Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr5
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: 39371879
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2227820 characters in sequence are not A, C, G, or T
File 25 of 103
Found at i:9212937 original size:21 final size:21
Alignment explanation
Indices: 9212912--9212989 Score: 68
Period size: 21 Copynumber: 3.5 Consensus size: 21
9212902 TTTTTCGCGT
9212912 CTGGCAGGGTGAAGGAGGTGC
1 CTGGCAGGGTGAAGGAGGTGC
* **
9212933 CTGGCAGGGTG-CGGAATTTTTGC
1 CTGGCAGGGTGAAGG-A--GGTGC
9212956 GTCTGGCAGGGTGAAGGAGGTGC
1 --CTGGCAGGGTGAAGGAGGTGC
*
9212979 CTAGCAGGGTG
1 CTGGCAGGGTG
9212990 CGTCCGCACC
Statistics
Matches: 44, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
20 2 0.05
21 22 0.50
23 6 0.14
25 12 0.27
26 2 0.05
ACGTcount: A:0.17, C:0.15, G:0.47, T:0.21
Consensus pattern (21 bp):
CTGGCAGGGTGAAGGAGGTGC
Found at i:9212967 original size:46 final size:47
Alignment explanation
Indices: 9212899--9212991 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 47
9212889 TGCCAGACGT
*
9212899 GAATTTTTCGCGTCTGGCAGGGTGAAGGAGGTGCCTGGCAGGGTGCG
1 GAATTTTTCGCGTCTGGCAGGGTGAAGGAGGTGCCTAGCAGGGTGCG
9212946 GAATTTTT-GCGTCTGGCAGGGTGAAGGAGGTGCCTAGCAGGGTGCG
1 GAATTTTTCGCGTCTGGCAGGGTGAAGGAGGTGCCTAGCAGGGTGCG
9212992 TCCGCACCCT
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
46 37 0.82
47 8 0.18
ACGTcount: A:0.16, C:0.16, G:0.44, T:0.24
Consensus pattern (47 bp):
GAATTTTTCGCGTCTGGCAGGGTGAAGGAGGTGCCTAGCAGGGTGCG
Found at i:9213278 original size:27 final size:27
Alignment explanation
Indices: 9213236--9213310 Score: 105
Period size: 27 Copynumber: 2.8 Consensus size: 27
9213226 TTTTGACAAG
* *
9213236 GCAAAACATGATAAGTTGAATGATGTA
1 GCAAAACATGACAAGTTGAATAATGTA
* *
9213263 GCAAAACATGACAAGTTGAACAATGTG
1 GCAAAACATGACAAGTTGAATAATGTA
*
9213290 GCAAAATATGACAAGTTGAAT
1 GCAAAACATGACAAGTTGAAT
9213311 TGCATGGTGA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.45, C:0.11, G:0.21, T:0.23
Consensus pattern (27 bp):
GCAAAACATGACAAGTTGAATAATGTA
Found at i:9213797 original size:24 final size:24
Alignment explanation
Indices: 9213751--9213798 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
9213741 AGTGCACATG
*
9213751 ATGTTACATGCTATATATAAAACC
1 ATGTTACACGCTATATATAAAACC
* * *
9213775 ATGTTACACGTTATGTATTAAACC
1 ATGTTACACGCTATATATAAAACC
9213799 TCTTTATATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (24 bp):
ATGTTACACGCTATATATAAAACC
Found at i:9213923 original size:26 final size:25
Alignment explanation
Indices: 9213894--9214020 Score: 73
Period size: 26 Copynumber: 4.9 Consensus size: 25
9213884 TACAAAAACA
9213894 TGTTACACGCTATGGTTAAAAAAAGT
1 TGTTACACGCTAT-GTTAAAAAAAGT
* * *
9213920 TGTTACACACCATGTTAAAAAAATATTAT
1 TGTTACACGCTATGTT-AAAAAA-A--GT
*
9213949 TGTTACACGCTATG-TACAAAAA-T
1 TGTTACACGCTATGTTAAAAAAAGT
* *
9213972 ATATTATACG-TCATGGTTAAAAAAAGT
1 -TGTTACACGCT-AT-GTTAAAAAAAGT
* *
9213999 TGTTATACG-TCATGTTGAAAAA
1 TGTTACACGCT-ATGTTAAAAAA
9214021 CAAAATATTT
Statistics
Matches: 81, Mismatches: 11, Indels: 19
0.73 0.10 0.17
Matches are distributed among these distances:
23 2 0.02
24 9 0.11
25 12 0.15
26 37 0.46
27 7 0.09
28 1 0.01
29 13 0.16
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (25 bp):
TGTTACACGCTATGTTAAAAAAAGT
Found at i:9213955 original size:29 final size:30
Alignment explanation
Indices: 9213919--9213978 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
9213909 TTAAAAAAAG
9213919 TTGTTACACACCATGTTA-AAAAA-ATATTA
1 TTGTTACACACCATG-TACAAAAATATATTA
* *
9213948 TTGTTACACGCTATGTACAAAAATATATTA
1 TTGTTACACACCATGTACAAAAATATATTA
9213978 T
1 T
9213979 ACGTCATGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 2 0.07
29 18 0.67
30 7 0.26
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.37
Consensus pattern (30 bp):
TTGTTACACACCATGTACAAAAATATATTA
Found at i:9214077 original size:83 final size:79
Alignment explanation
Indices: 9213842--9214147 Score: 267
Period size: 83 Copynumber: 3.8 Consensus size: 79
9213832 ATGCATATGA
* * * * * *** *
9213842 TGTTACATACCATGTT-GAAAAGTGTTATTGTTACAGGTTGTGTACAAAAACATGTTACACGCTA
1 TGTTACACACCATGTTAAAAAAATATTATTGTTACACGCCATGTACAAAAACATGTTACACGCCA
9213906 TGGTTAAAAAAAGT
66 TGGTTAAAAAAAGT
* * * * *
9213920 TGTTACACACCATGTTAAAAAAATATTATTGTTACACGCTATGTACAAAAATATATTATACGTCA
1 TGTTACACACCATGTTAAAAAAATATTATTGTTACACGCCATGTACAAAAACATGTTACACGCCA
9213985 TGGTTAAAAAAAGT
66 TGGTTAAAAAAAGT
* ** *
9213999 TGTTATACGTCATGTTGAAAAACAAAATATTTTTGTTACACGCCATGTACAAAAACATGTTACA-
1 TGTTACACACCATGTT---AAA-AAAATATTATTGTTACACGCCATGTACAAAAACATGTTACAC
*
9214063 GACCAT-ATTGAAAAAAATGTTGT
62 G-CCATGGTT-AAAAAAA----GT
* * * * * *
9214086 TGTTACACGCCATGTTGAAAAAATATTACTGTTAGACGCCATGTTCAAAAAAATTGTTACAC
1 TGTTACACACCATGTTAAAAAAATATTATTGTTACACGCCATGTACAAAAACA-TGTTACAC
9214148 TTTAATGCTT
Statistics
Matches: 185, Mismatches: 30, Indels: 19
0.79 0.13 0.08
Matches are distributed among these distances:
78 15 0.08
79 64 0.35
82 6 0.03
83 75 0.41
84 9 0.05
87 16 0.09
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (79 bp):
TGTTACACACCATGTTAAAAAAATATTATTGTTACACGCCATGTACAAAAACATGTTACACGCCA
TGGTTAAAAAAAGT
Found at i:9222125 original size:103 final size:103
Alignment explanation
Indices: 9222007--9222215 Score: 377
Period size: 105 Copynumber: 2.0 Consensus size: 103
9221997 TATATTATAT
9222007 TTTTAGCAGGTTTCGAAATTTTTGAGT-AAAAA-TGACCAAAATACCCCTGTGTGGTAGAAATTA
1 TTTTAGCAGGTTTCGAAATTTTTGAGTAAAAAATTGACCAAAATACCCCTGTGTGGTAGAAATTA
9222070 CTTTTTGATTGTCTTTGATTTGAAAATAGTCTATATTCC
66 CTTTTTGATT-TCTTTGATTTGAAAATAGTCTATATTCC
9222109 TNTTTAGCAGGTTTCGAAATTTTTGAGTAAAAAATTGACCAAAATACCCCTGTGTGGTAGAAATT
1 T-TTTAGCAGGTTTCGAAATTTTTGAGTAAAAAATTGACCAAAATACCCCTGTGTGGTAGAAATT
*
9222174 ACTTTTTGATTTCTTTGATTTGAAAATAGTTTATATTCC
65 ACTTTTTGATTTCTTTGATTTGAAAATAGTCTATATTCC
9222213 TTT
1 TTT
9222216 AAAACATGAT
Statistics
Matches: 103, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
102 1 0.01
103 28 0.27
104 33 0.32
105 41 0.40
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (103 bp):
TTTTAGCAGGTTTCGAAATTTTTGAGTAAAAAATTGACCAAAATACCCCTGTGTGGTAGAAATTA
CTTTTTGATTTCTTTGATTTGAAAATAGTCTATATTCC
Found at i:9232434 original size:54 final size:54
Alignment explanation
Indices: 9232376--9232596 Score: 361
Period size: 54 Copynumber: 4.1 Consensus size: 54
9232366 TGAGGGAGAT
* *
9232376 AGATGGGATGTCTGGCTATGTGCACGATATGGTGGGATGCACATGAGCTGGGTG
1 AGATGGGATGTCCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTG
* *
9232430 AGATGGGATGTCCGACTATGTGCACGATGTGGTGGGATGCACATGAGTTGGGTG
1 AGATGGGATGTCCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTG
* *
9232484 AGATGGGATGTCCGGCTTTGTGCATGATGTGGTGGGATGCACATGAGCTGGGTG
1 AGATGGGATGTCCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTG
* * *
9232538 AGATGGGATGTCCGTCTTTGTGCACAATGTGGTGGGATGCACATGAGCTGGGTG
1 AGATGGGATGTCCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTG
9232592 AGATG
1 AGATG
9232597 CACATAATGA
Statistics
Matches: 156, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 156 1.00
ACGTcount: A:0.19, C:0.13, G:0.41, T:0.27
Consensus pattern (54 bp):
AGATGGGATGTCCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTG
Found at i:9234365 original size:28 final size:28
Alignment explanation
Indices: 9234333--9234393 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
9234323 ATATTTAAAC
*
9234333 TTTATTTATATTT-GATGTAATTTATTTT
1 TTTATTTATATTTAG-TGTAATTTATTTG
*
9234361 TTTATTTATGTTTAGTGTAATTTATTTG
1 TTTATTTATATTTAGTGTAATTTATTTG
9234389 TTTAT
1 TTTAT
9234394 AACATGTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 29 0.97
29 1 0.03
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (28 bp):
TTTATTTATATTTAGTGTAATTTATTTG
Found at i:9237964 original size:8 final size:8
Alignment explanation
Indices: 9237920--9237982 Score: 62
Period size: 8 Copynumber: 8.2 Consensus size: 8
9237910 TAGGTCAAAC
9237920 CTTCCTTGT
1 CTTCCTT-T
9237929 CTT--TTT
1 CTTCCTTT
9237935 CTT-CTTT
1 CTTCCTTT
*
9237942 C-TCCATT
1 CTTCCTTT
*
9237949 CTTTCTTT
1 CTTCCTTT
9237957 CTTCCTTT
1 CTTCCTTT
9237965 CTTCCTTT
1 CTTCCTTT
*
9237973 TTTCCTTT
1 CTTCCTTT
9237981 CT
1 CT
9237983 CTCTTTGCTT
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
6 5 0.11
7 10 0.22
8 27 0.60
9 3 0.07
ACGTcount: A:0.02, C:0.32, G:0.02, T:0.65
Consensus pattern (8 bp):
CTTCCTTT
Found at i:9237988 original size:16 final size:15
Alignment explanation
Indices: 9237932--9237993 Score: 63
Period size: 16 Copynumber: 3.9 Consensus size: 15
9237922 TCCTTGTCTT
9237932 TTTCTTCTTTC-TCC
1 TTTCTTCTTTCTTCC
*
9237946 ATTCTTTCTTTCTTCC
1 TTTC-TTCTTTCTTCC
*
9237962 TTTCTTCCTTTTTTCC
1 TTTCTT-CTTTCTTCC
9237978 TTTCTCTCTTTGCTTC
1 TTTCT-TCTTT-CTTC
9237994 AAAGCTGATT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
14 3 0.08
15 9 0.23
16 23 0.59
17 4 0.10
ACGTcount: A:0.02, C:0.32, G:0.02, T:0.65
Consensus pattern (15 bp):
TTTCTTCTTTCTTCC
Found at i:9239343 original size:26 final size:25
Alignment explanation
Indices: 9239306--9239358 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 25
9239296 AATACATATA
** *
9239306 AAATTAAAATAACTCACTTGAAAAT
1 AAATTAAAATAAAACACTTAAAAAT
*
9239331 AAATTAATTATAAAACACTTAAAAAT
1 AAATTAA-AATAAAACACTTAAAAAT
9239357 AA
1 AA
9239359 CTAAGTTATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.60, C:0.09, G:0.02, T:0.28
Consensus pattern (25 bp):
AAATTAAAATAAAACACTTAAAAAT
Found at i:9239367 original size:26 final size:26
Alignment explanation
Indices: 9239320--9239369 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
9239310 TAAAATAACT
* *
9239320 CACTTGAAAATAAATTAATTATAAAA
1 CACTTAAAAATAAACTAATTATAAAA
9239346 CACTTAAAAAT-AACTAAGTTATAA
1 CACTTAAAAATAAACTAA-TTATAA
9239370 TTGAAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.56, C:0.10, G:0.04, T:0.30
Consensus pattern (26 bp):
CACTTAAAAATAAACTAATTATAAAA
Found at i:9248762 original size:35 final size:36
Alignment explanation
Indices: 9248680--9248867 Score: 131
Period size: 36 Copynumber: 5.2 Consensus size: 36
9248670 TCTCATCAGC
9248680 TCATGTGCACTCCCACA-CAGCACATAGCTAGA-ATCA
1 TCATGTGCACTCCCACATC-GCACATAGC-AGATATCA
* *
9248716 TCTTGTACACTCCCACATCGCACA-AGGCA-ATATCA
1 TCATGTGCACTCCCACATCGCACATA-GCAGATATCA
* *
9248751 TCATGTGCACTCCCACATCACACATAGCATATATCA
1 TCATGTGCACTCCCACATCGCACATAGCAGATATCA
* * * *
9248787 TCAGTGTGTGCACTCACACA--GCACACTA-C-TATCACCG
1 TCA---TGTGCACTCCCACATCGCACA-TAGCAGAT-ATCA
* * * *
9248824 TCATGTGCACTCCCGCACCGCACATGGCATATATCA
1 TCATGTGCACTCCCACATCGCACATAGCAGATATCA
9248860 TCAGTGTG
1 TCA-TGTG
9248868 TGCACTCACA
Statistics
Matches: 123, Mismatches: 14, Indels: 29
0.74 0.08 0.17
Matches are distributed among these distances:
34 13 0.11
35 31 0.25
36 46 0.37
37 18 0.15
38 2 0.02
39 13 0.11
ACGTcount: A:0.29, C:0.34, G:0.14, T:0.23
Consensus pattern (36 bp):
TCATGTGCACTCCCACATCGCACATAGCAGATATCA
Found at i:9248812 original size:39 final size:39
Alignment explanation
Indices: 9248754--9248885 Score: 123
Period size: 39 Copynumber: 3.5 Consensus size: 39
9248744 AATATCATCA
* *
9248754 TGTGCACTCCCACATCACACATAGCATATATCATCAGTG
1 TGTGCACTCACACAACACACATAGCATATATCATCAGTG
* * *
9248793 TGTGCACTCACACAGCACAC-TA-C---TATCA-CCGTCA
1 TGTGCACTCACACAACACACATAGCATATATCATCAGT-G
* * * * *
9248827 TGTGCACTCCCGCACCGCACATGGCATATATCATCAGTG
1 TGTGCACTCACACAACACACATAGCATATATCATCAGTG
9248866 TGTGCACTCACACAACACAC
1 TGTGCACTCACACAACACAC
9248886 CACTATCACA
Statistics
Matches: 71, Mismatches: 15, Indels: 14
0.71 0.15 0.14
Matches are distributed among these distances:
33 3 0.04
34 21 0.30
35 1 0.01
36 1 0.01
37 1 0.01
38 2 0.03
39 39 0.55
40 3 0.04
ACGTcount: A:0.29, C:0.35, G:0.14, T:0.22
Consensus pattern (39 bp):
TGTGCACTCACACAACACACATAGCATATATCATCAGTG
Found at i:9248831 original size:34 final size:34
Alignment explanation
Indices: 9248793--9248908 Score: 101
Period size: 34 Copynumber: 3.3 Consensus size: 34
9248783 ATCATCAGTG
*
9248793 TGTGCACTCACACAGCACACTACTATCACCGTCA
1 TGTGCACTCACACAGCACACTACTATCACAGTCA
* * *
9248827 TGTGCACTCCCGCACCGCACATGGCATA-TATCATCAGT-G
1 TGTGCACT--CACACAGCACA---C-TACTATCA-CAGTCA
* *
9248866 TGTGCACTCACACAACACACCACTATCACAGTCA
1 TGTGCACTCACACAGCACACTACTATCACAGTCA
9248900 TGTGCACTC
1 TGTGCACTC
9248909 CTACACTGCA
Statistics
Matches: 64, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
33 5 0.08
34 23 0.36
36 9 0.14
37 8 0.12
39 14 0.22
40 5 0.08
ACGTcount: A:0.28, C:0.36, G:0.15, T:0.22
Consensus pattern (34 bp):
TGTGCACTCACACAGCACACTACTATCACAGTCA
Found at i:9248920 original size:73 final size:73
Alignment explanation
Indices: 9248751--9248922 Score: 256
Period size: 73 Copynumber: 2.4 Consensus size: 73
9248741 GGCAATATCA
* * * *
9248751 TCATGTGCACTCCCACA-TCACACATAGCATATATCATCAGTGTGTGCACTCACACAGCACACTA
1 TCATGTGCACTCCCACACT-GCACATGGCATATATCATCAGTGTGTGCACTCACACAACACACCA
*
9248815 CTATCACCG
65 CTATCACAG
* *
9248824 TCATGTGCACTCCCGCACCGCACATGGCATATATCATCAGTGTGTGCACTCACACAACACACCAC
1 TCATGTGCACTCCCACACTGCACATGGCATATATCATCAGTGTGTGCACTCACACAACACACCAC
9248889 TATCACAG
66 TATCACAG
*
9248897 TCATGTGCACTCCTACACTGCACATG
1 TCATGTGCACTCCCACACTGCACATG
9248923 CACGGTTACA
Statistics
Matches: 88, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
73 88 1.00
ACGTcount: A:0.28, C:0.35, G:0.14, T:0.23
Consensus pattern (73 bp):
TCATGTGCACTCCCACACTGCACATGGCATATATCATCAGTGTGTGCACTCACACAACACACCAC
TATCACAG
Found at i:9249737 original size:14 final size:15
Alignment explanation
Indices: 9249704--9249746 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
9249694 AGGAGGAAGT
*
9249704 AAGAAAACAAAATAA
1 AAGAAAATAAAATAA
*
9249719 AAGAAAATAAAA-CA
1 AAGAAAATAAAATAA
9249733 AAGAAAATAAAATA
1 AAGAAAATAAAATA
9249747 GAAAAATACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.79, C:0.05, G:0.07, T:0.09
Consensus pattern (15 bp):
AAGAAAATAAAATAA
Found at i:9253313 original size:20 final size:20
Alignment explanation
Indices: 9253296--9253333 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
9253286 CCTCAAATCT
9253296 TACTCCAATAAGTCAAATTA
1 TACTCCAATAAGTCAAATTA
9253316 TACTCCAATAAGTCAAAT
1 TACTCCAATAAGTCAAAT
9253334 GGGGCCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.21, G:0.05, T:0.29
Consensus pattern (20 bp):
TACTCCAATAAGTCAAATTA
Found at i:9256557 original size:26 final size:26
Alignment explanation
Indices: 9256521--9256573 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
9256511 ATGGAGTTCA
9256521 TAGTATTAACATCACTTTTAGTGATT
1 TAGTATTAACATCACTTTTAGTGATT
9256547 TAGTATTAACATCACTTTTAGTGATT
1 TAGTATTAACATCACTTTTAGTGATT
9256573 T
1 T
9256574 CAGGAAGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.47
Consensus pattern (26 bp):
TAGTATTAACATCACTTTTAGTGATT
Found at i:9257187 original size:13 final size:13
Alignment explanation
Indices: 9257169--9257193 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9257159 TACAAGATAA
9257169 TTAGAGAGAGAAT
1 TTAGAGAGAGAAT
9257182 TTAGAGAGAGAA
1 TTAGAGAGAGAA
9257194 GCTCTCAAGT
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:0.48, C:0.00, G:0.32, T:0.20
Consensus pattern (13 bp):
TTAGAGAGAGAAT
Found at i:9265167 original size:29 final size:29
Alignment explanation
Indices: 9265134--9265189 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
9265124 GAGGTGTACA
*
9265134 AGAATAGGTACGAGAGAAGAAGCTGTATG
1 AGAATAGGTACAAGAGAAGAAGCTGTATG
*
9265163 AGAATAGGTACAAGAGAATAAGCTGTA
1 AGAATAGGTACAAGAGAAGAAGCTGTA
9265190 CATGAATAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.45, C:0.07, G:0.30, T:0.18
Consensus pattern (29 bp):
AGAATAGGTACAAGAGAAGAAGCTGTATG
Found at i:9265196 original size:29 final size:28
Alignment explanation
Indices: 9265128--9265197 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 28
9265118 AGAAAAGAGG
*
9265128 TGTACAAGAATAGGTACGAGAGAAGAAGC
1 TGTAC-AGAATAGGTACAAGAGAAGAAGC
* *
9265157 TGTATGAGAATAGGTACAAGAGAATAAGC
1 TGTA-CAGAATAGGTACAAGAGAAGAAGC
9265186 TGTACATGAATA
1 TGTACA-GAATA
9265198 AGTATACGAG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
28 1 0.03
29 34 0.97
ACGTcount: A:0.44, C:0.09, G:0.27, T:0.20
Consensus pattern (28 bp):
TGTACAGAATAGGTACAAGAGAAGAAGC
Found at i:9265506 original size:26 final size:26
Alignment explanation
Indices: 9265477--9265551 Score: 141
Period size: 26 Copynumber: 2.9 Consensus size: 26
9265467 AAGTAATACT
9265477 TGAAGTAGCGCTTCACTTGTTCTGCG
1 TGAAGTAGCGCTTCACTTGTTCTGCG
9265503 TGAAGTAGCGCTTCACTTGTTCTGCG
1 TGAAGTAGCGCTTCACTTGTTCTGCG
*
9265529 TGAAGTAACGCTTCACTTGTTCT
1 TGAAGTAGCGCTTCACTTGTTCT
9265552 AGTTATTCTG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 48 1.00
ACGTcount: A:0.17, C:0.23, G:0.24, T:0.36
Consensus pattern (26 bp):
TGAAGTAGCGCTTCACTTGTTCTGCG
Found at i:9265568 original size:35 final size:35
Alignment explanation
Indices: 9265522--9265595 Score: 112
Period size: 35 Copynumber: 2.1 Consensus size: 35
9265512 GCTTCACTTG
* *
9265522 TTCTGCGTGAAGTAACGCTTCACTTGTTCTAGTTA
1 TTCTGCGTGAAGTAACACTTCACTTATTCTAGTTA
* *
9265557 TTCTGCGTGAAGTAACACTTCACTTATTCTGGTTG
1 TTCTGCGTGAAGTAACACTTCACTTATTCTAGTTA
9265592 TTCT
1 TTCT
9265596 CTATATAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.19, C:0.20, G:0.19, T:0.42
Consensus pattern (35 bp):
TTCTGCGTGAAGTAACACTTCACTTATTCTAGTTA
Found at i:9265828 original size:58 final size:59
Alignment explanation
Indices: 9265717--9265894 Score: 159
Period size: 59 Copynumber: 3.0 Consensus size: 59
9265707 TGGTAGCTTT
* *
9265717 AACATGTTTGTCTTAATTTAGACAAAAAAAACATATTTGGTGTTAATTTAGACAA-AAA
1 AACATGTTTGTCTTAATTTAGACAAAAAAAACATATTTGATCTTAATTTAGACAAGAAA
* * * *
9265775 AACATGTTTGGTGTTAATTTAGAC-AAGAAAATATGTTT-ATCTTAATTTAAGACAAGAAA
1 AACATGTTT-GTCTTAATTTAGACAAAAAAAACATATTTGATCTTAATTT-AGACAAGAAA
* * * * * * * *
9265834 AATATTTTTTATCTTAGTCTAGA-TAAGAAAACATATTTG-TCTCAATTTAGACAAGATAA
1 AACA-TGTTTGTCTTAATTTAGACAAAAAAAACATATTTGATCTTAATTTAGACAAGA-AA
9265893 AA
1 AA
9265895 TATTTTTATC
Statistics
Matches: 98, Mismatches: 15, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
57 8 0.08
58 34 0.35
59 52 0.53
60 4 0.04
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.36
Consensus pattern (59 bp):
AACATGTTTGTCTTAATTTAGACAAAAAAAACATATTTGATCTTAATTTAGACAAGAAA
Found at i:9265838 original size:30 final size:29
Alignment explanation
Indices: 9265720--9265897 Score: 157
Period size: 29 Copynumber: 6.1 Consensus size: 29
9265710 TAGCTTTAAC
* *
9265720 ATGTTTGTCTTAATTTAGACAAAAAAAAC
1 ATGTTTGTCTTAATTTAGACAAGAAAAAT
* * *
9265749 ATATTTGGTGTTAATTTAGACAA-AAAAAC
1 ATGTTT-GTCTTAATTTAGACAAGAAAAAT
*
9265778 ATGTTTGGTGTTAATTTAGACAAG-AAAAT
1 ATGTTT-GTCTTAATTTAGACAAGAAAAAT
*
9265807 ATGTTTATCTTAATTTAAGACAAGAAAAAT
1 ATGTTTGTCTTAATTT-AGACAAGAAAAAT
* * * * *
9265837 ATTTTTTATCTTAGTCTAGATAAGAAAACAT
1 A-TGTTTGTCTTAATTTAGACAAGAAAA-AT
*
9265868 A--TTTGTCTCAATTTAGACAAGATAAAAT
1 ATGTTTGTCTTAATTTAGACAAGA-AAAAT
9265896 AT
1 AT
9265898 TTTTATCTCA
Statistics
Matches: 126, Mismatches: 15, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
28 27 0.21
29 53 0.42
30 31 0.25
31 15 0.12
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.37
Consensus pattern (29 bp):
ATGTTTGTCTTAATTTAGACAAGAAAAAT
Found at i:9265909 original size:30 final size:29
Alignment explanation
Indices: 9265790--9265910 Score: 122
Period size: 30 Copynumber: 4.1 Consensus size: 29
9265780 GTTTGGTGTT
* *
9265790 AATTTAGACAAG-AAAATATGTTTATCTT
1 AATTTAGACAAGAAAAATATTTTTATCTC
*
9265818 AATTTAAGACAAGAAAAATATTTTTTATCTT
1 AATTT-AGACAAGAAAAATA-TTTTTATCTC
* * * *
9265849 AGTCTAGATAAGAAAACATA--TTTGTCTC
1 AATTTAGACAAGAAAA-ATATTTTTATCTC
9265877 AATTTAGACAAGATAAAATATTTTTATCTC
1 AATTTAGACAAGA-AAAATATTTTTATCTC
9265907 AATT
1 AATT
9265911 AAAGACATGA
Statistics
Matches: 76, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
28 24 0.32
29 10 0.13
30 27 0.36
31 15 0.20
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (29 bp):
AATTTAGACAAGAAAAATATTTTTATCTC
Found at i:9266081 original size:17 final size:17
Alignment explanation
Indices: 9266061--9266093 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
9266051 ATAATAATAA
9266061 AATAA-GAGTTATTATTC
1 AATAAGGAGTT-TTATTC
9266078 AATAAGGAGTTTTATT
1 AATAAGGAGTTTTATT
9266094 TTATTAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (17 bp):
AATAAGGAGTTTTATTC
Found at i:9269972 original size:21 final size:22
Alignment explanation
Indices: 9269941--9269983 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
9269931 TAAAATTTAC
9269941 TTTATATATAT-ATTTAAGATTT
1 TTTATATATATAATTT-AGATTT
9269963 TTTA-ATATATAATTTAGATTT
1 TTTATATATATAATTTAGATTT
9269984 AAAATTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (22 bp):
TTTATATATATAATTTAGATTT
Found at i:9287776 original size:20 final size:21
Alignment explanation
Indices: 9287745--9287793 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
9287735 AAAATTATCA
*
9287745 CAAATAATTTT-GATTCTATTT
1 CAAAT-ATTTTGGATTCTACTT
9287766 CAAATATTTTGGATTCTACTT
1 CAAATATTTTGGATTCTACTT
9287787 CAAATAT
1 CAAATAT
9287794 ATAGCATTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 5 0.19
21 21 0.81
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.47
Consensus pattern (21 bp):
CAAATATTTTGGATTCTACTT
Found at i:9288517 original size:20 final size:21
Alignment explanation
Indices: 9288477--9288517 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
9288467 GGCCGAAGAT
9288477 GTTGAGCTGGCTGCAAGGGGC
1 GTTGAGCTGGCTGCAAGGGGC
9288498 GTTGAAGCT-GCTGC-AGGGGC
1 GTTG-AGCTGGCTGCAAGGGGC
9288518 TGCAACTGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
21 9 0.47
22 4 0.21
ACGTcount: A:0.15, C:0.20, G:0.46, T:0.20
Consensus pattern (21 bp):
GTTGAGCTGGCTGCAAGGGGC
Found at i:9323104 original size:76 final size:76
Alignment explanation
Indices: 9322997--9323160 Score: 240
Period size: 76 Copynumber: 2.1 Consensus size: 76
9322987 TGAATTTCTC
*
9322997 AAATTAAAATCCTATCCTTAATTTTAGGAATTTCTTTTAAAGTAGGAAACAATTTCCTA-TTTTT
1 AAATTAAAATCCTATCCTTAATTTTAGGAATTGCTTTTAAAGTA-GAAACAATTTCCTATTTTTT
9323061 ATAAATCACCCA
65 ATAAATCACCCA
* * *
9323073 AAATTAAAATTCTATTCTTAATTTTATGAATTGCTTTTAAAGTAGAAACAATTTCCTATTTTTTT
1 AAATTAAAATCCTATCCTTAATTTTAGGAATTGCTTTTAAAGTAGAAACAATTTCCTA--TTTTT
* *
9323138 TATGAATCATCCA
64 TATAAATCACCCA
9323151 AAATTAAAAT
1 AAATTAAAAT
9323161 AAATGATATT
Statistics
Matches: 79, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
75 14 0.18
76 40 0.51
78 25 0.32
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (76 bp):
AAATTAAAATCCTATCCTTAATTTTAGGAATTGCTTTTAAAGTAGAAACAATTTCCTATTTTTTA
TAAATCACCCA
Found at i:9325414 original size:27 final size:27
Alignment explanation
Indices: 9325384--9325441 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
9325374 TTGGAGTAAA
*
9325384 AGGGTAAAATGGTAATTTTGCCACC-CC
1 AGGGCAAAATGGTAATTTT-CCACCACC
*
9325411 AGGGGCAAAATTGTAATTTTCCACCACC
1 A-GGGCAAAATGGTAATTTTCCACCACC
9325439 AGG
1 AGG
9325442 ACATTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 8 0.30
28 19 0.70
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.24
Consensus pattern (27 bp):
AGGGCAAAATGGTAATTTTCCACCACC
Found at i:9326581 original size:13 final size:13
Alignment explanation
Indices: 9326563--9326587 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9326553 AGAGAAATTG
9326563 TGATTTTATAAAA
1 TGATTTTATAAAA
9326576 TGATTTTATAAA
1 TGATTTTATAAA
9326588 TTTTCTAAAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:9338250 original size:27 final size:27
Alignment explanation
Indices: 9338220--9338307 Score: 88
Period size: 27 Copynumber: 3.3 Consensus size: 27
9338210 TTGACAGGTT
* *
9338220 AAGTTATCTATCCACTTTTGGTGGGTA
1 AAGTTATCTATCCACTTATAGTGGGTA
* ***
9338247 AAGTTAT-TCATCCACTTCTAGTACATA
1 AAGTTATCT-ATCCACTTATAGTGGGTA
* *
9338274 AAGTTATCCATTCACTTATAGTGGGTA
1 AAGTTATCTATCCACTTATAGTGGGTA
9338301 AAGTTAT
1 AAGTTAT
9338308 TCTTAGAATT
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
26 1 0.02
27 47 0.98
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.39
Consensus pattern (27 bp):
AAGTTATCTATCCACTTATAGTGGGTA
Found at i:9345983 original size:28 final size:30
Alignment explanation
Indices: 9345942--9346006 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
9345932 GTCTATGGGC
*
9345942 AATTTTTCAGTTTT-T-GGGGCAAAAATGT
1 AATTTTTCACTTTTATAGGGGCAAAAATGT
* *
9345970 AATTTTTGACTTTTATAGGGGCAAAAGTGT
1 AATTTTTCACTTTTATAGGGGCAAAAATGT
*
9346000 AAATTTT
1 AATTTTT
9346007 AAAAATTACT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 12 0.39
29 1 0.03
30 18 0.58
ACGTcount: A:0.31, C:0.06, G:0.20, T:0.43
Consensus pattern (30 bp):
AATTTTTCACTTTTATAGGGGCAAAAATGT
Found at i:9351428 original size:27 final size:28
Alignment explanation
Indices: 9351371--9351428 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
9351361 GGAAAAATGT
*
9351371 CCTGGTGGTGGAAAATTACAATTTTGCC
1 CCTGGTGGTGGAAAATTACAATTTTGAC
*
9351399 CCTGG-GGTGGCAAAATTACCATTTT-AC
1 CCTGGTGGTGG-AAAATTACAATTTTGAC
9351426 CCT
1 CCT
9351429 TTTACTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 9 0.33
28 18 0.67
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.31
Consensus pattern (28 bp):
CCTGGTGGTGGAAAATTACAATTTTGAC
Found at i:9351499 original size:20 final size:20
Alignment explanation
Indices: 9351482--9351519 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
9351472 CCTCAAATCT
*
9351482 TACTCCAATGAGTCAAATTA
1 TACTCCAATAAGTCAAATTA
9351502 TACTCCAATAAGTCAAAT
1 TACTCCAATAAGTCAAAT
9351520 GGGGTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (20 bp):
TACTCCAATAAGTCAAATTA
Found at i:9371971 original size:2 final size:2
Alignment explanation
Indices: 9371964--9371993 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
9371954 CATTTCATAC
9371964 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9371994 TGAAAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9376693 original size:11 final size:11
Alignment explanation
Indices: 9376677--9376701 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
9376667 TCTTGAAGTG
9376677 TTACTTTTAAA
1 TTACTTTTAAA
9376688 TTACTTTTAAA
1 TTACTTTTAAA
9376699 TTA
1 TTA
9376702 AAAAATCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (11 bp):
TTACTTTTAAA
Found at i:9380643 original size:48 final size:48
Alignment explanation
Indices: 9380574--9380672 Score: 171
Period size: 48 Copynumber: 2.1 Consensus size: 48
9380564 TAAATCGTAA
*
9380574 CACATGATAGTGGAGCACAAAATCAAACACACGACCACCAACACACAC
1 CACATGATAGTGGAGCACAAAATCAAACACACAACCACCAACACACAC
* *
9380622 CACATGATAGTGGAGCTCAAAATCAAACACACAACCCCCAACACACAC
1 CACATGATAGTGGAGCACAAAATCAAACACACAACCACCAACACACAC
9380670 CAC
1 CAC
9380673 CACAAAATCA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.44, C:0.35, G:0.11, T:0.09
Consensus pattern (48 bp):
CACATGATAGTGGAGCACAAAATCAAACACACAACCACCAACACACAC
Found at i:9380971 original size:15 final size:15
Alignment explanation
Indices: 9380948--9380982 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
9380938 AAAAAGTAAG
*
9380948 ATTTCAGTACCATAC
1 ATTTTAGTACCATAC
*
9380963 ATTTTAGTACCGTAC
1 ATTTTAGTACCATAC
9380978 ATTTT
1 ATTTT
9380983 GACTGTGCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.29, C:0.20, G:0.09, T:0.43
Consensus pattern (15 bp):
ATTTTAGTACCATAC
Found at i:9386616 original size:3 final size:3
Alignment explanation
Indices: 9386592--9386630 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
9386582 TGTATCATTG
* *
9386592 AAT AA- AAT TAT AAT AAT TAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
9386631 GCATCTTATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:9390290 original size:29 final size:29
Alignment explanation
Indices: 9390218--9390290 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 29
9390208 TATAAATTGC
* *
9390218 TTAAAACATTTTTTATTACTTGATTTATCT
1 TTAAAA-ATTTTTTATTACATGACTTATCT
*
9390248 TATAAAAATATTTT-TTATCATGACTTATCT
1 T-TAAAAATTTTTTATTA-CATGACTTATCT
9390278 TTAAAAATTTTTT
1 TTAAAAATTTTTT
9390291 CTATAACGCC
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
29 14 0.38
30 18 0.49
31 5 0.14
ACGTcount: A:0.34, C:0.08, G:0.03, T:0.55
Consensus pattern (29 bp):
TTAAAAATTTTTTATTACATGACTTATCT
Found at i:9395726 original size:12 final size:12
Alignment explanation
Indices: 9395709--9395733 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9395699 CCTTCATTGT
9395709 TGTTATCTTATA
1 TGTTATCTTATA
9395721 TGTTATCTTATA
1 TGTTATCTTATA
9395733 T
1 T
9395734 ACTATTCCAG
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:0.24, C:0.08, G:0.08, T:0.60
Consensus pattern (12 bp):
TGTTATCTTATA
Found at i:9399761 original size:2 final size:2
Alignment explanation
Indices: 9399754--9399804 Score: 81
Period size: 2 Copynumber: 27.0 Consensus size: 2
9399744 TGTGTAAAAC
9399754 AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9399794 AT AT AT -T AT AT
1 AT AT AT AT AT AT
9399805 TGTGAATGTT
Statistics
Matches: 46, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 3 0.07
2 43 0.93
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9399776 original size:15 final size:15
Alignment explanation
Indices: 9399756--9399804 Score: 75
Period size: 15 Copynumber: 3.4 Consensus size: 15
9399746 TGTAAAACAT
9399756 ATATATATATATATA
1 ATATATATATATATA
9399771 ATATATATATATAT-
1 ATATATATATATATA
9399785 ATA-ATATATATATA
1 ATATATATATATATA
*
9399799 TTATAT
1 ATATAT
9399805 TGTGAATGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 10 0.32
14 5 0.16
15 16 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:9399776 original size:17 final size:17
Alignment explanation
Indices: 9399754--9399803 Score: 93
Period size: 17 Copynumber: 3.0 Consensus size: 17
9399744 TGTGTAAAAC
9399754 ATATATATATATATATA
1 ATATATATATATATATA
9399771 ATATATATATATATATA
1 ATATATATATATATATA
9399788 ATATATATATAT-TATA
1 ATATATATATATATATA
9399804 TTGTGAATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 4 0.12
17 29 0.88
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATATATATATATATA
Found at i:9405749 original size:23 final size:23
Alignment explanation
Indices: 9405712--9405755 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
9405702 AGAAATTGTT
9405712 AGAAATTTAGAAGAAGAAGAAGA
1 AGAAATTTAGAAGAAGAAGAAGA
9405735 AGAATATTTAG-AGAAGAAGAA
1 AGAA-ATTTAGAAGAAGAAGAA
9405756 AGAGTATGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.59, C:0.00, G:0.25, T:0.16
Consensus pattern (23 bp):
AGAAATTTAGAAGAAGAAGAAGA
Found at i:9406006 original size:33 final size:33
Alignment explanation
Indices: 9405960--9406025 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
9405950 AAAGGATTTA
* *
9405960 TTTCTTTTTATAATATGACT-TTTCAAATAATTAT
1 TTTCTTTTCATAATATAACTATTT--AATAATTAT
9405994 TTTC-TTTCATAATATAACTATTTAATAATTAT
1 TTTCTTTTCATAATATAACTATTTAATAATTAT
9406026 ATCTAATAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 9 0.31
33 13 0.45
34 7 0.24
ACGTcount: A:0.35, C:0.09, G:0.02, T:0.55
Consensus pattern (33 bp):
TTTCTTTTCATAATATAACTATTTAATAATTAT
Found at i:9411053 original size:47 final size:46
Alignment explanation
Indices: 9410984--9411078 Score: 127
Period size: 47 Copynumber: 2.0 Consensus size: 46
9410974 CTAATTTTAA
* *
9410984 TTTTCCCCGTTTCCTTTGTTGGGTTTGGGCCAACCACATCTTTCTT
1 TTTTCCCCGTTTCCTTTGTTGGGTTTGAGCCAACCACATCGTTCTT
* * * *
9411030 TTTTCCTCCGTTTTCTTTTTTGGGTTTGAGCCTACCACCTCGTTCTT
1 TTTTCC-CCGTTTCCTTTGTTGGGTTTGAGCCAACCACATCGTTCTT
9411077 TT
1 TT
9411079 CCTTTACATT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
46 6 0.14
47 36 0.86
ACGTcount: A:0.07, C:0.27, G:0.16, T:0.49
Consensus pattern (46 bp):
TTTTCCCCGTTTCCTTTGTTGGGTTTGAGCCAACCACATCGTTCTT
Found at i:9417108 original size:64 final size:63
Alignment explanation
Indices: 9417019--9417139 Score: 190
Period size: 64 Copynumber: 1.9 Consensus size: 63
9417009 TTTATTCTTG
* *
9417019 GATATTTCTATTACTAATCAAATGATCAATTCTTCTTTCAGGGTGGACAAGAAAATCAGCAATT
1 GATATTTCCATTACTAATCAAATGATCAATTCTT-TTTCAGGGTAGACAAGAAAATCAGCAATT
*
9417083 GATATTTCCATTA-TCAATCATATGATCAATTCTTTTTCAGGGTAGACAAGAAAATCA
1 GATATTTCCATTACT-AATCAAATGATCAATTCTTTTTCAGGGTAGACAAGAAAATCA
9417140 ACATATCAAC
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
63 23 0.43
64 30 0.57
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (63 bp):
GATATTTCCATTACTAATCAAATGATCAATTCTTTTTCAGGGTAGACAAGAAAATCAGCAATT
Found at i:9427907 original size:41 final size:41
Alignment explanation
Indices: 9427850--9427928 Score: 149
Period size: 41 Copynumber: 1.9 Consensus size: 41
9427840 GTTTAAGTAA
*
9427850 GCCTATATATCATGAGCTTACGTTCTCAACTCAAAAGATAT
1 GCCTATAAATCATGAGCTTACGTTCTCAACTCAAAAGATAT
9427891 GCCTATAAATCATGAGCTTACGTTCTCAACTCAAAAGA
1 GCCTATAAATCATGAGCTTACGTTCTCAACTCAAAAGA
9427929 CATGTCTAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.29
Consensus pattern (41 bp):
GCCTATAAATCATGAGCTTACGTTCTCAACTCAAAAGATAT
Found at i:9436008 original size:21 final size:21
Alignment explanation
Indices: 9435966--9436008 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
9435956 TTTATATTTA
* * *
9435966 TTTTATTGAAAATAGATTTAT
1 TTTTATTGAAAAAAAATATAT
*
9435987 TTTTTTTGAAAAAAAATATAT
1 TTTTATTGAAAAAAAATATAT
9436008 T
1 T
9436009 ATCGAGATAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (21 bp):
TTTTATTGAAAAAAAATATAT
Found at i:9443309 original size:23 final size:22
Alignment explanation
Indices: 9443266--9443310 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
9443256 CAGAAACTTC
9443266 AAAGAAAAAAAGAAAACTGAAG
1 AAAGAAAAAAAGAAAACTGAAG
*
9443288 AAAGAAAGAAAGATAAACTGAAG
1 AAAGAAAAAAAGA-AAACTGAAG
9443311 TACTCACATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.69, C:0.04, G:0.20, T:0.07
Consensus pattern (22 bp):
AAAGAAAAAAAGAAAACTGAAG
Found at i:9443426 original size:2 final size:2
Alignment explanation
Indices: 9443419--9443451 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
9443409 CAAGCAAGGA
9443419 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
9443452 CGGCCGATGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:9450868 original size:66 final size:65
Alignment explanation
Indices: 9450731--9450865 Score: 163
Period size: 66 Copynumber: 2.1 Consensus size: 65
9450721 CCTCTTCAAC
*
9450731 AATTTT-AAAATTTTTATACTTATTTTTATTTTTTTTAAAAAATATTTTAATTTCATCCTTATAA
1 AATTTTAAAAATTTTTATACATATTTTTATTTTTTTT-AAAAATATTTTAATTTCATCCTTATAA
9450795 A
65 A
* *
9450796 AATTTTAAAAATTTTT-TAACATATTTTTATTTTTTTT-GAAAT-TTTATAATTTTA-CCTCTAT
1 AATTTTAAAAATTTTTAT-ACATATTTTTATTTTTTTTAAAAATATTT-TAATTTCATCCT-TAT
*
9450857 AAT
63 AAA
9450860 AATTTT
1 AATTTT
9450866 TTATTTAGTA
Statistics
Matches: 62, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
63 6 0.10
64 22 0.35
65 7 0.11
66 27 0.44
ACGTcount: A:0.36, C:0.06, G:0.01, T:0.58
Consensus pattern (65 bp):
AATTTTAAAAATTTTTATACATATTTTTATTTTTTTTAAAAATATTTTAATTTCATCCTTATAAA
Found at i:9451817 original size:6 final size:6
Alignment explanation
Indices: 9451788--9451840 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
9451778 TCTCTATATT
* * * *
9451788 TATGTA TATGTA TATGTG TATGTG TATGTG --TGTG TGTGTG TGTGTG
1 TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG TATGTG
9451834 TATGTG T
1 TATGTG T
9451841 GAATAAATAT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
4 4 0.09
6 39 0.91
ACGTcount: A:0.15, C:0.00, G:0.34, T:0.51
Consensus pattern (6 bp):
TATGTG
Found at i:9451821 original size:2 final size:2
Alignment explanation
Indices: 9451802--9451841 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
9451792 TATATGTATA
* * *
9451802 TG TG TA TG TG TA TG TG TG TG TG TG TG TG TG TG TA TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
9451842 AATAAATATA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.07, C:0.00, G:0.42, T:0.50
Consensus pattern (2 bp):
TG
Found at i:9451908 original size:8 final size:8
Alignment explanation
Indices: 9451885--9452006 Score: 95
Period size: 8 Copynumber: 15.0 Consensus size: 8
9451875 ACATATGCAT
9451885 TATACATA
1 TATACATA
9451893 TGTATACATA
1 --TATACATA
9451903 TATACATA
1 TATACATA
* *
9451911 CATTCATA
1 TATACATA
*
9451919 TATATATA
1 TATACATA
*
9451927 TACATACGTA
1 T--ATACATA
9451937 TATACATA
1 TATACATA
*
9451945 CATACATA
1 TATACATA
*
9451953 TAT--TTA
1 TATACATA
*
9451959 TATATATA
1 TATACATA
9451967 TATACATA
1 TATACATA
* *
9451975 CATATATA
1 TATACATA
*
9451983 AATACATA
1 TATACATA
9451991 TATACATA
1 TATACATA
*
9451999 CATACATA
1 TATACATA
9452007 CAGGAGCGGA
Statistics
Matches: 89, Mismatches: 19, Indels: 10
0.75 0.16 0.08
Matches are distributed among these distances:
6 5 0.06
8 70 0.79
10 14 0.16
ACGTcount: A:0.48, C:0.13, G:0.02, T:0.38
Consensus pattern (8 bp):
TATACATA
Found at i:9451911 original size:12 final size:12
Alignment explanation
Indices: 9451896--9452008 Score: 100
Period size: 12 Copynumber: 9.1 Consensus size: 12
9451886 ATACATATGT
9451896 ATACATATATAC
1 ATACATATATAC
*
9451908 ATACATTCATATAT
1 ATACA-T-ATATAC
* *
9451922 ATATATACATAC
1 ATACATATATAC
* * *
9451934 GTATATACATAC
1 ATACATATATAC
*
9451946 ATACATATATTTAT
1 ATACATATA--TAC
*
9451960 ATATATATATAC
1 ATACATATATAC
*
9451972 ATACATATATAA
1 ATACATATATAC
9451984 ATACATATATAC
1 ATACATATATAC
*
9451996 ATACATACATAC
1 ATACATATATAC
9452008 A
1 A
9452009 GGAGCGGAGC
Statistics
Matches: 82, Mismatches: 15, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
12 61 0.74
13 2 0.02
14 19 0.23
ACGTcount: A:0.49, C:0.14, G:0.01, T:0.36
Consensus pattern (12 bp):
ATACATATATAC
Found at i:9451913 original size:4 final size:4
Alignment explanation
Indices: 9451896--9452008 Score: 77
Period size: 4 Copynumber: 28.2 Consensus size: 4
9451886 ATACATATGT
* * * * * *
9451896 ATAC ATAT ATAC ATAC ATTC AT-- ATAT ATAT ATAC ATAC GTAT ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * * * *
9451942 ATAC ATAC ATAT ATTTAT ATAT ATAT ATAC ATAC ATAT ATAA ATAC ATAT
1 ATAC ATAC ATAC A--TAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
9451992 ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC A
9452009 GGAGCGGAGC
Statistics
Matches: 90, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
2 2 0.02
4 84 0.93
6 4 0.04
ACGTcount: A:0.49, C:0.14, G:0.01, T:0.36
Consensus pattern (4 bp):
ATAC
Found at i:9452841 original size:37 final size:37
Alignment explanation
Indices: 9452783--9452853 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
9452773 ATATATGAGC
* **
9452783 AAATAGAATATAATTTTAAAAAA-TAAATAAAAATAA
1 AAATAGAATATAAATAAAAAAAATTAAATAAAAATAA
9452819 AAATAGTAATATAAATAAAAAAAATTAAATAAAAA
1 AAATAG-AATATAAATAAAAAAAATTAAATAAAAA
9452854 CTTTACCTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
36 6 0.20
37 14 0.47
38 10 0.33
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (37 bp):
AAATAGAATATAAATAAAAAAAATTAAATAAAAATAA
Found at i:9452850 original size:18 final size:17
Alignment explanation
Indices: 9452799--9452853 Score: 58
Period size: 20 Copynumber: 3.0 Consensus size: 17
9452789 AATATAATTT
9452799 TAAAAAATAAATAAAAA
1 TAAAAAATAAATAAAAA
9452816 TAAAAATAGTAATATAAATAA
1 TAAAAA-A-TAA-ATAAA-AA
9452837 -AAAAAATTAAATAAAAA
1 TAAAAAA-TAAATAAAAA
9452854 CTTTACCTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
17 8 0.24
18 6 0.18
19 7 0.21
20 10 0.30
21 2 0.06
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (17 bp):
TAAAAAATAAATAAAAA
Found at i:9452936 original size:185 final size:184
Alignment explanation
Indices: 9452732--9453100 Score: 661
Period size: 185 Copynumber: 2.0 Consensus size: 184
9452722 GTGGTTGATG
*
9452732 ATTAGTAGATATTTAAAAAAGAAAATCTATAGAAACTTAAAATATATGAGCAAATAGAATATAAT
1 ATTAGTAGAAATTTAAAAAAGAAAATCTATAGAAACTTAAAATATATGAGCAAATAGAATATAAT
9452797 TTT-AAAAAATAAATAAAAATAAAAATAG-TAATATAAATAAAAAAAATTAAATAAAAACTTTAC
66 TTTAAAAAAATAAATAAAAAT-AAAATAGTTAATATAAATAAAAAAAATT-AATAAAAACTTTAC
*
9452860 CTCTTTATAATTTCACAATACAAGGACAAGAAAGAAAAGAGGGAAAGATGGGTGGA
129 CTCTTTATAATTTCACAATACAAGGACAAGAAAGAAAAGAGAGAAAGATGGGTGGA
*
9452916 NATTAGTAGAAATTTAAAAAAGAAAATCTGTAGAAACTTAAAATATATGAGCAAATAGAATATAA
1 -ATTAGTAGAAATTTAAAAAAGAAAATCTATAGAAACTTAAAATATATGAGCAAATAGAATATAA
*
9452981 TTTTAAAAAAATAAATAAAAATAAAATAGTTAATATAAATTAAAAAAATTAATAAAAACTTTACC
65 TTTTAAAAAAATAAATAAAAATAAAATAGTTAATATAAATAAAAAAAATTAATAAAAACTTTACC
9453046 TCTTTATAATTTCACAATACAAGGACAAGAAAGAAAAGAGAGAAAGATGGGTGGA
130 TCTTTATAATTTCACAATACAAGGACAAGAAAGAAAAGAGAGAAAGATGGGTGGA
9453101 GAAAACATAA
Statistics
Matches: 178, Mismatches: 4, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
185 142 0.80
186 36 0.20
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.26
Consensus pattern (184 bp):
ATTAGTAGAAATTTAAAAAAGAAAATCTATAGAAACTTAAAATATATGAGCAAATAGAATATAAT
TTTAAAAAAATAAATAAAAATAAAATAGTTAATATAAATAAAAAAAATTAATAAAAACTTTACCT
CTTTATAATTTCACAATACAAGGACAAGAAAGAAAAGAGAGAAAGATGGGTGGA
Found at i:9453032 original size:19 final size:18
Alignment explanation
Indices: 9452983--9453037 Score: 65
Period size: 19 Copynumber: 3.0 Consensus size: 18
9452973 GAATATAATT
*
9452983 TTAAAAAAATAAATAAAA
1 TTAAAAAAATTAATAAAA
* * *
9453001 ATAAAATAGTTAATATAAA
1 TTAAAAAAATTAATA-AAA
9453020 TTAAAAAAATTAATAAAA
1 TTAAAAAAATTAATAAAA
9453038 ACTTTACCTC
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
18 14 0.48
19 15 0.52
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (18 bp):
TTAAAAAAATTAATAAAA
Found at i:9453340 original size:2 final size:2
Alignment explanation
Indices: 9453335--9453365 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
9453325 GTTTGTGTAT
9453335 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
9453366 TATATAAACA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:9457691 original size:61 final size:61
Alignment explanation
Indices: 9457559--9457725 Score: 253
Period size: 61 Copynumber: 2.7 Consensus size: 61
9457549 TTGATGTAAC
***
9457559 CGTGCATGTGCGGAGTGGGCAGTGCACATGCCGGTTGAATGACAATGTCGTGATAATTACAAT
1 CGTGCATGTGCGGAGTGGGCAGTGCACATGCCGG-T-AATGATGCTGTCGTGATAATTACAAT
* *
9457622 CGTGCATGTGCGGAGTGGGTAGTGCACATGCCGGTAATGATGCTGTCGTGATATTTACAAT
1 CGTGCATGTGCGGAGTGGGCAGTGCACATGCCGGTAATGATGCTGTCGTGATAATTACAAT
* *
9457683 CGTGCATGTACGGAGTGGGCAGTGCACATGCCGGTGATGATGC
1 CGTGCATGTGCGGAGTGGGCAGTGCACATGCCGGTAATGATGC
9457726 ACATGAGTTG
Statistics
Matches: 96, Mismatches: 8, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
61 62 0.65
62 1 0.01
63 33 0.34
ACGTcount: A:0.22, C:0.18, G:0.34, T:0.26
Consensus pattern (61 bp):
CGTGCATGTGCGGAGTGGGCAGTGCACATGCCGGTAATGATGCTGTCGTGATAATTACAAT
Found at i:9460072 original size:13 final size:13
Alignment explanation
Indices: 9460054--9460078 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9460044 AGAGAAATTG
9460054 TGATTTTATAAAA
1 TGATTTTATAAAA
9460067 TGATTTTATAAA
1 TGATTTTATAAA
9460079 TTTTCTGGAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:9462842 original size:17 final size:18
Alignment explanation
Indices: 9462815--9462852 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
9462805 TGAGGGATTA
9462815 CTCCTTCTTTAATATATG
1 CTCCTTCTTTAATATATG
*
9462833 CTCC-TCTTTAATATGTG
1 CTCCTTCTTTAATATATG
9462850 CTC
1 CTC
9462853 ACAAAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.18, C:0.26, G:0.08, T:0.47
Consensus pattern (18 bp):
CTCCTTCTTTAATATATG
Found at i:9465775 original size:43 final size:43
Alignment explanation
Indices: 9465727--9465862 Score: 159
Period size: 43 Copynumber: 3.2 Consensus size: 43
9465717 TTGTGTGATA
* * * *
9465727 ATGATGACTCAACTATGTGCGATGT-GGGAGTGCACATGAGCTG
1 ATGATGACTCGACTATGTGCGA-GTAGGGAGTGCGCATAAGCCG
* *
9465770 ATGATGGC-CTGACTATGTACGAGTAGGGAGTGCGCATAAGCCG
1 ATGATGACTC-GACTATGTGCGAGTAGGGAGTGCGCATAAGCCG
* * *
9465813 ATGATGACTCGGCCATGTGCGAGTAGGGGGTGCGCATAAGCCG
1 ATGATGACTCGACTATGTGCGAGTAGGGAGTGCGCATAAGCCG
9465856 ATGATGA
1 ATGATGA
9465863 TGAGCCAGCT
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
42 3 0.04
43 75 0.95
44 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.35, T:0.22
Consensus pattern (43 bp):
ATGATGACTCGACTATGTGCGAGTAGGGAGTGCGCATAAGCCG
Found at i:9466179 original size:22 final size:22
Alignment explanation
Indices: 9466147--9466202 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
9466137 GTGAGGAATT
9466147 TCGCTGTAGCGAAATTGGATTC
1 TCGCTGTAGCGAAATTGGATTC
*
9466169 TCGCTGCAGCGAAATTGGATTC
1 TCGCTGTAGCGAAATTGGATTC
*
9466191 TCGTTGTAGCGA
1 TCGCTGTAGCGA
9466203 GAAACTCTCG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (22 bp):
TCGCTGTAGCGAAATTGGATTC
Found at i:9469443 original size:31 final size:31
Alignment explanation
Indices: 9469369--9469450 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
9469359 TGACACATTA
* ** *
9469369 GTCTTTGGATTTCATATTTGTTTCGACTTTG
1 GTCTTTAGATTTGGTATTTGATTCGACTTTG
9469400 GTCTTTAGATTTGGTATTTGATTCGACTTT-
1 GTCTTTAGATTTGGTATTTGATTCGACTTTG
* *
9469430 GTTTTTTGAATTTGGTATTTG
1 GTCTTTAG-ATTTGGTATTTG
9469451 TTTCAATTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
30 6 0.14
31 38 0.86
ACGTcount: A:0.15, C:0.09, G:0.21, T:0.56
Consensus pattern (31 bp):
GTCTTTAGATTTGGTATTTGATTCGACTTTG
Found at i:9475047 original size:19 final size:19
Alignment explanation
Indices: 9475023--9475060 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
9475013 ACTTCTTAAC
9475023 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
9475042 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
9475061 AGTCAAATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:9476121 original size:21 final size:21
Alignment explanation
Indices: 9476097--9476159 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
9476087 GTTCATGCAA
*
9476097 TTCATGATAAAGAATGATGCC
1 TTCATGACAAAGAATGATGCC
* * * *
9476118 TTCATGGCAAAGACTGGTACC
1 TTCATGACAAAGAATGATGCC
* *
9476139 TACATGACAATGAATGATGCC
1 TTCATGACAAAGAATGATGCC
9476160 ATCAATTAAA
Statistics
Matches: 31, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (21 bp):
TTCATGACAAAGAATGATGCC
Found at i:9476388 original size:21 final size:21
Alignment explanation
Indices: 9476364--9476404 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
9476354 GATTAGTTAG
*
9476364 TTTAAGTTATTTTAGTTTAAT
1 TTTAAGTTATTTTACTTTAAT
*
9476385 TTTATGTTATTTTACTTTAA
1 TTTAAGTTATTTTACTTTAA
9476405 ATTACTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.02, G:0.07, T:0.63
Consensus pattern (21 bp):
TTTAAGTTATTTTACTTTAAT
Found at i:9480451 original size:19 final size:19
Alignment explanation
Indices: 9480408--9480451 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
9480398 AAATTTTTGA
** *
9480408 AATAAAATAATATTTTATT
1 AATAAAATAATATTAAAAT
9480427 AATAAAATAATATTAAAAT
1 AATAAAATAATATTAAAAT
*
9480446 ATTAAA
1 AATAAA
9480452 TATTTTATTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AATAAAATAATATTAAAAT
Found at i:9482756 original size:21 final size:20
Alignment explanation
Indices: 9482731--9482769 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
9482721 CGGCCATAAG
9482731 GAGAGAATAAGAAAGAAAATA
1 GAGAGAA-AAGAAAGAAAATA
* *
9482752 GAGAGGAAAGGAAGAAAA
1 GAGAGAAAAGAAAGAAAA
9482770 GAGAAAAACC
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:0.64, C:0.00, G:0.31, T:0.05
Consensus pattern (20 bp):
GAGAGAAAAGAAAGAAAATA
Found at i:9483164 original size:10 final size:11
Alignment explanation
Indices: 9483123--9483164 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
9483113 TTTTTATTTT
9483123 AAGAG-AAATG
1 AAGAGAAAATG
*
9483133 AAGTGAAAATG
1 AAGAGAAAATG
9483144 AAGAGAAAATG
1 AAGAGAAAATG
*
9483155 ATGA-AAAATG
1 AAGAGAAAATG
9483165 GTTAAATGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 10 0.36
11 18 0.64
ACGTcount: A:0.60, C:0.00, G:0.26, T:0.14
Consensus pattern (11 bp):
AAGAGAAAATG
Found at i:9485039 original size:54 final size:54
Alignment explanation
Indices: 9484966--9485071 Score: 185
Period size: 54 Copynumber: 2.0 Consensus size: 54
9484956 ATACTATCCA
*
9484966 GCTATGTGCACGATATGGTGGGATGCACATGAGCTGGGTGAGATGGGATGTCCG
1 GCTATGTGCACGATATGGTGGGATGCACATAAGCTGGGTGAGATGGGATGTCCG
* *
9485020 GCTATGTGCATGATGTGGTGGGATGCACATAAGCTGGGTGAGATGGGATGTC
1 GCTATGTGCACGATATGGTGGGATGCACATAAGCTGGGTGAGATGGGATGTC
9485072 AAGCCCAGCT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.21, C:0.13, G:0.41, T:0.25
Consensus pattern (54 bp):
GCTATGTGCACGATATGGTGGGATGCACATAAGCTGGGTGAGATGGGATGTCCG
Found at i:9485740 original size:10 final size:11
Alignment explanation
Indices: 9485713--9485747 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
9485703 TATGGCCTGC
*
9485713 CAAAGCAAGAA
1 CAAAGGAAGAA
9485724 CAAAGGAAGAA
1 CAAAGGAAGAA
9485735 -AAAGGAAGAA
1 CAAAGGAAGAA
9485745 CAA
1 CAA
9485748 GAACCTTAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.45
11 12 0.55
ACGTcount: A:0.66, C:0.11, G:0.23, T:0.00
Consensus pattern (11 bp):
CAAAGGAAGAA
Found at i:9488094 original size:54 final size:54
Alignment explanation
Indices: 9488026--9488136 Score: 204
Period size: 54 Copynumber: 2.1 Consensus size: 54
9488016 GGGTCTTGAC
*
9488026 ATGGGATGTCCGGCTATGTGCACGATGTGTTGGGATGCACATGAGCTGGGTGAG
1 ATGGGATGTCCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAG
*
9488080 ATGGGATGTTCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAG
1 ATGGGATGTCCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAG
9488134 ATG
1 ATG
9488137 CACATGATGA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.19, C:0.14, G:0.41, T:0.26
Consensus pattern (54 bp):
ATGGGATGTCCGGCTATGTGCACGATGTGGTGGGATGCACATGAGCTGGGTGAG
Found at i:9491503 original size:75 final size:75
Alignment explanation
Indices: 9491356--9491495 Score: 201
Period size: 75 Copynumber: 1.9 Consensus size: 75
9491346 ACCTGAGAGT
* * * * *
9491356 TTCTCGCTGTAGCGAAAACCAGGGTTGGGTCAAACCCCTAAGCAGTCGAAAGTTTCTTACTACAG
1 TTCTCACTGCAGCGAAAACCAGGGCTGGGTCAAACCCCTAAGCAGCCCAAAGTTTCTTACTACAG
9491421 CAAGAATGCA
66 CAAGAATGCA
* *
9491431 TTCTCACTGCAGCGAAAACCAGGGCTGGGTCAAACCCTTAAGCA-CCCAAGAGTTTCTTGCTACA
1 TTCTCACTGCAGCGAAAACCAGGGCTGGGTCAAACCCCTAAGCAGCCCAA-AGTTTCTTACTACA
9491495 G
65 G
9491496 TGAGAATGAA
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
74 3 0.05
75 54 0.95
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.22
Consensus pattern (75 bp):
TTCTCACTGCAGCGAAAACCAGGGCTGGGTCAAACCCCTAAGCAGCCCAAAGTTTCTTACTACAG
CAAGAATGCA
Found at i:9491571 original size:22 final size:22
Alignment explanation
Indices: 9491546--9491588 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
9491536 AGTTAAAAGA
*
9491546 ATTCTTGTTACAACGAAAATCC
1 ATTCTTGCTACAACGAAAATCC
*
9491568 ATTCTTGCTACAATGAAAATC
1 ATTCTTGCTACAACGAAAATC
9491589 AATTTGGAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.37, C:0.21, G:0.09, T:0.33
Consensus pattern (22 bp):
ATTCTTGCTACAACGAAAATCC
Found at i:9491749 original size:36 final size:36
Alignment explanation
Indices: 9491702--9491819 Score: 148
Period size: 36 Copynumber: 3.3 Consensus size: 36
9491692 GCTTACCAGC
*
9491702 TCATGTGCACTCCCACACTGCACATAGCTGAA-ATCA
1 TCATGTACACTCCCACACTGCACATAGCT-AATATCA
* * *
9491738 TCATGTACACTCCTACACTGCACATAGCTAATACCG
1 TCATGTACACTCCCACACTGCACATAGCTAATATCA
* * * *
9491774 TCATGTGCACTCCCACACCGCACATGGCAAATATCA
1 TCATGTACACTCCCACACTGCACATAGCTAATATCA
9491810 TCATGTACAC
1 TCATGTACAC
9491820 CCCCTCACCA
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
35 2 0.03
36 67 0.97
ACGTcount: A:0.31, C:0.34, G:0.13, T:0.23
Consensus pattern (36 bp):
TCATGTACACTCCCACACTGCACATAGCTAATATCA
Found at i:9491863 original size:67 final size:69
Alignment explanation
Indices: 9491703--9491866 Score: 194
Period size: 72 Copynumber: 2.4 Consensus size: 69
9491693 CTTACCAGCT
* * * *
9491703 CATGTGCACTCCCACACTGCACATAGCTGAAATCATCATGTACACTCCTACACTGCACATAGCTA
1 CATGTGCACTCCCACACCGCACATGGCTAAAATCATCATGTACACCCCTACAC-GCACATA-C-A
*
9491768 ATACCGT
63 ATACCGA
9491775 CATGTGCACTCCCACACCGCACATGGC-AAATATCATCATGTACACCCCCT-CAC-CACAT-C-A
1 CATGTGCACTCCCACACCGCACATGGCTAAA-ATCATCATGTACA-CCCCTACACGCACATACAA
9491835 TCACCGA
64 T-ACCGA
9491842 CATGTGCACTCCCACACCGCACATG
1 CATGTGCACTCCCACACCGCACATG
9491867 CACGGTTACA
Statistics
Matches: 84, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
66 2 0.02
67 29 0.35
68 1 0.01
70 5 0.06
71 2 0.02
72 41 0.49
73 4 0.05
ACGTcount: A:0.29, C:0.38, G:0.12, T:0.20
Consensus pattern (69 bp):
CATGTGCACTCCCACACCGCACATGGCTAAAATCATCATGTACACCCCTACACGCACATACAATA
CCGA
Found at i:9501818 original size:25 final size:25
Alignment explanation
Indices: 9501790--9501849 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
9501780 GTGATCGCAA
* **
9501790 CCACGTATATCAACTTGTGGCCTAG
1 CCACATATATCAACCCGTGGCCTAG
* *
9501815 CCACATTTATCAACCCGTGGCCTTG
1 CCACATATATCAACCCGTGGCCTAG
9501840 CCACATATAT
1 CCACATATAT
9501850 ACGTCACAGA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.25, C:0.32, G:0.15, T:0.28
Consensus pattern (25 bp):
CCACATATATCAACCCGTGGCCTAG
Found at i:9504193 original size:11 final size:11
Alignment explanation
Indices: 9504177--9504201 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
9504167 CTCAATAAGA
9504177 TATTATTATTT
1 TATTATTATTT
9504188 TATTATTATTT
1 TATTATTATTT
9504199 TAT
1 TAT
9504202 CGCATATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TATTATTATTT
Found at i:9528153 original size:21 final size:21
Alignment explanation
Indices: 9528107--9528147 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
9528097 GTTCATGCAA
9528107 TTCATGACAAAGACTGATGCC
1 TTCATGACAAAGACTGATGCC
*
9528128 TTCATGACAAGGACTGATGC
1 TTCATGACAAAGACTGATGC
9528148 TATCATTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (21 bp):
TTCATGACAAAGACTGATGCC
Found at i:9528768 original size:17 final size:17
Alignment explanation
Indices: 9528746--9528781 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
9528736 CTTACTTTTT
* *
9528746 TTTTATTTTTTTTATTA
1 TTTTATTTCTTTAATTA
9528763 TTTTATTTCTTTAATTA
1 TTTTATTTCTTTAATTA
9528780 TT
1 TT
9528782 AAATTGTTAA
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:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTATTTCTTTAATTA
Found at i:9529186 original size:24 final size:24
Alignment explanation
Indices: 9529159--9529224 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 24
9529149 ATTTACCTAC
*
9529159 TACCCACTTACTCACAAACCCACT
1 TACCCACTTACCCACAAACCCACT
* *
9529183 TACCCACTTACCCACTAACCCATT
1 TACCCACTTACCCACAAACCCACT
*
9529207 TATCCA-TTACCCAACAAA
1 TACCCACTTACCC-ACAAA
9529225 ATAAAAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
23 6 0.17
24 30 0.83
ACGTcount: A:0.35, C:0.42, G:0.00, T:0.23
Consensus pattern (24 bp):
TACCCACTTACCCACAAACCCACT
Found at i:9529189 original size:8 final size:8
Alignment explanation
Indices: 9529143--9529219 Score: 68
Period size: 8 Copynumber: 9.9 Consensus size: 8
9529133 GGACTATCCA
*
9529143 TTACCCAT
1 TTACCCAC
*
9529151 TTACCTAC
1 TTACCCAC
9529159 -TACCCAC
1 TTACCCAC
*
9529166 TTACTCAC
1 TTACCCAC
**
9529174 AAACCCAC
1 TTACCCAC
9529182 TTACCCAC
1 TTACCCAC
9529190 TTACCCAC
1 TTACCCAC
* *
9529198 TAACCCAT
1 TTACCCAC
*
9529206 TTATCCA-
1 TTACCCAC
9529213 TTACCCA
1 TTACCCA
9529220 ACAAAATAAA
Statistics
Matches: 54, Mismatches: 14, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
7 12 0.22
8 42 0.78
ACGTcount: A:0.30, C:0.43, G:0.00, T:0.27
Consensus pattern (8 bp):
TTACCCAC
Found at i:9530748 original size:21 final size:21
Alignment explanation
Indices: 9530722--9530761 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
9530712 ACTTTATCTC
9530722 TAGTAGTAGTAAT-AGTAATAG
1 TAGTAGTAGT-ATGAGTAATAG
9530743 TAGTAGTAGTATGAGTAAT
1 TAGTAGTAGTATGAGTAAT
9530762 TATATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.40, C:0.00, G:0.25, T:0.35
Consensus pattern (21 bp):
TAGTAGTAGTATGAGTAATAG
Found at i:9539615 original size:19 final size:19
Alignment explanation
Indices: 9539591--9539628 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
9539581 ACTTCTAAAC
9539591 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
9539610 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
9539629 AGTCAAATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:9541204 original size:23 final size:22
Alignment explanation
Indices: 9541177--9541231 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 22
9541167 AGGATAAATA
9541177 TCTCATTTCTTCCAGCACCTTC
1 TCTCATTTCTTCCAGCACCTTC
*
9541199 TCCTCA---CTTCCAGCAGCTTC
1 T-CTCATTTCTTCCAGCACCTTC
9541219 T-TCATCTTCTTCC
1 TCTCAT-TTCTTCC
9541232 CATCCTTTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
18 3 0.11
20 14 0.52
22 6 0.22
23 4 0.15
ACGTcount: A:0.13, C:0.42, G:0.05, T:0.40
Consensus pattern (22 bp):
TCTCATTTCTTCCAGCACCTTC
Found at i:9548630 original size:27 final size:27
Alignment explanation
Indices: 9548600--9548652 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
9548590 AGTGTTAAGT
* *
9548600 GGTGTAAAATTACAATTTTGCCCTTAG
1 GGTGGAAAATGACAATTTTGCCCTTAG
* *
9548627 GGTGGCAAATGACTATTTTGCCCTTA
1 GGTGGAAAATGACAATTTTGCCCTTA
9548653 TGCTCGAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (27 bp):
GGTGGAAAATGACAATTTTGCCCTTAG
Found at i:9549178 original size:43 final size:42
Alignment explanation
Indices: 9549075--9549202 Score: 157
Period size: 43 Copynumber: 3.0 Consensus size: 42
9549065 TTGTGTGAAA
* **
9549075 ATGATGACCCGACTATGTGCGGTATAAGAGTGCACATGAGCTG
1 ATGATGACCCGGCTATGTGCGGT-TGGGAGTGCACATGAGCTG
** *
9549118 ATGATGACCTAGTTATGTGCGGTGTGGGAGTGCACATGAGCTG
1 ATGATGACCCGGCTATGTGCGGT-TGGGAGTGCACATGAGCTG
* *
9549161 ATGATGACCCGGCTATGTGCGAGTAGGGAATGCACATGAGCT
1 ATGATGACCCGGCTATGTGCG-GTTGGGAGTGCACATGAGCT
9549203 AAGTGTGGTG
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
43 70 0.97
44 2 0.03
ACGTcount: A:0.25, C:0.17, G:0.34, T:0.24
Consensus pattern (42 bp):
ATGATGACCCGGCTATGTGCGGTTGGGAGTGCACATGAGCTG
Found at i:9553158 original size:71 final size:71
Alignment explanation
Indices: 9553013--9553179 Score: 203
Period size: 71 Copynumber: 2.4 Consensus size: 71
9553003 GGAAGTGCAC
* * * * *
9553013 ACATTCTGGTCCAAGATCGACTATAGACCTTCTGTAGTTGATCTTATGAAAGAAAAATGAATGAA
1 ACATTCTAGTCCAAGATCGACTATAAACCCTCTATAGTCGATCTTATGAAAGAAAAATGAATGAA
**
9553078 ATGTCA
66 ATCACA
* * *
9553084 ACATT-TCAGTCCAAGATCGATTATAAACCCTCTATAGTCGATCTTGTGAAGGAAAAATGAATGA
1 ACATTCT-AGTCCAAGATCGACTATAAACCCTCTATAGTCGATCTTATGAAAGAAAAATGAATGA
9553148 AA-CACGA
65 AATCAC-A
*
9553155 ACATTCTAGTCTAAGATCGACTATA
1 ACATTCTAGTCCAAGATCGACTATA
9553180 GATCCTTATA
Statistics
Matches: 81, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
70 2 0.02
71 78 0.96
72 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (71 bp):
ACATTCTAGTCCAAGATCGACTATAAACCCTCTATAGTCGATCTTATGAAAGAAAAATGAATGAA
ATCACA
Found at i:9556524 original size:85 final size:85
Alignment explanation
Indices: 9556381--9556553 Score: 328
Period size: 85 Copynumber: 2.0 Consensus size: 85
9556371 TAAATGAAAT
9556381 TGAACATGAGAATATACTTGTTTTCCAAGGCACCGTATTCTCAAATTCCTAACATACGGTTGTAC
1 TGAACATGAGAATATACTTGTTTTCCAAGGCACCGTATTCTCAAATTCCTAACATACGGTTGTAC
9556446 CATAAGCAGATGCATAGGTG
66 CATAAGCAGATGCATAGGTG
**
9556466 TGAACATGAGAATATACTTGTTTTCCAAGGCACCGTATTCTCAAATTTTTAACATACGGTTGTAC
1 TGAACATGAGAATATACTTGTTTTCCAAGGCACCGTATTCTCAAATTCCTAACATACGGTTGTAC
9556531 CATAAGCAGATGCATAGGTG
66 CATAAGCAGATGCATAGGTG
9556551 TGA
1 TGA
9556554 GATTAAGATT
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 86 1.00
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (85 bp):
TGAACATGAGAATATACTTGTTTTCCAAGGCACCGTATTCTCAAATTCCTAACATACGGTTGTAC
CATAAGCAGATGCATAGGTG
Found at i:9557916 original size:2 final size:2
Alignment explanation
Indices: 9557909--9557961 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
9557899 TGTTTGGTGA
9557909 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9557951 AT AT -T AT AT AT
1 AT AT AT AT AT AT
9557962 TTNNNNNNNN
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:9558699 original size:22 final size:23
Alignment explanation
Indices: 9558674--9558724 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
9558664 ATAAACACAG
*
9558674 TAAAAGATG-ATAATAA-TAAAAA
1 TAAAAAATGTATAA-AATTAAAAA
*
9558696 TAAAAAATGTATAAAATTTAAAA
1 TAAAAAATGTATAAAATTAAAAA
9558719 TAAAAA
1 TAAAAA
9558725 TTACCCATGC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 10 0.40
23 15 0.60
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (23 bp):
TAAAAAATGTATAAAATTAAAAA
Found at i:9561198 original size:2 final size:2
Alignment explanation
Indices: 9561187--9561226 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
9561177 ATATTTTATG
9561187 TA TA TA -A 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
9561227 TGAAGTTTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9569195 original size:28 final size:27
Alignment explanation
Indices: 9569157--9569209 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
9569147 ATTTGGAGTA
*
9569157 TAGGGGTAAAA-TGATAATTTTGCCACTC
1 TAGGGGCAAAATTG-TAATTTT-CCACTC
9569185 TAGGGGCAAAATTGTAATTTTCCAC
1 TAGGGGCAAAATTGTAATTTTCCAC
9569210 CACTAGGACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 4 0.17
28 17 0.74
29 2 0.09
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (27 bp):
TAGGGGCAAAATTGTAATTTTCCACTC
Found at i:9569215 original size:28 final size:28
Alignment explanation
Indices: 9569157--9569216 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
9569147 ATTTGGAGTA
* *
9569157 TAGGGGTAAAATGATAATTTTGCCACTC
1 TAGGGGCAAAATGATAATTTTGCCACAC
9569185 TAGGGGCAAAATTG-TAATTTT-CCACCAC
1 TAGGGGCAAAA-TGATAATTTTGCCA-CAC
9569213 TAGG
1 TAGG
9569217 ACAATTTTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 3 0.11
28 23 0.82
29 2 0.07
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.30
Consensus pattern (28 bp):
TAGGGGCAAAATGATAATTTTGCCACAC
Found at i:9569315 original size:9 final size:8
Alignment explanation
Indices: 9569284--9569313 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
9569274 GTGGTGGAGA
9569284 TAAAATGTT
1 TAAAAT-TT
9569293 TAAAATTT
1 TAAAATTT
9569301 TAAAATTT
1 TAAAATTT
9569309 TAAAA
1 TAAAA
9569314 ATGGACCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 15 0.71
9 6 0.29
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (8 bp):
TAAAATTT
Found at i:9593249 original size:17 final size:17
Alignment explanation
Indices: 9593224--9593256 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
9593214 TGGACAGCAA
*
9593224 AAACTCGTGCCTCTTCT
1 AAACCCGTGCCTCTTCT
9593241 AAACCCGTGCCTCTTC
1 AAACCCGTGCCTCTTC
9593257 CTCTGTCACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.39, G:0.12, T:0.30
Consensus pattern (17 bp):
AAACCCGTGCCTCTTCT
Found at i:9604554 original size:31 final size:31
Alignment explanation
Indices: 9604501--9604560 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
9604491 ATTGAAATTA
* *
9604501 AAGAAATGTTTGAAGGACCAAATTGTAAAGG
1 AAGAAAAGTTTGAAGGACCAAATGGTAAAGG
* **
9604532 AAGAAAAGTTTGGAGGGTCAAATGGTAAA
1 AAGAAAAGTTTGAAGGACCAAATGGTAAA
9604561 TAAGGAAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.45, C:0.05, G:0.28, T:0.22
Consensus pattern (31 bp):
AAGAAAAGTTTGAAGGACCAAATGGTAAAGG
Found at i:9607162 original size:20 final size:20
Alignment explanation
Indices: 9607117--9607154 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
9607107 TTTTGGCCCC
9607117 ATTTGACTTATTAGAGTATA
1 ATTTGACTTATTAGAGTATA
*
9607137 ATTTGACTTATTGGAGTA
1 ATTTGACTTATTAGAGTA
9607155 AGATTTGAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (20 bp):
ATTTGACTTATTAGAGTATA
Found at i:9607543 original size:30 final size:31
Alignment explanation
Indices: 9607509--9607568 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
9607499 AACCCTAGAA
9607509 AAGAAAATCAA-AGAAAAAGTGTGA-ATTTTC
1 AAGAAAATCAAGAGAAAAAG-GTGAGATTTTC
* *
9607539 AAGAAAATTAAGTGAAAAAGGTGAGATTTT
1 AAGAAAATCAAGAGAAAAAGGTGAGATTTT
9607569 TTCTATTAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 14 0.54
31 12 0.46
ACGTcount: A:0.52, C:0.03, G:0.20, T:0.25
Consensus pattern (31 bp):
AAGAAAATCAAGAGAAAAAGGTGAGATTTTC
Found at i:9620669 original size:13 final size:13
Alignment explanation
Indices: 9620651--9620675 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9620641 AGAGAAATTG
9620651 TGATTTTATAAAA
1 TGATTTTATAAAA
9620664 TGATTTTATAAA
1 TGATTTTATAAA
9620676 TTTTCTGGAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:9622980 original size:35 final size:35
Alignment explanation
Indices: 9622941--9623012 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
9622931 AAGTGCGTGA
**
9622941 GATGATATTGAAATGTGTGTGTAGGGAGTGCACAT
1 GATGATATTGAAATGTGCATGTAGGGAGTGCACAT
9622976 GATGATATTGAAATGTGCATGTAGGGAGTGCACAT
1 GATGATATTGAAATGTGCATGTAGGGAGTGCACAT
9623011 GA
1 GA
9623013 GTAAGCCGAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.31, C:0.07, G:0.33, T:0.29
Consensus pattern (35 bp):
GATGATATTGAAATGTGCATGTAGGGAGTGCACAT
Found at i:9626382 original size:20 final size:20
Alignment explanation
Indices: 9626357--9626402 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
9626347 TTTTGACCCC
9626357 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
*
9626377 ATTTGACTTATTGGAGTATG
1 ATTTGACTTATTGGAGTATA
9626397 ATTTGA
1 ATTTGA
9626403 GGTCTAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.04, G:0.22, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:9637972 original size:20 final size:20
Alignment explanation
Indices: 9637947--9637992 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
9637937 TTTTTATCCC
9637947 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
*
9637967 ATTTGACTTATTGGAGTATG
1 ATTTGACTTATTGGAGTATA
9637987 ATTTGA
1 ATTTGA
9637993 GGTTTAGAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.04, G:0.22, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:9638068 original size:28 final size:27
Alignment explanation
Indices: 9638037--9638089 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
9638027 TTTGGAGTAT
*
9638037 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTT-CCACCTC
*
9638065 AGGGGCAAAATTGTAATTTTCCACC
1 AGGGGCAAAATGGTAATTTTCCACC
9638090 ACCAGGATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (27 bp):
AGGGGCAAAATGGTAATTTTCCACCTC
Found at i:9638095 original size:28 final size:28
Alignment explanation
Indices: 9638037--9638095 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
9638027 TTTGGAGTAT
* *
9638037 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTTGCCACCCC
*
9638065 AGGGGCAAAATTGTAATTTT-CCACCACC
1 AGGGGCAAAATGGTAATTTTGCCACC-CC
9638093 AGG
1 AGG
9638096 ATATTTTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (28 bp):
AGGGGCAAAATGGTAATTTTGCCACCCC
Found at i:9641566 original size:38 final size:40
Alignment explanation
Indices: 9641524--9641626 Score: 138
Period size: 38 Copynumber: 2.6 Consensus size: 40
9641514 CTAGTGCCCG
* *
9641524 TGTGCACGATGTGGGGGGATGTACACTATGGC-ACTGAT-
1 TGTGCACGATGTGGGGGGATGTACACGATGGCGACGGATA
* * *
9641562 TGTGCACGATGTGGGGGGATGCACACGATGGCGCCGGCTA
1 TGTGCACGATGTGGGGGGATGTACACGATGGCGACGGATA
*
9641602 TGTGCATGATGTGGGGGGATGTACA
1 TGTGCACGATGTGGGGGGATGTACA
9641627 TGAGCCGAGT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
38 30 0.54
39 3 0.05
40 23 0.41
ACGTcount: A:0.19, C:0.17, G:0.41, T:0.23
Consensus pattern (40 bp):
TGTGCACGATGTGGGGGGATGTACACGATGGCGACGGATA
Found at i:9643884 original size:73 final size:73
Alignment explanation
Indices: 9643716--9643884 Score: 239
Period size: 73 Copynumber: 2.3 Consensus size: 73
9643706 TTAGTCAACC
* * *
9643716 AAGAAGGATAGTTAGTCGACTAAGAGCCTACTACCAGAAATCTGGACTTCAAGACAGAAACAACT
1 AAGAAGGA-AGTTAGTCGACTAAAAGCCTACTACCAGAAATCTGGACTTCAAAACAAAAACAACT
9643781 TAATCGACT
65 TAATCGACT
* * * * *
9643790 AATAAGGAAGTTAGTCAACTAAAAGCTTACTGCTAGAAATCTGGACTTCAAAACAAAAACAACTT
1 AAGAAGGAAGTTAGTCGACTAAAAGCCTACTACCAGAAATCTGGACTTCAAAACAAAAACAACTT
*
9643855 AATTGACT
66 AATCGACT
*
9643863 AAGAAGGAAGTTAGTTGACTAA
1 AAGAAGGAAGTTAGTCGACTAA
9643885 GTGCTCACTT
Statistics
Matches: 83, Mismatches: 12, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
73 76 0.92
74 7 0.08
ACGTcount: A:0.43, C:0.17, G:0.18, T:0.22
Consensus pattern (73 bp):
AAGAAGGAAGTTAGTCGACTAAAAGCCTACTACCAGAAATCTGGACTTCAAAACAAAAACAACTT
AATCGACT
Found at i:9644517 original size:32 final size:32
Alignment explanation
Indices: 9644373--9644509 Score: 161
Period size: 32 Copynumber: 4.2 Consensus size: 32
9644363 ACCATTGTTG
9644373 TAGGTTGTGGTTGAGCCTTTGAAAAACCACTT
1 TAGGTTGTGGTTGAGCCTTTGAAAAACCACTT
* *
9644405 TTGGTTGTGGTTGAGCTTTTGAAAAACCACTT
1 TAGGTTGTGGTTGAGCCTTTGAAAAACCACTT
* **
9644437 T-GGTTTTTGGTTGAGCCCATGAAAAACCA-TT
1 TAGG-TTGTGGTTGAGCCTTTGAAAAACCACTT
*
9644468 GTGAAAGGTTGTGGTTGAGCCTTTGAAAAATCACTT
1 -T---AGGTTGTGGTTGAGCCTTTGAAAAACCACTT
9644504 TAGGTT
1 TAGGTT
9644510 TTAGTTGATC
Statistics
Matches: 88, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
31 4 0.05
32 58 0.66
35 22 0.25
36 4 0.05
ACGTcount: A:0.25, C:0.13, G:0.26, T:0.36
Consensus pattern (32 bp):
TAGGTTGTGGTTGAGCCTTTGAAAAACCACTT
Done.