size:28
Alignment explanation
Indices: 1412804--1412857 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
1412794 ATAATCTAAT
*
1412804 ATATAACTTAAACTAACAAATTAATATA
1 ATATAACTTAAACTAACAAACTAATATA
1412832 ATATAACTTAAACTAACAAACTAATA
1 ATATAACTTAAACTAACAAACTAATA
1412858 ATTTATACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (28 bp):
ATATAACTTAAACTAACAAACTAATATA
Found at i:1412864 original size:28 final size:28
Alignment explanation
Indices: 1412800--1412864 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
1412790 TTATATAATC
*
1412800 TAATATATAACTTAAACTAACAAATTAA
1 TAATATATAACTTAAACTAACAAACTAA
1412828 T-ATAATATAACTTAAACTAACAAACTAA
1 TAAT-ATATAACTTAAACTAACAAACTAA
*
1412856 TAATTTATA
1 TAATATATA
1412865 CTAACAAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 29 0.88
29 2 0.06
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (28 bp):
TAATATATAACTTAAACTAACAAACTAA
Found at i:1412867 original size:21 final size:21
Alignment explanation
Indices: 1412834--1412882 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1412824 TTAATATAAT
1412834 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
1412855 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
1412876 ATTAACT
1 A-TAACT
1412883 AAATTTTTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:1416222 original size:40 final size:41
Alignment explanation
Indices: 1416173--1416266 Score: 140
Period size: 40 Copynumber: 2.3 Consensus size: 41
1416163 AGTTTCCATT
1416173 TTCGCAACGCGAATATGT-AAA-TCACAACACAGAAGTCAAA
1 TTCGCAACGCGAATA-GTCAAATTCACAACACAGAAGTCAAA
*
1416213 TTCGTAACGC-AATAGTCAAATTCACAACACAGAAGTCAAA
1 TTCGCAACGCGAATAGTCAAATTCACAACACAGAAGTCAAA
*
1416253 TTCGCAACACGAAT
1 TTCGCAACGCGAAT
1416267 TTAATTTCGC
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
38 2 0.04
39 7 0.15
40 36 0.75
41 3 0.06
ACGTcount: A:0.44, C:0.23, G:0.14, T:0.19
Consensus pattern (41 bp):
TTCGCAACGCGAATAGTCAAATTCACAACACAGAAGTCAAA
Found at i:1416249 original size:20 final size:20
Alignment explanation
Indices: 1416194--1416262 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
1416184 AATATGTAAA
1416194 TCACAACACAGAAGTCAAAT
1 TCACAACACAGAAGTCAAAT
** *
1416214 TCGTAACGCA-ATAGTCAAAT
1 TCACAACACAGA-AGTCAAAT
1416234 TCACAACACAGAAGTCAAAT
1 TCACAACACAGAAGTCAAAT
*
1416254 TCGCAACAC
1 TCACAACAC
1416263 GAATTTAATT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
19 1 0.03
20 38 0.95
21 1 0.03
ACGTcount: A:0.45, C:0.26, G:0.12, T:0.17
Consensus pattern (20 bp):
TCACAACACAGAAGTCAAAT
Found at i:1417451 original size:3 final size:3
Alignment explanation
Indices: 1417443--1417470 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1417433 ATATAACCCT
1417443 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1417471 TCCCCGAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1419055 original size:30 final size:30
Alignment explanation
Indices: 1419019--1419236 Score: 364
Period size: 30 Copynumber: 7.2 Consensus size: 30
1419009 TCCGAAGGAC
1419019 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1419049 CTATCCAGATGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1419079 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1419109 CTATCCAAAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1419139 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1419169 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* ** * *
1419199 CTATCCATAGGTCCCAAAGAACCTAGGTAAA
1 CTATCCAGAGGTCATAAAGATCCTCGGT-AA
1419230 CTATCCA
1 CTATCCA
1419237 TATGTTCCTT
Statistics
Matches: 178, Mismatches: 9, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
30 169 0.95
31 9 0.05
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:1419473 original size:4 final size:4
Alignment explanation
Indices: 1419464--1419492 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
1419454 ATATAACCAT
1419464 TACA TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA TACA T
1419493 GTCATCAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (4 bp):
TACA
Found at i:1420466 original size:64 final size:63
Alignment explanation
Indices: 1420350--1420490 Score: 167
Period size: 64 Copynumber: 2.2 Consensus size: 63
1420340 ACACTACACC
* * * *
1420350 ATGCATCGATACATAAATCCTATTCGATGTTTGTATTTAATGGGGATACATCGATGCACTCCTT
1 ATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAAT-GGAATACATCGATGCACTCCAT
* * * *
1420414 ATGCATCGATGCATAAATCCTATTCGATGTTTTCTTTTTAAAT-TAATGCATCGATGCACTGCAT
1 ATGCATCGATGCATAAATCCTATTCGATG-TTTCTATTT-AATGGAATACATCGATGCACTCCAT
*
1420478 GTGCATCGATGCA
1 ATGCATCGATGCA
1420491 CCTTAAAAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
64 56 0.85
65 7 0.11
66 3 0.05
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (63 bp):
ATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGAATACATCGATGCACTCCAT
Found at i:1424445 original size:18 final size:18
Alignment explanation
Indices: 1424424--1424459 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1424414 ATGGATCCTG
*
1424424 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
1424442 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
1424460 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:1425381 original size:18 final size:18
Alignment explanation
Indices: 1425360--1425396 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1425350 GTAATTGGAG
1425360 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
1425378 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
1425396 T
1 T
1425397 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:1425403 original size:24 final size:24
Alignment explanation
Indices: 1425352--1425404 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
1425342 TTTCATATGT
* * *
1425352 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
1425376 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
1425400 AATTT
1 AATTT
1425405 CGGTTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:1426386 original size:18 final size:18
Alignment explanation
Indices: 1426353--1426388 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1426343 AAGCAAAAGG
* *
1426353 AAATCAAAATCGCAATCA
1 AAATCAAAACCCCAATCA
1426371 AAATCAAAACCCCAATCA
1 AAATCAAAACCCCAATCA
1426389 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.28, G:0.03, T:0.14
Consensus pattern (18 bp):
AAATCAAAACCCCAATCA
Found at i:1428025 original size:21 final size:21
Alignment explanation
Indices: 1428001--1428099 Score: 92
Period size: 21 Copynumber: 4.7 Consensus size: 21
1427991 GCGGGCAGGA
* *
1428001 CCTCTTGAACGATGATAAGGG
1 CCTCTTGAATGATGAGAAGGG
* * * *
1428022 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAATGATGAGAAGGG
* * *
1428043 CTTCTTCAATGATGAGAATGG
1 CCTCTTGAATGATGAGAAGGG
*
1428064 CCTCTTGAATGAT-AGGAGGCG
1 CCTCTTGAATGATGAGAAGG-G
1428085 CCTCTTGAATGATGA
1 CCTCTTGAATGATGA
1428100 TAGATGCATC
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 4 0.07
21 56 0.92
22 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.26
Consensus pattern (21 bp):
CCTCTTGAATGATGAGAAGGG
Found at i:1428057 original size:42 final size:42
Alignment explanation
Indices: 1428001--1428101 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 42
1427991 GCGGGCAGGA
* * * * *
1428001 CCTCTTGAACGATGATAAGGGCCTCTTGAACGGTGGGAGGGG
1 CCTCTTCAATGATGATAAGGGCCTCTTGAACGATAGGAGGCG
* * * *
1428043 CTTCTTCAATGATGAGAATGGCCTCTTGAATGATAGGAGGCG
1 CCTCTTCAATGATGATAAGGGCCTCTTGAACGATAGGAGGCG
*
1428085 CCTCTTGAATGATGATA
1 CCTCTTCAATGATGATA
1428102 GATGCATCGG
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.27
Consensus pattern (42 bp):
CCTCTTCAATGATGATAAGGGCCTCTTGAACGATAGGAGGCG
Found at i:1428359 original size:21 final size:21
Alignment explanation
Indices: 1428333--1428382 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
1428323 AAACAAATTT
1428333 ACCTCATTGAGTAGAGTATGA
1 ACCTCATTGAGTAGAGTATGA
1428354 ACCTCATTGAGTAGAGTATGA
1 ACCTCATTGAGTAGAGTATGA
1428375 ACCTCATT
1 ACCTCATT
1428383 CTGCAACGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (21 bp):
ACCTCATTGAGTAGAGTATGA
Found at i:1430848 original size:20 final size:20
Alignment explanation
Indices: 1430823--1430921 Score: 135
Period size: 20 Copynumber: 5.0 Consensus size: 20
1430813 ATATTGTGTT
1430823 TCGCGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
*
1430843 TCGCGTTGCGAATTTGACTT
1 TCGCGTTGCGAATTTGACTA
* * * *
1430863 TTGTGTTGAGAATTTGACTT
1 TCGCGTTGCGAATTTGACTA
* *
1430883 TTGTGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
1430903 TCGCGTTGCGAATTTGACT
1 TCGCGTTGCGAATTTGACT
1430922 TCTATGTTGC
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 71 1.00
ACGTcount: A:0.18, C:0.15, G:0.25, T:0.41
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGACTA
Found at i:1430900 original size:60 final size:59
Alignment explanation
Indices: 1430822--1430978 Score: 192
Period size: 60 Copynumber: 2.6 Consensus size: 59
1430812 AATATTGTGT
* * * *
1430822 TTCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGTGTTGAGAATTTGAC-T
1 TTCGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTATGTTGAG-ATTT-ACAA
* *
1430882 TTTGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTATGTTGCGATTTACAAA
1 TTCGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTATGTTGAGATTTAC-AA
* *
1430942 TTCGTGTTGCGAAATTAGAGT-TCGCGTTGCGAATTTG
1 TTCGTGTTGCG-AATTTGACTATCGCGTTGCGAATTTG
1430979 TTGGTCATTT
Statistics
Matches: 85, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
58 2 0.02
59 4 0.05
60 72 0.85
61 7 0.08
ACGTcount: A:0.20, C:0.15, G:0.25, T:0.41
Consensus pattern (59 bp):
TTCGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTATGTTGAGATTTACAA
Found at i:1430922 original size:40 final size:40
Alignment explanation
Indices: 1430823--1430933 Score: 141
Period size: 40 Copynumber: 2.8 Consensus size: 40
1430813 ATATTGTGTT
* * * *
1430823 TCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTT
1 TCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTA
* * *
1430863 TTGTGTTGAGAATTTGACTTTTGTGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTA
* *
1430903 TCGCGTTGCGAATTTGACTTCTATGTTGCGA
1 TCGCGTTGCGAATTTGACTTTTGTGTTGCGA
1430934 TTTACAAATT
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 59 1.00
ACGTcount: A:0.18, C:0.15, G:0.25, T:0.41
Consensus pattern (40 bp):
TCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTA
Found at i:1430930 original size:20 final size:20
Alignment explanation
Indices: 1430827--1430933 Score: 128
Period size: 20 Copynumber: 5.3 Consensus size: 20
1430817 TGTGTTTCGC
*
1430827 GTTGCGAATTTGACTATC-GC
1 GTTGCGAATTTGACT-TCTGT
*
1430847 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTCTGT
* *
1430867 GTTGAGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTCTGT
*
1430887 GTTGCGAATTTGACTATC-GC
1 GTTGCGAATTTGACT-TCTGT
*
1430907 GTTGCGAATTTGACTTCTAT
1 GTTGCGAATTTGACTTCTGT
1430927 GTTGCGA
1 GTTGCGA
1430934 TTTACAAATT
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
19 3 0.04
20 72 0.95
21 1 0.01
ACGTcount: A:0.19, C:0.14, G:0.25, T:0.42
Consensus pattern (20 bp):
GTTGCGAATTTGACTTCTGT
Found at i:1430951 original size:40 final size:40
Alignment explanation
Indices: 1430827--1430954 Score: 118
Period size: 40 Copynumber: 3.2 Consensus size: 40
1430817 TGTGTTTCGC
** ** *
1430827 GTTGCGAATTTGACTATC-GCGTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACT-TCTATGTTGCGAATTTGACAATCGT
* * * * *
1430867 GTTGAGAATTTGACTTTTGTGTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTTCTATGTTGCGAATTTGACAATCGT
1430907 GTTGCGAATTTGACTTCTATGTTGCG-ATTT-ACAAATTCGT
1 GTTGCGAATTTGACTTCTATGTTGCGAATTTGAC-AA-TCGT
1430947 GTTGCGAA
1 GTTGCGAA
1430955 ATTAGAGTTC
Statistics
Matches: 74, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
38 2 0.03
39 6 0.08
40 66 0.89
ACGTcount: A:0.20, C:0.14, G:0.24, T:0.41
Consensus pattern (40 bp):
GTTGCGAATTTGACTTCTATGTTGCGAATTTGACAATCGT
Found at i:1431721 original size:2 final size:2
Alignment explanation
Indices: 1431714--1431749 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1431704 TTAACTGAAT
1431714 TA TA TA TA TA TA TA TA TA TA TA TA 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
1431750 GATAAGATCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1433868 original size:21 final size:21
Alignment explanation
Indices: 1433844--1433883 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1433834 GTTAATTAGT
1433844 TTGTTAGTTTAAGTTATATTA
1 TTGTTAGTTTAAGTTATATTA
1433865 TTGTTAGTTTAAGTTATAT
1 TTGTTAGTTTAAGTTATAT
1433884 CATACATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (21 bp):
TTGTTAGTTTAAGTTATATTA
Found at i:1433941 original size:40 final size:40
Alignment explanation
Indices: 1433897--1433996 Score: 116
Period size: 40 Copynumber: 2.5 Consensus size: 40
1433887 ACATAAATAT
1433897 AAATTATTTAATTAGTTTGTT-T-GATAGTTATATATTAAAA
1 AAATTATTTAATTAGTTTGTTATCGATAGTTATATA-T-AAA
* * * *
1433937 AAATTAATTAGTTTGTTTGTTAGTCGTTAGTTATATATAAA
1 AAATTATTTAATTAGTTTGTTA-TCGATAGTTATATATAAA
1433978 AAA-TATTTAATTAGTTTGT
1 AAATTATTTAATTAGTTTGT
1433997 AGTTAGTTAA
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
40 31 0.62
41 6 0.12
42 2 0.04
43 11 0.22
ACGTcount: A:0.37, C:0.01, G:0.12, T:0.50
Consensus pattern (40 bp):
AAATTATTTAATTAGTTTGTTATCGATAGTTATATATAAA
Found at i:1433951 original size:36 final size:42
Alignment explanation
Indices: 1433901--1433996 Score: 123
Period size: 36 Copynumber: 2.4 Consensus size: 42
1433891 AAATATAAAT
1433901 TATTTAATTAGTTTGTTTG-A-TAGTTA-TATAT-TAAAAAA
1 TATTTAATTAGTTTGTTTGTAGTAGTTAGTATATATAAAAAA
*
1433939 -A-TTAATTAGTTTGTTTGTTAGTCGTTAGTTATATATAAAAAA
1 TATTTAATTAGTTTGTTTG-TAGTAGTTAG-TATATATAAAAAA
1433981 TATTTAATTAGTTTGT
1 TATTTAATTAGTTTGT
1433997 AGTTAGTTAA
Statistics
Matches: 49, Mismatches: 1, Indels: 10
0.82 0.02 0.17
Matches are distributed among these distances:
36 16 0.33
37 1 0.02
38 1 0.02
39 5 0.10
41 5 0.10
42 7 0.14
43 1 0.02
44 13 0.27
ACGTcount: A:0.35, C:0.01, G:0.12, T:0.51
Consensus pattern (42 bp):
TATTTAATTAGTTTGTTTGTAGTAGTTAGTATATATAAAAAA
Found at i:1434002 original size:43 final size:43
Alignment explanation
Indices: 1433921--1434003 Score: 125
Period size: 43 Copynumber: 1.9 Consensus size: 43
1433911 GTTTGTTTGA
*
1433921 TAGTTATATATTAAAAAAATTAATTAGTTTGTTTGTTAGTCGT
1 TAGTTATATATTAAAAAAATTAATTAGTTTGTTAGTTAGTCGT
1433964 TAGTTATATA-TAAAAAATATTTAATTAGTTTG-TAGTTAGT
1 TAGTTATATATTAAAAAA-A-TTAATTAGTTTGTTAGTTAGT
1434004 TAAATAGTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
42 7 0.19
43 18 0.49
44 12 0.32
ACGTcount: A:0.37, C:0.01, G:0.13, T:0.48
Consensus pattern (43 bp):
TAGTTATATATTAAAAAAATTAATTAGTTTGTTAGTTAGTCGT
Found at i:1434012 original size:44 final size:43
Alignment explanation
Indices: 1433920--1434013 Score: 111
Period size: 44 Copynumber: 2.2 Consensus size: 43
1433910 AGTTTGTTTG
* **
1433920 ATAGTTATATATTAAAAAAATTAATTAGTTTGTTTGTTAGTCG
1 ATAGTTATATATTAAAAAAATTAATTAGTTTGTTAGTTAGTAA
*
1433963 TTAGTTATATA-TAAAAAATATTTAATTAGTTTG-TAGTTAGTTAA
1 ATAGTTATATATTAAAAAA-A-TTAATTAGTTTGTTAGTTAG-TAA
1434007 ATAGTTA
1 ATAGTTA
1434014 AGTTATATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
42 7 0.16
43 17 0.40
44 19 0.44
ACGTcount: A:0.39, C:0.01, G:0.13, T:0.47
Consensus pattern (43 bp):
ATAGTTATATATTAAAAAAATTAATTAGTTTGTTAGTTAGTAA
Found at i:1434447 original size:29 final size:28
Alignment explanation
Indices: 1434415--1434512 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 28
1434405 TTAATTAGTT
*
1434415 TTTAGTAGTAAATTATAATTTAAA-AATCG
1 TTTAGTAGTAAATTAT-A-TTAAAGAATAG
* *
1434444 TTTATTAGTTTAAGTTATATTAAAGAATAG
1 TTTAGTAG--TAAATTATATTAAAGAATAG
*
1434474 TTTAGTAGTTGAAGTTATATTAAAGAATAG
1 TTTAGTAG-T-AAATTATATTAAAGAATAG
*
1434504 TTTATTAGT
1 TTTAGTAGT
1434513 TGTTTAAGAG
Statistics
Matches: 60, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
29 15 0.25
30 38 0.63
31 7 0.12
ACGTcount: A:0.40, C:0.01, G:0.14, T:0.45
Consensus pattern (28 bp):
TTTAGTAGTAAATTATATTAAAGAATAG
Found at i:1434483 original size:30 final size:30
Alignment explanation
Indices: 1434434--1434514 Score: 128
Period size: 30 Copynumber: 2.7 Consensus size: 30
1434424 AAATTATAAT
* *
1434434 TTAAA-AATCGTTTATTAGTTTAAGTTATA
1 TTAAAGAATAGTTTATTAGTTGAAGTTATA
*
1434463 TTAAAGAATAGTTTAGTAGTTGAAGTTATA
1 TTAAAGAATAGTTTATTAGTTGAAGTTATA
1434493 TTAAAGAATAGTTTATTAGTTG
1 TTAAAGAATAGTTTATTAGTTG
1434515 TTTAAGAGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 5 0.11
30 42 0.89
ACGTcount: A:0.38, C:0.01, G:0.16, T:0.44
Consensus pattern (30 bp):
TTAAAGAATAGTTTATTAGTTGAAGTTATA
Done.