Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008504.1 Hibiscus syriacus cultivar Beakdansim tig00111356_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2056749
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 10
Found at i:1404449 original size:2 final size:2
Alignment explanation
Indices: 1404442--1404510 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
1404432 ATGCACCTCG
1404442 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1404484 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1404511 GCATTTGAAA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1404552 original size:25 final size:25
Alignment explanation
Indices: 1404517--1404581 Score: 94
Period size: 25 Copynumber: 2.6 Consensus size: 25
1404507 ATATGCATTT
*
1404517 GAAATTGCCTCGTAGAATTGAACTC
1 GAAAGTGCCTCGTAGAATTGAACTC
* * *
1404542 GAAAGTTCCTCGTAGTATTGTACTC
1 GAAAGTGCCTCGTAGAATTGAACTC
1404567 GAAAGTGCCTCGTAG
1 GAAAGTGCCTCGTAG
1404582 GATTCCACCA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (25 bp):
GAAAGTGCCTCGTAGAATTGAACTC
Found at i:1410994 original size:18 final size:20
Alignment explanation
Indices: 1410973--1411011 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
1410963 AAATGAAAAT
1410973 TCCAT-TTAAATTC-ACTGA
1 TCCATGTTAAATTCTACTGA
1410991 TCCATGTTAAATTCTACTGA
1 TCCATGTTAAATTCTACTGA
1411011 T
1 T
1411012 TAAAACTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.26
19 8 0.42
20 6 0.32
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.41
Consensus pattern (20 bp):
TCCATGTTAAATTCTACTGA
Found at i:1412794 original size:21 final size:22
Alignment explanation
Indices: 1412770--1412821 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 22
1412760 TGCCCTCTTG
*
1412770 TTTTCTTTTTATAATTTTTTT-T
1 TTTTCTTTTCA-AATTTTTTTAT
*
1412792 TTTTACTTTTC-AAGTTTTTTAT
1 TTTT-CTTTTCAAATTTTTTTAT
1412814 TTTTCTTT
1 TTTTCTTT
1412822 AAAAATACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 12 0.46
22 9 0.35
23 5 0.19
ACGTcount: A:0.13, C:0.08, G:0.02, T:0.77
Consensus pattern (22 bp):
TTTTCTTTTCAAATTTTTTTAT
Found at i:1413428 original size:13 final size:14
Alignment explanation
Indices: 1413402--1413438 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
1413392 TTTTCATCTC
1413402 AATTTATCTTCTTT
1 AATTTATCTTCTTT
1413416 AATTTAT-TTCTTT
1 AATTTATCTTCTTT
1413429 -ATTTACTCTT
1 AATTTA-TCTT
1413439 TACTCTTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 5 0.24
13 7 0.33
14 9 0.43
ACGTcount: A:0.22, C:0.14, G:0.00, T:0.65
Consensus pattern (14 bp):
AATTTATCTTCTTT
Found at i:1416423 original size:14 final size:15
Alignment explanation
Indices: 1416393--1416430 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
1416383 GAGACAACCC
*
1416393 ATTTTGTTTTCATTT
1 ATTTTATTTTCATTT
1416408 ATTTTATTTT-ATTT
1 ATTTTATTTTCATTT
1416422 A-TTTATTTT
1 ATTTTATTTT
1416431 TATTGAGTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 8 0.36
14 5 0.23
15 9 0.41
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (15 bp):
ATTTTATTTTCATTT
Found at i:1416739 original size:16 final size:16
Alignment explanation
Indices: 1416714--1416746 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1416704 ATTCATAAAG
1416714 AGCATCTGAATCATTC
1 AGCATCTGAATCATTC
*
1416730 AGCATTTGAATCATTC
1 AGCATCTGAATCATTC
1416746 A
1 A
1416747 ACGCTTAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.33
Consensus pattern (16 bp):
AGCATCTGAATCATTC
Found at i:1419289 original size:13 final size:13
Alignment explanation
Indices: 1419269--1419301 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
1419259 CCTTGATTTT
1419269 TTTA-TTTTTCTA
1 TTTATTTTTTCTA
1419281 TTTATTTTTTCTA
1 TTTATTTTTTCTA
1419294 TTTATTTT
1 TTTATTTT
1419302 CATTTTTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.20
13 16 0.80
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTATTTTTTCTA
Found at i:1423281 original size:15 final size:15
Alignment explanation
Indices: 1423261--1423297 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1423251 TATGTTTATA
*
1423261 TGAAAATGTTCTAAG
1 TGAAAATGTTCCAAG
*
1423276 TGAAAATGTTCCACG
1 TGAAAATGTTCCAAG
1423291 TGAAAAT
1 TGAAAAT
1423298 ATCTATGTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.30
Consensus pattern (15 bp):
TGAAAATGTTCCAAG
Found at i:1423461 original size:23 final size:23
Alignment explanation
Indices: 1423428--1423538 Score: 80
Period size: 23 Copynumber: 4.7 Consensus size: 23
1423418 AGTCGAGGGT
* * *
1423428 TCTACGCGGTCATTCGGGAAAAA
1 TCTACGTGGTCCTTCGGGACAAA
* ** *
1423451 TCTATGTGGTCCTTTAGGACAAT
1 TCTACGTGGTCCTTCGGGACAAA
1423474 TCTACGTGGTCCTTCGGGACAAA
1 TCTACGTGGTCCTTCGGGACAAA
* ***
1423497 TTATACACAGTCCTTCGGGACAAA
1 -TCTACGTGGTCCTTCGGGACAAA
*
1423521 TTCTATGTGG-CACTTCGG
1 -TCTACGTGGTC-CTTCGG
1423539 TGCAATTTAT
Statistics
Matches: 66, Mismatches: 20, Indels: 3
0.74 0.22 0.03
Matches are distributed among these distances:
23 36 0.55
24 30 0.45
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (23 bp):
TCTACGTGGTCCTTCGGGACAAA
Found at i:1428026 original size:18 final size:18
Alignment explanation
Indices: 1427993--1428074 Score: 76
Period size: 20 Copynumber: 4.3 Consensus size: 18
1427983 GAATTCCAGA
*
1427993 ATACTGAA-ATGGTATCG
1 ATACTGAAGAGGGTATCG
1428010 ATACTGAAGAGGGTATCG
1 ATACTGAAGAGGGTATCG
*
1428028 GTACCCTAGAAGAGAGGTATCG
1 ATA--CT-GAAGAG-GGTATCG
*
1428050 GTACTGTAAGAGGAGTATCG
1 ATACTG-AAGAGG-GTATCG
1428070 ATACT
1 ATACT
1428075 ATTCAGTGTG
Statistics
Matches: 55, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
17 8 0.15
18 10 0.18
19 2 0.04
20 19 0.35
21 6 0.11
22 10 0.18
ACGTcount: A:0.33, C:0.13, G:0.29, T:0.24
Consensus pattern (18 bp):
ATACTGAAGAGGGTATCG
Found at i:1428608 original size:15 final size:15
Alignment explanation
Indices: 1428588--1428635 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
1428578 TATGTTTATA
1428588 TGAAAATATTCTAAG
1 TGAAAATATTCTAAG
*
1428603 TGAAAATGTTC-AACG
1 TGAAAATATTCTAA-G
*
1428618 TGAAAATA-TCTATG
1 TGAAAATATTCTAAG
1428632 TGAA
1 TGAA
1428636 TGTGCTCTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 9 0.32
15 19 0.68
ACGTcount: A:0.44, C:0.08, G:0.17, T:0.31
Consensus pattern (15 bp):
TGAAAATATTCTAAG
Found at i:1428862 original size:46 final size:45
Alignment explanation
Indices: 1428754--1428865 Score: 116
Period size: 46 Copynumber: 2.4 Consensus size: 45
1428744 GAGTCGAGGG
*
1428754 TTCTACGCGGTTCTTCGGGATAAACCTATGTGATCCTTCGGGACAA
1 TTCTACGCGG-TCTTCGGGACAAACCTATGTGATCCTTCGGGACAA
* ** * ** * *
1428800 TTCTATGTAGTCCTTCGTGACAATTCTATGTGGTCCTTTGGGACAAA
1 TTCTACGCGGT-CTTCGGGACAAACCTATGTGATCCTTCGGGAC-AA
1428847 TTCTACGCGGTCTTCGGGA
1 TTCTACGCGGTCTTCGGGA
1428866 TAAATTCTAC
Statistics
Matches: 51, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
45 1 0.02
46 40 0.78
47 10 0.20
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.34
Consensus pattern (45 bp):
TTCTACGCGGTCTTCGGGACAAACCTATGTGATCCTTCGGGACAA
Found at i:1428865 original size:23 final size:24
Alignment explanation
Indices: 1428754--1428878 Score: 105
Period size: 23 Copynumber: 5.4 Consensus size: 24
1428744 GAGTCGAGGG
* * *
1428754 TTCTACGCGGTTCTTCGGGATAAA
1 TTCTACGTGGTCCTTCGGGACAAA
* * *
1428778 -CCTATGTGATCCTTCGGGAC-AA
1 TTCTACGTGGTCCTTCGGGACAAA
* * *
1428800 TTCTATGTAGTCCTTCGTGAC-AA
1 TTCTACGTGGTCCTTCGGGACAAA
* *
1428823 TTCTATGTGGTCCTTTGGGACAAA
1 TTCTACGTGGTCCTTCGGGACAAA
* *
1428847 TTCTACGCGGT-CTTCGGGATAAA
1 TTCTACGTGGTCCTTCGGGACAAA
1428870 TTCTACGTG
1 TTCTACGTG
1428879 ACACTTCGGT
Statistics
Matches: 81, Mismatches: 18, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
22 2 0.02
23 68 0.84
24 11 0.14
ACGTcount: A:0.21, C:0.22, G:0.23, T:0.34
Consensus pattern (24 bp):
TTCTACGTGGTCCTTCGGGACAAA
Found at i:1436332 original size:2 final size:2
Alignment explanation
Indices: 1436327--1436368 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1436317 ATAAAAAACC
1436327 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1436369 TAAACGTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1438080 original size:82 final size:82
Alignment explanation
Indices: 1437993--1439130 Score: 1181
Period size: 82 Copynumber: 14.1 Consensus size: 82
1437983 TGATAGGAAA
* * * * **
1437993 TCTGCTCCACTCTTCATTCAAGGGATATCAGACTTGATACGTGCCTCTTTTTTAGGTAGTCAGAT
1 TCTGCTCCACTATTCATTCAGGGGAGATCAGACTTGATATGTGCCTCTTTTTCGGGTAGTCAGAT
*
1438058 CAATTTTGGAAGACGGG
66 CAATTTTGGAAGACGTG
* * * * * *
1438075 CCTGCTTCGCTATTCATTCAGGGGAGATCAGACTTGATATGTTCCTC-TTTTCAGGTAGTCATAT
1 TCTGCTCCACTATTCATTCAGGGGAGATCAGACTTGATATGTGCCTCTTTTTCGGGTAGTCAGAT
* * * *
1438139 CTATTTTAGATGGCGTG
66 CAATTTTGGAAGACGTG
* *
1438156 TCTGCTCCACTATTCATTCAGGGGAGATCAGACTTGATTTTTGCCTCTTTTTCGGGTAGTCAGAT
1 TCTGCTCCACTATTCATTCAGGGGAGATCAGACTTGATATGTGCCTCTTTTTCGGGTAGTCAGAT
* * *
1438221 CTATTTTGTATGACGTG
66 CAATTTTGGAAGACGTG
* *
1438238 TCTACTCCACTATTCATTCAGGGGAGATCAGACTTGATCTGTGCCTC-TTTTCGGGTAGTCAGAT
1 TCTGCTCCACTATTCATTCAGGGGAGATCAGACTTGATATGTGCCTCTTTTTCGGGTAGTCAGAT
* * *
1438302 CTATTTTGGATGACATG
66 CAATTTTGGAAGACGTG
* * *
1438319 TCTGCTCTACTATTCATTCAGGGGAGATCAGACTTGATATGTACCTCTTTTTTGGGTAGTCAGAT
1 TCTGCTCCACTATTCATTCAGGGGAGATCAGACTTGATATGTGCCTCTTTTTCGGGTAGTCAGAT
*
1438384 CAATTTTGGAAGATGTG
66 CAATTTTGGAAGACGTG
* *
1438401 TCTGCTTCACTATTCATTTAGGGGAGATCAGACTTGATATGTGCCTCTTTTTCGGGTAGTCAGAT
1 TCTGCTCCACTATTCATTCAGGGGAGATCAGACTTGATATGTGCCTCTTTTTCGGGTAGTCAGAT
*
1438466 CAATTTTGAAAGACGTG
66 CAATTTTGGAAGACGTG
* * * * ** * *
1438483 TCTGCTCTAATATTCATTCAGGGGACATCAGACTTGATCTGTGTTTTTTTTTTCAGGTAGTCAGA
1 TCTGCTCCACTATTCATTCAGGGGAGATCAGACTTGATATGTG-CCTCTTTTTCGGGTAGTCAGA
1438548 TCAATTTTGGAAGA----
65 TCAATTTTGGAAGACGTG
* * * * *
1438562 -------CA-AATTCATTCAGGGGAGATTAAACTTAATTTTGTGCCTCTTTTTCGGGTAGTCAGA
1 TCTGCTCCACTATTCATTCAGGGGAGATCAGACTTGA-TATGTGCCTCTTTTTCGGGTAGTCAGA
***
1438619 TCAATTTTGGAAGACAAA
65 TCAATTTTGGAAGACGTG
* * * * * * * * *
1438637 TATGCTCTAATATTCATTCAGGGTATATCAGACTTGATCTGTACCTCTTTTTCGGCTAGTCAAAT
1 TCTGCTCCACTATTCATTCAGGGGAGATCAGACTTGATATGTGCCTCTTTTTCGGGTAGTCAGAT
****
1438702 CAATTTTGGAAGATAAA
66 CAATTTTGGAAGACGTG
* * * * * * *
1438719 TATGCTCTACTATTCATTCAGGGAAGATCAGACTTGATTTGTGCCTCTTTTTCAGGTACTCAAAT
1 TCTGCTCCACTATTCATTCAGGGGAGATCAGACTTGATATGTGCCTCTTTTTCGGGTAGTCAGAT
* **
1438784 CTATTTTGGATTACGTG
66 CAATTTTGGAAGACGTG
* * * * *
1438801 TCTGCTCTACTATTCATTCATGGGAGATTAAACTTGATATGTGTCT-TTTTTCGGGTAGTCTA-A
1 TCTGCTCCACTATTCATTCAGGGGAGATCAGACTTGATATGTGCCTCTTTTTCGGGTAGTC-AGA
* *
1438864 TCTATTTTGGATGACGTG
65 TCAATTTTGGAAGACGTG
* *
1438882 TCTGCTCCACTATTCATTCAAGGGAGATTAGACTTGATATGTGCCTCTTTTTCGGGTAGTCAGAT
1 TCTGCTCCACTATTCATTCAGGGGAGATCAGACTTGATATGTGCCTCTTTTTCGGGTAGTCAGAT
***
1438947 CAATTTTGGAAGACAAA
66 CAATTTTGGAAGACGTG
* * *
1438964 TCTTCTCCACTATTCATTCAAGGGAGATCAGAC--------TGCCTCTTTTTCAGGTAGTCAGAT
1 TCTGCTCCACTATTCATTCAGGGGAGATCAGACTTGATATGTGCCTCTTTTTCGGGTAGTCAGAT
****
1439021 CAATTTTGGAAGAAAAA
66 CAATTTTGGAAGACGTG
* ** * * * *
1439038 TATGCTATACTATTCATTTAGGGGAGATCGGACTTGATCTATGCCTCTTTTTCGGGTAGTCAGAT
1 TCTGCTCCACTATTCATTCAGGGGAGATCAGACTTGATATGTGCCTCTTTTTCGGGTAGTCAGAT
*
1439103 CAATTTTGGAAGACATG
66 CAATTTTGGAAGACGTG
1439120 TCTGCTCCACT
1 TCTGCTCCACT
1439131 CTTGTTTCAA
Statistics
Matches: 896, Mismatches: 133, Indels: 54
0.83 0.12 0.05
Matches are distributed among these distances:
71 53 0.06
72 6 0.01
74 65 0.07
81 216 0.24
82 505 0.56
83 51 0.06
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (82 bp):
TCTGCTCCACTATTCATTCAGGGGAGATCAGACTTGATATGTGCCTCTTTTTCGGGTAGTCAGAT
CAATTTTGGAAGACGTG
Found at i:1438263 original size:163 final size:164
Alignment explanation
Indices: 1437993--1439126 Score: 1191
Period size: 163 Copynumber: 7.0 Consensus size: 164
1437983 TGATAGGAAA
* * * * * **
1437993 TCTGCTCCACTCTTCATTCAAGGGATATCAGACTTGATACGTGCCTCTTTTTTAGGTAGTCAGAT
1 TCTGCTCTACTATTCATTCAGGGGAGATCAGACTTGATATGTGCCTCTTTTTCGGGTAGTCAGAT
* * * * *
1438058 CAATTTTGGAAGACGGGCCTGCTTCGCTATTCATTCAGGGGAGATCAGACTTGATATGTTCCTC-
66 CAATTTTGGAAGACGTGTCTGCTCCACTATTCATTCAGGGGAGATCAGACTTGATATGTGCCTCT
* * * * * * *
1438122 TTTTCAGGTAGTCATATCTATTTTAGATGGCGTG
131 TTTTCGGGTAGTCAGATCAATTTTGGAAGACATG
* * *
1438156 TCTGCTCCACTATTCATTCAGGGGAGATCAGACTTGATTTTTGCCTCTTTTTCGGGTAGTCAGAT
1 TCTGCTCTACTATTCATTCAGGGGAGATCAGACTTGATATGTGCCTCTTTTTCGGGTAGTCAGAT
* * * * *
1438221 CTATTTTGTATGACGTGTCTACTCCACTATTCATTCAGGGGAGATCAGACTTGATCTGTGCCTC-
66 CAATTTTGGAAGACGTGTCTGCTCCACTATTCATTCAGGGGAGATCAGACTTGATATGTGCCTCT
* *
1438285 TTTTCGGGTAGTCAGATCTATTTTGGATGACATG
131 TTTTCGGGTAGTCAGATCAATTTTGGAAGACATG
* *
1438319 TCTGCTCTACTATTCATTCAGGGGAGATCAGACTTGATATGTACCTCTTTTTTGGGTAGTCAGAT
1 TCTGCTCTACTATTCATTCAGGGGAGATCAGACTTGATATGTGCCTCTTTTTCGGGTAGTCAGAT
* * *
1438384 CAATTTTGGAAGATGTGTCTGCTTCACTATTCATTTAGGGGAGATCAGACTTGATATGTGCCTCT
66 CAATTTTGGAAGACGTGTCTGCTCCACTATTCATTCAGGGGAGATCAGACTTGATATGTGCCTCT
* *
1438449 TTTTCGGGTAGTCAGATCAATTTTGAAAGACGTG
131 TTTTCGGGTAGTCAGATCAATTTTGGAAGACATG
* * * ** * *
1438483 TCTGCTCTAATATTCATTCAGGGGACATCAGACTTGATCTGTGTTTTTTTTTTCAGGTAGTCAGA
1 TCTGCTCTACTATTCATTCAGGGGAGATCAGACTTGATATGTG-CCTCTTTTTCGGGTAGTCAGA
* * * * *
1438548 TCAATTTTGGAAGA-----------CA-AATTCATTCAGGGGAGATTAAACTTAATTTTGTGCCT
65 TCAATTTTGGAAGACGTGTCTGCTCCACTATTCATTCAGGGGAGATCAGACTTGA-TATGTGCCT
**
1438601 CTTTTTCGGGTAGTCAGATCAATTTTGGAAGACAAA
129 CTTTTTCGGGTAGTCAGATCAATTTTGGAAGACATG
* * * * * * * *
1438637 TATGCTCTAATATTCATTCAGGGTATATCAGACTTGATCTGTACCTCTTTTTCGGCTAGTCAAAT
1 TCTGCTCTACTATTCATTCAGGGGAGATCAGACTTGATATGTGCCTCTTTTTCGGGTAGTCAGAT
**** * * * *
1438702 CAATTTTGGAAGATAAATATGCTCTACTATTCATTCAGGGAAGATCAGACTTGATTTGTGCCTCT
66 CAATTTTGGAAGACGTGTCTGCTCCACTATTCATTCAGGGGAGATCAGACTTGATATGTGCCTCT
* * * * ** *
1438767 TTTTCAGGTACTCAAATCTATTTTGGATTACGTG
131 TTTTCGGGTAGTCAGATCAATTTTGGAAGACATG
* * * *
1438801 TCTGCTCTACTATTCATTCATGGGAGATTAAACTTGATATGTGTCT-TTTTTCGGGTAGTCTA-A
1 TCTGCTCTACTATTCATTCAGGGGAGATCAGACTTGATATGTGCCTCTTTTTCGGGTAGTC-AGA
* * * *
1438864 TCTATTTTGGATGACGTGTCTGCTCCACTATTCATTCAAGGGAGATTAGACTTGATATGTGCCTC
65 TCAATTTTGGAAGACGTGTCTGCTCCACTATTCATTCAGGGGAGATCAGACTTGATATGTGCCTC
**
1438929 TTTTTCGGGTAGTCAGATCAATTTTGGAAGACAAA
130 TTTTTCGGGTAGTCAGATCAATTTTGGAAGACATG
* * * *
1438964 TCTTCTCCACTATTCATTCAAGGGAGATCAGAC--------TGCCTCTTTTTCAGGTAGTCAGAT
1 TCTGCTCTACTATTCATTCAGGGGAGATCAGACTTGATATGTGCCTCTTTTTCGGGTAGTCAGAT
**** * ** * * * *
1439021 CAATTTTGGAAGAAAAATATGCTATACTATTCATTTAGGGGAGATCGGACTTGATCTATGCCTCT
66 CAATTTTGGAAGACGTGTCTGCTCCACTATTCATTCAGGGGAGATCAGACTTGATATGTGCCTCT
1439086 TTTTCGGGTAGTCAGATCAATTTTGGAAGACATG
131 TTTTCGGGTAGTCAGATCAATTTTGGAAGACATG
1439120 TCTGCTC
1 TCTGCTC
1439127 CACTCTTGTT
Statistics
Matches: 812, Mismatches: 141, Indels: 43
0.82 0.14 0.04
Matches are distributed among these distances:
153 51 0.06
154 81 0.10
155 5 0.01
156 103 0.13
163 377 0.46
164 143 0.18
165 52 0.06
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (164 bp):
TCTGCTCTACTATTCATTCAGGGGAGATCAGACTTGATATGTGCCTCTTTTTCGGGTAGTCAGAT
CAATTTTGGAAGACGTGTCTGCTCCACTATTCATTCAGGGGAGATCAGACTTGATATGTGCCTCT
TTTTCGGGTAGTCAGATCAATTTTGGAAGACATG
Found at i:1438427 original size:245 final size:244
Alignment explanation
Indices: 1437990--1439130 Score: 1228
Period size: 245 Copynumber: 4.7 Consensus size: 244
1437980 TTTTGATAGG
* * * *
1437990 AAATCTGCTCCACTCTTCATTCAAGGGATATCAGACTTGATAC-GTGCCTCTTTTTTAGGTAGTC
1 AAATCTGCTCCACTATTCATTCAGGGGAGATCAGACTTGAT-CTGTGCCTC-TTTTCAGGTAGTC
** * * *
1438054 AGATCAATTTTGGAAGACGGGCCTGCTTCGCTATTCATTCAGGGGAGATCAGACTTGATATGTTC
64 AGATCAATTTTGGAAGACATGTCTGCTT-ACTATTCATTCAGGGGAGATCAGACTTGATATGTGC
* * * * * *
1438119 CTC-TTTTCAGGTAGTCATATCTATTTTAGATGGCGTGTCTGCTCCACTATTCATTCAGGGGAGA
128 CTCTTTTTCGGGTAGTCAGATCAATTTTGGAAGACGTGTCTGCTCCACTATTCATTCAGGGGAGA
* * * * *
1438183 TCAGACTTGATTTTTGCCTCTTTTTCGGGTAGTCAGATCTATTTTGTATGAC
193 TCAGACTTGATATGTGCCTCTTTTTCGGGTAGTCAGATCAATTTTGGAAGAC
*** * *
1438235 GTGTCTACTCCACTATTCATTCAGGGGAGATCAGACTTGATCTGTGCCTCTTTTCGGGTAGTCAG
1 AAATCTGCTCCACTATTCATTCAGGGGAGATCAGACTTGATCTGTGCCTCTTTTCAGGTAGTCAG
* * *
1438300 ATCTATTTTGGATGACATGTCTGCTCTACTATTCATTCAGGGGAGATCAGACTTGATATGTACCT
66 ATCAATTTTGGAAGACATGTCTGCT-TACTATTCATTCAGGGGAGATCAGACTTGATATGTGCCT
* * * *
1438365 CTTTTTTGGGTAGTCAGATCAATTTTGGAAGATGTGTCTGCTTCACTATTCATTTAGGGGAGATC
130 CTTTTTCGGGTAGTCAGATCAATTTTGGAAGACGTGTCTGCTCCACTATTCATTCAGGGGAGATC
*
1438430 AGACTTGATATGTGCCTCTTTTTCGGGTAGTCAGATCAATTTTGAAAGAC
195 AGACTTGATATGTGCCTCTTTTTCGGGTAGTCAGATCAATTTTGGAAGAC
*** * * * ** *
1438480 GTGTCTGCTCTAATATTCATTCAGGGGACATCAGACTTGATCTGTGTTTTTTTTTTCAGGTAGTC
1 AAATCTGCTCCACTATTCATTCAGGGGAGATCAGACTTGATCTGTG--CCTCTTTTCAGGTAGTC
* * * *
1438545 AGATCAATTTTGGAAGACA---------A--ATTCATTCAGGGGAGATTAAACTTAATTTTGTGC
64 AGATCAATTTTGGAAGACATGTCTGCTTACTATTCATTCAGGGGAGATCAGACTTGA-TATGTGC
*** * * * * *
1438599 CTCTTTTTCGGGTAGTCAGATCAATTTTGGAAGACAAATATGCTCTAATATTCATTCAGGGTATA
128 CTCTTTTTCGGGTAGTCAGATCAATTTTGGAAGACGTGTCTGCTCCACTATTCATTCAGGGGAGA
* * * * *
1438664 TCAGACTTGATCTGTACCTCTTTTTCGGCTAGTCAAATCAATTTTGGAAGAT
193 TCAGACTTGATATGTGCCTCTTTTTCGGGTAGTCAGATCAATTTTGGAAGAC
* * * * *
1438716 AAATATGCTCTACTATTCATTCAGGGAAGATCAGACTTGATTTGTGCCTCTTTTTCAGGTACTCA
1 AAATCTGCTCCACTATTCATTCAGGGGAGATCAGACTTGATCTGTGCCTC-TTTTCAGGTAGTCA
* * ** * * * * *
1438781 AATCTATTTTGGATTACGTGTCTGCTCTACTATTCATTCATGGGAGATTAAACTTGATATGTGTC
65 GATCAATTTTGGAAGACATGTCTGCT-TACTATTCATTCAGGGGAGATCAGACTTGATATGTGCC
* * *
1438846 T-TTTTTCGGGTAGTCTA-ATCTATTTTGGATGACGTGTCTGCTCCACTATTCATTCAAGGGAGA
129 TCTTTTTCGGGTAGTC-AGATCAATTTTGGAAGACGTGTCTGCTCCACTATTCATTCAGGGGAGA
*
1438909 TTAGACTTGATATGTGCCTCTTTTTCGGGTAGTCAGATCAATTTTGGAAGAC
193 TCAGACTTGATATGTGCCTCTTTTTCGGGTAGTCAGATCAATTTTGGAAGAC
* * *
1438961 AAATCTTCTCCACTATTCATTCAAGGGAGATCAGAC-TG--C-CT--CT-TTTTCAGGTAGTCAG
1 AAATCTGCTCCACTATTCATTCAGGGGAGATCAGACTTGATCTGTGCCTCTTTTCAGGTAGTCAG
* ** * * * * *
1439019 ATCAATTTTGGAAGAAAAATATGCTATACTATTCATTTAGGGGAGATCGGACTTGATCTATGCCT
66 ATCAATTTTGGAAGACATGTCTGCT-TACTATTCATTCAGGGGAGATCAGACTTGATATGTGCCT
*
1439084 CTTTTTCGGGTAGTCAGATCAATTTTGGAAGACATGTCTGCTCCACT
130 CTTTTTCGGGTAGTCAGATCAATTTTGGAAGACGTGTCTGCTCCACT
1439131 CTTGTTTCAA
Statistics
Matches: 743, Mismatches: 131, Indels: 51
0.80 0.14 0.06
Matches are distributed among these distances:
234 1 0.00
235 49 0.07
236 142 0.19
237 63 0.08
238 41 0.06
239 2 0.00
241 1 0.00
244 73 0.10
245 309 0.42
246 8 0.01
247 54 0.07
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (244 bp):
AAATCTGCTCCACTATTCATTCAGGGGAGATCAGACTTGATCTGTGCCTCTTTTCAGGTAGTCAG
ATCAATTTTGGAAGACATGTCTGCTTACTATTCATTCAGGGGAGATCAGACTTGATATGTGCCTC
TTTTTCGGGTAGTCAGATCAATTTTGGAAGACGTGTCTGCTCCACTATTCATTCAGGGGAGATCA
GACTTGATATGTGCCTCTTTTTCGGGTAGTCAGATCAATTTTGGAAGAC
Found at i:1439388 original size:167 final size:166
Alignment explanation
Indices: 1439162--1439611 Score: 590
Period size: 167 Copynumber: 2.7 Consensus size: 166
1439152 TCGAGATTGT
*
1439162 TTTGATTCGCTACTTTTTC---AAGACCAAATTTGGATGAGAAGAATCTGTTCCACTACTCTTCC
1 TTTGATTCGCTACTTTTTCAGGAAGACCAAATTGGGATGAGAAGAATCTGTTCCACTACTCTTCC
* * ** * *
1439224 GTGGAGATCGGACTCGAGGTTTATTTGATTCGTTGCTTTTTCAGAAAGACCAAATATGG-GTAAG
66 GTGGAGATCAGACTCGAGGTTGATTTGATTCACTGCTTTTTCAGGAAGACCAAATATGGAATAAG
*
1439288 AAGAA-ATGTTCCACTACTCTTTCATTTGAGGTTGA
131 AAGAATATATTCCACTACTCTTTCATTTGAGGTTGA
* *
1439323 TTTGATTCGCTATTTCTTTTCAGGAAGACCAAATCTGGGATGAAAAGAATCTGTTCCACTACTCT
1 TTTGATTCGCTA-CT-TTTTCAGGAAGACCAAAT-TGGGATGAGAAGAATCTGTTCCACTACTCT
* * * *
1439388 TTCGTGGAGATCAGACTCAAGGTTGATTTTATTCACTG-TTTTTCTAGGAAGACCAAATCTGGAA
63 TCCGTGGAGATCAGACTCGAGGTTGATTTGATTCACTGCTTTTTC-AGGAAGACCAAATATGGAA
* *
1439452 TGAGAAGAATCTATTCCACTACTCTTTCATTTGAGGTTGA
127 TAAGAAGAATATATTCCACTACTCTTTCATTTGAGGTTGA
* *
1439492 TTTGATTCGCTACTTTTTCATGAAGACCAAATTTGGG-TGAGAAGAATTTGTTCCACTACTCTTC
1 TTTGATTCGCTACTTTTTCAGGAAGACCAAA-TTGGGATGAGAAGAATCTGTTCCACTACTCTTC
* * * * * *
1439556 TGTGGAGATCAGATTTGAGATTGATTTGATTCACTACTTTTCCAGGAAGACCAAAT
65 CGTGGAGATCAGACTCGAGGTTGATTTGATTCACTGCTTTTTCAGGAAGACCAAAT
1439612 CTGTAATATT
Statistics
Matches: 249, Mismatches: 29, Indels: 17
0.84 0.10 0.06
Matches are distributed among these distances:
161 12 0.05
162 1 0.00
163 5 0.02
166 82 0.33
167 99 0.40
168 10 0.04
169 40 0.16
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (166 bp):
TTTGATTCGCTACTTTTTCAGGAAGACCAAATTGGGATGAGAAGAATCTGTTCCACTACTCTTCC
GTGGAGATCAGACTCGAGGTTGATTTGATTCACTGCTTTTTCAGGAAGACCAAATATGGAATAAG
AAGAATATATTCCACTACTCTTTCATTTGAGGTTGA
Found at i:1439552 original size:77 final size:78
Alignment explanation
Indices: 1439407--1439554 Score: 201
Period size: 78 Copynumber: 1.9 Consensus size: 78
1439397 ATCAGACTCA
* *
1439407 AGGTTGATTTTATTCACTGTTTTTCTAGGAAGACCAAATCTGGAATGAGAAGAATCTATTCCACT
1 AGGTTGATTTGATTCACTCTTTTTCTAGGAAGACCAAATCTGGAATGAGAAGAATCTATTCCACT
1439472 ACTCTTTCATTTG
66 ACTCTTTCATTTG
* * * * * *
1439485 AGGTTGATTTGATTCGCTACTTTTTC-ATGAAGACCAAATTTGG-GTGAGAAGAATTTGTTCCAC
1 AGGTTGATTTGATTCACT-CTTTTTCTAGGAAGACCAAATCTGGAATGAGAAGAATCTATTCCAC
1439548 TACTCTT
65 TACTCTT
1439555 CTGTGGAGAT
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
77 24 0.39
78 31 0.51
79 6 0.10
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (78 bp):
AGGTTGATTTGATTCACTCTTTTTCTAGGAAGACCAAATCTGGAATGAGAAGAATCTATTCCACT
ACTCTTTCATTTG
Found at i:1439571 original size:77 final size:79
Alignment explanation
Indices: 1439426--1439573 Score: 178
Period size: 77 Copynumber: 1.9 Consensus size: 79
1439416 TTATTCACTG
* * *
1439426 TTTTTCTAGGAAGACCAAATCTGGAATGAGAAGAATCTATTCCACTACTCTTTCATTTGAGGTTG
1 TTTTTCTAGGAAGACCAAATCTGGAATGAGAAGAATCTATTCCACTACTCTTTCATTGGAGATAG
1439491 ATTTGATTCGCTAC
66 ATTTGATTCGCTAC
* * * * *
1439505 TTTTTC-ATGAAGACCAAATTTGG-GTGAGAAGAATTTGTTCCACTACTC-TTC-TGTGGAGATC
1 TTTTTCTAGGAAGACCAAATCTGGAATGAGAAGAATCTATTCCACTACTCTTTCAT-TGGAGAT-
1439566 AGATTTGA
64 AGATTTGA
1439574 GATTGATTTG
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
75 1 0.02
76 8 0.14
77 29 0.49
78 15 0.25
79 6 0.10
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (79 bp):
TTTTTCTAGGAAGACCAAATCTGGAATGAGAAGAATCTATTCCACTACTCTTTCATTGGAGATAG
ATTTGATTCGCTAC
Found at i:1439701 original size:62 final size:62
Alignment explanation
Indices: 1439625--1440002 Score: 258
Period size: 62 Copynumber: 6.1 Consensus size: 62
1439615 TAATATTAAT
* * * ** *
1439625 TTCTCTTCATGAGGAAGTCAATGATTGACTCTACTGGGGATTCAGGGATAATAAAGGTTGAC
1 TTCTCTTCACGAGGAAGTCAAAGATTGACTCTACTGGGGAGTCAGAAATAACAAAGGTTGAC
* * *
1439687 TTCTCTTCACGAGGAAGTCTAGGATTGACTCTATTGGGGAGTCAGAAATAACAAAGGTTG--
1 TTCTCTTCACGAGGAAGTCAAAGATTGACTCTACTGGGGAGTCAGAAATAACAAAGGTTGAC
* * * ***
1439747 --------ACGAGGAAGTCAAAGATTGGCTCCT-CTGGGGAGTTAGGGATAATAATAAAAAATGA
1 TTCTCTTCACGAGGAAGTCAAAGATTGACT-CTACTGGGGAGTCA--GA-AATAACAAAGGTTGA
1439803 C
62 C
* ** * * *
1439804 TTCTCTTTATAAGGAAGTCAAAAATTGACTCCT-CTTCACGAGGGAGTCAGAAATAACAAAGATA
1 TTCTCTTCACGAGGAAGTCAAAGATTGACT-CTAC-T---G-GGGAGTCAGAAATAACAAAGGTT
*
1439868 GGC
60 GAC
* * *
1439871 TTCTCTTTACGAGGAAGTCAAGGATTGACTTTACTGGGGAGTCAAGAAATAACAAAGGTTGAC
1 TTCTCTTCACGAGGAAGTCAAAGATTGACTCTACTGGGGAGTC-AGAAATAACAAAGGTTGAC
* * * * ** ** * *
1439934 TTCTCTTCATGAGAAAGTTAATGATTGACTCTACTATGGAGTCAGGGATAACAAAAGTTAAC
1 TTCTCTTCACGAGGAAGTCAAAGATTGACTCTACTGGGGAGTCAGAAATAACAAAGGTTGAC
1439996 TTCTCTT
1 TTCTCTT
1440003 TATGATAAAG
Statistics
Matches: 248, Mismatches: 47, Indels: 42
0.74 0.14 0.12
Matches are distributed among these distances:
52 28 0.11
53 2 0.01
54 2 0.01
55 10 0.04
62 81 0.33
63 52 0.21
65 22 0.09
66 3 0.01
67 38 0.15
68 2 0.01
69 1 0.00
70 7 0.03
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (62 bp):
TTCTCTTCACGAGGAAGTCAAAGATTGACTCTACTGGGGAGTCAGAAATAACAAAGGTTGAC
Found at i:1439960 original size:63 final size:62
Alignment explanation
Indices: 1439844--1440020 Score: 201
Period size: 63 Copynumber: 2.8 Consensus size: 62
1439834 CCTCTTCACG
* * * * * * *
1439844 AGGGAGTCAGAAATAACAAAGATAGGCTTCTCTTTACGAGGAAGTCAAGGATTGACTTTACT
1 AGGGAGTCAGAAATAACAAAGGTTGACTTCTCTTTATGAGAAAGTTAAGGATTGACTCTACT
* * *
1439906 GGGGAGTCAAGAAATAACAAAGGTTGACTTCTCTTCATGAGAAAGTTAATGATTGACTCTACT
1 AGGGAGTC-AGAAATAACAAAGGTTGACTTCTCTTTATGAGAAAGTTAAGGATTGACTCTACT
* ** * * *
1439969 ATGGAGTCAGGGATAACAAAAGTTAACTTCTCTTTATGATAAAGTTAAGGAT
1 AGGGAGTCAGAAATAACAAAGGTTGACTTCTCTTTATGAGAAAGTTAAGGAT
1440021 AACAAATATT
Statistics
Matches: 95, Mismatches: 19, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
62 44 0.46
63 51 0.54
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (62 bp):
AGGGAGTCAGAAATAACAAAGGTTGACTTCTCTTTATGAGAAAGTTAAGGATTGACTCTACT
Found at i:1440058 original size:38 final size:38
Alignment explanation
Indices: 1439973--1440058 Score: 93
Period size: 38 Copynumber: 2.3 Consensus size: 38
1439963 TCTACTATGG
* *
1439973 AGTCAGGGATAACAAAAGTTAACTTCTCTTTATGATAA
1 AGTCAAGGATAACAAAAGTTAACTTCTCTTTATGAGAA
* * * *
1440011 AGTTAAGGATAACAAATA-TTGACTTCTGTTTATGAGGA
1 AGTCAAGGATAACAAA-AGTTAACTTCTCTTTATGAGAA
*
1440049 AGTCCAGGAT
1 AGTCAAGGAT
1440059 TGACTCTAGG
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
38 38 0.97
39 1 0.03
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (38 bp):
AGTCAAGGATAACAAAAGTTAACTTCTCTTTATGAGAA
Found at i:1449836 original size:60 final size:60
Alignment explanation
Indices: 1449725--1449838 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 60
1449715 AGTCGGTGAC
* * *
1449725 CATTTTGTAACTTTTAATTGTCAAAGGACTGAACAAAACAACATTCCATAGTCAAGAGAT
1 CATTTTGTAACTTTTAATAGTCAAAGGACTCAACAAAACAACATCCCATAGTCAAGAGAT
* * * *
1449785 CATTTTGTAACTTTTAATAGTCGAGGGACTCAACAAAGCAATA-CCCTATAGTCA
1 CATTTTGTAACTTTTAATAGTCAAAGGACTCAACAAAACAACATCCC-ATAGTCA
1449839 GGGACCATTT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
59 2 0.04
60 44 0.96
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (60 bp):
CATTTTGTAACTTTTAATAGTCAAAGGACTCAACAAAACAACATCCCATAGTCAAGAGAT
Found at i:1449949 original size:3 final size:3
Alignment explanation
Indices: 1449941--1450048 Score: 153
Period size: 3 Copynumber: 36.0 Consensus size: 3
1449931 TGAAGAATCA
* * * * *
1449941 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATG ATG ATG ATG ATG
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
1449989 ATG ATG ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1450037 ATT ATT ATT ATT
1 ATT ATT ATT ATT
1450049 TAATTTTAAG
Statistics
Matches: 103, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 103 1.00
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:1453749 original size:21 final size:20
Alignment explanation
Indices: 1453663--1453820 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
1453653 AAATGACCAA
**
1453663 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
1453682 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
1453702 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
1453722 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
1453743 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1453764 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1453784 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1453805 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1453821 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1453811 original size:20 final size:20
Alignment explanation
Indices: 1453787--1454057 Score: 274
Period size: 20 Copynumber: 13.5 Consensus size: 20
1453777 CGATTTTCCA
* ** *
1453787 AAATCGCAACGCGAATATGA
1 AAATCGCAACGAGAATCCGT
* *
1453807 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGAGAATC-CGT
* * *
1453827 AAATCGCAACGCGTATCTGT
1 AAATCGCAACGAGAATCCGT
* *
1453847 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGAGAATCCGT
* * *
1453867 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGAGAATCCGT
* * *
1453887 AAATCGCAACGATAATACAT
1 AAATCGCAACGAGAATCCGT
* *
1453907 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGAGAATCCGT
*
1453928 AAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGT
*
1453948 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCCGT
*
1453968 AAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGT
**
1453988 AAATCGCAACGAGAATTTGT
1 AAATCGCAACGAGAATCCGT
*
1454008 AAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGT
*
1454028 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCCGT
*
1454048 AAATCACAAC
1 AAATCGCAAC
1454058 ACTGAAATTT
Statistics
Matches: 210, Mismatches: 38, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
20 194 0.92
21 16 0.08
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGAGAATCCGT
Found at i:1454779 original size:24 final size:24
Alignment explanation
Indices: 1454740--1454786 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1454730 AAATTTGGTC
1454740 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1454764 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1454787 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:1457372 original size:33 final size:33
Alignment explanation
Indices: 1457268--1457375 Score: 173
Period size: 33 Copynumber: 3.2 Consensus size: 33
1457258 CGGAAATTAC
1457268 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
* *
1457301 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACGA-GAGAATCGCAATGC-GAAATGAA
1457335 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1457368 AATCGCAA
1 AATCGCAA
1457376 TGCGAAATGA
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
32 1 0.01
33 37 0.54
34 29 0.43
35 1 0.01
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.13
Consensus pattern (33 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:1457373 original size:19 final size:19
Alignment explanation
Indices: 1457282--1457432 Score: 143
Period size: 19 Copynumber: 8.7 Consensus size: 19
1457272 GCAACGAGAG
1457282 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1457301 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
1457315 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
1457335 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1457349 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1457368 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1457387 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
1457401 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
1457420 AATCGCATTGCGA
1 AATCGCAATGCGA
1457433 TTCTCCCGTT
Statistics
Matches: 108, Mismatches: 8, Indels: 32
0.73 0.05 0.22
Matches are distributed among these distances:
14 32 0.30
15 2 0.02
16 5 0.05
17 4 0.04
18 3 0.03
19 49 0.45
20 13 0.12
ACGTcount: A:0.45, C:0.19, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1457395 original size:52 final size:52
Alignment explanation
Indices: 1457310--1457432 Score: 219
Period size: 52 Copynumber: 2.3 Consensus size: 52
1457300 AAATCCCAAC
1457310 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1457363 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
1457415 ATTAAAATCGCATTGCGA
1 ATGAAAATCGCAATGCGA
1457433 TTCTCCCGTT
Statistics
Matches: 68, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
52 52 0.76
53 16 0.24
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:1457481 original size:19 final size:19
Alignment explanation
Indices: 1457441--1457538 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
1457431 GATTCTCCCG
1457441 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1457461 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1457480 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1457494 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1457513 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1457532 TTGCGAT
1 TTGCGAT
1457539 AGTCAATTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1457535 original size:52 final size:53
Alignment explanation
Indices: 1457422--1457538 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
1457412 GAAATTAAAA
1457422 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
*
1457475 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1457527 TCGCATTGCGAT
1 TCGCATTGCGAT
1457539 AGTCAATTTT
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 30 0.48
53 33 0.52
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:1457664 original size:14 final size:14
Alignment explanation
Indices: 1457645--1457681 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1457635 CATCAATTAC
1457645 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1457659 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1457673 ACAAATCAA
1 ACAAATCAA
1457682 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1459681 original size:14 final size:14
Alignment explanation
Indices: 1459662--1459718 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1459652 GCGAAATGAA
*
1459662 AATCGCAACGACAG
1 AATCGCAACGAAAG
1459676 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
1459693 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1459709 AATCGCAACG
1 AATCGCAACG
1459719 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1459689 original size:33 final size:33
Alignment explanation
Indices: 1459643--1459735 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1459633 GCGAAACCAA
*
1459643 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
1459676 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1459709 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1459736 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:1459700 original size:19 final size:19
Alignment explanation
Indices: 1459606--1459740 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
1459596 TAGTTTACTT
* *
1459606 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
1459626 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1459645 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1459664 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
1459678 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1459697 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
1459711 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1459730 TCGCAATGCGA
1 TCGCAACGCGA
1459741 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1459758 original size:19 final size:19
Alignment explanation
Indices: 1459736--1459864 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1459726 AAAATCGCAA
1459736 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1459755 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
1459769 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1459788 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
1459802 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1459821 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1459840 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
1459860 TGCGA
1 TGCGA
1459865 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:1459778 original size:33 final size:33
Alignment explanation
Indices: 1459736--1459827 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
1459726 AAAATCGCAA
1459736 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
1459769 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
1459802 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
1459828 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:1460048 original size:93 final size:93
Alignment explanation
Indices: 1459912--1460287 Score: 718
Period size: 93 Copynumber: 4.1 Consensus size: 93
1459902 ATGGATTGCA
*
1459912 TTAC-TTCAACCAATAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1459976 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1460004 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1460069 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1460097 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1460162 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
*
1460190 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAATT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
1460255 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1460283 TTACT
1 TTACT
1460288 AAGCAATCTA
Statistics
Matches: 280, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 4 0.01
93 276 0.99
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:1462032 original size:19 final size:19
Alignment explanation
Indices: 1462008--1462058 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
1461998 GCAACGAGAG
*
1462008 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATAAA
1462027 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATAAA
*
1462046 AATCGCAATGCGA
1 AATCGCAACGCGA
1462059 TTTTGGTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATAAA
Found at i:1462089 original size:14 final size:14
Alignment explanation
Indices: 1462070--1462126 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1462060 TTTGGTTTCG
1462070 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1462084 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1462103 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1462117 CGTTGCGATT
1 CGTTGCGATT
1462127 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1462102 original size:33 final size:33
Alignment explanation
Indices: 1462054--1462134 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
1462044 AAAATCGCAA
**
1462054 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1462087 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1462120 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
1462135 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:1462137 original size:21 final size:21
Alignment explanation
Indices: 1462111--1462186 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
1462101 CGCGTTGCGA
1462111 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
1462132 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
1462152 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
1462173 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
1462187 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:1462167 original size:41 final size:41
Alignment explanation
Indices: 1462110--1462187 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
1462100 TCGCGTTGCG
*
1462110 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
1462151 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1462188 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:1462308 original size:33 final size:33
Alignment explanation
Indices: 1462266--1462336 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1462256 AATACTAACT
*
1462266 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
1462299 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
1462332 TGAAA
1 TGAAA
1462337 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:1462570 original size:22 final size:22
Alignment explanation
Indices: 1462518--1462572 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
1462508 TGGTTGTGAG
**
1462518 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
** *
1462540 GGAAATCTTCGGAGATGTGGAC
1 GGATTTCTTCGGAGATGGGGAC
1462562 GGATTTCTTCG
1 GGATTTCTTCG
1462573 CCGTAGAGAG
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.20, C:0.16, G:0.38, T:0.25
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:1462745 original size:20 final size:20
Alignment explanation
Indices: 1462720--1462873 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
1462710 CTTTAAATAT
1462720 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1462740 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1462762 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1462781 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
1462801 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1462821 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1462841 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1462861 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1462874 TGGAAAATCG
Statistics
Matches: 113, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 94 0.83
21 15 0.13
22 2 0.02
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1462847 original size:40 final size:40
Alignment explanation
Indices: 1462719--1462873 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
1462709 GCTTTAAATA
*
1462719 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTGT
** * *
1462760 TATCGTTGCGATTTACGGATACGCGTTGCGATATACG-GAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-T
* *
1462800 ACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
* ** *
1462840 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTT
1462874 TGGAAAATCG
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
40 66 0.69
41 30 0.31
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.37
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
Found at i:1462890 original size:21 final size:21
Alignment explanation
Indices: 1462860--1462942 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
1462850 ATTTTCATAT
*
1462860 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
1462881 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
1462902 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
1462923 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
1462943 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:1462933 original size:42 final size:43
Alignment explanation
Indices: 1462840--1462938 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
1462830 ATTTATGTGT
* *
1462840 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
1462881 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
1462923 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
1462939 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:1463708 original size:44 final size:44
Alignment explanation
Indices: 1463636--1463722 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 44
1463626 ATTAAAAAAT
*
1463636 TATTGATTTACTAATAAATAATAAAAAATGA-TAAATTTGTAATC
1 TATTAATTTACTAATAAATAATAAAAAAT-ACTAAATTTGTAATC
* *
1463680 TATTAATTTTCTAATAAATAACT-AAAAATACTAAATTTTTAAT
1 TATTAATTTACTAATAAATAA-TAAAAAATACTAAATTTGTAAT
1463723 TTAAAAATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
43 1 0.03
44 36 0.95
45 1 0.03
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.41
Consensus pattern (44 bp):
TATTAATTTACTAATAAATAATAAAAAATACTAAATTTGTAATC
Found at i:1463732 original size:44 final size:44
Alignment explanation
Indices: 1463641--1463733 Score: 109
Period size: 44 Copynumber: 2.1 Consensus size: 44
1463631 AAAATTATTG
* **
1463641 ATTTACTAATAAATAATAAAAAATGATAAATTTGTAATCTATTA
1 ATTTTCTAATAAATAATAAAAAATGATAAATTTGTAATCTAAAA
* *
1463685 ATTTTCTAATAAATAACT-AAAAAT-ACTAAATTTTTAATTTAAAA
1 ATTTTCTAATAAATAA-TAAAAAATGA-TAAATTTGTAATCTAAAA
1463729 ATTTT
1 ATTTT
1463734 TTGTTTTACT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
43 1 0.02
44 40 0.95
45 1 0.02
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (44 bp):
ATTTTCTAATAAATAATAAAAAATGATAAATTTGTAATCTAAAA
Found at i:1470248 original size:23 final size:23
Alignment explanation
Indices: 1470222--1470269 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1470212 ATAAAGTACA
*
1470222 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
1470245 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
1470268 AT
1 AT
1470270 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:1470947 original size:334 final size:336
Alignment explanation
Indices: 1470309--1470983 Score: 1219
Period size: 334 Copynumber: 2.0 Consensus size: 336
1470299 TTATACCGAT
*
1470309 AGCATTACAAATTTACCTATTACATTATATTATATTATATTGAAAGTGTCCATACTTTTTATAAA
1 AGCATTACAAATTTACCTATTAC----TATTATATTATATTGAAAGTATCCATACTTTTTATAAA
* *
1470374 AAGGATCGATATTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTTATG
62 AAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATG
*
1470439 TTTTCCACCTATAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATA
127 TTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATA
* *
1470504 TTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAATAAA
192 TTTTATAAAATAATATTTAGAATTTTTAATTTAATAATAATATATATCGTAACGAAAAAAATAAA
*
1470569 TCATTAGACGTCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTA
257 TCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTA
1470634 ATGTTTTCCACAGTG
322 ATGTTTTCCACAGTG
* *
1470649 AGCATTGCAAATTTACCTATTAC-ATTATATTATATTGAAAGTATCCATACTTTTTATAAAAATG
1 AGCATTACAAATTTACCTATTACTATTATATTATATTGAAAGTATCCATACTTTTTATAAAAAGG
1470713 ATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAA-TTTTTTTAATAGTGTTTCATGTTTT
66 ATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTT
1470777 CCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTT
131 CCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTT
1470842 ATAAAATAATATTTAGAATTTTTAATTTAATAATAATATATATCGTAACGAAAAAAATAAATCAT
196 ATAAAATAATATTTAGAATTTTTAATTTAATAATAATATATATCGTAACGAAAAAAATAAATCAT
1470907 TAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGT
261 TAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGT
1470972 TTTCCACAGTG
326 TTTCCACAGTG
1470983 A
1 A
1470984 AAAAAGTATG
Statistics
Matches: 326, Mismatches: 9, Indels: 6
0.96 0.03 0.02
Matches are distributed among these distances:
334 227 0.70
335 77 0.24
340 22 0.07
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.43
Consensus pattern (336 bp):
AGCATTACAAATTTACCTATTACTATTATATTATATTGAAAGTATCCATACTTTTTATAAAAAGG
ATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTT
CCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTGATATTTT
ATAAAATAATATTTAGAATTTTTAATTTAATAATAATATATATCGTAACGAAAAAAATAAATCAT
TAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGT
TTTCCACAGTG
Found at i:1471051 original size:21 final size:22
Alignment explanation
Indices: 1471026--1471077 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
1471016 ACACTTTACA
*
1471026 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
1471049 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
1471072 ATATAA
1 ATATAA
1471078 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:1471062 original size:23 final size:23
Alignment explanation
Indices: 1471036--1471098 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1471026 ATATAACCAC
1471036 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
1471059 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
1471082 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1471099 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1471556 original size:39 final size:39
Alignment explanation
Indices: 1471502--1471588 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
1471492 TCAAGTTGTA
*
1471502 GATTTTGATTTCCTTTTGCTTAGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTAGCACCATATGAGATTTG
* *
1471541 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTAGCACCATATGAGATTTG
1471580 GATTTTGAT
1 GATTTTGAT
1471589 GAGCATCGGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.18, C:0.14, G:0.20, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTAGCACCATATGAGATTTG
Found at i:1471870 original size:18 final size:18
Alignment explanation
Indices: 1471847--1471883 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1471837 CGAAATATAT
1471847 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
1471865 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
1471883 A
1 A
1471884 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:1472857 original size:33 final size:33
Alignment explanation
Indices: 1472820--1472885 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1472810 CATCTTAATA
*
1472820 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
1472853 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
1472886 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:1472959 original size:21 final size:21
Alignment explanation
Indices: 1472919--1472983 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
1472909 CCCCTTATGC
* *
1472919 CTCTCGAGTGTATCTTCGACT
1 CTCTCGAGTTTCTCTTCGACT
*
1472940 CTCTCGAGTTTCTCTACGACT
1 CTCTCGAGTTTCTCTTCGACT
* * *
1472961 TTATCAAGTTTCTCTTCGACT
1 CTCTCGAGTTTCTCTTCGACT
1472982 CT
1 CT
1472984 TGATTGTCTT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.15, C:0.29, G:0.14, T:0.42
Consensus pattern (21 bp):
CTCTCGAGTTTCTCTTCGACT
Found at i:1475229 original size:17 final size:18
Alignment explanation
Indices: 1475207--1475249 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
1475197 ATATATCCGG
1475207 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
1475224 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
1475244 TATCAT
1 TATCAT
1475250 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:1475258 original size:20 final size:19
Alignment explanation
Indices: 1475212--1475263 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
1475202 TCCGGTATCA
1475212 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
1475231 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
*
1475252 TTTTACCTGTTT
1 TTTTACCGGTTT
1475264 ATCGTTGTGG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.07
20 23 0.82
21 3 0.11
ACGTcount: A:0.17, C:0.15, G:0.12, T:0.56
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:1475404 original size:20 final size:20
Alignment explanation
Indices: 1475378--1475423 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
1475368 CACTTTTAAA
1475378 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
1475397 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
1475418 TTTACC
1 TTTACC
1475424 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:1475923 original size:226 final size:226
Alignment explanation
Indices: 1475493--1475933 Score: 769
Period size: 225 Copynumber: 2.0 Consensus size: 226
1475483 AACTGCTTTA
1475493 AAAGTTATATAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATATTAA
1 AAAGTTATATAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATATTAA
**
1475558 TTTAATAATTTAATTTACACAAAATTTTATTTGATTGTTTTGATATTTTATAAATATTATTTAGA
66 TTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAATATTATTTAGA
* *
1475623 ATTAAATTTAACAATATTAACCAAATATAATAATAAATATGTTTTCAACAGTGAAATAAGTATGG
131 ATTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCAACAGTGAAATAAGTATGG
*
1475688 ACACTTTTATAAAAATGATATATACTTTTTG
196 ACACTTTTATAAAAAGGATATATACTTTTTG
*
1475719 AAAGTTATGTAATTTATGTTTCAATTT-TTTAATAGTGTTTCATGTTTTCCACCTACAATATTAA
1 AAAGTTATATAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATATTAA
*
1475783 TTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAG
66 TTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTAT-AAATATTATTTAG
* *
1475848 ATTTTAAATTTAACAATATTAACTAAAGATAATAATAAATATATTTTC-ACAGTGAAATAAGTAT
130 A-ATTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCAACAGTGAAATAAGTAT
1475912 GGACACTTTTATAAAAAGGATA
194 GGACACTTTTATAAAAAGGATA
1475934 GATAATTTAC
Statistics
Matches: 204, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
225 85 0.42
226 77 0.38
227 42 0.21
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.44
Consensus pattern (226 bp):
AAAGTTATATAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATATTAA
TTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAATATTATTTAGA
ATTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCAACAGTGAAATAAGTATGG
ACACTTTTATAAAAAGGATATATACTTTTTG
Found at i:1476445 original size:25 final size:25
Alignment explanation
Indices: 1476394--1476464 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
1476384 GAAGGATTTA
* * * *
1476394 TATAAATTTTTAAAGGGAAATGCACT
1 TATAAAATTTTAGA-GGAAGTGAACT
1476420 TATAAAATTTTAGAGGAAGTGAACT
1 TATAAAATTTTAGAGGAAGTGAACT
*
1476445 TATAAAATTTTAGAGAAAGT
1 TATAAAATTTTAGAGGAAGT
1476465 TAAACTTTAG
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
25 28 0.70
26 12 0.30
ACGTcount: A:0.45, C:0.04, G:0.17, T:0.34
Consensus pattern (25 bp):
TATAAAATTTTAGAGGAAGTGAACT
Found at i:1479062 original size:21 final size:21
Alignment explanation
Indices: 1479037--1479086 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
1479027 ATGGACAGTA
*
1479037 GGAAACAAGAAGATATTTACT
1 GGAAAAAAGAAGATATTTACT
*
1479058 GGAAAAAAGAAGATATTTATT
1 GGAAAAAAGAAGATATTTACT
*
1479079 AGAAAAAA
1 GGAAAAAA
1479087 ACAATGAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
GGAAAAAAGAAGATATTTACT
Found at i:1480587 original size:14 final size:14
Alignment explanation
Indices: 1480568--1480620 Score: 60
Period size: 14 Copynumber: 4.1 Consensus size: 14
1480558 CGTTCGTGAA
1480568 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
1480582 CGTTCGGTTATG-T
1 CGTTCGGTTATGTT
*
1480595 --TT-GTTTATGTT
1 CGTTCGGTTATGTT
*
1480606 CGTTCGATTATGTT
1 CGTTCGGTTATGTT
1480620 C
1 C
1480621 TTTTATGTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
10 6 0.18
11 3 0.09
13 3 0.09
14 21 0.64
ACGTcount: A:0.09, C:0.13, G:0.25, T:0.53
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:1480602 original size:24 final size:24
Alignment explanation
Indices: 1480575--1480633 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
1480565 GAACGTTCGG
*
1480575 TTATGTTCGTTCGGTTATGTT-TGT
1 TTATGTTCGTTCGATTATGTTCT-T
1480599 TTATGTTCGTTCGATTATGTTCTT
1 TTATGTTCGTTCGATTATGTTCTT
1480623 TTATGTTCGTT
1 TTATGTTCGTT
1480634 TATTTATGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
24 32 0.97
25 1 0.03
ACGTcount: A:0.10, C:0.10, G:0.20, T:0.59
Consensus pattern (24 bp):
TTATGTTCGTTCGATTATGTTCTT
Found at i:1480640 original size:24 final size:23
Alignment explanation
Indices: 1480575--1480644 Score: 79
Period size: 24 Copynumber: 2.9 Consensus size: 23
1480565 GAACGTTCGG
*
1480575 TTATGTTCGTTCGGTTATGTTTGT
1 TTATGTTCGTTC-ATTATGTTTGT
1480599 TTATGTTCGTTCGATTATGTTCT-T
1 TTATGTTCGTTC-ATTATGTT-TGT
*
1480623 TTATGTTCGTTTATTTATGTTT
1 TTATGTTCGTTCA-TTATGTTT
1480645 AACTCAATCT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
23 2 0.05
24 39 0.93
25 1 0.02
ACGTcount: A:0.11, C:0.09, G:0.19, T:0.61
Consensus pattern (23 bp):
TTATGTTCGTTCATTATGTTTGT
Found at i:1481010 original size:16 final size:16
Alignment explanation
Indices: 1480989--1481024 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
1480979 GTCTCCAATG
1480989 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
1481005 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
1481021 TTTA
1 TTTA
1481025 ATTATTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.11, C:0.11, G:0.19, T:0.58
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:1482994 original size:21 final size:21
Alignment explanation
Indices: 1482978--1483031 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
1482968 TTAAGCACCA
*
1482978 AAGTGCCACCAAAAAGCATCG
1 AAGTGCCACCAAAAAGCAACG
**
1482999 AAGTGCCACCATTAAGCAACG
1 AAGTGCCACCAAAAAGCAACG
1483020 AAGTGCCACCAA
1 AAGTGCCACCAA
1483032 TAACGTTTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.41, C:0.30, G:0.19, T:0.11
Consensus pattern (21 bp):
AAGTGCCACCAAAAAGCAACG
Found at i:1482995 original size:42 final size:42
Alignment explanation
Indices: 1482943--1483031 Score: 117
Period size: 42 Copynumber: 2.1 Consensus size: 42
1482933 TAAGTTCCAA
* * *
1482943 ACCAATAAGCATC-AGAGTGCTACAATTAAGCACCAAAGTGCC
1 ACCAAAAAGCATCGA-AGTGCCACAATTAAGCAACAAAGTGCC
* *
1482985 ACCAAAAAGCATCGAAGTGCCACCATTAAGCAACGAAGTGCC
1 ACCAAAAAGCATCGAAGTGCCACAATTAAGCAACAAAGTGCC
1483027 ACCAA
1 ACCAA
1483032 TAACGTTTAG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
42 40 0.98
43 1 0.02
ACGTcount: A:0.42, C:0.28, G:0.17, T:0.13
Consensus pattern (42 bp):
ACCAAAAAGCATCGAAGTGCCACAATTAAGCAACAAAGTGCC
Found at i:1483675 original size:81 final size:81
Alignment explanation
Indices: 1483581--1484312 Score: 1051
Period size: 81 Copynumber: 9.1 Consensus size: 81
1483571 AAGCATTTAG
* ** * * * * * *
1483581 TCTTTTACCCAAAGACATTTAGCCTTTCATCTAACTTGCATGATTGACACCTTTTTGCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGC
*
1483646 ACAGCTAGGCATTTAA
66 ACAGCTAGGCAATTAA
* * *
1483662 TCTTTAACTCAAAGGCATTTAGCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGC
1483727 ACAGCTAGGCAATTAA
66 ACAGCTAGGCAATTAA
* * * * *
1483743 TCTTTTACTCAAATGTATTTAACCTTTCATCAAAGTGGCATAAATGACATATTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGC
*
1483808 ACAACTAGGCAATTAA
66 ACAGCTAGGCAATTAA
*
1483824 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGC----TTGACACCTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGC
*
1483885 ACAACTAGGCAATTAA
66 ACAGCTAGGCAATTAA
1483901 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGC
**
1483966 ACAGCTAGATAATTAA
66 ACAGCTAGGCAATTAA
* * * * *
1483982 TCTTATACTCAAATGTATTTAACCTTTCATCTAACTAGCATAATTGACACTTTTCTGTCAAATGT
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGC
* *
1484047 ACAACTAGGAAATTAA
66 ACAGCTAGGCAATTAA
*
1484063 TCATTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGC
*
1484128 ACAGCTAGACAATTAA
66 ACAGCTAGGCAATTAA
* ** *
1484144 TCTTTTACTCAAATGTATTTAACCTTTCATCTAGTTGGCATAATTGACACCTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGC
*
1484209 A-ACGTTAGGCAATTAA
66 ACA-GCTAGGCAATTAA
* * *
1484225 TCTCTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACATATTTCTGTCAAGTGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGC
*
1484290 ACAACTAGGCAATTAA
66 ACAGCTAGGCAATTAA
1484306 TCTTTTA
1 TCTTTTA
1484313 TTTAAAACAG
Statistics
Matches: 583, Mismatches: 62, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
77 74 0.13
80 1 0.00
81 507 0.87
82 1 0.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.35
Consensus pattern (81 bp):
TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGC
ACAGCTAGGCAATTAA
Found at i:1484857 original size:94 final size:95
Alignment explanation
Indices: 1484720--1484901 Score: 287
Period size: 94 Copynumber: 1.9 Consensus size: 95
1484710 ACCATGGTAT
* *
1484720 CGATACTTATATACTGTGGTACCGATACTCCCTTTCAGTATCGATACCATTTCT-ACATTCTG-G
1 CGATACTTATATACTATGGTACCGATACTCCCTTTCAGTATCGATACCATTT-TGACATTCTGAA
1484783 ATCCATGGTATCGATACTTTCCTTCTAGTAC
65 ATCCATGGTATCGATACTTTCCTTCTAGTAC
* * * *
1484814 CGATACTTCTATACTATGGTACCGGTACTCCCTTTCAGTATCGATACCATTTTGGCATTTTGAAA
1 CGATACTTATATACTATGGTACCGATACTCCCTTTCAGTATCGATACCATTTTGACATTCTGAAA
1484879 TCCATGGTATCGATACTTTCCTT
66 TCCATGGTATCGATACTTTCCTT
1484902 TTTGGTATTG
Statistics
Matches: 80, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
93 1 0.01
94 55 0.69
95 24 0.30
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.38
Consensus pattern (95 bp):
CGATACTTATATACTATGGTACCGATACTCCCTTTCAGTATCGATACCATTTTGACATTCTGAAA
TCCATGGTATCGATACTTTCCTTCTAGTAC
Found at i:1491032 original size:81 final size:81
Alignment explanation
Indices: 1490905--1491471 Score: 736
Period size: 81 Copynumber: 7.1 Consensus size: 81
1490895 AAGCATTTAG
* * * * * ** *
1490905 TCTTTTACCCAAAGGCATTTAGCCTTTCATCTAACTTGCATGATTGACACATTTCTACCAAATAC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGC
* *
1490970 ACAGCTAGGCATTTAA
66 ACAACTAGGCAATTAA
* * * * *
1490986 TCTTTAACTCAAAGGCATTTAGCCTTTCGTCTAACTGGCATAATTGACAC-TATTCTATCAAATG
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACAT-TTCTGTCAAATG
* * *
1491050 CATAGCTAGACAATTAA
65 CACAACTAGGCAATTAA
* **
1491067 TCTTTTACTCAAAGGTATTTAACCTCTCATCTAACTGGCATAATTGACACCCTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGC
*
1491132 ACAACTAGACAATTAA
66 ACAACTAGGCAATTAA
*
1491148 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAAATGGCATAATTGACACATTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGC
*
1491213 AAAACTAGGCAATTAA
66 ACAACTAGGCAATTAA
**
1491229 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGATATAATTGACACATTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGC
*
1491294 ACAACTAGACAATTAA
66 ACAACTAGGCAATTAA
* * * *
1491310 TCTTTTACTC-AA---ATGT-A--TTTCATCTAACTGACATAATTGACACCTTTCTTTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGC
*
1491368 ACAACTAGGTAATTAA
66 ACAACTAGGCAATTAA
* * *
1491384 TCTTTTACTCAAAGATATTTAACCTTTCATCTAACTGGCATAATTAACACCTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGC
* *
1491449 ACAACTAGACAATTAT
66 ACAACTAGGCAATTAA
1491465 TCTTTTA
1 TCTTTTA
1491472 TTTGAAACAA
Statistics
Matches: 434, Mismatches: 43, Indels: 18
0.88 0.09 0.04
Matches are distributed among these distances:
74 62 0.14
75 2 0.00
76 1 0.00
77 3 0.01
78 3 0.01
79 1 0.00
80 3 0.01
81 359 0.83
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.35
Consensus pattern (81 bp):
TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGC
ACAACTAGGCAATTAA
Found at i:1493576 original size:2 final size:2
Alignment explanation
Indices: 1493571--1493637 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
1493561 TTGAGGAATG
1493571 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1493613 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1493638 TGTTTTTTTT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1494674 original size:13 final size:12
Alignment explanation
Indices: 1494642--1494675 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1494632 ACTATTTTTT
*
1494642 ATAACTTTTTAA
1 ATAATTTTTTAA
1494654 ATAATTTTTTAA
1 ATAATTTTTTAA
*
1494666 ATTATTTTTT
1 ATAATTTTTT
1494676 CAAGGTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (12 bp):
ATAATTTTTTAA
Found at i:1497307 original size:54 final size:54
Alignment explanation
Indices: 1497249--1497638 Score: 513
Period size: 54 Copynumber: 7.2 Consensus size: 54
1497239 CCGTGGTTTA
* * *
1497249 CACACATAGTGTCAAAACGATTATTCATCCACATATGATGAATTCTGTGAAATG
1 CACACTTAGTGCCAAAACGATTATTCATCCACATAGGATGAATTCTGTGAAATG
* * *
1497303 CACACTTAGTGCCGAAAGCG-TTATTCATCCACCTAGGATGAATTCCGTGAAATG
1 CACACTTAGTGCC-AAAACGATTATTCATCCACATAGGATGAATTCTGTGAAATG
* * * *
1497357 GACACTTAGTGCCGAAAC-AGTTATTCATCCACCTAGGATGAATTCCGTGAAATG
1 CACACTTAGTGCCAAAACGA-TTATTCATCCACATAGGATGAATTCTGTGAAATG
* * *
1497411 CACACTTAGTGCCGAAACGATTATTCATCCACCTAGGATGAATTCTGTAAAATG
1 CACACTTAGTGCCAAAACGATTATTCATCCACATAGGATGAATTCTGTGAAATG
* ** *
1497465 CACACTTAGTGCCAAAAAGGCTATTCATCCA-ACTAGGATGAATTTTGTGAAATG
1 CACACTTAGTGCCAAAACGATTATTCATCCACA-TAGGATGAATTCTGTGAAATG
*
1497519 CACACTTAGTGCCAAAACGGTTATTCATCCACATAGGATGAATTCTGTGAAATG
1 CACACTTAGTGCCAAAACGATTATTCATCCACATAGGATGAATTCTGTGAAATG
*
1497573 CACACTTAGTGCCGAAATA-G-TTATTCATCCACATAGGATGAATT-TCGTGAAATA
1 CACACTTAGTGCC-AAA-ACGATTATTCATCCACATAGGATGAATTCT-GTGAAATG
1497627 CACACTTAGTGC
1 CACACTTAGTGC
1497639 ATATTTGGTA
Statistics
Matches: 304, Mismatches: 23, Indels: 18
0.88 0.07 0.05
Matches are distributed among these distances:
53 4 0.01
54 288 0.95
55 11 0.04
56 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (54 bp):
CACACTTAGTGCCAAAACGATTATTCATCCACATAGGATGAATTCTGTGAAATG
Found at i:1497530 original size:162 final size:162
Alignment explanation
Indices: 1497249--1497638 Score: 570
Period size: 162 Copynumber: 2.4 Consensus size: 162
1497239 CCGTGGTTTA
* * * *
1497249 CACACATAGTGTCAAAACGATTATTCATCCACATATGATGAATTCTGTGAAATGCACACTTAGTG
1 CACACTTAGTGCCGAAACGATTATTCATCCACATAGGATGAATTCTGTGAAATGCACACTTAGTG
* * * * *
1497314 CCGAAAGCGTTATTCATCCACCTAGGATGAATTCCGTGAAATGGACACTTAGTGCCGAAACAGTT
66 CCAAAAGCGCTATTCATCCAACTAGGATGAATTCCGTGAAATGCACACTTAGTGCCAAAACAGTT
*
1497379 ATTCATCCACCTAGGATGAATTCCGTGAAATG
131 ATTCATCCACATAGGATGAATTCCGTGAAATG
* *
1497411 CACACTTAGTGCCGAAACGATTATTCATCCACCTAGGATGAATTCTGTAAAATGCACACTTAGTG
1 CACACTTAGTGCCGAAACGATTATTCATCCACATAGGATGAATTCTGTGAAATGCACACTTAGTG
** *
1497476 CCAAAAAG-GCTATTCATCCAACTAGGATGAATTTTGTGAAATGCACACTTAGTGCCAAAACGGT
66 CC-AAAAGCGCTATTCATCCAACTAGGATGAATTCCGTGAAATGCACACTTAGTGCCAAAACAGT
*
1497540 TATTCATCCACATAGGATGAATTCTGTGAAATG
130 TATTCATCCACATAGGATGAATTCCGTGAAATG
* *
1497573 CACACTTAGTGCCGAAA-TAGTTATTCATCCACATAGGATGAATT-TCGTGAAATACACACTTAG
1 CACACTTAGTGCCGAAACGA-TTATTCATCCACATAGGATGAATTCT-GTGAAATGCACACTTAG
1497636 TGC
64 TGC
1497639 ATATTTGGTA
Statistics
Matches: 205, Mismatches: 20, Indels: 6
0.89 0.09 0.03
Matches are distributed among these distances:
161 2 0.01
162 199 0.97
163 4 0.02
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (162 bp):
CACACTTAGTGCCGAAACGATTATTCATCCACATAGGATGAATTCTGTGAAATGCACACTTAGTG
CCAAAAGCGCTATTCATCCAACTAGGATGAATTCCGTGAAATGCACACTTAGTGCCAAAACAGTT
ATTCATCCACATAGGATGAATTCCGTGAAATG
Found at i:1497880 original size:22 final size:22
Alignment explanation
Indices: 1497855--1497905 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
1497845 TGTATAATAT
1497855 CAATTATTAGTATATTTCCTAA
1 CAATTATTAGTATATTTCCTAA
1497877 CAATTATTAGTATATTTCCTAA
1 CAATTATTAGTATATTTCCTAA
1497899 CAATTAT
1 CAATTAT
1497906 ACTTAAACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.37, C:0.14, G:0.04, T:0.45
Consensus pattern (22 bp):
CAATTATTAGTATATTTCCTAA
Found at i:1498010 original size:20 final size:21
Alignment explanation
Indices: 1497985--1498025 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
1497975 TGGCTCCTCA
1497985 GTATCGATAC-CCATACTATG
1 GTATCGATACACCATACTATG
1498005 GTATCGATACTACCATACTAT
1 GTATCGATAC-ACCATACTAT
1498026 AGTACCGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
22 9 0.47
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (21 bp):
GTATCGATACACCATACTATG
Found at i:1498037 original size:22 final size:22
Alignment explanation
Indices: 1497995--1498038 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1497985 GTATCGATAC
* *
1497995 CCATACTATGGTATCGATACTA
1 CCATACTATAGTACCGATACTA
*
1498017 CCATACTATAGTACCGTTACTA
1 CCATACTATAGTACCGATACTA
1498039 TGCTATAGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.32, C:0.25, G:0.11, T:0.32
Consensus pattern (22 bp):
CCATACTATAGTACCGATACTA
Found at i:1499288 original size:19 final size:19
Alignment explanation
Indices: 1499252--1499288 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1499242 TGAAAATGAT
*
1499252 TTGATTTTGAAAGCCAAAG
1 TTGATTTTGAAAACCAAAG
*
1499271 TTGATTTTGAAAATCAAA
1 TTGATTTTGAAAACCAAA
1499289 ATGAAAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (19 bp):
TTGATTTTGAAAACCAAAG
Found at i:1503959 original size:73 final size:72
Alignment explanation
Indices: 1503823--1503990 Score: 216
Period size: 73 Copynumber: 2.3 Consensus size: 72
1503813 AGTTTGTTTC
* * *
1503823 AAGAGAAACAATCTCAAGTGAGATATAATTCGTTTTAAGGAAAACAATCTTAAGTGAGATAAAAT
1 AAGAAAAACAATCTCAAGTGAGAGATAATTCGTTTTAAGAAAAACAATCTTAAGTGAGATAAAAT
1503888 ATATTTT
66 ATATTTT
* *
1503895 AAGAAAAACAATCTCGAA-TGAGACGA-AATTTGTTTTAAGAAAAAACAATCTTGAGTGAGATAA
1 AAGAAAAACAATCTC-AAGTGAGA-GATAATTCGTTTTAAG-AAAAACAATCTTAAGTGAGATAA
*
1503958 AATCTATTTT
63 AATATATTTT
*
1503968 TAGAAAAATC-ATCTCAAGTGAGA
1 AAGAAAAA-CAATCTCAAGTGAGA
1503991 TAAAATCTTG
Statistics
Matches: 84, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
72 33 0.39
73 50 0.60
74 1 0.01
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.29
Consensus pattern (72 bp):
AAGAAAAACAATCTCAAGTGAGAGATAATTCGTTTTAAGAAAAACAATCTTAAGTGAGATAAAAT
ATATTTT
Found at i:1503995 original size:36 final size:36
Alignment explanation
Indices: 1503823--1503998 Score: 178
Period size: 36 Copynumber: 4.9 Consensus size: 36
1503813 AGTTTGTTTC
* * *
1503823 AAGAGAAACAATCTCAAGTGAGATATAAT-TCGTTTT
1 AAGAAAAACAATCTCAAGTGAGATAAAATCT-ATTTT
* * *
1503859 AAGGAAAACAATCTTAAGTGAGATAAAATATATTTT
1 AAGAAAAACAATCTCAAGTGAGATAAAATCTATTTT
** * *
1503895 AAGAAAAACAATCTCGAA-TGAGACGAAATTTGTTTT
1 AAGAAAAACAATCTC-AAGTGAGATAAAATCTATTTT
**
1503931 AAGAAAAAACAATCTTGAGTGAGATAAAATCTATTTT
1 AAG-AAAAACAATCTCAAGTGAGATAAAATCTATTTT
*
1503968 TAGAAAAATC-ATCTCAAGTGAGATAAAATCT
1 AAGAAAAA-CAATCTCAAGTGAGATAAAATCT
1503999 TGAGTGAAAT
Statistics
Matches: 115, Mismatches: 20, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
36 84 0.73
37 31 0.27
ACGTcount: A:0.47, C:0.10, G:0.15, T:0.29
Consensus pattern (36 bp):
AAGAAAAACAATCTCAAGTGAGATAAAATCTATTTT
Found at i:1505423 original size:99 final size:99
Alignment explanation
Indices: 1505287--1505482 Score: 250
Period size: 99 Copynumber: 2.0 Consensus size: 99
1505277 TCAATTTAGT
* * * * * *** * *
1505287 TTGCCTTTTTTTTGGCTAGCTGAAGGATCTATCCATAAAGCTATGGCTTTTAATCAATTTCTATA
1 TTGCCTTTTATTTAGCTAACTGAAGAATCTATCCATAAAGCCAAAACTTTTAACCAATTGCTATA
* *
1505352 GAGGAATAGCTCATCTTTATTGTTTATATATATA
66 GAGGAATACCTCAACTTTATTGTTTATATATATA
*
1505386 TTGCC-TTTATTTAGCTAACTGAAGAAATCTATCCATAAAGCCAAAACTTTTAACCAATTGCTTT
1 TTGCCTTTTATTTAGCTAACTGAAG-AATCTATCCATAAAGCCAAAACTTTTAACCAATTGCTAT
*
1505450 ATAGGAATACCTCAACTTTATTGTTTATATATA
65 AGAGGAATACCTCAACTTTATTGTTTATATATA
1505483 ATTATATTAA
Statistics
Matches: 82, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
98 16 0.20
99 66 0.80
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (99 bp):
TTGCCTTTTATTTAGCTAACTGAAGAATCTATCCATAAAGCCAAAACTTTTAACCAATTGCTATA
GAGGAATACCTCAACTTTATTGTTTATATATATA
Found at i:1505740 original size:28 final size:29
Alignment explanation
Indices: 1505691--1505749 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
1505681 TTTAATTTTT
*
1505691 TTATTTTTTAATTTGTACCTTATATTATA
1 TTATATTTTAATTTGTACCTTATATTATA
1505720 TTATATTTT-ATTT-TAGCCTTATATTATA
1 TTATATTTTAATTTGTA-CCTTATATTATA
1505748 TT
1 TT
1505750 TATGGTCTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 2 0.07
28 18 0.64
29 8 0.29
ACGTcount: A:0.27, C:0.07, G:0.03, T:0.63
Consensus pattern (29 bp):
TTATATTTTAATTTGTACCTTATATTATA
Found at i:1506826 original size:23 final size:23
Alignment explanation
Indices: 1506800--1506923 Score: 104
Period size: 23 Copynumber: 5.3 Consensus size: 23
1506790 ATTAGTAGCG
* *
1506800 AAACTATGCCCGTTTTTGTACCA
1 AAACTATGCCCATTTTTGTACTA
* *** *
1506823 AAACTTTGCATGTTTTTGTACCA
1 AAACTATGCCCATTTTTGTACTA
* * *
1506846 AAACTATACCCATTTTTGAACTG
1 AAACTATGCCCATTTTTGTACTA
* *
1506869 AAACTTTGCCAATTTTTGTACTA
1 AAACTATGCCCATTTTTGTACTA
* * *
1506892 AAACTCTACCCATTTTTCGCACTA
1 AAACTATGCCCATTTTT-GTACTA
1506916 AAACTATG
1 AAACTATG
1506924 TTCGCAAATC
Statistics
Matches: 78, Mismatches: 22, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
23 67 0.86
24 11 0.14
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.37
Consensus pattern (23 bp):
AAACTATGCCCATTTTTGTACTA
Found at i:1506862 original size:46 final size:46
Alignment explanation
Indices: 1506800--1506908 Score: 130
Period size: 46 Copynumber: 2.4 Consensus size: 46
1506790 ATTAGTAGCG
* * * *
1506800 AAACTATGCCCGTTTTTGTACCAAAACTTTG-CATGTTTTTGTACCA
1 AAACTATACCCATTTTTGAACCAAAACTTTGCCA-ATTTTTGTACCA
** *
1506846 AAACTATACCCATTTTTGAACTGAAACTTTGCCAATTTTTGTACTA
1 AAACTATACCCATTTTTGAACCAAAACTTTGCCAATTTTTGTACCA
*
1506892 AAACTCTACCCATTTTT
1 AAACTATACCCATTTTT
1506909 CGCACTAAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
46 52 0.96
47 2 0.04
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.39
Consensus pattern (46 bp):
AAACTATACCCATTTTTGAACCAAAACTTTGCCAATTTTTGTACCA
Found at i:1513977 original size:18 final size:16
Alignment explanation
Indices: 1513934--1513977 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 16
1513924 TGTTATAACC
1513934 TTATTTTTATTGTTTT
1 TTATTTTTATTGTTTT
1513950 TTATAGTTTTATTTGTTATT
1 TTAT--TTTTA-TTGTT-TT
1513970 TTATTTTT
1 TTATTTTT
1513978 TTTATCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
16 4 0.17
18 9 0.38
19 5 0.21
20 6 0.25
ACGTcount: A:0.16, C:0.00, G:0.07, T:0.77
Consensus pattern (16 bp):
TTATTTTTATTGTTTT
Found at i:1513978 original size:19 final size:18
Alignment explanation
Indices: 1513935--1513978 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
1513925 GTTATAACCT
1513935 TATTTTTATTGTTTTTTA
1 TATTTTTATTGTTTTTTA
*
1513953 TAGTTTTATTTGTTATTTTA
1 TATTTTTA-TTGTT-TTTTA
1513973 T-TTTTT
1 TATTTTT
1513979 TTATCTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 7 0.32
19 9 0.41
20 6 0.27
ACGTcount: A:0.16, C:0.00, G:0.07, T:0.77
Consensus pattern (18 bp):
TATTTTTATTGTTTTTTA
Found at i:1515250 original size:21 final size:21
Alignment explanation
Indices: 1515224--1515266 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1515214 GTTTTTTTAT
1515224 AAGATTTCATGTCAACTACAA
1 AAGATTTCATGTCAACTACAA
* **
1515245 AAGATTTTATGTGGACTACAA
1 AAGATTTCATGTCAACTACAA
1515266 A
1 A
1515267 GACCTTGTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (21 bp):
AAGATTTCATGTCAACTACAA
Found at i:1515455 original size:37 final size:37
Alignment explanation
Indices: 1515369--1515469 Score: 130
Period size: 37 Copynumber: 2.7 Consensus size: 37
1515359 TTCGTCCTAC
* **
1515369 TAGGATTCAAACTCCTAAAAATAGGATAGAATTTTGC
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTCTAA
*
1515406 TAGGATTCAAACTCCTAAAAATAGGATAGAGTTCTAA
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTCTAA
** * *
1515443 TATTATTTAAACTCCTAAAGATAGGAT
1 TAGGATTCAAACTCCTAAAAATAGGAT
1515470 CCACAAGCAT
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.31
Consensus pattern (37 bp):
TAGGATTCAAACTCCTAAAAATAGGATAGAATTCTAA
Found at i:1515909 original size:15 final size:14
Alignment explanation
Indices: 1515889--1515934 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
1515879 TATACATATA
1515889 TATTTAATTATATTT
1 TATTTAATT-TATTT
1515904 TATTT-ATTTA-TT
1 TATTTAATTTATTT
1515916 TATTATAATTT-TTT
1 TATT-TAATTTATTT
1515930 TATTT
1 TATTT
1515935 TCTTTGCGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
12 6 0.21
13 4 0.14
14 13 0.46
15 5 0.18
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TATTTAATTTATTT
Found at i:1515920 original size:22 final size:23
Alignment explanation
Indices: 1515889--1515934 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 23
1515879 TATACATATA
1515889 TATTTAATTAT-ATTTTATTTATT
1 TATTTAATTATAATTTT-TTTATT
1515912 TATTT-ATTATAATTTTTTTATT
1 TATTTAATTATAATTTTTTTATT
1515934 T
1 T
1515935 TCTTTGCGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (23 bp):
TATTTAATTATAATTTTTTTATT
Found at i:1516022 original size:13 final size:13
Alignment explanation
Indices: 1515980--1516029 Score: 55
Period size: 13 Copynumber: 3.5 Consensus size: 13
1515970 ATATATATAT
1515980 TATTTTTTTATCTA
1 TATTTTTTTA-CTA
1515994 TGATTACTTATTTACTA
1 T-ATT--TT-TTTACTA
1516011 TATTTTTTTACTA
1 TATTTTTTTACTA
1516024 TATTTT
1 TATTTT
1516030 CCTAACGTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
13 13 0.41
14 3 0.09
15 3 0.09
16 3 0.09
17 6 0.19
18 4 0.12
ACGTcount: A:0.24, C:0.08, G:0.02, T:0.66
Consensus pattern (13 bp):
TATTTTTTTACTA
Found at i:1516146 original size:33 final size:34
Alignment explanation
Indices: 1516099--1516163 Score: 89
Period size: 33 Copynumber: 1.9 Consensus size: 34
1516089 ATTACGATTT
1516099 TTTAGTTAATATTATATG-TA-TATTTATTTTTCA
1 TTTAGTTAATATTAT-TGTTACTATTTATTTTTCA
* *
1516132 TTTATTTATTATTATTGTTACTATTTATTTTT
1 TTTAGTTAATATTATTGTTACTATTTATTTTT
1516164 TTATTATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 2 0.07
33 15 0.54
34 11 0.39
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (34 bp):
TTTAGTTAATATTATTGTTACTATTTATTTTTCA
Found at i:1516207 original size:20 final size:19
Alignment explanation
Indices: 1516182--1516248 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 19
1516172 TTATACATAC
1516182 ATTTTTATATTTTTATATAT
1 ATTTTT-TATTTTTATATAT
*
1516202 ATTTTTTTATTTTTTTATACT
1 A-TTTTTTATTTTTATATA-T
1516223 ATTTATTTATTTTTAT-TAT
1 ATTT-TTTATTTTTATATAT
*
1516242 GTTTTTT
1 ATTTTTT
1516249 GTTTCTTTGC
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
18 3 0.07
19 4 0.10
20 17 0.41
21 17 0.41
ACGTcount: A:0.22, C:0.01, G:0.01, T:0.75
Consensus pattern (19 bp):
ATTTTTTATTTTTATATAT
Found at i:1516236 original size:22 final size:22
Alignment explanation
Indices: 1516131--1516241 Score: 68
Period size: 22 Copynumber: 4.9 Consensus size: 22
1516121 TTTATTTTTC
*
1516131 ATTTATTTATTATTATTGT-TACT
1 ATTTATTTATT-TT-TTTTATACT
*
1516154 ATTTATTTTTTTATTATATTATACAT
1 ATTTATTTATTT-TT-T-TTATAC-T
* *
1516180 ACATT-TTTATATTTTTATATA-T
1 A-TTTATTTAT-TTTTTTTATACT
*
1516202 ATTTTTTTA-TTTTTTTATACT
1 ATTTATTTATTTTTTTTATACT
*
1516223 ATTTATTTATTTTTATTAT
1 ATTTATTTATTTTTTTTAT
1516242 GTTTTTTGTT
Statistics
Matches: 69, Mismatches: 9, Indels: 21
0.70 0.09 0.21
Matches are distributed among these distances:
20 9 0.13
21 11 0.16
22 16 0.23
23 12 0.17
24 5 0.07
25 4 0.06
26 8 0.12
27 4 0.06
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.68
Consensus pattern (22 bp):
ATTTATTTATTTTTTTTATACT
Found at i:1516343 original size:18 final size:19
Alignment explanation
Indices: 1516322--1516373 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
1516312 TTTTTGTATA
*
1516322 TATTTTTTTTTCTTC-ATT
1 TATTTTTTTTTATTCAATT
*
1516340 TATTTTATTTTATTCAATT
1 TATTTTTTTTTATTCAATT
*
1516359 TCATTTTTTTATATT
1 T-ATTTTTTTTTATT
1516374 TGTTTCATCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 13 0.46
19 4 0.14
20 11 0.39
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (19 bp):
TATTTTTTTTTATTCAATT
Found at i:1520905 original size:9 final size:9
Alignment explanation
Indices: 1520876--1520956 Score: 60
Period size: 9 Copynumber: 8.9 Consensus size: 9
1520866 CCAATCAAGA
*
1520876 AAAAAAAAG
1 AAAAAAAAC
* *
1520885 AAAATAAGC
1 AAAAAAAAC
1520894 AAAAAAAAC
1 AAAAAAAAC
1520903 AAAAAAAA-
1 AAAAAAAAC
1520911 AACAAAGAAAC
1 AA-AAA-AAAC
* *
1520922 AAGAGAAAC
1 AAAAAAAAC
1520931 AAGAACAAAA-
1 AA-AA-AAAAC
1520941 AAAAAAAA-
1 AAAAAAAAC
1520949 AAAAAAAA
1 AAAAAAAA
1520957 AAGGGACAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
8 14 0.24
9 32 0.55
10 7 0.12
11 5 0.09
ACGTcount: A:0.84, C:0.07, G:0.07, T:0.01
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:1520968 original size:1 final size:1
Alignment explanation
Indices: 1520875--1520958 Score: 51
Period size: 1 Copynumber: 84.0 Consensus size: 1
1520865 TCCAATCAAG
* * ** * * * * * * * * *
1520875 AAAAAAAAAGAAAATAAGCAAAAAAAACAAAAAAAAAACAAAGAAACAAGAGAAACAAGAACAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1520940 AAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAA
1520959 GGGACAAAAA
Statistics
Matches: 58, Mismatches: 25, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 58 1.00
ACGTcount: A:0.85, C:0.07, G:0.07, T:0.01
Consensus pattern (1 bp):
A
Found at i:1521279 original size:172 final size:171
Alignment explanation
Indices: 1520993--1521336 Score: 625
Period size: 172 Copynumber: 2.0 Consensus size: 171
1520983 CCCTAAAGAC
*
1520993 AAATGGCACATCAAGCTTCAAACTATGAGATTGATCAAGCACAATCATTCCTGAATCACTGAATC
1 AAATGGCACATCAAGCTTCAAACTATGAGATTGATCAAGCACAATCATTCCCGAATCACTGAATC
* * *
1521058 ACTTCACTCGAAGATCATAGAGCATCAAGAGATAGAAACATTTTGAGCAGGATTGAAGACATCAT
66 ACTTCACTCAAAGATCATAGAGCATCAAGAGAGAGAAACATTTTGAGCAGGATTGAAGACATCAG
*
1521123 AATGAATTGATCCTTGGTTCAACACCCTGAAACACTTGTTTG
131 AATGAATTGATCATTGGTTCAACACCCTGAAACACTT-TTTG
1521165 AAATGGCACATCAAGCTTCAAACTATGAGATTGATCAAGCACAATCATTCCCGAATCACTGAATC
1 AAATGGCACATCAAGCTTCAAACTATGAGATTGATCAAGCACAATCATTCCCGAATCACTGAATC
*
1521230 ACTTCACTCAAAGATCATGGAGCATCAAGAGAGAGAAACATTTTGAGCAGGATTGAAGACATCAG
66 ACTTCACTCAAAGATCATAGAGCATCAAGAGAGAGAAACATTTTGAGCAGGATTGAAGACATCAG
1521295 AATGAATTGATCATTGGTTCAACACCCTGAAACACTTTTTG
131 AATGAATTGATCATTGGTTCAACACCCTGAAACACTTTTTG
1521336 A
1 A
1521337 GCCTATTTAT
Statistics
Matches: 166, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
171 5 0.03
172 161 0.97
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.25
Consensus pattern (171 bp):
AAATGGCACATCAAGCTTCAAACTATGAGATTGATCAAGCACAATCATTCCCGAATCACTGAATC
ACTTCACTCAAAGATCATAGAGCATCAAGAGAGAGAAACATTTTGAGCAGGATTGAAGACATCAG
AATGAATTGATCATTGGTTCAACACCCTGAAACACTTTTTG
Found at i:1521761 original size:22 final size:22
Alignment explanation
Indices: 1521730--1521773 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1521720 AAGCTACCCC
* *
1521730 ATCAATCCTTTGAGTATCAAAT
1 ATCAAACCTTTGAGCATCAAAT
1521752 ATCAAACCTTTGAGCATCAAAT
1 ATCAAACCTTTGAGCATCAAAT
1521774 GCCAAACACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (22 bp):
ATCAAACCTTTGAGCATCAAAT
Found at i:1521779 original size:22 final size:22
Alignment explanation
Indices: 1521736--1521780 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1521726 CCCCATCAAT
* *
1521736 CCTTTGAGTATCAAATATCAAA
1 CCTTTGAGCATCAAATACCAAA
*
1521758 CCTTTGAGCATCAAATGCCAAA
1 CCTTTGAGCATCAAATACCAAA
1521780 C
1 C
1521781 ACAATAACCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.38, C:0.24, G:0.11, T:0.27
Consensus pattern (22 bp):
CCTTTGAGCATCAAATACCAAA
Found at i:1524324 original size:106 final size:106
Alignment explanation
Indices: 1522730--1524323 Score: 2476
Period size: 106 Copynumber: 15.0 Consensus size: 106
1522720 ATATCGTGCC
* * * * *
1522730 ACTCGAGACAACTCAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTCTCAACAAATAACTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAACTTCC
*
1522794 CAAATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
1522836 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1522901 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
1522942 ACTCCAGACAACACAAGTTCAACTTTACGACGAAGGGACCTCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1523007 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
1523048 ACTCAAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1523113 AATTTCAGAGCCAATTTTAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
1523154 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGATCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1523219 AGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
1523260 ACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGATGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1523325 AATTTCGGAGCCAATTTCAACTTCACAGCGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
1523366 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1523431 AATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGA
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
1523472 ACTCCAGACAACGCAAGTTTAACTTCAAGACGAAGGGACCGTTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1523537 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
1523578 ACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTTAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1523643 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
1523684 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
1523749 AATATC-GAAGCCAATTTCAACTTCACAGCTAAAGATATTGG
66 AATTTCAG-AGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
1523790 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1523855 AATTTCGGAGCTAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* ** * * *
1523896 ACTCCAGACAACGCAAGTTCAACTTCACGATGAATAGATCACTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1523961 AATTTCAGAGCCAATTTCAACTTCACAACTAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
1524002 ACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTAGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1524067 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
1524108 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
1524173 AATTTCGGAGCCAATTTCAACTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
1524214 ACTCGAGAAAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAATTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAACTTCC
* *
1524278 CGATTTCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
1524320 ACTC
1 ACTC
1524324 GGAACAATGC
Statistics
Matches: 1370, Mismatches: 113, Indels: 10
0.92 0.08 0.01
Matches are distributed among these distances:
105 3 0.00
106 1364 1.00
107 3 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:1525127 original size:37 final size:37
Alignment explanation
Indices: 1525077--1525147 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
1525067 TTTCGTCCTA
1525077 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTTT
1525114 CTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1525148 CTAATATTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (37 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTTT
Found at i:1525164 original size:37 final size:37
Alignment explanation
Indices: 1525078--1525178 Score: 139
Period size: 37 Copynumber: 2.7 Consensus size: 37
1525068 TTCGTCCTAC
* **
1525078 TAGGATTCAAACTCCTAAAAATAGGATAGAATTTTTC
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTCTAA
1525115 TAGGATTCAAACTCCTAAAAATAGGATAGAATTCTAA
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTCTAA
** * *
1525152 TATTATTTAAACTCCTAAAGATAGGAT
1 TAGGATTCAAACTCCTAAAAATAGGAT
1525179 CCACAAGCAT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.32
Consensus pattern (37 bp):
TAGGATTCAAACTCCTAAAAATAGGATAGAATTCTAA
Found at i:1525591 original size:2 final size:2
Alignment explanation
Indices: 1525578--1525690 Score: 74
Period size: 2 Copynumber: 58.5 Consensus size: 2
1525568 CCTTATTATT
* * *
1525578 TA TA TG TA TA TA TA TA TA TA TA TA TA T- TA TA T- TT TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * * * *
1525618 TT TA TT TA TT TA T- TT TT TCA TA T- TA TT TA TT TT TC TA T- TA
1 TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA
1525658 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1525691 GTTTACTTAT
Statistics
Matches: 88, Mismatches: 17, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
1 5 0.06
2 82 0.93
3 1 0.01
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.61
Consensus pattern (2 bp):
TA
Found at i:1525627 original size:17 final size:17
Alignment explanation
Indices: 1525610--1525651 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
1525600 TATATTATAT
1525610 TTTATTTATTT-AT-TTA
1 TTTATTT-TTTCATATTA
1525626 TTTATTTTTTCATATTA
1 TTTATTTTTTCATATTA
1525643 TTTATTTTT
1 TTTATTTTT
1525652 CTATTATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.12
16 9 0.38
17 12 0.50
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTATTTTTTCATATTA
Found at i:1525913 original size:13 final size:13
Alignment explanation
Indices: 1525897--1525950 Score: 58
Period size: 13 Copynumber: 4.1 Consensus size: 13
1525887 TATATATATT
1525897 TTTTATTTTTTTA
1 TTTTATTTTTTTA
1525910 TTTTATTTATTTTA
1 TTTTATTT-TTTTA
*
1525924 -TTTATTCTATTTA
1 TTTTATT-TTTTTA
1525937 -TTTATTTTTATTA
1 TTTTATTTTT-TTA
1525950 T
1 T
1525951 GTTTTTAGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
12 2 0.06
13 27 0.77
14 6 0.17
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTATTTTTTTA
Found at i:1525918 original size:9 final size:9
Alignment explanation
Indices: 1525898--1525943 Score: 69
Period size: 9 Copynumber: 5.3 Consensus size: 9
1525888 ATATATATTT
1525898 TTTATTTT-
1 TTTATTTTA
1525906 TTTATTTTA
1 TTTATTTTA
1525915 TTTATTTTA
1 TTTATTTTA
*
1525924 TTTATTCTA
1 TTTATTTTA
1525933 TTTA-TTTA
1 TTTATTTTA
1525941 TTT
1 TTT
1525944 TTATTATGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
8 14 0.40
9 21 0.60
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTATTTTA
Found at i:1525920 original size:4 final size:4
Alignment explanation
Indices: 1525883--1525943 Score: 61
Period size: 4 Copynumber: 14.8 Consensus size: 4
1525873 TTTTTATATT
* * *
1525883 TTTA TATA TATA TTT- TTTA TTTT TTTA TTTTA TTTA TTTTA TTTA TTCTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA -TTTA TTTA TT-TA
1525933 TTTA TTTA TTT
1 TTTA TTTA TTT
1525944 TTATTATGTT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
3 3 0.06
4 34 0.69
5 12 0.24
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:1525950 original size:22 final size:22
Alignment explanation
Indices: 1525811--1525950 Score: 67
Period size: 22 Copynumber: 6.4 Consensus size: 22
1525801 TATATGTATA
*
1525811 TTTATTTTTC-ATTTATTTATT
1 TTTATTATTCTATTTATTTATT
* * *
1525832 ATTATTGTTACTATTTA-GTA-T
1 TTTATTATT-CTATTTATTTATT
** **
1525853 TTTATTATAT-TATACATACATT
1 TTTATTAT-TCTATTTATTTATT
* * *
1525875 TTTA-TATTTTTATATATATATTT
1 TTTATTA-TTCTATTTATTTA-TT
* *
1525898 TTTATTTTTTTATTTTATTTA-T
1 TTTATTATTCTA-TTTATTTATT
1525920 TTTATTTATTCTATTTATTTATT
1 TTTA-TTATTCTATTTATTTATT
1525943 TTTATTAT
1 TTTATTAT
1525951 GTTTTTAGTT
Statistics
Matches: 91, Mismatches: 16, Indels: 23
0.70 0.12 0.18
Matches are distributed among these distances:
20 4 0.04
21 18 0.20
22 35 0.38
23 27 0.30
24 7 0.08
ACGTcount: A:0.26, C:0.04, G:0.01, T:0.69
Consensus pattern (22 bp):
TTTATTATTCTATTTATTTATT
Found at i:1525955 original size:10 final size:10
Alignment explanation
Indices: 1525809--1525948 Score: 53
Period size: 12 Copynumber: 13.4 Consensus size: 10
1525799 ATTATATGTA
1525809 TATTTATTTT
1 TATTTATTTT
1525819 TCATTTATTTAT
1 T-ATTTATTT-T
1525831 TA-TTATTGTT
1 TATTTATT-TT
1525841 ACTATTTAGTATTT
1 --TATTTA-T-TTT
*
1525855 TATTATATTATA
1 TATT-TATT-TT
* **
1525867 CATACATTTT
1 TATTTATTTT
1525877 TA--TATTTT
1 TATTTATTTT
*
1525885 TATATATATATT
1 TAT-T-TATTTT
1525897 T-TTTA-TTT
1 TATTTATTTT
1525905 T-TTTA-TTT
1 TATTTATTTT
1525913 TATTTA-TTT
1 TATTTATTTT
1525922 TATTTATTCTATT
1 TATTTA-T-T-TT
1525935 TATTTATTTT
1 TATTTATTTT
1525945 TATT
1 TATT
1525949 ATGTTTTTAG
Statistics
Matches: 102, Mismatches: 9, Indels: 38
0.68 0.06 0.26
Matches are distributed among these distances:
8 18 0.18
9 15 0.15
10 16 0.16
11 16 0.16
12 20 0.20
13 13 0.13
14 3 0.03
15 1 0.01
ACGTcount: A:0.26, C:0.04, G:0.01, T:0.69
Consensus pattern (10 bp):
TATTTATTTT
Found at i:1526057 original size:18 final size:19
Alignment explanation
Indices: 1526033--1526078 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
1526023 TGTATATATA
*
1526033 TTTTTTTCTTC-ATTT-AT
1 TTTTTTTATTCAATTTCAT
1526050 TTTATTTTATTCAATTTCAT
1 TTT-TTTTATTCAATTTCAT
1526070 TTTTTTTAT
1 TTTTTTTAT
1526079 ATTTGTTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 3 0.12
18 7 0.28
19 10 0.40
20 5 0.20
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTTTTATTCAATTTCAT
Found at i:1529583 original size:316 final size:310
Alignment explanation
Indices: 1529016--1529648 Score: 1104
Period size: 316 Copynumber: 2.0 Consensus size: 310
1529006 AAGATCCAAC
* *
1529016 TCGATTAATTCTAATATAACTCTATTGAACCCCAAAAAAGAGCTAACCCTTTATTAAAGAAAGTG
1 TCGATTAATTCCAATATAACTCTATTGAACCCCAAAAAAGAGCTAACCCATTATTAAAGAAAGTG
1529081 GTGATGATGGAAATCATCAAGTGGATCGATATTGGAGTAATCTACCCAATATCCAATAATTCATG
66 GTGATGATGGAAATCATCAAGTGGATCGATATTGGAGTAATCTACCCAATATCCAATAATTCATG
* * * *
1529146 GGTCAGGCTGGTGCAATGCGTGCCCAAGAAAGGAGGCGTGATTGTGATGAGTAATGAAGACAATG
131 GGTCAGGCTGGTGCAATACGTGCCCAAGAAAAGAGGCATGATTGTGATGAGCAATGAAGACAATG
1529211 AACTATTACTGACGAGAACTTTCACAAGATGGAGGATATGTATAGATTATCAAAAGCTCAGCAAG
196 AACTATTACTGACGAGAACTTTCACAAGATGGAGGATATGTATAGATTATCAAAAGCTCAGCAAG
*
1529276 GCGATGAGGAATGATCATTTCCCTCTTCCTTTTATCTATCAAATGCTGGA
261 GCGATGAGGAATGATCATTTCCCTCTTCCTTTTATCTATCAAATGATGGA
* *
1529326 TCGATTAATTCCAATATAACTCTATTGAACCCCAAAAAAGAGCTAACGCATTATTAAATAAAGTG
1 TCGATTAATTCCAATATAACTCTATTGAACCCCAAAAAAGAGCTAACCCATTATTAAAGAAAGT-
1529391 GTGATGATGGTGATGGAAATCATCAAGTGGATCGATATTGGAGTAATCTACCCAATATCCAATAA
65 G-G-TGA---TGATGGAAATCATCAAGTGGATCGATATTGGAGTAATCTACCCAATATCCAATAA
*
1529456 TTCATGGGTCAGGCTGGTTCAATACGTGCCCAAGAAAAGAGGCATGATTGTGATGAGCAATGAAG
125 TTCATGGGTCAGGCTGGTGCAATACGTGCCCAAGAAAAGAGGCATGATTGTGATGAGCAATGAAG
*
1529521 ACAATGAACTATTACTGACGAGAACTTTCAGAAGATGGAGGATATGTATAGATTATCAAAAGCTC
190 ACAATGAACTATTACTGACGAGAACTTTCACAAGATGGAGGATATGTATAGATTATCAAAAGCTC
*
1529586 AGCAAGGCGATGATGAATGATCATTTCCCTCTTCCTTTTATCTATCAAATGATGGA
255 AGCAAGGCGATGAGGAATGATCATTTCCCTCTTCCTTTTATCTATCAAATGATGGA
1529642 TCGATTA
1 TCGATTA
1529649 GTGGGAAAAG
Statistics
Matches: 305, Mismatches: 12, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
310 60 0.20
311 1 0.00
312 1 0.00
313 3 0.01
316 240 0.79
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (310 bp):
TCGATTAATTCCAATATAACTCTATTGAACCCCAAAAAAGAGCTAACCCATTATTAAAGAAAGTG
GTGATGATGGAAATCATCAAGTGGATCGATATTGGAGTAATCTACCCAATATCCAATAATTCATG
GGTCAGGCTGGTGCAATACGTGCCCAAGAAAAGAGGCATGATTGTGATGAGCAATGAAGACAATG
AACTATTACTGACGAGAACTTTCACAAGATGGAGGATATGTATAGATTATCAAAAGCTCAGCAAG
GCGATGAGGAATGATCATTTCCCTCTTCCTTTTATCTATCAAATGATGGA
Found at i:1536204 original size:13 final size:13
Alignment explanation
Indices: 1536163--1536212 Score: 57
Period size: 13 Copynumber: 3.6 Consensus size: 13
1536153 TAGAAATAGT
1536163 TAAAATAACTAAAA
1 TAAAATAAC-AAAA
1536177 TATTAACATAA-AAAA
1 TA--AA-ATAACAAAA
1536192 TAAAATAACAAAA
1 TAAAATAACAAAA
1536205 TAAAATAA
1 TAAAATAA
1536213 AATTGCACGT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
12 4 0.12
13 14 0.44
14 2 0.06
15 6 0.19
16 2 0.06
17 4 0.12
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (13 bp):
TAAAATAACAAAA
Done.