Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008480.1 Hibiscus syriacus cultivar Beakdansim tig00111311_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: 2515485
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 13
Found at i:1303599 original size:20 final size:20
Alignment explanation
Indices: 1303574--1303620 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
1303564 GAAAAGGATT
*
1303574 GGTGGTGTTTGAATGTGGTA
1 GGTGGTGTTTGAACGTGGTA
1303594 GGTGGTGTTTGAACGTGGTA
1 GGTGGTGTTTGAACGTGGTA
*
1303614 TGTGGTG
1 GGTGGTG
1303621 GATTGAGTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.13, C:0.02, G:0.47, T:0.38
Consensus pattern (20 bp):
GGTGGTGTTTGAACGTGGTA
Found at i:1305533 original size:21 final size:24
Alignment explanation
Indices: 1305477--1305541 Score: 94
Period size: 24 Copynumber: 2.7 Consensus size: 24
1305467 TTGATATAAC
*
1305477 TATTATTAATTATTGTTGTTGTTAT
1 TATTATT-ATTATTATTGTTGTTAT
* *
1305502 TATTATTATTATTATTTTTTTTAT
1 TATTATTATTATTATTGTTGTTAT
1305526 TATTATTATTATTATT
1 TATTATTATTATTATT
1305542 AACTAATAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
24 30 0.81
25 7 0.19
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (24 bp):
TATTATTATTATTATTGTTGTTAT
Found at i:1305562 original size:3 final size:3
Alignment explanation
Indices: 1305477--1305542 Score: 78
Period size: 3 Copynumber: 21.7 Consensus size: 3
1305467 TTGATATAAC
* * * * *
1305477 TAT TAT TAAT TAT TGT TGT TGT TAT TAT TAT TAT TAT TAT TTT TTT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1305523 TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
1305543 ACTAATAATA
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
3 55 0.95
4 3 0.05
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1308755 original size:20 final size:22
Alignment explanation
Indices: 1308730--1308770 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1308720 CAATGTTCTG
1308730 TCTTTTC-GT-GTGATATTTTT
1 TCTTTTCTGTGGTGATATTTTT
*
1308750 TCTTTTCTTTGGTGATATTTT
1 TCTTTTCTGTGGTGATATTTT
1308771 GATGGTCGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 1 0.06
22 10 0.56
ACGTcount: A:0.10, C:0.10, G:0.15, T:0.66
Consensus pattern (22 bp):
TCTTTTCTGTGGTGATATTTTT
Found at i:1309801 original size:14 final size:14
Alignment explanation
Indices: 1309782--1309819 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
1309772 GTTGACAGCT
*
1309782 AGCCTGCTGAGCAG
1 AGCCTGCCGAGCAG
1309796 AGCCTGCCGAGCAG
1 AGCCTGCCGAGCAG
1309810 AGCCTGCCGA
1 AGCCTGCCGA
1309820 TGGAACATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.21, C:0.34, G:0.34, T:0.11
Consensus pattern (14 bp):
AGCCTGCCGAGCAG
Found at i:1311060 original size:19 final size:19
Alignment explanation
Indices: 1311032--1311070 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1311022 CAACCGCACT
*
1311032 ACCCTTATAATCAT-AAGCA
1 ACCCTAATAAT-ATAAAGCA
1311051 ACCCTAATAATATAAAGCA
1 ACCCTAATAATATAAAGCA
1311070 A
1 A
1311071 AACCAAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.49, C:0.23, G:0.05, T:0.23
Consensus pattern (19 bp):
ACCCTAATAATATAAAGCA
Found at i:1312165 original size:19 final size:21
Alignment explanation
Indices: 1312105--1312176 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 21
1312095 AAATGACCAA
* * *
1312105 CAAATTCGCAACGCGATA-GT
1 CAAATTCGCAACGTGAAATTT
1312125 CAAATTCGCAACGTGAAATTT
1 CAAATTCGCAACGTGAAATTT
*
1312146 CAAATTTGCAAC-TG-AATTT
1 CAAATTCGCAACGTGAAATTT
1312165 CAAATTCGCAAC
1 CAAATTCGCAAC
1312177 AGGTTTTAGT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
19 16 0.35
20 18 0.39
21 12 0.26
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (21 bp):
CAAATTCGCAACGTGAAATTT
Found at i:1312368 original size:16 final size:15
Alignment explanation
Indices: 1312333--1312371 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1312323 TCCCCATCTC
*
1312333 TAATTTTTTTTTACA
1 TAATTTTTTTCTACA
*
1312348 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
1312364 TAATTTTT
1 TAATTTTT
1312372 CAATGATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:1312945 original size:12 final size:12
Alignment explanation
Indices: 1312924--1312957 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1312914 ACCACATTTC
*
1312924 CAATACCAAACA
1 CAATATCAAACA
1312936 CAATATCAAACA
1 CAATATCAAACA
*
1312948 CAATCTCAAA
1 CAATATCAAA
1312958 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:1313135 original size:24 final size:24
Alignment explanation
Indices: 1313084--1313137 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1313074 GTATTCAAAA
* *
1313084 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGGCAATACCCAGAC
* * *
1313108 TTTGATCTTGGGGAATACTCAGAT
1 TTTGATCTTGGGCAATACCCAGAC
1313132 TTTGAT
1 TTTGAT
1313138 GATGTGATGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (24 bp):
TTTGATCTTGGGCAATACCCAGAC
Found at i:1315450 original size:20 final size:19
Alignment explanation
Indices: 1315414--1315572 Score: 124
Period size: 20 Copynumber: 8.0 Consensus size: 19
1315404 GCGTAAAAAC
*
1315414 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTT-GTGTTGCGA
*
1315434 ATTTGTCTTCTGTGTTGCG-
1 ATTTGACTT-TGTGTTGCGA
* *
1315453 ATTT-ACAAATTCGCGTTGCGA
1 ATTTGAC---TTTGTGTTGCGA
* *
1315474 ATATGACTTTCGTGTTGCAA
1 ATTTGACTTT-GTGTTGCGA
* *
1315494 ATTTGACTATTGCGTTGTGA
1 ATTTGACT-TTGTGTTGCGA
*
1315514 ATTTGACTTTGTGTTACGA
1 ATTTGACTTTGTGTTGCGA
*
1315533 ATTTGACTATCGTGTTGCGA
1 ATTTGACT-TTGTGTTGCGA
*
1315553 ATTTGACTAATGTGTTGCGA
1 ATTTGACT-TTGTGTTGCGA
1315573 TTTACAGATT
Statistics
Matches: 110, Mismatches: 20, Indels: 18
0.74 0.14 0.12
Matches are distributed among these distances:
18 1 0.01
19 22 0.20
20 77 0.70
21 8 0.07
22 2 0.02
ACGTcount: A:0.20, C:0.14, G:0.23, T:0.42
Consensus pattern (19 bp):
ATTTGACTTTGTGTTGCGA
Found at i:1315489 original size:40 final size:39
Alignment explanation
Indices: 1315414--1315597 Score: 180
Period size: 40 Copynumber: 4.7 Consensus size: 39
1315404 GCGTAAAAAC
*
1315414 ATTTGACT-TTCGCGTTGCGAATTTGTCTTCTGTGTTGCG
1 ATTTGACTATTCGCGTTGCGAATTTGACTT-TGTGTTGCG
* * *
1315453 ATTT-ACAAATTCGCGTTGCGAATATGACTTTCGTGTTGCAA
1 ATTTGAC-TATTCGCGTTGCGAATTTGACTTT-GTGTTGC-G
* *
1315494 ATTTGACTATT-GCGTTGTGAATTTGACTTTGTGTTACG
1 ATTTGACTATTCGCGTTGCGAATTTGACTTTGTGTTGCG
* *
1315532 AATTTGACTA-TCGTGTTGCGAATTTGACTAATGTGTTGCG
1 -ATTTGACTATTCGCGTTGCGAATTTGACT-TTGTGTTGCG
* *
1315572 ATTT-ACAGATTCGCGTTTCGAATTTG
1 ATTTGAC-TATTCGCGTTGCGAATTTG
1315598 GAAAAGCGCA
Statistics
Matches: 119, Mismatches: 16, Indels: 19
0.77 0.10 0.12
Matches are distributed among these distances:
38 5 0.04
39 40 0.34
40 65 0.55
41 7 0.06
42 2 0.02
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.42
Consensus pattern (39 bp):
ATTTGACTATTCGCGTTGCGAATTTGACTTTGTGTTGCG
Found at i:1315614 original size:21 final size:21
Alignment explanation
Indices: 1315590--1315697 Score: 198
Period size: 21 Copynumber: 5.1 Consensus size: 21
1315580 ATTCGCGTTT
1315590 CGAATTTGGAAAAGCGCAACG
1 CGAATTTGGAAAAGCGCAACG
1315611 CGAATTTGGAAAAGCGCAACG
1 CGAATTTGGAAAAGCGCAACG
1315632 CGAATTTGGAAAAGCGCAACG
1 CGAATTTGGAAAAGCGCAACG
1315653 CGAATTTGGAAAAGCGCAACG
1 CGAATTTGGAAAAGCGCAACG
* *
1315674 CGAATTTGGAAAATCGCAATG
1 CGAATTTGGAAAAGCGCAACG
1315695 CGA
1 CGA
1315698 TTTACATATT
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 85 1.00
ACGTcount: A:0.38, C:0.19, G:0.28, T:0.16
Consensus pattern (21 bp):
CGAATTTGGAAAAGCGCAACG
Found at i:1315899 original size:18 final size:18
Alignment explanation
Indices: 1315872--1315912 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
1315862 TGATTCGCAC
1315872 AAAAACATTT-TTT-TGAG
1 AAAAACATTTATTTAT-AG
1315889 AAAAACTATTTATTTATAG
1 AAAAAC-ATTTATTTATAG
1315908 AAAAA
1 AAAAA
1315913 TATATAACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 6 0.29
18 4 0.19
19 10 0.48
20 1 0.05
ACGTcount: A:0.51, C:0.05, G:0.07, T:0.37
Consensus pattern (18 bp):
AAAAACATTTATTTATAG
Found at i:1316242 original size:3 final size:3
Alignment explanation
Indices: 1316234--1316287 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
1316224 AATTATCCTG
1316234 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1316282 TAT TAT
1 TAT TAT
1316288 ACATTAATAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1316697 original size:25 final size:25
Alignment explanation
Indices: 1316646--1316699 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
1316636 TTATAATTAT
*
1316646 TAATATTATTATTCTTAAATAATAA
1 TAATATTATTATTCTAAAATAATAA
1316671 TAATATTATTA-T-TAAAATAAATAAA
1 TAATATTATTATTCTAAAAT-AAT-AA
1316696 TAAT
1 TAAT
1316700 GACAAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 5 0.19
24 4 0.15
25 17 0.65
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (25 bp):
TAATATTATTATTCTAAAATAATAA
Found at i:1317736 original size:22 final size:21
Alignment explanation
Indices: 1317696--1317736 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1317686 ATTTGTATTT
1317696 AAGTTTCATATCTTTAAAAAA
1 AAGTTTCATATCTTTAAAAAA
*
1317717 AAGTTTCATATCTTTTAAAA
1 AAGTTTCATATCTTTAAAAA
1317737 TCATTCTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (21 bp):
AAGTTTCATATCTTTAAAAAA
Found at i:1319813 original size:25 final size:24
Alignment explanation
Indices: 1319746--1319813 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
1319736 CTTTTACAAA
* * * *
1319746 AAAAAAAACTTTCATATCTTTTAC
1 AAAAAAAAGTTTAACATCTGTTAC
*
1319770 AAAAAAAAGTTTAATATCTGTTAC
1 AAAAAAAAGTTTAACATCTGTTAC
*
1319794 AAAAAGAAAGTTTTACATCT
1 AAAAA-AAAGTTTAACATCT
1319814 TTTAAAATCA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
24 26 0.68
25 12 0.32
ACGTcount: A:0.49, C:0.12, G:0.06, T:0.34
Consensus pattern (24 bp):
AAAAAAAAGTTTAACATCTGTTAC
Found at i:1322261 original size:21 final size:20
Alignment explanation
Indices: 1322237--1322304 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 20
1322227 TTCATACAAT
1322237 TTCAACCATCATAACATCAAA
1 TTCAACC-TCATAACATCAAA
* *
1322258 TTCAATCT-A-AATTCATGCAAT
1 TTCAACCTCATAA--CAT-CAAA
1322279 TTCAACCTTCATAACATCAAA
1 TTCAACC-TCATAACATCAAA
1322300 TTCAA
1 TTCAA
1322305 TCCAAATTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
18 2 0.05
19 1 0.03
20 4 0.11
21 23 0.62
22 4 0.11
23 1 0.03
24 2 0.05
ACGTcount: A:0.43, C:0.25, G:0.01, T:0.31
Consensus pattern (20 bp):
TTCAACCTCATAACATCAAA
Found at i:1322270 original size:42 final size:42
Alignment explanation
Indices: 1322223--1322322 Score: 157
Period size: 42 Copynumber: 2.4 Consensus size: 42
1322213 CTCCTATGAT
1322223 CAAATTCATACAATTTCAACCATCATAACATCAAATTCAATC
1 CAAATTCATACAATTTCAACCATCATAACATCAAATTCAATC
* * *
1322265 TAAATTCATGCAATTTCAACCTTCATAACATCAAATTCAATC
1 CAAATTCATACAATTTCAACCATCATAACATCAAATTCAATC
1322307 CAAATTCA-ACCAATTT
1 CAAATTCATA-CAATTT
1322323 ACATAAACCC
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.43, C:0.25, G:0.01, T:0.31
Consensus pattern (42 bp):
CAAATTCATACAATTTCAACCATCATAACATCAAATTCAATC
Found at i:1323207 original size:30 final size:30
Alignment explanation
Indices: 1323164--1323234 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 30
1323154 CAAAATATAT
* *
1323164 AACTTTTAAAAA-TTATATTCTTAGTCCCAA
1 AACTTTTAAAAATTTATACT-TTAGTCACAA
** *
1323194 AACTTTTCCAAATTTATACTTTGGTCACAA
1 AACTTTTAAAAATTTATACTTTAGTCACAA
*
1323224 AACTTTCAAAA
1 AACTTTTAAAA
1323235 CATGCATTTC
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
30 26 0.81
31 6 0.19
ACGTcount: A:0.39, C:0.18, G:0.04, T:0.38
Consensus pattern (30 bp):
AACTTTTAAAAATTTATACTTTAGTCACAA
Found at i:1325540 original size:17 final size:17
Alignment explanation
Indices: 1325504--1325543 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1325494 AAAACATAAA
* *
1325504 AAATAAAATAAGGGTTT
1 AAATAAAATAAGCGTAT
*
1325521 AAATAAAATACGCGTAT
1 AAATAAAATAAGCGTAT
1325538 AAATAA
1 AAATAA
1325544 GGTACCTACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.57, C:0.05, G:0.12, T:0.25
Consensus pattern (17 bp):
AAATAAAATAAGCGTAT
Found at i:1327388 original size:55 final size:55
Alignment explanation
Indices: 1327315--1327734 Score: 461
Period size: 55 Copynumber: 7.6 Consensus size: 55
1327305 AATAACGAGC
* * * * *
1327315 CCGCTCCCTACTCATTCAGAAAGTATA-AGACTCGAACAATCTTCATAAAATGTGT
1 CCGCTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCATAAAACGGGT
** * *
1327370 TTGCTCCCTATTCGTTCAGGGAGTATA-AGACTCGAACAATCTTCA-ATAAACGGGT
1 CCGCTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCATA-AAACGGGT
* * * * *
1327425 CCGCTCCCTATTCATTCAGGGAGTATAGAACTCGAACAATGTTTATAAAATGGGT
1 CCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGT
* * * * *
1327480 CCGCTCTCTATTCCTTTAGAGAGTATCGAACTCGAACAATTTTCA-ACAAATGGGT
1 CCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATA-AAACGGGT
** *
1327535 CCGCTTTCTATTTCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGT
1 CCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGT
** * * * *
1327590 ATGCTCCCAATTCCATCAAAGAGTATAGAACTCGAACAATCTTCGTAAAACGGGT
1 CCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGT
* * * *
1327645 CCGCTCTCTATTCCTTCAGAGAGTATAGAATTCGAACAATCTTCAAAAAACGTGT
1 CCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGT
* * *
1327700 CCGCTCCCTATTTCTTCAGAGAGTGTAGGACTCGA
1 CCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGA
1327735 TCTTCATAAA
Statistics
Matches: 309, Mismatches: 51, Indels: 10
0.84 0.14 0.03
Matches are distributed among these distances:
54 2 0.01
55 304 0.98
56 3 0.01
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (55 bp):
CCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGT
Found at i:1329086 original size:19 final size:19
Alignment explanation
Indices: 1329064--1329104 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1329054 TGGAACCCCC
1329064 TTTTTATTTTTC-TCTATTT
1 TTTTTATTTTTCATC-ATTT
*
1329083 TTTTTCTTTTTCATCATTT
1 TTTTTATTTTTCATCATTT
1329102 TTT
1 TTT
1329105 CTTTTCTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTTATTTTTCATCATTT
Found at i:1329102 original size:17 final size:15
Alignment explanation
Indices: 1329081--1329214 Score: 85
Period size: 15 Copynumber: 8.5 Consensus size: 15
1329071 TTTTCTCTAT
1329081 TTTTTTTCTTTTTCA
1 TTTTTTTCTTTTTCA
*
1329096 TCATTTTTTC-TTTTCT
1 T--TTTTTTCTTTTTCA
* *
1329112 TTTTTTTATTTTTCT
1 TTTTTTTCTTTTTCA
*
1329127 TCTTTTTTCCTTTTCA
1 T-TTTTTTCTTTTTCA
*
1329143 TTTTTCATCATTTTTCA
1 TTTTT-TTC-TTTTTCA
*
1329160 TTTTTTTATTTTTTTTCA
1 --TTTTT-TTCTTTTTCA
*
1329178 TTTTTTAT-TTTTTTA
1 TTTTTT-TCTTTTTCA
*
1329193 TTTTTAT-TTTTTCA
1 TTTTTTTCTTTTTCA
1329207 TTTCTTTT
1 TTT-TTTT
1329215 TCAGGCGAAA
Statistics
Matches: 95, Mismatches: 14, Indels: 20
0.74 0.11 0.16
Matches are distributed among these distances:
14 16 0.17
15 27 0.28
16 26 0.27
17 13 0.14
18 7 0.07
19 6 0.06
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTTTCTTTTTCA
Found at i:1329106 original size:30 final size:30
Alignment explanation
Indices: 1329070--1329166 Score: 81
Period size: 31 Copynumber: 3.2 Consensus size: 30
1329060 CCCCTTTTTA
*
1329070 TTTTTC-TCTATTTTTTTTCTTTTTCATCAT
1 TTTTTCTTCTATTTTTTTTATTTTTCATC-T
* * *
1329100 TTTTTCTTTTCTTTTTTTTATTTTTCTTCT
1 TTTTTCTTCTATTTTTTTTATTTTTCATCT
* * *
1329130 TTTTTCCTTTTCATTTTTCATCATTTTTCAT-T
1 TTTTT-CTTCT-ATTTTT-TTTATTTTTCATCT
1329162 TTTTT
1 TTTTT
1329167 ATTTTTTTTC
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
30 12 0.22
31 23 0.42
32 11 0.20
33 9 0.16
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.76
Consensus pattern (30 bp):
TTTTTCTTCTATTTTTTTTATTTTTCATCT
Found at i:1329118 original size:31 final size:31
Alignment explanation
Indices: 1329080--1329189 Score: 98
Period size: 31 Copynumber: 3.5 Consensus size: 31
1329070 TTTTTCTCTA
*
1329080 TTTTTTTTCTTTTTCATCATTTTTT-CTTTTC
1 TTTTTTTTATTTTTCATC-TTTTTTCCTTTTC
*
1329111 TTTTTTTTATTTTTCTTCTTTTTTCCTTTTC
1 TTTTTTTTATTTTTCATCTTTTTTCCTTTTC
* * ** *
1329142 ATTTTTCATCATTTTTCAT-TTTTTTATTTTTT
1 -TTTTT-TTTATTTTTCATCTTTTTTCCTTTTC
1329174 TTCATTTTTTATTTTT
1 TT--TTTTTTATTTTT
1329190 TTATTTTTAT
Statistics
Matches: 64, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
30 6 0.09
31 24 0.38
32 22 0.34
33 12 0.19
ACGTcount: A:0.09, C:0.13, G:0.00, T:0.78
Consensus pattern (31 bp):
TTTTTTTTATTTTTCATCTTTTTTCCTTTTC
Found at i:1329170 original size:8 final size:8
Alignment explanation
Indices: 1329153--1329214 Score: 58
Period size: 8 Copynumber: 7.8 Consensus size: 8
1329143 TTTTTCATCA
*
1329153 TTTTTCAT
1 TTTTTTAT
1329161 TTTTTTAT
1 TTTTTTAT
1329169 TTTTTT-T
1 TTTTTTAT
1329176 CATTTTTTAT
1 --TTTTTTAT
1329186 TTTTTTA-
1 TTTTTTAT
1329193 -TTTTTAT
1 TTTTTTAT
*
1329200 TTTTTCAT
1 TTTTTTAT
1329208 TTCTTTT
1 TT-TTTT
1329215 TCAGGCGAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
6 6 0.13
7 1 0.02
8 28 0.62
9 9 0.20
10 1 0.02
ACGTcount: A:0.11, C:0.06, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTTAT
Found at i:1338911 original size:45 final size:47
Alignment explanation
Indices: 1338836--1338946 Score: 129
Period size: 45 Copynumber: 2.4 Consensus size: 47
1338826 CCATGCTTTG
* *
1338836 TTATTCACAAAAAGAAATCCTAACAGCATGATACCTAATTCGCATGC-
1 TTATTCA-AAAAATAAATCCTAACAGCATGATACCTAATTCGCAAGCA
* * *
1338883 TTGTTCAAAAAATAAA-CCTAACCA-CATGATATCTAGTTCGCAAGCA
1 TTATTCAAAAAATAAATCCTAA-CAGCATGATACCTAATTCGCAAGCA
1338929 TTTATTCAAAAAATAAAT
1 -TTATTCAAAAAATAAAT
1338947 GACTCAAAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
45 23 0.43
46 10 0.19
47 21 0.39
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.28
Consensus pattern (47 bp):
TTATTCAAAAAATAAATCCTAACAGCATGATACCTAATTCGCAAGCA
Found at i:1344767 original size:3 final size:3
Alignment explanation
Indices: 1344684--1344747 Score: 74
Period size: 3 Copynumber: 20.7 Consensus size: 3
1344674 TTGATATAAC
* * * *
1344684 TAT TAT TAAT TAT TGT TGT TAT TAT TAT TATT TAT TAT AAT TAT TAC
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
1344731 TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
1344748 ACTAATAATA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
3 47 0.89
4 6 0.11
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:1344779 original size:22 final size:22
Alignment explanation
Indices: 1344739--1344780 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1344729 ACTATTATTA
*
1344739 TTATTATTAACTAATAATAATG
1 TTATTATTAAATAATAATAATG
1344761 TTATTATTAAAATAA-AATAA
1 TTATTATT-AAATAATAATAA
1344781 AAATTACATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
TTATTATTAAATAATAATAATG
Found at i:1348156 original size:24 final size:24
Alignment explanation
Indices: 1348103--1348193 Score: 146
Period size: 25 Copynumber: 3.7 Consensus size: 24
1348093 ATTTTTATTT
1348103 AAGTTTCATATCTTTTACAAAAAA
1 AAGTTTCATATCTTTTACAAAAAA
*
1348127 ATAGTTTCATATCTTTTACTAAAAA
1 A-AGTTTCATATCTTTTACAAAAAA
1348152 AAGTTTCATATCTTTTACAAAAAAA
1 AAGTTTCATATCTTTTAC-AAAAAA
*
1348177 AAGTTTTATATCTTTTA
1 AAGTTTCATATCTTTTA
1348194 AAATCATTCT
Statistics
Matches: 62, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
24 18 0.29
25 44 0.71
ACGTcount: A:0.42, C:0.11, G:0.04, T:0.43
Consensus pattern (24 bp):
AAGTTTCATATCTTTTACAAAAAA
Found at i:1350130 original size:2 final size:2
Alignment explanation
Indices: 1350123--1350152 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1350113 GTCAATGTAC
1350123 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1350153 GATAACATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1350367 original size:18 final size:18
Alignment explanation
Indices: 1350344--1350378 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1350334 GTTCAGTATT
1350344 TGTCCCAAAGGACCACTA
1 TGTCCCAAAGGACCACTA
*
1350362 TGTCCCGAAGGACCACT
1 TGTCCCAAAGGACCACT
1350379 GGATACATCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.34, G:0.20, T:0.17
Consensus pattern (18 bp):
TGTCCCAAAGGACCACTA
Found at i:1350392 original size:22 final size:22
Alignment explanation
Indices: 1350364--1350444 Score: 110
Period size: 22 Copynumber: 3.7 Consensus size: 22
1350354 GACCACTATG
*
1350364 TCCCGAAGGACCACTGGATACA
1 TCCCGAAGGACCACTGAATACA
1350386 TCCCGAAGGACCACTGAATAC-
1 TCCCGAAGGACCACTGAATACA
* *
1350407 GCCTCGAAAGACCACTGAATACA
1 TCC-CGAAGGACCACTGAATACA
*
1350430 TCCCGAATGACCACT
1 TCCCGAAGGACCACT
1350445 ATTCCCTCGA
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
21 2 0.04
22 48 0.92
23 2 0.04
ACGTcount: A:0.33, C:0.33, G:0.19, T:0.15
Consensus pattern (22 bp):
TCCCGAAGGACCACTGAATACA
Found at i:1350395 original size:40 final size:40
Alignment explanation
Indices: 1350346--1350450 Score: 115
Period size: 44 Copynumber: 2.5 Consensus size: 40
1350336 TCAGTATTTG
* * *
1350346 TCCCAAAGGACCACTATGTCCCGAAGGACCACTGGATACA
1 TCCCGAAGGACCACTATGTCCCGAAAGACCACTGAATACA
1350386 TCCCGAAGGACCACTGAATACG-CCTCGAAAGACCACTGAATACA
1 TCCCGAAGGACCACT--AT--GTCC-CGAAAGACCACTGAATACA
*
1350430 TCCCGAATGACCACTAT-TCCC
1 TCCCGAAGGACCACTATGTCCC
1350451 TCGACTCTTG
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
39 1 0.02
40 16 0.29
42 4 0.07
43 2 0.04
44 32 0.58
ACGTcount: A:0.32, C:0.34, G:0.17, T:0.16
Consensus pattern (40 bp):
TCCCGAAGGACCACTATGTCCCGAAAGACCACTGAATACA
Found at i:1351104 original size:63 final size:64
Alignment explanation
Indices: 1350994--1351137 Score: 150
Period size: 63 Copynumber: 2.3 Consensus size: 64
1350984 ATTCCTTAAC
* ** ** *
1350994 GGGTGCATCGATACACTACTTATGCATCGGTGCATGAATCATATTCGATGTTTGTATTTAAT-G
1 GGGTGCATCGATGCACTACTTATGCATCGACGCACCAATCATATTCGATGTTTGTATTTAATCA
* * * *
1351057 GGGTGCATCGATGCACT-CATTATGCATCGACGCACCAATGCCT-TTCGATGTTTTTGTTTTATC
1 GGGTGCATCGATGCACTAC-TTATGCATCGACGCACCAAT-CATATTCGATGTTTGTATTTAATC
1351120 A
64 A
*
1351121 GAGTGCATCGATGCACT
1 GGGTGCATCGATGCACT
1351138 TCATGTGCAT
Statistics
Matches: 67, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
62 1 0.01
63 48 0.72
64 18 0.27
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (64 bp):
GGGTGCATCGATGCACTACTTATGCATCGACGCACCAATCATATTCGATGTTTGTATTTAATCA
Found at i:1351209 original size:21 final size:21
Alignment explanation
Indices: 1351185--1351241 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
1351175 TTATCCTTGA
1351185 TGCATCGGTGCACATTGAATG
1 TGCATCGGTGCACATTGAATG
*
1351206 TGCATCGGTTCACATTGAATG
1 TGCATCGGTGCACATTGAATG
*
1351227 TGCATCGATGCACAT
1 TGCATCGGTGCACAT
1351242 AGCCCAGAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (21 bp):
TGCATCGGTGCACATTGAATG
Found at i:1357349 original size:18 final size:18
Alignment explanation
Indices: 1357326--1357361 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1357316 GTTCAGTATT
*
1357326 TGTCCCGAAGGACCACTA
1 TGTCCCGAAAGACCACTA
1357344 TGTCCCGAAAGACCACTA
1 TGTCCCGAAAGACCACTA
1357362 AAAACATCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.33, G:0.19, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAAGACCACTA
Found at i:1357382 original size:22 final size:22
Alignment explanation
Indices: 1357346--1357405 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
1357336 GACCACTATG
*
1357346 TCCCGAAAGACCACTAAAAACA
1 TCCCGAAGGACCACTAAAAACA
* * *
1357368 TCTCC-AAGGACCACTGAATACG
1 TC-CCGAAGGACCACTAAAAACA
1357390 TCCCGAAGGACCACTA
1 TCCCGAAGGACCACTA
1357406 TACCCTCAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
21 2 0.06
22 27 0.87
23 2 0.06
ACGTcount: A:0.38, C:0.33, G:0.15, T:0.13
Consensus pattern (22 bp):
TCCCGAAGGACCACTAAAAACA
Found at i:1358106 original size:19 final size:19
Alignment explanation
Indices: 1358082--1358133 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
1358072 TTTTATCAGA
1358082 GTGCATCGATACACTTCAT
1 GTGCATCGATACACTTCAT
1358101 GTGCATCGATACACTTCAT
1 GTGCATCGATACACTTCAT
1358120 GTGCATCGATACAC
1 GTGCATCGATACAC
1358134 CTTGAATAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (19 bp):
GTGCATCGATACACTTCAT
Found at i:1361609 original size:16 final size:17
Alignment explanation
Indices: 1361586--1361648 Score: 73
Period size: 16 Copynumber: 4.0 Consensus size: 17
1361576 TTGATATAAC
1361586 TATTATTAATTATT-TT
1 TATTATTAATTATTATT
*
1361602 TGTTATT-ATTATTATT
1 TATTATTAATTATTATT
*
1361618 TATTA-TAATTATTA-C
1 TATTATTAATTATTATT
1361633 TATTATT-ATTATTATT
1 TATTATTAATTATTATT
1361649 AACTAATAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
15 19 0.49
16 20 0.51
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (17 bp):
TATTATTAATTATTATT
Found at i:1361669 original size:3 final size:3
Alignment explanation
Indices: 1361586--1361649 Score: 74
Period size: 3 Copynumber: 20.7 Consensus size: 3
1361576 TTGATATAAC
* * * *
1361586 TAT TAT TAAT TAT TTT TGT TAT TAT TAT TATT TAT TAT AAT TAT TAC
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
1361633 TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
1361650 ACTAATAATA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
3 46 0.88
4 6 0.12
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1362269 original size:40 final size:40
Alignment explanation
Indices: 1362218--1362301 Score: 150
Period size: 40 Copynumber: 2.1 Consensus size: 40
1362208 CTTTAAAATT
*
1362218 ATATTCAAAAATTCATTCGAATATATTTTTAGAAAATATC
1 ATATTCAAAAATTCATTCGAATATATTTTCAGAAAATATC
*
1362258 ATATTCGAAAATTCATTCGAATATATTTTCAGAAAATATC
1 ATATTCAAAAATTCATTCGAATATATTTTCAGAAAATATC
1362298 ATAT
1 ATAT
1362302 AAAAACATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.44, C:0.11, G:0.06, T:0.39
Consensus pattern (40 bp):
ATATTCAAAAATTCATTCGAATATATTTTCAGAAAATATC
Found at i:1368683 original size:24 final size:24
Alignment explanation
Indices: 1368591--1368683 Score: 98
Period size: 24 Copynumber: 3.9 Consensus size: 24
1368581 ATCTGATTTT
* *
1368591 TGATTTGAATTCTGTTTTGACATC
1 TGATCTGAATTCTGTTTTGATATC
* *
1368615 TGATCTGAAATCTGTTCTGAT-TCC
1 TGATCTGAATTCTGTTTTGATAT-C
* * *
1368639 TAACCTGGATTCTGTTTTGATATC
1 TGATCTGAATTCTGTTTTGATATC
*
1368663 TGATCTGAATTATGTTTTGAT
1 TGATCTGAATTCTGTTTTGAT
1368684 TTTTGATATC
Statistics
Matches: 54, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
23 1 0.02
24 52 0.96
25 1 0.02
ACGTcount: A:0.22, C:0.14, G:0.17, T:0.47
Consensus pattern (24 bp):
TGATCTGAATTCTGTTTTGATATC
Found at i:1368690 original size:24 final size:24
Alignment explanation
Indices: 1368584--1368690 Score: 97
Period size: 24 Copynumber: 4.5 Consensus size: 24
1368574 ATATTTTATC
* *
1368584 TGATTTTTGATTTGAATTCTGTTT
1 TGATTTCTGATCTGAATTCTGTTT
** * *
1368608 TGACATCTGATCTGAAATCTGTTC
1 TGATTTCTGATCTGAATTCTGTTT
* * * *
1368632 TGATTCCTAACCTGGATTCTGTTT
1 TGATTTCTGATCTGAATTCTGTTT
* *
1368656 TGATATCTGATCTGAATTATGTTT
1 TGATTTCTGATCTGAATTCTGTTT
*
1368680 TGATTTTTGAT
1 TGATTTCTGAT
1368691 ATCTCCGTTT
Statistics
Matches: 61, Mismatches: 22, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
24 61 1.00
ACGTcount: A:0.21, C:0.12, G:0.17, T:0.50
Consensus pattern (24 bp):
TGATTTCTGATCTGAATTCTGTTT
Found at i:1370769 original size:8 final size:8
Alignment explanation
Indices: 1370756--1370809 Score: 58
Period size: 10 Copynumber: 6.5 Consensus size: 8
1370746 GTCACGACCC
1370756 GACCCGTT
1 GACCCGTT
1370764 GACCCGTT
1 GACCCGTT
1370772 GA-CCGTT
1 GACCCGTT
1370779 GA-CCGTT
1 GACCCGTT
1370786 GACCGGCGTT
1 GACC--CGTT
1370796 GACCACTGTT
1 GACC-C-GTT
1370806 GACC
1 GACC
1370810 AAAACTTTGA
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
7 14 0.34
8 11 0.27
9 1 0.02
10 15 0.37
ACGTcount: A:0.15, C:0.33, G:0.28, T:0.24
Consensus pattern (8 bp):
GACCCGTT
Found at i:1370779 original size:7 final size:7
Alignment explanation
Indices: 1370759--1370790 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
1370749 ACGACCCGAC
1370759 CCGTTGA
1 CCGTTGA
1370766 CCCGTTGA
1 -CCGTTGA
1370774 CCGTTGA
1 CCGTTGA
1370781 CCGTTGA
1 CCGTTGA
1370788 CCG
1 CCG
1370791 GCGTTGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.34, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:1375574 original size:23 final size:24
Alignment explanation
Indices: 1375484--1375571 Score: 126
Period size: 24 Copynumber: 3.7 Consensus size: 24
1375474 ATTTTTATTT
1375484 AAGTTTCATATCTTTTACAAAAAA
1 AAGTTTCATATCTTTTACAAAAAA
*
1375508 AAGTTTCATATCTTTTACTAAAAA
1 AAGTTTCATATCTTTTACAAAAAA
*
1375532 AAGTAT-ATATC-TTTACAAAAAAA
1 AAGTTTCATATCTTTTAC-AAAAAA
*
1375555 AAGTTTTATATCTTTTA
1 AAGTTTCATATCTTTTA
1375572 AAATCATTCT
Statistics
Matches: 57, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
22 5 0.09
23 15 0.26
24 33 0.58
25 4 0.07
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (24 bp):
AAGTTTCATATCTTTTACAAAAAA
Found at i:1377756 original size:22 final size:22
Alignment explanation
Indices: 1377728--1377809 Score: 146
Period size: 22 Copynumber: 3.7 Consensus size: 22
1377718 AGACCACTAT
* *
1377728 GTCCCGAAGAACCACTGGATAC
1 GTCCCGAAGGACCACTGAATAC
1377750 GTCCCGAAGGACCACTGAATAC
1 GTCCCGAAGGACCACTGAATAC
1377772 GTCCCGAAGGACCACTGAATAC
1 GTCCCGAAGGACCACTGAATAC
1377794 GTCCCGAAGGACCACT
1 GTCCCGAAGGACCACT
1377810 ATACCCTCGA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 58 1.00
ACGTcount: A:0.30, C:0.33, G:0.23, T:0.13
Consensus pattern (22 bp):
GTCCCGAAGGACCACTGAATAC
Found at i:1378473 original size:63 final size:62
Alignment explanation
Indices: 1378354--1378521 Score: 153
Period size: 63 Copynumber: 2.7 Consensus size: 62
1378344 GATGCATTCC
** * *
1378354 TTAATGGGTGCATCGATGCACT-ACTTATGCATCTG-TGCATGAATCATATTCGATGTTTGTAT
1 TTAATGGGTGCATCGATGCACTCA-TTATGCATC-GATGCACCAATCACATTCAATGTTTGTAT
** * *
1378416 TTAATGGGGTGCATCGATGCACTCATTATGCATCGATGCACCAATGGCATTCAATGTTTTTGT
1 TTAAT-GGGTGCATCGATGCACTCATTATGCATCGATGCACCAATCACATTCAATGTTTGTAT
* * * *
1378479 TTTATCAGAGTGCATCGATGCACTTCA-TGTGCATCGATACACC
1 TTAAT--GGGTGCATCGATGCAC-TCATTATGCATCGATGCACC
1378522 TTGAACAATT
Statistics
Matches: 88, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
62 6 0.07
63 49 0.56
64 30 0.34
65 3 0.03
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (62 bp):
TTAATGGGTGCATCGATGCACTCATTATGCATCGATGCACCAATCACATTCAATGTTTGTAT
Found at i:1382040 original size:3 final size:3
Alignment explanation
Indices: 1381962--1382020 Score: 57
Period size: 3 Copynumber: 19.7 Consensus size: 3
1381952 TTGATATAAC
* * * * *
1381962 TAT TAT AAT TAT TGT TGT TAT TAT TAT TAT T-T TAT AATT TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT
1382007 TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TA
1382021 ACTAATAATA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
2 2 0.04
3 42 0.91
4 2 0.04
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1382649 original size:40 final size:40
Alignment explanation
Indices: 1382599--1382682 Score: 150
Period size: 40 Copynumber: 2.1 Consensus size: 40
1382589 CTTTAAAATT
*
1382599 ATATTTGAAAATTCATTCGAATATATTTTCAGAAAATATC
1 ATATTCGAAAATTCATTCGAATATATTTTCAGAAAATATC
*
1382639 ATATTCGAAAATTCATTCGAATGTATTTTCAGAAAATATC
1 ATATTCGAAAATTCATTCGAATATATTTTCAGAAAATATC
1382679 ATAT
1 ATAT
1382683 AAAAACATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.39
Consensus pattern (40 bp):
ATATTCGAAAATTCATTCGAATATATTTTCAGAAAATATC
Found at i:1387856 original size:159 final size:157
Alignment explanation
Indices: 1387672--1388227 Score: 582
Period size: 159 Copynumber: 3.6 Consensus size: 157
1387662 TCTTCTTCTG
* * * * *
1387672 TTGAAGCTGCTGATTGTAATGGTGAATCATCACCACCAGCACCACCATCTTCTTCTTCTTCTGAA
1 TTGAAGTTGATGATTGCAATGGTGAATCACCACCACCATCACCACCATCTTCTTCTTCTTCTGAA
1387737 AATGGTGATTCCATCGGTGAATCTTCTTCTTCTTCATCCTCTCCACCACCATCCTCATCATCATC
66 AATGGTGATTCCATCGGTGAATCTTCTTCTTCTTCATCCTCTCCACCACCATCCTCATCATCATC
*
1387802 ATCACAATCTTCTTCTTCTTCTGTCGAAA
131 ATCACAATC-TATTCTTCTTCTGTCG-AA
* ** **** *
1387831 TTGAAGTTGATGATTGCAATGGTGAATCCCCACCACCATCTTCTTGTTCTTCTTCTTCTTCCGAA
1 TTGAAGTTGATGATTGCAATGGTGAATCACCACCACCATCACCACCATCTTCTTCTTCTTCTGAA
*
1387896 AATGGTGATTCCATCGGTGAATCTTCTTCTTCATT-ATCCTCTCCACCACCATGCTCATCATCAT
66 AATGGTGATTCCATCGGTGAATCTTCTTCTTC-TTCATCCTCTCCACCACCATCCTCATCATCAT
* *
1387960 CATCATAA--TATTCTTCTTCTGTTGAA
130 CATCACAATCTATTCTTCTTCTGTCGAA
1387986 GTTGAAGTTGATGATTGCAATGGTGAAT------CA-C--CACCACCA---TCTTCTTCTTCTGA
1 -TTGAAGTTGATGATTGCAATGGTGAATCACCACCACCATCACCACCATCTTCTTCTTCTTCTGA
* * * ** * *
1388039 AAATGGTGATTCCACCAGTGAATCTTCTTCTTCATCATCCTCTCCACCACCATCCTCCCCCTCCT
65 AAATGGTGATTCCATCGGTGAATCTTCTTCTTCTTCATCCTCTCCACCACCATCCTCATCATCAT
*
1388104 CATCATC-ATCATAATCTTCTTCT-TCTG--
130 CATCA-CAATC-TATTCTTCTTCTGTC-GAA
* * ** * *
1388131 TTGAA---GATGACTGCAATGGTGAATCACCACCACCATCAACTTCTTCTTCTTCTTCCTCTGAA
1 TTGAAGTTGATGATTGCAATGGTGAATCACCACCACCATCACCACCATCTTCTTCTTCTTCTGAA
* *
1388193 AGTGGTGATTCCA-CTGATGAATCTTCTTCTTCTTC
66 AATGGTGATTCCATC-GGTGAATCTTCTTCTTCTTC
1388228 TTTTTCTTCT
Statistics
Matches: 331, Mismatches: 45, Indels: 48
0.78 0.11 0.11
Matches are distributed among these distances:
141 18 0.05
143 1 0.00
144 79 0.24
146 1 0.00
147 16 0.05
148 1 0.00
149 1 0.00
150 6 0.02
152 1 0.00
153 43 0.13
155 2 0.01
156 41 0.12
159 119 0.36
160 2 0.01
ACGTcount: A:0.22, C:0.29, G:0.12, T:0.36
Consensus pattern (157 bp):
TTGAAGTTGATGATTGCAATGGTGAATCACCACCACCATCACCACCATCTTCTTCTTCTTCTGAA
AATGGTGATTCCATCGGTGAATCTTCTTCTTCTTCATCCTCTCCACCACCATCCTCATCATCATC
ATCACAATCTATTCTTCTTCTGTCGAA
Found at i:1388178 original size:144 final size:144
Alignment explanation
Indices: 1387711--1388180 Score: 526
Period size: 144 Copynumber: 3.2 Consensus size: 144
1387701 TCACCACCAG
*
1387711 CACCACCATCTTCTTCTTCTTCTGAAAATGGTGATTCCATCGGTGAATCTTCTTCTTCTTCATCC
1 CACCACCATCTTCTTCTTCTTCTGAAAATGGTGATTCCATCGGTGAATCTTCTTCTTCATCATCC
* *
1387776 TCTCCACCACCATCCT-CATCATCATCATCACAATCTTCTTCTTCTTCTGTC-GAAATTGAAGTT
66 TCTCCACCACCATCCTCCATCATCATCAT--C-ATCATATTCTTCTTCTGTCTG---TTGAA--T
*
1387839 GATGATTGCAATGGTGAATCCC
123 GATGATTGCAATGGTGAATCAC
1387861 CACCACCATCTTCTTGTTCTTCTTCTTCTTCCGAAAATGGTGATTCCATCGGTGAATCTTCTTCT
1 CACCACCA---TC---TTCTTCTTCTTC-T--GAAAATGGTGATTCCATCGGTGAATCTTCTTCT
* * *
1387926 TCATTATCCTCTCCACCACCATGCT-CATCATCATCATCATAATATTCTTCTTCTGT-TGAAGTT
57 TCATCATCCTCTCCACCACCATCCTCCATCATCATCATCATCATATTCTTCTTCTGTCT---GTT
1387989 GAAGTTGATGATTGCAATGGTGAATCAC
119 GAA--TGATGATTGCAATGGTGAATCAC
* *
1388017 CACCACCA---TCTTCTTCTTCTGAAAATGGTGATTCCACCAGTGAATCTTCTTCTTCATCATCC
1 CACCACCATCTTCTTCTTCTTCTGAAAATGGTGATTCCATCGGTGAATCTTCTTCTTCATCATCC
* * * *
1388079 TCTCCACCACCATCCTCCCCCTCCTCATCATCATCATAATCTTCTTCT-TCTGTTGAA-GATGAC
66 TCTCCACCACCATCCT--CCATCATCATCATCATCATATTCTTCTTCTGTCTGTTGAATGATGAT
1388142 TGCAATGGTGAATCAC
129 TGCAATGGTGAATCAC
**
1388158 CACCACCATCAACTTCTTCTTCT
1 CACCACCATCTTCTTCTTCTTCT
1388181 TCTTCCTCTG
Statistics
Matches: 283, Mismatches: 17, Indels: 46
0.82 0.05 0.13
Matches are distributed among these distances:
141 29 0.10
144 71 0.25
146 2 0.01
147 37 0.13
150 8 0.03
153 2 0.01
156 64 0.23
157 2 0.01
159 68 0.24
ACGTcount: A:0.22, C:0.31, G:0.11, T:0.36
Consensus pattern (144 bp):
CACCACCATCTTCTTCTTCTTCTGAAAATGGTGATTCCATCGGTGAATCTTCTTCTTCATCATCC
TCTCCACCACCATCCTCCATCATCATCATCATCATATTCTTCTTCTGTCTGTTGAATGATGATTG
CAATGGTGAATCAC
Found at i:1388222 original size:3 final size:3
Alignment explanation
Indices: 1388214--1388243 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1388204 CACTGATGAA
*
1388214 TCT TCT TCT TCT TCT TTT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1388244 ACGGTTGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TCT
Found at i:1391084 original size:18 final size:18
Alignment explanation
Indices: 1391061--1391142 Score: 157
Period size: 18 Copynumber: 4.6 Consensus size: 18
1391051 GAAACTTAAG
1391061 GAAGCTTAAAGATAATTA
1 GAAGCTTAAAGATAATTA
1391079 GAAGCTTAAAGATAATTA
1 GAAGCTTAAAGATAATTA
1391097 GAAGCTTAAAGATAATTA
1 GAAGCTTAAAGATAATTA
1391115 GAAGCTTAAAGATAATTA
1 GAAGCTTAAAGATAATTA
1391133 GAAGC-TAAAG
1 GAAGCTTAAAG
1391143 GAATTAGGAG
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
17 5 0.08
18 59 0.92
ACGTcount: A:0.50, C:0.06, G:0.18, T:0.26
Consensus pattern (18 bp):
GAAGCTTAAAGATAATTA
Found at i:1391397 original size:19 final size:18
Alignment explanation
Indices: 1391357--1391397 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
1391347 GGGGTTTTGG
*
1391357 TAAAAAGAGATTAAATAG
1 TAAAAAGAGATTAAATAA
1391375 TAAAAAGAGATTAAATGAA
1 TAAAAAGAGATTAAAT-AA
1391394 TAAA
1 TAAA
1391398 GACAACTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.63, C:0.00, G:0.15, T:0.22
Consensus pattern (18 bp):
TAAAAAGAGATTAAATAA
Found at i:1391398 original size:17 final size:18
Alignment explanation
Indices: 1391356--1391390 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1391346 AGGGGTTTTG
1391356 GTAAAAAGAGATTAAATA
1 GTAAAAAGAGATTAAATA
1391374 GTAAAAAGAGATTAAAT
1 GTAAAAAGAGATTAAAT
1391391 GAATAAAGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.17, T:0.23
Consensus pattern (18 bp):
GTAAAAAGAGATTAAATA
Found at i:1393530 original size:28 final size:28
Alignment explanation
Indices: 1393480--1393533 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
1393470 TATATATGAT
* *
1393480 AATGTGCTAAGTGAAAAGGTTCTACGTG
1 AATGTGATAAGTGAAAAGATTCTACGTG
1393508 AATGTGATAAGTGAACAA-ATTCTACG
1 AATGTGATAAGTGAA-AAGATTCTACG
1393534 CAAAGATACC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 21 0.91
29 2 0.09
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.28
Consensus pattern (28 bp):
AATGTGATAAGTGAAAAGATTCTACGTG
Found at i:1400610 original size:44 final size:44
Alignment explanation
Indices: 1400562--1400645 Score: 107
Period size: 44 Copynumber: 1.9 Consensus size: 44
1400552 AAAAAACTAC
1400562 TAATTTACTAACAAATAATAAAAAATGA-TAAATTACTAATATAT
1 TAATTTACTAACAAATAATAAAAAAT-ATTAAATTACTAATATAT
* * * * *
1400606 TAATTTTCTAATAAATATTTAAAAATATTAAATTATTAAT
1 TAATTTACTAACAAATAATAAAAAATATTAAATTACTAAT
1400646 GAATAATGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 1 0.03
44 33 0.97
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.40
Consensus pattern (44 bp):
TAATTTACTAACAAATAATAAAAAATATTAAATTACTAATATAT
Found at i:1400890 original size:28 final size:28
Alignment explanation
Indices: 1400856--1400909 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
1400846 GAGGTTAATG
* *
1400856 AGCAACGAGACGAGCAACGAGCTTAACA
1 AGCAACGAGACGAACAACAAGCTTAACA
*
1400884 AGCAACGAGTCGAACAACAAGCTTAA
1 AGCAACGAGACGAACAACAAGCTTAA
1400910 TGAGCTTAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.44, C:0.24, G:0.22, T:0.09
Consensus pattern (28 bp):
AGCAACGAGACGAACAACAAGCTTAACA
Found at i:1401035 original size:67 final size:67
Alignment explanation
Indices: 1400911--1401107 Score: 189
Period size: 67 Copynumber: 2.9 Consensus size: 67
1400901 CAAGCTTAAT
* * * * * ** **
1400911 GAGCTTAACGAGCAATGAGTTGAGCAACAAATTTTCTTAAAGATCACAAGTTAAGCAAAATTGAA
1 GAGCTTAACAAGCAACGAGTCGAGCAACAAATTTTCTTAACGAGCATGAGTCGAGCAAAATTGAA
1400976 AC
66 AC
* * ***
1400978 TAGCTTAACAAGCAACGAGTCGAGCAATAAATTTTCTTAACGAGCATGAGTCGAGCAAAATTTCT
1 GAGCTTAACAAGCAACGAGTCGAGCAACAAATTTTCTTAACGAGCATGAGTCGAGCAAAATTGAA
1401043 AC
66 AC
* *
1401045 GAGCTTAACGAACAACGAATCGAGTCGAGCAACGAAATTTT-TTAACGAGTATGAGTCGAGCAA
1 GAGCTTAAC--A-AGC-AA-CGAGTCGAGCAAC-AAATTTTCTTAACGAGCATGAGTCGAGCAA
1401108 TGGCCAACTT
Statistics
Matches: 106, Mismatches: 18, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
67 61 0.58
69 1 0.01
70 2 0.02
71 2 0.02
72 33 0.31
73 7 0.07
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (67 bp):
GAGCTTAACAAGCAACGAGTCGAGCAACAAATTTTCTTAACGAGCATGAGTCGAGCAAAATTGAA
AC
Found at i:1402429 original size:22 final size:23
Alignment explanation
Indices: 1402399--1402462 Score: 80
Period size: 22 Copynumber: 2.9 Consensus size: 23
1402389 GAAAAATACC
1402399 AAAAAATAAAGAGGATG-AAGA-
1 AAAAAATAAAGAGGATGAAAGAG
* *
1402420 AGAATAATAAAGAAG-TGAAAGAG
1 A-AAAAATAAAGAGGATGAAAGAG
1402443 AAAAAATAAAGAGGATGAAA
1 AAAAAATAAAGAGGATGAAA
1402463 ATACCAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
21 3 0.09
22 26 0.74
23 6 0.17
ACGTcount: A:0.66, C:0.00, G:0.23, T:0.11
Consensus pattern (23 bp):
AAAAAATAAAGAGGATGAAAGAG
Found at i:1411855 original size:19 final size:20
Alignment explanation
Indices: 1411828--1411875 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
1411818 TAAGGGATCC
1411828 ATCCTTTTTCAAGGGGATTG
1 ATCCTTTTTCAAGGGGATTG
1411848 ATCCTTTTTCAAGGGGATTG
1 ATCCTTTTTCAAGGGGATTG
*
1411868 ATCATTTT
1 ATCCTTTT
1411876 GTTAAGGGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.44
Consensus pattern (20 bp):
ATCCTTTTTCAAGGGGATTG
Found at i:1426936 original size:40 final size:40
Alignment explanation
Indices: 1426875--1426964 Score: 153
Period size: 40 Copynumber: 2.2 Consensus size: 40
1426865 TGAATGGAAT
*
1426875 AAACTAGATTGGGAGGGTCACCATCGCTTCTGCAGTACCC
1 AAACTGGATTGGGAGGGTCACCATCGCTTCTGCAGTACCC
* *
1426915 GAACTGGATTGGGAGGGTCACCCTCGCTTCTGCAGTACCC
1 AAACTGGATTGGGAGGGTCACCATCGCTTCTGCAGTACCC
1426955 AAACTGGATT
1 AAACTGGATT
1426965 AGTCAGTCAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.23, C:0.27, G:0.27, T:0.23
Consensus pattern (40 bp):
AAACTGGATTGGGAGGGTCACCATCGCTTCTGCAGTACCC
Found at i:1431593 original size:17 final size:17
Alignment explanation
Indices: 1431571--1431605 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1431561 TCATATTATT
1431571 AATGTGTTGTATTGTTG
1 AATGTGTTGTATTGTTG
1431588 AATGTGTTGTATTGTTG
1 AATGTGTTGTATTGTTG
1431605 A
1 A
1431606 CAGTGGCGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.20, C:0.00, G:0.29, T:0.51
Consensus pattern (17 bp):
AATGTGTTGTATTGTTG
Found at i:1432208 original size:12 final size:12
Alignment explanation
Indices: 1432191--1432217 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1432181 ACATTTTTAT
1432191 ATTAGGTGTGAC
1 ATTAGGTGTGAC
1432203 ATTAGGTGTGAC
1 ATTAGGTGTGAC
1432215 ATT
1 ATT
1432218 TGATTTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.07, G:0.30, T:0.37
Consensus pattern (12 bp):
ATTAGGTGTGAC
Found at i:1433287 original size:29 final size:29
Alignment explanation
Indices: 1433255--1433350 Score: 104
Period size: 30 Copynumber: 3.3 Consensus size: 29
1433245 TTTAAGTACC
*
1433255 TAAAGTATTTTTTTATCAAAATAAGTATT
1 TAAAGTATTTTTTTGTCAAAATAAGTATT
** * *
1433284 TAAAGTCATTTTTGGGTCAAAATAGGTACT
1 TAAAGT-ATTTTTTTGTCAAAATAAGTATT
* *
1433314 TAAAGTATTTTATTGTCAAAA-AAGTATC
1 TAAAGTATTTTTTTGTCAAAATAAGTATT
*
1433342 TAAAATATT
1 TAAAGTATT
1433351 CAATTTTTTC
Statistics
Matches: 54, Mismatches: 12, Indels: 3
0.78 0.17 0.04
Matches are distributed among these distances:
28 12 0.22
29 18 0.33
30 24 0.44
ACGTcount: A:0.41, C:0.06, G:0.11, T:0.42
Consensus pattern (29 bp):
TAAAGTATTTTTTTGTCAAAATAAGTATT
Found at i:1437741 original size:19 final size:19
Alignment explanation
Indices: 1437717--1437753 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1437707 TTTGTTTTTT
1437717 TGTATTTCTCT-TCTCTCTG
1 TGTATTT-TCTGTCTCTCTG
1437736 TGTATTTTCTGTCTCTCT
1 TGTATTTTCTGTCTCTCT
1437754 TTTCTCTGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.05, C:0.24, G:0.11, T:0.59
Consensus pattern (19 bp):
TGTATTTTCTGTCTCTCTG
Found at i:1438881 original size:31 final size:31
Alignment explanation
Indices: 1438843--1439027 Score: 327
Period size: 31 Copynumber: 6.0 Consensus size: 31
1438833 CCCGAAGGAC
* * *
1438843 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
1438874 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1438905 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1438936 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1438967 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1438998 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
1439028 CCCTCGACCC
Statistics
Matches: 150, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
31 149 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1443085 original size:31 final size:31
Alignment explanation
Indices: 1443047--1443231 Score: 309
Period size: 31 Copynumber: 6.0 Consensus size: 31
1443037 CCCGAAGGAC
* * *
1443047 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
1443078 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
1443109 CAGTCTATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1443140 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1443171 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
1443202 TAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
1443232 CCCTCGACCC
Statistics
Matches: 147, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
31 146 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1444838 original size:3 final size:3
Alignment explanation
Indices: 1444832--1444911 Score: 90
Period size: 3 Copynumber: 26.7 Consensus size: 3
1444822 TATATGTATT
* * *
1444832 TAA TAA TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
1444880 TTA TTA TAA TTA TAA TAA TAAA TAA -AA TAA TA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TA
1444912 TGGGTAAAAA
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
2 2 0.03
3 60 0.92
4 3 0.05
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:1444864 original size:21 final size:21
Alignment explanation
Indices: 1444832--1444910 Score: 104
Period size: 21 Copynumber: 3.8 Consensus size: 21
1444822 TATATGTATT
* *
1444832 TAATAATAATAATAATAATAA
1 TAATAATTATAATAATTATAA
*
1444853 TAATATTTATAATAATTATAA
1 TAATAATTATAATAATTATAA
*
1444874 TAATAATTATTATAATTATAA
1 TAATAATTATAATAATTATAA
* *
1444895 TAATAAATAAAATAAT
1 TAATAATTATAATAAT
1444911 ATGGGTAAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TAATAATTATAATAATTATAA
Found at i:1445493 original size:113 final size:113
Alignment explanation
Indices: 1445230--1445791 Score: 849
Period size: 113 Copynumber: 5.0 Consensus size: 113
1445220 ATAGAATTAT
* * * *
1445230 GCAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* ** * * * * *
1445295 ATTATGAA-CTTTTCTGG-AAATGTTGATCCATCAATTGATGAATTCAT
66 ATTATGAACCTTCTCTGGCAAA-AATAATCCATCAAGTGATGGATTTAA
* *
1445342 GTAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*** * *
1445407 ATTATGAACCTTCTCTGGCAAGGCTAATTCATCAAGTGATGGATTTGA
66 ATTATGAACCTTCTCTGGCAAAAATAATCCATCAAGTGATGGATTTAA
* *
1445455 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAAATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
1445520 ATTATGAACCTTCTCTGGCAAAAATAATCCATCAAGTGATGAATTCAA
66 ATTATGAACCTTCTCTGGCAAAAATAATCCATCAAGTGATGGATTTAA
1445568 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
1445633 ATTATGAACCTTCTCTGGAAAAAATAATCCATCAAGTGATGAATTCAA
66 ATTATGAACCTTCTCTGGCAAAAATAATCCATCAAGTGATGGATTTAA
1445681 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
1445746 ATTATGAACCTTCTCTGGCAAAAATAATCCATCAAATGATAGATTT
66 ATTATGAACCTTCTCTGGCAAAAATAATCCATCAAGTGATGGATTT
1445792 GAATCTTTGC
Statistics
Matches: 415, Mismatches: 33, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
112 69 0.17
113 344 0.83
114 2 0.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.38
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACCTTCTCTGGCAAAAATAATCCATCAAGTGATGGATTTAA
Found at i:1446652 original size:83 final size:83
Alignment explanation
Indices: 1446513--1446905 Score: 693
Period size: 83 Copynumber: 4.7 Consensus size: 83
1446503 GTAGTTCTTA
* *
1446513 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATTCATCTTTTA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTTTCA
1446577 AATTCAATGATTGGTTCTG
65 AATTCAATGATTGGTTCTG
1446596 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTTCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTTCAA
1446661 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
1446679 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTTCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTTCAA
1446744 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
*
1446762 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTTTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTTCAA
1446827 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* *
1446845 TCC-AACCAAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATTCATCTT
1 -CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTT
1446906 CCAGTTAATG
Statistics
Matches: 302, Mismatches: 5, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
82 2 0.01
83 296 0.98
84 4 0.01
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (83 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTTCAA
ATTCAATGATTGGTTCTG
Found at i:1448070 original size:14 final size:14
Alignment explanation
Indices: 1448051--1448083 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1448041 CCCTTTTTTC
1448051 TTTTTTTT-TTCTT
1 TTTTTTTTCTTCTT
1448064 TTTTTTTTCTTCTT
1 TTTTTTTTCTTCTT
1448078 TTTTTT
1 TTTTTT
1448084 CTTCAAGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (14 bp):
TTTTTTTTCTTCTT
Found at i:1448087 original size:12 final size:11
Alignment explanation
Indices: 1448044--1448086 Score: 77
Period size: 11 Copynumber: 3.8 Consensus size: 11
1448034 TTGACCCCCC
1448044 TTTTTTCTTTT
1 TTTTTTCTTTT
1448055 TTTTTTCTTTT
1 TTTTTTCTTTT
1448066 TTTTTTCTTCTT
1 TTTTTTCTT-TT
1448078 TTTTTTCTT
1 TTTTTTCTT
1448087 CAAGCATAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 20 0.65
12 11 0.35
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:1458750 original size:24 final size:23
Alignment explanation
Indices: 1458723--1458787 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 23
1458713 ATGAAATATT
*
1458723 AATAATATATATAAATACTATAAA
1 AATAATATATATAAATA-TAAAAA
* *
1458747 AATAATATGTATATATATAAAAA
1 AATAATATATATAAATATAAAAA
* *
1458770 AATTATAAAT-TAAATATA
1 AATAATATATATAAATATA
1458788 TGAAATTTTA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
22 7 0.21
23 12 0.35
24 15 0.44
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (23 bp):
AATAATATATATAAATATAAAAA
Found at i:1460381 original size:19 final size:19
Alignment explanation
Indices: 1460357--1460393 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1460347 TTTGTTTTTT
1460357 TGTATTTCTCT-TCTCTCTG
1 TGTATTT-TCTGTCTCTCTG
1460376 TGTATTTTCTGTCTCTCT
1 TGTATTTTCTGTCTCTCT
1460394 TTTCTCTGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.05, C:0.24, G:0.11, T:0.59
Consensus pattern (19 bp):
TGTATTTTCTGTCTCTCTG
Found at i:1460825 original size:3 final size:3
Alignment explanation
Indices: 1460819--1460910 Score: 123
Period size: 3 Copynumber: 30.7 Consensus size: 3
1460809 TATATGTATT
* *
1460819 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
1460867 TTA TAA TAA TAA TAA TTA TAA TTA TAA TAA TAAA TAA -AA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TA
1460911 TGGGTAAAAA
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
2 2 0.03
3 72 0.94
4 3 0.04
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:1465431 original size:31 final size:31
Alignment explanation
Indices: 1465387--1465486 Score: 96
Period size: 31 Copynumber: 3.2 Consensus size: 31
1465377 CCGAATAACC
*
1465387 TAGGTA-AACTGTCCATATGTTCCTTAGAACA
1 TAGGTATAA-TGTCCATATGTTCCCTAGAACA
* * * *
1465418 CAGGTATAATGTCCATAT-ATCCCGAAAGACA
1 TAGGTATAATGTCCATATGTTCCCTAGA-ACA
* *
1465449 TAGGTAATTATGTCCATATGTTCCGTAGAACA
1 TAGGT-ATAATGTCCATATGTTCCCTAGAACA
1465481 TAGGTA
1 TAGGTA
1465487 AACCCTCGAC
Statistics
Matches: 54, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
30 5 0.09
31 22 0.41
32 22 0.41
33 5 0.09
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (31 bp):
TAGGTATAATGTCCATATGTTCCCTAGAACA
Found at i:1465482 original size:32 final size:32
Alignment explanation
Indices: 1465387--1465487 Score: 109
Period size: 32 Copynumber: 3.2 Consensus size: 32
1465377 CCGAATAACC
* *
1465387 TAGGTAA-ACTGTCCATATGTTCCTTAGAACA
1 TAGGTAATAATGTCCATATGTTCCGTAGAACA
* * * *
1465418 CAGGT-ATAATGTCCATATATCCCG-AAAGACA
1 TAGGTAATAATGTCCATATGTTCCGTAGA-ACA
*
1465449 TAGGTAATTATGTCCATATGTTCCGTAGAACA
1 TAGGTAATAATGTCCATATGTTCCGTAGAACA
1465481 TAGGTAA
1 TAGGTAA
1465488 ACCCTCGACT
Statistics
Matches: 55, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
30 3 0.05
31 24 0.44
32 26 0.47
33 2 0.04
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.30
Consensus pattern (32 bp):
TAGGTAATAATGTCCATATGTTCCGTAGAACA
Found at i:1466943 original size:15 final size:15
Alignment explanation
Indices: 1466910--1467002 Score: 69
Period size: 16 Copynumber: 5.9 Consensus size: 15
1466900 TTTGGGATGT
* *
1466910 TTTCGGTTTGGGTTGC
1 TTTCGG-TTCGGTTAC
*
1466926 TTTTGGTTCGGTTAC
1 TTTCGGTTCGGTTAC
* *
1466941 TTTCGGCTCGAGTTGC
1 TTTCGGTTCG-GTTAC
**
1466957 TTTTAGTTCGGTTAC
1 TTTCGGTTCGGTTAC
* *
1466972 TTTCGGCTCGAGTTGC
1 TTTCGGTTCG-GTTAC
1466988 TTTCGGTTCAGGTTA
1 TTTCGGTTC-GGTTA
1467003 ATTTTGGATA
Statistics
Matches: 58, Mismatches: 16, Indels: 6
0.73 0.20 0.08
Matches are distributed among these distances:
15 26 0.45
16 31 0.53
17 1 0.02
ACGTcount: A:0.08, C:0.17, G:0.29, T:0.46
Consensus pattern (15 bp):
TTTCGGTTCGGTTAC
Found at i:1466945 original size:31 final size:31
Alignment explanation
Indices: 1466921--1467002 Score: 137
Period size: 31 Copynumber: 2.6 Consensus size: 31
1466911 TTCGGTTTGG
1466921 GTTGCTTTTGGTTCGGTTACTTTCGGCTCGA
1 GTTGCTTTTGGTTCGGTTACTTTCGGCTCGA
*
1466952 GTTGCTTTTAGTTCGGTTACTTTCGGCTCGA
1 GTTGCTTTTGGTTCGGTTACTTTCGGCTCGA
*
1466983 GTTGCTTTCGGTTCAGGTTA
1 GTTGCTTTTGGTTC-GGTTA
1467003 ATTTTGGATA
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
31 42 0.89
32 5 0.11
ACGTcount: A:0.09, C:0.18, G:0.28, T:0.45
Consensus pattern (31 bp):
GTTGCTTTTGGTTCGGTTACTTTCGGCTCGA
Found at i:1466992 original size:16 final size:15
Alignment explanation
Indices: 1466920--1466993 Score: 67
Period size: 15 Copynumber: 4.8 Consensus size: 15
1466910 TTTCGGTTTG
* *
1466920 GGTTGCTTTTGGTTC
1 GGTTGCTTTCGGCTC
*
1466935 GGTTACTTTCGGCTC
1 GGTTGCTTTCGGCTC
** *
1466950 GAGTTGCTTTTAGTTC
1 G-GTTGCTTTCGGCTC
*
1466966 GGTTACTTTCGGCTC
1 GGTTGCTTTCGGCTC
1466981 GAGTTGCTTTCGG
1 G-GTTGCTTTCGG
1466994 TTCAGGTTAA
Statistics
Matches: 45, Mismatches: 12, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
15 24 0.53
16 21 0.47
ACGTcount: A:0.07, C:0.19, G:0.30, T:0.45
Consensus pattern (15 bp):
GGTTGCTTTCGGCTC
Found at i:1469235 original size:20 final size:20
Alignment explanation
Indices: 1469208--1469257 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
1469198 GTTGAAAGTG
1469208 TCGATACTTTAATATAAGCA
1 TCGATACTTTAATATAAGCA
* *
1469228 TTGATACTTTAATATAAGTA
1 TCGATACTTTAATATAAGCA
1469248 TCGATACTTT
1 TCGATACTTT
1469258 TGGAATTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (20 bp):
TCGATACTTTAATATAAGCA
Found at i:1469552 original size:182 final size:181
Alignment explanation
Indices: 1469230--1469791 Score: 747
Period size: 182 Copynumber: 3.1 Consensus size: 181
1469220 TATAAGCATT
* * *
1469230 GATACTTTAATATAAGTATCGATACTTTTGGAATTTAAAAGAGAAACAGTAATAGCGCCTATAAA
1 GATACTTTATTATAAGTATCGACACTTTTGGAATTTAAAAGACAAACAGTAATAGCGCCTATAAA
* * *
1469295 GTGTCAAAATTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAAA-C
66 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAAATC
* *
1469359 TGGTTTCAAAATGACAAAACCGGTAAAGAGCTATCAGATATGTTGAAAGTGTC
131 -GGTCTCAAAATGACAAAACCGGTAAAGCGCTA-CAGATATGTTGAAAGTGTC
* * * *
1469412 GATAATTTATTATAAGTATCGACACTTATGTAATTTAAAAGACAAGCAGTAATAGCGCCTATAAA
1 GATACTTTATTATAAGTATCGACACTTTTGGAATTTAAAAGACAAACAGTAATAGCGCCTATAAA
*
1469477 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAATATGATAAAATC
66 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAAATC
* * *
1469542 GGTCTCAAAATGACAAAACTGGTAAAGCGTTACCGGATATGTTGAAAGTGTC
131 GGTCTCAAAATGACAAAACCGGTAAAGCGCTA-CAGATATGTTGAAAGTGTC
* * * * *
1469594 AATATTTTATTATAAGTATCAACATTTTTGGAATTTAAAAGACAAACAATAATAGCGCCTATAAA
1 GATACTTTATTATAAGTATCGACACTTTTGGAATTTAAAAGACAAACAGTAATAGCGCCTATAAA
* * * * *
1469659 GTGTCGATACTTTATAAAAATGTATC-AACACTTAATAATTTAATAGGTAAAAATATGATAAAAT
66 GTGTCGATACTTTATAAAAATGTATCGATC-CATAACAATATAACAGGTAAAAATATGATAAAAT
* ** * * *
1469723 CAG-CATTGAAATGACAAAACCGGTAAATCCCTACCGAATATGTTGAAAGTGTC
130 CGGTC-TCAAAATGACAAAACCGGTAAAGCGCTACAG-ATATGTTGAAAGTGTC
1469776 GATACTTTA--ATAAGTA
1 GATACTTTATTATAAGTA
1469792 CGCGTAAAAA
Statistics
Matches: 335, Mismatches: 41, Indels: 10
0.87 0.11 0.03
Matches are distributed among these distances:
180 7 0.02
181 5 0.01
182 322 0.96
183 1 0.00
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.30
Consensus pattern (181 bp):
GATACTTTATTATAAGTATCGACACTTTTGGAATTTAAAAGACAAACAGTAATAGCGCCTATAAA
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAAATC
GGTCTCAAAATGACAAAACCGGTAAAGCGCTACAGATATGTTGAAAGTGTC
Found at i:1474886 original size:201 final size:200
Alignment explanation
Indices: 1474521--1474941 Score: 626
Period size: 201 Copynumber: 2.1 Consensus size: 200
1474511 GTTAATAGAT
* * * * * *
1474521 GTGTCGACACAGTTATAAAAAGTATCGATCCCAAAAACATCAAAATCTATAATTATATTGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACAACAAAACCCATAATTATAATGTAATA
* *
1474586 GATAATTTTTCAATGTAACTGGTATAAATATACCGGTTTTATGAAAGAATAGGTTTACATAATGT
66 GATAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAAAGAATAGGTCTACATAATGT
* ** * *
1474651 ATCGACACTTGTGGAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAAGGAGTGGATG
131 ATCGACACTTGTGAAATTTCCGTCGATACTTTTTGTCCAGAATGAATGCCCAAAAGG-GTAGACG
1474716 CATAAA
195 CATAAA
* * *
1474722 GTGTCGATACATTTATAAAAAGTATCTATCCCAAGAACAACGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACAACAAAACCCATAATTATAATGTAATA
* * * *
1474787 GGTAATTTTTCAATGTAACCGGTATAAATATATCGGTTTTATGAGAGAATATGTCTACATAATGT
66 GATAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAAAGAATAGGTCTACATAATGT
* *
1474852 ATCGACACTTGTGAAATTTCCGTCGATGCTTTTTGTCCAGAATGAATGCCCAAAAGGGTATACGC
131 ATCGACACTTGTGAAATTTCCGTCGATACTTTTTGTCCAGAATGAATGCCCAAAAGGGTAGACGC
*
1474917 ATAAC
196 ATAAA
1474922 GTGTCGATACATTTATAAAA
1 GTGTCGATACATTTATAAAA
1474942 TTGTAAAGTT
Statistics
Matches: 197, Mismatches: 23, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
200 29 0.15
201 168 0.85
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (200 bp):
GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACAACAAAACCCATAATTATAATGTAATA
GATAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAAAGAATAGGTCTACATAATGT
ATCGACACTTGTGAAATTTCCGTCGATACTTTTTGTCCAGAATGAATGCCCAAAAGGGTAGACGC
ATAAA
Found at i:1475617 original size:21 final size:21
Alignment explanation
Indices: 1475591--1475635 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1475581 GATTTCTGGG
*
1475591 CAAGGGGAATCGATACCCATT
1 CAAGGGGAACCGATACCCATT
*
1475612 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1475633 CAA
1 CAA
1475636 ACGAACAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1476351 original size:31 final size:31
Alignment explanation
Indices: 1476313--1476435 Score: 203
Period size: 31 Copynumber: 4.0 Consensus size: 31
1476303 GAGTCGAGGG
1476313 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
1476344 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
1476375 TTACCTATGTTCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
1476406 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
1476436 GTCCTTCGGG
Statistics
Matches: 88, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
31 87 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:1477576 original size:202 final size:201
Alignment explanation
Indices: 1477209--1477616 Score: 602
Period size: 202 Copynumber: 2.0 Consensus size: 201
1477199 GGTGTTACAT
* * * * * *
1477209 TTTTTGTCCGGAATCAGTGCCCAACGAGGTGAACTCGTAAAGTGTCGATACATTTATAAAAAGTA
1 TTTTTCTCCAGAATCAATGCCCAACGAGGTGAACACATAAAGTGTCGATAAATTTATAAAAAGTA
* **** ** *
1477274 TCGATCCCAAAAACATCGAATCTGGTAATTATAATGTAATAGGTAAATTTCCAATGTAACCGGTA
66 TCGATCCCAAAAACATCGAAACCAAAAATTATAATGTAATAAATAAATTTACAATGTAACCGGTA
*
1477339 TAAATATACCGATTTAATTAGAAAAGCGGTCAACATAATGTATCGACACTTTTTAAATTTGTGTC
131 TAAATATACCGATTTAATTAGAAAAGCGATCAACATAATGTATCGACACTTTTTAAATTTGTGTC
1477404 GATA-C
196 GATACC
* *
1477409 TTTTTCTCCAGAATCAATGGCCAACGAGGTGCACACATAAAGTGTCGATAAATTTATAAAAAAAG
1 TTTTTCTCCAGAATCAATGCCCAACGAGGTGAACACATAAAGTGTCGATAAATTTAT--AAAAAG
1477474 TATCGATCCCAAAAACATCGAAACCAAAAATTATAATGTAATAAATAAATTTACAATGTAACCGG
64 TATCGATCCCAAAAACATCGAAACCAAAAATTATAATGTAATAAATAAATTTACAATGTAACCGG
* * * *
1477539 TATAAATATATCGGTTTAATTAGAAAAGCGATCAACATAATGTCTCGACACTTTTTAAATTTTTG
129 TATAAATATACCGATTTAATTAGAAAAGCGATCAACATAATGTATCGACACTTTTTAAATTTGTG
1477604 TCGATACC
194 TCGATACC
1477612 TTTTT
1 TTTTT
1477617 AAATTTCACG
Statistics
Matches: 184, Mismatches: 21, Indels: 3
0.88 0.10 0.01
Matches are distributed among these distances:
200 49 0.27
202 129 0.70
203 6 0.03
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (201 bp):
TTTTTCTCCAGAATCAATGCCCAACGAGGTGAACACATAAAGTGTCGATAAATTTATAAAAAGTA
TCGATCCCAAAAACATCGAAACCAAAAATTATAATGTAATAAATAAATTTACAATGTAACCGGTA
TAAATATACCGATTTAATTAGAAAAGCGATCAACATAATGTATCGACACTTTTTAAATTTGTGTC
GATACC
Found at i:1477925 original size:15 final size:15
Alignment explanation
Indices: 1477905--1477954 Score: 64
Period size: 15 Copynumber: 3.1 Consensus size: 15
1477895 GTCTTTCTCA
1477905 AAGCTCTTCTCAACC
1 AAGCTCTTCTCAACC
1477920 AAGCTCTTCTCAACGAC
1 AAGCTCTTCTCAAC--C
*
1477937 AACCTCCTTCTCAACC
1 AAGCT-CTTCTCAACC
1477953 AA
1 AA
1477955 TTGCTTCTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
15 14 0.45
16 3 0.10
17 5 0.16
18 9 0.29
ACGTcount: A:0.30, C:0.40, G:0.06, T:0.24
Consensus pattern (15 bp):
AAGCTCTTCTCAACC
Found at i:1479077 original size:12 final size:12
Alignment explanation
Indices: 1479060--1479095 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1479050 TAAGCGGTCA
1479060 ATGAAGATGATG
1 ATGAAGATGATG
*
1479072 ATGAAGATGAAG
1 ATGAAGATGATG
*
1479084 ATGATGATGATG
1 ATGAAGATGATG
1479096 TTGATCCAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.33, T:0.25
Consensus pattern (12 bp):
ATGAAGATGATG
Found at i:1481021 original size:19 final size:19
Alignment explanation
Indices: 1480997--1481044 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
1480987 ATGTAAGGGA
*
1480997 AATTTTGTATATAATTCAT
1 AATTTTGTATACAATTCAT
*
1481016 AATTTTGTATACAATTTAT
1 AATTTTGTATACAATTCAT
1481035 AATTTTGTAT
1 AATTTTGTAT
1481045 GTGAATGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.54
Consensus pattern (19 bp):
AATTTTGTATACAATTCAT
Found at i:1484109 original size:199 final size:198
Alignment explanation
Indices: 1483755--1484467 Score: 934
Period size: 199 Copynumber: 3.6 Consensus size: 198
1483745 ACAGGTAAAC
*
1483755 AAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACATATAATTATAATGTA
1 AAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACAGATAATTATAATGTA
* * * * * *
1483820 ATAGGTAAATTTTCAATGTAACTGGTAAAAAAATACC-GGTTAATTAGAAAACAAGTCTACATAA
66 ATAGGTAAATTTACAATGTAACCGGTATAAATATACCAGTTTAATTAGAAAACAGGTCTACATAA
* * * *
1483884 CGTATCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCAAGAATAAATGCTAAACGGGGTACA
131 TGTATCGACACTTTTTAAA-TTGTGTCGATA-TTTTTGTCCAGAATGAATGCTAAACGGGGTGCA
*
1483949 CACGT
194 CACAT
*
1483954 AAAGTGTCGATACATTTATTAAAAGTATTGATCCCAAAAACATCGAAACAGATAATTATAATGTA
1 AAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACAGATAATTATAATGTA
* * * **
1484019 ATAGGTAAATTTCCAATGTAATCGGTATATATATACCAGTTTAATTAGAAAACAGGTAAACATAA
66 ATAGGTAAATTTACAATGTAACCGGTATAAATATACCAGTTTAATTAGAAAACAGGTCTACATAA
* *
1484084 TGTATCGACACTTTTTCAATTGTGTCGATATTTTTTGTCCAGAATGAATG-TCAAAAGGGGTGCA
131 TGTATCGACACTTTTTAAATTGTGTCGATA-TTTTTGTCCAGAATGAATGCT-AAACGGGGTGCA
*
1484148 CGCAT
194 CACAT
* *
1484153 AAAGTGTCGATACATTTATTAACAA-TATCGATCCCAAAAACATCGAAACCGATAATTACAATGT
1 AAAGTGTCGATACATTTATTAA-AAGTATCGATCCCAAAAACATCGAAACAGATAATTATAATGT
* * * * * *
1484217 AATAGGTAAATTTACAATGTACCCGGTAGAAATATATCAGTTTTATGAGAAAATAGGTCTACATA
65 AATAGGTAAATTTACAATGTAACCGGTATAAATATACCAGTTTAATTAGAAAACAGGTCTACATA
* * ** *
1484282 ATGTATCGACACTTTTTAAGATTGTGTCAATATGTTTT-TCCAGAATGAATACCCAACGAGGTGC
130 ATGTATCGACACTTTTTAA-ATTGTGTCGATAT-TTTTGTCCAGAATGAATGCTAAACGGGGTGC
1484346 ACACAT
193 ACACAT
* * * *
1484352 AAAGTGTCGATACATTTA--AAATTGTATCGATCCCGAAAACATCGAAACTGATAATTATAATAT
1 AAAGTGTCGATACATTTATTAAA-AGTATCGATCCCAAAAACATCGAAACAGATAATTATAATGT
* * * *
1484415 AATAGGTAAATTTGCAATGTTACCGGTATAAATATACCGGTTTAGTTAGAAAA
65 AATAGGTAAATTTACAATGTAACCGGTATAAATATACCAGTTTAATTAGAAAA
1484468 TATGTCAATA
Statistics
Matches: 449, Mismatches: 57, Indels: 17
0.86 0.11 0.03
Matches are distributed among these distances:
196 1 0.00
197 2 0.00
198 80 0.18
199 309 0.69
200 57 0.13
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (198 bp):
AAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACAGATAATTATAATGTA
ATAGGTAAATTTACAATGTAACCGGTATAAATATACCAGTTTAATTAGAAAACAGGTCTACATAA
TGTATCGACACTTTTTAAATTGTGTCGATATTTTTGTCCAGAATGAATGCTAAACGGGGTGCACA
CAT
Found at i:1484566 original size:87 final size:87
Alignment explanation
Indices: 1484475--1484637 Score: 290
Period size: 87 Copynumber: 1.9 Consensus size: 87
1484465 AAATATGTCA
* *
1484475 ATATAAGCGCTACCTATTACATTATATAAGTGATGCCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGATACCTAATATGTTATTGTACTTGATAATATTT
1484540 CCGGTTAAATGCCTATTTTATT
66 CCGGTTAAATGCCTATTTTATT
*
1484562 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGATACCTAATATGTTATTGTACTTGATAATATTT
*
1484627 TCGGTTAAATG
66 CCGGTTAAATG
1484638 ATATAACATA
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGATACCTAATATGTTATTGTACTTGATAATATTT
CCGGTTAAATGCCTATTTTATT
Found at i:1484609 original size:23 final size:23
Alignment explanation
Indices: 1484559--1484603 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
1484549 TGCCTATTTT
*
1484559 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
1484582 ATTATATAAGCGCTACCTAATA
1 ATTATATAAGCGCTACCTAATA
1484604 TGTTATTGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:1485969 original size:23 final size:23
Alignment explanation
Indices: 1485943--1485987 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1485933 TAGACACGTG
* *
1485943 TTTACTTTAAAATTTAATTTTTT
1 TTTACTTTAAAATCTAAATTTTT
*
1485966 TTTATTTTAAAATCTAAATTTT
1 TTTACTTTAAAATCTAAATTTT
1485988 CTTATCAAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTACTTTAAAATCTAAATTTTT
Found at i:1485992 original size:22 final size:23
Alignment explanation
Indices: 1485948--1485992 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1485938 ACGTGTTTAC
* * *
1485948 TTTAAAATTTAATTTTTTTTTAT
1 TTTAAAATCTAATATTTTCTTAT
1485971 TTTAAAATCTAA-ATTTTCTTAT
1 TTTAAAATCTAATATTTTCTTAT
1485993 CAAACATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTAAAATCTAATATTTTCTTAT
Found at i:1492892 original size:17 final size:15
Alignment explanation
Indices: 1492846--1492884 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1492836 AAAATCCAGG
1492846 AAAAACAACTAAAAATC
1 AAAAACAAC--AAAATC
*
1492863 AAAAGCAACAAAATC
1 AAAAACAACAAAATC
1492878 AAAAACA
1 AAAAACA
1492885 TAACAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 12 0.60
17 8 0.40
ACGTcount: A:0.72, C:0.18, G:0.03, T:0.08
Consensus pattern (15 bp):
AAAAACAACAAAATC
Found at i:1494203 original size:2 final size:2
Alignment explanation
Indices: 1494196--1494272 Score: 154
Period size: 2 Copynumber: 38.5 Consensus size: 2
1494186 GGATTGAACA
1494196 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1494238 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1494273 TCTGTTAAGA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1510745 original size:19 final size:20
Alignment explanation
Indices: 1510714--1510752 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
1510704 ACCCCACTTA
1510714 CTTTTTACTTTTCACTTTCT
1 CTTTTTACTTTTCACTTTCT
1510734 CTTTTTAC-TTTCACTTTCT
1 CTTTTTACTTTTCACTTTCT
1510753 AGTTTCCTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.10, C:0.26, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTTACTTTTCACTTTCT
Found at i:1512793 original size:2 final size:2
Alignment explanation
Indices: 1512786--1512835 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
1512776 ACCCCGCATA
1512786 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1512828 AT AT -T AT A
1 AT AT AT AT A
1512836 AATAAATGCC
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1521378 original size:21 final size:21
Alignment explanation
Indices: 1521352--1521393 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1521342 AAGTAAGTCA
1521352 ACGATCCCTAAAACGGACTAT
1 ACGATCCCTAAAACGGACTAT
1521373 ACGATCCCTAAAACGGACTAT
1 ACGATCCCTAAAACGGACTAT
1521394 GTAATGTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.29, G:0.14, T:0.19
Consensus pattern (21 bp):
ACGATCCCTAAAACGGACTAT
Found at i:1524054 original size:18 final size:18
Alignment explanation
Indices: 1524013--1524060 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
1524003 TTTTTAATAT
*
1524013 TAAAAAATAATTTTACAAA
1 TAAAAAATAA-ATTACAAA
1524032 TAAAAAATAAATTA-AAA
1 TAAAAAATAAATTACAAA
1524049 TGAAAAAATAAA
1 T-AAAAAATAAA
1524061 CGTTTTAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 4 0.15
18 13 0.48
19 10 0.37
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (18 bp):
TAAAAAATAAATTACAAA
Found at i:1525401 original size:2 final size:2
Alignment explanation
Indices: 1525394--1525455 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
1525384 GCTTCATAAC
1525394 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1525436 AT AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
1525456 CACATATAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1525659 original size:29 final size:29
Alignment explanation
Indices: 1525617--1525673 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
1525607 ATGCAAAACA
* *
1525617 TAGGTCGCCATGCCCTCTGGGTGACCTTG
1 TAGGTCGCCATGCCATCTGGGCGACCTTG
*
1525646 TAGGTTGCCATGCCATCTGGGCGACCTT
1 TAGGTCGCCATGCCATCTGGGCGACCTT
1525674 ATTTGTAGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.12, C:0.30, G:0.30, T:0.28
Consensus pattern (29 bp):
TAGGTCGCCATGCCATCTGGGCGACCTTG
Found at i:1525889 original size:19 final size:19
Alignment explanation
Indices: 1525865--1525902 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1525855 CGACCAAGCT
1525865 TCTGCTCCCTCGTGCCATA
1 TCTGCTCCCTCGTGCCATA
*
1525884 TCTGCTCCCTCGTGTCATA
1 TCTGCTCCCTCGTGCCATA
1525903 GCTTCAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.11, C:0.39, G:0.16, T:0.34
Consensus pattern (19 bp):
TCTGCTCCCTCGTGCCATA
Found at i:1526860 original size:22 final size:23
Alignment explanation
Indices: 1526817--1526860 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
1526807 TATTGCGCTT
**
1526817 AAAAATATTTAGTGTTGTTTTAA
1 AAAAATATTTAGTGTTAATTTAA
*
1526840 AAAAATATTTTGT-TTAATTTA
1 AAAAATATTTAGTGTTAATTTA
1526861 TATTAGATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (23 bp):
AAAAATATTTAGTGTTAATTTAA
Found at i:1530139 original size:21 final size:21
Alignment explanation
Indices: 1530115--1530199 Score: 54
Period size: 21 Copynumber: 4.2 Consensus size: 21
1530105 AAAATTATAA
1530115 TAATTATTTAGTAATGATTAG
1 TAATTATTTAGTAATGATTAG
* * * *
1530136 TAA-TA-AT-GAAATTATTAT
1 TAATTATTTAGTAATGATTAG
* *
1530154 TAA-TATTTAATGATTTGA-TAG
1 TAATTATTTAGT-A-ATGATTAG
*
1530175 TAATGATTTAGTAATGATTAG
1 TAATTATTTAGTAATGATTAG
1530196 TAAT
1 TAAT
1530200 AATAAAATTA
Statistics
Matches: 45, Mismatches: 13, Indels: 12
0.64 0.19 0.17
Matches are distributed among these distances:
18 13 0.29
19 2 0.04
20 5 0.11
21 17 0.38
22 8 0.18
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (21 bp):
TAATTATTTAGTAATGATTAG
Found at i:1530180 original size:49 final size:49
Alignment explanation
Indices: 1530064--1530298 Score: 235
Period size: 49 Copynumber: 4.6 Consensus size: 49
1530054 TTTGATTTAG
* * ** *
1530064 TAATGATTTGATAATCATGATT--TAATAATGATTTTA-TATTTAAAATT
1 TAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTA-TTAATATT
* *
1530111 ATAATAATTAT-TTAGTAATGATTAGTAATAATGAAATTATTATTAATATT
1 -TAATGATT-TGATAGTAATGATTAGTAATAATGAAATTATTATTAATATT
*
1530161 TAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATAAAATTATTATTAATATT
1 T-A--A--TGAT--T--TGA--TAGTAATGATTAGTAATAATGAAATTATTATTAATATT
1530221 TAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATATT
1 TAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATATT
1530270 TAATGATTTGATAGTAATGATTTAGTAAT
1 TAATGATTTGATAGTAATGA-TTAGTAAT
1530299 TATTAGTAAT
Statistics
Matches: 160, Mismatches: 11, Indels: 30
0.80 0.05 0.15
Matches are distributed among these distances:
48 16 0.10
49 59 0.37
50 28 0.17
51 5 0.03
52 1 0.01
53 1 0.01
54 3 0.02
55 4 0.03
56 1 0.01
57 3 0.02
59 1 0.01
60 38 0.24
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (49 bp):
TAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATATT
Found at i:1530193 original size:60 final size:60
Alignment explanation
Indices: 1530115--1530248 Score: 243
Period size: 60 Copynumber: 2.2 Consensus size: 60
1530105 AAAATTATAA
* *
1530115 TAATTATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAG
1 TAATGATTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGATAG
1530175 TAATGATTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGATAG
1 TAATGATTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGATAG
1530235 TAATGA-TTAGTAAT
1 TAATGATTTAGTAAT
1530249 AATGAAATTA
Statistics
Matches: 72, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
59 8 0.11
60 64 0.89
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.46
Consensus pattern (60 bp):
TAATGATTTAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGATAG
Found at i:1530238 original size:21 final size:21
Alignment explanation
Indices: 1530129--1530238 Score: 58
Period size: 21 Copynumber: 5.5 Consensus size: 21
1530119 TATTTAGTAA
* *
1530129 TGATTAGTAATAATGAA-A-T
1 TGATTAGTAATATTTAATATT
*
1530148 T-ATTATTAATATTTAATGATT
1 TGATTAGTAATATTTAAT-ATT
* *
1530169 TGA-TAGTAATGATTTAGTA-A
1 TGATTAGTAAT-ATTTAATATT
* *
1530189 TGATTAGTAATA-ATAA-AAT
1 TGATTAGTAATATTTAATATT
*
1530208 T-ATTATTAATATTTAATGATT
1 TGATTAGTAATATTTAAT-ATT
1530229 TGA-TAGTAAT
1 TGATTAGTAAT
1530239 GATTAGTAAT
Statistics
Matches: 67, Mismatches: 13, Indels: 20
0.67 0.13 0.20
Matches are distributed among these distances:
18 22 0.33
19 7 0.10
20 5 0.07
21 25 0.37
22 8 0.12
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (21 bp):
TGATTAGTAATATTTAATATT
Found at i:1530247 original size:109 final size:109
Alignment explanation
Indices: 1530123--1530319 Score: 376
Period size: 109 Copynumber: 1.8 Consensus size: 109
1530113 AATAATTATT
1530123 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTA
1530188 ATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGA
66 ATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGA
1530232 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTA
* *
1530297 ATTATTAGTAATAATGAAATTAT
66 ATGATTAGTAATAATAAAATTAT
1530320 AATAATGATT
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
109 86 1.00
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (109 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTA
ATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGA
Found at i:1530264 original size:21 final size:21
Alignment explanation
Indices: 1530240--1530319 Score: 51
Period size: 21 Copynumber: 4.0 Consensus size: 21
1530230 GATAGTAATG
1530240 ATTAGTAATAATGAAATTATT
1 ATTAGTAATAATGAAATTATT
* * *
1530261 ATTAATATTTAATG--ATT-TG
1 ATTAGTA-ATAATGAAATTATT
* ** * *
1530280 A-TAGTAATGATTTAGTAATT
1 ATTAGTAATAATGAAATTATT
1530300 ATTAGTAATAATGAAATTAT
1 ATTAGTAATAATGAAATTAT
1530320 AATAATGATT
Statistics
Matches: 39, Mismatches: 15, Indels: 10
0.61 0.23 0.16
Matches are distributed among these distances:
17 3 0.08
18 4 0.10
19 3 0.08
20 5 0.13
21 19 0.49
22 5 0.13
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.45
Consensus pattern (21 bp):
ATTAGTAATAATGAAATTATT
Found at i:1530277 original size:35 final size:35
Alignment explanation
Indices: 1530126--1530228 Score: 91
Period size: 35 Copynumber: 3.2 Consensus size: 35
1530116 AATTATTTAG
1530126 TAATGATTAGTAATAATGAAATTATTATTAATATT
1 TAATGATTAGTAATAATGAAATTATTATTAATATT
* * * *
1530161 TAATGATT--TGAT-A-G---TAATGATT--TA-G
1 TAATGATTAGTAATAATGAAATTATTATTAATATT
*
1530186 TAATGATTAGTAATAATAAAATTATTATTAATATT
1 TAATGATTAGTAATAATGAAATTATTATTAATATT
1530221 TAATGATT
1 TAATGATT
1530229 TGATAGTAAT
Statistics
Matches: 49, Mismatches: 9, Indels: 20
0.63 0.12 0.26
Matches are distributed among these distances:
25 8 0.16
26 2 0.04
27 3 0.06
28 7 0.14
31 1 0.02
32 7 0.14
33 3 0.06
34 2 0.04
35 16 0.33
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.46
Consensus pattern (35 bp):
TAATGATTAGTAATAATGAAATTATTATTAATATT
Found at i:1530671 original size:11 final size:11
Alignment explanation
Indices: 1530655--1530905 Score: 62
Period size: 11 Copynumber: 20.6 Consensus size: 11
1530645 TAATAATTAT
*
1530655 ATGATTTAGTA
1 ATGATTTAATA
1530666 ATGATTTGATAATA
1 ATGA-TT--TAATA
1530680 ATGATTTAATA
1 ATGATTTAATA
1530691 ATGATTT--TA
1 ATGATTTAATA
1530700 AT-ATTTAATGA
1 ATGATTTAAT-A
**
1530711 TTTGATGATTTTGTA
1 ----ATGATTTAATA
1530726 ATGATTTGATAATA
1 ATGA-TT--TAATA
*
1530740 ATCATTATAATA
1 ATGATT-TAATA
* *
1530752 ATGGTTTAGTAAGA
1 AT-GATT--TAATA
*
1530766 ATCATTATAATA
1 ATGATT-TAATA
1530778 ATGATTTAATA
1 ATGATTTAATA
* *
1530789 ATAATGATAATA
1 ATGAT-TTAATA
* *
1530801 ATAATTTAGTA
1 ATGATTTAATA
1530812 ATGATTTGATAATA
1 ATGA-TT--TAATA
* *
1530826 ATAATTTATTA
1 ATGATTTAATA
* *
1530837 TTAATATT--TA
1 ATGAT-TTAATA
1530847 ATGATTTGATACTA
1 ATGATTT-A-A-TA
*
1530861 ATGATTTACTA
1 ATGATTTAATA
1530872 ATGATTACTAATA
1 ATGATT--TAATA
1530885 ATGAAATTATAATA
1 ATG--ATT-TAATA
1530899 ATGATTT
1 ATGATTT
1530906 GATACTAATA
Statistics
Matches: 181, Mismatches: 29, Indels: 60
0.67 0.11 0.22
Matches are distributed among these distances:
8 4 0.02
9 6 0.03
10 6 0.03
11 54 0.30
12 38 0.21
13 18 0.10
14 44 0.24
15 6 0.03
16 5 0.03
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.45
Consensus pattern (11 bp):
ATGATTTAATA
Found at i:1530708 original size:60 final size:59
Alignment explanation
Indices: 1530643--1530877 Score: 185
Period size: 60 Copynumber: 3.9 Consensus size: 59
1530633 CATATGATTT
1530643 TTTAATAATTATATGATTTAGTAATGATTTGATAATAATGATTTAATAATGATTTTAATA
1 TTTAATAATT-TATGATTTAGTAATGATTTGATAATAATGATTTAATAATGATTTTAATA
* * * * *
1530703 TTTAATGATTTGATGATTTTGTAATGATTTGATAATAATCATTATAATAATGGTTTAGTAAGAA
1 TTTAATAATTT-ATGATTTAGTAATGATTTGATAATAATGATT-TAATAATGATTT--TAA-TA
* * * * * *
1530767 TCATT-ATAA-TAATGATTTAATAAT-A-ATGATAATAATAATTTAGTAATGA-TTTGATA
1 T--TTAATAATTTATGATTTAGTAATGATTTGATAATAATGATTTAATAATGATTTTAATA
* * * * *
1530823 -ATAATAATTTATTATTAATATTTAATGATTTGATACTAATGATTTACTAATGATT
1 TTTAATAATTTATGATT--TA-GTAATGATTTGATAATAATGATTTAATAATGATT
1530878 ACTAATAATG
Statistics
Matches: 137, Mismatches: 23, Indels: 29
0.72 0.12 0.15
Matches are distributed among these distances:
53 1 0.01
54 4 0.03
55 6 0.04
56 1 0.01
57 4 0.03
58 4 0.03
59 4 0.03
60 65 0.47
61 25 0.18
62 1 0.01
63 14 0.10
64 3 0.02
65 3 0.02
66 2 0.01
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.46
Consensus pattern (59 bp):
TTTAATAATTTATGATTTAGTAATGATTTGATAATAATGATTTAATAATGATTTTAATA
Found at i:1530753 original size:26 final size:25
Alignment explanation
Indices: 1530724--1530925 Score: 102
Period size: 26 Copynumber: 8.1 Consensus size: 25
1530714 GATGATTTTG
1530724 TAATGATTTGATAATAATCATTATAA
1 TAATGATTT-ATAATAATCATTATAA
* *
1530750 TAATGGTTTAGTAAGAATCATTATAA
1 TAATGATTTA-TAATAATCATTATAA
* *
1530776 TAATGA-TT-TAATAATAATGATAA
1 TAATGATTTATAATAATCATTATAA
* *
1530799 TAATAATTTAGTAATGAT--TTGATAA
1 TAATGATTTA-TAATAATCATT-ATAA
* *
1530824 TAATAATTTATTATTAAT-A-T-T--
1 TAATGATTTA-TAATAATCATTATAA
* * *
1530845 TAATGATTTGATACTAATGATT-TAC
1 TAATGATTT-ATAATAATCATTATAA
*
1530870 TAATGA-TTACTAATAATGAAATTATAA
1 TAATGATTTA-TAATAAT--CATTATAA
* * *
1530897 TAATGATTTGATACTAATAATCATAA
1 TAATGATTT-ATAATAATCATTATAA
1530923 TAA
1 TAA
1530926 ATATGTCGAT
Statistics
Matches: 140, Mismatches: 19, Indels: 34
0.73 0.10 0.18
Matches are distributed among these distances:
21 14 0.10
22 2 0.01
23 21 0.15
24 11 0.08
25 29 0.21
26 46 0.33
27 8 0.06
28 8 0.06
29 1 0.01
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.42
Consensus pattern (25 bp):
TAATGATTTATAATAATCATTATAA
Done.