Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001991.1 Hibiscus syriacus cultivar Beakdansim tig00004072_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: 2373627
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 13
Found at i:1177125 original size:33 final size:34
Alignment explanation
Indices: 1177078--1177187 Score: 111
Period size: 33 Copynumber: 3.3 Consensus size: 34
1177068 GTTTATATTA
* *
1177078 ATAT-ATATATACTATGTATAAATTATATAGTTT
1 ATATAATATAAACTATGTATAAACTATATAGTTT
* * *
1177111 AT-TAATATAAACTATATATAAGCCATATAGTTT
1 ATATAATATAAACTATGTATAAACTATATAGTTT
* *
1177144 ATACTTATATACAACTATGTA-AAACTCTATAGTTT
1 ATA-TAATATA-AACTATGTATAAACTATATAGTTT
1177179 ATAT-ATATA
1 ATATAATATA
1177188 GTATATATGG
Statistics
Matches: 63, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
32 1 0.02
33 33 0.52
34 1 0.02
35 20 0.32
36 8 0.13
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.43
Consensus pattern (34 bp):
ATATAATATAAACTATGTATAAACTATATAGTTT
Found at i:1177266 original size:41 final size:39
Alignment explanation
Indices: 1177209--1177287 Score: 95
Period size: 41 Copynumber: 2.0 Consensus size: 39
1177199 TTAGGGTTAA
* ***
1177209 TTTATACAATTATATATAGTTTATATATAAACAATATAG
1 TTTATACAAGTATATATAAACTATATATAAACAATATAG
*
1177248 TTTATACATAGTAGTATATAAACTATATATAAACCATATA
1 TTTATACA-AGTA-TATATAAACTATATATAAACAATATA
1177288 TACTATGTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
39 8 0.24
40 3 0.09
41 22 0.67
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.41
Consensus pattern (39 bp):
TTTATACAAGTATATATAAACTATATATAAACAATATAG
Found at i:1178577 original size:24 final size:24
Alignment explanation
Indices: 1178548--1178595 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
1178538 TACAAACAAA
*
1178548 TTTATTTATTGACTTATTTATAAG
1 TTTATTTATCGACTTATTTATAAG
1178572 TTTATTTATCGACTTATTTATAAG
1 TTTATTTATCGACTTATTTATAAG
1178596 CTCGTTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.29, C:0.06, G:0.08, T:0.56
Consensus pattern (24 bp):
TTTATTTATCGACTTATTTATAAG
Found at i:1178603 original size:24 final size:24
Alignment explanation
Indices: 1178551--1178604 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1178541 AAACAAATTT
* * *
1178551 ATTTATTGACTTATTTATAAGTTT
1 ATTTATCGACTTATTTATAAGCTC
1178575 ATTTATCGACTTATTTATAAGCTC
1 ATTTATCGACTTATTTATAAGCTC
*
1178599 GTTTAT
1 ATTTAT
1178605 TCGATTAGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.54
Consensus pattern (24 bp):
ATTTATCGACTTATTTATAAGCTC
Found at i:1178816 original size:23 final size:23
Alignment explanation
Indices: 1178786--1178829 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1178776 GTTGGTTGAA
* *
1178786 GAATATATTCGCAGACGTTAAAC
1 GAATATATTCACAAACGTTAAAC
1178809 GAATATATTCACAAACGTTAA
1 GAATATATTCACAAACGTTAA
1178830 GCGTACACGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.27
Consensus pattern (23 bp):
GAATATATTCACAAACGTTAAAC
Found at i:1182304 original size:21 final size:20
Alignment explanation
Indices: 1182253--1182304 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1182243 TTTTTCCAGT
*
1182253 AGGTATCGATACTCTCTCAG
1 AGGTATCGATACTCACTCAG
* * *
1182273 AGGTATTGATAGTCACTCAT
1 AGGTATCGATACTCACTCAG
1182293 ATGGTATCGATA
1 A-GGTATCGATA
1182305 AGTTAGGGAG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (20 bp):
AGGTATCGATACTCACTCAG
Found at i:1188274 original size:18 final size:19
Alignment explanation
Indices: 1188228--1188304 Score: 70
Period size: 18 Copynumber: 4.2 Consensus size: 19
1188218 GCTATGAACT
*
1188228 TGAAAATAAGCTAT--ATC
1 TGAAAATAAGTTATGAATC
*
1188245 TGAAATTAAGTTATGAATC
1 TGAAAATAAGTTATGAATC
*
1188264 T-AAAATAAGTTATGAGTC
1 TGAAAATAAGTTATGAATC
* * *
1188282 CGAAAACAAGTTTCTGAATC
1 TGAAAATAAG-TTATGAATC
1188302 TGA
1 TGA
1188305 GAATGTTCTG
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
17 12 0.26
18 15 0.32
19 11 0.23
20 9 0.19
ACGTcount: A:0.43, C:0.10, G:0.16, T:0.31
Consensus pattern (19 bp):
TGAAAATAAGTTATGAATC
Found at i:1188476 original size:33 final size:36
Alignment explanation
Indices: 1188428--1188494 Score: 113
Period size: 33 Copynumber: 1.9 Consensus size: 36
1188418 TGATATGACT
1188428 ATTATGTATGATATTGTTTATCATGG-TTTGATATG
1 ATTATGTATGATATTGTTTATCATGGTTTTGATATG
1188463 ATTAT-TATG-TATTGTTTATCATGGTTTTGATA
1 ATTATGTATGATATTGTTTATCATGGTTTTGATA
1188495 AAGTCATGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
33 15 0.48
34 11 0.35
35 5 0.16
ACGTcount: A:0.25, C:0.03, G:0.18, T:0.54
Consensus pattern (36 bp):
ATTATGTATGATATTGTTTATCATGGTTTTGATATG
Found at i:1188915 original size:2 final size:2
Alignment explanation
Indices: 1188908--1188941 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1188898 TTTAGATAAA
1188908 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
1188942 TGATAGAGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1189530 original size:11 final size:12
Alignment explanation
Indices: 1189507--1189540 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
1189497 TCGGTTTAAC
1189507 AATAATTTATTA
1 AATAATTTATTA
1189519 AATAATTT-TTA
1 AATAATTTATTA
*
1189530 ATTAATTTATT
1 AATAATTTATT
1189541 GTTGTTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
AATAATTTATTA
Found at i:1191576 original size:35 final size:34
Alignment explanation
Indices: 1191502--1191582 Score: 94
Period size: 34 Copynumber: 2.4 Consensus size: 34
1191492 TATAGTTTTT
* *
1191502 TAATTTTTTATATTTAATGTATTAAATATCTTAA
1 TAATTTTTTATATTTAATATATTAAATATATTAA
*
1191536 TAATTTTTTATATTTTAA-AT-TTAAATTTATATAA
1 TAATTTTTTATA-TTTAATATATTAAATATAT-TAA
1191570 TGAATTTTTTATA
1 T-AATTTTTTATA
1191583 ATTATATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
33 8 0.20
34 17 0.41
35 16 0.39
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.58
Consensus pattern (34 bp):
TAATTTTTTATATTTAATATATTAAATATATTAA
Found at i:1191597 original size:34 final size:34
Alignment explanation
Indices: 1191502--1191598 Score: 92
Period size: 34 Copynumber: 2.9 Consensus size: 34
1191492 TATAGTTTTT
* * *
1191502 TAATTTTTTATAT-TTAATGTATTAAATATCT-TAA
1 TAATTTTTTATATATTAA-AT-TTAAATTTATATAA
*
1191536 TAATTTTTTATATTTTAAATTTAAATTTATATAA
1 TAATTTTTTATATATTAAATTTAAATTTATATAA
* *
1191570 TGAATTTTTTATA-ATTATATTTTAATTTA
1 T-AATTTTTTATATATTAAATTTAAATTTA
1191599 ATTATTGTTC
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
33 8 0.15
34 31 0.57
35 15 0.28
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.59
Consensus pattern (34 bp):
TAATTTTTTATATATTAAATTTAAATTTATATAA
Found at i:1191909 original size:18 final size:19
Alignment explanation
Indices: 1191883--1191938 Score: 62
Period size: 18 Copynumber: 2.9 Consensus size: 19
1191873 TTTTTTTATT
*
1191883 AAACCATTTA-AAATCGTA
1 AAACAATTTATAAATCGTA
*
1191901 AAACAATTTATAAAT-GAA
1 AAACAATTTATAAATCGTA
1191919 AACACAATTTCATAAATCGT
1 AA-ACAATTT-ATAAATCGT
1191939 TCATAAATTC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 13 0.42
19 11 0.35
20 6 0.19
21 1 0.03
ACGTcount: A:0.52, C:0.14, G:0.05, T:0.29
Consensus pattern (19 bp):
AAACAATTTATAAATCGTA
Found at i:1196718 original size:30 final size:31
Alignment explanation
Indices: 1196684--1196778 Score: 84
Period size: 31 Copynumber: 3.1 Consensus size: 31
1196674 AGAGGTCATA
* *
1196684 AAGAACCTCGGT-AACTGTTCATAGGTCCTG
1 AAGAACCTAGGTAAACTGTCCATAGGTCCTG
* **
1196714 AAGAACCTAGGTAAACTGTCCATATGTCCCA
1 AAGAACCTAGGTAAACTGTCCATAGGTCCTG
* * * * *
1196745 AAGGACATAGGTAATCATGTCCATATGTCTTG
1 AAGAACCTAGGTAAAC-TGTCCATAGGTCCTG
1196777 AA
1 AA
1196779 AGACATAGGT
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
30 11 0.21
31 27 0.52
32 14 0.27
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (31 bp):
AAGAACCTAGGTAAACTGTCCATAGGTCCTG
Found at i:1196768 original size:32 final size:31
Alignment explanation
Indices: 1196721--1196790 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 31
1196711 CTGAAGAACC
1196721 TAGGTAAACTGTCCATATGTC-CCAAAGGACA
1 TAGGTAAACTGTCCATATGTCTCCAAA-GACA
* **
1196752 TAGGTAATCATGTCCATATGTCTTGAAAGACA
1 TAGGTAAAC-TGTCCATATGTCTCCAAAGACA
1196784 TAGGTAA
1 TAGGTAA
1196791 CCCTCGACTC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 8 0.24
32 23 0.68
33 3 0.09
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (31 bp):
TAGGTAAACTGTCCATATGTCTCCAAAGACA
Found at i:1197225 original size:2 final size:2
Alignment explanation
Indices: 1197161--1197217 Score: 73
Period size: 2 Copynumber: 29.5 Consensus size: 2
1197151 ATCACACTAG
* *
1197161 TA TA TA AA TA TA TA TA TA TA TA CA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1197202 TA TA TA CA -A TA TA TA T
1 TA TA TA TA TA TA TA TA T
1197218 TCATATATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
1 2 0.04
2 46 0.96
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1198117 original size:2 final size:2
Alignment explanation
Indices: 1198110--1198161 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1198100 GTGGAACCAA
1198110 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
1198152 AT AT AT AT AT
1 AT AT AT AT AT
1198162 CATCTCTCAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1201813 original size:32 final size:31
Alignment explanation
Indices: 1201725--1201819 Score: 104
Period size: 32 Copynumber: 3.0 Consensus size: 31
1201715 GAACCTCGAC
*
1201725 AACTGTCCATA-GTTCCCG-AAGAACCTAGGTA
1 AACTGTCCATATG-TCCCGAAAG-ACATAGGTA
* *
1201756 AACTGTTCATATGTCCCGAATGACATAGGTA
1 AACTGTCCATATGTCCCGAAAGACATAGGTA
* *
1201787 ATCATGTCCATATGTCTCGAAAGACATAGGTA
1 AAC-TGTCCATATGTCCCGAAAGACATAGGTA
1201819 A
1 A
1201820 CCCTCAACTC
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
31 25 0.46
32 29 0.54
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (31 bp):
AACTGTCCATATGTCCCGAAAGACATAGGTA
Found at i:1201903 original size:22 final size:22
Alignment explanation
Indices: 1201878--1201938 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
1201868 AACATGGGCA
*
1201878 TTCTCTTATAATCACATATTTC
1 TTCTCTTATAATCACATATTCC
*
1201900 TTCTCTTATAATCACATGTTCC
1 TTCTCTTATAATCACATATTCC
*
1201922 TTCTCTTCT-ATCACATA
1 TTCTCTTATAATCACATA
1201939 CCCTATATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
21 7 0.20
22 28 0.80
ACGTcount: A:0.25, C:0.26, G:0.02, T:0.48
Consensus pattern (22 bp):
TTCTCTTATAATCACATATTCC
Found at i:1202165 original size:2 final size:2
Alignment explanation
Indices: 1202160--1202206 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
1202150 CACACACACA
1202160 AT AT AT AT AT -T 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
1202201 AT AT AT
1 AT AT AT
1202207 TCATACAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1204176 original size:10 final size:9
Alignment explanation
Indices: 1204158--1204187 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
1204148 TTTTAAGATT
1204158 AAATATTAA
1 AAATATTAA
1204167 AAATTATTAA
1 AAA-TATTAA
1204177 AAATATTAA
1 AAATATTAA
1204186 AA
1 AA
1204188 TTCTATGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
AAATATTAA
Found at i:1204279 original size:15 final size:15
Alignment explanation
Indices: 1204261--1204295 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1204251 GGAAATAAAG
*
1204261 AAAAATATAATTTTA
1 AAAAATATAATTTCA
*
1204276 AAAAATATACTTTCA
1 AAAAATATAATTTCA
1204291 AAAAA
1 AAAAA
1204296 AATGATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (15 bp):
AAAAATATAATTTCA
Found at i:1213237 original size:24 final size:24
Alignment explanation
Indices: 1213186--1213237 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
1213176 TTGTACTTTT
** * *
1213186 AATTGATAATATGTTTTTTCTCTC
1 AATTGATAATATGTTTTACCCCTA
1213210 AATTGATAATATGTTTTACCCCTA
1 AATTGATAATATGTTTTACCCCTA
1213234 AATT
1 AATT
1213238 TTATAAGTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.31, C:0.13, G:0.08, T:0.48
Consensus pattern (24 bp):
AATTGATAATATGTTTTACCCCTA
Found at i:1214457 original size:61 final size:63
Alignment explanation
Indices: 1214387--1214510 Score: 225
Period size: 61 Copynumber: 2.0 Consensus size: 63
1214377 AACTATCACT
*
1214387 TTTGTTCTTTTTCGGTCATTTAATTATTTTTTAGTTC-AAATCATA-TTAATATTTAGTTTTG
1 TTTGTTCTTTTTCGGTCATTTAACTATTTTTTAGTTCAAAATCATATTTAATATTTAGTTTTG
1214448 TTTGTTCTTTTTCGGTCATTTAACTATTTTTTAGTTCAAAATCATATTTAATATTTAGTTTTG
1 TTTGTTCTTTTTCGGTCATTTAACTATTTTTTAGTTCAAAATCATATTTAATATTTAGTTTTG
1214511 ATTTCATTTT
Statistics
Matches: 60, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
61 36 0.60
62 8 0.13
63 16 0.27
ACGTcount: A:0.23, C:0.09, G:0.10, T:0.58
Consensus pattern (63 bp):
TTTGTTCTTTTTCGGTCATTTAACTATTTTTTAGTTCAAAATCATATTTAATATTTAGTTTTG
Found at i:1215189 original size:24 final size:25
Alignment explanation
Indices: 1215151--1215198 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
1215141 AAAATTATTT
** *
1215151 TTTATTCTAGCATAA-ATTTTTTAA
1 TTTATTCTAAAATAATATATTTTAA
1215175 TTTATTCTAAAATAATATATTTTA
1 TTTATTCTAAAATAATATATTTTA
1215199 TGCCGCATAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (25 bp):
TTTATTCTAAAATAATATATTTTAA
Found at i:1217991 original size:18 final size:20
Alignment explanation
Indices: 1217970--1218015 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 20
1217960 ATCCTCTTTA
1217970 TTTTTTTCTCTTT-TCC-CT
1 TTTTTTTCTCTTTATCCTCT
* *
1217988 TTTTCTTCTTTTTATCCTCT
1 TTTTTTTCTCTTTATCCTCT
1218008 TTATTTTT
1 TT-TTTTT
1218016 TGATATTTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
18 11 0.50
19 3 0.14
20 4 0.18
21 4 0.18
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTTTTCTCTTTATCCTCT
Found at i:1225533 original size:18 final size:18
Alignment explanation
Indices: 1225507--1225541 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1225497 TAATATAATT
*
1225507 TTTAGTTTTTGATATTTA
1 TTTAGTTTTTAATATTTA
*
1225525 TTTATTTTTTAATATTT
1 TTTAGTTTTTAATATTT
1225542 TATATTTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (18 bp):
TTTAGTTTTTAATATTTA
Found at i:1228458 original size:26 final size:26
Alignment explanation
Indices: 1228429--1228482 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
1228419 TATTTTTTAA
1228429 TTTTGAAAATTCTGCAGAGCAATTGC
1 TTTTGAAAATTCTGCAGAGCAATTGC
1228455 TTTTGAAAATTCTGCAGAGCAATTGC
1 TTTTGAAAATTCTGCAGAGCAATTGC
1228481 TT
1 TT
1228483 CGGAGAGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.37
Consensus pattern (26 bp):
TTTTGAAAATTCTGCAGAGCAATTGC
Found at i:1237636 original size:3 final size:3
Alignment explanation
Indices: 1237630--1237689 Score: 95
Period size: 3 Copynumber: 19.7 Consensus size: 3
1237620 TAATAACATA
1237630 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
1237679 AA- AAT ATAT AA
1 AAT AAT A-AT AA
1237690 ATATAAATAA
Statistics
Matches: 54, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.04
3 46 0.85
4 6 0.11
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1237969 original size:3 final size:3
Alignment explanation
Indices: 1237961--1237986 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1237951 TTTCTTAACA
1237961 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
1237987 GTAGTAGTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1238148 original size:24 final size:24
Alignment explanation
Indices: 1238099--1238209 Score: 177
Period size: 24 Copynumber: 4.6 Consensus size: 24
1238089 CAACATCAAT
*
1238099 GTGCCACGTAGAATATGCACACAAA
1 GTGCCTCGTAGAAT-TGCACACAAA
*
1238124 GTGCCTCGTAGAATTGCACATAAA
1 GTGCCTCGTAGAATTGCACACAAA
* *
1238148 GTGTCTCATAGAATTGCACACAAA
1 GTGCCTCGTAGAATTGCACACAAA
1238172 GTGCCTCGTAGAATTGCACACAAA
1 GTGCCTCGTAGAATTGCACACAAA
1238196 GTGCCTCGTAGAAT
1 GTGCCTCGTAGAAT
1238210 ATGTCAAAAT
Statistics
Matches: 79, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
24 66 0.84
25 13 0.16
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.23
Consensus pattern (24 bp):
GTGCCTCGTAGAATTGCACACAAA
Found at i:1241709 original size:12 final size:12
Alignment explanation
Indices: 1241692--1241733 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
1241682 TGTTTATATA
1241692 AAAATAAAATTT
1 AAAATAAAATTT
1241704 AAAATAAAA-TT
1 AAAATAAAATTT
*
1241715 AATATAAAATTT
1 AAAATAAAATTT
1241727 AAAATAA
1 AAAATAA
1241734 TAATAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 10 0.37
12 17 0.63
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAATAAAATTT
Found at i:1241719 original size:29 final size:29
Alignment explanation
Indices: 1241687--1241748 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
1241677 TACTATGTTT
1241687 ATATAAAA-ATAAAATTTAA-AATAAAATTA
1 ATATAAAATATAAAA--TAATAATAAAATTA
* *
1241716 ATATAAAATTTAAAATAATAATAAATTTA
1 ATATAAAATATAAAATAATAATAAAATTA
1241745 ATAT
1 ATAT
1241749 GTATTAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 3 0.10
29 21 0.72
30 5 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (29 bp):
ATATAAAATATAAAATAATAATAAAATTA
Found at i:1241741 original size:17 final size:18
Alignment explanation
Indices: 1241708--1241745 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
1241698 AAATTTAAAA
1241708 TAAAATTAATATAAAATT
1 TAAAATTAATATAAAATT
1241726 TAAAA-TAATA-ATAAATT
1 TAAAATTAATATA-AAATT
1241743 TAA
1 TAA
1241746 TATGTATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 1 0.05
17 13 0.68
18 5 0.26
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TAAAATTAATATAAAATT
Found at i:1243570 original size:24 final size:23
Alignment explanation
Indices: 1243537--1243585 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
1243527 TTTATTAGTT
*
1243537 TAATTTAATATATAAAATTATTAA
1 TAATTGAATATATAAAATTA-TAA
* *
1243561 TAATTGAATATGTAATATTATAA
1 TAATTGAATATATAAAATTATAA
1243584 TA
1 TA
1243586 TATATATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (23 bp):
TAATTGAATATATAAAATTATAA
Found at i:1244065 original size:21 final size:21
Alignment explanation
Indices: 1244039--1244091 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1244029 TAAATATTTT
* *
1244039 TTAAATTTTAAAATATGAAAA
1 TTAAATATAAAAATATGAAAA
*
1244060 TTAAATATAAAAATATTAAAA
1 TTAAATATAAAAATATGAAAA
* *
1244081 ATAAAAATAAA
1 TTAAATATAAA
1244092 TATTAAAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
TTAAATATAAAAATATGAAAA
Found at i:1244079 original size:15 final size:14
Alignment explanation
Indices: 1244049--1244106 Score: 59
Period size: 13 Copynumber: 4.2 Consensus size: 14
1244039 TTAAATTTTA
*
1244049 AAATATGAAA-ATT
1 AAATATAAAATATT
1244062 AAATATAAAAATATT
1 AAATAT-AAAATATT
*
1244077 AAAAATAAAA-A-T
1 AAATATAAAATATT
1244089 AAATATTAAAATATT
1 AAATA-TAAAATATT
1244104 AAA
1 AAA
1244107 AAATAGAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
12 5 0.14
13 12 0.32
14 8 0.22
15 12 0.32
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (14 bp):
AAATATAAAATATT
Found at i:1244102 original size:8 final size:8
Alignment explanation
Indices: 1244041--1244107 Score: 51
Period size: 8 Copynumber: 9.4 Consensus size: 8
1244031 AATATTTTTT
*
1244041 AAATTTTA
1 AAATATTA
*
1244049 AAATA-TG
1 AAATATTA
1244056 AAA-ATT-
1 AAATATTA
*
1244062 AAATATAA
1 AAATATTA
1244070 AAATATTA
1 AAATATTA
1244078 AAA-A-TA
1 AAATATTA
1244084 AAA-A-T-
1 AAATATTA
1244089 AAATATTA
1 AAATATTA
1244097 AAATATTA
1 AAATATTA
1244105 AAA
1 AAA
1244108 AATAGAAATA
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
5 3 0.06
6 12 0.24
7 9 0.18
8 25 0.51
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.31
Consensus pattern (8 bp):
AAATATTA
Found at i:1244127 original size:28 final size:27
Alignment explanation
Indices: 1244041--1244143 Score: 93
Period size: 28 Copynumber: 3.7 Consensus size: 27
1244031 AATATTTTTT
* *
1244041 AAATTTTAAAATATGAAAATTAAATATAA
1 AAATATTAAAAAAT-AAAA-TAAATATAA
*
1244070 AAATATT-AAAAATAAAAATAAATATTA
1 AAATATTAAAAAAT-AAAATAAATATAA
*
1244097 AAATATTAAAAAATAGAAAT-ACTACTAA
1 AAATATTAAAAAATA-AAATAAATA-TAA
* *
1244125 AAAAATAAAAAAATAAAAT
1 AAATATTAAAAAATAAAAT
1244144 TATATCATAA
Statistics
Matches: 63, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
27 23 0.37
28 34 0.54
29 6 0.10
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (27 bp):
AAATATTAAAAAATAAAATAAATATAA
Found at i:1244533 original size:27 final size:27
Alignment explanation
Indices: 1244481--1244533 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
1244471 ACCTATTTTG
**
1244481 AATTTAAATACTTAATATAATGAAAAT
1 AATTTAAATACTTAATATAAAAAAAAT
*
1244508 AATTTATATACTTAA-ATGAAAAAAAA
1 AATTTAAATACTTAATAT-AAAAAAAA
1244534 ATATACCTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 2 0.09
27 20 0.91
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.34
Consensus pattern (27 bp):
AATTTAAATACTTAATATAAAAAAAAT
Found at i:1245222 original size:184 final size:185
Alignment explanation
Indices: 1245021--1245392 Score: 588
Period size: 184 Copynumber: 2.0 Consensus size: 185
1245011 AAATTAAATG
* *
1245021 TTTTTTAATTCAAAAAAA-AGTTTATAATTAATTTAAATAATATATAATTATAAAATAAAAATTT
1 TTTTTTAATTCAAAAAAATAGTTTACAATTAATTTAAATAATATATAATCATAAAATAAAAATTT
*
1245085 CAGATAATTTTTTTAATTAATTACTATTGATTTAGGTTTAAAAGTTATTAG-ATCTTAAATTATT
66 CAGATAA-TTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA-TAGAATCTTAAATTATT
* ** * *
1245149 AATTGGGTTTTAAATTTTTTGGGCTTAGCCCATATGTTATATATAATATATATAATA
129 AATTGGATTTTAAATAGTTTGGGCTGAGCCCATATGTTATATATAATATATATAAAA
1245206 TTTTTTAATT-AAAAAAATAGTTTACAATTAATTTAAATAATATATAATCATAAAATAAAAATTT
1 TTTTTTAATTCAAAAAAATAGTTTACAATTAATTTAAATAATATATAATCATAAAATAAAAATTT
* * *
1245270 TATATAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATCGAATCTTAAATTATTAA
66 CAGATAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATAGAATCTTAAATTATTAA
* *
1245335 TTGTATTTTAAATAGTTTGGGCTGAGCCCATATGTTATATATAATATATTTAAAA
131 TTGGATTTTAAATAGTTTGGGCTGAGCCCATATGTTATATATAATATATATAAAA
1245390 TTT
1 TTT
1245393 AAAATTTAAT
Statistics
Matches: 172, Mismatches: 13, Indels: 5
0.91 0.07 0.03
Matches are distributed among these distances:
183 2 0.01
184 111 0.65
185 59 0.34
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (185 bp):
TTTTTTAATTCAAAAAAATAGTTTACAATTAATTTAAATAATATATAATCATAAAATAAAAATTT
CAGATAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATAGAATCTTAAATTATTAA
TTGGATTTTAAATAGTTTGGGCTGAGCCCATATGTTATATATAATATATATAAAA
Found at i:1245549 original size:27 final size:30
Alignment explanation
Indices: 1245492--1245563 Score: 87
Period size: 27 Copynumber: 2.5 Consensus size: 30
1245482 ATTATTAATC
1245492 AATCAAATTAATTCGATAATCGAACCGAATT
1 AATCAAATTAATTCGAT-ATCGAACCGAATT
* *
1245523 AATCAAACTAATTCGAT-TCG-ATC-AATT
1 AATCAAATTAATTCGATATCGAACCGAATT
*
1245550 AATCGAATTAATTC
1 AATCAAATTAATTC
1245564 AATTATTTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
27 16 0.43
28 2 0.05
29 3 0.08
31 16 0.43
ACGTcount: A:0.43, C:0.17, G:0.08, T:0.32
Consensus pattern (30 bp):
AATCAAATTAATTCGATATCGAACCGAATT
Found at i:1253554 original size:40 final size:40
Alignment explanation
Indices: 1253438--1253555 Score: 98
Period size: 40 Copynumber: 2.9 Consensus size: 40
1253428 CGAACTCAAA
*
1253438 TTTCGCAACTC-AGTTTCCAAATTCGCAACACTGAATTTCAG
1 TTTCGCAACTCGA-TTTTCAAATTCGCAACA-TGAATTTCAG
* * ** ** *
1253479 ATTCGCAACTCGA-TTTCTTAATTCATAACGCGAATTT-TG
1 TTTCGCAACTCGATTTTC-AAATTCGCAACATGAATTTCAG
*
1253518 TTTTCGCAACTCGATTTTCGAATTCGCAACATGAATTT
1 -TTTCGCAACTCGATTTTCAAATTCGCAACATGAATTT
1253556 AATTTCCCAA
Statistics
Matches: 59, Mismatches: 14, Indels: 9
0.72 0.17 0.11
Matches are distributed among these distances:
39 1 0.02
40 35 0.59
41 22 0.37
42 1 0.02
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (40 bp):
TTTCGCAACTCGATTTTCAAATTCGCAACATGAATTTCAG
Found at i:1253750 original size:16 final size:15
Alignment explanation
Indices: 1253715--1253753 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1253705 TCCCCATCTC
*
1253715 TAATTTTTTTTTACA
1 TAATTTTTTTATACA
*
1253730 TAATTTTATTTATATA
1 TAATTTT-TTTATACA
1253746 TAATTTTT
1 TAATTTTT
1253754 CAATGATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (15 bp):
TAATTTTTTTATACA
Found at i:1254367 original size:12 final size:12
Alignment explanation
Indices: 1254346--1254379 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1254336 ACCACATTTC
*
1254346 CAATACCAAACA
1 CAATATCAAACA
1254358 CAATATCAAACA
1 CAATATCAAACA
*
1254370 CAATCTCAAA
1 CAATATCAAA
1254380 ATCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:1256834 original size:18 final size:18
Alignment explanation
Indices: 1256811--1256846 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1256801 AAGCAAAAGG
*
1256811 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
1256829 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
1256847 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:1257053 original size:20 final size:20
Alignment explanation
Indices: 1257025--1257064 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1257015 TTGTTTCGAT
1257025 TGTTGCGAAAGTCAAATTCG
1 TGTTGCGAAAGTCAAATTCG
*
1257045 TGTTTCGAAAGTCAAATTCG
1 TGTTGCGAAAGTCAAATTCG
1257065 AAATGCGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.33
Consensus pattern (20 bp):
TGTTGCGAAAGTCAAATTCG
Found at i:1257073 original size:20 final size:20
Alignment explanation
Indices: 1257028--1257074 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
1257018 TTTCGATTGT
***
1257028 TGCGAAAGTCAAATTCGTGT
1 TGCGAAAGTCAAATTCGAAA
*
1257048 TTCGAAAGTCAAATTCGAAA
1 TGCGAAAGTCAAATTCGAAA
1257068 TGCGAAA
1 TGCGAAA
1257075 ATCACAACAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (20 bp):
TGCGAAAGTCAAATTCGAAA
Found at i:1258655 original size:21 final size:21
Alignment explanation
Indices: 1258631--1258743 Score: 79
Period size: 21 Copynumber: 5.4 Consensus size: 21
1258621 GTGAATTGGA
*
1258631 CTCTCGAACGGTGGGAGGGAC
1 CTCTTGAACGGTGGGAGGGAC
* * ** *
1258652 CTCTTGAATGATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGAC
1258673 CTCTTGAACGGTGGGAGGGGA-
1 CTCTTGAACGGTGGGA-GGGAC
** *
1258694 CTCTTGAA-GGATGATAGGGGC
1 CTCTTGAACGG-TGGGAGGGAC
* *
1258715 CTCTTGAACGATAGGAGAGG-C
1 CTCTTGAACGGTGGGAG-GGAC
1258736 CTCTTGAA
1 CTCTTGAA
1258744 TGATGACAGG
Statistics
Matches: 69, Mismatches: 18, Indels: 10
0.71 0.19 0.10
Matches are distributed among these distances:
20 5 0.07
21 58 0.84
22 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGAC
Found at i:1258698 original size:42 final size:42
Alignment explanation
Indices: 1258631--1258749 Score: 168
Period size: 42 Copynumber: 2.8 Consensus size: 42
1258621 GTGAATTGGA
*
1258631 CTCTCGAACGGTGGGA-GGGACCTCTTGAATGATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGA-CTCTTGAATGATGATAGGGGC
*
1258673 CTCTTGAACGGTGGGAGGGGACTCTTGAAGGATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTTGAATGATGATAGGGGC
* * * *
1258715 CTCTTGAACGATAGGAGAGGCCTCTTGAATGATGA
1 CTCTTGAACGGTGGGAGGGGACTCTTGAATGATGA
1258750 CAGGTGAATC
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
42 65 0.94
43 4 0.06
ACGTcount: A:0.24, C:0.17, G:0.37, T:0.23
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGGACTCTTGAATGATGATAGGGGC
Found at i:1258912 original size:12 final size:12
Alignment explanation
Indices: 1258893--1258934 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
1258883 GGGCTGCTAA
*
1258893 AAATAAATTAAT
1 AAATAAATCAAT
*
1258905 ACATAAATCAAT
1 AAATAAATCAAT
1258917 AAATAAA-CAAAT
1 AAATAAATC-AAT
1258929 AAATAA
1 AAATAA
1258935 TACCGAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 1 0.04
12 25 0.96
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (12 bp):
AAATAAATCAAT
Found at i:1261184 original size:22 final size:22
Alignment explanation
Indices: 1261141--1261186 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
1261131 CATATTTCGC
* *
1261141 CGGAGATGGGGATGAATTTCGT
1 CGGAGATGGGGACGAATGTCGT
*
1261163 CGGAGATGGGGACGGATGTCGT
1 CGGAGATGGGGACGAATGTCGT
1261185 CG
1 CG
1261187 TAGAGAGTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.13, G:0.46, T:0.22
Consensus pattern (22 bp):
CGGAGATGGGGACGAATGTCGT
Found at i:1261353 original size:20 final size:20
Alignment explanation
Indices: 1261328--1261376 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
1261318 TAAACGCGCT
1261328 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTCTGTG
1261348 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTCTGTG
1261368 TTGCGAATT
1 TTGCGAATT
1261377 ACAAATTCGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.16, C:0.14, G:0.24, T:0.45
Consensus pattern (20 bp):
TTGCGAATTTGACTTCTGTG
Found at i:1261388 original size:20 final size:20
Alignment explanation
Indices: 1261365--1261416 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
1261355 TTTGACTTCT
1261365 GTGTTGCGAATTACAAATTC
1 GTGTTGCGAATTACAAATTC
* *
1261385 GTGTTGCGATTTACATATTC
1 GTGTTGCGAATTACAAATTC
*
1261405 GTGTAGCGAATT
1 GTGTTGCGAATT
1261417 TGGAAAATCG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.38
Consensus pattern (20 bp):
GTGTTGCGAATTACAAATTC
Found at i:1263133 original size:18 final size:18
Alignment explanation
Indices: 1263110--1263146 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1263100 GCTTAAAATC
1263110 TAAAATTATTATATATTT
1 TAAAATTATTATATATTT
*
1263128 TAAAATTTTTATATATTT
1 TAAAATTATTATATATTT
1263146 T
1 T
1263147 TATTAAAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TAAAATTATTATATATTT
Found at i:1264574 original size:20 final size:19
Alignment explanation
Indices: 1264536--1264574 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1264526 AAAAAATAAT
* *
1264536 TTTAAAAATATTAATTTAA
1 TTTAAAAACATTAAATTAA
1264555 TTTAAAAACATTAAAATTAA
1 TTTAAAAACATT-AAATTAA
1264575 AATCTTACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (19 bp):
TTTAAAAACATTAAATTAA
Found at i:1266055 original size:9 final size:8
Alignment explanation
Indices: 1266035--1266109 Score: 66
Period size: 8 Copynumber: 9.4 Consensus size: 8
1266025 GATGCTCATA
1266035 TTTT-TAT
1 TTTTATAT
1266042 TTTTATAGT
1 TTTTATA-T
*
1266051 TTTTATAA
1 TTTTATAT
1266059 TTTTATAT
1 TTTTATAT
*
1266067 TTTTACGA-
1 TTTTA-TAT
1266075 TTTTATA-
1 TTTTATAT
1266082 TTTTATAT
1 TTTTATAT
*
1266090 TTTTAAAT
1 TTTTATAT
*
1266098 GTTTTTTAT
1 -TTTTATAT
1266107 TTT
1 TTT
1266110 ACATAAAAAG
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
7 12 0.21
8 29 0.52
9 15 0.27
ACGTcount: A:0.24, C:0.01, G:0.04, T:0.71
Consensus pattern (8 bp):
TTTTATAT
Found at i:1266421 original size:22 final size:21
Alignment explanation
Indices: 1266375--1266420 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
1266365 TCAGCCGAGC
1266375 AAAATTAAATATTTTTATATA
1 AAAATTAAATATTTTTATATA
1266396 AAAATTAAATATTTTTATATA
1 AAAATTAAATATTTTTATATA
1266417 AAAA
1 AAAA
1266421 AATATATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AAAATTAAATATTTTTATATA
Found at i:1266429 original size:22 final size:21
Alignment explanation
Indices: 1266375--1266431 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
1266365 TCAGCCGAGC
*
1266375 AAAATTAAATATTTTTATATA
1 AAAAATAAATATTTTTATATA
*
1266396 AAAATTAAATATTTTTATATAA
1 AAAAATAAATATTTTTATAT-A
*
1266418 AAAAATATATATTT
1 AAAAATAAATATTT
1266432 AGTCAATGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
21 20 0.61
22 13 0.39
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AAAAATAAATATTTTTATATA
Found at i:1266965 original size:25 final size:26
Alignment explanation
Indices: 1266927--1266984 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 26
1266917 TATGCTTTCT
*
1266927 ATATTTTTACAAAATTAATA-TTTTA-
1 ATATTTTTA-AAAAATAATATTTTTAC
*
1266952 ATATTTTTAAAAAATAGTATTTTTAC
1 ATATTTTTAAAAAATAATATTTTTAC
1266978 ATATTTT
1 ATATTTT
1266985 AAATTTTATG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 8 0.28
25 14 0.48
26 7 0.24
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.53
Consensus pattern (26 bp):
ATATTTTTAAAAAATAATATTTTTAC
Found at i:1272163 original size:23 final size:23
Alignment explanation
Indices: 1272122--1272189 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
1272112 AACCTTATAT
*
1272122 GGCACTTCGGTGCATTTCTACGC
1 GGCACTACGGTGCATTTCTACGC
* * *
1272145 GGTACTACGGTGCAATTCTACGT
1 GGCACTACGGTGCATTTCTACGC
*
1272168 GGCACTTCGGTGCATTTCTACG
1 GGCACTACGGTGCATTTCTACG
1272190 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:0.16, C:0.26, G:0.26, T:0.31
Consensus pattern (23 bp):
GGCACTACGGTGCATTTCTACGC
Found at i:1277113 original size:23 final size:23
Alignment explanation
Indices: 1277080--1277142 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1277070 AACCTTATAT
1277080 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * * *
1277103 GGCACTACGGTGTAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
1277126 GGCACTTCGGTGCATTT
1 GGCACTTCGGTGCATTT
1277143 ATATGAGTTG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.32
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:1278827 original size:15 final size:15
Alignment explanation
Indices: 1278807--1278837 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1278797 AACTGTCCTT
*
1278807 TTATTTTATTTTTTA
1 TTATTTTATTATTTA
1278822 TTATTTTATTATTTA
1 TTATTTTATTATTTA
1278837 T
1 T
1278838 GTAGTACAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTATTTTATTATTTA
Found at i:1278830 original size:8 final size:8
Alignment explanation
Indices: 1278807--1278835 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
1278797 AACTGTCCTT
1278807 TTATTTTA
1 TTATTTTA
1278815 TT-TTTTA
1 TTATTTTA
1278822 TTATTTTA
1 TTATTTTA
1278830 TTATTT
1 TTATTT
1278836 ATGTAGTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (8 bp):
TTATTTTA
Found at i:1283972 original size:20 final size:20
Alignment explanation
Indices: 1283949--1284015 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
1283939 GTCCCAAAAC
*
1283949 ACCTATGTTTGTCCCGAAGG
1 ACCTATGTATGTCCCGAAGG
*
1283969 ACCTATATATGTCCCGAAGG
1 ACCTATGTATGTCCCGAAGG
* *
1283989 ACCTCTGTATGTCCCGAAAG
1 ACCTATGTATGTCCCGAAGG
1284009 ACCTATG
1 ACCTATG
1284016 AACCCTCGAC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (20 bp):
ACCTATGTATGTCCCGAAGG
Found at i:1283982 original size:40 final size:40
Alignment explanation
Indices: 1283938--1284014 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
1283928 ATATGAAATT
* *
1283938 TGTCCCAAAACACCTATGTTTGTCCCGAAGGACCTATATA
1 TGTCCCAAAACACCTATGTATGTCCCGAAAGACCTATATA
* ** *
1283978 TGTCCCGAAGGACCTCTGTATGTCCCGAAAGACCTAT
1 TGTCCCAAAACACCTATGTATGTCCCGAAAGACCTAT
1284015 GAACCCTCGA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.26
Consensus pattern (40 bp):
TGTCCCAAAACACCTATGTATGTCCCGAAAGACCTATATA
Found at i:1284735 original size:19 final size:19
Alignment explanation
Indices: 1284711--1284757 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
1284701 CCTTGACATG
1284711 TGCATCGATGCACTAACTA
1 TGCATCGATGCACTAACTA
1284730 TGCATCGATGCACTAACTA
1 TGCATCGATGCACTAACTA
1284749 TGCATCGAT
1 TGCATCGAT
1284758 ACACAAATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.28
Consensus pattern (19 bp):
TGCATCGATGCACTAACTA
Found at i:1288222 original size:20 final size:20
Alignment explanation
Indices: 1288179--1288274 Score: 151
Period size: 20 Copynumber: 4.9 Consensus size: 20
1288169 ATATGAAATT
*
1288179 TGTCCCAAAGGACCTAT-T-
1 TGTCCCGAAGGACCTATGTA
1288197 TGTCCCGAAGGACCTATGTA
1 TGTCCCGAAGGACCTATGTA
1288217 TGTCCCGAAGGACCTATGTA
1 TGTCCCGAAGGACCTATGTA
*
1288237 TGTCCCGAAGGACCTCTGTA
1 TGTCCCGAAGGACCTATGTA
*
1288257 TGTCCCGAAAGACCTATG
1 TGTCCCGAAGGACCTATG
1288275 AACCCTCGAC
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
18 16 0.22
19 1 0.01
20 55 0.76
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (20 bp):
TGTCCCGAAGGACCTATGTA
Found at i:1291690 original size:19 final size:18
Alignment explanation
Indices: 1291668--1291712 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1291658 TTAAAATACC
1291668 TAAAATCATGTAAATTTAA
1 TAAAA-CATGTAAATTTAA
* * *
1291687 TAAAACATTTTATTTTAA
1 TAAAACATGTAAATTTAA
1291705 TAAAACAT
1 TAAAACAT
1291713 TTTATTTTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.40
Consensus pattern (18 bp):
TAAAACATGTAAATTTAA
Found at i:1291705 original size:18 final size:18
Alignment explanation
Indices: 1291682--1291727 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
1291672 ATCATGTAAA
1291682 TTTAATAAAACATTTTAT
1 TTTAATAAAACATTTTAT
1291700 TTTAATAAAACATTTTAT
1 TTTAATAAAACATTTTAT
*
1291718 TTTACTAAAA
1 TTTAATAAAA
1291728 ATACCAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.48
Consensus pattern (18 bp):
TTTAATAAAACATTTTAT
Found at i:1292648 original size:138 final size:138
Alignment explanation
Indices: 1292255--1292648 Score: 610
Period size: 138 Copynumber: 2.9 Consensus size: 138
1292245 CTAAAAAAGT
*
1292255 AGGCTCTAATATTAATTCTAATTCATTTTAACCAATTATTGATTCGAATAATTAAAATGGAACCT
1 AGGCTCTAATATTAATCCTAATTCATTTTAACCAATTATTGATTCGAATAATTAAAATGGAACCT
* * * * *
1292320 CGAGCATATGTGAGGACCAAATTAAAAATTCTCCTAAATTAAAAGACTAAATATGAAATTAGACC
66 CGAGCATAAGCGAGGACCAAATTAAAAATTCTCCTAAATTAAAGGACTAAATTTGAAATTAAACC
1292385 TAAAGTGA
131 TAAAGTGA
* * *
1292393 AGGTTCTAACATTAATCCTAATTCATTTTAACCAATTATTGATTCGAATAATTAAAACGGAACCT
1 AGGCTCTAATATTAATCCTAATTCATTTTAACCAATTATTGATTCGAATAATTAAAATGGAACCT
*
1292458 CGAGCATAAGCGATGACCAAATTAAAAATTCTCCTAAATTAAAGGACTAAATTTGAAATTAAACC
66 CGAGCATAAGCGAGGACCAAATTAAAAATTCTCCTAAATTAAAGGACTAAATTTGAAATTAAACC
1292523 TAAAGTGA
131 TAAAGTGA
* * *** * *
1292531 AGGCCCTAATATTAATCCTAATTAATTTTAATTGATTATTGATTCGAATAATTAAAATAGAAACT
1 AGGCTCTAATATTAATCCTAATTCATTTTAACCAATTATTGATTCGAATAATTAAAATGGAACCT
*
1292596 CGAGCATAAGCGAGGACCAAATTAAAAATTC-CTCTAAATTAAAGGGCTAAATT
66 CGAGCATAAGCGAGGACCAAATTAAAAATTCTC-CTAAATTAAAGGACTAAATT
1292649 AAAAGGATCT
Statistics
Matches: 233, Mismatches: 22, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
137 1 0.00
138 232 1.00
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (138 bp):
AGGCTCTAATATTAATCCTAATTCATTTTAACCAATTATTGATTCGAATAATTAAAATGGAACCT
CGAGCATAAGCGAGGACCAAATTAAAAATTCTCCTAAATTAAAGGACTAAATTTGAAATTAAACC
TAAAGTGA
Found at i:1292662 original size:15 final size:14
Alignment explanation
Indices: 1292628--1292669 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
1292618 TAAAAATTCC
1292628 TCTAAATT-AAAGG
1 TCTAAATTAAAAGG
*
1292641 GCTAAATTAAAAGG
1 TCTAAATTAAAAGG
1292655 ATCTAAATCTAAAAG
1 -TCTAAAT-TAAAAG
1292670 TAAAGTAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 7 0.29
14 5 0.21
15 6 0.25
16 6 0.25
ACGTcount: A:0.50, C:0.10, G:0.14, T:0.26
Consensus pattern (14 bp):
TCTAAATTAAAAGG
Found at i:1292920 original size:28 final size:30
Alignment explanation
Indices: 1292863--1292935 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 30
1292853 GAAAATTTGA
*
1292863 AACTGGAATTTAAAGGACTGAAATGTAAAT
1 AACTGAAATTTAAAGGACTGAAATGTAAAT
1292893 -ACTGAAATTTAAAGG-CTGAAAT-TAAAAT
1 AACTGAAATTTAAAGGACTGAAATGT-AAAT
* *
1292921 AACAGAAAATTAAAG
1 AACTGAAATTTAAAG
1292936 TAAATGGAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
27 1 0.03
28 11 0.29
29 26 0.68
ACGTcount: A:0.52, C:0.07, G:0.16, T:0.25
Consensus pattern (30 bp):
AACTGAAATTTAAAGGACTGAAATGTAAAT
Found at i:1293013 original size:10 final size:10
Alignment explanation
Indices: 1292998--1293031 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
1292988 TTTAAAGTGC
1292998 ATAAAATTAA
1 ATAAAATTAA
*
1293008 ATAAAATAAA
1 ATAAAATTAA
1293018 ATAAAAATTAA
1 AT-AAAATTAA
1293029 ATA
1 ATA
1293032 TTAGTGTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (10 bp):
ATAAAATTAA
Found at i:1295382 original size:34 final size:34
Alignment explanation
Indices: 1295342--1295423 Score: 164
Period size: 34 Copynumber: 2.4 Consensus size: 34
1295332 CTGGGCTAAA
1295342 CTAGAACCTTTCCCTAGCTTTTACACGGGATTAG
1 CTAGAACCTTTCCCTAGCTTTTACACGGGATTAG
1295376 CTAGAACCTTTCCCTAGCTTTTACACGGGATTAG
1 CTAGAACCTTTCCCTAGCTTTTACACGGGATTAG
1295410 CTAGAACCTTTCCC
1 CTAGAACCTTTCCC
1295424 ATTTACAAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 48 1.00
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.32
Consensus pattern (34 bp):
CTAGAACCTTTCCCTAGCTTTTACACGGGATTAG
Found at i:1295798 original size:20 final size:20
Alignment explanation
Indices: 1295769--1295842 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
1295759 GCAGTCTTCG
* *
1295769 TGCATGGATGCACAGCAGGA
1 TGCATCGATGCACAACAGGA
**
1295789 TGCATCGATGCACAACCTTGA
1 TGCATCGATGCACAA-CAGGA
*
1295810 TGCATCGATGCACAAAAGGA
1 TGCATCGATGCACAACAGGA
1295830 TGCATCGATGCAC
1 TGCATCGATGCAC
1295843 TAATTGCATT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
20 28 0.61
21 18 0.39
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.19
Consensus pattern (20 bp):
TGCATCGATGCACAACAGGA
Found at i:1296041 original size:29 final size:29
Alignment explanation
Indices: 1296020--1296077 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
1296010 AAACTTTGAA
1296020 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
1296049 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
1296078 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:1296067 original size:30 final size:30
Alignment explanation
Indices: 1296020--1296079 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
1296010 AAACTTTGAA
1296020 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
1296049 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
1296080 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:1298725 original size:20 final size:20
Alignment explanation
Indices: 1298696--1298769 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
1298686 GCAACCTTCG
*
1298696 TGCATGGATGCACAGCAGGA
1 TGCATCGATGCACAGCAGGA
* *
1298716 TGCATCGATGCACAACCATGA
1 TGCATCGATGCAC-AGCAGGA
*
1298737 TGCATCGATGCACAGAAGGA
1 TGCATCGATGCACAGCAGGA
1298757 TGCATCGATGCAC
1 TGCATCGATGCAC
1298770 TAATTGCATT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
20 29 0.62
21 18 0.38
ACGTcount: A:0.31, C:0.24, G:0.27, T:0.18
Consensus pattern (20 bp):
TGCATCGATGCACAGCAGGA
Found at i:1298837 original size:22 final size:23
Alignment explanation
Indices: 1298804--1298846 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
1298794 ATGGATGCAC
1298804 TGCATGGTGCATCGATGCACTAG
1 TGCATGGTGCATCGATGCACTAG
*
1298827 TGCA-GGTGCATGGATGCACT
1 TGCATGGTGCATCGATGCACT
1298847 GCAGGGATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.21, C:0.21, G:0.33, T:0.26
Consensus pattern (23 bp):
TGCATGGTGCATCGATGCACTAG
Found at i:1298859 original size:21 final size:20
Alignment explanation
Indices: 1298790--1298888 Score: 128
Period size: 21 Copynumber: 4.8 Consensus size: 20
1298780 TGGTGTTTGA
*
1298790 GTGCATGGATGCACTGCATG
1 GTGCATGGATGCACTGCAGG
*
1298810 GTGCATCGATGCACTAGTGCA-G
1 GTGCATGGATGCAC---TGCAGG
1298832 GTGCATGGATGCACTGCAGG
1 GTGCATGGATGCACTGCAGG
1298852 GATGCATGGATGCACTGCAGGG
1 G-TGCATGGATGCACTGCA-GG
1298874 GTGCATGGATGCACT
1 GTGCATGGATGCACT
1298889 TTGACACCCT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
19 4 0.06
20 15 0.21
21 31 0.44
22 17 0.24
23 4 0.06
ACGTcount: A:0.21, C:0.20, G:0.36, T:0.22
Consensus pattern (20 bp):
GTGCATGGATGCACTGCAGG
Found at i:1299159 original size:21 final size:21
Alignment explanation
Indices: 1299091--1299188 Score: 112
Period size: 21 Copynumber: 4.7 Consensus size: 21
1299081 GGTGTTTGAG
*
1299091 TGCATGGATGCACTGCATGG-
1 TGCATGGATGCACTGCAGGGA
* *
1299111 TGCATCGATGCACT--AGTGCA
1 TGCATGGATGCACTGCAG-GGA
1299131 TGTGCATGGATGCACTGCAGGGA
1 --TGCATGGATGCACTGCAGGGA
*
1299154 TGCATGGATGCACTGCAGGGG
1 TGCATGGATGCACTGCAGGGA
1299175 TGCATGGATGCACT
1 TGCATGGATGCACT
1299189 TTGACACCCT
Statistics
Matches: 66, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
18 1 0.02
19 1 0.02
20 13 0.20
21 34 0.52
22 13 0.20
23 2 0.03
24 2 0.03
ACGTcount: A:0.21, C:0.20, G:0.35, T:0.23
Consensus pattern (21 bp):
TGCATGGATGCACTGCAGGGA
Found at i:1299170 original size:13 final size:14
Alignment explanation
Indices: 1299091--1299158 Score: 54
Period size: 13 Copynumber: 4.9 Consensus size: 14
1299081 GGTGTTTGAG
1299091 TGCATGGATGCA-C
1 TGCATGGATGCATC
1299104 TGCATGG-TGCATC
1 TGCATGGATGCATC
* *
1299117 GATGCACTAG-TGCATG
1 --TGCA-TGGATGCATC
1299133 TGCATGGATGCA-C
1 TGCATGGATGCATC
*
1299146 TGCAGGGATGCAT
1 TGCATGGATGCAT
1299159 GGATGCACTG
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
12 4 0.09
13 21 0.48
14 8 0.18
15 4 0.09
16 7 0.16
ACGTcount: A:0.22, C:0.21, G:0.32, T:0.25
Consensus pattern (14 bp):
TGCATGGATGCATC
Found at i:1299289 original size:29 final size:29
Alignment explanation
Indices: 1299268--1299325 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
1299258 AAACTTTGAA
1299268 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
1299297 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
1299326 TACCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:1299315 original size:30 final size:30
Alignment explanation
Indices: 1299268--1299326 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
1299258 AAACTTTGAA
1299268 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
1299297 TAAATTCAATTCAAGTCCAAAAACCATTTT
1 TAAATTCAATT-AAGTCCAAAAACCATTTT
1299327 ACCTTAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.44, C:0.17, G:0.05, T:0.34
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:1300283 original size:21 final size:22
Alignment explanation
Indices: 1300254--1300307 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
1300244 TATCAAAATT
*
1300254 GGAAAAAAATTTACCATTAAAA
1 GGAAAAAAATTAACCATTAAAA
*
1300276 GGAAAAAAATTAACCGTTAAAA
1 GGAAAAAAATTAACCATTAAAA
1300298 GGAAAAAAAT
1 GGAAAAAAAT
1300308 GATAAATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.61, C:0.07, G:0.13, T:0.19
Consensus pattern (22 bp):
GGAAAAAAATTAACCATTAAAA
Found at i:1300520 original size:51 final size:50
Alignment explanation
Indices: 1300452--1300560 Score: 128
Period size: 51 Copynumber: 2.2 Consensus size: 50
1300442 TAAAGCGCGT
* ** *
1300452 CCCCTGCACCGCGCTATACGATGATTTGGCACCACGTGGGGTATAGCACGC
1 CCCCTGCACCGCACTATACGATGAGCTGGCACCACGT-AGGTATAGCACGC
* * * * *
1300503 CCCCTGCACTGCACTATACGGTGAGCTGGCACCATGTAGGTATAGCGCGG
1 CCCCTGCACCGCACTATACGATGAGCTGGCACCACGTAGGTATAGCACGC
1300553 CCCCTGCA
1 CCCCTGCA
1300561 GCGTGCTATA
Statistics
Matches: 49, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
50 18 0.37
51 31 0.63
ACGTcount: A:0.19, C:0.34, G:0.28, T:0.19
Consensus pattern (50 bp):
CCCCTGCACCGCACTATACGATGAGCTGGCACCACGTAGGTATAGCACGC
Found at i:1300570 original size:50 final size:50
Alignment explanation
Indices: 1300445--1300571 Score: 123
Period size: 51 Copynumber: 2.5 Consensus size: 50
1300435 TTAGCAGTAA
* * ** *
1300445 AGCGCGTCCCCTGCACCGCGCTATACGATGATTTGGCACCACGTGGGGTAT
1 AGCGCGCCCCCTGCA-CGTGCTATACGATGAGCTGGCACCACGTGAGGTAT
* * *
1300496 AGCACGCCCCCTGCAC-TGCACTATACGGTGAGCTGGCACCATGT-AGGTAT
1 AGCGCGCCCCCTGCACGTG--CTATACGATGAGCTGGCACCACGTGAGGTAT
*
1300546 AGCGCGGCCCCTGCAGCGTGCTATAC
1 AGCGCGCCCCCTGCA-CGTGCTATAC
1300572 CTGTATATCT
Statistics
Matches: 62, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
49 1 0.02
50 25 0.40
51 34 0.55
52 2 0.03
ACGTcount: A:0.19, C:0.33, G:0.28, T:0.20
Consensus pattern (50 bp):
AGCGCGCCCCCTGCACGTGCTATACGATGAGCTGGCACCACGTGAGGTAT
Found at i:1300734 original size:12 final size:10
Alignment explanation
Indices: 1300693--1300733 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
1300683 TTTATCATAC
1300693 CAAATTCTCT
1 CAAATTCTCT
1300703 CAAATTCTCT
1 CAAATTCTCT
1300713 -AAATTTCTCT
1 CAAA-TTCTCT
*
1300723 CAAATACTCT
1 CAAATTCTCT
1300733 C
1 C
1300734 TTTTTAAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 22 0.79
11 3 0.11
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:1302606 original size:18 final size:18
Alignment explanation
Indices: 1302579--1302618 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
1302569 CCAGCATCCA
*
1302579 CCGCAGCCATATATGATG
1 CCGCAACCATATATGATG
1302597 CCGCAACCATATATGATG
1 CCGCAACCATATATGATG
1302615 CCGC
1 CCGC
1302619 CATCGCCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.28, C:0.33, G:0.20, T:0.20
Consensus pattern (18 bp):
CCGCAACCATATATGATG
Found at i:1304329 original size:47 final size:49
Alignment explanation
Indices: 1304222--1304330 Score: 161
Period size: 51 Copynumber: 2.2 Consensus size: 49
1304212 TTGTATAAAA
*
1304222 CGCGGTACCTGCCTCGCGCTATATAAAATTATGTCAGGAGTAAAGGTATGT
1 CGCGGTACCTGCCCCGCGCTATATAAAATTATGTC--GAGTAAAGGTATGT
1304273 CGCGGTACCTGCCCCGCGCTATATAAAATTATG-C-AGTAAAGGTATAG-
1 CGCGGTACCTGCCCCGCGCTATATAAAATTATGTCGAGTAAAGGTAT-GT
1304320 CGCGGTACCTG
1 CGCGGTACCTG
1304331 ATCCGTGATA
Statistics
Matches: 56, Mismatches: 1, Indels: 6
0.89 0.02 0.10
Matches are distributed among these distances:
47 22 0.39
48 1 0.02
50 1 0.02
51 32 0.57
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.25
Consensus pattern (49 bp):
CGCGGTACCTGCCCCGCGCTATATAAAATTATGTCGAGTAAAGGTATGT
Found at i:1304429 original size:50 final size:50
Alignment explanation
Indices: 1304366--1304479 Score: 142
Period size: 51 Copynumber: 2.3 Consensus size: 50
1304356 TATAGCGTGC
* * **
1304366 TGCAGGGGCCGCGCTATA-CCCACGTGGCTCCAGCTCACCGTATAGCGCAG
1 TGCAGGGG-CGCGCTATACCCCACGTGACGCCAAATCACCGTATAGCGCAG
* *
1304416 TGCAGGGCGCGCGCTATACCCCACGTGACGCCAAATCATCGTATAGCGCGG
1 TGCAGGG-GCGCGCTATACCCCACGTGACGCCAAATCACCGTATAGCGCAG
1304467 TGCAGGGG-GCGCT
1 TGCAGGGGCGCGCT
1304480 TTAATGCTAA
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
49 5 0.09
50 17 0.30
51 34 0.61
ACGTcount: A:0.18, C:0.33, G:0.32, T:0.16
Consensus pattern (50 bp):
TGCAGGGGCGCGCTATACCCCACGTGACGCCAAATCACCGTATAGCGCAG
Found at i:1307264 original size:15 final size:14
Alignment explanation
Indices: 1307246--1307284 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
1307236 TTTTTTTCCA
*
1307246 TTTTATTTTTATTAT
1 TTTTATATTTA-TAT
1307261 TTTTATATTTATAT
1 TTTTATATTTATAT
1307275 TTTGTATATT
1 TTT-TATATT
1307285 ATTTTCTTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.27
15 16 0.73
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (14 bp):
TTTTATATTTATAT
Found at i:1307394 original size:54 final size:53
Alignment explanation
Indices: 1307283--1307394 Score: 120
Period size: 54 Copynumber: 2.1 Consensus size: 53
1307273 ATTTTGTATA
* * * *
1307283 TTATTTTCTTAGTATTAATATTATATTTATACATACATGTTTCCTTCCTTTTAT
1 TTATTTTCTTAGTATTAATATTATATATATACATACATATTT-CATCATTTTAT
* *
1307337 TTATTTTCTTAGTATTAATATTAATATATATATATATATATATT-ATCATTATT-T
1 TTATTTTCTTAGTATTAATATT-ATATATATACATACATAT-TTCATCATT-TTAT
1307391 TTAT
1 TTAT
1307395 CTCCTTTATA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
54 31 0.63
55 16 0.33
56 2 0.04
ACGTcount: A:0.31, C:0.08, G:0.03, T:0.58
Consensus pattern (53 bp):
TTATTTTCTTAGTATTAATATTATATATATACATACATATTTCATCATTTTAT
Found at i:1312765 original size:125 final size:125
Alignment explanation
Indices: 1312538--1312794 Score: 462
Period size: 125 Copynumber: 2.1 Consensus size: 125
1312528 CTCACTTGAG
* *
1312538 ACAGTCTCATTTAATGCAGATGATTTATCTCACTTGAGGTTGTTATTCTTAAAACAAACTTTGTC
1 ACAGACTCATTTAATGCAGATGATTTATCTCACTTGAGATTGTTATTCTTAAAACAAACTTTGTC
*
1312603 TCACCTGAGACTGTTTTACTCGAAAGAAGATTTATTTCCCTCAAGATTGTTTTTATTAAA
66 TCACCTGAGACTGTTTTACTCGAAAAAAGATTTATTTCCCTCAAGATTGTTTTTATTAAA
1312663 ACAGACTCATTTAATGCAGATGATTTATCTCACTTGAGATTGTTATTCTTAAAACAAACTTTGTC
1 ACAGACTCATTTAATGCAGATGATTTATCTCACTTGAGATTGTTATTCTTAAAACAAACTTTGTC
*
1312728 TCA-CTCGAGACTGTTTTACTCGAAAAAAGATTTATTTCCCTCAAGATTGTTTTTCTTAAA
66 TCACCT-GAGACTGTTTTACTCGAAAAAAGATTTATTTCCCTCAAGATTGTTTTTATTAAA
1312788 ACAGACT
1 ACAGACT
1312795 TTGTCTTACT
Statistics
Matches: 127, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
124 2 0.02
125 125 0.98
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.39
Consensus pattern (125 bp):
ACAGACTCATTTAATGCAGATGATTTATCTCACTTGAGATTGTTATTCTTAAAACAAACTTTGTC
TCACCTGAGACTGTTTTACTCGAAAAAAGATTTATTTCCCTCAAGATTGTTTTTATTAAA
Found at i:1312811 original size:36 final size:36
Alignment explanation
Indices: 1312698--1312816 Score: 107
Period size: 36 Copynumber: 3.3 Consensus size: 36
1312688 TATCTCACTT
* * *
1312698 GAGATTGTTATTCTTAAAACAAACTTTGTCTCACTC
1 GAGATTGTTTTTCTTAAAACAGACTTTGTCTTACTC
* * * * * *
1312734 GAGACTGTTTTACTCGAAAAAAGA-TTTAT-TTCCCTC
1 GAGATTGTTTTTCT-TAAAACAGACTTTGTCTT-ACTC
* *
1312770 AAGATTGTTTTTCTTAAAACAGACTTTGTCTTACTT
1 GAGATTGTTTTTCTTAAAACAGACTTTGTCTTACTC
1312806 GAGATTGTTTT
1 GAGATTGTTTT
1312817 ACTCGAAAGA
Statistics
Matches: 61, Mismatches: 18, Indels: 8
0.70 0.21 0.09
Matches are distributed among these distances:
35 8 0.13
36 45 0.74
37 8 0.13
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (36 bp):
GAGATTGTTTTTCTTAAAACAGACTTTGTCTTACTC
Found at i:1312870 original size:36 final size:35
Alignment explanation
Indices: 1312750--1312867 Score: 105
Period size: 36 Copynumber: 3.3 Consensus size: 35
1312740 GTTTTACTCG
*
1312750 AAAA-AAGATTTATTTCCCTCAAGATTGTTTTTCTT
1 AAAACAAGATTTATTTTCCTCAAGATTG-TTTTCTT
* * * ** *
1312785 AAAAC-AGACTTTGTCTTACTTGAGATTGTTTTACTC
1 AAAACAAGA-TTTATTTTCCTCAAGATTGTTTT-CTT
* * *
1312821 GAAAGAAGATTTATTTTCCTCAATATTGTTTTCTT
1 AAAACAAGATTTATTTTCCTCAAGATTGTTTTCTT
1312856 AAAACAAGATTT
1 AAAACAAGATTT
1312868 TATCTCGCTT
Statistics
Matches: 61, Mismatches: 18, Indels: 8
0.70 0.21 0.09
Matches are distributed among these distances:
35 23 0.38
36 35 0.57
37 3 0.05
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (35 bp):
AAAACAAGATTTATTTTCCTCAAGATTGTTTTCTT
Found at i:1312879 original size:72 final size:72
Alignment explanation
Indices: 1312699--1312896 Score: 256
Period size: 72 Copynumber: 2.8 Consensus size: 72
1312689 ATCTCACTTG
* *
1312699 AGATTGTTATTCTTAAAACAA-ACTTTGTCTCACTCGAGACTGTTTTACTCGAAAAAAGATTTAT
1 AGATTGTT-TTCTTAAAACAAGACTTTGTCTCACTTGAGATTGTTTTACTCGAAAAAAGATTTAT
1312763 TTCCCTCA
65 TTCCCTCA
* *
1312771 AGATTGTTTTTCTTAAAAC-AGACTTTGTCTTACTTGAGATTGTTTTACTCGAAAGAAGATTTAT
1 AGATTG-TTTTCTTAAAACAAGACTTTGTCTCACTTGAGATTGTTTTACTCGAAAAAAGATTTAT
*
1312835 TTTCCTCA
65 TTCCCTCA
* * * * * **
1312843 ATATTGTTTTCTTAAAACAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAA
1 AGATTGTTTTCTTAAAACAAGACTTTGTCTCACTTGAGATTGTTTTACTCGAAA
1312897 TAGAAAATTT
Statistics
Matches: 110, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
71 13 0.12
72 95 0.86
73 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.41
Consensus pattern (72 bp):
AGATTGTTTTCTTAAAACAAGACTTTGTCTCACTTGAGATTGTTTTACTCGAAAAAAGATTTATT
TCCCTCA
Found at i:1313000 original size:36 final size:36
Alignment explanation
Indices: 1312953--1313037 Score: 107
Period size: 36 Copynumber: 2.4 Consensus size: 36
1312943 ATTGAAAACA
* * * *
1312953 TTTCCCTTGAAATGAGTTTAGTCTCTCTCGAGATAG
1 TTTCCCTTGAAATCAATTTAGTCTCCCTCGAGACAG
* *
1312989 TTTCCCTTGAAACCAATTTTGTCTCCCTCGAGACAG
1 TTTCCCTTGAAATCAATTTAGTCTCCCTCGAGACAG
*
1313025 TTTCTCTTGAAAT
1 TTTCCCTTGAAAT
1313038 ATAAACATTG
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (36 bp):
TTTCCCTTGAAATCAATTTAGTCTCCCTCGAGACAG
Found at i:1313056 original size:101 final size:101
Alignment explanation
Indices: 1312864--1313200 Score: 521
Period size: 101 Copynumber: 3.3 Consensus size: 101
1312854 TTAAAACAAG
* * * *
1312864 ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAATAGAAAATTTTGTCTCCCTTGAGACAGTTTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTG-AA-A-CAAATTTTGTCTCCCTTGAGACAGTTTCT
1312929 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
63 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
* * * * *
1312968 GTTTAGTCTCTCTCGAGATAGTTTCCCTTGAAACCAATTTTGTCTCCCTCGAGACAGTTTCTCTT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTT
* *
1313033 GAAATATAAACATTGAAAACATTTCCCTTGAAATAA
66 GAAACATAAACATTGAAAACATTTCCCTTGAAATGA
*
1313069 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAAACAGTTTCTCTT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTT
1313134 GAAACATAAACATTGAAAACATTTCCCTTGAAATGA
66 GAAACATAAACATTGAAAACATTTCCCTTGAAATGA
* *
1313170 ATTTTGTCTCTATTGAGATAGTTTCCTTTGA
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGA
1313201 GACAGTTTCT
Statistics
Matches: 212, Mismatches: 21, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
101 185 0.87
102 1 0.00
103 2 0.01
104 24 0.11
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.38
Consensus pattern (101 bp):
ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTT
GAAACATAAACATTGAAAACATTTCCCTTGAAATGA
Found at i:1313101 original size:36 final size:36
Alignment explanation
Indices: 1313049--1313139 Score: 130
Period size: 36 Copynumber: 2.6 Consensus size: 36
1313039 TAAACATTGA
* *
1313049 AAACA-TTTCCCTTGAAATAAATTTTGTCTCTCTTG
1 AAACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTG
* *
1313084 AGATAGTTTCCCTTGAAACAAATTTTGTCTCCCTTG
1 AAACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTG
*
1313120 AAACAGTTTCTCTTGAAACA
1 AAACAGTTTCCCTTGAAACA
1313140 TAAACATTGA
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
35 3 0.06
36 45 0.94
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (36 bp):
AAACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTG
Found at i:1313406 original size:35 final size:36
Alignment explanation
Indices: 1313314--1313422 Score: 112
Period size: 35 Copynumber: 2.9 Consensus size: 36
1313304 CTTTTGGAAG
*
1313314 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTT
1 TTTTGTCTCTCTTGAGACAGTTTC-CCTGAAACAAA--T
* * *
1313353 TATCTTCGTCTCTTTTGAGATAATTTCCCTGAAACAAA-
1 T-T-TT-GTCTCTCTTGAGACAGTTTCCCTGAAACAAAT
1313391 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCC-TGAAA
1313423 AAGAATCTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
35 19 0.32
36 7 0.12
37 1 0.02
38 1 0.02
39 1 0.02
40 1 0.02
41 12 0.20
42 17 0.29
ACGTcount: A:0.24, C:0.20, G:0.13, T:0.43
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTGAAACAAAT
Found at i:1313453 original size:65 final size:66
Alignment explanation
Indices: 1313382--1313587 Score: 195
Period size: 65 Copynumber: 3.1 Consensus size: 66
1313372 ATAATTTCCC
* * *
1313382 TGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAA-AAGAATCTTTGAATATGTTT-TA
1 TGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAACAACCTTTGAATATGTTTCT-
1313445 CAT
65 C-T
* * ** *
1313448 T-AAACAAATTTTATCTCCCCTGAGACAGTTTTTCTTGAAACACCAACCTTTGAATATGTTTCTC
1 TGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAACAACCTTTGAATATGTTTCTC
1313512 T
66 T
* * ** * *
1313513 TGAAACAAAATTTTGCCTCCCTAGAGACAGTTTCTTTTGAAACACAAAAAACTTTTGAA-ATCGT
1 TGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCCCTTG-AA-AC-AACAACCTTTGAATAT-GT
1313577 TTCTCT
61 TTCTCT
1313583 TGAAA
1 TGAAA
1313588 TACAAAGAAC
Statistics
Matches: 115, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
65 36 0.31
66 23 0.20
67 27 0.23
68 2 0.02
69 4 0.03
70 23 0.20
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (66 bp):
TGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAACAACCTTTGAATATGTTTCTC
T
Found at i:1313586 original size:33 final size:33
Alignment explanation
Indices: 1313542--1313616 Score: 114
Period size: 33 Copynumber: 2.3 Consensus size: 33
1313532 CCTAGAGACA
* *
1313542 GTTTCTTTTGAAACACAAAAAACTTTTGAAATC
1 GTTTCTCTTGAAACACAAAAAACCTTTGAAATC
* *
1313575 GTTTCTCTTGAAATACAAAGAACCTTTGAAATC
1 GTTTCTCTTGAAACACAAAAAACCTTTGAAATC
1313608 GTTTCTCTT
1 GTTTCTCTT
1313617 AAAAAACCTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (33 bp):
GTTTCTCTTGAAACACAAAAAACCTTTGAAATC
Found at i:1313631 original size:26 final size:26
Alignment explanation
Indices: 1313595--1313646 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
1313585 AAATACAAAG
1313595 AACCTTTGAAA-TCGTTTCTCTTAAAA
1 AACCTTTGAAACT-GTTTCTCTTAAAA
1313621 AACCTTTGAAACTGTTTCTCTTAAAA
1 AACCTTTGAAACTGTTTCTCTTAAAA
1313647 GACTAAGACC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 24 0.96
27 1 0.04
ACGTcount: A:0.35, C:0.19, G:0.08, T:0.38
Consensus pattern (26 bp):
AACCTTTGAAACTGTTTCTCTTAAAA
Found at i:1315362 original size:15 final size:16
Alignment explanation
Indices: 1315344--1315376 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
1315334 CCATTTAATT
1315344 TTTATTATTTT-TATA
1 TTTATTATTTTGTATA
1315359 TTTATTATTTTGTATA
1 TTTATTATTTTGTATA
1315375 TT
1 TT
1315377 ATTTTCTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (16 bp):
TTTATTATTTTGTATA
Found at i:1320846 original size:14 final size:14
Alignment explanation
Indices: 1320813--1320860 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
1320803 CACATAATTA
1320813 GATTTAGGGTTTAG
1 GATTTAGGGTTTAG
* * *
1320827 GGTTTAAGGTTTAT
1 GATTTAGGGTTTAG
*
1320841 GATTTAGGGTTTTG
1 GATTTAGGGTTTAG
1320855 GATTTA
1 GATTTA
1320861 TTACAAAGAC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.21, C:0.00, G:0.31, T:0.48
Consensus pattern (14 bp):
GATTTAGGGTTTAG
Found at i:1320860 original size:21 final size:22
Alignment explanation
Indices: 1320813--1320861 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
1320803 CACATAATTA
* *
1320813 GATTTAGGGTTTAGGGTTTAAG
1 GATTTATGATTTAGGGTTTAAG
*
1320835 G-TTTATGATTTAGGGTTT-TG
1 GATTTATGATTTAGGGTTTAAG
1320855 GATTTAT
1 GATTTAT
1320862 TACAAAGACA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 2 0.09
21 20 0.87
22 1 0.04
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.49
Consensus pattern (22 bp):
GATTTATGATTTAGGGTTTAAG
Found at i:1320928 original size:12 final size:12
Alignment explanation
Indices: 1320911--1320935 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1320901 AGGTAAGTAC
1320911 AATTTAGGGTTT
1 AATTTAGGGTTT
1320923 AATTTAGGGTTT
1 AATTTAGGGTTT
1320935 A
1 A
1320936 GGGTTTAAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (12 bp):
AATTTAGGGTTT
Found at i:1320935 original size:7 final size:7
Alignment explanation
Indices: 1320913--1320962 Score: 50
Period size: 7 Copynumber: 7.4 Consensus size: 7
1320903 GTAAGTACAA
1320913 TTTAGGG
1 TTTAGGG
*
1320920 TTTA--A
1 TTTAGGG
1320925 TTTAGGG
1 TTTAGGG
1320932 TTTAGGG
1 TTTAGGG
*
1320939 TTTAAGG
1 TTTAGGG
* *
1320946 TTTATGA
1 TTTAGGG
1320953 TTTAGGG
1 TTTAGGG
1320960 TTT
1 TTT
1320963 TGGATTTATT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
5 4 0.12
7 30 0.88
ACGTcount: A:0.20, C:0.00, G:0.30, T:0.50
Consensus pattern (7 bp):
TTTAGGG
Found at i:1320937 original size:110 final size:112
Alignment explanation
Indices: 1320814--1321054 Score: 459
Period size: 110 Copynumber: 2.2 Consensus size: 112
1320804 ACATAATTAG
1320814 ATTTAGGGTTTAGGGTTTAAGGTTTATGATTTAGGGTTTTGGATTTATTACAAAGACATTAATTA
1 ATTTAGGGTTTAGGGTTTAAGGTTTATGATTTAGGGTTTTGGATTTATTACAAAGACATTAATTA
1320879 ATCGACTTGGTATCGATTTATGAGGTAAGTACAATTTAGGG-TT-TA
66 ATCGACTTGGTATCGATTTATGAGGTAAGTACAATTTAGGGTTTATA
*
1320924 ATTTAGGGTTTAGGGTTTAAGGTTTATGATTTAGGGTTTTGGATTTATTACAAAGTCATTAATTA
1 ATTTAGGGTTTAGGGTTTAAGGTTTATGATTTAGGGTTTTGGATTTATTACAAAGACATTAATTA
1320989 ATCGACTTGGTATCGATTTATGAGGTAAGTACAATTTAGGGTTTATA
66 ATCGACTTGGTATCGATTTATGAGGTAAGTACAATTTAGGGTTTATA
1321036 ATTTAGGGTTTAGGGTTTA
1 ATTTAGGGTTTAGGGTTTA
1321055 TAATTTAGGG
Statistics
Matches: 128, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
110 105 0.82
111 2 0.02
112 21 0.16
ACGTcount: A:0.28, C:0.05, G:0.24, T:0.43
Consensus pattern (112 bp):
ATTTAGGGTTTAGGGTTTAAGGTTTATGATTTAGGGTTTTGGATTTATTACAAAGACATTAATTA
ATCGACTTGGTATCGATTTATGAGGTAAGTACAATTTAGGGTTTATA
Found at i:1320971 original size:21 final size:21
Alignment explanation
Indices: 1320912--1320962 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1320902 GGTAAGTACA
*
1320912 ATTTAGGGTTTAA--TTTAGG
1 ATTTAGGGTTTAAGGTTTATG
*
1320931 GTTTAGGGTTTAAGGTTTATG
1 ATTTAGGGTTTAAGGTTTATG
1320952 ATTTAGGGTTT
1 ATTTAGGGTTT
1320963 TGGATTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 12 0.44
21 15 0.56
ACGTcount: A:0.22, C:0.00, G:0.29, T:0.49
Consensus pattern (21 bp):
ATTTAGGGTTTAAGGTTTATG
Found at i:1321047 original size:7 final size:7
Alignment explanation
Indices: 1321023--1321093 Score: 54
Period size: 7 Copynumber: 10.3 Consensus size: 7
1321013 GTAAGTACAA
1321023 TTTAGGG
1 TTTAGGG
***
1321030 TTTATAA
1 TTTAGGG
1321037 TTTAGGG
1 TTTAGGG
1321044 TTTAGGG
1 TTTAGGG
***
1321051 TTTATAA
1 TTTAGGG
1321058 TTTAGGG
1 TTTAGGG
1321065 -TTAGGG
1 TTTAGGG
* **
1321071 CTTATAG
1 TTTAGGG
1321078 TTTAGGG
1 TTTAGGG
1321085 TTTAGGG
1 TTTAGGG
1321092 TT
1 TT
1321094 CATTGCAAAG
Statistics
Matches: 46, Mismatches: 17, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
6 6 0.13
7 40 0.87
ACGTcount: A:0.21, C:0.01, G:0.31, T:0.46
Consensus pattern (7 bp):
TTTAGGG
Found at i:1321049 original size:21 final size:21
Alignment explanation
Indices: 1321023--1321093 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
1321013 GTAAGTACAA
1321023 TTTAGGGTTTATAATTTAGGG
1 TTTAGGGTTTATAATTTAGGG
1321044 TTTAGGGTTTATAATTTAGGG
1 TTTAGGGTTTATAATTTAGGG
* *
1321065 -TTAGGGCTTATAGTTTAGGG
1 TTTAGGGTTTATAATTTAGGG
1321085 TTTAGGGTT
1 TTTAGGGTT
1321094 CATTGCAAAG
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 18 0.39
21 28 0.61
ACGTcount: A:0.21, C:0.01, G:0.31, T:0.46
Consensus pattern (21 bp):
TTTAGGGTTTATAATTTAGGG
Found at i:1321746 original size:162 final size:165
Alignment explanation
Indices: 1321479--1321805 Score: 633
Period size: 162 Copynumber: 2.0 Consensus size: 165
1321469 GTTCTTACAC
1321479 CAATATCAACTCTCTAACTAAGCTACCTATACTGACGCGACCTATTTATATTCATAAAAATATTT
1 CAATATCAACTCTCTAACTAAGCTACCTATACTGACGCGACCTATTTATATTCATAAAAATATTT
1321544 ATTTCAAATAAATTAGGATTAATCTAATATTTATTTTATTAAGTGATTTAGATGAATTA-GA-TT
66 ATTTCAAATAAATTAGGATTAATCTAATATTTATTTTATTAAGTGATTTAGATGAATTAGGATTT
1321607 -TTTTTATTTTATTAGTTTCATAGTTTAGTTCAAA
131 ATTTTTATTTTATTAGTTTCATAGTTTAGTTCAAA
1321641 CAATATCAACTCTCTAACTAAGCTACCTATACTGACGCGACCTATTTATATTCATAAAAATATTT
1 CAATATCAACTCTCTAACTAAGCTACCTATACTGACGCGACCTATTTATATTCATAAAAATATTT
1321706 ATTTCAAATAAATTAGGATTAATCTAATATTTATTTTATTAAGTGATTTAGATGAATTAGGATTT
66 ATTTCAAATAAATTAGGATTAATCTAATATTTATTTTATTAAGTGATTTAGATGAATTAGGATTT
1321771 ATTTTTATTTTATTAGTTTCATAGTTTAGTTCAAA
131 ATTTTTATTTTATTAGTTTCATAGTTTAGTTCAAA
1321806 ATATGATTTT
Statistics
Matches: 162, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
162 124 0.77
163 2 0.01
164 2 0.01
165 34 0.21
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.44
Consensus pattern (165 bp):
CAATATCAACTCTCTAACTAAGCTACCTATACTGACGCGACCTATTTATATTCATAAAAATATTT
ATTTCAAATAAATTAGGATTAATCTAATATTTATTTTATTAAGTGATTTAGATGAATTAGGATTT
ATTTTTATTTTATTAGTTTCATAGTTTAGTTCAAA
Found at i:1326374 original size:21 final size:21
Alignment explanation
Indices: 1326348--1326468 Score: 107
Period size: 21 Copynumber: 5.7 Consensus size: 21
1326338 TCGAGGGTTC
1326348 TATGTGGTCCTTCGGGACATA
1 TATGTGGTCCTTCGGGACATA
* * * *
1326369 TATGTGATTCTTTGGAACATA
1 TATGTGGTCCTTCGGGACATA
*
1326390 TATGAGGTCCTTCGGGACATA
1 TATGTGGTCCTTCGGGACATA
* * * *
1326411 TATTTGGTTCTTTGGAACATA
1 TATGTGGTCCTTCGGGACATA
* * * *
1326432 TATATGGTCTTTAGGGACAATTC
1 TATGTGGTCCTTCGGGAC-A-TA
1326455 TATGTGGTCCTTCG
1 TATGTGGTCCTTCG
1326469 AGAGAAACCT
Statistics
Matches: 75, Mismatches: 23, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
21 62 0.83
22 1 0.01
23 12 0.16
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.39
Consensus pattern (21 bp):
TATGTGGTCCTTCGGGACATA
Found at i:1326449 original size:42 final size:43
Alignment explanation
Indices: 1326348--1326450 Score: 149
Period size: 42 Copynumber: 2.5 Consensus size: 43
1326338 TCGAGGGTTC
1326348 TATG-TGGTCCTTCGGGACATATATGTGATTCTTTGGAACATA
1 TATGATGGTCCTTCGGGACATATATGTGATTCTTTGGAACATA
* *
1326390 TATGA-GGTCCTTCGGGACATATATTTGGTTCTTTGGAACATA
1 TATGATGGTCCTTCGGGACATATATGTGATTCTTTGGAACATA
* *
1326432 TAT-ATGGTCTTTAGGGACA
1 TATGATGGTCCTTCGGGACA
1326451 ATTCTATGTG
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
41 1 0.02
42 54 0.98
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.38
Consensus pattern (43 bp):
TATGATGGTCCTTCGGGACATATATGTGATTCTTTGGAACATA
Found at i:1326480 original size:23 final size:22
Alignment explanation
Indices: 1326454--1326532 Score: 79
Period size: 23 Copynumber: 3.5 Consensus size: 22
1326444 AGGGACAATT
1326454 CTATGTGGTCCTTCGAGAGAAAC
1 CTATGTGGTCCTTCG-GAGAAAC
*
1326477 CTATGTGG-CACTTCGGTGCAAAC
1 CTATGTGGTC-CTTCGGAG-AAAC
* * *
1326500 CTATGTGATCCTTCGGGACAAAA
1 CTATGTGGTCCTTC-GGAGAAAC
1326523 CTATGTGGTC
1 CTATGTGGTC
1326533 TTTTGGGACA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
22 3 0.07
23 40 0.87
24 3 0.07
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.28
Consensus pattern (22 bp):
CTATGTGGTCCTTCGGAGAAAC
Found at i:1326540 original size:23 final size:23
Alignment explanation
Indices: 1326445--1326543 Score: 67
Period size: 23 Copynumber: 4.3 Consensus size: 23
1326435 ATGGTCTTTA
** *
1326445 GGGACAATTCTATGTGGTCCTTC
1 GGGACAAAACTATGTGATCCTTC
* * * *
1326468 GAGAGAAACCTATGTG-GCACTTC
1 GGGACAAAACTATGTGATC-CTTC
*
1326491 GGTG-CAAACCTATGTGATCCTTC
1 GG-GACAAAACTATGTGATCCTTC
* * *
1326514 GGGACAAAACTATGTGGTCTTTT
1 GGGACAAAACTATGTGATCCTTC
1326537 GGGACAA
1 GGGACAA
1326544 TTAAGTGGCA
Statistics
Matches: 60, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
22 2 0.03
23 56 0.93
24 2 0.03
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.28
Consensus pattern (23 bp):
GGGACAAAACTATGTGATCCTTC
Found at i:1332667 original size:15 final size:15
Alignment explanation
Indices: 1332647--1332718 Score: 92
Period size: 15 Copynumber: 4.8 Consensus size: 15
1332637 GGGGTGATTT
1332647 GGAGGAAGAGGAAGA
1 GGAGGAAGAGGAAGA
*
1332662 GGAGGAAGAGGAGGA
1 GGAGGAAGAGGAAGA
*
1332677 GGAAGAAGAGGAAGA
1 GGAGGAAGAGGAAGA
* *
1332692 AGAGGAAGA-GCAGA
1 GGAGGAAGAGGAAGA
1332706 TGGAGGAAGAGGA
1 -GGAGGAAGAGGA
1332719 GTTGGAGGAT
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
14 4 0.09
15 42 0.89
16 1 0.02
ACGTcount: A:0.46, C:0.01, G:0.51, T:0.01
Consensus pattern (15 bp):
GGAGGAAGAGGAAGA
Done.