Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr4
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: 30015117
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1306243 characters in sequence are not A, C, G, or T
File 5 of 85
Found at i:1651018 original size:11 final size:11
Alignment explanation
Indices: 1651002--1651029 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1650992 TTTAATCTGC
1651002 AAAAAAAGAAA
1 AAAAAAAGAAA
1651013 AAAAAAAGAAA
1 AAAAAAAGAAA
1651024 AAAAAA
1 AAAAAA
1651030 GATGGCAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:1663236 original size:19 final size:19
Alignment explanation
Indices: 1663212--1663250 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1663202 TTTTGTCTGT
1663212 ATTCCTTGTTATCTTTGGA
1 ATTCCTTGTTATCTTTGGA
1663231 ATTCCTTGTTATCTTTGGA
1 ATTCCTTGTTATCTTTGGA
1663250 A
1 A
1663251 CATATGGTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.18, C:0.15, G:0.15, T:0.51
Consensus pattern (19 bp):
ATTCCTTGTTATCTTTGGA
Found at i:1669744 original size:28 final size:27
Alignment explanation
Indices: 1669709--1669761 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 27
1669699 ATTAACAGTT
1669709 AAACTTAAATT-TTAAAAATTAAAAAAA
1 AAACTTAAATTCTT-AAAATTAAAAAAA
1669736 AAACATTAAATTCTTAAAATTAAAAA
1 AAAC-TTAAATTCTTAAAATTAAAAA
1669762 TATAGGGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
27 4 0.17
28 18 0.75
29 2 0.08
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (27 bp):
AAACTTAAATTCTTAAAATTAAAAAAA
Found at i:1676952 original size:54 final size:54
Alignment explanation
Indices: 1676868--1676972 Score: 174
Period size: 54 Copynumber: 1.9 Consensus size: 54
1676858 ACAGTCTGTT
*
1676868 GGTACTACTGTTCACACCAAAACTCAGCAGGGTGAATACAGTGATCTGAATGAG
1 GGTACTACTGTTCACACCAAAACTCAGCAGGGTGAACACAGTGATCTGAATGAG
** *
1676922 GGTACTACTGTTCACACTGAAACTCGGCAGGGTGAACACAGTGATCTGAAT
1 GGTACTACTGTTCACACCAAAACTCAGCAGGGTGAACACAGTGATCTGAAT
1676973 TCTCAACAGG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (54 bp):
GGTACTACTGTTCACACCAAAACTCAGCAGGGTGAACACAGTGATCTGAATGAG
Found at i:1681936 original size:21 final size:20
Alignment explanation
Indices: 1681911--1681966 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
1681901 CTTAGATTTT
*
1681911 TATATTATTTATTTATATAAA
1 TATATTATTTAATTATA-AAA
* * *
1681932 TATATAAATTAATTATAAAG
1 TATATTATTTAATTATAAAA
*
1681952 TATATTATTAAATTA
1 TATATTATTTAATTA
1681967 ATTATATTAT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
TATATTATTTAATTATAAAA
Found at i:1681950 original size:11 final size:11
Alignment explanation
Indices: 1681934--1681972 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
1681924 TATATAAATA
1681934 TATAAATTAAT
1 TATAAATTAAT
*
1681945 TATAAAGTATAT
1 TATAAATTA-AT
1681957 TATTAAATTAAT
1 TA-TAAATTAAT
1681969 TATA
1 TATA
1681973 TTATAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 10 0.42
12 8 0.33
13 6 0.25
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (11 bp):
TATAAATTAAT
Found at i:1681961 original size:19 final size:20
Alignment explanation
Indices: 1681911--1681962 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
1681901 CTTAGATTTT
*
1681911 TATATTATTTATTTATATAAA
1 TATATTA-TTAATTATATAAA
* *
1681932 TATATAAATTAATTATA-AAG
1 TATAT-TATTAATTATATAAA
1681952 TATATTATTAA
1 TATATTATTAA
1681963 ATTAATTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 5 0.19
20 7 0.27
21 13 0.50
22 1 0.04
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
TATATTATTAATTATATAAA
Found at i:1681984 original size:14 final size:17
Alignment explanation
Indices: 1681952--1681989 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 17
1681942 AATTATAAAG
1681952 TATATTATTAAATTAAT
1 TATATTATTAAATTAAT
1681969 TATATTA-TAAA-T-AT
1 TATATTATTAAATTAAT
1681983 TATATTA
1 TATATTA
1681990 AGAAATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.43
15 1 0.05
16 4 0.19
17 7 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATTATTAAATTAAT
Found at i:1683182 original size:44 final size:41
Alignment explanation
Indices: 1683133--1683219 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 41
1683123 GGCTTTGCTG
1683133 ATCAGGCA-CTTTATGTGTCGTACGTCAGGCACTTTATGTGTCGT
1 ATCAGGCATC-TTATGTGTCGT--GTCAGGCAC-TTATGTGTCGT
* *
1683177 ATCAGGCATCTTGTGTGTCGTTTCAGGCACTTATGTGTCGT
1 ATCAGGCATCTTATGTGTCGTGTCAGGCACTTATGTGTCGT
1683218 AT
1 AT
1683220 ACTGATCATG
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
41 13 0.32
42 8 0.20
44 18 0.45
45 1 0.03
ACGTcount: A:0.17, C:0.20, G:0.25, T:0.38
Consensus pattern (41 bp):
ATCAGGCATCTTATGTGTCGTGTCAGGCACTTATGTGTCGT
Found at i:1683183 original size:21 final size:21
Alignment explanation
Indices: 1683133--1683219 Score: 115
Period size: 21 Copynumber: 4.1 Consensus size: 21
1683123 GGCTTTGCTG
1683133 ATCAGGCACTTTATGTGTCGT
1 ATCAGGCACTTTATGTGTCGT
1683154 ACGTCAGGCACTTTATGTGTCGT
1 A--TCAGGCACTTTATGTGTCGT
*
1683177 ATCAGGCA-TCTTGTGTGTCGT
1 ATCAGGCACT-TTATGTGTCGT
*
1683198 TTCAGGCAC-TTATGTGTCGT
1 ATCAGGCACTTTATGTGTCGT
1683218 AT
1 AT
1683220 ACTGATCATG
Statistics
Matches: 58, Mismatches: 4, Indels: 9
0.82 0.06 0.13
Matches are distributed among these distances:
20 12 0.21
21 25 0.43
23 21 0.36
ACGTcount: A:0.17, C:0.20, G:0.25, T:0.38
Consensus pattern (21 bp):
ATCAGGCACTTTATGTGTCGT
Found at i:1689791 original size:182 final size:179
Alignment explanation
Indices: 1689479--1689998 Score: 675
Period size: 181 Copynumber: 2.9 Consensus size: 179
1689469 TTACACTTAT
* * *
1689479 ACGTGAGTATTGTTAATTCGGGTTTTGAATCAAGATTTCTTAATTTCGAAAAGGTTTAAAAAATG
1 ACGTGAGTATTGTTAATTCGGGTTTTGGATCAAGAATTCTTAATTT-GAAAATGTTT-AAAAATG
* * * * *
1689544 TATATTTTTTTTATGACTAAGGTTT-CTTAATGTTCATTTTACGGTCTATGAAGACTAATATTTT
64 TATATATTTTTTATGACCAAGGTTTCCTTAATGTTTATTTTACGGTCTATAAAGATTAATATTTT
* *
1689608 TGAGATTCATGATTATCTTTCTAAAAACTGACATTTCCAGTCATATCTTTTAC
129 TGAGATTCATGATTATCTCTCTAAAAA-TGACATTTCCAGTAAT-TCTTTTAC
* * * * *
1689661 ACGTGAGTATTGTTAATTTGGGTTTTGGATTAAAAATCCTTAATTTGGAAAATGTTTAAAAATAT
1 ACGTGAGTATTGTTAATTCGGGTTTTGGATCAAGAATTCTTAATTT-GAAAATGTTTAAAAATGT
*
1689726 ATATATTTTTTATGACCAAGGTTTCCTTAATGTTTATTTTACGGTCTATAAAGATTAACATTTTT
65 ATATATTTTTTATGACCAAGGTTTCCTTAATGTTTATTTTACGGTCTATAAAGATTAATATTTTT
* * * * ** *
1689791 GAGGTCCATGATTATCCCTCTCAAAAATGATATTTCGTGTAATTTTTTTAC
130 GAGATTCATGATTATCTCTCT-AAAAATGACATTTCCAGTAATTCTTTTAC
* *
1689842 ACGTGAATATTGTTAATTCAGGTTTTGGATCAAGAATTCTTAATTTGAAAATTGTTTAAAAATGT
1 ACGTGAGTATTGTTAATTCGGGTTTTGGATCAAGAATTCTTAATTTGAAAA-TGTTTAAAAATGT
*
1689907 ATATATTTTTTATGACCAAGGTTTCCTTAATGTTTATTTTACTGTCTATAAA-ATACTAATATTT
65 ATATATTTTTTATGACCAAGGTTTCCTTAATGTTTATTTTACGGTCTATAAAGAT--TAATATTT
** * *
1689971 TAAAGTTTCATAATTATCTCTCTAAAAA
128 TTGAGATTCATGATTATCTCTCTAAAAA
1689999 AATAACATTT
Statistics
Matches: 294, Mismatches: 39, Indels: 11
0.85 0.11 0.03
Matches are distributed among these distances:
180 7 0.02
181 144 0.49
182 138 0.47
183 5 0.02
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.44
Consensus pattern (179 bp):
ACGTGAGTATTGTTAATTCGGGTTTTGGATCAAGAATTCTTAATTTGAAAATGTTTAAAAATGTA
TATATTTTTTATGACCAAGGTTTCCTTAATGTTTATTTTACGGTCTATAAAGATTAATATTTTTG
AGATTCATGATTATCTCTCTAAAAATGACATTTCCAGTAATTCTTTTAC
Found at i:1690545 original size:18 final size:18
Alignment explanation
Indices: 1690499--1690551 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
1690489 ATTGTAACAT
*
1690499 TATTTATATTTTAAATATT
1 TATTTA-ATTTTAAATATG
1690518 TATTTCAATTTT-AATAGTG
1 TATTT-AATTTTAAATA-TG
1690537 TATTTAATTTGTAAA
1 TATTTAATTT-TAAA
1690552 AATAGTGATA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 9 0.31
19 17 0.59
20 3 0.10
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.57
Consensus pattern (18 bp):
TATTTAATTTTAAATATG
Found at i:1715076 original size:106 final size:107
Alignment explanation
Indices: 1714941--1715157 Score: 427
Period size: 106 Copynumber: 2.0 Consensus size: 107
1714931 AATAAGAAAA
1714941 TTAAATATATTCCCTCATAGATTCCTTTACGATAAAGTTTTCATGATTTTAGTGGAATTAAAATT
1 TTAAATATATTCCCTCATAGATTCCTTTACGATAAAGTTTTCATGATTTTAGTGGAATTAAAATT
1715006 GGGTTGAGAAAATTATTTAATTAGAAAATTAATTTAGTTAAT
66 GGGTTGAGAAAATTATTTAATTAGAAAATTAATTTAGTTAAT
1715048 TTAAATATATT-CCTCATAGATTCCTTTACGATAAAGTTTTCATGATTTTAGTGGAATTAAAATT
1 TTAAATATATTCCCTCATAGATTCCTTTACGATAAAGTTTTCATGATTTTAGTGGAATTAAAATT
1715112 GGGTTGAGAAAATTATTTAATTAGAAAATTAATTTAGTTAAT
66 GGGTTGAGAAAATTATTTAATTAGAAAATTAATTTAGTTAAT
1715154 TTAA
1 TTAA
1715158 TTAATAATAT
Statistics
Matches: 110, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
106 99 0.90
107 11 0.10
ACGTcount: A:0.38, C:0.07, G:0.13, T:0.42
Consensus pattern (107 bp):
TTAAATATATTCCCTCATAGATTCCTTTACGATAAAGTTTTCATGATTTTAGTGGAATTAAAATT
GGGTTGAGAAAATTATTTAATTAGAAAATTAATTTAGTTAAT
Found at i:1717265 original size:59 final size:59
Alignment explanation
Indices: 1717206--1717533 Score: 299
Period size: 59 Copynumber: 5.6 Consensus size: 59
1717196 CCACAATTCT
* *
1717206 CACATTGAAGG-TTGAACTTTTTTTTGTCCAAGTTAGTCCTTAAACTTGGCAATTGTTCT
1 CACATT-AAGGCTTGAACTTTTTTTTGTCCAAGTTAGTCCTTGAACTTGGCAATTGTTCC
* ** * * * * * ** *
1717265 CACATTAGGGCTTGAACTTTTTAATATTCAAATTAATCCCTGAACTTAACAATTTTTCC
1 CACATTAAGGCTTGAACTTTTTTTTGTCCAAGTTAGTCCTTGAACTTGGCAATTGTTCC
** * * *
1717324 CACATTGGGGCTTGAAC-ATTTTTTATCCAAGTTAG-CCTCTAAACTTGGCAATTGTTCC
1 CACATTAAGGCTTGAACTTTTTTTTGTCCAAGTTAGTCCT-TGAACTTGGCAATTGTTCC
** * * * * * * *
1717382 CACATTGGGGCCTGAATTTTTTTTTGTTCAAGTTAGTCCTCGAACTTGACAATTATTCT
1 CACATTAAGGCTTGAACTTTTTTTTGTCCAAGTTAGTCCTTGAACTTGGCAATTGTTCC
* * *
1717441 TACATT-AGAGTTTGAACTTTTTTTTGTCCAAATTAGTCCTTGAACTTGGCAATTGTTCC
1 CACATTAAG-GCTTGAACTTTTTTTTGTCCAAGTTAGTCCTTGAACTTGGCAATTGTTCC
*
1717500 CACATT-AGAGTTTGAA-TTTTTTTTGTCCAAGTTA
1 CACATTAAG-GCTTGAACTTTTTTTTGTCCAAGTTA
1717534 ATCTCTAATA
Statistics
Matches: 216, Mismatches: 48, Indels: 11
0.79 0.17 0.04
Matches are distributed among these distances:
57 2 0.01
58 63 0.29
59 148 0.69
60 3 0.01
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.41
Consensus pattern (59 bp):
CACATTAAGGCTTGAACTTTTTTTTGTCCAAGTTAGTCCTTGAACTTGGCAATTGTTCC
Found at i:1717533 original size:117 final size:118
Alignment explanation
Indices: 1717217--1717536 Score: 387
Period size: 117 Copynumber: 2.7 Consensus size: 118
1717207 ACATTGAAGG
*
1717217 TTGAACTTTTTTTTGTCCAAGTTAGTCCTTAAACTTGGCAATTGTTCTCACATTAGGGCTTGAAC
1 TTGAACTTTTTTTTGTCCAAGTTAGTCCTTAAACTTGGCAATTGTTCCCACATTAGGGCTTGAAC
** * * * * *
1717282 TTTTTAATATTCAAATTAATCCCTGAACTTAACAATTTTTCCCACATTGGGGC
66 TTTTTTTTGTTCAAGTTAATCCCTGAACTTAACAATTATTCCCACATTAGAGC
* * * *
1717335 TTGAAC-ATTTTTTATCCAAGTTAG-CCTCTAAACTTGGCAATTGTTCCCACATTGGGGCCTGAA
1 TTGAACTTTTTTTTGTCCAAGTTAGTCCT-TAAACTTGGCAATTGTTCCCACATTAGGGCTTGAA
* * * ** *
1717398 TTTTTTTTTGTTCAAGTTAGT-CCTCGAACTTGACAATTATTCTTACATTAGAGT
65 CTTTTTTTTGTTCAAGTTAATCCCT-GAACTTAACAATTATTCCCACATTAGAGC
* * * *
1717452 TTGAACTTTTTTTTGTCCAAATTAGTCCTTGAACTTGGCAATTGTTCCCACATTAGAGTTTGAA-
1 TTGAACTTTTTTTTGTCCAAGTTAGTCCTTAAACTTGGCAATTGTTCCCACATTAGGGCTTGAAC
*
1717516 TTTTTTTTGTCCAAGTTAATC
66 TTTTTTTTGTTCAAGTTAATC
1717537 TCTAATATTT
Statistics
Matches: 169, Mismatches: 28, Indels: 10
0.82 0.14 0.05
Matches are distributed among these distances:
116 6 0.04
117 109 0.64
118 51 0.30
119 3 0.02
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.42
Consensus pattern (118 bp):
TTGAACTTTTTTTTGTCCAAGTTAGTCCTTAAACTTGGCAATTGTTCCCACATTAGGGCTTGAAC
TTTTTTTTGTTCAAGTTAATCCCTGAACTTAACAATTATTCCCACATTAGAGC
Found at i:1721879 original size:59 final size:59
Alignment explanation
Indices: 1721820--1722147 Score: 299
Period size: 59 Copynumber: 5.6 Consensus size: 59
1721810 CCACAATTCT
* *
1721820 CACATTGAAGG-TTGAACTTTTTTTTGTCCAAGTTAGTCCTTAAACTTGGCAATTGTTCT
1 CACATT-AAGGCTTGAACTTTTTTTTGTCCAAGTTAGTCCTTGAACTTGGCAATTGTTCC
* ** * * * * * ** *
1721879 CACATTAGGGCTTGAACTTTTTAATATTCAAATTAATCCCTGAACTTAACAATTTTTCC
1 CACATTAAGGCTTGAACTTTTTTTTGTCCAAGTTAGTCCTTGAACTTGGCAATTGTTCC
** * * *
1721938 CACATTGGGGCTTGAAC-ATTTTTTATCCAAGTTAG-CCTCTAAACTTGGCAATTGTTCC
1 CACATTAAGGCTTGAACTTTTTTTTGTCCAAGTTAGTCCT-TGAACTTGGCAATTGTTCC
** * * * * * * *
1721996 CACATTGGGGCCTGAATTTTTTTTTGTTCAAGTTAGTCCTCGAACTTGACAATTATTCT
1 CACATTAAGGCTTGAACTTTTTTTTGTCCAAGTTAGTCCTTGAACTTGGCAATTGTTCC
* * *
1722055 TACATT-AGAGTTTGAACTTTTTTTTGTCCAAATTAGTCCTTGAACTTGGCAATTGTTCC
1 CACATTAAG-GCTTGAACTTTTTTTTGTCCAAGTTAGTCCTTGAACTTGGCAATTGTTCC
*
1722114 CACATT-AGAGTTTGAA-TTTTTTTTGTCCAAGTTA
1 CACATTAAG-GCTTGAACTTTTTTTTGTCCAAGTTA
1722148 ATCTCTAATA
Statistics
Matches: 216, Mismatches: 48, Indels: 11
0.79 0.17 0.04
Matches are distributed among these distances:
57 2 0.01
58 63 0.29
59 148 0.69
60 3 0.01
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.41
Consensus pattern (59 bp):
CACATTAAGGCTTGAACTTTTTTTTGTCCAAGTTAGTCCTTGAACTTGGCAATTGTTCC
Found at i:1722147 original size:117 final size:118
Alignment explanation
Indices: 1721831--1722150 Score: 387
Period size: 117 Copynumber: 2.7 Consensus size: 118
1721821 ACATTGAAGG
*
1721831 TTGAACTTTTTTTTGTCCAAGTTAGTCCTTAAACTTGGCAATTGTTCTCACATTAGGGCTTGAAC
1 TTGAACTTTTTTTTGTCCAAGTTAGTCCTTAAACTTGGCAATTGTTCCCACATTAGGGCTTGAAC
** * * * * *
1721896 TTTTTAATATTCAAATTAATCCCTGAACTTAACAATTTTTCCCACATTGGGGC
66 TTTTTTTTGTTCAAGTTAATCCCTGAACTTAACAATTATTCCCACATTAGAGC
* * * *
1721949 TTGAAC-ATTTTTTATCCAAGTTAG-CCTCTAAACTTGGCAATTGTTCCCACATTGGGGCCTGAA
1 TTGAACTTTTTTTTGTCCAAGTTAGTCCT-TAAACTTGGCAATTGTTCCCACATTAGGGCTTGAA
* * * ** *
1722012 TTTTTTTTTGTTCAAGTTAGT-CCTCGAACTTGACAATTATTCTTACATTAGAGT
65 CTTTTTTTTGTTCAAGTTAATCCCT-GAACTTAACAATTATTCCCACATTAGAGC
* * * *
1722066 TTGAACTTTTTTTTGTCCAAATTAGTCCTTGAACTTGGCAATTGTTCCCACATTAGAGTTTGAA-
1 TTGAACTTTTTTTTGTCCAAGTTAGTCCTTAAACTTGGCAATTGTTCCCACATTAGGGCTTGAAC
*
1722130 TTTTTTTTGTCCAAGTTAATC
66 TTTTTTTTGTTCAAGTTAATC
1722151 TCTAATATTT
Statistics
Matches: 169, Mismatches: 28, Indels: 10
0.82 0.14 0.05
Matches are distributed among these distances:
116 6 0.04
117 109 0.64
118 51 0.30
119 3 0.02
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.42
Consensus pattern (118 bp):
TTGAACTTTTTTTTGTCCAAGTTAGTCCTTAAACTTGGCAATTGTTCCCACATTAGGGCTTGAAC
TTTTTTTTGTTCAAGTTAATCCCTGAACTTAACAATTATTCCCACATTAGAGC
Found at i:1727841 original size:73 final size:74
Alignment explanation
Indices: 1727721--1727867 Score: 287
Period size: 73 Copynumber: 2.0 Consensus size: 74
1727711 AGCTGTAAAT
1727721 GTGAATTGGGAGGGTGAGGTAGGTTGGGATGATATCATGAGAGTCATGAGAATGACTCTCTTTCA
1 GTGAATTGGGAGGGTGAGGTAGGTTGGGATGATATCATGAGAGTCATGAGAATGACTCTCTTTCA
1727786 TGGCAATGG
66 TGGCAATGG
1727795 GTGAATTGGG-GGGTGAGGTAGGTTGGGATGATATCATGAGAGTCATGAGAATGACTCTCTTTCA
1 GTGAATTGGGAGGGTGAGGTAGGTTGGGATGATATCATGAGAGTCATGAGAATGACTCTCTTTCA
1727859 TGGCAATGG
66 TGGCAATGG
1727868 TTGATGAATT
Statistics
Matches: 73, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
73 63 0.86
74 10 0.14
ACGTcount: A:0.25, C:0.10, G:0.37, T:0.29
Consensus pattern (74 bp):
GTGAATTGGGAGGGTGAGGTAGGTTGGGATGATATCATGAGAGTCATGAGAATGACTCTCTTTCA
TGGCAATGG
Found at i:1728465 original size:34 final size:34
Alignment explanation
Indices: 1728422--1728490 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
1728412 AGTTATATAC
1728422 ATTGTTATTCGATACGTTGGTGGTAGAATTTTTT
1 ATTGTTATTCGATACGTTGGTGGTAGAATTTTTT
1728456 ATTGTTATTCGATACGTTGGTGGTAGAATTTTTT
1 ATTGTTATTCGATACGTTGGTGGTAGAATTTTTT
1728490 A
1 A
1728491 ACTTCACAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.22, C:0.06, G:0.23, T:0.49
Consensus pattern (34 bp):
ATTGTTATTCGATACGTTGGTGGTAGAATTTTTT
Found at i:1734189 original size:25 final size:25
Alignment explanation
Indices: 1734142--1734188 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
1734132 TTGGAAAATT
*
1734142 ATATGAGTACACATATTATAAAAGA
1 ATATGAATACACATATTATAAAAGA
*
1734167 ATATGAATACATATA-TATAAAA
1 ATATGAATACACATATTATAAAA
1734189 ATTATAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.55, C:0.06, G:0.09, T:0.30
Consensus pattern (25 bp):
ATATGAATACACATATTATAAAAGA
Found at i:1734332 original size:13 final size:12
Alignment explanation
Indices: 1734295--1734347 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
1734285 AATCAAAACC
*
1734295 AAAACAATAATA
1 AAAATAATAATA
* *
1734307 ACAATAGTAATA
1 AAAATAATAATA
*
1734319 AAACTAATTAATA
1 AAAATAA-TAATA
1734332 AATAATAATAATA
1 AA-AATAATAATA
1734345 AAA
1 AAA
1734348 GGGACTAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
12 14 0.44
13 14 0.44
14 4 0.12
ACGTcount: A:0.68, C:0.06, G:0.02, T:0.25
Consensus pattern (12 bp):
AAAATAATAATA
Found at i:1739817 original size:36 final size:36
Alignment explanation
Indices: 1739770--1739838 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
1739760 CTACTAAAGT
* * *
1739770 TTTGAGATAAAAAGTGAAATGCTTGATCTTGCTGAA
1 TTTGAGATAAAAAGCGAAATACTTGAGCTTGCTGAA
*
1739806 TTTGAGATAAAAAGCGAACTACTTGAGCTTGCT
1 TTTGAGATAAAAAGCGAAATACTTGAGCTTGCT
1739839 TGATTAGGCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.32
Consensus pattern (36 bp):
TTTGAGATAAAAAGCGAAATACTTGAGCTTGCTGAA
Found at i:1749488 original size:2 final size:2
Alignment explanation
Indices: 1749481--1749517 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1749471 CAACTGTCAT
1749481 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1749518 GTATGTATGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1750282 original size:30 final size:31
Alignment explanation
Indices: 1750242--1750305 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
1750232 TAATTTTAAA
1750242 AAATATATTTTTAT-ATATTTTAGTACTTTTT
1 AAATATATTTTTATAATATTTTAGTA-TTTTT
* *
1750273 AAATA-ATTTTTATAATTTTTTTGTATTTTT
1 AAATATATTTTTATAATATTTTAGTATTTTT
1750303 AAA
1 AAA
1750306 ATTTAATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 16 0.53
31 14 0.47
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (31 bp):
AAATATATTTTTATAATATTTTAGTATTTTT
Found at i:1750320 original size:26 final size:27
Alignment explanation
Indices: 1750291--1750347 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 27
1750281 TTTATAATTT
**
1750291 TTTTGTATTTT-TAAAATTTAATTTAA
1 TTTTGTATTTTGTAAAATGCAATTTAA
* *
1750317 TTTT-TTTTTTGTAAAATGCCATTTAA
1 TTTTGTATTTTGTAAAATGCAATTTAA
1750343 TTTTG
1 TTTTG
1750348 AAGAATCTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.28, C:0.04, G:0.07, T:0.61
Consensus pattern (27 bp):
TTTTGTATTTTGTAAAATGCAATTTAA
Found at i:1754086 original size:22 final size:22
Alignment explanation
Indices: 1754060--1754103 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1754050 AATGAGATAA
*
1754060 AAAAAAACTCAAGTATCAAATTG
1 AAAAAAA-TCAAATATCAAATTG
*
1754083 AAAAAAATTAAATATCAAATT
1 AAAAAAATCAAATATCAAATT
1754104 AAACATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.61, C:0.09, G:0.05, T:0.25
Consensus pattern (22 bp):
AAAAAAATCAAATATCAAATTG
Found at i:1755623 original size:6 final size:6
Alignment explanation
Indices: 1755612--1755644 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
1755602 AATTTGAATC
1755612 CCAGTT CCAGTT CCAGTT CCAGTT CCAGTT CCA
1 CCAGTT CCAGTT CCAGTT CCAGTT CCAGTT CCA
1755645 ATTTGAATCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.36, G:0.15, T:0.30
Consensus pattern (6 bp):
CCAGTT
Found at i:1758880 original size:208 final size:208
Alignment explanation
Indices: 1758522--1759151 Score: 1244
Period size: 208 Copynumber: 3.0 Consensus size: 208
1758512 CATGAAAACT
1758522 AATGATGCAAAATTGTTTCAGATACTCATAGAGGGCCGAGAAACTTAACTGCAATTAGATAGGGG
1 AATGATGCAAAATTGTTTCAGATACTCATAGAGGGCCGAGAAACTTAACTGCAATTAGATAGGGG
1758587 ACTTCTTTGGGGAAAAAATGTACAAAAGAACCAGTACTGCTTAAGTAAAGGACTACCAACAATGA
66 ACTTCTTTGGGGAAAAAATGTACAAAAGAACCAGTACTGCTTAAGTAAAGGACTACCAACAATGA
1758652 AAATGTGACAAGAAATGGTAGAAAACAGGAAAGGCTTGCCCATACAACCGACAAAAAAAAACACC
131 AAATGTGACAAGAAATGGTAGAAAACAGGAAAGGCTTGCCCATACAACCGACAAAAAAAAACACC
1758717 CAATCAAGGGAAC
196 CAATCAAGGGAAC
1758730 AATGATGCAAAATTGTTTCAGATACTCATAGAGGGCCGAGAAACTTAACTGCAATTAGATAGGGG
1 AATGATGCAAAATTGTTTCAGATACTCATAGAGGGCCGAGAAACTTAACTGCAATTAGATAGGGG
1758795 ACTTCTTTGGGGAAAAAATGTACAAAAGAACCAGTACTGCTTAAGTAAAGGACTACCAACAATGA
66 ACTTCTTTGGGGAAAAAATGTACAAAAGAACCAGTACTGCTTAAGTAAAGGACTACCAACAATGA
1758860 AAATGTGACAAGAAATGGTAGAAAACAGGAAAGGCTTGCCCATACAACCGACAAAAAAAAACACC
131 AAATGTGACAAGAAATGGTAGAAAACAGGAAAGGCTTGCCCATACAACCGACAAAAAAAAACACC
1758925 CAATCAAGGGAAC
196 CAATCAAGGGAAC
1758938 AATGATGCAAAATTGTTTCAGATACTCATAGAGGGCCGAGAAACTTAACTGCAATTAGATAGGGG
1 AATGATGCAAAATTGTTTCAGATACTCATAGAGGGCCGAGAAACTTAACTGCAATTAGATAGGGG
1759003 ACTTCTTTGGGGAAAAAATGTACAAAAGAACCAGTACTGCTTAAGTAAAGGACTACCAACAATGA
66 ACTTCTTTGGGGAAAAAATGTACAAAAGAACCAGTACTGCTTAAGTAAAGGACTACCAACAATGA
*
1759068 AAATGTGACAAGAAATGGTAGAAAACAGGAAAGGCTTGCCCATACAACCGA-AAAAAAAAACACA
131 AAATGTGACAAGAAATGGTAGAAAACAGGAAAGGCTTGCCCATACAACCGACAAAAAAAAACACC
1759132 CAATCAAGGGAAC
196 CAATCAAGGGAAC
1759145 AATGATG
1 AATGATG
1759152 ACAATAATAC
Statistics
Matches: 421, Mismatches: 1, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
207 32 0.08
208 389 0.92
ACGTcount: A:0.44, C:0.17, G:0.21, T:0.18
Consensus pattern (208 bp):
AATGATGCAAAATTGTTTCAGATACTCATAGAGGGCCGAGAAACTTAACTGCAATTAGATAGGGG
ACTTCTTTGGGGAAAAAATGTACAAAAGAACCAGTACTGCTTAAGTAAAGGACTACCAACAATGA
AAATGTGACAAGAAATGGTAGAAAACAGGAAAGGCTTGCCCATACAACCGACAAAAAAAAACACC
CAATCAAGGGAAC
Found at i:1759602 original size:2 final size:2
Alignment explanation
Indices: 1759595--1759629 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1759585 CACCAACCAA
1759595 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1759630 TACCTCTGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1767144 original size:47 final size:47
Alignment explanation
Indices: 1767037--1767144 Score: 139
Period size: 47 Copynumber: 2.3 Consensus size: 47
1767027 ATTACCTAAC
* * *
1767037 TACAAAAATTATGACAACTTCTGTAATGTTTTGTATATTTATGTAAT
1 TACAAAAACTATTACAACTTCTGTAATGTTATGTATATTTATGTAAT
* *
1767084 TACAAAAACTATTACAACTTC-GTTAATGTTATGTGTATTTGTGTAAT
1 TACAAAAACTATTACAACTTCTG-TAATGTTATGTATATTTATGTAAT
1767131 TACAGAAAA-TATTA
1 TACA-AAAACTATTA
1767145 TTCAGTTGCA
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
46 1 0.02
47 49 0.91
48 4 0.07
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (47 bp):
TACAAAAACTATTACAACTTCTGTAATGTTATGTATATTTATGTAAT
Found at i:1773742 original size:164 final size:164
Alignment explanation
Indices: 1773555--1773879 Score: 524
Period size: 164 Copynumber: 2.0 Consensus size: 164
1773545 GAATTTAACT
* *
1773555 ATATTGATAAAAATGATCATGACCTCAATCAGAATCAAAACAGAAGATTCTCAACCAACAAGATC
1 ATATTGATAAAAATGACCATGACCTCAATCAGAATCAAAACAGAAGATTCTCAACCAACAAGAAC
** * ***
1773620 ATAGCCAATTAAAATGTTATTTATTGGCAGACAATAAGCAATCACTTTTTACTTCCTCTGCACCA
66 ATAGAAAATTAAAATGTTATTTATTGGCAGACAATAAGCAACCAAGGTTTACTTCCTCTGCACCA
*
1773685 TACTAAATCTAAAACCACATGATTTAGTGTTACC
131 TACTAAATCCAAAACCACATGATTTAGTGTTACC
1773719 ATATTGATAAAAATGACCATGACCTCAATCAGAATCAAAACAGAAGATTCTCAACCAACAAGAAC
1 ATATTGATAAAAATGACCATGACCTCAATCAGAATCAAAACAGAAGATTCTCAACCAACAAGAAC
* *
1773784 ATAGAAAATTTAAATGTTATTTATTGGCAGGCAATAAGCAACCAAGGTTTACTTCCTCTGCACCA
66 ATAGAAAATTAAAATGTTATTTATTGGCAGACAATAAGCAACCAAGGTTTACTTCCTCTGCACCA
* * *
1773849 TACTACATCCAAATCCGCATGATTTAGTGTT
131 TACTAAATCCAAAACCACATGATTTAGTGTT
1773880 GAAATTTTGA
Statistics
Matches: 147, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
164 147 1.00
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.28
Consensus pattern (164 bp):
ATATTGATAAAAATGACCATGACCTCAATCAGAATCAAAACAGAAGATTCTCAACCAACAAGAAC
ATAGAAAATTAAAATGTTATTTATTGGCAGACAATAAGCAACCAAGGTTTACTTCCTCTGCACCA
TACTAAATCCAAAACCACATGATTTAGTGTTACC
Found at i:1776000 original size:29 final size:29
Alignment explanation
Indices: 1775958--1776020 Score: 117
Period size: 29 Copynumber: 2.2 Consensus size: 29
1775948 TAACTCGATA
*
1775958 ATTAAGTTTAGAGTTAATAATATATACAT
1 ATTAAATTTAGAGTTAATAATATATACAT
1775987 ATTAAATTTAGAGTTAATAATATATACAT
1 ATTAAATTTAGAGTTAATAATATATACAT
1776016 ATTAA
1 ATTAA
1776021 GGGCAATAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.48, C:0.03, G:0.08, T:0.41
Consensus pattern (29 bp):
ATTAAATTTAGAGTTAATAATATATACAT
Found at i:1783161 original size:36 final size:36
Alignment explanation
Indices: 1783121--1783200 Score: 90
Period size: 36 Copynumber: 2.2 Consensus size: 36
1783111 TTTAATGTTT
* * * *
1783121 TTGTTACTATTTAACTATTATGCTATTA-TTATTTTA
1 TTGTTAATATTTAAATATT-TGATAATATTTATTTTA
* *
1783157 TTGTTAATGTTTAAATATTTTATAATATTTATTTTA
1 TTGTTAATATTTAAATATTTGATAATATTTATTTTA
1783193 TTGTTAAT
1 TTGTTAAT
1783201 TTCGTTACTA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
35 5 0.14
36 32 0.86
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.60
Consensus pattern (36 bp):
TTGTTAATATTTAAATATTTGATAATATTTATTTTA
Found at i:1783200 original size:18 final size:18
Alignment explanation
Indices: 1783149--1783200 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
1783139 TATGCTATTA
*
1783149 TTATTTTATTGTTAATGT
1 TTATTTTATTGTTAATAT
** *
1783167 TTA-AATATTTTATAATAT
1 TTATTTTATTGT-TAATAT
1783185 TTATTTTATTGTTAAT
1 TTATTTTATTGTTAAT
1783201 TTCGTTACTA
Statistics
Matches: 25, Mismatches: 7, Indels: 4
0.69 0.19 0.11
Matches are distributed among these distances:
17 5 0.20
18 15 0.60
19 5 0.20
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (18 bp):
TTATTTTATTGTTAATAT
Found at i:1786564 original size:20 final size:19
Alignment explanation
Indices: 1786532--1786589 Score: 68
Period size: 19 Copynumber: 3.1 Consensus size: 19
1786522 ATTGGTTGAA
1786532 TTGAATTTTTAATAATTTT
1 TTGAATTTTTAATAATTTT
*
1786551 TTG-TTCTATTTAAT--TTTT
1 TTGAAT-T-TTTAATAATTTT
1786569 TTGAATTTTTAATAATTTT
1 TTGAATTTTTAATAATTTT
1786588 TT
1 TT
1786590 TAATCAAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
17 6 0.19
18 9 0.28
19 11 0.34
20 6 0.19
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (19 bp):
TTGAATTTTTAATAATTTT
Found at i:1786590 original size:20 final size:20
Alignment explanation
Indices: 1786532--1786590 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
1786522 ATTGGTTGAA
1786532 TTGAATTTTTAATAA-TTTT
1 TTGAATTTTTAATAATTTTT
1786551 TTG--TTCTATT--TAATTTTT
1 TTGAATT-T-TTAATAATTTTT
1786569 TTGAATTTTTAATAATTTTT
1 TTGAATTTTTAATAATTTTT
1786589 TT
1 TT
1786591 AATCAAATCA
Statistics
Matches: 33, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
17 5 0.15
18 10 0.30
19 6 0.18
20 12 0.36
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (20 bp):
TTGAATTTTTAATAATTTTT
Found at i:1796626 original size:18 final size:19
Alignment explanation
Indices: 1796605--1796645 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
1796595 TTTATAAATT
* *
1796605 ATTTTTATCAT-ATTGATA
1 ATTTTTATAATAATTAATA
1796623 A-TTTTATAATAATTAATA
1 ATTTTTATAATAATTAATA
1796641 ATTTT
1 ATTTT
1796646 AAAAATATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 8 0.42
18 8 0.42
19 3 0.16
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.56
Consensus pattern (19 bp):
ATTTTTATAATAATTAATA
Found at i:1796629 original size:17 final size:18
Alignment explanation
Indices: 1796607--1796646 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1796597 TATAAATTAT
* *
1796607 TTTTATCAT-ATTGATAA
1 TTTTATAATAATTAATAA
1796624 TTTTATAATAATTAATAA
1 TTTTATAATAATTAATAA
1796642 TTTTA
1 TTTTA
1796647 AAAATATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (18 bp):
TTTTATAATAATTAATAA
Found at i:1803070 original size:34 final size:34
Alignment explanation
Indices: 1803032--1803101 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
1803022 TTATAAAAGA
1803032 ATGAAAAAATTCATTGTATATATACAAACTATTG
1 ATGAAAAAATTCATTGTATATATACAAACTATTG
1803066 ATGAAAAAATTCATTGTATATATACAAACTATTG
1 ATGAAAAAATTCATTGTATATATACAAACTATTG
1803100 AT
1 AT
1803102 AAATTGCAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.36
Consensus pattern (34 bp):
ATGAAAAAATTCATTGTATATATACAAACTATTG
Found at i:1806851 original size:32 final size:32
Alignment explanation
Indices: 1806782--1806851 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
1806772 ATACAATTTC
* * *
1806782 GTACTTGTACTTGATACTTTTTTCCTAATTTG
1 GTACTTGGACTTGACACTTTTTTCCTAATTCG
* *
1806814 ATACTTGGACTTGACACTTTTTTCTTAATTCG
1 GTACTTGGACTTGACACTTTTTTCCTAATTCG
1806846 GTACTT
1 GTACTT
1806852 AAATTTTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.20, C:0.17, G:0.13, T:0.50
Consensus pattern (32 bp):
GTACTTGGACTTGACACTTTTTTCCTAATTCG
Found at i:1814180 original size:25 final size:25
Alignment explanation
Indices: 1814123--1814180 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
1814113 ACATACCGCA
*
1814123 GCTCTTTATGAGCATCCTGATATAG
1 GCTCTTTGTGAGCATCCTGATATAG
* *
1814148 ACTCTTTGTGAGCTTCCTGATAT-G
1 GCTCTTTGTGAGCATCCTGATATAG
1814172 GCTCGTTTG
1 GCTC-TTTG
1814181 AACTTCCTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 4 0.14
25 24 0.86
ACGTcount: A:0.17, C:0.21, G:0.22, T:0.40
Consensus pattern (25 bp):
GCTCTTTGTGAGCATCCTGATATAG
Found at i:1815874 original size:24 final size:23
Alignment explanation
Indices: 1815847--1815898 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
1815837 CAGTCCTAAG
1815847 AGTAATGGGGGTCAAGTCATAAAC
1 AGTAAT-GGGGTCAAGTCATAAAC
* * * *
1815871 AGTACTGGGGTCATGTCGTGAAC
1 AGTAATGGGGTCAAGTCATAAAC
1815894 AGTAA
1 AGTAA
1815899 CAATATGTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.33, C:0.13, G:0.31, T:0.23
Consensus pattern (23 bp):
AGTAATGGGGTCAAGTCATAAAC
Found at i:1815880 original size:23 final size:23
Alignment explanation
Indices: 1815854--1815897 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1815844 AAGAGTAATG
1815854 GGGGTCAAGTCATAAACAGTACT
1 GGGGTCAAGTCATAAACAGTACT
* * *
1815877 GGGGTCATGTCGTGAACAGTA
1 GGGGTCAAGTCATAAACAGTA
1815898 ACAATATGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.30, C:0.16, G:0.32, T:0.23
Consensus pattern (23 bp):
GGGGTCAAGTCATAAACAGTACT
Found at i:1826840 original size:134 final size:133
Alignment explanation
Indices: 1826684--1826929 Score: 366
Period size: 134 Copynumber: 1.8 Consensus size: 133
1826674 GATGTTGTTC
* * * *
1826684 TGCTAACTGTGTGAAAATTGAAATTTTTGTTAATTTATTAGTGATCTTTTTATCTTGAGATTTCA
1 TGCTAACTGTGTGAAAACTGAAATTTTTGTCAATTTATTAGTGATCTTTTTATCATGAAATTTCA
* **
1826749 ATGTTTTCATGTAGACGAGAAGCAGTGGTCCGAAATTGAAGGAAAAAAAGTGTTGTTTTTTTTTT
66 ATGTTTCCATGTAGACGAGAAGCAGTGACCCGAAATTGAAGGAAAAAAAGTGTTGTTTTTTTTTT
1826814 TTT
131 TTT
* * *
1826817 TGCTAATTGGTGTGAAAACTGAAATTTTTGTCAATTTATTAGTGATTTTTTTGTCATGAAATTTC
1 TGCTAACT-GTGTGAAAACTGAAATTTTTGTCAATTTATTAGTGATCTTTTTATCATGAAATTTC
** *
1826882 AATGTTTCCATGTAGGTGAGAAGCCGTGACCCGAAATTGAAGGAAAAA
65 AATGTTTCCATGTAGACGAGAAGCAGTGACCCGAAATTGAAGGAAAAA
1826930 GATGTGAAGC
Statistics
Matches: 99, Mismatches: 13, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
133 7 0.07
134 92 0.93
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (133 bp):
TGCTAACTGTGTGAAAACTGAAATTTTTGTCAATTTATTAGTGATCTTTTTATCATGAAATTTCA
ATGTTTCCATGTAGACGAGAAGCAGTGACCCGAAATTGAAGGAAAAAAAGTGTTGTTTTTTTTTT
TTT
Found at i:1827586 original size:36 final size:36
Alignment explanation
Indices: 1827539--1827622 Score: 91
Period size: 36 Copynumber: 2.3 Consensus size: 36
1827529 GGGGACAGTG
*
1827539 AGGAAGAAGGAGAGTAA-GAGGAAGGCGCAAA-GAGAA
1 AGGAAGGAGGAGAG-AATGAGGAAGGCGCAAATG-GAA
*** *
1827575 AGGAAGGAGGAGAGAATGAGGGTTGCGGAAATGGAA
1 AGGAAGGAGGAGAGAATGAGGAAGGCGCAAATGGAA
1827611 AGGAAGGAGGAG
1 AGGAAGGAGGAG
1827623 TTGAAGCATT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
35 2 0.05
36 38 0.93
37 1 0.02
ACGTcount: A:0.44, C:0.04, G:0.46, T:0.06
Consensus pattern (36 bp):
AGGAAGGAGGAGAGAATGAGGAAGGCGCAAATGGAA
Found at i:1839334 original size:28 final size:27
Alignment explanation
Indices: 1839294--1839348 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
1839284 TATCAAACTG
1839294 AAAAAACTGAGGTGCCAAATTGAGACAA
1 AAAAAACTGAGGTGCCAAATTGA-ACAA
* * *
1839322 AAAAAATTTAGGTGTCAAATTGAACAA
1 AAAAAACTGAGGTGCCAAATTGAACAA
1839349 TTCAAGGTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 4 0.17
28 20 0.83
ACGTcount: A:0.51, C:0.11, G:0.18, T:0.20
Consensus pattern (27 bp):
AAAAAACTGAGGTGCCAAATTGAACAA
Found at i:1842597 original size:26 final size:26
Alignment explanation
Indices: 1842561--1842612 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
1842551 TCTTTTTTTC
1842561 TTTTTCTTGTTTGCTTCCTGAGAAAA
1 TTTTTCTTGTTTGCTTCCTGAGAAAA
1842587 TTTTTCTTGTTTGCTTCCTGAGAAAA
1 TTTTTCTTGTTTGCTTCCTGAGAAAA
1842613 GTAAAAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.19, C:0.15, G:0.15, T:0.50
Consensus pattern (26 bp):
TTTTTCTTGTTTGCTTCCTGAGAAAA
Found at i:1845951 original size:2 final size:2
Alignment explanation
Indices: 1845944--1845974 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1845934 AAAAATATTG
1845944 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1845975 TGAAAGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1846214 original size:2 final size:2
Alignment explanation
Indices: 1846207--1846237 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1846197 AAAAATATTG
1846207 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1846238 TGAAAGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1846217 original size:263 final size:263
Alignment explanation
Indices: 1845750--1846277 Score: 1047
Period size: 263 Copynumber: 2.0 Consensus size: 263
1845740 TTATATACTA
1845750 AACTGTCTTTTAATGTAGATATTTTGTAATAAAGACAAAATTATAATTCTCAGATATTTCATGAG
1 AACTGTCTTTTAATGTAGATATTTTGTAATAAAGACAAAATTATAATTCTCAGATATTTCATGAG
1845815 ATAATTTGTACCATTAATATGTGGTACTGGTCTTTGTTACAAGTAGCTAATTAAGTCTTCTTCTT
66 ATAATTTGTACCATTAATATGTGGTACTGGTCTTTGTTACAAGTAGCTAATTAAGTCTTCTTCTT
1845880 TTTCTTTTTCTTTTTTTTTAAAAAAAATCTAATTATTGCATAAATTAAGGCTAGAAAAATATTGT
131 TTTCTTTTTCTTTTTTTTTAAAAAAAATCTAATTATTGCATAAATTAAGGCTAGAAAAATATTGT
1845945 ATATATATATATATATATATATATATATATTGAAAGAAAAATAAATAAACACAAATCTATATGTA
196 ATATATATATATATATATATATATATATATTGAAAGAAAAATAAATAAACACAAATCTATATGTA
1846010 GAT
261 GAT
1846013 AACTGTCTTTTAATGTAGATATTTTGTAATAAAGACAAAATTATAATTCTCAGATATTTCATGAG
1 AACTGTCTTTTAATGTAGATATTTTGTAATAAAGACAAAATTATAATTCTCAGATATTTCATGAG
1846078 ATAATTTGTACCATTAATATGTGGTACTGGTCTTTGTTACAAGTAGCTAATTAAGTCTTCTTCTT
66 ATAATTTGTACCATTAATATGTGGTACTGGTCTTTGTTACAAGTAGCTAATTAAGTCTTCTTCTT
1846143 TTTCTTTTTCTTTTTTTTTAAAAAAAATCTAATTATTGCATAAATTAAGGCTAGAAAAATATTGT
131 TTTCTTTTTCTTTTTTTTTAAAAAAAATCTAATTATTGCATAAATTAAGGCTAGAAAAATATTGT
*
1846208 ATATATATATATATATATATATATATATATTGAAAGAAAAATAAATAACCACAAATCTATATGTA
196 ATATATATATATATATATATATATATATATTGAAAGAAAAATAAATAAACACAAATCTATATGTA
1846273 GAT
261 GAT
1846276 AA
1 AA
1846278 GCAGATGTGT
Statistics
Matches: 264, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
263 264 1.00
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.42
Consensus pattern (263 bp):
AACTGTCTTTTAATGTAGATATTTTGTAATAAAGACAAAATTATAATTCTCAGATATTTCATGAG
ATAATTTGTACCATTAATATGTGGTACTGGTCTTTGTTACAAGTAGCTAATTAAGTCTTCTTCTT
TTTCTTTTTCTTTTTTTTTAAAAAAAATCTAATTATTGCATAAATTAAGGCTAGAAAAATATTGT
ATATATATATATATATATATATATATATATTGAAAGAAAAATAAATAAACACAAATCTATATGTA
GAT
Found at i:1847897 original size:32 final size:31
Alignment explanation
Indices: 1847823--1847914 Score: 87
Period size: 31 Copynumber: 2.9 Consensus size: 31
1847813 TAACCTTGGT
* *
1847823 CCCTCCAAAATTTTGGAAAATTTTCATTACAC
1 CCCT-CAAAATTTTTGAAAATTTTAATTACAC
** *
1847855 CTTTCAAAATTTTTGAAAATTTTAATTAGCTC
1 CCCTCAAAATTTTTGAAAATTTTAATTA-CAC
* *
1847887 CCCTCGAAATTTTT-AAATATTCTAATTA
1 CCCTCAAAATTTTTGAAA-ATTTTAATTA
1847915 AACCTTCCAA
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
31 25 0.51
32 24 0.49
ACGTcount: A:0.35, C:0.18, G:0.05, T:0.41
Consensus pattern (31 bp):
CCCTCAAAATTTTTGAAAATTTTAATTACAC
Found at i:1847945 original size:22 final size:22
Alignment explanation
Indices: 1847909--1847955 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1847899 TTAAATATTC
*
1847909 TAATTAAACCTTCCAAAAGTTT
1 TAATTAAACCCTCCAAAAGTTT
* * *
1847931 TAATTAGACCCTCCAACATTTT
1 TAATTAAACCCTCCAAAAGTTT
1847953 TAA
1 TAA
1847956 AAATTCTCAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.38, C:0.21, G:0.04, T:0.36
Consensus pattern (22 bp):
TAATTAAACCCTCCAAAAGTTT
Found at i:1847962 original size:53 final size:51
Alignment explanation
Indices: 1847870--1848003 Score: 144
Period size: 53 Copynumber: 2.5 Consensus size: 51
1847860 AAAATTTTTG
* * *
1847870 AAAATTTTAATTAGCTCCCCTCGAAATTTTTAAATATTCTAATTAAACCT-TCC
1 AAAATTTTAATTAG--ACCCTCCAAATTTTTAAAAATTCTAATTAAACCTCT-C
* *
1847923 AAAAGTTTTAATTAGACCCTCCAACATTTTTAAAAATTCTCATTAATCCTCTC
1 AAAA-TTTTAATTAGACCCTCCAA-ATTTTTAAAAATTCTAATTAAACCTCTC
* * *
1847976 AAAATTTTAACTAAACCGTCCAAATTTT
1 AAAATTTTAATTAGACCCTCCAAATTTT
1848004 AATTAAATCC
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
51 5 0.07
52 23 0.33
53 31 0.44
54 11 0.16
ACGTcount: A:0.37, C:0.21, G:0.04, T:0.38
Consensus pattern (51 bp):
AAAATTTTAATTAGACCCTCCAAATTTTTAAAAATTCTAATTAAACCTCTC
Found at i:1850465 original size:32 final size:33
Alignment explanation
Indices: 1850426--1850502 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
1850416 CTCTACTTTT
1850426 ATTTATGAAATTTA-TTTTTTTAACTTTTTAAA
1 ATTTATGAAATTTATTTTTTTTAACTTTTTAAA
1850458 ATTTATGAAATTTATTTTTTTTAACTTTTTAAA
1 ATTTATGAAATTTATTTTTTTTAACTTTTTAAA
1850491 ATTTA--AAATTTA
1 ATTTATGAAATTTA
1850503 AGTCTGACAG
Statistics
Matches: 44, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
31 7 0.16
32 14 0.32
33 23 0.52
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (33 bp):
ATTTATGAAATTTATTTTTTTTAACTTTTTAAA
Found at i:1854844 original size:25 final size:26
Alignment explanation
Indices: 1854806--1854859 Score: 67
Period size: 24 Copynumber: 2.1 Consensus size: 26
1854796 ATTGATTTCT
* *
1854806 ATTTTTTAAAAT-AATAATAAAT-TA
1 ATTTTTAAAAATAAAAAATAAATATA
1854830 ATTTTTAAAATATAAAAAATAAATATA
1 ATTTTTAAAA-ATAAAAAATAAATATA
1854857 ATT
1 ATT
1854860 ATACCGGAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 9 0.36
25 2 0.08
26 9 0.36
27 5 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
ATTTTTAAAAATAAAAAATAAATATA
Found at i:1856799 original size:22 final size:21
Alignment explanation
Indices: 1856766--1856817 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
1856756 AATTTAACTC
*
1856766 TTAAATTATTTTATATTCTTTT
1 TTAAATTATTTTAGATT-TTTT
* *
1856788 TTGAATTCTTTTAGATTTTTT
1 TTAAATTATTTTAGATTTTTT
1856809 TTAAATTAT
1 TTAAATTAT
1856818 ATATTTTCTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (21 bp):
TTAAATTATTTTAGATTTTTT
Found at i:1867139 original size:34 final size:34
Alignment explanation
Indices: 1867101--1867168 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
1867091 TATACTATTC
* *
1867101 GGTACTTGAACTTGATTTCAATATTCAATTTGGT
1 GGTACATGAACTTGACTTCAATATTCAATTTGGT
** *
1867135 GGTACATGAGTTTGACTTCAATATTCATTTTGGT
1 GGTACATGAACTTGACTTCAATATTCAATTTGGT
1867169 ACCTTAGTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.44
Consensus pattern (34 bp):
GGTACATGAACTTGACTTCAATATTCAATTTGGT
Found at i:1868041 original size:8 final size:8
Alignment explanation
Indices: 1868028--1868054 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
1868018 AACCAAGTAA
1868028 ATTAAATC
1 ATTAAATC
1868036 ATTAAATC
1 ATTAAATC
1868044 ATTAAATC
1 ATTAAATC
1868052 ATT
1 ATT
1868055 TAACTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (8 bp):
ATTAAATC
Found at i:1868367 original size:38 final size:37
Alignment explanation
Indices: 1868315--1868406 Score: 105
Period size: 38 Copynumber: 2.5 Consensus size: 37
1868305 ACCAGATTGG
** *
1868315 CACCCAGTGCCTCATCGG-ATAGTTCGAAGCAAAGTTGA
1 CACCCAGTATCTCATCGGCATAG-CCGAAGCAAAG-TGA
* *
1868353 CACCCAGTATCTCATCGGCCTAGCCGAAGTAAAGTGA
1 CACCCAGTATCTCATCGGCATAGCCGAAGCAAAGTGA
*
1868390 TACCCAGTATCTCATCG
1 CACCCAGTATCTCATCG
1868407 AATCTATCCG
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
37 19 0.40
38 25 0.53
39 3 0.06
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (37 bp):
CACCCAGTATCTCATCGGCATAGCCGAAGCAAAGTGA
Found at i:1868444 original size:41 final size:38
Alignment explanation
Indices: 1868339--1868448 Score: 123
Period size: 41 Copynumber: 2.8 Consensus size: 38
1868329 TCGGATAGTT
* *
1868339 CGAAGCAAAGTTGACACCCAGTATCTCATCG-GCCTAGC
1 CGAAGTAAAG-TGACACCCAGTATCTCATCGAACCTAGC
* * *
1868377 CGAAGTAAAGTGATACCCAGTATCTCATCGAATCTATC
1 CGAAGTAAAGTGACACCCAGTATCTCATCGAACCTAGC
*
1868415 CGAAGTAAAATAGTGACACCCAGTGTCTCATCGA
1 CGAAGT--AA-AGTGACACCCAGTATCTCATCGA
1868449 CTCGAGGTCA
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
37 19 0.31
38 19 0.31
40 2 0.03
41 21 0.34
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (38 bp):
CGAAGTAAAGTGACACCCAGTATCTCATCGAACCTAGC
Found at i:1869172 original size:21 final size:20
Alignment explanation
Indices: 1869140--1869180 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1869130 TATACTAATT
1869140 TTCAAAATTTCAACT-TAAA
1 TTCAAAATTTCAACTCTAAA
1869159 TTCAATAATATTCAACTCTAAA
1 TTCAA-AAT-TTCAACTCTAAA
1869181 ACTCCAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.26
20 3 0.16
21 7 0.37
22 4 0.21
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.37
Consensus pattern (20 bp):
TTCAAAATTTCAACTCTAAA
Found at i:1869334 original size:21 final size:21
Alignment explanation
Indices: 1869310--1869352 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1869300 CGAATGGTTC
*
1869310 TGTTTTTTTTATGC-TTTATTT
1 TGTTTGTTTTAT-CTTTTATTT
1869331 TGTTTGTTTTATCTTTTATTT
1 TGTTTGTTTTATCTTTTATTT
1869352 T
1 T
1869353 ACTTTAGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.09, C:0.05, G:0.09, T:0.77
Consensus pattern (21 bp):
TGTTTGTTTTATCTTTTATTT
Found at i:1883208 original size:31 final size:28
Alignment explanation
Indices: 1883165--1883222 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 28
1883155 TCTTTAATCT
* *
1883165 TAAAATTGATAAATTTTTTAATAAAAAAA
1 TAAAATTGATAAA-ATTTTAACAAAAAAA
1883194 TAAAATATGAATAAAATTTTAACAAAAAA
1 TAAAAT-TG-ATAAAATTTTAACAAAAAA
1883223 TATTAATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 6 0.24
30 14 0.56
31 5 0.20
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (28 bp):
TAAAATTGATAAAATTTTAACAAAAAAA
Found at i:1883222 original size:113 final size:114
Alignment explanation
Indices: 1883082--1883308 Score: 447
Period size: 113 Copynumber: 2.0 Consensus size: 114
1883072 TTTTAATTAT
1883082 AAATATGAATAAAATTTTTAACAAAAAATATTAATTTACTCTTTGATTTATTGTATATTAATTAA
1 AAATATGAATAAAATTTTTAACAAAAAATATTAATTTACTCTTTGATTTATTGTATATTAATTAA
1883147 TTTATTATTCTTTAATCTTAAAATTGATAAATTTTTTAATAAAAAAATA
66 TTTATTATTCTTTAATCTTAAAATTGATAAATTTTTTAATAAAAAAATA
1883196 AAATATGAATAAAA-TTTTAACAAAAAATATTAATTTACTCTTTGATTTATTGTATATTAATTAA
1 AAATATGAATAAAATTTTTAACAAAAAATATTAATTTACTCTTTGATTTATTGTATATTAATTAA
1883260 TTTATTATTCTTTAATCTTAAAATTGATAAATTTTTTAATAAAAAAATA
66 TTTATTATTCTTTAATCTTAAAATTGATAAATTTTTTAATAAAAAAATA
1883309 CTAATTTACT
Statistics
Matches: 113, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
113 99 0.88
114 14 0.12
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (114 bp):
AAATATGAATAAAATTTTTAACAAAAAATATTAATTTACTCTTTGATTTATTGTATATTAATTAA
TTTATTATTCTTTAATCTTAAAATTGATAAATTTTTTAATAAAAAAATA
Found at i:1890619 original size:35 final size:34
Alignment explanation
Indices: 1890538--1890628 Score: 87
Period size: 35 Copynumber: 2.6 Consensus size: 34
1890528 CGGGATAAGT
* *
1890538 GTATATATATTATAAATATTTAAAGTTAAAATATA
1 GTATATATATTAT-AATATTAAAACTTAAAATATA
*
1890573 -TATAATAATATTATAATATTAAAACTTAAGAGTCA-A
1 GTAT-AT-ATATTATAATATTAAAACTTAA-AAT-ATA
*
1890609 GTATATATATTATTATATTA
1 GTATATATATTATAATATTA
1890629 TAATGATAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
34 3 0.06
35 28 0.60
36 12 0.26
37 4 0.09
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.43
Consensus pattern (34 bp):
GTATATATATTATAATATTAAAACTTAAAATATA
Found at i:1890720 original size:25 final size:25
Alignment explanation
Indices: 1890663--1890720 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
1890653 ATAAATAAAT
* * *
1890663 AAAAAGAATGAGAGAAAGAAACGAA
1 AAAAAGAAGGAAAGAAAGAAAAGAA
* * *
1890688 ACAGAGAAGGAAAGAAGGAAAAGAA
1 AAAAAGAAGGAAAGAAAGAAAAGAA
1890713 AAAAAGAA
1 AAAAAGAA
1890721 AGGAGGAGAA
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.69, C:0.03, G:0.26, T:0.02
Consensus pattern (25 bp):
AAAAAGAAGGAAAGAAAGAAAAGAA
Found at i:1891431 original size:24 final size:25
Alignment explanation
Indices: 1891377--1891431 Score: 62
Period size: 24 Copynumber: 2.2 Consensus size: 25
1891367 GTGTTTTACA
1891377 ATTGAAATTGATTGATTTACTATGTG
1 ATTG-AATTGATTGATTTACTATGTG
*
1891403 A-TGAATTTATTGAATTTA-TAT-TG
1 ATTGAATTGATTG-ATTTACTATGTG
1891426 ATTGAA
1 ATTGAA
1891432 GTGGTATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 3 0.12
24 15 0.58
25 7 0.27
26 1 0.04
ACGTcount: A:0.35, C:0.02, G:0.16, T:0.47
Consensus pattern (25 bp):
ATTGAATTGATTGATTTACTATGTG
Found at i:1894046 original size:24 final size:25
Alignment explanation
Indices: 1893992--1894046 Score: 62
Period size: 24 Copynumber: 2.2 Consensus size: 25
1893982 GTGTTTTACA
1893992 ATTGAAATTGATTGATTTACTATGTG
1 ATTG-AATTGATTGATTTACTATGTG
*
1894018 A-TGAATTTATTGAATTTA-TAT-TG
1 ATTGAATTGATTG-ATTTACTATGTG
1894041 ATTGAA
1 ATTGAA
1894047 GTGGTATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 3 0.12
24 15 0.58
25 7 0.27
26 1 0.04
ACGTcount: A:0.35, C:0.02, G:0.16, T:0.47
Consensus pattern (25 bp):
ATTGAATTGATTGATTTACTATGTG
Found at i:1902894 original size:7 final size:7
Alignment explanation
Indices: 1902882--1902920 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
1902872 TCAAGCACAC
1902882 CCTAAAT
1 CCTAAAT
1902889 CCTAAAT
1 CCTAAAT
1902896 CCTAAAT
1 CCTAAAT
1902903 CCTAAAT
1 CCTAAAT
* *
1902910 CTTAAAC
1 CCTAAAT
1902917 CCTA
1 CCTA
1902921 CAAATCTTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.41, C:0.31, G:0.00, T:0.28
Consensus pattern (7 bp):
CCTAAAT
Found at i:1903450 original size:3 final size:3
Alignment explanation
Indices: 1903442--1903467 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1903432 TTTAAGACAA
1903442 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
1903468 GTTGAATTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1905954 original size:23 final size:24
Alignment explanation
Indices: 1905937--1905984 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
1905927 CATAATTATT
*
1905937 ATTATTTTAA-AAAAATAACAATA
1 ATTATTTAAATAAAAATAACAATA
*
1905960 ATTATTTAAATAAAAATAAAAATA
1 ATTATTTAAATAAAAATAACAATA
1905984 A
1 A
1905985 AAAATGGGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (24 bp):
ATTATTTAAATAAAAATAACAATA
Found at i:1914204 original size:232 final size:232
Alignment explanation
Indices: 1913786--1914233 Score: 781
Period size: 232 Copynumber: 1.9 Consensus size: 232
1913776 TTTCTTAGGG
* *
1913786 CTTCCATAAATGGTTAATAAAAGAGTCCTCCTTTTATATGTGAGATTAGAAGGACATGAGGAAGC
1 CTTCCATAAATGGTTAATAAAAGAGCCCTCCTTTTATATGTGAGATTAGAAGGACACGAGGAAGC
1913851 TCTATGGTTTTATTGTGTTCCTAATATTTAATTAGTTTCACTTTTCTCCGAGCAGAGATTGTACG
66 TCTATGGTTTTATTGTGTTCCTAATATTTAATTAGTTTCACTTTTCTCCGAGCAGAGATTGTACG
* *
1913916 CAAATATTAAATATGGTACACCGGTTGAATGTAGTCCTGCTTTGATACTTAGTATATTGATGTTG
131 CAAATATTAAATATGGGACACCGGTTGAATGTAGTCCTGCTTTGATACTGAGTATATTGATGTTG
1913981 AGATTATGATATATTTGCTCCATTGCTATACTTGGGA
196 AGATTATGATATATTTGCTCCATTGCTATACTTGGGA
1914018 CTTCCATAAATGGTTAATAAAAGAGCCCTCCTTTTATATGTGAGATTAGAAGGACACGAGGAAGC
1 CTTCCATAAATGGTTAATAAAAGAGCCCTCCTTTTATATGTGAGATTAGAAGGACACGAGGAAGC
* * *
1914083 TGC-ATGGTTTTATTGTGTTCCTAATATTTATTTAGTTTCACTTTTCTCTGAGCAGAGATTGTAT
66 T-CTATGGTTTTATTGTGTTCCTAATATTTAATTAGTTTCACTTTTCTCCGAGCAGAGATTGTAC
* * *
1914147 GCAAATATTAAATGTGGGACACTGGTTGAATGTAGTCCTGCTTTGTTACTGAGTATATTGATGTT
130 GCAAATATTAAATATGGGACACCGGTTGAATGTAGTCCTGCTTTGATACTGAGTATATTGATGTT
*
1914212 GAGATTGTGATATATTTGCTCC
195 GAGATTATGATATATTTGCTCC
1914234 TAATATTTAA
Statistics
Matches: 204, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
232 203 1.00
233 1 0.00
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (232 bp):
CTTCCATAAATGGTTAATAAAAGAGCCCTCCTTTTATATGTGAGATTAGAAGGACACGAGGAAGC
TCTATGGTTTTATTGTGTTCCTAATATTTAATTAGTTTCACTTTTCTCCGAGCAGAGATTGTACG
CAAATATTAAATATGGGACACCGGTTGAATGTAGTCCTGCTTTGATACTGAGTATATTGATGTTG
AGATTATGATATATTTGCTCCATTGCTATACTTGGGA
Found at i:1922558 original size:86 final size:86
Alignment explanation
Indices: 1922413--1922571 Score: 282
Period size: 86 Copynumber: 1.8 Consensus size: 86
1922403 CTCTTAACAT
*
1922413 ATATTTGATAATATACTACAAAAAAAAAAAAAAACCACAACAGAATTCATGTATATGTACATAGC
1 ATATTTGAGAATATACTACAAAAAAAAAAAAAAACCACAACAGAATTCATGTATATGTACATAGC
1922478 ATTCATAGAAAACGCTCAAAA
66 ATTCATAGAAAACGCTCAAAA
* **
1922499 ATATTTGAGAATATTCTACAAAAAAAAAAAAAAACCAGTACAGAATTCATGTATATGTACATAGC
1 ATATTTGAGAATATACTACAAAAAAAAAAAAAAACCACAACAGAATTCATGTATATGTACATAGC
1922564 ATTCATAG
66 ATTCATAG
1922572 CCCCCTGGCA
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
86 69 1.00
ACGTcount: A:0.52, C:0.14, G:0.09, T:0.25
Consensus pattern (86 bp):
ATATTTGAGAATATACTACAAAAAAAAAAAAAAACCACAACAGAATTCATGTATATGTACATAGC
ATTCATAGAAAACGCTCAAAA
Found at i:1932665 original size:84 final size:85
Alignment explanation
Indices: 1932544--1932715 Score: 319
Period size: 84 Copynumber: 2.0 Consensus size: 85
1932534 AAATTAAAGG
* *
1932544 TTAATAAAAATAAATATTTAAAATAAATACAATGAAGGTCATATTGGTCAATTCAAAAGTTATCT
1 TTAATAAAAATAAAAAATTAAAATAAATACAATGAAGGTCATATTGGTCAATTCAAAAGTTATCT
1932609 AAATTCGTATTTTATTTAAA
66 AAATTCGTATTTTATTTAAA
1932629 TTAATAAAAA-AAAAAATTAAAATAAATACAATGAAGGTCATATTGGTCAATTCAAAAGTTATCT
1 TTAATAAAAATAAAAAATTAAAATAAATACAATGAAGGTCATATTGGTCAATTCAAAAGTTATCT
1932693 AAATTCGTATTTTATTTAAA
66 AAATTCGTATTTTATTTAAA
1932713 TTA
1 TTA
1932716 GTTTCTAATG
Statistics
Matches: 85, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
84 75 0.88
85 10 0.12
ACGTcount: A:0.48, C:0.07, G:0.08, T:0.37
Consensus pattern (85 bp):
TTAATAAAAATAAAAAATTAAAATAAATACAATGAAGGTCATATTGGTCAATTCAAAAGTTATCT
AAATTCGTATTTTATTTAAA
Found at i:1945961 original size:7 final size:7
Alignment explanation
Indices: 1945949--1945975 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1945939 TTTCCTCAGG
1945949 TTTTAAA
1 TTTTAAA
1945956 TTTTAAA
1 TTTTAAA
1945963 TTTTAAA
1 TTTTAAA
1945970 TTTTAA
1 TTTTAA
1945976 TTTCAATTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TTTTAAA
Found at i:1946454 original size:4 final size:4
Alignment explanation
Indices: 1946445--1946481 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
1946435 GTTTGGGCTG
*
1946445 GTTA GTTA GTTA GTTA GTTA GCTA GTTA GTTA GTTA G
1 GTTA GTTA GTTA GTTA GTTA GTTA GTTA GTTA GTTA G
1946482 AGTTGAGTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.24, C:0.03, G:0.27, T:0.46
Consensus pattern (4 bp):
GTTA
Found at i:1958809 original size:56 final size:57
Alignment explanation
Indices: 1958727--1958840 Score: 221
Period size: 56 Copynumber: 2.0 Consensus size: 57
1958717 TATAAAAATA
1958727 TATATTTTTATAATTTAATAATTTTAAATTTTAAAAAATTAATTAATTATTGATGTG
1 TATATTTTTATAATTTAATAATTTTAAATTTTAAAAAATTAATTAATTATTGATGTG
1958784 TATATTTTTA-AATTTAATAATTTTAAATTTTAAAAAATTAATTAATTATTGATGTG
1 TATATTTTTATAATTTAATAATTTTAAATTTTAAAAAATTAATTAATTATTGATGTG
1958840 T
1 T
1958841 TATCTACGTG
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
56 47 0.82
57 10 0.18
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (57 bp):
TATATTTTTATAATTTAATAATTTTAAATTTTAAAAAATTAATTAATTATTGATGTG
Found at i:1959483 original size:98 final size:98
Alignment explanation
Indices: 1959362--1959559 Score: 396
Period size: 98 Copynumber: 2.0 Consensus size: 98
1959352 TAGGGAGAAG
1959362 ACAATAACACAAGCAAAAAGTCTTGGTCTTCCAAAAATAATACTTAAATTCATTATGTAATTTAT
1 ACAATAACACAAGCAAAAAGTCTTGGTCTTCCAAAAATAATACTTAAATTCATTATGTAATTTAT
1959427 ACTATTATTTAAGCATTTTGTTGAGTTAATATC
66 ACTATTATTTAAGCATTTTGTTGAGTTAATATC
1959460 ACAATAACACAAGCAAAAAGTCTTGGTCTTCCAAAAATAATACTTAAATTCATTATGTAATTTAT
1 ACAATAACACAAGCAAAAAGTCTTGGTCTTCCAAAAATAATACTTAAATTCATTATGTAATTTAT
1959525 ACTATTATTTAAGCATTTTGTTGAGTTAATATC
66 ACTATTATTTAAGCATTTTGTTGAGTTAATATC
1959558 AC
1 AC
1959560 TCTCAATCAT
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 100 1.00
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (98 bp):
ACAATAACACAAGCAAAAAGTCTTGGTCTTCCAAAAATAATACTTAAATTCATTATGTAATTTAT
ACTATTATTTAAGCATTTTGTTGAGTTAATATC
Found at i:1960562 original size:167 final size:168
Alignment explanation
Indices: 1960275--1960610 Score: 665
Period size: 167 Copynumber: 2.0 Consensus size: 168
1960265 TTTATTTTAT
1960275 TATATTATAATAAAAATATAGATTGCTATTATATATTTAAATAAATTTCTCAATTTGAAAAAAAG
1 TATATTATAATAAAAATATAGATTGCTATTATATATTTAAATAAATTTCTCAATTTGAAAAAAAG
1960340 AAAAAGTTAAAACGGTAAACAAAGTCGTAATTTTATACCAAACTCAATTGACCCTCGTTCCCTAA
66 AAAAAGTTAAAACGGTAAACAAAGTCGTAATTTTATACCAAACTCAATTGACCCTCGTTCCCTAA
1960405 TTCTGCTCTTAGCCCCTATACTTTTCAGAATTCTAAAA
131 TTCTGCTCTTAGCCCCTATACTTTTCAGAATTCTAAAA
1960443 TATATTATAA-AAAAATATAGATTGCTATTATATATTTAAATAAATTTCTCAATTTGAAAAAAAG
1 TATATTATAATAAAAATATAGATTGCTATTATATATTTAAATAAATTTCTCAATTTGAAAAAAAG
1960507 AAAAAGTTAAAACGGTAAACAAAGTCGTAATTTTATACCAAACTCAATTGACCCTCGTTCCCTAA
66 AAAAAGTTAAAACGGTAAACAAAGTCGTAATTTTATACCAAACTCAATTGACCCTCGTTCCCTAA
1960572 TTCTGCTCTTAGCCCCTATACTTTTCAGAATTCTAAAA
131 TTCTGCTCTTAGCCCCTATACTTTTCAGAATTCTAAAA
1960610 T
1 T
1960611 TTAATCCCTC
Statistics
Matches: 168, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
167 158 0.94
168 10 0.06
ACGTcount: A:0.41, C:0.16, G:0.08, T:0.35
Consensus pattern (168 bp):
TATATTATAATAAAAATATAGATTGCTATTATATATTTAAATAAATTTCTCAATTTGAAAAAAAG
AAAAAGTTAAAACGGTAAACAAAGTCGTAATTTTATACCAAACTCAATTGACCCTCGTTCCCTAA
TTCTGCTCTTAGCCCCTATACTTTTCAGAATTCTAAAA
Found at i:1968699 original size:24 final size:24
Alignment explanation
Indices: 1968672--1968717 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
1968662 AACCTAATTC
1968672 TAATCAAA-GTTAAATATATTATGT
1 TAAT-AAATGTTAAATATATTATGT
1968696 TAATAAATGTTAAATATATTAT
1 TAATAAATGTTAAATATATTAT
1968718 ACTCATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (24 bp):
TAATAAATGTTAAATATATTATGT
Found at i:1968725 original size:24 final size:24
Alignment explanation
Indices: 1968671--1968727 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
1968661 AAACCTAATT
*
1968671 CTAATCAAA-GTTAAATATATTATG
1 CTAAT-AAATGTTAAATATATTATA
*
1968695 TTAATAAATGTTAAATATATTATA
1 CTAATAAATGTTAAATATATTATA
*
1968719 CTCATAAAT
1 CTAATAAAT
1968728 AATAAATCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 3 0.11
24 25 0.89
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.40
Consensus pattern (24 bp):
CTAATAAATGTTAAATATATTATA
Found at i:1968733 original size:24 final size:24
Alignment explanation
Indices: 1968682--1968734 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
1968672 TAATCAAAGT
** **
1968682 TAAATATATTATGTTAATAAATGT
1 TAAATATATTATACTAATAAATAA
*
1968706 TAAATATATTATACTCATAAATAA
1 TAAATATATTATACTAATAAATAA
1968730 TAAAT
1 TAAAT
1968735 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.42
Consensus pattern (24 bp):
TAAATATATTATACTAATAAATAA
Found at i:1970382 original size:21 final size:21
Alignment explanation
Indices: 1970356--1970395 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1970346 TGGGTTTAAA
*
1970356 AGTTTA-GAGTCTAGGGTTTCG
1 AGTTTATGA-TCTAGAGTTTCG
1970377 AGTTTATGATCTAGAGTTT
1 AGTTTATGATCTAGAGTTT
1970396 AAGGTTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.23, C:0.07, G:0.28, T:0.42
Consensus pattern (21 bp):
AGTTTATGATCTAGAGTTTCG
Found at i:1970786 original size:101 final size:102
Alignment explanation
Indices: 1970662--1970864 Score: 399
Period size: 101 Copynumber: 2.0 Consensus size: 102
1970652 CCCCAAAATG
1970662 ATAAAATTTTGATTTAATCATTTAAAAATTATAAAGATATAAATTATTAAAATGGTAAAATTATA
1 ATAAAATTTTGATTTAATCATTTAAAAATTATAAAGATATAAATTATTAAAATGGTAAAATTATA
1970727 TTTTTATTATAGTAAAAATATACAATTTAATTTCGAT
66 TTTTTATTATAGTAAAAATATACAATTTAATTTCGAT
1970764 ATAAAATTTT-ATTTAATCATTTAAAAATTATAAAGATATAAATTATTAAAATGGTAAAATTATA
1 ATAAAATTTTGATTTAATCATTTAAAAATTATAAAGATATAAATTATTAAAATGGTAAAATTATA
1970828 TTTTTATTATAGTAAAAATATACAATTTAATTTCGAT
66 TTTTTATTATAGTAAAAATATACAATTTAATTTCGAT
1970865 CCCCCTCAAA
Statistics
Matches: 101, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
101 91 0.90
102 10 0.10
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.43
Consensus pattern (102 bp):
ATAAAATTTTGATTTAATCATTTAAAAATTATAAAGATATAAATTATTAAAATGGTAAAATTATA
TTTTTATTATAGTAAAAATATACAATTTAATTTCGAT
Found at i:1976329 original size:25 final size:25
Alignment explanation
Indices: 1976301--1976349 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
1976291 GTAGACCAAT
*
1976301 AAGAAACGTGCCAAAGTGGCAGACG
1 AAGAAACGTGCCAAAGCGGCAGACG
1976326 AAGAAACGTGCCAAAGCGGCAGAC
1 AAGAAACGTGCCAAAGCGGCAGAC
1976350 TTTCTTCCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.41, C:0.22, G:0.31, T:0.06
Consensus pattern (25 bp):
AAGAAACGTGCCAAAGCGGCAGACG
Found at i:1993145 original size:14 final size:14
Alignment explanation
Indices: 1993126--1993156 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1993116 CTTAATTCAT
1993126 TTTCTGTAAATATA
1 TTTCTGTAAATATA
*
1993140 TTTCTGTAATTATA
1 TTTCTGTAAATATA
1993154 TTT
1 TTT
1993157 GTGAACTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.58
Consensus pattern (14 bp):
TTTCTGTAAATATA
Found at i:1996815 original size:14 final size:14
Alignment explanation
Indices: 1996792--1996826 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1996782 TACAATATCC
*
1996792 AAATAATAACAACA
1 AAATAGTAACAACA
1996806 AAATAGTAACAACA
1 AAATAGTAACAACA
*
1996820 TAATAGT
1 AAATAGT
1996827 GAAATGACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.63, C:0.11, G:0.06, T:0.20
Consensus pattern (14 bp):
AAATAGTAACAACA
Found at i:2002222 original size:19 final size:19
Alignment explanation
Indices: 2002198--2002238 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
2002188 TATTTTAAAG
2002198 TTATTTAGGTAGATAAATC
1 TTATTTAGGTAGATAAATC
*
2002217 TTATTTAGTTAGATAAATC
1 TTATTTAGGTAGATAAATC
2002236 TTA
1 TTA
2002239 GAATAAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.46
Consensus pattern (19 bp):
TTATTTAGGTAGATAAATC
Found at i:2002323 original size:41 final size:41
Alignment explanation
Indices: 2002276--2002356 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
2002266 ATATTTTATT
* * *
2002276 TTATCTTTTAGTAGTTTATTAGAATAGGGGAATTATTTTCC
1 TTATCTTTTAGTAATTTAATAGAATAAGGGAATTATTTTCC
2002317 TTATCTTTTAGTAATTTAATAGAATAAGGGAATTATTTTC
1 TTATCTTTTAGTAATTTAATAGAATAAGGGAATTATTTTC
2002357 TCAATTAGGT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.31, C:0.06, G:0.15, T:0.48
Consensus pattern (41 bp):
TTATCTTTTAGTAATTTAATAGAATAAGGGAATTATTTTCC
Found at i:2006170 original size:41 final size:41
Alignment explanation
Indices: 2006138--2006218 Score: 153
Period size: 41 Copynumber: 2.0 Consensus size: 41
2006128 ATATTTTATT
2006138 TTATCTTTTAGTAGTTTATTAGAATAAGAGAATTATTTTCC
1 TTATCTTTTAGTAGTTTATTAGAATAAGAGAATTATTTTCC
*
2006179 TTATCTTTTAGTAGTTTATTAGAATAAGGGAATTATTTTC
1 TTATCTTTTAGTAGTTTATTAGAATAAGAGAATTATTTTC
2006219 TCAATTCGGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.31, C:0.06, G:0.14, T:0.49
Consensus pattern (41 bp):
TTATCTTTTAGTAGTTTATTAGAATAAGAGAATTATTTTCC
Found at i:2006772 original size:3 final size:3
Alignment explanation
Indices: 2006764--2006791 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2006754 TATTTAGAGC
2006764 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2006792 AATACACACA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2011848 original size:15 final size:17
Alignment explanation
Indices: 2011816--2011848 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
2011806 CAGGGTGCTT
2011816 ATTGGATAAAAGACCAA
1 ATTGGATAAAAGACCAA
2011833 ATTGG-TAAAA-ACCAA
1 ATTGGATAAAAGACCAA
2011848 A
1 A
2011849 GTTGAGGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 5 0.31
17 5 0.31
ACGTcount: A:0.55, C:0.12, G:0.15, T:0.18
Consensus pattern (17 bp):
ATTGGATAAAAGACCAA
Found at i:2012956 original size:29 final size:30
Alignment explanation
Indices: 2012900--2012965 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
2012890 ATATAAAAAA
* *
2012900 TATATATGAATTTTGATTTAATTTGTAAT-T
1 TATATATGAAGTTTGATTT-ATGTGTAATCT
2012930 TGATATATGAAGTTTGATTT-TGTGTAATCT
1 T-ATATATGAAGTTTGATTTATGTGTAATCT
2012960 TATATA
1 TATATA
2012966 GTAAACTTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 12 0.38
30 3 0.09
31 17 0.53
ACGTcount: A:0.32, C:0.02, G:0.14, T:0.53
Consensus pattern (30 bp):
TATATATGAAGTTTGATTTATGTGTAATCT
Found at i:2016014 original size:8 final size:9
Alignment explanation
Indices: 2015991--2016017 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
2015981 TTTTTCTATT
2015991 TATTTTTAA
1 TATTTTTAA
2016000 TATTTTTAA
1 TATTTTTAA
2016009 TATTTTTAA
1 TATTTTTAA
2016018 AGTCACGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TATTTTTAA
Found at i:2018194 original size:23 final size:23
Alignment explanation
Indices: 2018167--2018216 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
2018157 GTTTTAAGAG
*
2018167 GTTAAAATATAATTTTATCATTT
1 GTTAAAATATAATTTCATCATTT
* *
2018190 GTTAATATATAGTTTCATCATTT
1 GTTAAAATATAATTTCATCATTT
2018213 -TTAA
1 GTTAA
2018217 GGGATTGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.52
Consensus pattern (23 bp):
GTTAAAATATAATTTCATCATTT
Found at i:2023312 original size:16 final size:16
Alignment explanation
Indices: 2023293--2023328 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
2023283 AGTTTAGATT
2023293 ATTTTAGGTTCAAATC
1 ATTTTAGGTTCAAATC
*
2023309 ATTTTAGGTTTAAATC
1 ATTTTAGGTTCAAATC
2023325 ATTT
1 ATTT
2023329 AAGTTTACCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.08, G:0.11, T:0.50
Consensus pattern (16 bp):
ATTTTAGGTTCAAATC
Found at i:2023334 original size:15 final size:16
Alignment explanation
Indices: 2023283--2023335 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
2023273 GGTTATTTCG
* *
2023283 AGTTTAGATTATTTTA
1 AGTTTAAATCATTTTA
* *
2023299 GGTTCAAATCATTTTA
1 AGTTTAAATCATTTTA
*
2023315 GGTTTAAATCA-TTTA
1 AGTTTAAATCATTTTA
2023330 AGTTTA
1 AGTTTA
2023336 CCGATCAGGA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
15 9 0.29
16 22 0.71
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.49
Consensus pattern (16 bp):
AGTTTAAATCATTTTA
Found at i:2032752 original size:23 final size:23
Alignment explanation
Indices: 2032726--2032773 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
2032716 AAGTGTTTAC
2032726 ATAATTTTCTTCTGTCAAAAGAA
1 ATAATTTTCTTCTGTCAAAAGAA
2032749 ATAATTTTCTTCTGTCAAAAGAA
1 ATAATTTTCTTCTGTCAAAAGAA
2032772 AT
1 AT
2032774 GATTCATCGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (23 bp):
ATAATTTTCTTCTGTCAAAAGAA
Found at i:2047219 original size:21 final size:21
Alignment explanation
Indices: 2047195--2047241 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
2047185 AGTAAGGTGA
*
2047195 TTAAATA-ATGTAATTTATTTT
1 TTAAATATATGTAATTTA-TAT
*
2047216 TTAAA-ATATTTAATTTATAT
1 TTAAATATATGTAATTTATAT
2047236 TTAAAT
1 TTAAAT
2047242 TAAAAACCGA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
TTAAATATATGTAATTTATAT
Found at i:2052021 original size:23 final size:24
Alignment explanation
Indices: 2051993--2052037 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
2051983 TGATTTAAAT
*
2051993 AAATATTCATA-TTTATATTATTA
1 AAATATTAATATTTTATATTATTA
2052016 AAATATTAATATTTTATATTAT
1 AAATATTAATATTTTATATTAT
2052038 AAATACATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (24 bp):
AAATATTAATATTTTATATTATTA
Found at i:2055615 original size:197 final size:193
Alignment explanation
Indices: 2055266--2055859 Score: 550
Period size: 197 Copynumber: 2.9 Consensus size: 193
2055256 GCGAAGTTTG
* * * * *
2055266 ATTGTTTTTGTTGTTGATCCATGAGTATGTTGCCTTCAATTTTTTAACAATATTTATCTTTGATG
1 ATTGTTTTTGTTGTTGATCCATGAATATGTTGACTT-AAGTTTTTAACAATGTTGATCTTTGATG
* * * * * * * *
2055331 GTGACGAGAAGGTTGTCACGTAATTTAATTTTCAGTTTCAGTTGAATTTGAATGCTTCGGTTCCG
65 ATGGCGA-AAGGTTGTTACGTAATTTAATTTCCA-TTTTAG-AGAAATTGAATGCTTCGATTCC-
* **
2055396 AATTTTTTTACCCTTAGATGCTTTACATTACAATTTCAAAATTTTTCAAAAAATAAT-A-GCGAA
126 -ATTTTTTCACTTTTAGATGCTTTACATTACAATTTCAAAATTTTTCAAAAAATAATGATGCGAA
2055459 ATATT
190 ATA-T
* *
2055464 ATTGTTTTTGTTGTTGATCTATGAATATGTTGACTTAAGTTTTCAACAATGTTGATCTTTGATGA
1 ATTGTTTTTGTTGTTGATCCATGAATATGTTGACTTAAGTTTTTAACAATGTTGATCTTTGATGA
2055529 TGGCTGAAAGGTT-TTACGTAATTTAAAATTTCCATTTTTAGAGAAATTGAATGCTTCGATTTCC
66 TGGC-GAAAGGTTGTTACGTAATTT--AATTTCCA-TTTTAGAGAAATTGAATGCTTCGA-TTCC
* * ** *
2055593 ATTTTTTCACTTTTTTGATGCTTTACGTTACAATTTCAAAA-TTTAAAAAAAAAAATCTTTTTTG
126 ATTTTTTCAC-TTTTAGATGCTTTACATTACAATTTCAAAATTTTTCAAAAAATAA-------TG
*
2055657 ATGCGAAGTAT
183 ATGCGAAATAT
* *
2055668 AGTTGTTTTTGTTG-TGATCCACGAATACGTTGACTTAAGTTTTTAACAATGTTGATCTTTGATG
1 A-TTGTTTTTGTTGTTGATCCATGAATATGTTGACTTAAGTTTTTAACAATGTTGATCTTTGATG
* * * * * *
2055732 TTTGGCCGAAATGTTGCTACCTAGTTTGATTTTCCATTTTAGAGTTAAATTTTGAATGCTTCGAT
65 -ATGG-CGAAAGGTTGTTACGTAATTT-AATTTCCATTTTAGAG--AAA--TTGAATGCTTCGAT
* * * *
2055797 TCTCAATTTTTCACTTTTAGATGCTTTACATTTCACTTTCAAATTTTTTCTAAAAAAATAATG
123 TC-CATTTTTTCACTTTTAGATGCTTTACATTACAATTTCAAAATTTTTC--AAAAAATAATG
2055860 TTTTCTTCTT
Statistics
Matches: 325, Mismatches: 45, Indels: 47
0.78 0.11 0.11
Matches are distributed among these distances:
196 30 0.09
197 74 0.23
198 51 0.16
203 3 0.01
204 57 0.18
205 36 0.11
206 12 0.04
207 28 0.09
208 26 0.08
210 8 0.02
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (193 bp):
ATTGTTTTTGTTGTTGATCCATGAATATGTTGACTTAAGTTTTTAACAATGTTGATCTTTGATGA
TGGCGAAAGGTTGTTACGTAATTTAATTTCCATTTTAGAGAAATTGAATGCTTCGATTCCATTTT
TTCACTTTTAGATGCTTTACATTACAATTTCAAAATTTTTCAAAAAATAATGATGCGAAATAT
Found at i:2055774 original size:204 final size:206
Alignment explanation
Indices: 2055465--2055839 Score: 501
Period size: 204 Copynumber: 1.8 Consensus size: 206
2055455 CGAAATATTA
* * *
2055465 TTGTTTTTGTTGTTGATCTATGAATATGTTGACTTAAGTTTTCAACAATGTTGATCTTTGATGAT
1 TTGTTTTTGTTGTTGATCCACGAATACGTTGACTTAAGTTTTCAACAATGTTGATCTTTGATGAT
* * *
2055530 GGCTGAAAGGTTTTACGTAATTTAAAATTTCCATTTTTAGAG-AAA-TTGAATGCTTCGATT-TC
66 GGCCGAAAGGTTCTACCTAATTTAAAATTTCCATTTTTAGAGTAAATTTGAATGCTTCGATTCT-
* * *
2055592 CATTTTTTCACTTTTTTGATGCTTTACGTTACAATTTCAAAATTTAAAAAAAAAAATCTTTTTTG
130 CAATTTTTCAC-TTTTAGATGCTTTACATTACAATTTCAAAATTTAAAAAAAAAAATCTTTTTTG
2055657 ATGCGAAGTATAG
194 ATGCGAAGTATAG
* *
2055670 TTGTTTTTGTTG-TGATCCACGAATACGTTGACTTAAGTTTTTAACAATGTTGATCTTTGATGTT
1 TTGTTTTTGTTGTTGATCCACGAATACGTTGACTTAAGTTTTCAACAATGTTGATCTTTGATG-A
* * * *
2055734 TGGCCGAAATGTTGCTACCTAGTTT-GATTTTCCA-TTTTAGAGTTAAATTTTGAATGCTTCGAT
65 TGGCCGAAAGGTT-CTACCTAATTTAAAATTTCCATTTTTAGAG-TAAA-TTTGAATGCTTCGAT
* *
2055797 TCTCAATTTTTCACTTTTAGATGCTTTACATTTCACTTTCAAA
127 TCTCAATTTTTCACTTTTAGATGCTTTACATTACAATTTCAAA
2055840 TTTTTTCTAA
Statistics
Matches: 146, Mismatches: 17, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
204 54 0.37
205 30 0.21
206 11 0.08
207 25 0.17
208 25 0.17
209 1 0.01
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.46
Consensus pattern (206 bp):
TTGTTTTTGTTGTTGATCCACGAATACGTTGACTTAAGTTTTCAACAATGTTGATCTTTGATGAT
GGCCGAAAGGTTCTACCTAATTTAAAATTTCCATTTTTAGAGTAAATTTGAATGCTTCGATTCTC
AATTTTTCACTTTTAGATGCTTTACATTACAATTTCAAAATTTAAAAAAAAAAATCTTTTTTGAT
GCGAAGTATAG
Found at i:2067452 original size:15 final size:13
Alignment explanation
Indices: 2067426--2067466 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
2067416 TTTTTACCAA
2067426 TAAT-TAAAAAAT
1 TAATATAAAAAAT
2067438 TAAATATATAAAAAT
1 T-AATATA-AAAAAT
2067453 T-ATATAAAAAAT
1 TAATATAAAAAAT
2067465 TA
1 TA
2067467 TTGTACCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
12 8 0.32
13 8 0.32
14 2 0.08
15 7 0.28
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
TAATATAAAAAAT
Found at i:2067657 original size:5 final size:6
Alignment explanation
Indices: 2067631--2067656 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2067621 TTTGTTTTCC
2067631 TTTCTT TTTCTT TTTCTT TTTCTT TT
1 TTTCTT TTTCTT TTTCTT TTTCTT TT
2067657 CCGTTTCTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTCTT
Found at i:2067730 original size:3 final size:3
Alignment explanation
Indices: 2067722--2067751 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2067712 TCTCAGAATA
2067722 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
2067752 ATCATCATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:2067955 original size:15 final size:16
Alignment explanation
Indices: 2067937--2067971 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
2067927 TTTTTTTTGG
*
2067937 ATTTGTTTTAC-GTTT
1 ATTTGATTTACTGTTT
2067952 ATTTGATTTACTGTTT
1 ATTTGATTTACTGTTT
2067968 ATTT
1 ATTT
2067972 AAGTGATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.17, C:0.06, G:0.11, T:0.66
Consensus pattern (16 bp):
ATTTGATTTACTGTTT
Found at i:2074198 original size:218 final size:217
Alignment explanation
Indices: 2073819--2074455 Score: 981
Period size: 218 Copynumber: 2.9 Consensus size: 217
2073809 AGCATGGTGG
2073819 ATCATGATTTGTACATTTTATATGTAGGGATAGTGTGTTTTATGTCGTA-AAAAGACCTGCAAAC
1 ATCATGATTTGTACATTTTATATGTAGGGATAGTGTGTTTTATGTC--ACAAAAGACCTGCAAAC
* * * *
2073883 TAGTTTAAGCTCCTTGGCC-CTGGAGGGTTTGTTTTTTGTATTTCTTTTGTGTAAAGTTGTTTTT
64 TAGTGTAAGCTCCTTGGCCTC-GGAGGGTTTGCTTTTTGTAATTCTTTTGCGTAAAGTTGTTTTT
* * *
2073947 GTTTTCGATGTGGATGGTAGTTGCATTTGAAACATTTTATAAGGAGAAAGGCCATCATTCATGTA
128 GTCTTCGATATGGATGGTAGTTGCATTTGAAACATTTTAAAAGGA-AAAGGCCATCATTCATGTA
*
2074012 TCTCGTCTTCATCCCTAGTTGAATGC
192 TCTCGTCTTCATCCCCAGTTGAATGC
* * *
2074038 ATCATGATTTGTACATTTTATATGTAGGGATAGTATGTTTTATGTCACAATAGACCTGCAAATTA
1 ATCATGATTTGTACATTTTATATGTAGGGATAGTGTGTTTTATGTCACAAAAGACCTGCAAACTA
* **
2074103 GTGTAAGCTCCTTGGCCTCGCAGGGTTTGCTTTTTGTAATTCTTTTGCACAAAGTTGTTTTTGTC
66 GTGTAAGCTCCTTGGCCTCGGAGGGTTTGCTTTTTGTAATTCTTTTGCGTAAAGTTGTTTTTGTC
*
2074168 TTCGATATGGATGGTAGTTGCATTTGAAACATTTTACAAAGGAAAAGGCCACCATTCATGTATCT
131 TTCGATATGGATGGTAGTTGCATTTGAAACATTTTA-AAAGGAAAAGGCCATCATTCATGTATCT
2074233 CGTCTTCATCCCCAGTTGAATGC
195 CGTCTTCATCCCCAGTTGAATGC
*
2074256 ATCATGATTTGTACATTTTATATGTAGGGATAGTGTGTTTTATGTCACAAAAGACCTGTAAACTA
1 ATCATGATTTGTACATTTTATATGTAGGGATAGTGTGTTTTATGTCACAAAAGACCTGCAAACTA
* * *
2074321 GTGTAAGCTCCTTGGCCTTGGAGGGTTTGCTTTTTGCAATTCTTTTGCGTAAAGTTGTGTTTGTC
66 GTGTAAGCTCCTTGGCCTCGGAGGGTTTGCTTTTTGTAATTCTTTTGCGTAAAGTTGTTTTTGTC
* * * * * * *
2074386 TTCAATAGGGATGGTAGTTGCATTTAAAACATTTTACAAGGAAAAGTCCGTCATTCATGTATCTT
131 TTCGATATGGATGGTAGTTGCATTTGAAACATTTTAAAAGGAAAAGGCCATCATTCATGTATCTC
2074451 GTCTT
196 GTCTT
2074456 TTTATGTAAA
Statistics
Matches: 382, Mismatches: 33, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
217 30 0.08
218 301 0.79
219 51 0.13
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.40
Consensus pattern (217 bp):
ATCATGATTTGTACATTTTATATGTAGGGATAGTGTGTTTTATGTCACAAAAGACCTGCAAACTA
GTGTAAGCTCCTTGGCCTCGGAGGGTTTGCTTTTTGTAATTCTTTTGCGTAAAGTTGTTTTTGTC
TTCGATATGGATGGTAGTTGCATTTGAAACATTTTAAAAGGAAAAGGCCATCATTCATGTATCTC
GTCTTCATCCCCAGTTGAATGC
Found at i:2077364 original size:151 final size:151
Alignment explanation
Indices: 2077090--2077396 Score: 533
Period size: 151 Copynumber: 2.0 Consensus size: 151
2077080 TTGTAGTTAC
*
2077090 AGTAGAGTTATATAACCGTAGTTCAATCAGTCTTATTCTAGGTCTTGAGCATTGGTTTGTTTTAT
1 AGTAGAGTTATATAACCGTAGTTCAATCAGTCTTATTCTAGGTCTTGAGCATTGGTTCGTTTTAT
*
2077155 CTACAACTTATCATCTACAATCATGGAATCCCAACCATTCACACTGGATCAATCCATCTAAATCT
66 CTACAACTTATCATCTACAATCATGGAATCCCAACCATTCACAATGGATCAATCCATCTAAATCT
* *
2077220 AATATTATCATCACTAGACCT
131 AATAATATCATCACTAAACCT
* * *
2077241 AGTAGAGTTATATAACTGTAGTTCAATCGGTCTTATTCTAGGTCTTGAGCATTGGTTCGTTTTGT
1 AGTAGAGTTATATAACCGTAGTTCAATCAGTCTTATTCTAGGTCTTGAGCATTGGTTCGTTTTAT
*
2077306 CTACAACTTATCATCTACAATCATGGAATCCCAACCATTCACAATGGATCAATCCATCTAGATCT
66 CTACAACTTATCATCTACAATCATGGAATCCCAACCATTCACAATGGATCAATCCATCTAAATCT
*
2077371 GATAATATCATCACTAAACCT
131 AATAATATCATCACTAAACCT
2077392 AGTAG
1 AGTAG
2077397 TTTTGGATAC
Statistics
Matches: 147, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
151 147 1.00
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (151 bp):
AGTAGAGTTATATAACCGTAGTTCAATCAGTCTTATTCTAGGTCTTGAGCATTGGTTCGTTTTAT
CTACAACTTATCATCTACAATCATGGAATCCCAACCATTCACAATGGATCAATCCATCTAAATCT
AATAATATCATCACTAAACCT
Found at i:2079433 original size:23 final size:23
Alignment explanation
Indices: 2079407--2079450 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2079397 ATTTAGTTCT
2079407 TTAAAAAATAATAAAATTATAAA
1 TTAAAAAATAATAAAATTATAAA
* *
2079430 TTAATACATAATAAAATTATA
1 TTAAAAAATAATAAAATTATA
2079451 TTTTGACATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (23 bp):
TTAAAAAATAATAAAATTATAAA
Found at i:2083404 original size:23 final size:21
Alignment explanation
Indices: 2083372--2083416 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
2083362 TTAAGAGATT
*
2083372 ATTATGTGTTCTATTTATTTTTA
1 ATTATGTGTT-T-TTAATTTTTA
*
2083395 ATTATTTGTTTTTAATTTTTA
1 ATTATGTGTTTTTAATTTTTA
2083416 A
1 A
2083417 ATCCACAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 10 0.50
22 1 0.05
23 9 0.45
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.67
Consensus pattern (21 bp):
ATTATGTGTTTTTAATTTTTA
Found at i:2083406 original size:14 final size:14
Alignment explanation
Indices: 2083383--2083415 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2083373 TTATGTGTTC
2083383 TATTTATTTTTAAT
1 TATTTATTTTTAAT
*
2083397 TATTTGTTTTTAAT
1 TATTTATTTTTAAT
2083411 T-TTTA
1 TATTTA
2083416 AATCCACAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 3 0.18
14 14 0.82
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (14 bp):
TATTTATTTTTAAT
Found at i:2083556 original size:14 final size:14
Alignment explanation
Indices: 2083537--2083574 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
2083527 CAAATATCAC
2083537 ATTAT-TTATATA-
1 ATTATATTATATAT
2083549 ATTATATTATATAT
1 ATTATATTATATAT
2083563 ATTATATTATAT
1 ATTATATTATAT
2083575 TTTTAAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 5 0.21
13 7 0.29
14 12 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
ATTATATTATATAT
Found at i:2083559 original size:5 final size:5
Alignment explanation
Indices: 2083537--2083575 Score: 50
Period size: 5 Copynumber: 8.6 Consensus size: 5
2083527 CAAATATCAC
2083537 ATTAT -TTAT A-TA- ATTAT ATTAT A-TAT ATTAT ATTAT ATT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATT
2083576 TTTAAATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
3 1 0.03
4 12 0.40
5 17 0.57
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:2083573 original size:19 final size:17
Alignment explanation
Indices: 2083537--2083575 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
2083527 CAAATATCAC
*
2083537 ATTATTTATATAATTAT
1 ATTATATATATAATTAT
2083554 ATTATATATATTATATTAT
1 ATTATATATA-TA-ATTAT
2083573 ATT
1 ATT
2083576 TTTAAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
18 2 0.11
19 8 0.42
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTATATATATAATTAT
Found at i:2087768 original size:55 final size:55
Alignment explanation
Indices: 2087684--2087951 Score: 306
Period size: 55 Copynumber: 4.8 Consensus size: 55
2087674 CAAATTAAAC
* * *
2087684 AAGAAACTAAAACTACCCATCAAGCCAAAAGGCAA-AAGAACCCTACAAACTAACA
1 AAGAAATTAAAACTACCCATCAAGCCAAAAGGCAAGAAAAACCC-ACAAAATAACA
* **
2087739 AAGAAATTAAAATTACCCATCAAATCAAAAGGCAAGAAAAAAAACCCACAAAATAACA
1 AAGAAATTAAAACTACCCATCAAGCCAAAAGGCAAG---AAAAACCCACAAAATAACA
* * * *
2087797 AAGAAATTAAAACTACACATCAAGCCGAAGGGCAAGAAGAAAAACCCACAAACTAA-A
1 AAGAAATTAAAACTACCCATCAAGCCAAAAGGC---AAGAAAAACCCACAAAATAACA
* *
2087854 CAAGATATTAAAACTACCCATCAAGCCAAAAGGCAAGAAAAACCCGCAAAATAACA
1 -AAGAAATTAAAACTACCCATCAAGCCAAAAGGCAAGAAAAACCCACAAAATAACA
* * * *
2087910 ATGAAATTAAAAGTACCCATCAAGTCAAAAGGCAACAAAAAC
1 AAGAAATTAAAACTACCCATCAAGCCAAAAGGCAAGAAAAAC
2087952 TCAAAAAAGA
Statistics
Matches: 180, Mismatches: 24, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
55 86 0.48
56 1 0.01
57 1 0.01
58 82 0.46
59 7 0.04
61 3 0.02
ACGTcount: A:0.56, C:0.22, G:0.10, T:0.11
Consensus pattern (55 bp):
AAGAAATTAAAACTACCCATCAAGCCAAAAGGCAAGAAAAACCCACAAAATAACA
Found at i:2087806 original size:58 final size:58
Alignment explanation
Indices: 2087684--2087950 Score: 307
Period size: 58 Copynumber: 4.7 Consensus size: 58
2087674 CAAATTAAAC
* * *
2087684 AAGAAACTAAAACTACCCATCAAGCCAAAAGGC----AAAAGAACCCTACAAACTAACA
1 AAGAAATTAAAACTACCCATCAAGCCAAAAGGCAAGAAAAAAAACCC-ACAAAATAACA
* **
2087739 AAGAAATTAAAATTACCCATCAAATCAAAAGGCAAGAAAAAAAACCCACAAAATAACA
1 AAGAAATTAAAACTACCCATCAAGCCAAAAGGCAAGAAAAAAAACCCACAAAATAACA
* * * * *
2087797 AAGAAATTAAAACTACACATCAAGCCGAAGGGCAAGAAGAAAAACCCACAAACTAA-A
1 AAGAAATTAAAACTACCCATCAAGCCAAAAGGCAAGAAAAAAAACCCACAAAATAACA
* *
2087854 CAAGATATTAAAACTACCCATCAAGCCAAAAGGCAAG---AAAAACCCGCAAAATAACA
1 -AAGAAATTAAAACTACCCATCAAGCCAAAAGGCAAGAAAAAAAACCCACAAAATAACA
* * * *
2087910 ATGAAATTAAAAGTACCCATCAAGTCAAAAGGCAACAAAAA
1 AAGAAATTAAAACTACCCATCAAGCCAAAAGGCAAGAAAAA
2087951 CTCAAAAAAG
Statistics
Matches: 178, Mismatches: 25, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
55 75 0.42
56 1 0.01
57 1 0.01
58 92 0.52
59 9 0.05
ACGTcount: A:0.57, C:0.22, G:0.10, T:0.11
Consensus pattern (58 bp):
AAGAAATTAAAACTACCCATCAAGCCAAAAGGCAAGAAAAAAAACCCACAAAATAACA
Found at i:2087808 original size:29 final size:29
Alignment explanation
Indices: 2087717--2087808 Score: 71
Period size: 29 Copynumber: 3.1 Consensus size: 29
2087707 GCCAAAAGGC
* *
2087717 AAAAGAACCCTACAAACTAACAAAGAAATT
1 AAAAAAACCC-ACAAAATAACAAAGAAATT
** * * **
2087747 AAAATTACCCATC-AAATCAA-AAGGCAAGA
1 AAAAAAACCCA-CAAAAT-AACAAAGAAATT
2087776 AAAAAAACCCACAAAATAACAAAGAAATT
1 AAAAAAACCCACAAAATAACAAAGAAATT
2087805 AAAA
1 AAAA
2087809 CTACACATCA
Statistics
Matches: 45, Mismatches: 13, Indels: 9
0.67 0.19 0.13
Matches are distributed among these distances:
28 3 0.07
29 31 0.69
30 11 0.24
ACGTcount: A:0.63, C:0.18, G:0.07, T:0.12
Consensus pattern (29 bp):
AAAAAAACCCACAAAATAACAAAGAAATT
Found at i:2088365 original size:19 final size:18
Alignment explanation
Indices: 2088324--2088367 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
2088314 GATTATTGTT
2088324 AATTT-TTTTATAATTTA
1 AATTTATTTTATAATTTA
*
2088341 AA-TTATTTTATATTTTA
1 AATTTATTTTATAATTTA
2088358 ATATTTATTT
1 A-ATTTATTT
2088368 ATTAATAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 2 0.09
17 14 0.61
18 1 0.04
19 6 0.26
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
AATTTATTTTATAATTTA
Found at i:2090590 original size:16 final size:16
Alignment explanation
Indices: 2090567--2090603 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
2090557 TTAAAATTTT
*
2090567 CAAA-TTTTAATATTA
1 CAAATTTTTAATAATA
2090582 CAAATTTTTAATAATA
1 CAAATTTTTAATAATA
2090598 -AAATTT
1 CAAATTT
2090604 CATATTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (16 bp):
CAAATTTTTAATAATA
Found at i:2101041 original size:14 final size:14
Alignment explanation
Indices: 2101022--2101057 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
2101012 CTTTGAAGGT
2101022 CCCATTTCAAATAA
1 CCCATTTCAAATAA
2101036 CCCATTTCAAATAA
1 CCCATTTCAAATAA
2101050 CCCATTTC
1 CCCATTTC
2101058 GAAAACCAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.31
Consensus pattern (14 bp):
CCCATTTCAAATAA
Done.