Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004803.1 Hibiscus syriacus cultivar Beakdansim tig00010821_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: 83633
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1293 original size:18 final size:19
Alignment explanation
Indices: 1270--1310 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
1260 CCCTCGAATC
1270 AGCTGAAA-CTGTTTTTAA
1 AGCTGAAACCTGTTTTTAA
1288 AGCTGAAACTCTGTTTTTAA
1 AGCTGAAAC-CTGTTTTTAA
1308 AGC
1 AGC
1311 AAAAAAACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 8 0.38
20 13 0.62
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.37
Consensus pattern (19 bp):
AGCTGAAACCTGTTTTTAA
Found at i:4386 original size:13 final size:13
Alignment explanation
Indices: 4368--4431 Score: 119
Period size: 13 Copynumber: 4.9 Consensus size: 13
4358 CCGGTCCAAC
4368 TGAGTCAACTCAT
1 TGAGTCAACTCAT
4381 TGAGTCAACTCAT
1 TGAGTCAACTCAT
4394 TGAGTCAACTCAT
1 TGAGTCAACTCAT
*
4407 TGAGTCAACTCGT
1 TGAGTCAACTCAT
4420 TGAGTCAACTCA
1 TGAGTCAACTCA
4432 AACAAAGTCT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 49 1.00
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (13 bp):
TGAGTCAACTCAT
Found at i:5240 original size:28 final size:28
Alignment explanation
Indices: 5208--5275 Score: 127
Period size: 28 Copynumber: 2.4 Consensus size: 28
5198 TTGATTAGTT
5208 GGTAATAATTTGTGATCGAAATTTAAAA
1 GGTAATAATTTGTGATCGAAATTTAAAA
5236 GGTAATAATTTGTGATCGAAATTTAAAA
1 GGTAATAATTTGTGATCGAAATTTAAAA
*
5264 GGTATTAATTTG
1 GGTAATAATTTG
5276 GTCAATAATC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.40, C:0.03, G:0.19, T:0.38
Consensus pattern (28 bp):
GGTAATAATTTGTGATCGAAATTTAAAA
Found at i:7166 original size:20 final size:20
Alignment explanation
Indices: 7141--7201 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 20
7131 AAGTAGTTAT
7141 GATGAAGAAGATGATTCTAG
1 GATGAAGAAGATGATTCTAG
* *
7161 GATG-A-AAG-T-AGT-TAT
1 GATGAAGAAGATGATTCTAG
7176 GATGAAGAAGATGATTCTAG
1 GATGAAGAAGATGATTCTAG
7196 GATGAA
1 GATGAA
7202 AGTAGTTCCG
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
15 6 0.19
16 3 0.09
17 4 0.12
18 4 0.12
19 3 0.09
20 12 0.38
ACGTcount: A:0.41, C:0.03, G:0.30, T:0.26
Consensus pattern (20 bp):
GATGAAGAAGATGATTCTAG
Found at i:7166 original size:35 final size:35
Alignment explanation
Indices: 7115--7270 Score: 237
Period size: 35 Copynumber: 4.5 Consensus size: 35
7105 GACGATGACT
7115 ATGATTCTGAGGATGAAAGTAGTTATGATGAAGAAG
1 ATGATTCT-AGGATGAAAGTAGTTATGATGAAGAAG
7151 ATGATTCTAGGATGAAAGTAGTTATGATGAAGAAG
1 ATGATTCTAGGATGAAAGTAGTTATGATGAAGAAG
**
7186 ATGATTCTAGGATGAAAGTAGTTCCGAT---GAAG
1 ATGATTCTAGGATGAAAGTAGTTATGATGAAGAAG
*
7218 ATGATTCTTAGGATGAAAGTAGTTCTGATGAAGAAG
1 ATGATTC-TAGGATGAAAGTAGTTATGATGAAGAAG
7254 ATGATTCTGAGGATGAA
1 ATGATTCT-AGGATGAA
7271 GATGAGTCTG
Statistics
Matches: 112, Mismatches: 3, Indels: 10
0.90 0.02 0.08
Matches are distributed among these distances:
32 11 0.10
33 20 0.18
35 54 0.48
36 27 0.24
ACGTcount: A:0.37, C:0.05, G:0.29, T:0.29
Consensus pattern (35 bp):
ATGATTCTAGGATGAAAGTAGTTATGATGAAGAAG
Found at i:7234 original size:18 final size:18
Alignment explanation
Indices: 7211--7281 Score: 74
Period size: 18 Copynumber: 3.9 Consensus size: 18
7201 AAGTAGTTCC
*
7211 GATGAAGATGATTCTTAG
1 GATGAAGATGATTCTGAG
*
7229 GATGAA-A-GTAGTTCTGAT
1 GATGAAGATG-A-TTCTGAG
*
7247 GAAGAAGATGATTCTGAG
1 GATGAAGATGATTCTGAG
*
7265 GATGAAGATGAGTCTGA
1 GATGAAGATGATTCTGA
7282 TGAGGTTTCT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
16 1 0.02
17 2 0.05
18 37 0.86
19 2 0.05
20 1 0.02
ACGTcount: A:0.35, C:0.06, G:0.31, T:0.28
Consensus pattern (18 bp):
GATGAAGATGATTCTGAG
Found at i:8459 original size:18 final size:18
Alignment explanation
Indices: 8436--8471 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
8426 TATTATCTTT
8436 GCTCATTATTTTCTATTA
1 GCTCATTATTTTCTATTA
8454 GCTCATTATTTTCTATTA
1 GCTCATTATTTTCTATTA
8472 TTTGGTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.17, G:0.06, T:0.56
Consensus pattern (18 bp):
GCTCATTATTTTCTATTA
Found at i:11471 original size:28 final size:28
Alignment explanation
Indices: 11427--11483 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
11417 TCGTCGTTGA
*
11427 TTTCAAGCACTAGCTCGACAACATAATG
1 TTTCAAACACTAGCTCGACAACATAATG
*
11455 TTTCAAACACT-GACTCGACGACATAATG
1 TTTCAAACACTAG-CTCGACAACATAATG
11483 T
1 T
11484 AAACGAAGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 1 0.04
28 25 0.96
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.26
Consensus pattern (28 bp):
TTTCAAACACTAGCTCGACAACATAATG
Found at i:12354 original size:31 final size:31
Alignment explanation
Indices: 12301--12360 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
12291 ACGTTGTTGA
* * *
12301 TGATGTGATATATGTCATATCATAATTTTAG
1 TGATGTGATACATGACACATCATAATTTTAG
* *
12332 TGATGTGCTACATGACACATCATTATTTT
1 TGATGTGATACATGACACATCATAATTTT
12361 TTTTTGGTGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.43
Consensus pattern (31 bp):
TGATGTGATACATGACACATCATAATTTTAG
Found at i:20557 original size:19 final size:20
Alignment explanation
Indices: 20521--20560 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
20511 CACATTAACC
**
20521 TATTAATAATTAGTCAAAAA
1 TATTAATAATTAACCAAAAA
20541 TATT-ATAATTAACCAAAAA
1 TATTAATAATTAACCAAAAA
20560 T
1 T
20561 TAAAAAGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.35
Consensus pattern (20 bp):
TATTAATAATTAACCAAAAA
Found at i:22225 original size:21 final size:21
Alignment explanation
Indices: 22200--22240 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
22190 AAATGTTAAA
* *
22200 AAATATTAATGTTTTAGGTAT
1 AAATAATAATGTTTAAGGTAT
22221 AAATAATAATGTTTAAGGTA
1 AAATAATAATGTTTAAGGTA
22241 ACTTTTTACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (21 bp):
AAATAATAATGTTTAAGGTAT
Found at i:22465 original size:19 final size:20
Alignment explanation
Indices: 22441--22481 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
22431 TATTTCTAGT
*
22441 TAATGTTAGA-ATAGTTAAA
1 TAATGTTACACATAGTTAAA
*
22460 TAATGTTACACATATTTAAA
1 TAATGTTACACATAGTTAAA
22480 TA
1 TA
22482 GTACTTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.39
Consensus pattern (20 bp):
TAATGTTACACATAGTTAAA
Found at i:30508 original size:29 final size:29
Alignment explanation
Indices: 30458--30537 Score: 126
Period size: 29 Copynumber: 2.8 Consensus size: 29
30448 AGGAATAGAG
* *
30458 AGGTCGCCATGCAG-CCTAGGCGACCTTGT
1 AGGTCGCCATGTAGTCC-CGGCGACCTTGT
30487 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
30516 AGGTCGCCATGTAGTCCCGGCG
1 AGGTCGCCATGTAGTCCCGGCG
30538 CCATTCCCAT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
29 46 0.96
30 2 0.04
ACGTcount: A:0.15, C:0.31, G:0.33, T:0.21
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:30754 original size:25 final size:25
Alignment explanation
Indices: 30724--30775 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
30714 TGTACAATTA
*
30724 TTGGTGAAATAATTGAGGCAGCCGG
1 TTGGTGAAATAATTGAGGCAGACGG
30749 TTGGTGAAATAATTGAGGCAGACGG
1 TTGGTGAAATAATTGAGGCAGACGG
30774 TT
1 TT
30776 ATAAAAGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.29, C:0.10, G:0.35, T:0.27
Consensus pattern (25 bp):
TTGGTGAAATAATTGAGGCAGACGG
Found at i:30816 original size:23 final size:23
Alignment explanation
Indices: 30788--30833 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
30778 AAAAGAAAGA
30788 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
30811 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
30834 CCGAGAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.04, G:0.39, T:0.09
Consensus pattern (23 bp):
AAGAAAGGGAGAAGAGATTGCAG
Found at i:30848 original size:25 final size:23
Alignment explanation
Indices: 30788--30848 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
30778 AAAAGAAAGA
**
30788 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
**
30811 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
*
30834 CCGAGAAAGAAAGAA
1 --AAGAAAGAAAGAA
30849 AGGGAGAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 23 0.70
25 10 0.30
ACGTcount: A:0.51, C:0.07, G:0.36, T:0.07
Consensus pattern (23 bp):
AAGAAAGAAAGAAGAGATTGCAG
Found at i:30862 original size:21 final size:21
Alignment explanation
Indices: 30838--30890 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
30828 TTGCAGCCGA
30838 GAAAGAAAGAAAGGGAGAAAG
1 GAAAGAAAGAAAGGGAGAAAG
30859 GAAAGAAAGAAAGGGAGAAAG
1 GAAAGAAAGAAAGGGAGAAAG
*
30880 GAAAGTAAGAA
1 GAAAGAAAGAA
30891 GAAGAAAGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.62, C:0.00, G:0.36, T:0.02
Consensus pattern (21 bp):
GAAAGAAAGAAAGGGAGAAAG
Found at i:30884 original size:17 final size:16
Alignment explanation
Indices: 30836--30867 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
30826 GATTGCAGCC
30836 GAGAAAGAAAGAAAGG
1 GAGAAAGAAAGAAAGG
30852 GAGAAAGGAAAGAAAG
1 GAGAAA-GAAAGAAAG
30868 AAAGGGAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (16 bp):
GAGAAAGAAAGAAAGG
Found at i:31156 original size:45 final size:45
Alignment explanation
Indices: 31053--31184 Score: 134
Period size: 45 Copynumber: 3.0 Consensus size: 45
31043 TACATAAATT
*
31053 AAAAATTATTTAATTAGTATATG-TTTG---ATAGTTA--TATAGTTA
1 AAAAATTATTTAATTAGT-T-TGTTTTGTTAATAGTTAGTTATA-TAA
*
31095 AAAAA-TAATTAATTAGTTTGTTTTGTTAATAGTTAGTTATATAA
1 AAAAATTATTTAATTAGTTTGTTTTGTTAATAGTTAGTTATATAA
*
31139 AAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAATTATTTAATTAGTTTGT-TTTGTT-AATAGTT-AGTTATAT
31185 TTGTTTGTTG
Statistics
Matches: 76, Mismatches: 4, Indels: 14
0.81 0.04 0.15
Matches are distributed among these distances:
39 2 0.03
40 5 0.07
41 11 0.14
42 5 0.07
43 7 0.09
44 7 0.09
45 19 0.25
46 5 0.07
47 7 0.09
48 8 0.11
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (45 bp):
AAAAATTATTTAATTAGTTTGTTTTGTTAATAGTTAGTTATATAA
Found at i:32644 original size:15 final size:15
Alignment explanation
Indices: 32600--32649 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 15
32590 ATAAACCTAA
*
32600 TAATGATTTGATAAT
1 TAATGATTTGATATT
*
32615 TAAT-A-TT-A-ATC
1 TAATGATTTGATATT
32626 TAATGATTTGATATT
1 TAATGATTTGATATT
32641 TAATGATTT
1 TAATGATTT
32650 AATAATAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
11 5 0.18
12 2 0.07
13 4 0.14
14 2 0.07
15 15 0.54
ACGTcount: A:0.38, C:0.02, G:0.10, T:0.50
Consensus pattern (15 bp):
TAATGATTTGATATT
Found at i:32655 original size:26 final size:24
Alignment explanation
Indices: 32597--32655 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 24
32587 CTAATAAACC
32597 TAATAATGATTTGATAATTAATAT
1 TAATAATGATTTGATAATTAATAT
*
32621 TAATCTAATGATTTGATATTTAATGATT
1 TAA--TAATGATTTGATAATTAAT-A-T
32649 TAATAAT
1 TAATAAT
32656 AATATGATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
24 3 0.10
26 22 0.73
27 1 0.03
28 4 0.13
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.47
Consensus pattern (24 bp):
TAATAATGATTTGATAATTAATAT
Found at i:33430 original size:40 final size:46
Alignment explanation
Indices: 33386--33485 Score: 115
Period size: 40 Copynumber: 2.3 Consensus size: 46
33376 GTTTAAAGAC
*
33386 ACTAACAAATTAATTAA-T-A-TTTTTATAT-T-TA-ATAACTTAA
1 ACTAACAAACTAATTAACTAATTTTTTATATATATATATAACTTAA
*
33426 ACTAAGAAACTAATTAACTAATTTTTTATATATAATATATAACTTAA
1 ACTAACAAACTAATTAACTAATTTTTTATATAT-ATATATAACTTAA
*
33473 ACTAA-TAACTAAT
1 ACTAACAAACTAAT
33486 ATAATATAAC
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
40 15 0.30
41 1 0.02
42 1 0.02
43 9 0.18
44 1 0.02
46 9 0.18
47 14 0.28
ACGTcount: A:0.49, C:0.09, G:0.01, T:0.41
Consensus pattern (46 bp):
ACTAACAAACTAATTAACTAATTTTTTATATATATATATAACTTAA
Found at i:33477 original size:47 final size:43
Alignment explanation
Indices: 33393--33485 Score: 116
Period size: 47 Copynumber: 2.1 Consensus size: 43
33383 GACACTAACA
*
33393 AATTAATTAATATTTTTATATTTAATAACTTAAACTAAGAAACT
1 AATTAACTAATATTTTTATATTTAATAACTTAAACTAA-AAACT
*
33437 AATTAACTAAT-TTTTTATATATAATATATAACTTAAACTAATAACT
1 AATTAACTAATATTTTTATAT-T--TA-ATAACTTAAACTAAAAACT
33483 AAT
1 AAT
33486 ATAATATAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
43 9 0.21
44 11 0.26
46 9 0.21
47 14 0.33
ACGTcount: A:0.48, C:0.08, G:0.01, T:0.43
Consensus pattern (43 bp):
AATTAACTAATATTTTTATATTTAATAACTTAAACTAAAAACT
Found at i:33498 original size:27 final size:28
Alignment explanation
Indices: 33462--33514 Score: 90
Period size: 27 Copynumber: 1.9 Consensus size: 28
33452 TATATATAAT
*
33462 ATATAACTTAAACTAA-TAACTAATATA
1 ATATAACTTAAACTAACAAACTAATATA
33489 ATATAACTTAAACTAACAAACTAATA
1 ATATAACTTAAACTAACAAACTAATA
33515 ATTTATACTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 16 0.67
28 8 0.33
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (28 bp):
ATATAACTTAAACTAACAAACTAATATA
Found at i:33515 original size:21 final size:21
Alignment explanation
Indices: 33491--33539 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
33481 CTAATATAAT
33491 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
33512 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
33533 ATTAACT
1 A-TAACT
33540 AGATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:34027 original size:15 final size:15
Alignment explanation
Indices: 34007--34070 Score: 74
Period size: 15 Copynumber: 4.1 Consensus size: 15
33997 GCATCCCCTC
34007 CCCCATGCATTCCCA
1 CCCCATGCATTCCCA
*
34022 CCCCATGCATTCTCA
1 CCCCATGCATTCCCA
* *
34037 CGTCCCATGCATCCCCTC
1 C--CCCATGCATTCCC-A
34055 CCCCATGCATTCCCA
1 CCCCATGCATTCCCA
34070 C
1 C
34071 GTCCCATGTT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
15 16 0.40
16 12 0.30
17 11 0.28
18 1 0.03
ACGTcount: A:0.17, C:0.53, G:0.08, T:0.22
Consensus pattern (15 bp):
CCCCATGCATTCCCA
Found at i:34045 original size:17 final size:16
Alignment explanation
Indices: 33994--34078 Score: 82
Period size: 16 Copynumber: 5.2 Consensus size: 16
33984 CAATGCACAG
* * *
33994 CATGCATCCCCTCCCC
1 CATGCATTCCCACTCC
34010 CATGCATTCCCAC-CC
1 CATGCATTCCCACTCC
*
34025 CATGCATTCTCACGTCC
1 CATGCATTCCCAC-TCC
* * *
34042 CATGCATCCCCTCCCC
1 CATGCATTCCCACTCC
34058 CATGCATTCCCACGTCC
1 CATGCATTCCCAC-TCC
34075 CATG
1 CATG
34079 TTGATTGCAT
Statistics
Matches: 56, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
15 14 0.25
16 24 0.43
17 18 0.32
ACGTcount: A:0.16, C:0.52, G:0.09, T:0.22
Consensus pattern (16 bp):
CATGCATTCCCACTCC
Found at i:34063 original size:33 final size:32
Alignment explanation
Indices: 34008--34078 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 32
33998 CATCCCCTCC
* *
34008 CCCATGCATTCCCACCCCATGCATTCTCACGT
1 CCCATGCATCCCCACCCCATGCATTCCCACGT
*
34040 CCCATGCATCCCCTCCCCCATGCATTCCCACGT
1 CCCATGCATCCCC-ACCCCATGCATTCCCACGT
34073 CCCATG
1 CCCATG
34079 TTGATTGCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
32 12 0.34
33 23 0.66
ACGTcount: A:0.17, C:0.51, G:0.10, T:0.23
Consensus pattern (32 bp):
CCCATGCATCCCCACCCCATGCATTCCCACGT
Found at i:34160 original size:29 final size:29
Alignment explanation
Indices: 34118--34207 Score: 171
Period size: 29 Copynumber: 3.1 Consensus size: 29
34108 AAATACACAC
*
34118 AGGTCGCCCGGATGCCATGGCGACCTCTA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
34147 AGGTCGCCCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
34176 AGGTCGCCCGGATGCCATGGCGACCTCCA
1 AGGTCGCCCGGATGCCATGGCGACCTCCA
34205 AGG
1 AGG
34208 CCACTGTAGA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 60 1.00
ACGTcount: A:0.18, C:0.36, G:0.32, T:0.14
Consensus pattern (29 bp):
AGGTCGCCCGGATGCCATGGCGACCTCCA
Found at i:34962 original size:32 final size:32
Alignment explanation
Indices: 34850--34995 Score: 132
Period size: 32 Copynumber: 4.6 Consensus size: 32
34840 ATCCAAGACC
* * *
34850 CAATCGTCGTCGTCCACACTCCATTAATGTTG
1 CAATCGTCGTCCTCCTCACTCCATTGATGTTG
* * * * *
34882 CAGTCGTCCTCCTCTTCATTCCATTGATGCTG
1 CAATCGTCGTCCTCCTCACTCCATTGATGTTG
* * **
34914 CAATTGTTGTTGTCCTCACTCCATTGATGTTG
1 CAATCGTCGTCCTCCTCACTCCATTGATGTTG
* *
34946 TAATCGTCCTCCTCCTCACTCC-TTGATGTTG
1 CAATCGTCGTCCTCCTCACTCCATTGATGTTG
* * *
34977 GAATCCTCGTCCTCTTCAC
1 CAATCGTCGTCCTCCTCAC
34996 CGGACCACTC
Statistics
Matches: 87, Mismatches: 27, Indels: 1
0.76 0.23 0.01
Matches are distributed among these distances:
31 24 0.28
32 63 0.72
ACGTcount: A:0.16, C:0.32, G:0.15, T:0.37
Consensus pattern (32 bp):
CAATCGTCGTCCTCCTCACTCCATTGATGTTG
Found at i:34975 original size:31 final size:32
Alignment explanation
Indices: 34926--34995 Score: 97
Period size: 31 Copynumber: 2.2 Consensus size: 32
34916 ATTGTTGTTG
* *
34926 TCCTCACTCCATTGATGTTGTAATCGTCCTCC
1 TCCTCACTCCATTGATGTTGGAATCCTCCTCC
*
34958 TCCTCACTCC-TTGATGTTGGAATCCTCGTCC
1 TCCTCACTCCATTGATGTTGGAATCCTCCTCC
*
34989 TCTTCAC
1 TCCTCAC
34996 CGGACCACTC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 24 0.71
32 10 0.29
ACGTcount: A:0.14, C:0.36, G:0.13, T:0.37
Consensus pattern (32 bp):
TCCTCACTCCATTGATGTTGGAATCCTCCTCC
Found at i:37906 original size:37 final size:37
Alignment explanation
Indices: 37833--37907 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 37
37823 GTTGAAAAAT
* *
37833 ATTTATATATATTTTTTAAAAATTTTAAATTCATAAA
1 ATTTATATATATTTTTTAAAAATTTAAAAATCATAAA
*
37870 ATTTATATAATTTTTTTTATAAAA-TTAAAAAT-ATAAA
1 ATTTATAT-ATATTTTTTA-AAAATTTAAAAATCATAAA
37907 A
1 A
37908 ATATTTAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 14 0.42
38 15 0.45
39 4 0.12
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (37 bp):
ATTTATATATATTTTTTAAAAATTTAAAAATCATAAA
Found at i:39052 original size:3 final size:3
Alignment explanation
Indices: 39044--39157 Score: 228
Period size: 3 Copynumber: 38.0 Consensus size: 3
39034 TCTACAATTC
39044 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
39092 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
39140 TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT
39158 AATATTAGAC
Statistics
Matches: 111, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 111 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:45311 original size:15 final size:15
Alignment explanation
Indices: 45291--45327 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
45281 TGAGACATTA
*
45291 CCCGCCCCGCATCCG
1 CCCGCCCCACATCCG
45306 CCCGCCCCACATCCG
1 CCCGCCCCACATCCG
45321 CCCGCCC
1 CCCGCCC
45328 AGCTAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.08, C:0.70, G:0.16, T:0.05
Consensus pattern (15 bp):
CCCGCCCCACATCCG
Found at i:49229 original size:29 final size:29
Alignment explanation
Indices: 49194--49275 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
49184 AAACTAAATT
* *
49194 GATGTCATTACCTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
49223 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
49252 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
49276 GTTAGGTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:53998 original size:29 final size:29
Alignment explanation
Indices: 53963--54044 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
53953 AAACTAAATT
* *
53963 GATGTCATTACCTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
53992 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
54021 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
54045 GTTAGGTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:57058 original size:22 final size:22
Alignment explanation
Indices: 57033--57130 Score: 72
Period size: 22 Copynumber: 4.3 Consensus size: 22
57023 TTAAAATAAA
57033 TTATTATAAAATATGGATTGAT
1 TTATTATAAAATATGGATTGAT
* ** * *
57055 TTATTTTAAAATAATTTATTTTAAA
1 TTATTATAAAAT-ATGGA--TTGAT
* * *
57080 TAATT-TATTAGTATGGATTGAT
1 TTATTATA-AAATATGGATTGAT
*
57102 TTATTTTAAAATATGGATTGAT
1 TTATTATAAAATATGGATTGAT
57124 TTATTAT
1 TTATTAT
57131 TGTAGTTGTA
Statistics
Matches: 55, Mismatches: 16, Indels: 10
0.68 0.20 0.12
Matches are distributed among these distances:
22 36 0.65
23 5 0.09
24 5 0.09
25 9 0.16
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (22 bp):
TTATTATAAAATATGGATTGAT
Found at i:57082 original size:14 final size:15
Alignment explanation
Indices: 56971--57088 Score: 130
Period size: 15 Copynumber: 7.5 Consensus size: 15
56961 TAATAAGGTT
56971 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
56986 ATTTATTTTAACATA
1 ATTTATTTTAAAATA
*
57001 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
57016 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
57031 AATTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
57050 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
57068 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
57082 ATTTATT
1 ATTTATT
57089 AGTATGGATT
Statistics
Matches: 88, Mismatches: 8, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
14 12 0.14
15 56 0.64
16 4 0.05
17 2 0.02
18 1 0.01
19 1 0.01
20 2 0.02
21 4 0.05
22 6 0.07
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.52
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:57179 original size:32 final size:32
Alignment explanation
Indices: 57138--57637 Score: 365
Period size: 32 Copynumber: 16.7 Consensus size: 32
57128 TATTGTAGTT
57138 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
57170 GTATGGATTGATTTA-CTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
57193 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
57224 GTATGTATTGATTTATTTT--A-AA---A-TA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
57249 -T-T-GATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
57278 GTATGGATTGATTTATTTTAAATAATTTATTT
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
57310 GTATGGATTGATTTATTTTAAA-ATATTGATT-
1 GTATGGATTGATTTATTTTAAATA-ATTTATTA
** *
57341 G-ATTTATT-ATTGTAGTTGT--ATAGATTTATTTA
1 GTATGGATTGATT-TA-TTTTAAATA-ATTTA-TTA
* ** * * * *
57373 -TTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAA
1 GTATGGATTGATTTATT--T-T-AAATAATTTA--TT--A
*
57412 ATATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
57444 GTATGCATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
57467 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
* *
57498 GTATAGATTGATTTATTTTAAATAATTTATTT
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
57530 GTATGGATCGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
57553 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
* *
57584 GTATAGATTGATTTATTTTAAATAATTTATTT
1 GTATGGATTGATTTATTTTAAATAATTTATTA
57616 GTATGGATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
57638 ATATGGATTG
Statistics
Matches: 374, Mismatches: 36, Indels: 116
0.71 0.07 0.22
Matches are distributed among these distances:
22 53 0.14
23 11 0.03
24 2 0.01
25 7 0.02
26 10 0.03
28 10 0.03
29 11 0.03
30 14 0.04
31 21 0.06
32 198 0.53
33 3 0.01
34 3 0.01
36 13 0.03
37 5 0.01
38 1 0.00
39 1 0.00
40 11 0.03
ACGTcount: A:0.34, C:0.01, G:0.12, T:0.53
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:57196 original size:22 final size:22
Alignment explanation
Indices: 57171--57213 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
57161 AATTTATTAG
57171 TATGGATTGATTTACTTTAAAA
1 TATGGATTGATTTACTTTAAAA
*
57193 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTACTTTAAA
57214 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.02, G:0.14, T:0.49
Consensus pattern (22 bp):
TATGGATTGATTTACTTTAAAA
Found at i:57206 original size:54 final size:54
Alignment explanation
Indices: 57139--57654 Score: 516
Period size: 54 Copynumber: 9.3 Consensus size: 54
57129 ATTGTAGTTG
*
57139 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTACTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
57193 TATGGATTGATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
57247 TATTGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT--A-AA---A
* * * ***
57307 TTTGTATGGATTGATTTATTTT-AA-AA--TATT-G-ATTGATTTA-TTATTGTAGTTG
1 ----TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTA-AAA
* * *
57359 TATAGATTTATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
57413 TATGGATTGATTTATTTTAAATAATTTATTAGTATGCATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
57467 TATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTT-AAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* * * ** * *
57520 TA---ATTTATTT-GTATGGATCGATTTATTTTAAAATATGGATTGATTTATTTTAAATAA
1 TATGGATTGATTTATTTTAAAT-AATTTA--TT--AGTATGGATTGATTTATTTT-AA-AA
*
57577 TTTATTAGTATAGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAA
1 --TA-T-G----GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
57639 TATGGATTGATTTATT
1 TATGGATTGATTTATT
57655 ATTGTAATTG
Statistics
Matches: 383, Mismatches: 42, Indels: 74
0.77 0.08 0.15
Matches are distributed among these distances:
48 16 0.04
49 6 0.02
50 14 0.04
52 6 0.02
53 6 0.02
54 235 0.61
55 8 0.02
56 2 0.01
57 10 0.03
58 8 0.02
59 4 0.01
60 7 0.02
62 4 0.01
63 4 0.01
64 35 0.09
66 2 0.01
68 12 0.03
69 4 0.01
ACGTcount: A:0.34, C:0.01, G:0.12, T:0.53
Consensus pattern (54 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
Found at i:57283 original size:86 final size:84
Alignment explanation
Indices: 57193--57734 Score: 504
Period size: 86 Copynumber: 6.5 Consensus size: 84
57183 TACTTTAAAA
**
57193 TATGGATTGATTTATTTT-AAATAATTTATTAGTATGTATTGATTTATTTTAAAATATTGATTGA
1 TATGGATTGATTTATTTTAAAAT-ATGGATT-G-ATGTATTGATTTATTTTAAAATATTGATTGA
57257 TTTATTTTAAATAATTTATTAG
63 TTTATTTTAAATAATTTATTAG
** *
57279 TATGGATTGATTTATTTT-AAATAATTTATTTGTATGGATTGATTTATTTTAAAATATTGATTGA
1 TATGGATTGATTTATTTTAAAAT-ATGGA-TTG-ATGTATTGATTTATTTTAAAATATTGATTGA
*
57343 TTTA--TT--AT--TGTAGTT-G
63 TTTATTTTAAATAATTTA-TTAG
* * ** * *
57359 TATAGATTTATTTATTTT-AAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGA
1 TATGGATTGATTTATTTTAAAAT-ATGGATT-G-ATGTATTGATTTATTTTAAAATATTGATTGA
57423 TTTATTTTAAATAATTTATTAG
63 TTTATTTTAAATAATTTATTAG
* * * ** * * * *
57445 TATGCATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGAT
1 TATGGATTGATTTATTTTAAAATATGGATTGATGTA-TTGATTTATTTTA-AAATATTGATTGAT
*
57510 TTATTTTAAATAATTTATTTG
64 TTATTTTAAATAATTTATTAG
* * * ** * * * *
57531 TATGGATCGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGAT
1 TATGGATTGATTTATTTTAAAATATGGATTGATGTA-TTGATTTATTTTA-AAATATTGATTGAT
*
57596 TTATTTTAAATAATTTATTTG
64 TTATTTTAAATAATTTATTAG
* *
57617 TATGGATTGATTTATTTTAAAATATGGATTGATTTATT-ATTGTAATTGT---ATA--GATTGAT
1 TATGGATTGATTTATTTTAAAATATGGATTGATGTATTGATT-T-ATTTTAAAATATTGATTGAT
57676 TTATTTTAAATAATTTATTAG
64 TTATTTTAAATAATTTATTAG
* *
57697 TAAGGATTGATTTATTTTAAAATATGGATTGATTTATT
1 TATGGATTGATTTATTTTAAAATATGGATTGATGTATT
57735 TTAAATAATT
Statistics
Matches: 409, Mismatches: 32, Indels: 36
0.86 0.07 0.08
Matches are distributed among these distances:
79 2 0.00
80 129 0.32
81 2 0.00
82 6 0.01
84 8 0.02
85 15 0.04
86 241 0.59
87 6 0.01
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.53
Consensus pattern (84 bp):
TATGGATTGATTTATTTTAAAATATGGATTGATGTATTGATTTATTTTAAAATATTGATTGATTT
ATTTTAAATAATTTATTAG
Found at i:57374 original size:220 final size:220
Alignment explanation
Indices: 57068--57654 Score: 996
Period size: 220 Copynumber: 2.6 Consensus size: 220
57058 TTTTAAAATA
*
57068 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
1 ATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
* *
57133 TAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTACTTTAAAATATGG
66 TAGTTGTATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGG
* *
57198 ATTGATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAAATATTGATTGATTTATT
131 ATTGATTTATTTTAAATAATTTATTAGTATGCATTGATTTATTTTAAAATATGGATTGATTTATT
*
57263 TTAAATAATTTATTAGTATGGATTG
196 TTAAATAATTTATTAGTATAGATTG
*
57288 ATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATTGATTGATTTATTATTG
1 ATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
* *
57353 TAGTTGTATAGATTTATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGG
66 TAGTTGTATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGG
57418 ATTGATTTATTTTAAATAATTTATTAGTATGCATTGATTTATTTTAAAATATGGATTGATTTATT
131 ATTGATTTATTTTAAATAATTTATTAGTATGCATTGATTTATTTTAAAATATGGATTGATTTATT
57483 TTAAATAATTTATTAGTATAGATTG
196 TTAAATAATTTATTAGTATAGATTG
*
57508 ATTTATTTTAAATAATTTATTTGTATGGATCGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTA--TT--
* *
57573 ATAATTTA-TTAGTATAGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAA
62 AT--TGTAGTT-GTATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAA
57637 AATATGGATTGATTTATT
124 AATATGGATTGATTTATT
57655 ATTGTAATTG
Statistics
Matches: 345, Mismatches: 15, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
220 268 0.78
222 2 0.01
224 2 0.01
225 2 0.01
226 71 0.21
ACGTcount: A:0.34, C:0.01, G:0.12, T:0.53
Consensus pattern (220 bp):
ATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
TAGTTGTATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGG
ATTGATTTATTTTAAATAATTTATTAGTATGCATTGATTTATTTTAAAATATGGATTGATTTATT
TTAAATAATTTATTAGTATAGATTG
Found at i:57416 original size:22 final size:22
Alignment explanation
Indices: 57391--57433 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
57381 AATTTATTAG
57391 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
57413 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
57434 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:57470 original size:22 final size:22
Alignment explanation
Indices: 57445--57487 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
57435 AATTTATTAG
57445 TATGCATTGATTTATTTTAAAA
1 TATGCATTGATTTATTTTAAAA
*
57467 TATGGATTGATTTATTTTAAA
1 TATGCATTGATTTATTTTAAA
57488 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGCATTGATTTATTTTAAAA
Found at i:57495 original size:14 final size:14
Alignment explanation
Indices: 57476--57529 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
57466 ATATGGATTG
57476 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
57490 ATTTATTAGTATAGATTG
1 ATTTATT--T-TA-AATA
57508 ATTTATTTTAAATA
1 ATTTATTTTAAATA
57522 ATTTATTT
1 ATTTATTT
57530 GTATGGATCG
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 17 0.53
15 2 0.06
16 2 0.06
17 2 0.06
18 9 0.28
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:57556 original size:22 final size:22
Alignment explanation
Indices: 57531--57573 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
57521 AATTTATTTG
57531 TATGGATCGATTTATTTTAAAA
1 TATGGATCGATTTATTTTAAAA
*
57553 TATGGATTGATTTATTTTAAA
1 TATGGATCGATTTATTTTAAA
57574 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.02, G:0.14, T:0.49
Consensus pattern (22 bp):
TATGGATCGATTTATTTTAAAA
Found at i:57581 original size:14 final size:14
Alignment explanation
Indices: 57562--57615 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
57552 ATATGGATTG
57562 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
57576 ATTTATTAGTATAGATTG
1 ATTTATT--T-TA-AATA
57594 ATTTATTTTAAATA
1 ATTTATTTTAAATA
57608 ATTTATTT
1 ATTTATTT
57616 GTATGGATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 17 0.53
15 2 0.06
16 2 0.06
17 2 0.06
18 9 0.28
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:57615 original size:306 final size:306
Alignment explanation
Indices: 57068--57749 Score: 1051
Period size: 306 Copynumber: 2.2 Consensus size: 306
57058 TTTTAAAATA
57068 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTA--TT--
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
* * ** ** *
57129 AT--TGTAGTT-GTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTACTTTAA
66 ATAATTTA-TTAGTATGCATTGATTTATTTTAAATAATGGATTAGTATGGATTGAAATAATTTAA
* * * *
57191 AATATGGATTGATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAAATATTGATTG
130 AATATAGATTGATTTATTTTAAATAATTTATTAGTATGGATCGATTTATTTTAAAATATGGATTG
*
57256 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGA
195 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAATAATTTATTTGTATGGATTGA
* * *
57321 TTTATTTTAAAATATTGATTGATTTATTATTGTAGTTGTATAGATTT
260 TTTATTTTAAAATATGGATTGATTTATTATTGTAATTGTATAGATTG
*
57368 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
** *
57433 ATAATTTATTAGTATGCATTGATTTATTTTAAA-ATATGGATT-G-ATTTATTTTAAATAATTTA
66 ATAATTTATTAGTATGCATTGATTTATTTTAAATA-ATGGATTAGTATGGA-TTGAAATAATTTA
* * *
57495 TTAGTATAGATTGATTTATTTTAAATAATTTATTTGTATGGATCGATTTATTTTAAAATATGGAT
129 -AAATATAGATTGATTTATTTTAAATAATTTATTAGTATGGATCGATTTATTTTAAAATATGGAT
57560 TGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAATAATTTATTTGTATGGATT
193 TGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAATAATTTATTTGTATGGATT
57625 GATTTATTTTAAAATATGGATTGATTTATTATTGTAATTGTATAGATTG
258 GATTTATTTTAAAATATGGATTGATTTATTATTGTAATTGTATAGATTG
*
57674 ATTTATTTTAAATAATTTATTAGTAAGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
57739 ATAATTTATTA
66 ATAATTTATTA
57750 TTTTAGTTGT
Statistics
Matches: 348, Mismatches: 24, Indels: 14
0.90 0.06 0.04
Matches are distributed among these distances:
300 58 0.17
302 2 0.01
304 5 0.01
305 13 0.04
306 270 0.78
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.53
Consensus pattern (306 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
ATAATTTATTAGTATGCATTGATTTATTTTAAATAATGGATTAGTATGGATTGAAATAATTTAAA
ATATAGATTGATTTATTTTAAATAATTTATTAGTATGGATCGATTTATTTTAAAATATGGATTGA
TTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAATAATTTATTTGTATGGATTGAT
TTATTTTAAAATATGGATTGATTTATTATTGTAATTGTATAGATTG
Found at i:57729 original size:220 final size:214
Alignment explanation
Indices: 57068--57748 Score: 767
Period size: 220 Copynumber: 3.1 Consensus size: 214
57058 TTTTAAAATA
*
57068 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
1 ATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
* *
57133 TAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTACTTTAAAATATGG
66 TAGTTGTATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGG
* * *
57198 ATTGATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAA-ATATTGATTGATTTA-
131 ATTGATTTATTTT-AATAA--T-TTAGTA-G-ATTGATTTATTTTAAATA-ATTTATT-AATAAG
* * ** * * *
57261 -TTTTAAATAATTTATTAGTATGGATTG
188 GATTGATTTATTTTA-AAATATGGATTG
*
57288 ATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATTGATTGATTTATTATTG
1 ATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
* *
57353 TAGTTGTATAGATTTATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGG
66 TAGTTGTATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGG
* * * *
57418 ATTGATTTATTTTAAATAATTTATTAG-TATGCATTGA-TTT--AT--TTTA-AAATATGGATTG
131 ATTGATTTATTTT-AATAATTTAGTAGAT-TG-ATTTATTTTAAATAATTTATTAATAAGGATTG
57476 ATTTATTTTAAATAATTTATTAGTATAGATTG
193 ATTTATTTT-AA-AA--TA-T-G----GATTG
*
57508 ATTTATTTTAAATAATTTATTTGTATGGATCGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTA--TT--
* *
57573 ATAATTTA-TTAGTATAGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAA
62 AT--TGTAGTT-GTATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAA
* *
57637 AATATGGATTGATTTATTATT-GTAATTGTA-TAGATTGATTTATTTTAAATAATTTATTAGTAA
124 AATATGGATTGATTTATT-TTAATAATT-TAGTAGATTGATTTATTTTAAATAATTTATTAATAA
57700 GGATTGATTTATTTTAAAATATGGATTG
187 GGATTGATTTATTTTAAAATATGGATTG
57728 ATTTATTTTAAATAATTTATT
1 ATTTATTTTAAATAATTTATT
57749 ATTTTAGTTG
Statistics
Matches: 399, Mismatches: 31, Indels: 62
0.81 0.06 0.13
Matches are distributed among these distances:
209 2 0.01
211 11 0.03
212 2 0.01
213 1 0.00
214 3 0.01
215 6 0.02
216 6 0.02
217 5 0.01
218 1 0.00
220 231 0.58
222 2 0.01
224 7 0.02
225 16 0.04
226 76 0.19
227 4 0.01
228 2 0.01
229 6 0.02
230 18 0.05
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.53
Consensus pattern (214 bp):
ATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
TAGTTGTATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGG
ATTGATTTATTTTAATAATTTAGTAGATTGATTTATTTTAAATAATTTATTAATAAGGATTGATT
TATTTTAAAATATGGATTG
Found at i:57735 original size:54 final size:54
Alignment explanation
Indices: 57503--57749 Score: 243
Period size: 54 Copynumber: 4.5 Consensus size: 54
57493 TATTAGTATA
* * *
57503 GATTGATTTATTTTAAATAATTTATTTGTATGGATCGATTTATTTTAAAATATG
1 GATTGATTTATTTTAAATAATTTATTAGTAAGGATTGATTTATTTTAAAATATG
57557 GATTGATTTATTTTAAATAATTTATTAGTATA-GATTGATTTATTTT-AAATA--
1 GATTGATTTATTTTAAATAATTTATTAGTA-AGGATTGATTTATTTTAAAATATG
* * * ** * * * * ** *
57608 -ATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAATTGTATA
1 GATTGATTTATTTTAAATAATTTA--TT--AGTAAGGATTGATTTA-T-TT-TAA-AATATG
57669 GATTGATTTATTTTAAATAATTTATTAGTAAGGATTGATTTATTTTAAAATATG
1 GATTGATTTATTTTAAATAATTTATTAGTAAGGATTGATTTATTTTAAAATATG
57723 GATTGATTTATTTTAAATAATTTATTA
1 GATTGATTTATTTTAAATAATTTATTA
57750 TTTTAGTTGT
Statistics
Matches: 153, Mismatches: 26, Indels: 28
0.74 0.13 0.14
Matches are distributed among these distances:
50 16 0.10
52 2 0.01
53 5 0.03
54 85 0.56
55 4 0.03
56 4 0.03
57 2 0.01
58 15 0.10
59 2 0.01
60 2 0.01
62 16 0.10
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (54 bp):
GATTGATTTATTTTAAATAATTTATTAGTAAGGATTGATTTATTTTAAAATATG
Found at i:59513 original size:18 final size:18
Alignment explanation
Indices: 59490--59525 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
59480 ATTAAGTATG
59490 AAGTTTCAAAACTATTAA
1 AAGTTTCAAAACTATTAA
*
59508 AAGTTTCAAAACTCTTAA
1 AAGTTTCAAAACTATTAA
59526 TAAAATTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.47, C:0.14, G:0.06, T:0.33
Consensus pattern (18 bp):
AAGTTTCAAAACTATTAA
Found at i:68511 original size:17 final size:17
Alignment explanation
Indices: 68491--68538 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 17
68481 ATTAAATTAA
68491 AATATATATATATATAT
1 AATATATATATATATAT
*
68508 AATAT-T-TATATATTT
1 AATATATATATATATAT
* *
68523 AATTTAAATATATATA
1 AATATATATATATATA
68539 CTCGGCTCGA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 12 0.48
16 1 0.04
17 12 0.48
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AATATATATATATATAT
Found at i:68532 original size:38 final size:37
Alignment explanation
Indices: 68454--68538 Score: 102
Period size: 38 Copynumber: 2.2 Consensus size: 37
68444 AATAATTATT
68454 ATATATATATAATATTAATAAATTTAAATTAAATTAAA
1 ATATATATATAATATTAAT-AATTTAAATTAAATTAAA
* *
68492 ATATATATAT-ATATATAAT-ATTTATATATTTAATTTAA
1 ATATATATATAATAT-TAATAATTTA-A-ATTAAATTAAA
68530 ATATATATA
1 ATATATATA
68539 CTCGGCTCGA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
36 5 0.12
37 5 0.12
38 32 0.76
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (37 bp):
ATATATATATAATATTAATAATTTAAATTAAATTAAA
Found at i:74975 original size:33 final size:34
Alignment explanation
Indices: 74932--74999 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 34
74922 AAAATTAACA
*
74932 ATGATATTGATAT-CA-ACTTAAGATAATGTCATG
1 ATGATATTGATATACACA-TTAAGATAATATCATG
*
74965 ATGATGTTGATATATCACATTAAGATAATATCATG
1 ATGATATTGATATA-CACATTAAGATAATATCATG
75000 TTATTATTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 12 0.40
35 17 0.57
36 1 0.03
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.37
Consensus pattern (34 bp):
ATGATATTGATATACACATTAAGATAATATCATG
Found at i:78726 original size:23 final size:22
Alignment explanation
Indices: 78683--78727 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
78673 TAATTAAGGA
*
78683 ATAATTAATCACAATATAATAT
1 ATAATTAATCACAATACAATAT
78705 ATAATTTAATCACTAAT-CAATAT
1 ATAA-TTAATCAC-AATACAATAT
78728 CATATTCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 4 0.20
23 13 0.65
24 3 0.15
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (22 bp):
ATAATTAATCACAATACAATAT
Found at i:79060 original size:18 final size:17
Alignment explanation
Indices: 79024--79076 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
79014 ATTTTAGGTG
*
79024 ATAAAAAAT-ATTTTCA
1 ATAAAAAATAATTTTAA
79040 ATAAAAATATAATTTTAA
1 ATAAAAA-ATAATTTTAA
* *
79058 ATATATAATAATTTTAA
1 ATAAAAAATAATTTTAA
79075 AT
1 AT
79077 TTTTATGGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
16 7 0.22
17 14 0.44
18 11 0.34
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAAAAAATAATTTTAA
Done.