Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1905
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: 79352
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:2433 original size:13 final size:13
Alignment explanation
Indices: 2415--2440 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2405 ATGGGAACAA
2415 TGTATCGATACAT
1 TGTATCGATACAT
2428 TGTATCGATACAT
1 TGTATCGATACAT
2441 AGCTTGTAAC
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:4766 original size:20 final size:20
Alignment explanation
Indices: 4741--4778 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
4731 TACTGCCAGT
4741 TTCATGTATCGATACAATTC
1 TTCATGTATCGATACAATTC
4761 TTCATGTATCGATACAAT
1 TTCATGTATCGATACAAT
4779 GAACATGTAT
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:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (20 bp):
TTCATGTATCGATACAATTC
Found at i:4787 original size:19 final size:19
Alignment explanation
Indices: 4743--4798 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
4733 CTGCCAGTTT
***
4743 CATGTATCGATACAATTCTT
1 CATGTATCGATACAA-TGAA
4763 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
4782 CATGTATCGATGCAATG
1 CATGTATCGATACAATG
4799 TATCGGTACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:6664 original size:17 final size:17
Alignment explanation
Indices: 6644--6695 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
6634 TGATCAGCTG
6644 AGAAAAAAAGAGAA-AAA
1 AGAAAAAAAGA-AAGAAA
* *
6661 AGAAAGAAAGAAAGACA
1 AGAAAAAAAGAAAGAAA
6678 AGAAAAAATA-AAAGAAA
1 AGAAAAAA-AGAAAGAAA
6695 A
1 A
6696 TAGGCAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 2 0.07
17 26 0.90
18 1 0.03
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (17 bp):
AGAAAAAAAGAAAGAAA
Found at i:7688 original size:162 final size:155
Alignment explanation
Indices: 7486--8086 Score: 633
Period size: 162 Copynumber: 3.8 Consensus size: 155
7476 CATATTAATC
* * * * *
7486 ATTTTTTAAATCTTTTATA-TTCTTATAGGATTTCGTAGGGGTATAAAAGATTTCAAAAATTTTT
1 ATTTTTTTAATCTTTTATATTTC-TATGGGGTCT-GTAGGGGTATAAAAGATTTCAAAAACTTTT
* *
7550 TGTATCTTTTTAGGTTTCCATTAAGGTACAAAATAGTATTTTTCAAAAATAAATAAATAAAATTA
64 CGTATCTTTTTGGGTTTCCATTAAGGTACAAAAT-GTATTTTT-AAAAATAAA-AAATAAAATTA
7615 AATTAACATTTTCATAATTGAAATAAATTTA
126 AATTAACATTTT-ATAATTGAAATAAATTTA
7646 ATAATTTTTTAATCTTTTATATTTCTATAGGGGTCTGTAGGGGTATAAAAGATTTCAAAAACTTT
1 AT--TTTTTTAATCTTTTATATTTCTAT-GGGGTCTGTAGGGGTATAAAAGATTTCAAAAACTTT
* * ** *
7711 TCGTATCTTTTTGGGTCTCCATTAAGGTACGAAATGGTATTTTT---TTTAAAAAATTAAATTAA
63 TCGTATCTTTTTGGGTTTCCATTAAGGTACAAAAT-GTATTTTTAAAAATAAAAAATAAAATTAA
7773 ATTAACACTTTTATAATTGAAATAAATATTA
127 ATTAACA-TTTTATAATTGAAATAAAT-TTA
* * * * *
7804 ATTTTTTTAATCTTTTATATTCCTATGGGGTCCGTAAGGGTATAAAACATTTCAAAAAATTTTCG
1 ATTTTTTTAATCTTTTATATTTCTATGGGGTCTGTAGGGGTATAAAAGATTTCAAAAACTTTTCG
* * * *
7869 TATC-TTTTCGGTTTCCATTAAGGTACGAAAATGTAATTTTTGAAAACAAATAAATAAAATTAAG
66 TATCTTTTTGGGTTTCCATTAAGGTAC-AAAATGT-ATTTTTAAAAATAAA-AAATAAAATTAAA
* * * * ** **
7933 CTAATACTTTAATAACCT-AGAGGAGCTTTA
128 TTAACA-TTTTATAA-TTGA-AATAAATTTA
* *
7963 ACTTTTTTTTATCTTTTATATTTTTATGGGGATCTGTAGGGGTATAAAAGATTTC-AAAACTTTT
1 A-TTTTTTTAATCTTTTATATTTCTATGGGG-TCTGTAGGGGTATAAAAGATTTCAAAAACTTTT
* * * *
8027 CATATCTTTTCGGGCTTT-CATTAAGGTACGAAATGAAATTTTTAAAAATAAAAAATAAAA
64 CGTATCTTTTTGGG-TTTCCATTAAGGTACAAAATG-TATTTTTAAAAATAAAAAATAAAA
8087 AATAAATAAA
Statistics
Matches: 374, Mismatches: 48, Indels: 39
0.81 0.10 0.08
Matches are distributed among these distances:
154 22 0.06
155 49 0.13
156 23 0.06
157 33 0.09
158 16 0.04
159 36 0.10
160 63 0.17
161 36 0.10
162 89 0.24
163 7 0.02
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.42
Consensus pattern (155 bp):
ATTTTTTTAATCTTTTATATTTCTATGGGGTCTGTAGGGGTATAAAAGATTTCAAAAACTTTTCG
TATCTTTTTGGGTTTCCATTAAGGTACAAAATGTATTTTTAAAAATAAAAAATAAAATTAAATTA
ACATTTTATAATTGAAATAAATTTA
Found at i:7928 original size:316 final size:317
Alignment explanation
Indices: 7486--8061 Score: 774
Period size: 316 Copynumber: 1.8 Consensus size: 317
7476 CATATTAATC
* * * * * * *
7486 ATTTTTTAAATCTTTTATATTCTTATAGGATTTCGTAGGGGTATAAAAGATTTCAAAAATTTTTT
1 ATTTTTTAAATCTTTTATATTCCTATAGGAGTCCGTAAGGGTATAAAACATTTCAAAAAATTTTC
*
7551 GTATCTTTTTAGGTTTCCATTAAGGTACAAAATAGTATTTTTCAAAAATAAATAAATAAAATTAA
66 GTATCTTTTTAGGTTTCCATTAAGGTACAAAATAGTATTTTTCAAAAACAAATAAATAAAATTAA
* * * * *
7616 ATTAACATTTTCATAA--TTGAAATAAATTTAA-TAATTTTTTAATCTTTTATATTTCTATAGGG
131 ACTAACACTTTAATAACCTAG-AAGAAATTTAACT--TTTTTTAATCTTTTATATTTCTAT-GGG
* *
7678 G-TCTGTAGGGGTATAAAAGATTTCAAAAACTTTTCGTATCTTTTTGGG-TCTCCATTAAGGTAC
192 GATCTGTAGGGGTATAAAAGATTTC-AAAACTTTTCATATCTTTTCGGGCT-TCCATTAAGGTAC
7741 GAAATGGTATTTTTTTTAAAAAATTAAATTAAATTAACACTTTTATAATTGAAATAAATATTA
255 GAAATGGTATTTTTTTTAAAAAATTAAATTAAATTAACACTTTTATAATTGAAATAAATATTA
* *
7804 ATTTTTTTAATCTTTTATATTCCTAT-GGGGTCCGTAAGGGTATAAAACATTTCAAAAAATTTTC
1 ATTTTTTAAATCTTTTATATTCCTATAGGAGTCCGTAAGGGTATAAAACATTTCAAAAAATTTTC
* *
7868 GTATC-TTTTCGGTTTCCATTAAGGTACGAAAAT-GTAATTTTT-GAAAACAAATAAATAAAATT
66 GTATCTTTTTAGGTTTCCATTAAGGTAC-AAAATAGT-ATTTTTCAAAAACAAATAAATAAAATT
* * * ** * *
7930 AAGCTAATACTTTAATAACCTAGAGGAGCTTTAACTTTTTTTTATCTTTTATATTTTTATGGGGA
129 AAACTAACACTTTAATAACCTAGAAGAAATTTAACTTTTTTTAATCTTTTATATTTCTATGGGGA
*
7995 TCTGTAGGGGTATAAAAGATTTCAAAACTTTTCATATCTTTTCGGGCTTTCATTAAGGTACGAAA
194 TCTGTAGGGGTATAAAAGATTTCAAAACTTTTCATATCTTTTCGGGCTTCCATTAAGGTACGAAA
8060 TG
259 TG
8062 AAATTTTTAA
Statistics
Matches: 224, Mismatches: 27, Indels: 17
0.84 0.10 0.06
Matches are distributed among these distances:
315 43 0.19
316 100 0.45
317 54 0.24
318 27 0.12
ACGTcount: A:0.35, C:0.09, G:0.13, T:0.43
Consensus pattern (317 bp):
ATTTTTTAAATCTTTTATATTCCTATAGGAGTCCGTAAGGGTATAAAACATTTCAAAAAATTTTC
GTATCTTTTTAGGTTTCCATTAAGGTACAAAATAGTATTTTTCAAAAACAAATAAATAAAATTAA
ACTAACACTTTAATAACCTAGAAGAAATTTAACTTTTTTTAATCTTTTATATTTCTATGGGGATC
TGTAGGGGTATAAAAGATTTCAAAACTTTTCATATCTTTTCGGGCTTCCATTAAGGTACGAAATG
GTATTTTTTTTAAAAAATTAAATTAAATTAACACTTTTATAATTGAAATAAATATTA
Found at i:10919 original size:154 final size:151
Alignment explanation
Indices: 10511--10899 Score: 473
Period size: 153 Copynumber: 2.5 Consensus size: 151
10501 GTCTTTAAAT
* *
10511 GCATTTTGGTAACTTTTTA-AAGTCAAGTCCT-ATGTAGTCACTAGGATACTTTTATGCCAAAGA
1 GCATTTTGGTAATTTTTTAGAA-TCAAGT-CTGATGTAGTCACT-GGATGCTTTTATGCCAAAGA
* * **
10574 TATGCATTTAGGATAAGTTCACTCTTTTATAATCATATTAGAGTCTTTTAAAGTTACCGAGATAC
63 TATGCATTTAGGATAGGTTCACTCTTTTATAATCATTTTAGAGTCCATTAAAGTTACCGAGATAC
* *
10639 TTTCATGTTGAAGATATCCCAAGA
128 TTTCATGTCGAACATATCCCAAGA
* * *
10663 TCATTTTGGTAATTTTTCTAGAATCGAGTCTGATGTAGTTACTGCGATGCTTTTATGCCCAAA-A
1 GCATTTTGGTAATTTTT-TAGAATCAAGTCTGATGTAGTCACTG-GATGCTTTTATG-CCAAAGA
* * * **
10727 TGTGCATTTAGGATAGGTTCACTCTTTCATAATCATTTTAGAGTCCATT-AGGTTTATTGAGATA
63 TATGCATTTAGGATAGGTTCACTCTTTTATAATCATTTTAGAGTCCATTAAAG-TTACCGAGATA
10791 CTTTCATGTCGAACATATACTCCAA-A
127 CTTTCATGTCGAACATAT-C-CCAAGA
* * *
10817 GGCGTTTTGGTAATTTTTTAGAATCAAGTCTGATGTAGTCACTGTGATGCTTTTATGCGAAAGTT
1 -GCATTTTGGTAATTTTTTAGAATCAAGTCTGATGTAGTCACTG-GATGCTTTTATGCCAAAGAT
10882 ATGCATTTAGGATAGGTT
64 ATGCATTTAGGATAGGTT
10900 AATCCTTTTA
Statistics
Matches: 203, Mismatches: 24, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
152 20 0.10
153 101 0.50
154 63 0.31
155 19 0.09
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.39
Consensus pattern (151 bp):
GCATTTTGGTAATTTTTTAGAATCAAGTCTGATGTAGTCACTGGATGCTTTTATGCCAAAGATAT
GCATTTAGGATAGGTTCACTCTTTTATAATCATTTTAGAGTCCATTAAAGTTACCGAGATACTTT
CATGTCGAACATATCCCAAGA
Found at i:13105 original size:13 final size:13
Alignment explanation
Indices: 13087--13117 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
13077 ACTTTTCACT
13087 ATGTATCGATACA
1 ATGTATCGATACA
13100 ATGTATCGATACA
1 ATGTATCGATACA
13113 ATGTA
1 ATGTA
13118 CTATGTATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:13106 original size:33 final size:33
Alignment explanation
Indices: 13064--13133 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 33
13054 AGCCGTTAGG
* *
13064 ACAATGTATCGATAC-TTTTCACTATGTATCGAT
1 ACAATGTATCGATACAATGT-ACTATGTATCGAT
*
13097 ACAATGTATCGATACAATGTACTATGTATTGAT
1 ACAATGTATCGATACAATGTACTATGTATCGAT
13130 ACAA
1 ACAA
13134 ACAGTGGTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 31 0.94
34 2 0.06
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.36
Consensus pattern (33 bp):
ACAATGTATCGATACAATGTACTATGTATCGAT
Found at i:13207 original size:19 final size:19
Alignment explanation
Indices: 13162--13217 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
13152 CTTCTAGTTT
* *
13162 CATGTATCGATACAATTTAG
1 CATGTATCGATACAA-TGAA
*
13182 TATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
13201 CATGTATCGATACAATG
1 CATGTATCGATACAATG
13218 TATCGATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:13220 original size:13 final size:13
Alignment explanation
Indices: 13202--13228 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
13192 TACAATGAAC
13202 ATGTATCGATACA
1 ATGTATCGATACA
13215 ATGTATCGATACA
1 ATGTATCGATACA
13228 A
1 A
13229 AGCATAATGT
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:15842 original size:13 final size:13
Alignment explanation
Indices: 15821--15855 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
15811 AGTCCCATTG
15821 TATCGATACAATA
1 TATCGATACAATA
* *
15834 TATCAATACAATG
1 TATCGATACAATA
15847 TATCGATAC
1 TATCGATAC
15856 TTAGAACATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.31
Consensus pattern (13 bp):
TATCGATACAATA
Found at i:16312 original size:27 final size:27
Alignment explanation
Indices: 16274--16328 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
16264 CTCCTAATGG
16274 TGCAAAATCTACTTTGGTCAAGAGGTT
1 TGCAAAATCTACTTTGGTCAAGAGGTT
*
16301 TGCAAAATCTACTTTGGTCAAGCGGTT
1 TGCAAAATCTACTTTGGTCAAGAGGTT
16328 T
1 T
16329 AGTGAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (27 bp):
TGCAAAATCTACTTTGGTCAAGAGGTT
Found at i:19816 original size:13 final size:13
Alignment explanation
Indices: 19798--19854 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
19788 CATAAAGTGT
19798 TGTATCGATACAA
1 TGTATCGATACAA
19811 TGTATCGATACATAA
1 TGTATCGATAC--AA
19826 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
19843 TGTATCGATACA
1 TGTATCGATACA
19855 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:19833 original size:32 final size:32
Alignment explanation
Indices: 19778--19878 Score: 184
Period size: 32 Copynumber: 3.1 Consensus size: 32
19768 TTCAATGATT
19778 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
19811 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
19843 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
19875 TGTA
1 TGTA
19879 AGCTATTGCC
Statistics
Matches: 67, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
32 54 0.81
33 13 0.19
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:19835 original size:19 final size:18
Alignment explanation
Indices: 19776--19873 Score: 90
Period size: 19 Copynumber: 5.8 Consensus size: 18
19766 ATTTCAATGA
19776 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
19795 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
19811 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
19827 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
19843 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
19859 TTTTGTATCGATACA
1 -TTTGTATCGATACA
19874 ATGTAAGCTA
Statistics
Matches: 66, Mismatches: 0, Indels: 26
0.72 0.00 0.28
Matches are distributed among these distances:
13 22 0.33
15 4 0.06
17 4 0.06
19 24 0.36
20 12 0.18
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:19934 original size:13 final size:13
Alignment explanation
Indices: 19916--19940 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19906 ATTACTCAAA
19916 TGTATCGATACAT
1 TGTATCGATACAT
19929 TGTATCGATACA
1 TGTATCGATACA
19941 CTGATCTTTG
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:25552 original size:13 final size:13
Alignment explanation
Indices: 25534--25565 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
25524 CCTTTTCACT
*
25534 ATGTATCGATATA
1 ATGTATCGATACA
25547 ATGTATCGATACA
1 ATGTATCGATACA
25560 ATGTAT
1 ATGTAT
25566 TATGTATCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:25654 original size:19 final size:20
Alignment explanation
Indices: 25609--25662 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 20
25599 CAGCCAATTT
*
25609 CATGTATCGATACAATTGAG
1 CATGTATCGATACAATTGAA
*
25629 TATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
25648 CATGTATCGATACAA
1 CATGTATCGATACAA
25663 AGCATAATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:25674 original size:20 final size:19
Alignment explanation
Indices: 25609--25679 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 19
25599 CAGCCAATTT
* *
25609 CATGTATCGATACAATTGAG
1 CATGTATCGATACAA-AGAA
* *
25629 TATGTATCGATACAATGAA
1 CATGTATCGATACAAAGAA
25648 CATGTATCGATACAAAGCATA
1 CATGTATCGATACAAAG-A-A
25669 -ATGTATCGATA
1 CATGTATCGATA
25680 TATCTGGATA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
19 18 0.40
20 26 0.58
21 1 0.02
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAAAGAA
Found at i:25814 original size:21 final size:22
Alignment explanation
Indices: 25790--25840 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 22
25780 TTTTTACTTG
* *
25790 AAAACATTTGAT-TTAAAGTTTA
1 AAAACATTT-ATATAAAACTTTA
*
25812 AAAACACTTATATAAAACTTT-
1 AAAACATTTATATAAAACTTTA
25833 AAAACATT
1 AAAACATT
25841 ATTGATATTG
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.51, C:0.10, G:0.04, T:0.35
Consensus pattern (22 bp):
AAAACATTTATATAAAACTTTA
Found at i:31269 original size:32 final size:32
Alignment explanation
Indices: 31220--31411 Score: 159
Period size: 32 Copynumber: 6.1 Consensus size: 32
31210 AACTCTTCAA
* *
31220 ATCTCTCTTT-CCTAAGTCCATGACTCAGTGGC
1 ATCTCT-TTTCCCAAAGTCCACGACTCAGTGGC
*
31252 ATCTCTTTTCCCAAAGTCCACGACTCAATGGC
1 ATCTCTTTTCCCAAAGTCCACGACTCAGTGGC
* *
31284 A--TC-TTTCCTTCAAAGACCACGACTTAGTGGC
1 ATCTCTTTTCC--CAAAGTCCACGACTCAGTGGC
* *
31315 A--TCTTTTCTTCAAAGTCCATGACTCAGTGGC
1 ATCTCTTTTC-CCAAAGTCCACGACTCAGTGGC
* * *
31346 ATCT-TTTCTTCCAAAGTCTACGACTAAGTGGC
1 ATCTCTTT-TCCCAAAGTCCACGACTCAGTGGC
* * *
31378 A--TCTTGTCCCATAGTCCACGATTCAGTGGC
1 ATCTCTTTTCCCAAAGTCCACGACTCAGTGGC
31408 ATCT
1 ATCT
31412 TGTCCTAAAG
Statistics
Matches: 128, Mismatches: 21, Indels: 22
0.75 0.12 0.13
Matches are distributed among these distances:
29 5 0.04
30 23 0.18
31 45 0.35
32 53 0.41
33 2 0.02
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.32
Consensus pattern (32 bp):
ATCTCTTTTCCCAAAGTCCACGACTCAGTGGC
Found at i:31304 original size:31 final size:31
Alignment explanation
Indices: 31233--31438 Score: 190
Period size: 31 Copynumber: 6.6 Consensus size: 31
31223 TCTCTTTCCT
*
31233 AAGTCCATGACTCAGTGGCATCTCTT--TTCCCA
1 AAGTCCACGACTCAGTGGCATCT-TTCCTT--CA
*
31265 AAGTCCACGACTCAATGGCATCTTTCCTTCA
1 AAGTCCACGACTCAGTGGCATCTTTCCTTCA
* * *
31296 AAGACCACGACTTAGTGGCATCTTTTCTTCA
1 AAGTCCACGACTCAGTGGCATCTTTCCTTCA
* *
31327 AAGTCCATGACTCAGTGGCATCTTTTCTTCCA
1 AAGTCCACGACTCAGTGGCATCTTTCCTT-CA
* *
31359 AAGTCTACGACTAAGTGGCATCTTGTCC--CA
1 AAGTCCACGACTCAGTGGCATCTT-TCCTTCA
* *
31389 TAGTCCACGATTCAGTGGCATCTTGTCC-T-A
1 AAGTCCACGACTCAGTGGCATCTT-TCCTTCA
* * *
31419 AAGCCCACAACTCCGTGGCA
1 AAGTCCACGACTCAGTGGCA
31439 CCCATTTTCT
Statistics
Matches: 147, Mismatches: 22, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
30 42 0.29
31 57 0.39
32 44 0.30
33 4 0.03
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.29
Consensus pattern (31 bp):
AAGTCCACGACTCAGTGGCATCTTTCCTTCA
Found at i:31521 original size:27 final size:29
Alignment explanation
Indices: 31480--31725 Score: 144
Period size: 27 Copynumber: 7.9 Consensus size: 29
31470 GGCCTTTGTT
*
31480 TCCTTTTAAGTCCACAACTCCGTGGCA-C
1 TCCTTTTAAGCCCACAACTCCGTGGCACC
31508 -CCTTTTAAGCCCACAACTCCGTGGCACTC
1 TCCTTTTAAGCCCACAACTCCGTGGCAC-C
* *
31537 TTTTTCCTTTTAAGTCCACAACTCTGTGGCACC
1 ----TCCTTTTAAGCCCACAACTCCGTGGCACC
31570 TTGTTCCTTTTTAAAGCCCACAACTCCGTGGCACCC
1 ----TCC-TTTT-AAGCCCACAACTCCGTGGCA-CC
*
31606 TTTTTCCTTTTAAGTCCACAACTCCGTGGCA-C
1 ----TCCTTTTAAGCCCACAACTCCGTGGCACC
* * *
31638 -CCTTTTAAGTCCACAATTTCGTGGCATCTTTC
1 TCCTTTTAAGCCCACAACTCCGTGGCA-C---C
* * *
31670 TCCTTCTAAGCCCACAAGTCAGTGGCA-C
1 TCCTTTTAAGCCCACAACTCCGTGGCACC
* *
31698 -CCTTTTCAAAGCCCACAAGTCAGTGGCA
1 TCCTTTT--AAGCCCACAACTCCGTGGCA
31726 ACCTTCAAAA
Statistics
Matches: 184, Mismatches: 16, Indels: 35
0.78 0.07 0.15
Matches are distributed among these distances:
27 54 0.29
28 1 0.01
29 21 0.11
32 2 0.01
33 28 0.15
34 48 0.26
35 22 0.12
36 8 0.04
ACGTcount: A:0.21, C:0.34, G:0.14, T:0.31
Consensus pattern (29 bp):
TCCTTTTAAGCCCACAACTCCGTGGCACC
Found at i:31521 original size:95 final size:96
Alignment explanation
Indices: 31419--31609 Score: 289
Period size: 95 Copynumber: 2.0 Consensus size: 96
31409 TCTTGTCCTA
* *
31419 AAGCCCACAACTCCGTGGCACCCATTTTCTTTTTAAAGCCCACAACTCTGTGGC-CTTTGTTTCC
1 AAGCCCACAACTCCGTGGCACCCATTTTCCTTTT-AAGCCCACAACTCTGTGGCACCTTG-TTCC
*
31483 -TTTT-AAGTCCACAACTCCGTGGCACCCTTTT
64 TTTTTAAAGCCCACAACTCCGTGGCACCCTTTT
* * *
31514 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGGCACCTTGTTCCTT
1 AAGCCCACAACTCCGTGGCACCCATTTTCCTTTTAAGCCCACAACTCTGTGGCACCTTGTTCCTT
31579 TTTAAAGCCCACAACTCCGTGGCACCCTTTT
66 TTTAAAGCCCACAACTCCGTGGCACCCTTTT
31610 TCCTTTTAAG
Statistics
Matches: 87, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
94 22 0.25
95 39 0.45
96 26 0.30
ACGTcount: A:0.20, C:0.34, G:0.14, T:0.32
Consensus pattern (96 bp):
AAGCCCACAACTCCGTGGCACCCATTTTCCTTTTAAGCCCACAACTCTGTGGCACCTTGTTCCTT
TTTAAAGCCCACAACTCCGTGGCACCCTTTT
Found at i:31546 original size:34 final size:33
Alignment explanation
Indices: 31419--31704 Score: 256
Period size: 34 Copynumber: 8.8 Consensus size: 33
31409 TCTTGTCCTA
* *
31419 AAGCCCACAACTCCGTGGCACCCATTTTCTTTTT
1 AAGCCCACAACTCCGTGGCA-CCTTTTTCCTTTT
* *
31453 AAAGCCCACAACTCTGTGGC-CTTTGTTTCCTTTT
1 -AAGCCCACAACTCCGTGGCACCTT-TTTCCTTTT
*
31487 AAGTCCACAACTCCGTGGCA-C-----CCTTTT
1 AAGCCCACAACTCCGTGGCACCTTTTTCCTTTT
31514 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTTT
1 AAGCCCACAACTCCGTGGCAC-CTTTTTCCTTTT
* * *
31548 AAGTCCACAACTCTGTGGCACCTTGTTCCTTTTT
1 AAGCCCACAACTCCGTGGCACCTTTTTCC-TTTT
31582 AAAGCCCACAACTCCGTGGCACCCTTTTTCCTTTT
1 -AAGCCCACAACTCCGTGGCA-CCTTTTTCCTTTT
*
31617 AAGTCCACAACTCCGTGGCA-C-----CCTTTT
1 AAGCCCACAACTCCGTGGCACCTTTTTCCTTTT
* * * * * *
31644 AAGTCCACAATTTCGTGGCATCTTTCTCCTTCT
1 AAGCCCACAACTCCGTGGCACCTTTTTCCTTTT
* * *
31677 AAGCCCACAAGTCAGTGGCACCCTTTTC
1 AAGCCCACAACTCCGTGGCACCTTTTTC
31705 AAAGCCCACA
Statistics
Matches: 208, Mismatches: 25, Indels: 38
0.77 0.09 0.14
Matches are distributed among these distances:
27 49 0.24
28 1 0.00
29 1 0.00
32 1 0.00
33 52 0.25
34 56 0.27
35 40 0.19
36 8 0.04
ACGTcount: A:0.20, C:0.34, G:0.14, T:0.33
Consensus pattern (33 bp):
AAGCCCACAACTCCGTGGCACCTTTTTCCTTTT
Found at i:31550 original size:61 final size:62
Alignment explanation
Indices: 31449--31725 Score: 321
Period size: 60 Copynumber: 4.4 Consensus size: 62
31439 CCCATTTTCT
*
31449 TTTTAAAGCCCACAACTCTGTGGC-CT-TTGTTTCCTTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAAGCCCACAACTCCGTGGCACTCTT-TTTCCTTTTAAGTCCACAACTCCGTGGCACCC
*
31510 TTTT-AAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGGCACCTTGT
1 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCA-C----
31574 TCC
61 -CC
*
31577 TTTTTAAAGCCCACAACTCCGTGGCACCCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCC
1 -TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCC
* * * * * * * *
31640 TTTT-AAGTCCACAATTTCGTGGCA-TCTTTCTCCTTCTAAGCCCACAAGTCAGTGGCACCC
1 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCC
* *
31700 TTTTCAAAGCCCACAAGTCAGTGGCA
1 TTTT-AAAGCCCACAACTCCGTGGCA
31726 ACCTTCAAAA
Statistics
Matches: 187, Mismatches: 17, Indels: 23
0.82 0.07 0.10
Matches are distributed among these distances:
60 52 0.28
61 51 0.27
62 23 0.12
63 2 0.01
67 2 0.01
68 5 0.03
69 52 0.28
ACGTcount: A:0.21, C:0.33, G:0.14, T:0.32
Consensus pattern (62 bp):
TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCC
Found at i:31589 original size:129 final size:127
Alignment explanation
Indices: 31419--31704 Score: 396
Period size: 129 Copynumber: 2.2 Consensus size: 127
31409 TCTTGTCCTA
* * *
31419 AAGCCCACAACTCCGTGGCACCCATTTTCTTTTTAAAGCCCACAACTCTGTGG-CCTTTGTTTCC
1 AAGCCCACAACTCAGTGGCA-CCATTTTCTTTTTAAAGCCCACAACTCCGTGGACCCTT-TTTCC
* *
31483 TTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTT
64 TTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGGCA-TCTTTCTCCTTCT
* *
31548 AAGTCCACAACTCTGTGGCACC-TTGTTCCTTTTTAAAGCCCACAACTCCGTGGCACCCTTTTTC
1 AAGCCCACAACTCAGTGGCACCATT-TT-CTTTTTAAAGCCCACAACTCCGTGG-ACCCTTTTTC
* * *
31612 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAATTTCGTGGCATCTTTCTCCTTCT
63 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGGCATCTTTCTCCTTCT
* *
31677 AAGCCCACAAGTCAGTGGCACCCTTTTC
1 AAGCCCACAACTCAGTGGCACCATTTTC
31705 AAAGCCCACA
Statistics
Matches: 140, Mismatches: 12, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
127 2 0.01
128 5 0.04
129 74 0.53
130 55 0.39
131 4 0.03
ACGTcount: A:0.20, C:0.34, G:0.14, T:0.33
Consensus pattern (127 bp):
AAGCCCACAACTCAGTGGCACCATTTTCTTTTTAAAGCCCACAACTCCGTGGACCCTTTTTCCTT
TTAAGTCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGGCATCTTTCTCCTTCT
Found at i:31592 original size:69 final size:68
Alignment explanation
Indices: 31510--31638 Score: 231
Period size: 69 Copynumber: 1.9 Consensus size: 68
31500 CGTGGCACCC
* *
31510 TTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGGCACCTTGTT
1 TTTTAAGCCCACAACTCCGTGGCACCCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTTGTT
31575 CCT
66 CCT
31578 TTTTAAAGCCCACAACTCCGTGGCACCCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACC
1 TTTT-AAGCCCACAACTCCGTGGCACCCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACC
31639 CTTTTAAGTC
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
68 4 0.07
69 54 0.93
ACGTcount: A:0.19, C:0.34, G:0.13, T:0.33
Consensus pattern (68 bp):
TTTTAAGCCCACAACTCCGTGGCACCCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTTGTT
CCT
Found at i:31753 original size:27 final size:28
Alignment explanation
Indices: 31701--31781 Score: 76
Period size: 28 Copynumber: 2.8 Consensus size: 28
31691 GTGGCACCCT
* **
31701 TTTC-AAAGCCCACAAGTCAGTGGCAACC
1 TTTCAAAAGCACACAAGTTGGT-GCAACC
31729 -TTCAAAAGCACACAAGTTGGTGCAACC
1 TTTCAAAAGCACACAAGTTGGTGCAACC
*
31756 TTTTTAAAAGCCCACACAAGTTGGTG
1 -TTTCAAAAG--CACACAAGTTGGTG
31782 GCATCTTCTT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
27 9 0.20
28 14 0.32
29 7 0.16
31 14 0.32
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (28 bp):
TTTCAAAAGCACACAAGTTGGTGCAACC
Found at i:31771 original size:29 final size:29
Alignment explanation
Indices: 31677--31771 Score: 113
Period size: 29 Copynumber: 3.3 Consensus size: 29
31667 TTCTCCTTCT
* *
31677 AAGCCCACAAGTCAGTGGCACCCTTTTCA
1 AAGCCCACAAGTCAGTGGCAACCTTTTAA
*
31706 AAGCCCACAAGTCAGTGGCAACC-TTCAA
1 AAGCCCACAAGTCAGTGGCAACCTTTTAA
* **
31734 AAGCACACAAGTTGGT-GCAACCTTTTTAA
1 AAGCCCACAAGTCAGTGGCAACC-TTTTAA
31763 AAGCCCACA
1 AAGCCCACA
31772 CAAGTTGGTG
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
27 6 0.11
28 16 0.29
29 34 0.61
ACGTcount: A:0.34, C:0.31, G:0.17, T:0.19
Consensus pattern (29 bp):
AAGCCCACAAGTCAGTGGCAACCTTTTAA
Found at i:31900 original size:39 final size:38
Alignment explanation
Indices: 31846--32000 Score: 139
Period size: 39 Copynumber: 3.8 Consensus size: 38
31836 ATCTTTAAAA
31846 CCAATGTCGCTGGCCTTGAATCAGCACATTAGCATAAG
1 CCAATGTCGCTGGCCTTGAATCAGCACATTAGCATAAG
* *
31884 CCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAG
1 -CCAATGTCGCTGGCCTTGAATCAGCACATT---A----G-C-ATAAG
* * * * *
31932 ACTATGTCGCTGGCCTTGAATTAGCACATTGGCACAAG
1 CCAATGTCGCTGGCCTTGAATCAGCACATTAGCATAAG
*
31970 ACCAATGTCGTTGGCCTTGAATCAGCACATT
1 -CCAATGTCGCTGGCCTTGAATCAGCACATT
32001 GGCACCTTCA
Statistics
Matches: 93, Mismatches: 13, Indels: 20
0.74 0.10 0.16
Matches are distributed among these distances:
38 3 0.03
39 56 0.60
40 1 0.01
42 1 0.01
46 1 0.01
47 27 0.29
48 4 0.04
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (38 bp):
CCAATGTCGCTGGCCTTGAATCAGCACATTAGCATAAG
Found at i:31976 original size:86 final size:86
Alignment explanation
Indices: 31811--32042 Score: 338
Period size: 86 Copynumber: 2.7 Consensus size: 86
31801 ATATCGTTGT
*
31811 CCTTGAATCAGCATATTGGCACCTTATCTTTAAAACCAATGTCGCTGGCCTTGAATCAGCACATT
1 CCTTGAATCAGCATATTGGCACCTTATCTTTAAGA-CAATGTCGCTGGCCTTGAATCAGCACATT
* *
31876 AGCATAAGCCCAATGTCGCTGG
65 AGCACAAGACCAATGTCGCTGG
* * * *
31898 CCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACTATGTCGCTGGCCTTGAATTAGCACATTG
1 CCTTGAATCAGCATATTGGCACCTTATCTTTAAGACAATGTCGCTGGCCTTGAATCAGCACATTA
*
31963 GCACAAGACCAATGTCGTTGG
66 GCACAAGACCAATGTCGCTGG
* * *
31984 CCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCA
1 CCTTGAATCAGCATATTGGCACCTT-ATCTTTAAG-ACAATGTCGCTGGCCTTGAATCA
32043 ACATATTGGC
Statistics
Matches: 129, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
86 69 0.53
87 41 0.32
88 19 0.15
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (86 bp):
CCTTGAATCAGCATATTGGCACCTTATCTTTAAGACAATGTCGCTGGCCTTGAATCAGCACATTA
GCACAAGACCAATGTCGCTGG
Found at i:32149 original size:101 final size:101
Alignment explanation
Indices: 31971--32819 Score: 1320
Period size: 101 Copynumber: 8.4 Consensus size: 101
31961 TGGCACAAGA
* *
31971 CCAATGTCGTTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATATCGCTGGCCT
* *
32036 TGAATCAACATATTGGCGCCTTTGTCATCTTTAAGT
66 TGAATCAGCATATTGGCGCCTTCGTCATCTTTAAGT
* * *
32072 GCAATGTCGCTGGCCCTGGATCAGCACATTGGCATCTTCATCTTTAAGTCCAATATCGCTGGCCT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATATCGCTGGCCT
*
32137 TGAATCAGCATATTGGCGCCTTCGTCATTTTTAAGT
66 TGAATCAGCATATTGGCGCCTTCGTCATCTTTAAGT
* * * *
32173 CCAATGTCACTGGCCTTGAATCAGCACATTGGCATCTTCATCCTTAAGTCCAGTATCACTGGCCT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATATCGCTGGCCT
*
32238 TGAATTAGCATATTGGCGCCTTCGTCATCTTTAAGT
66 TGAATCAGCATATTGGCGCCTTCGTCATCTTTAAGT
*
32274 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATTTTTAAGTCCAATATCGCTGGCCT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATATCGCTGGCCT
*
32339 TGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGT
66 TGAATCAGCATATTGGCGCCTTCGTCATCTTTAAGT
* * * * *
32375 GCAATGTCGCTGGCCCTAAATCAGCAAATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATATCGCTGGCCT
* *
32440 TGAATCAGCATATTAGCGCATTCGTCATCTTTAAGT
66 TGAATCAGCATATTGGCGCCTTCGTCATCTTTAAGT
* * * ** *
32476 CCAATGTCGTTGGCCTTGAATCAACACATTGGCATCTTCATCTTTATGTCCGGTATCGCTAGCCT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATATCGCTGGCCT
*
32541 TGAATCAGCATATTGGCACCTTCGTCATCTTTAAGT
66 TGAATCAGCATATTGGCGCCTTCGTCATCTTTAAGT
* **
32577 CCAATGTCGCTGGCCTTGAATCAACACATTGGCATCTTCATCTTTAAGTCCGGTATCGCTGGCCT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATATCGCTGGCCT
32642 TGAATCAGCATATTGGCGCCTTCGTCATCTTTAAGT
66 TGAATCAGCATATTGGCGCCTTCGTCATCTTTAAGT
* * * *
32678 CCAATTTCACTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGATGGCCT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATATCGCTGGCCT
**
32743 TGAATCAGCATATTGGCGCCTTCGTCATCTTTAAAAC
66 TGAATCAGCATATTGGCGCCTTCGTCATCTTT-AAGT
**
32780 CCAATGTCATTGGCCTTGAATCAGCACATTGGCATTCTTC
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-TCTTC
32820 TCATCTTCAA
Statistics
Matches: 683, Mismatches: 63, Indels: 2
0.91 0.08 0.00
Matches are distributed among these distances:
101 645 0.94
102 34 0.05
103 4 0.01
ACGTcount: A:0.23, C:0.26, G:0.18, T:0.33
Consensus pattern (101 bp):
CCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATATCGCTGGCCT
TGAATCAGCATATTGGCGCCTTCGTCATCTTTAAGT
Found at i:32904 original size:52 final size:51
Alignment explanation
Indices: 31981--32917 Score: 646
Period size: 52 Copynumber: 18.5 Consensus size: 51
31971 CCAATGTCGT
* * *
31981 TGGCCTTGAATCAGCACATTGGCA--CCTTCATCTTTAAGTCCAATATCGC
1 TGGCCTTGAATCAGCACATTGGCATTCTTTCATCTTTAAGCCCAATATCAC
* * * * ** * *
32030 TGGCCTTGAATCAACATATTGGCGCCTT-TGTCATCTTTAAGTGCAATGTCGC
1 TGGCCTTGAATCAGCACATT-G-GCATTCTTTCATCTTTAAGCCCAATATCAC
* * * *
32082 TGGCCCTGGATCAGCACATTGGCA-TC-TTCATCTTTAAGTCCAATATCGC
1 TGGCCTTGAATCAGCACATTGGCATTCTTTCATCTTTAAGCCCAATATCAC
* * * * * *
32131 TGGCCTTGAATCAGCATATTGGCGCCTTC-GTCATTTTTAAGTCCAATGTCAC
1 TGGCCTTGAATCAGCACATT-G-GCATTCTTTCATCTTTAAGCCCAATATCAC
* * *
32183 TGGCCTTGAATCAGCACATTGGCA-TC-TTCATCCTTAAGTCCAGTATCAC
1 TGGCCTTGAATCAGCACATTGGCATTCTTTCATCTTTAAGCCCAATATCAC
* * * * * * *
32232 TGGCCTTGAATTAGCATATTGGCGCCTTC-GTCATCTTTAAGTCCAATGTCGC
1 TGGCCTTGAATCAGCACATT-G-GCATTCTTTCATCTTTAAGCCCAATATCAC
* * *
32284 TGGCCTTGAATCAGCACATTGGCA-TC-TTCATTTTTAAGTCCAATATCGC
1 TGGCCTTGAATCAGCACATTGGCATTCTTTCATCTTTAAGCCCAATATCAC
* * * ** * *
32333 TGGCCTTGAATCAGCATATTGGCGCCTT-TGTCATCTTTAAGTGCAATGTCGC
1 TGGCCTTGAATCAGCACATT-G-GCATTCTTTCATCTTTAAGCCCAATATCAC
* * * * * *
32385 TGGCCCTAAATCAGCAAATTGGCA--CCTTCATCTTTAAGTCCAATATCGC
1 TGGCCTTGAATCAGCACATTGGCATTCTTTCATCTTTAAGCCCAATATCAC
* * * * **
32434 TGGCCTTGAATCAGCATATTAGCGCATTC-GTCATCTTTAAGTCCAATGTCGT
1 TGGCCTTGAATCAGCACATT-G-GCATTCTTTCATCTTTAAGCCCAATATCAC
* * * ** *
32486 TGGCCTTGAATCAACACATTGGCA-TC-TTCATCTTTATGTCCGGTATCGC
1 TGGCCTTGAATCAGCACATTGGCATTCTTTCATCTTTAAGCCCAATATCAC
* * * * * *
32535 TAGCCTTGAATCAGCATATTGGCACCTTC-GTCATCTTTAAGTCCAATGTCGC
1 TGGCCTTGAATCAGCACATTGGCA--TTCTTTCATCTTTAAGCCCAATATCAC
* * ** *
32587 TGGCCTTGAATCAACACATTGGCA-TC-TTCATCTTTAAGTCCGGTATCGC
1 TGGCCTTGAATCAGCACATTGGCATTCTTTCATCTTTAAGCCCAATATCAC
* * * * *
32636 TGGCCTTGAATCAGCATATTGGCGCCTTC-GTCATCTTTAAGTCCAATTTCAC
1 TGGCCTTGAATCAGCACATT-G-GCATTCTTTCATCTTTAAGCCCAATATCAC
* *
32688 TGGCCTTGAATCAGCACATTGGCA--CCTTCATCTTTAAGTCCAATATCGA-
1 TGGCCTTGAATCAGCACATTGGCATTCTTTCATCTTTAAGCCCAATATC-AC
* * * * * *
32737 TGGCCTTGAATCAGCATATTGGCGCCTTC-GTCATCTTTAAAACCCAATGTCAT
1 TGGCCTTGAATCAGCACATT-G-GCATTCTTTCATCTTT-AAGCCCAATATCAC
* * * * **
32790 TGGCCTTGAATCAGCACATTGGCATTCTTCTCATCTTCAAGGCTAATGTCGT
1 TGGCCTTGAATCAGCACATTGGCATTCTT-TCATCTTTAAGCCCAATATCAC
** * *
32842 TGATCGTGAATCAGCACATTGACATTCTTTACATCTTTAAGCCCAATATCAC
1 TGGCCTTGAATCAGCACATTGGCATTCTTT-CATCTTTAAGCCCAATATCAC
** * *
32894 TGGTTTTGAATTAGCATATTGGCA
1 TGGCCTTGAATCAGCACATTGGCA
32918 CCTTTATCAC
Statistics
Matches: 722, Mismatches: 129, Indels: 71
0.78 0.14 0.08
Matches are distributed among these distances:
48 1 0.00
49 289 0.40
50 21 0.03
51 27 0.04
52 347 0.48
53 37 0.05
ACGTcount: A:0.23, C:0.26, G:0.18, T:0.33
Consensus pattern (51 bp):
TGGCCTTGAATCAGCACATTGGCATTCTTTCATCTTTAAGCCCAATATCAC
Found at i:35778 original size:24 final size:26
Alignment explanation
Indices: 35751--35799 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
35741 TCAAAATTCT
35751 ATTCAT-CGA-GGACACTCCAACCCC
1 ATTCATCCGAGGGACACTCCAACCCC
*
35775 ATTCCTCCGAGGGGACACTCCAACC
1 ATTCATCCGA-GGGACACTCCAACC
35800 TCGTTTTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
25 3 0.14
27 13 0.62
ACGTcount: A:0.27, C:0.41, G:0.16, T:0.16
Consensus pattern (26 bp):
ATTCATCCGAGGGACACTCCAACCCC
Found at i:36603 original size:20 final size:20
Alignment explanation
Indices: 36580--36652 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
36570 ACAATTCAAA
36580 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
36600 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
36621 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
36641 GTATCGATACAT
1 GTATCGATACAT
36653 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:36624 original size:21 final size:21
Alignment explanation
Indices: 36598--36673 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
36588 ACATGTTGCA
36598 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
36619 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
36639 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
36660 ATGTATCGATACAT
1 ATGTATCGATACAT
36674 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:36631 original size:41 final size:41
Alignment explanation
Indices: 36580--36673 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
36570 ACAATTCAAA
*
36580 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
36621 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
36662 GTATCGATACAT
1 GTATCGATACAT
36674 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:36730 original size:13 final size:13
Alignment explanation
Indices: 36712--36737 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
36702 TACAGCAAGT
36712 ATGTATCGATACA
1 ATGTATCGATACA
36725 ATGTATCGATACA
1 ATGTATCGATACA
36738 CAAAAAATTG
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:40819 original size:15 final size:15
Alignment explanation
Indices: 40799--40829 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
40789 TAAAAATGTC
*
40799 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
40814 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
40829 C
1 C
40830 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:42927 original size:13 final size:13
Alignment explanation
Indices: 42909--42946 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
42899 CATTTTTATT
42909 TGTATCGATACAA
1 TGTATCGATACAA
*
42922 TGTATCGATACAC
1 TGTATCGATACAA
42935 TGTATCGATACA
1 TGTATCGATACA
42947 GGGTGTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:44775 original size:32 final size:32
Alignment explanation
Indices: 44739--44800 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
44729 AATTTTGATA
44739 TGAATTACTTGATTAAGGGGGAGATTTTTTTT
1 TGAATTACTTGATTAAGGGGGAGATTTTTTTT
44771 TGAATTACTTGATTAAGGGGGAGATTTTTT
1 TGAATTACTTGATTAAGGGGGAGATTTTTT
44801 AATAAACGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.26, C:0.03, G:0.26, T:0.45
Consensus pattern (32 bp):
TGAATTACTTGATTAAGGGGGAGATTTTTTTT
Found at i:45445 original size:20 final size:20
Alignment explanation
Indices: 45422--45494 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
45412 ACAATTCAAA
45422 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
45442 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
45463 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
45483 GTATCGATACAT
1 GTATCGATACAT
45495 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:45466 original size:21 final size:21
Alignment explanation
Indices: 45440--45515 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
45430 ACATGTTGCA
45440 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
45461 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
45481 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
45502 ATGTATCGATACAT
1 ATGTATCGATACAT
45516 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:45473 original size:41 final size:41
Alignment explanation
Indices: 45422--45515 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
45412 ACAATTCAAA
*
45422 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
45463 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
45504 GTATCGATACAT
1 GTATCGATACAT
45516 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:45572 original size:13 final size:13
Alignment explanation
Indices: 45554--45579 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
45544 TACAGCAAGT
45554 ATGTATCGATACA
1 ATGTATCGATACA
45567 ATGTATCGATACA
1 ATGTATCGATACA
45580 CAAAAAATTG
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:48136 original size:13 final size:13
Alignment explanation
Indices: 48118--48142 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48108 ACCAAAATCA
48118 TGTATCGATACAG
1 TGTATCGATACAG
48131 TGTATCGATACA
1 TGTATCGATACA
48143 AACCAATATG
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:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:48159 original size:33 final size:32
Alignment explanation
Indices: 48099--48161 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 32
48089 TAATTCGCTA
*
48099 TGTATCGATACCAAAATCATGTATCGATACAG
1 TGTATCGATACAAAAATCATGTATCGATACAG
48131 TGTATCGATACAAACCAAT-ATGTATCGATAC
1 TGTATCGATACAAA--AATCATGTATCGATAC
48162 TTCTGGGTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 13 0.46
33 12 0.43
34 3 0.11
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (32 bp):
TGTATCGATACAAAAATCATGTATCGATACAG
Found at i:49146 original size:16 final size:16
Alignment explanation
Indices: 49125--49159 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
49115 TTCATTAAGG
**
49125 AAAGTTAAGTACAAGC
1 AAAGTTAAAAACAAGC
49141 AAAGTTAAAAACAAGC
1 AAAGTTAAAAACAAGC
49157 AAA
1 AAA
49160 AAAACAAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.60, C:0.11, G:0.14, T:0.14
Consensus pattern (16 bp):
AAAGTTAAAAACAAGC
Found at i:52699 original size:13 final size:13
Alignment explanation
Indices: 52681--52710 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
52671 ACAATTCTTC
52681 ATGTATCGATACA
1 ATGTATCGATACA
52694 ATGTATCGATACA
1 ATGTATCGATACA
52707 ATGT
1 ATGT
52711 CCCATGTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:52702 original size:33 final size:33
Alignment explanation
Indices: 52660--52726 Score: 109
Period size: 33 Copynumber: 2.0 Consensus size: 33
52650 CGTTAGGCAT
*
52660 AATGTATCGATACAAT-TCTTCATGTATCGATAC
1 AATGTATCGATACAATGTC-CCATGTATCGATAC
52693 AATGTATCGATACAATGTCCCATGTATCGATAC
1 AATGTATCGATACAATGTCCCATGTATCGATAC
52726 A
1 A
52727 TTTCACTTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 30 0.94
34 2 0.06
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.33
Consensus pattern (33 bp):
AATGTATCGATACAATGTCCCATGTATCGATAC
Found at i:52781 original size:20 final size:20
Alignment explanation
Indices: 52755--52809 Score: 85
Period size: 19 Copynumber: 2.8 Consensus size: 20
52745 CTACTAATTT
*
52755 CATGTATCGATACAATTGAG
1 CATGTATCGATACAATTGAA
*
52775 TATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
52794 CATGTATCGATACAAT
1 CATGTATCGATACAAT
52810 ATATCGATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:52837 original size:33 final size:32
Alignment explanation
Indices: 52779--52840 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
52769 ATTGAGTATG
*
52779 TATCGATACAATGAACATGTATCGATACAATA
1 TATCGATACAAAGAACATGTATCGATACAATA
52811 TATCGATACAAAGCATA-ATGTATCGATACA
1 TATCGATACAAAG-A-ACATGTATCGATACA
52841 TCTGGATATG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 12 0.44
33 14 0.52
34 1 0.04
ACGTcount: A:0.44, C:0.16, G:0.13, T:0.27
Consensus pattern (32 bp):
TATCGATACAAAGAACATGTATCGATACAATA
Found at i:53516 original size:55 final size:55
Alignment explanation
Indices: 53456--53570 Score: 203
Period size: 55 Copynumber: 2.1 Consensus size: 55
53446 AGTTCTCCCC
53456 CTTTTTGTTATAAAAAATCTTTTTATTTCTTCCCCTTTGTCAAAAGCCAAAATTT
1 CTTTTTGTTATAAAAAATCTTTTTATTTCTTCCCCTTTGTCAAAAGCCAAAATTT
* *
53511 CTTTTTGTTATAAAAATTCTTTTTATTTCTTCCCCTTTGTCAAAATCCAAAATTT
1 CTTTTTGTTATAAAAAATCTTTTTATTTCTTCCCCTTTGTCAAAAGCCAAAATTT
*
53566 ATTTT
1 CTTTT
53571 CAAAAAATTT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.28, C:0.17, G:0.04, T:0.50
Consensus pattern (55 bp):
CTTTTTGTTATAAAAAATCTTTTTATTTCTTCCCCTTTGTCAAAAGCCAAAATTT
Found at i:61472 original size:20 final size:20
Alignment explanation
Indices: 61447--61495 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
61437 TTGGGCATAG
*
61447 TGTATCGATACAAT-TCTTCA
1 TGTATCGATACAATGTC-CCA
61467 TGTATCGATACAATGTCCCA
1 TGTATCGATACAATGTCCCA
61487 TGTATCGAT
1 TGTATCGAT
61496 GCATTTCATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 25 0.93
21 2 0.07
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (20 bp):
TGTATCGATACAATGTCCCA
Found at i:65917 original size:21 final size:21
Alignment explanation
Indices: 65861--65921 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
65851 ACTATCTTCC
* *
65861 AATTCAATTACCTTCTTTTCT
1 AATTCACTTACTTTCTTTTCT
*
65882 AATTCACTTATTTTCTTTTCT
1 AATTCACTTACTTTCTTTTCT
*
65903 AATTCTTCTT-CTTTCTTTT
1 AATTC-ACTTACTTTCTTTT
65922 TAAGCACATC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 31 0.91
22 3 0.09
ACGTcount: A:0.18, C:0.21, G:0.00, T:0.61
Consensus pattern (21 bp):
AATTCACTTACTTTCTTTTCT
Found at i:69229 original size:80 final size:79
Alignment explanation
Indices: 69127--69329 Score: 221
Period size: 79 Copynumber: 2.6 Consensus size: 79
69117 AATAACAGGG
* * * * *
69127 TTGGAGTGTTCCCTT-GAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA-TTA
1 TTGGAGT-ATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-ATTTA
*
69190 GAAAAAAAAAATCGGGA
64 G-AAAAAAAAACCGGGA
* * *
69207 TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGG
1 TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAGA
* * * *
69272 GAATAAAGCCGGGG
66 AAAAAAAACCGGGA
* * *
69286 TTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGAT
69330 GAAATAACGA
Statistics
Matches: 104, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
79 56 0.54
80 48 0.46
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.25
Consensus pattern (79 bp):
TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAGA
AAAAAAAACCGGGA
Found at i:69321 original size:28 final size:28
Alignment explanation
Indices: 69281--69352 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
69271 GGAATAAAGC
** *
69281 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
69309 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
69337 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
69353 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:69410 original size:52 final size:50
Alignment explanation
Indices: 69339--69465 Score: 146
Period size: 52 Copynumber: 2.5 Consensus size: 50
69329 TGAAATAACG
* * * *
69339 AGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATC
1 AGGTTGGAGTATCCCCGATTGTGAAAAATTGG-AGTTTTGAAAATAAAACC
** * *
69390 AGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACC
1 AG-GTTGGAGTATCCCCGATT-GTGAAAAATTGGAGTTTTGAAAATAAAACC
69442 AGGATTGGAGTATCCCCGATTGTG
1 AGG-TTGGAGTATCCCCGATTGTG
69466 GAGAATTGAT
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
51 4 0.06
52 50 0.79
53 9 0.14
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (50 bp):
AGGTTGGAGTATCCCCGATTGTGAAAAATTGGAGTTTTGAAAATAAAACC
Found at i:71843 original size:13 final size:13
Alignment explanation
Indices: 71825--71850 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
71815 ACAAAGATCC
71825 ATGTATCGATACA
1 ATGTATCGATACA
71838 ATGTATCGATACA
1 ATGTATCGATACA
71851 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:71846 original size:33 final size:33
Alignment explanation
Indices: 71804--71870 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
71794 AAAATTTCCA
***
71804 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
71837 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
71870 A
1 A
71871 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:71914 original size:19 final size:18
Alignment explanation
Indices: 71890--71989 Score: 103
Period size: 19 Copynumber: 5.9 Consensus size: 18
71880 CAGTAGCTAA
71890 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
71909 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
71924 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
71941 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
71956 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
71973 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
71990 TCGTTGAATT
Statistics
Matches: 69, Mismatches: 0, Indels: 25
0.73 0.00 0.27
Matches are distributed among these distances:
13 22 0.32
14 2 0.03
16 4 0.06
18 5 0.07
19 36 0.52
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:71930 original size:13 final size:13
Alignment explanation
Indices: 71912--71968 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
71902 ACAATACTTA
71912 TGTATCGATACAT
1 TGTATCGATACAT
71925 TGTATCGATACAAAACTT
1 TGTATCGATAC---A--T
71943 ATGTATCGATACAT
1 -TGTATCGATACAT
71957 TGTATCGATACA
1 TGTATCGATACA
71969 AAACTTATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
14 1 0.03
16 2 0.05
18 1 0.03
19 11 0.29
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:71934 original size:32 final size:32
Alignment explanation
Indices: 71893--71987 Score: 181
Period size: 32 Copynumber: 3.0 Consensus size: 32
71883 TAGCTAATTA
*
71893 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
71925 TGTATCGATACAAAACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
71957 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
71988 AATCGTTGAA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 62 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:72615 original size:55 final size:55
Alignment explanation
Indices: 72482--73035 Score: 696
Period size: 55 Copynumber: 10.0 Consensus size: 55
72472 TGGGAAGGTT
* *
72482 TGCCACTAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACTGGAAA--
1 TGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACT-GAAAGG
*
72536 TGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCTTGCTCTTTGAGGACTGAAAGG
1 TGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGAGGACTGAAAGG
* ** **
72591 TGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAAAA
1 TGCCACCAACTTGTGTGGGCTTT---AAG---AGGTGTCCTGCTCTTTGAGGACTGAAAGG
* * * *
72652 TGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTC-TTGAGGATTGGAAA-A
1 TGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACT-GAAAGG
* **
72706 TGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGGGGACTGAAAAA
1 TGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGAAAGG
* *
72761 TGCCACCAACTTGGGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGGGGACTGAAAGG
1 TGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGAGGACTGAAAGG
* * *
72816 TGCCACCAAATTTTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTTGGAAGG
1 TGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGAC-TGAAAGG
* * * *
72872 CGCCA-CAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTTTTTGAGGACTGGAAGA
1 TGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGAAAGG
*
72926 CGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGGAAA-G
1 TGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACT-GAAAGG
*
72981 CGCCACCAACTTGTGT-GGCTTTAAGAGGTGTCCTGCTCTTTG-GGACTGAAAGG
1 TGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGAAAGG
73034 TG
1 TG
73036 AGTTGACTTT
Statistics
Matches: 446, Mismatches: 36, Indels: 37
0.86 0.07 0.07
Matches are distributed among these distances:
52 4 0.01
53 11 0.02
54 133 0.30
55 234 0.52
56 15 0.03
57 2 0.00
58 2 0.00
61 45 0.10
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.29
Consensus pattern (55 bp):
TGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTTTGAGGACTGAAAGG
Found at i:77829 original size:17 final size:15
Alignment explanation
Indices: 77800--77862 Score: 65
Period size: 17 Copynumber: 4.0 Consensus size: 15
77790 TTCTCTTCAT
* *
77800 AAAAAAAAGAGCAAA
1 AAAAAAAAAAACAAA
77815 AAAAAAACAAAAGCAAA
1 AAAAAAA-AAAA-CAAA
77832 AAAAAAAAAAA-AAA
1 AAAAAAAAAAACAAA
77846 ACAAAAAACAAAACAAA
1 A-AAAAAA-AAAACAAA
77863 GCGAAAAAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
14 4 0.10
15 13 0.32
16 10 0.24
17 14 0.34
ACGTcount: A:0.86, C:0.10, G:0.05, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAACAAA
Found at i:77832 original size:12 final size:10
Alignment explanation
Indices: 77812--77853 Score: 52
Period size: 9 Copynumber: 4.4 Consensus size: 10
77802 AAAAAAGAGC
77812 AAAAAAA-AA
1 AAAAAAACAA
* *
77821 ACAAAAGCAA
1 AAAAAAACAA
77831 AAAAAAA-AA
1 AAAAAAACAA
77840 AAAAAAACAA
1 AAAAAAACAA
77850 AAAA
1 AAAA
77854 CAAAACAAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
9 14 0.52
10 13 0.48
ACGTcount: A:0.90, C:0.07, G:0.02, T:0.00
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:77834 original size:19 final size:18
Alignment explanation
Indices: 77812--77862 Score: 66
Period size: 19 Copynumber: 2.8 Consensus size: 18
77802 AAAAAAGAGC
*
77812 AAAAAAAAAACAAAAGCAA
1 AAAAAAAAAACAAAAAC-A
*
77831 AAAAAAAAAAAAAAAACA
1 AAAAAAAAAACAAAAACA
*
77849 AAAAACAAAACAAA
1 AAAAAAAAAACAAA
77863 GCGAAAAAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
18 13 0.46
19 15 0.54
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAACAAAAACA
Found at i:77840 original size:36 final size:36
Alignment explanation
Indices: 77800--77870 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
77790 TTCTCTTCAT
* * *
77800 AAAAAAAAGAGCAAAAAA-AAAACAAAAGCAAAAAAA
1 AAAAAAAAAAACAAAAAACAAAA-CAAAGCAAAAAAA
*
77836 AAAAAAAAAAACAAAAAACAAAACAAAGCGAAAAA
1 AAAAAAAAAAACAAAAAACAAAACAAAGCAAAAAA
77871 GATGAGGGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 26 0.87
37 4 0.13
ACGTcount: A:0.83, C:0.10, G:0.07, T:0.00
Consensus pattern (36 bp):
AAAAAAAAAAACAAAAAACAAAACAAAGCAAAAAAA
Found at i:77870 original size:19 final size:17
Alignment explanation
Indices: 77800--77870 Score: 56
Period size: 17 Copynumber: 4.1 Consensus size: 17
77790 TTCTCTTCAT
*
77800 AAAAAAA-AGAGC-AAA
1 AAAAAAACAAAGCAAAA
77815 AAAAAAACAAAAGCAAAAAA
1 AAAAAAAC-AAAGC--AAAA
* *
77835 AAAAAAAAAAAACAAAA
1 AAAAAAACAAAGCAAAA
* *
77852 AACAAAACAAAGCGAAA
1 AAAAAAACAAAGCAAAA
77869 AA
1 AA
77871 GATGAGGGAA
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
15 7 0.16
17 23 0.52
19 4 0.09
20 10 0.23
ACGTcount: A:0.83, C:0.10, G:0.07, T:0.00
Consensus pattern (17 bp):
AAAAAAACAAAGCAAAA
Found at i:79111 original size:57 final size:56
Alignment explanation
Indices: 78898--79352 Score: 442
Period size: 59 Copynumber: 8.0 Consensus size: 56
78888 CCTTCTCTTC
* *
78898 CACCATTTTCAGTCCTC-AAGAGCAGAGGACCACCTCTTAAAGCCTA-ACAAGTTGGTGG
1 CACC-TTTCCAGTCCTCAAAGAGC--AGGA-CACCTCTTAAAGCCCACACAAGTTGGTGG
* *
78956 CACCTTTCC--TCC-CCAAGAGCAGGACACCT-TTCCAAGCCCACAC-AGTTGGTGG
1 CACCTTTCCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGG
* *
79008 CA-TTTTCCATTCCTCAAAGAGCCAGGACA-CTCTTAAAGCCCACACAAGTTTGGTGG
1 CACCTTTCCAGTCCTCAAAGAG-CAGGACACCTCTTAAAGCCCACACAAG-TTGGTGG
* * *
79064 CACCTTTCAAGTCACCCAAAG-GCAGGACACCTCTTCAAGCCCACACAAGTTGTGGGTGG
1 CACCTTTCCAGTC-CTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAG-T-T-GGTGG
**
79123 CGTC-TTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAG-CCACA-ACA-TTGGTGG
1 CACCTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACA-AGTTGGTGG
* * *
79176 CGCC-TTCCAGTCCTCAAAGCAGCAGGGACACATCTTAAAGCCCACACAATTTGGTGGG
1 CACCTTTCCAGTCCTCAAAG-AGCA-GGACACCTCTTAAAGCCCACACAAGTTGGT-GG
*
79234 CA-TTTTCCCAGTGCCTCAAAGAGCAAGGACACCTCTTAAAAG-CCACACACAGTTGGTGG
1 CACCTTT-CCAGT-CCTCAAAGAGC-AGGACACCTCTT-AAAGCCCACACA-AGTTGGTGG
79293 CCCACC-TTCCAGTCCTCAAAGAGCAGGAACACCTCTTAAAGCCCACACAAGTTGGTGG
1 --CACCTTTCCAGTCCTCAAAGAGCAGG-ACACCTCTTAAAGCCCACACAAGTTGGTGG
79351 CA
1 CA
Statistics
Matches: 340, Mismatches: 23, Indels: 70
0.79 0.05 0.16
Matches are distributed among these distances:
51 7 0.02
52 22 0.06
53 32 0.09
54 24 0.07
55 35 0.10
56 25 0.07
57 50 0.15
58 56 0.16
59 61 0.18
60 24 0.07
61 4 0.01
ACGTcount: A:0.28, C:0.31, G:0.20, T:0.20
Consensus pattern (56 bp):
CACCTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGG
Found at i:79156 original size:115 final size:112
Alignment explanation
Indices: 78901--79352 Score: 499
Period size: 115 Copynumber: 4.0 Consensus size: 112
78891 TCTCTTCCAC
78901 CATTTT-CAGTCCTC-AAGAGCAGAGGACCACCTCTTAAAGCCTA-ACA-AGTTGGTGGCACCTT
1 CATTTTCCAGTCCTCAAAGAGCA-AGGA-CACCTCTTAAAGCC-ACACACAGTTGGTGGCACC-T
*
78962 TCC--TCCCC-AAGAGCAGGACACCT-TTCCAAGCCCACAC-AG-TTGGTGG
62 TCCAGTCCCCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTTGGTGG
* *
79008 CATTTTCCATTCCTCAAAGAGCCAGGACA-CTCTTAAAGCC-CACACAAGTTTGGTGGCACCTTT
1 CATTTTCCAGTCCTCAAAGAGCAAGGACACCTCTTAAAGCCACACAC-AG-TTGGTGGCACC-TT
* *
79071 CAAGTCACCCAAAG-GCAGGACACCTCTTCAAGCCCACACAAGTTGTGGGTGG
63 CCAGTC-CCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTT-T-GGTGG
* * *
79123 CGTCTTCCAGTCCTCAAAGAGC-AGGACACCTCTTAAAGCCACA-ACA-TTGGTGGCGCCTTCCA
1 CATTTTCCAGTCCTCAAAGAGCAAGGACACCTCTTAAAGCCACACACAGTTGGTGGCACCTTCCA
* *
79185 GTCCTCAAAGCAGCAGGGACACATCTTAAAGCCCACACAA-TTTGGTGGG
66 GTCCCCAAAG-AGCA-GGACACCTCTTAAAGCCCACACAAGTTTGGT-GG
79234 CATTTTCCCAGTGCCTCAAAGAGCAAGGACACCTCTTAAAAGCCACACACAGTTGGTGGCCCACC
1 CATTTT-CCAGT-CCTCAAAGAGCAAGGACACCTCTT-AAAGCCACACACAGTTGGTGG--CACC
*
79299 TTCCAGTCCTCAAAGAGCAGGAACACCTCTTAAAGCCCACACAAG-TTGGTGG
61 TTCCAGTCCCCAAAGAGCAGG-ACACCTCTTAAAGCCCACACAAGTTTGGTGG
79351 CA
1 CA
Statistics
Matches: 299, Mismatches: 15, Indels: 52
0.82 0.04 0.14
Matches are distributed among these distances:
105 3 0.01
106 11 0.04
107 10 0.03
108 26 0.09
109 6 0.02
110 11 0.04
111 39 0.13
112 27 0.09
113 34 0.11
114 20 0.07
115 46 0.15
116 5 0.02
117 13 0.04
118 30 0.10
119 18 0.06
ACGTcount: A:0.28, C:0.31, G:0.20, T:0.20
Consensus pattern (112 bp):
CATTTTCCAGTCCTCAAAGAGCAAGGACACCTCTTAAAGCCACACACAGTTGGTGGCACCTTCCA
GTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTTGGTGG
Done.