Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold25
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: 9553305
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 6276 characters in sequence are not A, C, G, or T
File 7 of 56
Found at i:1326015 original size:17 final size:18
Alignment explanation
Indices: 1325970--1326013 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
1325960 AATATGTTTA
1325970 AAATAT-TAAATAAATTT
1 AAATATATAAATAAATTT
1325987 AAATATATAAAT-AATTT
1 AAATATATAAATAAATTT
*
1326004 ATAT-TATAAA
1 AAATATATAAA
1326014 ATTTTTGATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 6 0.24
17 14 0.56
18 5 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAATATATAAATAAATTT
Found at i:1326212 original size:22 final size:21
Alignment explanation
Indices: 1326173--1326214 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
1326163 TACGACTACT
* *
1326173 TAAAATAATATTATAAAATTG
1 TAAAATAAAATTAAAAAATTG
1326194 TAAAATTAAAATTAAAAAATT
1 TAAAA-TAAAATTAAAAAATT
1326215 ATTATATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
TAAAATAAAATTAAAAAATTG
Found at i:1328797 original size:29 final size:30
Alignment explanation
Indices: 1328732--1328798 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
1328722 ATTAAAATTT
*
1328732 ATATAA-AT-ATAAAATATTTTAAATATAA
1 ATATAATATAATAAAATATTATAAATATAA
*
1328760 TTATAATATAATAAAATA-TATAAATA-AA
1 ATATAATATAATAAAATATTATAAATATAA
1328788 ATATAGATATA
1 ATATA-ATATA
1328799 TTAATTACCA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
28 11 0.33
29 14 0.42
30 8 0.24
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (30 bp):
ATATAATATAATAAAATATTATAAATATAA
Found at i:1328917 original size:15 final size:14
Alignment explanation
Indices: 1328897--1328955 Score: 57
Period size: 15 Copynumber: 4.0 Consensus size: 14
1328887 AATTTTTTAA
1328897 AAATATAATTTATT
1 AAATATAATTTATT
* *
1328911 CAAATATAA-ATATAA
1 -AAATATAATTTAT-T
1328926 AAATATAATTATATT
1 AAATATAATT-TATT
1328941 AAATATATATTTATT
1 AAATATA-ATTTATT
1328956 TTCGACATCA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 11 0.31
15 19 0.53
16 6 0.17
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (14 bp):
AAATATAATTTATT
Found at i:1329676 original size:9 final size:9
Alignment explanation
Indices: 1329653--1329685 Score: 57
Period size: 9 Copynumber: 3.6 Consensus size: 9
1329643 ATGCACCCAA
1329653 AAAACTTTCC
1 AAAACTTT-C
1329663 AAAACTTTC
1 AAAACTTTC
1329672 AAAACTTTC
1 AAAACTTTC
1329681 AAAAC
1 AAAAC
1329686 ACCCAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.27
Consensus pattern (9 bp):
AAAACTTTC
Found at i:1330930 original size:5 final size:5
Alignment explanation
Indices: 1330915--1330947 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
1330905 GACAGATTCG
1330915 AAAGAA AAAGA AAAGA AAAGA AAAGA AAA-A AAA
1 AAAG-A AAAGA AAAGA AAAGA AAAGA AAAGA AAA
1330948 TATTATAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 19 0.70
6 4 0.15
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:1335678 original size:136 final size:139
Alignment explanation
Indices: 1335437--1335712 Score: 420
Period size: 136 Copynumber: 2.0 Consensus size: 139
1335427 TTTTATTATA
*
1335437 TTTAATAAAAATAATACATTAAATATAAAAATTTTCTAAAATAAGTTATTAAAGAATTTTTAATG
1 TTTAATAAAAATAATACATTAAATATAAAAATATTCTAAAATAAGTTATTAAAGAATTTTTAATG
* * *
1335502 TGCTTATAAACACTAATTACAATAATTATTTTTGTAATTAAATTATTGCTTAATAAATTGTAAAA
66 TGATTATAAACACTAATTACAATAATTATTTTTATAATTAAATTATTGCTTAATAAATAGTAAAA
1335567 ATTAAATGC
131 ATTAAATGC
*
1335576 TTTAATAAAAATAATGCATTAAATATAAAAA-ATTC-ATAAATAAGTTATTAAA-AA-TTTT-AT
1 TTTAATAAAAATAATACATTAAATATAAAAATATTCTA-AAATAAGTTATTAAAGAATTTTTAAT
**
1335636 CGTGATTATAAGTACTAATTA-AATAGATTATTTTTATAATTAAATTATTGCTTAATAAATAGTA
65 -GTGATTATAAACACTAATTACAATA-ATTATTTTTATAATTAAATTATTGCTTAATAAATAGTA
1335700 AAAATTAAATGC
128 AAAATTAAATGC
1335712 T
1 T
1335713 AAAAATTAAG
Statistics
Matches: 127, Mismatches: 7, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
135 6 0.05
136 70 0.55
137 3 0.02
138 18 0.14
139 30 0.24
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.41
Consensus pattern (139 bp):
TTTAATAAAAATAATACATTAAATATAAAAATATTCTAAAATAAGTTATTAAAGAATTTTTAATG
TGATTATAAACACTAATTACAATAATTATTTTTATAATTAAATTATTGCTTAATAAATAGTAAAA
ATTAAATGC
Found at i:1339430 original size:58 final size:58
Alignment explanation
Indices: 1339340--1339451 Score: 170
Period size: 58 Copynumber: 1.9 Consensus size: 58
1339330 AATCAAGATG
* * *
1339340 TATTTGGAGACTGTCGAAACGAAAGTAAGCAATGGTTAGAGATTTAAGTGTTTTAACA
1 TATTTGGAGAATGTCGAAACGAAAGTAAGCAATAGTTAGAGATATAAGTGTTTTAACA
* * *
1339398 TATTTGGAGAATTTCGAAACGAAAGTCAGCAATAGTTGGAGATATAAGTGTTTT
1 TATTTGGAGAATGTCGAAACGAAAGTAAGCAATAGTTAGAGATATAAGTGTTTT
1339452 CTGATTTTGC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
58 48 1.00
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.32
Consensus pattern (58 bp):
TATTTGGAGAATGTCGAAACGAAAGTAAGCAATAGTTAGAGATATAAGTGTTTTAACA
Found at i:1348893 original size:88 final size:88
Alignment explanation
Indices: 1348770--1348965 Score: 317
Period size: 88 Copynumber: 2.2 Consensus size: 88
1348760 TCAATCAAGC
* * *
1348770 CAATCGAA-TTCAAAACCC-AAAATCCCAATCTAATTTAATAGAAGACCTTAAAACGAATTCTTG
1 CAATCTAATTTCAAAACCCAAAAATCCCAATCTAATTTAATAGAAAACCTTAAAAAGAATTCTTG
1348833 CATCAATCATAATTCAACTAAAT
66 CATCAATCATAATTCAACTAAAT
*
1348856 CAATCTAATTTCAAAACCCAAAAATCCGGAA-CTAATTTAATAGAAAACCTTAAAAAGAATTCTT
1 CAATCTAATTTCAAAACCCAAAAATCC-CAATCTAATTTAATAGAAAACCTTAAAAAGAATTCTT
*
1348920 GCTTCAATCATAATTCAACTAAAT
65 GCATCAATCATAATTCAACTAAAT
1348944 CAATCTAATTTCAAAACCCAAA
1 CAATCTAATTTCAAAACCCAAA
1348966 GTCCCATTAA
Statistics
Matches: 102, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
86 7 0.07
87 10 0.10
88 83 0.81
89 2 0.02
ACGTcount: A:0.46, C:0.21, G:0.05, T:0.27
Consensus pattern (88 bp):
CAATCTAATTTCAAAACCCAAAAATCCCAATCTAATTTAATAGAAAACCTTAAAAAGAATTCTTG
CATCAATCATAATTCAACTAAAT
Found at i:1353744 original size:16 final size:17
Alignment explanation
Indices: 1353719--1353751 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1353709 AATTATACAT
1353719 ATAATAAAAA-TTTTAA
1 ATAATAAAAACTTTTAA
*
1353735 ATAATTAAAACTTTTAA
1 ATAATAAAAACTTTTAA
1353752 TATGAAAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (17 bp):
ATAATAAAAACTTTTAA
Found at i:1353823 original size:19 final size:19
Alignment explanation
Indices: 1353781--1353835 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
1353771 TAGACGAATC
1353781 ATATTAAT-TTTATTTAAAT
1 ATATTAATATTTA-TTAAAT
*
1353800 ATATTAATATTTATTATAT
1 ATATTAATATTTATTAAAT
*
1353819 TTATTTAATATTATATT
1 ATA-TTAATATT-TATT
1353836 TTATATCGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 15 0.48
20 12 0.39
21 4 0.13
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
ATATTAATATTTATTAAAT
Found at i:1362959 original size:9 final size:9
Alignment explanation
Indices: 1362937--1362973 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
1362927 TATAATATCT
1362937 ATAATCTATA
1 ATAAT-TATA
1362947 ATAATTATA
1 ATAATTATA
*
1362956 ATAATAATA
1 ATAATTATA
1362965 ATAATTATA
1 ATAATTATA
1362974 TATATTGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 20 0.80
10 5 0.20
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (9 bp):
ATAATTATA
Found at i:1363167 original size:17 final size:17
Alignment explanation
Indices: 1363130--1363192 Score: 51
Period size: 16 Copynumber: 3.8 Consensus size: 17
1363120 TATTTTTATG
*
1363130 TATATTT-TAATAT-AA
1 TATATTTATATTATAAA
*
1363145 TGTATTTATATTATAAA
1 TATATTTATATTATAAA
* *
1363162 TATA-TTATTTTTTATAA
1 TATATTTATATTATA-AA
*
1363179 TATATTTTTATTAT
1 TATATTTATATTAT
1363193 TTTTATTATG
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
15 6 0.17
16 13 0.36
17 11 0.31
18 6 0.17
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
TATATTTATATTATAAA
Found at i:1363177 original size:23 final size:23
Alignment explanation
Indices: 1363149--1363196 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
1363139 ATATAATGTA
*
1363149 TTTATATTATAAATATATTATTT
1 TTTATAATATAAATATATTATTT
** *
1363172 TTTATAATATATTTTTATTATTT
1 TTTATAATATAAATATATTATTT
1363195 TT
1 TT
1363197 ATTATGTTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTATAATATAAATATATTATTT
Found at i:1369841 original size:23 final size:24
Alignment explanation
Indices: 1369815--1369892 Score: 70
Period size: 23 Copynumber: 3.1 Consensus size: 24
1369805 AAAAATATTT
1369815 TTATTTAAAT-TTAATTATAAAA-A
1 TTATTTAAATATTAA-TATAAAATA
*
1369838 TTATATAAATATTAATATAAAATA
1 TTATTTAAATATTAATATAAAATA
* *
1369862 TTTTTTATTAATATTTAAAATAATAATA
1 TTATTTA--AATA-TTAATATAA-AATA
1369890 TTA
1 TTA
1369893 AATTAAATCA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
23 16 0.36
24 10 0.23
26 4 0.09
27 8 0.18
28 6 0.14
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TTATTTAAATATTAATATAAAATA
Found at i:1370232 original size:9 final size:8
Alignment explanation
Indices: 1370213--1370237 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1370203 TCCGAGCTAG
1370213 TTTTTTAT
1 TTTTTTAT
1370221 TTTTTTAT
1 TTTTTTAT
1370229 TTTTTTAT
1 TTTTTTAT
1370237 T
1 T
1370238 GGGTTATAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTTAT
Found at i:1373801 original size:44 final size:46
Alignment explanation
Indices: 1373721--1373813 Score: 118
Period size: 45 Copynumber: 2.1 Consensus size: 46
1373711 AAATTTTTTA
* * * **
1373721 TTTATTTTAATTTAATTTAAATTATTATTTAATAATAAAAAT-ATT
1 TTTATTTAAATTTAATTAAAAATATTAAATAATAATAAAAATAATT
*
1373766 TTTATTTAAATTTAATTAAAAATA-TAAATATTAATAAAAATAATT
1 TTTATTTAAATTTAATTAAAAATATTAAATAATAATAAAAATAATT
1373811 TTT
1 TTT
1373814 TAATTTTTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
44 14 0.34
45 27 0.66
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (46 bp):
TTTATTTAAATTTAATTAAAAATATTAAATAATAATAAAAATAATT
Found at i:1373803 original size:18 final size:18
Alignment explanation
Indices: 1373772--1373807 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
1373762 TATTTTTATT
1373772 TAAATTTAATTAAAAATA
1 TAAATTTAATTAAAAATA
1373790 TAAATATTAA-TAAAAATA
1 TAAAT-TTAATTAAAAATA
1373808 ATTTTTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
TAAATTTAATTAAAAATA
Found at i:1374471 original size:2 final size:2
Alignment explanation
Indices: 1374466--1374490 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1374456 AAGAAAAGCA
1374466 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1374491 AATTCATTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1375027 original size:11 final size:11
Alignment explanation
Indices: 1375011--1375126 Score: 55
Period size: 11 Copynumber: 10.7 Consensus size: 11
1375001 AATATTATAT
1375011 ATTTTATATTA
1 ATTTTATATTA
1375022 ATTTTA-A-TA
1 ATTTTATATTA
** * *
1375031 AAGTAATAATTT
1 ATTTTAT-ATTA
*
1375043 ATTTTATATAA
1 ATTTTATATTA
*
1375054 ATTTTATATTT
1 ATTTTATATTA
*
1375065 ATTTTATATTT
1 ATTTTATATTA
*
1375076 ATATTAT-TT-
1 ATTTTATATTA
*
1375085 ATTTATATTTTA
1 ATTT-TATATTA
* *
1375097 ATTATTTTAAT-
1 ATT-TTATATTA
1375108 ATTTTAT-TTA
1 ATTTTATATTA
1375118 TATTTTATA
1 -ATTTTATA
1375127 ATCTATTGAT
Statistics
Matches: 77, Mismatches: 18, Indels: 19
0.68 0.16 0.17
Matches are distributed among these distances:
9 9 0.12
10 9 0.12
11 47 0.61
12 11 0.14
13 1 0.01
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (11 bp):
ATTTTATATTA
Found at i:1375064 original size:22 final size:22
Alignment explanation
Indices: 1375006--1375073 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 22
1374996 TTAAAAATAT
* *
1375006 TATATATTTTATATTAATTTTA
1 TATAAATTTTATATTTATTTTA
* *
1375028 -ATAAA-GTAATAATTTATTTTA
1 TATAAATTTTAT-ATTTATTTTA
1375049 TATAAATTTTATATTTATTTTA
1 TATAAATTTTATATTTATTTTA
1375071 TAT
1 TAT
1375074 TTATATTATT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
20 3 0.08
21 13 0.35
22 18 0.49
23 3 0.08
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (22 bp):
TATAAATTTTATATTTATTTTA
Found at i:1375076 original size:17 final size:16
Alignment explanation
Indices: 1375054--1375118 Score: 66
Period size: 17 Copynumber: 4.1 Consensus size: 16
1375044 TTTTATATAA
1375054 ATTTTATA-TTTATTTT
1 ATTTTATATTTTA-TTT
1375070 ATATTTATA--TTATTT
1 AT-TTTATATTTTATTT
*
1375085 A-TTTATATTTTAATT
1 ATTTTATATTTTATTT
1375100 ATTTTAATATTTTATTT
1 ATTTT-ATATTTTATTT
1375117 AT
1 AT
1375119 ATTTTATAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
13 6 0.14
15 10 0.24
16 8 0.19
17 18 0.43
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
ATTTTATATTTTATTT
Found at i:1375091 original size:19 final size:20
Alignment explanation
Indices: 1375060--1375103 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 20
1375050 ATAAATTTTA
1375060 TATTTATTTTATA-TTTATAT
1 TATTTATTTTATATTTTA-AT
1375080 TATTTA-TTTATATTTTAAT
1 TATTTATTTTATATTTTAAT
1375099 TATTT
1 TATTT
1375104 TAATATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TATTTATTTTATATTTTAAT
Found at i:1375102 original size:28 final size:27
Alignment explanation
Indices: 1375054--1375124 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 27
1375044 TTTTATATAA
*
1375054 ATTTTATATT-TATTTT-ATATTTATATT
1 ATTTTAT-TTATATTTTAATATTT-TAAT
1375081 A-TTTATTTATATTTTAATTATTTTAAT
1 ATTTTATTTATATTTTAA-TATTTTAAT
1375108 ATTTTATTTATATTTTA
1 ATTTTATTTATATTTTA
1375125 TAATCTATTG
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
25 2 0.05
26 11 0.28
27 6 0.15
28 20 0.51
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (27 bp):
ATTTTATTTATATTTTAATATTTTAAT
Found at i:1377196 original size:16 final size:16
Alignment explanation
Indices: 1377175--1377207 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1377165 GTCCTGCCCA
1377175 CTGTTAAGGAATTGTC
1 CTGTTAAGGAATTGTC
1377191 CTGTTAAGGAATTGTC
1 CTGTTAAGGAATTGTC
1377207 C
1 C
1377208 GTTTTAGCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.36
Consensus pattern (16 bp):
CTGTTAAGGAATTGTC
Found at i:1379225 original size:2 final size:2
Alignment explanation
Indices: 1379218--1379255 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1379208 ACCCAAATTA
1379218 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1379256 GAAAATACCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1394308 original size:30 final size:29
Alignment explanation
Indices: 1394274--1394333 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 29
1394264 TAATTTTAAG
1394274 TAAGGACAGATGTCCACTTCTTATGATCAC
1 TAAGGACAGATGTCCACTTCTTAT-ATCAC
1394304 TAAGGACAGATGTCCACTTCTTATATCAC
1 TAAGGACAGATGTCCACTTCTTATATCAC
1394333 T
1 T
1394334 CAAAACTATC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 6 0.20
30 24 0.80
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (29 bp):
TAAGGACAGATGTCCACTTCTTATATCAC
Found at i:1399231 original size:8 final size:8
Alignment explanation
Indices: 1399158--1399237 Score: 50
Period size: 8 Copynumber: 10.8 Consensus size: 8
1399148 CTTTGTCATA
1399158 TAAT-TAT
1 TAATATAT
1399165 TAA-AT-T
1 TAATATAT
1399171 TAATA-AT
1 TAATATAT
*
1399178 TCATAT-T
1 TAATATAT
1399185 TAATATAT
1 TAATATAT
1399193 TAATA-ATT
1 TAATATA-T
1399201 TAATTATAT
1 TAA-TATAT
*
1399210 AAAT-TA-
1 TAATATAT
*
1399216 TAAAATAT
1 TAATATAT
*
1399224 TCATATAT
1 TAATATAT
1399232 TAATAT
1 TAATAT
1399238 TATAGTGATT
Statistics
Matches: 55, Mismatches: 8, Indels: 19
0.67 0.10 0.23
Matches are distributed among these distances:
6 6 0.11
7 21 0.38
8 22 0.40
9 5 0.09
10 1 0.02
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (8 bp):
TAATATAT
Found at i:1399851 original size:7 final size:6
Alignment explanation
Indices: 1399839--1399962 Score: 57
Period size: 6 Copynumber: 21.2 Consensus size: 6
1399829 AGTATGTATA
**
1399839 AAATATT AAATAT ATAATAT AAATAT AAATATT AAA-AT TTATA- AAATAT
1 AAATA-T AAATAT A-AATAT AAATAT AAATA-T AAATAT AAATAT AAATAT
* * * * * *
1399888 AAATTAT TAATA- AATTA- AAATTT ATATAT -AATAT -ATTTT AAATAT
1 AAA-TAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
* *
1399933 AATTAT -AATAT -AATAA AATATAT AAATAT A
1 AAATAT AAATAT AAATAT AA-ATAT AAATAT A
1399963 TAAATTATAA
Statistics
Matches: 88, Mismatches: 20, Indels: 19
0.69 0.16 0.15
Matches are distributed among these distances:
5 26 0.30
6 37 0.42
7 25 0.28
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (6 bp):
AAATAT
Found at i:1399867 original size:27 final size:27
Alignment explanation
Indices: 1399835--1399965 Score: 92
Period size: 29 Copynumber: 4.8 Consensus size: 27
1399825 ATATAGTATG
1399835 TATAAAATATTAAATATATAATATAAA
1 TATAAAATATTAAATATATAATATAAA
*
1399862 TAT-AAATATTAAA-AT-TTATA-AAA
1 TATAAAATATTAAATATATAATATAAA
* * * * *
1399885 TATAAATTATTAATAAATTAAAATTTATA
1 TATAAAATATTAA-ATA-TATAATATAAA
* *
1399914 TATAATATATTTTAAATATA-ATTATAATA
1 TATAA-A-ATATTAAATATATAATATAA-A
1399943 TAATAAAATATATAAATATATAA
1 T-ATAAAATAT-TAAATATATAA
1399966 ATTATAAAAT
Statistics
Matches: 78, Mismatches: 14, Indels: 21
0.69 0.12 0.19
Matches are distributed among these distances:
23 6 0.08
24 12 0.15
25 3 0.04
26 11 0.14
27 4 0.05
28 9 0.12
29 20 0.26
30 8 0.10
31 5 0.06
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
TATAAAATATTAAATATATAATATAAA
Found at i:1399885 original size:17 final size:17
Alignment explanation
Indices: 1399865--1399913 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
1399855 ATATAAATAT
1399865 AAATATTAAAATTTATA
1 AAATATTAAAATTTATA
1399882 AAATA-T-AAA-TTATTA
1 AAATATTAAAATTTA-TA
1399897 ATAA-ATTAAAATTTATA
1 A-AATATTAAAATTTATA
1399914 TATAATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
14 3 0.11
15 7 0.26
16 4 0.15
17 10 0.37
18 3 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATATTAAAATTTATA
Found at i:1399888 original size:34 final size:34
Alignment explanation
Indices: 1399837--1399978 Score: 95
Period size: 32 Copynumber: 4.3 Consensus size: 34
1399827 ATAGTATGTA
*
1399837 TAAAATATTA-AATATATAATATAAATATAAATAT
1 TAAAAT-TTATAAAATATAATATAAATATAAATAT
* *
1399871 TAAAATTTATAAAATATAA-AT-TAT-TAATAAAT
1 TAAAATTTATAAAATATAATATAAATATAA-ATAT
* * *
1399903 TAAAATTTATATATAATATATTTTAAATATAATTA-
1 TAAAATTTATA-A-AATATAATATAAATATAAATAT
* *
1399938 TAATA-TAATAAAATAT-ATA-AATATATAAAT-T
1 TAAAATTTATAAAATATAATATAA-ATATAAATAT
1399969 ATAAAATTTA
1 -TAAAATTTA
1399979 AATTAATCTA
Statistics
Matches: 82, Mismatches: 15, Indels: 23
0.68 0.12 0.19
Matches are distributed among these distances:
30 2 0.02
31 11 0.13
32 25 0.30
33 9 0.11
34 24 0.29
35 5 0.06
36 3 0.04
37 3 0.04
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (34 bp):
TAAAATTTATAAAATATAATATAAATATAAATAT
Found at i:1399906 original size:23 final size:22
Alignment explanation
Indices: 1399837--1399969 Score: 82
Period size: 23 Copynumber: 6.1 Consensus size: 22
1399827 ATAGTATGTA
*
1399837 TAAAATATTAA-AT-ATATAA-
1 TAAAATATAAATATAATATAAT
* *
1399856 TATAAATATAAATATTAAAAT-TT
1 TA-AAATATAAATA-TAATATAAT
1399879 ATAAAATATAAATTATTAATA-AAT
1 -TAAAATATAAA-TA-TAATATAAT
* * *
1399903 TAAAATTTATATATAATATATT
1 TAAAATATAAATATAATATAAT
* *
1399925 TTAAATATAATTATAATATAAT
1 TAAAATATAAATATAATATAAT
*
1399947 AAAATATATAAATAT-ATA-AAT
1 TAAA-ATATAAATATAATATAAT
1399968 TA
1 TA
1399970 TAAAATTTAA
Statistics
Matches: 87, Mismatches: 17, Indels: 18
0.71 0.14 0.15
Matches are distributed among these distances:
19 2 0.02
20 8 0.09
21 10 0.11
22 27 0.31
23 30 0.34
24 10 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
TAAAATATAAATATAATATAAT
Found at i:1399969 original size:32 final size:31
Alignment explanation
Indices: 1399843--1399972 Score: 87
Period size: 34 Copynumber: 4.2 Consensus size: 31
1399833 TGTATAAAAT
*
1399843 ATTA-AATATATAATATAAATATAAATAT-TAAA
1 ATTATAATATATAA-A-ATATATAAATATAT-AA
* *
1399875 ATTTATAAAATATAAATTATTAATAAAT-TA-AA
1 A-TTATAATATATAAAATA-T-ATAAATATATAA
* * *
1399907 ATT-T-ATATATAATATATTTTAA-ATAT-A
1 ATTATAATATATAAAATATATAAATATATAA
1399934 ATTATAATATAATAAAATATATAAATATATAA
1 ATTATAATAT-ATAAAATATATAAATATATAA
1399966 ATTATAA
1 ATTATAA
1399973 AATTTAAATT
Statistics
Matches: 75, Mismatches: 11, Indels: 24
0.68 0.10 0.22
Matches are distributed among these distances:
27 9 0.12
28 2 0.03
29 13 0.17
30 12 0.16
31 6 0.08
32 13 0.17
33 6 0.08
34 14 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (31 bp):
ATTATAATATATAAAATATATAAATATATAA
Found at i:1399971 original size:27 final size:24
Alignment explanation
Indices: 1399877--1399972 Score: 65
Period size: 27 Copynumber: 3.8 Consensus size: 24
1399867 ATATTAAAAT
1399877 TTATAAA-ATATAAATTATTAATAAA
1 TTATAAATATATAAA-TA-TAATAAA
* *
1399902 TTA-AAAT-T-TATATATAATATA
1 TTATAAATATATAAATATAATAAA
*
1399923 TTTTAAATATAATTATAATATAATAAAA
1 TTATAAATAT-A-TA-AATATAAT-AAA
1399951 TATATAAATATATAAATTATAA
1 T-TATAAATATATAAA-TATAA
1399973 AATTTAAATT
Statistics
Matches: 55, Mismatches: 6, Indels: 18
0.70 0.08 0.23
Matches are distributed among these distances:
21 8 0.15
22 6 0.11
23 4 0.07
24 4 0.07
25 3 0.05
26 4 0.07
27 14 0.25
28 4 0.07
29 8 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
TTATAAATATATAAATATAATAAA
Found at i:1399973 original size:7 final size:7
Alignment explanation
Indices: 1399835--1399983 Score: 50
Period size: 7 Copynumber: 21.3 Consensus size: 7
1399825 ATATAGTATG
*
1399835 TATAAAA
1 TATAAAT
1399842 TATTAAA-
1 TA-TAAAT
1399849 TATATAA-
1 TATA-AAT
1399856 TATAAA-
1 TATAAAT
1399862 TATAAA-
1 TATAAAT
1399868 TATTAAAATT
1 TA-T-AAA-T
*
1399878 TATAAAA
1 TATAAAT
1399885 TATAAAT
1 TATAAAT
1399892 TAT---T
1 TATAAAT
*
1399896 AATAAAT
1 TATAAAT
1399903 TA-AAATT
1 TATAAA-T
*
1399910 TATATAT
1 TATAAAT
* *
1399917 AATATAT
1 TATAAAT
*
1399924 TTTAAA-
1 TATAAAT
1399930 TAT-AAT
1 TATAAAT
1399936 TATAATAT
1 TATAA-AT
*
1399944 AATAAAAT
1 TAT-AAAT
1399952 ATATAAAT
1 -TATAAAT
1399960 ATATAAAT
1 -TATAAAT
1399968 TATAAAAT
1 TAT-AAAT
1399976 T-TAAAT
1 TATAAAT
1399982 TA
1 TA
1399984 ATCTATCACA
Statistics
Matches: 112, Mismatches: 12, Indels: 36
0.70 0.08 0.22
Matches are distributed among these distances:
4 3 0.03
5 2 0.02
6 25 0.22
7 40 0.36
8 35 0.31
9 5 0.04
10 2 0.02
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
TATAAAT
Found at i:1399982 original size:14 final size:15
Alignment explanation
Indices: 1399839--1399983 Score: 71
Period size: 14 Copynumber: 9.9 Consensus size: 15
1399829 AGTATGTATA
1399839 AAATAT-TAAA-TAT
1 AAATATATAAATTAT
*
1399852 ATA-ATATAAA-TAT
1 AAATATATAAATTAT
1399865 AAATAT-TAAAATTTAT
1 AAATATAT-AAA-TTAT
1399881 AAA-ATATAAATTAT
1 AAATATATAAATTAT
* *
1399895 TAATAAATTAAAATT-T
1 AAATATA-T-AAATTAT
* *
1399911 ATATATAATATATT-T
1 AAATAT-ATAAATTAT
*
1399926 TAA-ATAT-AATTAT
1 AAATATATAAATTAT
1399939 -AATATAATAAAATATAT
1 AAATAT-AT-AAAT-TAT
1399956 AAATATATAAATTAT
1 AAATATATAAATTAT
*
1399971 AAA-ATTTAAATTA
1 AAATATATAAATTA
1399984 ATCTATCACA
Statistics
Matches: 103, Mismatches: 12, Indels: 33
0.70 0.08 0.22
Matches are distributed among these distances:
12 7 0.07
13 17 0.17
14 24 0.23
15 19 0.18
16 20 0.19
17 11 0.11
18 5 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AAATATATAAATTAT
Found at i:1403995 original size:18 final size:18
Alignment explanation
Indices: 1403974--1404008 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1403964 TTTATTAGCG
*
1403974 TGATAATTTTTTCATTAT
1 TGATAATTTTTTAATTAT
*
1403992 TGATATTTTTTTAATTA
1 TGATAATTTTTTAATTA
1404009 ATGTGTTATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.63
Consensus pattern (18 bp):
TGATAATTTTTTAATTAT
Found at i:1404604 original size:20 final size:20
Alignment explanation
Indices: 1404579--1404618 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1404569 TCGGAATAAG
1404579 AATGCATGGCCCCATCATCC
1 AATGCATGGCCCCATCATCC
*
1404599 AATGCATGGTCCCATCATCC
1 AATGCATGGCCCCATCATCC
1404619 TCTCTCTTAC
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:0.25, C:0.38, G:0.15, T:0.23
Consensus pattern (20 bp):
AATGCATGGCCCCATCATCC
Found at i:1406322 original size:2 final size:2
Alignment explanation
Indices: 1406315--1406359 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
1406305 TCTAACTTGG
* * *
1406315 AT AT AT AT AA AT AT AT AT AT AT AT AC AT AT AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1406357 AT A
1 AT A
1406360 CCAGTGTATG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (2 bp):
AT
Found at i:1406907 original size:20 final size:19
Alignment explanation
Indices: 1406882--1406948 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 19
1406872 ATTTATAATT
1406882 TATATATATTTAAATATAAA
1 TATATA-ATTTAAATATAAA
1406902 TATATAATTTGTAAA-ATAAA
1 TATATAA-TT-TAAATATAAA
*
1406922 TA-AAAATTT-AATATTAAA
1 TATATAATTTAAATA-TAAA
1406940 TATATAATT
1 TATATAATT
1406949 ATGCGAGACG
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
16 2 0.05
17 2 0.05
18 8 0.20
19 9 0.22
20 15 0.38
21 4 0.10
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (19 bp):
TATATAATTTAAATATAAA
Found at i:1407032 original size:2 final size:2
Alignment explanation
Indices: 1407025--1407050 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1407015 TAATGAGTAC
1407025 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1407051 GAGAGAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1407055 original size:2 final size:2
Alignment explanation
Indices: 1407050--1407085 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1407040 ATATATATAT
1407050 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1407086 TAAAGGAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1408280 original size:21 final size:21
Alignment explanation
Indices: 1408245--1408290 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1408235 AATTCAACTA
1408245 AAATTAATTTAAATATAAAAAT
1 AAATTAATTTAAATAT-AAAAT
* *
1408267 AAATT-ATTTTAATATTAAAT
1 AAATTAATTTAAATATAAAAT
1408287 AAAT
1 AAAT
1408291 AATAAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 8 0.36
21 9 0.41
22 5 0.23
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AAATTAATTTAAATATAAAAT
Found at i:1409034 original size:31 final size:30
Alignment explanation
Indices: 1408974--1409077 Score: 102
Period size: 30 Copynumber: 3.4 Consensus size: 30
1408964 ATTTTTATTG
* *
1408974 TATCCAAATAAATTTTTAATTTTTAAATTTA
1 TATCTAAATAAATTTTTAATCTTT-AATTTA
* * *
1409005 CATCTAAATAAAAATTTTAATCTTTAATTTG
1 TATCTAAAT-AAATTTTTAATCTTTAATTTA
* *
1409036 TATCAAAATATATTTTTAA-CTTTTAATTTA
1 TATCTAAATAAATTTTTAATC-TTTAATTTA
*
1409066 TATCTCAATAAA
1 TATCTAAATAAA
1409078 CTCTTAACAT
Statistics
Matches: 58, Mismatches: 13, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
29 1 0.02
30 25 0.43
31 19 0.33
32 13 0.22
ACGTcount: A:0.42, C:0.09, G:0.01, T:0.48
Consensus pattern (30 bp):
TATCTAAATAAATTTTTAATCTTTAATTTA
Found at i:1409061 original size:30 final size:29
Alignment explanation
Indices: 1408957--1409069 Score: 93
Period size: 31 Copynumber: 3.7 Consensus size: 29
1408947 TTATATAGGT
* * *
1408957 TTTTTATATTTTTA-TTGTATCCAAATAAA
1 TTTTTA-ATTTTAATTTATATCAAAATAAA
* *
1408986 TTTTTAATTTTTAAATTTACATCTAAATAAAA
1 TTTTTAA-TTTT-AATTTATATCAAAAT-AAA
* * *
1409018 ATTTTAATCTTTAATTTGTATCAAAATATA
1 TTTTTAAT-TTTAATTTATATCAAAATAAA
1409048 TTTTTAACTTTTAATTTATATC
1 TTTTTAA-TTTTAATTTATATC
1409070 TCAATAAACT
Statistics
Matches: 67, Mismatches: 11, Indels: 11
0.75 0.12 0.12
Matches are distributed among these distances:
28 1 0.01
29 10 0.15
30 21 0.31
31 23 0.34
32 12 0.18
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (29 bp):
TTTTTAATTTTAATTTATATCAAAATAAA
Found at i:1409145 original size:30 final size:32
Alignment explanation
Indices: 1409110--1409180 Score: 103
Period size: 30 Copynumber: 2.3 Consensus size: 32
1409100 TATTTGAAAC
*
1409110 AAAAATTTATTTAGATATAAA-TAAAAAAT-A
1 AAAAATTTATTTAAATATAAATTAAAAAATAA
*
1409140 AAAAATAT-TTTAAATATAAATTAAAAAATAA
1 AAAAATTTATTTAAATATAAATTAAAAAATAA
1409171 AAAAATTTAT
1 AAAAATTTAT
1409181 GAAAAAATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 11 0.31
30 15 0.43
31 8 0.23
32 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (32 bp):
AAAAATTTATTTAAATATAAATTAAAAAATAA
Found at i:1414019 original size:21 final size:21
Alignment explanation
Indices: 1413994--1414033 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1413984 TTTTTTTATA
1413994 AATTTAATTGAATTAAATTTT
1 AATTTAATTGAATTAAATTTT
** *
1414015 AATTTTTTTTAATTAAATT
1 AATTTAATTGAATTAAATT
1414034 AAGATCACTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (21 bp):
AATTTAATTGAATTAAATTTT
Found at i:1414238 original size:19 final size:18
Alignment explanation
Indices: 1414188--1414239 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
1414178 AATAAGAATG
1414188 AATATA-AATATAAAAAT
1 AATATATAATATAAAAAT
* *
1414205 AATATAATTACATAAAAAT
1 AATAT-ATAATATAAAAAT
1414224 ATATATATAATATAAA
1 A-ATATATAATATAAA
1414240 TTATTATGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 5 0.18
18 1 0.04
19 18 0.64
20 4 0.14
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
AATATATAATATAAAAAT
Found at i:1414278 original size:12 final size:14
Alignment explanation
Indices: 1414211--1414291 Score: 51
Period size: 14 Copynumber: 5.6 Consensus size: 14
1414201 AAATAATATA
*
1414211 ATTACATAAA-AAT
1 ATTATATAAATAAT
1414224 ATATATATAATATAA-
1 AT-TATATAA-ATAAT
* *
1414239 ATTATTATGTATTAAT
1 ATTA-TAT-AAATAAT
1414255 ATTATATAAATAAT
1 ATTATATAAATAAT
*
1414269 ATTTTA-AATATAAAT
1 ATTATATAA-AT-AAT
1414284 ATTATATA
1 ATTATATA
1414292 TTAAAATAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 15
0.70 0.09 0.20
Matches are distributed among these distances:
13 4 0.08
14 20 0.38
15 20 0.38
16 8 0.15
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (14 bp):
ATTATATAAATAAT
Found at i:1414289 original size:27 final size:28
Alignment explanation
Indices: 1414188--1414291 Score: 77
Period size: 29 Copynumber: 3.6 Consensus size: 28
1414178 AATAAGAATG
*
1414188 AATATAAATATA-A-AAATAATATAATTA
1 AATATAAATATATATAAATAATAT-TTTA
* * *
1414215 CATAAAAATATATATATAATATAAATTATTA
1 AATATAAATATATATA-AATA-ATATT-TTA
** *
1414246 TGTATTAATATTATATAAATAATATTTTA
1 AATATAAATA-TATATAAATAATATTTTA
1414275 AATATAAATATTATATA
1 AATATAAATA-TATATA
1414292 TTAAAATAAT
Statistics
Matches: 59, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
27 10 0.17
28 1 0.02
29 18 0.31
30 8 0.14
31 16 0.27
32 6 0.10
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (28 bp):
AATATAAATATATATAAATAATATTTTA
Found at i:1414290 original size:20 final size:18
Alignment explanation
Indices: 1414258--1414300 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
1414248 TATTAATATT
*
1414258 ATATAAATAATATTTTAA
1 ATATAAATAATATATTAA
1414276 ATATAAATATTATATATTAA
1 ATATAAATA--ATATATTAA
1414296 A-ATAA
1 ATATAA
1414301 TCGATGATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 9 0.41
19 4 0.18
20 9 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATATAAATAATATATTAA
Found at i:1414709 original size:22 final size:23
Alignment explanation
Indices: 1414661--1414721 Score: 106
Period size: 22 Copynumber: 2.7 Consensus size: 23
1414651 TTTTGTTCTC
1414661 TTTGTGATAATTAAATGATTATTT
1 TTTGTGATAATTAAATGA-TATTT
1414685 TTTGTGATAATTAAATGA-ATTT
1 TTTGTGATAATTAAATGATATTT
1414707 TTTGTGATAATTAAA
1 TTTGTGATAATTAAA
1414722 GGGTTTTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
22 19 0.51
24 18 0.49
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (23 bp):
TTTGTGATAATTAAATGATATTT
Found at i:1414729 original size:22 final size:22
Alignment explanation
Indices: 1414661--1414731 Score: 88
Period size: 22 Copynumber: 3.1 Consensus size: 22
1414651 TTTTGTTCTC
*
1414661 TTTGTGATAATTAAATGATTATTT
1 TTTGTGATAATTAAAGGA-T-TTT
* *
1414685 TTTGTGATAATTAAATGAATTT
1 TTTGTGATAATTAAAGGATTTT
*
1414707 TTTGTGATAATTAAAGGGTTTT
1 TTTGTGATAATTAAAGGATTTT
1414729 TTT
1 TTT
1414732 CTTTTTTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
22 25 0.58
24 18 0.42
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (22 bp):
TTTGTGATAATTAAAGGATTTT
Found at i:1422370 original size:2 final size:2
Alignment explanation
Indices: 1422363--1422397 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1422353 AGTACAATTC
1422363 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1422398 ATTTATCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1423615 original size:2 final size:2
Alignment explanation
Indices: 1423604--1423634 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1423594 TCTATATGTA
1423604 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1423635 CTTTTAATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1426550 original size:2 final size:2
Alignment explanation
Indices: 1426538--1426568 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1426528 TTTGTAGTAC
*
1426538 TA TA AA 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
1426569 CAGTACATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1427104 original size:17 final size:18
Alignment explanation
Indices: 1427078--1427115 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1427068 AAAAATAATT
* *
1427078 TAAAATATAATTTG-ATA
1 TAAAAAATAATATGAATA
1427095 TAAAAAATAATATGAATA
1 TAAAAAATAATATGAATA
1427113 TAA
1 TAA
1427116 TATATTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (18 bp):
TAAAAAATAATATGAATA
Found at i:1427124 original size:28 final size:28
Alignment explanation
Indices: 1427058--1427120 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 28
1427048 AGTTTATCTA
*
1427058 AATATA-ATATAAAAATAATTTAAAATAT
1 AATATATATA-AAAAATAATATAAAATAT
* *
1427086 AATTTGATATAAAAAATAATAT-GAATAT
1 AATAT-ATATAAAAAATAATATAAAATAT
1427114 AATATAT
1 AATATAT
1427121 TATATATAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
27 2 0.07
28 13 0.45
29 11 0.38
30 3 0.10
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (28 bp):
AATATATATAAAAAATAATATAAAATAT
Found at i:1427126 original size:40 final size:41
Alignment explanation
Indices: 1427082--1427192 Score: 104
Period size: 40 Copynumber: 2.6 Consensus size: 41
1427072 ATAATTTAAA
1427082 ATATAATTTGATATAAAAAATAATATGAA-TA-TAATATATT
1 ATATAATTT-ATATAAAAAATAATATGAATTATTAATATATT
*
1427122 ATATATAATTATATCAAAATTTATATAATATGAATTATTAATATATT
1 ATATA-ATTTATAT-AAAA---A-ATAATATGAATTATTAATATATT
*
1427169 A-A-AATTTATATAAATATATAATAT
1 ATATAATTTATATAAA-AAATAATAT
1427193 TTTAAATATG
Statistics
Matches: 59, Mismatches: 3, Indels: 18
0.74 0.04 0.22
Matches are distributed among these distances:
40 16 0.27
41 7 0.12
43 3 0.05
44 9 0.15
45 11 0.19
46 3 0.05
47 10 0.17
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (41 bp):
ATATAATTTATATAAAAAATAATATGAATTATTAATATATT
Found at i:1427489 original size:2 final size:2
Alignment explanation
Indices: 1427482--1427522 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1427472 AATTCTTCAC
1427482 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1427523 CACATACAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1427860 original size:2 final size:2
Alignment explanation
Indices: 1427853--1427879 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1427843 TTAAAAAGAG
1427853 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1427880 GATAGATAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1429313 original size:2 final size:2
Alignment explanation
Indices: 1429306--1429340 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1429296 TTAACTTTAA
1429306 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1429341 AGGAAAAGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1432767 original size:14 final size:14
Alignment explanation
Indices: 1432730--1432768 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1432720 TGTTCAATTT
*
1432730 CTTCTCTTTTTCCA
1 CTTCTCTTATTCCA
* *
1432744 CTTCTTTTATTCTA
1 CTTCTCTTATTCCA
1432758 CTTCTCTTATT
1 CTTCTCTTATT
1432769 TTTCTTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.10, C:0.28, G:0.00, T:0.62
Consensus pattern (14 bp):
CTTCTCTTATTCCA
Found at i:1435892 original size:3 final size:3
Alignment explanation
Indices: 1435884--1435910 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1435874 TATTAAATCA
1435884 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1435911 GTGTTTCAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1437313 original size:2 final size:2
Alignment explanation
Indices: 1437306--1437344 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1437296 ATTACTTGAA
1437306 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1437345 GAGATTTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1438602 original size:3 final size:3
Alignment explanation
Indices: 1438594--1438627 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1438584 TTCGTGTTGG
1438594 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1438628 AAAATAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1441849 original size:27 final size:27
Alignment explanation
Indices: 1441786--1441853 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
1441776 ATTAATATTA
* *
1441786 TCAAGAGGACCCGACATGAACCCTCTC
1 TCAATAGGACCCGACATAAACCCTCTC
* *
1441813 TCAATCGGACCCGACATAAACCCTCTT
1 TCAATAGGACCCGACATAAACCCTCTC
1441840 TCTAA-AGGACCCGA
1 TC-AATAGGACCCGA
1441854 GCCAGGAATG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 33 0.94
28 2 0.06
ACGTcount: A:0.31, C:0.35, G:0.16, T:0.18
Consensus pattern (27 bp):
TCAATAGGACCCGACATAAACCCTCTC
Found at i:1445287 original size:22 final size:20
Alignment explanation
Indices: 1445262--1445305 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
1445252 TAATAAAAAA
*
1445262 TATTTAATTTATTTTTTATAAT
1 TATTTAA-TTATTATTT-TAAT
1445284 TATTTAATTATTATTTTAAT
1 TATTTAATTATTATTTTAAT
1445304 TA
1 TA
1445306 ATATTATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.29
21 8 0.38
22 7 0.33
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TATTTAATTATTATTTTAAT
Found at i:1446513 original size:2 final size:2
Alignment explanation
Indices: 1446506--1446539 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1446496 AGCAACCACA
1446506 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1446540 TATTGGGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1447794 original size:33 final size:33
Alignment explanation
Indices: 1447757--1447829 Score: 128
Period size: 33 Copynumber: 2.2 Consensus size: 33
1447747 ACGTAACACA
*
1447757 AATATATTTAAACATAATTAATAAAATATATTT
1 AATATATTTAAACATAATTAATAAAACATATTT
*
1447790 AATATATTTAAATATAATTAATAAAACATATTT
1 AATATATTTAAACATAATTAATAAAACATATTT
1447823 AATATAT
1 AATATAT
1447830 GAATTATATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (33 bp):
AATATATTTAAACATAATTAATAAAACATATTT
Found at i:1448368 original size:13 final size:13
Alignment explanation
Indices: 1448350--1448374 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1448340 ACAAAAATTT
1448350 AAATATAAATATC
1 AAATATAAATATC
1448363 AAATATAAATAT
1 AAATATAAATAT
1448375 ATATTTAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATATAAATATC
Found at i:1448384 original size:17 final size:18
Alignment explanation
Indices: 1448364--1448399 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1448354 ATAAATATCA
*
1448364 AATATAAATATA-TATTT
1 AATAAAAATATATTATTT
1448381 AATAAAAATATATTATTT
1 AATAAAAATATATTATTT
1448399 A
1 A
1448400 TTTATATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AATAAAAATATATTATTT
Found at i:1448405 original size:28 final size:28
Alignment explanation
Indices: 1448374--1448438 Score: 89
Period size: 28 Copynumber: 2.3 Consensus size: 28
1448364 AATATAAATA
1448374 TATATTTAATAAA-AATATATTATTTATT
1 TATATTTAATAAAGAATATATT-TTTATT
*
1448402 TATATTT-ATAAAGTTATATATTTTTATT
1 TATATTTAATAAAG-AATATATTTTTATT
1448430 TATATTTAA
1 TATATTTAA
1448439 AAACATGTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
27 5 0.15
28 20 0.61
29 8 0.24
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (28 bp):
TATATTTAATAAAGAATATATTTTTATT
Found at i:1451543 original size:21 final size:21
Alignment explanation
Indices: 1451521--1451596 Score: 72
Period size: 20 Copynumber: 3.8 Consensus size: 21
1451511 TAAAAATCTA
1451521 AAAATAT-TAAATATAATTAT
1 AAAATATATAAATATAATTAT
* *
1451541 AAAATATAAAAATATAAATAT
1 AAAATATATAAATATAATTAT
*
1451562 -AAAT-TATTAATAT-ATTA-
1 AAAATATATAAATATAATTAT
*
1451579 AAATTTATATAAATATAA
1 AAA-ATATATAAATATAA
1451597 AATATATAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
18 5 0.11
19 8 0.18
20 19 0.43
21 12 0.27
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAATATATAAATATAATTAT
Found at i:1451603 original size:27 final size:28
Alignment explanation
Indices: 1451493--1451605 Score: 105
Period size: 27 Copynumber: 4.2 Consensus size: 28
1451483 ATGACTAGAT
* *
1451493 TATAAAATA-AAAAATAAATA-AAAATC
1 TATAAAATATAAATATAAATATAAAATA
*
1451519 TA-AAAATATTAAATATAATTATAAAATA
1 TATAAAATA-TAAATATAAATATAAAATA
*
1451547 TA-AAAATATAAATATAAAT-TATTAATA
1 TATAAAATATAAATATAAATATA-AAATA
*
1451574 TATTAAAAT-T-TATATAAATATAAAATA
1 TA-TAAAATATAAATATAAATATAAAATA
1451601 TATAA
1 TATAA
1451606 TTTCGATGTG
Statistics
Matches: 73, Mismatches: 7, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
25 6 0.08
26 7 0.10
27 39 0.53
28 16 0.22
29 5 0.07
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.35
Consensus pattern (28 bp):
TATAAAATATAAATATAAATATAAAATA
Found at i:1454969 original size:21 final size:24
Alignment explanation
Indices: 1454916--1454971 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 24
1454906 TTATAAAAAC
1454916 ATAAAAATTTATTTTTAATATATT
1 ATAAAAATTTATTTTTAATATATT
* *
1454940 ATTATAATTT-TTTTTAAT-T-TT
1 ATAAAAATTTATTTTTAATATATT
1454961 ATAAAAATTTA
1 ATAAAAATTTA
1454972 AAAATTTATC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
21 10 0.37
22 1 0.04
23 8 0.30
24 8 0.30
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
ATAAAAATTTATTTTTAATATATT
Found at i:1455348 original size:15 final size:16
Alignment explanation
Indices: 1455328--1455357 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1455318 TTGAATATTT
1455328 TAAAAAATA-AATTAA
1 TAAAAAATATAATTAA
1455343 TAAAAAATATAATTA
1 TAAAAAATATAATTA
1455358 TTATATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
TAAAAAATATAATTAA
Found at i:1455913 original size:3 final size:3
Alignment explanation
Indices: 1455907--1455950 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
1455897 ATCATCAGAT
*
1455907 TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1455951 TGTATTGTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1456537 original size:22 final size:23
Alignment explanation
Indices: 1456494--1456540 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
1456484 ATATAAGTTT
*
1456494 ATTAAAATTATATCCAAAAAAATC
1 ATTAAAATTACAT-CAAAAAAATC
1456518 ATTAAAATTACAT-AAAAAAATC
1 ATTAAAATTACATCAAAAAAATC
1456540 A
1 A
1456541 AAATCTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.45
24 12 0.55
ACGTcount: A:0.62, C:0.11, G:0.00, T:0.28
Consensus pattern (23 bp):
ATTAAAATTACATCAAAAAAATC
Found at i:1465041 original size:11 final size:10
Alignment explanation
Indices: 1465015--1465052 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
1465005 TATGATTATG
1465015 ATATATAAAA
1 ATATATAAAA
*
1465025 ATATATTAAA
1 ATATATAAAA
*
1465035 ATA-ATATAA
1 ATATATAAAA
1465044 ATATATAAA
1 ATATATAAA
1465053 TTGATAATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
9 7 0.30
10 16 0.70
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (10 bp):
ATATATAAAA
Found at i:1465923 original size:2 final size:2
Alignment explanation
Indices: 1465918--1465942 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1465908 TGTGTGTGTG
1465918 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 T
1465943 TTGGGGTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1468453 original size:17 final size:19
Alignment explanation
Indices: 1468431--1468473 Score: 63
Period size: 17 Copynumber: 2.3 Consensus size: 19
1468421 ACTATTTAAA
1468431 AATTAAAT-AATTT-ATTT
1 AATTAAATAAATTTAATTT
1468448 AATTAAATAAATTTAATTT
1 AATTAAATAAATTTAATTT
1468467 AAGTTAA
1 AA-TTAA
1468474 GCTGTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.35
18 5 0.22
19 6 0.26
20 4 0.17
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (19 bp):
AATTAAATAAATTTAATTT
Found at i:1468540 original size:16 final size:15
Alignment explanation
Indices: 1468521--1468572 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 15
1468511 TTATTAATAA
1468521 TTTATTAAAATAATAT
1 TTTATTAAAAT-ATAT
* *
1468537 TTTATTTAAATTTA-
1 TTTATTAAAATATAT
*
1468551 TTTATAAAAATATAT
1 TTTATTAAAATATAT
1468566 TTT-TTAA
1 TTTATTAA
1468573 TATTTTAATA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
14 14 0.48
15 5 0.17
16 10 0.34
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTATTAAAATATAT
Found at i:1468541 original size:27 final size:29
Alignment explanation
Indices: 1468511--1468579 Score: 74
Period size: 27 Copynumber: 2.5 Consensus size: 29
1468501 TCAGTTTTAA
1468511 TTATTAATAATTTA-TTA-AAATAATAT-T
1 TTATTAATAATTTATTTATAAA-AATATAT
*
1468538 TTATTTA-AATTTATTTATAAAAATATAT
1 TTATTAATAATTTATTTATAAAAATATAT
* *
1468566 TTTTTAATATTTTA
1 TTATTAATAATTTA
1468580 ATATATTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
26 6 0.18
27 14 0.41
28 9 0.26
29 5 0.15
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (29 bp):
TTATTAATAATTTATTTATAAAAATATAT
Found at i:1476059 original size:22 final size:22
Alignment explanation
Indices: 1476010--1476059 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
1476000 TTATAAAATA
* *
1476010 TTAAATTTTTACTTTTAATGAT
1 TTAAATTTATACTTTTAATAAT
*
1476032 TGAAATTTATA-TTTTAATAAT
1 TTAAATTTATACTTTTAATAAT
1476053 TATAAAT
1 T-TAAAT
1476060 ATTAAAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (22 bp):
TTAAATTTATACTTTTAATAAT
Found at i:1480226 original size:2 final size:2
Alignment explanation
Indices: 1480219--1480248 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1480209 AATTACACAA
1480219 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1480249 GTATAAAACG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1486201 original size:16 final size:17
Alignment explanation
Indices: 1486166--1486205 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
1486156 GAAGGTAACC
1486166 GATAGCCAATATGTTCT
1 GATAGCCAATATGTTCT
1486183 GATAGCCAATATG-TCT
1 GATAGCCAATATGTTCT
1486199 GATAGCC
1 GATAGCC
1486206 CATTGTCCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (17 bp):
GATAGCCAATATGTTCT
Found at i:1487881 original size:18 final size:19
Alignment explanation
Indices: 1487858--1487898 Score: 75
Period size: 18 Copynumber: 2.2 Consensus size: 19
1487848 TAAACCATAG
1487858 TTTATGATTAATTT-TTTT
1 TTTATGATTAATTTATTTT
1487876 TTTATGATTAATTTATTTT
1 TTTATGATTAATTTATTTT
1487895 TTTA
1 TTTA
1487899 CTTTAGTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (19 bp):
TTTATGATTAATTTATTTT
Found at i:1488583 original size:23 final size:26
Alignment explanation
Indices: 1488533--1488587 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 26
1488523 TTAAAATTTT
1488533 TTAATAAAATATCATAATTTAAATTA
1 TTAATAAAATATCATAATTTAAATTA
*
1488559 TTAATAATATAT-A-AATTTATATATTA
1 TTAATAAAATATCATAATTTA-A-ATTA
1488585 TTA
1 TTA
1488588 TCCATACATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 6 0.23
25 2 0.08
26 18 0.69
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (26 bp):
TTAATAAAATATCATAATTTAAATTA
Found at i:1489322 original size:23 final size:23
Alignment explanation
Indices: 1489296--1489350 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
1489286 AATTTGAGGA
*
1489296 TAAATATAAATATTAAAATTTAT
1 TAAATATAAATATTAAAATTAAT
* * *
1489319 TAAATATTATTTTTAAAATTAAT
1 TAAATATAAATATTAAAATTAAT
1489342 T--ATATAAAT
1 TAAATATAAAT
1489351 TAATTAAGTA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 6 0.23
23 20 0.77
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TAAATATAAATATTAAAATTAAT
Found at i:1494008 original size:24 final size:24
Alignment explanation
Indices: 1493981--1494028 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1493971 AAAAATTAAA
*
1493981 AAAATTAAA-TTAAATATATATAAT
1 AAAATAAAATTTAAA-ATATATAAT
*
1494005 AAAATAAAATTTAAAATATTTAAT
1 AAAATAAAATTTAAAATATATAAT
1494029 TTTTTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
AAAATAAAATTTAAAATATATAAT
Found at i:1497012 original size:2 final size:2
Alignment explanation
Indices: 1497007--1497042 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1496997 ACACTGCGTG
1497007 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1497043 TAATTGTAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1498731 original size:2 final size:2
Alignment explanation
Indices: 1498724--1498783 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
1498714 ATCTTGTCCT
1498724 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1498766 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
1498784 CATTCTGAGT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1504681 original size:13 final size:14
Alignment explanation
Indices: 1504647--1504693 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
1504637 TTATTTTTTA
*
1504647 ATTAAAATATATTT
1 ATTAAAATATAATT
*
1504661 ATTAAAATTTAATT
1 ATTAAAATATAATT
*
1504675 A-TAAAATAATAAAT
1 ATTAAAAT-ATAATT
1504689 ATTAA
1 ATTAA
1504694 TAAAAAGTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 6 0.22
14 18 0.67
15 3 0.11
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
ATTAAAATATAATT
Found at i:1509247 original size:16 final size:17
Alignment explanation
Indices: 1509216--1509267 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
1509206 ACGTTTAAAA
1509216 TTTTAAATTTTAATATT
1 TTTTAAATTTTAATATT
* *
1509233 TTTTAACTTTT-ATATAA
1 TTTTAAATTTTAATAT-T
1509250 TTTTAAATATTTAA-ATT
1 TTTTAAAT-TTTAATATT
1509267 T
1 T
1509268 GATAGAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
16 4 0.14
17 18 0.64
18 5 0.18
19 1 0.04
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTAAATTTTAATATT
Found at i:1514202 original size:2 final size:2
Alignment explanation
Indices: 1514195--1514242 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1514185 GAAGAGCAGG
1514195 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1514237 TC TC TC
1 TC TC TC
1514243 GCATAATGTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1515686 original size:14 final size:14
Alignment explanation
Indices: 1515655--1515694 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
1515645 TATATATTTA
1515655 AAATATTT-TATTTT
1 AAATATTTAT-TTTT
1515669 -AATATTTATTTTT
1 AAATATTTATTTTT
1515682 AAATATTTATTTT
1 AAATATTTATTTT
1515695 ACTTTAGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
AAATATTTATTTTT
Found at i:1516578 original size:20 final size:21
Alignment explanation
Indices: 1516546--1516595 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
1516536 GTTGAATAAA
1516546 AATTATAAT-AATTTAAATT-T
1 AATT-TAATAAATTTAAATTAT
1516566 AATTTAATAAATTTAAATTAT
1 AATTTAATAAATTTAAATTAT
*
1516587 TATTTAATA
1 AATTTAATA
1516596 TTTATATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 4 0.15
20 14 0.52
21 9 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AATTTAATAAATTTAAATTAT
Found at i:1516617 original size:18 final size:19
Alignment explanation
Indices: 1516573--1516622 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
1516563 TTTAATTTAA
1516573 TAAA-TTTAAATTATTATT
1 TAAATTTTAAATTATTATT
*
1516591 T-AATATTTATATT-TTATT
1 TAAAT-TTTAAATTATTATT
1516609 TAAATTTT-AATTAT
1 TAAATTTTAAATTAT
1516623 AAAATATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
17 5 0.19
18 11 0.42
19 10 0.38
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TAAATTTTAAATTATTATT
Found at i:1517512 original size:19 final size:19
Alignment explanation
Indices: 1517464--1517527 Score: 53
Period size: 18 Copynumber: 3.5 Consensus size: 19
1517454 TTATTTTTTA
*
1517464 ATTTAT-TTAAATATAAAAT
1 ATTTATATTAAATA-AATAT
*
1517483 -TTTATA-AAAATAAATAT
1 ATTTATATTAAATAAATAT
**
1517500 ATTTATATTAAATTTATAT
1 ATTTATATTAAATAAATAT
*
1517519 AATTATATT
1 ATTTATATT
1517528 TTATATTTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
17 4 0.11
18 16 0.44
19 16 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTTATATTAAATAAATAT
Found at i:1517564 original size:32 final size:32
Alignment explanation
Indices: 1517474--1517569 Score: 83
Period size: 33 Copynumber: 3.0 Consensus size: 32
1517464 ATTTATTTAA
* **
1517474 ATATAAAATTT-TATAAAAATAAA-TATATTT
1 ATATTAAATTTATATAATTATAAATTATATTT
**
1517504 ATATTAAATTTATATAATTATATTTTATATTT
1 ATATTAAATTTATATAATTATAAATTATATTT
*
1517536 ATTTTTAAATTTA-AGTAA-TATAAATTATAATTT
1 A-TATTAAATTTATA-TAATTATAAATTAT-ATTT
1517569 A
1 A
1517570 AAAAATATAA
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
30 10 0.19
31 8 0.15
32 17 0.32
33 18 0.34
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (32 bp):
ATATTAAATTTATATAATTATAAATTATATTT
Found at i:1519243 original size:19 final size:18
Alignment explanation
Indices: 1519221--1519264 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
1519211 AATTAAGTTT
*
1519221 AATTTAAATTATTATTTAA
1 AATTTAAATTATTACTT-A
* *
1519240 AATTTAATTTTTTACTTA
1 AATTTAAATTATTACTTA
1519258 AATTTAA
1 AATTTAA
1519265 TTTTAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
AATTTAAATTATTACTTA
Found at i:1519336 original size:19 final size:20
Alignment explanation
Indices: 1519287--1519341 Score: 51
Period size: 19 Copynumber: 2.8 Consensus size: 20
1519277 ATAAATTATT
** *
1519287 AATATATTTTTTTCATAATAT
1 AATATA-TTTTTAAATAATAA
1519308 AATATA-TTTTAAATAATAA
1 AATATATTTTTAAATAATAA
1519327 AATA-AGTTTTTAAAT
1 AATATA-TTTTTAAAT
1519342 TAAACTTAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 1 0.03
19 14 0.48
20 8 0.28
21 6 0.21
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (20 bp):
AATATATTTTTAAATAATAA
Found at i:1519458 original size:2 final size:2
Alignment explanation
Indices: 1519451--1519506 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
1519441 TCAACATGAA
1519451 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1519493 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
1519507 GAGAAAACAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1520601 original size:17 final size:20
Alignment explanation
Indices: 1520581--1520621 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
1520571 ATTTTCATCA
1520581 ATTTT-TATTTTT-TA-ATT
1 ATTTTATATTTTTATATATT
1520598 ATTTTATATTTTTATATATT
1 ATTTTATATTTTTATATATT
1520618 ATTT
1 ATTT
1520622 AATTATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.24
18 7 0.33
19 2 0.10
20 7 0.33
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (20 bp):
ATTTTATATTTTTATATATT
Found at i:1521970 original size:26 final size:29
Alignment explanation
Indices: 1521941--1522013 Score: 80
Period size: 32 Copynumber: 2.4 Consensus size: 29
1521931 TTTTTACGTA
1521941 TATTAAATAATTTTAT-A-TA-TTTAAAT
1 TATTAAATAATTTTATAAGTATTTTAAAT
1521967 TATTAAATAATAATTTATACAGTATTTTAAAT
1 TATTAAATAAT--TTTATA-AGTATTTTAAAT
1521999 TATTGAAGATAATTT
1 TATT-AA-ATAATTT
1522014 AAAATTTTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
26 11 0.28
28 5 0.13
30 1 0.03
31 2 0.05
32 13 0.33
33 2 0.05
34 5 0.13
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.49
Consensus pattern (29 bp):
TATTAAATAATTTTATAAGTATTTTAAAT
Found at i:1530579 original size:12 final size:12
Alignment explanation
Indices: 1530564--1530620 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
1530554 TTTAAATTTA
1530564 ATTTTTATTAAT
1 ATTTTTATTAAT
*
1530576 ATTTTTATCTAAA
1 ATTTTTAT-TAAT
*
1530589 ATTTTT-TTAAG
1 ATTTTTATTAAT
* *
1530600 ATTATTATTATT
1 ATTTTTATTAAT
*
1530612 ATTATTATT
1 ATTTTTATT
1530621 TATGTGTAGT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
11 8 0.21
12 21 0.55
13 9 0.24
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (12 bp):
ATTTTTATTAAT
Found at i:1532424 original size:2 final size:2
Alignment explanation
Indices: 1532417--1532447 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1532407 TTTTCTTTAC
1532417 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1532448 CATCAAAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1533067 original size:53 final size:53
Alignment explanation
Indices: 1532990--1533097 Score: 198
Period size: 53 Copynumber: 2.0 Consensus size: 53
1532980 GCTCTTTTTA
1532990 TTTTCTTCCACTGCTTTGTTGCACCAGCTCTAGATCCTAGGTTCTTCTTCTTC
1 TTTTCTTCCACTGCTTTGTTGCACCAGCTCTAGATCCTAGGTTCTTCTTCTTC
**
1533043 TTTTCTTCTGCTGCTTTGTTGCACCAGCTCTAGATCCTAGGTTCTTCTTCTTC
1 TTTTCTTCCACTGCTTTGTTGCACCAGCTCTAGATCCTAGGTTCTTCTTCTTC
1533096 TT
1 TT
1533098 AGTTCTTTCA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.10, C:0.29, G:0.14, T:0.47
Consensus pattern (53 bp):
TTTTCTTCCACTGCTTTGTTGCACCAGCTCTAGATCCTAGGTTCTTCTTCTTC
Found at i:1536667 original size:20 final size:20
Alignment explanation
Indices: 1536603--1536687 Score: 72
Period size: 20 Copynumber: 4.3 Consensus size: 20
1536593 TAATATTAAA
*
1536603 ATTTAAAATTTATTAAATATT
1 ATTT-AAATTTATTAAATAAT
*
1536624 ATTT---TTTA-AAAATAAT
1 ATTTAAATTTATTAAATAAT
*
1536640 CATATAAATTTATTAAATTAA-
1 -ATTTAAATTTATTAAA-TAAT
*
1536661 ATTTAAATTTGTTAAATAAT
1 ATTTAAATTTATTAAATAAT
1536681 ATTTAAA
1 ATTTAAA
1536688 ATTAAAAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
16 6 0.12
17 7 0.14
19 3 0.06
20 25 0.49
21 7 0.14
22 3 0.06
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (20 bp):
ATTTAAATTTATTAAATAAT
Found at i:1537268 original size:70 final size:70
Alignment explanation
Indices: 1537182--1537315 Score: 180
Period size: 70 Copynumber: 1.9 Consensus size: 70
1537172 ATTAAATGAC
* *
1537182 GATATATAATTAAAAATTACTTTATATATTAAAAAAAGGATAAAATTGA-TTTTTTAATAAAAAT
1 GATATAAAATTAAAAATTACTTTAAATATT-AAAAAAGGATAAAATTGATTTTTTTAATAAAAAT
1537246 TTAATT
65 TTAATT
* ** * * *
1537252 GATATAAAATTTAAAATTACTTTAAATATTTTAAGAGGATAAATTTGATTTTTTTTATAAAAAT
1 GATATAAAATTAAAAATTACTTTAAATATTAAAAAAGGATAAAATTGATTTTTTTAATAAAAAT
1537316 AATTATTATT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
69 14 0.25
70 41 0.75
ACGTcount: A:0.49, C:0.01, G:0.07, T:0.43
Consensus pattern (70 bp):
GATATAAAATTAAAAATTACTTTAAATATTAAAAAAGGATAAAATTGATTTTTTTAATAAAAATT
TAATT
Found at i:1537333 original size:68 final size:69
Alignment explanation
Indices: 1537182--1537333 Score: 175
Period size: 70 Copynumber: 2.2 Consensus size: 69
1537172 ATTAAATGAC
* * *
1537182 GATATATAATTAAAAATTACTTTATATATTAAAAAAAGGATAAAATTGATTTTTTAATAAAAATT
1 GATATAAAATTTAAAATTACTTTAAATATTAAAAAAAGGATAAAATTGATTTTTTAATAAAAA-T
1537247 TAATT
65 TAATT
** * * *
1537252 GATATAAAATTTAAAATTACTTTAAATATT-TTAAGAGGATAAATTTGATTTTTTTTATAAAAA-
1 GATATAAAATTTAAAATTACTTTAAATATTAAAAAAAGGATAAAATTGA-TTTTTTAATAAAAAT
1537315 TAATT
65 TAATT
*
1537320 -ATTATTAAATTTAA
1 GA-TATAAAATTTAA
1537334 TTATTGTTTA
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
67 1 0.01
68 16 0.23
69 14 0.20
70 40 0.56
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.44
Consensus pattern (69 bp):
GATATAAAATTTAAAATTACTTTAAATATTAAAAAAAGGATAAAATTGATTTTTTAATAAAAATT
AATT
Found at i:1537685 original size:18 final size:18
Alignment explanation
Indices: 1537662--1537701 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1537652 AATATGTAAT
*
1537662 TATAATTATATTTAAAT-A
1 TATAATT-TATTAAAATAA
1537680 TATAATTTATTAAAATAA
1 TATAATTTATTAAAATAA
1537698 TATA
1 TATA
1537702 TAAAATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TATAATTTATTAAAATAA
Found at i:1537712 original size:20 final size:20
Alignment explanation
Indices: 1537676--1537715 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1537666 ATTATATTTA
*
1537676 AATATATAATTTATTAAAAT
1 AATATATAAATTATTAAAAT
1537696 AATATATAAAATT-TTAAAAT
1 AATATAT-AAATTATTAAAAT
1537716 TTTAATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AATATATAAATTATTAAAAT
Found at i:1537737 original size:11 final size:11
Alignment explanation
Indices: 1537721--1537774 Score: 56
Period size: 11 Copynumber: 4.8 Consensus size: 11
1537711 AAAATTTTAA
1537721 TATATTTATAT
1 TATATTTATAT
*
1537732 TATATTAATAT
1 TATATTTATAT
*
1537743 TATTTTTCATA-
1 TATATTT-ATAT
*
1537754 TAAATATTATAT
1 TATAT-TTATAT
1537766 TATATTTAT
1 TATATTTAT
1537775 TTTTTTATCA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
11 25 0.74
12 9 0.26
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1538007 original size:19 final size:21
Alignment explanation
Indices: 1537966--1538013 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 21
1537956 GTATATTTAA
*
1537966 TTATTTATTAAATTAATTATT
1 TTATTTATTAAATTAATGATT
*
1537987 TTATTT-TT-AATTAATGGTT
1 TTATTTATTAAATTAATGATT
1538006 TTAATTTA
1 TT-ATTTA
1538014 AAACATTGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 11 0.48
20 6 0.26
21 6 0.26
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (21 bp):
TTATTTATTAAATTAATGATT
Found at i:1538348 original size:16 final size:17
Alignment explanation
Indices: 1538327--1538358 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1538317 TTGATTACTT
1538327 ATAAGTAAC-TTAAATC
1 ATAAGTAACTTTAAATC
1538343 ATAAGTAACTTTAAAT
1 ATAAGTAACTTTAAAT
1538359 TTTAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.34
Consensus pattern (17 bp):
ATAAGTAACTTTAAATC
Found at i:1544608 original size:2 final size:2
Alignment explanation
Indices: 1544601--1544634 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1544591 TTATCCTCAT
1544601 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1544635 ATATTATGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1546150 original size:16 final size:17
Alignment explanation
Indices: 1546129--1546166 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
1546119 AAAAAATTTT
1546129 AAATATTA-AATTTAAA
1 AAATATTATAATTTAAA
*
1546145 AAATATTATATTTTAAA
1 AAATATTATAATTTAAA
1546162 AAATA
1 AAATA
1546167 ATTACTTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATATTATAATTTAAA
Done.