Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003884.1 Hibiscus syriacus cultivar Beakdansim tig00008380_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: 153911
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:4626 original size:23 final size:22
Alignment explanation
Indices: 4582--4626 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
4572 CAATCTTATA
*
4582 TGGCACTACGTGCAATTCTACG
1 TGGCACTACGTGCAATTATACG
* *
4604 TGGCACTTCGGTGCATTTATACG
1 TGGCACTAC-GTGCAATTATACG
4627 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.31
Consensus pattern (22 bp):
TGGCACTACGTGCAATTATACG
Found at i:7939 original size:20 final size:21
Alignment explanation
Indices: 7901--7939 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
7891 TAAGTTTTAT
*
7901 GATTTGAGATTTTAAGGTTGG
1 GATTTGAGACTTTAAGGTTGG
*
7922 GATTT-AGACTTTATGGTT
1 GATTTGAGACTTTAAGGTT
7940 TATAAATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.23, C:0.03, G:0.28, T:0.46
Consensus pattern (21 bp):
GATTTGAGACTTTAAGGTTGG
Found at i:8222 original size:2 final size:2
Alignment explanation
Indices: 8217--8257 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
8207 TTTTTTTCAA
8217 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8258 AGCTACTCAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:8799 original size:2 final size:2
Alignment explanation
Indices: 8792--8826 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
8782 TATAATCCTA
8792 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8827 GTTTTTAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9310 original size:85 final size:86
Alignment explanation
Indices: 9201--9372 Score: 312
Period size: 85 Copynumber: 2.0 Consensus size: 86
9191 ACCATTATAT
9201 ATAATATTAAATCTTGATATTTATCTTAAAAATATAATATCTCTTTAC-T-TAATAATAATAATA
1 ATAATATTAAATCTTGATATTTATCTTAAAAATATAATATCTCTTTACTTATAATAATAATAATA
9264 ATAAATCCTTATCCACTAAAC
66 ATAAATCCTTATCCACTAAAC
9285 ATAATATTAAAATCTTGATATTTATCTTAAAAATATAATATCTCTTTACTTAATAATAATAATAA
1 ATAATATT-AAATCTTGATATTTATCTTAAAAATATAATATCTCTTTACTT-ATAATAATAATAA
9350 TAATAAATCCTTATCCACTAAAC
64 TAATAAATCCTTATCCACTAAAC
9373 TTCATTTCTT
Statistics
Matches: 84, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
84 8 0.10
85 40 0.48
86 1 0.01
88 35 0.42
ACGTcount: A:0.46, C:0.13, G:0.01, T:0.40
Consensus pattern (86 bp):
ATAATATTAAATCTTGATATTTATCTTAAAAATATAATATCTCTTTACTTATAATAATAATAATA
ATAAATCCTTATCCACTAAAC
Found at i:10614 original size:35 final size:35
Alignment explanation
Indices: 10563--10633 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
10553 GGACACGGGA
*
10563 CGCATACTTCATCAACTGCTGCCGGAACTTACGTG
1 CGCACACTTCATCAACTGCTGCCGGAACTTACGTG
10598 CGCACACTTCATCAACTGCTGCCGGAACTTACGTG
1 CGCACACTTCATCAACTGCTGCCGGAACTTACGTG
10633 C
1 C
10634 AAGATGCGTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.24
Consensus pattern (35 bp):
CGCACACTTCATCAACTGCTGCCGGAACTTACGTG
Found at i:12401 original size:22 final size:24
Alignment explanation
Indices: 12376--12426 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
12366 AGAGATATAT
12376 ATATT-TA-ATGTTTAAAAAGTTA
1 ATATTATATATGTTTAAAAAGTTA
*
12398 ATATTATATTATGTTTAAAAATTTA
1 ATATTATA-TATGTTTAAAAAGTTA
12423 ATAT
1 ATAT
12427 ATGACAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 5 0.20
23 2 0.08
25 18 0.72
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (24 bp):
ATATTATATATGTTTAAAAAGTTA
Found at i:12855 original size:2 final size:2
Alignment explanation
Indices: 12848--12874 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12838 AATTCAGTTT
12848 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 T
12875 GCATGTGTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20142 original size:4 final size:4
Alignment explanation
Indices: 20133--20159 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
20123 TCTTCATATT
20133 TAAA TAAA TAAA TAAA TAAA TAAA TAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAA
20160 GATACATAAT
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:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:25062 original size:31 final size:31
Alignment explanation
Indices: 25024--25101 Score: 147
Period size: 31 Copynumber: 2.5 Consensus size: 31
25014 ATTAACGGCG
25024 AGTGACCGATTTGTTATAAATCAATAATATT
1 AGTGACCGATTTGTTATAAATCAATAATATT
*
25055 AGTGACCGATTTGTTATAAATCAATAATGTT
1 AGTGACCGATTTGTTATAAATCAATAATATT
25086 AGTGACCGATTTGTTA
1 AGTGACCGATTTGTTA
25102 CTTTTGAAAC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (31 bp):
AGTGACCGATTTGTTATAAATCAATAATATT
Found at i:28590 original size:23 final size:25
Alignment explanation
Indices: 28542--28594 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
28532 CCAAAAAGAA
28542 AAATAAATAATATAAAATTTAGTTC
1 AAATAAATAATATAAAATTTAGTTC
28567 AAATAAATAATAT-AAA-TTAGTTC
1 AAATAAATAATATAAAATTTAGTTC
28590 AAATA
1 AAATA
28595 TTTGTGGGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 12 0.43
24 3 0.11
25 13 0.46
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.34
Consensus pattern (25 bp):
AAATAAATAATATAAAATTTAGTTC
Found at i:35139 original size:31 final size:31
Alignment explanation
Indices: 35092--35152 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
35082 TAAAATTTTC
*
35092 AAACTCAACTCGAACTCGAAAGATAATATTA
1 AAACTCAACTCAAACTCGAAAGATAATATTA
*
35123 AAACTCGACTCAAACTCGAAAGATAATATT
1 AAACTCAACTCAAACTCGAAAGATAATATT
35153 TATTTTAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.48, C:0.20, G:0.10, T:0.23
Consensus pattern (31 bp):
AAACTCAACTCAAACTCGAAAGATAATATTA
Found at i:35758 original size:11 final size:11
Alignment explanation
Indices: 35738--35804 Score: 61
Period size: 11 Copynumber: 6.4 Consensus size: 11
35728 TCATCAGATA
35738 AATA-ATTTTT
1 AATATATTTTT
35748 AATATATTTTT
1 AATATATTTTT
35759 AA-A-ATTTTAT
1 AATATATTTT-T
***
35769 AAT-TATCAAT
1 AATATATTTTT
*
35779 AGTATATTTTT
1 AATATATTTTT
35790 AATATATTTTT
1 AATATATTTTT
35801 AATA
1 AATA
35805 ATGTAATTTA
Statistics
Matches: 44, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
9 5 0.11
10 11 0.25
11 28 0.64
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (11 bp):
AATATATTTTT
Found at i:36298 original size:7 final size:7
Alignment explanation
Indices: 36286--36390 Score: 210
Period size: 7 Copynumber: 15.0 Consensus size: 7
36276 CTAAGTGCAG
36286 AAGCATC
1 AAGCATC
36293 AAGCATC
1 AAGCATC
36300 AAGCATC
1 AAGCATC
36307 AAGCATC
1 AAGCATC
36314 AAGCATC
1 AAGCATC
36321 AAGCATC
1 AAGCATC
36328 AAGCATC
1 AAGCATC
36335 AAGCATC
1 AAGCATC
36342 AAGCATC
1 AAGCATC
36349 AAGCATC
1 AAGCATC
36356 AAGCATC
1 AAGCATC
36363 AAGCATC
1 AAGCATC
36370 AAGCATC
1 AAGCATC
36377 AAGCATC
1 AAGCATC
36384 AAGCATC
1 AAGCATC
36391 GAATGAACTG
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 98 1.00
ACGTcount: A:0.43, C:0.29, G:0.14, T:0.14
Consensus pattern (7 bp):
AAGCATC
Found at i:39177 original size:15 final size:16
Alignment explanation
Indices: 39142--39177 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
39132 CCGTAATGCG
39142 CCCCCCACCTACAGCA
1 CCCCCCACCTACAGCA
*
39158 CCCCCCACGTACAGCA
1 CCCCCCACCTACAGCA
39174 CCCC
1 CCCC
39178 GCCTGGATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.22, C:0.64, G:0.08, T:0.06
Consensus pattern (16 bp):
CCCCCCACCTACAGCA
Found at i:45923 original size:15 final size:16
Alignment explanation
Indices: 45905--45942 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
45895 CAATTAAAAA
45905 TATTATTATTA-TTTT
1 TATTATTATTACTTTT
*
45920 TATTA-TGTTACTTTT
1 TATTATTATTACTTTT
45935 TATTATTA
1 TATTATTA
45943 ATTTATAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
14 4 0.21
15 14 0.74
16 1 0.05
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (16 bp):
TATTATTATTACTTTT
Found at i:46805 original size:2 final size:2
Alignment explanation
Indices: 46798--46919 Score: 116
Period size: 2 Copynumber: 65.0 Consensus size: 2
46788 TTAATTATTT
46798 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
* * * * *
46840 TA T- TA -A TA AA TT TA -A TT TA -A TT TA AA T- TA -A 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
* * *
46876 TA TA TA TA TA TA TA -A TA TA TA TA TA TT TA -A TT TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
46916 TA TA
1 TA TA
46920 CCCGGCCTGA
Statistics
Matches: 96, Mismatches: 16, Indels: 16
0.75 0.12 0.12
Matches are distributed among these distances:
1 8 0.08
2 88 0.92
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:52394 original size:23 final size:23
Alignment explanation
Indices: 52368--52444 Score: 91
Period size: 23 Copynumber: 3.3 Consensus size: 23
52358 TACCAAAGTG
* *
52368 CCACATAGAAATGTTTTGAAGGA
1 CCACATAGAAATGTCTCGAAGGA
* *
52391 CCACATAGTATTGTCTCGAAGGA
1 CCACATAGAAATGTCTCGAAGGA
* * *
52414 CCGCGTAGAAATGTCCCGAAGGA
1 CCACATAGAAATGTCTCGAAGGA
52437 CCACATAG
1 CCACATAG
52445 TTTTGTCCCG
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.21
Consensus pattern (23 bp):
CCACATAGAAATGTCTCGAAGGA
Found at i:52451 original size:23 final size:23
Alignment explanation
Indices: 52385--52461 Score: 100
Period size: 23 Copynumber: 3.3 Consensus size: 23
52375 GAAATGTTTT
*
52385 GAAGGACCACATAGTATTGTCTC
1 GAAGGACCACATAGTATTGTCCC
* * * *
52408 GAAGGACCGCGTAGAAATGTCCC
1 GAAGGACCACATAGTATTGTCCC
*
52431 GAAGGACCACATAGTTTTGTCCC
1 GAAGGACCACATAGTATTGTCCC
52454 GAAGGACC
1 GAAGGACC
52462 GCGTAGAATC
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.30, C:0.25, G:0.26, T:0.19
Consensus pattern (23 bp):
GAAGGACCACATAGTATTGTCCC
Found at i:53941 original size:30 final size:31
Alignment explanation
Indices: 53907--53965 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
53897 GAAAAATTCA
*
53907 GGGA-CAATTCTA-TAATTTTTGAAAAGTTAG
1 GGGACCAATT-TAGTAATTTTGGAAAAGTTAG
*
53937 GGGACCAATTTAGTAATTTTGGTAAAGTT
1 GGGACCAATTTAGTAATTTTGGAAAAGTT
53966 GGGAATAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 6 0.24
31 19 0.76
ACGTcount: A:0.34, C:0.07, G:0.22, T:0.37
Consensus pattern (31 bp):
GGGACCAATTTAGTAATTTTGGAAAAGTTAG
Found at i:54515 original size:24 final size:24
Alignment explanation
Indices: 54488--54557 Score: 131
Period size: 24 Copynumber: 2.9 Consensus size: 24
54478 TGCATGACAT
54488 TGTACATAGATGTTTTATACATCA
1 TGTACATAGATGTTTTATACATCA
*
54512 TGTACATAGAGGTTTTATACATCA
1 TGTACATAGATGTTTTATACATCA
54536 TGTACATAGATGTTTTATACAT
1 TGTACATAGATGTTTTATACAT
54558 TATCAGGAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.41
Consensus pattern (24 bp):
TGTACATAGATGTTTTATACATCA
Found at i:55088 original size:7 final size:7
Alignment explanation
Indices: 55076--55114 Score: 69
Period size: 7 Copynumber: 5.4 Consensus size: 7
55066 TTGGGCTATT
55076 GTTTATG
1 GTTTATG
55083 GTTTATG
1 GTTTATG
55090 GTTTATG
1 GTTTATG
55097 GTTTATG
1 GTTTATG
55104 GTTTATTG
1 GTTTA-TG
55112 GTT
1 GTT
55115 AATGAATGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 26 0.84
8 5 0.16
ACGTcount: A:0.13, C:0.00, G:0.28, T:0.59
Consensus pattern (7 bp):
GTTTATG
Found at i:62294 original size:24 final size:24
Alignment explanation
Indices: 62267--62315 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
62257 TGCATGACAT
62267 TGTACATAGATGTTTTATACATCA
1 TGTACATAGATGTTTTATACATCA
62291 TGTACATAGATGTTTTATACATCA
1 TGTACATAGATGTTTTATACATCA
62315 T
1 T
62316 CAGGAAGACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (24 bp):
TGTACATAGATGTTTTATACATCA
Found at i:62850 original size:14 final size:15
Alignment explanation
Indices: 62827--62867 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
62817 TATATTGGCC
62827 TATT-GTTTATGATT
1 TATTGGTTTATGATT
*
62841 TA-TGGTTTATGGTT
1 TATTGGTTTATGATT
*
62855 TATTGGTTAATGA
1 TATTGGTTTATGA
62868 ATGATAAACA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
13 1 0.05
14 13 0.59
15 8 0.36
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.56
Consensus pattern (15 bp):
TATTGGTTTATGATT
Found at i:65776 original size:21 final size:20
Alignment explanation
Indices: 65752--65802 Score: 75
Period size: 21 Copynumber: 2.5 Consensus size: 20
65742 TCTGAATCGT
*
65752 AGTATCGATATTGTTCTTGTG
1 AGTATCGATATTGCTCTTG-G
*
65773 AGTATCGACATTGCTCTTGG
1 AGTATCGATATTGCTCTTGG
65793 AGTATCGATA
1 AGTATCGATA
65803 CTCATATCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.39
Consensus pattern (20 bp):
AGTATCGATATTGCTCTTGG
Found at i:65846 original size:32 final size:32
Alignment explanation
Indices: 65782--65846 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
65772 GAGTATCGAC
* *
65782 ATTGCTCTTGGAGTATCGATACTCATATCAAT
1 ATTGCTCTTGGAGTACCGATACTCATACCAAT
* * **
65814 ATTGTTCTTTGAGTACCGATACTTGTACCAAT
1 ATTGCTCTTGGAGTACCGATACTCATACCAAT
65846 A
1 A
65847 CCCATACCAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.38
Consensus pattern (32 bp):
ATTGCTCTTGGAGTACCGATACTCATACCAAT
Found at i:65854 original size:12 final size:12
Alignment explanation
Indices: 65839--65871 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
65829 CCGATACTTG
65839 TACCAATACCCA
1 TACCAATACCCA
65851 TACCAATACCCA
1 TACCAATACCCA
*
65863 TATCAATAC
1 TACCAATAC
65872 TGTTAGAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.42, C:0.36, G:0.00, T:0.21
Consensus pattern (12 bp):
TACCAATACCCA
Found at i:67842 original size:20 final size:19
Alignment explanation
Indices: 67817--67883 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 19
67807 AGGTAATTAA
67817 TTGCGAAAATGAAATTCGCG
1 TTGCGAAAATGAAA-TCGCG
***
67837 TTGCGATTTTGGAGAATCGCG
1 TTGCGAAAAT-GA-AATCGCG
*
67858 TTGCGAAAACGAAAATCGCG
1 TTGCGAAAATG-AAATCGCG
*
67878 ATGCGA
1 TTGCGA
67884 TAGTACTGTT
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
20 20 0.56
21 14 0.39
22 2 0.06
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.24
Consensus pattern (19 bp):
TTGCGAAAATGAAATCGCG
Found at i:67959 original size:20 final size:20
Alignment explanation
Indices: 67934--68103 Score: 198
Period size: 20 Copynumber: 8.5 Consensus size: 20
67924 TAACTTCTGT
67934 GTTGCGATTTACATATTCGC
1 GTTGCGATTTACATATTCGC
* *
67954 GTTGCGATTTATATATTCGG
1 GTTGCGATTTACATATTCGC
**
67974 GTTGCGATTTACATATTATC
1 GTTGCGATTTACATATTCGC
*
67994 GTTGCGATTTACCTATTCGC
1 GTTGCGATTTACATATTCGC
*
68014 GTTGCGATTTACCTATTCGC
1 GTTGCGATTTACATATTCGC
* **
68034 GTTGCGAATTACATATTATC
1 GTTGCGATTTACATATTCGC
* * **
68054 ATTGCGAATTACATATTATC
1 GTTGCGATTTACATATTCGC
*
68074 ATTGCGATTTA-ACTATTCGC
1 GTTGCGATTTACA-TATTCGC
68094 GTTGCGATTT
1 GTTGCGATTT
68104 TAACTTTCGC
Statistics
Matches: 131, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
19 1 0.01
20 130 0.99
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.42
Consensus pattern (20 bp):
GTTGCGATTTACATATTCGC
Found at i:68002 original size:60 final size:59
Alignment explanation
Indices: 67934--68103 Score: 232
Period size: 60 Copynumber: 2.8 Consensus size: 59
67924 TAACTTCTGT
*
67934 GTTGCGATTTACATATTCGCGTTGCGATTTATATATTCGGGTTGCGATTTACATATTATC
1 GTTGCGATTTACATATTCGCGTTGCGATTTA-ATATTCGCGTTGCGATTTACATATTATC
* * *
67994 GTTGCGATTTACCTATTCGCGTTGCGATTTACCTATTCGCGTTGCGAATTACATATTATC
1 GTTGCGATTTACATATTCGCGTTGCGATTTA-ATATTCGCGTTGCGATTTACATATTATC
* * ** *
68054 ATTGCGAATTACATATTATCATTGCGATTTAACTATTCGCGTTGCGATTT
1 GTTGCGATTTACATATTCGCGTTGCGATTTAA-TATTCGCGTTGCGATTT
68104 TAACTTTCGC
Statistics
Matches: 96, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
60 96 1.00
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.42
Consensus pattern (59 bp):
GTTGCGATTTACATATTCGCGTTGCGATTTAATATTCGCGTTGCGATTTACATATTATC
Found at i:68112 original size:20 final size:21
Alignment explanation
Indices: 67995--68124 Score: 87
Period size: 20 Copynumber: 6.5 Consensus size: 21
67985 CATATTATCG
* *
67995 TTGCGA-TTTACCTATTCGCG
1 TTGCGATTTTAACTATTCGCA
* *
68015 TTGCGA-TTTACCTATTCGCG
1 TTGCGATTTTAACTATTCGCA
* **
68035 TTGCGA-ATT-ACATATTATCA
1 TTGCGATTTTAAC-TATTCGCA
* **
68055 TTGCGA-ATT-ACATATTATCA
1 TTGCGATTTTAAC-TATTCGCA
*
68075 TTGCGA-TTTAACTATTCGCG
1 TTGCGATTTTAACTATTCGCA
68095 TTGCGATTTTAACT-TTCGCA
1 TTGCGATTTTAACTATTCGCA
68115 TTGCGATTTT
1 TTGCGATTTT
68125 GGAACCTGTG
Statistics
Matches: 97, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
19 1 0.01
20 87 0.90
21 9 0.09
ACGTcount: A:0.22, C:0.19, G:0.16, T:0.42
Consensus pattern (21 bp):
TTGCGATTTTAACTATTCGCA
Found at i:68117 original size:40 final size:40
Alignment explanation
Indices: 67934--68123 Score: 149
Period size: 40 Copynumber: 4.8 Consensus size: 40
67924 TAACTTCTGT
* *
67934 GTTGCGATTT-ACATATTCGCGTTGCGATTTATA-TATTCGG
1 GTTGCGATTTAAC-TATTCGCATTGCGATTTA-ACTATTCGC
** * *
67974 GTTGCGATTT-ACATATTATCGTTGCGATTTACCTATTCGC
1 GTTGCGATTTAAC-TATTCGCATTGCGATTTAACTATTCGC
* * * **
68014 GTTGCGATTTACCTATTCGCGTTGCGAATT-ACATATTATC
1 GTTGCGATTTAACTATTCGCATTGCGATTTAAC-TATTCGC
* * **
68054 ATTGCGAATT-ACATATTATCATTGCGATTTAACTATTCGC
1 GTTGCGATTTAAC-TATTCGCATTGCGATTTAACTATTCGC
68094 GTTGCGATTTTAACT-TTCGCATTGCGATTT
1 GTTGCGA-TTTAACTATTCGCATTGCGATTT
68124 TGGAACCTGT
Statistics
Matches: 119, Mismatches: 24, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
39 2 0.02
40 109 0.92
41 6 0.05
42 2 0.02
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.42
Consensus pattern (40 bp):
GTTGCGATTTAACTATTCGCATTGCGATTTAACTATTCGC
Found at i:68576 original size:13 final size:13
Alignment explanation
Indices: 68558--68583 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
68548 TAATTATTAC
68558 AAGACAGTTTTAT
1 AAGACAGTTTTAT
68571 AAGACAGTTTTAT
1 AAGACAGTTTTAT
68584 TTTTAGGATA
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:0.08, G:0.15, T:0.38
Consensus pattern (13 bp):
AAGACAGTTTTAT
Found at i:71622 original size:27 final size:28
Alignment explanation
Indices: 71580--71634 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
71570 TTTGGATTTT
*
71580 TTAAAATAATAATTTT-AATTTTTGTAA
1 TTAAAATAATAATTTTAAAATTTTGTAA
71607 TTAAAATAA-AATTTTTAAAATTTTGTAA
1 TTAAAATAATAA-TTTTAAAATTTTGTAA
71635 AGGTGACATG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 2 0.08
27 13 0.52
28 10 0.40
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (28 bp):
TTAAAATAATAATTTTAAAATTTTGTAA
Found at i:76594 original size:19 final size:19
Alignment explanation
Indices: 76556--76595 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
76546 CGAATAATTT
* * *
76556 AATCGAATATATAATTTTA
1 AATCGAATAAAAAATCTTA
76575 AATCGAATAAAAAATCTTA
1 AATCGAATAAAAAATCTTA
76594 AA
1 AA
76596 ATTCATTTAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (19 bp):
AATCGAATAAAAAATCTTA
Found at i:76714 original size:13 final size:13
Alignment explanation
Indices: 76696--76729 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
76686 TAAGATTTTC
*
76696 TTTGAAAATCATT
1 TTTGAAAATCAAT
76709 TTTG-AAATCAAT
1 TTTGAAAATCAAT
76721 TTTGAAAAT
1 TTTGAAAAT
76730 TACTTCCTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (13 bp):
TTTGAAAATCAAT
Found at i:77901 original size:15 final size:15
Alignment explanation
Indices: 77881--77909 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
77871 AATTACTTTT
77881 TCATTATCTAAACCC
1 TCATTATCTAAACCC
77896 TCATTATCTAAACC
1 TCATTATCTAAACC
77910 AAAGATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (15 bp):
TCATTATCTAAACCC
Found at i:78609 original size:15 final size:17
Alignment explanation
Indices: 78579--78611 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
78569 ATATATATAT
78579 TTTTTTTATTTCAGAAA
1 TTTTTTTATTTCAGAAA
78596 TTTTTTT-TTT-AGAAA
1 TTTTTTTATTTCAGAAA
78611 T
1 T
78612 CTTGTGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 3 0.19
17 7 0.44
ACGTcount: A:0.27, C:0.03, G:0.06, T:0.64
Consensus pattern (17 bp):
TTTTTTTATTTCAGAAA
Found at i:85933 original size:28 final size:28
Alignment explanation
Indices: 85901--85988 Score: 83
Period size: 28 Copynumber: 3.2 Consensus size: 28
85891 AGATGACCTG
85901 TTGATAATAGGTAATGACATCAAATTGA
1 TTGATAATAGGTAATGACATCAAATTGA
* * * * **
85929 TTGAT-GTTGGTATATGTAGAT-GACCT-A
1 TTGATAATAGGTA-ATG-ACATCAAATTGA
85956 TTGATAATAGGTAATGACATCAAATTGA
1 TTGATAATAGGTAATGACATCAAATTGA
85984 TTGAT
1 TTGAT
85989 GAGTTAAAGG
Statistics
Matches: 43, Mismatches: 12, Indels: 10
0.66 0.18 0.15
Matches are distributed among these distances:
26 3 0.07
27 16 0.37
28 21 0.49
29 3 0.07
ACGTcount: A:0.36, C:0.07, G:0.20, T:0.36
Consensus pattern (28 bp):
TTGATAATAGGTAATGACATCAAATTGA
Found at i:85946 original size:55 final size:55
Alignment explanation
Indices: 85880--85989 Score: 211
Period size: 55 Copynumber: 2.0 Consensus size: 55
85870 TGTGATCTTA
*
85880 TTGGTATATGTAGATGACCTGTTGATAATAGGTAATGACATCAAATTGATTGATG
1 TTGGTATATGTAGATGACCTATTGATAATAGGTAATGACATCAAATTGATTGATG
85935 TTGGTATATGTAGATGACCTATTGATAATAGGTAATGACATCAAATTGATTGATG
1 TTGGTATATGTAGATGACCTATTGATAATAGGTAATGACATCAAATTGATTGATG
85990 AGTTAAAGGA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.34, C:0.07, G:0.23, T:0.36
Consensus pattern (55 bp):
TTGGTATATGTAGATGACCTATTGATAATAGGTAATGACATCAAATTGATTGATG
Found at i:88245 original size:17 final size:19
Alignment explanation
Indices: 88215--88251 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
88205 ATTTAGAAAC
88215 AATTGTAGTCAAAATACAA
1 AATTGTAGTCAAAATACAA
*
88234 AATTG-AGT-AAAATGCAA
1 AATTGTAGTCAAAATACAA
88251 A
1 A
88252 GTTAAGAGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 9 0.53
18 3 0.18
19 5 0.29
ACGTcount: A:0.54, C:0.08, G:0.14, T:0.24
Consensus pattern (19 bp):
AATTGTAGTCAAAATACAA
Found at i:89018 original size:158 final size:158
Alignment explanation
Indices: 88551--89554 Score: 1163
Period size: 158 Copynumber: 6.4 Consensus size: 158
88541 TGAATTGAAA
* *
88551 AAAAAAT-GAGGGACTAAATTGAAAAATAAAAAATTTGTTATCAAAAAAAAGGAATTGAAAGTAC
1 AAAAAATAGAGGGACTAAATTGAAAAATAAAAAAATTGTTAT-AAAAAAGAGGAATTGAAAGTAC
* *
88615 ATATGTATTCTACAATGGTTTAGGAGCATGTGGTTAAAATTTGGTAAAAAAAAGAACTTAAAATA
65 ATATGTATTCTACAATGGTTTAGGAGCATGTGGTTCAAATTTGGTAAAAAACAG-ACTTAAAATA
*
88680 AAGGATGAATCGAAGAAATAAAGAAATTAT
129 AAGGATGAATTGAAGAAATAAAGAAATTAT
* * * * *
88710 AAAACATTA-AGGGACTAAATTGAAAAATATAAAATTTGTTAT-CAAAATAGGAATTGAAAGTAC
1 AAAA-AATAGAGGGACTAAATTGAAAAATAAAAAAATTGTTATAAAAAAGAGGAATTGAAAGTAC
** * *
88773 ATATGTATTCTATGATGGTTTTAGGAGAATGTGGTTCAAATTTGGTAAAAAAATAGACTTAAAAT
65 ATATGTATTCTACAATGG-TTTAGGAGCATGTGGTTCAAATTTGGT-AAAAAACAGACTTAAAAT
* *
88838 AAAGGATGAATTGGAGAAATAAGGAAATTAT
128 AAAGGATGAATTGAAGAAATAAAGAAATTAT
* * * * * *
88869 GAAAAATAGGGGGACTGAATTGAAAAACAAAAAAATTATTATAAAAAAAGAGGAATTGAAAGCAC
1 AAAAAATAGAGGGACTAAATTGAAAAATAAAAAAATTGTTAT-AAAAAAGAGGAATTGAAAGTAC
* * *
88934 ATGTGTATTCTACAATGGTGTAGGAGCATGTGGTTCAAAGTTGGT-AAAAACAGACTTAAAATAA
65 ATATGTATTCTACAATGGTTTAGGAGCATGTGGTTCAAATTTGGTAAAAAACAGACTTAAAATAA
** *
88998 ATTATGAATTGAAGAAATAAGGAAATTAT
130 AGGATGAATTGAAGAAATAAAGAAATTAT
* * *
89027 AAAAAA-ATGAGGGACTAAATTG--AAA-AAAAATA-TGTTATCAAAAAGAGGAATTGAAAGTAT
1 AAAAAATA-GAGGGACTAAATTGAAAAATAAAAAAATTGTTATAAAAAAGAGGAATTGAAAGTAC
* * * ** **
89087 ATATGTATTCTACGATGGTTTAGGAGCATGTGGTTTAATTTTTTTTCAAAAC-GAACTTAAAATA
65 ATATGTATTCTACAATGGTTTAGGAGCATGTGGTTCAAATTTGGTAAAAAACAG-ACTTAAAATA
* * *
89151 AAAGATGAATCGATGAAATAAAGAAATTAT
129 AAGGATGAATTGAAGAAATAAAGAAATTAT
* * * *
89181 AAAAAATTGAGGGACTAAATTAAAAAATAGAAAAATTGTTATTAAAAAGAGGAATTGAAAGTACA
1 AAAAAATAGAGGGACTAAATTGAAAAATAAAAAAATTGTTATAAAAAAGAGGAATTGAAAGTACA
*
89246 TATGTATTAC-ACAATGGTATAGGAGCATGTGGTTCAAATTTGGTAAAAAA-AGACTTAAAATAA
66 TATGTATT-CTACAATGGTTTAGGAGCATGTGGTTCAAATTTGGTAAAAAACAGACTTAAAATAA
* * *
89309 AGAATGAATTTAAGAAATAAATAAATTAT
130 AGGATGAATTGAAGAAATAAAGAAATTAT
* * * * * * *
89338 AAAAAAATAGAGGGACTGAATTG-AAAATAGAAAATTTATTATTAAAAGGAGGAATTGAAAGAAC
1 -AAAAAATAGAGGGACTAAATTGAAAAATAAAAAAATTGTTATAAAAAAGAGGAATTGAAAGTAC
** ** * * * *
89402 ATATGTATTCTATGATGGTGCATGAGCAAGTGGTTCAAAGTTGGTAAAAAACAAACTTAAAATAA
65 ATATGTATTCTACAATGGTTTAGGAGCATGTGGTTCAAATTTGGTAAAAAACAGACTTAAAATAA
* * *
89467 AAGATAAATTGAAGAAATAAGGAAATTAT
130 AGGATGAATTGAAGAAATAAAGAAATTAT
* *
89496 AAAAAAAAATGAGGGACTAAATTGAAAAAATAGAAAAAA-TGTTATCAAAAAGAGGAATT
1 -AAAAAATA-GAGGGACTAAATTG-AAAAATA-AAAAAATTGTTATAAAAAAGAGGAATT
89555 TGTTGAAAAT
Statistics
Matches: 718, Mismatches: 103, Indels: 46
0.83 0.12 0.05
Matches are distributed among these distances:
153 57 0.08
154 64 0.09
155 6 0.01
156 7 0.01
157 119 0.17
158 229 0.32
159 110 0.15
160 66 0.09
161 56 0.08
162 4 0.01
ACGTcount: A:0.50, C:0.05, G:0.18, T:0.27
Consensus pattern (158 bp):
AAAAAATAGAGGGACTAAATTGAAAAATAAAAAAATTGTTATAAAAAAGAGGAATTGAAAGTACA
TATGTATTCTACAATGGTTTAGGAGCATGTGGTTCAAATTTGGTAAAAAACAGACTTAAAATAAA
GGATGAATTGAAGAAATAAAGAAATTAT
Found at i:89281 original size:471 final size:472
Alignment explanation
Indices: 88549--89554 Score: 1396
Period size: 471 Copynumber: 2.1 Consensus size: 472
88539 GGTGAATTGA
* *
88549 AAAAAAAATGAGGGACTAAATTGAAAAATAAAAAATTTGTTATCAAAAAAAAGGAATTGAAAGTA
1 AAAAAAAATGAGGGACTAAATTG--AAA-AAAAAATATGTTATC-AAAAAGAGGAATTGAAAGTA
88614 CATATGTATTCTACAATGGTTTAGGAGCATGTGGTTAAAATTTGGTAAAAAAAAGAACTTAAAAT
62 CATATGTATTCTACAATGGTTTAGGAGCATGTGGTTAAAATTTGGTAAAAAAAAGAACTTAAAAT
* * * *
88679 AAAGGATGAATCGAAGAAATAAAGAAATTATAAAACATTAAGGGACTAAATTGAAAAATATAAAA
127 AAAAGATGAATCGAAGAAATAAAGAAATTATAAAAAATTAAGGGACTAAATTAAAAAATAGAAAA
* * * ** *
88744 TTTGTTATCAAAATAGGAATTGAAAGTACATATGTATTCTATGATGGTTTTAGGAGAATGTGGTT
192 ATTGTTATAAAAAGAGGAATTGAAAGTACATATGTATTCTACAATGGTTATAGGAGAATGTGGTT
* * * *
88809 CAAATTTGGTAAAAAAATAGACTTAAAATAAAGGATGAATTGGAGAAATAAGGAAATTAT-GAAA
257 CAAATTTGGT-AAAAAA-AGACTTAAAATAAAGAATGAATTGAAGAAATAAAGAAATTATAAAAA
* * *
88873 AATAGGGGGACTGAATTGAAAAACAAAAAAATTATTATAAAAAAAGAGGAATTGAAAGCACATGT
320 AATAGAGGGACTGAATTG-AAAACAAAAAAATTATTAT-AAAAAAGAGGAATTGAAAGAACATAT
* * * **
88938 GTATTCTACAATGGTGTAGGAGCATGTGGTTCAAAGTTGGT-AAAAACAGACTTAAAATAAATTA
383 GTATTCTACAATGGTGCAGGAGCAAGTGGTTCAAAGTTGGTAAAAAACAAACTTAAAATAAAAGA
*
89002 TGAATTGAAGAAATAAGGAAATTAT
448 TAAATTGAAGAAATAAGGAAATTAT
*
89027 -AAAAAAATGAGGGACTAAATTG-AAAAAAAATATGTTATCAAAAAGAGGAATTGAAAGTATATA
1 AAAAAAAATGAGGGACTAAATTGAAAAAAAAATATGTTATCAAAAAGAGGAATTGAAAGTACATA
* * ** *** *
89090 TGTATTCTACGATGGTTTAGGAGCATGTGGTT-TAATTTTTTTTCAAAACGAACTTAAAATAAAA
66 TGTATTCTACAATGGTTTAGGAGCATGTGGTTAAAATTTGGTAAAAAAAAGAACTTAAAATAAAA
* *
89154 GATGAATCGATGAAATAAAGAAATTATAAAAAATTGAGGGACTAAATTAAAAAATAGAAAAATTG
131 GATGAATCGAAGAAATAAAGAAATTATAAAAAATTAAGGGACTAAATTAAAAAATAGAAAAATTG
*
89219 TTATTAAAAAGAGGAATTGAAAGTACATATGTATTAC-ACAATGG-TATAGGAGCATGTGGTTCA
196 TTA-TAAAAAGAGGAATTGAAAGTACATATGTATT-CTACAATGGTTATAGGAGAATGTGGTTCA
* *
89282 AATTTGGTAAAAAAAGACTTAAAATAAAGAATGAATTTAAGAAATAAATAAATTATAAAAAAATA
259 AATTTGGTAAAAAAAGACTTAAAATAAAGAATGAATTGAAGAAATAAAGAAATTATAAAAAAATA
* * * * *
89347 GAGGGACTGAATTGAAAATAGAAAATTTATTATTAAAAGGAGGAATTGAAAGAACATATGTATTC
324 GAGGGACTGAATTGAAAACAAAAAAATTATTATAAAAAAGAGGAATTGAAAGAACATATGTATTC
** *
89412 TATGATGGTGCATGAGCAAGTGGTTCAAAGTTGGTAAAAAACAAACTTAAAATAAAAGATAAATT
389 TACAATGGTGCAGGAGCAAGTGGTTCAAAGTTGGTAAAAAACAAACTTAAAATAAAAGATAAATT
89477 GAAGAAATAAGGAAATTAT
454 GAAGAAATAAGGAAATTAT
*
89496 AAAAAAAAATGAGGGACTAAATTGAAAAAATAGAAAAAATGTTATCAAAAAGAGGAATT
1 -AAAAAAAATGAGGGACTAAATTG--AAAA-A-AAAATATGTTATCAAAAAGAGGAATT
89555 TGTTGAAAAT
Statistics
Matches: 469, Mismatches: 48, Indels: 24
0.87 0.09 0.04
Matches are distributed among these distances:
468 58 0.12
469 97 0.21
470 26 0.06
471 133 0.28
472 87 0.19
473 15 0.03
474 5 0.01
475 1 0.00
476 25 0.05
477 22 0.05
ACGTcount: A:0.50, C:0.05, G:0.18, T:0.27
Consensus pattern (472 bp):
AAAAAAAATGAGGGACTAAATTGAAAAAAAAATATGTTATCAAAAAGAGGAATTGAAAGTACATA
TGTATTCTACAATGGTTTAGGAGCATGTGGTTAAAATTTGGTAAAAAAAAGAACTTAAAATAAAA
GATGAATCGAAGAAATAAAGAAATTATAAAAAATTAAGGGACTAAATTAAAAAATAGAAAAATTG
TTATAAAAAGAGGAATTGAAAGTACATATGTATTCTACAATGGTTATAGGAGAATGTGGTTCAAA
TTTGGTAAAAAAAGACTTAAAATAAAGAATGAATTGAAGAAATAAAGAAATTATAAAAAAATAGA
GGGACTGAATTGAAAACAAAAAAATTATTATAAAAAAGAGGAATTGAAAGAACATATGTATTCTA
CAATGGTGCAGGAGCAAGTGGTTCAAAGTTGGTAAAAAACAAACTTAAAATAAAAGATAAATTGA
AGAAATAAGGAAATTAT
Found at i:89920 original size:65 final size:63
Alignment explanation
Indices: 89804--90011 Score: 226
Period size: 65 Copynumber: 3.2 Consensus size: 63
89794 TTTTAAAGTG
** **
89804 ATGCATCGATGCACCAATCCATGCATCGATGCAC-CATGAAATAAATT-AAACATCGAATGTATT
1 ATGCATCGATGCA-CAA-CCATGCATCGATGCACTCA-G-GCTATTTTGAAACATCGAATGTATT
89867 TC
62 TC
*
89869 ATGCATCGATGCACATACCATGCATCGATGCACTCAAGG-T-TTTATGAAAACATCAAATGTATT
1 ATGCATCGATGCACA-ACCATGCATCGATGCACTC-AGGCTATTT-TG-AAACATCGAATGTATT
*
89932 TG
62 TC
* * *
89934 ATGCATCGATGCACCAGCCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTT
1 ATGCATCGATGCA-CAACCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGTATTTC
89998 ATGCATCGATGCAC
1 ATGCATCGATGCAC
90012 TTTTAGTGCA
Statistics
Matches: 125, Mismatches: 9, Indels: 20
0.81 0.06 0.13
Matches are distributed among these distances:
62 1 0.01
63 3 0.02
64 49 0.39
65 66 0.53
66 6 0.05
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (63 bp):
ATGCATCGATGCACAACCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGTATTTC
Found at i:90006 original size:18 final size:18
Alignment explanation
Indices: 89983--90031 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
89973 TATTTTGAAA
89983 CATCGAATGCATTTTA-TG
1 CATCG-ATGCATTTTAGTG
90001 CATCGATGCACTTTTAGTG
1 CATCGATGCA-TTTTAGTG
*
90020 CACCGATGCATT
1 CATCGATGCATT
90032 AAGGGTTCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 5 0.18
18 12 0.43
19 11 0.39
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.35
Consensus pattern (18 bp):
CATCGATGCATTTTAGTG
Found at i:90026 original size:19 final size:17
Alignment explanation
Indices: 89989--90031 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 17
89979 GAAACATCGA
*
89989 ATGCATTTTATGCATCG
1 ATGCATTTTATGCACCG
90006 ATGCACTTTTAGTGCACCG
1 ATGCA-TTTTA-TGCACCG
90025 ATGCATT
1 ATGCATT
90032 AAGGGTTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 5 0.22
18 7 0.30
19 11 0.48
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (17 bp):
ATGCATTTTATGCACCG
Found at i:91976 original size:22 final size:21
Alignment explanation
Indices: 91952--91991 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
91942 GAGAAATTGT
91952 TTTTAAAATAT-AAAAATGATA
1 TTTTAAAAT-TGAAAAATGATA
91973 TTTTAAAATTGAAAAATGA
1 TTTTAAAATTGAAAAATGA
91992 AAATAAACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (21 bp):
TTTTAAAATTGAAAAATGATA
Found at i:92262 original size:135 final size:134
Alignment explanation
Indices: 92020--92291 Score: 481
Period size: 135 Copynumber: 2.0 Consensus size: 134
92010 AACCAACAAC
92020 GATCTTGAAAGTAAAATCAAAGATTTACAAATCAAACTAGAAGAGTTTGAAAAGAAAAATTCAGA
1 GATCTTGAAAGTAAAATCAAAGATTTACAAATCAAACTAGAAGAGTTTGAAAAGAAAAATTCAGA
*
92085 TTTGTAAAATTTACTTTCAAAGTTCAATGATGATAATCAAAAGAAAATTGATGATCTTAAAGCTT
66 TTTGTAAAATTTACTTTCAAAGGTCAATGATGATAATCAAAAG-AAATTGATGATCTTAAAGCTT
92150 CTTTT
130 CTTTT
* * **
92155 GATCTTGAAAGTAAAATCAAAGATTTGCAAATCAAACTATAAGAGTTTGAAAAGAAAAATTTGGA
1 GATCTTGAAAGTAAAATCAAAGATTTACAAATCAAACTAGAAGAGTTTGAAAAGAAAAATTCAGA
*
92220 TTTGTAAAATTTACTTTCAAAGGTCAATGATGATCATCAAAAGAAATTGATGATCTTAAAGCTTC
66 TTTGTAAAATTTACTTTCAAAGGTCAATGATGATAATCAAAAGAAATTGATGATCTTAAAGCTTC
92285 TTTT
131 TTTT
92289 GAT
1 GAT
92292 AAAGTTGGAA
Statistics
Matches: 131, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
134 29 0.22
135 102 0.78
ACGTcount: A:0.44, C:0.10, G:0.14, T:0.32
Consensus pattern (134 bp):
GATCTTGAAAGTAAAATCAAAGATTTACAAATCAAACTAGAAGAGTTTGAAAAGAAAAATTCAGA
TTTGTAAAATTTACTTTCAAAGGTCAATGATGATAATCAAAAGAAATTGATGATCTTAAAGCTTC
TTTT
Found at i:95849 original size:15 final size:15
Alignment explanation
Indices: 95829--95864 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
95819 TATATGAGTT
95829 GCCAATACCACTAGA
1 GCCAATACCACTAGA
95844 GCCAATACCACTAGA
1 GCCAATACCACTAGA
95859 GCCAAT
1 GCCAAT
95865 TAATTTAGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.39, C:0.33, G:0.14, T:0.14
Consensus pattern (15 bp):
GCCAATACCACTAGA
Found at i:95945 original size:20 final size:20
Alignment explanation
Indices: 95920--95968 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
95910 TGCTTAATGT
95920 ATCGATACACTT-AACAGTGC
1 ATCGATACACTTGAACA-TGC
* *
95940 ATCGATGCA-TTGAATATGC
1 ATCGATACACTTGAACATGC
95959 ATCGATACAC
1 ATCGATACAC
95969 CATGAAGGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (20 bp):
ATCGATACACTTGAACATGC
Found at i:107410 original size:24 final size:24
Alignment explanation
Indices: 107376--107447 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 24
107366 AATTTTTTTA
* *
107376 TGATACTTGACCTGGATTCTGATT
1 TGATACTTGACATGGATTCTGATC
* * *
107400 TGATACGTGACTTGGATCCTGATC
1 TGATACTTGACATGGATTCTGATC
*
107424 TAATACTTGACATGGATTCTGATC
1 TGATACTTGACATGGATTCTGATC
107448 AGTGATAAAG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.38
Consensus pattern (24 bp):
TGATACTTGACATGGATTCTGATC
Found at i:110135 original size:87 final size:87
Alignment explanation
Indices: 109989--110163 Score: 350
Period size: 87 Copynumber: 2.0 Consensus size: 87
109979 ACTGAAATAA
109989 ATGATAAGTTTGAATTTAATAATAAGATCGGATGGAAGGAAAGGATTGAAATACATTGGATCTGT
1 ATGATAAGTTTGAATTTAATAATAAGATCGGATGGAAGGAAAGGATTGAAATACATTGGATCTGT
110054 AAAATGACCAGAATACCCCTTG
66 AAAATGACCAGAATACCCCTTG
110076 ATGATAAGTTTGAATTTAATAATAAGATCGGATGGAAGGAAAGGATTGAAATACATTGGATCTGT
1 ATGATAAGTTTGAATTTAATAATAAGATCGGATGGAAGGAAAGGATTGAAATACATTGGATCTGT
110141 AAAATGACCAGAATACCCCTTG
66 AAAATGACCAGAATACCCCTTG
110163 A
1 A
110164 ATGGAAATGA
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 88 1.00
ACGTcount: A:0.41, C:0.10, G:0.22, T:0.27
Consensus pattern (87 bp):
ATGATAAGTTTGAATTTAATAATAAGATCGGATGGAAGGAAAGGATTGAAATACATTGGATCTGT
AAAATGACCAGAATACCCCTTG
Found at i:111245 original size:24 final size:24
Alignment explanation
Indices: 111213--111284 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 24
111203 AATTTTGTTA
* *
111213 TGATACTTGACCTGGATTCTGATT
1 TGATACTTGACATGGATTCTGATC
** *
111237 TGATACTTGAGTTGGATCCTGATC
1 TGATACTTGACATGGATTCTGATC
*
111261 TAATACTTGACATGGATTCTGATC
1 TGATACTTGACATGGATTCTGATC
111285 AGTGATAAAG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.39
Consensus pattern (24 bp):
TGATACTTGACATGGATTCTGATC
Found at i:113111 original size:24 final size:24
Alignment explanation
Indices: 113084--113175 Score: 130
Period size: 24 Copynumber: 3.8 Consensus size: 24
113074 TCAGATATTA
* *
113084 ATTCTGTTATGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
* *
113108 ATTCTGATTTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
*
113132 ATTCTGATCTGATACTTGACATAG
1 ATTCTGATCTGATACTTGACATGG
*
113156 ATTCTGATCTTATACTTGAC
1 ATTCTGATCTGATACTTGAC
113176 CTGAATTATT
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 61 1.00
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.42
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:115004 original size:24 final size:25
Alignment explanation
Indices: 114977--115030 Score: 76
Period size: 23 Copynumber: 2.2 Consensus size: 25
114967 TCATGATTTA
114977 TATATTAAAATATTTATAGTA-AAT
1 TATATTAAAATATTTATAGTATAAT
* *
115001 TATA-TAAAATATTTTTATTATAAT
1 TATATTAAAATATTTATAGTATAAT
115025 TATATT
1 TATATT
115031 GTTTTATTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 14 0.54
24 11 0.42
25 1 0.04
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TATATTAAAATATTTATAGTATAAT
Found at i:115063 original size:19 final size:18
Alignment explanation
Indices: 115012--115065 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
115002 ATATAAAATA
* *
115012 TTTTTATTATAATTATAT
1 TTTTTATTATATTTTTAT
*
115030 TGTTTTATTTGTATTTTTAT
1 T-TTTTA-TTATATTTTTAT
115050 GTTTTTATTATATTTT
1 -TTTTTATTATATTTT
115066 AAATTGATAC
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
18 1 0.03
19 13 0.45
20 14 0.48
21 1 0.03
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (18 bp):
TTTTTATTATATTTTTAT
Found at i:116076 original size:15 final size:15
Alignment explanation
Indices: 116036--116083 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
116026 AAAATTGATG
116036 TTATTTTAATAAATA
1 TTATTTTAATAAATA
*
116051 --A-TTTAAAAAATA
1 TTATTTTAATAAATA
116063 TTATTTTAATAAATA
1 TTATTTTAATAAATA
116078 TATATT
1 T-TATT
116084 ATTTTAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
12 10 0.37
13 1 0.04
14 1 0.04
15 11 0.41
16 4 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTATTTTAATAAATA
Found at i:120365 original size:21 final size:20
Alignment explanation
Indices: 120340--120383 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
120330 ACTTGGAAAT
120340 AATTAAATAAGAAATAA-TTAA
1 AATTAAATAA-AAA-AATTTAA
*
120361 AATTAAGTAAAAAAATTTAA
1 AATTAAATAAAAAAATTTAA
120381 AAT
1 AAT
120384 AAGAAACAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 2 0.10
20 10 0.48
21 9 0.43
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.30
Consensus pattern (20 bp):
AATTAAATAAAAAAATTTAA
Found at i:123127 original size:21 final size:21
Alignment explanation
Indices: 123103--123303 Score: 166
Period size: 21 Copynumber: 9.7 Consensus size: 21
123093 GATTATTGCA
* *
123103 TTGCGATAGTCTAAGTTCACG
1 TTGCGATAGTCCAAGTTCGCG
*
123124 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
** *
123145 TTGCGATTTTCCAAATT--CG
1 TTGCGATAGTCCAAGTTCGCG
123164 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
* * *
123185 TTGCGATTTATTCCAAATT--TG
1 TTGCGA--TAGTCCAAGTTCGCG
123206 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
* * *
123227 TTGCGATTTATTACAAATT--CG
1 TTGCGA--TAGTCCAAGTTCGCG
123248 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
* *
123269 TTGCGATTTATTCCAAATT--CG
1 TTGCGA--TAGTCCAAGTTCGCG
123290 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
123304 AATCGCAACG
Statistics
Matches: 144, Mismatches: 24, Indels: 26
0.74 0.12 0.13
Matches are distributed among these distances:
19 40 0.28
21 78 0.54
23 26 0.18
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.35
Consensus pattern (21 bp):
TTGCGATAGTCCAAGTTCGCG
Found at i:123212 original size:42 final size:42
Alignment explanation
Indices: 123122--123303 Score: 323
Period size: 42 Copynumber: 4.4 Consensus size: 42
123112 TCTAAGTTCA
*
123122 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
123162 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
* *
123204 TGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
123246 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
123288 CGTTGCGATAGTCCAA
1 CGTTGCGATAGTCCAA
123304 AATCGCAACG
Statistics
Matches: 135, Mismatches: 5, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
40 28 0.21
41 2 0.01
42 105 0.78
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (42 bp):
CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
Found at i:124058 original size:15 final size:15
Alignment explanation
Indices: 124038--124071 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
124028 GCCGTCCGTC
124038 TCGTCTCGTCTCGGG
1 TCGTCTCGTCTCGGG
*
124053 TCGTCTCGTGTCGGG
1 TCGTCTCGTCTCGGG
124068 TCGT
1 TCGT
124072 GGTCGTGGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.00, C:0.29, G:0.35, T:0.35
Consensus pattern (15 bp):
TCGTCTCGTCTCGGG
Found at i:124203 original size:21 final size:21
Alignment explanation
Indices: 124177--124415 Score: 178
Period size: 21 Copynumber: 11.3 Consensus size: 21
124167 ATTTTGGACT
*
124177 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
124198 ATCGCAACGCGAACTTGGAATAA
1 ATCGCAA--CGAACTTGGAATAA
* *
124221 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
*
124242 ATCGCAACTCGAACTTGGACT--
1 ATCGCAA--CGAACTTGGAATAA
*
124263 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
124284 ATCGCAACGCGAACTTGGAATAA
1 ATCGCAA--CGAACTTGGAATAA
*
124307 ATCGCAACGCGAACTTGGACT--
1 ATCGCAA--CGAACTTGGAATAA
*
124328 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
*
124349 ATCGCAACGTGAACTTGGACT--
1 ATCGCAAC--GAACTTGGAATAA
*
124370 ATCGCAACACGAACTTGGACT--
1 ATCGC-A-ACGAACTTGGAATAA
*
124391 ATCGCAACGAATTTGG-A-AA
1 ATCGCAACGAACTTGGAATAA
124410 ATCGCA
1 ATCGCA
124416 TTGCGATAGT
Statistics
Matches: 189, Mismatches: 15, Indels: 30
0.81 0.06 0.13
Matches are distributed among these distances:
19 35 0.19
20 1 0.01
21 76 0.40
22 1 0.01
23 76 0.40
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.21
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATAA
Found at i:124315 original size:86 final size:86
Alignment explanation
Indices: 124170--124335 Score: 323
Period size: 86 Copynumber: 1.9 Consensus size: 86
124160 CGTTGCGATT
124170 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGAATAAATCGCAACGCGAAC
124235 TTCGACTATCGCAACTCGAAC
66 TTCGACTATCGCAACTCGAAC
124256 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGAATAAATCGCAACGCGAAC
*
124321 TTGGACTATCGCAAC
66 TTCGACTATCGCAAC
124336 GAATTTGGAA
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 79 1.00
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.21
Consensus pattern (86 bp):
TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGAATAAATCGCAACGCGAAC
TTCGACTATCGCAACTCGAAC
Found at i:124353 original size:86 final size:85
Alignment explanation
Indices: 124170--124388 Score: 309
Period size: 86 Copynumber: 2.6 Consensus size: 85
124160 CGTTGCGATT
*
124170 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGAATATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGAATAAATCGCAACGCGAAC
124235 TTCGACTATCGCAACTCGAAC
66 TTCGACTATCGCAAC-CGAAC
*
124256 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGAATATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGAATAAATCGCAACGCGAAC
* *
124321 TTGGACTATCGCAA-CGAAT
66 TTCGACTATCGCAACCGAAC
* * *
124340 TTGGAATAAATCGCAACGTGAACTTGGACT--ATCGCAACACGAACTTGGA
1 TTGGAAT--ATCGCAAC--GAATTTGGAATAAATCGCAACGCGAACTTGGA
124389 CTATCGCAAC
Statistics
Matches: 123, Mismatches: 6, Indels: 8
0.90 0.04 0.06
Matches are distributed among these distances:
84 10 0.08
86 104 0.85
88 9 0.07
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.21
Consensus pattern (85 bp):
TTGGAATATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGAATAAATCGCAACGCGAAC
TTCGACTATCGCAACCGAAC
Found at i:124443 original size:21 final size:21
Alignment explanation
Indices: 124419--124459 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
124409 AATCGCATTG
124419 CGATAGTCGAAGTTCGCGTTT
1 CGATAGTCGAAGTTCGCGTTT
*
124440 CGATAGTCGATGTTCGCGTT
1 CGATAGTCGAAGTTCGCGTT
124460 GTGAATCTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.17, C:0.20, G:0.29, T:0.34
Consensus pattern (21 bp):
CGATAGTCGAAGTTCGCGTTT
Found at i:134571 original size:20 final size:20
Alignment explanation
Indices: 134546--134594 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
134536 AAATTTGGTA
134546 TTATACTCTATCAATTTAAT
1 TTATACTCTATCAATTTAAT
*
134566 TTATACTCAATCAATTTAAT
1 TTATACTCTATCAATTTAAT
*
134586 ATATACTCT
1 TTATACTCT
134595 TTTAACTTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.37, C:0.16, G:0.00, T:0.47
Consensus pattern (20 bp):
TTATACTCTATCAATTTAAT
Found at i:138043 original size:12 final size:12
Alignment explanation
Indices: 138026--138056 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
138016 TTAAATATAT
138026 ATACCCGGCTCG
1 ATACCCGGCTCG
*
138038 ATACCCGGCTTG
1 ATACCCGGCTCG
138050 ATACCCG
1 ATACCCG
138057 TTTAAATAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.39, G:0.23, T:0.19
Consensus pattern (12 bp):
ATACCCGGCTCG
Found at i:138344 original size:2 final size:2
Alignment explanation
Indices: 138337--138361 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
138327 GAAAAACGTT
138337 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 T
138362 TCATCAACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:138803 original size:53 final size:53
Alignment explanation
Indices: 138745--138907 Score: 200
Period size: 57 Copynumber: 3.0 Consensus size: 53
138735 TTTTTAAGTA
* * * * *
138745 CTAAGATGTTGAGATATATACATATTTATACCAGTGTAAATATGTGTTAATTG
1 CTAAGATATTGAGAGATGTGCATACTTATACCAGTGTAAATATGTGTTAATTG
* *
138798 CTAAGATATTGAGAGATGTGCATACTTACACCTGTGTAAGTATGTATGTGTTAATTG
1 CTAAGATATTGAGAGATGTGCATACTTATACCAGTGTAA--A--TATGTGTTAATTG
* * *
138855 TTAAGATATTGAGAGATGTGCATACTTATATCGGTGTAAATATGTGTTAATTG
1 CTAAGATATTGAGAGATGTGCATACTTATACCAGTGTAAATATGTGTTAATTG
138908 TTACAATTTC
Statistics
Matches: 95, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
53 45 0.47
55 2 0.02
57 48 0.51
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.39
Consensus pattern (53 bp):
CTAAGATATTGAGAGATGTGCATACTTATACCAGTGTAAATATGTGTTAATTG
Found at i:142090 original size:17 final size:20
Alignment explanation
Indices: 142049--142085 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
142039 TGTTTGAATA
142049 AAATAATATATTTTTTATTC
1 AAATAATATATTTTTTATTC
*
142069 AAATAA-ATTTTTTTTAT
1 AAATAATATATTTTTTAT
142086 AAATATCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (20 bp):
AAATAATATATTTTTTATTC
Found at i:147876 original size:56 final size:56
Alignment explanation
Indices: 147790--147902 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
147780 GCTATTCCAC
147790 TAAAACAATTGGTTATAAAGGAAACTTAAAAGCCCCAGCTTTATGAATAGATTGTT
1 TAAAACAATTGGTTATAAAGGAAACTTAAAAGCCCCAGCTTTATGAATAGATTGTT
147846 TAAAACAATTGGTTATAAAGGAAACTTAAAAGCCCCAGCTTTATGAATAGATTGTT
1 TAAAACAATTGGTTATAAAGGAAACTTAAAAGCCCCAGCTTTATGAATAGATTGTT
147902 T
1 T
147903 GCTCGGGTAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (56 bp):
TAAAACAATTGGTTATAAAGGAAACTTAAAAGCCCCAGCTTTATGAATAGATTGTT
Found at i:149987 original size:29 final size:29
Alignment explanation
Indices: 149931--149987 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
149921 TGAAGCTTCA
* *
149931 ACTTGACTCCCTTACGAAGAGGAGTCAAT
1 ACTTGACTCCCTTACGAAGAGAAATCAAT
* **
149960 ACTTGACTTCCTTGTGAAGAGAAATCAA
1 ACTTGACTCCCTTACGAAGAGAAATCAA
149988 CCTTTGTTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.26
Consensus pattern (29 bp):
ACTTGACTCCCTTACGAAGAGAAATCAAT
Found at i:150046 original size:67 final size:67
Alignment explanation
Indices: 149938--150132 Score: 282
Period size: 67 Copynumber: 2.9 Consensus size: 67
149928 TCAACTTGAC
* * *
149938 TCCCTTACGAAGAGGAGTCAATACTTGACTTCCTTGTGAAGAGAAATCAACCTTTGTTATTCCTG
1 TCCCTTGCGAAGAAGAGTCAATACTTGACTTCCTCGTGAAGAGAAATCAACCTTTGTTATTCCTG
150003 AA
66 AA
* * *
150005 TCCCTTGCGAAGATGAGTCAATCCTTGACTTCCACGTGAAGAGAAATCAACCTTTGTTATTCCTG
1 TCCCTTGCGAAGAAGAGTCAATACTTGACTTCCTCGTGAAGAGAAATCAACCTTTGTTATTCCTG
*
150070 AC
66 AA
* * * * *
150072 TCCCTCGTGAAGAAGAGTCAATTCTTGACTTCCTCGTGAAGAGAAGTTAACCTTTGTTATT
1 TCCCTTGCGAAGAAGAGTCAATACTTGACTTCCTCGTGAAGAGAAATCAACCTTTGTTATT
150133 TTATGAATTT
Statistics
Matches: 115, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
67 115 1.00
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (67 bp):
TCCCTTGCGAAGAAGAGTCAATACTTGACTTCCTCGTGAAGAGAAATCAACCTTTGTTATTCCTG
AA
Found at i:150239 original size:26 final size:24
Alignment explanation
Indices: 150177--150239 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
150167 CATTGTAATC
150177 AAAATAT-TAATTATTAAAATATTT
1 AAAATATAT-ATTATTAAAATATTT
*
150201 AAAATATAT-TTATTAATAT-TTCT
1 AAAATATATATTATTAAAATATT-T
150224 AATAATATAATATTAT
1 AA-AATAT-ATATTAT
150240 ATTTTTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 12 0.36
24 12 0.36
25 3 0.09
26 4 0.12
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATATATTATTAAAATATTT
Found at i:150241 original size:22 final size:23
Alignment explanation
Indices: 150211--150257 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
150201 AAAATATATT
150211 TATTAATATTTCTAATAATATAA
1 TATTAATATTTCTAATAATATAA
* *
150234 TATT-ATATTTTTAATATTATAA
1 TATTAATATTTCTAATAATATAA
150256 TA
1 TA
150258 AAACAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTAATATTTCTAATAATATAA
Found at i:151581 original size:13 final size:13
Alignment explanation
Indices: 151565--151589 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
151555 TTAATCGTGA
151565 AAATTAAAATTTT
1 AAATTAAAATTTT
151578 AAATTAAAATTT
1 AAATTAAAATTT
151590 AAAAAATCTG
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATTAAAATTTT
Found at i:151725 original size:46 final size:46
Alignment explanation
Indices: 151639--151730 Score: 116
Period size: 46 Copynumber: 2.0 Consensus size: 46
151629 AATTACTACT
* * *
151639 GAAAAAAAAGTCAAAAATATGTTAAATGATAAAATAAAAATAAATAG
1 GAAAAAAAAG-CAAAAAAATATTAAATAATAAAATAAAAATAAATAG
151686 GAAAAAAAAG-AAAAAAATATTAATATAATAATAAT-AAAATAAATA
1 GAAAAAAAAGCAAAAAAATATTAA-ATAATAA-AATAAAAATAAATA
151731 AATAAAGATA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
45 11 0.28
46 16 0.40
47 13 0.32
ACGTcount: A:0.70, C:0.01, G:0.08, T:0.22
Consensus pattern (46 bp):
GAAAAAAAAGCAAAAAAATATTAAATAATAAAATAAAAATAAATAG
Found at i:151813 original size:24 final size:24
Alignment explanation
Indices: 151786--151836 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
151776 ATAATAACAA
** *
151786 AAAAGGGTTAAATTTTGAAAAAAT
1 AAAAGGGAAAAATGTTGAAAAAAT
*
151810 AAAATGGAAAAATGTTGAAAAAAT
1 AAAAGGGAAAAATGTTGAAAAAAT
151834 AAA
1 AAA
151837 TATTAACAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.24
Consensus pattern (24 bp):
AAAAGGGAAAAATGTTGAAAAAAT
Found at i:153171 original size:41 final size:40
Alignment explanation
Indices: 153122--153375 Score: 205
Period size: 41 Copynumber: 6.6 Consensus size: 40
153112 CAAAAACTGA
*
153122 TTTT-AAAAACTATATAATATATATGTGTTTTTAAAATGT
1 TTTTAAAAAACTATATAATATATATATGTTTTTAAAATGT
153161 TTTTAAAAAAACTATATAATATATATATGTTTTTAAAATG-
1 TTTT-AAAAAACTATATAATATATATATGTTTTTAAAATGT
* * *
153201 TTTT-AAGAACTATAT-AT-TATATAAG-TTTTCAAAT-T
1 TTTTAAAAAACTATATAATATATATATGTTTTTAAAATGT
*
153236 TTTTTAAAAACTATAT-ATATATATAT-TTTTTCAAAATGT
1 TTTTAAAAAACTATATAATATATATATGTTTTT-AAAATGT
* * * * *
153275 TTTT--AAAACTATATTATTATATATAT-ATTATATATATAT
1 TTTTAAAAAACTATA-TAATATATATATGTTTTTA-AAATGT
* * * * **
153314 ATATATATATA-TATATATATATATATATGTTTCCAAAATG-
1 TTTTA-AAAAACTATATA-ATATATATATGTTTTTAAAATGT
153354 TTTT-AAAAACTATATAATATAT
1 TTTTAAAAAACTATATAATATAT
153376 TCAAATGTTT
Statistics
Matches: 172, Mismatches: 26, Indels: 35
0.74 0.11 0.15
Matches are distributed among these distances:
35 12 0.07
36 19 0.11
37 21 0.12
38 25 0.15
39 33 0.19
40 8 0.05
41 49 0.28
42 5 0.03
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (40 bp):
TTTTAAAAAACTATATAATATATATATGTTTTTAAAATGT
Found at i:153299 original size:2 final size:2
Alignment explanation
Indices: 153284--153341 Score: 95
Period size: 2 Copynumber: 30.5 Consensus size: 2
153274 TTTTTAAAAC
153284 TA TA T- TA T- TA TA TA TA TA T- 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
153323 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
153342 GTTTCCAAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
1 3 0.06
2 50 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:153299 original size:116 final size:115
Alignment explanation
Indices: 153078--153375 Score: 292
Period size: 116 Copynumber: 2.6 Consensus size: 115
153068 TTTCCAAAAA
*
153078 TAAAATATTTTAAAAACTATATATTATAGGTTTTCAAAAACTGATTTTAAAAACTATATAATATA
1 TAAAATATTTTAAAAACTATATATTATAAGTTTTC-AAAACTGATTTTAAAAACTATATAATATA
*
153143 TATGTGTTTTTAAAATGTTTTTAAAAAAACTATATAATATATATATGTTTT
65 TATGTGTTTTCAAAATGTTTTTAAAAAAACTATATAATATATATATGTTTT
* * **
153194 TAAAATGTTTTAAGAACTATATATTATATAAGTTTTC-AAA-TTTTTTTAAAAACTATATATATA
1 TAAAATATTTTAAAAACTATATA-T-TATAAGTTTTCAAAACTGATTTTAAAAACTATATA-ATA
* *
153257 TATAT-T-TTTTCAAAATGTTTTT---AAAACTATATTATTATATATATATTATAT
63 TATATGTGTTTTCAAAATGTTTTTAAAAAAACTATA-TAATATATATATGTT-T-T
* * * * *
153308 ATATATATATATATATATATA-TATATATATATATGTTTCCAAAA-TG-TTTTAAAAACTATATA
1 -TA-A-A-ATAT-TTTAAAAACTATATAT-TATAAGTTTTCAAAACTGATTTTAAAAACTATATA
153370 ATATAT
60 ATATAT
153376 TCAAATGTTT
Statistics
Matches: 154, Mismatches: 16, Indels: 24
0.79 0.08 0.12
Matches are distributed among these distances:
111 9 0.06
112 13 0.08
113 1 0.01
114 16 0.10
115 20 0.13
116 39 0.25
117 29 0.19
118 23 0.15
119 4 0.03
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (115 bp):
TAAAATATTTTAAAAACTATATATTATAAGTTTTCAAAACTGATTTTAAAAACTATATAATATAT
ATGTGTTTTCAAAATGTTTTTAAAAAAACTATATAATATATATATGTTTT
Found at i:153403 original size:80 final size:80
Alignment explanation
Indices: 153247--153407 Score: 202
Period size: 80 Copynumber: 2.0 Consensus size: 80
153237 TTTTAAAAAC
* * * * * * *
153247 TATATATATATATATTTTTTCAAAATGTTTTTAAAACTATATTATTATATATATATTATATATAT
1 TATATATATATATATGTTTCCAAAATGTTTTAAAAACTATATTAATATATATAAATTATAAAAAT
153312 ATATATATATATATA
66 ATATATATATATATA
*
153327 TATATATATATATATGTTTCCAAAATGTTTTAAAAACTATA-TAATATAT-TCAAATGTTTAAAA
1 TATATATATATATATGTTTCCAAAATGTTTTAAAAACTATATTAATATATAT-AAAT-TATAAAA
153390 ACTATATAT-TATATATA
64 A-TATATATATATATATA
153407 T
1 T
153408 TTCAAAATCA
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 1 0.01
79 10 0.14
80 52 0.74
81 7 0.10
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.48
Consensus pattern (80 bp):
TATATATATATATATGTTTCCAAAATGTTTTAAAAACTATATTAATATATATAAATTATAAAAAT
ATATATATATATATA
Found at i:153405 original size:30 final size:29
Alignment explanation
Indices: 153349--153403 Score: 94
Period size: 28 Copynumber: 1.9 Consensus size: 29
153339 TATGTTTCCA
153349 AAATGTTTTAAAAACTATATAATATATTC
1 AAATGTTTTAAAAACTATATAATATATTC
*
153378 AAATG-TTTAAAAACTATATATTATAT
1 AAATGTTTTAAAAACTATATAATATAT
153404 ATATTTCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 20 0.80
29 5 0.20
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.42
Consensus pattern (29 bp):
AAATGTTTTAAAAACTATATAATATATTC
Done.