Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold386
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: 157506
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:4673 original size:18 final size:18
Alignment explanation
Indices: 4650--4699 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
4640 TCCATCTTCT
4650 TCTCTCCTC-CTCCTATCA
1 TCTCTCCTCTCT-CTATCA
*
4668 TCTCTCCTCTCTCTATTA
1 TCTCTCCTCTCTCTATCA
*
4686 TCTCTCCTGTCTCT
1 TCTCTCCTCTCTCT
4700 CCTCCTATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 27 0.93
19 2 0.07
ACGTcount: A:0.08, C:0.44, G:0.02, T:0.46
Consensus pattern (18 bp):
TCTCTCCTCTCTCTATCA
Found at i:4708 original size:42 final size:42
Alignment explanation
Indices: 4656--4774 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
4646 TTCTTCTCTC
* *
4656 CTCCTCCTATCATCTCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
4698 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
4740 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
4775 TTGAGGGCTA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.09, C:0.45, G:0.02, T:0.44
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:4715 original size:12 final size:11
Alignment explanation
Indices: 4689--4764 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
4679 TCTATTATCT
*
4689 CTCCTGTCTCTC
1 CTCCTATCTC-C
4701 CTCCTATCATCC
1 CTCCTATC-TCC
4713 CTCCTATCT--
1 CTCCTATCTCC
*
4722 CTACTATCT--
1 CTCCTATCTCC
*
4731 CTCCTGTCTCTC
1 CTCCTATCTC-C
4743 CTCCTATCATCC
1 CTCCTATC-TCC
*
4755 CTCCTCTCTC
1 CTCCTATCTC
4765 TTCTTTCTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 3 0.06
12 31 0.58
13 4 0.08
ACGTcount: A:0.09, C:0.49, G:0.03, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:4716 original size:24 final size:24
Alignment explanation
Indices: 4680--4765 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
4670 TCTCCTCTCT
* *
4680 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
4704 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
4725 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
4746 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
4766 TCTTTCTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 4 0.08
20 5 0.10
21 14 0.29
22 5 0.10
24 21 0.43
ACGTcount: A:0.10, C:0.45, G:0.02, T:0.42
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:4740 original size:9 final size:9
Alignment explanation
Indices: 4667--4744 Score: 54
Period size: 9 Copynumber: 9.0 Consensus size: 9
4657 TCCTCCTATC
4667 ATCTCTCCT
1 ATCTCTCCT
* **
4676 CTCTCTATT
1 ATCTCTCCT
4685 ATCTCTCCT
1 ATCTCTCCT
*
4694 GTCTCTCCT
1 ATCTCTCCT
* *
4703 -CCTAT-C-
1 ATCTCTCCT
*
4709 ATCCCTCCT
1 ATCTCTCCT
*
4718 ATCTCTACT
1 ATCTCTCCT
4727 ATCTCTCCT
1 ATCTCTCCT
*
4736 GTCTCTCCT
1 ATCTCTCCT
4745 CCTATCATCC
Statistics
Matches: 50, Mismatches: 16, Indels: 6
0.69 0.22 0.08
Matches are distributed among these distances:
7 3 0.06
8 4 0.08
9 43 0.86
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.44
Consensus pattern (9 bp):
ATCTCTCCT
Found at i:4740 original size:18 final size:18
Alignment explanation
Indices: 4667--4741 Score: 60
Period size: 18 Copynumber: 3.8 Consensus size: 18
4657 TCCTCCTATC
* *
4667 ATCTCTCCTCTCTCTATT
1 ATCTCTCCTGTCTCTACT
*
4685 ATCTCTCCTGTCTCTCCTCCT
1 ATCTCTCCTG--TCT-CTACT
*
4706 ATCATCCCTCCTATCTCTACT
1 ATC-T--CTCCTGTCTCTACT
4727 ATCTCTCCTGTCTCT
1 ATCTCTCCTGTCTCT
4742 CCTCCTATCA
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
18 19 0.42
20 4 0.09
21 13 0.29
22 4 0.09
24 5 0.11
ACGTcount: A:0.11, C:0.43, G:0.03, T:0.44
Consensus pattern (18 bp):
ATCTCTCCTGTCTCTACT
Found at i:12581 original size:12 final size:11
Alignment explanation
Indices: 12559--12634 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
12549 AGAGAAAGAA
*
12559 GAGAGAGGAGG
1 GAGATAGGAGG
12570 GATGATAGGAGG
1 GA-GATAGGAGG
*
12582 AGAGACAGGA--
1 -GAGATAGGAGG
*
12592 GAGATAGTA--
1 GAGATAGGAGG
12601 GAGATAGGAGG
1 GAGATAGGAGG
12612 GATGATAGGAGG
1 GA-GATAGGAGG
*
12624 AGAGACAGGAG
1 -GAGATAGGAG
12635 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:12591 original size:24 final size:24
Alignment explanation
Indices: 12558--12643 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
12548 AAGAGAAAGA
*
12558 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
12582 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
12600 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
12624 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
12644 AGAGAGGAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:12610 original size:42 final size:42
Alignment explanation
Indices: 12549--12667 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
12539 TAGCCCTCAA
* *
12549 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
12591 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
12633 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
12668 GAGAGAAGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.43, C:0.03, G:0.46, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:31163 original size:20 final size:20
Alignment explanation
Indices: 31125--31166 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
31115 TTTTTTCAAG
*
31125 AATACAAAAAAAAATGAAAA
1 AATACAAAAAAAAAGGAAAA
* *
31145 AATACAAAAAGAGAGGAAAA
1 AATACAAAAAAAAAGGAAAA
31165 AA
1 AA
31167 AACCAGTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.76, C:0.05, G:0.12, T:0.07
Consensus pattern (20 bp):
AATACAAAAAAAAAGGAAAA
Found at i:31865 original size:12 final size:11
Alignment explanation
Indices: 31843--31918 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
31833 AGAGAAAAAA
*
31843 GAGAGAGGAGG
1 GAGATAGGAGG
31854 GATGATAGGAGG
1 GA-GATAGGAGG
*
31866 AGAGACAGGA--
1 -GAGATAGGAGG
*
31876 GAGATAGTA--
1 GAGATAGGAGG
31885 GAGATAGGAGG
1 GAGATAGGAGG
31896 GATGATAGGAGG
1 GA-GATAGGAGG
*
31908 AGAGACAGGAG
1 -GAGATAGGAG
31919 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:31875 original size:24 final size:24
Alignment explanation
Indices: 31842--31927 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
31832 AAGAGAAAAA
*
31842 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
31866 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
31884 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
31908 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
31928 AGAGAGGAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:31894 original size:42 final size:42
Alignment explanation
Indices: 31833--31951 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
31823 TAGCCGTCAA
* *
31833 AGAGAAAAAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAATAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
31875 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAATAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
31917 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAATAGAGAGAGGAGGGATGATAGGAGGAG
31952 GAGAGAAGAA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.44, C:0.03, G:0.45, T:0.08
Consensus pattern (42 bp):
AGAGATAATAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:40897 original size:43 final size:42
Alignment explanation
Indices: 40819--40938 Score: 186
Period size: 43 Copynumber: 2.8 Consensus size: 42
40809 TAGCCCTCAA
* *
40819 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
40861 AGAGATAGTAGAGATAGGAGGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGA-GGGATGATAGGAGGAGAGACAGG
* *
40904 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
40939 GAGAGAAGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
42 31 0.44
43 40 0.56
ACGTcount: A:0.42, C:0.03, G:0.47, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:44766 original size:43 final size:42
Alignment explanation
Indices: 44688--44807 Score: 186
Period size: 43 Copynumber: 2.8 Consensus size: 42
44678 TAGCCCTCAA
* *
44688 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
44730 AGAGATAGTAGAGATAGGAGGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGA-GGGATGATAGGAGGAGAGACAGG
* *
44773 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
44808 GAGAGAAGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
42 31 0.44
43 40 0.56
ACGTcount: A:0.42, C:0.03, G:0.47, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:48647 original size:43 final size:42
Alignment explanation
Indices: 48569--48688 Score: 186
Period size: 43 Copynumber: 2.8 Consensus size: 42
48559 TAGCCCTCAA
* *
48569 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
48611 AGAGATAGTAGAGATAGGAGGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGA-GGGATGATAGGAGGAGAGACAGG
* *
48654 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
48689 GAGAGAAGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
42 31 0.44
43 40 0.56
ACGTcount: A:0.42, C:0.03, G:0.47, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:52529 original size:43 final size:42
Alignment explanation
Indices: 52451--52570 Score: 186
Period size: 43 Copynumber: 2.8 Consensus size: 42
52441 TAGCCCTCAA
* *
52451 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
52493 AGAGATAGTAGAGATAGGAGGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGA-GGGATGATAGGAGGAGAGACAGG
* *
52536 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
52571 GAGAGAAGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
42 31 0.44
43 40 0.56
ACGTcount: A:0.42, C:0.03, G:0.47, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:60992 original size:28 final size:28
Alignment explanation
Indices: 60941--61012 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 28
60931 TTATTCTTTA
* * *
60941 TTGATTTCTTTTCCTTTGAAATTTCTTG
1 TTGATTTCATTTCCTTTCAAATTTATTG
*
60969 CTT-ATTTCATTTCCTTTCATATTTATTG
1 -TTGATTTCATTTCCTTTCAAATTTATTG
*
60997 TTGATTTCACTTCCTT
1 TTGATTTCATTTCCTT
61013 GATCTTTCTT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
27 2 0.05
28 33 0.89
29 2 0.05
ACGTcount: A:0.15, C:0.18, G:0.07, T:0.60
Consensus pattern (28 bp):
TTGATTTCATTTCCTTTCAAATTTATTG
Found at i:70502 original size:38 final size:38
Alignment explanation
Indices: 70401--70502 Score: 179
Period size: 38 Copynumber: 2.7 Consensus size: 38
70391 TTACATAAGC
*
70401 TTTG-AAAATTGTAACTTCCTTGTCTAGACAGAAAGGG
1 TTTGAAAAATTGTAACTTCCTTGTCTGGACAGAAAGGG
*
70438 TTTGAAAAATTGTAATTTCCTTGTCTGGACAGAAAGGG
1 TTTGAAAAATTGTAACTTCCTTGTCTGGACAGAAAGGG
70476 TTTGAAAAATTGTAACTTCCTTGTCTG
1 TTTGAAAAATTGTAACTTCCTTGTCTG
70503 AATGACCCAA
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
37 4 0.07
38 57 0.93
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (38 bp):
TTTGAAAAATTGTAACTTCCTTGTCTGGACAGAAAGGG
Found at i:72344 original size:182 final size:181
Alignment explanation
Indices: 72033--72396 Score: 683
Period size: 182 Copynumber: 2.0 Consensus size: 181
72023 CCTTCCAAAT
72033 ATATGCAATTAACTAGCTTGGGCTCCTCTAACTCCAAATTGGGTCTACTTTCAAATAGGCCAGCA
1 ATATGCAATTAACTAGCTTGGGCTCCTCTAACTCCAAATTGGGTCTACTTTCAAATAGGCCAGCA
*
72098 ACCATCTTCTCTAGGTCTTCTTTTATCCTCTTTGCCTTTGCCCTCGTCATTGGTCCTCGAAACCC
66 ACCATCTTCTCTAGGTCTTCCTTTATCCTCTTTGCCTTTGCCCTCGTCATTGGTCCTCGAAACCC
72163 TTCCAATGCCTTCAGGTCATTGTATTCAATGGACCTTCCTTGGCTTTCATC
131 TTCCAATGCCTTCAGGTCATTGTATTCAATGGACCTTCCTTGGCTTTCATC
72214 ATATGCAATTAACTAGCTTGGGCTCCCTCTAACTCCAAATTGGGTCTACTTTCAAATAGGCCAGC
1 ATATGCAATTAACTAGCTTGGGCT-CCTCTAACTCCAAATTGGGTCTACTTTCAAATAGGCCAGC
*
72279 AACCATCTTCTCTAGGTCTTCCTTTATCCTCTTTGCCTTTGCCCTCGTCATTGGTCCTTGAAACC
65 AACCATCTTCTCTAGGTCTTCCTTTATCCTCTTTGCCTTTGCCCTCGTCATTGGTCCTCGAAACC
* *
72344 CTTCCAATGCTTTCAGGTCATTGTATTCAATGGACCTTCCTTGGTTTTCATC
130 CTTCCAATGCCTTCAGGTCATTGTATTCAATGGACCTTCCTTGGCTTTCATC
72396 A
1 A
72397 ACCCCTCATT
Statistics
Matches: 178, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
181 24 0.13
182 154 0.87
ACGTcount: A:0.20, C:0.29, G:0.15, T:0.36
Consensus pattern (181 bp):
ATATGCAATTAACTAGCTTGGGCTCCTCTAACTCCAAATTGGGTCTACTTTCAAATAGGCCAGCA
ACCATCTTCTCTAGGTCTTCCTTTATCCTCTTTGCCTTTGCCCTCGTCATTGGTCCTCGAAACCC
TTCCAATGCCTTCAGGTCATTGTATTCAATGGACCTTCCTTGGCTTTCATC
Found at i:74448 original size:12 final size:11
Alignment explanation
Indices: 74426--74501 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
74416 AGAGAAAGAA
*
74426 GAGAGAGGAGG
1 GAGATAGGAGG
74437 GATGATAGGAGG
1 GA-GATAGGAGG
*
74449 AGAGACAGGA--
1 -GAGATAGGAGG
*
74459 GAGATAGTA--
1 GAGATAGGAGG
74468 GAGATAGGAGG
1 GAGATAGGAGG
74479 GATGATAGGAGG
1 GA-GATAGGAGG
*
74491 AGAGACAGGAG
1 -GAGATAGGAG
74502 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:74458 original size:24 final size:24
Alignment explanation
Indices: 74425--74510 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
74415 AAGAGAAAGA
*
74425 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
74449 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
74467 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
74491 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
74511 AGAGAGGAGA
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:74460 original size:9 final size:9
Alignment explanation
Indices: 74446--74523 Score: 54
Period size: 9 Copynumber: 9.0 Consensus size: 9
74436 GGATGATAGG
*
74446 AGGAGAGAC
1 AGGAGAGAT
74455 AGGAGAGAT
1 AGGAGAGAT
*
74464 AGTAGAGAT
1 AGGAGAGAT
*
74473 AGGAGGGAT
1 AGGAGAGAT
* *
74482 --GATAG-G
1 AGGAGAGAT
*
74488 AGGAGAGAC
1 AGGAGAGAT
74497 AGGAGAGAT
1 AGGAGAGAT
** *
74506 AATAGAGAG
1 AGGAGAGAT
74515 AGGAGAGAT
1 AGGAGAGAT
74524 GATAGGAGGA
Statistics
Matches: 50, Mismatches: 16, Indels: 6
0.69 0.22 0.08
Matches are distributed among these distances:
7 3 0.06
8 4 0.08
9 43 0.86
ACGTcount: A:0.44, C:0.03, G:0.44, T:0.10
Consensus pattern (9 bp):
AGGAGAGAT
Found at i:74476 original size:18 final size:18
Alignment explanation
Indices: 74449--74523 Score: 60
Period size: 18 Copynumber: 3.8 Consensus size: 18
74439 TGATAGGAGG
74449 AGAGACAGGAGAGATAGT
1 AGAGACAGGAGAGATAGT
* *
74467 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGA--GA-GAT---AGT
*
74491 AGAGACAGGAGAGATAAT
1 AGAGACAGGAGAGATAGT
*
74509 AGAGAGAGGAGAGAT
1 AGAGACAGGAGAGAT
74524 GATAGGAGGA
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
18 24 0.53
20 2 0.04
21 6 0.13
22 2 0.04
24 11 0.24
ACGTcount: A:0.44, C:0.03, G:0.43, T:0.11
Consensus pattern (18 bp):
AGAGACAGGAGAGATAGT
Found at i:74477 original size:42 final size:42
Alignment explanation
Indices: 74416--74534 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
74406 TAGCCCTCAA
* *
74416 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
74458 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
74500 AGAGATAATAGAGAGAGGAGAGATGATAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
74535 GAGAGAAGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.44, C:0.02, G:0.45, T:0.09
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:74528 original size:18 final size:18
Alignment explanation
Indices: 74491--74540 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
74481 TGATAGGAGG
*
74491 AGAGACAGGAGAGATAAT
1 AGAGAGAGGAGAGATAAT
*
74509 AGAGAGAGGAGAGATGAT
1 AGAGAGAGGAGAGATAAT
74527 AG-GAGGAGGAGAGA
1 AGAGA-GAGGAGAGA
74541 AGAAGATGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 2 0.07
18 27 0.93
ACGTcount: A:0.46, C:0.02, G:0.44, T:0.08
Consensus pattern (18 bp):
AGAGAGAGGAGAGATAAT
Found at i:79354 original size:12 final size:11
Alignment explanation
Indices: 79332--79407 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
79322 AGAGAAAGAA
*
79332 GAGAGAGGAGG
1 GAGATAGGAGG
79343 GATGATAGGAGG
1 GA-GATAGGAGG
*
79355 AGAGACAGGA--
1 -GAGATAGGAGG
*
79365 GAGATAGTA--
1 GAGATAGGAGG
79374 GAGATAGGAGG
1 GAGATAGGAGG
79385 GATGATAGGAGG
1 GA-GATAGGAGG
*
79397 AGAGACAGGAG
1 -GAGATAGGAG
79408 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:79364 original size:24 final size:24
Alignment explanation
Indices: 79331--79416 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
79321 AAGAGAAAGA
*
79331 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
79355 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
79373 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
79397 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
79417 AGAGAGGAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:79383 original size:42 final size:42
Alignment explanation
Indices: 79322--79440 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
79312 TAGCCCTCAA
* *
79322 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
79364 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
79406 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
79441 GAGAGAAGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.43, C:0.03, G:0.46, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:82365 original size:12 final size:11
Alignment explanation
Indices: 82343--82414 Score: 53
Period size: 12 Copynumber: 6.5 Consensus size: 11
82333 AGAGAAAGAA
*
82343 GAGAGAGGAGG
1 GAGATAGGAGG
82354 GATGATAGGAGG
1 GA-GATAGGAGG
*
82366 AGAGACAGGA--
1 -GAGATAGGAGG
*
82376 GAGATAGTA--
1 GAGATAGGAGG
82385 GAGATAGGAGG
1 GAGATAGGAGG
82396 GATGATAGGAGG
1 GA-GATAGGAGG
82408 AGAGATA
1 -GAGATA
82415 ATAGAGAGAG
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
9 15 0.30
11 4 0.08
12 27 0.54
13 4 0.08
ACGTcount: A:0.40, C:0.01, G:0.47, T:0.11
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:82394 original size:42 final size:42
Alignment explanation
Indices: 82333--82412 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
82323 TAGCCCTCAA
82333 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* * *
82375 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGA
1 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGA
82413 TAATAGAGAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.44, C:0.01, G:0.46, T:0.09
Consensus pattern (42 bp):
AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:82409 original size:33 final size:33
Alignment explanation
Indices: 82372--82442 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
82362 GAGGAGAGAC
* * *
82372 AGGAGAGATAGTAGAGATAGGAGGGATGATAGG
1 AGGAGAGATAATAGAGAGAGGAGGGATGACAGG
82405 AGGAGAGATAATAGAGAGAGGAGGGATGACAGG
1 AGGAGAGATAATAGAGAGAGGAGGGATGACAGG
82438 AGGAG
1 AGGAG
82443 GAGAGAAGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.41, C:0.01, G:0.46, T:0.11
Consensus pattern (33 bp):
AGGAGAGATAATAGAGAGAGGAGGGATGACAGG
Found at i:82421 original size:42 final size:42
Alignment explanation
Indices: 82333--82421 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 42
82323 TAGCCCTCAA
*
82333 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAAG
* * * * *
82375 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGATAAT
1 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAAG
82417 AGAGA
1 AGAGA
82422 GAGGAGGGAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.45, C:0.01, G:0.44, T:0.10
Consensus pattern (42 bp):
AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAAG
Found at i:91767 original size:42 final size:42
Alignment explanation
Indices: 91688--91805 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
91678 TTCTTCTCTC
* *
91688 CTCCTCCTGTCATCCCTCC-CTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
91729 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
91771 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
91806 TTGAGGGCTA
Statistics
Matches: 70, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
41 18 0.26
42 52 0.74
ACGTcount: A:0.08, C:0.47, G:0.03, T:0.42
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:96667 original size:9 final size:9
Alignment explanation
Indices: 96655--96715 Score: 56
Period size: 9 Copynumber: 7.1 Consensus size: 9
96645 CTCTCTCTAT
96655 TATCTCTCC
1 TATCTCTCC
96664 TATCTCTCC
1 TATCTCTCC
* *
96673 T-CCTAT-C
1 TATCTCTCC
*
96680 -ATCCCTCC
1 TATCTCTCC
*
96688 TATCTCTAC
1 TATCTCTCC
*
96697 TATCTCTCT
1 TATCTCTCC
96706 TATCTCTCC
1 TATCTCTCC
96715 T
1 T
96716 CCTATCATCC
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
7 3 0.08
8 4 0.10
9 32 0.82
ACGTcount: A:0.13, C:0.43, G:0.00, T:0.44
Consensus pattern (9 bp):
TATCTCTCC
Found at i:96675 original size:12 final size:12
Alignment explanation
Indices: 96660--96736 Score: 71
Period size: 12 Copynumber: 6.9 Consensus size: 12
96650 TCTATTATCT
96660 CTCCTATCTCTC
1 CTCCTATCTCTC
96672 CTCCTATCATC-C
1 CTCCTATC-TCTC
96684 CTCCTA--TCT-
1 CTCCTATCTCTC
*
96693 CTACTATCTCT-
1 CTCCTATCTCTC
96704 CT--TATCTCTC
1 CTCCTATCTCTC
96714 CTCCTATCATC-C
1 CTCCTATC-TCTC
96726 CTCCTATCTCT
1 CTCCTATCTCT
96737 TCTTTCTCTT
Statistics
Matches: 55, Mismatches: 1, Indels: 18
0.74 0.01 0.24
Matches are distributed among these distances:
9 14 0.25
10 2 0.04
11 7 0.13
12 28 0.51
13 4 0.07
ACGTcount: A:0.13, C:0.45, G:0.00, T:0.42
Consensus pattern (12 bp):
CTCCTATCTCTC
Found at i:96682 original size:42 final size:42
Alignment explanation
Indices: 96627--96745 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
96617 TTCTTCTCTC
* * *
96627 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTATCT
1 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATCT
*
96669 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCTTATCT
1 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATCT
* *
96711 CTCCTCCTATCATCCCTCCTATCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCT
96746 TTGAGGGCTA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.11, C:0.45, G:0.01, T:0.44
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATCT
Found at i:99374 original size:42 final size:42
Alignment explanation
Indices: 99319--99437 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
99309 TTCTTCTCTC
* *
99319 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
99361 CTCCTCCTATCATCCCTCCTATCTCTACTATTTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
99403 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
99438 TTGAGGGCTA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.08, C:0.45, G:0.03, T:0.44
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:99379 original size:24 final size:24
Alignment explanation
Indices: 99343--99428 Score: 76
Period size: 24 Copynumber: 3.8 Consensus size: 24
99333 CCTCCTCTCT
* *
99343 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
99367 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
*
99388 CTAT--T-TCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
99409 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
99429 TCTTTCTCTT
Statistics
Matches: 47, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
18 4 0.09
19 1 0.02
20 4 0.09
21 12 0.26
22 4 0.09
23 1 0.02
24 21 0.45
ACGTcount: A:0.10, C:0.44, G:0.02, T:0.43
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:100210 original size:15 final size:15
Alignment explanation
Indices: 100174--100210 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
100164 AAATGCTGGC
100174 TTTTTTTCTCTCTTT
1 TTTTTTTCTCTCTTT
*
100189 TTGTTTTCTCTCTTT
1 TTTTTTTCTCTCTTT
100204 TTTTTTT
1 TTTTTTT
100211 TGTATTCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (15 bp):
TTTTTTTCTCTCTTT
Found at i:101310 original size:315 final size:315
Alignment explanation
Indices: 100738--101365 Score: 1193
Period size: 315 Copynumber: 2.0 Consensus size: 315
100728 TAACAAGCCT
100738 AACTCTTACATAAACCCAAATAACAAGTTTTTATGCTAAATAAAGCCCAAAGCAAGTCACAACCA
1 AACTCTTACATAAACCCAAATAACAAGTTTTTATGCTAAATAAAGCCCAAAGCAAGTCACAACCA
*
100803 GCAGGCCCTTTATTACAAAATAACCCAAGTCCTAATTCAATCCATTGGGGCCCATATCTTCCAAA
66 GCAGGCCCTTTATTACAAAATAACCCAAGTCCTAATTCAATCCATTGGAGCCCATATCTTCCAAA
* *
100868 TATATGCAATTAACTAGCTTGGGTTCTTCTAACTCCAAATTGGGTCTACTTTCAAATAGGCTAGC
131 TATATGCAATTAACTAGCTTGGGCTCTTCTAACTCCAAATTGGGTCTACTTTCAAATAGGCCAGC
100933 AACCATCTTCTCTAGGTCTTCCTTTATCCTCTTTGCCTTTGCCCTCGTTATTGGTCCTTGAAATC
196 AACCATCTTCTCTAGGTCTTCCTTTATCCTCTTTGCCTTTGCCCTCGTTATTGGTCCTTGAAATC
100998 CTTCCAACACCTTCAGGTCTTTGTCTTCAATGGACCTTCCTTGGTTTTCATCACC
261 CTTCCAACACCTTCAGGTCTTTGTCTTCAATGGACCTTCCTTGGTTTTCATCACC
*
101053 AACTCTTACTTAAACCCAAATAACAAGTTTTTATGCTAAATAAAGCCCAAAGCAAGTCACAACCA
1 AACTCTTACATAAACCCAAATAACAAGTTTTTATGCTAAATAAAGCCCAAAGCAAGTCACAACCA
*
101118 GCAGGCCCTTTATTACAAAATAACCCAAGTCCTAATTGAATCCATTGGAGCCCATATCTTCCAAA
66 GCAGGCCCTTTATTACAAAATAACCCAAGTCCTAATTCAATCCATTGGAGCCCATATCTTCCAAA
101183 TATATGCAATTAACTAGCTTGGGCTCTTCTAACTCCAAATTGGGTCTACTTTCAAATAGGCCAGC
131 TATATGCAATTAACTAGCTTGGGCTCTTCTAACTCCAAATTGGGTCTACTTTCAAATAGGCCAGC
*
101248 AACCATCTTCTCTAGGTCTTCCTTTATCCTTTTTGCCTTTGCCCTCGTTATTGGTCCTTGAAATC
196 AACCATCTTCTCTAGGTCTTCCTTTATCCTCTTTGCCTTTGCCCTCGTTATTGGTCCTTGAAATC
*
101313 CTTCCAACGCCTTCAGGTCTTTGTCTTCAATGGACCTTCCTTGGTTTTCATCA
261 CTTCCAACACCTTCAGGTCTTTGTCTTCAATGGACCTTCCTTGGTTTTCATCA
101366 ACCCCTCCTT
Statistics
Matches: 306, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
315 306 1.00
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.33
Consensus pattern (315 bp):
AACTCTTACATAAACCCAAATAACAAGTTTTTATGCTAAATAAAGCCCAAAGCAAGTCACAACCA
GCAGGCCCTTTATTACAAAATAACCCAAGTCCTAATTCAATCCATTGGAGCCCATATCTTCCAAA
TATATGCAATTAACTAGCTTGGGCTCTTCTAACTCCAAATTGGGTCTACTTTCAAATAGGCCAGC
AACCATCTTCTCTAGGTCTTCCTTTATCCTCTTTGCCTTTGCCCTCGTTATTGGTCCTTGAAATC
CTTCCAACACCTTCAGGTCTTTGTCTTCAATGGACCTTCCTTGGTTTTCATCACC
Found at i:105494 original size:51 final size:51
Alignment explanation
Indices: 105376--105559 Score: 210
Period size: 51 Copynumber: 3.6 Consensus size: 51
105366 TTTGGAAAGA
* * * * *
105376 AAATGTATCAATACATTTTTTTTTGTATCAATACATTTTGGG-TTTGATCC
1 AAATGTATCGATACATTATTTATTGTATCAATACATTCTGGGTTTTGACCC
* **
105426 AAATGTATCGATACATTATTTGTTGTATTGATACATTCTGGGTTTTGACCC
1 AAATGTATCGATACATTATTTATTGTATCAATACATTCTGGGTTTTGACCC
* * * *
105477 AGATGTATTGATACATTATTCATTGTATCAATACATTCTGGATTTTGACCC
1 AAATGTATCGATACATTATTTATTGTATCAATACATTCTGGGTTTTGACCC
* * * *
105528 AAATGCATCTATACATTCTTTA-TGTATTAATA
1 AAATGTATCGATACATTATTTATTGTATCAATA
105560 TATCCAGTTA
Statistics
Matches: 112, Mismatches: 21, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
50 45 0.40
51 67 0.60
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.44
Consensus pattern (51 bp):
AAATGTATCGATACATTATTTATTGTATCAATACATTCTGGGTTTTGACCC
Found at i:111939 original size:18 final size:19
Alignment explanation
Indices: 111897--111946 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
111887 TCCATCTTCT
111897 TCTCTCCTC-CTCTTGTCA
1 TCTCTCCTCTCTCTTGTCA
*
111915 TCCCTCCTCTCTCTAT-T-A
1 TCTCTCCTCTCTCT-TGTCA
*
111933 TCTCTCCTGTCTCT
1 TCTCTCCTCTCTCT
111947 CCTCCTATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 21 0.78
19 5 0.19
20 1 0.04
ACGTcount: A:0.06, C:0.44, G:0.04, T:0.46
Consensus pattern (19 bp):
TCTCTCCTCTCTCTTGTCA
Found at i:111958 original size:42 final size:42
Alignment explanation
Indices: 111903--112021 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
111893 TTCTTCTCTC
* * *
111903 CTCCTCTTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
111945 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
111987 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
112022 TTGAGGGCTA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.08, C:0.45, G:0.03, T:0.44
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:111962 original size:12 final size:11
Alignment explanation
Indices: 111936--112011 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
111926 TCTATTATCT
*
111936 CTCCTGTCTCTC
1 CTCCTATCTC-C
111948 CTCCTATCATCC
1 CTCCTATC-TCC
111960 CTCCTATCT--
1 CTCCTATCTCC
*
111969 CTACTATCT--
1 CTCCTATCTCC
*
111978 CTCCTGTCTCTC
1 CTCCTATCTC-C
111990 CTCCTATCATCC
1 CTCCTATC-TCC
*
112002 CTCCTCTCTC
1 CTCCTATCTC
112012 TTCTTTCTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 3 0.06
12 31 0.58
13 4 0.08
ACGTcount: A:0.09, C:0.49, G:0.03, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:111963 original size:24 final size:24
Alignment explanation
Indices: 111927--112012 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
111917 CCTCCTCTCT
* *
111927 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
111951 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
111972 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
111993 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
112013 TCTTTCTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 4 0.08
20 5 0.10
21 14 0.29
22 5 0.10
24 21 0.43
ACGTcount: A:0.10, C:0.45, G:0.02, T:0.42
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:111987 original size:18 final size:18
Alignment explanation
Indices: 111918--111988 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
111908 CTTGTCATCC
* *
111918 CTCCTCTCTCTATTATCT
1 CTCCTGTCTCTACTATCT
*
111936 CTCCTGTCTCTCCTCCTATCAT
1 CTCCTG--TCT-CTACTATC-T
*
111958 CCCTCCTATCTCTACTATCT
1 --CTCCTGTCTCTACTATCT
111978 CTCCTGTCTCT
1 CTCCTGTCTCT
111989 CCTCCTATCA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
18 15 0.37
20 4 0.10
21 13 0.32
22 4 0.10
24 5 0.12
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.44
Consensus pattern (18 bp):
CTCCTGTCTCTACTATCT
Found at i:114844 original size:12 final size:11
Alignment explanation
Indices: 114822--114897 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
114812 AGAGAAAGAA
*
114822 GAGAGAGGAGG
1 GAGATAGGAGG
114833 GATGATAGGAGG
1 GA-GATAGGAGG
*
114845 AGAGACAGGA--
1 -GAGATAGGAGG
*
114855 GAGATAGTA--
1 GAGATAGGAGG
114864 GAGATAGGAGG
1 GAGATAGGAGG
114875 GATGATAGGAGG
1 GA-GATAGGAGG
*
114887 AGAGACAGGAG
1 -GAGATAGGAG
114898 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:114854 original size:24 final size:24
Alignment explanation
Indices: 114821--114906 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
114811 AAGAGAAAGA
*
114821 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
114845 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
114863 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
114887 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
114907 AGAGAGGAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:114873 original size:42 final size:42
Alignment explanation
Indices: 114812--114930 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
114802 TAGCCCTGAA
* *
114812 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
114854 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
114896 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
114931 GAGAGAAGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.43, C:0.03, G:0.46, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:122273 original size:79 final size:79
Alignment explanation
Indices: 122141--122370 Score: 257
Period size: 79 Copynumber: 2.9 Consensus size: 79
122131 TGGAGATGAC
* * * * * *
122141 AACGGGGCTGGAGTATCCCCTAATTATAGGAAATCGACATTTTGAGAATAAAATCGGGGTTGGAG
1 AACGGGGTTGGAGTATCCCC-GATTGTAGAAAATCGATATTTTGAAAATAAAATCGGGGTTGGAG
*
122206 TATCCCCTTGAAAAT
65 TATCCCCTCGAAAAT
* * *
122221 AACGGGGTTGGAGTATCCCCGATTGTAGAAAATCGGTATTTTGAAAATAAAATCGGGATTGGAGC
1 AACGGGGTTGGAGTATCCCCGATTGTAGAAAATCGATATTTTGAAAATAAAATCGGGGTTGGAGT
*
122286 ATTCCCTCGAAAAT
66 ATCCCCTCGAAAAT
* * * ** **
122300 AACGGGGTTGAAGTATCCCTGATTGT-GAAAAATCGATGATTTAG-AAATAAGGTCGGGGTTAAA
1 AACGGGGTTGGAGTATCCCCGATTGTAG-AAAATCGAT-ATTTTGAAAATAAAATCGGGGTTGGA
122363 GTATCCCC
64 GTATCCCC
122371 GATTGTGAGA
Statistics
Matches: 126, Mismatches: 22, Indels: 5
0.82 0.14 0.03
Matches are distributed among these distances:
78 1 0.01
79 101 0.80
80 24 0.19
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.27
Consensus pattern (79 bp):
AACGGGGTTGGAGTATCCCCGATTGTAGAAAATCGATATTTTGAAAATAAAATCGGGGTTGGAGT
ATCCCCTCGAAAAT
Found at i:122369 original size:51 final size:51
Alignment explanation
Indices: 122302--122421 Score: 152
Period size: 51 Copynumber: 2.4 Consensus size: 51
122292 TCGAAAATAA
* * *
122302 CGGGGTTGAAGTATCCCTGATTGTGAAAAATCGATGATTTAG-AAATAAGGT
1 CGGGGTTGAAGTATCCCTGATTGTGAAAAATCAAT-ATTTAGAAAATAAAGC
* * * *
122353 CGGGGTTAAAGTATCCCCGATTGTGAGAAATCAATATTTTGAAAATAAAGC
1 CGGGGTTGAAGTATCCCTGATTGTGAAAAATCAATATTTAGAAAATAAAGC
*
122404 CGGGGTTGGAGTATCCCT
1 CGGGGTTGAAGTATCCCT
122422 CGAAAATAAC
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
50 5 0.09
51 53 0.91
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.28
Consensus pattern (51 bp):
CGGGGTTGAAGTATCCCTGATTGTGAAAAATCAATATTTAGAAAATAAAGC
Found at i:122465 original size:28 final size:27
Alignment explanation
Indices: 122404--122479 Score: 118
Period size: 28 Copynumber: 2.8 Consensus size: 27
122394 AAAATAAAGC
122404 CGGGGTTGGAGTATCCCTCGA-AAATAA
1 CGGGGTTGGAGTATCCC-CGATAAATAA
122431 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAT-AAATAA
*
122459 TGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
122480 TGTGAAAAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
26 3 0.07
27 17 0.37
28 26 0.57
ACGTcount: A:0.25, C:0.18, G:0.33, T:0.24
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCCGATAAATAA
Found at i:122530 original size:51 final size:51
Alignment explanation
Indices: 122463--122578 Score: 178
Period size: 51 Copynumber: 2.3 Consensus size: 51
122453 AAATAATGGG
* *
122463 GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTAGAAATAAAACCGGA
* * * *
122514 GTTGGAGTATCTCCGATTGTGGAGAATTGGTGTTTTAGAAATAAAACCGGG
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTAGAAATAAAACCGGA
122565 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
122579 TCGAAAATAA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 58 1.00
ACGTcount: A:0.28, C:0.12, G:0.29, T:0.31
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTAGAAATAAAACCGGA
Found at i:122614 original size:28 final size:28
Alignment explanation
Indices: 122561--122633 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 28
122551 GAAATAAAAC
*
122561 CGGGGTTGGAGTATCCCCTCGAAAATAA
1 CGGGGTTGGAGTATCCCATCGAAAATAA
*
122589 GGGGGTTGGAGTATCCACAAT-G-AAATAA
1 CGGGGTTGGAGTATCC-C-ATCGAAAATAA
*
122617 CGGGGTTAGAGTATCCC
1 CGGGGTTGGAGTATCCC
122634 TGATTGTGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
27 1 0.03
28 35 0.90
29 2 0.05
30 1 0.03
ACGTcount: A:0.29, C:0.18, G:0.32, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCATCGAAAATAA
Found at i:122639 original size:158 final size:156
Alignment explanation
Indices: 122296--122687 Score: 527
Period size: 158 Copynumber: 2.5 Consensus size: 156
122286 ATTCCCTCGA
* * * * ** *
122296 AAATAACGGGGTTGAAGTATCCCTGATTGTGAAAAATCGATGATTTAGAAATAAGGTCGGGGTTA
1 AAATAACGGGGTTG-AGTATCCCTGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGGAGTTA
* *
122361 AAGTATCCCCGATTGTGAGAAATCAATATTTTGAAAATAAAGCCGGGGTTGGAGTATCCCTCGAA
65 GAGTATCCCCGATTGTGAGAAATCAATATTTTGAAAATAAAACCGGGGTTGGAGTATCCCTCGAA
* *
122426 AATAACGGGGTTGGAGTATCCCCGATG
130 AATAACGGGGTTGGAGTATCCACAATG
* * *
122453 AAATAATGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGGAGTTG
1 AAATAACGGGGTT-GAGTATCCCTGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGGAGTTA
* *** *
122518 GAGTATCTCCGATTGTG-GAGAATTGGTGTTTT-AGAAATAAAACCGGGGTTGGAGTATCCCCTC
65 GAGTATCCCCGATTGTGAGA-AATCAATATTTTGA-AAATAAAACCGGGGTTGGAGTAT-CCCTC
*
122581 GAAAATAAGGGGGTTGGAGTATCCACAATG
127 GAAAATAACGGGGTTGGAGTATCCACAATG
*
122611 AAATAACGGGGTTAGAGTATCCCTGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGGAGTTT
1 AAATAACGGGGTT-GAGTATCCCTGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGGAGTTA
122676 GAGTATCCCCGA
65 GAGTATCCCCGA
122688 GATAAAAAAT
Statistics
Matches: 206, Mismatches: 25, Indels: 7
0.87 0.11 0.03
Matches are distributed among these distances:
156 3 0.01
157 98 0.48
158 105 0.51
ACGTcount: A:0.32, C:0.12, G:0.28, T:0.28
Consensus pattern (156 bp):
AAATAACGGGGTTGAGTATCCCTGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGGAGTTAG
AGTATCCCCGATTGTGAGAAATCAATATTTTGAAAATAAAACCGGGGTTGGAGTATCCCTCGAAA
ATAACGGGGTTGGAGTATCCACAATG
Found at i:122684 original size:51 final size:51
Alignment explanation
Indices: 122463--122684 Score: 171
Period size: 51 Copynumber: 4.3 Consensus size: 51
122453 AAATAATGGG
*
122463 GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCTGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGGA
* * * * *
122514 GTTGGAGTATCTCC-GATTGTGGAGAATTGGTGTTTTAGAAATAAAACCGGG
1 GTTGGAGTATC-CCTGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGGA
*** *** * * ** * *
122565 GTTGGAGTATCCCCTCGAAAAT-AAGGGGGTTGGAG-TATCCACAATGAAATAACGGG
1 GTTGGAGTAT-CCCT-GATTGTGAA--AAATTGGTGTTTTGGA-AAT-AAA-ATCGGA
*
122621 GTTAGAGTATCCCTGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCTGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGGA
*
122672 GTTTGAGTATCCC
1 GTTGGAGTATCCC
122685 CGAGATAAAA
Statistics
Matches: 130, Mismatches: 30, Indels: 22
0.71 0.16 0.12
Matches are distributed among these distances:
51 71 0.55
52 7 0.05
53 14 0.11
54 15 0.12
55 9 0.07
56 14 0.11
ACGTcount: A:0.30, C:0.12, G:0.28, T:0.30
Consensus pattern (51 bp):
GTTGGAGTATCCCTGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGGA
Found at i:129567 original size:24 final size:23
Alignment explanation
Indices: 129534--129625 Score: 79
Period size: 24 Copynumber: 4.2 Consensus size: 23
129524 AAGAGAAAGA
*
129534 AGAGAGAGGAGGGATGATAGGAAG
1 AGAGACAGGAGGGATGATAGG-AG
*
129558 AGAGACAGGA--GA-GATA-G-T
1 AGAGACAGGAGGGATGATAGGAG
*
129576 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGA-G
* *
129600 AGAGACAGGAGAGATAATA-GAG
1 AGAGACAGGAGGGATGATAGGAG
129622 AGAG
1 AGAG
129626 GAGGGATGAC
Statistics
Matches: 55, Mismatches: 7, Indels: 14
0.72 0.09 0.18
Matches are distributed among these distances:
18 9 0.16
20 3 0.05
21 8 0.15
22 8 0.15
23 2 0.04
24 25 0.45
ACGTcount: A:0.43, C:0.02, G:0.45, T:0.10
Consensus pattern (23 bp):
AGAGACAGGAGGGATGATAGGAG
Found at i:129640 original size:42 final size:42
Alignment explanation
Indices: 129534--129643 Score: 184
Period size: 42 Copynumber: 2.6 Consensus size: 42
129524 AAGAGAAAGA
* *
129534 AGAGAGAGGAGGGATGATAGGAAGAGAGACAGGAGAGATAGT
1 AGAGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
*
129576 AGAGATAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
1 AGAGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
*
129618 AGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGAGAGGAGGGATGATAGGAGGAG
129644 GAGAGAAGAA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.42, C:0.03, G:0.46, T:0.09
Consensus pattern (42 bp):
AGAGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
Found at i:136848 original size:30 final size:30
Alignment explanation
Indices: 136814--136893 Score: 126
Period size: 30 Copynumber: 2.7 Consensus size: 30
136804 TTCTCTCCTC
* *
136814 CTCCTGTCATC-CCTCCTCTCTCTATTATCT
1 CTCCTGTC-TCTCCTCCTATCTCTACTATCT
136844 CTCCTGTCTCTCCTCCTATCTCTACTATCT
1 CTCCTGTCTCTCCTCCTATCTCTACTATCT
136874 CTCCTGTCTCTCCTCCTATC
1 CTCCTGTCTCTCCTCCTATC
136894 ATCCCTCCTC
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
29 2 0.04
30 45 0.96
ACGTcount: A:0.09, C:0.45, G:0.04, T:0.42
Consensus pattern (30 bp):
CTCCTGTCTCTCCTCCTATCTCTACTATCT
Found at i:136865 original size:21 final size:21
Alignment explanation
Indices: 136839--136878 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
136829 CTCTCTCTAT
* *
136839 TATCTCTCCTGTCTCTCCTCC
1 TATCTCTACTATCTCTCCTCC
136860 TATCTCTACTATCTCTCCT
1 TATCTCTACTATCTCTCCT
136879 GTCTCTCCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.42, G:0.03, T:0.45
Consensus pattern (21 bp):
TATCTCTACTATCTCTCCTCC
Found at i:139290 original size:156 final size:155
Alignment explanation
Indices: 139076--139787 Score: 715
Period size: 156 Copynumber: 4.6 Consensus size: 155
139066 TAATTGCATT
* *
139076 GGACTTGGTTCTAATGCAAAATTATCAAAATATCCC-T-AGGATATACCTTCGACATGAAAGTAT
1 GGACTTGGTTCT-A-G-AAAATTATGAAAATA-CCCTTAAGG-TATACCTTCGATATGAAAGTAT
* * *
139139 TCTGGTAACTGTAAAGGACATAAAAATGATTATAAATGGGATGAACCTATCCTAAATGCACACTT
61 TCTGGTAACTCTAAAGGACATAAAAATGATCATAAATGGGATGAACCTATCCTAAATGCACACCT
* ** *
139204 TTGGCATAAAAGCATCTCGGTTACAACCTAA
126 TTGGCATAAAAGCATCCCAATGACAACCT-A
** * *
139235 GG-CTTGGTTCTAGTAAAATTACAAAAATACCCTTAAGGTATACGTTCGATGTGAAAGT-TTCTT
1 GGACTTGGTTCTAG-AAAATTATGAAAATACCCTTAAGGTATACCTTCGATATGAAAGTATTC-T
* * * * *
139298 GTTAAC-CTTAAAGGATACAAATATGATCATAAATGGGATGAACTTATCCTAAATGCACACCTTT
64 GGTAACTC-TAAAGGACATAAAAATGATCATAAATGGGATGAACCTATCCTAAATGCACACCTTT
*
139362 GGCATAAAATCATCCCAATGACAACCTA
128 GGCATAAAAGCATCCCAATGACAACCTA
* * * * * *
139390 GGACTTGGTTCTAAAAAAATTATGAAAATGCCCTTAGGGTATACTTTCGTTATGAAAGTGTTC-G
1 GGACTTGGTTCT-AGAAAATTATGAAAATACCCTTAAGGTATACCTTCGATATGAAAGTATTCTG
* * *
139454 AGTAACCCTAAAAGACTTAAAAATGATCATAAATGGGATGAACCTATCCTAAATGCACACCTTTG
65 -GTAACTCTAAAGGACATAAAAATGATCATAAATGGGATGAACCTATCCTAAATGCACACCTTTG
* *
139519 GCATAAGAGCATCCCAATGACAACTTA
129 GCATAAAAGCATCCCAATGACAACCTA
* * ***
139546 GGACTTGGTTTTAAGAAAATTATGAAAATACCCCTT-AGGTATACCTTCAACGGGAAAGTA-TCT
1 GGACTTGGTTCT-AGAAAATTATGAAAATA-CCCTTAAGGTATACCTTCGATATGAAAGTATTCT
** * * *
139609 CAATAACTCTAAAAGACTTAAAAATGATCATAAATGGGATGAACCTATCCTAAATGAACACCTTT
64 -GGTAACTCTAAAGGACATAAAAATGATCATAAATGGGATGAACCTATCCTAAATGCACACCTTT
* *
139674 GGCAT-AAAGCAT-CTAGGTGACAACCTA
128 GGCATAAAAGCATCCCA-ATGACAACCTA
* *** * * * * * * *
139701 GGCCTCAATTTTAGGAAAATTATGAAAACACCCTTAGGGTATACCTTTGATATGAAAATATCCTA
1 GGACTTGGTTCTA-GAAAATTATGAAAATACCCTTAAGGTATACCTTCGATATGAAAGTATTCTG
* *
139766 GTAACTTTAAAGGACATGAAAA
65 GTAACTCTAAAGGACATAAAAA
139788 GAATCTAGGA
Statistics
Matches: 463, Mismatches: 74, Indels: 36
0.81 0.13 0.06
Matches are distributed among these distances:
154 8 0.02
155 85 0.18
156 345 0.75
157 14 0.03
158 9 0.02
159 2 0.00
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (155 bp):
GGACTTGGTTCTAGAAAATTATGAAAATACCCTTAAGGTATACCTTCGATATGAAAGTATTCTGG
TAACTCTAAAGGACATAAAAATGATCATAAATGGGATGAACCTATCCTAAATGCACACCTTTGGC
ATAAAAGCATCCCAATGACAACCTA
Found at i:152508 original size:1 final size:1
Alignment explanation
Indices: 152498--152582 Score: 98
Period size: 1 Copynumber: 85.0 Consensus size: 1
152488 CTTAAGCAGA
* * * * * * *
152498 TTTTTCTTTTTTTTTTTTTGTTTTGTTTTTTGTTGTTTTTTTTTGTTTTTTTTTTTTTTTTTTGT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
152563 TTTTTTTGTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTT
152583 GAAGAGAAGG
Statistics
Matches: 68, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 68 1.00
ACGTcount: A:0.00, C:0.01, G:0.08, T:0.91
Consensus pattern (1 bp):
T
Found at i:152521 original size:10 final size:10
Alignment explanation
Indices: 152498--152579 Score: 116
Period size: 10 Copynumber: 8.5 Consensus size: 10
152488 CTTAAGCAGA
*
152498 TTTTTCTTTT
1 TTTTTGTTTT
152508 TTTTT-TTTT
1 TTTTTGTTTT
*
152517 GTTTTGTTTT
1 TTTTTGTTTT
*
152527 TTGTTGTTTT
1 TTTTTGTTTT
152537 TTTTTGTTTT
1 TTTTTGTTTT
152547 TTTTT-TTTT
1 TTTTTGTTTT
152556 TTTTTG-TTT
1 TTTTTGTTTT
152565 TTTTTGTTTT
1 TTTTTGTTTT
152575 TTTTT
1 TTTTT
152580 TTTGAAGAGA
Statistics
Matches: 65, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
9 26 0.40
10 39 0.60
ACGTcount: A:0.00, C:0.01, G:0.09, T:0.90
Consensus pattern (10 bp):
TTTTTGTTTT
Found at i:152537 original size:28 final size:25
Alignment explanation
Indices: 152498--152582 Score: 109
Period size: 25 Copynumber: 3.4 Consensus size: 25
152488 CTTAAGCAGA
* *
152498 TTTTTCTTTTTTTTTTTTTGTTTTG
1 TTTTTTTTTTTTTTTTTTTGTTTTT
* *
152523 TTTTTTGTTGTTTTTTTTTGTTTTT
1 TTTTTTTTTTTTTTTTTTTGTTTTT
* *
152548 TTTTTTTTTTTTTGTTTTT-TTTGT
1 TTTTTTTTTTTTTTTTTTTGTTTTT
152572 TTTTTTTTTTT
1 TTTTTTTTTTT
152583 GAAGAGAAGG
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
24 15 0.29
25 37 0.71
ACGTcount: A:0.00, C:0.01, G:0.08, T:0.91
Consensus pattern (25 bp):
TTTTTTTTTTTTTTTTTTTGTTTTT
Found at i:152580 original size:39 final size:39
Alignment explanation
Indices: 152498--152579 Score: 139
Period size: 39 Copynumber: 2.1 Consensus size: 39
152488 CTTAAGCAGA
152498 TTTTTCTTTTTTTTTTTTTGTTTTGTTTTTTGTTGTTTT
1 TTTTTCTTTTTTTTTTTTTGTTTTGTTTTTTGTTGTTTT
* *
152537 TTTTTGTTTTTTTTTTTTTTTTTTGTTTTTT-TTGTTTT
1 TTTTTCTTTTTTTTTTTTTGTTTTGTTTTTTGTTGTTTT
152575 TTTTT
1 TTTTT
152580 TTTGAAGAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
38 12 0.29
39 29 0.71
ACGTcount: A:0.00, C:0.01, G:0.09, T:0.90
Consensus pattern (39 bp):
TTTTTCTTTTTTTTTTTTTGTTTTGTTTTTTGTTGTTTT
Found at i:155987 original size:13 final size:13
Alignment explanation
Indices: 155969--155994 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
155959 ACAAAGATCC
155969 ATGTATCGATACA
1 ATGTATCGATACA
155982 ATGTATCGATACA
1 ATGTATCGATACA
155995 CCAAATCGTT
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
Done.