Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold14
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: 2879421
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 64274 characters in sequence are not A, C, G, or T
File 1 of 17
Found at i:11777 original size:28 final size:28
Alignment explanation
Indices: 11696--11777 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
11686 TTTTGGAGAT
*
11696 AATAACGAGGTTGGAGTGTTCCCTCG--GA
1 AATAACGAGGTTGGAGT-AT-CCTCGATGA
* * *
11724 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGAGGTTGGAGTATCCTCGATGA
11752 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCTCGAT
11778 TGTGAAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 4 0.09
27 1 0.02
28 40 0.89
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCTCGATGA
Found at i:11874 original size:53 final size:52
Alignment explanation
Indices: 11760--12306 Score: 235
Period size: 51 Copynumber: 10.4 Consensus size: 52
11750 GAAATAACGA
* * * *
11760 GGTTGGAGTATCCTCGATT--GTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTAAG-GAGAAATTGGT-GTTTTGAAAATAAAATCGG
** * *
11812 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-AAGGAGAAATTGGTGTTTTGAAAATAAAATCGG
* * * * * *
11865 GGTTGGAGTATCCCCGATT-ATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTAAGGAGAAATTGGTGTTTTGAAAATAAAATCGG
* * * ** ** *
11916 GGTTGGAGTATCCCCTCAGAAATAACGG-G--GTTGGAGTATCCCCGATGAT-TAA-CGG
1 GGTTGGAGTAT-CCC-C-G-ATTAA-GGAGAAATTGGTGT-T--TTGAAAATAAAATCGG
* ** * * *
11971 GGTTGGAGTGTCCCCGATTGTGAAG-AATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTAAGGAGAAATTGGT-GTTTTGAAAATAAAATCGG
** * *
12023 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-AAGGAGAAATTGGTGTTTTGAAAATAAAATCGG
* * * * * *
12076 GGTTGGAGTATCCCCGATT-ATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTAAGGAGAAATTGGTGTTTTGAAAATAAAATCGG
* * * * ** ** *
12127 GGTTGGAGTATCCCCTCAGAAATAACGAG--GTTGGAGTATCCCCGATGAT-TAA-CGG
1 GGTTGGAGTAT-CCC-C-G-ATTAAGGAGAAATTGGTGT-T--TTGAAAATAAAATCGG
* ** * *
12182 GGTTGGAGTGTCCCCGATTGTGAAGAAATTGGTGTTTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTAAGGAGAAATTGGTG---TTTTGAAAATAAAATCGG
* ** *
12237 AGTTGGAGTATCCCCGATTATA-GA-AAATTAATGTTTTGAAAGTAAAATCGG
1 GGTTGGAGTATCCCCGATTA-AGGAGAAATTGGTGTTTTGAAAATAAAATCGG
* * *
12288 AGTTGGAATATCCTCGATT
1 GGTTGGAGTATCCCCGATT
12307 GTGGAGAATT
Statistics
Matches: 355, Mismatches: 105, Indels: 71
0.67 0.20 0.13
Matches are distributed among these distances:
50 4 0.01
51 112 0.32
52 48 0.14
53 80 0.23
54 40 0.11
55 55 0.15
56 7 0.02
57 9 0.03
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.29
Consensus pattern (52 bp):
GGTTGGAGTATCCCCGATTAAGGAGAAATTGGTGTTTTGAAAATAAAATCGG
Found at i:11920 original size:51 final size:51
Alignment explanation
Indices: 11760--12141 Score: 288
Period size: 51 Copynumber: 7.3 Consensus size: 51
11750 GAAATAACGA
* * *
11760 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * *
11812 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
11865 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
* *** ** *
11916 GGTTGGAGTATCCCC--TCA-GAAATAACGGGGTTGGAGTATCCCCGATGAT-TAA-CGG
1 GGTTGGAGTATCCCCGATTATGAAA-AA-----TT-G-GTAT-TTTGAAAATAAAATCGG
* * * *
11971 GGTTGGAGTGTCCCCGATTGTGAAGAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * *
12023 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
12076 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
12127 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
12142 TCAGAAATAA
Statistics
Matches: 249, Mismatches: 62, Indels: 39
0.71 0.18 0.11
Matches are distributed among these distances:
48 4 0.02
49 4 0.02
50 6 0.02
51 82 0.33
52 37 0.15
53 64 0.26
54 20 0.08
55 18 0.07
56 4 0.02
57 7 0.03
58 3 0.01
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.28
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:11976 original size:27 final size:28
Alignment explanation
Indices: 11913--11988 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
11903 AAAATAAAGT
*
11913 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
11941 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
11968 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
11989 TGTGAAGAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:12069 original size:211 final size:211
Alignment explanation
Indices: 11704--12306 Score: 967
Period size: 211 Copynumber: 2.8 Consensus size: 211
11694 ATAATAACGA
* * * * * *
11704 GGTTGGAGTGTTCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGT
1 GGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACGGGGTTGGAGT
* * *
11769 ATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAATTGGAGTATCCCCGATTAAA
65 GTCCCCGATTGTGAAGAATTGGTATTTTTGGAAATAAAATCGGAATTGGAGTATCCCCGATTAAA
11834 GGAGAAATTGGTGTTGTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTATGAAAAATCGATAT
130 GGAGAAATTGGTGTTGTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTATGAAAAATCGATAT
11899 TTTGAAAATAAAGTCGG
195 TTTGAAAATAAAGTCGG
11916 GGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTG
1 GGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTG
11981 TCCCCGATTGTGAAGAATTGGTATTTTTGGAAATAAAATCGGAATTGGAGTATCCCCGATTAAAG
66 TCCCCGATTGTGAAGAATTGGTATTTTTGGAAATAAAATCGGAATTGGAGTATCCCCGATTAAAG
12046 GAGAAATTGGTGTTGTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTATGAAAAATCGATATT
131 GAGAAATTGGTGTTGTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTATGAAAAATCGATATT
12111 TTGAAAATAAAGTCGG
196 TTGAAAATAAAGTCGG
*
12127 GGTTGGAGTATCCCCTCAGAAATAACGAGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTG
1 GGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTG
* *
12192 TCCCCGATTGTGAAGAAATTGGTGTTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTA
66 TCCCCGATTGTGAAG-AATT-G-GTATTTTTGGAAATAAAATCGGAATTGGAGTATCCCCGATTA
* ** * * * * * *
12257 TA-GA-AAATTAATGTTTTGAAAGTAAAATCGGAGTTGGAATATCCTCGATT
128 AAGGAGAAATTGGTGTTGTGAAAATAAAACCGGGGTTGGAGTATCCCCGATT
12307 GTGGAGAATT
Statistics
Matches: 367, Mismatches: 21, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
211 238 0.65
212 85 0.23
213 3 0.01
214 41 0.11
ACGTcount: A:0.31, C:0.13, G:0.28, T:0.29
Consensus pattern (211 bp):
GGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGATTAACGGGGTTGGAGTG
TCCCCGATTGTGAAGAATTGGTATTTTTGGAAATAAAATCGGAATTGGAGTATCCCCGATTAAAG
GAGAAATTGGTGTTGTGAAAATAAAACCGGGGTTGGAGTATCCCCGATTATGAAAAATCGATATT
TTGAAAATAAAGTCGG
Found at i:12187 original size:27 final size:28
Alignment explanation
Indices: 12124--12199 Score: 93
Period size: 27 Copynumber: 2.8 Consensus size: 28
12114 AAAATAAAGT
*
12124 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
* *
12152 CGAGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
12179 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
12200 TGTGAAGAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
27 24 0.57
28 18 0.43
ACGTcount: A:0.22, C:0.21, G:0.33, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:14688 original size:13 final size:13
Alignment explanation
Indices: 14670--14695 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
14660 ACAAAGATCC
14670 ATGTATCGATACA
1 ATGTATCGATACA
14683 ATGTATCGATACA
1 ATGTATCGATACA
14696 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:14691 original size:33 final size:33
Alignment explanation
Indices: 14649--14715 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
14639 AAAATTTCCA
***
14649 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
14682 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
14715 A
1 A
14716 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:14759 original size:19 final size:18
Alignment explanation
Indices: 14735--14802 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
14725 CAGTAGCTAA
14735 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
14754 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
14769 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
14786 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
14803 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:14775 original size:13 final size:13
Alignment explanation
Indices: 14757--14781 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14747 ACAATACTTA
14757 TGTATCGATACAT
1 TGTATCGATACAT
14770 TGTATCGATACA
1 TGTATCGATACA
14782 AAACTTATGT
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:14779 original size:32 final size:32
Alignment explanation
Indices: 14738--14800 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
14728 TAGCTAATTA
*
14738 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
14770 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
14801 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:14882 original size:21 final size:21
Alignment explanation
Indices: 14858--14914 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
14848 CATTTGTAGG
14858 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
14879 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
14900 ATGTATCGATACATT
1 ATGTATCGATACATT
14915 TAAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:15219 original size:2 final size:2
Alignment explanation
Indices: 15206--15269 Score: 92
Period size: 2 Copynumber: 32.0 Consensus size: 2
15196 ATCGTTACAA
* * * *
15206 AT AT AT AA AT AT AT AT AT AT AT AT AT AT AC AC AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15248 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
15270 GTGAAGAACA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:16488 original size:16 final size:17
Alignment explanation
Indices: 16463--16497 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
16453 CTTAACCCAA
*
16463 TTCAATTAAAG-CTAAT
1 TTCAAGTAAAGTCTAAT
16479 TTCAAGTAAAGTCTAAT
1 TTCAAGTAAAGTCTAAT
16496 TT
1 TT
16498 TTTTATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (17 bp):
TTCAAGTAAAGTCTAAT
Found at i:16876 original size:32 final size:32
Alignment explanation
Indices: 16832--16907 Score: 118
Period size: 32 Copynumber: 2.4 Consensus size: 32
16822 TAATTACATT
* *
16832 TTATAAAT-TTAAAATAAATTTATAATTTATA
1 TTATAATTATTAAAATAAATTGATAATTTATA
*
16863 TTATAGTTATTAAAATAAATTGATAATTTATA
1 TTATAATTATTAAAATAAATTGATAATTTATA
16895 TTATAATTATTAA
1 TTATAATTATTAA
16908 TTTTATTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
31 6 0.15
32 34 0.85
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (32 bp):
TTATAATTATTAAAATAAATTGATAATTTATA
Found at i:17007 original size:16 final size:16
Alignment explanation
Indices: 16988--17018 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16978 TAAGTATGAA
16988 TTAATATAAATTTAAT
1 TTAATATAAATTTAAT
*
17004 TTAATTTAAATTTAA
1 TTAATATAAATTTAA
17019 ATTATTTCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAATATAAATTTAAT
Found at i:17418 original size:3 final size:3
Alignment explanation
Indices: 17410--17446 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
17400 TTTGATCTTG
17410 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
17447 GTTGCTATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:17874 original size:32 final size:32
Alignment explanation
Indices: 17838--17908 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
17828 TAAATGTATT
* *
17838 GATACATAAGTTTTAAATCGATATAATATATC
1 GATACATAAGTTTTAAATCGAAACAATATATC
*
17870 GATACATAAGTTTTGAATCGAAACAATATATC
1 GATACATAAGTTTTAAATCGAAACAATATATC
17902 GATACAT
1 GATACAT
17909 TAAGCTACCT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (32 bp):
GATACATAAGTTTTAAATCGAAACAATATATC
Found at i:20585 original size:23 final size:25
Alignment explanation
Indices: 20559--20605 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
20549 AGATTAAAAC
*
20559 TTTTATCCAAAA-TCAGG-ATTTGT
1 TTTTATACAAAATTCAGGCATTTGT
20582 TTTTATACAAAATTCAGGCATTTG
1 TTTTATACAAAATTCAGGCATTTG
20606 AAGGGATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 11 0.52
24 5 0.24
25 5 0.24
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.43
Consensus pattern (25 bp):
TTTTATACAAAATTCAGGCATTTGT
Found at i:21269 original size:2 final size:2
Alignment explanation
Indices: 21262--21290 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
21252 GAAAATAATG
21262 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
21291 TAATGTAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21392 original size:19 final size:18
Alignment explanation
Indices: 21364--21404 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
21354 TTAAATTGAA
21364 TAAAAAATAAAAAAATATT
1 TAAAAAATAAAAAAA-ATT
* *
21383 TAAAATATAAAACAAATT
1 TAAAAAATAAAAAAAATT
21401 TAAA
1 TAAA
21405 TGAATCATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (18 bp):
TAAAAAATAAAAAAAATT
Found at i:21394 original size:18 final size:17
Alignment explanation
Indices: 21367--21404 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
21357 AATTGAATAA
21367 AAAATAAAAA-AATATTT
1 AAAATAAAAACAA-ATTT
21384 AAAATATAAAACAAATTT
1 AAAATA-AAAACAAATTT
21402 AAA
1 AAA
21405 TGAATCATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 11 0.58
19 2 0.11
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAATAAAAACAAATTT
Found at i:22446 original size:16 final size:16
Alignment explanation
Indices: 22427--22460 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
22417 TAAAATTATC
22427 TTTAATCATCATTAAA
1 TTTAATCATCATTAAA
* *
22443 TTTAATTATTATTAAA
1 TTTAATCATCATTAAA
22459 TT
1 TT
22461 ATATTTTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTAATCATCATTAAA
Found at i:23283 original size:20 final size:19
Alignment explanation
Indices: 23250--23289 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
23240 TAAAATTTTG
23250 TATTATTTATTCTTTCTCTT
1 TATTATTTATTCTTTC-CTT
23270 TATT-TTTATCTCTTTCCTT
1 TATTATTTAT-TCTTTCCTT
23289 T
1 T
23290 CCTTTCCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.70
Consensus pattern (19 bp):
TATTATTTATTCTTTCCTT
Found at i:23401 original size:10 final size:11
Alignment explanation
Indices: 23361--23407 Score: 53
Period size: 10 Copynumber: 4.4 Consensus size: 11
23351 TCACTCTCAC
*
23361 TCTCTTT-CTA
1 TCTCTTTCCTT
*
23371 TCTATTTCTCTT
1 TCTCTTTC-CTT
23383 TCTCTTTCCTT
1 TCTCTTTCCTT
23394 TC-CTTTCCTT
1 TCTCTTTCCTT
23404 TCTC
1 TCTC
23408 CACCAAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
10 16 0.52
11 6 0.19
12 9 0.29
ACGTcount: A:0.04, C:0.34, G:0.00, T:0.62
Consensus pattern (11 bp):
TCTCTTTCCTT
Found at i:24772 original size:76 final size:78
Alignment explanation
Indices: 24662--24805 Score: 204
Period size: 76 Copynumber: 1.9 Consensus size: 78
24652 TGAATGCTTT
*
24662 TAAAAACTTCATTTTAACAAAAAAAAATACTAAAATGACTCTAA-AGATTTGATTTTGACATGAA
1 TAAAAACTCCATTTTAAC-AAAAAAAATACTAAAATGACTCTAAGAG-TTTGATTTTGACATGAA
24726 AGTGCTAAATGACCC
64 AGTGCTAAATGACCC
* * * *
24741 TAAAAAC-CCATTTTAAC-AAGAAAATATTAAAATGGCTCTAAGAGTTTGGTTTTGACATGAAAG
1 TAAAAACTCCATTTTAACAAAAAAAATACTAAAATGACTCTAAGAGTTTGATTTTGACATGAAAG
24804 TG
66 TG
24806 TTGGCATGAT
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
76 41 0.69
77 2 0.03
78 9 0.15
79 7 0.12
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.30
Consensus pattern (78 bp):
TAAAAACTCCATTTTAACAAAAAAAATACTAAAATGACTCTAAGAGTTTGATTTTGACATGAAAG
TGCTAAATGACCC
Found at i:26132 original size:20 final size:20
Alignment explanation
Indices: 26084--26132 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
26074 CAAATTAATG
* *
26084 TATCCATACATAAGTGAATG
1 TATCAATACATAAGTGAATA
* *
26104 TTTCAATACGTAAGTGAATA
1 TATCAATACATAAGTGAATA
*
26124 TATCGATAC
1 TATCAATAC
26133 TAGACCCTGT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (20 bp):
TATCAATACATAAGTGAATA
Found at i:29823 original size:24 final size:23
Alignment explanation
Indices: 29763--29825 Score: 99
Period size: 24 Copynumber: 2.7 Consensus size: 23
29753 CCGAGTTGTG
29763 TGTTTATTACTTAAAACAATCTA
1 TGTTTATTACTTAAAACAATCTA
*
29786 TGTTTCTTTACTTAAAACAATCTA
1 TGTTT-ATTACTTAAAACAATCTA
29810 TGTTTATTACCTTAAA
1 TGTTTATTA-CTTAAA
29826 GCTTTTATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
23 8 0.22
24 28 0.78
ACGTcount: A:0.35, C:0.14, G:0.05, T:0.46
Consensus pattern (23 bp):
TGTTTATTACTTAAAACAATCTA
Found at i:32228 original size:20 final size:20
Alignment explanation
Indices: 32200--32274 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 20
32190 TTTTACCCAG
32200 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
32220 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
32240 ATGTATAGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
32260 ATGTATCGATACATT
1 ATGTATCGATACATT
32275 CTATCTTTTT
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:36436 original size:2 final size:2
Alignment explanation
Indices: 36431--36474 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
36421 ATGAAAAAAT
36431 TA TA TA 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 TA TA TA
36473 TA
1 TA
36475 CTGTTGTTGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:36765 original size:23 final size:25
Alignment explanation
Indices: 36739--36787 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
36729 AAAATAATTA
36739 AAATACAACA-TAACAT-AAAATAT
1 AAATACAACATTAACATAAAAATAT
* *
36762 AAATACGACATTAATATAAAAATAT
1 AAATACAACATTAACATAAAAATAT
36787 A
1 A
36788 TCAAAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 9 0.41
24 5 0.23
25 8 0.36
ACGTcount: A:0.63, C:0.10, G:0.02, T:0.24
Consensus pattern (25 bp):
AAATACAACATTAACATAAAAATAT
Found at i:38484 original size:9 final size:9
Alignment explanation
Indices: 38463--38492 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
38453 ACATATAATA
38463 TTTATTTTAT
1 TTTATTTT-T
38473 TTTATTTTT
1 TTTATTTTT
38482 TTTATTTTT
1 TTTATTTTT
38491 TT
1 TT
38493 ATATATGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.60
10 8 0.40
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (9 bp):
TTTATTTTT
Found at i:38484 original size:14 final size:14
Alignment explanation
Indices: 38461--38494 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
38451 GGACATATAA
38461 TATTTATTTTATTT
1 TATTTATTTTATTT
*
38475 TATTTTTTTTATTT
1 TATTTATTTTATTT
38489 T-TTTAT
1 TATTTAT
38495 ATATGAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (14 bp):
TATTTATTTTATTT
Found at i:38560 original size:16 final size:16
Alignment explanation
Indices: 38507--38570 Score: 53
Period size: 16 Copynumber: 4.1 Consensus size: 16
38497 ATGAAAATAT
*
38507 TAAAA-TATACAT-AA
1 TAAAATTATATATAAA
*
38521 TATAAATTAT-TAAAATA
1 TA-AAATTATATATAA-A
38538 TAAAATTATATATAAA
1 TAAAATTATATATAAA
* *
38554 TAAAATTTTTTATAAA
1 TAAAATTATATATAAA
38570 T
1 T
38571 TTATAATCTT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
14 2 0.05
15 4 0.10
16 27 0.68
17 7 0.17
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (16 bp):
TAAAATTATATATAAA
Found at i:39042 original size:2 final size:2
Alignment explanation
Indices: 39031--39065 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
39021 TTTTTGGGTT
39031 TA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39066 AGTTTGTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:39397 original size:2 final size:2
Alignment explanation
Indices: 39390--39422 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
39380 ATTATCATGT
39390 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39423 TAAAATTTAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39913 original size:29 final size:29
Alignment explanation
Indices: 39872--39944 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 29
39862 ATAAATTTAC
* *
39872 TTAAATAAATAAAAATA-TAATAATAAAA
1 TTAAATCAATTAAAATATTAATAATAAAA
* *
39900 TTACATCAATTAAAATATTAATAATAAAT
1 TTAAATCAATTAAAATATTAATAATAAAA
*
39929 TTAAATC-ATTCAAATA
1 TTAAATCAATTAAAATA
39945 AGTATAATGG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 22 0.58
29 16 0.42
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.34
Consensus pattern (29 bp):
TTAAATCAATTAAAATATTAATAATAAAA
Found at i:40491 original size:15 final size:16
Alignment explanation
Indices: 40467--40499 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
40457 ATTTTGCATT
*
40467 AATTTATTTTAAATAA
1 AATTTATTTTAAAGAA
40483 AATTT-TTTTAAAGAA
1 AATTTATTTTAAAGAA
40498 AA
1 AA
40500 ATTAAAGGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
AATTTATTTTAAAGAA
Found at i:40531 original size:123 final size:126
Alignment explanation
Indices: 40372--40616 Score: 336
Period size: 123 Copynumber: 2.0 Consensus size: 126
40362 TTAAAAAAAA
* * * * *
40372 AAAAGATTGAAGGTAAATATATCTATTTTTTATAATTTTTTATTCCCTT-TATTTAGGGATTGAC
1 AAAAGATTAAAGGTAAATATATCCATTTTTTATAATTATCTACTCCCTTCTATTTAGGGA-TGAC
* * * *
40436 AAAATTTAATATGCTTTATAGATTTTGCATTAATTTATTTTAAAT-AAAAT-TTTTTTAAAG
65 AAAATTTAATATGCTTTACAGATTTTACATTAATGTATTTCAAATGAAAATGTTTTTTAAAG
* * *
40496 AAAA-ATTAAAGGTAATTCTATCCATTTTTTATAATTATCTACTCCCTTCTATTTAGGGATGATA
1 AAAAGATTAAAGGTAAATATATCCATTTTTTATAATTATCTACTCCCTTCTATTTAGGGATGACA
*
40560 AAATTTAATATGCTTTACAGATTTTACATTGATGTATTTCAAATGAAAATGTTTTTT
66 AAATTTAATATGCTTTACAGATTTTACATTAATGTATTTCAAATGAAAATGTTTTTT
40617 TTTTTTTTTT
Statistics
Matches: 105, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
123 80 0.76
124 19 0.18
125 6 0.06
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.47
Consensus pattern (126 bp):
AAAAGATTAAAGGTAAATATATCCATTTTTTATAATTATCTACTCCCTTCTATTTAGGGATGACA
AAATTTAATATGCTTTACAGATTTTACATTAATGTATTTCAAATGAAAATGTTTTTTAAAG
Found at i:40776 original size:19 final size:19
Alignment explanation
Indices: 40748--40784 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
40738 ATATATTAGA
*
40748 TATATGCTAAAATTATATC
1 TATATACTAAAATTATATC
40767 TATATACTAAAATTATAT
1 TATATACTAAAATTATAT
40785 ATGCTTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (19 bp):
TATATACTAAAATTATATC
Found at i:40917 original size:19 final size:17
Alignment explanation
Indices: 40881--40919 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
40871 ATTTATTTTA
*
40881 TATATTAAAAAATTATT
1 TATATTAAAAAATCATT
40898 TATATTAAAATATATCATT
1 TATATTAAAA-A-ATCATT
40917 TAT
1 TAT
40920 CATATTAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
18 1 0.05
19 8 0.42
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (17 bp):
TATATTAAAAAATCATT
Found at i:41221 original size:15 final size:15
Alignment explanation
Indices: 41174--41229 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 15
41164 AAATTTATAT
*
41174 TAATAAATTATTAATA
1 TAATATATT-TTAATA
* *
41190 TATTAATTTTTTAAATA
1 TAAT-ATATTTT-AATA
41207 TAATATATTTTAATA
1 TAATATATTTTAATA
41222 TAAT-TATT
1 TAATATATT
41230 AAAATAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
14 4 0.12
15 8 0.24
16 11 0.33
17 10 0.30
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TAATATATTTTAATA
Found at i:42422 original size:77 final size:77
Alignment explanation
Indices: 42326--42479 Score: 308
Period size: 77 Copynumber: 2.0 Consensus size: 77
42316 ATTACATATA
42326 TTAATATTTGATAAAATTAAAACATCTAGGAGCTAGTGATTCCTTGCATAGATTATCTAAAACGT
1 TTAATATTTGATAAAATTAAAACATCTAGGAGCTAGTGATTCCTTGCATAGATTATCTAAAACGT
42391 GTATAATACAGG
66 GTATAATACAGG
42403 TTAATATTTGATAAAATTAAAACATCTAGGAGCTAGTGATTCCTTGCATAGATTATCTAAAACGT
1 TTAATATTTGATAAAATTAAAACATCTAGGAGCTAGTGATTCCTTGCATAGATTATCTAAAACGT
42468 GTATAATACAGG
66 GTATAATACAGG
42480 GGGGTACCTG
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 77 1.00
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.34
Consensus pattern (77 bp):
TTAATATTTGATAAAATTAAAACATCTAGGAGCTAGTGATTCCTTGCATAGATTATCTAAAACGT
GTATAATACAGG
Found at i:44169 original size:21 final size:20
Alignment explanation
Indices: 44136--44176 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
44126 ATCAAAGAAA
*
44136 GGAAGAAGAAAAAAGAAAAAG
1 GGAAAAAGAAAAAA-AAAAAG
*
44157 GGAAAAAGGAAAAAAAAAAG
1 GGAAAAAGAAAAAAAAAAAG
44177 AGTGAAAGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (20 bp):
GGAAAAAGAAAAAAAAAAAG
Found at i:47392 original size:15 final size:14
Alignment explanation
Indices: 47377--47423 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 14
47367 AATTATATTA
47377 TATTATTTTA-TTT
1 TATTATTTTATTTT
47390 TATTATTTTTATTTT
1 TATTA-TTTTATTTT
47405 TATTATTTTTATATTT
1 TATTA-TTTTAT-TTT
47421 TAT
1 TAT
47424 GAAAGGATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
13 5 0.16
14 5 0.16
15 15 0.48
16 6 0.19
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TATTATTTTATTTT
Found at i:50150 original size:19 final size:20
Alignment explanation
Indices: 50113--50152 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
50103 GTAAGTTCTT
* *
50113 ATTTGCTTTTATTCGTTAAA
1 ATTTGCTTTTATGCATTAAA
50133 ATTT-CTTTTATGCATTAAA
1 ATTTGCTTTTATGCATTAAA
50152 A
1 A
50153 GTGTTAGCCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (20 bp):
ATTTGCTTTTATGCATTAAA
Found at i:60516 original size:21 final size:20
Alignment explanation
Indices: 60494--60546 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
60484 AATTTTAATA
*
60494 AAATAAAATAAAAATTAAAT
1 AAATAAAATAAAAATAAAAT
* *
60514 AAATAATAATCATAATAAAAT
1 AAATAA-AATAAAAATAAAAT
60535 AAATAAATATAA
1 AAATAAA-ATAA
60547 TCTTTTAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 7 0.26
21 20 0.74
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (20 bp):
AAATAAAATAAAAATAAAAT
Found at i:60518 original size:25 final size:25
Alignment explanation
Indices: 60490--60548 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
60480 AAATAATTTT
60490 AATAA-AAT-AAAATAAAAATTAAATA
1 AATAATAATCAAAAT-AAAA-TAAATA
*
60515 AATAATAATCATAATAAAATAAATA
1 AATAATAATCAAAATAAAATAAATA
60540 AAT-ATAATC
1 AATAATAATC
60549 TTTTAAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
24 6 0.19
25 14 0.45
26 7 0.23
27 4 0.13
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.27
Consensus pattern (25 bp):
AATAATAATCAAAATAAAATAAATA
Found at i:60563 original size:25 final size:24
Alignment explanation
Indices: 60502--60561 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 24
60492 TAAAATAAAA
60502 TAAAAATTAAATAAATAATAATCAT
1 TAAAAA-TAAATAAATAATAATCAT
* *
60527 AATAAAATAAATAAAT-ATAATCTTT
1 TA-AAAATAAATAAATAATAATC-AT
60552 TAAAAATAAA
1 TAAAAATAAA
60562 ATTTTCATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
24 14 0.47
25 12 0.40
26 4 0.13
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (24 bp):
TAAAAATAAATAAATAATAATCAT
Found at i:68014 original size:2 final size:2
Alignment explanation
Indices: 68007--68036 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
67997 TAATCTTTGA
*
68007 AT AT AT AT AC 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
68037 GTTTCCAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:69716 original size:30 final size:30
Alignment explanation
Indices: 69616--69739 Score: 112
Period size: 30 Copynumber: 4.2 Consensus size: 30
69606 ACGTTTCATT
* * *
69616 TTCATCAATAACCTTTAAAAATTATATTTA
1 TTCATCTATAACTTTTAAAAATTACATTTA
* * ** *
69646 TT-ATTTATAATTTTTATTAATGTATTATTT-
1 TTCATCTATAACTTTTAAAAAT-TA-CATTTA
* *
69676 GT-ATCCATAACTTTTAAAAATTACATTTA
1 TTCATCTATAACTTTTAAAAATTACATTTA
69705 TTCATCTATAACTTTTAAAAATTACATTTA
1 TTCATCTATAACTTTTAAAAATTACATTTA
69735 -TCATC
1 TTCATC
69740 AATATTTTTT
Statistics
Matches: 75, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
28 4 0.05
29 21 0.28
30 45 0.60
31 5 0.07
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (30 bp):
TTCATCTATAACTTTTAAAAATTACATTTA
Found at i:74026 original size:20 final size:20
Alignment explanation
Indices: 74001--74072 Score: 90
Period size: 20 Copynumber: 3.6 Consensus size: 20
73991 TACCCAGATG
74001 TATCGATACATTTTTCAATA
1 TATCGATACATTTTTCAATA
* * *
74021 TATCGATACATGTATGAATA
1 TATCGATACATTTTTCAATA
* * *
74041 TATCGATATATTCTTCAATG
1 TATCGATACATTTTTCAATA
74061 TATCGATACATT
1 TATCGATACATT
74073 ATGTCTTTTT
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.42
Consensus pattern (20 bp):
TATCGATACATTTTTCAATA
Found at i:88077 original size:14 final size:13
Alignment explanation
Indices: 88060--88111 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 13
88050 ACACAAAAAA
88060 AAAACAAAAAAAGC
1 AAAA-AAAAAAAGC
*
88074 AAAACAAAAAAAAC
1 AAAA-AAAAAAAGC
*
88088 TAAGAAAAAAATAGC
1 -AA-AAAAAAAAAGC
88103 AAAAAAAAA
1 AAAAAAAAA
88112 GAAAGAGGTC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
13 7 0.21
14 15 0.45
15 9 0.27
16 2 0.06
ACGTcount: A:0.81, C:0.10, G:0.06, T:0.04
Consensus pattern (13 bp):
AAAAAAAAAAAGC
Found at i:89365 original size:28 final size:28
Alignment explanation
Indices: 89325--90119 Score: 659
Period size: 28 Copynumber: 27.5 Consensus size: 28
89315 ATGTTCATCC
*
89325 CTTTCAAAGCCCACGAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
* *
89353 CTTTTAAAGCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
* *
89381 CTTTCAAAGCCCACAAGTTAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
89409 CTTTCAGAGCCCACGAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
* *
89437 CTTTCGAAGACCACAAGTCAGTGGCACTT
1 CTTTCAAAGCCCACAAGTCAGTGGCAC-T
* *
89466 TTTTCAAAGCCCACAATTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
89494 CTTTTCAAAGCCCACAAGTTAGTGGCACT
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
* *
89523 CTTTCAAAGCCCACAAGCCAGTGGCGC-
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
* *
89550 CTTTTC-GAGCCCACGAGTCAGTGGCACT
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
*
89578 CTTTCAAAGCCCATAAGTCAGTGGCA-T
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
* *
89605 CCTTTCAAAGCCCATGCAAGTTAGTGGCACC
1 -CTTTCAAAGCCCA--CAAGTCAGTGGCACT
*
89636 CTTTTAAAGCCCATGCAAGTCAGTGGCACT
1 CTTTCAAAGCCCA--CAAGTCAGTGGCACT
* ** *
89666 CATTTGAAAGCCCACACAAGTTGGTGGCAACC
1 C-TTTCAAAG-CC-CACAAGTCAGTGGC-ACT
*
89698 CATTTCAAAGCCCACAGAAG-CTGGTGGCAACCT
1 C-TTTCAAAGCCCAC--AAGTC-AGTGGC-A-CT
* **
89731 ATTTCAAAGCCCACACAAGTTGGTGGCAAC-
1 CTTTCAAAG-CC-CACAAGTCAGTGGC-ACT
* * *
89761 CATTTGAAACCCCATACAA-TCGGTGGCAACT
1 C-TTTCAAAGCCC--ACAAGTCAGTGGC-ACT
** *
89792 CATTTCAAAGCCCACACAAGTTGGTGGCAACC
1 C-TTTCAAAG-CC-CACAAGTCAGTGGC-ACT
89824 CATTTCAAAGCCCACACAAGTC-GATGGCA-T
1 C-TTTCAAAG-CC-CACAAGTCAG-TGGCACT
*
89854 CTTTTCAAAGCCCACAAGTCAGTGGCACC
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
89883 CTTTCAAAGCCCACAAGTCAGTGGCA-T
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
* * **
89910 CCTTTCAATGTCCACAAGTTGGTGGCA-T
1 -CTTTCAAAGCCCACAAGTCAGTGGCACT
* *
89938 CTTTTCAAAGCCCACAAGTCAATGGTA-T
1 C-TTTCAAAGCCCACAAGTCAGTGGCACT
**
89966 CTTTTCCGAGCCCACAAGTCAGTGGCAACT
1 C-TTTCAAAGCCCACAAGTCAGTGGC-ACT
*
89996 -TTTCAAAGCCCACGAGTCAGTGGCAACT
1 CTTTCAAAGCCCACAAGTCAGTGGC-ACT
* *
90024 -TTTCAAAGCCCACGAGTCAATGGCA-T
1 CTTTCAAAGCCCACAAGTCAGTGGCACT
*
90050 CCTTCCAAAGCCCACAAGTCAGTGGCA-T
1 -CTTTCAAAGCCCACAAGTCAGTGGCACT
*
90078 CCTTTCAAAGCCAACAAGTCAGTGGCATCT
1 -CTTTCAAAGCCCACAAGTCAGTGGCA-CT
90108 CTTT-AAAGCCCA
1 CTTTCAAAGCCCA
90120 AAGAAGTTAG
Statistics
Matches: 647, Mismatches: 82, Indels: 76
0.80 0.10 0.09
Matches are distributed among these distances:
26 1 0.00
27 25 0.04
28 364 0.56
29 59 0.09
30 65 0.10
31 44 0.07
32 80 0.12
33 6 0.01
34 3 0.00
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (28 bp):
CTTTCAAAGCCCACAAGTCAGTGGCACT
Found at i:89708 original size:32 final size:32
Alignment explanation
Indices: 89607--89897 Score: 289
Period size: 32 Copynumber: 9.4 Consensus size: 32
89597 AGTGGCATCC
** *
89607 TTTCAAAGCCCATGCAAGTTAGTGGC-ACCC-
1 TTTCAAAGCCCACACAAGTTGGTGGCAACCCA
* ** ** *
89637 TTTTAAAGCCCATGCAAGTCAGTGGC-ACTCA
1 TTTCAAAGCCCACACAAGTTGGTGGCAACCCA
*
89668 TTTGAAAGCCCACACAAGTTGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTTGGTGGCAACCCA
* * *
89700 TTTCAAAGCCCACAGAAGCTGGTGGCAACCTA
1 TTTCAAAGCCCACACAAGTTGGTGGCAACCCA
89732 TTTCAAAGCCCACACAAGTTGGTGGCAA-CCA
1 TTTCAAAGCCCACACAAGTTGGTGGCAACCCA
* * * * *
89763 TTTGAAACCCCATACAA-TCGGTGGCAACTCA
1 TTTCAAAGCCCACACAAGTTGGTGGCAACCCA
89794 TTTCAAAGCCCACACAAGTTGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTTGGTGGCAACCCA
* * * *
89826 TTTCAAAGCCCACACAAGTCGATGGC-A-TCT
1 TTTCAAAGCCCACACAAGTTGGTGGCAACCCA
**
89856 TTTCAAAG-CC-CACAAGTCAGTGGC-ACCC-
1 TTTCAAAGCCCACACAAGTTGGTGGCAACCCA
89884 TTTCAAAGCCCACA
1 TTTCAAAGCCCACA
89898 AGTCAGTGGC
Statistics
Matches: 221, Mismatches: 33, Indels: 14
0.82 0.12 0.05
Matches are distributed among these distances:
28 21 0.10
29 5 0.02
30 47 0.21
31 54 0.24
32 94 0.43
ACGTcount: A:0.31, C:0.30, G:0.19, T:0.21
Consensus pattern (32 bp):
TTTCAAAGCCCACACAAGTTGGTGGCAACCCA
Found at i:89817 original size:94 final size:95
Alignment explanation
Indices: 89565--89897 Score: 327
Period size: 94 Copynumber: 3.6 Consensus size: 95
89555 CGAGCCCACG
* * * * * **
89565 AGTCAGTGGCACTC-TTTCAAA-GCC-CATAAGTCAGTGGC-ATCC-TTTCAAAGCCCATGCAAG
1 AGTCAGTGGCACTCATTTGAAACCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAG
* * **
89625 TTAGTGGCACCCT-TTT-AAAGCCCATGCA
66 TTGGTGGCAACCTATTTCAAAGCCCACACA
* * *
89653 AGTCAGTGGCACTCATTTGAAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCCACAGAAG
1 AGTCAGTGGCACTCATTTGAAACCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAG
*
89718 CTGGTGGCAACCTATTTCAAAGCCCACACA
66 TTGGTGGCAACCTATTTCAAAGCCCACACA
** * *
89748 AGTTGGTGGCAAC-CATTTGAAACCCCATACAA-TCGGTGGCAACTCATTTCAAAGCCCACACAA
1 AGTCAGTGGC-ACTCATTTGAAACCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAA
*
89811 GTTGGTGGCAACCCATTTCAAAGCCCACACA
65 GTTGGTGGCAACCTATTTCAAAGCCCACACA
* * * *
89842 AGTC-GATGGCA-TCTTTTCAAA-GCC-CACAAGTCAGTGGC-ACCC-TTTCAAAGCCCACA
1 AGTCAG-TGGCACTCATTTGAAACCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACA
89898 AGTCAGTGGC
Statistics
Matches: 204, Mismatches: 30, Indels: 20
0.80 0.12 0.08
Matches are distributed among these distances:
88 14 0.07
89 6 0.03
90 16 0.08
91 18 0.09
92 12 0.06
93 34 0.17
94 67 0.33
95 35 0.17
96 2 0.01
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (95 bp):
AGTCAGTGGCACTCATTTGAAACCCCACACAAGTCGGTGGCAACCCATTTCAAAGCCCACACAAG
TTGGTGGCAACCTATTTCAAAGCCCACACA
Found at i:90737 original size:20 final size:20
Alignment explanation
Indices: 90709--90783 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 20
90699 TTTTACCCAG
90709 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
90729 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
90749 ATGTATCGATATATTCTTCA
1 ATGTATCGATACATTTTTCA
90769 ATGTATCGATACATT
1 ATGTATCGATACATT
90784 ATGTCTTTTT
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:90769 original size:40 final size:39
Alignment explanation
Indices: 90709--90786 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
90699 TTTTACCCAG
*
90709 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTTCAATATATCGATACAT-TATGA
* *
90749 ATGTATCGATATATTCTTCAATGTATCGATACATTATG
1 ATGTATCGATACATTCTTCAATATATCGATACATTATG
90787 TCTTTTTACC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (39 bp):
ATGTATCGATACATTCTTCAATATATCGATACATTATGA
Found at i:94834 original size:17 final size:17
Alignment explanation
Indices: 94789--94835 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
94779 AATTATAATG
94789 CAAAACAATAAATAATTT
1 CAAAA-AATAAATAATTT
* *
94807 GAAAAAGTAAATAA-TT
1 CAAAAAATAAATAATTT
94823 CAATAAAATAAAT
1 CAA-AAAATAAAT
94836 GAAGCAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 4 0.17
17 16 0.67
18 4 0.17
ACGTcount: A:0.64, C:0.06, G:0.04, T:0.26
Consensus pattern (17 bp):
CAAAAAATAAATAATTT
Found at i:95860 original size:4 final size:4
Alignment explanation
Indices: 95851--95877 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
95841 ATTTGCACAA
95851 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
95878 AGATGAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:96279 original size:26 final size:26
Alignment explanation
Indices: 96204--96309 Score: 107
Period size: 26 Copynumber: 4.2 Consensus size: 26
96194 TTTTATTTTT
*
96204 AATTATATTATATATAATATA-AATAA
1 AATTATA-TATATATAATATATATTAA
*
96230 AATTATATATATATAATA-GT-TTAA
1 AATTATATATATATAATATATATTAA
96254 AATTATATA-ATATAATATATCATTAA
1 AATTATATATATATAATATAT-ATTAA
* *
96280 TATTATAT-TATATAATA-ATATAAA
1 AATTATATATATATAATATATATTAA
96304 TAATTA
1 -AATTA
96310 ATACTTTAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
23 8 0.12
24 17 0.25
25 17 0.25
26 26 0.38
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (26 bp):
AATTATATATATATAATATATATTAA
Found at i:97729 original size:22 final size:21
Alignment explanation
Indices: 97704--97760 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 21
97694 TTCACAGAGA
97704 TATACATATATTTATAATACAT
1 TATACATATATTTA-AATACAT
97726 TATACA-AT-TTTAAAT-CAT
1 TATACATATATTTAAATACAT
97744 TATACATATTATTTAAA
1 TATACATA-TATTTAAA
97761 ATAAATATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
18 9 0.28
19 4 0.12
20 5 0.16
21 8 0.25
22 6 0.19
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.46
Consensus pattern (21 bp):
TATACATATATTTAAATACAT
Found at i:97762 original size:22 final size:22
Alignment explanation
Indices: 97704--97763 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
97694 TTCACAGAGA
*
97704 TATACATATATTTATAATACAT
1 TATACATATATTTAAAATACAT
97726 TATACA-AT-TTT-AAAT-CAT
1 TATACATATATTTAAAATACAT
97744 TATACATATTATTTAAAATA
1 TATACATA-TATTTAAAATA
97764 AATATATTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
18 9 0.28
19 4 0.12
20 4 0.12
21 5 0.16
22 10 0.31
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (22 bp):
TATACATATATTTAAAATACAT
Found at i:97769 original size:22 final size:21
Alignment explanation
Indices: 97703--97769 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 21
97693 ATTCACAGAG
*
97703 ATATACATATATTTATAATACA
1 ATATACATATATTTAAAATA-A
* *
97725 TTATACA-AT-TTT-AAATCA
1 ATATACATATATTTAAAATAA
*
97743 TTATACATATTATTTAAAATAA
1 ATATACATA-TATTTAAAATAA
97765 ATATA
1 ATATA
97770 TTAATTTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 8 0.22
19 4 0.11
20 4 0.11
21 5 0.14
22 15 0.42
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.43
Consensus pattern (21 bp):
ATATACATATATTTAAAATAA
Found at i:97864 original size:21 final size:21
Alignment explanation
Indices: 97838--97886 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
97828 AATAAATCAT
97838 ATTTAATAATTTAAA-AAAATC
1 ATTTAA-AATTTAAATAAAATC
97859 ATTTAAAATTTAAATAAAAT-
1 ATTTAAAATTTAAATAAAATC
97879 ATATTAAA
1 AT-TTAAA
97887 TAGTAATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
ATTTAAAATTTAAATAAAATC
Found at i:97870 original size:20 final size:22
Alignment explanation
Indices: 97838--97878 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
97828 AATAAATCAT
97838 ATTTAATAATTTAAA-AAAATC
1 ATTTAATAATTTAAATAAAATC
97859 ATTTAA-AATTTAAATAAAAT
1 ATTTAATAATTTAAATAAAAT
97879 ATATTAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
ATTTAATAATTTAAATAAAATC
Found at i:105879 original size:2 final size:2
Alignment explanation
Indices: 105872--105897 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
105862 AATGGAACTT
105872 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
105898 CGCGTGAGAG
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:105908 original size:2 final size:2
Alignment explanation
Indices: 105903--105965 Score: 101
Period size: 2 Copynumber: 32.0 Consensus size: 2
105893 GTGTGCGCGT
105903 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA -A
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
* *
105944 GA GA GA GA GG GA GA GA CA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA
105966 TCTATATTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
1 1 0.02
2 55 0.98
ACGTcount: A:0.49, C:0.02, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:115729 original size:20 final size:19
Alignment explanation
Indices: 115704--115751 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
115694 CTCATGTATT
*
115704 GATACAATTGTCCATTTATC
1 GATACAA-TGACCATTTATC
*
115724 GATACAATGAGCATTTATC
1 GATACAATGACCATTTATC
*
115743 GATATAATG
1 GATACAATG
115752 TATCGATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (19 bp):
GATACAATGACCATTTATC
Found at i:120503 original size:13 final size:13
Alignment explanation
Indices: 120485--120512 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
120475 ATACAAAGAT
120485 CAATGTATCGATA
1 CAATGTATCGATA
120498 CAATGTATCGATA
1 CAATGTATCGATA
120511 CA
1 CA
120513 TTTGAGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:120593 original size:13 final size:13
Alignment explanation
Indices: 120575--120599 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
120565 CAAAAAAATA
120575 TGTATCGATACAT
1 TGTATCGATACAT
120588 TGTATCGATACA
1 TGTATCGATACA
120600 ACATTTTATT
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:122993 original size:20 final size:21
Alignment explanation
Indices: 122968--123016 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
122958 GGAAAAGATT
*
122968 TTTTTATTATAAAATT-TATA
1 TTTTTATAATAAAATTATATA
*
122988 TTTTTATAATATAATTATATA
1 TTTTTATAATAAAATTATATA
123009 -TTTTATAA
1 TTTTTATAA
123017 GAATAGTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 22 0.85
21 4 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTTTATAATAAAATTATATA
Found at i:123546 original size:27 final size:29
Alignment explanation
Indices: 123512--123579 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 29
123502 TATCCTTAAA
123512 AAGTAAA-TTATTAAATTATTA-ATTTTT
1 AAGTAAATTTATTAAATTATTATATTTTT
*
123539 AAGTAAATTTTTATTATATTATTATATTTTT
1 AAGTAAA--TTTATTAAATTATTATATTTTT
*
123570 AA-TATATTTA
1 AAGTAAATTTA
123580 ATTATTTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
27 7 0.20
28 4 0.11
30 16 0.46
31 8 0.23
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (29 bp):
AAGTAAATTTATTAAATTATTATATTTTT
Found at i:123585 original size:19 final size:19
Alignment explanation
Indices: 123545--123586 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
123535 TTTTAAGTAA
* *
123545 ATTTTTATTATATTATTAT
1 ATTTTTAATATATTAATAT
123564 ATTTTTAATATATTTAAT-T
1 ATTTTTAATATA-TTAATAT
123583 ATTT
1 ATTT
123587 ATTTATTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
ATTTTTAATATATTAATAT
Found at i:123634 original size:18 final size:19
Alignment explanation
Indices: 123604--123642 Score: 71
Period size: 18 Copynumber: 2.1 Consensus size: 19
123594 GAAATCTATA
123604 TTTATATATAAATTAATTT
1 TTTATATATAAATTAATTT
123623 TTTATATA-AAATTAATTT
1 TTTATATATAAATTAATTT
123641 TT
1 TT
123643 CAAATAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTATATATAAATTAATTT
Found at i:123649 original size:18 final size:18
Alignment explanation
Indices: 123613--123649 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
123603 ATTTATATAT
* *
123613 AAATTAATTTTTTATATA
1 AAATTAATTTTTCAAATA
123631 AAATTAATTTTTCAAATA
1 AAATTAATTTTTCAAATA
123649 A
1 A
123650 TTTATTATTA
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:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (18 bp):
AAATTAATTTTTCAAATA
Found at i:124770 original size:77 final size:78
Alignment explanation
Indices: 124643--124839 Score: 209
Period size: 77 Copynumber: 2.5 Consensus size: 78
124633 AATAACGGGG
* * * * * ** * *
124643 TTGGAGTGTTCCCTTGAAAATAACGGGGCTGGAGTATCTCCGGTTGTGAGAAATCGATGA-TT-A
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAAT-ATTTGA
*
124706 GAAAAAAATCGAGA
65 GAAAAAAACCGAGA
*
124720 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGG
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATA-TTTGA
* * * *
124785 GAATAAAGCCGGGG
65 GAAAAAAACCGAGA
* *
124799 TTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCC
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCC
124840 GATGAAATAA
Statistics
Matches: 100, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
76 1 0.01
77 49 0.49
78 2 0.02
79 48 0.48
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.25
Consensus pattern (78 bp):
TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTGAG
AAAAAAACCGAGA
Found at i:124834 original size:28 final size:28
Alignment explanation
Indices: 124794--124865 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
124784 GGAATAAAGC
** *
124794 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
124822 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
124850 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
124866 TCGACTGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:125121 original size:27 final size:26
Alignment explanation
Indices: 125057--125132 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 26
125047 GAAATAAAGT
*
125057 CGGGGTTGGAGTATCCCCTCGAAAATAA
1 CGGGGTTGGAGTAT-CCC-CGATAATAA
*
125085 CGGGGTTGGAGTATCCCCGATGATCAA
1 CGGGGTTGGAGTATCCCCGATAAT-AA
125112 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
125133 TGTGAAGAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
26 5 0.11
27 26 0.58
28 14 0.31
ACGTcount: A:0.22, C:0.22, G:0.33, T:0.22
Consensus pattern (26 bp):
CGGGGTTGGAGTATCCCCGATAATAA
Found at i:125212 original size:263 final size:262
Alignment explanation
Indices: 124743--125243 Score: 799
Period size: 263 Copynumber: 1.9 Consensus size: 262
124733 TCGAAAATAA
* * * *
124743 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAGTAT
1 CGGGGTTGGAATATCCCCAATTATGAAAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTAT
* * *
124808 CCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGACTG
66 CCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATG-AATAACGAGGTTGGAGTATCCCCGACTG
*
124873 TGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGT
130 TGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTAGT
* *
124938 GTTTCGAAAATAAAATCGGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAA
195 GTTTCGAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAA
125003 AAC
260 AAC
* *
125006 CGGGGTTGGAATATCCCCGATTATGAAAAATCAATATTTTAGAAATAAAGTCGGGGTTGGAGTAT
1 CGGGGTTGGAATATCCCCAATTATGAAAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTAT
* *
125071 CCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATG-ATCAACGGGGTTGGAGTATCCCCGATTG
66 CCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGAAT-AACGAGGTTGGAGTATCCCCGACTG
* *
125135 TGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTATA-GAAAATTA
130 TGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTA
*
125199 GTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGGA
193 GTGTTTCGAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGGA
125244 GAATTGAGAA
Statistics
Matches: 218, Mismatches: 17, Indels: 6
0.90 0.07 0.02
Matches are distributed among these distances:
261 2 0.01
262 26 0.12
263 150 0.69
264 40 0.18
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (262 bp):
CGGGGTTGGAATATCCCCAATTATGAAAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTAT
CCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGAATAACGAGGTTGGAGTATCCCCGACTGT
GAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTAGTG
TTTCGAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAA
AC
Found at i:125220 original size:51 final size:52
Alignment explanation
Indices: 124853--125238 Score: 250
Period size: 52 Copynumber: 7.4 Consensus size: 52
124843 GAAATAACGA
* * * * * *
124853 GGTTGGAGTATCCTCGACTGT-GAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATAGAAAAATTAGT-GTTTTGAAAATAAAATCGG
* * * * *
124905 AGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTCGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATAGAAAAATTAGTGTTTTGAAAATAAAATCGG
* * * *
124957 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTT-AGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTATAGAAAAATTAGTGTTTTGA-AAATAAAATCGG
* * * * *
125009 GGTTGGAATATCCCCGATTAT-GAAAAATCAATATTTT-AGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATAGAAAAATTAGTGTTTTGA-AAATAAAATCGG
** **** * *** ** *
125060 GGTTGGAGTATCCCCTCGAAAATA-ACGGGGTTGGAGTATCCCCGATGAT-CAA-CGG
1 GGTTGGAGTAT-CCC-CGATTATAGA-AAAATT--AGTGT-TTTGAAAATAAAATCGG
* * *
125115 GGTTGGAGTATCCCCGATTGT-GAAGAAATTGGTGTTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATAGAA-AAATTAGTG--TTTTGAAAATAAAATCGG
*
125169 AGTTGGAGTATCCCCGATTATAG-AAAATTAGTGTTTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATAGAAAAATTAGTGTTTTGAAAATAAAATCGG
* *
125220 AGTTGGAATATCCCCGATT
1 GGTTGGAGTATCCCCGATT
125239 GTGGAGAATT
Statistics
Matches: 254, Mismatches: 63, Indels: 35
0.72 0.18 0.10
Matches are distributed among these distances:
51 72 0.28
52 98 0.39
53 34 0.13
54 27 0.11
55 15 0.06
56 5 0.02
57 2 0.01
58 1 0.00
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (52 bp):
GGTTGGAGTATCCCCGATTATAGAAAAATTAGTGTTTTGAAAATAAAATCGG
Found at i:127548 original size:13 final size:13
Alignment explanation
Indices: 127530--127555 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
127520 ACAAAGATCC
127530 ATGTATCGATACA
1 ATGTATCGATACA
127543 ATGTATCGATACA
1 ATGTATCGATACA
127556 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:127551 original size:33 final size:33
Alignment explanation
Indices: 127509--127575 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
127499 AAAATTTCCA
***
127509 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
127542 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
127575 A
1 A
127576 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:127616 original size:13 final size:13
Alignment explanation
Indices: 127598--127622 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
127588 TAGCTAATTA
127598 TGTATCGATACAT
1 TGTATCGATACAT
127611 TGTATCGATACA
1 TGTATCGATACA
127623 AAACTTATGT
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:127722 original size:21 final size:22
Alignment explanation
Indices: 127679--127756 Score: 108
Period size: 21 Copynumber: 3.7 Consensus size: 22
127669 GTTGGGACCC
* * *
127679 TGTATCGATACTTTTGTA-GAA
1 TGTATCGATACATTTCTACAAA
127700 TGTATCGATACATTTC-ACAAA
1 TGTATCGATACATTTCTACAAA
127721 TGTATCGATACA-TTCTACAAA
1 TGTATCGATACATTTCTACAAA
127742 TGTATCGATACATTT
1 TGTATCGATACATTT
127757 GGAAATTTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
20 4 0.08
21 45 0.88
22 2 0.04
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (22 bp):
TGTATCGATACATTTCTACAAA
Found at i:127879 original size:10 final size:10
Alignment explanation
Indices: 127864--127888 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
127854 TGTTGGTCTT
127864 AAATTGTCGA
1 AAATTGTCGA
127874 AAATTGTCGA
1 AAATTGTCGA
127884 AAATT
1 AAATT
127889 CATCCCCACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (10 bp):
AAATTGTCGA
Found at i:128696 original size:26 final size:26
Alignment explanation
Indices: 128667--128754 Score: 72
Period size: 26 Copynumber: 3.3 Consensus size: 26
128657 GTGGGCTTTA
128667 AAAGGTGTCCTGCTCTTTGGGGACTG
1 AAAGGTGTCCTGCTCTTTGGGGACTG
** * *
128693 AAAGGTG-CCACCAAC-TTGTGTGAGCTTTG
1 AAAGGTGTCCTGC-TCTTTG-GGGA-C--TG
*
128722 AAAGGGGTCCTGCTCTTTGGGGACTG
1 AAAGGTGTCCTGCTCTTTGGGGACTG
128748 AAAGGTG
1 AAAGGTG
128755 CCACCAACTT
Statistics
Matches: 45, Mismatches: 10, Indels: 14
0.65 0.14 0.20
Matches are distributed among these distances:
25 6 0.13
26 19 0.42
27 1 0.02
28 1 0.02
29 12 0.27
30 6 0.13
ACGTcount: A:0.20, C:0.18, G:0.34, T:0.27
Consensus pattern (26 bp):
AAAGGTGTCCTGCTCTTTGGGGACTG
Found at i:128869 original size:59 final size:59
Alignment explanation
Indices: 128509--129480 Score: 1107
Period size: 55 Copynumber: 16.9 Consensus size: 59
128499 ATAAAGTGTA
* * * * *
128509 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTT----G-AAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * *
128564 CCCTGCTCTTTGAGGACTGAAATGTGCCACCAACTTGTGTGGGCTTT--AAG---AGGTG
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* ** * *
128619 TCCTGCTCTTTAAGGACTGGAAAATGCCATCAACTTGTGTGGGCTTT-----AAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * *
128674 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGAGCTTT----G-AAAGGGG
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * *
128729 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCG
*
128790 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * *
128849 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCG
* *
128909 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGGGTGGACTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * *
128968 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAATGTG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * *
129027 TCCCGCTTTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTT--AAG---AGGTG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* ** * *
129081 TCCTGCTCTCTGAGGACTGGAAAATGACACCAACTTGTGTGGGCTTT----G-AAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* ** *
129136 ACCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT----G-AAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* *
129191 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCG
* *
129252 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTCGGGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * *
129311 TCCCGCTCTTTAAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCA
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* **
129370 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGGAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* *
129429 TCCTGCTCTTTGAGGACTGGGAA-GTGCCACCATCTTGTGTGGGTTTTAAAAG
1 TCCTGCTCTTTGAGGACT--GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAG
129481 GTGTCCTGCT
Statistics
Matches: 815, Mismatches: 74, Indels: 51
0.87 0.08 0.05
Matches are distributed among these distances:
53 1 0.00
54 21 0.03
55 304 0.37
56 1 0.00
57 4 0.00
59 302 0.37
60 134 0.16
61 48 0.06
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.26
Consensus pattern (59 bp):
TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
Found at i:129240 original size:462 final size:462
Alignment explanation
Indices: 128572--129480 Score: 1554
Period size: 462 Copynumber: 2.0 Consensus size: 462
128562 CGCCCTGCTC
* *
128572 TTTGAGGACTGAAATGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTAAGGACT
1 TTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTCTAAGGACT
* * * * *
128637 GGAAAATGCCATCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGGGGACTGAAAGGTGCC
66 GGAAAATGACACCAACTTGTGTGGGCTTTAAAAGGTGACCTGCTCTTTGAGGACTGAAAGATGCC
*
128702 ACCAACTTGTGTGAGCTTTGAAAGGGGTCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGT
131 ACCAACTTGTGTGAGCTTTGAAAGGGGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGT
*
128767 GTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGGGTGGG
196 GTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTCGGGTGGG
*
128832 CTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTGA
261 CTTTAAAAGAAAAGGCGTCCCGCTCTTTAAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTT-A
*
128897 AAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGGGTGGACTTTAAAAGAA
325 AAAGAAAAAGCATCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGGGTGGACTTTAAAAGAA
128962 AAGGCGTCCCGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAATGT
390 AAGGCGTCCCGCTCTTTGAGGACTGGAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGAAAATGT
129026 GTCCCGCTT
454 GTCCCGCTT
*
129035 TTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTCTGAGGACT
1 TTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTCTAAGGACT
*
129099 GGAAAATGACACCAACTTGTGTGGGCTTTGAAAGGTGACCTGCTCTTTGAGGACTGGAAA-ATGC
66 GGAAAATGACACCAACTTGTGTGGGCTTTAAAAGGTGACCTGCTCTTTGAGGACT-GAAAGATGC
* *
129163 CACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTG
130 CACCAACTTGTGTGAGCTTTGAAAGGGGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTG
129228 TGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTCGGGTGG
195 TGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTCGGGTGG
129293 GCTTTAAAAGAAAAGGCGTCCCGCTCTTTAAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTA
260 GCTTTAAAAGAAAAGGCGTCCCGCTCTTTAAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTA
* * * **
129358 AAAGAAAAGGCATCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGG
325 AAAGAAAAAGCATCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGGGTGGACTTTAAAAGAA
* * *
129423 AAGGCGTCCTGCTCTTTGAGGACTGGGAAGTGCCACCATCTTGTGTGGGTTTTAAAAG
390 AAGGCGTCCCGCTCTTTGAGGACT-GGAAGTGCCACCAACTTGTGTGGGCTTTAAAAG
129481 GTGTCCTGCT
Statistics
Matches: 420, Mismatches: 23, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
461 83 0.20
462 319 0.76
463 18 0.04
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (462 bp):
TTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTCTAAGGACT
GGAAAATGACACCAACTTGTGTGGGCTTTAAAAGGTGACCTGCTCTTTGAGGACTGAAAGATGCC
ACCAACTTGTGTGAGCTTTGAAAGGGGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGT
GTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTCGGGTGGG
CTTTAAAAGAAAAGGCGTCCCGCTCTTTAAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAA
AAGAAAAAGCATCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGGGTGGACTTTAAAAGAAA
AGGCGTCCCGCTCTTTGAGGACTGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAATGTGT
CCCGCTT
Found at i:130478 original size:1 final size:1
Alignment explanation
Indices: 130468--130528 Score: 50
Period size: 1 Copynumber: 61.0 Consensus size: 1
130458 CTTAAGCAGA
* * * * * * * *
130468 TTTTTCTTTTTTTTTTTGTTTGTTTTGTTTGTTTTGTTTTTTTTTTTTGTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
130529 GAAAAATAAT
Statistics
Matches: 44, Mismatches: 16, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.00, C:0.02, G:0.11, T:0.87
Consensus pattern (1 bp):
T
Found at i:130493 original size:9 final size:9
Alignment explanation
Indices: 130481--130529 Score: 57
Period size: 9 Copynumber: 5.6 Consensus size: 9
130471 TTCTTTTTTT
130481 TTTTGTTTG
1 TTTTGTTTG
130490 TTTTGTTTG
1 TTTTGTTTG
*
130499 TTTTGTTTT
1 TTTTGTTTG
*
130508 TTTTTTTTG
1 TTTTGTTTG
130517 TGTTT-TTT-
1 T-TTTGTTTG
130525 TTTTG
1 TTTTG
130530 AAAAATAATG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
7 3 0.09
8 1 0.03
9 28 0.80
10 3 0.09
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (9 bp):
TTTTGTTTG
Found at i:130493 original size:13 final size:13
Alignment explanation
Indices: 130468--130529 Score: 65
Period size: 14 Copynumber: 4.8 Consensus size: 13
130458 CTTAAGCAGA
*
130468 TTTTTCTTT-TTT
1 TTTTTGTTTGTTT
130480 TTTTTGTTTGTTT
1 TTTTTGTTTGTTT
*
130493 TGTTTGTTTTGTTT
1 TTTTTG-TTTGTTT
*
130507 TTTTTTTTTGTGTT
1 TTTTTGTTTGT-TT
130521 TTTTT-TTTG
1 TTTTTGTTTG
130530 AAAAATAATG
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
12 8 0.19
13 17 0.40
14 18 0.42
ACGTcount: A:0.00, C:0.02, G:0.13, T:0.85
Consensus pattern (13 bp):
TTTTTGTTTGTTT
Found at i:130504 original size:18 final size:17
Alignment explanation
Indices: 130481--130529 Score: 59
Period size: 15 Copynumber: 3.0 Consensus size: 17
130471 TTCTTTTTTT
130481 TTTTGTTTGTTTTGTTTG
1 TTTTGTTT-TTTTGTTTG
130499 TTTTGTTTTTTT-TTT-
1 TTTTGTTTTTTTGTTTG
*
130514 TTGTGTTTTTTT-TTTG
1 TTTTGTTTTTTTGTTTG
130530 AAAAATAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 14 0.48
16 3 0.10
17 4 0.14
18 8 0.28
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (17 bp):
TTTTGTTTTTTTGTTTG
Found at i:143130 original size:28 final size:27
Alignment explanation
Indices: 143076--143145 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 27
143066 AATAAAGCCG
*
143076 GGGTTGGAGTATCCCCTCAGAAGTAAC
1 GGGTTGGAGTATCCCCTCAGAAATAAC
*
143103 AGGGTTGGAGTATCCCC-GATGAAATAAC
1 -GGGTTGGAGTATCCCCTCA-GAAATAAC
*
143131 GACGTTGGAGTATCC
1 G-GGTTGGAGTATCC
143146 TCGACTGTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 2 0.05
28 35 0.95
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (27 bp):
GGGTTGGAGTATCCCCTCAGAAATAAC
Found at i:143197 original size:52 final size:52
Alignment explanation
Indices: 143134--143521 Score: 240
Period size: 52 Copynumber: 7.4 Consensus size: 52
143124 AAATAACGAC
* * * *
143134 GTTGGAGTATCCTCGACTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTAGTTTTGGAAATAAAATCGGG
** * * * *
143186 GTTGGAGTATCCCCGATTAAAGGAAAATTGGT-GTTTCGAAAATAAAACCGGG
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGTAGTTTTGGAAATAAAATCGGG
* * * * *
143238 GTTAGAGTATCCCCGATTGTGGAAAAATTAGT-GTTTTAGCAATAAAACCGGG
1 GTTGGAGTATCCCCGATTGT-GAAAAATTGGTAGTTTTGGAAATAAAATCGGG
* * *** * *
143290 GTTGGAATATCCCCGATTATGAAAAATCAATA-TTTTAGAAATAAAGTCGGG
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTAGTTTTGGAAATAAAATCGGG
** *** * *
143341 GTTGGAGTATCCCC---TCAGAAATAACGGGGTTGG-AGTATCCCCGATGAT-CAA-CGGG
1 GTTGGAGTATCCCCGATTGTGAAA-AA-----TTGGTAGT-T-TTGGA-AATAAAATCGGG
* *
143396 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTATTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAA-AAATTGGTA-GTTTTGGAAATAAAATCGGG
* * * * *
143450 GTTGGAGTATCCTCGATTAT-AGAAAATTAGT-GTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGA-AAAATTGGTAGTTTTGGAAATAAAATCGGG
*
143501 GTTGGAATATCCCCGATTGTG
1 GTTGGAGTATCCCCGATTGTG
143522 GAGAATTGAG
Statistics
Matches: 257, Mismatches: 56, Indels: 46
0.72 0.16 0.13
Matches are distributed among these distances:
48 5 0.02
49 2 0.01
51 73 0.28
52 92 0.36
53 27 0.11
54 26 0.10
55 20 0.08
56 3 0.01
57 2 0.01
58 6 0.02
59 1 0.00
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.29
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTAGTTTTGGAAATAAAATCGGG
Found at i:143401 original size:27 final size:26
Alignment explanation
Indices: 143337--143412 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 26
143327 GAAATAAAGT
143337 CGGGGTTGGAGTATCCCCTCAGA-AATAA
1 CGGGGTTGGAGTAT-CCC-C-GATAATAA
*
143365 CGGGGTTGGAGTATCCCCGATGATCAA
1 CGGGGTTGGAGTATCCCCGATAAT-AA
143392 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
143413 TGTGAAGAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
25 2 0.04
26 3 0.07
27 26 0.58
28 14 0.31
ACGTcount: A:0.22, C:0.22, G:0.33, T:0.22
Consensus pattern (26 bp):
CGGGGTTGGAGTATCCCCGATAATAA
Found at i:143493 original size:263 final size:262
Alignment explanation
Indices: 143026--143523 Score: 766
Period size: 263 Copynumber: 1.9 Consensus size: 262
143016 AAAATAACGA
* * * *
143026 GGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAGTATCCC
1 GGTTGGAATATCCCCAATTATGAAAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTATCCC
* *
143091 CTCAGAAGTAACAGGGTTGGAGTATCCCCGATGAAATAACGACGTTGGAGTATCCTCGACTGTGA
66 CTCAGAAATAACAGGGTTGGAGTATCCCCGATG-AATAACGACGTTGGAGTATCCCCGACTGTGA
*
143156 AAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTT
130 AAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTAGTGTT
* *
143221 TCGAAAATAAAACCGGGGTTAGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAAC
195 TCGAAAATAAAACCGGAGTTAGAATATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAAC
143286 CGG
260 CGG
* *
143289 GGTTGGAATATCCCCGATTATGAAAAATCAATATTTTAGAAATAAAGTCGGGGTTGGAGTATCCC
1 GGTTGGAATATCCCCAATTATGAAAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTATCCC
* ** *
143354 CTCAGAAATAACGGGGTTGGAGTATCCCCGATG-ATCAACGGGGTTGGAGTATCCCCGATTGTGA
66 CTCAGAAATAACAGGGTTGGAGTATCCCCGATGAAT-AACGACGTTGGAGTATCCCCGACTGTGA
* *
143418 AGAAATTGGTATTTTTTGGAAATAAAATCGGAGTTGGAGTATCCTCGATTATA-GAAAATTAGTG
130 A-AAATTGGTA-TTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTAGTG
* * *
143482 TTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGGA
193 TTTCGAAAATAAAACCGGAGTTAGAATATCCCCGATTGTGGA
143524 GAATTGAGAA
Statistics
Matches: 212, Mismatches: 20, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
261 2 0.01
262 25 0.12
263 146 0.69
264 39 0.18
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (262 bp):
GGTTGGAATATCCCCAATTATGAAAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTATCCC
CTCAGAAATAACAGGGTTGGAGTATCCCCGATGAATAACGACGTTGGAGTATCCCCGACTGTGAA
AAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGAAAATTAGTGTTT
CGAAAATAAAACCGGAGTTAGAATATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACC
GG
Found at i:152987 original size:16 final size:15
Alignment explanation
Indices: 152962--152992 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
152952 ATATTAACTT
152962 TATATTCTATTCTAC
1 TATATTCTATTCTAC
152977 TATATTGCTATTCTAC
1 TATATT-CTATTCTAC
152993 GTGTAATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.26, C:0.19, G:0.03, T:0.52
Consensus pattern (15 bp):
TATATTCTATTCTAC
Found at i:153117 original size:3 final size:3
Alignment explanation
Indices: 153109--153150 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
153099 CATTTCTTGA
*
153109 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAG AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
153151 TTCAAATAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:153681 original size:14 final size:14
Alignment explanation
Indices: 153642--153684 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
153632 TTAACTCAAA
153642 TTTAAATTTAAATTTT
1 TTTAAATTTAAA--TT
153658 TTTAAA--TAAATT
1 TTTAAATTTAAATT
153670 TTTAAATTTAAATT
1 TTTAAATTTAAATT
153684 T
1 T
153685 ATTTTATCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 8 0.32
14 11 0.44
16 6 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTTAAATTTAAATT
Found at i:162474 original size:14 final size:14
Alignment explanation
Indices: 162455--162484 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
162445 AGAAATTAAA
162455 GAGAACTTTAATTC
1 GAGAACTTTAATTC
162469 GAGAACTTTAATTC
1 GAGAACTTTAATTC
162483 GA
1 GA
162485 CAGGCTTATA
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:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (14 bp):
GAGAACTTTAATTC
Found at i:162498 original size:2 final size:2
Alignment explanation
Indices: 162491--162519 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
162481 TCGACAGGCT
162491 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
162520 GCTTATTGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:162655 original size:15 final size:15
Alignment explanation
Indices: 162634--162670 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
162624 AGTTGTGCTG
162634 CTCTTTTTTTTTCTTT
1 CTCTTTTTTTTT-TTT
162650 -TCTTTTTTTTTTTT
1 CTCTTTTTTTTTTTT
162664 CTCTTTT
1 CTCTTTT
162671 AAACAGAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 3 0.15
15 17 0.85
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (15 bp):
CTCTTTTTTTTTTTT
Found at i:164341 original size:26 final size:26
Alignment explanation
Indices: 164285--164341 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
164275 AATTAATAAT
* * *
164285 AATTTATTATATTTTTAAATATTTTA
1 AATTTATTATATTTATAAAGATTTAA
* * *
164311 TATTTATTTTATTTATAGAGATTTAA
1 AATTTATTATATTTATAAAGATTTAA
164337 AATTT
1 AATTT
164342 TGGATATTAA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (26 bp):
AATTTATTATATTTATAAAGATTTAA
Found at i:164906 original size:4 final size:4
Alignment explanation
Indices: 164887--164923 Score: 56
Period size: 4 Copynumber: 9.0 Consensus size: 4
164877 AGACTTAAAG
*
164887 CATA CCATA TATA CATA CATA CATA CATA CATA CATA
1 CATA -CATA CATA CATA CATA CATA CATA CATA CATA
164924 TATATATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
4 26 0.87
5 4 0.13
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (4 bp):
CATA
Found at i:164928 original size:4 final size:4
Alignment explanation
Indices: 164893--164953 Score: 68
Period size: 4 Copynumber: 15.2 Consensus size: 4
164883 AAAGCATACC
* * * * * *
164893 ATAT ATAC ATAC ATAC ATAC ATAC ATAC ATAT ATAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
164941 ATAT ATAT ATAT A
1 ATAT ATAT ATAT A
164954 AAAGATAATA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 55 1.00
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (4 bp):
ATAT
Found at i:165159 original size:3 final size:3
Alignment explanation
Indices: 165151--165180 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
165141 GTACCATAGC
165151 AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT
1 AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT
165181 TTATTAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
AGT
Found at i:166802 original size:14 final size:16
Alignment explanation
Indices: 166785--166826 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
166775 ATATATAAAC
*
166785 TTTTATAA-ATAAGT-
1 TTTTATAATATAAATA
166799 TTTTATAATATAAATA
1 TTTTATAATATAAATA
*
166815 TTTTATATTATA
1 TTTTATAATATA
166827 GTATGATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 8 0.33
15 5 0.21
16 11 0.46
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
TTTTATAATATAAATA
Found at i:166820 original size:16 final size:15
Alignment explanation
Indices: 166777--166826 Score: 57
Period size: 14 Copynumber: 3.3 Consensus size: 15
166767 TATATTCAAT
*
166777 ATATAAACTTTTATA
1 ATATAAATTTTTATA
*
166792 A-ATAAGTTTTTATA
1 ATATAAATTTTTATA
166806 ATATAAATATTTTATA
1 ATATAAAT-TTTTATA
*
166822 TTATA
1 ATATA
166827 GTATGATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
14 12 0.41
15 6 0.21
16 11 0.38
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (15 bp):
ATATAAATTTTTATA
Found at i:168189 original size:22 final size:21
Alignment explanation
Indices: 168164--168210 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 21
168154 AATAATTAAC
168164 TTTTTAAT-TTATTTTTAAATT
1 TTTTTAATATT-TTTTTAAATT
168185 ATTTTTAATATTTTTTTAAATT
1 -TTTTTAATATTTTTTTAAATT
168207 TTTT
1 TTTT
168211 ACTGTAATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 4 0.17
22 18 0.75
23 2 0.08
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTTAATATTTTTTTAAATT
Found at i:168210 original size:12 final size:11
Alignment explanation
Indices: 168164--168203 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
168154 AATAATTAAC
168164 TTTTTAATTTA
1 TTTTTAATTTA
*
168175 TTTTTAAATTA
1 TTTTTAATTTA
168186 TTTTTAATATT-
1 TTTTTAAT-TTA
168197 TTTTTAA
1 TTTTTAA
168204 ATTTTTTACT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 24 0.92
12 2 0.08
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTTTAATTTA
Found at i:168999 original size:16 final size:15
Alignment explanation
Indices: 168978--169037 Score: 56
Period size: 16 Copynumber: 4.1 Consensus size: 15
168968 ATTAATTACA
*
168978 TATTATTTATTAAGAT
1 TATTATTTAAT-AGAT
168994 TATTATTTAATAG--
1 TATTATTTAATAGAT
*
169007 -ATTATTTAATAAAT
1 TATTATTTAATAGAT
169021 TCATTATTTAATA-AT
1 T-ATTATTTAATAGAT
169036 TA
1 TA
169038 AATTAATATA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
12 11 0.29
14 1 0.03
15 5 0.13
16 21 0.55
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (15 bp):
TATTATTTAATAGAT
Found at i:169012 original size:28 final size:27
Alignment explanation
Indices: 168979--169037 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 27
168969 TTAATTACAT
*
168979 ATTATTTATTAAGATT-ATTATTTAATA
1 ATTATTTAATAA-ATTCATTATTTAATA
169006 GATTATTTAATAAATTCATTATTTAATA
1 -ATTATTTAATAAATTCATTATTTAATA
169034 ATTA
1 ATTA
169038 AATTAATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 7 0.24
28 22 0.76
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (27 bp):
ATTATTTAATAAATTCATTATTTAATA
Found at i:169337 original size:74 final size:73
Alignment explanation
Indices: 169176--169340 Score: 170
Period size: 74 Copynumber: 2.2 Consensus size: 73
169166 ATTTTAATTT
* * * * * *
169176 TTTAATTATTAATAAGATTTATTACATTTATAAATAAGTATTTTAATTCAATTAAAAGGCTTTGG
1 TTTATTTATTAATAA-ATTTATCACATTTATAAATAAGAATTCTAATTCAATTAAAAGACTTTAG
* **
169241 TTACATTTA
65 TTAAATGAA
* * ** *
169250 TTTACTTGA-TAATAAACTTTATCATATTTATAAATAAGAATTCTAATTTTATTGAAAGACTTTA
1 TTTA-TTTATTAATAAA-TTTATCACATTTATAAATAAGAATTCTAATTCAATTAAAAGACTTTA
169314 GTTAAATGAA
64 GTTAAATGAA
169324 TTTATTTATTAATAAAT
1 TTTATTTATTAATAAAT
169341 AAAAATTAAA
Statistics
Matches: 73, Mismatches: 15, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
73 5 0.07
74 66 0.90
75 2 0.03
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.47
Consensus pattern (73 bp):
TTTATTTATTAATAAATTTATCACATTTATAAATAAGAATTCTAATTCAATTAAAAGACTTTAGT
TAAATGAA
Found at i:169517 original size:18 final size:19
Alignment explanation
Indices: 169486--169533 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 19
169476 TATATTCAAT
169486 ATATATAAA-ATTTTATAA
1 ATATATAAATATTTTATAA
* *
169504 ATATATAAGTTTTTTAT-A
1 ATATATAAATATTTTATAA
169522 AT-T-TAAATATTT
1 ATATATAAATATTT
169534 AAATCGTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 7 0.28
17 1 0.04
18 11 0.44
19 6 0.24
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
ATATATAAATATTTTATAA
Found at i:170668 original size:13 final size:12
Alignment explanation
Indices: 170652--170685 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
170642 TTTTTTAAAA
170652 ATAATTTTAGAAG
1 ATAATTTTAG-AG
170665 ATAATTATTAGAG
1 ATAATT-TTAGAG
170678 ATAATTTT
1 ATAATTTT
170686 TCATCTCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 2 0.10
13 14 0.70
14 4 0.20
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (12 bp):
ATAATTTTAGAG
Found at i:173100 original size:16 final size:16
Alignment explanation
Indices: 173059--173118 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
173049 TTTAAAAATT
* *
173059 AATAAATCAAAATTCA
1 AATAAATCAAACTTCG
* *
173075 AACAATTCAAACTT-G
1 AATAAATCAAACTTCG
173090 AATAATATCAAA-TTCG
1 AATAA-ATCAAACTTCG
*
173106 AATGAATCAAACT
1 AATAAATCAAACT
173119 CAAATAAACT
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
15 12 0.35
16 22 0.65
ACGTcount: A:0.53, C:0.15, G:0.05, T:0.27
Consensus pattern (16 bp):
AATAAATCAAACTTCG
Found at i:174414 original size:20 final size:21
Alignment explanation
Indices: 174383--174421 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
174373 TAATATATAT
174383 ATATATATATATATTCTAATA
1 ATATATATATATATTCTAATA
174404 ATATA-ATATATATTCTAA
1 ATATATATATATATTCTAA
174422 ACACTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (21 bp):
ATATATATATATATTCTAATA
Found at i:175386 original size:28 final size:29
Alignment explanation
Indices: 175342--175397 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
175332 CATTTAATAA
*
175342 AAAATAATAAACGAAAAG-AAATAAAAAT
1 AAAATAATAAACGAAAAGTAAAAAAAAAT
*
175370 AAAATAAATAAA-TAAAAGTAAAAAAAAA
1 AAAAT-AATAAACGAAAAGTAAAAAAAAA
175398 AAGGAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 10 0.42
29 14 0.58
ACGTcount: A:0.79, C:0.02, G:0.05, T:0.14
Consensus pattern (29 bp):
AAAATAATAAACGAAAAGTAAAAAAAAAT
Found at i:176182 original size:17 final size:17
Alignment explanation
Indices: 176155--176197 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
176145 AAAATGCTTT
*
176155 TAAATTAAATTATGAAAA
1 TAAA-TAAATTATAAAAA
*
176173 TAAATAAATTGTAAAAA
1 TAAATAAATTATAAAAA
176190 TAAATAAA
1 TAAATAAA
176198 ATTCAAATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 19 0.83
18 4 0.17
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (17 bp):
TAAATAAATTATAAAAA
Done.