Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 37 of 210
Found at i:11840093 original size:105 final size:108
Alignment explanation
Indices: 11839805--11840112 Score: 358
Period size: 108 Copynumber: 2.9 Consensus size: 108
11839795 AAAAGAAAAT
* * *
11839805 TTTCTAAATAAGGCAATGTTTTGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGTTGGGTTT
1 TTTCAAAACAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGTTGGGTTT
* **
11839870 CGATTTCTCGTTTGACCAAAATAGCCAAATACCCTTTTTAAAC
66 CGATTTCTCGTTAGACCAAAATAGCCAAATACCCTTTCGAAAC
* * * * *
11839913 TTTCAAAATAAGACCATATTTCGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGTTGGGTTT
1 TTTCAAAACAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGTTGGGTTT
* * * *
11839978 CGATTACTCGTCTAG-CC-AAATAGTCGAATATCCTTTCGAAA-
66 CGATTTCTCGT-TAGACCAAAATAGCCAAATACCCTTTCGAAAC
* * * * * *
11840019 TTTTAAAACGAGGCAATGTTTTGC-TTTGGAAATTTGAGAGAATGTGCCCTAACGTGCTGGGTTT
1 TTTCAAAACAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGTTGGGTTT
*
11840083 CGATTTCTCGTTCA-A-CTAAATAGCCAAATA
66 CGATTTCTCGTT-AGACCAAAATAGCCAAATA
11840113 TCCTCTTAAA
Statistics
Matches: 169, Mismatches: 27, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
104 2 0.01
105 58 0.34
106 17 0.10
107 19 0.11
108 71 0.42
109 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (108 bp):
TTTCAAAACAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAACGTGTTGGGTTT
CGATTTCTCGTTAGACCAAAATAGCCAAATACCCTTTCGAAAC
Found at i:11842864 original size:22 final size:22
Alignment explanation
Indices: 11842764--11842866 Score: 125
Period size: 22 Copynumber: 4.6 Consensus size: 22
11842754 CAGCCTTCAC
*
11842764 AAGCATCTCATGTTTAACGAACT
1 AAGC-TCTCATGTTTAACGTACT
* * **
11842787 AAACCCTCATGGCTAACGTACT
1 AAGCTCTCATGTTTAACGTACT
**
11842809 AAGCTCTCATGGCTAACGTACT
1 AAGCTCTCATGTTTAACGTACT
*
11842831 AAGCTCTCATGTTTCACGTACT
1 AAGCTCTCATGTTTAACGTACT
11842853 AAGCTCTCATGTTT
1 AAGCTCTCATGTTT
11842867 GAACAATAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
22 67 0.96
23 3 0.04
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (22 bp):
AAGCTCTCATGTTTAACGTACT
Found at i:11854410 original size:21 final size:21
Alignment explanation
Indices: 11854386--11854449 Score: 51
Period size: 21 Copynumber: 3.0 Consensus size: 21
11854376 AGGGTTCAAT
11854386 GGAAGCTCATAAGAGCTTAAC
1 GGAAGCTCATAAGAGCTTAAC
* * *
11854407 GGAAACCCATAAG-GGTTAAAC
1 GGAAGCTCATAAGAGCTT-AAC
* *
11854428 AGAAGCTCA-ATAGAGCTGAAC
1 GGAAGCTCATA-AGAGCTTAAC
11854449 G
1 G
11854450 AAAACCCATT
Statistics
Matches: 31, Mismatches: 9, Indels: 6
0.67 0.20 0.13
Matches are distributed among these distances:
20 4 0.13
21 25 0.81
22 2 0.06
ACGTcount: A:0.41, C:0.19, G:0.25, T:0.16
Consensus pattern (21 bp):
GGAAGCTCATAAGAGCTTAAC
Found at i:11854412 original size:42 final size:42
Alignment explanation
Indices: 11854366--11854488 Score: 151
Period size: 42 Copynumber: 3.0 Consensus size: 42
11854356 GTGCTAAAAA
* *
11854366 GAAACCCATAAGGGTTCAATGGAAGCTCATAAGAGCTTAACG
1 GAAACCCATAAGGGTTAAACGGAAGCTCATAAGAGCTTAACG
* *
11854408 GAAACCCATAAGGGTTAAACAGAAGCTCA-ATAGAGCTGAACG
1 GAAACCCATAAGGGTTAAACGGAAGCTCATA-AGAGCTTAACG
* * * *
11854450 AAAACCCATTAGGGTTAAACGGAAACTCATATGAG-TTAA
1 GAAACCCATAAGGGTTAAACGGAAGCTCATAAGAGCTTAA
11854489 ACAGAAGTTT
Statistics
Matches: 69, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
41 4 0.06
42 64 0.93
43 1 0.01
ACGTcount: A:0.41, C:0.18, G:0.22, T:0.19
Consensus pattern (42 bp):
GAAACCCATAAGGGTTAAACGGAAGCTCATAAGAGCTTAACG
Found at i:11854475 original size:21 final size:21
Alignment explanation
Indices: 11854404--11854475 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
11854394 ATAAGAGCTT
*
11854404 AACGGAAACCCATAAGGGTTA
1 AACGGAAACCCATTAGGGTTA
* * * * * * *
11854425 AACAGAAGCTCAATAGAGCTG
1 AACGGAAACCCATTAGGGTTA
*
11854446 AACGAAAACCCATTAGGGTTA
1 AACGGAAACCCATTAGGGTTA
11854467 AACGGAAAC
1 AACGGAAAC
11854476 TCATATGAGT
Statistics
Matches: 34, Mismatches: 17, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.14
Consensus pattern (21 bp):
AACGGAAACCCATTAGGGTTA
Found at i:11860913 original size:26 final size:26
Alignment explanation
Indices: 11860883--11860932 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
11860873 AACATAGAAG
* *
11860883 TAAATACCGAAATGGGTTTACAAAAA
1 TAAATACCGAAATGAGTTCACAAAAA
11860909 TAAATACCGAAATGAGTTCACAAA
1 TAAATACCGAAATGAGTTCACAAA
11860933 TGTTTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.22
Consensus pattern (26 bp):
TAAATACCGAAATGAGTTCACAAAAA
Found at i:11867420 original size:38 final size:38
Alignment explanation
Indices: 11867378--11867455 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
11867368 ATTTAGCCGC
11867378 ATTCAAAATGGTTGAGAAACCTTCTGCACATAGTAGTA
1 ATTCAAAATGGTTGAGAAACCTTCTGCACATAGTAGTA
11867416 ATTCAAAATGGTTGAGAAACCTTCTGCACATAGTAGTA
1 ATTCAAAATGGTTGAGAAACCTTCTGCACATAGTAGTA
11867454 AT
1 AT
11867456 AAGTAAGGAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.29
Consensus pattern (38 bp):
ATTCAAAATGGTTGAGAAACCTTCTGCACATAGTAGTA
Found at i:11871774 original size:19 final size:19
Alignment explanation
Indices: 11871752--11871799 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
11871742 TAATTCCCAT
*
11871752 AAAAAAAATTTATTCTTAG
1 AAAATAAATTTATTCTTAG
11871771 AAAATAAATTTATTCTTAG
1 AAAATAAATTTATTCTTAG
*
11871790 GAAATAAATT
1 AAAATAAATT
11871800 ATCACTACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (19 bp):
AAAATAAATTTATTCTTAG
Found at i:11875473 original size:23 final size:23
Alignment explanation
Indices: 11875447--11875554 Score: 180
Period size: 23 Copynumber: 4.7 Consensus size: 23
11875437 GTGTTATTGA
*
11875447 TCAGTGGTAGCTTCGGCTACGTT
1 TCAGTGGTAGCTTCGGCTACATT
11875470 TCAGTGGTAGCTTCGGCTACATT
1 TCAGTGGTAGCTTCGGCTACATT
11875493 TCAGTGGTAGCTTCGGCTACATT
1 TCAGTGGTAGCTTCGGCTACATT
*
11875516 TCAGTGGTAGCTTCGGCTACAATA
1 TCAGTGGTAGCTTCGGCTAC-ATT
*
11875540 ACAGTGGTAGCTTCG
1 TCAGTGGTAGCTTCG
11875555 NNNNNNNNNN
Statistics
Matches: 81, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
23 65 0.80
24 16 0.20
ACGTcount: A:0.19, C:0.21, G:0.28, T:0.32
Consensus pattern (23 bp):
TCAGTGGTAGCTTCGGCTACATT
Found at i:11880253 original size:42 final size:42
Alignment explanation
Indices: 11880194--11880274 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
11880184 CTTCACAGAT
* *
11880194 TAGATAATGACCTAACCCCCACCATTAGTGGTTGGGTTACAG
1 TAGATAATGACCCAACCCCCACCATCAGTGGTTGGGTTACAG
11880236 TAGATAATGACCCAACCCCCACCATCAGTGGTTGGGTTA
1 TAGATAATGACCCAACCCCCACCATCAGTGGTTGGGTTA
11880275 AAGTGGTCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (42 bp):
TAGATAATGACCCAACCCCCACCATCAGTGGTTGGGTTACAG
Found at i:11883827 original size:16 final size:17
Alignment explanation
Indices: 11883796--11883830 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
11883786 CGATTTTCTC
*
11883796 TATTTTTTTAATATTTT
1 TATTTTTATAATATTTT
11883813 TATTTTTATAA-ATTTT
1 TATTTTTATAATATTTT
11883829 TA
1 TA
11883831 ATAATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TATTTTTATAATATTTT
Found at i:11886299 original size:21 final size:21
Alignment explanation
Indices: 11886275--11886399 Score: 151
Period size: 21 Copynumber: 6.0 Consensus size: 21
11886265 TGGGTGGATC
* *
11886275 AGCTCTCACGAGCTTCTGTTC
1 AGCTCTTACGAGCTTCTGTTT
* * *
11886296 AGCTCTCACGAGCTTCTATTA
1 AGCTCTTACGAGCTTCTGTTT
* *
11886317 AGCTGTTACAAGCTTCTGTTT
1 AGCTCTTACGAGCTTCTGTTT
* *
11886338 AGCTCTTATGAGCTTCTATTT
1 AGCTCTTACGAGCTTCTGTTT
*
11886359 AGCTCTTATGAGCTTCTGTTT
1 AGCTCTTACGAGCTTCTGTTT
*
11886380 AGCTCTTATGAGCTTCTGTT
1 AGCTCTTACGAGCTTCTGTT
11886400 GGCATGTTCG
Statistics
Matches: 92, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 92 1.00
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.42
Consensus pattern (21 bp):
AGCTCTTACGAGCTTCTGTTT
Found at i:11886567 original size:18 final size:18
Alignment explanation
Indices: 11886537--11886589 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
11886527 ATATTCTAAA
11886537 TGATAATACATGATATAT
1 TGATAATACATGATATAT
11886555 TGATATATA-ATGATATAT
1 TGATA-ATACATGATATAT
**
11886573 TGA-AATGGATGATATAT
1 TGATAATACATGATATAT
11886590 GTATATAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
16 2 0.06
17 10 0.31
18 17 0.53
19 3 0.09
ACGTcount: A:0.43, C:0.02, G:0.15, T:0.40
Consensus pattern (18 bp):
TGATAATACATGATATAT
Found at i:11897365 original size:21 final size:23
Alignment explanation
Indices: 11897333--11897374 Score: 54
Period size: 21 Copynumber: 1.9 Consensus size: 23
11897323 ATTTTACTAA
11897333 AATTTCATTCAA-AAA-TTGATC
1 AATTTCATTCAATAAACTTGATC
11897354 AATTTACA-TCAATAAACTTGA
1 AATTT-CATTCAATAAACTTGA
11897375 AAACAGGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
21 9 0.50
22 5 0.28
23 4 0.22
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (23 bp):
AATTTCATTCAATAAACTTGATC
Found at i:11898532 original size:16 final size:18
Alignment explanation
Indices: 11898500--11898532 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11898490 GTTAATAGAT
11898500 TAAATTTAGTGTTAATTG
1 TAAATTTAGTGTTAATTG
11898518 TAAATTT-GT-TTAATT
1 TAAATTTAGTGTTAATT
11898533 TATGAAATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 2 0.13
18 7 0.47
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (18 bp):
TAAATTTAGTGTTAATTG
Found at i:11899194 original size:30 final size:30
Alignment explanation
Indices: 11899160--11899222 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
11899150 ACTTAACAAG
11899160 CAAATGTCTCTAAAATAATAACAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
*
11899190 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
11899220 CAA
1 CAA
11899223 TAAAATAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.57, C:0.13, G:0.03, T:0.27
Consensus pattern (30 bp):
CAAATGTCTCTAAAATAATAACAAAATTAA
Found at i:11900521 original size:36 final size:36
Alignment explanation
Indices: 11900469--11900541 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
11900459 TTCCAGATCC
*
11900469 CTTTACTTTCCTAGTTCTCTACCATGTCTTCTCACA
1 CTTTACTTTCCCAGTTCTCTACCATGTCTTCTCACA
*
11900505 CTTTACTTTCCCAGTTCTCTCCCATGTCTTCTCACA
1 CTTTACTTTCCCAGTTCTCTACCATGTCTTCTCACA
11900541 C
1 C
11900542 CATAACTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.15, C:0.37, G:0.05, T:0.42
Consensus pattern (36 bp):
CTTTACTTTCCCAGTTCTCTACCATGTCTTCTCACA
Found at i:11902506 original size:31 final size:30
Alignment explanation
Indices: 11902468--11902540 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
11902458 GAAAATGTTA
11902468 ATTAGTGACTGATTTGTCACTTTTTAATAAC
1 ATTAGTGACTGATTTGTCA-TTTTTAATAAC
* * ** *
11902499 ATTAGTGACCGTTTTGTCATTTTTTTTAAG
1 ATTAGTGACTGATTTGTCATTTTTAATAAC
*
11902529 TTTAGTGACTGA
1 ATTAGTGACTGA
11902541 AATGAAATCA
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
30 17 0.50
31 17 0.50
ACGTcount: A:0.25, C:0.11, G:0.16, T:0.48
Consensus pattern (30 bp):
ATTAGTGACTGATTTGTCATTTTTAATAAC
Found at i:11909989 original size:28 final size:28
Alignment explanation
Indices: 11909935--11909990 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
11909925 ATGTATATGT
* *
11909935 GTATATATTTACAAAATAAAATGTATAA
1 GTATATATATACAAAATAAAATATATAA
* * *
11909963 GTATATATATATAATATAAAGTATATAA
1 GTATATATATACAAAATAAAATATATAA
11909991 AAATAAGAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.38
Consensus pattern (28 bp):
GTATATATATACAAAATAAAATATATAA
Found at i:11913853 original size:43 final size:44
Alignment explanation
Indices: 11913773--11913872 Score: 121
Period size: 43 Copynumber: 2.2 Consensus size: 44
11913763 TCAAGTATCA
* * *
11913773 CATTTCATATTATATTTCTCATTTCATATTCAGTTCTCATATTTGC
1 CATTTCA-A-TATATTTATCATCTCATAGTCAGTTCTCATATTTGC
* * *
11913819 CATTTCAATAT-TTTATCATCTCATAGTCATTTCTCATCTTTTC
1 CATTTCAATATATTTATCATCTCATAGTCAGTTCTCATATTTGC
11913862 CATTTCAATAT
1 CATTTCAATAT
11913873 CAATCACGAA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
43 37 0.77
44 3 0.06
45 1 0.02
46 7 0.15
ACGTcount: A:0.25, C:0.21, G:0.03, T:0.51
Consensus pattern (44 bp):
CATTTCAATATATTTATCATCTCATAGTCAGTTCTCATATTTGC
Found at i:11918651 original size:18 final size:18
Alignment explanation
Indices: 11918630--11918677 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
11918620 AAGATATGGG
*
11918630 AAATGATGTTCACATTTT
1 AAATGATGTTCACATTTC
11918648 AAATGATGTTCACATTTC
1 AAATGATGTTCACATTTC
11918666 AAATGATGTTCA
1 AAATGATGTTCA
11918678 AATTGATGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (18 bp):
AAATGATGTTCACATTTC
Found at i:11919185 original size:72 final size:72
Alignment explanation
Indices: 11919090--11919328 Score: 401
Period size: 72 Copynumber: 3.3 Consensus size: 72
11919080 CAATGCTAAA
*
11919090 CTAGTTTTATCAATAGTTATTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
11919155 GTGTAAT
66 GTGTAAT
*
11919162 CTAGTTTTATCAATGGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
11919227 GTGTAAT
66 GTGTAAT
* *
11919234 CTAGTTTTATTAATAGTTGTTTATGTTTGGTCTTTGGATATTGAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
* *
11919299 ACT-AAAT
66 -GTGTAAT
11919306 -TAGTTTTATCAATAGTTGTTTAT
1 CTAGTTTTATCAATAGTTGTTTAT
11919329 ATATGATTTT
Statistics
Matches: 158, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
71 22 0.14
72 135 0.85
73 1 0.01
ACGTcount: A:0.23, C:0.06, G:0.15, T:0.55
Consensus pattern (72 bp):
CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
GTGTAAT
Found at i:11921642 original size:17 final size:18
Alignment explanation
Indices: 11921620--11921653 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11921610 AGACGTCGGC
11921620 CTCTTTT-TTTTATTTCT
1 CTCTTTTCTTTTATTTCT
*
11921637 CTCTTTTCTTTTCTTTC
1 CTCTTTTCTTTTATTTC
11921654 AATTTGCATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.74
Consensus pattern (18 bp):
CTCTTTTCTTTTATTTCT
Found at i:11922837 original size:30 final size:30
Alignment explanation
Indices: 11922803--11922871 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
11922793 TAGGGGGATA
* *
11922803 GAAAATGGTAGCT-TCGTTAAGTTTGTAATG
1 GAAAATGGTAGCTCT-GTTAAGTCTGTAACG
*
11922833 GAAAATGGTAGCTCTGTTACGTCTGTAACG
1 GAAAATGGTAGCTCTGTTAAGTCTGTAACG
*
11922863 AAAAATGGT
1 GAAAATGGT
11922872 TAGTGGTGAC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 33 0.97
31 1 0.03
ACGTcount: A:0.32, C:0.10, G:0.26, T:0.32
Consensus pattern (30 bp):
GAAAATGGTAGCTCTGTTAAGTCTGTAACG
Found at i:11926872 original size:29 final size:29
Alignment explanation
Indices: 11926822--11926878 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
11926812 TGTGTAGCCC
*
11926822 GGATCAAATTAGTCCGTCTATTATTAAAT
1 GGATCAAATTAGTCCGTATATTATTAAAT
* *
11926851 GGATCAATTTAGTCAC-TATATTGTTAAA
1 GGATCAAATTAGTC-CGTATATTATTAAA
11926879 ATCTTCAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 23 0.96
30 1 0.04
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (29 bp):
GGATCAAATTAGTCCGTATATTATTAAAT
Found at i:11944696 original size:42 final size:42
Alignment explanation
Indices: 11944649--11944735 Score: 147
Period size: 42 Copynumber: 2.1 Consensus size: 42
11944639 TTTTTAATCC
*
11944649 GATCATCATGTAGGTGTAAGATTTATGAATTTTGCAACACTT
1 GATCATCATGTAGGTGTAAGATTTATAAATTTTGCAACACTT
* *
11944691 GATCATCATGTAGTTGTAAGATTTATAAATTTTGTAACACTT
1 GATCATCATGTAGGTGTAAGATTTATAAATTTTGCAACACTT
11944733 GAT
1 GAT
11944736 GAAATAAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.40
Consensus pattern (42 bp):
GATCATCATGTAGGTGTAAGATTTATAAATTTTGCAACACTT
Found at i:11945619 original size:17 final size:17
Alignment explanation
Indices: 11945599--11945633 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
11945589 ACTTTGGGAG
11945599 TTAGTTTCTTTTGTGCA
1 TTAGTTTCTTTTGTGCA
11945616 TTAGTTTCTTTTGTGCA
1 TTAGTTTCTTTTGTGCA
11945633 T
1 T
11945634 GATTGCTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.17, T:0.60
Consensus pattern (17 bp):
TTAGTTTCTTTTGTGCA
Found at i:11958586 original size:49 final size:49
Alignment explanation
Indices: 11958504--11958600 Score: 131
Period size: 49 Copynumber: 2.0 Consensus size: 49
11958494 TTATGCTATG
* * * *
11958504 CATTTCTAAACTTGGTCTTCCACTGTGTACACTCTTATCACTATTTATA
1 CATTGCTAAACTTAGTCTTCCACTGTCTACACTCTTATCAATATTTATA
* * *
11958553 CATTGCTAAACTTATTCTTCCCCTGTCTGCACTCTTATCAATATTTAT
1 CATTGCTAAACTTAGTCTTCCACTGTCTACACTCTTATCAATATTTAT
11958601 CTATTCTAGA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.24, C:0.26, G:0.07, T:0.43
Consensus pattern (49 bp):
CATTGCTAAACTTAGTCTTCCACTGTCTACACTCTTATCAATATTTATA
Found at i:11959186 original size:9 final size:9
Alignment explanation
Indices: 11959169--11959205 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
11959159 TGAGTTTTCG
11959169 AATTCGAAT
1 AATTCGAAT
*
11959178 AACTCGAAT
1 AATTCGAAT
11959187 AATTCGAAT
1 AATTCGAAT
11959196 AATTCGAAT
1 AATTCGAAT
11959205 A
1 A
11959206 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:11959584 original size:17 final size:17
Alignment explanation
Indices: 11959557--11959618 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
11959547 ACTCCCCCTA
*
11959557 TTTACTTCCCCTCAAACT
1 TTTACTTCCCC-AAAACT
11959575 TTTA-TTCCCCAAAACTT
1 TTTACTTCCCCAAAAC-T
* *
11959592 TTTATTTTCCCCCTAAACT
1 TTTA-CTT-CCCCAAAACT
11959611 TTTACTTC
1 TTTACTTC
11959619 TCACCCTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
16 4 0.11
17 12 0.32
18 6 0.16
19 7 0.19
20 8 0.22
ACGTcount: A:0.23, C:0.32, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTACTTCCCCAAAACT
Found at i:11964123 original size:66 final size:66
Alignment explanation
Indices: 11964017--11964150 Score: 232
Period size: 66 Copynumber: 2.0 Consensus size: 66
11964007 GTTTCAAACT
* *
11964017 TTGGATTTATCAAATCAACCTTTCAATCCTCATAAACCTTCTATGGAGGAACCTCCTACATTAGA
1 TTGGATTTATCAAATCAACCTTTCAATCCTCATAAACCTTCTATGGAAGAACCTCCTACACTAGA
11964082 G
66 G
**
11964083 TTGGATTTATCAAATCAACCTTTCAATCCTTTTAAACCTTCTATGGAAGAACCTCCTACACTAGA
1 TTGGATTTATCAAATCAACCTTTCAATCCTCATAAACCTTCTATGGAAGAACCTCCTACACTAGA
11964148 G
66 G
11964149 TT
1 TT
11964151 ACAACCTTTG
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.31, C:0.24, G:0.11, T:0.34
Consensus pattern (66 bp):
TTGGATTTATCAAATCAACCTTTCAATCCTCATAAACCTTCTATGGAAGAACCTCCTACACTAGA
G
Found at i:11971394 original size:36 final size:35
Alignment explanation
Indices: 11971322--11971394 Score: 85
Period size: 36 Copynumber: 2.1 Consensus size: 35
11971312 TCTTGCTCTC
* * *
11971322 TTTTTCAATTTGCTTTTCTTGCTCGCACTCTTTTT
1 TTTTTCAATTCGCTTTTCTTGCTCCCACTCTCTTT
*
11971357 TTTTTCAATCTCG-TTTTGCTTTCTCCCACTCTCTTT
1 TTTTTCAAT-TCGCTTTT-CTTGCTCCCACTCTCTTT
11971393 TT
1 TT
11971395 CTTTTTAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
35 13 0.41
36 19 0.59
ACGTcount: A:0.08, C:0.26, G:0.07, T:0.59
Consensus pattern (35 bp):
TTTTTCAATTCGCTTTTCTTGCTCCCACTCTCTTT
Found at i:11971426 original size:17 final size:17
Alignment explanation
Indices: 11971386--11971432 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
11971376 TTTCTCCCAC
*
11971386 TCTCTTTTTCTTTTTAAA
1 TCTCTTTTTC-TTTCAAA
* *
11971404 TTTCTTTTTCTTTCATA
1 TCTCTTTTTCTTTCAAA
11971421 TCTCTTTTTCTT
1 TCTCTTTTTCTT
11971433 CTCTAAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 16 0.64
18 9 0.36
ACGTcount: A:0.11, C:0.19, G:0.00, T:0.70
Consensus pattern (17 bp):
TCTCTTTTTCTTTCAAA
Found at i:11972397 original size:17 final size:17
Alignment explanation
Indices: 11972364--11972397 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
11972354 CTTCGTAAAA
* *
11972364 TTTTTTTATACTTCAAT
1 TTTTTTTAAACTACAAT
11972381 TTTTTTTAAACTACAAT
1 TTTTTTTAAACTACAAT
11972398 AAGATGAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTTTTTAAACTACAAT
Found at i:11976776 original size:159 final size:159
Alignment explanation
Indices: 11976487--11976805 Score: 593
Period size: 159 Copynumber: 2.0 Consensus size: 159
11976477 ACAATGTTGG
* *
11976487 ATACTATTTTGAACTAAAATTTTAATCTCCAACCCATGAATTAAATCTCATAGGGTTGGGGTTAC
1 ATACTATTTTGAACTAAAATTTTAATCTCCAACCCATGAATTAAATCTCATAGGGTTGAGATTAC
* *
11976552 ATGATGGAACTTTTATTTCCTTTAATGGTTGAAGCATATATTTGATTTAATCTACTGTTTCATTC
66 ATGATGAAACTTTTATTTCCTTTAATGGTTGAAACATATATTTGATTTAATCTACTGTTTCATTC
11976617 AATTGTTTTTATTTCCTAACTGTATGTGT
131 AATTGTTTTTATTTCCTAACTGTATGTGT
*
11976646 ATACTATTTTGAACTGAAATTTTAATCTCCAACCCATGAATTAAATCTCATAGGGTTGAGATTAC
1 ATACTATTTTGAACTAAAATTTTAATCTCCAACCCATGAATTAAATCTCATAGGGTTGAGATTAC
11976711 ATGATGAAACTTTTATTTCCTTTAATGGTTGAAACATATATTTGATTTAATCTACTGTTTCATTC
66 ATGATGAAACTTTTATTTCCTTTAATGGTTGAAACATATATTTGATTTAATCTACTGTTTCATTC
11976776 AATTGTTTTTATTTCCTAACTGTATGTGT
131 AATTGTTTTTATTTCCTAACTGTATGTGT
11976805 A
1 A
11976806 CATTCTTTAG
Statistics
Matches: 155, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
159 155 1.00
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.44
Consensus pattern (159 bp):
ATACTATTTTGAACTAAAATTTTAATCTCCAACCCATGAATTAAATCTCATAGGGTTGAGATTAC
ATGATGAAACTTTTATTTCCTTTAATGGTTGAAACATATATTTGATTTAATCTACTGTTTCATTC
AATTGTTTTTATTTCCTAACTGTATGTGT
Found at i:11977901 original size:16 final size:16
Alignment explanation
Indices: 11977878--11977910 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
11977868 ACATTAGTCT
11977878 TTTGAAACATAA-GTG
1 TTTGAAACATAATGTG
11977893 TTTGTAAACATAATGTG
1 TTTG-AAACATAATGTG
11977910 T
1 T
11977911 ACCAAACTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 8 0.50
17 4 0.25
ACGTcount: A:0.36, C:0.06, G:0.18, T:0.39
Consensus pattern (16 bp):
TTTGAAACATAATGTG
Found at i:11986794 original size:20 final size:21
Alignment explanation
Indices: 11986750--11986794 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
11986740 TTAAAATACT
* *
11986750 TTTAAAATAAATTTTTTTATT
1 TTTAAAATAAATTTTTTAATG
11986771 TTTAAAAT-AATTTTTTAATG
1 TTTAAAATAAATTTTTTAATG
11986791 TTTA
1 TTTA
11986795 TTTTAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
TTTAAAATAAATTTTTTAATG
Found at i:11992816 original size:13 final size:13
Alignment explanation
Indices: 11992798--11992836 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
11992788 TATACTTTTT
11992798 AATATTTTTTAAA
1 AATATTTTTTAAA
11992811 AATATTTTTTAAA
1 AATATTTTTTAAA
*
11992824 AAAATTTTTTAAA
1 AATATTTTTTAAA
11992837 TTAAAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
AATATTTTTTAAA
Found at i:11994527 original size:25 final size:25
Alignment explanation
Indices: 11994435--11994530 Score: 88
Period size: 25 Copynumber: 3.8 Consensus size: 25
11994425 TATTAGCATG
* * *
11994435 ATCAAAATCACATATCATTCTCAGA
1 ATCAGAATGACATATCATTATCAGA
*
11994460 ATCATG-ATGACATATCATTACCA-A
1 ATCA-GAATGACATATCATTATCAGA
* * * *
11994484 GATTAGAATAACCTTTCATTATCAGA
1 -ATCAGAATGACATATCATTATCAGA
11994510 ATCAGAATGACATATCATTAT
1 ATCAGAATGACATATCATTAT
11994531 TTACAATTGG
Statistics
Matches: 54, Mismatches: 13, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
24 2 0.04
25 51 0.94
26 1 0.02
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (25 bp):
ATCAGAATGACATATCATTATCAGA
Found at i:12005423 original size:20 final size:20
Alignment explanation
Indices: 12005398--12005435 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12005388 TAAAGTTATA
* *
12005398 TATTTTATATTGGATGGATG
1 TATTTTACATTAGATGGATG
12005418 TATTTTACATTAGATGGA
1 TATTTTACATTAGATGGA
12005436 GATGGAGAAT
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:0.29, C:0.03, G:0.21, T:0.47
Consensus pattern (20 bp):
TATTTTACATTAGATGGATG
Found at i:12005694 original size:41 final size:39
Alignment explanation
Indices: 12005639--12005835 Score: 135
Period size: 41 Copynumber: 4.8 Consensus size: 39
12005629 ACCTTTCGAG
*
12005639 GCTTTAGCAGCGTTTTTGAAAAAGCGCCGCTAATGCCCTA
1 GCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCCC-A
* * * ** * *
12005679 GTCTTTAGTGGCGTTTTTGGATAAGCGAAGCTATTGCTCAGA
1 G-CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC-C-CA
* * * *
12005721 GATTTAGCGGCGTTTTTGAAAAATCGCCGTTAATGCTCAAA
1 GCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC-C-CA
* * * * *
12005762 GCTTTAGCGGCGTTTTTGGAGAGGCGCTGCTAATGCTCAGA
1 GCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC-C-CA
* *
12005803 GCATTAGCGGCGATTTTTCAAAAA-CGCCGCTAA
1 GCTTTAGCGGCG-TTTTTGAAAAAGCGCCGCTAA
12005836 ATCTCTGAGC
Statistics
Matches: 121, Mismatches: 32, Indels: 7
0.76 0.20 0.04
Matches are distributed among these distances:
40 1 0.01
41 110 0.91
42 10 0.08
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (39 bp):
GCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCCCA
Found at i:12005737 original size:82 final size:82
Alignment explanation
Indices: 12005641--12005835 Score: 234
Period size: 82 Copynumber: 2.4 Consensus size: 82
12005631 CTTTCGAGGC
* ** * *
12005641 TTTAGCAGCGTTTTTGAAAAAGCGCCGCTAATGC-CCTAGTCTTTAGTGGCGTTTTTGGATAAGC
1 TTTAGCGGCGTTTTTGAAAAA-CGCCGCTAATGCTCAAAG-CTTTAGCGGCGTTTTTGGAGAAGC
*
12005705 GAAGCTATTGCTCAGAG-A
64 GAAGCTAATGCTCAGAGCA
* *
12005723 TTTAGCGGCGTTTTTGAAAAATCGCCGTTAATGCTCAAAGCTTTAGCGGCGTTTTTGGAGAGGCG
1 TTTAGCGGCGTTTTTGAAAAA-CGCCGCTAATGCTCAAAGCTTTAGCGGCGTTTTTGGAGAAGCG
**
12005788 CTGCTAATGCTCAGAGCA
65 AAGCTAATGCTCAGAGCA
*
12005806 -TTAGCGGCGATTTTTCAAAAACGCCGCTAA
1 TTTAGCGGCG-TTTTTGAAAAACGCCGCTAA
12005836 ATCTCTGAGC
Statistics
Matches: 97, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
82 83 0.86
83 14 0.14
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (82 bp):
TTTAGCGGCGTTTTTGAAAAACGCCGCTAATGCTCAAAGCTTTAGCGGCGTTTTTGGAGAAGCGA
AGCTAATGCTCAGAGCA
Found at i:12005851 original size:82 final size:82
Alignment explanation
Indices: 12005683--12005855 Score: 199
Period size: 82 Copynumber: 2.1 Consensus size: 82
12005673 GCCCTAGTCT
* * * *
12005683 TTAGTGGCGTTTTTGGATAAGCGAAGCTATTGCTCAGAGATTTAGCGGCGTTTTTGAAAAATCGC
1 TTAGCGGCGTTTTTGGAGAAGCGAAGCTAATGCTCAGAGATTTAGCGGCGTTTTTCAAAAATCGC
* *
12005748 CGTTAATGCTCAAAGCT
66 CGTAAATGCTCAAAGCA
* **
12005765 TTAGCGGCGTTTTTGGAGAGGCGCTGCTAATGCTCAGAGCA-TTAGCGGCGATTTTTCAAAAA-C
1 TTAGCGGCGTTTTTGGAGAAGCGAAGCTAATGCTCAGAG-ATTTAGCGGCG-TTTTTCAAAAATC
**
12005828 GCCGCTAAAT-CTCTGAGCA
64 GCCG-TAAATGCTCAAAGCA
12005847 TTAGCGGCG
1 TTAGCGGCG
12005856 CTTATCCAAA
Statistics
Matches: 77, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
82 62 0.81
83 15 0.19
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.29
Consensus pattern (82 bp):
TTAGCGGCGTTTTTGGAGAAGCGAAGCTAATGCTCAGAGATTTAGCGGCGTTTTTCAAAAATCGC
CGTAAATGCTCAAAGCA
Found at i:12005889 original size:41 final size:41
Alignment explanation
Indices: 12005797--12005896 Score: 130
Period size: 41 Copynumber: 2.4 Consensus size: 41
12005787 GCTGCTAATG
* * *
12005797 CTCAGAGCATTAGCGGCGATTTTTCAAAAACGCCGCTAAAT
1 CTCAGAGCATTAGCGGCGATTATCCAAAAACGCCGCTAAAA
* *
12005838 CTCTGAGCATTAGCGGCGCTTATCCAAAAACGCCGCTAAAGA
1 CTCAGAGCATTAGCGGCGATTATCCAAAAACGCCGCTAAA-A
*
12005880 CT-AGCGCATTAGCGGCG
1 CTCAGAGCATTAGCGGCG
12005897 TTTTTTATTT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
41 49 0.96
42 2 0.04
ACGTcount: A:0.29, C:0.27, G:0.23, T:0.21
Consensus pattern (41 bp):
CTCAGAGCATTAGCGGCGATTATCCAAAAACGCCGCTAAAA
Found at i:12005973 original size:41 final size:41
Alignment explanation
Indices: 12005904--12006057 Score: 184
Period size: 41 Copynumber: 3.8 Consensus size: 41
12005894 GCGTTTTTTA
* * * *
12005904 TTTAGCGGCATTTTTTGAGAAGCACCGCTAATGCTCAGATC
1 TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGATC
* *
12005945 TTTAGCTGCGTTTTTGGAAAAGCGCCGCTAATGCTCAAATC
1 TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGATC
* * * * **
12005986 TTTAGCAGCGTTTTTGAAAAAGAGACGCTAATGCTC-GGGC
1 TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGATC
12006026 TTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAA
1 -TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAA
12006058 AACATTTTAT
Statistics
Matches: 95, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
40 1 0.01
41 94 0.99
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.31
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCAGATC
Found at i:12006482 original size:14 final size:15
Alignment explanation
Indices: 12006454--12006486 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
12006444 AACGTTTATA
12006454 GATTATGGAATTAGG
1 GATTATGGAATTAGG
12006469 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
12006483 GATT
1 GATT
12006487 CTGGTTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:12006518 original size:7 final size:7
Alignment explanation
Indices: 12006506--12006572 Score: 53
Period size: 7 Copynumber: 9.4 Consensus size: 7
12006496 GGGTTGCGAT
12006506 TTAGGGG
1 TTAGGGG
12006513 TTAGGGG
1 TTAGGGG
* *
12006520 TTAGAGA
1 TTAGGGG
* *
12006527 TTAAGAG
1 TTAGGGG
*
12006534 TTAGGGAT
1 TTAGGG-G
* *
12006542 TTAAGGT
1 TTAGGGG
12006549 TTAGGGG
1 TTAGGGG
12006556 TTAGGGG
1 TTAGGGG
*
12006563 TTAGAGG
1 TTAGGGG
12006570 TTA
1 TTA
12006573 AGAGTTGTGA
Statistics
Matches: 46, Mismatches: 13, Indels: 2
0.75 0.21 0.03
Matches are distributed among these distances:
7 41 0.89
8 5 0.11
ACGTcount: A:0.25, C:0.00, G:0.42, T:0.33
Consensus pattern (7 bp):
TTAGGGG
Found at i:12006566 original size:43 final size:42
Alignment explanation
Indices: 12006505--12006594 Score: 144
Period size: 43 Copynumber: 2.1 Consensus size: 42
12006495 AGGGTTGCGA
12006505 TTTAGGGGTTAGGGGTTAGAGATTAAGAGTTAGGGATTTAAGG
1 TTTAGGGGTTAGGGGTTAGAGATTAAGAGTT-GGGATTTAAGG
* * *
12006548 TTTAGGGGTTAGGGGTTAGAGGTTAAGAGTTGTGATTTAGGG
1 TTTAGGGGTTAGGGGTTAGAGATTAAGAGTTGGGATTTAAGG
12006590 TTTAG
1 TTTAG
12006595 AGACTTGAGG
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
42 14 0.32
43 30 0.68
ACGTcount: A:0.24, C:0.00, G:0.40, T:0.36
Consensus pattern (42 bp):
TTTAGGGGTTAGGGGTTAGAGATTAAGAGTTGGGATTTAAGG
Found at i:12006696 original size:7 final size:7
Alignment explanation
Indices: 12006684--12006726 Score: 59
Period size: 7 Copynumber: 6.1 Consensus size: 7
12006674 ATTGTAAAAG
12006684 AGGGGTT
1 AGGGGTT
12006691 AGGGGTT
1 AGGGGTT
*
12006698 AGAGGTT
1 AGGGGTT
* *
12006705 AAGGATT
1 AGGGGTT
12006712 AGGGGTT
1 AGGGGTT
12006719 AGGGGTT
1 AGGGGTT
12006726 A
1 A
12006727 TGGATAGGTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.23, C:0.00, G:0.49, T:0.28
Consensus pattern (7 bp):
AGGGGTT
Found at i:12006715 original size:21 final size:21
Alignment explanation
Indices: 12006689--12006731 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
12006679 AAAAGAGGGG
12006689 TTAGGGGTTAGAGGTTAAGGA
1 TTAGGGGTTAGAGGTTAAGGA
* *
12006710 TTAGGGGTTAGGGGTTATGGA
1 TTAGGGGTTAGAGGTTAAGGA
12006731 T
1 T
12006732 AGGTAACTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.00, G:0.44, T:0.33
Consensus pattern (21 bp):
TTAGGGGTTAGAGGTTAAGGA
Found at i:12012104 original size:44 final size:42
Alignment explanation
Indices: 12011960--12012212 Score: 267
Period size: 43 Copynumber: 5.9 Consensus size: 42
12011950 AGTTTGTGTG
*
12011960 AAAAGCGCCGCTAAAGGT-CTGTTCTATAGCGGCGTTTATAGGA
1 AAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTT-T-GGA
* * * *
12012003 AAAAGCGCCGCTAAAAGTCTTTATCTATAGCAGCGTTTGTGGA
1 AAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTT-TGGA
* * *
12012046 ACAAGCGCCGCTAAAAGTCCTGATCTATAGCAGCGTTTTGTTGA
1 AAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTTG--GA
* * * *
12012090 AAAACCGTCGCTAAAGGTCCTGATCTATAGCTGC-ATTTGTGA
1 AAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTTG-GA
* * * *
12012132 AAAAGTGTCGTTAAAGGTCTTGATCTATAGCGGCGTTTTCGGA
1 AAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTT-GGA
* *
12012175 AAAAGCGCCGCTAAAGGTCATGATCTATAACGGCGTTT
1 AAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTT
12012213 ATTTCAAAAA
Statistics
Matches: 179, Mismatches: 26, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
42 34 0.19
43 97 0.54
44 48 0.27
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (42 bp):
AAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTTGGA
Found at i:12012152 original size:129 final size:129
Alignment explanation
Indices: 12011968--12012234 Score: 315
Period size: 129 Copynumber: 2.1 Consensus size: 129
12011958 TGAAAAGCGC
* * *
12011968 CGCTAAAGGTCTGTTCTATAGCGGCGTTTATAGGAAAAAGCGCCGCTAAAAGTCTTTATCTATAG
1 CGCTAAAGGTCTGATCTATAGCGGCATTTATA-GAAAAAGCGCCGCTAAAAGTCTTGATCTATAG
* * * * *
12012033 CAGCGTTTGT-GGAACAAGCGCCGCTAAAAGTCCTGATCTATAGCAGCGTTT-TGTTGAAAAACC
65 CAGCGTTT-TCGGAAAAAGCGCCGCTAAAAGTCATGATCTATAACAGCGTTTAT-TTCAAAAAAC
12012096 GT
128 GT
* * * * * *
12012098 CGCTAAAGGTCCTGATCTATAGCTGCATTTGT-GAAAAAGTGTCGTTAAAGGTCTTGATCTATAG
1 CGCTAAAGGT-CTGATCTATAGCGGCATTTATAGAAAAAGCGCCGCTAAAAGTCTTGATCTATAG
* * *
12012162 CGGCGTTTTCGGAAAAAGCGCCGCTAAAGGTCATGATCTATAACGGCGTTTATTTCAAAAAACGT
65 CAGCGTTTTCGGAAAAAGCGCCGCTAAAAGTCATGATCTATAACAGCGTTTATTTCAAAAAACGT
*
12012227 TGCTAAAG
1 CGCTAAAG
12012235 TTAGCGACGC
Statistics
Matches: 116, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
128 1 0.01
129 87 0.75
130 11 0.09
131 17 0.15
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (129 bp):
CGCTAAAGGTCTGATCTATAGCGGCATTTATAGAAAAAGCGCCGCTAAAAGTCTTGATCTATAGC
AGCGTTTTCGGAAAAAGCGCCGCTAAAAGTCATGATCTATAACAGCGTTTATTTCAAAAAACGT
Found at i:12020741 original size:20 final size:20
Alignment explanation
Indices: 12020716--12020754 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
12020706 TATAAAAGTT
12020716 ATAAATATTATATTATAAAC
1 ATAAATATTATATTATAAAC
*
12020736 ATAAATATTTTATTATAAA
1 ATAAATATTATATTATAAA
12020755 AATTAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (20 bp):
ATAAATATTATATTATAAAC
Found at i:12028643 original size:2 final size:2
Alignment explanation
Indices: 12028636--12028662 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12028626 ATACATGTAA
12028636 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
12028663 GTTTATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12029995 original size:43 final size:43
Alignment explanation
Indices: 12029873--12029992 Score: 129
Period size: 43 Copynumber: 2.8 Consensus size: 43
12029863 GGCTCGTACA
* * * *
12029873 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACTGATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACAAGAAAACACAGATCG
* *
12029916 ATGCC-ACTATCCCAGACAG-GGTCTTACACGAAAACACA-AGTCG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACAAGAAAACACAGA-TCG
12029959 ATGCCAACGTCCCAGACGTGGTCTTACAAAGAAA
1 ATGCCAACGTCCCAGACGTGGTCTTAC-AAGAAA
12029993 CACTTTTAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
42 4 0.06
43 52 0.81
44 8 0.12
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.20
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACAAGAAAACACAGATCG
Found at i:12032589 original size:45 final size:46
Alignment explanation
Indices: 12032461--12032589 Score: 138
Period size: 45 Copynumber: 2.8 Consensus size: 46
12032451 GCGCCTAAAG
* *
12032461 ATGAGTAAGACCATGGCTGAAAGACGCCATGGCATCA-CACTAACA
1 ATGAGTAAGACCATGGCTGAAAGACGCCATGACATCATGACTAACA
* ** * **
12032506 ATGAATAAGACCATAACTGAAAGATGTTATGACATCATGA-TATA-A
1 ATGAGTAAGACCATGGCTGAAAGACGCCATGACATCATGACTA-ACA
* *
12032551 TTGAGTAAGATCATGGCTGAAAGACGCCATGACATCATG
1 ATGAGTAAGACCATGGCTGAAAGACGCCATGACATCATG
12032590 GTAAACAAGA
Statistics
Matches: 66, Mismatches: 16, Indels: 4
0.77 0.19 0.05
Matches are distributed among these distances:
45 64 0.97
46 2 0.03
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.22
Consensus pattern (46 bp):
ATGAGTAAGACCATGGCTGAAAGACGCCATGACATCATGACTAACA
Found at i:12032617 original size:90 final size:90
Alignment explanation
Indices: 12032462--12032631 Score: 225
Period size: 90 Copynumber: 1.9 Consensus size: 90
12032452 CGCCTAAAGA
* * *
12032462 TGAGTAAGACCATGGCTGAAAGACGCCATGGCATCACACTAACAATGAATAAGACCATAACTGAA
1 TGAGTAAGACCATGGCTGAAAGACGCCATGACATCACACTAACAATGAATAAAAACATAACTGAA
*
12032527 AGATGTTATGACATCATGATATAAT
66 AGATGCTATGACATCATGATATAAT
* *** * **
12032552 TGAGTAAGATCATGGCTGAAAGACGCCATGACATCATGGTAAACAA-GATTAAAAACATAGTTGA
1 TGAGTAAGACCATGGCTGAAAGACGCCATGACATCACACT-AACAATGAATAAAAACATAACTGA
12032616 AAGATGCTATGACATC
65 AAGATGCTATGACATC
12032632 CTACGAAAGC
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
90 63 0.93
91 5 0.07
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.22
Consensus pattern (90 bp):
TGAGTAAGACCATGGCTGAAAGACGCCATGACATCACACTAACAATGAATAAAAACATAACTGAA
AGATGCTATGACATCATGATATAAT
Found at i:12032878 original size:27 final size:27
Alignment explanation
Indices: 12032846--12032919 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 27
12032836 ATAGTTTGGT
*
12032846 AGGACGTTAAATATGGGATAGTCC-A-
1 AGGACGTTAAACATGGGATAGTCCGAC
* *
12032871 ATGAGACGTTAAACACGAGATAGTCCGAC
1 A-G-GACGTTAAACATGGGATAGTCCGAC
12032900 AGGACGTTAAACATGGGATA
1 AGGACGTTAAACATGGGATA
12032920 ATCTGTCGAG
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
25 1 0.03
26 1 0.03
27 35 0.88
28 2 0.05
29 1 0.03
ACGTcount: A:0.38, C:0.15, G:0.27, T:0.20
Consensus pattern (27 bp):
AGGACGTTAAACATGGGATAGTCCGAC
Found at i:12033371 original size:31 final size:29
Alignment explanation
Indices: 12033307--12033375 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
12033297 CGATAATCGT
*** *
12033307 AAGTGACTAAAATGTAACATTTCAAACAT
1 AAGTGACTAAAATGTAACAAGACAAACAA
12033336 AAGTGACTAAAATGTAACCTAAGACAAACAA
1 AAGTGACTAAAATGTAA-C-AAGACAAACAA
12033367 AAGTGACTA
1 AAGTGACTA
12033376 TTTTGATAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 17 0.50
30 1 0.03
31 16 0.47
ACGTcount: A:0.51, C:0.14, G:0.13, T:0.22
Consensus pattern (29 bp):
AAGTGACTAAAATGTAACAAGACAAACAA
Found at i:12034080 original size:39 final size:40
Alignment explanation
Indices: 12034037--12034115 Score: 124
Period size: 39 Copynumber: 2.0 Consensus size: 40
12034027 TTAAAACTTG
* *
12034037 ACACTCGTATATACCGTGATAATCCT-AAAAAACGTATTT
1 ACACTCGTACATACCGTGATAATACTAAAAAAACGTATTT
*
12034076 ACACTCGTACATACGGTGATAATACTAAAAAAACGTATTT
1 ACACTCGTACATACCGTGATAATACTAAAAAAACGTATTT
12034116 TAAAAAATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 23 0.64
40 13 0.36
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (40 bp):
ACACTCGTACATACCGTGATAATACTAAAAAAACGTATTT
Found at i:12036023 original size:24 final size:24
Alignment explanation
Indices: 12035996--12036046 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
12035986 GCTACCTCAG
12035996 TTGGTGATCGAAAAAAAGATAAAT
1 TTGGTGATCGAAAAAAAGATAAAT
12036020 TTGGTGATCGAAAAAAAGATAAAT
1 TTGGTGATCGAAAAAAAGATAAAT
12036044 TTG
1 TTG
12036047 AATAGTTGGC
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:0.04, G:0.22, T:0.27
Consensus pattern (24 bp):
TTGGTGATCGAAAAAAAGATAAAT
Found at i:12037375 original size:20 final size:22
Alignment explanation
Indices: 12037350--12037391 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
12037340 CCATTATTGA
12037350 GAAATTGAT-G-AATTAAGCTT
1 GAAATTGATAGAAATTAAGCTT
12037370 GAAATTGATAGAAATTAAGCTT
1 GAAATTGATAGAAATTAAGCTT
12037392 AGATCATGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.45
21 1 0.05
22 10 0.50
ACGTcount: A:0.43, C:0.05, G:0.19, T:0.33
Consensus pattern (22 bp):
GAAATTGATAGAAATTAAGCTT
Found at i:12038034 original size:24 final size:24
Alignment explanation
Indices: 12038007--12038052 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
12037997 GAATTGATGA
12038007 TGAAT-TAAAATGAAATTATGAAAT
1 TGAATGTAAAATGAAA-TATGAAAT
* *
12038031 TGAATGTGAAATGATATATGAA
1 TGAATGTAAAATGAAATATGAA
12038053 TTGGATTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (24 bp):
TGAATGTAAAATGAAATATGAAAT
Found at i:12049102 original size:18 final size:18
Alignment explanation
Indices: 12049075--12049114 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
12049065 AATACTTGAG
*
12049075 TAAATCAGAATTAAAAAT
1 TAAATCAGAAATAAAAAT
*
12049093 TAAATTAGAAATAAAAAT
1 TAAATCAGAAATAAAAAT
12049111 TAAA
1 TAAA
12049115 ATTTGATAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.28
Consensus pattern (18 bp):
TAAATCAGAAATAAAAAT
Found at i:12049506 original size:6 final size:6
Alignment explanation
Indices: 12049495--12049524 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
12049485 AAAGAAAAAA
12049495 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
12049525 ATTCAATTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTCT
Found at i:12051515 original size:22 final size:22
Alignment explanation
Indices: 12051468--12051517 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
12051458 ACAAATGGCT
* *
12051468 TGTCTCGAGACAATTTACTCTG
1 TGTCTCGAGACAATCTACTCTA
12051490 TGTCTCGAGACAATCTA-TCGTA
1 TGTCTCGAGACAATCTACTC-TA
12051512 TGTCTC
1 TGTCTC
12051518 AAGATTAAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 2 0.08
22 23 0.92
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (22 bp):
TGTCTCGAGACAATCTACTCTA
Found at i:12054008 original size:17 final size:17
Alignment explanation
Indices: 12053962--12054009 Score: 51
Period size: 19 Copynumber: 2.7 Consensus size: 17
12053952 GAAACTCTTT
*
12053962 AAATTTCAAAAAATAAA
1 AAATTTCAAAATATAAA
* *
12053979 AATGGTTTTAAAATATAAA
1 AA--ATTTCAAAATATAAA
12053998 AAATTTCAAAAT
1 AAATTTCAAAAT
12054010 TCAATGTCAT
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
17 10 0.42
19 14 0.58
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.31
Consensus pattern (17 bp):
AAATTTCAAAATATAAA
Found at i:12054229 original size:23 final size:23
Alignment explanation
Indices: 12054197--12054246 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
12054187 AATTCAAAGC
12054197 AAATAAATTATTAAAACAT-TAA
1 AAATAAATTATTAAAACATATAA
12054219 AAATAGAATTATTAAAACATATAA
1 AAATA-AATTATTAAAACATATAA
12054243 AAAT
1 AAAT
12054247 CGGTCCAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 5 0.19
23 14 0.54
24 7 0.27
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (23 bp):
AAATAAATTATTAAAACATATAA
Found at i:12056839 original size:24 final size:24
Alignment explanation
Indices: 12056795--12056841 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
12056785 GTTTAAATGA
* **
12056795 TAGTTTTTGAATATATGGACTAAT
1 TAGTTTTTGAATACAAAGACTAAT
12056819 TAGTTTTTGAATACAAAGACTAA
1 TAGTTTTTGAATACAAAGACTAA
12056842 AGTATGAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.40
Consensus pattern (24 bp):
TAGTTTTTGAATACAAAGACTAAT
Found at i:12057323 original size:71 final size:71
Alignment explanation
Indices: 12057205--12057338 Score: 189
Period size: 71 Copynumber: 1.9 Consensus size: 71
12057195 AGTACGAATC
*
12057205 ATTCTTTATCGATGGCTAAGACCCAACATATGTTGCGGATTCGCGACAGCTTGAGTGAACAACGT
1 ATTCTTTATCGATGGCTAAGACCCAACATATATTGCGGATTCGCGACAGCTTGAGTGAACAACGT
12057270 CAAATT
66 CAAATT
* ** * * *
12057276 ATTCTTTATCGATGGTTGGGATCCAACATATATTGCGGATGT-TCGACAGCTTGAGTGAGCAAC
1 ATTCTTTATCGATGGCTAAGACCCAACATATATTGCGGAT-TCGCGACAGCTTGAGTGAACAAC
12057339 ATCGAATAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
71 54 0.98
72 1 0.02
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (71 bp):
ATTCTTTATCGATGGCTAAGACCCAACATATATTGCGGATTCGCGACAGCTTGAGTGAACAACGT
CAAATT
Found at i:12062211 original size:33 final size:33
Alignment explanation
Indices: 12062170--12062244 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 33
12062160 TAGTCTGTTA
* * *
12062170 GGACAGTAAATAAATAACATAAATAGTCCACTG
1 GGACAGTAAACAAAGAACAGAAATAGTCCACTG
* * * *
12062203 GGATAGTAAACACAGAATAGAGATAGTCCACTG
1 GGACAGTAAACAAAGAACAGAAATAGTCCACTG
12062236 GGACAGTAA
1 GGACAGTAA
12062245 CCACAGATAG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.45, C:0.15, G:0.21, T:0.19
Consensus pattern (33 bp):
GGACAGTAAACAAAGAACAGAAATAGTCCACTG
Found at i:12062250 original size:33 final size:32
Alignment explanation
Indices: 12062192--12062256 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 32
12062182 AATAACATAA
*
12062192 ATAGTCCACTGGGATAGTAAACACAGAATAGAG
1 ATAGTCCACTGGGACAGTAAACACAG-ATAGAG
*
12062225 ATAGTCCACTGGGACAGTAACCACAGATAGAG
1 ATAGTCCACTGGGACAGTAAACACAGATAGAG
12062257 TATGTGGGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 6 0.20
33 24 0.80
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (32 bp):
ATAGTCCACTGGGACAGTAAACACAGATAGAG
Found at i:12062948 original size:6 final size:6
Alignment explanation
Indices: 12062937--12062965 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
12062927 ACTTTTAGAC
12062937 TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
1 TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
12062966 AATTTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.66
Consensus pattern (6 bp):
TTTAGT
Found at i:12062989 original size:20 final size:20
Alignment explanation
Indices: 12062921--12062978 Score: 66
Period size: 18 Copynumber: 3.0 Consensus size: 20
12062911 ATTAAATTAT
* *
12062921 TTTTAGACTTTTAGACTTTAG
1 TTTTAGAATTTTAG-TTTTAG
12062942 TTTTAG--TTTTAGTTTTAG
1 TTTTAGAATTTTAGTTTTAG
*
12062960 TTTTAGAATTTTATTTTTA
1 TTTTAGAATTTTAGTTTTA
12062979 TTTATTAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
18 11 0.33
19 6 0.18
20 10 0.30
21 6 0.18
ACGTcount: A:0.22, C:0.03, G:0.12, T:0.62
Consensus pattern (20 bp):
TTTTAGAATTTTAGTTTTAG
Found at i:12073042 original size:49 final size:49
Alignment explanation
Indices: 12072970--12073063 Score: 152
Period size: 49 Copynumber: 1.9 Consensus size: 49
12072960 ATTCAAACAC
** *
12072970 CATTTTAAAGTTATGTACACTAAGGAGTGTCCTAGAAACAAGGTTTTTG
1 CATTTTAAAGCCATGTACACTAAGGAGTGTCCCAGAAACAAGGTTTTTG
*
12073019 CATTTTAAAGCCATGTACACTAAGGAGTGTCCCAGAAATAAGGTT
1 CATTTTAAAGCCATGTACACTAAGGAGTGTCCCAGAAACAAGGTT
12073064 CTTACATATG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (49 bp):
CATTTTAAAGCCATGTACACTAAGGAGTGTCCCAGAAACAAGGTTTTTG
Found at i:12075315 original size:95 final size:92
Alignment explanation
Indices: 12075184--12075354 Score: 227
Period size: 95 Copynumber: 1.8 Consensus size: 92
12075174 AATTTAATTT
* *
12075184 CTCGTTTTGGAAATAAAATAAAAAAAGGAATAAAATCTGCTGCACGGCGGGAATAAATCCCAAAA
1 CTCGTTTTGGAAATAAAATAAAAAAAGGAATAAAATCCGCTGAACGGCGGGAATAAAT-CCAAAA
12075249 CAGATTTTATTCTATATTTAAAAAGAAA
65 CAGATTTTATTCTATATTTAAAAAGAAA
** * * *
12075277 CTCGTTTTTGGAAATAAAAATCAAAATTA-GAATAAAATCCGTTGAACGGCGGGGATAAATCCGA
1 CTCG-TTTTGGAAAT-AAAAT-AAAAAAAGGAATAAAATCCGCTGAACGGCGGGAATAAATCCAA
*
12075341 AACATATTTTATTC
63 AACAGATTTTATTC
12075355 ACCTTTGTTA
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
93 4 0.06
94 26 0.39
95 32 0.48
96 5 0.07
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.27
Consensus pattern (92 bp):
CTCGTTTTGGAAATAAAATAAAAAAAGGAATAAAATCCGCTGAACGGCGGGAATAAATCCAAAAC
AGATTTTATTCTATATTTAAAAAGAAA
Found at i:12077430 original size:31 final size:32
Alignment explanation
Indices: 12077372--12077435 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
12077362 AGAGATAGAG
* *
12077372 ATCCCATGTATATCCCTTGTTTTTTTATGCTT
1 ATCCCAGGTATATCCCATGTTTTTTTATGCTT
12077404 ATCCCAGGTATATCCCATG-TTTTTTATGCTT
1 ATCCCAGGTATATCCCATGTTTTTTTATGCTT
12077435 A
1 A
12077436 ATATAACTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.19, C:0.22, G:0.11, T:0.48
Consensus pattern (32 bp):
ATCCCAGGTATATCCCATGTTTTTTTATGCTT
Found at i:12079774 original size:15 final size:15
Alignment explanation
Indices: 12079754--12079786 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
12079744 TTTACTCACC
12079754 GCTAATAAAAAAAAT
1 GCTAATAAAAAAAAT
12079769 GCTAATAAAAAAAAT
1 GCTAATAAAAAAAAT
12079784 GCT
1 GCT
12079787 TTTACCAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.61, C:0.09, G:0.09, T:0.21
Consensus pattern (15 bp):
GCTAATAAAAAAAAT
Found at i:12084633 original size:18 final size:19
Alignment explanation
Indices: 12084610--12084645 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
12084600 TTATACATTC
12084610 ATAATTTACATA-TATATA
1 ATAATTTACATACTATATA
12084628 ATAATTTACATACTATAT
1 ATAATTTACATACTATAT
12084646 GTTCTTAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.44
Consensus pattern (19 bp):
ATAATTTACATACTATATA
Found at i:12100971 original size:40 final size:39
Alignment explanation
Indices: 12100927--12101022 Score: 147
Period size: 40 Copynumber: 2.4 Consensus size: 39
12100917 GCGTTTGGAT
*
12100927 AAAAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTA
1 AAAAAACGCCGCTAAAGATCGAGCATTAGCAGCGCTTTA
12100966 CAAAAAACGCCGCTAAAGATCGAGCATTAGCAGCGCTTTA
1 -AAAAAACGCCGCTAAAGATCGAGCATTAGCAGCGCTTTA
* *
12101006 AGGAAAGCGCCGCTAAA
1 A-AAAAACGCCGCTAAA
12101023 AATAAGAATT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
39 1 0.02
40 51 0.98
ACGTcount: A:0.38, C:0.24, G:0.23, T:0.16
Consensus pattern (39 bp):
AAAAAACGCCGCTAAAGATCGAGCATTAGCAGCGCTTTA
Found at i:12101197 original size:41 final size:41
Alignment explanation
Indices: 12101099--12101293 Score: 293
Period size: 41 Copynumber: 4.8 Consensus size: 41
12101089 TGACCTTTTG
*
12101099 GGGCTTTAGCGGCGTTTTTGGAGAAGTGCCGCTAAT-CTCC
1 GGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCC
* *
12101139 GCGCTTTAGCGGTGTTTTTGGAGAAGCGCCGCTAATGCTCC
1 GGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCC
12101180 GGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCC
1 GGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCC
* *
12101221 GGGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCC
** * * *
12101262 ATGCTTTAGCGGCTTTTTTGAAAAAGCGCCGC
1 GGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGC
12101294 AAAAGCATTT
Statistics
Matches: 143, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
40 33 0.23
41 110 0.77
ACGTcount: A:0.17, C:0.23, G:0.31, T:0.29
Consensus pattern (41 bp):
GGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCC
Found at i:12101649 original size:14 final size:14
Alignment explanation
Indices: 12101624--12101666 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
12101614 AGTTTTATAT
12101624 ATTATGGGATTAGGG
1 ATTAT-GGATTAGGG
12101639 ATTATGGATTAGGG
1 ATTATGGATTAGGG
* *
12101653 GTTCTGGATTAGGG
1 ATTATGGATTAGGG
12101667 GTTCTGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 21 0.81
15 5 0.19
ACGTcount: A:0.23, C:0.02, G:0.40, T:0.35
Consensus pattern (14 bp):
ATTATGGATTAGGG
Found at i:12101667 original size:14 final size:14
Alignment explanation
Indices: 12101630--12101697 Score: 75
Period size: 14 Copynumber: 4.9 Consensus size: 14
12101620 ATATATTATG
* *
12101630 GGATTAGGGATTAT
1 GGATTAGGGGTTCT
12101644 GGATTAGGGGTTCT
1 GGATTAGGGGTTCT
12101658 GGATTAGGGGTTCT
1 GGATTAGGGGTTCT
* * *
12101672 GGTTTAAGGGTTGT
1 GGATTAGGGGTTCT
12101686 -GATTTAGGGGTT
1 GGA-TTAGGGGTT
12101698 AGGGTTAGAG
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
13 1 0.02
14 45 0.98
ACGTcount: A:0.18, C:0.03, G:0.41, T:0.38
Consensus pattern (14 bp):
GGATTAGGGGTTCT
Found at i:12101914 original size:21 final size:21
Alignment explanation
Indices: 12101890--12101957 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
12101880 TAAATAAGGT
12101890 TTAGGGGTTAGTAGTTAGGGG
1 TTAGGGGTTAGTAGTTAGGGG
*
12101911 TTAGGGGTTAG-AGCTTAGAGG
1 TTAGGGGTTAGTAG-TTAGGGG
* * * *
12101932 TTAAGAGTTAGTGATTTAGGGT
1 TTAGGGGTTAGT-AGTTAGGGG
12101954 TTAG
1 TTAG
12101958 AGATTCGGGG
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
20 2 0.05
21 26 0.70
22 8 0.22
23 1 0.03
ACGTcount: A:0.24, C:0.01, G:0.40, T:0.35
Consensus pattern (21 bp):
TTAGGGGTTAGTAGTTAGGGG
Found at i:12114853 original size:108 final size:108
Alignment explanation
Indices: 12114659--12114977 Score: 503
Period size: 108 Copynumber: 3.0 Consensus size: 108
12114649 ATTGGTTGTG
* * * *
12114659 GAACCATGAGAACTTTAAATAGATGAAGCATGAACTTGAGTTGATGATTGGCATAACAGAGCATA
1 GAACCATGAGAACTTTAAATAGACGAAGCTTGAACTTGAGTTGATGATTGGCATGACAGAGCATG
*
12114724 GTGGTCATAATCACTATCGGAGACAATTTTTGCATTTTCCCTA
66 GTGGTCATAATCACTACCGGAGACAATTTTTGCATTTTCCCTA
* * * * *
12114767 GAACCATGAGAGCTTTAAATGGACGAAGCTTGAACTTGAGTTGATGATTGGCGTGACAAAGCACG
1 GAACCATGAGAACTTTAAATAGACGAAGCTTGAACTTGAGTTGATGATTGGCATGACAGAGCATG
*
12114832 GTGGTCATACTCACTACCGGAGACAATTTTTGCATTTTCCCTA
66 GTGGTCATAATCACTACCGGAGACAATTTTTGCATTTTCCCTA
* * * *
12114875 GAACCATGAGAACTTTAAATAGACGAAACTTGAACTTGAATTGATGATTGGCATGATAGAGCTTG
1 GAACCATGAGAACTTTAAATAGACGAAGCTTGAACTTGAGTTGATGATTGGCATGACAGAGCATG
12114940 GTGGTCATAATCACTACCGGAGACAATTTTTGCATTTT
66 GTGGTCATAATCACTACCGGAGACAATTTTTGCATTTT
12114978 TTAAAAAGTA
Statistics
Matches: 190, Mismatches: 21, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
108 190 1.00
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (108 bp):
GAACCATGAGAACTTTAAATAGACGAAGCTTGAACTTGAGTTGATGATTGGCATGACAGAGCATG
GTGGTCATAATCACTACCGGAGACAATTTTTGCATTTTCCCTA
Found at i:12115132 original size:17 final size:17
Alignment explanation
Indices: 12115110--12115142 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
12115100 TTTTGGTCAT
12115110 CAAAAAATAAAATTTGC
1 CAAAAAATAAAATTTGC
12115127 CAAAAAATAAAATTTG
1 CAAAAAATAAAATTTG
12115143 AAACTAGGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.61, C:0.09, G:0.06, T:0.24
Consensus pattern (17 bp):
CAAAAAATAAAATTTGC
Found at i:12122254 original size:30 final size:30
Alignment explanation
Indices: 12122218--12122280 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
12122208 ACTTATTTTA
*
12122218 TTGTTAATTTTGTTATTTTTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
* *
12122248 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
12122278 TTG
1 TTG
12122281 CTTGTTAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.24, C:0.03, G:0.14, T:0.59
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:12122401 original size:17 final size:18
Alignment explanation
Indices: 12122362--12122402 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
12122352 GAAAATATTT
*
12122362 TTTTTGATGTCTTTAGTA
1 TTTTTGATGTATTTAGTA
12122380 TTTTTGATGTATTATA-TA
1 TTTTTGATGTATT-TAGTA
12122398 TTTTT
1 TTTTT
12122403 TAAAATTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 19 0.90
19 2 0.10
ACGTcount: A:0.20, C:0.02, G:0.12, T:0.66
Consensus pattern (18 bp):
TTTTTGATGTATTTAGTA
Found at i:12122434 original size:12 final size:12
Alignment explanation
Indices: 12122404--12122436 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
12122394 TATATTTTTT
12122404 AAAATT-ATATA
1 AAAATTAATATA
12122415 AAAA-TAATATA
1 AAAATTAATATA
12122426 AAAATTAATAT
1 AAAATTAATAT
12122437 GGGCAGGCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:12122603 original size:12 final size:12
Alignment explanation
Indices: 12122586--12122610 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12122576 ACCTCTAACC
12122586 TATTCTATGTAA
1 TATTCTATGTAA
12122598 TATTCTATGTAA
1 TATTCTATGTAA
12122610 T
1 T
12122611 TTTAGATTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (12 bp):
TATTCTATGTAA
Found at i:12124389 original size:17 final size:18
Alignment explanation
Indices: 12124364--12124399 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
12124354 TACCCTCAAA
*
12124364 ATAATATAATT-TATTTT
1 ATAAAATAATTATATTTT
12124381 ATAAAATAATTATATTTT
1 ATAAAATAATTATATTTT
12124399 A
1 A
12124400 ATCATTACCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATAAAATAATTATATTTT
Found at i:12124943 original size:3 final size:3
Alignment explanation
Indices: 12124935--12124982 Score: 69
Period size: 3 Copynumber: 15.7 Consensus size: 3
12124925 TAGCTAAAGG
* *
12124935 AGA AGA AGA AGA AGA GAGA TGA AGG AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA -AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
12124981 AG
1 AG
12124983 GTGGTGCGGA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.60, C:0.00, G:0.38, T:0.02
Consensus pattern (3 bp):
AGA
Found at i:12125310 original size:39 final size:38
Alignment explanation
Indices: 12125200--12125407 Score: 133
Period size: 39 Copynumber: 5.4 Consensus size: 38
12125190 GTTTAGTTAT
* * ***
12125200 TAATAATTATTGTTACTTAGTATTATTATTAGTAAAAAAT
1 TAATTATTATTGTTAGTTAGTA-TATT-TTAGTAAAACCC
* **
12125240 TAATATTATTATGGTTAGTTA-T-TAGGATTAGTAAAACCC
1 T-A-ATTATTATTGTTAGTTAGTATA-TTTTAGTAAAACCC
*** *
12125279 TAATTATTATT-TTAGTTAGTATGATTGTTAGTTTTTA-CA
1 TAATTATTATTGTTAGTTAGTAT-ATT-TTAG-TAAAACCC
* *
12125318 TTA-TATTATTGTTAGTTATTAT-TTTTAGTAAAACCC
1 TAATTATTATTGTTAGTTAGTATATTTTAGTAAAACCC
**
12125354 TAATTATTATTGTTAGTTAGTATTATTTTGAGTAAAAAAC
1 TAATTATTATTGTTAGTTAGTA-TATTTT-AGTAAAACCC
12125394 T-ATTATTATTGTTA
1 TAATTATTATTGTTA
12125408 TTGTGTTAGT
Statistics
Matches: 129, Mismatches: 25, Indels: 29
0.70 0.14 0.16
Matches are distributed among these distances:
35 2 0.02
36 14 0.11
37 28 0.22
38 10 0.08
39 47 0.36
40 12 0.09
41 2 0.02
42 14 0.11
ACGTcount: A:0.35, C:0.04, G:0.11, T:0.50
Consensus pattern (38 bp):
TAATTATTATTGTTAGTTAGTATATTTTAGTAAAACCC
Found at i:12133239 original size:8 final size:8
Alignment explanation
Indices: 12133226--12133260 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
12133216 AATAAAAATA
12133226 TATTATTT
1 TATTATTT
12133234 TATTATTT
1 TATTATTT
12133242 TATTATTT
1 TATTATTT
*
12133250 ACATTATTT
1 -TATTATTT
12133259 TA
1 TA
12133261 GTACATTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 17 0.71
9 7 0.29
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.69
Consensus pattern (8 bp):
TATTATTT
Found at i:12133407 original size:156 final size:157
Alignment explanation
Indices: 12133093--12133601 Score: 707
Period size: 156 Copynumber: 3.3 Consensus size: 157
12133083 GGCTGTTACA
*
12133093 ACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTGTGTTTTTTAAATAAATTTCAAA
1 ACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTGTGTTTTTTAAATAAATTTTAAA
** *
12133158 AATTAACCCTTATTTCGGCCCTTTGTTCACATTTTTCTTCGCGAATTTTATTACTTTCAATAAAA
66 AATTAACCCTTATTTCGGCCCTTTGTTCGTA-TTTT-TTCTCGAATTTTATTACTTTCAATAAAA
*
12133223 ATATATTATTTTAT-TATTTTATTA-TTT
129 ATATATTATTTTTTGTATTTTATTATTTT
12133250 ACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTGT-TTTTTTAAATAAATTTTAAA
1 ACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTGTGTTTTTTAAATAAATTTTAAA
*
12133314 AATTAACCCTTATTTCGGCCCTTTGTTTGTATTTTTTCTCGAATTTTATTACTTTCAATAAAAAT
66 AATTAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTCTCGAATTTTATTACTTTCAATAAAAAT
12133379 ATATTATTTTTTGTATTTTATTATTTT
131 ATATTATTTTTTGTATTTTATTATTTT
*
12133406 ACATTATTTCAGTACATTATGTTTGAAATGTATTAATTTAGTGTGTTTTTTAAATAAA-TTTAGT
1 ACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTGTGTTTTTTAAATAAATTTTA--
* * * ** * *
12133470 AAAA--AACTCTTATTTCGGCCATTTATTCGTATTTTTT-TACCGAAGCCTCATT-GTTTC-A-A
64 AAAATTAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTCT--CGAA-TTTTATTACTTTCAATA
* *
12133529 AAAATATATTA-TTTTCGTATTTTATCATTTT
126 AAAATATATTATTTTTTGTATTTTATTATTTT
** *
12133560 ACGCTATTTTAGTACATTATGTTTGAAATGCATTAATTTAGT
1 ACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGT
12133602 AAAAAACCCT
Statistics
Matches: 323, Mismatches: 21, Indels: 19
0.89 0.06 0.05
Matches are distributed among these distances:
154 96 0.30
155 27 0.08
156 127 0.39
157 65 0.20
158 8 0.02
ACGTcount: A:0.30, C:0.10, G:0.09, T:0.51
Consensus pattern (157 bp):
ACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTGTGTTTTTTAAATAAATTTTAAA
AATTAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTCTCGAATTTTATTACTTTCAATAAAAAT
ATATTATTTTTTGTATTTTATTATTTT
Found at i:12133956 original size:19 final size:19
Alignment explanation
Indices: 12133928--12133965 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
12133918 TTTTTTACAT
*
12133928 AAATATTACAAAAAAATTA
1 AAATAATACAAAAAAATTA
12133947 AAATAATACAAAAAAATTA
1 AAATAATACAAAAAAATTA
12133966 TCTTTACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (19 bp):
AAATAATACAAAAAAATTA
Found at i:12133991 original size:10 final size:10
Alignment explanation
Indices: 12133978--12134075 Score: 52
Period size: 10 Copynumber: 9.2 Consensus size: 10
12133968 TTTACTTATT
12133978 TTTTTCTTTC
1 TTTTTCTTTC
*
12133988 TTTTTCCTTC
1 TTTTTCTTTC
* **
12133998 TCTCCCTCTTC
1 TTTTTCT-TTC
* *
12134009 TTCTCCTTTC
1 TTTTTCTTTC
*
12134019 CTTTTCTTTC
1 TTTTTCTTTC
*
12134029 TTTTCCTTTC
1 TTTTTCTTTC
*
12134039 TTCTCCTTTCCTTCC
1 -T-T--TTT-CTTTC
*
12134054 CTTTTCTTTC
1 TTTTTCTTTC
12134064 TTTTTCTTTC
1 TTTTTCTTTC
12134074 TT
1 TT
12134076 CTCCTTCTTT
Statistics
Matches: 64, Mismatches: 18, Indels: 12
0.68 0.19 0.13
Matches are distributed among these distances:
10 45 0.70
11 11 0.17
12 1 0.02
13 1 0.02
14 2 0.03
15 4 0.06
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (10 bp):
TTTTTCTTTC
Found at i:12134022 original size:5 final size:5
Alignment explanation
Indices: 12134012--12134073 Score: 54
Period size: 5 Copynumber: 12.4 Consensus size: 5
12134002 CCTCTTCTTC
* * * *
12134012 TCCTT TCCTT TTCTT TCTTT TCCTT T-CTT CTCCTT TCCTT CCCTT TTCTT
1 TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT -TCCTT TCCTT TCCTT TCCTT
* *
12134062 TCTTT TTCTT TC
1 TCCTT TCCTT TC
12134074 TTCTCCTTCT
Statistics
Matches: 43, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
4 3 0.07
5 37 0.86
6 3 0.07
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (5 bp):
TCCTT
Found at i:12134057 original size:35 final size:36
Alignment explanation
Indices: 12133979--12134083 Score: 131
Period size: 35 Copynumber: 2.8 Consensus size: 36
12133969 TTACTTATTT
* *
12133979 TTTTCTTTCTTTTTCCTTCTCTCCCTCTTCTTCTCCTTTCC
1 TTTTCTTTC-TTTTCCTT-TCT---TCTCCTTCTCCTTCCC
12134020 TTTTCTTTCTTTTCCTTTCTTCTCCTT-TCCTTCCC
1 TTTTCTTTCTTTTCCTTTCTTCTCCTTCTCCTTCCC
*
12134055 TTTTCTTTCTTTTTCTTTCTTCTCCTTCT
1 TTTTCTTTCTTTTCCTTTCTTCTCCTTCT
12134084 TTCTTCTCTC
Statistics
Matches: 60, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
35 33 0.55
36 7 0.12
39 3 0.05
40 8 0.13
41 9 0.15
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (36 bp):
TTTTCTTTCTTTTCCTTTCTTCTCCTTCTCCTTCCC
Found at i:12134070 original size:41 final size:41
Alignment explanation
Indices: 12133976--12134072 Score: 98
Period size: 40 Copynumber: 2.4 Consensus size: 41
12133966 TCTTTACTTA
*
12133976 TTTT-TTTCTTTCT-TTTTCCTTCTCTCCCTCTTCTTCTCC
1 TTTTCTTTCTTTTTCTTTTCCTTCTCTCCCTCTTCTTCTCC
* *
12134015 TTTCCTTT-TCTTTCTTTTCCTT-TCTTCTCCT-TTCCTTC-CC
1 TTTTCTTTCTTTTTCTTTTCCTTCTC-TC-CCTCTT-CTTCTCC
12134055 TTTTCTTTCTTTTTCTTT
1 TTTTCTTTCTTTTTCTTT
12134073 CTTCTCCTTC
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
39 8 0.17
40 24 0.51
41 15 0.32
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (41 bp):
TTTTCTTTCTTTTTCTTTTCCTTCTCTCCCTCTTCTTCTCC
Found at i:12134091 original size:13 final size:13
Alignment explanation
Indices: 12134067--12134091 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12134057 TTCTTTCTTT
12134067 TTCTTTCTTCTCC
1 TTCTTTCTTCTCC
12134080 TTCTTTCTTCTC
1 TTCTTTCTTCTC
12134092 TCCAGTCGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (13 bp):
TTCTTTCTTCTCC
Found at i:12134419 original size:26 final size:26
Alignment explanation
Indices: 12134371--12134420 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
12134361 GTATTTTATT
*
12134371 TTTATTATTTTTAATTTTCTTTAAGG
1 TTTATTATTTTTAAATTTCTTTAAGG
12134397 TTTATTATTTTTATAATTT-TTTAA
1 TTTATTATTTTTA-AATTTCTTTAA
12134421 ATGATGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (26 bp):
TTTATTATTTTTAAATTTCTTTAAGG
Found at i:12143149 original size:9 final size:9
Alignment explanation
Indices: 12143132--12143162 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
12143122 TTGAGTTGAT
12143132 TCGAATAAC
1 TCGAATAAC
*
12143141 TCGATTAAC
1 TCGAATAAC
12143150 TCGAATAAC
1 TCGAATAAC
12143159 TCGA
1 TCGA
12143163 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:12144122 original size:23 final size:24
Alignment explanation
Indices: 12144096--12144146 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
12144086 AAAAATCAAA
* *
12144096 ATATGTAATATACA-AAATAATAT
1 ATATGTAATATAAATAAATAATAC
*
12144119 ATAT-TAATCTAAATAAATAATAC
1 ATATGTAATATAAATAAATAATAC
12144142 ATATG
1 ATATG
12144147 GAATGAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.35
Consensus pattern (24 bp):
ATATGTAATATAAATAAATAATAC
Found at i:12144301 original size:185 final size:185
Alignment explanation
Indices: 12144029--12144366 Score: 626
Period size: 185 Copynumber: 1.8 Consensus size: 185
12144019 ACAAATAATC
12144029 AATAAATACTATATGAAATGATAATATCAAAATGAATTTCAAAGTAAATATTGTATAAAAAATCA
1 AATAAATACTATATGAAATGATAATATCAAAATGAATTTCAAAGTAAATATTGTATAAAAAATCA
12144094 AAATATGTAATATACAAAATAATATATATTAATCTAAATAAATAATACATATGGAATGAAAAATT
66 AAATATGTAATATACAAAATAATATATATTAATCTAAATAAATAATACATATGGAATGAAAAATT
*
12144159 CGAAATAAATAA-A-TATATATACGAGTTTGAAATAGATAAAAAATGAAGATAAA
131 CCAAATAAATAATATTATATATACGAGTTTGAAATAGATAAAAAATGAAGATAAA
12144212 AATAAATACTATATGAAATGATAATATCAAAATGAATTTTCAAAGTAAATATTGTATAAAAAAAT
1 AATAAATACTATATGAAATGATAATATCAAAATGAA-TTTCAAAGTAAATATTGTAT-AAAAAAT
12144277 CAAAATATGTAATATACAAAATAATATATATTAATCTAAATAAATAATACATATGGAATGAAAAA
64 CAAAATATGTAATATACAAAATAATATATATTAATCTAAATAAATAATACATATGGAATGAAAAA
*
12144342 TTCCAAATAGATAATATTATATATA
129 TTCCAAATAAATAATATTATATATA
12144367 TATAAAGATA
Statistics
Matches: 149, Mismatches: 2, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
183 36 0.24
184 20 0.13
185 84 0.56
186 1 0.01
187 8 0.05
ACGTcount: A:0.56, C:0.05, G:0.08, T:0.31
Consensus pattern (185 bp):
AATAAATACTATATGAAATGATAATATCAAAATGAATTTCAAAGTAAATATTGTATAAAAAATCA
AAATATGTAATATACAAAATAATATATATTAATCTAAATAAATAATACATATGGAATGAAAAATT
CCAAATAAATAATATTATATATACGAGTTTGAAATAGATAAAAAATGAAGATAAA
Found at i:12144307 original size:23 final size:24
Alignment explanation
Indices: 12144281--12144331 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
12144271 AAAAATCAAA
* *
12144281 ATATGTAATATACA-AAATAATAT
1 ATATGTAATATAAATAAATAATAC
*
12144304 ATAT-TAATCTAAATAAATAATAC
1 ATATGTAATATAAATAAATAATAC
12144327 ATATG
1 ATATG
12144332 GAATGAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.35
Consensus pattern (24 bp):
ATATGTAATATAAATAAATAATAC
Found at i:12144880 original size:20 final size:20
Alignment explanation
Indices: 12144840--12144880 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
12144830 AAATGGATTT
* *
12144840 AAAACAAATTTAGAAAGAAA
1 AAAACAAAATTAAAAAGAAA
*
12144860 AAAACAAAATTAAAAATAAA
1 AAAACAAAATTAAAAAGAAA
12144880 A
1 A
12144881 TAAAGGACCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.15
Consensus pattern (20 bp):
AAAACAAAATTAAAAAGAAA
Found at i:12146659 original size:51 final size:51
Alignment explanation
Indices: 12146578--12146979 Score: 606
Period size: 51 Copynumber: 7.9 Consensus size: 51
12146568 CATAATTTGT
* * * *
12146578 AGCTTTAATCTATTCCGCTGTAACGTCAGGGAAATAAGATTCGCTGCCTTC
1 AGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* *
12146629 AGCTTTAATCTGTTCCACTACAACGCCAGGGAAATAAGATTCGTTGCCTTC
1 AGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* ** *
12146680 AGTTTTAATCTACTCCACTACAACGCCAGGGAAATAAGATTCGCTGCCTTC
1 AGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* * *
12146731 AGCTTTAATCTGTTCCACTGCAACGCCAGAGAAATAAAATTCGCTACCTTC
1 AGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* * *
12146782 AACTTTAATCTGCTCCACTGCAACGCCAGGGAAATAAGATTCGCTACCTTC
1 AGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* * *
12146833 AACTTTAATCTATTCCACTACAACGCCAGGGAAATAAGATTCGCTGCCTTC
1 AGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
* *
12146884 AACTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCACTGCCTTC
1 AGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
*
12146935 AGCTTTAATCTGTTCCACTGCAACACCAGGGAAATAAGATTCGCT
1 AGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCT
12146980 ATAATGACTT
Statistics
Matches: 320, Mismatches: 31, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 320 1.00
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (51 bp):
AGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGCCTTC
Found at i:12149283 original size:30 final size:31
Alignment explanation
Indices: 12149242--12149306 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
12149232 ATTTTCGAGC
12149242 TTGGGGACAAAAGTGTAATTATGC-AAAAGT
1 TTGGGGACAAAAGTGTAATTATGCAAAAAGT
* * * *
12149272 TTGGGGGCAAAATTGTAATTTTTCAAAAAGT
1 TTGGGGACAAAAGTGTAATTATGCAAAAAGT
12149303 TTGG
1 TTGG
12149307 TGGTGGATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 20 0.67
31 10 0.33
ACGTcount: A:0.35, C:0.06, G:0.26, T:0.32
Consensus pattern (31 bp):
TTGGGGACAAAAGTGTAATTATGCAAAAAGT
Found at i:12149787 original size:76 final size:75
Alignment explanation
Indices: 12149661--12149837 Score: 284
Period size: 76 Copynumber: 2.3 Consensus size: 75
12149651 TGATTCCCCC
* *
12149661 AAGGGGTTGCTAAGTGTTGATTCCCCGAATCATTGGTGGTTGTTAAGTGTTGATTCCACCATATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGTTGATTCCACCATATC
*
12149726 TTTGAATGTGA
66 -TTAAATGTGA
*
12149737 AAGGGGTTGCTAAGTGCTGATTCCCC-AATTCATTGGTGGTTGCTAAGTGTTGATTCCACCGTAT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAA-TCATTGGTGGTTGCTAAGTGTTGATTCCACCATAT
12149801 CTTAAATGTGA
65 CTTAAATGTGA
*
12149812 AGGGGGTTGCTAAGTGCTGATTCCCC
1 AAGGGGTTGCTAAGTGCTGATTCCCC
12149838 CGAGGGGTTG
Statistics
Matches: 95, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
75 36 0.38
76 59 0.62
ACGTcount: A:0.21, C:0.17, G:0.27, T:0.34
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGTTGATTCCACCATATC
TTAAATGTGA
Found at i:12149857 original size:102 final size:102
Alignment explanation
Indices: 12149738--12149939 Score: 334
Period size: 102 Copynumber: 2.0 Consensus size: 102
12149728 TGAATGTGAA
* ** *
12149738 AGGGGTTGCTAAGTGCTGATTCCCC-AATTCATTGGTGGTTGCTAAGTGTTGATTCCACCGTATC
1 AGGGGTTGCTAAGTGCTGATTCCCCGAA-TCATTGGTGGTTGCTAAGTGCTGAACCCACCGTAAC
*
12149802 TTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCG
65 TTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCCG
*
12149840 AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGTTAAGTGCTGAACCCACCGTAACT
1 AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGAACCCACCGTAACT
12149905 TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCC
66 TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCC
12149940 GATTCATTGG
Statistics
Matches: 93, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
102 91 0.98
103 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.31
Consensus pattern (102 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGAACCCACCGTAACT
TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCCG
Found at i:12149963 original size:75 final size:76
Alignment explanation
Indices: 12149840--12149979 Score: 246
Period size: 75 Copynumber: 1.9 Consensus size: 76
12149830 GATTCCCCCG
*
12149840 AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGTTAAGTGCTGAACCCACCG-TAAC
1 AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGAACCCACCGATAAC
12149904 TTAAATGTGAA
66 TTAAATGTGAA
* *
12149915 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGAATCCACCGATAAC
1 AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGAACCCACCGATAAC
12149980 GGTTAACATT
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
75 57 0.93
76 4 0.07
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (76 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGAACCCACCGATAAC
TTAAATGTGAA
Found at i:12151700 original size:24 final size:24
Alignment explanation
Indices: 12151653--12151700 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
12151643 TGGTAGACTT
* *
12151653 TAATGCATATGATGTAATGTAATG
1 TAATGCAAATGATGAAATGTAATG
12151677 TAATGCAAATGCATGAAATG-AATG
1 TAATGCAAATG-ATGAAATGTAATG
12151701 CAAAAATGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.42, C:0.06, G:0.21, T:0.31
Consensus pattern (24 bp):
TAATGCAAATGATGAAATGTAATG
Found at i:12154002 original size:20 final size:20
Alignment explanation
Indices: 12153953--12154024 Score: 56
Period size: 20 Copynumber: 3.5 Consensus size: 20
12153943 TAAAAATATA
* *
12153953 TAAAATAATGCATGATGAATT
1 TAAAATAATGCATGA-AAACT
12153974 TGAATAATAATGCATGAAAACT
1 T-AA-AATAATGCATGAAAACT
**
12153996 TAAAATATATG-AAAAAAACT
1 TAAAATA-ATGCATGAAAACT
*
12154016 TTAAATAAT
1 TAAAATAAT
12154025 AATGTACGAT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
19 2 0.05
20 17 0.40
21 6 0.14
22 6 0.14
23 12 0.28
ACGTcount: A:0.54, C:0.06, G:0.10, T:0.31
Consensus pattern (20 bp):
TAAAATAATGCATGAAAACT
Found at i:12161814 original size:13 final size:13
Alignment explanation
Indices: 12161788--12161851 Score: 60
Period size: 13 Copynumber: 4.9 Consensus size: 13
12161778 AGTTCTTCGT
12161788 TGCTTGTGAAAAG
1 TGCTTGTGAAAAG
* *
12161801 TGCTTTTGAGAAG
1 TGCTTGTGAAAAG
12161814 TG-TTGTGAAAAAG
1 TGCTTGTG-AAAAG
*
12161827 TGC-TGTAGAAAAT
1 TGCTTGT-GAAAAG
*
12161840 TGCTTTTGAAAA
1 TGCTTGTGAAAA
12161852 ATTTGAGTGT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
12 4 0.10
13 34 0.83
14 3 0.07
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.34
Consensus pattern (13 bp):
TGCTTGTGAAAAG
Found at i:12161851 original size:26 final size:26
Alignment explanation
Indices: 12161787--12161851 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
12161777 CAGTTCTTCG
* * *
12161787 TTGCTTGTGAAAAGTGCTTTTGAGAA
1 TTGCTTGTGAAAAGTGCTGTAGAAAA
*
12161813 GTG-TTGTGAAAAAGTGCTGTAGAAAA
1 TTGCTTGTG-AAAAGTGCTGTAGAAAA
*
12161839 TTGCTTTTGAAAA
1 TTGCTTGTGAAAA
12161852 ATTTGAGTGT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
25 5 0.16
26 22 0.71
27 4 0.13
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.35
Consensus pattern (26 bp):
TTGCTTGTGAAAAGTGCTGTAGAAAA
Found at i:12167932 original size:112 final size:116
Alignment explanation
Indices: 12167559--12168381 Score: 514
Period size: 113 Copynumber: 7.3 Consensus size: 116
12167549 TGTGTTTTCG
* * * * * * * * *
12167559 TCTTGATGTATCCTAAAAGTAGTGGCGTTTAC-GCAAAACGCCGTTAAAGGACAGTAATAGCGGC
1 TCTTGATGTATACTAGAATTAGTGGCGCTTACGGTAAAACGCCGCTAAAGCATAGTATTAGCGGC
* ** * * * * *
12167623 GCTTTTTGGC-AA-CGCCGCAAAATAGCTTAACCAAAACGCAGAG-TTTGG
66 GATTCATGGCTAAGCGCCACAAAATATCTTAACCAAAACACATAGTTTTGA
* * * * * * * * *
12167671 TCTTGAGGTAT-CTTAGAATTAGTGGCGTTTATGGGAAAACGCCGTTAAAGGACAGTAATAGTGG
1 TCTTGATGTATAC-TAGAATTAGTGGCGCTTACGGTAAAACGCCGCTAAAGCATAGTATTAGCGG
* * * * * * * * * *
12167735 CG-CT-AT-ACTGAAGCACCGCAAACTCTCTGAACCGAAACACATCGTTTTGG
65 CGATTCATGGCT-AAGCGCCACAAAATATCTTAACCAAAACACATAGTTTTGA
* * * * *
12167785 TCTTGATGTATACTAGAACTAGTGGCGCATGCGGTAAAACGCCGCTAAAGAATAGTATTAGCTGC
1 TCTTGATGTATACTAGAATTAGTGGCGCTTACGGTAAAACGCCGCTAAAGCATAGTATTAGCGGC
*
12167850 GATTCCTGGCT-AGCGCCACAAAATATCTTAACCAAAACAC-T-GTTTTGA
66 GATTCATGGCTAAGCGCCACAAAATATCTTAACCAAAACACATAGTTTTGA
* * * * * *
12167898 TCTTAATGTATA-TAAAATTAGTGGCGCTTACGGTAAACCGCCGCTAAAGAATATTTAATAGCGG
1 TCTTGATGTATACTAGAATTAGTGGCGCTTACGGTAAAACGCCGCTAAAGCATA-GTATTAGCGG
** * * * *
12167962 C-ACTTTGTGAC-AAGCGCCGCAAAATATCTTAACCAAAACGCATAATTTTGA
65 CGA-TTCATGGCTAAGCGCCACAAAATATCTTAACCAAAACACATAGTTTTGA
* * * * * *
12168013 CCTCGATGTATAGTAAAATTAGTGGCGCTTA-GG-GAAACGCCGTTAAAGCATAGTATTAGCGGC
1 TCTTGATGTATACTAGAATTAGTGGCGCTTACGGTAAAACGCCGCTAAAGCATAGTATTAGCGGC
* * * **
12168076 G--T-ATGGATAAAAGCGCCACCAAATATCTTAACCAAAACGCATAACTTTG-
66 GATTCATGGCT--AAGCGCCACAAAATATCTTAACCAAAACACATAGTTTTGA
* ** * * *
12168125 GCCCGATGTATAGTAGAATTAGTGGCGCTTA-GG-GAAACGCCGTTAAAGCATAGTATTAGCGGC
1 TCTTGATGTATACTAGAATTAGTGGCGCTTACGGTAAAACGCCGCTAAAGCATAGTATTAGCGGC
* * * * ** * *
12168188 G---CTTGGGTAAAAGCGCCACCAAATATCTGAACCAAAATGCATCGTTTTGG
66 GATTCATGGCT--AAGCGCCACAAAATATCTTAACCAAAACACATAGTTTTGA
* * *
12168238 TCTTGATGTATACTTGATTTAGTGGCGATTACGGTAAAACGCCGCTAAAGCATAGTATTAGCGGC
1 TCTTGATGTATACTAGAATTAGTGGCGCTTACGGTAAAACGCCGCTAAAGCATAGTATTAGCGGC
** * * * * * * * * *
12168303 GATTTTTTG-T-AGCGCCGCGACATACCATAAACAAAACGCA-ACGTTTTGG
66 GATTCATGGCTAAGCGCCACAAAATATCTTAACCAAAACACATA-GTTTTGA
* *
12168352 TCTTGATTTATACTAAAATTAGTGGCGCTT
1 TCTTGATGTATACTAGAATTAGTGGCGCTT
12168382 TGTTGAAAGC
Statistics
Matches: 577, Mismatches: 106, Indels: 54
0.78 0.14 0.07
Matches are distributed among these distances:
110 3 0.01
111 3 0.01
112 167 0.29
113 179 0.31
114 129 0.22
115 71 0.12
116 19 0.03
117 3 0.01
118 3 0.01
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.27
Consensus pattern (116 bp):
TCTTGATGTATACTAGAATTAGTGGCGCTTACGGTAAAACGCCGCTAAAGCATAGTATTAGCGGC
GATTCATGGCTAAGCGCCACAAAATATCTTAACCAAAACACATAGTTTTGA
Found at i:12168625 original size:23 final size:23
Alignment explanation
Indices: 12168571--12168614 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
12168561 ACGATGTAGG
12168571 TTTAGGGTTAGGGTATTAGGGCA
1 TTTAGGGTTAGGGTATTAGGGCA
12168594 TTTAGGGTTAGGGTATTAGGG
1 TTTAGGGTTAGGGTATTAGGG
12168615 TGTTTTAGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.20, C:0.02, G:0.41, T:0.36
Consensus pattern (23 bp):
TTTAGGGTTAGGGTATTAGGGCA
Found at i:12168643 original size:8 final size:7
Alignment explanation
Indices: 12168569--12168679 Score: 84
Period size: 7 Copynumber: 15.1 Consensus size: 7
12168559 TTACGATGTA
12168569 GGTTTAG
1 GGTTTAG
12168576 GG-TTAG
1 GGTTTAG
12168582 GGTATTAG
1 GGT-TTAG
12168590 GGCATTTAG
1 GG--TTTAG
12168599 GG-TTAG
1 GGTTTAG
12168605 GGTATTAGG
1 GGT-TTA-G
12168614 GTGTTTTA-
1 G-G-TTTAG
*
12168622 GGTTTAA
1 GGTTTAG
12168629 GGTTTAG
1 GGTTTAG
12168636 GAGTTTAG
1 G-GTTTAG
*
12168644 GGTTTAA
1 GGTTTAG
*
12168651 GGTTTAA
1 GGTTTAG
*
12168658 GGTTTAA
1 GGTTTAG
*
12168665 GGTTTGG
1 GGTTTAG
12168672 GGTTTAG
1 GGTTTAG
12168679 G
1 G
12168680 CTACTTTAGT
Statistics
Matches: 88, Mismatches: 5, Indels: 22
0.77 0.04 0.19
Matches are distributed among these distances:
6 16 0.18
7 41 0.47
8 17 0.19
9 8 0.09
10 5 0.06
11 1 0.01
ACGTcount: A:0.20, C:0.01, G:0.39, T:0.41
Consensus pattern (7 bp):
GGTTTAG
Found at i:12168657 original size:29 final size:28
Alignment explanation
Indices: 12168616--12168677 Score: 88
Period size: 29 Copynumber: 2.2 Consensus size: 28
12168606 GTATTAGGGT
* *
12168616 GTTTTAGGTTTAAGGTTTAGGAGTTTAGG
1 GTTTAAGGTTTAAGGTTTAAG-GTTTAGG
*
12168645 GTTTAAGGTTTAAGGTTTAAGGTTTGGG
1 GTTTAAGGTTTAAGGTTTAAGGTTTAGG
12168673 GTTTA
1 GTTTA
12168678 GGCTACTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 11 0.37
29 19 0.63
ACGTcount: A:0.21, C:0.00, G:0.34, T:0.45
Consensus pattern (28 bp):
GTTTAAGGTTTAAGGTTTAAGGTTTAGG
Done.