Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008709.1 Hibiscus syriacus cultivar Beakdansim tig00111758_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: 3030657
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 15
Found at i:558123 original size:20 final size:22
Alignment explanation
Indices: 558072--558128 Score: 73
Period size: 24 Copynumber: 2.6 Consensus size: 22
558062 ATGCATAAGT
*
558072 AGTGCATCGATGCACTTGTTAG
1 AGTGCATCGATACACTTGTTAG
558094 AGGATGCATCGATACAC-TG-TAG
1 A-G-TGCATCGATACACTTGTTAG
558116 AGTGCATCGATAC
1 AGTGCATCGATAC
558129 CTATATTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 11 0.34
21 1 0.03
22 5 0.16
23 3 0.09
24 12 0.38
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.26
Consensus pattern (22 bp):
AGTGCATCGATACACTTGTTAG
Found at i:558879 original size:18 final size:18
Alignment explanation
Indices: 558856--558908 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
558846 GTTCTTAAGG
558856 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
558874 AGTGGTCCATCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
558892 TGTGGTCCTTCAGGACA
1 AGTGGTCCTTCGGGACA
558909 AATATATTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.19, C:0.23, G:0.32, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:559337 original size:21 final size:21
Alignment explanation
Indices: 559300--559339 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
559290 TTAACTATGG
559300 AAAAGATATATAAATAAGTAT
1 AAAAGATATATAAATAAGTAT
*
559321 AAAAGGATAT-TAGATAAGT
1 AAAA-GATATATAAATAAGT
559340 TGTGTAGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.57, C:0.00, G:0.15, T:0.28
Consensus pattern (21 bp):
AAAAGATATATAAATAAGTAT
Found at i:562749 original size:19 final size:19
Alignment explanation
Indices: 562725--562814 Score: 135
Period size: 19 Copynumber: 4.7 Consensus size: 19
562715 GAATGCAATT
562725 AGTGCATCGATGCATAGTA
1 AGTGCATCGATGCATAGTA
* *
562744 AGTGCATTGATGCATAGTG
1 AGTGCATCGATGCATAGTA
*
562763 AGTGCATCGATGCATAGCA
1 AGTGCATCGATGCATAGTA
* *
562782 AGTGCATTGATGCATAGTG
1 AGTGCATCGATGCATAGTA
562801 AGTGCATCGATGCA
1 AGTGCATCGATGCA
562815 CCCCCTTAAG
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 62 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.27
Consensus pattern (19 bp):
AGTGCATCGATGCATAGTA
Found at i:562767 original size:38 final size:38
Alignment explanation
Indices: 562725--562814 Score: 171
Period size: 38 Copynumber: 2.4 Consensus size: 38
562715 GAATGCAATT
*
562725 AGTGCATCGATGCATAGTAAGTGCATTGATGCATAGTG
1 AGTGCATCGATGCATAGCAAGTGCATTGATGCATAGTG
562763 AGTGCATCGATGCATAGCAAGTGCATTGATGCATAGTG
1 AGTGCATCGATGCATAGCAAGTGCATTGATGCATAGTG
562801 AGTGCATCGATGCA
1 AGTGCATCGATGCA
562815 CCCCCTTAAG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 51 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.27
Consensus pattern (38 bp):
AGTGCATCGATGCATAGCAAGTGCATTGATGCATAGTG
Found at i:563672 original size:18 final size:18
Alignment explanation
Indices: 563649--563701 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
563639 GTTCTTAAGG
563649 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
563667 AGTGGTCCTTCGAGACAT
1 AGTGGTCCTTCGGGACAT
*
563685 AGTGGTCATTCGGGACA
1 AGTGGTCCTTCGGGACA
563702 AATATACAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.21, C:0.21, G:0.32, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:570269 original size:11 final size:10
Alignment explanation
Indices: 570246--570314 Score: 52
Period size: 11 Copynumber: 6.6 Consensus size: 10
570236 ATTAGATTGT
*
570246 AAAATAAAAA
1 AAAATATAAA
570256 AAAATATGAAA
1 AAAATAT-AAA
570267 AAAA-AT-AA
1 AAAATATAAA
*
570275 AAAATATTAAT
1 AAAATA-TAAA
570286 AAAATAATAATA
1 AAAAT-ATAA-A
*
570298 ATAATATAAA
1 AAAATATAAA
570308 AAGAATA
1 AA-AATA
570315 GAAATAAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
8 6 0.13
9 1 0.02
10 11 0.23
11 24 0.51
12 5 0.11
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (10 bp):
AAAATATAAA
Found at i:570276 original size:9 final size:9
Alignment explanation
Indices: 570245--570415 Score: 62
Period size: 9 Copynumber: 18.8 Consensus size: 9
570235 AATTAGATTG
*
570245 TAAAATAAA
1 TAAAAAAAA
*
570254 -AAAAAATA
1 TAAAAAAAA
570262 TGAAAAAAAA
1 T-AAAAAAAA
*
570272 TAAAAAATA
1 TAAAAAAAA
* *
570281 TTAATAAAA
1 TAAAAAAAA
* *
570290 TAATAATAA
1 TAAAAAAAA
570299 TAATATAAAAA
1 TAA-A-AAAAA
* * *
570310 GAATAGAAA
1 TAAAAAAAA
570319 TAAAAAAAA
1 TAAAAAAAA
*
570328 TAAACAAAAGG
1 TAAA-AAAA-A
* ***
570339 TTAAATTTA
1 TAAAAAAAA
570348 -AAAAAAAA
1 TAAAAAAAA
570356 TAAAAAAAA
1 TAAAAAAAA
***
570365 TGTTAAAAA
1 TAAAAAAAA
* *
570374 -AATAAATA
1 TAAAAAAAA
*
570382 TTAAAAAAA
1 TAAAAAAAA
570391 TCAAAAAAAA
1 T-AAAAAAAA
*
570401 T-AAATAAA
1 TAAAAAAAA
570409 TAAAAAA
1 TAAAAAA
570416 GGATCAAAAT
Statistics
Matches: 111, Mismatches: 41, Indels: 20
0.65 0.24 0.12
Matches are distributed among these distances:
8 22 0.20
9 59 0.53
10 21 0.19
11 9 0.08
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.20
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:570299 original size:14 final size:14
Alignment explanation
Indices: 570245--570331 Score: 63
Period size: 14 Copynumber: 6.3 Consensus size: 14
570235 AATTAGATTG
570245 TAAAATAAAAA-AA
1 TAAAATAAAAATAA
* *
570258 -AATATGAAAAAAAA
1 TAAAAT-AAAAATAA
* *
570272 TAAAA-AATATTAA
1 TAAAATAAAAATAA
*
570285 TAAAATAATAATAA
1 TAAAATAAAAATAA
* *
570299 TAATATAAAAAGAA
1 TAAAATAAAAATAA
*
570313 TAGAAATAAAAAAAA
1 TA-AAATAAAAATAA
570328 TAAA
1 TAAA
570332 CAAAAGGTTA
Statistics
Matches: 58, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
12 4 0.07
13 15 0.26
14 24 0.41
15 15 0.26
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (14 bp):
TAAAATAAAAATAA
Found at i:570314 original size:17 final size:15
Alignment explanation
Indices: 570273--570330 Score: 55
Period size: 17 Copynumber: 3.6 Consensus size: 15
570263 GAAAAAAAAT
*
570273 AAAAAATATTAATAA
1 AAAAAATAATAATAA
570288 AATAATAATAATAATATA
1 AA-AA-AATAATAATA-A
570306 AAAAGAATAGA-AATAA
1 AAAA-AATA-ATAATAA
570322 AAAAAATAA
1 AAAAAATAA
570331 ACAAAAGGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
14 1 0.03
15 6 0.16
16 7 0.19
17 19 0.51
18 4 0.11
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.22
Consensus pattern (15 bp):
AAAAAATAATAATAA
Found at i:570380 original size:15 final size:15
Alignment explanation
Indices: 570357--570391 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
570347 AAAAAAAAAT
*
570357 AAAAA-AAATGTTAA
1 AAAAATAAATATTAA
570371 AAAAATAAATATTAA
1 AAAAATAAATATTAA
570386 AAAAAT
1 AAAAAT
570392 CAAAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (15 bp):
AAAAATAAATATTAA
Found at i:570387 original size:26 final size:24
Alignment explanation
Indices: 570347--570424 Score: 70
Period size: 26 Copynumber: 3.1 Consensus size: 24
570337 GGTTAAATTT
**
570347 AAAAAA-AAATA-AAAAAAATGTTA
1 AAAAAATAAATATAAAAAAAT-CAA
570370 AAAAAATAAATATTAAAAAAATCAA
1 AAAAAATAAATA-TAAAAAAATCAA
570395 AAAAAATAAATAAATAAAAAAGGATCAA
1 AAAAAATAAAT--ATAAAAAA--ATCAA
570423 AA
1 AA
570425 TGAATGATGT
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
23 6 0.13
24 5 0.11
25 12 0.26
26 15 0.33
27 1 0.02
28 7 0.15
ACGTcount: A:0.77, C:0.03, G:0.04, T:0.17
Consensus pattern (24 bp):
AAAAAATAAATATAAAAAAATCAA
Found at i:574837 original size:28 final size:26
Alignment explanation
Indices: 574806--574857 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 26
574796 ATATCTAAAA
574806 TATTTTAT-TAATAATTTTAGACATATAT
1 TATTTT-TGTAAT-ATTTTAGA-ATATAT
574834 TATTTTTGTAATATTTTAGAATAT
1 TATTTTTGTAATATTTTAGAATAT
574858 TCTCAAGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 4 0.17
27 9 0.39
28 10 0.43
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.56
Consensus pattern (26 bp):
TATTTTTGTAATATTTTAGAATATAT
Found at i:576077 original size:15 final size:15
Alignment explanation
Indices: 576057--576090 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
576047 CTTTATCTTA
576057 TCCCTTAACGCACCT
1 TCCCTTAACGCACCT
576072 TCCCTTAACGCACCT
1 TCCCTTAACGCACCT
576087 TCCC
1 TCCC
576091 GATTACTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.18, C:0.50, G:0.06, T:0.26
Consensus pattern (15 bp):
TCCCTTAACGCACCT
Found at i:577201 original size:8 final size:7
Alignment explanation
Indices: 577184--577271 Score: 50
Period size: 6 Copynumber: 13.3 Consensus size: 7
577174 TTAGATAGAA
577184 AAATAAT
1 AAATAAT
577191 AAATCAAT
1 AAAT-AAT
577199 -AA-AA-
1 AAATAAT
577203 AAATAAT
1 AAATAAT
577210 AGAATAAT
1 A-AATAAT
577218 AAAAATAAT
1 --AAATAAT
577227 AAATAA-
1 AAATAAT
*
577233 AAACAA-
1 AAATAAT
*
577239 AAAAAAT
1 AAATAAT
577246 AAA-AAT
1 AAATAAT
*
577252 AAA-AAC
1 AAATAAT
577258 AAA-AA-
1 AAATAAT
577263 AAATAAT
1 AAATAAT
577270 AA
1 AA
577272 TAAACATAAA
Statistics
Matches: 68, Mismatches: 3, Indels: 20
0.75 0.03 0.22
Matches are distributed among these distances:
5 7 0.10
6 27 0.40
7 18 0.26
8 9 0.13
9 6 0.09
10 1 0.01
ACGTcount: A:0.78, C:0.03, G:0.01, T:0.17
Consensus pattern (7 bp):
AAATAAT
Found at i:577224 original size:36 final size:34
Alignment explanation
Indices: 577182--577256 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 34
577172 TGTTAGATAG
* *
577182 AAAAATAATAAATCAATAA-AAAAATAATAGAATAAT
1 AAAAATAATAAAT-AAAAACAAAAAAAATA-AA-AAT
577218 AAAAATAATAAATAAAAACAAAAAAAATAAAAAT
1 AAAAATAATAAATAAAAACAAAAAAAATAAAAAT
577252 AAAAA
1 AAAAA
577257 CAAAAAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
34 8 0.22
35 6 0.17
36 22 0.61
ACGTcount: A:0.79, C:0.03, G:0.01, T:0.17
Consensus pattern (34 bp):
AAAAATAATAAATAAAAACAAAAAAAATAAAAAT
Found at i:577240 original size:6 final size:6
Alignment explanation
Indices: 577196--577271 Score: 54
Period size: 6 Copynumber: 12.8 Consensus size: 6
577186 ATAATAAATC
* *
577196 AATAAA AA-AAT AATAGAA TAATAAA AATAATA AAT-AA AA-ACA AA-AAA
1 AATAAA AATAAA AATA-AA -AATAAA AATAA-A AATAAA AATAAA AATAAA
*
577243 AATAAA AATAAA AACAAA AA-AAA TAATAA
1 AATAAA AATAAA AATAAA AATAAA -AATAA
577272 TAAACATAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 15
0.74 0.06 0.19
Matches are distributed among these distances:
5 17 0.30
6 27 0.47
7 9 0.16
8 4 0.07
ACGTcount: A:0.80, C:0.03, G:0.01, T:0.16
Consensus pattern (6 bp):
AATAAA
Found at i:577242 original size:21 final size:22
Alignment explanation
Indices: 577218--577275 Score: 102
Period size: 21 Copynumber: 2.7 Consensus size: 22
577208 ATAGAATAAT
577218 AAAAATAATAAATAAAAACAAA
1 AAAAATAATAAATAAAAACAAA
577240 AAAAATAA-AAATAAAAACAAA
1 AAAAATAATAAATAAAAACAAA
577261 AAAAATAAT-AATAAA
1 AAAAATAATAAATAAA
577276 CATAAATCAG
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
21 27 0.77
22 8 0.23
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.14
Consensus pattern (22 bp):
AAAAATAATAAATAAAAACAAA
Found at i:577268 original size:15 final size:16
Alignment explanation
Indices: 577227--577265 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
577217 TAAAAATAAT
577227 AAATAAAAACAAAAA-
1 AAATAAAAACAAAAAC
*
577242 AAATAAAAATAAAAAC
1 AAATAAAAACAAAAAC
577258 AAA-AAAAA
1 AAATAAAAA
577266 TAATAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 19 0.86
16 3 0.14
ACGTcount: A:0.87, C:0.05, G:0.00, T:0.08
Consensus pattern (16 bp):
AAATAAAAACAAAAAC
Found at i:577276 original size:19 final size:19
Alignment explanation
Indices: 577185--577277 Score: 80
Period size: 21 Copynumber: 4.6 Consensus size: 19
577175 TAGATAGAAA
*
577185 AATAATAAATCAATAAAAA-
1 AATAATAAA-CAAAAAAAAT
* *
577204 AATAATAGAATAATAAAAAT
1 AATAATA-AACAAAAAAAAT
577224 AATAAATAAAAACAAAAAAAAT
1 AAT-AAT--AAACAAAAAAAAT
*
577246 AAAAATAAAAACAAAAAAAAT
1 AATAAT--AAACAAAAAAAAT
577267 AATAATAAACA
1 AATAATAAACA
577278 TAAATCAGAG
Statistics
Matches: 64, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
19 20 0.31
20 5 0.08
21 26 0.41
22 12 0.19
23 1 0.02
ACGTcount: A:0.77, C:0.04, G:0.01, T:0.17
Consensus pattern (19 bp):
AATAATAAACAAAAAAAAT
Found at i:577350 original size:3 final size:3
Alignment explanation
Indices: 577342--577370 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
577332 GAATAAGTCA
577342 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
577371 GAGAATAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:578799 original size:38 final size:37
Alignment explanation
Indices: 578668--578909 Score: 250
Period size: 38 Copynumber: 6.9 Consensus size: 37
578658 TTATAAAAAA
578668 TTAAAAACTATATATA-ATATATTTTCAAAAA-G---
1 TTAAAAACTATATATATATATATTTTCAAAAATGTTT
* *
578700 -TAAAAA-T-TATATA-ATATCTTTTCAAAAATATTT
1 TTAAAAACTATATATATATATATTTTCAAAAATGTTT
*
578733 TTAAAAA-T-TATATA-ATATATTTTAAAAAATGTTT
1 TTAAAAACTATATATATATATATTTTCAAAAATGTTT
*
578767 TTAAAAATTATATAATATATATATTTTCAAAAAATG-TT
1 TTAAAAACTATAT-ATATATATATTTTC-AAAAATGTTT
578805 TTAAAAACTATATATTATATATATTTTC-AAAATGTTT
1 TTAAAAACTATATA-TATATATATTTTCAAAAATGTTT
578842 TTAAAAAACTATATAT-TATATATTTTC-AAAATGTTT
1 TT-AAAAACTATATATATATATATTTTCAAAAATGTTT
* *
578878 TTCAAAAAACTAGATA-ATACATA-TTTCAAAAA
1 TT--AAAAACTATATATATATATATTTTCAAAAA
578910 AAAATGTTTT
Statistics
Matches: 185, Mismatches: 9, Indels: 27
0.84 0.04 0.12
Matches are distributed among these distances:
29 20 0.11
30 1 0.01
31 6 0.03
34 37 0.20
35 1 0.01
36 35 0.19
37 30 0.16
38 48 0.26
39 7 0.04
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.43
Consensus pattern (37 bp):
TTAAAAACTATATATATATATATTTTCAAAAATGTTT
Found at i:578902 original size:37 final size:36
Alignment explanation
Indices: 578670--578908 Score: 200
Period size: 36 Copynumber: 6.8 Consensus size: 36
578660 ATAAAAAATT
*
578670 AAAAACTATAT-ATAATATATTTTCAAAAAG----T-
1 AAAAACTATATAAT-ATATATTTTCAAAATGTTTTTA
* * *
578701 AAAAATTATAT-A-ATATCTTTTCAAAAATATTTTT-
1 AAAAACTATATAATATATATTTTC-AAAATGTTTTTA
* **
578735 AAAAATTATATAATATAT-TTTAAAAAATGTTTTT-
1 AAAAACTATATAATATATATTTTCAAAATGTTTTTA
*
578769 AAAAATTATATAATATATATATTTTCAAAAAATG-TTTT-
1 AAAAACTATAT-A-ATATATATTTTC--AAAATGTTTTTA
578807 AAAAACTATATATTATATATATTTTCAAAATGTTTTTA
1 AAAAACTATATA--ATATATATTTTCAAAATGTTTTTA
*
578845 AAAAACTATATATTATATATTTTCAAAATGTTTTTCA
1 AAAAACTATATAATATATATTTTCAAAATGTTTTT-A
* *
578882 AAAAACTAGATAATACATA-TTTCAAAA
1 AAAAACTATATAATATATATTTTCAAAA
578909 AAAAATGTTT
Statistics
Matches: 178, Mismatches: 14, Indels: 27
0.81 0.06 0.12
Matches are distributed among these distances:
29 9 0.05
30 4 0.02
31 11 0.06
34 33 0.19
35 5 0.03
36 46 0.26
37 25 0.14
38 39 0.22
39 6 0.03
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (36 bp):
AAAAACTATATAATATATATTTTCAAAATGTTTTTA
Found at i:578995 original size:38 final size:38
Alignment explanation
Indices: 578942--579027 Score: 95
Period size: 38 Copynumber: 2.3 Consensus size: 38
578932 TTTTCAAAAT
*
578942 TTTTTTAAAACTATA-TATTAT-ATATTTTCGAAAACCG
1 TTTTTAAAAACTATATTA-TATGATATTTTCGAAAACCG
* * *
578979 ATTTTTAAAAAGTATATTATATGTTTTTTTCGAAAACCG
1 -TTTTTAAAAACTATATTATATGATATTTTCGAAAACCG
*
579018 TTTTAAAAAA
1 TTTTTAAAAA
579028 TATTTTTCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
38 25 0.61
39 16 0.39
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.45
Consensus pattern (38 bp):
TTTTTAAAAACTATATTATATGATATTTTCGAAAACCG
Found at i:579158 original size:19 final size:19
Alignment explanation
Indices: 579119--579163 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
579109 AAAGTGTTAA
579119 TGAATTTTATGATTTTATAT
1 TGAATTTTA-GATTTTATAT
579139 TGAATTTTA-ATTTATATAT
1 TGAATTTTAGATTT-TATAT
*
579158 TCAATT
1 TGAATT
579164 AAATTATTCG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 10 0.43
20 9 0.39
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (19 bp):
TGAATTTTAGATTTTATAT
Found at i:579427 original size:73 final size:72
Alignment explanation
Indices: 579341--579505 Score: 231
Period size: 73 Copynumber: 2.3 Consensus size: 72
579331 ATACCTAAGT
* * * * *
579341 CATAGGTACCGATACCCTTATGTTGATTTTGGCTCCGAGAAAAACAGAATGCCAAACGGGTATCG
1 CATAGGTATCGATACCCTTATGTTAATTTTGGCTCCAAGAAAAACAAAATGCC-AACGGGTACCG
579406 ATACCCCC
65 ATACCCCC
* * *
579414 CATAGGTATCGATACCCTTGTGTTAATTTTGGCTCCAAGAAAAACAAAATGCCCATGGGTACCGA
1 CATAGGTATCGATACCCTTATGTTAATTTTGGCTCCAAGAAAAACAAAATGCCAACGGGTACCGA
579479 TACCCCC
66 TACCCCC
* *
579486 TAGAGGTATCGATACCCTTA
1 CATAGGTATCGATACCCTTA
579506 ATCTTTTAAC
Statistics
Matches: 81, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
72 33 0.41
73 48 0.59
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.25
Consensus pattern (72 bp):
CATAGGTATCGATACCCTTATGTTAATTTTGGCTCCAAGAAAAACAAAATGCCAACGGGTACCGA
TACCCCC
Found at i:585679 original size:20 final size:20
Alignment explanation
Indices: 585639--585676 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
585629 AGGACGAGAG
*
585639 CTTTTATATTCTCTCATTTC
1 CTTTTATATCCTCTCATTTC
585659 CTTTTAT-TCCTCTCATTT
1 CTTTTATATCCTCTCATTT
585677 TCCATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.13, C:0.26, G:0.00, T:0.61
Consensus pattern (20 bp):
CTTTTATATCCTCTCATTTC
Found at i:598188 original size:16 final size:16
Alignment explanation
Indices: 598167--598198 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
598157 TTTTATTTTG
*
598167 AAATCATGTTTGAAAT
1 AAATCAAGTTTGAAAT
598183 AAATCAAGTTTGAAAT
1 AAATCAAGTTTGAAAT
598199 TACTCCCACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.34
Consensus pattern (16 bp):
AAATCAAGTTTGAAAT
Found at i:598874 original size:18 final size:18
Alignment explanation
Indices: 598861--598896 Score: 63
Period size: 18 Copynumber: 1.9 Consensus size: 18
598851 TCCTCTAGTT
598861 GTGCTTGTTCCTCTGCTC
1 GTGCTTGTTCCTCTGCTC
598879 GTGCTTGTTCCTCGTGCT
1 GTGCTTGTTCCTC-TGCT
598897 GTTCTGGTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.00, C:0.31, G:0.25, T:0.44
Consensus pattern (18 bp):
GTGCTTGTTCCTCTGCTC
Found at i:598906 original size:18 final size:19
Alignment explanation
Indices: 598861--598911 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 19
598851 TCCTCTAGTT
*
598861 GTGCTTGTTCCTC-TGCTC
1 GTGCTGGTTCCTCGTGCTC
*
598879 GTGCTTGTTCCTCGTGCT-
1 GTGCTGGTTCCTCGTGCTC
* *
598897 GTTCTGGTTCATCGT
1 GTGCTGGTTCCTCGT
598912 TAGAGTCGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 25 0.86
19 4 0.14
ACGTcount: A:0.02, C:0.27, G:0.25, T:0.45
Consensus pattern (19 bp):
GTGCTGGTTCCTCGTGCTC
Found at i:600514 original size:22 final size:23
Alignment explanation
Indices: 600454--600515 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 23
600444 TAGAACTCTC
600454 AGGGGGTATCGATTCCCCTTCAA
1 AGGGGGTATCGATTCCCCTTCAA
*
600477 AGGGGGAATC-AGTTCCCCTTC-A
1 AGGGGGTATCGA-TTCCCCTTCAA
600499 AGGGGGTATCGATTCCC
1 AGGGGGTATCGATTCCC
600516 TCTGCACCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
22 16 0.46
23 19 0.54
ACGTcount: A:0.21, C:0.26, G:0.29, T:0.24
Consensus pattern (23 bp):
AGGGGGTATCGATTCCCCTTCAA
Found at i:603039 original size:21 final size:21
Alignment explanation
Indices: 603013--603057 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
603003 GATTTCTGGG
* *
603013 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
603034 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
603055 CAA
1 CAA
603058 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:604495 original size:23 final size:23
Alignment explanation
Indices: 604469--604536 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
604459 ATTATTATAT
604469 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
604492 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
* *
604515 GGCACTTCAGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
604537 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.19, C:0.26, G:0.25, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:609498 original size:23 final size:23
Alignment explanation
Indices: 609472--609539 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
609462 ATTATTATAT
609472 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
609495 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
* *
609518 GGCACTTCAGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
609540 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.19, C:0.26, G:0.25, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:612344 original size:22 final size:21
Alignment explanation
Indices: 612302--612341 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
612292 GAGTTTGTTT
*
612302 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
612323 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
612342 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:614535 original size:13 final size:13
Alignment explanation
Indices: 614517--614541 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
614507 TCGAATATAC
614517 TTAGAAAATCTTT
1 TTAGAAAATCTTT
614530 TTAGAAAATCTT
1 TTAGAAAATCTT
614542 AAAATTCATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (13 bp):
TTAGAAAATCTTT
Found at i:619011 original size:41 final size:41
Alignment explanation
Indices: 618919--619415 Score: 641
Period size: 41 Copynumber: 12.1 Consensus size: 41
618909 GTTTCCAGAT
* * **
618919 TCGCAACGCGATTTTGACTATCGCAATGCGA-ATATGTAA-A
1 TCGCAACGCGATTCTGACTATCGCAACGCGATA-ATACAAGA
618959 TCGCAACGCGATTCTGACTATCGCAACGCGATAATACAAGA
1 TCGCAACGCGATTCTGACTATCGCAACGCGATAATACAAGA
*
619000 TCGCAACGCGATTCTGATTATCGCAACGCGATAATACAAGA
1 TCGCAACGCGATTCTGACTATCGCAACGCGATAATACAAGA
*
619041 TCGCAACGCGATTCTGACTATCGCAACGTGATAATACAAGA
1 TCGCAACGCGATTCTGACTATCGCAACGCGATAATACAAGA
619082 TCGCAACGCGATTCTGACTATCGCAACGCGATAATACAAGA
1 TCGCAACGCGATTCTGACTATCGCAACGCGATAATACAAGA
* * *
619123 TCGCAACGAGATTCTGACTATCGCAACGTGATAATATAAGA
1 TCGCAACGCGATTCTGACTATCGCAACGCGATAATACAAGA
* ** *
619164 TCGCAACGCGATTCTGACTATCGCAACACGATTCTGAC--TA
1 TCGCAACGCGATTCTGACTATCGCAACGCGATAAT-ACAAGA
** * * ** *
619204 TCGCAACGCGATAAT-ACAAGATCGCAAAGCGATTCTGAC--TA
1 TCGCAACGCGATTCTGAC--TATCGCAACGCGATAAT-ACAAGA
** * *
619245 TCGCAACGCGATAAT-ACAAGATCGCAACGTGATAATACAAGA
1 TCGCAACGCGATTCTGAC--TATCGCAACGCGATAATACAAGA
619287 TCGCAACGCGATTCTGACTATCGCAACGCGATAATACAAGA
1 TCGCAACGCGATTCTGACTATCGCAACGCGATAATACAAGA
619328 TCGCAACGCGATTCTGACTATCGCAACGCGATAATACAAGA
1 TCGCAACGCGATTCTGACTATCGCAACGCGATAATACAAGA
* *
619369 TCGCAACGCGATTCTGACTATCGCAATGCGATAATACAAAA
1 TCGCAACGCGATTCTGACTATCGCAACGCGATAATACAAGA
619410 TCGCAA
1 TCGCAA
619416 TGCAATTTTC
Statistics
Matches: 415, Mismatches: 34, Indels: 15
0.89 0.07 0.03
Matches are distributed among these distances:
39 2 0.00
40 49 0.12
41 347 0.84
42 15 0.04
43 2 0.00
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (41 bp):
TCGCAACGCGATTCTGACTATCGCAACGCGATAATACAAGA
Found at i:619875 original size:19 final size:20
Alignment explanation
Indices: 619847--619937 Score: 87
Period size: 19 Copynumber: 4.4 Consensus size: 20
619837 CTTATTTTAG
*
619847 ATTTTCCACTATCGCAACAC
1 ATTTTTCACTATCGCAACAC
619867 -TTTTTCACTATCGCAACAAC
1 ATTTTTCACTATCGCAAC-AC
*
619887 ACGTTTTTCAAACTCTCGCAACAC
1 A--TTTTTC--ACTATCGCAACAC
* *
619911 A-TTTTAACTATTGCAACAC
1 ATTTTTCACTATCGCAACAC
619930 ATTTTTCA
1 ATTTTTCA
619938 AAATCGCGTT
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
19 28 0.48
20 7 0.12
21 4 0.07
23 6 0.10
24 3 0.05
25 10 0.17
ACGTcount: A:0.31, C:0.29, G:0.05, T:0.35
Consensus pattern (20 bp):
ATTTTTCACTATCGCAACAC
Found at i:619910 original size:44 final size:41
Alignment explanation
Indices: 619858--619939 Score: 110
Period size: 44 Copynumber: 1.9 Consensus size: 41
619848 TTTTCCACTA
* *
619858 TCGCAACACTTTTTCACTATCGCAACAACACGTTTTTCAAACTC
1 TCGCAACACATTTTAACTATCGCAAC-ACA--TTTTTCAAACTC
*
619902 TCGCAACACATTTTAACTATTGCAACACATTTTTCAAA
1 TCGCAACACATTTTAACTATCGCAACACATTTTTCAAA
619940 ATCGCGTTGC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
41 9 0.26
43 3 0.09
44 23 0.66
ACGTcount: A:0.33, C:0.28, G:0.06, T:0.33
Consensus pattern (41 bp):
TCGCAACACATTTTAACTATCGCAACACATTTTTCAAACTC
Found at i:626975 original size:13 final size:13
Alignment explanation
Indices: 626957--626981 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
626947 TACAGACTCG
626957 CATATGAAGACTA
1 CATATGAAGACTA
626970 CATATGAAGACT
1 CATATGAAGACT
626982 GTTCAACTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (13 bp):
CATATGAAGACTA
Found at i:630304 original size:34 final size:34
Alignment explanation
Indices: 630255--630323 Score: 113
Period size: 34 Copynumber: 2.0 Consensus size: 34
630245 TCACTTTCCA
*
630255 TCATCTTATCTCGCTAACAATGATAATGTGCATT
1 TCATCTTATCTCGCTAACAATGACAATGTGCATT
630289 TCATCTTAT-TACGCTAACAATGACAATGTGCATT
1 TCATCTTATCT-CGCTAACAATGACAATGTGCATT
630323 T
1 T
630324 GTGATGTAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
33 1 0.03
34 32 0.97
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (34 bp):
TCATCTTATCTCGCTAACAATGACAATGTGCATT
Found at i:631063 original size:42 final size:42
Alignment explanation
Indices: 630974--631098 Score: 162
Period size: 42 Copynumber: 2.9 Consensus size: 42
630964 AATTTGAACT
*** *
630974 ACGTAATTCGTTTTCTGGAAAATCCTGAAATCTCATATTTGTTTC
1 ACGTAATTCGTTTTCTGGAAAA---TGTTTTCTCATGTTTGTTTC
631019 ACGTAATTCGTTTTCTGGAAAATGTTTTCTCATGTTTGTTTC
1 ACGTAATTCGTTTTCTGGAAAATGTTTTCTCATGTTTGTTTC
*
631061 ACGTAATTCGTTTTCCGGAAAATGTTTTCT-AGTGTTTG
1 ACGTAATTCGTTTTCTGGAAAATGTTTTCTCA-TGTTTG
631099 GTTGGAGGAA
Statistics
Matches: 74, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
41 1 0.01
42 51 0.69
45 22 0.30
ACGTcount: A:0.22, C:0.15, G:0.17, T:0.46
Consensus pattern (42 bp):
ACGTAATTCGTTTTCTGGAAAATGTTTTCTCATGTTTGTTTC
Found at i:631335 original size:12 final size:12
Alignment explanation
Indices: 631306--631343 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
631296 AATTATTAAA
631306 ATATTTAA-AAT
1 ATATTTAATAAT
*
631317 ATATTTATTAAT
1 ATATTTAATAAT
*
631329 ATTTTTAATAAT
1 ATATTTAATAAT
631341 ATA
1 ATA
631344 ATATTATATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
ATATTTAATAAT
Found at i:631348 original size:23 final size:23
Alignment explanation
Indices: 631290--631368 Score: 81
Period size: 22 Copynumber: 3.4 Consensus size: 23
631280 TTTTAATCAA
* *
631290 AATATTAATTATTAAAATATTTAA-
1 AATA-TAA-TATTAATATTTTTAAT
*
631314 AATATATTTATTAATATTTTTAAT
1 AATATA-ATATTAATATTTTTAAT
631338 AATATAATATT-ATATTTTTAAT
1 AATATAATATTAATATTTTTAAT
*
631360 ATTATAATA
1 AATATAATA
631369 ATATAAGATA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
22 19 0.40
23 19 0.40
24 10 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATAATATTAATATTTTTAAT
Found at i:631380 original size:32 final size:31
Alignment explanation
Indices: 631316--631403 Score: 119
Period size: 30 Copynumber: 2.8 Consensus size: 31
631306 ATATTTAAAA
631316 TATATTTATTAATATTTTTAATAATAT-AATAT
1 TATATTT-TTAATA-TTTTAATAATATAAATAT
*
631348 TATATTTTTAATATTATAATAATATAAGATAT
1 TATATTTTTAATATTTTAATAATATAA-ATAT
631380 TATATTTTT--TATTTTAATAATATA
1 TATATTTTTAATATTTTAATAATATA
631404 TAAAAAATTA
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
30 25 0.48
31 7 0.13
32 20 0.38
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (31 bp):
TATATTTTTAATATTTTAATAATATAAATAT
Found at i:631414 original size:32 final size:32
Alignment explanation
Indices: 631312--631414 Score: 97
Period size: 32 Copynumber: 3.2 Consensus size: 32
631302 TAAAATATTT
*
631312 AAAA-TATATTTATTAATATTTTTAATAATAT--
1 AAAATTATATTT-TTAATA-TTATAATAATATAA
*
631343 AATATTATATTTTTAATATTATAATAATATAA
1 AAAATTATATTTTTAATATTATAATAATATAA
* * * *
631375 GATATTATATTTTTTATTTTAATAAT-ATATAA
1 AAAATTATATTTTTAATATT-ATAATAATATAA
631407 AAAATTAT
1 AAAATTAT
631415 TAATAAAATT
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
30 11 0.18
31 9 0.15
32 36 0.59
33 5 0.08
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (32 bp):
AAAATTATATTTTTAATATTATAATAATATAA
Found at i:631935 original size:14 final size:14
Alignment explanation
Indices: 631916--631972 Score: 60
Period size: 14 Copynumber: 4.0 Consensus size: 14
631906 TCCAGAAATG
*
631916 TAATTCATTTTTCA
1 TAATTCAATTTTCA
* *
631930 TAATTCAAATTCCA
1 TAATTCAATTTTCA
*
631944 GTAATTCATTTTTCA
1 -TAATTCAATTTTCA
*
631959 GAATTCAATTTTCA
1 TAATTCAATTTTCA
631973 AAAAAACCAA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
14 23 0.68
15 11 0.32
ACGTcount: A:0.33, C:0.16, G:0.04, T:0.47
Consensus pattern (14 bp):
TAATTCAATTTTCA
Found at i:632826 original size:12 final size:12
Alignment explanation
Indices: 632809--632835 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
632799 ATATACTCTG
632809 ATTTTCAATTTA
1 ATTTTCAATTTA
632821 ATTTTCAATTTA
1 ATTTTCAATTTA
632833 ATT
1 ATT
632836 ACTCAACTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.59
Consensus pattern (12 bp):
ATTTTCAATTTA
Found at i:639581 original size:22 final size:22
Alignment explanation
Indices: 639553--639598 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
639543 TTCGACCTTG
639553 GCTTAAATGAAGTATTCTACAA
1 GCTTAAATGAAGTATTCTACAA
639575 GCTTAAATGAAGTATTCTACAA
1 GCTTAAATGAAGTATTCTACAA
639597 GC
1 GC
639599 CTTAGAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.30
Consensus pattern (22 bp):
GCTTAAATGAAGTATTCTACAA
Found at i:640991 original size:65 final size:64
Alignment explanation
Indices: 640921--641073 Score: 218
Period size: 65 Copynumber: 2.4 Consensus size: 64
640911 CCCTATTTCG
* *
640921 AATGCATTTTGTGTACCGATGCACA-AGCCATGCATCGATGCACTCTTGAATATTTTGAAACATC
1 AATGCATTTAGTGTACCGATGCACATA-CCATGCATCGATGCACT-ATGAATATTTTGAAACATC
640985 A
64 A
** *
640986 AATGCATTTAGTGTACCGATGCACATACCATGCATCGATGCACTATGGCTATTTTGAAACATCG
1 AATGCATTTAGTGTACCGATGCACATACCATGCATCGATGCACTATGAATATTTTGAAACATCA
* *
641050 AATGTAATTAGTGTACCGATGCAC
1 AATGCATTTAGTGTACCGATGCAC
641074 CCCTAGTGTA
Statistics
Matches: 80, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
64 38 0.47
65 41 0.51
66 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (64 bp):
AATGCATTTAGTGTACCGATGCACATACCATGCATCGATGCACTATGAATATTTTGAAACATCA
Found at i:647364 original size:13 final size:13
Alignment explanation
Indices: 647346--647392 Score: 69
Period size: 13 Copynumber: 3.7 Consensus size: 13
647336 TACATCGTAA
647346 TTTTCAAACATTG
1 TTTTCAAACATTG
647359 TTTTCAAACATTG
1 TTTTCAAACATTG
*
647372 TTTTCAAA-ATTA
1 TTTTCAAACATTG
*
647384 TTTTTAAAC
1 TTTTCAAAC
647393 TTTGCCCATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
12 10 0.32
13 21 0.68
ACGTcount: A:0.34, C:0.13, G:0.04, T:0.49
Consensus pattern (13 bp):
TTTTCAAACATTG
Found at i:649582 original size:65 final size:65
Alignment explanation
Indices: 649503--649656 Score: 229
Period size: 65 Copynumber: 2.4 Consensus size: 65
649493 CCCTATTTCG
* *
649503 AATGCATTTTGTGTACCGATGCACA-AGCCATGCATCGATGCACTCTTGAATATTTTGAAACATC
1 AATGCATTTAGTGTACCGATGCACATA-CCATGCATCGATGCACTCATGAATATTTTGAAACATC
649567 A
65 A
** *
649568 AATGCATTTAGTGTACCGATGCACATACCATGCATCGATGCACTCATGGCTATTTTGAAACATCG
1 AATGCATTTAGTGTACCGATGCACATACCATGCATCGATGCACTCATGAATATTTTGAAACATCA
* *
649633 AATGTAATTAGTGTACCGATGCAC
1 AATGCATTTAGTGTACCGATGCAC
649657 CCCTAGTGTA
Statistics
Matches: 81, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
65 80 0.99
66 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (65 bp):
AATGCATTTAGTGTACCGATGCACATACCATGCATCGATGCACTCATGAATATTTTGAAACATCA
Found at i:650976 original size:43 final size:40
Alignment explanation
Indices: 650915--651091 Score: 214
Period size: 39 Copynumber: 4.4 Consensus size: 40
650905 TATCGATTAA
* * *
650915 GCACTTCAGTTCATATGGTGGGCATGACCTTATGTGTAATAAT
1 GCACTTCGGTGCATATGGTGGGCACGACCTTATGTG---TAAT
*
650958 GCACTTCGGTGCATATGGTGGACACGACCTTATGTGTAAT
1 GCACTTCGGTGCATATGGTGGGCACGACCTTATGTGTAAT
*
650998 GTACTTCGGTGCATATGGTGGGCACGACCTTATGTGTAA-
1 GCACTTCGGTGCATATGGTGGGCACGACCTTATGTGTAAT
* * * *
651037 GTACTTCGGTGCAAATGGTGGGCACAACCCTATGTGTAA-
1 GCACTTCGGTGCATATGGTGGGCACGACCTTATGTGTAAT
* *
651076 GCACTACGATGCATAT
1 GCACTTCGGTGCATAT
651092 ATTTGACTCG
Statistics
Matches: 121, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
39 48 0.40
40 41 0.34
43 32 0.26
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (40 bp):
GCACTTCGGTGCATATGGTGGGCACGACCTTATGTGTAAT
Found at i:651055 original size:39 final size:40
Alignment explanation
Indices: 650917--651075 Score: 212
Period size: 40 Copynumber: 3.9 Consensus size: 40
650907 TCGATTAAGC
* * * *
650917 ACTTCAGTTCATATGGTGGGCATGACCTTATGTGTAATAATGC
1 ACTTCGGTGCATATGGTGGGCACGACCTTATGTG---TAATGT
*
650960 ACTTCGGTGCATATGGTGGACACGACCTTATGTGTAATGT
1 ACTTCGGTGCATATGGTGGGCACGACCTTATGTGTAATGT
651000 ACTTCGGTGCATATGGTGGGCACGACCTTATGTGTAA-GT
1 ACTTCGGTGCATATGGTGGGCACGACCTTATGTGTAATGT
* * *
651039 ACTTCGGTGCAAATGGTGGGCACAACCCTATGTGTAA
1 ACTTCGGTGCATATGGTGGGCACGACCTTATGTGTAA
651076 GCACTACGAT
Statistics
Matches: 107, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
39 36 0.34
40 41 0.38
43 30 0.28
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (40 bp):
ACTTCGGTGCATATGGTGGGCACGACCTTATGTGTAATGT
Found at i:659326 original size:20 final size:19
Alignment explanation
Indices: 659298--659344 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
659288 TAATAAACAA
*
659298 AAAAT-AATTGGATGAAAA-
1 AAAATAAATTGAAT-AAAAT
659316 AAAATGAAATTGAATAAAAT
1 AAAAT-AAATTGAATAAAAT
659336 AAAATAAAT
1 AAAATAAAT
659345 GAAGATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 5 0.20
19 8 0.32
20 12 0.48
ACGTcount: A:0.66, C:0.00, G:0.11, T:0.23
Consensus pattern (19 bp):
AAAATAAATTGAATAAAAT
Found at i:659481 original size:21 final size:21
Alignment explanation
Indices: 659429--659499 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 21
659419 GCAAAGAAAC
659429 AAAAAATAT-AATGAAAATAAAT
1 AAAAAATATAAAT-AAAAT-AAT
* *
659451 AAATAGTATAAATAAAATAAT
1 AAAAAATATAAATAAAATAAT
*
659472 AAAAAATATATATATAAA-AAT
1 AAAAAATATAAATA-AAATAAT
*
659493 ATAAAAT
1 AAAAAAT
659500 TGTATGTATA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
21 23 0.56
22 15 0.37
23 3 0.07
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (21 bp):
AAAAAATATAAATAAAATAAT
Found at i:659718 original size:13 final size:11
Alignment explanation
Indices: 659691--659739 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
659681 ATAGATAAAA
659691 ATAATAATAAT
1 ATAATAATAAT
659702 ATAAT-AT-AT
1 ATAATAATAAT
659711 ATATATAATAAT
1 ATA-ATAATAAT
*
659723 AGGAA-AATAAT
1 A-TAATAATAAT
659734 ATAATA
1 ATAATA
659740 TAACACAAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
9 5 0.16
10 6 0.19
11 15 0.48
12 4 0.13
13 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (11 bp):
ATAATAATAAT
Found at i:660312 original size:37 final size:37
Alignment explanation
Indices: 660219--660322 Score: 154
Period size: 37 Copynumber: 2.8 Consensus size: 37
660209 ATGCTTGTGG
* * * *
660219 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
*
660256 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
*
660293 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
1 ATCCTATTTTTAGGAGTTTGAATCATAGTA
660323 GGACGAAAAG
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
Found at i:661258 original size:106 final size:106
Alignment explanation
Indices: 661073--662341 Score: 1874
Period size: 106 Copynumber: 12.0 Consensus size: 106
661063 GCATTGTTTC
* * * **
661073 GAGTCCAATATCCTTCGTTGTTAAGTTGAAATTGGCTCTGGAATCGGGAAACTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
661138 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** *
661179 GAGTCCAATATCCTTTATTGTGAAGTTGAAATTGGCT-TCGAAATTGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAAATTGGGAAGTTGTTTGTTGACA
* *
661243 ACCAGAGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
661285 GAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
661350 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGCCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
661391 GAGTCCAATATTCTTCGTCGTTGTGAAGTTGAATTTGGCTCTGAAATTGAGAAGTTGTTTGTTGA
1 GAGTCCAATA-TC--CTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGA
661456 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
63 CAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
661500 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
661565 CCACCGGTCCCTTCGTCGTGAAGTTGAA-TATGCGTTGTATG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACT-TGCGTTGTCTG
* * * * *
661606 AAGTCCGATATCTTTCGCTT-TGAAGTTAAAATTGGCT-TCGAAATTGGGAAATTGTTTGTTGAC
1 GAGTCCAATATCCTTCG-TTGTGAAGTTGAAATTGGCTCT-GAAATTGGGAAGTTGTTTGTTGAC
* * *
661669 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTTTC
64 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
661712 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
661777 CTAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
661818 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTAGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
661883 CCACCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
661924 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAGTTATTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
661989 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
662030 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
662095 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
662136 GAGTCCAATATCCTTCGTTGTGAA---G--ATTCGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
662196 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
662237 GAGTCCAATATCCTTCGCTATGAAGTTGAAATTGGCTCTGAATTTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
662302 CCAGTC-GTCCCTTTGTTGTGAAGTTGAACTTGTGTTGTCT
66 CCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
662342 CAAGTGGCAC
Statistics
Matches: 1055, Mismatches: 91, Indels: 34
0.89 0.08 0.03
Matches are distributed among these distances:
101 92 0.09
103 1 0.00
104 1 0.00
105 3 0.00
106 851 0.81
107 7 0.01
108 2 0.00
109 98 0.09
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.35
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:662369 original size:15 final size:15
Alignment explanation
Indices: 662349--662379 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
662339 TCTCAAGTGG
662349 CACGATATCCTCCGT
1 CACGATATCCTCCGT
662364 CACGATATCCTCCGT
1 CACGATATCCTCCGT
662379 C
1 C
662380 GTGGAGTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.42, G:0.13, T:0.26
Consensus pattern (15 bp):
CACGATATCCTCCGT
Found at i:663317 original size:22 final size:22
Alignment explanation
Indices: 663291--663344 Score: 108
Period size: 22 Copynumber: 2.5 Consensus size: 22
663281 TTGTGTTTGG
663291 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
663313 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
663335 TCAAAGGTTT
1 TCAAAGGTTT
663345 AATGGGGTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.24, C:0.13, G:0.26, T:0.37
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:663994 original size:15 final size:14
Alignment explanation
Indices: 663965--664030 Score: 69
Period size: 15 Copynumber: 4.4 Consensus size: 14
663955 TTTTTGATTC
*
663965 TTGTTCTTTCTTTTT
1 TTGTTTTTTC-TTTT
663980 TTGTTTTCTTCTTTT
1 TTGTTTT-TTCTTTT
663995 TTGCTTCTTTTCTTTT
1 TTG-TT-TTTTCTTTT
*
664011 TTGTTTTTTCCCTTT
1 TTGTTTTTT-CTTTT
664026 TTGTT
1 TTGTT
664031 CTGATTGAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
14 4 0.09
15 24 0.53
16 15 0.33
17 2 0.04
ACGTcount: A:0.00, C:0.15, G:0.08, T:0.77
Consensus pattern (14 bp):
TTGTTTTTTCTTTT
Found at i:664027 original size:31 final size:31
Alignment explanation
Indices: 663965--664032 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 31
663955 TTTTTGATTC
*
663965 TTGTTC-TTTCTTTTTTTGTTTTCTTCTTTT
1 TTGTTCTTTTCTTTTTTTGTTTTCTTCCTTT
663995 TTGCTTCTTTTC-TTTTTTGTTTT-TTCCCTTT
1 TTG-TTCTTTTCTTTTTTTGTTTTCTT-CCTTT
664026 TTGTTCT
1 TTGTTCT
664033 GATTGAATCT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
30 9 0.26
31 21 0.62
32 4 0.12
ACGTcount: A:0.00, C:0.16, G:0.07, T:0.76
Consensus pattern (31 bp):
TTGTTCTTTTCTTTTTTTGTTTTCTTCCTTT
Found at i:667499 original size:20 final size:20
Alignment explanation
Indices: 667470--667515 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
667460 CCGAGTTCTC
* *
667470 CTTGCTGGTGCCCCTTTGGG
1 CTTGCCGGTGCCCCCTTGGG
667490 CTTGCCGGTGCCCCCTTGGG
1 CTTGCCGGTGCCCCCTTGGG
667510 CTTGCC
1 CTTGCC
667516 AGGCCTTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.00, C:0.37, G:0.33, T:0.30
Consensus pattern (20 bp):
CTTGCCGGTGCCCCCTTGGG
Found at i:668382 original size:20 final size:20
Alignment explanation
Indices: 668331--668386 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
668321 AACCAAAAAT
668331 AATAAACATAAAAT--AATTG
1 AATAAA-ATAAAATAAAATTG
* *
668350 GATGAAAAAAAAATAAAATTG
1 AAT-AAAATAAAATAAAATTG
668371 AATAAAATAAAATAAA
1 AATAAAATAAAATAAA
668387 TGAAGATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
19 8 0.27
20 15 0.50
21 7 0.23
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.21
Consensus pattern (20 bp):
AATAAAATAAAATAAAATTG
Found at i:668537 original size:21 final size:22
Alignment explanation
Indices: 668488--668564 Score: 75
Period size: 22 Copynumber: 3.3 Consensus size: 22
668478 ATATAATGAA
*
668488 AATAAATAAATAGTATAAATAAAAT
1 AATAAA-AAATA-TATATAT-AAAT
668513 AATAAAAAATATATATATAAA-
1 AATAAAAAATATATATATAAAT
* *
668534 AATATAAAAATGTATGTATAATAT
1 AATA-AAAAATATATATATAA-AT
668558 AATAAAA
1 AATAAAA
668565 TACTAAATAG
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
21 4 0.09
22 17 0.37
23 10 0.22
24 9 0.20
25 6 0.13
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (22 bp):
AATAAAAAATATATATATAAAT
Found at i:668553 original size:22 final size:21
Alignment explanation
Indices: 668474--668564 Score: 69
Period size: 22 Copynumber: 4.1 Consensus size: 21
668464 CAAAGAAACT
*
668474 AAAA-ATATA-ATGAAAATAA
1 AAAATATATATATAAAAATAA
*
668493 ATAAATAGTATAAATAAAATAATAA
1 A-AAATA-TATATAT-AAA-AATAA
668518 AAAATATATATATAAAAATATA
1 AAAATATATATATAAAAATA-A
* *
668540 AAAATGTATGTATAATATAATAA
1 AAAATATATATATAA-A-AATAA
668563 AA
1 AA
668565 TACTAAATAG
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
19 1 0.02
20 3 0.05
21 5 0.08
22 21 0.36
23 12 0.20
24 11 0.19
25 6 0.10
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (21 bp):
AAAATATATATATAAAAATAA
Found at i:668713 original size:13 final size:13
Alignment explanation
Indices: 668695--668720 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
668685 TAACGTTAGG
668695 AAAATATAGTAAA
1 AAAATATAGTAAA
668708 AAAATATAGTAAA
1 AAAATATAGTAAA
668721 TAAGTAAACA
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:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (13 bp):
AAAATATAGTAAA
Found at i:668756 original size:5 final size:5
Alignment explanation
Indices: 668740--668790 Score: 50
Period size: 5 Copynumber: 9.8 Consensus size: 5
668730 ATAGATAAAA
* *
668740 ATAAT AATAAT ATAAT ATAAT AT-AT AATAAT AGGAAA ATAAT ATAAT
1 ATAAT -ATAAT ATAAT ATAAT ATAAT -ATAAT A-TAAT ATAAT ATAAT
668787 ATAA
1 ATAA
668791 CGCAAAGAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
4 2 0.05
5 26 0.68
6 10 0.26
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (5 bp):
ATAAT
Found at i:668768 original size:26 final size:26
Alignment explanation
Indices: 668739--668789 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
668729 CATAGATAAA
* *
668739 AATAATAATAATATAATATAATATAT
1 AATAATAAGAAAATAATATAATATAT
*
668765 AATAATAGGAAAATAATATAATATA
1 AATAATAAGAAAATAATATAATATA
668790 ACGCAAAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (26 bp):
AATAATAAGAAAATAATATAATATAT
Found at i:669359 original size:37 final size:37
Alignment explanation
Indices: 669266--669363 Score: 142
Period size: 37 Copynumber: 2.6 Consensus size: 37
669256 ATGCTTGTGG
* * * * *
669266 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGCAAAACTCT
*
669303 ATCCTATTTTTAGGAGTTTGAATCATAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGCAAAACTCT
669340 ATCCTATTTTTAGGAGTTTGAATC
1 ATCCTATTTTTAGGAGTTTGAATC
669364 CTAGTAGGAC
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGCAAAACTCT
Found at i:671427 original size:20 final size:19
Alignment explanation
Indices: 671404--671448 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
671394 GTATCAAGGG
*
671404 CTTTGTTGAAGCCATGAAAT
1 CTTTGTCGAAGCCAT-AAAT
671424 CTTTTGTCGAAGCCATAAAT
1 C-TTTGTCGAAGCCATAAAT
*
671444 ATTTG
1 CTTTG
671449 CAAAGAAGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 4 0.18
20 5 0.23
21 13 0.59
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.38
Consensus pattern (19 bp):
CTTTGTCGAAGCCATAAAT
Found at i:671430 original size:21 final size:20
Alignment explanation
Indices: 671405--671443 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
671395 TATCAAGGGC
*
671405 TTTGTTGAAGCCATGAAATCT
1 TTTGTCGAAGCCAT-AAATCT
671426 TTTGTCGAAGCCATAAAT
1 TTTGTCGAAGCCATAAAT
671444 ATTTGCAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (20 bp):
TTTGTCGAAGCCATAAATCT
Found at i:673108 original size:43 final size:44
Alignment explanation
Indices: 673047--673129 Score: 132
Period size: 43 Copynumber: 1.9 Consensus size: 44
673037 ATGGTATGAA
*
673047 GTGAAGTGAAGTGAGAAGATAATT-TTGTTGAGGCAAGAATTAT
1 GTGAAGTGAAATGAGAAGATAATTATTGTTGAGGCAAGAATTAT
* *
673090 GTGAAGTTAAATGAGAAGATAATTATTGTTGAGGCCAGAA
1 GTGAAGTGAAATGAGAAGATAATTATTGTTGAGGCAAGAA
673130 AAATATGCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
43 22 0.61
44 14 0.39
ACGTcount: A:0.39, C:0.04, G:0.29, T:0.29
Consensus pattern (44 bp):
GTGAAGTGAAATGAGAAGATAATTATTGTTGAGGCAAGAATTAT
Found at i:673735 original size:18 final size:18
Alignment explanation
Indices: 673712--673748 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
673702 CAAAACAACA
673712 ATAAACATAAATATACTT
1 ATAAACATAAATATACTT
673730 ATAAACATAAATATACTT
1 ATAAACATAAATATACTT
673748 A
1 A
673749 ATCATCCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (18 bp):
ATAAACATAAATATACTT
Found at i:675377 original size:11 final size:13
Alignment explanation
Indices: 675313--675376 Score: 128
Period size: 13 Copynumber: 4.9 Consensus size: 13
675303 TGAAAGAGGA
675313 AAAATGAAGAGAG
1 AAAATGAAGAGAG
675326 AAAATGAAGAGAG
1 AAAATGAAGAGAG
675339 AAAATGAAGAGAG
1 AAAATGAAGAGAG
675352 AAAATGAAGAGAG
1 AAAATGAAGAGAG
675365 AAAATGAAGAGA
1 AAAATGAAGAGA
675377 AGATGAAGAG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 51 1.00
ACGTcount: A:0.62, C:0.00, G:0.30, T:0.08
Consensus pattern (13 bp):
AAAATGAAGAGAG
Found at i:675382 original size:11 final size:11
Alignment explanation
Indices: 675322--675386 Score: 67
Period size: 13 Copynumber: 5.4 Consensus size: 11
675312 AAAAATGAAG
675322 AGAGAAAATGAA
1 AGAGAAAATG-A
675334 GAGAGAAAATGAA
1 -AGAGAAAATG-A
675347 GAGAGAAAATGAA
1 -AGAGAAAATG-A
675360 GAGAGAAAATGA
1 -AGAGAAAATGA
*
675372 AGAGAAGATGA
1 AGAGAAAATGA
675383 AGAG
1 AGAG
675387 TGTTTAGTGA
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
11 14 0.27
12 1 0.02
13 36 0.71
ACGTcount: A:0.60, C:0.00, G:0.32, T:0.08
Consensus pattern (11 bp):
AGAGAAAATGA
Found at i:675818 original size:4 final size:4
Alignment explanation
Indices: 675809--675834 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
675799 AACATAATAA
675809 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
675835 GAAAGAGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:684503 original size:2 final size:2
Alignment explanation
Indices: 684492--684534 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
684482 AAATTATTAA
684492 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
684531 -T AT A
1 AT AT A
684535 AACATATTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
1 4 0.11
2 33 0.89
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:685552 original size:15 final size:14
Alignment explanation
Indices: 685532--685570 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
685522 AGGAAATAGG
685532 TTTTTTTAAAAATAA
1 TTTTTTTAAAAAT-A
*
685547 TTTTTTTAAATATA
1 TTTTTTTAAAAATA
*
685561 TTTTTATAAA
1 TTTTTTTAAA
685571 GTGCCATGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTTTTTAAAAATA
Found at i:687270 original size:14 final size:14
Alignment explanation
Indices: 687251--687288 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
687241 AAAATCGGAC
687251 AGCAGATTCTGCAA
1 AGCAGATTCTGCAA
687265 AGCAGATTCTGCAA
1 AGCAGATTCTGCAA
*
687279 AACAGATTCT
1 AGCAGATTCT
687289 ATTGGTCAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.24
Consensus pattern (14 bp):
AGCAGATTCTGCAA
Found at i:688508 original size:44 final size:45
Alignment explanation
Indices: 688458--688896 Score: 708
Period size: 44 Copynumber: 9.8 Consensus size: 45
688448 GTAACCATAC
* *
688458 AAATAAGCTTACGAGCTAAAGGAAT-AATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
*
688502 AAATAAGCTTACGAGCTTATGGAAT-AATTGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
*
688546 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTAT-GGAATAAATGGTAAGTATATTGGTA
*
688592 AAATAAGCTTACGAACTTATGGAAT-AATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
*
688636 AAATAAGCTTACGAGCTTATGAGATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATG-GAATAAATGGTAAGTATATTGGTA
* *
688682 AAATAAGCTTATGAGCTTATGGAAT-AATGGAAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
*
688726 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTAT-GGAATAAATGGTAAGTATATTGGTA
688772 AAATAAGCTTACGAGCTTATGGAAT-AATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
*
688816 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTAT-GGAATAAATGGTAAGTATATTGGTA
*
688862 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
688897 AGATTTTATC
Statistics
Matches: 368, Mismatches: 19, Indels: 15
0.92 0.05 0.04
Matches are distributed among these distances:
44 176 0.48
45 39 0.11
46 153 0.42
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
Found at i:688589 original size:90 final size:90
Alignment explanation
Indices: 688458--688896 Score: 774
Period size: 90 Copynumber: 4.9 Consensus size: 90
688448 GTAACCATAC
** *
688458 AAATAAGCTTACGAGC-TAAAGGAAT-AATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
1 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
*
688521 TGGAATAATTGTAAGTATATTGGTA
66 TGGAATAATGGTAAGTATATTGGTA
*
688546 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTAAAATAAGCTTACGAACTTA
1 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
688611 TGGAATAATGGTAAGTATATTGGTA
66 TGGAATAATGGTAAGTATATTGGTA
* *
688636 AAATAAGCTTACGAGCTTATGAGATTAAATGGTAAGTATATTGGTAAAATAAGCTTATGAGCTTA
1 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
*
688701 TGGAATAATGGAAAGTATATTGGTA
66 TGGAATAATGGTAAGTATATTGGTA
688726 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
1 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
688791 TGGAATAATGGTAAGTATATTGGTA
66 TGGAATAATGGTAAGTATATTGGTA
688816 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
1 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
*
688881 TGGGATAAATGGTAAG
66 TGGAAT-AATGGTAAG
688897 AGATTTTATC
Statistics
Matches: 335, Mismatches: 13, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
88 16 0.05
89 6 0.02
90 304 0.91
91 9 0.03
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.31
Consensus pattern (90 bp):
AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
TGGAATAATGGTAAGTATATTGGTA
Found at i:694249 original size:24 final size:22
Alignment explanation
Indices: 694208--694286 Score: 71
Period size: 24 Copynumber: 3.7 Consensus size: 22
694198 GAATGCAATT
694208 AGTGCATCGATGCA---TAAGG
1 AGTGCATCGATGCACTGTAAGG
694227 AGTGCATCGATGCACATGTTAAGG
1 AGTGCATCGATGCAC-TG-TAAGG
*
694251 -GATGCATCGATACACTGT-A-G
1 AG-TGCATCGATGCACTGTAAGG
*
694271 AATGCATCGATGCACT
1 AGTGCATCGATGCACT
694287 TCAAGGGGAA
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
19 14 0.28
20 14 0.28
21 1 0.02
22 1 0.02
23 3 0.06
24 17 0.34
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (22 bp):
AGTGCATCGATGCACTGTAAGG
Found at i:698880 original size:3 final size:3
Alignment explanation
Indices: 698872--698952 Score: 69
Period size: 3 Copynumber: 26.7 Consensus size: 3
698862 GTATATAATG
* * *
698872 TAA TAA TAA TAA TACT TAA TAA -CA TAA T-A TAA TATA TTA TATA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TA-A TAA TA-A TAA
*
698918 TAA TATA TAA TAA TAG TAA TAA TAA T-A TAA TAA TA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
698953 TCAATTCGGA
Statistics
Matches: 63, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
2 5 0.08
3 48 0.76
4 10 0.16
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:698903 original size:5 final size:5
Alignment explanation
Indices: 698890--698949 Score: 50
Period size: 5 Copynumber: 11.2 Consensus size: 5
698880 ATAATACTTA
* *
698890 ATAAC ATAAT ATAAT ATATT AT-AT ATAAT AATATAT AATAAT AGTAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT -ATA-AT -ATAAT A-TAAT
698938 AATAAT ATAAT A
1 -ATAAT ATAAT A
698950 ATATCAATTC
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
4 3 0.06
5 24 0.51
6 13 0.28
7 7 0.15
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:698922 original size:17 final size:17
Alignment explanation
Indices: 698900--698953 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
698890 ATAACATAAT
698900 ATAATATATTATATATA
1 ATAATATATTATATATA
*
698917 ATAATATATAATA-ATA
1 ATAATATATTATATATA
*
698933 GTAATA-A-TA-ATATA
1 ATAATATATTATATATA
698947 ATAATAT
1 ATAATAT
698954 CAATTCGGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
13 1 0.03
14 9 0.29
15 1 0.03
16 8 0.26
17 12 0.39
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (17 bp):
ATAATATATTATATATA
Found at i:698923 original size:22 final size:23
Alignment explanation
Indices: 698874--698952 Score: 83
Period size: 22 Copynumber: 3.4 Consensus size: 23
698864 ATATAATGTA
*
698874 ATAATAATAATACTTAATAACATAAT
1 ATAATAATAATA-GTAAT-A-ATAAT
*
698900 ATAAT-ATATTA-TATATAATAAT
1 ATAATAATAATAGTA-ATAATAAT
698922 AT-ATAATAATAGTAATAATAAT
1 ATAATAATAATAGTAATAATAAT
698944 ATAATAATA
1 ATAATAATA
698953 TCAATTCGGA
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
21 2 0.04
22 22 0.47
23 11 0.23
24 2 0.04
25 5 0.11
26 5 0.11
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (23 bp):
ATAATAATAATAGTAATAATAAT
Found at i:699124 original size:20 final size:20
Alignment explanation
Indices: 699096--699149 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
699086 AAAACATCAT
* *
699096 ACCCTGAGGTTTTACAGATG
1 ACCCAGAGGTTTTACAAATG
699116 ACCCAGAGGTTTTACAAATG
1 ACCCAGAGGTTTTACAAATG
* *
699136 ACCCGGAGGATTTA
1 ACCCAGAGGTTTTA
699150 ATTTTCTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (20 bp):
ACCCAGAGGTTTTACAAATG
Found at i:699410 original size:101 final size:100
Alignment explanation
Indices: 699116--699539 Score: 636
Period size: 100 Copynumber: 4.2 Consensus size: 100
699106 TTTACAGATG
* * ** ** *
699116 ACCCAGAGGTTTTACAAATGACCCGGAGGATTTAATTTTCTAAAACATTAAATGAGAAACTCTGA
1 ACCCTGAGGTTTTACAGATGACCCAAAGGATTTAATTTTCTTGAACATTAAATGAGAAACTTTGA
* *
699181 AAATCACTATCTCATTTTTCATGTGAAAACATCCC
66 AAATCGCTATCTCATTTTTCATGTGAAAACATCCT
* * * * * *
699216 ACCCTAAGGCTTTAGAGATGACCTAGAGAATTTAATTTTCTTGAACATTAAATGAGAAACTTTGA
1 ACCCTGAGGTTTTACAGATGACCCAAAGGATTTAATTTTCTTGAACATTAAATGAGAAACTTTGA
699281 AAATCGCTATCTCATTTTTCATGTGAAAACATCCT
66 AAATCGCTATCTCATTTTTCATGTGAAAACATCCT
699316 ACCCTGAGGTTTTACAGATGACCCAAAGGATTTAATTTTCTTTGAACATTAAATGAGAAACTTTG
1 ACCCTGAGGTTTTACAGATGACCCAAAGGATTTAATTTTC-TTGAACATTAAATGAGAAACTTTG
699381 AAAATCGCTATCTCATTTTTCATGTGAAAACATCCT
65 AAAATCGCTATCTCATTTTTCATGTGAAAACATCCT
* **
699417 ACCCTGAGGTTTTACAAATGACCTGAAGGATTTAATTTTCTTGAACATTAAATGAGAAACTTT-A
1 ACCCTGAGGTTTTACAGATGACCCAAAGGATTTAATTTTCTTGAACATTAAATGAGAAACTTTGA
* *
699481 AATATCGTTATCTCA-TTTTCATGCGAAAACATCCT
66 AA-ATCGCTATCTCATTTTTCATGTGAAAACATCCT
699516 ACCCTGAGGTTTTACAGATGACCC
1 ACCCTGAGGTTTTACAGATGACCC
699540 GGAGGCATTA
Statistics
Matches: 296, Mismatches: 26, Indels: 5
0.91 0.08 0.02
Matches are distributed among these distances:
99 44 0.15
100 155 0.52
101 97 0.33
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (100 bp):
ACCCTGAGGTTTTACAGATGACCCAAAGGATTTAATTTTCTTGAACATTAAATGAGAAACTTTGA
AAATCGCTATCTCATTTTTCATGTGAAAACATCCT
Found at i:699465 original size:201 final size:199
Alignment explanation
Indices: 699116--699539 Score: 654
Period size: 201 Copynumber: 2.1 Consensus size: 199
699106 TTTACAGATG
* * **
699116 ACCCAGAGGTTTTACAAATGACCCGGAGGATTTAATTTTCTAAAACATTAAATGAGAAACTCTGA
1 ACCCTGAGGTTTTACAGATGACCCAAAGGATTTAATTTTCTAAAACATTAAATGAGAAACTCTGA
* *
699181 AAATCACTATCTCATTTTTCATGTGAAAACATCCCACCCTAAGGCTTTAGAGATGACCTAGAGAA
66 AAATCACTATCTCATTTTTCATGTGAAAACATCCCACCCTAAGGCTTTACAAATGACCTAGAGAA
*
699246 TTTAATTTTCTTGAACATTAAATGAGAAACTTTGAAA-ATCGCTATCTCATTTTTCATGTGAAAA
131 TTTAATTTTCTTGAACATTAAATGAGAAACTTT-AAATATCGCTATCTCA-TTTTCATGCGAAAA
699310 CATCCT
194 CATCCT
** *
699316 ACCCTGAGGTTTTACAGATGACCCAAAGGATTTAATTTTCTTTGAACATTAAATGAGAAACTTTG
1 ACCCTGAGGTTTTACAGATGACCCAAAGGATTTAATTTTC-TAAAACATTAAATGAGAAACTCTG
* * * *
699381 AAAATCGCTATCTCATTTTTCATGTGAAAACATCCTACCCTGAGGTTTTACAAATGACCT-GAAG
65 AAAATCACTATCTCATTTTTCATGTGAAAACATCCCACCCTAAGGCTTTACAAATGACCTAG-AG
* *
699445 GATTTAATTTTCTTGAACATTAAATGAGAAACTTTAAATATCGTTATCTCATTTTCATGCGAAAA
129 AATTTAATTTTCTTGAACATTAAATGAGAAACTTTAAATATCGCTATCTCATTTTCATGCGAAAA
699510 CATCCT
194 CATCCT
699516 ACCCTGAGGTTTTACAGATGACCC
1 ACCCTGAGGTTTTACAGATGACCC
699540 GGAGGCATTA
Statistics
Matches: 205, Mismatches: 16, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
200 83 0.40
201 122 0.60
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (199 bp):
ACCCTGAGGTTTTACAGATGACCCAAAGGATTTAATTTTCTAAAACATTAAATGAGAAACTCTGA
AAATCACTATCTCATTTTTCATGTGAAAACATCCCACCCTAAGGCTTTACAAATGACCTAGAGAA
TTTAATTTTCTTGAACATTAAATGAGAAACTTTAAATATCGCTATCTCATTTTCATGCGAAAACA
TCCT
Found at i:707211 original size:21 final size:21
Alignment explanation
Indices: 707152--707212 Score: 61
Period size: 23 Copynumber: 2.8 Consensus size: 21
707142 TAATAATATT
*
707152 TAATATAAATATTAATAATCC
1 TAATATAAATATAAATAATCC
*
707173 T-ATAATAAATTATAAAATTATCC
1 TAAT-ATAAA-TAT-AAATAATCC
*
707196 TAATATAAATGTAAATA
1 TAATATAAATATAAATA
707213 CTAATATTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
20 2 0.06
21 10 0.31
22 5 0.16
23 13 0.41
24 2 0.06
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.38
Consensus pattern (21 bp):
TAATATAAATATAAATAATCC
Found at i:708452 original size:3 final size:3
Alignment explanation
Indices: 708444--708515 Score: 76
Period size: 3 Copynumber: 23.7 Consensus size: 3
708434 GTATACGATG
* *
708444 TAA TAA TAA TAA TACT TAA TAA T-A TAA TATA TTA TATA TAA TAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TA-A TAA TA-A TAA TAA TAA
*
708491 TAA TAG TAA TAA TAA T-A TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
708516 TCAATTCGGA
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
2 4 0.07
3 47 0.81
4 7 0.12
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:709022 original size:16 final size:17
Alignment explanation
Indices: 708988--709026 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
708978 TTCCAATTCA
708988 TAAATAAATTAAAATGT
1 TAAATAAATTAAAATGT
709005 TAAA-AAATT-AAATCGT
1 TAAATAAATTAAAAT-GT
709021 TAAATA
1 TAAATA
709027 TGTAATATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 4 0.20
16 11 0.55
17 5 0.25
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (17 bp):
TAAATAAATTAAAATGT
Found at i:714780 original size:18 final size:18
Alignment explanation
Indices: 714745--714787 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
714735 AAATATATTA
*
714745 AAAT-AATAAAAGCGATT
1 AAATAAATAAAAGCAATT
*
714762 AAATAAATAAAAGTAATT
1 AAATAAATAAAAGCAATT
714780 AAAGTAAA
1 AAA-TAAA
714788 AATAAGAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 4 0.18
18 14 0.64
19 4 0.18
ACGTcount: A:0.65, C:0.02, G:0.09, T:0.23
Consensus pattern (18 bp):
AAATAAATAAAAGCAATT
Found at i:716494 original size:15 final size:14
Alignment explanation
Indices: 716476--716514 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
716466 GTTTTCCATT
*
716476 TTTTTCTTTCATGTC
1 TTTTTCTTTC-TCTC
*
716491 TTTTTTTTTCTCTC
1 TTTTTCTTTCTCTC
716505 TTTTTCTTTC
1 TTTTTCTTTC
716515 GAACAACTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.03, C:0.21, G:0.03, T:0.74
Consensus pattern (14 bp):
TTTTTCTTTCTCTC
Found at i:716533 original size:27 final size:27
Alignment explanation
Indices: 716493--716566 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 27
716483 TTCATGTCTT
716493 TTTTTTTCTCTCTTTTTCTTTCGAACAAC
1 TTTTTTT-T-TCTTTTTCTTTCGAACAAC
**
716522 TTTTTTTTTC-TTTT-TTTCGAACTGC
1 TTTTTTTTTCTTTTTCTTTCGAACAAC
716547 -TTTTTTTTCTTCTTTCTTTC
1 TTTTTTTTTCTT-TTTCTTTC
716567 ATTCAACATT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
24 9 0.22
25 10 0.25
26 7 0.17
27 6 0.15
28 1 0.03
29 7 0.17
ACGTcount: A:0.08, C:0.20, G:0.04, T:0.68
Consensus pattern (27 bp):
TTTTTTTTTCTTTTTCTTTCGAACAAC
Found at i:723048 original size:18 final size:18
Alignment explanation
Indices: 723013--723055 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
723003 AAATATATTA
*
723013 AAAT-AATAAAAGCGATT
1 AAATAAATAAAAGCAATT
*
723030 AAATAAATAAAAGTAATT
1 AAATAAATAAAAGCAATT
723048 AAAGTAAA
1 AAA-TAAA
723056 AATAAGAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 4 0.18
18 14 0.64
19 4 0.18
ACGTcount: A:0.65, C:0.02, G:0.09, T:0.23
Consensus pattern (18 bp):
AAATAAATAAAAGCAATT
Found at i:724514 original size:20 final size:20
Alignment explanation
Indices: 724489--724575 Score: 106
Period size: 20 Copynumber: 4.3 Consensus size: 20
724479 TTTTCCAAAT
*
724489 TCGCAATGTGAATA-GTTAAA
1 TCGCAACGTGAATATG-TAAA
724509 TCGCAACGAT-AATATGTAAA
1 TCGCAACG-TGAATATGTAAA
*
724529 TCGCAACGCGAATATGTAAA
1 TCGCAACGTGAATATGTAAA
* *
724549 TCGCAACGCGAATTTGTAAA
1 TCGCAACGTGAATATGTAAA
724569 TCGCAAC
1 TCGCAAC
724576 ACAGAAGTCA
Statistics
Matches: 61, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
20 59 0.97
21 2 0.03
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.24
Consensus pattern (20 bp):
TCGCAACGTGAATATGTAAA
Found at i:724704 original size:19 final size:20
Alignment explanation
Indices: 724670--724737 Score: 84
Period size: 20 Copynumber: 3.4 Consensus size: 20
724660 ATTTTCTAAA
724670 TCGCAACACGAATTTTGATT
1 TCGCAACACGAATTTTGATT
* * *
724690 TTGCAACTC-AATTTTTGAAT
1 TCGCAACACGAA-TTTTGATT
*
724710 TCGCAACACGAATTTTAATT
1 TCGCAACACGAATTTTGATT
724730 TCGCAACA
1 TCGCAACA
724738 GCTTTTATTT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
19 2 0.05
20 35 0.90
21 2 0.05
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (20 bp):
TCGCAACACGAATTTTGATT
Found at i:725708 original size:24 final size:24
Alignment explanation
Indices: 725681--725758 Score: 120
Period size: 24 Copynumber: 3.2 Consensus size: 24
725671 ATATTCGAAA
725681 TTTGATCTTGGTCAATACCCAGAC
1 TTTGATCTTGGTCAATACCCAGAC
**
725705 TTTGATCTTGGTCAATACCTGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
725729 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
725753 TTTGAT
1 TTTGAT
725759 GATGTTTCAG
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:728041 original size:6 final size:6
Alignment explanation
Indices: 728030--728065 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
728020 CAAGTAAAAG
**
728030 AAAATC AAAATC GCAATC AAAATC AAAATC AAAATC
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC
728066 TCAATCACAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.61, C:0.19, G:0.03, T:0.17
Consensus pattern (6 bp):
AAAATC
Found at i:728049 original size:12 final size:12
Alignment explanation
Indices: 728032--728072 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
728022 AGTAAAAGAA
*
728032 AATCAAAATCGC
1 AATCAAAATCAC
*
728044 AATCAAAATCAA
1 AATCAAAATCAC
*
728056 AATCAAAATCTC
1 AATCAAAATCAC
728068 AATCA
1 AATCA
728073 CAACCGACTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.56, C:0.22, G:0.02, T:0.20
Consensus pattern (12 bp):
AATCAAAATCAC
Found at i:728403 original size:20 final size:20
Alignment explanation
Indices: 728378--728510 Score: 187
Period size: 20 Copynumber: 6.7 Consensus size: 20
728368 AGGTACACTT
*
728378 TCGCAACGAGAAAGACAAAA
1 TCGCAACGCGAAAGACAAAA
728398 TCGCAACGCGAAAGACAAAA
1 TCGCAACGCGAAAGACAAAA
*
728418 TCGCAACGCGAAAGTCAAAA
1 TCGCAACGCGAAAGACAAAA
*
728438 TCGCAACACGAAA-ATCAAAA
1 TCGCAACGCGAAAGA-CAAAA
* *
728458 TCGCAACGTGAAAGTCAAAA
1 TCGCAACGCGAAAGACAAAA
*
728478 TCGCAACGCGAAAGTCAAAA
1 TCGCAACGCGAAAGACAAAA
*
728498 TTGCAACGCGAAA
1 TCGCAACGCGAAA
728511 ATCACAACGC
Statistics
Matches: 102, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
20 102 1.00
ACGTcount: A:0.48, C:0.23, G:0.19, T:0.10
Consensus pattern (20 bp):
TCGCAACGCGAAAGACAAAA
Found at i:728459 original size:60 final size:60
Alignment explanation
Indices: 728393--728514 Score: 208
Period size: 60 Copynumber: 2.0 Consensus size: 60
728383 ACGAGAAAGA
728393 CAAAATCGCAACGCGAAAGACAAAATCGCAACGCGAAAGTCAAAATCGCAACACGAAAAT
1 CAAAATCGCAACGCGAAAGACAAAATCGCAACGCGAAAGTCAAAATCGCAACACGAAAAT
* * * *
728453 CAAAATCGCAACGTGAAAGTCAAAATCGCAACGCGAAAGTCAAAATTGCAACGCGAAAAT
1 CAAAATCGCAACGCGAAAGACAAAATCGCAACGCGAAAGTCAAAATCGCAACACGAAAAT
728513 CA
1 CA
728515 CAACGCGAAT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.11
Consensus pattern (60 bp):
CAAAATCGCAACGCGAAAGACAAAATCGCAACGCGAAAGTCAAAATCGCAACACGAAAAT
Found at i:728729 original size:20 final size:20
Alignment explanation
Indices: 728704--728776 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
728694 TTCCTTGAAT
728704 TCGCAACGCGAAAGTCAAAA
1 TCGCAACGCGAAAGTCAAAA
*
728724 TCGCAACGTGAAAGTCAAAA
1 TCGCAACGCGAAAGTCAAAA
*
728744 TCACAACGCGAAAGTCAAAA
1 TCGCAACGCGAAAGTCAAAA
*
728764 TCGCAACACGAAA
1 TCGCAACGCGAAA
728777 ATTGCATCGC
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.47, C:0.25, G:0.18, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAGTCAAAA
Found at i:729065 original size:15 final size:15
Alignment explanation
Indices: 729045--729084 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
729035 GCAGAAACCA
729045 AACATTTTCTCAAAT
1 AACATTTTCTCAAAT
729060 AACATTTTCTCAAAT
1 AACATTTTCTCAAAT
*
729075 AACACTTTCT
1 AACATTTTCT
729085 ACACATCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (15 bp):
AACATTTTCTCAAAT
Found at i:730078 original size:21 final size:21
Alignment explanation
Indices: 730049--730098 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
730039 GTGAATCGGG
*
730049 CTCTCGAACGGTGGGAGGGAC
1 CTCTTGAACGGTGGGAGGGAC
*
730070 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGGTGGGAGGGAC
730091 CTCTTGAA
1 CTCTTGAA
730099 GGATGATAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.18, C:0.22, G:0.40, T:0.20
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGAC
Found at i:730109 original size:21 final size:21
Alignment explanation
Indices: 730064--730150 Score: 86
Period size: 21 Copynumber: 4.1 Consensus size: 21
730054 GAACGGTGGG
* * **
730064 AGGGACCTCTTGAACGGTGGG
1 AGGGGCCTCTTGAACGATGAT
*
730085 AGGGGCCTCTTGAAGGATGAT
1 AGGGGCCTCTTGAACGATGAT
* *
730106 AGGGGCCTCTTAAATGATAGA-
1 AGGGGCCTCTTGAACGAT-GAT
*
730127 AGAGGCCTCTTGAACGATGAT
1 AGGGGCCTCTTGAACGATGAT
730148 AGG
1 AGG
730151 TGCTTCGGGC
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
20 2 0.04
21 49 0.92
22 2 0.04
ACGTcount: A:0.26, C:0.16, G:0.36, T:0.22
Consensus pattern (21 bp):
AGGGGCCTCTTGAACGATGAT
Found at i:732302 original size:19 final size:18
Alignment explanation
Indices: 732274--732309 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
732264 TCTGAAACTT
*
732274 AAAATTGCAACGCGAAATG
1 AAAATCGCAACGC-AAATG
732293 AAAATCGCAACGCAAAT
1 AAAATCGCAACGCAAAT
732310 TTCATTTTCA
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:0.50, C:0.19, G:0.17, T:0.14
Consensus pattern (18 bp):
AAAATCGCAACGCAAATG
Found at i:732348 original size:20 final size:20
Alignment explanation
Indices: 732323--732370 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
732313 ATTTTCACAA
732323 CGTTGCGATTTTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
*
732343 CGTTGCGATTTTCATTTTTG
1 CGTTGCGATTTTCATTTTCG
*
732363 TGTTGCGA
1 CGTTGCGA
732371 ATTTAAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.10, C:0.17, G:0.23, T:0.50
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTTCG
Found at i:732884 original size:19 final size:20
Alignment explanation
Indices: 732862--732899 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
732852 AATATTGTGT
732862 TTCGAATT-CGAAAATAAAA
1 TTCGAATTGCGAAAATAAAA
**
732881 TTCGCGTTGCGAAAATAAA
1 TTCGAATTGCGAAAATAAA
732900 TGTGCTTTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (20 bp):
TTCGAATTGCGAAAATAAAA
Found at i:733049 original size:20 final size:20
Alignment explanation
Indices: 732925--733055 Score: 88
Period size: 20 Copynumber: 6.5 Consensus size: 20
732915 TGAATTATGT
* *
732925 GTTGCGATTTACAAATTTGC
1 GTTGCGATTTACATATTCGC
* *
732945 ATTTCGATTTACATATTCGC
1 GTTGCGATTTACATATTCGC
* * **
732965 GTAGCGATTTAAATATTATC
1 GTTGCGATTTACATATTCGC
732985 GTTGCGATTTA-ACTATTCGC
1 GTTGCGATTTACA-TATTCGC
* * * *
733005 TTTACGAATTTGGA-AAATT-GT
1 GTTGCG-ATTT--ACATATTCGC
*
733026 GTTGCGATTTACCTATTCGC
1 GTTGCGATTTACATATTCGC
733046 GTTGCGATTT
1 GTTGCGATTT
733056 TGGAACCTAT
Statistics
Matches: 83, Mismatches: 22, Indels: 12
0.71 0.19 0.10
Matches are distributed among these distances:
18 1 0.01
19 4 0.05
20 64 0.77
21 9 0.11
22 3 0.04
23 2 0.02
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.42
Consensus pattern (20 bp):
GTTGCGATTTACATATTCGC
Found at i:734346 original size:19 final size:19
Alignment explanation
Indices: 734322--734358 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
734312 TTTTACGAAC
734322 AGTACTATA-TGGTATGAAT
1 AGTACTATACT-GTATGAAT
734341 AGTACTATACTGTATGAA
1 AGTACTATACTGTATGAA
734359 CAATATTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 16 0.94
20 1 0.06
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.35
Consensus pattern (19 bp):
AGTACTATACTGTATGAAT
Found at i:734489 original size:22 final size:21
Alignment explanation
Indices: 734437--734494 Score: 107
Period size: 21 Copynumber: 2.7 Consensus size: 21
734427 AATGGTACTT
734437 ATACCTTGCTACAGTGTACCG
1 ATACCTTGCTACAGTGTACCG
734458 ATACCTTGCTACAGTGTACCG
1 ATACCTTGCTACAGTGTACCG
734479 ATATCCTTGCTACAGT
1 ATA-CCTTGCTACAGT
734495 AACTTTCGGC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 24 0.67
22 12 0.33
ACGTcount: A:0.24, C:0.28, G:0.17, T:0.31
Consensus pattern (21 bp):
ATACCTTGCTACAGTGTACCG
Found at i:738279 original size:13 final size:13
Alignment explanation
Indices: 738256--738280 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
738246 TTTTATCTCT
738256 ATTTTCTTATGTG
1 ATTTTCTTATGTG
738269 ATTTTCTTATGT
1 ATTTTCTTATGT
738281 TTGATGGATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.08, G:0.12, T:0.64
Consensus pattern (13 bp):
ATTTTCTTATGTG
Found at i:738839 original size:3 final size:3
Alignment explanation
Indices: 738805--738867 Score: 53
Period size: 3 Copynumber: 21.7 Consensus size: 3
738795 GTAAAACTTG
* *
738805 TAA TAA GTAA TAT TAA TAA -AA GTAA AAA TAA TAA TAA TAA TAA TAA
1 TAA TAA -TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA
*
738851 -AA T-A TAA T-T TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA
738868 TTTTTGTATA
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
2 7 0.15
3 36 0.75
4 5 0.10
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:739467 original size:30 final size:31
Alignment explanation
Indices: 739431--739489 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
739421 CAAAGATAAG
739431 AGAAACAAACTCAAAGATGTT-TTTGTTTCA
1 AGAAACAAACTCAAAGATGTTGTTTGTTTCA
* * *
739461 AGAAACAGACTTAAAGATTTTGTTTGTTT
1 AGAAACAAACTCAAAGATGTTGTTTGTTT
739490 TGTTTCAAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 18 0.72
31 7 0.28
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.37
Consensus pattern (31 bp):
AGAAACAAACTCAAAGATGTTGTTTGTTTCA
Found at i:740001 original size:33 final size:32
Alignment explanation
Indices: 739917--740036 Score: 105
Period size: 33 Copynumber: 3.4 Consensus size: 32
739907 GTGTTTCGAG
* *
739917 ATAAAATATCTCAAGCAAGACAAAATTTATTTTA
1 ATAAAATGTCTCAAGCGAGAC--AATTTATTTTA
* *
739951 AGAGAAATTGTCTCAAGCGAGACAATTTTTTTTA
1 ATA-AAA-TGTCTCAAGCGAGACAATTTATTTTA
739985 ATAAAACTGTCTCAAGCGAGACAAAATTTATTTTCA
1 ATAAAA-TGTCTCAAGCGAGAC--AATTTATTTT-A
*
740021 AAAGAAATTGTCTCAA
1 ATA-AAA-TGTCTCAA
740037 AGGAGATCGA
Statistics
Matches: 71, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
33 18 0.25
34 14 0.20
35 12 0.17
36 16 0.23
37 11 0.15
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (32 bp):
ATAAAATGTCTCAAGCGAGACAATTTATTTTA
Found at i:747869 original size:75 final size:75
Alignment explanation
Indices: 747746--747973 Score: 456
Period size: 75 Copynumber: 3.0 Consensus size: 75
747736 TTTACAGAGG
747746 TGGTTTCATAGCCATGGTTTACCTGGAGAACTTCGTCTTCAAGCGCTGGTTTGGAGTTTCAGTCA
1 TGGTTTCATAGCCATGGTTTACCTGGAGAACTTCGTCTTCAAGCGCTGGTTTGGAGTTTCAGTCA
747811 TGATCGGCAC
66 TGATCGGCAC
747821 TGGTTTCATAGCCATGGTTTACCTGGAGAACTTCGTCTTCAAGCGCTGGTTTGGAGTTTCAGTCA
1 TGGTTTCATAGCCATGGTTTACCTGGAGAACTTCGTCTTCAAGCGCTGGTTTGGAGTTTCAGTCA
747886 TGATCGGCAC
66 TGATCGGCAC
747896 TGGTTTCATAGCCATGGTTTACCTGGAGAACTTCGTCTTCAAGCGCTGGTTTGGAGTTTCAGTCA
1 TGGTTTCATAGCCATGGTTTACCTGGAGAACTTCGTCTTCAAGCGCTGGTTTGGAGTTTCAGTCA
747961 TGATCGGCAC
66 TGATCGGCAC
747971 TGG
1 TGG
747974 ATTCGGTTCC
Statistics
Matches: 153, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 153 1.00
ACGTcount: A:0.18, C:0.21, G:0.27, T:0.33
Consensus pattern (75 bp):
TGGTTTCATAGCCATGGTTTACCTGGAGAACTTCGTCTTCAAGCGCTGGTTTGGAGTTTCAGTCA
TGATCGGCAC
Done.