Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold936
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: 46820
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:8073 original size:51 final size:51
Alignment explanation
Indices: 7913--8083 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
7903 GAAATAACGA
* * *
7913 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * *
7965 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
8018 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
8069 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
8084 TCAGAAATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 39 0.40
52 16 0.16
53 32 0.33
54 10 0.10
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:10637 original size:13 final size:13
Alignment explanation
Indices: 10619--10644 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10609 ACAAAGATCC
10619 ATGTATCGATACA
1 ATGTATCGATACA
10632 ATGTATCGATACA
1 ATGTATCGATACA
10645 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:10640 original size:33 final size:33
Alignment explanation
Indices: 10598--10664 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
10588 AAAATTTCCA
***
10598 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
10631 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
10664 A
1 A
10665 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:10708 original size:19 final size:18
Alignment explanation
Indices: 10684--10751 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
10674 CAGTAGCTAA
10684 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
10703 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
10718 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
10735 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
10752 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:10724 original size:13 final size:13
Alignment explanation
Indices: 10706--10730 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10696 ACAATACTTA
10706 TGTATCGATACAT
1 TGTATCGATACAT
10719 TGTATCGATACA
1 TGTATCGATACA
10731 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:10728 original size:32 final size:32
Alignment explanation
Indices: 10687--10749 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
10677 TAGCTAATTA
*
10687 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
10719 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
10750 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:10831 original size:21 final size:21
Alignment explanation
Indices: 10807--10863 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
10797 CATTTGTAGG
10807 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
10828 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
10849 ATGTATCGATACATT
1 ATGTATCGATACATT
10864 TAAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:10874 original size:1 final size:1
Alignment explanation
Indices: 10868--10935 Score: 109
Period size: 1 Copynumber: 68.0 Consensus size: 1
10858 TACATTTAAA
***
10868 TTTTTTTTTTTTTTTTTTTTTTTTTCAATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
10933 TTT
1 TTT
10936 CAAACACTTT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
1 64 1.00
ACGTcount: A:0.03, C:0.01, G:0.00, T:0.96
Consensus pattern (1 bp):
T
Found at i:11162 original size:13 final size:13
Alignment explanation
Indices: 11144--11168 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11134 ATAATGCACA
11144 GTATCGATACATT
1 GTATCGATACATT
11157 GTATCGATACAT
1 GTATCGATACAT
11169 GACCACTATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:11278 original size:32 final size:33
Alignment explanation
Indices: 11237--11300 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
11227 CCTTAACTGT
11237 TTGTATCGATACAT-A-CAAGATGTATCGATACC
1 TTGTATCGATACATGACCAA-ATGTATCGATACC
11269 TTGTATCGATACATGACCAAATGTATCGATAC
1 TTGTATCGATACATGACCAAATGTATCGATAC
11301 ATTGGCTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
32 14 0.47
33 13 0.43
34 3 0.10
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (33 bp):
TTGTATCGATACATGACCAAATGTATCGATACC
Found at i:17126 original size:51 final size:51
Alignment explanation
Indices: 17061--17226 Score: 174
Period size: 51 Copynumber: 3.3 Consensus size: 51
17051 ATTTTTCATC
**
17061 TCGGGGATACTCCAA-TCCCGATTCCATTTCCAAAACATCAATTTTTCTTAA
1 TCGGGGATACTCCAACT-CCGATTTTATTTCCAAAACATCAATTTTTCTTAA
* * * * ** **
17112 TCGGGGATATTCCAACTCCGATTTTATTTCTAAAGCATTAATTTACCGCAA
1 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACATCAATTTTTCTTAA
* * *
17163 TCGGGGATACTCAAACTCCGATTTTATTTTCAAAACACCAA-TTTTCTATAA
1 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACATCAATTTTTCT-TAA
*
17214 TCAGGGATACTCC
1 TCGGGGATACTCC
17227 GACCCTGTTA
Statistics
Matches: 90, Mismatches: 23, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
50 3 0.03
51 86 0.96
52 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (51 bp):
TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACATCAATTTTTCTTAA
Found at i:17296 original size:79 final size:79
Alignment explanation
Indices: 17165--17385 Score: 336
Period size: 79 Copynumber: 2.8 Consensus size: 79
17155 TACCGCAATC
* * *
17165 GGGGATACTCAAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCAGGGATACTCCGAC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCAGGGATACTCCAAC
17230 CCTGTTATTTCCGA
66 CCTGTTATTTCCGA
* *
17244 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTCTATAATCAGGGATACTCCAAT
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCAGGGATACTCCAAC
**
17309 CCTGTTATTTTTGA
66 CCTGTTATTTCCGA
* * *
17323 GTGGATACTCCAACCCCGATTTTATTTTCAAAACACCGATTTT-TCATAATCGGGGATACTCCA
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCT-ATAATCAGGGATACTCCA
17386 GCCCCGTTGT
Statistics
Matches: 130, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
78 1 0.01
79 129 0.99
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.34
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCAGGGATACTCCAAC
CCTGTTATTTCCGA
Found at i:19834 original size:19 final size:19
Alignment explanation
Indices: 19788--19842 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
19778 TGCCAATTTT
**
19788 ATGTATCGATACAATTGTCC
1 ATGTATCGATACAA-TGAAC
*
19808 ACGTATCGATACAATGAAC
1 ATGTATCGATACAATGAAC
19827 ATGTATCGATACAATG
1 ATGTATCGATACAATG
19843 TATCGATACA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.58
20 13 0.42
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.29
Consensus pattern (19 bp):
ATGTATCGATACAATGAAC
Found at i:19845 original size:13 final size:13
Alignment explanation
Indices: 19827--19853 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
19817 TACAATGAAC
19827 ATGTATCGATACA
1 ATGTATCGATACA
19840 ATGTATCGATACA
1 ATGTATCGATACA
19853 A
1 A
19854 GGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:21536 original size:20 final size:19
Alignment explanation
Indices: 21511--21601 Score: 85
Period size: 20 Copynumber: 4.6 Consensus size: 19
21501 ACCCTAGAAA
21511 GTATCGATACATATCCAGAT
1 GTATCGATACATATCCA-AT
* **
21531 GTATCGATACATTATGCTTT
1 GTATCGATACA-TATCCAAT
* * *
21551 GTATCGATACATGTTCATT
1 GTATCGATACATATCCAAT
21570 GTATCGATACATA-CTCAATT
1 GTATCGATACATATC-CAA-T
21590 GTATCGATACAT
1 GTATCGATACAT
21602 GAAACTGGCA
Statistics
Matches: 59, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
19 19 0.32
20 36 0.61
21 4 0.07
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (19 bp):
GTATCGATACATATCCAAT
Found at i:21580 original size:39 final size:40
Alignment explanation
Indices: 21511--21602 Score: 109
Period size: 39 Copynumber: 2.3 Consensus size: 40
21501 ACCCTAGAAA
* *
21511 GTATCGATACATATCCAGATGTATCGATACATTA-TGC-TTT
1 GTATCGATACATGTCCAGATGTATCGATACA-TACT-CAATT
* *
21551 GTATCGATACATGTTCA-TTGTATCGATACATACTCAATT
1 GTATCGATACATGTCCAGATGTATCGATACATACTCAATT
21590 GTATCGATACATG
1 GTATCGATACATG
21603 AAACTGGCAG
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
38 3 0.07
39 28 0.61
40 15 0.33
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.37
Consensus pattern (40 bp):
GTATCGATACATGTCCAGATGTATCGATACATACTCAATT
Found at i:22138 original size:23 final size:23
Alignment explanation
Indices: 22095--22138 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
22085 GCATTCAACC
* *
22095 TTGGGTTATAATCTTTTAAGAAT
1 TTGGGGTATAATCTTTGAAGAAT
22118 TTGGGGTATAAT-TCTTGAAGA
1 TTGGGGTATAATCT-TTGAAGA
22139 GATTGTGAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 1 0.06
23 17 0.94
ACGTcount: A:0.30, C:0.05, G:0.23, T:0.43
Consensus pattern (23 bp):
TTGGGGTATAATCTTTGAAGAAT
Found at i:22698 original size:33 final size:33
Alignment explanation
Indices: 22654--22722 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
22644 CTACCACTGT
*
22654 TTGTATCGATACAT-AGGACATTGTATCGTTACA
1 TTGTATCGATACATGAGGA-ATTGTATCGATACA
* *
22687 TTGTATTGATACATGATGAATTGTATCGATACA
1 TTGTATCGATACATGAGGAATTGTATCGATACA
22720 TTG
1 TTG
22723 CTTGTAACGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 29 0.91
34 3 0.09
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (33 bp):
TTGTATCGATACATGAGGAATTGTATCGATACA
Found at i:28849 original size:21 final size:19
Alignment explanation
Indices: 28825--28872 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
28815 TAAATCCTTT
*
28825 TCAAAATTCATCATTTTCACA
1 TCAAAATACAT-ATTTT-ACA
*
28846 TCAAAACTACATATTTTTCA
1 TCAAAA-TACATATTTTACA
28866 TCAAAAT
1 TCAAAAT
28873 CTTCATCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 1 0.04
20 8 0.33
21 11 0.46
22 4 0.17
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.38
Consensus pattern (19 bp):
TCAAAATACATATTTTACA
Found at i:30300 original size:15 final size:15
Alignment explanation
Indices: 30280--30311 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
30270 TTACTTTTCC
*
30280 TCTAGTGATGATGAG
1 TCTAGTGACGATGAG
30295 TCTAGTGACGATGAG
1 TCTAGTGACGATGAG
30310 TC
1 TC
30312 ATAGGGTTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.12, G:0.31, T:0.31
Consensus pattern (15 bp):
TCTAGTGACGATGAG
Found at i:31274 original size:13 final size:13
Alignment explanation
Indices: 31256--31315 Score: 51
Period size: 13 Copynumber: 5.1 Consensus size: 13
31246 ACATTATGCT
31256 TTGTATCGATACA
1 TTGTATCGATACA
*
31269 TTGTATCAATACA
1 TTGTATCGATACA
*
31282 -TG---GGA--CA
1 TTGTATCGATACA
31289 TTGTATCGATACA
1 TTGTATCGATACA
*
31302 TTGTATAGATACA
1 TTGTATCGATACA
31315 T
1 T
31316 GGTAAAAAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 12
0.68 0.09 0.23
Matches are distributed among these distances:
7 2 0.06
8 2 0.06
9 1 0.03
11 2 0.06
12 2 0.06
13 27 0.75
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:31281 original size:33 final size:34
Alignment explanation
Indices: 31237--31315 Score: 92
Period size: 33 Copynumber: 2.4 Consensus size: 34
31227 CATATCTAGA
* * *
31237 TGTATCGATACATTATG-CTTTGTATCGATACAT
1 TGTATCAATACATTAGGACATTGTATCGATACAT
*
31270 TGTATCAATACA-TGGGACATTGTATCGATACAT
1 TGTATCAATACATTAGGACATTGTATCGATACAT
31303 TGTAT-AGATACAT
1 TGTATCA-ATACAT
31316 GGTAAAAAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
32 3 0.08
33 36 0.92
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (34 bp):
TGTATCAATACATTAGGACATTGTATCGATACAT
Found at i:31316 original size:33 final size:33
Alignment explanation
Indices: 31256--31336 Score: 110
Period size: 33 Copynumber: 2.5 Consensus size: 33
31246 ACATTATGCT
*
31256 TTGTATCGATACATTGTATCAATACATGGGACA
1 TTGTATCGATACATTGTATCAATACATGGGAAA
*
31289 TTGTATCGATACATTGTAT-AGATACATGGTAAA
1 TTGTATCGATACATTGTATCA-ATACATGGGAAA
**
31322 AAGTATCGATACATT
1 TTGTATCGATACATT
31337 ATGCTTTGTA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
32 1 0.02
33 42 0.98
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (33 bp):
TTGTATCGATACATTGTATCAATACATGGGAAA
Found at i:31341 original size:86 final size:86
Alignment explanation
Indices: 31238--31426 Score: 378
Period size: 86 Copynumber: 2.2 Consensus size: 86
31228 ATATCTAGAT
31238 GTATCGATACATTATGCTTTGTATCGATACATTGTATCAATACATGGGACATTGTATCGATACAT
1 GTATCGATACATTATGCTTTGTATCGATACATTGTATCAATACATGGGACATTGTATCGATACAT
31303 TGTATAGATACATGGTAAAAA
66 TGTATAGATACATGGTAAAAA
31324 GTATCGATACATTATGCTTTGTATCGATACATTGTATCAATACATGGGACATTGTATCGATACAT
1 GTATCGATACATTATGCTTTGTATCGATACATTGTATCAATACATGGGACATTGTATCGATACAT
31389 TGTATAGATACATGGTAAAAA
66 TGTATAGATACATGGTAAAAA
31410 GTATCGATACATTATGC
1 GTATCGATACATTATGC
31427 CCAACGGCTA
Statistics
Matches: 103, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 103 1.00
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.35
Consensus pattern (86 bp):
GTATCGATACATTATGCTTTGTATCGATACATTGTATCAATACATGGGACATTGTATCGATACAT
TGTATAGATACATGGTAAAAA
Found at i:31360 original size:13 final size:13
Alignment explanation
Indices: 31342--31401 Score: 51
Period size: 13 Copynumber: 5.1 Consensus size: 13
31332 ACATTATGCT
31342 TTGTATCGATACA
1 TTGTATCGATACA
*
31355 TTGTATCAATACA
1 TTGTATCGATACA
*
31368 -TG---GGA--CA
1 TTGTATCGATACA
31375 TTGTATCGATACA
1 TTGTATCGATACA
*
31388 TTGTATAGATACA
1 TTGTATCGATACA
31401 T
1 T
31402 GGTAAAAAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 12
0.68 0.09 0.23
Matches are distributed among these distances:
7 2 0.06
8 2 0.06
9 1 0.03
11 2 0.06
12 2 0.06
13 27 0.75
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:31361 original size:33 final size:34
Alignment explanation
Indices: 31324--31401 Score: 97
Period size: 33 Copynumber: 2.4 Consensus size: 34
31314 ATGGTAAAAA
* *
31324 GTATCGATACATTATG-CTTTGTATCGATACATT
1 GTATCGATACATTAGGACATTGTATCGATACATT
* *
31357 GTATCAATACA-TGGGACATTGTATCGATACATT
1 GTATCGATACATTAGGACATTGTATCGATACATT
*
31390 GTATAGATACAT
1 GTATCGATACAT
31402 GGTAAAAAGT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
32 2 0.05
33 35 0.95
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (34 bp):
GTATCGATACATTAGGACATTGTATCGATACATT
Found at i:31381 original size:53 final size:53
Alignment explanation
Indices: 31289--31389 Score: 150
Period size: 53 Copynumber: 1.9 Consensus size: 53
31279 ACATGGGACA
*
31289 TTGTATCGATACATTGTATAGATACATGGTAAAAAGTATCGATACATTATGCT
1 TTGTATCGATACATTGTATAGATACATGGGAAAAAGTATCGATACATTATGCT
* **
31342 TTGTATCGATACATTGTATCA-ATACATGGGACATTGTATCGATACATT
1 TTGTATCGATACATTGTAT-AGATACATGGGAAAAAGTATCGATACATT
31390 GTATAGATAC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
53 42 0.98
54 1 0.02
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.37
Consensus pattern (53 bp):
TTGTATCGATACATTGTATAGATACATGGGAAAAAGTATCGATACATTATGCT
Found at i:31402 original size:33 final size:33
Alignment explanation
Indices: 31342--31422 Score: 110
Period size: 33 Copynumber: 2.5 Consensus size: 33
31332 ACATTATGCT
*
31342 TTGTATCGATACATTGTATCAATACATGGGACA
1 TTGTATCGATACATTGTATCAATACATGGGAAA
*
31375 TTGTATCGATACATTGTAT-AGATACATGGTAAA
1 TTGTATCGATACATTGTATCA-ATACATGGGAAA
**
31408 AAGTATCGATACATT
1 TTGTATCGATACATT
31423 ATGCCCAACG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
32 1 0.02
33 42 0.98
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (33 bp):
TTGTATCGATACATTGTATCAATACATGGGAAA
Found at i:37142 original size:50 final size:51
Alignment explanation
Indices: 37020--37153 Score: 180
Period size: 50 Copynumber: 2.6 Consensus size: 51
37010 ATTTAACTGG
* * *
37020 ATGTATCGATACATTGAAGAATGTATCGATACATTTGGATCAAAAACCTAGA
1 ATGTATCGATATAATGAAAAATGTATCGATACATTTGGATC-AAAACCTAGA
* * * *
37072 ATGTGTCAATATAATAAAAAATGTATTGATACATTTGGATC-AAACCTAGA
1 ATGTATCGATATAATGAAAAATGTATCGATACATTTGGATCAAAACCTAGA
*
37122 ATGTATCGATATAATGAAAAAAGTATCGATAC
1 ATGTATCGATATAATGAAAAATGTATCGATAC
37154 CTTTTCTTTT
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
50 36 0.51
52 34 0.49
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.30
Consensus pattern (51 bp):
ATGTATCGATATAATGAAAAATGTATCGATACATTTGGATCAAAACCTAGA
Found at i:37745 original size:20 final size:20
Alignment explanation
Indices: 37720--37758 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
37710 GCACTTTGAA
37720 AAGTAAATGTATCAATATAT
1 AAGTAAATGTATCAATATAT
*
37740 AAGTAAATGTATCGATATA
1 AAGTAAATGTATCAATATA
37759 CTTACTGTTT
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:0.49, C:0.05, G:0.13, T:0.33
Consensus pattern (20 bp):
AAGTAAATGTATCAATATAT
Found at i:41419 original size:12 final size:12
Alignment explanation
Indices: 41389--41433 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
41379 GCAAAAGCGT
*
41389 AAAAGGAAAATG
1 AAAAGAAAAATG
41401 -AAA-AAAAATG
1 AAAAGAAAAATG
41411 AAAAGAAAAA-G
1 AAAAGAAAAATG
41422 AAAAAGAAAAAT
1 -AAAAGAAAAAT
41434 AAAGTGAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
10 6 0.21
11 7 0.25
12 15 0.54
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.07
Consensus pattern (12 bp):
AAAAGAAAAATG
Found at i:44157 original size:155 final size:153
Alignment explanation
Indices: 43861--44239 Score: 413
Period size: 155 Copynumber: 2.4 Consensus size: 153
43851 CTAAGTTCAA
* * ** * **
43861 GAAAAATTACGAAAATGCTCTTAAGGGATACCTTCGACGTAAAAGTACTCGATACCCCTAAAAAA
1 GAAAAATTATGAAAATGC-CCTAAGGGA-ATTTTCGACGTAAAAGTACCCGATACCCCTAAAGGA
* * * * *
43926 CTTAAAAAAGATAATAGATGAGATGAACCTATCATTAATATCTACCTTCGGCATAAAAGCAGACC
64 CTTAAAAAAGATAACAGATGAGATGAACCTATCATAAATATCTACCTCCGACATAAAAGCAAACC
*
43991 CAATGATAACCTAGGACGT-AATTCT
129 CAATGACAACCTAGGAC-TCAATTCT
* *
44016 GAAAAATTATGAAATTGCCCATAAGGGACATTTTCGACGTAAAAGTACCCGATATCCCTAAAGGA
1 GAAAAATTATGAAAATGCCC-TAAGGGA-ATTTTCGACGTAAAAGTACCCGATACCCCTAAAGGA
* * * *
44081 CTTAAAAAGGATAACATATGAGATGAGCCTATCCTAAATATCTACCTCCGACATAAAAGCAAACC
64 CTTAAAAAAGATAACAGATGAGATGAACCTATCATAAATATCTACCTCCGACATAAAAGCAAACC
** * *
44146 CGGTGACAACCTAGGACTCGATTTT
129 CAATGACAACCTAGGACTCAATTCT
* * * *
44171 AAAAAATTATGAAAATGACCCT-AGAGG-ATTACTTCAATGTAAAAGTACCCAATACCCCTAAAG
1 GAAAAATTATGAAAATG-CCCTAAG-GGAATT--TTCGACGTAAAAGTACCCGATACCCCTAAAG
44234 GACTTA
62 GACTTA
44240 GGATAATGCT
Statistics
Matches: 188, Mismatches: 30, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
153 3 0.02
154 4 0.02
155 178 0.95
156 3 0.02
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.23
Consensus pattern (153 bp):
GAAAAATTATGAAAATGCCCTAAGGGAATTTTCGACGTAAAAGTACCCGATACCCCTAAAGGACT
TAAAAAAGATAACAGATGAGATGAACCTATCATAAATATCTACCTCCGACATAAAAGCAAACCCA
ATGACAACCTAGGACTCAATTCT
Found at i:45601 original size:19 final size:19
Alignment explanation
Indices: 45577--45615 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
45567 TCCCGTGTAA
*
45577 ATGTATCGATACATTTTTG
1 ATGTATCGATACATATTTG
45596 ATGTATCGATACATATTTG
1 ATGTATCGATACATATTTG
45615 A
1 A
45616 AAATATAGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (19 bp):
ATGTATCGATACATATTTG
Found at i:45684 original size:13 final size:13
Alignment explanation
Indices: 45666--45691 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
45656 ACATTTTTTG
45666 TGTATCGATACAT
1 TGTATCGATACAT
45679 TGTATCGATACAT
1 TGTATCGATACAT
45692 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:45688 original size:32 final size:32
Alignment explanation
Indices: 45647--45709 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
45637 TACCAGCCAA
**
45647 TGTATCGATACATTTTTTG-TGTATCGATACAT
1 TGTATCGATACA-TACTTGCTGTATCGATACAT
45679 TGTATCGATACATACTTGCTGTATCGATACA
1 TGTATCGATACATACTTGCTGTATCGATACA
45710 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 4 0.14
32 24 0.86
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (32 bp):
TGTATCGATACATACTTGCTGTATCGATACAT
Found at i:45775 original size:20 final size:20
Alignment explanation
Indices: 45750--45821 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
45740 CAACTTTTTT
45750 ATGTATCGATACATTACAAC
1 ATGTATCGATACATTACAAC
****
45770 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TACAAC
*
45791 AT-TATCGATACATTGCAAC
1 ATGTATCGATACATTACAAC
45810 ATGTATCGATAC
1 ATGTATCGATAC
45822 TTTGGAATTG
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
19 4 0.10
20 34 0.81
21 4 0.10
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTACAAC
Found at i:45800 original size:40 final size:41
Alignment explanation
Indices: 45729--45821 Score: 152
Period size: 40 Copynumber: 2.3 Consensus size: 41
45719 ACTGCAAGAA
*
45729 ATGTATCGATACAACTTTTTTATGTATCGATACATTACAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTACAAC
* *
45770 ATGTATCGATACATCTTTTTCAT-TATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTACAAC
45810 ATGTATCGATAC
1 ATGTATCGATAC
45822 TTTGGAATTG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
40 28 0.57
41 21 0.43
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACAACTTTTTCATGTATCGATACATTACAAC
Done.