Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 46 of 318
Found at i:17103216 original size:3 final size:3
Alignment explanation
Indices: 17103208--17103233 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
17103198 TAATGATCTG
17103208 CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CA
17103234 CCGCTAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:17114210 original size:4 final size:4
Alignment explanation
Indices: 17114201--17114225 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
17114191 AGCACAGTAT
17114201 AGTC AGTC AGTC AGTC AGTC AGTC A
1 AGTC AGTC AGTC AGTC AGTC AGTC A
17114226 AGGGATGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (4 bp):
AGTC
Found at i:17115390 original size:22 final size:22
Alignment explanation
Indices: 17115362--17115407 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
17115352 GCCAGTGGGT
17115362 CACACCACTCGCTCCTCGGTAG
1 CACACCACTCGCTCCTCGGTAG
17115384 CACACCACTCGCTCCTCGGTAG
1 CACACCACTCGCTCCTCGGTAG
17115406 CA
1 CA
17115408 AACCGACTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.20, C:0.46, G:0.17, T:0.17
Consensus pattern (22 bp):
CACACCACTCGCTCCTCGGTAG
Found at i:17116033 original size:3 final size:3
Alignment explanation
Indices: 17116025--17116060 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
17116015 TTAACCTTAT
17116025 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
17116061 ACGACAACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:17118293 original size:12 final size:12
Alignment explanation
Indices: 17118272--17118316 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
17118262 TACAAGGAAG
17118272 GATG-TGATATT
1 GATGTTGATATT
* *
17118283 GATATTGATATC
1 GATGTTGATATT
*
17118295 GATGTTGATGTT
1 GATGTTGATATT
17118307 GATGTTGATA
1 GATGTTGATA
17118317 AACAAATTAG
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
11 3 0.11
12 24 0.89
ACGTcount: A:0.27, C:0.02, G:0.27, T:0.44
Consensus pattern (12 bp):
GATGTTGATATT
Found at i:17118308 original size:24 final size:23
Alignment explanation
Indices: 17118272--17118316 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
17118262 TACAAGGAAG
17118272 GATGTGATATTGATATTGATATC
1 GATGTGATATTGATATTGATATC
* *
17118295 GATGTTGATGTTGATGTTGATA
1 GATG-TGATATTGATATTGATA
17118317 AACAAATTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.27, C:0.02, G:0.27, T:0.44
Consensus pattern (23 bp):
GATGTGATATTGATATTGATATC
Found at i:17120497 original size:235 final size:235
Alignment explanation
Indices: 17120086--17120555 Score: 895
Period size: 235 Copynumber: 2.0 Consensus size: 235
17120076 TGGCTCTTTC
* *
17120086 TATTTGTACTGTTTGTAACAATCGAAAGTTCTCTTTCTCTTTTTTTTCTACAGTAGTTTTTTTCA
1 TATTTGTACTGTTTGTAACAATCGAAAGTTCTCTTTCCCTTTTTCTTCTACAGTAGTTTTTTTCA
*
17120151 TGAAATAACTTTGGACATCATGAATCAGCGAACCAAAATTTAAATAGTTTTTTTCTTCGATCTTC
66 TGAAATAACTTTGGACATCATGAATCAGCGAACCAAAATTCAAATAGTTTTTTTCTTCGATCTTC
17120216 AACATTGATCGTTTAGATCGGCTAGGATCTAAAGTATGTTTTTCTACTTGTCAAATTTCAAATTG
131 AACATTGATCGTTTAGATCGGCTAGGATCTAAAGTATGTTTTTCTACTTGTCAAATTTCAAATTG
* *
17120281 TCACTTAGAGTTCACTGATAGAATTTTTTTTTAGAAAAAA
196 TCACTTAGAGTTCACAGATAGAAATTTTTTTTAGAAAAAA
17120321 TATTTGTACTGTTTGTAACAATCGAAAGTTCTCTTTCCCTTTTTCTTCTACAGTAGTTTTTTTCA
1 TATTTGTACTGTTTGTAACAATCGAAAGTTCTCTTTCCCTTTTTCTTCTACAGTAGTTTTTTTCA
17120386 TGAAATAACTTTGGACATCATGAATCAGCGAACCAAAATTCAAATAGTTTTTTTCTTCGATCTTC
66 TGAAATAACTTTGGACATCATGAATCAGCGAACCAAAATTCAAATAGTTTTTTTCTTCGATCTTC
17120451 AACATTGATCGTTTAGATCGGCTAGGATCTAAAGTATGTTTTTCTACTTGTCAAATTTCAAATTG
131 AACATTGATCGTTTAGATCGGCTAGGATCTAAAGTATGTTTTTCTACTTGTCAAATTTCAAATTG
17120516 TCACTTAGAGTTCACAGATAGAAATTTTTTTTAGAAAAAA
196 TCACTTAGAGTTCACAGATAGAAATTTTTTTTAGAAAAAA
17120556 CTTAACAAGT
Statistics
Matches: 230, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
235 230 1.00
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (235 bp):
TATTTGTACTGTTTGTAACAATCGAAAGTTCTCTTTCCCTTTTTCTTCTACAGTAGTTTTTTTCA
TGAAATAACTTTGGACATCATGAATCAGCGAACCAAAATTCAAATAGTTTTTTTCTTCGATCTTC
AACATTGATCGTTTAGATCGGCTAGGATCTAAAGTATGTTTTTCTACTTGTCAAATTTCAAATTG
TCACTTAGAGTTCACAGATAGAAATTTTTTTTAGAAAAAA
Found at i:17120635 original size:31 final size:31
Alignment explanation
Indices: 17120573--17120635 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
17120563 AGTCAGTGAA
* * * *
17120573 TTAAATAAAAACTTTCGAATAATTTACTAAC
1 TTAAACAAAAACTTTCAAATAATTCAATAAC
*
17120604 TTAAACAAAAATTTTCAAATAATTCAATAAC
1 TTAAACAAAAACTTTCAAATAATTCAATAAC
17120635 T
1 T
17120636 AAATTATACT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.51, C:0.13, G:0.02, T:0.35
Consensus pattern (31 bp):
TTAAACAAAAACTTTCAAATAATTCAATAAC
Found at i:17129334 original size:19 final size:19
Alignment explanation
Indices: 17129307--17129343 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
17129297 CAAAATTTAT
* *
17129307 ATTTTTAAAAAATTATAAA
1 ATTTCTAAAAAAATATAAA
17129326 ATTTCTAAAAAAATATAA
1 ATTTCTAAAAAAATATAA
17129344 GAAATATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
ATTTCTAAAAAAATATAAA
Found at i:17129767 original size:29 final size:28
Alignment explanation
Indices: 17129721--17129782 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
17129711 TTGTTTCCAT
*
17129721 TTATTTCTTTGTTAATAAT-TTTGCTTTG
1 TTATTTCTTTGTAAATAATATTT-CTTTG
* *
17129749 TTATTTTTTTGGTAAATAATATTTTTTTG
1 TTATTTCTTT-GTAAATAATATTTCTTTG
17129778 TTATT
1 TTATT
17129783 AAAAAAAATG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 9 0.31
29 17 0.59
30 3 0.10
ACGTcount: A:0.21, C:0.03, G:0.10, T:0.66
Consensus pattern (28 bp):
TTATTTCTTTGTAAATAATATTTCTTTG
Found at i:17133276 original size:33 final size:33
Alignment explanation
Indices: 17133234--17133298 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
17133224 ATACATAAAT
17133234 AAGAGAACATGAATAATTATGGGGCATTTGAAG
1 AAGAGAACATGAATAATTATGGGGCATTTGAAG
17133267 AAGAGAACATGAATAATTATGGGGCATTTGAA
1 AAGAGAACATGAATAATTATGGGGCATTTGAA
17133299 AAACAAGTGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.43, C:0.06, G:0.26, T:0.25
Consensus pattern (33 bp):
AAGAGAACATGAATAATTATGGGGCATTTGAAG
Found at i:17138397 original size:35 final size:35
Alignment explanation
Indices: 17138358--17138550 Score: 230
Period size: 35 Copynumber: 5.5 Consensus size: 35
17138348 GGTAAAGTGC
* * * *
17138358 GAAATATAGGTATTGTATTATCCATACCGAGTCGT
1 GAAATGTAGGTATGGTATTATCCATACCGAGTTGA
*
17138393 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
1 GAAATGTAGGTATGGTATTATCCATACCGAGTTGA
* ** *
17138428 GAAATATAGGTATGGTATTATCCATATTGAGTTAA
1 GAAATGTAGGTATGGTATTATCCATACCGAGTTGA
* *
17138463 GAAATGTAGGTATGGCATT-TCCCATACCGAGTTGT
1 GAAATGTAGGTATGGTATTAT-CCATACCGAGTTGA
* *
17138498 GAAACGTAGGTATGGTATTTTCCATACCGAGTAT-A
1 GAAATGTAGGTATGGTATTATCCATACCGAGT-TGA
17138533 -AAATGTAGGTATGGTATT
1 GAAATGTAGGTATGGTATT
17138551 TCAATGAGGA
Statistics
Matches: 135, Mismatches: 20, Indels: 7
0.83 0.12 0.04
Matches are distributed among these distances:
34 18 0.13
35 115 0.85
36 2 0.01
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.33
Consensus pattern (35 bp):
GAAATGTAGGTATGGTATTATCCATACCGAGTTGA
Found at i:17140196 original size:24 final size:24
Alignment explanation
Indices: 17140164--17140222 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
17140154 ACCGGTGTTT
17140164 CTGGTGGTTTCCG-GAGTAAAGTAG
1 CTGGTGGTTTCCGCG-GTAAAGTAG
*
17140188 CTGGTGGTTTCTGCGGTAAAGTAG
1 CTGGTGGTTTCCGCGGTAAAGTAG
17140212 CTGGTGGTTTC
1 CTGGTGGTTTC
17140223 GGCAGTGAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
24 32 0.97
25 1 0.03
ACGTcount: A:0.15, C:0.14, G:0.37, T:0.34
Consensus pattern (24 bp):
CTGGTGGTTTCCGCGGTAAAGTAG
Found at i:17143282 original size:24 final size:24
Alignment explanation
Indices: 17143255--17143303 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
17143245 ATATAGTAAA
17143255 TGTTAATGTGAAATGATTGTAAGG
1 TGTTAATGTGAAATGATTGTAAGG
17143279 TGTTAATGTGAAATGATTGTAAGG
1 TGTTAATGTGAAATGATTGTAAGG
17143303 T
1 T
17143304 CAGCCATTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.29, T:0.39
Consensus pattern (24 bp):
TGTTAATGTGAAATGATTGTAAGG
Found at i:17143371 original size:23 final size:23
Alignment explanation
Indices: 17143345--17143389 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
17143335 TTGGTATGTG
*
17143345 ATGAGGTTATCTT-ATAAATATGC
1 ATGAAGTTATCTTGA-AAATATGC
*
17143368 ATGAATTTATCTTGAAAATATG
1 ATGAAGTTATCTTGAAAATATG
17143390 TTGAATTGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.40
Consensus pattern (23 bp):
ATGAAGTTATCTTGAAAATATGC
Found at i:17146867 original size:27 final size:27
Alignment explanation
Indices: 17146823--17146874 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
17146813 ATAAATTTTC
*
17146823 AAAAAATTATAAACATTATTAAAAATAA
1 AAAAAATGATAAACATTA-TAAAAATAA
*
17146851 AAAAAATGA-AAATATTATAAAAAT
1 AAAAAATGATAAACATTATAAAAAT
17146875 TAAATATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 7 0.32
27 7 0.32
28 8 0.36
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (27 bp):
AAAAAATGATAAACATTATAAAAATAA
Found at i:17146878 original size:27 final size:28
Alignment explanation
Indices: 17146823--17146878 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
17146813 ATAAATTTTC
* *
17146823 AAAAAATTATAAACATTATTAAAAATAA
1 AAAAAATGATAAACATTATAAAAAATAA
* *
17146851 AAAAAATGA-AAATATTATAAAAATTAA
1 AAAAAATGATAAACATTATAAAAAATAA
17146878 A
1 A
17146879 TATTTAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 16 0.67
28 8 0.33
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.27
Consensus pattern (28 bp):
AAAAAATGATAAACATTATAAAAAATAA
Found at i:17146889 original size:17 final size:17
Alignment explanation
Indices: 17146840--17146896 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
17146830 TATAAACATT
*
17146840 ATTAAAA-ATAAAAAAA
1 ATTAAAATATTAAAAAA
* *
17146856 ATGAAAATATTATAAAA
1 ATTAAAATATTAAAAAA
17146873 ATT-AAATATTTAAAAAA
1 ATTAAAATA-TTAAAAAA
*
17146890 ACTAAAA
1 ATTAAAA
17146897 AATAAAATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
16 11 0.34
17 18 0.56
18 3 0.09
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (17 bp):
ATTAAAATATTAAAAAA
Found at i:17155661 original size:21 final size:22
Alignment explanation
Indices: 17155620--17155670 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 22
17155610 AGAGATTCTT
*
17155620 TTAAAATAAACTCAGTAATTTTA-
1 TTAAAA-AAACTCAATAA-TTTAC
17155643 TTAAAAAAACT-AATAATTTAC
1 TTAAAAAAACTCAATAATTTAC
17155664 TTAAAAA
1 TTAAAAA
17155671 CATTATAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 4 0.15
21 11 0.42
22 5 0.19
23 6 0.23
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.35
Consensus pattern (22 bp):
TTAAAAAAACTCAATAATTTAC
Found at i:17156516 original size:6 final size:6
Alignment explanation
Indices: 17156505--17156534 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
17156495 AGAATTCTAA
17156505 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
17156535 CAGATGCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:17157308 original size:18 final size:18
Alignment explanation
Indices: 17157281--17157373 Score: 123
Period size: 18 Copynumber: 5.2 Consensus size: 18
17157271 TACGACCGTT
*
17157281 TACGGTACTATTCACGTA
1 TACGGCACTATTCACGTA
* *
17157299 TACGACACTATTCACATA
1 TACGGCACTATTCACGTA
*
17157317 TACGGTACTATTCACGTA
1 TACGGCACTATTCACGTA
*
17157335 TACGGCACTATTCGCGTA
1 TACGGCACTATTCACGTA
* *
17157353 TACGGTACTGTTCACGTA
1 TACGGCACTATTCACGTA
17157371 TAC
1 TAC
17157374 AGTAGTTGGG
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 64 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (18 bp):
TACGGCACTATTCACGTA
Found at i:17157328 original size:36 final size:36
Alignment explanation
Indices: 17157281--17157373 Score: 150
Period size: 36 Copynumber: 2.6 Consensus size: 36
17157271 TACGACCGTT
17157281 TACGGTACTATTCACGTATACGACACTATTCACATA
1 TACGGTACTATTCACGTATACGACACTATTCACATA
* * *
17157317 TACGGTACTATTCACGTATACGGCACTATTCGCGTA
1 TACGGTACTATTCACGTATACGACACTATTCACATA
*
17157353 TACGGTACTGTTCACGTATAC
1 TACGGTACTATTCACGTATAC
17157374 AGTAGTTGGG
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 53 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (36 bp):
TACGGTACTATTCACGTATACGACACTATTCACATA
Found at i:17161273 original size:37 final size:37
Alignment explanation
Indices: 17161164--17161274 Score: 204
Period size: 37 Copynumber: 3.0 Consensus size: 37
17161154 TACGTATGAT
* *
17161164 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAAC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
17161201 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
17161238 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
17161275 TAAAGCTATC
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 72 1.00
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (37 bp):
CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
Found at i:17161317 original size:52 final size:52
Alignment explanation
Indices: 17161238--17161408 Score: 279
Period size: 52 Copynumber: 3.2 Consensus size: 52
17161228 TAAGTGTAGC
* *
17161238 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTAT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTAT
**
17161291 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTAT
*
17161343 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTAT
17161395 CACTTTGTCACTTG
1 CACTTT-TCACTTG
17161409 ATCAGAAGTA
Statistics
Matches: 110, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
52 94 0.85
53 16 0.15
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (52 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTAT
Found at i:17178456 original size:19 final size:17
Alignment explanation
Indices: 17178422--17178456 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
17178412 CTAAAATAGG
17178422 AACAAAATTAACAATAA
1 AACAAAATTAACAATAA
17178439 AACAAGAATTATACAATA
1 AACAA-AATTA-ACAATA
17178457 TTCAAATACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 5 0.31
19 6 0.38
ACGTcount: A:0.66, C:0.11, G:0.03, T:0.20
Consensus pattern (17 bp):
AACAAAATTAACAATAA
Found at i:17178790 original size:26 final size:23
Alignment explanation
Indices: 17178740--17178790 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 23
17178730 ATAAAACTAC
*
17178740 CATAATATAATAGTAAAAGTGTG
1 CATAATATAATAGTAAAAGTATG
*
17178763 CATATATATATATATTAAAAGTTATG
1 CATA-ATATA-ATAGTAAAAG-TATG
17178789 CA
1 CA
17178791 CGTCCTTCGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 4 0.17
24 5 0.22
25 9 0.39
26 5 0.22
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (23 bp):
CATAATATAATAGTAAAAGTATG
Found at i:17181520 original size:13 final size:13
Alignment explanation
Indices: 17181501--17181563 Score: 85
Period size: 13 Copynumber: 4.9 Consensus size: 13
17181491 TAAATCAAAT
17181501 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
*
17181514 TTCTCAAAAGCAC
1 TTTTCAAAAGCAC
*
17181527 TTTTCCACAA-CAC
1 TTTT-CAAAAGCAC
17181540 TTTT-AAAAGCAC
1 TTTTCAAAAGCAC
17181552 TTTTCAAAAGCA
1 TTTTCAAAAGCA
17181564 TTGTCAAACT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
11 3 0.07
12 7 0.16
13 29 0.67
14 4 0.09
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.30
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:17181570 original size:12 final size:13
Alignment explanation
Indices: 17181504--17181571 Score: 61
Period size: 13 Copynumber: 5.4 Consensus size: 13
17181494 ATCAAATTTT
*
17181504 TCAAAAGCACTTC
1 TCAAAAGCACTTG
*
17181517 TCAAAAGCACTTT
1 TCAAAAGCACTTG
*
17181530 TCCACAA-CACTT-
1 T-CAAAAGCACTTG
* *
17181542 TTAAAAGCACTTT
1 TCAAAAGCACTTG
17181555 TCAAAAGCA-TTG
1 TCAAAAGCACTTG
17181567 TCAAA
1 TCAAA
17181572 CTAGCCCTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
11 3 0.07
12 13 0.28
13 26 0.57
14 4 0.09
ACGTcount: A:0.40, C:0.25, G:0.07, T:0.28
Consensus pattern (13 bp):
TCAAAAGCACTTG
Found at i:17186961 original size:29 final size:29
Alignment explanation
Indices: 17186928--17186987 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
17186918 GGTGAAAGTT
17186928 AGAAAGCTCACATCATTTGTTTTAATGAA
1 AGAAAGCTCACATCATTTGTTTTAATGAA
17186957 AGAAAGCTCACATCATTTGTTTTAATGAA
1 AGAAAGCTCACATCATTTGTTTTAATGAA
17186986 AG
1 AG
17186988 TCTTACTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.33
Consensus pattern (29 bp):
AGAAAGCTCACATCATTTGTTTTAATGAA
Found at i:17197734 original size:5 final size:5
Alignment explanation
Indices: 17197724--17197757 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
17197714 CTTTCACTAT
17197724 TATAG TATAG TATAG TATAG TATAG TATAG TATA
1 TATAG TATAG TATAG TATAG TATAG TATAG TATA
17197758 TGACAACTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (5 bp):
TATAG
Found at i:17197808 original size:27 final size:27
Alignment explanation
Indices: 17197770--17197823 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
17197760 ACAACTGAAG
17197770 GAGATTTTCATCTTCCTATGTGTTTTT
1 GAGATTTTCATCTTCCTATGTGTTTTT
17197797 GAGATTTTCATCTTCCTATGTGTTTTT
1 GAGATTTTCATCTTCCTATGTGTTTTT
17197824 TTCTGATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.56
Consensus pattern (27 bp):
GAGATTTTCATCTTCCTATGTGTTTTT
Found at i:17200009 original size:2 final size:2
Alignment explanation
Indices: 17200002--17200035 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
17199992 GTTACTAAAA
17200002 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
17200036 TATAACTTCA
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:17205479 original size:18 final size:19
Alignment explanation
Indices: 17205437--17205478 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
17205427 ATTTCTATAT
*
17205437 ATTTTTATAATATTTTACG
1 ATTTTTATAATAATTTACG
17205456 ATTTTTATAA-AATTTAC-
1 ATTTTTATAATAATTTACG
17205473 ATTTTT
1 ATTTTT
17205479 TTTACTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.27
18 6 0.27
19 10 0.45
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (19 bp):
ATTTTTATAATAATTTACG
Found at i:17205480 original size:57 final size:57
Alignment explanation
Indices: 17205364--17205498 Score: 143
Period size: 57 Copynumber: 2.4 Consensus size: 57
17205354 TTTTATGAGA
* * * * *
17205364 TTTATATTTCTTTACATTTTGTATAATTTTCTTATGACTTTATAAAATTTTATAATTT
1 TTTATATTTCTATATATTTT-TATAATATTCTTACGACTTTATAAAATTTCATAATTT
* *
17205422 TTTATATTTCTATATATTTTTATAATATT-TTACGATTTTTATAAAATTTACAT-TTTT
1 TTTATATTTCTATATATTTTTATAATATTCTTACGA-CTTTATAAAATTT-CATAATTT
17205479 TTTACTATTT-TATAT-TTTTT
1 TTTA-TATTTCTATATATTTTT
17205499 CCTAATTTTT
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
56 10 0.15
57 32 0.48
58 25 0.37
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63
Consensus pattern (57 bp):
TTTATATTTCTATATATTTTTATAATATTCTTACGACTTTATAAAATTTCATAATTT
Found at i:17205767 original size:92 final size:91
Alignment explanation
Indices: 17205607--17205808 Score: 246
Period size: 92 Copynumber: 2.2 Consensus size: 91
17205597 AAGAAAGGGT
* ** * * * * * *
17205607 TTAATTGCTTTTTTTTTGAAAATTTTTGAGGGTTTTTTTGATATATTTTGAAAGTTCAAGTATTC
1 TTAATTGCTTTTTTTTTTAAAAGGTTTGAAGGCTTTTTTGATACATTTTGAAAATTCAAGCACTC
*
17205672 AAATGAGTGTAAAAAAAAGAGCAGGGGC
66 AAATGAGTGCAAAAAAAA-A-CAGGGGC
* *
17205700 TTAATTGCTTTTTTTTTTAAAAGGTTTGAAGGCTTTTTT-ATGCATTTTGAAAATTTAAGCACTC
1 TTAATTGCTTTTTTTTTTAAAAGGTTTGAAGGCTTTTTTGATACATTTTGAAAATTCAAGCACTC
*
17205764 AAATGAGTGCAAAAAAAAATAGGGGC
66 AAATGAGTGCAAAAAAAAACAGGGGC
17205790 TTAATTTG-TTTTTTTTTTA
1 TTAA-TTGCTTTTTTTTTTA
17205809 TGTTTGAGGT
Statistics
Matches: 95, Mismatches: 13, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
90 21 0.22
91 4 0.04
92 36 0.38
93 34 0.36
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (91 bp):
TTAATTGCTTTTTTTTTTAAAAGGTTTGAAGGCTTTTTTGATACATTTTGAAAATTCAAGCACTC
AAATGAGTGCAAAAAAAAACAGGGGC
Found at i:17206047 original size:35 final size:35
Alignment explanation
Indices: 17206001--17206071 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
17205991 TCCATGTTAC
17206001 TGTTAAGATACATTCTTCAAATTCTCACTGATTGT
1 TGTTAAGATACATTCTTCAAATTCTCACTGATTGT
17206036 TGTTAAGATACATTCTTCAAATTCTCACTGATTGT
1 TGTTAAGATACATTCTTCAAATTCTCACTGATTGT
17206071 T
1 T
17206072 ATTTTTTGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.44
Consensus pattern (35 bp):
TGTTAAGATACATTCTTCAAATTCTCACTGATTGT
Found at i:17210785 original size:22 final size:23
Alignment explanation
Indices: 17210752--17210795 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 23
17210742 ATAATGGAAT
17210752 TTAATTAAAAAATAAAAATTAAA
1 TTAATTAAAAAATAAAAATTAAA
17210775 TTAA-TAAAAAATAAAAATTAA
1 TTAATTAAAAAATAAAAATTAA
17210796 GAGTTAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (23 bp):
TTAATTAAAAAATAAAAATTAAA
Found at i:17214058 original size:18 final size:18
Alignment explanation
Indices: 17214035--17214072 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
17214025 TATGGTTGAC
17214035 TTATTTAACTCAGTAAGT
1 TTATTTAACTCAGTAAGT
*
17214053 TTATTTAACTCATTAAGT
1 TTATTTAACTCAGTAAGT
17214071 TT
1 TT
17214073 GCTTAATTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.50
Consensus pattern (18 bp):
TTATTTAACTCAGTAAGT
Found at i:17214078 original size:18 final size:18
Alignment explanation
Indices: 17214039--17214078 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
17214029 GTTGACTTAT
*
17214039 TTAACTCAGTAAGTTTAT
1 TTAACTCAGTAAGTTTAC
* *
17214057 TTAACTCATTAAGTTTGC
1 TTAACTCAGTAAGTTTAC
17214075 TTAA
1 TTAA
17214079 TTCCTCGCAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (18 bp):
TTAACTCAGTAAGTTTAC
Found at i:17216940 original size:239 final size:243
Alignment explanation
Indices: 17216491--17216976 Score: 782
Period size: 239 Copynumber: 2.0 Consensus size: 243
17216481 TGAAGGGATC
**
17216491 CATGAAATGCTACGACTTATGCACGACCACCTTCTACGGCCGAGGTGGGTTACATTAGATGAAAT
1 CATGAAATGCTACGACTTATGCACGACCACCTTCTACAACCGAGGTGGGTTACATTAGATGAAAT
*
17216556 TTGACCACCTAAATGTATCTTTACTCACACAGTAGTTGGATTTGCAAGAAGCTGAAGAAAAATGC
66 TTGACCACCTAAATGTACCTTTACT-ACACAGTAGTTGGATTTGCAAGAAGCTGAAGAAAAATGC
* * *
17216621 AGTTTTTTTATGTCATCTAGGTTTTGGTTCACACAGCAGTCAAAATTCGCTGACTGTAGGCATCT
130 AGTTTTTTGATGTCATCTAGGTTTTGGTTCACACAGCACTCAAAATTCGCCGACTGTAGGCATCT
17216686 TGTGATGATCGACAGTGT-AAACTAACTGTCCACAAACTACACATACTT
195 TGTGATGATCGACAGTGTAAAACTAACTGTCCACAAACTACACATACTT
* * *
17216734 CATGAAATGCTACGACTTATGCACTACCACCTTCTACAACTGAGGTGGGTTACGTTAGATGAAA-
1 CATGAAATGCTACGACTTATGCACGACCACCTTCTACAACCGAGGTGGGTTACATTAGATGAAAT
** *
17216798 TTGACCACCTAAATGTACCTTTACT-CGTAGTAGTTGGATTTGCAAGAAGCTGAAGAAAAATGGA
66 TTGACCACCTAAATGTACCTTTACTACACAGTAGTTGGATTTGCAAGAAGCTGAAGAAAAATGCA
*
17216862 G-TTTTTGATGTCATCTAGGTTTTGGTTCACACAGCACTCAAAATTGGCCGACTGTAGGCATCTT
131 GTTTTTTGATGTCATCTAGGTTTTGGTTCACACAGCACTCAAAATTCGCCGACTGTAGGCATCTT
* * * *
17216926 TTGATGGTCGACAGTGTAAAACTAACTGTCCACAAACTACCCATAGTT
196 GTGATGATCGACAGTGTAAAACTAACTGTCCACAAACTACACATACTT
17216974 CAT
1 CAT
17216977 TATATTGCTA
Statistics
Matches: 225, Mismatches: 17, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
239 74 0.33
240 68 0.30
242 24 0.11
243 59 0.26
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (243 bp):
CATGAAATGCTACGACTTATGCACGACCACCTTCTACAACCGAGGTGGGTTACATTAGATGAAAT
TTGACCACCTAAATGTACCTTTACTACACAGTAGTTGGATTTGCAAGAAGCTGAAGAAAAATGCA
GTTTTTTGATGTCATCTAGGTTTTGGTTCACACAGCACTCAAAATTCGCCGACTGTAGGCATCTT
GTGATGATCGACAGTGTAAAACTAACTGTCCACAAACTACACATACTT
Found at i:17217333 original size:9 final size:9
Alignment explanation
Indices: 17217318--17217350 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
17217308 TTGAATCTCT
17217318 CTTCTTCTG
1 CTTCTTCTG
*
17217327 TTTCTTCTG
1 CTTCTTCTG
17217336 CTTCTTCTG
1 CTTCTTCTG
17217345 CTTCTT
1 CTTCTT
17217351 TTTTTCCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.00, C:0.30, G:0.09, T:0.61
Consensus pattern (9 bp):
CTTCTTCTG
Found at i:17228843 original size:14 final size:15
Alignment explanation
Indices: 17228809--17228845 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
17228799 TAGTTGAGAG
17228809 GAATGAAAATTAAAAT
1 GAAT-AAAATTAAAAT
17228825 G-ATAAAATTAAAA-
1 GAATAAAATTAAAAT
17228838 GAATAAAA
1 GAATAAAA
17228846 AATTTATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 1 0.05
14 16 0.80
15 2 0.10
16 1 0.05
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.22
Consensus pattern (15 bp):
GAATAAAATTAAAAT
Found at i:17234126 original size:13 final size:13
Alignment explanation
Indices: 17234108--17234133 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17234098 TTGAAAATAA
17234108 ATGAAACCAACTT
1 ATGAAACCAACTT
17234121 ATGAAACCAACTT
1 ATGAAACCAACTT
17234134 TGTTATTTAT
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:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (13 bp):
ATGAAACCAACTT
Found at i:17242077 original size:11 final size:11
Alignment explanation
Indices: 17242063--17242087 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
17242053 GAAACACCCA
17242063 CGAAAATCCGG
1 CGAAAATCCGG
17242074 CGAAAATCCGG
1 CGAAAATCCGG
17242085 CGA
1 CGA
17242088 GGGTGGTGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.28, G:0.28, T:0.08
Consensus pattern (11 bp):
CGAAAATCCGG
Found at i:17243345 original size:2 final size:2
Alignment explanation
Indices: 17243334--17243365 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
17243324 GCTGCACTGC
17243334 CT CT -T CT CT CT CT CT CT CT CT CT CT CT -T CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
17243366 TAGACTTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:17256629 original size:23 final size:23
Alignment explanation
Indices: 17256599--17256644 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
17256589 CTATCCTGTC
17256599 AGTAACTTGATAGTAATAATTCA
1 AGTAACTTGATAGTAATAATTCA
17256622 AGTAACTTGATAGTAATAATTCA
1 AGTAACTTGATAGTAATAATTCA
17256645 TTGCCACTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (23 bp):
AGTAACTTGATAGTAATAATTCA
Found at i:17263135 original size:18 final size:17
Alignment explanation
Indices: 17263112--17263161 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
17263102 TTCACTTATG
17263112 TTTTAAAAAATGAATAAA
1 TTTTAAAAAAT-AATAAA
*
17263130 TTTT--AAAATAATATA
1 TTTTAAAAAATAATAAA
17263145 TTTTATAAAAATAATAA
1 TTTTA-AAAAATAATAA
17263162 TTCTTCCAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
15 9 0.33
16 5 0.19
18 13 0.48
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (17 bp):
TTTTAAAAAATAATAAA
Found at i:17271171 original size:70 final size:71
Alignment explanation
Indices: 17271058--17271199 Score: 259
Period size: 72 Copynumber: 2.0 Consensus size: 71
17271048 TTACCTAGAC
17271058 CAATCTAAAGCTTTCTTTTCCCTTTTACAATTTAA-TTTTTTTTTATCAAGCAACTTTGAATTCA
1 CAATCTAAAGCTTTCTTTTCCCTTTTACAATTTAATTTTTTTTTTATCAAGCAACTTTGAATTCA
17271122 CAAATT
66 CAAATT
*
17271128 CAATCTAAAGCTTTCTTTTCCCTTTTACAATTTAGTTTTTTTTTTTATCAAGCAACTTTGAATTC
1 CAATCTAAAGCTTTCTTTTCCCTTTTACAATTTA-ATTTTTTTTTTATCAAGCAACTTTGAATTC
17271193 ACAAATT
65 ACAAATT
17271200 TATTAACTAA
Statistics
Matches: 69, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
70 34 0.49
72 35 0.51
ACGTcount: A:0.29, C:0.18, G:0.05, T:0.48
Consensus pattern (71 bp):
CAATCTAAAGCTTTCTTTTCCCTTTTACAATTTAATTTTTTTTTTATCAAGCAACTTTGAATTCA
CAAATT
Found at i:17271400 original size:31 final size:31
Alignment explanation
Indices: 17271355--17271426 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
17271345 AAAACTTATC
* *
17271355 AGTTTAGTGCCTTAAATAAAAAATTTCAAAT
1 AGTTCAGTGACTTAAATAAAAAATTTCAAAT
* * *
17271386 AGTTCAGTGACTTAAATGAAAACTTTCGAAT
1 AGTTCAGTGACTTAAATAAAAAATTTCAAAT
*
17271417 AATTCAGTGA
1 AGTTCAGTGA
17271427 TCATTTTGTA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (31 bp):
AGTTCAGTGACTTAAATAAAAAATTTCAAAT
Found at i:17277398 original size:18 final size:18
Alignment explanation
Indices: 17277375--17277411 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
17277365 AAACAATCAG
17277375 ATAACAACAACAACAATA
1 ATAACAACAACAACAATA
*
17277393 ATAACAACAACAACGATA
1 ATAACAACAACAACAATA
17277411 A
1 A
17277412 AGAAAAAGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.65, C:0.22, G:0.03, T:0.11
Consensus pattern (18 bp):
ATAACAACAACAACAATA
Found at i:17277411 original size:15 final size:15
Alignment explanation
Indices: 17277375--17277405 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
17277365 AAACAATCAG
17277375 ATAACAACAACAACA
1 ATAACAACAACAACA
*
17277390 ATAATAACAACAACA
1 ATAACAACAACAACA
17277405 A
1 A
17277406 CGATAAAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.68, C:0.23, G:0.00, T:0.10
Consensus pattern (15 bp):
ATAACAACAACAACA
Found at i:17292419 original size:3 final size:3
Alignment explanation
Indices: 17292411--17292436 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
17292401 TTAGTCAAGT
17292411 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
17292437 GCATTTTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:17342231 original size:9 final size:9
Alignment explanation
Indices: 17342202--17342238 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
17342192 TGAATTTTCG
17342202 AATTCGAAT
1 AATTCGAAT
*
17342211 AACTCGAAT
1 AATTCGAAT
17342220 AATTCGAAT
1 AATTCGAAT
*
17342229 AATTCAAAT
1 AATTCGAAT
17342238 A
1 A
17342239 TTAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:17342323 original size:29 final size:30
Alignment explanation
Indices: 17342281--17342340 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
17342271 ACTCCCAAAT
* *
17342281 CTTTTTACTTTTCCCTCAAAACTTTTACTC
1 CTTTCTACTTTTCCCCCAAAACTTTTACTC
17342311 CTTTCTAC-TTTCCCCCAAAACTTTTACTC
1 CTTTCTACTTTTCCCCCAAAACTTTTACTC
17342340 C
1 C
17342341 CCTTCTATCC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
29 21 0.75
30 7 0.25
ACGTcount: A:0.20, C:0.35, G:0.00, T:0.45
Consensus pattern (30 bp):
CTTTCTACTTTTCCCCCAAAACTTTTACTC
Found at i:17342347 original size:30 final size:29
Alignment explanation
Indices: 17342290--17342347 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
17342280 TCTTTTTACT
* *
17342290 TTTCCCTCAAAACTTTTACTCCTTTCTAC
1 TTTCCCCCAAAACTTTTACTCCCTTCTAC
17342319 TTTCCCCCAAAACTTTTACTCCCCTTCTA
1 TTTCCCCCAAAACTTTTACT-CCCTTCTA
17342348 TCCCAACCCC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 19 0.73
30 7 0.27
ACGTcount: A:0.21, C:0.38, G:0.00, T:0.41
Consensus pattern (29 bp):
TTTCCCCCAAAACTTTTACTCCCTTCTAC
Found at i:17343490 original size:24 final size:24
Alignment explanation
Indices: 17343458--17343505 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
17343448 GAAGTAAGAG
17343458 ACGACAAAGACAATATTATTACAA
1 ACGACAAAGACAATATTATTACAA
17343482 ACGACAAAGACAATATTATTACAA
1 ACGACAAAGACAATATTATTACAA
17343506 GCTTGTTCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.17, G:0.08, T:0.21
Consensus pattern (24 bp):
ACGACAAAGACAATATTATTACAA
Found at i:17349033 original size:21 final size:22
Alignment explanation
Indices: 17348981--17349023 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 22
17348971 AGTACTTGAT
17348981 TAAATTAAATTTTATATTATTAGA
1 TAAATT-AA-TTTATATTATTAGA
17349005 TAAATTAATTTA-ATTATTA
1 TAAATTAATTTATATTATTA
17349024 TATTATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 4 0.21
23 2 0.11
24 6 0.32
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
TAAATTAATTTATATTATTAGA
Found at i:17370461 original size:6 final size:6
Alignment explanation
Indices: 17370441--17370496 Score: 85
Period size: 6 Copynumber: 9.2 Consensus size: 6
17370431 ACACTTCTTC
* *
17370441 TCCCCTT TCCCCT TCCTCT TCCCCT TCCCCT TCCTCT TCCCCT TCCCCT
1 TCCCC-T TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT
17370490 TCCCCT T
1 TCCCCT T
17370497 TTGAAATCGG
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
6 40 0.89
7 5 0.11
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (6 bp):
TCCCCT
Found at i:17370468 original size:18 final size:18
Alignment explanation
Indices: 17370441--17370492 Score: 95
Period size: 18 Copynumber: 2.8 Consensus size: 18
17370431 ACACTTCTTC
17370441 TCCCCTTTCCCCTTCCTCT
1 TCCCC-TTCCCCTTCCTCT
17370460 TCCCCTTCCCCTTCCTCT
1 TCCCCTTCCCCTTCCTCT
17370478 TCCCCTTCCCCTTCC
1 TCCCCTTCCCCTTCC
17370493 CCTTTTGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 28 0.85
19 5 0.15
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (18 bp):
TCCCCTTCCCCTTCCTCT
Found at i:17371731 original size:17 final size:18
Alignment explanation
Indices: 17371698--17371734 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
17371688 TGTTTCCTTT
*
17371698 GAGGTCCATGATAATTGG
1 GAGGTCCAAGATAATTGG
17371716 GAGGTCCAAG-TAATTGG
1 GAGGTCCAAGATAATTGG
17371733 GA
1 GA
17371735 ATTCCATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.30, C:0.11, G:0.35, T:0.24
Consensus pattern (18 bp):
GAGGTCCAAGATAATTGG
Found at i:17374001 original size:19 final size:19
Alignment explanation
Indices: 17373957--17373995 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
17373947 ATCCAAACAC
*
17373957 CAGAAAAGTAAATCATTTT
1 CAGAAAAATAAATCATTTT
17373976 CAGAAAAATAAATCATTTT
1 CAGAAAAATAAATCATTTT
17373995 C
1 C
17373996 CAAAAATCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.49, C:0.13, G:0.08, T:0.31
Consensus pattern (19 bp):
CAGAAAAATAAATCATTTT
Found at i:17374002 original size:18 final size:19
Alignment explanation
Indices: 17373960--17374002 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
17373950 CAAACACCAG
* *
17373960 AAAAGTAAATCATTTTCAG
1 AAAAATAAATCATTTTCAC
17373979 AAAAATAAATCATTTTC-C
1 AAAAATAAATCATTTTCAC
17373997 AAAAAT
1 AAAAAT
17374003 CATTTTTCGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.53, C:0.12, G:0.05, T:0.30
Consensus pattern (19 bp):
AAAAATAAATCATTTTCAC
Found at i:17378851 original size:3 final size:3
Alignment explanation
Indices: 17378843--17378880 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
17378833 TATACGAACA
*
17378843 AAG AAG AAG AAG AAG AAG AAG CAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
17378881 ACGAGGCGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.66, C:0.03, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:17381997 original size:125 final size:126
Alignment explanation
Indices: 17381829--17382073 Score: 429
Period size: 125 Copynumber: 1.9 Consensus size: 126
17381819 AAAAGAAATT
17381829 AAAAGAACTTTAATCAAGCAGCCTTTTATACCTATTGCTTTACAAAAAACTGTGCCTAGGTGCAC
1 AAAAGAACTTTAATCAAGCAGCC-TTTATACCTATTGCTTTACAAAAAACTGTGCCTAGGTGCAC
*
17381894 CAAGAGTGCGCCTGATCAAATGAGTTTGAAGCACTTTTGTTGTCTAGTGCTAAGGAAAACTA
65 CAAGAGTGCGCCTGATCAAATGAGTTTGAAGCACTTTTGTTGCCTAGTGCTAAGGAAAACTA
* ** *
17381956 AAAAGAATTTTAATCAAGCAGCC-TTATACCTATTGCTTTACAAAAATGTGTGTCTAGGTGCACC
1 AAAAGAACTTTAATCAAGCAGCCTTTATACCTATTGCTTTACAAAAAACTGTGCCTAGGTGCACC
17382020 AAGAGTGCGCCTGATCAAATGAGTTTGAAGCACTTTTGTTGCCTAGTGCTAAGG
66 AAGAGTGCGCCTGATCAAATGAGTTTGAAGCACTTTTGTTGCCTAGTGCTAAGG
17382074 GACAAGCACA
Statistics
Matches: 113, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
125 91 0.81
127 22 0.19
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (126 bp):
AAAAGAACTTTAATCAAGCAGCCTTTATACCTATTGCTTTACAAAAAACTGTGCCTAGGTGCACC
AAGAGTGCGCCTGATCAAATGAGTTTGAAGCACTTTTGTTGCCTAGTGCTAAGGAAAACTA
Found at i:17385550 original size:29 final size:29
Alignment explanation
Indices: 17385483--17385559 Score: 81
Period size: 29 Copynumber: 2.7 Consensus size: 29
17385473 TTTTTTTAGA
*
17385483 TTCAA-AATTTAGT-TGTTATAGTTTTGTT
1 TTCAAGAATTTAGTCT-TTATAGTTTTATT
17385511 TTCAAGAATTTAGTCTTTATAGTTTTATGT
1 TTCAAGAATTTAGTCTTTATAGTTTTAT-T
17385541 TT-AATG-ATTTAGTCCTTTA
1 TTCAA-GAATTTAGT-CTTTA
17385560 ATTTTTAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
28 5 0.12
29 28 0.65
30 10 0.23
ACGTcount: A:0.26, C:0.06, G:0.13, T:0.55
Consensus pattern (29 bp):
TTCAAGAATTTAGTCTTTATAGTTTTATT
Found at i:17387378 original size:15 final size:16
Alignment explanation
Indices: 17387358--17387390 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
17387348 ATATATATTT
17387358 TTATTTT-ATTTTTAA
1 TTATTTTAATTTTTAA
17387373 TTATTTTAAATTTTTAA
1 TTATTTT-AATTTTTAA
17387390 T
1 T
17387391 ATAACCATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTTTAATTTTTAA
Found at i:17387463 original size:21 final size:22
Alignment explanation
Indices: 17387437--17387526 Score: 64
Period size: 22 Copynumber: 4.1 Consensus size: 22
17387427 GTTTTAAGAA
*
17387437 TTGTTTTAGTA-TTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
*
17387458 TTGTTTTAATATTTGTTTTTAT
1 TTGTTTTAATATTTATTTTTAT
*
17387480 GTT-TTTAAATATATTTGATTTATTAT
1 -TTGTTT-TA-ATATTT-ATTT-TTAT
*
17387506 AT-TTTTAA-ATTT-TTTTTAT
1 TTGTTTTAATATTTATTTTTAT
17387525 TT
1 TT
17387527 AATGAAATAA
Statistics
Matches: 56, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
19 5 0.09
20 3 0.05
21 10 0.18
22 16 0.29
23 4 0.07
24 7 0.12
25 7 0.12
26 4 0.07
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (22 bp):
TTGTTTTAATATTTATTTTTAT
Found at i:17387479 original size:22 final size:21
Alignment explanation
Indices: 17387451--17387526 Score: 66
Period size: 22 Copynumber: 3.4 Consensus size: 21
17387441 TTTAGTATTA
17387451 TTTTTATTTGTTTTAATATTTG
1 TTTTTATTT-TTTTAATATTTG
*
17387473 TTTTTATGTTTTTAAATATATTTG
1 TTTTTAT-TTTTT-TA-ATATTTG
*
17387497 ATTTATTATATTTTTAA-ATTT-
1 -TTT-TTATTTTTTTAATATTTG
17387518 TTTTTATTT
1 TTTTTATTT
17387527 AATGAAATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
19 5 0.11
20 3 0.07
22 14 0.31
23 4 0.09
24 8 0.18
25 7 0.16
26 4 0.09
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (21 bp):
TTTTTATTTTTTTAATATTTG
Found at i:17387527 original size:26 final size:26
Alignment explanation
Indices: 17387466--17387515 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
17387456 ATTTGTTTTA
*
17387466 ATATTTG-TTT-TTATGTTTTTAAAT
1 ATATTTGATTTATTATATTTTTAAAT
17387490 ATATTTGATTTATTATATTTTTAAAT
1 ATATTTGATTTATTATATTTTTAAAT
17387516 TTTTTTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (26 bp):
ATATTTGATTTATTATATTTTTAAAT
Found at i:17388418 original size:13 final size:13
Alignment explanation
Indices: 17388402--17388488 Score: 52
Period size: 13 Copynumber: 6.5 Consensus size: 13
17388392 GAAAAAAAAT
17388402 TATAAAATTTAAA
1 TATAAAATTTAAA
*
17388415 TATAAATTTTAAA
1 TATAAAATTTAAA
**
17388428 -ATAAATATAAAAAA
1 TATAAA-AT-TTAAA
** *
17388442 TATAATTAAAAATAAT
1 TAT-A--AAATTTAAA
17388458 TATAAAATTTAAA
1 TATAAAATTTAAA
*
17388471 TATAAATTTTAAA
1 TATAAAATTTAAA
17388484 -ATAAA
1 TATAAA
17388489 TATAAAAATA
Statistics
Matches: 57, Mismatches: 11, Indels: 13
0.70 0.14 0.16
Matches are distributed among these distances:
12 10 0.18
13 31 0.54
14 3 0.05
15 3 0.05
16 7 0.12
17 1 0.02
18 2 0.04
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
TATAAAATTTAAA
Found at i:17388421 original size:12 final size:12
Alignment explanation
Indices: 17388406--17388494 Score: 50
Period size: 12 Copynumber: 7.8 Consensus size: 12
17388396 AAAAATTATA
17388406 AAATTTAAATAT
1 AAATTTAAATAT
17388418 AAATTTTAAA-AT
1 AAA-TTTAAATAT
* *
17388430 AAATATAAAAAAT
1 AAAT-TTAAATAT
*
17388443 ATAA-TTAAAAAT
1 A-AATTTAAATAT
17388455 -AA-TT--ATA-
1 AAATTTAAATAT
17388462 AAATTTAAATAT
1 AAATTTAAATAT
17388474 AAATTTTAAA-AT
1 AAA-TTTAAATAT
*
17388486 AAATATAAA
1 AAATTTAAA
17388495 AATATAATTA
Statistics
Matches: 63, Mismatches: 4, Indels: 21
0.72 0.05 0.24
Matches are distributed among these distances:
8 4 0.06
9 2 0.03
10 4 0.06
11 9 0.14
12 27 0.43
13 15 0.24
14 2 0.03
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
AAATTTAAATAT
Found at i:17388434 original size:18 final size:18
Alignment explanation
Indices: 17388398--17388494 Score: 88
Period size: 18 Copynumber: 5.2 Consensus size: 18
17388388 TTAAGAAAAA
17388398 AAATTATAAAATTTAAATAT
1 AAATTATAAAA--TAAATAT
*
17388418 AAATTTTAAAATAAATAT
1 AAATTATAAAATAAATAT
** * *
17388436 AAAAAATATAATTAAAAAT
1 AAATTATA-AAATAAATAT
17388455 -AATTATAAAATTTAAATAT
1 AAATTATAAAA--TAAATAT
*
17388474 AAATTTTAAAATAAATAT
1 AAATTATAAAATAAATAT
17388492 AAA
1 AAA
17388495 AATATAATTA
Statistics
Matches: 62, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
17 2 0.03
18 27 0.44
19 14 0.23
20 19 0.31
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AAATTATAAAATAAATAT
Found at i:17388460 original size:56 final size:55
Alignment explanation
Indices: 17388393--17388518 Score: 207
Period size: 56 Copynumber: 2.3 Consensus size: 55
17388383 TATTATTAAG
*
17388393 AAAAAAAATTATAAAATTTAAATATAAATTTTAAAATAAATATAAAAAATATAATT
1 AAAAATAATTATAAAATTTAAATATAAATTTTAAAATAAATAT-AAAAATATAATT
17388449 AAAAATAATTATAAAATTTAAATATAAATTTTAAAATAAATATAAAAATATAATT
1 AAAAATAATTATAAAATTTAAATATAAATTTTAAAATAAATATAAAAATATAATT
* * *
17388504 ATAATTAATGATAAA
1 AAAAATAATTATAAA
17388519 TAAATAAAAT
Statistics
Matches: 66, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
55 24 0.36
56 42 0.64
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (55 bp):
AAAAATAATTATAAAATTTAAATATAAATTTTAAAATAAATATAAAAATATAATT
Found at i:17388498 original size:12 final size:12
Alignment explanation
Indices: 17388406--17388476 Score: 54
Period size: 12 Copynumber: 5.8 Consensus size: 12
17388396 AAAAATTATA
* *
17388406 AAATTTAAATAT
1 AAATATAAAAAT
* *
17388418 AAATTTTAAAAT
1 AAATATAAAAAT
17388430 AAATATAAAAAAT
1 AAATAT-AAAAAT
17388443 ATAAT-TAAAAAT
1 A-AATATAAAAAT
* *
17388455 AATTATAAAATTT
1 AAATATAAAA-AT
17388468 AAATATAAA
1 AAATATAAA
17388477 TTTTAAAATA
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
11 2 0.04
12 27 0.56
13 16 0.33
14 3 0.06
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
AAATATAAAAAT
Found at i:17392936 original size:5 final size:5
Alignment explanation
Indices: 17392928--17392956 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
17392918 TATAATATGG
17392928 TTAAT TTAAT TTAAT TTAAT TTAAT TTAA
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAA
17392957 ATAGTCATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TTAAT
Found at i:17396088 original size:17 final size:17
Alignment explanation
Indices: 17396055--17396088 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
17396045 TTTATAGTAC
*
17396055 TTTATATTATGTTATTT
1 TTTATATTATGTAATTT
*
17396072 TTTATATTTTGTAATTT
1 TTTATATTATGTAATTT
17396089 ACAACACATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (17 bp):
TTTATATTATGTAATTT
Found at i:17399123 original size:17 final size:18
Alignment explanation
Indices: 17399101--17399134 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17399091 TTAACTTAAC
17399101 TAAATTA-ATTTCTCAAA
1 TAAATTATATTTCTCAAA
*
17399118 TAAATTATTTTTCTCAA
1 TAAATTATATTTCTCAA
17399135 CTCAATTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (18 bp):
TAAATTATATTTCTCAAA
Found at i:17404766 original size:17 final size:18
Alignment explanation
Indices: 17404739--17404772 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
17404729 TCAACAAGTA
17404739 ATTTAAAAATTTAAAAAT
1 ATTTAAAAATTTAAAAAT
17404757 ATTT-AAAATTTAAAAA
1 ATTTAAAAATTTAAAAA
17404773 CTATAAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTTAAAAATTTAAAAAT
Found at i:17404767 original size:7 final size:8
Alignment explanation
Indices: 17404738--17404772 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
17404728 GTCAACAAGT
17404738 AATTTAAA
1 AATTTAAA
17404746 AATTTAAA
1 AATTTAAA
*
17404754 AATATTTAA
1 AAT-TTAAA
17404763 AATTTAAA
1 AATTTAAA
17404771 AA
1 AA
17404773 CTATAAAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 17 0.71
9 7 0.29
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
AATTTAAA
Found at i:17404781 original size:17 final size:17
Alignment explanation
Indices: 17404741--17404791 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
17404731 AACAAGTAAT
17404741 TTAAAAATTTAAAAATA
1 TTAAAAATTTAAAAATA
*
17404758 TTTAAAATTTAAAAACTA
1 TTAAAAATTTAAAAA-TA
* *
17404776 -TAAAAAGTTCAAAATA
1 TTAAAAATTTAAAAATA
17404792 ACTAGCACGT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 2 0.07
17 25 0.86
18 2 0.07
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (17 bp):
TTAAAAATTTAAAAATA
Found at i:17408214 original size:34 final size:34
Alignment explanation
Indices: 17408166--17408243 Score: 140
Period size: 34 Copynumber: 2.3 Consensus size: 34
17408156 TTTCTCATCT
*
17408166 TAAATTCCA-AAATTGGATTTGCGCCGGAAACCA
1 TAAATTTCATAAATTGGATTTGCGCCGGAAACCA
17408199 TAAATTTCATAAATTGGATTTGCGCCGGAAACCA
1 TAAATTTCATAAATTGGATTTGCGCCGGAAACCA
17408233 TAAATTTCATA
1 TAAATTTCATA
17408244 CACAATAGAA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 8 0.19
34 35 0.81
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.29
Consensus pattern (34 bp):
TAAATTTCATAAATTGGATTTGCGCCGGAAACCA
Found at i:17408438 original size:24 final size:24
Alignment explanation
Indices: 17408383--17408438 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
17408373 AAGATTTAAT
* *
17408383 ATTTATAAGTATAATATATTTAGC
1 ATTTATTAGTATAATATATTTAGA
17408407 ATTTATTAGTATAATATATTT-GA
1 ATTTATTAGTATAATATATTTAGA
17408430 ATTTGATTA
1 ATTT-ATTA
17408439 AAATTAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 5 0.17
24 24 0.83
ACGTcount: A:0.39, C:0.02, G:0.09, T:0.50
Consensus pattern (24 bp):
ATTTATTAGTATAATATATTTAGA
Found at i:17409664 original size:19 final size:19
Alignment explanation
Indices: 17409642--17409681 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
17409632 GTCGCTCACG
17409642 ACTCTCGGCCCCGCTCTCC
1 ACTCTCGGCCCCGCTCTCC
17409661 ACTCTCGGCCCCGCTCTCC
1 ACTCTCGGCCCCGCTCTCC
17409680 AC
1 AC
17409682 CGTTTCTTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.07, C:0.57, G:0.15, T:0.20
Consensus pattern (19 bp):
ACTCTCGGCCCCGCTCTCC
Found at i:17430748 original size:52 final size:52
Alignment explanation
Indices: 17430549--17430752 Score: 170
Period size: 52 Copynumber: 4.0 Consensus size: 52
17430539 TCATATATCA
* * * * * *
17430549 CACACCTAAGCCATAGCCCTGCCATGGTCTTACACG-GATCACATAT-A-AT
1 CACACCGATGCCATAGCCCAGCTATGGTCTTATACGAGAACACATATCACAT
* * * *
17430598 ---ACCGATGTCATATCCCAGATATGATCTTATACGA-AATCACATTATCACAT
1 CACACCGATGCCATAGCCCAGCTATGGTCTTATACGAGAA-CACA-TATCACAT
* * * *
17430648 CACACCGACGCCATAGCCCAGCTATGGTCTTATATGCGAACACGTATCACAT
1 CACACCGATGCCATAGCCCAGCTATGGTCTTATACGAGAACACATATCACAT
** * **
17430700 TGCACCGATGCCATAGCCCAGCTATGGTCTTATACGGGCGCACATATCACAT
1 CACACCGATGCCATAGCCCAGCTATGGTCTTATACGAGAACACATATCACAT
17430752 C
1 C
17430753 TTTTATGTCA
Statistics
Matches: 119, Mismatches: 27, Indels: 15
0.74 0.17 0.09
Matches are distributed among these distances:
46 25 0.21
47 4 0.03
48 3 0.03
49 1 0.01
50 2 0.02
52 52 0.44
53 30 0.25
54 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.24
Consensus pattern (52 bp):
CACACCGATGCCATAGCCCAGCTATGGTCTTATACGAGAACACATATCACAT
Found at i:17433405 original size:19 final size:18
Alignment explanation
Indices: 17433370--17433410 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 18
17433360 AATTAATTTT
17433370 TTAAAAAATTTAAAAATA
1 TTAAAAAATTTAAAAATA
17433388 TTAAAAAA-TTAATTAAATA
1 TTAAAAAATTTAA--AAATA
17433407 TTAA
1 TTAA
17433411 TGTATCATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.19
18 8 0.38
19 9 0.43
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TTAAAAAATTTAAAAATA
Found at i:17433515 original size:14 final size:14
Alignment explanation
Indices: 17433496--17433542 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
17433486 GATTTAATAA
17433496 AAAAATAAAAATTT
1 AAAAATAAAAATTT
*
17433510 AAAAATATAAAATAT
1 AAAAATA-AAAATTT
*
17433525 AAAAA-AATAATATT
1 AAAAATAAAAAT-TT
17433539 AAAA
1 AAAA
17433543 GCTAAAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
13 4 0.14
14 13 0.46
15 11 0.39
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAAATAAAAATTT
Found at i:17433521 original size:15 final size:15
Alignment explanation
Indices: 17433491--17433534 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
17433481 TAGGTGATTT
*
17433491 AATAAAAAAATA-AA
1 AATATAAAAATATAA
*
17433505 AATTTAAAAATATAA
1 AATATAAAAATATAA
*
17433520 AATATAAAAAAATAA
1 AATATAAAAATATAA
17433535 TATTAAAAGC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AATATAAAAATATAA
Found at i:17441679 original size:9 final size:9
Alignment explanation
Indices: 17441665--17441689 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
17441655 AAATAGAGTT
17441665 TTATATTAA
1 TTATATTAA
17441674 TTATATTAA
1 TTATATTAA
17441683 TTATATT
1 TTATATT
17441690 TTCATCATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
TTATATTAA
Found at i:17441764 original size:105 final size:105
Alignment explanation
Indices: 17441580--17441785 Score: 340
Period size: 105 Copynumber: 2.0 Consensus size: 105
17441570 TTTTAATAAA
* *
17441580 ATATTTTCATCATTAAGTAGATATTTATCAAAATTAAAAAACATTTATATACATTAAGATTTTAA
1 ATATTTTCATCATTAAATAGATATTTATCAAAATTAAAAAACATTTATATACATTAAGATTGTAA
* *
17441645 TATTTATTAAAAATAGAGTTTTATATTAATTATATTAATT
66 TATTTATTAAAAATAAAATTTTATATTAATTATATTAATT
** *
17441685 ATATTTTCATCATTAAATAGATATTTATCAAAATTAAAATGCATTTATATATATTAAGATTGTAA
1 ATATTTTCATCATTAAATAGATATTTATCAAAATTAAAAAACATTTATATACATTAAGATTGTAA
*
17441750 TATTTATTAGAAATAAAATTTTATATTAATTATATT
66 TATTTATTAAAAATAAAATTTTATATTAATTATATT
17441786 TTTTATGTGC
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
105 93 1.00
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (105 bp):
ATATTTTCATCATTAAATAGATATTTATCAAAATTAAAAAACATTTATATACATTAAGATTGTAA
TATTTATTAAAAATAAAATTTTATATTAATTATATTAATT
Found at i:17442885 original size:38 final size:38
Alignment explanation
Indices: 17442834--17442941 Score: 216
Period size: 38 Copynumber: 2.8 Consensus size: 38
17442824 GCCCTATTTA
17442834 ATCTATTAATCTCCATAGTACGTGAAAGAAAATAATAC
1 ATCTATTAATCTCCATAGTACGTGAAAGAAAATAATAC
17442872 ATCTATTAATCTCCATAGTACGTGAAAGAAAATAATAC
1 ATCTATTAATCTCCATAGTACGTGAAAGAAAATAATAC
17442910 ATCTATTAATCTCCATAGTACGTGAAAGAAAA
1 ATCTATTAATCTCCATAGTACGTGAAAGAAAA
17442942 GAATCAAATA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 70 1.00
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.29
Consensus pattern (38 bp):
ATCTATTAATCTCCATAGTACGTGAAAGAAAATAATAC
Found at i:17443695 original size:20 final size:18
Alignment explanation
Indices: 17443670--17443706 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
17443660 ATTGCTAAGT
17443670 TGTAAAATGAGTTGTAAATG
1 TGTAAAAT-AGTTG-AAATG
17443690 TGTAAAATAGTTGAAAT
1 TGTAAAATAGTTGAAAT
17443707 TATGAGTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
20 8 0.47
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (18 bp):
TGTAAAATAGTTGAAATG
Found at i:17454547 original size:25 final size:25
Alignment explanation
Indices: 17454513--17454576 Score: 112
Period size: 25 Copynumber: 2.6 Consensus size: 25
17454503 TCTGTAAAAT
17454513 CAATTGAAACGGTGCGTGGT-GGAAA
1 CAATTGAAACGGTGCGTGGTAGG-AA
17454538 CAATTGAAACGGTGCGTGGTAGGAA
1 CAATTGAAACGGTGCGTGGTAGGAA
17454563 CAATTGAAACGGTG
1 CAATTGAAACGGTG
17454577 AGTTTTGAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 36 0.95
26 2 0.05
ACGTcount: A:0.33, C:0.12, G:0.34, T:0.20
Consensus pattern (25 bp):
CAATTGAAACGGTGCGTGGTAGGAA
Found at i:17455742 original size:7 final size:7
Alignment explanation
Indices: 17455730--17455865 Score: 80
Period size: 7 Copynumber: 19.1 Consensus size: 7
17455720 ACTAATTAAT
17455730 CTAAACC
1 CTAAACC
17455737 CTAAACC
1 CTAAACC
*
17455744 TCTTAACTC
1 -CTAAAC-C
*
17455753 CT-ATCC
1 CTAAACC
*
17455759 CATAAACA
1 C-TAAACC
17455767 CTAAACC
1 CTAAACC
17455774 CTAAACC
1 CTAAACC
*
17455781 CTTAACC
1 CTAAACC
*
17455788 CTTAACC
1 CTAAACC
*
17455795 CCAAACC
1 CTAAACC
*
17455802 CTTACACC
1 C-TAAACC
*
17455810 TTAAACTC
1 CTAAAC-C
17455818 C--AACC
1 CTAAACC
*
17455823 CTAACCC
1 CTAAACC
*
17455830 CTAACCC
1 CTAAACC
17455837 CTAAACC
1 CTAAACC
* *
17455844 TTAAATC
1 CTAAACC
* *
17455851 ATAATCC
1 CTAAACC
17455858 CTAAACC
1 CTAAACC
17455865 C
1 C
17455866 ACAATTCATC
Statistics
Matches: 99, Mismatches: 22, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
5 2 0.02
6 5 0.05
7 76 0.77
8 15 0.15
9 1 0.01
ACGTcount: A:0.37, C:0.42, G:0.00, T:0.21
Consensus pattern (7 bp):
CTAAACC
Found at i:17455945 original size:46 final size:46
Alignment explanation
Indices: 17455892--17455985 Score: 161
Period size: 46 Copynumber: 2.0 Consensus size: 46
17455882 CTTCAAATAC
* * *
17455892 TAGTTAACTCCTAAACCTTAAACCCTAAACCATATATCTTAAACCA
1 TAGTTAACTCATAAACCATAAACCCTAAACCATATATATTAAACCA
17455938 TAGTTAACTCATAAACCATAAACCCTAAACCATATATATTAAACCA
1 TAGTTAACTCATAAACCATAAACCCTAAACCATATATATTAAACCA
17455984 TA
1 TA
17455986 AACCATAAAC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.45, C:0.26, G:0.02, T:0.28
Consensus pattern (46 bp):
TAGTTAACTCATAAACCATAAACCCTAAACCATATATATTAAACCA
Found at i:17455959 original size:7 final size:7
Alignment explanation
Indices: 17455903--17456000 Score: 63
Period size: 7 Copynumber: 13.4 Consensus size: 7
17455893 AGTTAACTCC
*
17455903 TAAACCT
1 TAAACCA
*
17455910 TAAACCC
1 TAAACCA
17455917 TAAACCA
1 TAAACCA
* * *
17455924 TATATCT
1 TAAACCA
17455931 TAAACCA
1 TAAACCA
17455938 TAGTTAACTCA
1 TA---AAC-CA
17455949 TAAACCA
1 TAAACCA
*
17455956 TAAACCC
1 TAAACCA
17455963 TAAACCA
1 TAAACCA
* *
17455970 TATA-TA
1 TAAACCA
17455976 TTAAACCA
1 -TAAACCA
17455984 TAAACCA
1 TAAACCA
*
17455991 TAAACTA
1 TAAACCA
17455998 TAA
1 TAA
17456001 TGATAATTAA
Statistics
Matches: 70, Mismatches: 15, Indels: 12
0.72 0.15 0.12
Matches are distributed among these distances:
6 1 0.01
7 58 0.83
8 4 0.06
10 3 0.04
11 4 0.06
ACGTcount: A:0.49, C:0.24, G:0.01, T:0.26
Consensus pattern (7 bp):
TAAACCA
Found at i:17456201 original size:41 final size:41
Alignment explanation
Indices: 17456156--17456374 Score: 300
Period size: 41 Copynumber: 5.4 Consensus size: 41
17456146 GTTATATGAC
*
17456156 TTTTAGCGGCGTTTTTCCAAAAGCGCCACTAATGCTCTGGT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
*
17456197 TTTTAGCGGCGTTTTGCC-AAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
* * *
17456237 TTTTAGCGGCGCTTTACGAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
* * *
17456278 TTTTAGCGGCGCTTTGCCAAAAGCGCCACTAATGCTCTGGT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
* ** *
17456319 TTTTGGCGGCGTTTTTCCAAAAGCATCGCTAATGCTCT-AT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
17456359 TTTTCA-CGGCGTTTTT
1 TTTT-AGCGGCGTTTTT
17456375 GGTAAAAACG
Statistics
Matches: 160, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
40 51 0.32
41 109 0.68
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.34
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
Found at i:17456294 original size:81 final size:82
Alignment explanation
Indices: 17456156--17456356 Score: 314
Period size: 81 Copynumber: 2.5 Consensus size: 82
17456146 GTTATATGAC
* *
17456156 TTTTAGCGGCGTTTTTCCAAAAGCGCCACTAATGCTCTGGTTTTTAGCGGCGTTTTGCC-AAAGC
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGCTTTGCCAAAAGC
*
17456220 GCCGCTAATGCTCTGGT
66 GCCACTAATGCTCTGGT
* * *
17456237 TTTTAGCGGCGCTTTACGAAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGCTTTGCCAAAAGC
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGCTTTGCCAAAAGC
17456302 GCCACTAATGCTCTGGT
66 GCCACTAATGCTCTGGT
* **
17456319 TTTTGGCGGCGTTTTTCCAAAAGCATCGCTAATGCTCT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCT
17456357 ATTTTTCACG
Statistics
Matches: 107, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
81 54 0.50
82 53 0.50
ACGTcount: A:0.18, C:0.25, G:0.24, T:0.32
Consensus pattern (82 bp):
TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGCTTTGCCAAAAGC
GCCACTAATGCTCTGGT
Found at i:17456403 original size:122 final size:122
Alignment explanation
Indices: 17456150--17456410 Score: 321
Period size: 122 Copynumber: 2.1 Consensus size: 122
17456140 TTAAGGGTTA
* * *
17456150 TATGACTTTTAGCGGCGTTTTTCCAAAAGCGCCACTAATGCTCTGGTTTTTAGCGGCGTTTTGCC
1 TATGATTTTTAGCGGCGCTTTGCCAAAAGCGCCACTAATGCTCTGGTTTTTAGCGGCGTTTTGCC
* * *
17456215 AAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGCTTTACGAAAAGCGCCGCTAATGC
66 AAAGCACCGCTAATGCTCTGATTTTTAGCGGCGCTTTACGAAAAACGCCGCTAATGC
* * * *
17456272 TCTGGTTTTTAGCGGCGCTTTGCCAAAAGCGCCACTAATGCTCTGGTTTTTGGCGGCGTTTTTCC
1 TATGATTTTTAGCGGCGCTTTGCCAAAAGCGCCACTAATGCTCTGGTTTTTAGCGGCGTTTTGCC
* * ** * *
17456337 AAAAGCATCGCTAATGCTCT-ATTTTTCA-CGGCGTTTTTGGTAAAAACGCTGCTATTGC
66 -AAAGCACCGCTAATGCTCTGATTTTT-AGCGGCGCTTTACG-AAAAACGCCGCTAATGC
*
17456395 TAT-ATTTTTAGTGGCG
1 TATGATTTTTAGCGGCG
17456411 TTTTTGGTAA
Statistics
Matches: 117, Mismatches: 19, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
122 83 0.71
123 34 0.29
ACGTcount: A:0.19, C:0.23, G:0.24, T:0.34
Consensus pattern (122 bp):
TATGATTTTTAGCGGCGCTTTGCCAAAAGCGCCACTAATGCTCTGGTTTTTAGCGGCGTTTTGCC
AAAGCACCGCTAATGCTCTGATTTTTAGCGGCGCTTTACGAAAAACGCCGCTAATGC
Found at i:17456483 original size:12 final size:12
Alignment explanation
Indices: 17456468--17456493 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
17456458 GTTTTTTGAT
17456468 AAAACGCCGCTA
1 AAAACGCCGCTA
17456480 AAAACGCCGCTA
1 AAAACGCCGCTA
17456492 AA
1 AA
17456494 GCCCTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAAACGCCGCTA
Found at i:17457117 original size:17 final size:17
Alignment explanation
Indices: 17457095--17457129 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
17457085 GAAAAGAAGA
**
17457095 AAAAGAAGGTAAAGACG
1 AAAAGAAGAAAAAGACG
17457112 AAAAGAAGAAAAAGACG
1 AAAAGAAGAAAAAGACG
17457129 A
1 A
17457130 GGATATGCTG
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:0.66, C:0.06, G:0.26, T:0.03
Consensus pattern (17 bp):
AAAAGAAGAAAAAGACG
Found at i:17458866 original size:18 final size:19
Alignment explanation
Indices: 17458845--17458894 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 19
17458835 ATGTATTAGA
17458845 TATTAAATAA-ATATTTAT
1 TATTAAATAAGATATTTAT
17458863 TATTTTATAA-AAGATATTTAT
1 TA--TTA-AATAAGATATTTAT
17458884 TAATTAAATAA
1 T-ATTAAATAA
17458895 TTATATTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
18 2 0.08
19 2 0.08
20 10 0.38
21 11 0.42
22 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
TATTAAATAAGATATTTAT
Found at i:17460955 original size:13 final size:13
Alignment explanation
Indices: 17460937--17460968 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
17460927 ATAGTTTAAT
17460937 AATAAAATAAAGA
1 AATAAAATAAAGA
17460950 AATAAAATAAAGA
1 AATAAAATAAAGA
17460963 AATAAA
1 AATAAA
17460969 TGAAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.16
Consensus pattern (13 bp):
AATAAAATAAAGA
Found at i:17460974 original size:18 final size:17
Alignment explanation
Indices: 17460949--17460983 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
17460939 TAAAATAAAG
*
17460949 AAATAAAATAAAGAAAT
1 AAATAAAAAAAAGAAAT
17460966 AAATGAAAAAAAAGAAAT
1 AAAT-AAAAAAAAGAAAT
17460984 GAAAAAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (17 bp):
AAATAAAAAAAAGAAAT
Found at i:17461034 original size:4 final size:4
Alignment explanation
Indices: 17461025--17461058 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
17461015 AGAACAGGTG
*
17461025 AGAA AGAA AGGAA AGAA AGAA AGAA AGAG AGAA A
1 AGAA AGAA A-GAA AGAA AGAA AGAA AGAA AGAA A
17461059 AGGGAAAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:17462227 original size:15 final size:15
Alignment explanation
Indices: 17462204--17462251 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
17462194 TATCAAATTT
17462204 ATATTGATTGAAATC
1 ATATTGATTGAAATC
* * *
17462219 ATTTTGATTGAATTT
1 ATATTGATTGAAATC
17462234 ATATTGATTGAAAT-
1 ATATTGATTGAAATC
17462248 ATAT
1 ATAT
17462252 ATTATATATA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (15 bp):
ATATTGATTGAAATC
Found at i:17462766 original size:23 final size:23
Alignment explanation
Indices: 17462740--17462797 Score: 107
Period size: 23 Copynumber: 2.5 Consensus size: 23
17462730 TTAATATCCG
17462740 GGTGTGTTTGGGTTGGATATTCT
1 GGTGTGTTTGGGTTGGATATTCT
*
17462763 GGTGTGTTTGGGTTGGGTATTCT
1 GGTGTGTTTGGGTTGGATATTCT
17462786 GGTGTGTTTGGG
1 GGTGTGTTTGGG
17462798 AGGAATCCAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.05, C:0.03, G:0.45, T:0.47
Consensus pattern (23 bp):
GGTGTGTTTGGGTTGGATATTCT
Found at i:17462915 original size:12 final size:12
Alignment explanation
Indices: 17462898--17462922 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17462888 AATGAAATGA
17462898 AATTGAATTGAG
1 AATTGAATTGAG
17462910 AATTGAATTGAG
1 AATTGAATTGAG
17462922 A
1 A
17462923 TATGAGATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.24, T:0.32
Consensus pattern (12 bp):
AATTGAATTGAG
Found at i:17486508 original size:23 final size:23
Alignment explanation
Indices: 17486482--17486544 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
17486472 TGATTTATAT
*
17486482 ATTTAAATTAA-ATTTTAAGAAC
1 ATTTAAATTAATATTTTAAAAAC
* *
17486504 AATTTATATTAATGTTTTAAAAAC
1 -ATTTAAATTAATATTTTAAAAAC
*
17486528 ATTTAAGATTTATATTT
1 ATTTAA-ATTAATATTT
17486545 CATGTATCAA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
23 15 0.47
24 17 0.53
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (23 bp):
ATTTAAATTAATATTTTAAAAAC
Found at i:17506173 original size:25 final size:25
Alignment explanation
Indices: 17506139--17506202 Score: 112
Period size: 25 Copynumber: 2.6 Consensus size: 25
17506129 ATCTGTAAAT
17506139 CAATTGAAACGGTGCGTGGT-GGAAA
1 CAATTGAAACGGTGCGTGGTAGG-AA
17506164 CAATTGAAACGGTGCGTGGTAGGAA
1 CAATTGAAACGGTGCGTGGTAGGAA
17506189 CAATTGAAACGGTG
1 CAATTGAAACGGTG
17506203 AGTTTTGAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 36 0.95
26 2 0.05
ACGTcount: A:0.33, C:0.12, G:0.34, T:0.20
Consensus pattern (25 bp):
CAATTGAAACGGTGCGTGGTAGGAA
Found at i:17507361 original size:7 final size:7
Alignment explanation
Indices: 17507349--17507484 Score: 80
Period size: 7 Copynumber: 19.1 Consensus size: 7
17507339 ACTAATTAAT
17507349 CTAAACC
1 CTAAACC
17507356 CTAAACC
1 CTAAACC
*
17507363 TCTTAACTC
1 -CTAAAC-C
*
17507372 CT-ATCC
1 CTAAACC
*
17507378 CATAAACA
1 C-TAAACC
17507386 CTAAACC
1 CTAAACC
17507393 CTAAACC
1 CTAAACC
*
17507400 CTTAACC
1 CTAAACC
*
17507407 CTTAACC
1 CTAAACC
*
17507414 CCAAACC
1 CTAAACC
*
17507421 CTTACACC
1 C-TAAACC
*
17507429 TTAAACTC
1 CTAAAC-C
17507437 C--AACC
1 CTAAACC
*
17507442 CTAACCC
1 CTAAACC
*
17507449 CTAACCC
1 CTAAACC
17507456 CTAAACC
1 CTAAACC
* *
17507463 TTAAATC
1 CTAAACC
* *
17507470 ATAATCC
1 CTAAACC
17507477 CTAAACC
1 CTAAACC
17507484 C
1 C
17507485 ACAATTCATC
Statistics
Matches: 99, Mismatches: 22, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
5 2 0.02
6 5 0.05
7 76 0.77
8 15 0.15
9 1 0.01
ACGTcount: A:0.37, C:0.42, G:0.00, T:0.21
Consensus pattern (7 bp):
CTAAACC
Found at i:17507564 original size:46 final size:46
Alignment explanation
Indices: 17507511--17507604 Score: 161
Period size: 46 Copynumber: 2.0 Consensus size: 46
17507501 CTTCAAATAC
* * *
17507511 TAGTTAACTCCTAAACCTTAAACCCTAAACCATATATCTTAAACCA
1 TAGTTAACTCATAAACCATAAACCCTAAACCATATATATTAAACCA
17507557 TAGTTAACTCATAAACCATAAACCCTAAACCATATATATTAAACCA
1 TAGTTAACTCATAAACCATAAACCCTAAACCATATATATTAAACCA
17507603 TA
1 TA
17507605 AACCATAAAC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.45, C:0.26, G:0.02, T:0.28
Consensus pattern (46 bp):
TAGTTAACTCATAAACCATAAACCCTAAACCATATATATTAAACCA
Found at i:17507578 original size:7 final size:7
Alignment explanation
Indices: 17507522--17507619 Score: 63
Period size: 7 Copynumber: 13.4 Consensus size: 7
17507512 AGTTAACTCC
*
17507522 TAAACCT
1 TAAACCA
*
17507529 TAAACCC
1 TAAACCA
17507536 TAAACCA
1 TAAACCA
* * *
17507543 TATATCT
1 TAAACCA
17507550 TAAACCA
1 TAAACCA
17507557 TAGTTAACTCA
1 TA---AAC-CA
17507568 TAAACCA
1 TAAACCA
*
17507575 TAAACCC
1 TAAACCA
17507582 TAAACCA
1 TAAACCA
* *
17507589 TATA-TA
1 TAAACCA
17507595 TTAAACCA
1 -TAAACCA
17507603 TAAACCA
1 TAAACCA
*
17507610 TAAACTA
1 TAAACCA
17507617 TAA
1 TAA
17507620 TGATAATTAA
Statistics
Matches: 70, Mismatches: 15, Indels: 12
0.72 0.15 0.12
Matches are distributed among these distances:
6 1 0.01
7 58 0.83
8 4 0.06
10 3 0.04
11 4 0.06
ACGTcount: A:0.49, C:0.24, G:0.01, T:0.26
Consensus pattern (7 bp):
TAAACCA
Found at i:17507820 original size:41 final size:41
Alignment explanation
Indices: 17507775--17507993 Score: 300
Period size: 41 Copynumber: 5.4 Consensus size: 41
17507765 GTTATATGAC
*
17507775 TTTTAGCGGCGTTTTTCCAAAAGCGCCACTAATGCTCTGGT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
*
17507816 TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
* * *
17507857 TTTTAGCGGCGCTTTACGAAAAGCGCCGCTAATGCTCTGG-
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
* * *
17507897 TTTTAGCGGCGCTTTGCCAAAAGCGCCACTAATGCTCTGGT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
* ** *
17507938 TTTTGGCGGCGTTTTTCCAAAAGCATCGCTAATGCTCT-AT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
17507978 TTTTCA-CGGCGTTTTT
1 TTTT-AGCGGCGTTTTT
17507994 GGTAAAAACG
Statistics
Matches: 160, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
40 52 0.32
41 108 0.68
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.34
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
Found at i:17507934 original size:81 final size:82
Alignment explanation
Indices: 17507775--17507975 Score: 314
Period size: 81 Copynumber: 2.5 Consensus size: 82
17507765 GTTATATGAC
* *
17507775 TTTTAGCGGCGTTTTTCCAAAAGCGCCACTAATGCTCTGGTTTTTAGCGGCGTTTTGCCAAAAGC
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGCTTTGCCAAAAGC
*
17507840 GCCGCTAATGCTCTGGT
66 GCCACTAATGCTCTGGT
* * *
17507857 TTTTAGCGGCGCTTTACGAAAAGCGCCGCTAATGCTCTGG-TTTTAGCGGCGCTTTGCCAAAAGC
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGCTTTGCCAAAAGC
17507921 GCCACTAATGCTCTGGT
66 GCCACTAATGCTCTGGT
* **
17507938 TTTTGGCGGCGTTTTTCCAAAAGCATCGCTAATGCTCT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCT
17507976 ATTTTTCACG
Statistics
Matches: 107, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
81 71 0.66
82 36 0.34
ACGTcount: A:0.19, C:0.25, G:0.24, T:0.32
Consensus pattern (82 bp):
TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGCTTTGCCAAAAGC
GCCACTAATGCTCTGGT
Found at i:17508023 original size:122 final size:122
Alignment explanation
Indices: 17507775--17508029 Score: 325
Period size: 122 Copynumber: 2.1 Consensus size: 122
17507765 GTTATATGAC
* *
17507775 TTTTAGCGGCGTTTTTCCAAAAGCGCCACTAATGCTCTGGTTTTTAGCGGCGTTTTGCCAAAAGC
1 TTTTAGCGGCGCTTTGCCAAAAGCGCCACTAATGCTCTGGTTTTTAGCGGCGTTTTGCCAAAAGC
* * * * *
17507840 GCCGCTAATGCTCTGGTTTTTAGCGGCGCTTTACGAAAAGCGCCGCTAATGCTCTGG
66 ACCGCTAATGCTCTGATTTTTAGCGGCGCTTTACGAAAAACGCCGCTAATGCTATAG
* *
17507897 TTTTAGCGGCGCTTTGCCAAAAGCGCCACTAATGCTCTGGTTTTTGGCGGCGTTTTTCCAAAAGC
1 TTTTAGCGGCGCTTTGCCAAAAGCGCCACTAATGCTCTGGTTTTTAGCGGCGTTTTGCCAAAAGC
* * ** * * *
17507962 ATCGCTAATGCTCT-ATTTTTCA-CGGCGTTTTTGGTAAAAACGCTGCTATTGCTATAT
66 ACCGCTAATGCTCTGATTTTT-AGCGGCGCTTTACG-AAAAACGCCGCTAATGCTATAG
*
17508019 TTTTAGTGGCG
1 TTTTAGCGGCG
17508030 TTTTTGGTAA
Statistics
Matches: 114, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
121 14 0.12
122 100 0.88
ACGTcount: A:0.19, C:0.23, G:0.24, T:0.34
Consensus pattern (122 bp):
TTTTAGCGGCGCTTTGCCAAAAGCGCCACTAATGCTCTGGTTTTTAGCGGCGTTTTGCCAAAAGC
ACCGCTAATGCTCTGATTTTTAGCGGCGCTTTACGAAAAACGCCGCTAATGCTATAG
Found at i:17508103 original size:12 final size:12
Alignment explanation
Indices: 17508088--17508112 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17508078 GTTTTTTGAT
17508088 AAACGCCGCTAA
1 AAACGCCGCTAA
17508100 AAACGCCGCTAA
1 AAACGCCGCTAA
17508112 A
1 A
17508113 GCCCTATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.32, G:0.16, T:0.08
Consensus pattern (12 bp):
AAACGCCGCTAA
Found at i:17508728 original size:17 final size:17
Alignment explanation
Indices: 17508701--17508743 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
17508691 GGCATTGCCG
* *
17508701 AAAAGAAGAAAAGAAGG
1 AAAAGACGAAAAGAAGA
*
17508718 TAAAGACGAAAAGAAGA
1 AAAAGACGAAAAGAAGA
17508735 AAAAGACGA
1 AAAAGACGA
17508744 GGATATGCTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.67, C:0.05, G:0.26, T:0.02
Consensus pattern (17 bp):
AAAAGACGAAAAGAAGA
Found at i:17510477 original size:18 final size:19
Alignment explanation
Indices: 17510456--17510505 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 19
17510446 ATGTATTAGA
17510456 TATTAAATAA-ATATTTAT
1 TATTAAATAAGATATTTAT
17510474 TATTTTATAA-AAGATATTTAT
1 TA--TTA-AATAAGATATTTAT
17510495 TAATTAAATAA
1 T-ATTAAATAA
17510506 TTATATTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
18 2 0.08
19 2 0.08
20 10 0.38
21 11 0.42
22 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
TATTAAATAAGATATTTAT
Found at i:17512565 original size:13 final size:13
Alignment explanation
Indices: 17512547--17512578 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
17512537 ATAGTTTAAT
17512547 AATAAAATAAAGA
1 AATAAAATAAAGA
17512560 AATAAAATAAAGA
1 AATAAAATAAAGA
17512573 AATAAA
1 AATAAA
17512579 TGAAAAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.16
Consensus pattern (13 bp):
AATAAAATAAAGA
Found at i:17512588 original size:17 final size:17
Alignment explanation
Indices: 17512559--17512592 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
17512549 TAAAATAAAG
17512559 AAATAAAATAAAGAAAT
1 AAATAAAATAAAGAAAT
17512576 AAATGAAAA-AAAGAAAT
1 AAAT-AAAATAAAGAAAT
17512593 GAAAAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (17 bp):
AAATAAAATAAAGAAAT
Done.