Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold68
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: 494511
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 3 of 3
Found at i:318628 original size:18 final size:16
Alignment explanation
Indices: 318591--318643 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 16
318581 AGTTCTTTTC
318591 TTTTCTTTTTTTTCTT
1 TTTTCTTTTTTTTCTT
*
318607 TTTTCTCTTTTTTTGTT
1 TTTTCT-TTTTTTTCTT
318624 GTTTT-TTTTTGTTT-TT
1 -TTTTCTTTTT-TTTCTT
318640 TTTT
1 TTTT
318644 AATTTTTGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
15 4 0.12
16 12 0.36
17 13 0.39
18 4 0.12
ACGTcount: A:0.00, C:0.08, G:0.06, T:0.87
Consensus pattern (16 bp):
TTTTCTTTTTTTTCTT
Found at i:318632 original size:13 final size:12
Alignment explanation
Indices: 318586--318643 Score: 55
Period size: 13 Copynumber: 4.6 Consensus size: 12
318576 AAGCAAGTTC
* *
318586 TTTTCTTTTCTT
1 TTTTTTTTTGTT
318598 TTTTTTCTTT-TT
1 TTTTTT-TTTGTT
318610 TCTCTTTTTTTGTT
1 T-T-TTTTTTTGTT
318624 GTTTTTTTTTGTT
1 -TTTTTTTTTGTT
318637 TTTTTTT
1 TTTTTTT
318644 AATTTTTGTT
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
12 15 0.38
13 17 0.43
14 7 0.17
15 1 0.03
ACGTcount: A:0.00, C:0.09, G:0.05, T:0.86
Consensus pattern (12 bp):
TTTTTTTTTGTT
Found at i:318632 original size:30 final size:29
Alignment explanation
Indices: 318596--318663 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 29
318586 TTTTCTTTTC
318596 TTTTTTTTCTTTTTTCTCTT-TTTTTGTTGT
1 TTTTTTTTCTTTTTT-T-TTATTTTTGTTGT
*
318626 TTTTTTTTGTTTTTTTTTAATTTTTGTTGT
1 TTTTTTTTCTTTTTTTTT-ATTTTTGTTGT
*
318656 TTTCTTTT
1 TTTTTTTT
318664 GTTTAGAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 2 0.06
29 1 0.03
30 31 0.91
ACGTcount: A:0.03, C:0.06, G:0.07, T:0.84
Consensus pattern (29 bp):
TTTTTTTTCTTTTTTTTTATTTTTGTTGT
Found at i:330899 original size:79 final size:76
Alignment explanation
Indices: 330801--331394 Score: 510
Period size: 79 Copynumber: 7.6 Consensus size: 76
330791 AATTTTAATA
* * * * *
330801 TTTTGGAGATAAAAGCGGGGTTGGAGTATCCTTTCAAAAAATAACAGGGATGGAGTATCCCCGAT
1 TTTTGGAAATAAAATCGGGGTTGGAGTATCC-CTC-AGAAATAAC-GGGTTGGAGTATCCCCGAT
* *
330866 TGTGGAAAATCATG
63 TGTGAAAAATGATG
* * * * * *
330880 TTCTGGAAATAAAATCGGGGTTAGAGTATTCCCTCGGAAATAATAGGGTTGCAGTATCCTCGATT
1 TTTTGGAAATAAAATCGGGGTTGGAGTA-TCCCTCAGAAATAA-CGGGTTGGAGTATCCCCGATT
* * * *
330945 ATGGAAAATCGGTA
64 GTGAAAAAT-GATG
** * * * * *
330959 TTTCAGAAATAAAATCGAGGTTAGAGTATTCCCTCAGAAATAATGGGGTTAGAGTATCCCCGATG
1 TTTTGGAAATAAAATCGGGGTTGGAGTA-TCCCTCAGAAATAA-CGGGTTGGAGTATCCCCGATT
*
331024 GTGAAAATTGATG
64 GTGAAAAATGATG
* * * *
331037 CTTTGGAAATAAAATCGGGGTTGGAGTATCCCCTTAAAAATAATTGGGTTGGAGTATCCCCGATT
1 TTTTGGAAATAAAATCGGGGTTGGAGTAT-CCCTCAGAAATAA-CGGGTTGGAGTATCCCCGATT
* *
331102 GTGAAAAATTGGTA
64 GTGAAAAA-TGATG
* *** * *
331116 TTTTGAAAATAAAATTACGGTCGGAGTATCCCTCAGAAATAACGAGGTTAGG-GTATCTCCGATT
1 TTTTGGAAATAAAATCGGGGTTGGAGTATCCCTCAGAAATAACG-GGTT-GGAGTATCCCCGATT
* *
331180 ATGAAAAATTAGTG
64 GTGAAAAATGA-TG
* * * *
331194 TTTTGGAAATAAAACCGGGGTTGGAGTATCCCCTCGGAAATAACGAGATTAGAGTATCCCCGATT
1 TTTTGGAAATAAAATCGGGGTTGGAGTAT-CCCTCAGAAATAACG-GGTTGGAGTATCCCCGATT
*
331259 GTGAAAAATTGGTG
64 GTGAAAAA-TGATG
* *
331273 TTTTGGAAATAAAA-CTGGTGTTGGAGCATCCTCTC-GAAAATAACGGGGTTGGAGTATCCCCGA
1 TTTTGGAAATAAAATC-GGGGTTGGAGTATCC-CTCAG-AAATAAC-GGGTTGGAGTATCCCCGA
* * *
331336 CTATGAAAAATTAGTG
62 TTGTGAAAAATGA-TG
*
331352 TTTTGGAAATAAAATCGGGGTTGGAGTATCCTCTCGGAAATAA
1 TTTTGGAAATAAAATCGGGGTTGGAGTATCC-CTCAGAAATAA
331395 AAACATAAAT
Statistics
Matches: 417, Mismatches: 80, Indels: 36
0.78 0.15 0.07
Matches are distributed among these distances:
77 3 0.01
78 156 0.37
79 251 0.60
80 7 0.02
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.28
Consensus pattern (76 bp):
TTTTGGAAATAAAATCGGGGTTGGAGTATCCCTCAGAAATAACGGGTTGGAGTATCCCCGATTGT
GAAAAATGATG
Found at i:331014 original size:157 final size:155
Alignment explanation
Indices: 330809--331394 Score: 603
Period size: 157 Copynumber: 3.7 Consensus size: 155
330799 TATTTTGGAG
* * * * * * * * *
330809 ATAAAAGCGGGGTTGGAGTATCCTTTCAAAAAATAACAGGGATGGAGTATCCCCGATTGTGGAAA
1 ATAAAATCGAGGTTGGAGTATCC-CTC-AGAAATAACGGGGTTAGAGTATCCCCGATTATGAAAA
* * * *
330874 ATCA-TGTTCTGGAAATAAAATCGGGGTTAGAGTATTCCCTCGGAAATAATAGGGTTGCAGTATC
64 ATTAGTGTTTTGGAAATAAAATCGGGGTTGGAGTATCCCCTCGGAAATAATAGGGTTG-AGTATC
* * * *
330938 CTCGATTATGGAAAATCGGTATTTCAGAA
128 CCCGATTGTGAAAAATTGGTATTT-AGAA
* * **
330967 ATAAAATCGAGGTTAGAGTATTCCCTCAGAAATAATGGGGTTAGAGTATCCCCGATGGTG-AAAA
1 ATAAAATCGAGGTTGGAGTA-TCCCTCAGAAATAACGGGGTTAGAGTATCCCCGATTATGAAAAA
* *** *
331031 TT-GATGCTTTGGAAATAAAATCGGGGTTGGAGTATCCCCTTAAAAATAATTGGGTTGGAGTATC
65 TTAG-TGTTTTGGAAATAAAATCGGGGTTGGAGTATCCCCTCGGAAATAATAGGGTT-GAGTATC
*
331095 CCCGATTGTGAAAAATTGGTATTTTGAAA
128 CCCGATTGTGAAAAATTGGTATTTAG-AA
* * * * *
331124 ATAAAAT-TACGGTCGGAGTATCCCTCAGAAATAACGAGGTTAGGGTATCTCCGATTATGAAAAA
1 ATAAAATCGA-GGTTGGAGTATCCCTCAGAAATAACGGGGTTAGAGTATCCCCGATTATGAAAAA
* * *
331188 TTAGTGTTTTGGAAATAAAACCGGGGTTGGAGTATCCCCTCGGAAATAA-CGAGATTAGAGTATC
65 TTAGTGTTTTGGAAATAAAATCGGGGTTGGAGTATCCCCTCGGAAATAATAG-GGTT-GAGTATC
* *
331252 CCCGATTGTGAAAAATTGGTGTTTTGGAA
128 CCCGATTGTGAAAAATTGGT-ATTTAGAA
* * *
331281 ATAAAA-CTG-GTGTTGGAGCATCCTCTC-GAAAATAACGGGGTTGGAGTATCCCCGACTATGAA
1 ATAAAATC-GAG-GTTGGAGTATCC-CTCAG-AAATAACGGGGTTAGAGTATCCCCGATTATGAA
*
331343 AAATTAGTGTTTTGGAAATAAAATCGGGGTTGGAGTATCCTCTCGGAAATAA
62 AAATTAGTGTTTTGGAAATAAAATCGGGGTTGGAGTATCCCCTCGGAAATAA
331395 AAACATAAAT
Statistics
Matches: 360, Mismatches: 53, Indels: 30
0.81 0.12 0.07
Matches are distributed among these distances:
156 42 0.12
157 209 0.58
158 106 0.29
159 3 0.01
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (155 bp):
ATAAAATCGAGGTTGGAGTATCCCTCAGAAATAACGGGGTTAGAGTATCCCCGATTATGAAAAAT
TAGTGTTTTGGAAATAAAATCGGGGTTGGAGTATCCCCTCGGAAATAATAGGGTTGAGTATCCCC
GATTGTGAAAAATTGGTATTTAGAA
Found at i:333759 original size:20 final size:20
Alignment explanation
Indices: 333734--333787 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
333724 AAATGCCTGG
*
333734 ATGTATCGATACATTGAAAA
1 ATGTATCGATACAATGAAAA
*
333754 ATGTATCGATACAATGAACA
1 ATGTATCGATACAATGAAAA
333774 ATGTATCGATACAA
1 ATGTATCGATACAA
333788 ATTGTGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (20 bp):
ATGTATCGATACAATGAAAA
Found at i:347193 original size:51 final size:51
Alignment explanation
Indices: 347136--347251 Score: 178
Period size: 51 Copynumber: 2.3 Consensus size: 51
347126 AATTAACTAG
* * * *
347136 ATGTATCGATACATTGAAAAATGTATTGATACATCTGGGTAAAAAAATAGA
1 ATGTATCGATACATTGAAAAATGAATCGATACATCTAGGTAAAAAAACAGA
*
347187 ATGTATCAATACATTGAAAAATGAATCGATACATCTAGGTAAAAAAACAGA
1 ATGTATCGATACATTGAAAAATGAATCGATACATCTAGGTAAAAAAACAGA
*
347238 ACGTATCGATACAT
1 ATGTATCGATACAT
347252 GTACTATTTA
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:0.47, C:0.11, G:0.16, T:0.27
Consensus pattern (51 bp):
ATGTATCGATACATTGAAAAATGAATCGATACATCTAGGTAAAAAAACAGA
Found at i:350783 original size:23 final size:25
Alignment explanation
Indices: 350738--350783 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
350728 AAAGTAAAAA
*
350738 GTAAAATAAATAAATAAATACAAGG
1 GTAAAATAAATAAATAAAAACAAGG
350763 GTAAAA-AAAT-AATAAAAACAA
1 GTAAAATAAATAAATAAAAACAA
350784 AAAAGGTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
24 4 0.20
25 6 0.30
ACGTcount: A:0.70, C:0.04, G:0.09, T:0.17
Consensus pattern (25 bp):
GTAAAATAAATAAATAAAAACAAGG
Found at i:353811 original size:163 final size:161
Alignment explanation
Indices: 353198--353818 Score: 592
Period size: 163 Copynumber: 3.8 Consensus size: 161
353188 TTATAATAAT
* * * *
353198 ATTTTATTTATTCTTTTTTTTGAAAAA-ATCATTTCGTACTTTAATAGAAACCCAAAAAGATACG
1 ATTTTATTTA-T-TTCTTTTTGAAAAATACCATTTCGTACCTTAATGGAAACCCAAAAAGATACG
* * * *
353262 AAAAGTTTTTGAAACCTATTATACCTTTACAAACCCCCAGAGGAATATAAAAGATTTAAAAAAAA
64 AAAAGTTTTTGAATCCT-TTATACCCTTACAGACCCCCATAGGAATATAAAAGA-TTAAAAAAAA
* * *
353327 TTATTTCTATTTATTTCAATCAATA-AAGTGTTAA-TTA
127 TTA-AT-T-TTTATTTCAAT-TATAGAAGTATTAATTTA
* * *
353364 ATTTTATTTATTTCTTTTTGAAAAATACCATTTCGTACCTTAATGAAAACTCGAAAAGATACGAA
1 ATTTTATTTATTTCTTTTTGAAAAATACCATTTCGTACCTTAATGGAAACCCAAAAAGATACGAA
** * * *
353429 AAGTTTTAAAATCCTTTATACCCCTACAGATCCCCATAGGAATATAAAAGATT-AAAAAGATTAA
66 AAGTTTTTGAATCCTTTATACCCTTACAGACCCCCATAGGAATATAAAAGATTAAAAAAAATTAA
** * ** * *
353493 AGTTTCTTTCGGTTGT-GTAAGTATTAATTTT
131 TTTTTATTTCAATTATAG-AAGTATTAATTTA
* * * * *
353524 ATTTTATTTA-TTCGTTTTCAAAAATACCTTTTCGTACCTTAATGGAGACCCAAAAAGATATGAA
1 ATTTTATTTATTTCTTTTTGAAAAATACCATTTCGTACCTTAATGGAAACCCAAAAAGATACGAA
* * * * *
353588 AAGTTTTTGAAATCCTTTATACCCTTACTGACCCCCACAAGAAAATAGAAGA-TAAAAAAATGAT
66 AAGTTTTTG-AATCCTTTATACCCTTACAGACCCCCATAGGAATATAAAAGATTAAAAAAA--AT
* * * *
353652 TAATTTTTATTTTAATTATAGGACTCTTAATTTA
128 TAATTTTTATTTCAATTATAGAAGTATTAATTTA
* * * * *
353686 ACTTTATTTATTTATTTTTAAAAAATATCATTTCGTACCTTAATGGAAA-TCAGAAAAGATACGA
1 ATTTTATTTATTTCTTTTTGAAAAATACCATTTCGTACCTTAATGGAAACCCA-AAAAGATACGA
* * * ** *
353750 AAAGTTTTTGAATTCTTATATACCTTTACGGACTTCTATAGGAATATAAAAGATTAAAAAATAAT
65 AAAGTTTTTGAATCCTT-TATACCCTTACAGACCCCCATAGGAATATAAAAGATTAAAAAA-AAT
353815 TAAT
128 TAAT
353819 ATGGAAATAT
Statistics
Matches: 367, Mismatches: 74, Indels: 31
0.78 0.16 0.07
Matches are distributed among these distances:
158 1 0.00
159 70 0.19
160 52 0.14
162 49 0.13
163 87 0.24
164 51 0.14
165 47 0.13
166 10 0.03
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.38
Consensus pattern (161 bp):
ATTTTATTTATTTCTTTTTGAAAAATACCATTTCGTACCTTAATGGAAACCCAAAAAGATACGAA
AAGTTTTTGAATCCTTTATACCCTTACAGACCCCCATAGGAATATAAAAGATTAAAAAAAATTAA
TTTTTATTTCAATTATAGAAGTATTAATTTA
Found at i:357492 original size:20 final size:20
Alignment explanation
Indices: 357467--357612 Score: 105
Period size: 20 Copynumber: 6.8 Consensus size: 20
357457 ATTTGCCTAC
357467 ATGTATCGATACATTGAATA
1 ATGTATCGATACATTGAATA
* *
357487 ATGTATTGATACATCGAATA
1 ATGTATCGATACATTGAATA
*
357507 ATGTATCGATACATAGAATA
1 ATGTATCGATACATTGAATA
* * *
357527 ATATATCGATTCTTCTAGGTAAAATTCCTA
1 ATGTATCGATACAT-T--G---AA----TA
**
357557 GATGTATCGATACAAAG-ATCA
1 -ATGTATCGATACATTGAAT-A
357578 ATGTATCGATACATTGAATA
1 ATGTATCGATACATTGAATA
357598 ATGTATCGATACATT
1 ATGTATCGATACATT
357613 TCCTTGGCAG
Statistics
Matches: 98, Mismatches: 15, Indels: 26
0.71 0.11 0.19
Matches are distributed among these distances:
20 78 0.80
21 3 0.03
23 1 0.01
24 1 0.01
26 2 0.02
28 1 0.01
30 2 0.02
31 10 0.10
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACATTGAATA
Found at i:357655 original size:13 final size:13
Alignment explanation
Indices: 357637--357662 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
357627 CAGGGCAGCT
357637 TTGTATCGATACA
1 TTGTATCGATACA
357650 TTGTATCGATACA
1 TTGTATCGATACA
357663 ACACTTATGT
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):
TTGTATCGATACA
Found at i:358242 original size:12 final size:12
Alignment explanation
Indices: 358219--358259 Score: 57
Period size: 12 Copynumber: 3.3 Consensus size: 12
358209 TTTTCTTCAA
358219 TTTTTCTCTTTT
1 TTTTTCTCTTTT
358231 TTTCTT-TCTTTT
1 TTT-TTCTCTTTT
358243 TTTTTCTCTCTTT
1 TTTTTCTCT-TTT
358256 TTTT
1 TTTT
358260 AGCTAACCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.08
12 15 0.58
13 9 0.35
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTTTCTCTTTT
Found at i:358244 original size:14 final size:14
Alignment explanation
Indices: 358221--358259 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
358211 TTCTTCAATT
*
358221 TTTCTCTTTTTTTC
1 TTTCTTTTTTTTTC
358235 TTTCTTTTTTTTTC
1 TTTCTTTTTTTTTC
*
358249 TCTCTTTTTTT
1 TTTCTTTTTTT
358260 AGCTAACCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTCTTTTTTTTTC
Found at i:358951 original size:166 final size:163
Alignment explanation
Indices: 358767--359363 Score: 688
Period size: 165 Copynumber: 3.6 Consensus size: 163
358757 GAGAAACTCG
* *
358767 TGAAAATGAATGAATTTTTGAAAACTAATTTAATATGATTTAAATAATAATATTTGATGAATTTT
1 TGAAAATGAATGAATTTTTGAAAACTGATTTAATATGAATTAAATAATAATATTTGATGAATTTT
* * * *
358832 AAAAAATAAAAAGC-AAGAAAAATCTCC-CCGAAAAAATTTAGGGAGTAGAAAACTCTGTATTTC
66 AAAAATTAAAAA-CTAAGAAAAATC-CCTCCG-AAAAATTTACGGAGTAGAAAACAC-ATATTTC
* *
358895 GAAAAAAAAGAAGTTTTAAGGAAAAAATAAAAAATTCA
127 GAAAAAGAAGAA-TTTCAAGGAAAAAATAAAAAATTCA
** * * * * * *
358933 TGATGATGAATTAATTTTTTAAAAATTATTTAATATGAATCAAATAATGATATTTGATGAATTTT
1 TGAAAATGAATGAATTTTTGAAAACTGATTTAATATGAATTAAATAATAATATTTGATGAATTTT
* *
358998 AAAAATTAAAAACTAAGAAAAATCCCTTCGAAAAA-TTACAGAGTAGAAAACACCATATTTCGAA
66 AAAAATTAAAAACTAAGAAAAATCCCTCCGAAAAATTTACGGAGTAGAAAACA-CATATTTCGAA
* * *
359062 AAAGGAGAATTTCAAGGAAACAAATTTAAAAATTTA
130 AAAGAAGAATTTCAAGGAAA-AAA-TAAAAAATTCA
* * * * *
359098 TGAAAATGAATGAATTTTTGCAAACTGATTTAATATGAATTAATTGATAGTATTTTATGAATTTT
1 TGAAAATGAATGAATTTTTGAAAACTGATTTAATATGAATTAAATAATAATATTTGATGAATTTT
* * *
359163 AAAAATTAAAAACTACGAAAAATCCCTCCG-AAAATTTACGAAGTAGAAAAAACATATTTCGGAA
66 AAAAATTAAAAACTAAGAAAAATCCCTCCGAAAAATTTACGGAGTAGAAAACACATATTTC-GAA
*
359227 AAAGGAA-AATTTCAA-GAAAAAATAAAAAA-TCC
130 AAA-GAAGAATTTCAAGGAAAAAATAAAAAATTCA
* * * * *
359259 TGAAAATGAATTAATTTTTGAGAACTGATTTAATATGAAATAAATAATGATATTTTATGAATTTT
1 TGAAAATGAATGAATTTTTGAAAACTGATTTAATATGAATTAAATAATAATATTTGATGAATTTT
* * *
359324 GAAAATTAAAAATTAATAAAAAT-CCTGCCGAAAAAATTTA
66 AAAAATTAAAAACTAAGAAAAATCCCT-CCG-AAAAATTTA
359364 TAAAGAAGAA
Statistics
Matches: 366, Mismatches: 54, Indels: 25
0.82 0.12 0.06
Matches are distributed among these distances:
160 3 0.01
161 80 0.22
162 6 0.02
163 21 0.06
164 49 0.13
165 126 0.34
166 81 0.22
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.31
Consensus pattern (163 bp):
TGAAAATGAATGAATTTTTGAAAACTGATTTAATATGAATTAAATAATAATATTTGATGAATTTT
AAAAATTAAAAACTAAGAAAAATCCCTCCGAAAAATTTACGGAGTAGAAAACACATATTTCGAAA
AAGAAGAATTTCAAGGAAAAAATAAAAAATTCA
Found at i:360399 original size:42 final size:42
Alignment explanation
Indices: 360346--360570 Score: 168
Period size: 42 Copynumber: 5.4 Consensus size: 42
360336 CTGACAAGTC
* **
360346 GATGAATAAGTCTCCTAAGTCAAAGTCGACGGGCAGACAAAG
1 GATGAAGAAGTCTCCTGGGTCAAAGTCGACGGGCAGACAAAG
* * * *
360388 GATGAAGAAGTCTCTTGGGTCAAAGTCAACTGGTAGACAAAG
1 GATGAAGAAGTCTCCTGGGTCAAAGTCGACGGGCAGACAAAG
* * * *
360430 GGTGAAGGAGTCTACC-AGGTCAAAG-CTGACTGGCAGACAAAG
1 GATGAAGAAGTCT-CCTGGGTCAAAGTC-GACGGGCAGACAAAG
* * * * * * *
360472 GGTAAAGGAGTCTCCCGGGTCAAAGTTGACGAGCAAACAAAG
1 GATGAAGAAGTCTCCTGGGTCAAAGTCGACGGGCAGACAAAG
* * ** * * *
360514 GGT-AAAAGAGTCTTTTGAGTCAAAGCCGACAGGCAGACAAAG
1 GATGAAGA-AGTCTCCTGGGTCAAAGTCGACGGGCAGACAAAG
*
360556 TATGAAGAAGTCTCC
1 GATGAAGAAGTCTCC
360571 CAGGTCTAAG
Statistics
Matches: 142, Mismatches: 35, Indels: 12
0.75 0.19 0.06
Matches are distributed among these distances:
41 5 0.04
42 133 0.94
43 4 0.03
ACGTcount: A:0.36, C:0.18, G:0.29, T:0.17
Consensus pattern (42 bp):
GATGAAGAAGTCTCCTGGGTCAAAGTCGACGGGCAGACAAAG
Found at i:360568 original size:84 final size:83
Alignment explanation
Indices: 360363--360576 Score: 214
Period size: 84 Copynumber: 2.6 Consensus size: 83
360353 AAGTCTCCTA
* * ** * *
360363 AGTCAAAGTCGACGGGCAGACAAAGGATGAAGAAGTCTCTTGGGTCAAAGTCAACTGGTAGACAA
1 AGTCAAAGCCGACAGGCAGACAAAGGATGAAGAAGTCTCCCGGGTCAAAGTCAACTGGCAAACAA
* *
360428 AGGGTGAAGGAGTCTACC
66 AGGGTAAAAGAGTCTACC
* * * * * **
360446 AGGTCAAAGCTGACTGGCAGACAAAGGGTAAAGGAGTCTCCCGGGTCAAAGTTGAC-GAGCAAAC
1 A-GTCAAAGCCGACAGGCAGACAAAGGATGAAGAAGTCTCCCGGGTCAAAGTCAACTG-GCAAAC
***
360510 AAAGGGTAAAAGAGTCTTTTG
64 AAAGGGTAAAAGAGTC-TACC
* *
360531 AGTCAAAGCCGACAGGCAGACAAAGTATGAAGAAGTCTCCCAGGTC
1 AGTCAAAGCCGACAGGCAGACAAAGGATGAAGAAGTCTCCCGGGTC
360577 TAAGCTGATA
Statistics
Matches: 104, Mismatches: 24, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
83 2 0.02
84 100 0.96
85 2 0.02
ACGTcount: A:0.36, C:0.18, G:0.30, T:0.16
Consensus pattern (83 bp):
AGTCAAAGCCGACAGGCAGACAAAGGATGAAGAAGTCTCCCGGGTCAAAGTCAACTGGCAAACAA
AGGGTAAAAGAGTCTACC
Found at i:360862 original size:18 final size:19
Alignment explanation
Indices: 360839--360878 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
360829 ATGTTCATGA
360839 TTTTATTC-ATTCTTTATT
1 TTTTATTCAATTCTTTATT
360857 TTTTATTCAATTCTTTATT
1 TTTTATTCAATTCTTTATT
360876 TTT
1 TTT
360879 CTTTATTAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTATTCAATTCTTTATT
Found at i:364991 original size:13 final size:13
Alignment explanation
Indices: 364973--364997 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
364963 CAAATTGCAA
364973 TGTATCGATACAT
1 TGTATCGATACAT
364986 TGTATCGATACA
1 TGTATCGATACA
364998 ACTTGCAATG
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:365004 original size:33 final size:32
Alignment explanation
Indices: 364954--365019 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 32
364944 CACATGAAAA
364954 TGTATCGTACAAATTGCAATGTATCGATACAT
1 TGTATCGTACAAATTGCAATGTATCGATACAT
* *
364986 TGTATCGATACAACTTGCAATGTATTGATACAT
1 TGTATCG-TACAAATTGCAATGTATCGATACAT
365019 T
1 T
365020 ATGTAAATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 7 0.23
33 24 0.77
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (32 bp):
TGTATCGTACAAATTGCAATGTATCGATACAT
Found at i:365090 original size:21 final size:21
Alignment explanation
Indices: 365064--365141 Score: 65
Period size: 21 Copynumber: 3.8 Consensus size: 21
365054 CTGCCCTTCA
365064 AATGTATCGATACACATAT-AG
1 AATGTATCGATACA-ATATCAG
* *
365085 AATGTATCGAAACAATTTCAG
1 AATGTATCGATACAATATCAG
*
365106 AATTTATCGAT---ATATCCAG
1 AATGTATCGATACAATAT-CAG
*
365125 AATTGTGTCGATACAAT
1 AA-TGTATCGATACAAT
365142 TAATCCAATG
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
18 3 0.07
19 5 0.11
20 10 0.23
21 24 0.55
23 2 0.05
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (21 bp):
AATGTATCGATACAATATCAG
Found at i:373165 original size:21 final size:21
Alignment explanation
Indices: 373118--373197 Score: 83
Period size: 22 Copynumber: 3.8 Consensus size: 21
373108 CTACCCTTCA
* *
373118 AATGTATCGATACAAATATAGG
1 AATGTATCGATACAATTCTA-G
*
373140 AATGTATCGATACAATTCCAG
1 AATGTATCGATACAATTCTAG
*
373161 AATGTATCTATAC-A-TCTAG
1 AATGTATCGATACAATTCTAG
*
373180 AATTGTATCGACACAATT
1 AA-TGTATCGATACAATT
373198 ACCCCAATGG
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
19 6 0.12
20 10 0.21
21 14 0.29
22 18 0.38
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.31
Consensus pattern (21 bp):
AATGTATCGATACAATTCTAG
Found at i:377792 original size:5 final size:6
Alignment explanation
Indices: 377763--377791 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
377753 TAAGTTGCAA
377763 CTTTTC CTTTTC CTTTTC CTTTT- CTTTTC
1 CTTTTC CTTTTC CTTTTC CTTTTC CTTTTC
377792 TGGCCTCCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (6 bp):
CTTTTC
Found at i:384544 original size:13 final size:13
Alignment explanation
Indices: 384526--384551 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
384516 TACACCAAGT
384526 ATGTATCGATACA
1 ATGTATCGATACA
384539 ATGTATCGATACA
1 ATGTATCGATACA
384552 CAAAAACTTG
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:384637 original size:20 final size:21
Alignment explanation
Indices: 384606--384644 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
384596 CTATATTTTT
384606 CAAATATGTATCGATACATCA
1 CAAATATGTATCGATACATCA
384627 CAAAT-TGTATCGATACAT
1 CAAATATGTATCGATACAT
384645 TTACACGGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (21 bp):
CAAATATGTATCGATACATCA
Found at i:385503 original size:22 final size:24
Alignment explanation
Indices: 385457--385507 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
385447 TTTCTACCTA
385457 TTTTCTTCTATTTTTCTCTTGCTT
1 TTTTCTTCTATTTTTCTCTTGCTT
*
385481 TCTTTC-TCTTTTTTTCTC-T-CTT
1 T-TTTCTTCTATTTTTCTCTTGCTT
385503 TTTTC
1 TTTTC
385508 AACTGACCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 4 0.16
22 4 0.16
23 1 0.04
24 12 0.48
25 4 0.16
ACGTcount: A:0.02, C:0.24, G:0.02, T:0.73
Consensus pattern (24 bp):
TTTTCTTCTATTTTTCTCTTGCTT
Found at i:386605 original size:13 final size:13
Alignment explanation
Indices: 386587--386613 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
386577 ACAATTGTCC
386587 ATGTATCGATACA
1 ATGTATCGATACA
386600 ATGTATCGATACA
1 ATGTATCGATACA
386613 A
1 A
386614 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:388938 original size:20 final size:23
Alignment explanation
Indices: 388913--388959 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
388903 TTTTGTTGAT
388913 GATTTTG-A-TGAAAAA-TGAAA
1 GATTTTGAAGTGAAAAAGTGAAA
388933 GATTTTGAAGTGAAAAAGTGAAA
1 GATTTTGAAGTGAAAAAGTGAAA
388956 -ATTT
1 GATTT
388960 ATGGAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.29
21 1 0.04
22 11 0.46
23 5 0.21
ACGTcount: A:0.47, C:0.00, G:0.21, T:0.32
Consensus pattern (23 bp):
GATTTTGAAGTGAAAAAGTGAAA
Found at i:395305 original size:33 final size:33
Alignment explanation
Indices: 395261--395325 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
395251 ATTAGAAGCT
*
395261 ATGTATCGATACATT-TCATCATGTATCGATACA
1 ATGTATCGATACATTGT-ACCATGTATCGATACA
* *
395294 ATGTATGGATACATTGTACCATGTATTGATAC
1 ATGTATCGATACATTGTACCATGTATCGATAC
395326 CAACAGTGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.37
Consensus pattern (33 bp):
ATGTATCGATACATTGTACCATGTATCGATACA
Found at i:395400 original size:19 final size:20
Alignment explanation
Indices: 395356--395405 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
395346 CAGCCAATCT
**
395356 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
395376 CATGTATCGATACAATT-AA
1 CATGTATCGATACAATTGAA
395395 CATGTATCGAT
1 CATGTATCGAT
395406 TCAAAGCATA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:397740 original size:20 final size:23
Alignment explanation
Indices: 397715--397761 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
397705 TTATGTTAAT
397715 GATTTTG-A-TGAAAAA-TGAAA
1 GATTTTGAAGTGAAAAAGTGAAA
397735 GATTTTGAAGTGAAAAAGTGAAA
1 GATTTTGAAGTGAAAAAGTGAAA
397758 -ATTT
1 GATTT
397762 GTGGAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.29
21 1 0.04
22 11 0.46
23 5 0.21
ACGTcount: A:0.47, C:0.00, G:0.21, T:0.32
Consensus pattern (23 bp):
GATTTTGAAGTGAAAAAGTGAAA
Found at i:404054 original size:13 final size:13
Alignment explanation
Indices: 404036--404066 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
404026 ACAATTCATC
404036 ATGTATCGATACA
1 ATGTATCGATACA
404049 ATGTATCGATACA
1 ATGTATCGATACA
*
404062 TTGTA
1 ATGTA
404067 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:404058 original size:33 final size:33
Alignment explanation
Indices: 404016--404080 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
404006 GTTAGAACCT
*
404016 ATGTATCGATACAATT-CATCATGTATCGATACA
1 ATGTATCGATAC-ATTGCACCATGTATCGATACA
*
404049 ATGTATCGATACATTGTACCATGTATCGATAC
1 ATGTATCGATACATTGCACCATGTATCGATAC
404081 CAACAGTGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 3 0.10
33 26 0.90
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (33 bp):
ATGTATCGATACATTGCACCATGTATCGATACA
Found at i:404136 original size:20 final size:20
Alignment explanation
Indices: 404111--404160 Score: 86
Period size: 18 Copynumber: 2.6 Consensus size: 20
404101 CTGCCAATCT
404111 CATGTATCGATATAATTGTC
1 CATGTATCGATATAATTGTC
404131 CATGTATCG--ATAATTGTC
1 CATGTATCGATATAATTGTC
404149 CATGTATCGATA
1 CATGTATCGATA
404161 CAATGTATCG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 18 0.64
20 10 0.36
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (20 bp):
CATGTATCGATATAATTGTC
Found at i:406508 original size:20 final size:23
Alignment explanation
Indices: 406483--406529 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
406473 TTCTGTTGAT
406483 GATTTTG-A-TGAAAAA-TGAAA
1 GATTTTGAAGTGAAAAAGTGAAA
406503 GATTTTGAAGTGAAAAAGTGAAA
1 GATTTTGAAGTGAAAAAGTGAAA
406526 -ATTT
1 GATTT
406530 GTGGAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.29
21 1 0.04
22 11 0.46
23 5 0.21
ACGTcount: A:0.47, C:0.00, G:0.21, T:0.32
Consensus pattern (23 bp):
GATTTTGAAGTGAAAAAGTGAAA
Found at i:406670 original size:13 final size:13
Alignment explanation
Indices: 406652--406677 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
406642 TAGTACCCAC
406652 TGTATCGATACAA
1 TGTATCGATACAA
406665 TGTATCGATACAA
1 TGTATCGATACAA
406678 GGAATATTGT
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):
TGTATCGATACAA
Found at i:412829 original size:13 final size:13
Alignment explanation
Indices: 412811--412836 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
412801 ACAATTCATC
412811 ATGTATCGATACA
1 ATGTATCGATACA
412824 ATGTATCGATACA
1 ATGTATCGATACA
412837 TTATACCATG
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:412829 original size:33 final size:32
Alignment explanation
Indices: 412791--412855 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
412781 GTTACAAGCT
412791 ATGTATCGATACAATTCAT-CATGTATCGATACA
1 ATGTATCGATAC-ATT-ATACATGTATCGATACA
412824 ATGTATCGATACATTATACCATGTATCGATAC
1 ATGTATCGATACATTATA-CATGTATCGATAC
412856 CAACAGTGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
31 2 0.07
32 3 0.10
33 25 0.83
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.34
Consensus pattern (32 bp):
ATGTATCGATACATTATACATGTATCGATACA
Found at i:412930 original size:19 final size:20
Alignment explanation
Indices: 412886--412940 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
412876 CTGCCAATCT
**
412886 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
412906 CATGTATCGATACAATT-AA
1 CATGTATCGATACAATTGAA
412925 CATGTATCGATACAAT
1 CATGTATCGATACAAT
412941 GTATCGATAC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:412944 original size:13 final size:13
Alignment explanation
Indices: 412926--412952 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
412916 TACAATTAAC
412926 ATGTATCGATACA
1 ATGTATCGATACA
412939 ATGTATCGATACA
1 ATGTATCGATACA
412952 A
1 A
412953 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:413898 original size:162 final size:159
Alignment explanation
Indices: 413519--414081 Score: 580
Period size: 163 Copynumber: 3.5 Consensus size: 159
413509 AAAAGAAATA
* * *
413519 AATTTTTGAAAATTGATTTAATATGATTTAAATAATAATATTTGATGAATTTTAAAAATTAAAAA
1 AATTTTAGAAAACTGATTTAATATGAATTAAATAATAATATTTGATGAATTTTAAAAATTAAAAA
* * * * *
413584 CAAAGAAAAATCTCCTAAAAAAAATTTACAGAGTAGAAAACTCCATATTTCGAAAAAAAAGTTTC
66 C-AAGAAAAATCCCCTCAAAAAAATTTACA-AGTAGAAAAC-ACATATTTCAAAAAAAAAATTTC
* * *
413649 AAGGAAAAAAATAAAAAATTGGTGAG-GATGAATT
128 AAGG-AAAAAATCAAAAATT--TAAGAAATGAATT
** * * *
413683 AATTTTTA-AAAAAAGATTTAATATGAATCAAATAATGATATTT-ATGAATTTTAAAAATTGAAA
1 AA-TTTTAGAAAACTGATTTAATATGAATTAAATAATAATATTTGATGAATTTTAAAAATTAAAA
* *
413746 TCGAGAAAAATCCCCTCAAAAAAATTGTA-AAGTAGAAAACACTATATTTCAAAAAAGGAAAATT
65 ACAAGAAAAATCCCCTCAAAAAAATT-TACAAGTAGAAAACAC-ATATTTCAAAAAA--AAAATT
* *
413810 TCAAGGAAAAATTCAAAAATTTAAGAAATGAATG
126 TCAAGGAAAAAATCAAAAATTTAAGAAATGAATT
* * * *
413844 AATTTTAGCAAACTGTTTTAATATGAATTAAATGATAATATTTGATGAATTTTAAAAATTAAAAC
1 AATTTTAGAAAACTGATTTAATATGAATTAAATAATAATATTTGATGAATTTTAAAAATTAAAAA
* * *
413909 CAAGAAAAATCCCTTCGAAAAAATTTACGAAGTAGAAAACAACGTATTTCAAAAAAAAGAATTTC
66 CAAGAAAAATCCCCTCAAAAAAATTTAC-AAGTAGAAAAC-ACATATTTCAAAAAAAA-AATTTC
* * * *
413974 AAGAAAAAAATCAAAAAATCATGAAAATGAATT
128 AAGGAAAAAATCAAAAATTTAAG-AAATGAATT
* * * * * * * *
414007 AATTTTTGAAAACTAATTTAATGTAAAAT-AATGAATGATATTTGATGAATTTT-GAAATTAAAC
1 AATTTTAGAAAACTGATTTAATATGAATTAAAT-AATAATATTTGATGAATTTTAAAAATTAAAA
414070 ACTAAGAAAAAT
65 AC-AAGAAAAAT
414082 TTTTCGAAAA
Statistics
Matches: 334, Mismatches: 50, Indels: 31
0.80 0.12 0.07
Matches are distributed among these distances:
160 9 0.03
161 62 0.19
162 112 0.34
163 113 0.34
164 34 0.10
165 4 0.01
ACGTcount: A:0.52, C:0.07, G:0.11, T:0.30
Consensus pattern (159 bp):
AATTTTAGAAAACTGATTTAATATGAATTAAATAATAATATTTGATGAATTTTAAAAATTAAAAA
CAAGAAAAATCCCCTCAAAAAAATTTACAAGTAGAAAACACATATTTCAAAAAAAAAATTTCAAG
GAAAAAATCAAAAATTTAAGAAATGAATT
Found at i:415000 original size:14 final size:14
Alignment explanation
Indices: 414981--415008 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
414971 TATTAGACTT
414981 CACATCATGCATTC
1 CACATCATGCATTC
414995 CACATCATGCATTC
1 CACATCATGCATTC
415009 ATATTACCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.36, G:0.07, T:0.29
Consensus pattern (14 bp):
CACATCATGCATTC
Found at i:415941 original size:155 final size:155
Alignment explanation
Indices: 415693--416092 Score: 543
Period size: 155 Copynumber: 2.6 Consensus size: 155
415683 ACCTTCACCG
* * * * * * *
415693 TTAAGTCC-AATATCACTAGCCGTGAATTAGCATATTAGCATCTTTTATCATCTTTAAGCCCAAC
1 TTAAGTCCAAATATCACTAGCCTTAAATCAGCACATTGGCATC-TTTATCATCTTTAAGTCCAAT
* * * * *
415757 ATCGCTGGTCTTGAATCAGCACATTGGCACCCTTATTGTTTTTAAGTCCAATGTCAATGGCCCTA
65 GTTGCTGGCCATGAATCAGCACATTGGCACCCTTATTGTCTTTAAGTCCAATGTCAATGGCCCTA
415822 AACCAGCACATTGGTAAACTCCATCT
130 AACCAGCACATTGGTAAACTCCATCT
* * * *
415848 TTAAGTCCAAATATCATTGGCCTTGAATCAAG-ACATTGGCATCTTTATCATCTTTAAGTCTAAT
1 TTAAGTCCAAATATCACTAGCCTTAAATC-AGCACATTGGCATCTTTATCATCTTTAAGTCCAAT
**
415912 GTTGCTGGCCATGAATCAGCACATTGGCACCCTTATTGTCTTTAAGTCCAATGTTGATGGCCCTA
65 GTTGCTGGCCATGAATCAGCACATTGGCACCCTTATTGTCTTTAAGTCCAATGTCAATGGCCCTA
* * *
415977 AACCAGTACATTGGTAACCTTCATCT
130 AACCAGCACATTGGTAAACTCCATCT
* * *
416003 TTAAGTCCAAATATCGCTAGCGTTAAATCAGCACATTGGCACCTTTATCATCTTTAAGTCCAATG
1 TTAAGTCCAAATATCACTAGCCTTAAATCAGCACATTGGCATCTTTATCATCTTTAAGTCCAATG
*
416068 TTGTTGGCCATGAATCAGCACATTG
66 TTGCTGGCCATGAATCAGCACATTG
416093 ACACTTTTAT
Statistics
Matches: 215, Mismatches: 27, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
154 2 0.01
155 186 0.87
156 25 0.12
157 2 0.01
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.33
Consensus pattern (155 bp):
TTAAGTCCAAATATCACTAGCCTTAAATCAGCACATTGGCATCTTTATCATCTTTAAGTCCAATG
TTGCTGGCCATGAATCAGCACATTGGCACCCTTATTGTCTTTAAGTCCAATGTCAATGGCCCTAA
ACCAGCACATTGGTAAACTCCATCT
Found at i:416086 original size:52 final size:52
Alignment explanation
Indices: 415655--416114 Score: 283
Period size: 52 Copynumber: 8.9 Consensus size: 52
415645 CACCCCGATA
* * * * *
415655 TCGCTGGCCTTGAATCAACACTTTGGCAACC--T-TCACCGTTAAGTCCAATA
1 TCGCTGGCCTTGAATCAGCACATTGGC-ACCTTTATCATCTTTAAGTCCAATG
* * * * * * * * **
415705 TCACTAGCCGTGAATTAGCATATTAGCATCTTTTATCATCTTTAAGCCCAACA
1 TCGCTGGCCTTGAATCAGCACATTGGCA-CCTTTATCATCTTTAAGTCCAATG
* * ** *
415758 TCGCTGGTCTTGAATCAGCACATTGGCACCCTTATTGTTTTTAAGTCCAATG
1 TCGCTGGCCTTGAATCAGCACATTGGCACCTTTATCATCTTTAAGTCCAATG
** * * * * * * *
415810 TCAATGGCCCTAAACCAGCACATTGGTAAAC--T-CCATCTTTAAGTCCAAATA
1 TCGCTGGCCTTGAATCAGCACATTGG-CACCTTTATCATCTTTAAGTCC-AATG
** * *
415861 TCATTGGCCTTGAATCAAG-ACATTGGCATCTTTATCATCTTTAAGTCTAATG
1 TCGCTGGCCTTGAATC-AGCACATTGGCACCTTTATCATCTTTAAGTCCAATG
* * * **
415913 TTGCTGGCCATGAATCAGCACATTGGCACCCTTATTGTCTTTAAGTCCAATG
1 TCGCTGGCCTTGAATCAGCACATTGGCACCTTTATCATCTTTAAGTCCAATG
* * * * * * * *
415965 TTGATGGCCCTAAACCAGTACATTGGTAACC--T-TCATCTTTAAGTCCAAATA
1 TCGCTGGCCTTGAATCAGCACATTGG-CACCTTTATCATCTTTAAGTCC-AATG
* * *
416016 TCGCTAGCGTTAAATCAGCACATTGGCACCTTTATCATCTTTAAGTCCAATG
1 TCGCTGGCCTTGAATCAGCACATTGGCACCTTTATCATCTTTAAGTCCAATG
* * * * * * *
416068 TTGTTGGCCATGAATCAGCACATTGACACTTTTATCACCCTTAAGTC
1 TCGCTGGCCTTGAATCAGCACATTGGCACCTTTATCATCTTTAAGTC
416115 TGATGTCATA
Statistics
Matches: 307, Mismatches: 87, Indels: 30
0.72 0.21 0.07
Matches are distributed among these distances:
49 1 0.00
50 47 0.15
51 48 0.16
52 145 0.47
53 66 0.21
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (52 bp):
TCGCTGGCCTTGAATCAGCACATTGGCACCTTTATCATCTTTAAGTCCAATG
Found at i:432722 original size:20 final size:20
Alignment explanation
Indices: 432693--432742 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
432683 CCTACATGTT
* * *
432693 TCGATTCATTGAATACTGTA
1 TCGATACATTGAATAATCTA
* *
432713 TCGATACATTTATTAATCTA
1 TCGATACATTGAATAATCTA
432733 TCGATACATT
1 TCGATACATT
432743 TCCTTGGCAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.42
Consensus pattern (20 bp):
TCGATACATTGAATAATCTA
Found at i:437736 original size:40 final size:41
Alignment explanation
Indices: 437663--437741 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 41
437653 ATTCTGAAAG
*
437663 GAAATTGTATCGATACAGTTTTTAAATATATCGATATATAA
1 GAAATTATATCGATACAGTTTTTAAATATATCGATATATAA
* * *
437704 GAAATTATATCGATACA-TTTTTCATTGTATCGATATAT
1 GAAATTATATCGATACAGTTTTTAAATATATCGATATAT
437742 TCTAGGTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
40 18 0.53
41 16 0.47
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (41 bp):
GAAATTATATCGATACAGTTTTTAAATATATCGATATATAA
Found at i:437775 original size:24 final size:20
Alignment explanation
Indices: 437757--437794 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
437747 GTTTTGATAG
437757 AAATGTATCGATACATTTTT
1 AAATGTATCGATACATTTTT
*
437777 CAATGTATCGATACATTT
1 AAATGTATCGATACATTT
437795 AGTCAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (20 bp):
AAATGTATCGATACATTTTT
Found at i:441330 original size:31 final size:31
Alignment explanation
Indices: 441289--441409 Score: 138
Period size: 31 Copynumber: 3.9 Consensus size: 31
441279 TTGGACTAAA
*
441289 GTGCCACCAACTCATGTGGGCTTTGACTTGG
1 GTGCCACCAACTCATGTGGGCTTTGACTAGG
*
441320 GTGCCTCCAACT--TGTGCGAGCTTTGACTAGG
1 GTGCCACCAACTCATGTG-G-GCTTTGACTAGG
* * *
441351 ATGCCACTAACTCATGTGGGCTCTGACTAGG
1 GTGCCACCAACTCATGTGGGCTTTGACTAGG
** *
441382 GTGCCACCAACTTGTGTGGGCTTAGACT
1 GTGCCACCAACTCATGTGGGCTTTGACT
441410 CTGGTGTCGC
Statistics
Matches: 74, Mismatches: 12, Indels: 8
0.79 0.13 0.09
Matches are distributed among these distances:
29 4 0.05
30 1 0.01
31 64 0.86
32 1 0.01
33 4 0.05
ACGTcount: A:0.18, C:0.26, G:0.28, T:0.28
Consensus pattern (31 bp):
GTGCCACCAACTCATGTGGGCTTTGACTAGG
Found at i:441423 original size:31 final size:31
Alignment explanation
Indices: 441388--441458 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
441378 TAGGGTGCCA
* * *
441388 CCAACTTGTGTGGGCTTAGACTCTG-GTGTCG
1 CCAACTTGTGTGAGCTTAGACTC-GACTATCG
*
441419 CCAACTAGTGTGAGCTTAGACTCGACTATCG
1 CCAACTTGTGTGAGCTTAGACTCGACTATCG
441450 CCAACTTGT
1 CCAACTTGT
441459 ACGGGCTTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 1 0.03
31 33 0.97
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.30
Consensus pattern (31 bp):
CCAACTTGTGTGAGCTTAGACTCGACTATCG
Found at i:441564 original size:34 final size:33
Alignment explanation
Indices: 441526--441630 Score: 111
Period size: 34 Copynumber: 3.1 Consensus size: 33
441516 AGGAAAAAAA
*
441526 GAAATGTAGTGCGTCCTGCTCTTTAAGGACAAAG
1 GAAATG-AGTGCGTCCTGCTCTTCAAGGACAAAG
* * *
441560 GAAATGAAGTGCGTCCTACTCTTGAAGGATGAAAG
1 GAAATG-AGTGCGTCCTGCTCTTCAAGGA-CAAAG
** *
441595 GAAAATGAGTATGTCCTGCTCTTCAAAGACAAAG
1 G-AAATGAGTGCGTCCTGCTCTTCAAGGACAAAG
441629 GA
1 GA
441631 TAAAGGCGAA
Statistics
Matches: 59, Mismatches: 10, Indels: 5
0.80 0.14 0.07
Matches are distributed among these distances:
33 1 0.02
34 31 0.53
35 22 0.37
36 5 0.08
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (33 bp):
GAAATGAGTGCGTCCTGCTCTTCAAGGACAAAG
Found at i:441829 original size:29 final size:27
Alignment explanation
Indices: 441795--441875 Score: 90
Period size: 29 Copynumber: 2.8 Consensus size: 27
441785 CAAAGTTGTA
*
441795 GACTTTAGAAGGGATGCCACTAAGTCGTG
1 GACTTTAAAAGGGATGCCACTAA-T-GTG
* *
441824 GACTTTGAAAAAGGATACCACTGAATGTG
1 GACTTT-AAAAGGGATGCCACT-AATGTG
441853 GACTTTTAAAAGGGATGCCACTA
1 GAC-TTTAAAAGGGATGCCACTA
441876 GGGGTTGTTG
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
28 1 0.02
29 25 0.57
30 16 0.36
31 2 0.05
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.25
Consensus pattern (27 bp):
GACTTTAAAAGGGATGCCACTAATGTG
Found at i:445314 original size:20 final size:20
Alignment explanation
Indices: 445288--445342 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
445278 AAAAAGACAG
* *
445288 AATGTATTGATACATTCATA
1 AATGTATCGATACATTCAAA
* *
445308 CATGTATCGATACATTGAAA
1 AATGTATCGATACATTCAAA
445328 AATGTATCGATACAT
1 AATGTATCGATACAT
445343 CTGGGTACTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCAAA
Found at i:446133 original size:45 final size:48
Alignment explanation
Indices: 446024--446133 Score: 118
Period size: 49 Copynumber: 2.3 Consensus size: 48
446014 CTAATGCACC
** *
446024 AATTCAAGGCCAGCGACATTGGGCTAAGGGAAAAGTGGACCAATGTGCT
1 AATTCAATACCAGCGACATTGGGCTAA-GGAAAAGTGGACCAATATGCT
* * * *
446073 GATTCAATGCCAGCGACATTGGGCTAA-TAAAGGT-G-CCAATATGCT
1 AATTCAATACCAGCGACATTGGGCTAAGGAAAAGTGGACCAATATGCT
*
446118 AATTCAATACTAGCGA
1 AATTCAATACCAGCGA
446134 TGTCAGACAG
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
45 22 0.42
46 1 0.02
47 5 0.09
49 25 0.47
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.22
Consensus pattern (48 bp):
AATTCAATACCAGCGACATTGGGCTAAGGAAAAGTGGACCAATATGCT
Found at i:446302 original size:28 final size:28
Alignment explanation
Indices: 446193--446978 Score: 751
Period size: 28 Copynumber: 27.1 Consensus size: 28
446183 TTTTTTTAAA
*
446193 GAAAAGGTGCCACTAACTTGTGTGGGCTTT
1 GAAAAGGTGCCACTGAC-T-TGTGGGCTTT
** *
446223 GAAAAAATTTGCCACCGACTCGTGTGGGCTTT
1 G--AAAAGGTGCCACTGACT--TGTGGGCTTT
*
446255 GAAAAGAGTGCCACTGACTTATGGGCTTT
1 GAAAAG-GTGCCACTGACTTGTGGGCTTT
*
446284 GAAAAGGTGCCACTAACTTGTGGGCTTT
1 GAAAAGGTGCCACTGACTTGTGGGCTTT
* * **
446312 GAAAGGGTGCCACTGACTTATAAGCTTT
1 GAAAAGGTGCCACTGACTTGTGGGCTTT
* * * *
446340 G-AATGTGCGCCACTAACTTGTGGGCATT
1 GAAAAG-GTGCCACTGACTTGTGGGCTTT
* **
446368 GAAAGGGTGCCACAAACTTGTGGGCTTT
1 GAAAAGGTGCCACTGACTTGTGGGCTTT
* *
446396 G-AAAGGATGCCACTAACTTATGGGCTTT
1 GAAAAGG-TGCCACTGACTTGTGGGCTTT
* *
446424 GAAAAGAATGCCACTGACTTATGGGCTTT
1 GAAAAG-GTGCCACTGACTTGTGGGCTTT
*
446453 GAAATGGTG-CACTGACTTGTGGGCTTT
1 GAAAAGGTGCCACTGACTTGTGGGCTTT
* *
446480 GAAAGGGTGCTACTGACTTGTGGGCTTT
1 GAAAAGGTGCCACTGACTTGTGGGCTTT
* *
446508 G-AAAGGATGACACTAACTTGTGGGCTTT
1 GAAAAGG-TGCCACTGACTTGTGGGCTTT
*
446536 GAAAAGAGTTGCCACCGACTCATGTGGGCTTT
1 GAAAAG-G-TGCCACTGACT--TGTGGGCTTT
**
446568 GAAAATAATGCCACTGACTTGTGGGCTTT
1 GAAAA-GGTGCCACTGACTTGTGGGCTTT
446597 G-AAAGGTTGCCACTGACTTGTGGGCTTT
1 GAAAAGG-TGCCACTGACTTGTGGGCTTT
* * *
446625 GAAAAGAGTTGCCACCGACTCGTGGGTTTT
1 GAAAAG-G-TGCCACTGACTTGTGGGCTTT
*
446655 G-AGAGGATGCCACTGACTTGTGGGCTTT
1 GAAAAGG-TGCCACTGACTTGTGGGCTTT
* *
446683 GAAAAGAATGCCACTGATTTGTGGGCTTT
1 GAAAAG-GTGCCACTGACTTGTGGGCTTT
*
446712 G-AAAGGATGCCATTGACTTGTGGGCTTT
1 GAAAAGG-TGCCACTGACTTGTGGGCTTT
* * **
446740 AAAAAGAGTTGCCACCGACTCATGGGCTTT
1 GAAAAG-G-TGCCACTGACTTGTGGGCTTT
*
446770 G-AAAGGATGCCACTGACTTGTGGCCTTT
1 GAAAAGG-TGCCACTGACTTGTGGGCTTT
*
446798 GAAAAGAGTGGCCACCGACTCGTGTGGGCTTT
1 GAAAAG-GT-GCCACTGACT--TGTGGGCTTT
* *
446830 GAAAAGAGTGCCACTAACTTGTGAGCTTT
1 GAAAAG-GTGCCACTGACTTGTGGGCTTT
* *
446859 GAAAGGGTGCCACTAACTTGTGGGCTTT
1 GAAAAGGTGCCACTGACTTGTGGGCTTT
*
446887 GAAAAGAGTTGCCACCGACTCGTGTGGGCTTT
1 GAAAAG-G-TGCCACTGACT--TGTGGGCTTT
*
446919 GAAAAGAGTGCCATTGACTTGTGGGCTTT
1 GAAAAG-GTGCCACTGACTTGTGGGCTTT
* *
446948 GAAAGGGTACCACTGACTTGTGGGCTTT
1 GAAAAGGTGCCACTGACTTGTGGGCTTT
446976 GAA
1 GAA
446979 GAGATGAACG
Statistics
Matches: 633, Mismatches: 90, Indels: 68
0.80 0.11 0.09
Matches are distributed among these distances:
27 36 0.06
28 276 0.44
29 136 0.21
30 72 0.11
31 38 0.06
32 75 0.12
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.28
Consensus pattern (28 bp):
GAAAAGGTGCCACTGACTTGTGGGCTTT
Found at i:446331 original size:56 final size:57
Alignment explanation
Indices: 446193--446978 Score: 803
Period size: 57 Copynumber: 13.5 Consensus size: 57
446183 TTTTTTTAAA
* * * * *
446193 GAAAAGGTGCCACTAACTTGTGTGGGCTTTGAAAAAATTTGCCACCGACTCGTGTGGGCTTT
1 GAAAGGGTGCCACTGAC-T-TGTGGGCTTTGAAAAGA-GTGCCACTGACT--TGTGGGCTTT
* * *
446255 GAAAAGAGTGCCACTGACTTATGGGCTTTGAAAAG-GTGCCACTAACTTGTGGGCTTT
1 G-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTT
* ** * * * * *
446312 GAAAGGGTGCCACTGACTTATAAGCTTTG-AATGTGCGCCACTAACTTGTGGGCATT
1 GAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTT
** * * *
446368 GAAAGGGTGCCACAAACTTGTGGGCTTTGAAAGGA-TGCCACTAACTTATGGGCTTT
1 GAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTT
** * *
446424 GAAAAGAATGCCACTGACTTATGGGCTTTGAAATG-GTG-CACTGACTTGTGGGCTTT
1 G-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTT
* * * *
446480 GAAAGGGTGCTACTGACTTGTGGGCTTTGAAAGGA-TGACACTAACTTGTGGGCTTT
1 GAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTT
* * * *
446536 GAAAAGAGTTGCCACCGACTCATGTGGGCTTTGAAAATAATGCCACTGACTTGTGGGCTTT
1 G-AAAG-GGTGCCACTGACT--TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTT
* * * *
446597 GAAAGGTTGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTCGTGGGTTTT
1 GAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAG-TGCCACTGACTTGTGGGCTTT
* * * *
446655 GAGAGGATGCCACTGACTTGTGGGCTTTGAAAAGAATGCCACTGATTTGTGGGCTTT
1 GAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTT
* * * * **
446712 GAAAGGATGCCATTGACTTGTGGGCTTTAAAAAGAGTTGCCACCGACTCATGGGCTTT
1 GAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAG-TGCCACTGACTTGTGGGCTTT
* * *
446770 GAAAGGATGCCACTGACTTGTGGCCTTTGAAAAGAGTGGCCACCGACTCGTGTGGGCTTT
1 GAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGT-GCCACTGACT--TGTGGGCTTT
* * * * *
446830 GAAAAGAGTGCCACTAACTTGTGAGCTTTG-AAAGGGTGCCACTAACTTGTGGGCTTT
1 G-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTT
* * *
446887 GAAAAGAGTTGCCACCGACTCGTGTGGGCTTTGAAAAGAGTGCCATTGACTTGTGGGCTTT
1 G-AAAG-GGTGCCACTGACT--TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTT
*
446948 GAAAGGGTACCACTGACTTGTGGGCTTTGAA
1 GAAAGGGTGCCACTGACTTGTGGGCTTTGAA
446979 GAGATGAACG
Statistics
Matches: 612, Mismatches: 90, Indels: 49
0.81 0.12 0.07
Matches are distributed among these distances:
55 33 0.05
56 123 0.20
57 142 0.23
58 130 0.21
59 39 0.06
60 48 0.08
61 82 0.13
62 2 0.00
63 13 0.02
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.28
Consensus pattern (57 bp):
GAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTT
Found at i:446593 original size:89 final size:86
Alignment explanation
Indices: 446213--446978 Score: 780
Period size: 89 Copynumber: 8.8 Consensus size: 86
446203 CACTAACTTG
* * *
446213 TGTGGGCTTTGAAAA-AATTTGCCACCGACTCGTGTGGGCTTTGAAAAGAGTGCCACTGACTTAT
1 TGTGGGCTTTGAAAAGAA--TGCCACTGACT--TGTGGGCTTTGAAAGGA-TGCCACTGACTTGT
**
446277 GGGCTTTGAAAAGG-TGCCACTAACT
61 GGGCTTTGAAAAGGTTGCCACCGACT
** * ** * * *
446302 TGTGGGCTTTG-AAAGGGTGCCACTGACTTATAAGCTTTGAATGTG-CGCCACTAACTTGTGGGC
1 TGTGGGCTTTGAAAAGAATGCCACTGACTTGTGGGCTTTGAAAG-GATGCCACTGACTTGTGGGC
* * **
446365 ATTG-AAAGGGTGCCACAAACT
65 TTTGAAAAGGTTGCCACCGACT
* * * * *
446386 TGTGGGCTTTG-AAAGGATGCCACTAACTTATGGGCTTTGAAAAGAATGCCACTGACTTATGGGC
1 TGTGGGCTTTGAAAAGAATGCCACTGACTTGTGGGCTTTG-AAAGGATGCCACTGACTTGTGGGC
* *
446450 TTTGAAATGG-TG-CACTGACT
65 TTTGAAAAGGTTGCCACCGACT
** * * *
446470 TGTGGGCTTTG-AAAGGGTGCTACTGACTTGTGGGCTTTGAAAGGATGACACTAACTTGTGGGCT
1 TGTGGGCTTTGAAAAGAATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCT
446534 TTGAAAAGAGTTGCCACCGACT
66 TTGAAAAG-GTTGCCACCGACT
* *
446556 CATGTGGGCTTTGAAAATAATGCCACTGACTTGTGGGCTTTGAAAGGTTGCCACTGACTTGTGGG
1 --TGTGGGCTTTGAAAAGAATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGG
446621 CTTTGAAAAGAGTTGCCACCGACT
64 CTTTGAAAAG-GTTGCCACCGACT
* * * * * *
446645 CGTGGGTTTTG-AGAGGATGCCACTGACTTGTGGGCTTTGAAAAGAATGCCACTGATTTGTGGGC
1 TGTGGGCTTTGAAAAGAATGCCACTGACTTGTGGGCTTTG-AAAGGATGCCACTGACTTGTGGGC
* **
446709 TTTG-AAAGGATGCCATTGACT
65 TTTGAAAAGGTTGCCACCGACT
* * * ** *
446730 TGTGGGCTTTAAAAAGAGTTGCCACCGACTCATGGGCTTTGAAAGGATGCCACTGACTTGTGGCC
1 TGTGGGCTTTGAAAAGA-ATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGC
*
446795 TTTGAAAAGAGTGGCCACCGACT
65 TTTGAAAAG-GTTGCCACCGACT
* * * * *
446818 CGTGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGAGCTTTGAAAGGGTGCCACTAACTTGTGGG
1 --TGTGGGCTTTGAAAAGAATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGG
446883 CTTTGAAAAGAGTTGCCACCGACT
64 CTTTGAAAAG-GTTGCCACCGACT
* * * *
446907 CGTGTGGGCTTTGAAAAGAGTGCCATTGACTTGTGGGCTTTGAAAGGGTACCACTGACTTGTGGG
1 --TGTGGGCTTTGAAAAGAATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGG
446972 CTTTGAA
64 CTTTGAA
446979 GAGATGAACG
Statistics
Matches: 572, Mismatches: 86, Indels: 38
0.82 0.12 0.05
Matches are distributed among these distances:
83 33 0.06
84 105 0.18
85 53 0.09
86 69 0.12
87 67 0.12
88 23 0.04
89 206 0.36
90 16 0.03
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.28
Consensus pattern (86 bp):
TGTGGGCTTTGAAAAGAATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCT
TTGAAAAGGTTGCCACCGACT
Found at i:448213 original size:20 final size:20
Alignment explanation
Indices: 448190--448227 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
448180 TTTTCCTTAT
*
448190 TTTTTTTCT-TTTTCTTTTGG
1 TTTTCTTCTATTTT-TTTTGG
448210 TTTTCTTCTATTTTTTTT
1 TTTTCTTCTATTTTTTTT
448228 TTTGGGTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.03, C:0.11, G:0.05, T:0.82
Consensus pattern (20 bp):
TTTTCTTCTATTTTTTTTGG
Found at i:460445 original size:24 final size:23
Alignment explanation
Indices: 460418--460467 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
460408 TGAAAAAGTC
*
460418 ACATTTTTATCTAAATGTATCGAT
1 ACATATTTAT-TAAATGTATCGAT
* * *
460442 ACATATTTCTTGAATGTATTGAT
1 ACATATTTATTAAATGTATCGAT
460465 ACA
1 ACA
460468 AGGTCCCAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (23 bp):
ACATATTTATTAAATGTATCGAT
Found at i:464444 original size:28 final size:28
Alignment explanation
Indices: 464404--464475 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
464394 GGAATAAAGC
** *
464404 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
464432 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
464460 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
464476 TTGACTATGA
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:464526 original size:80 final size:81
Alignment explanation
Indices: 464436--464614 Score: 245
Period size: 80 Copynumber: 2.2 Consensus size: 81
464426 AAGTAACGGG
**
464436 GTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTTGACTATGAA-AAATT-GGTATTT
1 GTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCCCGACTATGAAGAAATTGGGT-TTT
464499 TTGGAAATAAAATCGGA
65 TTGGAAATAAAATCGGA
*** * * *
464516 GTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGGGTTTT
1 GTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCCCGACTATGAAGAAATT-GGGTTTT
464581 TTGGAAATAAAATCGGA
65 TTGGAAATAAAATCGGA
*
464598 GTTAGAGTATCCCCGAT
1 GTTGGAGTATCCCCGAT
464615 TATAGAAAAT
Statistics
Matches: 84, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
80 43 0.51
81 5 0.06
82 33 0.39
83 3 0.04
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.29
Consensus pattern (81 bp):
GTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCCCGACTATGAAGAAATTGGGTTTTT
TGGAAATAAAATCGGA
Found at i:464609 original size:82 final size:80
Alignment explanation
Indices: 464453--464611 Score: 230
Period size: 82 Copynumber: 2.0 Consensus size: 80
464443 TATCCCCGAT
**
464453 GAAATAACGAGGTTGGAGTATCCTTGACTATGAAAAATTGGTATTTTTGGAAATAAAATCGGAGT
1 GAAATAACGAGGTTGGAGTATCCCCGACTATGAAAAATTGGTATTTTTGGAAATAAAATCGGAGT
*
464518 TGGAGTATCCCCTCG
66 TAGAGTATCCCCTCG
* * *
464533 GAAATAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGGGT-TTTTTGGAAATAAAATCGG
1 GAAATAACGAGGTTGGAGTATCCCCGACTATGAA-AAATT--GGTATTTTTGGAAATAAAATCGG
464597 AGTTAGAGTATCCCC
63 AGTTAGAGTATCCCC
464612 GATTATAGAA
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
80 29 0.41
81 5 0.07
82 33 0.47
83 3 0.04
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (80 bp):
GAAATAACGAGGTTGGAGTATCCCCGACTATGAAAAATTGGTATTTTTGGAAATAAAATCGGAGT
TAGAGTATCCCCTCG
Found at i:467051 original size:13 final size:13
Alignment explanation
Indices: 467033--467058 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
467023 ACAAAGATCC
467033 ATGTATCGATACA
1 ATGTATCGATACA
467046 ATGTATCGATACA
1 ATGTATCGATACA
467059 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:467054 original size:33 final size:33
Alignment explanation
Indices: 467012--467078 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
467002 AAAATTTCCA
***
467012 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
467045 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
467078 A
1 A
467079 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:467122 original size:19 final size:18
Alignment explanation
Indices: 467098--467165 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
467088 CAGTAGCTAA
467098 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
467117 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
467132 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
467149 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
467166 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:467138 original size:13 final size:13
Alignment explanation
Indices: 467120--467144 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
467110 ACAATACTTA
467120 TGTATCGATACAT
1 TGTATCGATACAT
467133 TGTATCGATACA
1 TGTATCGATACA
467145 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:467142 original size:32 final size:32
Alignment explanation
Indices: 467101--467163 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
467091 TAGCTAATTA
*
467101 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
467133 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
467164 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:467785 original size:77 final size:79
Alignment explanation
Indices: 467682--467881 Score: 215
Period size: 79 Copynumber: 2.6 Consensus size: 79
467672 AATAACGGGG
* * * * * * * *
467682 TTGGAGTGTTCCCTTGAAAATAACGGGGCTAGAGTATCCCCGGTTGTGAGAAATCGAT-GCTT-A
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAGCTTGA
*
467745 GAAAAAAATCGAGA
66 GAAAAAAACCGAGA
* * ** *
467759 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGGGTATCCCCAATTATGAGAAATCAATATTTTGG
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAGCTTGA
* * * *
467824 GAATAAAGCCGGGG
66 GAAAAAAACCGAGA
*
467838 TTGGAGTATCCCCTCGAAAGTAACGGGGTTGGAGTATCCCCGAT
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGAT
467882 GAAATAACGA
Statistics
Matches: 100, Mismatches: 21, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
77 48 0.48
78 2 0.02
79 50 0.50
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.25
Consensus pattern (79 bp):
TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAGCTTGA
GAAAAAAACCGAGA
Found at i:467866 original size:28 final size:27
Alignment explanation
Indices: 467833--467904 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 27
467823 GGAATAAAGC
467833 CGGGGTTGGAGTATCCCC-TCGAAAGTAA
1 CGGGGTTGGAGTATCCCCAT-GAAA-TAA
467861 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCC-ATGAAATAA
*
467889 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
467905 TTGACTATGA
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 36 0.88
29 4 0.10
30 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.22
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCCATGAAATAA
Found at i:467955 original size:80 final size:82
Alignment explanation
Indices: 467865--468043 Score: 254
Period size: 80 Copynumber: 2.2 Consensus size: 82
467855 AAGTAACGGG
**
467865 GTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTTGACTATGAA-AAATTGGT-ATTT
1 GTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCCCGACTATGAAGAAATTGGTGATTT
467928 TTGGAAATAAAATCGGA
66 TTGGAAATAAAATCGGA
*** * * * *
467945 GTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTT
1 GTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCCCGACTATGAAGAAATTGGTGATTT
468010 TTGGAAATAAAATCGGA
66 TTGGAAATAAAATCGGA
*
468027 GTTAGAGTATCCCCGAT
1 GTTGGAGTATCCCCGAT
468044 TATAGAAAAT
Statistics
Matches: 84, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
80 43 0.51
81 8 0.10
82 33 0.39
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.30
Consensus pattern (82 bp):
GTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCCCGACTATGAAGAAATTGGTGATTT
TTGGAAATAAAATCGGA
Found at i:468038 original size:82 final size:80
Alignment explanation
Indices: 467882--468040 Score: 237
Period size: 82 Copynumber: 2.0 Consensus size: 80
467872 TATCCCCGAT
**
467882 GAAATAACGAGGTTGGAGTATCCTTGACTATGAAAAATTGGTATTTTTGGAAATAAAATCGGAGT
1 GAAATAACGAGGTTGGAGTATCCCCGACTATGAAAAATTGGTATTTTTGGAAATAAAATCGGAGT
*
467947 TGGAGTATCCCCTCG
66 TAGAGTATCCCCTCG
* * * *
467962 GAAATAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GAAATAACGAGGTTGGAGTATCCCCGACTATGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGA
468027 GTTAGAGTATCCCC
64 GTTAGAGTATCCCC
468041 GATTATAGAA
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
80 29 0.41
81 8 0.11
82 33 0.47
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (80 bp):
GAAATAACGAGGTTGGAGTATCCCCGACTATGAAAAATTGGTATTTTTGGAAATAAAATCGGAGT
TAGAGTATCCCCTCG
Found at i:468069 original size:51 final size:53
Alignment explanation
Indices: 467977--468095 Score: 145
Period size: 51 Copynumber: 2.3 Consensus size: 53
467967 AACGGGGTTG
* * *
467977 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTATGAAGAAATTAGTG-TTTTTGAAAATAAAATCGGAGTTA
*
468031 GAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTATGAAG-AAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
* *
468082 GAATATCCACGATT
1 GAGTATCCCCGATT
468096 GTGGAGAATT
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
51 33 0.57
52 2 0.03
53 8 0.14
54 15 0.26
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (53 bp):
GAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCGGAGTTA
Found at i:470469 original size:20 final size:20
Alignment explanation
Indices: 470442--470496 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
470432 TAAAATTTCC
*
470442 AAATGTATCGATACAAAGAT
1 AAATGTATCGATACAAAGAA
** *
470462 CCATGTATCGATACACAGAA
1 AAATGTATCGATACAAAGAA
470482 AAATGTATCGATACA
1 AAATGTATCGATACA
470497 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.45, C:0.16, G:0.15, T:0.24
Consensus pattern (20 bp):
AAATGTATCGATACAAAGAA
Found at i:471244 original size:55 final size:55
Alignment explanation
Indices: 471114--471896 Score: 1083
Period size: 55 Copynumber: 13.9 Consensus size: 55
471104 TGGGAAGGTT
* *
471114 TGCCACTAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACTGG-AAA
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAA
* * *
471168 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCTTGATCTTTGAGGACT-GAAATG
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAA-A
** *
471223 TGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAAAA
1 TGCCACCAACTTGTGTGGGCTTTG-AAAG-----GTGTCCTGCTCTTTGAGGACTGGAAAA
* * *
471284 TGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGATTGGAAAA
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAA
**
471339 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAGGA
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAA
* * * *
471394 TGCTACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCCTGCTCTTTGAGGACTGGGAAG
1 TGCCACCAACTTGTGTGGGCTTT-----GA-AAGGTGTCCTGCTCTTTGAGGACTGGAAAA
* * *
471455 TGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCCTGCTCTTTGGGGAC--GAAAGG
1 TGCCACCAACTTGTGTGGGCTTT-----GA-AAGGTGTCCTGCTCTTTGAGGACTGGAAA-A
*
471515 TGCCACCAACTTGTGTGGGCTTTGAGAGGTGTCCTGCTCTTTGAGGACTGGAAAA
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAA
*
471570 TGCCACCGACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAA
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAA
471625 TGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGAGGACTGGAAAA
1 TGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGAGGACTGGAAAA
**
471680 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAGGA
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAA
* *
471735 TGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGATTGGAAAA
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAA
*
471790 TGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTTCTCTTTGAGGACTGGAAAA
1 TGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGAGGACTGGAAAA
471845 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGA
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGA
471897 GAGATACCGA
Statistics
Matches: 660, Mismatches: 47, Indels: 43
0.88 0.06 0.06
Matches are distributed among these distances:
53 1 0.00
54 71 0.11
55 424 0.64
56 12 0.02
59 3 0.00
60 30 0.05
61 116 0.18
62 3 0.00
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (55 bp):
TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAA
Found at i:471623 original size:27 final size:27
Alignment explanation
Indices: 471541--471623 Score: 62
Period size: 27 Copynumber: 3.0 Consensus size: 27
471531 GGGCTTTGAG
471541 AGGTGTCCTGCTCTTTGAGGACTGGAA
1 AGGTGTCCTGCTCTTTGAGGACTGGAA
* * * * * * *
471568 A-ATGCCACCGACT-TGTGTGGGCTTTGAA
1 AGGTGTC-CTG-CTCTTTGAGGAC-TGGAA
471596 AGGTGTCCTGCTCTTTGAGGACTGGAA
1 AGGTGTCCTGCTCTTTGAGGACTGGAA
471623 A
1 A
471624 ATGCCACCAA
Statistics
Matches: 37, Mismatches: 14, Indels: 10
0.61 0.23 0.16
Matches are distributed among these distances:
26 3 0.08
27 16 0.43
28 15 0.41
29 3 0.08
ACGTcount: A:0.20, C:0.19, G:0.31, T:0.29
Consensus pattern (27 bp):
AGGTGTCCTGCTCTTTGAGGACTGGAA
Found at i:474434 original size:52 final size:52
Alignment explanation
Indices: 474349--474473 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
474339 ATATGAAAAG
* *
474349 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
474401 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
474453 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
474474 AAGATCAGTG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:474486 original size:52 final size:51
Alignment explanation
Indices: 474349--474493 Score: 211
Period size: 52 Copynumber: 2.8 Consensus size: 51
474339 ATATGAAAAG
*
474349 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
474401 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
474453 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
474494 ATGTATCGAT
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 83 0.98
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:474500 original size:13 final size:13
Alignment explanation
Indices: 474482--474506 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
474472 CAAAGATCAG
474482 TGTATCGATACAA
1 TGTATCGATACAA
474495 TGTATCGATACA
1 TGTATCGATACA
474507 TGTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:474575 original size:20 final size:20
Alignment explanation
Indices: 474550--474604 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
474540 GTAGCTTACA
474550 ATGTATCGATACAAAAAAAT
1 ATGTATCGATACAAAAAAAT
* ***
474570 ATGTATCGATACAACATTTT
1 ATGTATCGATACAAAAAAAT
474590 ATGTATCGATACAAA
1 ATGTATCGATACAAA
474605 TCGTTGAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAAAAAAAT
Found at i:474844 original size:27 final size:27
Alignment explanation
Indices: 474806--474865 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
474796 GCTTTAAAGG
*
474806 AAAAGAGTGCCACGGAGTCGTGGACTT
1 AAAAGGGTGCCACGGAGTCGTGGACTT
* *
474833 AAAAGGGTGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTCGTGGACTT
*
474860 AGAAGG
1 AAAAGG
474866 AAAAGAAGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.28, C:0.15, G:0.38, T:0.18
Consensus pattern (27 bp):
AAAAGGGTGCCACGGAGTCGTGGACTT
Found at i:474954 original size:34 final size:34
Alignment explanation
Indices: 474833--475344 Score: 649
Period size: 34 Copynumber: 14.8 Consensus size: 34
474823 TCGTGGACTT
* * *
474833 AAAAGGGTGCCACGGAGTTGTGGGC-TTAGAAGG
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
**
474866 AAAAGAAGGTGCCATAGAGTTGTGGGCTTTAAAAAGGG
1 -AAA-AAGGTGCCACGGAGTTGTGGGCTTTAAAAA--G
474904 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAG
1 AAAAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAG
*
474939 AAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGG
1 AAAAAGGTGCCACGGAGTTGTGGGCTTT-AAAA-AG
**
474975 AAAAAGAGTGCCACAAAGTTGTGGGCTTTAAAAAG
1 AAAAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAG
*
475010 AAAAAGTGTGCCACAGAGTTGTGGGCTTT-AAAAG
1 AAAAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAG
*
475044 AAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGG
1 AAAAAGGTGCCACGGAGTTGTGGGCTTT-AAAA-AG
475080 AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAG
1 AAAAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAG
* *
475114 AAAAAGTGTGCCACAGAGTTGTGGGCTTTAAACAG
1 AAAAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAG
475149 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
* * *
475183 AAAAAGGTGCCATGGAGTTGTGGAC-TTAAAGATG
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAA-AAG
* *
475217 AAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAG
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
* *
475251 AAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAG
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
*
475285 AAGAAGGTGCCACGGAGTTGTGGGCTTT--AAAG
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
* * *
475317 GAAAAGGTGCCATGAAGTTGTGGGCTTT
1 AAAAAGGTGCCACGGAGTTGTGGGCTTT
475345 GAAGAAAAAA
Statistics
Matches: 428, Mismatches: 35, Indels: 32
0.86 0.07 0.06
Matches are distributed among these distances:
32 28 0.07
33 26 0.06
34 199 0.46
35 78 0.18
36 26 0.06
37 70 0.16
38 1 0.00
ACGTcount: A:0.33, C:0.11, G:0.34, T:0.21
Consensus pattern (34 bp):
AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
Found at i:475071 original size:105 final size:103
Alignment explanation
Indices: 474772--475378 Score: 710
Period size: 105 Copynumber: 5.9 Consensus size: 103
474762 AAAAAGTTAT
* * * *
474772 AAAAAGAGTGCCACATAGTTGTGGGCTTT-AAAGGAAAAGAGTGCCACGGAGTCGTGGAC-TTAA
1 AAAAAG-GTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
* *
474835 AAG-----GGTGCCACGGAGTTGTGGGC-TT-AGAAGGA
65 AAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGG
*
474867 AAAGAAGGTGCCATAGAGTTGTGGGCTTTAAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
1 AAA-AAGGTGCCACAGAGTTGTGGGCTTT-AAAA--GAAAAAGAGTGCCACGGAGTTGTGGGCTT
474932 TAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGG
62 T-AAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGG
* * *
474975 AAAAAGAGTGCCACAAAGTTGTGGGCTTTAAAAAGAAAAAGTGTGCCACAGAGTTGTGGGCTTTA
1 AAAAAG-GTGCCACAGAGTTGTGGGCTTT-AAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTA
475040 AAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGG
64 AAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGG
* * *
475080 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGTGTGCCACAGAGTTGTGGGCTTTAA
1 AAAAAG-GTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
*
475145 ACAGAAAAAGGTGCCACGGAGTTGTGGGCTTT-AAAA-AG
65 A-AGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGG
** *
475183 AAAAAGGTGCCATGGAGTTGTGGAC-TTAAAGATGAAAAA-AGTGCCACGGAGTTGTGGGCTTTG
1 AAAAAGGTGCCACAGAGTTGTGGGCTTTAAA-A-GAAAAAGAGTGCCACGGAGTTGTGGGCTTT-
*
475246 AAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAA--G
63 AAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGG
* * * * * *
475285 AAGAAGGTGCCACGGAGTTGTGGGCTTT-AAAGGAAAAG-GTGCCATGAAGTTGTGGGCTTT-GA
1 AAAAAGGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
** * * *
475347 AGAAAAAAATGCCACTGAGTCGTGGACTTTGA
66 AGAAAAAGGTGCCACGGAGTTGTGGGCTTTGA
475379 GACAAAATGC
Statistics
Matches: 458, Mismatches: 32, Indels: 41
0.86 0.06 0.08
Matches are distributed among these distances:
95 23 0.05
96 3 0.01
97 3 0.01
98 27 0.06
99 24 0.05
100 27 0.06
101 11 0.02
102 93 0.20
103 22 0.05
104 41 0.09
105 98 0.21
106 48 0.10
107 5 0.01
108 33 0.07
ACGTcount: A:0.34, C:0.12, G:0.33, T:0.21
Consensus pattern (103 bp):
AAAAAGGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
AGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGG
Found at i:475422 original size:94 final size:94
Alignment explanation
Indices: 475219--475503 Score: 265
Period size: 94 Copynumber: 3.0 Consensus size: 94
475209 TAAAGATGAA
* * * * * * *
475219 AAAAG-TGCCACGGAGTTGTGGGCTTTGA-AAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAA
1 AAAAGATGCCACTGAGTCGTGGACTTTGAGAAA-AA-AA--TGCCACTGAGTCGTGGACTTTGAG
* ** *
475282 AAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAGG
62 AAG-AGAA--TGCCACTGAGTCATGGACTTTAAAGG
* * *
475318 AAAAGGTGCCA-TGAAGTTGTGGGCTTTGAAGAAAAAAATGCCACTGAGTCGTGGACTTTGAGAC
1 AAAAGATGCCACTG-AGTCGTGGACTTTG-AGAAAAAAATGCCACTGAGTCGTGGACTTTGAGA-
475382 A-A-AATGCCACTGAGTCATGGACTTTAAAGG
63 AGAGAATGCCACTGAGTCATGGACTTTAAAGG
* * * *
475412 AAAAGATGCCACTGAGTCGTGGACTTTGAGCAGAGATTGCCACTGAGTCGTGGACTTTGAGAAGA
1 AAAAGATGCCACTGAGTCGTGGACTTTGAGAAAAAAATGCCACTGAGTCGTGGACTTTGAGAAGA
* *
475477 GATTGCCACTGAGTCGTGGACTTTAAA
66 GAATGCCACTGAGTCATGGACTTTAAA
475504 AAGGTATTTG
Statistics
Matches: 160, Mismatches: 18, Indels: 21
0.80 0.09 0.11
Matches are distributed among these distances:
92 1 0.01
93 31 0.19
94 68 0.43
95 2 0.01
96 2 0.01
97 1 0.01
98 21 0.13
99 7 0.04
100 21 0.13
101 3 0.02
102 3 0.02
ACGTcount: A:0.31, C:0.15, G:0.32, T:0.23
Consensus pattern (94 bp):
AAAAGATGCCACTGAGTCGTGGACTTTGAGAAAAAAATGCCACTGAGTCGTGGACTTTGAGAAGA
GAATGCCACTGAGTCATGGACTTTAAAGG
Found at i:475456 original size:31 final size:31
Alignment explanation
Indices: 475356--475500 Score: 197
Period size: 31 Copynumber: 4.7 Consensus size: 31
475346 AAGAAAAAAA
*
475356 TGCCACTGAGTCGTGGACTTTGAGACA-A-AA
1 TGCCACTGAGTCGTGGACTTTGAGA-AGAGAT
* * *
475386 TGCCACTGAGTCATGGACTTTAAAGGAAAAGA-
1 TGCCACTGAGTCGTGGACTTT-GA-GAAGAGAT
*
475418 TGCCACTGAGTCGTGGACTTTGAGCAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAGAAGAGAT
475449 TGCCACTGAGTCGTGGACTTTGAGAAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAGAAGAGAT
475480 TGCCACTGAGTCGTGGACTTT
1 TGCCACTGAGTCGTGGACTTT
475501 AAAAAGGTAT
Statistics
Matches: 103, Mismatches: 7, Indels: 9
0.87 0.06 0.08
Matches are distributed among these distances:
30 25 0.24
31 54 0.52
32 23 0.22
33 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.26
Consensus pattern (31 bp):
TGCCACTGAGTCGTGGACTTTGAGAAGAGAT
Found at i:476763 original size:55 final size:52
Alignment explanation
Indices: 476663--477192 Score: 485
Period size: 49 Copynumber: 10.7 Consensus size: 52
476653 GAAAAGTGAT
* * * * * * *
476663 AAAGATGCCAATATGTTGATTCACGGCCAACGATATT-AGGCTTAAAGATGAGAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGA-ACTTAAAGATG-G-A
* *
476717 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
1 AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* *
476770 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * * *
476813 AAAGGTGTCAATGTGCTGATTCAAAGCCAGCTACATTGGACTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* *
476863 --AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * *
476911 -AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT--A-ATGGT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * * *
476959 GAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* *
477009 -AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * *
477057 AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * * *
477107 -AAGATGCCTATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* *
477156 -AAGATGCCAATGTGCTGATTCAAGGCCAGCTACATTG
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTG
477193 GGCTTAGAAG
Statistics
Matches: 428, Mismatches: 30, Indels: 41
0.86 0.06 0.08
Matches are distributed among these distances:
43 37 0.09
44 1 0.00
46 3 0.01
47 2 0.00
48 46 0.11
49 255 0.60
51 3 0.01
52 34 0.08
53 6 0.01
54 5 0.01
55 35 0.08
56 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (52 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
Found at i:476935 original size:49 final size:49
Alignment explanation
Indices: 476726--477198 Score: 726
Period size: 49 Copynumber: 9.7 Consensus size: 49
476716 AAAAGGATGT
*
476726 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
* * *
476778 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGT
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
476821 CAATGTGCTGATTCAAAGCCAGCTACATTGGACTTAAAGATG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
476869 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * *
476918 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
476967 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
477016 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
477065 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
477114 CTATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
477163 CAATGTGCTGATTCAAGGCCAGCTACATTGGGCTTA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
477199 GAAGGGTTGC
Statistics
Matches: 387, Mismatches: 27, Indels: 17
0.90 0.06 0.04
Matches are distributed among these distances:
43 38 0.10
47 1 0.00
48 47 0.12
49 269 0.70
52 32 0.08
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
Found at i:477239 original size:32 final size:31
Alignment explanation
Indices: 477191--477269 Score: 124
Period size: 32 Copynumber: 2.5 Consensus size: 31
477181 CCAGCTACAT
477191 TGGGC-TTAGAAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAAGGGTTGCCACCGACTTGTG
*
477221 TGGGCTTTAGAGAGGGTTGCCATCGACTTGTG
1 TGGGCTTTAGA-AGGGTTGCCACCGACTTGTG
477253 TGGGCTTTAGAAAGGGT
1 TGGGCTTTAG-AAGGGT
477270 GAAAGATGCC
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
30 5 0.11
31 5 0.11
32 34 0.76
33 1 0.02
ACGTcount: A:0.18, C:0.15, G:0.38, T:0.29
Consensus pattern (31 bp):
TGGGCTTTAGAAGGGTTGCCACCGACTTGTG
Found at i:477382 original size:34 final size:35
Alignment explanation
Indices: 477251--478173 Score: 1040
Period size: 34 Copynumber: 27.3 Consensus size: 35
477241 CATCGACTTG
** *
477251 TGTGGGCTTTAGAAAGGGTGAAAGA-TGCCACGAAGT
1 TGTGGGCTTTA-AAA-GGAAAAAGAGTGCCACGGAGT
* * * *
477287 TGTGGAC-TTAAAAAGAACAAG-GTGCCACAGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
477320 TGTGGGCTTTAAAAAGGAAAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTT-AAAAGG--AAAAAGAGTGCCACGGAGT
* *
477358 TGTAGGC-TTAGAAGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
*
477392 TGTGGGC-TTAGAAGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
* *
477426 TGTGGGC-TTAGAAGG-AAAAGAGTGCCACGTAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
477459 TGTGGGCTTT-AAAGG-AAAAGAGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
* *
477492 CGTGGAC-TTAAAA-G-----G-GTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
*
477519 TGTGGGC-TTAGAAGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
* *
477553 TGTGGGC-TTAGAAGG-AAAAGAGTGCCACGTAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
477586 TGTGGGCTTT-AAAGG-AAAAGAGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
* *
477619 CGTGGAC-TTAAAA-G-----G-GTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
*
477646 TGTGGGCTTTAAAAAGAAAAAG-GTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
*
477680 TGTGGGCTTTGAAAAAGGAAAAAGGGTGCCACGGAGT
1 TGTGGGCTTT--AAAAGGAAAAAGAGTGCCACGGAGT
* * *
477717 TGTGGGCTTTAAAAAGAAAAAGTGTGCCACAGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
477752 TGTGGGCTTTAAAA-GAAAAAG-GTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
*
477785 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACAGAGT
1 TGTGGGCTTT-AAAA-GGAAAAAGAGTGCCACGGAGT
* * *
477822 TGTGGGCTTTAAAAAGAAAAAGTGTGCCACAGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
477857 TGTGGGCTTTAAAA-GAAAAAG-GTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
477890 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTT-AAAA-GGAAAAAGAGTGCCACGGAGT
* * *
477927 TGTGGGCTTTAAAAAGAAAAAGTGTGCCACAGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
*
477962 TGTGGGCTTTAAACA-GAAAAAG-GTGCCATGGAGT
1 TGTGGGCTTTAAA-AGGAAAAAGAGTGCCACGGAGT
*
477996 TGTGGGCTTTAAAAAGAAAAAG-GTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
* *
478030 TGTGGAC-TTAAAGATGAAAAA-AGTGCCACGGAGT
1 TGTGGGCTTTAAA-AGGAAAAAGAGTGCCACGGAGT
*
478064 TGTGGGCTTTGAAAA-GAAGAAG-GTGCCACGGAGT
1 TGTGGGCTTT-AAAAGGAAAAAGAGTGCCACGGAGT
*
478098 TGTGGGCTTTGAAAA-GAAGAAG-GTGCCACGGAGT
1 TGTGGGCTTT-AAAAGGAAAAAGAGTGCCACGGAGT
*
478132 TGTGGGCTTT-AAAGG-AAAAG-GTGCCACGAAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
478164 TGTGGGCTTT
1 TGTGGGCTTT
478174 GAAGAAAAAA
Statistics
Matches: 794, Mismatches: 50, Indels: 90
0.85 0.05 0.10
Matches are distributed among these distances:
27 39 0.05
28 9 0.01
29 1 0.00
32 34 0.04
33 175 0.22
34 281 0.35
35 118 0.15
36 48 0.06
37 72 0.09
38 17 0.02
ACGTcount: A:0.33, C:0.12, G:0.34, T:0.21
Consensus pattern (35 bp):
TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
Found at i:477393 original size:105 final size:102
Alignment explanation
Indices: 477271--478205 Score: 1041
Period size: 105 Copynumber: 9.3 Consensus size: 102
477261 AGAAAGGGTG
* * * * *
477271 AAAGATGCCACGAAGTTGTGGAC-TTAAAAAGAACAAGGTGCCACAGAGTTGTGGGCTTTAAAAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAA
* *
477335 GGAAAAAAAGAGTGCCACGGAGTTGTAGGC-TTAGAAGGAA
66 -G--AAAAAGAGTGCCACGGAGTTGTGGGCTTTA-AAAGAA
* * *
477375 AAAGAGTGCCACGGAGTTGTGGGC-TTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGC-TT-AG
1 AAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAG-GTGCCACGGAGTTGTGGGCTTTAAA
* * *
477437 AAGGAAAAGAGTGCCACGTAGTTGTGGGCTTT-AAAGGA
64 AAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAA
* * *
477475 AAAGAGTGCCACGGAGTCGTGGAC-TT-AAAAG-----GGTGCCACGGAGTTGTGGGC-TTAGAA
1 AAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAA
* * *
477532 GGAAAAAGAGTGCCACGGAGTTGTGGGC-TTAGAAGGA
65 AGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAA
* * * *
477569 AAAGAGTGCCACGTAGTTGTGGGCTTT--AAAGGAAAAGAGTGCCACGGAGTCGTGGAC-TT-AA
1 AAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAG-GTGCCACGGAGTTGTGGGCTTTAAA
477630 AAG-----G-GTGCCACGGAGTTGTGGGCTTTAAAAAGAA
64 AAGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAGAA
477664 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAAGGAAAAAGGGTGCCACGGAGTTGTGGGCTTTAA
1 AAAGGTGCCACGGAGTTGTGGGCTTT-AAAAA-GAAAAA-GGTGCCACGGAGTTGTGGGCTTTAA
* *
477729 AAAGAAAAAGTGTGCCACAGAGTTGTGGGCTTTAAAAGAA
63 AAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAA
* *
477769 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAA
1 AAAGGTGCCACGGAGTTGTGGGCTTT-AAAA-AGAAAAAG-GTGCCACGGAGTTGTGGGCTTTAA
* *
477834 AAAGAAAAAGTGTGCCACAGAGTTGTGGGCTTTAAAAGAA
63 AAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAA
*
477874 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AAAGGTGCCACGGAGTTGTGGGCTTT-AAAA-AGAAAAAG-GTGCCACGGAGTTGTGGGCTTTAA
* *
477939 AAAGAAAAAGTGTGCCACAGAGTTGTGGGCTTTAAACAGAA
63 AAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA-AGAA
* *
477980 AAAGGTGCCATGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGAC-TTAAAGA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAA-A
*
478044 TGAAAAA-AGTGCCACGGAGTTGTGGGCTTTGAAAAGAA
65 AGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAGAA
* * *
478082 GAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTT--AAA
1 AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAA
* * *
478145 GGAAAAG-GTGCCACGAAGTTGTGGGCTTT-GAAGAA
66 GAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAA
** * * *
478180 AAAAATGCCACTGAGTCGTGGACTTT
1 AAAGGTGCCACGGAGTTGTGGGCTTT
478206 GAGACAAAAT
Statistics
Matches: 736, Mismatches: 61, Indels: 74
0.85 0.07 0.08
Matches are distributed among these distances:
93 42 0.06
94 81 0.11
95 11 0.01
97 3 0.00
98 47 0.06
99 10 0.01
100 79 0.11
101 24 0.03
102 84 0.11
103 31 0.04
104 15 0.02
105 241 0.33
106 68 0.09
ACGTcount: A:0.33, C:0.12, G:0.34, T:0.21
Consensus pattern (102 bp):
AAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAA
GAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAA
Found at i:477512 original size:27 final size:27
Alignment explanation
Indices: 477474--477533 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
477464 GCTTTAAAGG
*
477474 AAAAGAGTGCCACGGAGTCGTGGACTT
1 AAAAGGGTGCCACGGAGTCGTGGACTT
* *
477501 AAAAGGGTGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTCGTGGACTT
*
477528 AGAAGG
1 AAAAGG
477534 AAAAAGAGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.28, C:0.15, G:0.38, T:0.18
Consensus pattern (27 bp):
AAAAGGGTGCCACGGAGTCGTGGACTT
Found at i:477639 original size:27 final size:28
Alignment explanation
Indices: 477601--477659 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
477591 GCTTTAAAGG
477601 AAAAGAGTGCCACGGAGTCGTGGAC-TT
1 AAAAGAGTGCCACGGAGTCGTGGACTTT
* * *
477628 AAAAGGGTGCCACGGAGTTGTGGGCTTT
1 AAAAGAGTGCCACGGAGTCGTGGACTTT
477656 AAAA
1 AAAA
477660 AGAAAAAGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 22 0.79
28 6 0.21
ACGTcount: A:0.31, C:0.15, G:0.34, T:0.20
Consensus pattern (28 bp):
AAAAGAGTGCCACGGAGTCGTGGACTTT
Found at i:478206 original size:32 final size:32
Alignment explanation
Indices: 478009--478329 Score: 172
Period size: 34 Copynumber: 10.0 Consensus size: 32
477999 GGGCTTTAAA
** * * *
478009 AAGAAAAAGGTGCCACGGAGTTGTGGAC-TTA
1 AAGAAAAAAATGCCACTGAGTCGTGGACTTTG
* * *
478040 AAGATGAAAAAAGTGCCACGGAGTTGTGGGCTTTG
1 AAGA--AAAAAA-TGCCACTGAGTCGTGGACTTTG
* * * *
478075 AA-AAGAAGAAGGTGCCACGGAGTTGTGGGCTTTG
1 AAGAA-AA-AA-ATGCCACTGAGTCGTGGACTTTG
* * * * *
478109 AA-AAGAAGAAGGTGCCACGGAGTTGTGGGCTTTA
1 AAGAA-AA-AA-ATGCCACTGAGTCGTGGACTTTG
* ** * *
478143 AAGGAAAAGGTGCCAC-GAAGTTGTGGGCTTTG
1 AAGAAAAAAATGCCACTG-AGTCGTGGACTTTG
478175 AAGAAAAAAATGCCACTGAGTCGTGGACTTTG
1 AAGAAAAAAATGCCACTGAGTCGTGGACTTTG
* * * *
478207 -AG-ACAAAATGCCATTGAGTCATGGACTTTA
1 AAGAAAAAAATGCCACTGAGTCGTGGACTTTG
* *
478237 AAGGAAAAGATGCCACTGAGTCGTGGACTTTG
1 AAGAAAAAAATGCCACTGAGTCGTGGACTTTG
* * * * *
478269 -AGCAGAGATTGCCACTGAGTCGTCGACTTTG
1 AAGAAAAAAATGCCACTGAGTCGTGGACTTTG
* * *
478300 -AGAAGAGATTGCCACTGAGTCGTGGACTTT
1 AAGAAAAAAATGCCACTGAGTCGTGGACTTT
478330 AAAAAGGTAT
Statistics
Matches: 247, Mismatches: 31, Indels: 24
0.82 0.10 0.08
Matches are distributed among these distances:
30 24 0.10
31 62 0.25
32 69 0.28
33 8 0.03
34 79 0.32
35 5 0.02
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.23
Consensus pattern (32 bp):
AAGAAAAAAATGCCACTGAGTCGTGGACTTTG
Found at i:478251 original size:94 final size:94
Alignment explanation
Indices: 478138--478332 Score: 243
Period size: 94 Copynumber: 2.1 Consensus size: 94
478128 GAGTTGTGGG
* * * *
478138 CTTTAAAGGAAAAGGTGCCAC-GAAGTTGTGGGCTTTGAAGAAAAAAATGCCACTGAGTCGTGGA
1 CTTTAAAGGAAAAGATGCCACTG-AGTCGTGGACTTTG-AGAAAAAAATGCCACTGAGTCGTCGA
*
478202 CTTTGAGACA-A-AATGCCATTGAGTCATGGA
64 CTTTGAGA-AGAGAATGCCACTGAGTCATGGA
* * * *
478232 CTTTAAAGGAAAAGATGCCACTGAGTCGTGGACTTTGAGCAGAGATTGCCACTGAGTCGTCGACT
1 CTTTAAAGGAAAAGATGCCACTGAGTCGTGGACTTTGAGAAAAAAATGCCACTGAGTCGTCGACT
* *
478297 TTGAGAAGAGATTGCCACTGAGTCGTGGA
66 TTGAGAAGAGAATGCCACTGAGTCATGGA
478326 CTTTAAA
1 CTTTAAA
478333 AAGGTATTTG
Statistics
Matches: 87, Mismatches: 11, Indels: 6
0.84 0.11 0.06
Matches are distributed among these distances:
92 1 0.01
93 30 0.34
94 55 0.63
95 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.25
Consensus pattern (94 bp):
CTTTAAAGGAAAAGATGCCACTGAGTCGTGGACTTTGAGAAAAAAATGCCACTGAGTCGTCGACT
TTGAGAAGAGAATGCCACTGAGTCATGGA
Found at i:478285 original size:31 final size:31
Alignment explanation
Indices: 478185--478329 Score: 179
Period size: 31 Copynumber: 4.7 Consensus size: 31
478175 AAGAAAAAAA
*
478185 TGCCACTGAGTCGTGGACTTTGAGACA-A-AA
1 TGCCACTGAGTCGTGGACTTTGAGA-AGAGAT
* * * *
478215 TGCCATTGAGTCATGGACTTTAAAGGAAAAGA-
1 TGCCACTGAGTCGTGGACTTT-GA-GAAGAGAT
*
478247 TGCCACTGAGTCGTGGACTTTGAGCAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAGAAGAGAT
*
478278 TGCCACTGAGTCGTCGACTTTGAGAAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAGAAGAGAT
478309 TGCCACTGAGTCGTGGACTTT
1 TGCCACTGAGTCGTGGACTTT
478330 AAAAAGGTAT
Statistics
Matches: 99, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
30 24 0.24
31 52 0.53
32 22 0.22
33 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.26
Consensus pattern (31 bp):
TGCCACTGAGTCGTGGACTTTGAGAAGAGAT
Found at i:479716 original size:13 final size:13
Alignment explanation
Indices: 479698--479723 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
479688 ACAAAGATCC
479698 ATGTATCGATACA
1 ATGTATCGATACA
479711 ATGTATCGATACA
1 ATGTATCGATACA
479724 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:479719 original size:33 final size:33
Alignment explanation
Indices: 479677--479743 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
479667 AAAATTTCCA
***
479677 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
479710 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
479743 A
1 A
479744 TTTCCTTGGT
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:479787 original size:19 final size:18
Alignment explanation
Indices: 479763--479830 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
479753 TAGTAGCTAA
479763 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
479782 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
479797 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
479814 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
479831 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:479803 original size:13 final size:13
Alignment explanation
Indices: 479785--479809 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
479775 ACAATACTTA
479785 TGTATCGATACAT
1 TGTATCGATACAT
479798 TGTATCGATACA
1 TGTATCGATACA
479810 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:479807 original size:32 final size:32
Alignment explanation
Indices: 479766--479828 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
479756 TAGCTAATTA
*
479766 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
479798 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
479829 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:484929 original size:30 final size:31
Alignment explanation
Indices: 484894--485043 Score: 161
Period size: 30 Copynumber: 5.0 Consensus size: 31
484884 AACTCCCATG
*
484894 GTGGCATCTCTTCTCTAAGTCCACGACTCTA
1 GTGGCATCTCTTCTCAAAGTCCACGACTCTA
*
484925 -TGGCATCTCTTCTCTAAGTCCACGACT-TA
1 GTGGCATCTCTTCTCAAAGTCCACGACTCTA
* *
484954 GTGGCATCTCTTCTCCAAGTCCATGACTC-A
1 GTGGCATCTCTTCTCAAAGTCCACGACTCTA
* *
484984 GTGGTATC-CTTTTTCAAAGTCCACGACTC-A
1 GTGGCATCTC-TTCTCAAAGTCCACGACTCTA
*
485014 ATGGCAAT-T-TTCTTCAAAGTCCACGACTCT
1 GTGGC-ATCTCTTC-TCAAAGTCCACGACTCT
485044 GTAGCACCCT
Statistics
Matches: 103, Mismatches: 9, Indels: 14
0.82 0.07 0.11
Matches are distributed among these distances:
29 5 0.05
30 96 0.93
31 2 0.02
ACGTcount: A:0.22, C:0.30, G:0.15, T:0.33
Consensus pattern (31 bp):
GTGGCATCTCTTCTCAAAGTCCACGACTCTA
Found at i:485088 original size:33 final size:33
Alignment explanation
Indices: 484994--485460 Score: 231
Period size: 33 Copynumber: 14.8 Consensus size: 33
484984 GTGGTATCCT
* * *
484994 TTTTCAAAGTCCACGACTCAATGGCA--ATTTTC
1 TTTT-AAAGTCCACAACTCCATGGCACCTTTTTC
* * ** *
485026 -TTCAAAGTCCACGACTCTGTAGCACCCTTTTTC
1 TTTTAAAGTCCACAACTCCATGGCA-CCTTTTTC
*
485059 TTTTTAAGTCCACAACTCCATGGCACCTTTTTCC
1 TTTTAAAGTCCACAACTCCATGGCACCTTTTT-C
* * *
485093 ATTT-ATGTCCATAA---C-T-----CTTTTTC
1 TTTTAAAGTCCACAACTCCATGGCACCTTTTTC
* * * **
485116 TTTTTAAGTCCACAACTCTATGGCACATTTCCC
1 TTTTAAAGTCCACAACTCCATGGCACCTTTTTC
* *
485149 TTTTAAAGTCCACAACTTCGTGGCACCTTTCTTCC
1 TTTTAAAGTCCACAACTCCATGGCACCTTT-TT-C
* * * * *
485184 CTTTGAAGTCCATAACTCCGTGG-A-CTCTTTCC
1 TTTTAAAGTCCACAACTCCATGGCACCT-TTTTC
* *
485216 TTTTTAAAGTCCACAACTCCGTGGCACATTTTTC
1 -TTTTAAAGTCCACAACTCCATGGCACCTTTTTC
* *
485250 -TTCAAAGTCCATAACTCCATGGCACC-TTTT-
1 TTTTAAAGTCCACAACTCCATGGCACCTTTTTC
*
485280 TTTTAAAGTCCACAACTCCGTGGCACC-----C
1 TTTTAAAGTCCACAACTCCATGGCACCTTTTTC
* * * ** **
485308 TTTCAAAGTCTACGACTCTGTGGTGCC-----C
1 TTTTAAAGTCCACAACTCCATGGCACCTTTTTC
*
485336 TTTT-AAGTCTACAACTCCATGGCACTCTTTTTC
1 TTTTAAAGTCCACAACTCCATGGCAC-CTTTTTC
* * * *
485369 TTTTGATGTCCATAACTCTATGGCACCTTTTTCC
1 TTTTAAAGTCCACAACTCCATGGCACCTTTTT-C
*
485403 TTTTAAA-TCCATAACTCCATGGCACCTTTTTC
1 TTTTAAAGTCCACAACTCCATGGCACCTTTTTC
* * *
485435 -TTCAAAGTCCACAACACTATGGCACC
1 TTTTAAAGTCCACAACTCCATGGCACC
485461 CTTCTCTAAA
Statistics
Matches: 335, Mismatches: 68, Indels: 64
0.72 0.15 0.14
Matches are distributed among these distances:
23 4 0.01
24 14 0.04
27 16 0.05
28 27 0.08
29 1 0.00
30 19 0.06
31 34 0.10
32 40 0.12
33 106 0.32
34 53 0.16
35 21 0.06
ACGTcount: A:0.23, C:0.30, G:0.11, T:0.36
Consensus pattern (33 bp):
TTTTAAAGTCCACAACTCCATGGCACCTTTTTC
Found at i:485115 original size:90 final size:92
Alignment explanation
Indices: 485021--485201 Score: 215
Period size: 90 Copynumber: 2.0 Consensus size: 92
485011 TCAATGGCAA
* * * ** *
485021 TTTTC-TTCAAAGTCCACGACTCTGTAGCACCCTTTTTCTTTTTAAGTCCACAACTCCATGGCAC
1 TTTTCTTTCAAAGTCCACAACTCTATAGCA-CATTTCCCTTTTAAAGTCCACAACTCCATGGCAC
*
485085 CTTT-TTCCATTT-ATGTCCATAACTCT
65 CTTTCTTCCATTTGAAGTCCATAACTCT
** * * *
485111 TTTTCTTTTTAAGTCCACAACTCTATGGCACATTTCCCTTTTAAAGTCCACAACTTCGTGGCACC
1 TTTTCTTTCAAAGTCCACAACTCTATAGCACATTTCCCTTTTAAAGTCCACAACTCCATGGCACC
*
485176 TTTCTTCCCTTTGAAGTCCATAACTC
66 TTTCTTCCATTTGAAGTCCATAACTC
485202 CGTGGACTCT
Statistics
Matches: 75, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
90 37 0.49
91 26 0.35
92 12 0.16
ACGTcount: A:0.22, C:0.30, G:0.09, T:0.39
Consensus pattern (92 bp):
TTTTCTTTCAAAGTCCACAACTCTATAGCACATTTCCCTTTTAAAGTCCACAACTCCATGGCACC
TTTCTTCCATTTGAAGTCCATAACTCT
Found at i:485121 original size:24 final size:24
Alignment explanation
Indices: 485085--485134 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
485075 TCCATGGCAC
* *
485085 CTTTTTCCATTTATGTCCATAACT
1 CTTTTTCCATTTAAGTCCACAACT
**
485109 CTTTTTCTTTTTAAGTCCACAACT
1 CTTTTTCCATTTAAGTCCACAACT
485133 CT
1 CT
485135 ATGGCACATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.20, C:0.26, G:0.04, T:0.50
Consensus pattern (24 bp):
CTTTTTCCATTTAAGTCCACAACT
Found at i:485160 original size:57 final size:57
Alignment explanation
Indices: 485052--485165 Score: 158
Period size: 57 Copynumber: 2.0 Consensus size: 57
485042 CTGTAGCACC
* * * *
485052 CTTTTTCTTTTTAAGTCCACAACTCCATGGCACCTTTTTCCATTTATGTCCATAACT
1 CTTTTTCTTTTTAAGTCCACAACTCCATGGCACCATTTCCCATTTAAGTCCACAACT
* *
485109 CTTTTTCTTTTTAAGTCCACAACTCTATGGCA-CATTTCCCTTTTAAAGTCCACAACT
1 CTTTTTCTTTTTAAGTCCACAACTCCATGGCACCATTTCCCATTT-AAGTCCACAACT
485166 TCGTGGCACC
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
56 9 0.18
57 41 0.82
ACGTcount: A:0.23, C:0.28, G:0.07, T:0.42
Consensus pattern (57 bp):
CTTTTTCTTTTTAAGTCCACAACTCCATGGCACCATTTCCCATTTAAGTCCACAACT
Found at i:485201 original size:68 final size:66
Alignment explanation
Indices: 485121--485460 Score: 241
Period size: 68 Copynumber: 5.3 Consensus size: 66
485111 TTTTCTTTTT
* * * * *
485121 AAGTCCACAACTCTATGGCACATTTCCCTTTTAAAGTCCACAACTTCGTGGCACCTTTCTTCCCT
1 AAGTCCATAACTCCATGGCACCTTTCCTTTTTAAAGTCCACAACTCCGTGGCACCTTTCTT--CT
**
485186 TTG
64 TCA
* *
485189 AAGTCCATAACTCCGTGG-ACTCTTTCCTTTTTAAAGTCCACAACTCCGTGGCACATTT-TTCTT
1 AAGTCCATAACTCCATGGCAC-CTTTCCTTTTTAAAGTCCACAACTCCGTGGCACCTTTCTTCTT
485252 CA
65 CA
485254 AAGTCCATAACTCCATGGCACCTTT--TTTTTAAAGTCCACAACTCCGTGGCACC---C-T-TTC
1 AAGTCCATAACTCCATGGCACCTTTCCTTTTTAAAGTCCACAACTCCGTGGCACCTTTCTTCTTC
485312 A
66 A
* ** ** * * * *
485313 AAGTCTACGACTCTGTGG-----TGCCCTTTT-AAGTCTACAACTCCATGGCACTCTTT-TTCTT
1 AAGTCCATAACTCCATGGCACCTTTCCTTTTTAAAGTCCACAACTCCGTGGCAC-CTTTCTTC-T
**
485371 TTG
64 TCA
* * * *
485374 ATGTCCATAACTCTATGGCACCTTTTTCC-TTTTAAA-TCCATAACTCCATGGCACCTTT-TTCT
1 AAGTCCATAACTCCATGGCACC--TTTCCTTTTTAAAGTCCACAACTCCGTGGCACCTTTCTTCT
485436 TCA
64 TCA
* * *
485439 AAGTCCACAACACTATGGCACC
1 AAGTCCATAACTCCATGGCACC
485461 CTTCTCTAAA
Statistics
Matches: 217, Mismatches: 35, Indels: 43
0.74 0.12 0.15
Matches are distributed among these distances:
54 1 0.00
55 19 0.09
56 5 0.02
59 18 0.08
60 1 0.00
61 15 0.07
63 27 0.12
65 45 0.21
66 9 0.04
67 24 0.11
68 53 0.24
ACGTcount: A:0.23, C:0.30, G:0.12, T:0.34
Consensus pattern (66 bp):
AAGTCCATAACTCCATGGCACCTTTCCTTTTTAAAGTCCACAACTCCGTGGCACCTTTCTTCTTC
A
Found at i:485325 original size:28 final size:27
Alignment explanation
Indices: 485281--485365 Score: 89
Period size: 27 Copynumber: 3.1 Consensus size: 27
485271 GCACCTTTTT
*
485281 TTTAAAGTCCACAACTCCGTGGCACCC
1 TTTAAAGTCTACAACTCCGTGGCACCC
* * **
485308 TTTCAAAGTCTACGACTCTGTGGTGCCC
1 TTT-AAAGTCTACAACTCCGTGGCACCC
* * *
485336 TTTTAAGTCTACAACTCCATGGCACTC
1 TTTAAAGTCTACAACTCCGTGGCACCC
485363 TTT
1 TTT
485366 TTCTTTTGAT
Statistics
Matches: 45, Mismatches: 12, Indels: 2
0.76 0.20 0.03
Matches are distributed among these distances:
27 23 0.51
28 22 0.49
ACGTcount: A:0.22, C:0.31, G:0.15, T:0.32
Consensus pattern (27 bp):
TTTAAAGTCTACAACTCCGTGGCACCC
Found at i:485352 original size:27 final size:27
Alignment explanation
Indices: 485280--485366 Score: 84
Period size: 28 Copynumber: 3.1 Consensus size: 27
485270 GGCACCTTTT
*
485280 TTTTAAAGTCCACAACTCCGTGGCACCC
1 TTTT-AAGTCTACAACTCCGTGGCACCC
* * * **
485308 TTTCAAAGTCTACGACTCTGTGGTGCCC
1 TTT-TAAGTCTACAACTCCGTGGCACCC
* *
485336 TTTTAAGTCTACAACTCCATGGCACTC
1 TTTTAAGTCTACAACTCCGTGGCACCC
485363 TTTT
1 TTTT
485367 TCTTTTGATG
Statistics
Matches: 45, Mismatches: 13, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
27 21 0.47
28 24 0.53
ACGTcount: A:0.22, C:0.30, G:0.15, T:0.33
Consensus pattern (27 bp):
TTTTAAGTCTACAACTCCGTGGCACCC
Found at i:485541 original size:33 final size:32
Alignment explanation
Indices: 485454--485619 Score: 158
Period size: 33 Copynumber: 5.2 Consensus size: 32
485444 CACAACACTA
485454 TGGC-ACCCTTCTCTAAAGCCCACACAAGTCGG
1 TGGCAACCCTT-TCTAAAGCCCACACAAGTCGG
*
485486 TGGCAACCC-TTCTAAAGTCCACACAAGTCGG
1 TGGCAACCCTTTCTAAAGCCCACACAAGTCGG
* **
485517 TGGTAACCCCTTTCTAAAGCCCACACAAGTTAG
1 TGGCAA-CCCTTTCTAAAGCCCACACAAGTCGG
* * * ** * *
485550 TGACAACCCCCTTCAAAAGCATACACGAGTCGA
1 TGGCAA-CCCTTTCTAAAGCCCACACAAGTCGG
* *
485583 TGGCAACCCTCTC-AATAGCCCACACAAGTTGG
1 TGGCAACCCTTTCTAA-AGCCCACACAAGTCGG
485615 TGGCA
1 TGGCA
485620 TCTTCTTCTA
Statistics
Matches: 107, Mismatches: 23, Indels: 8
0.78 0.17 0.06
Matches are distributed among these distances:
31 27 0.25
32 29 0.27
33 51 0.48
ACGTcount: A:0.30, C:0.33, G:0.18, T:0.19
Consensus pattern (32 bp):
TGGCAACCCTTTCTAAAGCCCACACAAGTCGG
Found at i:485763 original size:52 final size:52
Alignment explanation
Indices: 485704--486258 Score: 261
Period size: 52 Copynumber: 10.5 Consensus size: 52
485694 AATATCGCTG
* *
485704 GCCTTGAATCAGCACATTGGCACCTTTTTCTTTCTTAAGTCCAGTATCACTA
1 GCCTTGAATCAGCACATTGGCACCTTTTTCTTTCTTAAGTCCAATGTCACTA
** * ** * * * * *
485756 GCCTTGAATCAGCATTTTTGACACGGTTGTC-ATCTTTAAGTCTAATATCGCTA
1 GCCTTGAATCAGCA-CATTGGCACCTTTTTCTTTC-TTAAGTCCAATGTCACTA
* * * * * * * * *
485809 GCCTTGGATCAGTATATTGGCATCTTTATCATCCCTAAGCCCAATGTCACTA
1 GCCTTGAATCAGCACATTGGCACCTTTTTCTTTCTTAAGTCCAATGTCACTA
* * * **
485861 GCCTTGAATCAGCAGATTGGCA--TTCTTCTAATTTTTAAGTCCAATGTTGC-A
1 GCCTTGAATCAGCACATTGGCACCTTTTTCT--TTCTTAAGTCCAATGTCACTA
* * ** * *
485912 GGCCTTCAATCAGCACATTAGCATTTTTTTC-ATCTTCAAGTCTAATGTCACTA
1 -GCCTTGAATCAGCACATTGGCACCTTTTTCTTTCTT-AAGTCCAATGTCACTA
* * ** ** * *
485965 GCCATGAATCAGCACATTGGCACTCTTCTTACCCTTATCATCTTTAAGTCTGACATCATTG
1 GCCTTGAATCAGCACATTGGCAC-CTT-TT--TC-T-T--TC-TTAAGTCCAATGTCACTA
* ** *
486026 GCCTTGAATC-G-ACATATCGGCACCTTTATCTCTTT-TTAAGTCTAATGTTGCTG
1 GCCTTGAATCAGCACAT-T-GGCACCTTT-T-TCTTTCTTAAGTCCAATGTCACTA
* * * ** *
486079 GCCTTGAATCAGCACATAGGCACCTTTATCATTT-TTAAGCCCAATGTTGCTG
1 GCCTTGAATCAGCACATTGGCACCTTTTTC-TTTCTTAAGTCCAATGTCACTA
* * * * ** *
486131 GCCTTGAATCAGCACATTAGCACCCTTGTCATTT-TTAAGTCTAATGTTGCTG
1 GCCTTGAATCAGCACATTGGCACCTTTTTC-TTTCTTAAGTCCAATGTCACTA
* * * *
486183 GCCTTGAATCAACACATTGGCA--TTTTTCTCATCTTCAAGTCCAATGTCATTG
1 GCCTTGAATCAGCACATTGGCACCTTTTTCT-TTCTT-AAGTCCAATGTCACTA
*
486235 GCCTTGAATCAACACATTGGCACC
1 GCCTTGAATCAGCACATTGGCACC
486259 CTTCTCATCT
Statistics
Matches: 387, Mismatches: 85, Indels: 60
0.73 0.16 0.11
Matches are distributed among these distances:
49 1 0.00
50 9 0.02
51 8 0.02
52 239 0.62
53 72 0.19
54 8 0.02
55 5 0.01
56 1 0.00
57 1 0.00
58 1 0.00
59 7 0.02
60 6 0.02
61 27 0.07
62 2 0.01
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (52 bp):
GCCTTGAATCAGCACATTGGCACCTTTTTCTTTCTTAAGTCCAATGTCACTA
Found at i:486125 original size:270 final size:270
Alignment explanation
Indices: 485790--486285 Score: 668
Period size: 270 Copynumber: 1.8 Consensus size: 270
485780 GGTTGTCATC
* * * * *
485790 TTTAAGTCTAATATCGCTAGCCTTGGATCAGTATATTGGCATCTTTATCATCCCTAAGCCCAATG
1 TTTAAGTCTAATATCGCTAGCCTTGAATCAGCACATAGGCACCTTTATCATCCCTAAGCCCAATG
* * **
485855 TCACTAGCCTTGAATCAGCAGATTGGCATTCTTCTAATTTTTAAGTCCAATGTTGCAGGCCTTCA
66 TCACTAGCCTTGAATCAGCACATTAGCACCCTTCTAATTTTTAAGTCCAATGTTGCAGGCCTTCA
* * * *
485920 ATCAGCACATTAGCATTTTTTTCATCTTCAAGTCTAATGTCACTAGCCATGAATCAGCACATTGG
131 ATCAACACATTAGCATTTTTCTCATCTTCAAGTCCAATGTCACTAGCCATGAATCAACACATTGG
* *
485985 CACTCTTCTTACCCTTATCATCTTTAAGTCTGACATCATTGGCCTTGAATCGACATATCGGCACC
196 CACCCTTCTCACCCTTATCATCTTTAAGTCTGACATCATTGGCCTTGAATCGACATATCGGCACC
486050 TTTATCTCTT
261 TTTATCTCTT
* * * ***
486060 TTTAAGTCTAATGTTGCTGGCCTTGAATCAGCACATAGGCACCTTTATCATTTTTAAGCCCAATG
1 TTTAAGTCTAATATCGCTAGCCTTGAATCAGCACATAGGCACCTTTATCATCCCTAAGCCCAATG
** * * * * * *
486125 TTGCTGGCCTTGAATCAGCACATTAGCACCCTTGTCATTTTTAAGTCTAATGTTGCTGGCCTTGA
66 TCACTAGCCTTGAATCAGCACATTAGCACCCTTCTAATTTTTAAGTCCAATGTTGCAGGCCTTCA
* * * *
486190 ATCAACACATTGGCATTTTTCTCATCTTCAAGTCCAATGTCATTGGCCTTGAATCAACACATTGG
131 ATCAACACATTAGCATTTTTCTCATCTTCAAGTCCAATGTCACTAGCCATGAATCAACACATTGG
* * *
486255 CACCCTTCTCATCTTTATTATCTTTAAGTCT
196 CACCCTTCTCACCCTTATCATCTTTAAGTCT
486286 ACTATCGTAG
Statistics
Matches: 190, Mismatches: 36, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
270 190 1.00
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.36
Consensus pattern (270 bp):
TTTAAGTCTAATATCGCTAGCCTTGAATCAGCACATAGGCACCTTTATCATCCCTAAGCCCAATG
TCACTAGCCTTGAATCAGCACATTAGCACCCTTCTAATTTTTAAGTCCAATGTTGCAGGCCTTCA
ATCAACACATTAGCATTTTTCTCATCTTCAAGTCCAATGTCACTAGCCATGAATCAACACATTGG
CACCCTTCTCACCCTTATCATCTTTAAGTCTGACATCATTGGCCTTGAATCGACATATCGGCACC
TTTATCTCTT
Found at i:486191 original size:104 final size:104
Alignment explanation
Indices: 486054--486271 Score: 294
Period size: 104 Copynumber: 2.1 Consensus size: 104
486044 GGCACCTTTA
* * *
486054 TCTC-TTTTTAAGTCTAATGTTGCTGGCCTTGAATCAGCACATAGGCACCTTTATCATTTTTAAG
1 TCTCATTTTTAAGTCTAATGTTGCTGGCCTTGAATCAACACATAGGCACCTTTATCATCTTCAAG
** *
486118 CCCAATGTTGCTGGCCTTGAATCAGCACATTAGCACCCT
66 CCCAATGTCACTGGCCTTGAATCAACACATTAGCACCCT
* * ** *
486157 TGTCATTTTTAAGTCTAATGTTGCTGGCCTTGAATCAACACATTGGCATTTTTCTCATCTTCAAG
1 TCTCATTTTTAAGTCTAATGTTGCTGGCCTTGAATCAACACATAGGCACCTTTATCATCTTCAAG
* * *
486222 TCCAATGTCATTGGCCTTGAATCAACACATTGGCACCCT
66 CCCAATGTCACTGGCCTTGAATCAACACATTAGCACCCT
*
486261 TCTCATCTTTA
1 TCTCATTTTTA
486272 TTATCTTTAA
Statistics
Matches: 98, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
103 3 0.03
104 95 0.97
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.37
Consensus pattern (104 bp):
TCTCATTTTTAAGTCTAATGTTGCTGGCCTTGAATCAACACATAGGCACCTTTATCATCTTCAAG
CCCAATGTCACTGGCCTTGAATCAACACATTAGCACCCT
Found at i:486870 original size:21 final size:21
Alignment explanation
Indices: 486823--486878 Score: 80
Period size: 20 Copynumber: 2.7 Consensus size: 21
486813 TACAAATAGT
486823 AAATGTATCGATACATAACTG
1 AAATGTATCGATACATAACTG
*
486844 -AATGTATCGATACAT-GCTTG
1 AAATGTATCGATACATAAC-TG
486864 AAATGTATCGATACA
1 AAATGTATCGATACA
486879 AAACCACTCT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 1 0.03
20 17 0.53
21 14 0.44
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (21 bp):
AAATGTATCGATACATAACTG
Found at i:489449 original size:462 final size:461
Alignment explanation
Indices: 488533--489455 Score: 1765
Period size: 462 Copynumber: 2.0 Consensus size: 461
488523 CCATGACTCG
* *
488533 AGTGTAGACCAATAAACACTAAGAAAACTGAAATCCTCCTCTATTTTACTTTGTCCATTACTGGC
1 AGTGTAGACCAATAAACACTAAGAAAACTGAAATCCTCCTCTATTTTACTGTGTCCACTACTGGC
488598 AGCACCTCTATTGCATATTGGAAAATCATTTTAAAATACTAATCCATTTTCATGAATTTTAGAAC
66 AGCACCTCTATTGCATATTGGAAAATCATTTTAAAATACTAATCCATTTTCATGAATTTTAGAAC
*
488663 ATTTTGCCTTGAAAGTGTGTTAAAATAGCTTTCAAACAGTGTCTTATTCATCCGTAGATCATTCT
131 ATTTTGCCTTGAAAGTGTGTTAAAATAGCTTTCAAACAGTGTCTTATTCATCCCTAGATCATTCT
*
488728 AGATAAGGGAGTTGTGATTTTTCAAACCTAAGCTATCAGAATCCCTAGAACTAGGAAAATGCATT
196 AGATAAGGGAGTTGTGATTTTTCAAACCTAAGCTATCAGAATCCCTAGAACTAGCAAAATGCATT
488793 CTGGTTGGGCCGTTTAGGCCCATTAGACGATTTTCCAAATTTTTTGAAAATTTATCCTAAAATTT
261 CTGGTTGGGCCGTTTAGGCCCATTAGACGATTTTCCAAATTTTTTGAAAATTTATCCTAAAATTT
488858 CATAAAATTTCCTTTCCGAAAAGGTATCATTTATAATTTTTCGATGCTAAACTAGTATGGGGCGA
326 CATAAAATTTCCTTTCCGAAAAGGTATCATTTATAATTTTTCGATGCTAAACTAGTATGGGGCGA
488923 TTTTTCAAAGTTTGACATACCTTTTACTTCATGTGTTTTGCCAGCAATGCAATTAACCCAACTCC
391 TTTTTCAAAGTTTGACATACCTTTTACTTCATGTGTTTTGCCAGCAATGCAATTAACCCAACTCC
488988 AAGAAT
456 AAGAAT
488994 AGTGTAGACCAATAAACACTAAGAAAACTGAAATCCTCCTCTATTTTACTGTGTCCACTACTGGC
1 AGTGTAGACCAATAAACACTAAGAAAACTGAAATCCTCCTCTATTTTACTGTGTCCACTACTGGC
489059 AGCACCTCTATTGCATATTGGAAAATCATTTTAAAATACTAATCCATTTTCATGAATTTTAGAAC
66 AGCACCTCTATTGCATATTGGAAAATCATTTTAAAATACTAATCCATTTTCATGAATTTTAGAAC
489124 ATTTTGCCTTGAAAGTGTGTTAAAATAGCTTTCAAACAGTGTCTTATTCATCCCTAGATCATTCT
131 ATTTTGCCTTGAAAGTGTGTTAAAATAGCTTTCAAACAGTGTCTTATTCATCCCTAGATCATTCT
* *
489189 AGATAAGGGAGTTGTGGTTTTTTAAACCTAAGCTATCCAGAATCCCTAGAACTAGCAAAATGCAT
196 AGATAAGGGAGTTGTGATTTTTCAAACCTAAGCTAT-CAGAATCCCTAGAACTAGCAAAATGCAT
489254 TCTGGTTGGGCCGTTTAGGCCCATTAGACGATTTTCCAAATTTTTTGAAAATTTATCCTAAAATT
260 TCTGGTTGGGCCGTTTAGGCCCATTAGACGATTTTCCAAATTTTTTGAAAATTTATCCTAAAATT
*
489319 TCATAAAATTTCCTTTCCGAAAAGGTATCATTTATAATTTTTTGATGCTAAACTAGTATGGGGCG
325 TCATAAAATTTCCTTTCCGAAAAGGTATCATTTATAATTTTTCGATGCTAAACTAGTATGGGGCG
*
489384 ATTTTTCAAAGTTTGACATACCTTTTACTTCATGTGTTTTGCCAGCAATGCAATTAACTCAACTC
390 ATTTTTCAAAGTTTGACATACCTTTTACTTCATGTGTTTTGCCAGCAATGCAATTAACCCAACTC
489449 CAAGAAT
455 CAAGAAT
489456 TTATTCCACT
Statistics
Matches: 453, Mismatches: 8, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
461 226 0.50
462 227 0.50
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (461 bp):
AGTGTAGACCAATAAACACTAAGAAAACTGAAATCCTCCTCTATTTTACTGTGTCCACTACTGGC
AGCACCTCTATTGCATATTGGAAAATCATTTTAAAATACTAATCCATTTTCATGAATTTTAGAAC
ATTTTGCCTTGAAAGTGTGTTAAAATAGCTTTCAAACAGTGTCTTATTCATCCCTAGATCATTCT
AGATAAGGGAGTTGTGATTTTTCAAACCTAAGCTATCAGAATCCCTAGAACTAGCAAAATGCATT
CTGGTTGGGCCGTTTAGGCCCATTAGACGATTTTCCAAATTTTTTGAAAATTTATCCTAAAATTT
CATAAAATTTCCTTTCCGAAAAGGTATCATTTATAATTTTTCGATGCTAAACTAGTATGGGGCGA
TTTTTCAAAGTTTGACATACCTTTTACTTCATGTGTTTTGCCAGCAATGCAATTAACCCAACTCC
AAGAAT
Found at i:492887 original size:13 final size:13
Alignment explanation
Indices: 492869--492893 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
492859 CAAAGATCAG
492869 TGTATCGATACAA
1 TGTATCGATACAA
492882 TGTATCGATACA
1 TGTATCGATACA
492894 TTTTCTTGGC
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:492949 original size:19 final size:18
Alignment explanation
Indices: 492925--492987 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
492915 AGCGATACGT
492925 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
492944 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
492957 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
492976 TGTATCGATACA
1 TGTATCGATACA
492988 TTGTATCGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
16 2 0.05
18 1 0.03
19 23 0.61
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:492960 original size:32 final size:32
Alignment explanation
Indices: 492917--493002 Score: 154
Period size: 32 Copynumber: 2.7 Consensus size: 32
492907 AGTTTCGTAG
*
492917 CGATACGTTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
492949 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
492981 CGATACATTGTATCGATACAAA
1 CGATACATTGTATCGATACAAA
493003 TCGTTGAAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:492962 original size:13 final size:13
Alignment explanation
Indices: 492944--493000 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
492934 ACAAAACTTA
492944 TGTATCGATACAT
1 TGTATCGATACAT
492957 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
492975 ATGTATCGATACAT
1 -TGTATCGATACAT
492989 TGTATCGATACA
1 TGTATCGATACA
493001 AATCGTTGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:493100 original size:21 final size:21
Alignment explanation
Indices: 493040--493094 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
493030 TGGGACCTTA
*
493040 TATCGATACATTCAAACAATG
1 TATCGATACATTTAAACAATG
493061 TATCGATACATTTAAACAATG
1 TATCGATACATTTAAACAATG
493082 TATCGATACATTT
1 TATCGATACATTT
493095 GGACAAAACT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (21 bp):
TATCGATACATTTAAACAATG
Done.