Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr12
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: 39383930
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.32
Warning! 780790 characters in sequence are not A, C, G, or T
File 4 of 126
Found at i:863053 original size:305 final size:305
Alignment explanation
Indices: 862498--863113 Score: 1054
Period size: 305 Copynumber: 2.0 Consensus size: 305
862488 TTGAACTAAA
862498 ATATCGATAAATACACAGGTAGTACACACAAAGTGTACAAATCTATAATCCATCAATTCATATAT
1 ATATCGATAAATACACAGGTAGTACACACAAAGTGTACAAATCTATAATCCATCAATTCATATAT
* * *
862563 TATCCTTCAATTCATATTCAGGAATACTTATATGAGCATGTAAACGGGAAGATCTTCCGAGCTAT
66 TATCCGTCAATTCATATTCAGGAATACTCATACGAGCATGTAAACGGGAAGATCTTCCGAGCTAT
* * *
862628 ATATAACGGGAAGCTCATGTGAGTCATGTAACGGGAAGCTCATAAGAGCTGTAATCAGGAAGCTC
131 ATATAACGGAAAGCTCATGTGAGTCATGTAACAGGAAGCTCATAAGAGCTGTAATCAAGAAGCTC
* *
862693 ATGCGAGCTAATATCGGAAAGCTCCGGAGAATCGTTAATCAGGAAGCTTATGAGAGCCAGATATC
196 ATGCGAGCTAATATCGGAAAGCTCCGGAGAATCGTTAATCAGAAAGCTCATGAGAGCCAGATATC
862758 AGGAAGCTCGTGAGAGCCAAATAACAGGAAGCTCAAGAGAGCCAT
261 AGGAAGCTCGTGAGAGCCAAATAACAGGAAGCTCAAGAGAGCCAT
* * * *
862803 ATATCGATAAATACACATGTAGTACACACAAAGTGTATAAATCTGTAATCCGTCAATTCATATAT
1 ATATCGATAAATACACAGGTAGTACACACAAAGTGTACAAATCTATAATCCATCAATTCATATAT
* *
862868 TATCCGTCAATTCATATTCAGGAATACTCATACGAGCATGTAAACGGGAAGCTCTTCCTAGCTAT
66 TATCCGTCAATTCATATTCAGGAATACTCATACGAGCATGTAAACGGGAAGATCTTCCGAGCTAT
* *
862933 ATATAACGGAAATCTCATGTGAGTCATGTAACAGGAAGCTCATAAGAGCTGTAATCAATAAGCTC
131 ATATAACGGAAAGCTCATGTGAGTCATGTAACAGGAAGCTCATAAGAGCTGTAATCAAGAAGCTC
*
862998 ATGTGAGCTAATATCGGAAAGCTCCGGAGAA-CTGTTAATCAGAAAGCTCATGAGAGCCAGATAT
196 ATGCGAGCTAATATCGGAAAGCTCCGGAGAATC-GTTAATCAGAAAGCTCATGAGAGCCAGATAT
*
863062 CGGGAAGCTCGTGAGAGCCAAATAACAGGAAGCTCAAGAGAGCCAT
260 CAGGAAGCTCGTGAGAGCCAAATAACAGGAAGCTCAAGAGAGCCAT
863108 ATATCG
1 ATATCG
863114 GGATGTTCAT
Statistics
Matches: 292, Mismatches: 18, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
304 1 0.00
305 291 1.00
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.24
Consensus pattern (305 bp):
ATATCGATAAATACACAGGTAGTACACACAAAGTGTACAAATCTATAATCCATCAATTCATATAT
TATCCGTCAATTCATATTCAGGAATACTCATACGAGCATGTAAACGGGAAGATCTTCCGAGCTAT
ATATAACGGAAAGCTCATGTGAGTCATGTAACAGGAAGCTCATAAGAGCTGTAATCAAGAAGCTC
ATGCGAGCTAATATCGGAAAGCTCCGGAGAATCGTTAATCAGAAAGCTCATGAGAGCCAGATATC
AGGAAGCTCGTGAGAGCCAAATAACAGGAAGCTCAAGAGAGCCAT
Found at i:863069 original size:25 final size:25
Alignment explanation
Indices: 863041--863179 Score: 127
Period size: 25 Copynumber: 5.6 Consensus size: 25
863031 GTTAATCAGA
*
863041 AAGCTCATGAGAGCCAGATATCGGG
1 AAGCTCATGAGAGCCAAATATCGGG
* * *
863066 AAGCTCGTGAGAGCCAAATAACAGG
1 AAGCTCATGAGAGCCAAATATCGGG
* *
863091 AAGCTCAAGAGAGCCATATATCGGG
1 AAGCTCATGAGAGCCAAATATCGGG
* * * * *
863116 ATGTTCATAAGAGCTAAATAACGGG
1 AAGCTCATGAGAGCCAAATATCGGG
* * *
863141 AAGATCGTGAGAGCCATATATCGGG
1 AAGCTCATGAGAGCCAAATATCGGG
*
863166 ACA-CTCATAAGAGC
1 A-AGCTCATGAGAGC
863180 TGTGGTGAGT
Statistics
Matches: 87, Mismatches: 26, Indels: 2
0.76 0.23 0.02
Matches are distributed among these distances:
25 86 0.99
26 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.27, T:0.17
Consensus pattern (25 bp):
AAGCTCATGAGAGCCAAATATCGGG
Found at i:863095 original size:50 final size:50
Alignment explanation
Indices: 863041--863179 Score: 172
Period size: 50 Copynumber: 2.8 Consensus size: 50
863031 GTTAATCAGA
* * *
863041 AAGCTCATGAGAGCCAGATATCGGGAAGCTCGTGAGAGCCAAATAACAGG
1 AAGCTCATGAGAGCCATATATCGGGAAGCTCATAAGAGCCAAATAACAGG
* * * * *
863091 AAGCTCAAGAGAGCCATATATCGGGATGTTCATAAGAGCTAAATAACGGG
1 AAGCTCATGAGAGCCATATATCGGGAAGCTCATAAGAGCCAAATAACAGG
* *
863141 AAGATCGTGAGAGCCATATATCGGGACA-CTCATAAGAGC
1 AAGCTCATGAGAGCCATATATCGGGA-AGCTCATAAGAGC
863180 TGTGGTGAGT
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
50 75 1.00
ACGTcount: A:0.37, C:0.19, G:0.27, T:0.17
Consensus pattern (50 bp):
AAGCTCATGAGAGCCATATATCGGGAAGCTCATAAGAGCCAAATAACAGG
Found at i:865598 original size:25 final size:25
Alignment explanation
Indices: 865570--865678 Score: 130
Period size: 25 Copynumber: 4.4 Consensus size: 25
865560 TAAACTCCGC
*
865570 CGAGCTGAATAACGATAAGCTCTTT
1 CGAGCTGAATAACGATAAGCTCATT
* *
865595 CGAGGTGAATAACGATAAGCTCTTT
1 CGAGCTGAATAACGATAAGCTCATT
*
865620 CGAGCTGAATAACGGTAAGCTCATT
1 CGAGCTGAATAACGATAAGCTCATT
* * * *
865645 CAAGCTGAGTATC-AGTAAGCTCATA
1 CGAGCTGAATAACGA-TAAGCTCATT
865670 CGAGCTGAA
1 CGAGCTGAA
865679 ATCGGTAACC
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
25 72 1.00
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (25 bp):
CGAGCTGAATAACGATAAGCTCATT
Found at i:869998 original size:787 final size:789
Alignment explanation
Indices: 868460--870043 Score: 2956
Period size: 787 Copynumber: 2.0 Consensus size: 789
868450 CAAATGACAA
868460 TATTCAAACATGTATTTTCATATATATATATATCTATATATATATTATAACCAAATAAACCATCA
1 TATTCAAACATGTATTTTC--A-ATATATATA-CTATATATATATTATAACCAAATAAACCATCA
*
868525 ATTTACCAAGCTAATTTGAGTCCTTTAATACCAATTCATTTATCTACCAAAACACACCATTTGAT
62 ATTTACCAAGCTAATTTGAATCCTTTAATACCAATTCATTTATCTACCAAAACACACCATTTGAT
868590 ACCAAAAAGCATTTCAAATACTAACATATTTAGACATATATATACCTTAAATATCAAGGTACCAA
127 ACCAAAAAGCATTTCAAATACTAACATATTTAGACATATATATACCTTAAATATCAAGGTACCAA
*
868655 TTTATCACCAATTCTTCACATCACAAACATATGTACAAAATGCACATTTAGCTAACATTTACCTT
192 TTCATCACCAATTCTTCACATCACAAACATATGTACAAAATGCACATTTAGCTAACATTTACCTT
*
868720 TCATTATTCTATCACAAATCAAGCCACACACCAAATATGATAAGGCCATTTGTATATACACAGAG
257 TCATTATTCTATCACAAATCAAGCCACACACCAAATATGATAAGGCCATTTATATATACACAGAG
868785 CAAAATATATCAAAACACAAGCCAAAACATATGGCCACAACCACAACATCACACATAGGCCAACA
322 CAAAATATATCAAAACACAAGCCAAAACATATGGCCACAACCACAACATCACACATAGGCCAACA
* *
868850 TTAGTCAAAATAACCTATACATGCCATTATAACCAAAATGTAACCAACTAAAAGTACCAAAAGAG
387 TTAGCCAAAATAACATATACATGCCATTATAACCAAAATGTAACCAACTAAAAGTACCAAAAGAG
*
868915 ACGATGGATAGTGTGATATAACTCCGAGAAGCTTTCAACCCGAACGAGCTTCCGAATCACTATAA
452 ACGATGGATAGTGTGATATAACTCCGAGAAGCTTTCAACCCGAACGAGCCTCCGAATCACTATAA
*
868980 AACACGGAAAATAACACATAGTAAGCATTTAAGCTTAGTAAGTTCGTATAACTTAGAATTTAACT
517 AACACAGAAAATAACACATAGTAAGCATTTAAGCTTAGTAAGTTCGTATAACTTAGAATTTAACT
869045 TACCATTTTAAATCACAATTAAGTTAAGCTAACATAACATATCCCAACCAATTTGGCTAAAAGCC
582 TACCATTTTAAATCACAATTAAGTTAAGCTAACATAACATATCCCAACCAATTTGGCTAAAAGCC
869110 TAAACACAAGTTCATCAACATATTAGCCATGTAAATAATATATAAAATCCAATATACATGGATGA
647 TAAACACAAGTTCATCAACATATTAGCCATGTAAATAATATATAAAATCCAATATACATGGATGA
*
869175 ATTTAACAAGTAATCACATTTCATATACACGAATTATTCATTTCATAAATCAATGTATCATGTAA
712 ATTCAACAAGTAATCACATTTCATATACACGAATTATTCATTTCATAAATCAATGTATCATGTAA
869240 CATCACTTTCATG
777 CATCACTTTCATG
869253 TATTCAAACATGTATTTTC-ATATATATA-TATATATATATTATAACCAAATAAACCATCAATTT
1 TATTCAAACATGTATTTTCAATATATATACTATATATATATTATAACCAAATAAACCATCAATTT
* *
869316 ACCAAGCTAATTTGAATCTTTTCATACCAATTCATTTATCTACCAAAACACACCATTTGATACCA
66 ACCAAGCTAATTTGAATCCTTTAATACCAATTCATTTATCTACCAAAACACACCATTTGATACCA
* *
869381 AAACGCATTTCAAATACTAACATATTTAGACATATATATACCTTACATATCAAGGTACCAATTCA
131 AAAAGCATTTCAAATACTAACATATTTAGACATATATATACCTTAAATATCAAGGTACCAATTCA
869446 TCACCAATTCTTCACATCACAAACATATGTACAAAATGCACATTTAGCTAACATTTACCTTTCAT
196 TCACCAATTCTTCACATCACAAACATATGTACAAAATGCACATTTAGCTAACATTTACCTTTCAT
* *
869511 TATTCTATCATAAATCAAGCCACACACCAAATATGATAAGGCCATTTATATATACACATAGCAAA
261 TATTCTATCACAAATCAAGCCACACACCAAATATGATAAGGCCATTTATATATACACAGAGCAAA
869576 ATATATCAAAACACAAGCCAAAACATATGGCCACAACCACAACATCACACATAGGCCAACATTAG
326 ATATATCAAAACACAAGCCAAAACATATGGCCACAACCACAACATCACACATAGGCCAACATTAG
869641 CCAAAATAACATATACATGCCATTATAACCAAAATGTAACCAACTAAAAGTACCAAAAGAGACGA
391 CCAAAATAACATATACATGCCATTATAACCAAAATGTAACCAACTAAAAGTACCAAAAGAGACGA
*
869706 TGGATAGTGTGATATAACTCTGAGAAGCTTTCAACCCGAACGAGCCTCCGAATCACTATAAAACA
456 TGGATAGTGTGATATAACTCCGAGAAGCTTTCAACCCGAACGAGCCTCCGAATCACTATAAAACA
* *
869771 CAGAAAATAACATATAGTAAGTATTTAAGCTTAGTAAGTTCGTATAACTTAGAATTTAACTTACC
521 CAGAAAATAACACATAGTAAGCATTTAAGCTTAGTAAGTTCGTATAACTTAGAATTTAACTTACC
869836 ATTTTAAATCACAATTAAGTTAAGCTAACATAACATATCCCAACCAATTTGGCTAAAAGCCTAAA
586 ATTTTAAATCACAATTAAGTTAAGCTAACATAACATATCCCAACCAATTTGGCTAAAAGCCTAAA
*
869901 CACAAGTTCATCAACATATTAGCCATGTAAATCATATATAAAATCCAATATACATGGATGAATTC
651 CACAAGTTCATCAACATATTAGCCATGTAAATAATATATAAAATCCAATATACATGGATGAATTC
869966 AACAAGTAATCACATTTCATATACACGAATTATTCATTTCATAAATCAATGTATCATGTAACATC
716 AACAAGTAATCACATTTCATATACACGAATTATTCATTTCATAAATCAATGTATCATGTAACATC
870031 ACTTTCATG
781 ACTTTCATG
870040 TATT
1 TATT
870044 TCATGTAAAT
Statistics
Matches: 773, Mismatches: 18, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
787 745 0.96
789 9 0.01
793 19 0.02
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (789 bp):
TATTCAAACATGTATTTTCAATATATATACTATATATATATTATAACCAAATAAACCATCAATTT
ACCAAGCTAATTTGAATCCTTTAATACCAATTCATTTATCTACCAAAACACACCATTTGATACCA
AAAAGCATTTCAAATACTAACATATTTAGACATATATATACCTTAAATATCAAGGTACCAATTCA
TCACCAATTCTTCACATCACAAACATATGTACAAAATGCACATTTAGCTAACATTTACCTTTCAT
TATTCTATCACAAATCAAGCCACACACCAAATATGATAAGGCCATTTATATATACACAGAGCAAA
ATATATCAAAACACAAGCCAAAACATATGGCCACAACCACAACATCACACATAGGCCAACATTAG
CCAAAATAACATATACATGCCATTATAACCAAAATGTAACCAACTAAAAGTACCAAAAGAGACGA
TGGATAGTGTGATATAACTCCGAGAAGCTTTCAACCCGAACGAGCCTCCGAATCACTATAAAACA
CAGAAAATAACACATAGTAAGCATTTAAGCTTAGTAAGTTCGTATAACTTAGAATTTAACTTACC
ATTTTAAATCACAATTAAGTTAAGCTAACATAACATATCCCAACCAATTTGGCTAAAAGCCTAAA
CACAAGTTCATCAACATATTAGCCATGTAAATAATATATAAAATCCAATATACATGGATGAATTC
AACAAGTAATCACATTTCATATACACGAATTATTCATTTCATAAATCAATGTATCATGTAACATC
ACTTTCATG
Found at i:870277 original size:25 final size:25
Alignment explanation
Indices: 870248--870331 Score: 80
Period size: 25 Copynumber: 3.4 Consensus size: 25
870238 TAAACTCCTC
870248 CGAGCTGAATAACGATAAGCTCTTT
1 CGAGCTGAATAACGATAAGCTCTTT
* *
870273 CGAGCTGAATAACGGTAAGTTCATTT
1 CGAGCTGAATAACGATAAGCTC-TTT
* * * * * *
870299 -GAACTGAGTATCAATAAGCTCATA
1 CGAGCTGAATAACGATAAGCTCTTT
870323 CGAGCTGAA
1 CGAGCTGAA
870332 ATCGGTAACC
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
24 1 0.02
25 41 0.91
26 3 0.07
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (25 bp):
CGAGCTGAATAACGATAAGCTCTTT
Found at i:877129 original size:57 final size:55
Alignment explanation
Indices: 877059--877174 Score: 155
Period size: 57 Copynumber: 2.1 Consensus size: 55
877049 ATATTTAGGG
* *
877059 AATGATTATGATTTTCTCCAAATGAAAATGAAAATAGAGAAAATGGAA-TCATTTGGA
1 AATGATTATGATTTTCTCAAAATGAAAATGAAAAT-GAG-AAAT-GAATTCATTTAGA
*
877116 AATGAATT-TGATTTTCTCAAAATGGAAATGAAAATGAGAAATGAATTCATTTAGA
1 AATG-ATTATGATTTTCTCAAAATGAAAATGAAAATGAGAAATGAATTCATTTAGA
877171 AATG
1 AATG
877175 GAAAATGAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
54 3 0.06
55 16 0.30
56 3 0.06
57 29 0.54
58 3 0.06
ACGTcount: A:0.46, C:0.06, G:0.17, T:0.31
Consensus pattern (55 bp):
AATGATTATGATTTTCTCAAAATGAAAATGAAAATGAGAAATGAATTCATTTAGA
Found at i:877188 original size:55 final size:57
Alignment explanation
Indices: 877066--877192 Score: 145
Period size: 57 Copynumber: 2.3 Consensus size: 57
877056 GGGAATGATT
* * * *
877066 ATGATTTTCTCCAAATGAAAATGAAAATAGAGAAAATGGAATCATTTGGAAATGAAT
1 ATGATATTCTCAAAATGAAAATGAAAATAGAGAAAATGGAATCATTTAGAAATGAAA
* * *
877123 TTGATTTTCTCAAAATGGAAATGAAAAT-GAG-AAAT-GAATTCATTTAGAAATGGAAA
1 ATGATATTCTCAAAATGAAAATGAAAATAGAGAAAATGGAA-TCATTTAGAAAT-GAAA
877179 ATGA-ATTCTCAAAA
1 ATGATATTCTCAAAA
877193 ATAATCAGAA
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
54 3 0.05
55 24 0.39
56 9 0.15
57 25 0.41
ACGTcount: A:0.47, C:0.07, G:0.17, T:0.29
Consensus pattern (57 bp):
ATGATATTCTCAAAATGAAAATGAAAATAGAGAAAATGGAATCATTTAGAAATGAAA
Found at i:878043 original size:27 final size:27
Alignment explanation
Indices: 878009--878067 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
877999 GTTATACTTC
* ** *
878009 TTTG-TCAAAAATCAAGTGATATAACT
1 TTTGATCAAAAACCAAAAGATATAAAT
*
878035 TTTGATCAATAACCAAAAGATATAAAT
1 TTTGATCAAAAACCAAAAGATATAAAT
878062 TTTGAT
1 TTTGAT
878068 TAATTACACC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 4 0.15
27 23 0.85
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (27 bp):
TTTGATCAAAAACCAAAAGATATAAAT
Found at i:878909 original size:6 final size:6
Alignment explanation
Indices: 878893--878955 Score: 99
Period size: 6 Copynumber: 10.3 Consensus size: 6
878883 TTTCTTTCCA
*
878893 TTCTCTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTC
1 TTCT-TT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT
*
878942 TTATTT TTCTTT TT
1 TTCTTT TTCTTT TT
878956 ACTTGTTTCC
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
6 48 0.92
7 4 0.08
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (6 bp):
TTCTTT
Found at i:885608 original size:87 final size:87
Alignment explanation
Indices: 885462--885643 Score: 337
Period size: 87 Copynumber: 2.1 Consensus size: 87
885452 CAACAAATGA
885462 TAAAATCATCAATGCATAAAAACTCATAAAATATAGAACTTGACTGATGCACTTTAACAAATTGT
1 TAAAATCATCAATGCATAAAAACTCATAAAATATAGAACTTGACTGATGCACTTTAACAAATTGT
885527 TTAAACTTAAACCAGATAAGTG
66 TTAAACTTAAACCAGATAAGTG
* *
885549 TAAAATCATCAATGCATAAAAACTTATAAAATATAGAACTTGACTGATGCATTTTAACAAATTGT
1 TAAAATCATCAATGCATAAAAACTCATAAAATATAGAACTTGACTGATGCACTTTAACAAATTGT
885614 TTAAACTTAAACCAGATAAGTG
66 TTAAACTTAAACCAGATAAGTG
*
885636 TAATATCA
1 TAAAATCA
885644 ATGTTAGTCA
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 92 1.00
ACGTcount: A:0.46, C:0.14, G:0.10, T:0.30
Consensus pattern (87 bp):
TAAAATCATCAATGCATAAAAACTCATAAAATATAGAACTTGACTGATGCACTTTAACAAATTGT
TTAAACTTAAACCAGATAAGTG
Found at i:888093 original size:13 final size:14
Alignment explanation
Indices: 888077--888105 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
888067 TATATATTAT
888077 TAAAATATTAA-TA
1 TAAAATATTAAGTA
888090 TAAAATATTAAGTA
1 TAAAATATTAAGTA
888104 TA
1 TA
888106 TATTTAAATT
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:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (14 bp):
TAAAATATTAAGTA
Found at i:888149 original size:19 final size:19
Alignment explanation
Indices: 888109--888159 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
888099 AAGTATATAT
* *
888109 TTAAATTTAAAA-TTATTT
1 TTAAAATTAAAATTTATTA
**
888127 TTAATGTTAAAATTTATTA
1 TTAAAATTAAAATTTATTA
888146 TTAAAATTAAAATT
1 TTAAAATTAAAATT
888160 GTAATTTTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 10 0.37
19 17 0.63
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
TTAAAATTAAAATTTATTA
Found at i:888248 original size:13 final size:15
Alignment explanation
Indices: 888213--888243 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
888203 TGTATGTTTA
888213 ATAATATTGAAAATT
1 ATAATATTGAAAATT
*
888228 ATAATATTTAAAATT
1 ATAATATTGAAAATT
888243 A
1 A
888244 ATATTATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (15 bp):
ATAATATTGAAAATT
Found at i:888788 original size:10 final size:10
Alignment explanation
Indices: 888773--888797 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
888763 TACGCCCTTT
888773 TATATTTATA
1 TATATTTATA
888783 TATATTTATA
1 TATATTTATA
888793 TATAT
1 TATAT
888798 ATTTCGGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
TATATTTATA
Found at i:889827 original size:11 final size:11
Alignment explanation
Indices: 889813--889842 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
889803 TTTTATTTTT
889813 TAATTTTAAAA
1 TAATTTTAAAA
889824 TAATTTTAAAA
1 TAATTTTAAAA
889835 TAATTTTA
1 TAATTTTA
889843 TTTTTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TAATTTTAAAA
Found at i:891379 original size:43 final size:43
Alignment explanation
Indices: 891307--891432 Score: 134
Period size: 43 Copynumber: 2.9 Consensus size: 43
891297 AGGATTTCAT
891307 TATGTG-TTATCGTGTAAGACCACGTCTGGGACGTTGGCATCGAC
1 TATGTGATTA-CGTGTAAGACCACGTCTGGGACGTTGGCATCG-C
** * *
891351 T-TGTGACTTA-GTGTAAGACCTTGTCTGGGATAG-TGGCATCGT
1 TATGTGA-TTACGTGTAAGACCACGTCTGGGA-CGTTGGCATCGC
* *
891393 TATGTGATTACATGTAAGACCACGTCTAGGACGTTGGCAT
1 TATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCAT
891433 TGTACGAAAT
Statistics
Matches: 67, Mismatches: 9, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
42 5 0.07
43 57 0.85
44 2 0.03
45 3 0.04
ACGTcount: A:0.22, C:0.17, G:0.29, T:0.32
Consensus pattern (43 bp):
TATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCATCGC
Found at i:894722 original size:16 final size:15
Alignment explanation
Indices: 894701--894730 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
894691 GTGAGTTGGA
894701 TATATATATGTATAAT
1 TATATATA-GTATAAT
894717 TATATATAGTATAA
1 TATATATAGTATAA
894731 ATGTGAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (15 bp):
TATATATAGTATAAT
Found at i:897225 original size:50 final size:50
Alignment explanation
Indices: 897117--897413 Score: 319
Period size: 50 Copynumber: 5.8 Consensus size: 50
897107 ATTTGGATAA
* * * *
897117 AGAGATCCCATGTAAGACCATGTTTGGGACATGACATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATG
*
897173 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
897223 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * *
897273 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * * * *
897323 AGAACTCCCATGTAAGACCATATTTGGGATATGACATTGGCA--GTACAAG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* ** *
897372 AAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
897414 TGTTATTATC
Statistics
Matches: 209, Mismatches: 31, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
48 1 0.00
49 36 0.17
50 130 0.62
53 3 0.01
55 1 0.00
56 38 0.18
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:899743 original size:21 final size:21
Alignment explanation
Indices: 899703--899743 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
899693 TCAAAGGTAA
*
899703 ATAAACAATATCATACACTTT
1 ATAAACAATATCATAAACTTT
899724 ATAAA-AATATCATCAAACTT
1 ATAAACAATATCAT-AAACTT
899744 ACAACTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (21 bp):
ATAAACAATATCATAAACTTT
Found at i:900479 original size:57 final size:58
Alignment explanation
Indices: 900380--900505 Score: 166
Period size: 57 Copynumber: 2.2 Consensus size: 58
900370 AAGGCATCGC
* *
900380 AACACATCCCTTCTAAACACACCAAAGCGCACCTAAGTGCTAAACCCAAAGGCAAGAG
1 AACACATCCCTTCTAAACACACCAAAGAGCACCTAAGTGCTAAACCCAAAGGCAACAG
* *** *
900438 ATCACATCCCTTC-AAACACACTTGAGAGCACAC-AAGTGCTAAACCCGAAGGCAACAG
1 AACACATCCCTTCTAAACACACCAAAGAGCAC-CTAAGTGCTAAACCCAAAGGCAACAG
900495 AACACATCCCT
1 AACACATCCCT
900506 ATTGGCATGC
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
57 46 0.78
58 13 0.22
ACGTcount: A:0.40, C:0.33, G:0.13, T:0.13
Consensus pattern (58 bp):
AACACATCCCTTCTAAACACACCAAAGAGCACCTAAGTGCTAAACCCAAAGGCAACAG
Found at i:901341 original size:20 final size:20
Alignment explanation
Indices: 901318--901362 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
901308 AAGATGTTCA
901318 ATAATCCAATAAGAAATTCT
1 ATAATCCAATAAGAAATTCT
***
901338 ATAATTTTATAAGAAATTCT
1 ATAATCCAATAAGAAATTCT
901358 ATAAT
1 ATAAT
901363 TTTTAATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (20 bp):
ATAATCCAATAAGAAATTCT
Found at i:901362 original size:40 final size:40
Alignment explanation
Indices: 901286--901362 Score: 91
Period size: 40 Copynumber: 1.9 Consensus size: 40
901276 TTATAATATG
* * **
901286 ATAAGAGATTCAATAATGTTGTAAGATGTTCAATAATCCA
1 ATAAGAAATTCAATAATGTTATAAGAAATTCAATAATCCA
* * *
901326 ATAAGAAATTCTATAATTTTATAAGAAATTCTATAAT
1 ATAAGAAATTCAATAATGTTATAAGAAATTCAATAAT
901363 TTTTAATAAT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 30 1.00
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.36
Consensus pattern (40 bp):
ATAAGAAATTCAATAATGTTATAAGAAATTCAATAATCCA
Found at i:901363 original size:20 final size:20
Alignment explanation
Indices: 901326--901365 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
901316 CAATAATCCA
901326 ATAAGAAATTCTATAATTTT
1 ATAAGAAATTCTATAATTTT
901346 ATAAGAAATTCTATAATTTT
1 ATAAGAAATTCTATAATTTT
901366 TAATAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (20 bp):
ATAAGAAATTCTATAATTTT
Found at i:901374 original size:30 final size:30
Alignment explanation
Indices: 901338--901394 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
901328 AAGAAATTCT
*
901338 ATAATTTTATAA-GAAATTCTATAATTTTTA
1 ATAATTTTA-AAGGAAATTCAATAATTTTTA
*
901368 ATAATTTTAAAGGAGATTCAATAATTT
1 ATAATTTTAAAGGAAATTCAATAATTT
901395 ACAAAATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 22 0.92
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.46
Consensus pattern (30 bp):
ATAATTTTAAAGGAAATTCAATAATTTTTA
Found at i:902868 original size:11 final size:11
Alignment explanation
Indices: 902839--902871 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
902829 AAAGAAAAAA
*
902839 TTATAAAATTA
1 TTATAAAATTT
902850 TT-TAAAATTT
1 TTATAAAATTT
902860 TTATAAAATTT
1 TTATAAAATTT
902871 T
1 T
902872 AACATTTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TTATAAAATTT
Found at i:903038 original size:19 final size:19
Alignment explanation
Indices: 903014--903069 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 19
903004 GTAGATTATG
903014 AATTTTTTAATTTTTTAAT
1 AATTTTTTAATTTTTTAAT
** *
903033 AATTTTCGAA-GTTTTAAT
1 AATTTTTTAATTTTTTAAT
*
903051 -ATTTTTTGAGTTTTTTAAT
1 AATTTTTT-AATTTTTTAAT
903070 TTTTTAAAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
17 5 0.18
18 8 0.29
19 15 0.54
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.62
Consensus pattern (19 bp):
AATTTTTTAATTTTTTAAT
Found at i:903065 original size:18 final size:18
Alignment explanation
Indices: 903015--903074 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
903005 TAGATTATGA
* *
903015 ATTTTTTAATTTTTTAAT
1 ATTTTTTGAGTTTTTAAT
* *
903033 AATTTTCGAAG-TTTTAAT
1 ATTTTTTG-AGTTTTTAAT
903051 ATTTTTTGAGTTTTTTAAT
1 ATTTTTTGAG-TTTTTAAT
903070 -TTTTT
1 ATTTTT
903075 AAAAACTTTC
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
17 2 0.06
18 23 0.70
19 8 0.24
ACGTcount: A:0.25, C:0.02, G:0.07, T:0.67
Consensus pattern (18 bp):
ATTTTTTGAGTTTTTAAT
Found at i:910229 original size:40 final size:39
Alignment explanation
Indices: 910192--910283 Score: 132
Period size: 39 Copynumber: 2.3 Consensus size: 39
910182 GCTACTCGTT
*
910192 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGG-CATAGCCCGGAAT-TAGTAACTCGCA
* *
910232 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCATAGCCCGGAATTAGTAACTCGCA
910271 CAAATGCCTTCGG
1 CAAATGCCTTCGG
910284 ATCTTAGTCC
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
39 33 0.69
40 15 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGGCATAGCCCGGAATTAGTAACTCGCA
Found at i:910263 original size:39 final size:40
Alignment explanation
Indices: 910173--910336 Score: 176
Period size: 40 Copynumber: 4.1 Consensus size: 40
910163 CGGAATTTAA
** *
910173 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
*
910213 CCGGTTATAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
910252 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
910292 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
910332 CCGGA
1 CCGGA
910337 CATCATTCAA
Statistics
Matches: 105, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
38 3 0.03
39 32 0.30
40 58 0.55
41 12 0.11
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:914183 original size:21 final size:21
Alignment explanation
Indices: 914158--914205 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
914148 CTAAACATGG
*
914158 CCGTGTGGCTA-TCTCACACAC
1 CCGTGTGACTACTC-CACACAC
914179 CCGTGTGACTACTCCACACAC
1 CCGTGTGACTACTCCACACAC
914200 CCGTGT
1 CCGTGT
914206 ATCCAACCGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.19, C:0.40, G:0.19, T:0.23
Consensus pattern (21 bp):
CCGTGTGACTACTCCACACAC
Found at i:914223 original size:147 final size:147
Alignment explanation
Indices: 913964--914252 Score: 479
Period size: 147 Copynumber: 2.0 Consensus size: 147
913954 ACACGCCGTC
* *
913964 TGTCCAGAACGTTTGATAGAGCCCAGACCGTATGGCTCCAAACATGGCTGTGTGGTTATCCCACA
1 TGTCCAGAACGTTTGATAGAGCCCAGACCGTATGGCTCCAAACATGGCCGTGTGGCTATCCCACA
* * * **
914029 CGCCCGTGTGACTACTCCACACACCCATGTGTCCAACCGTGTGCTTACCTGTGTAACTCACTGAC
66 CACCCGTGTGACTACTCCACACACCCATGTATCCAACCGTGTACTTACCCATGTAACTCACTGAC
914094 TTGGCTCACACGTCATG
131 TTGGCTCACACGTCATG
* * *
914111 TGTCCAGAACGTTTGATAGAGCCCAGACTGTATGGCTCTAAACATGGCCGTGTGGCTATCTCACA
1 TGTCCAGAACGTTTGATAGAGCCCAGACCGTATGGCTCCAAACATGGCCGTGTGGCTATCCCACA
*
914176 CACCCGTGTGACTACTCCACACACCCGTGTATCCAACCGTGTACTTACCCATGTAACTCACTGAC
66 CACCCGTGTGACTACTCCACACACCCATGTATCCAACCGTGTACTTACCCATGTAACTCACTGAC
914241 TTGGCTCACACG
131 TTGGCTCACACG
914253 CCCGTGTCTC
Statistics
Matches: 131, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
147 131 1.00
ACGTcount: A:0.23, C:0.31, G:0.21, T:0.25
Consensus pattern (147 bp):
TGTCCAGAACGTTTGATAGAGCCCAGACCGTATGGCTCCAAACATGGCCGTGTGGCTATCCCACA
CACCCGTGTGACTACTCCACACACCCATGTATCCAACCGTGTACTTACCCATGTAACTCACTGAC
TTGGCTCACACGTCATG
Found at i:919047 original size:90 final size:89
Alignment explanation
Indices: 918888--919139 Score: 233
Period size: 90 Copynumber: 2.8 Consensus size: 89
918878 ATAAGCTCAT
* * * * * * *
918888 TGCTCTTAATAAGTTCATAGCCCAGATTTTGGGTGGTCTTGCT-AGGACGGACTTGATGAATTCA
1 TGCTCTTAATGAGTTCATAACCCAG-GTTTGGGTGGTCCTACTGA-GACGAACTTGATGAACTCA
* *
918952 CCGAATTTATAAGATGAAG-TACTAGA
64 CCGAATTTATAAGAT-AAGCCACTAAA
*
918978 TGCTCTTAATGAGTTCATAACCCATGGTTTGGGTGGTCCTATTGAGACGAACTTGATGAAC-CTA
1 TGCTCTTAATGAGTTCATAACCCA-GGTTTGGGTGGTCCTACTGAGACGAACTTGATGAACTC-A
* * *
919042 TCGAATTTATAGGGTAAGCCACTAAA
64 CCGAATTTATAAGATAAGCCACTAAA
* * * * * *
919068 TGTTCTTAATGAATTCATATCCCAGGCTTTAGGTGGTCCTAGTGAGAC-AGACTTGATGAATTCA
1 TGCTCTTAATGAGTTCATAACCCAGG-TTTGGGTGGTCCTACTGAGACGA-ACTTGATGAACTCA
*
919132 CTGAATTT
64 CCGAATTT
919140 TTAAACTGAG
Statistics
Matches: 134, Mismatches: 21, Indels: 14
0.79 0.12 0.08
Matches are distributed among these distances:
89 7 0.05
90 124 0.93
91 3 0.02
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (89 bp):
TGCTCTTAATGAGTTCATAACCCAGGTTTGGGTGGTCCTACTGAGACGAACTTGATGAACTCACC
GAATTTATAAGATAAGCCACTAAA
Found at i:920018 original size:45 final size:46
Alignment explanation
Indices: 919967--920072 Score: 112
Period size: 44 Copynumber: 2.4 Consensus size: 46
919957 TTTTTAAGTA
*
919967 TGTATTAATTAGGGTTATAAG-GTTTGTTAAATTATGGTTAATGATT
1 TGTATTAATTAGGGTTATAAGTGTTTGTT-AATTAGGGTTAATGATT
* * * * *
920013 T-TATT-ATTATGGTCATTAGTGTTTGTTAATTAGGGTTTATGGTT
1 TGTATTAATTAGGGTTATAAGTGTTTGTTAATTAGGGTTAATGATT
*
920057 TGT-TAAATTAGGGTTA
1 TGTATTAATTAGGGTTA
920073 ATGATTTTAT
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
44 27 0.56
45 20 0.42
46 1 0.02
ACGTcount: A:0.26, C:0.01, G:0.23, T:0.50
Consensus pattern (46 bp):
TGTATTAATTAGGGTTATAAGTGTTTGTTAATTAGGGTTAATGATT
Found at i:920057 original size:21 final size:21
Alignment explanation
Indices: 919971--920071 Score: 71
Period size: 23 Copynumber: 4.6 Consensus size: 21
919961 TAAGTATGTA
*
919971 TTAATTAGGGTTATAAGGTTTG
1 TTAATTAGGGTT-TATGGTTTG
* * *
919993 TTAAATTATGGTTAATGATTT-
1 TT-AATTAGGGTTTATGGTTTG
* *
920014 TATTATTATGGTCATTA-GTGTTTG
1 T-TAATTAGGGT--TTATG-GTTTG
920038 TTAATTAGGGTTTATGGTTTG
1 TTAATTAGGGTTTATGGTTTG
920059 TTAAATTAGGGTT
1 TT-AATTAGGGTT
920072 AATGATTTTA
Statistics
Matches: 62, Mismatches: 9, Indels: 16
0.71 0.10 0.18
Matches are distributed among these distances:
21 19 0.31
22 20 0.32
23 22 0.35
24 1 0.02
ACGTcount: A:0.26, C:0.01, G:0.23, T:0.50
Consensus pattern (21 bp):
TTAATTAGGGTTTATGGTTTG
Found at i:920064 original size:66 final size:66
Alignment explanation
Indices: 919969--920154 Score: 237
Period size: 66 Copynumber: 2.8 Consensus size: 66
919959 TTTAAGTATG
* *
919969 TATTAATTAGGGTTATAAGGTTTGTTAAATTATGGTTAATGATTTTATTATTATGGTCATTAGTG
1 TATTAATTAGGGTT-TAAGGTTTGTTAAATTAAGGTTAATGATTTTATTATTAGGGTCATTAGTG
920034 TT
65 TT
* * * * **
920036 TGTTAATTAGGGTTTATGGTTTGTTAAATTAGGGTTAATGATTTTATTATGAGGGTTTTTAGTGT
1 TATTAATTAGGGTTTAAGGTTTGTTAAATTAAGGTTAATGATTTTATTATTAGGGTCATTAGTGT
920101 T
66 T
* * * * * *
920102 TATAAATTAAGGTTTAAAGTTTATTAATTTAAGATTAATGATTTTATTATTAG
1 TATTAATTAGGGTTTAAGGTTTGTTAAATTAAGGTTAATGATTTTATTATTAG
920155 AGTTTTAGGG
Statistics
Matches: 102, Mismatches: 17, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
66 89 0.87
67 13 0.13
ACGTcount: A:0.30, C:0.01, G:0.19, T:0.51
Consensus pattern (66 bp):
TATTAATTAGGGTTTAAGGTTTGTTAAATTAAGGTTAATGATTTTATTATTAGGGTCATTAGTGT
T
Found at i:920706 original size:36 final size:36
Alignment explanation
Indices: 920655--920726 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
920645 TTTTAGAAGA
*
920655 ATAGAAGTTCGTAGGGAAGACATAAGTTGGAGCAAT
1 ATAGAAGTTCATAGGGAAGACATAAGTTGGAGCAAT
*
920691 ATAGAAGTTCATAGGGAAGGCATAAGTTGGAGCAAT
1 ATAGAAGTTCATAGGGAAGACATAAGTTGGAGCAAT
920727 GGTACTATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.39, C:0.08, G:0.31, T:0.22
Consensus pattern (36 bp):
ATAGAAGTTCATAGGGAAGACATAAGTTGGAGCAAT
Found at i:927114 original size:50 final size:50
Alignment explanation
Indices: 927006--927243 Score: 230
Period size: 50 Copynumber: 4.7 Consensus size: 50
926996 ATTTGGGTAA
927006 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--TGAG---ATG
* *
927062 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGAGATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATG
* * * * *
927112 AGAGGTCCC-TCGTAAGACCATGTTTGGGACATGGCATGGGCACCGATATG
1 AGAGATCCCAT-GTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATG
* * * ** * *
927162 AGA-ACTCCCATGTAAGACCATATCTGGGATATGACATTGGCGGT-ACAAG
1 AGAGA-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATG
* * *
927211 AAACATCACATGTAAGACCATGTCTGGGACATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATG
927244 AATTTGGCAT
Statistics
Matches: 156, Mismatches: 22, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
49 31 0.20
50 79 0.51
51 1 0.01
53 4 0.03
55 1 0.01
56 40 0.26
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (50 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATG
Found at i:927410 original size:22 final size:22
Alignment explanation
Indices: 927384--927428 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
927374 TTATAAGAGT
927384 TAAGAACATATTCTGTTATCAA
1 TAAGAACATATTCTGTTATCAA
927406 TAAGAACATATTCTGTTATCAA
1 TAAGAACATATTCTGTTATCAA
927428 T
1 T
927429 TGAAAACCAA
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:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (22 bp):
TAAGAACATATTCTGTTATCAA
Found at i:933462 original size:16 final size:17
Alignment explanation
Indices: 933438--933470 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
933428 CAAAATCTAA
*
933438 CCATTTTAACC-TAAAT
1 CCATGTTAACCATAAAT
933454 CCATGTTAACCATAAAT
1 CCATGTTAACCATAAAT
933471 GCAAGGGACC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.39, C:0.24, G:0.03, T:0.33
Consensus pattern (17 bp):
CCATGTTAACCATAAAT
Found at i:942905 original size:12 final size:12
Alignment explanation
Indices: 942888--942919 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
942878 TACCCAATTA
942888 AATTAATTCTAT
1 AATTAATTCTAT
942900 AATTAATTCTAT
1 AATTAATTCTAT
942912 AATTAATT
1 AATTAATT
942920 TAATTTAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (12 bp):
AATTAATTCTAT
Found at i:947003 original size:42 final size:41
Alignment explanation
Indices: 946949--947085 Score: 132
Period size: 42 Copynumber: 3.3 Consensus size: 41
946939 CAGTACACAT
*
946949 AGTGCATTATCAGACAAGTCGAAGCAAATATACTAGCACGTA
1 AGTGCATCATCAGACAA-TCGAAGCAAATATACTAGCACGTA
* * * *
946991 AGTGCATCATCAGATGAATTGAAGCAAATATACTAGTACATA
1 AGTGCATCATCAGA-CAATCGAAGCAAATATACTAGCACGTA
* * * * *
947033 AGTGAATCATC-GAATAAACCAAAACAAATATACTAGCACGTA
1 AGTGCATCATCAG-A-CAATCGAAGCAAATATACTAGCACGTA
*
947075 AGTACATCATC
1 AGTGCATCATC
947086 GGATAAACTG
Statistics
Matches: 78, Mismatches: 15, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
41 1 0.01
42 75 0.96
43 2 0.03
ACGTcount: A:0.44, C:0.18, G:0.15, T:0.23
Consensus pattern (41 bp):
AGTGCATCATCAGACAATCGAAGCAAATATACTAGCACGTA
Found at i:948964 original size:17 final size:17
Alignment explanation
Indices: 948942--948974 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
948932 TAATTTCTCA
948942 TTATTTATTTCTTTTTG
1 TTATTTATTTCTTTTTG
948959 TTATTTATTTCTTTTT
1 TTATTTATTTCTTTTT
948975 ATTCCTCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.06, G:0.03, T:0.79
Consensus pattern (17 bp):
TTATTTATTTCTTTTTG
Found at i:951571 original size:20 final size:20
Alignment explanation
Indices: 951543--951582 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
951533 GGGATGATAA
*
951543 TGATGATTTTAAAATCATTT
1 TGATAATTTTAAAATCATTT
951563 TGATAATTTTAAAATCATTT
1 TGATAATTTTAAAATCATTT
951583 GCTGACGTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (20 bp):
TGATAATTTTAAAATCATTT
Found at i:957786 original size:16 final size:16
Alignment explanation
Indices: 957765--957797 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
957755 ACTATAGTGG
*
957765 AATGAGTTTATGATTA
1 AATGAGTTTATAATTA
957781 AATGAGTTTATAATTA
1 AATGAGTTTATAATTA
957797 A
1 A
957798 TAGTAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.42
Consensus pattern (16 bp):
AATGAGTTTATAATTA
Found at i:960210 original size:18 final size:18
Alignment explanation
Indices: 960189--960223 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
960179 TTAAAAATTC
*
960189 ATATTTTTTATTTTTAAT
1 ATATTTTTTAATTTTAAT
960207 ATATTTTTTAATTTTAA
1 ATATTTTTTAATTTTAA
960224 AATACATAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
ATATTTTTTAATTTTAAT
Found at i:975046 original size:7 final size:7
Alignment explanation
Indices: 975034--975058 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
975024 AGTCGATTGA
975034 TATTTAG
1 TATTTAG
975041 TATTTAG
1 TATTTAG
975048 TATTTAG
1 TATTTAG
975055 TATT
1 TATT
975059 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:975736 original size:18 final size:18
Alignment explanation
Indices: 975710--975744 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
975700 AGGTGCGTTT
*
975710 CCTAGCCCTTATATGTAC
1 CCTAACCCTTATATGTAC
975728 CCTAACCCTTATATGTA
1 CCTAACCCTTATATGTA
975745 TCATTTTTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.31, G:0.09, T:0.34
Consensus pattern (18 bp):
CCTAACCCTTATATGTAC
Found at i:976184 original size:43 final size:45
Alignment explanation
Indices: 976128--976213 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 45
976118 ATATTTTGAA
*
976128 TATTTTGAAATTATTTTATGTAA-AAAAAAGAAATTT-TTTGAGT
1 TATTTTGAAATTATTTGATGTAATAAAAAAGAAATTTATTTGAGT
* * *
976171 TATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGA
1 TATTTTGAAATTATTTGATGTAATAAAAAAGAAATTTATTTGA
976214 TGTAATAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
43 21 0.57
44 11 0.30
45 5 0.14
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.48
Consensus pattern (45 bp):
TATTTTGAAATTATTTGATGTAATAAAAAAGAAATTTATTTGAGT
Found at i:976215 original size:25 final size:25
Alignment explanation
Indices: 976181--976293 Score: 123
Period size: 25 Copynumber: 4.7 Consensus size: 25
976171 TATTTTGATA
976181 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
*
976206 TTATTTGATGTAATAAAATAGAAAT
1 TTATTTGATGTAATAAAATAGAAGT
** *
976231 TT-TTTCGA-GT--T-ATTTTG-A-T
1 TTATTT-GATGTAATAAAATAGAAGT
976250 ATTATTTGATGTAATAAAATAGAAGT
1 -TTATTTGATGTAATAAAATAGAAGT
976276 TTATTTGATGTAATAAAA
1 TTATTTGATGTAATAAAA
976294 ACCCTAACCT
Statistics
Matches: 72, Mismatches: 7, Indels: 18
0.74 0.07 0.19
Matches are distributed among these distances:
19 1 0.01
20 5 0.07
21 8 0.11
22 1 0.01
23 1 0.01
24 8 0.11
25 47 0.65
26 1 0.01
ACGTcount: A:0.41, C:0.01, G:0.14, T:0.44
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:976248 original size:70 final size:69
Alignment explanation
Indices: 976138--976294 Score: 280
Period size: 70 Copynumber: 2.3 Consensus size: 69
976128 TATTTTGAAA
*
976138 TTATTTTATGTAA-AAAAAAGAAATTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAATAG
1 TTATTTGATGTAATAAAAAAGAAATTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAATAG
976202 AAGT
66 AAGT
*
976206 TTATTTGATGTAATAAAATAGAAATTTTTTCGAGTTATTTTGATATTATTTGATGTAATAAAATA
1 TTATTTGATGTAATAAAAAAGAAATTTTTT-GAGTTATTTTGATATTATTTGATGTAATAAAATA
976271 GAAGT
65 GAAGT
976276 TTATTTGATGTAATAAAAA
1 TTATTTGATGTAATAAAAA
976295 CCCTAACCTA
Statistics
Matches: 84, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
68 12 0.14
69 15 0.18
70 57 0.68
ACGTcount: A:0.41, C:0.01, G:0.13, T:0.45
Consensus pattern (69 bp):
TTATTTGATGTAATAAAAAAGAAATTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAATAG
AAGT
Found at i:976355 original size:29 final size:30
Alignment explanation
Indices: 976303--976385 Score: 150
Period size: 29 Copynumber: 2.8 Consensus size: 30
976293 AACCCTAACC
*
976303 TAATTAAAAACCCTAAACCCTAACCTAATT
1 TAATTAAAAACCCTAAACCTTAACCTAATT
976333 TAATTAAAAACCCT-AACCTTAACCTAATT
1 TAATTAAAAACCCTAAACCTTAACCTAATT
976362 TAATTAAAAACCCTAAACCTTAAC
1 TAATTAAAAACCCTAAACCTTAAC
976386 TTAAAAACCC
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
29 28 0.55
30 23 0.45
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.28
Consensus pattern (30 bp):
TAATTAAAAACCCTAAACCTTAACCTAATT
Found at i:976390 original size:21 final size:21
Alignment explanation
Indices: 976361--976487 Score: 120
Period size: 21 Copynumber: 5.9 Consensus size: 21
976351 TTAACCTAAT
976361 TTAA-TTAAAAACCCTAAACC
1 TTAACTTAAAAACCCTAAACC
976381 TTAACTTAAAAACCCTAAACC
1 TTAACTTAAAAACCCTAAACC
976402 TTAACTTTAAAAACCCT-AACC
1 TTAAC-TTAAAAACCCTAAACC
* *
976423 -TAATTTAATACAAAACTCT-AACC
1 TTAA-CT--TA-AAAACCCTAAACC
976446 TAATTTAA-TTAAAAACCCTAAACC
1 ----TTAACTTAAAAACCCTAAACC
976470 TTAACTTAAAAACCCTAA
1 TTAACTTAAAAACCCTAA
976488 CCTAATTTAA
Statistics
Matches: 91, Mismatches: 3, Indels: 25
0.76 0.03 0.21
Matches are distributed among these distances:
20 12 0.13
21 38 0.42
22 13 0.14
23 18 0.20
24 6 0.07
26 1 0.01
28 3 0.03
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (21 bp):
TTAACTTAAAAACCCTAAACC
Found at i:976474 original size:89 final size:92
Alignment explanation
Indices: 976317--976564 Score: 310
Period size: 89 Copynumber: 2.6 Consensus size: 92
976307 TAAAAACCCT
976317 AAACCCTAACCTAATTTAATTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAAACCT
1 AAACCCTAACCTAATTTAATTAAAAA-CCT-A-CTTAACCTAATTTAATTAAAAACCCTAAACCT
976382 TAACTTAAAAACCCTAAACCTTAACTT-TA-A
63 TAACTTAAAAACCCT-AACC-TAACTTATACA
976412 AAACCCTAACCTAATTTAA-TACAAAA-CT-C-TAACCTAATTTAATTAAAAACCCTAAACCTTA
1 AAACCCTAACCTAATTTAATTA-AAAACCTACTTAACCTAATTTAATTAAAAACCCTAAACCTTA
*
976473 ACTTAAAAACCCTAACCTAATTTAATACA
65 ACTTAAAAACCCTAACCTAACTT-ATACA
* * *
976502 AAACCCTAACCTAAACCTTAATTAAAAACCCTAACCCTAACCTAAATTAATTAAAAACCCTAA
1 AAACCCTAACCT-AA-TTTAATTAAAAA-CCT-A-CTTAACCTAATTTAATTAAAAACCCTAA
976565 CCCTAACCTA
Statistics
Matches: 137, Mismatches: 3, Indels: 23
0.84 0.02 0.14
Matches are distributed among these distances:
87 5 0.04
88 4 0.03
89 47 0.34
90 14 0.10
91 2 0.01
92 8 0.06
93 4 0.03
94 4 0.03
95 23 0.17
97 1 0.01
98 25 0.18
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.27
Consensus pattern (92 bp):
AAACCCTAACCTAATTTAATTAAAAACCTACTTAACCTAATTTAATTAAAAACCCTAAACCTTAA
CTTAAAAACCCTAACCTAACTTATACA
Found at i:976497 original size:67 final size:70
Alignment explanation
Indices: 976373--976535 Score: 278
Period size: 67 Copynumber: 2.4 Consensus size: 70
976363 AATTAAAAAC
976373 CCTAAACCTTAACTTAAAAACCCTAAACCTTAACTTTAAAAACCCTAACCTAATTTAATACAAAA
1 CCTAAACCTTAA-TTAAAAACCCTAAACCTTAACTTTAAAAACCCTAACCTAATTTAATACAAAA
*
976438 CTCTAA
65 CCCTAA
*
976444 CCT-AA-TTTAATTAAAAACCCTAAACCTTAAC-TTAAAAACCCTAACCTAATTTAATACAAAAC
1 CCTAAACCTTAATTAAAAACCCTAAACCTTAACTTTAAAAACCCTAACCTAATTTAATACAAAAC
976506 CCTAA
66 CCTAA
976511 CCTAAACCTTAATTAAAAACCCTAA
1 CCTAAACCTTAATTAAAAACCCTAA
976536 CCCTAACCTA
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
67 38 0.44
68 23 0.26
69 21 0.24
70 2 0.02
71 3 0.03
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.26
Consensus pattern (70 bp):
CCTAAACCTTAATTAAAAACCCTAAACCTTAACTTTAAAAACCCTAACCTAATTTAATACAAAAC
CCTAA
Found at i:976526 original size:29 final size:29
Alignment explanation
Indices: 976480--977034 Score: 758
Period size: 29 Copynumber: 19.1 Consensus size: 29
976470 TTAACTTAAA
976480 AACCCTAACCTAATTTAA-TACAAAACCCT
1 AACCCTAACCTAATTTAATTA-AAAACCCT
976509 AA-CCTAAACC----TTAATTAAAAACCCT
1 AACCCT-AACCTAATTTAATTAAAAACCCT
*
976534 AACCCTAACCTAAATTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
976563 AACCCTAACCTAAATTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
* *
976592 AACCCTAACATAAATTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
976621 AACCCTAACCTAATTTAATTAAAAATCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
976650 ACCCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
976679 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
976708 AACCCTAACCTAAATTAATTAAAAACCCTAACCCT
1 AACCCTAACCTAATTTAATT--AAA----AACCCT
976743 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
976772 AACCCTAACCTAATTTAATTAAAAAACCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
* *
976801 AACACTAACCTAATTTAATTAAAGACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
976830 AACCCTAACCTAAATTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
* *
976859 AATCCTAACCTAAATTAATT-AAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
976887 AAACCCTAACCTAATTTAATTAAAGACCCT
1 -AACCCTAACCTAATTTAATTAAAAACCCT
976917 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
976946 AACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
976975 AACCCTAACCCCAACCTAATTTAATTAAAAACCCT
1 AACCCT------AACCTAATTTAATTAAAAACCCT
977010 AA-CCT-A---AA-TTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
977033 AA
1 AA
977035 ACTAAGTTAA
Statistics
Matches: 484, Mismatches: 21, Indels: 48
0.88 0.04 0.09
Matches are distributed among these distances:
23 17 0.04
24 2 0.00
25 18 0.04
26 5 0.01
27 1 0.00
28 11 0.02
29 364 0.75
30 7 0.01
31 3 0.01
33 3 0.01
34 3 0.01
35 50 0.10
ACGTcount: A:0.46, C:0.27, G:0.00, T:0.26
Consensus pattern (29 bp):
AACCCTAACCTAATTTAATTAAAAACCCT
Found at i:977013 original size:23 final size:23
Alignment explanation
Indices: 976981--977044 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
976971 CCCTAACCCT
* *
976981 AACCCCAACCTAATTTAATTAAA
1 AACCCTAACCTAAATTAATTAAA
977004 AACCCTAACCTAAATTAATTAAA
1 AACCCTAACCTAAATTAATTAAA
* *
977027 AACCCTAAACTAAGTTAA
1 AACCCTAACCTAAATTAA
977045 CAATGTTACA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.50, C:0.23, G:0.02, T:0.25
Consensus pattern (23 bp):
AACCCTAACCTAAATTAATTAAA
Found at i:977194 original size:116 final size:116
Alignment explanation
Indices: 977041--977394 Score: 609
Period size: 116 Copynumber: 3.1 Consensus size: 116
977031 CTAAACTAAG
* * * *
977041 TTAACAATGTTACATTCACGTAATGTTAGATTGGGAAAAATGTTTTGACTGGTACTAACAATTAA
1 TTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
*
977106 TAATTTTACATAATTTGATAATTTTACTAACCACTAATACAATTTTTTGAC
66 TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
*
977157 TTAATAATTTTACATTCACATAATGGTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
1 TTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
977222 TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
66 TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
* * * *
977273 TAAATAATTTTACATTCACATAATGTTAGATTTCGAAAAATGTTTTGATTGGTACTAGCAATTAA
1 TTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
*
977338 TAATTTTATATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
66 TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
977389 TTAATA
1 TTAATA
977395 CAATTTATCA
Statistics
Matches: 225, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
116 225 1.00
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (116 bp):
TTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
Found at i:977411 original size:17 final size:18
Alignment explanation
Indices: 977370--977411 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
977360 TTTACTAACC
* *
977370 ATTAATACAATTTTTTGA
1 ATTAATACAATTTTATCA
*
977388 CTTAATACAA-TTTATCA
1 ATTAATACAATTTTATCA
977405 ATTAATA
1 ATTAATA
977412 ATTTCACAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTAATACAATTTTATCA
Found at i:985045 original size:64 final size:64
Alignment explanation
Indices: 984944--985071 Score: 229
Period size: 64 Copynumber: 2.0 Consensus size: 64
984934 ATATGTCACC
984944 GGATCAACAAAAGAACAAAATCGATACGTGATAGACAGAACTTTCATTGGCATAGTTCTGAAAA
1 GGATCAACAAAAGAACAAAATCGATACGTGATAGACAGAACTTTCATTGGCATAGTTCTGAAAA
* * *
985008 GGATCAACAGAAGAACAAAATCGATACGTGATAGACAGAACTTTCATTGGCGTCGTTCTGAAAA
1 GGATCAACAAAAGAACAAAATCGATACGTGATAGACAGAACTTTCATTGGCATAGTTCTGAAAA
985072 TTTTACGCCT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.22
Consensus pattern (64 bp):
GGATCAACAAAAGAACAAAATCGATACGTGATAGACAGAACTTTCATTGGCATAGTTCTGAAAA
Found at i:985483 original size:124 final size:125
Alignment explanation
Indices: 985323--985676 Score: 557
Period size: 124 Copynumber: 2.8 Consensus size: 125
985313 CCCAAACAAG
*
985323 CTACTGTAGCAAAAGCGCGTCTACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
*
985388 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAT-TTTATTTCTTACATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAATAATTATTTCTTACATGAC
* * * *
985447 CTACTGTAGCAAAAGTGCGTCCACAAGGCCACGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* *
985512 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATAATTATTTCTTCCGTGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTC--AAAAAATAATTATTTCTTACATGAC
* *
985574 CTACTGTAGCAAAAACGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAAGCATCCTT
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAAT-AGCATCCTG
** *
985639 CTAGAAGCGATTTTATACTATTTTATCAGAAATGTCAA
65 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAA
985677 CTCGAAATTA
Statistics
Matches: 209, Mismatches: 17, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
124 95 0.45
126 9 0.04
127 64 0.31
128 41 0.20
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAATAATTATTTCTTACATGAC
Found at i:986959 original size:17 final size:17
Alignment explanation
Indices: 986937--986970 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
986927 ATATTTATCA
986937 ATAAAATAAAAATAATT
1 ATAAAATAAAAATAATT
986954 ATAAAATAAAAATAATT
1 ATAAAATAAAAATAATT
986971 TTTTTAATTT
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:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAATAAAAATAATT
Found at i:993451 original size:19 final size:19
Alignment explanation
Indices: 993429--993475 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
993419 ATTGGAACGT
* *
993429 AAAGTGCATATTGGCGCAC
1 AAAGTGCATACTGGCACAC
*
993448 AAAGCGCATACTGGCACAC
1 AAAGTGCATACTGGCACAC
*
993467 GAAGTGCAT
1 AAAGTGCAT
993476 CTTGACGTGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.34, C:0.23, G:0.26, T:0.17
Consensus pattern (19 bp):
AAAGTGCATACTGGCACAC
Found at i:1000479 original size:41 final size:41
Alignment explanation
Indices: 1000417--1000587 Score: 213
Period size: 41 Copynumber: 4.2 Consensus size: 41
1000407 ATTATTGCTT
*
1000417 AATTGCACATATGTGCTCC-TGTTTGTACTTCGGTACCCCTA
1 AATTGCACATACGTGC-CCTTGTTTGTACTTCGGTACCCCTA
* *
1000458 AATTGAACATACGTGTCCC-TGTTTGTACTTCGGTAACCCTA
1 AATTGCACATACGTG-CCCTTGTTTGTACTTCGGTACCCCTA
* * *
1000499 AATTGCACATATGTGCCCTTATTTGTACTTCGGTACCCCTG
1 AATTGCACATACGTGCCCTTGTTTGTACTTCGGTACCCCTA
* * * *
1000540 AATTGCACATACATGCCCTTTTTTATACTTCGGTACCTCTA
1 AATTGCACATACGTGCCCTTGTTTGTACTTCGGTACCCCTA
1000581 AA-TGCAC
1 AATTGCAC
1000588 TTTTTTCCTG
Statistics
Matches: 114, Mismatches: 14, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
40 8 0.07
41 105 0.92
42 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.36
Consensus pattern (41 bp):
AATTGCACATACGTGCCCTTGTTTGTACTTCGGTACCCCTA
Found at i:1007981 original size:27 final size:27
Alignment explanation
Indices: 1007945--1008022 Score: 138
Period size: 27 Copynumber: 2.9 Consensus size: 27
1007935 AAATGTGAAG
*
1007945 GGGGTTGCTAAGTGCTGATTCCCGCAA
1 GGGGTTGCTAAGTGCTGATTCCCCCAA
1007972 GGGGTTGCTAAGTGCTGATTCCCCCAA
1 GGGGTTGCTAAGTGCTGATTCCCCCAA
*
1007999 GAGGTTGCTAAGTGCTGATTCCCC
1 GGGGTTGCTAAGTGCTGATTCCCC
1008023 GACTCATTGG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.18, C:0.24, G:0.31, T:0.27
Consensus pattern (27 bp):
GGGGTTGCTAAGTGCTGATTCCCCCAA
Found at i:1008078 original size:129 final size:130
Alignment explanation
Indices: 1007843--1008098 Score: 415
Period size: 129 Copynumber: 2.0 Consensus size: 130
1007833 GAATATAAAG
* * *
1007843 GGGGTTGCTAAGTGCTTATTCCCCCAAGGGGTTTCTAAGTGCTGATTCCCCGAATCATTGGTGGT
1 GGGGTTGCTAAGTGCTGATTCCCCCAAGAGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGT
* * * *
1007908 TGTTAAGTGCTGATTCCACCGTATTTTAAATGTGAAGGGGGTTGCTAAGTGCTGA-TTCCCGCAA
66 TGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTTCCCGCAA
*
1007972 GGGGTTGCTAAGTGCTGATTCCCCCAAGAGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGT
1 GGGGTTGCTAAGTGCTGATTCCCCCAAGAGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGT
* *
1008037 TGCTAAGTGCTGATCCCATCGTATCTTAAATGTGAAAGGGGTTGCTAAGTGTTGATTTCCCG
66 TGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTTCCCG
1008099 AATCACTGGT
Statistics
Matches: 116, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
129 110 0.95
130 6 0.05
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.32
Consensus pattern (130 bp):
GGGGTTGCTAAGTGCTGATTCCCCCAAGAGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGT
TGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTTCCCGCAA
Found at i:1013095 original size:22 final size:22
Alignment explanation
Indices: 1013067--1013116 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
1013057 GGGTCATGTC
*
1013067 TTGTCTCAAGACATAAGAC-CAT
1 TTGTCTCAAGACAT-ACACTCAT
*
1013089 TTGTCTCAAGATATACACTCAT
1 TTGTCTCAAGACATACACTCAT
1013111 TTGTCT
1 TTGTCT
1013117 TGAGATAGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 3 0.12
22 22 0.88
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (22 bp):
TTGTCTCAAGACATACACTCAT
Found at i:1019088 original size:32 final size:32
Alignment explanation
Indices: 1019033--1019131 Score: 128
Period size: 32 Copynumber: 3.1 Consensus size: 32
1019023 AGGACCGGCC
* *
1019033 TAAATCAAGCCTTCATATGGCATTGATTTAAT
1 TAAATCAAGCCTTAATATAGCATTGATTTAAT
* *
1019065 TAAATCAAACCTTAATATAGCATTCATTTAAT
1 TAAATCAAGCCTTAATATAGCATTGATTTAAT
*
1019097 TAAATCAAGGCTTAAT-TAAGCATTGATTTTAAT
1 TAAATCAAGCCTTAATAT-AGCATTGA-TTTAAT
1019130 TA
1 TA
1019132 CCAATAGTTA
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
31 1 0.02
32 49 0.84
33 8 0.14
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.38
Consensus pattern (32 bp):
TAAATCAAGCCTTAATATAGCATTGATTTAAT
Found at i:1027630 original size:217 final size:217
Alignment explanation
Indices: 1027132--1027652 Score: 927
Period size: 217 Copynumber: 2.4 Consensus size: 217
1027122 CAAGTCCCAC
* * *
1027132 AGCTTGAGCCAAAAAGCTTTGATGATTGCGTATAACTCAAAAACCACATTAAAATCAACTTTTGG
1 AGCTTCAGTCAAAAAGCTTTGATGATTGCATATAACTCAAAAACCACATTAAAATCAACTTTTGG
1027197 TTGTTCTCATTCAACATGAAAATGGGATTGAAATGCTAAAAAACAATTTAGGAACAACAAACAAT
66 TTGTTCTCATTCAACATGAAAATGGGATTGAAATGCTAAAAAACAATTTAGGAACAACAAACAAT
*
1027262 AACATAAAGGTATGCTACCATACTATCGGCACCAAAATACCTCAACAAGCAATCAACATAATATT
131 AACATAAAAGTATGCTACCATACTATCGGCACCAAAATACCTCAACAAGCAATCAACATAATATT
1027327 ATAAAACAACCTCAACTTACAT
196 ATAAAACAACCTCAACTTACAT
*
1027349 AGCTTCAGTCAAAAAGCTTTGATGATTGCATATAACTCAAAAACCACATTGAAATCAACTTTTGG
1 AGCTTCAGTCAAAAAGCTTTGATGATTGCATATAACTCAAAAACCACATTAAAATCAACTTTTGG
1027414 TTGTTCTCATTCAACATGAAAATGGGATTGAAATGCTAAAAAACAATTTAGG-ACAACAAACAAT
66 TTGTTCTCATTCAACATGAAAATGGGATTGAAATGCTAAAAAACAATTTAGGAACAACAAACAAT
*
1027478 AACATAAAAGTATGCTACCATACTATTGGCACCAAAATACCTCAACAAGCAATCAACATAATATT
131 AACATAAAAGTATGCTACCATACTATCGGCACCAAAATACCTCAACAAGCAATCAACATAATATT
1027543 ATAAAACAACCTCAACTTACAT
196 ATAAAACAACCTCAACTTACAT
*
1027565 AGCTTCAGTCAAAAAGCTTTGATGATTGCATATAACTCAAAAACCACCATTAAAATCATCTTTTG
1 AGCTTCAGTCAAAAAGCTTTGATGATTGCATATAACTCAAAAACCA-CATTAAAATCAACTTTTG
** * *
1027630 GTCATTTTCGTTCAACATGAAAA
65 GTTGTTCTCATTCAACATGAAAA
1027653 AAGGATAGAA
Statistics
Matches: 291, Mismatches: 12, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
216 143 0.49
217 148 0.51
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.26
Consensus pattern (217 bp):
AGCTTCAGTCAAAAAGCTTTGATGATTGCATATAACTCAAAAACCACATTAAAATCAACTTTTGG
TTGTTCTCATTCAACATGAAAATGGGATTGAAATGCTAAAAAACAATTTAGGAACAACAAACAAT
AACATAAAAGTATGCTACCATACTATCGGCACCAAAATACCTCAACAAGCAATCAACATAATATT
ATAAAACAACCTCAACTTACAT
Found at i:1043081 original size:126 final size:126
Alignment explanation
Indices: 1042856--1043095 Score: 444
Period size: 126 Copynumber: 1.9 Consensus size: 126
1042846 TTTGAGTAAT
*
1042856 TTCATTTGACTGCTTTGACTCAAAAGCCAAACACTAGTTTCAATTCAAGGTTATATCTTTTTCAC
1 TTCATTTGACTGCTTTGACTCAAAAGCCAAACACTAGTTCCAATTCAAGGTTATATCTTTTTCAC
* *
1042921 TTTCTTTTCAGATTTCTTAGCTTGTTTGGTTGCTGAGAAAAAAAAAAAAAAGAAGAACCAA
66 TTTCCTTTCAGATTTCTTAGCTCGTTTGGTTGCTGAGAAAAAAAAAAAAAAGAAGAACCAA
*
1042982 TTCATTTGACTGCTTTGTCTCAAAAGCCAAACACTAGTTCCAATTCAAGGTTATATCTTTTTCAC
1 TTCATTTGACTGCTTTGACTCAAAAGCCAAACACTAGTTCCAATTCAAGGTTATATCTTTTTCAC
1043047 TTTCCTTTCAGATTTCTTAGCTCGTTTGGTTGCTGAGAAAAAAAAAAAA
66 TTTCCTTTCAGATTTCTTAGCTCGTTTGGTTGCTGAGAAAAAAAAAAAA
1043096 CCCAATTCTC
Statistics
Matches: 110, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
126 110 1.00
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (126 bp):
TTCATTTGACTGCTTTGACTCAAAAGCCAAACACTAGTTCCAATTCAAGGTTATATCTTTTTCAC
TTTCCTTTCAGATTTCTTAGCTCGTTTGGTTGCTGAGAAAAAAAAAAAAAAGAAGAACCAA
Found at i:1054744 original size:24 final size:24
Alignment explanation
Indices: 1054717--1054768 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
1054707 TTAGTAAGTC
*
1054717 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
1054741 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
1054765 AAAT
1 AAAT
1054769 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:1059744 original size:18 final size:17
Alignment explanation
Indices: 1059721--1059769 Score: 71
Period size: 18 Copynumber: 2.8 Consensus size: 17
1059711 TCCAATTTTT
* *
1059721 ATTAAATTATTTATTTA
1 ATTAAATTAATTATATA
1059738 ATATAAATTAATTATATA
1 AT-TAAATTAATTATATA
1059756 ATTAAATTAATTAT
1 ATTAAATTAATTAT
1059770 GTGGATTGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 14 0.48
18 15 0.52
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTAAATTAATTATATA
Found at i:1059760 original size:22 final size:21
Alignment explanation
Indices: 1059725--1059768 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
1059715 ATTTTTATTA
* *
1059725 AATTATTTATTTAATATAAATT
1 AATTATATAATTAA-ATAAATT
*
1059747 AATTATATAATTAAATTAATT
1 AATTATATAATTAAATAAATT
1059768 A
1 A
1059769 TGTGGATTGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AATTATATAATTAAATAAATT
Found at i:1062741 original size:21 final size:21
Alignment explanation
Indices: 1062715--1062755 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1062705 ATCTGCTCAA
* *
1062715 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
1062736 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
1062756 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:1068086 original size:19 final size:19
Alignment explanation
Indices: 1068062--1068109 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
1068052 TTTTTCGCTC
1068062 CAACTTGAAATGATCCAAA
1 CAACTTGAAATGATCCAAA
1068081 CAACTTGAAA-GA-CCAAA
1 CAACTTGAAATGATCCAAA
*
1068098 -AA-TTGAAGTGAT
1 CAACTTGAAATGAT
1068110 TATAACCTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 5 0.19
16 4 0.15
17 5 0.19
18 2 0.08
19 10 0.38
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.21
Consensus pattern (19 bp):
CAACTTGAAATGATCCAAA
Found at i:1071313 original size:20 final size:20
Alignment explanation
Indices: 1071288--1071337 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
1071278 TGGCTTAAAA
1071288 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
1071308 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
1071325 GTGGTAGTGGATT
1 TTGGTAGTGGATT
1071338 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:1075952 original size:20 final size:20
Alignment explanation
Indices: 1075927--1075976 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
1075917 TGGCTTAAAA
1075927 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
1075947 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
1075964 GTGGTAGTGGATT
1 TTGGTAGTGGATT
1075977 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:1077537 original size:40 final size:40
Alignment explanation
Indices: 1077493--1077591 Score: 128
Period size: 40 Copynumber: 2.5 Consensus size: 40
1077483 AAAAACGCTA
*
1077493 CTAAAAATCAAGCATTAGCGGCGCTTTTATAAAAACACAG
1 CTAAAAATCAAGCATTAGCGGCGCTTTTAGAAAAACACAG
* * * * *
1077533 CTAAAGATCGAGCATTAGCGGCGCTTTTCGAAAAACGCCG
1 CTAAAAATCAAGCATTAGCGGCGCTTTTAGAAAAACACAG
*
1077573 CTAAAAAT-AAGAATTAGCG
1 CTAAAAATCAAGCATTAGCG
1077592 CGTTTTCCGA
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
39 9 0.18
40 41 0.82
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.21
Consensus pattern (40 bp):
CTAAAAATCAAGCATTAGCGGCGCTTTTAGAAAAACACAG
Found at i:1077796 original size:41 final size:41
Alignment explanation
Indices: 1077652--1077811 Score: 221
Period size: 41 Copynumber: 3.9 Consensus size: 41
1077642 TGAGTTTTTG
* * * *
1077652 GGGCCTTTAGCGGTGTTTTTGGAGTAGTGCCACTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAATAGCGCCACTAATGCTC
* * * *
1077693 GGTCCTTTAGCAGCGTTTTTGAGATAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAATAGCGCCACTAATGCTC
*
1077734 GGGCCTTTAGCGGCTTTTTTGAAATAGCGCCACTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAATAGCGCCACTAATGCTC
* *
1077775 GGGCCTTTAGCGGCGTTTTTGAAATAGCACCGCTAAT
1 GGGCCTTTAGCGGCGTTTTTGAAATAGCGCCACTAAT
1077812 AATAATAAAA
Statistics
Matches: 103, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 103 1.00
ACGTcount: A:0.18, C:0.23, G:0.28, T:0.32
Consensus pattern (41 bp):
GGGCCTTTAGCGGCGTTTTTGAAATAGCGCCACTAATGCTC
Found at i:1078972 original size:11 final size:11
Alignment explanation
Indices: 1078948--1078992 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
1078938 GTATAGGACC
*
1078948 AAAATATAAGAA
1 AAAATA-AAAAA
1078960 AAAATAAAAAA
1 AAAATAAAAAA
*
1078971 AAAATAAAAAT
1 AAAATAAAAAA
*
1078982 GAAATAAAAAA
1 AAAATAAAAAA
1078993 CTAAAATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 23 0.79
12 6 0.21
ACGTcount: A:0.82, C:0.00, G:0.04, T:0.13
Consensus pattern (11 bp):
AAAATAAAAAA
Found at i:1078999 original size:18 final size:17
Alignment explanation
Indices: 1078959--1078998 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 17
1078949 AAATATAAGA
1078959 AAAAATAAAAAAAAAAT
1 AAAAATAAAAAAAAAAT
*
1078976 AAAAATGAAATAAAAAACT
1 AAAAAT-AAA-AAAAAAAT
1078995 AAAA
1 AAAA
1078999 TTTATACATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 6 0.30
18 3 0.15
19 11 0.55
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.12
Consensus pattern (17 bp):
AAAAATAAAAAAAAAAT
Found at i:1079087 original size:4 final size:4
Alignment explanation
Indices: 1079078--1079103 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1079068 TGAAAGATAC
1079078 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
1079104 ATATTTGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:1085253 original size:20 final size:20
Alignment explanation
Indices: 1085228--1085277 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
1085218 TGGCTTAAAA
1085228 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
1085248 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
1085265 GTGGTAGTGGATT
1 TTGGTAGTGGATT
1085278 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:1089892 original size:20 final size:20
Alignment explanation
Indices: 1089867--1089916 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
1089857 TGGCTTAAAA
1089867 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
1089887 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
1089904 GTGGTAGTGGATT
1 TTGGTAGTGGATT
1089917 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:1094163 original size:17 final size:19
Alignment explanation
Indices: 1094141--1094176 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
1094131 CTAAAATAGT
1094141 AACAAAA-TTA-ACAATAA
1 AACAAAAGTTATACAATAA
1094158 AACAAAAGTTATACAATAA
1 AACAAAAGTTATACAATAA
1094177 CAAAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 3 0.18
19 7 0.41
ACGTcount: A:0.67, C:0.11, G:0.03, T:0.19
Consensus pattern (19 bp):
AACAAAAGTTATACAATAA
Found at i:1094263 original size:23 final size:23
Alignment explanation
Indices: 1094214--1094262 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
1094204 AAATAGTAGC
*
1094214 AAAATAGTGAGAAAAAAAACAAG
1 AAAATAGTGAGAAAAAAAACAAA
1094237 AAAATAG-GA-AAAAAAAAGCAAA
1 AAAATAGTGAGAAAAAAAA-CAAA
1094259 AAAA
1 AAAA
1094263 AAAACTACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 8 0.33
22 9 0.38
23 7 0.29
ACGTcount: A:0.76, C:0.04, G:0.14, T:0.06
Consensus pattern (23 bp):
AAAATAGTGAGAAAAAAAACAAA
Found at i:1105296 original size:9 final size:9
Alignment explanation
Indices: 1105284--1105308 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1105274 TTTTTAATTT
1105284 AAAATTTTA
1 AAAATTTTA
1105293 AAAATTTTA
1 AAAATTTTA
1105302 AAAATTT
1 AAAATTT
1105309 AAATAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
AAAATTTTA
Found at i:1109221 original size:20 final size:20
Alignment explanation
Indices: 1109196--1109235 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1109186 CGTAAAATGA
*
1109196 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
1109216 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
1109236 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:1109225 original size:34 final size:35
Alignment explanation
Indices: 1109181--1109247 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
1109171 CAGTAAAATA
*
1109181 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
1109215 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
1109248 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:1109251 original size:14 final size:15
Alignment explanation
Indices: 1109175--1109251 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
1109165 GATTGCCAGT
* *
1109175 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
1109189 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
1109203 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
1109223 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
1109238 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
1109252 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:1124165 original size:31 final size:33
Alignment explanation
Indices: 1124127--1124202 Score: 93
Period size: 37 Copynumber: 2.2 Consensus size: 33
1124117 AAAGTTGAAA
*
1124127 ATCAGACA-GG-AAGGAAGATTAAGGTTCTCCG
1 ATCAGACAGGGAAAGGAAGATTAAGGATCTCCG
1124158 ATCAGACAACGGTGGAAAGGAAGATTAAGGATCTCCG
1 ATCAGAC-A--G-GGAAAGGAAGATTAAGGATCTCCG
1124195 ATCAGACA
1 ATCAGACA
1124203 ACGGTGGAGA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
31 7 0.18
32 1 0.03
36 3 0.08
37 27 0.71
ACGTcount: A:0.38, C:0.17, G:0.28, T:0.17
Consensus pattern (33 bp):
ATCAGACAGGGAAAGGAAGATTAAGGATCTCCG
Found at i:1124187 original size:37 final size:37
Alignment explanation
Indices: 1124137--1124210 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
1124127 ATCAGACAGG
*
1124137 AAGGAAGATTAAGGTTCTCCGATCAGACAACGGTGGA
1 AAGGAAGATTAAGGATCTCCGATCAGACAACGGTGGA
1124174 AAGGAAGATTAAGGATCTCCGATCAGACAACGGTGGA
1 AAGGAAGATTAAGGATCTCCGATCAGACAACGGTGGA
1124211 GAATATAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.36, C:0.16, G:0.30, T:0.18
Consensus pattern (37 bp):
AAGGAAGATTAAGGATCTCCGATCAGACAACGGTGGA
Found at i:1124728 original size:21 final size:22
Alignment explanation
Indices: 1124699--1124745 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
1124689 CAGAAGGAGT
*
1124699 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
1124721 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
1124742 GAGT
1 GAGT
1124746 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:1139100 original size:3 final size:3
Alignment explanation
Indices: 1139089--1139141 Score: 63
Period size: 3 Copynumber: 17.7 Consensus size: 3
1139079 CAATAATACC
* * *
1139089 AAT ACT AAT AAT AGT AA- AGAT GAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
1139134 AAT AAT AA
1 AAT AAT AA
1139142 AGTTAACAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
2 1 0.02
3 41 0.98
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:1141146 original size:88 final size:88
Alignment explanation
Indices: 1141011--1141398 Score: 717
Period size: 88 Copynumber: 4.4 Consensus size: 88
1141001 ATCGATGGAT
* * * *
1141011 GCAAGGCTTTGT-T-TTCGATCTGCTTCGCTGTTAATGTAGGAAGGCAAGATCTTTTGTCTTCAA
1 GCAAGG-TTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGAAAAGCAAGATCTTTTGTCTTCAA
1141074 CCAGCTCTATCACAACCGAAAGAG
65 CCAGCTCTATCACAACCGAAAGAG
1141098 GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGAAAAGCAAGATCTTTTGTCTTCAAC
1 GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGAAAAGCAAGATCTTTTGTCTTCAAC
1141163 CAGCTCTATCACAACCGAAAGAG
66 CAGCTCTATCACAACCGAAAGAG
1141186 GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGAAAAGCAAGATCTTTTGTCTTCAAC
1 GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGAAAAGCAAGATCTTTTGTCTTCAAC
1141251 CAGCTCTATCACAACCGAAAGAG
66 CAGCTCTATCACAACCGAAAGAG
1141274 GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGAAAAGCAAGATCTTTTGTCTTCAAC
1 GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGAAAAGCAAGATCTTTTGTCTTCAAC
1141339 CAGCTCTATCACAACCGAAAGAG
66 CAGCTCTATCACAACCGAAAGAG
1141362 GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATG
1 GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATG
1141399 NNNNNNNNNN
Statistics
Matches: 295, Mismatches: 4, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
86 5 0.02
87 7 0.02
88 283 0.96
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (88 bp):
GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGAAAAGCAAGATCTTTTGTCTTCAAC
CAGCTCTATCACAACCGAAAGAG
Found at i:1148708 original size:3 final size:3
Alignment explanation
Indices: 1148700--1148736 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1148690 NNNNNNNNNN
1148700 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1148737 AGTTAACAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1149674 original size:20 final size:20
Alignment explanation
Indices: 1149638--1149677 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1149628 TCCTATTGTT
1149638 GTTTTGTTACTGTTTGCTGC
1 GTTTTGTTACTGTTTGCTGC
*
1149658 GTTTCTGTTTCTG-TTGCTGC
1 GTTT-TGTTACTGTTTGCTGC
1149678 TTCCGTCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.03, C:0.17, G:0.25, T:0.55
Consensus pattern (20 bp):
GTTTTGTTACTGTTTGCTGC
Found at i:1161648 original size:29 final size:28
Alignment explanation
Indices: 1161615--1161697 Score: 96
Period size: 29 Copynumber: 2.9 Consensus size: 28
1161605 TATTTTTAAA
1161615 TTTTCTATATTTTT-TATTATTGTTTGCAC
1 TTTTCTATATTTTTATATTATTGTTT--AC
* * *
1161644 TTTTCAATATTTTTATAATATTGTTTAT
1 TTTTCTATATTTTTATATTATTGTTTAC
*
1161672 TTTTTTAATATTTTTATATTATTGTT
1 TTTTCT-ATATTTTTATATTATTGTT
1161698 ATTGCTCCTG
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
28 5 0.11
29 31 0.67
30 10 0.22
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.67
Consensus pattern (28 bp):
TTTTCTATATTTTTATATTATTGTTTAC
Found at i:1161674 original size:18 final size:17
Alignment explanation
Indices: 1161651--1161688 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
1161641 CACTTTTCAA
1161651 TATTTTTATAATATTGTT
1 TATTTTTATAATATT-TT
*
1161669 TATTTTTTTAATATTTT
1 TATTTTTATAATATTTT
1161686 TAT
1 TAT
1161689 ATTATTGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (17 bp):
TATTTTTATAATATTTT
Found at i:1166490 original size:91 final size:91
Alignment explanation
Indices: 1166335--1166516 Score: 355
Period size: 91 Copynumber: 2.0 Consensus size: 91
1166325 AATATCAGCA
*
1166335 TCAATCATAGCCCAAAGATTTTGTTTCAAAAATTGACAACTTTAAGCACAAGTAAGCTTTATGTC
1 TCAATCATAGCCCAAAGATTTTGTTTCAAAAATTGACAACTTTAAACACAAGTAAGCTTTATGTC
1166400 GTTGTGATGACCGTAGTGGCCACTTT
66 GTTGTGATGACCGTAGTGGCCACTTT
1166426 TCAATCATAGCCCAAAGATTTTGTTTCAAAAATTGACAACTTTAAACACAAGTAAGCTTTATGTC
1 TCAATCATAGCCCAAAGATTTTGTTTCAAAAATTGACAACTTTAAACACAAGTAAGCTTTATGTC
1166491 GTTGTGATGACCGTAGTGGCCACTTT
66 GTTGTGATGACCGTAGTGGCCACTTT
1166517 CATTGGCACG
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 90 1.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (91 bp):
TCAATCATAGCCCAAAGATTTTGTTTCAAAAATTGACAACTTTAAACACAAGTAAGCTTTATGTC
GTTGTGATGACCGTAGTGGCCACTTT
Found at i:1166688 original size:33 final size:33
Alignment explanation
Indices: 1166647--1166712 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
1166637 CTATAAAGTA
1166647 AAAAAAAGCTTAACCATCCCATGCTTTTTATTT
1 AAAAAAAGCTTAACCATCCCATGCTTTTTATTT
1166680 AAAAAAAGCTTAACCATCCCATGCTTTTTATTT
1 AAAAAAAGCTTAACCATCCCATGCTTTTTATTT
1166713 TGAAACTTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.36
Consensus pattern (33 bp):
AAAAAAAGCTTAACCATCCCATGCTTTTTATTT
Found at i:1173309 original size:33 final size:35
Alignment explanation
Indices: 1173272--1173342 Score: 101
Period size: 33 Copynumber: 2.1 Consensus size: 35
1173262 AATATAAATG
* *
1173272 TAAGTAGTCCATTAACAAAA-TTTTAAGCA-AACA
1 TAAGTAATCCATTAACAAAACTTTCAAGCATAACA
*
1173305 TAAGTAATCCCTTAACAAAACTTTCAAGCATAACA
1 TAAGTAATCCATTAACAAAACTTTCAAGCATAACA
1173340 TAA
1 TAA
1173343 CAAAAGAGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 18 0.55
34 8 0.24
35 7 0.21
ACGTcount: A:0.48, C:0.18, G:0.07, T:0.27
Consensus pattern (35 bp):
TAAGTAATCCATTAACAAAACTTTCAAGCATAACA
Found at i:1176287 original size:3 final size:3
Alignment explanation
Indices: 1176279--1176381 Score: 179
Period size: 3 Copynumber: 34.3 Consensus size: 3
1176269 ATTGGGTATT
*
1176279 ACA ACA ACA ACA ACA ACA ACA ATA ACA ACA ACA ACA ACA ACA ACA ACA
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA
* *
1176327 ACA ACA ACA ACA ACA ATA ACA AGA ACA ACA ACA ACA ACA ACA ACA ACA
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA
1176375 ACA ACA A
1 ACA ACA A
1176382 TAATAATAAT
Statistics
Matches: 94, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 94 1.00
ACGTcount: A:0.67, C:0.30, G:0.01, T:0.02
Consensus pattern (3 bp):
ACA
Found at i:1180183 original size:50 final size:50
Alignment explanation
Indices: 1180124--1180224 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
1180114 GAAAAATCGC
1180124 AACTTGTACATCTTTCAAGGAAAAGCTATGAATCCGAAGGAAGTCATCAA
1 AACTTGTACATCTTTCAAGGAAAAGCTATGAATCCGAAGGAAGTCATCAA
1180174 AACTTGTACATCTTTCAAGGAAAAGCTATGAATCCGAAGGAAGTCATCAA
1 AACTTGTACATCTTTCAAGGAAAAGCTATGAATCCGAAGGAAGTCATCAA
1180224 A
1 A
1180225 GTTTCGTATT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.24
Consensus pattern (50 bp):
AACTTGTACATCTTTCAAGGAAAAGCTATGAATCCGAAGGAAGTCATCAA
Found at i:1181416 original size:90 final size:90
Alignment explanation
Indices: 1181258--1181438 Score: 281
Period size: 90 Copynumber: 2.0 Consensus size: 90
1181248 GGGATTAGGT
* * * *
1181258 TATAAATTGTAAGTGTTTAGTTTAGGGTTTTGTGATTTTTTAGTAATGTAATTTTTTAAAAAAAT
1 TATAAATTGTAAGTGGTTAGTTTAGGGTTTCGTGACTTTTTAGTAATGAAATTTTTTAAAAAAAT
*
1181323 AATTTTATAGTTATTTTGTTAGTAA
66 AATTTTATAGTTATTTTGCTAGTAA
* * * *
1181348 TATAAATTGTTAGTGGTTAGTTTAGTGTTTCGTGACTTTTTAGTAATGAAATTTTTTTAAAAATT
1 TATAAATTGTAAGTGGTTAGTTTAGGGTTTCGTGACTTTTTAGTAATGAAATTTTTTAAAAAAAT
1181413 AATTTTATAGTTATTTTGCTAGTAA
66 AATTTTATAGTTATTTTGCTAGTAA
1181438 T
1 T
1181439 TTATGATTAG
Statistics
Matches: 82, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
90 82 1.00
ACGTcount: A:0.31, C:0.02, G:0.15, T:0.52
Consensus pattern (90 bp):
TATAAATTGTAAGTGGTTAGTTTAGGGTTTCGTGACTTTTTAGTAATGAAATTTTTTAAAAAAAT
AATTTTATAGTTATTTTGCTAGTAA
Found at i:1185609 original size:16 final size:16
Alignment explanation
Indices: 1185588--1185642 Score: 76
Period size: 16 Copynumber: 3.4 Consensus size: 16
1185578 GTTTGGTTCA
1185588 CTGTAA-TGAAATAGAG
1 CTGTAATTG-AATAGAG
1185604 CTGTAATTGAATAGAG
1 CTGTAATTGAATAGAG
* *
1185620 TTGTAATTGAATAAAG
1 CTGTAATTGAATAGAG
1185636 CTGTAAT
1 CTGTAAT
1185643 CAGTAATTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
16 33 0.94
17 2 0.06
ACGTcount: A:0.40, C:0.05, G:0.22, T:0.33
Consensus pattern (16 bp):
CTGTAATTGAATAGAG
Found at i:1185713 original size:44 final size:46
Alignment explanation
Indices: 1185628--1185717 Score: 123
Period size: 44 Copynumber: 2.0 Consensus size: 46
1185618 AGTTGTAATT
*
1185628 GAATAAAGCTGTAATCAGTAATTCAATTGTTTGGTTGAATGGAATG
1 GAATAAAACTGTAATCAGTAATTCAATTGTTTGGTTGAATGGAATG
* *
1185674 GAATAAAACTGTAAT-AGT-ATTC-TTGTGTTTGTTTGAATGGAATG
1 GAATAAAACTGTAATCAGTAATTCAAT-TGTTTGGTTGAATGGAATG
1185718 TTGTAATAGC
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
43 1 0.03
44 22 0.55
45 3 0.08
46 14 0.35
ACGTcount: A:0.33, C:0.06, G:0.23, T:0.38
Consensus pattern (46 bp):
GAATAAAACTGTAATCAGTAATTCAATTGTTTGGTTGAATGGAATG
Found at i:1185908 original size:36 final size:37
Alignment explanation
Indices: 1185868--1185944 Score: 86
Period size: 36 Copynumber: 2.1 Consensus size: 37
1185858 TTAACCATAT
* *
1185868 TTTAACATAATTATTATTAAATATAATT-TTATAT-AA
1 TTTAACAAAATTATTAATAAA-ATAATTATTATATGAA
* * *
1185904 TTTAATAAAATTCTTAATAAAATTATTATTATATGAA
1 TTTAACAAAATTATTAATAAAATAATTATTATATGAA
1185941 TTTA
1 TTTA
1185945 CTAAAATCAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
35 5 0.15
36 23 0.68
37 6 0.18
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (37 bp):
TTTAACAAAATTATTAATAAAATAATTATTATATGAA
Found at i:1189091 original size:21 final size:21
Alignment explanation
Indices: 1189036--1189096 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
1189026 AGCAGTATAT
*
1189036 GACACATAAAGTGCCTGAA-AC
1 GACACATATAGTGCCT-AATAC
* ** *
1189057 AACACACGTGGTGCCTAATAC
1 GACACATATAGTGCCTAATAC
1189078 GACACATATAGTGCCTAAT
1 GACACATATAGTGCCTAAT
1189097 CGGCAAAGCT
Statistics
Matches: 30, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
20 2 0.07
21 28 0.93
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (21 bp):
GACACATATAGTGCCTAATAC
Found at i:1195129 original size:52 final size:48
Alignment explanation
Indices: 1195110--1195312 Score: 265
Period size: 46 Copynumber: 4.3 Consensus size: 48
1195100 TGACAAGTGG
* *
1195110 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
1195156 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-A---A
* *
1195208 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
** *
1195254 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
1195300 AAAGTGATAAGTG
1 AAAGTGATAAGTG
1195313 GCTACACTTA
Statistics
Matches: 144, Mismatches: 7, Indels: 12
0.88 0.04 0.07
Matches are distributed among these distances:
46 100 0.69
52 44 0.31
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (48 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
Found at i:1195164 original size:98 final size:98
Alignment explanation
Indices: 1195044--1195312 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
1195034 TTTGAGTACT
*
1195044 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
1195109 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
**
1195142 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
1195207 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* *
1195240 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGAC-AAGT
*
1195305 GATAAGTG
65 GAAAAGTG
1195313 GCTACACTTA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 149 0.93
99 11 0.07
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:1195320 original size:37 final size:37
Alignment explanation
Indices: 1195276--1195421 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
1195266 GATAGCTTTA
*
1195276 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1195313 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
1195350 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
1195387 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1195422 ATCATACGTA
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 89 0.86
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:1196672 original size:15 final size:15
Alignment explanation
Indices: 1196652--1196682 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1196642 AAAACAACAT
1196652 AACTCTTAACCTTTC
1 AACTCTTAACCTTTC
*
1196667 AACTCTTGACCTTTC
1 AACTCTTAACCTTTC
1196682 A
1 A
1196683 CTTACATAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.32, G:0.03, T:0.39
Consensus pattern (15 bp):
AACTCTTAACCTTTC
Found at i:1200841 original size:17 final size:18
Alignment explanation
Indices: 1200815--1200853 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1200805 CAAATTGTGG
1200815 AAAA-TGTTCTC-AATAT
1 AAAATTGTTCTCTAATAT
*
1200831 AAAATTGTTCTCTCATAT
1 AAAATTGTTCTCTAATAT
1200849 AAAAT
1 AAAAT
1200854 CAAAAGCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 7 0.35
18 9 0.45
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38
Consensus pattern (18 bp):
AAAATTGTTCTCTAATAT
Found at i:1201978 original size:4 final size:4
Alignment explanation
Indices: 1201961--1202003 Score: 77
Period size: 4 Copynumber: 10.8 Consensus size: 4
1201951 AACTGTAGGG
*
1201961 CATA CATT CATA CATA CATA CATA CATA CATA CATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CAT
1202004 TTCCTAACTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.28
Consensus pattern (4 bp):
CATA
Found at i:1203859 original size:17 final size:17
Alignment explanation
Indices: 1203837--1203892 Score: 69
Period size: 17 Copynumber: 3.3 Consensus size: 17
1203827 GCATTAACGT
1203837 AGATAATAATAATAATA
1 AGATAATAATAATAATA
1203854 AGATAATAATAATAATA
1 AGATAATAATAATAATA
* * *
1203871 TGCTTA-AATAATAATA
1 AGATAATAATAATAATA
1203887 TAGATA
1 -AGATA
1203893 TAGATTCATG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
16 10 0.31
17 22 0.69
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.32
Consensus pattern (17 bp):
AGATAATAATAATAATA
Found at i:1203861 original size:14 final size:14
Alignment explanation
Indices: 1203842--1203868 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1203832 AACGTAGATA
1203842 ATAATAATAATAAG
1 ATAATAATAATAAG
1203856 ATAATAATAATAA
1 ATAATAATAATAA
1203869 TATGCTTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.30
Consensus pattern (14 bp):
ATAATAATAATAAG
Found at i:1207948 original size:49 final size:49
Alignment explanation
Indices: 1207891--1207985 Score: 172
Period size: 49 Copynumber: 1.9 Consensus size: 49
1207881 AAAATCAAGT
1207891 CTGATTCAAAATGTAGCAAGAGCAGGCTCAGGTGGATCAACCAGGAGAC
1 CTGATTCAAAATGTAGCAAGAGCAGGCTCAGGTGGATCAACCAGGAGAC
* *
1207940 CTGATTCAAAATGTAGCGAGAGCAGGCTTAGGTGGATCAACCAGGA
1 CTGATTCAAAATGTAGCAAGAGCAGGCTCAGGTGGATCAACCAGGA
1207986 AAACATCGAG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.34, C:0.19, G:0.29, T:0.18
Consensus pattern (49 bp):
CTGATTCAAAATGTAGCAAGAGCAGGCTCAGGTGGATCAACCAGGAGAC
Found at i:1210373 original size:28 final size:31
Alignment explanation
Indices: 1210332--1210389 Score: 86
Period size: 28 Copynumber: 2.0 Consensus size: 31
1210322 ATCTTAAATA
*
1210332 ATTATAAAAAATTATTAAA-C-AATATTTAT
1 ATTATAAAAAATTAATAAAGCGAATATTTAT
1210361 ATTA-AAAAAATTAATAAAGCGAATATTTA
1 ATTATAAAAAATTAATAAAGCGAATATTTA
1210390 AAAAATTGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 13 0.50
29 5 0.19
30 8 0.31
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.36
Consensus pattern (31 bp):
ATTATAAAAAATTAATAAAGCGAATATTTAT
Found at i:1210416 original size:15 final size:15
Alignment explanation
Indices: 1210396--1210424 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1210386 TTTAAAAAAT
1210396 TGAATTAAATAAAGG
1 TGAATTAAATAAAGG
1210411 TGAATTAAATAAAG
1 TGAATTAAATAAAG
1210425 AATGAAAGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.17, T:0.28
Consensus pattern (15 bp):
TGAATTAAATAAAGG
Done.