Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A07
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: 93829987
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4250000 characters in sequence are not A, C, G, or T
File 138 of 295
Found at i:42545413 original size:37 final size:37
Alignment explanation
Indices: 42545354--42545462 Score: 182
Period size: 37 Copynumber: 2.9 Consensus size: 37
42545344 AGCTCAGACG
* * *
42545354 AAATCTCCACATGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
42545391 AAATCTCCACACGTAGTCATCGGGTCTTACTCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
42545428 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
42545463 ATATATTTCC
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 67 1.00
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.24
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:42545755 original size:47 final size:47
Alignment explanation
Indices: 42545663--42546049 Score: 490
Period size: 47 Copynumber: 8.1 Consensus size: 47
42545653 ACACGTTTCG
* * *
42545663 CATTAGCCATTCAGCCTTA-C-CACATATTCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCA
* *
42545708 CATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCA
* * *
42545755 CATTGGCTATTCGGCCTTATCACACATACGCATGTTCACGTTCATCA
1 CATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCA
*
42545802 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCA
* * *
42545849 CATTGGCCATTCGGCCTTATCACGCATATATATATACAGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCA--C----ACATATGCATGTTCACATTCATCA
* *
42545902 CATTGGCCATTCGGCCTTATCACGCATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCA
* * **
42545949 CATTAGCGATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATATGCAT----GTTCACATTCATCA
* *
42546000 CATTGGCCATTCGGCCTTATCACACATAAGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCA
42546047 CAT
1 CAT
42546050 AAAATCCTAA
Statistics
Matches: 298, Mismatches: 32, Indels: 22
0.85 0.09 0.06
Matches are distributed among these distances:
45 17 0.06
46 1 0.00
47 194 0.65
49 1 0.00
51 43 0.14
53 42 0.14
ACGTcount: A:0.26, C:0.29, G:0.13, T:0.32
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCA
Found at i:42545915 original size:53 final size:53
Alignment explanation
Indices: 42545835--42546027 Score: 258
Period size: 53 Copynumber: 3.8 Consensus size: 53
42545825 ACATACGCAT
42545835 GTTCACATTCATCACATTGGCCATTCGGCCTTATCACGCATATATATATACAG
1 GTTCACATTCATCACATTGGCCATTCGGCCTTATCACGCATATATATATACAG
** *
42545888 GTTCACATTCATCACATTGGCCATTCGGCCTTATCACGC------ATACGCAT
1 GTTCACATTCATCACATTGGCCATTCGGCCTTATCACGCATATATATATACAG
* * * *
42545935 GTTCACATTCATCACATTAGCGATTCGGCCTTATCA--CACATATATATACGG
1 GTTCACATTCATCACATTGGCCATTCGGCCTTATCACGCATATATATATACAG
*
42545986 GTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATA
1 GTTCACATTCATCACATTGGCCATTCGGCCTTATCACGCATA
42546028 AGCATGTTCA
Statistics
Matches: 120, Mismatches: 12, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
45 1 0.01
47 39 0.32
51 38 0.32
53 42 0.35
ACGTcount: A:0.27, C:0.28, G:0.13, T:0.31
Consensus pattern (53 bp):
GTTCACATTCATCACATTGGCCATTCGGCCTTATCACGCATATATATATACAG
Found at i:42552153 original size:43 final size:43
Alignment explanation
Indices: 42552103--42552258 Score: 181
Period size: 43 Copynumber: 3.7 Consensus size: 43
42552093 TATCCTAGAT
* * *
42552103 ATGGTCTTACATGTTATCACATATCGATGCCACTGTCCCAGAC
1 ATGGTCTTACACGTAATCACATATCGATGCCAATGTCCCAGAC
* * * * *
42552146 AAGGTCTTACACGTATTGA-TTAACGATGCCAATGTCCCAGAC
1 ATGGTCTTACACGTAATCACATATCGATGCCAATGTCCCAGAC
* *
42552188 ATGGTCTTACACATAATCACA-ATACAATGCCAATGTCCCAGAC
1 ATGGTCTTACACGTAATCACATAT-CGATGCCAATGTCCCAGAC
* *
42552231 ATGGTCTTACATGTAATCACATCTCGAT
1 ATGGTCTTACACGTAATCACATATCGAT
42552259 AACCTAATGT
Statistics
Matches: 91, Mismatches: 19, Indels: 6
0.78 0.16 0.05
Matches are distributed among these distances:
42 36 0.40
43 54 0.59
44 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (43 bp):
ATGGTCTTACACGTAATCACATATCGATGCCAATGTCCCAGAC
Found at i:42562282 original size:63 final size:63
Alignment explanation
Indices: 42562181--42562314 Score: 142
Period size: 63 Copynumber: 2.1 Consensus size: 63
42562171 GAGACACTTG
* * * * *
42562181 GGCGTGTGTGCAGGCCGTGTAACTTACTAAGTTCATATTAGAGTCACACGAGTGAGACATACA
1 GGCGTGTGTCCAGGCCGTGTAACTCACTAAGTTCATATTAGAGACACACGAGTAAGACACACA
** * * * * * * *
42562244 GGCGTGTGTCCAGGTTGTGTGACTCACTGAGTTTATATTTGAGACATACGGGTAAGGCACACA
1 GGCGTGTGTCCAGGCCGTGTAACTCACTAAGTTCATATTAGAGACACACGAGTAAGACACACA
42562307 GGCGTGTG
1 GGCGTGTG
42562315 CAGACCATGT
Statistics
Matches: 57, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.27
Consensus pattern (63 bp):
GGCGTGTGTCCAGGCCGTGTAACTCACTAAGTTCATATTAGAGACACACGAGTAAGACACACA
Found at i:42563607 original size:30 final size:30
Alignment explanation
Indices: 42563571--42563630 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
42563561 TTCCCGAGCC
42563571 TAGGGGCAAAA-GTGTAATTATGCAAAAGTT
1 TAGGGGCAAAATG-GTAATTATGCAAAAGTT
* *
42563601 TAGGGGCAAAATGGTAATTTTGCCAAAGTT
1 TAGGGGCAAAATGGTAATTATGCAAAAGTT
42563631 CGTATTAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.37, C:0.08, G:0.27, T:0.28
Consensus pattern (30 bp):
TAGGGGCAAAATGGTAATTATGCAAAAGTT
Found at i:42564408 original size:51 final size:51
Alignment explanation
Indices: 42564284--42564530 Score: 304
Period size: 51 Copynumber: 4.9 Consensus size: 51
42564274 GTGAGGTCTG
* * ** * *
42564284 GTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGAT-TGTTGGTTGCA-
1 GTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAACTTCGAT-CAC
*
42564334 -TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCTGATAACTTCGATCAC
1 GTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAACTTCGATCAC
*
42564384 GTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCTGATAACTTCGATCAC
1 GTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAACTTCGATCAC
* * * ** * *
42564435 GTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGAT-GGTTAGGTCAC
1 GTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAACTTCGATCAC
* *
42564485 GTGTGTAGTACTAAGTGCAGGCTACTATGGGTACCAGATAGCTTCG
1 GTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAACTTCG
42564531 GCTACAAGTG
Statistics
Matches: 173, Mismatches: 20, Indels: 7
0.87 0.10 0.04
Matches are distributed among these distances:
49 37 0.21
50 47 0.27
51 89 0.51
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (51 bp):
GTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAACTTCGATCAC
Found at i:42564510 original size:101 final size:101
Alignment explanation
Indices: 42564284--42564530 Score: 302
Period size: 101 Copynumber: 2.5 Consensus size: 101
42564274 GTGAGGTCTG
* * ** * *
42564284 GTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGAT-TGTTGGTTGCATGTGTAGTACTAAG
1 GTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAACTTCGATGCATGTGTAGTACTAAG
* * *
42564348 TGCAGGCTACTATGCGTACCTGATAACTTCGATCAC
66 TGCAGGCTACTACGCGTACCAGATAACTTAGATCAC
*
42564384 GTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCTGATAACTTCGAT-CACGTGTGTAGTACTA
1 GTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAACTTCGATGCA--TGTGTAGTACTA
* * ** *
42564448 AGTGCAGGCTACTACGTGTATCAGAT-GGTTAGGTCAC
64 AGTGCAGGCTACTACGCGTACCAGATAACTTAGATCAC
* *
42564485 GTGTGTAGTACTAAGTGCAGGCTACTATGGGTACCAGATAGCTTCG
1 GTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAACTTCG
42564531 GCTACAAGTG
Statistics
Matches: 126, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
100 38 0.30
101 54 0.43
102 34 0.27
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (101 bp):
GTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAACTTCGATGCATGTGTAGTACTAAG
TGCAGGCTACTACGCGTACCAGATAACTTAGATCAC
Found at i:42568365 original size:19 final size:19
Alignment explanation
Indices: 42568341--42568384 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
42568331 GTAAAAGTAA
42568341 AGTGTGAGCTAACAAGCTC
1 AGTGTGAGCTAACAAGCTC
*
42568360 AGTGTGAGCTAATAAGCTC
1 AGTGTGAGCTAACAAGCTC
42568379 AGTGTG
1 AGTGTG
42568385 TGTAACTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.25
Consensus pattern (19 bp):
AGTGTGAGCTAACAAGCTC
Found at i:42570101 original size:22 final size:23
Alignment explanation
Indices: 42570067--42570110 Score: 54
Period size: 22 Copynumber: 1.9 Consensus size: 23
42570057 AGAACCAGAT
**
42570067 CAATTCACTAAAC-AAATTTTAA
1 CAATTCAAAAAACAAAATTTTAA
42570089 CAATTCAAAAAACTAAAATTTT
1 CAATTCAAAAAAC-AAAATTTT
42570111 GGGGTGTTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 11 0.61
24 7 0.39
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (23 bp):
CAATTCAAAAAACAAAATTTTAA
Found at i:42572745 original size:15 final size:15
Alignment explanation
Indices: 42572727--42572756 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
42572717 ATGCGTTTAA
42572727 TTTTTAATTAATATT
1 TTTTTAATTAATATT
*
42572742 TTTTTAATTATTATT
1 TTTTTAATTAATATT
42572757 GCTTAACATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTTAATTAATATT
Found at i:42574847 original size:27 final size:27
Alignment explanation
Indices: 42574795--42574883 Score: 92
Period size: 26 Copynumber: 3.4 Consensus size: 27
42574785 AGTAAATAAT
* * *
42574795 AATTTAAAA-AAATTAGTATACAAAAC
1 AATTTAAAATAAAATAATATATAAAAC
42574821 AATTTAAAATAAAATAATATATAAAAC
1 AATTTAAAATAAAATAATATATAAAAC
** * * *
42574848 AATCCAAAAT-GACTAATTTATAAAAC
1 AATTTAAAATAAAATAATATATAAAAC
42574874 AATTTAAAAT
1 AATTTAAAAT
42574884 GACATATAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
26 30 0.58
27 22 0.42
ACGTcount: A:0.61, C:0.08, G:0.02, T:0.29
Consensus pattern (27 bp):
AATTTAAAATAAAATAATATATAAAAC
Found at i:42574973 original size:26 final size:25
Alignment explanation
Indices: 42574944--42575016 Score: 58
Period size: 25 Copynumber: 2.8 Consensus size: 25
42574934 TACATAATAT
42574944 ATAAAAAATATAAAACAATTTTAAA
1 ATAAAAAATATAAAACAATTTTAAA
* * * *
42574969 A-ATAATAATGTAAAAGAAATTTAAA
1 ATA-AAAAATATAAAACAATTTTAAA
* *
42574994 GTAAATAACATATAAAATAATTT
1 ATAAA-AA-ATATAAAACAATTT
42575017 AAACCAAGTA
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
24 1 0.03
25 21 0.60
26 2 0.06
27 11 0.31
ACGTcount: A:0.63, C:0.03, G:0.04, T:0.30
Consensus pattern (25 bp):
ATAAAAAATATAAAACAATTTTAAA
Found at i:42575100 original size:27 final size:26
Alignment explanation
Indices: 42574944--42575135 Score: 110
Period size: 26 Copynumber: 7.4 Consensus size: 26
42574934 TACATAATAT
* * *
42574944 ATAAAAAATA-TAAAACAATTTTAAA
1 ATAAATAATAGTAAAAAAAATTTAAA
*
42574969 A-ATAATAAT-GTAAAAGAAATTTAAA
1 ATA-AATAATAGTAAAAAAAATTTAAA
* * *
42574994 GTAAATAACA-TATAAAATAATTTAAA
1 ATAAATAATAGTA-AAAAAAATTTAAA
** * * * *
42575020 CCAAGTAATA-CATATAAAACTTTAAA
1 ATAAATAATAGTA-AAAAAAATTTAAA
* * *
42575046 ATAGATAATA-TACACAAAGATTTAAA
1 ATAAATAATAGTA-AAAAAAATTTAAA
*
42575072 ATAAATCATA-TAAGGAAAAAATTTAAA
1 ATAAATAATAGTAA--AAAAAATTTAAA
*
42575099 ATAAATAATATGTAAAAATAATTTAAA
1 ATAAATAATA-GTAAAAAAAATTTAAA
42575126 ATAAATAATA
1 ATAAATAATA
42575136 CACAAAATTT
Statistics
Matches: 128, Mismatches: 30, Indels: 16
0.74 0.17 0.09
Matches are distributed among these distances:
24 1 0.01
25 27 0.21
26 57 0.45
27 40 0.31
29 3 0.02
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.29
Consensus pattern (26 bp):
ATAAATAATAGTAAAAAAAATTTAAA
Found at i:42575106 original size:22 final size:25
Alignment explanation
Indices: 42575065--42575134 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 25
42575055 ATACACAAAG
* * *
42575065 ATTTAAAATAAATCATATAAGGAAAAA
1 ATTTAAAATAAATAATGTAA--AAATA
42575092 ATTTAAAATAAATAATATGTAAAAATA
1 ATTTAAAATAAAT-A-ATGTAAAAATA
42575119 ATTTAAAATAAATAAT
1 ATTTAAAATAAATAAT
42575135 ACACAAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
25 2 0.05
26 1 0.03
27 30 0.79
29 5 0.13
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.31
Consensus pattern (25 bp):
ATTTAAAATAAATAATGTAAAAATA
Found at i:42575133 original size:14 final size:14
Alignment explanation
Indices: 42575065--42575134 Score: 56
Period size: 14 Copynumber: 5.1 Consensus size: 14
42575055 ATACACAAAG
*
42575065 ATTTAAAATAAATC
1 ATTTAAAATAAATA
* *
42575079 ATATAAGGA-AAA-A
1 ATTTAA-AATAAATA
42575092 ATTTAAAATAAATA
1 ATTTAAAATAAATA
* **
42575106 ATATGTAA-AAATA
1 ATTTAAAATAAATA
42575119 ATTTAAAATAAATA
1 ATTTAAAATAAATA
42575133 AT
1 AT
42575135 ACACAAAATT
Statistics
Matches: 41, Mismatches: 11, Indels: 8
0.68 0.18 0.13
Matches are distributed among these distances:
12 1 0.02
13 18 0.44
14 21 0.51
15 1 0.02
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.31
Consensus pattern (14 bp):
ATTTAAAATAAATA
Found at i:42575142 original size:27 final size:26
Alignment explanation
Indices: 42574979--42575142 Score: 114
Period size: 26 Copynumber: 6.2 Consensus size: 26
42574969 AATAATAATG
* * *
42574979 TAAAAGAAATTTAAAGTAAATAACATA
1 TAAAA-AAATTTAAAATAAATAATACA
* ** *
42575006 TAAAATAATTTAAACCAAGTAATACA
1 TAAAAAAATTTAAAATAAATAATACA
* * * *
42575032 TATAAAACTTTAAAATAGATAATATA
1 TAAAAAAATTTAAAATAAATAATACA
* * *
42575058 CACAAAGATTTAAAATAAATCATATA-A
1 TAAAAAAATTTAAAATAAAT-A-ATACA
** **
42575085 GGAAAAAATTTAAAATAAATAATATG
1 TAAAAAAATTTAAAATAAATAATACA
42575111 TAAAAATAATTTAAAATAAATAATACA
1 TAAAAA-AATTTAAAATAAATAATACA
*
42575138 CAAAA
1 TAAAA
42575143 TTTTAAAGTA
Statistics
Matches: 104, Mismatches: 29, Indels: 8
0.74 0.21 0.06
Matches are distributed among these distances:
25 3 0.03
26 53 0.51
27 45 0.43
28 3 0.03
ACGTcount: A:0.62, C:0.06, G:0.05, T:0.27
Consensus pattern (26 bp):
TAAAAAAATTTAAAATAAATAATACA
Found at i:42577001 original size:44 final size:44
Alignment explanation
Indices: 42576932--42577880 Score: 324
Period size: 44 Copynumber: 21.1 Consensus size: 44
42576922 CAAAGAGACT
* * * *
42576932 AGACTTGTAGCTT-TAATCTACTCCACTGTAACTTTAGGGAGATA
1 AGACTTGTAACTTCT-ATCTGCTCCACTGCAACTTCAGGGAGATA
* * *
42576976 AAACTTGTGACTTCTATCTGCTCCACTGCAACTTCATGGAGATA
1 AGACTTGTAACTTCTATCTGCTCCACTGCAACTTCAGGGAGATA
* * * * *
42577020 AGATTTGTAA-TCTGTAGTTTGCTCCATTGCAACTTCAGGGGGATA
1 AGACTTGTAACT-TCTA-TCTGCTCCACTGCAACTTCAGGGAGATA
*
42577065 AGACTTGTAACTTCTATCTACTCCACTGCAACTTCAGGGAGATA
1 AGACTTGTAACTTCTATCTGCTCCACTGCAACTTCAGGGAGATA
* * * *
42577109 AGACTTGTAACTTCAACCTGCTCCACTGCAACTTTAGAGAGATA
1 AGACTTGTAACTTCTATCTGCTCCACTGCAACTTCAGGGAGATA
** * * *
42577153 AGGTTTGTTATA-TAC-AGTCTACTCCATTGCAACTTCAGGGAGATA
1 AGACTTG-TA-ACTTCTA-TCTGCTCCACTGCAACTTCAGGGAGATA
* * * * * *
42577198 AGATTCGCCATGGTAGA-TT-TGATCTGAC-CTACTACTACTTTAGAGG-TATA
1 AGA-----C-TTGTA-ACTTCT-ATCTG-CTCCACTGCAACTTCAG-GGAGATA
* * * * * *
42577248 GGATTTATAGCTT-TAATCTGCTCTACTGCAACTTCAGAGAGATA
1 AGACTTGTAACTTCT-ATCTGCTCCACTGCAACTTCAGGGAGATA
* * * *
42577292 AGA-TTCGCTATC-TCCAGTCTGCTCCACTACAACTTTAGGGAGATA
1 AGACTT-G-TAACTTCTA-TCTGCTCCACTGCAACTTCAGGGAGATA
* * * *
42577337 AGACTTGTAACTTC-AACTTGCTCTACTGCAACTTTAGAGAGATA
1 AGACTTGTAACTTCTATC-TGCTCCACTGCAACTTCAGGGAGATA
* ** * ** *
42577381 AG-GTTAGTGGCTTCAATCTGCTCCACTATAACTTCAGAGAGATA
1 AGACTT-GTAACTTCTATCTGCTCCACTGCAACTTCAGGGAGATA
* * * * *
42577425 AGATTCGCCATGGTAGA-TT-TGATCCGAC-CTACTGTAACTTCAGAGG-TATA
1 AGA-----C-TTGTA-ACTTCT-ATCTG-CTCCACTGCAACTTCAG-GGAGATA
* ** * * * *
42577475 GGGTTTATAGCTT-TAATCTG-TCTACTGCAACTTCAGAGAGATA
1 AGACTTGTAACTTCT-ATCTGCTCCACTGCAACTTCAGGGAGATA
* * ** *
42577518 AGA-TT-TACTATTTTTAGTCCACTCTACTGCAACTTCAGGGAGATA
1 AGACTTGTA--ACTTCTA-TCTGCTCCACTGCAACTTCAGGGAGATA
* *
42577563 AGACTTGTAACTTC-AACTTGCTCCACTGCAACTTCAAGGAGATA
1 AGACTTGTAACTTCTATC-TGCTCCACTGCAACTTCAGGGAGATA
* ** * *
42577607 AG-GTTAGTGGCTTCGATCTGCTCCACTACAACTTCAGGGAGATA
1 AGACTT-GTAACTTCTATCTGCTCCACTGCAACTTCAGGGAGATA
* ** *
42577651 AGATTTGCCATGGTAGA-TT-TGATCTGAC-CTGCTGCAACTTCAGAGG-TATA
1 AGA-----C-TTGTA-ACTTCT-ATCTG-CTCCACTGCAACTTCAG-GGAGATA
* * * * * *
42577701 GGATTTATAGCTT-TAATCTGCTCTACTGCAACTTCAGAGAGATA
1 AGACTTGTAACTTCT-ATCTGCTCCACTGCAACTTCAGGGAGATA
** * *
42577745 AGA-TTCGCTATTTTC-AGTCTGCTCCGCTGCAACTTCAGAGAGATA
1 AGACTT-G-TAACTTCTA-TCTGCTCCACTGCAACTTCAGGGAGATA
* ** * *
42577790 AG-GTTAGTGGCTTCGATCTGCTCCACTGCAACTTTAGGGAGATA
1 AGACTT-GTAACTTCTATCTGCTCCACTGCAACTTCAGGGAGATA
* ** *
42577834 AG-GTTAGTGGCTTCGATCTGCTCCACTGCAACTTCAGGGAGATA
1 AGACTT-GTAACTTCTATCTGCTCCACTGCAACTTCAGGGAGATA
42577878 AGA
1 AGA
42577881 TTCACCATGG
Statistics
Matches: 680, Mismatches: 151, Indels: 147
0.70 0.15 0.15
Matches are distributed among these distances:
41 2 0.00
42 3 0.00
43 36 0.05
44 378 0.56
45 167 0.25
46 6 0.01
47 2 0.00
50 73 0.11
51 13 0.02
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (44 bp):
AGACTTGTAACTTCTATCTGCTCCACTGCAACTTCAGGGAGATA
Found at i:42577160 original size:133 final size:133
Alignment explanation
Indices: 42576932--42577200 Score: 362
Period size: 133 Copynumber: 2.0 Consensus size: 133
42576922 CAAAGAGACT
* * * * * *
42576932 AGACTTGTAGCTTTAATCTACTCCACTGTAACTTTAGGGAGATAAAACTTGTGACTTCTATCTGC
1 AGACTTGTAACTTTAATCTACTCCACTGCAACTTCAGGGAGATAAAACTTGTAACTTCAACCTGC
* ** * * *
42576997 TCCACTGCAACTTCATGGAGATAAGATTTGTAATCTGTAGTTTGCTCCATTGCAACTTCAGGGGG
66 TCCACTGCAACTTCATGGAGATAAGATTTGTAATATACAGTCTACTCCATTGCAACTTCAGGGAG
42577062 ATA
131 ATA
*
42577065 AGACTTGTAACTTCT-ATCTACTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTG
1 AGACTTGTAACTT-TAATCTACTCCACTGCAACTTCAGGGAGATAAAACTTGTAACTTCAACCTG
* * *
42577129 CTCCACTGCAACTTTA-GAGAGATAAGGTTTGTTATATACAGTCTACTCCATTGCAACTTCAGGG
65 CTCCACTGCAACTTCATG-GAGATAAGATTTGTAATATACAGTCTACTCCATTGCAACTTCAGGG
42577193 AGATA
129 AGATA
42577198 AGA
1 AGA
42577201 TTCGCCATGG
Statistics
Matches: 118, Mismatches: 16, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
132 1 0.01
133 116 0.98
134 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.32
Consensus pattern (133 bp):
AGACTTGTAACTTTAATCTACTCCACTGCAACTTCAGGGAGATAAAACTTGTAACTTCAACCTGC
TCCACTGCAACTTCATGGAGATAAGATTTGTAATATACAGTCTACTCCATTGCAACTTCAGGGAG
ATA
Found at i:42577367 original size:89 final size:88
Alignment explanation
Indices: 42576952--42577427 Score: 318
Period size: 89 Copynumber: 5.3 Consensus size: 88
42576942 CTTTAATCTA
** * * *
42576952 CTCCACTGTAACTTTAGGGAGATAAAACTTGTGACTTCTATCTGCTCCACTGCAACTTCATG-GA
1 CTCCACTACAACTTTAGGGAGATAAGACTTGTAACTTCAATCTGCTCCACTGCAACTTCA-GAGA
* *
42577016 GATAAGATTTGTAATCTGT-AGTTTG
65 GATAAGATTCGT-ATCT-TCAGTCTG
* * * * * * *
42577041 CTCCATTGCAACTTCAGGGGGATAAGACTTGTAACTTCTATCTACTCCACTGCAACTTCAGGGAG
1 CTCCACTACAACTTTAGGGAGATAAGACTTGTAACTTCAATCTGCTCCACTGCAACTTCAGAGAG
* **
42577106 ATAAGACTT-GTAACTTCAACCTG
66 ATAAGA-TTCGTATCTTCAGTCTG
* * ** * * * * *
42577129 CTCCACTGCAACTTTAGAGAGATAAGGTTTGTTATA-TACAGTCTACTCCATTGCAACTTCAGGG
1 CTCCACTACAACTTTAGGGAGATAAGACTTG-TA-ACTTCAATCTGCTCCACTGCAACTTCAGAG
* ** *
42577193 AGATAAGATTCGCCATGGT-AGATTTG
64 AGATAAGATTCG-TATCTTCAG-TCTG
* * * * * * * *
42577219 ATCTGACCTACTACTACTTTAGAGG-TATAGGATTTATAGCTTTAATCTGCTCTACTGCAACTTC
1 --CT--CC-ACTACAACTTTAG-GGAGATAAGACTTGTAACTTCAATCTGCTCCACTGCAACTTC
*
42577283 AGAGAGATAAGATTCGCTATCTCCAGTCTG
60 AGAGAGATAAGATTCG-TATCTTCAGTCTG
* *
42577313 CTCCACTACAACTTTAGGGAGATAAGACTTGTAACTTCAA-CTTGCTCTACTGCAACTTTAGAGA
1 CTCCACTACAACTTTAGGGAGATAAGACTTGTAACTTCAATC-TGCTCCACTGCAACTTCAGAGA
* * ** *
42577377 GATAAGGTTAGTGGCTTCAATCTG
65 GATAAGATTCGTATCTTCAGTCTG
* * *
42577401 CTCCACTATAACTTCAGAGAGATAAGA
1 CTCCACTACAACTTTAGGGAGATAAGA
42577428 TTCGCCATGG
Statistics
Matches: 304, Mismatches: 65, Indels: 37
0.75 0.16 0.09
Matches are distributed among these distances:
87 1 0.00
88 70 0.23
89 156 0.51
90 9 0.03
92 4 0.01
94 43 0.14
95 20 0.07
96 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (88 bp):
CTCCACTACAACTTTAGGGAGATAAGACTTGTAACTTCAATCTGCTCCACTGCAACTTCAGAGAG
ATAAGATTCGTATCTTCAGTCTG
Found at i:42577456 original size:227 final size:227
Alignment explanation
Indices: 42577085--42578163 Score: 1466
Period size: 227 Copynumber: 4.8 Consensus size: 227
42577075 CTTCTATCTA
*
42577085 CTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCAACTTTAGAGAG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACTTGCTCCACTGCAACTTTAGAGAG
* ** * * *
42577150 ATAAGGTTTGT-TATATACAGTCTACTCCATTGCAACTTCAGGGAGATAAGATTCGCCATGGTAG
66 ATAAGGTTAGTGGCT-T-CAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATGGTAG
* *
42577214 ATTTGATCTGACCTACTACTACTTTAGAGGTATAGGATTTATAGCTTTAATCTGCTCTACTGCAA
129 ATTTGATCTGACCTGCTACAACTTTAGAGGTATAGGATTTATAGCTTTAATCTGCTCTACTGCAA
* * *
42577279 CTTCAGAGAGATAAGATTCGCTATCTCCAGTCTG
194 CTTCAGAGAGATAAGATTCACTATTTTCAGTCTG
* * *
42577313 CTCCACTACAACTTTAGGGAGATAAGACTTGTAACTTCAACTTGCTCTACTGCAACTTTAGAGAG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACTTGCTCCACTGCAACTTTAGAGAG
** *
42577378 ATAAGGTTAGTGGCTTCAATCTGCTCCACTATAACTTCAGAGAGATAAGATTCGCCATGGTAGAT
66 ATAAGGTTAGTGGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATGGTAGAT
* * ** * *
42577443 TTGATCCGACCTACTGTAACTTCAGAGGTATAGGGTTTATAGCTTTAATCTG-TCTACTGCAACT
131 TTGATCTGACCTGCTACAACTTTAGAGGTATAGGATTTATAGCTTTAATCTGCTCTACTGCAACT
* * **
42577507 TCAGAGAGATAAGATTTACTATTTTTAGTCCA
196 TCAGAGAGATAAGATTCACTATTTTCAGTCTG
* *
42577539 CTCTACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACTTGCTCCACTGCAACTTCA-AGGA
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACTTGCTCCACTGCAACTTTAGA-GA
* * *
42577603 GATAAGGTTAGTGGCTTCGATCTGCTCCACTACAACTTCAGGGAGATAAGATTTGCCATGGTAGA
65 GATAAGGTTAGTGGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATGGTAGA
* *
42577668 TTTGATCTGACCTGCTGCAACTTCAGAGGTATAGGATTTATAGCTTTAATCTGCTCTACTGCAAC
130 TTTGATCTGACCTGCTACAACTTTAGAGGTATAGGATTTATAGCTTTAATCTGCTCTACTGCAAC
*
42577733 TTCAGAGAGATAAGATTCGCTATTTTCAGTCTG
195 TTCAGAGAGATAAGATTCACTATTTTCAGTCTG
* * * ** * *
42577766 CTCCGCTGCAACTTCAGAGAGATAAG-GTTAGTGGCTTCGA-TCTGCTCCACTGCAACTTTAGGG
1 CTCCACTGCAACTTCAGGGAGATAAGACTT-GTAACTTCAACT-TGCTCCACTGCAACTTTAGAG
* *
42577829 AGATAAGGTTAGTGGCTTCGATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCACCATGGTAG
64 AGATAAGGTTAGTGGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATGGTAG
* * **
42577894 ATTTGATCAGACCTGCTACAACTTTAGAGGTATAGGATTTATAGTTTTAATCTGCTCTACTATAA
129 ATTTGATCTGACCTGCTACAACTTTAGAGGTATAGGATTTATAGCTTTAATCTGCTCTACTGCAA
42577959 CTTCAGAGAGATAAGATTCACTATTTTCAGTCTG
194 CTTCAGAGAGATAAGATTCACTATTTTCAGTCTG
** * * * ** * *
42577993 CTCTGCTGCAACTTCAAGGAGATAAGACTTGGAACTTTAACTTGCTCCACTAAAACTTCAGGGAG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACTTGCTCCACTGCAACTTTAGAGAG
* * * * * * * *
42578058 ATAAAGTTTGTGGCTTCAATCTACTCCACCGCAATTTTAGGGAGATAAGATTTGCCAAGGTAGAT
66 ATAAGGTTAGTGGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATGGTAGAT
* *
42578123 TTGATCTGACCTGCTGCAATTTTAGAGGTATAGGATTTATA
131 TTGATCTGACCTGCTACAACTTTAGAGGTATAGGATTTATA
42578164 ACTTCAATGA
Statistics
Matches: 755, Mismatches: 88, Indels: 17
0.88 0.10 0.02
Matches are distributed among these distances:
225 1 0.00
226 207 0.27
227 471 0.62
228 75 0.10
229 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.31
Consensus pattern (227 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACTTGCTCCACTGCAACTTTAGAGAG
ATAAGGTTAGTGGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATGGTAGAT
TTGATCTGACCTGCTACAACTTTAGAGGTATAGGATTTATAGCTTTAATCTGCTCTACTGCAACT
TCAGAGAGATAAGATTCACTATTTTCAGTCTG
Found at i:42577807 original size:183 final size:183
Alignment explanation
Indices: 42577499--42577835 Score: 477
Period size: 183 Copynumber: 1.8 Consensus size: 183
42577489 AATCTGTCTA
** * *
42577499 CTGCAACTTCAGAGAGATAAGATTTACTATTTTTAGTCCACTCTACTGCAACTTCAGGGAGATAA
1 CTGCAACTTCAGAGAGATAAGATTTACTAGCTTTAATCCACTCTACTGCAACTTCAGAGAGATAA
42577564 GACTTGTAACTTCAACTTGCTCCACTGCAACTTCAAGGAGATAAGGTTAGTGGCTTCGATCTGCT
66 GACTTGTAACTTCAACTTGCTCCACTGCAACTTCAAGGAGATAAGGTTAGTGGCTTCGATCTGCT
42577629 CCACTACAACTTCAGGGAGATAAGATTTGCCATGGTAGATTTGATCTGACCTG
131 CCACTACAACTTCAGGGAGATAAGATTTGCCATGGTAGATTTGATCTGACCTG
* **
42577682 CTGCAACTTCAGAG-GTATAGGATTTA-TAGCTTTAATCTGCTCTACTGCAACTTCAGAGAGATA
1 CTGCAACTTCAGAGAG-ATAAGATTTACTAGCTTTAATCCACTCTACTGCAACTTCAGAGAGATA
** * *
42577745 AGA-TTCGCTATTTTC-AGTCTGCTCCGCTGCAACTTC-AGAGAGATAAGGTTAGTGGCTTCGAT
65 AGACTT-G-TAACTTCAACT-TGCTCCACTGCAACTTCAAG-GAGATAAGGTTAGTGGCTTCGAT
* *
42577807 CTGCTCCACTGCAACTTTAGGGAGATAAG
126 CTGCTCCACTACAACTTCAGGGAGATAAG
42577836 GTTAGTGGCT
Statistics
Matches: 136, Mismatches: 13, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
181 2 0.01
182 40 0.29
183 94 0.69
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (183 bp):
CTGCAACTTCAGAGAGATAAGATTTACTAGCTTTAATCCACTCTACTGCAACTTCAGAGAGATAA
GACTTGTAACTTCAACTTGCTCCACTGCAACTTCAAGGAGATAAGGTTAGTGGCTTCGATCTGCT
CCACTACAACTTCAGGGAGATAAGATTTGCCATGGTAGATTTGATCTGACCTG
Found at i:42577893 original size:453 final size:453
Alignment explanation
Indices: 42577084--42578163 Score: 1540
Period size: 453 Copynumber: 2.4 Consensus size: 453
42577074 ACTTCTATCT
* * *
42577084 ACTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCAACTT-TAGAG
1 ACTCTACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACTTGCTCCACTGCAACTTCAAG-G
** * *
42577148 AGATAAGGTTTGT-TATATACAGTCTACTCCATTGCAACTTCAGGGAGATAAGATTCGCCATGGT
65 AGATAAGGTTTGTGGCT-T-CA-TCTACTCCACTGCAACTTCAGGGAGATAAGATTTGCCATGGT
* * *
42577212 AGATTTGATCTGACCTACTACTACTTTAGAGGTATAGGATTTATAGCTTTAATCTGCTCTACTGC
127 AGATTTGATCTGACCTGCTGCAACTTTAGAGGTATAGGATTTATAGCTTTAATCTGCTCTACTGC
* *
42577277 AACTTCAGAGAGATAAGATTCGCTATCTCCAGTCTGCTCCACTACAACTTTAGGGAGATAAGACT
192 AACTTCAGAGAGATAAGATTCGCTATCTCCAGTCTGCTCCACTACAACTTCAGAGAGATAAGACT
*
42577342 TGTAACTTCAACTTGCTCTACTGCAACTTTAGAGAGATAAGGTTAGTGGCTTCAATCTGCTCCAC
257 TGTAACTTCAACTTGCTCCACTGCAACTTTAGAGAGATAAGGTTAGTGGCTTCAATCTGCTCCAC
* * * **
42577407 TATAACTTCAGAGAGATAAGATTCGCCATGGTAGATTTGATCCGACCTACTGTAACTTCAGAGGT
322 TACAACTTCAGAGAGATAAGATTCACCATGGTAGATTTGATCAGACCTACTACAACTTCAGAGGT
* * * *
42577472 ATAGGGTTTATAGCTTTAATCTG-TCTACTGCAACTTCAGAGAGATAAGATTTACTATTTTTAGT
387 ATAGGATTTATAGCTTTAATCTGCTCTACTACAACTTCAGAGAGATAAGATTCACTATTTTCAGT
42577536 CC
452 CC
42577538 ACTCTACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACTTGCTCCACTGCAACTTCAAGGA
1 ACTCTACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACTTGCTCCACTGCAACTTCAAGGA
* * *
42577603 GATAAGGTTAGTGGCTTCGATCTGCTCCACTACAACTTCAGGGAGATAAGATTTGCCATGGTAGA
66 GATAAGGTTTGTGGCTTC-ATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGCCATGGTAGA
*
42577668 TTTGATCTGACCTGCTGCAACTTCAGAGGTATAGGATTTATAGCTTTAATCTGCTCTACTGCAAC
130 TTTGATCTGACCTGCTGCAACTTTAGAGGTATAGGATTTATAGCTTTAATCTGCTCTACTGCAAC
* * * * *
42577733 TTCAGAGAGATAAGATTCGCTATTTTCAGTCTGCTCCGCTGCAACTTCAGAGAGATAAG-GTTAG
195 TTCAGAGAGATAAGATTCGCTATCTCCAGTCTGCTCCACTACAACTTCAGAGAGATAAGACTT-G
** * * *
42577797 TGGCTTCGA-TCTGCTCCACTGCAACTTTAGGGAGATAAGGTTAGTGGCTTCGATCTGCTCCACT
259 TAACTTCAACT-TGCTCCACTGCAACTTTAGAGAGATAAGGTTAGTGGCTTCAATCTGCTCCACT
* * * *
42577861 GCAACTTCAGGGAGATAAGATTCACCATGGTAGATTTGATCAGACCTGCTACAACTTTAGAGGTA
323 ACAACTTCAGAGAGATAAGATTCACCATGGTAGATTTGATCAGACCTACTACAACTTCAGAGGTA
* *
42577926 TAGGATTTATAGTTTTAATCTGCTCTACTATAACTTCAGAGAGATAAGATTCACTATTTTCAGTC
388 TAGGATTTATAGCTTTAATCTGCTCTACTACAACTTCAGAGAGATAAGATTCACTATTTTCAGTC
*
42577991 T
453 C
* * * * * ** *
42577992 GCTCTGCTGCAACTTCAAGGAGATAAGACTTGGAACTTTAACTTGCTCCACTAAAACTTCAGGGA
1 ACTCTACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACTTGCTCCACTGCAACTTCAAGGA
* * * * *
42578057 GATAAAGTTTGTGGCTTCAATCTACTCCACCGCAATTTTAGGGAGATAAGATTTGCCAAGGTAGA
66 GATAAGGTTTGTGGCTTC-ATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGCCATGGTAGA
*
42578122 TTTGATCTGACCTGCTGCAATTTTAGAGGTATAGGATTTATA
130 TTTGATCTGACCTGCTGCAACTTTAGAGGTATAGGATTTATA
42578164 ACTTCAATGA
Statistics
Matches: 558, Mismatches: 62, Indels: 12
0.88 0.10 0.02
Matches are distributed among these distances:
452 3 0.01
453 289 0.52
454 263 0.47
455 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (453 bp):
ACTCTACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACTTGCTCCACTGCAACTTCAAGGA
GATAAGGTTTGTGGCTTCATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGCCATGGTAGAT
TTGATCTGACCTGCTGCAACTTTAGAGGTATAGGATTTATAGCTTTAATCTGCTCTACTGCAACT
TCAGAGAGATAAGATTCGCTATCTCCAGTCTGCTCCACTACAACTTCAGAGAGATAAGACTTGTA
ACTTCAACTTGCTCCACTGCAACTTTAGAGAGATAAGGTTAGTGGCTTCAATCTGCTCCACTACA
ACTTCAGAGAGATAAGATTCACCATGGTAGATTTGATCAGACCTACTACAACTTCAGAGGTATAG
GATTTATAGCTTTAATCTGCTCTACTACAACTTCAGAGAGATAAGATTCACTATTTTCAGTCC
Found at i:42579379 original size:6 final size:6
Alignment explanation
Indices: 42579368--42579402 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
42579358 TGTCCTCTCC
*
42579368 TTTTCT TTTTCT TTTTCT TCTTCTT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTC-T TTTTCT TTTT
42579403 TATTATACGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTCT
Found at i:42582513 original size:19 final size:19
Alignment explanation
Indices: 42582472--42582517 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
42582462 GTGAAAGTTT
**
42582472 AATGCAAATGATGCGATGC
1 AATGCAAATGATGAAATGC
42582491 AATGCAAATGCATGAAATG-
1 AATGCAAATG-ATGAAATGC
42582510 AATGCAAA
1 AATGCAAA
42582518 AGAAAAAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.46, C:0.13, G:0.22, T:0.20
Consensus pattern (19 bp):
AATGCAAATGATGAAATGC
Found at i:42587305 original size:18 final size:17
Alignment explanation
Indices: 42587274--42587307 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
42587264 TATAAGTGAT
*
42587274 TTTTTTAATTTATATTG
1 TTTTTAAATTTATATTG
42587291 TTTTTAAATTATATATT
1 TTTTTAAATT-TATATT
42587308 AAATAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (17 bp):
TTTTTAAATTTATATTG
Found at i:42592678 original size:91 final size:88
Alignment explanation
Indices: 42592494--42592744 Score: 398
Period size: 86 Copynumber: 2.8 Consensus size: 88
42592484 TTTTGAAGAT
* * *
42592494 ATTATTTTATTTTAGTTTAATCACGATAAATATTTTGTCTACTTTTATTTTAATTTTAAATTACC
1 ATTATTTTATTTTATTTTAATCACGAAAAATATTTTGTCTACTTTTATTTTATTTTTAAATTACC
42592559 TAATTAAATTAAATTGTATTTAA
66 TAATTAAATTAAATTGTATTTAA
* * *
42592582 A--ATTTTATTTTATTTTAACCAGGAAAAATATTTTGTCTACATTTATTTTATTTTTAAATTACC
1 ATTATTTTATTTTATTTTAATCACGAAAAATATTTTGTCTACTTTTATTTTATTTTTAAATTACC
42592645 TAATTAAATTAAATTGTATTTAAA
66 TAATTAAATTAAATTGTATTT-AA
*
42592669 ATTTTATTTTATTTTATTTTAATCACGAAAAATATTTTTTCTACTTTTATTTTATTTTTAAATTA
1 A--TTATTTTATTTTATTTTAATCACGAAAAATATTTTGTCTACTTTTATTTTATTTTTAAATTA
42592734 CCTAATTAAAT
64 CCTAATTAAAT
42592745 AATCATTATT
Statistics
Matches: 148, Mismatches: 10, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
86 77 0.52
87 3 0.02
88 1 0.01
91 67 0.45
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.54
Consensus pattern (88 bp):
ATTATTTTATTTTATTTTAATCACGAAAAATATTTTGTCTACTTTTATTTTATTTTTAAATTACC
TAATTAAATTAAATTGTATTTAA
Found at i:42592904 original size:9 final size:9
Alignment explanation
Indices: 42592888--42592941 Score: 54
Period size: 9 Copynumber: 6.0 Consensus size: 9
42592878 ATATCATATC
42592888 TTACATAAT
1 TTACATAAT
*
42592897 TTACATAAG
1 TTACATAAT
* * *
42592906 ATAAATAAC
1 TTACATAAT
42592915 TTACATAAT
1 TTACATAAT
*
42592924 TTACATAAC
1 TTACATAAT
*
42592933 CTACATAAT
1 TTACATAAT
42592942 ACATAAATAT
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.48, C:0.15, G:0.02, T:0.35
Consensus pattern (9 bp):
TTACATAAT
Found at i:42592931 original size:18 final size:18
Alignment explanation
Indices: 42592888--42592941 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
42592878 ATATCATATC
* *
42592888 TTACATAATTTACATAAG
1 TTACATAACTTACATAAT
* *
42592906 ATAAATAACTTACATAAT
1 TTACATAACTTACATAAT
*
42592924 TTACATAACCTACATAAT
1 TTACATAACTTACATAAT
42592942 ACATAAATAT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.48, C:0.15, G:0.02, T:0.35
Consensus pattern (18 bp):
TTACATAACTTACATAAT
Found at i:42592940 original size:27 final size:27
Alignment explanation
Indices: 42592882--42592947 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
42592872 AAATATATAT
* *
42592882 CATATCTTACATAATTTACATAAGATA
1 CATAACTTACATAATTTACATAACATA
* *
42592909 AATAACTTACATAATTTACATAACCTA
1 CATAACTTACATAATTTACATAACATA
42592936 CATAA--TACATAA
1 CATAACTTACATAA
42592948 ATATATATCA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
25 7 0.21
27 27 0.79
ACGTcount: A:0.48, C:0.17, G:0.02, T:0.33
Consensus pattern (27 bp):
CATAACTTACATAATTTACATAACATA
Found at i:42598024 original size:13 final size:14
Alignment explanation
Indices: 42598008--42598036 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
42597998 TTATTCTAAA
42598008 TATTTATAATT-TT
1 TATTTATAATTGTT
42598021 TATTTATAATTGTT
1 TATTTATAATTGTT
42598035 TA
1 TA
42598037 ATTCAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (14 bp):
TATTTATAATTGTT
Found at i:42598977 original size:43 final size:42
Alignment explanation
Indices: 42598916--42599076 Score: 171
Period size: 43 Copynumber: 3.8 Consensus size: 42
42598906 AAAAACGTCA
* * * * *
42598916 CTAAAAGTCATGGCTTTTATCGGCACTTTTTGCACAAACACCG
1 CTAAAAGTCATGACTTTTAGCGGCGCTTTTT-TACAAACGCCG
* * **
42598959 CTAAAAGCCATGACTTTTAGCGGTGCTTTTTTACAAACGTAG
1 CTAAAAGTCATGACTTTTAGCGGCGCTTTTTTACAAACGCCG
* *
42599001 CTAAAATTCATTACTTTTAGCGGCGCTTTTTTTACAAACGCCG
1 CTAAAAGTCATGACTTTTAGCGGCGC-TTTTTTACAAACGCCG
* *
42599044 CTAAAAGTTATGGCTTTTAGCGGCG-TTTATTTA
1 CTAAAAGTCATGACTTTTAGCGGCGCTTT-TTTA
42599077 AATAAACACC
Statistics
Matches: 97, Mismatches: 19, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
41 3 0.03
42 33 0.34
43 61 0.63
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.35
Consensus pattern (42 bp):
CTAAAAGTCATGACTTTTAGCGGCGCTTTTTTACAAACGCCG
Found at i:42602508 original size:46 final size:46
Alignment explanation
Indices: 42602449--42602575 Score: 163
Period size: 46 Copynumber: 2.8 Consensus size: 46
42602439 CATCGATATT
*
42602449 GAGACG-AGAGCTAGTGTAAGACATGTCTAGGACATGTATTGGCCT-C
1 GAGACGTA-AGCTAGTGTAAGACATGTCTAGGACATGCATTGG-CTAC
42602495 GAGACGTAAGCTAGTGTAAGACATGTCTAGGACATGCATTGGCTAC
1 GAGACGTAAGCTAGTGTAAGACATGTCTAGGACATGCATTGGCTAC
* * *
42602541 GAGATGT--GTTAGTGTAAGACCATGTCTGGGACATG
1 GAGACGTAAGCTAGTGTAAGA-CATGTCTAGGACATG
42602576 GCAGCGGCAC
Statistics
Matches: 74, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
44 11 0.15
45 16 0.22
46 46 0.62
47 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.31, T:0.25
Consensus pattern (46 bp):
GAGACGTAAGCTAGTGTAAGACATGTCTAGGACATGCATTGGCTAC
Found at i:42608083 original size:17 final size:17
Alignment explanation
Indices: 42608061--42608094 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
42608051 TTGTTGATTC
42608061 AATTTTGGAATTGTCTT
1 AATTTTGGAATTGTCTT
42608078 AATTTTGGAATTGTCTT
1 AATTTTGGAATTGTCTT
42608095 TCTTTCTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.06, G:0.18, T:0.53
Consensus pattern (17 bp):
AATTTTGGAATTGTCTT
Found at i:42608104 original size:21 final size:21
Alignment explanation
Indices: 42608080--42608120 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
42608070 ATTGTCTTAA
*
42608080 TTTTGGAATTGTCTTTCTTTC
1 TTTTGGAATTGTCTTCCTTTC
42608101 TTTTGGAATTGTCTTCCTTT
1 TTTTGGAATTGTCTTCCTTT
42608121 GTTGGACCTC
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:0.10, C:0.15, G:0.15, T:0.61
Consensus pattern (21 bp):
TTTTGGAATTGTCTTCCTTTC
Found at i:42608120 original size:17 final size:17
Alignment explanation
Indices: 42608063--42608120 Score: 62
Period size: 17 Copynumber: 3.2 Consensus size: 17
42608053 GTTGATTCAA
**
42608063 TTTTGGAATTGTCTTAA
1 TTTTGGAATTGTCTTCC
42608080 TTTTGGAATTGTCTTTCTTTC
1 TTTTGGAATTGTC-TTC---C
42608101 TTTTGGAATTGTCTTCC
1 TTTTGGAATTGTCTTCC
42608118 TTT
1 TTT
42608121 GTTGGACCTC
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
17 17 0.49
18 2 0.06
20 3 0.09
21 13 0.37
ACGTcount: A:0.14, C:0.12, G:0.16, T:0.59
Consensus pattern (17 bp):
TTTTGGAATTGTCTTCC
Found at i:42610034 original size:20 final size:20
Alignment explanation
Indices: 42610003--42610064 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
42609993 GTTTGATGTG
*
42610003 TTAAAATGATTTTAACTTGA
1 TTAAAATAATTTTAACTTGA
* * *
42610023 TTGAAATCATTTTGACTTCG-
1 TTAAAATAATTTTAACTT-GA
*
42610043 TTAAAATAATTTTCACTTGA
1 TTAAAATAATTTTAACTTGA
42610063 TT
1 TT
42610065 TTAAAATTGT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
19 1 0.03
20 32 0.94
21 1 0.03
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.47
Consensus pattern (20 bp):
TTAAAATAATTTTAACTTGA
Found at i:42612328 original size:80 final size:79
Alignment explanation
Indices: 42612180--42612376 Score: 252
Period size: 80 Copynumber: 2.5 Consensus size: 79
42612170 ACCCAAGTTT
* * * * * * * *
42612180 CTTCGGAAT-TTAGCCGGATATAACCACAAGCACAAATGCCTTCGGGTCTTAGCCTGGATTTAGT
1 CTTCGG-ATCTTAGCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGATATAGC
*
42612244 AACTCGCACAAAAGC
65 AACTCACACAAAAGC
*
42612259 CTTCGGATCTTAGTCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGC
1 CTTCGGATCTTAG-CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGATATAGC
*
42612324 AACTCACACAAATGC
65 AACTCACACAAAAGC
*
42612339 CTTCGGGTCTTAGCCCGGATAAAATCACTAGCACAATT
1 CTTCGGATCTTAG-CCGGATAAAATCACTAGCACAATT
42612377 TGTAACACCC
Statistics
Matches: 103, Mismatches: 13, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
78 2 0.02
79 10 0.10
80 91 0.88
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.25
Consensus pattern (79 bp):
CTTCGGATCTTAGCCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTAACCCGGATATAGCA
ACTCACACAAAAGC
Found at i:42612374 original size:40 final size:40
Alignment explanation
Indices: 42612189--42612374 Score: 180
Period size: 40 Copynumber: 4.7 Consensus size: 40
42612179 TCTTCGGAAT
* * *
42612189 TTAG-CCGGATATAACCACAAGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTC
* ** * * * * *
42612228 TTAGCCTGGATTTAGTAACTCGCACAAAAGCCTTCGGATC
1 TTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTC
* *
42612268 TTAGTCCGGATAAAATCACTAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTC
* * * *
42612308 TTAACCCGGGT-ATAGCAACTCA-CACAAATGCCTTCGGGTC
1 TTAGCCCGGATAAAATC-ACT-AGCACAAATGCCTTCGGGTC
42612348 TTAGCCCGGATAAAATCACTAGCACAA
1 TTAGCCCGGATAAAATCACTAGCACAA
42612375 TTTGTAACAC
Statistics
Matches: 113, Mismatches: 29, Indels: 9
0.75 0.19 0.06
Matches are distributed among these distances:
39 8 0.07
40 101 0.89
41 4 0.04
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (40 bp):
TTAGCCCGGATAAAATCACTAGCACAAATGCCTTCGGGTC
Found at i:42613904 original size:119 final size:120
Alignment explanation
Indices: 42613722--42613944 Score: 308
Period size: 119 Copynumber: 1.9 Consensus size: 120
42613712 TCCTCGTTCA
*
42613722 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
* * *
42613787 TTTGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATGGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* * * **
42613842 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTCGGGTCTTAGTCCGGA
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
* *
42613905 TATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
65 TATGGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
42613945 CACCATTCAA
Statistics
Matches: 90, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
118 1 0.01
119 69 0.77
120 20 0.22
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATGGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:42613944 original size:40 final size:40
Alignment explanation
Indices: 42613720--42613944 Score: 285
Period size: 40 Copynumber: 5.7 Consensus size: 40
42613710 GCTCCTCGTT
* *
42613720 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * *
42613760 CAAATGCCTTCGGGACTTAACCCGGATTTTGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
42613800 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
42613840 CCAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * * *
42613879 CAAATGCCTTCGGGTCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAAC-TCGCA
42613920 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
42613945 CACCATTCAA
Statistics
Matches: 163, Mismatches: 18, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
39 34 0.21
40 120 0.74
41 9 0.06
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:42621860 original size:39 final size:40
Alignment explanation
Indices: 42621703--42621927 Score: 260
Period size: 40 Copynumber: 5.7 Consensus size: 40
42621693 GCTCGTCGTT
* *
42621703 CAAATGCCTTCGGGACATATCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
* *
42621743 CAAATGCCTTCGGGACTTAACTCGGATTTTGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
42621783 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
42621823 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
42621862 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
42621903 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
42621928 CATCATTCAA
Statistics
Matches: 161, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
38 2 0.01
39 32 0.20
40 114 0.71
41 13 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:42621888 original size:119 final size:120
Alignment explanation
Indices: 42621705--42621927 Score: 285
Period size: 119 Copynumber: 1.9 Consensus size: 120
42621695 TCGTCGTTCA
* *
42621705 AATGCCTTCGGGACATATCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACTCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACTCGGAT
* * *
42621770 TTTGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATGGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* * *
42621825 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTT-AGTCCG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACT-CG
* *
42621886 GATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
63 GATATGGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
42621928 CATCATTCAA
Statistics
Matches: 89, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
118 6 0.07
119 63 0.71
120 20 0.22
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACTCGGAT
ATGGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:42630056 original size:12 final size:12
Alignment explanation
Indices: 42630041--42630074 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
42630031 GCCGCCAAGG
*
42630041 CCACCACCAACT
1 CCACCTCCAACT
*
42630053 CCACCTCCACCT
1 CCACCTCCAACT
42630065 CCACCTCCAA
1 CCACCTCCAA
42630075 GACCGGTTCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.62, G:0.00, T:0.12
Consensus pattern (12 bp):
CCACCTCCAACT
Found at i:42630431 original size:24 final size:24
Alignment explanation
Indices: 42630403--42630454 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
42630393 CATCATGTCC
*
42630403 TTTAGAAACCTTAATCTATGACCT
1 TTTAGAAACCTTAATCTAAGACCT
*
42630427 TTTAGAAACCTTAATTTAAGACCT
1 TTTAGAAACCTTAATCTAAGACCT
42630451 TTTA
1 TTTA
42630455 ATGAACTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.35, C:0.17, G:0.08, T:0.40
Consensus pattern (24 bp):
TTTAGAAACCTTAATCTAAGACCT
Found at i:42633320 original size:13 final size:13
Alignment explanation
Indices: 42633302--42633327 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42633292 TTTTGTACTG
42633302 AATAAGTGGATGT
1 AATAAGTGGATGT
42633315 AATAAGTGGATGT
1 AATAAGTGGATGT
42633328 GGTTGTGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (13 bp):
AATAAGTGGATGT
Found at i:42635490 original size:22 final size:22
Alignment explanation
Indices: 42635464--42635508 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
42635454 ATTATATGTA
42635464 TTAATTCATAATATAA-TTAATT
1 TTAATTCAT-ATATAAGTTAATT
* *
42635486 TTAATTTATATCTAAGTTAATT
1 TTAATTCATATATAAGTTAATT
42635508 T
1 T
42635509 GGGTTAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (22 bp):
TTAATTCATATATAAGTTAATT
Found at i:42652897 original size:19 final size:17
Alignment explanation
Indices: 42652863--42652904 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
42652853 GTAAGACCGT
42652863 ATTTTTTCTTAAATTTTA
1 ATTTTTTCTTAAA-TTTA
42652881 ATTTTATTC-TAATATTTA
1 ATTTT-TTCTTAA-ATTTA
42652899 ATTTTT
1 ATTTTT
42652905 CAATTTATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 1 0.05
18 17 0.77
19 4 0.18
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTTTTTCTTAAATTTA
Found at i:42658288 original size:20 final size:18
Alignment explanation
Indices: 42658245--42658279 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42658235 TTCTTGTCAA
**
42658245 AAAATAATTAATTTGCAT
1 AAAATAATTAAAGTGCAT
42658263 AAAATAATTAAAGTGCA
1 AAAATAATTAAAGTGCA
42658280 CTTAAAATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.06, G:0.09, T:0.31
Consensus pattern (18 bp):
AAAATAATTAAAGTGCAT
Found at i:42661749 original size:16 final size:16
Alignment explanation
Indices: 42661728--42661759 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
42661718 ATGAAATAGC
*
42661728 ATAAATAAACAATTAA
1 ATAAATAAAAAATTAA
42661744 ATAAATAAAAAATTAA
1 ATAAATAAAAAATTAA
42661760 GTTAAATTGG
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:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (16 bp):
ATAAATAAAAAATTAA
Found at i:42664736 original size:40 final size:39
Alignment explanation
Indices: 42664692--42664877 Score: 232
Period size: 40 Copynumber: 4.7 Consensus size: 39
42664682 AAGTGACCAT
42664692 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAA
1 ATCCGGACTAAG-TCCGAAGGCATTTGTGCGAGATACTAA
42664732 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAA
1 ATCCGGACTAAG-TCCGAAGGCATTTGTGCGAGATACTAA
* * * *
42664772 TTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 ATCCGGACTAAGTCCGAAGGCATTTGTGCGAGATACTAA
** *
42664811 ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
1 ATCCGGACTAAGT-CCGAAGGCATTTGTGCGAGATACTA-A
*
42664852 A-CCAGG-CTATGTCCCGAAGGCATTTG
1 ATCC-GGACTAAGT-CCGAAGGCATTTG
42664878 AACGAGGAGC
Statistics
Matches: 134, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
39 35 0.26
40 95 0.71
41 4 0.03
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (39 bp):
ATCCGGACTAAGTCCGAAGGCATTTGTGCGAGATACTAA
Found at i:42664809 original size:79 final size:80
Alignment explanation
Indices: 42664659--42664877 Score: 245
Period size: 79 Copynumber: 2.8 Consensus size: 80
42664649 GATGTCCAGG
* * *
42664659 CTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATATCC-GGACTAAGAT-CCGAAGGCATTTGT
1 CTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTATAACCAGG-CTAAG-TCCCGAAGGCATTTGT
42664720 GCGAGATACTAAATCCGGA
62 GCGAGATACTAAATCCGGA
* *
42664739 CTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATTCCGGGCTAAG-CCCGAAGGCATTTGTGC
1 CTAAG-TCCCGAAGGCATTTGTGCGAGATACTATA-ACCAGGCTAAGTCCCGAAGGCATTTGTGC
* *
42664801 GAGTTACTAAATCCGGG
64 GAGATACTAAATCCGGA
* * *
42664818 TTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCAGGCTATGTCCCGAAGGCATTTG
1 CTAAGTCCCGAAGGCATTTGTGCGAGATACTATAACCAGGCTAAGTCCCGAAGGCATTTG
42664878 AACGAGGAGC
Statistics
Matches: 121, Mismatches: 9, Indels: 18
0.82 0.06 0.12
Matches are distributed among these distances:
78 1 0.01
79 68 0.56
80 39 0.32
81 12 0.10
82 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (80 bp):
CTAAGTCCCGAAGGCATTTGTGCGAGATACTATAACCAGGCTAAGTCCCGAAGGCATTTGTGCGA
GATACTAAATCCGGA
Found at i:42664896 original size:119 final size:120
Alignment explanation
Indices: 42664657--42664883 Score: 277
Period size: 119 Copynumber: 1.9 Consensus size: 120
42664647 ATGATGTCCA
*
42664657 GGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTTGTGC
1 GGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTTGTGC
**
42664722 GAGATACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAATTCCG
66 GAGATACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGATACTAATTCCG
* * * **
42664777 GGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATTTGT
1 GGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCATTTGT
* *
42664839 GCGAGTTACTATAA-CCAGG-CTATG-TCCCGAAGGCATTTGAACGAG
64 GCGAGATACTA-AATCC-GGACTAAGAT-CCGAAGGCATTTGAACGAG
42664884 GAGCTATATC
Statistics
Matches: 92, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
118 2 0.02
119 72 0.78
120 18 0.20
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (120 bp):
GGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTTGTGC
GAGATACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGATACTAATTCCG
Found at i:42664899 original size:79 final size:79
Alignment explanation
Indices: 42664706--42664900 Score: 202
Period size: 79 Copynumber: 2.5 Consensus size: 79
42664696 GGACTAAGAT
** **
42664706 CCGAAGGCATTTGTGCGAGAT-ACTAAATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC
1 CCGAAGGCATTTGAACGAG-TGACTAAATCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGATAC
* *
42664769 TAATTCCGGGCTAAGC
64 TAATACCAGGCTAAGC
** * *
42664785 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-
1 CCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTA
*
42664849 ATAACCAGGCTATGTC
66 AT-ACCAGGCTAAG-C
*
42664865 CCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAA
1 CCGAAGGCATTTGAACGAGTGA-CTAAATCCGGGTTAA
42664901 ACTCCGAAGG
Statistics
Matches: 101, Mismatches: 10, Indels: 10
0.83 0.08 0.08
Matches are distributed among these distances:
78 4 0.04
79 72 0.71
80 25 0.25
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTA
ATACCAGGCTAAGC
Found at i:42679131 original size:6 final size:6
Alignment explanation
Indices: 42679087--42679137 Score: 52
Period size: 6 Copynumber: 8.5 Consensus size: 6
42679077 AAAGTCTAAG
* *
42679087 AAAATA ACAATA AACATA AAAATA GAAAA-A AAAACTA AAAAT- AAAATA
1 AAAATA AAAATA AAAATA AAAATA -AAAATA AAAA-TA AAAATA AAAATA
42679135 AAA
1 AAA
42679138 TGAATAGACT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
5 9 0.24
6 19 0.51
7 9 0.24
ACGTcount: A:0.78, C:0.06, G:0.02, T:0.14
Consensus pattern (6 bp):
AAAATA
Found at i:42680593 original size:23 final size:28
Alignment explanation
Indices: 42680538--42680596 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 28
42680528 ACTAATAATG
*
42680538 AGCAATAATAATCATAAAGAAGTAGACT
1 AGCAAGAATAATCATAAAGAAGTAGACT
42680566 AGCAAGAATAAT-ATAAA-AA-TAG-C-
1 AGCAAGAATAATCATAAAGAAGTAGACT
42680589 AGCAAGAA
1 AGCAAGAA
42680597 ACAAGTAAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 8 0.27
24 1 0.03
25 3 0.10
26 2 0.07
27 5 0.17
28 11 0.37
ACGTcount: A:0.58, C:0.10, G:0.15, T:0.17
Consensus pattern (28 bp):
AGCAAGAATAATCATAAAGAAGTAGACT
Found at i:42681040 original size:12 final size:13
Alignment explanation
Indices: 42681017--42681045 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
42681007 GCGCGGGAAA
42681017 GAAAAAGAAAAGG
1 GAAAAAGAAAAGG
42681030 GAAAAAG-AAAGG
1 GAAAAAGAAAAGG
42681042 GAAA
1 GAAA
42681046 GGTCTGGTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (13 bp):
GAAAAAGAAAAGG
Found at i:42694497 original size:22 final size:22
Alignment explanation
Indices: 42694470--42694514 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
42694460 GAGTTAAAGG
42694470 TAAATCATTAGAAAGAAGAAAA
1 TAAATCATTAGAAAGAAGAAAA
42694492 TAAATCATTAGAAAGAAGAAAA
1 TAAATCATTAGAAAGAAGAAAA
42694514 T
1 T
42694515 GACTTCACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.62, C:0.04, G:0.13, T:0.20
Consensus pattern (22 bp):
TAAATCATTAGAAAGAAGAAAA
Found at i:42697500 original size:34 final size:34
Alignment explanation
Indices: 42697456--42697537 Score: 114
Period size: 34 Copynumber: 2.4 Consensus size: 34
42697446 TTAGCCCCTT
*
42697456 TTTCAATAACAGTATCAGTCTGGGCCTGAGCCCA
1 TTTCAGTAACAGTATCAGTCTGGGCCTGAGCCCA
* *
42697490 TTTCAGTAACAG-AGGCAGTCTGGGCCTTAGCCCA
1 TTTCAGTAACAGTA-TCAGTCTGGGCCTGAGCCCA
42697524 TTTCAGT-ACAGTAT
1 TTTCAGTAACAGTAT
42697538 GCAAACAAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
33 5 0.12
34 37 0.88
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (34 bp):
TTTCAGTAACAGTATCAGTCTGGGCCTGAGCCCA
Found at i:42700778 original size:28 final size:28
Alignment explanation
Indices: 42700734--42700788 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
42700724 CCCAAAAACT
42700734 CATCCTCTAACTATTTACTCTTAATCTA
1 CATCCTCTAACTATTTACTCTTAATCTA
* *
42700762 CATCCTCTAATTGTTTACTCTTAATCT
1 CATCCTCTAACTATTTACTCTTAATCT
42700789 GCTCAATCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.25, C:0.27, G:0.02, T:0.45
Consensus pattern (28 bp):
CATCCTCTAACTATTTACTCTTAATCTA
Found at i:42707374 original size:46 final size:45
Alignment explanation
Indices: 42707271--42707442 Score: 176
Period size: 46 Copynumber: 3.8 Consensus size: 45
42707261 ACATTATGAG
*
42707271 AGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCATTGAGA-T
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC-TTGAGAGT
*
42707316 GAGCACTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGTCTTGATACGT
1 -AGC-C-AGTGTAAGACCATGTCTGGGACATGGCATCGG-CTTGAGA-GT
* *
42707364 AAGCCAGTGTAAGA-CATGTTTGGGACAT-GCATCGGCTACGAGATGT
1 -AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCT-TGAGA-GT
*
42707410 -GTCAGTGTAAGACCATGTCTGGGACATGGCATC
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATC
42707443 AGCACAGATA
Statistics
Matches: 109, Mismatches: 9, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
44 11 0.10
45 15 0.14
46 54 0.50
47 16 0.15
48 13 0.12
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (45 bp):
AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTTGAGAGT
Found at i:42707472 original size:50 final size:50
Alignment explanation
Indices: 42707414--42707546 Score: 230
Period size: 50 Copynumber: 2.7 Consensus size: 50
42707404 AGATGTGTCA
*
42707414 GTGTAAGACCATGTCTGGGACATGGCATCAGCACAGATATACTAGATATT
1 GTGTAAGACCATGTCTGGGACATGGCATCAGCACAGATATACTAGAGATT
* * *
42707464 GTGTAAGACCATGTTTGGGACATGGCATCAGCACATATATACTAGAGCTT
1 GTGTAAGACCATGTCTGGGACATGGCATCAGCACAGATATACTAGAGATT
42707514 GTGTAAGACCATGTCTGGGACATGGCATCAGCA
1 GTGTAAGACCATGTCTGGGACATGGCATCAGCA
42707547 TCTGACCCAT
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 78 1.00
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.26
Consensus pattern (50 bp):
GTGTAAGACCATGTCTGGGACATGGCATCAGCACAGATATACTAGAGATT
Found at i:42711710 original size:21 final size:21
Alignment explanation
Indices: 42711682--42711733 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
42711672 ATTTTCCTAA
42711682 GATG-TAAATTGGATTGAA-TT
1 GATGTTAAATTGGATT-AACTT
* *
42711702 GATTTTAAATTGTATTAACTT
1 GATGTTAAATTGGATTAACTT
42711723 GATGTTAAATT
1 GATGTTAAATT
42711734 TACTCGTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.19
21 22 0.81
ACGTcount: A:0.35, C:0.02, G:0.17, T:0.46
Consensus pattern (21 bp):
GATGTTAAATTGGATTAACTT
Found at i:42712801 original size:26 final size:26
Alignment explanation
Indices: 42712762--42712812 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
42712752 ATTATGAAAA
*
42712762 TATACTTGTAATATAAATATATGATT
1 TATACATGTAATATAAATATATGATT
* * *
42712788 TATACATGTTATATGAATATGTGAT
1 TATACATGTAATATAAATATATGAT
42712813 ACGAAATGTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.39, C:0.04, G:0.12, T:0.45
Consensus pattern (26 bp):
TATACATGTAATATAAATATATGATT
Found at i:42718387 original size:21 final size:21
Alignment explanation
Indices: 42718359--42718410 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
42718349 ATTTTCCTAA
*
42718359 GATG-TAAATTCG-ATTGAATT
1 GATGTTAAATT-GTATTAAATT
42718379 GA-GTTTAAATTGTATTAAATT
1 GATG-TTAAATTGTATTAAATT
42718400 GATGTTAAATT
1 GATGTTAAATT
42718411 TAATCGTATG
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
19 1 0.04
20 3 0.11
21 22 0.81
22 1 0.04
ACGTcount: A:0.37, C:0.02, G:0.17, T:0.44
Consensus pattern (21 bp):
GATGTTAAATTGTATTAAATT
Found at i:42722226 original size:61 final size:59
Alignment explanation
Indices: 42722147--42722314 Score: 189
Period size: 60 Copynumber: 2.8 Consensus size: 59
42722137 CCTTAGAAAA
* * * * * *
42722147 ATTTTAATATGATAATTATTGAATATACTTTAATAAAAAATAATAAAAATAATTTAATCAT
1 ATTTTAATATAATTATTATTAAATATAATTTAATAAAAAATAAT--AAATAATTTAATAAC
**
42722208 ATTTTAATATAATTATTATTAAATATAATTTAAT-AAAAATAATATTTAATTTAATAAC
1 ATTTTAATATAATTATTATTAAATATAATTTAATAAAAAATAATAAATAATTTAATAAC
* *
42722266 ATTCTCAATATAATTATTATTAAAATATAAATTAAT-AAAAATAA-AAATA
1 ATT-TTAATATAATTATTATT-AAATATAATTTAATAAAAAATAATAAATA
42722315 TATAATATAT
Statistics
Matches: 93, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
58 14 0.15
59 19 0.20
60 30 0.32
61 30 0.32
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (59 bp):
ATTTTAATATAATTATTATTAAATATAATTTAATAAAAAATAATAAATAATTTAATAAC
Found at i:42722239 original size:26 final size:26
Alignment explanation
Indices: 42722210--42722302 Score: 71
Period size: 29 Copynumber: 3.3 Consensus size: 26
42722200 TTAATCATAT
42722210 TTTAATATAATTATTATTAAATATAA
1 TTTAATATAATTATTATTAAATATAA
* *
42722236 TTTAATAAAAATAATATTTAATTTAATA-ACA
1 TTTAAT-ATAAT--TA-TT-ATTAAATATA-A
42722267 TTCTCAATATAATTATTATTAAAATATAA
1 TT-T-AATATAATTATTATT-AAATATAA
*
42722296 ATTAATA
1 TTTAATA
42722303 AAAATAAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 19
0.68 0.07 0.25
Matches are distributed among these distances:
26 6 0.12
27 8 0.15
28 4 0.08
29 10 0.19
30 6 0.12
31 10 0.19
32 5 0.10
33 3 0.06
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (26 bp):
TTTAATATAATTATTATTAAATATAA
Found at i:42731167 original size:65 final size:65
Alignment explanation
Indices: 42731063--42731185 Score: 201
Period size: 65 Copynumber: 1.9 Consensus size: 65
42731053 GGCAAAGCAC
*
42731063 GGGAAACAAGTTGAACAAAGCTAAAACACAAATGGAAAGGACTCAAACCTTTCGGTTACTAATAT
1 GGGAAACAAGATGAACAAAGCTAAAACACAAATGGAAAGGACTCAAACCTTTCGGTTACTAATAT
** **
42731128 GGGAAACAAGATGAACAAAGCTAAAACATGAATGGAAAGGACTTGAACCTTTCGGTTA
1 GGGAAACAAGATGAACAAAGCTAAAACACAAATGGAAAGGACTCAAACCTTTCGGTTA
42731186 TTAGCATGAA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
65 53 1.00
ACGTcount: A:0.44, C:0.15, G:0.21, T:0.20
Consensus pattern (65 bp):
GGGAAACAAGATGAACAAAGCTAAAACACAAATGGAAAGGACTCAAACCTTTCGGTTACTAATAT
Found at i:42731469 original size:3 final size:3
Alignment explanation
Indices: 42731463--42731490 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
42731453 AAAAGGGTAA
42731463 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
42731491 TCGTCACTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:42736804 original size:22 final size:23
Alignment explanation
Indices: 42736753--42736805 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
42736743 AGAAAACCAT
42736753 TTTAT-GTGTTAAATGCTGAAAA
1 TTTATGGTGTTAAATGCTGAAAA
*
42736775 TTTA-GGTGTTAAATGCTG-CAA
1 TTTATGGTGTTAAATGCTGAAAA
42736796 TTTATGGTGT
1 TTTATGGTGT
42736806 CTGAAAGTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 6 0.21
22 22 0.79
ACGTcount: A:0.28, C:0.06, G:0.23, T:0.43
Consensus pattern (23 bp):
TTTATGGTGTTAAATGCTGAAAA
Found at i:42737659 original size:10 final size:10
Alignment explanation
Indices: 42737646--42737681 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
42737636 TTTTCATGAC
*
42737646 TTTTACAATA
1 TTTTATAATA
42737656 TTTTATAATA
1 TTTTATAATA
42737666 TTTTATAATA
1 TTTTATAATA
42737676 TTTTAT
1 TTTTAT
42737682 TTTTTTTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (10 bp):
TTTTATAATA
Found at i:42737822 original size:43 final size:43
Alignment explanation
Indices: 42737702--42737885 Score: 248
Period size: 43 Copynumber: 4.3 Consensus size: 43
42737692 TTTTATGACC
* *
42737702 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCCCAG-CT
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGT-CAAGACT
** * *
42737745 TTTAATGGCGTTTGT-GGAGAAGCGCCGCTAAAGGTCACA-ATT
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCA-AGACT
42737787 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCAAGACT
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCAAGACT
* *
42737830 TTTAGCGGCGTTTGTGAGAAAAGCGCCGTTAAAGGTCAAGACT
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCAAGACT
*
42737873 TTTAGCGGTGTTT
1 TTTAGCGGCGTTT
42737886 TTTAAAATAA
Statistics
Matches: 124, Mismatches: 13, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
41 1 0.01
42 34 0.27
43 89 0.72
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.27
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCAAGACT
Found at i:42737845 original size:85 final size:86
Alignment explanation
Indices: 42737702--42737885 Score: 257
Period size: 85 Copynumber: 2.2 Consensus size: 86
42737692 TTTTATGACC
* * *
42737702 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCCCAGCTTTTAATGGCGTTTGTG-GAGAA
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCCAAGCTTTTAACGGCGTTTGTGAGAAAA
*
42737766 GCGCCGCTAAAGGTCACA-ATT
66 GCGCCGCTAAAGGTCA-AGACT
* *
42737787 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGT-CAAGACTTTTAGCGGCGTTTGTGAGAAA
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCCAAG-CTTTTAACGGCGTTTGTGAGAAA
*
42737851 AGCGCCGTTAAAGGTCAAGACT
65 AGCGCCGCTAAAGGTCAAGACT
*
42737873 TTTAGCGGTGTTT
1 TTTAGCGGCGTTT
42737886 TTTAAAATAA
Statistics
Matches: 88, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
84 3 0.03
85 52 0.59
86 33 0.38
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.27
Consensus pattern (86 bp):
TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCCAAGCTTTTAACGGCGTTTGTGAGAAAA
GCGCCGCTAAAGGTCAAGACT
Found at i:42738060 original size:10 final size:10
Alignment explanation
Indices: 42738045--42738074 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
42738035 AATTTGATTG
42738045 TTTTTTTAAA
1 TTTTTTTAAA
42738055 TTTTTTTAAA
1 TTTTTTTAAA
*
42738065 TTTATTTAAA
1 TTTTTTTAAA
42738075 AAAATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTTTTTAAA
Found at i:42742956 original size:48 final size:46
Alignment explanation
Indices: 42742899--42743022 Score: 146
Period size: 48 Copynumber: 2.7 Consensus size: 46
42742889 ATATTCATAC
* *
42742899 CGATGCCATGTCCCAGACATGGTCTTACACTGACACAT-TTATACGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTAACACATCTCATA-GT
* * *
42742945 GCTGATGCCATGTCCCAGATATGGTTTTACACTAACACATCTCGTAGT
1 -C-GATGCCATGTCCCAGACATGGTCTTACACTAACACATCTCATAGT
*
42742993 CGATG-CATGTCCCAGACAT-GTCCTACACTA
1 CGATGCCATGTCCCAGACATGGTCTTACACTA
42743023 GCTCTCGACT
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
44 9 0.13
45 13 0.19
46 4 0.06
47 2 0.03
48 36 0.54
49 3 0.04
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (46 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTAACACATCTCATAGT
Found at i:42743057 original size:47 final size:45
Alignment explanation
Indices: 42742995--42743118 Score: 144
Period size: 47 Copynumber: 2.7 Consensus size: 45
42742985 CTCGTAGTCG
* *
42742995 ATGCATGTCCCAGACATGTCCTACACTAGCTCTCGACTCAA-T-GCCA
1 ATGCATGTCCTAGACATGTCTTACACTAGCTCTC-A-T-AAGTGGCCA
* *
42743041 ATGCCATGTCCTAGACATGGTCTTACACTGGCTCTCATAATGTGGCCG
1 ATG-CATGTCCTAGACAT-GTCTTACACTAGCTCTCATAA-GTGGCCA
42743089 ATGCATGTCCTAGACATGTCTTACACTAGC
1 ATGCATGTCCTAGACATGTCTTACACTAGC
42743119 ACACAAATAA
Statistics
Matches: 68, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
45 2 0.03
46 16 0.24
47 29 0.43
48 21 0.31
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (45 bp):
ATGCATGTCCTAGACATGTCTTACACTAGCTCTCATAAGTGGCCA
Found at i:42744277 original size:11 final size:10
Alignment explanation
Indices: 42744249--42744282 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
42744239 AGCCTGTAAG
42744249 TATTCTGAAT
1 TATTCTGAAT
*
42744259 TTTTCTGAAT
1 TATTCTGAAT
42744269 ATATTCTGAAT
1 -TATTCTGAAT
42744280 TAT
1 TAT
42744283 CTGTCTGTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.53
Consensus pattern (10 bp):
TATTCTGAAT
Found at i:42749482 original size:24 final size:24
Alignment explanation
Indices: 42749455--42749501 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
42749445 TTGTCAGGAG
**
42749455 AGGATTTAAGAGTTGATAAGGGAT
1 AGGATTTAAGAGCAGATAAGGGAT
*
42749479 AGGATTTAGGAGCAGATAAGGGA
1 AGGATTTAAGAGCAGATAAGGGA
42749502 GGAAATCTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.38, C:0.02, G:0.36, T:0.23
Consensus pattern (24 bp):
AGGATTTAAGAGCAGATAAGGGAT
Found at i:42750955 original size:27 final size:27
Alignment explanation
Indices: 42750915--42751019 Score: 106
Period size: 27 Copynumber: 3.9 Consensus size: 27
42750905 AGGAAGCGTC
*
42750915 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
*
42750942 CTGGTGGCTCTGCCAC-ATATATCTGTT
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
* * * *
42750969 CCGGTGGTTCTGCCACGATTAACTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
* *
42750997 CTGGTGACTCTGTCA-AATTATCT
1 CTGGTGGCTCTGCCACAATTATCT
42751020 ATTCTGGCAG
Statistics
Matches: 63, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
26 2 0.03
27 47 0.75
28 14 0.22
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:42762887 original size:12 final size:12
Alignment explanation
Indices: 42762872--42762902 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
42762862 CATGTCCTAG
*
42762872 CCCGTGTCTTTA
1 CCCGTGTCCTTA
42762884 CCCGTGTCCTTA
1 CCCGTGTCCTTA
42762896 CCCGTGT
1 CCCGTGT
42762903 AACACCCTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.06, C:0.39, G:0.19, T:0.35
Consensus pattern (12 bp):
CCCGTGTCCTTA
Found at i:42772498 original size:43 final size:43
Alignment explanation
Indices: 42772445--42772712 Score: 218
Period size: 43 Copynumber: 6.4 Consensus size: 43
42772435 GAAACGCCAT
* * *
42772445 TAAAAAACATGACCTTTAGTGGCTCTTTTCCCACAAACTCCGC
1 TAAAGAACATGACCTTTAGCGGCACTTTTCCCACAAACTCCGC
* * ** * *
42772488 TAAAGAACATGACCTTTAGTGGCGCTTTTATCACAAACGCCGT
1 TAAAGAACATGACCTTTAGCGGCACTTTTCCCACAAACTCCGC
* * * *
42772531 TAAAGAACATGACCTTTAACGGCACTTTTCCCACAAGCCCCAC
1 TAAAGAACATGACCTTTAGCGGCACTTTTCCCACAAACTCCGC
**
42772574 TAAAGAACATGACCTTT------ACTTTTCCCACAAA-TGTTGC
1 TAAAGAACATGACCTTTAGCGGCACTTTTCCCACAAACT-CCGC
* * *
42772611 TAAAGAACATGACCTTTAGCGACGC-TTTCCCACAAA-TGCCAC
1 TAAAGAACATGACCTTTAGCGGCACTTTTCCCACAAACT-CCGC
* * *
42772653 TATA-AA-ATAAACCTTTAGCGGCACTTTTCTCACAAACGT-CGC
1 TAAAGAACAT-GACCTTTAGCGGCACTTTTCCCACAAAC-TCCGC
*
42772695 TAAAGAATATGACCTTTA
1 TAAAGAACATGACCTTTA
42772713 AAAATATATA
Statistics
Matches: 180, Mismatches: 32, Indels: 26
0.76 0.13 0.11
Matches are distributed among these distances:
37 31 0.17
40 2 0.01
41 14 0.08
42 32 0.18
43 98 0.54
44 3 0.02
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (43 bp):
TAAAGAACATGACCTTTAGCGGCACTTTTCCCACAAACTCCGC
Found at i:42772899 original size:27 final size:26
Alignment explanation
Indices: 42772834--42772899 Score: 62
Period size: 27 Copynumber: 2.5 Consensus size: 26
42772824 ATTAATTAAA
**
42772834 TTAAATTTTCTATAAAAATTTTAACT
1 TTAAATTTAATATAAAAATTTTAACT
* *
42772860 TTAAAACTAAATATAAAAATTTATGAA-T
1 TT-AAATTTAATATAAAAATTT-T-AACT
42772888 TTAAATTTAATA
1 TTAAATTTAATA
42772900 CATAAACATT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
26 2 0.06
27 23 0.74
28 4 0.13
29 2 0.06
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.44
Consensus pattern (26 bp):
TTAAATTTAATATAAAAATTTTAACT
Found at i:42774939 original size:14 final size:14
Alignment explanation
Indices: 42774920--42774951 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
42774910 ATAAGTCGAG
42774920 ATTATGTATATGAT
1 ATTATGTATATGAT
42774934 ATTATGTATATGAT
1 ATTATGTATATGAT
42774948 ATTA
1 ATTA
42774952 ATACCATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (14 bp):
ATTATGTATATGAT
Found at i:42776655 original size:14 final size:14
Alignment explanation
Indices: 42776619--42776668 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
42776609 TGCTAAAATA
* *
42776619 TTAATATTAAATTT
1 TTAATTTTAATTTT
42776633 TTAAGTTTTAATTTT
1 TTAA-TTTTAATTTT
*
42776648 TTAATTTTTATTTT
1 TTAATTTTAATTTT
*
42776662 TAAATTT
1 TTAATTT
42776669 CAAAATTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
14 19 0.61
15 12 0.39
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (14 bp):
TTAATTTTAATTTT
Found at i:42777354 original size:21 final size:21
Alignment explanation
Indices: 42777330--42777376 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
42777320 CCCAAATATC
* *
42777330 AAACCCCAAATCCTAGTCCAT
1 AAACCCCAAATCATAGACCAT
*
42777351 AAACCCTAAATCATAGACCAT
1 AAACCCCAAATCATAGACCAT
42777372 AAACC
1 AAACC
42777377 TACACCCTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.45, C:0.34, G:0.04, T:0.17
Consensus pattern (21 bp):
AAACCCCAAATCATAGACCAT
Found at i:42777748 original size:7 final size:7
Alignment explanation
Indices: 42777738--42777768 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
42777728 AAACCCTAAA
42777738 CCCCTAT
1 CCCCTAT
42777745 CCCCTAT
1 CCCCTAT
42777752 CCCCTAT
1 CCCCTAT
42777759 CCCCTAT
1 CCCCTAT
42777766 CCC
1 CCC
42777769 ATAAACCCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.13, C:0.61, G:0.00, T:0.26
Consensus pattern (7 bp):
CCCCTAT
Found at i:42777777 original size:21 final size:21
Alignment explanation
Indices: 42777726--42777779 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
42777716 ACTAATTAAT
42777726 ATAAACCCTAAACCCCTATCCC
1 ATAAACCCT-AACCCCTATCCC
* ** *
42777748 CTATCCCCTATCCCCTATCCC
1 ATAAACCCTAACCCCTATCCC
42777769 ATAAACCCTAA
1 ATAAACCCTAA
42777780 ATCATAAAAT
Statistics
Matches: 24, Mismatches: 8, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.31, C:0.46, G:0.00, T:0.22
Consensus pattern (21 bp):
ATAAACCCTAACCCCTATCCC
Found at i:42777806 original size:8 final size:7
Alignment explanation
Indices: 42777767--42777873 Score: 58
Period size: 7 Copynumber: 15.3 Consensus size: 7
42777757 ATCCCCTATC
42777767 CCATAAA
1 CCATAAA
*
42777774 CCCTAAA
1 CCATAAA
*
42777781 TCATAAA
1 CCATAAA
**
42777788 ATATAAA
1 CCATAAA
42777795 CCATAAA
1 CCATAAA
42777802 CCCAT-AA
1 -CCATAAA
*
42777809 CCATTAAT
1 CCA-TAAA
*
42777817 CCCT-AA
1 CCATAAA
*
42777823 CTCCT-AA
1 C-CATAAA
*
42777830 CCTTAAA
1 CCATAAA
** *
42777837 CCCCAAC
1 CCATAAA
*
42777844 CCTTAAA
1 CCATAAA
42777851 CCATAAA
1 CCATAAA
42777858 CCATAAA
1 CCATAAA
42777865 CCATAAA
1 CCATAAA
42777872 CC
1 CC
42777874 CTAATGATAA
Statistics
Matches: 77, Mismatches: 18, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
6 7 0.09
7 63 0.82
8 7 0.09
ACGTcount: A:0.47, C:0.34, G:0.00, T:0.20
Consensus pattern (7 bp):
CCATAAA
Found at i:42777871 original size:21 final size:21
Alignment explanation
Indices: 42777767--42777873 Score: 67
Period size: 21 Copynumber: 5.1 Consensus size: 21
42777757 ATCCCCTATC
*
42777767 CCATAAACCCTAAATCATAAA
1 CCATAAACCCTAAACCATAAA
** *
42777788 ATATAAACCATAAACCCAT-AA
1 CCATAAACCCTAAA-CCATAAA
* *
42777809 CCATTAATCCCT-AACTCCT-AA
1 CCA-TAAACCCTAAAC-CATAAA
* * * *
42777830 CCTTAAACCCCAACCCTTAAA
1 CCATAAACCCTAAACCATAAA
*
42777851 CCATAAACCATAAACCATAAA
1 CCATAAACCCTAAACCATAAA
42777872 CC
1 CC
42777874 CTAATGATAA
Statistics
Matches: 62, Mismatches: 19, Indels: 10
0.68 0.21 0.11
Matches are distributed among these distances:
20 9 0.15
21 44 0.71
22 9 0.15
ACGTcount: A:0.47, C:0.34, G:0.00, T:0.20
Consensus pattern (21 bp):
CCATAAACCCTAAACCATAAA
Found at i:42778235 original size:40 final size:40
Alignment explanation
Indices: 42778180--42778362 Score: 199
Period size: 40 Copynumber: 4.6 Consensus size: 40
42778170 TTTTGCGGCG
* * *
42778180 TTTTCATAAA-CGCCGCTAAAGCTCGATCTATAGCGGCAT
1 TTTTCAAAAACCGCCGCTAATGCTCGACCTATAGCGGCAT
* * * *
42778219 TTTTCAAAAAGCGCCGCTAATGGTCGACCTATAGTGGCGT
1 TTTTCAAAAACCGCCGCTAATGCTCGACCTATAGCGGCAT
* *
42778259 TTTTCAAAAACCGTCC-CTAATGGTCGACCTATAACGGCATT
1 TTTTCAAAAACCG-CCGCTAATGCTCGACCTATAGCGGCA-T
* * * * *
42778300 TTTTTAAAAACCGCCGCTAATGCTCAATCTATAGCAGCGT
1 TTTTCAAAAACCGCCGCTAATGCTCGACCTATAGCGGCAT
*
42778340 TTTTCAAAAAGCGCCGCTAATGC
1 TTTTCAAAAACCGCCGCTAATGC
42778363 CTCTAAAGCT
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
39 9 0.07
40 80 0.66
41 32 0.26
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.28
Consensus pattern (40 bp):
TTTTCAAAAACCGCCGCTAATGCTCGACCTATAGCGGCAT
Found at i:42778360 original size:81 final size:79
Alignment explanation
Indices: 42778180--42778362 Score: 215
Period size: 81 Copynumber: 2.3 Consensus size: 79
42778170 TTTTGCGGCG
* * * * * * *
42778180 TTTTCATAAACGCCGCTAAAGCTCGATCTATAGCGGCATTTTTCAAAAAGCGCCGCTAATGGTCG
1 TTTTCAAAAACGCCGCTAATGCTCGACCTATAACGGCATTTTTCAAAAACCGCCGCTAATGCTCA
**
42778245 ACCTATAGTGGCGT
66 ACCTATAGCAGCGT
* *
42778259 TTTTCAAAAACCGTCC-CTAATGGTCGACCTATAACGGCATTTTTTTAAAAACCGCCGCTAATGC
1 TTTTCAAAAA-CG-CCGCTAATGCTCGACCTATAACGGCA-TTTTTCAAAAACCGCCGCTAATGC
*
42778323 TCAATCTATAGCAGCGT
63 TCAACCTATAGCAGCGT
42778340 TTTTCAAAAAGCGCCGCTAATGC
1 TTTTCAAAAA-CGCCGCTAATGC
42778363 CTCTAAAGCT
Statistics
Matches: 86, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
79 9 0.10
80 23 0.27
81 54 0.63
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.28
Consensus pattern (79 bp):
TTTTCAAAAACGCCGCTAATGCTCGACCTATAACGGCATTTTTCAAAAACCGCCGCTAATGCTCA
ACCTATAGCAGCGT
Found at i:42778427 original size:75 final size:75
Alignment explanation
Indices: 42778333--42778511 Score: 277
Period size: 75 Copynumber: 2.4 Consensus size: 75
42778323 TCAATCTATA
* * *
42778333 GCAGCGTTTTTCAAAAAGCGCCGCTAATGCCTCTAAAGCTCAACACAAAACAATAGCGTTGTGCT
1 GCAGCGTTTTTCAAAAAGCGCCGCTAATGCCACTAAAACTCAACACAAAACAACAGCGTTGTGCT
42778398 AAATTTTTTT
66 AAATTTTTTT
*
42778408 GCAGCGTTTTTCAAAAAGCGCCACTAATGCCACTAAAACTCAACACAAAACAACAGCGTTGTGCT
1 GCAGCGTTTTTCAAAAAGCGCCGCTAATGCCACTAAAACTCAACACAAAACAACAGCGTTGTGCT
*
42778473 TAATTTTTTT
66 AAATTTTTTT
** * *
42778483 GTGGCGTTTTTCAAAAAGTGCCGCCAATG
1 GCAGCGTTTTTCAAAAAGCGCCGCTAATG
42778512 GTCGACCTAT
Statistics
Matches: 94, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
75 94 1.00
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (75 bp):
GCAGCGTTTTTCAAAAAGCGCCGCTAATGCCACTAAAACTCAACACAAAACAACAGCGTTGTGCT
AAATTTTTTT
Found at i:42778529 original size:40 final size:40
Alignment explanation
Indices: 42778485--42778564 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
42778475 ATTTTTTTGT
*
42778485 GGCGTTTTTCAAAAAGTGCCGCCAATGGTCGACCTATAGC
1 GGCGTTTTTCAAAAAGTGCCGCCAATGCTCGACCTATAGC
* * * * *
42778525 GGCGTTTTTTAGAAGGTGCCGCTAATGCTCGATCTATAGC
1 GGCGTTTTTCAAAAAGTGCCGCCAATGCTCGACCTATAGC
42778565 TAATGCTCGA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.29
Consensus pattern (40 bp):
GGCGTTTTTCAAAAAGTGCCGCCAATGCTCGACCTATAGC
Found at i:42778568 original size:18 final size:18
Alignment explanation
Indices: 42778545--42778582 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
42778535 AGAAGGTGCC
42778545 GCTAATGCTCGATCTATA
1 GCTAATGCTCGATCTATA
42778563 GCTAATGCTCGATCTATA
1 GCTAATGCTCGATCTATA
42778581 GC
1 GC
42778583 GGCGTTTGGA
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:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (18 bp):
GCTAATGCTCGATCTATA
Found at i:42782602 original size:19 final size:19
Alignment explanation
Indices: 42782578--42782619 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
42782568 TAAGAAAAAT
42782578 CAATAGCATACAACTTTTA
1 CAATAGCATACAACTTTTA
42782597 CAATAGCATACAACTTTTA
1 CAATAGCATACAACTTTTA
42782616 CAAT
1 CAAT
42782620 TTTTACGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (19 bp):
CAATAGCATACAACTTTTA
Found at i:42802846 original size:40 final size:41
Alignment explanation
Indices: 42802727--42802946 Score: 222
Period size: 40 Copynumber: 5.5 Consensus size: 41
42802717 CTCAAGTAAT
* * * * *
42802727 CTTCGGGATTTAG-CCGGATATA-ACTACTTGCAC-AAGGC
1 CTTCGGGACTTAGCCCGGATATAGTCAACTAGCACAAATGC
* * * *
42802765 CTTCGGGTCTTAGCCC-GATGTGGTC-ACTAGCATAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCAACTAGCACAAATGC
*
42802804 CTTCGGGACTTAGCCCGGATATAGTC-GCTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCAACTAGCACAAATGC
* * *
42802844 CTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCAACTAGCACAAATGC
* * * *
42802884 CTTC-GGATCTTAGTCCGGTTATAGTCACCTAGCACAAAAGC
1 CTTCGGGA-CTTAGCCCGGATATAGTCAACTAGCACAAATGC
42802925 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
42802947 CATTCGAATA
Statistics
Matches: 148, Mismatches: 26, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
38 21 0.14
39 25 0.17
40 71 0.48
41 28 0.19
42 3 0.02
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (41 bp):
CTTCGGGACTTAGCCCGGATATAGTCAACTAGCACAAATGC
Found at i:42802932 original size:121 final size:117
Alignment explanation
Indices: 42802727--42802946 Score: 289
Period size: 121 Copynumber: 1.8 Consensus size: 117
42802717 CTCAAGTAAT
* * * * *
42802727 CTTCGGGATTTAGCCGGATATAACTACTTGCACAAGGCCTTCGGGTCTTAGCCCGATGTGGTCAC
1 CTTCGGGATTTAGCCGGATATAACAACTCGCACAAGGCCTTCGGATCTTAGCCCGATATAGTCAC
* *
42802792 TAGCATAAATGCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
66 TAGCACAAAAGCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
* * * *
42802844 CTTCGGG-TCTTAGCCCGGATATAGCAACTCGCACGAATGCCTTCGGATCTTAGTCCGGTTATAG
1 CTTCGGGAT-TTAG-CCGGATATAACAACTCGCAC-AAGGCCTTCGGATCTTAG-CCCGATATAG
42802908 TCACCTAGCACAAAAGCCTTCGGGACTTAGCCCGGATAT
62 TCA-CTAGCACAAAAGCCTTCGGGACTTAGCCCGGATAT
42802947 CATTCGAATA
Statistics
Matches: 87, Mismatches: 11, Indels: 6
0.84 0.11 0.06
Matches are distributed among these distances:
116 1 0.01
117 11 0.13
118 17 0.20
119 16 0.18
120 9 0.10
121 33 0.38
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (117 bp):
CTTCGGGATTTAGCCGGATATAACAACTCGCACAAGGCCTTCGGATCTTAGCCCGATATAGTCAC
TAGCACAAAAGCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
Found at i:42807460 original size:15 final size:16
Alignment explanation
Indices: 42807440--42807469 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
42807430 CAATTTTCTC
42807440 CCCTTTTA-CCTTTTA
1 CCCTTTTACCCTTTTA
42807455 CCCTTTTACCCTTTT
1 CCCTTTTACCCTTTT
42807470 CTTTATCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.10, C:0.37, G:0.00, T:0.53
Consensus pattern (16 bp):
CCCTTTTACCCTTTTA
Found at i:42807461 original size:8 final size:8
Alignment explanation
Indices: 42807440--42807469 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
42807430 CAATTTTCTC
42807440 CCCTTTTA
1 CCCTTTTA
42807448 -CCTTTTA
1 CCCTTTTA
42807455 CCCTTTTA
1 CCCTTTTA
42807463 CCCTTTT
1 CCCTTTT
42807470 CTTTATCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.10, C:0.37, G:0.00, T:0.53
Consensus pattern (8 bp):
CCCTTTTA
Found at i:42809167 original size:5 final size:6
Alignment explanation
Indices: 42809148--42809204 Score: 60
Period size: 6 Copynumber: 9.3 Consensus size: 6
42809138 ATTGAGTCCA
* * * *
42809148 TTTATT TTTATT TTTATT TTTAGTA ATTATT TTTATT TTTCTG TTTATT
1 TTTATT TTTATT TTTATT TTTA-TT TTTATT TTTATT TTTATT TTTATT
*
42809197 TGTATT TT
1 TTTATT TT
42809205 CTTGGACTTT
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
6 36 0.90
7 4 0.10
ACGTcount: A:0.18, C:0.02, G:0.05, T:0.75
Consensus pattern (6 bp):
TTTATT
Found at i:42812254 original size:24 final size:23
Alignment explanation
Indices: 42812194--42812257 Score: 74
Period size: 23 Copynumber: 2.6 Consensus size: 23
42812184 TAAAGGCTCG
*
42812194 CTTAAAATATGAAAGGGATTCGGTAA
1 CTTAAAATAT--AA-GGATTCAGTAA
*
42812220 CTTTAAATATAAGGATTCAGTAA
1 CTTAAAATATAAGGATTCAGTAA
42812243 CTTAAAATTATAAGG
1 CTTAAAA-TATAAGG
42812258 TTAAATTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 16 0.47
24 9 0.26
26 9 0.26
ACGTcount: A:0.44, C:0.08, G:0.17, T:0.31
Consensus pattern (23 bp):
CTTAAAATATAAGGATTCAGTAA
Found at i:42813010 original size:21 final size:21
Alignment explanation
Indices: 42812969--42813011 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
42812959 AAGCATGAAA
***
42812969 AGTAACTATACATATTGTTGC
1 AGTAACTATACATAACATTGC
42812990 AGTAACTATACATAACATTGC
1 AGTAACTATACATAACATTGC
42813011 A
1 A
42813012 AGACGATCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.33
Consensus pattern (21 bp):
AGTAACTATACATAACATTGC
Found at i:42815042 original size:18 final size:17
Alignment explanation
Indices: 42815002--42815042 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
42814992 CACTTTTTGA
*
42815002 ATCATCCCTCATCCTTC
1 ATCATCCCTCATCATTC
42815019 ATTCATCCCTCACTCATTC
1 A-TCATCCCTCA-TCATTC
42815038 ATCAT
1 ATCAT
42815043 TCTCTTCTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 14 0.67
19 6 0.29
ACGTcount: A:0.22, C:0.41, G:0.00, T:0.37
Consensus pattern (17 bp):
ATCATCCCTCATCATTC
Found at i:42823371 original size:40 final size:40
Alignment explanation
Indices: 42823344--42823438 Score: 136
Period size: 40 Copynumber: 2.4 Consensus size: 40
42823334 CGTTTTAATG
* *
42823344 AAAATGCCGTTAAAGAACGAGAATTAGCGGCGCTTTTTCA
1 AAAACGCCGCTAAAGAACGAGAATTAGCGGCGCTTTTTCA
* * *
42823384 AAAACGCCGCTAAAGAACGAGCATTAGCGGCGCTTTCTAA
1 AAAACGCCGCTAAAGAACGAGAATTAGCGGCGCTTTTTCA
*
42823424 AAAACACCGCTAAAG
1 AAAACGCCGCTAAAG
42823439 GTGTACCTAT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.19
Consensus pattern (40 bp):
AAAACGCCGCTAAAGAACGAGAATTAGCGGCGCTTTTTCA
Found at i:42823687 original size:40 final size:41
Alignment explanation
Indices: 42823606--42823691 Score: 113
Period size: 41 Copynumber: 2.1 Consensus size: 41
42823596 CGAGCATTAG
*
42823606 ATTAGTGCCGCTTTTTCTAAAAACGTCGCTATAGGTAGAGT
1 ATTAGTGCCGCTTTTTCTAAAAACGCCGCTATAGGTAGAGT
* * *
42823647 ATTAGTGGCG-TTTTTTTGAAAAACGCCGCTATATGT-GAGT
1 ATTAGTGCCGCTTTTTCT-AAAAACGCCGCTATAGGTAGAGT
42823687 ATTAG
1 ATTAG
42823692 CGACGTTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
40 15 0.38
41 25 0.62
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (41 bp):
ATTAGTGCCGCTTTTTCTAAAAACGCCGCTATAGGTAGAGT
Found at i:42824074 original size:15 final size:15
Alignment explanation
Indices: 42824053--42824091 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
42824043 AATATTTTAA
42824053 GGTTTAGGGATTATG
1 GGTTTAGGGATTATG
*
42824068 TGTTTAGGGATTATG
1 GGTTTAGGGATTATG
42824083 GGTTTAGGG
1 GGTTTAGGG
42824092 GTTGTGGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.41, T:0.41
Consensus pattern (15 bp):
GGTTTAGGGATTATG
Found at i:42824154 original size:15 final size:15
Alignment explanation
Indices: 42824126--42824225 Score: 80
Period size: 15 Copynumber: 6.6 Consensus size: 15
42824116 AATGGGTAAA
*
42824126 GGTTAAGCGTTTTAAG
1 GGTTAAG-GGTTTAAG
*
42824142 GGTTATGGGTTTAAG
1 GGTTAAGGGTTTAAG
*
42824157 GGTTAAGGG-TTATG
1 GGTTAAGGGTTTAAG
*
42824171 GGTTTAATGG-TTAAGG
1 GG-TTAAGGGTTTAA-G
* *
42824187 GGATAAGGG-TTAGG
1 GGTTAAGGGTTTAAG
*
42824201 GGTTAAGGGGTTTAAT
1 GGTTAA-GGGTTTAAG
42824217 GGTTAAGGG
1 GGTTAAGGG
42824226 GACATAGGCT
Statistics
Matches: 68, Mismatches: 12, Indels: 9
0.76 0.13 0.10
Matches are distributed among these distances:
14 12 0.18
15 38 0.56
16 18 0.26
ACGTcount: A:0.24, C:0.01, G:0.41, T:0.34
Consensus pattern (15 bp):
GGTTAAGGGTTTAAG
Found at i:42824162 original size:7 final size:7
Alignment explanation
Indices: 42824137--42824225 Score: 79
Period size: 7 Copynumber: 12.0 Consensus size: 7
42824127 GTTAAGCGTT
42824137 TTAAGGG
1 TTAAGGG
*
42824144 TTATGGG
1 TTAAGGG
42824151 TTTAAGGG
1 -TTAAGGG
42824159 TTAAGGG
1 TTAAGGG
*
42824166 TTATGGG
1 TTAAGGG
*
42824173 TTTAATGG
1 -TTAAGGG
42824181 TTAAGGGG
1 TTAA-GGG
*
42824189 ATAAGGG
1 TTAAGGG
*
42824196 TTAGGGG
1 TTAAGGG
42824203 TTAAGGGG
1 TTAA-GGG
*
42824211 TTTAATGG
1 -TTAAGGG
42824219 TTAAGGG
1 TTAAGGG
42824226 GACATAGGCT
Statistics
Matches: 65, Mismatches: 12, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
7 40 0.62
8 21 0.32
9 4 0.06
ACGTcount: A:0.25, C:0.00, G:0.42, T:0.34
Consensus pattern (7 bp):
TTAAGGG
Found at i:42824162 original size:22 final size:22
Alignment explanation
Indices: 42824137--42824209 Score: 94
Period size: 22 Copynumber: 3.3 Consensus size: 22
42824127 GTTAAGCGTT
42824137 TTAAGGGTTATGGGTTTAAGGG
1 TTAAGGGTTATGGGTTTAAGGG
*
42824159 TTAAGGGTTATGGGTTTAATGG
1 TTAAGGGTTATGGGTTTAAGGG
* * *
42824181 TTAAGGGGATAAGGG-TTAGGGG
1 TTAA-GGGTTATGGGTTTAAGGG
42824203 TTAAGGG
1 TTAAGGG
42824210 GTTTAATGGT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
21 3 0.07
22 34 0.76
23 8 0.18
ACGTcount: A:0.25, C:0.00, G:0.42, T:0.33
Consensus pattern (22 bp):
TTAAGGGTTATGGGTTTAAGGG
Found at i:42824356 original size:22 final size:22
Alignment explanation
Indices: 42824331--42824372 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
42824321 TTGAAGGGCT
42824331 GGGATGTAAAG-TTTAGGGTTTA
1 GGGAT-TAAAGATTTAGGGTTTA
*
42824353 GGGATTAAGGATTTAGGGTT
1 GGGATTAAAGATTTAGGGTT
42824373 AATGGGATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.26, C:0.00, G:0.38, T:0.36
Consensus pattern (22 bp):
GGGATTAAAGATTTAGGGTTTA
Found at i:42824422 original size:14 final size:14
Alignment explanation
Indices: 42824389--42824437 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
42824379 ATAGTGGATG
*
42824389 AGGGTTATAGGGTCA
1 AGGGTTAT-GGGTTA
42824404 AGGGTTATGGGTTA
1 AGGGTTATGGGTTA
* *
42824418 TGGGTTATGGGTTT
1 AGGGTTATGGGTTA
42824432 AGGGTT
1 AGGGTT
42824438 TAAGGTTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
14 22 0.73
15 8 0.27
ACGTcount: A:0.18, C:0.02, G:0.43, T:0.37
Consensus pattern (14 bp):
AGGGTTATGGGTTA
Found at i:42824643 original size:26 final size:26
Alignment explanation
Indices: 42824553--42824641 Score: 135
Period size: 26 Copynumber: 3.4 Consensus size: 26
42824543 AGAATTAAAG
*
42824553 ATTTCAAATTTAGAATAATTTTCAAG
1 ATTTCAAATTTAGAATAATTTTCAAT
* *
42824579 AATTCAAATTTAGAATAAGTTTCAAT
1 ATTTCAAATTTAGAATAATTTTCAAT
42824605 ATTTCAAATTTTA-AATAATTTTCAAT
1 ATTTCAAA-TTTAGAATAATTTTCAAT
42824631 ATTTCAAATTT
1 ATTTCAAATTT
42824642 TATCTAATTC
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
25 3 0.05
26 50 0.88
27 4 0.07
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (26 bp):
ATTTCAAATTTAGAATAATTTTCAAT
Found at i:42826219 original size:25 final size:25
Alignment explanation
Indices: 42826191--42826241 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
42826181 GTTAGTAGGT
42826191 TAAAATATGCTACAATTCCTTAGAA
1 TAAAATATGCTACAATTCCTTAGAA
42826216 TAAAATATGCTACAATTCCTTAGAA
1 TAAAATATGCTACAATTCCTTAGAA
42826241 T
1 T
42826242 TCAATCTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.43, C:0.16, G:0.08, T:0.33
Consensus pattern (25 bp):
TAAAATATGCTACAATTCCTTAGAA
Found at i:42827623 original size:44 final size:44
Alignment explanation
Indices: 42827560--42827648 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
42827550 AGTGATGATC
42827560 AATCTTTCAATTTATAATGGCAAACCACAAAGACAACTAAGATT
1 AATCTTTCAATTTATAATGGCAAACCACAAAGACAACTAAGATT
*
42827604 AATCTTTCAATTTATAATGGCAAACCACATAGACAACTAAGATT
1 AATCTTTCAATTTATAATGGCAAACCACAAAGACAACTAAGATT
42827648 A
1 A
42827649 GCCATTGGAG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.45, C:0.18, G:0.09, T:0.28
Consensus pattern (44 bp):
AATCTTTCAATTTATAATGGCAAACCACAAAGACAACTAAGATT
Found at i:42828567 original size:19 final size:20
Alignment explanation
Indices: 42828542--42828635 Score: 75
Period size: 19 Copynumber: 4.8 Consensus size: 20
42828532 TCAATCTTAT
*
42828542 TTTAATTAATATAATTCGTA
1 TTTAATTAATATAATTAGTA
* * * *
42828562 -TTAATTTATTTAAATATTA
1 TTTAATTAATATAATTAGTA
* *
42828581 TTTAATTAATATAATTTGGA
1 TTTAATTAATATAATTAGTA
* * * *
42828601 -TTAATTTATTTAAATATTA
1 TTTAATTAATATAATTAGTA
42828620 TTTAATTAATATAATT
1 TTTAATTAATATAATT
42828636 TTTATAAGTA
Statistics
Matches: 52, Mismatches: 20, Indels: 4
0.68 0.26 0.05
Matches are distributed among these distances:
19 27 0.52
20 25 0.48
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (20 bp):
TTTAATTAATATAATTAGTA
Found at i:42828607 original size:24 final size:24
Alignment explanation
Indices: 42828580--42828635 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
42828570 TTTAAATATT
*
42828580 ATTTAATT-AATATAATTTGGATTA
1 ATTTAATTAAATATAATTT-AATTA
* *
42828604 ATTTATTTAAATATTATTTAATTA
1 ATTTAATTAAATATAATTTAATTA
*
42828628 ATATAATT
1 ATTTAATT
42828636 TTTATAAGTA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 17 0.65
25 9 0.35
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (24 bp):
ATTTAATTAAATATAATTTAATTA
Found at i:42828636 original size:39 final size:39
Alignment explanation
Indices: 42828542--42828636 Score: 172
Period size: 39 Copynumber: 2.4 Consensus size: 39
42828532 TCAATCTTAT
* *
42828542 TTTAATTAATATAATTCGTATTAATTTATTTAAATATTA
1 TTTAATTAATATAATTTGGATTAATTTATTTAAATATTA
42828581 TTTAATTAATATAATTTGGATTAATTTATTTAAATATTA
1 TTTAATTAATATAATTTGGATTAATTTATTTAAATATTA
42828620 TTTAATTAATATAATTT
1 TTTAATTAATATAATTT
42828637 TTATAAGTAT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 54 1.00
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (39 bp):
TTTAATTAATATAATTTGGATTAATTTATTTAAATATTA
Found at i:42828640 original size:20 final size:20
Alignment explanation
Indices: 42828542--42828640 Score: 78
Period size: 20 Copynumber: 5.0 Consensus size: 20
42828532 TCAATCTTAT
**
42828542 TTTAATTAATATAATTCGTA
1 TTTAATTAATATAATTATTA
* * *
42828562 -TTAATTTATTTAAATATTA
1 TTTAATTAATATAATTATTA
*
42828581 TTTAATTAATATAATT-TGGA
1 TTTAATTAATATAATTAT-TA
* * *
42828601 -TTAATTTATTTAAATATTA
1 TTTAATTAATATAATTATTA
*
42828620 TTTAATTAATATAATTTTTA
1 TTTAATTAATATAATTATTA
42828640 T
1 T
42828641 AAGTATAATT
Statistics
Matches: 58, Mismatches: 17, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
19 28 0.48
20 30 0.52
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (20 bp):
TTTAATTAATATAATTATTA
Found at i:42828651 original size:29 final size:29
Alignment explanation
Indices: 42828602--42828662 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
42828592 TAATTTGGAT
* *
42828602 TAATTTATTTAAATATTATTTAATTAATA
1 TAATTTATTTAAATATAATTTAATTAAAA
*
42828631 TAATTT-TTATAAGTATAATTTAATTAAAA
1 TAATTTATT-TAAATATAATTTAATTAAAA
42828660 TAA
1 TAA
42828663 AATTTTTTCC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 2 0.07
29 26 0.93
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (29 bp):
TAATTTATTTAAATATAATTTAATTAAAA
Found at i:42828951 original size:9 final size:9
Alignment explanation
Indices: 42828937--42829005 Score: 102
Period size: 9 Copynumber: 7.7 Consensus size: 9
42828927 TATATACTTG
42828937 AACTTACAT
1 AACTTACAT
*
42828946 AACTTAAAT
1 AACTTACAT
42828955 AACTTACAT
1 AACTTACAT
*
42828964 GACTTACAT
1 AACTTACAT
*
42828973 AACTCACAT
1 AACTTACAT
*
42828982 AACTTACAG
1 AACTTACAT
42828991 AACTTACAT
1 AACTTACAT
42829000 AACTTA
1 AACTTA
42829006 ATTATACTTA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 52 1.00
ACGTcount: A:0.45, C:0.22, G:0.03, T:0.30
Consensus pattern (9 bp):
AACTTACAT
Done.