Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009608.1 Hibiscus syriacus cultivar Beakdansim tig00116994_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: 1053610
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 7
Found at i:192303 original size:18 final size:18
Alignment explanation
Indices: 192280--192317 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
192270 GTCAATACCA
*
192280 AAAACAAGAAAATAAAGC
1 AAAACAAGAAAAGAAAGC
*
192298 AAAACAAGAAGAGAAAGC
1 AAAACAAGAAAAGAAAGC
192316 AA
1 AA
192318 CAAAGCAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.71, C:0.11, G:0.16, T:0.03
Consensus pattern (18 bp):
AAAACAAGAAAAGAAAGC
Found at i:199128 original size:170 final size:168
Alignment explanation
Indices: 198810--199136 Score: 417
Period size: 170 Copynumber: 1.9 Consensus size: 168
198800 AGTTTTCCGA
* ***
198810 GTCATCTATAAGACCTTCAGACAAGATGATTTTATATGATATTTGTGAAAGATAAAAGTGATTTA
1 GTCATCTATAAGACCTTCAGACAAGATGATTTTATATGATATTTGTGAAAAATAAAAACAATTTA
*
198875 TAAAGTTTCTCATTTTTAGAAAATAAAATTTATGAAAAGTAAGAAAGTGATTTCCAAAATTTCTT
66 TAAAGTTTCTCATTTTCAGAAAATAAAATTTATGAAAAGTAAGAAAGTGATTTCCAAAATTTCTT
* * **
198940 AACTAGTAGACTATTTCCAAAATTAGTAAGTATTTTAG
131 AACTAATAAAAAATTTCCAAAATTAGTAAGTATTTTAG
* * *
198978 GTCATCTATAAGACCTT-TGAGCATGGTG-TTTTCATATGATATTTGTGAAAAATGAGAAAACAA
1 GTCATCTATAAGACCTTCAGA-CAAGATGATTTT-ATATGATATTTGTGAAAAAT-A-AAAACAA
* * * * *
199041 TTT-TCAAAGTTTCTTATTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAGTGATTTTCAAAGT
62 TTTAT-AAAGTTTCTCATTTTCAGAAAATAAAATTTATGAAAAGTAAGAAAGTGATTTCCAAAAT
* *
199105 TTCTTATCTAATAAAAAATTTCCAAAGTTAGT
126 TTCTTAACTAATAAAAAATTTCCAAAATTAGT
199137 GAATCATTTG
Statistics
Matches: 135, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
167 6 0.04
168 41 0.30
169 2 0.01
170 86 0.64
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.37
Consensus pattern (168 bp):
GTCATCTATAAGACCTTCAGACAAGATGATTTTATATGATATTTGTGAAAAATAAAAACAATTTA
TAAAGTTTCTCATTTTCAGAAAATAAAATTTATGAAAAGTAAGAAAGTGATTTCCAAAATTTCTT
AACTAATAAAAAATTTCCAAAATTAGTAAGTATTTTAG
Found at i:201851 original size:32 final size:32
Alignment explanation
Indices: 201771--201885 Score: 126
Period size: 32 Copynumber: 3.6 Consensus size: 32
201761 TAGTATTAGC
*
201771 ATTGCATTCAGATAA--TACACACTAGAGTCAAT
1 ATTGCATTCAGATAATGTATA-AC-AGAGTCAAT
*
201803 ATTTCATTCAGATAATGTATAACAGAGTCAAT
1 ATTGCATTCAGATAATGTATAACAGAGTCAAT
* * *
201835 ATTGCATTCAGATAATGGATAGCAGAGTTAAT
1 ATTGCATTCAGATAATGTATAACAGAGTCAAT
* * *
201867 GTTACATTCAGATGATGTA
1 ATTGCATTCAGATAATGTA
201886 CAGGAACATC
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
32 66 0.93
33 2 0.03
34 3 0.04
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (32 bp):
ATTGCATTCAGATAATGTATAACAGAGTCAAT
Found at i:205308 original size:20 final size:21
Alignment explanation
Indices: 205285--205324 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
205275 TACCTTATGT
*
205285 AGGGTATCGATACT-TAAGAG
1 AGGGTATCCATACTGTAAGAG
205305 AGGGTATCCATACTGTAAGA
1 AGGGTATCCATACTGTAAGA
205325 CCAGTATCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.35, C:0.12, G:0.28, T:0.25
Consensus pattern (21 bp):
AGGGTATCCATACTGTAAGAG
Found at i:206234 original size:21 final size:21
Alignment explanation
Indices: 206191--206258 Score: 82
Period size: 21 Copynumber: 3.1 Consensus size: 21
206181 CTACTAGGGG
*
206191 CACATAATATTATCCCAAAAGAC
1 CACAT-AT-TTATCCCGAAAGAC
* *
206214 CACATATTTGTCTCGAAAGAC
1 CACATATTTATCCCGAAAGAC
*
206235 CACATATTTATCCCGAATGAC
1 CACATATTTATCCCGAAAGAC
206256 CAC
1 CAC
206259 TCCTTAAGGA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 32 0.82
22 2 0.05
23 5 0.13
ACGTcount: A:0.38, C:0.28, G:0.09, T:0.25
Consensus pattern (21 bp):
CACATATTTATCCCGAAAGAC
Found at i:206297 original size:21 final size:21
Alignment explanation
Indices: 206264--206359 Score: 77
Period size: 21 Copynumber: 4.6 Consensus size: 21
206254 ACCACTCCTT
* *
206264 AAGGATCACATATATATTCCA
1 AAGGACCACATATATGTTCCA
* * *
206285 AAGGACCAAATATGTGTCCCA
1 AAGGACCACATATATGTTCCA
* *
206306 AAGAACCGCATATATGTTCCA
1 AAGGACCACATATATGTTCCA
** *
206327 AAGGATTACATATAT-ATCTCA
1 AAGGACCACATATATGTTC-CA
*
206348 AAGGGCCACATA
1 AAGGACCACATA
206360 GAACCCTCAA
Statistics
Matches: 56, Mismatches: 18, Indels: 2
0.74 0.24 0.03
Matches are distributed among these distances:
20 2 0.04
21 54 0.96
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.24
Consensus pattern (21 bp):
AAGGACCACATATATGTTCCA
Found at i:206774 original size:7 final size:7
Alignment explanation
Indices: 206762--206793 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
206752 TCACACAGAT
206762 CATATAA
1 CATATAA
206769 CATAT-A
1 CATATAA
206775 CA-ATAA
1 CATATAA
206781 CATATAA
1 CATATAA
206788 CATATA
1 CATATA
206794 TATTAATATC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
5 2 0.09
6 6 0.26
7 15 0.65
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (7 bp):
CATATAA
Found at i:211555 original size:18 final size:19
Alignment explanation
Indices: 211532--211575 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
211522 CATAGAGTTA
* *
211532 TGAGGG-CAGTATCGATAC
1 TGAGGGTCAGTACCGAAAC
211550 TGAGGGTTCAGTACCGAAAC
1 TGAGGG-TCAGTACCGAAAC
211570 TGAGGG
1 TGAGGG
211576 GCATGGTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 6 0.27
20 16 0.73
ACGTcount: A:0.27, C:0.16, G:0.36, T:0.20
Consensus pattern (19 bp):
TGAGGGTCAGTACCGAAAC
Found at i:211571 original size:20 final size:20
Alignment explanation
Indices: 211538--211575 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
211528 GTTATGAGGG
* *
211538 CAGTATCGATACTGAGGGTT
1 CAGTACCGAAACTGAGGGTT
211558 CAGTACCGAAACTGAGGG
1 CAGTACCGAAACTGAGGG
211576 GCATGGTATT
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:0.29, C:0.18, G:0.32, T:0.21
Consensus pattern (20 bp):
CAGTACCGAAACTGAGGGTT
Found at i:214670 original size:22 final size:22
Alignment explanation
Indices: 214645--214713 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 22
214635 TGTTATGAAG
* *
214645 CTTTTGTATCAGTGCAGATGCA
1 CTTTAGTATCAGTGCAGAGGCA
* *
214667 CTTTCGTATCAGTGCTGAGGCA
1 CTTTAGTATCAGTGCAGAGGCA
*
214689 CTTTAGTATTAGTGCCA-AGGCA
1 CTTTAGTATCAGTG-CAGAGGCA
214711 CTT
1 CTT
214714 CCATTATTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
22 39 0.98
23 1 0.03
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (22 bp):
CTTTAGTATCAGTGCAGAGGCA
Found at i:218493 original size:22 final size:22
Alignment explanation
Indices: 218468--218592 Score: 65
Period size: 22 Copynumber: 5.6 Consensus size: 22
218458 AAAGGTACTG
218468 ATACCCCTATGAATGGGTATCA
1 ATACCCCTATGAATGGGTATCA
* ** *
218490 ATACCCCTAAGAATAAGTA-CTG
1 ATACCCCTATGAATGGGTATC-A
* * *** *
218512 ATACCCATATCAATACCCCTATAA
1 ATACCCCTATGAAT--GGGTATCA
* * * * *
218536 ATAACTCTTATGAATGGTTACCG
1 AT-ACCCCTATGAATGGGTATCA
218559 ATACCCCTATGAATGGGTATCA
1 ATACCCCTATGAATGGGTATCA
218581 ATACCCC-ATGAA
1 ATACCCCTATGAA
218593 GGCTCAAATT
Statistics
Matches: 72, Mismatches: 26, Indels: 11
0.66 0.24 0.10
Matches are distributed among these distances:
21 6 0.08
22 49 0.68
23 4 0.06
24 4 0.06
25 9 0.12
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.26
Consensus pattern (22 bp):
ATACCCCTATGAATGGGTATCA
Found at i:221810 original size:21 final size:18
Alignment explanation
Indices: 221762--221820 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 18
221752 TCAACAATAG
*
221762 TTAAAAATTGGTATCTTT
1 TTAACAATTGGTATCTTT
221780 TTAACAATTGGTATCCTTT
1 TTAACAATTGGTAT-CTTT
* *
221799 TGTAATCAATTGATATATTT
1 T-TAA-CAATTGGTATCTTT
221819 TT
1 TT
221821 CATTAAACAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 13 0.37
19 6 0.17
20 7 0.20
21 9 0.26
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.51
Consensus pattern (18 bp):
TTAACAATTGGTATCTTT
Found at i:222057 original size:22 final size:22
Alignment explanation
Indices: 222032--222088 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
222022 AATATTAAGA
222032 GGTACTGATACCCATATGAATG
1 GGTACTGATACCCATATGAATG
* *
222054 GGTA-TCAATACCCCTATGAATG
1 GGTACT-GATACCCATATGAATG
*
222076 GGTACCGATACCC
1 GGTACTGATACCC
222089 TTATCAATAC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 1 0.03
22 28 0.97
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (22 bp):
GGTACTGATACCCATATGAATG
Found at i:222100 original size:12 final size:12
Alignment explanation
Indices: 222083--222117 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
222073 ATGGGTACCG
222083 ATACCCTTATCA
1 ATACCCTTATCA
*
222095 ATACCCCTATCA
1 ATACCCTTATCA
222107 ATACCTCTTAT
1 ATACC-CTTAT
222118 GAACAGGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (12 bp):
ATACCCTTATCA
Found at i:222367 original size:20 final size:20
Alignment explanation
Indices: 222344--222385 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
222334 CCCCAAATAG
222344 CTCCAAAACAACCCCAACGA
1 CTCCAAAACAACCCCAACGA
*
222364 CTCCAAAACATCCCCAACGA
1 CTCCAAAACAACCCCAACGA
222384 CT
1 CT
222386 ATATACGACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.40, C:0.45, G:0.05, T:0.10
Consensus pattern (20 bp):
CTCCAAAACAACCCCAACGA
Found at i:222638 original size:33 final size:33
Alignment explanation
Indices: 222601--222670 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 33
222591 TTTTGTAAAG
*
222601 GGGAAAGGTTCTAG-CTAATCCCGTGAAAAGCTA
1 GGGAAAAGTTCTAGTCTAA-CCCGTGAAAAGCTA
* *
222634 GGGAAAAGTTCTAGTTTAACCCGTGAAAATCTA
1 GGGAAAAGTTCTAGTCTAACCCGTGAAAAGCTA
222667 GGGA
1 GGGA
222671 GTTTGTAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 30 0.91
34 3 0.09
ACGTcount: A:0.34, C:0.16, G:0.27, T:0.23
Consensus pattern (33 bp):
GGGAAAAGTTCTAGTCTAACCCGTGAAAAGCTA
Found at i:224856 original size:55 final size:55
Alignment explanation
Indices: 224797--224902 Score: 153
Period size: 57 Copynumber: 1.9 Consensus size: 55
224787 AATTGGTGTT
*
224797 AATGAAAATG-ATCTCTCTAACAATTCATATC-AACTTTTCAAATATTTTGATTTTA
1 AATGAAAATGAATCTCTCTAACAATTCATATCAAAATTTT-AAAT-TTTTGATTTTA
*
224852 AATGAAAATGATATCTCTCTAACAATTGATATCAAAATTTTAAATTTTTGA
1 AATGAAAATGA-ATCTCTCTAACAATTCATATCAAAATTTTAAATTTTTGA
224903 CCTAAACTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
55 10 0.22
56 6 0.13
57 24 0.52
58 6 0.13
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.41
Consensus pattern (55 bp):
AATGAAAATGAATCTCTCTAACAATTCATATCAAAATTTTAAATTTTTGATTTTA
Found at i:225634 original size:22 final size:22
Alignment explanation
Indices: 225609--225684 Score: 143
Period size: 22 Copynumber: 3.5 Consensus size: 22
225599 AGAGGTACTG
225609 ATACCCCTATGAATGGGTATCA
1 ATACCCCTATGAATGGGTATCA
225631 ATACCCCTATGAATGGGTATCA
1 ATACCCCTATGAATGGGTATCA
*
225653 ATACCCCTATGAATGGGTATCG
1 ATACCCCTATGAATGGGTATCA
225675 ATACCCCTAT
1 ATACCCCTAT
225685 CAATACCTCT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (22 bp):
ATACCCCTATGAATGGGTATCA
Found at i:225708 original size:35 final size:34
Alignment explanation
Indices: 225648--225719 Score: 108
Period size: 35 Copynumber: 2.1 Consensus size: 34
225638 TATGAATGGG
* *
225648 TATCAATACCCCTATGAATGGGTATCGATACCCC
1 TATCAATACCCCTATGAACGAGTATCGATACCCC
*
225682 TATCAATACCTCTTATGAACGAGTATCGATACCCC
1 TATCAATACC-CCTATGAACGAGTATCGATACCCC
225717 TAT
1 TAT
225720 GAATGTGTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
34 10 0.29
35 24 0.71
ACGTcount: A:0.31, C:0.28, G:0.12, T:0.29
Consensus pattern (34 bp):
TATCAATACCCCTATGAACGAGTATCGATACCCC
Found at i:225713 original size:23 final size:22
Alignment explanation
Indices: 225682--225743 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
225672 TCGATACCCC
*
225682 TATCAATACCTCTTATGAACGAG
1 TATCAATACC-CCTATGAACGAG
* * *
225705 TATCGATACCCCTATGAATGTG
1 TATCAATACCCCTATGAACGAG
*
225727 TATCCATACCCC-ATGAA
1 TATCAATACCCCTATGAA
225744 GGCTCAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 5 0.15
22 20 0.59
23 9 0.26
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (22 bp):
TATCAATACCCCTATGAACGAG
Found at i:225714 original size:57 final size:56
Alignment explanation
Indices: 225626--225738 Score: 163
Period size: 57 Copynumber: 2.0 Consensus size: 56
225616 TATGAATGGG
* * *
225626 TATCAATACCCCTATGAATGGGTATCAATACCCCTATGAATGGGTATCGATACCCC
1 TATCAATACCCCTATGAACGAGTATCAATACCCCTATGAATGGGTATCCATACCCC
* * *
225682 TATCAATACCTCTTATGAACGAGTATCGATACCCCTATGAATGTGTATCCATACCCC
1 TATCAATACC-CCTATGAACGAGTATCAATACCCCTATGAATGGGTATCCATACCCC
225739 ATGAAGGCTC
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
56 10 0.20
57 40 0.80
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.28
Consensus pattern (56 bp):
TATCAATACCCCTATGAACGAGTATCAATACCCCTATGAATGGGTATCCATACCCC
Found at i:225729 original size:22 final size:22
Alignment explanation
Indices: 225695--225743 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
225685 CAATACCTCT
*
225695 TATGAACGAGTATCGATACCCC
1 TATGAACGAGTATCCATACCCC
* *
225717 TATGAATGTGTATCCATACCCC
1 TATGAACGAGTATCCATACCCC
225739 -ATGAA
1 TATGAA
225744 GGCTCAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (22 bp):
TATGAACGAGTATCCATACCCC
Found at i:226687 original size:45 final size:46
Alignment explanation
Indices: 226616--226722 Score: 164
Period size: 45 Copynumber: 2.3 Consensus size: 46
226606 GGTGCACTAA
*
226616 GAGTGCATCGATGCATAAAATACATTCGATG-TTTCA-AAATAGCCT
1 GAGTGCATCGATGCATAAAATACATTCGATGTTTTCATAAA-ACCCT
* *
226661 GAGTGCATCGATGCATTAAATGCATTCGATGTTTTCATAAAACCCT
1 GAGTGCATCGATGCATAAAATACATTCGATGTTTTCATAAAACCCT
226707 GAGTGCATCGATGCAT
1 GAGTGCATCGATGCAT
226723 GGTATGTGCA
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
45 29 0.51
46 25 0.44
47 3 0.05
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.30
Consensus pattern (46 bp):
GAGTGCATCGATGCATAAAATACATTCGATGTTTTCATAAAACCCT
Found at i:226797 original size:65 final size:64
Alignment explanation
Indices: 226663--226806 Score: 168
Period size: 65 Copynumber: 2.2 Consensus size: 64
226653 AATAGCCTGA
* *
226663 GTGCATCGATGCATTAAATGCATTCGATGTTTTCATAAAACCCTGAGTGCATCGATGCATGGTAT
1 GTGCATCGATGCATAAAATGCATTCGATG-TTTCATAAAACCATGAGTGCATCGATGCATGGTAT
* **
226728 GTGCATCGATGCATAAAATGCATTCGATG-TTCAATTTATTCCAT-AGTGCATCGATGCATGG-A
1 GTGCATCGATGCATAAAATGCATTCGATGTTTC-A-TAAAACCATGAGTGCATCGATGCATGGTA
226790 TT
64 -T
*
226792 GGTGCATCGGTGCAT
1 -GTGCATCGATGCAT
226807 CACTTTGAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
63 4 0.06
64 19 0.28
65 46 0.67
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTCATAAAACCATGAGTGCATCGATGCATGGTAT
Found at i:229473 original size:20 final size:20
Alignment explanation
Indices: 229448--229499 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
229438 ACCCGACGGA
229448 TGCATCGATGCATAGCCTTG
1 TGCATCGATGCATAGCCTTG
*
229468 TGCATCGATGCATGGCCTTG
1 TGCATCGATGCATAGCCTTG
229488 TGCATCGATGCA
1 TGCATCGATGCA
229500 CATTCAAGGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.19, C:0.25, G:0.27, T:0.29
Consensus pattern (20 bp):
TGCATCGATGCATAGCCTTG
Found at i:229517 original size:23 final size:22
Alignment explanation
Indices: 229487--229568 Score: 76
Period size: 23 Copynumber: 3.6 Consensus size: 22
229477 GCATGGCCTT
229487 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
229509 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
* *
229531 GTGTATCGATGCATATTCAAAGG
1 GTGCATCGATGCACATTC-AAGG
*
229554 GATGGATCGATGCAC
1 G-TGCATCGATGCAC
229569 TGTTAAGTGT
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
21 14 0.30
22 2 0.04
23 19 0.41
24 11 0.24
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:233910 original size:15 final size:13
Alignment explanation
Indices: 233889--233922 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 13
233879 CTCATATTCT
233889 TCTTCTTCTCTGTC
1 TCTTCTTCTC-GTC
233903 TGCTTCTTCTCGTC
1 T-CTTCTTCTCGTC
233917 TCTTCT
1 TCTTCT
233923 CTCAAGGTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 5 0.26
14 5 0.26
15 9 0.47
ACGTcount: A:0.00, C:0.35, G:0.09, T:0.56
Consensus pattern (13 bp):
TCTTCTTCTCGTC
Found at i:235428 original size:64 final size:64
Alignment explanation
Indices: 235353--235531 Score: 193
Period size: 64 Copynumber: 2.8 Consensus size: 64
235343 TGACCATTAG
* * *
235353 ACCCTTAGTGCATCGGTGCACTAAG-AGTACATCGATGCATAAAATGCATTCGATGTTTT-A-AA
1 ACCCTGAGTGCATCGATGCA-T-AGTAGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAA
235415 A
64 A
** * * * *
235416 TAGTCTGAGTGCATCGATGCATAGCTGGTGCATCAATACATCAAATGCATTCGATGTTTTCATAA
1 -ACCCTGAGTGCATCGATGCATAG-TAGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAA
235481 A
64 A
* *
235482 ACCCTGAGTGCATCGATGCATGGTATGCGCATCGATGCATAAAATGCATT
1 ACCCTGAGTGCATCGATGCATAGTA-GTGCATCGATGCATAAAATGCATT
235532 TGATTTTCAA
Statistics
Matches: 93, Mismatches: 17, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
62 2 0.02
63 1 0.01
64 46 0.49
65 41 0.44
66 3 0.03
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.29
Consensus pattern (64 bp):
ACCCTGAGTGCATCGATGCATAGTAGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAA
Found at i:235514 original size:65 final size:64
Alignment explanation
Indices: 235390--235531 Score: 171
Period size: 65 Copynumber: 2.2 Consensus size: 64
235380 TACATCGATG
** *
235390 CATAAAATGCATTCGATGTTTTAAAATAGTCTGAGTGCATCGATGCATAGCTGGTGCATCAATA
1 CATAAAATGCATTCGATGTTTTAAAATACCCTGAGTGCATCGATGCATAGCTGGCGCATCAATA
* * * *
235454 CATCAAATGCATTCGATGTTTTCATAAA-ACCCTGAGTGCATCGATGCAT-GGTATGCGCATCGA
1 CATAAAATGCATTCGATGTTTT-A-AAATACCCTGAGTGCATCGATGCATAGCT-GGCGCATCAA
*
235517 TG
63 TA
235519 CATAAAATGCATT
1 CATAAAATGCATT
235532 TGATTTTCAA
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
64 23 0.35
65 40 0.61
66 3 0.05
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (64 bp):
CATAAAATGCATTCGATGTTTTAAAATACCCTGAGTGCATCGATGCATAGCTGGCGCATCAATA
Found at i:239120 original size:22 final size:22
Alignment explanation
Indices: 239087--239145 Score: 91
Period size: 22 Copynumber: 2.7 Consensus size: 22
239077 TATTAAGAGT
*
239087 TACCGATACCCCTATGAATGGG
1 TACCAATACCCCTATGAATGGG
*
239109 TATCAATACCCCTATGAATGGG
1 TACCAATACCCCTATGAATGGG
*
239131 TACCGATACCCCTAT
1 TACCAATACCCCTAT
239146 CAATACCTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (22 bp):
TACCAATACCCCTATGAATGGG
Found at i:239167 original size:35 final size:34
Alignment explanation
Indices: 239109--239180 Score: 99
Period size: 35 Copynumber: 2.1 Consensus size: 34
239099 TATGAATGGG
* *
239109 TATCAATACCCCTATGAATGGGTACCGATACCCC
1 TATCAATACCCCTATGAACGGGTACCAATACCCC
* *
239143 TATCAATACCTCTTATGAACGGGTATCAATACCCC
1 TATCAATACC-CCTATGAACGGGTACCAATACCCC
239178 TAT
1 TAT
239181 GAATGGGTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
34 10 0.30
35 23 0.70
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.28
Consensus pattern (34 bp):
TATCAATACCCCTATGAACGGGTACCAATACCCC
Found at i:239188 original size:22 final size:22
Alignment explanation
Indices: 239143--239204 Score: 90
Period size: 22 Copynumber: 2.8 Consensus size: 22
239133 CCGATACCCC
*
239143 TATCAATACCTCTTATGAACGGG
1 TATCAATACC-CCTATGAACGGG
*
239166 TATCAATACCCCTATGAATGGG
1 TATCAATACCCCTATGAACGGG
239188 TATCAATACCCC-ATGAA
1 TATCAATACCCCTATGAA
239205 GGCTCAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.14
22 22 0.59
23 10 0.27
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (22 bp):
TATCAATACCCCTATGAACGGG
Found at i:239656 original size:33 final size:33
Alignment explanation
Indices: 239609--239680 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 33
239599 CCTTTTGTAA
* *
239609 AGGGTAAAGGTTCTAGCTGATCCCATGAAAAGCT
1 AGGG-AAAGGTTCTAGCTGAACCCATGAAAAACT
* * *
239643 AGGGAAAGGTTCTAGTTTAACCCGTGAAAAACT
1 AGGGAAAGGTTCTAGCTGAACCCATGAAAAACT
239676 AGGGA
1 AGGGA
239681 TTTTATAAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
33 29 0.88
34 4 0.12
ACGTcount: A:0.35, C:0.15, G:0.28, T:0.22
Consensus pattern (33 bp):
AGGGAAAGGTTCTAGCTGAACCCATGAAAAACT
Found at i:243372 original size:6 final size:6
Alignment explanation
Indices: 243361--243398 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
243351 TACAACATAC
243361 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA AT
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA AT
243399 ATTCTAGCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
ATTAAA
Found at i:245111 original size:18 final size:20
Alignment explanation
Indices: 245088--245133 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
245078 ATTTTGGTAC
245088 CGATACTCAT-GG-GAGTAT
1 CGATACTCATAGGAGAGTAT
245106 CGATAC-CATAGGGAGAGTAT
1 CGATACTCATA-GGAGAGTAT
245126 CGATACTC
1 CGATACTC
245134 TCCACCAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 3 0.12
18 6 0.25
19 2 0.08
20 12 0.50
21 1 0.04
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (20 bp):
CGATACTCATAGGAGAGTAT
Found at i:245212 original size:18 final size:19
Alignment explanation
Indices: 245186--245232 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
245176 GCGAAATTTG
*
245186 GTATTGATA-CTAAGGCCA
1 GTATCGATACCTAAGGCCA
245204 GTATCGATACCCTAAGGCCA
1 GTATCGATA-CCTAAGGCCA
*
245224 GTTTCGATA
1 GTATCGATA
245233 TTGACAGGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 8 0.32
20 17 0.68
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (19 bp):
GTATCGATACCTAAGGCCA
Found at i:245220 original size:20 final size:20
Alignment explanation
Indices: 245195--245232 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
245185 GGTATTGATA
245195 CTAAGGCCAGTATCGATACC
1 CTAAGGCCAGTATCGATACC
*
245215 CTAAGGCCAGTTTCGATA
1 CTAAGGCCAGTATCGATA
245233 TTGACAGGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (20 bp):
CTAAGGCCAGTATCGATACC
Found at i:245543 original size:23 final size:23
Alignment explanation
Indices: 245516--245577 Score: 117
Period size: 23 Copynumber: 2.7 Consensus size: 23
245506 TTCCAGTGTC
245516 ATGACACTTTTGTATCAGTGCGG
1 ATGACACTTTTGTATCAGTGCGG
245539 ATGACACTTTTGTATCAGTGCGG
1 ATGACACTTTTGTATCAGTGCGG
245562 ATG-CACTTTTGTATCA
1 ATGACACTTTTGTATCA
245578 ATGCTGAGGC
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
22 13 0.33
23 26 0.67
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.37
Consensus pattern (23 bp):
ATGACACTTTTGTATCAGTGCGG
Found at i:245571 original size:22 final size:22
Alignment explanation
Indices: 245520--245597 Score: 111
Period size: 22 Copynumber: 3.5 Consensus size: 22
245510 AGTGTCATGA
245520 CACTTTTGTATCAGTGCGGATG
1 CACTTTTGTATCAGTGCGGATG
245542 ACACTTTTGTATCAGTGCGGATG
1 -CACTTTTGTATCAGTGCGGATG
* * *
245565 CACTTTTGTATCAATGCTGAGG
1 CACTTTTGTATCAGTGCGGATG
*
245587 CACTTTAGTAT
1 CACTTTTGTAT
245598 TAATGCCAAG
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 29 0.57
23 22 0.43
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (22 bp):
CACTTTTGTATCAGTGCGGATG
Found at i:245631 original size:24 final size:22
Alignment explanation
Indices: 245564--245623 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
245554 CAGTGCGGAT
* * **
245564 GCACTTTTGTATCAATGCTGAG
1 GCACTTTAGTATTAATGCCAAG
245586 GCACTTTAGTATTAATGCCAAG
1 GCACTTTAGTATTAATGCCAAG
*
245608 GCACTTCTATTATTAA
1 GCACTT-TAGTATTAA
245624 ATGGCAAGCC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 24 0.75
23 8 0.25
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (22 bp):
GCACTTTAGTATTAATGCCAAG
Found at i:247332 original size:18 final size:18
Alignment explanation
Indices: 247309--247351 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
247299 TTCCACTCAA
*
247309 ATTCAATACTATCATCAT
1 ATTCAACACTATCATCAT
247327 ATTCAACACTATCATCAT
1 ATTCAACACTATCATCAT
247345 ATTCAAC
1 ATTCAAC
247352 CATTCTTACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.40, C:0.26, G:0.00, T:0.35
Consensus pattern (18 bp):
ATTCAACACTATCATCAT
Found at i:250155 original size:22 final size:21
Alignment explanation
Indices: 250123--250163 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
250113 CCATCTCCAT
250123 TTCATCATCAAAACCATCATC
1 TTCATCATCAAAACCATCATC
*
250144 TTCATCCATCAAGACCATCA
1 TTCAT-CATCAAAACCATCA
250164 ATTTCCGTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.37, C:0.34, G:0.02, T:0.27
Consensus pattern (21 bp):
TTCATCATCAAAACCATCATC
Found at i:250502 original size:11 final size:11
Alignment explanation
Indices: 250488--250526 Score: 78
Period size: 11 Copynumber: 3.5 Consensus size: 11
250478 CAAAAAGAAA
250488 AGAAAAAAATC
1 AGAAAAAAATC
250499 AGAAAAAAATC
1 AGAAAAAAATC
250510 AGAAAAAAATC
1 AGAAAAAAATC
250521 AGAAAA
1 AGAAAA
250527 GAAGAAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.74, C:0.08, G:0.10, T:0.08
Consensus pattern (11 bp):
AGAAAAAAATC
Found at i:250504 original size:22 final size:23
Alignment explanation
Indices: 250479--250544 Score: 89
Period size: 22 Copynumber: 2.8 Consensus size: 23
250469 TTTGGAGTAC
250479 AAAAAGAAAAGAAAAAAATCAGA
1 AAAAAGAAAAGAAAAAAATCAGA
**
250502 AAAAA-ATCAGAAAAAAATCAGA
1 AAAAAGAAAAGAAAAAAATCAGA
250524 AAAGAAGAAAAGAAAAGAAAT
1 AAA-AAGAAAAGAAAA-AAAT
250545 TCAAAAGAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
22 18 0.50
23 7 0.19
24 7 0.19
25 4 0.11
ACGTcount: A:0.76, C:0.05, G:0.14, T:0.06
Consensus pattern (23 bp):
AAAAAGAAAAGAAAAAAATCAGA
Found at i:261727 original size:9 final size:9
Alignment explanation
Indices: 261696--261737 Score: 52
Period size: 8 Copynumber: 4.8 Consensus size: 9
261686 AAATTTTGGA
261696 TTTTTTTGGC
1 TTTTTTT-GC
261706 TTTTTTTG-
1 TTTTTTTGC
261714 TTTTTTTGC
1 TTTTTTTGC
*
261723 CTTTTTTG-
1 TTTTTTTGC
261731 TTTTTTT
1 TTTTTTT
261738 TTTTTGAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 14 0.48
9 8 0.28
10 7 0.24
ACGTcount: A:0.00, C:0.07, G:0.12, T:0.81
Consensus pattern (9 bp):
TTTTTTTGC
Found at i:261738 original size:18 final size:18
Alignment explanation
Indices: 261696--261737 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
261686 AAATTTTGGA
*
261696 TTTTTTTGGCTTTTTTTG
1 TTTTTTTGCCTTTTTTTG
261714 TTTTTTTGCC-TTTTTTG
1 TTTTTTTGCCTTTTTTTG
261731 TTTTTTT
1 TTTTTTT
261738 TTTTTGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.00, C:0.07, G:0.12, T:0.81
Consensus pattern (18 bp):
TTTTTTTGCCTTTTTTTG
Found at i:264106 original size:22 final size:21
Alignment explanation
Indices: 264080--264120 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
264070 TTGCGGAAAT
264080 TGATGGTCTTGATGGATGAAGA
1 TGATGGTCTTGAT-GATGAAGA
*
264102 TGATGGTTTTGATGATGAA
1 TGATGGTCTTGATGATGAA
264121 ATAGAGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.27, C:0.02, G:0.34, T:0.37
Consensus pattern (21 bp):
TGATGGTCTTGATGATGAAGA
Found at i:268473 original size:42 final size:42
Alignment explanation
Indices: 268386--268544 Score: 132
Period size: 42 Copynumber: 3.9 Consensus size: 42
268376 AAAACGATCT
* *
268386 CAAATTCGCAACGCG-ATCT-CCAATTTCGCAACACAGTTTC
1 CAAATTCGCAACGCGAATTTCCCAAATTCGCAACACAGTTTC
* * *
268426 CAAATTTGCAACGCGAATTTCCCAAATTCGCAACATAGTTTT
1 CAAATTCGCAACGCGAATTTCCCAAATTCGCAACACAGTTTC
* * *** * *
268468 GAAATTCGCAACTCGAATTT--CTTTTTCGCAACGCGATTTTC
1 CAAATTCGCAACGCGAATTTCCCAAATTCGCAACAC-AGTTTC
* * *
268509 TAAATTCGCAACGCG-GTTT-TCAAATTCGCAACACAG
1 CAAATTCGCAACGCGAATTTCCCAAATTCGCAACACAG
268545 AAGTCAAATT
Statistics
Matches: 92, Mismatches: 23, Indels: 8
0.75 0.19 0.07
Matches are distributed among these distances:
40 27 0.29
41 30 0.33
42 35 0.38
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (42 bp):
CAAATTCGCAACGCGAATTTCCCAAATTCGCAACACAGTTTC
Found at i:268535 original size:20 final size:20
Alignment explanation
Indices: 268385--268540 Score: 109
Period size: 20 Copynumber: 7.7 Consensus size: 20
268375 TAAAACGATC
*
268385 TCAAATTCGCAACGCGATCT
1 TCAAATTCGCAACGCGATTT
* * *
268405 CCAATTTCGCAACAC-AGTTT
1 TCAAATTCGCAACGCGA-TTT
* *
268425 CCAAATTTGCAACGCGAATTT
1 TCAAATTCGCAACGCG-ATTT
* **
268446 CCCAAATTCGCAAC-ATAGTTT
1 -TCAAATTCGCAACGCGA-TTT
* * *
268467 TGAAATTCGCAACTCGAATT
1 TCAAATTCGCAACGCGATTT
***
268487 TCTTTTTCGCAACGCGATTT
1 TCAAATTCGCAACGCGATTT
*
268507 TCTAAATTCGCAACGCGGTTT
1 TC-AAATTCGCAACGCGATTT
268528 TCAAATTCGCAAC
1 TCAAATTCGCAAC
268541 ACAGAAGTCA
Statistics
Matches: 104, Mismatches: 25, Indels: 14
0.73 0.17 0.10
Matches are distributed among these distances:
19 1 0.01
20 67 0.64
21 23 0.22
22 13 0.12
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.31
Consensus pattern (20 bp):
TCAAATTCGCAACGCGATTT
Found at i:268591 original size:20 final size:20
Alignment explanation
Indices: 268566--268615 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
268556 GTAAAGCGCG
**
268566 TTTATTTTCGCAATGCGAAT
1 TTTATTTTCGCAACACGAAT
*
268586 TTTATTTTCGCAACATGAAT
1 TTTATTTTCGCAACACGAAT
268606 TTTATTTTCG
1 TTTATTTTCG
268616 AATTCGAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.24, C:0.14, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTATTTTCGCAACACGAAT
Found at i:268626 original size:26 final size:26
Alignment explanation
Indices: 268592--268641 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
268582 GAATTTTATT
* * * *
268592 TTCGCAACATGAATTTTATTTTCGAA
1 TTCGAAACACGAATATTAATTTCGAA
268618 TTCGAAACACGAATATTAATTTCG
1 TTCGAAACACGAATATTAATTTCG
268642 CAACACAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (26 bp):
TTCGAAACACGAATATTAATTTCGAA
Found at i:268757 original size:22 final size:22
Alignment explanation
Indices: 268732--268786 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
268722 TCTCTCACTC
268732 TCTCCGGCGACATCCATCCCCA
1 TCTCCGGCGACATCCATCCCCA
* *
268754 TCTCCGACGACATCCGTCCCCA
1 TCTCCGGCGACATCCATCCCCA
*
268776 TATCCGGCGAC
1 TCTCCGGCGAC
268787 CCCCTCCATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.18, C:0.47, G:0.16, T:0.18
Consensus pattern (22 bp):
TCTCCGGCGACATCCATCCCCA
Found at i:269150 original size:20 final size:20
Alignment explanation
Indices: 269127--269177 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
269117 TTTGAAACTT
269127 AAATTCGCAACACGAAAATG
1 AAATTCGCAACACGAAAATG
*
269147 AAATTTGCAACACGAAAATG
1 AAATTCGCAACACGAAAATG
269167 AAATTCGCAAC
1 AAATTCGCAAC
269178 GCGATTTTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.49, C:0.20, G:0.14, T:0.18
Consensus pattern (20 bp):
AAATTCGCAACACGAAAATG
Found at i:270827 original size:18 final size:18
Alignment explanation
Indices: 270806--270845 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
270796 ACTTCGACAC
*
270806 CGAGATCCATCACCTGAT
1 CGAGAGCCATCACCTGAT
270824 CGAGAGCCATCACCTGAT
1 CGAGAGCCATCACCTGAT
270842 CGAG
1 CGAG
270846 TCGATTCTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.28, C:0.33, G:0.23, T:0.17
Consensus pattern (18 bp):
CGAGAGCCATCACCTGAT
Found at i:270863 original size:60 final size:60
Alignment explanation
Indices: 270764--270880 Score: 153
Period size: 60 Copynumber: 1.9 Consensus size: 60
270754 ACTTCGGCAC
* ** * * * *
270764 CGAGATCCATCACCTCATCGAGCCTCTTCTCCACTTCGACACCGAGATCCATCACCTGAT
1 CGAGAGCCATCACCTCATCGAGCCGATTCTACACCTCGACACCAAGAGCCATCACCTGAT
* *
270824 CGAGAGCCATCACCTGATCGAGTCGATTCTACACCTCGACACCAAGAGCCATCACCT
1 CGAGAGCCATCACCTCATCGAGCCGATTCTACACCTCGACACCAAGAGCCATCACCT
270881 ATTCCATCAC
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.26, C:0.38, G:0.15, T:0.21
Consensus pattern (60 bp):
CGAGAGCCATCACCTCATCGAGCCGATTCTACACCTCGACACCAAGAGCCATCACCTGAT
Found at i:271019 original size:21 final size:21
Alignment explanation
Indices: 270995--271047 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
270985 GTTAGGAGAG
270995 TTACGTGATGAGGTC-AGTGCT
1 TTACGTGATGAGGTCGA-TGCT
*
271016 TTACGTGATAAGGTCGATGCT
1 TTACGTGATGAGGTCGATGCT
*
271037 TTACCTGATGA
1 TTACGTGATGA
271048 CAATGGTGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.34
Consensus pattern (21 bp):
TTACGTGATGAGGTCGATGCT
Found at i:271141 original size:21 final size:21
Alignment explanation
Indices: 271117--271162 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
271107 ATAACAATGG
* *
271117 TGCTTTACGTGGTGAGGTATC
1 TGCTTTACGTGATGAGGTAAC
271138 TGCTTTACGTGATGAGGTAAC
1 TGCTTTACGTGATGAGGTAAC
271159 TGCT
1 TGCT
271163 CTGCGTGAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.17, C:0.15, G:0.30, T:0.37
Consensus pattern (21 bp):
TGCTTTACGTGATGAGGTAAC
Found at i:271169 original size:21 final size:21
Alignment explanation
Indices: 271117--271170 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
271107 ATAACAATGG
* * *
271117 TGCTTTACGTGGTGAGGTATC
1 TGCTCTACGTGATGAGGTAAC
*
271138 TGCTTTACGTGATGAGGTAAC
1 TGCTCTACGTGATGAGGTAAC
*
271159 TGCTCTGCGTGA
1 TGCTCTACGTGA
271171 GATTGTTTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.17, C:0.17, G:0.31, T:0.35
Consensus pattern (21 bp):
TGCTCTACGTGATGAGGTAAC
Found at i:271267 original size:4 final size:4
Alignment explanation
Indices: 271258--271303 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
271248 TTTTTCGGCA
* * * *
271258 TTAT TTAT TTAT TTAT TTAT TTAC TGAT TTAT GTAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
271304 TTAGCGGCCC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.67
Consensus pattern (4 bp):
TTAT
Found at i:271508 original size:42 final size:42
Alignment explanation
Indices: 271437--271590 Score: 132
Period size: 42 Copynumber: 3.7 Consensus size: 42
271427 GAAGAAGCTC
* * * *
271437 GATCCACCTACCATTGTTTAGAATCCACCTACCATTGTTCAG
1 GATCCACCTCCCATTGTTCAGGATCCACCTACCATCGTTCAG
* ** * * *
271479 GATCCACCTCCCATTGTTCAGGATTCACCTGTCATCATTTAA
1 GATCCACCTCCCATTGTTCAGGATCCACCTACCATCGTTCAG
* * * * *
271521 GAGGCC-CCTCCCATCGTTCAAGAGGCC-CCTCCCATCGTTCAG
1 GA-TCCACCTCCCATTGTTCAGGA-TCCACCTACCATCGTTCAG
*
271563 GATCCACCTCCCACTGTTCAGGATCCAC
1 GATCCACCTCCCATTGTTCAGGATCCAC
271591 ATGGTATACT
Statistics
Matches: 83, Mismatches: 25, Indels: 8
0.72 0.22 0.07
Matches are distributed among these distances:
41 4 0.05
42 76 0.92
43 3 0.04
ACGTcount: A:0.22, C:0.36, G:0.15, T:0.27
Consensus pattern (42 bp):
GATCCACCTCCCATTGTTCAGGATCCACCTACCATCGTTCAG
Found at i:271572 original size:21 final size:21
Alignment explanation
Indices: 271437--271590 Score: 116
Period size: 21 Copynumber: 7.3 Consensus size: 21
271427 GAAGAAGCTC
* * *
271437 GATCCACCTACCATTGTTTAG
1 GATCCACCTCCCATCGTTCAG
* * *
271458 AATCCACCTACCATTGTTCAG
1 GATCCACCTCCCATCGTTCAG
*
271479 GATCCACCTCCCATTGTTCAG
1 GATCCACCTCCCATCGTTCAG
* ** * * *
271500 GATTCACCTGTCATCATTTAA
1 GATCCACCTCCCATCGTTCAG
* *
271521 GAGGCC-CCTCCCATCGTTCAA
1 GA-TCCACCTCCCATCGTTCAG
*
271542 GAGGCC-CCTCCCATCGTTCAG
1 GA-TCCACCTCCCATCGTTCAG
271563 GATCCACCTCCCA-CTGTTCAG
1 GATCCACCTCCCATC-GTTCAG
271584 GATCCAC
1 GATCCAC
271591 ATGGTATACT
Statistics
Matches: 111, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
20 3 0.03
21 107 0.96
22 1 0.01
ACGTcount: A:0.22, C:0.36, G:0.15, T:0.27
Consensus pattern (21 bp):
GATCCACCTCCCATCGTTCAG
Found at i:273026 original size:16 final size:16
Alignment explanation
Indices: 272997--273032 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
272987 TGTAAATAAA
* *
272997 AATTGTTTTTTTGTTT
1 AATTGATTTGTTGTTT
273013 AATTGATTTGTTGTTT
1 AATTGATTTGTTGTTT
273029 AATT
1 AATT
273033 TCAATATGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.14, T:0.67
Consensus pattern (16 bp):
AATTGATTTGTTGTTT
Found at i:273429 original size:12 final size:12
Alignment explanation
Indices: 273414--273454 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
273404 AAGGCGGCTG
*
273414 TGATTGGGATTT
1 TGATTGTGATTT
*
273426 TGATTTTGATTT
1 TGATTGTGATTT
273438 TGATTGTGATTT
1 TGATTGTGATTT
273450 TGATT
1 TGATT
273455 TCCTTTTGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.17, C:0.00, G:0.24, T:0.59
Consensus pattern (12 bp):
TGATTGTGATTT
Found at i:273430 original size:6 final size:6
Alignment explanation
Indices: 273421--273455 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
273411 CTGTGATTGG
*
273421 GATTTT GATTTT GATTTT GATTGT GATTTT GATTT
1 GATTTT GATTTT GATTTT GATTTT GATTTT GATTT
273456 CCTTTTGCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.17, C:0.00, G:0.20, T:0.63
Consensus pattern (6 bp):
GATTTT
Found at i:276225 original size:17 final size:17
Alignment explanation
Indices: 276203--276237 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
276193 AACCATCGTC
276203 ATCTAGCCCAAAATGTG
1 ATCTAGCCCAAAATGTG
276220 ATCTAGCCCAAAATGTG
1 ATCTAGCCCAAAATGTG
276237 A
1 A
276238 AGCTATCGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (17 bp):
ATCTAGCCCAAAATGTG
Found at i:277330 original size:23 final size:23
Alignment explanation
Indices: 277303--277381 Score: 60
Period size: 23 Copynumber: 3.5 Consensus size: 23
277293 GCATGGCTTT
277303 GTGCATCGATGCACATTCAAGGA
1 GTGCATCGATGCACATTCAAGGA
*
277326 GTGCATC-AGTGCATC-TTC-ATGA
1 GTGCATCGA-TGCA-CATTCAAGGA
* *
277348 -TGTATCGATGCACATATAAAGG-
1 GTGCATCGATGCACAT-TCAAGGA
277370 GATGCATCGATG
1 G-TGCATCGATG
277382 TACTGTTCAG
Statistics
Matches: 43, Mismatches: 5, Indels: 15
0.68 0.08 0.24
Matches are distributed among these distances:
20 1 0.02
21 10 0.23
22 6 0.14
23 16 0.37
24 10 0.23
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (23 bp):
GTGCATCGATGCACATTCAAGGA
Found at i:281483 original size:23 final size:23
Alignment explanation
Indices: 281432--281506 Score: 120
Period size: 23 Copynumber: 3.3 Consensus size: 23
281422 AGGGTGTCAA
281432 AGTGCATCCATGCACC--CCAGC-
1 AGTGCATCCATGCACCTGCCA-CT
281453 AGTGCATCCATGCACCTGCCACT
1 AGTGCATCCATGCACCTGCCACT
281476 AGTGCATCCATGCACCTGCCACT
1 AGTGCATCCATGCACCTGCCACT
281499 AGTGCATC
1 AGTGCATC
281507 GATGTATCAG
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
21 16 0.31
22 1 0.02
23 34 0.67
ACGTcount: A:0.23, C:0.39, G:0.19, T:0.20
Consensus pattern (23 bp):
AGTGCATCCATGCACCTGCCACT
Found at i:281578 original size:20 final size:20
Alignment explanation
Indices: 281553--281607 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
281543 AATGCAATTA
*
281553 GTGCATCAATGCACCCTGCT
1 GTGCATCCATGCACCCTGCT
* *
281573 GTGCATCCATGCAACCTGTT
1 GTGCATCCATGCACCCTGCT
281593 GTGCATCCATGCACC
1 GTGCATCCATGCACC
281608 AAGGCTGTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.20, C:0.35, G:0.20, T:0.25
Consensus pattern (20 bp):
GTGCATCCATGCACCCTGCT
Found at i:284008 original size:48 final size:48
Alignment explanation
Indices: 283956--284051 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
283946 TTATTGAGGG
283956 GGAGCTTTGTTTTTTCAAATAAGTTTTAAAATGTCAAATTTACTACTT
1 GGAGCTTTGTTTTTTCAAATAAGTTTTAAAATGTCAAATTTACTACTT
284004 GGAGCTTTGTTTTTTCAAATAAGTTTTAAAATGTCAAATTTACTACTT
1 GGAGCTTTGTTTTTTCAAATAAGTTTTAAAATGTCAAATTTACTACTT
284052 ACTCTCCAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.46
Consensus pattern (48 bp):
GGAGCTTTGTTTTTTCAAATAAGTTTTAAAATGTCAAATTTACTACTT
Found at i:286526 original size:12 final size:12
Alignment explanation
Indices: 286511--286535 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
286501 TTTTCGAGGA
286511 CTTTTTCTTCTT
1 CTTTTTCTTCTT
286523 CTTTTTCTTCTT
1 CTTTTTCTTCTT
286535 C
1 C
286536 AGGGTTATAT
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:286749 original size:24 final size:24
Alignment explanation
Indices: 286722--286787 Score: 123
Period size: 24 Copynumber: 2.8 Consensus size: 24
286712 CAAAATCTGA
*
286722 GTATTGGCCAAGATCAAAGTCCGG
1 GTATTGACCAAGATCAAAGTCCGG
286746 GTATTGACCAAGATCAAAGTCCGG
1 GTATTGACCAAGATCAAAGTCCGG
286770 GTATTGACCAAGATCAAA
1 GTATTGACCAAGATCAAA
286788 TTTCGAATAC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.21
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTCCGG
Found at i:286801 original size:24 final size:24
Alignment explanation
Indices: 286729--286801 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 24
286719 TGAGTATTGG
** *
286729 CCAAGATCAAAGTCCGGGTATTGA
1 CCAAGATCAAAGTCCGAATACTGA
** *
286753 CCAAGATCAAAGTCCGGGTATTGA
1 CCAAGATCAAAGTCCGAATACTGA
* *
286777 CCAAGATCAAATTTCGAATACTGA
1 CCAAGATCAAAGTCCGAATACTGA
286801 C
1 C
286802 TAGTACTCAC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.22
Consensus pattern (24 bp):
CCAAGATCAAAGTCCGAATACTGA
Found at i:286934 original size:12 final size:12
Alignment explanation
Indices: 286913--286946 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
286903 GGTTGTGGGT
*
286913 TTTGAGATTGTG
1 TTTGATATTGTG
286925 TTTGATATTGTG
1 TTTGATATTGTG
*
286937 TTTGGTATTG
1 TTTGATATTG
286947 GAAATGTGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:287731 original size:15 final size:15
Alignment explanation
Indices: 287711--287739 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
287701 TACCCAAAAC
287711 ATTTGTGTTGCGAAA
1 ATTTGTGTTGCGAAA
287726 ATTTGTGTTGCGAA
1 ATTTGTGTTGCGAA
287740 TTCGGAAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.07, G:0.28, T:0.41
Consensus pattern (15 bp):
ATTTGTGTTGCGAAA
Found at i:287836 original size:40 final size:39
Alignment explanation
Indices: 287722--287880 Score: 113
Period size: 40 Copynumber: 3.9 Consensus size: 39
287712 TTTGTGTTGC
*** *
287722 GAAAATTTGTGTTGCGAATTCGGAAATCGAGTTGCGAAAA
1 GAAAA-TTGTGTTGCGAATTTAAAAATCGTGTTGCGAAAA
* * * *
287762 CAAAATTCGTGTTGTGAA-TTAGAAATTCTTGTTGCGAAAA
1 GAAAATT-GTGTTGCGAATTTA-AAAATCGTGTTGCGAAAA
* * *
287802 GGAAACTTGTGTTGCGAATTTAAAAATCGCGTTGCTAAAAA
1 -GAAAATTGTGTTGCGAATTTAAAAATCGTGTTGC-GAAAA
* ** * *
287843 GAAATTTGCATTGCGAATTTGAAATTCCGTGTTGCGAA
1 GAAAATTGTGTTGCGAATTTAAAAAT-CGTGTTGCGAA
287881 CGAATTTGGA
Statistics
Matches: 91, Mismatches: 22, Indels: 12
0.73 0.18 0.10
Matches are distributed among these distances:
39 3 0.03
40 69 0.76
41 19 0.21
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.31
Consensus pattern (39 bp):
GAAAATTGTGTTGCGAATTTAAAAATCGTGTTGCGAAAA
Found at i:287848 original size:80 final size:81
Alignment explanation
Indices: 287728--287880 Score: 184
Period size: 80 Copynumber: 1.9 Consensus size: 81
287718 TTGCGAAAAT
** ** * *
287728 TTGTGTTGCGAATTCGGAAATCGAGTTGCGAAAACAAAATTCGTGTTGTGAATTAGAAATT-CTT
1 TTGTGTTGCGAATTCAAAAATCGAGTTGCGAAAACAAAATTCGCATTGCGAATTAGAAATTCCGT
287792 GTTGCGAAAAGGAAAC
66 GTTGCGAAAAGGAAAC
* * * * *
287808 TTGTGTTGCGAATTTAAAAATCGCGTTGCTAAAA-AGAAATTTGCATTGCGAATTTGAAATTCCG
1 TTGTGTTGCGAATTCAAAAATCGAGTTGCGAAAACA-AAATTCGCATTGCGAATTAGAAATTCCG
287872 TGTTGCGAA
65 TGTTGCGAA
287881 CGAATTTGGA
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
79 1 0.02
80 49 0.82
81 10 0.17
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.32
Consensus pattern (81 bp):
TTGTGTTGCGAATTCAAAAATCGAGTTGCGAAAACAAAATTCGCATTGCGAATTAGAAATTCCGT
GTTGCGAAAAGGAAAC
Found at i:287946 original size:20 final size:21
Alignment explanation
Indices: 287921--287965 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
287911 GTTCGTGTTC
287921 CGAATTT-GAAAACCGCATTG
1 CGAATTTAGAAAACCGCATTG
* *
287941 CGAATTTAGAAAATCGCGTTG
1 CGAATTTAGAAAACCGCATTG
287962 CGAA
1 CGAA
287966 AAAGAAATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (21 bp):
CGAATTTAGAAAACCGCATTG
Found at i:288007 original size:20 final size:21
Alignment explanation
Indices: 287976--288028 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
287966 AAAGAAATTC
*
287976 GAGTTGTG-AATTTCAAAACT
1 GAGTTGCGAAATTTCAAAACT
**
287996 GAGTTGC-AAATTTGGAAACT
1 GAGTTGCGAAATTTCAAAACT
*
288016 GTGTTGCGAAATT
1 GAGTTGCGAAATT
288029 GGAGATCGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 22 0.81
21 5 0.19
ACGTcount: A:0.32, C:0.09, G:0.25, T:0.34
Consensus pattern (21 bp):
GAGTTGCGAAATTTCAAAACT
Found at i:288030 original size:20 final size:21
Alignment explanation
Indices: 287991--288049 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 21
287981 GTGAATTTCA
*
287991 AAACTGAGTTGC-AAATTTGG
1 AAACTGTGTTGCGAAATTTGG
288011 AAACTGTGTTGCGAAA-TTGG
1 AAACTGTGTTGCGAAATTTGG
*
288031 AGA-TCGTGTTGCG-AATTTG
1 AAACT-GTGTTGCGAAATTTG
288050 TTGGTTATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 3 0.09
20 28 0.82
21 3 0.09
ACGTcount: A:0.29, C:0.10, G:0.29, T:0.32
Consensus pattern (21 bp):
AAACTGTGTTGCGAAATTTGG
Found at i:288038 original size:121 final size:123
Alignment explanation
Indices: 287813--288049 Score: 320
Period size: 121 Copynumber: 1.9 Consensus size: 123
287803 GAAACTTGTG
* * * * *
287813 TTGCGAATTTAAAAATCGCGTTGCTAAAAAGAAATTTGCATTGCGAATTTGAAATTCCGTGTTGC
1 TTGCGAATTTAAAAATCGCGTTGCGAAAAAGAAATTCGCATTGCGAATTTCAAATACCGAGTTGC
*
287878 GAACGAATTTGGAAACTGCGTTGCGAAATTGGAGTTCGTGTTCCGAATTTGAAAACCGCA
66 -AAC-AATTTGGAAACTGCGTTGCGAAATTGGAGATCGTGTTCCGAATTTGAAAACCGCA
* *
287938 TTGCGAATTTAGAAAATCGCGTTGCGAAAAAGAAATTCG-AGTTGTGAATTTCAAA-ACTGAGTT
1 TTGCGAATTTA-AAAATCGCGTTGCGAAAAAGAAATTCGCA-TTGCGAATTTCAAATACCGAGTT
* *
288001 GC-A-AATTTGGAAACTGTGTTGCGAAATTGGAGATCGTGTTGCGAATTTG
64 GCAACAATTTGGAAACTGCGTTGCGAAATTGGAGATCGTGTTCCGAATTTG
288050 TTGGTTATTT
Statistics
Matches: 100, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
121 43 0.43
123 1 0.01
125 19 0.19
126 37 0.37
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (123 bp):
TTGCGAATTTAAAAATCGCGTTGCGAAAAAGAAATTCGCATTGCGAATTTCAAATACCGAGTTGC
AACAATTTGGAAACTGCGTTGCGAAATTGGAGATCGTGTTCCGAATTTGAAAACCGCA
Found at i:293351 original size:64 final size:64
Alignment explanation
Indices: 293250--293373 Score: 155
Period size: 64 Copynumber: 1.9 Consensus size: 64
293240 ATGCACTCTT
* * *
293250 TTAAAATAAAAATATCGAATGCAATTAGTACATCGATGCATAAGGCA-TGCATCGATGCATCCCA
1 TTAAAATAAAAACATCGAATGCAATTAGTACACCGATGCACAA-GCAGTGCATCGATGCATCCCA
* *
293314 TTAATAAT-AAAACATCGAATGCAATTTA-TGCACCGATGCACAAGTAGTGCATCGATGCAT
1 TTAA-AATAAAAACATCGAATGCAA-TTAGTACACCGATGCACAAGCAGTGCATCGATGCAT
293374 ACCTTCATTA
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
63 2 0.04
64 44 0.85
65 6 0.12
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.26
Consensus pattern (64 bp):
TTAAAATAAAAACATCGAATGCAATTAGTACACCGATGCACAAGCAGTGCATCGATGCATCCCA
Found at i:293794 original size:29 final size:29
Alignment explanation
Indices: 293756--293830 Score: 134
Period size: 29 Copynumber: 2.6 Consensus size: 29
293746 ATATGAGATC
*
293756 ATGACATGAGCTACATGATCACAAGAGAG
1 ATGACATGAGCTACATGATCACAAGAGAA
293785 ATGACATGAGCTACATGATCACAAGAGAA
1 ATGACATGAGCTACATGATCACAAGAGAA
293814 ATGACATGAG-TACATGA
1 ATGACATGAGCTACATGA
293831 ACATATGAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
28 7 0.16
29 38 0.84
ACGTcount: A:0.43, C:0.16, G:0.23, T:0.19
Consensus pattern (29 bp):
ATGACATGAGCTACATGATCACAAGAGAA
Found at i:296198 original size:32 final size:32
Alignment explanation
Indices: 296162--296225 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
296152 AAAGAAAGAC
296162 AAATTAGTGAATTTGTGGAAAATCCTTAGTGT
1 AAATTAGTGAATTTGTGGAAAATCCTTAGTGT
296194 AAATTAGTGAATTTGTGGAAAATCCTTAGTGT
1 AAATTAGTGAATTTGTGGAAAATCCTTAGTGT
296226 GGATAGCTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.06, G:0.22, T:0.38
Consensus pattern (32 bp):
AAATTAGTGAATTTGTGGAAAATCCTTAGTGT
Found at i:301494 original size:21 final size:21
Alignment explanation
Indices: 301468--301507 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
301458 CCCCCTTTGA
*
301468 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
301489 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
301508 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:309647 original size:36 final size:36
Alignment explanation
Indices: 309600--309671 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
309590 CTATCTTACC
309600 TCCCCCTTACCCCATTACATATGGGAACAAGGGAGA
1 TCCCCCTTACCCCATTACATATGGGAACAAGGGAGA
309636 TCCCCCTTACCCCATTACATATGGGAACAAGGGAGA
1 TCCCCCTTACCCCATTACATATGGGAACAAGGGAGA
309672 GCCATTTGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.31, C:0.31, G:0.19, T:0.19
Consensus pattern (36 bp):
TCCCCCTTACCCCATTACATATGGGAACAAGGGAGA
Found at i:309940 original size:17 final size:17
Alignment explanation
Indices: 309918--309963 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 17
309908 TTGGAAGAAT
*
309918 GTTTTGGGATATACTGG
1 GTTTTGGGATATACCGG
*
309935 GTTTTGGTATCTATACCGG
1 GTTTTGGGA--TATACCGG
309954 GTTTTGGGAT
1 GTTTTGGGAT
309964 GCATATGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 9 0.38
19 15 0.62
ACGTcount: A:0.15, C:0.09, G:0.33, T:0.43
Consensus pattern (17 bp):
GTTTTGGGATATACCGG
Found at i:311997 original size:37 final size:37
Alignment explanation
Indices: 311871--312011 Score: 157
Period size: 37 Copynumber: 3.9 Consensus size: 37
311861 TGGTTGGAAC
311871 ATAAAATATTTTAAGGTAATCAAATTAAAATATCAAT
1 ATAAAATATTTTAAGGTAATCAAATTAAAATATCAAT
* ** ** *
311908 AT--AGTA-CAT-AGGATAATCGTATTAAAATATC-GT
1 ATAAAATATTTTAAGG-TAATCAAATTAAAATATCAAT
*
311941 ATTATCAATATTTTAAGGTAATCAAATTAAAATATCAAT
1 A-TA-AAATATTTTAAGGTAATCAAATTAAAATATCAAT
311980 ATAAAATATTTTAAGGTAATCAAATTAAAATA
1 ATAAAATATTTTAAGGTAATCAAATTAAAATA
312012 CAGCATCCAT
Statistics
Matches: 83, Mismatches: 13, Indels: 16
0.74 0.12 0.14
Matches are distributed among these distances:
33 5 0.06
34 18 0.22
35 3 0.04
37 33 0.40
38 19 0.23
39 5 0.06
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.35
Consensus pattern (37 bp):
ATAAAATATTTTAAGGTAATCAAATTAAAATATCAAT
Found at i:314448 original size:12 final size:12
Alignment explanation
Indices: 314431--314455 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
314421 CCTTCATTCA
314431 AATTCCCTAGCC
1 AATTCCCTAGCC
314443 AATTCCCTAGCC
1 AATTCCCTAGCC
314455 A
1 A
314456 GTTGTGCCTT
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:0.28, C:0.40, G:0.08, T:0.24
Consensus pattern (12 bp):
AATTCCCTAGCC
Found at i:317544 original size:154 final size:154
Alignment explanation
Indices: 317363--317670 Score: 616
Period size: 154 Copynumber: 2.0 Consensus size: 154
317353 AGGGAGAACA
317363 CACGCAAGCAGAAAAAAATCACATTTATTTATTTTCTTTTCCTTTCTTCTTCCTTGGTATATTCC
1 CACGCAAGCAGAAAAAAATCACATTTATTTATTTTCTTTTCCTTTCTTCTTCCTTGGTATATTCC
317428 TCCATTGAAAAGCTCCAAGGAGTGGCAAGCTAGGCACCGAAAGGAGCTAGCAAGCTAGGTGGTTC
66 TCCATTGAAAAGCTCCAAGGAGTGGCAAGCTAGGCACCGAAAGGAGCTAGCAAGCTAGGTGGTTC
317493 GTGGTGGCCGAGAGGAGACCTCCG
131 GTGGTGGCCGAGAGGAGACCTCCG
317517 CACGCAAGCAGAAAAAAATCACATTTATTTATTTTCTTTTCCTTTCTTCTTCCTTGGTATATTCC
1 CACGCAAGCAGAAAAAAATCACATTTATTTATTTTCTTTTCCTTTCTTCTTCCTTGGTATATTCC
317582 TCCATTGAAAAGCTCCAAGGAGTGGCAAGCTAGGCACCGAAAGGAGCTAGCAAGCTAGGTGGTTC
66 TCCATTGAAAAGCTCCAAGGAGTGGCAAGCTAGGCACCGAAAGGAGCTAGCAAGCTAGGTGGTTC
317647 GTGGTGGCCGAGAGGAGACCTCCG
131 GTGGTGGCCGAGAGGAGACCTCCG
317671 GTGGCGCGTC
Statistics
Matches: 154, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
154 154 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (154 bp):
CACGCAAGCAGAAAAAAATCACATTTATTTATTTTCTTTTCCTTTCTTCTTCCTTGGTATATTCC
TCCATTGAAAAGCTCCAAGGAGTGGCAAGCTAGGCACCGAAAGGAGCTAGCAAGCTAGGTGGTTC
GTGGTGGCCGAGAGGAGACCTCCG
Found at i:318372 original size:16 final size:16
Alignment explanation
Indices: 318336--318369 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
318326 CAAGTGAGGA
318336 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
318352 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
318369 T
1 T
318370 ATTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:324548 original size:19 final size:21
Alignment explanation
Indices: 324511--324553 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
324501 TAACTTTTTC
324511 TTTTATCTTTCATTATTAA-T
1 TTTTATCTTTCATTATTAACT
*
324531 TTTTCTCTTTCATT-TTAACT
1 TTTTATCTTTCATTATTAACT
324551 TTT
1 TTT
324554 ACCTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCTTTCATTATTAACT
Found at i:324559 original size:19 final size:20
Alignment explanation
Indices: 324510--324559 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
324500 TTAACTTTTT
*
324510 CTTTTATCTTTCATTATTAA
1 CTTTTACCTTTCATTATTAA
*
324530 -TTTTTCTCTTTCATT-TTAA
1 CTTTTAC-CTTTCATTATTAA
324549 CTTTTACCTTT
1 CTTTTACCTTT
324560 TCTCTTCTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTACCTTTCATTATTAA
Found at i:331839 original size:40 final size:40
Alignment explanation
Indices: 331783--331862 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
331773 GTCGTTGGTC
*
331783 TGGTTGAAGATGCTGCCGACAGTGACGGGAATTTTCCCGA
1 TGGTTGAAGATACTGCCGACAGTGACGGGAATTTTCCCGA
331823 TGGTTGAAGATACTGCCGACAGTGACGGGAATTTTCCCGA
1 TGGTTGAAGATACTGCCGACAGTGACGGGAATTTTCCCGA
331863 CACGAAAACT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.25
Consensus pattern (40 bp):
TGGTTGAAGATACTGCCGACAGTGACGGGAATTTTCCCGA
Found at i:332379 original size:16 final size:16
Alignment explanation
Indices: 332358--332390 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
332348 TAATAAATAA
332358 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
332374 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
332390 A
1 A
332391 AATTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:332499 original size:14 final size:13
Alignment explanation
Indices: 332482--332526 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
332472 AAACACAATC
332482 GAACAAACATAAAT
1 GAACAAA-ATAAAT
*
332496 GAACATAATAAAT
1 GAACAAAATAAAT
* *
332509 GAACACAATAAAC
1 GAACAAAATAAAT
332522 GAACA
1 GAACA
332527 TAAACGAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
13 22 0.79
14 6 0.21
ACGTcount: A:0.62, C:0.16, G:0.09, T:0.13
Consensus pattern (13 bp):
GAACAAAATAAAT
Found at i:332508 original size:13 final size:13
Alignment explanation
Indices: 332490--332529 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
332480 TCGAACAAAC
332490 ATAAATGAACATA
1 ATAAATGAACATA
*
332503 ATAAATGAACACA
1 ATAAATGAACATA
*
332516 ATAAACGAACATA
1 ATAAATGAACATA
332529 A
1 A
332530 ACGAACAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.62, C:0.12, G:0.07, T:0.17
Consensus pattern (13 bp):
ATAAATGAACATA
Found at i:333278 original size:20 final size:20
Alignment explanation
Indices: 333253--333345 Score: 118
Period size: 20 Copynumber: 4.7 Consensus size: 20
333243 TTTTCCTAAT
333253 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
333273 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATACGTAAA
*
333293 TCGCAATGCGAAT-C-TGACTA
1 TCGCAATGCGAATACGT-A-AA
*
333313 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATACGTAAA
*
333333 TCGCAACGCGAAT
1 TCGCAATGCGAAT
333346 TGACTATCGC
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
18 1 0.02
19 1 0.02
20 59 0.94
21 1 0.02
22 1 0.02
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:333303 original size:40 final size:40
Alignment explanation
Indices: 333212--333357 Score: 145
Period size: 40 Copynumber: 3.6 Consensus size: 40
333202 GTTTCCAGAT
* * * * * * * *
333212 TCGCAACGCGATTCTGACTATCGCATTGCGATTTTCCTAAT
1 TCGCAATGCGAATCTGACAATCGCAATGCGAATAT-GTAAA
333253 TCGCAATGCGAATAC-GTA-AATCGCAATGCGAATATGTAAA
1 TCGCAATGCGAAT-CTG-ACAATCGCAATGCGAATATGTAAA
*
333293 TCGCAATGCGAATCTGACTATCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATCTGACAATCGCAATGCGAATATGTAAA
* *
333333 TCGCAACGCGAAT-TGACTATCGCAA
1 TCGCAATGCGAATCTGACAATCGCAA
333358 CGAGATTCTG
Statistics
Matches: 91, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
39 14 0.15
40 50 0.55
41 25 0.27
42 2 0.02
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (40 bp):
TCGCAATGCGAATCTGACAATCGCAATGCGAATATGTAAA
Found at i:333332 original size:60 final size:59
Alignment explanation
Indices: 333253--333382 Score: 172
Period size: 60 Copynumber: 2.2 Consensus size: 59
333243 TTTTCCTAAT
* * *
333253 TCGCAATGCGAATACGTAAATCGCAATGCGAATATGTA-AATCGCAATGCGAATCTGACTA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAAT-TG-ACAATCGCAACGAGAATCTGACTA
* * *
333313 TCGCAATGCGAATATGTAAATCGCAACGCGAATTGACTATCGCAACGAGATTCTGACTA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAATTGACAATCGCAACGAGAATCTGACTA
*
333372 TCGCAACGCGA
1 TCGCAATGCGA
333383 TTCTGACTAT
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
58 1 0.02
59 30 0.48
60 31 0.50
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (59 bp):
TCGCAATGCGAATACGTAAATCGCAACGCGAATTGACAATCGCAACGAGAATCTGACTA
Found at i:333371 original size:20 final size:20
Alignment explanation
Indices: 333292--333396 Score: 115
Period size: 20 Copynumber: 5.3 Consensus size: 20
333282 GAATATGTAA
* *
333292 ATCGCAATGCGAATCTGACT
1 ATCGCAACGCGATTCTGACT
* * * *
333312 ATCGCAATGCGAATATGTA-A
1 ATCGCAACGCGATTCTG-ACT
*
333332 ATCGCAACGCGAAT-TGACT
1 ATCGCAACGCGATTCTGACT
*
333351 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
333371 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
333391 ATCGCA
1 ATCGCA
333397 GTACTGAATT
Statistics
Matches: 75, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
18 1 0.01
19 14 0.19
20 59 0.79
21 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:333375 original size:39 final size:40
Alignment explanation
Indices: 333272--333396 Score: 146
Period size: 40 Copynumber: 3.1 Consensus size: 40
333262 GAATACGTAA
* * *
333272 ATCGCAATGCGAATATGTAAATCGCAATGCGAATCTGACT
1 ATCGCAACGAGAATATGTAAATCGCAACGCGAATCTGACT
* *
333312 ATCGCAATGCGAATATGTAAATCGCAACGCGAAT-TGACT
1 ATCGCAACGAGAATATGTAAATCGCAACGCGAATCTGACT
* * * *
333351 ATCGCAACGAGATTCTG-ACTATCGCAACGCGATTCTGACT
1 ATCGCAACGAGAATATGTA-AATCGCAACGCGAATCTGACT
333391 ATCGCA
1 ATCGCA
333397 GTACTGAATT
Statistics
Matches: 76, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
38 1 0.01
39 31 0.41
40 44 0.58
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (40 bp):
ATCGCAACGAGAATATGTAAATCGCAACGCGAATCTGACT
Found at i:336732 original size:20 final size:20
Alignment explanation
Indices: 336707--336820 Score: 185
Period size: 20 Copynumber: 5.7 Consensus size: 20
336697 GACATTCATT
336707 TGACTATCGCAACGC-GAATA
1 TGACTATCGCAACGCGGAA-A
*
336727 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACGCGGAAA
336747 TGACTATCGCAACGCGGAAA
1 TGACTATCGCAACGCGGAAA
336767 TGACTATCGCAACGCGGAAA
1 TGACTATCGCAACGCGGAAA
* *
336787 TGACTATCGCAACGTGAAAA
1 TGACTATCGCAACGCGGAAA
336807 TGACTATCGCAACG
1 TGACTATCGCAACG
336821 AGAGAATCGC
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
20 86 0.97
21 3 0.03
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.18
Consensus pattern (20 bp):
TGACTATCGCAACGCGGAAA
Found at i:337016 original size:14 final size:14
Alignment explanation
Indices: 336997--337033 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
336987 AATCAATTAA
336997 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
337011 ACAAATCATCTTTT
1 ACAAATCAACATTT
337025 ACAAATCAA
1 ACAAATCAA
337034 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:338522 original size:42 final size:42
Alignment explanation
Indices: 338415--338526 Score: 111
Period size: 42 Copynumber: 2.7 Consensus size: 42
338405 TCTAGAATGT
* * **
338415 TGGGAG-GGACCTCTTCAACGATGACAGTGGCCTCTTGAACGG
1 TGGGAGAGG-CCTCTTGAACGATGACAGGGGCCTCTTGAACCA
* * ** *
338457 TGGGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACCA
1 TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACCA
338499 TAGGG-GAGGCCTCTTGAACGATGACAGG
1 T-GGGAGAGGCCTCTTGAACGATGACAGG
338527 TGAGTCGGGC
Statistics
Matches: 55, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
42 50 0.91
43 5 0.09
ACGTcount: A:0.22, C:0.20, G:0.38, T:0.21
Consensus pattern (42 bp):
TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACCA
Found at i:339168 original size:22 final size:20
Alignment explanation
Indices: 339006--339210 Score: 280
Period size: 20 Copynumber: 10.4 Consensus size: 20
338996 GAAACTTAAA
339006 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
339026 ATCGCAACACGGAAATGACT
1 ATCGCAACGCGAAAATGACT
339046 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
339066 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
339086 ATCGCAACGC-AGAAATGACT
1 ATCGCAACGCGA-AAATGACT
*
339106 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
339126 ATCGCAA--C-AAGA-GA--
1 ATCGCAACGCGAAAATGACT
339140 ATCGCAATGCGCGAAAATGACT
1 ATCGCAA--CGCGAAAATGACT
339162 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
339182 ATCGCAACGTGAAAATGACT
1 ATCGCAACGCGAAAATGACT
339202 ATCGCAACG
1 ATCGCAACG
339211 AGAGAATCGT
Statistics
Matches: 165, Mismatches: 10, Indels: 20
0.85 0.05 0.10
Matches are distributed among these distances:
14 7 0.04
16 2 0.01
17 3 0.02
18 2 0.01
19 3 0.02
20 140 0.85
21 1 0.01
22 7 0.04
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:339283 original size:20 final size:20
Alignment explanation
Indices: 339255--339293 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
339245 GATTCTTTCG
*
339255 TTGCGATAGTCATTTTCGCA
1 TTGCAATAGTCATTTTCGCA
339275 TTGCAATAGTCATTTTCGC
1 TTGCAATAGTCATTTTCGC
339294 GTTACGATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.41
Consensus pattern (20 bp):
TTGCAATAGTCATTTTCGCA
Found at i:339315 original size:14 final size:14
Alignment explanation
Indices: 339286--339329 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
339276 TGCAATAGTC
* *
339286 ATTTTCGCGTTACG
1 ATTTTCTCGTTGCG
* *
339300 ATTTTGTTGTTGCG
1 ATTTTCTCGTTGCG
339314 ATTTTCTCGTTGCG
1 ATTTTCTCGTTGCG
339328 AT
1 AT
339330 AGTCATTTTC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.50
Consensus pattern (14 bp):
ATTTTCTCGTTGCG
Found at i:339339 original size:20 final size:20
Alignment explanation
Indices: 339314--339372 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
339304 TGTTGTTGCG
*
339314 ATTTTCTCGTTGCGATAGTC
1 ATTTTCGCGTTGCGATAGTC
339334 ATTTTCGCGTTGCGATAGTC
1 ATTTTCGCGTTGCGATAGTC
*
339354 ATTTTCGCATTGCGATAGT
1 ATTTTCGCGTTGCGATAGT
339373 AAACTATTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGTC
Found at i:341273 original size:20 final size:20
Alignment explanation
Indices: 341253--341379 Score: 127
Period size: 20 Copynumber: 6.4 Consensus size: 20
341243 GAAACTTAAA
**
341253 ATCGCAACAGGAAAATGAAA
1 ATCGCAACAGGAAAATGACT
341273 ATCGCAACACGG-AAATGACT
1 ATCGCAACA-GGAAAATGACT
*
341293 ATCGCAACATGAAAATGACT
1 ATCGCAACAGGAAAATGACT
**
341313 ATCGCAAC-GCGAATTTGACT
1 ATCGCAACAG-GAAAATGACT
**
341333 ATCGCAAC-GCG-AAATGAAA
1 ATCGCAACAG-GAAAATGACT
*
341352 ATCGCAACACGAAAATGACT
1 ATCGCAACAGGAAAATGACT
341372 ATCGCAAC
1 ATCGCAAC
341380 GCAAGAATTG
Statistics
Matches: 89, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
19 14 0.16
20 73 0.82
21 2 0.02
ACGTcount: A:0.43, C:0.23, G:0.18, T:0.16
Consensus pattern (20 bp):
ATCGCAACAGGAAAATGACT
Found at i:341308 original size:40 final size:40
Alignment explanation
Indices: 341253--341379 Score: 159
Period size: 40 Copynumber: 3.2 Consensus size: 40
341243 GAAACTTAAA
*
341253 ATCGCAACAGGAAAATGAAAATCGCAACACGGAAATGACT
1 ATCGCAACACGAAAATGAAAATCGCAACACGGAAATGACT
* ** * *
341293 ATCGCAACATGAAAATGACTATCGCAACGC-GAATTTGACT
1 ATCGCAACACGAAAATGAAAATCGCAACACGGAA-ATGACT
* *
341333 ATCGCAACGCG-AAATGAAAATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGAAAATCGCAACACGGAAATGACT
341372 ATCGCAAC
1 ATCGCAAC
341380 GCAAGAATTG
Statistics
Matches: 73, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
39 31 0.42
40 42 0.58
ACGTcount: A:0.43, C:0.23, G:0.18, T:0.16
Consensus pattern (40 bp):
ATCGCAACACGAAAATGAAAATCGCAACACGGAAATGACT
Found at i:341811 original size:22 final size:22
Alignment explanation
Indices: 341749--341814 Score: 114
Period size: 22 Copynumber: 3.0 Consensus size: 22
341739 TGACCGTGAA
*
341749 TGATTTCGTCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
*
341771 TGATATCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
341793 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
341815 GGATGTCACC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.21, C:0.14, G:0.39, T:0.26
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:342033 original size:20 final size:20
Alignment explanation
Indices: 342010--342066 Score: 114
Period size: 20 Copynumber: 2.9 Consensus size: 20
342000 CGATAGTCAG
342010 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
342030 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
342050 ATTCGCATTGCGATTTA
1 ATTCGCATTGCGATTTA
342067 GGAAAATCGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:342083 original size:21 final size:20
Alignment explanation
Indices: 342059--342105 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 20
342049 TATTCGCATT
342059 GCGATTTAGGAAAATCGCAAC
1 GCGATTT-GGAAAATCGCAAC
*
342080 GCGAATTTGGAAAATCGCAAT
1 GCG-ATTTGGAAAATCGCAAC
342101 GCGAT
1 GCGAT
342106 AGTCAGAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 2 0.08
21 18 0.75
22 4 0.17
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21
Consensus pattern (20 bp):
GCGATTTGGAAAATCGCAAC
Found at i:350678 original size:16 final size:16
Alignment explanation
Indices: 350657--350689 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
350647 TGACCAGATA
350657 TGACATTTACCTAACT
1 TGACATTTACCTAACT
*
350673 TGACATTTACCTGACT
1 TGACATTTACCTAACT
350689 T
1 T
350690 ATATTATCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.24, G:0.09, T:0.39
Consensus pattern (16 bp):
TGACATTTACCTAACT
Found at i:351366 original size:12 final size:12
Alignment explanation
Indices: 351349--351374 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
351339 TCATGCTGAA
351349 TTGCATTTCATG
1 TTGCATTTCATG
351361 TTGCATTTCATG
1 TTGCATTTCATG
351373 TT
1 TT
351375 AGATAGTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.54
Consensus pattern (12 bp):
TTGCATTTCATG
Found at i:351600 original size:29 final size:29
Alignment explanation
Indices: 351567--351651 Score: 161
Period size: 29 Copynumber: 2.9 Consensus size: 29
351557 TCCCAACACA
351567 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCCCTCCGGGCGACCTTG
351596 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCCCTCCGGGCGACCTTG
*
351625 TAGGTCGCCATGCACTCCGGGCGACCT
1 TAGGTCGCCATGCCCTCCGGGCGACCT
351652 ACCCTCGCTC
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 55 1.00
ACGTcount: A:0.12, C:0.38, G:0.31, T:0.20
Consensus pattern (29 bp):
TAGGTCGCCATGCCCTCCGGGCGACCTTG
Found at i:351727 original size:23 final size:23
Alignment explanation
Indices: 351669--351728 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
351659 CTCGGCTTCC
* *
351669 CTCGGATTCCCTCGCATAGCTTG
1 CTCGGATGCCCTCGCATAGCTCG
*
351692 CTCGGTTGCCCTCGCATAGCTCG
1 CTCGGATGCCCTCGCATAGCTCG
* *
351715 TTCGGATGGCCTCG
1 CTCGGATGCCCTCG
351729 AATGCCTAGC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.10, C:0.35, G:0.27, T:0.28
Consensus pattern (23 bp):
CTCGGATGCCCTCGCATAGCTCG
Found at i:351809 original size:29 final size:29
Alignment explanation
Indices: 351772--351829 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
351762 GCAATCTCTT
* *
351772 GTAGCTCGCCGGGAAGACATGGCGACCTA
1 GTAGCTCGCCCGGAAGACATGACGACCTA
* *
351801 GTAGGTCGCCCGGAAGGCATGACGACCTA
1 GTAGCTCGCCCGGAAGACATGACGACCTA
351830 CGGCCAACAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.24, C:0.28, G:0.34, T:0.14
Consensus pattern (29 bp):
GTAGCTCGCCCGGAAGACATGACGACCTA
Found at i:352527 original size:12 final size:11
Alignment explanation
Indices: 352500--352636 Score: 67
Period size: 12 Copynumber: 11.5 Consensus size: 11
352490 CTTCAAAGAG
*
352500 ATTTTATATTTC
1 ATTTTATA-TTA
352512 ATTTTATATTA
1 ATTTTATATTA
* *
352523 TATTTGATTTTA
1 -ATTTTATATTA
352535 ATTTTAATATTA
1 ATTTT-ATATTA
* *
352547 ATTTTTAAATAA
1 A-TTTTATATTA
**
352559 ATTAAATATTA
1 ATTTTATATTA
* *
352570 ATTTTTAAATAA
1 A-TTTTATATTA
**
352582 ATTAAATATTA
1 ATTTTATATTA
352593 ATTTTTAATATTA
1 A-TTTT-ATATTA
*
352606 TATTATAGATATTA
1 -ATT-T-TATATTA
352620 ATTTTAATATTA
1 ATTTT-ATATTA
352632 ATTTT
1 ATTTT
352637 TTAAATAAAT
Statistics
Matches: 92, Mismatches: 23, Indels: 20
0.68 0.17 0.15
Matches are distributed among these distances:
11 20 0.22
12 49 0.53
13 15 0.16
14 8 0.09
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (11 bp):
ATTTTATATTA
Found at i:352623 original size:27 final size:23
Alignment explanation
Indices: 352540--352624 Score: 125
Period size: 23 Copynumber: 3.5 Consensus size: 23
352530 TTTTAATTTT
352540 AATATTAATTTTTAAATAAATTA
1 AATATTAATTTTTAAATAAATTA
352563 AATATTAATTTTTAAATAAATTA
1 AATATTAATTTTTAAATAAATTA
*
352586 AATATTAATTTTTAATATTATATTA
1 AATATTAATTTTTAA-A-TAAATTA
352611 TAGATATTAATTTT
1 -A-ATATTAATTTT
352625 AATATTAATT
Statistics
Matches: 57, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
23 38 0.67
24 1 0.02
25 6 0.11
26 1 0.02
27 11 0.19
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (23 bp):
AATATTAATTTTTAAATAAATTA
Done.