Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A12
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: 102106374
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3186644 characters in sequence are not A, C, G, or T
File 8 of 311
Found at i:2219129 original size:63 final size:64
Alignment explanation
Indices: 2218977--2219129 Score: 213
Period size: 63 Copynumber: 2.4 Consensus size: 64
2218967 TAAATATCTC
* *
2218977 TTACACGGCCTGGACACACGCCCGTG-TCTCAGGCCCATGTGACTCTAATTCACAAATAGTGAG
1 TTACACGGCCTAGACACACGCCCGTGTTCTCAGGCCCATGTGACTCTAATTCACAAACAGTGAG
* **
2219040 TTACACGGCTTAGACACACGTTCGTGTTC-CTA-GCCCATGTGACTCTAATTCACAAACAGTGAG
1 TTACACGGCCTAGACACACGCCCGTGTTCTC-AGGCCCATGTGACTCTAATTCACAAACAGTGAG
* *
2219103 TTACATGGCCTAGACACATGCCCGTGT
1 TTACACGGCCTAGACACACGCCCGTGT
2219130 GACTTTAATT
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
63 75 0.96
64 3 0.04
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (64 bp):
TTACACGGCCTAGACACACGCCCGTGTTCTCAGGCCCATGTGACTCTAATTCACAAACAGTGAG
Found at i:2220727 original size:21 final size:20
Alignment explanation
Indices: 2220681--2220736 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
2220671 AATTATTTGT
* *
2220681 TTAATAACTTTTTTTATCATG
1 TTAATAA-TTTTTTTATAATA
*
2220702 GTAATAATTTTTTTATAATAA
1 TTAATAATTTTTTTATAAT-A
2220723 TTAAT-ATTTTTTTA
1 TTAATAATTTTTTTA
2220737 AAAATATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 20 0.67
21 10 0.33
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.59
Consensus pattern (20 bp):
TTAATAATTTTTTTATAATA
Found at i:2231181 original size:17 final size:18
Alignment explanation
Indices: 2231161--2231196 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
2231151 TAATCAAATT
2231161 TAATTATTATATT-TTTA
1 TAATTATTATATTATTTA
2231178 TAATTATTATATTATTTA
1 TAATTATTATATTATTTA
2231196 T
1 T
2231197 TAAGTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TAATTATTATATTATTTA
Found at i:2231438 original size:23 final size:21
Alignment explanation
Indices: 2231412--2231465 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 21
2231402 GATAAATCTT
2231412 TATTTTAATTGTAATGCATTTAA
1 TATTTTAATT-TAATGCATTT-A
* *
2231435 TATTATTTATTTAATGTATTTA
1 TATT-TTAATTTAATGCATTTA
2231457 TATGTTTAA
1 TAT-TTTAA
2231466 ATATAGTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
22 7 0.27
23 14 0.54
24 5 0.19
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.57
Consensus pattern (21 bp):
TATTTTAATTTAATGCATTTA
Found at i:2231796 original size:7 final size:7
Alignment explanation
Indices: 2231784--2231828 Score: 90
Period size: 7 Copynumber: 6.4 Consensus size: 7
2231774 TTTTATTATG
2231784 TTTAAAT
1 TTTAAAT
2231791 TTTAAAT
1 TTTAAAT
2231798 TTTAAAT
1 TTTAAAT
2231805 TTTAAAT
1 TTTAAAT
2231812 TTTAAAT
1 TTTAAAT
2231819 TTTAAAT
1 TTTAAAT
2231826 TTT
1 TTT
2231829 TATTTTTAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
TTTAAAT
Found at i:2231810 original size:21 final size:21
Alignment explanation
Indices: 2231784--2231837 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
2231774 TTTTATTATG
2231784 TTTAAATTTTAAATTTTAAAT
1 TTTAAATTTTAAATTTTAAAT
2231805 TTTAAATTTTAAATTTTAAAT
1 TTTAAATTTTAAATTTTAAAT
* *
2231826 TTTTATTTTTAA
1 TTTAAATTTTAA
2231838 CATAATTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTAAATTTTAAATTTTAAAT
Found at i:2232119 original size:18 final size:17
Alignment explanation
Indices: 2232093--2232126 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2232083 AATTTTAATA
*
2232093 AATATTTTTATAATTTTT
1 AATAATTTTAT-ATTTTT
2232111 AATAATTTTATATTTT
1 AATAATTTTATATTTT
2232127 GAAAGATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
AATAATTTTATATTTTT
Found at i:2234350 original size:14 final size:15
Alignment explanation
Indices: 2234331--2234361 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
2234321 AATATGATAG
2234331 AAATCTTTGTA-TAA
1 AAATCTTTGTATTAA
2234345 AAATCTTTGTATTAA
1 AAATCTTTGTATTAA
2234360 AA
1 AA
2234362 GTTGAATTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.42
Consensus pattern (15 bp):
AAATCTTTGTATTAA
Found at i:2237457 original size:7 final size:7
Alignment explanation
Indices: 2237447--2237476 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
2237437 TTAATAAATA
2237447 ATATTAT
1 ATATTAT
2237454 ATATTAT
1 ATATTAT
2237461 ATATTAT
1 ATATTAT
2237468 ATATTAT
1 ATATTAT
2237475 AT
1 AT
2237477 GTATTAGACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
ATATTAT
Found at i:2241293 original size:46 final size:46
Alignment explanation
Indices: 2241242--2241607 Score: 572
Period size: 46 Copynumber: 8.0 Consensus size: 46
2241232 AGTGTGCTCT
*
2241242 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGT
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
*
2241288 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGT
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
*
2241334 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
2241380 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
*
2241426 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
*
2241472 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
* *** *
2241518 GTGATATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
* * * * * *
2241564 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
2241608 TCATGTCAAA
Statistics
Matches: 304, Mismatches: 15, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
45 1 0.00
46 303 1.00
ACGTcount: A:0.38, C:0.14, G:0.25, T:0.23
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
Found at i:2245016 original size:20 final size:19
Alignment explanation
Indices: 2244969--2245072 Score: 62
Period size: 18 Copynumber: 5.6 Consensus size: 19
2244959 CAAGATAAAC
2244969 ATTAAATT-A-AATTTAAT
1 ATTAAATTAATAATTTAAT
2244986 ATTAAGA-TAATAACTTTAAT
1 ATTAA-ATTAATAA-TTTAAT
* *
2245006 ATTAAATTAATAA-ATACT
1 ATTAAATTAATAATTTAAT
*
2245024 ATTAAAATAAGT-A-TTAA-
1 ATTAAATTAA-TAATTTAAT
*
2245041 ATTAAATTTAAT-ATTAAACT
1 ATTAAA-TTAATAATTTAA-T
*
2245061 ATTAAAATAATA
1 ATTAAATTAATA
2245073 TTAATTTTAA
Statistics
Matches: 68, Mismatches: 8, Indels: 19
0.72 0.08 0.20
Matches are distributed among these distances:
17 14 0.21
18 23 0.34
19 8 0.12
20 23 0.34
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (19 bp):
ATTAAATTAATAATTTAAT
Found at i:2245046 original size:17 final size:17
Alignment explanation
Indices: 2244981--2245088 Score: 83
Period size: 18 Copynumber: 5.9 Consensus size: 17
2244971 TAAATTAAAT
*
2244981 TTAATATTAAGATAATAA
1 TTAATATTAAAATAAT-A
*
2244999 CTTTAATATTAAATTAATAA
1 --TTAATATTAAAATAAT-A
* *
2245019 ATACTATTAAAATAAGTA
1 TTAATATTAAAATAA-TA
*
2245037 TTAA-ATTAAATTTAATA
1 TTAATATTAAA-ATAATA
2245054 TTAAACTATTAAAATAATA
1 TT-AA-TATTAAAATAATA
*
2245073 TTAATTTTAAAATAAT
1 TTAATATTAAAATAAT
2245089 TAATCTGAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
17 21 0.29
18 22 0.30
19 8 0.11
20 22 0.30
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.42
Consensus pattern (17 bp):
TTAATATTAAAATAATA
Found at i:2245063 original size:25 final size:25
Alignment explanation
Indices: 2245001--2245083 Score: 66
Period size: 25 Copynumber: 3.4 Consensus size: 25
2244991 GATAATAACT
* * *
2245001 TTAATATTAAATTAAT-AAATACTA
1 TTAATATTAAACTATTAAAATAATA
* * *
2245025 TTAA-AAT-AAGTATTAAATTAA-A
1 TTAATATTAAACTATTAAAATAATA
2245047 TTTAATATTAAACTATTAAAATAATA
1 -TTAATATTAAACTATTAAAATAATA
*
2245073 TTAATTTTAAA
1 TTAATATTAAA
2245084 ATAATTAATC
Statistics
Matches: 45, Mismatches: 9, Indels: 9
0.71 0.14 0.14
Matches are distributed among these distances:
22 6 0.13
23 10 0.22
24 6 0.13
25 22 0.49
26 1 0.02
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.42
Consensus pattern (25 bp):
TTAATATTAAACTATTAAAATAATA
Found at i:2245083 original size:37 final size:36
Alignment explanation
Indices: 2245001--2245088 Score: 110
Period size: 36 Copynumber: 2.4 Consensus size: 36
2244991 GATAATAACT
2245001 TTAATATTAAATTAATAAATACTATTAAAATAAGTA
1 TTAATATTAAATTAATAAATACTATTAAAATAAGTA
2245037 TTAA-ATTAAATTTAATATTAA-ACTATTAAAATAA-TA
1 TTAATATTAAA-TTAATA--AATACTATTAAAATAAGTA
* *
2245073 TTAATTTTAAAATAAT
1 TTAATATTAAATTAAT
2245089 TAATCTGAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
35 6 0.13
36 20 0.43
37 18 0.39
38 2 0.04
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (36 bp):
TTAATATTAAATTAATAAATACTATTAAAATAAGTA
Found at i:2245092 original size:15 final size:17
Alignment explanation
Indices: 2245025--2245088 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
2245015 ATAAATACTA
*
2245025 TTAAAATAAGTATTAA-A
1 TTAAAATAA-TATTAATT
* *
2245042 TTAAATTTAATATTAAACTA
1 TTAAA-ATAATATT-AA-TT
2245062 TTAAAATAATATTAATT
1 TTAAAATAATATTAATT
2245079 TTAAAATAAT
1 TTAAAATAAT
2245089 TAATCTGAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
17 20 0.50
18 7 0.17
19 7 0.17
20 6 0.15
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (17 bp):
TTAAAATAATATTAATT
Found at i:2246689 original size:15 final size:15
Alignment explanation
Indices: 2246665--2246696 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2246655 TATGCATGAA
*
2246665 AAATATAAAAGACAT
1 AAATACAAAAGACAT
2246680 AAATACAAAAGACAT
1 AAATACAAAAGACAT
2246695 AA
1 AA
2246697 TAGTGAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATACAAAAGACAT
Found at i:2258622 original size:14 final size:13
Alignment explanation
Indices: 2258588--2258613 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2258578 CAAATGGGTA
2258588 GTTTTCTGCAAAT
1 GTTTTCTGCAAAT
2258601 GTTTTCTGCAAAT
1 GTTTTCTGCAAAT
2258614 CAGTTTCTGG
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:0.23, C:0.15, G:0.15, T:0.46
Consensus pattern (13 bp):
GTTTTCTGCAAAT
Found at i:2260211 original size:34 final size:35
Alignment explanation
Indices: 2260145--2260211 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
2260135 CAAACACCAG
*
2260145 AAAATATTTTCCAGTAAGTCATTTTACAGAAAAGT
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
*
2260180 AAAATATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAA
2260212 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 16 0.53
35 14 0.47
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (35 bp):
AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:2261964 original size:21 final size:21
Alignment explanation
Indices: 2261922--2261964 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
2261912 AAACTTTAAA
* *
2261922 AATAGTTATTTTTATTTTTTT
1 AATAGTTATTTTTAGTTATTT
2261943 AATA-TTATATTTTAGTTATTT
1 AATAGTTAT-TTTTAGTTATTT
2261964 A
1 A
2261965 TGTTTGAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (21 bp):
AATAGTTATTTTTAGTTATTT
Found at i:2339525 original size:16 final size:15
Alignment explanation
Indices: 2339499--2339533 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
2339489 TGATGTGAAT
2339499 AATATAAAATATTAA
1 AATATAAAATATTAA
*
2339514 AATATCAAAATATTAG
1 AATAT-AAAATATTAA
2339530 AATA
1 AATA
2339534 ATAATAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (15 bp):
AATATAAAATATTAA
Found at i:2339715 original size:20 final size:21
Alignment explanation
Indices: 2339676--2339718 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
2339666 CCTTTTTTAG
*
2339676 AATAATAATTAAATATACAAA
1 AATAATAATTAAATACACAAA
*
2339697 AATAAT-ATTATATACACAAA
1 AATAATAATTAAATACACAAA
2339717 AA
1 AA
2339719 GGTATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (21 bp):
AATAATAATTAAATACACAAA
Found at i:2339935 original size:11 final size:11
Alignment explanation
Indices: 2339919--2339948 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
2339909 TAACATTAAG
2339919 AATATATATAT
1 AATATATATAT
*
2339930 AATATAAATAT
1 AATATATATAT
2339941 AATATATA
1 AATATATA
2339949 CAATATACGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AATATATATAT
Found at i:2340418 original size:13 final size:13
Alignment explanation
Indices: 2340369--2340424 Score: 60
Period size: 13 Copynumber: 4.2 Consensus size: 13
2340359 GGCCGAAAAA
*
2340369 TATAATTTTTTA-
1 TATATTTTTTTAT
*
2340381 TATATTTGTTTTGT
1 TATATTT-TTTTAT
*
2340395 ATATATATTTTTAT
1 -TATATTTTTTTAT
2340409 TATATTTTTTTAT
1 TATATTTTTTTAT
2340422 TAT
1 TAT
2340425 GATGTATATA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
12 6 0.17
13 19 0.53
14 5 0.14
15 6 0.17
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.70
Consensus pattern (13 bp):
TATATTTTTTTAT
Found at i:2340510 original size:18 final size:16
Alignment explanation
Indices: 2340464--2340516 Score: 56
Period size: 17 Copynumber: 3.3 Consensus size: 16
2340454 AAAAACGAAA
*
2340464 AAAATAAAAA-AATA-
1 AAAATAAAAAGAAGAT
*
2340478 AAAATAAAAATAAGAGT
1 AAAATAAAAAGAAGA-T
2340495 AAAATAATAAAGAAGAT
1 AAAATAA-AAAGAAGAT
2340512 AAAAT
1 AAAAT
2340517 CACCTTTAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
14 10 0.30
15 3 0.09
17 13 0.39
18 7 0.21
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.17
Consensus pattern (16 bp):
AAAATAAAAAGAAGAT
Found at i:2346272 original size:78 final size:78
Alignment explanation
Indices: 2346143--2346301 Score: 300
Period size: 78 Copynumber: 2.0 Consensus size: 78
2346133 TTAGGTGTTC
*
2346143 AATACTCTTGTGAATGTTGATGTTTTCTGCCTTGTATGTATTGTGATTTCTTCTTCTTGTAGGCC
1 AATACTCTTGTGAATGTTGATGTTTTCTACCTTGTATGTATTGTGATTTCTTCTTCTTGTAGGCC
2346208 AACGGTTGCATGA
66 AACGGTTGCATGA
*
2346221 AATACTCTTGTGAATGTTGATGTTTTCTACCTTGTATTTATTGTGATTTCTTCTTCTTGTAGGCC
1 AATACTCTTGTGAATGTTGATGTTTTCTACCTTGTATGTATTGTGATTTCTTCTTCTTGTAGGCC
2346286 AACGGTTGCATGA
66 AACGGTTGCATGA
2346299 AAT
1 AAT
2346302 GAAACTGAAT
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
78 79 1.00
ACGTcount: A:0.19, C:0.15, G:0.20, T:0.45
Consensus pattern (78 bp):
AATACTCTTGTGAATGTTGATGTTTTCTACCTTGTATGTATTGTGATTTCTTCTTCTTGTAGGCC
AACGGTTGCATGA
Found at i:2347602 original size:2 final size:2
Alignment explanation
Indices: 2347595--2347636 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
2347585 ATCAGTCTTT
*
2347595 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CG CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
2347637 TGTATTAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.50, G:0.02, T:0.00
Consensus pattern (2 bp):
CA
Found at i:2347815 original size:18 final size:19
Alignment explanation
Indices: 2347781--2347817 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2347771 TCCCGACACT
2347781 ATAGCTTCTCCTTCCCATG
1 ATAGCTTCTCCTTCCCATG
*
2347800 ATAGCTTCT-GTTCCCATG
1 ATAGCTTCTCCTTCCCATG
2347818 GTTCTTCCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.16, C:0.32, G:0.14, T:0.38
Consensus pattern (19 bp):
ATAGCTTCTCCTTCCCATG
Found at i:2349152 original size:16 final size:18
Alignment explanation
Indices: 2349114--2349153 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
2349104 ATTATAAATA
2349114 ATAATGTGTAAAAATTGCT
1 ATAAT-TGTAAAAATTGCT
2349133 -TAATTGTAAAAA-TG-T
1 ATAATTGTAAAAATTGCT
2349148 ATAATT
1 ATAATT
2349154 TCATGATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
15 1 0.05
16 7 0.35
17 8 0.40
18 4 0.20
ACGTcount: A:0.45, C:0.03, G:0.12, T:0.40
Consensus pattern (18 bp):
ATAATTGTAAAAATTGCT
Found at i:2351749 original size:10 final size:11
Alignment explanation
Indices: 2351723--2351761 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
2351713 TATATTTTCC
2351723 TATTTTTATAA
1 TATTTTTATAA
2351734 TATTTTTATAA
1 TATTTTTATAA
2351745 T-TTTTTAATAA
1 TATTTTT-ATAA
*
2351756 AATTTT
1 TATTTT
2351762 AAAAAATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
10 5 0.20
11 16 0.64
12 4 0.16
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TATTTTTATAA
Found at i:2353087 original size:20 final size:21
Alignment explanation
Indices: 2353064--2353104 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
2353054 GGTAGTTATT
*
2353064 TGTTAGTTAGTAG-TTGTTAA
1 TGTTAGTTAGCAGTTTGTTAA
2353084 TGTTAGTTAGCAGTTTGTTAA
1 TGTTAGTTAGCAGTTTGTTAA
2353105 AGTCAGCTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.24, C:0.02, G:0.24, T:0.49
Consensus pattern (21 bp):
TGTTAGTTAGCAGTTTGTTAA
Found at i:2355491 original size:17 final size:16
Alignment explanation
Indices: 2355469--2355506 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
2355459 CAATATTAAC
*
2355469 AATAACGACAATAATA
1 AATAACAACAATAATA
2355485 GAATAACAACAATAATA
1 -AATAACAACAATAATA
2355502 AATAA
1 AATAA
2355507 AGAATAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.66, C:0.11, G:0.05, T:0.18
Consensus pattern (16 bp):
AATAACAACAATAATA
Found at i:2355618 original size:25 final size:23
Alignment explanation
Indices: 2355581--2355633 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 23
2355571 AAATATAAGA
*
2355581 AATAATAGAATAATGGCAA-TAAT
1 AATAATAGAATAATAG-AATTAAT
2355604 AATAAGTAGTAATAATAGAATTAAT
1 AATAA-TAG-AATAATAGAATTAAT
2355629 AATAA
1 AATAA
2355634 AAATAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 5 0.19
24 5 0.19
25 16 0.62
ACGTcount: A:0.58, C:0.02, G:0.11, T:0.28
Consensus pattern (23 bp):
AATAATAGAATAATAGAATTAAT
Found at i:2364203 original size:20 final size:21
Alignment explanation
Indices: 2364165--2364203 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
2364155 AAAATCAATT
*
2364165 AATATTTATATAATTAAAATA
1 AATATTTATATAATGAAAATA
*
2364186 AATA-TTATATTATGAAAA
1 AATATTTATATAATGAAAA
2364204 ATAATATACA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (21 bp):
AATATTTATATAATGAAAATA
Found at i:2369013 original size:138 final size:138
Alignment explanation
Indices: 2368823--2369101 Score: 540
Period size: 138 Copynumber: 2.0 Consensus size: 138
2368813 ATTAGGTATG
2368823 TATTTTTGTCCCGTTTTTAATGATTTCTATGTTTCTGAGATCATAGTAGCTTAATCTAGCTAGCT
1 TATTTTTGTCCCGTTTTTAATGATTTCTATGTTTCTGAGATCATAGTAGCTTAATCTAGCTAGCT
2368888 CGGGGATTAATTTGCAAAACTGTTAAAGTATTAAGGTTTTTCCATTGATGAGTATGCTTGAATTT
66 CGGGGATTAATTTGCAAAACTGTTAAAGTATTAAGGTTTTTCCATTGATGAGTATGCTTGAATTT
2368953 TGAAGTTT
131 TGAAGTTT
* *
2368961 TATTTTTGTCCCGTTTTTAATGATTTCTATGTTTCTGAGATCGTAGTAGCTTAATCTAGTTAGCT
1 TATTTTTGTCCCGTTTTTAATGATTTCTATGTTTCTGAGATCATAGTAGCTTAATCTAGCTAGCT
2369026 CGGGGATTAATTTGCAAAACTGTTAAAGTATTAAGGTTTTTCCATTGATGAGTATGCTTGAATTT
66 CGGGGATTAATTTGCAAAACTGTTAAAGTATTAAGGTTTTTCCATTGATGAGTATGCTTGAATTT
2369091 TGAAGTTT
131 TGAAGTTT
2369099 TAT
1 TAT
2369102 GATAGAAAAT
Statistics
Matches: 139, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
138 139 1.00
ACGTcount: A:0.25, C:0.11, G:0.19, T:0.45
Consensus pattern (138 bp):
TATTTTTGTCCCGTTTTTAATGATTTCTATGTTTCTGAGATCATAGTAGCTTAATCTAGCTAGCT
CGGGGATTAATTTGCAAAACTGTTAAAGTATTAAGGTTTTTCCATTGATGAGTATGCTTGAATTT
TGAAGTTT
Found at i:2369753 original size:25 final size:25
Alignment explanation
Indices: 2369716--2369771 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
2369706 AGACACACCA
* *
2369716 CAGCTCATATGAGCTTCTCGATATT
1 CAGCTCATATGAGCTTCCCGATACT
*
2369741 CAGCTCACT-TGAGCTTCCCGTTACT
1 CAGCTCA-TATGAGCTTCCCGATACT
2369766 CAGCTC
1 CAGCTC
2369772 GGAGGAGCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 26 0.96
26 1 0.04
ACGTcount: A:0.20, C:0.32, G:0.16, T:0.32
Consensus pattern (25 bp):
CAGCTCATATGAGCTTCCCGATACT
Found at i:2371611 original size:21 final size:21
Alignment explanation
Indices: 2371587--2371656 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
2371577 CGTGTATCTC
2371587 AGTCACACAGGCTTGTGTCTT
1 AGTCACACAGGCTTGTGTCTT
2371608 AGTCACACA-G-TTGTGTCCCTT
1 AGTCACACAGGCTTGTGT--CTT
* * * *
2371629 CGTTACAC-GGCGTGTGTCTC
1 AGTCACACAGGCTTGTGTCTT
2371649 AGTCACAC
1 AGTCACAC
2371657 GACCGTGTAG
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
19 6 0.15
20 9 0.23
21 19 0.49
22 5 0.13
ACGTcount: A:0.19, C:0.29, G:0.23, T:0.30
Consensus pattern (21 bp):
AGTCACACAGGCTTGTGTCTT
Found at i:2380139 original size:15 final size:16
Alignment explanation
Indices: 2380111--2380143 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2380101 ATATTTAAAA
*
2380111 TTTTAGTTTATATATT
1 TTTTAATTTATATATT
2380127 TTTTAATTT-TATATT
1 TTTTAATTTATATATT
2380142 TT
1 TT
2380144 AACCCATTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (16 bp):
TTTTAATTTATATATT
Found at i:2381650 original size:29 final size:29
Alignment explanation
Indices: 2381606--2381663 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
2381596 GCTTAGTTGC
*
2381606 AATTGACGATAGATATGGCTACATTCTCT
1 AATTGACGATAAATATGGCTACATTCTCT
2381635 AATTGACGATAAATATGGCTACATTCTCT
1 AATTGACGATAAATATGGCTACATTCTCT
2381664 TGAGTTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (29 bp):
AATTGACGATAAATATGGCTACATTCTCT
Found at i:2385976 original size:78 final size:78
Alignment explanation
Indices: 2385837--2385992 Score: 249
Period size: 78 Copynumber: 2.0 Consensus size: 78
2385827 TAAGAAGTAC
2385837 TTATAATTGGACCAAATACGAGAGAAACCCAAAAGATCCTAATGATAATGCTAAGGATGACAAAC
1 TTATAATTGGACCAAATACGAGAGAAACCCAAAAGATCCTAATGATAATGCTAAGGATGACAAAC
2385902 CTTAGTATAATTA
66 CTTAGTATAATTA
* * * * * * *
2385915 TTATAATTGGACCCAATACGGGAGAGACCCAAAAGATCCTCATGATAATGTTAGGGGTGACAAAC
1 TTATAATTGGACCAAATACGAGAGAAACCCAAAAGATCCTAATGATAATGCTAAGGATGACAAAC
2385980 CTTAGTATAATTA
66 CTTAGTATAATTA
2385993 ACTAGGGTTA
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
78 71 1.00
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (78 bp):
TTATAATTGGACCAAATACGAGAGAAACCCAAAAGATCCTAATGATAATGCTAAGGATGACAAAC
CTTAGTATAATTA
Found at i:2396092 original size:29 final size:26
Alignment explanation
Indices: 2396026--2396082 Score: 69
Period size: 29 Copynumber: 2.1 Consensus size: 26
2396016 ACTTTTTATA
2396026 TATTTAAAATTAAGTCCTTTTATTTT
1 TATTTAAAATTAAGTCCTTTTATTTT
* *
2396052 TATTTCAAAAAATTTAGTCTTTTTATTTT
1 TATTT---AAAATTAAGTCCTTTTATTTT
2396081 TA
1 TA
2396083 GGATTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 5 0.19
29 21 0.81
ACGTcount: A:0.32, C:0.07, G:0.04, T:0.58
Consensus pattern (26 bp):
TATTTAAAATTAAGTCCTTTTATTTT
Found at i:2398849 original size:23 final size:25
Alignment explanation
Indices: 2398818--2398871 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
2398808 TATATATTCA
2398818 CATTCAAT-ATCAAAATCACAAT-TCT
1 CATT-AATAATCAAAA-CACAATATCT
*
2398843 -ATTAATAATCAACACACAATATCT
1 CATTAATAATCAAAACACAATATCT
2398867 CATTA
1 CATTA
2398872 TAAACGTGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
23 9 0.36
24 12 0.48
25 4 0.16
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.31
Consensus pattern (25 bp):
CATTAATAATCAAAACACAATATCT
Found at i:2402134 original size:71 final size:72
Alignment explanation
Indices: 2402040--2402190 Score: 168
Period size: 72 Copynumber: 2.1 Consensus size: 72
2402030 CATTTGGGTT
* ** *
2402040 AAATAATGGTAAAATTATTTTTGGTCCC-CAAAGT-TTTTAATATTGTT-AATTTATCCTTGTAT
1 AAATAATGGTAAAATTATATTTGG-CCCTCAAA-TCTTTTAATATT-TTAAACCTATCCTTCTAT
*
2402102 CATTATTTAA
63 CACTATTTAA
2402112 AAATAAT-GTAAAATT-TGATTTGGCCCTTCAAATCTTTTAATATTTTAAACCTATCCTTCTATC
1 AAATAATGGTAAAATTAT-ATTTGGCCC-TCAAATCTTTTAATATTTTAAACCTATCCTTCTATC
2402175 ACTATTTAA
64 ACTATTTAA
*
2402184 AAGTAAT
1 AAATAAT
2402191 ATAATTTACA
Statistics
Matches: 68, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
70 4 0.06
71 16 0.24
72 48 0.71
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (72 bp):
AAATAATGGTAAAATTATATTTGGCCCTCAAATCTTTTAATATTTTAAACCTATCCTTCTATCAC
TATTTAA
Found at i:2404309 original size:90 final size:90
Alignment explanation
Indices: 2404152--2404345 Score: 212
Period size: 90 Copynumber: 2.2 Consensus size: 90
2404142 TTCTGGCAGA
* ** * * *
2404152 ATATTAATCTGCAATTCTGGTGGTTCATCCACATATTATCTAGTAGCTTTTATCCGCAATTAAGT
1 ATATTAACCTGCAACACCGGTGGTTCATCCACATATTATCTAGCAACTTTTATCCGCAATTAAGT
* *
2404217 TGTGTATTCATAACCATCTAG-CAGT
66 TGTGTATTCACAACCAT-TAGACAGC
* * * ** * *
2404242 GTATTAACCTGCAACACCGGTGGTTCGTCCACCA-ATTATCTGGCAACTTTTATTTGCATTTATG
1 ATATTAACCTGCAACACCGGTGGTTCATCCA-CATATTATCTAGCAACTTTTATCCGCAATTAAG
*
2404306 TTGTGTATTCACAACCATTTGACAGC
65 TTGTGTATTCACAACCATTAGACAGC
2404332 ATATTAACCTGCAA
1 ATATTAACCTGCAA
2404346 ATTTACGATT
Statistics
Matches: 85, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
89 2 0.02
90 81 0.95
91 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (90 bp):
ATATTAACCTGCAACACCGGTGGTTCATCCACATATTATCTAGCAACTTTTATCCGCAATTAAGT
TGTGTATTCACAACCATTAGACAGC
Found at i:2409545 original size:26 final size:26
Alignment explanation
Indices: 2409516--2409575 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
2409506 AAAAGAATTC
*
2409516 AATATTTTATCTATATATTAATTTAA
1 AATATTTTATCTAAATATTAATTTAA
*
2409542 AATATTTTATCTAAATTTTAATTTAA
1 AATATTTTATCTAAATATTAATTTAA
*
2409568 TATATTTT
1 AATATTTT
2409576 TAAATGAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (26 bp):
AATATTTTATCTAAATATTAATTTAA
Found at i:2417027 original size:20 final size:20
Alignment explanation
Indices: 2416991--2417028 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2416981 TTTTATTTAA
*
2416991 TTTTTTTATCTTCTTCTTTT
1 TTTTTTTATCTTATTCTTTT
2417011 TTTTTTTAAT-TTATTCTT
1 TTTTTTT-ATCTTATTCTT
2417029 GATCCAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTTTTATCTTATTCTTTT
Found at i:2419610 original size:18 final size:17
Alignment explanation
Indices: 2419565--2419610 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 17
2419555 GTTTTCAATT
2419565 TTTTTTACATTTTTAATA
1 TTTTTTAC-TTTTTAATA
*
2419583 TATTTATACTTTTTAATAA
1 T-TTTTTACTTTTTAAT-A
2419602 TTTTTTACT
1 TTTTTTACT
2419611 AATTTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTTTACTTTTTAATA
Found at i:2419654 original size:10 final size:10
Alignment explanation
Indices: 2419573--2419657 Score: 54
Period size: 10 Copynumber: 8.7 Consensus size: 10
2419563 TTTTTTTTAC
2419573 ATTTTTAAT-
1 ATTTTTAATA
*
2419582 ATATTT-ATA
1 ATTTTTAATA
*
2419591 CTTTTTAATA
1 ATTTTTAATA
*
2419601 ATTTTTTACTA
1 A-TTTTTAATA
2419612 ATTTTTAA-A
1 ATTTTTAATA
*
2419621 ATTCTTACA-A
1 ATTTTTA-ATA
* *
2419631 GTTCTTTTAT-
1 ATT-TTTAATA
2419641 ATTTTTAATA
1 ATTTTTAATA
2419651 ATTTTTA
1 ATTTTTA
2419658 CTATTAATAT
Statistics
Matches: 57, Mismatches: 12, Indels: 13
0.70 0.15 0.16
Matches are distributed among these distances:
8 2 0.04
9 21 0.37
10 23 0.40
11 11 0.19
ACGTcount: A:0.33, C:0.06, G:0.01, T:0.60
Consensus pattern (10 bp):
ATTTTTAATA
Found at i:2420370 original size:51 final size:51
Alignment explanation
Indices: 2420307--2420439 Score: 158
Period size: 51 Copynumber: 2.6 Consensus size: 51
2420297 CAATCAAATC
* * * * * *
2420307 TCTAAGAATATAAAATCATATCTTCTAAGATTACCTATCTTATCTAAGATA
1 TCTAAGATTATAAAATAATATCTTATAAGATTACATATCATATCTAAGACA
* ** *
2420358 TGTAATCTTATAAAATAATATCTTATAAGATTACATATCATATCTAAGACC
1 TCTAAGATTATAAAATAATATCTTATAAGATTACATATCATATCTAAGACA
* *
2420409 TCTAAGATTATAAAATTATATCTTTTAAGAT
1 TCTAAGATTATAAAATAATATCTTATAAGAT
2420440 CATGTTTCCA
Statistics
Matches: 67, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
51 67 1.00
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.39
Consensus pattern (51 bp):
TCTAAGATTATAAAATAATATCTTATAAGATTACATATCATATCTAAGACA
Found at i:2425571 original size:51 final size:51
Alignment explanation
Indices: 2425508--2425640 Score: 167
Period size: 51 Copynumber: 2.6 Consensus size: 51
2425498 CAATCAAATC
* * * * *
2425508 TCTAAGAATATAAAATCATATCTTCTAAGATTACCTATCTTATCTAAGATA
1 TCTAAGATTATAAAATAATATCTTATAAGATTACATATCATATCTAAGATA
* ** *
2425559 TGTAATCTTATAAAATAATATCTTATAAGATTACATATCATATCTAAGATC
1 TCTAAGATTATAAAATAATATCTTATAAGATTACATATCATATCTAAGATA
* *
2425610 TCTAAGATTATAAAATTATATCTTTTAAGAT
1 TCTAAGATTATAAAATAATATCTTATAAGAT
2425641 CATGTTTCCA
Statistics
Matches: 68, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 68 1.00
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.40
Consensus pattern (51 bp):
TCTAAGATTATAAAATAATATCTTATAAGATTACATATCATATCTAAGATA
Found at i:2433406 original size:17 final size:17
Alignment explanation
Indices: 2433352--2433406 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
2433342 TGGTAGATCG
*
2433352 TGTGGGTCACA-AGGTCC
1 TGTGGGTCACATAGG-CA
* *
2433369 TGTGGGTCACAT-GACTG
1 TGTGGGTCACATAGGC-A
2433386 TGTGGGTCACATAGGCA
1 TGTGGGTCACATAGGCA
2433403 TGTG
1 TGTG
2433407 TCAGGTTGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
16 1 0.03
17 28 0.90
18 2 0.06
ACGTcount: A:0.18, C:0.18, G:0.36, T:0.27
Consensus pattern (17 bp):
TGTGGGTCACATAGGCA
Found at i:2435136 original size:32 final size:32
Alignment explanation
Indices: 2435099--2435162 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
2435089 TTAAAGAGTT
2435099 AAAATCAGGAAGAGAACCTCAGCAACAAAACC
1 AAAATCAGGAAGAGAACCTCAGCAACAAAACC
2435131 AAAATCAGGAAGAGAACCTCAGCAACAAAACC
1 AAAATCAGGAAGAGAACCTCAGCAACAAAACC
2435163 CTCCACCCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.53, C:0.25, G:0.16, T:0.06
Consensus pattern (32 bp):
AAAATCAGGAAGAGAACCTCAGCAACAAAACC
Found at i:2436493 original size:29 final size:28
Alignment explanation
Indices: 2436455--2436509 Score: 92
Period size: 29 Copynumber: 1.9 Consensus size: 28
2436445 AATATTATGT
*
2436455 TAAATGTAATAACTAATAGCATAATTTA
1 TAAATGTAATAACTAATAACATAATTTA
2436483 TAAATTGTAATAACTAATAACATAATT
1 TAAA-TGTAATAACTAATAACATAATT
2436510 ATACATAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 4 0.16
29 21 0.84
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.36
Consensus pattern (28 bp):
TAAATGTAATAACTAATAACATAATTTA
Found at i:2436728 original size:20 final size:19
Alignment explanation
Indices: 2436689--2436729 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
2436679 TTTTAATTAG
*
2436689 ATTTGTTTTTAATCAATTT
1 ATTTGTTTTTAAACAATTT
*
2436708 ATTTGATTTTTAAACATTTT
1 ATTTG-TTTTTAAACAATTT
2436728 AT
1 AT
2436730 ATATACTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.61
Consensus pattern (19 bp):
ATTTGTTTTTAAACAATTT
Found at i:2436921 original size:23 final size:23
Alignment explanation
Indices: 2436889--2436939 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
2436879 TGAGAGAGAG
2436889 AAAAAAATATT-AGAATGGATAAA
1 AAAAAAATATTGAGAATGGA-AAA
* *
2436912 AAATAAATATTGAGAATTGAAAA
1 AAAAAAATATTGAGAATGGAAAA
2436935 AAAAA
1 AAAAA
2436940 TCAATACTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.22
Consensus pattern (23 bp):
AAAAAAATATTGAGAATGGAAAA
Found at i:2438819 original size:40 final size:40
Alignment explanation
Indices: 2438758--2438836 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
2438748 ATGACAGTTG
2438758 GTACCACACCCATGACAGCAGTAATAGCATGCAACCACCA
1 GTACCACACCCATGACAGCAGTAATAGCATGCAACCACCA
** * *
2438798 GTACCACACCCATGATTGCAGTAGTAGTATGCAACCACC
1 GTACCACACCCATGACAGCAGTAATAGCATGCAACCACC
2438837 GATTTTAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.34, C:0.33, G:0.16, T:0.16
Consensus pattern (40 bp):
GTACCACACCCATGACAGCAGTAATAGCATGCAACCACCA
Found at i:2441129 original size:20 final size:20
Alignment explanation
Indices: 2441104--2441143 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2441094 CTTTACAAAA
2441104 ACTCTAGCAAAAGGGTAAGG
1 ACTCTAGCAAAAGGGTAAGG
2441124 ACTCTAGCAAAAGGGTAAGG
1 ACTCTAGCAAAAGGGTAAGG
2441144 GCTGGAGTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.15, G:0.30, T:0.15
Consensus pattern (20 bp):
ACTCTAGCAAAAGGGTAAGG
Found at i:2441526 original size:18 final size:18
Alignment explanation
Indices: 2441505--2441543 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
2441495 AATTCGAAAT
* *
2441505 AATTTTTAAATTTTAAAA
1 AATTTTAAAAATTTAAAA
*
2441523 AATTTTAAAAATTTATAA
1 AATTTTAAAAATTTAAAA
2441541 AAT
1 AAT
2441544 ATATATAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AATTTTAAAAATTTAAAA
Found at i:2447901 original size:21 final size:21
Alignment explanation
Indices: 2447828--2447920 Score: 73
Period size: 22 Copynumber: 4.1 Consensus size: 21
2447818 ATGTCTTATA
*
2447828 TTTTTATATTTTACAATAATT
1 TTTTTATATTTTATAATAATT
* *
2447849 TTCTATACATTTT-TAATAATTTCCT
1 TT-TTTATATTTTATAATAA--T--T
2447874 ATTTTTATATTTTATAATAATT
1 -TTTTTATATTTTATAATAATT
2447896 TTTTTATGATTTTTATAAT-ATT
1 TTTTTAT-A-TTTTATAATAATT
2447918 TTT
1 TTT
2447921 AAGAAAAATT
Statistics
Matches: 58, Mismatches: 5, Indels: 17
0.73 0.06 0.21
Matches are distributed among these distances:
21 14 0.24
22 16 0.28
23 10 0.17
24 1 0.02
25 9 0.16
26 8 0.14
ACGTcount: A:0.30, C:0.05, G:0.01, T:0.63
Consensus pattern (21 bp):
TTTTTATATTTTATAATAATT
Found at i:2447908 original size:47 final size:46
Alignment explanation
Indices: 2447826--2447914 Score: 126
Period size: 47 Copynumber: 1.9 Consensus size: 46
2447816 TTATGTCTTA
2447826 TATTTTTATATTTTACAATAATTTTCTATACATTTTTAATAATTTCC
1 TATTTTTATATTTTACAATAATTTTCTATACATTTTT-ATAATTTCC
* * *
2447873 TATTTTTATATTTTATAATAATTTT-TTTATGATTTTTATAAT
1 TATTTTTATATTTTACAATAATTTTCTATA-CATTTTTATAAT
2447915 ATTTTTAAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
46 8 0.21
47 30 0.79
ACGTcount: A:0.31, C:0.06, G:0.01, T:0.62
Consensus pattern (46 bp):
TATTTTTATATTTTACAATAATTTTCTATACATTTTTATAATTTCC
Found at i:2447909 original size:23 final size:20
Alignment explanation
Indices: 2447875--2447920 Score: 65
Period size: 23 Copynumber: 2.1 Consensus size: 20
2447865 TAATTTCCTA
2447875 TTTTTATATTTTATAATAATT
1 TTTTTATATTTTATAAT-ATT
2447896 TTTTTATGATTTTTATAATATT
1 TTTTTAT-A-TTTTATAATATT
2447918 TTT
1 TTT
2447921 AAGAAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.30
22 7 0.30
23 9 0.39
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (20 bp):
TTTTTATATTTTATAATATT
Found at i:2447913 original size:20 final size:21
Alignment explanation
Indices: 2447825--2447921 Score: 67
Period size: 21 Copynumber: 4.4 Consensus size: 21
2447815 TTTATGTCTT
*
2447825 ATATTTTTATATTTTACAATA
1 ATATTTTTATATTTTATAATA
*
2447846 AT-TTTCTATACATTTT-TAATA
1 ATATTT-T-TATATTTTATAATA
2447867 ATTTCCTATTTTTATATTTTATAATA
1 A-----TATTTTTATATTTTATAATA
*
2447893 ATTTTTTTATGATTTT-T-ATA
1 ATATTTTTAT-ATTTTATAATA
2447913 ATATTTTTA
1 ATATTTTTA
2447922 AGAAAAATTC
Statistics
Matches: 61, Mismatches: 5, Indels: 21
0.70 0.06 0.24
Matches are distributed among these distances:
20 14 0.23
21 17 0.28
22 12 0.20
25 7 0.11
26 8 0.13
27 3 0.05
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.62
Consensus pattern (21 bp):
ATATTTTTATATTTTATAATA
Found at i:2447974 original size:13 final size:13
Alignment explanation
Indices: 2447956--2447983 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2447946 AATTTAAATA
2447956 TTTTTCTATATTT
1 TTTTTCTATATTT
2447969 TTTTTCTATATTT
1 TTTTTCTATATTT
2447982 TT
1 TT
2447984 ATATTTTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTTCTATATTT
Found at i:2448016 original size:21 final size:21
Alignment explanation
Indices: 2447948--2448017 Score: 74
Period size: 20 Copynumber: 3.4 Consensus size: 21
2447938 TTTTAATAAA
2447948 TTTA-AATAT-TTTTCTATATT
1 TTTATAATATATTTT-TATATT
* **
2447968 TTTTTTCTATATTTTTATA-T
1 TTTATAATATATTTTTATATT
*
2447988 TTTCTAATATATTTTTATATT
1 TTTATAATATATTTTTATATT
2448009 TTTATAATA
1 TTTATAATA
2448018 ATTGGGTAGC
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
20 20 0.50
21 16 0.40
22 4 0.10
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTATAATATATTTTTATATT
Found at i:2450585 original size:13 final size:13
Alignment explanation
Indices: 2450567--2450592 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2450557 GGATAGCTCT
2450567 AGCTACTACTAAG
1 AGCTACTACTAAG
2450580 AGCTACTACTAAG
1 AGCTACTACTAAG
2450593 TGAGTTTTTT
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:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (13 bp):
AGCTACTACTAAG
Found at i:2450700 original size:29 final size:27
Alignment explanation
Indices: 2450668--2450744 Score: 75
Period size: 28 Copynumber: 2.7 Consensus size: 27
2450658 CAATTTAACT
2450668 TAAATTTTAAAATTTAAAAGGAGAAGA-AA
1 TAAATTTTAAAA--TAAAAGGA-AAGAGAA
* *
2450697 TAAATTTTTAAAATAAAAGTAAAGAGAC
1 TAAA-TTTTAAAATAAAAGGAAAGAGAA
2450725 TAAATTTTAAATATATAAAG
1 TAAATTTTAAA-ATA-AAAG
2450745 AGTATAGGGA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
27 11 0.26
28 15 0.36
29 8 0.19
30 8 0.19
ACGTcount: A:0.57, C:0.01, G:0.10, T:0.31
Consensus pattern (27 bp):
TAAATTTTAAAATAAAAGGAAAGAGAA
Found at i:2456336 original size:14 final size:16
Alignment explanation
Indices: 2456310--2456343 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
2456300 AAATAAAAAC
2456310 ATAAAATATGACAA-A
1 ATAAAATATGACAATA
2456325 ATAAAA-ATGACAATA
1 ATAAAATATGACAATA
2456340 ATAA
1 ATAA
2456344 TGAAAACAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.68, C:0.06, G:0.06, T:0.21
Consensus pattern (16 bp):
ATAAAATATGACAATA
Found at i:2456345 original size:12 final size:12
Alignment explanation
Indices: 2456322--2456368 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
2456312 AAAATATGAC
*
2456322 AAAATAAAAATG
1 AAAATAATAATG
*
2456334 ACAATAATAATG
1 AAAATAATAATG
*
2456346 AAAACAATAAT-
1 AAAATAATAATG
2456357 AATAATAATAAT
1 AA-AATAATAAT
2456369 AATACTAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
11 2 0.07
12 27 0.93
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.23
Consensus pattern (12 bp):
AAAATAATAATG
Found at i:2456352 original size:15 final size:15
Alignment explanation
Indices: 2456320--2456424 Score: 70
Period size: 15 Copynumber: 6.8 Consensus size: 15
2456310 ATAAAATATG
* *
2456320 ACAA-AATAAAAATG
1 ACAATAATAATAATA
2456334 ACAATAATAATGAA-A
1 ACAATAATAAT-AATA
2456349 ACAATAATAATAATA
1 ACAATAATAATAATA
* *
2456364 ATAATAATACTAATA
1 ACAATAATAATAATA
* * *
2456379 GTAGTAATAGTAATAGTA
1 --A-CAATAATAATAATA
*
2456397 AAAAGTAATAATAATA
1 ACAA-TAATAATAATA
*
2456413 ATAATAATAATA
1 ACAATAATAATA
2456425 GTAATGGAAA
Statistics
Matches: 73, Mismatches: 11, Indels: 13
0.75 0.11 0.13
Matches are distributed among these distances:
14 6 0.08
15 40 0.55
16 15 0.21
17 1 0.01
18 11 0.15
ACGTcount: A:0.63, C:0.04, G:0.07, T:0.27
Consensus pattern (15 bp):
ACAATAATAATAATA
Found at i:2456464 original size:3 final size:3
Alignment explanation
Indices: 2456336--2456448 Score: 95
Period size: 3 Copynumber: 37.3 Consensus size: 3
2456326 TAAAAATGAC
* * *
2456336 AAT AAT AAT GAA- AAC AAT AAT AAT AAT AAT AAT AAT ACT AAT AGT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
2456381 AGT AAT AGT AAT AGT AAA AAGT AAT AAT AAT AAT AAT AAT AAT AGT
1 AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT
* *
2456427 AAT GGA- AAT AAT AGT AAT AAT A
1 AAT -AAT AAT AAT AAT AAT AAT A
2456449 TGCTAAATAA
Statistics
Matches: 88, Mismatches: 17, Indels: 10
0.77 0.15 0.09
Matches are distributed among these distances:
2 3 0.03
3 80 0.91
4 5 0.06
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:2457441 original size:28 final size:28
Alignment explanation
Indices: 2457401--2457457 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
2457391 CTCGTTCTAG
*
2457401 TCCACTACGTCTTGTTGCTTGGATCCAC
1 TCCACTACGTCTTGTTGCTTCGATCCAC
*
2457429 TCCACTGCGTCTTGTTGCTTCGATCCAC
1 TCCACTACGTCTTGTTGCTTCGATCCAC
2457457 T
1 T
2457458 TCATGCAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.12, C:0.33, G:0.18, T:0.37
Consensus pattern (28 bp):
TCCACTACGTCTTGTTGCTTCGATCCAC
Found at i:2457560 original size:45 final size:45
Alignment explanation
Indices: 2457504--2457618 Score: 117
Period size: 44 Copynumber: 2.6 Consensus size: 45
2457494 ATATGCTTCG
* * **
2457504 CTGCAATTTTAGGGAAATAAGATTTGCTATCTTCAGTCTACTCCA
1 CTGCAACTTTAGGGAAATAAGATTTGCTAACTTCAACCTACTCCA
* * * *
2457549 CTGCAACTTTAGGGAGATAAGA-CTACTAACTTCAACCTGCTCCA
1 CTGCAACTTTAGGGAAATAAGATTTGCTAACTTCAACCTACTCCA
* *
2457593 CTGCAACTTCA-GGAAGATAAGGTTTG
1 CTGCAACTTTAGGGAA-ATAAGATTTG
2457619 TTTTGATCTG
Statistics
Matches: 55, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
43 3 0.05
44 31 0.56
45 21 0.38
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (45 bp):
CTGCAACTTTAGGGAAATAAGATTTGCTAACTTCAACCTACTCCA
Found at i:2457660 original size:55 final size:55
Alignment explanation
Indices: 2457585--2457696 Score: 188
Period size: 55 Copynumber: 2.0 Consensus size: 55
2457575 TAACTTCAAC
*
2457585 CTGCTCCACTGCAACTTCAGGAAGATAAGGTTTGTTTTGATCTGCTCTACTGCAA
1 CTGCTCCACTGCAACTTCAGGAAGATAAGGTTTGTTTTGACCTGCTCTACTGCAA
* * *
2457640 CTGCTCCACTGTAACTTCAGGGAGATAAGGTTTGTTTTGACCTGTTCTACTGCAA
1 CTGCTCCACTGCAACTTCAGGAAGATAAGGTTTGTTTTGACCTGCTCTACTGCAA
2457695 CT
1 CT
2457697 TCAGAGAGAT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (55 bp):
CTGCTCCACTGCAACTTCAGGAAGATAAGGTTTGTTTTGACCTGCTCTACTGCAA
Found at i:2457956 original size:183 final size:182
Alignment explanation
Indices: 2457643--2458192 Score: 823
Period size: 182 Copynumber: 3.0 Consensus size: 182
2457633 ACTGCAACTG
* * *
2457643 CTCCACTGTAACTTCAGGGAGATAAGGTTTGTTTTGACCTGTTCTACTGCAACTTCAGAGAGATA
1 CTCCACTGCAACTTCAGGGAGATAAGGTTTGTTTTGATCTGCTCTACTGCAACTTCAGAGAGATA
* * * *
2457708 AGATCTGTTTATTTATAGCTTCAATCGGTTCTATTTCAACTTCAAGGAAATAAGATTTGCTATCT
66 AGATCTGTTTATTTATAGCTTCAATCTGTTCTACTGCAACTTCAGGGAAATAAGATTTGCTATCT
* *
2457773 TCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGTAACTTCAACCTA
131 TCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTGACTTCAACCTA
* * *
2457825 CTCCACTGCAACTTTAGGGAGATAAGGTTTGTTTTGATTTGCTCTACTGCAAACTTTAGAGAGAT
1 CTCCACTGCAACTTCAGGGAGATAAGGTTTGTTTTGATCTGCTCTACTGC-AACTTCAGAGAGAT
* **
2457890 AAGATCTGTTTATTTATAGCTTTAATCTGTTCTACTGCAACTTCAGGGAAATAAGATTCACTATC
65 AAGATCTGTTTATTTATAGCTTCAATCTGTTCTACTGCAACTTCAGGGAAATAAGATTTGCTATC
** * *
2457955 TT-TAGTCTATTCCACTGGAACTTCAGGGAGATAAGACTTGTGACTTCAACCTG
130 TTCT-GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTGACTTCAACCTA
* *
2458008 CTCCATTGCAACTTCAGGGAGATAAGGTTTGTTTTGATCTGCTCTACTGCAACTTCAGAAAGATA
1 CTCCACTGCAACTTCAGGGAGATAAGGTTTGTTTTGATCTGCTCTACTGCAACTTCAGAGAGATA
* * *
2458073 AGATCTGTTTATTCATAGCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAAATTTGCTATCT
66 AGATCTGTTTATTTATAGCTTCAATCTGTTCTACTGCAACTTCAGGGAAATAAGATTTGCTATCT
** * *
2458138 TCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTGACTTCAATCTA
131 TCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTGACTTCAACCTA
2458190 CTC
1 CTC
2458193 TGCTGAAACT
Statistics
Matches: 327, Mismatches: 38, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
182 164 0.50
183 163 0.50
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (182 bp):
CTCCACTGCAACTTCAGGGAGATAAGGTTTGTTTTGATCTGCTCTACTGCAACTTCAGAGAGATA
AGATCTGTTTATTTATAGCTTCAATCTGTTCTACTGCAACTTCAGGGAAATAAGATTTGCTATCT
TCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTGACTTCAACCTA
Found at i:2458082 original size:41 final size:41
Alignment explanation
Indices: 2458005--2458082 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
2457995 TGACTTCAAC
* ** * *
2458005 CTGCTCCATTGCAACTTCAGGGAGATAAGGTTTGTTTTGAT
1 CTGCTCCACTGCAACTTCAGAAAGATAAGATCTGTTTTGAT
*
2458046 CTGCTCTACTGCAACTTCAGAAAGATAAGATCTGTTT
1 CTGCTCCACTGCAACTTCAGAAAGATAAGATCTGTTT
2458083 ATTCATAGCT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.35
Consensus pattern (41 bp):
CTGCTCCACTGCAACTTCAGAAAGATAAGATCTGTTTTGAT
Found at i:2458155 original size:45 final size:44
Alignment explanation
Indices: 2458091--2458188 Score: 144
Period size: 45 Copynumber: 2.2 Consensus size: 44
2458081 TTATTCATAG
*
2458091 CTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAAATTTGCT-A
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAAATTTG-TGA
* *
2458135 TCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTGA
1 -CTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAAATTTGTGA
2458180 CTTCAATCT
1 CTTCAATCT
2458189 ACTCTGCTGA
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
44 10 0.20
45 39 0.80
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (44 bp):
CTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAAATTTGTGA
Found at i:2458161 original size:182 final size:182
Alignment explanation
Indices: 2457640--2458185 Score: 831
Period size: 183 Copynumber: 3.0 Consensus size: 182
2457630 TCTACTGCAA
* * *
2457640 CTGCTCCACTGTAACTTCAGGGAGATAAGGTTTGTTTTGACCTGTTCTACTGCAACTTCAGAGAG
1 CTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTTTTGATCTGCTCTACTGCAACTTCAGAGAG
* * * *
2457705 ATAAGATCTGTTTATTTATAGCTTCAATCGGTTCTATTTCAACTTCAAGGAAATAAGATTTGCTA
66 ATAAGATCTGTTTATTTATAGCTTCAATCTGTTCTACTGCAACTTCAGGGAAATAAGATTTGCTA
* * *
2457770 TCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGTAACTTCAAC
131 TCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTGACTTCAAC
* * * *
2457822 CTACTCCACTGCAACTTTAGGGAGATAAGGTTTGTTTTGATTTGCTCTACTGCAAACTTTAGAGA
1 CTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTTTTGATCTGCTCTACTGC-AACTTCAGAGA
* **
2457887 GATAAGATCTGTTTATTTATAGCTTTAATCTGTTCTACTGCAACTTCAGGGAAATAAGATTCACT
65 GATAAGATCTGTTTATTTATAGCTTCAATCTGTTCTACTGCAACTTCAGGGAAATAAGATTTGCT
* ** *
2457952 ATCTTTAGTCTATTCCACTGGAACTTCAGGGAGATAAGACTTGTGACTTCAAC
130 ATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTGACTTCAAC
* *
2458005 CTGCTCCATTGCAACTTCAGGGAGATAAGGTTTGTTTTGATCTGCTCTACTGCAACTTCAGAAAG
1 CTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTTTTGATCTGCTCTACTGCAACTTCAGAGAG
* * *
2458070 ATAAGATCTGTTTATTCATAGCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAAATTTGCTA
66 ATAAGATCTGTTTATTTATAGCTTCAATCTGTTCTACTGCAACTTCAGGGAAATAAGATTTGCTA
* *
2458135 TCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTGACTTCAA
131 TCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTGACTTCAA
2458186 TCTACTCTGC
Statistics
Matches: 324, Mismatches: 39, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
182 161 0.50
183 163 0.50
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (182 bp):
CTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTTTTGATCTGCTCTACTGCAACTTCAGAGAG
ATAAGATCTGTTTATTTATAGCTTCAATCTGTTCTACTGCAACTTCAGGGAAATAAGATTTGCTA
TCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTGACTTCAAC
Found at i:2458203 original size:44 final size:45
Alignment explanation
Indices: 2458091--2458212 Score: 122
Period size: 45 Copynumber: 2.7 Consensus size: 45
2458081 TTATTCATAG
** *
2458091 CTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAAATTTGCTAT
1 CTTCAATCTACTCCACTGAAACTTCAGGGAAATAAAATTTGCTAT
* * * *
2458136 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TGA-
1 CTTCAATCTACTCCACTGAAACTTCAGGGAAATAAAATTTGCT-AT
** * *
2458180 CTTCAATCTACTCTGCTGAAACTTTAAGGAAAT
1 CTTCAATCTACTCCACTGAAACTTCAGGGAAAT
2458213 CTGCTGTGGC
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
44 27 0.41
45 39 0.59
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (45 bp):
CTTCAATCTACTCCACTGAAACTTCAGGGAAATAAAATTTGCTAT
Found at i:2458406 original size:86 final size:86
Alignment explanation
Indices: 2458247--2459087 Score: 1004
Period size: 86 Copynumber: 9.7 Consensus size: 86
2458237 ACGCCATTTC
* * * *
2458247 AGGGAGA-AGAGATTTGTAATTCCCAGCCTGTTACCCTATTGCTTAGGGGGTTAAGGCTTACCGT
1 AGGGAGATA-AGATCTGTAATT--CAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCATCGT
**
2458311 CTTTAATCTGCTCCACTACTGCTT
63 CTTCGATCTGCTCCACTACTGCTT
* **
2458335 AGGGAGATAAGATCTGTAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCACCTT
1 AGGGAGATAAGATCTGTAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCATCGTCTT
* *
2458400 CGATCTGTTCCCCTACTGCTT
66 CGATCTGCTCCACTACTGCTT
* * * * *
2458421 AGGGTGATAAGATCTATAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAAGCTTATTGTCT
1 AGGGAGATAAGATCTGT-AATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCATCGTCT
* * *
2458486 TCAATCCGCTACACTACTGCTT
65 TCGATCTGCTCCACTACTGCTT
** * * * **
2458508 AGGGAGATAAGATCTAAAATTTTCAACCTGTTACCATACTGCTTA-GGGGTTAAGGCCCATTATC
1 AGGGAGATAAGATCTGTAA--TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCATCGTC
2458572 TTCGATCTGCTCCACTACTGCTT
64 TTCGATCTGCTCCACTACTGCTT
* * * * * **
2458595 AGAGAGACAAGATCTGAAATTTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATTATC
1 AGGGAGATAAGATCTGTAA--TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCATCGTC
* *
2458660 TTCGGTCTGTTCCACTACTGCTT
64 TTCGATCTGCTCCACTACTGCTT
* * * * * * *
2458683 AGGGTGACAAGATCTGTAATTCGGCCTGTTACCCTACTGCTTAGAGGGTTAAAGCTTATTGTCTT
1 AGGGAGATAAGATCTGTAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCATCGTCTT
*
2458748 CGATCCGCTCCACTACTGCTT
66 CGATCTGCTCCACTACTGCTT
** * * ** *
2458769 AGGGAGATAAGATCTAAAATTTCTAGCCTGTTACACTA-TCACTTAGAAGGTTAAGGCTCACCGT
1 AGGGAGATAAGATCTGTAA-TTC-AGCCTGTTACCCTACT-GCTTAGGGGGTTAAGGCTCATCGT
*
2458833 CTTTGATCTGCTCCACTACTGCTT
63 CTTCGATCTGCTCCACTACTGCTT
* * * *
2458857 AGGGAGACAATATCTGTAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGTTCACCGTCTT
1 AGGGAGATAAGATCTGTAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCATCGTCTT
2458922 CGATCTGCTCCACTACTGCTT
66 CGATCTGCTCCACTACTGCTT
* *
2458943 AGGGAGATAAGATCTGTAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTACCGTCTT
1 AGGGAGATAAGATCTGTAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCATCGTCTT
*
2459008 CGATCTGCTCTACTACTGCTT
66 CGATCTGCTCCACTACTGCTT
* *
2459029 AGGGTGACAAGATCTGTAATTCTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTC
1 AGGGAGATAAGATCTGTAA-T-TCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTC
2459088 GTGAATTCAC
Statistics
Matches: 654, Mismatches: 88, Indels: 22
0.86 0.12 0.03
Matches are distributed among these distances:
86 298 0.46
87 156 0.24
88 199 0.30
89 1 0.00
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.32
Consensus pattern (86 bp):
AGGGAGATAAGATCTGTAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCATCGTCTT
CGATCTGCTCCACTACTGCTT
Found at i:2458734 original size:174 final size:173
Alignment explanation
Indices: 2458270--2459085 Score: 1037
Period size: 174 Copynumber: 4.7 Consensus size: 173
2458260 TTGTAATTCC
* **
2458270 CAGCCTGTTACCCTATTGCTTAGGGGGTTAAGGCTTACCGTCTTTAATCTGCTCCACTACTGCTT
1 CAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTACCGTCTTCGATCTGCTCCACTACTGCTT
* *
2458335 AGGGAGATAAGATCTGTAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCACCTT
66 AGGGAGACAAGATCTGTAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCATCTT
* * * *
2458400 CGATCTGTTCCCCTACTGCTTAGGGTGATAAGATCT-ATAAATT
131 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGA-AATTT
* ** * * *
2458443 CAGCCTGTTACCCTACTGCTTAGGGGGTTAAAGCTTATTGTCTTCAATCCGCTACACTACTGCTT
1 CAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTACCGTCTTCGATCTGCTCCACTACTGCTT
* ** * * *
2458508 AGGGAGATAAGATCTAAAATTTTCAACCTGTTACCATACTGCTTA-GGGGTTAAGGCCCATTATC
66 AGGGAGACAAGATCTGTAA--TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCATC
* *
2458572 TTCGATCTGCTCCACTACTGCTTAGAGAGACAAGATCTGAAATTTT
129 TTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAA-TTT
* ** *** * *
2458618 TAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATTATCTTCGGTCTGTTCCACTACTGCTT
1 CAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTACCGTCTTCGATCTGCTCCACTACTGCTT
* * * * ** **
2458683 AGGGTGACAAGATCTGTAATTCGGCCTGTTACCCTACTGCTTAGAGGGTTAAAGCTTATTGTCTT
66 AGGGAGACAAGATCTGTAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCATCTT
* *
2458748 CGATCCGCTCCACTACTGCTTAGGGAGATAAGATCTAAAATTT
131 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATTT
* * ** * *
2458791 CTAGCCTGTTACACTA-TCACTTAGAAGGTTAAGGCTCACCGTCTTTGATCTGCTCCACTACTGC
1 C-AGCCTGTTACCCTACT-GCTTAGGGGGTTAAGGCTTACCGTCTTCGATCTGCTCCACTACTGC
* ** * *
2458855 TTAGGGAGACAATATCTGTAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGTTCACCGTC
64 TTAGGGAGACAAGATCTGTAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCATC
*
2458920 TTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAA-TT
129 TTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATTT
*
2458964 CAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTACCGTCTTCGATCTGCTCTACTACTGCTT
1 CAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTACCGTCTTCGATCTGCTCCACTACTGCTT
*
2459029 AGGGTGACAAGATCTGTAATTCTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGC
66 AGGGAGACAAGATCTGTAA-T-TCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGC
2459086 TCGTGAATTC
Statistics
Matches: 554, Mismatches: 79, Indels: 19
0.85 0.12 0.03
Matches are distributed among these distances:
172 72 0.13
173 105 0.19
174 282 0.51
175 95 0.17
ACGTcount: A:0.23, C:0.24, G:0.21, T:0.32
Consensus pattern (173 bp):
CAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTACCGTCTTCGATCTGCTCCACTACTGCTT
AGGGAGACAAGATCTGTAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCATCTT
CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATTT
Found at i:2458806 original size:44 final size:43
Alignment explanation
Indices: 2458324--2459076 Score: 215
Period size: 44 Copynumber: 17.3 Consensus size: 43
2458314 TAATCTGCTC
*
2458324 CACTACTGCTTAGGGAGATAAGATCTGTAA-TTCAGCCTGTTA
1 CACTACTGCTTAGGGAGATAAGATCTATAATTTCAGCCTGTTA
* * * ** * ** * *
2458366 CCCTACTGCTTAGGGGGTTAAGGCCCATCACCTTC-GATCTGTTC
1 CACTACTGCTTAGGGAGATAAGATCTAT-AATTTCAG-CCTGTTA
* * *
2458410 CCCTACTGCTTAGGGTGATAAGATCTATAAATTCAGCCTGTTA
1 CACTACTGCTTAGGGAGATAAGATCTATAATTTCAGCCTGTTA
* * * * ** * *
2458453 CCCTACTGCTTAGGGGGTTAA-AGCTTATTGTCTTCAATCC-GCTA
1 CACTACTGCTTAGGGAGATAAGATC-TATAAT-TTC-AGCCTGTTA
* *
2458497 CACTACTGCTTAGGGAGATAAGATCTAAAATTTTCAACCTGTTA
1 CACTACTGCTTAGGGAGATAAGATCTATAA-TTTCAGCCTGTTA
* ** * * * * *
2458541 C-CATACTGCTTAGGG-GTTAAGGCCCATTATCTTC-GATCTGCTC
1 CAC-TACTGCTTAGGGAGATAAGATCTATAAT-TTCAG-CCTGTTA
* * *
2458584 CACTACTGCTTAGAGAGACAAGATCTGA-AATTTTTAGCCTGTTA
1 CACTACTGCTTAGGGAGATAAGATCT-ATAA-TTTCAGCCTGTTA
* * * ** * * * * *
2458628 CCCTACTGCTTAGGGGGTTAAGGCCCATTATCTTCGGTCTGTTC
1 CACTACTGCTTAGGGAGATAAGATCTATAAT-TTCAGCCTGTTA
* * * *
2458672 CACTACTGCTTAGGGTGACAAGATCTGTAA-TTCGGCCTGTTA
1 CACTACTGCTTAGGGAGATAAGATCTATAATTTCAGCCTGTTA
* * * ** * * *
2458714 CCCTACTGCTTAGAGG-GTTAA-AGCTTATTGTCTTCGATCC-GCTC
1 CACTACTGCTTAG-GGAGATAAGATC-TATAAT-TTC-AGCCTGTTA
*
2458758 CACTACTGCTTAGGGAGATAAGATCTAAAATTTCTAGCCTGTTA
1 CACTACTGCTTAGGGAGATAAGATCTATAATTTC-AGCCTGTTA
* * * * * * * * *
2458802 CACTA-TCACTTA-GAAGGTTAAG-GCTCACCGT-CTTTGA-TCTGCTC
1 CACTACT-GCTTAGGGA-GATAAGATCT-A---TAATTTCAGCCTGTTA
* * *
2458846 CACTACTGCTTAGGGAGACAATATCTGTAA-TTCAGCCTGTTA
1 CACTACTGCTTAGGGAGATAAGATCTATAATTTCAGCCTGTTA
* * * * *** * * *
2458888 CCCTACTGCTTAGGGGGTTAAGGT-TCACCGTCTTC-GATCTGCTC
1 CACTACTGCTTAGGGAGATAAGATCT-ATAAT-TTCAG-CCTGTTA
*
2458932 CACTACTGCTTAGGGAGATAAGATCTGTAA-TTCAGCCTGTTA
1 CACTACTGCTTAGGGAGATAAGATCTATAATTTCAGCCTGTTA
* * * * * * *
2458974 CCCTACTGCTTAGGGGGTTAAG-GCT-TACCGTCTTC-GATCTGCT-
1 CACTACTGCTTAGGGAGATAAGATCTATA--AT-TTCAG-CCTGTTA
* * *
2459017 CTACTACTGCTTAGGGTGACAAGATCTGTAATTCTCAGCCTGTTA
1 C-ACTACTGCTTAGGGAGATAAGATCTATAATT-TCAGCCTGTTA
*
2459062 CCCTACTGCTTAGGG
1 CACTACTGCTTAGGG
2459077 GGTTAAGGCT
Statistics
Matches: 491, Mismatches: 164, Indels: 110
0.64 0.21 0.14
Matches are distributed among these distances:
40 2 0.00
41 9 0.02
42 99 0.20
43 86 0.18
44 266 0.54
45 24 0.05
46 5 0.01
ACGTcount: A:0.23, C:0.24, G:0.21, T:0.32
Consensus pattern (43 bp):
CACTACTGCTTAGGGAGATAAGATCTATAATTTCAGCCTGTTA
Found at i:2458994 original size:260 final size:259
Alignment explanation
Indices: 2458270--2459087 Score: 1124
Period size: 260 Copynumber: 3.1 Consensus size: 259
2458260 TTGTAATTCC
* * *
2458270 CAGCCTGTTACCCTATTGCTTAGGGGGTTAAGGCTTACCGTCTTTAATCTGCTCCACTACTGCTT
1 CAGCCTGTTA-CCTATCGCTTA-GGGGTTAAGGCTCACCGTCTTTGATCTGCTCCACTACTGCTT
* *
2458335 AGGGAGATAAGATCTGTAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCACCTT
64 AGGGAGACAAGATCTGTAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCATCTT
* *
2458400 CGATCTGTTCCCCTACTGCTTAGGGTGATAAGATCTATAAATTCAGCCTGTTACCCTACTGCTTA
129 CGATCTGTTCCACTACTGCTTAGGGTGATAAGATCTGT-AATTCAGCCTGTTACCCTACTGCTTA
* *
2458465 GGGGGTTAAAGCTTATTGTCTTCAATCCGCTACACTACTGCTTAGGGAGATAAGATCTAAAATTT
193 GGGGGTTAAAGCTTATTGTCTTCGATCCGCTCCACTACTGCTTAGGGAGATAAGATCTAAAATTT
2458530 -T
258 CT
* * *** *
2458531 CAACCTGTTACC-ATACTGCTTAGGGGTTAAGGCCCATTATCTTCGATCTGCTCCACTACTGCTT
1 CAGCCTGTTACCTAT-C-GCTTAGGGGTTAAGGCTCACCGTCTTTGATCTGCTCCACTACTGCTT
* * * *
2458595 AGAGAGACAAGATCTGAAATTTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATTATC
64 AGGGAGACAAGATCTGTAA--TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCATC
* * *
2458660 TTCGGTCTGTTCCACTACTGCTTAGGGTGACAAGATCTGTAATTCGGCCTGTTACCCTACTGCTT
127 TTCGATCTGTTCCACTACTGCTTAGGGTGATAAGATCTGTAATTCAGCCTGTTACCCTACTGCTT
*
2458725 AGAGGGTTAAAGCTTATTGTCTTCGATCCGCTCCACTACTGCTTAGGGAGATAAGATCTAAAATT
192 AGGGGGTTAAAGCTTATTGTCTTCGATCCGCTCCACTACTGCTTAGGGAGATAAGATCTAAAATT
2458790 TCT
257 TCT
* *
2458793 -AGCCTGTTACACTATCACTTAGAAGGTTAAGGCTCACCGTCTTTGATCTGCTCCACTACTGCTT
1 CAGCCTGTTAC-CTATCGCTTAG-GGGTTAAGGCTCACCGTCTTTGATCTGCTCCACTACTGCTT
* ** * *
2458857 AGGGAGACAATATCTGTAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGTTCACCGTCTT
64 AGGGAGACAAGATCTGTAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCATCTT
* *
2458922 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTCAGCCTGTTACCCTACTGCTTAG
129 CGATCTGTTCCACTACTGCTTAGGGTGATAAGATCTGTAATTCAGCCTGTTACCCTACTGCTTAG
* ** * * * * **
2458987 GGGGTTAAGGCTTACCGTCTTCGATCTGCTCTACTACTGCTTAGGGTGACAAGATCTGTAA-TTC
194 GGGGTTAAAGCTTATTGTCTTCGATCCGCTCCACTACTGCTTAGGGAGATAAGATCTAAAATTTC
2459051 T
259 T
2459052 CAGCCTGTTACCCTA-CTGCTTAGGGGGTTAAGGCTC
1 CAGCCTGTTA-CCTATC-GCTTA-GGGGTTAAGGCTC
2459088 GTGAATTCAC
Statistics
Matches: 488, Mismatches: 57, Indels: 25
0.86 0.10 0.04
Matches are distributed among these distances:
259 7 0.01
260 231 0.47
261 117 0.24
262 131 0.27
263 2 0.00
ACGTcount: A:0.23, C:0.24, G:0.21, T:0.32
Consensus pattern (259 bp):
CAGCCTGTTACCTATCGCTTAGGGGTTAAGGCTCACCGTCTTTGATCTGCTCCACTACTGCTTAG
GGAGACAAGATCTGTAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCATCTTCG
ATCTGTTCCACTACTGCTTAGGGTGATAAGATCTGTAATTCAGCCTGTTACCCTACTGCTTAGGG
GGTTAAAGCTTATTGTCTTCGATCCGCTCCACTACTGCTTAGGGAGATAAGATCTAAAATTTCT
Found at i:2464384 original size:14 final size:16
Alignment explanation
Indices: 2464358--2464391 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
2464348 AAATAAAAAC
2464358 ATAAAATATGACAA-A
1 ATAAAATATGACAATA
2464373 ATAAAA-ATGACAATA
1 ATAAAATATGACAATA
2464388 ATAA
1 ATAA
2464392 TGAAAACAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.68, C:0.06, G:0.06, T:0.21
Consensus pattern (16 bp):
ATAAAATATGACAATA
Found at i:2464407 original size:3 final size:3
Alignment explanation
Indices: 2464401--2464678 Score: 97
Period size: 3 Copynumber: 92.7 Consensus size: 3
2464391 ATGAAAACAG
* * * *
2464401 TAA TAA TAA TAA TAC TAA TAG TAA AAA GTAG TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA
* ** * * ** *
2464447 TAG TAA TGG CAA TAA TAG TAA TAA T-A TGC TAAA TAA TAA TAA GAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
* * * * * *
2464492 -AA -AA CAA TAG TAA TAG TAA TTA CAA -AA GTGA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA
** * * * * *
2464535 -AA TAGGA TGG TAA TAA TAA TAC TAA TGAA -AC TAA AAA TAG TAG TAA
1 TAA TA--A TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
* * * * * * *
2464581 TAG TAA TAA TAA TAA GACCG TAA TAA AAA GAA AAA GAAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TA--A TAA TAA TAA TAA TAA -TAA TAA TAA TAA
* * *
2464629 TAA TAA T-A TAT TAA TAA GAA -AA TAA TAA T-C TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2464674 TAA TA
1 TAA TA
2464679 GAAATGGAAT
Statistics
Matches: 199, Mismatches: 59, Indels: 34
0.68 0.20 0.12
Matches are distributed among these distances:
2 16 0.08
3 172 0.86
4 8 0.04
5 3 0.02
ACGTcount: A:0.59, C:0.04, G:0.09, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:2464436 original size:28 final size:29
Alignment explanation
Indices: 2464384--2464452 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 29
2464374 TAAAAATGAC
2464384 AATAATAAT-G-AAAACAGTAATAATAAT
1 AATAATAATAGTAAAACAGTAATAATAAT
* *
2464411 AATACTAATAGTAAAA-AGTAGTAATAAT
1 AATAATAATAGTAAAACAGTAATAATAAT
2464439 AATAATAATAGTAA
1 AATAATAATAGTAA
2464453 TGGCAATAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 8 0.22
28 25 0.68
29 4 0.11
ACGTcount: A:0.61, C:0.03, G:0.09, T:0.28
Consensus pattern (29 bp):
AATAATAATAGTAAAACAGTAATAATAAT
Found at i:2466889 original size:16 final size:17
Alignment explanation
Indices: 2466854--2466890 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
2466844 TTTTGTTTGT
2466854 TTTTCATTGTTAATAAG
1 TTTTCATTGTTAATAAG
2466871 TTTTCAATT-TTAA-AAG
1 TTTTC-ATTGTTAATAAG
2466887 TTTT
1 TTTT
2466891 TATCTAACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.37
17 9 0.47
18 3 0.16
ACGTcount: A:0.30, C:0.05, G:0.08, T:0.57
Consensus pattern (17 bp):
TTTTCATTGTTAATAAG
Found at i:2467368 original size:32 final size:32
Alignment explanation
Indices: 2467327--2467388 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
2467317 TTAAAGATTC
2467327 GTTGGTTTTGATAGACGAAGAAATGAATTTGT
1 GTTGGTTTTGATAGACGAAGAAATGAATTTGT
2467359 GTTGGTTTTGATAGACGAAGAAATGAATTT
1 GTTGGTTTTGATAGACGAAGAAATGAATTT
2467389 ATTTTTAGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.32, C:0.03, G:0.27, T:0.37
Consensus pattern (32 bp):
GTTGGTTTTGATAGACGAAGAAATGAATTTGT
Found at i:2474817 original size:27 final size:27
Alignment explanation
Indices: 2474779--2474832 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
2474769 TTGCTTTGTA
*
2474779 ACACTGTTAAATATACATAGCAGAAAT
1 ACACTGTTAAATATACACAGCAGAAAT
2474806 ACACTGTTAAATATACACAGCAGAAAT
1 ACACTGTTAAATATACACAGCAGAAAT
2474833 CATAATTATG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.48, C:0.17, G:0.11, T:0.24
Consensus pattern (27 bp):
ACACTGTTAAATATACACAGCAGAAAT
Found at i:2488397 original size:312 final size:316
Alignment explanation
Indices: 2487988--2488617 Score: 1216
Period size: 312 Copynumber: 2.0 Consensus size: 316
2487978 GTACCTAAAT
2487988 AACCCTTTAATCGTTAACTTAAATCCAACTAAATAGTTATTGCATAAAAGTATGCTATTATCTGC
1 AACCCTTTAATCGTTAACTTAAATCCAACTAAATAGTTATTGCATAAAAGTATGCTATTATCTGC
2488053 ATTTAAAGTATTTAATATTTAATATACAAACAGTACGAAAAGAAGTAGGTAGAATAGCTTTCTAG
66 ATTTAAAGTATTTAATATTTAATATACAAACAGTACGAAAAGAAGTAGGTAGAATAGCTTTCTAG
2488118 CTCTTTACAATGATTTCATGAGAGAGTTTTTTTTTAAATGAAAAATGATATAAATTAAATAAATC
131 CTCTTTACAATGATTTCATGAGAGAGTTTTTTTTTAAATGAAAAATGATATAAATTAAA-AAATC
2488183 ATGAACTTCGATCATGGTTTAGTACACTTGATTCATGGCGTTAACTTCTTTAGTTTGAATATTTG
195 ATGAACTTCGATCATGGTTTAGTACACTTGATTCATGGCGTTAACTTCTTTAGTTTGAATATTTG
2488248 AATCTCAACATCCATAA-TTTGCTAATTTTGGATTGGG-TTTTTTTTTTTTTTATAA
260 AATCTCAACATCCATAACTTTGCTAATTTTGGATTGGGTTTTTTTTTTTTTTTATAA
2488303 AACCCTTTAATCGTTAACTTAAAT-CAACTAAATAGTTATTGCA-AAAAGTATGCTATTATCTGC
1 AACCCTTTAATCGTTAACTTAAATCCAACTAAATAGTTATTGCATAAAAGTATGCTATTATCTGC
2488366 ATTT-AAGTATTTAATATTTAATATACAAACAGTACGAAAAGAAGTAGGTAGAATAGCTTTCTAG
66 ATTTAAAGTATTTAATATTTAATATACAAACAGTACGAAAAGAAGTAGGTAGAATAGCTTTCTAG
2488430 CTCTTTACAATGATTTCATGAGAGAGTTTTTTTTTAAATGAAAAATGATATAAATTAAAAAATCA
131 CTCTTTACAATGATTTCATGAGAGAGTTTTTTTTTAAATGAAAAATGATATAAATTAAAAAATCA
2488495 TGAACTTCGATCATGGTTTAGTACACTTGATTCATGGCGTTAACTTCTTTAGTTTGAATATTTGA
196 TGAACTTCGATCATGGTTTAGTACACTTGATTCATGGCGTTAACTTCTTTAGTTTGAATATTTGA
2488560 ATCTCAACATCCATAACTTTGCTAATTTTGGATTGGGTTTTTTTTTTTTTTTATAA
261 ATCTCAACATCCATAACTTTGCTAATTTTGGATTGGGTTTTTTTTTTTTTTTATAA
2488616 AA
1 AA
2488618 TAACACAAAA
Statistics
Matches: 313, Mismatches: 0, Indels: 6
0.98 0.00 0.02
Matches are distributed among these distances:
311 87 0.28
312 139 0.44
313 44 0.14
314 19 0.06
315 24 0.08
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (316 bp):
AACCCTTTAATCGTTAACTTAAATCCAACTAAATAGTTATTGCATAAAAGTATGCTATTATCTGC
ATTTAAAGTATTTAATATTTAATATACAAACAGTACGAAAAGAAGTAGGTAGAATAGCTTTCTAG
CTCTTTACAATGATTTCATGAGAGAGTTTTTTTTTAAATGAAAAATGATATAAATTAAAAAATCA
TGAACTTCGATCATGGTTTAGTACACTTGATTCATGGCGTTAACTTCTTTAGTTTGAATATTTGA
ATCTCAACATCCATAACTTTGCTAATTTTGGATTGGGTTTTTTTTTTTTTTTATAA
Found at i:2490050 original size:133 final size:133
Alignment explanation
Indices: 2489812--2490193 Score: 629
Period size: 133 Copynumber: 2.9 Consensus size: 133
2489802 TAGGTACATA
* * * * * *
2489812 AGTTAATCATGGCTATTTTTTAAATCATGTGTGTTATACTTATTCTATTATCTGATTTGTTAAGC
1 AGTTAAGCATGACTATTTTGTAAATCATGTGTGTTATACTTATTCTGTTATCTGTTTTGATAAGC
* *
2489877 TATTTGATTCAGTTATGTAATATGAACATATGATATTATGATTTTGCATGTCCATGTGCATTGAG
66 TATTTGATTCAATTATGTAATATGAACATATGATATTATGATTCTGCATGTCCATGTGCATTGAG
2489942 GTG
131 GTG
* * *
2489945 AGTTAAGCATGATTGTTTTGTAAATCATGTGCGTTATACTTATTCTGTTATCTGTTTTGATAAGC
1 AGTTAAGCATGACTATTTTGTAAATCATGTGTGTTATACTTATTCTGTTATCTGTTTTGATAAGC
* * *
2490010 TATTTGATTCAATTATGTAATATGAACCTATGATATTATGATTCTACATGTCCATGTGCATTGGG
66 TATTTGATTCAATTATGTAATATGAACATATGATATTATGATTCTGCATGTCCATGTGCATTGAG
2490075 GTG
131 GTG
2490078 AGTTAAGCATGACTATTTTGTAAATCATGTGTGTTATACTTATTCTGTTATCTGTTTTGATAAGC
1 AGTTAAGCATGACTATTTTGTAAATCATGTGTGTTATACTTATTCTGTTATCTGTTTTGATAAGC
*
2490143 TATTTGATTCAATTATGTAATATGAACATATGATATTATGATCCTGCATGT
66 TATTTGATTCAATTATGTAATATGAACATATGATATTATGATTCTGCATGT
2490194 GCATTGGGCT
Statistics
Matches: 229, Mismatches: 20, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
133 229 1.00
ACGTcount: A:0.27, C:0.10, G:0.17, T:0.45
Consensus pattern (133 bp):
AGTTAAGCATGACTATTTTGTAAATCATGTGTGTTATACTTATTCTGTTATCTGTTTTGATAAGC
TATTTGATTCAATTATGTAATATGAACATATGATATTATGATTCTGCATGTCCATGTGCATTGAG
GTG
Found at i:2493220 original size:192 final size:192
Alignment explanation
Indices: 2492893--2493650 Score: 1309
Period size: 192 Copynumber: 3.9 Consensus size: 192
2492883 GATAAATGTG
* * *
2492893 GCTTAATGGAGTTTCCTAAGCCTAGGCCTCCCCATGCTTCTTGCAACTCTCTCTCCCTTGCTTCT
1 GCTTAATGGAGTTTCCTAAGCTTAAGCCGCCCCATGCTTCTTGCAACTCTCTCTCCCTTGCTTCT
*
2492958 CTACGAGATAGAGAGAATCTAATCTGCTCACTTGGTTGCTCAGAAGTAGCCATCTTCTCTTTCTC
66 CTACGAGATACAGAGAATCTAATCTGCTCACTTGGTTGCTCAGAAGTAGCCATCTTCTCTTTCTC
*
2493023 TAATTTTGATTTGTGTTTAACCAAAATTTGGTCCAGACTACCCCGATCATCCGCCACCTGTT
131 TAATTTTGATTTGTGTTTAACCAAAATTTGGTCCAGACTACCCTGATCATCCGCCACCTGTT
* *
2493085 GCTTAATGGAGTTTCCTAAGCTTAAACCGCCCCATGCTTCTTGCAACTCTCTCTCCCTTGCTTGT
1 GCTTAATGGAGTTTCCTAAGCTTAAGCCGCCCCATGCTTCTTGCAACTCTCTCTCCCTTGCTTCT
*
2493150 CTACGAGATACAGAGAATCTAATCTGCTCACTTGGTTGCTCAGAAGTAGCCATCTTCTCTTTTTC
66 CTACGAGATACAGAGAATCTAATCTGCTCACTTGGTTGCTCAGAAGTAGCCATCTTCTCTTTCTC
* *
2493215 TAATTTTGATTTGTGTTTAACTAAAATTTGGCCCAGACTACCCTGATCATCCGCCACCTGTT
131 TAATTTTGATTTGTGTTTAACCAAAATTTGGTCCAGACTACCCTGATCATCCGCCACCTGTT
* *
2493277 GCTTAATGGAGTTTTCTAAGCTTAAGCCGCCCCATGCTTCTTGCAACTCTCTCTCCCTTGCTTGT
1 GCTTAATGGAGTTTCCTAAGCTTAAGCCGCCCCATGCTTCTTGCAACTCTCTCTCCCTTGCTTCT
*
2493342 CTACGAGATACAGAGAATCTAATCTGCTCACTTGGTTGCTCAGAAGTAGCCATCTTCTCTTTTTC
66 CTACGAGATACAGAGAATCTAATCTGCTCACTTGGTTGCTCAGAAGTAGCCATCTTCTCTTTCTC
*
2493407 TAATTTTGATTTGTGTTTAACTAAAATTTGGTCCAGACTACCCTGATCATCCGCCACCTGTT
131 TAATTTTGATTTGTGTTTAACCAAAATTTGGTCCAGACTACCCTGATCATCCGCCACCTGTT
*
2493469 GCTTAATGGAGTTTTCTAAGCTTAAGCCGCCCCATGCTTCTTGCAACTCTCTCTCCCTTGCTTCT
1 GCTTAATGGAGTTTCCTAAGCTTAAGCCGCCCCATGCTTCTTGCAACTCTCTCTCCCTTGCTTCT
* * * * * * *
2493534 CTACGAGATACAGATAATCTAATTTGCTCGCTTGCTTGCTCAGAACTTGTCATCTTCTCTTTCTC
66 CTACGAGATACAGAGAATCTAATCTGCTCACTTGGTTGCTCAGAAGTAGCCATCTTCTCTTTCTC
*
2493599 TAATTTTGATTTGTGTTTAACCAAAATTTGATCCAGACTACCCTGATCATCC
131 TAATTTTGATTTGTGTTTAACCAAAATTTGGTCCAGACTACCCTGATCATCC
2493651 ACTTGTGGCG
Statistics
Matches: 542, Mismatches: 24, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
192 542 1.00
ACGTcount: A:0.21, C:0.27, G:0.15, T:0.36
Consensus pattern (192 bp):
GCTTAATGGAGTTTCCTAAGCTTAAGCCGCCCCATGCTTCTTGCAACTCTCTCTCCCTTGCTTCT
CTACGAGATACAGAGAATCTAATCTGCTCACTTGGTTGCTCAGAAGTAGCCATCTTCTCTTTCTC
TAATTTTGATTTGTGTTTAACCAAAATTTGGTCCAGACTACCCTGATCATCCGCCACCTGTT
Found at i:2498729 original size:13 final size:14
Alignment explanation
Indices: 2498708--2498736 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2498698 TAGGTTTGAG
2498708 GCTTTTTTTTATTT
1 GCTTTTTTTTATTT
2498722 GCTTTTTTTTATTT
1 GCTTTTTTTTATTT
2498736 G
1 G
2498737 TGGTTTGATG
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:0.07, C:0.07, G:0.10, T:0.76
Consensus pattern (14 bp):
GCTTTTTTTTATTT
Found at i:2500080 original size:19 final size:20
Alignment explanation
Indices: 2500043--2500080 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
2500033 TGCTAATTTT
* *
2500043 TTTTTTACAATTTATAATAA
1 TTTTTTACAAGTTAGAATAA
2500063 TTTTTTA-AAGTTAGAATA
1 TTTTTTACAAGTTAGAATA
2500081 GGGGAATTCG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (20 bp):
TTTTTTACAAGTTAGAATAA
Found at i:2506198 original size:19 final size:21
Alignment explanation
Indices: 2506160--2506212 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 21
2506150 TCGTATCAAC
*
2506160 AAATAATTTAAAAATTATAAA
1 AAATAATTTAAAAATAATAAA
2506181 AAAT-ATTT-AAAATAATAAA
1 AAATAATTTAAAAATAATAAA
2506200 TAAA-AATTATAAA
1 -AAATAATT-TAAA
2506213 TTTCAGAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
19 10 0.37
20 10 0.37
21 5 0.19
22 2 0.07
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
AAATAATTTAAAAATAATAAA
Found at i:2508009 original size:33 final size:33
Alignment explanation
Indices: 2507970--2508040 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
2507960 AATATATATA
* *
2507970 TAAATTAGTTTAAATTGTGAGTAAAAATAAATT
1 TAAATTAGTTTAAATTGTGAATAAAAATAAAAT
2508003 TAAATTAGTTTAAATTGTGAATAAAAATAAAAT
1 TAAATTAGTTTAAATTGTGAATAAAAATAAAAT
2508036 TAAAT
1 TAAAT
2508041 AGGTAAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (33 bp):
TAAATTAGTTTAAATTGTGAATAAAAATAAAAT
Found at i:2516920 original size:39 final size:39
Alignment explanation
Indices: 2516862--2516938 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 39
2516852 TAGGGTTTCA
*
2516862 GTTTAGCTCTAATGAGCTTCAGTTAGCCTTCGGGCTTCT
1 GTTTAGCACTAATGAGCTTCAGTTAGCCTTCGGGCTTCT
* * *
2516901 GTTTAGCACTTATGTGCTTCAGTTAGCCTTCTGGCTTC
1 GTTTAGCACTAATGAGCTTCAGTTAGCCTTCGGGCTTC
2516939 AGATCACGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.14, C:0.23, G:0.22, T:0.40
Consensus pattern (39 bp):
GTTTAGCACTAATGAGCTTCAGTTAGCCTTCGGGCTTCT
Found at i:2516939 original size:18 final size:18
Alignment explanation
Indices: 2516877--2516940 Score: 74
Period size: 18 Copynumber: 3.4 Consensus size: 18
2516867 GCTCTAATGA
*
2516877 GCTTCAGTTAGCCTTCGG
1 GCTTCAGTTAGCCTTCTG
* *
2516895 GCTTCTGTTTAGCACTTATG
1 GCTTCAG-TTAGC-CTTCTG
2516915 TGCTTCAGTTAGCCTTCTG
1 -GCTTCAGTTAGCCTTCTG
2516934 GCTTCAG
1 GCTTCAG
2516941 ATCACGATGT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
18 13 0.34
19 10 0.26
20 9 0.24
21 6 0.16
ACGTcount: A:0.12, C:0.25, G:0.23, T:0.39
Consensus pattern (18 bp):
GCTTCAGTTAGCCTTCTG
Found at i:2520198 original size:32 final size:32
Alignment explanation
Indices: 2520157--2520220 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
2520147 TATCATGACA
2520157 TAGTTCAACAATTCCGGGTCAATAAGTAATGT
1 TAGTTCAACAATTCCGGGTCAATAAGTAATGT
2520189 TAGTTCAACAATTCCGGGTCAATAAGTAATGT
1 TAGTTCAACAATTCCGGGTCAATAAGTAATGT
2520221 ACATACAGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (32 bp):
TAGTTCAACAATTCCGGGTCAATAAGTAATGT
Found at i:2522973 original size:24 final size:24
Alignment explanation
Indices: 2522946--2523007 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 24
2522936 GGAGTGCAAC
*
2522946 GGAGACGAAGATGAAGTCGATGGT
1 GGAGACGAAGATGAAGACGATGGT
* * *
2522970 GGAGACAAAAATAAAGACGATGGT
1 GGAGACGAAGATGAAGACGATGGT
* *
2522994 AGAGATGAAGATGA
1 GGAGACGAAGATGA
2523008 CTACAATGAT
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.35, T:0.15
Consensus pattern (24 bp):
GGAGACGAAGATGAAGACGATGGT
Found at i:2525340 original size:31 final size:31
Alignment explanation
Indices: 2525292--2525362 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
2525282 TAATATACTG
*
2525292 TTTGGTACTTATATTTGA-TTTGAATGTTTAA
1 TTTGGTACTTATATTTGACTTT-AATGTTCAA
*
2525323 TTTGGTACTTA-AGTTTGACTTTAGTGTTCAA
1 TTTGGTACTTATA-TTTGACTTTAATGTTCAA
*
2525354 TTTGATACT
1 TTTGGTACT
2525363 CTAAATTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 1 0.03
31 31 0.89
32 3 0.09
ACGTcount: A:0.24, C:0.07, G:0.17, T:0.52
Consensus pattern (31 bp):
TTTGGTACTTATATTTGACTTTAATGTTCAA
Found at i:2530584 original size:19 final size:19
Alignment explanation
Indices: 2530547--2530584 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2530537 CCCCTTGGCT
*
2530547 GTGTGTGCTCCAAGCCAAG
1 GTGTGTGCTCCAAGACAAG
2530566 GTGTGTGCCTCCAA-ACAAG
1 GTGTGTG-CTCCAAGACAAG
2530585 CTTCCCGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.24, C:0.26, G:0.29, T:0.21
Consensus pattern (19 bp):
GTGTGTGCTCCAAGACAAG
Found at i:2534828 original size:33 final size:30
Alignment explanation
Indices: 2534774--2534835 Score: 79
Period size: 33 Copynumber: 2.0 Consensus size: 30
2534764 CTATATAAGA
*
2534774 TAAAAATATATAAATTATTAAATATTAAAT
1 TAAAAATATATAAATTATTAAAAATTAAAT
*
2534804 TAAAAATAATATAAATATTGTTAAAAATTAAA
1 TAAAAAT-ATAT-AA-ATTATTAAAAATTAAA
2534836 AAAATTGCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 7 0.26
31 4 0.15
32 2 0.07
33 14 0.52
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (30 bp):
TAAAAATATATAAATTATTAAAAATTAAAT
Found at i:2538567 original size:51 final size:51
Alignment explanation
Indices: 2538442--2538619 Score: 286
Period size: 51 Copynumber: 3.5 Consensus size: 51
2538432 CCATGGCAAC
*
2538442 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGATAAGTG-A
1 AAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGGATAAGTGAA
2538492 AAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGGATAAGTGAA
1 AAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGGATAAGTGAA
* * *
2538543 AAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGAC
1 AAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGGATAAGTGAA
* **
2538594 AAGTGAAAAGTGGTAGCTTCGGCTAC
1 AAGTGATAAGTAATAGCTTCGGCTAC
2538620 CTGATCAGTG
Statistics
Matches: 120, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
50 48 0.40
51 72 0.60
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.26
Consensus pattern (51 bp):
AAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGGATAAGTGAA
Found at i:2538633 original size:31 final size:31
Alignment explanation
Indices: 2538595--2538836 Score: 340
Period size: 31 Copynumber: 7.8 Consensus size: 31
2538585 ACAAATGACA
2538595 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
2538626 AGTGAAAAGTGGTAGCTTTGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* * *
2538657 AGTGAAAAGTGGTAGCTTCTGCTACCCGATA
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* * *
2538688 AGTGAAAAGTGGTAGCTTCTGCTACCCGATA
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
2538719 AGTGAAAAGTGGTAGCTTCTGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* * *
2538750 AGTGAAAAATGGTAGCTCCGACTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* * * *
2538781 AATAAAAAATGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
2538812 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
2538837 AAGTGACAAG
Statistics
Matches: 192, Mismatches: 19, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 192 1.00
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:2538908 original size:46 final size:49
Alignment explanation
Indices: 2538858--2538983 Score: 186
Period size: 49 Copynumber: 2.6 Consensus size: 49
2538848 GATTTCCGTA
* * *
2538858 TAAGACCATATCTGGGATATGACATC-A-GTGAGATATGTGATT-CGTG
1 TAAGACCATAGCTGGGCTATGACATCGATATGAGATATGTGATTACGTG
* *
2538904 TAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATTACGTG
1 TAAGACCATAGCTGGGCTATGACATCGATATGAGATATGTGATTACGTG
2538953 TAAGACCATAGCTGGGCTATGACATCGATAT
1 TAAGACCATAGCTGGGCTATGACATCGATAT
2538984 ATGAAGATGT
Statistics
Matches: 71, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
46 23 0.32
47 1 0.01
48 13 0.18
49 34 0.48
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.29
Consensus pattern (49 bp):
TAAGACCATAGCTGGGCTATGACATCGATATGAGATATGTGATTACGTG
Found at i:2540086 original size:46 final size:46
Alignment explanation
Indices: 2540010--2540193 Score: 215
Period size: 46 Copynumber: 4.0 Consensus size: 46
2540000 TAAGGCTTAA
* * * *
2540010 TATTCTTGTATTCTCGAGTCCGCAACATATGCAGGAGCTCAAAACC
1 TATTCATGTATTCTCAAGTCTGCAACATATGCAGGAGCTCAGAACC
** ** * *
2540056 TAAACATGTATTCTTGAGTCTGCAATATATGTAGGAGCTCAGAACC
1 TATTCATGTATTCTCAAGTCTGCAACATATGCAGGAGCTCAGAACC
* * * * *
2540102 TATTCTTCTATTCTCAAGTTTGCAACATATGCAGGAACTCGGAACC
1 TATTCATGTATTCTCAAGTCTGCAACATATGCAGGAGCTCAGAACC
* *
2540148 TATTCATGTATTCTCAAGTTTGCAACATATGCAGGAGCTTAGAACC
1 TATTCATGTATTCTCAAGTCTGCAACATATGCAGGAGCTCAGAACC
2540194 ATGGCAAAAC
Statistics
Matches: 114, Mismatches: 24, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
46 114 1.00
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (46 bp):
TATTCATGTATTCTCAAGTCTGCAACATATGCAGGAGCTCAGAACC
Found at i:2541515 original size:24 final size:24
Alignment explanation
Indices: 2541488--2541538 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
2541478 TCACCTACAT
2541488 CAACACTTAAATACATTTACAAGC
1 CAACACTTAAATACATTTACAAGC
2541512 CAACACTTAAATACATTTACAAGC
1 CAACACTTAAATACATTTACAAGC
2541536 CAA
1 CAA
2541539 TATAAAACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.47, C:0.25, G:0.04, T:0.24
Consensus pattern (24 bp):
CAACACTTAAATACATTTACAAGC
Found at i:2543623 original size:24 final size:24
Alignment explanation
Indices: 2543591--2543640 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
2543581 ATCATCATAC
2543591 TTATCTACTAACTCCTCTTAATGG
1 TTATCTACTAACTCCTCTTAATGG
2543615 TTATCTACTAACTCCTCTTAATGG
1 TTATCTACTAACTCCTCTTAATGG
2543639 TT
1 TT
2543641 TATTTGCTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.24, G:0.08, T:0.44
Consensus pattern (24 bp):
TTATCTACTAACTCCTCTTAATGG
Found at i:2552025 original size:14 final size:14
Alignment explanation
Indices: 2551996--2552024 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2551986 TTAAAAAATG
2551996 AATTAAAATATAAA
1 AATTAAAATATAAA
2552010 AATTAAAA-ATAAA
1 AATTAAAATATAAA
2552023 AA
1 AA
2552025 AACTTGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
AATTAAAATATAAA
Found at i:2553359 original size:11 final size:12
Alignment explanation
Indices: 2553342--2553371 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
2553332 TTTCTACATT
2553342 TTTCTTCAGTTC
1 TTTCTTCAGTTC
2553354 -TTCTTCAGTTC
1 TTTCTTCAGTTC
2553365 TTTCTTC
1 TTTCTTC
2553372 TTTAGTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.07, C:0.27, G:0.07, T:0.60
Consensus pattern (12 bp):
TTTCTTCAGTTC
Found at i:2553371 original size:15 final size:14
Alignment explanation
Indices: 2553351--2553384 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
2553341 TTTTCTTCAG
2553351 TTCTTCTTCAGTTCT
1 TTCTTCTTCAGTT-T
*
2553366 TTCTTCTTTAGTTT
1 TTCTTCTTCAGTTT
2553380 TTCTT
1 TTCTT
2553385 TTTTCTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.06, C:0.21, G:0.06, T:0.68
Consensus pattern (14 bp):
TTCTTCTTCAGTTT
Found at i:2554537 original size:9 final size:9
Alignment explanation
Indices: 2554519--2554611 Score: 123
Period size: 9 Copynumber: 10.3 Consensus size: 9
2554509 TCAGTTGAAC
2554519 TAAATCGGT
1 TAAATCGGT
*
2554528 TAAGTCGGT
1 TAAATCGGT
*
2554537 TAAGTCGGT
1 TAAATCGGT
2554546 TAAATCGGT
1 TAAATCGGT
*
2554555 TAAATTGGT
1 TAAATCGGT
*
2554564 TAAGTCGGT
1 TAAATCGGT
*
2554573 TAAATCAGT
1 TAAATCGGT
2554582 TAAATCGGT
1 TAAATCGGT
* *
2554591 TAAGTCAGT
1 TAAATCGGT
2554600 TAAATCGGT
1 TAAATCGGT
2554609 TAA
1 TAA
2554612 TTTTTAACCA
Statistics
Matches: 72, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 72 1.00
ACGTcount: A:0.32, C:0.10, G:0.24, T:0.34
Consensus pattern (9 bp):
TAAATCGGT
Found at i:2554557 original size:27 final size:27
Alignment explanation
Indices: 2554519--2554611 Score: 150
Period size: 27 Copynumber: 3.4 Consensus size: 27
2554509 TCAGTTGAAC
*
2554519 TAAATCGGTTAAGTCGGTTAAGTCGGT
1 TAAATCGGTTAAATCGGTTAAGTCGGT
*
2554546 TAAATCGGTTAAATTGGTTAAGTCGGT
1 TAAATCGGTTAAATCGGTTAAGTCGGT
* *
2554573 TAAATCAGTTAAATCGGTTAAGTCAGT
1 TAAATCGGTTAAATCGGTTAAGTCGGT
2554600 TAAATCGGTTAA
1 TAAATCGGTTAA
2554612 TTTTTAACCA
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 60 1.00
ACGTcount: A:0.32, C:0.10, G:0.24, T:0.34
Consensus pattern (27 bp):
TAAATCGGTTAAATCGGTTAAGTCGGT
Found at i:2557423 original size:3 final size:3
Alignment explanation
Indices: 2557408--2557442 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
2557398 TATTTATTAA
*
2557408 ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2557443 CAAATAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2557812 original size:17 final size:17
Alignment explanation
Indices: 2557774--2557812 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
2557764 CAGGGGAGAA
2557774 AGAAAGAAAGGAAAAAG
1 AGAAAGAAAGGAAAAAG
*
2557791 GGAAAGAAA-GAAAAGAG
1 AGAAAGAAAGGAAAA-AG
2557808 AGAAA
1 AGAAA
2557813 TAGGGATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (17 bp):
AGAAAGAAAGGAAAAAG
Found at i:2558674 original size:18 final size:18
Alignment explanation
Indices: 2558653--2558716 Score: 85
Period size: 18 Copynumber: 3.6 Consensus size: 18
2558643 AACGACTAAC
*
2558653 TGTTATTGAATAATTGAT
1 TGTTACTGAATAATTGAT
2558671 TGTTACTGAATAATTGAT
1 TGTTACTGAATAATTGAT
* *
2558689 TGCTACTGAAAAATTGAT
1 TGTTACTGAATAATTGAT
*
2558707 T-TTAATGAAT
1 TGTTACTGAAT
2558717 GATATTGATA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
17 6 0.15
18 34 0.85
ACGTcount: A:0.36, C:0.05, G:0.16, T:0.44
Consensus pattern (18 bp):
TGTTACTGAATAATTGAT
Found at i:2572650 original size:3 final size:3
Alignment explanation
Indices: 2572642--2572670 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2572632 GTGTTATTTT
2572642 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2572671 TTATTATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2572783 original size:3 final size:3
Alignment explanation
Indices: 2572764--2572838 Score: 55
Period size: 3 Copynumber: 24.0 Consensus size: 3
2572754 AACGTAATAG
* * *
2572764 TAT TTT TAT TAT T-T TAT TAT TAT T-T TCACCT TTT TAT TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-A--T TAT TAT TAT TAT TAT
*
2572810 TAT TAACC TAT TAT TAT TAT TAT TAT TAT
1 TAT T-A-T TAT TAT TAT TAT TAT TAT TAT
2572839 AGTGTTATTT
Statistics
Matches: 57, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
2 4 0.07
3 48 0.84
4 2 0.04
5 1 0.02
6 2 0.04
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:2572789 original size:20 final size:20
Alignment explanation
Indices: 2572764--2572864 Score: 60
Period size: 20 Copynumber: 5.0 Consensus size: 20
2572754 AACGTAATAG
2572764 TATTTTTATTATTTTATTAT
1 TATTTTTATTATTTTATTAT
* * *
2572784 TATTTTCACCT-TTTTATTAC
1 TATTTTTA-TTATTTTATTAT
* ***
2572804 TATTATTATTAACCTATTAT
1 TATTTTTATTATTTTATTAT
* * * *
2572824 TATTATTATTATTATAGTGT
1 TATTTTTATTATTTTATTAT
* *
2572844 TATTTTCATTTCTTTTATTAT
1 TATTTTTA-TTATTTTATTAT
2572865 CATTATTAAC
Statistics
Matches: 57, Mismatches: 21, Indels: 5
0.69 0.25 0.06
Matches are distributed among these distances:
19 1 0.02
20 47 0.82
21 9 0.16
ACGTcount: A:0.26, C:0.08, G:0.02, T:0.64
Consensus pattern (20 bp):
TATTTTTATTATTTTATTAT
Found at i:2572798 original size:60 final size:58
Alignment explanation
Indices: 2572729--2572864 Score: 137
Period size: 60 Copynumber: 2.3 Consensus size: 58
2572719 CTATCACTGA
* * * * *
2572729 TTTCTTTTTTTTTATTATTAGTAGTAACGTAATAGTATTTTTATTATTTTATTATTAT
1 TTTCATTTTTTTTATTATTAGTAGTAACCTAATAGTATTATTATTATTATAGTATTAT
* * * * * * *
2572787 TTTCACCTTTTTATTACTATTATTATTAACCTATTATTATTATTATTATTATAGTGTTAT
1 TTTCA--TTTTTTTTATTATTAGTAGTAACCTAATAGTATTATTATTATTATAGTATTAT
*
2572847 TTTCATTTCTTTTATTAT
1 TTTCATTTTTTTTATTAT
2572865 CATTATTAAC
Statistics
Matches: 61, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
58 14 0.23
60 47 0.77
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.62
Consensus pattern (58 bp):
TTTCATTTTTTTTATTATTAGTAGTAACCTAATAGTATTATTATTATTATAGTATTAT
Found at i:2572908 original size:29 final size:29
Alignment explanation
Indices: 2572844--2572909 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
2572834 ATTATAGTGT
* *
2572844 TATTTTCATTTCTTTTATTATCATTATTA
1 TATTATCATTTCTTTTATTATCATTAATA
*
2572873 -ACATATCATTTCTATTT-TTATCATTAATA
1 TA-TTATCATTTCT-TTTATTATCATTAATA
2572902 TATTATCA
1 TATTATCA
2572910 CGCTTATTAG
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
28 1 0.03
29 25 0.83
30 4 0.13
ACGTcount: A:0.30, C:0.12, G:0.00, T:0.58
Consensus pattern (29 bp):
TATTATCATTTCTTTTATTATCATTAATA
Done.