Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007776.1 Hibiscus syriacus cultivar Beakdansim tig00110057_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2207776
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 11
Found at i:1355319 original size:22 final size:22
Alignment explanation
Indices: 1355293--1355352 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
1355283 TAAGGAGAGG
1355293 TAAATAACATATATAATATATA
1 TAAATAACATATATAATATATA
*
1355315 TAAATAACATATATATTATATA
1 TAAATAACATATATAATATATA
*
1355337 TAAGATAATATATATA
1 TAA-ATAACATATATA
1355353 TATTTTATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 24 0.69
23 11 0.31
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (22 bp):
TAAATAACATATATAATATATA
Found at i:1356474 original size:42 final size:43
Alignment explanation
Indices: 1356394--1356491 Score: 144
Period size: 42 Copynumber: 2.3 Consensus size: 43
1356384 ATGTATAATT
* * *
1356394 GGTACGATAACGTCTGTCGTGGAGTTGAAATCATGGATTTGTG
1 GGTACGATATCCTCTGTCGTGGAGTTAAAATCATGGATTTGTG
*
1356437 GGTACGATATCCTCTGTCGT-GAGTTAAAATCGTGGATTTGTG
1 GGTACGATATCCTCTGTCGTGGAGTTAAAATCATGGATTTGTG
*
1356479 GGTATGATATCCT
1 GGTACGATATCCT
1356492 TCATCATGGA
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
42 32 0.64
43 18 0.36
ACGTcount: A:0.22, C:0.13, G:0.30, T:0.35
Consensus pattern (43 bp):
GGTACGATATCCTCTGTCGTGGAGTTAAAATCATGGATTTGTG
Found at i:1357490 original size:8 final size:7
Alignment explanation
Indices: 1357462--1357508 Score: 53
Period size: 7 Copynumber: 6.7 Consensus size: 7
1357452 AACCACCTTA
1357462 TTTTTCT
1 TTTTTCT
*
1357469 TTTCTCT
1 TTTTTCT
1357476 TTTTTCT
1 TTTTTCT
1357483 TTTGTTCT
1 TTT-TTCT
1357491 TTTTT-T
1 TTTTTCT
1357497 TTCTTT-T
1 TT-TTTCT
1357504 TTTTT
1 TTTTT
1357509 AATTTAGGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
6 6 0.17
7 23 0.64
8 7 0.19
ACGTcount: A:0.00, C:0.13, G:0.02, T:0.85
Consensus pattern (7 bp):
TTTTTCT
Found at i:1357556 original size:78 final size:78
Alignment explanation
Indices: 1357468--1357619 Score: 209
Period size: 78 Copynumber: 1.9 Consensus size: 78
1357458 CTTATTTTTC
* * * ** *
1357468 TTTTCTCTTTTTTCTTTTGTTCTTTTTTTTTCTTTT-TTTTT-AATTTAGGGTGCCCTTTCGGGT
1 TTTTCTCTTTTTT-TTTTCTT-TTCTTTTTTCTTTTCTTTTTCAACTTAGGACGCCCTCTCGGGT
1357531 TTTCACCCTAAACGT
64 TTTCACCCTAAACGT
1357546 TTTTCTCTTTTTTTTTTCTTTTCTTTTTTCTTTTCTTTTTCAACTTAGGACGCCCTCTCGGGTTT
1 TTTTCTCTTTTTTTTTTCTTTTCTTTTTTCTTTTCTTTTTCAACTTAGGACGCCCTCTCGGGTTT
*
1357611 TCATCCTAA
66 TCACCCTAA
1357620 GCAACTTATT
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
76 13 0.20
77 11 0.17
78 41 0.63
ACGTcount: A:0.09, C:0.20, G:0.10, T:0.61
Consensus pattern (78 bp):
TTTTCTCTTTTTTTTTTCTTTTCTTTTTTCTTTTCTTTTTCAACTTAGGACGCCCTCTCGGGTTT
TCACCCTAAACGT
Found at i:1357565 original size:11 final size:11
Alignment explanation
Indices: 1357545--1357586 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
1357535 ACCCTAAACG
*
1357545 TTTTTCTCTTT
1 TTTTTTTCTTT
1357556 TTTTTTTCTTT
1 TTTTTTTCTTT
1357567 TCTTTTTTCTTT
1 T-TTTTTTCTTT
*
1357579 TCTTTTTC
1 TTTTTTTC
1357587 AACTTAGGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 17 0.61
12 11 0.39
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:1357572 original size:12 final size:12
Alignment explanation
Indices: 1357545--1357585 Score: 66
Period size: 12 Copynumber: 3.4 Consensus size: 12
1357535 ACCCTAAACG
1357545 TTTTTCTCTTTT-
1 TTTTT-TCTTTTC
1357557 TTTTTTCTTTTC
1 TTTTTTCTTTTC
1357569 TTTTTTCTTTTC
1 TTTTTTCTTTTC
1357581 TTTTT
1 TTTTT
1357586 CAACTTAGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 6 0.21
12 22 0.79
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTTCTTTTC
Found at i:1357579 original size:17 final size:16
Alignment explanation
Indices: 1357551--1357584 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
1357541 AACGTTTTTC
1357551 TCTTTTTTTTTTCTTT
1 TCTTTTTTTTTTCTTT
1357567 TCTTTTTTCTTTTCTTT
1 TCTTTTTT-TTTTCTTT
1357584 T
1 T
1357585 TCAACTTAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (16 bp):
TCTTTTTTTTTTCTTT
Found at i:1366882 original size:17 final size:15
Alignment explanation
Indices: 1366774--1366898 Score: 78
Period size: 17 Copynumber: 8.1 Consensus size: 15
1366764 AATGTGTTGG
1366774 AAAA-AAATGAAAATA
1 AAAATAAAT-AAAATA
*
1366789 AATAATAAAGAAAATA
1 AA-AATAAATAAAATA
* *
1366805 AAAAAACGAATGAAATA
1 AAAATA--AATAAAATA
* *
1366822 AAGA-AAATAATAT-
1 AAAATAAATAAAATA
*
1366835 AAAATAAAGAAAATA
1 AAAATAAATAAAATA
* *
1366850 AATTATTAA-AAAATA
1 AA-AATAAATAAAATA
1366865 AAAATAAAGTAAAGATA
1 AAAATAAA-TAAA-ATA
*
1366882 AAAATGAATAAAATA
1 AAAATAAATAAAATA
1366897 AA
1 AA
1366899 TAAAATGAAG
Statistics
Matches: 85, Mismatches: 15, Indels: 20
0.71 0.12 0.17
Matches are distributed among these distances:
13 3 0.04
14 17 0.20
15 20 0.24
16 22 0.26
17 23 0.27
ACGTcount: A:0.74, C:0.01, G:0.07, T:0.18
Consensus pattern (15 bp):
AAAATAAATAAAATA
Found at i:1366900 original size:9 final size:9
Alignment explanation
Indices: 1366774--1366904 Score: 71
Period size: 9 Copynumber: 14.6 Consensus size: 9
1366764 AATGTGTTGG
1366774 AAAA-AAAT
1 AAAATAAAT
1366782 GAAAATAAAT
1 -AAAATAAAT
*
1366792 --AATAAAG
1 AAAATAAAT
1366799 AAAATAAA-
1 AAAATAAAT
**
1366807 AAAACGAAT
1 AAAATAAAT
* *
1366816 GAAATAAAG
1 AAAATAAAT
1366825 AAAATAATAT
1 AAAATAA-AT
*
1366835 AAAATAAAG
1 AAAATAAAT
1366844 AAAATAAATT
1 AAAATAAA-T
1366854 ATTAAA-AAAT
1 A--AAATAAAT
1366864 AAAAATAAAGT
1 -AAAATAAA-T
1366875 AAAGAT--A-
1 AAA-ATAAAT
*
1366882 AAAATGAAT
1 AAAATAAAT
1366891 AAAATAAAT
1 AAAATAAAT
1366900 AAAAT
1 AAAAT
1366905 GAAGAAAGAT
Statistics
Matches: 95, Mismatches: 12, Indels: 30
0.69 0.09 0.22
Matches are distributed among these distances:
6 2 0.02
7 9 0.09
8 7 0.07
9 47 0.49
10 20 0.21
11 7 0.07
12 3 0.03
ACGTcount: A:0.73, C:0.01, G:0.07, T:0.19
Consensus pattern (9 bp):
AAAATAAAT
Found at i:1366918 original size:18 final size:18
Alignment explanation
Indices: 1366865--1366919 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
1366855 TTAAAAAATA
*
1366865 AAAATAAAGTAAAGAT-A-
1 AAAATGAAG-AAAGATAAT
*
1366882 AAAATGAATAAA-ATAAAT
1 AAAATGAAGAAAGAT-AAT
1366900 AAAATGAAGAAAGATAAT
1 AAAATGAAGAAAGATAAT
1366918 AA
1 AA
1366920 TAATAATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
15 2 0.06
16 3 0.10
17 8 0.26
18 16 0.52
19 2 0.06
ACGTcount: A:0.71, C:0.00, G:0.11, T:0.18
Consensus pattern (18 bp):
AAAATGAAGAAAGATAAT
Found at i:1367067 original size:3 final size:3
Alignment explanation
Indices: 1367059--1367086 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1367049 AAAATAGAAA
1367059 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1367087 TAAAATAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1367167 original size:26 final size:25
Alignment explanation
Indices: 1367138--1367193 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
1367128 TAAAATAGGA
* *
1367138 AATATAATAATTATATATATATATAT
1 AATATAATAATGATA-AAATATATAT
*
1367164 AATAATACTAATGATAAAATATATAT
1 AAT-ATAATAATGATAAAATATATAT
1367190 AATA
1 AATA
1367194 AAATTAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 1 0.04
26 15 0.58
27 10 0.38
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (25 bp):
AATATAATAATGATAAAATATATAT
Found at i:1368215 original size:2 final size:2
Alignment explanation
Indices: 1368203--1368256 Score: 55
Period size: 2 Copynumber: 29.5 Consensus size: 2
1368193 TGTAAATAAC
* *
1368203 AT AT AT A- AT AT AT AT AT A- AC AT AT AA AT -T AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1368241 AT A- AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
1368257 GTTATTTATG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
1 5 0.11
2 39 0.89
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1368215 original size:7 final size:7
Alignment explanation
Indices: 1368203--1368256 Score: 53
Period size: 7 Copynumber: 8.0 Consensus size: 7
1368193 TGTAAATAAC
1368203 ATATATA
1 ATATATA
1368210 ATATAT-
1 ATATATA
1368216 ATATA-A
1 ATATATA
1368222 CATATA-A
1 -ATATATA
1368229 ATTATATA
1 A-TATATA
*
1368237 TTATATA
1 ATATATA
1368244 ATATAT-
1 ATATATA
1368250 ATATATA
1 ATATATA
1368257 GTTATTTATG
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
6 12 0.30
7 27 0.68
8 1 0.03
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (7 bp):
ATATATA
Found at i:1369141 original size:30 final size:30
Alignment explanation
Indices: 1369096--1369183 Score: 131
Period size: 30 Copynumber: 2.9 Consensus size: 30
1369086 CTATTAATTT
* *
1369096 TTCATCGATAGATGATTAAAATAAAAACAC
1 TTCAACGAAAGATGATTAAAATAAAAACAC
*
1369126 TTCAACGAAAGATGATTTAAATAAAAACAC
1 TTCAACGAAAGATGATTAAAATAAAAACAC
* *
1369156 TTCAACGAAAGATGATCAAAACAAAAAC
1 TTCAACGAAAGATGATTAAAATAAAAAC
1369184 GTTGAATATG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.53, C:0.15, G:0.10, T:0.22
Consensus pattern (30 bp):
TTCAACGAAAGATGATTAAAATAAAAACAC
Found at i:1373489 original size:8 final size:8
Alignment explanation
Indices: 1373478--1373507 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
1373468 TTGTTTTTTG
1373478 TTTTAAAT
1 TTTTAAAT
1373486 TTTTAAATT
1 TTTTAAA-T
1373495 TTTTAAAT
1 TTTTAAAT
1373503 TTTTA
1 TTTTA
1373508 TAACTCTGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TTTTAAAT
Found at i:1373499 original size:9 final size:9
Alignment explanation
Indices: 1373478--1373506 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1373468 TTGTTTTTTG
1373478 TTTTAAA-T
1 TTTTAAATT
1373486 TTTTAAATT
1 TTTTAAATT
1373495 TTTTAAATT
1 TTTTAAATT
1373504 TTT
1 TTT
1373507 ATAACTCTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 7 0.35
9 13 0.65
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
TTTTAAATT
Found at i:1375106 original size:48 final size:48
Alignment explanation
Indices: 1375051--1375145 Score: 172
Period size: 48 Copynumber: 2.0 Consensus size: 48
1375041 TATCTATGAA
*
1375051 TTTTACTATGTTAATTTATTAATCAAAAGTTAGTTTTAATTTCCACCT
1 TTTTACTATGTTAATTTATTAATCAAAAGTTAGTTTTAACTTCCACCT
*
1375099 TTTTACTATGTTATTTTATTAATCAAAAGTTAGTTTTAACTTCCACC
1 TTTTACTATGTTAATTTATTAATCAAAAGTTAGTTTTAACTTCCACC
1375146 CTTTATCATT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.31, C:0.14, G:0.06, T:0.49
Consensus pattern (48 bp):
TTTTACTATGTTAATTTATTAATCAAAAGTTAGTTTTAACTTCCACCT
Found at i:1376879 original size:38 final size:38
Alignment explanation
Indices: 1376828--1376903 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
1376818 TTTTTCTTAC
1376828 AAACGCCGCAATAGGTGTGGACATTTA-GCGGCGTTTGT
1 AAACGCCGCAATAGGTGTGGACA-TTACGCGGCGTTTGT
* *
1376866 AAACGCCGCAATAGGTTTTGACATTACGCGGCGTTTGT
1 AAACGCCGCAATAGGTGTGGACATTACGCGGCGTTTGT
1376904 CTTACCAACG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 3 0.09
38 32 0.91
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.28
Consensus pattern (38 bp):
AAACGCCGCAATAGGTGTGGACATTACGCGGCGTTTGT
Found at i:1376940 original size:43 final size:40
Alignment explanation
Indices: 1376822--1376941 Score: 113
Period size: 38 Copynumber: 2.9 Consensus size: 40
1376812 GCGGTATTTT
*
1376822 TCTTACAAACGCCGCAATAGGTGTGGACATTTAGCGGCGTTTG
1 TCTTAC-AACGCCGCAATAGGTTTGG-CA-TTAGCGGCGTTTG
*
1376865 ---TA-AACGCCGCAATAGGTTTTGACATTACGCGGCGTTTG
1 TCTTACAACGCCGCAATAGG-TTTGGCATTA-GCGGCGTTTG
*
1376903 TCTTACCAACGCCGCAATAGGATTTGGTATATAGCGGCG
1 TCTTA-CAACGCCGCAATAGG-TTTGGCAT-TAGCGGCG
1376942 GTTTTAGGAT
Statistics
Matches: 64, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
37 3 0.05
38 26 0.41
39 3 0.05
40 2 0.03
41 2 0.03
43 26 0.41
44 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.28
Consensus pattern (40 bp):
TCTTACAACGCCGCAATAGGTTTGGCATTAGCGGCGTTTG
Found at i:1377132 original size:44 final size:43
Alignment explanation
Indices: 1377083--1377183 Score: 125
Period size: 43 Copynumber: 2.3 Consensus size: 43
1377073 TTGTAACAAA
* * *
1377083 AAACGCCGCTATGGATGT-TAATATTTTGCTGCGTTTTTTGAT-AC
1 AAACGCCGCTA--AATGTCTAATATATTGCAGCGTTTTTT-ATGAC
*
1377127 AAACGCCGCTAAATGTCTTATATATTGCAGCGTTTTTTATGAC
1 AAACGCCGCTAAATGTCTAATATATTGCAGCGTTTTTTATGAC
1377170 AAACGCCGCTAAAT
1 AAACGCCGCTAAAT
1377184 AACACATAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
42 6 0.12
43 34 0.67
44 11 0.22
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.36
Consensus pattern (43 bp):
AAACGCCGCTAAATGTCTAATATATTGCAGCGTTTTTTATGAC
Found at i:1383880 original size:22 final size:22
Alignment explanation
Indices: 1383855--1383900 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
1383845 ACATTTTCAG
*
1383855 AAGCTATTATTTTCCTATTCGA
1 AAGCAATTATTTTCCTATTCGA
*
1383877 AAGCAATTATTTTTCTATTCGA
1 AAGCAATTATTTTCCTATTCGA
1383899 AA
1 AA
1383901 AAAAACACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.43
Consensus pattern (22 bp):
AAGCAATTATTTTCCTATTCGA
Found at i:1385270 original size:30 final size:30
Alignment explanation
Indices: 1385236--1385312 Score: 77
Period size: 30 Copynumber: 2.6 Consensus size: 30
1385226 AAATGGATTT
* *
1385236 AGTTTAGTGA-TCAAATTATAAGATTTTG-AA
1 AGTTTAGTGACT-AAAGTATAA-ACTTTGAAA
*
1385266 AGTTTGGTGACTAAAGTATAAACTTTGAAA
1 AGTTTAGTGACTAAAGTATAAACTTTGAAA
* *
1385296 AGTTTAGGGACCAAAGT
1 AGTTTAGTGACTAAAGT
1385313 GTAATTTTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
29 5 0.13
30 33 0.85
31 1 0.03
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.34
Consensus pattern (30 bp):
AGTTTAGTGACTAAAGTATAAACTTTGAAA
Found at i:1386986 original size:18 final size:18
Alignment explanation
Indices: 1386963--1386998 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1386953 ATTCCATTAC
1386963 TGGAATTTCTTGAATTTA
1 TGGAATTTCTTGAATTTA
* *
1386981 TGGAATTTTTTGTATTTA
1 TGGAATTTCTTGAATTTA
1386999 AAATTTAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.03, G:0.17, T:0.56
Consensus pattern (18 bp):
TGGAATTTCTTGAATTTA
Found at i:1388116 original size:38 final size:38
Alignment explanation
Indices: 1388028--1388123 Score: 131
Period size: 38 Copynumber: 2.5 Consensus size: 38
1388018 TATAAGACAT
* *
1388028 ATGATAGGTCC-TAAGGGACACAGATTACATCCTTCGGG
1 ATGATAGGTCCTTCA-GGACACAGATGACATCCTTCGGG
* *
1388066 ATGACAGGTCCTTCAGGACACAGATGACATCCTTTGGG
1 ATGATAGGTCCTTCAGGACACAGATGACATCCTTCGGG
*
1388104 ATGATAGGTCCTTCGGGACA
1 ATGATAGGTCCTTCAGGACA
1388124 TTTATACGAG
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
38 49 0.96
39 2 0.04
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (38 bp):
ATGATAGGTCCTTCAGGACACAGATGACATCCTTCGGG
Found at i:1389257 original size:41 final size:40
Alignment explanation
Indices: 1389196--1389429 Score: 173
Period size: 41 Copynumber: 5.8 Consensus size: 40
1389186 AACTTTAGCG
* *
1389196 GCGTTTTT-TCAACAAACGCCGCAATAGGGTGGTAATTTAGCT
1 GCGTTTTTAT-AA-AAACGCCGCAATAGAGTTGTAATTTAG-T
*
1389238 GCGTTTTTATATAAACGCCGCAATAGAGTTGT--TTATAGT
1 GCGTTTTTATAAAAACGCCGCAATAGAGTTGTAATT-TAGT
* * * *
1389277 GACGTTTTCTAAAAAAACACCGCAATAGAGTAGTAATTTAGCG
1 G-CGTTTT-TATAAAAACGCCGCAATAGAGTTGTAATTTAG-T
1389320 GCG--TTTATAAAAACGCCGCAATAGAGTTGT--TTATAGT
1 GCGTTTTTATAAAAACGCCGCAATAGAGTTGTAATT-TAGT
* * * *
1389357 GGCG-TTTTACAAGAAACGTCGCAA-ATGGGTCGTACA-TTAGT
1 -GCGTTTTTATAA-AAACGCCGCAATA-GAGTTGTA-ATTTAGT
*
1389398 GGCGTTTTTATATAAACGCCGCAATAGAGTTG
1 -GCGTTTTTATAAAAACGCCGCAATAGAGTTG
1389430 CTTATAGTGT
Statistics
Matches: 154, Mismatches: 21, Indels: 35
0.73 0.10 0.17
Matches are distributed among these distances:
37 2 0.01
38 6 0.04
39 33 0.21
40 26 0.17
41 61 0.40
42 22 0.14
43 4 0.03
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.31
Consensus pattern (40 bp):
GCGTTTTTATAAAAACGCCGCAATAGAGTTGTAATTTAGT
Found at i:1389437 original size:81 final size:81
Alignment explanation
Indices: 1389200--1389503 Score: 345
Period size: 81 Copynumber: 3.8 Consensus size: 81
1389190 TTAGCGGCGT
* * *
1389200 TTTTTCAACAAACGCCGC-AATAGGGTGGTA-ATTTAGCT-GCGTTTTTATATAAACGCCGCAAT
1 TTTTACAAGAAACGCCGCAAAT-GGGTCGTACA-TTAG-TGGCGTTTTTATATAAACGCCGCAAT
1389262 AGAGTTGTTTATAGTGACG
63 AGAGTTGTTTATAGTGACG
* * * * * *
1389281 TTTT-CTAAAAAAACACCGC-AATAGAGTAGTA-ATTTAGCGGCG--TTTATAAAAACGCCGCAA
1 TTTTAC--AAGAAACGCCGCAAAT-GGGTCGTACA-TTAGTGGCGTTTTTATATAAACGCCGCAA
*
1389341 TAGAGTTGTTTATAGTGGCG
62 TAGAGTTGTTTATAGTGACG
*
1389361 TTTTACAAGAAACGTCGCAAATGGGTCGTACATTAGTGGCGTTTTTATATAAACGCCGCAATAGA
1 TTTTACAAGAAACGCCGCAAATGGGTCGTACATTAGTGGCGTTTTTATATAAACGCCGCAATAGA
* *
1389426 GTTGCTTATAGTGTCG
66 GTTGTTTATAGTGACG
* * *
1389442 TTTTACAAGAAACGCCGCAAATGGGTCGTACATTAGTGGCGATTTTCTGTAAACGCCGCAAT
1 TTTTACAAGAAACGCCGCAAATGGGTCGTACATTAGTGGCGTTTTTATATAAACGCCGCAAT
1389504 TGATTTTAAC
Statistics
Matches: 195, Mismatches: 20, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
79 23 0.12
80 45 0.23
81 98 0.50
82 29 0.15
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (81 bp):
TTTTACAAGAAACGCCGCAAATGGGTCGTACATTAGTGGCGTTTTTATATAAACGCCGCAATAGA
GTTGTTTATAGTGACG
Found at i:1389496 original size:41 final size:40
Alignment explanation
Indices: 1389353--1389502 Score: 112
Period size: 41 Copynumber: 3.7 Consensus size: 40
1389343 GAGTTGTTTA
* *
1389353 TAGTGGCGTTTTACAAG-AAACGTCGCAAATGGGTCGTACAT
1 TAGTGGCGTTTT-C-TGTAAACGCCGCAAATGGGTCGTACAT
* * * * *
1389394 TAGTGGCGTTTTTATATAAACGCCGC-AATAGAGT--TGCTT
1 TAGTGGCG-TTTTCTGTAAACGCCGCAAAT-GGGTCGTACAT
* *
1389433 ATAGTGTCGTTTTACAAG-AAACGCCGCAAATGGGTCGTACAT
1 -TAGTGGCGTTTT-C-TGTAAACGCCGCAAATGGGTCGTACAT
1389475 TAGTGGCGATTTTCTGTAAACGCCGCAA
1 TAGTGGCG-TTTTCTGTAAACGCCGCAA
1389503 TTGATTTTAA
Statistics
Matches: 82, Mismatches: 16, Indels: 22
0.68 0.13 0.18
Matches are distributed among these distances:
39 7 0.09
40 23 0.28
41 41 0.50
42 11 0.13
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (40 bp):
TAGTGGCGTTTTCTGTAAACGCCGCAAATGGGTCGTACAT
Found at i:1391073 original size:43 final size:42
Alignment explanation
Indices: 1391016--1391235 Score: 192
Period size: 43 Copynumber: 5.1 Consensus size: 42
1391006 CTAAAATTTT
*
1391016 GTTTGTA-GAAAAACGCCGCTAAATATCAACATCTTCTGCGGC
1 GTTTGTAGGAAAAACGCCGCTAAATATCAACACCTT-TGCGGC
* * * * *
1391058 GTTTGTAGGAAAAACGCCGGTAAAAATAAACATCTACTGCGGC
1 GTTTGTAGGAAAAACGCCGCTAAATATCAACACCT-TTGCGGC
* * * *
1391101 GTTTGT-GAAGAAAACGCCGCTAAACATCAACGCCTATTGCAGC
1 GTTTGTAGGA-AAAACGCCGCTAAATATCAACACCT-TTGCGGC
** ** * *
1391144 GTTTGTCTGCCAAATGCCGTTAAATATCAACACCTATTGCGGC
1 GTTTGTAGGAAAAACGCCGCTAAATATCAACACCT-TTGCGGC
* ** *
1391187 GTTTTTCTGAAAAACGCCGCTAAATATCAATACCTTTTGCGGC
1 GTTTGTAGGAAAAACGCCGCTAAATATCAACACC-TTTGCGGC
1391230 GTTTGT
1 GTTTGT
1391236 TATGTTGTCA
Statistics
Matches: 145, Mismatches: 28, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
42 9 0.06
43 135 0.93
44 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (42 bp):
GTTTGTAGGAAAAACGCCGCTAAATATCAACACCTTTGCGGC
Found at i:1391120 original size:86 final size:84
Alignment explanation
Indices: 1391023--1391235 Score: 221
Period size: 86 Copynumber: 2.5 Consensus size: 84
1391013 TTTGTTTGTA
*
1391023 GAAAAACGCCGCTAAATATCAACATCTTCTGCGGCGTTTGTAGGAAAAACGCCGGTAAAAATAAA
1 GAAAAACGCCGCTAAATATCAACACCTT-TGCGGCGTTTGTAGGAAAAACGCCGGTAAAAATAAA
* *
1391088 CATCTACTGCGGCG-TTTGT
65 CACCTACTGCGGCGTTTTCT
* * * ** ** * * * *
1391107 GAAGAAAACGCCGCTAAACATCAACGCCTATTGCAGCGTTTGTCTGCCAAATGCCGTTAAATATC
1 G-A-AAAACGCCGCTAAATATCAACACCT-TTGCGGCGTTTGTAGGAAAAACGCCGGTAAAAATA
*
1391172 AACACCTATTGCGGCGTTTTTCT
63 AACACCTACTGCGGCG-TTTTCT
*
1391195 GAAAAACGCCGCTAAATATCAATACCTTTTGCGGCGTTTGT
1 GAAAAACGCCGCTAAATATCAACACC-TTTGCGGCGTTTGT
1391236 TATGTTGTCA
Statistics
Matches: 104, Mismatches: 19, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
84 1 0.01
85 1 0.01
86 94 0.90
87 3 0.03
88 5 0.05
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (84 bp):
GAAAAACGCCGCTAAATATCAACACCTTTGCGGCGTTTGTAGGAAAAACGCCGGTAAAAATAAAC
ACCTACTGCGGCGTTTTCT
Found at i:1391256 original size:27 final size:25
Alignment explanation
Indices: 1391218--1391267 Score: 73
Period size: 27 Copynumber: 1.9 Consensus size: 25
1391208 AAATATCAAT
*
1391218 ACCTTTTGCGGCGTTTGTTATGTTGTC
1 ACCTATTGCGGCGTTT-TT-TGTTGTC
1391245 ACCTATTGCGGCGTTTTTTGTTG
1 ACCTATTGCGGCGTTTTTTGTTG
1391268 AAAAACGCCG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 5 0.23
26 2 0.09
27 15 0.68
ACGTcount: A:0.08, C:0.18, G:0.26, T:0.48
Consensus pattern (25 bp):
ACCTATTGCGGCGTTTTTTGTTGTC
Found at i:1398008 original size:31 final size:31
Alignment explanation
Indices: 1397943--1398002 Score: 106
Period size: 30 Copynumber: 2.0 Consensus size: 31
1397933 CAATTTAAGG
1397943 CAAAATGGTTTTTGGACTTGAATTGAATTTT
1 CAAAATGGTTTTTGGACTTGAATTGAATTTT
1397974 CAAAAT-GTTTTTGGACTT-AATTGAATTTT
1 CAAAATGGTTTTTGGACTTGAATTGAATTTT
1398003 TTCAAACCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.47
Consensus pattern (31 bp):
CAAAATGGTTTTTGGACTTGAATTGAATTTT
Found at i:1400196 original size:21 final size:21
Alignment explanation
Indices: 1400170--1400211 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1400160 CTATGATAGG
*
1400170 GGGTATCGGTACCCCTTCATA
1 GGGTATCGATACCCCTTCATA
*
1400191 GGGTATCGATACTCCTTCATA
1 GGGTATCGATACCCCTTCATA
1400212 AAATTCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.31
Consensus pattern (21 bp):
GGGTATCGATACCCCTTCATA
Found at i:1402983 original size:44 final size:44
Alignment explanation
Indices: 1402934--1403034 Score: 143
Period size: 44 Copynumber: 2.3 Consensus size: 44
1402924 GTACCATCAG
*
1402934 GGGGTATCGATACCCATTC-AAGGATGGTATCGATACCTATT-GAA
1 GGGGTATCGATACCCATTCAAAGG-GGGTATCGATACC-ATTCGAA
* *
1402978 GGGGTATCGATACCTATTCAAAGGGGGTATCGATACCATTCTAA
1 GGGGTATCGATACCCATTCAAAGGGGGTATCGATACCATTCGAA
1403022 GGGGTATCGATAC
1 GGGGTATCGATAC
1403035 TCTATGCACA
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
43 3 0.06
44 45 0.87
45 4 0.08
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27
Consensus pattern (44 bp):
GGGGTATCGATACCCATTCAAAGGGGGTATCGATACCATTCGAA
Found at i:1402985 original size:21 final size:22
Alignment explanation
Indices: 1402934--1403039 Score: 128
Period size: 23 Copynumber: 4.8 Consensus size: 22
1402924 GTACCATCAG
*
1402934 GGGGTATCGATACCCATTC-AA
1 GGGGTATCGATACCTATTCAAA
*
1402955 GGATGGTATCGATACCTATT-GAA
1 GG--GGTATCGATACCTATTCAAA
1402978 GGGGTATCGATACCTATTCAAA
1 GGGGTATCGATACCTATTCAAA
*
1403000 GGGGGTATCGATACC-ATTCTAA
1 -GGGGTATCGATACCTATTCAAA
1403022 GGGGTATCGATACTCTAT
1 GGGGTATCGATAC-CTAT
1403040 GCACAAAAAT
Statistics
Matches: 75, Mismatches: 3, Indels: 12
0.83 0.03 0.13
Matches are distributed among these distances:
21 31 0.41
22 9 0.12
23 35 0.47
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.28
Consensus pattern (22 bp):
GGGGTATCGATACCTATTCAAA
Found at i:1407457 original size:19 final size:20
Alignment explanation
Indices: 1407432--1407489 Score: 66
Period size: 19 Copynumber: 3.0 Consensus size: 20
1407422 CCAACAATAG
* * *
1407432 GTAACAATTGGTTTTCTTTT
1 GTAACAATTAGTATCCTTTT
1407452 -TAACAATTAGTATCCTTTT
1 GTAACAATTAGTATCCTTTT
*
1407471 GTAACAATTTGTAT-CTTTT
1 GTAACAATTAGTATCCTTTT
1407490 TCATTAAACA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 21 0.64
20 12 0.36
ACGTcount: A:0.26, C:0.12, G:0.10, T:0.52
Consensus pattern (20 bp):
GTAACAATTAGTATCCTTTT
Found at i:1407817 original size:33 final size:34
Alignment explanation
Indices: 1407765--1407828 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 34
1407755 GCTCGGAGGG
*
1407765 TATCTATACCCCCCAGGGGTATCCATACCCCGGA
1 TATCGATACCCCCCAGGGGTATCCATACCCCGGA
* *
1407799 TATCGATA-CCCCCTGGGGTATCTATACCCC
1 TATCGATACCCCCCAGGGGTATCCATACCCC
1407829 CTGGCTGCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 20 0.74
34 7 0.26
ACGTcount: A:0.22, C:0.38, G:0.17, T:0.23
Consensus pattern (34 bp):
TATCGATACCCCCCAGGGGTATCCATACCCCGGA
Found at i:1407830 original size:18 final size:18
Alignment explanation
Indices: 1407762--1407832 Score: 76
Period size: 18 Copynumber: 4.1 Consensus size: 18
1407752 ATTGCTCGGA
*
1407762 GGGTATCTATACCCCCCAG
1 GGGTATCTATA-CCCCCTG
*
1407781 GGGTATCCATA-CCCC--
1 GGGTATCTATACCCCCTG
* *
1407796 GGATATCGATACCCCCTG
1 GGGTATCTATACCCCCTG
1407814 GGGTATCTATACCCCCTG
1 GGGTATCTATACCCCCTG
1407832 G
1 G
1407833 CTGCAACGAC
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
15 9 0.20
16 4 0.09
17 4 0.09
18 17 0.39
19 10 0.23
ACGTcount: A:0.20, C:0.35, G:0.23, T:0.23
Consensus pattern (18 bp):
GGGTATCTATACCCCCTG
Found at i:1407886 original size:21 final size:21
Alignment explanation
Indices: 1407860--1407901 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1407850 ATTTGAATTT
*
1407860 TATGAAGGAGTATCGATACCC
1 TATGAAGGAGTACCGATACCC
*
1407881 TATGAAGGGGTACCGATACCC
1 TATGAAGGAGTACCGATACCC
1407902 CTATCGTAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.21
Consensus pattern (21 bp):
TATGAAGGAGTACCGATACCC
Found at i:1410470 original size:34 final size:34
Alignment explanation
Indices: 1410411--1410539 Score: 174
Period size: 34 Copynumber: 3.9 Consensus size: 34
1410401 GAAAAATAAG
* *
1410411 TTGGCCATCTACCAA-A-GAATTTTCCAATGAGT
1 TTGGCCACCAACCAAGATGAATTTTCCAATGAGT
1410443 TTGGCCACCAACCAAGATGAATTTTCCAATGAGT
1 TTGGCCACCAACCAAGATGAATTTTCCAATGAGT
* *
1410477 TTGGCCACCAACCAAGATGAATTTTTCAATAAG-
1 TTGGCCACCAACCAAGATGAATTTTCCAATGAGT
* * *
1410510 TTGGTCACCAACCAAAATGAAATTTCCAAT
1 TTGGCCACCAACCAAGATGAATTTTCCAAT
1410540 CTTGCCAAAC
Statistics
Matches: 87, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.15
33 27 0.31
34 47 0.54
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (34 bp):
TTGGCCACCAACCAAGATGAATTTTCCAATGAGT
Found at i:1410530 original size:67 final size:66
Alignment explanation
Indices: 1410411--1410539 Score: 170
Period size: 67 Copynumber: 1.9 Consensus size: 66
1410401 GAAAAATAAG
* * * * *
1410411 TTGGCCATCTACCAAAGAATTTTCCAATGAGTTTGGCCACCAACCAAGATGAATTTTCCAATGAG
1 TTGGCCACCAACCAAAGAATTTTCCAATAAGTTTGGCCACCAACCAAAATGAAATTTCCAATGAG
1410476 T
66 T
* *
1410477 TTGGCCACCAACCAAGATGAATTTTTCAATAAG-TTGGTCACCAACCAAAATGAAATTTCCAAT
1 TTGGCCACCAACCAA-A-GAATTTTCCAATAAGTTTGGCCACCAACCAAAATGAAATTTCCAAT
1410540 CTTGCCAAAC
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
66 13 0.24
67 28 0.52
68 13 0.24
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (66 bp):
TTGGCCACCAACCAAAGAATTTTCCAATAAGTTTGGCCACCAACCAAAATGAAATTTCCAATGAG
T
Found at i:1415135 original size:34 final size:33
Alignment explanation
Indices: 1415040--1415140 Score: 134
Period size: 33 Copynumber: 3.1 Consensus size: 33
1415030 AAACATGAAA
* * *
1415040 AATAAGTTGGCCATCTACCAA-A-GAATTTTCC
1 AATAAGTTGGCCACCAACCAAGATGAATTTTTC
*
1415071 AATGAGTTTGGCCACCAACCAAGATGAATTTTTC
1 AATAAG-TTGGCCACCAACCAAGATGAATTTTTC
*
1415105 AATAAGTTGGCCACCAACCAAGATGAAATTTTC
1 AATAAGTTGGCCACCAACCAAGATGAATTTTTC
1415138 AAT
1 AAT
1415141 CTTGCCAATT
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
31 5 0.08
32 13 0.21
33 30 0.49
34 13 0.21
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.28
Consensus pattern (33 bp):
AATAAGTTGGCCACCAACCAAGATGAATTTTTC
Found at i:1416870 original size:16 final size:16
Alignment explanation
Indices: 1416833--1416893 Score: 79
Period size: 17 Copynumber: 3.8 Consensus size: 16
1416823 GTTTTTTAGG
*
1416833 TTCGGGTTACTTTTG-
1 TTCGGGTTGCTTTTGT
*
1416848 GTCGGGTTGCTTTTGT
1 TTCGGGTTGCTTTTGT
1416864 TTCGGGTTGCTTTTTGT
1 TTCGGGTTGC-TTTTGT
*
1416881 TTCAGGTTGCTTT
1 TTCGGGTTGCTTT
1416894 CAGTCCAACT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
15 13 0.32
16 12 0.30
17 15 0.38
ACGTcount: A:0.03, C:0.13, G:0.30, T:0.54
Consensus pattern (16 bp):
TTCGGGTTGCTTTTGT
Found at i:1421150 original size:16 final size:16
Alignment explanation
Indices: 1421127--1421159 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1421117 GATTTTGGTT
1421127 ATTTTTTATT-TTAAA
1 ATTTTTTATTATTAAA
1421142 ATTTATTTATTATTAAA
1 ATTT-TTTATTATTAAA
1421159 A
1 A
1421160 AATAATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 6 0.38
17 6 0.38
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTTTTATTATTAAA
Found at i:1422193 original size:37 final size:37
Alignment explanation
Indices: 1422065--1422203 Score: 142
Period size: 37 Copynumber: 3.8 Consensus size: 37
1422055 ATTTTTCGTC
* * *
1422065 CTACTACGATTTAAACTCCTAAAAATATGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
*
1422102 -T--TAGGATTCAAACTCATAAAAATAGGATA-ACATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGA-ATT
* * *
1422136 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * * *
1422173 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
1422204 CCACAAGCAC
Statistics
Matches: 85, Mismatches: 12, Indels: 10
0.79 0.11 0.09
Matches are distributed among these distances:
33 1 0.01
34 27 0.32
35 1 0.01
36 1 0.01
37 54 0.64
38 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:1422904 original size:4 final size:4
Alignment explanation
Indices: 1422895--1423039 Score: 56
Period size: 4 Copynumber: 34.2 Consensus size: 4
1422885 TTTTCTATGC
*
1422895 TTTA TTTA TTTA TTTA -TTA TTTTA TTTTA TTTTA TTT- CTT- TTTA TTT-
1 TTTA TTTA TTTA TTTA TTTA -TTTA -TTTA -TTTA TTTA TTTA TTTA TTTA
*
1422942 TGGTTGAA TTTA TTTA TTTA -TTA TTTTAA TTTA TTTTA TTT- CTT- TTTA
1 T--TT--A TTTA TTTA TTTA TTTA -TTT-A TTTA -TTTA TTTA TTTA TTTA
1422990 TTT- TGGTTGAA TTTA TTTA TTTA TTTTA TTTA TTTTA TTTTA TTT- TTTA
1 TTTA T--TT--A TTTA TTTA TTTA -TTTA TTTA -TTTA -TTTA TTTA TTTA
1423039 T
1 T
1423040 ATCTAACATG
Statistics
Matches: 116, Mismatches: 4, Indels: 42
0.72 0.02 0.26
Matches are distributed among these distances:
3 19 0.16
4 51 0.44
5 39 0.34
6 5 0.04
8 2 0.02
ACGTcount: A:0.21, C:0.01, G:0.04, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:1422921 original size:5 final size:5
Alignment explanation
Indices: 1422911--1423035 Score: 91
Period size: 5 Copynumber: 25.4 Consensus size: 5
1422901 TATTTATTTA
** * *
1422911 TTATT TTATT TTATT TTATT TCT-TT TTATT TTGGT TGAAT TTA-T TTATTT
1 TTATT TTATT TTATT TTATT T-TATT TTATT TTATT TTATT TTATT TTA-TT
* ** * *
1422961 ATTATT TTAAT TTATT TTATT TCT-TT TTATT TTGGT TGAAT TTA-T TTA-T
1 -TTATT TTATT TTATT TTATT T-TATT TTATT TTATT TTATT TTATT TTATT
1423010 TTATT TTA-T TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TT
1423036 TTATATCTAA
Statistics
Matches: 97, Mismatches: 14, Indels: 18
0.75 0.11 0.14
Matches are distributed among these distances:
4 18 0.19
5 71 0.73
6 5 0.05
7 3 0.03
ACGTcount: A:0.20, C:0.02, G:0.05, T:0.74
Consensus pattern (5 bp):
TTATT
Found at i:1422958 original size:51 final size:51
Alignment explanation
Indices: 1422898--1423034 Score: 247
Period size: 51 Copynumber: 2.7 Consensus size: 51
1422888 TCTATGCTTT
1422898 ATTTATTTATTTATTATTTTATTTTATTTTATTTCTTTTTATTTTGGTTGA
1 ATTTATTTATTTATTATTTTATTTTATTTTATTTCTTTTTATTTTGGTTGA
*
1422949 ATTTATTTATTTATTATTTTAATTTATTTTATTTCTTTTTATTTTGGTTGA
1 ATTTATTTATTTATTATTTTATTTTATTTTATTTCTTTTTATTTTGGTTGA
*
1423000 ATTTATTTATTTATTTTATTTATTTTATTTTATTT
1 ATTTATTTATTTATTAT-TTTATTTTATTTTATTT
1423035 TTTATATCTA
Statistics
Matches: 82, Mismatches: 3, Indels: 1
0.95 0.03 0.01
Matches are distributed among these distances:
51 66 0.80
52 16 0.20
ACGTcount: A:0.21, C:0.01, G:0.04, T:0.73
Consensus pattern (51 bp):
ATTTATTTATTTATTATTTTATTTTATTTTATTTCTTTTTATTTTGGTTGA
Found at i:1426080 original size:18 final size:16
Alignment explanation
Indices: 1426044--1426086 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
1426034 AGATCCAATC
*
1426044 AAGAAGAAAAAAAGAA
1 AAGAAGAAAAAAAAAA
1426060 AAGAAGCAAAAAAAAACA
1 AAGAAG-AAAAAAAAA-A
1426078 AAGAA-AAAA
1 AAGAAGAAAA
1426087 GAGAAACAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 10 0.42
17 8 0.33
18 6 0.25
ACGTcount: A:0.81, C:0.05, G:0.14, T:0.00
Consensus pattern (16 bp):
AAGAAGAAAAAAAAAA
Found at i:1426097 original size:16 final size:15
Alignment explanation
Indices: 1426051--1426109 Score: 57
Period size: 15 Copynumber: 3.7 Consensus size: 15
1426041 ATCAAGAAGA
*
1426051 AAAAAAGAAAAGAAG
1 AAAAAAGAAAACAAG
*
1426066 CAAAAA-AAAACAAAG
1 AAAAAAGAAAAC-AAG
1426081 AAAAAAGAGAAACAAG
1 AAAAAAGA-AAACAAG
1426097 AACAAAAGGAAAA
1 AA-AAAA-GAAAA
1426110 AACAAGAATC
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 4 0.11
15 13 0.36
16 6 0.17
17 11 0.31
18 2 0.06
ACGTcount: A:0.78, C:0.07, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAACAAG
Found at i:1426110 original size:7 final size:7
Alignment explanation
Indices: 1426051--1426111 Score: 52
Period size: 8 Copynumber: 7.9 Consensus size: 7
1426041 ATCAAGAAGA
1426051 AAAAAAG
1 AAAAAAG
1426058 AAAAGAAG
1 AAAA-AAG
1426066 CAAAAAA-
1 -AAAAAAG
1426073 AAACAAAG
1 AAA-AAAG
1426081 AAAAAAG
1 AAAAAAG
1426088 AGAAACAAG
1 A-AAA-AAG
1426097 AACAAAAGG
1 AA-AAAA-G
1426106 AAAAAA
1 AAAAAA
1426112 CAAGAATCAA
Statistics
Matches: 46, Mismatches: 0, Indels: 15
0.75 0.00 0.25
Matches are distributed among these distances:
6 3 0.07
7 12 0.26
8 18 0.39
9 13 0.28
ACGTcount: A:0.79, C:0.07, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:1426112 original size:19 final size:18
Alignment explanation
Indices: 1426070--1426128 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 18
1426060 AAGAAGCAAA
1426070 AAAAAACAAAGAA-AAAAG
1 AAAAAAC-AAGAACAAAAG
*
1426088 -AGAAACAAGAACAAAAGG
1 AAAAAACAAGAACAAAA-G
1426106 AAAAAACAAGAATCAAAAAG
1 AAAAAACAAGAA-C-AAAAG
1426126 AAA
1 AAA
1426129 GAGGAGCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
16 5 0.15
17 9 0.26
18 1 0.03
19 10 0.29
20 5 0.15
21 4 0.12
ACGTcount: A:0.76, C:0.08, G:0.14, T:0.02
Consensus pattern (18 bp):
AAAAAACAAGAACAAAAG
Found at i:1426789 original size:22 final size:22
Alignment explanation
Indices: 1426761--1426815 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
1426751 GCTATCCCAT
1426761 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
*
1426783 CAAACCTTTGAGTATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
1426805 CAAACCTTTGA
1 CAAACCTTTGA
1426816 CCAAACACAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.25
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:1427676 original size:37 final size:36
Alignment explanation
Indices: 1427620--1427871 Score: 247
Period size: 37 Copynumber: 7.2 Consensus size: 36
1427610 TGCTTTTTTA
*
1427620 AAACAAATTTCGTCTCTCTTGAGATAGTTTCCCTTG
1 AAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTG
*
1427656 AAACAAGATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAA-ATTTCGTCTCTCTTGAGACAGTTTCCCTTG
*
1427693 AAATAAAGTTT-G-C-CTCTTGAGACAGTTTCCCTTG
1 AAACAAA-TTTCGTCTCTCTTGAGACAGTTTCCCTTG
* * * * *
1427727 AAACAAA------ATAT-TTGA-ATATGTTTTCTTTG
1 AAACAAATTTCGTCTCTCTTGAGACA-GTTTCCCTTG
* **
1427756 AAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTG
1 AAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTG
* * * *
1427792 GAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 AAAC-AAATTTCGTCTCTCTTGAGACAGTTTCCCTTG
*
1427829 AAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTG
1 AAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTG
1427865 AAACAAA
1 AAACAAA
1427872 ATCTTCAAAT
Statistics
Matches: 178, Mismatches: 25, Indels: 26
0.78 0.11 0.11
Matches are distributed among these distances:
28 2 0.01
29 19 0.11
30 1 0.01
34 27 0.15
35 2 0.01
36 58 0.33
37 69 0.39
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (36 bp):
AAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTG
Found at i:1427719 original size:17 final size:16
Alignment explanation
Indices: 1427672--1427727 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 16
1427662 GATTTTGTCT
1427672 CTCTTGAGACAGTTTC
1 CTCTTGAGACAGTTTC
* *
1427688 C-CTTGAAATAAAGTTTGC
1 CTCTTG--AGACAGTTT-C
1427706 CTCTTGAGACAGTTTC
1 CTCTTGAGACAGTTTC
1427722 C-CTTGA
1 CTCTTGA
1427728 AACAAAATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 9
0.71 0.09 0.20
Matches are distributed among these distances:
15 9 0.28
16 3 0.09
17 14 0.44
18 2 0.06
19 4 0.12
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (16 bp):
CTCTTGAGACAGTTTC
Found at i:1428770 original size:105 final size:105
Alignment explanation
Indices: 1428576--1428991 Score: 551
Period size: 105 Copynumber: 4.0 Consensus size: 105
1428566 GTGGCACTCG
* *
1428576 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTCAATTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGCTTGTCAACAAACAACTTC-CCATTT
1428641 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTC
65 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTC
* * *
1428682 AGACAACGCAAGTTCAACTTCACGATGAAGGGATC-GCTGCTTGTCAAC-AACAACTTCCCAATT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGA-CGGCTGCTTGTCAACAAACAACTTCCC-ATT
* *
1428745 TCAGAGCCAATTTTAACTTCACAACGAAGGATATTGGACTCC
64 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTC
* * * * *
1428787 AGACAACGCAAGTTCAAATTCACGACGAAGGGACCGCTGCTTGTCAAC-AA-AA-TT-TCA-TTC
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGCTTGTCAACAAACAACTTCCCATTTC
**
1428847 AGATTCAATTTCAACTTCACAACGAAGGATATTGGAC-TC
66 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTC
* * **
1428886 GAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCGGTT
1 -AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGCTTGTCAACAAACAACTTCCCATTT
* *
1428951 CAAGAGCCAATTTCAACTTCACGACGGAGGATATTGGACTT
65 C-AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTT
1428992 GGAACAATGC
Statistics
Matches: 274, Mismatches: 25, Indels: 21
0.86 0.08 0.07
Matches are distributed among these distances:
99 1 0.00
100 80 0.29
101 3 0.01
102 3 0.01
103 4 0.01
104 5 0.02
105 101 0.37
106 75 0.27
107 2 0.01
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (105 bp):
AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGCTTGTCAACAAACAACTTCCCATTTC
AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTC
Found at i:1428934 original size:205 final size:212
Alignment explanation
Indices: 1428571--1428990 Score: 581
Period size: 205 Copynumber: 2.0 Consensus size: 212
1428561 ATTTCGTGGC
* * * *
1428571 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACACAAGTTCAAATTCACAACGAAGGGACCGCTGCTTGTCAACAAACAACTTCTC
*
1428636 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACACAAGTTCAACT
* * * *
1428701 TCACGATGAAGGGATCGCTGCTTGTCAAC-AACAACTTCCCAATTTC-AGAGCCAATTTTAACTT
131 TCACAACGAAGGGATCGCTGCTTGTCAACAAACAACTTCCC-AGTTCAAGAGCCAATTTCAACTT
1428764 CACAACGAAGGATATTGG
195 CACAACGAAGGATATTGG
* *
1428782 ACTCCAGACAACGCAAGTTCAAATTCACGACGAAGGGACCGCTGCTTGTCAAC-AA-AA-TT-TC
1 ACTCCAGACAACACAAGTTCAAATTCACAACGAAGGGACCGCTGCTTGTCAACAAACAACTTCTC
**
1428843 -A-TTCAGATTCAATTTCAACTTCACAACGAAGGATATTGGAC-TCGAGACAACACAAGTTCAAC
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTC-AGACAACACAAGTTCAAC
* * *
1428905 TTCACAACGAAGGGA-CGGCTGGTTGTCAACAAACAATTTCCCGGTTCAAGAGCCAATTTCAACT
130 TTCACAACGAAGGGATC-GCTGCTTGTCAACAAACAACTTCCCAGTTCAAGAGCCAATTTCAACT
* *
1428969 TCACGACGGAGGATATTGG
194 TCACAACGAAGGATATTGG
1428988 ACT
1 ACT
1428991 TGGAACAATG
Statistics
Matches: 187, Mismatches: 18, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
204 3 0.02
205 83 0.44
206 46 0.25
207 2 0.01
208 2 0.01
209 2 0.01
210 2 0.01
211 47 0.25
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (212 bp):
ACTCCAGACAACACAAGTTCAAATTCACAACGAAGGGACCGCTGCTTGTCAACAAACAACTTCTC
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACACAAGTTCAACT
TCACAACGAAGGGATCGCTGCTTGTCAACAAACAACTTCCCAGTTCAAGAGCCAATTTCAACTTC
ACAACGAAGGATATTGG
Found at i:1429582 original size:34 final size:37
Alignment explanation
Indices: 1429538--1429639 Score: 167
Period size: 34 Copynumber: 2.8 Consensus size: 37
1429528 TTTCGTCCTA
1429538 CTAGGATTCAAACTCCTAAAAATAGGATAGA-A-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
1429573 -TAGGATTCAAACTCCTAAAAATAGGATA-ACATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
1429608 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
1429640 GTTCTACTAA
Statistics
Matches: 62, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
33 1 0.02
34 29 0.47
35 3 0.05
37 28 0.45
38 1 0.02
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (37 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
Found at i:1429663 original size:37 final size:37
Alignment explanation
Indices: 1429535--1429665 Score: 171
Period size: 37 Copynumber: 3.6 Consensus size: 37
1429525 ATTTTTCGTC
1429535 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1429572 -T--TAGGATTCAAACTCCTAAAAATAGGATA-ACATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGA-ATT
* * *
1429606 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
1429643 CTACTAAGATTTAAATTCCTAAA
1 CTACTAGGATTCAAACTCCTAAA
1429666 GATATGATCC
Statistics
Matches: 83, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
33 1 0.01
34 31 0.37
35 1 0.01
36 1 0.01
37 48 0.58
38 1 0.01
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:1430350 original size:23 final size:23
Alignment explanation
Indices: 1430298--1430350 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 23
1430288 TTATGTGTAT
*
1430298 TTTATTTATTTATATATATTACC
1 TTTATTTATTTATATATATTAAC
1430321 TTT-TTTATTT-TATAT-TTATAC
1 TTTATTTATTTATATATATTA-AC
1430342 TATTATTTA
1 T-TTATTTA
1430351 CTATAATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 3 0.12
21 7 0.27
22 9 0.35
23 7 0.27
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (23 bp):
TTTATTTATTTATATATATTAAC
Found at i:1430377 original size:4 final size:4
Alignment explanation
Indices: 1430368--1430462 Score: 54
Period size: 4 Copynumber: 22.2 Consensus size: 4
1430358 TTTTCTATGC
*
1430368 TTTA TTTA TTTA TTTA -TTA TTTTA TTTTA TTTTA TTT- CTT- TTTA TTT-
1 TTTA TTTA TTTA TTTA TTTA -TTTA -TTTA -TTTA TTTA TTTA TTTA TTTA
*
1430415 TGGTTGAA TTTA TTTA TTTA TTTTA TTTA TTTTA TTTTA TTTT TTTA T
1 T--TT--A TTTA TTTA TTTA -TTTA TTTA -TTTA -TTTA TTTA TTTA T
1430463 ATCTAACATG
Statistics
Matches: 77, Mismatches: 4, Indels: 20
0.76 0.04 0.20
Matches are distributed among these distances:
3 8 0.10
4 38 0.49
5 28 0.36
6 2 0.03
8 1 0.01
ACGTcount: A:0.20, C:0.01, G:0.03, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:1430394 original size:5 final size:5
Alignment explanation
Indices: 1430384--1430457 Score: 75
Period size: 5 Copynumber: 15.4 Consensus size: 5
1430374 TATTTATTTA
** * *
1430384 TTATT TTATT TTATT TTATT TCT-TT TTATT TTGGT TGAAT TTA-T TTA-T
1 TTATT TTATT TTATT TTATT T-TATT TTATT TTATT TTATT TTATT TTATT
1430432 TTATT TTA-T TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TT
1430458 TTTATATCTA
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
4 13 0.22
5 45 0.76
6 1 0.02
ACGTcount: A:0.19, C:0.01, G:0.04, T:0.76
Consensus pattern (5 bp):
TTATT
Found at i:1431622 original size:24 final size:24
Alignment explanation
Indices: 1431586--1431736 Score: 135
Period size: 24 Copynumber: 6.4 Consensus size: 24
1431576 AATGCTAAAC
* *
1431586 GAACATGTTCATGAACACGTTCGT
1 GAACATATACATGAACACGTTCGT
***
1431610 GAACATATACATGAATGTGTTCGT
1 GAACATATACATGAACACGTTCGT
**
1431634 GAACATATACATGAACGTGTTCGT
1 GAACATATACATGAACACGTTCGT
*
1431658 GAACATATACATGAACACATTCGT
1 GAACATATACATGAACACGTTCGT
* * ***
1431682 GAACAT-TAAAGGAACAC-TAAAT
1 GAACATATACATGAACACGTTCGT
* * *
1431704 GAACATGTTCATGAACACATTCGT
1 GAACATATACATGAACACGTTCGT
*
1431728 GAATATATA
1 GAACATATA
1431737 AACAAACACC
Statistics
Matches: 102, Mismatches: 23, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
22 8 0.08
23 17 0.17
24 77 0.75
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (24 bp):
GAACATATACATGAACACGTTCGT
Found at i:1431624 original size:12 final size:12
Alignment explanation
Indices: 1431609--1431674 Score: 51
Period size: 12 Copynumber: 5.5 Consensus size: 12
1431599 AACACGTTCG
1431609 TGAACATATACA
1 TGAACATATACA
** * * *
1431621 TGAATGTGTTCG
1 TGAACATATACA
1431633 TGAACATATACA
1 TGAACATATACA
* * * *
1431645 TGAACGTGTTCG
1 TGAACATATACA
1431657 TGAACATATACA
1 TGAACATATACA
1431669 TGAACA
1 TGAACA
1431675 CATTCGTGAA
Statistics
Matches: 36, Mismatches: 18, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (12 bp):
TGAACATATACA
Found at i:1431879 original size:30 final size:30
Alignment explanation
Indices: 1431779--1431890 Score: 113
Period size: 30 Copynumber: 3.7 Consensus size: 30
1431769 GTTCGTAAAC
*
1431779 AATAAATAAATGAACACGAACATCC-TCAAA
1 AATAAATAAACGAACACGAACA-CCTTCAAA
* **
1431809 AATAAATAAACGAACACGAACACGATATTGAA
1 AATAAATAAACGAACACGAACAC-CT-TCAAA
* *
1431841 AAT--TTAAACGAACACGAGCACCTTCAAA
1 AATAAATAAACGAACACGAACACCTTCAAA
*
1431869 AATAAATAAACAAACACGAACA
1 AATAAATAAACGAACACGAACA
1431891 TAATCTTATT
Statistics
Matches: 65, Mismatches: 12, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
28 6 0.09
29 2 0.03
30 51 0.78
32 6 0.09
ACGTcount: A:0.56, C:0.20, G:0.09, T:0.15
Consensus pattern (30 bp):
AATAAATAAACGAACACGAACACCTTCAAA
Found at i:1433338 original size:18 final size:18
Alignment explanation
Indices: 1433317--1433360 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
1433307 ATAAACATCT
*
1433317 TTATCATGATCTCTGTCA
1 TTATCATGATCTCTATCA
1433335 TTATCATGATCTCTATCA
1 TTATCATGATCTCTATCA
*
1433353 CTATCATG
1 TTATCATG
1433361 TATTAACATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.25, C:0.23, G:0.09, T:0.43
Consensus pattern (18 bp):
TTATCATGATCTCTATCA
Found at i:1433651 original size:21 final size:20
Alignment explanation
Indices: 1433610--1433704 Score: 92
Period size: 21 Copynumber: 4.8 Consensus size: 20
1433600 TGAAATTTTC
1433610 CCCGAAGGACCAC--TATAT
1 CCCGAAGGACCACTGTATAT
*
1433628 CCCGTAGGACCACTGTATTAT
1 CCCGAAGGACCACTGTA-TAT
*
1433649 CCCGAAGGACCACTGTATTGT
1 CCCGAAGGACCACTGTA-TAT
* *
1433670 CCCGAAGAACCAC--TATGT
1 CCCGAAGGACCACTGTATAT
1433688 CCC-ATAGGACCACTGTA
1 CCCGA-AGGACCACTGTA
1433705 ACCCTCGACT
Statistics
Matches: 66, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
17 1 0.02
18 25 0.38
19 2 0.03
20 4 0.06
21 34 0.52
ACGTcount: A:0.28, C:0.32, G:0.19, T:0.21
Consensus pattern (20 bp):
CCCGAAGGACCACTGTATAT
Found at i:1437247 original size:84 final size:84
Alignment explanation
Indices: 1437065--1437305 Score: 301
Period size: 83 Copynumber: 2.9 Consensus size: 84
1437055 ATACTTTAGC
* * *
1437065 GGCGTTTCTT-CAACAAACGTCGTGATAGAGTT-GTACTTTAGCGGC-GTTTTTATACAAACGCC
1 GGCGTTT-TTCCAACAAACGCCGTGATAGA-TTAGTACTTTAGCGGCATTTTTTATACAAATGCC
* * *
1437127 GCAATAAGGATCGTTTATAAT
64 GCAATAGGGTTCGTTCATAAT
* * *
1437148 GGCGTTTTTCTAACAAACGCCATGATAGATTAGTACTTTAGCGGCATTTTTTATACAAATGTCGC
1 GGCGTTTTTCCAACAAACGCCGTGATAGATTAGTACTTTAGCGGCATTTTTTATACAAATGCCGC
*
1437213 AATAGGGTTCGTTCATAGT
66 AATAGGGTTCGTTCATAAT
* * ** *
1437232 GGTGTTTTTCCAACAAATGCCGTGATA-AAGAGTACTTTAGCGGCATTTTTTATATAAATGCCGC
1 GGCGTTTTTCCAACAAACGCCGTGATAGATTAGTACTTTAGCGGCATTTTTTATACAAATGCCGC
1437296 AATAGGGTTC
66 AATAGGGTTC
1437306 TTTAGCGACA
Statistics
Matches: 137, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
82 4 0.03
83 79 0.58
84 54 0.39
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (84 bp):
GGCGTTTTTCCAACAAACGCCGTGATAGATTAGTACTTTAGCGGCATTTTTTATACAAATGCCGC
AATAGGGTTCGTTCATAAT
Found at i:1440566 original size:43 final size:42
Alignment explanation
Indices: 1440518--1440827 Score: 325
Period size: 43 Copynumber: 7.2 Consensus size: 42
1440508 AAGGTAATTA
* * **
1440518 GCGGCGTTTGTATCAAAAAATGCCGCTATAGATCTGATATTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCTGACCTTTT
* *
1440561 GCGGCGTTTGTATCCAAAAACGCCGCCATAGATCTGACTTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCTGACCTTTT
* * * * *
1440604 GCGGCATTTGTTCAAAAAACGCAGCTATAGATTTTACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTT
* * * *
1440646 GCGGCGTTTGTATCCTAAAATGCCGCTATAGATATCAACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCT-GACCTTTT
* * *
1440690 GCGGCGTTTGTTCCAAAAACGTCACTATAGATATTGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGAT-CTGACCTTTT
* *
1440733 GCAGCGTTTGTTCCAAAAACGCCGCTAGAGATAGC-GACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGAT--CTGACCTTTT
* * * *
1440776 GCGGCGTTTGTTCCAAAAATGCCGCGATAGATCTTAACCTATT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATC-TGACCTTTT
1440819 GCGGCGTTT
1 GCGGCGTTT
1440828 TTTGTTCTCA
Statistics
Matches: 224, Mismatches: 37, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
41 1 0.00
42 35 0.16
43 169 0.75
44 19 0.08
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (42 bp):
GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTT
Found at i:1440795 original size:129 final size:129
Alignment explanation
Indices: 1440518--1440827 Score: 385
Period size: 129 Copynumber: 2.4 Consensus size: 129
1440508 AAGGTAATTA
* *
1440518 GCGGCGTTTGTATCAAAAAATGCCGCTATAGATCTGATA--TTTTGCGGCGTTTGTATCCAAAAA
1 GCGGCGTTTGTATCCAAAAATGCCGCTATAGATCTCA-ACCTTTTGCGGCGTTTGTATCCAAAAA
* * * * ***
1440581 CGCCGCCATAGATCTGACTTTTTGCGGCATTTGTTCAAAAAACGCAGCTATAGATTTTACCTTTT
65 CGCCACCATAGATCTGACCTTTTGCAGCATTTGTTCAAAAAACGCAGCTAGAGATGCGACCTTTT
* *
1440646 GCGGCGTTTGTATCCTAAAATGCCGCTATAGATATCAACCTTTTGCGGCGTTTGT-TCCAAAAAC
1 GCGGCGTTTGTATCCAAAAATGCCGCTATAGATCTCAACCTTTTGCGGCGTTTGTATCCAAAAAC
* * * * * *
1440710 GTCACTATAGATATTGACCTTTTGCAGCGTTTGTTCCAAAAACGCCGCTAGAGATAGCGACCTTT
66 GCCACCATAGAT-CTGACCTTTTGCAGCATTTGTTCAAAAAACGCAGCTAGAGAT-GCGACCTTT
1440775 T
129 T
* * *
1440776 GCGGCGTTTGT-TCCAAAAATGCCGCGATAGATCTTAACCTATTGCGGCGTTT
1 GCGGCGTTTGTATCCAAAAATGCCGCTATAGATCTCAACCTTTTGCGGCGTTT
1440828 TTTGTTCTCA
Statistics
Matches: 156, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
127 1 0.01
128 51 0.33
129 86 0.55
130 18 0.12
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (129 bp):
GCGGCGTTTGTATCCAAAAATGCCGCTATAGATCTCAACCTTTTGCGGCGTTTGTATCCAAAAAC
GCCACCATAGATCTGACCTTTTGCAGCATTTGTTCAAAAAACGCAGCTAGAGATGCGACCTTTT
Found at i:1444109 original size:14 final size:14
Alignment explanation
Indices: 1444083--1444126 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
1444073 TATAAATTAT
*
1444083 AATAATAATAATAA
1 AATAATTATAATAA
1444097 TAA-AATTATAATAA
1 -AATAATTATAATAA
*
1444111 AATATTTATAATAA
1 AATAATTATAATAA
1444125 AA
1 AA
1444127 CTCGGACGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 2 0.08
14 22 0.85
15 2 0.08
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
AATAATTATAATAA
Found at i:1448587 original size:26 final size:26
Alignment explanation
Indices: 1448553--1448606 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
1448543 TTCTACAAAT
1448553 ATCTAAGACATACTTTGATAGCCCAA
1 ATCTAAGACATACTTTGATAGCCCAA
*
1448579 ATCTAAGACGTACTTTGATAGCCCAA
1 ATCTAAGACATACTTTGATAGCCCAA
1448605 AT
1 AT
1448607 GACTAAAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (26 bp):
ATCTAAGACATACTTTGATAGCCCAA
Found at i:1456993 original size:21 final size:21
Alignment explanation
Indices: 1456975--1457021 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
1456965 CTTCTGAAGC
1456975 AGAACCAGCACTTGATGAAAA
1 AGAACCAGCACTTGATGAAAA
*
1456996 AGAACCAGCACTTGATGAACA
1 AGAACCAGCACTTGATGAAAA
1457017 AGAAC
1 AGAAC
1457022 TAGAGAGTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.13
Consensus pattern (21 bp):
AGAACCAGCACTTGATGAAAA
Found at i:1458815 original size:2 final size:2
Alignment explanation
Indices: 1458808--1458863 Score: 87
Period size: 2 Copynumber: 28.5 Consensus size: 2
1458798 AGGTGGGAAA
1458808 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
1458849 CT AA AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
1458864 ATTCCACCAA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1464292 original size:150 final size:147
Alignment explanation
Indices: 1464025--1464831 Score: 534
Period size: 150 Copynumber: 5.4 Consensus size: 147
1464015 GTAGTTGTAA
* * * * ** * * *
1464025 ATACTGCATACGTTACATAACGTGTAACTGTAATTATGAGTGTGA--T-TTTCAAAAAAAAATGT
1 ATACTACAGACGTTACATAATGTGTAACGGTCGTTACGAGTGTGATTTGTTTC-TAAAAAATTGT
* * * * * * ** * *
1464087 ACAAGTTCAATGTTATATGATTTATAATATTAAATTATAGTTACAATATTTGTCACGAAAGTAAT
65 ACAAATTCAATGTTTTCTTATTCATAATATTAAA-AACGGTTACGATATTTGTCACGAAAGTGAT
1464152 TACAATATCGCGATTGTGG
129 TACAATATCGCGATTGTGG
* * * *
1464171 ATACTACAGACGTTACATAATGTGTAACGGTTGTTACGTGTGTGAATTGTTTTTAAAGAAAATTG
1 ATACTACAGACGTTACATAATGTGTAACGGTCGTTACGAGTGTGATTTGTTTCT-AA-AAAATTG
* *
1464236 TACAAATTTAATGTTTTCTTATTCATAATATTAAACAACGGTTACGATATTTGTCACGAATACTA
64 TACAAATTCAATGTTTTCTTATTCATAATATTAAA-AACGGTTACGATATTTGTCACGAA-AGT-
* * * *
1464301 CAAACGTTACGTTACATAACATGTAACGGTTGTGA
126 --GA--TTAC---A-ATATC--G---CGATTGTGG
* ** * * *
1464336 ATACTACAAACGTTACATAACATGTAACGGTTGTTACGAGTGTGATTTATTTCTAAAAAATTGTG
1 ATACTACAGACGTTACATAATGTGTAACGGTCGTTACGAGTGTGATTTGTTTCTAAAAAATTGTA
* * * * * ***
1464401 CAAATTCAATATTTT-TTATTCATAATATTAAATTACGGTTACGGTGTCTGTCACGGTTGTGATT
66 CAAATTCAATGTTTTCTTATTCATAATATTAAA-AACGGTTACGATATTTGTCACGAAAGTGATT
* * *
1464465 ACAATATCGCTACTATGG
130 ACAATATCGCGATTGTGG
* * ** * *
1464483 ATACTAAAGACGTTAGATAATGCATAACGGTCATTATGA--GTGATTTTGTTTCTAAAAAATTGT
1 ATACTACAGACGTTACATAATGTGTAACGGTCGTTACGAGTGTGA-TTTGTTTCTAAAAAATTGT
* * * * * *
1464546 ACAAATACAAAGTTATCTTATTCATAATATTTATAAATTACGATTAC-AGTGTCTGTCAC-AAAT
65 ACAAATTCAATGTTTTCTTATTCATAATA-TTA-AAA--ACGGTTACGA-TATTTGTCACGAAA-
* * *
1464609 GTGATTACAATATCACAATTGTGA
124 GTGATTACAATATCGCGATTGTGG
* * * **
1464633 ATATTGCAGACGTTACATAATGTGTAACGGTCATTACGAGAATGATTTGTTTCTAAAAAAATTGT
1 ATACTACAGACGTTACATAATGTGTAACGGTCGTTACGAGTGTGATTTGTTTCT-AAAAAATTGT
* * *
1464698 ATAAATTCAATGTTTTCTGATTCATAATATT--AAA---TTACG----TTGTCAC-AGATGTGAT
65 ACAAATTCAATGTTTTCTTATTCATAATATTAAAAACGGTTACGATATTTGTCACGA-AAGTGAT
1464753 TACAATATCGCGATTGTGG
129 TACAATATCGCGATTGTGG
* * * * * * *
1464772 ATCCTACAAACGTTTCATAACGCGTAACGGTCGTTACGAGTGTGATTTATCTCTAAAAAA
1 ATACTACAGACGTTACATAATGTGTAACGGTCGTTACGAGTGTGATTTGTTTCTAAAAAA
1464832 CATTATTTTT
Statistics
Matches: 519, Mismatches: 109, Indels: 74
0.74 0.16 0.11
Matches are distributed among these distances:
138 6 0.01
139 70 0.13
140 1 0.00
143 4 0.01
145 4 0.01
146 67 0.13
147 45 0.09
148 6 0.01
149 7 0.01
150 124 0.24
151 13 0.03
152 41 0.08
153 1 0.00
154 2 0.00
156 8 0.02
158 1 0.00
159 1 0.00
160 4 0.01
161 1 0.00
162 36 0.07
163 21 0.04
164 2 0.00
165 54 0.10
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (147 bp):
ATACTACAGACGTTACATAATGTGTAACGGTCGTTACGAGTGTGATTTGTTTCTAAAAAATTGTA
CAAATTCAATGTTTTCTTATTCATAATATTAAAAACGGTTACGATATTTGTCACGAAAGTGATTA
CAATATCGCGATTGTGG
Found at i:1472794 original size:46 final size:49
Alignment explanation
Indices: 1472741--1472832 Score: 118
Period size: 48 Copynumber: 1.9 Consensus size: 49
1472731 TACATTGTCT
* **
1472741 CTATTA-TTAGAAATT-TAAGAATTCAAAATATAT-TTAATTTATAATC
1 CTATTATTTAAAAATTATAAGAATGAAAAATATATATTAATTTATAATC
**
1472787 CTATTATTTAAAAATTATAATTATGAAAAATATATATTAATTTATA
1 CTATTATTTAAAAATTATAAGAATGAAAAATATATATTAATTTATA
1472833 TATTTATAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
46 6 0.16
47 8 0.21
48 14 0.37
49 10 0.26
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (49 bp):
CTATTATTTAAAAATTATAAGAATGAAAAATATATATTAATTTATAATC
Found at i:1472953 original size:20 final size:19
Alignment explanation
Indices: 1472914--1472965 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
1472904 TTTCTTTGAT
1472914 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
1472933 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
*
1472953 ATTTATAAAATAA
1 A-TTAAAAAATAA
1472966 GATATTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 7 0.26
20 15 0.56
21 5 0.19
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:1473028 original size:120 final size:119
Alignment explanation
Indices: 1472822--1473058 Score: 266
Period size: 120 Copynumber: 2.0 Consensus size: 119
1472812 AAAAATATAT
* * * *
1472822 ATTAATTTATATATTTATAAATAAAATATTTATTTATTTAGAAATATAAGAAAAGGACTTATAGG
1 ATTAATATATATATTTATAAATAAAATATTTATTTATTTAAAAATATAAGAAAAGGACATACAGG
* * *
1472887 TGCCTTAAGACAGCTCTTTTCTTTGATATTAAAAAATAAATAA-ATA-ATTAAAACA
66 TACCTTAAGACAGCTCCTTTC-TTAATATT-AAAAATAAA-AATATATATTAAAACA
* * *
1472942 ATTAATATATA-ATTTATAAAATAAGATATTTATTTATTTAAAAATATCAGAAAATGGACATCCA
1 ATTAATATATATATTTAT-AAATAAAATATTTATTTATTTAAAAATATAAGAAAA-GGACATACA
* ** * *
1473006 GTTATTTTAAGACTGC-CCTTTCTTAATATTGAAAATAAAAATATATATTAAAA
64 GGTACCTTAAGACAGCTCCTTTCTTAATATTAAAAATAAAAATATATATTAAAA
1473059 TATGATTATT
Statistics
Matches: 98, Mismatches: 15, Indels: 9
0.80 0.12 0.07
Matches are distributed among these distances:
117 2 0.02
118 11 0.11
119 20 0.20
120 48 0.49
121 17 0.17
ACGTcount: A:0.47, C:0.07, G:0.08, T:0.38
Consensus pattern (119 bp):
ATTAATATATATATTTATAAATAAAATATTTATTTATTTAAAAATATAAGAAAAGGACATACAGG
TACCTTAAGACAGCTCCTTTCTTAATATTAAAAATAAAAATATATATTAAAACA
Found at i:1473211 original size:15 final size:15
Alignment explanation
Indices: 1473193--1473234 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 15
1473183 AATATTGCAA
1473193 ATAATAATTAAAAAT
1 ATAATAATTAAAAAT
1473208 ATAAT-ATT-AAAAT
1 ATAATAATTAAAAAT
1473221 ATAA-AATATAAAAA
1 ATAATAAT-TAAAAA
1473235 AATTTGAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 11 0.46
14 4 0.17
15 9 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
ATAATAATTAAAAAT
Found at i:1473220 original size:26 final size:26
Alignment explanation
Indices: 1473166--1473242 Score: 72
Period size: 26 Copynumber: 3.0 Consensus size: 26
1473156 GATAAAAAGT
*
1473166 AATAATAATAATAAAATAATATTGCA
1 AATAATAATAATAAAATAATATTGAA
1473192 AATAATAATTAA-AAATATAATATT-AA
1 AATAATAA-TAATAAA-ATAATATTGAA
* *
1473218 AAT-ATAAAATATAAAAAAAT-TTGAA
1 AATAATAATA-ATAAAATAATATTGAA
1473243 TGATTAAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
24 3 0.07
25 11 0.26
26 18 0.42
27 11 0.26
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (26 bp):
AATAATAATAATAAAATAATATTGAA
Found at i:1474415 original size:3 final size:3
Alignment explanation
Indices: 1474407--1474478 Score: 76
Period size: 3 Copynumber: 24.0 Consensus size: 3
1474397 AATTACTTTT
*
1474407 TAA TAA TAA TAA TAA TAA T-A TATA TAA TAA T-A TATA TAA TAA TTA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TA-A TAA TAA TAA
* * *
1474452 TAA TTA TAA TTA TAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1474479 ATAAATAAAT
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
2 4 0.07
3 47 0.82
4 6 0.11
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:1474490 original size:18 final size:19
Alignment explanation
Indices: 1474408--1474490 Score: 64
Period size: 21 Copynumber: 4.3 Consensus size: 19
1474398 ATTACTTTTT
1474408 AATAATAAT-AATAATAATA
1 AATAATAATAAAT-ATAATA
*
1474427 TATATAATAATATATATAATA
1 -A-ATAATAATAAATATAATA
* *
1474448 ATTATAATTATAATTATAAT-
1 A--ATAATAATAAATATAATA
*
1474468 TATAATAATAAATA-AATA
1 AATAATAATAAATATAATA
1474486 AATAA
1 AATAA
1474491 AATGGGTAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
17 3 0.06
18 15 0.29
20 2 0.04
21 29 0.57
22 2 0.04
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AATAATAATAAATATAATA
Found at i:1474877 original size:113 final size:113
Alignment explanation
Indices: 1474754--1475428 Score: 1050
Period size: 113 Copynumber: 6.0 Consensus size: 113
1474744 AGAGTCATGA
*
1474754 AAAAGGTTGAACAAAATT-TTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCA
1 AAAAGGTTGAAC-AAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * * * * * *
1474818 TTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTTAAAC
65 TTATGAACTTTTCCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGC
1474867 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
1474932 TATGAAC-TTTCTCTGGAAAAGCTGATTCATCAAGTGATGGATTTGAGA
66 TATGAACTTTTC-CTGGAAAAGCTGATCCATCAAATGATGGATTTGAGC
* *
1474980 AAAATGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
1475045 TATGAACTTTTTCTGGAAAAGCTGATCCATCAAATAATGGATTTGAGC
66 TATGAACTTTTCCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGC
*
1475093 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* **
1475158 TATAAACTTTTTTTGGAAAAGCTGATCCATCAAATGATGGATTTGAGC
66 TATGAACTTTTCCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGC
*
1475206 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
1475271 TATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGC
66 TATGAACTTTTCCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGC
*
1475319 AAAAGGTTGATCAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * **
1475384 TATGAACTCTTCC-AGAAATGTTGATCCATTGAATGATGGATTTGA
66 TATGAACTTTTCCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
1475429 ACTTTGCTAA
Statistics
Matches: 525, Mismatches: 34, Indels: 7
0.93 0.06 0.01
Matches are distributed among these distances:
112 34 0.06
113 488 0.93
114 3 0.01
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTTCCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGC
Found at i:1475276 original size:339 final size:346
Alignment explanation
Indices: 1474645--1475391 Score: 1096
Period size: 339 Copynumber: 2.2 Consensus size: 346
1474635 TTGGGATTAG
* *
1474645 TTCTTCTAATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * ** ** **
1474710 GAAAAGTTGATGCTGATCTATCTCCTTTTATGATAGAGTCATGAAAAAGGTTGAACAAAATTTTC
66 GAAAAGCTGATGCTCATCTAAATCAATGGAT-ATAGAGTC---AAAAAGGTTGAACAAAATTTTC
* * * *
1474775 TCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATG
127 TCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATAAACTCTACCTGGAAAAG
*
1474840 TTGATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTC
192 CTGATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTC
* *
1474905 TTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATTCATCAAGTGAT
257 TTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGAT
*
1474970 GGATTTGAGAAAAATGTTGAACAAA
322 GGATTTGAGAAAAAGGTTGAACAAA
* *
1474995 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
*
1475060 GAAAAGCTGAT-C-CATC-AAAT-AATGGAT-TTGAG-C-AAAAGGTTGAAC-AAATTCTTCTCA
66 GAAAAGCTGATGCTCATCTAAATCAATGGATATAGAGTCAAAAAGGTTGAACAAAATT-TTCTCA
* * ***
1475117 TTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATAAACTTTTTTTGGAAAAGCTG
130 TTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATAAACTCTACCTGGAAAAGCTG
* * * *
1475182 ATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTC
195 ATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
*
1475247 CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGA
260 CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGA
* *
1475312 TTTGAGCAAAAGGTTGATCAAA
325 TTTGAGAAAAAGGTTGAACAAA
1475334 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
1475392 CTTCCAGAAA
Statistics
Matches: 362, Mismatches: 34, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
338 5 0.01
339 272 0.75
343 1 0.00
344 4 0.01
346 3 0.01
347 2 0.01
348 3 0.01
349 1 0.00
350 71 0.20
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (346 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GAAAAGCTGATGCTCATCTAAATCAATGGATATAGAGTCAAAAAGGTTGAACAAAATTTTCTCAT
TATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATAAACTCTACCTGGAAAAGCTGA
TCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCC
TTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGAT
TTGAGAAAAAGGTTGAACAAA
Found at i:1475851 original size:22 final size:22
Alignment explanation
Indices: 1475826--1475880 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
1475816 GATAAAGCTT
*
1475826 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* *
1475848 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
1475870 TCATCTTTGAA
1 TCATCTTTGAA
1475881 GAGTGTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:1476329 original size:54 final size:54
Alignment explanation
Indices: 1476247--1476402 Score: 233
Period size: 54 Copynumber: 2.9 Consensus size: 54
1476237 AGAATAGCAG
* * * *
1476247 GTTCGTAAAACATTTTACAGCGCATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGCTCAGAT
*
1476301 GTTCGTAAAACATTTGAAAACACATTCATCCTTTCCTGTGGTTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGCTCAGAT
* *
1476355 GTCCGTAAAGA-ATTTGACAACACATTCATCCTTTTCTGTGGTTTCTGC
1 GTTCGTAAA-ACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGC
1476403 CAAGATTTCT
Statistics
Matches: 93, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
54 92 0.99
55 1 0.01
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.37
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGCTCAGAT
Found at i:1480898 original size:10 final size:10
Alignment explanation
Indices: 1480844--1480911 Score: 55
Period size: 10 Copynumber: 6.4 Consensus size: 10
1480834 CTTGATTCAA
1480844 TTTTTTTCTT
1 TTTTTTTCTT
*
1480854 TTTCTTTTTTT
1 TTT-TTTTCTT
1480865 GTTTATTTTCTAT
1 -TTT-TTTTCT-T
* *
1480878 TTCTTTCCTT
1 TTTTTTTCTT
1480888 TTTTTTTCTT
1 TTTTTTTCTT
**
1480898 TTTTCCTCTT
1 TTTTTTTCTT
1480908 TTTT
1 TTTT
1480912 CTTTTTTCCT
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
10 24 0.52
11 11 0.24
12 10 0.22
13 1 0.02
ACGTcount: A:0.03, C:0.15, G:0.01, T:0.81
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:1480918 original size:29 final size:30
Alignment explanation
Indices: 1480845--1480927 Score: 71
Period size: 29 Copynumber: 2.7 Consensus size: 30
1480835 TTGATTCAAT
* *
1480845 TTTTTTCTTTTTCTTTTTTTGTTTATTTTCTA
1 TTTTTTC-TTTT-TTTTTTTCTTTATTTCCTA
* *
1480877 TTTCTTTC-CTTTTTTTTTCTTT-TTTCCTC
1 TTT-TTTCTTTTTTTTTTTCTTTATTTCCTA
**
1480906 TTTTTTCTTTTTTCCTTTCTTT
1 TTTTTTCTTTTTTTTTTTCTTT
1480928 GCTGGATTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
28 4 0.10
29 19 0.45
30 10 0.24
31 2 0.05
32 3 0.07
33 4 0.10
ACGTcount: A:0.02, C:0.17, G:0.01, T:0.80
Consensus pattern (30 bp):
TTTTTTCTTTTTTTTTTTCTTTATTTCCTA
Found at i:1480919 original size:17 final size:17
Alignment explanation
Indices: 1480889--1480921 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1480879 TCTTTCCTTT
1480889 TTTTTTCTTTTTTCCTC
1 TTTTTTCTTTTTTCCTC
1480906 TTTTTTCTTTTTTCCT
1 TTTTTTCTTTTTTCCT
1480922 TTCTTTGCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTTCTTTTTTCCTC
Found at i:1480937 original size:27 final size:26
Alignment explanation
Indices: 1480907--1480960 Score: 99
Period size: 26 Copynumber: 2.0 Consensus size: 26
1480897 TTTTTCCTCT
1480907 TTTTTCTTTTTTCCTTTCTTTGCTGGA
1 TTTTTCTTTTTT-CTTTCTTTGCTGGA
1480934 TTTTTCTTTTTTCTTTCTTTGCTGGA
1 TTTTTCTTTTTTCTTTCTTTGCTGGA
1480960 T
1 T
1480961 GAGTATAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 15 0.56
27 12 0.44
ACGTcount: A:0.04, C:0.17, G:0.11, T:0.69
Consensus pattern (26 bp):
TTTTTCTTTTTTCTTTCTTTGCTGGA
Found at i:1484285 original size:14 final size:14
Alignment explanation
Indices: 1484251--1484307 Score: 69
Period size: 14 Copynumber: 4.0 Consensus size: 14
1484241 CATAAAAATA
* *
1484251 CAAATGCAAAGATG
1 CAAATGTAAATATG
1484265 CCAAATGTAAATATG
1 -CAAATGTAAATATG
*
1484280 CAAATGTAAAAATG
1 CAAATGTAAATATG
*
1484294 TAAATGTAAATATG
1 CAAATGTAAATATG
1484308 TGAATACCAG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
14 25 0.68
15 12 0.32
ACGTcount: A:0.51, C:0.09, G:0.16, T:0.25
Consensus pattern (14 bp):
CAAATGTAAATATG
Found at i:1486521 original size:46 final size:49
Alignment explanation
Indices: 1486468--1486559 Score: 118
Period size: 48 Copynumber: 1.9 Consensus size: 49
1486458 TACATTGTCT
* **
1486468 CTATTA-TTAGAAATT-TAAGAATTCAAAATATAT-TTAATTTATAATC
1 CTATTATTTAAAAATTATAAGAATGAAAAATATATATTAATTTATAATC
**
1486514 CTATTATTTAAAAATTATAATTATGAAAAATATATATTAATTTATA
1 CTATTATTTAAAAATTATAAGAATGAAAAATATATATTAATTTATA
1486560 TATTTATAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
46 6 0.16
47 8 0.21
48 14 0.37
49 10 0.26
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (49 bp):
CTATTATTTAAAAATTATAAGAATGAAAAATATATATTAATTTATAATC
Found at i:1486680 original size:20 final size:19
Alignment explanation
Indices: 1486641--1486692 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
1486631 TTTCTTTGAT
1486641 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
1486660 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
*
1486680 ATTTATAAAATAA
1 A-TTAAAAAATAA
1486693 GATATTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 7 0.26
20 15 0.56
21 5 0.19
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:1486940 original size:15 final size:15
Alignment explanation
Indices: 1486922--1486963 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 15
1486912 AATATTGCAA
1486922 ATAATAATTAAAAAT
1 ATAATAATTAAAAAT
1486937 ATAAT-ATT-AAAAT
1 ATAATAATTAAAAAT
1486950 ATAA-AATATAAAAA
1 ATAATAAT-TAAAAA
1486964 AATTTGAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 11 0.46
14 4 0.17
15 9 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
ATAATAATTAAAAAT
Found at i:1486949 original size:26 final size:26
Alignment explanation
Indices: 1486895--1486971 Score: 72
Period size: 26 Copynumber: 3.0 Consensus size: 26
1486885 GATAAAAAGT
*
1486895 AATAATAATAATAAAATAATATTGCA
1 AATAATAATAATAAAATAATATTGAA
1486921 AATAATAATTAA-AAATATAATATT-AA
1 AATAATAA-TAATAAA-ATAATATTGAA
* *
1486947 AAT-ATAAAATATAAAAAAAT-TTGAA
1 AATAATAATA-ATAAAATAATATTGAA
1486972 TGATTAAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
24 3 0.07
25 11 0.26
26 18 0.42
27 11 0.26
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (26 bp):
AATAATAATAATAAAATAATATTGAA
Found at i:1488161 original size:3 final size:3
Alignment explanation
Indices: 1488153--1488222 Score: 88
Period size: 3 Copynumber: 23.0 Consensus size: 3
1488143 AATTATTTTT
*
1488153 TAA TAA TAA TAA TAA TAA TATA TAA TAA T-A TATA TAA TAA TTA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TA-A TAA TAA TAA TAA
* *
1488199 TAA TAA TTA TAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
1488223 ATAAATAAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.03
3 50 0.86
4 6 0.10
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:1493144 original size:85 final size:85
Alignment explanation
Indices: 1492998--1493556 Score: 219
Period size: 83 Copynumber: 6.6 Consensus size: 85
1492988 ATGTGTCATC
* * ***
1492998 GAGCTGAGTGGAATCAAACTCGAAAGTTTTTGTTGACAGATAGTTTTTCTCGACTTAAGCTATGA
1 GAGCTGAATGGAATCAAACTCGAAAGTATTTGTTGACAGATAGCCCTTCTCGACTTAAGCTATGA
*
1493063 TGTATATTTGACCTGCCCTT
66 TGTAAATTTGACCTGCCCTT
* * *
1493083 GAGCTGAATGGAATCAAACTC-AAAGGTATTTGTTGACAGATAGCCCTTCTTGCCTTTAGCTATG
1 GAGCTGAATGGAATCAAACTCGAAA-GTATTTGTTGACAGATAGCCCTTCTCGACTTAAGCTATG
* **
1493147 TTGTAAATTTGATTTG-CCTCT
65 ATGTAAATTTGACCTGCCCT-T
* * * * * * * * * *
1493168 AAGCTGAGTGTGTAATCGAACTCGAAGGTCTTTTGTTTG-TAGATAGGCTTTCTCGCCTTGAGCT
1 GAGCTGAATG-G-AATCAAACTCGAAAGT-ATTTG-TTGACAGATAGCCCTTCTCGACTTAAGCT
* ** ** * *
1493232 ATGCTACAAA--TGATGTACCTTT
62 ATGATGTAAATTTGACCTGCCCTT
* * * * * * * * * * * * *
1493254 AAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATATCTCTTCTCGCCTTGAGGTATGC
1 GAGCTGAATGGAATCAAACTCGAAAGTATTTGTTGACAGATAGCCCTTCTCGACTTAAGCTATGA
** ** *
1493319 TACAAA--TGATGTGCCTTT
66 TGTAAATTTGACCTGCCCTT
* * * * * * * *
1493337 GAGCTGAGTGTAATCAAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGCCTTGAGCTAT-
1 GAGCTGAATGGAATCAAACTCGAAAGTATTT-GTTGACAGATAGCCCTTCTCGACTTAAGCTATG
* ** **
1493401 ATTGCAAA--TGATGTGCATTT
65 A-TGTAAATTTGACCTGCCCTT
* * * * * * * * * *
1493421 GAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGA
1 GAGCTGAATGGAATCAAACTCGAAAGTATTTGTTGACAGATAGCCCTTCTCGACTTAAGCTATGA
** *
1493486 TGTAAA--TGATGTGCCTTT
66 TGTAAATTTGACCTGCCCTT
* * * * *
1493504 GAGCT-AAGTGTAATCGAACTC-AAAGGTTTTTTGTTGGCAGATAACCCTTCTCG
1 GAGCTGAA-TGGAATCAAACTCGAAA-G-TATTTGTTGACAGATAGCCCTTCTCG
1493557 TCTTGAGTTA
Statistics
Matches: 400, Mismatches: 59, Indels: 31
0.82 0.12 0.06
Matches are distributed among these distances:
82 6 0.01
83 136 0.34
84 119 0.30
85 73 0.18
86 17 0.04
87 13 0.03
88 33 0.08
89 3 0.01
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (85 bp):
GAGCTGAATGGAATCAAACTCGAAAGTATTTGTTGACAGATAGCCCTTCTCGACTTAAGCTATGA
TGTAAATTTGACCTGCCCTT
Found at i:1493365 original size:167 final size:168
Alignment explanation
Indices: 1493076--1494206 Score: 1313
Period size: 167 Copynumber: 6.7 Consensus size: 168
1493066 ATATTTGACC
* * * * * * * * * *
1493076 TGCCCTTGAGCTGAATGGAATCAAACTCAAAGGTATTT-GTTGACAGATAGCCCTTCTTGCCTTT
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGCCTTG
* ** ** * *
1493140 AGCTATGTTGTAAATTTGATTTGCCTCTAAGCTGAGTGTGTAATCGAACTCGAAGGTCTTTTGTT
66 AGCTATGCTACAAA--TGATGCGCCTTTGAGCTGA--GTGTAATCGAACTCGAAGGTCTTTTGTT
* * ** * *
1493205 TGTAGATAGGCTTTCTCGCCTTGAGCTATGCTACAAATGATG
127 GGCAGATAACCCTTCTCGCCTTGAGCTATGCTGCAAATGATG
* * * * *
1493247 TACCTTTAAGCTGAGTGTAATCGAACTCGAAGGTC-TTGGTTGACAGATATCTCTTCTCGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGCCTTG
* * * *
1493311 AGGTATGCTACAAATGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTGGTTGGCA
66 AGCTATGCTACAAATGATGCGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCA
**
1493376 GATAACCCTTCTCGCCTTGAGCTATATTGCAAATGATG
131 GATAACCCTTCTCGCCTTGAGCTATGCTGCAAATGATG
* *
1493414 TGCATTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTGGTTGACAGATAACCCTTCTCGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGCCTTG
* * ** * * * *
1493478 AGTTATGATGTAAATGATGTGCCTTTGAGCTAAGTGTAATCGAACTCAAAGGTTTTTTGTTGGCA
66 AGCTATGCTACAAATGATGCGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCA
* * *
1493543 GATAACCCTTCTCGTCTTGAGTTATGCTTCAAATGATG
131 GATAACCCTTCTCGCCTTGAGCTATGCTGCAAATGATG
* * * * *
1493581 TGCCTTTGAGTTGAGTGTAATCGAACTCGAAGGTCTTTTGTTTGCATATAACCCTTCTCACCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGCCTTG
* * * *
1493646 AGCTATGTTACAAATGATGCGCCTTTGAGCTGAGTGTAATTGAACTCGAAGGTC-TTGGTTGACA
66 AGCTATGCTACAAATGATGCGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCA
* *
1493710 GATAACCCTTTCTCGCCTTGAGTTATGCTGTAAATGATG
131 GATAACCC-TTCTCGCCTTGAGCTATGCTGCAAATGATG
* * * * *
1493749 TGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGGTAGATAGCCATTCTCGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGCCTTG
* * *
1493814 AGCTATGCTGCAAACGATGCGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC--TTGATTGAC
66 AGCTATGCTACAAATGATGCGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTG-TTGGC
* * *
1493877 AGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATAATG
130 AGATAACCCTTCTCGCCTTGAGCTATGCTGCAAATGATG
* * * * *
1493916 TGCCTTTGAGCTTAGTGTAATTGAACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTCGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGCCTTG
* *
1493981 AGCTATGCTACAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTATTGGCA
66 AGCTATGCTACAAATGATGCGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCA
* *
1494046 GATAGCCCTTCTAGCCTT-ATGCTATGCTGCAAATGATG
131 GATAACCCTTCTCGCCTTGA-GCTATGCTGCAAATGATG
* * * * * * ** * *
1494084 CGCCTTTGAGCTGAGTATAATTGAACTCGAAGGTTTTTTGTTGGCATATAACATTTATTGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGCCTTG
* * * * *
1494149 AGTTATGCTGCAAATGATACGCCTTTGAGCTGAGTGTAATCGAACTCAAAGGTATTTT
66 AGCTATGCTACAAATGATGCGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTT
1494207 ACTCAAGGTG
Statistics
Matches: 838, Mismatches: 115, Indels: 17
0.86 0.12 0.02
Matches are distributed among these distances:
167 399 0.48
168 360 0.43
169 18 0.02
170 2 0.00
171 59 0.07
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (168 bp):
TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGCCTTG
AGCTATGCTACAAATGATGCGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCA
GATAACCCTTCTCGCCTTGAGCTATGCTGCAAATGATG
Found at i:1493413 original size:84 final size:84
Alignment explanation
Indices: 1493076--1494206 Score: 1349
Period size: 84 Copynumber: 13.5 Consensus size: 84
1493066 ATATTTGACC
* * * * * * * * * *
1493076 TGCCCTTGAGCTGAATGGAATCAAACTCAAAGGT-ATTTGTTGACAGATAGCCCTTCTTGCCTTT
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTG
* * *
1493140 AGCTATGTTGTAAATTTGATT
66 AGCTATGCTGCAAA--TGATG
* * * * ** *
1493161 TGCCTCTAAGCTGAGTGTGTAATCGAACTCGAAGGTCTTTTGTTTGTAGATAGGCTTTCTCGCCT
1 TGCCTTTGAGCTGA--GTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCT
*
1493226 TGAGCTATGCTACAAATGATG
64 TGAGCTATGCTGCAAATGATG
* * * * * *
1493247 TACCTTTAAGCTGAGTGTAATCGAACTCGAAGGTC-TTGGTTGACAGATATCTCTTCTCGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTG
* *
1493311 AGGTATGCTACAAATGATG
66 AGCTATGCTGCAAATGATG
* *
1493330 TGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTG
**
1493395 AGCTATATTGCAAATGATG
66 AGCTATGCTGCAAATGATG
* * *
1493414 TGCATTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTGGTTGACAGATAACCCTTCTCGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTG
* * *
1493478 AGTTATGATGTAAATGATG
66 AGCTATGCTGCAAATGATG
* * * *
1493497 TGCCTTTGAGCTAAGTGTAATCGAACTCAAAGGTTTTTTGTTGGCAGATAACCCTTCTCGTCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTG
* *
1493562 AGTTATGCTTCAAATGATG
66 AGCTATGCTGCAAATGATG
* * * *
1493581 TGCCTTTGAGTTGAGTGTAATCGAACTCGAAGGTCTTTTGTTTGCATATAACCCTTCTCACCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTG
* *
1493646 AGCTATGTTACAAATGATG
66 AGCTATGCTGCAAATGATG
* * * *
1493665 CGCCTTTGAGCTGAGTGTAATTGAACTCGAAGGTC-TTGGTTGACAGATAACCCTTTCTCGCCTT
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCC-TTCTCGCCTT
* *
1493729 GAGTTATGCTGTAAATGATG
65 GAGCTATGCTGCAAATGATG
* * * *
1493749 TGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGGTAGATAGCCATTCTCGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTG
*
1493814 AGCTATGCTGCAAACGATG
66 AGCTATGCTGCAAATGATG
* *
1493833 CGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC--TTGATTGACAGATAACCCTTCTCGCCTT
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTG-TTGGCAGATAACCCTTCTCGCCTT
* * *
1493896 GAGTTATGCTGTAAATAATG
65 GAGCTATGCTGCAAATGATG
* * * *
1493916 TGCCTTTGAGCTTAGTGTAATTGAACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTCGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTG
*
1493981 AGCTATGCTACAAATGATG
66 AGCTATGCTGCAAATGATG
* * *
1494000 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTATTGGCAGATAGCCCTTCTAGCCTT-
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTG
1494064 ATGCTATGCTGCAAATGATG
66 A-GCTATGCTGCAAATGATG
* * * * * ** * *
1494084 CGCCTTTGAGCTGAGTATAATTGAACTCGAAGGTTTTTTGTTGGCATATAACATTTATTGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTG
* *
1494149 AGTTATGCTGCAAATGATA
66 AGCTATGCTGCAAATGATG
* * *
1494168 CGCCTTTGAGCTGAGTGTAATCGAACTCAAAGGTATTTT
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTT
1494207 ACTCAAGGTG
Statistics
Matches: 900, Mismatches: 134, Indels: 25
0.85 0.13 0.02
Matches are distributed among these distances:
82 3 0.00
83 228 0.25
84 576 0.64
85 28 0.03
86 16 0.02
87 16 0.02
88 33 0.04
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (84 bp):
TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTG
AGCTATGCTGCAAATGATG
Found at i:1493957 original size:419 final size:419
Alignment explanation
Indices: 1493076--1494206 Score: 1527
Period size: 419 Copynumber: 2.7 Consensus size: 419
1493066 ATATTTGACC
* * * * * * * *
1493076 TGCCCTTGAGCTGAA-TGGAATCAAACTCAAAGGT-ATTTGTTGACAGATAGCCCTTCTTGCCTT
1 TGCCTTTGAGCT-AAGTGTAATCGAACTCAAAGGTCTTTTGTTGGCAAATAACCCTTCTCGCCTT
* * ** * * *
1493139 TAGCTATGTTGTAAATTTGATTTGCCTCTAAGCTGAGTGTGTAATCGAACTCGAAGGTCTTTTGT
65 GAGCTATGCTACAAA--TGATGTGCCTTTGAGCTGA--GTGTAATCGAACTCGAAGGTCTTTTGT
* * * * ** * *
1493204 TTGTAGATAGGCTTTCTCGCCTTGAGCTATGCTACAAATGATGTACCTTTAAGCTGAGTGTAATC
126 TTGCAGATAGCCCTTCTCACCTTGAGCTATGCTACAAATGATGCGCCTTTGAGCTGAGTGTAATT
* * * *
1493269 GAACTCGAAGGTCTTGGTTGACAGATATCTC-TTCTCGCCTTGAGGTATGCTACAAATGATGTGC
191 GAACTCGAAGGTCTTGGTTGACAGATAACCCTTTCTCGCCTTGAGTTATGCTGCAAATGATGTGC
* *
1493333 CTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGCCTTGAGC
256 CTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGGCAGATAACCATTCTCGCCTTGAGC
* * * *
1493398 TATATTGCAAATGATGTGCATTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATA
321 TATACTGCAAACGATGCGCATTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGATTGACAGATA
*
1493463 ACCCTTCTCGCCTTGAGTTATGATGTAAATGATG
386 ACCCTTCTCGCCTTGAGTTATGATGTAAATAATG
* * *
1493497 TGCCTTTGAGCTAAGTGTAATCGAACTCAAAGGTTTTTTGTTGGCAGATAACCCTTCTCGTCTTG
1 TGCCTTTGAGCTAAGTGTAATCGAACTCAAAGGTCTTTTGTTGGCAAATAACCCTTCTCGCCTTG
* * *
1493562 AGTTATGCTTCAAATGATGTGCCTTTGAGTTGAGTGTAATCGAACTCGAAGGTCTTTTGTTTGCA
66 AGCTATGCTACAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTTGCA
* * *
1493627 TATAACCCTTCTCACCTTGAGCTATGTTACAAATGATGCGCCTTTGAGCTGAGTGTAATTGAACT
131 GATAGCCCTTCTCACCTTGAGCTATGCTACAAATGATGCGCCTTTGAGCTGAGTGTAATTGAACT
*
1493692 CGAAGGTCTTGGTTGACAGATAACCCTTTCTCGCCTTGAGTTATGCTGTAAATGATGTGCCTTTG
196 CGAAGGTCTTGGTTGACAGATAACCCTTTCTCGCCTTGAGTTATGCTGCAAATGATGTGCCTTTG
* * *
1493757 AGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGGTAGATAGCCATTCTCGCCTTGAGCTATGC
261 AGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGGCAGATAACCATTCTCGCCTTGAGCTATAC
*
1493822 TGCAAACGATGCGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGATTGACAGATAACCCT
326 TGCAAACGATGCGCATTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGATTGACAGATAACCCT
*
1493887 TCTCGCCTTGAGTTATGCTGTAAATAATG
391 TCTCGCCTTGAGTTATGATGTAAATAATG
* * * *
1493916 TGCCTTTGAGCTTAGTGTAATTGAACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTCGCCTTG
1 TGCCTTTGAGCTAAGTGTAATCGAACTCAAAGGTCTTTTGTTGGCAAATAACCCTTCTCGCCTTG
* *
1493981 AGCTATGCTACAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTATTGGCA
66 AGCTATGCTACAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTTGCA
* *
1494046 GATAGCCCTTCT-AGCCTT-ATGCTATGCTGCAAATGATGCGCCTTTGAGCTGAGTATAATTGAA
131 GATAGCCCTTCTCA-CCTTGA-GCTATGCTACAAATGATGCGCCTTTGAGCTGAGTGTAATTGAA
* * * * * * * **
1494109 CTCGAAGGTTTTTTGTTGGCATATAA-CATTTATTGCCTTGAGTTATGCTGCAAATGATACGCCT
194 CTCGAAGG-TCTTGGTTGACAGATAACCCTTTCTCGCCTTGAGTTATGCTGCAAATGATGTGCCT
* * *
1494173 TTGAGCTGAGTGTAATCGAACTCAAAGGTATTTT
258 TTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTT
1494207 ACTCAAGGTG
Statistics
Matches: 629, Mismatches: 75, Indels: 14
0.88 0.10 0.02
Matches are distributed among these distances:
418 112 0.18
419 425 0.68
420 30 0.05
421 28 0.04
422 34 0.05
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (419 bp):
TGCCTTTGAGCTAAGTGTAATCGAACTCAAAGGTCTTTTGTTGGCAAATAACCCTTCTCGCCTTG
AGCTATGCTACAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTTGCA
GATAGCCCTTCTCACCTTGAGCTATGCTACAAATGATGCGCCTTTGAGCTGAGTGTAATTGAACT
CGAAGGTCTTGGTTGACAGATAACCCTTTCTCGCCTTGAGTTATGCTGCAAATGATGTGCCTTTG
AGCTGAGTGTAATCAAACTCGAAGGTCTTTTGTTGGCAGATAACCATTCTCGCCTTGAGCTATAC
TGCAAACGATGCGCATTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGATTGACAGATAACCCT
TCTCGCCTTGAGTTATGATGTAAATAATG
Found at i:1495187 original size:95 final size:95
Alignment explanation
Indices: 1495003--1495265 Score: 296
Period size: 95 Copynumber: 2.7 Consensus size: 95
1494993 GGCTAGCTGG
* * * * * * * *
1495003 ATCCATAAAGCTGGGGCGTTTAACCAATTTCTCTAAAAGGATAGCTCAATATCGTTGTA-TAGAT
1 ATCCATAAAGCTGGGGAGTTTAACCAATTGCTCTAGAGGGACAACTC-A-AGC-TT-TATTATAT
* * *
1495067 ATTCTAATCACTTTTATCAGTCTAGCTGAATATT
62 ATTATAATCACCTTTATCAGGCTAGCTGAATATT
* * * *
1495101 ATCTATAAAGCCT-GGGAGTTTAACCAATTGCTCTAGCGGGACAACTCGAGCTTTATTGTATATT
1 ATCCATAAAG-CTGGGGAGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTATATATT
*
1495165 ATAATCACCTTTATCAGGCTAGCTGAATCTT
65 ATAATCACCTTTATCAGGCTAGCTGAATATT
* *
1495196 ATCCATAAAGCTGGGGCGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTATATATAT
1 ATCCATAAAGCTGGGGAGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTATATAT-T
1495261 ATAAT
65 ATAAT
1495266 ATTATAATCT
Statistics
Matches: 139, Mismatches: 22, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
94 4 0.03
95 89 0.64
96 8 0.06
98 36 0.26
99 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (95 bp):
ATCCATAAAGCTGGGGAGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTATATATTA
TAATCACCTTTATCAGGCTAGCTGAATATT
Found at i:1502455 original size:37 final size:37
Alignment explanation
Indices: 1502411--1502506 Score: 138
Period size: 37 Copynumber: 2.6 Consensus size: 37
1502401 CTTTTCGTCG
* *
1502411 TACTAGGATTCAAACTCCTAAAAATATGATAGAATTT
1 TACTAGGATTCAAACTCCTAAAAATAAGATAGAATTC
* *
1502448 TGCTAGGATTCAAACTCCTAAAAATAAGATAGAGTTC
1 TACTAGGATTCAAACTCCTAAAAATAAGATAGAATTC
* *
1502485 TACTATGATTTAAACTCCTAAA
1 TACTAGGATTCAAACTCCTAAA
1502507 GATAGGATCC
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 52 1.00
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.31
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATAAGATAGAATTC
Found at i:1503123 original size:12 final size:13
Alignment explanation
Indices: 1503092--1503174 Score: 50
Period size: 12 Copynumber: 6.5 Consensus size: 13
1503082 TTTGCATTTT
*
1503092 TATTATTACTATTG
1 TATT-TTACTATTA
*
1503106 TA-TTTATTATTA
1 TATTTTACTATTA
1503118 T-TTTTACTATTA
1 TATTTTACTATTA
*
1503130 TATTTTCCT-TT-
1 TATTTTACTATTA
*
1503141 TATTCTACTTATTTA
1 TATTTTAC-TA-TTA
*
1503156 TATTATA-TATGTA
1 TATTTTACTAT-TA
1503169 TATTTT
1 TATTTT
1503175 TATATTTTAT
Statistics
Matches: 54, Mismatches: 8, Indels: 15
0.70 0.10 0.19
Matches are distributed among these distances:
11 6 0.11
12 22 0.41
13 16 0.30
14 4 0.07
15 6 0.11
ACGTcount: A:0.27, C:0.07, G:0.02, T:0.64
Consensus pattern (13 bp):
TATTTTACTATTA
Found at i:1503202 original size:26 final size:27
Alignment explanation
Indices: 1503150--1503199 Score: 79
Period size: 24 Copynumber: 2.0 Consensus size: 27
1503140 TTATTCTACT
1503150 TATTTATATTATATATGTATATTTTTA
1 TATTTATATTATATATGTATATTTTTA
1503177 TATTT-TATTAT-TAT-TATATTTTT
1 TATTTATATTATATATGTATATTTTT
1503200 TTACTTTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 9 0.39
25 3 0.13
26 6 0.26
27 5 0.22
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (27 bp):
TATTTATATTATATATGTATATTTTTA
Found at i:1503469 original size:2 final size:2
Alignment explanation
Indices: 1503462--1503492 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1503452 TTACTATTAC
1503462 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1503493 TCTACACAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1503653 original size:2 final size:2
Alignment explanation
Indices: 1503646--1503726 Score: 162
Period size: 2 Copynumber: 40.5 Consensus size: 2
1503636 GTATTGTTAC
1503646 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1503688 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1503727 TGTAATTATC
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 79 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1503824 original size:12 final size:11
Alignment explanation
Indices: 1503807--1503926 Score: 53
Period size: 11 Copynumber: 10.1 Consensus size: 11
1503797 AATTTATATA
1503807 TATTTACTTTTT
1 TATTTA-TTTTT
*
1503819 TATTTATTTTA
1 TATTTATTTTT
* * *
1503830 TATATATATAT
1 TATTTATTTTT
*
1503841 TATTCGTACTTTGT
1 TATT--TA-TTTTT
1503855 TA-TTATTATTT
1 TATTTATT-TTT
*
1503866 TGTTTATTTGTTT
1 TATTTA-TT-TTT
1503879 TATTTATTTTCT
1 TATTTATTTT-T
* *
1503891 TTTTCTTTTTTT
1 TATT-TATTTTT
*
1503903 TATATATTTTAT
1 TATTTATTTT-T
*
1503915 TATTTGTTTTT
1 TATTTATTTTT
1503926 T
1 T
1503927 TACTTACTAT
Statistics
Matches: 80, Mismatches: 19, Indels: 19
0.68 0.16 0.16
Matches are distributed among these distances:
10 2 0.03
11 28 0.35
12 27 0.34
13 18 0.22
14 5 0.06
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.72
Consensus pattern (11 bp):
TATTTATTTTT
Found at i:1503885 original size:22 final size:21
Alignment explanation
Indices: 1503850--1503928 Score: 63
Period size: 24 Copynumber: 3.6 Consensus size: 21
1503840 TTATTCGTAC
1503850 TTTGTTATTA-TTATTTTGTTTA
1 TTTGTT-TTATTTATTTT-TTTA
*
1503872 TTTGTTTTATTTATTTTCTTTTTC
1 TTTGTTTTATTTA--TT-TTTTTA
* * *
1503896 TTTTTTTTATATATTTTATTA
1 TTTGTTTTATTTATTTTTTTA
1503917 TTTGTTTT-TTTA
1 TTTGTTTTATTTA
1503929 CTTACTATTT
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
20 3 0.07
21 14 0.30
22 11 0.24
24 16 0.35
25 2 0.04
ACGTcount: A:0.15, C:0.03, G:0.05, T:0.77
Consensus pattern (21 bp):
TTTGTTTTATTTATTTTTTTA
Found at i:1503903 original size:24 final size:25
Alignment explanation
Indices: 1503876--1503927 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
1503866 TGTTTATTTG
* *
1503876 TTTTATTTATTTTCTT-TTTCTTTT
1 TTTTATATATTTTATTATTTCTTTT
*
1503900 TTTTATATATTTTATTATTTGTTTT
1 TTTTATATATTTTATTATTTCTTTT
1503925 TTT
1 TTT
1503928 ACTTACTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.13, C:0.04, G:0.02, T:0.81
Consensus pattern (25 bp):
TTTTATATATTTTATTATTTCTTTT
Found at i:1508423 original size:14 final size:14
Alignment explanation
Indices: 1508406--1508461 Score: 57
Period size: 13 Copynumber: 4.1 Consensus size: 14
1508396 GGGAAAAAAC
1508406 AAAAAAGAAGC-AA
1 AAAAAAGAAGCAAA
*
1508419 AAAAAAGAAAACAAA
1 AAAAAAG-AAGCAAA
1508434 AAAAAAGAA-CAAA
1 AAAAAAGAAGCAAA
1508447 AATAAAA-AAG-AAA
1 AA-AAAAGAAGCAAA
1508460 AA
1 AA
1508462 GGGACAAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
13 20 0.53
14 9 0.24
15 9 0.24
ACGTcount: A:0.84, C:0.05, G:0.09, T:0.02
Consensus pattern (14 bp):
AAAAAAGAAGCAAA
Found at i:1508424 original size:15 final size:14
Alignment explanation
Indices: 1508401--1508454 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 14
1508391 AAAAAGGGAA
1508401 AAAACAAAAAAGAAGC
1 AAAA-AAAAAAGAA-C
1508417 AAAAAAAAGAA-AAC
1 AAAAAAAA-AAGAAC
1508431 -AAAAAAAAAGAAC
1 AAAAAAAAAAGAAC
1508444 AAAAATAAAAA
1 AAAAA-AAAAA
1508455 AGAAAAAGGG
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
12 2 0.06
13 10 0.29
14 5 0.15
15 11 0.32
16 6 0.18
ACGTcount: A:0.83, C:0.07, G:0.07, T:0.02
Consensus pattern (14 bp):
AAAAAAAAAAGAAC
Found at i:1508429 original size:25 final size:24
Alignment explanation
Indices: 1508401--1508462 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 24
1508391 AAAAAGGGAA
1508401 AAAACAAAAAAGAAGCAAAAAAAAG
1 AAAACAAAAAAGAAG-AAAAAAAAG
* * *
1508426 AAAACAAAAAAAAAGAACAAAAAT
1 AAAACAAAAAAGAAGAAAAAAAAG
*
1508450 AAAAAAGAAAAAG
1 AAAACA-AAAAAG
1508463 GGACAAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
24 12 0.39
25 19 0.61
ACGTcount: A:0.82, C:0.06, G:0.10, T:0.02
Consensus pattern (24 bp):
AAAACAAAAAAGAAGAAAAAAAAG
Found at i:1509134 original size:22 final size:22
Alignment explanation
Indices: 1509071--1509137 Score: 125
Period size: 22 Copynumber: 3.0 Consensus size: 22
1509061 CAAATCGTTC
*
1509071 AGCATCAAATGCCAAACCTATG
1 AGCATCAAATGCCAAACCTTTG
1509093 AGCATCAAATGCCAAACCTTTG
1 AGCATCAAATGCCAAACCTTTG
1509115 AGCATCAAATGCCAAACCTTTG
1 AGCATCAAATGCCAAACCTTTG
1509137 A
1 A
1509138 CCAAACATAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.39, C:0.27, G:0.13, T:0.21
Consensus pattern (22 bp):
AGCATCAAATGCCAAACCTTTG
Found at i:1510216 original size:106 final size:106
Alignment explanation
Indices: 1510028--1511433 Score: 2069
Period size: 106 Copynumber: 13.3 Consensus size: 106
1510018 CAATTTTCCA
* * * *
1510028 AGCCAATTTCAACTTCACACCAAAAGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* * *
1510093 AAGGGACCGCTGATTGTCAATAAACAATTTCCCAATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAG
* * *
1510134 AGCCAATTTCAACTTCACAGCGAAGGATATTGGACTTCAGATAACACAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
** * *
1510199 AAGGGACATCTGGTTGTCAATAAACAACTTTCCAATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAG
* **
1510240 AGCCAATTTTAACTTCACAGATAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* *
1510305 AAGGGGCCGCTGGTTGTCAACAAACAACTTCTCAATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAG
* * * *
1510346 AGCCAATTTTAACTTCACAACGAATGATATTGGACTCCAAACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
1510411 AAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAG
* *
1510452 AGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACATCACAACG
1 AGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
1510517 AAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAG
* * *
1510558 AGCCAATTTCAACTTTACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATG
1 AGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* * *
1510623 AAGGGACTGTTGGTTGTCAACAAACAACTTCTCAATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAG
* *
1510664 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGAAAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* * * *
1510729 AAGGAACCGCTGGTTGTTAACAAATAATTTCCCAATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAG
* *
1510770 AGCCAATTTCAACTTCACAGTGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* **
1510835 AAGGGACCGCTGGTTGTCAATAATTAACTTCCCAATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAG
1510876 AGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* *
1510941 AAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTTAG
66 AAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAG
* *
1510982 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACTCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* *
1511047 AAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAG
* * *
1511088 AGCCAATTTCAACTTCACAGCGTAGGATATTGGACTCAAGACAACGAAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
1511153 AAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAG
* * * * *
1511194 AGCCAATTTTAACTTCTCAGCGAAGGATCTTGGAC-CCAAGACAACACAAGCTCAACTTCACGAC
1 AGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC-AGACAACGCAAGTTCAACTTCACGAC
* * *
1511258 GAAAGG---GCTGATTGTCAAC-AA-AA-TT-TC-A-TTCAG
65 GAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAG
* * * *
1511291 AGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACG
1 AGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* * ** *
1511356 AAGGGACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAG
66 AAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAG
*
1511397 AGCCAATTTCAACTTCAC-GACGGAGGATATTGGACTC
1 AGCCAATTTCAACTTCACAG-CGAAGGATATTGGACTC
1511434 GGAACAATGC
Statistics
Matches: 1177, Mismatches: 111, Indels: 24
0.90 0.08 0.02
Matches are distributed among these distances:
97 65 0.06
98 2 0.00
99 1 0.00
100 14 0.01
101 4 0.00
102 4 0.00
103 13 0.01
104 1 0.00
105 2 0.00
106 1071 0.91
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
AGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
AAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAG
Found at i:1512899 original size:23 final size:24
Alignment explanation
Indices: 1512858--1512904 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
1512848 TTATTCTACT
1512858 TATTTATATTATATATATTTTTTA
1 TATTTATATTATATATATTTTTTA
1512882 TATTT-TATTAT-TATTATTTTTTA
1 TATTTATATTATATA-TATTTTTTA
1512905 CTTTCTCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 2 0.09
23 15 0.68
24 5 0.23
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (24 bp):
TATTTATATTATATATATTTTTTA
Found at i:1512936 original size:11 final size:11
Alignment explanation
Indices: 1512920--1512958 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
1512910 TCTTTCTTTT
1512920 TATTATTCTTG
1 TATTATTCTTG
*
1512931 TATTATACTTG
1 TATTATTCTTG
*
1512942 TATTATT-TTA
1 TATTATTCTTG
1512952 TATTATT
1 TATTATT
1512959 TATTTTGTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.64
Consensus pattern (11 bp):
TATTATTCTTG
Found at i:1513493 original size:29 final size:27
Alignment explanation
Indices: 1513426--1513480 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
1513416 TTGTCATTTA
* *
1513426 ATTTATTAATT-TATATATATTTACTT
1 ATTTATTTATTATATATATATATACTT
1513452 ATTTATTTATTATATATATATATA-TT
1 ATTTATTTATTATATATATATATACTT
1513478 ATT
1 ATT
1513481 CTTACTTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 15 0.58
27 11 0.42
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (27 bp):
ATTTATTTATTATATATATATATACTT
Found at i:1513521 original size:22 final size:22
Alignment explanation
Indices: 1513486--1513547 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
1513476 TTATTCTTAC
*
1513486 TTTGTTATTA-TTATTTTGTTTA
1 TTTGTT-TTATTTATTTTCTTTA
*
1513508 TTTGTTTTATTTATTTTCTTTT
1 TTTGTTTTATTTATTTTCTTTA
* *
1513530 TCTTTTTTTATATATTTT
1 T-TTGTTTTATTTATTTT
1513548 ATTATTATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 3 0.09
22 17 0.50
23 14 0.41
ACGTcount: A:0.15, C:0.03, G:0.05, T:0.77
Consensus pattern (22 bp):
TTTGTTTTATTTATTTTCTTTA
Found at i:1513561 original size:23 final size:23
Alignment explanation
Indices: 1513512--1513561 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
1513502 TGTTTATTTG
* * * * *
1513512 TTTTATTTATTTTCTTTTTCTTT
1 TTTTATATATTTTATTATTATTA
1513535 TTTTATATATTTTATTATTATTA
1 TTTTATATATTTTATTATTATTA
1513558 TTTT
1 TTTT
1513562 TACTTACTAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (23 bp):
TTTTATATATTTTATTATTATTA
Found at i:1515236 original size:30 final size:31
Alignment explanation
Indices: 1515200--1515261 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
1515190 CCCGAAGTAC
*
1515200 CAGTCCATA-ATCCCGAAGAACCTAGGTAAA
1 CAGTCCATATATCCCGAAGAACATAGGTAAA
* *
1515230 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATATCCCGAAGAACATAGGTAAA
1515261 C
1 C
1515262 CCTCGACCCT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 9 0.32
31 19 0.68
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (31 bp):
CAGTCCATATATCCCGAAGAACATAGGTAAA
Done.