Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000235.1 Hibiscus syriacus cultivar Beakdansim tig00000405_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: 589249
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:831 original size:20 final size:20
Alignment explanation
Indices: 806--879 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 20
796 CCTTGAAGTA
806 CATCGATGCACTCTACAGTG
1 CATCGATGCACTCTACAGTG
*
826 CATCGATGCATTCTTTAACATGTG
1 CATCGATGCA--CTCT-ACA-GTG
*
850 CATCGATGCACTAC-CCA-TG
1 CATCGATGCACT-CTACAGTG
869 CATCGATGCAC
1 CATCGATGCAC
880 AATTACCTTC
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
19 13 0.28
20 10 0.22
21 2 0.04
22 5 0.11
23 3 0.07
24 13 0.28
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.27
Consensus pattern (20 bp):
CATCGATGCACTCTACAGTG
Found at i:961 original size:45 final size:46
Alignment explanation
Indices: 866--969 Score: 122
Period size: 45 Copynumber: 2.3 Consensus size: 46
856 TGCACTACCC
** * *
866 ATGCATCGATGCA-CAATTACCTTCGATGTTTTTTATTTTAAGGGG
1 ATGCATCGATGCACCAATTACCTTCGATGTTCCTTATTTTAAAGAG
* * *
911 ATGCATCGATGCACCAATTGCTTTCGATGTTCCTTCTTTTAAAGAG
1 ATGCATCGATGCACCAATTACCTTCGATGTTCCTTATTTTAAAGAG
*
957 -TGCATTGATGCAC
1 ATGCATCGATGCAC
970 ATTCAATAGC
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
45 25 0.50
46 25 0.50
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (46 bp):
ATGCATCGATGCACCAATTACCTTCGATGTTCCTTATTTTAAAGAG
Found at i:8148 original size:50 final size:50
Alignment explanation
Indices: 8090--8199 Score: 139
Period size: 50 Copynumber: 2.2 Consensus size: 50
8080 TTAGCAGGAA
* * * *
8090 AACGCGCCCCCTGCACCGTGTTATATGCTGATTTGGCGCCACGTGGGTAT
1 AACGCGCCCCCTGCACCGCGATATACGCTGATCTGGCGCCACGTGGGTAT
* * *
8140 AACGCGCCCCCTGCCCCGCGATATACGGTGATCTGGCGTCACGTGGGTAT
1 AACGCGCCCCCTGCACCGCGATATACGCTGATCTGGCGCCACGTGGGTAT
**
8190 AGTGCGCCCC
1 AACGCGCCCC
8200 TTAATCCGCG
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.15, C:0.34, G:0.29, T:0.22
Consensus pattern (50 bp):
AACGCGCCCCCTGCACCGCGATATACGCTGATCTGGCGCCACGTGGGTAT
Found at i:8209 original size:50 final size:50
Alignment explanation
Indices: 8118--8215 Score: 115
Period size: 50 Copynumber: 2.0 Consensus size: 50
8108 TGTTATATGC
* **
8118 TGATTTGGCGCCACGTGGGTATAACGCGCCCCCTGCCCCGCGATATACGG
1 TGATCTGGCGCCACGTGGGTATAACGCGCCCCCTAACCCGCGATATACGG
* ** * * *
8168 TGATCTGGCGTCACGTGGGTATAGTGCGCCCCTTAATCCGCGCTATAC
1 TGATCTGGCGCCACGTGGGTATAACGCGCCCCCTAACCCGCGATATAC
8216 CTGAATATCT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
50 39 1.00
ACGTcount: A:0.16, C:0.32, G:0.29, T:0.23
Consensus pattern (50 bp):
TGATCTGGCGCCACGTGGGTATAACGCGCCCCCTAACCCGCGATATACGG
Found at i:8379 original size:12 final size:10
Alignment explanation
Indices: 8338--8378 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
8328 TTTATCACAC
8338 CAAATTCTCT
1 CAAATTCTCT
8348 CAAATTCTCT
1 CAAATTCTCT
8358 -AAATTTCTCT
1 CAAA-TTCTCT
*
8368 CAAATACTCT
1 CAAATTCTCT
8378 C
1 C
8379 TTTTTAAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 22 0.79
11 3 0.11
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:8696 original size:111 final size:111
Alignment explanation
Indices: 8502--8723 Score: 390
Period size: 111 Copynumber: 2.0 Consensus size: 111
8492 TGGAAATCAT
* *
8502 ATATCTCTACACTTTGCTGATACGGTAACATTTTAAAGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTACTGATACGGTAACATTTTAAAGTTTTAATTTAATTTAAATTATTAGTAA
* *
8567 TATTTAGTTGATTTATTTAATGCATCATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATTTAATGCATCATTATTAGATTAAGAATTAA
*
8613 ATATCTCGACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTACTGATACGGTAACATTTTAAAGTTTTAATTTAATTTAAATTATTAGTAA
*
8678 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATTTAATGCATCATTATTAGATTAAGAATTAA
8724 TTTTTGTAAT
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 105 1.00
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTACTGATACGGTAACATTTTAAAGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTCATTTAATGCATCATTATTAGATTAAGAATTAA
Found at i:10255 original size:18 final size:18
Alignment explanation
Indices: 10232--10283 Score: 104
Period size: 18 Copynumber: 2.9 Consensus size: 18
10222 GCCACCACAA
10232 CCATATATGATGCCGCAG
1 CCATATATGATGCCGCAG
10250 CCATATATGATGCCGCAG
1 CCATATATGATGCCGCAG
10268 CCATATATGATGCCGC
1 CCATATATGATGCCGC
10284 CATCGCCTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (18 bp):
CCATATATGATGCCGCAG
Found at i:18281 original size:18 final size:18
Alignment explanation
Indices: 18258--18294 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
18248 AAACACTCCT
18258 ATATATCTATATAAACTA
1 ATATATCTATATAAACTA
18276 ATATATCTATATAAACTA
1 ATATATCTATATAAACTA
18294 A
1 A
18295 CATCAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (18 bp):
ATATATCTATATAAACTA
Found at i:18437 original size:24 final size:24
Alignment explanation
Indices: 18410--18465 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
18400 AACCACCATT
18410 TAAGCAAATCAAAGAAAAGGGATA
1 TAAGCAAATCAAAGAAAAGGGATA
18434 TAAGCAAATCAAAGAAAAGGGATA
1 TAAGCAAATCAAAGAAAAGGGATA
*
18458 AAAGCAAA
1 TAAGCAAA
18466 AAATAAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.61, C:0.09, G:0.20, T:0.11
Consensus pattern (24 bp):
TAAGCAAATCAAAGAAAAGGGATA
Found at i:20863 original size:13 final size:13
Alignment explanation
Indices: 20845--20870 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20835 TACAGACGCA
20845 CATATGAAGACTG
1 CATATGAAGACTG
20858 CATATGAAGACTG
1 CATATGAAGACTG
20871 TTCAACTATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (13 bp):
CATATGAAGACTG
Found at i:23724 original size:13 final size:13
Alignment explanation
Indices: 23706--23770 Score: 76
Period size: 13 Copynumber: 5.0 Consensus size: 13
23696 GTTATAAATC
*
23706 TATGACGCGTATT
1 TATGACGCGCATT
**
23719 TATGACATGCATT
1 TATGACGCGCATT
23732 TATGACGCGCATT
1 TATGACGCGCATT
* *
23745 TATGATGTGCATT
1 TATGACGCGCATT
*
23758 TATGACGCTCATT
1 TATGACGCGCATT
23771 GCGCGTCATT
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 42 1.00
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:23745 original size:26 final size:26
Alignment explanation
Indices: 23706--23770 Score: 94
Period size: 26 Copynumber: 2.5 Consensus size: 26
23696 GTTATAAATC
*
23706 TATGACGCGTATTTATGACATGCATT
1 TATGACGCGCATTTATGACATGCATT
**
23732 TATGACGCGCATTTATGATGTGCATT
1 TATGACGCGCATTTATGACATGCATT
*
23758 TATGACGCTCATT
1 TATGACGCGCATT
23771 GCGCGTCATT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (26 bp):
TATGACGCGCATTTATGACATGCATT
Found at i:23934 original size:2 final size:2
Alignment explanation
Indices: 23927--23965 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
23917 TTTCGTAAAT
23927 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
23966 TGTAGATTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:28823 original size:31 final size:30
Alignment explanation
Indices: 28767--28838 Score: 99
Period size: 31 Copynumber: 2.4 Consensus size: 30
28757 GTTCCGAAGA
*
28767 ACATAGGTAACTGTCCATATATCTTGAAAG
1 ACATAGGTAACTATCCATATATCTTGAAAG
* *
28797 ACATAGGTAAGTTATCCATATGTCTTGAAAG
1 ACATAGGTAA-CTATCCATATATCTTGAAAG
*
28828 ACATAGATAAC
1 ACATAGGTAAC
28839 CCTCGACTCT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
30 10 0.28
31 26 0.72
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (30 bp):
ACATAGGTAACTATCCATATATCTTGAAAG
Found at i:28993 original size:15 final size:16
Alignment explanation
Indices: 28967--29010 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
28957 TATCTCATAT
28967 CATATAACATGT-ATCA
1 CATAT-ACATGTAATCA
*
28983 CTTATACATGTAATCA
1 CATATACATGTAATCA
28999 CATATATCATGT
1 CATATA-CATGT
29011 CTCATAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 6 0.25
16 13 0.54
17 5 0.21
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.36
Consensus pattern (16 bp):
CATATACATGTAATCA
Found at i:43706 original size:20 final size:19
Alignment explanation
Indices: 43681--43718 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
43671 AAGTTATTAA
*
43681 ATTTTATTTTTTATTTTTTT
1 ATTTTA-TTATTATTTTTTT
43701 ATTTTATTATTATTTTTT
1 ATTTTATTATTATTTTTT
43719 CTTTCATTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (19 bp):
ATTTTATTATTATTTTTTT
Found at i:43801 original size:4 final size:4
Alignment explanation
Indices: 43792--43827 Score: 56
Period size: 4 Copynumber: 9.0 Consensus size: 4
43782 AGCTTTTTGG
43792 TTAT TTAT TTATT TTAT TTAT TTAT TTAT TT-T TTAT
1 TTAT TTAT TTA-T TTAT TTAT TTAT TTAT TTAT TTAT
43828 CTAACCTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 3 0.10
4 23 0.77
5 4 0.13
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTAT
Found at i:43806 original size:17 final size:17
Alignment explanation
Indices: 43786--43823 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
43776 CTAACTAGCT
*
43786 TTTTGGTTATTTATTTA
1 TTTTAGTTATTTATTTA
*
43803 TTTTATTTATTTATTTA
1 TTTTAGTTATTTATTTA
43820 TTTT
1 TTTT
43824 TTATCTAACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.76
Consensus pattern (17 bp):
TTTTAGTTATTTATTTA
Found at i:46149 original size:9 final size:9
Alignment explanation
Indices: 46128--46175 Score: 62
Period size: 9 Copynumber: 5.2 Consensus size: 9
46118 CAAGTGCATC
46128 TTTTTATTT-
1 TTTTT-TTTA
46137 TTTTTTTTA
1 TTTTTTTTA
46146 TTTTTTTTA
1 TTTTTTTTA
46155 TTTTTTTTCA
1 TTTTTTTT-A
*
46165 TTTATTTTA
1 TTTTTTTTA
46174 TT
1 TT
46176 CACTTTGTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
8 3 0.08
9 25 0.69
10 8 0.22
ACGTcount: A:0.12, C:0.02, G:0.00, T:0.85
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:46149 original size:10 final size:10
Alignment explanation
Indices: 46128--46172 Score: 54
Period size: 10 Copynumber: 4.3 Consensus size: 10
46118 CAAGTGCATC
46128 TTTTTATTTT
1 TTTTTATTTT
*
46138 TTTTTTTATTT
1 TTTTTAT-TTT
46149 TTTTTATTTT
1 TTTTTATTTT
*
46159 TTTTCATTTAT
1 TTTTTATTT-T
46170 TTT
1 TTT
46173 ATTCACTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
10 17 0.57
11 13 0.43
ACGTcount: A:0.11, C:0.02, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTATTTT
Found at i:46153 original size:21 final size:22
Alignment explanation
Indices: 46128--46172 Score: 74
Period size: 21 Copynumber: 2.0 Consensus size: 22
46118 CAAGTGCATC
46128 TTTTTATTTTTTTT-TTTATTT
1 TTTTTATTTTTTTTATTTATTT
46149 TTTTTATTTTTTTTCATTTATTT
1 TTTTTATTTTTTTT-ATTTATTT
46172 T
1 T
46173 ATTCACTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 14 0.64
23 8 0.36
ACGTcount: A:0.11, C:0.02, G:0.00, T:0.87
Consensus pattern (22 bp):
TTTTTATTTTTTTTATTTATTT
Found at i:46158 original size:19 final size:19
Alignment explanation
Indices: 46136--46175 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
46126 TCTTTTTATT
* *
46136 TTTTTTTTTATTTTTTTTA
1 TTTTTTTTCATTTATTTTA
46155 TTTTTTTTCATTTATTTTA
1 TTTTTTTTCATTTATTTTA
46174 TT
1 TT
46176 CACTTTGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (19 bp):
TTTTTTTTCATTTATTTTA
Found at i:53146 original size:21 final size:20
Alignment explanation
Indices: 53107--53157 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
53097 CTTCGGATTA
* *
53107 TGAAAAATTATTTTTAAAAT
1 TGAAAAATGATTTTCAAAAT
53127 AT-AAAAATGATGTTTCAAAAT
1 -TGAAAAATGAT-TTTCAAAAT
53148 TGAAAAATGA
1 TGAAAAATGA
53158 AAACAAACTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.53, C:0.02, G:0.10, T:0.35
Consensus pattern (20 bp):
TGAAAAATGATTTTCAAAAT
Found at i:56977 original size:20 final size:20
Alignment explanation
Indices: 56952--57004 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
56942 TTTTGGTGCA
*
56952 GAGGGAATCGATCCCCCCTT
1 GAGGGAATCGATCCCCCCAT
*
56972 GAGGGAACCGATTCCCCCCAT
1 GAGGGAATCGA-TCCCCCCAT
56993 -AGGGGAATCGAT
1 GA-GGGAATCGAT
57005 ACCACCTAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.25, C:0.30, G:0.28, T:0.17
Consensus pattern (20 bp):
GAGGGAATCGATCCCCCCAT
Found at i:56989 original size:21 final size:20
Alignment explanation
Indices: 56952--56990 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
56942 TTTTGGTGCA
*
56952 GAGGGAATCGATCCCCCCTT
1 GAGGGAACCGATCCCCCCTT
56972 GAGGGAACCGATTCCCCCC
1 GAGGGAACCGA-TCCCCCC
56991 ATAGGGGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.21, C:0.38, G:0.26, T:0.15
Consensus pattern (20 bp):
GAGGGAACCGATCCCCCCTT
Found at i:62524 original size:19 final size:21
Alignment explanation
Indices: 62500--62551 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
62490 TAAGCAAAAT
62500 GGTATCGGTACC-A-AAGGGA
1 GGTATCGGTACCAACAAGGGA
*
62519 GGTATCGATACCAACCAAGGGA
1 GGTATCGGTACCAA-CAAGGGA
*
62541 AGTATCGGTAC
1 GGTATCGGTAC
62552 TGTTGAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 11 0.41
20 1 0.04
22 15 0.56
ACGTcount: A:0.33, C:0.19, G:0.31, T:0.17
Consensus pattern (21 bp):
GGTATCGGTACCAACAAGGGA
Found at i:63165 original size:23 final size:23
Alignment explanation
Indices: 63139--63203 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 23
63129 GTGATCATTT
*
63139 GGGATACTTCTACGTGGTCCTTA
1 GGGATAATTCTACGTGGTCCTTA
** *
63162 GGGATAAATTCTACACGGTCCTTC
1 GGGAT-AATTCTACGTGGTCCTTA
*
63186 GGGACAAATTCTACGTGG
1 GGGA-TAATTCTACGTGG
63204 CACTTCGGTG
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
23 5 0.15
24 28 0.85
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (23 bp):
GGGATAATTCTACGTGGTCCTTA
Found at i:63209 original size:24 final size:24
Alignment explanation
Indices: 63146--63219 Score: 80
Period size: 24 Copynumber: 3.1 Consensus size: 24
63136 TTTGGGATAC
* *
63146 TTCTACGTGGTCCTTAGGGATAAA
1 TTCTACGTGGTCCTTCGGGACAAA
**
63170 TTCTACACGGTCCTTCGGGACAAA
1 TTCTACGTGGTCCTTCGGGACAAA
63194 TTCTACGTGG-CACTTCGGTG-CAAA
1 TTCTACGTGGTC-CTTCGG-GACAAA
63218 TT
1 TT
63220 ATATGAGCTG
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
23 1 0.02
24 40 0.95
25 1 0.02
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (24 bp):
TTCTACGTGGTCCTTCGGGACAAA
Found at i:65623 original size:20 final size:21
Alignment explanation
Indices: 65573--65623 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
65563 TTATATTTTG
*
65573 TTCTATATGTTTCTATATATAT
1 TTCT-TATTTTTCTATATATAT
65595 TTCTTATTTTTCTAT-TATTAT
1 TTCTTATTTTTCTATATA-TAT
65616 TT-TTATTT
1 TTCTTATTT
65624 AATACTATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 8 0.30
21 15 0.56
22 4 0.15
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.69
Consensus pattern (21 bp):
TTCTTATTTTTCTATATATAT
Found at i:69871 original size:183 final size:183
Alignment explanation
Indices: 69563--69912 Score: 637
Period size: 183 Copynumber: 1.9 Consensus size: 183
69553 ATTAAATCCG
69563 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTATATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTATATGA
** *
69628 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAACTCGGTGTTTGCTCCACTGCTT
66 ATAGATTACATTCAAACCATGACACTGCTCGGACACTTGGCAACTCGGTGTTTGCTCCACTGCTT
69693 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
*
69746 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTATATGA
* *
69811 ATAGATTACATTCAAACCATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTACATTCAAACCATGACACTGCTCGGACACTTGGCAACTCGGTGTTTGCTCCACTGCTT
*
69876 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTT
131 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTT
69913 TAGTTAAACC
Statistics
Matches: 160, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
183 160 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTATATGA
ATAGATTACATTCAAACCATGACACTGCTCGGACACTTGGCAACTCGGTGTTTGCTCCACTGCTT
TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
Found at i:71254 original size:37 final size:37
Alignment explanation
Indices: 71187--71273 Score: 113
Period size: 37 Copynumber: 2.4 Consensus size: 37
71177 ATTGAAAACA
** * *
71187 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
*
71223 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAT
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
*
71260 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
71274 TAAACATTGA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
36 12 0.27
37 32 0.73
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.41
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:71276 original size:102 final size:102
Alignment explanation
Indices: 71098--71402 Score: 461
Period size: 102 Copynumber: 3.0 Consensus size: 102
71088 TTAAAACAAG
* * * *
71098 ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAGAAAGTTTTGTCTCACTTGAGACAATTTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA-AAA-TTTTGTCTCCCTTGAGACAATTTCT
*
71163 CTTTAAACATAAACATTGAAAACATTTCCCTTGAAATGA
64 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
*
71202 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACATTTTCTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAATTTCTCT
71267 TGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
66 TGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
* * *
71304 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAA-TAAATTTTGTCTCCTTTGAGA-AAGTTTCTA
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAA-TTTCTC
* *
71367 TTGAAACATAAACTTTGAAAACAGTTTCCCATGAAA
65 TTGAAACATAAACATTGAAAACA-TTTCCCTTGAAA
71403 CAAAATCTTT
Statistics
Matches: 187, Mismatches: 12, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
100 1 0.01
101 46 0.25
102 105 0.56
103 3 0.02
104 32 0.17
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.38
Consensus pattern (102 bp):
ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAATTTCTCT
TGAAACATAAACATTGAAAACATTTCCCTTGAAATGA
Found at i:71336 original size:36 final size:36
Alignment explanation
Indices: 71289--71364 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 36
71279 ATTGAAAACA
* *
71289 TTTCCCTTGAAATGAATTTTGTCT-CTCTTGAGATAG
1 TTTCCCTTGAAATAAATTTTGTCTCCT-TTGAGAAAG
71325 TTTCCCTTGAAATAAATTTTGTCTCCTTTGAGAAAG
1 TTTCCCTTGAAATAAATTTTGTCTCCTTTGAGAAAG
71361 TTTC
1 TTTC
71365 TATTGAAACA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 35 0.95
37 2 0.05
ACGTcount: A:0.24, C:0.17, G:0.14, T:0.45
Consensus pattern (36 bp):
TTTCCCTTGAAATAAATTTTGTCTCCTTTGAGAAAG
Found at i:71394 original size:30 final size:29
Alignment explanation
Indices: 71350--71415 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 29
71340 ATTTTGTCTC
* *
71350 CTTTGAGAAAGTTT-CTATTGAAACATAAA-
1 CTTTGAAAAAGTTTCCCA-TGAAACA-AAAT
71379 CTTTGAAAACAGTTTCCCATGAAACAAAAT
1 CTTTGAAAA-AGTTTCCCATGAAACAAAAT
71409 CTTTGAA
1 CTTTGAA
71416 TATGTTTTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 11 0.34
30 19 0.59
31 2 0.06
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (29 bp):
CTTTGAAAAAGTTTCCCATGAAACAAAAT
Found at i:71543 original size:37 final size:36
Alignment explanation
Indices: 71429--71543 Score: 158
Period size: 36 Copynumber: 3.1 Consensus size: 36
71419 GTTTTACATT
*
71429 AAACAAATTTCGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* * *
71465 AAACAAATTTTGTCTCTCTTAAGACATGTTTTTCTTA
1 AAACAAATTTTGTCTCTCTTGAGACA-GTTTCTCTTG
* *
71502 AAACAAAATTTTGTCTCCCTTGATACAGTTTCTCTTG
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
71539 AAACA
1 AAACA
71544 TCAATCCTTG
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
36 25 0.37
37 24 0.35
38 19 0.28
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
Found at i:71632 original size:36 final size:35
Alignment explanation
Indices: 71585--71673 Score: 137
Period size: 33 Copynumber: 2.6 Consensus size: 35
71575 CCTTGATACA
*
71585 GTTTCTCTTGAAACACAAAAAGAAACCTTTGAAATT
1 GTTTCTCTTGAAACACAAAAA-AAACCTTTGAAAAT
*
71621 GTTTCTCTTGAAATAC--AAAAAACCTTTGAAAAT
1 GTTTCTCTTGAAACACAAAAAAAACCTTTGAAAAT
71654 GTTTCTCTTGAAACACAAAA
1 GTTTCTCTTGAAACACAAAA
71674 CCTTTGAGAT
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
33 28 0.58
34 3 0.06
35 2 0.04
36 15 0.31
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.31
Consensus pattern (35 bp):
GTTTCTCTTGAAACACAAAAAAAACCTTTGAAAAT
Found at i:71649 original size:33 final size:32
Alignment explanation
Indices: 71585--71701 Score: 139
Period size: 31 Copynumber: 3.6 Consensus size: 32
71575 CCTTGATACA
71585 GTTTCTCTTGAAACACAAAAAGAAACCTTTGAAATT
1 GTTTCTCTTGAAA-AC--AAA-AAACCTTTGAAATT
*
71621 GTTTCTCTTGAAATACAAAAAACCTTTGAAAAT
1 GTTTCTCTTGAAA-ACAAAAAACCTTTGAAATT
* *
71654 GTTTCTCTTG-AAACACAAAACCTTTGAGATT
1 GTTTCTCTTGAAAACAAAAAACCTTTGAAATT
*
71685 GTTTCCCTTG-AAACAAA
1 GTTTCTCTTGAAAACAAA
71702 TTTCATCTCC
Statistics
Matches: 74, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
31 31 0.42
32 2 0.03
33 23 0.31
34 3 0.04
36 15 0.20
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.32
Consensus pattern (32 bp):
GTTTCTCTTGAAAACAAAAAACCTTTGAAATT
Found at i:71746 original size:67 final size:67
Alignment explanation
Indices: 71654--71840 Score: 230
Period size: 67 Copynumber: 2.7 Consensus size: 67
71644 CTTTGAAAAT
*
71654 GTTTCTCTTGAAACACAAAACCTTTGAGATTGTTTCCCTTGAAACAAATTTCATCTCCCTTGAGA
1 GTTTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAACAAATTTCATCTCCCTTGAGA
71719 CA
66 CA
* * * **
71721 GTTTCTCTTGAAACACAAAATCTTTGAGTTTATTTCCCTTAAAACAAAATTTTGTCTCCCTTGAG
1 GTTTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAAC-AAATTTCATCTCCCTTGAG
* *
71786 GCC
65 ACA
* * * * *
71789 GTTTCTCATGAAACAACATATATCTTTAAGATCGTTTCCCTTGAAACGAATT
1 GTTTCTCTTGAAAC-ACA-AAATCTTTGAGATTGTTTCCCTTGAAACAAATT
71841 CTGTCTTTTT
Statistics
Matches: 101, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
67 41 0.41
68 31 0.31
69 7 0.07
70 22 0.22
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (67 bp):
GTTTCTCTTGAAACACAAAATCTTTGAGATTGTTTCCCTTGAAACAAATTTCATCTCCCTTGAGA
CA
Found at i:72336 original size:106 final size:107
Alignment explanation
Indices: 72145--72377 Score: 333
Period size: 106 Copynumber: 2.2 Consensus size: 107
72135 GGTTTTAGCT
*
72145 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAGCGAAGGACATTGGACTCAAGACAACACAAGTTCAACTTCACAA
* ** *
72210 CGAAGGGACTGCTGGTTGTCAAC-AAACAATTTCCCAATTTC
66 CGAAGGGACGGCTGACTGTCAACAAAACAATTTCCCAATTCC
* ** * * *
72251 GGAGCCAATTTCAACTTCACATTGAAGGGCATTGGACTCGAGACAGCACAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAGCGAAGGACATTGGACTCAAGACAACACAAGTTCAACTTCACAA
*
72316 CGAAGGGACGGCTGACTGTCAACAAAACAATTTCCCAGTTCC
66 CGAAGGGACGGCTGACTGTCAACAAAACAATTTCCCAATTCC
* *
72358 AGAACCAACTTCAACTTCAC
1 AGAGCCAATTTCAACTTCAC
72378 GACAGAAGAT
Statistics
Matches: 111, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
106 78 0.70
107 33 0.30
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (107 bp):
AGAGCCAATTTCAACTTCACAGCGAAGGACATTGGACTCAAGACAACACAAGTTCAACTTCACAA
CGAAGGGACGGCTGACTGTCAACAAAACAATTTCCCAATTCC
Found at i:72404 original size:107 final size:105
Alignment explanation
Indices: 72149--72405 Score: 329
Period size: 106 Copynumber: 2.4 Consensus size: 105
72139 TTAGCTAGAG
* *
72149 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAA
1 CCAATTTCAACTTCACA-CGAAGGATATTGGACTCGAGACAGCACAAGTTCAACTTCACAACGAA
* ** * * *
72214 GGGACTGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAG
65 GGGACGGCTGACTGTCAACAAACAATTTCCCAATTCCAGAA
* **
72255 CCAATTTCAACTTCACATTGAAGGGCATTGGACTCGAGACAGCACAAGTTCAACTTCACAACGAA
1 CCAATTTCAACTTCACA-CGAAGGATATTGGACTCGAGACAGCACAAGTTCAACTTCACAACGAA
*
72320 GGGACGGCTGACTGTCAACAAAACAATTTCCCAGTTCCAGAA
65 GGGACGGCTGACTGTCAAC-AAACAATTTCCCAATTCCAGAA
*
72362 CCAACTTCAACTTCACGACAGAA-GATATTGGACTCG-GAACAGCA
1 CCAATTTCAACTTCAC-AC-GAAGGATATTGGACTCGAG-ACAGCA
72406 GGACCTGCAT
Statistics
Matches: 130, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
106 76 0.58
107 50 0.38
108 4 0.03
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (105 bp):
CCAATTTCAACTTCACACGAAGGATATTGGACTCGAGACAGCACAAGTTCAACTTCACAACGAAG
GGACGGCTGACTGTCAACAAACAATTTCCCAATTCCAGAA
Found at i:73967 original size:20 final size:21
Alignment explanation
Indices: 73917--73967 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
73907 TTATATTTTG
*
73917 TTCTATATGTTTCTATATATAT
1 TTCT-TATTTTTCTATATATAT
73939 TTCTTATTTTTCTAT-TATTAT
1 TTCTTATTTTTCTATATA-TAT
73960 TT-TTATTT
1 TTCTTATTT
73968 AATACTATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 8 0.30
21 15 0.56
22 4 0.15
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.69
Consensus pattern (21 bp):
TTCTTATTTTTCTATATATAT
Found at i:91347 original size:16 final size:17
Alignment explanation
Indices: 91308--91354 Score: 69
Period size: 16 Copynumber: 2.8 Consensus size: 17
91298 TGTTTCTGAG
91308 GGAATTGGAATCTGTGA
1 GGAATTGGAATCTGTGA
* *
91325 AGAATTGAAATCTGT-A
1 GGAATTGGAATCTGTGA
91341 GGAATTGGAATCTG
1 GGAATTGGAATCTG
91355 AAACATGTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
16 13 0.50
17 13 0.50
ACGTcount: A:0.34, C:0.06, G:0.30, T:0.30
Consensus pattern (17 bp):
GGAATTGGAATCTGTGA
Found at i:92139 original size:33 final size:32
Alignment explanation
Indices: 91914--92140 Score: 275
Period size: 28 Copynumber: 7.4 Consensus size: 32
91904 CACCCTAAAC
* *
91914 CCGAACCGACCCGAATATCACACTTAAAAAAC
1 CCGACCCGACCCGAATATCACACTTAAAAAAA
91946 CCGA-CCGACCCGAATATCACACTTAAAAAAA
1 CCGACCCGACCCGAATATCACACTTAAAAAAA
*
91977 CCTGACCCGACCCAAATATCACACTTAAAAAAA
1 CC-GACCCGACCCGAATATCACACTTAAAAAAA
*
92010 CCCGACCCGACCCAAATATCACACTT-AAAAAA
1 -CCGACCCGACCCGAATATCACACTTAAAAAAA
*
92042 ---ACCCGACCCGAATATCACACTT-AACAAA
1 CCGACCCGACCCGAATATCACACTTAAAAAAA
92070 ---ACCCGACCCGAATATCACACTT-AAAAAA
1 CCGACCCGACCCGAATATCACACTTAAAAAAA
92098 ---A-CCGACCCGAATATCACACTTAAAAAAA
1 CCGACCCGACCCGAATATCACACTTAAAAAAA
*
92126 CTCGACCCCACCCGA
1 C-CGACCCGACCCGA
92141 TCAAAATATG
Statistics
Matches: 180, Mismatches: 6, Indels: 17
0.89 0.03 0.08
Matches are distributed among these distances:
27 20 0.11
28 60 0.33
31 28 0.16
32 13 0.07
33 57 0.32
34 2 0.01
ACGTcount: A:0.44, C:0.35, G:0.08, T:0.13
Consensus pattern (32 bp):
CCGACCCGACCCGAATATCACACTTAAAAAAA
Found at i:92548 original size:27 final size:28
Alignment explanation
Indices: 92518--92573 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
92508 CAGTCGGATT
*
92518 TTTTTTAAA-TTTCAGGTTCGGGTCGGG
1 TTTTTTAAAGTTTCAGATTCGGGTCGGG
* *
92545 TTTTTTAAAGTTTGATATTCGGGTCGGG
1 TTTTTTAAAGTTTCAGATTCGGGTCGGG
92573 T
1 T
92574 CAGGTTTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 9 0.36
28 16 0.64
ACGTcount: A:0.16, C:0.09, G:0.29, T:0.46
Consensus pattern (28 bp):
TTTTTTAAAGTTTCAGATTCGGGTCGGG
Found at i:92573 original size:33 final size:33
Alignment explanation
Indices: 92535--92612 Score: 95
Period size: 33 Copynumber: 2.3 Consensus size: 33
92525 AATTTCAGGT
* * *
92535 TCGGGTCGGGTTTTT-TAAAGTTTGATATTCGGG
1 TCGGGTCAGGTTTTTGT-AAGTGTGATATTCGAG
*
92568 TCGGGTCAGGTTTTTGTAAGTGTGATATTTGAG
1 TCGGGTCAGGTTTTTGTAAGTGTGATATTCGAG
92601 TCGGGTTCAGGT
1 TCGGG-TCAGGT
92613 CGGGTCAGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
33 32 0.82
34 7 0.18
ACGTcount: A:0.15, C:0.09, G:0.35, T:0.41
Consensus pattern (33 bp):
TCGGGTCAGGTTTTTGTAAGTGTGATATTCGAG
Found at i:96553 original size:142 final size:142
Alignment explanation
Indices: 96340--96619 Score: 443
Period size: 142 Copynumber: 2.0 Consensus size: 142
96330 AAAAATTGAC
* * *
96340 TGTTTGAATTATTATTTCACAAATCAATACATAACCCTCTGAAATTATATAATTCAAGAAGACCT
1 TGTTTGAATTATTATTTCACAAATCAATACATAACCATATGAAATTATAGAATTCAAGAAGACCT
*
96405 CATAGGCACCCTATAAATATCAGAAGAAATGTTCCTTCACACTCCTTTCTTTTGTTTTGTGAAAA
66 CATAGGCACCCTATAAATATCAGAAGAAATGTTCCTTCACAATCCTTTCTTTTGTTTTGTGAAAA
96470 TTCCTTACTGAA
131 TTCCTTACTGAA
* ** * *
96482 TGTTTGAATTATTATTTCAGAAATCAATACATAATTATATGAAATTATAGAATTCAAGCAGATCT
1 TGTTTGAATTATTATTTCACAAATCAATACATAACCATATGAAATTATAGAATTCAAGAAGACCT
* * * *
96547 CTTAGGCACCTTATAAATATCAGAAGAAATGTTTCTTTACAATCCTTTCTTTTGTTTTGTGAAAA
66 CATAGGCACCCTATAAATATCAGAAGAAATGTTCCTTCACAATCCTTTCTTTTGTTTTGTGAAAA
96612 TTCCTTAC
131 TTCCTTAC
96620 GAAGCATGAG
Statistics
Matches: 125, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
142 125 1.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (142 bp):
TGTTTGAATTATTATTTCACAAATCAATACATAACCATATGAAATTATAGAATTCAAGAAGACCT
CATAGGCACCCTATAAATATCAGAAGAAATGTTCCTTCACAATCCTTTCTTTTGTTTTGTGAAAA
TTCCTTACTGAA
Found at i:97856 original size:31 final size:31
Alignment explanation
Indices: 97820--97881 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
97810 ACATATAATA
97820 ATATCAAACGGGTTTAGTAAAGTACGAACAT
1 ATATCAAACGGGTTTAGTAAAGTACGAACAT
97851 ATATCAAACGGGTTTAGTAAAGTACGAACAT
1 ATATCAAACGGGTTTAGTAAAGTACGAACAT
97882 GGAGAACTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.26
Consensus pattern (31 bp):
ATATCAAACGGGTTTAGTAAAGTACGAACAT
Found at i:98452 original size:83 final size:83
Alignment explanation
Indices: 98309--98630 Score: 424
Period size: 83 Copynumber: 4.0 Consensus size: 83
98299 GAATTTCAAT
* *
98309 AGAGTTTTACTCCAACTAAAACT-TTTTAATATCT-AA---AAATAGATAATAATATCTTTTAAA
1 AGAGTTTTACTCCAACCAAAACTCTTTTAATATCTAAATTTAAACAGATAATAATATCTTTTAAA
98369 TTTAAAATATTAAATCTG
66 TTTAAAATATTAAATCTG
* * * *
98387 AGTGTTTTACTCTAACCAAAACTCTTTTAATATCTAAATTTAAACAGATTATAATATATTTTAAA
1 AGAGTTTTACTCCAACCAAAACTCTTTTAATATCTAAATTTAAACAGATAATAATATCTTTTAAA
** *
98452 TTTCTAATATTAAACCTG
66 TTTAAAATATTAAATCTG
*
98470 AGAGTTTTACTCCAACCAAAACTCTTTTAATATCTAAATTTAAACAGATTATAATATCTTTTAAA
1 AGAGTTTTACTCCAACCAAAACTCTTTTAATATCTAAATTTAAACAGATAATAATATCTTTTAAA
* *
98535 TTTATAATATTAAATATG
66 TTTAAAATATTAAATCTG
* * ** * *
98553 AGAATTTTACTCAAACCAAAACTCTTTTAATAAATAAACTTAAATAGATAATAATAT-TGTTTAA
1 AGAGTTTTACTCCAACCAAAACTCTTTTAATATCTAAATTTAAACAGATAATAATATCT-TTTAA
98617 ATTT-AAATATTAAA
65 ATTTAAAATATTAAA
98631 CATATATTTC
Statistics
Matches: 215, Mismatches: 23, Indels: 8
0.87 0.09 0.03
Matches are distributed among these distances:
78 20 0.09
79 11 0.05
80 2 0.01
82 10 0.05
83 172 0.80
ACGTcount: A:0.44, C:0.11, G:0.05, T:0.40
Consensus pattern (83 bp):
AGAGTTTTACTCCAACCAAAACTCTTTTAATATCTAAATTTAAACAGATAATAATATCTTTTAAA
TTTAAAATATTAAATCTG
Found at i:105086 original size:24 final size:20
Alignment explanation
Indices: 105059--105116 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
105049 ATGTAATTAG
*
105059 TGCATCGATGCACATGTTAAGGGA
1 TGCATCGATGCAC-TG-T-A-GAA
*
105083 TGCATCGATACACTGTAGAA
1 TGCATCGATGCACTGTAGAA
105103 TGCATCGATGCACT
1 TGCATCGATGCACT
105117 TCAAGGGGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 15 0.48
21 1 0.03
22 1 0.03
23 2 0.06
24 12 0.39
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:107964 original size:57 final size:57
Alignment explanation
Indices: 107852--108115 Score: 158
Period size: 57 Copynumber: 4.5 Consensus size: 57
107842 CAAGACGTTC
* ***
107852 AAGAAATAAAGTCAACAATTTATTTCTTTTTACAAGATAGAATCATACTTTATTCTT
1 AAGAAATAAAGTCAACAATTTATTTCTTTTTACAAGACAGAATCATACAAGATTCTT
*
107909 AAGAAATAAA-TCCAACGATTTAATTTCTTTTATA-AA-ACAGAATCATACAAGATTC-T
1 AAGAAATAAAGT-CAACAATTT-ATTTCTTTT-TACAAGACAGAATCATACAAGATTCTT
* * * * *
107965 ATGAAA-ATAATTTAACAATTTAGTTTC-TTTTACAAGA-TGAAATCGAT-CTAGATT-TT
1 AAGAAATA-AAGTCAACAATTTA-TTTCTTTTTACAAGACAG-AATC-ATACAAGATTCTT
**
108021 CAAGAAAATAAA-TCTAACAATTTATTTCCTTTTTGA-AAGTTAGAATCA-ACGCAAGATTC-T
1 -AAG-AAATAAAGTC-AACAATTTATTT-CTTTTT-ACAAGACAGAATCATA--CAAGATTCTT
*
108081 AAGGTGAAATAAATTCAACAATTTATTTCTCTTTT
1 AA---GAAATAAAGTCAACAATTTATTTCT-TTTT
108116 TCCACTGTTA
Statistics
Matches: 164, Mismatches: 15, Indels: 52
0.71 0.06 0.23
Matches are distributed among these distances:
54 2 0.01
55 8 0.05
56 32 0.20
57 42 0.26
58 27 0.16
59 16 0.10
60 11 0.07
61 23 0.14
62 3 0.02
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (57 bp):
AAGAAATAAAGTCAACAATTTATTTCTTTTTACAAGACAGAATCATACAAGATTCTT
Found at i:109708 original size:83 final size:82
Alignment explanation
Indices: 109597--109875 Score: 341
Period size: 83 Copynumber: 3.4 Consensus size: 82
109587 ATAAAAATAG
* * *
109597 ATAATAATATCTTTAAATTTAAAATATTAAATATTAGAGTTTTAATATAACAAAAATTCTTTTAA
1 ATAAT-ATATATTTAAATTTATAATATTAAAT-TTAGAGTTTTACTATAAC-AAAATTCTTTTAA
*
109662 TATCTAAATTTAAACAAATT
63 TATCTAAATTTAAACAGATT
* * ** *
109682 ATAATATAT-TTTAAATTTATAATATTAAACCTAAGAGTTTTACTCCAACCAAAACTCTTTTAAT
1 ATAATATATATTTAAATTTATAATATTAAA-TTTAGAGTTTTACTATAA-CAAAATTCTTTTAAT
109746 ATCTAAATTTAAACAGATT
64 ATCTAAATTTAAACAGATT
* *
109765 GTAATATAT-TTTAAATTTATAATATTAAATTTGAGAGTTTTACTTTAAGCAAAATTCTTTTAAT
1 ATAATATATATTTAAATTTATAATATTAAATTT-AGAGTTTTACTATAA-CAAAATTCTTTTAAT
* * *
109829 ATCTAAACTTAAATAGATA
64 ATCTAAATTTAAACAGATT
109848 ATAATAT-TATTTAAATTTA-AATATTAAA
1 ATAATATATATTTAAATTTATAATATTAAA
109876 CATATATTTT
Statistics
Matches: 171, Mismatches: 19, Indels: 11
0.85 0.09 0.05
Matches are distributed among these distances:
82 11 0.06
83 150 0.88
84 5 0.03
85 5 0.03
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.43
Consensus pattern (82 bp):
ATAATATATATTTAAATTTATAATATTAAATTTAGAGTTTTACTATAACAAAATTCTTTTAATAT
CTAAATTTAAACAGATT
Found at i:112441 original size:20 final size:21
Alignment explanation
Indices: 112418--112459 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
112408 AAATAAAATA
112418 ATAATTTTA-AAAACATTTAG
1 ATAATTTTATAAAACATTTAG
112438 ATAATTTTATTAAAACATTTAG
1 ATAATTTTA-TAAAACATTTAG
112460 CTTCATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.45
22 11 0.55
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (21 bp):
ATAATTTTATAAAACATTTAG
Found at i:113310 original size:18 final size:19
Alignment explanation
Indices: 113276--113311 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
113266 TTTTAGAAAA
*
113276 ATAAAATATACATTATATT
1 ATAAAATATAAATTATATT
113295 ATAAAATA-AAATTATAT
1 ATAAAATATAAATTATAT
113312 AATTGATGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (19 bp):
ATAAAATATAAATTATATT
Found at i:117449 original size:34 final size:34
Alignment explanation
Indices: 117401--117466 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
117391 CTATTACTTA
*
117401 TATTATATCAATTTGGTCCTAATTTTAATAAATT
1 TATTATATCAATTTGATCCTAATTTTAATAAATT
* *
117435 TATTCTATCAATTTGATCTTAATTTTAATAAA
1 TATTATATCAATTTGATCCTAATTTTAATAAA
117467 CTAAAATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.50
Consensus pattern (34 bp):
TATTATATCAATTTGATCCTAATTTTAATAAATT
Found at i:124467 original size:20 final size:20
Alignment explanation
Indices: 124444--124483 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
124434 TGGGGCCTAA
124444 GAGCCTACCTAAGGGTCGCC
1 GAGCCTACCTAAGGGTCGCC
124464 GAGCCTACCTAAGGGTCGCC
1 GAGCCTACCTAAGGGTCGCC
124484 TTAGGTCCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.35, G:0.30, T:0.15
Consensus pattern (20 bp):
GAGCCTACCTAAGGGTCGCC
Found at i:124609 original size:66 final size:66
Alignment explanation
Indices: 124495--124624 Score: 181
Period size: 66 Copynumber: 2.0 Consensus size: 66
124485 TAGGTCCATA
* *
124495 AGGAATTACGACTCGGTGATGAACCTATACAAGGAATTAACAGCAGCGACTGAA-CTTGCCAGAG
1 AGGAATTACCACTCGGTGATGAACCTATACAAGGAATTAACAGCAGCGACTAAACCTT-CCAGAG
124559 AT
65 AT
* * * * *
124561 AGGAATTACCAGTCGGTGTTGAACCTATACGAGGAATTACCAGGAGCGACTAAACCTTCCAGAG
1 AGGAATTACCACTCGGTGATGAACCTATACAAGGAATTAACAGCAGCGACTAAACCTTCCAGAG
124625 TCTTTATACC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
66 53 0.95
67 3 0.05
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.20
Consensus pattern (66 bp):
AGGAATTACCACTCGGTGATGAACCTATACAAGGAATTAACAGCAGCGACTAAACCTTCCAGAGA
T
Found at i:128799 original size:14 final size:15
Alignment explanation
Indices: 128769--128812 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
128759 GAAATTCAAA
128769 AAGAAGAATGAAGAAG
1 AAGAAGAAT-AAGAAG
128785 AAGAAGAAT-AGAAG
1 AAGAAGAATAAGAAG
* *
128799 AATAAGAAAAAGAA
1 AAGAAGAATAAGAA
128813 TGAGGTGGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 12 0.48
15 4 0.16
16 9 0.36
ACGTcount: A:0.68, C:0.00, G:0.25, T:0.07
Consensus pattern (15 bp):
AAGAAGAATAAGAAG
Found at i:129304 original size:19 final size:20
Alignment explanation
Indices: 129282--129320 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
129272 TTTTAAAGCA
129282 AAAATGG-ATTTTGAAAAAC
1 AAAATGGAATTTTGAAAAAC
129301 AAAATGGAAATTTTGAAAAA
1 AAAATGG-AATTTTGAAAAA
129321 TGATTTTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
21 11 0.61
ACGTcount: A:0.56, C:0.03, G:0.15, T:0.26
Consensus pattern (20 bp):
AAAATGGAATTTTGAAAAAC
Found at i:132819 original size:64 final size:64
Alignment explanation
Indices: 132709--132867 Score: 162
Period size: 64 Copynumber: 2.5 Consensus size: 64
132699 TTCAAGGTGC
* * * * **
132709 ATCGATGCACATGAAGTGCATCGATGCA-CTCCTTTAAAATAAAAACATCGAATTTCA-TCAGTG
1 ATCGATGCA-AAGTAGTGCATCGATGCACCCCCCTTAAAATAAAAACATCGAATAGCATTCA-TG
132772 T
64 T
** * *
132773 ATCGATGCAGAAGTAGTGCATCGATGCACCCCCCTT-AAATGCAAACATCGAATAGGATTTATGT
1 ATCGATGCA-AAGTAGTGCATCGATGCACCCCCCTTAAAATAAAAACATCGAATAGCATTCATGT
*
132837 ATCGATGCATAGATAGTGCATCGATGCACCC
1 ATCGATGCAAAG-TAGTGCATCGATGCACCC
132868 GTCAAGGGAT
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
63 2 0.03
64 71 0.89
65 7 0.09
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (64 bp):
ATCGATGCAAAGTAGTGCATCGATGCACCCCCCTTAAAATAAAAACATCGAATAGCATTCATGT
Found at i:138655 original size:3 final size:3
Alignment explanation
Indices: 138647--138681 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
138637 TTTTAATTTT
* *
138647 TTA TTA TTA TTA TTA TTA GTA TTA CTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
138682 TATATTAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:155487 original size:22 final size:22
Alignment explanation
Indices: 155436--155489 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
155426 CCAGCTGTTT
* *
155436 GTAACTCATGTAATAAAGCTTT
1 GTAACTCTTGTAATAAAGCTTC
*
155458 GTAACTCTTGTATTAAAGCTTC
1 GTAACTCTTGTAATAAAGCTTC
155480 GTAACTCTTG
1 GTAACTCTTG
155490 CATTCATTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.39
Consensus pattern (22 bp):
GTAACTCTTGTAATAAAGCTTC
Found at i:155810 original size:12 final size:13
Alignment explanation
Indices: 155782--155814 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
155772 ACACGTATTG
*
155782 CCACGAGCCATGA
1 CCACGAGCCAAGA
155795 CCACGA-CCAAGA
1 CCACGAGCCAAGA
155807 CCACGAGC
1 CCACGAGC
155815 ATGTCCATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.33, C:0.42, G:0.21, T:0.03
Consensus pattern (13 bp):
CCACGAGCCAAGA
Found at i:156257 original size:2 final size:2
Alignment explanation
Indices: 156214--156244 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
156204 AATGTGTAAG
156214 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
156245 CAAAAGTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:158112 original size:40 final size:40
Alignment explanation
Indices: 158033--158113 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 40
158023 ATAGGAGTCA
* * * *
158033 AATATTGCACCGAAGTGCTGAAGTCGAGCTTTGCTCACCT
1 AATAATGCACCGAAGTGCTGAAGTCGAGATTTACCCACCT
* * *
158073 AATAATGCACCGTAGTGCTGAGGTCGGGATTTACCCACCT
1 AATAATGCACCGAAGTGCTGAAGTCGAGATTTACCCACCT
158113 A
1 A
158114 GTACACCGTA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.26
Consensus pattern (40 bp):
AATAATGCACCGAAGTGCTGAAGTCGAGATTTACCCACCT
Found at i:158956 original size:20 final size:20
Alignment explanation
Indices: 158931--158997 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
158921 CCCCAACAAT
158931 ACAAATATTGTACTTAAACC
1 ACAAATATTGTACTTAAACC
* * * ** **
158951 ACAAATCTTTTCCCCAATAAT
1 ACAAATATTGTACTTAA-ACC
*
158972 ACAAATAGTGTACTTAAACC
1 ACAAATATTGTACTTAAACC
158992 ACAAAT
1 ACAAAT
158998 CTTTTCAAAC
Statistics
Matches: 31, Mismatches: 15, Indels: 2
0.65 0.31 0.04
Matches are distributed among these distances:
20 19 0.61
21 12 0.39
ACGTcount: A:0.45, C:0.22, G:0.04, T:0.28
Consensus pattern (20 bp):
ACAAATATTGTACTTAAACC
Found at i:158978 original size:41 final size:41
Alignment explanation
Indices: 158921--159003 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
158911 CATTTAAGTA
*
158921 CCCCAACAATACAAATATTGTACTTAAACCACAAATCTTTT
1 CCCCAACAATACAAATAGTGTACTTAAACCACAAATCTTTT
*
158962 CCCCAATAATACAAATAGTGTACTTAAACCACAAATCTTTT
1 CCCCAACAATACAAATAGTGTACTTAAACCACAAATCTTTT
159003 C
1 C
159004 AAACTTCCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.41, C:0.27, G:0.04, T:0.29
Consensus pattern (41 bp):
CCCCAACAATACAAATAGTGTACTTAAACCACAAATCTTTT
Found at i:159814 original size:16 final size:16
Alignment explanation
Indices: 159793--159824 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
159783 CATGAATCCT
159793 ATCATGAACACAAACC
1 ATCATGAACACAAACC
159809 ATCATGAACACAAACC
1 ATCATGAACACAAACC
159825 CTTAGATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.31, G:0.06, T:0.12
Consensus pattern (16 bp):
ATCATGAACACAAACC
Found at i:164746 original size:24 final size:24
Alignment explanation
Indices: 164719--164795 Score: 59
Period size: 24 Copynumber: 3.1 Consensus size: 24
164709 TGCACTGGAA
164719 TAACTAATTTCAATTTTGCTGTCG
1 TAACTAATTTCAATTTTGCTGTCG
** ***
164743 TAAC--ATTTCTTTCTATTGCACTGGAA
1 TAACTAATTTCAAT-T-TTG--CTGTCG
164769 TAACTAATTTCAATTTTGCTGTCG
1 TAACTAATTTCAATTTTGCTGTCG
164793 TAA
1 TAA
164796 AATGTATTAA
Statistics
Matches: 37, Mismatches: 10, Indels: 12
0.63 0.17 0.20
Matches are distributed among these distances:
22 6 0.16
23 1 0.03
24 13 0.35
26 10 0.27
27 1 0.03
28 6 0.16
ACGTcount: A:0.27, C:0.17, G:0.12, T:0.44
Consensus pattern (24 bp):
TAACTAATTTCAATTTTGCTGTCG
Found at i:164770 original size:50 final size:50
Alignment explanation
Indices: 164695--164795 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
164685 GTTAAGGACT
164695 ACATTTCTTTCTATTGCACTGGAATAACTAATTTCAATTTTGCTGTCGTA
1 ACATTTCTTTCTATTGCACTGGAATAACTAATTTCAATTTTGCTGTCGTA
164745 ACATTTCTTTCTATTGCACTGGAATAACTAATTTCAATTTTGCTGTCGTA
1 ACATTTCTTTCTATTGCACTGGAATAACTAATTTCAATTTTGCTGTCGTA
164795 A
1 A
164796 AATGTATTAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.44
Consensus pattern (50 bp):
ACATTTCTTTCTATTGCACTGGAATAACTAATTTCAATTTTGCTGTCGTA
Found at i:164772 original size:26 final size:26
Alignment explanation
Indices: 164695--164772 Score: 65
Period size: 26 Copynumber: 3.1 Consensus size: 26
164685 GTTAAGGACT
164695 ACATTTCTTTCTATTGCACTGGAATA
1 ACATTTCTTTCTATTGCACTGGAATA
** ***
164721 ACTAATTTCAAT-T-TTG--CTGTCGTA
1 AC--ATTTCTTTCTATTGCACTGGAATA
164745 ACATTTCTTTCTATTGCACTGGAATA
1 ACATTTCTTTCTATTGCACTGGAATA
164771 AC
1 AC
164773 TAATTTCAAT
Statistics
Matches: 36, Mismatches: 10, Indels: 12
0.62 0.17 0.21
Matches are distributed among these distances:
22 6 0.17
23 1 0.03
24 10 0.28
26 12 0.33
27 1 0.03
28 6 0.17
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (26 bp):
ACATTTCTTTCTATTGCACTGGAATA
Found at i:164787 original size:26 final size:26
Alignment explanation
Indices: 164708--164787 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 26
164698 TTTCTTTCTA
164708 TTGCACTGGAATAACTAATTTCAATT
1 TTGCACTGGAATAACTAATTTCAATT
*** **
164734 TTG--CTGTCGTAAC--ATTTCTTTCT
1 TTGCACTGGAATAACTAATTTCAAT-T
164757 ATTGCACTGGAATAACTAATTTCAATT
1 -TTGCACTGGAATAACTAATTTCAATT
164784 TTGC
1 TTGC
164788 TGTCGTAAAA
Statistics
Matches: 38, Mismatches: 10, Indels: 12
0.63 0.17 0.20
Matches are distributed among these distances:
22 6 0.16
23 1 0.03
24 10 0.26
26 14 0.37
27 1 0.03
28 6 0.16
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.42
Consensus pattern (26 bp):
TTGCACTGGAATAACTAATTTCAATT
Found at i:169460 original size:4 final size:4
Alignment explanation
Indices: 169451--169477 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
169441 TTCAACTATG
169451 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
169478 ACATGCATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:170429 original size:26 final size:25
Alignment explanation
Indices: 170375--170426 Score: 59
Period size: 27 Copynumber: 1.9 Consensus size: 25
170365 CTAAATTTCT
170375 AAAAAAATTTGGGGCCAAATTATTTTA
1 AAAAAAATTTGGGGCCAAATTA--TTA
*
170402 AAAAAAATTTAGGGGCTTAAATTAT
1 AAAAAAATTT-GGGGC-CAAATTAT
170427 AAATTTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
27 11 0.50
28 5 0.23
29 6 0.27
ACGTcount: A:0.46, C:0.06, G:0.15, T:0.33
Consensus pattern (25 bp):
AAAAAAATTTGGGGCCAAATTATTA
Found at i:173031 original size:135 final size:136
Alignment explanation
Indices: 172783--173050 Score: 475
Period size: 135 Copynumber: 2.0 Consensus size: 136
172773 GCTTAATATA
* *
172783 AAAATAAGGACCTAAATTAGATCGTTTTTCTTAAATATGTGTCTAATTTTTTTATTCAATCTAAG
1 AAAATAAGGACCTAAATTAAATCGTTTTTCTTAAATATGCGTCTAATTTTTTTATTCAATCTAAG
* * *
172848 TGTTTAACATTAAACATGTTATATTTTTAGGTGCTCAAATTATTATCGCCGTTAAAATATTTCGT
66 TGTTTAACATTAAACACGTTATATTTTTAGGTGCTCAAATCATAATCGCCGTTAAAATATTTCGT
172913 TAAATG
131 TAAATG
172919 AAAATAAGGACCTAAATTAAATCGTTTTTCTTAAATATGCGTCTAA-TTTTTTATTCAATCTAAG
1 AAAATAAGGACCTAAATTAAATCGTTTTTCTTAAATATGCGTCTAATTTTTTTATTCAATCTAAG
*
172983 TGTTTAACATTATACACGTTATATTTTTAGGTGCTCAAATCATAATCGCCGTTAAAATATTTCGT
66 TGTTTAACATTAAACACGTTATATTTTTAGGTGCTCAAATCATAATCGCCGTTAAAATATTTCGT
173048 TAA
131 TAA
173051 GTAACAATGT
Statistics
Matches: 126, Mismatches: 6, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
135 82 0.65
136 44 0.35
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.42
Consensus pattern (136 bp):
AAAATAAGGACCTAAATTAAATCGTTTTTCTTAAATATGCGTCTAATTTTTTTATTCAATCTAAG
TGTTTAACATTAAACACGTTATATTTTTAGGTGCTCAAATCATAATCGCCGTTAAAATATTTCGT
TAAATG
Found at i:173294 original size:15 final size:15
Alignment explanation
Indices: 173274--173308 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
173264 TAATCAATCG
173274 TCATTGCTTTTATCA
1 TCATTGCTTTTATCA
*
173289 TCATTGCTTTTGTCA
1 TCATTGCTTTTATCA
173304 TCATT
1 TCATT
173309 TGACAAAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.17, C:0.20, G:0.09, T:0.54
Consensus pattern (15 bp):
TCATTGCTTTTATCA
Found at i:176789 original size:17 final size:17
Alignment explanation
Indices: 176764--176799 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
176754 TTTCACATGC
176764 ATTATTATATATTACTTT
1 ATTATTATATATTA-TTT
176782 ATTA-TATATATTATTT
1 ATTATTATATATTATTT
176798 AT
1 AT
176800 ATAATACGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.28
17 9 0.50
18 4 0.22
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTATTATATATTATTT
Found at i:187057 original size:113 final size:113
Alignment explanation
Indices: 186853--188271 Score: 2025
Period size: 113 Copynumber: 12.6 Consensus size: 113
186843 GCCGTCACTC
** * * * *
186853 AGGGAATATCAAATCTTGGACGAGAGGGATATGTTCCACTTGCTCTGAAGGGAATATCAGATCTG
1 AGGGAATATCAAATCTTGGAAAAGAGAGACATGTTCCGCTTACTCTGAAGGGAATATCAGATCTG
* * * * *
186918 GGGAAGTTGATCCATTAAATCGGGGCAGTCTTGTTCCACATACTCTTA
66 GGGGAGTTGATCCATTGAATCGGGGCAGACTTGTTCCACTTACTCTGA
* * * *
186966 AGGGAATATCAAATCTTGGAAAAGATATACCTGTTCCGCTTACTCTGAAGGGAAAATCAGATCTG
1 AGGGAATATCAAATCTTGGAAAAGAGAGACATGTTCCGCTTACTCTGAAGGGAATATCAGATCTG
* ** *
187031 GGGGAGTGGATCCATTGAATTAGGGCAGACTTATTCCACTTACTCTGA
66 GGGGAGTTGATCCATTGAATCGGGGCAGACTTGTTCCACTTACTCTGA
* * * *
187079 AGGGAATATCAAATCTTGGAAAAGAAATACATGTTTCGCTTACTCTGAAGGGAATATTAGATCTG
1 AGGGAATATCAAATCTTGGAAAAGAGAGACATGTTCCGCTTACTCTGAAGGGAATATCAGATCTG
*
187144 GGGGAGTTGATCCATTGAATCGGGGCAGACTTGTTCTACTTACTCTGA
66 GGGGAGTTGATCCATTGAATCGGGGCAGACTTGTTCCACTTACTCTGA
* * * * * * *
187192 AGGGAATATCAAATCATGGAAAAGAGAAACTTGTTTCGCTTACTCTGAAGGGAAAATCATATATG
1 AGGGAATATCAAATCTTGGAAAAGAGAGACATGTTCCGCTTACTCTGAAGGGAATATCAGATCTG
* *
187257 GGGGAGTTGATCCATTGAATCGGGACAGACTTGTTCCACTTACTCTAA
66 GGGGAGTTGATCCATTGAATCGGGGCAGACTTGTTCCACTTACTCTGA
*
187305 AGGGAATATCAAATCTTGGAAAAGAGAGACATGTTCCGCTTACTCTGAAGGGAATATCATATCT-
1 AGGGAATATCAAATCTTGGAAAAGAGAGACATGTTCCGCTTACTCTGAAGGGAATATCAGATCTG
**
187369 GGGGAGTTGATCCATTGAATTAGGGCAGACTTGTTCCACTTACTCTGA
66 GGGGAGTTGATCCATTGAATCGGGGCAGACTTGTTCCACTTACTCTGA
* * *
187417 AGGGAATATCAAATCTTGGAAAAGAGAGACATGTTTCGTTTACTCTGAAGGGAATATCATATCTG
1 AGGGAATATCAAATCTTGGAAAAGAGAGACATGTTCCGCTTACTCTGAAGGGAATATCAGATCTG
* * * * **
187482 AGGGAGTTGATCCGTTGAATCGGGGTAGACTTGTTTCGTTTACTCTGA
66 GGGGAGTTGATCCATTGAATCGGGGCAGACTTGTTCCACTTACTCTGA
* * * *
187530 AGAGAATATTAAATCTTGGAAAAGAGAGACATGTTTCGCTTACTCTGAAGGGAATATCAGATCTA
1 AGGGAATATCAAATCTTGGAAAAGAGAGACATGTTCCGCTTACTCTGAAGGGAATATCAGATCTG
* *
187595 GGGGAATTGATCCATTGAATC-GGGCAGACTTGTTCCATTTACTCTGA
66 GGGGAGTTGATCCATTGAATCGGGGCAGACTTGTTCCACTTACTCTGA
* * * *
187642 AGGGAATATCAAATCTTGGAAAAGAGAGACCTATTCCGCTTACTCTTAAGGGAAAATCAGATCTG
1 AGGGAATATCAAATCTTGGAAAAGAGAGACATGTTCCGCTTACTCTGAAGGGAATATCAGATCTG
* * * *
187707 GGGGAGTTGATCTATTGAATCGGGACAGAATTGTTCCAGTTACTCTGA
66 GGGGAGTTGATCCATTGAATCGGGGCAGACTTGTTCCACTTACTCTGA
* * * *
187755 AGGGAATATCAAATCTTGGAATAGAGAGACATGTTTCGCTTACTTTGAAGGGAATATCAAAGT-T
1 AGGGAATATCAAATCTTGGAAAAGAGAGACATGTTCCGCTTACTCTGAAGGGAATATCAGA-TCT
* **
187819 GGGGGAGTTGATCCATTGAATCGGGGTAGACTTGTTAAACTTACTCTGA
65 GGGGGAGTTGATCCATTGAATCGGGGCAGACTTGTTCCACTTACTCTGA
* * * * * *
187868 AAGGAATATTAAATCTTGGAAAAGAGAGACTTGTCCCGCTTACTCTGAAGGGAATATCATATATG
1 AGGGAATATCAAATCTTGGAAAAGAGAGACATGTTCCGCTTACTCTGAAGGGAATATCAGATCTG
* * * * *
187933 GGGGAGTTGATTCATTGAATTGGGGTAGACTTGTTCCGCATACTCTGA
66 GGGGAGTTGATCCATTGAATCGGGGCAGACTTGTTCCACTTACTCTGA
* * *
187981 AGGGAATATCAAATCTTGGAAAAAAGAGATATGTTCCGTTTACTCTGAAGGGAATATCAGATCTG
1 AGGGAATATCAAATCTTGGAAAAGAGAGACATGTTCCGCTTACTCTGAAGGGAATATCAGATCTG
188046 GGGGAGTTGATCCATTGAATCGGGGCAGACTTGTTCCACTTACTCTGA
66 GGGGAGTTGATCCATTGAATCGGGGCAGACTTGTTCCACTTACTCTGA
* *
188094 AGGGAATATCAAATCTTGGAAAAGAGAGACTTGTTCCGCATACTCTGAAGGGAATATCAGATCTG
1 AGGGAATATCAAATCTTGGAAAAGAGAGACATGTTCCGCTTACTCTGAAGGGAATATCAGATCTG
* * *
188159 GGGGAGTTGAACCATTGAATCGGGGCAGACTTGTTCCACTTAATCTAA
66 GGGGAGTTGATCCATTGAATCGGGGCAGACTTGTTCCACTTACTCTGA
* *
188207 AGGGAATATCAAATCTTGGAAAAGAGAGACATGTTTCTCTTACTCTGAAGGGAATATCAGATCTG
1 AGGGAATATCAAATCTTGGAAAAGAGAGACATGTTCCGCTTACTCTGAAGGGAATATCAGATCTG
188272 CAAATTAAAC
Statistics
Matches: 1163, Mismatches: 139, Indels: 8
0.89 0.11 0.01
Matches are distributed among these distances:
112 206 0.18
113 956 0.82
114 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.29
Consensus pattern (113 bp):
AGGGAATATCAAATCTTGGAAAAGAGAGACATGTTCCGCTTACTCTGAAGGGAATATCAGATCTG
GGGGAGTTGATCCATTGAATCGGGGCAGACTTGTTCCACTTACTCTGA
Found at i:187489 original size:338 final size:339
Alignment explanation
Indices: 186853--188268 Score: 2043
Period size: 338 Copynumber: 4.2 Consensus size: 339
186843 GCCGTCACTC
** * * * * * *
186853 AGGGAATATCAAATCTTGGACGAGAGGGATATGTTCCACTTGCTCTGAAGGGAATATCAGATCTG
1 AGGGAATATCAAATCTTGGAAAAGAGAGACATGTTTCGCTTACTCTGAAGGGAATATCAGATATG
* * * *
186918 GGGAAGTTGATCCATTAAATCGGGGCAGTCTTGTTCCACATACTCTTAAGGGAATATCAAATCTT
66 GGGGAGTTGATCCATTGAATCGGGGCAGACTTGTTCCACATACTCTGAAGGGAATATCAAATCTT
* * * *
186983 GGAAAAGATATACCTGTTCCGCTTACTCTGAAGGGAAAATCAGATCTGGGGGAGTGGATCCATTG
131 GGAAAAGAGAGACATGTTCCGCTTACTCTGAAGGGAAAATCAGATCTGGGGGAGTTGATCCATTG
* * *
187048 AATTAGGGCAGACTTATTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAAATACATGT
196 AATTAGGGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACATGT
*
187113 TTCGCTTACTCTGAAGGGAATATTAGATCTGGGGGAGTTGATCCATTGAATCGGGGCAGACTTGT
261 TTCGCTTACTCTGAAGGGAATATCAGATCTGGGGGAGTTGATCCATTGAATCGGGGCAGACTTGT
187178 TCTACTTACTCTGA
326 TCTACTTACTCTGA
* * * * *
187192 AGGGAATATCAAATCATGGAAAAGAGAAACTTGTTTCGCTTACTCTGAAGGGAAAATCATATATG
1 AGGGAATATCAAATCTTGGAAAAGAGAGACATGTTTCGCTTACTCTGAAGGGAATATCAGATATG
* * *
187257 GGGGAGTTGATCCATTGAATCGGGACAGACTTGTTCCACTTACTCTAAAGGGAATATCAAATCTT
66 GGGGAGTTGATCCATTGAATCGGGGCAGACTTGTTCCACATACTCTGAAGGGAATATCAAATCTT
* *
187322 GGAAAAGAGAGACATGTTCCGCTTACTCTGAAGGGAATATCATATCT-GGGGAGTTGATCCATTG
131 GGAAAAGAGAGACATGTTCCGCTTACTCTGAAGGGAAAATCAGATCTGGGGGAGTTGATCCATTG
187386 AATTAGGGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACATGT
196 AATTAGGGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACATGT
* * * * *
187451 TTCGTTTACTCTGAAGGGAATATCATATCTGAGGGAGTTGATCCGTTGAATCGGGGTAGACTTGT
261 TTCGCTTACTCTGAAGGGAATATCAGATCTGGGGGAGTTGATCCATTGAATCGGGGCAGACTTGT
187516 T-T-CGTTTACTCTGA
326 TCTAC--TTACTCTGA
* * * *
187530 AGAGAATATTAAATCTTGGAAAAGAGAGACATGTTTCGCTTACTCTGAAGGGAATATCAGATCTA
1 AGGGAATATCAAATCTTGGAAAAGAGAGACATGTTTCGCTTACTCTGAAGGGAATATCAGATATG
* **
187595 GGGGAATTGATCCATTGAATC-GGGCAGACTTGTTCCATTTACTCTGAAGGGAATATCAAATCTT
66 GGGGAGTTGATCCATTGAATCGGGGCAGACTTGTTCCACATACTCTGAAGGGAATATCAAATCTT
* * * *
187659 GGAAAAGAGAGACCTATTCCGCTTACTCTTAAGGGAAAATCAGATCTGGGGGAGTTGATCTATTG
131 GGAAAAGAGAGACATGTTCCGCTTACTCTGAAGGGAAAATCAGATCTGGGGGAGTTGATCCATTG
* * * *
187724 AA-TCGGGACAGAATTGTTCCAGTTACTCTGAAGGGAATATCAAATCTTGGAATAGAGAGACATG
196 AATTAGGG-CAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACATG
* * *
187788 TTTCGCTTACTTTGAAGGGAATATCAAAGT-TGGGGGAGTTGATCCATTGAATCGGGGTAGACTT
260 TTTCGCTTACTCTGAAGGGAATATCAGA-TCTGGGGGAGTTGATCCATTGAATCGGGGCAGACTT
**
187852 GTTAAACTTACTCTGA
324 GTTCTACTTACTCTGA
* * * ** *
187868 AAGGAATATTAAATCTTGGAAAAGAGAGACTTGTCCCGCTTACTCTGAAGGGAATATCATATATG
1 AGGGAATATCAAATCTTGGAAAAGAGAGACATGTTTCGCTTACTCTGAAGGGAATATCAGATATG
* * * *
187933 GGGGAGTTGATTCATTGAATTGGGGTAGACTTGTTCCGCATACTCTGAAGGGAATATCAAATCTT
66 GGGGAGTTGATCCATTGAATCGGGGCAGACTTGTTCCACATACTCTGAAGGGAATATCAAATCTT
* * * *
187998 GGAAAAAAGAGATATGTTCCGTTTACTCTGAAGGGAATATCAGATCTGGGGGAGTTGATCCATTG
131 GGAAAAGAGAGACATGTTCCGCTTACTCTGAAGGGAAAATCAGATCTGGGGGAGTTGATCCATTG
** *
188063 AATCGGGGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACTTGT
196 AATTAGGGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACATGT
* * *
188128 TCCGCATACTCTGAAGGGAATATCAGATCTGGGGGAGTTGAACCATTGAATCGGGGCAGACTTGT
261 TTCGCTTACTCTGAAGGGAATATCAGATCTGGGGGAGTTGATCCATTGAATCGGGGCAGACTTGT
* * *
188193 TCCACTTAATCTAA
326 TCTACTTACTCTGA
*
188207 AGGGAATATCAAATCTTGGAAAAGAGAGACATGTTTCTCTTACTCTGAAGGGAATATCAGAT
1 AGGGAATATCAAATCTTGGAAAAGAGAGACATGTTTCGCTTACTCTGAAGGGAATATCAGAT
188269 CTGCAAATTA
Statistics
Matches: 958, Mismatches: 109, Indels: 20
0.88 0.10 0.02
Matches are distributed among these distances:
336 1 0.00
337 87 0.09
338 439 0.46
339 427 0.45
340 4 0.00
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (339 bp):
AGGGAATATCAAATCTTGGAAAAGAGAGACATGTTTCGCTTACTCTGAAGGGAATATCAGATATG
GGGGAGTTGATCCATTGAATCGGGGCAGACTTGTTCCACATACTCTGAAGGGAATATCAAATCTT
GGAAAAGAGAGACATGTTCCGCTTACTCTGAAGGGAAAATCAGATCTGGGGGAGTTGATCCATTG
AATTAGGGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACATGT
TTCGCTTACTCTGAAGGGAATATCAGATCTGGGGGAGTTGATCCATTGAATCGGGGCAGACTTGT
TCTACTTACTCTGA
Found at i:188921 original size:41 final size:41
Alignment explanation
Indices: 188788--188972 Score: 178
Period size: 42 Copynumber: 4.5 Consensus size: 41
188778 AGGTCTTATG
** *
188788 GATGACCCGAATTACTTATCATCTTGCTCGAAAGACTTAC-A
1 GATGACCCGAAGGACTTATCATCATGCTCGAAAGACTT-CTA
* * * * *
188829 GATGACCCGAAGAAATTAAGCATCATGCTCGAAAAACTTCTT
1 GATGACCCGAAGGACTT-ATCATCATGCTCGAAAGACTTCTA
* *
188871 GATGGCCCGAATGACTTATCAT-ATTGCTCGAAAGACTTAC-A
1 GATGACCCGAAGGACTTATCATCA-TGCTCGAAAGACTT-CTA
* * *
188912 GATGACCCGAAGGAATTAAGCATCATGCTCGAAAGACTTCTT
1 GATGACCCGAAGGACTT-ATCATCATGCTCGAAAGACTTCTA
*
188954 GATGGCCCGAAGGACTTAT
1 GATGACCCGAAGGACTTAT
188973 AAATTTTGGA
Statistics
Matches: 115, Mismatches: 22, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
40 1 0.01
41 48 0.42
42 65 0.57
43 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.25
Consensus pattern (41 bp):
GATGACCCGAAGGACTTATCATCATGCTCGAAAGACTTCTA
Found at i:188932 original size:83 final size:83
Alignment explanation
Indices: 188788--188972 Score: 316
Period size: 83 Copynumber: 2.2 Consensus size: 83
188778 AGGTCTTATG
* * *
188788 GATGACCCGAATTACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGAAATTAAGCATC
1 GATGGCCCGAATGACTTATCATATTGCTCGAAAGACTTACAGATGACCCGAAGAAATTAAGCATC
188853 ATGCTCGAAAAACTTCTT
66 ATGCTCGAAAAACTTCTT
*
188871 GATGGCCCGAATGACTTATCATATTGCTCGAAAGACTTACAGATGACCCGAAGGAATTAAGCATC
1 GATGGCCCGAATGACTTATCATATTGCTCGAAAGACTTACAGATGACCCGAAGAAATTAAGCATC
*
188936 ATGCTCGAAAGACTTCTT
66 ATGCTCGAAAAACTTCTT
*
188954 GATGGCCCGAAGGACTTAT
1 GATGGCCCGAATGACTTAT
188973 AAATTTTGGA
Statistics
Matches: 96, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 96 1.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.25
Consensus pattern (83 bp):
GATGGCCCGAATGACTTATCATATTGCTCGAAAGACTTACAGATGACCCGAAGAAATTAAGCATC
ATGCTCGAAAAACTTCTT
Found at i:191163 original size:18 final size:19
Alignment explanation
Indices: 191140--191180 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
191130 CAGTAATCCT
191140 ATTCT-CTGGTAATCTTAC
1 ATTCTACTGGTAATCTTAC
191158 ATTCTCACTGGTAATCTTAC
1 ATTCT-ACTGGTAATCTTAC
191178 ATT
1 ATT
191181 TCGTGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 5 0.24
20 16 0.76
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.44
Consensus pattern (19 bp):
ATTCTACTGGTAATCTTAC
Found at i:194904 original size:17 final size:17
Alignment explanation
Indices: 194882--194924 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
194872 AATGAATATA
194882 GAACCAAAAGAATTTGG
1 GAACCAAAAGAATTTGG
194899 GAACCAAAAGAATTTGG
1 GAACCAAAAGAATTTGG
*
194916 GTACCAAAA
1 GAACCAAAA
194925 ATTAGAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.49, C:0.14, G:0.21, T:0.16
Consensus pattern (17 bp):
GAACCAAAAGAATTTGG
Found at i:198355 original size:23 final size:23
Alignment explanation
Indices: 198313--198418 Score: 128
Period size: 23 Copynumber: 4.7 Consensus size: 23
198303 TTAGTGCAGA
* *
198313 GGGAATCGATACCCCC-TTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
198335 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
*
198358 GGGAACCGATTCCCCCTTTGCAG
1 GGGAACCGATTCCCCCTTTGAAG
* *
198381 GGGAACCAATTCCCCCTAT-AA-
1 GGGAACCGATTCCCCCTTTGAAG
* *
198402 GGGAATCGATACCCCCT
1 GGGAACCGATTCCCCCT
198419 GAGGGTTCTG
Statistics
Matches: 74, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
21 14 0.19
22 15 0.20
23 45 0.61
ACGTcount: A:0.25, C:0.32, G:0.24, T:0.20
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAG
Found at i:198393 original size:46 final size:44
Alignment explanation
Indices: 198312--198418 Score: 144
Period size: 46 Copynumber: 2.4 Consensus size: 44
198302 TTTAGTGCAG
* *
198312 AGGGAATCGATACCCCC-TTGAAGGGGAACCGATTCCCCCTTTGA
1 AGGGAATCGATACCCCCTTTGAAGGGGAACCAATTCCCCCTAT-A
* * *
198356 AGGGGAACCGATTCCCCCTTTGCAGGGGAACCAATTCCCCCTATA
1 A-GGGAATCGATACCCCCTTTGAAGGGGAACCAATTCCCCCTATA
198401 AGGGAATCGATACCCCCT
1 AGGGAATCGATACCCCCT
198419 GAGGGTTCTG
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
44 16 0.30
45 16 0.30
46 22 0.41
ACGTcount: A:0.25, C:0.32, G:0.23, T:0.20
Consensus pattern (44 bp):
AGGGAATCGATACCCCCTTTGAAGGGGAACCAATTCCCCCTATA
Found at i:202182 original size:22 final size:23
Alignment explanation
Indices: 202157--202205 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 23
202147 GTAAATTGTT
* * *
202157 AATTAGTTTTATTTA-TTTATTA
1 AATTAGTATTATTAATTTTAGTA
*
202179 AATTTGTATTATTAATTTTAGTA
1 AATTAGTATTATTAATTTTAGTA
202202 AATT
1 AATT
202206 TAGATTTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (23 bp):
AATTAGTATTATTAATTTTAGTA
Found at i:206672 original size:18 final size:20
Alignment explanation
Indices: 206624--206673 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
206614 GGCATGTGTG
*
206624 CCTACTTTGTAACTGGGCCAT
1 CCTA-TTTGTAAATGGGCCAT
*
206645 CCTCTTTGTAAATGGGCC-T
1 CCTATTTGTAAATGGGCCAT
206664 -CTATTTGTAA
1 CCTATTTGTAA
206674 TAATAATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 9 0.35
19 1 0.04
20 13 0.50
21 3 0.12
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.38
Consensus pattern (20 bp):
CCTATTTGTAAATGGGCCAT
Found at i:206688 original size:10 final size:10
Alignment explanation
Indices: 206673--206716 Score: 70
Period size: 10 Copynumber: 4.3 Consensus size: 10
206663 TCTATTTGTA
206673 ATAATAATAT
1 ATAATAATAT
206683 ATAATAATAT
1 ATAATAATAT
*
206693 ATATTTAATAT
1 ATA-ATAATAT
206704 ATAATAATAT
1 ATAATAATAT
206714 ATA
1 ATA
206717 TATATATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
10 22 0.71
11 9 0.29
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
ATAATAATAT
Found at i:206703 original size:21 final size:21
Alignment explanation
Indices: 206677--206717 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
206667 TTTGTAATAA
206677 TAATATATAATAATATATATT
1 TAATATATAATAATATATATT
206698 TAATATATAATAATATATAT
1 TAATATATAATAATATATAT
206718 ATATATTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TAATATATAATAATATATATT
Found at i:207475 original size:20 final size:20
Alignment explanation
Indices: 207436--207528 Score: 98
Period size: 20 Copynumber: 4.6 Consensus size: 20
207426 AGACTGATAG
207436 ATGACCCG-AGGAATTTTACAA
1 ATGACCCGAAGG-A-TTTACAA
* * *
207457 ATTACCAGAAGGCTTTACAA
1 ATGACCCGAAGGATTTACAA
* *
207477 ATTACCCGGAGGATTTACAA
1 ATGACCCGAAGGATTTACAA
*
207497 ATGACCCGGAGGATTTACAA
1 ATGACCCGAAGGATTTACAA
*
207517 ATGACCTGAAGG
1 ATGACCCGAAGG
207529 CTTTTAATTT
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
20 53 0.85
21 6 0.10
22 3 0.05
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.23
Consensus pattern (20 bp):
ATGACCCGAAGGATTTACAA
Found at i:214997 original size:35 final size:37
Alignment explanation
Indices: 214931--215035 Score: 155
Period size: 35 Copynumber: 2.9 Consensus size: 37
214921 AGATACAATC
214931 TGTCCATCACCATTATCACGCCTATATCATCACCAT-
1 TGTCCATCACCATTATCACGCCTATATCATCACCATA
*
214967 TGTCCATCACCATTAT-ACACCTATATCATCACCATA
1 TGTCCATCACCATTATCACGCCTATATCATCACCATA
* *
215003 T-TCCATTACCA-TATCACGCCTATATTATCACCA
1 TGTCCATCACCATTATCACGCCTATATCATCACCA
215036 ACTTATAAAT
Statistics
Matches: 63, Mismatches: 4, Indels: 5
0.88 0.06 0.07
Matches are distributed among these distances:
34 3 0.05
35 43 0.68
36 17 0.27
ACGTcount: A:0.30, C:0.34, G:0.04, T:0.31
Consensus pattern (37 bp):
TGTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:216544 original size:13 final size:13
Alignment explanation
Indices: 216516--216555 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 13
216506 ATAAGGACTA
216516 AAATATAAATATACC
1 AAAT-TAAA-ATACC
216531 AAATTAAAATACC
1 AAATTAAAATACC
216544 AAATTAAAATAC
1 AAATTAAAATAC
216556 GAATAAACCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 17 0.68
14 4 0.16
15 4 0.16
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.25
Consensus pattern (13 bp):
AAATTAAAATACC
Found at i:217681 original size:2 final size:2
Alignment explanation
Indices: 217674--217731 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
217664 ATTTGTGATA
217674 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
217716 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
217732 TAACATAACA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:218264 original size:47 final size:46
Alignment explanation
Indices: 218237--218413 Score: 166
Period size: 45 Copynumber: 4.3 Consensus size: 46
218227 ATTTTTGCAA
218237 ATATATATATATATATAATATAGTTTTT-AAAAACATTTTGAAAAT
1 ATATATATATATATATAATATAGTTTTTAAAAAACATTTTGAAAAT
218282 ATATATATATATATATAATATAGTTTTT--AAAA-A-TTTG-AAA-
1 ATATATATATATATATAATATAGTTTTTAAAAAACATTTTGAAAAT
*
218322 A-A-ATATATATA-AT-ATATAGTTTTT--ATAACATTTTG---A-
1 ATATATATATATATATAATATAGTTTTTAAAAAACATTTTGAAAAT
*
218358 A-A-A-A-ATATATATAATATAGTTTTT-AAAAACATTTTTGAAAAC
1 ATATATATATATATATAATATAGTTTTTAAAAAACA-TTTTGAAAAT
218400 ATATATA-ATATATA
1 ATATATATATATATA
218414 GTTTTGAAAA
Statistics
Matches: 117, Mismatches: 2, Indels: 26
0.81 0.01 0.18
Matches are distributed among these distances:
34 5 0.04
35 3 0.03
36 29 0.25
37 8 0.07
38 18 0.15
39 1 0.01
40 1 0.01
41 4 0.03
42 5 0.04
43 2 0.02
44 5 0.04
45 36 0.31
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.44
Consensus pattern (46 bp):
ATATATATATATATATAATATAGTTTTTAAAAAACATTTTGAAAAT
Found at i:218301 original size:45 final size:42
Alignment explanation
Indices: 218229--218443 Score: 207
Period size: 38 Copynumber: 5.5 Consensus size: 42
218219 AAAAATCGAT
*
218229 TTTTGCAAATATATATATATATATAATATAGTTTTTAAAAACA
1 TTTTGAAAATATATATATATATATAATATAGTTTTT-AAAACA
218272 TTTTGAAAATATATATATATATATATAATATAGTTTTTAAAA-A
1 TTTTG-AAA-ATATATATATATATATAATATAGTTTTTAAAACA
*
218315 -TTTGAAAA-A-ATATATATA-AT-ATATAGTTTTTATAACA
1 TTTTGAAAATATATATATATATATAATATAGTTTTTAAAACA
218352 TTTTG--AA-A-A-A-ATATATATAATATAGTTTTTAAAAACA
1 TTTTGAAAATATATATATATATATAATATAGTTTTT-AAAACA
* *
218389 TTTTTG--AA-A-ACATATATA-AT-ATATAGTTTTGAAAACA
1 -TTTTGAAAATATATATATATATATAATATAGTTTTTAAAACA
*
218426 TTTTAAAAATA-ATATATA
1 TTTTGAAAATATATATATA
218444 ATTTTTTAAA
Statistics
Matches: 153, Mismatches: 6, Indels: 30
0.81 0.03 0.16
Matches are distributed among these distances:
34 5 0.03
35 3 0.02
36 33 0.22
37 14 0.09
38 34 0.22
39 11 0.07
40 6 0.04
41 3 0.02
42 4 0.03
43 6 0.04
44 6 0.04
45 28 0.18
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (42 bp):
TTTTGAAAATATATATATATATATAATATAGTTTTTAAAACA
Found at i:218328 original size:36 final size:37
Alignment explanation
Indices: 218243--218445 Score: 197
Period size: 36 Copynumber: 5.4 Consensus size: 37
218233 GCAAATATAT
218243 ATATATATATAATATAGTTTTTAAAAACATTTTGAAAATATATA
1 ATATATATATAATATAGTTTTT-AAAACA-TTTG--AA-A-A-A
218287 TATATATATATAATATAGTTTTTAAAA-ATTTGAAAAA
1 -ATATATATATAATATAGTTTTTAAAACATTTGAAAAA
*
218324 ATATATATA-ATATATAGTTTTTATAACATTTTG-AAAA
1 ATATATATATA-ATATAGTTTTTAAAACA-TTTGAAAAA
*
218361 A-ATATATATAATATAGTTTTTAAAAACATTTTTGAAAAC
1 ATATATATATAATATAGTTTTT-AAAACA--TTTGAAAAA
* *
218400 ATATATA-AT-ATATAGTTTTGAAAACATTT-TAAAA
1 ATATATATATAATATAGTTTTTAAAACATTTGAAAAA
218434 ATA-ATATATAAT
1 ATATATATATAAT
218446 TTTTTAAAAT
Statistics
Matches: 142, Mismatches: 6, Indels: 30
0.80 0.03 0.17
Matches are distributed among these distances:
33 3 0.02
34 8 0.06
35 6 0.04
36 41 0.29
37 19 0.13
38 20 0.14
39 7 0.05
40 7 0.05
42 4 0.03
43 1 0.01
44 4 0.03
45 22 0.15
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (37 bp):
ATATATATATAATATAGTTTTTAAAACATTTGAAAAA
Found at i:218501 original size:31 final size:31
Alignment explanation
Indices: 218366--218538 Score: 129
Period size: 31 Copynumber: 5.3 Consensus size: 31
218356 GAAAAAATAT
* *
218366 ATATAATATAGTTTTTAAAAACATTTTTGAAAACA
1 ATATAATATA-ATTTTGAAAACATTTTTG--AA-A
*
218401 TATATAATATATAGTTTTGAAAACA-TTTTAAAA
1 -ATATAATATA-A-TTTTGAAAACATTTTTGAAA
* * **
218434 ATA-ATATATAATTTTTTAAAATATTTTTGAGT
1 ATATA-ATATAA-TTTTGAAAACATTTTTGAAA
*
218466 ATATAATATAATTTTGAAAATATTTTTGAAA
1 ATATAATATAATTTTGAAAACATTTTTGAAA
*
218497 ATAT-ATATTAGTTTT-AAAACAATTTTTGAAA
1 ATATAATA-TAATTTTGAAAAC-ATTTTTGAAA
218528 ATATATATATA
1 ATATA-ATATA
218539 TTGTATGGTT
Statistics
Matches: 114, Mismatches: 15, Indels: 20
0.77 0.10 0.13
Matches are distributed among these distances:
30 7 0.06
31 52 0.46
32 24 0.21
33 5 0.04
34 2 0.02
36 14 0.12
37 10 0.09
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (31 bp):
ATATAATATAATTTTGAAAACATTTTTGAAA
Found at i:218522 original size:62 final size:64
Alignment explanation
Indices: 218327--218539 Score: 175
Period size: 62 Copynumber: 3.2 Consensus size: 64
218317 TGAAAAAATA
* *
218327 TATATAATATATAGTTTTTATAACATTTTGAAAAA-ATATATATAATATAGTTTTTAAAAACATT
1 TATATAATATATAGTTTTGAAAACATTTT-AAAAATA-ATATAT-A-AT-G-TTTTAAAAA-ATT
*
218391 TTTGAAAACA
59 TTTG---A-G
* *
218401 TATATAATATATAGTTTTGAAAACATTTTAAAAATAATATATAATTTTTTAAAATATTTTTGAG
1 TATATAATATATAGTTTTGAAAACATTTTAAAAATAATATATAATGTTTTAAAAAATTTTTGAG
* * *
218465 TATATAATATA-A-TTTTGAAAATATTTTTGAAAAT-ATATATTA-GTTTTAAAACAATTTTTGA
1 TATATAATATATAGTTTTGAAAACA-TTTTAAAAATAATATATAATGTTTTAAAA-AATTTTTGA
*
218526 A
64 G
*
218527 AATATATATATAT
1 TATATA-ATATAT
218540 TGTATGGTTT
Statistics
Matches: 122, Mismatches: 12, Indels: 20
0.79 0.08 0.13
Matches are distributed among these distances:
61 8 0.07
62 30 0.25
63 15 0.12
64 11 0.09
65 1 0.01
68 7 0.06
69 8 0.07
71 2 0.02
72 1 0.01
73 11 0.09
74 28 0.23
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (64 bp):
TATATAATATATAGTTTTGAAAACATTTTAAAAATAATATATAATGTTTTAAAAAATTTTTGAG
Found at i:218600 original size:38 final size:34
Alignment explanation
Indices: 218288--218592 Score: 177
Period size: 37 Copynumber: 8.7 Consensus size: 34
218278 AAATATATAT
* **
218288 ATATATATATAATATAGTTTTTAAAAATTTGAAAAAA
1 ATATATA-AT-ATATAGTTTTAAAAAATTT-TTAAAA
* * *
218325 TATATATAATATATAGTTTTTATAACATTTTGAAAA
1 -ATATATAATATATAG-TTTTAAAAAATTTTTAAAA
218361 A-ATATATATAATATAGTTTTTAAAAACATTTTTGAAAA
1 ATATATA-AT-ATATAG-TTTTAAAAA-ATTTTT-AAAA
*
218399 CATATATAATATATAGTTTTGAAAACA-TTTTAAAA
1 -ATATATAATATATAGTTTT-AAAAAATTTTTAAAA
* * *
218434 ATA-AT-ATATA-ATTTTTTAAAATATTTTT--GA
1 ATATATAATATATA-GTTTTAAAAAATTTTTAAAA
* * *
218464 GTATATAATATA-A-TTTTGAAAATATTTTT-GAA
1 ATATATAATATATAGTTTT-AAAAAATTTTTAAAA
218496 A-ATAT-ATAT-TAGTTTTAAAACAATTTTTGAAAA
1 ATATATAATATATAGTTTTAAAA-AATTTTT-AAAA
* * *
218529 TATATATATATTGTATGGTTTAAAAACAATTTTTAAAA
1 -ATATATA-A-TATATAGTTTTAAAA-AATTTTTAAAA
218567 GCATATATAATATATAGTTTTAAAAA
1 --ATATATAATATATAGTTTTAAAAA
218593 TGATTTTTTA
Statistics
Matches: 217, Mismatches: 24, Indels: 54
0.74 0.08 0.18
Matches are distributed among these distances:
30 16 0.07
31 33 0.15
32 20 0.09
33 4 0.02
34 9 0.04
35 11 0.05
36 29 0.13
37 35 0.16
38 28 0.13
39 27 0.12
40 5 0.02
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (34 bp):
ATATATAATATATAGTTTTAAAAAATTTTTAAAA
Found at i:219783 original size:30 final size:28
Alignment explanation
Indices: 219749--219819 Score: 83
Period size: 30 Copynumber: 2.5 Consensus size: 28
219739 TTTTTAAATT
*
219749 TTTTTATTTTATTTTTTCCTTTGATTTTTA
1 TTTTTATTTTATTTTTCCCTTTGA--TTTA
*
219779 TTTTTATGTTT-TTCTTCCCTTTGATTTA
1 TTTTTAT-TTTATTTTTCCCTTTGATTTA
219807 TTTTTA-TTTATTT
1 TTTTTATTTTATTT
219820 ATTATTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
26 3 0.08
27 2 0.06
28 10 0.28
30 18 0.50
31 3 0.08
ACGTcount: A:0.13, C:0.08, G:0.04, T:0.75
Consensus pattern (28 bp):
TTTTTATTTTATTTTTCCCTTTGATTTA
Found at i:222336 original size:24 final size:24
Alignment explanation
Indices: 222274--222336 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 24
222264 GTGTTTGTCT
*
222274 ATTTAT-TGTTCATGAACATGTTC
1 ATTTATATGTTCACGAACATGTTC
* **
222297 ATTTA-ATGTTCGCGAATGTGTTC
1 ATTTATATGTTCACGAACATGTTC
*
222320 GTTTATATGTTCACGAA
1 ATTTATATGTTCACGAA
222337 ATTATTCATG
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
23 22 0.69
24 10 0.31
ACGTcount: A:0.25, C:0.13, G:0.17, T:0.44
Consensus pattern (24 bp):
ATTTATATGTTCACGAACATGTTC
Found at i:222485 original size:22 final size:22
Alignment explanation
Indices: 222421--222485 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
222411 TTAATGAATA
*
222421 TGTTCGTTTAGCATTCGTTTAG
1 TGTTCGTTTAGTATTCGTTTAG
222443 TGTTCGTTTAGTATT-GTTTTAG
1 TGTTCGTTTAGTATTCG-TTTAG
* *
222465 TGTTCGTTTATTGTTCGTTTA
1 TGTTCGTTTAGTATTCGTTTA
222486 TATATTCAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
21 1 0.03
22 36 0.95
23 1 0.03
ACGTcount: A:0.12, C:0.09, G:0.22, T:0.57
Consensus pattern (22 bp):
TGTTCGTTTAGTATTCGTTTAG
Found at i:222486 original size:11 final size:11
Alignment explanation
Indices: 222421--222485 Score: 78
Period size: 11 Copynumber: 5.9 Consensus size: 11
222411 TTAATGAATA
222421 TGTTCGTTTAG
1 TGTTCGTTTAG
**
222432 CATTCGTTTAG
1 TGTTCGTTTAG
222443 TGTTCGTTTAG
1 TGTTCGTTTAG
*
222454 TATT-GTTTTAG
1 TGTTCG-TTTAG
*
222465 TGTTCGTTTAT
1 TGTTCGTTTAG
222476 TGTTCGTTTA
1 TGTTCGTTTA
222486 TATATTCAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
10 1 0.02
11 43 0.96
12 1 0.02
ACGTcount: A:0.12, C:0.09, G:0.22, T:0.57
Consensus pattern (11 bp):
TGTTCGTTTAG
Found at i:226347 original size:14 final size:13
Alignment explanation
Indices: 226262--226350 Score: 80
Period size: 14 Copynumber: 7.0 Consensus size: 13
226252 TTCATTTTAC
226262 TTAAATTATTATTA
1 TTAAA-TATTATTA
**
226276 TTAAA-ATTAAAA
1 TTAAATATTATTA
*
226288 TT-ATTATTATTA
1 TTAAATATTATTA
226300 -TAAATATTATTA
1 TTAAATATTATTA
226312 TT--ATATTATTA
1 TTAAATATTATTA
*
226323 TTATTATATTATTA
1 TTA-AATATTATTA
226337 TTAAATAATTATTA
1 TTAAAT-ATTATTA
226351 CAAACCCAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
11 13 0.21
12 21 0.34
13 3 0.05
14 24 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TTAAATATTATTA
Found at i:226350 original size:3 final size:3
Alignment explanation
Indices: 226266--226339 Score: 80
Period size: 3 Copynumber: 25.3 Consensus size: 3
226256 TTTTACTTAA
** ** * *
226266 ATT ATT ATT ATT AAA ATT AAA ATT ATT ATT ATT ATA AAT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
226314 A-T ATT ATT ATT ATT A-T ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
226340 AATAATTATT
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
2 4 0.07
3 53 0.93
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:227063 original size:13 final size:13
Alignment explanation
Indices: 227045--227073 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
227035 ACCACCGTTA
227045 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
227058 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
227071 CGG
1 CGG
227074 AGTACGGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.31, G:0.62, T:0.07
Consensus pattern (13 bp):
CGGTGGCCGGCGG
Found at i:227663 original size:19 final size:19
Alignment explanation
Indices: 227625--227662 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
227615 TATAATTTAG
227625 TCATTTATTTTATATGTTT
1 TCATTTATTTTATATGTTT
227644 TCATTTATTTTAT-TGTTT
1 TCATTTATTTTATATGTTT
227662 T
1 T
227663 TAAAATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.71
Consensus pattern (19 bp):
TCATTTATTTTATATGTTT
Found at i:227778 original size:13 final size:13
Alignment explanation
Indices: 227760--227798 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
227750 GTAATTAAAT
227760 TTTTAAATATTTA
1 TTTTAAATATTTA
*
227773 TTTTAAATGAATTA
1 TTTTAAAT-ATTTA
227787 TTTT-AATATTTA
1 TTTTAAATATTTA
227799 GCTTTCAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 4 0.17
13 11 0.48
14 8 0.35
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (13 bp):
TTTTAAATATTTA
Found at i:228444 original size:20 final size:21
Alignment explanation
Indices: 228421--228472 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
228411 AGAAATTAAA
228421 AATTCATTTATTT-AATTTTT
1 AATTCATTTATTTAAATTTTT
* *
228441 AATTCTTTTCTTTCAAATTTTT
1 AATTCATTTATTT-AAATTTTT
228463 -ATT-ATTTATT
1 AATTCATTTATT
228473 ATTTTTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 16 0.62
21 3 0.12
22 7 0.27
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (21 bp):
AATTCATTTATTTAAATTTTT
Found at i:228478 original size:16 final size:16
Alignment explanation
Indices: 228457--228505 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 16
228447 TTTCTTTCAA
228457 ATTTTTATTATTTATT
1 ATTTTTATTATTTATT
*
228473 ATTTTTA-TA-TTAAT
1 ATTTTTATTATTTATT
*
228487 ATTGTT-TTATTTATCT
1 ATTTTTATTATTTAT-T
228503 ATT
1 ATT
228506 AGAGGTTTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
14 11 0.41
15 5 0.19
16 11 0.41
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (16 bp):
ATTTTTATTATTTATT
Found at i:235569 original size:83 final size:83
Alignment explanation
Indices: 235430--235684 Score: 483
Period size: 83 Copynumber: 3.1 Consensus size: 83
235420 GTAATTGGGA
235430 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGAA
1 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGAA
235495 TTTAGAAGATGAATGTGC
66 TTTAGAAGATGAATGTGC
235513 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGAA
1 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGAA
235578 TTTAGAAGATGAATGTGC
66 TTTAGAAGATGAATGTGC
*
235596 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTATACAGAACCAATCATTGAA
1 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGAA
* *
235661 TTTAAAAGATGAATTTGC
66 TTTAGAAGATGAATGTGC
235679 TCATAG
1 TCATAG
235685 GAGAAATAAG
Statistics
Matches: 169, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 169 1.00
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (83 bp):
TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGAA
TTTAGAAGATGAATGTGC
Found at i:237047 original size:75 final size:75
Alignment explanation
Indices: 236887--237056 Score: 182
Period size: 75 Copynumber: 2.3 Consensus size: 75
236877 AACAAGAAGC
* ** * *
236887 AAATATTGGGGCATGCTGAAAACCTTTTTTCAAACAGAATCAAAAATGTTGAAATATTCTGAATA
1 AAATGTTGGGGCATGCTGAAAACCTCATTTCAAACAGAATCAAAAATGTTGAAACATTCTGAACA
236952 TTTATCAGCA
66 TTTATCAGCA
* * * * ** *
236962 AAATGCTGGGGCATGCTGAAAACC-CATTTCAATCAGAATCAGAACTGTTGATGCATTTTGAACA
1 AAATGTTGGGGCATGCTGAAAACCTCATTTCAAACAGAATCAAAAATGTTGAAACATTCTGAACA
*
237026 CTTGTATTAGC-
66 -TT-TATCAGCA
*
237037 CAATGTTGGGGCATGCTGAA
1 AAATGTTGGGGCATGCTGAA
237057 GGCCCACAAT
Statistics
Matches: 78, Mismatches: 15, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
74 30 0.38
75 42 0.54
76 6 0.08
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (75 bp):
AAATGTTGGGGCATGCTGAAAACCTCATTTCAAACAGAATCAAAAATGTTGAAACATTCTGAACA
TTTATCAGCA
Found at i:238459 original size:22 final size:22
Alignment explanation
Indices: 238391--238470 Score: 70
Period size: 22 Copynumber: 3.6 Consensus size: 22
238381 TACATCTGCA
* *
238391 CTTTTTAAAGATAATAGATTCT
1 CTTTTCAAAGATGATAGATTCT
** * * * *
238413 CACTTCAGAGATGACAAATTTT
1 CTTTTCAAAGATGATAGATTCT
*
238435 CTTTTTAAAGATGATAGATTCT
1 CTTTTCAAAGATGATAGATTCT
*
238457 CTTTTCAAAAATGA
1 CTTTTCAAAGATGA
238471 AAGCTTTATG
Statistics
Matches: 41, Mismatches: 17, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.40
Consensus pattern (22 bp):
CTTTTCAAAGATGATAGATTCT
Found at i:239286 original size:76 final size:76
Alignment explanation
Indices: 239139--239701 Score: 1029
Period size: 76 Copynumber: 7.4 Consensus size: 76
239129 CTATTTCTCA
*
239139 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCC--AAAAAGCCTTCGGGAGCTTTTTGATGTTTTC
239204 AAAGCCTTCGGGT
64 AAAGCCTTCGGGT
* *
239217 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGTAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
239282 AGCCTTCGGGT
66 AGCCTTCGGGT
239293 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
239358 AGCCTTCGGGT
66 AGCCTTCGGGT
*
239369 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGTAGC-TTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
239433 AGCCTTCGGGT
66 AGCCTTCGGGT
239444 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
239509 AGCCTTCGGGT
66 AGCCTTCGGGT
*
239520 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGTAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
239585 AGCCTTCGGGT
66 AGCCTTCGGGT
239596 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
239661 ATCCTTCGGGT
66 AGCCTTCGGGT
* *
239672 CATCTGTAAGTCCTGCAGTGCATGATGTTT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTT
239702 TTAAGACCTC
Statistics
Matches: 474, Mismatches: 10, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
75 74 0.16
76 368 0.78
78 32 0.07
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:239537 original size:227 final size:228
Alignment explanation
Indices: 239139--239701 Score: 1038
Period size: 227 Copynumber: 2.5 Consensus size: 228
239129 CTATTTCTCA
*
239139 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCC--AAAAAGCCTTCGGGAGCTTTTTGATGTTTTC
*
239204 AAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGTAGCTTT
64 AAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTT
239269 TTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCT
129 TTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCT
239334 TCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
194 TCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
*
239369 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGTAGC-TTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
239433 AGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
239498 GATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
131 GATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
*
239563 GGTAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
196 GGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
239596 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
239661 ATCCTTCGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTT
66 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTT
239702 TTAAGACCTC
Statistics
Matches: 323, Mismatches: 9, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
227 223 0.69
228 69 0.21
230 31 0.10
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.35
Consensus pattern (228 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
GATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
GGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
Found at i:239916 original size:21 final size:21
Alignment explanation
Indices: 239876--239933 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
239866 TAAAATTAAA
*
239876 ATTATTATTATTA-TAAATATT
1 ATTATTA-TATTATTATATATT
239897 ATTATTATATTATTATATATT
1 ATTATTATATTATTATATATT
* *
239918 ATTATTAAATAATTAT
1 ATTATTATATTATTAT
239934 TACAAACCCA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 5 0.15
21 28 0.85
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTATTATATTATTATATATT
Found at i:239935 original size:3 final size:3
Alignment explanation
Indices: 239855--239924 Score: 70
Period size: 3 Copynumber: 23.3 Consensus size: 3
239845 TTTTACTTAA
** ** * *
239855 ATT ATT ATT ATT AAA ATT AAA ATT ATT ATT ATT ATA AAT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
239903 A-T ATT ATT ATAT ATT ATT ATT A
1 ATT ATT ATT AT-T ATT ATT ATT A
239925 AATAATTATT
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
2 2 0.04
3 48 0.91
4 3 0.06
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (3 bp):
ATT
Found at i:240642 original size:13 final size:13
Alignment explanation
Indices: 240624--240652 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
240614 ACCACCGTTA
240624 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
240637 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
240650 CGG
1 CGG
240653 AGTACGGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.31, G:0.62, T:0.07
Consensus pattern (13 bp):
CGGTGGCCGGCGG
Found at i:241242 original size:18 final size:19
Alignment explanation
Indices: 241205--241241 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
241195 TATAATTTAG
241205 TCATTTATTTTATATGTTT
1 TCATTTATTTTATATGTTT
241224 TCATTTA-TTTAT-TGTTT
1 TCATTTATTTTATATGTTT
241241 T
1 T
241242 TAAAATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
18 5 0.28
19 7 0.39
ACGTcount: A:0.19, C:0.05, G:0.05, T:0.70
Consensus pattern (19 bp):
TCATTTATTTTATATGTTT
Found at i:241359 original size:13 final size:13
Alignment explanation
Indices: 241341--241379 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
241331 GTAATTAAAT
241341 TTTTAAATATTTA
1 TTTTAAATATTTA
*
241354 TTTTAAATGAATTA
1 TTTTAAAT-ATTTA
241368 TTTT-AATATTTA
1 TTTTAAATATTTA
241380 GCTTTCAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 4 0.17
13 11 0.48
14 8 0.35
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (13 bp):
TTTTAAATATTTA
Found at i:249474 original size:38 final size:38
Alignment explanation
Indices: 249432--249526 Score: 145
Period size: 38 Copynumber: 2.4 Consensus size: 38
249422 TTAGAGTAAA
* * *
249432 TATATAATATTTTAAGTTAAAATTCATTGTAGTTTCAT
1 TATATAATATTTTAAATTAAAATTCATTGCAATTTCAT
249470 TATATAATATTTTAAATTAAAATTCATTGCAATTTCAT
1 TATATAATATTTTAAATTAAAATTCATTGCAATTTCAT
249508 TATATTTAATATTTTAAAT
1 TATA--TAATATTTTAAAT
249527 CCATCGTAGT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
38 39 0.75
40 13 0.25
ACGTcount: A:0.40, C:0.05, G:0.04, T:0.51
Consensus pattern (38 bp):
TATATAATATTTTAAATTAAAATTCATTGCAATTTCAT
Done.