Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold59
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: 3999109
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.32
Warning! 268233 characters in sequence are not A, C, G, or T
File 19 of 25
Found at i:2788875 original size:34 final size:34
Alignment explanation
Indices: 2788819--2788975 Score: 181
Period size: 34 Copynumber: 4.6 Consensus size: 34
2788809 TAGTGTTGGT
*
2788819 TAAAT-GATGATTTGGTAGTTTGCCATTGTTGAC
1 TAAATGGAAGATTTGGTAGTTTGCCATTGTTGAC
* * *
2788852 TAAATGAAAGATTTGGTACTTTGCCATTGTTGAT
1 TAAATGGAAGATTTGGTAGTTTGCCATTGTTGAC
** *
2788886 TAAATGGGTGATTTGGTGGTTTGCCATTGTTGAC
1 TAAATGGAAGATTTGGTAGTTTGCCATTGTTGAC
* * * *
2788920 TAAATGGGAGATTTGATAGTTTACCATTGTTGAT
1 TAAATGGAAGATTTGGTAGTTTGCCATTGTTGAC
** *
2788954 TAAATGGGTGATTTGGTGGTTT
1 TAAATGGAAGATTTGGTAGTTT
2788976 TTACCAAACC
Statistics
Matches: 105, Mismatches: 18, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
33 5 0.05
34 100 0.95
ACGTcount: A:0.24, C:0.07, G:0.27, T:0.42
Consensus pattern (34 bp):
TAAATGGAAGATTTGGTAGTTTGCCATTGTTGAC
Found at i:2788920 original size:68 final size:68
Alignment explanation
Indices: 2788812--2788975 Score: 249
Period size: 68 Copynumber: 2.4 Consensus size: 68
2788802 ACGTTGTTAG
* * * * *
2788812 TGTTGGTTAAAT-GATGATTTGGTAGTTTGCCATTGTTGACTAAATGAAAGATTTGGTACTTTGC
1 TGTTGATTAAATGGGTGATTTGGTGGTTTGCCATTGTTGACTAAATGAAAGATTTGATACTTTAC
2788876 CAT
66 CAT
** *
2788879 TGTTGATTAAATGGGTGATTTGGTGGTTTGCCATTGTTGACTAAATGGGAGATTTGATAGTTTAC
1 TGTTGATTAAATGGGTGATTTGGTGGTTTGCCATTGTTGACTAAATGAAAGATTTGATACTTTAC
2788944 CAT
66 CAT
2788947 TGTTGATTAAATGGGTGATTTGGTGGTTT
1 TGTTGATTAAATGGGTGATTTGGTGGTTT
2788976 TTACCAAACC
Statistics
Matches: 88, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
67 11 0.12
68 77 0.88
ACGTcount: A:0.23, C:0.07, G:0.27, T:0.43
Consensus pattern (68 bp):
TGTTGATTAAATGGGTGATTTGGTGGTTTGCCATTGTTGACTAAATGAAAGATTTGATACTTTAC
CAT
Found at i:2789310 original size:19 final size:19
Alignment explanation
Indices: 2789272--2789335 Score: 85
Period size: 19 Copynumber: 3.4 Consensus size: 19
2789262 TTAGTTATCG
*
2789272 AGGTACTATTCACAGTATAT
1 AGGTACTATTCA-TGTATAT
*
2789292 AGGTGCTATTCATGTATAT
1 AGGTACTATTCATGTATAT
*
2789311 AGATACTATTCATGTATAT
1 AGGTACTATTCATGTATAT
2789330 -GGTACT
1 AGGTACT
2789336 GTGCACGTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
18 5 0.13
19 23 0.59
20 11 0.28
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.39
Consensus pattern (19 bp):
AGGTACTATTCATGTATAT
Found at i:2792986 original size:34 final size:34
Alignment explanation
Indices: 2792932--2793013 Score: 119
Period size: 34 Copynumber: 2.4 Consensus size: 34
2792922 GTTTGGTAAA
*
2792932 AAACCACCAAATCACCCATTTAATCGACAATGGC
1 AAACCACCAAATCACCCATTTAATCAACAATGGC
* * * *
2792966 AAACTACCAAATCTCTCATTTAGTCAACAATGGC
1 AAACCACCAAATCACCCATTTAATCAACAATGGC
2793000 AAACCACCAAATCA
1 AAACCACCAAATCA
2793014 ACAATGGCAA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.43, C:0.30, G:0.07, T:0.20
Consensus pattern (34 bp):
AAACCACCAAATCACCCATTTAATCAACAATGGC
Found at i:2793017 original size:22 final size:22
Alignment explanation
Indices: 2792989--2793057 Score: 129
Period size: 22 Copynumber: 3.1 Consensus size: 22
2792979 TCTCATTTAG
2792989 TCAACAATGGCAAACCACCAAA
1 TCAACAATGGCAAACCACCAAA
2793011 TCAACAATGGCAAACCACCAAA
1 TCAACAATGGCAAACCACCAAA
*
2793033 TCAACAATGGCAAACTACCAAA
1 TCAACAATGGCAAACCACCAAA
2793055 TCA
1 TCA
2793058 CCATTTAATC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.49, C:0.30, G:0.09, T:0.12
Consensus pattern (22 bp):
TCAACAATGGCAAACCACCAAA
Found at i:2797578 original size:34 final size:34
Alignment explanation
Indices: 2797503--2797580 Score: 86
Period size: 34 Copynumber: 2.3 Consensus size: 34
2797493 GGTAAAAAAT
*
2797503 CACCAAATCACCCATTTAATCAACAATGACAAAC
1 CACCAAATCACCCATTTAATCAACAACGACAAAC
** * * *
2797537 CTA-CAAATCTTCCATTTAGTCAACAACGGCAAGC
1 C-ACCAAATCACCCATTTAATCAACAACGACAAAC
2797571 CACCAAATCA
1 CACCAAATCA
2797581 TTGATTAAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
33 1 0.03
34 33 0.94
35 1 0.03
ACGTcount: A:0.42, C:0.32, G:0.06, T:0.19
Consensus pattern (34 bp):
CACCAAATCACCCATTTAATCAACAACGACAAAC
Found at i:2797619 original size:34 final size:34
Alignment explanation
Indices: 2797581--2797709 Score: 204
Period size: 34 Copynumber: 3.8 Consensus size: 34
2797571 CACCAAATCA
2797581 TTGATTAAATGAGAGATTTGGTAGTTTGCCATTG
1 TTGATTAAATGAGAGATTTGGTAGTTTGCCATTG
* *
2797615 TTGATTAAATGAGTGATTTGGTGGTTTGCCATTG
1 TTGATTAAATGAGAGATTTGGTAGTTTGCCATTG
* *
2797649 TTGACTAAATGGGAGATTTGGTAGTTTGCCATTG
1 TTGATTAAATGAGAGATTTGGTAGTTTGCCATTG
* *
2797683 TTGATTAAATGGGTGATTTGGTAGTTT
1 TTGATTAAATGAGAGATTTGGTAGTTT
2797710 TTACCAAATC
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 87 1.00
ACGTcount: A:0.23, C:0.05, G:0.29, T:0.43
Consensus pattern (34 bp):
TTGATTAAATGAGAGATTTGGTAGTTTGCCATTG
Found at i:2803244 original size:17 final size:17
Alignment explanation
Indices: 2803224--2803259 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2803214 AAGGAAGATG
* *
2803224 AAGAAGAAAGAAAGAAA
1 AAGAAAAAAAAAAGAAA
2803241 AAGAAAAAAAAAAGAAA
1 AAGAAAAAAAAAAGAAA
2803258 AA
1 AA
2803260 ATATGAAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AAGAAAAAAAAAAGAAA
Found at i:2803637 original size:2 final size:2
Alignment explanation
Indices: 2803624--2803662 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
2803614 TTATTTTATT
*
2803624 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2803663 TTTGAAAATC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2809771 original size:36 final size:35
Alignment explanation
Indices: 2809691--2809771 Score: 85
Period size: 36 Copynumber: 2.3 Consensus size: 35
2809681 AAAATGACAA
* *
2809691 AAAAAAAAAAGTCAAAAGCAAAAGCACAAAAAATG
1 AAAACAAAAAGTCAAAAGCAAAAGCACAAAAAAGG
* *
2809726 AAAAGAAAAAGTGCAAAAGCAAAA-TA-AAAAAAGGG
1 AAAACAAAAAGT-CAAAAGCAAAAGCACAAAAAA-GG
2809761 AACAACAAAAA
1 AA-AACAAAAA
2809772 TAAAAAAACG
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
34 6 0.15
35 15 0.38
36 18 0.46
ACGTcount: A:0.72, C:0.10, G:0.14, T:0.05
Consensus pattern (35 bp):
AAAACAAAAAGTCAAAAGCAAAAGCACAAAAAAGG
Found at i:2810042 original size:13 final size:13
Alignment explanation
Indices: 2810024--2810049 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2810014 TAATCCTAAA
2810024 AAAAAAAAAAACC
1 AAAAAAAAAAACC
2810037 AAAAAAAAAAACC
1 AAAAAAAAAAACC
2810050 TTTTCACCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAACC
Found at i:2811144 original size:27 final size:27
Alignment explanation
Indices: 2811101--2812056 Score: 1410
Period size: 27 Copynumber: 34.9 Consensus size: 27
2811091 GTGGCATTTT
* *
2811101 CTTTTAAAGTCCACAACTCTGTGGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
2811129 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
2811156 CTTTTAAAGTCCACAACTCCATGGTACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
2811184 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
2811211 CTTTTAAAATCCACAACTCCGTGGTACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* *
2811239 CTTTTTAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
2811266 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
2811293 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* * *
2811320 CTTTTAAGTCCATAACTCTGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* *
2811348 TTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
2811375 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* *
2811403 CTTTTTAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
2811430 CTTTTAAGTCCACAACTCCGTGGTACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
2811457 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
2811484 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
2811511 CTTTTAAGTCCAGAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
** *
2811538 CTTTTAAGTCCACAACTCTATGGCATTC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
2811566 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
2811593 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
2811620 CTTTTAAGTCCACAACTCTGTGGCATTC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
2811648 CTTTTAA-TACCACAACTCCGTGGCACC
1 CTTTTAAGT-CCACAACTCCGTGGCACC
2811675 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
2811702 CTTTTAAGTCCACAACTCCGTGGCACT
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
2811729 CTTTTAAGTCCATAACTCCATGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
2811757 CTTTTAAGTCCACAACTCCGTAGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
2811784 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* * *
2811811 CTTTTAAGTCCATAACTCTGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* *
2811839 TTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
2811866 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* *
2811894 CTTTTTAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
2811921 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
2811949 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
2811977 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
2812004 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* * * *
2812032 CTTTTAAATTCACAAATCGGTGGCA
1 CTTTTAAGTCCACAACTCCGTGGCA
2812057 ACCCATTCCA
Statistics
Matches: 847, Mismatches: 68, Indels: 26
0.90 0.07 0.03
Matches are distributed among these distances:
27 545 0.64
28 302 0.36
ACGTcount: A:0.23, C:0.33, G:0.14, T:0.30
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:2811169 original size:55 final size:54
Alignment explanation
Indices: 2811101--2812056 Score: 1419
Period size: 55 Copynumber: 17.5 Consensus size: 54
2811091 GTGGCATTTT
* *
2811101 CTTTTAAAGTCCACAACTCTGTGGCATCCTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACC
* *
2811156 CTTTTAAAGTCCACAACTCCATGGTACCCTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACC
* * *
2811211 CTTTTAAAATCCACAACTCCGTGGTACCCTTTTTAGTCCACAACTCTGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACC
* *
2811266 CTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACC
* * **
2811320 CTTTTAAGTCCATAACTCTGTGGCATCTTTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCTGTGGCACC
*
2811375 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTTAGTCCACAACTCTGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACC
*
2811430 CTTTTAAGTCCACAACTCCGTGGTACCCTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACC
* *
2811484 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCAGAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACC
** * *
2811538 CTTTTAAGTCCACAACTCTATGGCATTCCTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCTGTGGCACC
*
2811593 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCATTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCA-CC
*
2811648 CTTTTAA-TACCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGT-CCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACC
* * **
2811702 CTTTTAAGTCCACAACTCCGTGGCACTCTTTTAAGTCCATAACTCCATGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCA-CC
* *
2811757 CTTTTAAGTCCACAACTCCGTAGCACCCTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACC
* * **
2811811 CTTTTAAGTCCATAACTCTGTGGCATCTTTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCTGTGGCACC
*
2811866 CTTTTAAAGTCCACAACTCCGTGGCACCCTTTTTAGTCCACAACTCTGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACC
*
2811921 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCTGTGGCA-CC
*
2811977 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCA-CC
* * * *
2812032 CTTTTAAATTCACAAATCGGTGGCA
1 CTTTTAAGTCCACAACTCCGTGGCA
2812057 ACCCATTCCA
Statistics
Matches: 829, Mismatches: 61, Indels: 22
0.91 0.07 0.02
Matches are distributed among these distances:
54 307 0.37
55 459 0.55
56 63 0.08
ACGTcount: A:0.23, C:0.33, G:0.14, T:0.30
Consensus pattern (54 bp):
CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACC
Found at i:2811201 original size:82 final size:81
Alignment explanation
Indices: 2811101--2812056 Score: 1410
Period size: 82 Copynumber: 11.6 Consensus size: 81
2811091 GTGGCATTTT
* * *
2811101 CTTTTAAAGTCCACAACTCTGTGGCATCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGT
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGT
* *
2811166 CCACAACTCCATGGTACC
64 CCACAACTCCGTGGCACC
* * * *
2811184 CTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAATCCACAACTCCGTGGTACCCTTTTTAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTC
*
2811249 CACAACTCTGTGGCACC
65 CACAACTCCGTGGCACC
*
2811266 CTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
* * *
2811331 ATAACTCTGTGGCATCT
66 ACAACTCCGTGGCA-CC
* * *
2811348 TTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTTAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTC
*
2811413 CACAACTCTGTGGCACC
65 CACAACTCCGTGGCACC
* *
2811430 CTTTTAAGTCCACAACTCCGTGGTACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
2811495 ACAACTCCGTGGCACC
66 ACAACTCCGTGGCACC
* ** *
2811511 CTTTTAAGTCCAGAACTCCGTGGCACCCTTTTAAGTCCACAACTCTATGGCATTCCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTC
2811576 CACAACTCCGTGGCACC
65 CACAACTCCGTGGCACC
* *
2811593 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCATTCCTTTTAA-TA
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGT-
2811657 CCACAACTCCGTGGCACC
64 CCACAACTCCGTGGCACC
*
2811675 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACTCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
* *
2811740 ATAACTCCATGGCATCC
66 ACAACTCCGTGGCA-CC
*
2811757 CTTTTAAGTCCACAACTCCGTAGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
* * *
2811822 ATAACTCTGTGGCATCT
66 ACAACTCCGTGGCA-CC
* * *
2811839 TTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTTAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTC
*
2811904 CACAACTCTGTGGCACC
65 CACAACTCCGTGGCACC
2811921 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAGT
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGT
2811986 CCACAACTCCGTGGCACC
64 CCACAACTCCGTGGCACC
* * * *
2812004 CTTTTAAGTCCACAACTCCGTGGCATCCCTTTTAAATTCACAAATCGGTGGCA
1 CTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTCCACAACTCCGTGGCA
2812057 ACCCATTCCA
Statistics
Matches: 810, Mismatches: 53, Indels: 20
0.92 0.06 0.02
Matches are distributed among these distances:
81 160 0.20
82 448 0.55
83 202 0.25
ACGTcount: A:0.23, C:0.33, G:0.14, T:0.30
Consensus pattern (81 bp):
CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
ACAACTCCGTGGCACC
Found at i:2812084 original size:32 final size:32
Alignment explanation
Indices: 2812042--2812516 Score: 772
Period size: 32 Copynumber: 14.8 Consensus size: 32
2812032 CTTTTAAATT
* *
2812042 CACAAATCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
2812074 CACAAGTCGGTGGAAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
2812106 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
2812138 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
2812170 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
2812202 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
2812234 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
2812266 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
2812298 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
2812330 CACAAGTCGGTGGCAACCCA-TTCTAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTC-AAAGCCCA
*
2812362 CACAAGTAGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
** *
2812394 CACAAGTCGGTGGCAACCTTTTTCAAAGCCCC
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * *
2812426 CAGAAGTTGGTGGCAACCCATTTAAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
2812458 CGCAAGTCGGTGGCAACCCATTTAAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * *
2812490 CGCAAGTCAGTGGCAACCCTTTTCAAA
1 CACAAGTCGGTGGCAACCCATTTCAAA
2812517 TCACCATTTT
Statistics
Matches: 420, Mismatches: 21, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
31 3 0.01
32 414 0.99
33 3 0.01
ACGTcount: A:0.32, C:0.34, G:0.19, T:0.16
Consensus pattern (32 bp):
CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
Found at i:2813792 original size:12 final size:13
Alignment explanation
Indices: 2813764--2813798 Score: 54
Period size: 12 Copynumber: 2.7 Consensus size: 13
2813754 GAAGATGAAG
2813764 AAGAAAGAAAGAAA
1 AAGAAA-AAAGAAA
2813778 AAGAAAAAA-AAA
1 AAGAAAAAAGAAA
2813790 AAGAAAAAA
1 AAGAAAAAA
2813799 TATGAAATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.57
13 3 0.14
14 6 0.29
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (13 bp):
AAGAAAAAAGAAA
Found at i:2819474 original size:12 final size:13
Alignment explanation
Indices: 2819457--2819487 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
2819447 AAAAAAATAA
2819457 AAATTTTAT-ATT
1 AAATTTTATAATT
2819469 AAATTTTATAATT
1 AAATTTTATAATT
2819482 AAATTT
1 AAATTT
2819488 AAATAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.50
13 9 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
AAATTTTATAATT
Found at i:2819535 original size:5 final size:5
Alignment explanation
Indices: 2819518--2819577 Score: 50
Period size: 5 Copynumber: 10.8 Consensus size: 5
2819508 ATTTAAAAAA
2819518 TAATT TAAATT TAATT TAA-T TAATT TATATTT TAAAATT TATATT TAAATT
1 TAATT T-AATT TAATT TAATT TAATT TA-A-TT T--AATT TA-ATT T-AATT
2819569 TAATT TAAT
1 TAATT TAAT
2819578 AGGAGGGGAA
Statistics
Matches: 47, Mismatches: 0, Indels: 16
0.75 0.00 0.25
Matches are distributed among these distances:
4 4 0.09
5 20 0.43
6 14 0.30
7 7 0.15
8 1 0.02
9 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
TAATT
Found at i:2819544 original size:14 final size:15
Alignment explanation
Indices: 2819525--2819575 Score: 54
Period size: 14 Copynumber: 3.4 Consensus size: 15
2819515 AAATAATTTA
2819525 AATTTA-ATTTAATT
1 AATTTATATTTAATT
2819539 AATTTATATTTTAA--
1 AATTTATA-TTTAATT
2819553 AATTTATATTTAAATTT
1 AATTTATATTT-AA-TT
2819570 AATTTA
1 AATTTA
2819576 ATAGGAGGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
13 3 0.10
14 16 0.52
15 1 0.03
16 5 0.16
17 6 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
AATTTATATTTAATT
Found at i:2823515 original size:2 final size:2
Alignment explanation
Indices: 2823508--2823546 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2823498 AATTGATTTT
2823508 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2823547 TTTAAAGATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2824063 original size:13 final size:12
Alignment explanation
Indices: 2824034--2824073 Score: 64
Period size: 13 Copynumber: 3.3 Consensus size: 12
2824024 TTTTAATAAT
2824034 ATATTTATA-TC
1 ATATTTATATTC
2824045 ATATTTATATTC
1 ATATTTATATTC
2824057 ATCATTTATATTC
1 AT-ATTTATATTC
2824070 ATAT
1 ATAT
2824074 CATACAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 9 0.33
12 6 0.22
13 12 0.44
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (12 bp):
ATATTTATATTC
Found at i:2826412 original size:22 final size:22
Alignment explanation
Indices: 2826365--2826412 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
2826355 TAAATATATT
* *
2826365 ATTATAATATAATGTACAAACC
1 ATTATAATATAATATACAAACA
*
2826387 ATTATAATA-ACATATACAATCA
1 ATTATAATATA-ATATACAAACA
2826409 ATTA
1 ATTA
2826413 CTTATTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.52, C:0.12, G:0.02, T:0.33
Consensus pattern (22 bp):
ATTATAATATAATATACAAACA
Found at i:2826488 original size:20 final size:21
Alignment explanation
Indices: 2826451--2826489 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
2826441 TCGACAAAAT
* *
2826451 TTAAGAAATTATATATTTAAA
1 TTAAGAAATAATAAATTTAAA
2826472 TTAA-AAATAATAAATTTA
1 TTAAGAAATAATAAATTTA
2826490 TCTTAAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (21 bp):
TTAAGAAATAATAAATTTAAA
Found at i:2826652 original size:15 final size:16
Alignment explanation
Indices: 2826632--2826669 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
2826622 TTTTATATGT
2826632 TATATTTT-AAAATAA
1 TATATTTTAAAAATAA
2826647 TATATTTTTAAAAAATAA
1 TATA-TTTT-AAAAATAA
2826665 TATAT
1 TATAT
2826670 CATATTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 4 0.20
16 4 0.20
17 1 0.05
18 11 0.55
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATATTTTAAAAATAA
Found at i:2826674 original size:23 final size:23
Alignment explanation
Indices: 2826648--2826700 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
2826638 TTAAAATAAT
*
2826648 ATATTTTTAAAAAATAATATATC
1 ATATTTTAAAAAAATAATATATC
2826671 ATATTTTAAAAAAATAATATAT-
1 ATATTTTAAAAAAATAATATATC
*
2826693 TTATTTTA
1 ATATTTTA
2826701 TGTAATATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
22 7 0.25
23 21 0.75
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
ATATTTTAAAAAAATAATATATC
Found at i:2826680 original size:22 final size:21
Alignment explanation
Indices: 2826632--2826700 Score: 76
Period size: 23 Copynumber: 3.4 Consensus size: 21
2826622 TTTTATATGT
2826632 TATATTTT--AAAAT-A-ATA
1 TATATTTTAAAAAATAATATA
2826649 TAT-TTTTAAAAAATAATATA
1 TATATTTTAAAAAATAATATA
2826669 TCATATTTTAAAAAAATAATATA
1 T-ATATTTT-AAAAAATAATATA
*
2826692 TTTATTTTA
1 TATATTTTA
2826701 TGTAATATGT
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
16 4 0.09
17 3 0.07
18 5 0.11
19 1 0.02
20 4 0.09
21 3 0.07
22 10 0.23
23 14 0.32
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (21 bp):
TATATTTTAAAAAATAATATA
Found at i:2827386 original size:16 final size:18
Alignment explanation
Indices: 2827365--2827404 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
2827355 TTAGTGTTAT
*
2827365 TATTTTATTAAAT-T-AA
1 TATTTTATAAAATATAAA
2827381 TATTTT-TAAAATATAAA
1 TATTTTATAAAATATAAA
2827398 TATTTTA
1 TATTTTA
2827405 ATTTAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
15 5 0.25
16 7 0.35
17 8 0.40
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TATTTTATAAAATATAAA
Found at i:2827425 original size:34 final size:32
Alignment explanation
Indices: 2827365--2827433 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
2827355 TTAGTGTTAT
2827365 TATTTTATTAAATTAATATTTTTAAAATATAAA
1 TATTTTATTAAATT-ATATTTTTAAAATATAAA
*
2827398 TATTTTAATTTAAATT-TATTATTTAAAATTTAAA
1 TATTTT-A-TTAAATTATATT-TTTAAAATATAAA
2827432 TA
1 TA
2827434 GATAAGATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
33 10 0.31
34 15 0.47
35 7 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (32 bp):
TATTTTATTAAATTATATTTTTAAAATATAAA
Found at i:2830180 original size:18 final size:18
Alignment explanation
Indices: 2830157--2830194 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
2830147 CAGATCGTTT
2830157 GAAACATTAACTTAGTTA
1 GAAACATTAACTTAGTTA
2830175 GAAACATTAACTTAGTTA
1 GAAACATTAACTTAGTTA
2830193 GA
1 GA
2830195 GTCAAAATAT
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:0.45, C:0.11, G:0.13, T:0.32
Consensus pattern (18 bp):
GAAACATTAACTTAGTTA
Found at i:2834828 original size:2 final size:2
Alignment explanation
Indices: 2834821--2834848 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2834811 AGTTTTTCCT
2834821 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2834849 AAACCAAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2841113 original size:2 final size:2
Alignment explanation
Indices: 2841106--2841162 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
2841096 ATGTGCATTC
2841106 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2841148 CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT C
2841163 GTCTGCTTCT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:2841770 original size:8 final size:8
Alignment explanation
Indices: 2841759--2841807 Score: 50
Period size: 8 Copynumber: 6.5 Consensus size: 8
2841749 AATTATAAAA
2841759 ATAATAAT
1 ATAATAAT
2841767 ATAA-AA-
1 ATAATAAT
*
2841773 ATAATATT
1 ATAATAAT
*
2841781 TTAATAAT
1 ATAATAAT
2841789 ATAATAA-
1 ATAATAAT
*
2841796 ATAATAAA
1 ATAATAAT
2841804 ATAA
1 ATAA
2841808 AATTTTAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
6 4 0.12
7 10 0.29
8 20 0.59
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
ATAATAAT
Found at i:2841813 original size:31 final size:28
Alignment explanation
Indices: 2841745--2841816 Score: 83
Period size: 31 Copynumber: 2.5 Consensus size: 28
2841735 AAATTTAATT
*
2841745 ATAAAATTATAAAAATAATAATATAAAA
1 ATAAAATTTTAAAAATAATAATATAAAA
*
2841773 ATAATATTTTAATAATATAATAA-ATAATAAA
1 ATAAAATTTTAA-AA-ATAATAATAT-A-AAA
2841804 ATAAAATTTTAAA
1 ATAAAATTTTAAA
2841817 TTAATCTGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
28 10 0.27
29 4 0.11
30 9 0.24
31 14 0.38
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (28 bp):
ATAAAATTTTAAAAATAATAATATAAAA
Found at i:2844074 original size:2 final size:2
Alignment explanation
Indices: 2844067--2844100 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2844057 TTGTATCTTA
*
2844067 AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2844101 GTTTTTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2844309 original size:15 final size:15
Alignment explanation
Indices: 2844289--2844347 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
2844279 TCTAATAAAA
2844289 AAATTTTAAATTTAT
1 AAATTTTAAATTTAT
* * *
2844304 AAATTTAAAAATGAT
1 AAATTTTAAATTTAT
* *
2844319 AAATTTCAAATCTA-
1 AAATTTTAAATTTAT
2844333 AAATTTTAAAATTTA
1 AAATTTT-AAATTTA
2844348 AATCTAAATC
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
14 6 0.18
15 28 0.82
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (15 bp):
AAATTTTAAATTTAT
Found at i:2846404 original size:19 final size:18
Alignment explanation
Indices: 2846366--2846405 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
2846356 TATTTTTGTA
* *
2846366 TTATATTTATATTATTTT
1 TTATATTTATATCATATT
2846384 TTATATATTATATCATATT
1 TTATAT-TTATATCATATT
2846403 TTA
1 TTA
2846406 ACTTTTCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (18 bp):
TTATATTTATATCATATT
Found at i:2846671 original size:19 final size:19
Alignment explanation
Indices: 2846649--2846712 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
2846639 AATAAATTAA
2846649 ATATTATTAAAATTATATT
1 ATATTATTAAAATTATATT
* * *
2846668 ATATTATTTAATTTAAATT
1 ATATTATTAAAATTATATT
2846687 A-ATTATTATTAAA-TATATTT
1 ATATTATTA--AAATTATA-TT
2846707 ATATTA
1 ATATTA
2846713 ATTTTTAATC
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
18 6 0.17
19 20 0.57
20 5 0.14
21 4 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATATTATTAAAATTATATT
Found at i:2846712 original size:21 final size:20
Alignment explanation
Indices: 2846666--2846733 Score: 52
Period size: 21 Copynumber: 3.4 Consensus size: 20
2846656 TAAAATTATA
* * *
2846666 TTATATTA-TTTAATTTAAA
1 TTATATTATTTTAAATCAAT
2846685 TTA-ATTATTATTAAAT-ATAT
1 TTATATTATT-TTAAATCA-AT
*
2846705 TTATATTAATTTTTAATCAAT
1 TTATATT-ATTTTAAATCAAT
2846726 TTATATTA
1 TTATATTA
2846734 ATAAAATATA
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
18 4 0.10
19 5 0.12
20 10 0.25
21 17 0.43
22 4 0.10
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (20 bp):
TTATATTATTTTAAATCAAT
Found at i:2846812 original size:22 final size:25
Alignment explanation
Indices: 2846764--2846819 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 25
2846754 TTGATTATAC
*
2846764 AATAATAAATTTTATTTATTATATTA
1 AATAAAAAATTTTA-TTATTATATTA
2846790 AATAAAAAATTTTA-TATT-T-TTA
1 AATAAAAAATTTTATTATTATATTA
2846812 AATAAAAA
1 AATAAAAA
2846820 TTATAAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 11 0.38
23 1 0.03
24 4 0.14
26 13 0.45
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
AATAAAAAATTTTATTATTATATTA
Found at i:2847602 original size:2 final size:2
Alignment explanation
Indices: 2847595--2847643 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
2847585 AAATTCTCAT
*
2847595 TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA T- TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
2847635 TT TA TA TA T
1 TA TA TA TA T
2847644 TAAAATTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (2 bp):
TA
Found at i:2847619 original size:15 final size:15
Alignment explanation
Indices: 2847595--2847645 Score: 77
Period size: 15 Copynumber: 3.5 Consensus size: 15
2847585 AAATTCTCAT
2847595 TATA-TATATATATA
1 TATATTATATATATA
2847609 TATATTATATATATA
1 TATATTATATATATA
* *
2847624 TATATTATGTATTTA
1 TATATTATATATATA
2847639 TATATTA
1 TATATTA
2847646 AAATTTTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
14 4 0.12
15 30 0.88
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (15 bp):
TATATTATATATATA
Found at i:2848479 original size:14 final size:13
Alignment explanation
Indices: 2848453--2848489 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
2848443 AATAAATAAA
2848453 TAAAAAAAT-TTT
1 TAAAAAAATATTT
2848465 TAATAAAAATATTT
1 TAA-AAAAATATTT
2848479 TAAAAAAATAT
1 TAAAAAAATAT
2848490 AACGTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 3 0.13
13 14 0.61
14 6 0.26
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAAAAATATTT
Found at i:2849851 original size:35 final size:35
Alignment explanation
Indices: 2849759--2849856 Score: 94
Period size: 35 Copynumber: 2.7 Consensus size: 35
2849749 CTTATTTTAT
** *
2849759 TATTTA-TTATGTTATTAAAATATTATTTTTAATAAA
1 TATTTATTTAT-TTATT-AAATAAAATTTTTAAAAAA
*
2849795 TATTTATCTATTT-TTATAATAAAATTTTTAAAAAA
1 TATTTATTTATTTATTA-AATAAAATTTTTAAAAAA
2849830 TA-TTATTTATATTATTAAATAATAATT
1 TATTTATTTAT-TTATTAAATAA-AATT
2849857 CGAGTAAAGT
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
34 8 0.15
35 26 0.50
36 15 0.29
37 3 0.06
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (35 bp):
TATTTATTTATTTATTAAATAAAATTTTTAAAAAA
Found at i:2850100 original size:16 final size:16
Alignment explanation
Indices: 2850079--2850110 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2850069 CTGAAAATTT
*
2850079 TGAATTTAGATTTTTA
1 TGAATTTAAATTTTTA
2850095 TGAATTTAAATTTTTA
1 TGAATTTAAATTTTTA
2850111 ATTTTTTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.56
Consensus pattern (16 bp):
TGAATTTAAATTTTTA
Found at i:2852813 original size:29 final size:30
Alignment explanation
Indices: 2852750--2852818 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
2852740 ACTTTACGTC
* * *
2852750 TAAAAATCAACAAAATTAAAAGTGTAATGG
1 TAAAATTCAACAAAATTAAAAGTATAATGA
* *
2852780 CAAAATTCAACAAAATTAAAA-TATAATTA
1 TAAAATTCAACAAAATTAAAAGTATAATGA
2852809 TAAAATTCAA
1 TAAAATTCAA
2852819 TTTTGATTCA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 14 0.42
30 19 0.58
ACGTcount: A:0.59, C:0.09, G:0.06, T:0.26
Consensus pattern (30 bp):
TAAAATTCAACAAAATTAAAAGTATAATGA
Found at i:2853400 original size:48 final size:48
Alignment explanation
Indices: 2853348--2853440 Score: 150
Period size: 48 Copynumber: 1.9 Consensus size: 48
2853338 TCCAATCTAG
* *
2853348 ATTATTGAAAATTTTATCCAAAATTCAGTGATGAGTAAATTTAATCGT
1 ATTATAGAAAATTTTATCCAAAATTCAGTGACGAGTAAATTTAATCGT
**
2853396 ATTATAGAAAATTTTATTTAAAATTCAGTGACGAGTAAATTTAAT
1 ATTATAGAAAATTTTATCCAAAATTCAGTGACGAGTAAATTTAAT
2853441 AGCAGTCAGT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.40
Consensus pattern (48 bp):
ATTATAGAAAATTTTATCCAAAATTCAGTGACGAGTAAATTTAATCGT
Found at i:2855294 original size:12 final size:12
Alignment explanation
Indices: 2855277--2855302 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2855267 TAATATATTG
2855277 AGAAAAAAAAAA
1 AGAAAAAAAAAA
2855289 AGAAAAAAAAAA
1 AGAAAAAAAAAA
2855301 AG
1 AG
2855303 GTACAATACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (12 bp):
AGAAAAAAAAAA
Found at i:2859473 original size:27 final size:27
Alignment explanation
Indices: 2859439--2859503 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
2859429 ACTACCCATT
2859439 TGTTTGTCAAAAATAGTG-TTTATTTTG
1 TGTTTGTCAAAAATAGTGATTT-TTTTG
2859466 TGTTTGTCAAAAATAGTGATTTTTTTG
1 TGTTTGTCAAAAATAGTGATTTTTTTG
* *
2859493 TATTTATCAAA
1 TGTTTGTCAAA
2859504 TATGGAGACT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
27 32 0.91
28 3 0.09
ACGTcount: A:0.29, C:0.05, G:0.15, T:0.51
Consensus pattern (27 bp):
TGTTTGTCAAAAATAGTGATTTTTTTG
Found at i:2862110 original size:21 final size:22
Alignment explanation
Indices: 2862081--2862126 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2862071 CGTTCAGACA
** *
2862081 AGTAGTACTCCGTAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
2862103 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
2862124 AGT
1 AGT
2862127 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.22
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:2864748 original size:19 final size:19
Alignment explanation
Indices: 2864724--2864762 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2864714 ATCTTTCTGA
*
2864724 TTTGGTGTT-GTTTTCTGTT
1 TTTGGTCTTCGTTTT-TGTT
2864743 TTTGGTCTTCGTTTTTGTT
1 TTTGGTCTTCGTTTTTGTT
2864762 T
1 T
2864763 ACTTTATGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.00, C:0.08, G:0.23, T:0.69
Consensus pattern (19 bp):
TTTGGTCTTCGTTTTTGTT
Found at i:2865005 original size:14 final size:14
Alignment explanation
Indices: 2864947--2865010 Score: 52
Period size: 12 Copynumber: 5.1 Consensus size: 14
2864937 ATTATATATG
2864947 AATATA-ATA-TAA
1 AATATATATATTAA
*
2864959 AA-AAATA-ATTAA
1 AATATATATATTAA
*
2864971 AATATA-ATATAAA
1 AATATATATATTAA
*
2864984 AAAATATATATTAA
1 AATATATATATTAA
2864998 AAT-T-TATATTAA
1 AATATATATATTAA
2865010 A
1 A
2865011 TAAATCGTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
11 3 0.07
12 18 0.44
13 12 0.29
14 8 0.20
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
AATATATATATTAA
Found at i:2865010 original size:27 final size:26
Alignment explanation
Indices: 2864947--2865000 Score: 85
Period size: 24 Copynumber: 2.1 Consensus size: 26
2864937 ATTATATATG
2864947 AATATAATAT-AAAAAA-ATAATTAA
1 AATATAATATAAAAAAATATAATTAA
2864971 AATATAATATAAAAAAATATATATTAA
1 AATATAATATAAAAAAATATA-ATTAA
2864998 AAT
1 AAT
2865001 TTATATTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
24 10 0.37
25 6 0.22
26 3 0.11
27 8 0.30
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (26 bp):
AATATAATATAAAAAAATATAATTAA
Found at i:2865355 original size:11 final size:11
Alignment explanation
Indices: 2865339--2865381 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
2865329 TAATATTATA
*
2865339 AATATAATTAT
1 AATATAAATAT
*
2865350 AATATAAAAAT
1 AATATAAATAT
2865361 AATATAAATAT
1 AATATAAATAT
*
2865372 AAAATAAATA
1 AATATAAATA
2865382 AGAGAATCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AATATAAATAT
Found at i:2865357 original size:17 final size:16
Alignment explanation
Indices: 2865335--2865382 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
2865325 TAAATAATAT
2865335 TATAAATATAAT-TATAA
1 TATAAA-ATAATATA-AA
2865352 TATAAAAATAATATAAA
1 TAT-AAAATAATATAAA
2865369 TATAAAATAA-ATAA
1 TATAAAATAATATAA
2865383 GAGAATCAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 4 0.14
16 7 0.24
17 13 0.45
18 5 0.17
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TATAAAATAATATAAA
Found at i:2865381 original size:28 final size:29
Alignment explanation
Indices: 2865323--2865382 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 29
2865313 TTAAATTTTT
* *
2865323 TATAAATAATATTATAAATATAATTATAA
1 TATAAATAATAATATAAATATAAATATAA
2865352 TATAAA-AATAATATAAATATAAA-ATAA
1 TATAAATAATAATATAAATATAAATATAA
2865379 -ATAA
1 TATAA
2865383 GAGAATCAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 4 0.14
27 4 0.14
28 15 0.52
29 6 0.21
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (29 bp):
TATAAATAATAATATAAATATAAATATAA
Found at i:2866752 original size:2 final size:2
Alignment explanation
Indices: 2866747--2866789 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
2866737 GTGTGTGTGT
* * *
2866747 GA GA GA GA GA GA GA GA GA GA GA CA GA CA GA GA GA GA GA TA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2866789 G
1 G
2866790 GCACTTCAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.05, G:0.44, T:0.02
Consensus pattern (2 bp):
GA
Found at i:2871269 original size:20 final size:21
Alignment explanation
Indices: 2871246--2871284 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
2871236 TTTTATTTTG
*
2871246 TTTAGTTTTATT-TTTTAAAA
1 TTTAATTTTATTATTTTAAAA
*
2871266 TTTAATTTTTTTATTTTAA
1 TTTAATTTTATTATTTTAA
2871285 TTTTTAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (21 bp):
TTTAATTTTATTATTTTAAAA
Found at i:2871294 original size:29 final size:30
Alignment explanation
Indices: 2871240--2871297 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
2871230 TAAATTTTTT
*
2871240 ATTTTGTTTAGTTTTATTTTTTAAAATTTA
1 ATTTTGTTTAGTTTTATTTTTAAAAATTTA
2871270 ATTTT-TTTA-TTTTAATTTTTAAAAATTT
1 ATTTTGTTTAGTTTT-ATTTTTAAAAATTT
2871298 TTTAATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 4 0.15
29 17 0.65
30 5 0.19
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.67
Consensus pattern (30 bp):
ATTTTGTTTAGTTTTATTTTTAAAAATTTA
Found at i:2871885 original size:14 final size:14
Alignment explanation
Indices: 2871846--2871892 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
2871836 TTATTAATTT
2871846 TAAAT-ATTAAATA
1 TAAATAATTAAATA
2871859 TAAATAATATAAAT-
1 TAAATAAT-TAAATA
*
2871873 TAAATAAATTAAAAA
1 TAAAT-AATTAAATA
2871888 TAAAT
1 TAAAT
2871893 TTAAATAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
13 5 0.17
14 11 0.38
15 13 0.45
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
TAAATAATTAAATA
Found at i:2872148 original size:22 final size:22
Alignment explanation
Indices: 2872121--2872186 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 22
2872111 TATTATCATA
*
2872121 TTATAATTATATTTAAAATATT
1 TTATAATTATATTTAAAATAAT
* *
2872143 TTATAATAATA-TAAAAATAAT
1 TTATAATTATATTTAAAATAAT
*
2872164 TTATATTATATATTTTAAAATAA
1 TTATAAT-TATA-TTTAAAATAA
2872187 ATATTTATAT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 14 0.40
22 13 0.37
24 8 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TTATAATTATATTTAAAATAAT
Found at i:2872800 original size:17 final size:17
Alignment explanation
Indices: 2872778--2872864 Score: 63
Period size: 17 Copynumber: 5.0 Consensus size: 17
2872768 TTGACTTGAT
2872778 TTTATTTATTTA-AATTA
1 TTTA-TTATTTATAATTA
2872795 TTTATTATTTATAATTA
1 TTTATTATTTATAATTA
* * ** *
2872812 ATAAAAATTTAAAATT-
1 TTTATTATTTATAATTA
2872828 TTTATT-TTTATAATAATA
1 TTTATTATTTATAAT--TA
2872846 TTTATATATTTTATAATTA
1 TTTAT-TA-TTTATAATTA
2872865 AATTTAAATA
Statistics
Matches: 53, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
15 7 0.13
16 9 0.17
17 21 0.40
18 5 0.09
19 3 0.06
21 8 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTATTATTTATAATTA
Found at i:2872832 original size:33 final size:31
Alignment explanation
Indices: 2872785--2872845 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 31
2872775 GATTTTATTT
2872785 ATTTAAATTATTTATTATTTATAATTAATAAAA
1 ATTTAAATTATTTATT-TTTATAA-TAATAAAA
2872818 ATTTAAAATT-TTTATTTTTATAATAATA
1 ATTT-AAATTATTTATTTTTATAATAATA
2872846 TTTATATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
31 5 0.19
32 7 0.26
33 10 0.37
34 5 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (31 bp):
ATTTAAATTATTTATTTTTATAATAATAAAA
Found at i:2872855 original size:22 final size:21
Alignment explanation
Indices: 2872823--2872870 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
2872813 TAAAAATTTA
*
2872823 AAATTTTTAT-TTTTATAA-T
1 AAATTTATATATTTTATAATT
2872842 AATATTTATATATTTTATAATT
1 AA-ATTTATATATTTTATAATT
2872864 AAATTTA
1 AAATTTA
2872871 AATAAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 2 0.08
20 7 0.28
21 13 0.52
22 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
AAATTTATATATTTTATAATT
Found at i:2873600 original size:23 final size:21
Alignment explanation
Indices: 2873549--2873601 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 21
2873539 AATACTATTA
*
2873549 TTTA-ATTAATAAAAATATTT
1 TTTATATTAATAAAAATAATT
2873569 TTTAAATATTAATATAAAATAAATT
1 TTT--ATATTAATA-AAAAT-AATT
2873594 TTTATATT
1 TTTATATT
2873602 TTTATATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
20 3 0.11
22 1 0.04
23 12 0.44
24 5 0.19
25 6 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTATATTAATAAAAATAATT
Found at i:2874275 original size:22 final size:22
Alignment explanation
Indices: 2874236--2874279 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2874226 TTATAAATGT
*
2874236 ATTATTATAATATAATATACAA
1 ATTATTATAATAAAATATACAA
2874258 ATTATTATAA-AAACATATACAA
1 ATTATTATAATAAA-ATATACAA
2874280 TCAATTACCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 2 0.10
22 18 0.90
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (22 bp):
ATTATTATAATAAAATATACAA
Found at i:2875203 original size:17 final size:17
Alignment explanation
Indices: 2875183--2875277 Score: 61
Period size: 17 Copynumber: 5.2 Consensus size: 17
2875173 AATAATTTAT
2875183 AATTATTATTTTAATTA
1 AATTATTATTTTAATTA
*
2875200 AATTAATATTTTAA--A
1 AATTATTATTTTAATTA
*
2875215 AATATAAATATTTTTAATTTAA
1 AAT-T-ATTA-TTTTAA-TT-A
2875237 AATTAAATTATTTTAAATT-
1 AATT--ATTATTTT-AATTA
*
2875256 AATTATTTATATTAATTA
1 AATTA-TTATTTTAATTA
2875274 AATT
1 AATT
2875278 TAAATTTAAA
Statistics
Matches: 64, Mismatches: 3, Indels: 21
0.73 0.03 0.24
Matches are distributed among these distances:
15 4 0.06
16 1 0.02
17 22 0.34
18 16 0.25
19 4 0.06
21 7 0.11
22 10 0.16
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AATTATTATTTTAATTA
Found at i:2875221 original size:37 final size:37
Alignment explanation
Indices: 2875180--2875283 Score: 101
Period size: 37 Copynumber: 2.8 Consensus size: 37
2875170 ATTAATAATT
2875180 TATAATTATTATTTTAATTAAATT-AA-TATTTTAAAAA
1 TATAATTATTATTTTAATTAAATTAAATTATTTT--AAA
*
2875217 TATAAATA-T-TTTTAATTTAAAATTAAATTATTTTAAA
1 TATAATTATTATTTTAA-TT-AAATTAAATTATTTTAAA
*
2875254 T-TAATTATTTATATTAATTAAATTTAAATT
1 TATAATTA-TTATTTTAATTAAA-TTAAATT
2875284 TAAATCAATT
Statistics
Matches: 56, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
35 6 0.11
36 8 0.14
37 19 0.34
38 12 0.21
39 11 0.20
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (37 bp):
TATAATTATTATTTTAATTAAATTAAATTATTTTAAA
Found at i:2875243 original size:21 final size:23
Alignment explanation
Indices: 2875213--2875255 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
2875203 TAATATTTTA
*
2875213 AAAATATAAA-TATTTTTAATTT
1 AAAATATAAATTATTTTAAATTT
2875235 AAAAT-TAAATTATTTTAAATT
1 AAAATATAAATTATTTTAAATT
2875256 AATTATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
AAAATATAAATTATTTTAAATTT
Found at i:2875249 original size:15 final size:14
Alignment explanation
Indices: 2875231--2875273 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
2875221 AATATTTTTA
2875231 ATTTAAAATTAAATT
1 ATTTAAAATT-AATT
*
2875246 ATTTTAAATTAATT
1 ATTTAAAATTAATT
*
2875260 ATTT-ATATTAATT
1 ATTTAAAATTAATT
2875273 A
1 A
2875274 AATTTAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 9 0.35
14 8 0.31
15 9 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATTTAAAATTAATT
Found at i:2875269 original size:13 final size:14
Alignment explanation
Indices: 2875231--2875283 Score: 54
Period size: 15 Copynumber: 3.7 Consensus size: 14
2875221 AATATTTTTA
*
2875231 ATTTAAAATTAAATT
1 ATTTTAAATT-AATT
2875246 ATTTTAAATTAATT
1 ATTTTAAATTAATT
*
2875260 A-TTTATATTAATT
1 ATTTTAAATTAATT
*
2875273 AAATTTAAATT
1 -ATTTTAAATT
2875284 TAAATCAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
13 11 0.33
14 6 0.18
15 16 0.48
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATTTTAAATTAATT
Found at i:2877436 original size:2 final size:2
Alignment explanation
Indices: 2877429--2877469 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2877419 TTCCTTTAAT
2877429 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2877470 GCATTTTTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2880479 original size:15 final size:15
Alignment explanation
Indices: 2880461--2880497 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
2880451 AAATCATAAA
*
2880461 AAATAATAAAAAATT
1 AAATAATAAAAAACT
2880476 AAATAATAAAAAACT
1 AAATAATAAAAAACT
2880491 AAATAAT
1 AAATAAT
2880498 TTAATCAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (15 bp):
AAATAATAAAAAACT
Found at i:2882574 original size:49 final size:49
Alignment explanation
Indices: 2882519--2882615 Score: 149
Period size: 49 Copynumber: 2.0 Consensus size: 49
2882509 ATTTCTCAAT
* *
2882519 ATTCAAGTCAAAACAGCTGCCAATACATTTTTAAGGCCGGTCCAATTTG
1 ATTCAAGTCAAAACAACTACCAATACATTTTTAAGGCCGGTCCAATTTG
** *
2882568 ATTCAAGTCAAAACAACTACCAATTTATTTTTAAGGCCGGTCCTATTT
1 ATTCAAGTCAAAACAACTACCAATACATTTTTAAGGCCGGTCCAATTT
2882616 TTCTATTTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.32
Consensus pattern (49 bp):
ATTCAAGTCAAAACAACTACCAATACATTTTTAAGGCCGGTCCAATTTG
Found at i:2888525 original size:26 final size:26
Alignment explanation
Indices: 2888491--2888546 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
2888481 GTATAAAAGT
2888491 AAGAGGTAGGAAAAACTAAAAATTGG
1 AAGAGGTAGGAAAAACTAAAAATTGG
* *
2888517 AAGATGTAGGAAAAGCTAAAAATTGG
1 AAGAGGTAGGAAAAACTAAAAATTGG
2888543 AAGA
1 AAGA
2888547 ATCTAAAGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.54, C:0.04, G:0.27, T:0.16
Consensus pattern (26 bp):
AAGAGGTAGGAAAAACTAAAAATTGG
Found at i:2896480 original size:27 final size:28
Alignment explanation
Indices: 2896450--2896514 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 28
2896440 TTTTTGAAAA
2896450 TAATTAAATTTAAATTTGATTATT-TTT
1 TAATTAAATTTAAATTTGATTATTATTT
* *
2896477 TAA-T--AGTTAAATTTGTTTATTATTT
1 TAATTAAATTTAAATTTGATTATTATTT
2896502 T-ATTAAATTTAAA
1 TAATTAAATTTAAA
2896515 AATATTATCT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
24 16 0.52
25 5 0.16
26 1 0.03
27 9 0.29
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (28 bp):
TAATTAAATTTAAATTTGATTATTATTT
Found at i:2896544 original size:24 final size:23
Alignment explanation
Indices: 2896492--2896556 Score: 60
Period size: 24 Copynumber: 2.7 Consensus size: 23
2896482 GTTAAATTTG
2896492 TTTATTATTTTATTAAATTTAAA
1 TTTATTATTTTATTAAATTTAAA
** *
2896515 AATATTATCTGTTA-TATATTTAAA
1 TTTATTAT-T-TTATTAAATTTAAA
*
2896539 TTTATTAATTTTTTTAAA
1 TTTATT-ATTTTATTAAA
2896557 ATAAATATAT
Statistics
Matches: 31, Mismatches: 7, Indels: 7
0.69 0.16 0.16
Matches are distributed among these distances:
23 8 0.26
24 18 0.58
25 5 0.16
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (23 bp):
TTTATTATTTTATTAAATTTAAA
Found at i:2896554 original size:51 final size:51
Alignment explanation
Indices: 2896452--2896554 Score: 118
Period size: 51 Copynumber: 2.0 Consensus size: 51
2896442 TTTGAAAATA
** * * * *
2896452 ATTAAATTTAAATTTGATTATTTTTTAATAGTTAAATTTGTTTATTATTTT
1 ATTAAATTTAAAAATGATTATCTGTTAATAGTTAAATTTATTAATTATTTT
* *
2896503 ATTAAATTTAAAAAT-ATTATCTGTTATATATTTAAATTTATTAATTTTTTT
1 ATTAAATTTAAAAATGATTATCTGTTA-ATAGTTAAATTTATTAATTATTTT
2896554 A
1 A
2896555 AAATAAATAT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
50 9 0.21
51 34 0.79
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (51 bp):
ATTAAATTTAAAAATGATTATCTGTTAATAGTTAAATTTATTAATTATTTT
Found at i:2897849 original size:17 final size:17
Alignment explanation
Indices: 2897827--2897859 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2897817 TAATAACGAA
2897827 TATATTT-TTAATAATTT
1 TATATTTATT-ATAATTT
2897844 TATATTTATTATAATT
1 TATATTTATTATAATT
2897860 ATAAATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TATATTTATTATAATTT
Found at i:2897896 original size:24 final size:26
Alignment explanation
Indices: 2897849--2897902 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
2897839 AATTTTATAT
2897849 TTATTATAATTATAAATATAATAAATA
1 TTATTATAATTAT-AATATAATAAATA
*
2897876 TTATTATAATTAT-GTAT-ATAAATA
1 TTATTATAATTATAATATAATAAATA
2897900 TTA
1 TTA
2897903 ATAATAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 10 0.38
25 3 0.12
27 13 0.50
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (26 bp):
TTATTATAATTATAATATAATAAATA
Found at i:2900128 original size:6 final size:6
Alignment explanation
Indices: 2900117--2900146 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
2900107 CATCATCTTT
2900117 TTTTTC TTTTTC TTTTTC TTTCTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TTT-TTC TTTTT
2900147 GACAGAATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTC
Found at i:2900134 original size:12 final size:13
Alignment explanation
Indices: 2900112--2900146 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
2900102 TTGCTCATCA
*
2900112 TCTTTTTTTTCTT
1 TCTTCTTTTTCTT
2900125 T-TTCTTTTTCTT
1 TCTTCTTTTTCTT
2900137 TCTTCTTTTT
1 TCTTCTTTTT
2900147 GACAGAATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
TCTTCTTTTTCTT
Found at i:2904737 original size:4 final size:4
Alignment explanation
Indices: 2904728--2904755 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
2904718 TTGATAAAAG
2904728 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
2904756 AACCGCAACG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:2906889 original size:28 final size:28
Alignment explanation
Indices: 2906853--2906908 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
2906843 ACCATAAACT
* *
2906853 AACATCTGGAAGACTGATAATTGATATC
1 AACACCTGGAAGACTGATAATCGATATC
2906881 AACACCTGGAAGACTGATAATCGATATC
1 AACACCTGGAAGACTGATAATCGATATC
2906909 TAACTCTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (28 bp):
AACACCTGGAAGACTGATAATCGATATC
Found at i:2909264 original size:2 final size:2
Alignment explanation
Indices: 2909257--2909291 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2909247 CAATGTTTGA
2909257 AT AT AT AT 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 AT AT AT AT A
2909292 AAAGATAACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2912259 original size:23 final size:24
Alignment explanation
Indices: 2912232--2912296 Score: 75
Period size: 23 Copynumber: 2.8 Consensus size: 24
2912222 ATTTAATAAA
*
2912232 AATATTAAAAATATTTTTAT-ATT
1 AATATTATAAATATTTTTATAATT
*
2912255 AATATT-TATATATTTTTATAATT
1 AATATTATAAATATTTTTATAATT
2912278 AA-ATCTATAAA-ATTTTTAT
1 AATAT-TATAAATATTTTTAT
2912297 TATAAATAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
22 13 0.36
23 20 0.56
24 3 0.08
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (24 bp):
AATATTATAAATATTTTTATAATT
Found at i:2912267 original size:22 final size:23
Alignment explanation
Indices: 2912241--2912296 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
2912231 AAATATTAAA
*
2912241 AATATTTTTAT-ATTAATATTTAT
1 AATATTTTTATAATTAA-ATCTAT
2912264 -ATATTTTTATAATTAAATCTAT
1 AATATTTTTATAATTAAATCTAT
*
2912286 AAAATTTTTAT
1 AATATTTTTAT
2912297 TATAAATAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 15 0.52
23 14 0.48
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (23 bp):
AATATTTTTATAATTAAATCTAT
Found at i:2916621 original size:31 final size:32
Alignment explanation
Indices: 2916583--2916643 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
2916573 GAACCGAAAA
*
2916583 CCAAACC-AAACTGAATATATATCATTAATAT
1 CCAAACCAAAACCGAATATATATCATTAATAT
2916614 CCAAACCAAAACCGAATATATATCATTAAT
1 CCAAACCAAAACCGAATATATATCATTAAT
2916644 TTCTATTGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 7 0.25
32 21 0.75
ACGTcount: A:0.49, C:0.21, G:0.03, T:0.26
Consensus pattern (32 bp):
CCAAACCAAAACCGAATATATATCATTAATAT
Found at i:2918293 original size:20 final size:20
Alignment explanation
Indices: 2918278--2918317 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2918268 ATTTTATTTA
*
2918278 AAATATT-ATATATTTATAT
1 AAATATTAAAATATTTATAT
2918297 AAATATTAAAATATTTATAT
1 AAATATTAAAATATTTATAT
2918317 A
1 A
2918318 TTTATATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATATTAAAATATTTATAT
Found at i:2918295 original size:28 final size:28
Alignment explanation
Indices: 2918262--2918331 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
2918252 GTAAGATTCC
*
2918262 TTTATAATTTTATTTAAAATA-TTATATA
1 TTTAT-ATTATATTTAAAATATTTATATA
*
2918290 TTTATA-TAAATATTAAAATATTTATATA
1 TTTATATTATAT-TTAAAATATTTATATA
2918318 TTTATATTATATTT
1 TTTATATTATATTT
2918332 TAATTTTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
26 3 0.08
27 9 0.25
28 20 0.56
29 4 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (28 bp):
TTTATATTATATTTAAAATATTTATATA
Found at i:2918515 original size:23 final size:23
Alignment explanation
Indices: 2918478--2918536 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
2918468 TTATATTGTG
*
2918478 TTTATATTATTTTTTGAGA-TATT
1 TTTATATTATATTTT-AGATTATT
*
2918501 TTTA-ATTAATATTTTATATTATT
1 TTTATATT-ATATTTTAGATTATT
2918524 TTTATATTATATT
1 TTTATATTATATT
2918537 CTTAATTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
22 5 0.16
23 23 0.74
24 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (23 bp):
TTTATATTATATTTTAGATTATT
Found at i:2918528 original size:11 final size:11
Alignment explanation
Indices: 2918467--2918533 Score: 57
Period size: 11 Copynumber: 5.9 Consensus size: 11
2918457 ACATCATGTA
* *
2918467 TTTATATTGTG
1 TTTATATTATT
2918478 TTTATATTATT
1 TTTATATTATT
*
2918489 TTT-TGAGATATT
1 TTTAT-A-TTATT
2918501 TTTA-ATTAATAT
1 TTTATATT-AT-T
2918513 TTTATATTATT
1 TTTATATTATT
2918524 TTTATATTAT
1 TTTATATTAT
2918534 ATTCTTAATT
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
10 2 0.04
11 27 0.59
12 14 0.30
13 3 0.07
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (11 bp):
TTTATATTATT
Found at i:2918881 original size:2 final size:2
Alignment explanation
Indices: 2918876--2918911 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
2918866 TTAGATAACA
* *
2918876 AT AT AT AT AT AT AT AA AT AT AT AA AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2918912 TGTTTCATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:2919074 original size:46 final size:45
Alignment explanation
Indices: 2919012--2919102 Score: 107
Period size: 46 Copynumber: 2.0 Consensus size: 45
2919002 ATTAAAGTTA
2919012 ATATTTAATAATAAATTTTATTTTT-ATTTAAT-TTAATTATAAAAT
1 ATATTTAATAATAAA--TTATTTTTAATTTAATATTAATTATAAAAT
**
2919057 ATATATTAAT-ATAAAATTATTTTTAATTTTTTATTAATTATAAAAT
1 ATAT-TTAATAAT-AAATTATTTTTAATTTAATATTAATTATAAAAT
2919103 TAAATATGAG
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
44 8 0.20
45 11 0.28
46 21 0.52
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (45 bp):
ATATTTAATAATAAATTATTTTTAATTTAATATTAATTATAAAAT
Found at i:2920887 original size:29 final size:25
Alignment explanation
Indices: 2920842--2920909 Score: 73
Period size: 29 Copynumber: 2.5 Consensus size: 25
2920832 TGATACATAA
*
2920842 TAATATTAATGTATTTTAATATATTATTT
1 TAAT-TTAATATATTTTAA-ATA-T-TTT
2920871 TAAATTTAATATATTTTAAATATTTT
1 T-AATTTAATATATTTTAAATATTTT
2920897 TAATTTATATATA
1 TAATTTA-ATATA
2920910 AATAAAAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
25 6 0.17
26 9 0.25
27 1 0.03
28 3 0.08
29 14 0.39
30 3 0.08
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (25 bp):
TAATTTAATATATTTTAAATATTTT
Found at i:2920949 original size:14 final size:15
Alignment explanation
Indices: 2920925--2920954 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
2920915 AAAATATCTT
2920925 TAAATATAAAATAAA
1 TAAATATAAAATAAA
2920940 TAAA-ATAAAATAAA
1 TAAATATAAAATAAA
2920954 T
1 T
2920955 TTTATATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
TAAATATAAAATAAA
Found at i:2921033 original size:18 final size:19
Alignment explanation
Indices: 2920991--2921027 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2920981 TATATAATAT
**
2920991 TATAAAAAATTTTATCAAA
1 TATAAAAAATCATATCAAA
2921010 TATAAAAAATCATATCAA
1 TATAAAAAATCATATCAA
2921028 TCTAAATAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.32
Consensus pattern (19 bp):
TATAAAAAATCATATCAAA
Found at i:2922025 original size:23 final size:25
Alignment explanation
Indices: 2921986--2922031 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
2921976 AAATAAATTT
*
2921986 TAAAATTATATAAATATTTAATATC
1 TAAAATTATATAAATATTAAATATC
2922011 TAAAATT-T-TAAATATTAAATA
1 TAAAATTATATAAATATTAAATA
2922032 ATAAAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 12 0.60
24 1 0.05
25 7 0.35
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (25 bp):
TAAAATTATATAAATATTAAATATC
Found at i:2922050 original size:33 final size:32
Alignment explanation
Indices: 2921979--2922050 Score: 74
Period size: 33 Copynumber: 2.2 Consensus size: 32
2921969 TATCTATAAA
* * * *
2921979 TAAATTTTAAAATTATATAAATATTTAATATC
1 TAAATTTTAAAATTAAATAAAAAATAAATATC
2922011 TAAAATTTTAAATATTAAATAATAAAATAAATAT-
1 T-AAATTTTAAA-ATTAAATAA-AAAATAAATATC
2922045 TAAATT
1 TAAATT
2922051 ATTATTACCT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
32 1 0.03
33 15 0.45
34 9 0.27
35 8 0.24
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (32 bp):
TAAATTTTAAAATTAAATAAAAAATAAATATC
Found at i:2922053 original size:8 final size:7
Alignment explanation
Indices: 2921996--2922054 Score: 50
Period size: 7 Copynumber: 8.3 Consensus size: 7
2921986 TAAAATTATA
2921996 TAAATAT
1 TAAATAT
*
2922003 TTAATAT
1 TAAATAT
*
2922010 CTAAAATTT
1 -T-AAATAT
2922019 TAAATAT
1 TAAATAT
*
2922026 TAAATAA
1 TAAATAT
2922033 TAAA-A-
1 TAAATAT
2922038 TAAATAT
1 TAAATAT
2922045 TAAATTAT
1 TAAA-TAT
2922053 TA
1 TA
2922055 TTACCTAGAT
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
5 4 0.10
6 2 0.05
7 25 0.60
8 7 0.17
9 4 0.10
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (7 bp):
TAAATAT
Found at i:2922165 original size:16 final size:16
Alignment explanation
Indices: 2922146--2922178 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2922136 AAAATTTATT
2922146 AAAAA-TTAAATAAATA
1 AAAAATTTAAA-AAATA
2922162 AAAAATTTAAAAAATA
1 AAAAATTTAAAAAATA
2922178 A
1 A
2922179 TTAATATCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAAATTTAAAAAATA
Found at i:2923295 original size:2 final size:2
Alignment explanation
Indices: 2923288--2923324 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2923278 TCGACATTGT
2923288 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2923325 GTGACAGCCG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:2928318 original size:21 final size:21
Alignment explanation
Indices: 2928294--2928333 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2928284 AAAACAATTT
2928294 TATTTTAATATAAAATAATAA
1 TATTTTAATATAAAATAATAA
*
2928315 TATTTTTATATAAAATAAT
1 TATTTTAATATAAAATAAT
2928334 TTTTATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TATTTTAATATAAAATAATAA
Found at i:2931821 original size:2 final size:2
Alignment explanation
Indices: 2931814--2931844 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2931804 CAAATAATCC
2931814 AT AT 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 AT AT A
2931845 AACTGAAACG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2932921 original size:29 final size:29
Alignment explanation
Indices: 2932854--2932923 Score: 74
Period size: 28 Copynumber: 2.4 Consensus size: 29
2932844 TTATTGTTAA
*
2932854 AATTTAAATAATATATTTTTATTAAAATTT
1 AATTTAAA-AATACATTTTTATTAAAATTT
*
2932884 AATAT-AAAATACATTTCCTT-TTAAAA-TT
1 AATTTAAAAATACATTT--TTATTAAAATTT
2932912 AATTTAAAAATA
1 AATTTAAAAATA
2932924 ATAATTTAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
28 14 0.41
29 14 0.41
30 6 0.18
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (29 bp):
AATTTAAAAATACATTTTTATTAAAATTT
Found at i:2933717 original size:23 final size:22
Alignment explanation
Indices: 2933686--2933759 Score: 69
Period size: 23 Copynumber: 3.3 Consensus size: 22
2933676 TATTTTGTTC
*
2933686 ATTTAATAATAAATAAATTACAT
1 ATTT-ATAATAAATAAATTAAAT
* *
2933709 ATTATATAATAATTAATTTAAAT
1 ATT-TATAATAAATAAATTAAAT
* *
2933732 ATTTAT-ATAAATATATAAAAT
1 ATTTATAATAAATAAATTAAAT
2933753 AATTTAT
1 -ATTTAT
2933760 GTTAAAATTT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
21 11 0.26
22 9 0.21
23 21 0.50
24 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (22 bp):
ATTTATAATAAATAAATTAAAT
Found at i:2936516 original size:17 final size:18
Alignment explanation
Indices: 2936477--2936518 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
2936467 AATTCGGTGA
2936477 TTGATTTAGTTGCAGCAT
1 TTGATTTAGTTGCAGCAT
2936495 TTGATTTAGTTGCAGC-T
1 TTGATTTAGTTGCAGCAT
2936512 TTGATTT
1 TTGATTT
2936519 GATTGGATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.19, C:0.10, G:0.21, T:0.50
Consensus pattern (18 bp):
TTGATTTAGTTGCAGCAT
Found at i:2941386 original size:2 final size:2
Alignment explanation
Indices: 2941379--2941428 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
2941369 ACCCTTTAGT
2941379 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2941421 TC TC TC TC
1 TC TC TC TC
2941429 CCCTTGGAAC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2946652 original size:31 final size:30
Alignment explanation
Indices: 2946600--2946659 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
2946590 ATAAAATATA
2946600 TTAAAAAATATATAAGAATATTATATTTAT
1 TTAAAAAATATATAAGAATATTATATTTAT
* *
2946630 TTAAAACAATATTTTAAG-ATATTGTATTTA
1 TTAAAA-AATA-TATAAGAATATTATATTTA
2946660 ATAATATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 6 0.23
31 15 0.58
32 5 0.19
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (30 bp):
TTAAAAAATATATAAGAATATTATATTTAT
Found at i:2948820 original size:13 final size:13
Alignment explanation
Indices: 2948802--2948826 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2948792 TCATCTACCA
2948802 CCTTTTTTTTTTT
1 CCTTTTTTTTTTT
2948815 CCTTTTTTTTTT
1 CCTTTTTTTTTT
2948827 GGGGGGGGGG
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:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
CCTTTTTTTTTTT
Found at i:2950447 original size:5 final size:5
Alignment explanation
Indices: 2950437--2950462 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
2950427 AATGTATTTT
2950437 TTTAA TTTAA TTTAA TTTAA TTTAA T
1 TTTAA TTTAA TTTAA TTTAA TTTAA T
2950463 AAAAATATAT
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTTAA
Found at i:2957655 original size:2 final size:2
Alignment explanation
Indices: 2957648--2957678 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2957638 ATAAATAATG
2957648 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2957679 TTTCAGGTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2958622 original size:10 final size:10
Alignment explanation
Indices: 2958600--2958658 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
2958590 GTTTAGATAA
2958600 ATTTAAAA-T
1 ATTTAAAATT
*
2958609 -TTTATAATT
1 ATTTAAAATT
2958618 ATTTAAAATAAT
1 ATTTAAAAT--T
2958630 ATTTAAAA--
1 ATTTAAAATT
2958638 ATTTAAAATT
1 ATTTAAAATT
*
2958648 ATTTAATATT
1 ATTTAAAATT
2958658 A
1 A
2958659 ATATGTATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
8 14 0.34
9 1 0.02
10 17 0.41
12 9 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (10 bp):
ATTTAAAATT
Found at i:2958634 original size:30 final size:31
Alignment explanation
Indices: 2958596--2958662 Score: 93
Period size: 30 Copynumber: 2.2 Consensus size: 31
2958586 CAAAGTTTAG
* *
2958596 ATAA-ATTTAAAATTTTATAATTATTTAA-A
1 ATAATATTTAAAAATTTAAAATTATTTAATA
2958625 ATAATATTTAAAAATTTAAAATTATTTAATA
1 ATAATATTTAAAAATTTAAAATTATTTAATA
*
2958656 TTAATAT
1 ATAATAT
2958663 GTATAATTAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 4 0.12
30 22 0.67
31 7 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (31 bp):
ATAATATTTAAAAATTTAAAATTATTTAATA
Found at i:2958652 original size:18 final size:18
Alignment explanation
Indices: 2958598--2958653 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 18
2958588 AAGTTTAGAT
2958598 AAATTTAAAATT-TTATAA
1 AAATTTAAAATTATT-TAA
**
2958616 TTATTTAAAATAATATTTAA
1 AAATTTAAAAT--TATTTAA
2958636 AAATTTAAAATTATTTAA
1 AAATTTAAAATTATTTAA
2958654 TATTAATATG
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
18 16 0.52
20 13 0.42
21 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AAATTTAAAATTATTTAA
Found at i:2958927 original size:21 final size:21
Alignment explanation
Indices: 2958890--2958929 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2958880 TTAGACTGCC
*
2958890 AAATTTAATTAATTTAAATAA
1 AAATTTAATTAAATTAAATAA
2958911 AAATTT-ATTCAAATTAAAT
1 AAATTTAATT-AAATTAAAT
2958930 TTTATAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (21 bp):
AAATTTAATTAAATTAAATAA
Found at i:2959472 original size:22 final size:21
Alignment explanation
Indices: 2959447--2959497 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
2959437 TTTATTTATT
2959447 TTATTTTATGTATTTTTTAAAA
1 TTATTTTAT-TATTTTTTAAAA
*
2959469 TTATTATT-TTATTTTTTGAAA
1 TTATT-TTATTATTTTTTAAAA
2959490 -TATTTTAT
1 TTATTTTAT
2959498 AGTTTATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 2 0.08
20 5 0.19
21 11 0.42
22 6 0.23
23 2 0.08
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (21 bp):
TTATTTTATTATTTTTTAAAA
Found at i:2959900 original size:11 final size:11
Alignment explanation
Indices: 2959886--2960021 Score: 64
Period size: 11 Copynumber: 13.0 Consensus size: 11
2959876 ATAAATAAAT
2959886 ATTAAAATATA
1 ATTAAAATATA
2959897 ATTAAAATATA
1 ATTAAAATATA
*
2959908 A--AACAATAAA
1 ATTAA-AATATA
2959918 ACTTATAAATATA
1 A-TTA-AAATATA
* *
2959931 TTTTTAAATAT-
1 -ATTAAAATATA
2959942 A-TAAAATATAA
1 ATTAAAATAT-A
*
2959953 ATTATTAATAT-
1 ATTA-AAATATA
*
2959964 ATTAAAAT-TT
1 ATTAAAATATA
*
2959974 A-TATAA-AT-
1 ATTAAAATATA
2959982 -TTAAAATAT-
1 ATTAAAATATA
*
2959991 -TTTAAATATA
1 ATTAAAATATA
2960001 ATTAAAATATA
1 ATTAAAATATA
2960012 A-TAAAATATA
1 ATTAAAATATA
2960022 TAAATATATT
Statistics
Matches: 97, Mismatches: 12, Indels: 33
0.68 0.08 0.23
Matches are distributed among these distances:
8 4 0.04
9 25 0.26
10 19 0.20
11 27 0.28
12 8 0.08
13 13 0.13
14 1 0.01
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (11 bp):
ATTAAAATATA
Found at i:2959929 original size:34 final size:32
Alignment explanation
Indices: 2959878--2960019 Score: 108
Period size: 34 Copynumber: 4.2 Consensus size: 32
2959868 AAAATTATAT
2959878 AAATAAATATTA-AAATATAATTAAAATATAAA
1 AAATAAA-ATTATAAATATAATTAAAATATAAA
* * *
2959910 ACAATAAAACTTATAAATATATTTTTAAATATATA
1 A-AATAAAA-TTATAAATATA-ATTAAAATATAAA
*
2959945 AAATATAAATTATTAATAT-ATTAAAATTTATATAA
1 AAATA-AAATTATAAATATAATTAAAA--TATA-AA
** *
2959980 ATTTAAAATATTTTAAATATAATTAAAATATAATA
1 AAAT-AAA-ATTATAAATATAATTAAAATATAA-A
2960015 AAATA
1 AAATA
2960020 TATAAATATA
Statistics
Matches: 85, Mismatches: 13, Indels: 22
0.71 0.11 0.18
Matches are distributed among these distances:
32 7 0.08
33 9 0.11
34 26 0.31
35 26 0.31
36 10 0.12
37 7 0.08
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (32 bp):
AAATAAAATTATAAATATAATTAAAATATAAA
Found at i:2959942 original size:46 final size:45
Alignment explanation
Indices: 2959866--2959953 Score: 115
Period size: 46 Copynumber: 1.9 Consensus size: 45
2959856 ATAATATTAG
*
2959866 ATAAAATTATATAAATAAATATTAAAATATAATTAAAATATAAAACA
1 ATAAAACTATATAAATAAATATTAAAATAT-A-TAAAATATAAAACA
* * *
2959913 ATAAAACT-TATAAATATATTTTTAAATATATAAAATATAAA
1 ATAAAACTATATAAATAAATATTAAAATATATAAAATATAAA
2959954 TTATTAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
44 11 0.30
45 1 0.03
46 18 0.49
47 7 0.19
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (45 bp):
ATAAAACTATATAAATAAATATTAAAATATATAAAATATAAAACA
Found at i:2959946 original size:20 final size:19
Alignment explanation
Indices: 2959921--2960031 Score: 61
Period size: 20 Copynumber: 5.6 Consensus size: 19
2959911 CAATAAAACT
2959921 TATAAATATATTTTTAAATA
1 TATAAA-ATATTTTTAAATA
2959941 TATAAAATATAAATTATT-AATA
1 TATAAAATAT---TT-TTAAATA
*
2959963 TATTAAAAT-TTATATAAAT-
1 TA-TAAAATATT-TTTAAATA
2959982 T-TAAAATA-TTTTAAATA
1 TATAAAATATTTTTAAATA
** *
2959999 TAATTAAAATATAATAAAATA
1 T-A-TAAAATATTTTTAAATA
2960020 TATAAATATATT
1 TATAAA-ATATT
2960032 AAAACATCGC
Statistics
Matches: 71, Mismatches: 6, Indels: 28
0.68 0.06 0.27
Matches are distributed among these distances:
16 6 0.08
17 8 0.11
19 11 0.15
20 22 0.31
21 7 0.10
22 9 0.13
23 8 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TATAAAATATTTTTAAATA
Done.