Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005089.1 Hibiscus syriacus cultivar Beakdansim tig00011445_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: 89612
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1245 original size:18 final size:19
Alignment explanation
Indices: 1222--1263 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
1212 TTTCAGGCTT
* *
1222 AGGATGA-TCGTCGGTGGG
1 AGGATGATTCGCCAGTGGG
1240 AGGATGATTCGCCAGTGGG
1 AGGATGATTCGCCAGTGGG
1259 AGGAT
1 AGGAT
1264 AATCATTGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.21, C:0.12, G:0.45, T:0.21
Consensus pattern (19 bp):
AGGATGATTCGCCAGTGGG
Found at i:1794 original size:53 final size:53
Alignment explanation
Indices: 1714--1824 Score: 195
Period size: 53 Copynumber: 2.1 Consensus size: 53
1704 TTATTTATCA
* * *
1714 GTAATGATATCTTCCGTGACCGTTATTGAAAGATTGTGATACTCATAATCATT
1 GTAATGATATCTTCCGTGACCATTATTGAAAGATTGCGATACTCATAATCACT
1767 GTAATGATATCTTCCGTGACCATTATTGAAAGATTGCGATACTCATAATCACT
1 GTAATGATATCTTCCGTGACCATTATTGAAAGATTGCGATACTCATAATCACT
1820 GTAAT
1 GTAAT
1825 AGCGTCTGTT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (53 bp):
GTAATGATATCTTCCGTGACCATTATTGAAAGATTGCGATACTCATAATCACT
Found at i:3542 original size:3 final size:3
Alignment explanation
Indices: 3534--3574 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
3524 AAACTTTATG
3534 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
3575 TACTACTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:5040 original size:46 final size:46
Alignment explanation
Indices: 4968--5061 Score: 179
Period size: 46 Copynumber: 2.0 Consensus size: 46
4958 TGATCTTTGC
4968 GTTTTTTGGTGAGAATTCCAACTTTTTTATGTTTTTATTTTTTTCA
1 GTTTTTTGGTGAGAATTCCAACTTTTTTATGTTTTTATTTTTTTCA
*
5014 GTTTTTTGGTGAGAATTCCAATTTTTTTATGTTTTTATTTTTTTCA
1 GTTTTTTGGTGAGAATTCCAACTTTTTTATGTTTTTATTTTTTTCA
5060 GT
1 GT
5062 AACGGTTGAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.17, C:0.07, G:0.14, T:0.62
Consensus pattern (46 bp):
GTTTTTTGGTGAGAATTCCAACTTTTTTATGTTTTTATTTTTTTCA
Found at i:9956 original size:28 final size:28
Alignment explanation
Indices: 9924--9978 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
9914 TTGTCGTTAC
* *
9924 TTTCAAGCACTGCCTTGACAACATAATG
1 TTTCAAGCACTGACTCGACAACATAATG
* *
9952 TTTCAAGCATTGACTCGACGACATAAT
1 TTTCAAGCACTGACTCGACAACATAAT
9979 ATAAATTGAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.29
Consensus pattern (28 bp):
TTTCAAGCACTGACTCGACAACATAATG
Found at i:10200 original size:29 final size:30
Alignment explanation
Indices: 10167--10224 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
10157 ATGCCTCTTT
* * *
10167 TTCCAGTTTAGTGTCTAAC-GTTTATTTCA
1 TTCCAATTTAGTGCCTAACACTTTATTTCA
*
10196 TTCCAATTTGGTGCCTAACACTTTATTTC
1 TTCCAATTTAGTGCCTAACACTTTATTTC
10225 GTTACTCAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.47
Consensus pattern (30 bp):
TTCCAATTTAGTGCCTAACACTTTATTTCA
Found at i:13988 original size:201 final size:200
Alignment explanation
Indices: 13724--14130 Score: 661
Period size: 201 Copynumber: 2.0 Consensus size: 200
13714 TGAACGGTAC
* * *
13724 AAATTAGATTGAAAGGGTAGCCTTTGCCTCTACGATACCTAATCCTGATTAATCAATTAATAAAT
1 AAATTAGATTGAAAGGGTAGCCCTCGCCTCTACGATACCTAATCCAGATTAATCAATTAATAAAT
*
13789 CACATATCAATGATTATACATAAAAAATACAACACCAAAATTTGACCTAATTTGAATATTTTTTT
66 CACATACCAATGATTATACATAAAAAATACAACACCAAAATTTGACCTAATTTGAATA-TTTTTT
*
13854 AATTATAATAAATTATATTTTATATAACTCGATGTAACTTATAATATAGAAATATATATACTATT
130 AATTATAATAAATTATATTTTATATAACTCGATGTAACTTATAATATAGAAATATATATAATATT
13919 ATGCTT
195 ATGCTT
* * *
13925 AAATTAGATTGAAAGTGTAGCCCTCGCCTCTACGATATCTAATCCAGATTAATCAGTTAATAAAT
1 AAATTAGATTGAAAGGGTAGCCCTCGCCTCTACGATACCTAATCCAGATTAATCAATTAATAAAT
* * * ** * * *
13990 CATATGCCATTGATTATATTTAAGACATACAACATCAAAATTTGACCTAATTTGAATATTTTTTA
66 CACATACCAATGATTATACATAAAAAATACAACACCAAAATTTGACCTAATTTGAATATTTTTTA
14055 ATTATAATAAATTATATTTTATATAACTCGATGTAACTTATAATATAGAAATATATATAATATTA
131 ATTATAATAAATTATATTTTATATAACTCGATGTAACTTATAATATAGAAATATATATAATATTA
14120 TGCTT
196 TGCTT
14125 AAATTA
1 AAATTA
14131 AGCTATTTAT
Statistics
Matches: 190, Mismatches: 16, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
200 82 0.43
201 108 0.57
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.38
Consensus pattern (200 bp):
AAATTAGATTGAAAGGGTAGCCCTCGCCTCTACGATACCTAATCCAGATTAATCAATTAATAAAT
CACATACCAATGATTATACATAAAAAATACAACACCAAAATTTGACCTAATTTGAATATTTTTTA
ATTATAATAAATTATATTTTATATAACTCGATGTAACTTATAATATAGAAATATATATAATATTA
TGCTT
Found at i:16483 original size:41 final size:41
Alignment explanation
Indices: 16424--16505 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
16414 AACATGCAAA
* *
16424 CATTGATTGATTTGCATCTCTTTAATTTTTAGATTTTGTCT
1 CATTGATTGATTTGCATCTCTATAATTTATAGATTTTGTCT
* * **
16465 CATTGTTTGATTTTCATCTCTATGGTTTATAGATTTTGTCT
1 CATTGATTGATTTGCATCTCTATAATTTATAGATTTTGTCT
16506 TTTCTCTTGT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.18, C:0.12, G:0.13, T:0.56
Consensus pattern (41 bp):
CATTGATTGATTTGCATCTCTATAATTTATAGATTTTGTCT
Found at i:16525 original size:3 final size:3
Alignment explanation
Indices: 16517--16541 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
16507 TTCTCTTGTT
16517 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
16542 ACATGATAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:16915 original size:28 final size:30
Alignment explanation
Indices: 16857--16916 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 30
16847 GGGGCCATTT
* *
16857 TGCTCCAAAATAAAACAATGAAGGCTAAAA
1 TGCTCCAAAATAAAACAATAAAGGATAAAA
*
16887 TGCTCCAAAA-CAAA-AATAAAGGATAAAA
1 TGCTCCAAAATAAAACAATAAAGGATAAAA
16915 TG
1 TG
16917 ACCATATGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 14 0.52
29 3 0.11
30 10 0.37
ACGTcount: A:0.55, C:0.15, G:0.13, T:0.17
Consensus pattern (30 bp):
TGCTCCAAAATAAAACAATAAAGGATAAAA
Found at i:18511 original size:18 final size:18
Alignment explanation
Indices: 18455--18502 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
18445 TATGTGGCAT
*
18455 TGTTATGTCAGCGTGCGA
1 TGTTATGTAAGCGTGCGA
18473 TGTTATGTAAGCGTGCGA
1 TGTTATGTAAGCGTGCGA
18491 TGTTATGTAAGC
1 TGTTATGTAAGC
18503 TTGTCATGTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.21, C:0.12, G:0.31, T:0.35
Consensus pattern (18 bp):
TGTTATGTAAGCGTGCGA
Found at i:18688 original size:19 final size:19
Alignment explanation
Indices: 18664--18702 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
18654 ATTTTGTTGC
*
18664 ATTATGTCATAATT-TTATT
1 ATTATGCCAT-ATTATTATT
18683 ATTATGCCATATTATTATT
1 ATTATGCCATATTATTATT
18702 A
1 A
18703 GTAGTAGTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.33, C:0.08, G:0.05, T:0.54
Consensus pattern (19 bp):
ATTATGCCATATTATTATT
Found at i:30440 original size:17 final size:17
Alignment explanation
Indices: 30427--30460 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
30417 ATAATATTCG
*
30427 TATTAAATATATATTAA
1 TATTAAAGATATATTAA
30444 TATTAAAGATATATTAA
1 TATTAAAGATATATTAA
30461 CCGATCAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
TATTAAAGATATATTAA
Found at i:33445 original size:17 final size:17
Alignment explanation
Indices: 33423--33472 Score: 82
Period size: 17 Copynumber: 2.9 Consensus size: 17
33413 AGTAGAGGGA
33423 TCTTTCGGTTATTTTGG
1 TCTTTCGGTTATTTTGG
* *
33440 TCTTTCGATTATTTTGT
1 TCTTTCGGTTATTTTGG
33457 TCTTTCGGTTATTTTG
1 TCTTTCGGTTATTTTG
33473 ACATTTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.08, C:0.12, G:0.18, T:0.62
Consensus pattern (17 bp):
TCTTTCGGTTATTTTGG
Found at i:35898 original size:12 final size:13
Alignment explanation
Indices: 35872--35901 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
35862 TTTTAATTCC
35872 ATGTTTAATGTTG
1 ATGTTTAATGTTG
35885 ATGTTTAATG-TG
1 ATGTTTAATGTTG
35897 ATGTT
1 ATGTT
35902 GGTATGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.53
Consensus pattern (13 bp):
ATGTTTAATGTTG
Found at i:37612 original size:14 final size:15
Alignment explanation
Indices: 37584--37612 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
37574 ATCTATTAAT
37584 CATATTTTAGTTATG
1 CATATTTTAGTTATG
37599 CATATTTT-GTTATG
1 CATATTTTAGTTATG
37613 ATTATAGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.24, C:0.07, G:0.14, T:0.55
Consensus pattern (15 bp):
CATATTTTAGTTATG
Found at i:38088 original size:17 final size:17
Alignment explanation
Indices: 38048--38082 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
38038 GAAAGTAGAG
38048 GACATTTCGATTATTTT
1 GACATTTCGATTATTTT
38065 GACATTTCGATTATTTT
1 GACATTTCGATTATTTT
38082 G
1 G
38083 TGATTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.11, G:0.14, T:0.51
Consensus pattern (17 bp):
GACATTTCGATTATTTT
Found at i:40809 original size:28 final size:28
Alignment explanation
Indices: 40777--40834 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
40767 TTTCGTCCTA
* *
40777 TAAAACTTTACATGTTCAAATTCGCTCC
1 TAAAACTTTACAAGTTCAAATTCACTCC
* *
40805 TAAAATTTTATAAGTTCAAATTCACTCC
1 TAAAACTTTACAAGTTCAAATTCACTCC
40833 TA
1 TA
40835 CACAAATTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.36, C:0.21, G:0.05, T:0.38
Consensus pattern (28 bp):
TAAAACTTTACAAGTTCAAATTCACTCC
Found at i:41230 original size:21 final size:21
Alignment explanation
Indices: 41205--41248 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
41195 GGAAATTTTA
* *
41205 AAAAACATTAATGTTTTAGGT
1 AAAAACAATAATGTTTTAAGT
*
41226 AAAAATAATAATGTTTTAAGT
1 AAAAACAATAATGTTTTAAGT
41247 AA
1 AA
41249 TTTTTTTTAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.36
Consensus pattern (21 bp):
AAAAACAATAATGTTTTAAGT
Found at i:42542 original size:20 final size:20
Alignment explanation
Indices: 42517--42645 Score: 68
Period size: 21 Copynumber: 6.3 Consensus size: 20
42507 GATTCGTAAC
*
42517 GCGATTATGACTATCGCAAT
1 GCGATTATGACAATCGCAAT
** *
42537 GCGATT-TTCCAATTTCGCATT
1 GCGATTATGACAA--TCGCAAT
* **
42558 GCGATTTTCCCAATTCGCAAT
1 GCGATTATGACAA-TCGCAAT
* *
42579 GCGAATAAGTA-AATCGCAAT
1 GCGATTATG-ACAATCGCAAT
*
42599 GCGAATT-TAGAAAATCGCAAT
1 GCG-ATTAT-GACAATCGCAAT
*
42620 GCGA-TATTGACTATCGCAAT
1 GCGATTA-TGACAATCGCAAT
42640 GCGATT
1 GCGATT
42646 TTCCTAATTC
Statistics
Matches: 84, Mismatches: 15, Indels: 19
0.71 0.13 0.16
Matches are distributed among these distances:
19 4 0.05
20 32 0.38
21 43 0.51
22 5 0.06
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (20 bp):
GCGATTATGACAATCGCAAT
Found at i:42560 original size:21 final size:21
Alignment explanation
Indices: 42530--42705 Score: 90
Period size: 21 Copynumber: 8.5 Consensus size: 21
42520 ATTATGACTA
42530 TCGCAATGCGATTTT-CCAATT
1 TCGCAATGCGATTTTCCCAA-T
*
42551 TCGCATTGCGATTTTCCCAAT
1 TCGCAATGCGATTTTCCCAAT
* **** *
42572 TCGCAATGCGA-ATAAGTAAA
1 TCGCAATGCGATTTTCCCAAT
* *** *
42592 TCGCAATGCGAATTTAGAAAA
1 TCGCAATGCGATTTTCCCAAT
* ** *
42613 TCGCAATGCGATATTGACTA-
1 TCGCAATGCGATTTTCCCAAT
*
42633 TCGCAATGCGATTTTCCTAAT
1 TCGCAATGCGATTTTCCCAAT
* * **
42654 TCGCATTGCGA-TTTACGTAT
1 TCGCAATGCGATTTTCCCAAT
** **
42674 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGATTTTCCCAAT
42695 TCGCAATGCGA
1 TCGCAATGCGA
42706 ATACGTAAAT
Statistics
Matches: 118, Mismatches: 33, Indels: 8
0.74 0.21 0.05
Matches are distributed among these distances:
20 45 0.38
21 69 0.58
22 4 0.03
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCCAAT
Found at i:42596 original size:41 final size:41
Alignment explanation
Indices: 42551--42722 Score: 143
Period size: 41 Copynumber: 4.2 Consensus size: 41
42541 TTTTCCAATT
* *
42551 TCGCATTGCGATTTTCCCAATTCGCAATGCGAATAAGTAAA
1 TCGCAATGCGATTTTCCTAATTCGCAATGCGAATAAGTAAA
* *** * * *
42592 TCGCAATGCGAATTTAGAAAATCGCAATGCG-AT-ATTGACTA
1 TCGCAATGCGATTTTCCTAATTCGCAATGCGAATAAGT-A-AA
* * * *
42633 TCGCAATGCGATTTTCCTAATTCGCATTGCGATTTACGT-AT
1 TCGCAATGCGATTTTCCTAATTCGCAATGCGA-ATAAGTAAA
** * *
42674 TCGCGTTGCGATTTTCATAATTCGCAATGCGAATACGTAAA
1 TCGCAATGCGATTTTCCTAATTCGCAATGCGAATAAGTAAA
42715 TCGCAATG
1 TCGCAATG
42723 TGAATCTTAC
Statistics
Matches: 98, Mismatches: 27, Indels: 12
0.72 0.20 0.09
Matches are distributed among these distances:
39 2 0.02
40 8 0.08
41 86 0.88
43 1 0.01
44 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (41 bp):
TCGCAATGCGATTTTCCTAATTCGCAATGCGAATAAGTAAA
Found at i:43369 original size:33 final size:33
Alignment explanation
Indices: 43323--43419 Score: 149
Period size: 33 Copynumber: 2.9 Consensus size: 33
43313 CAAAATCGCA
**
43323 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
*
43356 TTGCGATAGTCATTTCGCGTTGTGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
*
43389 TTGCAATAGTCATTTCCGCGTTGCGATTCTC
1 TTGCGATAGTCATTT-CGCGTTGCGATTCTC
43420 ATTATCTCGT
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
33 44 0.76
34 14 0.24
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.42
Consensus pattern (33 bp):
TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
Found at i:43421 original size:20 final size:20
Alignment explanation
Indices: 43398--43444 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
43388 GTTGCAATAG
43398 TCATTTCCGCGTTGCGATTC
1 TCATTTCCGCGTTGCGATTC
* *
43418 TCATTAT-CTCGTTGCGATTT
1 TCATT-TCCGCGTTGCGATTC
43438 TCATTTC
1 TCATTTC
43445 AACCAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 1 0.04
20 21 0.91
21 1 0.04
ACGTcount: A:0.13, C:0.26, G:0.15, T:0.47
Consensus pattern (20 bp):
TCATTTCCGCGTTGCGATTC
Found at i:45723 original size:9 final size:9
Alignment explanation
Indices: 45709--45791 Score: 76
Period size: 9 Copynumber: 8.8 Consensus size: 9
45699 GGCTGCTGGA
45709 AACCGGTTT
1 AACCGGTTT
45718 AACCGGTTCT
1 AACCGGTT-T
*
45728 GACCGGTTT
1 AACCGGTTT
*
45737 GACCGGTTT
1 AACCGGTTT
*
45746 CAACCGGTTCG
1 -AACCGGTT-T
45757 AACCGGTTT
1 AACCGGTTT
* *
45766 GACCGGTCTG
1 AACCGGT-TT
45776 AACCGGTTT
1 AACCGGTTT
*
45785 GACCGGT
1 AACCGGT
45792 CAGACCCGAC
Statistics
Matches: 61, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
9 31 0.51
10 30 0.49
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.28
Consensus pattern (9 bp):
AACCGGTTT
Found at i:45734 original size:19 final size:18
Alignment explanation
Indices: 45710--45791 Score: 94
Period size: 19 Copynumber: 4.3 Consensus size: 18
45700 GCTGCTGGAA
*
45710 ACCGGTTTAACCGGTTCTG
1 ACCGGTTGAACCGGTT-TG
*
45729 ACCGGTTTG-ACCGGTTTCA
1 ACCGG-TTGAACCGGTTT-G
45748 ACCGGTTCGAACCGGTTTG
1 ACCGGTT-GAACCGGTTTG
45767 ACCGGTCTGAACCGGTTTG
1 ACCGGT-TGAACCGGTTTG
45786 ACCGGT
1 ACCGGT
45792 CAGACCCGAC
Statistics
Matches: 55, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
18 3 0.05
19 41 0.75
20 11 0.20
ACGTcount: A:0.16, C:0.27, G:0.29, T:0.28
Consensus pattern (18 bp):
ACCGGTTGAACCGGTTTG
Found at i:45754 original size:29 final size:28
Alignment explanation
Indices: 45710--45791 Score: 114
Period size: 29 Copynumber: 2.9 Consensus size: 28
45700 GCTGCTGGAA
45710 ACCGGTTTAACCGGTTCTGACCGGTTTG
1 ACCGGTTTAACCGGTTCTGACCGGTTTG
45738 ACCGGTTTCAACCGGTTC-GAACCGGTTTG
1 ACCGGTTT-AACCGGTTCTG-ACCGGTTTG
*
45767 ACCGGTCTGAACCGGTT-TGACCGGT
1 ACCGGT-TTAACCGGTTCTGACCGGT
45792 CAGACCCGAC
Statistics
Matches: 49, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
28 15 0.31
29 33 0.67
30 1 0.02
ACGTcount: A:0.16, C:0.27, G:0.29, T:0.28
Consensus pattern (28 bp):
ACCGGTTTAACCGGTTCTGACCGGTTTG
Found at i:45804 original size:5 final size:5
Alignment explanation
Indices: 45794--45871 Score: 61
Period size: 5 Copynumber: 14.8 Consensus size: 5
45784 TGACCGGTCA
* *
45794 GACCC GACCC GACCGTT GACCC GACCC GA-CC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
*
45842 GA-CC GACCGTT GACCC GACCC GACCC GACC
1 GACCC GACC--C GACCC GACCC GACCC GACC
45872 GTTGACCGTT
Statistics
Matches: 59, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
4 8 0.14
5 39 0.66
7 12 0.20
ACGTcount: A:0.19, C:0.50, G:0.23, T:0.08
Consensus pattern (5 bp):
GACCC
Found at i:45828 original size:21 final size:22
Alignment explanation
Indices: 45794--45878 Score: 156
Period size: 21 Copynumber: 4.0 Consensus size: 22
45784 TGACCGGTCA
45794 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
45816 GACCCGA-CCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
45837 GACCCGA-CCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
45858 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
45879 GTTGACCGTT
Statistics
Matches: 62, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
21 42 0.68
22 20 0.32
ACGTcount: A:0.19, C:0.48, G:0.24, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:53084 original size:10 final size:9
Alignment explanation
Indices: 53049--53141 Score: 87
Period size: 10 Copynumber: 9.7 Consensus size: 9
53039 GCTGCTGGAA
*
53049 ACCGGTTTA
1 ACCGGTTTG
*
53058 ACCGGTTTTCA
1 ACCGG-TTT-G
53069 ACCGGTTCTG
1 ACCGGTT-TG
53079 ACCGGTTTG
1 ACCGGTTTG
*
53088 ACCGGTTTCA
1 ACCGGTTT-G
*
53098 ACCGGTTCG
1 ACCGGTTTG
53107 AACCGGTTTG
1 -ACCGGTTTG
*
53117 ACCGGTCTG
1 ACCGGTTTG
53126 AACCGGTTTG
1 -ACCGGTTTG
53136 ACCGGT
1 ACCGGT
53142 CAGACCCGAC
Statistics
Matches: 71, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
9 29 0.41
10 35 0.49
11 7 0.10
ACGTcount: A:0.16, C:0.27, G:0.28, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:53093 original size:19 final size:20
Alignment explanation
Indices: 53049--53141 Score: 104
Period size: 19 Copynumber: 4.8 Consensus size: 20
53039 GCTGCTGGAA
* * *
53049 ACCGGTTTAACCGGTTTTCA
1 ACCGGTTTGACCGGTTCTGA
53069 ACCGGTTCTGACCGGTT-TG-
1 ACCGGTT-TGACCGGTTCTGA
*
53088 ACCGGTTTCAACCGGTTC-GA
1 ACCGGTTT-GACCGGTTCTGA
53108 ACCGGTTTGACCGG-TCTGA
1 ACCGGTTTGACCGGTTCTGA
53127 ACCGGTTTGACCGGT
1 ACCGGTTTGACCGGT
53142 CAGACCCGAC
Statistics
Matches: 63, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
18 3 0.05
19 36 0.57
20 16 0.25
21 8 0.13
ACGTcount: A:0.16, C:0.27, G:0.28, T:0.29
Consensus pattern (20 bp):
ACCGGTTTGACCGGTTCTGA
Found at i:53111 original size:29 final size:28
Alignment explanation
Indices: 53049--53141 Score: 123
Period size: 29 Copynumber: 3.2 Consensus size: 28
53039 GCTGCTGGAA
*
53049 ACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGG-TTTCAACCGGTTC-G
53079 ACCGGTTTGACCGGTTTCAACCGGTTCG
1 ACCGGTTTGACCGGTTTCAACCGGTTCG
* * *
53107 AACCGGTTTGACCGGTCTGAACCGGTTTG
1 -ACCGGTTTGACCGGTTTCAACCGGTTCG
53136 ACCGGT
1 ACCGGT
53142 CAGACCCGAC
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
28 7 0.12
29 38 0.66
30 13 0.22
ACGTcount: A:0.16, C:0.27, G:0.28, T:0.29
Consensus pattern (28 bp):
ACCGGTTTGACCGGTTTCAACCGGTTCG
Found at i:53147 original size:9 final size:9
Alignment explanation
Indices: 53069--53147 Score: 52
Period size: 9 Copynumber: 8.3 Consensus size: 9
53059 CCGGTTTTCA
53069 ACCGGTTCTG
1 ACCGG-TCTG
*
53079 ACCGGTTTG
1 ACCGGTCTG
* *
53088 ACCGGTTTCA
1 ACCGGTCT-G
53098 ACCGGT-TCG
1 ACCGGTCT-G
*
53107 AACCGGTTTG
1 -ACCGGTCTG
53117 ACCGGTCTG
1 ACCGGTCTG
*
53126 AACCGGTTTG
1 -ACCGGTCTG
*
53136 ACCGGTCAG
1 ACCGGTCTG
53145 ACC
1 ACC
53148 CGACCCGACC
Statistics
Matches: 58, Mismatches: 7, Indels: 9
0.78 0.09 0.12
Matches are distributed among these distances:
9 31 0.53
10 26 0.45
11 1 0.02
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.25
Consensus pattern (9 bp):
ACCGGTCTG
Found at i:53154 original size:5 final size:5
Alignment explanation
Indices: 53144--53223 Score: 79
Period size: 5 Copynumber: 14.8 Consensus size: 5
53134 TGACCGGTCA
* *
53144 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
*
53193 GACCC GACCGTT GACCC GACCC GACCC GACC
1 GACCC GACC--C GACCC GACCC GACCC GACC
53224 GTTGACCGTT
Statistics
Matches: 63, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
5 51 0.81
7 12 0.19
ACGTcount: A:0.19, C:0.51, G:0.23, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:53170 original size:22 final size:22
Alignment explanation
Indices: 53144--53230 Score: 174
Period size: 22 Copynumber: 4.0 Consensus size: 22
53134 TGACCGGTCA
53144 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
53166 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
53188 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
53210 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
53231 GTTGACCGTT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 65 1.00
ACGTcount: A:0.18, C:0.49, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:53230 original size:17 final size:15
Alignment explanation
Indices: 53144--53223 Score: 79
Period size: 17 Copynumber: 4.9 Consensus size: 15
53134 TGACCGGTCA
*
53144 GACCCGACCCGACCGTT
1 GACCCGACCCGACC--C
53161 GACCCGACCCGACCC
1 GACCCGACCCGACCC
*
53176 GACCGTTGACCCGACCC
1 GACC--CGACCCGACCC
*
53193 GACCCGACCGTTGACCC
1 GACCCGACC--CGACCC
53210 GACCCGACCCGACC
1 GACCCGACCCGACC
53224 GTTGACCGTT
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
15 12 0.22
17 42 0.78
ACGTcount: A:0.19, C:0.51, G:0.23, T:0.07
Consensus pattern (15 bp):
GACCCGACCCGACCC
Found at i:55388 original size:21 final size:21
Alignment explanation
Indices: 55364--55430 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
55354 TCATTCCTCG
55364 AGAGTCCCCTCTCACCGTTCA
1 AGAGTCCCCTCTCACCGTTCA
* * * * *
55385 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCTCACCGTTCA
* *
55406 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCTCACCGTTCA
55427 AGAG
1 AGAG
55431 CCCGATTCAC
Statistics
Matches: 33, Mismatches: 12, Indels: 3
0.69 0.25 0.06
Matches are distributed among these distances:
20 1 0.03
21 31 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.34, G:0.21, T:0.21
Consensus pattern (21 bp):
AGAGTCCCCTCTCACCGTTCA
Found at i:56781 original size:14 final size:14
Alignment explanation
Indices: 56761--56797 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
56751 GATTGTTTAA
56761 TTGATTTGTAAAA-
1 TTGATTTGTAAAAG
56774 TATGATTTGTAAAAG
1 T-TGATTTGTAAAAG
56789 TTGATTTGT
1 TTGATTTGT
56798 TTAATTGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.05
14 20 0.91
15 1 0.05
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:56928 original size:19 final size:19
Alignment explanation
Indices: 56904--57021 Score: 96
Period size: 19 Copynumber: 6.7 Consensus size: 19
56894 AAAAAGTACT
*
56904 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
56923 ATCGCAACGCGAAATAAAA
1 ATCGCAACGCGAAATGAAA
*
56942 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
*
56956 ATCGTAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
56975 ATCGCAA--CG--A-CAAA
1 ATCGCAACGCGAAATGAAA
*
56989 ATCGTAACGCGAAACT-AAA
1 ATCGCAACGCGAAA-TGAAA
57008 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
57022 CTAAATTCGC
Statistics
Matches: 78, Mismatches: 10, Indels: 22
0.71 0.09 0.20
Matches are distributed among these distances:
14 17 0.22
15 2 0.03
16 4 0.05
17 4 0.05
18 2 0.03
19 49 0.63
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.12
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:56965 original size:33 final size:32
Alignment explanation
Indices: 56920--57016 Score: 140
Period size: 33 Copynumber: 2.9 Consensus size: 32
56910 ATGCGAAATG
* *
56920 AAAATCGCAACGCGAAATAAAAATCGCAACGAG
1 AAAATCGTAACGCGAAAT-AAAATCGCAACGAC
*
56953 AGAATCGTAACGCGAAATGAAAATCGCAACGAC
1 AAAATCGTAACGCGAAAT-AAAATCGCAACGAC
56986 AAAATCGTAACGCGAAACTAAAATCGCAACG
1 AAAATCGTAACGCGAAA-TAAAATCGCAACG
57017 CGAAACTAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 57 0.98
34 1 0.02
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.11
Consensus pattern (32 bp):
AAAATCGTAACGCGAAATAAAATCGCAACGAC
Found at i:57049 original size:19 final size:19
Alignment explanation
Indices: 57027--57144 Score: 76
Period size: 19 Copynumber: 6.7 Consensus size: 19
57017 CGAAACTAAA
57027 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
57046 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
57061 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
57079 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
57094 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
57112 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
57131 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
57145 AGACATTAAG
Statistics
Matches: 73, Mismatches: 15, Indels: 21
0.67 0.14 0.19
Matches are distributed among these distances:
14 17 0.23
16 6 0.08
17 6 0.08
19 34 0.47
20 10 0.14
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:57073 original size:33 final size:33
Alignment explanation
Indices: 57031--57124 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
57021 ACTAAATTCG
57031 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
57064 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
57097 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
57125 AGTAATTTCC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:59037 original size:12 final size:12
Alignment explanation
Indices: 59020--59044 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
59010 TCTTTGGGGA
59020 CTTTTTCTTCTT
1 CTTTTTCTTCTT
59032 CTTTTTCTTCTT
1 CTTTTTCTTCTT
59044 C
1 C
59045 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:60076 original size:20 final size:21
Alignment explanation
Indices: 60051--60102 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
60041 TTTTCCTAAT
*
60051 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
60071 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
60092 TCGCAATGCGA
1 TCGCAATGCGA
60103 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:60124 original size:20 final size:20
Alignment explanation
Indices: 60091--60169 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 20
60081 AATTTGGAAA
* *
60091 ATCGCAATGCGATACTGACT
1 ATCGCAACGAGATACTGACT
* *
60111 ATCGCAACGAGATAAT-ACAAA
1 ATCGCAACGAGATACTGAC--T
*
60132 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATACTGACT
* *
60152 TTCGCAACGAGATTCTGA
1 ATCGCAACGAGATACTGA
60170 AAAATCGCAA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
19 2 0.04
20 30 0.62
21 14 0.29
22 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGAGATACTGACT
Found at i:60179 original size:21 final size:21
Alignment explanation
Indices: 60111--60179 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
60101 GATACTGACT
**
60111 ATCGCAACGAGATAAT-ACAAA
1 ATCGCAACGAGATTCTGA-AAA
**
60132 ATCGCAACGAGATTCTG-ACT
1 ATCGCAACGAGATTCTGAAAA
*
60152 TTCGCAACGAGATTCTGAAAA
1 ATCGCAACGAGATTCTGAAAA
60173 ATCGCAA
1 ATCGCAA
60180 TCATCTTCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
20 17 0.45
21 21 0.55
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGAGATTCTGAAAA
Found at i:60418 original size:20 final size:20
Alignment explanation
Indices: 60393--60480 Score: 97
Period size: 20 Copynumber: 4.4 Consensus size: 20
60383 CAACGGGGAA
*
60393 ATCGCAATGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
*
60413 ATCGCAACGCAAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
** ***
60433 ATCGCAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
60453 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
60473 ATCGCAAC
1 ATCGCAAC
60481 TAGAAAATCG
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
19 5 0.09
20 43 0.81
21 5 0.09
ACGTcount: A:0.40, C:0.23, G:0.20, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:60531 original size:14 final size:16
Alignment explanation
Indices: 60511--60584 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
60501 TGAAAATCGC
60511 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
60526 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
60543 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
60562 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
60578 -TTGCGAT
1 ATTGCGAT
60585 AGTCAGCTTC
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 18 0.33
16 3 0.06
17 3 0.06
19 30 0.56
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:60548 original size:19 final size:19
Alignment explanation
Indices: 60507--60574 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
60497 GAAATGAAAA
60507 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
60523 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
60540 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
60559 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
60575 TCGTTGCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
17 3 0.06
19 30 0.64
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:62612 original size:20 final size:19
Alignment explanation
Indices: 62597--62710 Score: 79
Period size: 19 Copynumber: 6.5 Consensus size: 19
62587 CACGAAACTT
62597 AAAATCGCAATGCGAAAATG
1 AAAATCGCAATGCG-AAATG
** *
62617 ACTATCGCAACGCGAAATG
1 AAAATCGCAATGCGAAATG
*
62636 AAAATCGCAAT--G--A-C
1 AAAATCGCAATGCGAAATG
* *
62650 AAAATCGTAATGCTAAATG
1 AAAATCGCAATGCGAAATG
*
62669 AAAATCGCAA--CG--A-C
1 AAAATCGCAATGCGAAATG
62683 AAAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
62702 -AAATCGCAA
1 AAAATCGCAA
62711 CGATAAAATC
Statistics
Matches: 70, Mismatches: 14, Indels: 22
0.66 0.13 0.21
Matches are distributed among these distances:
14 20 0.29
15 2 0.03
16 2 0.03
17 2 0.03
18 11 0.16
19 22 0.31
20 11 0.16
ACGTcount: A:0.47, C:0.19, G:0.18, T:0.16
Consensus pattern (19 bp):
AAAATCGCAATGCGAAATG
Found at i:62642 original size:19 final size:19
Alignment explanation
Indices: 62581--62645 Score: 67
Period size: 20 Copynumber: 3.3 Consensus size: 19
62571 TAGTTTACTT
* *
62581 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
* **
62601 TCGCAATGCGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
62621 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
62640 TCGCAA
1 TCGCAA
62646 TGACAAAATC
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
19 13 0.36
20 20 0.56
21 3 0.08
ACGTcount: A:0.45, C:0.23, G:0.17, T:0.15
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:62711 original size:32 final size:33
Alignment explanation
Indices: 62620--62731 Score: 163
Period size: 33 Copynumber: 3.4 Consensus size: 33
62610 GAAAATGACT
*
62620 ATCGCAACGCGAAATGAAAATCGCAATGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
* * *
62653 ATCGTAATGCTAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
* *
62686 ATCGCAATGCGAAATG-AAATCGCAACGATAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
62718 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
62732 CACAAATCGC
Statistics
Matches: 71, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
32 28 0.39
33 43 0.61
ACGTcount: A:0.47, C:0.21, G:0.18, T:0.14
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:62721 original size:14 final size:14
Alignment explanation
Indices: 62669--62726 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
62659 ATGCTAAATG
*
62669 AAAATCGCAACGAC
1 AAAATCGCAACGAT
62683 AAAATCGCAATGCGAAAT
1 AAAATCGCAA--CG--AT
*
62701 GAAATCGCAACGAT
1 AAAATCGCAACGAT
62715 AAAATCGCAACG
1 AAAATCGCAACG
62727 CGAAACACAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 23 0.62
16 4 0.11
18 10 0.27
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAT
Found at i:62779 original size:14 final size:14
Alignment explanation
Indices: 62760--62817 Score: 62
Period size: 14 Copynumber: 3.8 Consensus size: 14
62750 TTTCATATCG
62760 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
62774 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
62791 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
62807 CGTTGCGATTT
1 CGTTGCGATTT
62818 GCATTTCGCA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 17 0.46
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:62799 original size:33 final size:33
Alignment explanation
Indices: 62743--62834 Score: 148
Period size: 33 Copynumber: 2.8 Consensus size: 33
62733 ACAAATCGCA
* * *
62743 TTGCAATTTTCATATCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
62776 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
62809 TTGCGATTTGCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
62835 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.14, C:0.18, G:0.22, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:62800 original size:19 final size:19
Alignment explanation
Indices: 62738--62834 Score: 70
Period size: 19 Copynumber: 5.6 Consensus size: 19
62728 GAAACACAAA
* *
62738 TCGCATTGCAATTTTCATA
1 TCGCATTGCGATTTTCATG
*
62757 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATG
*
62773 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATG
62790 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATG
* *
62806 TCG--TTGCGATTTGCATT
1 TCGCATTGCGATTTTCATG
62823 TCGCATTGCGAT
1 TCGCATTGCGAT
62835 AGCCATTTCC
Statistics
Matches: 61, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
14 12 0.20
15 5 0.08
16 8 0.13
17 8 0.13
18 6 0.10
19 22 0.36
ACGTcount: A:0.14, C:0.20, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATG
Found at i:62853 original size:20 final size:19
Alignment explanation
Indices: 62819--62873 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
62809 TTGCGATTTG
*
62819 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
62838 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
62858 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
62874 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:63375 original size:18 final size:18
Alignment explanation
Indices: 63349--63393 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
63339 GTCGATCAGA
*
63349 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
63367 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
63385 TGATGGCTC
1 TGATGGCTC
63394 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:64738 original size:20 final size:20
Alignment explanation
Indices: 64713--64766 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
64703 AATAGTTTCT
64713 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
** *
64733 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACAC
*
64753 GAAACT-AAAATCGC
1 GAAAATGAAAATCGC
64767 GTTGCGATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:65024 original size:22 final size:22
Alignment explanation
Indices: 64997--65040 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
64987 GATGGAGATA
64997 GACGGATTTCACCGGAGATGGG
1 GACGGATTTCACCGGAGATGGG
**
65019 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCACCGGAGATGGG
65041 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGGATTTCACCGGAGATGGG
Found at i:65254 original size:20 final size:20
Alignment explanation
Indices: 65228--65362 Score: 155
Period size: 20 Copynumber: 6.7 Consensus size: 20
65218 GATTATGTAT
* *
65228 TATCGCGTTGCGAAAGTCAG
1 TATCGCATTGCGATAGTCAG
* * *
65248 AATCGCGTTGCGAAAGTCAG
1 TATCGCATTGCGATAGTCAG
* * * *
65268 TATCTCGTTGCGATTTTGT-AT
1 TATCGCATTGCGA--TAGTCAG
*
65289 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTCAG
65309 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTCAG
65329 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTCAG
65349 TATCGCATTGCGAT
1 TATCGCATTGCGAT
65363 TTTCCCAATT
Statistics
Matches: 101, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
19 3 0.03
20 84 0.83
21 12 0.12
22 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (20 bp):
TATCGCATTGCGATAGTCAG
Found at i:65278 original size:40 final size:40
Alignment explanation
Indices: 65211--65362 Score: 155
Period size: 40 Copynumber: 3.8 Consensus size: 40
65201 TTTGAAAATT
* * * *
65211 GCATTGCGATTATGT-ATTATCGCGTTGCGAAAGTCAGAATC
1 GCATTGCGA-TA-GTCAGTATCGCATTGCGATAGTCAGTATC
* * * * * *
65252 GCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGT-ATTATC
1 GCATTGCGATAGTCAGTATCGCATTGCGA--TAGTCAGTATC
*
65293 GCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATC
1 GCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGTATC
65333 GCATTGCGATAGTCAGTATCGCATTGCGAT
1 GCATTGCGATAGTCAGTATCGCATTGCGAT
65363 TTTCCCAATT
Statistics
Matches: 91, Mismatches: 16, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
39 5 0.05
40 48 0.53
41 36 0.40
42 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (40 bp):
GCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGTATC
Found at i:65314 original size:61 final size:61
Alignment explanation
Indices: 65211--65361 Score: 189
Period size: 61 Copynumber: 2.5 Consensus size: 61
65201 TTTGAAAATT
* * *
65211 GCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATC
1 GCATTGCGATTATGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATC
* * * * * *
65272 TCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATC
1 GCATTGCGATTATGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATC
*
65333 GCATTGCGA-TA-GTCAGTATCGCATTGCGA
1 GCATTGCGATTATGT-ATTATCGCATTGCGA
65362 TTTTCCCAAT
Statistics
Matches: 76, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
59 2 0.03
60 15 0.20
61 59 0.78
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (61 bp):
GCATTGCGATTATGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATC
Found at i:65347 original size:81 final size:82
Alignment explanation
Indices: 65211--65365 Score: 215
Period size: 81 Copynumber: 1.9 Consensus size: 82
65201 TTTGAAAATT
* * * * *
65211 GCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGT
1 GCATTGCGATTATGTAGTATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCGCAT
65276 TGCGATTTTGTATTATC
66 TGCGATTTTGTATTATC
* * *
65293 GCATTGCGA-TA-GTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGTATCGCA
1 GCATTGCGATTATGT-AGTATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCGCA
65356 TTGCGATTTT
65 TTGCGATTTT
65366 CCCAATTCGC
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
80 2 0.03
81 53 0.83
82 9 0.14
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (82 bp):
GCATTGCGATTATGTAGTATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCGCAT
TGCGATTTTGTATTATC
Found at i:65402 original size:81 final size:81
Alignment explanation
Indices: 65211--65383 Score: 197
Period size: 81 Copynumber: 2.1 Consensus size: 81
65201 TTTGAAAATT
* * * * *
65211 GCATTGCGATTATGT-ATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCG
1 GCATTGCGA-TA-GTAAGTATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCGCA
** *
65275 TTGCGATTTTGTATTATC
64 TTGCGATTTTCCAATATC
* * *
65293 GCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGTATCGCATT
1 GCATTGCGATAGTAAGTATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATT
65358 GCGATTTTCCCAAT-TC
66 GCGATTTT-CCAATATC
*
65374 GCGTTGCGAT
1 GCATTGCGAT
65384 TTACTTATTC
Statistics
Matches: 77, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
80 2 0.03
81 64 0.83
82 11 0.14
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (81 bp):
GCATTGCGATAGTAAGTATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATT
GCGATTTTCCAATATC
Found at i:65473 original size:21 final size:21
Alignment explanation
Indices: 65433--65473 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
65423 ACTGTAGACC
** *
65433 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
65454 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
65474 GCGAATTTGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:66507 original size:20 final size:20
Alignment explanation
Indices: 66482--66528 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
66472 TTTCCAGAAA
*
66482 CGCAACGCGAATATGA-AAAT
1 CGCAACGCGAACAT-ATAAAT
66502 CGCAACGCGAACATATAAAT
1 CGCAACGCGAACATATAAAT
66522 CGCAACG
1 CGCAACG
66529 TGATTCTGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.43, C:0.26, G:0.19, T:0.13
Consensus pattern (20 bp):
CGCAACGCGAACATATAAAT
Found at i:66582 original size:61 final size:61
Alignment explanation
Indices: 66540--66692 Score: 236
Period size: 61 Copynumber: 2.5 Consensus size: 61
66530 GATTCTGACT
** **
66540 ATCGCAACGAGTATCCGTAAAATCGCAACGTTTATCCGTAAATCGCAACGACAATACGTAAA
1 ATCGCAACGACAATCCGT-AAATCGCAACGCATATCCGTAAATCGCAACGACAATACGTAAA
66602 ATCGCAACGACAATCCGTAAATCGCAACGCATATCCGTAAATCGCAACGACAATACGTAAA
1 ATCGCAACGACAATCCGTAAATCGCAACGCATATCCGTAAATCGCAACGACAATACGTAAA
*
66663 ATCGCAACG-CGTATCCGTAAATCGCAACGC
1 ATCGCAACGAC-AATCCGTAAATCGCAACGC
66693 GGTTTTTAAA
Statistics
Matches: 85, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
60 1 0.01
61 68 0.80
62 16 0.19
ACGTcount: A:0.38, C:0.27, G:0.16, T:0.18
Consensus pattern (61 bp):
ATCGCAACGACAATCCGTAAATCGCAACGCATATCCGTAAATCGCAACGACAATACGTAAA
Found at i:66584 original size:20 final size:20
Alignment explanation
Indices: 66540--66691 Score: 173
Period size: 20 Copynumber: 7.5 Consensus size: 20
66530 GATTCTGACT
*
66540 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGACTATCCGT-AA
**
66561 ATCGCAACGTTTATCCGTAA
1 ATCGCAACGACTATCCGTAA
* *
66581 ATCGCAACGACAATACGTAAA
1 ATCGCAACGACTATCCGT-AA
*
66602 ATCGCAACGACAATCCGTAA
1 ATCGCAACGACTATCCGTAA
66622 ATCGCAACG-CATATCCGTAA
1 ATCGCAACGAC-TATCCGTAA
* *
66642 ATCGCAACGACAATACGTAAA
1 ATCGCAACGACTATCCGT-AA
66663 ATCGCAACG-CGTATCCGTAA
1 ATCGCAACGAC-TATCCGTAA
66683 ATCGCAACG
1 ATCGCAACG
66692 CGGTTTTTAA
Statistics
Matches: 114, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
19 1 0.01
20 61 0.54
21 52 0.46
ACGTcount: A:0.38, C:0.27, G:0.16, T:0.18
Consensus pattern (20 bp):
ATCGCAACGACTATCCGTAA
Found at i:66585 original size:41 final size:40
Alignment explanation
Indices: 66540--66691 Score: 189
Period size: 41 Copynumber: 3.7 Consensus size: 40
66530 GATTCTGACT
***
66540 ATCGCAACGAGTATCCGTAAAATCGCAACGTTTATCCGTAA
1 ATCGCAACGAGTATCCGT-AAATCGCAACGACAATCCGTAA
** *
66581 ATCGCAACGACAATACGTAAAATCGCAACGACAATCCGTAA
1 ATCGCAACGAGTATCCGT-AAATCGCAACGACAATCCGTAA
*
66622 ATCGCAACGCA-TATCCGTAAATCGCAACGACAATACGTAAA
1 ATCGCAACG-AGTATCCGTAAATCGCAACGACAATCCGT-AA
*
66663 ATCGCAACGCGTATCCGTAAATCGCAACG
1 ATCGCAACGAGTATCCGTAAATCGCAACG
66692 CGGTTTTTAA
Statistics
Matches: 98, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
40 19 0.19
41 78 0.80
42 1 0.01
ACGTcount: A:0.38, C:0.27, G:0.16, T:0.18
Consensus pattern (40 bp):
ATCGCAACGAGTATCCGTAAATCGCAACGACAATCCGTAA
Found at i:67311 original size:21 final size:21
Alignment explanation
Indices: 67250--67328 Score: 85
Period size: 20 Copynumber: 3.9 Consensus size: 21
67240 TTCTAAACTT
67250 AAAATCGCAA-GATGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
67270 AAAATCGCAAC-ACGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
**
67290 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGAGAAATG
*
67311 AAAATCGCAATGAGAGAA
1 AAAATCGCAACGAGAGAA
67329 TCGCAACGCG
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
20 29 0.58
21 21 0.42
ACGTcount: A:0.52, C:0.15, G:0.20, T:0.13
Consensus pattern (21 bp):
AAAATCGCAACGAGAGAAATG
Found at i:67366 original size:19 final size:19
Alignment explanation
Indices: 67327--67368 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
67317 GCAATGAGAG
* **
67327 AATCGCAACGCGAAATGAA
1 AATCACAACGCGAAACCAA
67346 AATCACAACGCGAAACCAA
1 AATCACAACGCGAAACCAA
67365 AATC
1 AATC
67369 GCATTGCGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.50, C:0.26, G:0.14, T:0.10
Consensus pattern (19 bp):
AATCACAACGCGAAACCAA
Found at i:67389 original size:19 final size:19
Alignment explanation
Indices: 67367--67431 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
67357 GAAACCAAAA
67367 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
67386 TCGCGTTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
67402 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
67419 TCGCATTGCGATT
1 TCGCATTGCGATT
67432 CTCTCATTGC
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 6 0.16
16 7 0.18
17 7 0.18
19 18 0.47
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:67414 original size:33 final size:33
Alignment explanation
Indices: 67372--67493 Score: 145
Period size: 33 Copynumber: 3.5 Consensus size: 33
67362 CAAAATCGCA
67372 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
67405 TTGCGATTTTCATTTCGCATTGCGATTCTCTCA
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
**
67438 TTGCGATAGTCATTTCCGCGTTGCGATAATCATTCTCTCG
1 TTGCGATTTTCATTT-CGCGTTGCG------ATTCTCTCG
67478 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
67494 AACCAAAAGA
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
33 44 0.59
34 8 0.11
39 1 0.01
40 21 0.28
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:67491 original size:20 final size:20
Alignment explanation
Indices: 67429--67484 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
67419 TCGCATTGCG
* *
67429 ATTCTCTCATTGCGATAGTC
1 ATTCTCTCGTTGCGATAATC
*
67449 ATT-TCCGCGTTGCGATAATC
1 ATTCT-CTCGTTGCGATAATC
67469 ATTCTCTCGTTGCGAT
1 ATTCTCTCGTTGCGAT
67485 TTTCATTTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.03
20 28 0.93
21 1 0.03
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATAATC
Found at i:69350 original size:94 final size:93
Alignment explanation
Indices: 69189--69662 Score: 795
Period size: 94 Copynumber: 5.1 Consensus size: 93
69179 TAGATTGCTT
* * *
69189 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACATTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
69254 ATTTGTCTTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGA
* *
69283 AGTAAATTTATTCGGTTGCTGTCAATTTTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
69348 ATTTGTCTTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGA
69377 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
69442 GTTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * *
69471 AGTAAATTTGTTCGGTTACTGCCAATTCTTCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
69536 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * * *
69565 AGTAAATTTGTTCGGTTGCTGTCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
69630 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
69658 AGTAA
1 AGTAA
69663 TGCAATCCAT
Statistics
Matches: 362, Mismatches: 17, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
93 26 0.07
94 336 0.93
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.48
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:69515 original size:17 final size:17
Alignment explanation
Indices: 69495--69527 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
69485 GTTACTGCCA
69495 ATTCTTCTAA-ACTGTGT
1 ATTCTT-TAACACTGTGT
69512 ATTCTTTAACACTGTG
1 ATTCTTTAACACTGTG
69528 AAGTTAGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.45
Consensus pattern (17 bp):
ATTCTTTAACACTGTGT
Found at i:69787 original size:14 final size:14
Alignment explanation
Indices: 69765--69822 Score: 53
Period size: 14 Copynumber: 3.8 Consensus size: 14
69755 AACGCGAAAT
69765 GAATCGCAACGAGA
1 GAATCGCAACGAGA
*
69779 GAATTGCAACGAGAAATGA
1 GAATCGCAAC--G--A-GA
*
69798 GAATCACAACGAGA
1 GAATCGCAACGAGA
69812 GAATCGCAACG
1 GAATCGCAACG
69823 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
14 21 0.60
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.19, G:0.26, T:0.10
Consensus pattern (14 bp):
GAATCGCAACGAGA
Found at i:69850 original size:33 final size:32
Alignment explanation
Indices: 69750--69860 Score: 125
Period size: 33 Copynumber: 3.4 Consensus size: 32
69740 AAAAATGACT
69750 ATCGCAACGCGAAATG-AATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAATCGCAACGAGAGA
* * *
69781 ATTGCAACGAGAAATGAGAATCACAACGAGAGA
1 ATCGCAACGCGAAATGA-AATCGCAACGAGAGA
** * *
69814 ATCGCAACGCGAAATGAAAATCGTGACGACAAA
1 ATCGCAACGCGAAATG-AAATCGCAACGAGAGA
*
69847 ATCGCAACGTGAAA
1 ATCGCAACGCGAAA
69861 CTATAATCGC
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
31 14 0.21
33 51 0.77
34 1 0.02
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (32 bp):
ATCGCAACGCGAAATGAAATCGCAACGAGAGA
Found at i:69930 original size:20 final size:20
Alignment explanation
Indices: 69905--69971 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
69895 GATTCTCTCG
**
69905 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
69925 TTGCGATAGTCATTTTTGCA
1 TTGCGATAGTCATTTTCGCA
*
69945 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
69965 TTGCGAT
1 TTGCGAT
69972 TTTAAGTTTC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:70543 original size:21 final size:21
Alignment explanation
Indices: 70452--70556 Score: 95
Period size: 21 Copynumber: 5.0 Consensus size: 21
70442 GACTCACCTG
*
70452 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
70474 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
70494 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
70515 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
70536 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
70557 CCAACATTCT
Statistics
Matches: 63, Mismatches: 19, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
20 3 0.05
21 59 0.94
22 1 0.02
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:70549 original size:42 final size:42
Alignment explanation
Indices: 70449--70559 Score: 118
Period size: 42 Copynumber: 2.6 Consensus size: 42
70439 CCCGACTCAC
* * * *
70449 CTGTCATCGTTCAAGAGGCCTCC-CCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGTCC-CCTCCCACCGTTCAAGAGGCCA
* **
70491 CTATCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
*
70533 CTGTCATCGTTGAAGAGGT-CCCTCCCA
1 CTGTCATCGTTCAAGA-GTCCCCTCCCA
70560 ACATTCTAGA
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
41 2 0.04
42 52 0.93
43 2 0.04
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.23
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
Found at i:72138 original size:34 final size:33
Alignment explanation
Indices: 72061--72145 Score: 116
Period size: 33 Copynumber: 2.5 Consensus size: 33
72051 TCGCATCGCG
** * *
72061 GAAATGACTATCGCAACGAGAGAATCGCAATGT
1 GAAATGAAAATCGCAATGAGAGAATCGCAATGC
*
72094 GAAATGAAAATCGCAATGAGTGAATCGCAATGC
1 GAAATGAAAATCGCAATGAGAGAATCGCAATGC
72127 GAAAATGAAAATCGCAATG
1 G-AAATGAAAATCGCAATG
72146 CGAAACTAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 29 0.63
34 17 0.37
ACGTcount: A:0.44, C:0.15, G:0.24, T:0.18
Consensus pattern (33 bp):
GAAATGAAAATCGCAATGAGAGAATCGCAATGC
Found at i:72176 original size:19 final size:19
Alignment explanation
Indices: 72162--72241 Score: 98
Period size: 19 Copynumber: 4.4 Consensus size: 19
72152 TAATTTCGTG
72162 TTGCGATTTTCATTTTCGCA
1 TTGCGATTTTCA-TTTCGCA
*
72182 TTGCGA--TTCA-CTCG--
1 TTGCGATTTTCATTTCGCA
*
72196 TTGTGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
72215 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
72234 TTGCGATT
1 TTGCGATT
72242 CTCTCGTTGC
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
14 5 0.10
16 7 0.14
17 3 0.06
18 4 0.08
19 26 0.51
20 6 0.12
ACGTcount: A:0.15, C:0.20, G:0.17, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:72261 original size:52 final size:53
Alignment explanation
Indices: 72162--72261 Score: 157
Period size: 52 Copynumber: 1.9 Consensus size: 53
72152 TAATTTCGTG
* **
72162 TTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGTGATTTTCATTTCGCA
1 TTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATAGTCATTTCGCA
*
72215 TTGCGATTTTCA-TTTCGCATTGCGATTCTCTCGTTGCGATAGTCATT
1 TTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATAGTCATT
72262 ACATGCAGGG
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
52 31 0.72
53 12 0.28
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (53 bp):
TTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATAGTCATTTCGCA
Found at i:73162 original size:18 final size:19
Alignment explanation
Indices: 73128--73177 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
73118 CAAAACATTT
73128 GTGTTGCGAAATT-AAAATC
1 GTGTTGCG-AATTAAAAATC
73147 -TGTTGCGAATTCAAAAATC
1 GTGTTGCGAATT-AAAAATC
*
73166 GAGTTGCGAATT
1 GTGTTGCGAATT
73178 TGAAATTCAG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 4 0.15
18 7 0.26
19 6 0.22
20 10 0.37
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32
Consensus pattern (19 bp):
GTGTTGCGAATTAAAAATC
Found at i:73223 original size:20 final size:20
Alignment explanation
Indices: 73208--73643 Score: 181
Period size: 20 Copynumber: 21.5 Consensus size: 20
73198 GTCAGAATCT
*
73208 CGTTGCGATTTACAG-ATTCA
1 CGTTGCGATTTAC-GTATTCG
*
73228 CATTGCGATTTACGTATTCG
1 CGTTGCGATTTACGTATTCG
73248 CGTTGCGATTTACGTATTCG
1 CGTTGCGATTTACGTATTCG
*
73268 CGTTGCGATTTACGTAATCG
1 CGTTGCGATTTACGTATTCG
73288 CGTTGCGATTTACGTATTCG
1 CGTTGCGATTTACGTATTCG
* * * * *
73308 CATTGCGAATTAGGAAAATCG
1 CGTTGCGATTTACG-TATTCG
*** ** * *
73329 CAACGCGAATTTGGGAAATCG
1 CGTTGCG-ATTTACGTATTCG
** * * *
73350 CAATGCGATAGT-CAG-AATAG
1 CGTTGCGAT-TTAC-GTATTCG
* * **
73370 CGTTGCGA-AT-CTGGAAACTG
1 CGTTGCGATTTAC-GTATTC-G
** * * *
73390 ATTTGCGATAT-CGGAGATCG
1 CGTTGCGATTTACGTA-TTCG
73410 CGTTGCGATTTTACGTATT-G
1 CGTTGCGA-TTTACGTATTCG
* * *
73430 TCATTTGCGATTTACGGATACG
1 -C-GTTGCGATTTACGTATTCG
* *
73452 CATTGCGATTTACGTATTCT
1 CGTTGCGATTTACGTATTCG
*
73472 CGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACGTATTCG
* *
73492 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGTATTCG
* **
73512 TGTTGCGATTTTACGTATTAT
1 CGTTGCGA-TTTACGTATTCG
* *
73533 CGTTACGATTTAC-TGATACG
1 CGTTGCGATTTACGT-ATTCG
* * *
73553 CGTTGCGATTTTACGGATACT
1 CGTTGCGA-TTTACGTATTCG
* * *
73574 CGTTGCGATAGT-CAG-AATCA
1 CGTTGCGAT-TTAC-GTATTCG
** *
73594 CGTTGCGATTTATATGTTCG
1 CGTTGCGATTTACGTATTCG
* *
73614 CGTTGCGATTTTCATATTCG
1 CGTTGCGATTTACGTATTCG
73634 CGTTGCGATT
1 CGTTGCGATT
73644 CTGAAAAATC
Statistics
Matches: 325, Mismatches: 69, Indels: 44
0.74 0.16 0.10
Matches are distributed among these distances:
18 3 0.01
19 5 0.02
20 228 0.70
21 74 0.23
22 15 0.05
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (20 bp):
CGTTGCGATTTACGTATTCG
Found at i:73336 original size:21 final size:21
Alignment explanation
Indices: 73312--73357 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
73302 TATTCGCATT
73312 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
73333 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
73354 GCGA
1 GCGA
73358 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:73440 original size:42 final size:41
Alignment explanation
Indices: 73390--73469 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 41
73380 CTGGAAACTG
*
73390 ATTTGCGATAT-CGGAGATCGCGTTGCGATTTTACGTATTGTC
1 ATTTGCGATATACGGAGA-CGCATTGCGA-TTTACGTATTGTC
* *
73432 ATTTGCGATTTACGGATACGCATTGCGATTTACGTATT
1 ATTTGCGATATACGGAGACGCATTGCGATTTACGTATT
73470 CTCGTTGCGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
41 10 0.29
42 19 0.56
43 5 0.15
ACGTcount: A:0.21, C:0.16, G:0.24, T:0.39
Consensus pattern (41 bp):
ATTTGCGATATACGGAGACGCATTGCGATTTACGTATTGTC
Found at i:73530 original size:61 final size:61
Alignment explanation
Indices: 73410--73582 Score: 208
Period size: 61 Copynumber: 2.8 Consensus size: 61
73400 TCGGAGATCG
* * ** *
73410 CGTTGCGATTTTACGTATTGTCATTTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCT
1 CGTTGCGA-TTTACGTATTCTC-GTTGCGATTTACGGATACGTGTTGCGATTTTACGTATTAT
73472 CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGTGTTGCGATTTTACGTATTAT
1 CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGTGTTGCGATTTTACGTATTAT
* * *
73533 CGTTACGATTTAC-TGATACGCGTTGCGATTTTACGGATAC-TCGTTGCGAT
1 CGTTGCGATTTACGT-ATTCTCGTTGCGA-TTTACGGATACGT-GTTGCGAT
73583 AGTCAGAATC
Statistics
Matches: 99, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
60 25 0.25
61 47 0.47
62 27 0.27
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.40
Consensus pattern (61 bp):
CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGTGTTGCGATTTTACGTATTAT
Found at i:73577 original size:41 final size:39
Alignment explanation
Indices: 73434--73582 Score: 156
Period size: 41 Copynumber: 3.7 Consensus size: 39
73424 GTATTGTCAT
* * * *
73434 TTGCGATTTACGGATACGCATTGCGATTTACGTATTCTCG
1 TTGCGATTTACGGATACTCGTTGCGATTTACG-ATACGCG
* * *
73474 TTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGTG
1 TTGCGATTTACGGATACTCGTTGCGATTTAC-GATACGCG
* *
73514 TTGCGATTTTACGTATTA-TCGTTACGATTTACTGATACGCG
1 TTGCGA-TTTACGGA-TACTCGTTGCGATTTAC-GATACGCG
73555 TTGCGATTTTACGGATACTCGTTGCGAT
1 TTGCGA-TTTACGGATACTCGTTGCGAT
73583 AGTCAGAATC
Statistics
Matches: 92, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
40 39 0.42
41 52 0.57
42 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.40
Consensus pattern (39 bp):
TTGCGATTTACGGATACTCGTTGCGATTTACGATACGCG
Found at i:73603 original size:61 final size:62
Alignment explanation
Indices: 73434--73625 Score: 168
Period size: 61 Copynumber: 3.2 Consensus size: 62
73424 GTATTGTCAT
** * * *
73434 TTGCGA-TTTACGGATACGCATTGCGAT-TTACGTATTC-TCGTTGCGATTTAC-GTATTCTCG
1 TTGCGATTTTACGGATACGTGTTGCGATGTCACG-AATCATCGTTGCGATTTACTG-ATTCGCG
* * * * * *
73494 TTGCGA-TTTACGGATACGTGTTGCGATTTTACGTATTATCGTTACGATTTACTGATACGCG
1 TTGCGATTTTACGGATACGTGTTGCGATGTCACGAATCATCGTTGCGATTTACTGATTCGCG
*
73555 TTGCGATTTTACGGATAC-TCGTTGCGATAGTCA-GAATCA-CGTTGCGATTTATATG-TTCGCG
1 TTGCGATTTTACGGATACGT-GTTGCGAT-GTCACGAATCATCGTTGCGATTTA-CTGATTCGCG
73616 TTGCGATTTT
1 TTGCGATTTT
73626 CATATTCGCG
Statistics
Matches: 110, Mismatches: 15, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
60 26 0.24
61 56 0.51
62 26 0.24
63 2 0.02
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.40
Consensus pattern (62 bp):
TTGCGATTTTACGGATACGTGTTGCGATGTCACGAATCATCGTTGCGATTTACTGATTCGCG
Found at i:73704 original size:42 final size:42
Alignment explanation
Indices: 73611--73704 Score: 95
Period size: 42 Copynumber: 2.3 Consensus size: 42
73601 ATTTATATGT
*
73611 TCGCGTTGCG-ATTTTCATATTCGCGTTGCGATTCTGAAAAA
1 TCGCGTTGCGAATTTTCATATTCGCATTGCGATTCTGAAAAA
** ** *
73652 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTCTTCATAA
1 TCGCGTTGCGAATTT-TCA-TATTCGCATTGCGATTCTGAAAAA
73694 TCGCGTTGCGA
1 TCGCGTTGCGA
73705 TTCTGGGAAC
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
41 8 0.19
42 31 0.74
43 3 0.07
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.35
Consensus pattern (42 bp):
TCGCGTTGCGAATTTTCATATTCGCATTGCGATTCTGAAAAA
Found at i:82609 original size:14 final size:15
Alignment explanation
Indices: 82590--82621 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
82580 CTCAACATAC
82590 AAATCAGAAGAA-AA
1 AAATCAGAAGAAGAA
82604 AAATCAGAAGAAGAA
1 AAATCAGAAGAAGAA
82619 AAA
1 AAA
82622 ATTGTAGCGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.72, C:0.06, G:0.16, T:0.06
Consensus pattern (15 bp):
AAATCAGAAGAAGAA
Found at i:83647 original size:29 final size:30
Alignment explanation
Indices: 83577--83635 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
83567 AATTTAAGGT
83577 AAAATGGTTTTTGGACTTGAATTGAATTTAC
1 AAAAT-GTTTTTGGACTTGAATTGAATTTAC
83608 AAAATGTTTTTGGACTT-AATTGAATTTA
1 AAAATGTTTTTGGACTTGAATTGAATTTA
83636 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.39
30 12 0.43
31 5 0.18
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.44
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTAC
Found at i:83749 original size:15 final size:15
Alignment explanation
Indices: 83729--83758 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
83719 GATTGCCAGG
83729 GGGTACAGATACCCC
1 GGGTACAGATACCCC
83744 GGGTACAGATACCCC
1 GGGTACAGATACCCC
83759 CCCAGGGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.33, G:0.27, T:0.13
Consensus pattern (15 bp):
GGGTACAGATACCCC
Found at i:83858 original size:20 final size:21
Alignment explanation
Indices: 83814--83856 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
83804 AACAGAATGT
83814 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
83835 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
83856 C
1 C
83857 AGTTCAACAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.44, G:0.28, T:0.14
Consensus pattern (21 bp):
CCAGGGGGTACCGATTCCCCC
Found at i:83918 original size:21 final size:21
Alignment explanation
Indices: 83892--83934 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
83882 ATTTGAATAT
* *
83892 TATGAAGGGGTATCGATTCCC
1 TATGAAGAGGTACCGATTCCC
83913 TATGAAGAGGTACCGATTCCC
1 TATGAAGAGGTACCGATTCCC
83934 T
1 T
83935 CTATTCTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (21 bp):
TATGAAGAGGTACCGATTCCC
Found at i:84000 original size:20 final size:22
Alignment explanation
Indices: 83962--84001 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
83952 TTTGAGTATA
83962 AAAATCATCCCCAAACGGCTCT
1 AAAATCATCCCCAAACGGCTCT
83984 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
84002 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCT
Found at i:84251 original size:33 final size:33
Alignment explanation
Indices: 84213--84299 Score: 156
Period size: 33 Copynumber: 2.6 Consensus size: 33
84203 TTTTGTAAAG
84213 GGGAAAGGTTCTAGCTTAGCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCGTGTAAAAGCTA
84246 GGGAAAGGTTCTAGCTTAGCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCGTGTAAAAGCTA
* *
84279 GGGAAATGTTCTAGTTTAGCC
1 GGGAAAGGTTCTAGCTTAGCC
84300 CGGAAAAACT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.29, C:0.15, G:0.30, T:0.26
Consensus pattern (33 bp):
GGGAAAGGTTCTAGCTTAGCCGTGTAAAAGCTA
Found at i:85782 original size:19 final size:20
Alignment explanation
Indices: 85744--85784 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
85734 CCCAGAATAG
*
85744 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATA-CCCTTCAT
85765 AGGGAATCGATA-CCTTCAT
1 AGGGAATCGATACCCTTCAT
85784 A
1 A
85785 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
21 11 0.58
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.24
Consensus pattern (20 bp):
AGGGAATCGATACCCTTCAT
Found at i:85844 original size:20 final size:20
Alignment explanation
Indices: 85819--85857 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
85809 CTGTTGAACA
85819 GGGGGAATCGATACCCCTGG
1 GGGGGAATCGATACCCCTGG
*
85839 GGGGGAATCGGTACCCCTG
1 GGGGGAATCGATACCCCTG
85858 AACATTCGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.26, G:0.41, T:0.15
Consensus pattern (20 bp):
GGGGGAATCGATACCCCTGG
Found at i:85914 original size:20 final size:20
Alignment explanation
Indices: 85889--85966 Score: 78
Period size: 20 Copynumber: 4.1 Consensus size: 20
85879 AAAAACTGCA
85889 GGGGGTATCTGTACCCCCTG
1 GGGGGTATCTGTACCCCCTG
85909 GGGGGTATCTGTA---CC--
1 GGGGGTATCTGTACCCCCTG
85924 -GGGGTATCTGTACCCCCTGGG
1 GGGGGTATCTGTACCCCCT--G
* *
85945 GGGGGAATCTATACCCCCTG
1 GGGGGTATCTGTACCCCCTG
85965 GG
1 GG
85967 CAATCTTGAA
Statistics
Matches: 48, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
14 12 0.25
17 4 0.08
20 16 0.33
22 16 0.33
ACGTcount: A:0.13, C:0.27, G:0.37, T:0.23
Consensus pattern (20 bp):
GGGGGTATCTGTACCCCCTG
Found at i:85929 original size:14 final size:14
Alignment explanation
Indices: 85910--85937 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
85900 TACCCCCTGG
85910 GGGGTATCTGTACC
1 GGGGTATCTGTACC
85924 GGGGTATCTGTACC
1 GGGGTATCTGTACC
85938 CCCTGGGGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.36, T:0.29
Consensus pattern (14 bp):
GGGGTATCTGTACC
Found at i:85949 original size:22 final size:22
Alignment explanation
Indices: 85924--85966 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
85914 TATCTGTACC
* *
85924 GGGGTATCTGTACCCCCTGGGG
1 GGGGAATCTATACCCCCTGGGG
85946 GGGGAATCTATACCCCCTGGG
1 GGGGAATCTATACCCCCTGGG
85967 CAATCTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.14, C:0.28, G:0.37, T:0.21
Consensus pattern (22 bp):
GGGGAATCTATACCCCCTGGGG
Found at i:86088 original size:29 final size:31
Alignment explanation
Indices: 86056--86113 Score: 102
Period size: 29 Copynumber: 1.9 Consensus size: 31
86046 AAACTTTGAA
86056 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
86085 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAACCATTT
86114 GCCTAAATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.41
30 11 0.41
31 5 0.19
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:88737 original size:34 final size:33
Alignment explanation
Indices: 88675--88746 Score: 92
Period size: 34 Copynumber: 2.2 Consensus size: 33
88665 ACCTTACAAC
* *
88675 TCCCTAGTTTTTCCGGGCTAAACTAGAACC-TT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTTT
*
88707 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTTT
88742 TCCCT
1 TCCCT
88747 TTACAAAAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 15 0.44
35 7 0.21
ACGTcount: A:0.22, C:0.29, G:0.15, T:0.33
Consensus pattern (33 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTTT
Found at i:88981 original size:20 final size:21
Alignment explanation
Indices: 88956--88994 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
88946 AGTCGTATAT
88956 AGCCG-TTGGGGATGTTTTGG
1 AGCCGTTTGGGGATGTTTTGG
88976 AGCCGTTTGGGGATGTTTT
1 AGCCGTTTGGGGATGTTTT
88995 ATACTCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.10, C:0.10, G:0.41, T:0.38
Consensus pattern (21 bp):
AGCCGTTTGGGGATGTTTTGG
Found at i:89045 original size:20 final size:21
Alignment explanation
Indices: 89020--89061 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
89010 CCCAGAATAG
*
89020 AGGGAATCGGTA-CCCTTCAT
1 AGGGAATCGATACCCCTTCAT
89040 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
89061 A
1 A
89062 TATTCAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:89136 original size:21 final size:20
Alignment explanation
Indices: 89095--89132 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
89085 CTGTTGAACA
89095 GGGGGGAATCGGTACCCCTG
1 GGGGGGAATCGGTACCCCTG
89115 GGGGGGAATCGGTACCCC
1 GGGGGGAATCGGTACCCC
89133 CTGGACATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.16, C:0.26, G:0.45, T:0.13
Consensus pattern (20 bp):
GGGGGGAATCGGTACCCCTG
Found at i:89195 original size:21 final size:20
Alignment explanation
Indices: 89170--89247 Score: 85
Period size: 21 Copynumber: 4.0 Consensus size: 20
89160 AAAACCTGCA
89170 GGGGGTATCTGTACCCCCTGG
1 GGGGGTATCTGTA-CCCCTGG
89191 GGGGGTATCTGTA-CCC---
1 GGGGGTATCTGTACCCCTGG
89207 -GGGGTATCTGTACCCCCTGG
1 GGGGGTATCTGTA-CCCCTGG
* *
89227 GGGGGAATCTATACCCCTGG
1 GGGGGTATCTGTACCCCTGG
89247 G
1 G
89248 CAATCTTGAA
Statistics
Matches: 49, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
15 12 0.24
17 3 0.06
19 3 0.06
20 8 0.16
21 23 0.47
ACGTcount: A:0.13, C:0.27, G:0.37, T:0.23
Consensus pattern (20 bp):
GGGGGTATCTGTACCCCTGG
Found at i:89211 original size:36 final size:36
Alignment explanation
Indices: 89171--89242 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
89161 AAACCTGCAG
* *
89171 GGGGTATCTGTACCCCCTGGGGGGGTATCTGTACCC
1 GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
89207 GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
1 GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
89243 CTGGGCAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.14, C:0.28, G:0.35, T:0.24
Consensus pattern (36 bp):
GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
Found at i:89212 original size:15 final size:15
Alignment explanation
Indices: 89192--89221 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
89182 ACCCCCTGGG
89192 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
89207 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
89222 CCTGGGGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:89368 original size:28 final size:30
Alignment explanation
Indices: 89337--89393 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 30
89327 ACTTTGAATA
89337 AATTCAATT-AAGTCCAAAAA-CATTTTGT
1 AATTCAATTCAAGTCCAAAAACCATTTTGT
89365 AATTCAATTCAAGTCCAAAAACCATTTTG
1 AATTCAATTCAAGTCCAAAAACCATTTTG
89394 CCTTAAATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 9 0.33
29 11 0.41
30 7 0.26
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.33
Consensus pattern (30 bp):
AATTCAATTCAAGTCCAAAAACCATTTTGT
Found at i:89451 original size:19 final size:20
Alignment explanation
Indices: 89427--89474 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
89417 TAGTTCACAC
*
89427 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
89446 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
89466 TTTTGAAAA
1 TTTTGAAAA
89475 AAGGATTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Done.