Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007741.1 Hibiscus syriacus cultivar Beakdansim tig00110004_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: 1550271
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 7
Found at i:1351846 original size:3 final size:3
Alignment explanation
Indices: 1351833--1351920 Score: 88
Period size: 3 Copynumber: 28.7 Consensus size: 3
1351823 TTTCGTCAAG
* * *
1351833 TTA TCTA TTA TTA TTA TTA TTA TTA TTA TTA TTC TTA TCA TTA TCA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
1351879 TTA TCA TTA TCA TTA TTA TTA TTAA TTAA TTT TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TT-A TT-A TTA TTA TTA TTA TT
1351921 TACATGCCAA
Statistics
Matches: 70, Mismatches: 12, Indels: 6
0.80 0.14 0.07
Matches are distributed among these distances:
2 2 0.03
3 58 0.83
4 10 0.14
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1359436 original size:2 final size:2
Alignment explanation
Indices: 1359429--1359458 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1359419 AATGAAATCA
1359429 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
1359459 GTCTAATATC
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:1363290 original size:12 final size:12
Alignment explanation
Indices: 1363272--1363318 Score: 76
Period size: 12 Copynumber: 3.9 Consensus size: 12
1363262 TTCTACCTTT
**
1363272 TCTTCTTCCTTA
1 TCTTCTTCCTCC
1363284 TCTTCTTCCTCC
1 TCTTCTTCCTCC
1363296 TCTTCTTCCTCC
1 TCTTCTTCCTCC
1363308 TCTTCTTCCTC
1 TCTTCTTCCTC
1363319 TTCCCCATTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.02, C:0.45, G:0.00, T:0.53
Consensus pattern (12 bp):
TCTTCTTCCTCC
Found at i:1363302 original size:15 final size:15
Alignment explanation
Indices: 1363271--1363322 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
1363261 CTTCTACCTT
*
1363271 TTCTTCTTCCT-TATC
1 TTCTTCCTCCTCT-TC
1363286 TTCTTCCTCCTCTTC
1 TTCTTCCTCCTCTTC
* *
1363301 TTCCTCCTCTTCTTC
1 TTCTTCCTCCTCTTC
*
1363316 CTCTTCC
1 TTCTTCC
1363323 CCATTGCCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
15 30 0.97
16 1 0.03
ACGTcount: A:0.02, C:0.44, G:0.00, T:0.54
Consensus pattern (15 bp):
TTCTTCCTCCTCTTC
Found at i:1365444 original size:20 final size:20
Alignment explanation
Indices: 1365419--1365468 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
1365409 GCACTTTACC
*
1365419 GGTTTTTTCATATTGAAACT
1 GGTTTTGTCATATTGAAACT
1365439 GGTTTTGTCATATTGAAACT
1 GGTTTTGTCATATTGAAACT
1365459 GGTTTTGTCA
1 GGTTTTGTCA
1365469 AATTTCAACA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.22, C:0.10, G:0.20, T:0.48
Consensus pattern (20 bp):
GGTTTTGTCATATTGAAACT
Found at i:1365879 original size:20 final size:21
Alignment explanation
Indices: 1365856--1365908 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
1365846 ATTGAAATCG
1365856 GTTTTGTCAAATTT-CAACCA
1 GTTTTGTCAAATTTCCAACCA
* *
1365876 GTTTTGTC-AATTTCCAATCG
1 GTTTTGTCAAATTTCCAACCA
1365896 GTTTTGTCAAATT
1 GTTTTGTCAAATT
1365909 CGTTACATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 5 0.17
20 20 0.69
21 4 0.14
ACGTcount: A:0.25, C:0.17, G:0.13, T:0.45
Consensus pattern (21 bp):
GTTTTGTCAAATTTCCAACCA
Found at i:1378713 original size:45 final size:45
Alignment explanation
Indices: 1378662--1378753 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
1378652 AAGTGATAAA
1378662 TTTAAAAAATTATAAAAATACCAAAAACTCTGAAAGGTACAAAAT
1 TTTAAAAAATTATAAAAATACCAAAAACTCTGAAAGGTACAAAAT
1378707 TTTAAAAAATTATAAAAATACCAAAAACTCTGAAAGGTACAAAAT
1 TTTAAAAAATTATAAAAATACCAAAAACTCTGAAAGGTACAAAAT
1378752 TT
1 TT
1378754 ATTTTTTAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.57, C:0.11, G:0.07, T:0.26
Consensus pattern (45 bp):
TTTAAAAAATTATAAAAATACCAAAAACTCTGAAAGGTACAAAAT
Found at i:1379210 original size:2 final size:2
Alignment explanation
Indices: 1379203--1379252 Score: 91
Period size: 2 Copynumber: 24.5 Consensus size: 2
1379193 AAATATTTAT
1379203 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
1379245 TA TGA TA T
1 TA T-A TA T
1379253 TTTATGATAG
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 45 0.96
3 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1380436 original size:12 final size:12
Alignment explanation
Indices: 1380419--1380443 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1380409 TTCTTTCTTC
1380419 GGAGCTAGAGCT
1 GGAGCTAGAGCT
1380431 GGAGCTAGAGCT
1 GGAGCTAGAGCT
1380443 G
1 G
1380444 CCCCATCCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.44, T:0.16
Consensus pattern (12 bp):
GGAGCTAGAGCT
Found at i:1392814 original size:18 final size:18
Alignment explanation
Indices: 1392770--1392814 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
1392760 CGCGTAGGAC
1392770 AAAGGACCACTATGTCCG
1 AAAGGACCACTATGTCCG
*
1392788 -AAGGACCACTATGTTTCG
1 AAAGGACCACTATG-TCCG
1392806 AAAGG-CCAC
1 AAAGGACCAC
1392815 ATATCACACA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 13 0.54
18 7 0.29
19 4 0.17
ACGTcount: A:0.33, C:0.27, G:0.22, T:0.18
Consensus pattern (18 bp):
AAAGGACCACTATGTCCG
Found at i:1396951 original size:19 final size:19
Alignment explanation
Indices: 1396927--1396966 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1396917 TCATGCCTTA
1396927 TATTCATCACATATTCACG
1 TATTCATCACATATTCACG
1396946 TATTCATCACATATTCACG
1 TATTCATCACATATTCACG
1396965 TA
1 TA
1396967 GTCACATAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.38
Consensus pattern (19 bp):
TATTCATCACATATTCACG
Found at i:1404330 original size:66 final size:66
Alignment explanation
Indices: 1404205--1404330 Score: 162
Period size: 66 Copynumber: 1.9 Consensus size: 66
1404195 GTCTATAAGG
* * * * * * *
1404205 AATTACCAGTCGGTGCTGAACATATCCAAGGAATTACCAACCGTGACTGAACTTGCCAGATATGG
1 AATTACCAATCGGTGCTGAACATATACAAGGAATTACCAACAGCGACTAAACCTACCAGATATGG
1404270 A
66 A
* * *
1404271 AATTACCAATCGGTGTTGAACCTATACAAGGAATTACCAGCAGCGACTAAACCTACCAGA
1 AATTACCAATCGGTGCTGAACATATACAAGGAATTACCAACAGCGACTAAACCTACCAGA
1404331 GTCTTTATAC
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
66 50 1.00
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (66 bp):
AATTACCAATCGGTGCTGAACATATACAAGGAATTACCAACAGCGACTAAACCTACCAGATATGG
A
Found at i:1411505 original size:46 final size:46
Alignment explanation
Indices: 1411422--1411528 Score: 137
Period size: 46 Copynumber: 2.3 Consensus size: 46
1411412 GTTGAGTAAT
1411422 TTTAGTTTTCGAATAAATGCATGAGAACTAGAAAGCATGCA-GTTAGGA
1 TTTA-TTTTCGAATAAATG-ATGAGAACTAGAAAGCATG-AGGTTAGGA
* *
1411470 TTTACTTTTCGAATAAATG-TGTGAACTAGAAAGCATGAGGTTAGGG
1 TTTA-TTTTCGAATAAATGATGAGAACTAGAAAGCATGAGGTTAGGA
1411516 TTTATTTTACGAA
1 TTTATTTT-CGAA
1411529 CAAAGCATGA
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
45 5 0.09
46 31 0.57
48 18 0.33
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.34
Consensus pattern (46 bp):
TTTATTTTCGAATAAATGATGAGAACTAGAAAGCATGAGGTTAGGA
Found at i:1422778 original size:19 final size:19
Alignment explanation
Indices: 1422740--1422778 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1422730 ACAAACAAAA
* *
1422740 TAAATAAAAAGTTCATAAT
1 TAAATAAAAACTTCACAAT
*
1422759 TAAATAAAAACTTTACAAT
1 TAAATAAAAACTTCACAAT
1422778 T
1 T
1422779 GCTGGTAAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.56, C:0.08, G:0.03, T:0.33
Consensus pattern (19 bp):
TAAATAAAAACTTCACAAT
Found at i:1425030 original size:29 final size:29
Alignment explanation
Indices: 1424955--1425030 Score: 66
Period size: 29 Copynumber: 2.5 Consensus size: 29
1424945 CTACAAAAAG
1424955 TAATAAAAATATTAGTATAATAAAATTTAATA
1 TAATAAAAATATT--T-TAATAAAATTTAATA
* * *
1424987 AAATAATACAT-TTTTAA-ATAATTATAATA
1 TAATAA-AAATATTTTAATAAAATT-TAATA
1425016 TAATAAAAATATTTT
1 TAATAAAAATATTTT
1425031 GCCTTATTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
28 8 0.22
29 17 0.47
30 1 0.03
32 7 0.19
33 3 0.08
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (29 bp):
TAATAAAAATATTTTAATAAAATTTAATA
Found at i:1431766 original size:15 final size:15
Alignment explanation
Indices: 1431743--1431773 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1431733 TTAATTTTTT
*
1431743 AAAATATAAAATAAA
1 AAAAAATAAAATAAA
1431758 AAAAAATAAAATAAA
1 AAAAAATAAAATAAA
1431773 A
1 A
1431774 TTTTAATTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (15 bp):
AAAAAATAAAATAAA
Found at i:1433316 original size:17 final size:17
Alignment explanation
Indices: 1433276--1433317 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1433266 AAAAACAACA
1433276 TAAAAAT-ATTTAATAT
1 TAAAAATAATTTAATAT
** *
1433292 TATTAATAATTTAATTT
1 TAAAAATAATTTAATAT
1433309 TAAAAATAA
1 TAAAAATAA
1433318 AAAATTTAAT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAAAATAATTTAATAT
Found at i:1433374 original size:26 final size:26
Alignment explanation
Indices: 1433338--1433388 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
1433328 ATTTAACTTT
1433338 GACTTTCTCATCAGCTTTCCAAATCA
1 GACTTTCTCATCAGCTTTCCAAATCA
1433364 GACTTTCTCATCAGCTTTCCAAATC
1 GACTTTCTCATCAGCTTTCCAAATC
1433389 GGGAATCAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.25, C:0.31, G:0.08, T:0.35
Consensus pattern (26 bp):
GACTTTCTCATCAGCTTTCCAAATCA
Found at i:1433376 original size:13 final size:12
Alignment explanation
Indices: 1433340--1433382 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 12
1433330 TTAACTTTGA
1433340 CTTTCTCATCAG
1 CTTTCTCATCAG
1433352 CTTTC-CAAATCAG
1 CTTTCTC--ATCAG
1433365 ACTTTCTCATCAG
1 -CTTTCTCATCAG
1433378 CTTTC
1 CTTTC
1433383 CAAATCGGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
11 1 0.04
12 10 0.37
13 10 0.37
14 5 0.19
15 1 0.04
ACGTcount: A:0.21, C:0.33, G:0.07, T:0.40
Consensus pattern (12 bp):
CTTTCTCATCAG
Found at i:1434433 original size:16 final size:16
Alignment explanation
Indices: 1434389--1434449 Score: 86
Period size: 16 Copynumber: 3.6 Consensus size: 16
1434379 TCACGGAATG
1434389 TAAGATTACCAGTGGGAA
1 TAAGATTACCA--GGGAA
1434407 TAAAGGATTACCAGGGAA
1 T-AA-GATTACCAGGGAA
1434425 TAAGATTACCAGGGAA
1 TAAGATTACCAGGGAA
1434441 TAAGATTAC
1 TAAGATTAC
1434450 TGGGAATGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
16 22 0.54
17 2 0.05
18 7 0.17
19 2 0.05
20 8 0.20
ACGTcount: A:0.43, C:0.11, G:0.25, T:0.21
Consensus pattern (16 bp):
TAAGATTACCAGGGAA
Found at i:1436610 original size:29 final size:29
Alignment explanation
Indices: 1436568--1436679 Score: 206
Period size: 29 Copynumber: 3.9 Consensus size: 29
1436558 TACCGGGGGT
*
1436568 AGGTCGCCATGCACGCCCGGAGACCAACC
1 AGGTCGCCATGCACGCCCGGCGACCAACC
1436597 AGGTCGCCATGCACGCCCGGCGACCAACC
1 AGGTCGCCATGCACGCCCGGCGACCAACC
1436626 AGGTCGCCATGCACGCCCGGCGACCAACC
1 AGGTCGCCATGCACGCCCGGCGACCAACC
*
1436655 AGGTCGCCATGCACGCCCTGCGACC
1 AGGTCGCCATGCACGCCCGGCGACC
1436680 TACCCCACGA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 81 1.00
ACGTcount: A:0.21, C:0.44, G:0.28, T:0.08
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGACCAACC
Found at i:1436722 original size:30 final size:30
Alignment explanation
Indices: 1436686--1436766 Score: 126
Period size: 30 Copynumber: 2.7 Consensus size: 30
1436676 GACCTACCCC
* *
1436686 ACGACCTCCATGCATGCCCAGGCACGTCCA
1 ACGACCTCCATGCACGCCCAGGCACGCCCA
* *
1436716 ACGACCTCCATGCACGGCCATGCACGCCCA
1 ACGACCTCCATGCACGCCCAGGCACGCCCA
1436746 ACGACCTCCATGCACGCCCAG
1 ACGACCTCCATGCACGCCCAG
1436767 CTCGCCAAAG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.23, C:0.46, G:0.20, T:0.11
Consensus pattern (30 bp):
ACGACCTCCATGCACGCCCAGGCACGCCCA
Found at i:1437427 original size:28 final size:29
Alignment explanation
Indices: 1437396--1437460 Score: 105
Period size: 28 Copynumber: 2.3 Consensus size: 29
1437386 GTTAGTATAA
*
1437396 ATATTAGTTTGTTAGTTTAAGT-TATATT
1 ATATTAATTTGTTAGTTTAAGTATATATT
1437424 ATATTAATTTGTTAGTTTAAGTATATATT
1 ATATTAATTTGTTAGTTTAAGTATATATT
*
1437453 AGATTAAT
1 ATATTAAT
1437461 AAAAATTAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
28 21 0.62
29 13 0.38
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.54
Consensus pattern (29 bp):
ATATTAATTTGTTAGTTTAAGTATATATT
Found at i:1437527 original size:41 final size:46
Alignment explanation
Indices: 1437426--1437527 Score: 115
Period size: 41 Copynumber: 2.3 Consensus size: 46
1437416 GTTATATTAT
*
1437426 ATTAATTTGTTAGTTTAAGTATATATTAGATTAATAAAAATTAGTTA
1 ATTAATTTGTTAGTTTAAG-ATATATTAGAATAATAAAAATTAGTTA
* * * *
1437473 ATTAGTTTCTTAGTTTAAG-T-TATTA-AAT-GTAAAAA-TATTTA
1 ATTAATTTGTTAGTTTAAGATATATTAGAATAATAAAAATTAGTTA
1437514 ATTAATTTGTTAGT
1 ATTAATTTGTTAGT
1437528 GTGTTTAAAC
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
41 17 0.35
42 6 0.12
43 2 0.04
44 5 0.10
45 1 0.02
47 17 0.35
ACGTcount: A:0.39, C:0.01, G:0.11, T:0.49
Consensus pattern (46 bp):
ATTAATTTGTTAGTTTAAGATATATTAGAATAATAAAAATTAGTTA
Found at i:1440220 original size:11 final size:11
Alignment explanation
Indices: 1440204--1440234 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
1440194 AATGATTTGA
1440204 TAGTAATGATT
1 TAGTAATGATT
1440215 TAGTAATGA-T
1 TAGTAATGATT
1440225 TAGTAATGAT
1 TAGTAATGAT
1440235 GAAATTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.39, C:0.00, G:0.19, T:0.42
Consensus pattern (11 bp):
TAGTAATGATT
Found at i:1440222 original size:60 final size:60
Alignment explanation
Indices: 1440151--1440286 Score: 247
Period size: 60 Copynumber: 2.3 Consensus size: 60
1440141 GTATTTATAA
*
1440151 GATTTAGTAATGATTAGTAATGATGAAATTATTATTAATT-TTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATGATGAAATTATTATTAATTATGT-ATGATTTGATAGTAAT
1440211 GATTTAGTAATGATTAGTAATGATGAAATTATTATTAATTATGTATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATGATGAAATTATTATTAATTATGTATGATTTGATAGTAAT
1440271 GATTTAGTAATGATTA
1 GATTTAGTAATGATTA
1440287 ATTTCTATGT
Statistics
Matches: 74, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
60 72 0.97
61 2 0.03
ACGTcount: A:0.38, C:0.00, G:0.16, T:0.46
Consensus pattern (60 bp):
GATTTAGTAATGATTAGTAATGATGAAATTATTATTAATTATGTATGATTTGATAGTAAT
Found at i:1441037 original size:12 final size:12
Alignment explanation
Indices: 1441012--1441064 Score: 63
Period size: 12 Copynumber: 4.3 Consensus size: 12
1441002 TTTTTCATTA
*
1441012 TAATATACT-AC
1 TAATAAACTAAC
*
1441023 TAATAAACTTAC
1 TAATAAACTAAC
1441035 TAACTAAAACTAAC
1 TAA-T-AAACTAAC
1441049 TAATAAACTAAC
1 TAATAAACTAAC
1441061 TAAT
1 TAAT
1441065 TTTTTATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
11 8 0.22
12 17 0.46
13 2 0.05
14 10 0.27
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (12 bp):
TAATAAACTAAC
Found at i:1441149 original size:37 final size:39
Alignment explanation
Indices: 1441099--1441219 Score: 122
Period size: 41 Copynumber: 3.0 Consensus size: 39
1441089 CAAATATAAC
*
1441099 TTAACTATTTAACTAAC-AAAAACTAATTAAATAATTTT
1 TTAACTATATAACTAACAAAAAACTAATTAAATAATTTT
* * *
1441137 TTTA-TATCTAACTATTAACAAAAAACTAATT-AATTATTTT
1 TTAACTATATAAC---TAACAAAAAACTAATTAAATAATTTT
*
1441177 TTAACTATATAACTATCAAACATATACTAATTAAATAATTTT
1 TTAACTATATAACTAACAAA-A-A-ACTAATTAAATAATTTT
1441219 T
1 T
1441220 AATTTATGTA
Statistics
Matches: 67, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
37 7 0.10
38 9 0.13
39 1 0.01
40 16 0.24
41 25 0.37
42 9 0.13
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (39 bp):
TTAACTATATAACTAACAAAAAACTAATTAAATAATTTT
Found at i:1441167 original size:41 final size:42
Alignment explanation
Indices: 1441112--1441219 Score: 125
Period size: 41 Copynumber: 2.6 Consensus size: 42
1441102 ACTATTTAAC
* *
1441112 TAAC-AAAAACTAATTAAATAATTTTTTTA-TATCTAACTAT
1 TAACAAAAAACTAATTAAATAATTTTTTAACTATATAACTAT
*
1441152 TAACAAAAAACTAATT-AATTATTTTTTAACTATATAACTAT
1 TAACAAAAAACTAATTAAATAATTTTTTAACTATATAACTAT
* * *
1441193 CAA-ACATATACTAATTAAATAATTTTT
1 TAACA-AAAAACTAATTAAATAATTTTT
1441220 AATTTATGTA
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
40 16 0.28
41 32 0.56
42 9 0.16
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (42 bp):
TAACAAAAAACTAATTAAATAATTTTTTAACTATATAACTAT
Found at i:1441247 original size:41 final size:40
Alignment explanation
Indices: 1441112--1441247 Score: 116
Period size: 41 Copynumber: 3.3 Consensus size: 40
1441102 ACTATTTAAC
* *
1441112 TAACAAAAACTAATTAAATAATTTTT--TTATATCTAACTA
1 TAACATAAACTAATTAAATAATTTTTAATT-TATATAACTA
* * * *
1441151 TTAACAAAAAACTAATTAATTATTTTTTAA-CTATATAACTA
1 -TAAC-ATAAACTAATTAAATAATTTTTAATTTATATAACTA
* *
1441192 TCAAACATATACTAATTAAATAATTTTTAATTTATGTATACTA
1 T--AACATAAACTAATTAAATAATTTTTAATTTATATA-ACTA
*
1441235 TAACTTAAACTAA
1 TAACATAAACTAA
1441248 CAATCATATA
Statistics
Matches: 77, Mismatches: 12, Indels: 13
0.75 0.12 0.13
Matches are distributed among these distances:
40 5 0.06
41 59 0.77
42 8 0.10
43 5 0.06
ACGTcount: A:0.48, C:0.10, G:0.01, T:0.41
Consensus pattern (40 bp):
TAACATAAACTAATTAAATAATTTTTAATTTATATAACTA
Found at i:1441312 original size:16 final size:18
Alignment explanation
Indices: 1441283--1441321 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
1441273 ACTAATTAAC
*
1441283 ATTTATAATAATAAACTA
1 ATTTATAATAATAAACAA
1441301 ATTTA-AAT-ATAAACAA
1 ATTTATAATAATAAACAA
1441317 ATTTA
1 ATTTA
1441322 CCTTATCTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 3 0.15
18 5 0.25
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTTATAATAATAAACAA
Found at i:1441647 original size:49 final size:49
Alignment explanation
Indices: 1441532--1441637 Score: 182
Period size: 49 Copynumber: 2.2 Consensus size: 49
1441522 TAGGATCACA
*
1441532 TGGCATGC-TGTAGGCATGCAGCGGGAGCAGGAGCACGTGAAGTTATCT
1 TGGCATGCATGCAGGCATGCAGCGGGAGCAGGAGCACGTGAAGTTATCT
1441580 TGGCATGCATGCAGGCATGCAGCGGGAGCAGGAGCACGTGAAGTTAT-T
1 TGGCATGCATGCAGGCATGCAGCGGGAGCAGGAGCACGTGAAGTTATCT
1441628 TGGC-TGCATG
1 TGGCATGCATG
1441638 TGCATGCATG
Statistics
Matches: 56, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
47 6 0.11
48 13 0.23
49 37 0.66
ACGTcount: A:0.23, C:0.19, G:0.38, T:0.21
Consensus pattern (49 bp):
TGGCATGCATGCAGGCATGCAGCGGGAGCAGGAGCACGTGAAGTTATCT
Found at i:1441705 original size:29 final size:29
Alignment explanation
Indices: 1441672--1441795 Score: 221
Period size: 29 Copynumber: 4.3 Consensus size: 29
1441662 TGGACGCCGG
1441672 GGCGACCTACAAGGTCGCCGGGACTACAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
1441701 GGCGACCTACAAGGTCGCCGGGACTACAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
1441730 GGCGACCTACAAGGTCGCCGGGACTACAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
** *
1441759 GGCGACCTACAAGGTCGCCCAGACTGCAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
1441788 GGCGACCT
1 GGCGACCT
1441796 CTCTATTGGC
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 92 1.00
ACGTcount: A:0.23, C:0.32, G:0.31, T:0.14
Consensus pattern (29 bp):
GGCGACCTACAAGGTCGCCGGGACTACAT
Found at i:1441824 original size:32 final size:32
Alignment explanation
Indices: 1441782--1441853 Score: 117
Period size: 32 Copynumber: 2.2 Consensus size: 32
1441772 GTCGCCCAGA
*
1441782 CTGCATGGCGACCTCTCTATTGGCTGGCTCGT
1 CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
* *
1441814 TTGCATGGCGACCTCTCCGTTGGCTGGCTCGT
1 CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
1441846 CTGCATGG
1 CTGCATGG
1441854 TGAGTATATG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.08, C:0.31, G:0.31, T:0.31
Consensus pattern (32 bp):
CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
Found at i:1441918 original size:24 final size:19
Alignment explanation
Indices: 1441868--1441905 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1441858 TATATGGCTT
1441868 GTATGGCTCGTCTGCATGG
1 GTATGGCTCGTCTGCATGG
1441887 GTATGGCTCGTCTGCATGG
1 GTATGGCTCGTCTGCATGG
1441906 TGAGTATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.11, C:0.21, G:0.37, T:0.32
Consensus pattern (19 bp):
GTATGGCTCGTCTGCATGG
Found at i:1444748 original size:28 final size:29
Alignment explanation
Indices: 1444681--1444782 Score: 125
Period size: 29 Copynumber: 3.6 Consensus size: 29
1444671 TTTAACATAA
* * **
1444681 TTACCAGAATAGCACAAAAACCAAATTAT
1 TTACTAGAATAGCACCAAAACTGAATTAT
* *
1444710 TTATTAAAATAGCACCAAAA-TGAATTAT
1 TTACTAGAATAGCACCAAAACTGAATTAT
*
1444738 TTACTAGAATAGCACTAAAACTGAATTAT
1 TTACTAGAATAGCACCAAAACTGAATTAT
*
1444767 TTACTAGAATATCACC
1 TTACTAGAATAGCACC
1444783 GGTCAACGGG
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
28 23 0.38
29 38 0.62
ACGTcount: A:0.47, C:0.17, G:0.08, T:0.28
Consensus pattern (29 bp):
TTACTAGAATAGCACCAAAACTGAATTAT
Found at i:1444801 original size:13 final size:13
Alignment explanation
Indices: 1444783--1444838 Score: 112
Period size: 13 Copynumber: 4.3 Consensus size: 13
1444773 GAATATCACC
1444783 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1444796 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1444809 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1444822 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1444835 GGTC
1 GGTC
1444839 GTGACCGGTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 43 1.00
ACGTcount: A:0.14, C:0.23, G:0.46, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1452177 original size:29 final size:29
Alignment explanation
Indices: 1452088--1452189 Score: 118
Period size: 29 Copynumber: 3.6 Consensus size: 29
1452078 TTTAAAATAA
* **
1452088 TTACCAGAATAGAACCAAAACCAAATTAT
1 TTACCAGAATAGCACCAAAACTGAATTAT
**
1452117 TTA-TTGAAATAGCACCAAAA-TGAATTAT
1 TTACCAG-AATAGCACCAAAACTGAATTAT
*
1452145 TTACCAGAATAGCACTAAAACTGAATTAT
1 TTACCAGAATAGCACCAAAACTGAATTAT
*
1452174 TTACTAGAATAGCACC
1 TTACCAGAATAGCACC
1452190 GATCAACGGG
Statistics
Matches: 60, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
28 22 0.37
29 38 0.63
ACGTcount: A:0.46, C:0.18, G:0.10, T:0.26
Consensus pattern (29 bp):
TTACCAGAATAGCACCAAAACTGAATTAT
Found at i:1452210 original size:13 final size:13
Alignment explanation
Indices: 1452192--1452219 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1452182 ATAGCACCGA
1452192 TCAACGGGTCGGG
1 TCAACGGGTCGGG
1452205 TCAACGGGTCGGG
1 TCAACGGGTCGGG
1452218 TC
1 TC
1452220 GGGTCAACCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.25, G:0.43, T:0.18
Consensus pattern (13 bp):
TCAACGGGTCGGG
Found at i:1452219 original size:18 final size:18
Alignment explanation
Indices: 1452196--1452238 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
1452186 CACCGATCAA
* *
1452196 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACCGAT
1452214 CGGGTCGGGTCAACCGAT
1 CGGGTCGGGTCAACCGAT
1452232 CGGGTCG
1 CGGGTCG
1452239 TGACCGGTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.12, C:0.26, G:0.47, T:0.16
Consensus pattern (18 bp):
CGGGTCGGGTCAACCGAT
Found at i:1453610 original size:14 final size:15
Alignment explanation
Indices: 1453573--1453610 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1453563 ATGGAGTCTC
*
1453573 TAATTATTAACCTAAT
1 TAATT-TTAACCAAAT
1453589 TAATTTTAACCAAAT
1 TAATTTTAACCAAAT
1453604 T-ATTTTA
1 TAATTTTA
1453611 TTCGAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.29
15 10 0.48
16 5 0.24
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (15 bp):
TAATTTTAACCAAAT
Found at i:1453787 original size:139 final size:139
Alignment explanation
Indices: 1453462--1453874 Score: 509
Period size: 139 Copynumber: 3.0 Consensus size: 139
1453452 ATTTTTAATG
* * * *
1453462 AATTATTGAATT-GAATAA-TAAAAT-GAACCTCGAGCATAAGCGAGGACCAAATCAAAAATTCT
1 AATTATTTAATTCGAATAATTAAAATGGAACCTCGAGCAAAAGTGAGGACCAAATTAAAAATT-T
* * *
1453524 -CCTAAATTTAAAAGACT-AGTTATGAAATTAA-ACCTAAAAATGGAGTCTCTAATTATTAACCT
65 ACCTAAATTT-AAGGATTAAGTT-TGAAATTAATA--T-AAAATGGAGGCTCTAATTATTAACCT
1453586 AATT-AATTTTAACCA
125 -ATTCAATTTTAACCA
* *
1453601 AATTATTTTATTCGAATAATTAAAATGGAACCTCGAGAAAAAGTGAGGACCAAATTAAAAATTTA
1 AATTATTTAATTCGAATAATTAAAATGGAACCTCGAGCAAAAGTGAGGACCAAATTAAAAATTTA
* *
1453666 ACTAAATTTAAGGATTAAGTTTGAAATTAATTATAAAATGAAGGCTCTAATTATTAACCTATTCA
66 CCTAAATTTAAGGATTAAGTTTGAAATTAA-TATAAAATGGAGGCTCTAATTATTAACCTATTCA
1453731 ATTTTAACC-
130 ATTTTAACCA
* * * * * *
1453740 AATTATTTAATTCAAATAATTAAAATGGAACATCAAGCAAAAGTGAGGATCAAATTAAATATTCA
1 AATTATTTAATTCGAATAATTAAAATGGAACCTCGAGCAAAAGTGAGGACCAAATTAAAAATTTA
* * *
1453805 CCTAAATTTAAGGATTAAGTTTGAAATTAATACTAAAATGGAGGCTCTAATTACTGACCTAGTCA
66 CCTAAATTTAAGGATTAAGTTTGAAATTAATA-TAAAATGGAGGCTCTAATTATTAACCTATTCA
1453870 ATTTT
130 ATTTT
1453875 GATCAAGTTT
Statistics
Matches: 241, Mismatches: 24, Indels: 18
0.85 0.08 0.06
Matches are distributed among these distances:
138 2 0.01
139 132 0.55
140 40 0.17
141 22 0.09
142 44 0.18
143 1 0.00
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.32
Consensus pattern (139 bp):
AATTATTTAATTCGAATAATTAAAATGGAACCTCGAGCAAAAGTGAGGACCAAATTAAAAATTTA
CCTAAATTTAAGGATTAAGTTTGAAATTAATATAAAATGGAGGCTCTAATTATTAACCTATTCAA
TTTTAACCA
Found at i:1454119 original size:26 final size:27
Alignment explanation
Indices: 1454072--1454128 Score: 62
Period size: 26 Copynumber: 2.1 Consensus size: 27
1454062 AAAAATGACT
* *
1454072 AAATTGAAACAATGAAAAAAAGAATTA
1 AAATTAAAACAATGAAAAAAAGAACTA
* * *
1454099 AAATTAAAAC-ATTAAATAAAGGACTA
1 AAATTAAAACAATGAAAAAAAGAACTA
1454125 AAAT
1 AAAT
1454129 GAAAGAAATC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 16 0.64
27 9 0.36
ACGTcount: A:0.65, C:0.05, G:0.09, T:0.21
Consensus pattern (27 bp):
AAATTAAAACAATGAAAAAAAGAACTA
Found at i:1454342 original size:113 final size:113
Alignment explanation
Indices: 1454134--1454342 Score: 328
Period size: 113 Copynumber: 1.8 Consensus size: 113
1454124 AAAATGAAAG
* * *
1454134 AAATCAGAATATAAAGATTAAATTAAAACAATTCAGAAAATTAAAAGCTAAAGTTTAAAGGACTG
1 AAATCAGAATATAAAGATTAAATTAAAACAATGCAGAAAATTAAAAGCTAAAATTTAAAGGACTA
** * *
1454199 AAATATAAATGCTGAAATTTAAAGATCAAAACTGTAAATAACAAAAAT
66 AAATATAAACACTGAAATTAAAAGAACAAAACTGTAAATAACAAAAAT
*
1454247 AAATCAGAATATAAAGATTAAATTAAAACAATGCAGAAAATTAAATGCTAAAATTTAAAGGACTA
1 AAATCAGAATATAAAGATTAAATTAAAACAATGCAGAAAATTAAAAGCTAAAATTTAAAGGACTA
* *
1454312 AAATATAGACACTGAAATTAAAATAACAAAA
66 AAATATAAACACTGAAATTAAAAGAACAAAA
1454343 ATTTAAAGGG
Statistics
Matches: 86, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
113 86 1.00
ACGTcount: A:0.58, C:0.08, G:0.10, T:0.24
Consensus pattern (113 bp):
AAATCAGAATATAAAGATTAAATTAAAACAATGCAGAAAATTAAAAGCTAAAATTTAAAGGACTA
AAATATAAACACTGAAATTAAAAGAACAAAACTGTAAATAACAAAAAT
Found at i:1454514 original size:22 final size:21
Alignment explanation
Indices: 1454489--1454529 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1454479 ATATTTTCTT
*
1454489 TTAGAAATTAGTAAGTTAGTGG
1 TTAGAAATTAG-AAATTAGTGG
*
1454511 TTAGAAGTTAGAAATTAGT
1 TTAGAAATTAGAAATTAGT
1454530 AAAATGTTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.37
Consensus pattern (21 bp):
TTAGAAATTAGAAATTAGTGG
Found at i:1454677 original size:28 final size:28
Alignment explanation
Indices: 1454625--1454691 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
1454615 AACTAGAGCA
*
1454625 ATAATAAATTAAAAACAATGACTAAAGT
1 ATAATAAAATAAAAACAATGACTAAAGT
* *
1454653 ATAATAAAATAAAACACAGTG-CTAAATT
1 ATAATAAAATAAAA-ACAATGACTAAAGT
1454681 A-AAGTAAAATA
1 ATAA-TAAAATA
1454692 GCATGAATGC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 2 0.06
28 27 0.79
29 5 0.15
ACGTcount: A:0.61, C:0.07, G:0.07, T:0.24
Consensus pattern (28 bp):
ATAATAAAATAAAAACAATGACTAAAGT
Found at i:1455572 original size:3 final size:3
Alignment explanation
Indices: 1455564--1455597 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1455554 TTTTTTAATA
1455564 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1455598 TTTTACATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1456580 original size:20 final size:21
Alignment explanation
Indices: 1456557--1456596 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1456547 ATATCATTGT
1456557 ATTTAATAGTA-ATTTTCAAC
1 ATTTAATAGTATATTTTCAAC
* *
1456577 ATTTACTCGTATATTTTCAA
1 ATTTAATAGTATATTTTCAA
1456597 GTTTCTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.35, C:0.12, G:0.05, T:0.47
Consensus pattern (21 bp):
ATTTAATAGTATATTTTCAAC
Found at i:1460789 original size:2 final size:2
Alignment explanation
Indices: 1460782--1460807 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1460772 ATCCTTTCAA
1460782 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
1460808 CCCTTGTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1461078 original size:21 final size:21
Alignment explanation
Indices: 1461068--1461109 Score: 75
Period size: 22 Copynumber: 2.0 Consensus size: 21
1461058 AAACACACAA
1461068 AAAGAAAGAAAAAAAAAAAAG
1 AAAGAAAGAAAAAAAAAAAAG
1461089 AAAGAAAGATAAAAAAAAAAA
1 AAAGAAAGA-AAAAAAAAAAA
1461110 AACGCGGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (21 bp):
AAAGAAAGAAAAAAAAAAAAG
Found at i:1461086 original size:17 final size:19
Alignment explanation
Indices: 1461066--1461106 Score: 68
Period size: 17 Copynumber: 2.3 Consensus size: 19
1461056 AAAAACACAC
1461066 AAAAAGAAAGAAA-A-AAA
1 AAAAAGAAAGAAAGATAAA
1461083 AAAAAGAAAGAAAGATAAA
1 AAAAAGAAAGAAAGATAAA
1461102 AAAAA
1 AAAAA
1461107 AAAAACGCGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 13 0.59
18 1 0.05
19 8 0.36
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.02
Consensus pattern (19 bp):
AAAAAGAAAGAAAGATAAA
Found at i:1461139 original size:52 final size:53
Alignment explanation
Indices: 1461074--1461200 Score: 136
Period size: 53 Copynumber: 2.4 Consensus size: 53
1461064 ACAAAAAGAA
**
1461074 AGAAAAAA-A-AAAAAGAAAGA-AAGATAAAAAAAAAAAAAC-GCGGAAAAAAG
1 AGAAAAAAGAGAAAAA-AAAGAGAAGATAAAAAAAAAAAAACAGAAGAAAAAAG
* * * *
1461124 AGAAAAAAGGGAAAAAAAATAGAAGATATAAAGAAAAAAACAGAAGAAAAAAG
1 AGAAAAAAGAGAAAAAAAAGAGAAGATAAAAAAAAAAAAACAGAAGAAAAAAG
* *
1461177 TGAAAGAAGAGAAAAAAAGAGAGA
1 AGAAAAAAGAGAAAAAAA-AGAGA
1461201 GAGAAAGAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
50 8 0.13
51 4 0.06
52 22 0.35
53 24 0.39
54 4 0.06
ACGTcount: A:0.74, C:0.02, G:0.20, T:0.04
Consensus pattern (53 bp):
AGAAAAAAGAGAAAAAAAAGAGAAGATAAAAAAAAAAAAACAGAAGAAAAAAG
Found at i:1461186 original size:16 final size:14
Alignment explanation
Indices: 1461154--1461222 Score: 50
Period size: 16 Copynumber: 4.5 Consensus size: 14
1461144 AGAAGATATA
*
1461154 AAGAAAAAA-ACAG
1 AAGAAAAAAGAAAG
1461167 AAGAAAAAAGTGAAAG
1 AAGAAAAAA--GAAAG
*
1461183 AAGAGAAAAAAAGAGAG
1 -A-AG-AAAAAAGAAAG
1461200 AGAGAAAGAAAGAAAG
1 A-AGAAA-AAAGAAAG
1461216 AAGAAAA
1 AAGAAAA
1461223 TAGACAGATC
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
13 9 0.20
14 1 0.02
15 8 0.17
16 15 0.33
17 5 0.11
18 2 0.04
19 6 0.13
ACGTcount: A:0.72, C:0.01, G:0.25, T:0.01
Consensus pattern (14 bp):
AAGAAAAAAGAAAG
Found at i:1461194 original size:33 final size:33
Alignment explanation
Indices: 1461157--1461219 Score: 76
Period size: 33 Copynumber: 1.9 Consensus size: 33
1461147 AGATATAAAG
1461157 AAAAAAACAGA-AGAAA-AAAGTGAAAGAAGAGAA
1 AAAAAAACAGAGAGAAAGAAA--GAAAGAAGAGAA
* *
1461190 AAAAAGAGAGAGAGAAAGAAAGAAAGAAGA
1 AAAAAAACAGAGAGAAAGAAAGAAAGAAGA
1461220 AAATAGACAG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
33 18 0.69
34 5 0.19
35 3 0.12
ACGTcount: A:0.71, C:0.02, G:0.25, T:0.02
Consensus pattern (33 bp):
AAAAAAACAGAGAGAAAGAAAGAAAGAAGAGAA
Found at i:1463948 original size:36 final size:36
Alignment explanation
Indices: 1463896--1464032 Score: 127
Period size: 36 Copynumber: 3.8 Consensus size: 36
1463886 TTTAAACTTC
*
1463896 GTCTCGCTTGAGACAGTTTCTCTTGAAACAAATTTT
1 GTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTT
* * * *
1463932 CTCTCTCTCGAGACAGTTTCCCTTGAAACAAGTTTT
1 GTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTT
* * *
1463968 GTTTCCCTTGAGACA-TTTTTCTT-AAA-AACATTTTT
1 GTCTCTCTTGAGACAGTTTCTCTTGAAACAA-A-TTTT
* * * *
1464003 GTCTTTCTTTAGATAGTTTCTCTTGGAACA
1 GTCTCTCTTGAGACAGTTTCTCTTGAAACA
1464033 CAAAATCTTT
Statistics
Matches: 77, Mismatches: 19, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
33 2 0.03
34 3 0.04
35 20 0.26
36 49 0.64
37 2 0.03
38 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.14, T:0.42
Consensus pattern (36 bp):
GTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTT
Found at i:1464174 original size:138 final size:138
Alignment explanation
Indices: 1463911--1464174 Score: 304
Period size: 138 Copynumber: 1.9 Consensus size: 138
1463901 GCTTGAGACA
* * * *
1463911 GTTTCTCTTGAAACAAATTTTCTCTCTCTCGAGACAGTTTCCCTTGAAACAAGTTTTGTTTCCCT
1 GTTTCTCTTGAAACAAATTTTCTCTCCCTCGAGACAATTTCCCTTGAAAAAAGTTTTGTCTCCCT
** * ** * *
1463976 TGAGACATTTTTCTTAAAAACATTTTTGTCTTTCTTTAGATAGTTTCTCTTGGAACACAAAATCT
66 TGAGACATTTCCCTTAAAAACATTTTTATCTCACTTGAGATAGTTTCTCTTGCAACACAAAATCT
1464041 TTGAATAT
131 TTGAATAT
* * *
1464049 GTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAATTT-CTTTGGAAATAAAGTTTTGTCT-C
1 GTTTCTCTTGAAACAAATTTTCTCTCCCTCGAGACAATTTCCCTT-GAAA-AAAGTTTTGTCTCC
* *
1464112 TTTAGAGACAGTTTCCCTT-GAAACATGTTTTATCTCACTTGAGATAGTTTCTCTT-CAA-ACAA
64 CTT-GAGACA-TTTCCCTTAAAAACAT-TTTTATCTCACTTGAGATAGTTTCTCTTGCAACACAA
1464174 A
126 A
1464175 TTTCTTTTGA
Statistics
Matches: 105, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
137 3 0.03
138 48 0.46
139 24 0.23
140 30 0.29
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (138 bp):
GTTTCTCTTGAAACAAATTTTCTCTCCCTCGAGACAATTTCCCTTGAAAAAAGTTTTGTCTCCCT
TGAGACATTTCCCTTAAAAACATTTTTATCTCACTTGAGATAGTTTCTCTTGCAACACAAAATCT
TTGAATAT
Found at i:1464930 original size:139 final size:140
Alignment explanation
Indices: 1464459--1465301 Score: 854
Period size: 139 Copynumber: 6.2 Consensus size: 140
1464449 ATTTCCAGTA
* ** *
1464459 GAGAGTTCATAATGAGAAAAACTCATCCGA-TGAGGGAGAAGAAGTTCATAATGAGAAGAACTTG
1 GAGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAAGTTCATAATGAGAAGAGCTTG
* * * *
1464523 TTTAACCTTAGCTCGATTCATCACATATGGAGTTGAATTATCAACACCTCACTTGAGGGATCAAC
66 TTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAATACCTCACTTGAGGGATCAAC
*
1464588 ATTTCTAATG
131 ATTTCAAATG
* *
1464598 GAAAGTTCATAATGAGAATAACTCATCCGACAAAGGGAGAAGAAGTTCATAATGAGAAGAGCTTG
1 GAGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAAGTTCATAATGAGAAGAGCTTG
* * * ** * *
1464663 TTCGACCTATCA-CTTGATTCAT-A-ATAT---TTTGAATCAGTGATGCCTCGCTTGAGGGATCA
66 TTCAACCT-T-AGCTCGATTCATCACATATGGAGTTGAATCAGCAATACCTCACTTGAGGGATCA
*
1464722 ACA-TTAAAATG
129 ACATTTCAAATG
*
1464733 GAGAGTTCATAATGAAAAGAACTCATCCGACAAAGGGAGAAGAAGTTCATAATGAGAAGAGCTTG
1 GAGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAAGTTCATAATGAGAAGAGCTTG
* ** * * *
1464798 TTCAACCTTTGCTTAATTAATCAGATATGGAGTTGAATCAGCAATACCTCACTCGAGGGATCAAC
66 TTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAATACCTCACTTGAGGGATCAAC
* *
1464863 ATTTCTAGTG
131 ATTTCAAATG
* * *
1464873 GAGAGTTCATAATGAGAAGAACTCATCCGA-AGAGGGAGAAGAAGTTCATAATGAGAAGAACATG
1 GAGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAAGTTCATAATGAGAAGAGCTTG
* * * * * * *
1464937 TTCAACCTTAGCTCGATTCATCACATTTGGAGTTGAATCAACCACACCTTACTCGAGGGATCAAT
66 TTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAATACCTCACTTGAGGGATCAAC
* *
1465002 ATTTCCAGTG
131 ATTTCAAATG
* * * *
1465012 GAGAGTTCATAATGAGAAAAACTCATCCGATAAAGGGAGAAGTAGTTCATAATGAGAAGAGCTTA
1 GAGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAAGTTCATAATGAGAAGAGCTTG
* * * * * * * *
1465077 ATCAACCTATTGCTCGATTCATGACAT-T----TTGAATCAGCGATGCCTCGCTTGAGGGGTTAA
66 TTCAACCT-TAGCTCGATTCATCACATATGGAGTTGAATCAGCAATACCTCACTTGAGGGATCAA
* *
1465137 CACTTCAAATA
130 CATTTCAAATG
* * *
1465148 GAGAGTTCATAATGAGAAGAAATCATCCGAC-GA-GG-G-AGAAGTTCATAATGAGAAGAGGTTG
1 GAGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAAGTTCATAATGAGAAGAGCTTG
* * * * **
1465209 TTCGACCTATCA-CTCGATTCAT-A-ATACT----TCGAATCATCAACACCTCACTCAAGGGATC
66 TTCAACCT-T-AGCTCGATTCATCACATA-TGGAGTTGAATCAGCAATACCTCACTTGAGGGATC
* * *
1465267 AACATGTCCAAGG
128 AACATTTCAAATG
1465280 GAGAAGTTCATAATGAGAAGAA
1 GAG-AGTTCATAATGAGAAGAA
1465302 GTTGTTCAAC
Statistics
Matches: 590, Mismatches: 98, Indels: 38
0.81 0.13 0.05
Matches are distributed among these distances:
130 2 0.00
131 1 0.00
132 72 0.12
133 19 0.03
134 11 0.02
135 77 0.13
136 88 0.15
139 184 0.31
140 109 0.18
141 26 0.04
142 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (140 bp):
GAGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAAGTTCATAATGAGAAGAGCTTG
TTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAATACCTCACTTGAGGGATCAAC
ATTTCAAATG
Found at i:1465368 original size:41 final size:42
Alignment explanation
Indices: 1465323--1465426 Score: 131
Period size: 41 Copynumber: 2.5 Consensus size: 42
1465313 TTAGTGTGTT
*
1465323 TCCATCACATAAGGAGTTGGAACAACACCAAC-TTTTGCTCA-
1 TCCATCACATAAGGAGTTGGAACAACACCAACATTTCGCT-AG
* *** *
1465364 TCCATCACATAAGGAGTTGGATCAATGTCATCATTTCGCTAG
1 TCCATCACATAAGGAGTTGGAACAACACCAACATTTCGCTAG
1465406 TCCATCACATAAGGAGTTGGA
1 TCCATCACATAAGGAGTTGGA
1465427 TCAGCATCAC
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
41 28 0.51
42 27 0.49
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (42 bp):
TCCATCACATAAGGAGTTGGAACAACACCAACATTTCGCTAG
Found at i:1465423 original size:42 final size:41
Alignment explanation
Indices: 1465323--1465429 Score: 135
Period size: 42 Copynumber: 2.6 Consensus size: 41
1465313 TTAGTGTGTT
* *
1465323 TCCATCACATAAGGAGTTGGAACAACACCAACTTTTGCTCA
1 TCCATCACATAAGGAGTTGGATCAACACCAACTTTCGCTCA
*** *
1465364 TCCATCACATAAGGAGTTGGATCAATGTCATCATTTCGCT-A
1 TCCATCACATAAGGAGTTGGATCAACACCAAC-TTTCGCTCA
1465405 GTCCATCACATAAGGAGTTGGATCA
1 -TCCATCACATAAGGAGTTGGATCA
1465430 GCATCACCTT
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
41 28 0.48
42 30 0.52
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (41 bp):
TCCATCACATAAGGAGTTGGATCAACACCAACTTTCGCTCA
Found at i:1465443 original size:16 final size:16
Alignment explanation
Indices: 1465422--1465452 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1465412 ACATAAGGAG
*
1465422 TTGGATCAGCATCACC
1 TTGGATCAACATCACC
1465438 TTGGATCAACATCAC
1 TTGGATCAACATCAC
1465453 TATATCTGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (16 bp):
TTGGATCAACATCACC
Found at i:1465713 original size:17 final size:17
Alignment explanation
Indices: 1465691--1465737 Score: 85
Period size: 17 Copynumber: 2.8 Consensus size: 17
1465681 AAACATTATC
1465691 ATTTTAAATAAAAATTA
1 ATTTTAAATAAAAATTA
1465708 ATTTTAAATAAAAATTA
1 ATTTTAAATAAAAATTA
*
1465725 ATTTTAATTAAAA
1 ATTTTAAATAAAA
1465738 CAACAAATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATTTTAAATAAAAATTA
Found at i:1468989 original size:214 final size:214
Alignment explanation
Indices: 1468619--1469791 Score: 1581
Period size: 214 Copynumber: 5.5 Consensus size: 214
1468609 ATATCCTGCT
* * * * * * *
1468619 CGAAGGTCTTATGGATGATCCGAAGGATTTATTC-TCTTGCTCGAGAGACTCACAAATGACTCGA
1 CGAAGGTCTTATGGATGACCCGAAGGACTTA-TCATCTTGCTCTAAAGACTTACAGATGACCCGA
* * * **
1468683 ATGATTTAAGCATCGTGCTTGAAAGACTTACTGATGGCTTGAAGGACTTATAAATTGTGAAATTT
65 AGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAAATTT
* * * * * *
1468748 TGAAAATTGCATTCTTAGTTTTCAAAAATTTCATCTTTTTAAAATATCATTTTTCATTTTCAAAT
130 TGAAAATCGAATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTCATTTTCAAAT
*
1468813 TCATGTGAAAAAATCCTACC
195 TCATGTGAAAACATCCTACC
* * * * * * * *
1468833 GGAAGGTCTTATAGATGATCCGAAGGATTTATTC-TCTTGCTCGAGAGACTCACAAATGACCCGA
1 CGAAGGTCTTATGGATGACCCGAAGGACTTA-TCATCTTGCTCTAAAGACTTACAGATGACCCGA
* *
1468897 AGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCTCGAAGGACTTATAAATTGTGAAAATT
65 AGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAAATTT
* *
1468962 TGAAAATCGAATTCTTAGTTTTCAAAAATTTCATCTTCTTAAAACATCATTTTTCATTTTCAAAT
130 TGAAAATCGAATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTCATTTTCAAAT
1469027 TCATGTGAAAACATCCTACC
195 TCATGTGAAAACATCCTACC
* * * *
1469047 CGAAGGTCTTATGGATGACCCGAAGGACTTGTCATCTTGCT-TAAAAGGCTTATATATGACCCGA
1 CGAAGGTCTTATGGATGACCCGAAGGACTTATCATCTTGCTCT-AAAGACTTACAGATGACCCGA
* * * *
1469111 AGGATTTAAACATCCTGCTCGAAAGACTTACTGATGACCCAAAGGACTTATAAATTGTGAAATTT
65 AGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAAATTT
* *
1469176 TGAAAATTGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTTTCATTTTCAA
130 TGAAAATCGAATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCA--TTTTTCATTTTCAA
*
1469241 ATTCATGTGAAAGCATCCTACC
193 ATTCATGTGAAAACATCCTACC
* * * *
1469263 CGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTATAGATAACCCGAA
1 CGAAGGTCTTATGGATGACCCGAAGGACTTATCATCTTGCTCTAAAGACTTACAGATGACCCGAA
*
1469328 GGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTATGAAATTTT
66 GGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAAATTTT
* * * *
1469393 GAAAATTC-TATTTTTCGTTTTAAAAAATTCCATCTTCTTAAAACATCAATTTTCATTTTCAAAT
131 GAAAA-TCGAATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTCATTTTCAAAT
1469457 TCATGTGAAAACATCCTACC
195 TCATGTGAAAACATCCTACC
* * * * * * *
1469477 CGAAGGTTTTACGGATGGCTCAAAGGACTTATCATCTTGCTCTAAAGGCTTATAGATGACCCGAA
1 CGAAGGTCTTATGGATGACCCGAAGGACTTATCATCTTGCTCTAAAGACTTACAGATGACCCGAA
*
1469542 GGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAAGACTTATAAATTAG-GAAATTT
66 GGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATT-GTGAAATTT
* * *
1469606 TGAAAAT-TACATTTTTCGTTTTAAAAAATTCCATCTTCTTAAAACATCATTTTCTCATTCTTCA
130 TGAAAATCGA-ATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTT-TCATT-TTCA
1469670 AATTCATGTGAAAACATCCTACC
192 AATTCATGTGAAAACATCCTACC
* * * *
1469693 TGAAGGTCTTATGGATGGCTC-AAGGACTTATCATCTTGCT-TAAAGACTTACAGAT-AGCTCGA
1 CGAAGGTCTTATGGATGACCCGAAGGACTTATCATCTTGCTCTAAAGACTTACAGATGA-CCCGA
*
1469755 AGGATTTAAGCATCATGCTCGAAAGACTTATTGATGG
65 AGGATTTAAGCATCATGCTCGAAAGACTTACTGATGG
1469792 AACTTACCGA
Statistics
Matches: 881, Mismatches: 66, Indels: 24
0.91 0.07 0.02
Matches are distributed among these distances:
213 4 0.00
214 610 0.69
215 24 0.03
216 241 0.27
217 2 0.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Consensus pattern (214 bp):
CGAAGGTCTTATGGATGACCCGAAGGACTTATCATCTTGCTCTAAAGACTTACAGATGACCCGAA
GGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAAATTTT
GAAAATCGAATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTCATTTTCAAATT
CATGTGAAAACATCCTACC
Found at i:1469368 original size:42 final size:41
Alignment explanation
Indices: 1469270--1469376 Score: 117
Period size: 42 Copynumber: 2.6 Consensus size: 41
1469260 ACCCGAAGGT
* * * * *
1469270 CTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGG
1 CTTATAGATGGCCCGAAGGACTTAGCATCATGCTCGAAAGA
** *
1469311 CTTATAGATAACCCGAAGGATTTAAGCATCATGCTCGAAAGA
1 CTTATAGATGGCCCGAAGGACTT-AGCATCATGCTCGAAAGA
1469353 CTTACT-GATGGCCCGAAGGACTTA
1 CTTA-TAGATGGCCCGAAGGACTTA
1469377 TAAATTATGA
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
41 20 0.38
42 32 0.60
43 1 0.02
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.26
Consensus pattern (41 bp):
CTTATAGATGGCCCGAAGGACTTAGCATCATGCTCGAAAGA
Found at i:1469421 original size:430 final size:428
Alignment explanation
Indices: 1468619--1469791 Score: 1651
Period size: 430 Copynumber: 2.7 Consensus size: 428
1468609 ATATCCTGCT
* * * * * * * *
1468619 CGAAGGTCTTATGGATGATCCGAAGGATTTATTC-TCTTGCTCGAGAGACTCACAAATGACTCGA
1 CGAAGGTCTTATGGATGACCCGAAGGACTTA-TCATCTTGCT-TAAAGGCTTATAAATGACCCGA
* * * ***
1468683 ATGATTTAAGCATCGTGCTTGAAAGACTTACTGATGGCTTGAAGGACTTATAAATTGTGAAATTT
64 AGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTATAAATTGTGAAATTT
* * * *
1468748 TGAAAATTGCATTCTTAGTTTTCAAAAATTTCATCTTTTTAAAATATCA-TTTTTCATTTTCAAA
129 TGAAAATTGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTTCATTTTCAAA
* * * ** * *
1468812 TTCATGTGAAAAAATCCTACCGGAAGGTCTTATAGATGATCCGAAGGATTTATTC-TCTTGCTCG
194 TTCATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTA-TCATCTTGCTCT
* * * * *
1468876 AGAGACTCACAAATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCTCGAAG
258 AAAGACTTACAGATAACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAG
* * *
1468941 GACTTATAAATTGTGAAAATTTGAAAATCGAATTCTTAGTTTTCAAAAATTTCATCTTCTTAAAA
323 GACTTATAAATTATGAAAATTTGAAAATCGAATTCTTAGTTTTAAAAAATTCCATCTTCTTAAAA
*
1469006 CATCATTTTTCATTTTCAAATTCATGTGAAAACATCCTACC
388 CATCAATTTTCATTTTCAAATTCATGTGAAAACATCCTACC
* *
1469047 CGAAGGTCTTATGGATGACCCGAAGGACTTGTCATCTTGCTTAAAAGGCTTATATATGACCCGAA
1 CGAAGGTCTTATGGATGACCCGAAGGACTTATCATCTTGCTT-AAAGGCTTATAAATGACCCGAA
* * *
1469112 GGATTTAAACATCCTGCTCGAAAGACTTACTGATGACCCAAAGGACTTATAAATTGTGAAATTTT
65 GGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTATAAATTGTGAAATTTT
1469177 GAAAATTGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTTTCATTTTCAAA
130 GAAAATTGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCA-TTTTTTCATTTTCAAA
*
1469242 TTCATGTGAAAGCATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTA
194 TTCATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTA
* *
1469307 AAGGCTTATAGATAACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
259 AAGACTTACAGATAACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
* * * *
1469372 ACTTATAAATTATGAAATTTTGAAAATTC-TATTTTTCGTTTTAAAAAATTCCATCTTCTTAAAA
324 ACTTATAAATTATGAAAATTTGAAAA-TCGAATTCTTAGTTTTAAAAAATTCCATCTTCTTAAAA
1469436 CATCAATTTTCATTTTCAAATTCATGTGAAAACATCCTACC
388 CATCAATTTTCATTTTCAAATTCATGTGAAAACATCCTACC
* * * * * *
1469477 CGAAGGTTTTACGGATGGCTCAAAGGACTTATCATCTTGCTCTAAAGGCTTATAGATGACCCGAA
1 CGAAGGTCTTATGGATGACCCGAAGGACTTATCATCTTGCT-TAAAGGCTTATAAATGACCCGAA
1469542 GGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAA-GACTTATAAATTAG-GAAATT
65 GGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCC-AAAGGACTTATAAATT-GTGAAATT
* * * *
1469605 TTGAAAATTACATTTTTCGTTTTAAAAAATTCCATCTTCTTAAAACATCATTTTCTCATTCTTCA
128 TTGAAAATTGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTTCATT-TTCA
* *
1469670 AATTCATGTGAAAACATCCTACCTGAAGGTCTTATGGATGGCTC-AAGGACTTATCATCTTGCT-
192 AATTCATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTC
* * *
1469733 TAAAGACTTACAGATAGCTCGAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGG
257 TAAAGACTTACAGATAACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGG
1469792 AACTTACCGA
Statistics
Matches: 668, Mismatches: 67, Indels: 20
0.88 0.09 0.03
Matches are distributed among these distances:
427 2 0.00
428 206 0.31
429 30 0.04
430 423 0.63
431 7 0.01
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Consensus pattern (428 bp):
CGAAGGTCTTATGGATGACCCGAAGGACTTATCATCTTGCTTAAAGGCTTATAAATGACCCGAAG
GATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTATAAATTGTGAAATTTTG
AAAATTGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTTTCATTTTCAAATT
CATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAA
GACTTACAGATAACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGAC
TTATAAATTATGAAAATTTGAAAATCGAATTCTTAGTTTTAAAAAATTCCATCTTCTTAAAACAT
CAATTTTCATTTTCAAATTCATGTGAAAACATCCTACC
Found at i:1470738 original size:125 final size:125
Alignment explanation
Indices: 1470567--1470888 Score: 421
Period size: 125 Copynumber: 2.6 Consensus size: 125
1470557 AGTTGTGAGA
* * ** * * *
1470567 CTCATTC-TCAATGACTTCTTGGTCTGAATCTTGTTTTCTCATCATGACGTGGGTTCAGTCGTGC
1 CTCATTCTTC-ATGCCTCCTTGGTCTGAATCTTGTCATCTAAACATGATGTGGGTTCAGTCGTGC
* * *
1470631 CCCAACCTTATCTTATACTGGTGCAAGCCTTCAAAATGCCCCATCACCTCAAATTGTAAGG
65 CCCAACATTATCTTATACTAGTACAAGCCTTCAAAATGCCCCATCACCTCAAATTGTAAGG
* * *
1470692 GTCATTCTTCATTCCTCCTTGGTCTGAATCTTGTCATCTTAACATGATGTGGGTTCAGTCGTGCC
1 CTCATTCTTCATGCCTCCTTGGTCTGAATCTTGTCATCTAAACATGATGTGGGTTCAGTCGTGCC
* ** * *
1470757 CCCACATTATCTTATACTAGTACGGGCCTTCCAAATGCCTCATCACCTCAAATTGTAAGG
66 CCAACATTATCTTATACTAGTACAAGCCTTCAAAATGCCCCATCACCTCAAATTGTAAGG
** * * *
1470817 CTCATTCTTCATGCCTCCTTGGTCTGAAAGTTTTCATCTAAACATAATGTGGGTTCAATCGTGCC
1 CTCATTCTTCATGCCTCCTTGGTCTGAATCTTGTCATCTAAACATGATGTGGGTTCAGTCGTGCC
1470882 CCAACAT
66 CCAACAT
1470889 ATCCTAACTT
Statistics
Matches: 170, Mismatches: 26, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
125 168 0.99
126 2 0.01
ACGTcount: A:0.22, C:0.27, G:0.16, T:0.34
Consensus pattern (125 bp):
CTCATTCTTCATGCCTCCTTGGTCTGAATCTTGTCATCTAAACATGATGTGGGTTCAGTCGTGCC
CCAACATTATCTTATACTAGTACAAGCCTTCAAAATGCCCCATCACCTCAAATTGTAAGG
Found at i:1480401 original size:13 final size:13
Alignment explanation
Indices: 1480383--1480407 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1480373 TTTTTTAATA
1480383 TATTATTATTATT
1 TATTATTATTATT
1480396 TATTATTATTAT
1 TATTATTATTAT
1480408 ACTAATAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TATTATTATTATT
Found at i:1492106 original size:20 final size:21
Alignment explanation
Indices: 1492083--1492122 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1492073 ACATCTTTGT
1492083 ATTTAATAGTA-ATTTTCAAC
1 ATTTAATAGTATATTTTCAAC
* *
1492103 ATTTACTTGTATATTTTCAA
1 ATTTAATAGTATATTTTCAA
1492123 GTTTCTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.35, C:0.10, G:0.05, T:0.50
Consensus pattern (21 bp):
ATTTAATAGTATATTTTCAAC
Found at i:1494370 original size:17 final size:18
Alignment explanation
Indices: 1494350--1494385 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1494340 ATAATATAAG
1494350 TTTATA-TATAAACTATA
1 TTTATATTATAAACTATA
1494367 TTTATATTATAAACTATA
1 TTTATATTATAAACTATA
1494385 T
1 T
1494386 AATTATTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTATATTATAAACTATA
Found at i:1494372 original size:15 final size:15
Alignment explanation
Indices: 1494354--1494471 Score: 68
Period size: 13 Copynumber: 7.9 Consensus size: 15
1494344 TATAAGTTTA
1494354 TATATAAACTATATTT
1 TATATAAACTATA-TT
1494370 ATATTATAAACTATATAAT
1 -TA-TATAAACTATAT--T
* *
1494389 TATTATAAGC--TATG
1 TA-TATAAACTATATT
* *
1494403 TATATAAATTATGTT
1 TATATAAACTATATT
*
1494418 TATATGAACTATA--
1 TATATAAACTATATT
1494431 TATATAAACTATA--
1 TATATAAACTATATT
* *
1494444 TATGTAAACTATATG
1 TATATAAACTATATT
*
1494459 TGTATAAACTATA
1 TATATAAACTATA
1494472 AAAAGTATAT
Statistics
Matches: 81, Mismatches: 13, Indels: 16
0.74 0.12 0.15
Matches are distributed among these distances:
13 29 0.36
14 2 0.02
15 23 0.28
16 3 0.04
17 3 0.04
18 20 0.25
19 1 0.01
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (15 bp):
TATATAAACTATATT
Found at i:1494392 original size:18 final size:17
Alignment explanation
Indices: 1494351--1494401 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
1494341 TAATATAAGT
*
1494351 TTATATATAAACTATATT
1 TTAT-TATAAACTATATA
1494369 TATATTATAAACTATATAA
1 T-TATTATAAACTATAT-A
*
1494388 TTATTATAAGCTAT
1 TTATTATAAACTAT
1494402 GTATATAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 25 0.86
19 4 0.14
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (17 bp):
TTATTATAAACTATATA
Found at i:1494897 original size:2 final size:2
Alignment explanation
Indices: 1494890--1495059 Score: 108
Period size: 2 Copynumber: 87.0 Consensus size: 2
1494880 TTTAATTTTC
1494890 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
* * * * * *
1494932 TA TG TA TA TA AA CTA TA TA TG TA TA AA CTA TA -A AA AA 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
* * * *
1494975 GTT TA TA AA T- TA TA -A TT TA TA T- TA -A TA TA GTA TA TA TA TG
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* *
1495015 TA TA TA -A CTA -A TA TA -A GTA -A TC TA TA GA T- 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
1495054 TA TA TA
1 TA TA TA
1495060 GTTTATAGAA
Statistics
Matches: 131, Mismatches: 21, Indels: 32
0.71 0.11 0.17
Matches are distributed among these distances:
1 10 0.08
2 114 0.87
3 7 0.05
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1494988 original size:25 final size:24
Alignment explanation
Indices: 1494893--1494989 Score: 77
Period size: 25 Copynumber: 3.9 Consensus size: 24
1494883 AATTTTCTAT
* * *
1494893 ATATATATATATATATATATATATAT
1 ATATATATATATAAAT-TATA-AAAA
* *
1494919 ATATATATATATATATGTATATAAA
1 ATATATATATATAAAT-TATAAAAA
* * *
1494944 CTATATATGTATAAACTATAAAAA
1 ATATATATATATAAATTATAAAAA
*
1494968 ATATATAGTTTATAAATTATAA
1 ATATATA-TATATAAATTATAA
1494990 TTTATATTAA
Statistics
Matches: 58, Mismatches: 12, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
24 13 0.22
25 25 0.43
26 20 0.34
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (24 bp):
ATATATATATATAAATTATAAAAA
Found at i:1495266 original size:49 final size:49
Alignment explanation
Indices: 1495158--1495252 Score: 147
Period size: 48 Copynumber: 2.0 Consensus size: 49
1495148 ATAGTACATT
* **
1495158 TATGTATAAACTATATAAAGTAAATTACTTATATAGTTTATAGAAACAC
1 TATGTATAAACTATATAAAGTAAATAAAGTATATAGTTTATAGAAACAC
*
1495207 TATGCATAAACTATATAAAGT-AATAAAGTATATAGTTTATAGAAAC
1 TATGTATAAACTATATAAAGTAAATAAAGTATATAGTTTATAGAAAC
1495253 CCTAAATTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
48 22 0.52
49 20 0.48
ACGTcount: A:0.48, C:0.07, G:0.09, T:0.35
Consensus pattern (49 bp):
TATGTATAAACTATATAAAGTAAATAAAGTATATAGTTTATAGAAACAC
Found at i:1495481 original size:35 final size:36
Alignment explanation
Indices: 1495413--1495486 Score: 105
Period size: 37 Copynumber: 2.1 Consensus size: 36
1495403 ACAATAGTTA
*
1495413 ATATATGTAACCTATAGTATATGTATACATATAAACT
1 ATATATGTAACCTATAGTACATGTATA-ATATAAACT
* *
1495450 ATATATGTAACTTATAGTACATGTAT-GTATAAACT
1 ATATATGTAACCTATAGTACATGTATAATATAAACT
1495485 AT
1 AT
1495487 GTATAGTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 10 0.29
37 24 0.71
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.39
Consensus pattern (36 bp):
ATATATGTAACCTATAGTACATGTATAATATAAACT
Found at i:1495580 original size:57 final size:55
Alignment explanation
Indices: 1495414--1495581 Score: 131
Period size: 57 Copynumber: 2.9 Consensus size: 55
1495404 CAATAGTTAA
* * * *
1495414 TATATGTAACCTATAGTATATGTATACATATAAACTATATATGTAACTTATAGTACATG
1 TATATATAAACTAT-GTATA-GTAT--ATATAAAATATATATGTAACATATAGTACATG
* * * ** *
1495473 TATGTATAAACTATGTATAGTATATATGAACTATATCTACATAACATATAGTATATG
1 TATATATAAACTATGTATAGTATATAT-AA-AATATATATGTAACATATAGTACATG
* * *
1495530 TATATATATAATCTATTTTTATGT-TATATAAAATATATATGTAACGTATAGT
1 TATATATA-AA-CTATGTATA-GTATATATAAAATATATATGTAACATATAGT
1495582 TTATAAACAA
Statistics
Matches: 86, Mismatches: 18, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
55 4 0.05
56 2 0.02
57 46 0.53
58 9 0.10
59 23 0.27
60 2 0.02
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.42
Consensus pattern (55 bp):
TATATATAAACTATGTATAGTATATATAAAATATATATGTAACATATAGTACATG
Found at i:1496234 original size:15 final size:15
Alignment explanation
Indices: 1496214--1496250 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
1496204 CCGAAATACA
1496214 GAAATCAGATATT-AG
1 GAAATCA-ATATTCAG
1496229 GAAATCAATATTCAG
1 GAAATCAATATTCAG
1496244 G-AATCAA
1 GAAATCAA
1496251 GTATCATGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.49, C:0.11, G:0.16, T:0.24
Consensus pattern (15 bp):
GAAATCAATATTCAG
Found at i:1496840 original size:22 final size:22
Alignment explanation
Indices: 1496815--1496863 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
1496805 AGTCAACGGG
*
1496815 TTTGGAGACTTTCGGGTTCGGA
1 TTTGGAGACTTTCGGGTTCGAA
1496837 TTTGGAGACTTTCGGGTTCGAA
1 TTTGGAGACTTTCGGGTTCGAA
1496859 TTTGG
1 TTTGG
1496864 TGAAACGGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.14, C:0.12, G:0.35, T:0.39
Consensus pattern (22 bp):
TTTGGAGACTTTCGGGTTCGAA
Found at i:1497060 original size:29 final size:28
Alignment explanation
Indices: 1497010--1497078 Score: 93
Period size: 29 Copynumber: 2.4 Consensus size: 28
1497000 TATTTTACAA
*
1497010 AAAATAGCACCCTTTTTAAATTAATTACT
1 AAAATAGCA-CCTTTTCAAATTAATTACT
*
1497039 AAAATAGCACCTATTTCGAATTAATTACT
1 AAAATAGCACCT-TTTCAAATTAATTACT
*
1497068 AAACTAGCACC
1 AAAATAGCACC
1497079 CGATCAACGA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 3 0.08
29 33 0.92
ACGTcount: A:0.42, C:0.20, G:0.06, T:0.32
Consensus pattern (28 bp):
AAAATAGCACCTTTTCAAATTAATTACT
Found at i:1503060 original size:15 final size:16
Alignment explanation
Indices: 1503040--1503076 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
1503030 CCGAAATACA
1503040 GAAATCAAATATT-AG
1 GAAATCAAATATTCAG
1503055 GAAATC-AATATTCAG
1 GAAATCAAATATTCAG
1503070 G-AATCAA
1 GAAATCAA
1503077 GTATCATGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.51, C:0.11, G:0.14, T:0.24
Consensus pattern (16 bp):
GAAATCAAATATTCAG
Found at i:1503852 original size:29 final size:30
Alignment explanation
Indices: 1503820--1503887 Score: 104
Period size: 29 Copynumber: 2.3 Consensus size: 30
1503810 CATTTTACAG
*
1503820 AAATAACACCCT-TTTTAAATTAATTACTA
1 AAATAGCACCCTATTTTAAATTAATTACTA
*
1503849 AAATAGCA-CCTATTTTGAATTAATTACTA
1 AAATAGCACCCTATTTTAAATTAATTACTA
1503878 AAATAGCACC
1 AAATAGCACC
1503888 TAGTCAACGG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
28 3 0.09
29 31 0.89
30 1 0.03
ACGTcount: A:0.44, C:0.18, G:0.04, T:0.34
Consensus pattern (30 bp):
AAATAGCACCCTATTTTAAATTAATTACTA
Found at i:1503888 original size:29 final size:29
Alignment explanation
Indices: 1503832--1503889 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
1503822 ATAACACCCT
1503832 TTTTAAATTAATTACTAAAATAGCACCTA
1 TTTTAAATTAATTACTAAAATAGCACCTA
*
1503861 TTTTGAATTAATTACTAAAATAGCACCTA
1 TTTTAAATTAATTACTAAAATAGCACCTA
1503890 GTCAACGGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.43, C:0.14, G:0.05, T:0.38
Consensus pattern (29 bp):
TTTTAAATTAATTACTAAAATAGCACCTA
Found at i:1503912 original size:17 final size:17
Alignment explanation
Indices: 1503890--1503926 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1503880 ATAGCACCTA
* *
1503890 GTCAACGGTCGGGTTGG
1 GTCAACAGTCGGGTCGG
1503907 GTCAACAGTCGGGTCGG
1 GTCAACAGTCGGGTCGG
1503924 GTC
1 GTC
1503927 GGTCAACGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.14, C:0.22, G:0.43, T:0.22
Consensus pattern (17 bp):
GTCAACAGTCGGGTCGG
Found at i:1503921 original size:22 final size:23
Alignment explanation
Indices: 1503896--1503950 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
1503886 CCTAGTCAAC
*
1503896 GGTCGGGTTGGGTCAAC-AGTCG
1 GGTCGGGTTGGGTCAACGAGTCA
* *
1503918 GGTCGGG-TCGGTCAACGGGTCA
1 GGTCGGGTTGGGTCAACGAGTCA
1503940 GGTCGGGTTGG
1 GGTCGGGTTGG
1503951 AACGGGTCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 8 0.30
22 17 0.63
23 2 0.07
ACGTcount: A:0.11, C:0.18, G:0.49, T:0.22
Consensus pattern (23 bp):
GGTCGGGTTGGGTCAACGAGTCA
Found at i:1504791 original size:20 final size:21
Alignment explanation
Indices: 1504751--1504792 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1504741 ATTTATAAGC
*
1504751 TATAGTTTATATTAATGTGCTA
1 TATAATTTATATTAA-GTGCTA
1504773 TATAATTTATATTAA-TGCTA
1 TATAATTTATATTAAGTGCTA
1504793 ATTATCTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
22 14 0.74
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.50
Consensus pattern (21 bp):
TATAATTTATATTAAGTGCTA
Found at i:1504860 original size:65 final size:63
Alignment explanation
Indices: 1504779--1505059 Score: 207
Period size: 65 Copynumber: 4.3 Consensus size: 63
1504769 GCTATATAAT
** *
1504779 TTATATTAATGCTAATTATCTTAACTATAATTTATACTAATATAATATATAGTTTATAAACTATA
1 TTATATTAATATTAATTAT-TTAACTATAATTTATA-TAATATAATATATAATTTATAAACTATA
* * * * *
1504844 CTATATTAATATTAATTAAATTAACTATAGTTTATA-AACTATACTATATAATTTATAAAATATA
1 TTATATTAATATTAATT-ATTTAACTATAATTTATATAA-TATAATATATAATTTATAAACTATA
* * *
1504908 GTTTATATTAATATTAATT-TTATAGACTATATTTTATATTAATATTAAT-TACAAATTATAAAC
1 --TTATATTAATATTAATTATT-TA-ACTATAATTTATA-TAATA-TAATATATAATTTATAAAC
*
1504971 TTTA
60 TATA
* **
1504975 TTATATTAATA-TAAGTTAATATTAA-TATTAA-TTATATTAATATTAAT-TATAATATATAATT
1 TTATATTAATATTAA-TT-AT-TTAACTA-TAATTTATA-TAATA-TAATATATAATTTATAAAC
1505036 TATA
60 TATA
* *
1505040 TTAATTTTAATTTTAATTAT
1 TT-ATATTAATATTAATTAT
1505060 AAATAGTTTA
Statistics
Matches: 175, Mismatches: 25, Indels: 32
0.75 0.11 0.14
Matches are distributed among these distances:
63 2 0.01
64 26 0.15
65 78 0.45
66 41 0.23
67 22 0.13
68 6 0.03
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.49
Consensus pattern (63 bp):
TTATATTAATATTAATTATTTAACTATAATTTATATAATATAATATATAATTTATAAACTATA
Found at i:1504914 original size:21 final size:21
Alignment explanation
Indices: 1504804--1504907 Score: 79
Period size: 21 Copynumber: 4.9 Consensus size: 21
1504794 TTATCTTAAC
* *
1504804 TATAATTTATACTAATATAATA
1 TATAATTTATA-AAATATACTA
* *
1504826 TATAGTTTATAAACTATACTA
1 TATAATTTATAAAATATACTA
*
1504847 TATTAATATTAATTAAAT-TA--A
1 TA-TAAT-TT-ATAAAATATACTA
* *
1504868 CTATAGTTTATAAACTATACTA
1 -TATAATTTATAAAATATACTA
1504890 TATAATTTATAAAATATA
1 TATAATTTATAAAATATA
1504908 GTTTATATTA
Statistics
Matches: 63, Mismatches: 12, Indels: 15
0.70 0.13 0.17
Matches are distributed among these distances:
19 5 0.08
20 4 0.06
21 29 0.46
22 16 0.25
23 4 0.06
24 5 0.08
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (21 bp):
TATAATTTATAAAATATACTA
Found at i:1504944 original size:31 final size:31
Alignment explanation
Indices: 1504845--1505054 Score: 110
Period size: 31 Copynumber: 6.6 Consensus size: 31
1504835 TAAACTATAC
** * *
1504845 TATATTAATATTAATTAAATTAACTATAGTT
1 TATATTAATATTAATTTTATAAAATATAGTT
*
1504876 TATAAACTATACTATATAA-TTTATAAAATATAGTT
1 TAT--A-T-TAATAT-TAATTTTATAAAATATAGTT
* * *
1504911 TATATTAATATTAATTTTATAGACTATATTT
1 TATATTAATATTAATTTTATAAAATATAGTT
* *
1504942 TATATTAATATTAATTACAAATTATAAACTTTA--T
1 TATATTAATATTAATT-----TTATAAAATATAGTT
* * * *
1504976 TATATTAATA-TAAGTTAATATTAATATTA-AT
1 TATATTAATATTAATTTTATA-AAATA-TAGTT
* *
1505007 TATATTAATATTAA--TTATAATATATAATT
1 TATATTAATATTAATTTTATAAAATATAGTT
*
1505036 TATATTAATTTTAATTTTA
1 TATATTAATATTAATTTTA
1505055 ATTATAAATA
Statistics
Matches: 140, Mismatches: 21, Indels: 36
0.71 0.11 0.18
Matches are distributed among these distances:
28 6 0.04
29 19 0.14
30 9 0.06
31 51 0.36
32 4 0.03
33 6 0.04
34 12 0.09
35 20 0.14
36 13 0.09
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (31 bp):
TATATTAATATTAATTTTATAAAATATAGTT
Found at i:1504998 original size:16 final size:14
Alignment explanation
Indices: 1504974--1505085 Score: 84
Period size: 15 Copynumber: 7.5 Consensus size: 14
1504964 TATAAACTTT
1504974 ATTATATTAATATA
1 ATTATATTAATATA
1504988 AGTTAATATTAATATTA
1 A-TT-ATATTAATA-TA
1505005 ATTATATTAATATTA
1 ATTATATTAATA-TA
*
1505020 ATTATAAT-ATATA
1 ATTATATTAATATA
*
1505033 ATTTATATTAATTTTA
1 A-TTATATTAA-TATA
* *
1505049 ATTTTAATTATAAATA
1 ATTAT-ATTA-ATATA
*
1505065 GTT-TATTAATATAA
1 ATTATATTAATAT-A
1505079 ATTATAT
1 ATTATAT
1505086 AGGGATGAAA
Statistics
Matches: 79, Mismatches: 9, Indels: 19
0.74 0.08 0.18
Matches are distributed among these distances:
13 6 0.08
14 17 0.22
15 29 0.37
16 23 0.29
17 4 0.05
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (14 bp):
ATTATATTAATATA
Found at i:1504999 original size:6 final size:6
Alignment explanation
Indices: 1504973--1505056 Score: 60
Period size: 6 Copynumber: 15.2 Consensus size: 6
1504963 TTATAAACTT
*
1504973 TATT-A TATTAA TA-TAA -GTTAA TATTAA TATT-A -ATT-A TATTAA
1 TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA
* *
1505015 TATTAA T-TATAA TATATAA T-TT-A TATTAA TTTTAA TTTTAA T
1 TATTAA TAT-TAA TAT-TAA TATTAA TATTAA TATTAA TATTAA T
1505057 TATAAATAGT
Statistics
Matches: 67, Mismatches: 3, Indels: 17
0.77 0.03 0.20
Matches are distributed among these distances:
4 6 0.09
5 18 0.27
6 37 0.55
7 6 0.09
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (6 bp):
TATTAA
Found at i:1505010 original size:131 final size:124
Alignment explanation
Indices: 1504772--1505054 Score: 288
Period size: 131 Copynumber: 2.2 Consensus size: 124
1504762 TTAATGTGCT
** * **
1504772 ATATAATTTATATTAATGCTAATTATCT-TAACTATAATTTATACTAATATAATATATAGTTTAT
1 ATATAATTTATATTAATATTAATT-T-TATAACTATAATTTATACTAATATAATATACAAATTAT
* *
1504836 AAACTATACTATATTAATATTAATTAAATTAACTATAGTTTATAAACTATACTATATAATTTATA
64 AAACTATACTATATTAATATTAATTAAATTAACTATAGATTAT--A-T-TAATAT-TAA-TTATA
1504901 AA
123 AA
* * *
1504903 ATATAGTTTATATTAATATTAATTTTATAGACTATATTTTATATTAATATTAAT-TACAAATTAT
1 ATATAATTTATATTAATATTAATTTTATA-ACTATAATTTATACTAATA-TAATATACAAATTAT
* * *
1504967 AAACTTTATTATATTAATA-TAAGTTAATATTAA-TATTA-ATTATATTAATATTAATTATAAT
64 AAACTATACTATATTAATATTAA-TTAA-ATTAACTA-TAGATTATATTAATATTAATTATAAA
*
1505028 ATATAATTTATATTAATTTTAATTTTA
1 ATATAATTTATATTAATATTAATTTTA
1505055 ATTATAAATA
Statistics
Matches: 131, Mismatches: 15, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
125 31 0.24
126 3 0.02
127 5 0.04
128 1 0.01
129 2 0.02
130 6 0.05
131 72 0.55
132 11 0.08
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (124 bp):
ATATAATTTATATTAATATTAATTTTATAACTATAATTTATACTAATATAATATACAAATTATAA
ACTATACTATATTAATATTAATTAAATTAACTATAGATTATATTAATATTAATTATAAA
Found at i:1505041 original size:29 final size:29
Alignment explanation
Indices: 1504997--1505084 Score: 94
Period size: 29 Copynumber: 3.1 Consensus size: 29
1504987 AAGTTAATAT
1504997 TAATAT-TAA-TTATATTAATATTAATTA
1 TAATATATAATTTATATTAATATTAATTA
* *
1505024 TAATATATAATTTATATTAATTTTAATTT
1 TAATATATAATTTATATTAATATTAATTA
*
1505053 TAAT-TATAAATAGTT-TATTAATATAAATTA
1 TAATATAT-AAT--TTATATTAATATTAATTA
1505083 TA
1 TA
1505085 TAGGGATGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
27 6 0.12
28 6 0.12
29 23 0.45
30 14 0.27
31 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (29 bp):
TAATATATAATTTATATTAATATTAATTA
Found at i:1505771 original size:13 final size:14
Alignment explanation
Indices: 1505753--1505828 Score: 67
Period size: 13 Copynumber: 5.9 Consensus size: 14
1505743 ACACCTAATG
1505753 TAACATG-AATTAA
1 TAACATGCAATTAA
*
1505766 TAACATGCAA-T-G
1 TAACATGCAATTAA
*
1505778 CAACATG-AATTAA
1 TAACATGCAATTAA
1505791 TAACATGCAA-T-A
1 TAACATGCAATTAA
* *
1505803 TCACAT-TAATTAA
1 TAACATGCAATTAA
1505816 TAACATGCAATTA
1 TAACATGCAATTA
1505829 TTATTTAATA
Statistics
Matches: 48, Mismatches: 8, Indels: 13
0.70 0.12 0.19
Matches are distributed among these distances:
11 4 0.08
12 14 0.29
13 21 0.44
14 9 0.19
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.29
Consensus pattern (14 bp):
TAACATGCAATTAA
Found at i:1505777 original size:25 final size:25
Alignment explanation
Indices: 1505749--1505826 Score: 120
Period size: 25 Copynumber: 3.1 Consensus size: 25
1505739 TTTAACACCT
1505749 AATGTAACATGAATTAATAACATGC
1 AATGTAACATGAATTAATAACATGC
*
1505774 AATGCAACATGAATTAATAACATGC
1 AATGTAACATGAATTAATAACATGC
* * *
1505799 AATATCACATTAATTAATAACATGC
1 AATGTAACATGAATTAATAACATGC
1505824 AAT
1 AAT
1505827 TATTATTTAA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 48 1.00
ACGTcount: A:0.49, C:0.14, G:0.09, T:0.28
Consensus pattern (25 bp):
AATGTAACATGAATTAATAACATGC
Found at i:1505831 original size:21 final size:23
Alignment explanation
Indices: 1505760--1505838 Score: 81
Period size: 25 Copynumber: 3.3 Consensus size: 23
1505750 ATGTAACATG
* *
1505760 AATTAATAACATGCAATGCAACATG
1 AATTAATAACATGCAAT--ATCATT
1505785 AATTAATAACATGCAATATCACATT
1 AATTAATAACATGCAATAT--CATT
1505810 AATTAATAACATGCAAT-T-ATT
1 AATTAATAACATGCAATATCATT
*
1505831 ATTTAATA
1 AATTAATA
1505839 CACTATAATA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
21 10 0.20
23 1 0.02
24 1 0.02
25 37 0.76
ACGTcount: A:0.48, C:0.13, G:0.06, T:0.33
Consensus pattern (23 bp):
AATTAATAACATGCAATATCATT
Found at i:1506413 original size:12 final size:11
Alignment explanation
Indices: 1506385--1506424 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
1506375 TTGAATTAAC
1506385 TCAAATGTTAT
1 TCAAATGTTAT
*
1506396 TCAAATTTTAT
1 TCAAATGTTAT
1506407 ATCAAATGTTAT
1 -TCAAATGTTAT
*
1506419 TTAAAT
1 TCAAAT
1506425 TATCATTATC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.47
Consensus pattern (11 bp):
TCAAATGTTAT
Found at i:1506634 original size:23 final size:24
Alignment explanation
Indices: 1506607--1506657 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 24
1506597 TTATTTTTTC
*
1506607 TTTACTTAAATTAAACTAT-ATAA
1 TTTACATAAATTAAACTATAATAA
1506630 TTTACATAAATTAAACTATAATAA
1 TTTACATAAATTAAACTATAATAA
1506654 TTTA
1 TTTA
1506658 TATTTAATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 18 0.69
24 8 0.31
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (24 bp):
TTTACATAAATTAAACTATAATAA
Found at i:1507965 original size:23 final size:23
Alignment explanation
Indices: 1507938--1507982 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
1507928 GTTCCACCCA
1507938 CGTAGCCCAAATCAACTTAACAC
1 CGTAGCCCAAATCAACTTAACAC
*
1507961 CGTAGCCCAAATTAACTTAACA
1 CGTAGCCCAAATCAACTTAACA
1507983 TTTCACTCGC
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:0.40, C:0.31, G:0.09, T:0.20
Consensus pattern (23 bp):
CGTAGCCCAAATCAACTTAACAC
Found at i:1508949 original size:29 final size:29
Alignment explanation
Indices: 1508902--1508984 Score: 130
Period size: 29 Copynumber: 2.8 Consensus size: 29
1508892 CTCACCTAAC
*
1508902 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGAAATGACATCATTAAT
*
1508932 TAAATGATGTAAGAAATGACATCTTTAAT
1 TAAATGATGTAAGAAATGACATCATTAAT
*
1508961 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGAAATGACATCA
1508985 ATTTAGTTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 45 0.92
30 4 0.08
ACGTcount: A:0.45, C:0.08, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGAAATGACATCATTAAT
Found at i:1512372 original size:15 final size:15
Alignment explanation
Indices: 1512352--1512381 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1512342 CTTTCTCATA
1512352 GTTATTGTTGGAATT
1 GTTATTGTTGGAATT
*
1512367 GTTATTGTTGTAATT
1 GTTATTGTTGGAATT
1512382 CTAGCCTCGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.00, G:0.23, T:0.57
Consensus pattern (15 bp):
GTTATTGTTGGAATT
Found at i:1513709 original size:29 final size:29
Alignment explanation
Indices: 1513666--1513748 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
1513656 CTCACCTAAC
1513666 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
1513696 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
1513725 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
1513749 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:1515280 original size:157 final size:158
Alignment explanation
Indices: 1515040--1515345 Score: 587
Period size: 157 Copynumber: 1.9 Consensus size: 158
1515030 GAGGGGTATT
*
1515040 CCAATGATCTTGGGCGAGAGTCGTGTATGCACTTTTTAATGGAGAATTACAGCAAGACATCAAGA
1 CCAATGATCTTGGACGAGAGTCGTGTATGCACTTTTTAATGGAGAATTACAGCAAGACATCAAGA
1515105 ATATTTTCAATTGTAATAGCTTGATTCAAATCGGGTTTAGCATAGAGGATAAGGTCGTTAGCG-A
66 ATATTTTCAATTGTAATAGCTTGATTCAAATCGGGTTTAGCATAGAGGATAAGGTCGTTAGCGAA
1515169 AAAAAGATGGGAAATTAGCGCGCCATTA
131 AAAAAGATGGGAAATTAGCGCGCCATTA
1515197 CCAATGATCTTGGACGAGAGTCGTGTATGCACTTTTTAATGGAGAATTACAGCAAGACATCAAGA
1 CCAATGATCTTGGACGAGAGTCGTGTATGCACTTTTTAATGGAGAATTACAGCAAGACATCAAGA
*
1515262 ATATTTTCAATTGTAATAGCTTGATTCATATCGGGTTTAGCATAGAGGATAAGGTCGTTAGCGAA
66 ATATTTTCAATTGTAATAGCTTGATTCAAATCGGGTTTAGCATAGAGGATAAGGTCGTTAGCGAA
1515327 AAAAAGATGGGAAATTAGC
131 AAAAAGATGGGAAATTAGC
1515346 AACGAACTTG
Statistics
Matches: 146, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
157 126 0.86
158 20 0.14
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.28
Consensus pattern (158 bp):
CCAATGATCTTGGACGAGAGTCGTGTATGCACTTTTTAATGGAGAATTACAGCAAGACATCAAGA
ATATTTTCAATTGTAATAGCTTGATTCAAATCGGGTTTAGCATAGAGGATAAGGTCGTTAGCGAA
AAAAAGATGGGAAATTAGCGCGCCATTA
Found at i:1517104 original size:118 final size:117
Alignment explanation
Indices: 1516886--1517118 Score: 279
Period size: 118 Copynumber: 2.0 Consensus size: 117
1516876 CAAACGCCGC
* **
1516886 AATATGTTTGATATTAATAATCGTTTTGCAGAAACATGTTCGATATTTAGCGGCGTTTGTAGTAA
1 AATATGTTTGATATTAATAATCGTTTTGCAGAAACATGTTCGATATTTAGCAGCGTTTGTACCAA
** * * ** * * * *
1516951 AAACTGTTGCAATATATTTGATATATAGCGCCGTTTTTAGTTACAAATGCCAT
66 AAACTGCCGCAATAGAATAAATATATAACGACGTTTGTAG-TAAAAATGCCAT
* * *
1517004 AATATGTTTGATATTAATAATCGTTTTGCATAAACATGTTTGATATTTAGCAGCGTTTTTGACCA
1 AATATGTTTGATATTAATAATCGTTTTGCAGAAACATGTTCGATATTTAGCAGCGTTTGT-ACCA
* *
1517069 CAAAC-GCCGCAATAGAATAAATATTTAACGACGTTTGTAGTAAAAATGCC
65 AAAACTGCCGCAATAGAATAAATATATAACGACGTTTGTAGTAAAAATGCC
1517119 GCAATATTTG
Statistics
Matches: 96, Mismatches: 18, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
117 9 0.09
118 81 0.84
119 6 0.06
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (117 bp):
AATATGTTTGATATTAATAATCGTTTTGCAGAAACATGTTCGATATTTAGCAGCGTTTGTACCAA
AAACTGCCGCAATAGAATAAATATATAACGACGTTTGTAGTAAAAATGCCAT
Found at i:1526525 original size:41 final size:41
Alignment explanation
Indices: 1526480--1526574 Score: 181
Period size: 41 Copynumber: 2.3 Consensus size: 41
1526470 TTTCGAGTGT
1526480 AAACGCCGCTATATGTTTAAAGTTAGTGGCGTTTACTCTCA
1 AAACGCCGCTATATGTTTAAAGTTAGTGGCGTTTACTCTCA
*
1526521 AAACGCCGCTATATGTTTAAAGTTAGTGGCGTTTACTCTCT
1 AAACGCCGCTATATGTTTAAAGTTAGTGGCGTTTACTCTCA
1526562 AAACGCCGCTATA
1 AAACGCCGCTATA
1526575 GAACAATTTT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (41 bp):
AAACGCCGCTATATGTTTAAAGTTAGTGGCGTTTACTCTCA
Found at i:1538606 original size:7 final size:7
Alignment explanation
Indices: 1538596--1538666 Score: 51
Period size: 7 Copynumber: 10.4 Consensus size: 7
1538586 ATTTTCTAGC
1538596 AAATATA
1 AAATATA
1538603 AAATAT-
1 AAATATA
*
1538609 -AATTTA
1 AAATATA
1538615 AAATATA
1 AAATATA
*
1538622 AAAAATA
1 AAATATA
*
1538629 AATTATAA
1 AAATAT-A
1538637 AAATATTA
1 AAATA-TA
*
1538645 AATTATA
1 AAATATA
*
1538652 AAA-GT-
1 AAATATA
1538657 AAATATA
1 AAATATA
1538664 AAA
1 AAA
1538667 ATACAAGTTG
Statistics
Matches: 48, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
5 7 0.15
6 2 0.04
7 28 0.58
8 10 0.21
9 1 0.02
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (7 bp):
AAATATA
Found at i:1538620 original size:19 final size:21
Alignment explanation
Indices: 1538596--1538652 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 21
1538586 ATTTTCTAGC
1538596 AAATATAAAATATAATT-T-A
1 AAATATAAAATATAATTATAA
*
1538615 AAATATAAAAAATAAATTATAA
1 AAATATAAAATAT-AATTATAA
*
1538637 AAATATTAAATTATAA
1 AAATA-TAAAATATAA
1538653 AAGTAAATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 12 0.39
20 4 0.13
21 1 0.03
22 8 0.26
23 6 0.19
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
AAATATAAAATATAATTATAA
Found at i:1538638 original size:13 final size:13
Alignment explanation
Indices: 1538622--1538669 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 13
1538612 TTAAAATATA
1538622 AAAAATAAATTAT
1 AAAAATAAATTAT
1538635 AAAAATATTAAATTAT
1 -AAAA-A-TAAATTAT
*
1538651 AAAAGTAAA-TAT
1 AAAAATAAATTAT
1538663 AAAAATA
1 AAAAATA
1538670 CAAGTTGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
12 9 0.30
13 4 0.13
14 4 0.13
15 5 0.17
16 8 0.27
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (13 bp):
AAAAATAAATTAT
Found at i:1538648 original size:16 final size:15
Alignment explanation
Indices: 1538612--1538654 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
1538602 AAAATATAAT
*
1538612 TTAAAATATAAAAAA
1 TTAAATTATAAAAAA
1538627 -TAAATTATAAAAATA
1 TTAAATTATAAAAA-A
1538642 TTAAATTATAAAA
1 TTAAATTATAAAA
1538655 GTAAATATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 12 0.48
15 1 0.04
16 12 0.48
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TTAAATTATAAAAAA
Found at i:1538652 original size:30 final size:28
Alignment explanation
Indices: 1538596--1538669 Score: 85
Period size: 28 Copynumber: 2.5 Consensus size: 28
1538586 ATTTTCTAGC
1538596 AAATATAAAATATAATTTAAAATATAAAAAAT
1 AAATATAAAA-AT-A-TTAAAATAT-AAAAAT
* *
1538628 AAATTATAAAAATATTAAATTATAAAAGT
1 AAA-TATAAAAATATTAAAATATAAAAAT
1538657 AAATATAAAAATA
1 AAATATAAAAATA
1538670 CAAGTTGTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
28 10 0.26
29 8 0.21
30 8 0.21
31 1 0.03
32 5 0.13
33 7 0.18
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (28 bp):
AAATATAAAAATATTAAAATATAAAAAT
Found at i:1538679 original size:21 final size:21
Alignment explanation
Indices: 1538655--1538695 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1538645 AATTATAAAA
1538655 GTAAAT-ATAAAAATACAAGTT
1 GTAAATCATAAAAATA-AAGTT
1538676 GTAAATCATAAAAATAAAGT
1 GTAAATCATAAAAATAAAGT
1538696 AAATATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.59, C:0.05, G:0.10, T:0.27
Consensus pattern (21 bp):
GTAAATCATAAAAATAAAGTT
Found at i:1538712 original size:17 final size:18
Alignment explanation
Indices: 1538652--1538713 Score: 56
Period size: 17 Copynumber: 3.3 Consensus size: 18
1538642 TTAAATTATA
1538652 AAAGTAAAT-ATAAAAAT
1 AAAGTAAATCATAAAAAT
1538669 ACAAGTTGTAAATCATAAAAAT
1 A-AA---GTAAATCATAAAAAT
* *
1538691 AAAGTAAAT-ATTAAATT
1 AAAGTAAATCATAAAAAT
1538708 AAAGTA
1 AAAGTA
1538714 TATAATTTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
17 13 0.34
18 8 0.21
21 8 0.21
22 9 0.24
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.27
Consensus pattern (18 bp):
AAAGTAAATCATAAAAAT
Done.