Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold75
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: 1998514
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
File 12 of 12
Found at i:1893150 original size:14 final size:14
Alignment explanation
Indices: 1893131--1893179 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
1893121 TTTCATATGT
1893131 TTTTTCTTTTTTTC
1 TTTTTCTTTTTTTC
*
1893145 TTTTTCTTTCTTTC
1 TTTTTCTTTTTTTC
* * *
1893159 TTATTCATCTTTT-
1 TTTTTCTTTTTTTC
1893172 TTTTTCTT
1 TTTTTCTT
1893180 ACTATAAATA
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
13 6 0.21
14 22 0.79
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTTCTTTTTTTC
Found at i:1900994 original size:116 final size:116
Alignment explanation
Indices: 1900790--1901019 Score: 343
Period size: 116 Copynumber: 2.0 Consensus size: 116
1900780 ATGATAAGAA
* ** *
1900790 ATATTTTTAGATTAAGTAGGGAAGGTTGACAGATAAATCACTTATCCAACTGATCCTCGACGGTC
1 ATATTTTTAGATTAAGTAGGGAAGGTCGACAGATAAATCACCCATCCAACCGATCCTCGACGGTC
* * *
1900855 ACCATGAAGTGGCTGAAGGTTTGGAGTTGCACCGCTCATTTCAGGCTAAGC
66 ACCATGAAGTGGCCGAAGGTTTGGAGTTACACCACTCATTTCAGGCTAAGC
* * * *
1900906 ATATTTTTAGATTAAGTGGGGAATGTCGACAGATGAATCGCCCATCCAACCGATCCTCGACGGTC
1 ATATTTTTAGATTAAGTAGGGAAGGTCGACAGATAAATCACCCATCCAACCGATCCTCGACGGTC
* *
1900971 ACCATGAGGTGGCCGAAGGTTTGGAGTTACACTACTCATTTCAGGCTAA
66 ACCATGAAGTGGCCGAAGGTTTGGAGTTACACCACTCATTTCAGGCTAA
1901020 TCATGATCGT
Statistics
Matches: 101, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
116 101 1.00
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.27
Consensus pattern (116 bp):
ATATTTTTAGATTAAGTAGGGAAGGTCGACAGATAAATCACCCATCCAACCGATCCTCGACGGTC
ACCATGAAGTGGCCGAAGGTTTGGAGTTACACCACTCATTTCAGGCTAAGC
Found at i:1911053 original size:18 final size:18
Alignment explanation
Indices: 1911027--1911061 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1911017 AAAGAAACCT
* *
1911027 ATAATAAAATGACCAAAC
1 ATAAAAAAAGGACCAAAC
1911045 ATAAAAAAAGGACCAAA
1 ATAAAAAAAGGACCAAA
1911062 TATTCATAAT
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:0.66, C:0.14, G:0.09, T:0.11
Consensus pattern (18 bp):
ATAAAAAAAGGACCAAAC
Found at i:1917491 original size:18 final size:19
Alignment explanation
Indices: 1917470--1917507 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1917460 ATCAAAAATT
1917470 TCAA-TAAATGATAAAAAA
1 TCAATTAAATGATAAAAAA
* *
1917488 TCAATTAATTTATAAAAAA
1 TCAATTAAATGATAAAAAA
1917507 T
1 T
1917508 TAAAAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.32
Consensus pattern (19 bp):
TCAATTAAATGATAAAAAA
Found at i:1918537 original size:2 final size:2
Alignment explanation
Indices: 1918530--1918563 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1918520 CAACCAAGGC
1918530 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1918564 GTCTTTGTTT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1918798 original size:23 final size:26
Alignment explanation
Indices: 1918772--1918818 Score: 64
Period size: 23 Copynumber: 1.9 Consensus size: 26
1918762 TAAATTTTAA
1918772 AAAAATTT-AATTT-AA-AATTATGT
1 AAAAATTTGAATTTCAATAATTATGT
*
1918795 AAAATTTTGAATTTCAATAATTAT
1 AAAAATTTGAATTTCAATAATTAT
1918819 TCATAAATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 7 0.35
24 5 0.25
25 2 0.10
26 6 0.30
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (26 bp):
AAAAATTTGAATTTCAATAATTATGT
Found at i:1919164 original size:2 final size:2
Alignment explanation
Indices: 1919157--1919183 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1919147 TCCGTATAGT
1919157 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1919184 TTGTATATGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1927492 original size:22 final size:23
Alignment explanation
Indices: 1927459--1927506 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 23
1927449 GATTTAACTA
1927459 TTAAAACTGAACCA-GAAAAACG
1 TTAAAACTGAACCAGGAAAAACG
1927481 TTAAAA-TCGAACCAGGAAAAACG
1 TTAAAACT-GAACCAGGAAAAACG
1927504 TTA
1 TTA
1927507 TTTCTCACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 1 0.04
22 12 0.50
23 11 0.46
ACGTcount: A:0.52, C:0.17, G:0.15, T:0.17
Consensus pattern (23 bp):
TTAAAACTGAACCAGGAAAAACG
Found at i:1930225 original size:16 final size:16
Alignment explanation
Indices: 1930206--1930239 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1930196 AAATAAGAGA
1930206 TAATTGAAATTATCCC
1 TAATTGAAATTATCCC
1930222 TAATTGAAATTATCCC
1 TAATTGAAATTATCCC
1930238 TA
1 TA
1930240 GTATTATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.38, C:0.18, G:0.06, T:0.38
Consensus pattern (16 bp):
TAATTGAAATTATCCC
Found at i:1938062 original size:16 final size:16
Alignment explanation
Indices: 1938032--1938075 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
1938022 TCTAAGATAG
*
1938032 TTCAAACTCAAAATGA
1 TTCAAACTTAAAATGA
1938048 TT-AAGACTTAAAATGA
1 TTCAA-ACTTAAAATGA
1938064 TTCAAACTTAAA
1 TTCAAACTTAAA
1938076 TTAACTTGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 2 0.08
16 21 0.84
17 2 0.08
ACGTcount: A:0.50, C:0.14, G:0.07, T:0.30
Consensus pattern (16 bp):
TTCAAACTTAAAATGA
Found at i:1940350 original size:30 final size:31
Alignment explanation
Indices: 1940303--1940375 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 31
1940293 ATTTTAAAAG
*
1940303 TTATTTAAA-TATAAATTAAAAATT-AAGAC
1 TTATTTAAAGTGTAAATTAAAAATTAAAGAC
*
1940332 TTATTTAAAGTGTAAATTAAAAATTAAAGAT
1 TTATTTAAAGTGTAAATTAAAAATTAAAGAC
1940363 TTATTT-AAGTGTA
1 TTATTTAAAGTGTA
1940376 TAAAAATGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
29 9 0.22
30 21 0.52
31 10 0.25
ACGTcount: A:0.49, C:0.01, G:0.08, T:0.41
Consensus pattern (31 bp):
TTATTTAAAGTGTAAATTAAAAATTAAAGAC
Found at i:1942878 original size:2 final size:2
Alignment explanation
Indices: 1942871--1942898 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1942861 AAGCCTTCGG
1942871 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
1942899 GTTATACTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1946068 original size:17 final size:18
Alignment explanation
Indices: 1946036--1946069 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1946026 ATGCAAAATT
*
1946036 AATCATTTTAGTCTCTTA
1 AATCATTTTAGACTCTTA
1946054 AATCATTTT-GACTCTT
1 AATCATTTTAGACTCTT
1946070 GTACTATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.18, G:0.06, T:0.50
Consensus pattern (18 bp):
AATCATTTTAGACTCTTA
Found at i:1946254 original size:13 final size:12
Alignment explanation
Indices: 1946238--1946293 Score: 51
Period size: 13 Copynumber: 4.4 Consensus size: 12
1946228 CATAATTTTT
1946238 TTAAATAAAATAA
1 TTAAATAAAA-AA
1946251 TTAAATAATAAAAA
1 TTAAAT-A-AAAAA
*
1946265 TATAAATATAAAA
1 T-TAAATAAAAAA
*
1946278 TTAAA-AATAAA
1 TTAAATAAAAAA
1946289 TTAAA
1 TTAAA
1946294 AATTTTAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
11 9 0.24
12 4 0.11
13 11 0.30
14 5 0.14
15 8 0.22
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
TTAAATAAAAAA
Found at i:1947057 original size:17 final size:17
Alignment explanation
Indices: 1947031--1947065 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1947021 TTAATAGTTG
1947031 TTATTAATTATATGAAA
1 TTATTAATTATATGAAA
* *
1947048 TTATTTATTATATTAAA
1 TTATTAATTATATGAAA
1947065 T
1 T
1947066 AAAAATAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
TTATTAATTATATGAAA
Found at i:1947832 original size:2 final size:2
Alignment explanation
Indices: 1947825--1947850 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1947815 TGCAATTCGC
1947825 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
1947851 TTAGGGCATC
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):
AT
Found at i:1953006 original size:2 final size:2
Alignment explanation
Indices: 1953001--1953050 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
1952991 TATATAATTT
1953001 TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1953042 TA TA TA TA T
1 TA TA TA TA T
1953051 TTGGAAGAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1953014 original size:31 final size:33
Alignment explanation
Indices: 1952976--1953049 Score: 89
Period size: 31 Copynumber: 2.3 Consensus size: 33
1952966 ACTGGGGTGT
* * *
1952976 TATATATATAGGCCATATATA-AT-TTTATATA
1 TATATATATAGACAATATATATATATATATATA
* *
1953007 TATATATATATATAATATATATATATATATATA
1 TATATATATAGACAATATATATATATATATATA
1953040 TATATATATA
1 TATATATATA
1953050 TTTGGAAGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
31 17 0.47
32 2 0.06
33 17 0.47
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (33 bp):
TATATATATAGACAATATATATATATATATATA
Found at i:1957025 original size:2 final size:2
Alignment explanation
Indices: 1957018--1957048 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1957008 ATAAACACTA
1957018 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
1957049 AAAGAAAACA
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:1960053 original size:26 final size:27
Alignment explanation
Indices: 1960024--1960080 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 27
1960014 TTGAATTAAA
* *
1960024 TAAATTTTTAT-TAATTATTAATATAT
1 TAAATTTTTATATAAATATAAATATAT
*
1960050 TAAA-TTTTATATAAATATAAATATTT
1 TAAATTTTTATATAAATATAAATATAT
1960076 TAAAT
1 TAAAT
1960081 ATAATTATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 6 0.23
26 20 0.77
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
TAAATTTTTATATAAATATAAATATAT
Found at i:1966613 original size:24 final size:25
Alignment explanation
Indices: 1966580--1966643 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 25
1966570 CTAATTCTCC
*
1966580 TTATATATATTTTTTTATTTTTT-A
1 TTATAGATATTTTTTTATTTTTTGA
1966604 TTATAGATATAATTTTTTATTTTTTGA
1 TTATAGATAT--TTTTTTATTTTTTGA
1966631 TTAT-G-TATTTTTT
1 TTATAGATATTTTTT
1966644 GGATTTTCAG
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
23 5 0.14
24 9 0.25
25 3 0.08
26 14 0.39
27 5 0.14
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (25 bp):
TTATAGATATTTTTTTATTTTTTGA
Found at i:1966620 original size:26 final size:27
Alignment explanation
Indices: 1966584--1966634 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
1966574 TTCTCCTTAT
*
1966584 ATATATTTTTTTATTTTTT-ATTATAG
1 ATATAATTTTTTATTTTTTGATTATAG
1966610 ATATAATTTTTTATTTTTTGATTAT
1 ATATAATTTTTTATTTTTTGATTAT
1966635 GTATTTTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (27 bp):
ATATAATTTTTTATTTTTTGATTATAG
Found at i:1967374 original size:15 final size:15
Alignment explanation
Indices: 1967344--1967399 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 15
1967334 TCTCTTTTTT
1967344 TATTTATTATTATTTAA
1 TATTT-TTATT-TTTAA
*
1967361 TTTTTTTATTTTTAA
1 TATTTTTATTTTTAA
* *
1967376 AATTTTTATATTTAA
1 TATTTTTATTTTTAA
1967391 TATATTTTA
1 TAT-TTTTA
1967400 AATATAAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
15 19 0.58
16 10 0.30
17 4 0.12
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TATTTTTATTTTTAA
Found at i:1967380 original size:22 final size:23
Alignment explanation
Indices: 1967338--1967380 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1967328 ATATTTTCTC
**
1967338 TTTTTTTATTTATTATTATTTAA
1 TTTTTTTATTTATTAAAATTTAA
1967361 TTTTTTTATTT-TTAAAATTT
1 TTTTTTTATTTATTAAAATTT
1967381 TTATATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (23 bp):
TTTTTTTATTTATTAAAATTTAA
Found at i:1967715 original size:2 final size:2
Alignment explanation
Indices: 1967708--1967734 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1967698 AAACCTAAAT
1967708 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1967735 TGCCCATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1971073 original size:22 final size:21
Alignment explanation
Indices: 1971022--1971077 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
1971012 ATTAATTGTG
*
1971022 TTTTAAATTTTTAATTTTTATGA
1 TTTTAAA--TTTAATTTTTATAA
*
1971045 -TTAAAATTTAATTTTTAATAA
1 TTTTAAATTTAATTTTT-ATAA
1971066 TTTTAAATTTAA
1 TTTTAAATTTAA
1971078 AAAAATTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 10 0.36
21 3 0.11
22 15 0.54
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTAAATTTAATTTTTATAA
Found at i:1972448 original size:2 final size:2
Alignment explanation
Indices: 1972441--1972469 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1972431 CCAAAACTAC
1972441 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1972470 CACTTTCGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1974593 original size:34 final size:34
Alignment explanation
Indices: 1974547--1974731 Score: 257
Period size: 34 Copynumber: 5.5 Consensus size: 34
1974537 GTAAAAACCA
*
1974547 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
1974581 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
1974615 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
1974649 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
1974683 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
1974716 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
1974732 TCTCCCACTT
Statistics
Matches: 135, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
33 18 0.13
34 113 0.84
35 4 0.03
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:1978824 original size:19 final size:19
Alignment explanation
Indices: 1978797--1978859 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
1978787 TCACGTGTAC
* *
1978797 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
1978816 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
**
1978835 AGTACCTATATACGTGAAT
1 AGTACCCGTATACGTGAAT
1978854 AGTACC
1 AGTACC
1978860 TCGACAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:1979209 original size:34 final size:34
Alignment explanation
Indices: 1979163--1979345 Score: 253
Period size: 34 Copynumber: 5.4 Consensus size: 34
1979153 GGTAAAAATA
*
1979163 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
1979197 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
1979231 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
1979265 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
1979299 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
1979332 CCATTTAATCAACA
1 CCATTTAATCAACA
1979346 CTCTGTGGCA
Statistics
Matches: 133, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
33 16 0.12
34 113 0.85
35 4 0.03
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:1983588 original size:18 final size:19
Alignment explanation
Indices: 1983567--1983613 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
1983557 TAAAAAAAAG
1983567 AATAAAAATAAATA-ATAA
1 AATAAAAATAAATACATAA
*
1983585 AATAAAAA-ATATACATAA
1 AATAAAAATAAATACATAA
*
1983603 AATAATAATAA
1 AATAAAAATAA
1983614 TAAATTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 4 0.17
18 19 0.79
19 1 0.04
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (19 bp):
AATAAAAATAAATACATAA
Found at i:1983616 original size:14 final size:14
Alignment explanation
Indices: 1983562--1983622 Score: 58
Period size: 13 Copynumber: 4.6 Consensus size: 14
1983552 ATTTTTAAAA
* *
1983562 AAAAGAATAAAAAT
1 AAAATAATAATAAT
1983576 -AAATAATAA-AAT
1 AAAATAATAATAAT
1983588 AAAA-AAT-ATACAT
1 AAAATAATAATA-AT
1983601 AAAATAATAATAAT
1 AAAATAATAATAAT
*
1983615 AAATTAAT
1 AAAATAAT
1983623 TAAAAGAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
11 1 0.03
12 7 0.17
13 17 0.43
14 12 0.30
15 3 0.08
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.25
Consensus pattern (14 bp):
AAAATAATAATAAT
Found at i:1983837 original size:21 final size:20
Alignment explanation
Indices: 1983796--1983850 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 20
1983786 ACAAAAACAG
*
1983796 AACAAAAAGAAGAAAGGAATCGA
1 AACAAAAA-AA-AAA-GAATCAA
1983819 AACAAGAAAAAAAAGAATCAA
1 AACAA-AAAAAAAAGAATCAA
1983840 AACAAAAAAAA
1 AACAAAAAAAA
1983851 GAAAACAAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 6 0.20
21 11 0.37
22 3 0.10
23 7 0.23
24 3 0.10
ACGTcount: A:0.75, C:0.09, G:0.13, T:0.04
Consensus pattern (20 bp):
AACAAAAAAAAAAGAATCAA
Found at i:1984146 original size:12 final size:13
Alignment explanation
Indices: 1984115--1984147 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1984105 AAAGCAATGC
1984115 AAAAACAACAGTT
1 AAAAACAACAGTT
*
1984128 GAAAACAACAG-T
1 AAAAACAACAGTT
1984140 AAAAACAA
1 AAAAACAA
1984148 AAGAGAAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.67, C:0.15, G:0.09, T:0.09
Consensus pattern (13 bp):
AAAAACAACAGTT
Found at i:1990916 original size:90 final size:86
Alignment explanation
Indices: 1990634--1990956 Score: 263
Period size: 89 Copynumber: 3.6 Consensus size: 86
1990624 TTCAAGGAAA
** * **
1990634 ACACATTTCTTAATCATATCCCCTTCAATCAGCC-CTTAGATGGTATTGATGCATCTTAAAGCTT
1 ACACA-TTCTTAATCATAT-CCCTTCACCCAACCAC-TAGATGGTATTGATGCATCACAAAG-TT
* * *
1990698 GGTTTCTTGGGGGTAAGATGCAGCCC
62 GATTTCTT-GGGGCAAGGTGCAGCCC
* ** * *
1990724 ACATATTCCCAATCATATTCCCTTCACCCAACCACTAGATGGTATTAATGCATTACAAAGTTGAT
1 ACACATTCTTAATCATA-TCCCTTCACCCAACCACTAGATGGTATTGATGCATCACAAAGTTGAT
* ** *
1990789 CTCATT-GAACAAAGGTGTAGCCC
65 TTC-TTGGGGC-AAGGTGCAGCCC
** * * * *
1990812 ATGCATTCTTAATCATATCCTTTTTTACCCGACCACTAGATGGTATTGGTGCATCACAAAGTTTG
1 ACACATTCTTAATCATATCC--CTTCACCCAACCACTAGATGGTATTGATGCATCACAAAG-TTG
1990877 ATTTGCTTGGGGCAAGGTGCAGCCC
63 ATTT-CTTGGGGCAAGGTGCAGCCC
* * * * *
1990902 ACACATTCTTAATCATATCCCCTTTATCCAACCACTAGATAGTACTAATGCATCA
1 ACACATTCTTAATCATAT-CCCTTCACCCAACCACTAGATGGTATTGATGCATCA
1990957 AAATTTGTCT
Statistics
Matches: 182, Mismatches: 41, Indels: 21
0.75 0.17 0.09
Matches are distributed among these distances:
87 4 0.02
88 28 0.15
89 104 0.57
90 41 0.23
91 5 0.03
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (86 bp):
ACACATTCTTAATCATATCCCTTCACCCAACCACTAGATGGTATTGATGCATCACAAAGTTGATT
TCTTGGGGCAAGGTGCAGCCC
Found at i:1991173 original size:47 final size:47
Alignment explanation
Indices: 1991106--1991644 Score: 500
Period size: 47 Copynumber: 11.5 Consensus size: 47
1991096 TCCACCTTCG
* * * * *
1991106 TTTGACTGTATTGGCATTAGGACCTAGCCAAACTCTTCTTATGCTCG
1 TTTGACTGTATTGGCGTTAGGACCTGGTCAAACTCTTCTTATCCTCA
* * * * * *
1991153 TTTGATTGTATTAGTGTTAGGAGCTGGTTAAA-TACTTCTCA-CCTCA
1 TTTGACTGTATTGGCGTTAGGACCTGGTCAAACT-CTTCTTATCCTCA
* * * * *
1991199 TTTGACTCTATTAGCATTAGGACCTAGTCAAACTCTT-TTCA-CCTTCG
1 TTTGACTGTATTGGCGTTAGGACCTGGTCAAACTCTTCTT-ATCC-TCA
* * *
1991246 TTTGACTGTATTAGTGTTAGGACCTGGTCAAACTCTT-TTCATACTCA
1 TTTGACTGTATTGGCGTTAGGACCTGGTCAAACTCTTCTT-ATCCTCA
* ** * * ** *
1991293 TTTGATTGTATTGGCGTTAAAACCTGGTCAAACTTTTCTCATATTCG
1 TTTGACTGTATTGGCGTTAGGACCTGGTCAAACTCTTCTTATCCTCA
* * * * * *
1991340 TTTGAC-ATATTGGTGTTAGGGCTTGATCAAACTCTTTTTATCCTCA
1 TTTGACTGTATTGGCGTTAGGACCTGGTCAAACTCTTCTTATCCTCA
* * * * * *
1991386 TTTGACTGTATTGGCATTAAGACTTGGTCAAACTCTTATTATTCTCG
1 TTTGACTGTATTGGCGTTAGGACCTGGTCAAACTCTTCTTATCCTCA
* * *
1991433 TTTGACTATATTGGCGTTAGGACCTGGTCAAACTCTTCTCA-CATTCA
1 TTTGACTGTATTGGCGTTAGGACCTGGTCAAACTCTTCTTATC-CTCA
* * * * *
1991480 TTTGACTATATTAGCGTTAAGACCTGGTCAAATTCTTCTTATCCTCG
1 TTTGACTGTATTGGCGTTAGGACCTGGTCAAACTCTTCTTATCCTCA
* *
1991527 TTTGACTGTATTAGCGTTAGGACATGGTCAAACTCTTCTTATCCTCA
1 TTTGACTGTATTGGCGTTAGGACCTGGTCAAACTCTTCTTATCCTCA
* * * *
1991574 TTTGACTATATTGGTGTTAGGACCTGGTCAAACTCTTCTCA-CTTCA
1 TTTGACTGTATTGGCGTTAGGACCTGGTCAAACTCTTCTTATCCTCA
1991620 TTTGACTGTATTGGCGTTAGGACCT
1 TTTGACTGTATTGGCGTTAGGACCT
1991645 AGTTAAACAT
Statistics
Matches: 397, Mismatches: 86, Indels: 19
0.79 0.17 0.04
Matches are distributed among these distances:
45 1 0.00
46 95 0.24
47 298 0.75
48 3 0.01
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (47 bp):
TTTGACTGTATTGGCGTTAGGACCTGGTCAAACTCTTCTTATCCTCA
Found at i:1991436 original size:187 final size:186
Alignment explanation
Indices: 1991134--1991644 Score: 539
Period size: 187 Copynumber: 2.7 Consensus size: 186
1991124 AGGACCTAGC
* * * * * * * * *
1991134 CAAACTCTTCTTATGCTCGTTTGATTGTATTAGTGTTAGGAGC-TGGTTAAA-TACTTCTCA-CC
1 CAAATTCTTCTCATACTCGTTTGACTATATTAGCGTTAGGA-CATGATCAAACT-CTTCTTATCC
* * * * * *
1991196 TCATTTGACTCTATTAGCATTAGGACCTAGTCAAACTCTTTTCACCTTCGTTTGACTGTATTAGT
64 TCATTTGACTATATTGGCATTAGGACCTGGTCAAACTCTTTT-ATC-TCGTTTGACTGTATTGGC
* * * * *
1991261 GTTAGGACCTGGTCAAACTCTTTTCATACTCATTTGATTGTATTGGCGTTAAAACCTGGT
127 GTTAGGACCTGGTCAAACTCTTCTCACACTCATTTGACTATATTAGCGTTAAAACCTGGT
* * * * * *
1991321 CAAACTT-TTCTCATATTCGTTTGAC-ATATTGGTGTTAGGGCTTGATCAAACTCTTTTTATCCT
1 CAAA-TTCTTCTCATACTCGTTTGACTATATTAGCGTTAGGACATGATCAAACTCTTCTTATCCT
* * * *
1991384 CATTTGACTGTATTGGCATTAAGACTTGGTCAAACTCTTATTATTCTCGTTTGACTATATTGGCG
65 CATTTGACTATATTGGCATTAGGACCTGGTCAAACTCTT-TTA-TCTCGTTTGACTGTATTGGCG
* *
1991449 TTAGGACCTGGTCAAACTCTTCTCACATTCATTTGACTATATTAGCGTTAAGACCTGGT
128 TTAGGACCTGGTCAAACTCTTCTCACACTCATTTGACTATATTAGCGTTAAAACCTGGT
* * * *
1991508 CAAATTCTTCTTATCCTCGTTTGACTGTATTAGCGTTAGGACATGGTCAAACTCTTCTTATCCTC
1 CAAATTCTTCTCATACTCGTTTGACTATATTAGCGTTAGGACATGATCAAACTCTTCTTATCCTC
** * *
1991573 ATTTGACTATATTGGTGTTAGGACCTGGTCAAACTCTTCTCA-CTTCATTTGACTGTATTGGCGT
66 ATTTGACTATATTGGCATTAGGACCTGGTCAAACTCTT-TTATC-TCGTTTGACTGTATTGGCGT
1991637 TAGGACCT
129 TAGGACCT
1991645 AGTTAAACAT
Statistics
Matches: 268, Mismatches: 47, Indels: 18
0.80 0.14 0.05
Matches are distributed among these distances:
185 1 0.00
186 26 0.10
187 170 0.63
188 71 0.26
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (186 bp):
CAAATTCTTCTCATACTCGTTTGACTATATTAGCGTTAGGACATGATCAAACTCTTCTTATCCTC
ATTTGACTATATTGGCATTAGGACCTGGTCAAACTCTTTTATCTCGTTTGACTGTATTGGCGTTA
GGACCTGGTCAAACTCTTCTCACACTCATTTGACTATATTAGCGTTAAAACCTGGT
Found at i:1991557 original size:234 final size:234
Alignment explanation
Indices: 1991199--1991634 Score: 579
Period size: 234 Copynumber: 1.9 Consensus size: 234
1991189 TCTCACCTCA
* * * * * *
1991199 TTTGACTCTATTAGCATTAGGACCTAGTCAAACTCTTTTCACCTTCGTTTGACTGTATTAGTGTT
1 TTTGACTATATTAGCATTAGGACCTAGTCAAACTCTTCTCACATTCATTTGACTATATTAGCGTT
* * * * *
1991264 AGGACCTGGTCAAACTCTTTTCATACTCATTTGATTGTATTGGCGTTAAAACCTGGTCAAACTTT
66 AAGACCTGGTCAAACTCTTTTCATACTCATTTGACTGTATTAGCGTTAAAACATGGTCAAACTCT
* * * * * *
1991329 TCTCATATTCGTTTGAC-ATATTGGTGTTAGGGCTTGATCAAACTCTTTTTATCCTCATTTGACT
131 TCTCATACTCATTTGACTATATTGGTGTTAGGACCTGATCAAACTCTTCTCA-CCTCATTTGACT
1991393 GTATTGGCATTAAGACTTGGTCAAACTCTTATTATTCTCG
195 GTATTGGCATTAAGACTTGGTCAAACTCTTATTATTCTCG
* * *
1991433 TTTGACTATATTGGCGTTAGGACCTGGTCAAACTCTTCTCACATTCATTTGACTATATTAGCGTT
1 TTTGACTATATTAGCATTAGGACCTAGTCAAACTCTTCTCACATTCATTTGACTATATTAGCGTT
* * * **
1991498 AAGACCTGGTCAAATTCTTCTT-ATCCTCGTTTGACTGTATTAGCGTTAGGACATGGTCAAACTC
66 AAGACCTGGTCAAACTCTT-TTCATACTCATTTGACTGTATTAGCGTTAAAACATGGTCAAACTC
* * * *
1991562 TTCTTATCCTCATTTGACTATATTGGTGTTAGGACCTGGTCAAACTCTTCTCACTTCATTTGACT
130 TTCTCATACTCATTTGACTATATTGGTGTTAGGACCTGATCAAACTCTTCTCACCTCATTTGACT
1991627 GTATTGGC
195 GTATTGGC
1991635 GTTAGGACCT
Statistics
Matches: 171, Mismatches: 29, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
234 140 0.82
235 31 0.18
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (234 bp):
TTTGACTATATTAGCATTAGGACCTAGTCAAACTCTTCTCACATTCATTTGACTATATTAGCGTT
AAGACCTGGTCAAACTCTTTTCATACTCATTTGACTGTATTAGCGTTAAAACATGGTCAAACTCT
TCTCATACTCATTTGACTATATTGGTGTTAGGACCTGATCAAACTCTTCTCACCTCATTTGACTG
TATTGGCATTAAGACTTGGTCAAACTCTTATTATTCTCG
Found at i:1991992 original size:43 final size:43
Alignment explanation
Indices: 1991665--1993164 Score: 470
Period size: 42 Copynumber: 35.6 Consensus size: 43
1991655 TACTCATTTC
* * ** *
1991665 AGTTTGTCTGTCGACTTTGACCCTAAAGACTTTCTTACCC-TC
1 AGTTTGCCTGTCGACTTTGACCTTGGAGACTTTCTTACCCTTA
* * * * * * *
1991707 AGTCTACTTGTC-AGCTTTAACCTTGGAGAC-TACTT-CATCTCA
1 AGTTTGCCTGTCGA-CTTTGACCTTGGAGACTTTCTTAC-CCTTA
* * * * *
1991749 AGTCTACCTGTCGACTTTGACCTTGGAAACATTCTTA-CCTTC
1 AGTTTGCCTGTCGACTTTGACCTTGGAGACTTTCTTACCCTTA
* * * ** * *
1991791 AGTCTGCCTGTCGGCTTTGA-CTCTAGAGACTGCCTCATTCC--A
1 AGTTTGCCTGTCGACTTTGACCT-TGGAGACTTTCTTA-CCCTTA
* * * *
1991833 AGTTTGCCTGTCGGCTTTGACCCTAGAGACTTTATTA-CCTTCA
1 AGTTTGCCTGTCGACTTTGACCTTGGAGACTTTCTTACCCTT-A
* * * ** * * *
1991876 A-TCTGTCTGTCGACTTTAACCTTGGAGACTACCTCA-TCTCA
1 AGTTTGCCTGTCGACTTTGACCTTGGAGACTTTCTTACCCTTA
* * * * *
1991917 AGTCTGTCTATTGGCTTTGACCTTGGAGACTTTCTTACCCTTA
1 AGTTTGCCTGTCGACTTTGACCTTGGAGACTTTCTTACCCTTA
* * * * *
1991960 AGTTTGCCTATCAACTTTGACCCTCGAGACTTTCTTACCTTTA
1 AGTTTGCCTGTCGACTTTGACCTTGGAGACTTTCTTACCCTTA
* * *
1992003 A-TCTT-CCTGTCGACTTTGACCTTGGAAACTTCCTTACCCTCA
1 AGT-TTGCCTGTCGACTTTGACCTTGGAGACTTTCTTACCCTTA
* * * *
1992045 AGTCTGCCTGTCGACTTTGACCTTAGAGATTTTCTTA-CCTTC
1 AGTTTGCCTGTCGACTTTGACCTTGGAGACTTTCTTACCCTTA
* * * * * * * * *
1992087 AGTCTGCCTGTTGGCTTTAACCTTAGAGA-TTACCT-CATCTCA
1 AGTTTGCCTGTCGACTTTGACCTTGGAGACTTTCTTAC-CCTTA
* * * * *
1992129 AGTGTGTCTGTCGACTTTAACATTGGAGACTTTCTTA-CCTTC
1 AGTTTGCCTGTCGACTTTGACCTTGGAGACTTTCTTACCCTTA
* * * * *
1992171 AGTCTGCCTATC-AGCTTTGATCTTAGAGACTTTCTTACCCTCA
1 AGTTTGCCTGTCGA-CTTTGACCTTGGAGACTTTCTTACCCTTA
* ** ** * * *
1992214 AGTTTGTCTGTTAACTTTGACAGTGGAGAC-TGCTT-CATCTCA
1 AGTTTGCCTGTCGACTTTGACCTTGGAGACTTTCTTAC-CCTTA
* * * * * *
1992256 AGTCTACATGTTCG-CTTTGACCCTCGAGACTTTCTTA-CCTTT
1 AGTTTGCCTG-TCGACTTTGACCTTGGAGACTTTCTTACCCTTA
* * ** * * * ** * * *
1992298 AGTCTGTCTGTCGGTTTTAACCCTAGAGACTGCCTCA-TCTCA
1 AGTTTGCCTGTCGACTTTGACCTTGGAGACTTTCTTACCCTTA
* * * * * *
1992340 AGTCTGCCTATCGGCTTTGACATTGGAGACTTCCTTACCCTCA
1 AGTTTGCCTGTCGACTTTGACCTTGGAGACTTTCTTACCCTTA
* * * * * * * *
1992383 AATCTGTCTGTTGACTTTGATCTTAGAAACTTTCTTA-CCTTT
1 AGTTTGCCTGTCGACTTTGACCTTGGAGACTTTCTTACCCTTA
* * * * * * *
1992425 AGTCTACCTATCGACTTTGACCTTGGAGA-TTGCCT-CATCTCA
1 AGTTTGCCTGTCGACTTTGACCTTGGAGACTTTCTTAC-CCTTA
* * ** * *
1992467 AGTCTGCCTATCGGTTTTGACCTTGGAGA-TTTTTCTA-CCTTC
1 AGTTTGCCTGTCGACTTTGACCTTGGAGACTTTCT-TACCCTTA
* * * ** * *
1992509 AGTCTGCCTGTC-AGCTTTGACCCTAGAGACTGCCTTA-TCTCA
1 AGTTTGCCTGTCGA-CTTTGACCTTGGAGACTTTCTTACCCTTA
* * * * ** *
1992551 AGTATGCTTGTCGGCTTTAACCTTGGAGACTTTCTTACTATTT
1 AGTTTGCCTGTCGACTTTGACCTTGGAGACTTTCTTACCCTTA
* * * * * *
1992594 TGTCTGCCTGTCGGCTTTGACTTTAGAGACTTT-TCTA-CCTCA
1 AGTTTGCCTGTCGACTTTGACCTTGGAGACTTTCT-TACCCTTA
* ** * *
1992636 AGTCTGTTTGTCGGCTTTGACCTTGAAGACTTTCTTA-CCTTA
1 AGTTTGCCTGTCGACTTTGACCTTGGAGACTTTCTTACCCTTA
* * * * * * *
1992678 AGTCTGCTTGTCGGCTTTGACCTTGGAGA-TTGCCT-CATCTCA
1 AGTTTGCCTGTCGACTTTGACCTTGGAGACTTTCTTAC-CCTTA
* * * * * *
1992720 AGTCTGCTTGTCGACTTTGACCTTGGAAATTTTCATA-CCTTC
1 AGTTTGCCTGTCGACTTTGACCTTGGAGACTTTCTTACCCTTA
* * * * * ** *
1992762 AGTCTACCTGTCGGCTTTGACCCTAGAGACTGGCTTA-TCTTA
1 AGTTTGCCTGTCGACTTTGACCTTGGAGACTTTCTTACCCTTA
* * * * * * *
1992804 AGTCTGTCTGTCGGCTATGACCTTGGAGACTTTCTT-GCTTTC
1 AGTTTGCCTGTCGACTTTGACCTTGGAGACTTTCTTACCCTTA
* * * * * * * *
1992846 AGTCTGCCTATCGACTTTAACCCTGGAGATTTTTTTA-TCTTC
1 AGTTTGCCTGTCGACTTTGACCTTGGAGACTTTCTTACCCTTA
* * * * *
1992888 AGTCTGCCTGTC-AGCTTTGACCTTGGAGAC-TGCCT-CGTCTCA
1 AGTTTGCCTGTCGA-CTTTGACCTTGGAGACTTTCTTAC-CCTTA
* * * * *
1992930 AGTTTGCTTATCGGCTTTGACCTTCGAGACTTTCTTA-CCTTC
1 AGTTTGCCTGTCGACTTTGACCTTGGAGACTTTCTTACCCTTA
* * * * * * * *
1992972 AGTCTACCCGTCGGCTTTGACCCTGGAGACTGTCTTA-TCTCA
1 AGTTTGCCTGTCGACTTTGACCTTGGAGACTTTCTTACCCTTA
* * * *
1993014 AGTCTGCCTATC-AGCTTTAACCTTGGAGAC-TTCTTTATCCTTA
1 AGTTTGCCTGTCGA-CTTTGACCTTGGAGACTTTC-TTACCCTTA
* * * *
1993057 AGTCTGTCTGTCGACTTTGACCTTAGAGATTTTCTTA-CCTTCA
1 AGTTTGCCTGTCGACTTTGACCTTGGAGACTTTCTTACCCTT-A
* *** * * * * *
1993100 A-TCTATTTGTCGGCTTTTACCTTGGAGACTTCCTCA-TCTTA
1 AGTTTGCCTGTCGACTTTGACCTTGGAGACTTTCTTACCCTTA
* *
1993141 AGTTTGTCTATCGACTTTGACCTT
1 AGTTTGCCTGTCGACTTTGACCTT
1993165 TGTAGACACC
Statistics
Matches: 1070, Mismatches: 328, Indels: 120
0.70 0.22 0.08
Matches are distributed among these distances:
40 3 0.00
41 34 0.03
42 813 0.76
43 213 0.20
44 7 0.01
ACGTcount: A:0.18, C:0.26, G:0.17, T:0.38
Consensus pattern (43 bp):
AGTTTGCCTGTCGACTTTGACCTTGGAGACTTTCTTACCCTTA
Found at i:1992006 original size:127 final size:128
Alignment explanation
Indices: 1991746--1992234 Score: 340
Period size: 127 Copynumber: 3.9 Consensus size: 128
1991736 CTACTTCATC
* * * * * * *
1991746 TCAAGTCTACCTGTCGACTTTGACCTTGGAAAC-ATTCTTACCTTC-AGTCTGCCTGTCGGCTTT
1 TCAA-TCTTCCTGTCGACTTTAACCTTGGAAACTA-CCTCACCCTCAAGTCTGCCTATCGACTTT
** * * * **
1991809 GA-CTCTAGAGACTGCCTCATTCC--AAGTTTGCCTGTCGGCTTTGACCCTAGAGACTTTATTAC
64 GACCT-TAGAGACTTTCTTA-CCCTTAAGTTTGCCTATCAACTTTGACCCTAGAGACTTTATTAC
1991871 CT
127 CT
* * * * *
1991873 TCAATCTGT-CTGTCGACTTTAACCTTGGAGACTACCTCA-TCTCAAGTCTGTCTATTGGCTTTG
1 TCAATCT-TCCTGTCGACTTTAACCTTGGAAACTACCTCACCCTCAAGTCTGCCTATCGACTTTG
* * *
1991936 ACCTTGGAGACTTTCTTACCCTTAAGTTTGCCTATCAACTTTGACCCTCGAGACTTTCTTACCT
65 ACCTTAGAGACTTTCTTACCCTTAAGTTTGCCTATCAACTTTGACCCTAGAGACTTTATTACCT
* * * * *
1992000 TTAATCTTCCTGTCGACTTTGACCTTGGAAACTTCCTTACCCTCAAGTCTGCCTGTCGACTTTGA
1 TCAATCTTCCTGTCGACTTTAACCTTGGAAACTACCTCACCCTCAAGTCTGCCTATCGACTTTGA
* * * * *** * * * *
1992065 CCTTAGAGATTTTCTTA-CCTTCAGTCTGCCTGTTGGCTTTAACCTTAGAGA--TTACCT-CAT
66 CCTTAGAGACTTTCTTACCCTTAAGTTTGCCTATCAACTTTGACCCTAGAGACTTTA-TTACCT
* * * ** * *
1992125 CTCAAGTGTGT-CTGTCGACTTTAACATTGGAGACTTTCTTACCTTC-AGTCTGCCTATC-AGCT
1 -TCAA-TCT-TCCTGTCGACTTTAACCTTGGAAACTACCTCACCCTCAAGTCTGCCTATCGA-CT
* * * * *
1992187 TTGATCTTAGAGACTTTCTTACCCTCAAGTTTGTCTGTTAACTTTGAC
62 TTGACCTTAGAGACTTTCTTACCCTTAAGTTTGCCTATCAACTTTGAC
1992235 AGTGGAGACT
Statistics
Matches: 287, Mismatches: 61, Indels: 28
0.76 0.16 0.07
Matches are distributed among these distances:
125 9 0.03
126 91 0.32
127 151 0.53
128 36 0.13
ACGTcount: A:0.19, C:0.27, G:0.16, T:0.38
Consensus pattern (128 bp):
TCAATCTTCCTGTCGACTTTAACCTTGGAAACTACCTCACCCTCAAGTCTGCCTATCGACTTTGA
CCTTAGAGACTTTCTTACCCTTAAGTTTGCCTATCAACTTTGACCCTAGAGACTTTATTACCT
Found at i:1992165 original size:169 final size:169
Alignment explanation
Indices: 1991974--1993164 Score: 797
Period size: 169 Copynumber: 7.1 Consensus size: 169
1991964 TGCCTATCAA
* * * * *
1991974 CTTTGACCCTCGAGACTTTCTTACCTTTAATCTTCCTGTCGACTTTGACCTTGGAAACTTCCTTA
1 CTTTGACCTTGGAGACTTTCTTACCTTCAATCTGCCTGTCGACTTTGACCTTGGAGACTTCCTTA
* * * *
1992039 CCCTCAAGTCTGCCTGTCGACTTTGACCTTAGAGATTTTCTTACCTTCAGTCTGCCTGTTGGCTT
66 CCCTCAAGTCTGCCTGTCGACTTTGACCTTGGAGACTTTCTTACCTTCAGTCTACCTGTCGGCTT
* * * *
1992104 TAACCTTAGAGATTACCTCATCTCAAGTGTGTCTGTCGA
131 TGACCTTAGAGATTGCCTCATCTCAAGTCTGTCTGTCGG
* * * * * * *
1992143 CTTTAACATTGGAGACTTTCTTACCTTCAGTCTGCCTATC-AGCTTTGATCTTAGAGACTTTCTT
1 CTTTGACCTTGGAGACTTTCTTACCTTCAATCTGCCTGTCGA-CTTTGACCTTGGAGACTTCCTT
* * ** ** * * *
1992207 ACCCTCAAGTTTGTCTGTTAACTTTGACAGTGGAGAC-TGCTT-CATCTCAAGTCTACATGTTC-
65 ACCCTCAAGTCTGCCTGTCGACTTTGACCTTGGAGACTTTCTTACCT-TC-AGTCTACCTG-TCG
* * * * * **
1992269 GCTTTGACCCTCGAGACTT-TCTTACCTTTAGTCTGTCTGTCGG
127 GCTTTGACCTTAGAGA-TTGCCTCATCTCAAGTCTGTCTGTCGG
* * * * ** * * * * *
1992312 TTTTAACCCTAGAGACTGCCTCATC-TCAAGTCTGCCTATCGGCTTTGACATTGGAGACTTCCTT
1 CTTTGACCTTGGAGACTTTCTTACCTTCAA-TCTGCCTGTCGACTTTGACCTTGGAGACTTCCTT
* * * * * * * * *
1992376 ACCCTCAAATCTGTCTGTTGACTTTGATCTTAGAAACTTTCTTACCTTTAGTCTACCTATCGACT
65 ACCCTCAAGTCTGCCTGTCGACTTTGACCTTGGAGACTTTCTTACCTTCAGTCTACCTGTCGGCT
* * *
1992441 TTGACCTTGGAGATTGCCTCATCTCAAGTCTGCCTATCGG
130 TTGACCTTAGAGATTGCCTCATCTCAAGTCTGTCTGTCGG
* * * * * *
1992481 TTTTGACCTTGGAGA-TTTTTCTACCTTCAGTCTGCCTGTC-AGCTTTGACCCTAGAGACTGCCT
1 CTTTGACCTTGGAGACTTTCT-TACCTTCAATCTGCCTGTCGA-CTTTGACCTTGGAGACTTCCT
* * * * * * ** *
1992544 TA-TCTCAAGTATGCTTGTCGGCTTTAACCTTGGAGACTTTCTTACTATTTTGTCTGCCTGTCGG
64 TACCCTCAAGTCTGCCTGTCGACTTTGACCTTGGAGACTTTCTTAC-CTTCAGTCTACCTGTCGG
* ** * *
1992608 CTTTGACTTTAGAGACTTTTCT-ACCTCAAGTCTGTTTGTCGG
128 CTTTGACCTTAGAGA-TTGCCTCATCTCAAGTCTGTCTGTCGG
* * *
1992650 CTTTGACCTTGAAGACTTTCTTACCTT-AAGTCTGCTTGTCGGCTTTGACCTTGGAGA-TTGCCT
1 CTTTGACCTTGGAGACTTTCTTACCTTCAA-TCTGCCTGTCGACTTTGACCTTGGAGACTT-CCT
* * * * * *
1992713 CA-TCTCAAGTCTGCTTGTCGACTTTGACCTTGGAAATTTTCATACCTTCAGTCTACCTGTCGGC
64 TACCCTCAAGTCTGCCTGTCGACTTTGACCTTGGAGACTTTCTTACCTTCAGTCTACCTGTCGGC
* * * * *
1992777 TTTGACCCTAGAGACTGGCTTATCTTAAGTCTGTCTGTCGG
129 TTTGACCTTAGAGATTGCCTCATCTCAAGTCTGTCTGTCGG
* * * * * * * * **
1992818 CTATGACCTTGGAGACTTTCTTGCTTTCAGTCTGCCTATCGACTTTAACCCTGGAGATTTTTTTA
1 CTTTGACCTTGGAGACTTTCTTACCTTCAATCTGCCTGTCGACTTTGACCTTGGAGACTTCCTTA
* * * * * * * * *
1992883 TCTTC-AGTCTGCCTGTC-AGCTTTGACCTTGGAGAC-TGCCT-CGTCTCAAGTTTGCTTATCGG
66 CCCTCAAGTCTGCCTGTCGA-CTTTGACCTTGGAGACTTTCTTACCT-TC-AGTCTACCTGTCGG
* * * * ** *
1992944 CTTTGACCTTCGAGACTT-TCTTACCTTC-AGTCTACCCGTCGG
128 CTTTGACCTTAGAGA-TTGCCTCATC-TCAAGTCTGTCTGTCGG
* * * * * *
1992986 CTTTGACCCTGGAGACTGTCTTATC-TCAAGTCTGCCTATC-AGCTTTAACCTTGGAGACTTCTT
1 CTTTGACCTTGGAGACTTTCTTACCTTCAA-TCTGCCTGTCGA-CTTTGACCTTGGAGACTTCCT
* * * * * * **
1993049 TATCCTTAAGTCTGTCTGTCGACTTTGACCTTAGAGATTTTCTTACCTTCAATCTATTTGTCGGC
64 TACCCTCAAGTCTGCCTGTCGACTTTGACCTTGGAGACTTTCTTACCTTCAGTCTACCTGTCGGC
* * * * * *
1993114 TTTTACCTTGGAGACTT-CCTCATCTTAAGTTTGTCTATCGA
129 TTTGACCTTAGAGA-TTGCCTCATCTCAAGTCTGTCTGTCGG
1993155 CTTTGACCTT
1 CTTTGACCTT
1993165 TGTAGACACC
Statistics
Matches: 777, Mismatches: 209, Indels: 72
0.73 0.20 0.07
Matches are distributed among these distances:
166 2 0.00
167 15 0.02
168 258 0.33
169 473 0.61
170 25 0.03
171 4 0.01
ACGTcount: A:0.18, C:0.26, G:0.18, T:0.39
Consensus pattern (169 bp):
CTTTGACCTTGGAGACTTTCTTACCTTCAATCTGCCTGTCGACTTTGACCTTGGAGACTTCCTTA
CCCTCAAGTCTGCCTGTCGACTTTGACCTTGGAGACTTTCTTACCTTCAGTCTACCTGTCGGCTT
TGACCTTAGAGATTGCCTCATCTCAAGTCTGTCTGTCGG
Found at i:1992698 original size:253 final size:254
Alignment explanation
Indices: 1992341--1992863 Score: 698
Period size: 253 Copynumber: 2.1 Consensus size: 254
1992331 CTCATCTCAA
* * *
1992341 GTCTGCCTATCGGCTTTGACATTGGAGACTTCCTTACCCTCAAATCTGTCTGTTGACTTTGATCT
1 GTCTGCCTATCGGCTTTGACATTAGAGACTTCCTTACCCTCAAATCTGTCTGTCGACTTTGACCT
*
1992406 TAGAAACTTTCTTACCTTTAGTCTACCTATCGACTTTGACCTTGGAGATTGCCTCATCTCAAGTC
66 TAGAAACTTTCTTACCTTAAGTCTACCTATCGACTTTGACCTTGGAGATTGCCTCATCTCAAGTC
** * *
1992471 TGCCTATCGGTTTTGACCTTGGAGATTTTTC-TACCTTCAGTCTGCCTGTCAGCTTTGACCCTAG
131 TGCCTATCGACTTTGACCTTGGA-AATTTTCATACCTTCAGTCTACCTGTCAGCTTTGACCCTAG
*
1992535 AGACTGCCTTATCTCAAGTATG-CTTGTCGGCTTTAACCTTGGAGACTTTCTTACTATTTT
195 AGACTGCCTTATCTCAAGTATGTC-TGTCGGCTATAACCTTGGAGACTTTCTTACTATTTT
* * * * * *
1992595 GTCTGCCTGTCGGCTTTGACTTTAGAGACTT-TTCTA-CCTCAAGTCTGTTTGTCGGCTTTGACC
1 GTCTGCCTATCGGCTTTGACATTAGAGACTTCCT-TACCCTCAAATCTGTCTGTCGACTTTGACC
* * * *
1992658 TT-GAAGACTTTCTTACCTTAAGTCTGCTTGTCGGCTTTGACCTTGGAGATTGCCTCATCTCAAG
65 TTAGAA-ACTTTCTTACCTTAAGTCTACCTATCGACTTTGACCTTGGAGATTGCCTCATCTCAAG
* * *
1992722 TCTGCTTGTCGACTTTGACCTTGGAAATTTTCATACCTTCAGTCTACCTGTCGGCTTTGACCCTA
129 TCTGCCTATCGACTTTGACCTTGGAAATTTTCATACCTTCAGTCTACCTGTCAGCTTTGACCCTA
* * * * * **
1992787 GAGACTGGCTTATCTTAAGTCTGTCTGTCGGCTATGACCTTGGAGACTTTCTTGCT-TTCA
194 GAGACTGCCTTATCTCAAGTATGTCTGTCGGCTATAACCTTGGAGACTTTCTTACTATTTT
*
1992847 GTCTGCCTATCGACTTT
1 GTCTGCCTATCGGCTTT
1992864 AACCCTGGAG
Statistics
Matches: 234, Mismatches: 31, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
252 26 0.11
253 177 0.76
254 31 0.13
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.39
Consensus pattern (254 bp):
GTCTGCCTATCGGCTTTGACATTAGAGACTTCCTTACCCTCAAATCTGTCTGTCGACTTTGACCT
TAGAAACTTTCTTACCTTAAGTCTACCTATCGACTTTGACCTTGGAGATTGCCTCATCTCAAGTC
TGCCTATCGACTTTGACCTTGGAAATTTTCATACCTTCAGTCTACCTGTCAGCTTTGACCCTAGA
GACTGCCTTATCTCAAGTATGTCTGTCGGCTATAACCTTGGAGACTTTCTTACTATTTT
Found at i:1992726 original size:211 final size:209
Alignment explanation
Indices: 1991713--1992708 Score: 762
Period size: 211 Copynumber: 4.7 Consensus size: 209
1991703 CCTCAGTCTA
* * * * * * * * * *
1991713 CTTGTCAGCTTTAACCTTGGAGAC-TACTTCATCTCAAGTCTACCTGTCGACTTTGACCTTGGAA
1 CTTGTCGGCTTTAACATTGGAGACTTTCTT-ACCTTAAGTCTGCCTGTCGGCTTTGATCTTAGAG
* * * * * * * *
1991777 ACATTCTTACCTTC-AGTCTGCCTGTCGGCTTTGACTCTAG-AGACTGCCTCA-TTCCAAGTTTG
65 ACTTTCTTACC-TCAAGTCTGTCTGTCGACTTTGAC-CTTGAAGACTTCCTTACCT-CAAGTCTG
* * * * * * * * *
1991839 CCTGTCGGCTTTGACCCTAGAGACTTTATTACCTTCAATCTGTCTGTCGACTTTAACCTTGGAGA
127 CCTGTCGGCTTTGACCTTGGAGA-TTTCTCACCTTCAGTCTGCCTGTCGGCTTTAACCCTAGAGA
* *
1991904 CTACCTCATCTCAAGTCTG
191 CTGCCTCATCTCAAGTATG
* * * * ** * * *
1991923 TCTAT-T-GGCTTTGACCTTGGAGACTTTCTTACCCTTAAGTTTGCCTATCAACTTTGACCCTCG
1 -CT-TGTCGGCTTTAACATTGGAGACTTTCTTA-CCTTAAGTCTGCCTGTCGGCTTTGATCTTAG
*
1991986 AGACTTTCTTACCTTTAA-TCT-TCCTGTCGACTTTGACCTTGGAA-ACTTCCTTACCCTCAAGT
63 AGACTTTCTTACC-TCAAGTCTGT-CTGTCGACTTTGACCTT-GAAGACTTCCTTA-CCTCAAGT
* * * * *
1992048 CTGCCTGTCGACTTTGACCTTAGAGATTTTCTTACCTTCAGTCTGCCTGTTGGCTTTAACCTTAG
124 CTGCCTGTCGGCTTTGACCTTGGAGA-TTTCTCACCTTCAGTCTGCCTGTCGGCTTTAACCCTAG
* * *
1992113 AGATTACCTCATCTCAAGTGTG
188 AGACTGCCTCATCTCAAGTATG
* * * *
1992135 -TCTGTCGACTTTAACATTGGAGACTTTCTTACCTTCAGTCTGCCTATCAGCTTTGATCTTAGAG
1 CT-TGTCGGCTTTAACATTGGAGACTTTCTTACCTTAAGTCTGCCTGTCGGCTTTGATCTTAGAG
* ** ** * * * *
1992199 ACTTTCTTACCCTCAAGTTTGTCTGTTAACTTTGACAGTGGAGAC-TGCTTCATCTCAAGTCTAC
65 ACTTTCTTA-CCTCAAGTCTGTCTGTCGACTTTGACCTTGAAGACTTCCTT-ACCTCAAGTCTGC
* * * * * * *
1992263 ATGTTC-GCTTTGACCCTCGAGACTTTCTTACCTTTAGTCTGTCTGTCGGTTTTAACCCTAGAGA
128 CTG-TCGGCTTTGACCTTGGAGA-TTTCTCACCTTCAGTCTGCCTGTCGGCTTTAACCCTAGAGA
*
1992327 CTGCCTCATCTCAAGTCTG
191 CTGCCTCATCTCAAGTATG
* * * * * * * * * *
1992346 CCTATCGGCTTTGACATTGGAGACTTCCTTACCCTCAAATCTGTCTGTTGACTTTGATCTTAGAA
1 CTTGTCGGCTTTAACATTGGAGACTTTCTTA-CCTTAAGTCTGCCTGTCGGCTTTGATCTTAGAG
** ** * * * *
1992411 ACTTTCTTACCTTTAGTCTACCTATCGACTTTGACCTTGGAGA-TTGCCTCATCTCAAGTCTGCC
65 ACTTTCTTACCTCAAGTCTGTCTGTCGACTTTGACCTTGAAGACTT-CCTTACCTCAAGTCTGCC
* * * * *
1992475 TATCGGTTTTGACCTTGGAGATTTTTCTACCTTCAGTCTGCCTGTCAGCTTTGACCCTAGAGACT
129 TGTCGGCTTTGACCTTGGAGATTTCTC-ACCTTCAGTCTGCCTGTCGGCTTTAACCCTAGAGACT
*
1992540 GCCTTATCTCAAGTATG
193 GCCTCATCTCAAGTATG
* * **
1992557 CTTGTCGGCTTTAACCTTGGAGACTTTCTTACTATTTTGTCTGCCTGTCGGCTTTGA-CTTTAGA
1 CTTGTCGGCTTTAACATTGGAGACTTTCTTAC-CTTAAGTCTGCCTGTCGGCTTTGATC-TTAGA
* * * *
1992621 GACTTT-TCTACCTCAAGTCTGTTTGTCGGCTTTGACCTTGAAGACTTTCTTACCTTAAGTCTGC
64 GACTTTCT-TACCTCAAGTCTGTCTGTCGACTTTGACCTTGAAGACTTCCTTACCTCAAGTCTGC
*
1992685 TTGTCGGCTTTGACCTTGGAGATT
128 CTGTCGGCTTTGACCTTGGAGATT
1992709 GCCTCATCTC
Statistics
Matches: 623, Mismatches: 135, Indels: 54
0.77 0.17 0.07
Matches are distributed among these distances:
210 30 0.05
211 427 0.69
212 164 0.26
213 2 0.00
ACGTcount: A:0.19, C:0.26, G:0.17, T:0.38
Consensus pattern (209 bp):
CTTGTCGGCTTTAACATTGGAGACTTTCTTACCTTAAGTCTGCCTGTCGGCTTTGATCTTAGAGA
CTTTCTTACCTCAAGTCTGTCTGTCGACTTTGACCTTGAAGACTTCCTTACCTCAAGTCTGCCTG
TCGGCTTTGACCTTGGAGATTTCTCACCTTCAGTCTGCCTGTCGGCTTTAACCCTAGAGACTGCC
TCATCTCAAGTATG
Found at i:1992919 original size:126 final size:126
Alignment explanation
Indices: 1991673--1993127 Score: 652
Period size: 126 Copynumber: 11.5 Consensus size: 126
1991663 TCAGTTTGTC
* * ** ** * * * *
1991673 TGTCGACTTTGACCCTAAAGACTTTCTTACCCTCAGTCTACTTGTCAGCTTTAACCTTGGAGACT
1 TGTCGGCTTTGACCTTGGAGACTTTCTTACTTTCAGTCTGCCTGTCGGCTTTGACCTTGGAGA-T
** * * * * * * *
1991738 ACTTC-ATC-TCAAGTCTACCTGTC-GACTTTGACCTTGGAAACAT-TCTTACCTTCAGTCTGCC
65 TTTTCTACCTTC-AGTCTGCCTGTCAG-CTTTGACCTTGGAGAC-TGCCTTATCTTAAGTCTGCT
* ** * * * * *
1991799 TGTCGGCTTTGA-CTCTAGAGACTGCCTCA-TTCCAAGTTTGCCTGTCGGCTTTGACCCTAGAGA
1 TGTCGGCTTTGACCT-TGGAGACTTTCTTACTTTC-AGTCTGCCTGTCGGCTTTGACCTTGGAGA
* * * * * * *
1991862 CTTTAT-TACCTTCAATCTGTCTGTC-GACTTTAACCTTGGAGACTACCTCATCTCAAGTCTGTC
64 -TTTTTCTACCTTCAGTCTGCCTGTCAG-CTTTGACCTTGGAGACTGCCTTATCTTAAGTCTG-C
1991925 T
126 T
* * * * ** * *
1991926 AT-T-GGCTTTGACCTTGGAGACTTTCTTACCCTTAAGTTTGCCTATCAACTTTGACCCTCGAGA
1 -TGTCGGCTTTGACCTTGGAGACTTTCTTA-CTTTCAGTCTGCCTGTCGGCTTTGACCTTGGAGA
* * * * * * * *
1991989 -CTTTCTTACCTTTAATCTTCCTGTC-GACTTTGACCTTGGAAACTTCCTTACCCTCAAGTCTGC
64 TTTTTC-TACCTTCAGTCTGCCTGTCAG-CTTTGACCTTGGAGACTGCCTTA-TCTTAAGTCTGC
*
1992052 C
126 T
* * * * * * *
1992053 TGTCGACTTTGACCTTAGAGATTTTCTTACCTTCAGTCTGCCTGTTGGCTTTAACCTTAGAGA-T
1 TGTCGGCTTTGACCTTGGAGACTTTCTTACTTTCAGTCTGCCTGTCGGCTTTGACCTTGGAGATT
** * * * * * ** * * *
1992117 TACCT-CATCTCAAGTGTGTCTGTC-GACTTTAACATTGGAGACTTTCTTACCTTCAGTCTGCC
66 TTTCTACCT-TC-AGTCTGCCTGTCAG-CTTTGACCTTGGAGACTGCCTTATCTTAAGTCTGCT
* * * * ** * * *** **
1992179 TATCAGCTTTGATCTTAGAGACTTTCTTACCCTCAAGTTTGTCTGTTAACTTTGACAGTGGAGAC
1 TGTCGGCTTTGACCTTGGAGACTTTCTTACTTTC-AGTCTGCCTGTCGGCTTTGACCTTGGAGA-
** * * * * * ** * *
1992244 TGCTTC-ATC-TCAAGTCTACATGTTC-GCTTTGACCCTCGAGACTTTCTTACCTTTAGTCTG-T
64 TTTTTCTACCTTC-AGTCTGCCTG-TCAGCTTTGACCTTGGAGACTGCCTTATCTTAAGTCTGCT
* * * * ** * * * *
1992305 CTGTCGGTTTTAACCCTAGAGACTGCCTCA-TCTCAAGTCTGCCTATCGGCTTTGACATTGGAGA
1 -TGTCGGCTTTGACCTTGGAGACTTTCTTACTTTC-AGTCTGCCTGTCGGCTTTGACCTTGGAGA
* * * * * * * * * ** * * *
1992369 -CTTCCTTACCCTCAAATCTGTCTGT-TGACTTTGATCTTAGAAACTTTCTTACCTTTAGTCTAC
64 TTTTTC-TACCTTC-AGTCTGCCTGTCAG-CTTTGACCTTGGAGACTGCCTTATCTTAAGTCTGC
*
1992432 C
126 T
* * * * * * *
1992433 TATCGACTTTGACCTTGGAGA-TTGCCT-CATCTCAAGTCTGCCTATCGGTTTTGACCTTGGAGA
1 TGTCGGCTTTGACCTTGGAGACTTTCTTAC-TTTC-AGTCTGCCTGTCGGCTTTGACCTTGGAGA
* * * *
1992496 TTTTTCTACCTTCAGTCTGCCTGTCAGCTTTGACCCTAGAGACTGCCTTATCTCAAGTATGCT
64 TTTTTCTACCTTCAGTCTGCCTGTCAGCTTTGACCTTGGAGACTGCCTTATCTTAAGTCTGCT
* ** * * *
1992559 TGTCGGCTTTAACCTTGGAGACTTTCTTACTATTTTGTCTGCCTGTCGGCTTTGACTTTAGAGAC
1 TGTCGGCTTTGACCTTGGAGACTTTCTTACT-TTCAGTCTGCCTGTCGGCTTTGACCTTGGAGAT
** * * ** *
1992624 TTTTCTACC-TCAAGTCTGTTTGTCGGCTTTGACCTTGAAGACTTTCTTACCTTAAGTCTGCT
65 TTTTCTACCTTC-AGTCTGCCTGTCAGCTTTGACCTTGGAGACTGCCTTATCTTAAGTCTGCT
* * * * *
1992686 TGTCGGCTTTGACCTTGGAGA-TTGCCT-CATCTCAAGTCTGCTTGTCGACTTTGACCTTGGA-A
1 TGTCGGCTTTGACCTTGGAGACTTTCTTAC-TTTC-AGTCTGCCTGTCGGCTTTGACCTTGGAGA
* * * * * *
1992748 ATTTTCATACCTTCAGTCTACCTGTCGGCTTTGACCCTAGAGACTGGCTTATCTTAAGTCTG-T
64 TTTTTC-TACCTTCAGTCTGCCTGTCAGCTTTGACCTTGGAGACTGCCTTATCTTAAGTCTGCT
* * * * * *
1992811 CTGTCGGCTATGACCTTGGAGACTTTCTTGCTTTCAGTCTGCCTATCGACTTTAACCCTGGAGAT
1 -TGTCGGCTTTGACCTTGGAGACTTTCTTACTTTCAGTCTGCCTGTCGGCTTTGACCTTGGAGAT
* * ** * *
1992876 TTTTTTATCTTCAGTCTGCCTGTCAGCTTTGACCTTGGAGACTGCCTCGTCTCAAGTTTGCT
65 TTTTCTACCTTCAGTCTGCCTGTCAGCTTTGACCTTGGAGACTGCCTTATCTTAAGTCTGCT
* * * * * * *
1992938 TATCGGCTTTGACCTTCGAGACTTTCTTACCTTCAGTCTACCCGTCGGCTTTGACCCTGGAGA-C
1 TGTCGGCTTTGACCTTGGAGACTTTCTTACTTTCAGTCTGCCTGTCGGCTTTGACCTTGGAGATT
* * * * * *
1993002 TGTCTTATC-TCAAGTCTGCCTATCAGCTTTAACCTTGGAGACTTCTTTATCCTTAAGTCTG-T
66 TTTC-TACCTTC-AGTCTGCCTGTCAGCTTTGACCTTGGAGACTGCCTTAT-CTTAAGTCTGCT
* * * * * *** *
1993064 CTGTCGACTTTGACCTTAGAGATTTTCTTACCTTCAATCTATTTGTCGGCTTTTACCTTGGAGA
1 -TGTCGGCTTTGACCTTGGAGACTTTCTTACTTTCAGTCTGCCTGTCGGCTTTGACCTTGGAGA
1993128 CTTCCTCATC
Statistics
Matches: 1014, Mismatches: 265, Indels: 99
0.74 0.19 0.07
Matches are distributed among these distances:
124 2 0.00
125 20 0.02
126 478 0.47
127 470 0.46
128 43 0.04
129 1 0.00
ACGTcount: A:0.18, C:0.26, G:0.18, T:0.38
Consensus pattern (126 bp):
TGTCGGCTTTGACCTTGGAGACTTTCTTACTTTCAGTCTGCCTGTCGGCTTTGACCTTGGAGATT
TTTCTACCTTCAGTCTGCCTGTCAGCTTTGACCTTGGAGACTGCCTTATCTTAAGTCTGCT
Found at i:1993371 original size:1 final size:1
Alignment explanation
Indices: 1993365--1993403 Score: 51
Period size: 1 Copynumber: 39.0 Consensus size: 1
1993355 AAAGTGTTTG
***
1993365 AAAAAAAAAAAAAAAATTGAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1993404 TTTAAATGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.92, C:0.00, G:0.03, T:0.05
Consensus pattern (1 bp):
A
Found at i:1993386 original size:19 final size:19
Alignment explanation
Indices: 1993362--1993399 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1993352 GATAAAGTGT
1993362 TTGAAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAAA
1993381 TTGAAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAAA
1993400 AAAATTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.05, T:0.11
Consensus pattern (19 bp):
TTGAAAAAAAAAAAAAAAA
Found at i:1993432 original size:21 final size:21
Alignment explanation
Indices: 1993408--1993464 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
1993398 AAAAAATTTA
1993408 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
1993429 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
1993450 AATGTATCGATACAT
1 AATGTATCGATACAT
1993465 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:1993544 original size:19 final size:19
Alignment explanation
Indices: 1993520--1993587 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
1993510 AATTCAACAA
1993520 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1993539 TTTGTATCGAT--ATAA--
1 TTTGTATCGATACATAAGT
1993554 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
1993571 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
1993588 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 9 0.21
15 4 0.09
17 4 0.09
19 26 0.60
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1993558 original size:32 final size:32
Alignment explanation
Indices: 1993522--1993582 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
1993512 TTCAACAATT
*
1993522 TGTATCGATACATAAGTTTTGTATCGATATAA
1 TGTATCGATACATAAGTATTGTATCGATATAA
1993554 TGTATCGATACATAAGTATTGTATCGATA
1 TGTATCGATACATAAGTATTGTATCGATA
1993583 CATAATTAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATATAA
Found at i:1993645 original size:13 final size:13
Alignment explanation
Indices: 1993627--1993652 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1993617 CATTTTTCTG
1993627 TGTATCGATACAT
1 TGTATCGATACAT
1993640 TGTATCGATACAT
1 TGTATCGATACAT
1993653 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1993649 original size:33 final size:33
Alignment explanation
Indices: 1993607--1993673 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1993597 GCCAAGGAAA
***
1993607 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
1993640 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
1993673 T
1 T
1993674 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:1996298 original size:52 final size:50
Alignment explanation
Indices: 1996129--1996298 Score: 173
Period size: 52 Copynumber: 3.3 Consensus size: 50
1996119 TTATTTTCGA
* *
1996129 GGGGATACTCCAACTCCGATTTTATCGTT-AAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACTCTGATTTTAT--TTCAAAACACCAATTTTT-CACAATC
* * * **
1996181 GGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATC
1 GGGGATACTCCAACT-CTGATTTTA-TTTCAAAACACCAATTTTTC-ACAATC
*
1996233 GGGGATACTCCAACTCTGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACTCTGATTTTATTT-C-AAAACACCAATTTTTCACAATC
*
1996285 GAGGATACTCCAAC
1 GGGGATACTCCAAC
1996299 CTCGTTATTT
Statistics
Matches: 97, Mismatches: 14, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
51 7 0.07
52 75 0.77
53 15 0.15
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (50 bp):
GGGGATACTCCAACTCTGATTTTATTTCAAAACACCAATTTTTCACAATC
Found at i:1996318 original size:28 final size:28
Alignment explanation
Indices: 1996282--1996358 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
1996272 ATTTTTCACA
* * *
1996282 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
1996310 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
1996338 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
1996359 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:1996432 original size:28 final size:28
Alignment explanation
Indices: 1996392--1996445 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
1996382 TCTCATAATT
1996392 AGGGATACTCCAACCCCG-TTATTTTCGA
1 AGGGATACTCCAACCCCGATT-TTTTCGA
*
1996420 AGGGATACTCCAATCCCGATTTTTTC
1 AGGGATACTCCAACCCCGATTTTTTC
1996446 TAATCATCGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 22 0.92
29 2 0.08
ACGTcount: A:0.24, C:0.28, G:0.17, T:0.31
Consensus pattern (28 bp):
AGGGATACTCCAACCCCGATTTTTTCGA
Found at i:1996491 original size:76 final size:78
Alignment explanation
Indices: 1996312--1996513 Score: 223
Period size: 76 Copynumber: 2.6 Consensus size: 78
1996302 GTTATTTCAT
* * * *
1996312 CGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCC-GATTTATTCCCAAAATAT
* * *
1996377 TGATTTCTCATAAT
65 CGATTTCTCACAAC
** * * *
1996391 TAGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAATCCCGATTT-TT-TC-TAATCAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGATTTATTCCCAAAAT-AT
1996453 CGATTTCTCACAAC
65 CGATTTCTCACAAC
* *
1996467 CGGGGATACTCCAGCCCCGTTATTTTC-AAGGGAACACTCCAACCCCG
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGG-ATACTCCAACCCCG
1996514 TTATTATCTC
Statistics
Matches: 104, Mismatches: 17, Indels: 7
0.81 0.13 0.05
Matches are distributed among these distances:
75 8 0.08
76 50 0.48
77 2 0.02
78 4 0.04
79 40 0.38
ACGTcount: A:0.25, C:0.31, G:0.16, T:0.28
Consensus pattern (78 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGATTTATTCCCAAAATATC
GATTTCTCACAAC
Done.