Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 77 of 202
Found at i:22813513 original size:25 final size:26
Alignment explanation
Indices: 22813480--22813539 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
22813470 TTTAAAATAC
* *
22813480 TTTTAAAAT-AATTTTTATTTTTTAT
1 TTTTAAAATAAATTTTTAATGTTTAT
22813505 TTTTAAAATAAATTTTTAATGTTTAT
1 TTTTAAAATAAATTTTTAATGTTTAT
*
22813531 TTTAAAAAT
1 TTTTAAAAT
22813540 GGGCCGGGCC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
25 9 0.29
26 22 0.71
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (26 bp):
TTTTAAAATAAATTTTTAATGTTTAT
Found at i:22817502 original size:52 final size:52
Alignment explanation
Indices: 22817419--22817519 Score: 159
Period size: 52 Copynumber: 1.9 Consensus size: 52
22817409 TAAGGAAACG
* *
22817419 TAATGGACAGCAGCTTAAGATCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
1 TAATAGACAGCAGCTTAAGATCTCATCTCTAGCTCGGTTGAAGCTCAAACAA
*
22817471 TAATAGACAGCAGCTTAAGA-CTTCATCTCTAGCTCGGTTGAAGGTCAAA
1 TAATAGACAGCAGCTTAAGATC-TCATCTCTAGCTCGGTTGAAGCTCAAA
22817520 TATGTGCATG
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 1 0.02
52 44 0.98
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.27
Consensus pattern (52 bp):
TAATAGACAGCAGCTTAAGATCTCATCTCTAGCTCGGTTGAAGCTCAAACAA
Found at i:22828114 original size:28 final size:27
Alignment explanation
Indices: 22828071--22828139 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
22828061 AAATAAAAAA
*
22828071 TTACCAAAATGT-TATAACTTTTTTTAT
1 TTACCAAAATATATATAA-TTTTTTTAT
22828098 TTACCAAAATATATATAATTTTTTTAT
1 TTACCAAAATATATATAATTTTTTTAT
22828125 TTACCAAAATATATA
1 TTACCAAAATATATA
22828140 AAAAAATAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
27 35 0.88
28 5 0.12
ACGTcount: A:0.41, C:0.10, G:0.01, T:0.48
Consensus pattern (27 bp):
TTACCAAAATATATATAATTTTTTTAT
Found at i:22828226 original size:27 final size:27
Alignment explanation
Indices: 22828196--22828262 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
22828186 AAGGAAGCAG
22828196 GTTGGCGGCACCAAACAAGGGATCCCT
1 GTTGGCGGCACCAAACAAGGGATCCCT
****
22828223 GTTGGCGGCACCAGTGGAGGGATCCCT
1 GTTGGCGGCACCAAACAAGGGATCCCT
22828250 GTTGGCGGCACCA
1 GTTGGCGGCACCA
22828263 CCCTTGAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.19, C:0.28, G:0.36, T:0.16
Consensus pattern (27 bp):
GTTGGCGGCACCAAACAAGGGATCCCT
Found at i:22828332 original size:18 final size:17
Alignment explanation
Indices: 22828309--22828386 Score: 72
Period size: 18 Copynumber: 4.5 Consensus size: 17
22828299 GAAGGAGAGG
22828309 GGAAG-AAGAAGAAAGAAA
1 GGAAGAAAGAA-AAAG-AA
22828327 GGAAGAAAGAAAAAGAA
1 GGAAGAAAGAAAAAGAA
* *
22828344 GG-A-AAAGGAAAGGAGA
1 GGAAGAAAGAAAAAGA-A
22828360 GGAAAGAAAGAAAAAGAA
1 GG-AAGAAAGAAAAAGAA
22828378 GGAAAGAAA
1 GG-AAGAAA
22828387 AGGAAAGGGG
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
15 9 0.18
16 4 0.08
17 4 0.08
18 20 0.39
19 14 0.27
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (17 bp):
GGAAGAAAGAAAAAGAA
Found at i:22828342 original size:10 final size:10
Alignment explanation
Indices: 22828311--22828382 Score: 54
Period size: 10 Copynumber: 6.6 Consensus size: 10
22828301 AGGAGAGGGG
*
22828311 AAGAAGAAGA
1 AAGAAAAAGA
22828321 AAGAAAGGAAGA
1 AAGAAA--AAGA
22828333 AAGAAAAAGA
1 AAGAAAAAGA
* *
22828343 AGGAAAAGGA
1 AAGAAAAAGA
22828353 AAGGAGAGGAAAGA
1 AA-GA-A--AAAGA
22828367 AAGAAAAAGA
1 AAGAAAAAGA
*
22828377 AGGAAA
1 AAGAAA
22828383 GAAAAGGAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
10 28 0.56
11 2 0.04
12 12 0.24
13 2 0.04
14 6 0.12
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (10 bp):
AAGAAAAAGA
Found at i:22828342 original size:22 final size:23
Alignment explanation
Indices: 22828311--22828393 Score: 71
Period size: 24 Copynumber: 3.6 Consensus size: 23
22828301 AGGAGAGGGG
*
22828311 AAGAAGAAGAAAG-AAAGGAAGA
1 AAGAAAAAGAAAGAAAAGGAAGA
*
22828333 AAGAAAAAGAAGGAAAAGGAA-A
1 AAGAAAAAGAAAGAAAAGGAAGA
* * *
22828355 GGAGAGGAAAGAAAGAAAAAGAAGGA
1 -AAGA-AAAAGAAAGAAAAGGAA-GA
*
22828381 AAGAAAAGGAAAG
1 AAGAAAAAGAAAG
22828394 GGGAGGAAAT
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
22 12 0.26
23 10 0.21
24 21 0.45
25 3 0.06
26 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (23 bp):
AAGAAAAAGAAAGAAAAGGAAGA
Found at i:22828348 original size:14 final size:13
Alignment explanation
Indices: 22828314--22828387 Score: 51
Period size: 14 Copynumber: 5.1 Consensus size: 13
22828304 AGAGGGGAAG
22828314 AAGAAGAAAG-AA
1 AAGAAGAAAGAAA
*
22828326 AGGAAGAAAGAAA
1 AAGAAGAAAGAAA
22828339 AAGAAGGAAAAGGAAA
1 AAGAA-G-AAA-GAAA
22828355 GGAGAGGAAAGAAAGAAA
1 --A-A-G-AAGAAAGAAA
22828373 AAGAAGGAAAGAAA
1 AAGAA-GAAAGAAA
22828387 A
1 A
22828388 GGAAAGGGGA
Statistics
Matches: 50, Mismatches: 2, Indels: 18
0.71 0.03 0.26
Matches are distributed among these distances:
12 9 0.18
13 8 0.16
14 11 0.22
15 4 0.08
16 5 0.10
18 5 0.10
19 4 0.08
20 2 0.04
21 2 0.04
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (13 bp):
AAGAAGAAAGAAA
Found at i:22828369 original size:28 final size:28
Alignment explanation
Indices: 22828314--22828393 Score: 85
Period size: 34 Copynumber: 2.8 Consensus size: 28
22828304 AGAGGGGAAG
22828314 AAGAA-GAAAG-AAAGG-AAGAAAGAAA
1 AAGAAGGAAAGAAAAGGAAAGAAAGAAA
22828339 AAGAAGGAAAAGGAAAGGAGAGGAAAGAAAGAAA
1 AAGAAGG-AAA-G-AA--A-AGGAAAGAAAGAAA
22828373 AAGAAGGAAAGAAAAGGAAAG
1 AAGAAGGAAAGAAAAGGAAAG
22828394 GGGAGGAAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 15
0.75 0.00 0.25
Matches are distributed among these distances:
25 5 0.11
26 1 0.02
27 3 0.07
28 8 0.17
29 1 0.02
30 1 0.02
31 2 0.04
32 2 0.04
33 6 0.13
34 17 0.37
ACGTcount: A:0.68, C:0.00, G:0.33, T:0.00
Consensus pattern (28 bp):
AAGAAGGAAAGAAAAGGAAAGAAAGAAA
Found at i:22828387 original size:38 final size:36
Alignment explanation
Indices: 22828329--22828487 Score: 137
Period size: 38 Copynumber: 4.3 Consensus size: 36
22828319 GAAAGAAAGG
22828329 AAGAAAGAAAAAGAAG--GAAAAGGAAAGGAGAGGA
1 AAGAAAGAAAAAGAAGAAGAAAAGGAAAGGAGAGGA
*
22828363 AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGGGAGGA
1 AAGAAAGAAAAAGAA-G-AAGAAAAGGAAAGGAGAGGA
* * * *
22828401 AATAAAGAAAAATAAGGAAAGAAGAGGAAATGAGAAGAGA
1 AAGAAAGAAAAAGAA-G-AAGAAAAGGAAAGGAG-AG-GA
* * *
22828441 AA-AAAAAAGAAAGAAGAAGAAGAGGGAAGGA-AGGAA
1 AAGAAAGAA-AAAGAAGAAGAAAAGGAAAGGAGAGG-A
*
22828477 AAAAAAGAAAA
1 AAGAAAGAAAA
22828488 TAAGGTAATT
Statistics
Matches: 105, Mismatches: 11, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
34 15 0.14
35 2 0.02
36 7 0.07
37 5 0.05
38 59 0.56
39 8 0.08
40 9 0.09
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (36 bp):
AAGAAAGAAAAAGAAGAAGAAAAGGAAAGGAGAGGA
Found at i:22828389 original size:10 final size:10
Alignment explanation
Indices: 22828331--22828455 Score: 64
Period size: 10 Copynumber: 12.7 Consensus size: 10
22828321 AAGAAAGGAA
*
22828331 GAAAGAAAAA
1 GAAAGAAAAG
*
22828341 GAAGGAAAAG
1 GAAAGAAAAG
* *
22828351 GAAAGGAGAG
1 GAAAGAAAAG
22828361 GAAAG-AAA-
1 GAAAGAAAAG
22828369 GAAA-AAGAAG
1 GAAAGAA-AAG
22828379 GAAAGAAAAG
1 GAAAGAAAAG
***
22828389 GAAAGGGGAG
1 GAAAGAAAAG
*
22828399 GAAA-TAAA-
1 GAAAGAAAAG
22828407 GAAA-AATAAG
1 GAAAGAA-AAG
*
22828417 GAAAGAAGAG
1 GAAAGAAAAG
*
22828427 GAAATGAGAAG
1 GAAA-GAAAAG
* *
22828438 AGAAAAAAAAA
1 -GAAAGAAAAG
22828449 GAAAGAA
1 GAAAGAA
22828456 GAAGAAGAGG
Statistics
Matches: 86, Mismatches: 20, Indels: 18
0.69 0.16 0.15
Matches are distributed among these distances:
8 10 0.12
9 7 0.08
10 54 0.63
11 11 0.13
12 4 0.05
ACGTcount: A:0.66, C:0.00, G:0.31, T:0.02
Consensus pattern (10 bp):
GAAAGAAAAG
Found at i:22828393 original size:18 final size:19
Alignment explanation
Indices: 22828345--22828393 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
22828335 GAAAAAGAAG
22828345 GAAAAGGAAAGGAGAGGAAA
1 GAAAAGGAAA-GAGAGGAAA
*
22828365 G-AAA-GAAAAAGAAGGAAA
1 GAAAAGGAAAGAG-AGGAAA
22828383 GAAAAGGAAAG
1 GAAAAGGAAAG
22828394 GGGAGGAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
17 2 0.08
18 11 0.46
19 6 0.25
20 5 0.21
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (19 bp):
GAAAAGGAAAGAGAGGAAA
Found at i:22829197 original size:19 final size:19
Alignment explanation
Indices: 22829172--22829213 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
22829162 AATATTTTGG
* *
22829172 TATTTTTTTAATATTTTTAT
1 TATTTTTGTAAT-GTTTTAT
22829192 TATTTTTGTAATGTTTTAT
1 TATTTTTGTAATGTTTTAT
22829211 TAT
1 TAT
22829214 GGGTTTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (19 bp):
TATTTTTGTAATGTTTTAT
Found at i:22829308 original size:9 final size:9
Alignment explanation
Indices: 22829296--22829330 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
22829286 TCAAAAAAGT
22829296 AAAAACAAA
1 AAAAACAAA
*
22829305 AAAAATAAA
1 AAAAACAAA
22829314 AAAAACAGAA
1 AAAAACA-AA
22829324 AAAAACA
1 AAAAACA
22829331 CACTAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.86, C:0.09, G:0.03, T:0.03
Consensus pattern (9 bp):
AAAAACAAA
Found at i:22830651 original size:17 final size:17
Alignment explanation
Indices: 22830629--22830665 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
22830619 ATGGGGTAAG
22830629 ATGCTATTCTAATATTC
1 ATGCTATTCTAATATTC
22830646 ATGCTATTCTAATATTC
1 ATGCTATTCTAATATTC
22830663 ATG
1 ATG
22830666 ACATCTTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.16, G:0.08, T:0.46
Consensus pattern (17 bp):
ATGCTATTCTAATATTC
Found at i:22831662 original size:15 final size:14
Alignment explanation
Indices: 22831622--22831650 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
22831612 TTTTTGTATC
22831622 AATTTAATTATTCT
1 AATTTAATTATTCT
22831636 AATTTAATTATTCT
1 AATTTAATTATTCT
22831650 A
1 A
22831651 GTTTTAGTTA
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:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (14 bp):
AATTTAATTATTCT
Found at i:22835205 original size:27 final size:27
Alignment explanation
Indices: 22835137--22835188 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
22835127 GGTTGGCAGG
*
22835137 ACTGGTGCCGCCAACAGGGATTCCTCC
1 ACTGGTGCCGCCAACAGGGATCCCTCC
22835164 ACTGGTGCCGCCAACAGGGATCCCT
1 ACTGGTGCCGCCAACAGGGATCCCT
22835189 TGTTTGGTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.19, C:0.37, G:0.27, T:0.17
Consensus pattern (27 bp):
ACTGGTGCCGCCAACAGGGATCCCTCC
Found at i:22835252 original size:1 final size:1
Alignment explanation
Indices: 22835246--22835288 Score: 50
Period size: 1 Copynumber: 43.0 Consensus size: 1
22835236 TCAGTTCAGG
* * * *
22835246 TTTTTTTTTCTGTTTTTTTTTTTTTTTGTTTGTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
22835289 GATATATTTT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.02, G:0.07, T:0.91
Consensus pattern (1 bp):
T
Found at i:22835271 original size:20 final size:20
Alignment explanation
Indices: 22835246--22835288 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
22835236 TCAGTTCAGG
*
22835246 TTTTTTTT-TCTGTTTTTTT
1 TTTTTTTTGTTTGTTTTTTT
22835265 TTTTTTTTGTTTGTTTTTTT
1 TTTTTTTTGTTTGTTTTTTT
22835285 TTTT
1 TTTT
22835289 GATATATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.00, C:0.02, G:0.07, T:0.91
Consensus pattern (20 bp):
TTTTTTTTGTTTGTTTTTTT
Found at i:22835288 original size:16 final size:16
Alignment explanation
Indices: 22835245--22835289 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
22835235 ATCAGTTCAG
*
22835245 GTTTTTTTTTCTGTTT
1 GTTTTTTTTTTTGTTT
*
22835261 TTTTTTTTTTTTGTTT
1 GTTTTTTTTTTTGTTT
22835277 GTTTTTTTTTTTG
1 GTTTTTTTTTTTG
22835290 ATATATTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.00, C:0.02, G:0.11, T:0.87
Consensus pattern (16 bp):
GTTTTTTTTTTTGTTT
Found at i:22835320 original size:27 final size:29
Alignment explanation
Indices: 22835290--22835354 Score: 109
Period size: 27 Copynumber: 2.3 Consensus size: 29
22835280 TTTTTTTTTG
22835290 ATATATTTTGGTAAAT-AAAAAAA-TTAT
1 ATATATTTTGGTAAATAAAAAAAAGTTAT
22835317 ATATATTTTGGTAAATAAAAAAAAGTTAT
1 ATATATTTTGGTAAATAAAAAAAAGTTAT
22835346 A-ATATTTTG
1 ATATATTTTG
22835355 ATAATTTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
27 16 0.44
28 15 0.42
29 5 0.14
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (29 bp):
ATATATTTTGGTAAATAAAAAAAAGTTAT
Found at i:22841738 original size:41 final size:42
Alignment explanation
Indices: 22841693--22841776 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
22841683 TTAATTTCTA
* * *
22841693 TAATTCAAATT-AGATGTTTTGGTCCTTCTACTTTTAAAATG
1 TAATTCAAATTGACATGTTTTGATACTTCTACTTTTAAAATG
22841734 TAATTCAAATTGACATGTTTTGATACTTCTACTTTTAAAATG
1 TAATTCAAATTGACATGTTTTGATACTTCTACTTTTAAAATG
22841776 T
1 T
22841777 TATAATCATC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 11 0.28
42 28 0.72
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.46
Consensus pattern (42 bp):
TAATTCAAATTGACATGTTTTGATACTTCTACTTTTAAAATG
Found at i:22844929 original size:76 final size:74
Alignment explanation
Indices: 22844779--22844932 Score: 175
Period size: 76 Copynumber: 2.1 Consensus size: 74
22844769 TCATAAAAGT
* * * * *
22844779 TATTTTATTGTATTTTACATCAATAATATATTTATTTACAATCTAAGAAAAAAATCAAAAAATTA
1 TATTCTATTGTATTTCACATAAATAATATACTTATTTACAATATAAGAAAAAAATCAAAAAATTA
* **
22844844 TTTGTATTG
66 CTTACATTG
* * *
22844853 TATTCTATTGTATTTCATATAAATAATATAGACTTATTTACAATATATGAAAAAAAAT-GAAAAA
1 TATTCTATTGTATTTCACATAAATAATAT--ACTTATTTACAATATAAG-AAAAAAATCAAAAAA
22844917 TTACTTACATTG
63 TTACTTACATTG
22844929 TATT
1 TATT
22844933 TTACATCAAT
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
74 25 0.38
76 33 0.50
77 8 0.12
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.43
Consensus pattern (74 bp):
TATTCTATTGTATTTCACATAAATAATATACTTATTTACAATATAAGAAAAAAATCAAAAAATTA
CTTACATTG
Found at i:22857106 original size:3 final size:3
Alignment explanation
Indices: 22857098--22857125 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
22857088 TTTAAAAACC
22857098 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
22857126 TTAAAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:22857874 original size:12 final size:12
Alignment explanation
Indices: 22857844--22857900 Score: 78
Period size: 12 Copynumber: 4.6 Consensus size: 12
22857834 CGCCTTCTTC
22857844 TCCCCTTTCCCCTT
1 TCCCCTTT-CCC-T
22857858 TCCCCTTTCCCT
1 TCCCCTTTCCCT
*
22857870 TCCCCTTCCCCT
1 TCCCCTTTCCCT
*
22857882 TCCCTTTTCCCT
1 TCCCCTTTCCCT
22857894 TCCCCTT
1 TCCCCTT
22857901 GGGTTGCAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
12 28 0.72
13 3 0.08
14 8 0.21
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (12 bp):
TCCCCTTTCCCT
Found at i:22857875 original size:6 final size:6
Alignment explanation
Indices: 22857844--22857900 Score: 69
Period size: 6 Copynumber: 9.2 Consensus size: 6
22857834 CGCCTTCTTC
* * *
22857844 TCCCCTT TCCCCTT TCCCCT TTCCCT TCCCCT TCCCCT TCCCTT TTCCCT
1 TCCCC-T TCCCC-T TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT
22857894 TCCCCT T
1 TCCCCT T
22857901 GGGTTGCAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
6 32 0.73
7 12 0.27
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (6 bp):
TCCCCT
Found at i:22858216 original size:11 final size:11
Alignment explanation
Indices: 22858200--22858225 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
22858190 TTGCTGGATG
22858200 ATATTTTGGTT
1 ATATTTTGGTT
22858211 ATATTTTGGTT
1 ATATTTTGGTT
22858222 ATAT
1 ATAT
22858226 ACAGATGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (11 bp):
ATATTTTGGTT
Found at i:22860558 original size:22 final size:20
Alignment explanation
Indices: 22860515--22860553 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
22860505 TAATTTAAAA
22860515 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
*
22860535 TATATAAATTTATTAATAT
1 TATAAAAATTTATTAATAT
22860554 ATGTAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:22860658 original size:14 final size:15
Alignment explanation
Indices: 22860636--22860712 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
22860626 CAATCAAACA
22860636 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
22860650 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
22860665 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
22860685 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
22860699 ACGGAAAA-CATTTT
1 CCAGAAAATCATTTT
22860713 ACTGCCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 22 0.44
15 14 0.28
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:22860677 original size:20 final size:20
Alignment explanation
Indices: 22860652--22860691 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
22860642 AATATTTTCC
*
22860652 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
22860672 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
22860692 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:22860697 original size:34 final size:35
Alignment explanation
Indices: 22860640--22860706 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
22860630 CAAACACCAG
*
22860640 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
22860675 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
22860707 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:22860713 original size:14 final size:14
Alignment explanation
Indices: 22860675--22860714 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
22860665 ACAGAAAAGT
*
22860675 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
22860689 AAATCATTTTACGG
1 AAAACATTTTACAG
22860703 AAAACATTTTAC
1 AAAACATTTTAC
22860715 TGCCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:22861016 original size:23 final size:23
Alignment explanation
Indices: 22860989--22861039 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
22860979 AGATTTAAAT
22860989 AAATACTCATA-TTTATATTACTA
1 AAATACTCATATTTTATATTA-TA
* *
22861012 AAATATTTATATTTTATATTATA
1 AAATACTCATATTTTATATTATA
22861035 AAATA
1 AAATA
22861040 TTTTTTAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 16 0.64
24 9 0.36
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (23 bp):
AAATACTCATATTTTATATTATA
Found at i:22861093 original size:18 final size:20
Alignment explanation
Indices: 22861054--22861092 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
22861044 TTAATCATAA
22861054 TATATATTAATATAAAATTT
1 TATATATTAATATAAAATTT
*
22861074 TATATATTACT-TAAAATTT
1 TATATATTAATATAAAATTT
22861093 AAATTCTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (20 bp):
TATATATTAATATAAAATTT
Found at i:22861248 original size:22 final size:21
Alignment explanation
Indices: 22861206--22861255 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
22861196 ATTTTTTTAA
*
22861206 TATTTTAAAATATTAAAATTT
1 TATTTTAAAATAATAAAATTT
* *
22861227 TATTATTAATATAATAATATTT
1 TATT-TTAAAATAATAAAATTT
*
22861249 GATTTTA
1 TATTTTA
22861256 TTTAAGTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
TATTTTAAAATAATAAAATTT
Found at i:22861684 original size:21 final size:19
Alignment explanation
Indices: 22861641--22861685 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
22861631 TTATTTTTAT
**
22861641 TTTTTAAATTTAAAATACT
1 TTTTTAAATTTAAAATAAA
22861660 TTTTTAAATTTTTAAAATAAA
1 TTTTTAAA--TTTAAAATAAA
22861681 TTTTT
1 TTTTT
22861686 GGTGTTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 8 0.36
21 14 0.64
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTTTAAATTTAAAATAAA
Found at i:22863075 original size:14 final size:14
Alignment explanation
Indices: 22863056--22863092 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
22863046 ACTAGTAATT
22863056 GAATTTAACCAAAA
1 GAATTTAACCAAAA
22863070 GAATTTAACCAAAA
1 GAATTTAACCAAAA
22863084 GAATTTAAC
1 GAATTTAAC
22863093 TGCTTCTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.54, C:0.14, G:0.08, T:0.24
Consensus pattern (14 bp):
GAATTTAACCAAAA
Found at i:22867263 original size:29 final size:29
Alignment explanation
Indices: 22867178--22867341 Score: 109
Period size: 29 Copynumber: 5.9 Consensus size: 29
22867168 AACACCGTAA
* *
22867178 ATGTGGAAAGTCCGCCAAAACTATCT--T
1 ATGTGGAAAGTCTGCCAGAACTATCTGAT
* *
22867205 ATGTGGAAA-TCCATG--AGGATTATCTGAT
1 ATGTGGAAAGT-C-TGCCAGAACTATCTGAT
22867233 ATGTGGAAAGTCTGCCAGAACTATCTGAT
1 ATGTGGAAAGTCTGCCAGAACTATCTGAT
22867262 ATGTGGAAAGT-TCGCCA-AGACTATCT--T
1 ATGTGGAAAGTCT-GCCAGA-ACTATCTGAT
*** * *
22867289 ATGT-G-AAGTCTATGAGGACTATATGAT
1 ATGTGGAAAGTCTGCCAGAACTATCTGAT
*
22867316 ATGTGGAAAGTCAGCCA-AGACTATCT
1 ATGTGGAAAGTCTGCCAGA-ACTATCT
22867342 TAATATGGGA
Statistics
Matches: 104, Mismatches: 17, Indels: 30
0.69 0.11 0.20
Matches are distributed among these distances:
25 11 0.11
26 10 0.10
27 22 0.21
28 15 0.14
29 46 0.44
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (29 bp):
ATGTGGAAAGTCTGCCAGAACTATCTGAT
Found at i:22867341 original size:83 final size:84
Alignment explanation
Indices: 22867178--22867341 Score: 242
Period size: 83 Copynumber: 2.0 Consensus size: 84
22867168 AACACCGTAA
* *
22867178 ATGTGGAAAGTCCGCCAAAACTATCTTATGTGGAAATCCATGAGGATTATCTGATATGTGGAAAG
1 ATGTGGAAAGTCCGCCAAAACTATCTTATGTGGAAATCCATGAGGACTATATGATATGTGGAAAG
*
22867243 TCTGCCAGAACTATCTGAT
66 TCAGCCAGAACTATCTGAT
* * * *
22867262 ATGTGGAAAGTTCGCCAAGACTATCTTATGT-GAAGTCTATGAGGACTATATGATATGTGGAAAG
1 ATGTGGAAAGTCCGCCAAAACTATCTTATGTGGAAATCCATGAGGACTATATGATATGTGGAAAG
22867326 TCAGCCA-AGACTATCT
66 TCAGCCAGA-ACTATCT
22867342 TAATATGGGA
Statistics
Matches: 72, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
82 1 0.01
83 42 0.58
84 29 0.40
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (84 bp):
ATGTGGAAAGTCCGCCAAAACTATCTTATGTGGAAATCCATGAGGACTATATGATATGTGGAAAG
TCAGCCAGAACTATCTGAT
Found at i:22868398 original size:4 final size:4
Alignment explanation
Indices: 22868389--22868415 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
22868379 ATTTTAGTGT
22868389 TTAA TTAA TTAA TTAA TTAA TTAA TTA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTA
22868416 GGATTAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:22872624 original size:22 final size:22
Alignment explanation
Indices: 22872599--22872652 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
22872589 CAAGGCGATG
*
22872599 ATGGCATGTTCTATTAGCTTTT
1 ATGGCATATTCTATTAGCTTTT
* *
22872621 ATGGCATATTCTTTTAGTTTTT
1 ATGGCATATTCTATTAGCTTTT
* *
22872643 GTGGCGTATT
1 ATGGCATATT
22872653 TCATATGTTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.17, C:0.11, G:0.20, T:0.52
Consensus pattern (22 bp):
ATGGCATATTCTATTAGCTTTT
Found at i:22877924 original size:27 final size:27
Alignment explanation
Indices: 22877863--22877925 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
22877853 TAACATCCTA
* *
22877863 ATGGACTATCTCGTTTTTAATATCCCG
1 ATGGACTATCTCATGTTTAATATCCCG
*** *
22877890 ACAAACTATCTCATGTTTAATGTCCCG
1 ATGGACTATCTCATGTTTAATATCCCG
22877917 ATGGACTAT
1 ATGGACTAT
22877926 TTATGGTGCT
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (27 bp):
ATGGACTATCTCATGTTTAATATCCCG
Found at i:22880224 original size:24 final size:24
Alignment explanation
Indices: 22880182--22880239 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
22880172 ACCGAGGTAA
*
22880182 CTTGTTGG-CTTATCGTAGTAGAC
1 CTTGGTGGCCTTATCGTAGTAGAC
*
22880205 CTTGGTGGCCTTATCTTAGTAGAC
1 CTTGGTGGCCTTATCGTAGTAGAC
22880229 CTTGGTGGCCT
1 CTTGGTGGCCT
22880240 ACTTTTTCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 7 0.22
24 25 0.78
ACGTcount: A:0.14, C:0.21, G:0.28, T:0.38
Consensus pattern (24 bp):
CTTGGTGGCCTTATCGTAGTAGAC
Found at i:22889556 original size:55 final size:55
Alignment explanation
Indices: 22889497--22889608 Score: 197
Period size: 55 Copynumber: 2.0 Consensus size: 55
22889487 ATGATAAGAT
* *
22889497 AATGATGATAAATGAAATAAATAATTAAAATAAGTCATTTTTCATCATCTTTCCC
1 AATGATGATAAAAGAAACAAATAATTAAAATAAGTCATTTTTCATCATCTTTCCC
*
22889552 AATGATGATAAAAGAAACAAATAATTAAAATAAGTCATTTTTCATTATCTTTCCC
1 AATGATGATAAAAGAAACAAATAATTAAAATAAGTCATTTTTCATCATCTTTCCC
22889607 AA
1 AA
22889609 ATAAAAACAT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.35
Consensus pattern (55 bp):
AATGATGATAAAAGAAACAAATAATTAAAATAAGTCATTTTTCATCATCTTTCCC
Found at i:22890489 original size:49 final size:48
Alignment explanation
Indices: 22890412--22890507 Score: 115
Period size: 49 Copynumber: 2.0 Consensus size: 48
22890402 TATATATATA
*
22890412 GCTCTTATGAGCATCCCGATTAAAGGCTCTC-TGGAGCTTCCCGATTATG
1 GCTCTTATGAGCATCCCGATTAAAGGCTCACAT-GAGCTTCCCG-TTATG
* * *
22890461 GCTCTTATGAGC-TTCCTATTACATGGCTCACATGAGCTTCCCGTTAT
1 GCTCTTATGAGCATCCCGATTA-AAGGCTCACATGAGCTTCCCGTTAT
22890508 ATGGCACGAG
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
48 11 0.27
49 29 0.71
50 1 0.02
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (48 bp):
GCTCTTATGAGCATCCCGATTAAAGGCTCACATGAGCTTCCCGTTATG
Found at i:22890511 original size:25 final size:25
Alignment explanation
Indices: 22890445--22890512 Score: 75
Period size: 25 Copynumber: 2.8 Consensus size: 25
22890435 AGGCTCTCTG
* **
22890445 GAGCTTCCCGAT-TATGGCTCTTAT
1 GAGCTTCCCGTTATATGGCTCACAT
** *
22890469 GAGCTTCCTATTACATGGCTCACAT
1 GAGCTTCCCGTTATATGGCTCACAT
22890494 GAGCTTCCCGTTATATGGC
1 GAGCTTCCCGTTATATGGC
22890513 ACGAGAGAGA
Statistics
Matches: 34, Mismatches: 9, Indels: 1
0.77 0.20 0.02
Matches are distributed among these distances:
24 9 0.26
25 25 0.74
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.34
Consensus pattern (25 bp):
GAGCTTCCCGTTATATGGCTCACAT
Found at i:22894577 original size:16 final size:16
Alignment explanation
Indices: 22894531--22894583 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 16
22894521 ACAACGGATA
22894531 AAAGAGAAAACATGAT
1 AAAGAGAAAACATGAT
**** *
22894547 AAAGATTCCATATGAT
1 AAAGAGAAAACATGAT
22894563 AAAGAGAAAACATGAT
1 AAAGAGAAAACATGAT
22894579 AAAGA
1 AAAGA
22894584 CAACGGAAGT
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.58, C:0.08, G:0.17, T:0.17
Consensus pattern (16 bp):
AAAGAGAAAACATGAT
Found at i:22907050 original size:29 final size:30
Alignment explanation
Indices: 22906991--22907057 Score: 102
Period size: 29 Copynumber: 2.3 Consensus size: 30
22906981 ATTTAAAAAA
*
22906991 CAATAAATTTATTTCAGAAATAAAAACAAT
1 CAATAAATTTATTTCAGAAAAAAAAACAAT
22907021 CAATAAATTT-TGTTCA-AAAAAAAAACAAT
1 CAATAAATTTAT-TTCAGAAAAAAAAACAAT
22907050 CAATAAAT
1 CAATAAAT
22907058 AATAGTGAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
29 21 0.60
30 14 0.40
ACGTcount: A:0.58, C:0.10, G:0.03, T:0.28
Consensus pattern (30 bp):
CAATAAATTTATTTCAGAAAAAAAAACAAT
Found at i:22907868 original size:2 final size:2
Alignment explanation
Indices: 22907863--22907887 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
22907853 ATTTTTTTTC
22907863 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
22907888 GAAATAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22910743 original size:2 final size:2
Alignment explanation
Indices: 22910736--22910760 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
22910726 ACCATCCTTT
22910736 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
22910761 TTGAAGTTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22911718 original size:86 final size:85
Alignment explanation
Indices: 22911576--22911742 Score: 210
Period size: 86 Copynumber: 2.0 Consensus size: 85
22911566 GTAAAAGGCT
* * * * * ** * *
22911576 CTTAATTTTTTCAAAAAAGTAATTCAACCCCTTTTTTTTTTGCGCTGGATTGGGTACTTGAACTT
1 CTTAATTTTTTCAAAAAAGCAATTAAACCCCCTTTCTTTTTGCACTCAATTAGGTACTT-AAATT
* *
22911641 -TTAAAATGCATCAAAAGACC
65 GTCAAAATGCATAAAAAGACC
22911661 CTTAATTTTTTCAAAAAAAGCAATTAAACCCCCTTTCTTTTTGCACTCAATTAGGTACTTAAATT
1 CTTAATTTTTTC-AAAAAAGCAATTAAACCCCCTTTCTTTTTGCACTCAATTAGGTACTTAAATT
22911726 GTCAAAATGCATAAAAA
65 GTCAAAATGCATAAAAA
22911743 AAATACTCTT
Statistics
Matches: 69, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
85 16 0.23
86 53 0.77
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (85 bp):
CTTAATTTTTTCAAAAAAGCAATTAAACCCCCTTTCTTTTTGCACTCAATTAGGTACTTAAATTG
TCAAAATGCATAAAAAGACC
Found at i:22922325 original size:26 final size:25
Alignment explanation
Indices: 22922289--22922356 Score: 111
Period size: 26 Copynumber: 2.7 Consensus size: 25
22922279 AAATAAAAAA
22922289 TTACCAAAATATTATAACTTTTTTAT
1 TTACCAAAATATTATAA-TTTTTTAT
22922315 TTACCAAAATATATATAATTTTTTAT
1 TTACCAAAATAT-TATAATTTTTTAT
22922341 TTACCAAAATA-TATAA
1 TTACCAAAATATTATAA
22922357 AAAAACAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
24 5 0.12
26 31 0.76
27 5 0.12
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (25 bp):
TTACCAAAATATTATAATTTTTTAT
Found at i:22922438 original size:18 final size:18
Alignment explanation
Indices: 22922415--22922457 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
22922405 CCTGGTCACG
22922415 CCAATGGCATTGGCGGCA
1 CCAATGGCATTGGCGGCA
22922433 CCAATGGCATTGGCGGCA
1 CCAATGGCATTGGCGGCA
22922451 CCAATGG
1 CCAATGG
22922458 TGCCAATACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.23, C:0.28, G:0.33, T:0.16
Consensus pattern (18 bp):
CCAATGGCATTGGCGGCA
Found at i:22922535 original size:4 final size:4
Alignment explanation
Indices: 22922526--22922682 Score: 94
Period size: 4 Copynumber: 37.8 Consensus size: 4
22922516 GAAGGAGAGG
* *
22922526 GAAA GAAA GAAA GAAA GGAGAG GAAA GAAA GGTAAA GAAG GAAA GAAAA
1 GAAA GAAA GAAA GAAA -GA-AA GAAA GAAA -G-AAA GAAA GAAA G-AAA
* *
22922575 GTAAA G-GA GAAGA GAAA AAAA GAAA GAAA GAAA G-AA G-AA GAAAA GGAAAA
1 G-AAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAAA GAAA G-AAA -G-AAA
* *
22922625 GAGAA GAAA -AAA GAAA GAAA GAAG GAAA GAAA GGAAA G-GA GAAGA GAAA
1 GA-AA GAAA GAAA GAAA GAAA GAAA GAAA GAAA -GAAA GAAA GAA-A GAAA
22922674 -AAA -AAA GAA
1 GAAA GAAA GAA
22922683 GAGGGAAGGA
Statistics
Matches: 124, Mismatches: 13, Indels: 32
0.73 0.08 0.19
Matches are distributed among these distances:
3 19 0.15
4 63 0.51
5 33 0.27
6 9 0.07
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.01
Consensus pattern (4 bp):
GAAA
Found at i:22922544 original size:23 final size:23
Alignment explanation
Indices: 22922517--22922706 Score: 101
Period size: 23 Copynumber: 8.1 Consensus size: 23
22922507 GGTGGGGCAG
*
22922517 AAGGAGAGGGAAAGAAAGAAAGA
1 AAGGAGAAGGAAAGAAAGAAAGA
22922540 AAGGAG-AGGAAAGAAAGGTAAAG-
1 AAGGAGAAGGAAAGAAA-G-AAAGA
*
22922563 AAGGA-AAGAAAAGTAAAGGAGAAGA
1 AAGGAGAAGGAAAG-AAA-GA-AAGA
* *
22922588 GAA--AAAAAGAAAGAAAGAAAGA
1 -AAGGAGAAGGAAAGAAAGAAAGA
* *
22922610 AGAAGAAAAGGAAAAGAGAAGAAA-A
1 A-AGGAGAAGG-AAAGA-AAGAAAGA
* * *
22922635 AAGAAAGAAAGAAGGAAAGAAAGGA
1 AAG-GAGAAGGAAAGAAAGAAA-GA
22922660 AAGGAGAAGAGAAA-AAA-AAAGA
1 AAGGAGAAG-GAAAGAAAGAAAGA
* *
22922682 AGAGG-GAAGGAAGGAAAAAAAGA
1 A-AGGAGAAGGAAAGAAAGAAAGA
22922705 AA
1 AA
22922707 AAAAGGTATT
Statistics
Matches: 133, Mismatches: 14, Indels: 41
0.71 0.07 0.22
Matches are distributed among these distances:
21 4 0.03
22 25 0.19
23 39 0.29
24 33 0.25
25 24 0.18
26 8 0.06
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.01
Consensus pattern (23 bp):
AAGGAGAAGGAAAGAAAGAAAGA
Found at i:22922551 original size:18 final size:16
Alignment explanation
Indices: 22922530--22922662 Score: 101
Period size: 18 Copynumber: 7.8 Consensus size: 16
22922520 GAGAGGGAAA
22922530 GAAAGAAAGAAAGGAGAG
1 GAAAGAAAGAAA-GA-AG
22922548 GAAAGAAAGGTAAAGAAG
1 GAAAGAAA-G-AAAGAAG
*
22922566 GAAAGAAAAGTAAAGGA-
1 GAAAG-AAAG-AAAGAAG
* *
22922583 GAAGAGAAAAAAAGAAA
1 GAA-AGAAAGAAAGAAG
22922600 GAAAGAAAG-AAGAAG
1 GAAAGAAAGAAAGAAG
*
22922615 AAAAGGAAAAGAGAAGAA-
1 GAAA-G-AAAGA-AAGAAG
*
22922633 AAAAGAAAGAAAGAAG
1 GAAAGAAAGAAAGAAG
22922649 GAAAGAAAGGAAAG
1 GAAAGAAA-GAAAG
22922663 GAGAAGAGAA
Statistics
Matches: 97, Mismatches: 7, Indels: 23
0.76 0.06 0.18
Matches are distributed among these distances:
15 13 0.13
16 23 0.24
17 19 0.20
18 28 0.29
19 11 0.11
20 3 0.03
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.02
Consensus pattern (16 bp):
GAAAGAAAGAAAGAAG
Found at i:22922580 original size:5 final size:5
Alignment explanation
Indices: 22922567--22922682 Score: 51
Period size: 5 Copynumber: 22.2 Consensus size: 5
22922557 GTAAAGAAGG
* *
22922567 AAAGA AAAGTA AAGGA GAAGA GAAA-A AAAG- AAAG- AAAG- AAAGA AGAAGA
1 AAAGA AAAG-A AAAGA AAAGA -AAAGA AAAGA AAAGA AAAGA AAAGA A-AAGA
* * * *
22922616 AAAGGA AAAGA GAAGA AAAAA GAAAGAA AGAAGG AAAGA AAGGA AAGGAGA
1 AAA-GA AAAGA AAAGA AAAGA -AAAG-A A-AAGA AAAGA AAAGA AA--AGA
* *
22922667 AGAGA AAAAA AAAGA A
1 AAAGA AAAGA AAAGA A
22922683 GAGGGAAGGA
Statistics
Matches: 84, Mismatches: 16, Indels: 22
0.69 0.13 0.18
Matches are distributed among these distances:
4 15 0.18
5 41 0.49
6 21 0.25
7 7 0.08
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.01
Consensus pattern (5 bp):
AAAGA
Found at i:22922601 original size:38 final size:37
Alignment explanation
Indices: 22922530--22922677 Score: 140
Period size: 38 Copynumber: 3.8 Consensus size: 37
22922520 GAGAGGGAAA
*
22922530 GAAAGAAA-GAAAGGAG-AG-GAAAGAAAGGTAAAGAAG
1 GAAAGAAAGGAAAGGAGAAGAGAAA-AAAAG-AAAGAAG
*
22922566 GAAAGAAAAGTAAAGGAGAAGAGAAAAAAAGAAAGAAAG
1 GAAAG-AAAGGAAAGGAGAAGAGAAAAAAAGAAAG-AAG
* *
22922605 AAAGAAGAAGAAAAGGAAAAGAGAAGAAAAAAGAAAGAAAGAAG
1 ---G-A-AAG-AAAGGAAAGGAGAAGAGAAAA-AAAGAAAGAAG
22922649 GAAAGAAAGGAAAGGAGAAGAGAAAAAAA
1 GAAAGAAAGGAAAGGAGAAGAGAAAAAAA
22922678 AAGAAGAGGG
Statistics
Matches: 94, Mismatches: 7, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
36 5 0.05
37 6 0.06
38 30 0.32
39 12 0.13
40 5 0.05
41 1 0.01
42 1 0.01
43 1 0.01
44 25 0.27
45 8 0.09
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.01
Consensus pattern (37 bp):
GAAAGAAAGGAAAGGAGAAGAGAAAAAAAGAAAGAAG
Found at i:22922643 original size:33 final size:33
Alignment explanation
Indices: 22922594--22922709 Score: 101
Period size: 38 Copynumber: 3.3 Consensus size: 33
22922584 AAGAGAAAAA
22922594 AAGAAAGAAAGAAAGAAGAAGAAAAGGAAAAGAG
1 AAGAAA-AAAGAAAGAAGAAGAAAAGGAAAAGAG
*
22922628 AAGAAAAAAGAAAGAAAGAAGGAAAGAAAGGAAAGGAG
1 AAGAAAAAAGAAAG-AAGAA-G--A-AAAGGAAAAGAG
* *
22922666 AAGAGAAAAAAAAAGAAGAGGGAAGGAAGGAAAA-A-
1 AAGA-AAAAAGAAAGAAGA-AGAA--AAGGAAAAGAG
22922701 AAGAAAAAA
1 AAGAAAAAA
22922710 AGGTATTTTA
Statistics
Matches: 69, Mismatches: 4, Indels: 18
0.76 0.04 0.20
Matches are distributed among these distances:
33 8 0.12
34 16 0.23
35 6 0.09
36 2 0.03
37 8 0.12
38 20 0.29
39 9 0.13
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (33 bp):
AAGAAAAAAGAAAGAAGAAGAAAAGGAAAAGAG
Found at i:22922707 original size:83 final size:85
Alignment explanation
Indices: 22922549--22922707 Score: 218
Period size: 83 Copynumber: 1.9 Consensus size: 85
22922539 AAAGGAGAGG
* *
22922549 AAAGAAAGGTAAAGAAGGAAAGAAAAGTAAAGGAGAAGAGAAAAAAAGAAAGAAAGAAAGAAGAA
1 AAAGAAAGGTAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAAAAGAAAGAAAGAAGAA
*
22922614 GAAAAGGAAAAGAGAAGAAA
66 GAAAAAGAAAAGAGAAGAAA
** *
22922634 AAAGAAA-G-AAAGAAGGAAAG-AAAGGAAAGGAGAAGAGAAAAAAAAAGAAGAGGGAAGGAAGG
1 AAAGAAAGGTAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAA-AAGAAAGAAAGAA-G
22922696 AA-AAAAAGAAAA
64 AAGAAAAAGAAAA
22922708 AAAGGTATTT
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
82 24 0.36
83 31 0.47
84 4 0.06
85 7 0.11
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.01
Consensus pattern (85 bp):
AAAGAAAGGTAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAAAAGAAAGAAAGAAGAA
GAAAAAGAAAAGAGAAGAAA
Found at i:22929297 original size:19 final size:21
Alignment explanation
Indices: 22929273--22929311 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
22929263 ACTAAAACAA
*
22929273 AAAAT-ATTACAA-AATATAC
1 AAAATAATAACAACAATATAC
22929292 AAAATAATAACAACAATATA
1 AAAATAATAACAACAATATA
22929312 ATCAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAATAATAACAACAATATAC
Found at i:22929490 original size:27 final size:27
Alignment explanation
Indices: 22929444--22929520 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 27
22929434 AATACGAATA
22929444 GTGCCGCCAAT--CAATATGGCACCATTG
1 GTGCCGCCAATGGC-AT-TGGCACCATTG
22929471 GTGCCGCCAATGGCATTGGCACCATTG
1 GTGCCGCCAATGGCATTGGCACCATTG
* **
22929498 GTACCGCCAATGGTTTTGGCACC
1 GTGCCGCCAATGGCATTGGCACC
22929521 TTGACCAAGG
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
27 42 0.93
28 2 0.04
29 1 0.02
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (27 bp):
GTGCCGCCAATGGCATTGGCACCATTG
Found at i:22929643 original size:27 final size:22
Alignment explanation
Indices: 22929579--22929623 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
22929569 TGTTTTTTTG
22929579 ATATATTTTGGTAAATAAAAAA
1 ATATATTTTGGTAAATAAAAAA
22929601 ATATATTTTGGTAAATAAAAAA
1 ATATATTTTGGTAAATAAAAAA
22929623 A
1 A
22929624 GTTATAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.36
Consensus pattern (22 bp):
ATATATTTTGGTAAATAAAAAA
Found at i:22935493 original size:18 final size:17
Alignment explanation
Indices: 22935472--22935507 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
22935462 TTTAATGCAA
22935472 TATTATATATTAAAATTT
1 TATTATA-ATTAAAATTT
*
22935490 TATTTTAATTAAAATTT
1 TATTATAATTAAAATTT
22935507 T
1 T
22935508 CAAAAATAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATTATAATTAAAATTT
Found at i:22942111 original size:21 final size:22
Alignment explanation
Indices: 22942087--22942128 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
22942077 TGATTTTTTA
22942087 AAATATTAAAATATT-AATATC
1 AAATATTAAAATATTCAATATC
*
22942108 AAATATTATAATATTCAATAT
1 AAATATTAAAATATTCAATAT
22942129 TATTTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (22 bp):
AAATATTAAAATATTCAATATC
Found at i:22942175 original size:19 final size:17
Alignment explanation
Indices: 22942145--22942210 Score: 62
Period size: 19 Copynumber: 3.6 Consensus size: 17
22942135 AAATACATGT
*
22942145 TAAATTATTTATATTTAA
1 TAAATAATTTAT-TTTAA
22942163 TAATATAATTTATTATTAA
1 TAA-ATAATTTATT-TTAA
22942182 TAAAATTAA-TTATTTTAA
1 T-AAA-TAATTTATTTTAA
*
22942200 TAAATTATTTA
1 TAAATAATTTA
22942211 ATATTAAAGT
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
16 2 0.05
17 6 0.15
18 9 0.22
19 19 0.46
20 5 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TAAATAATTTATTTTAA
Found at i:22942210 original size:36 final size:38
Alignment explanation
Indices: 22942146--22942217 Score: 103
Period size: 36 Copynumber: 1.9 Consensus size: 38
22942136 AATACATGTT
* *
22942146 AAATTATTTATATTTAATAATATAATTTATTATTAATA
1 AAATTAATTATATTTAATAATATAATTTAATATTAATA
*
22942184 AAATTAATTAT-TTTAATAA-ATTATTTAATATTAA
1 AAATTAATTATATTTAATAATATAATTTAATATTAA
22942218 AGTTTTATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
36 13 0.42
37 8 0.26
38 10 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (38 bp):
AAATTAATTATATTTAATAATATAATTTAATATTAATA
Found at i:22942559 original size:17 final size:18
Alignment explanation
Indices: 22942539--22942576 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
22942529 TTTATATATG
*
22942539 ATATTAAT-TATTATAGA
1 ATATTAATGTATTATAAA
22942556 ATATTAATGTATTATAAA
1 ATATTAATGTATTATAAA
22942574 ATA
1 ATA
22942577 AATTTTGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (18 bp):
ATATTAATGTATTATAAA
Found at i:22943172 original size:22 final size:22
Alignment explanation
Indices: 22943139--22943199 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
22943129 GCCTGGCCCG
* *
22943139 TTTTTAATTAAAATTAAAATTAT
1 TTTTTAA-TAAAATTAAAACTAA
22943162 TTTTTAATAAAATTAAAACTAA
1 TTTTTAATAAAATTAAAACTAA
* *
22943184 TTGTTATTAAAATTAA
1 TTTTTAATAAAATTAA
22943200 TTGTTAGTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 27 0.79
23 7 0.21
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
TTTTTAATAAAATTAAAACTAA
Found at i:22943212 original size:16 final size:16
Alignment explanation
Indices: 22943175--22943214 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
22943165 TTAATAAAAT
* *
22943175 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
22943191 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
22943207 TAAAATTA
1 TAAAATTA
22943215 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:22943293 original size:59 final size:59
Alignment explanation
Indices: 22943225--22943394 Score: 322
Period size: 59 Copynumber: 2.9 Consensus size: 59
22943215 TCAAATTATT
*
22943225 AATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
22943284 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
*
22943343 AATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTAAA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAA
22943395 ACAAACTTGA
Statistics
Matches: 109, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 109 1.00
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (59 bp):
AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
Found at i:22943485 original size:23 final size:23
Alignment explanation
Indices: 22943459--22943510 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
22943449 GTAAATAAAC
22943459 TTAAAATA-AAAAACTAT-TATATT
1 TTAAAATATAAAAA-TATATATA-T
22943482 TTAAAA-ATAAAAATATATATAT
1 TTAAAATATAAAAATATATATAT
22943504 TTAAAAT
1 TTAAAAT
22943511 TTTTCGGGCC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
22 11 0.42
23 15 0.58
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
TTAAAATATAAAAATATATATAT
Found at i:22943490 original size:24 final size:22
Alignment explanation
Indices: 22943461--22943509 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 22
22943451 AAATAAACTT
22943461 AAAATAAAAA-ACTATTATATTTTA
1 AAAATAAAAATA-TA-TATA-TTTA
22943485 AAAATAAAAATATATATATTTA
1 AAAATAAAAATATATATATTTA
22943507 AAA
1 AAA
22943510 TTTTTCGGGC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 7 0.29
23 4 0.17
24 12 0.50
25 1 0.04
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (22 bp):
AAAATAAAAATATATATATTTA
Found at i:22947231 original size:23 final size:25
Alignment explanation
Indices: 22947205--22947252 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
22947195 TCAATTTTTT
22947205 TAATTAAA-ATATTAATA-AATATC
1 TAATTAAATATATTAATATAATATC
22947228 TAATTAAATTATATTAATATAATAT
1 TAATTAAA-TATATTAATATAATAT
22947253 TTTTTATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 8 0.36
25 9 0.41
26 5 0.23
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (25 bp):
TAATTAAATATATTAATATAATATC
Found at i:22948843 original size:20 final size:21
Alignment explanation
Indices: 22948798--22948843 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 21
22948788 AATCTCTTAA
22948798 TCTTTTAGTGGTTGCTTTGTG
1 TCTTTTAGTGGTTGCTTTGTG
* * *
22948819 T-TTTTGGTGTTTTCTTTGT-
1 TCTTTTAGTGGTTGCTTTGTG
22948838 TCTTTT
1 TCTTTT
22948844 CCAGATTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.05
20 19 0.90
21 1 0.05
ACGTcount: A:0.02, C:0.09, G:0.22, T:0.67
Consensus pattern (21 bp):
TCTTTTAGTGGTTGCTTTGTG
Found at i:22952414 original size:20 final size:21
Alignment explanation
Indices: 22952385--22952428 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
22952375 GAACAAAAAA
22952385 AAAAGAAGGAAGA-GAAGAAG
1 AAAAGAAGGAAGAGGAAGAAG
* * *
22952405 AAAAGTAGGATGAGGAGGAAG
1 AAAAGAAGGAAGAGGAAGAAG
22952426 AAA
1 AAA
22952429 TTGAAGATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.59, C:0.00, G:0.36, T:0.05
Consensus pattern (21 bp):
AAAAGAAGGAAGAGGAAGAAG
Found at i:22966823 original size:21 final size:21
Alignment explanation
Indices: 22966797--22966838 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
22966787 GTAATTTTGT
22966797 AATTAAA-TGGAAATTAAAACA
1 AATTAAAGT-GAAATTAAAACA
22966818 AATTAAAGTGAAATTAAAACA
1 AATTAAAGTGAAATTAAAACA
22966839 TTTTAACTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.24
Consensus pattern (21 bp):
AATTAAAGTGAAATTAAAACA
Found at i:22967792 original size:33 final size:33
Alignment explanation
Indices: 22967748--22967817 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
22967738 TACACTATGT
* *
22967748 TTGGTGTGTTGGTTAGATTAGCTCTTATGAGCA
1 TTGGTGCGTTGGTTAGATTAACTCTTATGAGCA
*
22967781 TTGGTGCGTTGGTTGGATTAACTCTTATGAGCA
1 TTGGTGCGTTGGTTAGATTAACTCTTATGAGCA
22967814 TTGG
1 TTGG
22967818 AGTGATGGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.17, C:0.10, G:0.31, T:0.41
Consensus pattern (33 bp):
TTGGTGCGTTGGTTAGATTAACTCTTATGAGCA
Found at i:22967832 original size:33 final size:33
Alignment explanation
Indices: 22967763--22967832 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
22967753 GTGTTGGTTA
* * * **
22967763 GATTAGCTCTTATGAGCATTGGTGCGTTGGTTG
1 GATTAACTCTTATGAGCATTGGAGCGATGGAGG
*
22967796 GATTAACTCTTATGAGCATTGGAGTGATGGAGG
1 GATTAACTCTTATGAGCATTGGAGCGATGGAGG
22967829 GATT
1 GATT
22967833 GGCTCATGTG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.33, T:0.36
Consensus pattern (33 bp):
GATTAACTCTTATGAGCATTGGAGCGATGGAGG
Found at i:22968317 original size:11 final size:10
Alignment explanation
Indices: 22968286--22968319 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
22968276 TATTATACAA
22968286 AAGAAACGGT
1 AAGAAACGGT
*
22968296 AAGAAAAGGT
1 AAGAAACGGT
22968306 AATGAAACGGT
1 AA-GAAACGGT
22968317 AAG
1 AAG
22968320 TTCATAATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.53, C:0.06, G:0.29, T:0.12
Consensus pattern (10 bp):
AAGAAACGGT
Found at i:22969531 original size:13 final size:13
Alignment explanation
Indices: 22969513--22969550 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
22969503 ACACGGGCGT
22969513 GTGTCTCAGCCGA
1 GTGTCTCAGCCGA
22969526 GTGTCTCAGCCGA
1 GTGTCTCAGCCGA
22969539 GTGTCTCAGCCG
1 GTGTCTCAGCCG
22969551 TGTGAGTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.13, C:0.32, G:0.32, T:0.24
Consensus pattern (13 bp):
GTGTCTCAGCCGA
Found at i:22971399 original size:11 final size:11
Alignment explanation
Indices: 22971368--22971403 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
22971358 AAGTGAACGT
*
22971368 AAGAAAAGCTA
1 AAGAAAAACTA
22971379 AAGTAAAAACTA
1 AAG-AAAAACTA
22971391 AAGAAAAACTA
1 AAGAAAAACTA
22971402 AA
1 AA
22971404 AATTTAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.69, C:0.08, G:0.11, T:0.11
Consensus pattern (11 bp):
AAGAAAAACTA
Found at i:22971926 original size:22 final size:22
Alignment explanation
Indices: 22971898--22971940 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
22971888 TTTATTGTTC
22971898 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
22971920 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
22971941 TAGCCATAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:22996289 original size:18 final size:21
Alignment explanation
Indices: 22996266--22996303 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
22996256 TTCTCTTTTT
22996266 AATT-AAT-TTATA-ATAAAA
1 AATTAAATATTATATATAAAA
22996284 AATTAAATATTATATATAAA
1 AATTAAATATTATATATAAA
22996304 TTAGAGAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.24
19 3 0.18
20 5 0.29
21 5 0.29
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
AATTAAATATTATATATAAAA
Found at i:23002878 original size:6 final size:6
Alignment explanation
Indices: 23002864--23002951 Score: 115
Period size: 6 Copynumber: 14.3 Consensus size: 6
23002854 GAAGTACGAG
* * *
23002864 AAAAGA AAAATA AAACA-A AACAACTA AAAATA AAAATA AACATA AACATA
1 AAAATA AAAATA AAA-ATA AA-AA-TA AAAATA AAAATA AAAATA AAAATA
23002914 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AA
23002952 CAAATAAAAT
Statistics
Matches: 75, Mismatches: 3, Indels: 8
0.87 0.03 0.09
Matches are distributed among these distances:
6 68 0.91
7 4 0.05
8 3 0.04
ACGTcount: A:0.80, C:0.06, G:0.01, T:0.14
Consensus pattern (6 bp):
AAAATA
Found at i:23004654 original size:5 final size:5
Alignment explanation
Indices: 23004640--23004684 Score: 51
Period size: 5 Copynumber: 9.4 Consensus size: 5
23004630 ATTAATAAAG
*
23004640 AAATA AAATA CAATA AAAT- -AATA AAATA ATAAT- AAATA AAATA AA
1 AAATA AAATA AAATA AAATA AAATA AAATA A-AATA AAATA AAATA AA
23004685 TAGGAAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
3 3 0.09
4 3 0.09
5 25 0.74
6 3 0.09
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (5 bp):
AAATA
Found at i:23004654 original size:18 final size:16
Alignment explanation
Indices: 23004633--23004686 Score: 65
Period size: 18 Copynumber: 3.2 Consensus size: 16
23004623 AAAATGAATT
23004633 AATAAAGAAATAAAATA
1 AATAAA-AAATAAAATA
23004650 CAATAAAATAATAAAAT-
1 -AATAAAA-AATAAAATA
*
23004667 AATAATAAATAAAATA
1 AATAAAAAATAAAATA
23004683 AATA
1 AATA
23004687 GGAAAATAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
15 8 0.24
16 10 0.30
17 1 0.03
18 14 0.42
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (16 bp):
AATAAAAAATAAAATA
Found at i:23004656 original size:10 final size:9
Alignment explanation
Indices: 23004640--23004686 Score: 57
Period size: 8 Copynumber: 5.6 Consensus size: 9
23004630 ATTAATAAAG
23004640 AAATAAAAT
1 AAATAAAAT
23004649 ACAATAAAAT
1 A-AATAAAAT
23004659 -AATAAAAT
1 AAATAAAAT
23004667 -AAT--AAT
1 AAATAAAAT
23004673 AAATAAAAT
1 AAATAAAAT
23004682 AAATA
1 AAATA
23004687 GGAAAATAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
6 3 0.09
7 3 0.09
8 11 0.32
9 9 0.26
10 8 0.24
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (9 bp):
AAATAAAAT
Found at i:23004659 original size:23 final size:22
Alignment explanation
Indices: 23004633--23004684 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 22
23004623 AAAATGAATT
23004633 AATAAAGAAATAA-AATACAATAA
1 AATAAA-AAATAATAATA-AATAA
23004656 AATAATAAAATAATAATAAATAA
1 AATAA-AAAATAATAATAAATAA
23004679 AATAAA
1 AATAAA
23004685 TAGGAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
22 1 0.04
23 21 0.78
24 5 0.19
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (22 bp):
AATAAAAAATAATAATAAATAA
Found at i:23011402 original size:12 final size:12
Alignment explanation
Indices: 23011385--23011426 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
23011375 AATTAGAATG
*
23011385 TAAAAATTAAAC
1 TAAAAATTAAAA
*
23011397 TAAAAACTAAAA
1 TAAAAATTAAAA
*
23011409 T-AAAATAAAAA
1 TAAAAATTAAAA
23011420 TAAAAAT
1 TAAAAAT
23011427 AAATGGCTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (12 bp):
TAAAAATTAAAA
Found at i:23011417 original size:17 final size:17
Alignment explanation
Indices: 23011385--23011429 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
23011375 AATTAGAATG
*
23011385 TAAAAATTAAACTAAAAA
1 TAAAAA-TAAAATAAAAA
23011403 CT-AAAATAAAATAAAAA
1 -TAAAAATAAAATAAAAA
23011420 TAAAAATAAA
1 TAAAAATAAA
23011430 TGGCTAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 1 0.04
17 18 0.75
18 4 0.17
19 1 0.04
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (17 bp):
TAAAAATAAAATAAAAA
Found at i:23012994 original size:19 final size:19
Alignment explanation
Indices: 23012970--23013006 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
23012960 GAGTCAGGCA
23012970 TACGGGTCATCAAAACAAT
1 TACGGGTCATCAAAACAAT
*
23012989 TACGGGTCATCGAAACAA
1 TACGGGTCATCAAAACAA
23013007 CAGAAAATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.19
Consensus pattern (19 bp):
TACGGGTCATCAAAACAAT
Found at i:23014358 original size:5 final size:5
Alignment explanation
Indices: 23014344--23014373 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
23014334 GTTTCTCTCC
23014344 CTTTT C-TTT CTTTT CTTTT CTTTT CTTTT C
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT C
23014374 CCTGGTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (5 bp):
CTTTT
Found at i:23015405 original size:2 final size:2
Alignment explanation
Indices: 23015398--23015426 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
23015388 TTTGTTATTT
23015398 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
23015427 TAAGATGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:23015805 original size:11 final size:12
Alignment explanation
Indices: 23015773--23015810 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 12
23015763 GGGGGTAGGA
23015773 ATCTGCATCTAT
1 ATCTGCATCTAT
*
23015785 ATCTAC-TCTAT
1 ATCTGCATCTAT
23015796 -TCTGCATCTAT
1 ATCTGCATCTAT
23015807 ATCT
1 ATCT
23015811 TATATGTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 4 0.18
11 10 0.45
12 8 0.36
ACGTcount: A:0.24, C:0.26, G:0.05, T:0.45
Consensus pattern (12 bp):
ATCTGCATCTAT
Found at i:23015820 original size:22 final size:22
Alignment explanation
Indices: 23015774--23015823 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
23015764 GGGGTAGGAA
*
23015774 TCTGCATCTATATCTACTCTAT
1 TCTGCATCTATATCTACTATAT
*
23015796 TCTGCATCTATATCTTA-TATGT
1 TCTGCATCTATATC-TACTATAT
23015818 TCTGCA
1 TCTGCA
23015824 ACTGTACCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 23 0.92
23 2 0.08
ACGTcount: A:0.22, C:0.24, G:0.08, T:0.46
Consensus pattern (22 bp):
TCTGCATCTATATCTACTATAT
Found at i:23022785 original size:17 final size:17
Alignment explanation
Indices: 23022752--23022785 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
23022742 ATTCACAAAT
*
23022752 TATTTTTATAATATATA
1 TATTTTTACAATATATA
*
23022769 TATTTTTACAATTTATA
1 TATTTTTACAATATATA
23022786 ATATAATAAA
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:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (17 bp):
TATTTTTACAATATATA
Found at i:23026565 original size:6 final size:6
Alignment explanation
Indices: 23026556--23026580 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
23026546 CCTTAATCAT
23026556 AATTAC AATTAC AATTAC AATTAC A
1 AATTAC AATTAC AATTAC AATTAC A
23026581 TAACCATACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (6 bp):
AATTAC
Found at i:23028932 original size:17 final size:17
Alignment explanation
Indices: 23028899--23028932 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
23028889 TTGTGTTTTG
*
23028899 TGCAAAAAGGGCTAAAT
1 TGCAAAAAGGGCAAAAT
*
23028916 TGCAAAAAGTGCAAAAT
1 TGCAAAAAGGGCAAAAT
23028933 GTTAGGGGCA
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:0.50, C:0.12, G:0.21, T:0.18
Consensus pattern (17 bp):
TGCAAAAAGGGCAAAAT
Found at i:23029826 original size:41 final size:41
Alignment explanation
Indices: 23029730--23029844 Score: 131
Period size: 41 Copynumber: 2.8 Consensus size: 41
23029720 AAATGTAATA
* *
23029730 CGGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAATAATT
1 CGGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAACAATT
* * * *
23029771 CAGACTTTATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CGGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAACAATT
* * * * *
23029812 CGGACTATAGGTCTAGTAGGCTAAAAGCCGGTG
1 CGGACTTTACGTCTAGCAGGCTTAATGCCGGTG
23029845 TACTGAATCA
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 62 1.00
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (41 bp):
CGGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAACAATT
Found at i:23030154 original size:2 final size:2
Alignment explanation
Indices: 23030147--23030173 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
23030137 TGCAATTGGG
23030147 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
23030174 AATGTACTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23034798 original size:34 final size:34
Alignment explanation
Indices: 23034755--23034823 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
23034745 ATCGCGATTT
23034755 TGGAAGAAATTACAAGATGCTTTAGGTACGAAAC
1 TGGAAGAAATTACAAGATGCTTTAGGTACGAAAC
23034789 TGGAAGAAATTACAAGATGCTTTAGGTACGAAAC
1 TGGAAGAAATTACAAGATGCTTTAGGTACGAAAC
23034823 T
1 T
23034824 ACATTTTAGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.41, C:0.12, G:0.23, T:0.25
Consensus pattern (34 bp):
TGGAAGAAATTACAAGATGCTTTAGGTACGAAAC
Found at i:23036514 original size:17 final size:17
Alignment explanation
Indices: 23036481--23036514 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
23036471 TTGTGTTTTG
*
23036481 TGCAAAAAGGGCTAAAT
1 TGCAAAAAGGGCAAAAT
*
23036498 TGCAAAAAGTGCAAAAT
1 TGCAAAAAGGGCAAAAT
23036515 GTTAGGGGCA
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:0.50, C:0.12, G:0.21, T:0.18
Consensus pattern (17 bp):
TGCAAAAAGGGCAAAAT
Found at i:23041045 original size:109 final size:108
Alignment explanation
Indices: 23040854--23041075 Score: 399
Period size: 109 Copynumber: 2.0 Consensus size: 108
23040844 GGTTTAATTT
* *
23040854 CTAAAAATGATGGGAGAGAATGATGACTGGAGTGTAAAACCCCTGACTACATCGCAGAAGGGCAA
1 CTAAAAATGACGGGAGAGAATGATGACTGGAGTGTAAAACCCCTGACTACATCGCAGAAGGGAAA
23040919 ACGCCCTGGTCAGAGTAGTAATACGGGTGTAAATCACAGTGGTG
66 ACGCCCTGGTCAGAGTAGTAATAC-GGTGTAAATCACAGTGGTG
23040963 CTAAAAATGACGGGAGAGAATGATGACTGGAGTGTAAAACCCCTGACTACATCGCAGAAGGGAAA
1 CTAAAAATGACGGGAGAGAATGATGACTGGAGTGTAAAACCCCTGACTACATCGCAGAAGGGAAA
* *
23041028 ACGCCGTGGTCAGAGTAGTAATACGGTGTAAATCGCAGTGGTG
66 ACGCCCTGGTCAGAGTAGTAATACGGTGTAAATCACAGTGGTG
23041071 CTAAA
1 CTAAA
23041076 GACACGACTA
Statistics
Matches: 109, Mismatches: 4, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
108 23 0.21
109 86 0.79
ACGTcount: A:0.35, C:0.17, G:0.29, T:0.19
Consensus pattern (108 bp):
CTAAAAATGACGGGAGAGAATGATGACTGGAGTGTAAAACCCCTGACTACATCGCAGAAGGGAAA
ACGCCCTGGTCAGAGTAGTAATACGGTGTAAATCACAGTGGTG
Found at i:23044676 original size:50 final size:50
Alignment explanation
Indices: 23044557--23044798 Score: 324
Period size: 50 Copynumber: 4.8 Consensus size: 50
23044547 GATAATAACA
* ** *
23044557 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * * ** ***
23044608 TGCCCATGCAATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTTTA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
23044658 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
** *
23044708 TGCCAACGCCATGTCCCAGGTATGATCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
23044758 TGCCAACGCCATGTCCCTGAC-TGGTCTTACATGGGACCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
23044799 TTACCCAAAT
Statistics
Matches: 165, Mismatches: 26, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
49 19 0.12
50 114 0.69
51 32 0.19
ACGTcount: A:0.20, C:0.31, G:0.22, T:0.26
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:23050902 original size:2 final size:2
Alignment explanation
Indices: 23050897--23050926 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
23050887 TACGAAATGA
23050897 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23050927 GCTTAACAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23051478 original size:41 final size:41
Alignment explanation
Indices: 23051433--23051568 Score: 200
Period size: 41 Copynumber: 3.3 Consensus size: 41
23051423 GCAATTAGCT
* * * *
23051433 TGCTAGACTTAAAGTCCGAATTATTTCACCGGCCTTAAACC
1 TGCTAGACTTTAAGTCTGAATTATATCATCGGCCTTAAACC
* * *
23051474 TGCTAGACTTTAAGTCTGAATTATATCATTGGCGTTAAGCC
1 TGCTAGACTTTAAGTCTGAATTATATCATCGGCCTTAAACC
*
23051515 TGCTAGACTTTAAGTCTGAATTATATCATCAGCCTTAAACC
1 TGCTAGACTTTAAGTCTGAATTATATCATCGGCCTTAAACC
23051556 TGCTAGACTTTAA
1 TGCTAGACTTTAA
23051569 AAATTTCAAT
Statistics
Matches: 84, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 84 1.00
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.34
Consensus pattern (41 bp):
TGCTAGACTTTAAGTCTGAATTATATCATCGGCCTTAAACC
Found at i:23058836 original size:17 final size:18
Alignment explanation
Indices: 23058811--23058848 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
23058801 TTATTTCCTG
23058811 TTTTCAG-TTTAGTTTAT
1 TTTTCAGTTTTAGTTTAT
* *
23058828 TTTTGAGTTTTATTTTAT
1 TTTTCAGTTTTAGTTTAT
23058846 TTT
1 TTT
23058849 GTTTAATTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.16, C:0.03, G:0.11, T:0.71
Consensus pattern (18 bp):
TTTTCAGTTTTAGTTTAT
Found at i:23063603 original size:27 final size:27
Alignment explanation
Indices: 23063559--23063620 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 27
23063549 GAGCCCTATT
*
23063559 CAGTAACAGTACAGTGT-GGCCTTAGCC
1 CAGT-ACAGTACAATGTGGGCCTTAGCC
23063586 CAGTACAGTAACAATGTGGGCCTTAGCC
1 CAGTACAGT-ACAATGTGGGCCTTAGCC
*
23063614 CAATACA
1 CAGTACA
23063621 ATATCAGTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
26 5 0.16
27 10 0.32
28 16 0.52
ACGTcount: A:0.31, C:0.26, G:0.23, T:0.21
Consensus pattern (27 bp):
CAGTACAGTACAATGTGGGCCTTAGCC
Found at i:23063744 original size:26 final size:26
Alignment explanation
Indices: 23063710--23063816 Score: 135
Period size: 26 Copynumber: 4.1 Consensus size: 26
23063700 AACACACCAA
* *
23063710 TATCACAGCAAAGCTGCCCGTAATAG
1 TATCGCAGCAAAGCTGCCAGTAATAG
* *
23063736 TATCGCAGCAAAGCTACTAGTAATAG
1 TATCGCAGCAAAGCTGCCAGTAATAG
*
23063762 TATCGCAGCAAAGCTGCCAAT-ATCAG
1 TATCGCAGCAAAGCTGCCAGTAAT-AG
* *
23063788 TATCGCAGCAAAGTTGCCAGTAACAG
1 TATCGCAGCAAAGCTGCCAGTAATAG
23063814 TAT
1 TAT
23063817 ACTTCCTCCA
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
25 2 0.03
26 66 0.96
27 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (26 bp):
TATCGCAGCAAAGCTGCCAGTAATAG
Found at i:23066266 original size:18 final size:18
Alignment explanation
Indices: 23066245--23066284 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
23066235 AGGATCTGTG
* *
23066245 TCTGCATTTGTATCTGAA
1 TCTGAATTTGCATCTGAA
*
23066263 TCTGAATTTGCATCTGTA
1 TCTGAATTTGCATCTGAA
23066281 TCTG
1 TCTG
23066285 TATCTGATTA
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:0.20, C:0.17, G:0.17, T:0.45
Consensus pattern (18 bp):
TCTGAATTTGCATCTGAA
Found at i:23066289 original size:12 final size:12
Alignment explanation
Indices: 23066238--23066290 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
23066228 ATAGGGTAGG
*
23066238 ATCTGTGTCTGC
1 ATCTGTATCTGC
* *
23066250 ATTTGTATCTGA
1 ATCTGTATCTGC
* *
23066262 ATCTGAATTTGC
1 ATCTGTATCTGC
*
23066274 ATCTGTATCTGT
1 ATCTGTATCTGC
23066286 ATCTG
1 ATCTG
23066291 ATTATGAAAA
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.19, C:0.17, G:0.19, T:0.45
Consensus pattern (12 bp):
ATCTGTATCTGC
Found at i:23070285 original size:20 final size:20
Alignment explanation
Indices: 23070260--23070307 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
23070250 TATGCTCTAA
*
23070260 CATCTTGTTGCTGTTGAGGG
1 CATCTTGCTGCTGTTGAGGG
23070280 CATCTTGCTGCTGTTGAGGG
1 CATCTTGCTGCTGTTGAGGG
*
23070300 CGTCTTGC
1 CATCTTGC
23070308 GTGATCAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.08, C:0.21, G:0.33, T:0.38
Consensus pattern (20 bp):
CATCTTGCTGCTGTTGAGGG
Found at i:23076728 original size:22 final size:22
Alignment explanation
Indices: 23076685--23076733 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
23076675 AGATAAGAGT
* *
23076685 CATAAACAGGATAGCTATAAGC
1 CATAAACAGAATAGCTACAAGC
*
23076707 TATAAACAGAAT-GACTACAAGC
1 CATAAACAGAATAG-CTACAAGC
23076729 CATAA
1 CATAA
23076734 GTACAGTAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.49, C:0.18, G:0.14, T:0.18
Consensus pattern (22 bp):
CATAAACAGAATAGCTACAAGC
Found at i:23076864 original size:31 final size:32
Alignment explanation
Indices: 23076725--23076894 Score: 157
Period size: 32 Copynumber: 5.4 Consensus size: 32
23076715 GAATGACTAC
* * * *
23076725 AAGCCATAAGT-ACAGTAATGTGATTGGCACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
* * *** * *
23076756 AAGCTATCATTAGTAGTGATATGAGCGGCACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
* *
23076788 CAA-CCATCAGTAACAGTAAAATGATCGGCACA
1 -AAGCCATCAGTAACGGTAATATGATCGGCACA
* * *
23076820 TAGCCATCGGTAACGGTAATATGATAGGC-CA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
*
23076851 AAGCCATCAGTAACGGTACTATGATCGGCACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
23076883 AAGCCATCAGTA
1 AAGCCATCAGTA
23076895 GCATCGCAGT
Statistics
Matches: 110, Mismatches: 25, Indels: 7
0.77 0.18 0.05
Matches are distributed among these distances:
31 36 0.33
32 72 0.65
33 2 0.02
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.21
Consensus pattern (32 bp):
AAGCCATCAGTAACGGTAATATGATCGGCACA
Found at i:23076968 original size:27 final size:27
Alignment explanation
Indices: 23076938--23077001 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
23076928 AACAAAGCTG
* *
23076938 CCAGTAATAGT-ATATGTGGCTAAGCCA
1 CCAGTAACAGTGAT-TGTGGCAAAGCCA
23076965 CCAGTAACAGTGATTGTGGCAAAGCCA
1 CCAGTAACAGTGATTGTGGCAAAGCCA
*
23076992 TCAGT-ACAGT
1 CCAGTAACAGT
23077002 ACTTCCTCCA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 5 0.15
27 26 0.79
28 2 0.06
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.23
Consensus pattern (27 bp):
CCAGTAACAGTGATTGTGGCAAAGCCA
Found at i:23077207 original size:27 final size:27
Alignment explanation
Indices: 23077169--23077292 Score: 137
Period size: 27 Copynumber: 4.7 Consensus size: 27
23077159 GGCAAAAATA
23077169 GTCA-TTTA-CCTACCA-GGGCATTACG
1 GTCATTTTACCCTA-CAGGGGCATTACG
* * *
23077194 GTCATTTTACCCTACATGGGTATTACA
1 GTCATTTTACCCTACAGGGGCATTACG
*
23077221 GTCATTTTACCCTACAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* * *
23077248 ATTATTTTACCCTATAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
23077275 ATCATTTTACTCTACAGG
1 GTCATTTTACCCTACAGG
23077293 TACCCTATAA
Statistics
Matches: 85, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
25 4 0.05
26 6 0.07
27 75 0.88
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGCATTACG
Found at i:23079550 original size:20 final size:21
Alignment explanation
Indices: 23079528--23079575 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
23079518 TTTTTTGTCT
*
23079528 TTATTTATTTATT-TTTATTT
1 TTATTTATTTATTATTTATAT
23079548 TTATTTATTTATTATTTATAT
1 TTATTTATTTATTATTTATAT
23079569 TT-TTTAT
1 TTATTTAT
23079576 GCTTTAGGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (21 bp):
TTATTTATTTATTATTTATAT
Found at i:23079552 original size:16 final size:17
Alignment explanation
Indices: 23079531--23079575 Score: 67
Period size: 16 Copynumber: 2.8 Consensus size: 17
23079521 TTTGTCTTTA
23079531 TTTATTTATTT-TTATT
1 TTTATTTATTTATTATT
23079547 TTTATTTATTTATTATT
1 TTTATTTATTTATTATT
*
23079564 TATATTT-TTTAT
1 TTTATTTATTTAT
23079576 GCTTTAGGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 16 0.59
17 11 0.41
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTATTTATTTATTATT
Found at i:23079575 original size:24 final size:24
Alignment explanation
Indices: 23079527--23079572 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
23079517 TTTTTTTGTC
*
23079527 TTTATTTATTTATTTTTATTTTTA
1 TTTATTTATTTATTTATATTTTTA
23079551 TTTATTTA-TTATTTATATTTTT
1 TTTATTTATTTATTTATATTTTT
23079573 TATGCTTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (24 bp):
TTTATTTATTTATTTATATTTTTA
Done.