Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168049.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_30, 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: 11202444
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 44000 characters in sequence are not A, C, G, or T
File 11 of 64
Found at i:1101605 original size:12 final size:12
Alignment explanation
Indices: 1101582--1101612 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1101572 TTTTTCAAAA
1101582 ATTTTA-TAATT
1 ATTTTATTAATT
1101593 ATTTTATTAATT
1 ATTTTATTAATT
1101605 ATTTTATT
1 ATTTTATT
1101613 TTTAATTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.32
12 13 0.68
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATTTTATTAATT
Found at i:1102474 original size:13 final size:12
Alignment explanation
Indices: 1102456--1102493 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
1102446 TTCATTTTTC
1102456 CTTTCTTCTCCTT
1 CTTTCTTCT-CTT
1102469 CTTTCTTCT-TT
1 CTTTCTTCTCTT
1102480 CTTTCTCTCTCTT
1 CTTTCT-TCTCTT
1102493 C
1 C
1102494 CAGAATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 8 0.35
12 3 0.13
13 12 0.52
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (12 bp):
CTTTCTTCTCTT
Found at i:1102486 original size:21 final size:21
Alignment explanation
Indices: 1102441--1102482 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
1102431 AAACACCTAA
1102441 TCTCCTTCATTTTTCCTTTCT
1 TCTCCTTCATTTTTCCTTTCT
1102462 TCTCCTTC-TTTCTT-CTTTCT
1 TCTCCTTCATTT-TTCCTTTCT
1102482 T
1 T
1102483 TCTCTCTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.64
Consensus pattern (21 bp):
TCTCCTTCATTTTTCCTTTCT
Found at i:1103152 original size:3 final size:3
Alignment explanation
Indices: 1103146--1103191 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
1103136 TATTTTTTTA
* ** *
1103146 ATT ATT ATT ATT ATT AAT ATT ATT ATT AAA ATT ATT ATT AAT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1103192 AACTAAAAAT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:1103161 original size:12 final size:12
Alignment explanation
Indices: 1103146--1103191 Score: 74
Period size: 12 Copynumber: 3.8 Consensus size: 12
1103136 TATTTTTTTA
*
1103146 ATTATTATTATT
1 ATTAATATTATT
1103158 ATTAATATTATT
1 ATTAATATTATT
*
1103170 ATTAAAATTATT
1 ATTAATATTATT
1103182 ATTAATATTA
1 ATTAATATTA
1103192 AACTAAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
ATTAATATTATT
Found at i:1103200 original size:24 final size:24
Alignment explanation
Indices: 1103152--1103201 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1103142 TTTAATTATT
* *
1103152 ATTATTATTAATATTATTATTAAA
1 ATTATTATTAATATTATAATAAAA
1103176 ATTATTATTAATATTA-AACTAAAA
1 ATTATTATTAATATTATAA-TAAAA
1103200 AT
1 AT
1103202 GAAGACAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 22 0.96
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
ATTATTATTAATATTATAATAAAA
Found at i:1110006 original size:18 final size:19
Alignment explanation
Indices: 1109983--1110018 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
1109973 ATAAATTGAA
1109983 AAAAAATATTTTT-TAATG
1 AAAAAATATTTTTATAATG
1110001 AAAAAATATTTTTATAAT
1 AAAAAATATTTTTATAAT
1110019 TTTTAAAAAT
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:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (19 bp):
AAAAAATATTTTTATAATG
Found at i:1117741 original size:2 final size:2
Alignment explanation
Indices: 1117734--1117759 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1117724 ATAAATAACA
1117734 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
1117760 TTCAAGGTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1126782 original size:37 final size:35
Alignment explanation
Indices: 1126737--1126820 Score: 86
Period size: 35 Copynumber: 2.4 Consensus size: 35
1126727 TATTTTAATT
* *
1126737 TTTA-AATTAATATTTTTAAATAATTATCTA-TATTT
1 TTTATAATTAATATTTTT-AATAAATAT-TATTATTC
*
1126772 TATTATAATTATTA-TTTTAATAAATATTATTATTC
1 T-TTATAATTAATATTTTTAATAAATATTATTATTC
1126807 TTTATAA-TAATATT
1 TTTATAATTAATATT
1126821 CAATTAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
33 4 0.10
34 9 0.22
35 14 0.34
36 7 0.17
37 7 0.17
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (35 bp):
TTTATAATTAATATTTTTAATAAATATTATTATTC
Found at i:1126805 original size:21 final size:21
Alignment explanation
Indices: 1126779--1126820 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1126769 TTTTATTATA
1126779 ATTATTATTT-TAATAAATATT
1 ATTATTATTTATAAT-AATATT
*
1126800 ATTATTCTTTATAATAATATT
1 ATTATTATTTATAATAATATT
1126821 CAATTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTATTATTTATAATAATATT
Found at i:1126815 original size:18 final size:18
Alignment explanation
Indices: 1126717--1126805 Score: 58
Period size: 18 Copynumber: 4.8 Consensus size: 18
1126707 TTGAATAAAT
1126717 TAAATATTATTATTTTAA
1 TAAATATTATTATTTTAA
* *
1126735 TTTTTAAATTAATATT-TTTAAA
1 ----TAAA-TATTATTATTTTAA
* *
1126757 TAATTATCTA-TATTTTAT
1 TAAATAT-TATTATTTTAA
*
1126775 TATA-ATTATTATTTTAA
1 TAAATATTATTATTTTAA
1126792 TAAATATTATTATT
1 TAAATATTATTATT
1126806 CTTTATAATA
Statistics
Matches: 52, Mismatches: 10, Indels: 14
0.68 0.13 0.18
Matches are distributed among these distances:
16 2 0.04
17 15 0.29
18 20 0.38
22 9 0.17
23 6 0.12
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (18 bp):
TAAATATTATTATTTTAA
Found at i:1126820 original size:18 final size:17
Alignment explanation
Indices: 1126747--1126820 Score: 60
Period size: 18 Copynumber: 4.1 Consensus size: 17
1126737 TTTAAATTAA
1126747 TATTTTTA-AATAATTAT
1 TATTTTTATAATAA-TAT
*
1126764 CTATATTTTATTATAATTAT
1 -TAT-TTTTATAATAA-TAT
* *
1126784 TATTTTAATAAATATTAT
1 TATTTTTAT-AATAATAT
1126802 TATTCTTTATAATAATAT
1 TATT-TTTATAATAATAT
1126820 T
1 T
1126821 CAATTAAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
18 23 0.50
19 15 0.33
20 8 0.17
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
TATTTTTATAATAATAT
Found at i:1134806 original size:39 final size:39
Alignment explanation
Indices: 1134732--1134806 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
1134722 TATATTGAAA
* *
1134732 ATATTTATTATTAAATCATAACAAAAATATTATTTATTT
1 ATATTTATTATTAAATAATAACAAAAATATCATTTATTT
* *
1134771 ATATTTATTATTAAAATAATAATATAAATA-CATTTA
1 ATATTTATTATT-AAATAATAACAAAAATATCATTTA
1134807 GAAATAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 17 0.55
40 14 0.45
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (39 bp):
ATATTTATTATTAAATAATAACAAAAATATCATTTATTT
Found at i:1136393 original size:13 final size:13
Alignment explanation
Indices: 1136375--1136402 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1136365 AATTAACATA
1136375 AATCTTAAATAAG
1 AATCTTAAATAAG
1136388 AATCTTAAATAAG
1 AATCTTAAATAAG
1136401 AA
1 AA
1136403 ATCCATTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (13 bp):
AATCTTAAATAAG
Found at i:1139982 original size:9 final size:9
Alignment explanation
Indices: 1139959--1139989 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
1139949 CACTTTATTG
1139959 TTTTTTCTT
1 TTTTTTCTT
1139968 TCTTTTTCTT
1 T-TTTTTCTT
1139978 TTTTTTCTT
1 TTTTTTCTT
1139987 TTT
1 TTT
1139990 CACAGTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:1139984 original size:15 final size:16
Alignment explanation
Indices: 1139960--1139990 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1139950 ACTTTATTGT
1139960 TTTTTCTTTCTTTTTC
1 TTTTTCTTTCTTTTTC
1139976 TTTTT-TTTCTTTTTC
1 TTTTTCTTTCTTTTTC
1139991 ACAGTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTCTTTCTTTTTC
Found at i:1140913 original size:40 final size:40
Alignment explanation
Indices: 1140863--1140943 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 40
1140853 ATCAATATGT
* * *
1140863 ACAAAAAAAAACATAACCAA-ATGACCAAATGAATAAATGA
1 ACAAAAAAAAA-ATAAACAATATAACCAAATGAACAAATGA
* *
1140903 ACAAAGAAAAATTAAACAATATAACCAAATGAACAAATGA
1 ACAAAAAAAAAATAAACAATATAACCAAATGAACAAATGA
1140943 A
1 A
1140944 AACATCAACA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
39 6 0.17
40 29 0.83
ACGTcount: A:0.65, C:0.14, G:0.07, T:0.14
Consensus pattern (40 bp):
ACAAAAAAAAAATAAACAATATAACCAAATGAACAAATGA
Found at i:1140941 original size:8 final size:8
Alignment explanation
Indices: 1140880--1140943 Score: 53
Period size: 8 Copynumber: 8.0 Consensus size: 8
1140870 AAAACATAAC
*
1140880 CAAATGAC
1 CAAATGAA
1140888 CAAATGAA
1 CAAATGAA
*
1140896 TAAATGAA
1 CAAATGAA
1140904 CAAA-GAA
1 CAAATGAA
*
1140911 -AAATTAAA
1 CAAA-TGAA
1140919 CAATAT-AA
1 CAA-ATGAA
1140927 CCAAATGAA
1 -CAAATGAA
1140936 CAAATGAA
1 CAAATGAA
1140944 AACATCAACA
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
6 3 0.07
7 3 0.07
8 31 0.67
9 8 0.17
10 1 0.02
ACGTcount: A:0.62, C:0.12, G:0.09, T:0.16
Consensus pattern (8 bp):
CAAATGAA
Found at i:1142594 original size:198 final size:197
Alignment explanation
Indices: 1142251--1142931 Score: 707
Period size: 200 Copynumber: 3.4 Consensus size: 197
1142241 AGTTTTTGTC
* * *
1142251 AGCTATTTATGAAAAAAAAAATTATTAAAGGCTATAATCGTCACAAAATAAATGATAAAATCTGA
1 AGCTATTTATGAAAAAAAATATCATTAAAAGCTATAATCGTCACAAAATAAATGATAAAATCTGA
* * * * * *
1142316 TATATTAAT-AACAAA-AAATAACTCATCACATTATT-AGTGACACAATTATCATCACTAATGAT
66 TATATTAATGATCAAAGGAA-AAC-CATCACAATATTGA-TGACATAATTATCGTCACAAATGAT
* * * *
1142378 TGTAAGATAATATCAAATGTGATAATAAAATTAAACATTACTTTATGCTTTTTTTTTATGTTAAT
128 TGTAAGATAATGTCAAATGTGATAATAAAATCAAACATTACCTTAT-CTTTTTTTTGATGTTAAT
1142443 TTGCATA
192 TT-CATA
* * * *
1142450 AGCTATTTATGAAAAGAAATGTCATTAAAAGCTATAATTGTCACAAAATAAATGAT-AAATTTGA
1 AGCTATTTATGAAAAAAAATATCATTAAAAGCTATAATCGTCACAAAATAAATGATAAAATCTGA
* * *
1142514 TATATTAATGATGAAAGGAAAACCATCACAATATTGATGACATAATTATCGTCACCAATGATTAT
66 TATATTAATGATCAAAGGAAAACCATCACAATATTGATGACATAATTATCGTCACAAATGATTGT
* * *
1142579 AAGATAATGTCAAATGTGATAATAAAATCAAACATTACCTTATCCTTCTTTTATGGTGTTAGTTT
131 AAGATAATGTCAAATGTGATAATAAAATCAAACATTACCTTAT-CTT-TTTTTTGATGTTA-ATT
**
1142644 TTGTCA
193 TCAT-A
* * * *
1142650 A-CTATTTATG-AAAAAAATATCATTGAAAGTTATAATCATCATCAAAATAAATGATAAAATATG
1 AGCTATTTATGAAAAAAAATATCATTAAAAGCTATAATCGTCA-CAAAATAAATGATAAAATCTG
* * * *
1142713 ATATATTAGTGA-CAACAGGTAAATCATCACAATATTTG-TGACATAATTAAT-GTCAAAAATGA
65 ATATATTAATGATCAA-AGGAAAACCATCACAATA-TTGATGACATAATT-ATCGTCACAAATGA
* * * * * * **
1142775 TTGTAAGATAACGTCAAACGTGATAGTAAAATCAAACGTCACCTTATATTTTTTTGTGACATTAG
127 TTGTAAGATAATGTCAAATGTGATAATAAAATCAAACATTACCTTATCTTTTTTT-TGATGTTA-
1142840 ATTTCATA
190 ATTTCATA
* * * *
1142848 AGCTATATATGAAAAAAAA-AGGTCATTAAATGCTATAATTGTCATAAAATAAATGATAAAATCT
1 AGCTATTTATGAAAAAAAATA--TCATTAAAAGCTATAATCGTCACAAAATAAATGATAAAATCT
* * *
1142912 AATATATTAGTGATGAAAGG
64 GATATATTAATGATCAAAGG
1142932 TAAATTGTCA
Statistics
Matches: 403, Mismatches: 62, Indels: 33
0.81 0.12 0.07
Matches are distributed among these distances:
198 125 0.31
199 114 0.28
200 140 0.35
201 24 0.06
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.34
Consensus pattern (197 bp):
AGCTATTTATGAAAAAAAATATCATTAAAAGCTATAATCGTCACAAAATAAATGATAAAATCTGA
TATATTAATGATCAAAGGAAAACCATCACAATATTGATGACATAATTATCGTCACAAATGATTGT
AAGATAATGTCAAATGTGATAATAAAATCAAACATTACCTTATCTTTTTTTTGATGTTAATTTCA
TA
Found at i:1144431 original size:14 final size:15
Alignment explanation
Indices: 1144409--1144446 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
1144399 TATTTCTTTA
1144409 TTTTCTTGCATTTTC
1 TTTTCTTGCATTTTC
1144424 TTTT-TTGCATTTTAC
1 TTTTCTTGCATTTT-C
1144439 ATTTTCTT
1 -TTTTCTT
1144447 AGTTACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 9 0.45
15 5 0.25
16 4 0.20
17 2 0.10
ACGTcount: A:0.11, C:0.16, G:0.05, T:0.68
Consensus pattern (15 bp):
TTTTCTTGCATTTTC
Found at i:1159905 original size:517 final size:517
Alignment explanation
Indices: 1158926--1159957 Score: 1832
Period size: 517 Copynumber: 2.0 Consensus size: 517
1158916 TAAATGATCC
* *
1158926 GTTGTCATTAACTTTCCTAGCTATAGACTTATCCTTTGCCTCCACTATCTCTTCCTCTATAACTT
1 GTTGTCATTAACTTTCCTAGCCATAGACTTATCCTTTGCCTCCACTATCTCTTCCTCCATAACTT
*
1158991 TAATAAAATGTGGTACTTCCACCACAATGGGCTCTTTATTATCATCAATCAACATCAGACCTCCT
66 TAACAAAATGTGGTACTTCCACCACAATGGGCTCTTTATTATCATCAATCAACATCAGACCTCCT
*
1159056 TTCCTCGAGTGGTCCCTTAATGCATGCTCATTCTTCTTTTCCCAACAAGGTGTTAACTTTATAGT
131 TTCCTCGAGTGGTCCCCTAATGCATGCTCATTCTTCTTTTCCCAACAAGGTGTTAACTTTATAGT
*
1159121 ACTAGGCATGGAATATTGAGGACAAATAATTAAGGTATATGCATTATGAACCCGTTGCCCAGGAG
196 ACTAGGCATGGAATATTGAGGACAAATAATTAAGGTATATGCATTATGAACCCGTTGCCCAAGAG
* *
1159186 TCCTTATGAATACCTTTTGGTTTTGTTAGAGTTTTTCTTGAGTCTAGAGCAATTCAATAAGCATC
261 TCCTCATGAATACCTCTTGGTTTTGTTAGAGTTTTTCTTGAGTCTAGAGCAATTCAATAAGCATC
1159251 TCCTTAAAGGATGATGTTTTTTCTTATATAGAAGGTAATAGTGAATATGGTGTAGATAGAAAGTG
326 TCCTTAAAGGATGATGTTTTTTCTTATATAGAAGGTAATAGTGAATATGGTGTAGATAGAAAGTG
* *
1159316 ATATGAAGATTAATGGTATTATGATGAAACAAAATGTTGCTATGGTGGGAAATAGTGTGGCATTT
391 ATATAAACATTAATGGTATTATGATGAAACAAAATGTTGCTATGGTGGGAAATAGTGTGGCATTT
*
1159381 ACGAGACTTATAATGATGGTAGAGAATATTGAGATGATAGAGGGTATTGTAAAAGTGAATTT
456 ACGAGACTTATAATGATGGTAAAGAATATTGAGATGATAGAGGGTATTGTAAAAGTGAATTT
1159443 GTTGTCATTAACTTTCCTAGCCATAGACTTATCCTTTGCCTCCACTATCTCTTCCTCCATAACTT
1 GTTGTCATTAACTTTCCTAGCCATAGACTTATCCTTTGCCTCCACTATCTCTTCCTCCATAACTT
* *
1159508 TAACAAAATGTGGTACTTCCACTACAATGGGCTCTTTATTATCATTAATCAACATCAGACCTCCT
66 TAACAAAATGTGGTACTTCCACCACAATGGGCTCTTTATTATCATCAATCAACATCAGACCTCCT
*
1159573 TTCCTCGAGTGGTCCCCTAATGTATGCTCATTCTTCTTTTCCCAACAAGGTGTTAACTTTATAGT
131 TTCCTCGAGTGGTCCCCTAATGCATGCTCATTCTTCTTTTCCCAACAAGGTGTTAACTTTATAGT
* * *
1159638 ACTAGGCATGGAATCTTGAGGACAAGTAATTAAGGTATATGCATTATGACCCCGTTGCCCAAGAG
196 ACTAGGCATGGAATATTGAGGACAAATAATTAAGGTATATGCATTATGAACCCGTTGCCCAAGAG
* *
1159703 TCCTCATGAATACCTCTTGGTTTTGTTAGAGTTTTTCTTGAGTTTGGAGCAATTCAATAAGCATC
261 TCCTCATGAATACCTCTTGGTTTTGTTAGAGTTTTTCTTGAGTCTAGAGCAATTCAATAAGCATC
* * *
1159768 T-CTTCAAAGGATGGTGTTTTTTCTTATATAGAAGGTAATGGTGAATATGGTGTAGATGGAAAGT
326 TCCTT-AAAGGATGATGTTTTTTCTTATATAGAAGGTAATAGTGAATATGGTGTAGATAGAAAGT
**
1159832 GATATAAACATTAATGGTATTATGATGAAGTAAAATGTTGCTATGGTGGGAAATAGTGTGGCATT
390 GATATAAACATTAATGGTATTATGATGAAACAAAATGTTGCTATGGTGGGAAATAGTGTGGCATT
*
1159897 TGCGAGACTTATAATGATGGTAAAGAATATTGAGATGATAGAGGGTATTGTAAAAGTGAAT
455 TACGAGACTTATAATGATGGTAAAGAATATTGAGATGATAGAGGGTATTGTAAAAGTGAAT
1159958 GCTTGTAGGA
Statistics
Matches: 490, Mismatches: 24, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
516 3 0.01
517 487 0.99
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.35
Consensus pattern (517 bp):
GTTGTCATTAACTTTCCTAGCCATAGACTTATCCTTTGCCTCCACTATCTCTTCCTCCATAACTT
TAACAAAATGTGGTACTTCCACCACAATGGGCTCTTTATTATCATCAATCAACATCAGACCTCCT
TTCCTCGAGTGGTCCCCTAATGCATGCTCATTCTTCTTTTCCCAACAAGGTGTTAACTTTATAGT
ACTAGGCATGGAATATTGAGGACAAATAATTAAGGTATATGCATTATGAACCCGTTGCCCAAGAG
TCCTCATGAATACCTCTTGGTTTTGTTAGAGTTTTTCTTGAGTCTAGAGCAATTCAATAAGCATC
TCCTTAAAGGATGATGTTTTTTCTTATATAGAAGGTAATAGTGAATATGGTGTAGATAGAAAGTG
ATATAAACATTAATGGTATTATGATGAAACAAAATGTTGCTATGGTGGGAAATAGTGTGGCATTT
ACGAGACTTATAATGATGGTAAAGAATATTGAGATGATAGAGGGTATTGTAAAAGTGAATTT
Found at i:1164680 original size:14 final size:15
Alignment explanation
Indices: 1164652--1164691 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1164642 AGAAGCAAAA
*
1164652 CAAGAAGAAATAGAT-
1 CAAG-AGAAAGAGATC
1164667 CAAGAGAAAGAGATC
1 CAAGAGAAAGAGATC
1164682 CAAGAGAAAG
1 CAAGAGAAAG
1164692 TTCAATCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.39
15 14 0.61
ACGTcount: A:0.57, C:0.10, G:0.25, T:0.07
Consensus pattern (15 bp):
CAAGAGAAAGAGATC
Found at i:1174074 original size:20 final size:19
Alignment explanation
Indices: 1174049--1174094 Score: 69
Period size: 17 Copynumber: 2.5 Consensus size: 19
1174039 ATGGCATATG
1174049 GAAGAGTTGAAGATCCTATA
1 GAAGAGTTG-AGATCCTATA
1174069 GAAGAG-T-AGATCCTATA
1 GAAGAGTTGAGATCCTATA
1174086 GAAGAGTTG
1 GAAGAGTTG
1174095 GTGGAAGAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 16 0.67
18 1 0.04
19 1 0.04
20 6 0.25
ACGTcount: A:0.39, C:0.09, G:0.28, T:0.24
Consensus pattern (19 bp):
GAAGAGTTGAGATCCTATA
Found at i:1178296 original size:31 final size:31
Alignment explanation
Indices: 1178268--1178349 Score: 130
Period size: 31 Copynumber: 2.6 Consensus size: 31
1178258 TATTCATATG
1178268 AAATTTGAAATTTAGTCCATATGCTCATACA
1 AAATTTGAAATTTAGTCCATATGCTCATACA
* *
1178299 AAATTTCAAATTTAGTCTC-TATTCTCATACA
1 AAATTTGAAATTTAGTC-CATATGCTCATACA
1178330 AAATTTGAAATTTAGTCCAT
1 AAATTTGAAATTTAGTCCAT
1178350 TTAATACAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
30 1 0.02
31 44 0.96
32 1 0.02
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.39
Consensus pattern (31 bp):
AAATTTGAAATTTAGTCCATATGCTCATACA
Found at i:1181229 original size:162 final size:161
Alignment explanation
Indices: 1180962--1181286 Score: 542
Period size: 162 Copynumber: 2.0 Consensus size: 161
1180952 TACAAACTTC
* * * *
1180962 TTGTAGATTGATGGTTTATTTACCTTAAAGGATCAATCTGGAGCTAGATTGCTTGAGGTTTTAAT
1 TTGTAGATTGACGGTCTATTTACCTTAAAGGATCAATATGAAGCTAGATTGCTTGAGGTTTTAAT
* * *
1181027 TCTAGGCATTTCCATCATTCATTTTTGTTCTAATTTGATATGCCATTGCCCAGTTGTGCCAATTT
66 TCTAGGCATTTCCATCATTCACTTTTATTCTAATTTGATATGCCATTGCCCAATTGTGCC-ATTT
*
1181092 TTTACTTGTCTCTTTAGATAAAAATAGTAACT
130 TTTACTTGTCTCTTTAGACAAAAATAGTAACT
1181124 TTGTAGATTGACGGTCTATTTACCTTAAAGGATCAATATGAAGCTAGATTGCTTGAGGTTTTAAT
1 TTGTAGATTGACGGTCTATTTACCTTAAAGGATCAATATGAAGCTAGATTGCTTGAGGTTTTAAT
*
1181189 TCTAGGTATTTCCATCATTCACTTTTATTCTAATTTGATATGCCATTGCCCAATTGTGCCATTTT
66 TCTAGGCATTTCCATCATTCACTTTTATTCTAATTTGATATGCCATTGCCCAATTGTGCCATTTT
* *
1181254 TTGCTTGTCTTTTTAGACAAAAATAGTAACT
131 TTACTTGTCTCTTTAGACAAAAATAGTAACT
1181285 TT
1 TT
1181287 ATTCCAAAAT
Statistics
Matches: 152, Mismatches: 11, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
161 35 0.23
162 117 0.77
ACGTcount: A:0.26, C:0.15, G:0.16, T:0.43
Consensus pattern (161 bp):
TTGTAGATTGACGGTCTATTTACCTTAAAGGATCAATATGAAGCTAGATTGCTTGAGGTTTTAAT
TCTAGGCATTTCCATCATTCACTTTTATTCTAATTTGATATGCCATTGCCCAATTGTGCCATTTT
TTACTTGTCTCTTTAGACAAAAATAGTAACT
Found at i:1188345 original size:23 final size:23
Alignment explanation
Indices: 1188295--1188338 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 23
1188285 TTTATATAAA
1188295 TATATATATATATAACTAAAGTC
1 TATATATATATATAACTAAAGTC
1188318 TATATATATA-ATAACTAAAGT
1 TATATATATATATAACTAAAGT
1188339 TTTATATTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.39
Consensus pattern (23 bp):
TATATATATATATAACTAAAGTC
Found at i:1188921 original size:21 final size:22
Alignment explanation
Indices: 1188881--1188923 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1188871 ATTTAGAAAA
* *
1188881 AAATTTTCTTAAATTTATTTTT
1 AAATTTTCTTAAACTAATTTTT
1188903 AAATTTT-TTAAACTAATTTTT
1 AAATTTTCTTAAACTAATTTTT
1188924 TTAAATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (22 bp):
AAATTTTCTTAAACTAATTTTT
Found at i:1194035 original size:333 final size:333
Alignment explanation
Indices: 1193427--1194036 Score: 907
Period size: 333 Copynumber: 1.8 Consensus size: 333
1193417 TTTTGCCTTT
* *
1193427 TTGTTGGATTATGAGGTCCAACGGTCTCCTTTAGAGATTCAGTATGTCGATTCATCTGGGTGAGG
1 TTGTTGGATTATGAGGTCCAACGATCTCCTTTAGAGAATCAGTATGTCGATTCATCTGGGTGAGG
* * *
1193492 TATCCCATGGTGGATCGGATTCCAATGTATGGTAACCCAACCTATCAAAACCCAATGGGTGAGGT
66 TATCCCAAGATGGATCGGATTCCAATGTATGGCAACCCAACCTATCAAAACCCAATGGGTGAGGT
* * * * * * *
1193557 ATCTCATGAAAGCTTTGCAAAGCTCTTTATGTCTACCTGTCGCTTAGTATGGGGCTCTGCGTTAC
131 ATCCCATGAAAGCTTTGCAAAGCCCCTTATGTCCACCTGTCACTTAGTATGAGGCTCTGCGCTAC
* *
1193622 CAAAAGAGAATAAGAAAATTAAGTTGTGCCTTCATTATTAGCTATAGCTTTTGGTGTAGTGGTAA
196 CAAAAGAGAATAAAAAAATAAAGTTGTGCCTTCATTATTAGCTATAGCTTTTGGTGTAGTGGTAA
*
1193687 GTGCTTAAACCTGAAAATTACTATTAGAGCGAGATTGCATGTTCGAGTCCCCCAAGTGCCACTGG
261 GTGCTCAAACCTGAAAATTACTATTAGAGCGAGATTGCATGTTCGAGTCCCCCAAGTGCCACTGG
1193752 AAGGGAGA
326 AAGGGAGA
* * * * * *
1193760 TTGTTGGATTATGGGGTCTAGCGATCT-CTCTTAGGGAATCGGTATGTTGATTCATCTGGGTGAG
1 TTGTTGGATTATGAGGTCCAACGATCTCCT-TTAGAGAATCAGTATGTCGATTCATCTGGGTGAG
* * * * ** *
1193824 GTATCCCAAGATGGATCGGATTTCGATGTATGGCAACCCAACCTGTCGAGGCCCGATGGGTGAGG
65 GTATCCCAAGATGGATCGGATTCCAATGTATGGCAACCCAACCTATCAAAACCCAATGGGTGAGG
** *
1193889 TATCCCATGAAAGCTTTGTGAAGCCCCTTATGTCCACTTGTCACTTAGTATGAGGCTCTGCGCTA
130 TATCCCATGAAAGCTTTGCAAAGCCCCTTATGTCCACCTGTCACTTAGTATGAGGCTCTGCGCTA
*
1193954 CCAAAAGAGAATAAAAAAATAAAGTTGTGCTTTCATTATTAGCTATAGCTTTTGGTGTAGTGGTA
195 CCAAAAGAGAATAAAAAAATAAAGTTGTGCCTTCATTATTAGCTATAGCTTTTGGTGTAGTGGTA
*
1194019 AGTGCTCAATCCTGAAAA
260 AGTGCTCAAACCTGAAAA
1194037 CTTTGTTAGC
Statistics
Matches: 243, Mismatches: 33, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
332 2 0.01
333 241 0.99
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.30
Consensus pattern (333 bp):
TTGTTGGATTATGAGGTCCAACGATCTCCTTTAGAGAATCAGTATGTCGATTCATCTGGGTGAGG
TATCCCAAGATGGATCGGATTCCAATGTATGGCAACCCAACCTATCAAAACCCAATGGGTGAGGT
ATCCCATGAAAGCTTTGCAAAGCCCCTTATGTCCACCTGTCACTTAGTATGAGGCTCTGCGCTAC
CAAAAGAGAATAAAAAAATAAAGTTGTGCCTTCATTATTAGCTATAGCTTTTGGTGTAGTGGTAA
GTGCTCAAACCTGAAAATTACTATTAGAGCGAGATTGCATGTTCGAGTCCCCCAAGTGCCACTGG
AAGGGAGA
Found at i:1196358 original size:16 final size:16
Alignment explanation
Indices: 1196324--1196358 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1196314 ATACAAGCTC
**
1196324 ATACCAATTGTTATGG
1 ATACCAATTGTTAAAG
1196340 ATACCAATTGTTAAAG
1 ATACCAATTGTTAAAG
1196356 ATA
1 ATA
1196359 TGTTATTAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.34
Consensus pattern (16 bp):
ATACCAATTGTTAAAG
Found at i:1198536 original size:32 final size:32
Alignment explanation
Indices: 1198500--1198567 Score: 136
Period size: 32 Copynumber: 2.1 Consensus size: 32
1198490 TCCACACAAG
1198500 AGAAGAAATAAATCTTGAATTAATAAGGATAA
1 AGAAGAAATAAATCTTGAATTAATAAGGATAA
1198532 AGAAGAAATAAATCTTGAATTAATAAGGATAA
1 AGAAGAAATAAATCTTGAATTAATAAGGATAA
1198564 AGAA
1 AGAA
1198568 TTAAAGCATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.57, C:0.03, G:0.16, T:0.24
Consensus pattern (32 bp):
AGAAGAAATAAATCTTGAATTAATAAGGATAA
Found at i:1198570 original size:17 final size:17
Alignment explanation
Indices: 1198516--1198571 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
1198506 AATAAATCTT
1198516 GAATTAATAAGGATAAA
1 GAATTAATAAGGATAAA
** ***
1198533 GAAGAAATAA--ATCTT
1 GAATTAATAAGGATAAA
1198548 GAATTAATAAGGATAAA
1 GAATTAATAAGGATAAA
1198565 GAATTAA
1 GAATTAA
1198572 AGCATATTTC
Statistics
Matches: 27, Mismatches: 10, Indels: 4
0.66 0.24 0.10
Matches are distributed among these distances:
15 10 0.37
17 17 0.63
ACGTcount: A:0.57, C:0.02, G:0.16, T:0.25
Consensus pattern (17 bp):
GAATTAATAAGGATAAA
Found at i:1202669 original size:16 final size:16
Alignment explanation
Indices: 1202628--1202682 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
1202618 TATTTTAATA
*
1202628 TTTTATATAATGAAAAT
1 TTTTAAATAAT-AAAAT
* *
1202645 TTATGAATAATAAAAT
1 TTTTAAATAATAAAAT
* *
1202661 TTTTAAATAAAAAAAA
1 TTTTAAATAATAAAAT
1202677 TTTTAA
1 TTTTAA
1202683 GCTTTCAATT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
16 23 0.74
17 8 0.26
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (16 bp):
TTTTAAATAATAAAAT
Found at i:1202879 original size:23 final size:23
Alignment explanation
Indices: 1202853--1202899 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1202843 AAATATATAA
1202853 ATATATTGATTTCAAATTTCTTT
1 ATATATTGATTTCAAATTTCTTT
1202876 ATATATTGATTTCAAATTTCTTT
1 ATATATTGATTTCAAATTTCTTT
1202899 A
1 A
1202900 GGATTAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.09, G:0.04, T:0.55
Consensus pattern (23 bp):
ATATATTGATTTCAAATTTCTTT
Found at i:1217131 original size:21 final size:20
Alignment explanation
Indices: 1217098--1217137 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1217088 TCAAATAAGA
*
1217098 AAATTAAAATAAAGTTAAAC
1 AAATTAAAATAAAATTAAAC
*
1217118 AAATTCAATATAAAATTAAA
1 AAATT-AAAATAAAATTAAA
1217138 TTAAACACAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.28
Consensus pattern (20 bp):
AAATTAAAATAAAATTAAAC
Found at i:1217795 original size:63 final size:63
Alignment explanation
Indices: 1217663--1217812 Score: 164
Period size: 63 Copynumber: 2.4 Consensus size: 63
1217653 ATAAAAAATA
* * ** * * *
1217663 TCTTAAACAATCATTTTATATTTTTATAAATGGATTATTTAAGAAATTTTTTGTACAGAAATG
1 TCTTAAATAATCTTTTTATATTTTTATAAAAAGATTATTTAAGAAATTTTATATACAGAAACG
*
1217726 TCTTAAATAAT-TTGTTTATATTTTTATAAAAAGATTATTT-A-AAGTGTTTATATACAGAAAAC
1 TCTTAAATAATCTT-TTTATATTTTTATAAAAAGATTATTTAAGAAAT-TTTATATACAG-AAAC
1217788 G
63 G
1217789 -CTTTAAATAATCTTTTTATATTTT
1 TC-TTAAATAATCTTTTTATATTTT
1217813 AAAGTTTAGG
Statistics
Matches: 74, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
61 3 0.04
62 12 0.16
63 57 0.77
64 2 0.03
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48
Consensus pattern (63 bp):
TCTTAAATAATCTTTTTATATTTTTATAAAAAGATTATTTAAGAAATTTTATATACAGAAACG
Found at i:1217925 original size:85 final size:80
Alignment explanation
Indices: 1217808--1217984 Score: 205
Period size: 85 Copynumber: 2.1 Consensus size: 80
1217798 ATCTTTTTAT
* * *
1217808 ATTTTAAAGTTTAGGGTCTAAAGTTAATATTTTTATAAAAAAATTATTTAAGACATTT-TTTGTA
1 ATTTTATATTTTAGGGTCTAAAGTTAATATTTTTAT-AAAAAATTA--TAAGACATTTCTGTGT-
1217872 CAGAAAATACC-TTAAATAATC
62 -AG-AAA-ACCTTTAAATAATC
* * * * *
1217893 TTTTTATATTTTAGGGTTTAAGGTTAATATTTTTATAAAAGATTATAAGGCATTTCTGTGTAGAA
1 ATTTTATATTTTAGGGTCTAAAGTTAATATTTTTATAAAAAATTATAAGACATTTCTGTGTAGAA
1217958 AACCTTTAAATAATC
66 AACCTTTAAATAATC
1217973 ATTTTATATTTT
1 ATTTTATATTTT
1217985 TATAAATGGA
Statistics
Matches: 81, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
79 3 0.04
80 24 0.30
81 2 0.02
82 9 0.11
83 4 0.05
84 8 0.10
85 31 0.38
ACGTcount: A:0.38, C:0.06, G:0.11, T:0.45
Consensus pattern (80 bp):
ATTTTATATTTTAGGGTCTAAAGTTAATATTTTTATAAAAAATTATAAGACATTTCTGTGTAGAA
AACCTTTAAATAATC
Found at i:1218092 original size:125 final size:120
Alignment explanation
Indices: 1217919--1218170 Score: 328
Period size: 125 Copynumber: 2.1 Consensus size: 120
1217909 TTTAAGGTTA
* *
1217919 ATATTTTTATAAAAGATTATAAGGCATTTCTGTGTAGAAAACCTTTAAATAATCATTTTATATTT
1 ATATTTTTATAAAAGATTATAAGGCATTTCTATATAGAAAACCTTTAAATAATCATTTTATATTT
* * * **
1217984 TTATAAATGGATTATTTAAGACG-TTCTATATAGAAAACGCCTTAAATAATCATTTT
66 TTATAAATAGATTATTTAAAACGTTTCTACA-A-AAAAAACCTTAAATAATCATTTT
*
1218040 ATATTTTTATAAAAGTATTATTTAAGGCATTTTCTATATAGAAATACC-TTAAATAATCCTTTTA
1 ATATTTTTATAAAAG-ATTA--TAAGGCA-TTTCTATATAGAAA-ACCTTTAAATAATCATTTTA
* * *
1218104 TATTTTTATAAATAGATTATTTAAAATGTTTCTACAAAAAAAACTTTAAATAATCTTTTT
61 TATTTTTATAAATAGATTATTTAAAACGTTTCTACAAAAAAAACCTTAAATAATCATTTT
1218164 ATATTTT
1 ATATTTT
1218171 AAGGTTTATG
Statistics
Matches: 114, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
121 15 0.13
122 4 0.04
124 33 0.29
125 53 0.46
126 9 0.08
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.45
Consensus pattern (120 bp):
ATATTTTTATAAAAGATTATAAGGCATTTCTATATAGAAAACCTTTAAATAATCATTTTATATTT
TTATAAATAGATTATTTAAAACGTTTCTACAAAAAAAACCTTAAATAATCATTTT
Found at i:1218114 original size:63 final size:60
Alignment explanation
Indices: 1217919--1218170 Score: 271
Period size: 62 Copynumber: 4.1 Consensus size: 60
1217909 TTTAAGGTTA
* *
1217919 ATATTTTTATAAAAGATTA--TAAGGCA-TTTCTGTGTAGAAAACCTTTAAATAATCATTTT
1 ATATTTTTATAAAAGATTATTTAA-GCATTTTCTATATAGAAAACC-TTAAATAATCATTTT
* **
1217978 ATATTTTTATAAATGGATTATTTAAG-ACGTTCTATATAGAAAACGCCTTAAATAATCATTTT
1 ATATTTTTATAAA-AGATTATTTAAGCATTTTCTATATAGAAAA--CCTTAAATAATCATTTT
*
1218040 ATATTTTTATAAAAGTATTATTTAAGGCATTTTCTATATAGAAATACCTTAAATAATCCTTTT
1 ATATTTTTATAAAAG-ATTATTTAA-GCATTTTCTATATAGAAA-ACCTTAAATAATCATTTT
* * * * * *
1218103 ATATTTTTATAAATAGATTATTTAA-AATGTTTCTACAAAAAAAACTTTAAATAATCTTTTT
1 ATATTTTTATAAA-AGATTATTTAAGCAT-TTTCTATATAGAAAACCTTAAATAATCATTTT
1218164 ATATTTT
1 ATATTTT
1218171 AAGGTTTATG
Statistics
Matches: 167, Mismatches: 14, Indels: 22
0.82 0.07 0.11
Matches are distributed among these distances:
59 13 0.08
60 6 0.04
61 39 0.23
62 51 0.31
63 41 0.25
64 16 0.10
65 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.45
Consensus pattern (60 bp):
ATATTTTTATAAAAGATTATTTAAGCATTTTCTATATAGAAAACCTTAAATAATCATTTT
Found at i:1228979 original size:23 final size:25
Alignment explanation
Indices: 1228930--1228979 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 25
1228920 ATAATTTGAA
*
1228930 TAATTTGAATTTAAGTAGCTTATTAG
1 TAATTTGAATTT-AGTAGCTTAATAG
*
1228956 TAATTT-AATTT-GTATCTTAATAG
1 TAATTTGAATTTAGTAGCTTAATAG
1228979 T
1 T
1228980 TAACACGGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 11 0.50
25 5 0.23
26 6 0.27
ACGTcount: A:0.34, C:0.04, G:0.12, T:0.50
Consensus pattern (25 bp):
TAATTTGAATTTAGTAGCTTAATAG
Found at i:1231517 original size:46 final size:46
Alignment explanation
Indices: 1231429--1231517 Score: 108
Period size: 46 Copynumber: 1.9 Consensus size: 46
1231419 TTATCCGGTT
* * * *
1231429 ATGGCCCTATACATGGGTGGCTTATGACATCTTCCTTAACCTAATC
1 ATGGCCCTATACAAGGGTGGCTCATGACATCCTCCTCAACCTAATC
* *
1231475 ATGGTCCTATACAAGGTTGGCTCATGACATCCTCC-CACACCTA
1 ATGGCCCTATACAAGGGTGGCTCATGACATCCTCCTCA-ACCTA
1231518 TCCTGTCAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
45 1 0.03
46 35 0.97
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.29
Consensus pattern (46 bp):
ATGGCCCTATACAAGGGTGGCTCATGACATCCTCCTCAACCTAATC
Found at i:1239272 original size:128 final size:128
Alignment explanation
Indices: 1239044--1239303 Score: 502
Period size: 128 Copynumber: 2.0 Consensus size: 128
1239034 CAGGGTATGT
1239044 TATAGTTACCACTATTAGTGGTAGAAATGGTCAACCTAAACAGGTATATATTTTCTTAAATGCAA
1 TATAGTTACCACTATTAGTGGTAGAAATGGTCAACCTAAACAGGTATATATTTTCTTAAATGCAA
1239109 CTATAATCTAATTATGCATGTTATAAAAGCCATTACATCACACTATTATTCATGTCTTTGTCA
66 CTATAATCTAATTATGCATGTTATAAAAGCCATTACATCACACTATTATTCATGTCTTTGTCA
1239172 TATAGTTACCACTATTAGTGGTAGAAATGGTCAACCTAAACAGGTATATATTTTCTTAAATGCAA
1 TATAGTTACCACTATTAGTGGTAGAAATGGTCAACCTAAACAGGTATATATTTTCTTAAATGCAA
* *
1239237 CTGTAATCTAATTCTGCATGTTATAAAAGCCATTACATCACACTATTATTCATGTCTTTGTCA
66 CTATAATCTAATTATGCATGTTATAAAAGCCATTACATCACACTATTATTCATGTCTTTGTCA
1239300 TATA
1 TATA
1239304 ATTTGTCTTC
Statistics
Matches: 130, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
128 130 1.00
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.37
Consensus pattern (128 bp):
TATAGTTACCACTATTAGTGGTAGAAATGGTCAACCTAAACAGGTATATATTTTCTTAAATGCAA
CTATAATCTAATTATGCATGTTATAAAAGCCATTACATCACACTATTATTCATGTCTTTGTCA
Found at i:1251795 original size:14 final size:13
Alignment explanation
Indices: 1251772--1251803 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
1251762 CAAAACTTGG
1251772 AAAAACCAAAAAT
1 AAAAACCAAAAAT
1251785 AAAAACTCAAAAAT
1 AAAAAC-CAAAAAT
1251799 AAAAA
1 AAAAA
1251804 AGAAAGAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.78, C:0.12, G:0.00, T:0.09
Consensus pattern (13 bp):
AAAAACCAAAAAT
Found at i:1252151 original size:16 final size:13
Alignment explanation
Indices: 1252116--1252163 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 13
1252106 ATGCAAAATA
*
1252116 AAAAAAAAAAGAG
1 AAAAAAGAAAGAG
1252129 AAAAAAGACAAGAG
1 AAAAAAGA-AAGAG
1252143 AAAGGAAAGAAATGAG
1 AAA--AAAGAAA-GAG
1252159 AAAAA
1 AAAAA
1252164 TGTGATGATG
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 7 0.23
14 10 0.33
15 2 0.07
16 11 0.37
ACGTcount: A:0.75, C:0.02, G:0.21, T:0.02
Consensus pattern (13 bp):
AAAAAAGAAAGAG
Found at i:1252532 original size:54 final size:54
Alignment explanation
Indices: 1252453--1252558 Score: 194
Period size: 54 Copynumber: 2.0 Consensus size: 54
1252443 TTTTGATGAA
*
1252453 TTTTGAATACTTAAGTGCATGATGCGACAATCAAGAAAAATAAAAGGAAAAAAT
1 TTTTGAATACTTAAGTGCATGATGCGACAATCAAGAAAAACAAAAGGAAAAAAT
*
1252507 TTTTGAATACTTAAGTGCATGATGCGACAATCCAGAAAAACAAAAGGAAAAA
1 TTTTGAATACTTAAGTGCATGATGCGACAATCAAGAAAAACAAAAGGAAAAA
1252559 TAATAAAGTC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.49, C:0.11, G:0.17, T:0.23
Consensus pattern (54 bp):
TTTTGAATACTTAAGTGCATGATGCGACAATCAAGAAAAACAAAAGGAAAAAAT
Found at i:1254614 original size:149 final size:149
Alignment explanation
Indices: 1254401--1254686 Score: 382
Period size: 149 Copynumber: 1.9 Consensus size: 149
1254391 AAGAGCAAGA
* * *
1254401 TTCATAAGTCTTTCTAGTTGAATCTGTTTTACTCCAAGCATAGTTTTTAAGTCATTTGGATAAGA
1 TTCATAAGTCTTTCGAGTTGAATCTGTTTTACTCCAAGCATAGTCTCTAAGTCATTTGGATAAGA
* * * *
1254466 TTCATAAGTCTTTT-AAGTTGAATCTCTTTTAGTATTAAGATTTGTAAGACCTCCGACCATAGTC
66 TTCATAAG-CTTTTCAAGTTGAATCTATTTTAGTATCAAGATTTGCAAGACCTCCAACCATAGTC
*
1254530 TTTAAGTCCTACGAATATGG
130 TCTAAGTCCTACGAATATGG
* * *
1254550 TTCATAAGTTTTTCGAGCTT-AATTTGTTTTACTCCAAGCATAGTCTCTAAG-CCTTTCAGG-TA
1 TTCATAAGTCTTTCGAG-TTGAATCTGTTTTACTCCAAGCATAGTCTCTAAGTCATTT--GGATA
** *
1254612 AGATTTGTAAGCTTTTCAAGTTGAATCTATTTTAGTATCAAGATTTGCAAGACCTCCAAGCATAG
63 AGATTCATAAGCTTTTCAAGTTGAATCTATTTTAGTATCAAGATTTGCAAGACCTCCAACCATAG
1254677 TCTCTAAGTC
128 TCTCTAAGTC
1254687 TTCTAAGAAA
Statistics
Matches: 119, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
148 9 0.08
149 106 0.89
150 4 0.03
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (149 bp):
TTCATAAGTCTTTCGAGTTGAATCTGTTTTACTCCAAGCATAGTCTCTAAGTCATTTGGATAAGA
TTCATAAGCTTTTCAAGTTGAATCTATTTTAGTATCAAGATTTGCAAGACCTCCAACCATAGTCT
CTAAGTCCTACGAATATGG
Found at i:1254707 original size:149 final size:148
Alignment explanation
Indices: 1254363--1254695 Score: 370
Period size: 149 Copynumber: 2.2 Consensus size: 148
1254353 TGAGATTCTT
* * * ** * * * *
1254363 AAGACCTCTAAGCATAGTCTCTAAG-CCCAAGAGCAAGATTCATAAGTCTTTCTAG-TTGAATCT
1 AAGACCTCCAACCATAGTCTCTAAGTCCTAAGAATATG-TTCATAAGTTTTTCGAGCTT-AATTT
* *
1254426 GTTTTACTCCAAGCATAGTTTTTAAGTCATTTGGATAAGATTCATAAGTCTTTTAAGTTGAATCT
64 GTTTTACTCCAAGCATAGTCTCTAAGTCATTTGGATAAGATTCATAAGTCTTTTAAGTTGAATCT
* * *
1254491 CTTTTAGTATTAAGATTTGT
129 ATTTTAGTATCAAGATTTGC
* * *
1254511 AAGACCTCCGACCATAGTCTTTAAGTCCTACGAATATGGTTCATAAGTTTTTCGAGCTTAATTTG
1 AAGACCTCCAACCATAGTCTCTAAGTCCTAAGAATAT-GTTCATAAGTTTTTCGAGCTTAATTTG
* **
1254576 TTTTACTCCAAGCATAGTCTCTAAG-CCTTTCAGG-TAAGATTTGTAAG-CTTTTCAAGTTGAAT
65 TTTTACTCCAAGCATAGTCTCTAAGTCATTT--GGATAAGATTCATAAGTCTTTT-AAGTTGAAT
1254638 CTATTTTAGTATCAAGATTTGC
127 CTATTTTAGTATCAAGATTTGC
*
1254660 AAGACCTCCAAGCATAGTCTCTAAGTCTTCTAAGAA
1 AAGACCTCCAACCATAGTCTCTAAGTC--CTAAGAA
1254696 ATATTTGTAA
Statistics
Matches: 153, Mismatches: 24, Indels: 13
0.81 0.13 0.07
Matches are distributed among these distances:
148 30 0.20
149 112 0.73
150 5 0.03
151 6 0.04
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.37
Consensus pattern (148 bp):
AAGACCTCCAACCATAGTCTCTAAGTCCTAAGAATATGTTCATAAGTTTTTCGAGCTTAATTTGT
TTTACTCCAAGCATAGTCTCTAAGTCATTTGGATAAGATTCATAAGTCTTTTAAGTTGAATCTAT
TTTAGTATCAAGATTTGC
Found at i:1262944 original size:31 final size:30
Alignment explanation
Indices: 1262871--1262953 Score: 94
Period size: 31 Copynumber: 2.7 Consensus size: 30
1262861 TTATATAATG
*
1262871 ATTTACTTGCATGATATGGTTTGCATGAATAT
1 ATTTATTTGCATGATAT--TTTGCATGAATAT
* * *
1262903 ATATATTTGCATGATATTTTGCATGGATCT
1 ATTTATTTGCATGATATTTTGCATGAATAT
*
1262933 AATTTATTTGCATGATTTTTT
1 -ATTTATTTGCATGATATTTT
1262954 TTACATAATT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
30 11 0.25
31 18 0.41
32 15 0.34
ACGTcount: A:0.27, C:0.08, G:0.16, T:0.49
Consensus pattern (30 bp):
ATTTATTTGCATGATATTTTGCATGAATAT
Found at i:1263024 original size:26 final size:25
Alignment explanation
Indices: 1262993--1263065 Score: 77
Period size: 26 Copynumber: 3.0 Consensus size: 25
1262983 TTTGCATGAC
1262993 TATTGCATGATTTTTTTATGATATT
1 TATTGCATGATTTTTTTATGATATT
1263018 TATTTGCATGA-----TTATGATA-T
1 TA-TTGCATGATTTTTTTATGATATT
1263038 TATTGCATGATATTTTTCTATGATATT
1 TATTGCATGAT-TTTTT-TATGATATT
1263065 T
1 T
1263066 TGATAGTATT
Statistics
Matches: 39, Mismatches: 0, Indels: 16
0.71 0.00 0.29
Matches are distributed among these distances:
19 8 0.21
20 3 0.08
21 8 0.21
25 3 0.08
26 15 0.38
27 2 0.05
ACGTcount: A:0.26, C:0.05, G:0.12, T:0.56
Consensus pattern (25 bp):
TATTGCATGATTTTTTTATGATATT
Found at i:1263045 original size:19 final size:21
Alignment explanation
Indices: 1263008--1263048 Score: 68
Period size: 19 Copynumber: 2.0 Consensus size: 21
1262998 CATGATTTTT
1263008 TTATGATATTTATTTGCATGA
1 TTATGATATTTATTTGCATGA
1263029 TTATGATA-TTA-TTGCATGA
1 TTATGATATTTATTTGCATGA
1263048 T
1 T
1263049 ATTTTTCTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 9 0.45
20 3 0.15
21 8 0.40
ACGTcount: A:0.29, C:0.05, G:0.15, T:0.51
Consensus pattern (21 bp):
TTATGATATTTATTTGCATGA
Found at i:1263049 original size:13 final size:13
Alignment explanation
Indices: 1263030--1263067 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
1263020 TTTGCATGAT
1263030 TATGATATTATTGC
1 TATGATATT-TTGC
*
1263044 -ATGATATTTTTC
1 TATGATATTTTGC
1263056 TATGATATTTTG
1 TATGATATTTTG
1263068 ATAGTATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 3 0.14
13 18 0.86
ACGTcount: A:0.26, C:0.05, G:0.13, T:0.55
Consensus pattern (13 bp):
TATGATATTTTGC
Found at i:1263712 original size:44 final size:44
Alignment explanation
Indices: 1263661--1263786 Score: 146
Period size: 44 Copynumber: 2.9 Consensus size: 44
1263651 ATGTAATCAT
* * * * *
1263661 TTATGATTTTTCATGTACACTAACCTATTTGGTTATTTTGTTGC
1 TTATGATTTTTCATGTGCACTAACTTATTTGATTATTTTGTAGA
* * *
1263705 TTATGATTCTTT-ATGTGTACTAATTTATTTGTTTATTTTGTAGA
1 TTATGATT-TTTCATGTGCACTAACTTATTTGATTATTTTGTAGA
* *
1263749 TTTTGATTTTTCATGTGCACTAAGTTATTTGATTATTT
1 TTATGATTTTTCATGTGCACTAACTTATTTGATTATTT
1263787 AGGTTGGCAT
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
43 3 0.04
44 63 0.91
45 3 0.04
ACGTcount: A:0.21, C:0.09, G:0.13, T:0.56
Consensus pattern (44 bp):
TTATGATTTTTCATGTGCACTAACTTATTTGATTATTTTGTAGA
Found at i:1269228 original size:18 final size:17
Alignment explanation
Indices: 1269205--1269272 Score: 66
Period size: 18 Copynumber: 3.8 Consensus size: 17
1269195 AAAGAAAAGG
1269205 AAAAGAAAAAGTGAAAAA
1 AAAAGAAAAA-TGAAAAA
*
1269223 AAAAGAAAATAAGGAAAAA
1 AAAAG-AAA-AATGAAAAA
**
1269242 GGAAG-AAAATGAAAGAA
1 AAAAGAAAAATGAAA-AA
1269259 AAAAGAAAAATGAA
1 AAAAGAAAAATGAA
1269273 TAAGGTGAGC
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
16 6 0.15
17 7 0.17
18 13 0.32
19 12 0.30
20 2 0.05
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (17 bp):
AAAAGAAAAATGAAAAA
Found at i:1269229 original size:29 final size:33
Alignment explanation
Indices: 1269195--1269267 Score: 82
Period size: 35 Copynumber: 2.2 Consensus size: 33
1269185 AAATCCATTT
*
1269195 AAAGAAAAGG-AAAA-GAA-AAAGTGAAA-AAA
1 AAAGAAAAGGAAAAAGGAAGAAAATGAAAGAAA
1269224 AAAGAAAATAAGGAAAAAGGAAGAAAATGAAAGAAA
1 AAAG--AA-AAGGAAAAAGGAAGAAAATGAAAGAAA
1269260 AAAGAAAA
1 AAAGAAAA
1269268 ATGAATAAGG
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
29 4 0.11
31 2 0.06
32 4 0.11
33 6 0.17
34 5 0.14
35 8 0.22
36 7 0.19
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.04
Consensus pattern (33 bp):
AAAGAAAAGGAAAAAGGAAGAAAATGAAAGAAA
Found at i:1269239 original size:19 final size:19
Alignment explanation
Indices: 1269205--1269262 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
1269195 AAAGAAAAGG
1269205 AAAAG-AAA-AAGTGAAAAA
1 AAAAGAAAATAAG-GAAAAA
1269223 AAAAGAAAATAAGGAAAAA
1 AAAAGAAAATAAGGAAAAA
** *
1269242 GGAAGAAAATGAAAGAAAAA
1 AAAAGAAAAT-AAGGAAAAA
1269262 A
1 A
1269263 GAAAAATGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 5 0.15
19 17 0.52
20 11 0.33
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (19 bp):
AAAAGAAAATAAGGAAAAA
Found at i:1269316 original size:15 final size:15
Alignment explanation
Indices: 1269296--1269326 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1269286 AAAAAAAAAG
*
1269296 AAAGAAAGGAAAGAA
1 AAAGAAAAGAAAGAA
1269311 AAAGAAAAGAAAGAA
1 AAAGAAAAGAAAGAA
1269326 A
1 A
1269327 TGATTGAATA
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:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAAGAA
Found at i:1274747 original size:20 final size:19
Alignment explanation
Indices: 1274722--1274786 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
1274712 ATTTATCATG
1274722 AAACCTTAAATCCAAACCCT
1 AAACC-TAAATCCAAACCCT
* * *
1274742 AAACCTACACTCTAAAACCT
1 AAACCTA-AATCCAAACCCT
*
1274762 AAACCCT-AACCCAAGACCCT
1 AAA-CCTAAATCCAA-ACCCT
1274782 AAACC
1 AAACC
1274787 AAACTCTAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
19 8 0.23
20 24 0.69
21 3 0.09
ACGTcount: A:0.45, C:0.38, G:0.02, T:0.15
Consensus pattern (19 bp):
AAACCTAAATCCAAACCCT
Found at i:1274756 original size:13 final size:13
Alignment explanation
Indices: 1274722--1274798 Score: 61
Period size: 13 Copynumber: 5.9 Consensus size: 13
1274712 ATTTATCATG
*
1274722 AAACCTTAAATCC-
1 AAACCCTAAA-CCT
1274735 AAACCCTAAACCT
1 AAACCCTAAACCT
* *
1274748 ACACTCTAAAACCT
1 AAACCCT-AAACCT
*
1274762 AAACCCT-AACCC
1 AAACCCTAAACCT
1274774 AAGACCCTAAACC-
1 AA-ACCCTAAACCT
*
1274787 AAACTCTAAACC
1 AAACCCTAAACC
1274799 AACCCCATAC
Statistics
Matches: 53, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
12 17 0.32
13 21 0.40
14 15 0.28
ACGTcount: A:0.45, C:0.38, G:0.01, T:0.16
Consensus pattern (13 bp):
AAACCCTAAACCT
Found at i:1275652 original size:41 final size:41
Alignment explanation
Indices: 1275578--1275777 Score: 165
Period size: 42 Copynumber: 4.8 Consensus size: 41
1275568 TCTCAAGCGG
* * * *
1275578 AGGG-AGCATCTTATTTTCTAAAAGTTTCCAAGCCACTAGT
1 AGGGAAGCATTTTATTTTTTGAAAGTTTCAAAGCCACTAGT
*
1275618 AGTGGAAGCATTTTA-TTTTTGAAAGTTTCAAAGCCACTAATT
1 AG-GGAAGCATTTTATTTTTTGAAAGTTTCAAAGCCACT-AGT
* * ** * *
1275660 GGGGGAGCATTTTATTTTTTGAAAGTTTTGAAGCC-TTCGGT
1 AGGGAAGCATTTTATTTTTTGAAAGTTTCAAAGCCACT-AGT
* **
1275701 AAGGGAACCATTTTATTTTTTGAAAGTTTGTAAGCCACT-GTT
1 -AGGGAAGCATTTTATTTTTTGAAAGTTTCAAAGCCACTAG-T
* * *
1275743 AGGAGGAGCACTTTATTTTTTGAAACTTTCAAAGC
1 AGG-GAAGCATTTTATTTTTTGAAAGTTTCAAAGC
1275778 ATCTGGTGGG
Statistics
Matches: 127, Mismatches: 25, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
40 2 0.02
41 39 0.31
42 85 0.67
43 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (41 bp):
AGGGAAGCATTTTATTTTTTGAAAGTTTCAAAGCCACTAGT
Found at i:1277313 original size:4 final size:4
Alignment explanation
Indices: 1277304--1277336 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
1277294 TGTTTATTTG
*
1277304 TTAT TTAT TTAT TT-T CTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1277337 TCTTATGTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
3 2 0.08
4 24 0.92
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:1277316 original size:15 final size:15
Alignment explanation
Indices: 1277296--1277332 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1277286 TTTGATTTTG
1277296 TTTATTTGT-TATTTA
1 TTTATTT-TCTATTTA
1277311 TTTATTTTCTATTTA
1 TTTATTTTCTATTTA
1277326 TTTATTT
1 TTTATTT
1277333 ATTTTCTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 1 0.05
15 20 0.95
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.76
Consensus pattern (15 bp):
TTTATTTTCTATTTA
Found at i:1277350 original size:19 final size:19
Alignment explanation
Indices: 1277309--1277351 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1277299 ATTTGTTATT
* *
1277309 TATTTATTTTCTATTTATT
1 TATTTATTTTCTATGTATC
1277328 TATTTATTTTCTTATGTA-C
1 TATTTATTTTC-TATGTATC
1277347 TATTT
1 TATTT
1277352 TTAAGTGTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.21, C:0.07, G:0.02, T:0.70
Consensus pattern (19 bp):
TATTTATTTTCTATGTATC
Found at i:1282036 original size:12 final size:12
Alignment explanation
Indices: 1281995--1282061 Score: 59
Period size: 12 Copynumber: 5.6 Consensus size: 12
1281985 TTTCTTTGAG
1281995 AATAT-TAAACA
1 AATATATAAACA
1282006 AATATATTTATAA-A
1 AATATA--TA-AACA
*
1282020 CATATATAAACA
1 AATATATAAACA
*
1282032 AATATATTAACA
1 AATATATAAACA
*
1282044 AATA-ATAAATA
1 AATATATAAACA
1282055 AATATAT
1 AATATAT
1282062 TCATGAACAA
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
11 16 0.36
12 19 0.42
14 8 0.18
15 2 0.04
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (12 bp):
AATATATAAACA
Found at i:1282136 original size:26 final size:26
Alignment explanation
Indices: 1282106--1282160 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
1282096 TACAATTAAA
*
1282106 AAATTAAGAAATCCTATATAAAAACC
1 AAATTAAGAAATCCTACATAAAAACC
*
1282132 AAATTAAGAAATCTTACATAAAAACC
1 AAATTAAGAAATCCTACATAAAAACC
1282158 AAA
1 AAA
1282161 ACCATTTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.60, C:0.15, G:0.04, T:0.22
Consensus pattern (26 bp):
AAATTAAGAAATCCTACATAAAAACC
Found at i:1292078 original size:108 final size:108
Alignment explanation
Indices: 1291952--1292165 Score: 263
Period size: 108 Copynumber: 2.0 Consensus size: 108
1291942 TTTGGACAAG
* * * *
1291952 TTTAATATAATGTGTTTAAGCTATCTAAACTATTAAAACATAAATATAACT-ATAAAATTATA-T
1 TTTAATATAATGTATTTAAGCTATCTAAACTATTAAAACAGAAATATAAATGA-AAAATTACATT
*
1292015 TTTGACCTTGTAACAGCATAAAA-AGTGCTAAATATACATAAACTA
65 TTTG-CCTTGTAACAGCATAAAATA-TGCTAAATAGACATAAACTA
* * * *
1292060 TTTAATATCATGTATTTAAGTTATCTAAACTTTTAAAATAGAAATATAAATGAAAAATTACATTT
1 TTTAATATAATGTATTTAAGCTATCTAAACTATTAAAACAGAAATATAAATGAAAAATTACATTT
* * * *
1292125 TTGCCTTTTAATAGTATAAAATATTCTAAATAGACATAAAC
66 TTGCCTTGTAACAGCATAAAATATGCTAAATAGACATAAAC
1292166 AATAATTTTT
Statistics
Matches: 90, Mismatches: 13, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
108 83 0.92
109 7 0.08
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.37
Consensus pattern (108 bp):
TTTAATATAATGTATTTAAGCTATCTAAACTATTAAAACAGAAATATAAATGAAAAATTACATTT
TTGCCTTGTAACAGCATAAAATATGCTAAATAGACATAAACTA
Found at i:1292251 original size:161 final size:160
Alignment explanation
Indices: 1292060--1293610 Score: 1123
Period size: 161 Copynumber: 9.6 Consensus size: 160
1292050 ACATAAACTA
* * * * * *
1292060 TTTAATATCATGTATTTAAGTTATCTAAACTTTTAAAATAGAAATATAAATGAAAAATTACATTT
1 TTTAATATTATGTATTGAAGCTATCTAAACTGTTAAAATAGAAATATAACTGAAAACTTACATTT
* * * * * * *
1292125 TTGCCTTTTAATAGTATAAAATA-TTCTAAATAGACATAAACAATAATTTTTTCGCACATATAAA
66 TTGCCTTTTAATAGCACAAAA-AGTCCTAAACAGACATAAACAATAACTTTTTCACACATATCAA
* * *
1292189 CTGTGGAAAAGAACATCAATCATTCGAACAAG
130 CTAT-GAAAACAAGATCAATCATTCGAACAAG
* * * * * * *
1292221 TTTAATTTTATGTATTGAAGCTATCTAAACTGTTAAAACA-AAACAATAATTGCAAATTTATATT
1 TTTAATATTATGTATTGAAGCTATCTAAACTGTTAAAATAGAAA-TATAACTGAAAACTTACATT
* * * * * *
1292285 ATTTACCTTTTAATGGTACAAAAAGTCCTAAACAAACATAAACGATAATTTTTTCACACATATCA
65 -TTTGCCTTTTAATAGCACAAAAAGTCCTAAACAGACATAAACAATAACTTTTTCACACATATCA
* *
1292350 A-T-TGCAGAAATCAAGTTCAATTATTCGAACAAG
129 ACTATG-A-AAA-CAAGATCAATCATTCGAACAAG
* * * * * * *
1292383 TTTAATATTATATATTTAAGCTATGTAAACTATTAAAACAAAAATATAACT-ACAAAGTTATC-T
1 TTTAATATTATGTATTGAAGCTATCTAAACTGTTAAAATAGAAATATAACTGA-AAACTTA-CAT
* * * * * *
1292446 TTTTATCC-TTTAAT-GACACAAAAAGTCTTAAAGAGACATAAATAGTAACTTTTTCATACATAT
64 TTTT-GCCTTTTAATAG-CACAAAAAGTCCTAAACAGACATAAACAATAACTTTTTCACACATAT
* ** *
1292509 CAACTATGAAAACAAAGTTTTATCATTC-AGACAAA
127 CAACTATGAAAAC-AAGATCAATCATTCGA-ACAAG
* ** * * * *
1292544 TTTAAATATCATGTATCAAAGCTATCTAAACTATTAAAATA-TAATAATAATTGCAAACTTGA-A
1 TTT-AATATTATGTATTGAAGCTATCTAAACTGTTAAAATAGAAAT-ATAACTGAAAACTT-ACA
* ** * * * * *
1292607 -TTTTGCTTTTTAACGGCATAAAAAGTCCTAAACAAAAATAAATC-ACAACTTTTTCACACAAAT
63 TTTTTGCCTTTTAATAGCACAAAAAGTCCTAAACAGACATAAA-CAATAACTTTTTCACACATAT
* *
1292670 CAACCATGAAAACCAAGTTCAATCATTC-AGACAAG
127 CAACTATGAAAA-CAAGATCAATCATTCGA-ACAAG
* * * * *
1292705 TTTAATATTATGTATTGAAGCTATCCAAACTGTTAAAAT-GAAACAATAACTGCAAATTTGCATT
1 TTTAATATTATGTATTGAAGCTATCTAAACTGTTAAAATAGAAA-TATAACTGAAAACTTACATT
* * * * *
1292769 TTTACCTTTTAACAGCATAAAAAGTCAC-AAACAGACATAAACGATAATTTTTTCACACATATCA
65 TTTGCCTTTTAATAGCACAAAAAGTC-CTAAACAGACATAAACAATAACTTTTTCACACATATCA
1292833 A-TAGTGAAAATCAA-ATTCAATCATTCGAACAAG
129 ACTA-TGAAAA-CAAGA-TCAATCATTCGAACAAG
* * * * * * **
1292866 TTTAATATAATGTATTTAAGCTATGTAAATTGTTAAAACA-ACAATATAACT-ATAAAGTTACCC
1 TTTAATATTATGTATTGAAGCTATCTAAACTGTTAAAATAGA-AATATAACTGA-AAACTTACAT
* * * * *
1292929 TTTTG-CTCTTTAACAACACAAAAAGTCTTAAATAGACATAAACAATAACTTTTTCATACATATC
64 TTTTGCCT-TTTAATAGCACAAAAAGTCCTAAACAGACATAAACAATAACTTTTTCACACATATC
* * * *
1292993 AACTATGGAAACAAAGTTCAATCATTTGGACAAG
128 AACTATGAAAAC-AAGATCAATCATTCGAACAAG
* * *
1293027 TTTAATATCATGTATTGAAG-TCATCTAAAGTGTTAAAATAGAACA-ATAACT-ACAAACTTGCA
1 TTTAATATTATGTATTGAAGCT-ATCTAAACTGTTAAAATAGAA-ATATAACTGA-AAACTTACA
* * * * *
1293089 TTTTTG-CTTATTAATAGCACAAAAAGTCCTAAACTGATATAAACCATTACTTTTTTACACATAT
63 TTTTTGCCTT-TTAATAGCACAAAAAGTCCTAAACAGACATAAACAATAACTTTTTCACACATAT
* * * * * * *
1293153 CAACCATAAAAACCAAGTTTAATCATTTGGATAAG
127 CAACTATGAAAA-CAAGATCAATCATTCGAACAAG
* * * * * * * * * **
1293188 TTTAATATCT-TATATTAAAGCTATTTGAATTGTTAAAATGGAACA-ATAGCTGCAAATTTGTAT
1 TTTAATAT-TATGTATTGAAGCTATCTAAACTGTTAAAATAGAA-ATATAACTGAAAACTTACAT
** * * *** *
1293251 TTTTATCTTTTAATGGCACAAAAAGTCCTAAACAAACATAAATGGTAACTTTTTCACATATAT-A
64 TTTTGCCTTTTAATAGCACAAAAAGTCCTAAACAGACATAAACAATAACTTTTTCACACATATCA
* * *
1293315 AATCGTGAAAACCAA-ATTCAATCATTCAAACAAG
129 ACT-ATGAAAA-CAAGA-TCAATCATTCGAACAAG
* * * * * **
1293349 TTTAATATTATGTATTTATGCTATGTAAATTGTTAAAACAGAAATATAACT-ATAAA-TTACCCT
1 TTTAATATTATGTATTGAAGCTATCTAAACTGTTAAAATAGAAATATAACTGA-AAACTTACATT
* * * * * *
1293412 TTTGCCCTTTAATAACACAAAAAGTTCTAAACAGATATAAACGATAACTTTTTCATACATATCAA
65 TTTGCCTTTTAATAGCACAAAAAGTCCTAAACAGACATAAACAATAACTTTTTCACACATATCAA
* *
1293477 CTATGGAAACAAAGATCAATCATTTGAACAAG
130 CTATGAAAAC-AAGATCAATCATTCGAACAAG
* * * * * *
1293509 TTTAATATTATTTATTGAAGCTATATAGACTGTTAAAATAGAGCA-ATAACTGTAAACTTGCATT
1 TTTAATATTATGTATTGAAGCTATCTAAACTGTTAAAATAGA-AATATAACTGAAAACTTACATT
* * *
1293573 TTTGCCTTTTAATAGCATAAAAATATCCTAAATAGACA
65 TTTGCCTTTTAATAGCACAAAAA-GTCCTAAACAGACA
1293611 CAAAGTCAAG
Statistics
Matches: 1102, Mismatches: 226, Indels: 123
0.76 0.16 0.08
Matches are distributed among these distances:
159 2 0.00
160 185 0.17
161 719 0.65
162 190 0.17
163 6 0.01
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (160 bp):
TTTAATATTATGTATTGAAGCTATCTAAACTGTTAAAATAGAAATATAACTGAAAACTTACATTT
TTGCCTTTTAATAGCACAAAAAGTCCTAAACAGACATAAACAATAACTTTTTCACACATATCAAC
TATGAAAACAAGATCAATCATTCGAACAAG
Found at i:1293115 original size:483 final size:479
Alignment explanation
Indices: 1292060--1293604 Score: 1798
Period size: 483 Copynumber: 3.2 Consensus size: 479
1292050 ACATAAACTA
* * * * * * *
1292060 TTTAATATCATGTATTTAAGTTATCTAAACTTTTAAAATAGAA-ATATAAATGAAAAATTACATT
1 TTTAATATCATGTATTGAAGCTATCTAAACTGTTAAAATAGAACA-ATAACTGCAAACTTGCATT
* * * * * * * * * * *
1292124 TTTGCCTTTTAATAGTATAAAATA-TTCTAAATAGACATAAACAATAATTTTTTCGCACATATAA
65 TTTG-CTTTTAATAGCATAAAA-AGTCCTAAACAAAAATAAACCACAACTTTTTCACACAAATCA
** * * ** *
1292188 ACTGTGGAAAA-GAACATCAATCATTCGAACAAGTTTAATTTTATGTATTGAAGCTATCTAAACT
128 ACCAT-AAAAACCAAGTTCAATCATTCG-ACAAGTTTAATATTATGTATTGAAGCTATCTAAACT
** * * *
1292252 GTTAAAACAAAACAATAATTGCAAATTTATATTATTTACCTTTTAATGGTACAAAAAGTCCTAAA
191 GTTAAAATGAAACAATAACTGCAAATTTGTATT-TTTACCTTTTAATGGCACAAAAAGTCCTAAA
* *
1292317 CAAACATAAACGATAATTTTTTCACACATATCAAT-TGCAGAAATCAAGTTCAATTATTCGAACA
255 CAAACATAAACGATAATTTTTTCACACATATCAATGTG-A-AAATCAAATTCAATCATTCGAACA
* * * * *
1292381 AGTTTAATATTATATATTTAAGCTATGTAAACTATTAAAACAAAAATATAACTACAAAGTTA-TC
318 AGTTTAATATTATGTATTTAAGCTATGTAAATTGTTAAAAC-AAAATATAACTATAAAGTTACCC
** * * * *
1292445 TTTTTATCCTTTAATGACACAAAAAGTCTTAAAGAGACATAAATAGTAACTTTTTCATACATATC
382 TTTTGCT-CTTTAATAACACAAAAAGTCTTAAACAGACATAAACAATAACTTTTTCATACATATC
* ** ** *
1292510 AACTATGAAAACAAAGTTTTATCATTCAGACAAA
446 AACTATGGAAACAAAGTTCAATCATTTGGACAAG
** * * * * *
1292544 TTTAAATATCATGTATCAAAGCTATCTAAACTATTAAAATATAATAATAATTGCAAACTTG-AAT
1 TTT-AATATCATGTATTGAAGCTATCTAAACTGTTAAAATAGAACAATAACTGCAAACTTGCATT
** *
1292608 TTTGCTTTTTAACGGCATAAAAAGTCCTAAACAAAAATAAATCACAACTTTTTCACACAAATCAA
65 TTTGC-TTTTAATAGCATAAAAAGTCCTAAACAAAAATAAACCACAACTTTTTCACACAAATCAA
* *
1292673 CCATGAAAACCAAGTTCAATCATTCAGACAAGTTTAATATTATGTATTGAAGCTATCCAAACTGT
129 CCATAAAAACCAAGTTCAATCATTC-GACAAGTTTAATATTATGTATTGAAGCTATCTAAACTGT
* ** *
1292738 TAAAATGAAACAATAACTGCAAATTTGCATTTTTACCTTTTAACAGCATAAAAAGTCAC-AAACA
193 TAAAATGAAACAATAACTGCAAATTTGTATTTTTACCTTTTAATGGCACAAAAAGTC-CTAAACA
*
1292802 GACATAAACGATAATTTTTTCACACATATCAATAGTGAAAATCAAATTCAATCATTCGAACAAGT
257 AACATAAACGATAATTTTTTCACACATATCAAT-GTGAAAATCAAATTCAATCATTCGAACAAGT
*
1292867 TTAATATAATGTATTTAAGCTATGTAAATTGTTAAAACAACAATATAACTATAAAGTTACCCTTT
321 TTAATATTATGTATTTAAGCTATGTAAATTGTTAAAACAA-AATATAACTATAAAGTTACCCTTT
* *
1292932 TGCTCTTTAACAACACAAAAAGTCTTAAATAGACATAAACAATAACTTTTTCATACATATCAACT
385 TGCTCTTTAATAACACAAAAAGTCTTAAACAGACATAAACAATAACTTTTTCATACATATCAACT
1292997 ATGGAAACAAAGTTCAATCATTTGGACAAG
450 ATGGAAACAAAGTTCAATCATTTGGACAAG
* *
1293027 TTTAATATCATGTATTGAAG-TCATCTAAAGTGTTAAAATAGAACAATAACTACAAACTTGCATT
1 TTTAATATCATGTATTGAAGCT-ATCTAAACTGTTAAAATAGAACAATAACTGCAAACTTGCATT
* ** * ** * *
1293091 TTTGCTTATTAATAGCACAAAAAGTCCTAAACTGATATAAACCATTACTTTTTTACACATATCAA
65 TTTGCTT-TTAATAGCATAAAAAGTCCTAAACAAAAATAAACCACAACTTTTTCACACAAATCAA
* * * * * * * *
1293156 CCATAAAAACCAAGTTTAATCATTTGGATAAGTTTAATATCT-TATATTAAAGCTATTTGAATTG
129 CCATAAAAACCAAGTTCAATCA-TTCGACAAGTTTAATAT-TATGTATTGAAGCTATCTAAACTG
* * *
1293220 TTAAAATGGAACAATAGCTGCAAATTTGTATTTTTATCTTTTAATGGCACAAAAAGTCCTAAACA
192 TTAAAATGAAACAATAACTGCAAATTTGTATTTTTACCTTTTAATGGCACAAAAAGTCCTAAACA
* * * * * * *
1293285 AACATAAATGGTAACTTTTTCACATATATAAATCGTGAAAACCAAATTCAATCATTCAAACAAGT
257 AACATAAACGATAATTTTTTCACACATATCAAT-GTGAAAATCAAATTCAATCATTCGAACAAGT
*
1293350 TTAATATTATGTATTTATGCTATGTAAATTGTTAAAACAGAAATATAACTATAAA-TTACCCTTT
321 TTAATATTATGTATTTAAGCTATGTAAATTGTTAAAACA-AAATATAACTATAAAGTTACCCTTT
* * *
1293414 TGCCCTTTAATAACACAAAAAGT-TCTAAACAGATATAAACGATAACTTTTTCATACATATCAAC
385 TGCTCTTTAATAACACAAAAAGTCT-TAAACAGACATAAACAATAACTTTTTCATACATATCAAC
* *
1293478 TATGGAAACAAAGATCAATCATTTGAACAAG
449 TATGGAAACAAAGTTCAATCATTTGGACAAG
* * * * * *
1293509 TTTAATATTATTTATTGAAGCTATATAGACTGTTAAAATAGAGCAATAACTGTAAACTTGCATTT
1 TTTAATATCATGTATTGAAGCTATCTAAACTGTTAAAATAGAACAATAACTGCAAACTTGCATTT
*
1293574 TTGCCTTTTAATAGCATAAAAATATCCTAAA
66 TTG-CTTTTAATAGCATAAAAA-GTCCTAAA
1293605 TAGACACAAA
Statistics
Matches: 912, Mismatches: 127, Indels: 45
0.84 0.12 0.04
Matches are distributed among these distances:
481 2 0.00
482 219 0.24
483 501 0.55
484 140 0.15
485 49 0.05
486 1 0.00
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (479 bp):
TTTAATATCATGTATTGAAGCTATCTAAACTGTTAAAATAGAACAATAACTGCAAACTTGCATTT
TTGCTTTTAATAGCATAAAAAGTCCTAAACAAAAATAAACCACAACTTTTTCACACAAATCAACC
ATAAAAACCAAGTTCAATCATTCGACAAGTTTAATATTATGTATTGAAGCTATCTAAACTGTTAA
AATGAAACAATAACTGCAAATTTGTATTTTTACCTTTTAATGGCACAAAAAGTCCTAAACAAACA
TAAACGATAATTTTTTCACACATATCAATGTGAAAATCAAATTCAATCATTCGAACAAGTTTAAT
ATTATGTATTTAAGCTATGTAAATTGTTAAAACAAAATATAACTATAAAGTTACCCTTTTGCTCT
TTAATAACACAAAAAGTCTTAAACAGACATAAACAATAACTTTTTCATACATATCAACTATGGAA
ACAAAGTTCAATCATTTGGACAAG
Found at i:1297067 original size:21 final size:21
Alignment explanation
Indices: 1297021--1297068 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1297011 TTCTCATCAC
*
1297021 TTTGAATATCAACATCACTAA
1 TTTGAATATCAACATCACCAA
* * *
1297042 CTTGAGTATCAGCATCACCAA
1 TTTGAATATCAACATCACCAA
1297063 TTTGAA
1 TTTGAA
1297069 GAATAGGAGG
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (21 bp):
TTTGAATATCAACATCACCAA
Found at i:1299780 original size:22 final size:22
Alignment explanation
Indices: 1299752--1299795 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1299742 CTAAATCTTC
*
1299752 CTTAATTCTAGGGATACAAATA
1 CTTAATTCTAGAGATACAAATA
1299774 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
1299796 TAAATATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:1303556 original size:23 final size:23
Alignment explanation
Indices: 1303443--1303550 Score: 162
Period size: 23 Copynumber: 4.6 Consensus size: 23
1303433 TTGAAAGGGT
* *
1303443 TCGGCAATGAAGGCCTAAACAGGAT
1 TCGGCAATGAAGGCCTAAA-A-AAG
1303468 TCGGCAATGAAGGCCTAAAAAAG
1 TCGGCAATGAAGGCCTAAAAAAG
1303491 TCGGCAATGAAGGCCTAAAAAAG
1 TCGGCAATGAAGGCCTAAAAAAG
*
1303514 TCGGCAATGAAGACCTAAAAAAG
1 TCGGCAATGAAGGCCTAAAAAAG
*
1303537 TCAGCAATGAAGGC
1 TCGGCAATGAAGGC
1303551 TGAAAATTTT
Statistics
Matches: 78, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
23 58 0.74
24 1 0.01
25 19 0.24
ACGTcount: A:0.42, C:0.19, G:0.26, T:0.14
Consensus pattern (23 bp):
TCGGCAATGAAGGCCTAAAAAAG
Found at i:1303725 original size:22 final size:22
Alignment explanation
Indices: 1303697--1303740 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1303687 CTAAATCTTC
*
1303697 CTTAATTCTAGGGATACAAATA
1 CTTAATTCTAGAGATACAAATA
1303719 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
1303741 TAAATATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:1312911 original size:152 final size:152
Alignment explanation
Indices: 1312635--1312941 Score: 578
Period size: 152 Copynumber: 2.0 Consensus size: 152
1312625 ATCCCAAAAT
*
1312635 GAACCCCGATCAAGGATCATCTTTTACATTAGGGGGCAAAATCAGGATATCTTCAAGAGCCCAAC
1 GAACCCCGATCAAAGATCATCTTTTACATTAGGGGGCAAAATCAGGATATCTTCAAGAGCCCAAC
*
1312700 TTTAAGGGAAGTGTTTGATATTGAGAACGTTTAACACGCACTTCAGAGATGAGAGTCTAGGGTAA
66 TTTAAGAGAAGTGTTTGATATTGAGAACGTTTAACACGCACTTCAGAGATGAGAGTCTAGGGTAA
1312765 AAAGTGAATGAGGCTTTAATTG
131 AAAGTGAATGAGGCTTTAATTG
*
1312787 GAACCCCGATCAAAGATCATCTTTTACATTAGGGGGTAAAATCAGGATATCTTCAAGAGCCCAAC
1 GAACCCCGATCAAAGATCATCTTTTACATTAGGGGGCAAAATCAGGATATCTTCAAGAGCCCAAC
1312852 TTTAAGAGAAGTGTTTGATATTGAGAACGTTTAACACGCACTTCAGAGATGAGAGTCTAGGGTAA
66 TTTAAGAGAAGTGTTTGATATTGAGAACGTTTAACACGCACTTCAGAGATGAGAGTCTAGGGTAA
*
1312917 AAAGTGAATGAGGTTTTAATTG
131 AAAGTGAATGAGGCTTTAATTG
1312939 GAA
1 GAA
1312942 TCCATAAAAT
Statistics
Matches: 151, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
152 151 1.00
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.27
Consensus pattern (152 bp):
GAACCCCGATCAAAGATCATCTTTTACATTAGGGGGCAAAATCAGGATATCTTCAAGAGCCCAAC
TTTAAGAGAAGTGTTTGATATTGAGAACGTTTAACACGCACTTCAGAGATGAGAGTCTAGGGTAA
AAAGTGAATGAGGCTTTAATTG
Found at i:1313302 original size:153 final size:152
Alignment explanation
Indices: 1312949--1313316 Score: 462
Period size: 153 Copynumber: 2.4 Consensus size: 152
1312939 GAATCCATAA
* * * * * * *
1312949 AATTCAAGAAAGTAGAATGCTAAAGTTGAAGGCAAATGTTTTCATAAAAGAAATAGCGAGGAAAG
1 AATTCAAGAAAGTAGAATGCAAAAGTTGAAGTCAAATGTTTCCAAAAAAGAAAAAGCAAAGAAAG
* * * ***
1313014 AAAGACATGCATCTCGAAGATGAGAGTCTGGGGTAAAAAAATGAATAAAGATTCAGTTAGAATTC
66 AAAGACATGCACCTCAAAGATGAGAATCCAAGGTAAAAAAATGAATAAAGATTCAGTTAGAATTC
1313079 AAAAAGAATAAAAAGAAAGATAG
131 AAAAAG-ATAAAAAGAAAGATAG
*
1313102 AATTCAAGAAAGTAGAATG-ATAAAGTTGAAGTCAGATGTTTCCAAAAAAGAAAAAGCAAAGAAA
1 AATTCAAGAAAGTAGAATGCA-AAAGTTGAAGTCAAATGTTTCCAAAAAAGAAAAAGCAAAGAAA
* *
1313166 GAAAGACATGCACCTCAAATATGAGAATCCAAGGT-AAAAAATGAATGAAA-CTTCAGTTAGAAT
65 GAAAGACATGCACCTCAAAGATGAGAATCCAAGGTAAAAAAATGAAT-AAAGATTCAGTTAGAAT
** *
1313229 TCAAAAAG-TAAAAAGGGATATAG
129 TCAAAAAGATAAAAAGAAAGATAG
* * *
1313252 AATTCAAGAATGTATAATGCAAAAGTTGAATTCAAATGTTTCCAAAAAA-AAAAA--AAAGAAAG
1 AATTCAAGAAAGTAGAATGCAAAAGTTGAAGTCAAATGTTTCCAAAAAAGAAAAAGCAAAGAAAG
1313314 AAA
66 AAA
1313317 CAAGACTTTT
Statistics
Matches: 189, Mismatches: 23, Indels: 12
0.84 0.10 0.05
Matches are distributed among these distances:
147 11 0.06
149 5 0.03
150 55 0.29
151 1 0.01
152 31 0.16
153 86 0.46
ACGTcount: A:0.52, C:0.09, G:0.19, T:0.20
Consensus pattern (152 bp):
AATTCAAGAAAGTAGAATGCAAAAGTTGAAGTCAAATGTTTCCAAAAAAGAAAAAGCAAAGAAAG
AAAGACATGCACCTCAAAGATGAGAATCCAAGGTAAAAAAATGAATAAAGATTCAGTTAGAATTC
AAAAAGATAAAAAGAAAGATAG
Found at i:1314345 original size:41 final size:38
Alignment explanation
Indices: 1314300--1314393 Score: 106
Period size: 35 Copynumber: 2.5 Consensus size: 38
1314290 CATGAAATAA
*
1314300 ACATTCACATTTGCATCACTTGCATCTATATCATGAGA-AAG
1 ACATTCACATTTGCATCA---GCATCTATATCAT-AAACAAG
1314341 ACATTCACATTT--A-CAGCATCTATATCATAAACAAG
1 ACATTCACATTTGCATCAGCATCTATATCATAAACAAG
*
1314376 GCATTCACATTTGCATCA
1 ACATTCACATTTGCATCA
1314394 TAAAAAAGAT
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
34 2 0.04
35 27 0.57
37 1 0.02
38 4 0.09
39 1 0.02
41 12 0.26
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.31
Consensus pattern (38 bp):
ACATTCACATTTGCATCAGCATCTATATCATAAACAAG
Found at i:1314360 original size:35 final size:35
Alignment explanation
Indices: 1314255--1314387 Score: 105
Period size: 35 Copynumber: 3.7 Consensus size: 35
1314245 TCACATGGAC
* *
1314255 ATCATGAGAAAGAAATTCACA-TT-CA-CATCTAAA
1 ATCATGAGAAAGACATTCACATTTACAGCATCT-AT
*
1314288 ATCATGA-AATAAACATTCACATTTGCATCACTTGCATCTAT
1 ATCATGAGAA-AGACATTCACATTT--A-CA---GCATCTAT
1314329 ATCATGAGAAAGACATTCACATTTACAGCATCTAT
1 ATCATGAGAAAGACATTCACATTTACAGCATCTAT
* *
1314364 ATCAT-AAACAAGGCATTCACATTT
1 ATCATGAGA-AAGACATTCACATTT
1314388 GCATCATAAA
Statistics
Matches: 82, Mismatches: 6, Indels: 22
0.75 0.05 0.20
Matches are distributed among these distances:
32 2 0.02
33 16 0.20
34 4 0.05
35 27 0.33
38 4 0.05
39 1 0.01
41 21 0.26
42 7 0.09
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.29
Consensus pattern (35 bp):
ATCATGAGAAAGACATTCACATTTACAGCATCTAT
Found at i:1314700 original size:13 final size:12
Alignment explanation
Indices: 1314658--1314700 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 12
1314648 TTTAAGTAGT
1314658 AAAAAGAAGAAG
1 AAAAAGAAGAAG
*
1314670 AAAAAAAAAGAA-
1 -AAAAAGAAGAAG
1314682 AAAAAGAGAGAAG
1 AAAAAGA-AGAAG
1314695 AAAAAG
1 AAAAAG
1314701 TAGTAAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 6 0.23
12 4 0.15
13 16 0.62
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (12 bp):
AAAAAGAAGAAG
Found at i:1315068 original size:22 final size:22
Alignment explanation
Indices: 1315040--1315141 Score: 96
Period size: 22 Copynumber: 4.6 Consensus size: 22
1315030 TAGATCAAAT
*
1315040 TAAGCCTAGTTTAGTTGACACC
1 TAAGCCTAGATTAGTTGACACC
****
1315062 TAAGCCTAGATTAGTTGGTGTC
1 TAAGCCTAGATTAGTTGACACC
* *
1315084 TAAGCCTAGATTAGCTGACGCC
1 TAAGCCTAGATTAGTTGACACC
* * *
1315106 CAAGCCTAGATTAATTGACACTT
1 TAAGCCTAGATTAGTTGACAC-C
*
1315129 TAAGCCTATATTA
1 TAAGCCTAGATTA
1315142 ACTGGTATCT
Statistics
Matches: 63, Mismatches: 16, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
22 52 0.83
23 11 0.17
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (22 bp):
TAAGCCTAGATTAGTTGACACC
Found at i:1315159 original size:67 final size:66
Alignment explanation
Indices: 1315041--1315178 Score: 177
Period size: 67 Copynumber: 2.1 Consensus size: 66
1315031 AGATCAAATT
* * ** * * *
1315041 AAGCCTAGTTTAGTTGACACCTAAGCCTAGATTAGTTGGTGTCTAAGCCTAGATTAGCTGACGCC
1 AAGCCTAGATTAATTGACACCTAAGCCTAGATTAACTGGTATCTAAACCTAGATTAGCTGACACC
1315106 C
66 C
* * *
1315107 AAGCCTAGATTAATTGACACTTTAAGCCTATATTAACTGGTATCTAAACCTAGATTAGCTGGCAC
1 AAGCCTAGATTAATTGACAC-CTAAGCCTAGATTAACTGGTATCTAAACCTAGATTAGCTGACAC
1315172 CC
65 CC
1315174 AAGCC
1 AAGCC
1315179 CAGTCTAACT
Statistics
Matches: 61, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
66 18 0.30
67 43 0.70
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (66 bp):
AAGCCTAGATTAATTGACACCTAAGCCTAGATTAACTGGTATCTAAACCTAGATTAGCTGACACC
C
Found at i:1315246 original size:22 final size:23
Alignment explanation
Indices: 1315221--1315263 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
1315211 CCGTTTAGCT
1315221 GGCAC-TTAAGCCTAGATTAGTG
1 GGCACTTTAAGCCTAGATTAGTG
1315243 GGCACTTTAAGCCTAGATTAG
1 GGCACTTTAAGCCTAGATTAG
1315264 CTAGCACCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.28
Consensus pattern (23 bp):
GGCACTTTAAGCCTAGATTAGTG
Found at i:1315282 original size:22 final size:22
Alignment explanation
Indices: 1315215--1315298 Score: 80
Period size: 22 Copynumber: 3.8 Consensus size: 22
1315205 TAGGCTCCGT
* *
1315215 TTAGCTGGCACTTAAGCCTAGA
1 TTAGCTAGCACCTAAGCCTAGA
* *
1315237 TTAG-TGGGCACTTTAAGCCTAGA
1 TTAGCT-AGCAC-CTAAGCCTAGA
*
1315260 TTAGCTAGCACCTAAGCCCAGA
1 TTAGCTAGCACCTAAGCCTAGA
* *
1315282 TCAGCTAGTACCTAAGC
1 TTAGCTAGCACCTAAGC
1315299 TTAGTCTAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
21 1 0.02
22 33 0.61
23 19 0.35
24 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (22 bp):
TTAGCTAGCACCTAAGCCTAGA
Found at i:1315522 original size:22 final size:22
Alignment explanation
Indices: 1315476--1315603 Score: 98
Period size: 22 Copynumber: 5.8 Consensus size: 22
1315466 AGGTTAACTA
* * *
1315476 GCACCTAAGCCCAGATCAGCAG
1 GCACCTAAGCCCAAATTAGCTG
*
1315498 GCACCTAAGCCCAAATTAGTTG
1 GCACCTAAGCCCAAATTAGCTG
* *
1315520 GCACCCAAGCCCAAATTAGCTA
1 GCACCTAAGCCCAAATTAGCTG
* * *
1315542 GCATCC-AAGCCCATATTTGTTG
1 GCA-CCTAAGCCCAAATTAGCTG
* ** *
1315564 GCACTTTAAGCCCAGTTTAGCTA
1 GCAC-CTAAGCCCAAATTAGCTG
*
1315587 GCACCTAA-ACCAAATTA
1 GCACCTAAGCCCAAATTA
1315604 AACCTAATCA
Statistics
Matches: 82, Mismatches: 21, Indels: 7
0.75 0.19 0.06
Matches are distributed among these distances:
21 7 0.09
22 58 0.71
23 17 0.21
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.21
Consensus pattern (22 bp):
GCACCTAAGCCCAAATTAGCTG
Found at i:1315524 original size:44 final size:44
Alignment explanation
Indices: 1315476--1315603 Score: 136
Period size: 44 Copynumber: 2.9 Consensus size: 44
1315466 AGGTTAACTA
*
1315476 GCACCTAAGCCCAGATCAGC-AGGCACCTAAGCCCAAATTAGTTG
1 GCACCTAAGCCCAGATTAGCTA-GCACCTAAGCCCAAATTAGTTG
* * * *
1315520 GCACCCAAGCCCAAATTAGCTAGCATCC-AAGCCCATATTTGTTG
1 GCACCTAAGCCCAGATTAGCTAGCA-CCTAAGCCCAAATTAGTTG
* * *
1315564 GCACTTTAAGCCCAGTTTAGCTAGCACCTAA-ACCAAATTA
1 GCAC-CTAAGCCCAGATTAGCTAGCACCTAAGCCCAAATTA
1315604 AACCTAATCA
Statistics
Matches: 68, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
44 46 0.68
45 22 0.32
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.21
Consensus pattern (44 bp):
GCACCTAAGCCCAGATTAGCTAGCACCTAAGCCCAAATTAGTTG
Found at i:1315828 original size:104 final size:104
Alignment explanation
Indices: 1315646--1315974 Score: 365
Period size: 104 Copynumber: 3.2 Consensus size: 104
1315636 GGCCTCTGAG
* * ** * * * * *
1315646 CATAATCTCTAAGACCTTATGGTAAAACATTTTAAATTTTCAAAATTTTAATGCCTTTAATACAA
1 CATAATCTCTAAAACTTTCGGGAAAAACATTTTAAATTTTCAAAGTTTCAATGCCTCTGATACAA
* *
1315711 GGAGTATTCAAAGATGTTGAGATTTGTAAGACCTCTAAC
66 GGAGCATTCAAAGATGTTGAGATTTGTAAGACCTCTAAA
* * * * *
1315750 CATAATCTTTAAAACTTTCGGGCAAAATATTTTAAAATTTCAAAGTTTCAATGCCTCTGATTCAA
1 CATAATCTCTAAAACTTTCGGGAAAAACATTTTAAATTTTCAAAGTTTCAATGCCTCTGATACAA
* * * * *
1315815 AGAGCATTGAAAGATGTTGAGATTTGTAAGACCTTTGAG
66 GGAGCATTCAAAGATGTTGAGATTTGTAAGACCTCTAAA
* * * * * * *
1315854 TATAATATCT-AATCCTCCGGGAAAAACATTTTAAATTTTTAAAGTTTCAATGCCTCTGATACGA
1 CATAATCTCTAAAACTTTCGGGAAAAACATTTTAAATTTTCAAAGTTTCAATGCCTCTGATACAA
*
1315918 GGAGCATTCAAAGATGTTGAGATTTGTAATACCTAC-AAA
66 GGAGCATTCAAAGATGTTGAGATTTGTAAGACCT-CTAAA
*
1315957 CATAATCTCTAAGACTTT
1 CATAATCTCTAAAACTTT
1315975 TGAGCATAAT
Statistics
Matches: 180, Mismatches: 43, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
103 85 0.47
104 95 0.53
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (104 bp):
CATAATCTCTAAAACTTTCGGGAAAAACATTTTAAATTTTCAAAGTTTCAATGCCTCTGATACAA
GGAGCATTCAAAGATGTTGAGATTTGTAAGACCTCTAAA
Found at i:1315923 original size:103 final size:104
Alignment explanation
Indices: 1315669--1315968 Score: 352
Period size: 103 Copynumber: 2.9 Consensus size: 104
1315659 ACCTTATGGT
* * * * *
1315669 AAAACATTTTAAATTTTCAAAATTTTAATGCCTTTAATACAAGGAGTATTCAAAGATGTTGAGAT
1 AAAACATTTTAAATTTTCAAAGTTTCAATGCCTCTGATACAAGGAGCATTCAAAGATGTTGAGAT
* * * * *
1315734 TTGTAAGACCTCTAACCATAATCTTTAAAACTTTCGGGC
66 TTGTAAGACCTCTAACCATAATATCTAAAACCTCCGGGA
* * * * *
1315773 AAAATATTTTAAAATTTCAAAGTTTCAATGCCTCTGATTCAAAGAGCATTGAAAGATGTTGAGAT
1 AAAACATTTTAAATTTTCAAAGTTTCAATGCCTCTGATACAAGGAGCATTCAAAGATGTTGAGAT
* * ** *
1315838 TTGTAAGACCTTTGAGTATAATATCT-AATCCTCCGGGA
66 TTGTAAGACCTCTAACCATAATATCTAAAACCTCCGGGA
* *
1315876 AAAACATTTTAAATTTTTAAAGTTTCAATGCCTCTGATACGAGGAGCATTCAAAGATGTTGAGAT
1 AAAACATTTTAAATTTTCAAAGTTTCAATGCCTCTGATACAAGGAGCATTCAAAGATGTTGAGAT
* * *
1315941 TTGTAATACCTAC-AAACATAATCTCTAA
66 TTGTAAGACCT-CTAACCATAATATCTAA
1315969 GACTTTTGAG
Statistics
Matches: 161, Mismatches: 33, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
103 85 0.53
104 76 0.47
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.34
Consensus pattern (104 bp):
AAAACATTTTAAATTTTCAAAGTTTCAATGCCTCTGATACAAGGAGCATTCAAAGATGTTGAGAT
TTGTAAGACCTCTAACCATAATATCTAAAACCTCCGGGA
Found at i:1316087 original size:126 final size:126
Alignment explanation
Indices: 1315876--1316204 Score: 414
Period size: 126 Copynumber: 2.6 Consensus size: 126
1315866 TCCTCCGGGA
*
1315876 AAAACATTTTAAATTTTTAAAGTTTCAATGCCTCTGATACGAGGAGCATTCAAAGATGTTGAGAT
1 AAAACATTTTAAATTTTCAAAGTTTCAATGCCTCTGATACGAGGAGCATTCAAAGATGTTGAGAT
* * *
1315941 TTGTAATACCTACAAACATAATCTCTAAGA-CTTTTGAGCATAATCTCTT-AGACCTTCAG-GC
66 TTGTAAGACCTACAAACATAATCTCTAAGACCTCTAG-GCATAAT-TCTTGAGA-CTTCAGAGC
* * * *
1316002 AAAATATTTTAAATTTTCAAAGTTTCAATGCCTCTTATACGAGGAGCATTCATAGCTGTTGAGAT
1 AAAACATTTTAAATTTTCAAAGTTTCAATGCCTCTGATACGAGGAGCATTCAAAGATGTTGAGAT
* *** * *
1316067 TTGTAAGACCTCCTGGCATAATCTCTAAGACCTCTAGGCATAATTTTTGAGACTTCCGAGC
66 TTGTAAGACCTACAAACATAATCTCTAAGACCTCTAGGCATAATTCTTGAGACTTCAGAGC
* * * * *
1316128 AAAACATTTTAAATTTTCAAAGTTTCAATGCCTTTGATTGCAATGAGCATTCAAAGAT-TTTATG
1 AAAACATTTTAAATTTTCAAAGTTTCAATGCCTCTGA-TACGAGGAGCATTCAAAGATGTTGA-G
1316192 ATTTGTAAGACCT
64 ATTTGTAAGACCT
1316205 CTAGGCATAA
Statistics
Matches: 175, Mismatches: 23, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
125 8 0.05
126 134 0.77
127 33 0.19
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (126 bp):
AAAACATTTTAAATTTTCAAAGTTTCAATGCCTCTGATACGAGGAGCATTCAAAGATGTTGAGAT
TTGTAAGACCTACAAACATAATCTCTAAGACCTCTAGGCATAATTCTTGAGACTTCAGAGC
Found at i:1316410 original size:20 final size:18
Alignment explanation
Indices: 1316385--1316436 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 18
1316375 TTATTAATTT
1316385 AGAAAAAAAACAAAAATTCA
1 AGAAAAAAAA-AAAAA-TCA
1316405 AGAAAAACAAAAAAAATCA
1 AGAAAAA-AAAAAAAATCA
1316424 A-AAAATAAAAAAA
1 AGAAAA-AAAAAAA
1316437 TAAAAAAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
18 10 0.33
19 5 0.17
20 12 0.40
21 3 0.10
ACGTcount: A:0.81, C:0.08, G:0.04, T:0.08
Consensus pattern (18 bp):
AGAAAAAAAAAAAAATCA
Found at i:1316444 original size:16 final size:16
Alignment explanation
Indices: 1316414--1316444 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1316404 AAGAAAAACA
*
1316414 AAAAAAATCAAAAAAT
1 AAAAAAATAAAAAAAT
1316430 AAAAAAATAAAAAAA
1 AAAAAAATAAAAAAA
1316445 ACCAAAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.87, C:0.03, G:0.00, T:0.10
Consensus pattern (16 bp):
AAAAAAATAAAAAAAT
Found at i:1319030 original size:19 final size:16
Alignment explanation
Indices: 1318988--1319019 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1318978 AGCATGGAAT
1318988 ATTAATAATTAAAAAA
1 ATTAATAATTAAAAAA
1319004 ATTAATAATTAAAAAA
1 ATTAATAATTAAAAAA
1319020 TTACTTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
ATTAATAATTAAAAAA
Found at i:1325313 original size:7 final size:7
Alignment explanation
Indices: 1325301--1325330 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
1325291 TTAAAAGGTG
1325301 AATAAGA
1 AATAAGA
1325308 AATAAGA
1 AATAAGA
1325315 AATAAGA
1 AATAAGA
1325322 AATAAGA
1 AATAAGA
1325329 AA
1 AA
1325331 CCTAAAGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.13
Consensus pattern (7 bp):
AATAAGA
Found at i:1328282 original size:50 final size:49
Alignment explanation
Indices: 1328207--1328310 Score: 147
Period size: 50 Copynumber: 2.1 Consensus size: 49
1328197 AAAATTGAAA
* *
1328207 ATTTTAAAGTTTTAAAGCATTTGTTT-CGAATGAGCTTTTCAAATATGAG
1 ATTTTAAAGTTTTAAAACATATGTTTACGAA-GAGCTTTTCAAATATGAG
* *
1328256 ATTTTGAAAGTTTTAAAACCTATGTTTAGGAAGAGCTTTTCAAATATGAG
1 ATTTT-AAAGTTTTAAAACATATGTTTACGAAGAGCTTTTCAAATATGAG
1328306 ATTTT
1 ATTTT
1328311 TTTTTTTTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
49 5 0.10
50 41 0.84
51 3 0.06
ACGTcount: A:0.34, C:0.08, G:0.16, T:0.42
Consensus pattern (49 bp):
ATTTTAAAGTTTTAAAACATATGTTTACGAAGAGCTTTTCAAATATGAG
Found at i:1328393 original size:50 final size:50
Alignment explanation
Indices: 1328318--1328659 Score: 241
Period size: 50 Copynumber: 6.9 Consensus size: 50
1328308 TTTTTTTTTT
* *
1328318 TTTTTAAGTTTCTAAG-CTCCTATTTAAAAGAAACTTTTCAAAAATGAAAA
1 TTTTAAAGTTTCAAAGCCT-CTATTTAAAAGAAACTTTTCAAAAATGAAAA
* * *
1328368 TTTTAAAGTTTCAAAGCCTTTATTTAACAAG-AGCTTTTCAAAAATTAAAA
1 TTTTAAAGTTTCAAAGCCTCTATTTAA-AAGAAACTTTTCAAAAATGAAAA
* * *
1328418 TTTT-TAGTTTCAAAGCCTCTATTTAGGAAGAGA-TTTTCAAAAATGAAAA
1 TTTTAAAGTTTCAAAGCCTCTATTTA-AAAGAAACTTTTCAAAAATGAAAA
* * * ** * *
1328467 TTTTAAAGTCTCAAAGCATCTGTTTAGAAAGTGTA-TTTT-AAAGAT-AAGAT
1 TTTTAAAGTTTCAAAGCCTCTATTTA-AAAG-AAACTTTTCAAAAATGAA-AA
* * * * * * *
1328517 TTTTAAAGTTTTAAAGTCTTTATTTAAGAGAAGCTTTTCAAAAATGAGAT
1 TTTTAAAGTTTCAAAGCCTCTATTTAAAAGAAACTTTTCAAAAATGAAAA
* * ** * * ** * *
1328567 TTTTAAAGTTTCAAAGCCTTTGTTTAGGATAAGCCTTTTCAAAGTTCAAAT
1 TTTTAAAGTTTCAAAGCCTCTATTTAAAAGAA-ACTTTTCAAAAATGAAAA
** **
1328618 TTTTAAAGTTTTGAAGCCTCTATTT-AAAGAAGTTTTTCAAAA
1 TTTTAAAGTTTCAAAGCCTCTATTTAAAAGAAACTTTTCAAAA
1328660 TTAAAAAAAG
Statistics
Matches: 229, Mismatches: 52, Indels: 23
0.75 0.17 0.08
Matches are distributed among these distances:
49 58 0.25
50 126 0.55
51 45 0.20
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.39
Consensus pattern (50 bp):
TTTTAAAGTTTCAAAGCCTCTATTTAAAAGAAACTTTTCAAAAATGAAAA
Found at i:1328574 original size:100 final size:99
Alignment explanation
Indices: 1328337--1328659 Score: 334
Period size: 100 Copynumber: 3.2 Consensus size: 99
1328327 TTCTAAGCTC
* * *
1328337 CTATTTAAAAGAAACTTTTCAAAAATGAAAATTTTAAAGTTTCAAAGCCTTTATTTA-ACAAGAG
1 CTATTTAAGAGAAGCTTTTCAAAAATGAAAATTTTAAAGTTTCAAAGCCTTTGTTTAGACAAGAG
* *
1328401 CTTTTCAAAAATTAAAATTTTT--AGTTTCAAAGCCT
66 -TTTTCAAAGA-T-AAATTTTTAAAGTTTTAAAGCCT
* * * * * *
1328436 CTATTTAGGA-AGAGATTTTCAAAAATGAAAATTTTAAAGTCTCAAAGCATCTGTTTAGA-AAGT
1 CTATTTAAGAGA-AGCTTTTCAAAAATGAAAATTTTAAAGTTTCAAAGCCTTTGTTTAGACAAGA
* *
1328499 GTATTTTAAAGATAAGATTTTTAAAGTTTTAAAGTCT
65 GT-TTTCAAAGATAA-ATTTTTAAAGTTTTAAAGCCT
* * * * *
1328536 TTATTTAAGAGAAGCTTTTCAAAAATGAGATTTTTAAAGTTTCAAAGCCTTTGTTTAGGATAAGC
1 CTATTTAAGAGAAGCTTTTCAAAAATGAAAATTTTAAAGTTTCAAAGCCTTTGTTTA-GACAAGA
* * *
1328601 CTTTTCAAAGTTCAAATTTTTAAAGTTTTGAAGCCT
65 GTTTTCAAAGAT-AAATTTTTAAAGTTTTAAAGCCT
*
1328637 CTATTTAA-AGAAGTTTTTCAAAA
1 CTATTTAAGAGAAGCTTTTCAAAA
1328660 TTAAAAAAAG
Statistics
Matches: 185, Mismatches: 29, Indels: 19
0.79 0.12 0.08
Matches are distributed among these distances:
97 2 0.01
98 9 0.05
99 58 0.31
100 73 0.39
101 37 0.20
102 6 0.03
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (99 bp):
CTATTTAAGAGAAGCTTTTCAAAAATGAAAATTTTAAAGTTTCAAAGCCTTTGTTTAGACAAGAG
TTTTCAAAGATAAATTTTTAAAGTTTTAAAGCCT
Found at i:1330926 original size:62 final size:61
Alignment explanation
Indices: 1330825--1331020 Score: 241
Period size: 61 Copynumber: 3.2 Consensus size: 61
1330815 TTTGTTTCCA
*
1330825 TGTT-CATGCATTCCCCATGCACCAAAGTTTGCATTTTTATCAATAGCATTTTGGTAATTTT
1 TGTTACATGCATTCCCCATGCATCAAAGTTTGCATTTTTATCAATAGCATTTTGGTAA-TTT
* *
1330886 TGTTACATGCATTCCCCATGCATCAAACTTTGCATTTTTATCAATAGCATTTTGGTAGTTT
1 TGTTACATGCATTCCCCATGCATCAAAGTTTGCATTTTTATCAATAGCATTTTGGTAATTT
* ** ** * * * * * **
1330947 TCTTACATGCATTTTCCATGCATTGAAGTTTGAATTTTTGTTAATGGCATCTCAGTAATTT
1 TGTTACATGCATTCCCCATGCATCAAAGTTTGCATTTTTATCAATAGCATTTTGGTAATTT
1331008 TGTTACATGCATT
1 TGTTACATGCATT
1331021 TCCAAACCTT
Statistics
Matches: 116, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
61 66 0.57
62 50 0.43
ACGTcount: A:0.24, C:0.18, G:0.14, T:0.44
Consensus pattern (61 bp):
TGTTACATGCATTCCCCATGCATCAAAGTTTGCATTTTTATCAATAGCATTTTGGTAATTT
Found at i:1331047 original size:13 final size:13
Alignment explanation
Indices: 1331024--1331248 Score: 173
Period size: 13 Copynumber: 17.2 Consensus size: 13
1331014 ATGCATTTCC
* *
1331024 AAACCTTAACCCT
1 AAACCCTAAACCT
*
1331037 AAA-CCAAAACCCT
1 AAACCCTAAA-CCT
*
1331050 AAACCCTAAACTT
1 AAACCCTAAACCT
1331063 AAACCCTAAATCCT
1 AAACCCTAAA-CCT
1331077 AAA-CC--AACCTT
1 AAACCCTAAACC-T
*
1331088 AAA-CCTAAATTCT
1 AAACCCTAAA-CCT
1331101 AAACCCTAAAACCT
1 AAACCCT-AAACCT
*
1331115 AAACCCTAACCCT
1 AAACCCTAAACCT
1331128 AAACCCTTAAACCT
1 AAACCC-TAAACCT
1331142 AAACCCTAAACCT
1 AAACCCTAAACCT
1331155 AAACCCTAAACC-
1 AAACCCTAAACCT
* * *
1331167 AAAACTTAAACTCC
1 AAACCCTAAAC-CT
1331181 AAA-CCTCAAACCTT
1 AAACCCT-AAACC-T
*
1331195 AAA-CATAAACCCT
1 AAACCCTAAA-CCT
1331208 AAACCCT-AACCT
1 AAACCCTAAACCT
*
1331220 AGACCCTAAA-CT
1 AAACCCTAAACCT
*
1331232 AACCCCTAAACCCT
1 AAACCCTAAA-CCT
1331246 AAA
1 AAA
1331249 ACCAACTTGA
Statistics
Matches: 173, Mismatches: 20, Indels: 37
0.75 0.09 0.16
Matches are distributed among these distances:
10 2 0.01
11 8 0.05
12 31 0.18
13 74 0.43
14 55 0.32
15 3 0.02
ACGTcount: A:0.46, C:0.36, G:0.00, T:0.18
Consensus pattern (13 bp):
AAACCCTAAACCT
Found at i:1331056 original size:20 final size:20
Alignment explanation
Indices: 1331031--1331248 Score: 179
Period size: 20 Copynumber: 11.1 Consensus size: 20
1331021 TCCAAACCTT
*
1331031 AACCCTAAACCAAAACCCTA
1 AACCCTAAACCTAAACCCTA
*
1331051 AACCCTAAACTTAAACCCTA
1 AACCCTAAACCTAAACCCTA
* *
1331071 AATCCTAAACC--AACCTTA
1 AACCCTAAACCTAAACCCTA
*
1331089 AA-CCTAAATTCTAAACCCTA
1 AACCCTAAA-CCTAAACCCTA
*
1331109 AAACCTAAACCCT-AACCCTA
1 AACCCTAAA-CCTAAACCCTA
1331129 AACCCTTAAACCTAAACCCTA
1 AACCC-TAAACCTAAACCCTA
1331150 AA-CCTAAACCCTAAA-CC-A
1 AACCCTAAA-CCTAAACCCTA
* * *
1331168 AAACTTAAACTCCAAA-CCTCA
1 AACCCTAAAC-CTAAACCCT-A
* *
1331189 AACCTTAAACATAAACCCTA
1 AACCCTAAACCTAAACCCTA
*
1331209 AACCCT-AACCTAGACCCTA
1 AACCCTAAACCTAAACCCTA
*
1331228 AA--CTAACCCCTAAACCCTA
1 AACCCTAA-ACCTAAACCCTA
1331247 AA
1 AA
1331249 ACCAACTTGA
Statistics
Matches: 164, Mismatches: 20, Indels: 29
0.77 0.09 0.14
Matches are distributed among these distances:
17 8 0.05
18 14 0.09
19 42 0.26
20 66 0.40
21 34 0.21
ACGTcount: A:0.46, C:0.36, G:0.00, T:0.17
Consensus pattern (20 bp):
AACCCTAAACCTAAACCCTA
Found at i:1331251 original size:8 final size:7
Alignment explanation
Indices: 1331031--1331248 Score: 166
Period size: 7 Copynumber: 33.3 Consensus size: 7
1331021 TCCAAACCTT
1331031 AACCCTA
1 AACCCTA
*
1331038 AA-CCAA
1 AACCCTA
1331044 AACCCTA
1 AACCCTA
1331051 AACCCTA
1 AACCCTA
*
1331058 AA-CTTA
1 AACCCTA
1331064 AACCCTA
1 AACCCTA
*
1331071 AATCCTA
1 AACCCTA
1331078 AA-CC--
1 AACCCTA
*
1331082 AACCTTA
1 AACCCTA
1331089 AA-CCTA
1 AACCCTA
**
1331095 AATTCTA
1 AACCCTA
1331102 AACCCTA
1 AACCCTA
*
1331109 AAACCTA
1 AACCCTA
1331116 AACCCT-
1 AACCCTA
1331122 AACCCTA
1 AACCCTA
1331129 AACCCTTA
1 AACCC-TA
1331137 AA-CCTA
1 AACCCTA
1331143 AACCCTA
1 AACCCTA
1331150 AA-CCTA
1 AACCCTA
1331156 AACCCTA
1 AACCCTA
1331163 AA-CC-A
1 AACCCTA
* *
1331168 AAACTTA
1 AACCCTA
1331175 AACTCC-A
1 AAC-CCTA
1331182 AA-CCTCA
1 AACCCT-A
*
1331189 AACCTTA
1 AACCCTA
*
1331196 AA-CATA
1 AACCCTA
1331202 AACCCTA
1 AACCCTA
1331209 AACCCT-
1 AACCCTA
1331215 AA-CCTA
1 AACCCTA
*
1331221 GACCCTA
1 AACCCTA
1331228 AA--CTA
1 AACCCTA
*
1331233 ACCCCTA
1 AACCCTA
1331240 AACCCTA
1 AACCCTA
1331247 AA
1 AA
1331249 ACCAACTTGA
Statistics
Matches: 168, Mismatches: 22, Indels: 42
0.72 0.09 0.18
Matches are distributed among these distances:
4 2 0.01
5 13 0.08
6 44 0.26
7 102 0.61
8 7 0.04
ACGTcount: A:0.46, C:0.36, G:0.00, T:0.17
Consensus pattern (7 bp):
AACCCTA
Found at i:1331251 original size:59 final size:60
Alignment explanation
Indices: 1331082--1331251 Score: 154
Period size: 59 Copynumber: 2.9 Consensus size: 60
1331072 ATCCTAAACC
* ** * * * *
1331082 AACCTTAAACCTAAATTCTAAACCCTAAAACCTAAA-CCCTAACCCTAAACCCTTAAACCTA
1 AACCCTAAACCTAAACCCTAAA-CC-AAAACTTAAACCCCAAACCCTAAAACCTTAAACATA
* *
1331143 AACCCTAAACCTAAACCCTAAACCAAAACTTAAACTCCAAA-CCTCAAACCTTAAACATA
1 AACCCTAAACCTAAACCCTAAACCAAAACTTAAACCCCAAACCCTAAAACCTTAAACATA
* *
1331202 AACCCTAAACCCT-AA-CCTAGACCCTAAAC-T-AACCCCTAAACCCTAAAACC
1 AACCCTAAA-CCTAAACCCTA-AACCAAAACTTAAACCCC-AAACCCTAAAACC
1331252 AACTTGATCC
Statistics
Matches: 91, Mismatches: 13, Indels: 12
0.78 0.11 0.10
Matches are distributed among these distances:
57 5 0.05
58 8 0.09
59 50 0.55
60 9 0.10
61 19 0.21
ACGTcount: A:0.45, C:0.36, G:0.01, T:0.18
Consensus pattern (60 bp):
AACCCTAAACCTAAACCCTAAACCAAAACTTAAACCCCAAACCCTAAAACCTTAAACATA
Found at i:1332797 original size:22 final size:24
Alignment explanation
Indices: 1332757--1332803 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
1332747 AAAAGAACGT
1332757 AAAAAAAAAAGGCCCAAAAC-TAAAA
1 AAAAAAAAAAGG--CAAAACGTAAAA
1332782 AAAAAAAAAAGG-AAAACGTAAA
1 AAAAAAAAAAGGCAAAACGTAAA
1332804 CCCAACTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 5 0.24
23 4 0.19
25 12 0.57
ACGTcount: A:0.74, C:0.11, G:0.11, T:0.04
Consensus pattern (24 bp):
AAAAAAAAAAGGCAAAACGTAAAA
Found at i:1334045 original size:31 final size:31
Alignment explanation
Indices: 1334010--1334071 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
1334000 AAATAATTTA
* *
1334010 CTCATTAATGAGGTATTATCAT-TAGATTCAC
1 CTCATTAATAAGGTATCATCATCT-GATTCAC
*
1334041 CTCATTAATAAGTTATCATCATCTGATTCAC
1 CTCATTAATAAGGTATCATCATCTGATTCAC
1334072 TGACAGTGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 26 0.96
32 1 0.04
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.39
Consensus pattern (31 bp):
CTCATTAATAAGGTATCATCATCTGATTCAC
Found at i:1335199 original size:13 final size:13
Alignment explanation
Indices: 1335168--1335209 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
1335158 TTATGCCTAG
*
1335168 ATCATGCTAAAAT
1 ATCATGCAAAAAT
1335181 ATTCATGCAAAAAT
1 A-TCATGCAAAAAT
*
1335195 ATCATGCAAATAT
1 ATCATGCAAAAAT
1335208 AT
1 AT
1335210 TAATTATCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 14 0.54
14 12 0.46
ACGTcount: A:0.48, C:0.14, G:0.07, T:0.31
Consensus pattern (13 bp):
ATCATGCAAAAAT
Found at i:1335219 original size:20 final size:19
Alignment explanation
Indices: 1335194--1335262 Score: 58
Period size: 17 Copynumber: 3.8 Consensus size: 19
1335184 CATGCAAAAA
1335194 TATCATGCAAATATATTAAT
1 TATCATGCAAATATA-TAAT
*
1335214 TATCATAC-AATA-ATAAT
1 TATCATGCAAATATATAAT
* *
1335231 AATCATG-TAA-ATATAA-
1 TATCATGCAAATATATAAT
*
1335247 TATCATGTAAATATAT
1 TATCATGCAAATATAT
1335263 TATCATGCGA
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
16 7 0.17
17 17 0.43
18 5 0.12
19 4 0.10
20 7 0.17
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (19 bp):
TATCATGCAAATATATAAT
Found at i:1335253 original size:16 final size:16
Alignment explanation
Indices: 1335226--1335269 Score: 70
Period size: 16 Copynumber: 2.7 Consensus size: 16
1335216 TCATACAATA
1335226 ATAATAATCATGTAAAT
1 ATAAT-ATCATGTAAAT
1335243 ATAATATCATGTAAAT
1 ATAATATCATGTAAAT
*
1335259 ATATTATCATG
1 ATAATATCATG
1335270 CGATAAGACA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 21 0.81
17 5 0.19
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.39
Consensus pattern (16 bp):
ATAATATCATGTAAAT
Found at i:1335634 original size:41 final size:41
Alignment explanation
Indices: 1335582--1335695 Score: 147
Period size: 41 Copynumber: 2.8 Consensus size: 41
1335572 ATGCAAATAG
* * *
1335582 ACATGCAATTAAATATATAATTATGCAATTAACAATGTAAA
1 ACATGCAATTAAATATATAATCATGCAAATAACAATATAAA
* * *
1335623 ACATACAATTAAATATATGATCATGCAAATAATAATATAAA
1 ACATGCAATTAAATATATAATCATGCAAATAACAATATAAA
* * *
1335664 TCATGCAATTAAATATATAATAATGGAAATAA
1 ACATGCAATTAAATATATAATCATGCAAATAA
1335696 ACATACAATT
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 62 1.00
ACGTcount: A:0.54, C:0.09, G:0.07, T:0.31
Consensus pattern (41 bp):
ACATGCAATTAAATATATAATCATGCAAATAACAATATAAA
Found at i:1335681 original size:21 final size:21
Alignment explanation
Indices: 1335583--1335683 Score: 102
Period size: 21 Copynumber: 4.9 Consensus size: 21
1335573 TGCAAATAGA
1335583 CATGCAATTAAATATAT-AAT
1 CATGCAATTAAATATATAAAT
* * *
1335603 TATGCAATTAACA-ATGTAAAA
1 CATGCAATTAA-ATATATAAAT
* *
1335624 CATACAATTAAATATAT-GAT
1 CATGCAATTAAATATATAAAT
*
1335644 CATGCAAAT-AATAATATAAAT
1 CATGCAATTAAAT-ATATAAAT
1335665 CATGCAATTAAATATATAA
1 CATGCAATTAAATATATAA
1335684 TAATGGAAAT
Statistics
Matches: 63, Mismatches: 12, Indels: 11
0.73 0.14 0.13
Matches are distributed among these distances:
19 3 0.05
20 26 0.41
21 31 0.49
22 3 0.05
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.32
Consensus pattern (21 bp):
CATGCAATTAAATATATAAAT
Found at i:1335698 original size:73 final size:77
Alignment explanation
Indices: 1335621--1335818 Score: 231
Period size: 73 Copynumber: 2.7 Consensus size: 77
1335611 TAACAATGTA
* *
1335621 AAACATACAATTAAATATATGATCATGCAAAT-AATA-A-T-ATAAATCATGCAATTAAATATA-
1 AAACATACAATTAAATATATAATCATGCAAATAAATATATTAAT-AATCAAGCAATTAAATATAT
1335681 TAATAATGGAAAT
65 TAATAATGGAAAT
*
1335694 AAACATACAATTAAATATATAATCGTGCAAATAAATATATTAATAATCAAGCAATTAAATATATT
1 AAACATACAATTAAATATATAATCATGCAAATAAATATATTAATAATCAAGCAATTAAATATATT
*
1335759 AATAAT---TAT
66 AATAATGGAAAT
* * *
1335768 ACA-AT-CGAATT-AA-ATATAATCATACAAATAAATATATTAATAATCATGCAA
1 AAACATAC-AATTAAATATATAATCATGCAAATAAATATATTAATAATCAAGCAA
1335819 ATATATTAAT
Statistics
Matches: 111, Mismatches: 8, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
71 35 0.32
72 3 0.03
73 36 0.32
74 8 0.07
75 1 0.01
76 19 0.17
77 9 0.08
ACGTcount: A:0.55, C:0.09, G:0.05, T:0.31
Consensus pattern (77 bp):
AAACATACAATTAAATATATAATCATGCAAATAAATATATTAATAATCAAGCAATTAAATATATT
AATAATGGAAAT
Found at i:1335726 original size:32 final size:33
Alignment explanation
Indices: 1335659--1335729 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 33
1335649 AAATAATAAT
* *
1335659 ATAAATCATGCAATTAAATATATAATAATGGAA
1 ATAAATCATACAATTAAATATATAATAATGCAA
**
1335692 ATAAA-CATACAATTAAATATATAATCGTGCAA
1 ATAAATCATACAATTAAATATATAATAATGCAA
1335724 ATAAAT
1 ATAAAT
1335730 ATATTAATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 28 0.85
33 5 0.15
ACGTcount: A:0.55, C:0.08, G:0.07, T:0.30
Consensus pattern (33 bp):
ATAAATCATACAATTAAATATATAATAATGCAA
Found at i:1335739 original size:24 final size:24
Alignment explanation
Indices: 1335712--1335872 Score: 135
Period size: 24 Copynumber: 7.0 Consensus size: 24
1335702 AATTAAATAT
*
1335712 ATAATCGTGCAAATAAATATATTA
1 ATAATCATGCAAATAAATATATTA
* *
1335736 ATAATCAAGCAATTAAATATATTA
1 ATAATCATGCAAATAAATATATTA
* * * *
1335760 ATAATTATAC-AATCGAAT-TA-AA
1 ATAATCATGCAAAT-AAATATATTA
*
1335782 TATAATCATACAAATAAATATATTA
1 -ATAATCATGCAAATAAATATATTA
1335807 ATAATCATGC----AAATATATTA
1 ATAATCATGCAAATAAATATATTA
**
1335827 ATAAATCACACAAATAAATATA-T-
1 AT-AATCATGCAAATAAATATATTA
1335850 -TAATCATGCAAATAAATATATTA
1 ATAATCATGCAAATAAATATATTA
1335873 GACAAATAAA
Statistics
Matches: 108, Mismatches: 17, Indels: 25
0.72 0.11 0.17
Matches are distributed among these distances:
20 12 0.11
21 23 0.21
22 3 0.03
23 16 0.15
24 46 0.43
25 8 0.07
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.33
Consensus pattern (24 bp):
ATAATCATGCAAATAAATATATTA
Found at i:1335801 original size:47 final size:45
Alignment explanation
Indices: 1335726--1335872 Score: 142
Period size: 47 Copynumber: 3.2 Consensus size: 45
1335716 TCGTGCAAAT
* *
1335726 AAATATATT-A-ATAATCAAGCAATTAAATATATTAATAATTATAC
1 AAATATATTAATATAATCAA-CAAATAAATATATTAATAATCATAC
*
1335770 -AATCGA-ATTAAATATAATCATACAAATAAATATATTAATAATCATGC
1 AAAT--ATATT-AATATAATCA-ACAAATAAATATATTAATAATCATAC
* * *
1335817 AAATATATTAATA-AATCACACAAATAAATATATTAATCATGCAAAT
1 AAATATATTAATATAATCA-ACAAATAAATATATTAATAAT-CATAC
1335863 AAATATATTA
1 AAATATATTA
1335873 GACAAATAAA
Statistics
Matches: 86, Mismatches: 8, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
43 3 0.03
44 3 0.03
45 26 0.30
46 18 0.21
47 32 0.37
48 4 0.05
ACGTcount: A:0.55, C:0.09, G:0.03, T:0.33
Consensus pattern (45 bp):
AAATATATTAATATAATCAACAAATAAATATATTAATAATCATAC
Found at i:1335840 original size:21 final size:20
Alignment explanation
Indices: 1335797--1335842 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
1335787 TCATACAAAT
**
1335797 AAATATATTAATAATCATGC
1 AAATATATTAATAATCACAC
1335817 AAATATATTAATAAATCACAC
1 AAATATATTAAT-AATCACAC
1335838 AAATA
1 AAATA
1335843 AATATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (20 bp):
AAATATATTAATAATCACAC
Found at i:1335854 original size:21 final size:21
Alignment explanation
Indices: 1335784--1335872 Score: 81
Period size: 21 Copynumber: 4.1 Consensus size: 21
1335774 GAATTAAATA
*
1335784 TAATCATACAAATAAATATAT
1 TAATCACACAAATAAATATAT
* *
1335805 TAATAATCATGCAAATATAT-TAAT
1 TAATCA-CA--CAAATAAATAT-AT
*
1335829 AAATCACACAAATAAATATAT
1 TAATCACACAAATAAATATAT
**
1335850 TAATCATGCAAATAAATATAT
1 TAATCACACAAATAAATATAT
1335871 TA
1 TA
1335873 GACAAATAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
21 35 0.65
22 2 0.04
23 3 0.06
24 14 0.26
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (21 bp):
TAATCACACAAATAAATATAT
Found at i:1335881 original size:71 final size:67
Alignment explanation
Indices: 1335691--1335872 Score: 178
Period size: 66 Copynumber: 2.7 Consensus size: 67
1335681 TAATAATGGA
* * * *
1335691 AATAAA-CATACAATTAAATATATAATCGTGCAAATAAATATATTAATAATCAAGCAATTAAATA
1 AATAAATCACACAAATAAATATATAATCATGCAAATAAATATATTAA-AAT-AAGCAATCAAATA
1335755 TATT
64 TATT
* * * *
1335759 AATAATTAT-ACAATCGAATTAA-ATATAATCATACAAATAAATATATT--AATAATC-ATGCAA
1 AATAA--ATCAC-A-CAAATAAATATATAATCATGCAAATAAATATATTAAAATAAGCAAT-CAA
1335819 ATATATT
61 ATATATT
1335826 AATAAATCACACAAATAAATATATTAATCATGCAAATAAATATATTA
1 AATAAATCACACAAATAAATATA-TAATCATGCAAATAAATATATTA
1335873 GACAAATAAA
Statistics
Matches: 93, Mismatches: 11, Indels: 21
0.74 0.09 0.17
Matches are distributed among these distances:
64 6 0.06
65 6 0.06
66 25 0.27
67 17 0.18
68 8 0.09
70 2 0.02
71 24 0.26
72 5 0.05
ACGTcount: A:0.55, C:0.09, G:0.03, T:0.32
Consensus pattern (67 bp):
AATAAATCACACAAATAAATATATAATCATGCAAATAAATATATTAAAATAAGCAATCAAATATA
TT
Found at i:1336543 original size:12 final size:13
Alignment explanation
Indices: 1336526--1336561 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
1336516 ACTTAAAAAA
1336526 CAAAAATTAAAC-
1 CAAAAATTAAACT
1336538 CAAAAATTAAACT
1 CAAAAATTAAACT
*
1336551 AAAAAATTAAA
1 CAAAAATTAAA
1336562 ATATAAATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.69, C:0.11, G:0.00, T:0.19
Consensus pattern (13 bp):
CAAAAATTAAACT
Found at i:1337149 original size:133 final size:132
Alignment explanation
Indices: 1336915--1337224 Score: 345
Period size: 133 Copynumber: 2.4 Consensus size: 132
1336905 AACTTTTTGA
* * * * * *
1336915 AAAATAAAATGCTCCCCCATAACTA-AGACTTTGGAACTTTGGAAAAATAAA---ATTCTCCCCC
1 AAAATAAAATGCTCCCCCACAA-TAGAGGCTTTGAAACTTTTGAAAAATAAATGTATTC-CCACA
* ** *
1336976 AC-AA---TTGAGGCTTTGAAACTTTGAAAAATAAAATGTTCCCCCGTAATTGAGGCTTT-AGAA
64 ACTAAGGCTTGAGGATTTGAAACTTTGAAAAATAAAATGTTCCCCCACAACTGAGGCTTTGA-AA
*
1337036 CTTTTG
128 C-TTCG
* * * *
1337042 AAAATAAAATGCT-CCCTATGACTAG-GGCTTTGAAACTTTTGAAAATTAAATGTATTCCCACAA
1 AAAATAAAATGCTCCCCCA-CAATAGAGGCTTTGAAACTTTTGAAAAATAAATGTATTCCCACAA
1337105 CTAAGGCTTGAGGATTTGAAACTTTTGAAAAATAAAATGTTCCCCCACAACTGAGGCTTTGAAAC
65 CTAAGGCTTGAGGATTTGAAAC-TTTGAAAAATAAAATGTTCCCCCACAACTGAGGCTTTGAAAC
1337170 TTCG
129 TTCG
*
1337174 AAAATAAAATGCTCCCCCACAATTGAGGCTTTGAAACTTTTGAAAAATAAA
1 AAAATAAAATGCTCCCCCACAATAGAGGCTTTGAAACTTTTGAAAAATAAA
1337225 ATGAGATCAT
Statistics
Matches: 151, Mismatches: 19, Indels: 20
0.79 0.10 0.11
Matches are distributed among these distances:
126 27 0.18
127 14 0.09
128 5 0.03
129 6 0.04
132 33 0.22
133 65 0.43
134 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.29
Consensus pattern (132 bp):
AAAATAAAATGCTCCCCCACAATAGAGGCTTTGAAACTTTTGAAAAATAAATGTATTCCCACAAC
TAAGGCTTGAGGATTTGAAACTTTGAAAAATAAAATGTTCCCCCACAACTGAGGCTTTGAAACTT
CG
Found at i:1337153 original size:50 final size:49
Alignment explanation
Indices: 1337070--1337227 Score: 139
Period size: 41 Copynumber: 3.5 Consensus size: 49
1337060 TGACTAGGGC
* *
1337070 TTTGAAACTTTTGAAAATTAAATGTATTCCCACAACTAAGGCTTGAGGA
1 TTTGAAACTTTTGAAAATAAAATGTATCCCCACAACTAAGGCTTGAGGA
*
1337119 TTTGAAACTTTTGAAAAATAAAATGT-TCCCC-C-AC-AA--C-TGAGGC
1 TTTGAAACTTTTG-AAAATAAAATGTATCCCCACAACTAAGGCTTGAGGA
* * *
1337162 TTTGAAAC-TTCGAAAATAAAATG-CTCCCC-C-AC-AA---TTGAGGC
1 TTTGAAACTTTTGAAAATAAAATGTATCCCCACAACTAAGGCTTGAGGA
1337203 TTTGAAACTTTTGAAAAATAAAATG
1 TTTGAAACTTTTG-AAAATAAAATG
1337228 AGATCATTCT
Statistics
Matches: 99, Mismatches: 5, Indels: 16
0.82 0.04 0.13
Matches are distributed among these distances:
41 35 0.35
42 6 0.06
43 24 0.24
44 1 0.01
46 2 0.02
47 2 0.02
48 1 0.01
49 17 0.17
50 11 0.11
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.30
Consensus pattern (49 bp):
TTTGAAACTTTTGAAAATAAAATGTATCCCCACAACTAAGGCTTGAGGA
Found at i:1337190 original size:41 final size:43
Alignment explanation
Indices: 1336812--1337227 Score: 368
Period size: 43 Copynumber: 9.7 Consensus size: 43
1336802 TCTTCGATAA
* * *
1336812 AGGC-TTGAAACTTTTG-AAAATAAAATGCTTCCCCACAATTT
1 AGGCTTTGAAACTTTTGAAAAATAAAATGCTCCCCCACAACTG
* * * * *
1336853 AGGGC-TTCATACTTTTGAAAAATAAAATGCTCTCCCATAACTC
1 A-GGCTTTGAAACTTTTGAAAAATAAAATGCTCCCCCACAACTG
* * * * *
1336896 ATGCCTTAAAACTTTTTGAAAAATAAAATGCTCCCCCATAACTA
1 AGGCTTTGAAAC-TTTTGAAAAATAAAATGCTCCCCCACAACTG
* * * * *
1336940 AGACTTTGGAACTTTGGAAAAATAAAATTCTCCCCCACAATTG
1 AGGCTTTGAAACTTTTGAAAAATAAAATGCTCCCCCACAACTG
* ** *
1336983 AGGCTTTGAAAC-TTTGAAAAATAAAATGTTCCCCCGTAATTG
1 AGGCTTTGAAACTTTTGAAAAATAAAATGCTCCCCCACAACTG
* **
1337025 AGGCTTT-AGAACTTTTG-AAAATAAAATGCT-CCCTATGACT-
1 AGGCTTTGA-AACTTTTGAAAAATAAAATGCTCCCCCACAACTG
* * *
1337065 AGGGCTTTGAAACTTTTG-AAAATTAAATGTATTCCCACAACTAAGGCTTG
1 A-GGCTTTGAAACTTTTGAAAAATAAAATG--CTCCC-CCAC-AA--C-TG
* *
1337115 AGGATTTGAAACTTTTGAAAAATAAAATGTTCCCCCACAACTG
1 AGGCTTTGAAACTTTTGAAAAATAAAATGCTCCCCCACAACTG
* *
1337158 AGGCTTTGAAAC-TTCG-AAAATAAAATGCTCCCCCACAATTG
1 AGGCTTTGAAACTTTTGAAAAATAAAATGCTCCCCCACAACTG
1337199 AGGCTTTGAAACTTTTGAAAAATAAAATG
1 AGGCTTTGAAACTTTTGAAAAATAAAATG
1337228 AGATCATTCT
Statistics
Matches: 308, Mismatches: 47, Indels: 38
0.78 0.12 0.10
Matches are distributed among these distances:
40 1 0.00
41 67 0.22
42 69 0.22
43 91 0.30
44 39 0.13
45 2 0.01
46 3 0.01
47 3 0.01
48 6 0.02
49 16 0.05
50 11 0.04
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (43 bp):
AGGCTTTGAAACTTTTGAAAAATAAAATGCTCCCCCACAACTG
Found at i:1344629 original size:14 final size:14
Alignment explanation
Indices: 1344610--1344651 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1344600 CATGCCTAGA
1344610 TCATGCTAAAATAT
1 TCATGCTAAAATAT
*
1344624 TCATGCAAAAATA-
1 TCATGCTAAAATAT
1344637 TCATG-TAAATATAT
1 TCATGCTAAA-ATAT
1344651 T
1 T
1344652 AATTATCATG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 3 0.12
13 8 0.33
14 13 0.54
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.36
Consensus pattern (14 bp):
TCATGCTAAAATAT
Found at i:1344660 original size:20 final size:18
Alignment explanation
Indices: 1344633--1344744 Score: 81
Period size: 18 Copynumber: 6.2 Consensus size: 18
1344623 TTCATGCAAA
1344633 AATATCATGTAAATATATT
1 AATATCATGTAAATATA-T
*
1344652 AATTATCATG-CAATA-AT
1 AA-TATCATGTAAATATAT
*
1344669 AATATTCATATAAATATAT
1 AATA-TCATGTAAATATAT
*
1344688 AAAATCATGTAAATATAT
1 AATATCATGTAAATATAT
*
1344706 --TATCATG-CAATAATAT
1 AATATCATGTAAAT-ATAT
* *
1344722 AAAATGCCATGCAAATATAT
1 AATAT--CATGTAAATATAT
1344742 AAT
1 AAT
1344745 CATTAAATCA
Statistics
Matches: 73, Mismatches: 10, Indels: 19
0.72 0.10 0.19
Matches are distributed among these distances:
15 3 0.04
16 12 0.16
17 7 0.10
18 20 0.27
19 11 0.15
20 17 0.23
21 3 0.04
ACGTcount: A:0.50, C:0.09, G:0.05, T:0.36
Consensus pattern (18 bp):
AATATCATGTAAATATAT
Found at i:1344720 original size:18 final size:18
Alignment explanation
Indices: 1344653--1344722 Score: 51
Period size: 16 Copynumber: 4.1 Consensus size: 18
1344643 AAATATATTA
1344653 ATTATCATGCAATAATAAT
1 ATTATCATGCAATAAT-AT
*
1344672 ATTCAT-AT-AAAT-ATAT
1 ATT-ATCATGCAATAATAT
** *
1344688 AAAATCATG-TA-AATAT
1 ATTATCATGCAATAATAT
1344704 ATTATCATGCAATAATAT
1 ATTATCATGCAATAATAT
1344722 A
1 A
1344723 AAATGCCATG
Statistics
Matches: 38, Mismatches: 7, Indels: 13
0.66 0.12 0.22
Matches are distributed among these distances:
15 2 0.05
16 17 0.45
17 3 0.08
18 9 0.24
19 5 0.13
20 2 0.05
ACGTcount: A:0.50, C:0.09, G:0.04, T:0.37
Consensus pattern (18 bp):
ATTATCATGCAATAATAT
Found at i:1344891 original size:25 final size:24
Alignment explanation
Indices: 1344847--1344893 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
1344837 ATCATTCAAC
*
1344847 TATAATATTAATCATCCAATAACA
1 TATAATATCAATCATCCAATAACA
*
1344871 TATAATATCATATCATGCAATAA
1 TATAATATCA-ATCATCCAATAA
1344894 AATAAAATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.49, C:0.15, G:0.02, T:0.34
Consensus pattern (24 bp):
TATAATATCAATCATCCAATAACA
Found at i:1344893 original size:18 final size:18
Alignment explanation
Indices: 1344872--1344913 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1344862 CCAATAACAT
* *
1344872 ATAATATCATATCATGCA
1 ATAATATAAAATCATGCA
*
1344890 ATAAAATAAAATCATGCA
1 ATAATATAAAATCATGCA
1344908 ATAATA
1 ATAATA
1344914 ATAATAAATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.55, C:0.12, G:0.05, T:0.29
Consensus pattern (18 bp):
ATAATATAAAATCATGCA
Found at i:1344922 original size:21 final size:18
Alignment explanation
Indices: 1344882--1344917 Score: 63
Period size: 18 Copynumber: 1.9 Consensus size: 18
1344872 ATAATATCAT
1344882 ATCATGCAATAAAATAAA
1 ATCATGCAATAAAATAAA
1344900 ATCATGCAATAATAATAA
1 ATCATGCAATAA-AATAA
1344918 TAAATAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.58, C:0.11, G:0.06, T:0.25
Consensus pattern (18 bp):
ATCATGCAATAAAATAAA
Done.