Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008074.1 Hibiscus syriacus cultivar Beakdansim tig00110576_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: 348028
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:123100 original size:142 final size:137
Alignment explanation
Indices: 122912--123256 Score: 516
Period size: 142 Copynumber: 2.5 Consensus size: 137
122902 GAAATGAAAA
*
122912 TCGCAATGCG-TTTATAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGAT
1 TCGCATTGCGATTT-TAATTTCGCATTGCGATT-T-TCGTTGCGATTTTCATTTCGCATTGCGAT
*
122976 TTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
63 TTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
*
123041 TGCGATTTTCATT
128 TGCGA--TTC-TC
123054 TCGCATTGCGATTTTAATTTCGCATTGCGATTCTGTCGTTGCGATTTTCATTTCGCATTGCGATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATT-T-TCGTTGCGATTTTCATTTCGCATTGCGATT
123119 TTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATT
64 TTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATT
123184 GCGATTCTC
129 GCGATTCTC
* * *
123193 TCG--TTGCGATTTTCATTTCCGCATTGCGATTTTCATGTTGGGATTTTCATTTCGCGTTGCGAT
1 TCGCATTGCGATTTTAATTT-CGCATTGCGATTTTC--GTTGCGATTTTCATTTCGCATTGCGAT
123256 T
63 T
123257 GTATTTTCCG
Statistics
Matches: 191, Mismatches: 8, Indels: 12
0.91 0.04 0.06
Matches are distributed among these distances:
136 2 0.01
137 15 0.08
138 38 0.20
139 4 0.02
140 3 0.02
142 126 0.66
143 3 0.02
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (137 bp):
TCGCATTGCGATTTTAATTTCGCATTGCGATTTTCGTTGCGATTTTCATTTCGCATTGCGATTTT
CATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
GATTCTC
Found at i:123195 original size:52 final size:52
Alignment explanation
Indices: 122950--123228 Score: 388
Period size: 52 Copynumber: 5.2 Consensus size: 52
122940 GATTATCTCG
*
122950 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
*
123002 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* *
123059 TTGCGATTTTAATTTCGCATTGCGATTCTGTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
123111 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
123163 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCA
123216 TTGCGATTTTCAT
1 TTGCGATTTTCAT
123229 GTTGGGATTT
Statistics
Matches: 217, Mismatches: 4, Indels: 11
0.94 0.02 0.05
Matches are distributed among these distances:
52 161 0.74
53 17 0.08
54 7 0.03
55 8 0.04
57 24 0.11
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:125761 original size:24 final size:24
Alignment explanation
Indices: 125727--125773 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
125717 CTGAAACATC
125727 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
125751 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
125774 GACCAAATTT
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:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:126484 original size:20 final size:20
Alignment explanation
Indices: 126456--126824 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
126446 AAATTTCAGT
* * * *
126456 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
126476 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
126496 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
126516 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
126536 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
126556 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
126576 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
126596 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
126616 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
126636 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
126656 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
126676 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
126696 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
126716 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
126736 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
126756 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
126776 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
126796 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
126816 GTTGCGATT
1 GTTGCGATT
126825 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:130279 original size:21 final size:20
Alignment explanation
Indices: 130193--130350 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
130183 AAATGACCAA
**
130193 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
130212 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
130232 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
130252 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
130273 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
130294 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
130314 ACAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
130335 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
130351 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:130379 original size:20 final size:20
Alignment explanation
Indices: 130317--130546 Score: 223
Period size: 20 Copynumber: 11.5 Consensus size: 20
130307 CGATTTTACA
* ** *
130317 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
130337 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
*
130357 AAATCGCAACTCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
130377 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
130397 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
130417 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
130437 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
130457 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
130477 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
130497 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
130517 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
130537 AAATCACAAC
1 AAATCGCAAC
130547 ACTGAAATCT
Statistics
Matches: 174, Mismatches: 30, Indels: 12
0.81 0.14 0.06
Matches are distributed among these distances:
19 2 0.01
20 170 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:133778 original size:19 final size:19
Alignment explanation
Indices: 133756--134010 Score: 245
Period size: 19 Copynumber: 14.7 Consensus size: 19
133746 CGGAAATTAC
*
133756 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
133775 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
133789 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
133809 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
133823 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
133842 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
133861 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
133875 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
133894 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
133913 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
133927 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
133946 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
133965 AATCGCAA----AGA-GAG
1 AATCGCAATGCGAAATGAA
133979 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
133998 AAACGCATTGCGA
1 AATCGCAATGCGA
134011 TTCTCTCGTT
Statistics
Matches: 196, Mismatches: 14, Indels: 52
0.75 0.05 0.20
Matches are distributed among these distances:
14 52 0.27
15 5 0.03
16 7 0.04
17 6 0.03
18 6 0.03
19 107 0.55
20 13 0.07
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:133843 original size:33 final size:33
Alignment explanation
Indices: 133756--133953 Score: 201
Period size: 33 Copynumber: 5.8 Consensus size: 33
133746 CGGAAATTAC
* *
133756 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAA
*
133789 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAA
133823 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
*
133861 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
*
133894 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAA
133927 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
133954 TGCGAAATGA
Statistics
Matches: 146, Mismatches: 7, Indels: 24
0.82 0.04 0.14
Matches are distributed among these distances:
33 84 0.58
34 31 0.21
35 5 0.03
36 4 0.03
37 2 0.01
38 20 0.14
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAA
Found at i:133871 original size:52 final size:52
Alignment explanation
Indices: 133784--134010 Score: 418
Period size: 52 Copynumber: 4.3 Consensus size: 52
133774 AAATCCCAAC
133784 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
133837 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
133889 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
133941 ATGAAAATCGCAATGCGAAATGAAAATCGCAAAGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
133993 ATGAAAAACGCATTGCGA
1 ATGAAAATCGCAATGCGA
134011 TTCTCTCGTT
Statistics
Matches: 171, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
52 155 0.91
53 16 0.09
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:133983 original size:33 final size:33
Alignment explanation
Indices: 133842--134004 Score: 154
Period size: 33 Copynumber: 4.8 Consensus size: 33
133832 GCGAAATGAA
*
133842 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAAAGAGAG
* *
133875 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA----AGA-GAG
* * *
133913 AATCGCAACGAGAGAATCG-CAAT-GCGAAATGA-A-
1 AATCGCAATGCGA-AAT-GAAAATCGC-AAA-GAGAG
133946 AATCGCAATGCGAAATGAAAATCGCAAAGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAAAGAGAG
*
133979 AATCGCAATGCGAAATGAAAAACGCA
1 AATCGCAATGCGAAATGAAAATCGCA
134005 TTGCGATTCT
Statistics
Matches: 106, Mismatches: 11, Indels: 26
0.74 0.08 0.18
Matches are distributed among these distances:
31 3 0.03
32 10 0.09
33 65 0.61
34 1 0.01
35 1 0.01
36 1 0.01
37 1 0.01
38 15 0.14
39 8 0.08
40 1 0.01
ACGTcount: A:0.47, C:0.17, G:0.23, T:0.13
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAAAGAGAG
Found at i:134059 original size:19 final size:20
Alignment explanation
Indices: 134019--134059 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
134009 GATTCTCTCG
*
134019 TTGCGATTTTCATTTCCGCA
1 TTGCAATTTTCATTTCCGCA
134039 TTGCAATTTTCATTT-CGCA
1 TTGCAATTTTCATTTCCGCA
134058 TT
1 TT
134060 ACGATTCTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.17, C:0.22, G:0.12, T:0.49
Consensus pattern (20 bp):
TTGCAATTTTCATTTCCGCA
Found at i:134096 original size:19 final size:19
Alignment explanation
Indices: 134019--134097 Score: 87
Period size: 19 Copynumber: 4.4 Consensus size: 19
134009 GATTCTCTCG
134019 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
*
134039 TTGCAATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
134058 TTACGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
134072 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
134091 TTGCGAT
1 TTGCGAT
134098 AGTCATTTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
14 5 0.10
16 7 0.15
17 7 0.15
19 15 0.31
20 14 0.29
ACGTcount: A:0.16, C:0.23, G:0.15, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:134223 original size:14 final size:14
Alignment explanation
Indices: 134204--134240 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
134194 CATCAATTAC
134204 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
134218 ACAAATCATCTTTT
1 ACAAATCAACTTTT
134232 ACAAATCAA
1 ACAAATCAA
134241 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:136203 original size:19 final size:19
Alignment explanation
Indices: 136163--136278 Score: 99
Period size: 19 Copynumber: 6.6 Consensus size: 19
136153 TAGTTTACTT
* *
136163 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
136183 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
136202 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
* *
136216 TCGCAATGCGAAAGGAAAA
1 TCGCAACGCGAAATGAAAA
136235 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
136249 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
136268 TCGCAATGCGA
1 TCGCAACGCGA
136279 TTTTGGTTTC
Statistics
Matches: 81, Mismatches: 5, Indels: 21
0.76 0.05 0.20
Matches are distributed among these distances:
14 16 0.20
16 11 0.14
17 11 0.14
19 31 0.38
20 12 0.15
ACGTcount: A:0.46, C:0.22, G:0.21, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:136219 original size:14 final size:14
Alignment explanation
Indices: 136200--136256 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
136190 GCGAAATGAA
*
136200 AATCGCAACGACAG
1 AATCGCAACGAAAG
136214 AATCGCAATGCGAAAGG
1 AATCGCAA--CGAAA-G
136231 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
136247 AATCGCAACG
1 AATCGCAACG
136257 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:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:136227 original size:33 final size:33
Alignment explanation
Indices: 136181--136273 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
136171 CGAAACTTAA
*
136181 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
* *
136214 AATCGCAATGCGAAAGGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
136247 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
136274 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:0.47, C:0.22, G:0.22, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:136296 original size:19 final size:18
Alignment explanation
Indices: 136274--136383 Score: 83
Period size: 19 Copynumber: 6.3 Consensus size: 18
136264 AAAATCGCAA
136274 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
136293 TGCGATCTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
136307 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
136326 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
136340 TGCGATTTTTATTTCGCGT
1 TGCGA-TTTTGTTTCGCGT
*
136359 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT--GTTTCGCGT
136379 TGCGA
1 TGCGA
136384 AAGTAAACTA
Statistics
Matches: 72, Mismatches: 7, Indels: 23
0.71 0.07 0.23
Matches are distributed among these distances:
14 19 0.26
15 4 0.06
16 2 0.03
17 2 0.03
18 6 0.08
19 27 0.38
20 12 0.17
ACGTcount: A:0.09, C:0.16, G:0.28, T:0.46
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:136316 original size:33 final size:33
Alignment explanation
Indices: 136274--136365 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
136264 AAAATCGCAA
136274 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
136307 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
136340 TGCGATTTTTATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
136366 TTAAGTTTCG
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:0.17, G:0.28, T:0.47
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:136547 original size:93 final size:93
Alignment explanation
Indices: 136431--137085 Score: 1285
Period size: 93 Copynumber: 7.1 Consensus size: 93
136421 ATGGATTGCA
136431 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
136495 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
136523 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
136588 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
136616 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
136681 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
136709 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
136774 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
136802 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
136867 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
*
136895 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAATT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
136960 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
136988 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
137053 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
137081 TTACT
1 TTACT
137086 AAGCAATCTA
Statistics
Matches: 559, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 4 0.01
93 555 0.99
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:138813 original size:14 final size:14
Alignment explanation
Indices: 138791--138880 Score: 54
Period size: 14 Copynumber: 5.7 Consensus size: 14
138781 TTGAAATGAA
*
138791 AATCACAACGAGAG
1 AATCGCAACGAGAG
*
138805 AATCGCAACGTGAAATGAC
1 AATCGCAAC--G--A-GAG
138824 AATCGCAACGAGAG
1 AATCGCAACGAGAG
* *
138838 AATCGCAACGCGAAATAAA
1 AATCGCAA--CG--A-GAG
138857 AATCGCAACGAGAG
1 AATCGCAACGAGAG
138871 AATCGCAACG
1 AATCGCAACG
138881 CGAAATGAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
14 29 0.49
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 20 0.34
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.10
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:138833 original size:33 final size:33
Alignment explanation
Indices: 138783--138897 Score: 194
Period size: 33 Copynumber: 3.5 Consensus size: 33
138773 TCTTTTGGTT
* *
138783 GAAATGAAAATCACAACGAGAGAATCGCAACGT
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
138816 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
138849 GAAATAAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
138882 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
138898 TGCGATTTTG
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 76 1.00
ACGTcount: A:0.48, C:0.20, G:0.22, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:138862 original size:19 final size:19
Alignment explanation
Indices: 138805--138902 Score: 72
Period size: 19 Copynumber: 5.7 Consensus size: 19
138795 ACAACGAGAG
* *
138805 AATCGCAACGTGAAATGAC
1 AATCGCAACGCGAAATGAA
*
138824 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
*
138838 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATGAA
*
138857 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
138871 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
138890 AATCGCAATGCGA
1 AATCGCAACGCGA
138903 TTTTGGTTTC
Statistics
Matches: 61, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
14 19 0.31
15 2 0.03
16 4 0.07
17 3 0.05
18 2 0.03
19 31 0.51
ACGTcount: A:0.45, C:0.21, G:0.22, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:138973 original size:21 final size:20
Alignment explanation
Indices: 138921--139016 Score: 104
Period size: 21 Copynumber: 4.8 Consensus size: 20
138911 TCGCGTTGCG
*
138921 ATTCTCTCGTTGCAATTTTC
1 ATTCTCTCGTTGCGATTTTC
* *
138941 A-TATCGCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
***
138960 ATTTCTCTCGTTGCGACAGTC
1 A-TTCTCTCGTTGCGATTTTC
138981 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
139001 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
139017 CTCTTCTGCA
Statistics
Matches: 61, Mismatches: 12, Indels: 5
0.78 0.15 0.06
Matches are distributed among these distances:
19 16 0.26
20 18 0.30
21 27 0.44
ACGTcount: A:0.15, C:0.24, G:0.17, T:0.45
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:139138 original size:33 final size:33
Alignment explanation
Indices: 139096--139166 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
139086 AATACTAACT
*
139096 TGAAAATCGCAACGAGAAAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAAAATAGCAACGCGAAA
* * *
139129 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAAAATAGCAACGCGAAA
139162 TGAAA
1 TGAAA
139167 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.49, C:0.18, G:0.21, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAAAATAGCAACGCGAAA
Found at i:139400 original size:22 final size:22
Alignment explanation
Indices: 139348--139402 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
139338 TGGTTGTGAG
**
139348 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
139370 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
139392 GGATTTCTTCG
1 GGATTTCTTCG
139403 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:139574 original size:20 final size:20
Alignment explanation
Indices: 139549--139742 Score: 212
Period size: 20 Copynumber: 9.7 Consensus size: 20
139539 CTTTAAATAT
139549 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
139569 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
139591 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
139610 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
139630 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
139650 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
139670 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
139690 CGAGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
139710 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
139730 CGCGTTGCGATTT
1 CGCGTTGCGATTT
139743 TGGAAAATCG
Statistics
Matches: 145, Mismatches: 24, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:139736 original size:60 final size:60
Alignment explanation
Indices: 139549--139742 Score: 237
Period size: 60 Copynumber: 3.2 Consensus size: 60
139539 CTTTAAATAT
* **
139549 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGAGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* *** *
139610 CGCGTTGCGATATACGGATACGCA-TTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACG-AGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
139670 CACGTTGCGATTTACGGATACGAGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGAGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
139730 CGCGTTGCGATTT
1 CGCGTTGCGATTT
139743 TGGAAAATCG
Statistics
Matches: 111, Mismatches: 20, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
59 1 0.01
60 83 0.75
61 27 0.24
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGAGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:140224 original size:42 final size:44
Alignment explanation
Indices: 140123--140226 Score: 124
Period size: 42 Copynumber: 2.4 Consensus size: 44
140113 AAGGAGCCAA
* * * *
140123 CTATAGATCT-GACCTTTTGCGGCGTTTTTTTACAAAAATGCCG
1 CTATAGATCTCGACCTTTTACGGCATTTGTTTACAAAAACGCCG
* *
140166 CTATATATCTCAACCTTTTACGGCATTTGTTT-C-AAAACGCCG
1 CTATAGATCTCGACCTTTTACGGCATTTGTTTACAAAAACGCCG
*
140208 CTATAGATATCGACCTTTT
1 CTATAGATCTCGACCTTTT
140227 GTGATGTTTG
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
42 24 0.47
43 10 0.20
44 17 0.33
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (44 bp):
CTATAGATCTCGACCTTTTACGGCATTTGTTTACAAAAACGCCG
Found at i:142466 original size:5 final size:5
Alignment explanation
Indices: 142456--142533 Score: 61
Period size: 5 Copynumber: 15.8 Consensus size: 5
142446 TTGGGTTTGA
** * * ** * *
142456 AAAAT AAAAT AAAAT AAAAT ATTAT TAATT ATTAT -ATAT AATAT AATAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA-AAT
142506 AAAAT AAAAT -AAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
142534 AAGACAACTC
Statistics
Matches: 58, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
4 7 0.12
5 47 0.81
6 4 0.07
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (5 bp):
AAAAT
Found at i:142522 original size:14 final size:14
Alignment explanation
Indices: 142503--142532 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
142493 ATAATATAAT
142503 AATAAAATAAAATA
1 AATAAAATAAAATA
142517 AATAAAATAAAATA
1 AATAAAATAAAATA
142531 AA
1 AA
142533 AAAGACAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (14 bp):
AATAAAATAAAATA
Found at i:144043 original size:30 final size:30
Alignment explanation
Indices: 143967--144043 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 30
143957 AGATGGCCTT
* *
143967 AGTCCATGTACCATTTAACATTGGTGGCTA
1 AGTCCATGTATCATTTAACATTAGTGGCTA
* * * * *
143997 ATTCCCTATATTATTTAACCTTAGTGGCTA
1 AGTCCATGTATCATTTAACATTAGTGGCTA
144027 AGTCCATGTATCATTTA
1 AGTCCATGTATCATTTA
144044 GTGCTTAGCT
Statistics
Matches: 36, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.39
Consensus pattern (30 bp):
AGTCCATGTATCATTTAACATTAGTGGCTA
Found at i:144435 original size:25 final size:24
Alignment explanation
Indices: 144401--144476 Score: 86
Period size: 21 Copynumber: 3.2 Consensus size: 24
144391 TTATGAAAGA
144401 ATGAAAGAATTTCGAAAAATGTTTG
1 ATGAAAGAATTTCG-AAAATGTTTG
*
144426 ATGAAAGAATTTTGAAAATGTTTG
1 ATGAAAGAATTTCGAAAATGTTTG
* * *
144450 AT--AAG-TTTTTGAAAATTTTTG
1 ATGAAAGAATTTCGAAAATGTTTG
144471 ATGAAA
1 ATGAAA
144477 TTTTTGAAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
21 16 0.35
22 3 0.07
23 2 0.04
24 12 0.26
25 13 0.28
ACGTcount: A:0.42, C:0.01, G:0.18, T:0.38
Consensus pattern (24 bp):
ATGAAAGAATTTCGAAAATGTTTG
Found at i:144468 original size:10 final size:10
Alignment explanation
Indices: 144435--144485 Score: 57
Period size: 10 Copynumber: 4.8 Consensus size: 10
144425 GATGAAAGAA
144435 TTTTGAAAAT
1 TTTTGAAAAT
* *
144445 GTTTGATAAGT
1 TTTTGA-AAAT
144456 TTTTGAAAAT
1 TTTTGAAAAT
144466 TTTTGATGAAAT
1 TTTTGA--AAAT
144478 TTTTGAAA
1 TTTTGAAA
144486 TTGATGTCCC
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
10 16 0.47
11 8 0.24
12 10 0.29
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (10 bp):
TTTTGAAAAT
Found at i:144487 original size:21 final size:22
Alignment explanation
Indices: 144416--144485 Score: 88
Period size: 21 Copynumber: 3.1 Consensus size: 22
144406 AGAATTTCGA
*
144416 AAAATGTTTGATGAAAGAATTTTG
1 AAAATGTTTGATG-AA-ATTTTTG
*
144440 AAAATGTTTGAT-AAGTTTTTG
1 AAAATGTTTGATGAAATTTTTG
*
144461 AAAATTTTTGATGAAATTTTTG
1 AAAATGTTTGATGAAATTTTTG
144483 AAA
1 AAA
144486 TTGATGTCCC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
21 16 0.39
22 13 0.32
24 12 0.29
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (22 bp):
AAAATGTTTGATGAAATTTTTG
Found at i:145165 original size:19 final size:21
Alignment explanation
Indices: 145141--145188 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
145131 ATATACATTT
**
145141 TATGAACAGT-AA-AATATGG
1 TATGAACAGTGAACAATACCG
*
145160 TATGAATAGTGAACAATACCG
1 TATGAACAGTGAACAATACCG
145181 TATGAACA
1 TATGAACA
145189 ATGCCATAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 9 0.39
20 2 0.09
21 12 0.52
ACGTcount: A:0.46, C:0.10, G:0.19, T:0.25
Consensus pattern (21 bp):
TATGAACAGTGAACAATACCG
Found at i:145778 original size:17 final size:19
Alignment explanation
Indices: 145736--145780 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 19
145726 TATTTATCAG
145736 TAATCATATTATTATCACT
1 TAATCATATTATTATCACT
*
145755 TATTCAT-TT-TTATCA-T
1 TAATCATATTATTATCACT
145771 ATAATCATAT
1 -TAATCATAT
145781 GTTGAACATT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
16 1 0.05
17 12 0.55
18 3 0.14
19 6 0.27
ACGTcount: A:0.36, C:0.13, G:0.00, T:0.51
Consensus pattern (19 bp):
TAATCATATTATTATCACT
Found at i:146058 original size:22 final size:22
Alignment explanation
Indices: 146033--146093 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
146023 GGCATATGAA
*
146033 ATTTGTCCCGAATGACCTA-TGT
1 ATTTGTCCCGAAGGACC-ACTGT
*
146055 ATTTATCCCGAAGGACCACTGT
1 ATTTGTCCCGAAGGACCACTGT
*
146077 ATATGTCCCGAAGGACC
1 ATTTGTCCCGAAGGACC
146094 GCGTAAACCC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 1 0.03
22 33 0.97
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (22 bp):
ATTTGTCCCGAAGGACCACTGT
Found at i:146612 original size:2 final size:2
Alignment explanation
Indices: 146561--146600 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
146551 ATAAGAATAA
146561 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
146601 CCATTATATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:148061 original size:2 final size:2
Alignment explanation
Indices: 148054--148111 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
148044 AACTTTATTG
148054 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
148096 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
148112 CAGTAACTTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:151742 original size:21 final size:21
Alignment explanation
Indices: 151718--151777 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
151708 ACTTTGAAAG
151718 AATGGTTTTCAAAGTTTGGTA
1 AATGGTTTTCAAAGTTTGGTA
*
151739 AAT-G-TTTC----TTT-GAA
1 AATGGTTTTCAAAGTTTGGTA
151753 AATGGTTTTCAAAGTTTGGTA
1 AATGGTTTTCAAAGTTTGGTA
151774 AATG
1 AATG
151778 TTTCTTTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
14 5 0.17
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 9 0.30
ACGTcount: A:0.30, C:0.05, G:0.22, T:0.43
Consensus pattern (21 bp):
AATGGTTTTCAAAGTTTGGTA
Found at i:151808 original size:37 final size:36
Alignment explanation
Indices: 151709--151828 Score: 181
Period size: 35 Copynumber: 3.3 Consensus size: 36
151699 TGGTAACCAA
151709 CTTTGAAAGAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAA-AATGGTTTTCAAAGTTTGGTAAATGTTT
151746 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
151781 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
*
151818 -GTTGAAAAATG
1 CTTTGAAAAATG
151829 ATAATGGGAT
Statistics
Matches: 78, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
35 34 0.44
36 16 0.21
37 28 0.36
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:156237 original size:21 final size:20
Alignment explanation
Indices: 156212--156307 Score: 63
Period size: 21 Copynumber: 5.2 Consensus size: 20
156202 GAAAGTATTA
156212 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAA-TTTGGT
*
156233 AAAT-G-TTTC---TTT-GA
1 AAATGGTTTTCAAATTTGGT
156247 AAATGGTTTTCAAAATTTGGT
1 AAATGGTTTTC-AAATTTGGT
*
156268 AAAT-G-TTTC---TTT-GA
1 AAATGGTTTTCAAATTTGGT
156282 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAA-TTTGGT
156303 AAATG
1 AAATG
156308 TTTCTTTGAA
Statistics
Matches: 57, Mismatches: 4, Indels: 28
0.64 0.04 0.31
Matches are distributed among these distances:
14 10 0.18
15 8 0.14
16 8 0.14
19 8 0.14
20 8 0.14
21 15 0.26
ACGTcount: A:0.31, C:0.05, G:0.20, T:0.44
Consensus pattern (20 bp):
AAATGGTTTTCAAATTTGGT
Found at i:156357 original size:36 final size:35
Alignment explanation
Indices: 156211--156355 Score: 229
Period size: 35 Copynumber: 4.1 Consensus size: 35
156201 TGAAAGTATT
156211 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
*
156246 AAAATGGTTTTCAAAATTTGGTAAATGTTTCTTTG
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
156281 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
* * *
156316 AAAAATAGTTTTTCAAAGTTTGGTAGATGTTT-GTTG
1 -AAAAT-GGTTTTCAAAGTTTGGTAAATGTTTCTTTG
156352 AAAA
1 AAAA
156356 ATGATAATGG
Statistics
Matches: 103, Mismatches: 5, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
35 72 0.70
36 8 0.08
37 23 0.22
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (35 bp):
AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
Found at i:158562 original size:32 final size:33
Alignment explanation
Indices: 158504--158570 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 33
158494 GCGACCTACC
* *
158504 CTCGCTCGGCTTTCCTCGGATTCCCTCGCATAG
1 CTCGCTCGGCTTGCCTCGGATGCCCTCGCATAG
158537 CTCGCTCGG-TTGCCTCGGATGCCCTCGCATAG
1 CTCGCTCGGCTTGCCTCGGATGCCCTCGCATAG
158569 CT
1 CT
158571 TGTTCGGATG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 23 0.72
33 9 0.28
ACGTcount: A:0.09, C:0.39, G:0.24, T:0.28
Consensus pattern (33 bp):
CTCGCTCGGCTTGCCTCGGATGCCCTCGCATAG
Found at i:158599 original size:20 final size:20
Alignment explanation
Indices: 158574--158611 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
158564 CATAGCTTGT
158574 TCGGATGGCCTCGAATGCTC
1 TCGGATGGCCTCGAATGCTC
*
158594 TCGGATGGCCTCGGATGC
1 TCGGATGGCCTCGAATGC
158612 CCAGCGTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.29, G:0.34, T:0.24
Consensus pattern (20 bp):
TCGGATGGCCTCGAATGCTC
Found at i:172649 original size:91 final size:91
Alignment explanation
Indices: 172484--172658 Score: 269
Period size: 91 Copynumber: 1.9 Consensus size: 91
172474 CAAGAAACTC
* * *
172484 ATGTAACATTCTCAGTTGTAACCGAAATTATTACCAATTATGTAACTTTTTAGAGTAGATATGGT
1 ATGTAACATTCTCAGTTGTAACCGAAATTATTACCAATTATGTAACTTTTTAGAGTAGACAAGAT
*
172549 AACATTTTAGGTTAAAACCGGCCGCA
66 AACAGTTTAGGTTAAAACCGGCCGCA
* * * *
172575 ATGTAACATTCTCGGTTGTAACTGAAATTATTATCAATTGTGTAACTTTTTAGAGTAGACAAGAT
1 ATGTAACATTCTCAGTTGTAACCGAAATTATTACCAATTATGTAACTTTTTAGAGTAGACAAGAT
*
172640 AATAGTTTAGGTTAAAACC
66 AACAGTTTAGGTTAAAACC
172659 CACCGCAAAT
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
91 75 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (91 bp):
ATGTAACATTCTCAGTTGTAACCGAAATTATTACCAATTATGTAACTTTTTAGAGTAGACAAGAT
AACAGTTTAGGTTAAAACCGGCCGCA
Found at i:175767 original size:15 final size:16
Alignment explanation
Indices: 175743--175775 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
175733 GCTCTTTTCT
175743 TTGATATT-AATAAAA
1 TTGATATTAAATAAAA
*
175758 TTGATTTTAAATAAAA
1 TTGATATTAAATAAAA
175774 TT
1 TT
175776 AAATAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (16 bp):
TTGATATTAAATAAAA
Found at i:175899 original size:24 final size:25
Alignment explanation
Indices: 175862--175908 Score: 62
Period size: 23 Copynumber: 1.9 Consensus size: 25
175852 TTCGATATTG
175862 AAAAATATTAAAATAATTTATTTAAA
1 AAAAATATTAAAATAA-TTATTTAAA
*
175888 AAAAATA-T-AAATTATTATTTA
1 AAAAATATTAAAATAATTATTTA
175909 TCATATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 7 0.35
24 5 0.25
25 1 0.05
26 7 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
AAAAATATTAAAATAATTATTTAAA
Found at i:177341 original size:3 final size:3
Alignment explanation
Indices: 177333--177373 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
177323 ATTTTTTATT
*
177333 TAA TAA TAA TAA T-A TAA TAA -AT TAA TAA TTAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA
177374 AATGAACTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
2 3 0.09
3 27 0.82
4 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:177629 original size:76 final size:76
Alignment explanation
Indices: 177503--178214 Score: 1261
Period size: 76 Copynumber: 9.4 Consensus size: 76
177493 GAAATGTTGA
* *
177503 AAACATCATGCACTGAAGGGCTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCTGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
177568 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
177579 AAACATCATGCACTGTATGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
177644 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
177655 AAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
177720 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
177731 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
177796 AGGCTTTTTGG
66 AGGCTTTTTGG
*
177807 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTAAAAACATCAAAAAGCT-CCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
177871 AGGCTTTTTGG
66 AGGCTTTTTGG
177882 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
177947 AGGCTTTTTGG
66 AGGCTTTTTGG
177958 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
178023 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
178034 AAACATCATGCACTGAAGGACTTATAGATGACCCGAAGGCTTT-AAAACATCAAAAAGCT-CCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
178097 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
178108 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT-AAGAACATCAAAAAGCTCTCG
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAA-AACATCAAAAAGCTCCCG
178172 AAGGCTTTTTGG
65 AAGGCTTTTTGG
*
178184 AAACATCATGCACTGAAGGACTTATAGATGA
1 AAACATCATGCACTGAAGGACTTACAGATGA
178215 GGGAAATAGT
Statistics
Matches: 618, Mismatches: 15, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
74 59 0.10
75 104 0.17
76 455 0.74
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (76 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:177979 original size:227 final size:226
Alignment explanation
Indices: 177503--178214 Score: 1273
Period size: 227 Copynumber: 3.1 Consensus size: 226
177493 GAAATGTTGA
* *
177503 AAACATCATGCACTGAAGGGCTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCTGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
* *
177568 AGGCTTTTTGGAAACATCATGCACTGTATGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTT-AAAACATCAA
*
177633 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTT
130 AAAGCT-CCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT
177698 GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
194 GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
* *
177731 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
177796 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTAAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTT-AAAACATCAA
*
177861 AAAGCTCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTG
130 AAAGCTCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTG
177926 AAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
195 AAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
177958 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
* *
178023 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTATAGATGACCCGAAGGCTTTAAAACATCAAA
66 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTAAAACATCAAA
178088 AAGCTCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT-A
131 AAGCTCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGA
*
178152 AGAACATCAAAAAGCTCTCGAAGGCTTTTTGG
196 A-AACATCAAAAAGCTCCCGAAGGCTTTTTGG
*
178184 AAACATCATGCACTGAAGGACTTATAGATGA
1 AAACATCATGCACTGAAGGACTTACAGATGA
178215 GGGAAATAGT
Statistics
Matches: 467, Mismatches: 16, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
225 2 0.00
226 132 0.28
227 204 0.44
228 129 0.28
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (226 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTAAAACATCAAA
AAGCTCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGA
AAACATCAAAAAGCTCCCGAAGGCTTTTTGG
Found at i:179124 original size:24 final size:23
Alignment explanation
Indices: 179089--179133 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
179079 TGAACAAATT
179089 CTTCTCATTATGAACTTCTTCTTC
1 CTTCTCATTATG-ACTTCTTCTTC
*
179113 CTTCTTCA-TATGAGTTCTTCT
1 CTTC-TCATTATGACTTCTTCT
179134 CATTATGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 8 0.42
24 8 0.42
25 3 0.16
ACGTcount: A:0.16, C:0.27, G:0.07, T:0.51
Consensus pattern (23 bp):
CTTCTCATTATGACTTCTTCTTC
Found at i:179269 original size:112 final size:112
Alignment explanation
Indices: 178619--179289 Score: 912
Period size: 113 Copynumber: 6.0 Consensus size: 112
178609 ATAGAATTAT
* *
178619 GCAAAAAGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * **
178684 ATTATGAA--CTTCTCTAGAAAAGCTGTTCCATCAAGTGATGTATTTGA
66 ATTATGAACTCTTCTCTGGAAATG-TGATCCATCAA-TGATGGATTCAA
*
178731 GCAAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
** * *
178796 ATTATGAAC-CTTCTCTGGCAAAAATAATCCATCAAGTGATGAATTC-A
66 ATTATGAACTCTTCTCTGG-AAATGTGATCCATCAA-TGATGGATTCAA
178843 GACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 G-CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* *
178908 CATTATGAACT-TTCTCTGGAAATGATGATCCATCAAATAATAGATTCAA
65 CATTATGAACTCTTCTCTGGAAATG-TGATCCATC-AATGATGGATTCAA
* *
178957 GTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
179022 ATTATGAACT-TTCTCTGGAAATGATGATCCATCAAATGATGGATTCAA
66 ATTATGAACTCTTCTCTGGAAATG-TGATCCATC-AATGATGGATTCAA
* *
179070 GTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCATATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * **
179135 ATTATGAA--CTTCTATAGAAATGTCAATCCATCGAATGATGGATTGGA
66 ATTATGAACTCTTCTCTGGAAATGT-GATCCATC-AATGATGGATTCAA
*
179182 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
** *
179247 ATTATGAACTCGAC-CTGG-AATGTTGATCCATGAATGATGGATT
66 ATTATGAACTCTTCTCTGGAAATG-TGATCCATCAATGATGGATT
179290 TGAACTTTGC
Statistics
Matches: 512, Mismatches: 35, Indels: 25
0.90 0.06 0.04
Matches are distributed among these distances:
111 12 0.02
112 187 0.37
113 303 0.59
114 10 0.02
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (112 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTCTTCTCTGGAAATGTGATCCATCAATGATGGATTCAA
Found at i:179715 original size:22 final size:22
Alignment explanation
Indices: 179690--179744 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
179680 CATAAAGTTT
*
179690 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
*
179712 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
179734 TCATCTTTGAA
1 TCATCTTTGAA
179745 GAGTGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:180195 original size:54 final size:54
Alignment explanation
Indices: 180130--180277 Score: 278
Period size: 54 Copynumber: 2.7 Consensus size: 54
180120 TTTGATAGTG
*
180130 CATTCATCCTTTCCTGTGGCTTCTGTTCAGATGTTCGTAAAACATTTGACAACA
1 CATTCATCCTTTCCTGTGGTTTCTGTTCAGATGTTCGTAAAACATTTGACAACA
*
180184 CATTCATCCTTTCCTGTGGTTTCTGTTTAGATGTTCGTAAAACATTTGACAACA
1 CATTCATCCTTTCCTGTGGTTTCTGTTCAGATGTTCGTAAAACATTTGACAACA
180238 CATTCATCCTTTCCTGTGGTTTCTGTTCAGATGTTCGTAA
1 CATTCATCCTTTCCTGTGGTTTCTGTTCAGATGTTCGTAA
180278 TTATTGAAGT
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 91 1.00
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.41
Consensus pattern (54 bp):
CATTCATCCTTTCCTGTGGTTTCTGTTCAGATGTTCGTAAAACATTTGACAACA
Found at i:182523 original size:83 final size:83
Alignment explanation
Indices: 182384--182639 Score: 467
Period size: 83 Copynumber: 3.1 Consensus size: 83
182374 CTTATTTCTC
*
182384 CTATGAGCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTATAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
182449 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
*
182467 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
*
182532 AAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* *
182550 CTATGAGCAGATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
182615 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
182633 CTATGAG
1 CTATGAG
182640 TCTCTTTCAG
Statistics
Matches: 167, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
83 167 1.00
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.29
Consensus pattern (83 bp):
CTATGAGCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:190047 original size:15 final size:16
Alignment explanation
Indices: 190023--190055 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
190013 GCTCTTTTCT
190023 TTGATATT-AATAAAA
1 TTGATATTAAATAAAA
*
190038 TTGATTTTAAATAAAA
1 TTGATATTAAATAAAA
190054 TT
1 TT
190056 AAATAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (16 bp):
TTGATATTAAATAAAA
Found at i:190178 original size:24 final size:25
Alignment explanation
Indices: 190141--190187 Score: 62
Period size: 23 Copynumber: 1.9 Consensus size: 25
190131 TTCGATATTG
190141 AAAAATATTAAAATAATTTATTTAAA
1 AAAAATATTAAAATAA-TTATTTAAA
*
190167 AAAAATA-T-AAATTATTATTTA
1 AAAAATATTAAAATAATTATTTA
190188 TCATATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 7 0.35
24 5 0.25
25 1 0.05
26 7 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
AAAAATATTAAAATAATTATTTAAA
Found at i:191265 original size:13 final size:13
Alignment explanation
Indices: 191247--191272 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
191237 GAACTCAATC
191247 ATTCTGAACTCCT
1 ATTCTGAACTCCT
191260 ATTCTGAACTCCT
1 ATTCTGAACTCCT
191273 GAACTCAATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.31, G:0.08, T:0.38
Consensus pattern (13 bp):
ATTCTGAACTCCT
Found at i:194605 original size:21 final size:22
Alignment explanation
Indices: 194572--194635 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 22
194562 TAATTATTAA
* *
194572 AATATTTAAAATATAT-GTATT
1 AATATTTATAATATATAATATT
*
194593 AATATTTCTAATAATATAATATT
1 AATATTTATAAT-ATATAATATT
*
194616 -ATATTTTTAATATTATAATA
1 AATATTTATAATA-TATAATA
194636 AAATAATCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
21 11 0.31
22 21 0.58
23 4 0.11
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (22 bp):
AATATTTATAATATATAATATT
Found at i:194616 original size:53 final size:53
Alignment explanation
Indices: 194557--194667 Score: 120
Period size: 53 Copynumber: 2.1 Consensus size: 53
194547 TTTTAATCAA
* ** *
194557 AATATTA-ATTATTAA-AATAT-TTAAAATATATGTATTAATATTTCTAATAATAT
1 AATATTATATTATTAATAATATAATAAAATA-ATCAATT-ATA-TTATAATAATAT
* *
194610 AATATTATATTTTTAATATTATAATAAAATAATCAATTATATTATAATAATAT
1 AATATTATATTATTAATAATATAATAAAATAATCAATTATATTATAATAATAT
194663 AATAT
1 AATAT
194668 GTTATATTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
53 23 0.47
54 10 0.20
55 9 0.18
56 7 0.14
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (53 bp):
AATATTATATTATTAATAATATAATAAAATAATCAATTATATTATAATAATAT
Found at i:194619 original size:22 final size:23
Alignment explanation
Indices: 194589--194635 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
194579 AAAATATATG
194589 TATTAATATTTCTAATAATATAA
1 TATTAATATTTCTAATAATATAA
* *
194612 TATT-ATATTTTTAATATTATAA
1 TATTAATATTTCTAATAATATAA
194634 TA
1 TA
194636 AAATAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTAATATTTCTAATAATATAA
Found at i:194776 original size:19 final size:18
Alignment explanation
Indices: 194752--194820 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 18
194742 ATATTATTAA
194752 ATTATTAATAATGAATAAT
1 ATTATTAATAAT-AATAAT
* *
194771 ATTATTTAT-ATATTTAAT
1 ATTATTAATAATA-ATAAT
194789 ATTAATATAATAATCTAATAAT
1 ATT-AT-TAATAA--TAATAAT
194811 ATT-TTAATAA
1 ATTATTAATAA
194821 AGATATTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
17 1 0.03
18 9 0.22
19 16 0.40
20 4 0.10
21 1 0.03
22 7 0.17
23 2 0.05
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (18 bp):
ATTATTAATAATAATAAT
Found at i:194795 original size:27 final size:27
Alignment explanation
Indices: 194715--194800 Score: 70
Period size: 27 Copynumber: 3.1 Consensus size: 27
194705 AATAAAATTT
* *
194715 ATATTATTTAT-TAATTTCATAGAAATA
1 ATATTATTTATAT-ATTTAATATAAATA
* *
194742 ATATTA-TTAAAT-TATTAATAATGAATA
1 ATATTATTTATATAT-TTAAT-ATAAATA
194769 ATATTATTTATATATTTAATATTAATATA
1 ATATTATTTATATATTTAATA-TAA-ATA
194798 ATA
1 ATA
194801 ATCTAATAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
25 1 0.02
26 7 0.15
27 19 0.41
28 12 0.26
29 7 0.15
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (27 bp):
ATATTATTTATATATTTAATATAAATA
Found at i:194841 original size:23 final size:23
Alignment explanation
Indices: 194815--194859 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
194805 AATAATATTT
194815 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
194838 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
194860 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:195501 original size:14 final size:15
Alignment explanation
Indices: 195475--195505 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
195465 TAAAAATGAA
195475 AAAATGAAGATAAAG
1 AAAATGAAGATAAAG
195490 AAAATG-AGATAAAG
1 AAAATGAAGATAAAG
195504 AA
1 AA
195506 GGATAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.68, C:0.00, G:0.19, T:0.13
Consensus pattern (15 bp):
AAAATGAAGATAAAG
Found at i:195506 original size:23 final size:24
Alignment explanation
Indices: 195467--195512 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
195457 AAAAGTGTTA
195467 AAAATGAAAAAATGAA-GATAAAG
1 AAAATGAAAAAATGAAGGATAAAG
*
195490 AAAATGAGATAAA-GAAGGATAAA
1 AAAATGA-AAAAATGAAGGATAAA
195513 AATAAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.20, T:0.13
Consensus pattern (24 bp):
AAAATGAAAAAATGAAGGATAAAG
Found at i:211505 original size:2 final size:2
Alignment explanation
Indices: 211498--211569 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
211488 TCTTCTATTC
211498 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
211540 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
211570 GAAATTTAGA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:215280 original size:2 final size:2
Alignment explanation
Indices: 215273--215327 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
215263 TTATAGTTTG
215273 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
215315 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
215328 GGGCTAGGAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:216784 original size:39 final size:39
Alignment explanation
Indices: 216730--216808 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
216720 TTTATACTCC
* *
216730 ATATGGCACAAAAATATGTATGCATGCATGTAGGGATGG
1 ATATGACACAAAAATATGTACGCATGCATGTAGGGATGG
*
216769 ATATGACACAGAAATATGTACGCATGCATGTAGGGATGG
1 ATATGACACAAAAATATGTACGCATGCATGTAGGGATGG
216808 A
1 A
216809 CTAGAGGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.37, C:0.11, G:0.28, T:0.24
Consensus pattern (39 bp):
ATATGACACAAAAATATGTACGCATGCATGTAGGGATGG
Found at i:272268 original size:26 final size:26
Alignment explanation
Indices: 272239--272296 Score: 116
Period size: 26 Copynumber: 2.2 Consensus size: 26
272229 AATTCATAAA
272239 TAAAATTTTATATGAAGTTCAGGGGT
1 TAAAATTTTATATGAAGTTCAGGGGT
272265 TAAAATTTTATATGAAGTTCAGGGGT
1 TAAAATTTTATATGAAGTTCAGGGGT
272291 TAAAAT
1 TAAAAT
272297 AAATTTTACC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.38, C:0.03, G:0.21, T:0.38
Consensus pattern (26 bp):
TAAAATTTTATATGAAGTTCAGGGGT
Found at i:272670 original size:8 final size:8
Alignment explanation
Indices: 272649--272684 Score: 63
Period size: 8 Copynumber: 4.4 Consensus size: 8
272639 TGTTAGGAAA
272649 TAAAATTT
1 TAAAATTT
272657 TAAAAATTT
1 T-AAAATTT
272666 TAAAATTT
1 TAAAATTT
272674 TAAAATTT
1 TAAAATTT
272682 TAA
1 TAA
272685 GTTATGACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 19 0.70
9 8 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (8 bp):
TAAAATTT
Found at i:286370 original size:2 final size:2
Alignment explanation
Indices: 286363--286393 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
286353 AAATACATGC
286363 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
286394 AGTGTTCTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:287134 original size:6 final size:6
Alignment explanation
Indices: 287123--287170 Score: 87
Period size: 6 Copynumber: 8.0 Consensus size: 6
287113 GATGCATGTA
*
287123 CCTATG CCTATG CCTATG CCTATG CCTATG CCTATG CCTATA CCTATG
1 CCTATG CCTATG CCTATG CCTATG CCTATG CCTATG CCTATG CCTATG
287171 AGATGCGACC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.19, C:0.33, G:0.15, T:0.33
Consensus pattern (6 bp):
CCTATG
Found at i:298871 original size:18 final size:19
Alignment explanation
Indices: 298830--298871 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
298820 TAACCATTTC
**
298830 ATCTAATATTTAATTGTTT
1 ATCTAATATTTAATTAATT
298849 A-CTAAT-TTTAATTAATT
1 ATCTAATATTTAATTAATT
298866 ATCTAA
1 ATCTAA
298872 ATTATAACGT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 10 0.50
18 9 0.45
19 1 0.05
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.52
Consensus pattern (19 bp):
ATCTAATATTTAATTAATT
Found at i:300324 original size:31 final size:31
Alignment explanation
Indices: 300259--300324 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
300249 AAATTACATA
* * *
300259 TTTAGTATCTAAACTATTTATTTTATTTTGT
1 TTTAATATCTAAACTATTCATTTTATTTTAT
*
300290 TTTAATATCTAAACT-TTCATTTATTTTTTAT
1 TTTAATATCTAAACTATTCATTT-TATTTTAT
300321 TTTA
1 TTTA
300325 TTTTGGTACC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 6 0.20
31 24 0.80
ACGTcount: A:0.27, C:0.08, G:0.03, T:0.62
Consensus pattern (31 bp):
TTTAATATCTAAACTATTCATTTTATTTTAT
Found at i:306231 original size:2 final size:2
Alignment explanation
Indices: 306224--306256 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
306214 GTAAAGAAAC
306224 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
306257 ATTATCACAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:306315 original size:16 final size:16
Alignment explanation
Indices: 306287--306329 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
306277 ATCCTTATTT
306287 ATTTTCTCA-TTTTTC-
1 ATTTT-TCATTTTTTCA
306302 ATTTTTCATTTTTTCA
1 ATTTTTCATTTTTTCA
*
306318 ATTTTTGATTTT
1 ATTTTTCATTTT
306330 GATTTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 3 0.12
15 11 0.44
16 11 0.44
ACGTcount: A:0.16, C:0.12, G:0.02, T:0.70
Consensus pattern (16 bp):
ATTTTTCATTTTTTCA
Found at i:306321 original size:23 final size:22
Alignment explanation
Indices: 306287--306346 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 22
306277 ATCCTTATTT
*
306287 ATTTTCTC-ATTTTTCATTTTTC
1 ATTTTTTCAATTTTTCA-TTTTC
* *
306309 ATTTTTTCAATTTTTGATTTTG
1 ATTTTTTCAATTTTTCATTTTC
*
306331 ATTTTTTTTAATTTTT
1 A-TTTTTTCAATTTTT
306347 AAAATAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 12 0.38
23 20 0.62
ACGTcount: A:0.17, C:0.08, G:0.03, T:0.72
Consensus pattern (22 bp):
ATTTTTTCAATTTTTCATTTTC
Found at i:306336 original size:7 final size:7
Alignment explanation
Indices: 306287--306329 Score: 50
Period size: 8 Copynumber: 5.7 Consensus size: 7
306277 ATCCTTATTT
306287 ATTTTCTC
1 ATTTT-TC
306295 ATTTTTC
1 ATTTTTC
306302 ATTTTTC
1 ATTTTTC
306309 ATTTTTTC
1 A-TTTTTC
*
306317 AATTTTTG
1 -ATTTTTC
306325 ATTTT
1 ATTTT
306330 GATTTTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
7 15 0.47
8 16 0.50
9 1 0.03
ACGTcount: A:0.16, C:0.12, G:0.02, T:0.70
Consensus pattern (7 bp):
ATTTTTC
Found at i:308242 original size:24 final size:24
Alignment explanation
Indices: 308215--308277 Score: 108
Period size: 24 Copynumber: 2.6 Consensus size: 24
308205 TTCATAAAGC
*
308215 TCGGACATTACCTCCATAGTTTCT
1 TCGGACATTACCTCCATAATTTCT
308239 TCGGACATTACCTCCATAATTTCT
1 TCGGACATTACCTCCATAATTTCT
*
308263 TCAGACATTACCTCC
1 TCGGACATTACCTCC
308278 GAAGAGTAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.24, C:0.32, G:0.10, T:0.35
Consensus pattern (24 bp):
TCGGACATTACCTCCATAATTTCT
Found at i:309369 original size:64 final size:62
Alignment explanation
Indices: 309301--309457 Score: 152
Period size: 64 Copynumber: 2.5 Consensus size: 62
309291 TTCAGTGTGT
* * *
309301 ATCGATGCACAGGAAGTGCATCGATGCACCCATTAAAAATGGAAACATCGAATGCAATTAGTGC
1 ATCGATGCAAAGG-AGTGCATCGATGCACCCATT-AAAATGAAAACATCGAAGGCAATTAGTGC
* * * ** * *
309365 ATCGATGTATAAGGAGTGCATCGATGCACCCCCTTAAAATTAAAACATCGAAGGTGATTTGTGT
1 ATCGATGCA-AAGGAGTGCATCGATGCA-CCCATTAAAATGAAAACATCGAAGGCAATTAGTGC
** *
309429 ATCGATGCATGGGTAGTGTATCGATGCAC
1 ATCGATGCAAAGG-AGTGCATCGATGCAC
309458 ATGTTAAAGA
Statistics
Matches: 76, Mismatches: 14, Indels: 7
0.78 0.14 0.07
Matches are distributed among these distances:
63 3 0.04
64 65 0.86
65 8 0.11
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (62 bp):
ATCGATGCAAAGGAGTGCATCGATGCACCCATTAAAATGAAAACATCGAAGGCAATTAGTGC
Found at i:309490 original size:20 final size:20
Alignment explanation
Indices: 309465--309502 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
309455 CACATGTTAA
309465 AGAATGCATCGATACACTGT
1 AGAATGCATCGATACACTGT
* *
309485 AGAATGTATCGATGCACT
1 AGAATGCATCGATACACT
309503 TCAAGGGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.26
Consensus pattern (20 bp):
AGAATGCATCGATACACTGT
Found at i:310959 original size:23 final size:23
Alignment explanation
Indices: 310923--310982 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
310913 CATTTTATAT
*
310923 GGCACTTCGATGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
* * *
310946 GGCACTTTGGTGCAATTCTATGT
1 GGCACTTCGGTGCAATTCTACGC
310969 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
310983 TTTATACTAG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.18, C:0.25, G:0.27, T:0.30
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:316245 original size:331 final size:332
Alignment explanation
Indices: 315518--316512 Score: 1879
Period size: 331 Copynumber: 3.0 Consensus size: 332
315508 TTATACCGAT
*
315518 AGCATTGCAAATTTACCTATTACATTATATTATATTGAAAGTGTCCATACTTTTTATAAAAATGA
1 AGCATTGCAAATTTACCTATTACATTATATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGA
*
315583 TCGATATTTCTTTTAAAGTTATGTAATTTATGTTTCAA-TTTTTTAATAGTGTTTCATGTTTTCC
66 TCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCC
315647 ACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTTAT
131 ACCTACAATATTAATTTAATAATTTCATTTGCAC-AAAAATTATTTGATTGTTTTGATATTTTAT
*
315712 AAAATATTATTTAGAATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAATCATTA
195 AAAATAATATTTAGAATTTTTAATTTAATAATAATATATATCGTAACG-AAAAAATAAATCATTA
315777 GACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTT
259 GACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTT
315842 TCCACAGTG
324 TCCACAGTG
315851 AGCATTGCAAATTTACCTATTACATTATATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGA
1 AGCATTGCAAATTTACCTATTACATTATATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGA
315916 TCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCC
66 TCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCC
315981 ACCTACAATATTAATTTAATAATTTCATTTGCACAAAAATTATTTGATTGTTTTGATATTTTATA
131 ACCTACAATATTAATTTAATAATTTCATTTGCACAAAAATTATTTGATTGTTTTGATATTTTATA
316046 AAATAATATTTAGAATTTTTAATTTAATAAT-A-ATATATCGTAACGAAAAAAATAAATCATTAG
196 AAATAATATTTAGAATTTTTAATTTAATAATAATATATATCGTAACG-AAAAAATAAATCATTAG
316109 ACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTT
260 ACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTT
316174 CCACAGTG
325 CCACAGTG
316182 AGCATTGCAAATTTACCTATTACATTATATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGA
1 AGCATTGCAAATTTACCTATTACATTATATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGA
316247 TCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCC
66 TCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCC
316312 ACCTACAATATTAATTTAATAATTTCATTTGCACAAGAAATTATTTGATTGTTTTGATATTTTAT
131 ACCTACAATATTAATTTAATAATTTCATTTGCACAA-AAATTATTTGATTGTTTTGATATTTTAT
* *
316377 AAAATAATATTTAGAATTTTTAATTTAATCATAATATATATCGTAATGAAAAAATAAATCATTAG
195 AAAATAATATTTAGAATTTTTAATTTAATAATAATATATATCGTAACGAAAAAATAAATCATTAG
*
316442 ACGCCTATAATTACTAAATTAATATATTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTT
260 ACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTT
316507 CCACAG
325 CCACAG
316513 GGAAAAAAGT
Statistics
Matches: 651, Mismatches: 7, Indels: 8
0.98 0.01 0.01
Matches are distributed among these distances:
331 269 0.41
332 60 0.09
333 250 0.38
334 72 0.11
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.42
Consensus pattern (332 bp):
AGCATTGCAAATTTACCTATTACATTATATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGA
TCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCC
ACCTACAATATTAATTTAATAATTTCATTTGCACAAAAATTATTTGATTGTTTTGATATTTTATA
AAATAATATTTAGAATTTTTAATTTAATAATAATATATATCGTAACGAAAAAATAAATCATTAGA
CGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTC
CACAGTG
Found at i:316594 original size:23 final size:23
Alignment explanation
Indices: 316568--316630 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
316558 ATATAACCAC
316568 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* * *
316591 TACCTATTAAATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
316614 TACCTATTACATCATAT
1 TACCTATTACATTATAT
316631 GTTTACCTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.40, C:0.19, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:317090 original size:39 final size:39
Alignment explanation
Indices: 317036--317121 Score: 154
Period size: 39 Copynumber: 2.2 Consensus size: 39
317026 CAAGTTGTAT
*
317036 ATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTGG
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGG
*
317075 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTGG
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGG
317114 ATTTTGAT
1 ATTTTGAT
317122 GAGCATCGGA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.17, C:0.14, G:0.20, T:0.49
Consensus pattern (39 bp):
ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGG
Found at i:317403 original size:18 final size:18
Alignment explanation
Indices: 317380--317416 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
317370 CGAAATATAT
317380 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
317398 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
317416 A
1 A
317417 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:318107 original size:23 final size:23
Alignment explanation
Indices: 318044--318116 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 23
318034 ACATTTTACA
* *
318044 ATATAACCACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
* *
318067 ATATAAACGATACATATTACATT
1 ATATAAACGCTACCTATTACATT
** *
318090 ATATAAGGGCTACCTATTACATC
1 ATATAAACGCTACCTATTACATT
318113 ATAT
1 ATAT
318117 GTTTACCTAT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.41, C:0.19, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:318519 original size:25 final size:25
Alignment explanation
Indices: 318462--318527 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
318452 CACTCAAAAG
*
318462 ATGTATATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
***
318487 ACAAACATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
*
318512 TTGTACATACCTAAAT
1 ATGTACATACCTAAAT
318528 TTAATGATAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (25 bp):
ATGTACATACCTAAATATGTAGTTA
Found at i:321659 original size:362 final size:362
Alignment explanation
Indices: 320994--321673 Score: 1261
Period size: 362 Copynumber: 1.9 Consensus size: 362
320984 TTAAAATTAC
* *
320994 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
* *
321059 ATTATAAAGTGTCGATATATGTTGTAGACCTATTCGCGCATAAAACCGGTATATGTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATGTATACCGGTT
* *
321124 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGTCGATACTTTTTT
131 ATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGTCGACACTTTTTT
321189 AAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGT
196 AAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGT
321254 CGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTACTAAAT
261 CGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTACTAAAT
321319 TATCTATTACATTATATGGGTTCCGATGTGTAAATGT
326 TATCTATTACATTATATGGGTTCCGATGTGTAAATGT
321356 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
* *
321421 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATATCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATGTATACCGGTT
* * *
321486 ATATTACTAAATTATCTCTTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTT
131 ATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGTCGACACTTTTTT
321551 AAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGT
196 AAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGT
321616 CGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATATT
261 CGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATATT
321674 GCAAATTTAC
Statistics
Matches: 307, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
362 307 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (362 bp):
CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATGTATACCGGTT
ATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGTCGACACTTTTTT
AAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTAAAAAGTGT
CGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTACTAAAT
TATCTATTACATTATATGGGTTCCGATGTGTAAATGT
Found at i:321698 original size:183 final size:183
Alignment explanation
Indices: 320994--321673 Score: 1233
Period size: 183 Copynumber: 3.7 Consensus size: 183
320984 TTAAAATTAC
* *
320994 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
* * *
321059 ATTATAAAGTGTCGATATATGTTGTAGACCTATTCGCGCATAAAACCGGTATATGTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
* * *
321124 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
131 ATATTACTAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
*
321177 CGATACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
321242 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
321307 ATATTACTAAATTATCTATTACA-T-T-A-TATGGGTTCCGATGTGTAAATGT
131 ATATTACTAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
321356 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
*
321421 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATATCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
*
321486 ATATTACTAAATTATCTCTTACATTATAATTATGGGTTCCGATGTGTAAATGT
131 ATATTACTAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
321539 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
321604 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
321669 ATATT
131 ATATT
321674 GCAAATTTAC
Statistics
Matches: 481, Mismatches: 12, Indels: 8
0.96 0.02 0.02
Matches are distributed among these distances:
179 172 0.36
180 2 0.00
181 2 0.00
182 2 0.00
183 303 0.63
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (183 bp):
CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
ATATTACTAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
Found at i:323632 original size:17 final size:18
Alignment explanation
Indices: 323610--323652 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
323600 ATATATCCGG
323610 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
323627 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
323647 TATCAT
1 TATCAT
323653 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:323670 original size:20 final size:19
Alignment explanation
Indices: 323615--323661 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
323605 TCCGGTATCA
323615 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
323634 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
323655 TTTTACC
1 TTTTACC
323662 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:323809 original size:20 final size:20
Alignment explanation
Indices: 323783--323828 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
323773 CACTTTTAAA
323783 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
323802 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
323823 TTTACC
1 TTTACC
323829 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:324931 original size:19 final size:19
Alignment explanation
Indices: 324907--324944 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
324897 TAATAAAAAA
*
324907 AACATTTTTATATTTGCAT
1 AACATTGTTATATTTGCAT
324926 AACATTGTTATATTTGCAT
1 AACATTGTTATATTTGCAT
324945 GCCAAGTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.50
Consensus pattern (19 bp):
AACATTGTTATATTTGCAT
Found at i:326152 original size:29 final size:29
Alignment explanation
Indices: 326109--326191 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
326099 CTCACCTAAC
326109 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
326139 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
326168 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
326192 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:330907 original size:29 final size:29
Alignment explanation
Indices: 330864--330946 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
330854 CTCACCTAAC
330864 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
330894 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
330923 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
330947 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:331770 original size:32 final size:32
Alignment explanation
Indices: 331729--331793 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 32
331719 TATAATAATC
* *
331729 AATGTATGAACTTTT-AGATGAATTTTGTTGTA
1 AATGTATGAACTTTTGA-ATGAAGTTTGGTGTA
331761 AATGTATGAACTTTTGAATGAAGTTTGGTGTA
1 AATGTATGAACTTTTGAATGAAGTTTGGTGTA
331793 A
1 A
331794 TAAACAGATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 29 0.97
33 1 0.03
ACGTcount: A:0.32, C:0.03, G:0.22, T:0.43
Consensus pattern (32 bp):
AATGTATGAACTTTTGAATGAAGTTTGGTGTA
Found at i:334411 original size:7 final size:7
Alignment explanation
Indices: 334401--334427 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
334391 AAACCTCTTA
334401 TCTCCAC
1 TCTCCAC
334408 TCTCCAC
1 TCTCCAC
334415 TCTCCAC
1 TCTCCAC
334422 TCTCCA
1 TCTCCA
334428 ACTCAAGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.56, G:0.00, T:0.30
Consensus pattern (7 bp):
TCTCCAC
Found at i:336963 original size:12 final size:12
Alignment explanation
Indices: 336939--336969 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
336929 TAGCGTCTTC
336939 TATTAAA-AAAA
1 TATTAAACAAAA
336950 TATTAAACAAAA
1 TATTAAACAAAA
336962 TATTAAAC
1 TATTAAAC
336970 TTTTTTTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.37
12 12 0.63
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (12 bp):
TATTAAACAAAA
Found at i:340457 original size:2 final size:2
Alignment explanation
Indices: 340450--340474 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
340440 ATTTGTTTAG
340450 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
340475 CATTTTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:346462 original size:132 final size:128
Alignment explanation
Indices: 346300--346560 Score: 459
Period size: 132 Copynumber: 2.0 Consensus size: 128
346290 GTAACTATGT
*
346300 TAATTTGTTATTATCCTTCTATGGAAACAATTGTAATTGTTGAATAGTGGATACTTTTATCTATT
1 TAATTTGTTATTATCCTTCTACGGAAACAATTGTAATTGTTGAATAGTGGATAC-TTTATCTATT
346365 TTCTTCTGAACCACAGTTGAAGTTTCTTTCTACATTAGTAATTTTTACGAGGGGATGAAAGTTTT
65 TTCTTCTGAACCACAGTTGAAGTTTC-TT-TACATTAGTAATTTTTACGAGGGGATGAAAGTTTT
346430 G
128 G
346431 TAATTATGTTATTATCCTTCTACGGAAACAATTGTAATTGTTGAATAGTGGATACTTTATCTATT
1 TAATT-TGTTATTATCCTTCTACGGAAACAATTGTAATTGTTGAATAGTGGATACTTTATCTATT
* *
346496 TTCTTCTGATCCACAGTTGAAGTTTCTTTACATTAGTAATTTTTATGAGGGGATGAAAGTTTTG
65 TTCTTCTGAACCACAGTTGAAGTTTCTTTACATTAGTAATTTTTACGAGGGGATGAAAGTTTTG
346560 T
1 T
346561 CTTTTAATTA
Statistics
Matches: 126, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
129 36 0.29
130 2 0.02
131 40 0.32
132 48 0.38
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.44
Consensus pattern (128 bp):
TAATTTGTTATTATCCTTCTACGGAAACAATTGTAATTGTTGAATAGTGGATACTTTATCTATTT
TCTTCTGAACCACAGTTGAAGTTTCTTTACATTAGTAATTTTTACGAGGGGATGAAAGTTTTG
Done.