Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004216.1 Hibiscus syriacus cultivar Beakdansim tig00009236_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: 66009
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:1167 original size:3 final size:3
Alignment explanation
Indices: 1159--1191 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
1149 TATGACTACT
*
1159 TAA TAA TAA TAA -AA TAA TAA TAA AAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1192 TTAAACATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:1176 original size:11 final size:12
Alignment explanation
Indices: 1160--1250 Score: 62
Period size: 14 Copynumber: 7.2 Consensus size: 12
1150 ATGACTACTT
1160 AATAATAAT-AA
1 AATAATAATAAA
1171 AATAATAATAAA
1 AATAATAATAAA
1183 AATAATAATTTAAA
1 AATAATAA--TAAA
* *
1197 CATATTGGAATAAA
1 AATAAT--AATAAA
1211 AGATAATAAT-AA
1 A-ATAATAATAAA
*
1223 AAT-GTAATAAA
1 AATAATAATAAA
*
1234 TACTAATTAATAAA
1 -AATAA-TAATAAA
1248 AAT
1 AAT
1251 TAAATAACAA
Statistics
Matches: 62, Mismatches: 8, Indels: 18
0.70 0.09 0.20
Matches are distributed among these distances:
10 4 0.06
11 13 0.21
12 15 0.24
13 5 0.08
14 19 0.31
15 4 0.06
16 2 0.03
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (12 bp):
AATAATAATAAA
Found at i:1190 original size:23 final size:23
Alignment explanation
Indices: 1160--1248 Score: 72
Period size: 23 Copynumber: 3.6 Consensus size: 23
1150 ATGACTACTT
1160 AATAATAATAAAATAATAATAAA
1 AATAATAATAAAATAATAATAAA
*
1183 AATAATAATTTAAACATATTGGAATAAA
1 AATAATAA--TAAA-ATAAT--AATAAA
*
1211 AGATAATAATAAAAT-GTAATAAA
1 A-ATAATAATAAAATAATAATAAA
*
1234 TACTAATTAATAAAA
1 -AATAA-TAATAAAA
1249 ATTAAATAAC
Statistics
Matches: 55, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
23 17 0.31
24 9 0.16
25 5 0.09
26 6 0.11
27 4 0.07
28 7 0.13
29 7 0.13
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.29
Consensus pattern (23 bp):
AATAATAATAAAATAATAATAAA
Found at i:1232 original size:13 final size:13
Alignment explanation
Indices: 1159--1224 Score: 53
Period size: 13 Copynumber: 4.8 Consensus size: 13
1149 TATGACTACT
*
1159 TAATAATAATAAAA
1 TAATAATAA-AAGA
1173 TAATAATAAAA-A
1 TAATAATAAAAGA
* *
1185 TAATAATTTAAACA
1 TAATAA-TAAAAGA
*
1199 TATTGGAATAAAAGA
1 TAAT--AATAAAAGA
1214 TAATAATAAAA
1 TAATAATAAAA
1225 TGTAATAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
12 7 0.16
13 13 0.30
14 13 0.30
15 8 0.19
16 2 0.05
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.29
Consensus pattern (13 bp):
TAATAATAAAAGA
Found at i:3196 original size:73 final size:73
Alignment explanation
Indices: 3037--3644 Score: 804
Period size: 73 Copynumber: 8.4 Consensus size: 73
3027 GATGGAAATG
* * * ** * * *
3037 TTGAAAA-ATCATGCACTGAAGGGCTTACAGATGATCCAAAGGTTTTGAAAACATCAAAAATCTC
1 TTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTT---AAGATCAAAAAGCTC
*
3101 CCGAAGGCCTT
63 CCGAAGGCTTT
* * * * *
3112 TTAAAAACATCATGCACTGAAGGGCTTACAGATGGCCCTGAGGTTTTAAGATCAAAAAGCTCCCG
1 TTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCG
*
3177 AAGGCCTT
66 AAGGCTTT
* *
3185 TTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGACTTTAAGATCAAAAAGCTCCTG
1 TTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCG
3250 AAGGCTTT
66 AAGGCTTT
** * *
3258 TTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAATCTTTAAGATAAAAAAAACTCCC
1 TTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGAT-CAAAAAGCTCCC
3323 GAAGGCTTT
65 GAAGGCTTT
3332 TTGAAAACATCATGCACTGTAGGTCTTAC--A-GACCCTGAGGCTTTAAGATCAAAAAGCTCCCG
1 TTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCG
3394 AAGGC-TT
66 AAGGCTTT
* * *
3401 TTGAAAACATAATGCACTGTAGGTCTTACAGATGACCCTAAAGCTTTAAGATCAAAAAAGCTCCC
1 TTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATC-AAAAAGCTCCC
*
3466 AAAGGCTTT
65 GAAGGCTTT
* *
3475 TTGAAAACATCATGCACTATA-GTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGATCCCG
1 TTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCG
3539 AAGGCTTT
66 AAGGCTTT
*
3547 TTAAAAACATCATGC-CTGTAGGTCTTAC--ATGACCCTGAGGCTTTAAGATC-AAAAGCTCCCG
1 TTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCG
**
3608 AAGTTTTTT
66 AAG-GCTTT
* *
3617 TTGAAAACATCCTGCACTGCAGGTCTTA
1 TTGAAAACATCATGCACTGTAGGTCTTA
3645 TGGATGTTGG
Statistics
Matches: 481, Mismatches: 42, Indels: 24
0.88 0.08 0.04
Matches are distributed among these distances:
69 43 0.09
70 54 0.11
71 33 0.07
72 58 0.12
73 184 0.38
74 68 0.14
75 6 0.01
76 35 0.07
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.26
Consensus pattern (73 bp):
TTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCG
AAGGCTTT
Found at i:3433 original size:216 final size:216
Alignment explanation
Indices: 3092--3644 Score: 819
Period size: 216 Copynumber: 2.5 Consensus size: 216
3082 TGAAAACATC
* * * * *
3092 AAAAATCTCCCGAAGGCCTTTTAAAAACATCATGCACTGAAGGGCTTACAGATGGCCCTGAGGTT
1 AAAAAACTCCCGAAGGCTTTTTAAAAACATCATGCACTGTAGGTCTTACAGA---CCCTGAGGCT
3157 TTAAGATCAAAAAGCTCCCGAAGGCCTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACC
63 TTAAGATCAAAAAGCTCCCGAAGG-CTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACC
* ** *
3222 CT-GAGACTTTAAGATC-AAAAAGCTCCTGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTT
127 CTAAAG-CTTTAAGATCAAAAAAGCTCCCAAAGGCTTTTTGAAAACATCATGCACTATA-GTCTT
*
3285 ACAGATGACCCTGAATCTTTAAGATAA
190 ACAGATGACCCTGAAGCTTTAAGATAA
*
3312 AAAAAACTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGACCCTGAGGCTTTA
1 AAAAAACTCCCGAAGGCTTTTTAAAAACATCATGCACTGTAGGTCTTACAGACCCTGAGGCTTTA
*
3377 AGATCAAAAAGCTCCCGAAGGCTTTTGAAAACATAATGCACTGTAGGTCTTACAGATGACCCTAA
66 AGATCAAAAAGCTCCCGAAGGCTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTAA
3442 AGCTTTAAGATCAAAAAAGCTCCCAAAGGCTTTTTGAAAACATCATGCACTATAGTCTTACAGAT
131 AGCTTTAAGATCAAAAAAGCTCCCAAAGGCTTTTTGAAAACATCATGCACTATAGTCTTACAGAT
* *
3507 GACCCTGAGGCTTTAAGATCA
196 GACCCTGAAGCTTTAAGATAA
*
3528 AAAAGA-TCCCGAAGGCTTTTTAAAAACATCATGC-CTGTAGGTCTTACATGACCCTGAGGCTTT
1 AAAAAACTCCCGAAGGCTTTTTAAAAACATCATGCACTGTAGGTCTTACA-GACCCTGAGGCTTT
** * *
3591 AAGATC-AAAAGCTCCCGAAGTTTTTTTTGAAAACATCCTGCACTGCAGGTCTTA
65 AAGATCAAAAAGCTCCCGAAG--GCTTTTGAAAACATCATGCACTGTAGGTCTTA
3645 TGGATGTTGG
Statistics
Matches: 307, Mismatches: 21, Indels: 14
0.90 0.06 0.04
Matches are distributed among these distances:
214 28 0.09
215 47 0.15
216 112 0.36
217 73 0.24
220 47 0.15
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (216 bp):
AAAAAACTCCCGAAGGCTTTTTAAAAACATCATGCACTGTAGGTCTTACAGACCCTGAGGCTTTA
AGATCAAAAAGCTCCCGAAGGCTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTAA
AGCTTTAAGATCAAAAAAGCTCCCAAAGGCTTTTTGAAAACATCATGCACTATAGTCTTACAGAT
GACCCTGAAGCTTTAAGATAA
Found at i:3458 original size:143 final size:145
Alignment explanation
Indices: 3089--3644 Score: 786
Period size: 143 Copynumber: 3.9 Consensus size: 145
3079 TTTTGAAAAC
* * * * * *
3089 ATCAAAAATCTCCCGAAGGCCTTTTAAAAACATCATGCACTGAAGGGCTTACAGATGGCCCTGAG
1 ATCAAAAAGCTCCCGAAGGCTTTTTAAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAA
* *
3154 GTTTTAAGATCAAAAAGCTCCCGAAGGCCTTTTGAAAACATCATGCACTGTAGGTCTTACAGATG
66 GCTTTAAGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACA-ATG
*
3219 ACCCTGAGACTTTAAG
130 ACCCTGAGGCTTTAAG
* *
3235 ATCAAAAAGCTCCTGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAA
1 ATCAAAAAGCTCCCGAAGGCTTTTTAAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAA
* * *
3300 TCTTTAAGATAAAAAAAACTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTAC-A-G
66 GCTTTAAGAT-CAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAATG
3363 ACCCTGAGGCTTTAAG
130 ACCCTGAGGCTTTAAG
* * *
3379 ATCAAAAAGCTCCCGAAGGC-TTTTGAAAACATAATGCACTGTAGGTCTTACAGATGACCCTAAA
1 ATCAAAAAGCTCCCGAAGGCTTTTTAAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAA
* *
3443 GCTTTAAGATCAAAAAAGCTCCCAAAGGCTTTTTGAAAACATCATGCACTATA-GTCTTACAGAT
66 GCTTTAAGATC-AAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACA-AT
3507 GACCCTGAGGCTTTAAG
129 GACCCTGAGGCTTTAAG
* *
3524 ATCAAAAAGATCCCGAAGGCTTTTTAAAAACATCATGC-CTGTAGGTCTTAC--ATGACCCTGAG
1 ATCAAAAAGCTCCCGAAGGCTTTTTAAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAA
** * *
3586 GCTTTAAGATC-AAAAGCTCCCGAAGTTTTTTTTGAAAACATCCTGCACTGCAGGTCTTA
66 GCTTTAAGATCAAAAAGCTCCCGAAG-GCTTTTTGAAAACATCATGCACTGTAGGTCTTA
3645 TGGATGTTGG
Statistics
Matches: 369, Mismatches: 33, Indels: 19
0.88 0.08 0.05
Matches are distributed among these distances:
141 13 0.04
142 28 0.08
143 115 0.31
144 36 0.10
145 50 0.14
146 80 0.22
147 47 0.13
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (145 bp):
ATCAAAAAGCTCCCGAAGGCTTTTTAAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAA
GCTTTAAGATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAATGA
CCCTGAGGCTTTAAG
Found at i:5902 original size:149 final size:149
Alignment explanation
Indices: 5630--6112 Score: 776
Period size: 149 Copynumber: 3.2 Consensus size: 149
5620 GGCCTTCAAT
* *
5630 ATGCCCCAACATTGGCTGATACA-AGCGTTCAAAATGTGTCAATATTCCTGATTATGATTGAAAT
1 ATGCCCCAACATTTGCTGATACAGA-TGTT-AAAA-GTGTCAATATTCCTGATTATGATTGAAAT
* * * *
5694 GGGCTTT--G-ATGCTTCATCATTTGCTTCTTGTTAATTTGATCCTTCAAAATGTCCCACATGGA
63 GGGCTTTCAGCATGCTCCATCATTTGCTTCTTGTTAATCTGACCCTTCAAAATGCCCCACATGGA
5756 TCTGTCTGAAGTAACCTTTAAA
128 TCTGTCTGAAGTAACCTTTAAA
* * *
5778 ATACCCCAACATTTGTTGATATAGATGTTAAAAGTGTCAATATTCCTGATTATGATTGAAATGGG
1 ATGCCCCAACATTTGCTGATACAGATGTTAAAAGTGTCAATATTCCTGATTATGATTGAAATGGG
* *
5843 CTTTCAGCATGCTCCATCATTTGCTTCTTGTTAATCTGAGCCTTAAAAATGCCCCACATGGATCT
66 CTTTCAGCATGCTCCATCATTTGCTTCTTGTTAATCTGACCCTTCAAAATGCCCCACATGGATCT
*
5908 ATCTGAAGTAACCTTTAAA
131 GTCTGAAGTAACCTTTAAA
*
5927 ATGCCCCAACATTTGCTGATACAAATGTTAAAAGTGTCAATATTCCTGATTATGATTGAAATGGG
1 ATGCCCCAACATTTGCTGATACAGATGTTAAAAGTGTCAATATTCCTGATTATGATTGAAATGGG
*
5992 CTTTCAGCATGCTCCATTATTTGCTTCTTGTTAATCTGACCCTTCAAAATGCCCCACATGGATCT
66 CTTTCAGCATGCTCCATCATTTGCTTCTTGTTAATCTGACCCTTCAAAATGCCCCACATGGATCT
6057 GTCTGAAGTAACCTTTAAA
131 GTCTGAAGTAACCTTTAAA
*
6076 ATGCTCCAACATTTGCTGATACAGATGTTAAAAGTGT
1 ATGCCCCAACATTTGCTGATACAGATGTTAAAAGTGT
6113 GCTCAACATT
Statistics
Matches: 310, Mismatches: 21, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
146 36 0.12
147 4 0.01
148 23 0.07
149 247 0.80
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (149 bp):
ATGCCCCAACATTTGCTGATACAGATGTTAAAAGTGTCAATATTCCTGATTATGATTGAAATGGG
CTTTCAGCATGCTCCATCATTTGCTTCTTGTTAATCTGACCCTTCAAAATGCCCCACATGGATCT
GTCTGAAGTAACCTTTAAA
Found at i:14268 original size:28 final size:28
Alignment explanation
Indices: 14229--14296 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 28
14219 AATAAAATAA
** *
14229 AAATATTAAAAAAATAAT-A-TACATAT
1 AAATATTATGAAAATAATAAGTATATAT
14255 AAATATTATGAAAATAATAAGTATATAT
1 AAATATTATGAAAATAATAAGTATATAT
* *
14283 AAAAATTTTGAAAA
1 AAATATTATGAAAA
14297 GAAAGAATTA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
26 16 0.46
27 1 0.03
28 18 0.51
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.32
Consensus pattern (28 bp):
AAATATTATGAAAATAATAAGTATATAT
Found at i:14280 original size:26 final size:25
Alignment explanation
Indices: 14215--14281 Score: 68
Period size: 26 Copynumber: 2.7 Consensus size: 25
14205 ATTTAATACT
14215 TGAAAATAA-AATA-A-AAATATTA
1 TGAAAATAATAATATATAAATATTA
** *
14237 AAAAAATAATATACATATAAATATTA
1 TGAAAATAATA-ATATATAAATATTA
14263 TGAAAATAATAAGTATATA
1 TGAAAATAATAA-TATATA
14282 TAAAAATTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
22 7 0.21
23 1 0.03
24 2 0.06
25 2 0.06
26 22 0.65
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.30
Consensus pattern (25 bp):
TGAAAATAATAATATATAAATATTA
Found at i:15091 original size:148 final size:147
Alignment explanation
Indices: 14805--15076 Score: 377
Period size: 148 Copynumber: 1.8 Consensus size: 147
14795 ATTTATATTT
* *
14805 AAATAAGATATTTGTTTACTTAGAAATATCAGAAAAGGACTTCTAGGTGCTTTAAGACATCACAT
1 AAATAAGATATTTATTTACTTAGAAATATCAGAAAAAGACTTCTAGGTGCTTTAAGACATCACAT
* * *
14870 TTCTTAATATTTAAAAATAAATAAATATTAGTAAAACATTTTTCTAAAATTAATTAAAATAAATT
66 TTCTTAATATTAAAAAATAAATAAATATTAATAAAACATTTTTCTAAAAGTAATTAAAATAAATT
14935 AATATATAATTTATAAAA
131 -ATATATAATTTATAAAA
* * *
14953 AAATAGGATATTTATTTATTTA-AGAATATTAGAAAAAGACTTCTAGGTGCTTTAAGACATTC-C
1 AAATAAGATATTTATTTACTTAGA-AATATCAGAAAAAGACTTCTAGGTGCTTTAAGACA-TCAC
**
15016 ATTTCTTAATATTAAAAAATAAATAAATATTAAAATATAATTATTTTTCTTAAAAGTAATT
64 ATTTCTTAATATTAAAAAATAAATAAATATT--AATA-AAACATTTTTC-TAAAAGTAATT
15077 TATATGATTT
Statistics
Matches: 108, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
147 1 0.01
148 83 0.77
149 2 0.02
150 3 0.03
151 9 0.08
152 10 0.09
ACGTcount: A:0.47, C:0.07, G:0.08, T:0.39
Consensus pattern (147 bp):
AAATAAGATATTTATTTACTTAGAAATATCAGAAAAAGACTTCTAGGTGCTTTAAGACATCACAT
TTCTTAATATTAAAAAATAAATAAATATTAATAAAACATTTTTCTAAAAGTAATTAAAATAAATT
ATATATAATTTATAAAA
Found at i:15184 original size:36 final size:36
Alignment explanation
Indices: 15138--15216 Score: 149
Period size: 36 Copynumber: 2.2 Consensus size: 36
15128 TAAAAATAAG
15138 TAAATAAATATTATTTATTATATATATTTATATGAC
1 TAAATAAATATTATTTATTATATATATTTATATGAC
15174 TAAATAAATATTATTTATTATATATATTTATATGAC
1 TAAATAAATATTATTTATTATATATATTTATATGAC
*
15210 TACATAA
1 TAAATAA
15217 TAATAATAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.48
Consensus pattern (36 bp):
TAAATAAATATTATTTATTATATATATTTATATGAC
Found at i:15241 original size:12 final size:11
Alignment explanation
Indices: 15215--15246 Score: 55
Period size: 12 Copynumber: 2.8 Consensus size: 11
15205 ATGACTACAT
15215 AATAATAATAA
1 AATAATAATAA
15226 AATAATAATGAA
1 AATAATAAT-AA
15238 AATAATAAT
1 AATAATAAT
15247 TTAAACATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (11 bp):
AATAATAATAA
Found at i:16902 original size:3 final size:3
Alignment explanation
Indices: 16888--16953 Score: 71
Period size: 3 Copynumber: 21.7 Consensus size: 3
16878 ATATTTATTA
* * **
16888 AAT AAT AGT AAT AAT AAT ATAT AAT ATAT AAT AAT AAT GAT AAT TTT
1 AAT AAT AAT AAT AAT AAT A-AT AAT A-AT AAT AAT AAT AAT AAT AAT
16935 AAT AAT AAT AAT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AA
16954 AATGAAAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
2 2 0.04
3 44 0.85
4 6 0.12
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:19070 original size:21 final size:23
Alignment explanation
Indices: 19030--19080 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
19020 TTTTCCAGAA
*
19030 TGCTACAGTGGTATCGATACCC-
1 TGCTACAGTGGTACCGATACCCT
19052 TGCTACAGT-GTACCGATACCCT
1 TGCTACAGTGGTACCGATACCCT
19074 TGCTACA
1 TGCTACA
19081 ATAATTTTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 11 0.41
22 16 0.59
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (23 bp):
TGCTACAGTGGTACCGATACCCT
Found at i:19742 original size:22 final size:22
Alignment explanation
Indices: 19717--19778 Score: 115
Period size: 22 Copynumber: 2.8 Consensus size: 22
19707 GGCATATGAA
19717 ATTTGTCCCGAAGGACCTATGT
1 ATTTGTCCCGAAGGACCTATGT
*
19739 ATTTATCCCGAAGGACCTATGT
1 ATTTGTCCCGAAGGACCTATGT
19761 ATTTGTCCCGAAGGACCT
1 ATTTGTCCCGAAGGACCT
19779 CTATATATTG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (22 bp):
ATTTGTCCCGAAGGACCTATGT
Found at i:19802 original size:29 final size:29
Alignment explanation
Indices: 19758--19835 Score: 111
Period size: 29 Copynumber: 2.7 Consensus size: 29
19748 GAAGGACCTA
* *
19758 TGTATTTGTCCCGAAGGACCTCTATATAT
1 TGTATATGTCCCGAAGGACCTCTATATAC
* *
19787 TGTATATGTCCTGAAGGACCTCTGTATAC
1 TGTATATGTCCCGAAGGACCTCTATATAC
*
19816 TATATATGTCCCGAAGGACC
1 TGTATATGTCCCGAAGGACC
19836 GCGTAGACCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (29 bp):
TGTATATGTCCCGAAGGACCTCTATATAC
Found at i:20564 original size:21 final size:22
Alignment explanation
Indices: 20504--20564 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 22
20494 GTACCCTCTA
20504 TAGGGTATCGATACACCCTTAAC
1 TAGGGTATCGATAC-CCCTTAAC
* * *
20527 T-GAGGTATTGGTA-CCCTT-CC
1 TAG-GGTATCGATACCCCTTAAC
20547 TAGGGTATCGATACCCCT
1 TAGGGTATCGATACCCCT
20565 ATTGAAATCT
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
20 10 0.33
21 10 0.33
22 1 0.03
23 9 0.30
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (22 bp):
TAGGGTATCGATACCCCTTAAC
Found at i:21452 original size:39 final size:38
Alignment explanation
Indices: 21396--21469 Score: 121
Period size: 39 Copynumber: 1.9 Consensus size: 38
21386 ACGCTCATCA
* *
21396 GCTTTGTGCTCAGGGTAAGTCCTTACTACAATCTCCGTG
1 GCTTTATGCTCAAGGTAAGTCCTTACTACAA-CTCCGTG
21435 GCTTTATGCTCAAGGTAAGTCCTTACTACAACTCC
1 GCTTTATGCTCAAGGTAAGTCCTTACTACAACTCC
21470 TCTGGTTTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
38 4 0.12
39 29 0.88
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.32
Consensus pattern (38 bp):
GCTTTATGCTCAAGGTAAGTCCTTACTACAACTCCGTG
Found at i:21902 original size:8 final size:8
Alignment explanation
Indices: 21889--22723 Score: 1174
Period size: 8 Copynumber: 104.9 Consensus size: 8
21879 TGGTTTTCTG
21889 ATGTATGT
1 ATGTATGT
21897 ATGTATGT
1 ATGTATGT
21905 ATGTATGT
1 ATGTATGT
21913 ATGTATGT
1 ATGTATGT
*
21921 ATGCATGT
1 ATGTATGT
*
21929 ATGCATGT
1 ATGTATGT
*
21937 ATGCATGT
1 ATGTATGT
*
21945 ATGCATGT
1 ATGTATGT
*
21953 ATGCATGT
1 ATGTATGT
*
21961 ATGCATGT
1 ATGTATGT
*
21969 ATGCATGT
1 ATGTATGT
*
21977 ATGCATGT
1 ATGTATGT
*
21985 ATGCATGT
1 ATGTATGT
*
21993 ATGCATGT
1 ATGTATGT
*
22001 ATGCATGT
1 ATGTATGT
*
22009 ATGCATGT
1 ATGTATGT
*
22017 ATGCATGT
1 ATGTATGT
* *
22025 ATGCATGC
1 ATGTATGT
*
22033 ATGTATGC
1 ATGTATGT
*
22041 ATGTATGC
1 ATGTATGT
*
22049 ATGTATGC
1 ATGTATGT
*
22057 ATGCATGT
1 ATGTATGT
*
22065 ATGCATGT
1 ATGTATGT
*
22073 ATGCATGT
1 ATGTATGT
* *
22081 ATGCATGC
1 ATGTATGT
*
22089 ATGTATGA
1 ATGTATGT
22097 ATGTATGT
1 ATGTATGT
22105 ATGTATGT
1 ATGTATGT
22113 ATGTATGT
1 ATGTATGT
22121 ATGTATGT
1 ATGTATGT
22129 ATGTATGT
1 ATGTATGT
22137 ATGTATGT
1 ATGTATGT
22145 ATGTATGT
1 ATGTATGT
22153 ATGTATGT
1 ATGTATGT
22161 ATGTATGT
1 ATGTATGT
22169 ATGTATGT
1 ATGTATGT
*
22177 ATGTACGT
1 ATGTATGT
*
22185 ATGTACGT
1 ATGTATGT
*
22193 ATGTACGT
1 ATGTATGT
*
22201 ATGTACGT
1 ATGTATGT
*
22209 ATGTACGT
1 ATGTATGT
*
22217 ATGTACGT
1 ATGTATGT
*
22225 ATGTACGT
1 ATGTATGT
*
22233 ATGTACGT
1 ATGTATGT
*
22241 ATGTACGT
1 ATGTATGT
*
22249 ATGTACGT
1 ATGTATGT
*
22257 ATGTGTGT
1 ATGTATGT
*
22265 ATGTGTGT
1 ATGTATGT
*
22273 ATGTGTGT
1 ATGTATGT
*
22281 ATGTGTGT
1 ATGTATGT
*
22289 ATGTGTGT
1 ATGTATGT
*
22297 ATGTGTGT
1 ATGTATGT
*
22305 ATGTGTGT
1 ATGTATGT
*
22313 ATGTGTGT
1 ATGTATGT
22321 ATGTATGT
1 ATGTATGT
22329 ATG--TGT
1 ATGTATGT
22335 ATGTATGT
1 ATGTATGT
22343 ATGTATGT
1 ATGTATGT
22351 ATGTATGT
1 ATGTATGT
22359 ATGTATGT
1 ATGTATGT
*
22367 ATGTGTGT
1 ATGTATGT
22375 ATGTATGT
1 ATGTATGT
*
22383 ATGTGTGT
1 ATGTATGT
*
22391 ATGTGTGT
1 ATGTATGT
*
22399 ATGTGTGT
1 ATGTATGT
*
22407 ATGTGTGT
1 ATGTATGT
*
22415 ATGTGTGT
1 ATGTATGT
*
22423 ATGTGTGT
1 ATGTATGT
*
22431 ATGTGTGT
1 ATGTATGT
*
22439 ATGTGTGT
1 ATGTATGT
*
22447 ATGTGTGT
1 ATGTATGT
22455 ATG--TGT
1 ATGTATGT
22461 ATGTATGT
1 ATGTATGT
22469 ATGTATGT
1 ATGTATGT
22477 ATGTATGT
1 ATGTATGT
22485 ATGTATGT
1 ATGTATGT
22493 ATGTATGT
1 ATGTATGT
22501 ATGTATGT
1 ATGTATGT
22509 ATGTATGT
1 ATGTATGT
22517 ATGTATGT
1 ATGTATGT
22525 ATGTATGT
1 ATGTATGT
22533 ATGTATGT
1 ATGTATGT
22541 ATGTATGT
1 ATGTATGT
22549 ATGTATGT
1 ATGTATGT
22557 ATGTATGT
1 ATGTATGT
22565 ATGTATGT
1 ATGTATGT
22573 ATGTATGT
1 ATGTATGT
22581 ATGTATGT
1 ATGTATGT
22589 ATGTATGT
1 ATGTATGT
22597 ATGTATGT
1 ATGTATGT
22605 ATGTATGT
1 ATGTATGT
22613 ATGTATGT
1 ATGTATGT
22621 ATGTATGT
1 ATGTATGT
22629 ATGTATGT
1 ATGTATGT
22637 ATGTATGT
1 ATGTATGT
22645 ATGTATGT
1 ATGTATGT
22653 ATGTATGT
1 ATGTATGT
22661 ATGTATGT
1 ATGTATGT
22669 ATGTATGT
1 ATGTATGT
22677 ATGTATGT
1 ATGTATGT
22685 ATGTATGT
1 ATGTATGT
22693 ATGTATGT
1 ATGTATGT
22701 ATGTATGT
1 ATGTATGT
22709 ATGTATGT
1 ATGTATGT
22717 ATGTATG
1 ATGTATG
22724 AATCCTAATT
Statistics
Matches: 807, Mismatches: 16, Indels: 8
0.97 0.02 0.01
Matches are distributed among these distances:
6 12 0.01
8 795 0.99
ACGTcount: A:0.23, C:0.04, G:0.27, T:0.46
Consensus pattern (8 bp):
ATGTATGT
Found at i:33939 original size:46 final size:47
Alignment explanation
Indices: 33885--33974 Score: 146
Period size: 46 Copynumber: 1.9 Consensus size: 47
33875 TCTAATAAAT
*
33885 GCATGCGAACTAGATATCATGCGGTTAGG-TTTATTTTTTTGAACAA
1 GCATGCGAACTAGATATCATGCGGTTAGGATTTATTTTTGTGAACAA
* *
33931 GCATGCGAATTAGATATCATGTGGTTAGGATTTATTTTTGTGAA
1 GCATGCGAACTAGATATCATGCGGTTAGGATTTATTTTTGTGAA
33975 TAACAAAGCA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
46 27 0.68
47 13 0.32
ACGTcount: A:0.28, C:0.10, G:0.23, T:0.39
Consensus pattern (47 bp):
GCATGCGAACTAGATATCATGCGGTTAGGATTTATTTTTGTGAACAA
Found at i:43660 original size:16 final size:17
Alignment explanation
Indices: 43641--43679 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
43631 GAAAAAATGA
43641 AAAAATGA-GAAAAAAC
1 AAAAATGAGGAAAAAAC
43657 AAAAATGATGGAAAAAAC
1 AAAAATGA-GGAAAAAAC
43675 AAAAA
1 AAAAA
43680 GAAAGAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 8 0.38
18 13 0.62
ACGTcount: A:0.74, C:0.05, G:0.13, T:0.08
Consensus pattern (17 bp):
AAAAATGAGGAAAAAAC
Found at i:43661 original size:18 final size:18
Alignment explanation
Indices: 43625--43679 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
43615 AAGAAGAAAT
**
43625 AAAA-GAGAAAAAATGAA
1 AAAATGAGAAAAAACAAA
43642 AAAATGAGAAAAAACAAA
1 AAAATGAGAAAAAACAAA
*
43660 AATGATG-GAAAAAACAAA
1 AA-AATGAGAAAAAACAAA
43678 AA
1 AA
43680 GAAAGAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
17 4 0.12
18 26 0.79
19 3 0.09
ACGTcount: A:0.75, C:0.04, G:0.15, T:0.07
Consensus pattern (18 bp):
AAAATGAGAAAAAACAAA
Found at i:43687 original size:17 final size:18
Alignment explanation
Indices: 43648--43689 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
43638 TGAAAAAATG
*
43648 AGAAAAAACAAAAATGAT
1 AGAAAAAACAAAAATGAA
*
43666 GGAAAAAACAAAAA-GAA
1 AGAAAAAACAAAAATGAA
43683 AGAAAAA
1 AGAAAAA
43690 TAAGAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.76, C:0.05, G:0.14, T:0.05
Consensus pattern (18 bp):
AGAAAAAACAAAAATGAA
Found at i:43689 original size:18 final size:18
Alignment explanation
Indices: 43641--43700 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
43631 GAAAAAATGA
43641 AAAAATG-AG-AAAAAAC
1 AAAAATGAAGAAAAAAAC
* *
43657 AAAAATGATGGAAAAAAC
1 AAAAATGAAGAAAAAAAC
*
43675 AAAAA-GAAAGAAAAATAAG
1 AAAAATG-AAGAAAAA-AAC
43694 AAAAATG
1 AAAAATG
43701 GAAAAGGGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
16 7 0.20
17 2 0.06
18 18 0.51
19 7 0.20
20 1 0.03
ACGTcount: A:0.73, C:0.03, G:0.15, T:0.08
Consensus pattern (18 bp):
AAAAATGAAGAAAAAAAC
Found at i:43712 original size:18 final size:19
Alignment explanation
Indices: 43691--43726 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
43681 AAAGAAAAAT
*
43691 AAGA-AAAATGGAAAAGGG
1 AAGAGAAAATGAAAAAGGG
43709 AAGAGAAAATGAAAAAGG
1 AAGAGAAAATGAAAAAGG
43727 AAAAATGGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.64, C:0.00, G:0.31, T:0.06
Consensus pattern (19 bp):
AAGAGAAAATGAAAAAGGG
Found at i:43728 original size:18 final size:18
Alignment explanation
Indices: 43691--43739 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
43681 AAAGAAAAAT
*
43691 AAGAAAAATGGAAAAGGG
1 AAGAAAAATGGAAAAAGG
43709 AAGAGAAAAT-GAAAAA-G
1 AAGA-AAAATGGAAAAAGG
43726 --GAAAAATGGAAAAA
1 AAGAAAAATGGAAAAA
43740 AAGAGAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
14 5 0.18
15 8 0.29
17 1 0.04
18 9 0.32
19 5 0.18
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.06
Consensus pattern (18 bp):
AAGAAAAATGGAAAAAGG
Found at i:43747 original size:18 final size:18
Alignment explanation
Indices: 43692--43747 Score: 50
Period size: 14 Copynumber: 3.3 Consensus size: 18
43682 AAGAAAAATA
*
43692 AGAAAAATGGAAAAGGGAAG
1 AGAAAAATGGAAAA--AAAG
43712 AG-AAAAT-G--AAAAAG
1 AGAAAAATGGAAAAAAAG
43726 -GAAAAATGGAAAAAAAG
1 AGAAAAATGGAAAAAAAG
43743 AGAAA
1 AGAAA
43748 TAAAAGGAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 12
0.70 0.02 0.28
Matches are distributed among these distances:
13 1 0.03
14 8 0.27
15 1 0.03
16 2 0.07
17 6 0.20
18 5 0.17
19 5 0.17
20 2 0.07
ACGTcount: A:0.68, C:0.00, G:0.27, T:0.05
Consensus pattern (18 bp):
AGAAAAATGGAAAAAAAG
Found at i:45598 original size:55 final size:55
Alignment explanation
Indices: 45066--45624 Score: 600
Period size: 55 Copynumber: 10.5 Consensus size: 55
45056 GAAGCAAATT
* * *
45066 CGTTTGTTGAAGA---TT-GAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACA
1 CGTTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACA
* * * *
45117 AGTTTGTCGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACA
* * * *
45168 AGTTCGTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACA
* * *
45219 CGTTTATTGAAGA----TCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACC
1 CGTTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACA
* * *
45270 CGTTTGTTGAAGATTATTCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGACA
1 CGTTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACA
* * * *
45325 CGTTTGTTGAAGATTGTTCAAGTCTTATACTCTCTGAAAGAATAGGGAGCGGACC
1 CGTTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACA
* * *
45380 CGTTTGTTGAAGATTATTCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGACA
1 CGTTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACA
* ** *
45435 CGTTTGTTGAAGATTGTTCAAGTCTTATACTCTCTGAATAAATAGAGAGCAGACA
1 CGTTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACA
* * * *
45490 CATTT-TATGAAGATTGTTCAAGTCTTATACTCTCTGAATGAATAGAGAGCAGACA
1 CGTTTGT-TGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACA
* * *
45545 CATTT-TATGAAGATTGTTCGAGTCTTATACT-TCCTGAAGGAATAGGGAACAGACT
1 CGTTTGT-TGAAGATTGTTCGAGTCTTATACTCT-CTGAAGGAATAGGGAGCAGACA
* * *
45600 CGTCAT-TTGAAGATTTTTCAAGTCT
1 CGT-TTGTTGAAGATTGTTCGAGTCT
45625 CACTTATCCC
Statistics
Matches: 456, Mismatches: 44, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
50 1 0.00
51 153 0.34
54 2 0.00
55 298 0.65
56 2 0.00
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (55 bp):
CGTTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACA
Found at i:48928 original size:40 final size:41
Alignment explanation
Indices: 48849--48928 Score: 99
Period size: 43 Copynumber: 1.9 Consensus size: 41
48839 GTAACTAATG
* **
48849 AATAAAATAATAATAAATTAAAGATGTTTTTATTCTAATTTCT
1 AATAAAATAATAATAAACTAAAGA--TTAATATTCTAATTTCT
*
48892 AATAAAATAATAATAAACTAAAGA-TAATATTTTAATT
1 AATAAAATAATAATAAACTAAAGATTAATATTCTAATT
48929 CTATCTTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
40 10 0.30
43 23 0.70
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.40
Consensus pattern (41 bp):
AATAAAATAATAATAAACTAAAGATTAATATTCTAATTTCT
Found at i:50378 original size:21 final size:20
Alignment explanation
Indices: 50354--50396 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
50344 TTTTTTCCTT
*
50354 AATCGAGAATATTATACTTGA
1 AATCAAGAA-ATTATACTTGA
*
50375 AATCAAGTAATTATACTTGA
1 AATCAAGAAATTATACTTGA
50395 AA
1 AA
50397 GCAGCTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.33
Consensus pattern (20 bp):
AATCAAGAAATTATACTTGA
Found at i:51239 original size:53 final size:52
Alignment explanation
Indices: 51165--51266 Score: 150
Period size: 53 Copynumber: 1.9 Consensus size: 52
51155 ATTCACATCT
* *
51165 TTTGTTTTTCATTGACATATCACCTAAAATCAAATCAAGTAAAATAATATTC
1 TTTGTTTTTCACTGAAATATCACCTAAAATCAAATCAAGTAAAATAATATTC
* * *
51217 TTTGCTTTTTCACTGAAATATCACCTCAAATCAGATCAAGTAATATAATA
1 TTTG-TTTTTCACTGAAATATCACCTAAAATCAAATCAAGTAAAATAATA
51267 ATTTTAAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
52 4 0.09
53 40 0.91
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (52 bp):
TTTGTTTTTCACTGAAATATCACCTAAAATCAAATCAAGTAAAATAATATTC
Found at i:51402 original size:18 final size:18
Alignment explanation
Indices: 51325--51558 Score: 138
Period size: 18 Copynumber: 12.6 Consensus size: 18
51315 GTAATACAAT
*
51325 AATTAGGGTTTCTCAGTG
1 AATTAGGGTTTCTTAGTG
* *
51343 AATTAAGGTTTCTCAGTG
1 AATTAGGGTTTCTTAGTG
* * * *
51361 AATTAAGATTTTTTTGTG
1 AATTAGGGTTTCTTAGTG
51379 AATTAGGGTTTCTTAGTG
1 AATTAGGGTTTCTTAGTG
*
51397 AATTAGGAG-TT-TTAATG
1 AATTAGG-GTTTCTTAGTG
* * *
51414 AATTAGGTTTTTTTTTTGTG
1 AATTAGG--GTTTCTTAGTG
* *
51434 AA-AAGGGTTT-TTTGTG
1 AATTAGGGTTTCTTAGTG
51450 AATTAGGGTTT-TTAGTG
1 AATTAGGGTTTCTTAGTG
** * *
51467 AATTAAGTTTTTTTTTAATTG
1 AATT-AG-GGTTTCTT-AGTG
*
51488 AATTAGGGTTCAACGTATAGTATTG
1 AATTAGGGTT--TC-T-TAG---TG
*
51513 AATTAAGGTTTCTTAGTG
1 AATTAGGGTTTCTTAGTG
51531 AATTAGGGTTT-TTAGTG
1 AATTAGGGTTTCTTAGTG
51548 AATTAGGGTTT
1 AATTAGGGTTT
51559 AAAATCAAAT
Statistics
Matches: 171, Mismatches: 29, Indels: 33
0.73 0.12 0.14
Matches are distributed among these distances:
16 8 0.05
17 48 0.28
18 68 0.40
19 11 0.06
20 10 0.06
21 10 0.06
22 3 0.02
23 2 0.01
25 11 0.06
ACGTcount: A:0.26, C:0.03, G:0.24, T:0.47
Consensus pattern (18 bp):
AATTAGGGTTTCTTAGTG
Found at i:51427 original size:54 final size:53
Alignment explanation
Indices: 51325--51497 Score: 190
Period size: 54 Copynumber: 3.2 Consensus size: 53
51315 GTAATACAAT
* * *
51325 AATTAGGGTTTCTCAGTGAATTAAGGTTTCTCAGTGAATTAAG-ATTTTTTTGTG
1 AATTAGGGTTTCTTAGTGAATTAGGGTTT-T-AGTGAATTAAGTTTTTTTTTGTG
* *
51379 AATTAGGGTTTCTTAGTGAATTAGGAGTTTTAATGAATTAGGTTTTTTTTTTGTG
1 AATTAGGGTTTCTTAGTGAATTAGG-GTTTTAGTGAATTAAG-TTTTTTTTTGTG
* * *
51434 AA-AAGGGTTT-TTTGTGAATTAGGGTTTTTAGTGAATTAAGTTTTTTTTTAATTG
1 AATTAGGGTTTCTTAGTGAATTAGGG-TTTTAGTGAATTAAGTTTTTTTTT--GTG
51488 AATTAGGGTT
1 AATTAGGGTT
51498 CAACGTATAG
Statistics
Matches: 101, Mismatches: 11, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
52 10 0.10
53 34 0.34
54 35 0.35
55 22 0.22
ACGTcount: A:0.25, C:0.03, G:0.23, T:0.49
Consensus pattern (53 bp):
AATTAGGGTTTCTTAGTGAATTAGGGTTTTAGTGAATTAAGTTTTTTTTTGTG
Found at i:51444 original size:16 final size:17
Alignment explanation
Indices: 51425--51469 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
51415 ATTAGGTTTT
51425 TTTTTTGTGAA-AAGGG
1 TTTTTTGTGAATAAGGG
*
51441 TTTTTTGTGAATTAGGG
1 TTTTTTGTGAATAAGGG
*
51458 TTTTTAGTGAAT
1 TTTTTTGTGAAT
51470 TAAGTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 11 0.42
17 15 0.58
ACGTcount: A:0.22, C:0.00, G:0.27, T:0.51
Consensus pattern (17 bp):
TTTTTTGTGAATAAGGG
Found at i:51451 original size:53 final size:55
Alignment explanation
Indices: 51329--51482 Score: 174
Period size: 53 Copynumber: 2.9 Consensus size: 55
51319 TACAATAATT
* * * * * *
51329 AGGGTTTCTCAGTGAATTAAGGTTTCTCAGTGAATTAAG--ATTTTTTTGTGAATT
1 AGGGTTTCTTAGTGAATTAGGGTTT-TTAATGAATTAAGTTTTTTTTTTGTGAATA
*
51383 AGGGTTTCTTAGTGAATTAGGAG-TTTTAATGAATTAGGTTTTTTTTTTGTGAA-A
1 AGGGTTTCTTAGTGAATTAGG-GTTTTTAATGAATTAAGTTTTTTTTTTGTGAATA
* *
51437 AGGGTTT-TTTGTGAATTAGGGTTTTTAGTGAATTAAGTTTTTTTTT
1 AGGGTTTCTTAGTGAATTAGGGTTTTTAATGAATTAAGTTTTTTTTT
51483 AATTGAATTA
Statistics
Matches: 86, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
52 1 0.01
53 44 0.51
54 28 0.33
55 13 0.15
ACGTcount: A:0.24, C:0.03, G:0.23, T:0.49
Consensus pattern (55 bp):
AGGGTTTCTTAGTGAATTAGGGTTTTTAATGAATTAAGTTTTTTTTTTGTGAATA
Found at i:52029 original size:167 final size:167
Alignment explanation
Indices: 51573--52101 Score: 716
Period size: 167 Copynumber: 3.2 Consensus size: 167
51563 TCAAATACAA
* * * *
51573 TACAATAATAATTTCATATGATGAAGAATCTAAACTATTCATGTCCTTTTTTCAGTGAAATGTCC
1 TACAATAATAATTTCAAATGATGAAGAATCTGAACTATTCATGTCATTTTTTCAGTGAAATGTCA
* * * * * *
51638 CCTCAAATAAAAATCGGTACAATAATAATTTCAAATGACAGATAATCTTAACTATTTATGTCAAT
66 CCTCAAATCAGAACCGGTACAATAATAATTTCAAATGACAGATAATCTTAACTATTCATATCATT
* * *
51703 TTCTTTTCAGTCAATTATCACATCAAATTAGATACGG
131 TTCTTTTCAATCAATTACCACATCAAATCAGATACGG
* * *
51740 TAAAATAATAATTTCAAATGATGAAGAATATGAACTATTCATGTCAATTTTTTCAGTGAATTGTC
1 TACAATAATAATTTCAAATGATGAAGAATCTGAACTATTCATGTC-ATTTTTTCAGTGAAATGTC
* * * *
51805 ACCTCAAATCAGAACTGGTACAATAATAATTTCAAATGACACATAATCTTTACTATTCACATCAT
65 ACCTCAAATCAGAACCGGTACAATAATAATTTCAAATGACAGATAATCTTAACTATTCATATCAT
* *
51870 TTTCTTTTCAATTAATTACCACTTCAAATCAGATACGG
130 TTTCTTTTCAATCAATTACCACATCAAATCAGATACGG
* **
51908 TACAATATTAATTTCAAATGACAAAGAATCTGAACTATTCATGTCATTTTTTCAGTGAAATGTCA
1 TACAATAATAATTTCAAATGATGAAGAATCTGAACTATTCATGTCATTTTTTCAGTGAAATGTCA
* * *
51973 CCTCAAATCAGAACCGGTATAATAATAATTTCAAATGATAGAGAATCTTAACTATTCATATCATT
66 CCTCAAATCAGAACCGGTACAATAATAATTTCAAATGACAGATAATCTTAACTATTCATATCATT
* ** * * * **
52038 TTCTTTTCAATCACTTGTCACATCAAAACATAAACAA
131 TTCTTTTCAATCAATTACCACATCAAATCAGATACGG
52075 TACAATAATAATTTCAAATGATAGAAG
1 TACAATAATAATTTCAAATGAT-GAAG
52102 TTGGCCATGA
Statistics
Matches: 312, Mismatches: 48, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
167 165 0.53
168 147 0.47
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (167 bp):
TACAATAATAATTTCAAATGATGAAGAATCTGAACTATTCATGTCATTTTTTCAGTGAAATGTCA
CCTCAAATCAGAACCGGTACAATAATAATTTCAAATGACAGATAATCTTAACTATTCATATCATT
TTCTTTTCAATCAATTACCACATCAAATCAGATACGG
Found at i:52099 original size:85 final size:84
Alignment explanation
Indices: 51573--52095 Score: 488
Period size: 85 Copynumber: 6.2 Consensus size: 84
51563 TCAAATACAA
* * * * * *
51573 TACAATAATAATTTCATATGA-TGAAGAATCTAAACTATTCATGTC-CTT-TTTTCAGTGAAATG
1 TACAATAATAATTTCAAATGACAG-AGAATCTTAACTATTCATGTCATTTCTTTTCAGTCAATTG
* * *
51635 TCCCCTCAAAT-AAAAATCGG
65 TCACATCAAATCAGAAA-CGG
* * *
51655 TACAATAATAATTTCAAATGACAGATAATCTTAACTATTTATGTCAATTTCTTTTCAGTCAATTA
1 TACAATAATAATTTCAAATGACAGAGAATCTTAACTATTCATGTC-ATTTCTTTTCAGTCAATTG
* *
51720 TCACATCAAATTAGATACGG
65 TCACATCAAATCAGAAACGG
* * * * * *
51740 TAAAATAATAATTTCAAATGA-TGAAGAATATGAACTATTCATGTCAATT-TTTTCAGTGAATTG
1 TACAATAATAATTTCAAATGACAG-AGAATCTTAACTATTCATGTCATTTCTTTTCAGTCAATTG
*
51803 TCACCTCAAATCAG-AACTGG
65 TCACATCAAATCAGAAAC-GG
* * * ** * * *
51823 TACAATAATAATTTCAAATGACACATAATCTTTACTATTCACATCATTTTCTTTTCAATTAATTA
1 TACAATAATAATTTCAAATGACAGAGAATCTTAACTATTCATGTCA-TTTCTTTTCAGTCAATTG
* * *
51888 CCACTTCAAATCAGATACGG
65 TCACATCAAATCAGAAACGG
* * * * *
51908 TACAATATTAATTTCAAATGACAAAGAATCTGAACTATTCATGTCA-TT-TTTTCAGTGAAATGT
1 TACAATAATAATTTCAAATGACAGAGAATCTTAACTATTCATGTCATTTCTTTTCAGTCAATTGT
* *
51971 CACCTCAAATCAGAACCGG
66 CACATCAAATCAGAAACGG
* * * * *
51990 TATAATAATAATTTCAAATGATAGAGAATCTTAACTATTCATATCATTTTCTTTTCAATCACTTG
1 TACAATAATAATTTCAAATGACAGAGAATCTTAACTATTCATGTCA-TTTCTTTTCAGTCAATTG
* * **
52055 TCACATCAAAACATAAACAA
65 TCACATCAAATCAGAAACGG
52075 TACAATAATAATTTCAAATGA
1 TACAATAATAATTTCAAATGA
52096 TAGAAGTTGG
Statistics
Matches: 354, Mismatches: 73, Indels: 25
0.78 0.16 0.06
Matches are distributed among these distances:
82 106 0.30
83 65 0.18
84 10 0.03
85 168 0.47
86 5 0.01
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (84 bp):
TACAATAATAATTTCAAATGACAGAGAATCTTAACTATTCATGTCATTTCTTTTCAGTCAATTGT
CACATCAAATCAGAAACGG
Found at i:53488 original size:41 final size:41
Alignment explanation
Indices: 53443--53521 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 41
53433 TGTAACGTTG
* *
53443 TGTAATGTAGTCTCGTGTAGTCTAGGAGTTAATGCTTCTAA
1 TGTAATGCAATCTCGTGTAGTCTAGGAGTTAATGCTTCTAA
* * *
53484 TGTAATGCAATGTCGTGTATTGTAGGAGTTAATGCTTC
1 TGTAATGCAATCTCGTGTAGTCTAGGAGTTAATGCTTC
53522 CAAACTTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.24, C:0.11, G:0.25, T:0.39
Consensus pattern (41 bp):
TGTAATGCAATCTCGTGTAGTCTAGGAGTTAATGCTTCTAA
Found at i:59313 original size:20 final size:22
Alignment explanation
Indices: 59280--59323 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
59270 TGTATAGCAT
*
59280 AATATATGTAATAGTTTTTGAA
1 AATATATGTAATAGGTTTTGAA
59302 AATATA-GT-ATAGGTTTTGAA
1 AATATATGTAATAGGTTTTGAA
59322 AA
1 AA
59324 CGTATTTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.62
21 2 0.10
22 6 0.29
ACGTcount: A:0.43, C:0.00, G:0.16, T:0.41
Consensus pattern (22 bp):
AATATATGTAATAGGTTTTGAA
Found at i:59333 original size:13 final size:13
Alignment explanation
Indices: 59315--59341 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
59305 ATAGTATAGG
59315 TTTTGAAAACGTA
1 TTTTGAAAACGTA
59328 TTTTGAAAACGTA
1 TTTTGAAAACGTA
59341 T
1 T
59342 ATATATAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (13 bp):
TTTTGAAAACGTA
Found at i:59333 original size:33 final size:31
Alignment explanation
Indices: 59295--59409 Score: 117
Period size: 32 Copynumber: 3.5 Consensus size: 31
59285 ATGTAATAGT
59295 TTTTGAAAATATAGTATAGGTTTTGAAAACGTA
1 TTTTGAAAATATA-TATA-GTTTTGAAAACGTA
59328 TTTTGAAAACGTATATATATAGTTTTGAAAACG--
1 TTTTG-AAA---ATATATATAGTTTTGAAAACGTA
*
59361 TTTTGAAAAAATATAATATAGTTTTGAAAGCGTA
1 TTTTG--AAAATAT-ATATAGTTTTGAAAACGTA
*
59395 TTTTGAAAACATATA
1 TTTTGAAAATATATA
59410 ATATATAGTT
Statistics
Matches: 72, Mismatches: 2, Indels: 18
0.78 0.02 0.20
Matches are distributed among these distances:
31 7 0.10
32 22 0.31
33 10 0.14
34 12 0.17
35 12 0.17
36 4 0.06
37 5 0.07
ACGTcount: A:0.42, C:0.04, G:0.15, T:0.39
Consensus pattern (31 bp):
TTTTGAAAATATATATAGTTTTGAAAACGTA
Found at i:59476 original size:36 final size:36
Alignment explanation
Indices: 59304--59499 Score: 179
Period size: 36 Copynumber: 5.5 Consensus size: 36
59294 TTTTTGAAAA
*
59304 TATAGTATAGGTTTTGAAAACGTATTTTGAAAACGTA-
1 TATA-TATAGTTTTTGAAAACG-ATTTTGAAAACGTAT
**
59341 TATATATAG-TTTTGAAAACG-TTTTGAAAAAATA-
1 TATATATAGTTTTTGAAAACGATTTTGAAAACGTAT
* *
59374 TA-ATATAG-TTTTGAAAGCGTATTTTGAAAACATAT
1 TATATATAGTTTTTGAAAACG-ATTTTGAAAACGTAT
* * * * *
59409 AATATATAGTTTTTTAAAATGGTTTTGAAAATGTAT
1 TATATATAGTTTTTGAAAACGATTTTGAAAACGTAT
* *
59445 TATATATAGTTTTTAAAAACGATTTTGAAAATGTAT
1 TATATATAGTTTTTGAAAACGATTTTGAAAACGTAT
* * * *
59481 AATATGTGGTTTTTAAAAA
1 TATATATAGTTTTTGAAAA
59500 AAAAAGGTTT
Statistics
Matches: 136, Mismatches: 18, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
32 16 0.12
33 13 0.10
34 12 0.09
35 12 0.09
36 71 0.52
37 12 0.09
ACGTcount: A:0.41, C:0.03, G:0.14, T:0.42
Consensus pattern (36 bp):
TATATATAGTTTTTGAAAACGATTTTGAAAACGTAT
Found at i:59559 original size:38 final size:37
Alignment explanation
Indices: 59507--59606 Score: 114
Period size: 38 Copynumber: 2.6 Consensus size: 37
59497 AAAAAAAAGG
*
59507 TTTTTGGAAAACATATATA-ATTTAATTTTTGAAAACGTA
1 TTTTT-GAAAACATATATATATATAATTTTTGAAAA--TA
* *
59546 TTTTTGAAAACATATA-ATATATGATTTTTTAAAATA
1 TTTTTGAAAACATATATATATATAATTTTTGAAAATA
*
59582 TTTTTAAAAACATATATATTATATA
1 TTTTTGAAAACATATATA-TATATA
59607 TATAGTTTCT
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
36 17 0.32
37 2 0.04
38 29 0.55
39 5 0.09
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (37 bp):
TTTTTGAAAACATATATATATATAATTTTTGAAAATA
Found at i:59584 original size:36 final size:35
Alignment explanation
Indices: 59328--59607 Score: 115
Period size: 36 Copynumber: 7.7 Consensus size: 35
59318 TGAAAACGTA
* * * **
59328 TTTTGAAAACGTAT-ATATATAGTTTTGAAAA-CG
1 TTTTGAAAACATATAATATATATTTTTTAAAATAT
* * * *
59361 TTTTGAAAAAATAT-A-ATATAGTTTTGAAAGCGTA-
1 TTTTGAAAACATATAATATATATTTTTTAAA--ATAT
**
59395 TTTTGAAAACATATAATATATAGTTTTTTAAAATGG
1 TTTTGAAAACATATAATATATA-TTTTTTAAAATAT
** * * *
59431 TTTTGAAAATGTATTATATATAGTTTTTAAAA-ACGA
1 TTTTGAAAACATATAATATATATTTTTTAAAATA--T
** * * * *
59467 TTTTGAAAATGTATAATATGTGGTTTTTAAAAAAAAAAGGT
1 TTTTGAAAACATATAATATAT-ATTTTT---TAAAATA--T
* *
59508 TTTTGGAAAACATAT-ATAATTTAATTTTTGAAAACGTAT
1 TTTT-GAAAACATATAAT-ATAT-ATTTTTTAAAA--TAT
59547 TTTTGAAAACATATAATATATGATTTTTTAAAATAT
1 TTTTGAAAACATATAATATAT-ATTTTTTAAAATAT
*
59583 TTTTAAAAACATATATATTATATAT
1 TTTTGAAAACATATA-A-TATATAT
59608 ATAGTTTCTT
Statistics
Matches: 193, Mismatches: 33, Indels: 38
0.73 0.12 0.14
Matches are distributed among these distances:
32 14 0.07
33 13 0.07
34 13 0.07
35 11 0.06
36 60 0.31
37 14 0.07
38 28 0.15
39 11 0.06
40 4 0.02
41 9 0.05
42 16 0.08
ACGTcount: A:0.43, C:0.03, G:0.11, T:0.43
Consensus pattern (35 bp):
TTTTGAAAACATATAATATATATTTTTTAAAATAT
Found at i:61033 original size:5 final size:5
Alignment explanation
Indices: 61025--61058 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
61015 AATTTAATAC
* *
61025 ATTTT ATTTT GTTTT GTTTT ATTTT ATTTT ATTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTT
61059 AACATTAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (5 bp):
ATTTT
Found at i:64745 original size:24 final size:24
Alignment explanation
Indices: 64718--64781 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 24
64708 TCAAGGAGAC
*
64718 TCATCTGTTGCAAAAGCACAAGCT
1 TCATCTGCTGCAAAAGCACAAGCT
* * *
64742 TCATATACTGCAAAGGCACAAGCT
1 TCATCTGCTGCAAAAGCACAAGCT
*
64766 TCATCGGCTGCAAAAG
1 TCATCTGCTGCAAAAG
64782 TAAAATCTTC
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (24 bp):
TCATCTGCTGCAAAAGCACAAGCT
Done.