Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 76 of 185
Found at i:23394690 original size:20 final size:20
Alignment explanation
Indices: 23394644--23394690 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
23394634 AGCTCGTTTC
*
23394644 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
23394664 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
23394684 CAGCTCA
1 CAGCTCA
23394691 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:23397319 original size:18 final size:18
Alignment explanation
Indices: 23397293--23397333 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
23397283 AAATTGAAAG
*
23397293 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
*
23397311 AAAAGAAAAAGAAATCGA
1 AAAAGAAAAAGAAAACGA
23397329 AAAAG
1 AAAAG
23397334 TGAGAGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.76, C:0.07, G:0.15, T:0.02
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:23397361 original size:15 final size:15
Alignment explanation
Indices: 23397338--23397380 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
23397328 AAAAAGTGAG
23397338 AGAAAAAGAAAATGA
1 AGAAAAAGAAAATGA
* *
23397353 AGAACAAGAAATTGA
1 AGAAAAAGAAAATGA
*
23397368 AAAAGAAAGAAAA
1 AGAA-AAAGAAAA
23397381 GACAATGAGT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.72, C:0.02, G:0.19, T:0.07
Consensus pattern (15 bp):
AGAAAAAGAAAATGA
Found at i:23397375 original size:6 final size:6
Alignment explanation
Indices: 23397289--23397349 Score: 52
Period size: 6 Copynumber: 10.3 Consensus size: 6
23397279 AAAGAAATTG
* * ** **
23397289 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATCGAA AAAGTG
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
*
23397336 AGAGAA AAAGAA AA
1 AAAGAA AAAGAA AA
23397350 TGAAGAACAA
Statistics
Matches: 41, Mismatches: 14, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
5 3 0.07
6 38 0.93
ACGTcount: A:0.74, C:0.05, G:0.18, T:0.03
Consensus pattern (6 bp):
AAAGAA
Found at i:23399090 original size:20 final size:20
Alignment explanation
Indices: 23399044--23399090 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
23399034 AGCTCGTTTC
*
23399044 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
23399064 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
23399084 CAGCTCA
1 CAGCTCA
23399091 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:23403515 original size:20 final size:20
Alignment explanation
Indices: 23403492--23403545 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
23403482 AGTTTTTCCC
*
23403492 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
23403512 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
23403532 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
23403546 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:23403527 original size:30 final size:30
Alignment explanation
Indices: 23403492--23403565 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
23403482 AGTTTTTCCC
23403492 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
23403522 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
23403552 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
23403566 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:23403555 original size:20 final size:20
Alignment explanation
Indices: 23403492--23403556 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
23403482 AGTTTTTCCC
* * * *
23403492 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
23403512 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
23403531 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
23403552 AGCTC
1 AGCTC
23403557 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:23405220 original size:12 final size:11
Alignment explanation
Indices: 23405156--23405249 Score: 53
Period size: 11 Copynumber: 7.6 Consensus size: 11
23405146 TTGGAGTAAC
*
23405156 AAAAAAATCAA
1 AAAAAAATGAA
23405167 AAAAAAATTCGAA
1 AAAAAAA-T-GAA
23405180 AAAAAAATTGATTGA
1 AAAAAAA-TGA---A
*
23405195 AAAAAAATTCAA
1 AAAAAAA-TGAA
*
23405207 AAAAAAGTGAA
1 AAAAAAATGAA
*
23405218 AAAAAATTGAGCA
1 AAAAAAATGA--A
*
23405231 AAAAAAAAGAA
1 AAAAAAATGAA
23405242 AAGAAAAA
1 AA-AAAAA
23405250 AAAAGGTGAG
Statistics
Matches: 68, Mismatches: 7, Indels: 15
0.76 0.08 0.17
Matches are distributed among these distances:
11 22 0.32
12 15 0.22
13 20 0.29
15 11 0.16
ACGTcount: A:0.73, C:0.04, G:0.10, T:0.13
Consensus pattern (11 bp):
AAAAAAATGAA
Found at i:23405235 original size:37 final size:39
Alignment explanation
Indices: 23405156--23405238 Score: 102
Period size: 37 Copynumber: 2.2 Consensus size: 39
23405146 TTGGAGTAAC
*
23405156 AAAAAAATCAAAAAAAAATTCGAAAAAAAAATTGATTG-AA
1 AAAAAAATCAAAAAAAAAGTCGAAAAAAAAATTGA--GCAA
*
23405196 AAAAAATTC-AAAAAAAAGT-G-AAAAAAAATTGAGCAA
1 AAAAAAATCAAAAAAAAAGTCGAAAAAAAAATTGAGCAA
23405232 AAAAAAA
1 AAAAAAA
23405239 GAAAAGAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
35 1 0.03
36 8 0.21
37 12 0.31
38 1 0.03
39 9 0.23
40 8 0.21
ACGTcount: A:0.72, C:0.05, G:0.08, T:0.14
Consensus pattern (39 bp):
AAAAAAATCAAAAAAAAAGTCGAAAAAAAAATTGAGCAA
Found at i:23405236 original size:13 final size:11
Alignment explanation
Indices: 23405190--23405227 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
23405180 AAAAAAATTG
23405190 ATTGAAAAAAA
1 ATTGAAAAAAA
*
23405201 ATTCAAAAAAA
1 ATTGAAAAAAA
*
23405212 AGTGAAAAAAA
1 ATTGAAAAAAA
23405223 ATTGA
1 ATTGA
23405228 GCAAAAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.68, C:0.03, G:0.11, T:0.18
Consensus pattern (11 bp):
ATTGAAAAAAA
Found at i:23406213 original size:15 final size:16
Alignment explanation
Indices: 23406193--23406224 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
23406183 AGAAAATGAA
23406193 AAAGAAAAAGAA-ATG
1 AAAGAAAAAGAAGATG
23406208 AAAGAAAAAGAAGATG
1 AAAGAAAAAGAAGATG
23406224 A
1 A
23406225 GTGTGAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (16 bp):
AAAGAAAAAGAAGATG
Found at i:23406339 original size:17 final size:18
Alignment explanation
Indices: 23406307--23406340 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
23406297 AAAAGAGAGT
*
23406307 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
23406325 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
23406341 GGAGTGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.03, G:0.35, T:0.09
Consensus pattern (18 bp):
GAGAGTGAAGGAAGAAAC
Found at i:23407621 original size:10 final size:10
Alignment explanation
Indices: 23407606--23407670 Score: 51
Period size: 10 Copynumber: 6.5 Consensus size: 10
23407596 AGTTTTTCCC
23407606 AGCTCAATTT
1 AGCTCAATTT
** *
23407616 AGCTCACGTG
1 AGCTCAATTT
*
23407626 AGCTTAATTT
1 AGCTCAATTT
*
23407636 AGCTC-GTTT
1 AGCTCAATTT
23407645 GAGCTCAATTT
1 -AGCTCAATTT
* *
23407656 AGCTTACTTT
1 AGCTCAATTT
23407666 AGCTC
1 AGCTC
23407671 GTTTGAGCTT
Statistics
Matches: 40, Mismatches: 13, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
9 3 0.08
10 34 0.85
11 3 0.08
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (10 bp):
AGCTCAATTT
Found at i:23407629 original size:20 final size:20
Alignment explanation
Indices: 23407606--23407659 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
23407596 AGTTTTTCCC
23407606 AGCTCAATTTAGCTCACGTG
1 AGCTCAATTTAGCTCACGTG
* ***
23407626 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACGTG
23407646 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
23407660 TACTTTAGCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACGTG
Found at i:23407650 original size:30 final size:30
Alignment explanation
Indices: 23407616--23407679 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
23407606 AGCTCAATTT
*
23407616 AGCTCACGTGAGCTTAATTTAGCTCGTTTG
1 AGCTCAAGTGAGCTTAATTTAGCTCGTTTG
* * *
23407646 AGCTCAATTTAGCTTACTTTAGCTCGTTTG
1 AGCTCAAGTGAGCTTAATTTAGCTCGTTTG
23407676 AGCT
1 AGCT
23407680 TGGCTTAAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.39
Consensus pattern (30 bp):
AGCTCAAGTGAGCTTAATTTAGCTCGTTTG
Found at i:23407669 original size:20 final size:20
Alignment explanation
Indices: 23407606--23407670 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
23407596 AGTTTTTCCC
* * *
23407606 AGCTCAATTTAGCTCACGTG
1 AGCTCAATTTAGCTTACTTT
*
23407626 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
23407645 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
23407666 AGCTC
1 AGCTC
23407671 GTTTGAGCTT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 29 0.81
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:23421239 original size:19 final size:18
Alignment explanation
Indices: 23421203--23421242 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
23421193 TTTCCACTCG
*
23421203 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
23421221 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
23421240 TTT
1 TTT
23421243 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:23422317 original size:15 final size:15
Alignment explanation
Indices: 23422297--23422336 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
23422287 TAGCTTCTTC
23422297 TTTTTTTTCACGAAA
1 TTTTTTTTCACGAAA
*
23422312 TTTTTTTTCACGAAT
1 TTTTTTTTCACGAAA
23422327 TTTTTTTTCA
1 TTTTTTTTCA
23422337 ACTTGATATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.20, C:0.12, G:0.05, T:0.62
Consensus pattern (15 bp):
TTTTTTTTCACGAAA
Found at i:23422391 original size:12 final size:12
Alignment explanation
Indices: 23422374--23422422 Score: 80
Period size: 12 Copynumber: 3.9 Consensus size: 12
23422364 ATGGAAACCA
23422374 AATTTTTTTTTG
1 AATTTTTTTTTG
23422386 AATTTTTTTTTG
1 AATTTTTTTTTG
23422398 AATTTTTTTTTTTG
1 AA--TTTTTTTTTG
23422412 AATTTTTTTTT
1 AATTTTTTTTT
23422423 CGAGTTGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
12 23 0.66
14 12 0.34
ACGTcount: A:0.16, C:0.00, G:0.06, T:0.78
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:23422395 original size:14 final size:14
Alignment explanation
Indices: 23422376--23422422 Score: 80
Period size: 14 Copynumber: 3.5 Consensus size: 14
23422366 GGAAACCAAA
23422376 TTTTTTTTTGAA--
1 TTTTTTTTTGAATT
23422388 TTTTTTTTTGAATT
1 TTTTTTTTTGAATT
23422402 TTTTTTTTTGAATT
1 TTTTTTTTTGAATT
23422416 TTTTTTT
1 TTTTTTT
23422423 CGAGTTGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.36
14 21 0.64
ACGTcount: A:0.13, C:0.00, G:0.06, T:0.81
Consensus pattern (14 bp):
TTTTTTTTTGAATT
Found at i:23422433 original size:26 final size:26
Alignment explanation
Indices: 23422378--23422435 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
23422368 AAACCAAATT
* *
23422378 TTTTTTTGAATTTTTTTTTGAATTTT
1 TTTTTTTGAATTTTTTTTTGAAGTTG
23422404 TTTTTTTGAATTTTTTTTTCG-AGTTG
1 TTTTTTTGAATTTTTTTTT-GAAGTTG
23422430 TTTTTT
1 TTTTTT
23422436 CGAGAAACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 28 0.97
27 1 0.03
ACGTcount: A:0.12, C:0.02, G:0.10, T:0.76
Consensus pattern (26 bp):
TTTTTTTGAATTTTTTTTTGAAGTTG
Found at i:23432521 original size:21 final size:23
Alignment explanation
Indices: 23432476--23432522 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
23432466 TCACCTGCAA
* *
23432476 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
23432499 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
23432520 TAA
1 TAA
23432523 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:23434474 original size:14 final size:13
Alignment explanation
Indices: 23434439--23434464 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
23434429 CGTAGCTTCA
23434439 AAAAAAAAAGGTT
1 AAAAAAAAAGGTT
23434452 AAAAAAAAAGGTT
1 AAAAAAAAAGGTT
23434465 TCGAAAAAAA
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:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (13 bp):
AAAAAAAAAGGTT
Found at i:23434484 original size:15 final size:14
Alignment explanation
Indices: 23434465--23434520 Score: 53
Period size: 14 Copynumber: 4.1 Consensus size: 14
23434455 AAAAAAGGTT
23434465 TCGAAAAAAAAAAA
1 TCGAAAAAAAAAAA
*
23434479 TCCGAAAAAAAAGAA
1 T-CGAAAAAAAAAAA
*
23434494 --GGAAAAAAAAAA
1 TCGAAAAAAAAAAA
* *
23434506 TTGCAAAAAAAAAA
1 TCGAAAAAAAAAAA
23434520 T
1 T
23434521 TGCATACGGT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
12 10 0.29
14 13 0.37
15 12 0.34
ACGTcount: A:0.73, C:0.07, G:0.11, T:0.09
Consensus pattern (14 bp):
TCGAAAAAAAAAAA
Found at i:23434521 original size:14 final size:14
Alignment explanation
Indices: 23434496--23434524 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
23434486 AAAAAGAAGG
23434496 AAAAAAAAAATTGC
1 AAAAAAAAAATTGC
23434510 AAAAAAAAAATTGC
1 AAAAAAAAAATTGC
23434524 A
1 A
23434525 TACGGTCTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.72, C:0.07, G:0.07, T:0.14
Consensus pattern (14 bp):
AAAAAAAAAATTGC
Found at i:23435279 original size:15 final size:15
Alignment explanation
Indices: 23435247--23435280 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
23435237 GTTCAACGAA
*
23435247 GAGGCCAACGCAACC
1 GAGGCCAACGAAACC
*
23435262 GAGGCCAACGAAATC
1 GAGGCCAACGAAACC
23435277 GAGG
1 GAGG
23435281 GAGGTTCGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.32, T:0.03
Consensus pattern (15 bp):
GAGGCCAACGAAACC
Found at i:23444245 original size:23 final size:22
Alignment explanation
Indices: 23444193--23444245 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
23444183 TCCACGTCTT
*
23444193 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
23444215 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
23444238 TTTCTTTT
1 TTTCTTTT
23444246 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:23449392 original size:30 final size:30
Alignment explanation
Indices: 23449330--23449393 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
23449320 ACTTAAGCCA
*
23449330 AGCTCAAACGAGCTAAAGTAAGCTAAATTG
1 AGCTCAAACGAGCTAAAGTAAGCTAAAGTG
* * *
23449360 AGCTCAAACGAGCTAAATTAAGCTCACGTG
1 AGCTCAAACGAGCTAAAGTAAGCTAAAGTG
23449390 AGCT
1 AGCT
23449394 AATTCGAGCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.20
Consensus pattern (30 bp):
AGCTCAAACGAGCTAAAGTAAGCTAAAGTG
Found at i:23451216 original size:32 final size:32
Alignment explanation
Indices: 23451179--23451240 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
23451169 GATTACTCAC
23451179 TTCACTCG-TTTCTTTTACAAACTCTCTTTCTT
1 TTCACTCGATTTCTTTT-CAAACTCTCTTTCTT
* *
23451211 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAACTCTCTTTC
23451241 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 19 0.70
33 8 0.30
ACGTcount: A:0.15, C:0.27, G:0.05, T:0.53
Consensus pattern (32 bp):
TTCACTCGATTTCTTTTCAAACTCTCTTTCTT
Found at i:23451267 original size:21 final size:21
Alignment explanation
Indices: 23451238--23451293 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
23451228 CAAGCTCTCT
*
23451238 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
23451259 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
23451280 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
23451294 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:23451286 original size:14 final size:14
Alignment explanation
Indices: 23451237--23451293 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
23451227 TCAAGCTCTC
23451237 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
23451250 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
23451264 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
23451278 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
23451292 TT
1 TT
23451294 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:23451327 original size:24 final size:25
Alignment explanation
Indices: 23451257--23451337 Score: 69
Period size: 24 Copynumber: 3.2 Consensus size: 25
23451247 TTTTTTCGCT
*
23451257 TTTTCTTTTTCAATTTTCTTTTCTTCA
1 TTTTCTTTTTCAA-TCTC-TTTCTTCA
** *
23451284 TTTTCTTTTTCTCTCACTTT-TTCGA
1 TTTTCTTTTTCAATCTCTTTCTTC-A
*
23451309 -TTTCTTTTTCAATCTCTTTC-TCC
1 TTTTCTTTTTCAATCTCTTTCTTCA
23451332 TTTTCT
1 TTTTCT
23451338 CGCTCAATGG
Statistics
Matches: 43, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
24 26 0.60
25 4 0.09
26 2 0.05
27 11 0.26
ACGTcount: A:0.09, C:0.23, G:0.01, T:0.67
Consensus pattern (25 bp):
TTTTCTTTTTCAATCTCTTTCTTCA
Found at i:23452401 original size:11 final size:11
Alignment explanation
Indices: 23452383--23452421 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
23452373 TTTTTTTTGC
23452383 TCAATTTTTTT
1 TCAATTTTTTT
*
23452394 TCACTTTTTTT
1 TCAATTTTTTT
*
23452405 TGAATTTTTTTT
1 TCAA-TTTTTTT
23452417 TCAAT
1 TCAAT
23452422 CAAATTTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.18, C:0.10, G:0.03, T:0.69
Consensus pattern (11 bp):
TCAATTTTTTT
Found at i:23452401 original size:32 final size:31
Alignment explanation
Indices: 23452340--23452405 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 31
23452330 TTAAACTTGA
* *
23452340 TTTTTTTTTGCTCACCTTTTTTTTTCTTTTCT
1 TTTTTTTTTGCTCACATTTTTTTTACTTTT-T
23452372 TTTTTTTTTGCTCA-ATTTTTTTTCACTTTTT
1 TTTTTTTTTGCTCACATTTTTTTT-ACTTTTT
23452403 TTT
1 TTT
23452406 GAATTTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
31 12 0.39
32 19 0.61
ACGTcount: A:0.06, C:0.15, G:0.03, T:0.76
Consensus pattern (31 bp):
TTTTTTTTTGCTCACATTTTTTTTACTTTTT
Found at i:23455144 original size:15 final size:15
Alignment explanation
Indices: 23455124--23455162 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
23455114 CTTCTTCTTC
*
23455124 TTTTTTTCACGAATT
1 TTTTTTTCACGAAAT
23455139 TTTTTTTCACGAAAT
1 TTTTTTTCACGAAAT
23455154 TTTTTTTCA
1 TTTTTTTCA
23455163 ACTTGATATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.05, T:0.62
Consensus pattern (15 bp):
TTTTTTTCACGAAAT
Found at i:23455215 original size:11 final size:11
Alignment explanation
Indices: 23455199--23455245 Score: 76
Period size: 11 Copynumber: 4.2 Consensus size: 11
23455189 AAAGGAAACC
23455199 AATTTTTTTTG
1 AATTTTTTTTG
*
23455210 AATTTTTATTG
1 AATTTTTTTTG
23455221 AATTTTTTTTCG
1 AATTTTTTTT-G
23455233 AATTTTTTTTG
1 AATTTTTTTTG
23455244 AA
1 AA
23455246 GAAACTACTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
11 22 0.67
12 11 0.33
ACGTcount: A:0.23, C:0.02, G:0.09, T:0.66
Consensus pattern (11 bp):
AATTTTTTTTG
Found at i:23455235 original size:23 final size:22
Alignment explanation
Indices: 23455199--23455245 Score: 76
Period size: 23 Copynumber: 2.1 Consensus size: 22
23455189 AAAGGAAACC
23455199 AATTTTTTTTGAATTTTTATTG
1 AATTTTTTTTGAATTTTTATTG
*
23455221 AATTTTTTTTCGAATTTTTTTTG
1 AATTTTTTTT-GAATTTTTATTG
23455244 AA
1 AA
23455246 GAAACTACTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.23, C:0.02, G:0.09, T:0.66
Consensus pattern (22 bp):
AATTTTTTTTGAATTTTTATTG
Found at i:23457401 original size:18 final size:18
Alignment explanation
Indices: 23457378--23457437 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
23457368 TCGACCTCAC
23457378 TCTTTTTTGATTTCTTTT
1 TCTTTTTTGATTTCTTTT
** *
23457396 TCTTTTTCAATCTCTTTT
1 TCTTTTTTGATTTCTTTT
23457414 TCTTTTCTTTCGATTTCTTTT
1 TC-TTT-TTT-GATTTCTTTT
23457435 TCT
1 TCT
23457438 CGCTCGTACT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
18 17 0.52
19 3 0.09
20 3 0.09
21 10 0.30
ACGTcount: A:0.07, C:0.18, G:0.03, T:0.72
Consensus pattern (18 bp):
TCTTTTTTGATTTCTTTT
Found at i:23459054 original size:12 final size:12
Alignment explanation
Indices: 23459039--23459071 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
23459029 AAAAAAAAGG
23459039 AAAAAAATTCAA
1 AAAAAAATTCAA
23459051 AAAAAAATTCAA
1 AAAAAAATTCAA
23459063 AAAAAAATT
1 AAAAAAATT
23459072 TGTATTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (12 bp):
AAAAAAATTCAA
Found at i:23460090 original size:15 final size:16
Alignment explanation
Indices: 23460070--23460099 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
23460060 AAAATGAAAA
23460070 AGAAAAAGAA-ATGAC
1 AGAAAAAGAAGATGAC
23460085 AGAAAAAGAAGATGA
1 AGAAAAAGAAGATGA
23460100 GTGTGAGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.67, C:0.03, G:0.23, T:0.07
Consensus pattern (16 bp):
AGAAAAAGAAGATGAC
Found at i:23462201 original size:16 final size:15
Alignment explanation
Indices: 23462182--23462211 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
23462172 AGTATCAATT
23462182 TTTGATTGGTGATGAC
1 TTTGATTGG-GATGAC
23462198 TTTGATTGGGATGA
1 TTTGATTGGGATGA
23462212 TGGATTGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.20, C:0.03, G:0.33, T:0.43
Consensus pattern (15 bp):
TTTGATTGGGATGAC
Found at i:23463120 original size:20 final size:20
Alignment explanation
Indices: 23463095--23463149 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
23463085 TGTGGTTCAA
*
23463095 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
23463115 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
23463135 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
23463150 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:23468226 original size:20 final size:20
Alignment explanation
Indices: 23468203--23468249 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
23468193 GGGTTAAGAT
*
23468203 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
23468223 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
23468243 TGAGCTG
1 TGAGCTG
23468250 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:23469559 original size:48 final size:48
Alignment explanation
Indices: 23469504--23469609 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 48
23469494 TTGTCTTTTC
*
23469504 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
23469552 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
23469600 TTTCTTTTTC
1 TTTCTTTTTC
23469610 CATGACACTC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.14, C:0.25, G:0.02, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:23469667 original size:18 final size:18
Alignment explanation
Indices: 23469585--23469669 Score: 55
Period size: 18 Copynumber: 4.6 Consensus size: 18
23469575 TTTTCACATC
* *
23469585 CTTTTTCAATCTCAATTT
1 CTTTTTCAATCTCACTCT
* **
23469603 CTTTTTCCATGACACTCGTTT
1 CTTTTTCAATCTCACTC---T
* * *
23469624 CTTTTACACTCTC-CTTT
1 CTTTTTCAATCTCACTCT
23469641 CTTTCTTCAATCTCACTCT
1 CTTT-TTCAATCTCACTCT
23469660 CTTTTTCAAT
1 CTTTTTCAAT
23469670 TTCTTGTTCC
Statistics
Matches: 48, Mismatches: 14, Indels: 10
0.67 0.19 0.14
Matches are distributed among these distances:
17 5 0.10
18 25 0.52
19 7 0.15
20 2 0.04
21 9 0.19
ACGTcount: A:0.16, C:0.29, G:0.02, T:0.52
Consensus pattern (18 bp):
CTTTTTCAATCTCACTCT
Found at i:23472254 original size:20 final size:20
Alignment explanation
Indices: 23472231--23472277 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
23472221 GGGTTAAGAT
*
23472231 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
23472251 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
23472271 TGAGCTG
1 TGAGCTG
23472278 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:23473586 original size:33 final size:33
Alignment explanation
Indices: 23473548--23473610 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
23473538 GATTACTCAC
23473548 TTCACTCG-TTTCTTTT-ACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
23473581 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
23473611 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.27, G:0.06, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:23473633 original size:15 final size:13
Alignment explanation
Indices: 23473607--23473663 Score: 62
Period size: 14 Copynumber: 4.2 Consensus size: 13
23473597 TCAAGCTCTC
*
23473607 TTTCAATTTCTTT
1 TTTCATTTTCTTT
23473620 TTTCACTTTT-TCTT
1 TTTCA-TTTTCT-TT
23473634 TTTCAATTTTCTTT
1 TTTC-ATTTTCTTT
23473648 TCTTCATTTTCTTT
1 T-TTCATTTTCTTT
23473662 TT
1 TT
23473664 CTCTCACTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
13 7 0.18
14 26 0.68
15 5 0.13
ACGTcount: A:0.11, C:0.18, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTCATTTTCTTT
Found at i:23473637 original size:27 final size:27
Alignment explanation
Indices: 23473607--23473732 Score: 89
Period size: 27 Copynumber: 4.6 Consensus size: 27
23473597 TCAAGCTCTC
23473607 TTTCAATTTCTTTTTTCACTTTTTCTT
1 TTTCAATTTCTTTTTTCACTTTTTCTT
23473634 TTTCAATTTTCTTTTCTTCA--TTTTCTT
1 TTTCAA-TTTCTTTT-TTCACTTTTTCTT
** ** *
23473661 TTTCTCTCACTTTTTTGATTTCTTTTTCTT
1 TTTCAATTTCTTTTTTCA---CTTTTTCTT
* * *
23473691 TTGCAATTTC-TTTTTC-TTTTTGTTTT
1 TTTCAATTTCTTTTTTCACTTTT-TCTT
23473717 CTTTCAATTTCTTTTT
1 -TTTCAATTTCTTTTT
23473733 CAATCTCTTT
Statistics
Matches: 75, Mismatches: 14, Indels: 19
0.69 0.13 0.18
Matches are distributed among these distances:
25 7 0.09
26 9 0.12
27 26 0.35
28 12 0.16
29 9 0.12
30 12 0.16
ACGTcount: A:0.10, C:0.17, G:0.02, T:0.71
Consensus pattern (27 bp):
TTTCAATTTCTTTTTTCACTTTTTCTT
Found at i:23473691 original size:18 final size:18
Alignment explanation
Indices: 23473670--23473720 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
23473660 TTTTCTCTCA
23473670 CTTTTTTGATTTCTTTTT
1 CTTTTTTGATTTCTTTTT
***
23473688 CTTTTGCAATTTCTTTTT
1 CTTTTTTGATTTCTTTTT
*
23473706 C-TTTTTGTTTTCTTT
1 CTTTTTTGATTTCTTT
23473721 CAATTTCTTT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
17 10 0.38
18 16 0.62
ACGTcount: A:0.06, C:0.14, G:0.06, T:0.75
Consensus pattern (18 bp):
CTTTTTTGATTTCTTTTT
Found at i:23473733 original size:6 final size:6
Alignment explanation
Indices: 23473625--23473720 Score: 52
Period size: 6 Copynumber: 15.7 Consensus size: 6
23473615 TCTTTTTTCA
* * * **
23473625 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
* * ** *
23473676 -TGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT -GTTTT CTTT
1 CT-TTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTT
23473721 CAATTTCTTT
Statistics
Matches: 64, Mismatches: 21, Indels: 10
0.67 0.22 0.11
Matches are distributed among these distances:
5 5 0.08
6 46 0.72
7 10 0.16
8 3 0.05
ACGTcount: A:0.07, C:0.18, G:0.03, T:0.72
Consensus pattern (6 bp):
CTTTTT
Found at i:23474774 original size:15 final size:15
Alignment explanation
Indices: 23474756--23474806 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
23474746 TTTAACTTGA
23474756 TTTTTTTTTGCTCAC
1 TTTTTTTTTGCTCAC
**
23474771 TTTTTTTTT-CTTTC
1 TTTTTTTTTGCTCAC
23474785 TTTTTTTTTGCTCGA-
1 TTTTTTTTTGCTC-AC
23474800 TTTTTTT
1 TTTTTTT
23474807 CACTTTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
14 12 0.40
15 18 0.60
ACGTcount: A:0.04, C:0.14, G:0.06, T:0.76
Consensus pattern (15 bp):
TTTTTTTTTGCTCAC
Found at i:23474788 original size:29 final size:28
Alignment explanation
Indices: 23474742--23474820 Score: 88
Period size: 29 Copynumber: 2.8 Consensus size: 28
23474732 ACTTTTCATT
* *
23474742 TTTTTTTAACTTGATTTTTTTTTGCTC-A
1 TTTTTTTCACTT-TTTTTTTTTTGCTCGA
**
23474770 CTTTTTTTTTCTTTCTTTTTTTTTGCTCGA
1 -TTTTTTTCACTTT-TTTTTTTTTGCTCGA
23474800 TTTTTTTCACTTTTTTTTTTT
1 TTTTTTTCACTTTTTTTTTTT
23474821 GAATTTTTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
28 8 0.19
29 34 0.79
30 1 0.02
ACGTcount: A:0.08, C:0.13, G:0.05, T:0.75
Consensus pattern (28 bp):
TTTTTTTCACTTTTTTTTTTTTGCTCGA
Found at i:23474817 original size:14 final size:14
Alignment explanation
Indices: 23474800--23474833 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
23474790 TTTTGCTCGA
*
23474800 TTTTTTTCACTTTT
1 TTTTTTTCAATTTT
*
23474814 TTTTTTTGAATTTT
1 TTTTTTTCAATTTT
23474828 TTTTTT
1 TTTTTT
23474834 GAATTTCGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.09, C:0.06, G:0.03, T:0.82
Consensus pattern (14 bp):
TTTTTTTCAATTTT
Found at i:23474834 original size:13 final size:13
Alignment explanation
Indices: 23474811--23474839 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
23474801 TTTTTTCACT
23474811 TTTTTTTTTTGAA
1 TTTTTTTTTTGAA
23474824 TTTTTTTTTTGAA
1 TTTTTTTTTTGAA
23474837 TTT
1 TTT
23474840 CGATTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (13 bp):
TTTTTTTTTTGAA
Found at i:23476289 original size:13 final size:13
Alignment explanation
Indices: 23476253--23476290 Score: 67
Period size: 13 Copynumber: 2.8 Consensus size: 13
23476243 ACCGTATGCA
23476253 ATTTTTTTTTCTCG
1 ATTTTTTTTT-TCG
23476267 ATTTTTTTTTTCG
1 ATTTTTTTTTTCG
23476280 ATTTTTTTTTT
1 ATTTTTTTTTT
23476291 AATCTACAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 14 0.58
14 10 0.42
ACGTcount: A:0.08, C:0.08, G:0.05, T:0.79
Consensus pattern (13 bp):
ATTTTTTTTTTCG
Found at i:23484355 original size:18 final size:18
Alignment explanation
Indices: 23484334--23484368 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
23484324 TTTTTCTTTT
23484334 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
23484352 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
23484369 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:23486763 original size:10 final size:10
Alignment explanation
Indices: 23486703--23486763 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
23486693 ACCAATAAAA
23486703 TAAA-TGAGC
1 TAAATTGAGC
*
23486712 TGAATTGTAGC
1 TAAATTG-AGC
23486723 TAAATTGAGC
1 TAAATTGAGC
**
23486733 TCGATTGAGC
1 TAAATTGAGC
23486743 TGAAATT-AGC
1 T-AAATTGAGC
*
23486753 TCAATTGAGC
1 TAAATTGAGC
23486763 T
1 T
23486764 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 7 0.17
10 22 0.54
11 12 0.29
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.31
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:23486764 original size:20 final size:20
Alignment explanation
Indices: 23486704--23486764 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
23486694 CCAATAAAAT
* *
23486704 AAATGAGCTGAATTGTAGCT-
1 AAATTAGCTCAATTG-AGCTG
*
23486724 AAATTGAGCTCGATTGAGCTG
1 AAATT-AGCTCAATTGAGCTG
23486745 AAATTAGCTCAATTGAGCTG
1 AAATTAGCTCAATTGAGCTG
23486765 GTCGGAGTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 22 0.63
21 13 0.37
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (20 bp):
AAATTAGCTCAATTGAGCTG
Found at i:23487227 original size:20 final size:20
Alignment explanation
Indices: 23487202--23487248 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
23487192 AATTGAGCTT
* *
23487202 GAATGAGCTGACTTGCGCAC
1 GAATGAGCTAACTTGAGCAC
*
23487222 GAATGAGCTAACTTGAGCTC
1 GAATGAGCTAACTTGAGCAC
23487242 GAATGAG
1 GAATGAG
23487249 TTTAACCACA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.19, G:0.30, T:0.21
Consensus pattern (20 bp):
GAATGAGCTAACTTGAGCAC
Found at i:23494681 original size:39 final size:40
Alignment explanation
Indices: 23494636--23494807 Score: 222
Period size: 40 Copynumber: 4.3 Consensus size: 40
23494626 GCTCCTCGTT
* * *
23494636 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
*
23494676 C-AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
23494715 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
23494755 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCA
23494795 CAAATGCCTTCGG
1 CAAATGCCTTCGG
23494808 ATCTTAGTCC
Statistics
Matches: 119, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.29
40 80 0.67
41 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:23494736 original size:40 final size:39
Alignment explanation
Indices: 23494638--23494860 Score: 216
Period size: 40 Copynumber: 5.6 Consensus size: 39
23494628 TCCTCGTTCA
* * * *
23494638 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
23494677 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
23494716 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
23494756 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
23494796 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
23494837 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
23494861 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
39 40 0.25
40 105 0.67
41 12 0.08
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:23494820 original size:80 final size:79
Alignment explanation
Indices: 23494636--23494860 Score: 240
Period size: 80 Copynumber: 2.8 Consensus size: 79
23494626 GCTCCTCGTT
* * * * *
23494636 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGG-
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGT-ACTCGCACAAAGCCTTCGGGACTTAACCCGGA
23494700 ATTTAATAACTCGCA
65 ATTTAATAACTCGCA
* * *
23494715 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTA-CTCGCACAAA-GCCTTCGGGACTTAACCCGG
* *
23494780 AATTT-GTATCTCGCA
64 AATTTAATAACTCGCA
* * * * *
23494795 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-AC-TCGCACAAAGCCTTCGGGACTTAACCCG
23494859 GA
63 GA
23494861 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
78 1 0.01
79 39 0.32
80 69 0.57
81 13 0.11
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACTCGCACAAAGCCTTCGGGACTTAACCCGGAA
TTTAATAACTCGCA
Found at i:23494869 original size:41 final size:41
Alignment explanation
Indices: 23494792--23494869 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
23494782 TTTGTATCTC
* * *
23494792 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
23494833 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
23494870 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:23497720 original size:6 final size:6
Alignment explanation
Indices: 23497709--23497740 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
23497699 AGTTGTAAAG
23497709 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TT
23497741 ATTTATTTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTAT
Found at i:23497749 original size:18 final size:18
Alignment explanation
Indices: 23497710--23497749 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
23497700 GTTGTAAAGT
*
23497710 TTTATTTTTATTTTTATT
1 TTTATTTTTATTTTTATA
23497728 TTTATTTTTATTTATT-TA
1 TTTATTTTTATTT-TTATA
23497746 TTTA
1 TTTA
23497750 CTTAGTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTATTTTTATTTTTATA
Found at i:23500023 original size:30 final size:30
Alignment explanation
Indices: 23499989--23500085 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
23499979 TAAACTAAAA
*
23499989 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
23500019 TGAGCTGAGGGTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
23500049 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
23500078 ATGAGCTA
1 -TGAGCTA
23500086 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:23502283 original size:12 final size:12
Alignment explanation
Indices: 23502268--23502298 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
23502258 TTCTTTTTGC
23502268 TTTTCAAAGGCT
1 TTTTCAAAGGCT
23502280 TTTTCAAAGGCT
1 TTTTCAAAGGCT
23502292 TTTTCAA
1 TTTTCAA
23502299 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:23502375 original size:6 final size:6
Alignment explanation
Indices: 23502359--23502408 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
23502349 TTTCTTTTTA
*
23502359 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
23502408 T
1 T
23502409 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:23502391 original size:37 final size:37
Alignment explanation
Indices: 23502348--23502418 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
23502338 CTTGCCTCTC
23502348 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
23502385 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
23502419 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:23502419 original size:16 final size:16
Alignment explanation
Indices: 23502344--23502404 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
23502334 GCCTCTTGCC
*
23502344 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
23502360 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
23502376 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
23502392 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
23502405 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:23503361 original size:10 final size:11
Alignment explanation
Indices: 23503337--23503386 Score: 52
Period size: 10 Copynumber: 4.6 Consensus size: 11
23503327 TTAACTCGAT
23503337 TTTTTTTGTCAC
1 TTTTTTT-TCAC
23503349 TTTTTTTTC-C
1 TTTTTTTTCAC
23503359 TTTTTTTTCGA-
1 TTTTTTTTC-AC
*
23503370 TTTTTTTTGA-
1 TTTTTTTTCAC
23503380 TTTTTTT
1 TTTTTTT
23503387 GTTACTCCAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
10 18 0.51
11 10 0.29
12 7 0.20
ACGTcount: A:0.06, C:0.10, G:0.06, T:0.78
Consensus pattern (11 bp):
TTTTTTTTCAC
Found at i:23503373 original size:11 final size:11
Alignment explanation
Indices: 23503349--23503386 Score: 53
Period size: 10 Copynumber: 3.6 Consensus size: 11
23503339 TTTTTGTCAC
*
23503349 TTTTTTTTC-C
1 TTTTTTTTCGA
23503359 TTTTTTTTCGA
1 TTTTTTTTCGA
23503370 TTTTTTTT-GA
1 TTTTTTTTCGA
23503380 TTTTTTT
1 TTTTTTT
23503387 GTTACTCCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 18 0.69
11 8 0.31
ACGTcount: A:0.05, C:0.08, G:0.05, T:0.82
Consensus pattern (11 bp):
TTTTTTTTCGA
Found at i:23505102 original size:30 final size:30
Alignment explanation
Indices: 23505068--23505164 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
23505058 TAAACTAAAA
*
23505068 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
23505098 TGAGCTGAGGGTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
23505128 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
23505157 ATGAGCTA
1 -TGAGCTA
23505165 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:23506354 original size:13 final size:13
Alignment explanation
Indices: 23506336--23506360 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23506326 TGGTCATCAT
23506336 GGTGTGAACACAA
1 GGTGTGAACACAA
23506349 GGTGTGAACACA
1 GGTGTGAACACA
23506361 TGATCAATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:23522343 original size:12 final size:12
Alignment explanation
Indices: 23522326--23522356 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
23522316 GAAACCAAAT
23522326 TTTTTTTTTGAA
1 TTTTTTTTTGAA
23522338 TTTTTTTTTGAA
1 TTTTTTTTTGAA
23522350 TTTTTTT
1 TTTTTTT
23522357 GAAGAAACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.13, C:0.00, G:0.06, T:0.81
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:23523392 original size:21 final size:23
Alignment explanation
Indices: 23523348--23523394 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
23523338 TCACCTGCAA
*
23523348 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGTTTAT
23523371 TAAACACATTAAAA-CA-TTTAT
1 TAAACACATTAAAATCAGTTTAT
23523392 TAA
1 TAA
23523395 TCATAACACA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.35
22 1 0.04
23 14 0.61
ACGTcount: A:0.51, C:0.11, G:0.04, T:0.34
Consensus pattern (23 bp):
TAAACACATTAAAATCAGTTTAT
Found at i:23528761 original size:11 final size:11
Alignment explanation
Indices: 23528745--23528801 Score: 80
Period size: 11 Copynumber: 5.0 Consensus size: 11
23528735 GAAACCAAAT
23528745 TTTTTTTTGAA
1 TTTTTTTTGAA
23528756 TTTTTTTTGAA
1 TTTTTTTTGAA
23528767 TTTTTTTTTTGAA
1 --TTTTTTTTGAA
23528780 -TTTTTTTGAAA
1 TTTTTTTTG-AA
23528791 TTTTTTTTGAA
1 TTTTTTTTGAA
23528802 GAAACTACTA
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
10 8 0.19
11 15 0.36
12 8 0.19
13 11 0.26
ACGTcount: A:0.19, C:0.00, G:0.09, T:0.72
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:23528762 original size:13 final size:13
Alignment explanation
Indices: 23528744--23528786 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
23528734 GGAAACCAAA
23528744 TTTTTTTTTGAA-
1 TTTTTTTTTGAAT
23528756 -TTTTTTTTGAAT
1 TTTTTTTTTGAAT
23528768 TTTTTTTTTGAAT
1 TTTTTTTTTGAAT
23528781 TTTTTT
1 TTTTTT
23528787 GAAATTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.38
13 18 0.62
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (13 bp):
TTTTTTTTTGAAT
Found at i:23528776 original size:24 final size:23
Alignment explanation
Indices: 23528741--23528798 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
23528731 AATGGAAACC
23528741 AAATTTTTTTTTGAATTTTTTTTG
1 AAATTTTTTTTTGAA-TTTTTTTG
*
23528765 AATTTTTTTTTTGAATTTTTTTG
1 AAATTTTTTTTTGAATTTTTTTG
23528788 AAATTTTTTTT
1 AAATTTTTTTT
23528799 GAAGAAACTA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 18 0.56
24 14 0.44
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.72
Consensus pattern (23 bp):
AAATTTTTTTTTGAATTTTTTTG
Found at i:23529836 original size:21 final size:23
Alignment explanation
Indices: 23529791--23529837 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
23529781 TCACCTGCAA
* *
23529791 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
23529814 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
23529835 TAA
1 TAA
23529838 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:23535631 original size:24 final size:23
Alignment explanation
Indices: 23535606--23535650 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
23535596 TTGAGCGAGA
23535606 AAAGAACA-AAGAAAATGAAAATG
1 AAAGAA-AGAAGAAAATGAAAATG
23535629 AAAGAAATGAAGAAAATGAAAA
1 AAAGAAA-GAAGAAAATGAAAA
23535651 AGATGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 1 0.05
23 6 0.30
24 13 0.65
ACGTcount: A:0.71, C:0.02, G:0.18, T:0.09
Consensus pattern (23 bp):
AAAGAAAGAAGAAAATGAAAATG
Found at i:23535689 original size:18 final size:19
Alignment explanation
Indices: 23535668--23535708 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
23535658 AATGAGATAT
23535668 AAAAAAC-AAAAGAGAGTG
1 AAAAAACGAAAAGAGAGTG
* *
23535686 -AAAAGCGAAAAGAGATTG
1 AAAAAACGAAAAGAGAGTG
23535704 AAAAA
1 AAAAA
23535709 GAATTTGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 5 0.26
18 10 0.53
19 4 0.21
ACGTcount: A:0.66, C:0.05, G:0.22, T:0.07
Consensus pattern (19 bp):
AAAAAACGAAAAGAGAGTG
Found at i:23535718 original size:18 final size:19
Alignment explanation
Indices: 23535697--23535732 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
23535687 AAAGCGAAAA
*
23535697 GAGATTGA-AAAAGAATTT
1 GAGATTGAGAAAAAAATTT
23535715 GAGATTGAGAAAAAAATT
1 GAGATTGAGAAAAAAATT
23535733 GACACAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.53, C:0.00, G:0.22, T:0.25
Consensus pattern (19 bp):
GAGATTGAGAAAAAAATTT
Found at i:23536716 original size:21 final size:21
Alignment explanation
Indices: 23536690--23536756 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
23536680 TTGGCATTTG
23536690 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
23536711 GGAATTGGTATGAAATAGTAT
1 GGAATTGGTACGAAATGGTAT
* *
23536732 GGTATTTGGTACGAATTGGTTAT
1 GG-AATTGGTACGAAATGG-TAT
23536755 GG
1 GG
23536757 TTCAAAGAGG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 21 0.55
22 12 0.32
23 5 0.13
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.34
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:23540567 original size:13 final size:13
Alignment explanation
Indices: 23540510--23540571 Score: 63
Period size: 13 Copynumber: 4.5 Consensus size: 13
23540500 TTGGAGTAAC
23540510 AAAAAAAA-TCAA
1 AAAAAAAATTCAA
23540522 AAAAAAAATTCGAAA
1 AAAAAAAATTC--AA
*
23540537 AAAAAAATTGATTGAA
1 AAAAAAA---ATTCAA
23540553 AAAAAAAATTCAA
1 AAAAAAAATTCAA
23540566 AAAAAA
1 AAAAAA
23540572 GTGAAAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
12 8 0.19
13 13 0.31
15 9 0.21
16 9 0.21
18 3 0.07
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.15
Consensus pattern (13 bp):
AAAAAAAATTCAA
Found at i:23540580 original size:13 final size:12
Alignment explanation
Indices: 23540510--23540599 Score: 54
Period size: 12 Copynumber: 6.7 Consensus size: 12
23540500 TTGGAGTAAC
*
23540510 AAAAAAAATCAA
1 AAAAAAAATGAA
23540522 AAAAAAAATTCGAAA
1 AAAAAAAA-T-G-AA
23540537 AAAAAAATTGATTGAA
1 AAAAAAA---A-TGAA
**
23540553 AAAAAAAATTCA
1 AAAAAAAATGAA
*
23540565 AAAAAAAGTGAA
1 AAAAAAAATGAA
23540577 AAAAAAAATCGAGCA
1 AAAAAAAAT-GA--A
23540592 AAAAAAAA
1 AAAAAAAA
23540600 AAAGGGTGAC
Statistics
Matches: 62, Mismatches: 7, Indels: 15
0.74 0.08 0.18
Matches are distributed among these distances:
12 27 0.44
13 4 0.06
15 18 0.29
16 9 0.15
17 1 0.02
18 3 0.05
ACGTcount: A:0.74, C:0.06, G:0.08, T:0.12
Consensus pattern (12 bp):
AAAAAAAATGAA
Found at i:23540595 original size:24 final size:24
Alignment explanation
Indices: 23540509--23540585 Score: 75
Period size: 31 Copynumber: 3.0 Consensus size: 24
23540499 ATTGGAGTAA
*
23540509 CAAAAAAAA-TCAAAAAAAAAATT
1 CAAAAAAAAGTGAAAAAAAAAATT
23540532 CGAAAAAAAAAATTGATTGAAAAAAAAAATT
1 C---AAAAAAAA--G--TGAAAAAAAAAATT
23540563 CAAAAAAAAGTGAAAAAAAAAAT
1 CAAAAAAAAGTGAAAAAAAAAAT
23540586 CGAGCAAAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 15
0.74 0.02 0.25
Matches are distributed among these distances:
23 1 0.02
24 13 0.29
26 9 0.20
28 8 0.18
31 14 0.31
ACGTcount: A:0.74, C:0.05, G:0.06, T:0.14
Consensus pattern (24 bp):
CAAAAAAAAGTGAAAAAAAAAATT
Found at i:23540596 original size:41 final size:42
Alignment explanation
Indices: 23540522--23540601 Score: 108
Period size: 41 Copynumber: 1.9 Consensus size: 42
23540512 AAAAAATCAA
* * ***
23540522 AAAAAAAATTCGAAAAAAAAAATTGATTGAAAAAAAAAATTC
1 AAAAAAAAGTCGAAAAAAAAAATCGAGCAAAAAAAAAAATTC
23540564 AAAAAAAAGT-GAAAAAAAAAATCGAGCAAAAAAAAAAA
1 AAAAAAAAGTCGAAAAAAAAAATCGAGCAAAAAAAAAAA
23540602 AGGGTGACCA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
41 24 0.73
42 9 0.27
ACGTcount: A:0.74, C:0.05, G:0.09, T:0.12
Consensus pattern (42 bp):
AAAAAAAAGTCGAAAAAAAAAATCGAGCAAAAAAAAAAATTC
Found at i:23541537 original size:18 final size:19
Alignment explanation
Indices: 23541516--23541551 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
23541506 AGAAAAGAAA
*
23541516 ATTGAA-AAAGAAATTGAG
1 ATTGAAGAAAAAAATTGAG
23541534 ATTGAAGAAAAAAATTGA
1 ATTGAAGAAAAAAATTGA
23541552 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.58, C:0.00, G:0.19, T:0.22
Consensus pattern (19 bp):
ATTGAAGAAAAAAATTGAG
Found at i:23541570 original size:31 final size:32
Alignment explanation
Indices: 23541492--23541577 Score: 97
Period size: 31 Copynumber: 2.7 Consensus size: 32
23541482 AATAGTGAGT
* *
23541492 GAAAAAGAAAATGAAGAAAAGAAAATTGAAAAA
1 GAAAAAGAGATTGAAG-AAAGAAAATTGAAAAA
**
23541525 GAAATTGAGATTGAAGAAA-AAAATTGAAAAA
1 GAAAAAGAGATTGAAGAAAGAAAATTGAAAAA
23541556 GAAAAAGATG-TTGAAG-AAGAAA
1 GAAAAAGA-GATTGAAGAAAGAAA
23541578 CGAGAGAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
30 2 0.04
31 27 0.60
32 4 0.09
33 12 0.27
ACGTcount: A:0.65, C:0.00, G:0.21, T:0.14
Consensus pattern (32 bp):
GAAAAAGAGATTGAAGAAAGAAAATTGAAAAA
Found at i:23547170 original size:17 final size:16
Alignment explanation
Indices: 23547118--23547171 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
23547108 TCTCTTTTCA
* *
23547118 TTCTCTTTTTTGAATT
1 TTCTTTTTTTTGTATT
*
23547134 TTCTTTTTTTTATCATTT
1 TTCTTTTTTTTGT-A-TT
23547152 TTCTTTTCTTTTGTATT
1 TTCTTTT-TTTTGTATT
23547169 TTC
1 TTC
23547172 GCTCTTTTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
16 10 0.32
17 6 0.19
18 10 0.32
19 5 0.16
ACGTcount: A:0.09, C:0.13, G:0.04, T:0.74
Consensus pattern (16 bp):
TTCTTTTTTTTGTATT
Found at i:23549420 original size:13 final size:13
Alignment explanation
Indices: 23549402--23549445 Score: 63
Period size: 12 Copynumber: 3.3 Consensus size: 13
23549392 TTTTTTTCAA
23549402 TTTTTCAATTTTT
1 TTTTTCAATTTTT
23549415 TTTTTCAA-TTTT
1 TTTTTCAATTTTT
23549427 TTTTTCGAACTTTTT
1 TTTTTC-AA-TTTTT
23549442 TTTT
1 TTTT
23549446 ACGCACCTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 10 0.36
13 10 0.36
15 8 0.29
ACGTcount: A:0.14, C:0.09, G:0.02, T:0.75
Consensus pattern (13 bp):
TTTTTCAATTTTT
Found at i:23549762 original size:24 final size:23
Alignment explanation
Indices: 23549708--23549785 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 23
23549698 GGATAATTAA
**
23549708 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGAATTGGTAC
***
23549731 GTTTTGGTATTTGGGAATTGGTAC
1 GAAATGGTATTT-GGAATTGGTAC
*
23549755 GAAATGGTA--TGGAATTGGTAT
1 GAAATGGTATTTGGAATTGGTAC
*
23549776 GAAATAGTAT
1 GAAATGGTAT
23549786 GGTATTTGGT
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
21 18 0.42
22 1 0.02
23 9 0.21
24 15 0.35
ACGTcount: A:0.27, C:0.03, G:0.31, T:0.40
Consensus pattern (23 bp):
GAAATGGTATTTGGAATTGGTAC
Found at i:23549770 original size:21 final size:21
Alignment explanation
Indices: 23549744--23549810 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
23549734 TTGGTATTTG
23549744 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
23549765 GGAATTGGTATGAAATAGTAT
1 GGAATTGGTACGAAATGGTAT
* *
23549786 GGTATTTGGTACGAATTGGTTAT
1 GG-AATTGGTACGAAATGG-TAT
23549809 GG
1 GG
23549811 TTCAAAGAGG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 21 0.55
22 12 0.32
23 5 0.13
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.34
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:23555860 original size:22 final size:21
Alignment explanation
Indices: 23555827--23555868 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
23555817 TTTGAACCAT
*
23555827 TACCAATTCGTATCAACTTCCA
1 TACCAATTCGTACCAA-TTCCA
23555849 TACC-ATTACGTACCAATTCC
1 TACCAATT-CGTACCAATTCC
23555869 TAAATGCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.31, C:0.33, G:0.05, T:0.31
Consensus pattern (21 bp):
TACCAATTCGTACCAATTCCA
Found at i:23556187 original size:10 final size:10
Alignment explanation
Indices: 23556169--23556237 Score: 88
Period size: 10 Copynumber: 6.9 Consensus size: 10
23556159 AGTAGACTTG
23556169 TGAAAAAAAA
1 TGAAAAAAAA
23556179 TTGAAAAAAAA
1 -TGAAAAAAAA
23556190 T-AAAAAAAA
1 TGAAAAAAAA
*
23556199 TCAAAAAAAA
1 TGAAAAAAAA
23556209 T-AAAAAAAA
1 TGAAAAAAAA
23556218 TTGAAAAAAAA
1 -TGAAAAAAAA
*
23556229 AGAAAAAAA
1 TGAAAAAAA
23556238 TTGTATACGG
Statistics
Matches: 54, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
9 17 0.31
10 19 0.35
11 18 0.33
ACGTcount: A:0.81, C:0.01, G:0.06, T:0.12
Consensus pattern (10 bp):
TGAAAAAAAA
Found at i:23556196 original size:20 final size:20
Alignment explanation
Indices: 23556171--23556240 Score: 108
Period size: 20 Copynumber: 3.5 Consensus size: 20
23556161 TAGACTTGTG
23556171 AAAAAAAATTGAAAAAAAAT
1 AAAAAAAATTGAAAAAAAAT
*
23556191 AAAAAAAA-TCAAAAAAAAT
1 AAAAAAAATTGAAAAAAAAT
23556210 AAAAAAAATTGAAAAAAAA-
1 AAAAAAAATTGAAAAAAAAT
23556229 AGAAAAAAATTG
1 A-AAAAAAATTG
23556241 TATACGGTCT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.41
20 27 0.59
ACGTcount: A:0.80, C:0.01, G:0.06, T:0.13
Consensus pattern (20 bp):
AAAAAAAATTGAAAAAAAAT
Found at i:23559173 original size:12 final size:12
Alignment explanation
Indices: 23559143--23559173 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
23559133 ATGAGATTGT
23559143 AAAAAAA-TCGA
1 AAAAAAATTCGA
23559154 AAAAAAATTCGA
1 AAAAAAATTCGA
23559166 AAAAAAAT
1 AAAAAAAT
23559174 ATTATTTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.37
12 12 0.63
ACGTcount: A:0.74, C:0.06, G:0.06, T:0.13
Consensus pattern (12 bp):
AAAAAAATTCGA
Found at i:23571187 original size:15 final size:14
Alignment explanation
Indices: 23571151--23571195 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
23571141 TCTATTGAGC
23571151 GAGAAAAAGAAAAA
1 GAGAAAAAGAAAAA
*
23571165 GAGAAAAACAAAAA
1 GAGAAAAAGAAAAA
*
23571179 GAGTGAAAAGAAAAA
1 GAG-AAAAAGAAAAA
23571194 GA
1 GA
23571196 AAGAAACGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 16 0.59
15 11 0.41
ACGTcount: A:0.73, C:0.02, G:0.22, T:0.02
Consensus pattern (14 bp):
GAGAAAAAGAAAAA
Found at i:23571201 original size:15 final size:15
Alignment explanation
Indices: 23571151--23571201 Score: 61
Period size: 14 Copynumber: 3.5 Consensus size: 15
23571141 TCTATTGAGC
23571151 GAGA-AAAAGAAAAA
1 GAGAGAAAAGAAAAA
*
23571165 GAGA-AAAACAAAAA
1 GAGAGAAAAGAAAAA
*
23571179 GAGTGAAAAGAAAAA
1 GAGAGAAAAGAAAAA
*
23571194 GAAAGAAA
1 GAGAGAAA
23571202 CGAATGATGA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
14 16 0.52
15 15 0.48
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (15 bp):
GAGAGAAAAGAAAAA
Found at i:23574066 original size:12 final size:13
Alignment explanation
Indices: 23574049--23574083 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
23574039 TTGTAGAATC
23574049 AAAAAAAATTGA-
1 AAAAAAAATTGAG
*
23574061 AAAAAAAATCGAG
1 AAAAAAAATTGAG
23574074 AAAAAAAATT
1 AAAAAAAATT
23574084 TCATACGGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.74, C:0.03, G:0.09, T:0.14
Consensus pattern (13 bp):
AAAAAAAATTGAG
Found at i:23581491 original size:12 final size:13
Alignment explanation
Indices: 23581470--23581520 Score: 70
Period size: 13 Copynumber: 4.1 Consensus size: 13
23581460 TAAATTGTAG
23581470 ATTC-AAAAAAAA
1 ATTCGAAAAAAAA
23581482 A-TCGAAAAAAAA
1 ATTCGAAAAAAAA
*
23581494 ATTGGAAAAAAAA
1 ATTCGAAAAAAAA
*
23581507 ATTTGAAAAAAAA
1 ATTCGAAAAAAAA
23581520 A
1 A
23581521 ATTTGCATAC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
11 2 0.06
12 10 0.29
13 23 0.66
ACGTcount: A:0.73, C:0.04, G:0.08, T:0.16
Consensus pattern (13 bp):
ATTCGAAAAAAAA
Found at i:23583800 original size:17 final size:18
Alignment explanation
Indices: 23583761--23583802 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
23583751 AAGAAGAAAA
23583761 ACAAAA-AGATGAGTGAT
1 ACAAAAGAGATGAGTGAT
*
23583778 AAAAAAGAGA-GAGTGAT
1 ACAAAAGAGATGAGTGAT
*
23583795 TCAAAAGA
1 ACAAAAGA
23583803 AAATGAAATG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.57, C:0.05, G:0.24, T:0.14
Consensus pattern (18 bp):
ACAAAAGAGATGAGTGAT
Found at i:23586145 original size:14 final size:14
Alignment explanation
Indices: 23586114--23586158 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
23586104 TTCATTTCTT
*
23586114 TCTTTTTCTTTTCAC
1 TCTTTTTCTTTT-TC
*
23586129 TCTTTTTGTTTTTC
1 TCTTTTTCTTTTTC
23586143 TCTTTTTCTTTTTC
1 TCTTTTTCTTTTTC
23586157 TC
1 TC
23586159 GCTCAATAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 16 0.59
15 11 0.41
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.73
Consensus pattern (14 bp):
TCTTTTTCTTTTTC
Found at i:23587982 original size:20 final size:20
Alignment explanation
Indices: 23587957--23588011 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
23587947 TGTGGTTCAA
* *
23587957 CTCATTCGAGCTCAAGTTAG
1 CTCATTCAAGCTCAAGTCAG
23587977 CTCATTCAAGCTCAAGTCAG
1 CTCATTCAAGCTCAAGTCAG
23587997 CTCATTCAAGCTCAA
1 CTCATTCAAGCTCAA
23588012 TTTAACTCGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (20 bp):
CTCATTCAAGCTCAAGTCAG
Found at i:23592536 original size:13 final size:13
Alignment explanation
Indices: 23592518--23592542 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23592508 GTATTGATCA
23592518 TGTGTTCACACCT
1 TGTGTTCACACCT
23592531 TGTGTTCACACC
1 TGTGTTCACACC
23592543 ATGATGACCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:23596958 original size:17 final size:18
Alignment explanation
Indices: 23596919--23596960 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
23596909 AAGAAGAAAA
23596919 ACAAAA-AGATGAGTGAT
1 ACAAAAGAGATGAGTGAT
*
23596936 AAAAAAGAGA-GAGTGAT
1 ACAAAAGAGATGAGTGAT
*
23596953 TCAAAAGA
1 ACAAAAGA
23596961 AAAAGAAACG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.57, C:0.05, G:0.24, T:0.14
Consensus pattern (18 bp):
ACAAAAGAGATGAGTGAT
Found at i:23606980 original size:468 final size:468
Alignment explanation
Indices: 23606104--23607016 Score: 1603
Period size: 468 Copynumber: 2.0 Consensus size: 468
23606094 AAAGAATCAA
* *
23606104 CCAAATAGCTACTCACCACATTTGAGCAACTACCACTATCAATAATGAGTGAACATAAGTTACCT
1 CCAAATAACTACTCACCACATTCGAGCAACTACCACTATCAATAATGAGTGAACATAAGTTACCT
23606169 TTAATAAAACACCGAGAATGGAAAATATTGGCCCTTTGGCTATCATCATCTTTCATCTGAATGTT
66 TTAATAAAACACCGAGAATGGAAAATATTGGCCCTTTGGCTATCATCATCTTTCATCTGAATGTT
*
23606234 AAGGGTTCGACGAACTACAAGACATTGAAAATCAGCAAAGTCTCCTTCTCTGGGTGGTTCAACCA
131 AAGGGTTCGACGAACTACAAGACATTGAAAATCAGCAAAGTCCCCTTCTCTGGGTGGTTCAACCA
* * *
23606299 ACTCTTCGCCATTATCACTGTCATCAACATGTTCTGGCATATCTGGATCTGTTTTATCAGAGTCG
196 ACTCGTCGCCATTATCACTGTCATCAACAAGTTCTGGCATATCTGGATCTGTATTATCAGAGTCG
23606364 GAAGTATACTCACCATTATCTTTTAGAAGAAGGAATCTCGTGTTAGGGCATTCCCTACTATAATG
261 GAAGTATACTCACCATTATCTTTTAGAAGAAGGAATCTCGTGTTAGGGCATTCCCTACTATAATG
23606429 ACCACGCCCTTTGCACTTAAAACATTCAACCTCACGAGTCCTCTTCACACTCGAATCACCTAAAT
326 ACCACGCCCTTTGCACTTAAAACATTCAACCTCACGAGTCCTCTTCACACTCGAATCACCTAAAT
23606494 TGGGCTGCTTAGAAGGTGTTTGCGTTTTAGCAGGAGCCCCTTTTTTCCAATCTGACTGCTTGTTA
391 TGGGCTGCTTAGAAGGTGTTTGCGTTTTAGCAGGAGCCCCTTTTTTCCAATCTGACTGCTTGTTA
23606559 CTCAAAGAAGACT
456 CTCAAAGAAGACT
* *
23606572 CCAAATAACTACTCACTACATTCGAGCAACTCCCACTATCAATAATGAGTGAACATAAGTTACCT
1 CCAAATAACTACTCACCACATTCGAGCAACTACCACTATCAATAATGAGTGAACATAAGTTACCT
* *
23606637 TTAATAAAACACCGAGAATGGAAAATATTGGCCCTTTGGCTCTCATCATCTTTTATCTGAATGTT
66 TTAATAAAACACCGAGAATGGAAAATATTGGCCCTTTGGCTATCATCATCTTTCATCTGAATGTT
* * * *
23606702 AAGGGTTCGACGAACTACAAGGCATTGAAAATTAGCAAAGTCCCCTTC-CTTTGGTGGTTCGACC
131 AAGGGTTCGACGAACTACAAGACATTGAAAATCAGCAAAGTCCCCTTCTC-TGGGTGGTTCAACC
*
23606766 AACTCGTCGCCATTATCACTGTCATCCACAAGTTCTGGCATATCTGGATCTGTATTATCAGAGTC
195 AACTCGTCGCCATTATCACTGTCATCAACAAGTTCTGGCATATCTGGATCTGTATTATCAGAGTC
* * * *
23606831 GGAAGTGTACTCACCGTTATCTTTTAGAAGAAGTAATCTCGTGTTAGGGCATTCTCTACTATAAT
260 GGAAGTATACTCACCATTATCTTTTAGAAGAAGGAATCTCGTGTTAGGGCATTCCCTACTATAAT
* * *
23606896 GACCACGCCCTTTGCACTTAAAGCATTCAATCTCACGAGTCCTCTTCGCACTCGAATCACCTAAA
325 GACCACGCCCTTTGCACTTAAAACATTCAACCTCACGAGTCCTCTTCACACTCGAATCACCTAAA
*
23606961 TTGGGCTGCTTAGAAGGTGTTTGCGTTTTTGCAGGAGCCCCTTTTTTCCAATCTGA
390 TTGGGCTGCTTAGAAGGTGTTTGCGTTTTAGCAGGAGCCCCTTTTTTCCAATCTGA
23607017 TTGTTTACTT
Statistics
Matches: 421, Mismatches: 23, Indels: 2
0.94 0.05 0.00
Matches are distributed among these distances:
467 1 0.00
468 420 1.00
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.30
Consensus pattern (468 bp):
CCAAATAACTACTCACCACATTCGAGCAACTACCACTATCAATAATGAGTGAACATAAGTTACCT
TTAATAAAACACCGAGAATGGAAAATATTGGCCCTTTGGCTATCATCATCTTTCATCTGAATGTT
AAGGGTTCGACGAACTACAAGACATTGAAAATCAGCAAAGTCCCCTTCTCTGGGTGGTTCAACCA
ACTCGTCGCCATTATCACTGTCATCAACAAGTTCTGGCATATCTGGATCTGTATTATCAGAGTCG
GAAGTATACTCACCATTATCTTTTAGAAGAAGGAATCTCGTGTTAGGGCATTCCCTACTATAATG
ACCACGCCCTTTGCACTTAAAACATTCAACCTCACGAGTCCTCTTCACACTCGAATCACCTAAAT
TGGGCTGCTTAGAAGGTGTTTGCGTTTTAGCAGGAGCCCCTTTTTTCCAATCTGACTGCTTGTTA
CTCAAAGAAGACT
Found at i:23608455 original size:10 final size:9
Alignment explanation
Indices: 23608422--23608475 Score: 56
Period size: 9 Copynumber: 6.0 Consensus size: 9
23608412 CGCTGAATCT
*
23608422 TTTTTTTAA
1 TTTTTTTGA
23608431 TTTTTATTGA
1 TTTTT-TTGA
* *
23608441 ATTTTGT-A
1 TTTTTTTGA
23608449 TTTTTTTGA
1 TTTTTTTGA
23608458 TTTTTTTGA
1 TTTTTTTGA
*
23608467 CTTTTTTGA
1 TTTTTTTGA
23608476 CTGATTTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
8 6 0.16
9 24 0.65
10 7 0.19
ACGTcount: A:0.17, C:0.02, G:0.09, T:0.72
Consensus pattern (9 bp):
TTTTTTTGA
Found at i:23609220 original size:12 final size:12
Alignment explanation
Indices: 23609203--23609256 Score: 92
Period size: 12 Copynumber: 4.6 Consensus size: 12
23609193 TAGTTTCTCG
*
23609203 AAAAAAACTCAA
1 AAAAAAATTCAA
23609215 AAAAAAATTCAA
1 AAAAAAATTCAA
23609227 AAAAAAATTC-A
1 AAAAAAATTCAA
23609238 AAAAAAATTCAA
1 AAAAAAATTCAA
23609250 AAAAAAA
1 AAAAAAA
23609257 ACTTTTGGTT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
11 11 0.28
12 29 0.73
ACGTcount: A:0.78, C:0.09, G:0.00, T:0.13
Consensus pattern (12 bp):
AAAAAAATTCAA
Found at i:23609232 original size:23 final size:23
Alignment explanation
Indices: 23609203--23609256 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
23609193 TAGTTTCTCG
23609203 AAAAAAACTCAAAAAAAAATTCAA
1 AAAAAAACTC-AAAAAAAATTCAA
*
23609227 AAAAAAATTCAAAAAAAATTCAA
1 AAAAAAACTCAAAAAAAATTCAA
23609250 AAAAAAA
1 AAAAAAA
23609257 ACTTTTGGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 20 0.69
24 9 0.31
ACGTcount: A:0.78, C:0.09, G:0.00, T:0.13
Consensus pattern (23 bp):
AAAAAAACTCAAAAAAAATTCAA
Found at i:23609322 original size:14 final size:14
Alignment explanation
Indices: 23609303--23609344 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
23609293 TCAAGTTGTG
23609303 AAAAAAAAAATTGA
1 AAAAAAAAAATTGA
*
23609317 AAAAAAAAATTGTGA
1 AAAAAAAAAAT-TGA
*
23609332 AAAAAAAATATTG
1 AAAAAAAAAATTG
23609345 TGAAAAAAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (14 bp):
AAAAAAAAAATTGA
Found at i:23609323 original size:15 final size:15
Alignment explanation
Indices: 23609299--23609352 Score: 67
Period size: 16 Copynumber: 3.7 Consensus size: 15
23609289 GATATCAAGT
23609299 TGTG-AAAAAAAAAA
1 TGTGAAAAAAAAAAA
*
23609313 T-TGAAAAAAAAAAT
1 TGTGAAAAAAAAAAA
*
23609327 TGTGAAAAAAAAATAT
1 TGTGAAAAAAAAA-AA
23609343 TGTGAAAAAA
1 TGTGAAAAAA
23609353 GAGAGAGCTA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
13 2 0.06
14 11 0.31
15 11 0.31
16 12 0.33
ACGTcount: A:0.67, C:0.00, G:0.13, T:0.20
Consensus pattern (15 bp):
TGTGAAAAAAAAAAA
Found at i:23609335 original size:16 final size:15
Alignment explanation
Indices: 23609298--23609352 Score: 87
Period size: 13 Copynumber: 3.7 Consensus size: 15
23609288 GGATATCAAG
23609298 TTGTGAAAAAAAAAA
1 TTGTGAAAAAAAAAA
23609313 -T-TGAAAAAAAAAA
1 TTGTGAAAAAAAAAA
23609326 TTGTGAAAAAAAAATA
1 TTGTGAAAAAAAAA-A
23609342 TTGTGAAAAAA
1 TTGTGAAAAAA
23609353 GAGAGAGCTA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
13 12 0.32
14 2 0.05
15 11 0.30
16 12 0.32
ACGTcount: A:0.65, C:0.00, G:0.13, T:0.22
Consensus pattern (15 bp):
TTGTGAAAAAAAAAA
Found at i:23617914 original size:56 final size:55
Alignment explanation
Indices: 23617798--23617915 Score: 159
Period size: 55 Copynumber: 2.1 Consensus size: 55
23617788 TGCATGCTTT
* * * *
23617798 CATT-AATGCCGTCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCC
1 CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
*
23617852 CTTTAAATGCCGTTCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCA
1 CATTAAATGCCG-TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCA
23617908 CATTAAAT
1 CATTAAAT
23617916 CAGCAAGCAG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
54 3 0.05
55 28 0.51
56 24 0.44
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (55 bp):
CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
Found at i:23618996 original size:20 final size:20
Alignment explanation
Indices: 23618973--23619026 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
23618963 AGTTTTTCCC
*
23618973 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
23618993 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
23619013 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
23619027 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:23619008 original size:30 final size:30
Alignment explanation
Indices: 23618973--23619046 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
23618963 AGTTTTTCCC
23618973 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
23619003 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
23619033 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
23619047 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:23619036 original size:20 final size:20
Alignment explanation
Indices: 23618973--23619037 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
23618963 AGTTTTTCCC
* * * *
23618973 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
23618993 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
23619012 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
23619033 AGCTC
1 AGCTC
23619038 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Done.