Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009070.1 Hibiscus syriacus cultivar Beakdansim tig00112498_pilon, whole genome shotgun sequence
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: 2268343
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 9
Found at i:1122225 original size:106 final size:106
Alignment explanation
Indices: 1122041--1123122 Score: 1600
Period size: 106 Copynumber: 10.3 Consensus size: 106
1122031 CACGAATTGG
* *
1122041 ATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAAA-TCGGAAATTGTTTGTTGACAACCAGCGG
1 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGG
*
1122105 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTTCA
66 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* *
1122146 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATCGGGAAATTGTTTATTGACAACCAGCGG
1 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGG
* * * *
1122211 TCCCTTCGTTGTGAAGTTGAACTTGTGTTATCCGGAGTCCA
66 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
*
1122252 ATATCCTTCG-T-T---G-TG-AA---G-T-TGAAATTGGGAAATTGTTTATTGACAACCAGCGG
1 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGG
*
1122305 TCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCA
66 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* *
1122346 ATATCCTTCGTTGTGAAGTTGAAATTAGCTCCGAAATTGGGAAATTGTTTGTTGACAACCAGCGG
1 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGG
1122411 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
66 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* * * *
1122452 ATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCAG
1 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGG
* *
1122517 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAATCCA
66 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* * * * * *
1122558 ATATCATTTGCTGTGAAGTTGAAATTGGCTATGAAATTGGGAAGTTGTTTGTTGATAACCAGCGG
1 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGG
*
1122623 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCA
66 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* * *
1122664 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAACGG
1 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGG
1122729 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
66 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* *
1122770 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGG
1 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGG
*
1122835 TCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCA
66 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* * * *
1122876 ATATCCTTCGCTGTGAAGCTGAAATTGACTCTGAAATT-GGAAAGTTGTTTATTGACAACCAGCG
1 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAA-TTGTTTGTTGACAACCAGCG
*
1122940 GTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCA
65 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* * * * * * *
1122982 CTATCATTCGCTGTGAAGTTGAAATTGGCTCT-AGTATTGGAAAATTGTTTATTAACAACCAGCG
1 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA-AATTGGGAAATTGTTTGTTGACAACCAGCG
1123046 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
65 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* * * * *
1123088 ATTTTCTTCGTTGCGAAGTTGAAATAGACTCTGAA
1 ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAA
1123123 TGAAATTGGA
Statistics
Matches: 891, Mismatches: 69, Indels: 33
0.90 0.07 0.03
Matches are distributed among these distances:
94 81 0.09
95 2 0.00
96 2 0.00
99 3 0.00
100 4 0.00
101 3 0.00
104 2 0.00
105 41 0.05
106 748 0.84
107 5 0.01
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGG
TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
Found at i:1127016 original size:6 final size:6
Alignment explanation
Indices: 1127000--1127031 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
1126990 TTTAATTGCG
1127000 AAAATT AAAAATT AAAATT AAAATT AAAATT A
1 AAAATT -AAAATT AAAATT AAAATT AAAATT A
1127032 TTCGATTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AAAATT
Found at i:1128091 original size:3 final size:3
Alignment explanation
Indices: 1128083--1128142 Score: 65
Period size: 3 Copynumber: 20.7 Consensus size: 3
1128073 CCTGCAAAAT
*
1128083 TAA TAA TAA TAA AAA TTAA TAA TAA TAA TAA T-A TAAA TAA T-A TAA
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
1128128 T-A TAA TAA T-A TAA TA
1 TAA TAA TAA TAA TAA TA
1128143 TTTTTTGTAG
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
2 8 0.16
3 37 0.76
4 4 0.08
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1128099 original size:16 final size:16
Alignment explanation
Indices: 1128078--1128124 Score: 67
Period size: 16 Copynumber: 2.8 Consensus size: 16
1128068 AAAATCCTGC
1128078 AAAATTAATAATAATA
1 AAAATTAATAATAATA
1128094 AAAATTAATAATAATA
1 AAAATTAATAATAATA
*
1128110 ATAATATAAATAATA
1 A-AA-ATTAATAATA
1128125 TAATATAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
16 17 0.61
17 2 0.07
18 9 0.32
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAAATTAATAATAATA
Found at i:1128104 original size:13 final size:14
Alignment explanation
Indices: 1128085--1128137 Score: 54
Period size: 16 Copynumber: 3.6 Consensus size: 14
1128075 TGCAAAATTA
1128085 ATAATAATAAAAATT
1 ATAATAATAAAAA-T
*
1128100 AATAATAATAATAAT
1 -ATAATAATAAAAAT
*
1128115 ATAAATAAT-ATAAT
1 AT-AATAATAAAAAT
1128129 ATAATAATA
1 ATAATAATA
1128138 TAATATTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
13 6 0.18
14 9 0.26
15 7 0.21
16 12 0.35
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAATAATAAAAAT
Found at i:1128111 original size:25 final size:26
Alignment explanation
Indices: 1128084--1128142 Score: 81
Period size: 25 Copynumber: 2.4 Consensus size: 26
1128074 CTGCAAAATT
1128084 AATAATAATAAA-AAT-TAATAATAAT
1 AATAATAATAAATAATATAAT-ATAAT
1128109 AATAAT-ATAAATAATATAATATAAT
1 AATAATAATAAATAATATAATATAAT
1128134 AAT-ATAATA
1 AATAATAATA
1128143 TTTTTTGTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
24 7 0.23
25 20 0.65
26 4 0.13
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (26 bp):
AATAATAATAAATAATATAATATAAT
Found at i:1128127 original size:5 final size:5
Alignment explanation
Indices: 1128099--1128143 Score: 51
Period size: 5 Copynumber: 9.2 Consensus size: 5
1128089 TAATAAAAAT
1128099 TAATAA TAATAA TAATA TAA-A TAATA TAATA T-A-A TAATA TAATA T
1 TAAT-A TAAT-A TAATA TAATA TAATA TAATA TAATA TAATA TAATA T
1128144 TTTTTGTAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
3 2 0.06
4 6 0.17
5 18 0.50
6 10 0.28
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
TAATA
Found at i:1128138 original size:22 final size:22
Alignment explanation
Indices: 1128083--1128140 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 22
1128073 CCTGCAAAAT
* *
1128083 TAATAATAATAAAAATTAATAA
1 TAATAATAATATAAATAAATAA
1128105 TAATAATAATATAAATAATATAA
1 TAATAATAATATAAATAA-ATAA
1128128 T-ATAATAATATAA
1 TAATAATAATATAA
1128141 TATTTTTTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
22 28 0.85
23 5 0.15
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
TAATAATAATATAAATAAATAA
Found at i:1128929 original size:12 final size:13
Alignment explanation
Indices: 1128912--1128979 Score: 57
Period size: 14 Copynumber: 5.2 Consensus size: 13
1128902 AACCTTAAAT
1128912 TTAGAGTTTAA-G
1 TTAGAGTTTAAGG
*
1128924 TTAGAGATTAAGG
1 TTAGAGTTTAAGG
* *
1128937 TTAGGGTTTAGGGG
1 TTAGAGTTTA-AGG
* *
1128951 TTATAGTTTAGGG
1 TTAGAGTTTAAGG
*
1128964 TTAGCAATTTAAGG
1 TTAG-AGTTTAAGG
1128978 TT
1 TT
1128980 TTAAGTTATG
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
12 10 0.23
13 15 0.34
14 19 0.43
ACGTcount: A:0.28, C:0.01, G:0.31, T:0.40
Consensus pattern (13 bp):
TTAGAGTTTAAGG
Found at i:1130028 original size:29 final size:29
Alignment explanation
Indices: 1129994--1130064 Score: 124
Period size: 29 Copynumber: 2.4 Consensus size: 29
1129984 TGTTACTCTT
1129994 AAACTTCTTAAAAAATCAATATTACCCTC
1 AAACTTCTTAAAAAATCAATATTACCCTC
* *
1130023 AAACTTCTTAAAAAATCTATGTTACCCTC
1 AAACTTCTTAAAAAATCAATATTACCCTC
1130052 AAACTTCTTAAAA
1 AAACTTCTTAAAA
1130065 GACCAAATGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.44, C:0.23, G:0.01, T:0.32
Consensus pattern (29 bp):
AAACTTCTTAAAAAATCAATATTACCCTC
Found at i:1135360 original size:220 final size:216
Alignment explanation
Indices: 1135057--1135488 Score: 559
Period size: 220 Copynumber: 2.0 Consensus size: 216
1135047 TTGTGTATTT
* * * * * **
1135057 TTAAACATTAATTTATACAAGATTAAAATAAAAATTAAATTTAAGTTTTGCAGGTGATTAAAATC
1 TTAAACATTAATTTATACAAAATTAAAAGAAAAACTAAATTTAAGATTTACACATGATTAAAATC
* ** *
1135122 GATTCTTAATTACACATTTTAATTATGCAATTTAATAAAAA-TAATTAAAATATAAATGATTCAC
66 GATTCTTAATTACACATTTTAACTATGCAATCCAATAAAAATTAATTAAAATATAAAT-AATCA-
*
1135186 A-TATTTTATTTTTCAATAAAAAATAAAATTATTAATTAAATTAAAATGATTAT-AAATTTTAGA
129 ATTATTTTATTTTT-AAT-AAAAATAAAATTATTAATTAAATTAAAA--AGTATCAAATTTTAGA
1135249 CTATATATATAATCATTAAATTATAAATG
190 CTATATATATAA-C-TTAAATTATAAATG
* * *
1135278 TTAAACATTAGTTTATACAAAATT-AAAGAAAAACTATATTTAAGATTTACACATGATTAAATTC
1 TTAAACATTAATTTATACAAAATTAAAAGAAAAACTAAATTTAAGATTTACACATGATTAAAATC
* *
1135342 GACTTC-TAATTACACATTTTAACTATGTAATCCAATAAAAATTTAATTGAAATATAAATAATCA
66 GA-TTCTTAATTACACATTTTAACTATGCAATCCAATAAAAA-TTAATTAAAATATAAATAATCA
* *
1135406 ATTTATTTTATTTTTAATAAAAGTAAAATTATTAATTAAATTAAAAAGTATCAATTTTTAGACTA
129 A-TTATTTTATTTTTAATAAAAATAAAATTATTAATTAAATTAAAAAGTATCAAATTTTAGACTA
1135471 TATATATAACTTAAATTA
193 TATATATAACTTAAATTA
1135489 ATTTTTCTTT
Statistics
Matches: 186, Mismatches: 19, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
217 8 0.04
218 5 0.03
219 21 0.11
220 93 0.50
221 32 0.17
222 27 0.15
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.40
Consensus pattern (216 bp):
TTAAACATTAATTTATACAAAATTAAAAGAAAAACTAAATTTAAGATTTACACATGATTAAAATC
GATTCTTAATTACACATTTTAACTATGCAATCCAATAAAAATTAATTAAAATATAAATAATCAAT
TATTTTATTTTTAATAAAAATAAAATTATTAATTAAATTAAAAAGTATCAAATTTTAGACTATAT
ATATAACTTAAATTATAAATG
Found at i:1136366 original size:15 final size:15
Alignment explanation
Indices: 1136342--1136377 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1136332 GTACTATTAA
*
1136342 ATTAATTTATAAAAT
1 ATTAAATTATAAAAT
*
1136357 ATTAAATTATAAAGT
1 ATTAAATTATAAAAT
1136372 ATTAAA
1 ATTAAA
1136378 CGTATAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (15 bp):
ATTAAATTATAAAAT
Found at i:1137020 original size:2 final size:2
Alignment explanation
Indices: 1137008--1137039 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
1136998 TAATACGATA
1137008 AT AT GAT 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
1137040 CACACACATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1138219 original size:15 final size:15
Alignment explanation
Indices: 1138191--1138237 Score: 67
Period size: 15 Copynumber: 3.0 Consensus size: 15
1138181 TTTTCAACTA
1138191 ATTTATATACATTTAAT
1 ATTT-TATA-ATTTAAT
1138208 ATTTTATAATTTAAT
1 ATTTTATAATTTAAT
*
1138223 ATTTTATAAATTAAT
1 ATTTTATAATTTAAT
1138238 TTAATGATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 21 0.72
16 4 0.14
17 4 0.14
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTTTATAATTTAAT
Found at i:1138259 original size:16 final size:16
Alignment explanation
Indices: 1138238--1138268 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1138228 ATAAATTAAT
*
1138238 TTAATGATATTCATCA
1 TTAATGATACTCATCA
1138254 TTAATGATACTCATC
1 TTAATGATACTCATC
1138269 CGTATTCGTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.42
Consensus pattern (16 bp):
TTAATGATACTCATCA
Found at i:1140940 original size:114 final size:114
Alignment explanation
Indices: 1140800--1141019 Score: 334
Period size: 114 Copynumber: 1.9 Consensus size: 114
1140790 TTCTCGGTAT
1140800 CAATGGTACTGCTTGCTGTTCCGGACAA-AGATTTCGTCTCAGCTTTGTAATCATCCATCTGTTC
1 CAATGGTACTGCTTGCTGTTCCGGACAAGA-ATTTCGTCTCAGCTTTGTAATCATCCATCTGTTC
* * * * *
1140864 TGTATCCTTTCCCGAGTCAGCATCGATCTTATTGCCTGATTCAGAATCAA
65 CGTACCCTTTCCCGAATCAGCATCAATCTTATTGACTGATTCAGAATCAA
* * * *
1140914 CAATGGTACTGCTTGCTGTTTCGGACAAGAATTTCTTCTCGGCTTTGTATTCATCCATCTGTTCC
1 CAATGGTACTGCTTGCTGTTCCGGACAAGAATTTCGTCTCAGCTTTGTAATCATCCATCTGTTCC
*
1140979 GTACCCTTTTCCGAATCAGCATCAATCTTATTGACTGATTC
66 GTACCCTTTCCCGAATCAGCATCAATCTTATTGACTGATTC
1141020 CAAATCGACG
Statistics
Matches: 95, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
114 94 0.99
115 1 0.01
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.37
Consensus pattern (114 bp):
CAATGGTACTGCTTGCTGTTCCGGACAAGAATTTCGTCTCAGCTTTGTAATCATCCATCTGTTCC
GTACCCTTTCCCGAATCAGCATCAATCTTATTGACTGATTCAGAATCAA
Found at i:1145531 original size:12 final size:12
Alignment explanation
Indices: 1145515--1145545 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1145505 GTTATTTAAA
1145515 CGGGTATCGGGC
1 CGGGTATCGGGC
*
1145527 TGGGTATCGGGC
1 CGGGTATCGGGC
1145539 CGGGTAT
1 CGGGTAT
1145546 ATATATTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.10, C:0.19, G:0.48, T:0.23
Consensus pattern (12 bp):
CGGGTATCGGGC
Found at i:1145580 original size:2 final size:2
Alignment explanation
Indices: 1145569--1145637 Score: 69
Period size: 2 Copynumber: 37.5 Consensus size: 2
1145559 AAATATCTAA
* *
1145569 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT -T AA AT -T AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1145608 AT TT AT -T A- AT AT -T 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 A
1145638 ATAATTATTT
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
1 6 0.11
2 49 0.89
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1145744 original size:35 final size:36
Alignment explanation
Indices: 1145704--1145772 Score: 104
Period size: 35 Copynumber: 1.9 Consensus size: 36
1145694 CGTCCCATTC
*
1145704 CCGTTTAACATAAAC-AGTTTTCCCCGTCTCCGTCT
1 CCGTTTAACATAAACGAGTTTTCCCCGTCCCCGTCT
* *
1145739 CCGTTTAACATAAACGATTTTTTCCCGTCCCCGT
1 CCGTTTAACATAAACGAGTTTTCCCCGTCCCCGT
1145773 TTAATTCGGT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 15 0.50
36 15 0.50
ACGTcount: A:0.20, C:0.33, G:0.12, T:0.35
Consensus pattern (36 bp):
CCGTTTAACATAAACGAGTTTTCCCCGTCCCCGTCT
Found at i:1148377 original size:15 final size:16
Alignment explanation
Indices: 1148340--1148381 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
1148330 TAAAAATAAA
1148340 AAATAGATTCATATTTT
1 AAATA-ATTCATATTTT
* *
1148357 AGATAATTTATA-TTT
1 AAATAATTCATATTTT
1148372 AAATAATTCA
1 AAATAATTCA
1148382 AAAAATTTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 11 0.52
16 6 0.29
17 4 0.19
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (16 bp):
AAATAATTCATATTTT
Found at i:1148669 original size:17 final size:17
Alignment explanation
Indices: 1148647--1148682 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1148637 GATTACGTAC
* *
1148647 AATATTTAAAAAAGTTA
1 AATATTAAAAAAAATTA
1148664 AATATTAAAAAAAATTA
1 AATATTAAAAAAAATTA
1148681 AA
1 AA
1148683 ATGTCCAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (17 bp):
AATATTAAAAAAAATTA
Found at i:1153843 original size:16 final size:16
Alignment explanation
Indices: 1153822--1153855 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1153812 GTTAAAATAC
1153822 AAAATATTAATAAT-TA
1 AAAATATT-ATAATATA
1153838 AAAATATTATAATATA
1 AAAATATTATAATATA
1153854 AA
1 AA
1153856 TTGAAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAATATTATAATATA
Found at i:1167559 original size:20 final size:21
Alignment explanation
Indices: 1167534--1167579 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
1167524 TTGTTCTGGA
1167534 TTTTAAAA-A-ATCATTTTAAT
1 TTTTAAAATATATC-TTTTAAT
1167554 TTTTAAAATATTATCTTTTAAT
1 TTTTAAAATA-TATCTTTTAAT
1167576 TTTT
1 TTTT
1167580 TCAGACTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 8 0.35
21 1 0.04
22 11 0.48
23 3 0.13
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTTAAAATATATCTTTTAAT
Found at i:1169161 original size:21 final size:22
Alignment explanation
Indices: 1169131--1169179 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
1169121 AACAATCAAA
1169131 ATATAATTTTATA-TTAATATTT
1 ATATAATTTTATAGTTAA-ATTT
1169153 ATAT-ATTTTATAGTTAAATTT
1 ATATAATTTTATAGTTAAATTT
*
1169174 AAATAA
1 ATATAA
1169180 AATATATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
ATATAATTTTATAGTTAAATTT
Found at i:1171186 original size:19 final size:19
Alignment explanation
Indices: 1171162--1171217 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
1171152 GAACGCTGGA
1171162 AACCGGTTTTGACCGGTTT
1 AACCGGTTTTGACCGGTTT
1171181 AACCGGTTTTGAACCGGTTTT
1 AACCGGTTTTG-ACCGG-TTT
*
1171202 GACCGG-TTTGACCGGT
1 AACCGGTTTTGACCGGT
1171218 CACGATCCGT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
18 1 0.03
19 16 0.47
20 9 0.26
21 8 0.24
ACGTcount: A:0.16, C:0.21, G:0.29, T:0.34
Consensus pattern (19 bp):
AACCGGTTTTGACCGGTTT
Found at i:1171197 original size:11 final size:11
Alignment explanation
Indices: 1171162--1171210 Score: 70
Period size: 10 Copynumber: 4.8 Consensus size: 11
1171152 GAACGCTGGA
1171162 AACCGGTTTTG
1 AACCGGTTTTG
1171173 -ACCGG-TTT-
1 AACCGGTTTTG
1171181 AACCGGTTTTG
1 AACCGGTTTTG
1171192 AACCGGTTTTG
1 AACCGGTTTTG
1171203 -ACCGGTTT
1 AACCGGTTT
1171211 GACCGGTCAC
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
9 8 0.23
10 16 0.46
11 11 0.31
ACGTcount: A:0.16, C:0.20, G:0.27, T:0.37
Consensus pattern (11 bp):
AACCGGTTTTG
Found at i:1171213 original size:9 final size:10
Alignment explanation
Indices: 1171163--1171217 Score: 78
Period size: 9 Copynumber: 5.6 Consensus size: 10
1171153 AACGCTGGAA
1171163 ACCGGTTTTG
1 ACCGGTTTTG
*
1171173 ACCGG-TTTA
1 ACCGGTTTTG
1171182 ACCGGTTTTG
1 ACCGGTTTTG
1171192 AACCGGTTTTG
1 -ACCGGTTTTG
1171203 ACCGG-TTTG
1 ACCGGTTTTG
1171212 ACCGGT
1 ACCGGT
1171218 CACGATCCGT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
9 17 0.43
10 13 0.32
11 10 0.25
ACGTcount: A:0.15, C:0.22, G:0.29, T:0.35
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:1171271 original size:13 final size:13
Alignment explanation
Indices: 1171230--1171260 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1171220 CGATCCGTTT
*
1171230 ACCCGTTTACCCG
1 ACCCGTTGACCCG
1171243 ACCCGTTGACCCG
1 ACCCGTTGACCCG
1171256 ACCCG
1 ACCCG
1171261 ACCCGTTGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.48, G:0.19, T:0.16
Consensus pattern (13 bp):
ACCCGTTGACCCG
Found at i:1171333 original size:29 final size:29
Alignment explanation
Indices: 1171272--1171347 Score: 107
Period size: 29 Copynumber: 2.6 Consensus size: 29
1171262 CCCGTTGACC
** *
1171272 GGTGCTATTCTGGGAATTAATTCGATTTT
1 GGTGCTATTCTGGGAATTAATTCGAAATG
1171301 GGTGCTATTCTGGGAATTAATTCGAAATG
1 GGTGCTATTCTGGGAATTAATTCGAAATG
* *
1171330 GGTGCTATTTTGGTAATT
1 GGTGCTATTCTGGGAATT
1171348 TTTTTAAAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.22, C:0.09, G:0.26, T:0.42
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATTCGAAATG
Found at i:1178462 original size:9 final size:10
Alignment explanation
Indices: 1178431--1178466 Score: 56
Period size: 11 Copynumber: 3.6 Consensus size: 10
1178421 AACGCTGGAA
1178431 ACCGGTTTTG
1 ACCGGTTTTG
1178441 AACCGGTTTTG
1 -ACCGGTTTTG
1178452 ACCGG-TTTG
1 ACCGGTTTTG
1178461 ACCGGT
1 ACCGGT
1178467 CACGACCCGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 9 0.38
10 5 0.21
11 10 0.42
ACGTcount: A:0.14, C:0.22, G:0.31, T:0.33
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:1178497 original size:13 final size:13
Alignment explanation
Indices: 1178479--1178515 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
1178469 CGACCCGTTT
*
1178479 ACCCGTTTACCCG
1 ACCCGTTGACCCG
1178492 ACCCGTTGACCCG
1 ACCCGTTGACCCG
1178505 ACCCGTTGACC
1 ACCCGTTGACC
1178516 GTTGACCGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.16, C:0.46, G:0.19, T:0.19
Consensus pattern (13 bp):
ACCCGTTGACCCG
Found at i:1178584 original size:29 final size:29
Alignment explanation
Indices: 1178523--1178598 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
1178513 ACCGTTGACC
*** *
1178523 GGTGCTATTCTGGGAATTAATTCGGCTTT
1 GGTGCTATTCTGGGAATTAATTCGAAATG
1178552 GGTGCTATTCTGGGAATTAATTCGAAATG
1 GGTGCTATTCTGGGAATTAATTCGAAATG
* *
1178581 GGTGCTATTTTGGTAATT
1 GGTGCTATTCTGGGAATT
1178599 TTTTTTAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.21, C:0.11, G:0.28, T:0.41
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATTCGAAATG
Found at i:1183526 original size:20 final size:20
Alignment explanation
Indices: 1183432--1183800 Score: 449
Period size: 20 Copynumber: 18.4 Consensus size: 20
1183422 GATTTTCCAT
* ** *
1183432 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
1183452 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
1183472 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1183492 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
1183512 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
1183532 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1183552 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1183572 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1183592 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1183612 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1183632 AATCGCAATGCGTATTCGTA
1 AATCGCAACGCGTATCCGTA
1183652 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1183672 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
1183692 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1183712 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1183732 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1183752 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1183772 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1183792 AATCACAAC
1 AATCGCAAC
1183801 ACTGAAATTT
Statistics
Matches: 303, Mismatches: 38, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
19 3 0.01
20 297 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1184522 original size:24 final size:24
Alignment explanation
Indices: 1184483--1184529 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1184473 AAATTTGGTC
1184483 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1184507 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1184530 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:1186939 original size:33 final size:33
Alignment explanation
Indices: 1186897--1187093 Score: 242
Period size: 33 Copynumber: 5.8 Consensus size: 33
1186887 GCGAAATGAA
*
1186897 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1186930 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATG
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAAA-G
* *
1186966 AAAATCGCAA--CGACA-G--AATCGCAATGCGAAATTAA
1 --AATCGCAATGCGAAATGAAAATCGCAA--CG-AA--AG
1187001 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1187034 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1187067 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
1187094 TGCGAAATGA
Statistics
Matches: 146, Mismatches: 5, Indels: 26
0.82 0.03 0.15
Matches are distributed among these distances:
33 108 0.74
34 2 0.01
35 11 0.08
36 9 0.06
38 16 0.11
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAAAG
Found at i:1186948 original size:52 final size:52
Alignment explanation
Indices: 1186886--1187112 Score: 338
Period size: 52 Copynumber: 4.4 Consensus size: 52
1186876 GGATTTTATG
1186886 TGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAA
1 TGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAA
*
1186938 TGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAA
1 TGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAA
* *
1186990 TGCGAAATTAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAA
1 TGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAA
*
1187042 TGCGAAATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAA
1 TGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAA
1187094 TGCGAAATGAAAATCGCAA
1 TGCGAAATGAAAATCGCAA
1187113 CGAGATAATC
Statistics
Matches: 164, Mismatches: 6, Indels: 10
0.91 0.03 0.06
Matches are distributed among these distances:
47 8 0.05
49 3 0.02
50 5 0.03
51 1 0.01
52 147 0.90
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (52 bp):
TGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAA
Found at i:1187040 original size:85 final size:85
Alignment explanation
Indices: 1186897--1187134 Score: 351
Period size: 85 Copynumber: 2.8 Consensus size: 85
1186887 GCGAAATGAA
*
1186897 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAAA-G--AATCGCAA
*
1186957 TGCGAAATGAAAATCGCAACGACAG
61 TGCGAAATGAAAATCGCAACGAAAG
*
1186982 AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
1187047 AATGAAAATCGCAACGAAAG
66 AATGAAAATCGCAACGAAAG
* *
1187067 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
1187132 AAT
66 AAT
1187135 TATAAACGCA
Statistics
Matches: 142, Mismatches: 6, Indels: 10
0.90 0.04 0.06
Matches are distributed among these distances:
85 123 0.87
87 3 0.02
88 5 0.04
89 1 0.01
90 10 0.07
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (85 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
AATGAAAATCGCAACGAAAG
Found at i:1187150 original size:52 final size:52
Alignment explanation
Indices: 1186930--1187134 Score: 214
Period size: 52 Copynumber: 3.9 Consensus size: 52
1186920 GCAACGAGAG
*
1186930 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAA
*
1186982 AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAAAATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAA
1187034 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAA
* *
1187086 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAAT
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAAT
1187135 TATAAACGCA
Statistics
Matches: 143, Mismatches: 5, Indels: 10
0.91 0.03 0.06
Matches are distributed among these distances:
47 8 0.06
49 6 0.04
50 6 0.04
52 123 0.86
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAA
Found at i:1187166 original size:20 final size:19
Alignment explanation
Indices: 1187141--1187243 Score: 144
Period size: 20 Copynumber: 5.6 Consensus size: 19
1187131 AAATTATAAA
1187141 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1187160 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
1187180 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
1187196 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1187213 CGCATTGCGATTTTTCATTT
1 CGCATTGCGA-TTTTCATTT
1187233 CGCATTGCGAT
1 CGCATTGCGAT
1187244 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 13
0.83 0.02 0.14
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 17 0.23
20 38 0.51
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:1187369 original size:14 final size:14
Alignment explanation
Indices: 1187350--1187386 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1187340 CATCAATTAC
1187350 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1187364 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1187378 ACAAATCAA
1 ACAAATCAA
1187387 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1189384 original size:14 final size:14
Alignment explanation
Indices: 1189367--1189423 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1189357 GCAAAATTAA
*
1189367 AATCGCAACGACAG
1 AATCGCAACGAAAG
1189381 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
1189398 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1189414 AATCGCAACG
1 AATCGCAACG
1189424 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1189385 original size:33 final size:33
Alignment explanation
Indices: 1189348--1189440 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
1189338 GCGAAACCAA
* * *
1189348 AATCGCAACGCAAAATTAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
1189381 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1189414 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1189441 TGCGATTTTG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:1189405 original size:19 final size:19
Alignment explanation
Indices: 1189311--1189445 Score: 110
Period size: 19 Copynumber: 7.6 Consensus size: 19
1189301 TAGTTTACTT
* *
1189311 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
1189331 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
* *
1189350 TCGCAACGCAAAATTAAAA
1 TCGCAACGCGAAATGAAAA
*
1189369 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
1189383 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1189402 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
1189416 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1189435 TCGCAATGCGA
1 TCGCAACGCGA
1189446 TTTTGGTTTC
Statistics
Matches: 94, Mismatches: 11, Indels: 21
0.75 0.09 0.17
Matches are distributed among these distances:
14 16 0.17
16 10 0.11
17 10 0.11
19 46 0.49
20 12 0.13
ACGTcount: A:0.47, C:0.24, G:0.18, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1189463 original size:19 final size:19
Alignment explanation
Indices: 1189441--1189569 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1189431 AAAATCGCAA
1189441 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1189460 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
1189474 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1189493 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
1189507 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1189526 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1189545 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
1189565 TGCGA
1 TGCGA
1189570 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:1189483 original size:33 final size:33
Alignment explanation
Indices: 1189441--1189532 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
1189431 AAAATCGCAA
1189441 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
1189474 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
1189507 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
1189533 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:1189760 original size:93 final size:93
Alignment explanation
Indices: 1189601--1190067 Score: 909
Period size: 93 Copynumber: 5.0 Consensus size: 93
1189591 GCAAATTGAA
1189601 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1189666 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
1189694 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1189759 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
*
1189787 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCATAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1189852 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
1189880 ACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1189944 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
1189972 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
*
1190037 GCAGAATTGGCAGCAACCGAATAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
1190065 ACT
1 ACT
1190068 AAGCAATCTA
Statistics
Matches: 370, Mismatches: 3, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
92 91 0.25
93 279 0.75
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
GCAGAATTGGCAGCAACCGAACAAATTT
Found at i:1190020 original size:185 final size:186
Alignment explanation
Indices: 1189601--1190067 Score: 909
Period size: 185 Copynumber: 2.5 Consensus size: 186
1189591 GCAAATTGAA
1189601 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1189666 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
66 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
1189731 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
131 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
*
1189787 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCATAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1189852 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TAT
66 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
1189916 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
131 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
1189972 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
*
1190037 GCAGAATTGGCAGCAACCGAATAAATTTACT
66 GCAGAATTGGCAGCAACCGAACAAATTTACT
1190068 AAGCAATCTA
Statistics
Matches: 278, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
185 153 0.55
186 125 0.45
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
Found at i:1191793 original size:14 final size:14
Alignment explanation
Indices: 1191774--1191863 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
1191764 TTGAAATGAA
1191774 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1191788 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
1191805 ATAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
1191821 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1191840 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1191854 AATCGCAACG
1 AATCGCAACG
1191864 CGAAAGGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.22, G:0.26, T:0.10
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1191811 original size:33 final size:33
Alignment explanation
Indices: 1191766--1191880 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
1191756 TCTTTTGGTT
1191766 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
1191799 GAGATGATAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1191832 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
1191865 GAAAGGAAAATCGCAA
1 GAAATGAAAATCGCAA
1191881 TGCGATTTTG
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 77 1.00
ACGTcount: A:0.45, C:0.20, G:0.25, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1191812 original size:19 final size:18
Alignment explanation
Indices: 1191773--1191885 Score: 79
Period size: 19 Copynumber: 6.8 Consensus size: 18
1191763 GTTGAAATGA
1191773 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
1191788 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
1191805 ATAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
1191821 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
1191838 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
* *
1191854 -AATCGCAACGCGAAAGG
1 AAATCGCAACGCGAGATG
*
1191871 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
1191886 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.21, G:0.26, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:1191916 original size:14 final size:14
Alignment explanation
Indices: 1191897--1191951 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1191887 TTTGGTTTCG
1191897 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1191911 CGTTGCGATTTTCATTTCA
1 CGTTGCGA--TTC---TCT
1191930 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1191944 CGTTGCGA
1 CGTTGCGA
1191952 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.11, C:0.25, G:0.22, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1191934 original size:33 final size:33
Alignment explanation
Indices: 1191881--1191951 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1191871 AAAATCGCAA
** *
1191881 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCACGTTGCGATTCTCTCGT
1191914 TGCGATTTTCATTTCACGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCACGTTGCGATTCTCTCGT
1191947 TGCGA
1 TGCGA
1191952 CAGTCATTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.10, C:0.23, G:0.24, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCACGTTGCGATTCTCTCGT
Found at i:1191959 original size:33 final size:33
Alignment explanation
Indices: 1191892--1191973 Score: 110
Period size: 33 Copynumber: 2.5 Consensus size: 33
1191882 GCGATTTTGG
* ***
1191892 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCACGTTGCGATTCTCTCGTTGCGACAGTCA
1191925 TTTCACGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCACGTTGCGATTCTCTCGTTGCGACAGTCA
*
1191958 TTCTCTCGTTGCGATT
1 TT-TCACGTTGCGATT
1191974 TTCATTTATC
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 31 0.72
34 12 0.28
ACGTcount: A:0.11, C:0.26, G:0.21, T:0.43
Consensus pattern (33 bp):
TTTCACGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:1191978 original size:20 final size:20
Alignment explanation
Indices: 1191904--1191992 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
1191894 TCGCGTTGCG
1191904 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
1191924 ATT-TCACGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
1191937 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
1191957 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
1191977 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
1191993 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.13, C:0.25, G:0.18, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:1192114 original size:32 final size:32
Alignment explanation
Indices: 1192075--1192143 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
1192065 ACTAACTTGA
*
1192075 AAATCGCAACGAGAGAATAGCAACGCGAAATG
1 AAATCGCAACGACAGAATAGCAACGCGAAATG
* *
1192107 AAATCGCAACGACAGAATCGTAACGCGAAATG
1 AAATCGCAACGACAGAATAGCAACGCGAAATG
1192139 AAATC
1 AAATC
1192144 TAAGTGAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.12
Consensus pattern (32 bp):
AAATCGCAACGACAGAATAGCAACGCGAAATG
Found at i:1192117 original size:18 final size:18
Alignment explanation
Indices: 1192094--1192143 Score: 54
Period size: 16 Copynumber: 3.0 Consensus size: 18
1192084 CGAGAGAATA
1192094 GCAACGCGAAATGAAATC
1 GCAACGCGAAATGAAATC
*
1192112 GCAA--CGACA-G-AATC
1 GCAACGCGAAATGAAATC
*
1192126 GTAACGCGAAATGAAATC
1 GCAACGCGAAATGAAATC
1192144 TAAGTGAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 8
0.69 0.08 0.22
Matches are distributed among these distances:
14 7 0.28
15 1 0.04
16 8 0.32
17 1 0.04
18 8 0.32
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (18 bp):
GCAACGCGAAATGAAATC
Found at i:1192375 original size:22 final size:22
Alignment explanation
Indices: 1192323--1192377 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1192313 TGGTTGTGAG
**
1192323 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
1192345 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
1192367 GGATTTCTTCG
1 GGATTTCTTCG
1192378 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:1192548 original size:20 final size:20
Alignment explanation
Indices: 1192523--1192715 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
1192513 CTTTAAATAT
1192523 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1192543 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1192565 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1192584 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
1192604 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1192624 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1192644 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1192664 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1192684 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1192704 CGCGTTGCGATT
1 CGCGTTGCGATT
1192716 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1192710 original size:60 final size:60
Alignment explanation
Indices: 1192523--1192715 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
1192513 CTTTAAATAT
**
1192523 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
1192584 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
1192644 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
1192704 CGCGTTGCGATT
1 CGCGTTGCGATT
1192716 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:1192796 original size:20 final size:20
Alignment explanation
Indices: 1192771--1192822 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1192761 AAGAATCGCG
*
1192771 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
1192791 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
1192811 TTGCGATTCTGG
1 TTGCGATTCTGG
1192823 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:1193814 original size:2 final size:2
Alignment explanation
Indices: 1193809--1193841 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1193799 TATTTTTTAC
1193809 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 T
1193842 TTAAATTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1198830 original size:30 final size:31
Alignment explanation
Indices: 1198796--1198854 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
1198786 AAAAAAATTA
*
1198796 AGGACC-ATTATG-TAATTTTTGAAAAGTTGG
1 AGGACCAATT-TGATAATTTTAGAAAAGTTGG
1198826 AGGACCAATTTGATAATTTTAGAAAAGTT
1 AGGACCAATTTGATAATTTTAGAAAAGTT
1198855 TTGAATGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 8 0.31
31 18 0.69
ACGTcount: A:0.37, C:0.07, G:0.20, T:0.36
Consensus pattern (31 bp):
AGGACCAATTTGATAATTTTAGAAAAGTTGG
Found at i:1199880 original size:31 final size:31
Alignment explanation
Indices: 1199842--1199917 Score: 125
Period size: 31 Copynumber: 2.5 Consensus size: 31
1199832 GAGTCGAGGG
1199842 TTACCTATGTTCTTCGGAACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGA
* *
1199873 TTACCTATGTTATTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGA
*
1199904 TTACCTAGGTTCTT
1 TTACCTATGTTCTT
1199918 ATGGACCTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGAACATATGGACTGA
Found at i:1199929 original size:31 final size:31
Alignment explanation
Indices: 1199842--1199933 Score: 103
Period size: 31 Copynumber: 3.0 Consensus size: 31
1199832 GAGTCGAGGG
* * * *
1199842 TTACCTATGTTCTTCGGAACATATGGACTGA
1 TTACCTAGGTTATTAGGGACATATGGACTGA
* *
1199873 TTACCTATGTTATTCGGGACATATGGACTGA
1 TTACCTAGGTTATTAGGGACATATGGACTGA
* * *
1199904 TTACCTAGGTTCTTATGGACCTATGGACTG
1 TTACCTAGGTTATTAGGGACATATGGACTG
1199934 GTTCTTCGGG
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 54 1.00
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (31 bp):
TTACCTAGGTTATTAGGGACATATGGACTGA
Found at i:1210908 original size:14 final size:14
Alignment explanation
Indices: 1210874--1210911 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
1210864 TTATCATTGT
*
1210874 AAAGAGAGAGGAAA
1 AAAGAGCGAGGAAA
1210888 AAAGAGCGAGGAAA
1 AAAGAGCGAGGAAA
1210902 AAAGAGCGAG
1 AAAGAGCGAG
1210912 AAGAGTGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.58, C:0.05, G:0.37, T:0.00
Consensus pattern (14 bp):
AAAGAGCGAGGAAA
Found at i:1212278 original size:2 final size:2
Alignment explanation
Indices: 1212271--1212299 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1212261 AAATTAAAAG
1212271 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
1212300 CAAAATAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1215665 original size:121 final size:122
Alignment explanation
Indices: 1215517--1215739 Score: 322
Period size: 121 Copynumber: 1.8 Consensus size: 122
1215507 GTCATCATCC
* ** *
1215517 CATGCAATGATAAAATCAAAGATAAACGGTTATTTTGATCCTTCAAATTAAAAATAAAAG-TTTT
1 CATGCAATGACAAAATCAAAGATAAACGGAGATCTTGATCCTTCAAATTAAAAATAAAAGTTTTT
* *
1215581 ATAATTTTTTAAAATCTCATAAAATTGTAAAATAATCAAATTTGACAACCTTCATAT
66 ATAATTATTTAAAAACTCATAAAATTGTAAAATAATCAAATTTGACAACCTTCATAT
* * * * * *
1215638 CATGCAATGACAGAATTAAAGATAAACGGAGATCTTGATCTTTTAAATTAATAATAAATGTTTTT
1 CATGCAATGACAAAATCAAAGATAAACGGAGATCTTGATCCTTCAAATTAAAAATAAAAGTTTTT
*
1215703 ATAATTATTTAAAAACTCATAAAATTGTAAATTAATC
66 ATAATTATTTAAAAACTCATAAAATTGTAAAATAATC
1215740 CAATAAAAAA
Statistics
Matches: 88, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
121 50 0.57
122 38 0.43
ACGTcount: A:0.45, C:0.10, G:0.09, T:0.36
Consensus pattern (122 bp):
CATGCAATGACAAAATCAAAGATAAACGGAGATCTTGATCCTTCAAATTAAAAATAAAAGTTTTT
ATAATTATTTAAAAACTCATAAAATTGTAAAATAATCAAATTTGACAACCTTCATAT
Found at i:1221856 original size:32 final size:31
Alignment explanation
Indices: 1221773--1221877 Score: 90
Period size: 31 Copynumber: 3.4 Consensus size: 31
1221763 ACCTAAGGGA
*
1221773 ACATCTTAGGGCCTGAGAGCCTACCCAAG-AT
1 ACATCTTAGGGCC-GAGGGCCTACCCAAGAAT
* * * *
1221804 AGAT-TTCGGGGCCGTGGGGCCTACCTAAGAAT
1 ACATCTT-AGGGCCG-AGGGCCTACCCAAGAAT
*
1221836 ACATCTTAGGGCCGCAGGGCCTACCCGAGAAT
1 ACATCTTAGGGCCG-AGGGCCTACCCAAGAAT
*
1221868 -GATCTTAGGG
1 ACATCTTAGGG
1221878 GTTAAATTTA
Statistics
Matches: 58, Mismatches: 12, Indels: 8
0.74 0.15 0.10
Matches are distributed among these distances:
30 3 0.05
31 28 0.48
32 25 0.43
33 2 0.03
ACGTcount: A:0.25, C:0.26, G:0.30, T:0.20
Consensus pattern (31 bp):
ACATCTTAGGGCCGAGGGCCTACCCAAGAAT
Found at i:1223026 original size:30 final size:30
Alignment explanation
Indices: 1222990--1223117 Score: 193
Period size: 30 Copynumber: 4.2 Consensus size: 30
1222980 TCCGAAGGAC
*
1222990 CTATCCAAAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1223020 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1223050 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* * * * *
1223080 CTATCCATAGGTCCTGAAGAACCTAGGTAAA
1 CTATCCAGAGGTCATAAAGATCCTCGGT-AA
1223111 CTATCCA
1 CTATCCA
1223118 TATGTTCCTT
Statistics
Matches: 91, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
30 82 0.90
31 9 0.10
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:1223132 original size:31 final size:32
Alignment explanation
Indices: 1223078--1223153 Score: 102
Period size: 31 Copynumber: 2.4 Consensus size: 32
1223068 GATCCTCGGT
* *
1223078 AACTATCCATA-GGTCCTGAAGAACCTAGGTA
1 AACTATCCATATGTTCCTGAAGAACATAGGTA
*
1223109 AACTATCCATATGTTCCT-TAGAACATAGGTA
1 AACTATCCATATGTTCCTGAAGAACATAGGTA
*
1223140 TACTATCCATATGT
1 AACTATCCATATGT
1223154 CTCGAAAGAC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 35 0.88
32 5 0.12
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.30
Consensus pattern (32 bp):
AACTATCCATATGTTCCTGAAGAACATAGGTA
Found at i:1223166 original size:31 final size:31
Alignment explanation
Indices: 1223078--1223170 Score: 91
Period size: 31 Copynumber: 3.0 Consensus size: 31
1223068 GATCCTCGGT
* * *
1223078 AACTATCCATA-GGTCCTGAAGAACCTAGGTA
1 AACTATCCATATGTTCC-AAAGAACATAGGTA
**
1223109 AACTATCCATATGTTCCTTAGAACATAGGTA
1 AACTATCCATATGTTCCAAAGAACATAGGTA
* *
1223140 TACTATCCATATGTCTCGAAAG-ACATAGGTA
1 AACTATCCATATGT-TCCAAAGAACATAGGTA
1223171 GTTCTTTGAC
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
31 44 0.85
32 8 0.15
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.28
Consensus pattern (31 bp):
AACTATCCATATGTTCCAAAGAACATAGGTA
Found at i:1223354 original size:4 final size:4
Alignment explanation
Indices: 1223345--1223369 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1223335 ATATAACCCT
1223345 TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA T
1223370 GTCATCATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (4 bp):
TACA
Found at i:1224262 original size:24 final size:24
Alignment explanation
Indices: 1224230--1224290 Score: 83
Period size: 21 Copynumber: 2.7 Consensus size: 24
1224220 TTTCATTATG
* *
1224230 GGGGAATCGGTTCCCCCCCCCCTT
1 GGGGTATCGATTCCCCCCCCCCTT
1224254 GGGGTATCGATT---CCCCCCCTT
1 GGGGTATCGATTCCCCCCCCCCTT
1224275 GGGGTATCGATTCCCC
1 GGGGTATCGATTCCCC
1224291 TCTAGCATTC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 21 0.66
24 11 0.34
ACGTcount: A:0.10, C:0.39, G:0.26, T:0.25
Consensus pattern (24 bp):
GGGGTATCGATTCCCCCCCCCCTT
Found at i:1224271 original size:21 final size:21
Alignment explanation
Indices: 1224245--1224290 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
1224235 ATCGGTTCCC
1224245 CCCCCCCTTGGGGTATCGATT
1 CCCCCCCTTGGGGTATCGATT
1224266 CCCCCCCTTGGGGTATCGATT
1 CCCCCCCTTGGGGTATCGATT
1224287 CCCC
1 CCCC
1224291 TCTAGCATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.09, C:0.43, G:0.22, T:0.26
Consensus pattern (21 bp):
CCCCCCCTTGGGGTATCGATT
Found at i:1224342 original size:21 final size:21
Alignment explanation
Indices: 1224318--1224360 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1224308 TCATATTCGT
* *
1224318 TTGAGGGGGGATCGATTCCCC
1 TTGAAGGGGGACCGATTCCCC
* *
1224339 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGGACCGATTCCCC
1224360 T
1 T
1224361 AGCCCAGAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.16, C:0.26, G:0.30, T:0.28
Consensus pattern (21 bp):
TTGAAGGGGGACCGATTCCCC
Found at i:1227714 original size:30 final size:30
Alignment explanation
Indices: 1227678--1227780 Score: 170
Period size: 30 Copynumber: 3.4 Consensus size: 30
1227668 TCCGAATGAC
1227678 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1227708 CTATCCAGAGATCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1227738 CTATCCAGAGGTCATAAAGATCCTCAGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
1227768 CTGTCCATAGGTC
1 CTATCCAGAGGTC
1227781 CCGAAGAACC
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 68 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:1227797 original size:60 final size:61
Alignment explanation
Indices: 1227678--1227805 Score: 168
Period size: 60 Copynumber: 2.1 Consensus size: 61
1227668 TCCGAATGAC
* * * *
1227678 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGATCATAAAGATCCTCGGT-AA
1 CTATCCAGAGGTCATAAAGATCCTCAGTAACTATCCAGAGATCACAAAGAACCTAGGTAAA
* * * * *
1227738 CTATCCAGAGGTCATAAAGATCCTCAGTAACTGTCCATAGGTCCCGAAGAACCTAGGTAAA
1 CTATCCAGAGGTCATAAAGATCCTCAGTAACTATCCAGAGATCACAAAGAACCTAGGTAAA
1227799 CTATCCA
1 CTATCCA
1227806 TATGTTCCTT
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
60 49 0.84
61 9 0.16
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (61 bp):
CTATCCAGAGGTCATAAAGATCCTCAGTAACTATCCAGAGATCACAAAGAACCTAGGTAAA
Found at i:1227806 original size:31 final size:31
Alignment explanation
Indices: 1227766--1227858 Score: 98
Period size: 31 Copynumber: 3.0 Consensus size: 31
1227756 GATCCTCAGT
* * *
1227766 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* **
1227797 AACTATCCATATGTTCCTTAGAACATAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* *
1227828 TACTATCCATATGTCTCGAA-AGACATAGGTA
1 AACTATCCATATGTCCCGAAGA-ACATAGGTA
1227859 GTTCTTTGAC
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
30 1 0.02
31 49 0.98
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (31 bp):
AACTATCCATATGTCCCGAAGAACATAGGTA
Found at i:1228996 original size:21 final size:21
Alignment explanation
Indices: 1228972--1229014 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1228962 TCATATTCGT
* *
1228972 TTGAGGGGGGATCGATTCCCC
1 TTGAAGGGGGACCGATTCCCC
* *
1228993 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGGACCGATTCCCC
1229014 T
1 T
1229015 AGCCCAGAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.16, C:0.26, G:0.30, T:0.28
Consensus pattern (21 bp):
TTGAAGGGGGACCGATTCCCC
Found at i:1233104 original size:59 final size:60
Alignment explanation
Indices: 1233035--1233166 Score: 169
Period size: 59 Copynumber: 2.2 Consensus size: 60
1233025 TTTTAAAATG
* ** *
1233035 ATCCTTAAACTTTTAAATGTTTCAATTTCATCCTTAAACTATGA-C-TATATTATAAATTA
1 ATCCTCAAACTTTTAAACATTTCAATTTCATCCTTAAAATATGACCTTA-ATTATAAATTA
* * *
1233094 ATCCTCAAACTTTTGAACATTTCAATTTCATCCTTAAAATATGACCTTAATTCTAAATTG
1 ATCCTCAAACTTTTAAACATTTCAATTTCATCCTTAAAATATGACCTTAATTATAAATTA
*
1233154 GTCCTCAAACTTT
1 ATCCTCAAACTTT
1233167 AAAAGAATTC
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
59 39 0.62
60 22 0.35
61 2 0.03
ACGTcount: A:0.35, C:0.19, G:0.05, T:0.42
Consensus pattern (60 bp):
ATCCTCAAACTTTTAAACATTTCAATTTCATCCTTAAAATATGACCTTAATTATAAATTA
Found at i:1235911 original size:2 final size:2
Alignment explanation
Indices: 1235904--1235931 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1235894 CATGCATGTG
1235904 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
1235932 GGAATGTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1236222 original size:32 final size:31
Alignment explanation
Indices: 1236186--1236278 Score: 107
Period size: 32 Copynumber: 2.9 Consensus size: 31
1236176 ACAAACTTTA
1236186 AAACTGATCTGAAGCCTAAGATAAAAATGAGT
1 AAACTGATCTGAAGCCTAAGATAAAAAT-AGT
* *
1236218 AAACTGATCTGAAGCCTAAGAGACAAACTAGT
1 AAACTGATCTGAAGCCTAAGATA-AAAATAGT
* * *
1236250 AGACTGATGC-CAATCCTAAGATAAAAATA
1 AAACTGAT-CTGAAGCCTAAGATAAAAATA
1236279 CGAATTATTG
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
31 5 0.10
32 42 0.81
33 5 0.10
ACGTcount: A:0.46, C:0.16, G:0.17, T:0.20
Consensus pattern (31 bp):
AAACTGATCTGAAGCCTAAGATAAAAATAGT
Found at i:1241296 original size:91 final size:91
Alignment explanation
Indices: 1241000--1241676 Score: 904
Period size: 91 Copynumber: 7.5 Consensus size: 91
1240990 GTTGGATGAT
* * * * * * *
1241000 TCGTCGGATGAGTTCTTCTCATTATGAACTCTCCGCTAG-AATATCGAGCCAAGATTAAACAAG-
1 TCGTTGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGAGCCAAGGTTGAACAAGT
* *
1241063 --TTAT--TTATGAACTTCTTTTCCC
66 TCTTCTCATTATGAACTTCTTCTCCC
* * * *
1241085 TCGTTGGACGAGTTATTCTCATTATGAACTCTCCACTGGAATTGTTGAGCCAATGTTGAACAAGT
1 TCGTTGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGAGCCAAGGTTGAACAAGT
* * *
1241150 TATTCTTATTATGAACTT-TTTTCCC
66 TCTTCTCATTATGAACTTCTTCTCCC
* * * * * *
1241175 TTGTTGGATGAGTTCTTCTCATTATGAACTCTTCACAGGAAAAGCTGAGCCAAGGTTGAATAAGT
1 TCGTTGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGAGCCAAGGTTGAACAAGT
* *
1241240 TCTTCTCATTATGAACTTCTTTTCTC
66 TCTTCTCATTATGAACTTCTTCTCCC
* * *
1241266 TCGTTGGATGAGTTCTTTTCATTATGAACTCTCAACTGGAAATGTTGAGCCAATGTTGAACAAGT
1 TCGTTGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGAGCCAAGGTTGAACAAGT
1241331 TCTTCTCATTATGAACTTCTTCTCCC
66 TCTTCTCATTATGAACTTCTTCTCCC
* * *
1241357 TCGTTGGATGAGTTATTCTCA-TATGAACTCTCCAGTAGAAATGTTGATG-CAAGGTTGAACAAG
1 TCGTTGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGA-GCCAAGGTTGAACAAG
*
1241420 TTCTTCTTATTATGAACTTCTTCTCCC
65 TTCTTCTCATTATGAACTTCTTCTCCC
* *
1241447 TCATTGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAATTGTTGAGCCAAGGTTGAACAAGT
1 TCGTTGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGAGCCAAGGTTGAACAAGT
1241512 TCTTCTCATTATGAACTTCTTCTCCC
66 TCTTCTCATTATGAACTTCTTCTCCC
* * * *
1241538 TCGTTGGATGAGTTCTTCTCATTGTGAACTCTCCACTGGAAATGCTGAACCAAGGTTGGACAAGT
1 TCGTTGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGAGCCAAGGTTGAACAAGT
* *
1241603 TCTTCTTATTATGAACTTATTCTCCC
66 TCTTCTCATTATGAACTTCTTCTCCC
* * *
1241629 TTGTTGGATGAGTTCTTCTCATTATGAACTCTCCATTAGAAATGTTGA
1 TCGTTGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGA
1241677 TCGATTTATC
Statistics
Matches: 520, Mismatches: 62, Indels: 14
0.87 0.10 0.02
Matches are distributed among these distances:
85 34 0.07
86 18 0.03
89 3 0.01
90 160 0.31
91 305 0.59
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (91 bp):
TCGTTGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAATGTTGAGCCAAGGTTGAACAAGT
TCTTCTCATTATGAACTTCTTCTCCC
Found at i:1241306 original size:181 final size:182
Alignment explanation
Indices: 1241000--1241663 Score: 904
Period size: 181 Copynumber: 3.7 Consensus size: 182
1240990 GTTGGATGAT
* * * * *
1241000 TCGTCGGATGAGTTCTTCTCATTATGAACTCTCCGCTA-GAATAT-C-GAGCCAAGATTAAACAA
1 TCGTTGGATGAGTTCTTCTCATTATGAACTCTTCAC-AGGAA-ATGCTGAGCCAAGGTTGAACAA
* * * *
1241062 G---TT-AT-TTATGAACTTCTTTTCCCTCGTTGGACGAGTTATTCTCATTATGAACTCTCCACT
64 GTTCTTCTTATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCACT
* * *
1241122 GGAATTGTTGAGCCAATGTTGAACAAGTTATTCTTATTATGAACTT-TTTTCCC
129 GGAATTGTTGAGCCAATGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCC
* * *
1241175 TTGTTGGATGAGTTCTTCTCATTATGAACTCTTCACAGGAAAAGCTGAGCCAAGGTTGAATAAGT
1 TCGTTGGATGAGTTCTTCTCATTATGAACTCTTCACAGGAAATGCTGAGCCAAGGTTGAACAAGT
* * * * *
1241240 TCTTCTCATTATGAACTTCTTTTCTCTCGTTGGATGAGTTCTTTTCATTATGAACTCTCAACTGG
66 TCTTCTTATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCACTGG
*
1241305 AAATGTTGAGCCAATGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCC
131 AATTGTTGAGCCAATGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCC
* *
1241357 TCGTTGGATGAGTTATTCTCA-TATGAACTC-TC-CAGTAGAAATGTTGATG-CAAGGTTGAACA
1 TCGTTGGATGAGTTCTTCTCATTATGAACTCTTCACAG--GAAATGCTGA-GCCAAGGTTGAACA
*
1241418 AGTTCTTCTTATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAACTCTCCAC
63 AGTTCTTCTTATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCAC
*
1241483 TGGAATTGTTGAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCC
128 TGGAATTGTTGAGCCAATGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCC
* * * * *
1241538 TCGTTGGATGAGTTCTTCTCATTGTGAACTCTCCACTGGAAATGCTGAACCAAGGTTGGACAAGT
1 TCGTTGGATGAGTTCTTCTCATTATGAACTCTTCACAGGAAATGCTGAGCCAAGGTTGAACAAGT
* *
1241603 TCTTCTTATTATGAACTTATTCTCCCTTGTTGGATGAGTTCTTCTCATTATGAACTCTCCA
66 TCTTCTTATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCA
1241664 TTAGAAATGT
Statistics
Matches: 431, Mismatches: 42, Indels: 25
0.87 0.08 0.05
Matches are distributed among these distances:
174 2 0.00
175 36 0.08
176 15 0.03
179 5 0.01
180 2 0.00
181 253 0.59
182 115 0.27
183 1 0.00
184 2 0.00
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (182 bp):
TCGTTGGATGAGTTCTTCTCATTATGAACTCTTCACAGGAAATGCTGAGCCAAGGTTGAACAAGT
TCTTCTTATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCACTGG
AATTGTTGAGCCAATGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCC
Found at i:1241458 original size:272 final size:273
Alignment explanation
Indices: 1240947--1241677 Score: 933
Period size: 272 Copynumber: 2.7 Consensus size: 273
1240937 AATGTTATTG
1240947 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGATTCGTCGGATGAG
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTC-------G--T--T-GGATGAG
** * * * * *
1241012 TTCTTCTCATTATGAACTCTCCGCTAGAATAT-C-GAGCCAAGATTAAACAAG---TTAT--TTA
54 TTCTTCTCATTATGAACTCTCAACTGGAA-ATGCTGAACCAAGGTTGAACAAGTTCTTCTCATTA
* * * *
1241070 TGAACTTCTTTTCCCTCGTTGGACGAGTTATTCTCATTATGAACTCTCCACTGGAATTGTTGA-G
118 TGAACTTCTTCTCCCTCGTTGGATGAGTTATTCTCATTATGAACTCTCCACTAGAAATGTTGATG
* * **
1241134 CCAATGTTGAACAAGTTATTCTTATTATGAACTTTTTTCCCTTGTTGGATGAGTTCTTCTCATTA
183 CCAAGGTTGAACAAGTTATTCTTATTATGAACTTTTCTCCCTCATTGGATGAGTTCTTCTCATTA
*
1241199 TGAACTCTTCACAGGAAAAGCTGAGC
248 TGAACTCTCCACAGGAAAAGCTGAGC
* * * *
1241225 CAAGGTTGAATAAGTTCTTCTCATTATGAACTTCTTTTCTCTCGTTGGATGAGTTCTTTTCATTA
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTA
* * *
1241290 TGAACTCTCAACTGGAAATGTTGAGCCAATGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTC
66 TGAACTCTCAACTGGAAATGCTGAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTC
*
1241355 CCTCGTTGGATGAGTTATTCTCA-TATGAACTCTCCAGTAGAAATGTTGATG-CAAGGTTGAACA
131 CCTCGTTGGATGAGTTATTCTCATTATGAACTCTCCACTAGAAATGTTGATGCCAAGGTTGAACA
*
1241418 AGTTCTTCTTATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAACTCTCCAC
196 AGTTATTCTTATTATGAACTT-TTCTCCCTCATTGGATGAGTTCTTCTCATTATGAACTCTCCAC
* ** *
1241483 TGGAATTGTTGAGC
260 AGGAAAAGCTGAGC
*
1241497 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTG
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTA
* * * *
1241562 TGAACTCTCCACTGGAAATGCTGAACCAAGGTTGGACAAGTTCTTCTTATTATGAACTTATTCTC
66 TGAACTCTCAACTGGAAATGCTGAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTC
* * *
1241627 CCTTGTTGGATGAGTTCTTCTCATTATGAACTCTCCATTAGAAATGTTGAT
131 CCTCGTTGGATGAGTTATTCTCATTATGAACTCTCCACTAGAAATGTTGAT
1241678 CGATTTATCT
Statistics
Matches: 401, Mismatches: 42, Indels: 25
0.86 0.09 0.05
Matches are distributed among these distances:
265 2 0.00
266 32 0.08
267 16 0.04
269 1 0.00
270 3 0.01
271 55 0.14
272 226 0.56
273 26 0.06
278 40 0.10
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.38
Consensus pattern (273 bp):
CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTA
TGAACTCTCAACTGGAAATGCTGAACCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTC
CCTCGTTGGATGAGTTATTCTCATTATGAACTCTCCACTAGAAATGTTGATGCCAAGGTTGAACA
AGTTATTCTTATTATGAACTTTTCTCCCTCATTGGATGAGTTCTTCTCATTATGAACTCTCCACA
GGAAAAGCTGAGC
Found at i:1242147 original size:66 final size:67
Alignment explanation
Indices: 1242032--1242473 Score: 334
Period size: 66 Copynumber: 6.6 Consensus size: 67
1242022 GTTTCAGGGG
* ** * * *
1242032 GAAACTATCTCAAGATAGACAAAATTCGTTTCAAGG-GAA-ATGATCTCAAAGATTTGTGTTTCA
1 GAAACTGTCTCAAGGGAGACAAAATTTGTTTAAAGGAAAACAT-ATCTCAAAGATTTGTGTTTCA
1242095 AGA
65 AGA
* * *
1242098 GAAACTGTATCTAGGGAGACAAAATTTGTTTAAAGGAAAACATAT-TCAAAGA-TTGATGTCTCA
1 GAAACTGTCTCAAGGGAGACAAAATTTGTTTAAAGGAAAACATATCTCAAAGATTTG-TGTTTCA
1242161 AG-
65 AGA
* ** * * * *
1242163 GAAACTGTCTCAAGAGAGACAAAATTCATTTTAAGG-GAAC-TGATGTCAAAGATTTTTGTTTCA
1 GAAACTGTCTCAAGGGAGACAAAATTTGTTTAAAGGAAAACAT-ATCTCAAAGATTTGTGTTTCA
1242226 AGA
65 AGA
* ** * * * *
1242229 GAAACTGTCTCAAGGTAGACAAAACATGTTTAAAGGGAAATA-ATCTCAAATATTTTGAGTTTCA
1 GAAACTGTCTCAAGGGAGACAAAATTTGTTTAAAGGAAAACATATCTCAAAGA-TTTGTGTTTCA
*
1242293 GGA
65 AGA
* * * * * *
1242296 GAAACTATCTCAAGAGAGAC-AACTTTGTTTTAAGGGAAACAGAT-TCAAAGATTTTGTGTTTCA
1 GAAACTGTCTCAAGGGAGACAAAATTTGTTTAAAGGAAAACATATCTCAAAGA-TTTGTGTTTCA
1242359 AGA
65 AGA
* * * * *
1242362 GAAACTATCTCAAGGGAGACAAAACTTGTTTCAA-GAGAAAC-TCTCTCAAGAGAGACAAAATT-
1 GAAACTGTCTCAAGGGAGACAAAATTTGTTTAAAGGA-AAACATATCTC-A-A-AG----ATTTG
*
1242424 TGCTTCAAGA
58 TGTTTCAAGA
*
1242434 GAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGAGAAA
1 GAAACTGTCTCAAGGGAGACAAAATTTGTTTAAAG-GAAA
1242474 CTGTCTCAAG
Statistics
Matches: 299, Mismatches: 54, Indels: 39
0.76 0.14 0.10
Matches are distributed among these distances:
63 1 0.00
64 5 0.02
65 48 0.16
66 139 0.46
67 52 0.17
68 3 0.01
69 1 0.00
70 2 0.01
72 41 0.14
73 4 0.01
74 3 0.01
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.27
Consensus pattern (67 bp):
GAAACTGTCTCAAGGGAGACAAAATTTGTTTAAAGGAAAACATATCTCAAAGATTTGTGTTTCAA
GA
Found at i:1242367 original size:133 final size:133
Alignment explanation
Indices: 1242021--1242402 Score: 465
Period size: 131 Copynumber: 2.9 Consensus size: 133
1242011 AGATACATTT
* *
1242021 TGTTTCAGGGGGAAACTATCTCAAGATAGACAAAATTCGTTTCAAGGGAAA-TGATCTCAAAGA-
1 TGTTTCA--GGGAAACTATCTCAAGAGAGACAAAATTCGTTTTAAGGGAAACTGATCTCAAAGAT
* * * *
1242084 TTTGTGTTTCAAGAGAAACTGTATCTAGGGAGACAAAATTTGTTTAAAGGAAAACATATTCAAAG
64 TTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTTGTTTAAAGGGAAACATATTCAAAG
1242149 ATTGA
129 ATTGA
* * * * *
1242154 TGTCTCAAGGAAACTGTCTCAAGAGAGACAAAATTCATTTTAAGGG-AACTGATGTCAAAGATTT
1 TGTTTCAGGGAAACTATCTCAAGAGAGACAAAATTCGTTTTAAGGGAAACTGATCTCAAAGATTT
* * * *
1242218 T-TGTTTCAAGAGAAACTGTCTCAAGGTAGACAAAACATGTTTAAAGGGAAATA-ATCTCAAATA
66 TGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTTGTTTAAAGGGAAACATAT-TCAAAGA
1242281 TTTTGA
130 --TTGA
* * *
1242287 -GTTTCAGGAGAAACTATCTCAAGAGAGAC-AACTTTGTTTTAAGGGAAACAGAT-TCAAAGATT
1 TGTTTCAGG-GAAACTATCTCAAGAGAGACAAAATTCGTTTTAAGGGAAACTGATCTCAAAGATT
* * *
1242349 TTGTGTTTCAAGAGAAACTATCTCAAGGGAGACAAAACTTGTTTCAAGAGAAAC
65 TTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTTGTTTAAAGGGAAAC
1242403 TCTCTCAAGA
Statistics
Matches: 213, Mismatches: 28, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
130 4 0.02
131 96 0.45
132 33 0.15
133 80 0.38
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (133 bp):
TGTTTCAGGGAAACTATCTCAAGAGAGACAAAATTCGTTTTAAGGGAAACTGATCTCAAAGATTT
TGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTTGTTTAAAGGGAAACATATTCAAAGAT
TGA
Found at i:1242399 original size:36 final size:35
Alignment explanation
Indices: 1242352--1242872 Score: 268
Period size: 36 Copynumber: 15.4 Consensus size: 35
1242342 AAAGATTTTG
1242352 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAACT
1 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAA-T
* *
1242388 TGTTTCAAGAGAAACTCTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAA-T
* *
1242424 TGCTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAA-T
* * *
1242460 TGTTTCAAGAGAAACTGTCTCAAGAGACACAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAA-T
* ***
1242496 TGTTTCAAG-GAAAACGT-TTTCAA---AG--TTTA-
1 TGTTTCAAGAG-AAAC-TATCTCAAGGGAGACAAAAT
1242525 TGTTTCAAGAGAAAC-AGTCTCAAGGGAG--AAAAT
1 TGTTTCAAGAGAAACTA-TCTCAAGGGAGACAAAAT
* * ***
1242558 TCG-TTCAAAGGGAAA-TGATTTCAA---AG--TTTA-
1 T-GTTTC-AAGAGAAACT-ATCTCAAGGGAGACAAAAT
* *
1242588 TGTTTTAAGAGAAACTATCTCAAGAGAGACAAAAT
1 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAAT
* *
1242623 TCGTTTCAAGA-AAA--A-CTCAAGGGAGATGAAATT
1 T-GTTTCAAGAGAAACTATCTCAAGGGAGA-CAAAAT
* * *
1242656 TGTTTCAAGGGAAACTATCTCAAGAGAGACTAAACT
1 TGTTTCAAGAGAAACTATCTCAAGGGAGAC-AAAAT
* * * ***
1242692 CGTTTCAAGGGAAAC-ATTATCAA---AG--TTTA-
1 TGTTTCAAGAGAAACTA-TCTCAAGGGAGACAAAAT
*
1242721 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAA-T
* * * *
1242757 TATTTCAAGAGAAACTGTTTCAAGAGAGACAAAAT
1 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAAT
* ***
1242792 TCGTTTCAAGAGAAACAATCTCAA---AG--TTTA-
1 T-GTTTCAAGAGAAACTATCTCAAGGGAGACAAAAT
* * *
1242822 TGTTTTAAGAGAGACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAA-T
1242858 TGTTTCAAGAGAAAC
1 TGTTTCAAGAGAAAC
1242873 AATATCAAAG
Statistics
Matches: 371, Mismatches: 69, Indels: 90
0.70 0.13 0.17
Matches are distributed among these distances:
29 68 0.18
30 6 0.02
31 5 0.01
32 27 0.07
33 18 0.05
34 16 0.04
35 10 0.03
36 220 0.59
37 1 0.00
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.26
Consensus pattern (35 bp):
TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAAT
Found at i:1242539 original size:65 final size:65
Alignment explanation
Indices: 1242460--1242770 Score: 296
Period size: 65 Copynumber: 4.8 Consensus size: 65
1242450 AGACAAAATT
* *
1242460 TGTTTCAAGAGAAACTGTCTCAAGAGACACAAAATTTGTTTCAAGGAAAACGTTTTCAAAGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGAAAACGTTTTCAAAGTTTA
* * * * *
1242525 TGTTTCAAGAGAAACAGTCTCAAG-G-GAGAAAATTCG-TTCAAAGGGAAATGATTTCAAAGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTC-AAGGAAAACGTTTTCAAAGTTT
1242587 A
65 A
* * *
1242588 TGTTTTAAGAGAAACTATCTCAAGAGAGACAAAATTCGTTTCAAGAAAAAC----TCAAGGGAGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGAAAACGTTTTCAA---AG-
1242649 TGAAATT-
62 T----TTA
* * * * * * *
1242656 TGTTTCAAGGGAAACTATCTCAAGAGAGACTAAACTCGTTTCAAGGGAAACATTATCAAAGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGAAAACGTTTTCAAAGTTTA
* **
1242721 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTATTTCAAGAGAAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAG-GAAA
1242771 CTGTTTCAAG
Statistics
Matches: 200, Mismatches: 28, Indels: 35
0.76 0.11 0.13
Matches are distributed among these distances:
61 4 0.02
62 3 0.01
63 49 0.25
64 6 0.03
65 78 0.39
66 6 0.03
68 46 0.23
69 4 0.02
72 4 0.02
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGAAAACGTTTTCAAAGTTTA
Found at i:1242642 original size:32 final size:33
Alignment explanation
Indices: 1242597--1242700 Score: 93
Period size: 32 Copynumber: 3.1 Consensus size: 33
1242587 ATGTTTTAAG
*
1242597 AGAAACTATCTCAAGAGAGACAAAATTCGTTTCA
1 AGAAAC-AACTCAAGAGAGACAAAATTCGTTTCA
* ** *
1242631 AGAAA-AACTCAAGGGAGATGAAATTTGTTTCA
1 AGAAACAACTCAAGAGAGACAAAATTCGTTTCA
* * *
1242663 AGGGAAACTATCTCAAGAGAGACTAAACTCGTTTCA
1 A--GAAAC-AACTCAAGAGAGACAAAATTCGTTTCA
1242699 AG
1 AG
1242701 GGAAACATTA
Statistics
Matches: 55, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
32 23 0.42
34 10 0.18
36 22 0.40
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.23
Consensus pattern (33 bp):
AGAAACAACTCAAGAGAGACAAAATTCGTTTCA
Found at i:1242731 original size:133 final size:131
Alignment explanation
Indices: 1242525--1242815 Score: 345
Period size: 133 Copynumber: 2.2 Consensus size: 131
1242515 TCAAAGTTTA
* * *
1242525 TGTTTCAAGAGAAACAGTCTCAAGGGAGAAAATTCGTTCAAAGGGAAATGATTTCAAAGTTTATG
1 TGTTTCAAGAGAAACAGTCTCAAGAGAGAAAACTCGTTCAAAGGGAAATCATTTCAAAGTTTATG
* *
1242590 TTTTAAGAGAAACTATCTCAAGAGAGACAAAATTCGTTTCAAGAAAAACTCAAGGGAGATGAAAT
66 TTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGAAAAACTCAAGGGAGATGAAAT
1242655 T
131 T
*
1242656 TGTTTCAAGGGAAACTA-TCTCAAGAGAGACTAAACTCGTTTC-AAGGGAAA-CATTATCAAAGT
1 TGTTTCAAGAGAAAC-AGTCTCAAGAGAGA--AAACTCG-TTCAAAGGGAAATCATT-TCAAAGT
* * * * *
1242718 TTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTATTTCAAGAGAAACTGTTTCAAGAG
61 TTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGAAAAAC----TCAAGGG
**
1242783 AGACAAAATT
122 AGATGAAATT
* *
1242793 CGTTTCAAGAGAAACAATCTCAA
1 TGTTTCAAGAGAAACAGTCTCAA
1242816 AGTTTATGTT
Statistics
Matches: 135, Mismatches: 15, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
131 25 0.19
132 4 0.03
133 69 0.51
134 3 0.02
136 1 0.01
137 33 0.24
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.26
Consensus pattern (131 bp):
TGTTTCAAGAGAAACAGTCTCAAGAGAGAAAACTCGTTCAAAGGGAAATCATTTCAAAGTTTATG
TTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGAAAAACTCAAGGGAGATGAAAT
T
Found at i:1242732 original size:196 final size:198
Alignment explanation
Indices: 1242388--1242749 Score: 539
Period size: 196 Copynumber: 1.8 Consensus size: 198
1242378 AGACAAAACT
* * *
1242388 TGTTTCAAGAGAAACTCTCTCAAGAGAGACAAAATTTGCTTCAAGAGAAACTGTCTCAAGGGAGA
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCGCTTCAAGAGAAAC--ACTCAAGGGAGA
* * * * *
1242453 CAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGACACAAAATTTGTTTCAAGGAAAACGTTTTCA
64 CAAAATTTGTTTCAAGAGAAACTATCTCAAGAGACACAAAACTCGTTTCAAGGAAAACATTATCA
1242518 AAGTTTATGTTTCAAGAGAAACAGTCTCAAGGGAGAAAATTCGTTCAAAGGGAAATGATTTCAAA
129 AAGTTTATGTTTCAAGAGAAACAGTCTCAAGGGAGAAAATTCGTTCAAAGGGAAATGATTTCAAA
1242583 GTTTA
194 GTTTA
* * **
1242588 TGTTTTAAGAGAAACTATCTCAAGAGAGACAAAATTCGTTTCAAGA-AAA-ACTCAAGGGAGATG
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCGCTTCAAGAGAAACACTCAAGGGAGACA
* * * *
1242651 AAATTTGTTTCAAGGGAAACTATCTCAAGAGAGACTAAACTCGTTTCAAGGGAAACATTATCAAA
66 AAATTTGTTTCAAGAGAAACTATCTCAAGAGACACAAAACTCGTTTCAAGGAAAACATTATCAAA
*
1242716 GTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGA
131 GTTTATGTTTCAAGAGAAACAGTCTCAAGGGAGA
1242750 CAAAATTTAT
Statistics
Matches: 145, Mismatches: 17, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
196 100 0.69
199 3 0.02
200 42 0.29
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.27
Consensus pattern (198 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCGCTTCAAGAGAAACACTCAAGGGAGACA
AAATTTGTTTCAAGAGAAACTATCTCAAGAGACACAAAACTCGTTTCAAGGAAAACATTATCAAA
GTTTATGTTTCAAGAGAAACAGTCTCAAGGGAGAAAATTCGTTCAAAGGGAAATGATTTCAAAGT
TTA
Found at i:1242763 original size:101 final size:101
Alignment explanation
Indices: 1242352--1242872 Score: 416
Period size: 101 Copynumber: 5.1 Consensus size: 101
1242342 AAAGATTTTG
*
1242352 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAACTT-GTTTCAAGAGAAAC-TCTCTCAAGAGA
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAA-TTCGTTTCAAGAGAAACAT-TCTC-A-A-A
* *
1242415 GACAAAATT-TGCTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
61 G-----TTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
* * * * *
1242460 TGTTTCAAGAGAAACTGTCTCAAGAGACACAAAATTTGTTTCAAG-GAAAACGTTTTCAAAGTTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCGTTTCAAGAG-AAACATTCTCAAAGTTT
*
1242524 ATGTTTCAAGAGAAACAGTCTCAAGGGAG--AAAATT
65 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
* * * *** *
1242559 CG-TTCAAAGGGAAA-TGATTTC-A-A-AG--TTTA-T-GTTTTAAGAGAAAC-TATCTCAAGAG
1 TGTTTC-AAGAGAAACT-ATCTCAAGAGAGACAAAATTCGTTTCAAGAGAAACAT-TCTC-A-A-
*** * **
1242614 AGACAAAATTCGTTTCAAGA-AAA---ACTCAAGGGAGATGAAATT
60 AG--TTTA-T-GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
* * * * *
1242656 TGTTTCAAGGGAAACTATCTCAAGAGAGACTAAACTCGTTTCAAGGGAAACATTATCAAAGTTTA
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCGTTTCAAGAGAAACATTCTCAAAGTTTA
1242721 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
* * * *
1242757 TATTTCAAGAGAAACTGTTTCAAGAGAGACAAAATTCGTTTCAAGAGAAACAATCTCAAAGTTTA
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCGTTTCAAGAGAAACATTCTCAAAGTTTA
* *
1242822 TGTTTTAAGAGAGACTGTCTCAAGGGAGACAAAATT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
1242858 TGTTTCAAGAGAAAC
1 TGTTTCAAGAGAAAC
1242873 AATATCAAAG
Statistics
Matches: 335, Mismatches: 47, Indels: 69
0.74 0.10 0.15
Matches are distributed among these distances:
91 1 0.00
92 14 0.04
93 3 0.01
94 2 0.01
95 12 0.04
96 1 0.00
97 29 0.09
98 18 0.05
99 28 0.08
100 4 0.01
101 148 0.44
102 3 0.01
103 2 0.01
104 15 0.04
105 3 0.01
106 1 0.00
107 4 0.01
108 46 0.14
109 1 0.00
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.26
Consensus pattern (101 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCGTTTCAAGAGAAACATTCTCAAAGTTTA
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
Found at i:1242867 original size:65 final size:65
Alignment explanation
Indices: 1242763--1242887 Score: 205
Period size: 65 Copynumber: 1.9 Consensus size: 65
1242753 AATTTATTTC
* *
1242763 AAGAGAAACTGTTTCAAGAGAGACAAAATTCGTTTCAAGAGAAACAATCTCAAAGTTTATGTTTT
1 AAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGAGAAACAATATCAAAGTTTATGTTTT
* * *
1242828 AAGAGAGACTGTCTCAAGGGAGACAAAATTTGTTTCAAGAGAAACAATATCAAAGTTTAT
1 AAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGAGAAACAATATCAAAGTTTAT
1242888 CAATTTTGTT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 55 1.00
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.27
Consensus pattern (65 bp):
AAGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGAGAAACAATATCAAAGTTTATGTTTT
Found at i:1243752 original size:36 final size:36
Alignment explanation
Indices: 1243685--1243757 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
1243675 ACTTATCTTG
* * ** *
1243685 TTTGAAAAAGTTTTTCTTCCTTTGAATTTTCAAAAT
1 TTTGAAAAAATTTTGCTTCCTTCAAAATTTCAAAAT
*
1243721 TTTGAAAAAATTTTGCTTCCTTCAAAATTTCACAAT
1 TTTGAAAAAATTTTGCTTCCTTCAAAATTTCAAAAT
1243757 T
1 T
1243758 GAAACAAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.33, C:0.14, G:0.07, T:0.47
Consensus pattern (36 bp):
TTTGAAAAAATTTTGCTTCCTTCAAAATTTCAAAAT
Found at i:1245851 original size:148 final size:149
Alignment explanation
Indices: 1245583--1245866 Score: 448
Period size: 148 Copynumber: 1.9 Consensus size: 149
1245573 CAAAGCTTTC
* *
1245583 ACTTCATCTCATACTTTCAGAAGTCTTTCAATCTGGTTCATGATCTTCAACTGTTGGCTTCAGCG
1 ACTTCATCTCATACTTTCAGAAATCTTTCAAGCTGGTTCATGATCTTCAACTGTTGGCTTCAGCG
*
1245648 TCGAATCATCTCGAGTCTAACTTGTTACCTCAGCAGACAGATGTCTGGCTCGTCTCATTGGT-AG
66 TCGAATCATCTCGAGTCTAACTTGTTACCTCAGCAGACAGAGGTCTGGCTCGTCTCATTGGTAAG
1245712 TAGACTCCCTCTAGCTCCT
131 TAGACTCCCTCTAGCTCCT
* * *
1245731 ACTTCATCTCATA-TTTCCATAAATCTTTCGAGCTGGTTCGTGATCTTCAACTGTTGGCTTCAGC
1 ACTTCATCTCATACTTT-CAGAAATCTTTCAAGCTGGTTCATGATCTTCAACTGTTGGCTTCAGC
* * *
1245795 GTCGAATCGTCTCGAGTTTAACTTGTTACCTCAGCAGGA-AGAGGTCTGGCTTGTCTCATTGGTA
65 GTCGAATCATCTCGAGTCTAACTTGTTACCTCAGCA-GACAGAGGTCTGGCTCGTCTCATTGGTA
1245859 AGTAGACT
129 AGTAGACT
1245867 TAGGGGTGTT
Statistics
Matches: 124, Mismatches: 9, Indels: 5
0.90 0.07 0.04
Matches are distributed among these distances:
147 3 0.02
148 111 0.90
149 10 0.08
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (149 bp):
ACTTCATCTCATACTTTCAGAAATCTTTCAAGCTGGTTCATGATCTTCAACTGTTGGCTTCAGCG
TCGAATCATCTCGAGTCTAACTTGTTACCTCAGCAGACAGAGGTCTGGCTCGTCTCATTGGTAAG
TAGACTCCCTCTAGCTCCT
Found at i:1247020 original size:17 final size:17
Alignment explanation
Indices: 1246998--1247036 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
1246988 TGAATAAAAT
1246998 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
1247015 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
1247032 -AATTA
1 TAATTA
1247037 ATTATAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:1250783 original size:15 final size:15
Alignment explanation
Indices: 1250750--1250792 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
1250740 AAAATAATAT
* *
1250750 TAAAATTAAAACTAA
1 TAAAAATAAAACAAA
1250765 -AAAAATAAAACAAA
1 TAAAAATAAAACAAA
1250779 TAAAAAT-AAACAAA
1 TAAAAATAAAACAAA
1250793 CAAACACTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 19 0.76
15 6 0.24
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.16
Consensus pattern (15 bp):
TAAAAATAAAACAAA
Found at i:1257882 original size:31 final size:30
Alignment explanation
Indices: 1257837--1257912 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 30
1257827 TACTTACATA
1257837 TATTATTATT-AAATTAAAAGATAAATTTATT
1 TATTATT-TTAAAATTAAAAGAT-AATTTATT
* *
1257868 TATTATTTTAAAATT---ATATTATTTATT
1 TATTATTTTAAAATTAAAAGATAATTTATT
1257895 TATTATTTTAAAATTAAA
1 TATTATTTTAAAATTAAA
1257913 TAATTAACAT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
27 22 0.56
28 3 0.08
30 2 0.05
31 12 0.31
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (30 bp):
TATTATTTTAAAATTAAAAGATAATTTATT
Found at i:1257889 original size:19 final size:19
Alignment explanation
Indices: 1257858--1257895 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
1257848 AATTAAAAGA
*
1257858 TAAATTTATTTA-TTATTT
1 TAAAATTATTTATTTATTT
1257876 TAAAATTATATTATTTATTT
1 TAAAATTAT-TTATTTATTT
1257896 ATTATTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 3 0.18
20 6 0.35
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TAAAATTATTTATTTATTT
Found at i:1258003 original size:19 final size:19
Alignment explanation
Indices: 1257975--1258067 Score: 55
Period size: 19 Copynumber: 4.5 Consensus size: 19
1257965 ATATATTAAA
*
1257975 AAAATAAAATAAATGT-TTT
1 AAAATTAAATAAAT-TATTT
1257994 AAAATTAAATAATATTATTT
1 AAAATTAAATAA-ATTATTT
* *
1258014 CAAATAAATAAATAATATAATTTT
1 --AA-AATTAAATAA-ATTA-TTT
1258038 AAATATTAAATAATATTATTT
1 AAA-ATTAAATAA-ATTATTT
*
1258059 CAAA-TAAAT
1 AAAATTAAAT
1258068 TAATAATATG
Statistics
Matches: 61, Mismatches: 6, Indels: 14
0.75 0.07 0.17
Matches are distributed among these distances:
19 17 0.28
20 6 0.10
21 6 0.10
22 16 0.26
23 13 0.21
24 3 0.05
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (19 bp):
AAAATTAAATAAATTATTT
Found at i:1258009 original size:38 final size:42
Alignment explanation
Indices: 1257967--1258085 Score: 113
Period size: 45 Copynumber: 2.8 Consensus size: 42
1257957 TAAGTTTGAT
*
1257967 ATATTA-AAA-AAATAAAATAA-AT-GTTTTAAA-ATTAAATA
1 ATATTATAAATAAAT-AAATAATATAATTTTAAATATTAAATA
1258005 ATATTATTTCAAATAAATAAATAATATAATTTTAAATATTAAATA
1 ATATTA--T-AAATAAATAAATAATATAATTTTAAATATTAAATA
* *
1258050 ATATTATTTCAAATAAATTAATAATATGATTTTAAA
1 ATATTA--T-AAATAAATAAATAATATAATTTTAAA
1258086 AATATTTTTA
Statistics
Matches: 70, Mismatches: 3, Indels: 9
0.85 0.04 0.11
Matches are distributed among these distances:
38 6 0.09
42 9 0.13
43 6 0.09
44 7 0.10
45 42 0.60
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (42 bp):
ATATTATAAATAAATAAATAATATAATTTTAAATATTAAATA
Found at i:1258029 original size:23 final size:23
Alignment explanation
Indices: 1257999--1258081 Score: 114
Period size: 23 Copynumber: 3.7 Consensus size: 23
1257989 GTTTTAAAAT
1257999 TAAATAATATTATTTCAAATAAA
1 TAAATAATATTATTTCAAATAAA
* * *
1258022 TAAATAATATAATTTTAAAT-AT
1 TAAATAATATTATTTCAAATAAA
1258044 TAAATAATATTATTTCAAATAAA
1 TAAATAATATTATTTCAAATAAA
* *
1258067 TTAATAATATGATTT
1 TAAATAATATTATTT
1258082 TAAAAATATT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
22 19 0.37
23 32 0.63
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.43
Consensus pattern (23 bp):
TAAATAATATTATTTCAAATAAA
Found at i:1258048 original size:45 final size:44
Alignment explanation
Indices: 1257990--1258086 Score: 167
Period size: 45 Copynumber: 2.2 Consensus size: 44
1257980 AAAATAAATG
1257990 TTTTAAAATTAAATAATATTATTTCAAATAAATAAATAATATAA
1 TTTTAAAATTAAATAATATTATTTCAAATAAATAAATAATATAA
* *
1258034 TTTTAAATATTAAATAATATTATTTCAAATAAATTAATAATATGA
1 TTTTAAA-ATTAAATAATATTATTTCAAATAAATAAATAATATAA
1258079 TTTTAAAA
1 TTTTAAAA
1258087 ATATTTTTAA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
44 8 0.16
45 42 0.84
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (44 bp):
TTTTAAAATTAAATAATATTATTTCAAATAAATAAATAATATAA
Found at i:1260122 original size:38 final size:38
Alignment explanation
Indices: 1260063--1260168 Score: 157
Period size: 35 Copynumber: 2.9 Consensus size: 38
1260053 TCCCATTATA
*
1260063 ATTTTTC-AACAAACATCTACCAAACTTTGAAAAAACC
1 ATTTTTCAAACAAACATTTACCAAACTTTGAAAAAACC
*
1260100 ATTTTTCAAATAAACATTTACCAAACTTTG--AAAACC
1 ATTTTTCAAACAAACATTTACCAAACTTTGAAAAAACC
*
1260136 A-TTTTCAAAGAAACATTTACCAAACTTTGAAAA
1 ATTTTTCAAACAAACATTTACCAAACTTTGAAAA
1260169 CTATTTTTTC
Statistics
Matches: 63, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
35 27 0.43
36 7 0.11
37 9 0.14
38 20 0.32
ACGTcount: A:0.46, C:0.20, G:0.04, T:0.30
Consensus pattern (38 bp):
ATTTTTCAAACAAACATTTACCAAACTTTGAAAAAACC
Found at i:1260138 original size:21 final size:21
Alignment explanation
Indices: 1260114--1260174 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1260104 TTCAAATAAA
1260114 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
1260135 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
1260149 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
1260170 TATTT
1 CATTT
1260175 TTTCAAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 14
0.64 0.06 0.30
Matches are distributed among these distances:
14 5 0.17
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 9 0.30
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.33
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:1265273 original size:25 final size:24
Alignment explanation
Indices: 1265236--1265282 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
1265226 ATATTATACA
* *
1265236 AAATTAAATATAATATTATAATAT
1 AAATTAAATATAAAAATATAATAT
1265260 AAATATAAATATAAAAATATAAT
1 AAAT-TAAATATAAAAATATAAT
1265283 CAAACTGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (24 bp):
AAATTAAATATAAAAATATAATAT
Found at i:1269116 original size:28 final size:26
Alignment explanation
Indices: 1269080--1269134 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 26
1269070 ACATATGTAT
*
1269080 AAATATATTTATATAAAAATATAAATTTA
1 AAATATATTAAT-TAAAAA-AT-AATTTA
1269109 AAAT-TATTAATTAAAAAATAATTTA
1 AAATATATTAATTAAAAAATAATTTA
1269134 A
1 A
1269135 TTTCATCACA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 7 0.28
26 2 0.08
27 6 0.24
28 6 0.24
29 4 0.16
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (26 bp):
AAATATATTAATTAAAAAATAATTTA
Found at i:1272003 original size:30 final size:31
Alignment explanation
Indices: 1271936--1272005 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
1271926 AATTTTGAAT
* * *
1271936 TATCATTTTCATCTTAACTTGTCCCTAAACT
1 TATCATTTTCATCTCAACTTGACCCTAAACG
*
1271967 TATCATTTTCATCTCAACTT-ACCCTTTAA-G
1 TATCATTTTCATCTCAACTTGACCC-TAAACG
1271997 TATCATTTT
1 TATCATTTT
1272006 TGTCTTAGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 12 0.35
31 22 0.65
ACGTcount: A:0.26, C:0.24, G:0.03, T:0.47
Consensus pattern (31 bp):
TATCATTTTCATCTCAACTTGACCCTAAACG
Found at i:1276935 original size:15 final size:16
Alignment explanation
Indices: 1276899--1276941 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
1276889 ATACAAAACT
*
1276899 TTTGAATCATTCAATA
1 TTTGAATTATTCAATA
*
1276915 TTTGAATTATTCAA-C
1 TTTGAATTATTCAATA
1276930 TTTGAATTATTC
1 TTTGAATTATTC
1276942 TAAAATAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.49
Consensus pattern (16 bp):
TTTGAATTATTCAATA
Found at i:1280263 original size:2 final size:2
Alignment explanation
Indices: 1280256--1280286 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1280246 TTTTATTATT
1280256 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
1280287 TTTTCAAAAA
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:1280331 original size:26 final size:27
Alignment explanation
Indices: 1280273--1280336 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 27
1280263 ATATATATAT
* * **
1280273 ATATATATATATATTTTTCAAAAATAA
1 ATATTTATTTATATTTTAAAAAAATAA
* *
1280300 ATATTTTTTTATATTTTAAAAAAATCA
1 ATATTTATTTATATTTTAAAAAAATAA
1280327 A-ATTTATTTA
1 ATATTTATTTA
1280337 AAATTTTTAA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 8 0.27
27 22 0.73
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (27 bp):
ATATTTATTTATATTTTAAAAAAATAA
Found at i:1306279 original size:21 final size:21
Alignment explanation
Indices: 1306234--1306279 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
1306224 ATTAAGTTAA
*
1306234 AATT-TATTTCTAATAACTTT
1 AATTATATTTCTAATAAATTT
*
1306254 CATTATATTT-TAATAAATATT
1 AATTATATTTCTAATAAAT-TT
1306275 AATTA
1 AATTA
1306280 ATAAGTTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (21 bp):
AATTATATTTCTAATAAATTT
Found at i:1307627 original size:36 final size:38
Alignment explanation
Indices: 1307556--1307628 Score: 123
Period size: 38 Copynumber: 2.0 Consensus size: 38
1307546 TTTTAGTTAT
1307556 AACTAAAAATATTATAAAAATGTAACATTTTAAATTAC
1 AACTAAAAATATTATAAAAATGTAACATTTTAAATTAC
*
1307594 AACTGAAAATATTATAAAAAT-T-ACATTTTAAATTA
1 AACTAAAAATATTATAAAAATGTAACATTTTAAATTA
1307629 ATGTCAACCT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
36 13 0.38
37 1 0.03
38 20 0.59
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.36
Consensus pattern (38 bp):
AACTAAAAATATTATAAAAATGTAACATTTTAAATTAC
Found at i:1322181 original size:31 final size:31
Alignment explanation
Indices: 1322145--1322205 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
1322135 GTTAAATTTT
1322145 ATTTAATTGAACCCATCAAATAACTTCAATA
1 ATTTAATTGAACCCATCAAATAACTTCAATA
* *
1322176 ATTTAATTGAATCCATCAAATGACTTCAAT
1 ATTTAATTGAACCCATCAAATAACTTCAAT
1322206 GATAAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.43, C:0.18, G:0.05, T:0.34
Consensus pattern (31 bp):
ATTTAATTGAACCCATCAAATAACTTCAATA
Found at i:1325695 original size:12 final size:13
Alignment explanation
Indices: 1325674--1325712 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
1325664 TAACAACTGT
*
1325674 TATTCTCATCTTC
1 TATTATCATCTTC
*
1325687 TATTA-CATCTGC
1 TATTATCATCTTC
1325699 TATTATCATCTTC
1 TATTATCATCTTC
1325712 T
1 T
1325713 TCCTCTAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.21, C:0.26, G:0.03, T:0.51
Consensus pattern (13 bp):
TATTATCATCTTC
Found at i:1331227 original size:2 final size:2
Alignment explanation
Indices: 1331220--1331248 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1331210 GAAGTTTGTT
1331220 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 T
1331249 TAATTACAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1331432 original size:2 final size:2
Alignment explanation
Indices: 1331425--1331469 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1331415 AAAAGATTAA
1331425 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
1331467 AT A
1 AT A
1331470 ACAGCAGATG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1333386 original size:2 final size:2
Alignment explanation
Indices: 1333379--1333429 Score: 52
Period size: 2 Copynumber: 26.5 Consensus size: 2
1333369 TCAGGCCAGG
* * * *
1333379 TA TA TA TA TA TA TT TA AA T- TA AA TA TA TA AA TA T- 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
1333419 TA TA TA TA TA T
1 TA TA TA TA TA T
1333430 TTAATTTAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1333406 original size:17 final size:17
Alignment explanation
Indices: 1333384--1333440 Score: 51
Period size: 17 Copynumber: 3.1 Consensus size: 17
1333374 CCAGGTATAT
1333384 ATATATATTTAAATTAA
1 ATATATATTTAAATTAA
* *
1333401 ATATATAAATATTATATATAT
1 ATATAT--AT-TTAAAT-TAA
*
1333422 ATATATATTTAATTTAA
1 ATATATATTTAAATTAA
1333439 AT
1 AT
1333441 TAAATTTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
17 10 0.32
18 4 0.13
19 4 0.13
20 5 0.16
21 8 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATATATATTTAAATTAA
Done.