Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold25
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: 9553305
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 6276 characters in sequence are not A, C, G, or T
File 2 of 56
Found at i:137799 original size:16 final size:15
Alignment explanation
Indices: 137778--137839 Score: 67
Period size: 15 Copynumber: 4.1 Consensus size: 15
137768 AATATTTATA
137778 AAAATTATAATTAAAT
1 AAAATT-TAATTAAAT
137794 AAAATTATAATT-AAT
1 AAAATT-TAATTAAAT
137809 AAAATTTAATTTAAA-
1 AAAATTTAA-TTAAAT
*
137824 AATATTTAA-TAAAT
1 AAAATTTAATTAAAT
137838 AA
1 AA
137840 TTTTAAAGTT
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
13 4 0.10
14 5 0.12
15 19 0.45
16 14 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAAATTTAATTAAAT
Found at i:137923 original size:255 final size:255
Alignment explanation
Indices: 137652--138165 Score: 1001
Period size: 255 Copynumber: 2.0 Consensus size: 255
137642 TTATATTTTG
137652 ATATATTTATGTATTCGTATTAGATTCATGTTATTTTTATGTTATATATTAATTTTTATATATAT
1 ATATATTTATGTATTCGTATTAGATTCATGTTATTTTTATGTTATATATTAATTTTTATATATAT
137717 TGAGTTCATATCATGTCTCAATTTATTTTTCTCTCGTTTCACTGAGTTTTTAATATTTATAAAAA
66 TGAGTTCATATCATGTCTCAATTTATTTTTCTCTCGTTTCACTGAGTTTTTAATATTTATAAAAA
137782 TTATAATTAAATAAAATTATAATTAATAAAATTTAATTTAAAAATATTTAATAAATAATTTTAAA
131 TTATAATTAAATAAAATTATAATTAATAAAATTTAATTTAAAAATATTTAATAAATAATTTTAAA
137847 GTTAAAATTTAATCATTAAAAAATTATATAAAATATAAAATAAATTGAGACATAGTACAA
196 GTTAAAATTTAATCATTAAAAAATTATATAAAATATAAAATAAATTGAGACATAGTACAA
137907 ATATATTTATGTATTCGTATTAGATTCATGTTATTTTTATGTTATATATTAATTTTTATATATAT
1 ATATATTTATGTATTCGTATTAGATTCATGTTATTTTTATGTTATATATTAATTTTTATATATAT
*
137972 TGAGTTCATATCATGTCTCAATTTATTTTTTTCTCGTTTCACTGAGTTTTTAATATTTATAAAAA
66 TGAGTTCATATCATGTCTCAATTTATTTTTCTCTCGTTTCACTGAGTTTTTAATATTTATAAAAA
*
138037 TTTTAATTAAATAAAATTATAATTAATAAAATTTAATTTAAAAATATTTAATAAATAATTTTAAA
131 TTATAATTAAATAAAATTATAATTAATAAAATTTAATTTAAAAATATTTAATAAATAATTTTAAA
*
138102 GTTAAAATTTAATCATTAAAAAATTATATAGAATATAAAATAAATTGAGACATAGTACAA
196 GTTAAAATTTAATCATTAAAAAATTATATAAAATATAAAATAAATTGAGACATAGTACAA
138162 ATAT
1 ATAT
138166 TATATTAAAA
Statistics
Matches: 256, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
255 256 1.00
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.46
Consensus pattern (255 bp):
ATATATTTATGTATTCGTATTAGATTCATGTTATTTTTATGTTATATATTAATTTTTATATATAT
TGAGTTCATATCATGTCTCAATTTATTTTTCTCTCGTTTCACTGAGTTTTTAATATTTATAAAAA
TTATAATTAAATAAAATTATAATTAATAAAATTTAATTTAAAAATATTTAATAAATAATTTTAAA
GTTAAAATTTAATCATTAAAAAATTATATAAAATATAAAATAAATTGAGACATAGTACAA
Found at i:138054 original size:16 final size:15
Alignment explanation
Indices: 138033--138094 Score: 65
Period size: 15 Copynumber: 4.1 Consensus size: 15
138023 AATATTTATA
138033 AAAATTTTAATTAAAT
1 AAAATTTTAATT-AAT
*
138049 AAAATTATAATTAAT
1 AAAATTTTAATTAAT
*
138064 AAAA-TTTAATTTA-
1 AAAATTTTAATTAAT
*
138077 AAAATATTTAATAAAT
1 AAAAT-TTTAATTAAT
138093 AA
1 AA
138095 TTTTAAAGTT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
13 4 0.11
14 7 0.18
15 14 0.37
16 13 0.34
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AAAATTTTAATTAAT
Found at i:138108 original size:29 final size:27
Alignment explanation
Indices: 138023--138100 Score: 79
Period size: 30 Copynumber: 2.8 Consensus size: 27
138013 CTGAGTTTTT
138023 AATATTT-ATAAA-AATTTTAATTAAA
1 AATATTTAATAAATAATTTTAATTAAA
* * *
138048 TAAAATTATAATTAATAAAATTTAATTTAAA
1 -AATATT-TAATAAAT-AATTTTAA-TTAAA
138079 AATATTTAATAAATAATTTTAA
1 AATATTTAATAAATAATTTTAA
138101 AGTTAAAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
26 5 0.12
27 1 0.02
28 11 0.27
29 7 0.17
30 12 0.29
31 5 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
AATATTTAATAAATAATTTTAATTAAA
Found at i:138550 original size:11 final size:12
Alignment explanation
Indices: 138536--138569 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
138526 AAACACAACA
138536 TAAAAAATAAT-
1 TAAAAAATAATG
*
138547 TAAAATATAATG
1 TAAAAAATAATG
138559 TAAAAAATAAT
1 TAAAAAATAAT
138570 ATGAATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (12 bp):
TAAAAAATAATG
Found at i:139467 original size:15 final size:17
Alignment explanation
Indices: 139431--139469 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
139421 ATATTTACAA
139431 AATTTTTATATCATATT
1 AATTTTTATATCATATT
139448 -A-TTTTATAT-A-ATT
1 AATTTTTATATCATATT
139461 AATTTTTAT
1 AATTTTTAT
139470 TAAAAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
13 3 0.15
14 2 0.10
15 14 0.70
16 1 0.05
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
AATTTTTATATCATATT
Found at i:139651 original size:14 final size:13
Alignment explanation
Indices: 139633--139659 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
139623 AAAATTATGA
139633 TAAAAATTTTTAT
1 TAAAAATTTTTAT
139646 TAAAAATTTTTAT
1 TAAAAATTTTTAT
139659 T
1 T
139660 TTAATTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAAAATTTTTAT
Found at i:139933 original size:6 final size:6
Alignment explanation
Indices: 139922--139949 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
139912 TCTTGAGATG
139922 AAAGTC AAAGTC AAAGTC AAAGTC AAAG
1 AAAGTC AAAGTC AAAGTC AAAGTC AAAG
139950 GGACAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.54, C:0.14, G:0.18, T:0.14
Consensus pattern (6 bp):
AAAGTC
Found at i:140216 original size:2 final size:2
Alignment explanation
Indices: 140209--140239 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
140199 TGAGAGTGAG
140209 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 A
140240 CACACACTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:141110 original size:58 final size:58
Alignment explanation
Indices: 141033--141145 Score: 145
Period size: 58 Copynumber: 1.9 Consensus size: 58
141023 AATAACACGC
* * * * *
141033 TTAAAAATATAATAAAATATAAAAAGATAAGATAAACACGATATAAAAAATAATAAAA
1 TTAAAAATACAATAAAATATAAAAAAATAAAATAAACACAATACAAAAAATAATAAAA
* * * *
141091 TTAAAAATACGATATAATATAAAAAAATAAAATAAATATAATACAAAAAATAATA
1 TTAAAAATACAATAAAATATAAAAAAATAAAATAAACACAATACAAAAAATAATA
141146 CGAATATAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
58 46 1.00
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.24
Consensus pattern (58 bp):
TTAAAAATACAATAAAATATAAAAAAATAAAATAAACACAATACAAAAAATAATAAAA
Found at i:141128 original size:19 final size:21
Alignment explanation
Indices: 141106--141164 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 21
141096 AATACGATAT
141106 AATATAAAAAAATAA-AATA-
1 AATATAAAAAAATAATAATAC
141125 AATATAATACAAAA-AATAATAC
1 AATATAA-A-AAAATAATAATAC
141147 GAATATAAAAAAATAATA
1 -AATATAAAAAAATAATA
141165 TGACCTAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
19 7 0.21
20 3 0.09
21 12 0.35
22 5 0.15
23 7 0.21
ACGTcount: A:0.73, C:0.03, G:0.02, T:0.22
Consensus pattern (21 bp):
AATATAAAAAAATAATAATAC
Found at i:141151 original size:23 final size:24
Alignment explanation
Indices: 141096--141154 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
141086 TAAAATTAAA
141096 AATACG-ATATAATATAAAAAAAT
1 AATACGAATATAATATAAAAAAAT
* ** *
141119 AAAATAAATATAATA-CAAAAAAT
1 AATACGAATATAATATAAAAAAAT
141142 AATACGAATATAA
1 AATACGAATATAA
141155 AAAAATAATA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
23 20 0.71
24 8 0.29
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (24 bp):
AATACGAATATAATATAAAAAAAT
Found at i:141158 original size:76 final size:75
Alignment explanation
Indices: 141073--141220 Score: 174
Period size: 76 Copynumber: 2.0 Consensus size: 75
141063 GATAAACACG
* * *
141073 ATAT-AAAAAATAATA-AAATTAAAAATACGATATAATATAAAAAAATAAAATAAATATAATACA
1 ATATAAAAAAATAATATAAACTAAAAAT--GATACAATACAAAAAAATAAAATAAATATAATA-A
141136 AAAAATAATACGA
63 AAAAATAATACGA
* * ** * *
141149 ATATAAAAAAATAATATGACCTAAACGTGATACAATACAAAAAAATAAAATCAATATGATAAAAA
1 ATATAAAAAAATAATATAAACTAAAAATGATACAATACAAAAAAATAAAATAAATATAATAAAAA
141214 AATAATA
66 AATAATA
141221 AAAATCTAAA
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
75 11 0.18
76 33 0.54
77 11 0.18
78 6 0.10
ACGTcount: A:0.67, C:0.06, G:0.04, T:0.23
Consensus pattern (75 bp):
ATATAAAAAAATAATATAAACTAAAAATGATACAATACAAAAAAATAAAATAAATATAATAAAAA
AATAATACGA
Found at i:141311 original size:17 final size:17
Alignment explanation
Indices: 141291--141323 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
141281 TTTTGGTATC
*
141291 ATATTTTAGGTCATGTA
1 ATATTTTAAGTCATGTA
141308 ATATTTTAAGTCATGT
1 ATATTTTAAGTCATGT
141324 TTTTGTTGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.06, G:0.15, T:0.48
Consensus pattern (17 bp):
ATATTTTAAGTCATGTA
Found at i:141433 original size:26 final size:23
Alignment explanation
Indices: 141403--141460 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 23
141393 TGTTATTTTT
141403 TTTATTTATGTTATTTTCATATCGTG
1 TTTATTTAT-TT-TTTT-ATATCGTG
*
141429 TTTATTTTATTTTTTTATATTGTG
1 TTTA-TTTATTTTTTTATATCGTG
141453 TTGTATTT
1 TT-TATTT
141461 TCAATCATGT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
24 12 0.41
25 6 0.21
26 6 0.21
27 5 0.17
ACGTcount: A:0.17, C:0.03, G:0.10, T:0.69
Consensus pattern (23 bp):
TTTATTTATTTTTTTATATCGTG
Found at i:141479 original size:41 final size:39
Alignment explanation
Indices: 141399--141476 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 39
141389 GTCATGTTAT
*
141399 TTTTTTTATTTATGTTATTTTCATATCGTGTTTATTTTA
1 TTTTTTTATTTATGTTATTTTCATATCATGTTTATTTTA
*
141438 TTTTTTTATATTGTGTTGTATTTTCA-ATCATG-TTATTTT
1 TTTTTTTAT-TTATG-T-TATTTTCATATCATGTTTATTTT
141477 TATGTCATGT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
39 9 0.26
40 11 0.32
41 6 0.18
42 8 0.24
ACGTcount: A:0.18, C:0.05, G:0.09, T:0.68
Consensus pattern (39 bp):
TTTTTTTATTTATGTTATTTTCATATCATGTTTATTTTA
Found at i:141495 original size:22 final size:22
Alignment explanation
Indices: 141470--141530 Score: 61
Period size: 24 Copynumber: 2.7 Consensus size: 22
141460 TTCAATCATG
*
141470 TTATTTTTATGTCATGTTTGTT
1 TTATTTTTATGTCATGTTTATT
*
141492 TTATTTTTTCATGTCGTGTTTATT
1 TTA-TTTTT-ATGTCATGTTTATT
*
141516 TT-TTTATCATGTCAT
1 TTATTT-TTATGTCAT
141531 ATTTTAGATC
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
22 12 0.38
23 6 0.19
24 14 0.44
ACGTcount: A:0.15, C:0.08, G:0.11, T:0.66
Consensus pattern (22 bp):
TTATTTTTATGTCATGTTTATT
Found at i:141505 original size:24 final size:22
Alignment explanation
Indices: 141473--141530 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
141463 AATCATGTTA
*
141473 TTTTT-ATGTCATGTTTGTTTTAT
1 TTTTTCATGTCATGTTT-ATTT-T
*
141496 TTTTTCATGTCGTGTTTATTTT
1 TTTTTCATGTCATGTTTATTTT
*
141518 TTTATCATGTCAT
1 TTTTTCATGTCAT
141531 ATTTTAGATC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 12 0.40
23 8 0.27
24 10 0.33
ACGTcount: A:0.14, C:0.09, G:0.12, T:0.66
Consensus pattern (22 bp):
TTTTTCATGTCATGTTTATTTT
Found at i:141525 original size:57 final size:58
Alignment explanation
Indices: 141399--141550 Score: 150
Period size: 57 Copynumber: 2.6 Consensus size: 58
141389 GTCATGTTAT
* * * * * *
141399 TTTTTTTATTTATGTTATTTTCATATCGTGTTTATTTTATTTTTTTATATTGTGTTGTA
1 TTTTTTTA-TCATGTTATTTTTATGTCATGTTTATTTTATTTTTTCATATCGTGTTGTA
** * *
141458 -TTTTCAATCATGTTATTTTTATGTCATGTTTGTTTTATTTTTTCATGTCGTGTT-TA
1 TTTTTTTATCATGTTATTTTTATGTCATGTTTATTTTATTTTTTCATATCGTGTTGTA
*
141514 TTTTTTTATCATGTCATATTTTA-GATCATG-TTATTTT
1 TTTTTTTATCATGTTAT-TTTTATG-TCATGTTTATTTT
141551 TTTCATATCA
Statistics
Matches: 76, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
56 2 0.03
57 59 0.78
58 15 0.20
ACGTcount: A:0.18, C:0.07, G:0.11, T:0.65
Consensus pattern (58 bp):
TTTTTTTATCATGTTATTTTTATGTCATGTTTATTTTATTTTTTCATATCGTGTTGTA
Found at i:141535 original size:17 final size:17
Alignment explanation
Indices: 141515--141564 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
141505 TCGTGTTTAT
141515 TTTTTTATCATGTCATA
1 TTTTTTATCATGTCATA
**
141532 TTTTAGATCATGT--TA
1 TTTTTTATCATGTCATA
*
141547 TTTTTT-TCATATCATA
1 TTTTTTATCATGTCATA
141563 TT
1 TT
141565 CGTTTTATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
14 5 0.19
15 6 0.23
16 4 0.15
17 11 0.42
ACGTcount: A:0.24, C:0.10, G:0.06, T:0.60
Consensus pattern (17 bp):
TTTTTTATCATGTCATA
Found at i:141948 original size:28 final size:28
Alignment explanation
Indices: 141917--141980 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 28
141907 ATTACGTGGC
* * *
141917 AAAAATATCATATTTTAATAGTATATTT
1 AAAAATATAATATTTCAATAATATATTT
*
141945 AAAAGA-ATAATATTTCAATAATTTATTT
1 AAAA-ATATAATATTTCAATAATATATTT
141973 AATAAATA
1 AA-AAATA
141981 AGGATAGTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
28 25 0.86
29 4 0.14
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (28 bp):
AAAAATATAATATTTCAATAATATATTT
Found at i:142180 original size:15 final size:15
Alignment explanation
Indices: 142160--142224 Score: 60
Period size: 15 Copynumber: 4.3 Consensus size: 15
142150 CTCGAACCCG
*
142160 AAATGATGCAAACCT
1 AAATGATCCAAACCT
*
142175 AAATGA-CTCAACCCT
1 AAATGATC-CAAACCT
* *
142190 AAATAATCCAAATCCG
1 AAATGATCCAAA-CCT
*
142206 AAATGATCCAAACTT
1 AAATGATCCAAACCT
142221 AAAT
1 AAAT
142225 TTAAGTATTA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
15 25 0.64
16 14 0.36
ACGTcount: A:0.48, C:0.23, G:0.08, T:0.22
Consensus pattern (15 bp):
AAATGATCCAAACCT
Found at i:142210 original size:31 final size:31
Alignment explanation
Indices: 142149--142211 Score: 74
Period size: 30 Copynumber: 2.0 Consensus size: 31
142139 CCTAAAAGTA
* * *
142149 ACTCGAACCCGAAATGATGCAAACCTAAATG
1 ACTCGAACCCGAAATAATCCAAACCGAAATG
*
142180 ACTC-AACCCTAAATAATCCAAATCCGAAATG
1 ACTCGAACCCGAAATAATCCAAA-CCGAAATG
142211 A
1 A
142212 TCCAAACTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 15 0.56
31 12 0.44
ACGTcount: A:0.44, C:0.27, G:0.11, T:0.17
Consensus pattern (31 bp):
ACTCGAACCCGAAATAATCCAAACCGAAATG
Found at i:144144 original size:3 final size:3
Alignment explanation
Indices: 144136--144161 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
144126 ACAAAACAAA
144136 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
144162 AACATCGCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:144642 original size:2 final size:2
Alignment explanation
Indices: 144581--144631 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
144571 CTGGTACTTC
*
144581 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
144623 AT AT AT AT A
1 AT AT AT AT A
144632 AGTACATATA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:145134 original size:2 final size:2
Alignment explanation
Indices: 145127--145158 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
145117 TATTCAACTG
145127 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
145159 CTTCCCTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:152267 original size:19 final size:19
Alignment explanation
Indices: 152245--152341 Score: 59
Period size: 19 Copynumber: 5.4 Consensus size: 19
152235 ATTAAATTTT
152245 ATTAATTATTAAAATTTAA
1 ATTAATTATTAAAATTTAA
*
152264 ATTAATTA-AAATAATTTAA
1 ATTAATTATTAA-AATTTAA
*
152283 ATT--TTATTCAAA---AA
1 ATTAATTATTAAAATTTAA
152297 ATTAATTA--AAAAGTTGTAA
1 ATTAATTATTAAAA-TT-TAA
* * *
152316 AATAA-AATTTAAATTTAA
1 ATTAATTATTAAAATTTAA
152334 ATTAATTA
1 ATTAATTA
152342 AATAACAAAT
Statistics
Matches: 57, Mismatches: 9, Indels: 24
0.63 0.10 0.27
Matches are distributed among these distances:
14 8 0.14
16 3 0.05
17 5 0.09
18 11 0.19
19 27 0.47
20 3 0.05
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (19 bp):
ATTAATTATTAAAATTTAA
Found at i:152518 original size:21 final size:20
Alignment explanation
Indices: 152467--152518 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 20
152457 TAATTAATCT
152467 AAAATTTTAATTAATTTATA
1 AAAATTTTAATTAATTTATA
*
152487 AATATCTTTTAA-TAATTTTATA
1 AA-A-ATTTTAATTAA-TTTATA
152509 AAAATATTTA
1 AAAAT-TTTA
152519 TCTTAATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
20 3 0.12
21 9 0.35
22 14 0.54
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
AAAATTTTAATTAATTTATA
Found at i:153231 original size:27 final size:27
Alignment explanation
Indices: 153200--153288 Score: 76
Period size: 27 Copynumber: 3.3 Consensus size: 27
153190 TATAAAAATA
*
153200 AAATAATATTAAATAATCATATAATTT
1 AAATAATATTAAATAATAATATAATTT
* *
153227 AAAT-ATA-AAAATAAAATAAAATAAATTT
1 AAATAATATTAAAT--AATAATAT-AATTT
* *
153255 AAAAAATTATTAAA-AATAATAAAATTT
1 AAATAA-TATTAAATAATAATATAATTT
153282 AAATAAT
1 AAATAAT
153289 TTTTTAAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 13
0.70 0.12 0.19
Matches are distributed among these distances:
25 4 0.08
26 4 0.08
27 20 0.42
28 14 0.29
29 1 0.02
30 2 0.04
31 3 0.06
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (27 bp):
AAATAATATTAAATAATAATATAATTT
Found at i:153270 original size:28 final size:28
Alignment explanation
Indices: 153239--153298 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
153229 ATATAAAAAT
153239 AAAATAAAATAAATTTAAA-AAATTATTA
1 AAAATAAAA-AAATTTAAATAAATTATTA
* * *
153267 AAAATAATAAAATTTAAATAATTTTTTA
1 AAAATAAAAAAATTTAAATAAATTATTA
153295 AAAA
1 AAAA
153299 AATTTAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 9 0.32
28 19 0.68
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (28 bp):
AAAATAAAAAAATTTAAATAAATTATTA
Found at i:154188 original size:15 final size:14
Alignment explanation
Indices: 154168--154197 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
154158 ATTTTTTAAA
154168 TTATTTTTATATTTT
1 TTATTTTT-TATTTT
154183 TTATTTTTTATTTT
1 TTATTTTTTATTTT
154197 T
1 T
154198 CTCTGTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (14 bp):
TTATTTTTTATTTT
Found at i:154197 original size:7 final size:7
Alignment explanation
Indices: 154168--154197 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
154158 ATTTTTTAAA
154168 TTATTTT
1 TTATTTT
154175 TATATTTT
1 T-TATTTT
154183 TTATTTT
1 TTATTTT
154190 TTATTTT
1 TTATTTT
154197 T
1 T
154198 CTCTGTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (7 bp):
TTATTTT
Found at i:154398 original size:2 final size:2
Alignment explanation
Indices: 154386--154423 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
154376 ATATCTGTAC
*
154386 TA TA TA CA 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
154424 AAGAACAGGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:154677 original size:14 final size:15
Alignment explanation
Indices: 154658--154686 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
154648 ATGTTTAAAA
154658 TATTA-TATAAAATT
1 TATTATTATAAAATT
154672 TATTATTATAAAATT
1 TATTATTATAAAATT
154687 ATATAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTATTATAAAATT
Found at i:154738 original size:13 final size:13
Alignment explanation
Indices: 154722--154775 Score: 73
Period size: 13 Copynumber: 4.5 Consensus size: 13
154712 TTATTTAATA
154722 TATATTTTTATAT
1 TATATTTTTATAT
154735 TATA--TTTATA-
1 TATATTTTTATAT
154745 T-TATTTTTA-AT
1 TATATTTTTATAT
154756 TATATTTTTATAT
1 TATATTTTTATAT
154769 TATATTT
1 TATATTT
154776 ACATCTTGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
9 2 0.06
10 2 0.06
11 11 0.31
12 8 0.22
13 13 0.36
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TATATTTTTATAT
Found at i:154740 original size:24 final size:21
Alignment explanation
Indices: 154708--154776 Score: 77
Period size: 23 Copynumber: 3.1 Consensus size: 21
154698 TAAGTATAAA
154708 TAATT-TATTTAATATATATTTT
1 TAATTATATTT-ATAT-TATTTT
154730 TATATTATATTTATATTATTTT
1 TA-ATTATATTTATATTATTTT
*
154752 TAATTATATTTTTATATTATATT
1 TAATTATA--TTTATATTATTTT
154775 TA
1 TA
154777 CATCTTGTAT
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
21 6 0.14
22 10 0.24
23 21 0.50
24 5 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TAATTATATTTATATTATTTT
Found at i:154742 original size:11 final size:11
Alignment explanation
Indices: 154713--154776 Score: 67
Period size: 11 Copynumber: 5.5 Consensus size: 11
154703 ATAAATAATT
154713 TATTTAATATATA
1 TATTT-ATAT-TA
*
154726 TTTTTATATTA
1 TATTTATATTA
154737 TATTTATATTA
1 TATTTATATTA
*
154748 TTTTTA-ATTA
1 TATTTATATTA
154758 TATTTTTATATTA
1 TA--TTTATATTA
154771 TATTTA
1 TATTTA
154777 CATCTTGTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
10 5 0.11
11 21 0.48
12 8 0.18
13 10 0.23
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TATTTATATTA
Found at i:154984 original size:18 final size:19
Alignment explanation
Indices: 154961--155028 Score: 76
Period size: 18 Copynumber: 3.8 Consensus size: 19
154951 GTTTAAAGTA
154961 TTTTAA-ATTTATATAAAT
1 TTTTAATATTTATATAAAT
*
154979 TTTTAATAATTA-ATAAA-
1 TTTTAATATTTATATAAAT
154996 --TTAAT-TTTATATAAAT
1 TTTTAATATTTATATAAAT
155012 TTTTATATATTTATATA
1 TTTTA-ATATTTATATA
155029 TTCATATTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
14 3 0.07
15 10 0.24
18 14 0.34
19 6 0.15
20 8 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTAATATTTATATAAAT
Found at i:154989 original size:20 final size:20
Alignment explanation
Indices: 154966--155028 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 20
154956 AAGTATTTTA
154966 AATTTATATAAATTTTTAAT
1 AATTTATATAAATTTTTAAT
154986 AA-TTA-ATAAA---TTAAT
1 AATTTATATAAATTTTTAAT
155001 --TTTATATAAATTTTT-AT
1 AATTTATATAAATTTTTAAT
155018 ATATTTATATA
1 A-ATTTATATA
155029 TTCATATTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 16
0.69 0.00 0.31
Matches are distributed among these distances:
14 3 0.09
15 10 0.29
17 2 0.06
18 7 0.20
19 3 0.09
20 10 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
AATTTATATAAATTTTTAAT
Found at i:155555 original size:24 final size:27
Alignment explanation
Indices: 155521--155589 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 27
155511 CATGTTCAAT
*
155521 TTTAAATAATTATCATAA-AT-TTA-A
1 TTTATATAATTATCATAATATATTAGA
* *
155545 TTTTTATAATTAACATAATATATTAGA
1 TTTATATAATTATCATAATATATTAGA
*
155572 TTTATATTATTAT-ATAAT
1 TTTATATAATTATCATAAT
155590 TGAAAAATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
24 15 0.42
25 2 0.06
26 8 0.22
27 11 0.31
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (27 bp):
TTTATATAATTATCATAATATATTAGA
Found at i:155820 original size:28 final size:29
Alignment explanation
Indices: 155760--155820 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 29
155750 AAAATAATTT
* * *
155760 ATAATATAAAGAAATATTTTAAACAATTT
1 ATAATATAAAGAAATATTTTAAAAAAATA
155789 ATAATATAAA-AAAT-TATTTAAAAAAATA
1 ATAATATAAAGAAATAT-TTTAAAAAAATA
155817 ATAA
1 ATAA
155821 ATGTAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 1 0.04
28 17 0.61
29 10 0.36
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (29 bp):
ATAATATAAAGAAATATTTTAAAAAAATA
Found at i:156304 original size:4 final size:4
Alignment explanation
Indices: 156295--156320 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
156285 AAAGACGAGT
156295 CTTC CTTC CTTC CTTC CTTC CTTC CT
1 CTTC CTTC CTTC CTTC CTTC CTTC CT
156321 GTCCAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (4 bp):
CTTC
Found at i:157969 original size:3 final size:3
Alignment explanation
Indices: 157961--157997 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
157951 ATGGGCGCAT
157961 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
157998 GTTTGATTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:160160 original size:2 final size:2
Alignment explanation
Indices: 160153--160185 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
160143 ATTAAAATAG
160153 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
160186 ACCTTCAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:166013 original size:5 final size:5
Alignment explanation
Indices: 166003--166033 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
165993 TAATCAACAG
*
166003 AAGCA AAGCA AAGCA AAGCA AAGCA GAGCA A
1 AAGCA AAGCA AAGCA AAGCA AAGCA AAGCA A
166034 TCCAATCACG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.58, C:0.19, G:0.23, T:0.00
Consensus pattern (5 bp):
AAGCA
Found at i:166489 original size:3 final size:3
Alignment explanation
Indices: 166481--166511 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
166471 TCTCCAACGT
166481 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
166512 ACCTCTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:169127 original size:22 final size:22
Alignment explanation
Indices: 169062--169133 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 22
169052 AAAATTTAAT
* *
169062 TTATATTTTAT-ATATAATGAAA
1 TTATATTTTATCAAAAAAT-AAA
* * * *
169084 TAATAATTTATCAAAGAGTAAA
1 TTATATTTTATCAAAAAATAAA
169106 TTATATTTTATCAAAAAATAAA
1 TTATATTTTATCAAAAAATAAA
169128 TTATAT
1 TTATAT
169134 CATGAGTTTT
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
22 36 0.90
23 4 0.10
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.43
Consensus pattern (22 bp):
TTATATTTTATCAAAAAATAAA
Found at i:169233 original size:2 final size:2
Alignment explanation
Indices: 169226--169258 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
169216 ATTGAGAGCT
169226 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
169259 TAGTAGTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:170804 original size:16 final size:16
Alignment explanation
Indices: 170785--170815 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
170775 CAAAAAATCT
*
170785 TAAATTTAAAATAACC
1 TAAATATAAAATAACC
170801 TAAATATAAAATAAC
1 TAAATATAAAATAAC
170816 TCAATTCGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (16 bp):
TAAATATAAAATAACC
Found at i:170920 original size:417 final size:422
Alignment explanation
Indices: 170212--171057 Score: 1278
Period size: 417 Copynumber: 2.0 Consensus size: 422
170202 AAATAAAAAA
* * * *
170212 TAATATAAAACATACTCGAACTAAAAACTAATTTAAACTCGAATTTAAATCGAAAAAAGTCCAAA
1 TAATATAAAACACACTCAAACTAAAAACTAACTTAAACTCGAATCTAAATCGAAAAAAGTCCAAA
* * **
170277 CTCGAAAAGCTTGAACGCGAAATAACTCTAACTTGAAAAAGATCAAACTCAAATATATTTAAATT
66 CTCGAAAAGCTTGAACGCGAAACAACTCTAACTCGAAAAAGATCAAACTCAAATATATCCAAATT
** *
170342 CAAATAAGCTCAAGCCCATAAAAATTTGGATTTAAAATAATCTAAATATAAAATAACCCAATCTG
131 CAAATAAGCTCAAGCCCATAAAAATTTAAATTTAAAATAACCTAAATATAAAATAACCCAATCTG
* * * *
170407 AATCTACTCAAGCTTATCTAATTAGTATCTCTAATGAGAGGATGAACCCTAAATTTTAATATTCT
196 AATCTACTCAAACCTATCTAATTAGTATCTCTAATGAAAAGATGAACCCTAAATTTTAATATTCT
* *
170472 ATTTCCATTAAACCTCTTAAATTTTAAAACAAATATTGATATATATATA-TTTTTTATAGAACTA
261 ATTTCCATTAAACCTCTTAAATTTTAAAACAAATATTGATATATATAAATTTTTTTATAAAACTA
*
170536 AATTATTAGTATC-T-AT-ATAATAATAATAATAATAATAATTTAAAATAATATTATACGTTTTT
326 AATTATTAGTATCATAATAATAATAATAATAATAATAATAATTTAAAATAATATTATACATTTTT
*
170598 ATTTAATTTTGAAATCAAACTTTCTTTATAAG
391 ATTTAATTTTAAAATCAAACTTTCTTTATAAG
* * * * *
170630 TAATGTAAAACACACTCAAACTCAAAATTAACTTAAACTCGAATCTAAAT-TAAAAAATGTCGAA
1 TAATATAAAACACACTCAAACTAAAAACTAACTTAAACTCGAATCTAAATCGAAAAAA-GTCCAA
* * * * *
170694 ACTCGAAAAGCTTGAATGCGAGACAGCTCTAACTCGAAAAAGATCAAAGTCGAATATATCCAAA-
65 ACTCGAAAAGCTTGAACGCGAAACAACTCTAACTCGAAAAAGATCAAACTCAAATATATCCAAAT
*
170758 TCAAATAAGCTCAAGCCCA-AAAAATCTTAAATTTAAAATAACCTAAATATAAAATAACTCAAT-
130 TCAAATAAGCTCAAGCCCATAAAAAT-TTAAATTTAAAATAACCTAAATATAAAATAACCCAATC
*
170821 TCGAATCTACTCAAACCTA-CTTAATTAGTATCTCTAATGAAAAGATGAACCTTAAATTTTAATA
194 T-GAATCTACTCAAACCTATC-TAATTAGTATCTCTAATGAAAAGATGAACCCTAAATTTTAATA
170885 TTCTATTTCCATTAAACCTCTTAAATTTTAAAACAAATATTGATATATATAAATTTTTTTATAAA
257 TTCTATTTCCATTAAACCTCTTAAATTTTAAAACAAATATTGATATATATAAATTTTTTTATAAA
170950 ACTAAATTATTAGTATCTATATAATAATAATAATAATAATAATAATAATTTAAAATAATATTATA
322 ACTAAATTATTAGTATC---ATAATAATAATAATAATAATAATAATAATTTAAAATAATATTATA
*
171015 TATTTTTATTTAATTTTAAAATCAAACTTTCTTTATAAG
384 CATTTTTATTTAATTTTAAAATCAAACTTTCTTTATAAG
171054 TAAT
1 TAAT
171058 TGGAATGAAA
Statistics
Matches: 385, Mismatches: 32, Indels: 16
0.89 0.07 0.04
Matches are distributed among these distances:
416 8 0.02
417 165 0.43
418 130 0.34
422 1 0.00
423 2 0.01
424 79 0.21
ACGTcount: A:0.46, C:0.13, G:0.06, T:0.34
Consensus pattern (422 bp):
TAATATAAAACACACTCAAACTAAAAACTAACTTAAACTCGAATCTAAATCGAAAAAAGTCCAAA
CTCGAAAAGCTTGAACGCGAAACAACTCTAACTCGAAAAAGATCAAACTCAAATATATCCAAATT
CAAATAAGCTCAAGCCCATAAAAATTTAAATTTAAAATAACCTAAATATAAAATAACCCAATCTG
AATCTACTCAAACCTATCTAATTAGTATCTCTAATGAAAAGATGAACCCTAAATTTTAATATTCT
ATTTCCATTAAACCTCTTAAATTTTAAAACAAATATTGATATATATAAATTTTTTTATAAAACTA
AATTATTAGTATCATAATAATAATAATAATAATAATAATAATTTAAAATAATATTATACATTTTT
ATTTAATTTTAAAATCAAACTTTCTTTATAAG
Found at i:171009 original size:3 final size:3
Alignment explanation
Indices: 170970--170998 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
170960 TAGTATCTAT
170970 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
170999 TTAAAATAAT
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:171471 original size:2 final size:2
Alignment explanation
Indices: 171464--171489 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
171454 CATTATTGTT
171464 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
171490 AATAATGTAT
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:173608 original size:48 final size:48
Alignment explanation
Indices: 173555--173759 Score: 272
Period size: 48 Copynumber: 4.3 Consensus size: 48
173545 TGCAGCTCCT
*
173555 GCTGTTGTTGATCCTGTTCCTCCTGTTGCAGCTCAC-GCTGTTGCCAA-A
1 GCTGTTGTTGATCCTGTTCCTCATGTTGCAGCTC-CTGCTGTTG-CAATA
* *
173603 GCTGTTGTTGATGCTGTTCCTCATGTTGCAGCTCCTGCTGTTGCAATG
1 GCTGTTGTTGATCCTGTTCCTCATGTTGCAGCTCCTGCTGTTGCAATA
* *
173651 GCTGTTGTTGATCCTGTTCCTCGTGTTGCAGCTCAC-GCTGTTGCAAAA
1 GCTGTTGTTGATCCTGTTCCTCATGTTGCAGCTC-CTGCTGTTGCAATA
* * * * *
173699 TCTGTTGTTGATGCTGCTCCTCATGCTGCAGCTCCTGCTGTTGCAATG
1 GCTGTTGTTGATCCTGTTCCTCATGTTGCAGCTCCTGCTGTTGCAATA
173747 GCTGTTGTTGATC
1 GCTGTTGTTGATC
173760 ACCCTGCCAA
Statistics
Matches: 137, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
47 5 0.04
48 131 0.96
49 1 0.01
ACGTcount: A:0.12, C:0.25, G:0.25, T:0.38
Consensus pattern (48 bp):
GCTGTTGTTGATCCTGTTCCTCATGTTGCAGCTCCTGCTGTTGCAATA
Found at i:173672 original size:96 final size:96
Alignment explanation
Indices: 173555--173759 Score: 365
Period size: 96 Copynumber: 2.1 Consensus size: 96
173545 TGCAGCTCCT
* *
173555 GCTGTTGTTGATCCTGTTCCTCCTGTTGCAGCTCACGCTGTTGCCAAAGCTGTTGTTGATGCTGT
1 GCTGTTGTTGATCCTGTTCCTCCTGTTGCAGCTCACGCTGTTGCAAAAGCTGTTGTTGATGCTGC
*
173620 TCCTCATGTTGCAGCTCCTGCTGTTGCAATG
66 TCCTCATGCTGCAGCTCCTGCTGTTGCAATG
* *
173651 GCTGTTGTTGATCCTGTTCCTCGTGTTGCAGCTCACGCTGTTGCAAAATCTGTTGTTGATGCTGC
1 GCTGTTGTTGATCCTGTTCCTCCTGTTGCAGCTCACGCTGTTGCAAAAGCTGTTGTTGATGCTGC
173716 TCCTCATGCTGCAGCTCCTGCTGTTGCAATG
66 TCCTCATGCTGCAGCTCCTGCTGTTGCAATG
173747 GCTGTTGTTGATC
1 GCTGTTGTTGATC
173760 ACCCTGCCAA
Statistics
Matches: 104, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
96 104 1.00
ACGTcount: A:0.12, C:0.25, G:0.25, T:0.38
Consensus pattern (96 bp):
GCTGTTGTTGATCCTGTTCCTCCTGTTGCAGCTCACGCTGTTGCAAAAGCTGTTGTTGATGCTGC
TCCTCATGCTGCAGCTCCTGCTGTTGCAATG
Found at i:176803 original size:18 final size:18
Alignment explanation
Indices: 176780--176814 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
176770 AAGCTATTTT
176780 AAAAA-TAATTAAAAATAA
1 AAAAATTAA-TAAAAATAA
176798 AAAAATTAATAAAAATA
1 AAAAATTAATAAAAATA
176815 TTAACTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAAATTAATAAAAATAA
Found at i:177992 original size:31 final size:31
Alignment explanation
Indices: 177946--178100 Score: 170
Period size: 31 Copynumber: 5.0 Consensus size: 31
177936 ATAGATTAAA
*
177946 ACAAAAACTATTATTTTTATCCGGTGGCACG
1 ACAAAAACTACTATTTTTATCCGGTGGCACG
* * *
177977 ACAAAAA-TCACTATTTTTATTCGTTGGCACA
1 ACAAAAACT-ACTATTTTTATCCGGTGGCACG
*
178008 ACAAAAA-TCACTATTTTTATCCGATGGCACG
1 ACAAAAACT-ACTATTTTTATCCGGTGGCACG
** * * **
178039 ATGAAAACTACTATTATTACCCGGTGGCATA
1 ACAAAAACTACTATTTTTATCCGGTGGCACG
*
178070 ACAAAAACTACTATTCTTATCCGGTGGCACG
1 ACAAAAACTACTATTTTTATCCGGTGGCACG
178101 GCGAAAACCA
Statistics
Matches: 102, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
30 1 0.01
31 100 0.98
32 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.30
Consensus pattern (31 bp):
ACAAAAACTACTATTTTTATCCGGTGGCACG
Found at i:178107 original size:62 final size:63
Alignment explanation
Indices: 177945--178112 Score: 200
Period size: 62 Copynumber: 2.7 Consensus size: 63
177935 TATAGATTAA
* * * ** *
177945 AACAAAAACTATTATTTTTATCCGGTGGCACGAC-AAAAATCACTATTTTTATTCGTTGGCAC
1 AACAAAAACTACTATTTTTATCCGGTGGCACGACGAAAACTCACTATTATTACCCGGTGGCAC
* * *
178007 AACAAAAA-TCACTATTTTTATCCGATGGCACGATGAAAACT-ACTATTATTACCCGGTGGCAT
1 AACAAAAACT-ACTATTTTTATCCGGTGGCACGACGAAAACTCACTATTATTACCCGGTGGCAC
* *
178069 AACAAAAACTACTATTCTTATCCGGTGGCACGGCGAAAAC-CACT
1 AACAAAAACTACTATTTTTATCCGGTGGCACGACGAAAACTCACT
178113 TTTCTTAATC
Statistics
Matches: 89, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
61 1 0.01
62 82 0.92
63 6 0.07
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (63 bp):
AACAAAAACTACTATTTTTATCCGGTGGCACGACGAAAACTCACTATTATTACCCGGTGGCAC
Found at i:178776 original size:52 final size:52
Alignment explanation
Indices: 178701--178801 Score: 193
Period size: 52 Copynumber: 1.9 Consensus size: 52
178691 GCTATTACTC
*
178701 TATCTAAATAGACCAACGCATTTCTCGGACTAATCTAAGACACTTAGGGTAT
1 TATCTAAATAGACCAACACATTTCTCGGACTAATCTAAGACACTTAGGGTAT
178753 TATCTAAATAGACCAACACATTTCTCGGACTAATCTAAGACACTTAGGG
1 TATCTAAATAGACCAACACATTTCTCGGACTAATCTAAGACACTTAGGG
178802 CATGTGACGA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.28
Consensus pattern (52 bp):
TATCTAAATAGACCAACACATTTCTCGGACTAATCTAAGACACTTAGGGTAT
Found at i:184553 original size:3 final size:3
Alignment explanation
Indices: 184545--184577 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
184535 CTAATACCGA
184545 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
184578 TTAAGATAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:184702 original size:4 final size:4
Alignment explanation
Indices: 184693--184752 Score: 102
Period size: 4 Copynumber: 15.0 Consensus size: 4
184683 ATCTTCAATG
* *
184693 TTTC TTTC TTTC TCTC TTTC TATC TTTC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
184741 TTTC TTTC TTTC
1 TTTC TTTC TTTC
184753 ATCATTTTAT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 52 1.00
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTC
Found at i:184862 original size:2 final size:2
Alignment explanation
Indices: 184855--184884 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
184845 GCATGCAAAT
*
184855 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
184885 GTAACATTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:184960 original size:26 final size:24
Alignment explanation
Indices: 184937--184982 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
184927 TATATAAATT
* *
184937 ATAATATATGTAAAAAAAATTAAA
1 ATAACATAGGTAAAAAAAATTAAA
*
184961 ATTACATAGGTAAAAAAAATTA
1 ATAACATAGGTAAAAAAAATTA
184983 CGAATATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.28
Consensus pattern (24 bp):
ATAACATAGGTAAAAAAAATTAAA
Found at i:185471 original size:2 final size:2
Alignment explanation
Indices: 185464--185501 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
185454 CTGCTTTGGG
185464 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
185502 TGATTAGTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:185570 original size:2 final size:2
Alignment explanation
Indices: 185563--185592 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
185553 GAAGCAAACA
*
185563 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
185593 TATGATTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:187073 original size:3 final size:3
Alignment explanation
Indices: 187065--187095 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
187055 TTTATACATG
187065 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
187096 CAGGATATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:187324 original size:2 final size:2
Alignment explanation
Indices: 187319--187358 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
187309 ATAAATATAA
187319 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
187359 TTAGATATAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:188613 original size:21 final size:21
Alignment explanation
Indices: 188589--188629 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
188579 TCCATCATCC
*
188589 CCTCTTCCTCCGACCCCTCCA
1 CCTCCTCCTCCGACCCCTCCA
*
188610 CCTCCTCCTCCGCCCCCTCC
1 CCTCCTCCTCCGACCCCTCC
188630 TCCTTCCATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.05, C:0.68, G:0.05, T:0.22
Consensus pattern (21 bp):
CCTCCTCCTCCGACCCCTCCA
Found at i:190335 original size:2 final size:2
Alignment explanation
Indices: 190330--190368 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
190320 ATATATAGAT
*
190330 AG AG AG AG AG AG AG AG AG AG AG AG A- AG AA AG A- AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
190369 AGGTTATGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (2 bp):
AG
Found at i:191607 original size:15 final size:15
Alignment explanation
Indices: 191582--191619 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
191572 GAAATTGAAA
*
191582 TTAAAATTTAATTT-
1 TTAAAAATTAATTTC
191596 TGTAAAAATTAATTTC
1 T-TAAAAATTAATTTC
191612 TTAAAAAT
1 TTAAAAAT
191620 GGACGAATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 1 0.05
15 19 0.90
16 1 0.05
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (15 bp):
TTAAAAATTAATTTC
Found at i:192486 original size:2 final size:2
Alignment explanation
Indices: 192479--192515 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
192469 AGGCTTCATA
192479 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 A
192516 CACCCCATCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:193816 original size:6 final size:6
Alignment explanation
Indices: 193803--193858 Score: 76
Period size: 6 Copynumber: 9.3 Consensus size: 6
193793 ATGGAATTCA
* * * *
193803 ATATAT AAATAT AAATAT ATATAT ATATAT ATATAT ATATAT ACATAA
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
193851 ATATAT AT
1 ATATAT AT
193859 GTGTCTGCGC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (6 bp):
ATATAT
Found at i:193821 original size:14 final size:14
Alignment explanation
Indices: 193802--193855 Score: 58
Period size: 14 Copynumber: 4.0 Consensus size: 14
193792 AATGGAATTC
193802 AATATATAAATATA
1 AATATATAAATATA
193816 AATATAT--ATATA
1 AATATATAAATATA
* *
193828 TATATATATATATA
1 AATATATAAATATA
* *
193842 TATACATAAATATA
1 AATATATAAATATA
193856 TATGTGTCTG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
12 11 0.31
14 24 0.69
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
AATATATAAATATA
Found at i:193826 original size:4 final size:4
Alignment explanation
Indices: 193803--193858 Score: 76
Period size: 4 Copynumber: 14.0 Consensus size: 4
193793 ATGGAATTCA
* * * *
193803 ATAT ATAA ATAT AAAT ATAT ATAT ATAT ATAT ATAT ATAT ATAC ATAA
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
193851 ATAT ATAT
1 ATAT ATAT
193859 GTGTCTGCGC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (4 bp):
ATAT
Found at i:194424 original size:2 final size:2
Alignment explanation
Indices: 194417--194454 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
194407 ATACATGCAC
194417 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
194455 CAGAGAAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:195438 original size:14 final size:15
Alignment explanation
Indices: 195419--195447 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
195409 TTTAATCTAA
195419 TATCTAATA-ATATT
1 TATCTAATATATATT
195433 TATCTAATATATATT
1 TATCTAATATATATT
195448 AATATTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (15 bp):
TATCTAATATATATT
Found at i:195439 original size:21 final size:21
Alignment explanation
Indices: 195407--195455 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
195397 CCCATGGGCT
*
195407 TATTTAATCTAATATCTAATAA
1 TATTT-ATCTAATATATAATAA
*
195429 TATTTATCTAATATATATTAA
1 TATTTATCTAATATATAATAA
195450 TATTTA
1 TATTTA
195456 AAAATTAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (21 bp):
TATTTATCTAATATATAATAA
Found at i:199900 original size:24 final size:24
Alignment explanation
Indices: 199873--199932 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
199863 AAAAAATATG
*
199873 TTTAATAATAATACTTATAT-ATTT
1 TTTAATAATAA-ACTTAAATAATTT
*
199897 TTT-ATAATTAAATTTAAATAATTT
1 TTTAATAA-TAAACTTAAATAATTT
*
199921 TTTATTAATAAA
1 TTTAATAATAAA
199933 TATTAATTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
23 10 0.33
24 17 0.57
25 3 0.10
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (24 bp):
TTTAATAATAAACTTAAATAATTT
Found at i:200190 original size:18 final size:18
Alignment explanation
Indices: 200168--200216 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
200158 TAAAATTACA
*
200168 AATAATATATAAATTTTTTAT
1 AATAATATA-AAA-ATTTT-T
*
200189 AATAAAATAAAAATTTTT
1 AATAATATAAAAATTTTT
200207 AATAATATAA
1 AATAATATAA
200217 TTCATGTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 10 0.40
19 4 0.16
20 3 0.12
21 8 0.32
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AATAATATAAAAATTTTT
Found at i:200202 original size:21 final size:21
Alignment explanation
Indices: 200168--200213 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
200158 TAAAATTACA
* * *
200168 AATAATATATAAATTTTTTAT
1 AATAAAATAAAAATTTTTAAT
200189 AATAAAATAAAAATTTTTAAT
1 AATAAAATAAAAATTTTTAAT
200210 AATA
1 AATA
200214 TAATTCATGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AATAAAATAAAAATTTTTAAT
Found at i:206214 original size:2 final size:2
Alignment explanation
Indices: 206203--206236 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
206193 GGCCTGATTT
*
206203 TA TA TA -A TA TA TA TA TA TA TA TA TA CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
206237 TACTATACCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:214207 original size:21 final size:21
Alignment explanation
Indices: 214183--214231 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
214173 AATATAGATA
214183 ATTTTTTAGAAGTAAAT-GATT
1 ATTTTTTAGAAG-AAATCGATT
* *
214204 A-TTTTTAGAAGAGATCGTTT
1 ATTTTTTAGAAGAAATCGATT
214224 ATTTTTTA
1 ATTTTTTA
214232 AAATAGATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 3 0.12
20 14 0.58
21 7 0.29
ACGTcount: A:0.33, C:0.02, G:0.14, T:0.51
Consensus pattern (21 bp):
ATTTTTTAGAAGAAATCGATT
Found at i:214338 original size:19 final size:19
Alignment explanation
Indices: 214314--214357 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
214304 TTTTAAGAAA
214314 TTTTAAAAAAGTTATAATT
1 TTTTAAAAAAGTTATAATT
* * *
214333 TTTTAATATATTTATAATT
1 TTTTAAAAAAGTTATAATT
214352 TTTTAA
1 TTTTAA
214358 TTTTAATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
TTTTAAAAAAGTTATAATT
Found at i:219841 original size:3 final size:3
Alignment explanation
Indices: 219833--219861 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
219823 AATAAGCTTC
219833 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
219862 AATACATAAC
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:221094 original size:2 final size:2
Alignment explanation
Indices: 221087--221118 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
221077 CCTTTTCCTC
221087 TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
221119 TATCAACTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:230025 original size:5 final size:5
Alignment explanation
Indices: 230015--230041 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
230005 CTCTTAATGG
230015 TATTT TATTT TATTT TATTT TATTT TA
1 TATTT TATTT TATTT TATTT TATTT TA
230042 CTTCACAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (5 bp):
TATTT
Found at i:230260 original size:3 final size:3
Alignment explanation
Indices: 230252--230281 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
230242 TAAGCCTTAA
230252 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
230282 CAAATCAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:234262 original size:3 final size:3
Alignment explanation
Indices: 234254--234283 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
234244 ATATTGTTCT
234254 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
234284 ATTTCATATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:239231 original size:13 final size:13
Alignment explanation
Indices: 239213--239256 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
239203 AGGATTTCGA
239213 ATTAAAGTTTTAG
1 ATTAAAGTTTTAG
*
239226 ATTAAAGTTTAAG
1 ATTAAAGTTTTAG
* *
239239 ATTTAGAGTTTTAA
1 A-TTAAAGTTTTAG
239253 ATTA
1 ATTA
239257 GGTTGATGTG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 16 0.62
14 10 0.38
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (13 bp):
ATTAAAGTTTTAG
Found at i:239707 original size:19 final size:20
Alignment explanation
Indices: 239679--239719 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
239669 AGTCACAATA
* *
239679 TTAAGGTTTAGAATTTA-GG
1 TTAAGATTTAAAATTTACGG
239698 TTAAGATTTAAAATTTACGG
1 TTAAGATTTAAAATTTACGG
239718 TT
1 TT
239720 TAATTTTCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.34, C:0.02, G:0.20, T:0.44
Consensus pattern (20 bp):
TTAAGATTTAAAATTTACGG
Found at i:239898 original size:6 final size:6
Alignment explanation
Indices: 239889--239967 Score: 54
Period size: 6 Copynumber: 12.2 Consensus size: 6
239879 AATAAAAGGC
* *
239889 ATAAAA ATAATTAA ATTAAA ATAAAA ATATAA AT-AAA ATGAAAA CA-AATAA
1 ATAAAA ATAA--AA ATAAAA ATAAAA ATAAAA ATAAAA AT-AAAA -ATAA-AA
239940 ATTAAGAA ATAAAA ATAAAA ATTAAAA A
1 A-TAA-AA ATAAAA ATAAAA A-TAAAA A
239968 GATTTGGTTT
Statistics
Matches: 59, Mismatches: 5, Indels: 17
0.73 0.06 0.21
Matches are distributed among these distances:
5 4 0.07
6 30 0.51
7 14 0.24
8 11 0.19
ACGTcount: A:0.73, C:0.01, G:0.03, T:0.23
Consensus pattern (6 bp):
ATAAAA
Found at i:247341 original size:44 final size:44
Alignment explanation
Indices: 247270--247393 Score: 230
Period size: 44 Copynumber: 2.8 Consensus size: 44
247260 TTGTATCTCC
* *
247270 ATGTATCAACAATAGGTTGGGACTGAGGTTGAGTGGGTCGTAAG
1 ATGTGTCAACAATAGGTTGGGATTGAGGTTGAGTGGGTCGTAAG
247314 ATGTGTCAACAATAGGTTGGGATTGAGGTTGAGTGGGTCGTAAG
1 ATGTGTCAACAATAGGTTGGGATTGAGGTTGAGTGGGTCGTAAG
247358 ATGTGTCAACAATAGGTTGGGATTGAGGTTGAGTGG
1 ATGTGTCAACAATAGGTTGGGATTGAGGTTGAGTGG
247394 CTTGTATACA
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
44 78 1.00
ACGTcount: A:0.26, C:0.07, G:0.38, T:0.29
Consensus pattern (44 bp):
ATGTGTCAACAATAGGTTGGGATTGAGGTTGAGTGGGTCGTAAG
Found at i:256953 original size:2 final size:2
Alignment explanation
Indices: 256946--256977 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
256936 GTACATGTAA
256946 TC 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 TC
256978 AGGCGCAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:259228 original size:34 final size:34
Alignment explanation
Indices: 259185--259262 Score: 147
Period size: 34 Copynumber: 2.3 Consensus size: 34
259175 ATTTTGCCGG
259185 GCTTAATTTATATGTGCTTTTAGTTGCTAATGAT
1 GCTTAATTTATATGTGCTTTTAGTTGCTAATGAT
259219 GCTTAATTTATATGTGCTTTTAGTTGCTAATGAT
1 GCTTAATTTATATGTGCTTTTAGTTGCTAATGAT
259253 GCTTAGATTT
1 GCTTA-ATTT
259263 GATTGTCTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
34 39 0.91
35 4 0.09
ACGTcount: A:0.23, C:0.09, G:0.18, T:0.50
Consensus pattern (34 bp):
GCTTAATTTATATGTGCTTTTAGTTGCTAATGAT
Found at i:267444 original size:3 final size:3
Alignment explanation
Indices: 267436--267468 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
267426 ATAAGGACTT
267436 TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TT
267469 GTTGTTGTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:267954 original size:31 final size:32
Alignment explanation
Indices: 267887--267969 Score: 105
Period size: 32 Copynumber: 2.6 Consensus size: 32
267877 ATAACATGTT
* *
267887 TTTAAAAAAATTTAAAAAAAAAATTTATAAGT
1 TTTAAAAAAATTTAAATAAAAAATTTATAAGA
***
267919 TTTAAAAAAATTTAAATAATTTATTTATAA-A
1 TTTAAAAAAATTTAAATAAAAAATTTATAAGA
*
267950 TTTAAAAAAATATAAATAAA
1 TTTAAAAAAATTTAAATAAA
267970 TTTTAAATTT
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
31 18 0.41
32 26 0.59
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (32 bp):
TTTAAAAAAATTTAAATAAAAAATTTATAAGA
Found at i:267978 original size:7 final size:7
Alignment explanation
Indices: 267966--267990 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
267956 AAAATATAAA
267966 TAAATTT
1 TAAATTT
267973 TAAATTT
1 TAAATTT
267980 TAAATTT
1 TAAATTT
267987 TAAA
1 TAAA
267991 ATAAATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
TAAATTT
Found at i:267981 original size:28 final size:29
Alignment explanation
Indices: 267907--267983 Score: 95
Period size: 31 Copynumber: 2.6 Consensus size: 29
267897 TTTAAAAAAA
* *
267907 AAATTTATAAGTTTTAAAAAAATTTAAAT
1 AAATTTATAAATTTTAAAAAAATATAAAT
267936 AATTTATTTATAAA-TTTAAAAAAATATAAAT
1 AA---ATTTATAAATTTTAAAAAAATATAAAT
267967 AAATTT-TAAATTTTAAA
1 AAATTTATAAATTTTAAA
267984 TTTTAAAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
27 4 0.10
28 10 0.24
29 2 0.05
31 18 0.43
32 8 0.19
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (29 bp):
AAATTTATAAATTTTAAAAAAATATAAAT
Found at i:275419 original size:8 final size:8
Alignment explanation
Indices: 275404--275434 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
275394 CCTCTTTCGT
275404 ACAAAAAA
1 ACAAAAAA
*
275412 AAAAAAAA
1 ACAAAAAA
275420 ACAAAAAA
1 ACAAAAAA
275428 ACAAAAA
1 ACAAAAA
275435 TTCTTCAGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (8 bp):
ACAAAAAA
Found at i:280871 original size:3 final size:3
Alignment explanation
Indices: 280863--280914 Score: 79
Period size: 3 Copynumber: 17.7 Consensus size: 3
280853 ATTAAAGGAA
* *
280863 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT ATT AAT ATT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
280910 AAT AA
1 AAT AA
280915 AAAAAGAGAG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:281078 original size:2 final size:2
Alignment explanation
Indices: 281071--281113 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
281061 GACAGGGAGG
281071 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
281113 G
1 G
281114 TATTTGTGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:283853 original size:40 final size:40
Alignment explanation
Indices: 283809--283887 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 40
283799 TAGCATGACC
**
283809 ACAAGAATTATCTAACACATCAAGAACAAAGGGGAAAAAA
1 ACAAGAAAAATCTAACACATCAAGAACAAAGGGGAAAAAA
*
283849 ACAAGAAAAATCTAACACATCAAGAACAAAGGGTAAAAA
1 ACAAGAAAAATCTAACACATCAAGAACAAAGGGGAAAAA
283888 GTTATCCTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.59, C:0.15, G:0.14, T:0.11
Consensus pattern (40 bp):
ACAAGAAAAATCTAACACATCAAGAACAAAGGGGAAAAAA
Found at i:286826 original size:17 final size:17
Alignment explanation
Indices: 286806--286845 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
286796 ACATAAAATA
*
286806 AAATAATTAATTTATAT
1 AAATAATTAAATTATAT
286823 AAAT-A-TAAATTATAT
1 AAATAATTAAATTATAT
286838 AAA-AATTA
1 AAATAATTA
286846 TTATAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 5
0.77 0.04 0.19
Matches are distributed among these distances:
15 13 0.65
16 3 0.15
17 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATAATTAAATTATAT
Found at i:293946 original size:1 final size:1
Alignment explanation
Indices: 293940--293965 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
293930 ACTTAATTAT
293940 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
293966 CCTTGCTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:294626 original size:2 final size:2
Alignment explanation
Indices: 294619--294657 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
294609 AAGTTACATG
* * *
294619 TA TA TA TA CA TA TA CA TA TA TA TA TA TA TA CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
294658 CGGTAGCAAG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:294640 original size:16 final size:16
Alignment explanation
Indices: 294619--294657 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
294609 AAGTTACATG
294619 TATATATACATATACA
1 TATATATACATATACA
*
294635 TATATATATATATACA
1 TATATATACATATACA
294651 TATATAT
1 TATATAT
294658 CGGTAGCAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.44
Consensus pattern (16 bp):
TATATATACATATACA
Found at i:294655 original size:12 final size:12
Alignment explanation
Indices: 294613--294657 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
294603 AAATAGAAGT
*
294613 TACATGTATATA
1 TACATATATATA
*
294625 TACATATACATA
1 TACATATATATA
294637 T--ATATATATA
1 TACATATATATA
294647 TACATATATAT
1 TACATATATAT
294658 CGGTAGCAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
10 9 0.32
12 19 0.68
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.42
Consensus pattern (12 bp):
TACATATATATA
Found at i:295534 original size:46 final size:46
Alignment explanation
Indices: 295467--295556 Score: 153
Period size: 46 Copynumber: 2.0 Consensus size: 46
295457 CCAAATACAT
* *
295467 GAAGATTAGTCAAGGTATAACTTCTAGTGAAACACCCTTTTAAGAG
1 GAAGACTAGTCAAGGTATAACTTCTAGTGAAACACCCTCTTAAGAG
*
295513 GAAGACTAGTCATGGTATAACTTCTAGTGAAACACCCTCTTAAG
1 GAAGACTAGTCAAGGTATAACTTCTAGTGAAACACCCTCTTAAG
295557 CAGAGCTAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.28
Consensus pattern (46 bp):
GAAGACTAGTCAAGGTATAACTTCTAGTGAAACACCCTCTTAAGAG
Found at i:298173 original size:31 final size:31
Alignment explanation
Indices: 298112--298171 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
298102 TCTAGATGAC
*
298112 TTTGTTTTATTTTATTATGGTTTATTTTTTA
1 TTTGTTTTATTTCATTATGGTTTATTTTTTA
298143 TTTGTTTTA-TTCA-TATGGTTCTATTTTTT
1 TTTGTTTTATTTCATTATGGTT-TATTTTTT
298172 TACATATTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 7 0.26
30 11 0.41
31 9 0.33
ACGTcount: A:0.15, C:0.03, G:0.10, T:0.72
Consensus pattern (31 bp):
TTTGTTTTATTTCATTATGGTTTATTTTTTA
Found at i:302152 original size:18 final size:20
Alignment explanation
Indices: 302129--302167 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
302119 AATAAAAAAA
302129 TATTTAATTTT-TTA-ATTT
1 TATTTAATTTTATTATATTT
*
302147 TATTTAGTTTTATTATATTT
1 TATTTAATTTTATTATATTT
302167 T
1 T
302168 CATAAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 10 0.56
19 3 0.17
20 5 0.28
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (20 bp):
TATTTAATTTTATTATATTT
Found at i:303791 original size:18 final size:18
Alignment explanation
Indices: 303757--303791 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
303747 TACGACAGAA
*
303757 TATTTATCAAAATTTAAT
1 TATTTATCAAAACTTAAT
*
303775 TATTTATCAAAGCTTAA
1 TATTTATCAAAACTTAA
303792 AAAATATATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.46
Consensus pattern (18 bp):
TATTTATCAAAACTTAAT
Found at i:305227 original size:18 final size:19
Alignment explanation
Indices: 305192--305229 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
305182 TATGTAATAT
*
305192 ATAAAGTTATTTAATTATA
1 ATAAAGTTATCTAATTATA
*
305211 ATAAAGTT-TCTATTTATA
1 ATAAAGTTATCTAATTATA
305229 A
1 A
305230 CTATTATCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (19 bp):
ATAAAGTTATCTAATTATA
Found at i:308317 original size:2 final size:2
Alignment explanation
Indices: 308310--308354 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
308300 GTGTCTGTGC
308310 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
308352 AT A
1 AT A
308355 ATCAAACTAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:310116 original size:11 final size:11
Alignment explanation
Indices: 310100--310124 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
310090 TATCTAAAAG
310100 TGTGATCCTTC
1 TGTGATCCTTC
310111 TGTGATCCTTC
1 TGTGATCCTTC
310122 TGT
1 TGT
310125 CTTTACCTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.24, G:0.20, T:0.48
Consensus pattern (11 bp):
TGTGATCCTTC
Found at i:310607 original size:3 final size:3
Alignment explanation
Indices: 310599--310631 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
310589 TACAAGCTTT
310599 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
310632 GTTTTCCTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:310902 original size:22 final size:22
Alignment explanation
Indices: 310877--310919 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
310867 AAAAGTTGGT
310877 TTTAAGTTTTGAGCAGTTATGG
1 TTTAAGTTTTGAGCAGTTATGG
310899 TTTAAGTTTTGAGCAGTTATG
1 TTTAAGTTTTGAGCAGTTATG
310920 ACCAGATTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.05, G:0.26, T:0.47
Consensus pattern (22 bp):
TTTAAGTTTTGAGCAGTTATGG
Found at i:318149 original size:74 final size:74
Alignment explanation
Indices: 318028--318179 Score: 295
Period size: 74 Copynumber: 2.1 Consensus size: 74
318018 AATCAAGAAA
318028 AAGAGCCTAAAGATGGCCCAGTCTCCTTCCTACCTGCACCCTTTTATCTTTTTGTTTCTTTTGGT
1 AAGAGCCTAAAGATGGCCCAGTCTCCTTCCTACCTGCACCCTTTTATCTTTTTGTTTCTTTTGGT
318093 CTTTGATTT
66 CTTTGATTT
*
318102 AAGAGCCTAAAGATGGCCCAGTCTTCTTCCTACCTGCACCCTTTTATCTTTTTGTTTCTTTTGGT
1 AAGAGCCTAAAGATGGCCCAGTCTCCTTCCTACCTGCACCCTTTTATCTTTTTGTTTCTTTTGGT
318167 CTTTGATTT
66 CTTTGATTT
318176 AAGA
1 AAGA
318180 CTTTTTCTGC
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 77 1.00
ACGTcount: A:0.18, C:0.24, G:0.15, T:0.43
Consensus pattern (74 bp):
AAGAGCCTAAAGATGGCCCAGTCTCCTTCCTACCTGCACCCTTTTATCTTTTTGTTTCTTTTGGT
CTTTGATTT
Found at i:322295 original size:2 final size:2
Alignment explanation
Indices: 322243--322278 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
322233 GTGAAGCTGG
*
322243 TA TA TA AA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
322279 TCAACTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:322469 original size:14 final size:14
Alignment explanation
Indices: 322452--322479 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
322442 CAAAGACCTG
322452 AACACAATGGTGAT
1 AACACAATGGTGAT
322466 AACACAATGGTGAT
1 AACACAATGGTGAT
322480 TGGCATGGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.21
Consensus pattern (14 bp):
AACACAATGGTGAT
Found at i:325750 original size:2 final size:2
Alignment explanation
Indices: 325743--325776 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
325733 ATATGCGCAA
325743 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
325777 CTGAAACTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:329066 original size:345 final size:345
Alignment explanation
Indices: 328435--329125 Score: 1319
Period size: 345 Copynumber: 2.0 Consensus size: 345
328425 AGTAGAGAGC
328435 TGTTGATCTACAGTTTTGGCTGCAATTTGACGAATAACGGAGAGAGATTCAGATCTGATGAACTC
1 TGTTGATCTACAGTTTTGGCTGCAATTTGACGAATAACGGAGAGAGATTCAGATCTGATGAACTC
*
328500 TTTCAAGCTCATCCGTATTTGAAAAAGCAATTTAACGTCATTGGAGGCGAAAACTGATTCAAGAA
66 TTTCAAGCTCATCCGTATTTGAAAAAGCAATTTAACGTCAGTGGAGGCGAAAACTGATTCAAGAA
328565 TGCGGAGAGAATCGTCATTGAATCTGCGAAGATCGAAAGGAAGGGAATTAAACATCGTTAAAGCG
131 TGCGGAGAGAATCGTCATTGAATCTGCGAAGATCGAAAGGAAGGGAATTAAACATCGTTAAAGCG
328630 AGATGATGGAATAAATGAACATTTTGTTGAGAGATTAAGTGAACCTTTTCTCGCTAATTTGGGAG
196 AGATGATGGAATAAATGAACATTTTGTTGAGAGATTAAGTGAACCTTTTCTCGCTAATTTGGGAG
*
328695 CTGAAGAGAGAGATTTGCTGAGCTACTCCAGAGTCCGAGTCCGACATCTTGGCTTGGGGAATGAA
261 CGGAAGAGAGAGATTTGCTGAGCTACTCCAGAGTCCGAGTCCGACATCTTGGCTTGGGGAATGAA
328760 TTGGAAAGGGAATTGGCGGG
326 TTGGAAAGGGAATTGGCGGG
328780 TGTTGATCTACAGTTTTGGCTGCAATTTGACGAATAACGGAGAGAGATTCAGATCTGATGAACTC
1 TGTTGATCTACAGTTTTGGCTGCAATTTGACGAATAACGGAGAGAGATTCAGATCTGATGAACTC
* *
328845 TTTCAAGCTCATCCGTATTTGAAAAAGCAATTTAACGTCAGTGGAGGCGAGAACTGATTCAGGAA
66 TTTCAAGCTCATCCGTATTTGAAAAAGCAATTTAACGTCAGTGGAGGCGAAAACTGATTCAAGAA
*
328910 TGCGGAGAGAATCGTCATTGAATCTGCGAAGATCGAAAGGAAGGGAATTAAACGTCGTTAAAGCG
131 TGCGGAGAGAATCGTCATTGAATCTGCGAAGATCGAAAGGAAGGGAATTAAACATCGTTAAAGCG
* *
328975 AGATGATGTAATAAATGAACATTTTGTTGAGAGATTGAGTGAACCTTTTCTCGCTAATTTGGGAG
196 AGATGATGGAATAAATGAACATTTTGTTGAGAGATTAAGTGAACCTTTTCTCGCTAATTTGGGAG
329040 CGGAAGAGAGAGATTTGCTGAGCTACTCCAGAGTCCGAGTCCGACATCTTGGCTTGGGGAATGAA
261 CGGAAGAGAGAGATTTGCTGAGCTACTCCAGAGTCCGAGTCCGACATCTTGGCTTGGGGAATGAA
329105 TTGGAAAGGGAATTGGCGGG
326 TTGGAAAGGGAATTGGCGGG
329125 T
1 T
329126 AAGGGATTAG
Statistics
Matches: 339, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
345 339 1.00
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.27
Consensus pattern (345 bp):
TGTTGATCTACAGTTTTGGCTGCAATTTGACGAATAACGGAGAGAGATTCAGATCTGATGAACTC
TTTCAAGCTCATCCGTATTTGAAAAAGCAATTTAACGTCAGTGGAGGCGAAAACTGATTCAAGAA
TGCGGAGAGAATCGTCATTGAATCTGCGAAGATCGAAAGGAAGGGAATTAAACATCGTTAAAGCG
AGATGATGGAATAAATGAACATTTTGTTGAGAGATTAAGTGAACCTTTTCTCGCTAATTTGGGAG
CGGAAGAGAGAGATTTGCTGAGCTACTCCAGAGTCCGAGTCCGACATCTTGGCTTGGGGAATGAA
TTGGAAAGGGAATTGGCGGG
Done.