Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003294.1 Hibiscus syriacus cultivar Beakdansim tig00006927_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: 86753
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:1198 original size:21 final size:22
Alignment explanation
Indices: 1154--1198 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1144 ATATAATTTT
*
1154 TATATTTTTAATGATTAAAGAA
1 TATATTTTTAATAATTAAAGAA
1176 TATA-TTTTAATAATATAAA-AA
1 TATATTTTTAATAAT-TAAAGAA
1197 TA
1 TA
1199 AAAATCCCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (22 bp):
TATATTTTTAATAATTAAAGAA
Found at i:3901 original size:5 final size:5
Alignment explanation
Indices: 3874--4023 Score: 69
Period size: 5 Copynumber: 28.6 Consensus size: 5
3864 TTTTAAGATA
3874 ATAAT ATAA- AT-AT ATAAT AATAAT ATAAT AAATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT -ATAAT ATAAT --ATAAT ATAAT ATAAT
* * * *
3920 ATATGT ATTAT ATAAT ATAA- ATACTAT ATAGT GTAA- ATAA- ATACTAT
1 ATA-AT ATAAT ATAAT ATAAT ATA--AT ATAAT ATAAT ATAAT ATA--AT
* * * *
3967 ATAAT ATAAT GT-GT ATATT ATACCAT ATAAT ATAAT ATGTAAT ACAAT
1 ATAAT ATAAT ATAAT ATAAT ATA--AT ATAAT ATAAT A--TAAT ATAAT
4015 AATAAT ATA
1 -ATAAT ATA
4024 TGCAAAGGGT
Statistics
Matches: 112, Mismatches: 15, Indels: 36
0.69 0.09 0.22
Matches are distributed among these distances:
3 1 0.01
4 15 0.13
5 62 0.55
6 14 0.12
7 20 0.18
ACGTcount: A:0.54, C:0.03, G:0.04, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:3904 original size:22 final size:23
Alignment explanation
Indices: 3871--3949 Score: 78
Period size: 22 Copynumber: 3.5 Consensus size: 23
3861 AGGTTTTAAG
3871 ATAATA-ATATAAAT-ATATAAT
1 ATAATATATATAAATAATATAAT
3892 AATAATATA-ATAAATAATATAAT
1 -ATAATATATATAAATAATATAAT
* *
3915 ATAATATATGT--ATTATATAAT
1 ATAATATATATAAATAATATAAT
3936 ATAAATACTATATA
1 AT-AATA-TATATA
3950 GTGTAAATAA
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
21 11 0.23
22 24 0.50
23 13 0.27
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (23 bp):
ATAATATATATAAATAATATAAT
Found at i:3947 original size:16 final size:16
Alignment explanation
Indices: 3873--3976 Score: 63
Period size: 16 Copynumber: 6.4 Consensus size: 16
3863 GTTTTAAGAT
3873 AATAATATA-AATATA
1 AATAATATATAATATA
*
3888 TAATAATAATATAATAAA
1 -AATAAT-ATATAATATA
3906 TAAT-ATAATATAATATA
1 -AATAAT-ATATAATATA
** *
3923 TGTATTATATAATATA
1 AATAATATATAATATA
* * *
3939 AATACTATATAGTGTA
1 AATAATATATAATATA
3955 AATAA-ATACT-ATATA
1 AATAATATA-TAATATA
3970 ATATAAT
1 A-ATAAT
3977 GTGTATATTA
Statistics
Matches: 69, Mismatches: 13, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
15 7 0.10
16 37 0.54
17 16 0.23
18 9 0.13
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (16 bp):
AATAATATATAATATA
Found at i:3986 original size:57 final size:57
Alignment explanation
Indices: 3874--3988 Score: 137
Period size: 57 Copynumber: 2.0 Consensus size: 57
3864 TTTTAAGATA
*
3874 ATAATATAAATATATAATAATAATATAATAAATAATATAATATAATATATGTATTAT
1 ATAATATAAATATATAATAATAATATAATAAATAATATAATATAATATATATATTAT
* * * *
3931 ATAATATAAATACTAT-ATAGT-GTA-AATAAATACTATATAATATAATGTGTATATTAT
1 ATAATATAAATA-TATAATAATAATATAATAAATA--ATATAATATAATATATATATTAT
3988 A
1 A
3989 CCATATAATA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
55 8 0.16
56 2 0.04
57 37 0.74
58 3 0.06
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (57 bp):
ATAATATAAATATATAATAATAATATAATAAATAATATAATATAATATATATATTAT
Found at i:9562 original size:19 final size:20
Alignment explanation
Indices: 9538--9585 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
9528 AACAATTTTC
* *
9538 TTTTGAAAGCAAAAATG-GA
1 TTTTGAAAACAAAAATGAAA
*
9557 TTTTGAAAACCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
9577 TTTTGAAAA
1 TTTTGAAAA
9586 AGGATTTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.50, C:0.06, G:0.15, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:11505 original size:17 final size:17
Alignment explanation
Indices: 11483--11515 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
11473 GGGGAGAGGG
11483 ATCGATACCCCCTGGGA
1 ATCGATACCCCCTGGGA
11500 ATCGATACCCCCTGGG
1 ATCGATACCCCCTGGG
11516 GTTCTGGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.36, G:0.24, T:0.18
Consensus pattern (17 bp):
ATCGATACCCCCTGGGA
Found at i:13521 original size:22 final size:21
Alignment explanation
Indices: 13478--13532 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
13468 AACATTTTGA
* *
13478 ATGTTTTTGGATTATTTTACTT
1 ATGTTGTTGGA-TATTTAACTT
13500 ATGTTGTTGGATATTTGAACTT
1 ATGTTGTTGGATATTT-AACTT
*
13522 AT-TTGATGGAT
1 ATGTTGTTGGAT
13533 TATGGATGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 13 0.45
22 16 0.55
ACGTcount: A:0.22, C:0.04, G:0.20, T:0.55
Consensus pattern (21 bp):
ATGTTGTTGGATATTTAACTT
Found at i:16351 original size:37 final size:36
Alignment explanation
Indices: 16290--16361 Score: 108
Period size: 37 Copynumber: 2.0 Consensus size: 36
16280 CAATGCTAAA
**
16290 GTGTATCGATACCCCTATGAGTGTATCCATACACTG
1 GTGTATCGATACCCCTACAAGTGTATCCATACACTG
*
16326 GTGTATCGATATCCCCTGCAAGTGTATCCATACACT
1 GTGTATCGATA-CCCCTACAAGTGTATCCATACACT
16362 CATGACTGCT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 11 0.34
37 21 0.66
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (36 bp):
GTGTATCGATACCCCTACAAGTGTATCCATACACTG
Found at i:19617 original size:47 final size:40
Alignment explanation
Indices: 19521--19597 Score: 118
Period size: 41 Copynumber: 1.9 Consensus size: 40
19511 AGTTCGTTTA
* *
19521 TGTTCATTTATTTATTAAATGAACGAACATGAACAAGATT
1 TGTTCATTTATTTATTAAACGAACGAACACGAACAAGATT
*
19561 TTTTCATTTATTTAATTAAACGAACGAACACGAACAA
1 TGTTCATTTATTT-ATTAAACGAACGAACACGAACAA
19598 ATGACTCGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
40 12 0.36
41 21 0.64
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (40 bp):
TGTTCATTTATTTATTAAACGAACGAACACGAACAAGATT
Found at i:19960 original size:10 final size:10
Alignment explanation
Indices: 19942--20015 Score: 67
Period size: 10 Copynumber: 7.1 Consensus size: 10
19932 GTGTTTGTGT
19942 TGTTCGTTTA
1 TGTTCGTTTA
*
19952 TGTTTGTTTA
1 TGTTCGTTTA
**
19962 TGTTAATTTATTA
1 TGTT--CGT-TTA
*
19975 TGTTCGTTTG
1 TGTTCGTTTA
19985 TGTTCGTTTA
1 TGTTCGTTTA
* *
19995 CGTTCATTTA
1 TGTTCGTTTA
20005 TGTTCGTTTA
1 TGTTCGTTTA
20015 T
1 T
20016 TATTTAAATG
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
10 41 0.80
11 1 0.02
12 2 0.04
13 7 0.14
ACGTcount: A:0.14, C:0.08, G:0.18, T:0.61
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:19981 original size:33 final size:33
Alignment explanation
Indices: 19942--20005 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
19932 GTGTTTGTGT
* *
19942 TGTTCGTTTATGTTTGTTTATGTTAATTTATTA
1 TGTTCGTTTATGTTCGTTTACGTTAATTTATTA
* *
19975 TGTTCGTTTGTGTTCGTTTACGTTCATTTAT
1 TGTTCGTTTATGTTCGTTTACGTTAATTTAT
20006 GTTCGTTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.14, C:0.08, G:0.17, T:0.61
Consensus pattern (33 bp):
TGTTCGTTTATGTTCGTTTACGTTAATTTATTA
Found at i:23260 original size:9 final size:9
Alignment explanation
Indices: 23246--23271 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
23236 CAACAATGGT
23246 TACAGCAGA
1 TACAGCAGA
23255 TACAGCAGA
1 TACAGCAGA
23264 TACAGCAG
1 TACAGCAG
23272 CACCAGCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.42, C:0.23, G:0.23, T:0.12
Consensus pattern (9 bp):
TACAGCAGA
Found at i:25161 original size:21 final size:22
Alignment explanation
Indices: 25118--25166 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
25108 TAATTTTCAA
*
25118 ACATTATTGCACCTAATTTTTG
1 ACATTGTTGCACCTAATTTTTG
25140 ACATTGTTGCACCTAA-TTTTG
1 ACATTGTTGCACCTAATTTTTG
25161 ACATTG
1 ACATTG
25167 CAATATTAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.43
Consensus pattern (22 bp):
ACATTGTTGCACCTAATTTTTG
Found at i:29697 original size:21 final size:21
Alignment explanation
Indices: 29667--29714 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
29657 TAATTTTCAA
*
29667 ACATTATTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
29688 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
29709 ACATTG
1 ACATTG
29715 CAATATTATG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:37235 original size:3 final size:3
Alignment explanation
Indices: 37223--37270 Score: 51
Period size: 3 Copynumber: 15.3 Consensus size: 3
37213 CATAATAATA
* * *
37223 ATT ATA ATT ATT ATT AAT ATA ATAT ATT ATT ATT ATT ATTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT A-TT ATT ATT
37270 A
1 A
37271 AATATATATA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
3 32 0.86
4 5 0.14
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:37241 original size:22 final size:22
Alignment explanation
Indices: 37215--37260 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
37205 TTTTTTTTCA
37215 TAATAATAAT-TATAATTATTAT
1 TAAT-ATAATATATAATTATTAT
*
37237 TAATATAATATATTATTATTAT
1 TAATATAATATATAATTATTAT
37259 TA
1 TA
37261 TTTATTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TAATATAATATATAATTATTAT
Found at i:37274 original size:28 final size:27
Alignment explanation
Indices: 37214--37285 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 27
37204 TTTTTTTTTC
*
37214 ATAATA-ATAATTATAATTATTATTAAT
1 ATAATATAT-ATTATTATTATTATTAAT
*
37241 ATAATATATTATTATTATTATTTATTATT
1 ATAATATA-TATTATTATTA-TTATTAAT
37270 A-AATATATATATATTA
1 ATAATATATAT-TATTA
37286 CAAATTACAT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
27 9 0.23
28 21 0.54
29 9 0.23
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
ATAATATATATTATTATTATTATTAAT
Found at i:42331 original size:4 final size:4
Alignment explanation
Indices: 42322--42392 Score: 60
Period size: 4 Copynumber: 17.8 Consensus size: 4
42312 CTCATCCAAC
*
42322 AAAG AAAG AAAA AAAG AAA- AATCCAG CAAAG AAAG -AAG AAAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AA---AG -AAAG AAAG AAAG AAAG AAAG
*
42368 -AAG AAAG AAAG AAA- AAAA AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAA
42393 AAAAAATATG
Statistics
Matches: 56, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
3 11 0.20
4 40 0.71
5 2 0.04
6 1 0.02
8 2 0.04
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.01
Consensus pattern (4 bp):
AAAG
Found at i:42365 original size:11 final size:11
Alignment explanation
Indices: 42349--42391 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
42339 AAAATCCAGC
42349 AAAGAAAGAAG
1 AAAGAAAGAAG
42360 AAAGAAAGAAG
1 AAAGAAAGAAG
*
42371 AAAGAAAGAAA
1 AAAGAAAGAAG
*
42382 AAAAAAAGAA
1 AAAGAAAGAA
42392 AAAAAAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (11 bp):
AAAGAAAGAAG
Found at i:42367 original size:15 final size:15
Alignment explanation
Indices: 42349--42392 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
42339 AAAATCCAGC
42349 AAAGAAAGAAGAAAG
1 AAAGAAAGAAGAAAG
42364 AAAG-AAGAAAGAAAG
1 AAAGAAAG-AAGAAAG
* *
42379 AAAAAAAAAAGAAA
1 AAAGAAAGAAGAAA
42393 AAAAAATATG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 3 0.12
15 20 0.80
16 2 0.08
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
AAAGAAAGAAGAAAG
Found at i:42368 original size:30 final size:27
Alignment explanation
Indices: 42315--42394 Score: 85
Period size: 26 Copynumber: 3.0 Consensus size: 27
42305 TCTTATACTC
42315 ATCCAACAAAGAAAGAAAAAAAGAAAA
1 ATCCAACAAAGAAAGAAAAAAAGAAAA
* *
42342 ATCCAGCAAAGAAAG-AAGAAAGAAAGA
1 ATCCAACAAAGAAAGAAAAAAAGAAA-A
** *
42369 A-GAAAGAAAGAAA-AAAAAAAGAAAA
1 ATCCAACAAAGAAAGAAAAAAAGAAAA
42394 A
1 A
42395 AAAATATGAA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
25 2 0.05
26 26 0.59
27 16 0.36
ACGTcount: A:0.74, C:0.07, G:0.16, T:0.03
Consensus pattern (27 bp):
ATCCAACAAAGAAAGAAAAAAAGAAAA
Found at i:42392 original size:11 final size:11
Alignment explanation
Indices: 42353--42429 Score: 61
Period size: 11 Copynumber: 7.3 Consensus size: 11
42343 TCCAGCAAAG
* *
42353 AAAGAAGAAAG
1 AAAGAAAAAAA
* *
42364 AAAGAAGAAAG
1 AAAGAAAAAAA
42375 AAAGAAAAAAA
1 AAAGAAAAAAA
42386 AAAG--AAAAA
1 AAAGAAAAAAA
* **
42395 AAA-ATATGAA
1 AAAGAAAAAAA
*
42405 AAAGGAAAAAA
1 AAAGAAAAAAA
42416 AAAGAAAAAAA
1 AAAGAAAAAAA
42427 AAA
1 AAA
42430 AGAGGAAAAT
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
9 8 0.15
10 6 0.11
11 40 0.74
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.03
Consensus pattern (11 bp):
AAAGAAAAAAA
Found at i:42393 original size:7 final size:7
Alignment explanation
Indices: 42349--42432 Score: 62
Period size: 7 Copynumber: 11.7 Consensus size: 7
42339 AAAATCCAGC
42349 AAAGAAA
1 AAAGAAA
*
42356 GAAGAAA
1 AAAGAAA
*
42363 GAAAGAAG
1 -AAAGAAA
42371 AAAGAAA
1 AAAGAAA
*
42378 GAAAAAAA
1 -AAAGAAA
42386 AAAGAAA
1 AAAGAAA
42393 AAA-AAA
1 AAAGAAA
* *
42399 TATGAAA
1 AAAGAAA
*
42406 AAGGAAA
1 AAAGAAA
*
42413 AAAAAAGA
1 AAAGAA-A
*
42421 AAAAAAA
1 AAAGAAA
42428 AAAGA
1 AAAGA
42433 GGAAAATTGA
Statistics
Matches: 60, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
6 4 0.07
7 38 0.63
8 18 0.30
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (7 bp):
AAAGAAA
Found at i:42438 original size:12 final size:12
Alignment explanation
Indices: 42360--42427 Score: 50
Period size: 12 Copynumber: 5.2 Consensus size: 12
42350 AAGAAAGAAG
42360 AAAGAAAGAAGAAA
1 AAAGAAA-AA-AAA
42374 GAAAG-AAAAAAA
1 -AAAGAAAAAAAA
42386 AAAGAAAAAAAA
1 AAAGAAAAAAAA
*
42398 ATATGAAAAAGGAAA
1 A-AAGAAAAA--AAA
42413 AAA-AAAGAAAAA
1 AAAGAAA-AAAAA
42425 AAA
1 AAA
42428 AAAGAGGAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 13
0.75 0.03 0.21
Matches are distributed among these distances:
11 4 0.09
12 17 0.37
13 12 0.26
14 5 0.11
15 8 0.17
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (12 bp):
AAAGAAAAAAAA
Found at i:46042 original size:75 final size:74
Alignment explanation
Indices: 45868--46042 Score: 219
Period size: 74 Copynumber: 2.4 Consensus size: 74
45858 AGTAAGAAGT
* * * *
45868 AAATGTTGGGGCATGCTGAAAACCCTTTTCAATCAGAATCAGAAATGTTGAAATATTCTGAATAT
1 AAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAGAAATGTTGAAACATTCTGAACAT
45933 TTATCAGCA
66 TTATCAGCA
* **
45942 AAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAGAACTGTTGATGCA-TCTTGAACA
1 AAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAGAAATGTTGAAACATTC-TGAACA
*
46006 CTTGTATTAGC-
65 -TT-TATCAGCA
* *
46017 CAATGTTGGGGCATGCTGAAGGCCCA
1 AAATGTTGGGGCATGCTGAAAGCCCA
46043 CAACATCTTT
Statistics
Matches: 88, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
73 2 0.02
74 54 0.61
75 26 0.30
76 6 0.07
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.29
Consensus pattern (74 bp):
AAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAGAAATGTTGAAACATTCTGAACAT
TTATCAGCA
Found at i:47403 original size:22 final size:22
Alignment explanation
Indices: 47374--47428 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
47364 ATCTACACTC
*
47374 TTCAAAGATGATATATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
47396 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
47418 TTCAAAGATGA
1 TTCAAAGATGA
47429 AAGCTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.42
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:48254 original size:165 final size:167
Alignment explanation
Indices: 47943--48267 Score: 476
Period size: 165 Copynumber: 2.0 Consensus size: 167
47933 AAAATGAGCA
* *
47943 TTATCTTCAGAGTGGGTCGTGTTACCCAATCAACATGTTATTTCAAAAAACAGAATGAGAAAACG
1 TTATCTTCAGAGTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAACAGAATGAGAAAACG
* * ** *
48008 ATTTTCATATTTTCTCATTTTATCTTTTCTAAAATGAAATTATTGAAAAGTAAGAAAATGATTTT
66 ATTTCCATAGTTTCTCATTCAATCTTTTCTAAAATGAAATTATTGAAAAGTAAGAAAACGATTTT
* * *
48073 CTTAGTTTTTTTACTTAGTAAACTATTTCCAACAACC
131 CATAGTTTTCTTACTTAGTAAACCATTTCCAACAACC
* * ** *
48110 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTT-TGAAAA-ATAATGAGAAAACG
1 TTATCTTCAGAGTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAACAGAATGAGAAAACG
*
48173 ATTTCCATAGTTTCTCATTCAATCTTTTCTAAAAATGAAATTGTTGAAAAGTAAGAAAACGATTT
66 ATTTCCATAGTTTCTCATTCAATCTTTTCT-AAAATGAAATTATTGAAAAGTAAGAAAACGATTT
48238 TCATAG-TTTCTTACTTAGTAAACCATTTCC
130 TCATAGTTTTCTTACTTAGTAAACCATTTCC
48268 CACATCTGTA
Statistics
Matches: 141, Mismatches: 16, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
165 61 0.43
166 41 0.29
167 39 0.28
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.38
Consensus pattern (167 bp):
TTATCTTCAGAGTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAACAGAATGAGAAAACG
ATTTCCATAGTTTCTCATTCAATCTTTTCTAAAATGAAATTATTGAAAAGTAAGAAAACGATTTT
CATAGTTTTCTTACTTAGTAAACCATTTCCAACAACC
Found at i:48396 original size:76 final size:76
Alignment explanation
Indices: 48270--48913 Score: 1103
Period size: 76 Copynumber: 8.5 Consensus size: 76
48260 CCATTTCCCA
48270 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
48335 AGCCTTAGGGT
66 AGCCTTAGGGT
*
48346 CATCTGTAAGTTCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
48411 AGCCTTAGGGT
66 AGCCTTAGGGT
48422 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAG-TTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
48486 AGCCTTAGGGT
66 AGCCTTAGGGT
*
48497 CATCTGTAAGTCCTGTAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
48562 AGCCTTAGGGT
66 AGCCTTAGGGT
*
48573 TATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
48638 AGCCTTAGGGT
66 AGCCTTAGGGT
*
48649 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
48713 AGCCTTCGGGT
66 AGCCTTAGGGT
* *
48724 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTTATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
48789 AACCTTAGGGT
66 AGCCTTAGGGT
* *
48800 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC--
* *
48865 AAAAACCTTCGGGT
64 -AAAGCCTTAGGGT
* * * *
48879 CATCTATAAGCCCTTCAGTGCATGATGTTTTCAAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAA
48914 CATTTTCATC
Statistics
Matches: 545, Mismatches: 18, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
75 147 0.27
76 355 0.65
79 43 0.08
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:48545 original size:151 final size:152
Alignment explanation
Indices: 48270--48913 Score: 1103
Period size: 151 Copynumber: 4.2 Consensus size: 152
48260 CCATTTCCCA
48270 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
48335 AGCCTTAGGGTCATCTGTAAGTTCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
48400 GATGTTTTCAAAGCCTTAGGGT
131 GATGTTTTCAAAGCCTTAGGGT
48422 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAG-TTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
**
48486 AGCCTTAGGGTCATCTGTAAGTCCTGTAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
48551 GATGTTTTCAAAGCCTTAGGGT
131 GATGTTTTCAAAGCCTTAGGGT
*
48573 TATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
48638 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
*
48703 GATGTTTTC-AAGCCTTCGGGT
131 GATGTTTTCAAAGCCTTAGGGT
* *
48724 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTTATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
48789 AACCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
* *
48854 GATGTTTTCAAAAAAACCTTCGGGT
131 GATGTTTTC---AAAGCCTTAGGGT
* * * *
48879 CATCTATAAGCCCTTCAGTGCATGATGTTTTCAAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAA
48914 CATTTTCATC
Statistics
Matches: 471, Mismatches: 16, Indels: 7
0.95 0.03 0.01
Matches are distributed among these distances:
151 293 0.62
152 136 0.29
155 42 0.09
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.35
Consensus pattern (152 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
GATGTTTTCAAAGCCTTAGGGT
Found at i:48670 original size:227 final size:227
Alignment explanation
Indices: 48270--48913 Score: 1101
Period size: 227 Copynumber: 2.8 Consensus size: 227
48260 CCATTTCCCA
48270 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
48335 AGCCTTAGGGTCATCTGTAAGTTCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
*
48400 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTC
131 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTC
48465 GGGAG-TTTTTGATGTTTTCAAAGCCTTAGGGT
196 GGGAGCTTTTTGATGTTTTC-AAGCCTTAGGGT
*
48497 CATCTGTAAGTCCTGTAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
48562 AGCCTTAGGGTTATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
48627 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTC
131 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTC
*
48692 GGGAGCTTTTTGATGTTTTCAAGCCTTCGGGT
196 GGGAGCTTTTTGATGTTTTCAAGCCTTAGGGT
* *
48724 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTTATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* * *
48789 AACCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTTT
66 AGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
* * * * * *
48854 GATGTTTTCAAAAAAACCTTCGGGTCATCTATAAGCCCTTCAGTGCATGATGTTTTCAAA
131 GATGTTTTC---AAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAA
48914 CATTTTCATC
Statistics
Matches: 395, Mismatches: 18, Indels: 5
0.94 0.04 0.01
Matches are distributed among these distances:
227 339 0.86
228 14 0.04
230 42 0.11
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.35
Consensus pattern (227 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTC
GGGAGCTTTTTGATGTTTTCAAGCCTTAGGGT
Found at i:49035 original size:3 final size:3
Alignment explanation
Indices: 49029--49080 Score: 52
Period size: 3 Copynumber: 16.7 Consensus size: 3
49019 AATTTTTTTC
* *
49029 ATA ATA ATA ATA ATA ATT ATA ATTA ATA TTA AT- ATA ATA TATA ATA
1 ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA -ATA ATA
49075 TATA AT
1 -ATA AT
49081 TATTATTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
2 2 0.05
3 30 0.73
4 9 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
ATA
Found at i:49056 original size:22 final size:22
Alignment explanation
Indices: 49030--49073 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
49020 ATTTTTTTCA
49030 TAATAATAATAATAAT-TATAAT
1 TAATAATAAT-ATAATATATAAT
*
49052 TAATATTAATATAATATATAAT
1 TAATAATAATATAATATATAAT
49074 ATATAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TAATAATAATATAATATATAAT
Found at i:49111 original size:35 final size:35
Alignment explanation
Indices: 49029--49114 Score: 106
Period size: 35 Copynumber: 2.5 Consensus size: 35
49019 AATTTTTTTC
49029 ATAATA-ATAATA-ATAATTATAATTAATATTAAT
1 ATAATATATAATATATAATTATAATTAATATTAAT
* *
49062 ATAATATATAATATATAATTATTATTATTTATTAA-
1 ATAATATATAATATATAATTATAATTA-ATATTAAT
49097 ATATATATATATATATAT
1 ATA-ATATATA-ATATAT
49115 TACAAATTAC
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
33 6 0.13
34 6 0.13
35 15 0.33
36 13 0.28
37 6 0.13
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (35 bp):
ATAATATATAATATATAATTATAATTAATATTAAT
Found at i:50422 original size:3 final size:3
Alignment explanation
Indices: 50409--50457 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
50399 TTATTTGCAA
* *
50409 TAT TAT T-T TAT TAT TAT TAT TAT T-T AAT TAT TAT T-T AAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
50454 TAT T
1 TAT T
50458 TTTAGTATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 4 0.10
3 35 0.90
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:50425 original size:11 final size:11
Alignment explanation
Indices: 50416--50454 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
50406 CAATATTATT
50416 TTATTA-TT-A
1 TTATTATTTAA
50425 TTATTATTTAA
1 TTATTATTTAA
50436 TTATTATTTAA
1 TTATTATTTAA
50447 TTATTATT
1 TTATTATT
50455 ATTTTTAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 6 0.21
10 2 0.07
11 20 0.71
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TTATTATTTAA
Found at i:50428 original size:14 final size:14
Alignment explanation
Indices: 50409--50459 Score: 68
Period size: 14 Copynumber: 3.6 Consensus size: 14
50399 TTATTTGCAA
50409 TATTATTTTATTAT
1 TATTATTTTATTAT
*
50423 TATTATTATT-TAAT
1 TATTATT-TTATTAT
*
50437 TATTATTTAATTAT
1 TATTATTTTATTAT
50451 TATTATTTT
1 TATTATTTT
50460 TAGTATTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
13 1 0.03
14 28 0.90
15 2 0.06
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TATTATTTTATTAT
Found at i:50719 original size:107 final size:107
Alignment explanation
Indices: 50569--50767 Score: 280
Period size: 107 Copynumber: 1.9 Consensus size: 107
50559 TTTTAATATA
* *
50569 TATTTATTTTTTCAATATTAAGAAAAGGATTGTCTTAAAGCACCTAGAAGTCCGTTTTCTGATAT
1 TATTTATTTATTCAATATAAAGAAAAGGATTGTCTTAAAGCACCTAGAAGTCC-TTTTCTGATAT
* * *
50634 TT-TTACTAAATATCCTA-TTTTATAAATTATAATTGTTTTAAT
65 TTCTAAATAAATAT-ATATTTTTATAAATTATAATTGTTTTAAT
*
50676 TATTTATTTATT-AATATCAAAGAAAA-GAGTTGTCTTAAGGCACCTAGAAGTCCTTTTCTGATA
1 TATTTATTTATTCAATAT-AAAGAAAAGGA-TTGTCTTAAAGCACCTAGAAGTCCTTTTCTGATA
50739 TTTCTAAATAAATATATATTTTTATAAAT
64 TTTCTAAATAAATATATATTTTTATAAAT
50768 ATATTTAAAT
Statistics
Matches: 82, Mismatches: 6, Indels: 8
0.85 0.06 0.08
Matches are distributed among these distances:
106 22 0.27
107 60 0.73
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.45
Consensus pattern (107 bp):
TATTTATTTATTCAATATAAAGAAAAGGATTGTCTTAAAGCACCTAGAAGTCCTTTTCTGATATT
TCTAAATAAATATATATTTTTATAAATTATAATTGTTTTAAT
Found at i:50787 original size:107 final size:108
Alignment explanation
Indices: 50566--50787 Score: 276
Period size: 107 Copynumber: 2.1 Consensus size: 108
50556 ATATTTTAAT
* *
50566 ATATATTTATTTTTTCAATATTAAGAAAAGGATTGTCTTAAAGCACCTAGAAGTCCGTTTTCTGA
1 ATATATTTATTTATTCAATATAAAGAAAAGGATTGTCTTAAAGCACCTAGAAGTCCGTTTTCTGA
* * * ***
50631 TATTTTTACTAAATATCCTATTTTATAAATTATAATTGTTTTA
66 TATTTTAAATAAATATCATATTTTATAAATTATAATTAAATTA
*
50674 AT-TATTTATTTATT-AATATCAAAGAAAA-GAGTTGTCTTAAGGCACCTAGAAGTCC-TTTTCT
1 ATATATTTATTTATTCAATAT-AAAGAAAAGGA-TTGTCTTAAAGCACCTAGAAGTCCGTTTTCT
*
50735 GATATTTCTAAATAAATAT-ATATTTTTATAAA-TATATTTAAATTA
64 GATATTT-TAAATAAATATCATA-TTTTATAAATTATAATTAAATTA
50780 ATATATTT
1 ATATATTT
50788 TCTTAAAAAT
Statistics
Matches: 99, Mismatches: 10, Indels: 11
0.82 0.08 0.09
Matches are distributed among these distances:
106 33 0.33
107 64 0.65
108 2 0.02
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.45
Consensus pattern (108 bp):
ATATATTTATTTATTCAATATAAAGAAAAGGATTGTCTTAAAGCACCTAGAAGTCCGTTTTCTGA
TATTTTAAATAAATATCATATTTTATAAATTATAATTAAATTA
Found at i:57322 original size:16 final size:16
Alignment explanation
Indices: 57301--57337 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
57291 AGATTTCGAG
57301 TCGAGCTCAACAATAC
1 TCGAGCTCAACAATAC
* *
57317 TCGAGCTTAGCAATAC
1 TCGAGCTCAACAATAC
57333 TCGAG
1 TCGAG
57338 TTTGACTAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (16 bp):
TCGAGCTCAACAATAC
Found at i:58217 original size:13 final size:13
Alignment explanation
Indices: 58195--58248 Score: 51
Period size: 13 Copynumber: 4.4 Consensus size: 13
58185 ACCGTTGACC
*
58195 TGACCTGACCCAT
1 TGACCCGACCCAT
58208 TGACCCGACCC--
1 TGACCCGACCCAT
*
58219 -GACCTGACCCAT
1 TGACCCGACCCAT
* *
58231 TGACTCGACCCGT
1 TGACCCGACCCAT
58244 TGACC
1 TGACC
58249 GTTAACTTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
10 9 0.28
13 23 0.72
ACGTcount: A:0.20, C:0.43, G:0.19, T:0.19
Consensus pattern (13 bp):
TGACCCGACCCAT
Found at i:58222 original size:23 final size:23
Alignment explanation
Indices: 58191--58242 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
58181 CCCGACCGTT
*
58191 GACCTGACCTGACCCATTGACCC
1 GACCCGACCTGACCCATTGACCC
*
58214 GACCCGACCTGACCCATTGACTC
1 GACCCGACCTGACCCATTGACCC
58237 GACCCG
1 GACCCG
58243 TTGACCGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.21, C:0.44, G:0.19, T:0.15
Consensus pattern (23 bp):
GACCCGACCTGACCCATTGACCC
Found at i:60669 original size:24 final size:24
Alignment explanation
Indices: 60635--60719 Score: 109
Period size: 24 Copynumber: 3.6 Consensus size: 24
60625 TCCAATTTGA
* * *
60635 ATTATGGTATGATACCTGACATGG
1 ATTATGATATGATACTTGACCTGG
60659 ATTATGATATGATACTTGACCTGG
1 ATTATGATATGATACTTGACCTGG
* *
60683 ATTTTGATTTGATACTTGACCTGG
1 ATTATGATATGATACTTGACCTGG
*
60707 ATTCTGAT-TGATA
1 ATTATGATATGATA
60720 TGACCTACTT
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
23 5 0.09
24 50 0.91
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.40
Consensus pattern (24 bp):
ATTATGATATGATACTTGACCTGG
Found at i:62593 original size:14 final size:14
Alignment explanation
Indices: 62574--62603 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
62564 ATAACATAAT
*
62574 ATTATATTGTTATA
1 ATTATATTATTATA
62588 ATTATATTATTATA
1 ATTATATTATTATA
62602 AT
1 AT
62604 ACATAATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (14 bp):
ATTATATTATTATA
Found at i:62752 original size:23 final size:22
Alignment explanation
Indices: 62722--62785 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 22
62712 TATATGCTCC
62722 TTAA-AATATAATAATTTTTATT
1 TTAACAATATAAT-ATTTTTATT
*
62744 TTAACAATATAAGT-TTTAATATT
1 TTAACAATATAA-TATTT-TTATT
*
62767 TTAACAATATTATTATTTT
1 TTAACAATA-TAATATTTT
62786 AATAAATAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
22 7 0.21
23 21 0.62
24 6 0.18
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (22 bp):
TTAACAATATAATATTTTTATT
Found at i:62760 original size:20 final size:22
Alignment explanation
Indices: 62732--62776 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
62722 TTAAAATATA
62732 ATAA-TTTT-TATTTTAACAAT
1 ATAAGTTTTATATTTTAACAAT
62752 ATAAGTTTTAATATTTTAACAAT
1 ATAAGTTTT-ATATTTTAACAAT
62775 AT
1 AT
62777 TATTATTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 4 0.18
21 4 0.18
23 14 0.64
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.51
Consensus pattern (22 bp):
ATAAGTTTTATATTTTAACAAT
Found at i:62831 original size:42 final size:42
Alignment explanation
Indices: 62774--62861 Score: 135
Period size: 42 Copynumber: 2.1 Consensus size: 42
62764 ATTTTAACAA
*
62774 TATTATTATTTTAATAAATAATTAATATAGTTAATAATATAT
1 TATTATTATTTTAATAAATAATTAATATAATTAATAATATAT
* *
62816 TATTCTTATTTTAATAAATAATTAATATAATTTATAATA-AT
1 TATTATTATTTTAATAAATAATTAATATAATTAATAATATAT
62857 T-TTAT
1 TATTAT
62862 ATTAATAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
40 3 0.07
41 3 0.07
42 36 0.86
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (42 bp):
TATTATTATTTTAATAAATAATTAATATAATTAATAATATAT
Found at i:62853 original size:23 final size:22
Alignment explanation
Indices: 62781--62855 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 22
62771 CAATATTATT
62781 ATTTTAATAAATAATTAATAT-
1 ATTTTAATAAATAATTAATATA
* * * *
62802 A-GTTAAT-AATATATTATTCTT
1 ATTTTAATAAATA-ATTAATATA
62823 ATTTTAATAAATAATTAATATA
1 ATTTTAATAAATAATTAATATA
62845 ATTTATAATAA
1 ATTT-TAATAA
62856 TTTTATATTA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
19 4 0.10
20 11 0.26
21 2 0.05
22 15 0.36
23 10 0.24
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (22 bp):
ATTTTAATAAATAATTAATATA
Found at i:62875 original size:31 final size:29
Alignment explanation
Indices: 62839--62902 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 29
62829 ATAAATAATT
62839 AATAT-AATTTATAATAATTTTATATTAATAA
1 AATATAAATTT-TAA-AATTTT-TATTAATAA
*
62870 AATATAAAATTTTAAAATTTTTATTTATAA
1 AATAT-AAATTTTAAAATTTTTATTAATAA
62900 AAT
1 AAT
62903 TATAGCTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 11 0.37
31 11 0.37
32 3 0.10
33 5 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
AATATAAATTTTAAAATTTTTATTAATAA
Found at i:63322 original size:15 final size:14
Alignment explanation
Indices: 63308--63358 Score: 59
Period size: 14 Copynumber: 3.4 Consensus size: 14
63298 AATTTAAAAT
63308 TTAAAATAATTAAA
1 TTAAAATAATTAAA
63322 TTAAGAATAATTTGAAA
1 TTAA-AATAA-TT-AAA
63339 GTT-AAATAATTAAA
1 -TTAAAATAATTAAA
63353 TTAAAA
1 TTAAAA
63359 AATAAAACTT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
13 2 0.06
14 10 0.31
15 7 0.22
16 7 0.22
17 4 0.12
18 2 0.06
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (14 bp):
TTAAAATAATTAAA
Found at i:63666 original size:25 final size:26
Alignment explanation
Indices: 63627--63679 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 26
63617 GACAACCACT
*
63627 TGTCTATACATTCGGCAAGAAATATA
1 TGTCTACACATTCGGCAAGAAATATA
*
63653 TGTCTACA-ATTCGGCATGAAATATA
1 TGTCTACACATTCGGCAAGAAATATA
63678 TG
1 TG
63680 CGTCTGAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 18 0.72
26 7 0.28
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (26 bp):
TGTCTACACATTCGGCAAGAAATATA
Found at i:64520 original size:31 final size:31
Alignment explanation
Indices: 64454--64549 Score: 128
Period size: 31 Copynumber: 3.2 Consensus size: 31
64444 AGGGGTTCTA
* * *
64454 TTTTTT-ATTTTTTTAATTAGGGCTCCTA--
1 TTTTTTCATCTTTGTAATTAGGCCTCCTATT
64482 TTTTTTCATCTTTGTAATTAGGCCTCCTATT
1 TTTTTTCATCTTTGTAATTAGGCCTCCTATT
64513 TTTTTTCATCTTTGTAATTAGGCCT-CTAATT
1 TTTTTTCATCTTTGTAATTAGGCCTCCT-ATT
64544 TTTTTT
1 TTTTTT
64550 AAAACAAATT
Statistics
Matches: 61, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
28 6 0.10
29 19 0.31
30 2 0.03
31 34 0.56
ACGTcount: A:0.17, C:0.15, G:0.09, T:0.59
Consensus pattern (31 bp):
TTTTTTCATCTTTGTAATTAGGCCTCCTATT
Found at i:64671 original size:43 final size:42
Alignment explanation
Indices: 64558--64951 Score: 247
Period size: 44 Copynumber: 8.9 Consensus size: 42
64548 TTAAAACAAA
*** **
64558 TTTACCTTTATAATTGATATCCTAATTTTATTCAATCTCACCT
1 TTTACCTTTATAATTGAGGCCCTAATTTT-TTCAATCTCATTT
** * * *
64601 TTTATTTTTATAATTGAAGTCTCTAA-TTTTTCAATCTCTTTTT
1 TTTACCTTTATAATTG-AGGCCCTAATTTTTTCAATCTC-ATTT
* * **
64644 TTTACCTTTATAATTGAGGCCCATAATTTCTT-AATCCCACGT
1 TTTACCTTTATAATTGAGGCCC-TAATTTTTTCAATCTCATTT
* * *
64686 TTTAGCTTTATAATTGAGTCCCTTAAGTTTTTTCATTCTCACTTCTACCTT
1 TTTACCTTTATAATTGAGGCCC-TAA-TTTTTTCAATCTCA----T---TT
** *
64737 TTCTACCTTTACCATTGAGGCTCCTAAATTTTTTTAATCTCGA-TT
1 TT-TACCTTTATAATTGAGGC-CCT-AATTTTTTCAATCTC-ATTT
* * * * *
64782 TCTACCTTTATAACTGAGGTCCTTAATTTTTTTAATCCCACTTT
1 TTTACCTTTATAATTGAGG-CCCTAATTTTTTCAATCTCA-TTT
* * *
64826 TTTAACTTTATAATTGAGTCTCCTAAGTTTTTTCAATCTCACTT
1 TTTACCTTTATAATTGAGGC-CCTAA-TTTTTTCAATCTCATTT
* * * *
64870 TCTACCTTTATAATTGATGCTCCTAAGTTTTTCAATCTCA-AT
1 TTTACCTTTATAATTGAGGC-CCTAATTTTTTCAATCTCATTT
* *
64912 TATACCTTTATAATTGAGGCCCCTATTTTTTTCAATCTCA
1 TTTACCTTTATAATTGAGG-CCCTAATTTTTTCAATCTCA
64952 ATTTCTATAG
Statistics
Matches: 272, Mismatches: 56, Indels: 47
0.73 0.15 0.13
Matches are distributed among these distances:
42 73 0.27
43 74 0.27
44 75 0.28
45 16 0.06
51 3 0.01
52 26 0.10
53 5 0.02
ACGTcount: A:0.24, C:0.21, G:0.07, T:0.48
Consensus pattern (42 bp):
TTTACCTTTATAATTGAGGCCCTAATTTTTTCAATCTCATTT
Found at i:70279 original size:73 final size:73
Alignment explanation
Indices: 69871--70354 Score: 484
Period size: 73 Copynumber: 6.5 Consensus size: 73
69861 CAACATATCC
* *
69871 GATAGGTAGTTTAATGTAATAGGTAGTGCC-TATTTTTTTTACCGTTTACATTATTAACAACCTT
1 GATAGGTATTTTAATGTAATAGGTA--GCCATATTTTTTTTACCGTTTACATTATTAGCAACCTT
69935 CAAAAAA-CT
64 CAAAAAATCT
* * ** *
69944 GGTAGGTATTTTAATGTAATAGGTAGCACCTATTTTTTTTTTTTACATTTTACATTATTAACAAC
1 GATAGGTATTTTAATGTAATAGGTAG--CC-A--TATTTTTTTTACCGTTTACATTATTAGCAAC
70009 CTTCAAAAAAATC-
61 CTTC-AAAAAATCT
* * *
70022 GGTATGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTTTTTACCGTTTACATTATTAGCAAC
1 GATAGGTATTTTAATGTAATAGGTA--GCC-A--TATTTTTTTTACCGTTTACATTATTAGCAAC
70087 CTT-AAAAAATC-
61 CTTCAAAAAATCT
* * * * * *
70098 GTTAAGTATTTTAATGTAA-ATGTAGCGCTTATTTTATTTTACCGTTTACATTATTAGTAATCTT
1 GATAGGTATTTTAATGTAATAGGTAGC-CATATTTT-TTTTACCGTTTACATTATTAGCAACCTT
*
70162 TAAATAAA-CT
64 CAAA-AAATCT
* * *
70172 GATAGGTAGTTTAATATAATAGGTAGTGCC-TATTTTTTTTACCGTTTACATTATTAGTAACCTT
1 GATAGGTATTTTAATGTAATAGGTA--GCCATATTTTTTTTACCGTTTACATTATTAGCAACCTT
70236 CAAAAAATCT
64 CAAAAAATCT
* * *
70246 G-TAGGTAGTTTAATGTAATAGGTATCACATATTTTTTTTACCGTTTACATTATTAGCAACTTTC
1 GATAGGTATTTTAATGTAATAGGTAGC-CATATTTTTTTTACCGTTTACATTATTAGCAACCTTC
70310 AAAAAAAT-T
65 -AAAAAATCT
* *
70319 GATAGGTATTTTAATATAATAGGTAGCGCTTATTTT
1 GATAGGTATTTTAATGTAATAGGTAGC-CATATTTT
70355 ATATTTCTGG
Statistics
Matches: 356, Mismatches: 32, Indels: 45
0.82 0.07 0.10
Matches are distributed among these distances:
71 7 0.02
72 27 0.08
73 91 0.26
74 88 0.25
75 14 0.04
76 26 0.07
77 34 0.10
78 67 0.19
79 1 0.00
80 1 0.00
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (73 bp):
GATAGGTATTTTAATGTAATAGGTAGCCATATTTTTTTTACCGTTTACATTATTAGCAACCTTCA
AAAAATCT
Found at i:70295 original size:147 final size:145
Alignment explanation
Indices: 69871--70354 Score: 571
Period size: 147 Copynumber: 3.2 Consensus size: 145
69861 CAACATATCC
* * *
69871 GATAGGTAGTTTAATGTAATAGGTAGTGCCTATTTTTTTTACCGTTTACATTATTAACAACCTTC
1 GATAGGTAGTTTAATATAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTC
* **
69936 AAAAAA-CTGGTAGGTATTTTAATGTAATAGGTAGCACCTATTTTTTTTTTTTACATTTTACATT
66 AAAAAATCT-GTAGGTATTTTAATGTAATAGGTAGCA-C-A--TATTTTTTTTACCGTTTACATT
* *
70000 ATTAACAACCTTCAAAAAAAT
126 ATTAGCAA-CTTTAAAAAAAT
* * * *
70021 CGGTATGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTTTTTACCGTTTACATTATTAGCAA
1 -GATAGGTAGTTTAATATAATAGGTAGCGCCTA----TTTTTTTTACCGTTTACATTATTAGCAA
* * * *
70086 CCTT-AAAAAATC-GTTAAGTATTTTAATGTAA-ATGTAGCGCTTATTTTATTTTACCGTTTACA
61 CCTTCAAAAAATCTG-TAGGTATTTTAATGTAATAGGTAGCACATATTTT-TTTTACCGTTTACA
* *
70148 TTATTAGTAATCTTTAAATAAACT
124 TTATTAGCAA-CTTTAAA-AAAAT
* *
70172 GATAGGTAGTTTAATATAATAGGTAGTGCCTATTTTTTTTACCGTTTACATTATTAGTAACCTTC
1 GATAGGTAGTTTAATATAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTC
* *
70237 AAAAAATCTGTAGGTAGTTTAATGTAATAGGTATCACATATTTTTTTTACCGTTTACATTATTAG
66 AAAAAATCTGTAGGTATTTTAATGTAATAGGTAGCACATATTTTTTTTACCGTTTACATTATTAG
70302 CAACTTTCAAAAAAATT
131 CAACTTT-AAAAAAA-T
* *
70319 GATAGGTATTTTAATATAATAGGTAGCGCTTATTTT
1 GATAGGTAGTTTAATATAATAGGTAGCGCCTATTTT
70355 ATATTTCTGG
Statistics
Matches: 286, Mismatches: 34, Indels: 30
0.82 0.10 0.09
Matches are distributed among these distances:
146 38 0.13
147 83 0.29
148 13 0.05
149 5 0.02
150 53 0.19
151 32 0.11
152 1 0.00
153 7 0.02
154 22 0.08
155 32 0.11
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (145 bp):
GATAGGTAGTTTAATATAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTC
AAAAAATCTGTAGGTATTTTAATGTAATAGGTAGCACATATTTTTTTTACCGTTTACATTATTAG
CAACTTTAAAAAAAT
Found at i:81935 original size:22 final size:22
Alignment explanation
Indices: 81909--81969 Score: 95
Period size: 22 Copynumber: 2.8 Consensus size: 22
81899 ATAGGGCAGA
*
81909 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATTCCCCCTTGAAG
* *
81931 GGGAACCGATTCCCCTTTGAAG
1 GGGAATCGATTCCCCCTTGAAG
81953 GGGAATCGATTCCCCCT
1 GGGAATCGATTCCCCCT
81970 AGGTTCTGGT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.23, C:0.30, G:0.26, T:0.21
Consensus pattern (22 bp):
GGGAATCGATTCCCCCTTGAAG
Done.