Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A13
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: 109233746
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2708888 characters in sequence are not A, C, G, or T
File 10 of 332
Found at i:2761582 original size:73 final size:73
Alignment explanation
Indices: 2761447--2761670 Score: 340
Period size: 74 Copynumber: 3.0 Consensus size: 73
2761437 CGAACAGAGA
* * *
2761447 TTGAAGAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAACAGAAATTGAAAATACCTCAGCATGT--CCCGAGGCTCAACTCACCTCTCGCAATAT
*
2761512 GAGTTAATTT
64 GAGTTGATTT
* *
2761522 TTGACAAACAGAAATTGAAATTACCTCAGCATGTCCCGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCATGTCCCGAGGCTCAACTCACCTCTCGCAATATGA
2761587 GTTGATTT
66 GTTGATTT
* * *
2761595 TTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAA-TTGAAAATACCTCAGCATGTCCCGAGGCTCAACTCACCTCTCGCAATATG
2761660 AGTTGATTT
65 AGTTGATTT
2761669 TT
1 TT
2761671 TTTTTACGAA
Statistics
Matches: 137, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
73 50 0.36
74 57 0.42
75 30 0.22
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.27
Consensus pattern (73 bp):
TTGAAAAACAGAAATTGAAAATACCTCAGCATGTCCCGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTT
Found at i:2761683 original size:240 final size:240
Alignment explanation
Indices: 2761260--2762148 Score: 1620
Period size: 240 Copynumber: 3.7 Consensus size: 240
2761250 ATCTGTAAAA
*
2761260 CTCTCGCAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAACGTGTCCCGAGGCT
1 CTCTCGCAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCT
* *
2761325 CAACTCACCTTTTGCAATATGAGTTGATTTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTG
66 CAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTG
*
2761390 TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTTTACGAACAGAGATTGAAGA
130 TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTACGAACAGAAATTGAAGA
2761454 ACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCAC
195 ACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCAC
*
2761500 CTCTCGCAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCATGTCCCGAGGCT
1 CTCTCGCAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCT
2761565 CAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGT
66 CAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGT
*
2761630 CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTACGAACAGAAATTGAAAAA
131 CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTACGAACAGAAATTGAAGAA
*
2761695 TAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCAC
196 CAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCAC
2761740 CTCTCGCAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCT
1 CTCTCGCAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCT
*
2761805 CAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTTAAAAATACCTCAGCGTGT
66 CAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGT
*
2761870 CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTACGAATAGAAATTGAAGAA
131 CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTACGAACAGAAATTGAAGAA
*
2761935 CAGAAATTGAAAAGATCTCAGCATGTGAGCCGAGGCTCAACTCAC
196 CAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCAC
2761980 CTCTCGCAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCT
1 CTCTCGCAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCT
* * * *
2762045 CAACTCACCTCTCGTAATATGAGTTGATTTTTGACAAACAGAAA-TTGAAATTACCTCAGCGTGT
66 CAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGT
*
2762109 CCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTT
131 CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
2762149 GAAAAAAAAT
Statistics
Matches: 629, Mismatches: 19, Indels: 3
0.97 0.03 0.00
Matches are distributed among these distances:
239 131 0.21
240 498 0.79
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (240 bp):
CTCTCGCAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCT
CAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGT
CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTACGAACAGAAATTGAAGAA
CAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCAC
Found at i:2761753 original size:93 final size:92
Alignment explanation
Indices: 2761595--2761763 Score: 252
Period size: 93 Copynumber: 1.8 Consensus size: 92
2761585 GAGTTGATTT
* *
2761595 TTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAATTTAAAAAGACCTCAGCGTGGCCTGAGGCTCAACTCACCTCTCGCAATATG
*
2761660 AGTTGATTTTTTTTTTACGAACAGAAA
66 AGTTAATTTTTTTTTTACGAACAGAAA
* *
2761687 TTGAAAAATAGAAA-TTGAAAAGACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTCGCAAT
1 TTGAAAAACAGAAATTTAAAAAGACCTCAGC--GTG-GCCTGAGGCTCAACTCACCTCTCGCAAT
2761750 ATGAGTTAATTTTT
63 ATGAGTTAATTTTT
2761764 GACAAACAGA
Statistics
Matches: 69, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
91 14 0.20
92 13 0.19
93 40 0.58
94 2 0.03
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.29
Consensus pattern (92 bp):
TTGAAAAACAGAAATTTAAAAAGACCTCAGCGTGGCCTGAGGCTCAACTCACCTCTCGCAATATG
AGTTAATTTTTTTTTTACGAACAGAAA
Found at i:2761835 original size:166 final size:165
Alignment explanation
Indices: 2761522--2761836 Score: 515
Period size: 166 Copynumber: 1.9 Consensus size: 165
2761512 GAGTTAATTT
* **
2761522 TTGACAAACAGAAATTGAAATTACCTCAGCATGTCCCGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAAGACCTCAGCATGTCCCGAGGCTCAACTCACCTCTCGCAATATGA
* *
2761587 GTTGATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTC
66 GTTAATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTC
2761652 GCAATATGAGTTGATTTTTTTTTTACGAACAGAAA
131 GCAATATGAGTTGATTTTTTTTTTACGAACAGAAA
* *
2761687 TTGAAAAATAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAACAGAAATTGAAAAGACCTCAGCATGT--CCCGAGGCTCAACTCACCTCTCGCAATAT
* * *
2761752 GAGTTAATTTTTGACAAACAGAAA-TTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTC
64 GAGTTAATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTC
2761816 TCGCAATATGAGTTGATTTTT
129 TCGCAATATGAGTTGATTTTT
2761837 GAAAAACAAA
Statistics
Matches: 138, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
165 30 0.22
166 58 0.42
167 50 0.36
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (165 bp):
TTGAAAAACAGAAATTGAAAAGACCTCAGCATGTCCCGAGGCTCAACTCACCTCTCGCAATATGA
GTTAATTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTC
GCAATATGAGTTGATTTTTTTTTTACGAACAGAAA
Found at i:2761844 original size:73 final size:73
Alignment explanation
Indices: 2761687--2762217 Score: 453
Period size: 73 Copynumber: 7.0 Consensus size: 73
2761677 CGAACAGAAA
* * **
2761687 TTGAAAAATAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAACAGAAATTGAAAATACCTCAGC--GTGTCCCGAGGCTCAACTCACCTCTCGCAATAT
*
2761752 GAGTTAATTT
64 GAGTTGATTT
* *
2761762 TTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGA
2761827 GTTGATTT
66 GTTGATTT
* * *
2761835 TTGAAAAACAAAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAA-TTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATG
2761900 AGTTGATTTTTTT
65 AGTTGA----TTT
* ** * * ** * ** * * * *
2761913 TTTACGAATAGAAATTGAAGAACAGAAATTGAAAAGATCTCAGCATGTGAGC-CGAGGCTCAACT
1 TTGAAAAACAGAAATTG-A-AA-A-TACCT-CAGCG-TGTC--C-CGAG-GCTC-A-ACTC----
*
2761977 CACCTCTCGCAATATGAGTTAATTT
50 -ACCTCTCGCAATATGAGTTGATTT
* * *
2762002 TTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGTAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGA
2762067 GTTGATTT
66 GTTGATTT
* * * *
2762075 TTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGA
2762140 GTTGA-TT
66 GTTGATTT
* ** ** *
2762147 TTG-AAAA-A-AAATT-AAAAGTACCTTAATGTGTCTTGAGGCTCAACTCATCTCTCGCAATATG
1 TTGAAAAACAGAAATTGAAAA-TACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATG
2762208 AGTTGATTT
65 AGTTGATTT
2762217 T
1 T
2762218 CCTTGAAAAG
Statistics
Matches: 376, Mismatches: 55, Indels: 55
0.77 0.11 0.11
Matches are distributed among these distances:
68 3 0.01
69 48 0.13
70 4 0.01
71 3 0.01
72 5 0.01
73 141 0.38
74 53 0.14
75 26 0.07
77 2 0.01
78 16 0.04
79 5 0.01
80 4 0.01
81 3 0.01
82 2 0.01
83 6 0.02
84 2 0.01
85 3 0.01
86 4 0.01
87 5 0.01
88 4 0.01
89 17 0.05
93 20 0.05
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (73 bp):
TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTT
Found at i:2770554 original size:16 final size:15
Alignment explanation
Indices: 2770533--2770580 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
2770523 GATGTGAATA
2770533 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
2770549 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
* *
2770564 ATCAAAACATTAGAAT
1 AT-AAAATATTAAAAT
2770580 A
1 A
2770581 ATAATAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 8 0.28
16 21 0.72
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:2770563 original size:8 final size:8
Alignment explanation
Indices: 2770529--2770580 Score: 52
Period size: 8 Copynumber: 6.5 Consensus size: 8
2770519 TAATGATGTG
*
2770529 AATAATAA
1 AATATTAA
2770537 AATATATAA
1 AATAT-TAA
2770546 AATA-TAA
1 AATATTAA
2770553 AATATTAA
1 AATATTAA
*
2770561 AATATCAA
1 AATATTAA
* *
2770569 AACATTAG
1 AATATTAA
2770577 AATA
1 AATA
2770581 ATAATAATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
7 7 0.19
8 22 0.61
9 7 0.19
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (8 bp):
AATATTAA
Found at i:2770580 original size:24 final size:24
Alignment explanation
Indices: 2770528--2770584 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
2770518 ATAATGATGT
2770528 GAATAATAAAATATATAAAATATA
1 GAATAATAAAATATATAAAATATA
* *
2770552 AAATATTAAAATATCA-AAACAT-TA
1 GAATAATAAAATAT-ATAAA-ATATA
2770576 GAATAATAA
1 GAATAATAA
2770585 TAATTAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
24 24 0.89
25 3 0.11
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.28
Consensus pattern (24 bp):
GAATAATAAAATATATAAAATATA
Found at i:2770775 original size:23 final size:23
Alignment explanation
Indices: 2770728--2770942 Score: 111
Period size: 23 Copynumber: 9.0 Consensus size: 23
2770718 TAAATACGTG
2770728 ATAATATTAAAAATATGTACATAAT
1 ATAATATTAAAAATA--TACATAAT
* *
2770753 ATAGTGTTAAAAATATACATAAT
1 ATAATATTAAAAATATACATAAT
* * *
2770776 AT-A-GTTAAGATATATACATAAG
1 ATAATATTAA-AAATATACATAAT
* *
2770798 ATAACATGTAAAAATATATATAAATAAT
1 ATAATAT-T--AAA-A-ATATACATAAT
*
2770826 ATAATATTAAAGATATATACATAAA
1 ATAATATTAAA-A-ATATACATAAT
* * *
2770851 ATAGTA-TAATATATATACGTAAT
1 ATAATATTAA-AAATATACATAAT
* * *
2770874 CTAGA-ATTTAAAATATACCTAAT
1 ATA-ATATTAAAAATATACATAAT
* *
2770897 AT-AT-TAAAAGAATATATATAAT
1 ATAATATTAAA-AATATACATAAT
2770919 ATAATATTAAGAAATATA-ATAAT
1 ATAATATTAA-AAATATACATAAT
2770942 A
1 A
2770943 ACAAAAAAGG
Statistics
Matches: 146, Mismatches: 28, Indels: 34
0.70 0.13 0.16
Matches are distributed among these distances:
21 9 0.06
22 25 0.17
23 43 0.29
24 15 0.10
25 35 0.24
26 1 0.01
27 3 0.02
28 15 0.10
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.34
Consensus pattern (23 bp):
ATAATATTAAAAATATACATAAT
Found at i:2770819 original size:28 final size:27
Alignment explanation
Indices: 2770785--2770844 Score: 75
Period size: 28 Copynumber: 2.2 Consensus size: 27
2770775 TATAGTTAAG
*
2770785 ATATATACATAAGATAACATGTAAAAAT
1 ATATATAAATAAGATAACAT-TAAAAAT
* * *
2770813 ATATATAAATAATATAATATTAAAGAT
1 ATATATAAATAAGATAACATTAAAAAT
2770840 ATATA
1 ATATA
2770845 CATAAAATAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 11 0.39
28 17 0.61
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.33
Consensus pattern (27 bp):
ATATATAAATAAGATAACATTAAAAAT
Found at i:2771515 original size:30 final size:30
Alignment explanation
Indices: 2771481--2771549 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
2771471 TGGAGCAAGT
*
2771481 GTGGCTAGTGGATTTGGTGGTGGAAAAGGA
1 GTGGCTAGTGGAGTTGGTGGTGGAAAAGGA
*
2771511 GTGGCTAGTGGAGTTGGTGGTGGAAAAGGT
1 GTGGCTAGTGGAGTTGGTGGTGGAAAAGGA
2771541 GTGGCTAGT
1 GTGGCTAGT
2771550 TGAGAAAAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.20, C:0.04, G:0.48, T:0.28
Consensus pattern (30 bp):
GTGGCTAGTGGAGTTGGTGGTGGAAAAGGA
Found at i:2778442 original size:31 final size:31
Alignment explanation
Indices: 2778381--2778444 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
2778371 ATTTTCATCC
* *
2778381 AATTAAGTCTTTGAATTTAGTTTTAAGATTT
1 AATTAAGTATTTGAATTTAGATTTAAGATTT
* *
2778412 AATTTAGTATTTGAATTT-GATTTATTGATTT
1 AATTAAGTATTTGAATTTAGATTTA-AGATTT
2778443 AA
1 AA
2778445 ATTGATACTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 5 0.18
31 23 0.82
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.53
Consensus pattern (31 bp):
AATTAAGTATTTGAATTTAGATTTAAGATTT
Found at i:2778447 original size:19 final size:18
Alignment explanation
Indices: 2778394--2778447 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
2778384 TAAGTCTTTG
2778394 AATTTAGT-TTTAAGATTT
1 AATTTAGTATTTAA-ATTT
*
2778412 AATTTAGTATTTGAATTT
1 AATTTAGTATTTAAATTT
* *
2778430 GATTTATTGATTTAAATT
1 AATTTAGT-ATTTAAATT
2778448 GATACTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 18 0.60
19 12 0.40
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (18 bp):
AATTTAGTATTTAAATTT
Found at i:2787194 original size:39 final size:40
Alignment explanation
Indices: 2787084--2787237 Score: 258
Period size: 39 Copynumber: 3.9 Consensus size: 40
2787074 ATAAAGTATG
*
2787084 GTTTTAATTAATAATAAAAACAAAATAGTATGGGGGAATG
1 GTTTTAATTAATAATAAAAACAAAATAGTATGGGGGAATA
2787124 GTTTTAATTAATAATAAAAACAAAATAGTATGGGGGAATA
1 GTTTTAATTAATAATAAAAACAAAATAGTATGGGGGAATA
*
2787164 GTTTTAATTAATAAT-AAAACAAAATAGTATGGGGGAGTA
1 GTTTTAATTAATAATAAAAACAAAATAGTATGGGGGAATA
* *
2787203 GTTTTAATTAATAAT-AAACCAAAGTAGTATGGGGG
1 GTTTTAATTAATAATAAAAACAAAATAGTATGGGGG
2787238 GAGTGGAATC
Statistics
Matches: 110, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
39 56 0.51
40 54 0.49
ACGTcount: A:0.46, C:0.03, G:0.20, T:0.31
Consensus pattern (40 bp):
GTTTTAATTAATAATAAAAACAAAATAGTATGGGGGAATA
Found at i:2787239 original size:79 final size:80
Alignment explanation
Indices: 2787084--2787237 Score: 258
Period size: 79 Copynumber: 1.9 Consensus size: 80
2787074 ATAAAGTATG
*
2787084 GTTTTAATTAATAATAAAAACAAAATAGTATGGGGGAATGGTTTTAATTAATAATAAAAACAAAA
1 GTTTTAATTAATAATAAAAACAAAATAGTATGGGGGAATAGTTTTAATTAATAATAAAAACAAAA
2787149 TAGTATGGGGGAATA
66 TAGTATGGGGGAATA
* * *
2787164 GTTTTAATTAATAAT-AAAACAAAATAGTATGGGGGAGTAGTTTTAATTAATAAT-AAACCAAAG
1 GTTTTAATTAATAATAAAAACAAAATAGTATGGGGGAATAGTTTTAATTAATAATAAAAACAAAA
2787227 TAGTATGGGGG
66 TAGTATGGGGG
2787238 GAGTGGAATC
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
78 18 0.26
79 37 0.53
80 15 0.21
ACGTcount: A:0.46, C:0.03, G:0.20, T:0.31
Consensus pattern (80 bp):
GTTTTAATTAATAATAAAAACAAAATAGTATGGGGGAATAGTTTTAATTAATAATAAAAACAAAA
TAGTATGGGGGAATA
Found at i:2790981 original size:29 final size:26
Alignment explanation
Indices: 2790941--2790995 Score: 65
Period size: 29 Copynumber: 2.0 Consensus size: 26
2790931 AAACTGCTAC
2790941 TTTTTCTTTTTACTGTTCTTGCTTTTT
1 TTTTTCTTTTTACTGTTCTTG-TTTTT
* *
2790968 TTTTTGCTATTTTATTGTTGTTGTTTTT
1 TTTTT-CT-TTTTACTGTTCTTGTTTTT
2790996 CACTATTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 5 0.21
28 7 0.29
29 12 0.50
ACGTcount: A:0.05, C:0.09, G:0.11, T:0.75
Consensus pattern (26 bp):
TTTTTCTTTTTACTGTTCTTGTTTTT
Found at i:2791013 original size:11 final size:11
Alignment explanation
Indices: 2790997--2791038 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
2790987 GTTGTTTTTC
2790997 ACTATTTTGCT
1 ACTATTTTGCT
**
2791008 ACTATTTCACT
1 ACTATTTTGCT
*
2791019 ACTATGTTGCT
1 ACTATTTTGCT
2791030 ACTATTTTG
1 ACTATTTTG
2791039 TTGCTATTGT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.21, C:0.19, G:0.10, T:0.50
Consensus pattern (11 bp):
ACTATTTTGCT
Found at i:2791087 original size:17 final size:19
Alignment explanation
Indices: 2791054--2791088 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
2791044 ATTGTTTGTA
2791054 TATTGTATAACTTTTGTTT
1 TATTGTATAACTTTTGTTT
2791073 TATTGT-TAA-TTTTGTT
1 TATTGTATAACTTTTGTT
2791089 ACTATTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.20, C:0.03, G:0.11, T:0.66
Consensus pattern (19 bp):
TATTGTATAACTTTTGTTT
Found at i:2805016 original size:23 final size:25
Alignment explanation
Indices: 2804990--2805042 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 25
2804980 TTTTCTATAT
* *
2804990 CTTATGGTCATTTCGGTAC-TTA-A
1 CTTATCGTCATTTCGGAACTTTAGA
*
2805013 CTTACCGTCATTTCGGAACTTTAGA
1 CTTATCGTCATTTCGGAACTTTAGA
2805038 CTTAT
1 CTTAT
2805043 ATCGACACTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 16 0.67
24 3 0.12
25 5 0.21
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.42
Consensus pattern (25 bp):
CTTATCGTCATTTCGGAACTTTAGA
Found at i:2808827 original size:46 final size:44
Alignment explanation
Indices: 2808767--2808881 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
2808757 ACAGGACAGA
* *
2808767 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
2808813 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
2808857 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
2808882 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:2808862 original size:44 final size:45
Alignment explanation
Indices: 2808767--2808900 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
2808757 ACAGGACAGA
* *
2808767 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
2808813 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
2808857 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
2808901 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:2817095 original size:36 final size:36
Alignment explanation
Indices: 2817055--2817123 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
2817045 TGCGTCGATG
* *
2817055 CCCTCCTGGTGGATCTCCTACTTACAGCTCTGGATA
1 CCCTCCTGGTGGATCTCCCACTTACAGCACTGGATA
*
2817091 CCCTCCTGGTGGATCTCCCACTTTCAGCACTGG
1 CCCTCCTGGTGGATCTCCCACTTACAGCACTGG
2817124 GAGCCAGTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.14, C:0.36, G:0.20, T:0.29
Consensus pattern (36 bp):
CCCTCCTGGTGGATCTCCCACTTACAGCACTGGATA
Found at i:2825458 original size:26 final size:26
Alignment explanation
Indices: 2825429--2825481 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
2825419 TCTTAGAAGA
2825429 AAGCCTGTGGAAAATACCTAAATGAT
1 AAGCCTGTGGAAAATACCTAAATGAT
2825455 AAGCCTGTGGAAAATACCTAAATGAT
1 AAGCCTGTGGAAAATACCTAAATGAT
2825481 A
1 A
2825482 TACATTCAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.43, C:0.15, G:0.19, T:0.23
Consensus pattern (26 bp):
AAGCCTGTGGAAAATACCTAAATGAT
Found at i:2829416 original size:11 final size:11
Alignment explanation
Indices: 2829400--2829439 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
2829390 GTTTTCTTTA
2829400 CTATTTTCTTG
1 CTATTTTCTTG
2829411 CTATTTTCTTG
1 CTATTTTCTTG
* * *
2829422 TTCTTTTCTTA
1 CTATTTTCTTG
2829433 CTATTTT
1 CTATTTT
2829440 ACTACAATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.10, C:0.17, G:0.05, T:0.68
Consensus pattern (11 bp):
CTATTTTCTTG
Found at i:2839482 original size:21 final size:21
Alignment explanation
Indices: 2839443--2839483 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2839433 ATTTTCCTGT
*
2839443 AAAAGATTGAAGGAAATAAAG
1 AAAAGATTGAAAGAAATAAAG
* *
2839464 AAAAGATTTAAAGATATAAA
1 AAAAGATTGAAAGAAATAAA
2839484 AAGTCAGATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.17, T:0.20
Consensus pattern (21 bp):
AAAAGATTGAAAGAAATAAAG
Found at i:2841763 original size:3 final size:3
Alignment explanation
Indices: 2841755--2841797 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
2841745 TACTGCATTC
*
2841755 ATG ATG ATG ATG ATG ATG AT- ATT ATG ATG ATG ATG ATG -TG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
2841798 GCTTCAGTGA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
2 4 0.11
3 33 0.89
ACGTcount: A:0.33, C:0.00, G:0.30, T:0.37
Consensus pattern (3 bp):
ATG
Found at i:2848279 original size:17 final size:18
Alignment explanation
Indices: 2848257--2848305 Score: 64
Period size: 17 Copynumber: 2.7 Consensus size: 18
2848247 ACACGTGGCA
2848257 AAAAATTAATAAAAA-AT
1 AAAAATTAATAAAAATAT
*
2848274 AAAAATCAATAAAAATTAT
1 AAAAATTAATAAAAA-TAT
*
2848293 AAAAATTATTAAA
1 AAAAATTAATAAA
2848306 TTTTAATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 14 0.52
19 13 0.48
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (18 bp):
AAAAATTAATAAAAATAT
Found at i:2848313 original size:29 final size:29
Alignment explanation
Indices: 2848281--2848350 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 29
2848271 AATAAAAATC
2848281 AATAAAAATTATAAAAAT-TATTAAATTTT
1 AATAAAAATTATAAAAATAT-TTAAATTTT
* *
2848310 AATAAAAGAATATAAAAATATTTAATTTTT
1 AATAAAA-ATTATAAAAATATTTAAATTTT
*
2848340 ATTAAAAATTA
1 AATAAAAATTA
2848351 GGAAACAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
29 10 0.29
30 24 0.69
31 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (29 bp):
AATAAAAATTATAAAAATATTTAAATTTT
Found at i:2848326 original size:30 final size:28
Alignment explanation
Indices: 2848281--2848348 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 28
2848271 AATAAAAATC
*
2848281 AATAAAAATTATAAAAATTATTAAATTTT
1 AATAAAAAATATAAAAA-TATTAAATTTT
*
2848310 AATAAAAGAATATAAAAATATTTAATTTT
1 AATAAAA-AATATAAAAATATTAAATTTT
* *
2848339 TATTAAAAAT
1 AATAAAAAAT
2848349 TAGGAAACAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 3 0.09
29 22 0.65
30 9 0.26
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (28 bp):
AATAAAAAATATAAAAATATTAAATTTT
Found at i:2848549 original size:9 final size:9
Alignment explanation
Indices: 2848505--2848547 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
2848495 AAAAGAAGCA
2848505 TTTTATAAT
1 TTTTATAAT
2848514 TTTTATTAAT
1 TTTTA-TAAT
* *
2848524 TTTTTTATT
1 TTTTATAAT
*
2848533 TTTTATCAT
1 TTTTATAAT
2848542 TTTTAT
1 TTTTAT
2848548 CACATTTCAC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
9 20 0.71
10 8 0.29
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (9 bp):
TTTTATAAT
Found at i:2853059 original size:31 final size:29
Alignment explanation
Indices: 2852990--2853060 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 29
2852980 AAATCCTAAT
*
2852990 TTAAAAA-AATTCAAAGAAATATATAAAA
1 TTAAAAATATTTCAAAGAAATATATAAAA
2853018 TTACATAAATATTTCAAA-AAATATAATATTAAA
1 TTA-A-AAATATTTCAAAGAAATAT-ATA--AAA
2853051 TTAAAAATAT
1 TTAAAAATAT
2853061 AAAAATAAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
28 3 0.08
29 1 0.03
30 9 0.25
31 16 0.44
32 1 0.03
33 6 0.17
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.32
Consensus pattern (29 bp):
TTAAAAATATTTCAAAGAAATATATAAAA
Found at i:2855187 original size:14 final size:15
Alignment explanation
Indices: 2855168--2855198 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
2855158 TAATTAAAAC
2855168 AATAAAGT-AAATAA
1 AATAAAGTAAAATAA
2855182 AATAAAGTAAAATAA
1 AATAAAGTAAAATAA
2855197 AA
1 AA
2855199 GAAACTAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.19
Consensus pattern (15 bp):
AATAAAGTAAAATAA
Found at i:2855243 original size:16 final size:15
Alignment explanation
Indices: 2855205--2855249 Score: 58
Period size: 16 Copynumber: 3.1 Consensus size: 15
2855195 AAAAGAAACT
*
2855205 AAAGAAATAA-AAGA
1 AAAGAAAAAAGAAGA
2855219 AAA-AAAAAAGAAGTA
1 AAAGAAAAAAGAAG-A
2855234 AAAGAAAAAAGAAGA
1 AAAGAAAAAAGAAGA
2855249 A
1 A
2855250 GAGCGGAAGC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 5 0.19
14 6 0.22
15 6 0.22
16 10 0.37
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (15 bp):
AAAGAAAAAAGAAGA
Found at i:2855250 original size:19 final size:20
Alignment explanation
Indices: 2855186--2855243 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
2855176 AAATAAAATA
*
2855186 AAGTAAAATAAAAGAAACTAAAG
1 AAGTAAAAGAAAA-AAA--AAAG
*
2855209 AAATAAAAGAAAAAAAAAAG
1 AAGTAAAAGAAAAAAAAAAG
2855229 AAGTAAAAGAAAAAA
1 AAGTAAAAGAAAAAA
2855244 GAAGAAGAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 18 0.56
22 3 0.09
23 11 0.34
ACGTcount: A:0.78, C:0.02, G:0.12, T:0.09
Consensus pattern (20 bp):
AAGTAAAAGAAAAAAAAAAG
Found at i:2856156 original size:44 final size:44
Alignment explanation
Indices: 2856106--2856197 Score: 116
Period size: 44 Copynumber: 2.1 Consensus size: 44
2856096 TGCTCAGGGA
*
2856106 TACTTCGACCTT-GAGTTGATAAGGCA-CTATAAGTGTCGTACTGT
1 TACTTCGA-CTTCGAGTCGATAAGGCACCT-TAAGTGTCGTACTGT
* **
2856150 TACTTCGACTTCGAGTCGATGAGGCACCTTGTGTGTCGTACTGT
1 TACTTCGACTTCGAGTCGATAAGGCACCTTAAGTGTCGTACTGT
2856194 TACT
1 TACT
2856198 GTTATTTCGG
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
43 3 0.07
44 37 0.88
45 2 0.05
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.35
Consensus pattern (44 bp):
TACTTCGACTTCGAGTCGATAAGGCACCTTAAGTGTCGTACTGT
Found at i:2856437 original size:18 final size:18
Alignment explanation
Indices: 2856382--2856439 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
2856372 ATTACCGGAC
2856382 TGAATAACTGATTGTTAT
1 TGAATAACTGATTGTTAT
* * *
2856400 TG-AT--C-GTTTGATAC
1 TGAATAACTGATTGTTAT
2856414 TGAATAACTGATTGTTAT
1 TGAATAACTGATTGTTAT
2856432 TGAATAAC
1 TGAATAAC
2856440 AATAATCAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
14 8 0.27
15 3 0.10
17 3 0.10
18 16 0.53
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.41
Consensus pattern (18 bp):
TGAATAACTGATTGTTAT
Found at i:2858461 original size:29 final size:29
Alignment explanation
Indices: 2858405--2858461 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
2858395 TTATTTAGTT
*
2858405 TTATTTAATAGCAAAGAGATTAAATTGAC
1 TTATTTAATAGCAAAGAGAATAAATTGAC
* *
2858434 TTATTTAATAGTACAAGA-AATAATTTGA
1 TTATTTAATAGCA-AAGAGAATAAATTGA
2858462 TACATATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 20 0.83
30 4 0.17
ACGTcount: A:0.46, C:0.05, G:0.12, T:0.37
Consensus pattern (29 bp):
TTATTTAATAGCAAAGAGAATAAATTGAC
Found at i:2871982 original size:46 final size:46
Alignment explanation
Indices: 2871811--2872023 Score: 202
Period size: 46 Copynumber: 4.6 Consensus size: 46
2871801 TCATTTGTGT
* * *
2871811 GCTAATGTAAGACATGTCTGGGACATGCATCAGCCA-C-A-ATATGAAA
1 GCTAGTGTAAGACATGTCTAGGACATGCATC-GGCATCGAGATAT--AA
* * *
2871857 GATAGTGTAAGACATGTTTAGGACATGCATCGGCCTCGAGATATTTAA
1 GCTAGTGTAAGACATGTCTAGGACATGCATCGGCATCGAGATA--TAA
* * *
2871905 GCTAGTGTAAGACATGTCTAGGACATGCATCGGCATTGAGGTGA-GA
1 GCTAGTGTAAGACATGTCTAGGACATGCATCGGCATCGAGAT-ATAA
* * *
2871951 GCTAGTGTAAGACATGTCTCGGACATGCATCGGCATCGCGAGATACA
1 GCTAGTGTAAGACATGTCTAGGACATGCATCGGCATCGAGATATA-A
* *
2871998 GCTAGTGTAA-ACCTGTCTGGGACATG
1 GCTAGTGTAAGACATGTCTAGGACATG
2872024 GCGTCAACTT
Statistics
Matches: 139, Mismatches: 20, Indels: 16
0.79 0.11 0.09
Matches are distributed among these distances:
45 3 0.02
46 80 0.58
47 12 0.09
48 42 0.30
49 1 0.01
50 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.24
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCTAGGACATGCATCGGCATCGAGATATAA
Found at i:2875180 original size:42 final size:44
Alignment explanation
Indices: 2875103--2875256 Score: 123
Period size: 42 Copynumber: 3.6 Consensus size: 44
2875093 AAATCGTACA
*
2875103 ATGCCAAC-GTCCCAGAC-GTGGTCTT--ACATGTAATCAATATCG
1 ATGCCAACTGTCCCAGACAG-GGTCTTAAACA-GAAATCAATATCG
*
2875145 ATGCC-ACTGTCCCAGACAGGGTTTTAAAC-GAAATCAAATAT-G
1 ATGCCAACTGTCCCAGACAGGGTCTTAAACAGAAATC-AATATCG
* * * *
2875187 ATGCCGA-TGTCCCAGACATGGTCTTATACATAAATCTCAA-ATCG
1 ATGCCAACTGTCCCAGACAGGGTCTTAAACAGAAA--TCAATATCG
2875231 ATGCCAAC-GTCCCAGAC-GTGGTCTTA
1 ATGCCAACTGTCCCAGACAG-GGTCTTA
2875257 CACGATAACA
Statistics
Matches: 92, Mismatches: 8, Indels: 22
0.75 0.07 0.18
Matches are distributed among these distances:
41 2 0.02
42 49 0.53
43 12 0.13
44 27 0.29
45 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (44 bp):
ATGCCAACTGTCCCAGACAGGGTCTTAAACAGAAATCAATATCG
Found at i:2880770 original size:39 final size:39
Alignment explanation
Indices: 2880726--2880810 Score: 152
Period size: 39 Copynumber: 2.2 Consensus size: 39
2880716 ACATCGTGAT
2880726 CTGAAGCACATAAGTGCTAAACGGAAGCCCGAAGGCTAA
1 CTGAAGCACATAAGTGCTAAACGGAAGCCCGAAGGCTAA
* *
2880765 TTGAAGCACATAAGTGCTAAACGGAAGCTCGAAGGCTAA
1 CTGAAGCACATAAGTGCTAAACGGAAGCCCGAAGGCTAA
2880804 CTGAAGC
1 CTGAAGC
2880811 TCATCAGAGC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.38, C:0.21, G:0.26, T:0.15
Consensus pattern (39 bp):
CTGAAGCACATAAGTGCTAAACGGAAGCCCGAAGGCTAA
Found at i:2880792 original size:21 final size:21
Alignment explanation
Indices: 2880728--2880792 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
2880718 ATCGTGATCT
2880728 GAAGCACATAAGTGCTAAACG
1 GAAGCACATAAGTGCTAAACG
** **
2880749 GAAGC-CCGAAG-GCT-AATT
1 GAAGCACATAAGTGCTAAACG
2880767 GAAGCACATAAGTGCTAAACG
1 GAAGCACATAAGTGCTAAACG
2880788 GAAGC
1 GAAGC
2880793 TCGAAGGCTA
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
18 7 0.21
19 7 0.21
20 7 0.21
21 12 0.36
ACGTcount: A:0.40, C:0.20, G:0.26, T:0.14
Consensus pattern (21 bp):
GAAGCACATAAGTGCTAAACG
Found at i:2880811 original size:18 final size:18
Alignment explanation
Indices: 2880749--2880812 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
2880739 GTGCTAAACG
* *
2880749 GAAGCCCGAAGGCTAATT
1 GAAGCTCGAAGGCTAACT
* * *
2880767 GAAGCACATAAGTGCTAAACG
1 GAAGCTC-GAAG-GCT-AACT
2880788 GAAGCTCGAAGGCTAACT
1 GAAGCTCGAAGGCTAACT
2880806 GAAGCTC
1 GAAGCTC
2880813 ATCAGAGCTG
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
18 16 0.44
19 6 0.17
20 6 0.17
21 8 0.22
ACGTcount: A:0.36, C:0.22, G:0.27, T:0.16
Consensus pattern (18 bp):
GAAGCTCGAAGGCTAACT
Found at i:2882049 original size:16 final size:18
Alignment explanation
Indices: 2882018--2882052 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
2882008 CAATTAACCC
2882018 CTCAATTAAGATAATTTT
1 CTCAATTAAGATAATTTT
2882036 CTCAATT-A-ATAATTTT
1 CTCAATTAAGATAATTTT
2882052 C
1 C
2882053 ATAAACATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 1 0.06
18 7 0.41
ACGTcount: A:0.37, C:0.14, G:0.03, T:0.46
Consensus pattern (18 bp):
CTCAATTAAGATAATTTT
Found at i:2888011 original size:76 final size:76
Alignment explanation
Indices: 2887887--2888035 Score: 235
Period size: 76 Copynumber: 2.0 Consensus size: 76
2887877 ACCCTTTATA
** * * **
2887887 TTGGGCACAATGACTTTGCTTTAATGAAGACATGGTCCATTTTATGAGAAATAGGAATCCATTTA
1 TTGGGCACAAACACATTGCTTTAATGAAGACATGATCCATTTTATGAGAAATAGGAATCCATCAA
2887952 TTTACTTTAGG
66 TTTACTTTAGG
*
2887963 TTGGGCACAAACACATTGCTTTAATGAAGACATGATCCATTTTTTGAGAAATAGGAATCCATCAA
1 TTGGGCACAAACACATTGCTTTAATGAAGACATGATCCATTTTATGAGAAATAGGAATCCATCAA
2888028 TTTACTTT
66 TTTACTTT
2888036 CTATGTAGAT
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
76 66 1.00
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (76 bp):
TTGGGCACAAACACATTGCTTTAATGAAGACATGATCCATTTTATGAGAAATAGGAATCCATCAA
TTTACTTTAGG
Found at i:2888852 original size:19 final size:17
Alignment explanation
Indices: 2888812--2888855 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
2888802 AAGAAGATTT
*
2888812 AAATGAAAATTGTTAAA
1 AAATGAAAATTATTAAA
*
2888829 TAATGAAAAGTTATATAAA
1 AAATGAAAA-TTAT-TAAA
2888848 AAATGAAA
1 AAATGAAA
2888856 TGACAGGGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 8 0.36
18 3 0.14
19 11 0.50
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.27
Consensus pattern (17 bp):
AAATGAAAATTATTAAA
Found at i:2888955 original size:38 final size:38
Alignment explanation
Indices: 2888911--2888987 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
2888901 ATCCTGAAGT
2888911 ACCTATTCAAGAAAAACTAAAACTTTTCCTAAGTACCA
1 ACCTATTCAAGAAAAACTAAAACTTTTCCTAAGTACCA
2888949 ACCTATTCAAGAAAAACTAAAACTTTTCCTAAGTACCA
1 ACCTATTCAAGAAAAACTAAAACTTTTCCTAAGTACCA
2888987 A
1 A
2888988 AAGTCAAGGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.45, C:0.23, G:0.05, T:0.26
Consensus pattern (38 bp):
ACCTATTCAAGAAAAACTAAAACTTTTCCTAAGTACCA
Found at i:2902063 original size:25 final size:26
Alignment explanation
Indices: 2902028--2902076 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
2902018 TTTATTTAAA
*
2902028 AAATAGTTTG-TAAAATCTATAATTAT
1 AAATAGTTTGTTAAAA-ATATAATTAT
2902054 AAAT-GTTTGTTAAAAATATAATT
1 AAATAGTTTGTTAAAAATATAATT
2902077 TAACCTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.43
Consensus pattern (26 bp):
AAATAGTTTGTTAAAAATATAATTAT
Found at i:2907487 original size:24 final size:25
Alignment explanation
Indices: 2907442--2907488 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
2907432 TATTATGGAT
* * *
2907442 AATAATTATAAGATAATCCCAAACA
1 AATAATTATAAAAAAATACCAAACA
2907467 AATAA-TATAAAAAAATACCAAA
1 AATAATTATAAAAAAATACCAAA
2907489 ACATAAATAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 14 0.74
25 5 0.26
ACGTcount: A:0.64, C:0.13, G:0.02, T:0.21
Consensus pattern (25 bp):
AATAATTATAAAAAAATACCAAACA
Found at i:2907932 original size:91 final size:91
Alignment explanation
Indices: 2907777--2907958 Score: 364
Period size: 91 Copynumber: 2.0 Consensus size: 91
2907767 CATATTATAA
2907777 ATACAAATAATAAGACCAAATTAACATATTGATAGATTCCACTTGCTCTAGTCAATGCCAATGGT
1 ATACAAATAATAAGACCAAATTAACATATTGATAGATTCCACTTGCTCTAGTCAATGCCAATGGT
2907842 AAATTATGTTTCTTGACAGCATAGTC
66 AAATTATGTTTCTTGACAGCATAGTC
2907868 ATACAAATAATAAGACCAAATTAACATATTGATAGATTCCACTTGCTCTAGTCAATGCCAATGGT
1 ATACAAATAATAAGACCAAATTAACATATTGATAGATTCCACTTGCTCTAGTCAATGCCAATGGT
2907933 AAATTATGTTTCTTGACAGCATAGTC
66 AAATTATGTTTCTTGACAGCATAGTC
2907959 TAACCAGGCC
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 91 1.00
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (91 bp):
ATACAAATAATAAGACCAAATTAACATATTGATAGATTCCACTTGCTCTAGTCAATGCCAATGGT
AAATTATGTTTCTTGACAGCATAGTC
Found at i:2922422 original size:57 final size:56
Alignment explanation
Indices: 2922350--2922468 Score: 152
Period size: 57 Copynumber: 2.1 Consensus size: 56
2922340 TCTTTTTCAC
2922350 TTTTCATTTTCATTTTGGAAAAACCACAT-CCATTTCCAAATGATTT-CATTTCTCCA
1 TTTTCATTTTCATTTTGGAAAAACC-CATACCATTTCCAAATG-TTTCCATTTCTCCA
* * *
2922406 TTTTCATTTTTCATTTTGGAGAAACCCATAATCGTTTCCAAATGTTTCCCATTTCTCCA
1 TTTTCA-TTTTCATTTTGGAAAAACCCAT-ACCATTTCCAAATGTTT-CCATTTCTCCA
2922465 TTTT
1 TTTT
2922469 TCACCATTTC
Statistics
Matches: 55, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
56 9 0.16
57 21 0.38
58 11 0.20
59 14 0.25
ACGTcount: A:0.25, C:0.23, G:0.07, T:0.45
Consensus pattern (56 bp):
TTTTCATTTTCATTTTGGAAAAACCCATACCATTTCCAAATGTTTCCATTTCTCCA
Found at i:2924975 original size:43 final size:43
Alignment explanation
Indices: 2924914--2925022 Score: 141
Period size: 43 Copynumber: 2.5 Consensus size: 43
2924904 TAAAGATAGA
* *
2924914 ATTTAGCCTGGACTGGTAATTCTGATCT-TACGTT-GAAATCGGG
1 ATTTAGCCTGGACTGGTAATCCTGAT-TATACGTTAGAAAT-GAG
* * *
2924957 ATTTAGCCTGGATTGGTAATCCTGATTATATGTTAGAGATGAG
1 ATTTAGCCTGGACTGGTAATCCTGATTATACGTTAGAAATGAG
2925000 ATTTAGCCTGGACTGGTAATCCT
1 ATTTAGCCTGGACTGGTAATCCT
2925023 TATCTCACTG
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
42 1 0.02
43 53 0.91
44 4 0.07
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.36
Consensus pattern (43 bp):
ATTTAGCCTGGACTGGTAATCCTGATTATACGTTAGAAATGAG
Found at i:2928090 original size:23 final size:23
Alignment explanation
Indices: 2928064--2928111 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
2928054 TAATCTTTCC
2928064 ATGAAACTAGCAAGATAATAAGT
1 ATGAAACTAGCAAGATAATAAGT
2928087 ATGAAACTAGCAAGATAATAAGT
1 ATGAAACTAGCAAGATAATAAGT
2928110 AT
1 AT
2928112 AAGGAATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.52, C:0.08, G:0.17, T:0.23
Consensus pattern (23 bp):
ATGAAACTAGCAAGATAATAAGT
Found at i:2943864 original size:17 final size:17
Alignment explanation
Indices: 2943831--2943870 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 17
2943821 CCCGGCCCAC
2943831 TAAACAAAATAATATAA
1 TAAACAAAATAATATAA
*
2943848 TAAATAAAAT--TA-AA
1 TAAACAAAATAATATAA
2943862 TAAACAAAA
1 TAAACAAAA
2943871 GTCTAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 10 0.48
15 2 0.10
17 9 0.43
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (17 bp):
TAAACAAAATAATATAA
Found at i:2944882 original size:3 final size:3
Alignment explanation
Indices: 2944858--2944960 Score: 65
Period size: 3 Copynumber: 35.7 Consensus size: 3
2944848 TGTGCTTTTG
* * *
2944858 TAT T-T TAT TAT CAT TAT CAT TAT TAT TAT TAT T-T TAT TAT GCA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
* * **
2944901 TAT TAG TAT TAT GATT TAT TAT TA- TAT T-T TAT TAT GCT TAT TAT
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
2944945 TA- TAC CAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
2944961 CAAATTGATG
Statistics
Matches: 75, Mismatches: 17, Indels: 16
0.69 0.16 0.15
Matches are distributed among these distances:
2 11 0.15
3 61 0.81
4 3 0.04
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:2944905 original size:38 final size:36
Alignment explanation
Indices: 2944863--2944960 Score: 117
Period size: 38 Copynumber: 2.6 Consensus size: 36
2944853 TTTTGTATTT
2944863 TATTATCATTATCATTATTATTATTATTTTATTATGCA
1 TATTAT-ATTATCATTATTATTA-TATTTTATTATGCA
* *
2944901 TATTAGTATTATGATTTATTATTATATTTTATTATGCT
1 TATTA-TATTATCA-TTATTATTATATTTTATTATGCA
*
2944939 TATTAT-TATACCATTATTATTA
1 TATTATAT-TATCATTATTATTA
2944961 CAAATTGATG
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
36 10 0.19
37 4 0.08
38 29 0.55
39 10 0.19
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.58
Consensus pattern (36 bp):
TATTATATTATCATTATTATTATATTTTATTATGCA
Found at i:2944910 original size:29 final size:29
Alignment explanation
Indices: 2944858--2944925 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
2944848 TGTGCTTTTG
* *
2944858 TATTTTATTATCATTATCATTATTATTAT
1 TATTTTATTATCATTATCAGTATTATGAT
*
2944887 TATTTTATTATGCA-TATTAGTATTATGAT
1 TATTTTATTAT-CATTATCAGTATTATGAT
*
2944916 T-TATTATTAT
1 TATTTTATTAT
2944926 ATTTTATTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 8 0.24
29 24 0.71
30 2 0.06
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.60
Consensus pattern (29 bp):
TATTTTATTATCATTATCAGTATTATGAT
Found at i:2961675 original size:39 final size:39
Alignment explanation
Indices: 2961614--2961692 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 39
2961604 ACCCTTCATG
* *
2961614 CTGCTGTTGCTGCCGCTACTTTTGCTGCCCCTATTTTCA
1 CTGCTGCTGCCGCCGCTACTTTTGCTGCCCCTATTTTCA
* *
2961653 CTGCTGCTGCCGCTGCTGCTTTTGCTGCCCCTATTTTCA
1 CTGCTGCTGCCGCCGCTACTTTTGCTGCCCCTATTTTCA
2961692 C
1 C
2961693 CATGCATGAG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.06, C:0.35, G:0.19, T:0.39
Consensus pattern (39 bp):
CTGCTGCTGCCGCCGCTACTTTTGCTGCCCCTATTTTCA
Found at i:2961999 original size:16 final size:18
Alignment explanation
Indices: 2961963--2961999 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
2961953 TAGTGTTTTG
*
2961963 TATTTTGTTATAGTTATT
1 TATTTTGTTATAGTAATT
2961981 TATTTTGTTA-A-TAATT
1 TATTTTGTTATAGTAATT
2961997 TAT
1 TAT
2962000 GGGATTAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 1 0.06
18 10 0.56
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (18 bp):
TATTTTGTTATAGTAATT
Found at i:2962214 original size:113 final size:107
Alignment explanation
Indices: 2961980--2962655 Score: 709
Period size: 107 Copynumber: 6.2 Consensus size: 107
2961970 TTATAGTTAT
* *
2961980 TTATTTTGTTAATAATTTATGGGATTAGGTTAC--AAATTGTTAGTGTTTAGTTGTTTAAG-GTA
1 TTATTTTGTTAGTAATTTAT--GATTAGGTTACATAAATTGTTAGTGTTTAGTGGTTT-AGTGTA
* * * * *
2962042 TTGTG-A--TTTTTAGGAATGTAATTTTTTTTAAAAATAATTTTATAG
63 TTATGTATTTTTTTAGTAA--T-ATATATTTAAAAAATAATTTTATAG
* *
2962087 TTATTTTGTTAGTAATTTATGATTAGGTTATAAAAATTGTTAGTGTTTAGTGGTTTAGTGTATTA
1 TTATTTTGTTAGTAATTTATGATTAGGTTACATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTA
**
2962152 GTGTATTGTGGGTTTTTTTAATAATATATTTAAAAAATAATTTTATAG
66 -TGTATT-T---TTTTAGTAAT-ATATATTTAAAAAATAATTTTATAG
* * * *
2962200 CTATTTTATTAGTAATTTATGATTAGGTTACGTAAATTGCTAGTGTTTAGTGGTTTAGTGTATTA
1 TTATTTTGTTAGTAATTTATGATTAGGTTACATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTA
* *
2962265 --TAATTTTTTAGTAATGTAT-TTTAAAAAAAATAATTTTATAG
66 TGTATTTTTTTAGTAATATATATTT--AAAAAATAATTTTATAG
* *
2962306 TTATTTTGTTAGTAATTTATGATTAGGTTAACATAAATTGCTAGTGTTTAGTGGTTCAGTGTATT
1 TTATTTTGTTAGTAATTTATGATTAGGTT-ACATAAATTGTTAGTGTTTAGTGGTTTAGTGTATT
* * *
2962371 ATG-A-TTTTTTAGTAATGTATTTTTTAAAAAA-AA-TTTATAA
65 ATGTATTTTTTTAGTAATATA-TATTTAAAAAATAATTTTATAG
*
2962411 TTATTTTGTTAGTAATTTATGATTAGGTTACATAAATTGTTAGTGTTTAGTGGTTTAGAGTATTA
1 TTATTTTGTTAGTAATTTATGATTAGGTTACATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTA
2962476 GTGTATTGTGATTTTTTAGTAATAATATATTTTTAAAAAATAATTTTATAG
66 -TGTA---T--TTTTTTAGTAAT-ATATA--TTTAAAAAATAATTTTATAG
* * * * *
2962527 CTATTTTATTAGTAATTTATGATTAGATTATATAAATTGTTAGTATTTAGTGGTTTAGTGTATTA
1 TTATTTTGTTAGTAATTTATGATTAGGTTACATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTA
* * *
2962592 TG-A-TTTTTTAGTAATGTAT-TTAAAAATAATAATTTTTTAG
66 TGTATTTTTTTAGTAATATATATTTAAAA-AATAATTTTATAG
2962632 TTATTTTGTGTTAGTAATTTATGA
1 TTA-TTT-TGTTAGTAATTTATGA
2962656 CTATAAATTG
Statistics
Matches: 493, Mismatches: 42, Indels: 68
0.82 0.07 0.11
Matches are distributed among these distances:
104 42 0.09
105 64 0.13
106 60 0.12
107 119 0.24
108 16 0.03
109 5 0.01
110 3 0.01
112 14 0.03
113 85 0.17
114 10 0.02
115 10 0.02
116 65 0.13
ACGTcount: A:0.32, C:0.01, G:0.16, T:0.51
Consensus pattern (107 bp):
TTATTTTGTTAGTAATTTATGATTAGGTTACATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTA
TGTATTTTTTTAGTAATATATATTTAAAAAATAATTTTATAG
Found at i:2962600 original size:327 final size:322
Alignment explanation
Indices: 2961980--2962655 Score: 1002
Period size: 327 Copynumber: 2.1 Consensus size: 322
2961970 TTATAGTTAT
* * * *
2961980 TTATTTTGTTAATAATTTATGGGATTAGGTTACAAATTGTTAGTGTTTAGTTGTTTAAGGTATTG
1 TTATTTTGTTAGTAATTTAT--GATTAGGTTACAAATTGCTAGTGTTTAGTTGGTTAAGGTATTA
* *
2962045 TGATTTTTAGGAATGTAATTTTTTTTAAAAATAATTTTATAGTTATTTTGTTAGTAATTTATGAT
64 TGATTTTTAGGAATGTAA-TTTTTTTAAAAATAAATTTATAATTATTTTGTTAGTAATTTATGAT
* * *
2962110 TAGGTTATAAAAATTGTTAGTGTTTAGTGGTTTAGTGTATTAGTGTATTGTGGGTTTTTTTAATA
128 TAGGTTACAAAAATTGTTAGTGTTTAGTGGTTTAGAGTATTAGTGTATTGTGGATTTTTTTAATA
* *
2962175 ATATATTTAAAAAATAATTTTATAGCTATTTTATTAGTAATTTATGATTAGGTTACGTAAATTGC
193 ATATATTTAAAAAATAATTTTATAGCTATTTTATTAGTAATTTATGATTAGATTACATAAATTGC
*
2962240 TAGTGTTTAGTGGTTTAGTGTATTATAATTTTTTAGTAATGTATTTTAAAAAAAATAATTTTATA
258 TAGTATTTAGTGGTTTAGTGTATTATAATTTTTTAGTAATGTA-TTTAAAAAAAATAATTTTATA
2962305 G
322 G
*
2962306 TTATTTTGTTAGTAATTTATGATTAGGTTAACATAAATTGCTAGTGTTTAG-TGGTTCAGTGTAT
1 TTATTTTGTTAGTAATTTATGATTAGGTT-AC--AAATTGCTAGTGTTTAGTTGGTTAAG-GTAT
*
2962370 TATGATTTTTTAGTAATGT-A-TTTTTTAAAAA-AAATTTATAATTATTTTGTTAGTAATTTATG
62 TATGA-TTTTTAGGAATGTAATTTTTTTAAAAATAAATTTATAATTATTTTGTTAGTAATTTATG
*
2962432 ATTAGGTTACATAAATTGTTAGTGTTTAGTGGTTTAGAGTATTAGTGTATTGT-GATTTTTTAGT
126 ATTAGGTTACAAAAATTGTTAGTGTTTAGTGGTTTAGAGTATTAGTGTATTGTGGATTTTTT--T
*
2962496 AATAATATATTTTTAAAAAATAATTTTATAGCTATTTTATTAGTAATTTATGATTAGATTATATA
189 AATAATATA--TTTAAAAAATAATTTTATAGCTATTTTATTAGTAATTTATGATTAGATTACATA
* * *
2962561 AATTGTTAGTATTTAGTGGTTTAGTGTATTATGATTTTTTAGTAATGTATTTAAAAATAATAATT
252 AATTGCTAGTATTTAGTGGTTTAGTGTATTATAATTTTTTAGTAATGTATTTAAAAAAAATAATT
*
2962626 TTTTAG
317 TTATAG
2962632 TTATTTTGTGTTAGTAATTTATGA
1 TTA-TTT-TGTTAGTAATTTATGA
2962656 CTATAAATTG
Statistics
Matches: 319, Mismatches: 20, Indels: 20
0.89 0.06 0.06
Matches are distributed among these distances:
323 7 0.02
324 88 0.28
325 23 0.07
326 48 0.15
327 125 0.39
328 28 0.09
ACGTcount: A:0.32, C:0.01, G:0.16, T:0.51
Consensus pattern (322 bp):
TTATTTTGTTAGTAATTTATGATTAGGTTACAAATTGCTAGTGTTTAGTTGGTTAAGGTATTATG
ATTTTTAGGAATGTAATTTTTTTAAAAATAAATTTATAATTATTTTGTTAGTAATTTATGATTAG
GTTACAAAAATTGTTAGTGTTTAGTGGTTTAGAGTATTAGTGTATTGTGGATTTTTTTAATAATA
TATTTAAAAAATAATTTTATAGCTATTTTATTAGTAATTTATGATTAGATTACATAAATTGCTAG
TATTTAGTGGTTTAGTGTATTATAATTTTTTAGTAATGTATTTAAAAAAAATAATTTTATAG
Found at i:2962612 original size:220 final size:218
Alignment explanation
Indices: 2961980--2962655 Score: 775
Period size: 220 Copynumber: 3.1 Consensus size: 218
2961970 TTATAGTTAT
* *
2961980 TTATTTTGTTAATAATTTATGGGATTAGGTTAC-AAATTGTTAGTGTTTAGTTG-TT---TA--A
1 TTATTTTGTTAGTAATTTAT--GATTAGGTTACTAAATTGTTAGTGTTTAGTGGTTTAGGTATTA
* *
2962038 GGTATTGTGA-TTTTTAGGAATGTAAT-TTTTTTTAAAAATAATTTTATAGTTATTTTGTTAGTA
64 GGTATTGTGATTTTTTAGTAA--TAATATTTTTTAAAAAATAATTTTATAGTTATTTTGTTAGTA
*
2962101 ATTTATGATTAGGTTATAAAAATTGTTAGTGTTTAGTGGTTTAGTGTATTAGTGTATTGTGGGTT
127 ATTTATGATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTA-TG-A-T-T---TT
** * *
2962166 TTTTTAAT-AATATATTTAAAAAATAATTTTATAG
185 TTAGTAATGTAT-TTTTTAAAAAATAATTTTATAG
* * *
2962200 CTATTTTATTAGTAATTTATGATTAGGTTACGTAAATTGCTAGTGTTTAGTGGTTTAGTGTATTA
1 TTATTTTGTTAGTAATTTATGATTAGGTTAC-TAAATTGTTAGTGTTTAGTGGTTTAG-GTATTA
* **
2962265 --TA-----ATTTTTTAGTAAT-GTATTTTAAAAAAAATAATTTTATAGTTATTTTGTTAGTAAT
64 GGTATTGTGATTTTTTAGTAATAATATTTTTTAAAAAATAATTTTATAGTTATTTTGTTAGTAAT
* * *
2962322 TTATGATTAGGTTAACATAAATTGCTAGTGTTTAGTGGTTCAGTGTATTATGATTTTTTAGTAAT
129 TTATGATTAGGTT-ATATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTATGATTTTTTAGTAAT
*
2962387 GTATTTTTTAAAAAA-AA-TTTATAA
193 GTATTTTTTAAAAAATAATTTTATAG
2962411 TTATTTTGTTAGTAATTTATGATTAGGTTACATAAATTGTTAGTGTTTAGTGGTTTAGAGTATTA
1 TTATTTTGTTAGTAATTTATGATTAGGTTAC-TAAATTGTTAGTGTTTAGTGGTTTAG-GTATTA
* *
2962476 GTGTATTGTGATTTTTTAGTAATAATATATTTTTAAAAAATAATTTTATAGCTATTTTATTAGTA
64 G-GTATTGTGATTTTTTAGTAATAATAT-TTTTTAAAAAATAATTTTATAGTTATTTTGTTAGTA
* *
2962541 ATTTATGATTAGATTATATAAATTGTTAGTATTTAGTGGTTTAGTGTATTATGATTTTTTAGTAA
127 ATTTATGATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTATGATTTTTTAGTAA
* *
2962606 TGTA--TTTAAAAATAATAATTTTTTAG
192 TGTATTTTTTAAAA-AATAATTTTATAG
2962632 TTATTTTGTGTTAGTAATTTATGA
1 TTA-TTT-TGTTAGTAATTTATGA
2962656 CTATAAATTG
Statistics
Matches: 391, Mismatches: 37, Indels: 53
0.81 0.08 0.11
Matches are distributed among these distances:
211 66 0.17
212 2 0.01
213 18 0.05
214 4 0.01
216 1 0.00
217 1 0.00
218 20 0.05
219 67 0.17
220 123 0.31
221 65 0.17
222 3 0.01
223 16 0.04
225 4 0.01
227 1 0.00
ACGTcount: A:0.32, C:0.01, G:0.16, T:0.51
Consensus pattern (218 bp):
TTATTTTGTTAGTAATTTATGATTAGGTTACTAAATTGTTAGTGTTTAGTGGTTTAGGTATTAGG
TATTGTGATTTTTTAGTAATAATATTTTTTAAAAAATAATTTTATAGTTATTTTGTTAGTAATTT
ATGATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTATGATTTTTTAGTAATGTA
TTTTTTAAAAAATAATTTTATAG
Found at i:2962725 original size:100 final size:98
Alignment explanation
Indices: 2962232--2962735 Score: 231
Period size: 107 Copynumber: 4.8 Consensus size: 98
2962222 TTAGGTTACG
* * * * *
2962232 TAAATTGCTAGTGTTTAGTGGTTTAGTGTATTATAATTTTTTAGTAATGTATTTTAAAAAAAATA
1 TAAATTGTTAGTATTTAGTAGTTTAGTGTATTATGATTTTTTA-TAATGTA-TTTAAAAATAATA
*
2962297 ATTTTATAGTTA-TTT-TGTTAGTAATTTATGATTAGGTTAACA
64 ATTTTATA-TTATTTTGTGTTAGTAATTTATG---A--CT---A
* * * * *
2962339 TAAATTGCTAGTGTTTAGTGGTTCAGTGTATTATGATTTTTTAGTAATGTATTTTTTAAAA-AA-
1 TAAATTGTTAGTATTTAGTAGTTTAGTGTATTATGATTTTTTA-TAATGTA--TTTAAAAATAAT
*
2962402 AA-TTTATAATTA-TTT-TGTTAGTAATTTATGATTAGGTTACA
63 AATTTTAT-ATTATTTTGTGTTAGTAATTTATG---A--CT--A
* * *
2962443 TAAATTGTTAGTGTTTAGTGGTTTAGAGTATTAGTGTATTGTGATTTTTTAGTAATAATATATTT
1 TAAATTGTTAGTATTTA---G--T--AGT-TTAGTGTATTATGA-TTTTT--T-ATAATGTATTT
** * * * *
2962508 TTAAAAAATAATTTTATAGCTA-TTT-TATTAGTAATTTATGATTAGATTATA
54 AAAAATAATAATTTTATA-TTATTTTGTGTTAGTAA-TT-T-A-T-GA--CTA
*
2962559 TAAATTGTTAGTATTTAGTGGTTTAGTGTATTATGATTTTTTAGTAATGTATTTAAAAATAATAA
1 TAAATTGTTAGTATTTAGTAGTTTAGTGTATTATGATTTTTTA-TAATGTATTTAAAAATAATAA
*
2962624 TTTTTTAGTTATTTTGTGTTAGTAATTTATGACTA
65 TTTTATA-TTATTTTGTGTTAGTAATTTATGACTA
* * * ** *
2962659 TAAATTGTTTA-TGTTTA-TAGTTTAGTGTTTTGTGATTTTTT-TAATGTAATTTTTATATAATG
1 TAAATTG-TTAGTATTTAGTAGTTTAGTGTATTATGATTTTTTATAATGT-ATTTAAAAATAA--
2962721 TAATTTTATATTATT
62 TAATTTTATATTATT
2962736 ATTTATTTTA
Statistics
Matches: 334, Mismatches: 33, Indels: 68
0.77 0.08 0.16
Matches are distributed among these distances:
97 6 0.02
98 9 0.03
99 26 0.08
100 23 0.07
101 3 0.01
102 2 0.01
103 1 0.00
104 21 0.06
105 62 0.19
106 8 0.02
107 65 0.19
108 21 0.06
109 3 0.01
111 3 0.01
112 12 0.04
113 13 0.04
114 2 0.01
115 10 0.03
116 36 0.11
117 2 0.01
118 3 0.01
119 1 0.00
120 1 0.00
121 1 0.00
ACGTcount: A:0.32, C:0.01, G:0.14, T:0.52
Consensus pattern (98 bp):
TAAATTGTTAGTATTTAGTAGTTTAGTGTATTATGATTTTTTATAATGTATTTAAAAATAATAAT
TTTATATTATTTTGTGTTAGTAATTTATGACTA
Found at i:2962727 original size:15 final size:16
Alignment explanation
Indices: 2962700--2962731 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
2962690 GTGATTTTTT
2962700 TAATGTAATTTTTATA
1 TAATGTAATTTTTATA
2962716 TAATGTAA-TTTTATA
1 TAATGTAATTTTTATA
2962731 T
1 T
2962732 TATTATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
TAATGTAATTTTTATA
Found at i:2962737 original size:23 final size:23
Alignment explanation
Indices: 2962711--2962760 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
2962701 AATGTAATTT
2962711 TTATATAATGTAATTTTATATTA
1 TTATATAATGTAATTTTATATTA
* * *
2962734 TTATTTATTTTAATTTTATATTA
1 TTATATAATGTAATTTTATATTA
2962757 TTAT
1 TTAT
2962761 TTATTTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (23 bp):
TTATATAATGTAATTTTATATTA
Found at i:2962739 original size:13 final size:13
Alignment explanation
Indices: 2962709--2962762 Score: 51
Period size: 15 Copynumber: 4.2 Consensus size: 13
2962699 TTAATGTAAT
*
2962709 TTTTATATAATGTAA
1 TTTTATATTAT-T-A
2962724 TTTTATATTATTA
1 TTTTATATTATTA
*
2962737 -TTTAT-TT-TAA
1 TTTTATATTATTA
2962747 TTTTATATTATTA
1 TTTTATATTATTA
2962760 TTT
1 TTT
2962763 ATTTATTTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
10 2 0.06
11 7 0.21
12 7 0.21
13 6 0.18
14 1 0.03
15 10 0.30
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (13 bp):
TTTTATATTATTA
Found at i:2962761 original size:23 final size:23
Alignment explanation
Indices: 2962721--2962766 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
2962711 TTATATAATG
2962721 TAATTTTATATTATTATTTATTT
1 TAATTTTATATTATTATTTATTT
2962744 TAATTTTATATTATTATTTATTT
1 TAATTTTATATTATTATTTATTT
2962767 ATTTGATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (23 bp):
TAATTTTATATTATTATTTATTT
Found at i:2962768 original size:11 final size:12
Alignment explanation
Indices: 2962725--2962769 Score: 58
Period size: 11 Copynumber: 3.9 Consensus size: 12
2962715 ATAATGTAAT
2962725 TTTATATTATTA
1 TTTATATTATTA
* *
2962737 TTTATTTTAAT-
1 TTTATATTATTA
2962748 TTTATATTATTA
1 TTTATATTATTA
2962760 TTTAT-TTATT
1 TTTATATTATT
2962770 TGATAATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
11 14 0.50
12 14 0.50
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTATATTATTA
Found at i:2962781 original size:30 final size:26
Alignment explanation
Indices: 2962729--2962784 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 26
2962719 TGTAATTTTA
2962729 TATTATTATTTATTTTAATTTTATAT
1 TATTATTATTTATTTTAATTTTATAT
2962755 TATTATTTATTTATTTGATAATTTT-TAT
1 TATTA-TTATTTATTT--TAATTTTATAT
2962783 TA
1 TA
2962785 ATTTATTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
26 5 0.19
27 10 0.37
28 5 0.19
29 7 0.26
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (26 bp):
TATTATTATTTATTTTAATTTTATAT
Found at i:2964902 original size:33 final size:34
Alignment explanation
Indices: 2964827--2964921 Score: 106
Period size: 33 Copynumber: 2.9 Consensus size: 34
2964817 CAATACTCTG
**
2964827 GCCCGTATCCACCATCGTACTCTACT-CTTCTAAA
1 GCCCGTATCCACCGCCGTACTCTACTCCTTC-AAA
* *
2964861 G-CCATATCCACCGCCGTACTCTACTCCTTC-CA
1 GCCCGTATCCACCGCCGTACTCTACTCCTTCAAA
**
2964893 GCCCGTATCCACCGCCGTGTTCTACTCCT
1 GCCCGTATCCACCGCCGTACTCTACTCCT
2964922 CTTGACTCAA
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
32 2 0.04
33 45 0.87
34 5 0.10
ACGTcount: A:0.18, C:0.43, G:0.12, T:0.27
Consensus pattern (34 bp):
GCCCGTATCCACCGCCGTACTCTACTCCTTCAAA
Found at i:2970183 original size:25 final size:23
Alignment explanation
Indices: 2970157--2970201 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2970147 TATACTAAAT
* *
2970157 ATATATATTTTTTATTTTTAATC
1 ATATTTATATTTTATTTTTAATC
2970180 ATATTTATATTTTATTTTTAAT
1 ATATTTATATTTTATTTTTAAT
2970202 TTTAATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (23 bp):
ATATTTATATTTTATTTTTAATC
Found at i:2970198 original size:29 final size:27
Alignment explanation
Indices: 2970165--2970219 Score: 74
Period size: 29 Copynumber: 2.0 Consensus size: 27
2970155 ATATATATAT
* *
2970165 TTTTTATTTTTAATCATATTTATATTTTA
1 TTTTTAATTTTAAT-ATAATTA-ATTTTA
2970194 TTTTTAATTTTAATATAATTAATTTT
1 TTTTTAATTTTAATATAATTAATTTT
2970220 TATTATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 5 0.21
28 6 0.25
29 13 0.54
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (27 bp):
TTTTTAATTTTAATATAATTAATTTTA
Found at i:2970285 original size:28 final size:29
Alignment explanation
Indices: 2970253--2970328 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 29
2970243 TGTTTTAAGA
*
2970253 ATTGTTTTAATATATTTTTT-ATTTATTT
1 ATTGTTTTAATATATTTTTTAATGTATTT
*
2970281 CTTGTTTTAATAT-TTATTTTAAATGTATTT
1 ATTGTTTTAATATATT-TTTT-AATGTATTT
* *
2970311 AATGATTTAATATATTTT
1 ATTGTTTTAATATATTTT
2970329 AAATTTTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
27 2 0.05
28 16 0.41
30 19 0.49
31 2 0.05
ACGTcount: A:0.29, C:0.01, G:0.05, T:0.64
Consensus pattern (29 bp):
ATTGTTTTAATATATTTTTTAATGTATTT
Found at i:2970339 original size:28 final size:28
Alignment explanation
Indices: 2970258--2970339 Score: 83
Period size: 28 Copynumber: 2.9 Consensus size: 28
2970248 TAAGAATTGT
** ** *
2970258 TTTAATATATTTTTTATTTATTTCTTGT
1 TTTAATATATTTTAAATTTATTTAATGA
*
2970286 TTTAATATTTATTTTAAATGTATTTAATGA
1 TTTAATA--TATTTTAAATTTATTTAATGA
*
2970316 TTTAATATATTTTAAATTTTTTTA
1 TTTAATATATTTTAAATTTATTTA
2970340 TTTAATGAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
28 22 0.50
30 22 0.50
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.65
Consensus pattern (28 bp):
TTTAATATATTTTAAATTTATTTAATGA
Found at i:2970787 original size:36 final size:37
Alignment explanation
Indices: 2970747--2970841 Score: 88
Period size: 36 Copynumber: 2.6 Consensus size: 37
2970737 TTGAGTGACT
2970747 TTTTAAAAATTTTAAATTA-ATAAAATTAAAATT-ATA
1 TTTTAAAAATTTTAAATTATA-AAAATTAAAATTAATA
** * * *
2970783 TTTT-AACCTCTTAAAATTATAAAAATTTAATTTAATA
1 TTTTAAAAAT-TTTAAATTATAAAAATTAAAATTAATA
*
2970820 TTTTAAAAATTATAAATATATA
1 TTTTAAAAATTTTAAAT-TATA
2970842 TACTATAAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
35 3 0.07
36 22 0.49
37 13 0.29
38 7 0.16
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (37 bp):
TTTTAAAAATTTTAAATTATAAAAATTAAAATTAATA
Found at i:2970816 original size:29 final size:31
Alignment explanation
Indices: 2970774--2970835 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 31
2970764 TAATAAAATT
* *
2970774 AAAATTATATTTTAACCTCTT-AAAATTATA
1 AAAATTATAATTTAACATCTTAAAAATTATA
* *
2970804 AAAATT-TAATTTAATATTTTAAAAATTATA
1 AAAATTATAATTTAACATCTTAAAAATTATA
2970834 AA
1 AA
2970836 TATATATACT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.44
Consensus pattern (31 bp):
AAAATTATAATTTAACATCTTAAAAATTATA
Found at i:2970919 original size:19 final size:19
Alignment explanation
Indices: 2970878--2970918 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
2970868 GTACTCCTAC
2970878 AAAATAGATATTAATATAA
1 AAAATAGATATTAATATAA
*
2970897 AAAATGGATA-TAATATAA
1 AAAATAGATATTAATATAA
2970915 AAAA
1 AAAA
2970919 AAGTTGGGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (19 bp):
AAAATAGATATTAATATAA
Found at i:2974049 original size:25 final size:25
Alignment explanation
Indices: 2974015--2974066 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
2974005 TAGGAGAATA
2974015 TGTCTGACTTCAAAAATAATGTAGT
1 TGTCTGACTTCAAAAATAATGTAGT
2974040 TGTCTGACTTCAAAAATAATGTAGT
1 TGTCTGACTTCAAAAATAATGTAGT
2974065 TG
1 TG
2974067 CTTGTGGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.37
Consensus pattern (25 bp):
TGTCTGACTTCAAAAATAATGTAGT
Found at i:2976941 original size:29 final size:29
Alignment explanation
Indices: 2976899--2976958 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
2976889 GGCGTTGATA
2976899 TTCTTCTACCGTCCCAGTTTGTCTCAAGT
1 TTCTTCTACCGTCCCAGTTTGTCTCAAGT
*
2976928 TTCTTCTACGGTCCCAGTTTGTCTCAAGT
1 TTCTTCTACCGTCCCAGTTTGTCTCAAGT
2976957 TT
1 TT
2976959 GCAAGTTCTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.13, C:0.28, G:0.15, T:0.43
Consensus pattern (29 bp):
TTCTTCTACCGTCCCAGTTTGTCTCAAGT
Found at i:3005270 original size:28 final size:29
Alignment explanation
Indices: 3005213--3005270 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
3005203 TCACTCAAAC
*
3005213 ATCGAGAAATCTTAAGTTAAAATTCGGTG
1 ATCGAGAAATCTTAAGTTAAAATTCAGTG
3005242 ATCGAGAAATCTTAA-TTAAAATTCAGTG
1 ATCGAGAAATCTTAAGTTAAAATTCAGTG
3005270 A
1 A
3005271 AAATAACGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 13 0.46
29 15 0.54
ACGTcount: A:0.41, C:0.10, G:0.17, T:0.31
Consensus pattern (29 bp):
ATCGAGAAATCTTAAGTTAAAATTCAGTG
Found at i:3006458 original size:5 final size:5
Alignment explanation
Indices: 3006448--3006473 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
3006438 TAAATAAATC
3006448 TTTAT TTTAT TTTAT TTTAT TTTAT T
1 TTTAT TTTAT TTTAT TTTAT TTTAT T
3006474 GCAAATTTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:3014406 original size:48 final size:48
Alignment explanation
Indices: 3014325--3014488 Score: 220
Period size: 48 Copynumber: 3.4 Consensus size: 48
3014315 TGACAACATG
* * ** * *
3014325 TGATTTGTGGTTTCCGTATAAGATTATATCTGGGATATGGCATCGGTA
1 TGATATGTGATTTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTA
3014373 TGATATGTGATTTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTA
1 TGATATGTGATTTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTA
* * * *
3014421 TGATATGTAATTTCCGTATAAGACCATAGTTGGGCTATGGCATTGGTG
1 TGATATGTGATTTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTA
* *
3014469 TGATACGTGATTCCCGTATA
1 TGATATGTGATTTCCGTATA
3014489 GATGATGGAT
Statistics
Matches: 103, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 103 1.00
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.35
Consensus pattern (48 bp):
TGATATGTGATTTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTA
Found at i:3015247 original size:25 final size:25
Alignment explanation
Indices: 3015213--3015263 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
3015203 GTTTTGCTTT
3015213 ATAGCAAGCACAATATAACAACCAA
1 ATAGCAAGCACAATATAACAACCAA
3015238 ATAGCAAGCACAATATAACAACCAA
1 ATAGCAAGCACAATATAACAACCAA
3015263 A
1 A
3015264 CATTTGATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.57, C:0.24, G:0.08, T:0.12
Consensus pattern (25 bp):
ATAGCAAGCACAATATAACAACCAA
Found at i:3017311 original size:21 final size:21
Alignment explanation
Indices: 3017286--3017326 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3017276 ATTAGTTGAG
3017286 AAATTT-ACACATTAAATGTGT
1 AAATTTAACACATT-AATGTGT
*
3017307 AAATTTAACAGATTAATGTG
1 AAATTTAACACATTAATGTG
3017327 ATCATAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (21 bp):
AAATTTAACACATTAATGTGT
Found at i:3022344 original size:15 final size:15
Alignment explanation
Indices: 3022324--3022380 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
3022314 ATTCAATACT
3022324 AATATTTTAATAATA
1 AATATTTTAATAATA
*
3022339 AATATTTATTAAAATTATA
1 AATA-TT-TT--AATAATA
*
3022358 AATATATTAATAATA
1 AATATTTTAATAATA
*
3022373 AATGTTTT
1 AATATTTT
3022381 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:3022362 original size:34 final size:35
Alignment explanation
Indices: 3022289--3022375 Score: 97
Period size: 34 Copynumber: 2.5 Consensus size: 35
3022279 ATTCCAATTT
*
3022289 TATTTTAATAATAAATTTAAATAATATTCAATACTAA
1 TATTTTAATAATAAATTTAAATAAAATT-AATAC-AA
* *
3022326 TATTTTAATAATAAATATTTATTAAAATT-ATA-AA
1 TATTTTAATAATAAAT-TTAAATAAAATTAATACAA
*
3022360 TATATTAATAATAAAT
1 TATTTTAATAATAAAT
3022376 GTTTTGTAGT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
34 17 0.38
36 3 0.07
37 16 0.36
38 9 0.20
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (35 bp):
TATTTTAATAATAAATTTAAATAAAATTAATACAA
Found at i:3022616 original size:20 final size:21
Alignment explanation
Indices: 3022577--3022619 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3022567 CATCCAAACA
3022577 CAAAAAAAAAATTAACTTTTT
1 CAAAAAAAAAATTAACTTTTT
3022598 CAAAAAAATAAATT-A-TTTTT
1 CAAAAAAA-AAATTAACTTTTT
3022618 CA
1 CA
3022620 GAAATTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.33
21 9 0.43
22 5 0.24
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (21 bp):
CAAAAAAAAAATTAACTTTTT
Found at i:3024073 original size:12 final size:12
Alignment explanation
Indices: 3024056--3024120 Score: 64
Period size: 12 Copynumber: 5.5 Consensus size: 12
3024046 GCGTAAGCCA
3024056 TTATAATAATTT
1 TTATAATAATTT
*
3024068 TTATAATAATAT
1 TTATAATAATTT
* *
3024080 ATATAAT-TTTT
1 TTATAATAATTT
3024091 TTATAAT--TTT
1 TTATAATAATTT
3024101 TTATAATATTATTT
1 TTATAATA--ATTT
3024115 TTATAA
1 TTATAA
3024121 ATGTACTAGC
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
10 10 0.23
11 8 0.18
12 17 0.39
14 9 0.20
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTATAATAATTT
Found at i:3024115 original size:24 final size:24
Alignment explanation
Indices: 3024056--3024120 Score: 66
Period size: 23 Copynumber: 2.8 Consensus size: 24
3024046 GCGTAAGCCA
3024056 TTATAATA--ATTTTTATAATAAT
1 TTATAATATTATTTTTATAATAAT
* **
3024078 ATAT-ATAATT-TTTTTATAATTTT
1 TTATAAT-ATTATTTTTATAATAAT
3024101 TTATAATATTATTTTTATAA
1 TTATAATATTATTTTTATAA
3024121 ATGTACTAGC
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
21 2 0.06
22 4 0.12
23 17 0.50
24 11 0.32
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TTATAATATTATTTTTATAATAAT
Found at i:3024210 original size:16 final size:16
Alignment explanation
Indices: 3024158--3024211 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 16
3024148 CATTATAGGT
*
3024158 TTTTATATATTTAGATA
1 TTTTATA-ATTTATATA
3024175 TTTTAATAAATTTATA-A
1 TTTT-AT-AATTTATATA
3024192 TTTTATAATTTATATA
1 TTTTATAATTTATATA
3024208 TTTT
1 TTTT
3024212 TCAAAATAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
15 8 0.24
16 7 0.21
17 9 0.27
18 8 0.24
19 1 0.03
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (16 bp):
TTTTATAATTTATATA
Found at i:3024212 original size:17 final size:17
Alignment explanation
Indices: 3024157--3024212 Score: 62
Period size: 18 Copynumber: 3.3 Consensus size: 17
3024147 GCATTATAGG
*
3024157 TTTTTATATATTTAGATA
1 TTTTTATA-ATTTATATA
*
3024175 TTTTAATAAATTTATA-A
1 TTTTTAT-AATTTATATA
3024192 -TTTTATAATTTATATA
1 TTTTTATAATTTATATA
3024208 TTTTT
1 TTTTT
3024213 CAAAATAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
15 8 0.25
16 6 0.19
17 5 0.16
18 12 0.38
19 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (17 bp):
TTTTTATAATTTATATA
Found at i:3039788 original size:27 final size:29
Alignment explanation
Indices: 3039731--3039790 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 29
3039721 ATCCTTTCCA
3039731 ATAATATAATATAATTAATTTATTAAATT
1 ATAATATAATATAATTAATTTATTAAATT
3039760 ATAATTATAA-AT-ATTAA-TTA-TAAATTT
1 ATAA-TATAATATAATTAATTTATTAAA-TT
3039787 ATAA
1 ATAA
3039791 CACAATAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
26 4 0.14
27 9 0.31
28 5 0.17
29 6 0.21
30 5 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
ATAATATAATATAATTAATTTATTAAATT
Found at i:3051128 original size:15 final size:15
Alignment explanation
Indices: 3051105--3051140 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
3051095 TTTATTTAAA
*
3051105 ATTTAAAAATAAATT
1 ATTTCAAAATAAATT
3051120 ATTTCAAAATAAATT
1 ATTTCAAAATAAATT
3051135 ATTTCA
1 ATTTCA
3051141 TTTTATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (15 bp):
ATTTCAAAATAAATT
Found at i:3051771 original size:22 final size:24
Alignment explanation
Indices: 3051746--3051801 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 24
3051736 AATTAAATTG
3051746 TATATTTTTACTACTATAA-A-AA
1 TATATTTTTACTACTATAATAGAA
* * * *
3051768 TATAATTTTATTATTATAATAGCA
1 TATATTTTTACTACTATAATAGAA
3051792 TATATTTTTA
1 TATATTTTTA
3051802 TAAATTTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 16 0.59
23 1 0.04
24 10 0.37
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (24 bp):
TATATTTTTACTACTATAATAGAA
Found at i:3051892 original size:17 final size:18
Alignment explanation
Indices: 3051853--3051894 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
3051843 GCTAAAGTTC
* *
3051853 TATATAATTATTATTAAT
1 TATAAAATTATTATAAAT
3051871 T-TAAAATT-TTATAAAT
1 TATAAAATTATTATAAAT
3051887 TATAAAAT
1 TATAAAAT
3051895 GCCTAAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 8 0.38
17 12 0.57
18 1 0.05
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TATAAAATTATTATAAAT
Found at i:3071245 original size:23 final size:23
Alignment explanation
Indices: 3071177--3071263 Score: 110
Period size: 21 Copynumber: 4.0 Consensus size: 23
3071167 CCTGATCAGT
*
3071177 ATACGACACATAAAGTGCCT-AA
1 ATACGACACATGAAGTGCCTGAA
*
3071199 A-ACGACACATGAGGTGCCTG--
1 ATACGACACATGAAGTGCCTGAA
* *
3071219 ATACGACACACGAGGTGCCTGAA
1 ATACGACACATGAAGTGCCTGAA
3071242 ATACGACACATGAAGTGCCTGA
1 ATACGACACATGAAGTGCCTGA
3071264 TCGATAAAGC
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
20 1 0.02
21 34 0.61
22 1 0.02
23 20 0.36
ACGTcount: A:0.37, C:0.24, G:0.23, T:0.16
Consensus pattern (23 bp):
ATACGACACATGAAGTGCCTGAA
Found at i:3071260 original size:44 final size:42
Alignment explanation
Indices: 3071177--3071264 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 42
3071167 CCTGATCAGT
* *
3071177 ATACGACACATAAAGTGCCTAAAACGACACATGAGGTGCCTG
1 ATACGACACACAAAGTGCCTAAAACGACACATGAAGTGCCTG
* *
3071219 ATACGACACACGAGGTGCCTGAAATACGACACATGAAGTGCCTG
1 ATACGACACACAAAGTGCCT-AAA-ACGACACATGAAGTGCCTG
3071263 AT
1 AT
3071265 CGATAAAGCC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 17 0.43
43 3 0.08
44 20 0.50
ACGTcount: A:0.36, C:0.24, G:0.23, T:0.17
Consensus pattern (42 bp):
ATACGACACACAAAGTGCCTAAAACGACACATGAAGTGCCTG
Found at i:3092086 original size:19 final size:19
Alignment explanation
Indices: 3092044--3092088 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
3092034 ATTAAACAAT
*
3092044 AACAACAAAACAGTATAAT
1 AACAACAAAACAGTATAAA
*
3092063 GACAACAAAACAGTA-AGAA
1 AACAACAAAACAGTATA-AA
3092082 AACAACA
1 AACAACA
3092089 GTAAAATAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 1 0.05
19 21 0.95
ACGTcount: A:0.64, C:0.18, G:0.09, T:0.09
Consensus pattern (19 bp):
AACAACAAAACAGTATAAA
Found at i:3104475 original size:18 final size:18
Alignment explanation
Indices: 3104452--3104489 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
3104442 CTATTAAATA
3104452 GCCTGAAATCTCAAACCT
1 GCCTGAAATCTCAAACCT
3104470 GCCTGAAATCTCAAACCT
1 GCCTGAAATCTCAAACCT
3104488 GC
1 GC
3104490 TATGTGGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.34, G:0.13, T:0.21
Consensus pattern (18 bp):
GCCTGAAATCTCAAACCT
Found at i:3106009 original size:18 final size:18
Alignment explanation
Indices: 3105973--3106011 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3105963 AGGTAAGCTA
3105973 ATTGGCGCAAAATCTCTT
1 ATTGGCGCAAAATCTCTT
*
3105991 ATTGG-GCAAACTCTACTT
1 ATTGGCGCAAAATCT-CTT
3106009 ATT
1 ATT
3106012 ACCCCCCCCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (18 bp):
ATTGGCGCAAAATCTCTT
Found at i:3107416 original size:16 final size:15
Alignment explanation
Indices: 3107392--3107446 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 15
3107382 ATAAAATTTT
3107392 AATTA-ATTAATATAA
1 AATTATATTAA-ATAA
*
3107407 AATTATATTAAATTA
1 AATTATATTAAATAA
*
3107422 AATTTTAATTAAATAA
1 AATTAT-ATTAAATAA
3107438 TAATT-TATT
1 -AATTATATT
3107447 TAAAAGCTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
15 16 0.47
16 14 0.41
17 4 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTATATTAAATAA
Found at i:3107420 original size:21 final size:20
Alignment explanation
Indices: 3107378--3107424 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
3107368 TTCTAAATTT
*
3107378 TTAAATAAAATTTTAATTAA
1 TTAAATAAAATTATAATTAA
3107398 TTAATATAAAATTAT-ATTAAA
1 TTAA-ATAAAATTATAATT-AA
3107419 TTAAAT
1 TTAAAT
3107425 TTTAATTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTAAATAAAATTATAATTAA
Found at i:3107514 original size:70 final size:70
Alignment explanation
Indices: 3107432--3107575 Score: 270
Period size: 70 Copynumber: 2.1 Consensus size: 70
3107422 AATTTTAATT
*
3107432 AAATAATAATTTATTTAAAAGCTTTATTTTTTAAATGTTGTAATAATATTAATACATTTTGTTAA
1 AAATAATAATTTATTTAAAAGCTTTATTTTTTAAATGTTGTAATAATATTAATACATTTTATTAA
3107497 TTATG
66 TTATG
*
3107502 AAATAATCATTTATTTAAAAGCTTTATTTTTTAAATGTTGTAATAATATTAATACATTTTATTAA
1 AAATAATAATTTATTTAAAAGCTTTATTTTTTAAATGTTGTAATAATATTAATACATTTTATTAA
3107567 TTATG
66 TTATG
3107572 AAAT
1 AAAT
3107576 TAAATCTATC
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 72 1.00
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.49
Consensus pattern (70 bp):
AAATAATAATTTATTTAAAAGCTTTATTTTTTAAATGTTGTAATAATATTAATACATTTTATTAA
TTATG
Found at i:3107876 original size:60 final size:59
Alignment explanation
Indices: 3107812--3107929 Score: 130
Period size: 60 Copynumber: 2.0 Consensus size: 59
3107802 CTATGTACCT
* * *
3107812 TGAAGG-ATATTTCCTTCAAGGTACATAGAATTAGGATCAAATTGATAGAATTTGTAAACG
1 TGAAGGCATATTT-ATTCAA-GTACATAGAATTAAGATCAAATTGATAGAATATGTAAACG
* * ** *
3107872 TGAAGGTCATATTTATTGAATTATTTAGAATTAAGATCAAATTGATGGAATATGTAAA
1 TGAAGG-CATATTTATTCAAGTACATAGAATTAAGATCAAATTGATAGAATATGTAAA
3107930 TATTGAAGAC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
60 38 0.79
61 4 0.08
62 6 0.12
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.35
Consensus pattern (59 bp):
TGAAGGCATATTTATTCAAGTACATAGAATTAAGATCAAATTGATAGAATATGTAAACG
Found at i:3111395 original size:5 final size:5
Alignment explanation
Indices: 3111385--3111409 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3111375 TATATATATG
3111385 TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA
3111410 AAGGAACGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:3111848 original size:4 final size:5
Alignment explanation
Indices: 3111821--3111845 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3111811 GGGACGACTA
3111821 TATTT TATTT TATTT TATTT TATTT
1 TATTT TATTT TATTT TATTT TATTT
3111846 ATTAATAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TATTT
Found at i:3112947 original size:40 final size:40
Alignment explanation
Indices: 3112899--3112980 Score: 137
Period size: 40 Copynumber: 2.0 Consensus size: 40
3112889 GTACATTGAC
* *
3112899 CAATATAAATCATTTTAGCACTTCAATGAACAATATAAAA
1 CAATATAAATCATTTTAGAACTTCAATGAACAAAATAAAA
*
3112939 CAATATAAATCATTTTAGAACTTCAATGAGCAAAATAAAA
1 CAATATAAATCATTTTAGAACTTCAATGAACAAAATAAAA
3112979 CA
1 CA
3112981 TACTTTTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.51, C:0.15, G:0.06, T:0.28
Consensus pattern (40 bp):
CAATATAAATCATTTTAGAACTTCAATGAACAAAATAAAA
Found at i:3113590 original size:20 final size:20
Alignment explanation
Indices: 3113565--3113602 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3113555 GACATGGCAA
*
3113565 TGTTGACCAATGATATGGTG
1 TGTTGACCAATGACATGGTG
*
3113585 TGTTGACCGATGACATGG
1 TGTTGACCAATGACATGG
3113603 CACATTGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.13, G:0.32, T:0.32
Consensus pattern (20 bp):
TGTTGACCAATGACATGGTG
Found at i:3113702 original size:24 final size:24
Alignment explanation
Indices: 3113657--3113727 Score: 61
Period size: 24 Copynumber: 2.8 Consensus size: 24
3113647 TGACCAGTAA
**
3113657 AAAAAAATAAAAAATTTTAAAATT
1 AAAAAAATAAAAAATTAAAAAATT
**
3113681 AAAAAAATTTAAAATTAAAAAAATT
1 AAAAAAATAAAAAATT-AAAAAATT
3113706 GCAAAAAATAGTAAAAAATTAA
1 --AAAAAA-A-TAAAAAATTAA
3113728 TTAGAGATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
24 14 0.39
25 6 0.17
27 6 0.17
28 3 0.08
29 7 0.19
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.25
Consensus pattern (24 bp):
AAAAAAATAAAAAATTAAAAAATT
Found at i:3113711 original size:17 final size:16
Alignment explanation
Indices: 3113659--3113705 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
3113649 ACCAGTAAAA
* *
3113659 AAAAATAAAAAATTTT
1 AAAATTAAAAAAATTT
3113675 AAAATTAAAAAAATTT
1 AAAATTAAAAAAATTT
3113691 AAAATTAAAAAAATT
1 AAAATTAAAAAAATT
3113706 GCAAAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAATTAAAAAAATTT
Found at i:3113789 original size:20 final size:20
Alignment explanation
Indices: 3113758--3113810 Score: 65
Period size: 19 Copynumber: 2.6 Consensus size: 20
3113748 TTTAAAAATT
3113758 AATTTGTAAAAATTCTA-AAAA
1 AATTT-TAAAAATT-TACAAAA
3113779 AATTTTAAAAA-TTACAAAA
1 AATTTTAAAAATTTACAAAA
*
3113798 AATATTAAAAATT
1 AATTTTAAAAATT
3113811 ATTGTAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 2 0.07
19 15 0.52
20 7 0.24
21 5 0.17
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (20 bp):
AATTTTAAAAATTTACAAAA
Found at i:3114095 original size:9 final size:9
Alignment explanation
Indices: 3114081--3114122 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
3114071 AATCTTTGCA
3114081 ATTTTTAAT
1 ATTTTTAAT
*
3114090 ATTTTTAAA
1 ATTTTTAAT
*
3114099 AGTTTTAAT
1 ATTTTTAAT
3114108 GA-TTTTAAT
1 -ATTTTTAAT
3114117 ATTTTT
1 ATTTTT
3114123 TTACATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
8 1 0.04
9 26 0.93
10 1 0.04
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (9 bp):
ATTTTTAAT
Found at i:3114122 original size:18 final size:18
Alignment explanation
Indices: 3114080--3114136 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
3114070 TAATCTTTGC
3114080 AATTTTTAATATTTTTAA
1 AATTTTTAATATTTTTAA
*
3114098 AAGTTTTAATGA-TTTTAA
1 AATTTTTAAT-ATTTTTAA
* * *
3114116 TATTTTTTTACATTTTTAA
1 -AATTTTTAATATTTTTAA
3114135 AA
1 AA
3114137 ATTAAAATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
18 17 0.57
19 13 0.43
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.58
Consensus pattern (18 bp):
AATTTTTAATATTTTTAA
Found at i:3116697 original size:75 final size:80
Alignment explanation
Indices: 3116612--3116768 Score: 234
Period size: 81 Copynumber: 2.0 Consensus size: 80
3116602 TATAAATTAA
3116612 AGAAATAATTTTCATGTCATTTTTTAAACAAT-AA-A-T-G-CTATTCCAATTTTACCCTATTTG
1 AGAAATAATTTTCATGTCATTTTTTAAACAATAAATACTAGCCTATTCCAATTTTACCCTATTTG
3116672 ATTCTTTTTAATAGT
66 ATTCTTTTTAATAGT
** * *
3116687 AGAAATAATTTTCATGTCATTTTTTAAACCGTAAATACTAGCTCTATTCCAATTTTATCCTGTTT
1 AGAAATAATTTTCATGTCATTTTTTAAACAATAAATACTAGC-CTATTCCAATTTTACCCTATTT
3116752 GATTCTTTTTAATAGT
65 GATTCTTTTTAATAGT
3116768 A
1 A
3116769 CACGGCTACA
Statistics
Matches: 72, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
75 30 0.42
76 2 0.03
77 1 0.01
78 1 0.01
79 1 0.01
81 37 0.51
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.46
Consensus pattern (80 bp):
AGAAATAATTTTCATGTCATTTTTTAAACAATAAATACTAGCCTATTCCAATTTTACCCTATTTG
ATTCTTTTTAATAGT
Found at i:3117994 original size:126 final size:126
Alignment explanation
Indices: 3117768--3117995 Score: 368
Period size: 126 Copynumber: 1.8 Consensus size: 126
3117758 GGATATTCGA
* * *
3117768 ATATTCAAAACAAACAAAGAAAGCGAAGCCCAGTACGTTAGGGCATGATTCTTCGAATTCTTTAA
1 ATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATCCTTCGAATTCTTTAA
* * **
3117833 ATACCGAACATTGCCTTTATTTTGAAAAATTTTGAGAGTGAACCAGTAAAGGGATGCTCTG
66 ATACCGAACATAGCCATTATTTTGAAAAAAATTGAGAGTGAACCAGTAAAGGGATGCTCTG
*
3117894 ATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATCCTTTGAATTCTTTAA
1 ATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATCCTTCGAATTCTTTAA
3117959 ATACCGAACATAGCCATTATTTT-AAAAACAATTGAGA
66 ATACCGAACATAGCCATTATTTTGAAAAA-AATTGAGA
3117996 ATAAATCTGT
Statistics
Matches: 93, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
125 5 0.05
126 88 0.95
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26
Consensus pattern (126 bp):
ATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATCCTTCGAATTCTTTAA
ATACCGAACATAGCCATTATTTTGAAAAAAATTGAGAGTGAACCAGTAAAGGGATGCTCTG
Found at i:3118538 original size:18 final size:18
Alignment explanation
Indices: 3118515--3118556 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
3118505 ATAATGCTAC
*
3118515 AATAACCA-TAAACATAGT
1 AATAACCATTAAA-ATAAT
*
3118533 AATAACGATTAAAATAAT
1 AATAACCATTAAAATAAT
3118551 AATAAC
1 AATAAC
3118557 AACAACAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.60, C:0.12, G:0.05, T:0.24
Consensus pattern (18 bp):
AATAACCATTAAAATAAT
Found at i:3118583 original size:3 final size:3
Alignment explanation
Indices: 3118577--3118751 Score: 89
Period size: 3 Copynumber: 60.0 Consensus size: 3
3118567 TAGAAGACAT
* * *
3118577 TAA TAA TAA T-A TAT TAA TAA AAA TAA TAA TAA T-A TAA AAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * ** ** *
3118623 AAA TAA CAA T-A TGT TTC TAA TAA TAA TAA -AA -AA TTAA TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA
* * * * *
3118666 TAA AAA AAA TATA TAA -AA TAA TAG TAA CAG TAA TAA -AA TAA -ATA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
* * *
3118710 TAA T-A TAA TAA TAA TATA TAA TAA TAA CAA TAT TAA AAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
3118752 CACTTTTCCT
Statistics
Matches: 129, Mismatches: 31, Indels: 24
0.70 0.17 0.13
Matches are distributed among these distances:
2 17 0.13
3 103 0.80
4 9 0.07
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:3118603 original size:17 final size:17
Alignment explanation
Indices: 3118578--3118751 Score: 68
Period size: 16 Copynumber: 10.3 Consensus size: 17
3118568 AGAAGACATT
3118578 AATAATAATATATTAATAAA
1 AATAATAATA-A-T-ATAAA
3118598 AATAATAATAATATAAA
1 AATAATAATAATATAAA
3118615 AATAATAA-AA-ATAACA
1 AATAATAATAATATAA-A
**
3118631 ATATGTTTCTAATAATAATAAA
1 A-A---TAATAATAAT-ATAAA
*
3118653 AA-ATTAATAATGAT-AA
1 AATAATAATAAT-ATAAA
3118669 AA-AA-AAT-ATAT-AA
1 AATAATAATAATATAAA
* * *
3118682 AATAATAGTAACAGTAAT
1 AATAATAATAATA-TAAA
3118700 AA-AAT-A-AATAT-AA
1 AATAATAATAATATAAA
* *
3118713 TATAATAATAATAT-AT
1 AATAATAATAATATAAA
*
3118729 AATAATAACAATATTAAA
1 AATAATAATAATA-TAAA
3118747 AATAA
1 AATAA
3118752 CACTTTTCCT
Statistics
Matches: 119, Mismatches: 17, Indels: 38
0.68 0.10 0.22
Matches are distributed among these distances:
13 8 0.07
14 8 0.07
15 13 0.11
16 28 0.24
17 28 0.24
18 10 0.08
19 1 0.01
20 14 0.12
21 3 0.03
22 2 0.02
23 4 0.03
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (17 bp):
AATAATAATAATATAAA
Found at i:3118607 original size:23 final size:24
Alignment explanation
Indices: 3118577--3118736 Score: 94
Period size: 23 Copynumber: 6.4 Consensus size: 24
3118567 TAGAAGACAT
**
3118577 TAATAATAATATATTAATAA-AAA
1 TAATAATAATATAAAAATAATAAA
3118600 TAATAATAATATAAAAATAATAAA
1 TAATAATAATATAAAAATAATAAA
* *
3118624 -AATAACAATATGTTTCTAATAATAATAAA
1 TAATAATAATA------TAAAAATAATAAA
* * *
3118653 AAATTAATAATGATAAAAAAAATATA
1 TAA-TAATAAT-ATAAAAATAATAAA
* *
3118679 TAA-AATAATAGTAACAGTAATAAAA
1 TAATAATAATA-TAAAAATAAT-AAA
* *
3118704 TAA-ATATAATATAATAATAATATA
1 TAATA-ATAATATAAAAATAATAAA
3118728 TAATAATAA
1 TAATAATAA
3118737 CAATATTAAA
Statistics
Matches: 107, Mismatches: 16, Indels: 27
0.71 0.11 0.18
Matches are distributed among these distances:
23 28 0.26
24 25 0.23
25 15 0.14
26 18 0.17
29 12 0.11
30 2 0.02
31 6 0.06
32 1 0.01
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (24 bp):
TAATAATAATATAAAAATAATAAA
Found at i:3118725 original size:20 final size:20
Alignment explanation
Indices: 3118577--3118735 Score: 75
Period size: 20 Copynumber: 8.0 Consensus size: 20
3118567 TAGAAGACAT
*
3118577 TAATAATAATATAT-TAATAA
1 TAATAATAATAAATATAAT-A
* *
3118597 AAATAATAAT-AATATAAAAA
1 TAATAATAATAAATAT-AATA
* ** *
3118617 TAATAAAAATAACAATATGTTTC
1 TAATAATAAT-A-AATAT-AATA
3118640 TAATAATAATAAA-A-AAT-
1 TAATAATAATAAATATAATA
* * *
3118657 TAATAATGATAAAAAAAATA
1 TAATAATAATAAATATAATA
*
3118677 T-ATAA-AAT-AATAGTAACA
1 TAATAATAATAAATA-TAATA
3118695 GTAATAA-AATAAATATAATA
1 -TAATAATAATAAATATAATA
*
3118715 TAATAATAATATATAATAATA
1 TAATAATAATAAAT-ATAATA
3118736 ACAATATTAA
Statistics
Matches: 105, Mismatches: 20, Indels: 27
0.69 0.13 0.18
Matches are distributed among these distances:
17 15 0.14
18 7 0.07
19 16 0.15
20 38 0.36
21 14 0.13
22 1 0.01
23 14 0.13
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (20 bp):
TAATAATAATAAATATAATA
Found at i:3119002 original size:24 final size:24
Alignment explanation
Indices: 3118967--3119016 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
3118957 TTTTTTTGTA
*
3118967 GGCAAGTGGGGTGATAGAGTTAGT
1 GGCAAGTGGGGTAATAGAGTTAGT
* *
3118991 GGCAAGTTGGGTAATGGAGTTAGT
1 GGCAAGTGGGGTAATAGAGTTAGT
3119015 GG
1 GG
3119017 GATGGTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.24, C:0.04, G:0.46, T:0.26
Consensus pattern (24 bp):
GGCAAGTGGGGTAATAGAGTTAGT
Done.