Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011501.1 Kokia drynarioides strain JFW-HI SEQ_126486, 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: 248941
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Warning! 53 characters in sequence are not A, C, G, or T
Found at i:10209 original size:14 final size:14
Alignment explanation
Indices: 10190--10235 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
10180 TCATCTCCTC
10190 TCTTTTCTTAGTTT
1 TCTTTTCTTAGTTT
10204 TCTTTTC---GTCTT
1 TCTTTTCTTAGT-TT
*
10216 TCTTTTTTTAGTTT
1 TCTTTTCTTAGTTT
10230 TCTTTT
1 TCTTTT
10236 TCATTTGATT
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
11 2 0.07
12 8 0.30
14 15 0.56
15 2 0.07
ACGTcount: A:0.04, C:0.15, G:0.07, T:0.74
Consensus pattern (14 bp):
TCTTTTCTTAGTTT
Found at i:11588 original size:29 final size:29
Alignment explanation
Indices: 11534--11589 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
11524 GGTTGGATAG
11534 GAGAGGAGTAAAAGTTTTAGGAGGAAAGT
1 GAGAGGAGTAAAAGTTTTAGGAGGAAAGT
*
11563 GAGAGAGAGTAAAAGTTTT-GGGGGAAA
1 GAGAG-GAGTAAAAGTTTTAGGAGGAAA
11590 ATTAAGAGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.41, C:0.00, G:0.39, T:0.20
Consensus pattern (29 bp):
GAGAGGAGTAAAAGTTTTAGGAGGAAAGT
Found at i:11825 original size:18 final size:18
Alignment explanation
Indices: 11802--11838 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
11792 TACAGTTTAA
*
11802 TATTCGGTTTATTCAAAT
1 TATTCGGGTTATTCAAAT
*
11820 TATTCGGGTTATTCGAAT
1 TATTCGGGTTATTCAAAT
11838 T
1 T
11839 CGAAAACTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.11, G:0.16, T:0.49
Consensus pattern (18 bp):
TATTCGGGTTATTCAAAT
Found at i:11914 original size:18 final size:18
Alignment explanation
Indices: 11877--11922 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
11867 ATTTTAAAAA
* *
11877 AATTCGAGTTGACTCGAAT
1 AATTCGA-TTAACTCAAAT
11896 AATTCGATTAACTCAAAT
1 AATTCGATTAACTCAAAT
*
11914 AACTCGATT
1 AATTCGATT
11923 CGTTTAACTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (18 bp):
AATTCGATTAACTCAAAT
Found at i:37431 original size:21 final size:21
Alignment explanation
Indices: 37407--37495 Score: 85
Period size: 21 Copynumber: 4.3 Consensus size: 21
37397 CACACATATA
37407 TATATATATATAAACTACTGT
1 TATATATATATAAACTACTGT
* **
37428 TATATACAT-TTTA-TACAT-T
1 TATATATATATAAACTAC-TGT
* * *
37447 TCTTTTTCATATAAACTACTGT
1 TATATAT-ATATAAACTACTGT
37469 TATATATATATAAACTACTGT
1 TATATATATATAAACTACTGT
37490 TATATA
1 TATATA
37496 CATTTTATAC
Statistics
Matches: 51, Mismatches: 12, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
19 7 0.14
20 5 0.10
21 31 0.61
22 8 0.16
ACGTcount: A:0.38, C:0.11, G:0.03, T:0.47
Consensus pattern (21 bp):
TATATATATATAAACTACTGT
Found at i:37483 original size:62 final size:62
Alignment explanation
Indices: 37407--37535 Score: 249
Period size: 62 Copynumber: 2.1 Consensus size: 62
37397 CACACATATA
37407 TATATATATATAAACTACTGTTATATACATTTTATACATTTCTTTTTCATATAAACTACTGT
1 TATATATATATAAACTACTGTTATATACATTTTATACATTTCTTTTTCATATAAACTACTGT
*
37469 TATATATATATAAACTACTGTTATATACATTTTATACATTTCTTTTTCATATAAACTACTTT
1 TATATATATATAAACTACTGTTATATACATTTTATACATTTCTTTTTCATATAAACTACTGT
37531 TATAT
1 TATAT
37536 TTGTAATATA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
62 66 1.00
ACGTcount: A:0.36, C:0.12, G:0.02, T:0.50
Consensus pattern (62 bp):
TATATATATATAAACTACTGTTATATACATTTTATACATTTCTTTTTCATATAAACTACTGT
Found at i:37548 original size:2 final size:2
Alignment explanation
Indices: 37541--37584 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
37531 TATATTTGTA
*
37541 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
37583 AT
1 AT
37585 TTATTTTACA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:48222 original size:257 final size:257
Alignment explanation
Indices: 47760--48264 Score: 809
Period size: 257 Copynumber: 2.0 Consensus size: 257
47750 AACTTTACTG
* * *
47760 TAAAAAAATCTATGAGAAAATATATTTAATTTCTACATTCAACTAATTCACAATAATCAATTAAT
1 TAAAAAAATCTACGAGAAAATATATTTAATTTCTACATTCAACGAATTCACAATAACCAATTAAT
*
47825 TTAATTCCCATTTCTAACTTCAATTAATTAAATAATAATTTGATAAACTTAAATTAATTCTCAGG
66 TTAATTCCCATTTCTAACTTCAATTAATGAAATAATAATTTGATAAACTTAAATTAATTCTCAGG
** * * *
47890 TCATTTCCATACTTTGTGAGAAACCACATTCCTTTCGAATGTAACCCATTTTTCTAACTTCATCA
131 TCATTTCCATACTTAATGAGAAACCACATTCATTTCAAATGTAACCCATTGTTCTAACTTCATCA
* * * *
47955 TTTCTATTCATTTATGTTCATTTGATTTAACATGCAATTCATTTTTTGTTTCAACGAAACCA
196 TTTCTATTCATTTACGTTCATTTGATTCAACATGCAATTCATTTCTGGTTTCAACGAAACCA
48017 TAAAAAAATCTACGAGAAAATATATTTAATTTCTACATTCAACGAATTCACAATAACCAATTAAT
1 TAAAAAAATCTACGAGAAAATATATTTAATTTCTACATTCAACGAATTCACAATAACCAATTAAT
* *
48082 TTAATT-CCATTTTTTAACTTCAATTAATGAAATAATAATTTG-TAAAACTTAAATTAATTCTTA
66 TTAATTCCCA-TTTCTAACTTCAATTAATGAAATAATAATTTGAT-AAACTTAAATTAATTCTCA
*
48145 GGTCATTTCCATACTTAAT-AGAAACCACATTCATTTCTAAATGTAACTCATTGTTCTAACTTCA
129 GGTCATTTCCATACTTAATGAGAAACCACATTCATTTC-AAATGTAACCCATTGTTCTAACTTCA
*
48209 TCATTTTTATTCATTTACGTTCATTTGATTCAACATGCAATTCATTTCTGGTTTCA
193 TCATTTCTATTCATTTACGTTCATTTGATTCAACATGCAATTCATTTCTGGTTTCA
48265 GCGAGCTAGC
Statistics
Matches: 228, Mismatches: 17, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
256 21 0.09
257 207 0.91
ACGTcount: A:0.37, C:0.17, G:0.06, T:0.41
Consensus pattern (257 bp):
TAAAAAAATCTACGAGAAAATATATTTAATTTCTACATTCAACGAATTCACAATAACCAATTAAT
TTAATTCCCATTTCTAACTTCAATTAATGAAATAATAATTTGATAAACTTAAATTAATTCTCAGG
TCATTTCCATACTTAATGAGAAACCACATTCATTTCAAATGTAACCCATTGTTCTAACTTCATCA
TTTCTATTCATTTACGTTCATTTGATTCAACATGCAATTCATTTCTGGTTTCAACGAAACCA
Found at i:52780 original size:37 final size:36
Alignment explanation
Indices: 52707--52779 Score: 96
Period size: 38 Copynumber: 2.0 Consensus size: 36
52697 AAAAACTACT
52707 TATAAAAATAAAAAAATCATTAAAATTATTAAAAAA
1 TATAAAAATAAAAAAATCATTAAAATTATTAAAAAA
52743 TATAAATAATAAAAATATAT-ATTAAAAATT-TTAAAAA
1 TATAAA-AATAAAAA-A-ATCATT-AAAATTATTAAAAA
52780 TTAATTAAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
36 6 0.18
37 8 0.24
38 11 0.33
39 8 0.24
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (36 bp):
TATAAAAATAAAAAAATCATTAAAATTATTAAAAAA
Found at i:52926 original size:24 final size:22
Alignment explanation
Indices: 52872--52926 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
52862 GATGATTTAA
* *
52872 CAAAAAATACAAATTTAAAAAC
1 CAAAAAATAAAAAATTAAAAAC
*
52894 TAAAAAAATAAAAAATTAAAAGAC
1 -CAAAAAATAAAAAATTAAAA-AC
52918 CAAATAAAT
1 CAAA-AAAT
52927 CATTATCACA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.71, C:0.09, G:0.02, T:0.18
Consensus pattern (22 bp):
CAAAAAATAAAAAATTAAAAAC
Found at i:54606 original size:6 final size:6
Alignment explanation
Indices: 54595--54627 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
54585 ATTGCAGAAA
54595 GGAGAT GGAGAT GGAGAT GGAGAT GGAGAT GGA
1 GGAGAT GGAGAT GGAGAT GGAGAT GGAGAT GGA
54628 AGGAAGGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.52, T:0.15
Consensus pattern (6 bp):
GGAGAT
Found at i:55091 original size:19 final size:21
Alignment explanation
Indices: 55058--55096 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
55048 TATCTTTAAC
*
55058 TAAGATATATTATT-ATTTTT
1 TAAGATATATAATTAATTTTT
55078 TAAGA-ATATAATTAATTTT
1 TAAGATATATAATTAATTTT
55097 ACAAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (21 bp):
TAAGATATATAATTAATTTTT
Found at i:56403 original size:12 final size:12
Alignment explanation
Indices: 56386--56411 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
56376 ATTTTCACAA
56386 AATTATTGATAT
1 AATTATTGATAT
56398 AATTATTGATAT
1 AATTATTGATAT
56410 AA
1 AA
56412 CTTCATTTTG
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:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (12 bp):
AATTATTGATAT
Found at i:56563 original size:14 final size:14
Alignment explanation
Indices: 56544--56590 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 14
56534 ATTGCACAAA
56544 ATCAAAGTTCATAT
1 ATCAAAGTTCATAT
56558 ATCAAA-TTGCATATT
1 ATCAAAGTT-CATA-T
56573 GAATCAAAGTTCATAT
1 --ATCAAAGTTCATAT
56589 AT
1 AT
56591 AATTTTGATA
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
13 2 0.07
14 12 0.43
15 1 0.04
16 1 0.04
17 10 0.36
18 2 0.07
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.36
Consensus pattern (14 bp):
ATCAAAGTTCATAT
Found at i:56587 original size:17 final size:16
Alignment explanation
Indices: 56543--56593 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
56533 AATTGCACAA
56543 AATCAAAGTTCATA-T
1 AATCAAAGTTCATATT
56558 -ATCAAA-TTGCATATT
1 AATCAAAGTT-CATATT
56573 GAATCAAAGTTCATATAT
1 -AATCAAAGTTCATAT-T
56591 AAT
1 AAT
56594 TTTGATATCT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
13 2 0.07
14 10 0.33
15 1 0.03
17 14 0.47
18 3 0.10
ACGTcount: A:0.45, C:0.12, G:0.08, T:0.35
Consensus pattern (16 bp):
AATCAAAGTTCATATT
Found at i:57779 original size:2 final size:2
Alignment explanation
Indices: 57774--57799 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
57764 TAATTTAACC
57774 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
57800 AAATATTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:75924 original size:17 final size:18
Alignment explanation
Indices: 75892--75925 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
75882 ATAAAGAAAT
*
75892 ATTTTCATCTATAAAGCA
1 ATTTACATCTATAAAGCA
75910 ATTTACATC-ATAAAGC
1 ATTTACATCTATAAAGC
75926 TGCATGCCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (18 bp):
ATTTACATCTATAAAGCA
Found at i:81912 original size:23 final size:24
Alignment explanation
Indices: 81886--81983 Score: 94
Period size: 24 Copynumber: 4.1 Consensus size: 24
81876 AATCACGGTA
*
81886 TTGCACAGAAGTGTCAC-TTTCAT
1 TTGCACAGAAGTGCCACATTTCAT
** * *
81909 TTGCATTGAAGTGCCACATTCCAA
1 TTGCACAGAAGTGCCACATTTCAT
81933 TTGCATCA-AAGTGCCACATTTCGA-
1 TTGCA-CAGAAGTGCCACATTTC-AT
* *
81957 TTGCACCGAAGTGCCTCATTTCAT
1 TTGCACAGAAGTGCCACATTTCAT
81981 TTG
1 TTG
81984 TGCGCATAGA
Statistics
Matches: 60, Mismatches: 10, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
23 16 0.27
24 43 0.72
25 1 0.02
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (24 bp):
TTGCACAGAAGTGCCACATTTCAT
Found at i:83419 original size:27 final size:28
Alignment explanation
Indices: 83389--83453 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 28
83379 TTTACAGCAG
* *
83389 TCTATGAAAAGGAAA-CCTTTGTGGCAA
1 TCTATGAAAAGGAAAGCATTTGTGACAA
**
83416 TCTAT-AAAAATAAAGCATTTGTGACAA
1 TCTATGAAAAGGAAAGCATTTGTGACAA
*
83443 TCTATGGAAAG
1 TCTATGAAAAG
83454 TTCATCTTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
26 7 0.23
27 20 0.67
28 3 0.10
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.28
Consensus pattern (28 bp):
TCTATGAAAAGGAAAGCATTTGTGACAA
Found at i:93201 original size:20 final size:21
Alignment explanation
Indices: 93178--93221 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
93168 AAACTAAGTA
* *
93178 TAAATGGGTTTAATTAAGA-T
1 TAAAAGGGATTAATTAAGACT
*
93198 TAAAAGTGATTAATTAAGACT
1 TAAAAGGGATTAATTAAGACT
93219 TAA
1 TAA
93222 TGATGAAAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.45, C:0.02, G:0.16, T:0.36
Consensus pattern (21 bp):
TAAAAGGGATTAATTAAGACT
Found at i:93735 original size:72 final size:72
Alignment explanation
Indices: 93639--93782 Score: 261
Period size: 72 Copynumber: 2.0 Consensus size: 72
93629 GTATTGACTT
93639 GTAAATAAAGGTGTGAAGAAGTGGGATAAACACCCTAAAGAATTCAGCTAAGGTTAGTTATGTGA
1 GTAAATAAAGGTGTGAAGAAGTGGGATAAACACCCTAAAGAATTCAGCTAAGGTTAGTTATGTGA
93704 GAAAATG
66 GAAAATG
** *
93711 GTAAATAAAGGTGTGAAGGGGTGGGATAAACACCCTAGAGAATTCAGCTAAGGTTAGTTATGTGA
1 GTAAATAAAGGTGTGAAGAAGTGGGATAAACACCCTAAAGAATTCAGCTAAGGTTAGTTATGTGA
93776 GAAAATG
66 GAAAATG
93783 ATTATTTTGC
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 69 1.00
ACGTcount: A:0.40, C:0.08, G:0.28, T:0.24
Consensus pattern (72 bp):
GTAAATAAAGGTGTGAAGAAGTGGGATAAACACCCTAAAGAATTCAGCTAAGGTTAGTTATGTGA
GAAAATG
Found at i:112746 original size:12 final size:12
Alignment explanation
Indices: 112729--112754 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
112719 AGTTTGTTTG
112729 TTGTTTTAATAT
1 TTGTTTTAATAT
112741 TTGTTTTAATAT
1 TTGTTTTAATAT
112753 TT
1 TT
112755 TTTAACTGTA
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:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (12 bp):
TTGTTTTAATAT
Found at i:118011 original size:35 final size:34
Alignment explanation
Indices: 117944--118048 Score: 201
Period size: 34 Copynumber: 3.1 Consensus size: 34
117934 AGAGATAATT
117944 TATTGCTAACAAAATACTTGATTTTTTTTTATAA
1 TATTGCTAACAAAATACTTGATTTTTTTTTATAA
117978 TATTGCTAACAAAATACTTGATTTTTTTTTTATAA
1 TATTGCTAACAAAATACTTGA-TTTTTTTTTATAA
118013 TATTGCTAACAAAATACTTGATTTTTTTTTATAA
1 TATTGCTAACAAAATACTTGATTTTTTTTTATAA
118047 TA
1 TA
118049 ATTCTATATA
Statistics
Matches: 70, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
34 36 0.51
35 34 0.49
ACGTcount: A:0.35, C:0.09, G:0.06, T:0.50
Consensus pattern (34 bp):
TATTGCTAACAAAATACTTGATTTTTTTTTATAA
Found at i:118078 original size:69 final size:69
Alignment explanation
Indices: 117944--118078 Score: 148
Period size: 69 Copynumber: 2.0 Consensus size: 69
117934 AGAGATAATT
**** ** * *
117944 TATTGCTAACAAAATACTTGATTTTTTTTTATAATATTGCTAACAAAATACTTGATTTTTTTTTT
1 TATTGCTAACAAAATACTTGATTTTTTTTTATAATATTGCTAACAAAATAAAAAAAATATCTTTT
118009 ATAA
66 ATAA
* *
118013 TATTGCTAACAAAATACTTGATTTTTTTTTATAATAATT-CTATA-TATATAAAAAAAATATCTT
1 TATTGCTAACAAAATACTTGATTTTTTTTTATAAT-ATTGCTA-ACAAAATAAAAAAAATATCTT
118076 TTA
64 TTA
118079 AGGAAAATTC
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
69 50 0.93
70 4 0.07
ACGTcount: A:0.39, C:0.08, G:0.04, T:0.49
Consensus pattern (69 bp):
TATTGCTAACAAAATACTTGATTTTTTTTTATAATATTGCTAACAAAATAAAAAAAATATCTTTT
ATAA
Found at i:121383 original size:21 final size:21
Alignment explanation
Indices: 121354--121393 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
121344 TAATGCCAAA
*
121354 TCAACATTTTCCTCTTGAATT
1 TCAACATTTTCATCTTGAATT
* *
121375 TCAATATTTTTATCTTGAA
1 TCAACATTTTCATCTTGAA
121394 AAAGATCAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.17, G:0.05, T:0.50
Consensus pattern (21 bp):
TCAACATTTTCATCTTGAATT
Found at i:131569 original size:16 final size:17
Alignment explanation
Indices: 131540--131572 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
131530 TATCATTCTG
131540 AATTAAGTAATTTATTC
1 AATTAAGTAATTTATTC
*
131557 AATT-AGTATTTTATTC
1 AATTAAGTAATTTATTC
131573 CATAGAAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.52
Consensus pattern (17 bp):
AATTAAGTAATTTATTC
Found at i:131850 original size:15 final size:15
Alignment explanation
Indices: 131830--131868 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
131820 GCACATCAAA
*
131830 CAAGAATTAATATAT
1 CAAGAATTAATAAAT
*
131845 CAAGAA-TACTAAAT
1 CAAGAATTAATAAAT
131859 CAAGAATTAA
1 CAAGAATTAA
131869 GCACACATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.56, C:0.10, G:0.08, T:0.26
Consensus pattern (15 bp):
CAAGAATTAATAAAT
Found at i:132281 original size:25 final size:23
Alignment explanation
Indices: 132249--132294 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
132239 GTTGGATCCA
132249 AATTAAATTCTAAAAAGATAATTGG
1 AATTAAA-TCTAAAAA-ATAATTGG
*
132274 AATTAAATCTAAATAATAATT
1 AATTAAATCTAAAAAATAATT
132295 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.35
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTGG
Found at i:132381 original size:13 final size:13
Alignment explanation
Indices: 132360--132393 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
132350 ACAATATAAT
132360 AATAATAATCCTA
1 AATAATAATCCTA
*
132373 AATATTAATCCTA
1 AATAATAATCCTA
*
132386 AAAAATAA
1 AATAATAA
132394 ATTTTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATCCTA
Found at i:141750 original size:17 final size:17
Alignment explanation
Indices: 141728--141761 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
141718 TACTAGAGCC
141728 TTTCTT-TCCTTTCTTCT
1 TTTCTTCTCC-TTCTTCT
141745 TTTCTTCTCCTTCTTCT
1 TTTCTTCTCCTTCTTCT
141762 CTGTTCTGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTCTTCTCCTTCTTCT
Found at i:142512 original size:2 final size:2
Alignment explanation
Indices: 142505--142534 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
142495 CACCCAACAT
142505 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
142535 GCAGGCCTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:145162 original size:5 final size:5
Alignment explanation
Indices: 145152--145208 Score: 70
Period size: 5 Copynumber: 12.2 Consensus size: 5
145142 GACATTGCTC
145152 TCTCT TCTCT TCTCT TCTCT TCTCT TCTCT TCTACT T-TCT T-TCT T-TCT
1 TCTCT TCTCT TCTCT TCTCT TCTCT TCTCT TCT-CT TCTCT TCTCT TCTCT
145200 T-TCT T-TCT T
1 TCTCT TCTCT T
145209 GCCTATGCAG
Statistics
Matches: 51, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
4 19 0.37
5 29 0.57
6 3 0.06
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65
Consensus pattern (5 bp):
TCTCT
Found at i:149394 original size:18 final size:18
Alignment explanation
Indices: 149368--149406 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
149358 GTTTTTTGTC
* *
149368 TTACTTATTTCTCTTATT
1 TTACGTATTTCTATTATT
*
149386 TTACGTATTTTTATTATT
1 TTACGTATTTCTATTATT
149404 TTA
1 TTA
149407 TAAAAACCCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.10, G:0.03, T:0.67
Consensus pattern (18 bp):
TTACGTATTTCTATTATT
Found at i:154872 original size:23 final size:22
Alignment explanation
Indices: 154846--154935 Score: 108
Period size: 23 Copynumber: 4.0 Consensus size: 22
154836 GCTCTCCGTT
154846 ATTAGCACTTCGTGTGCTCTACG
1 ATTAGCACTTCGTGTGCTCT-CG
154869 ATTAGCACTTCGTGTGCTCTTCG
1 ATTAGCACTTCGTGTGCTC-TCG
* * *
154892 ATTAGTACTTTGTGTACTCTCTG
1 ATTAGCACTTCGTGTGCTCTC-G
* *
154915 TTTAGCACTTAGTGTGCTCTC
1 ATTAGCACTTCGTGTGCTCTC
154936 TGTTACCCAG
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
22 2 0.03
23 55 0.95
24 1 0.02
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.41
Consensus pattern (22 bp):
ATTAGCACTTCGTGTGCTCTCG
Found at i:156446 original size:24 final size:24
Alignment explanation
Indices: 156397--156446 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
156387 TCTACTTTAG
* **
156397 TTTAGGTTTTTGTCTTTTTTTTTT
1 TTTAGGTTTTAGTCTTTTTTCGTT
156421 TTTAGGTTTTAGT-TTATTTTCGTT
1 TTTAGGTTTTAGTCTT-TTTTCGTT
156445 TT
1 TT
156447 ATCTTTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 2 0.09
24 20 0.91
ACGTcount: A:0.08, C:0.04, G:0.14, T:0.74
Consensus pattern (24 bp):
TTTAGGTTTTAGTCTTTTTTCGTT
Found at i:159240 original size:30 final size:29
Alignment explanation
Indices: 159198--159361 Score: 118
Period size: 30 Copynumber: 5.5 Consensus size: 29
159188 TTAATCCTTA
*
159198 AACTATTCAAAAATT-ATGTTTTGACCCTCG
1 AACT-TTCAAAAATTCAT-ATTTGACCCTCG
159228 AACTTTCTAAAAATTCATATTTGACCCTCG
1 AACTTTC-AAAAATTCATATTTGACCCTCG
* *
159258 AACTTCCAAAAAATTCATATTTGA-CCTTG
1 AACTTTC-AAAAATTCATATTTGACCCTCG
* * * *
159287 AACTTCCCAAAAATTTAGATTT-ATCCCCCG
1 AACTT-TCAAAAATTCATATTTGA-CCCTCG
* * * * *
159317 AACTTTAAAAAAATTTAGATTTGACCCCCA
1 AACTTT-CAAAAATTCATATTTGACCCTCG
*
159347 AACTTCCCAAAAATT
1 AACTT-TCAAAAATT
159362 TGAATTTGGC
Statistics
Matches: 113, Mismatches: 13, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
28 1 0.01
29 24 0.21
30 85 0.75
31 3 0.03
ACGTcount: A:0.37, C:0.23, G:0.07, T:0.33
Consensus pattern (29 bp):
AACTTTCAAAAATTCATATTTGACCCTCG
Found at i:159289 original size:29 final size:30
Alignment explanation
Indices: 159217--159361 Score: 141
Period size: 30 Copynumber: 4.9 Consensus size: 30
159207 AAAATTATGT
* *
159217 TTTGACCCTCGAACTTTCTAAAAATTCATA
1 TTTGACCCTCGAACTTCCAAAAAATTCATA
159247 TTTGACCCTCGAACTTCCAAAAAATTCATA
1 TTTGACCCTCGAACTTCCAAAAAATTCATA
* * * *
159277 TTTGA-CCTTGAACTTCCCAAAAATTTAGA
1 TTTGACCCTCGAACTTCCAAAAAATTCATA
* ** * *
159306 TTT-ATCCCCCGAACTTTAAAAAAATTTAGA
1 TTTGA-CCCTCGAACTTCCAAAAAATTCATA
* * *
159336 TTTGACCCCCAAACTTCCCAAAAATT
1 TTTGACCCTCGAACTTCCAAAAAATT
159362 TGAATTTGGC
Statistics
Matches: 97, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
28 1 0.01
29 23 0.24
30 72 0.74
31 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.32
Consensus pattern (30 bp):
TTTGACCCTCGAACTTCCAAAAAATTCATA
Found at i:159301 original size:59 final size:60
Alignment explanation
Indices: 159217--159361 Score: 159
Period size: 59 Copynumber: 2.4 Consensus size: 60
159207 AAAATTATGT
* * * * * *
159217 TTTGACCCTCGAACTTTCTAAAAATTCATATTTGA-CCCTCGAACTTCCAAAAAATTCATA
1 TTTGACCCTCGAACTTCCCAAAAATTCAGATTT-ATCCCCCGAACTTCAAAAAAATTCAGA
* * * *
159277 TTTGA-CCTTGAACTTCCCAAAAATTTAGATTTATCCCCCGAACTTTAAAAAAATTTAGA
1 TTTGACCCTCGAACTTCCCAAAAATTCAGATTTATCCCCCGAACTTCAAAAAAATTCAGA
* *
159336 TTTGACCCCCAAACTTCCCAAAAATT
1 TTTGACCCTCGAACTTCCCAAAAATT
159362 TGAATTTGGC
Statistics
Matches: 70, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
58 1 0.01
59 47 0.67
60 22 0.31
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.32
Consensus pattern (60 bp):
TTTGACCCTCGAACTTCCCAAAAATTCAGATTTATCCCCCGAACTTCAAAAAAATTCAGA
Found at i:159375 original size:29 final size:30
Alignment explanation
Indices: 159217--159385 Score: 112
Period size: 30 Copynumber: 5.7 Consensus size: 30
159207 AAAATTATGT
* * * * * *
159217 TTTGACCCTCGAACTTTCTAAAAATTCATA
1 TTTGACCCCCAAACTTCCCAAAAATTTAGA
* * * * *
159247 TTTGACCCTCGAACTTCCAAAAAATTCATA
1 TTTGACCCCCAAACTTCCCAAAAATTTAGA
***
159277 TTTGA-CCTTGAACTTCCCAAAAATTTAGA
1 TTTGACCCCCAAACTTCCCAAAAATTTAGA
* ***
159306 TTT-ATCCCCCGAACTTTAAAAAAATTTAGA
1 TTTGA-CCCCCAAACTTCCCAAAAATTTAGA
159336 TTTGACCCCCAAACTTCCCAAAAATTT-GAA
1 TTTGACCCCCAAACTTCCCAAAAATTTAG-A
* *
159366 TTTG-GCCCCAAACTTTCCAA
1 TTTGACCCCCAAACTTCCCAA
159386 GATTTCATTT
Statistics
Matches: 118, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
28 1 0.01
29 38 0.32
30 78 0.66
31 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.08, T:0.32
Consensus pattern (30 bp):
TTTGACCCCCAAACTTCCCAAAAATTTAGA
Found at i:176088 original size:40 final size:41
Alignment explanation
Indices: 176003--176112 Score: 163
Period size: 41 Copynumber: 2.7 Consensus size: 41
175993 TATTTTACCT
*
176003 AAAAAAAGGATCGAGATGAAAACCCGCAAAGGGCGTCTCGA
1 AAAAAAAGGATCGAGATGAAAACCAGCAAAGGGCGTCTCGA
*
176044 AAAAAAGGGATCGAGATGAAAACCAGCAAAGGGCGTCTCGA
1 AAAAAAAGGATCGAGATGAAAACCAGCAAAGGGCGTCTCGA
*
176085 AAAAAAA-G-TCAAGATGAAAAACCA-CAAA
1 AAAAAAAGGATCGAGATG-AAAACCAGCAAA
176113 TGGCATCTTG
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
39 11 0.17
40 8 0.12
41 45 0.70
ACGTcount: A:0.50, C:0.17, G:0.24, T:0.09
Consensus pattern (41 bp):
AAAAAAAGGATCGAGATGAAAACCAGCAAAGGGCGTCTCGA
Found at i:177015 original size:124 final size:124
Alignment explanation
Indices: 176795--177904 Score: 1073
Period size: 124 Copynumber: 9.0 Consensus size: 124
176785 TGTTTTACAA
* * *
176795 GAAGCAAAGCTCAATGTGAGTGAAACTTCAAATCCCCATCTTCTTAATGAGATATAGAGAAGTGG
1 GAAGCAAAGCTCAATGTGAGTGAAACTTCAAATCCCCATCTTCCTGATGAGATACAGAGAAGTGG
* *
176860 ATCAAAATGGTGAAGCGGTCATTTTCTTGATGAGATACAGAGAAGTGAACCAAAATAAT
66 ATCAAAATGGTGAAGCGGTCATTTTCCTGATGAGATATAGAGAAGTGAACCAAAATAAT
* * * * *
176919 GAAGCAAAGCTCAATATGAGTGAAACTTCAAATCTCCATCTTCTTGATAAGATACAGAGAAGTGA
1 GAAGCAAAGCTCAATGTGAGTGAAACTTCAAATCCCCATCTTCCTGATGAGATACAGAGAAGTGG
* *
176984 ATCAAAATGGTGAAGCAGTCATTTTCCTGATGAGATATAAAGAAGTGAACCAAAATAAT
66 ATCAAAATGGTGAAGCGGTCATTTTCCTGATGAGATATAGAGAAGTGAACCAAAATAAT
* * *
177043 GAAGCGAAGCTCAATGTGAGTGAAACTTCAAATCCCCATTTTCCTGATGAGATACATAGAAGTGG
1 GAAGCAAAGCTCAATGTGAGTGAAACTTCAAATCCCCATCTTCCTGATGAGATACAGAGAAGTGG
* * * * * *
177108 ATCAAAATGATGAACCGATCATCTTCCTGATGAGATACAGAGAAATGAACCAAAATAAT
66 ATCAAAATGGTGAAGCGGTCATTTTCCTGATGAGATATAGAGAAGTGAACCAAAATAAT
* * * *
177167 GAAGTGAAA-CTCAATGTGAGTGAAACTTTAAATCCTCATCTTCCTGATGAGATATAGAGAAGTG
1 GAAG-CAAAGCTCAATGTGAGTGAAACTTCAAATCCCCATCTTCCTGATGAGATACAGAGAAGTG
* *
177231 GATCAAAATGGTGAAGTGGTCATTTTCTTGATGAGATATAGAGAAGTGAACCAAAATAAT
65 GATCAAAATGGTGAAGCGGTCATTTTCCTGATGAGATATAGAGAAGTGAACCAAAATAAT
* *
177291 GAAGCAAAGCTCAATTTGAGTGAAACTTCAAATCCCCATCTTCCTAATGAGATACAGAGAAGTGG
1 GAAGCAAAGCTCAATGTGAGTGAAACTTCAAATCCCCATCTTCCTGATGAGATACAGAGAAGTGG
* *
177356 ATCAAAATGGTAAAGCTGTCATTTTCCTGATGAGATATAGAGAAGTGAACCAAAATAAT
66 ATCAAAATGGTGAAGCGGTCATTTTCCTGATGAGATATAGAGAAGTGAACCAAAATAAT
* * * * *
177415 GAAGCGAAGCTCAATGTGAGTGAAACTTCAAATCCCCATCTTCTTGATAAGATGCAGAGAAGTAG
1 GAAGCAAAGCTCAATGTGAGTGAAACTTCAAATCCCCATCTTCCTGATGAGATACAGAGAAGTGG
* * * ** * * * *
177480 ACCAAAACAATGAAGTGAAGC--TCA--ATGC-GAGTGA-A-ACTTCA-AA---ACCTCATATTC
66 ATC--AA-AATG--GTGAAGCGGTCATTTTCCTGA-TGAGATA-TAGAGAAGTGAAC-CAAAATA
*
177534 TT
123 AT
* * * * **** *
177536 GATGAG-ATACA-CTGAA-GTGGGTCAAAACAAT-AAAGTGGTTATCTTCCTGATGAGATATAGA
1 GA--AGCA-A-AGCTCAATGTGAGT-GAAAC-TTCAAA-TCCCCATCTTCCTGATGAGATACAGA
* * ** * * *
177597 GAAGTGAATCAAAATGGTGAAGCGGTCATCTTCCTGATGAGATGCAGAGAAGAGGACCAAAAAAA
59 GAAGTGGATCAAAATGGTGAAGCGGTCATTTTCCTGATGAGATATAGAGAAGTGAACCAAAATAA
177662 T
124 T
* * * * *
177663 GAAGCGAAGCTCAATGTGATTGAAACTTCAAA--CCCATCTTCTTAATGAGATACAAAG-AGCTA
1 GAAGCAAAGCTCAATGTGAGTGAAACTTCAAATCCCCATCTTCCTGATGAGATACAGAGAAG-T-
* *
177725 GG-TCAGACAA---TGAAGCGATCATTTTCCTGATGAGATACAGAGAAGT-AGACCAAAATAAT
64 GGATCA-A-AATGGTGAAGCGGTCATTTTCCTGATGAGATATAGAGAAGTGA-ACCAAAATAAT
* * * ** * *
177784 GAAACAAAGCTCAATTTGAGTGAAACTTCAAAACCTTATATTCCTGATGAGATACAGAGAAATGG
1 GAAGCAAAGCTCAATGTGAGTGAAACTTCAAATCCCCATCTTCCTGATGAGATACAGAGAAGTGG
* *** * * * * * * *
177849 GT-AAAACAATAAAGTGATCCTCTTCTTGATGAGATACAGAGAAGTGAACCAAAATA
66 ATCAAAATGGTGAAGCGGTCATTTTCCTGATGAGATATAGAGAAGTGAACCAAAATA
177905 TAAAGCTACA
Statistics
Matches: 807, Mismatches: 134, Indels: 91
0.78 0.13 0.09
Matches are distributed among these distances:
119 7 0.01
120 4 0.00
121 87 0.11
122 32 0.04
123 88 0.11
124 540 0.67
125 23 0.03
126 6 0.01
127 13 0.02
128 1 0.00
129 6 0.01
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.24
Consensus pattern (124 bp):
GAAGCAAAGCTCAATGTGAGTGAAACTTCAAATCCCCATCTTCCTGATGAGATACAGAGAAGTGG
ATCAAAATGGTGAAGCGGTCATTTTCCTGATGAGATATAGAGAAGTGAACCAAAATAAT
Found at i:177294 original size:48 final size:48
Alignment explanation
Indices: 177202--177294 Score: 132
Period size: 48 Copynumber: 1.9 Consensus size: 48
177192 CTTTAAATCC
* * **
177202 TCATCTTCCTGATGAGATATAGAGAAGTGGATCAAAATGGTGAAGTGG
1 TCATCTTCCTGATGAGATATAGAGAAGTGAACCAAAATAATGAAGTGG
* *
177250 TCATTTTCTTGATGAGATATAGAGAAGTGAACCAAAATAATGAAG
1 TCATCTTCCTGATGAGATATAGAGAAGTGAACCAAAATAATGAAG
177295 CAAAGCTCAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.38, C:0.10, G:0.25, T:0.28
Consensus pattern (48 bp):
TCATCTTCCTGATGAGATATAGAGAAGTGAACCAAAATAATGAAGTGG
Found at i:177503 original size:200 final size:200
Alignment explanation
Indices: 177255--177620 Score: 484
Period size: 200 Copynumber: 1.8 Consensus size: 200
177245 AGTGGTCATT
* * * **
177255 TTCTTGATGAGATATAGAGAAGTGAACCAAAATAATGAAGCAAAGCTCAATTTGAGTGAAACTTC
1 TTCTTGATAAGATACAGAGAAGTGAACCAAAACAATGAAGCAAAGCTCAATGCGAGTGAAACTTC
* * * *** *
177320 AAATCCCCATCTTCCTAATGAGATACAGAGAAGTGGATCAAAATGGTAAAGCT-GTCATTTTCCT
66 AAAACCCCATATTCCTAATGAGATACACAGAAGTGGATCAAAACAATAAAG-TGGTCATCTTCCT
177384 GATGAGATATAGAGAAGTGAACCAAAATAATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAATC
130 GATGAGATATAGAGAAGTGAACCAAAATAATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAATC
177449 CCCATC
195 CCCATC
* **
177455 TTCTTGATAAGATGCAGAGAAGT-AGACCAAAACAATGAAGTGAAGCTCAATGCGAGTGAAACTT
1 TTCTTGATAAGATACAGAGAAGTGA-ACCAAAACAATGAAGCAAAGCTCAATGCGAGTGAAACTT
* * * * * *
177519 CAAAACCTCATATTCTTGATGAGATACACTGAAGTGGGTCAAAACAATAAAGTGGTTATCTTCCT
65 CAAAACCCCATATTCCTAATGAGATACACAGAAGTGGATCAAAACAATAAAGTGGTCATCTTCCT
* **
177584 GATGAGATATAGAGAAGTGAATCAAAATGGTGAAGCG
130 GATGAGATATAGAGAAGTGAACCAAAATAATGAAGCG
177621 GTCATCTTCC
Statistics
Matches: 140, Mismatches: 24, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
199 2 0.01
200 138 0.99
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.24
Consensus pattern (200 bp):
TTCTTGATAAGATACAGAGAAGTGAACCAAAACAATGAAGCAAAGCTCAATGCGAGTGAAACTTC
AAAACCCCATATTCCTAATGAGATACACAGAAGTGGATCAAAACAATAAAGTGGTCATCTTCCTG
ATGAGATATAGAGAAGTGAACCAAAATAATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAATCC
CCATC
Found at i:177520 original size:76 final size:76
Alignment explanation
Indices: 177394--177543 Score: 221
Period size: 76 Copynumber: 2.0 Consensus size: 76
177384 GATGAGATAT
* * * *
177394 AGAGAAGTGAACCAAAATAATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAATCCCCATCTTCT
1 AGAGAAGTGAACCAAAACAATGAAGCGAAGCTCAATGCGAGTGAAACTTCAAAACCCCATATTCT
177459 TGATAAGATGC
66 TGATAAGATGC
* *
177470 AGAGAAGT-AGACCAAAACAATGAAGTGAAGCTCAATGCGAGTGAAACTTCAAAACCTCATATTC
1 AGAGAAGTGA-ACCAAAACAATGAAGCGAAGCTCAATGCGAGTGAAACTTCAAAACCCCATATTC
*
177534 TTGATGAGAT
65 TTGATAAGAT
177544 ACACTGAAGT
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
75 1 0.02
76 65 0.98
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (76 bp):
AGAGAAGTGAACCAAAACAATGAAGCGAAGCTCAATGCGAGTGAAACTTCAAAACCCCATATTCT
TGATAAGATGC
Found at i:177553 original size:76 final size:76
Alignment explanation
Indices: 177396--177572 Score: 212
Period size: 76 Copynumber: 2.3 Consensus size: 76
177386 TGAGATATAG
* * * * *
177396 AGAAGT-GAACCAAAATAATGAAGCGAAGCTCAATGTGAGTGAAACTTCAAATCCCCATCTTCTT
1 AGAAGTAG-ACCAAAACAATGAAGTGAAGCTCAATGCGAGTGAAACTTCAAAACCCCATATTCTT
* *
177460 GATAAGATGCAG
65 GATAAGATACAC
*
177472 AGAAGTAGACCAAAACAATGAAGTGAAGCTCAATGCGAGTGAAACTTCAAAACCTCATATTCTTG
1 AGAAGTAGACCAAAACAATGAAGTGAAGCTCAATGCGAGTGAAACTTCAAAACCCCATATTCTTG
*
177537 ATGAGATACAC
66 ATAAGATACAC
* * ** *
177548 TGAAGTGGGTCAAAACAATAAAGTG
1 AGAAGTAGACCAAAACAATGAAGTG
177573 GTTATCTTCC
Statistics
Matches: 86, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
76 85 0.99
77 1 0.01
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.21
Consensus pattern (76 bp):
AGAAGTAGACCAAAACAATGAAGTGAAGCTCAATGCGAGTGAAACTTCAAAACCCCATATTCTTG
ATAAGATACAC
Found at i:177582 original size:372 final size:369
Alignment explanation
Indices: 176804--177844 Score: 1203
Period size: 372 Copynumber: 2.8 Consensus size: 369
176794 AGAAGCAAAG
* * * * *
176804 CTCAATGTGAGTGAAAC-TTCAAATCCCCATCTTCTTAATGAGATATAGAGAAGTGGATCAAAAT
1 CTCAATGTGAGTAAAACAAT-AAATCCTCATCTTCCTGATGAGATATAGAGAAGTGGATCAAAAT
176868 GGTGAAGCGGTCATTTTCTTGATGAGATACAGAGAAGTGAACCAAAATAATGAAGCAAAGCTCAA
65 GGTGAAGCGGTCATTTTCTTGATGAGATACAGAGAAGTGAACCAAAATAATGAAGCAAAGCTCAA
* * * *
176933 TATGAGTGAAACTTCAAATCTCCATCTTCTTGATAAGATACAGAGAAGTGAATCAAAATGGTGAA
130 TATGAGTGAAACTTCAAATCCCCATCTTCTTAATGAGATACAGAGAAGTGGATCAAAATGGT-AA
*
176998 GCAGTCATTTTCCTGATGAGATATAAAGAAGTGAACCAAAATAATGAAGCGAAGCTCAATGTGAG
194 GC-GTCATTTTCCTGATGAGATATAGAGAAGTGAACCAAAATAATGAAGCGAAGCTCAATGTGAG
* * * * * ** *
177063 TGAAACTTCAAATCCCCATTTTCCTGATGAGATACATAGAAGTGGATCAAAATGATGAACCGATC
258 TGAAACTTCAAATCCCCATCTTCCTGATAAGATACAGAGAAGTAGACCAAAACAATGAACCGAGC
* * *
177128 ATCTTCCTGATGAGATACAGAGAAATGAACCAAAATAATGAAGTGAAA
323 ATCATCCTGATGAGATACAGACAAA-GAACCAAAATAATGAAGAGAAA
* **
177176 CTCAATGTGAGTGAAACTTTAAATCCTCATCTTCCTGATGAGATATAGAGAAGTGGATCAAAATG
1 CTCAATGTGAGTAAAACAATAAATCCTCATCTTCCTGATGAGATATAGAGAAGTGGATCAAAATG
* *
177241 GTGAAGTGGTCATTTTCTTGATGAGATATAGAGAAGTGAACCAAAATAATGAAGCAAAGCTCAAT
66 GTGAAGCGGTCATTTTCTTGATGAGATACAGAGAAGTGAACCAAAATAATGAAGCAAAGCTCAAT
* *
177306 TTGAGTGAAACTTCAAATCCCCATCTTCCTAATGAGATACAGAGAAGTGGATCAAAATGGTAAAG
131 ATGAGTGAAACTTCAAATCCCCATCTTCTTAATGAGATACAGAGAAGTGGATCAAAATGGT-AAG
177371 CTGTCATTTTCCTGATGAGATATAGAGAAGTGAACCAAAATAATGAAGCGAAGCTCAATGTGAGT
195 C-GTCATTTTCCTGATGAGATATAGAGAAGTGAACCAAAATAATGAAGCGAAGCTCAATGTGAGT
* * **
177436 GAAACTTCAAATCCCCATCTTCTTGATAAGATGCAGAGAAGTAGACCAAAACAATGAAGTGAAGC
259 GAAACTTCAAATCCCCATCTTCCTGATAAGATACAGAGAAGTAGACCAAAACAATGAACCG-AGC
* ** * * * ** *
177501 -TCAATGC-GAGTGA-A-AC-TTCAAA-ACCTCATATTCTTGATGAGATACA
323 ATC-ATCCTGA-TGAGATACAGACAAAGAAC-CAAAATAATGAAGAGA-A-A
* * ** * *
177547 CTGAA-GTGGGTCAAAACAATAAAGTGGTTATCTTCCTGATGAGATATAGAGAAGTGAATCAAAA
1 CTCAATGTGAGT-AAAACAATAAA-TCCTCATCTTCCTGATGAGATATAGAGAAGTGGATCAAAA
* * * * * * *
177611 TGGTGAAGCGGTCATCTTCCTGATGAGATGCAGAGAAGAGGACCAAAAAAATGAAGCGAAGCTCA
64 TGGTGAAGCGGTCATTTTCTTGATGAGATACAGAGAAGTGAACCAAAATAATGAAGCAAAGCTCA
* * *
177676 ATGTGATTGAAACTTCAAA--CCCATCTTCTTAATGAGATACAAAG-AGCTAGG-TCAGACAAT-
129 ATATGAGTGAAACTTCAAATCCCCATCTTCTTAATGAGATACAGAGAAG-T-GGATCA-A-AATG
* * *
177736 G-AAGCGATCATTTTCCTGATGAGATACAGAGAAGT-AGACCAAAATAATGAAACAAAGCTCAAT
190 GTAAGCG-TCATTTTCCTGATGAGATATAGAGAAGTGA-ACCAAAATAATGAAGCGAAGCTCAAT
* * ** * *
177799 TTGAGTGAAACTTCAAAACCTTATATTCCTGATGAGATACAGAGAA
253 GTGAGTGAAACTTCAAATCCCCATCTTCCTGATAAGATACAGAGAA
177845 ATGGGTAAAA
Statistics
Matches: 583, Mismatches: 71, Indels: 33
0.85 0.10 0.05
Matches are distributed among these distances:
368 4 0.01
369 105 0.18
370 36 0.06
371 19 0.03
372 410 0.70
373 9 0.02
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (369 bp):
CTCAATGTGAGTAAAACAATAAATCCTCATCTTCCTGATGAGATATAGAGAAGTGGATCAAAATG
GTGAAGCGGTCATTTTCTTGATGAGATACAGAGAAGTGAACCAAAATAATGAAGCAAAGCTCAAT
ATGAGTGAAACTTCAAATCCCCATCTTCTTAATGAGATACAGAGAAGTGGATCAAAATGGTAAGC
GTCATTTTCCTGATGAGATATAGAGAAGTGAACCAAAATAATGAAGCGAAGCTCAATGTGAGTGA
AACTTCAAATCCCCATCTTCCTGATAAGATACAGAGAAGTAGACCAAAACAATGAACCGAGCATC
ATCCTGATGAGATACAGACAAAGAACCAAAATAATGAAGAGAAA
Found at i:177601 original size:48 final size:48
Alignment explanation
Indices: 177526--177648 Score: 120
Period size: 48 Copynumber: 2.6 Consensus size: 48
177516 CTTCAAAACC
* * ** ** *
177526 TCATATTCTTGATGAGATACACTGAAGTGGGTCAAAACAATAAAGTGG
1 TCATCTTCCTGATGAGATACAGAGAAGTGAATCAAAACAATAAAGCGG
* * *** *
177574 TTATCTTCCTGATGAGATATAGAGAAGTGAATCAAAATGGTGAAGCGG
1 TCATCTTCCTGATGAGATACAGAGAAGTGAATCAAAACAATAAAGCGG
*
177622 TCATCTTCCTGATGAGATGCAGAGAAG
1 TCATCTTCCTGATGAGATACAGAGAAG
177649 AGGACCAAAA
Statistics
Matches: 59, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
48 59 1.00
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.27
Consensus pattern (48 bp):
TCATCTTCCTGATGAGATACAGAGAAGTGAATCAAAACAATAAAGCGG
Found at i:177666 original size:48 final size:48
Alignment explanation
Indices: 177558--177668 Score: 114
Period size: 48 Copynumber: 2.3 Consensus size: 48
177548 TGAAGTGGGT
* * * * * * *
177558 CAAAACAATAAAGTGGTTATCTTCCTGATGAGATATAGAGAAGTGAAT
1 CAAAAAAATGAAGCGGTCATCTTCCTGATGAGATACAGAGAAGAGAAC
*** * *
177606 CAAAATGGTGAAGCGGTCATCTTCCTGATGAGATGCAGAGAAGAGGAC
1 CAAAAAAATGAAGCGGTCATCTTCCTGATGAGATACAGAGAAGAGAAC
177654 CAAAAAAATGAAGCG
1 CAAAAAAATGAAGCG
177669 AAGCTCAATG
Statistics
Matches: 49, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.41, C:0.14, G:0.25, T:0.21
Consensus pattern (48 bp):
CAAAAAAATGAAGCGGTCATCTTCCTGATGAGATACAGAGAAGAGAAC
Found at i:179082 original size:29 final size:29
Alignment explanation
Indices: 179000--179141 Score: 131
Period size: 30 Copynumber: 4.8 Consensus size: 29
178990 AAAATTATGT
* * * * *
179000 TTTGACTCTCGAACTTTCTAAAGATTCATA
1 TTTGAC-CTCAAACTTCCCAAAAATTCAGA
*
179030 TTTGACTCTCAAACTTCCCAAAAATTCATA
1 TTTGAC-CTCAAACTTCCCAAAAATTCAGA
* **
179060 TTTGACCTCGAACTTCCCAAAAATTTGGA
1 TTTGACCTCAAACTTCCCAAAAATTCAGA
* * *
179089 TTTGAACCTTAAACTTTCCAAAAATTTAGA
1 TTTG-ACCTCAAACTTCCCAAAAATTCAGA
*
179119 TTTGACCCTTAAACTTCCCAAAA
1 TTTGA-CCTCAAACTTCCCAAAA
179142 TTTTGAATTT
Statistics
Matches: 97, Mismatches: 13, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
29 24 0.25
30 73 0.75
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.35
Consensus pattern (29 bp):
TTTGACCTCAAACTTCCCAAAAATTCAGA
Found at i:179162 original size:59 final size:59
Alignment explanation
Indices: 179039--179168 Score: 154
Period size: 59 Copynumber: 2.2 Consensus size: 59
179029 ATTTGACTCT
* * * * *
179039 CAAACTTCCCAAAAATTCATATTTGACCTCGAACTTCCCAAAAATTTGGATTTGAACCT
1 CAAACTTTCCAAAAATTCAGATTTGACCTCAAACTTCCCAAAAATTTGAATTTGAACCC
* * * * *
179098 TAAACTTTCCAAAAATTTAGATTTGACCCTTAAACTTCCCAAAATTTTGAATTT-AGCCC
1 CAAACTTTCCAAAAATTCAGATTTGA-CCTCAAACTTCCCAAAAATTTGAATTTGAACCC
179157 CAAACTTTCCAA
1 CAAACTTTCCAA
179169 GATTTCATTT
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
59 36 0.61
60 23 0.39
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.32
Consensus pattern (59 bp):
CAAACTTTCCAAAAATTCAGATTTGACCTCAAACTTCCCAAAAATTTGAATTTGAACCC
Found at i:186102 original size:28 final size:28
Alignment explanation
Indices: 186055--186132 Score: 86
Period size: 27 Copynumber: 2.7 Consensus size: 28
186045 ATTGAAAATT
* *
186055 AAAATTATTTAATAATTTTATA-TTTAA
1 AAAAATATTTAAAAATTTTATATTTTAA
*
186082 AAAAATATTTAAAAATATTTATATTTTTA
1 AAAAATATTTAAAAAT-TTTATATTTTAA
*
186111 AAAAATAATTTTAATAATTTTA
1 AAAAAT-A-TTTAAAAATTTTA
186133 AAATCATTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
27 14 0.33
28 6 0.14
29 10 0.23
30 5 0.12
31 8 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (28 bp):
AAAAATATTTAAAAATTTTATATTTTAA
Found at i:186121 original size:20 final size:21
Alignment explanation
Indices: 186092--186135 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
186082 AAAAATATTT
*
186092 AAAAATA-TTT-ATATTTTTA
1 AAAAATATTTTAATAATTTTA
186111 AAAAATAATTTTAATAATTTTA
1 AAAAAT-ATTTTAATAATTTTA
186133 AAA
1 AAA
186136 TCATTTATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 6 0.29
20 1 0.05
21 3 0.14
22 11 0.52
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AAAAATATTTTAATAATTTTA
Found at i:186130 original size:29 final size:28
Alignment explanation
Indices: 186062--186132 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 28
186052 ATTAAAATTA
186062 TTTAATAATTTTATATTTAAAAAAATA-
1 TTTAATAATTTTATATTTAAAAAAATAT
* *
186089 TTTAAAAATATTTATATTTTTAAAAAATAAT
1 TTTAATAAT-TTTATA-TTTAAAAAAAT-AT
186120 TTTAATAATTTTA
1 TTTAATAATTTTA
186133 AAATCATTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 8 0.22
28 6 0.16
29 10 0.27
30 5 0.14
31 8 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
TTTAATAATTTTATATTTAAAAAAATAT
Found at i:193979 original size:21 final size:18
Alignment explanation
Indices: 193953--193991 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 18
193943 GAATCTTAAC
193953 GTTTGAGATCGTTGTTTTTTT
1 GTTTGA-ATC-TT-TTTTTTT
193974 GTTTGAATCTTTTTTTTT
1 GTTTGAATCTTTTTTTTT
193992 ATTTAATAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 2 0.11
20 3 0.17
21 6 0.33
ACGTcount: A:0.10, C:0.05, G:0.18, T:0.67
Consensus pattern (18 bp):
GTTTGAATCTTTTTTTTT
Found at i:197188 original size:22 final size:24
Alignment explanation
Indices: 197162--197224 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 24
197152 AATTATAAAA
197162 TGAAAATAATTTTAAAAT-ATA-G
1 TGAAAATAATTTTAAAATGATATG
** *
197184 TGAAAATAGCTTTAAAATGTTATG
1 TGAAAATAATTTTAAAATGATATG
* *
197208 TAAAAATTATTTTAAAA
1 TGAAAATAATTTTAAAA
197225 AAAATATGAG
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
22 16 0.50
23 2 0.06
24 14 0.44
ACGTcount: A:0.51, C:0.02, G:0.10, T:0.38
Consensus pattern (24 bp):
TGAAAATAATTTTAAAATGATATG
Found at i:198022 original size:31 final size:30
Alignment explanation
Indices: 197987--198046 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
197977 CCCTCTCATA
* *
197987 TTATTTTTTTAATTTTTTAA-AATGTTTATAT
1 TTATTATTTTAA-TATTTAATAAT-TTTATAT
198018 TTATTATTTTAATATTTAATAATTTTATA
1 TTATTATTTTAATATTTAATAATTTTATA
198047 CATTTTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (30 bp):
TTATTATTTTAATATTTAATAATTTTATAT
Found at i:204573 original size:20 final size:20
Alignment explanation
Indices: 204542--204589 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
204532 TATCTAATTG
204542 TATGAA-AGGGGCACGGATT
1 TATGAATAGGGGCACGGATT
204561 TATGAATAGGGGCACGGATT
1 TATGAATAGGGGCACGGATT
204581 TATGAATAG
1 TATGAATAG
204590 AGGATCTAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.33, C:0.08, G:0.33, T:0.25
Consensus pattern (20 bp):
TATGAATAGGGGCACGGATT
Found at i:205907 original size:60 final size:60
Alignment explanation
Indices: 205843--206037 Score: 264
Period size: 60 Copynumber: 3.2 Consensus size: 60
205833 CTACAATAAC
* * * * * * ** * *
205843 TTATTTAAATAAGTTCTTATAATATCTTTTTATCTAAATAAGCTTTTTAGCTATAATGAT
1 TTATTTAAATAAGCTATTATAGTATATTTTTACCTAAATAAACCCTTAAGCTATAACGAT
*
205903 TTATTTAAATAAGCTATTATAGTATATTTTTACCTAAATAAACCCTTAAGTTATAACGAT
1 TTATTTAAATAAGCTATTATAGTATATTTTTACCTAAATAAACCCTTAAGCTATAACGAT
**
205963 TTATTTAAATAAGCTATTATAGTATATTTTTACCTAAATAAACCCTTAATTTATAACGAT
1 TTATTTAAATAAGCTATTATAGTATATTTTTACCTAAATAAACCCTTAAGCTATAACGAT
*
206023 ATATTTAAATAAGCT
1 TTATTTAAATAAGCT
206038 CTCAAATCTA
Statistics
Matches: 122, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 122 1.00
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (60 bp):
TTATTTAAATAAGCTATTATAGTATATTTTTACCTAAATAAACCCTTAAGCTATAACGAT
Found at i:205912 original size:31 final size:30
Alignment explanation
Indices: 205871--205988 Score: 87
Period size: 31 Copynumber: 3.9 Consensus size: 30
205861 ATAATATCTT
205871 TTTATCTAAATAAGCTTTTTAGCTATAATGA
1 TTTATCTAAATAAGCTTTTTAG-TATAATGA
* * *
205902 TTTATTTAAATAAGCTATTATAGTAT-AT-T
1 TTTATCTAAATAAGCT-TTTTAGTATAATGA
* * ** * *
205931 TTTACCTAAATAAACCCTTAAGTTATAACGA
1 TTTATCTAAATAAGCTTTTTAG-TATAATGA
* *
205962 TTTATTTAAATAAGCTATTATAGTATA
1 TTTATCTAAATAAGCT-TTTTAGTATA
205989 TTTTTACCTA
Statistics
Matches: 63, Mismatches: 19, Indels: 10
0.68 0.21 0.11
Matches are distributed among these distances:
28 3 0.05
29 15 0.24
30 3 0.05
31 34 0.54
32 8 0.13
ACGTcount: A:0.39, C:0.09, G:0.08, T:0.44
Consensus pattern (30 bp):
TTTATCTAAATAAGCTTTTTAGTATAATGA
Found at i:206017 original size:29 final size:29
Alignment explanation
Indices: 205925--206017 Score: 71
Period size: 29 Copynumber: 3.1 Consensus size: 29
205915 GCTATTATAG
*
205925 TATATTTTTACCTAAATAAACCCTTAAGT
1 TATATTTTTACCTAAATAAACCCTTAATT
** ** * ** *
205954 TATAACGATTTATTTAAATAAGCTATT-ATAG
1 TAT-A-TTTTTACCTAAATAAACCCTTAAT-T
205985 TATATTTTTACCTAAATAAACCCTTAATT
1 TATATTTTTACCTAAATAAACCCTTAATT
206014 TATA
1 TATA
206018 ACGATATATT
Statistics
Matches: 43, Mismatches: 17, Indels: 8
0.63 0.25 0.12
Matches are distributed among these distances:
29 21 0.49
30 5 0.12
31 17 0.40
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.43
Consensus pattern (29 bp):
TATATTTTTACCTAAATAAACCCTTAATT
Found at i:208547 original size:22 final size:23
Alignment explanation
Indices: 208511--208569 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 23
208501 TTGTGTACAA
* *
208511 ACCCAAAACCATAAAAACCTAAT-
1 ACCC-AAACCCTAAAAACCAAATC
*
208534 ACCCAAACCCT-AAAGCCAAATC
1 ACCCAAACCCTAAAAACCAAATC
*
208556 ATCCAAACCCTAAA
1 ACCCAAACCCTAAA
208570 CCCAACTCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
21 8 0.27
22 16 0.53
23 6 0.20
ACGTcount: A:0.51, C:0.36, G:0.02, T:0.12
Consensus pattern (23 bp):
ACCCAAACCCTAAAAACCAAATC
Found at i:208591 original size:7 final size:7
Alignment explanation
Indices: 208581--208641 Score: 79
Period size: 7 Copynumber: 8.7 Consensus size: 7
208571 CCAACTCAAT
208581 TTGACAG
1 TTGACAG
*
208588 TTGACTG
1 TTGACAG
208595 TTGACAG
1 TTGACAG
*
208602 TTGATAG
1 TTGACAG
208609 TTGATC-G
1 TTGA-CAG
208616 TTGACAG
1 TTGACAG
208623 TTGACAG
1 TTGACAG
*
208630 TTGACCG
1 TTGACAG
208637 TTGAC
1 TTGAC
208642 TTTTTAGGTT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
6 1 0.02
7 46 0.98
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.34
Consensus pattern (7 bp):
TTGACAG
Found at i:208610 original size:21 final size:21
Alignment explanation
Indices: 208581--208641 Score: 88
Period size: 21 Copynumber: 2.9 Consensus size: 21
208571 CCAACTCAAT
208581 TTGACAGTTGACTGTTGACAG
1 TTGACAGTTGACTGTTGACAG
*
208602 TTGATAGTTGA-TCGTTGACAG
1 TTGACAGTTGACT-GTTGACAG
*
208623 TTGACAGTTGACCGTTGAC
1 TTGACAGTTGACTGTTGAC
208642 TTTTTAGGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.03
21 34 0.97
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.34
Consensus pattern (21 bp):
TTGACAGTTGACTGTTGACAG
Found at i:215647 original size:21 final size:21
Alignment explanation
Indices: 215623--215664 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
215613 GTTGATTTTA
*
215623 ATTTTGGGGATTTTAA-TATTT
1 ATTTT-GGAATTTTAATTATTT
215644 ATTTTGGAATTTTAATTATTT
1 ATTTTGGAATTTTAATTATTT
215665 TATTCAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (21 bp):
ATTTTGGAATTTTAATTATTT
Found at i:220342 original size:14 final size:14
Alignment explanation
Indices: 220323--220362 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
220313 CTAATTTGAT
* *
220323 TTGACAGTTGATCG
1 TTGACAGTTGACCA
220337 TTGACAGTTGACCA
1 TTGACAGTTGACCA
*
220351 TTGACAATTGAC
1 TTGACAGTTGAC
220363 TGTTGGGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.33
Consensus pattern (14 bp):
TTGACAGTTGACCA
Found at i:222881 original size:17 final size:17
Alignment explanation
Indices: 222859--222891 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
222849 TCTGTGTTGA
222859 CTCAAGCACCGATTTTG
1 CTCAAGCACCGATTTTG
222876 CTCAAGCACCGATTTT
1 CTCAAGCACCGATTTT
222892 AATCCAACCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.30, G:0.15, T:0.30
Consensus pattern (17 bp):
CTCAAGCACCGATTTTG
Found at i:225614 original size:21 final size:22
Alignment explanation
Indices: 225589--225640 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
225579 CAAAACCATG
*
225589 AAAACCCAAT-ATCCAAACCCT
1 AAAACCCAATCACCCAAACCCT
**
225610 AAAACTAAATCACCCAAACCCT
1 AAAACCCAATCACCCAAACCCT
225632 -AAACCCAAT
1 AAAACCCAAT
225641 TCAATTTGAC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.50, C:0.37, G:0.00, T:0.13
Consensus pattern (22 bp):
AAAACCCAATCACCCAAACCCT
Found at i:225691 original size:20 final size:20
Alignment explanation
Indices: 225666--225703 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
225656 ATCGTTAACC
225666 GTTGATCATTGACTTTTTGG
1 GTTGATCATTGACTTTTTGG
*
225686 GTTGATCGTTGACTTTTT
1 GTTGATCATTGACTTTTT
225704 CGAGAAACCT
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:0.13, C:0.11, G:0.24, T:0.53
Consensus pattern (20 bp):
GTTGATCATTGACTTTTTGG
Found at i:228243 original size:3 final size:3
Alignment explanation
Indices: 228235--228259 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
228225 TCCCTTTGAA
228235 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
228260 CTGGAATGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:228861 original size:3 final size:3
Alignment explanation
Indices: 228853--228881 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
228843 TTTAATTTGA
228853 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
228882 ACGAGAGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:235316 original size:117 final size:117
Alignment explanation
Indices: 235110--235355 Score: 465
Period size: 117 Copynumber: 2.1 Consensus size: 117
235100 ATCAAATACT
*
235110 TGGATTTGAGTGTAGTTATTTGTCATTATACATTTTTGATATATTTAAATAATTATAGTAATATC
1 TGGATTCGAGTGTAGTTATTTGTCATTATACATTTTTGATATATTTAAATAATTATAGTAATATC
235175 GATTGAGTTTTAGTTTGATTCACATCAATTTTATTGCTACTGTAGGAAGACG
66 GATTGAGTTTTAGTTTGATTCACATCAATTTTATTGCTACTGTAGGAAGACG
235227 TGGATTCGAGTGTAGTTATTTGTCATTATACATTTTTGATATATTTAAATAATTATAGTAATATC
1 TGGATTCGAGTGTAGTTATTTGTCATTATACATTTTTGATATATTTAAATAATTATAGTAATATC
*
235292 GATTGAGTTTTAGTTTGATTCACATCAATTTTATTGTTACTGTAGGAAGACG
66 GATTGAGTTTTAGTTTGATTCACATCAATTTTATTGCTACTGTAGGAAGACG
*
235344 TGGGTTCGAGTG
1 TGGATTCGAGTG
235356 CGATGAAGTG
Statistics
Matches: 126, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
117 126 1.00
ACGTcount: A:0.29, C:0.08, G:0.19, T:0.45
Consensus pattern (117 bp):
TGGATTCGAGTGTAGTTATTTGTCATTATACATTTTTGATATATTTAAATAATTATAGTAATATC
GATTGAGTTTTAGTTTGATTCACATCAATTTTATTGCTACTGTAGGAAGACG
Done.