Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007911.1 Hibiscus syriacus cultivar Beakdansim tig00110307_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: 1972160
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 9
Found at i:1408293 original size:36 final size:38
Alignment explanation
Indices: 1408218--1408294 Score: 104
Period size: 36 Copynumber: 2.1 Consensus size: 38
1408208 TCGTACGGAG
* *
1408218 CACCTAATCATATTTAATTCGGATGACTCGCACGGGAA
1 CACCTAATCATATTTAATTCGGATAACTCGCACGAGAA
* *
1408256 CACCTAATCATA-TT-ATTTGGGTAACTCGCACGAGAA
1 CACCTAATCATATTTAATTCGGATAACTCGCACGAGAA
1408292 CAC
1 CAC
1408295 TGAAGAATAG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 21 0.60
37 2 0.06
38 12 0.34
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (38 bp):
CACCTAATCATATTTAATTCGGATAACTCGCACGAGAA
Found at i:1409049 original size:25 final size:26
Alignment explanation
Indices: 1409020--1409089 Score: 97
Period size: 27 Copynumber: 2.7 Consensus size: 26
1409010 CCCTACGCGC
*
1409020 CCCTCTCCCCTTCTCTCTCAT-CCAT
1 CCCTCTCCCCTTCCCTCTCATCCCAT
* *
1409045 CCCTCTCCCTTTCCCTCTCATCCCCGT
1 CCCTCTCCCCTTCCCTCTCAT-CCCAT
1409072 CCCTCTCCCCTTCCCTCT
1 CCCTCTCCCCTTCCCTCT
1409090 TAGGGAACAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
25 19 0.49
27 20 0.51
ACGTcount: A:0.04, C:0.60, G:0.01, T:0.34
Consensus pattern (26 bp):
CCCTCTCCCCTTCCCTCTCATCCCAT
Found at i:1411174 original size:2 final size:2
Alignment explanation
Indices: 1411167--1411206 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1411157 GTAGTAAATC
*
1411167 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA 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
1411207 CTAATTTATG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1412212 original size:18 final size:20
Alignment explanation
Indices: 1412167--1412223 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 20
1412157 CGAGGGATTA
1412167 TCAGTGGTCCTTCAGGACAG
1 TCAGTGGTCCTTCAGGACAG
*
1412187 TCAGTGGTCCTTCGGGACA-
1 TCAGTGGTCCTTCAGGACAG
*
1412206 T-AGTGGTCATTCAGGACA
1 TCAGTGGTCCTTCAGGACA
1412224 AATATTCAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
18 15 0.44
19 1 0.03
20 18 0.53
ACGTcount: A:0.21, C:0.23, G:0.30, T:0.26
Consensus pattern (20 bp):
TCAGTGGTCCTTCAGGACAG
Found at i:1412458 original size:23 final size:24
Alignment explanation
Indices: 1412432--1412478 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
1412422 TAAGATCATA
*
1412432 TGATAAAAAGGAATAT-ATGATAT
1 TGATAAAAAGGAAGATGATGATAT
*
1412455 TGATAAAAATGAAGATGATGATAT
1 TGATAAAAAGGAAGATGATGATAT
1412479 AGTTGCTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.51, C:0.00, G:0.19, T:0.30
Consensus pattern (24 bp):
TGATAAAAAGGAAGATGATGATAT
Found at i:1417486 original size:18 final size:18
Alignment explanation
Indices: 1417445--1417533 Score: 97
Period size: 18 Copynumber: 4.7 Consensus size: 18
1417435 GGATTATCAT
*
1417445 TGGTCCTTCGGGACAAACAG
1 TGGTCCTTCGGGAC--ATAG
1417465 TGGTCCTTCGGGACATAG
1 TGGTCCTTCGGGACATAG
* * *
1417483 TGGTTCTTCGGAATAGTCAG
1 TGGTCCTTCGGGACA-T-AG
*
1417503 TGGTCCTTCAGGACATAG
1 TGGTCCTTCGGGACATAG
1417521 TGGTCCTTCGGGA
1 TGGTCCTTCGGGA
1417534 TAACTATTCA
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
18 29 0.50
19 2 0.03
20 27 0.47
ACGTcount: A:0.19, C:0.21, G:0.31, T:0.28
Consensus pattern (18 bp):
TGGTCCTTCGGGACATAG
Found at i:1429864 original size:43 final size:43
Alignment explanation
Indices: 1429816--1430067 Score: 247
Period size: 43 Copynumber: 5.9 Consensus size: 43
1429806 TTTTTTGACA
* * *
1429816 AAAAACGCCGCAATAGGTATTGATATTTAGAGGCGTTTGTCAG
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCAC
* *
1429859 AAAAACGCCACAATAGGTGTTGATATTTAGCGGCGTTTGTCAT
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCAC
* * * * *
1429902 AAAAATGCCGCAATAGGTGTTGATATTTAGCGGCATTTTTTAG
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCAC
* * * * *
1429945 ACAAACGCCGCAGTAGGTGTTGATGTTTTGCGGCGTTT-TCCC
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCAC
* * * * * *
1429987 ACAAACGCCGCAGTAGGTGTTGATGTTTTGCGGCGTTTTTCTC
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCAC
* * * * *
1430030 ACAAGCGCCGCAGTAGGTATTGA-ATTTTTGCGGCGTTT
1 AAAAACGCCGCAATAGGTGTTGATA-TTTAGCGGCGTTT
1430068 TTGCTAAAGG
Statistics
Matches: 184, Mismatches: 23, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
42 39 0.21
43 145 0.79
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (43 bp):
AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCAC
Found at i:1430026 original size:85 final size:84
Alignment explanation
Indices: 1429816--1430068 Score: 283
Period size: 86 Copynumber: 3.0 Consensus size: 84
1429806 TTTTTTGACA
* * * * * * *
1429816 AAAAACGCCGCAATAGGTATTGATATTTAGAGGCGTTTGTCAGAAAAACGCCACAATAGGTGTTG
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTTAGACAAACGCCGCAGTAGGTGTTG
* *
1429881 ATATTTAGCGGCGTTTGTCAT
66 AT-TTTTGCGGCGTTT-TCAC
* *
1429902 AAAAATGCCGCAATAGGTGTTGATATTTAGCGGCATTTTTTAGACAAACGCCGCAGTAGGTGTTG
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTTAGACAAACGCCGCAGTAGGTGTTG
*
1429967 ATGTTTTGCGGCGTTTTCCC
66 AT-TTTTGCGGCGTTTTCAC
* * * * * * *
1429987 ACAAACGCCGCAGTAGGTGTTGATGTTTTGCGGCGTTTTTCT-CACAAGCGCCGCAGTAGGTATT
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTT-TAGACAAACGCCGCAGTAGGTGTT
1430051 GAATTTTTGCGGCGTTTT
65 G-ATTTTTGCGGCGTTTT
1430069 TGCTAAAGGT
Statistics
Matches: 143, Mismatches: 22, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
85 70 0.49
86 73 0.51
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (84 bp):
AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTTAGACAAACGCCGCAGTAGGTGTTG
ATTTTTGCGGCGTTTTCAC
Found at i:1430497 original size:21 final size:21
Alignment explanation
Indices: 1430473--1430538 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
1430463 TTGCTGATAT
1430473 GCTGCTTCTCTCTGTGCTACC
1 GCTGCTTCTCTCTGTGCTACC
* *
1430494 GCTGCTTCTCTCTGTGTTACT
1 GCTGCTTCTCTCTGTGCTACC
* * *
1430515 GCTGCTTCTTTCTCTGCTTCC
1 GCTGCTTCTCTCTGTGCTACC
1430536 GCT
1 GCT
1430539 ACTGTTCTGG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.03, C:0.35, G:0.18, T:0.44
Consensus pattern (21 bp):
GCTGCTTCTCTCTGTGCTACC
Found at i:1438579 original size:185 final size:187
Alignment explanation
Indices: 1438262--1438641 Score: 595
Period size: 185 Copynumber: 2.0 Consensus size: 187
1438252 CTATCGCTGT
1438262 GTTTTTTGAAGAAACGTCGCTATTTGATAAACATTAAATTAAATGTATGTATGTACCTATTGCGG
1 GTTTTTTGAAGAAACGTCGCTATTTGATAAACATTAAATTAAA--TATGTATGTACCTATTGCGG
* * * *
1438327 CGTTTTTTGAAAAAACGCCACGATTGATAAAGTCTATTGCGGCTTTTGAAGACAAACGCCACTAA
64 CGTTTTTTGAAAAAACACCACGATTGATAAAGCCTATCGCGGCGTTTGAAGACAAACGCCACTAA
* *
1438392 AGTACACTTTATTACGGTGTTTGTTACTAAAACGCCACTATTAATGAACCTATTGTGGC
129 AGTACACTTTATTACGGCGTTTGTTACTAAAACGCCACTATTAATGAACCTATTGCGGC
*
1438451 GTTTTTTGAAGAAACG-CTGCTATTTGATAAACATTAAATT-AA-ATGTATGTACCTATTGTGGC
1 GTTTTTTGAAGAAACGTC-GCTATTTGATAAACATTAAATTAAATATGTATGTACCTATTGCGGC
* * * *
1438513 TTTTTTTGAAAAAACACCATGATTGATAAAGCCTATCGCGGCGTTTGTAGACAAACGCCGCTAAA
65 GTTTTTTGAAAAAACACCACGATTGATAAAGCCTATCGCGGCGTTTGAAGACAAACGCCACTAAA
* *
1438578 GTACACTTTATTACGGCGTTTGTTACTAAAATGCCACTATTAATGAACTTATTGCGGC
130 GTACACTTTATTACGGCGTTTGTTACTAAAACGCCACTATTAATGAACCTATTGCGGC
1438636 GTTTTT
1 GTTTTT
1438642 AGATACAAAC
Statistics
Matches: 177, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
185 136 0.77
188 3 0.02
189 38 0.21
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (187 bp):
GTTTTTTGAAGAAACGTCGCTATTTGATAAACATTAAATTAAATATGTATGTACCTATTGCGGCG
TTTTTTGAAAAAACACCACGATTGATAAAGCCTATCGCGGCGTTTGAAGACAAACGCCACTAAAG
TACACTTTATTACGGCGTTTGTTACTAAAACGCCACTATTAATGAACCTATTGCGGC
Found at i:1439382 original size:37 final size:37
Alignment explanation
Indices: 1439341--1439414 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
1439331 CATCGGTTAT
* *
1439341 TTATCCATTCCTCTATCATCGTTCTCAATAAGTTTCG
1 TTATCCATTCCTCTATCATCATTCTCAATAAGCTTCG
1439378 TTATCCATTCCTCTATCATCATTCTCAATAAGCTTCG
1 TTATCCATTCCTCTATCATCATTCTCAATAAGCTTCG
1439415 AAGATCCTAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.23, C:0.28, G:0.07, T:0.42
Consensus pattern (37 bp):
TTATCCATTCCTCTATCATCATTCTCAATAAGCTTCG
Found at i:1440113 original size:42 final size:42
Alignment explanation
Indices: 1440054--1440144 Score: 128
Period size: 42 Copynumber: 2.2 Consensus size: 42
1440044 GCATTTTAGA
* * * *
1440054 TATAAACGCCGCTAATTTATCACTATATTATGGTATTTGTGG
1 TATAAACGCCACTAATTTATAAATATATTATGGCATTTGTGG
* *
1440096 TATAAACGCCACTAATTTATAAATATATTGTGGCGTTTGTGG
1 TATAAACGCCACTAATTTATAAATATATTATGGCATTTGTGG
1440138 TATAAAC
1 TATAAAC
1440145 TCGCTAAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.38
Consensus pattern (42 bp):
TATAAACGCCACTAATTTATAAATATATTATGGCATTTGTGG
Found at i:1445958 original size:20 final size:20
Alignment explanation
Indices: 1445930--1445967 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1445920 TTTTGCAGAA
1445930 AAATAATCCCCAACGGCTCC
1 AAATAATCCCCAACGGCTCC
*
1445950 AAATCATCCCCAACGGCT
1 AAATAATCCCCAACGGCT
1445968 AGAAACAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.39, G:0.11, T:0.16
Consensus pattern (20 bp):
AAATAATCCCCAACGGCTCC
Found at i:1448661 original size:3 final size:3
Alignment explanation
Indices: 1448655--1448680 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1448645 TCATCAATAG
1448655 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
1448681 ACACAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1450152 original size:27 final size:28
Alignment explanation
Indices: 1450122--1450174 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
1450112 AATAACCGAA
*
1450122 AAGAAC-GAAAAGGAGCATTCAATAAAG
1 AAGAACTGAAAAGAAGCATTCAATAAAG
* *
1450149 AAGAGCTTAAAAGAAGCATTCAATAA
1 AAGAACTGAAAAGAAGCATTCAATAA
1450175 TCGCCGGTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 5 0.23
28 17 0.77
ACGTcount: A:0.55, C:0.11, G:0.19, T:0.15
Consensus pattern (28 bp):
AAGAACTGAAAAGAAGCATTCAATAAAG
Found at i:1451474 original size:5 final size:5
Alignment explanation
Indices: 1451464--1451489 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1451454 TGACTTAGAA
1451464 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
1451490 AATAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:1456687 original size:3 final size:3
Alignment explanation
Indices: 1456681--1456706 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1456671 TTAGATAATA
1456681 ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG AT
1456707 AATAATAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:1456711 original size:3 final size:3
Alignment explanation
Indices: 1456705--1456795 Score: 182
Period size: 3 Copynumber: 30.3 Consensus size: 3
1456695 GATGATGATG
1456705 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1456753 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1456796 ATTAATAAGC
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 88 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1457240 original size:136 final size:135
Alignment explanation
Indices: 1457008--1457424 Score: 504
Period size: 136 Copynumber: 3.1 Consensus size: 135
1456998 ACACTACTCA
* * * * *
1457008 TACGTGATGAAGAGTTCTGGTCATTTTTA-GG-TAAATGGAGACAACACGGTTCCTACGTGATGA
1 TACGTGATGAAGA--TCTGGCCATCTTTAGGGATAATTGGAGATAACACGGTTCCTAAGTGATGA
* * *
1457071 GGAAATCTGGTTATCTAAAGG-TGACACTACTCCTACGTGATGAGGAGATCTTGTCGGTGGATGA
64 GGAAATCTGGCTATCT-AAGGATGACGCTGCTCCTACGTGATGAGGAGATC-TGTCGGTGGATGA
*
1457135 CACTGTTCC
127 CACAGTTCC
* * ** * *
1457144 TACATGATGATGCCATCTTTCCATCTTTAGGGATAA-T-GAGATAACACGATTCCTATGTGATGA
1 TACGTGATGAAG--ATCTGGCCATCTTTAGGGATAATTGGAGATAACACGGTTCCTAAGTGATGA
* *
1457207 GGAAATCTGACTATCTAAGGATGACGCTGCTCCTACGTGATGAGGAGATCTGATCGATGGATGAC
64 GGAAATCTGGCTATCTAAGGATGACGCTGCTCCTACGTGATGAGGAGATCTG-TCGGTGGATGAC
*
1457272 ACAATTCC
128 ACAGTTCC
* * * *
1457280 TACGTGATGAAGGTCTGGCCATCTTTAGGGATAATTGGAGATAACATGGTTCCTAAGCGAAGA-G
1 TACGTGATGAAGATCTGGCCATCTTTAGGGATAATTGGAGATAACACGGTTCCTAAGTGATGAGG
* *
1457344 AAAGTCTGGCTATCTAAGGATGACGCGGCTCCTACGTGATGAGGAGATCAGTCGGTGGATGACAC
66 AAA-TCTGGCTATCTAAGGATGACGCTGCTCCTACGTGATGAGGAGATCTGTCGGTGGATGACAC
1457409 AGTTCC
130 AGTTCC
1457415 TACGTGATGA
1 TACGTGATGA
1457425 GGATGTCTGG
Statistics
Matches: 241, Mismatches: 31, Indels: 19
0.83 0.11 0.07
Matches are distributed among these distances:
134 19 0.08
135 39 0.16
136 176 0.73
137 3 0.01
138 4 0.02
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.28
Consensus pattern (135 bp):
TACGTGATGAAGATCTGGCCATCTTTAGGGATAATTGGAGATAACACGGTTCCTAAGTGATGAGG
AAATCTGGCTATCTAAGGATGACGCTGCTCCTACGTGATGAGGAGATCTGTCGGTGGATGACACA
GTTCC
Found at i:1457465 original size:82 final size:83
Alignment explanation
Indices: 1457347--1457518 Score: 283
Period size: 82 Copynumber: 2.1 Consensus size: 83
1457337 CGAAGAGAAA
* ** *
1457347 GTCTGGCTATCTAAGGATGACGCGGCTCCTACGTGATGAGGAGATC-AGTCGGTGGATGACACAG
1 GTCTGGCTATCCAAGGATGACGCGGCTCAAACGTGATGAGGAGATCTAGTCGATGGATGACACAG
*
1457411 TTCCTACGTGATGAGGAT
66 TTCCTACGTAATGAGGAT
*
1457429 GTCTGGCTATCCAAGGATGACGCGGCTCAAACGTGATGAGGAGATCTGGTCGATGGATGACACAG
1 GTCTGGCTATCCAAGGATGACGCGGCTCAAACGTGATGAGGAGATCTAGTCGATGGATGACACAG
1457494 TTCCTACGTAATGAGGAT
66 TTCCTACGTAATGAGGAT
1457512 GTCTGGC
1 GTCTGGC
1457519 CATCATTAGG
Statistics
Matches: 83, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
82 43 0.52
83 40 0.48
ACGTcount: A:0.24, C:0.20, G:0.33, T:0.24
Consensus pattern (83 bp):
GTCTGGCTATCCAAGGATGACGCGGCTCAAACGTGATGAGGAGATCTAGTCGATGGATGACACAG
TTCCTACGTAATGAGGAT
Found at i:1457477 original size:43 final size:43
Alignment explanation
Indices: 1457348--1457477 Score: 126
Period size: 43 Copynumber: 3.1 Consensus size: 43
1457338 GAAGAGAAAG
*
1457348 TCTGGCTATCTAAGGATGACGCGGCTCCTACGTGATGAGGAGA
1 TCTGGCTATCCAAGGATGACGCGGCTCCTACGTGATGAGGAGA
* *** * * *
1457391 TC-AG---TCGGTGGATGACACAGTTCCTACGTGATGAGGATG-
1 TCTGGCTATCCAAGGATGACGCGGCTCCTACGTGATGAGGA-GA
**
1457430 TCTGGCTATCCAAGGATGACGCGGCTCAAACGTGATGAGGAGA
1 TCTGGCTATCCAAGGATGACGCGGCTCCTACGTGATGAGGAGA
1457473 TCTGG
1 TCTGG
1457478 TCGATGGATG
Statistics
Matches: 65, Mismatches: 16, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
39 29 0.45
40 2 0.03
42 2 0.03
43 32 0.49
ACGTcount: A:0.24, C:0.20, G:0.33, T:0.23
Consensus pattern (43 bp):
TCTGGCTATCCAAGGATGACGCGGCTCCTACGTGATGAGGAGA
Found at i:1457517 original size:40 final size:40
Alignment explanation
Indices: 1457373--1457510 Score: 136
Period size: 43 Copynumber: 3.4 Consensus size: 40
1457363 ATGACGCGGC
* *
1457373 TCCTACGTGATGAGGAGATC-AGTCGGTGGATGACACAGT
1 TCCTACGTGATGAGGAGATCTGGTCGATGGATGACACAGT
* * * * *
1457412 TCCTACGTGATGAGGATG-TCTGGCTATCCAAGGATGACGCGGC
1 TCCTACGTGATGAGGA-GATCTGG---TCGATGGATGACACAGT
**
1457455 TCAAACGTGATGAGGAGATCTGGTCGATGGATGACACAGT
1 TCCTACGTGATGAGGAGATCTGGTCGATGGATGACACAGT
*
1457495 TCCTACGTAATGAGGA
1 TCCTACGTGATGAGGA
1457511 TGTCTGGCCA
Statistics
Matches: 76, Mismatches: 17, Indels: 11
0.73 0.16 0.11
Matches are distributed among these distances:
39 18 0.24
40 27 0.36
42 1 0.01
43 30 0.39
ACGTcount: A:0.26, C:0.19, G:0.32, T:0.23
Consensus pattern (40 bp):
TCCTACGTGATGAGGAGATCTGGTCGATGGATGACACAGT
Found at i:1457773 original size:66 final size:65
Alignment explanation
Indices: 1457536--1457875 Score: 278
Period size: 66 Copynumber: 5.2 Consensus size: 65
1457526 AGGGATAATT
* * * * * * * * *
1457536 TGTTTCAAGAGAAACTGTCTAATAGAGACAAAAATTGTTTCAAGGGAAACTATCTCAATGTTTTT
1 TGTTTCAAGAGAAATTGTTTAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTTAAAG-GTTC
1457601 A
65 A
** * * * * * * * * *
1457602 TGTTTTGAGAGAAACTATCTCAAGAGAGAC--AA-TT-TTTAAAAGGAAACATTCTCAAAGATGC
1 TGTTTCAAGAGAAATTGT-TTAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTTAAAGGTTC
1457663 A
65 A
* * * *
1457664 TGTTTCAAGAGAAATTGTCTAAGAGAGGCAAAACTTGTTTCAAGGGAAATAATCTTAAAGG-TCA
1 TGTTTCAAGAGAAATTGTTTAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTTAAAGGTTCA
*
1457728 CTGTTTCAAGAGAAATTGTGTTAAGAGAGACAAAATTTGTTTCAAGGGAAACAATC-TCAAGGTT
1 -TGTTTCAAGAGAAATTGT-TTAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTTAAAGG-T
*
1457792 TTA
63 TCA
* * * * * *
1457795 TGTTTCAAGAGAAACTGTCTCAAGAGAAACAAAATTTGTTTCAAGGGAAACAATCTCAATGTTTT
1 TGTTTCAAGAGAAATTGT-TTAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTTAAAG-GTT
*
1457860 TA
64 CA
1457862 TGTTTCAAGAGAAA
1 TGTTTCAAGAGAAA
1457876 CAATTTCCAA
Statistics
Matches: 221, Mismatches: 42, Indels: 21
0.78 0.15 0.07
Matches are distributed among these distances:
61 8 0.04
62 16 0.07
63 20 0.09
64 6 0.03
65 43 0.19
66 98 0.44
67 30 0.14
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (65 bp):
TGTTTCAAGAGAAATTGTTTAAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTTAAAGGTTCA
Found at i:1457801 original size:30 final size:30
Alignment explanation
Indices: 1457765--1457879 Score: 88
Period size: 30 Copynumber: 3.6 Consensus size: 30
1457755 AGACAAAATT
*
1457765 TGTTTCAAGGGAAACAATCTCAAGGTTTTA
1 TGTTTCAAGAGAAACAATCTCAAGGTTTTA
** **
1457795 TGTTTCAAGAGAAACTGTCTCAAGAGAAACAAAATT-
1 TGTTTCAAGAGAAACAATCTCAAG-G------TTTTA
* *
1457831 TGTTTCAAGGGAAACAATCTCAATGTTTTTA
1 TGTTTCAAGAGAAACAATCTCAA-GGTTTTA
1457862 TGTTTCAAGAGAAACAAT
1 TGTTTCAAGAGAAACAAT
1457880 TTCCAAATTT
Statistics
Matches: 64, Mismatches: 12, Indels: 17
0.69 0.13 0.18
Matches are distributed among these distances:
30 23 0.36
31 18 0.28
36 20 0.31
37 3 0.05
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.31
Consensus pattern (30 bp):
TGTTTCAAGAGAAACAATCTCAAGGTTTTA
Found at i:1457852 original size:36 final size:35
Alignment explanation
Indices: 1457750--1457853 Score: 94
Period size: 36 Copynumber: 3.1 Consensus size: 35
1457740 AAATTGTGTT
1457750 AAGAGAGACAAAATTTGTTTCAAGGGAAACAATCTC
1 AAGAGA-ACAAAATTTGTTTCAAGGGAAACAATCTC
** * **
1457786 AAG-G-----TTTTATGTTTCAAGAGAAACTGTCTC
1 AAGAGAACAAAATT-TGTTTCAAGGGAAACAATCTC
1457816 AAGAGAAACAAAATTTGTTTCAAGGGAAACAATCTC
1 AAGAG-AACAAAATTTGTTTCAAGGGAAACAATCTC
1457852 AA
1 AA
1457854 TGTTTTTATG
Statistics
Matches: 50, Mismatches: 10, Indels: 16
0.66 0.13 0.21
Matches are distributed among these distances:
29 2 0.04
30 21 0.42
31 1 0.02
35 1 0.02
36 23 0.46
37 2 0.04
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.26
Consensus pattern (35 bp):
AAGAGAACAAAATTTGTTTCAAGGGAAACAATCTC
Found at i:1460422 original size:12 final size:11
Alignment explanation
Indices: 1460407--1460474 Score: 61
Period size: 12 Copynumber: 5.9 Consensus size: 11
1460397 TTTTCATGTG
1460407 TTTTTTGTCTTC
1 TTTTTT-TCTTC
1460419 TTTTCTTTCTT-
1 TTTT-TTTCTTC
1460430 TATTTTTTGCTTC
1 T-TTTTTT-CTTC
1460443 TTTTTTTCCTTGC
1 TTTTTTT-CTT-C
1460456 TTTTTTT-TT-
1 TTTTTTTCTTC
1460465 TTTTTTTCTT
1 TTTTTTTCTT
1460475 TTTGCTTATT
Statistics
Matches: 49, Mismatches: 1, Indels: 14
0.77 0.02 0.22
Matches are distributed among these distances:
9 7 0.14
10 2 0.04
11 6 0.12
12 23 0.47
13 11 0.22
ACGTcount: A:0.01, C:0.15, G:0.04, T:0.79
Consensus pattern (11 bp):
TTTTTTTCTTC
Found at i:1460459 original size:24 final size:25
Alignment explanation
Indices: 1460407--1460475 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 25
1460397 TTTTCATGTG
*
1460407 TTTTTTGTCTTCTTTTCTTTCTTTA
1 TTTTTTGTCTTCTTTTCTTTCTTGA
*
1460432 TTTTTTG-CTTCTTTT-TTTCCTTGC
1 TTTTTTGTCTTCTTTTCTTT-CTTGA
* * *
1460456 TTTTTTTTTTTTTTTTCTTT
1 TTTTTTGTCTTCTTTTCTTT
1460476 TTGCTTATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
23 3 0.08
24 17 0.47
25 13 0.36
26 3 0.08
ACGTcount: A:0.01, C:0.14, G:0.04, T:0.80
Consensus pattern (25 bp):
TTTTTTGTCTTCTTTTCTTTCTTGA
Found at i:1460475 original size:17 final size:17
Alignment explanation
Indices: 1460466--1460525 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 17
1460456 TTTTTTTTTT
1460466 TTTTTTCTTTTTGCTTA
1 TTTTTTCTTTTTGCTTA
1460483 TTTTTTC--TTTGCTCT-
1 TTTTTTCTTTTTGCT-TA
1460498 TTGTTTT-TTATTTGCTTA
1 TT-TTTTCTT-TTTGCTTA
*
1460516 TTTTCTCTTT
1 TTTTTTCTTT
1460526 GTTTTTCTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 14
0.70 0.02 0.28
Matches are distributed among these distances:
15 8 0.23
16 5 0.14
17 12 0.34
18 10 0.29
ACGTcount: A:0.05, C:0.13, G:0.07, T:0.75
Consensus pattern (17 bp):
TTTTTTCTTTTTGCTTA
Found at i:1460498 original size:24 final size:24
Alignment explanation
Indices: 1460452--1460499 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1460442 CTTTTTTTCC
* * **
1460452 TTGCTTTTTTTTTTTTTTTTCTTT
1 TTGCTTATTTTTTCTTTGCTCTTT
1460476 TTGCTTATTTTTTCTTTGCTCTTT
1 TTGCTTATTTTTTCTTTGCTCTTT
1460500 GTTTTTTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.02, C:0.12, G:0.06, T:0.79
Consensus pattern (24 bp):
TTGCTTATTTTTTCTTTGCTCTTT
Found at i:1463256 original size:17 final size:17
Alignment explanation
Indices: 1463232--1463275 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
1463222 AACACAAACA
1463232 ATCC-AAACAACCAAAT
1 ATCCAAAACAACCAAAT
*
1463248 ATCCAAAACAAGCAAAT
1 ATCCAAAACAACCAAAT
*
1463265 ATTCAAAACAA
1 ATCCAAAACAA
1463276 ACATCCAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 4 0.16
17 21 0.84
ACGTcount: A:0.59, C:0.25, G:0.02, T:0.14
Consensus pattern (17 bp):
ATCCAAAACAACCAAAT
Found at i:1463278 original size:21 final size:21
Alignment explanation
Indices: 1463253--1463292 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1463243 CAAATATCCA
*
1463253 AAACAAGCAAATATTCAAAAC
1 AAACAACCAAATATTCAAAAC
*
1463274 AAACATCCAAATATTCAAA
1 AAACAACCAAATATTCAAA
1463293 TACATAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.60, C:0.20, G:0.03, T:0.17
Consensus pattern (21 bp):
AAACAACCAAATATTCAAAAC
Found at i:1473678 original size:3 final size:3
Alignment explanation
Indices: 1473654--1473700 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
1473644 TAACCTGTAA
* *
1473654 AAT AAA AAT AA- AAT AGAT AAT AAT AAT AAT AAT AAT AAT AAA AAT
1 AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1473699 AA
1 AA
1473701 ATTAATAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:1477202 original size:12 final size:12
Alignment explanation
Indices: 1477185--1477233 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
1477175 ATTAATATTA
*
1477185 TTATATATGTAT
1 TTATATATATAT
1477197 TTATATATATAT
1 TTATATATATAT
* *
1477209 TTATATGTATAAAA
1 TTATA--TATATAT
1477223 TTATATATATA
1 TTATATATATA
1477234 CTTTTTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
12 21 0.68
14 10 0.32
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (12 bp):
TTATATATATAT
Found at i:1477677 original size:27 final size:27
Alignment explanation
Indices: 1477647--1477735 Score: 99
Period size: 27 Copynumber: 3.3 Consensus size: 27
1477637 TATACATTAC
*
1477647 ATATATACTCATGTACATACATCATAT
1 ATATATACTTATGTACATACATCATAT
* *
1477674 ATATACACTTATGTACACACATCATACAT
1 ATATATACTTATGTACATACATCAT--AT
* * *
1477703 ATATATACTTATGTATATAC-TTATAA
1 ATATATACTTATGTACATACATCATAT
1477729 ATATATA
1 ATATATA
1477736 TAGCCCATAT
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
26 8 0.15
27 22 0.42
28 3 0.06
29 19 0.37
ACGTcount: A:0.43, C:0.16, G:0.03, T:0.38
Consensus pattern (27 bp):
ATATATACTTATGTACATACATCATAT
Found at i:1477707 original size:31 final size:29
Alignment explanation
Indices: 1477638--1477717 Score: 85
Period size: 27 Copynumber: 2.8 Consensus size: 29
1477628 TAATGTATAT
* * * *
1477638 ATACATTACATATATACTCATGTACATAC
1 ATACATCATATATATACTTATGTACACAC
*
1477667 AT-CAT-ATATATACACTTATGTACACAC
1 ATACATCATATATATACTTATGTACACAC
1477694 AT-CATACATATATATACTTATGTA
1 ATACAT-CATATATATACTTATGTA
1477718 TATACTTATA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
27 23 0.52
28 3 0.07
29 18 0.41
ACGTcount: A:0.41, C:0.19, G:0.04, T:0.36
Consensus pattern (29 bp):
ATACATCATATATATACTTATGTACACAC
Found at i:1486858 original size:18 final size:19
Alignment explanation
Indices: 1486835--1486870 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
1486825 TTTATTTGTA
1486835 AATTTTTTTA-TCATTTTC
1 AATTTTTTTATTCATTTTC
1486853 AATTTTTTTATTCATTTT
1 AATTTTTTTATTCATTTT
1486871 TTAACATATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.69
Consensus pattern (19 bp):
AATTTTTTTATTCATTTTC
Found at i:1492713 original size:23 final size:24
Alignment explanation
Indices: 1492671--1492720 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
1492661 TTATGGTATC
* **
1492671 TTTACTTTTTCAAATTTGCTAT-T
1 TTTACTTTTCCAAACATGCTATAT
1492694 TTTACTTTTCCAAACATGCTATAT
1 TTTACTTTTCCAAACATGCTATAT
1492718 TTT
1 TTT
1492721 TCCTTGTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.24, C:0.16, G:0.04, T:0.56
Consensus pattern (24 bp):
TTTACTTTTCCAAACATGCTATAT
Found at i:1493118 original size:30 final size:30
Alignment explanation
Indices: 1493072--1493141 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
1493062 AATTCATCTA
*
1493072 CATTACATTTCTAAATAAAAATTGTTACTCT
1 CATTA-ATTCCTAAATAAAAATTGTTACTCT
*
1493103 CATTAATTCCTAAATAAGAATTGTTACTCT
1 CATTAATTCCTAAATAAAAATTGTTACTCT
* *
1493133 TACTAATTC
1 CATTAATTC
1493142 TTATTAATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
30 30 0.86
31 5 0.14
ACGTcount: A:0.37, C:0.17, G:0.04, T:0.41
Consensus pattern (30 bp):
CATTAATTCCTAAATAAAAATTGTTACTCT
Found at i:1493810 original size:19 final size:19
Alignment explanation
Indices: 1493747--1493813 Score: 55
Period size: 19 Copynumber: 3.4 Consensus size: 19
1493737 TAAATTTTGT
*
1493747 AAAAAATATATATATA-TA
1 AAAAAATATATATAAATTA
** *
1493765 AATTTAATATATTTAAATTTTA
1 AA-AAAATATATATAAA--TTA
*
1493787 TAAAAATATATATAAATTA
1 AAAAAATATATATAAATTA
1493806 AAAAAATA
1 AAAAAATA
1493814 ATGTATTTCC
Statistics
Matches: 36, Mismatches: 9, Indels: 7
0.69 0.17 0.13
Matches are distributed among these distances:
18 2 0.06
19 20 0.56
21 11 0.31
22 3 0.08
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAAAATATATATAAATTA
Found at i:1506609 original size:64 final size:64
Alignment explanation
Indices: 1506508--1506635 Score: 220
Period size: 64 Copynumber: 2.0 Consensus size: 64
1506498 TATGTTATAT
*
1506508 CATTTAACAGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATAAAATAGG
1 CATTTAACAGGAAATATTATCAAATACAATAACATATTAGGTAGCGCTTATATAATAAAATAGG
* * *
1506572 CATTTAACCGGAAATATTATCAAATATAATAACATATTAGGTAGCGCTTATATAATATAATAGG
1 CATTTAACAGGAAATATTATCAAATACAATAACATATTAGGTAGCGCTTATATAATAAAATAGG
1506636 TAGCGCTTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 60 1.00
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (64 bp):
CATTTAACAGGAAATATTATCAAATACAATAACATATTAGGTAGCGCTTATATAATAAAATAGG
Found at i:1506646 original size:21 final size:23
Alignment explanation
Indices: 1506600--1506647 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
1506590 ATCAAATATA
*
1506600 ATAACATATTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
*
1506623 ATAATATAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
1506646 AT
1 AT
1506648 TGACCTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:1507034 original size:199 final size:199
Alignment explanation
Indices: 1506650--1507364 Score: 960
Period size: 199 Copynumber: 3.6 Consensus size: 199
1506640 GCTTATATTG
* ** * *
1506650 ACCTATTTTCTAACT-AAACCGGTTTATTTATACCGGTAACATTGCAAATTTACCTATTACATTA
1 ACCTATTTTCTCA-TAAAACCGGTAAATTTATACCGGTTACATTGTAAATTTACCTATTACATTA
* * * *
1506714 TAATTATCGGTTTCGATATTTTTGGGATTGATACAATTT-TAAATGTATCGACACTTTATGCATG
65 TAATTATCGGTTTCGATGTTTTTGGGATCGATACATTTTATAAATGTATCGACACTTTATGCGTG
* * * * * *
1506778 CACCTCGTTGGGCATTCATTCTGGAAAAAAGTATCGACACAAACTT-AAAAAGTGTCGATACATT
130 CACCCCGTTTGGCATTCATTCTGGACAAAAGTATCGACAC-AAGTTCCACAAGTGTCGATACATT
1506842 ATGCAA
194 ATGCAA
* * * * * *
1506848 AACTATTTTCTCATAAAACGGGTATATTTATATCAGG-TACAGTGTAAATTTACCTATTACATTG
1 ACCTATTTTCTCATAAAACCGGTAAATTTATA-CCGGTTACATTGTAAATTTACCTATTACATTA
* *
1506912 TAATTATCAGTTTCGATGTTTTTGGGATCGATAC-TTTTAATAAATGTATCGACATTTTATGCGT
65 TAATTATCGGTTTCGATGTTTTTGGGATCGATACATTTT-ATAAATGTATCGACACTTTATGCGT
1506976 GCACCCCGTTTGGCATTCATTCTGGACAAAAGTATCGACACAAGTTCCACAAGTGTCGATACATT
129 GCACCCCGTTTGGCATTCATTCTGGACAAAAGTATCGACACAAGTTCCACAAGTGTCGATACATT
* *
1507041 ATGTAG
194 ATGCAA
* * **
1507047 ACCTATTTTTTCATAAAACCGGTAAATTTCTACCGGTTACA-TGTAAATTTATATATTACATTAT
1 ACCTATTTTCTCATAAAACCGGTAAATTTATACCGGTTACATTGTAAATTTACCTATTACATTAT
* *
1507111 AATTATGGGTTTCGATGTTTTTGGGATCGATACATTTTATAAATGTATCGACACTTTATGTGTGC
66 AATTATCGGTTTCGATGTTTTTGGGATCGATACATTTTATAAATGTATCGACACTTTATGCGTGC
** * *
1507176 A-CCATTTTGGGTATTCATTTTGGACAACAAGTATCGACACAAGTTCCACAAGTGTCGATACATT
131 ACCCCGTTT-GGCATTCATTCTGGACAA-AAGTATCGACACAAGTTCCACAAGTGTCGATACATT
*
1507240 ATGCAT
194 ATGCAA
*
1507246 ACCTATTTTCTCATAAAACCGGTAAATTTATACCGGTTACATTGTAAATTTACCAATTACATTAT
1 ACCTATTTTCTCATAAAACCGGTAAATTTATACCGGTTACATTGTAAATTTACCTATTACATTAT
* *
1507311 AATTATGGGTTTCGATGTTTTTGGGATC-AGTACTTTTTATAAATGTATCGACAC
66 AATTATCGGTTTCGATGTTTTTGGGATCGA-TACATTTTATAAATGTATCGACAC
1507365 ATATTTAGGT
Statistics
Matches: 458, Mismatches: 48, Indels: 20
0.87 0.09 0.04
Matches are distributed among these distances:
197 9 0.02
198 180 0.39
199 198 0.43
200 71 0.16
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (199 bp):
ACCTATTTTCTCATAAAACCGGTAAATTTATACCGGTTACATTGTAAATTTACCTATTACATTAT
AATTATCGGTTTCGATGTTTTTGGGATCGATACATTTTATAAATGTATCGACACTTTATGCGTGC
ACCCCGTTTGGCATTCATTCTGGACAAAAGTATCGACACAAGTTCCACAAGTGTCGATACATTAT
GCAA
Found at i:1509868 original size:19 final size:19
Alignment explanation
Indices: 1509837--1509888 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
1509827 CCTATTACAT
1509837 TCATATACAAAATTATAAA
1 TCATATACAAAATTATAAA
* * *
1509856 TCGTATACTAAATTATGAA
1 TCATATACAAAATTATAAA
1509875 TCATATACAAAATT
1 TCATATACAAAATT
1509889 TCCCTACATT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.50, C:0.12, G:0.04, T:0.35
Consensus pattern (19 bp):
TCATATACAAAATTATAAA
Found at i:1511955 original size:198 final size:198
Alignment explanation
Indices: 1511488--1512679 Score: 1412
Period size: 198 Copynumber: 6.0 Consensus size: 198
1511478 GCGTAATTTA
* * * *
1511488 AAAAAAGTATCGACACAACTTTAAAAGTGTCAATACATTATGCAGACCTATTTTCTAGTTAACCG
1 AAAAAA-TATCGACACAA-TTCAAAAGTGTCGATACATTATACAGACCTATTTTCTAATTAACCG
* *
1511553 ATATATTTCTACCGGTTACATTGGAAA-TTGACCTATTACATTATACTTATATTATTCGATGTTT
64 ATATATTTCTACCGGTTACATTGTAAAGTT-ACCTATTACATTATAATTATATTATTCGATGTTT
*
1511617 GTGGGATCGATACTTTTTATAAATGTATCGACACTTTATTCGTGCACCTCGGTTGGTCATTCATT
128 ATGGGATCGATACTTTTTATAAATGTATCGACACTTTATTCGTGCACCTCGGTTGGTCATTCATT
*
1511682 ATGGAC
193 CTGGAC
* ** ** *
1511688 AAAAAATATCGACACAATTTAAAACGTGTCGATACATTATGTAGACCTATTTTCGGATCAACCGA
1 AAAAAATATCGACACAATTCAAAA-GTGTCGATACATTATACAGACCTATTTTCTAATTAACCGA
* * * *
1511753 TATATTTCTACCGGTTATATTGTAAAGTTACATATTACATTATGATTATCGGTT-TT-GATGTTT
65 TATATTTCTACCGGTTACATTGTAAAGTTACCTATTACATTATAATTAT--ATTATTCGATGTTT
** ** **
1511816 ATGGGATCGATACAATTT-TAAATGTATCGACACTTTATGAGTGCA-CTCTTTTAGG-CATTCAT
128 ATGGGATCGATACTTTTTATAAATGTATCGACACTTTATTCGTGCACCTCGGTT-GGTCATTCAT
1511878 TCTGGAC
192 TCTGGAC
* * * *
1511885 AAAAAATATCGACATAAATTCCACAAGTGTCGATACATGATACAAACCTATTTTCTAATTAACCG
1 AAAAAATATCGACA-CAATT-CAAAAGTGTCGATACATTATACAGACCTATTTTCTAATTAACCG
*
1511950 ATATATTTCTACCGGTTACATTG-AAAATTGACCTATTACATTATAATTATATTATTCGATGTTT
64 ATATATTTCTACCGGTTACATTGTAAAGTT-ACCTATTACATTATAATTATATTATTCGATG-TT
*
1512014 TGTGGGATCGATACTTTTTATAAATGTATCGACACTTTATTCGTGCACCTCGGTTGGTCATTCAT
127 TATGGGATCGATACTTTTTATAAATGTATCGACACTTTATTCGTGCACCTCGGTTGGTCATTCAT
1512079 TCTGGAC
192 TCTGGAC
* * *
1512086 AAAAAATATCGACACAATTTAAAACGTGTCGATACATTATATAGACCTATTTT-TGGATTAACCG
1 AAAAAATATCGACACAATTCAAAA-GTGTCGATACATTATACAGACCTATTTTCT-AATTAACCG
* *
1512150 GTATATTTCTACCGGTTACATTGTAAAGTTACCTATTACATTATAATTATCGGTT-TT-GATGTT
64 ATATATTTCTACCGGTTACATTGTAAAGTTACCTATTACATTATAATTAT--ATTATTCGATGTT
* ** ** ** **
1512213 TATGGGATTGATACAATTT-TAAATGTATCGACACTTTATGAGTATA-CTCTTTTAGG-CATTCA
127 TATGGGATCGATACTTTTTATAAATGTATCGACACTTTATTCGTGCACCTCGGTT-GGTCATTCA
1512275 TTCTGGAC
191 TTCTGGAC
* * * * *
1512283 AAAAAGTATCGACATAAATTTCACAAGTGTCGATACATGATACATACCTATTTTCTAATTAACCT
1 AAAAAATATCGACA-CAA-TTCAAAAGTGTCGATACATTATACAGACCTATTTTCTAATTAACC-
* *
1512348 G-TATATTTCTACCGGTTACATTGAAAATTTACCTATTACATTATAATTATATTATTCGATGGTT
63 GATATATTTCTACCGGTTACATTGTAAAGTTACCTATTACATTATAATTATATTATTCGAT-GTT
* *
1512412 T-TGGGATCGATACTTTTTATAAATGTATCAACACTTTATTCCTGCACCTCGGTTGGTCATTCAT
127 TATGGGATCGATACTTTTTATAAATGTATCGACACTTTATTCGTGCACCTCGGTTGGTCATTCAT
*
1512476 TCTGAAC
192 TCTGGAC
* * * **
1512483 AAAAAGTATCGACACAATTTAAAAAGTGTCGATA-TTTATGTAGACCTATTTTCTAATTAACCGA
1 AAAAAATATCGACACAA-TTCAAAAGTGTCGATACATTATACAGACCTATTTTCTAATTAACCGA
* ** * * *
1512547 TATATATCTACATGTTACATTGTAAATTTACCTATTACATTATAATTATCTTATTTGATG-TTAT
65 TATATTTCTACCGGTTACATTGTAAAGTTACCTATTACATTATAATTATATTATTCGATGTTTA-
* ** * * *
1512611 TGGGATCGATA-TTTTTAATAAATGTATCGGCACTTTATTCGTTTACCTTGGTTGGGCATTCGTT
129 TGGGATCGATACTTTTT-ATAAATGTATCGACACTTTATTCGTGCACCTCGGTTGGTCATTCATT
1512675 CTGGA
193 CTGGA
1512680 GATTACTGAA
Statistics
Matches: 850, Mismatches: 108, Indels: 70
0.83 0.11 0.07
Matches are distributed among these distances:
196 6 0.01
197 80 0.09
198 367 0.43
199 201 0.24
200 152 0.18
201 42 0.05
202 2 0.00
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (198 bp):
AAAAAATATCGACACAATTCAAAAGTGTCGATACATTATACAGACCTATTTTCTAATTAACCGAT
ATATTTCTACCGGTTACATTGTAAAGTTACCTATTACATTATAATTATATTATTCGATGTTTATG
GGATCGATACTTTTTATAAATGTATCGACACTTTATTCGTGCACCTCGGTTGGTCATTCATTCTG
GAC
Found at i:1512679 original size:398 final size:398
Alignment explanation
Indices: 1511489--1512648 Score: 1834
Period size: 398 Copynumber: 2.9 Consensus size: 398
1511479 CGTAATTTAA
* * * * * * * *
1511489 AAAAAGTATCGACACAACTTT-AAAAGTGTCAATACATTATGCAGACCTATTTTCTAGTTAACCG
1 AAAAAGTATCGACATAAATTTCACAAGTGTCGATACATGATACAAACCTATTTTCTAATTAACCG
* *
1511553 ATATATTTCTACCGGTTACATTGGAAATTGACCTATTACATTATACTTATATTATTCGAT-GTTT
66 ATATATTTCTACCGGTTACATTGAAAATTGACCTATTACATTATAATTATATTATTCGATGGTTT
1511617 GTGGGATCGATACTTTTTATAAATGTATCGACACTTTATTCGTGCACCTCGGTTGGTCATTCATT
131 GTGGGATCGATACTTTTTATAAATGTATCGACACTTTATTCGTGCACCTCGGTTGGTCATTCATT
* * *
1511682 ATGGACAAAAAATATCGACACAATTTAAAACGTGTCGATACATTATGTAGACCTATTTTCGGATC
196 CTGGACAAAAAATATCGACACAATTTAAAACGTGTCGATACATTATGTAGACCTATTTTCTGATT
* * *
1511747 AACCGATATATTTCTACCGGTTATATTGTAAAGTTACATATTACATTATGATTATCGGTTTTGAT
261 AACCGATATATTTCTACCGGTTACATTGTAAAGTTACCTATTACATTATAATTATCGGTTTTGAT
**
1511812 GTTTATGGGATCGATACAATTTTAAATGTATCGACACTTTATGAGTGCACTCTTTTAGGCATTCA
326 GTTTATGGGATCGATACAATTTTAAATGTATCGACACTTTATGAGTATACTCTTTTAGGCATTCA
1511877 TTCTGGAC
391 TTCTGGAC
* *
1511885 AAAAAATATCGACATAAATTCCACAAGTGTCGATACATGATACAAACCTATTTTCTAATTAACCG
1 AAAAAGTATCGACATAAATTTCACAAGTGTCGATACATGATACAAACCTATTTTCTAATTAACCG
*
1511950 ATATATTTCTACCGGTTACATTGAAAATTGACCTATTACATTATAATTATATTATTCGATGTTTT
66 ATATATTTCTACCGGTTACATTGAAAATTGACCTATTACATTATAATTATATTATTCGATGGTTT
1512015 GTGGGATCGATACTTTTTATAAATGTATCGACACTTTATTCGTGCACCTCGGTTGGTCATTCATT
131 GTGGGATCGATACTTTTTATAAATGTATCGACACTTTATTCGTGCACCTCGGTTGGTCATTCATT
*
1512080 CTGGACAAAAAATATCGACACAATTTAAAACGTGTCGATACATTATATAGACCTATTTT-TGGAT
196 CTGGACAAAAAATATCGACACAATTTAAAACGTGTCGATACATTATGTAGACCTATTTTCT-GAT
*
1512144 TAACCGGTATATTTCTACCGGTTACATTGTAAAGTTACCTATTACATTATAATTATCGGTTTTGA
260 TAACCGATATATTTCTACCGGTTACATTGTAAAGTTACCTATTACATTATAATTATCGGTTTTGA
*
1512209 TGTTTATGGGATTGATACAATTTTAAATGTATCGACACTTTATGAGTATACTCTTTTAGGCATTC
325 TGTTTATGGGATCGATACAATTTTAAATGTATCGACACTTTATGAGTATACTCTTTTAGGCATTC
1512274 ATTCTGGAC
390 ATTCTGGAC
*
1512283 AAAAAGTATCGACATAAATTTCACAAGTGTCGATACATGATACATACCTATTTTCTAATTAACCT
1 AAAAAGTATCGACATAAATTTCACAAGTGTCGATACATGATACAAACCTATTTTCTAATTAACC-
*
1512348 G-TATATTTCTACCGGTTACATTGAAAATTTACCTATTACATTATAATTATATTATTCGATGGTT
65 GATATATTTCTACCGGTTACATTGAAAATTGACCTATTACATTATAATTATATTATTCGATGGTT
* *
1512412 T-TGGGATCGATACTTTTTATAAATGTATCAACACTTTATTCCTGCACCTCGGTTGGTCATTCAT
130 TGTGGGATCGATACTTTTTATAAATGTATCGACACTTTATTCGTGCACCTCGGTTGGTCATTCAT
* * * * *
1512476 TCTGAACAAAAAGTATCGACACAATTTAAAAAGTGTCGATA-TTTATGTAGACCTATTTTCTAAT
195 TCTGGACAAAAAATATCGACACAATTTAAAACGTGTCGATACATTATGTAGACCTATTTTCTGAT
* ** * *
1512540 TAACCGATATATATCTACATGTTACATTGTAAATTTACCTATTACATTATAATTATC-TTATTTG
260 TAACCGATATATTTCTACCGGTTACATTGTAAAGTTACCTATTACATTATAATTATCGGT-TTTG
** *
1512604 ATG-TTATTGGGATCGATA-TTTTTAATAAATGTATCGGCACTTTAT
324 ATGTTTA-TGGGATCGATACAATTT--TAAATGTATCGACACTTTAT
1512649 TCGTTTACCT
Statistics
Matches: 708, Mismatches: 47, Indels: 17
0.92 0.06 0.02
Matches are distributed among these distances:
395 7 0.01
396 104 0.15
397 214 0.30
398 382 0.54
399 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.39
Consensus pattern (398 bp):
AAAAAGTATCGACATAAATTTCACAAGTGTCGATACATGATACAAACCTATTTTCTAATTAACCG
ATATATTTCTACCGGTTACATTGAAAATTGACCTATTACATTATAATTATATTATTCGATGGTTT
GTGGGATCGATACTTTTTATAAATGTATCGACACTTTATTCGTGCACCTCGGTTGGTCATTCATT
CTGGACAAAAAATATCGACACAATTTAAAACGTGTCGATACATTATGTAGACCTATTTTCTGATT
AACCGATATATTTCTACCGGTTACATTGTAAAGTTACCTATTACATTATAATTATCGGTTTTGAT
GTTTATGGGATCGATACAATTTTAAATGTATCGACACTTTATGAGTATACTCTTTTAGGCATTCA
TTCTGGAC
Found at i:1513858 original size:199 final size:197
Alignment explanation
Indices: 1513514--1514194 Score: 965
Period size: 199 Copynumber: 3.4 Consensus size: 197
1513504 CATACGTCCG
* * * * *
1513514 AAATTTACCTATTACATTATAATTATGGGTTTTGATATTTTTGGGATCAATATTTTTTATAAATG
1 AAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGATACTATTTATAAATG
** *
1513579 TATCGACACTTTATGCGTGTGCCCCTTTGGGCATT-GATTCTGGACAAAATGTATCGACAAAAGT
66 TATCGACACTTTATGCGTGCACCCCTTTGGGCATTCG-TTCTGGACAAAA-GTATCGACACAAGT
* *
1513643 TCTACAAGTGTCGATATATTATGTAGACCTGTTTTCTCATAAACC-AGTAAATTTCTATCGGTTA
129 TCAACAAGTGTCGATATATTATGTAGACCTATTTTCTCATAAACCGA-TAAATTTCTA-CGGTTA
1513707 CATTGT
192 CATTGT
*
1513713 AAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGATACTTTTTATAAATG
1 AAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGATACTATTTATAAATG
*
1513778 TATCGACACTTTATGCGTGCACCCCTCTGGGCATTCGTTCTGGACGAAAAGTATCGACACAAGTT
66 TATCGACACTTTATGCGTGCACCCCTTTGGGCATTCGTTCTGGAC-AAAAGTATCGACACAAGTT
* * * *
1513843 CAAAAAGTATCGATATATTATGTAGACCAATTTTCTCTTAAACCGATAAATTTCTACCGGTTACA
130 CAACAAGTGTCGATATATTATGTAGACCTATTTTCTCATAAACCGATAAATTTCTA-CGGTTACA
*
1513908 TTTT
194 TTGT
* * *
1513912 AAATTTACATATTACATTATAATTATGGGTTTCGATGTTTTTTGGATAGATAC-ATTTATAAATG
1 AAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGATACTATTTATAAATG
* * * *
1513976 TATCGACACTTTATGCGTGCACCCCTTTTGGCATTCATTATGGACAAAAAGTATCGACACATGTT
66 TATCGACACTTTATGCGTGCACCCCTTTGGGCATTCGTTCTGGAC-AAAAGTATCGACACAAGTT
* * * *
1514041 -ACACAAGTGTCGATACATTATGCAGACCTATTTTCTCATAAACGGATAAATTTATACTGGTTAC
130 CA-ACAAGTGTCGATATATTATGTAGACCTATTTTCTCATAAACCGATAAATTTCTAC-GGTTAC
*
1514105 ATTGA
193 ATTGT
* *
1514110 AAAATTGCCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGATACTATTTATAAATG
1 AAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGATACTATTTATAAATG
*
1514175 TATCGACACTTTATGTGTGC
66 TATCGACACTTTATGCGTGC
1514195 CTATTCTCTA
Statistics
Matches: 434, Mismatches: 42, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
197 2 0.00
198 172 0.40
199 254 0.59
200 6 0.01
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.39
Consensus pattern (197 bp):
AAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGATACTATTTATAAATG
TATCGACACTTTATGCGTGCACCCCTTTGGGCATTCGTTCTGGACAAAAGTATCGACACAAGTTC
AACAAGTGTCGATATATTATGTAGACCTATTTTCTCATAAACCGATAAATTTCTACGGTTACATT
GT
Found at i:1514499 original size:18 final size:19
Alignment explanation
Indices: 1514484--1514539 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
1514474 ACATAATTAC
1514484 ATTCATATACAAAATTATA
1 ATTCATATACAAAATTATA
**
1514503 ATTTGTATACAAAATTATA
1 ATTCATATACAAAATTATA
**
1514522 AACCTATATACAAAATTA
1 ATTC-ATATACAAAATTA
1514540 ACCCTACATT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 18 0.60
20 12 0.40
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.36
Consensus pattern (19 bp):
ATTCATATACAAAATTATA
Found at i:1514545 original size:18 final size:20
Alignment explanation
Indices: 1514488--1514539 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1514478 AATTACATTC
**
1514488 ATATACAAAATTAT-AATTT
1 ATATACAAAATTATAAACCT
*
1514507 GTATACAAAATTATAAACCT
1 ATATACAAAATTATAAACCT
1514527 ATATACAAAATTA
1 ATATACAAAATTA
1514540 ACCCTACATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.35
Consensus pattern (20 bp):
ATATACAAAATTATAAACCT
Found at i:1515770 original size:24 final size:24
Alignment explanation
Indices: 1515702--1515762 Score: 122
Period size: 24 Copynumber: 2.5 Consensus size: 24
1515692 AATACATATA
1515702 TGTCCCGAAGGACAACGTAGAATT
1 TGTCCCGAAGGACAACGTAGAATT
1515726 TGTCCCGAAGGACAACGTAGAATT
1 TGTCCCGAAGGACAACGTAGAATT
1515750 TGTCCCGAAGGAC
1 TGTCCCGAAGGAC
1515763 CGTGTAGACC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.31, C:0.23, G:0.26, T:0.20
Consensus pattern (24 bp):
TGTCCCGAAGGACAACGTAGAATT
Found at i:1520978 original size:22 final size:22
Alignment explanation
Indices: 1520952--1520995 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1520942 AAAATACGGT
* *
1520952 ATGAACATTACCGTAAATAGTA
1 ATGAACAATACCATAAATAGTA
1520974 ATGAACAATACCATAAATAGTA
1 ATGAACAATACCATAAATAGTA
1520996 CTACAGTACC
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:0.50, C:0.14, G:0.11, T:0.25
Consensus pattern (22 bp):
ATGAACAATACCATAAATAGTA
Found at i:1521019 original size:20 final size:20
Alignment explanation
Indices: 1520996--1521044 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
1520986 ATAAATAGTA
1520996 CTACAGTACCGTGAACAATG
1 CTACAGTACCGTGAACAATG
*
1521016 CTACAGTACCGTGAACAGTG
1 CTACAGTACCGTGAACAATG
1521036 CTACAGTAC
1 CTACAGTAC
1521045 ATCGATGCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (20 bp):
CTACAGTACCGTGAACAATG
Found at i:1521073 original size:21 final size:21
Alignment explanation
Indices: 1521034--1521075 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1521024 CCGTGAACAG
* *
1521034 TGCTACAGTACATCGATGCAT
1 TGCTACAGTACACCAATGCAT
*
1521055 TGCTACAGTGCACCAATGCAT
1 TGCTACAGTACACCAATGCAT
1521076 AAACTTCGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (21 bp):
TGCTACAGTACACCAATGCAT
Found at i:1521695 original size:24 final size:23
Alignment explanation
Indices: 1521671--1521748 Score: 77
Period size: 23 Copynumber: 3.3 Consensus size: 23
1521661 TCATATAAAT
1521671 TTGCACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
** *
1521694 TTTGTC-CCGAAGAACCGCGTAGAA
1 -TTG-CACCGAAGTGCCACGTAGAA
* * *
1521718 ATACACTGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
1521741 TTGCACCG
1 TTGCACCG
1521749 TAGTTCCGTA
Statistics
Matches: 40, Mismatches: 12, Indels: 5
0.70 0.21 0.09
Matches are distributed among these distances:
22 1 0.03
23 20 0.50
24 18 0.45
25 1 0.03
ACGTcount: A:0.31, C:0.26, G:0.24, T:0.19
Consensus pattern (23 bp):
TTGCACCGAAGTGCCACGTAGAA
Found at i:1522031 original size:30 final size:31
Alignment explanation
Indices: 1521997--1522060 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
1521987 TTATATTGCG
1521997 TAGACATATCA-TTTCCATAACTTTATCACA
1 TAGACATATCATTTTCCATAACTTTATCACA
*
1522027 TAGACATATCATTTTCCATACCTTTATCACA
1 TAGACATATCATTTTCCATAACTTTATCACA
1522058 TAG
1 TAG
1522061 CTCATATAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 11 0.34
31 21 0.66
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.38
Consensus pattern (31 bp):
TAGACATATCATTTTCCATAACTTTATCACA
Found at i:1527862 original size:182 final size:183
Alignment explanation
Indices: 1527458--1527865 Score: 599
Period size: 182 Copynumber: 2.2 Consensus size: 183
1527448 TTTTGAGACA
* * *
1527458 TGTTATATTGTTAAGTTTCAATACATTTTTT-TAAGTATCGACACTTTATAGGCGCTATTACTGC
1 TGTTATATTGTTAAGTGTCGATACATTTTTTATAAGTATCGACACTTTATAGCCGCTATTACTGC
* * *
1527522 TTGTCTTTTAAATTCCAAAAGTCTGTCGACATTTATAATAAAGTATCGACACTTTCAATATATCC
66 TTGTCTTTTAAATTCCAAAAGTCTGTCGACACTTATAATAAAGTATCGACACTATCAACATATCC
* * ** *
1527587 GGTATCTCTTTACAGTTTTTTCATTTTGAGACCGGTTTTATCATATTTTTACC
131 GGTAGCACTTTACAGTTTGGTCATTTTGAGACCGATTTTATCATATTTTTACC
*
1527640 TGTTATATTGTTAAGTGTCGATACATTTTTTA-AAGTATCGACACTTTATAGCCGCTCTTACTGC
1 TGTTATATTGTTAAGTGTCGATACATTTTTTATAAGTATCGACACTTTATAGCCGCTATTACTGC
* * *
1527704 TTGTCTTTTAAATTCCAAAAGT-T-TCGATACTTATTATGAAGTATCGACACTATCAACATATCC
66 TTGTCTTTTAAATTCCAAAAGTCTGTCGACACTTATAATAAAGTATCGACACTATCAACATATCC
* * *
1527767 TGTAGCACTTTACCGGTTTGGTCATTTTGAGACCGATTTTGTCATATTTTTACC
131 GGTAGCACTTTA-CAGTTTGGTCATTTTGAGACCGATTTTATCATATTTTTACC
**
1527821 TGTTATATTGTTAAGTGTCGATACATTTTTTATTTGTATCGACAC
1 TGTTATATTGTTAAGTGTCGATACATTTTTTATAAGTATCGACAC
1527866 AAACCGACAA
Statistics
Matches: 203, Mismatches: 20, Indels: 6
0.89 0.09 0.03
Matches are distributed among these distances:
180 43 0.21
181 69 0.34
182 91 0.45
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.44
Consensus pattern (183 bp):
TGTTATATTGTTAAGTGTCGATACATTTTTTATAAGTATCGACACTTTATAGCCGCTATTACTGC
TTGTCTTTTAAATTCCAAAAGTCTGTCGACACTTATAATAAAGTATCGACACTATCAACATATCC
GGTAGCACTTTACAGTTTGGTCATTTTGAGACCGATTTTATCATATTTTTACC
Found at i:1528324 original size:14 final size:14
Alignment explanation
Indices: 1528305--1528333 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1528295 ATAGTATGGT
1528305 TTTTTGAAAACATA
1 TTTTTGAAAACATA
1528319 TTTTTGAAAACATA
1 TTTTTGAAAACATA
1528333 T
1 T
1528334 ACTATATAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (14 bp):
TTTTTGAAAACATA
Found at i:1528361 original size:38 final size:36
Alignment explanation
Indices: 1528319--1528439 Score: 154
Period size: 38 Copynumber: 3.3 Consensus size: 36
1528309 TGAAAACATA
1528319 TTTTTGAAAACATATACTATATAGTTTTTAAAAATGTT
1 TTTTTGAAAACATATA-TATATAGTTTTT-AAAATGTT
* ** *
1528357 TTTTTGAAAATATATATAATATAGTTTTTGAAAACATA
1 TTTTTGAAAACATATAT-ATATAGTTTTT-AAAATGTT
*
1528395 TTTTTGAAAACATATA-ATATAGTTATTAAAATGTT
1 TTTTTGAAAACATATATATATAGTTTTTAAAATGTT
1528430 TTTTTGAAAA
1 TTTTTGAAAA
1528440 AACATATTTT
Statistics
Matches: 72, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
35 15 0.21
36 10 0.14
37 1 0.01
38 46 0.64
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.46
Consensus pattern (36 bp):
TTTTTGAAAACATATATATATAGTTTTTAAAATGTT
Found at i:1528370 original size:36 final size:36
Alignment explanation
Indices: 1528284--1528418 Score: 153
Period size: 38 Copynumber: 3.6 Consensus size: 36
1528274 ATATATAGTC
* *
1528284 TTTGAAAATATATAGTATGGTTTTTTGAAAACATATT
1 TTTGAAAATATATAATATAG-TTTTTGAAAACATATT
* * ** *
1528321 TTTGAAAACATATACTATATAGTTTTTAAAAATGTTTT
1 TTTGAAAATATATA--ATATAGTTTTTGAAAACATATT
1528359 TTTGAAAATATATATAATATAGTTTTTGAAAACATATT
1 TTTG-AAA-ATATATAATATAGTTTTTGAAAACATATT
*
1528397 TTTGAAAACATATAATATAGTT
1 TTTGAAAATATATAATATAGTT
1528419 ATTAAAATGT
Statistics
Matches: 81, Mismatches: 13, Indels: 9
0.79 0.13 0.09
Matches are distributed among these distances:
36 14 0.17
37 16 0.20
38 38 0.47
39 7 0.09
40 6 0.07
ACGTcount: A:0.41, C:0.04, G:0.10, T:0.45
Consensus pattern (36 bp):
TTTGAAAATATATAATATAGTTTTTGAAAACATATT
Found at i:1528400 original size:14 final size:14
Alignment explanation
Indices: 1528381--1528409 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1528371 TATAATATAG
1528381 TTTTTGAAAACATA
1 TTTTTGAAAACATA
1528395 TTTTTGAAAACATA
1 TTTTTGAAAACATA
1528409 T
1 T
1528410 AATATAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (14 bp):
TTTTTGAAAACATA
Found at i:1528447 original size:51 final size:49
Alignment explanation
Indices: 1528380--1528488 Score: 159
Period size: 51 Copynumber: 2.2 Consensus size: 49
1528370 ATATAATATA
*
1528380 GTTTTTG--AAAACATATTTTTGAAAACATATAATATAGTTATTAAAATG
1 GTTTTTGAAAAAACATATTTTTGAAAACATAT-ATATAGTTATTAAAACG
* *
1528428 TTTTTTTGAAAAAACATATTTTTGAAAACATATATATAGTTTTTAAAACG
1 -GTTTTTGAAAAAACATATTTTTGAAAACATATATATAGTTATTAAAACG
1528478 GTTTTTGAAAA
1 GTTTTTGAAAA
1528489 CGTATATAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
49 16 0.30
50 15 0.28
51 23 0.43
ACGTcount: A:0.42, C:0.05, G:0.10, T:0.43
Consensus pattern (49 bp):
GTTTTTGAAAAAACATATTTTTGAAAACATATATATAGTTATTAAAACG
Found at i:1528540 original size:19 final size:21
Alignment explanation
Indices: 1528494--1528541 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
1528484 GAAAACGTAT
1528494 ATAATATATATAATTTTTGAA
1 ATAATATATATAATTTTTGAA
* *
1528515 ATCATAT-TATAGTTTTTGAA
1 ATAATATATATAATTTTTGAA
1528535 A-AATATA
1 ATAATATA
1528542 GATTTTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 4 0.17
20 13 0.57
21 6 0.26
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (21 bp):
ATAATATATATAATTTTTGAA
Found at i:1528547 original size:16 final size:17
Alignment explanation
Indices: 1528522--1528559 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1528512 GAAATCATAT
* *
1528522 TATAGTTTTTGAA-AAA
1 TATAGATTTTAAATAAA
1528538 TATAGATTTTAAATAAA
1 TATAGATTTTAAATAAA
1528555 TATAG
1 TATAG
1528560 TGTACGTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (17 bp):
TATAGATTTTAAATAAA
Found at i:1536050 original size:18 final size:19
Alignment explanation
Indices: 1536004--1536043 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1535994 CAACTCTGAC
*
1536004 CAAAGTCAACGGGTCGGGT
1 CAAAGTCAACGGTTCGGGT
*
1536023 CAAAGTCAACGGTTTGGGT
1 CAAAGTCAACGGTTCGGGT
1536042 CA
1 CA
1536044 GGTCAACAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.20, G:0.33, T:0.20
Consensus pattern (19 bp):
CAAAGTCAACGGTTCGGGT
Found at i:1537663 original size:21 final size:22
Alignment explanation
Indices: 1537639--1537679 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1537629 ATGGAGGAAA
*
1537639 AAATCAAG-TAGTTGGAAGATC
1 AAATCAAGATAGTTAGAAGATC
*
1537660 AAATGAAGATAGTTAGAAGA
1 AAATCAAGATAGTTAGAAGA
1537680 GATGATAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.49, C:0.05, G:0.24, T:0.22
Consensus pattern (22 bp):
AAATCAAGATAGTTAGAAGATC
Found at i:1546544 original size:93 final size:95
Alignment explanation
Indices: 1546385--1546605 Score: 331
Period size: 93 Copynumber: 2.3 Consensus size: 95
1546375 TACTGATGAG
* * *
1546385 GTAGTATCGATACCATGGTAAGGGTATCGATACTAGGTAACGTCGAACCTAATTTTGGTATCGAT
1 GTAGTATCGATACCATGGTAAGGGTATCGATACCAAGTAACATCGAACCTAATTTTGGTATCGAT
* *
1546450 ACCGG-AG-GGGTATCGGTACCATAGTATA
66 ACCGGAAGAGGGTATCGATACCATAGTAGA
* * *
1546478 GTAGTATCGATACCATGGTGAGGATATCGATACCAAG-ACACATCGAAGCTAATTTTGGTATCGA
1 GTAGTATCGATACCATGGTAAGGGTATCGATACCAAGTA-ACATCGAACCTAATTTTGGTATCGA
*
1546542 TACCGGAAGAGGGTATCGATACCATAGTAGG
65 TACCGGAAGAGGGTATCGATACCATAGTAGA
1546573 GTAGTATCGATACCATGGTAAGGGTATCGATAC
1 GTAGTATCGATACCATGGTAAGGGTATCGATAC
1546606 TGAAGACCAG
Statistics
Matches: 114, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
92 1 0.01
93 62 0.54
94 2 0.02
95 49 0.43
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.26
Consensus pattern (95 bp):
GTAGTATCGATACCATGGTAAGGGTATCGATACCAAGTAACATCGAACCTAATTTTGGTATCGAT
ACCGGAAGAGGGTATCGATACCATAGTAGA
Found at i:1546573 original size:19 final size:19
Alignment explanation
Indices: 1546534--1546605 Score: 67
Period size: 22 Copynumber: 3.6 Consensus size: 19
1546524 AGCTAATTTT
1546534 GGTATCGATACCGGA-AG-AG
1 GGTATCGATACC--ATAGTAG
1546553 GGTATCGATACCATAGTAGG
1 GGTATCGATACCATAGTA-G
*
1546573 GTAGTATCGATACCATGGTAAG
1 G--GTATCGATACCATAGT-AG
1546595 GGTATCGATAC
1 GGTATCGATAC
1546606 TGAAGACCAG
Statistics
Matches: 46, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
17 1 0.02
18 2 0.04
19 13 0.28
20 12 0.26
22 17 0.37
23 1 0.02
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.24
Consensus pattern (19 bp):
GGTATCGATACCATAGTAG
Found at i:1546582 original size:22 final size:20
Alignment explanation
Indices: 1546551--1546605 Score: 74
Period size: 22 Copynumber: 2.6 Consensus size: 20
1546541 ATACCGGAAG
1546551 AGGGTATCGATACCATAGTA
1 AGGGTATCGATACCATAGTA
* *
1546571 GGGTAGTATCGATACCATGGTA
1 AGG--GTATCGATACCATAGTA
1546593 AGGGTATCGATAC
1 AGGGTATCGATAC
1546606 TGAAGACCAG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 12 0.40
22 18 0.60
ACGTcount: A:0.31, C:0.15, G:0.29, T:0.25
Consensus pattern (20 bp):
AGGGTATCGATACCATAGTA
Found at i:1546993 original size:59 final size:59
Alignment explanation
Indices: 1546927--1547398 Score: 615
Period size: 59 Copynumber: 8.0 Consensus size: 59
1546917 GATTACCAAA
* *
1546927 AGGGCACTTCGTGTGCTAACATGAGAAATAATTCATACTAAGTGTATGCATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAAGAATTCATACTAAGTGTATGAATTTCCATAT
1546986 AGGGCACTTCGTGTGCTAACATGAGAAAGAATTCATACTAAGTGTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAAGAATTCATACTAAGTGTATGAATTTCCATAT
*
1547045 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAAGAATTCATACTAAGTGTATGAATTTCCATAT
* * * * *
1547104 AGGGCAATTTGTGTGCTAACATTAGAAGGAATTCATACTAAGTGTATGAATTTTCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAAGAATTCATACTAAGTGTATGAATTTCCATAT
* * * * *
1547163 AGGACACTTTGTGCGCTAACATGAGAAGGAATTCATACTAAGTGAATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAAGAATTCATACTAAGTGTATGAATTTCCATAT
* **
1547222 AGGGCACTTCGTGTGCTAACATGAGAAAGAATTCAAACTAAGTGTATGAATTTCTGTAT
1 AGGGCACTTCGTGTGCTAACATGAGAAAGAATTCATACTAAGTGTATGAATTTCCATAT
* * * * * * * * *
1547281 AGGGTACTTCGTGTGCTAAAATAAGAATA-AATTCATAATAAATATATGACTTTTCGTATT
1 AGGGCACTTCGTGTGCTAACATGAGAA-AGAATTCATACTAAGTGTATGAATTTCCATA-T
* * * * ** * *
1547341 A-GACACCTAGTGTGCTAAAATGATTAGGAATTCATATTAAGTGTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAAGAATTCATACTAAGTGTATGAATTTCCATAT
1547399 GGGAAATAAA
Statistics
Matches: 365, Mismatches: 45, Indels: 7
0.88 0.11 0.02
Matches are distributed among these distances:
58 1 0.00
59 361 0.99
60 3 0.01
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (59 bp):
AGGGCACTTCGTGTGCTAACATGAGAAAGAATTCATACTAAGTGTATGAATTTCCATAT
Found at i:1548978 original size:14 final size:14
Alignment explanation
Indices: 1548911--1548976 Score: 78
Period size: 14 Copynumber: 4.7 Consensus size: 14
1548901 AACTTGGTCC
* *
1548911 GAGTCAACTAATTT
1 GAGTCAACTCATAT
**
1548925 GAGTCAACTCATCC
1 GAGTCAACTCATAT
1548939 GAGTCAACTCATAT
1 GAGTCAACTCATAT
* *
1548953 GAGTTAACTCGTAT
1 GAGTCAACTCATAT
1548967 GAGTCAACTC
1 GAGTCAACTC
1548977 GTTAACTTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 44 1.00
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.29
Consensus pattern (14 bp):
GAGTCAACTCATAT
Found at i:1549903 original size:26 final size:26
Alignment explanation
Indices: 1549866--1549916 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
1549856 GGATTTATAG
1549866 AAATGCCCTAAAGTGT-AAATGACCA
1 AAATGCCCTAAAGTGTAAAATGACCA
1549891 AAATGCTCCTAAAGTGTAAAATGACC
1 AAATGC-CCTAAAGTGTAAAATGACC
1549917 TAAAGTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 6 0.25
26 10 0.42
27 8 0.33
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.22
Consensus pattern (26 bp):
AAATGCCCTAAAGTGTAAAATGACCA
Found at i:1553412 original size:14 final size:14
Alignment explanation
Indices: 1553350--1553415 Score: 53
Period size: 14 Copynumber: 4.6 Consensus size: 14
1553340 GGTCTAGTCA
*
1553350 CCGAGTCAACTTGGT
1 CCGAGTCAAC-TCGT
1553365 CCGAGTCAACTCGT
1 CCGAGTCAACTCGT
* * *
1553379 CTGAGTAAAC-CTTT
1 CCGAGTCAACTC-GT
**
1553393 TTGAGTCAACTCGT
1 CCGAGTCAACTCGT
1553407 CCGAGTCAA
1 CCGAGTCAA
1553416 TCTGTTGACT
Statistics
Matches: 40, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
13 1 0.03
14 28 0.70
15 11 0.28
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.27
Consensus pattern (14 bp):
CCGAGTCAACTCGT
Found at i:1554368 original size:26 final size:26
Alignment explanation
Indices: 1554330--1554380 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
1554320 GGATTTATAG
1554330 AAATGCCATAAAGTGT-AAATGACCA
1 AAATGCCATAAAGTGTAAAATGACCA
*
1554355 AAATGTCCCTAAAGTGTAAAATGACC
1 AAATG-CCATAAAGTGTAAAATGACC
1554381 TAAAGTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 5 0.22
26 10 0.43
27 8 0.35
ACGTcount: A:0.45, C:0.18, G:0.16, T:0.22
Consensus pattern (26 bp):
AAATGCCATAAAGTGTAAAATGACCA
Found at i:1556488 original size:9 final size:9
Alignment explanation
Indices: 1556469--1556515 Score: 51
Period size: 9 Copynumber: 5.1 Consensus size: 9
1556459 ACGTATTATT
1556469 TATTATATTA
1 TATTAT-TTA
1556479 TATTATTTA
1 TATTATTTA
*
1556488 TATTATTTT
1 TATTATTTA
*
1556497 TATT-TTTT
1 TATTATTTA
1556505 TCATTATTTA
1 T-ATTATTTA
1556515 T
1 T
1556516 TTGTTTCTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
8 5 0.15
9 18 0.55
10 10 0.30
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (9 bp):
TATTATTTA
Found at i:1556488 original size:14 final size:12
Alignment explanation
Indices: 1556462--1556517 Score: 55
Period size: 12 Copynumber: 4.7 Consensus size: 12
1556452 ATAATTTACG
1556462 TATTATTTATTA
1 TATTATTTATTA
1556474 TATTATATTATTTA
1 TATTAT-TTA-TTA
1556488 TATTATTT-TTA
1 TATTATTTATTA
*
1556499 T-TTTTTTCATTA
1 TATTATTT-ATTA
1556511 T-TTATTT
1 TATTATTT
1556518 GTTTCTAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
10 5 0.13
11 4 0.11
12 15 0.39
13 5 0.13
14 9 0.24
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (12 bp):
TATTATTTATTA
Found at i:1557876 original size:20 final size:20
Alignment explanation
Indices: 1557853--1557891 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1557843 TTTGAATTTT
1557853 CTTTTT-TTTCATTTAATATC
1 CTTTTTGTTT-ATTTAATATC
*
1557873 CTTTTTGTTTATTTTATAT
1 CTTTTTGTTTATTTAATAT
1557892 TATTTTATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.18, C:0.10, G:0.03, T:0.69
Consensus pattern (20 bp):
CTTTTTGTTTATTTAATATC
Found at i:1559448 original size:17 final size:17
Alignment explanation
Indices: 1559426--1559463 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1559416 ATTTTAATAG
*
1559426 AATTTTAATTAAATTAT
1 AATTTTAATTAAATAAT
*
1559443 AATTTTTATTAAATAAT
1 AATTTTAATTAAATAAT
1559460 AATT
1 AATT
1559464 CATTTAAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AATTTTAATTAAATAAT
Found at i:1567357 original size:35 final size:35
Alignment explanation
Indices: 1567318--1567387 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
1567308 TTGATGCTAT
*
1567318 TTATAATAAGTCATGTCACTTGGTGAATAGACTTA
1 TTATAATAAGTCATGTAACTTGGTGAATAGACTTA
*
1567353 TTATAATAAGTCATGTAACTTGGTGAATGGACTTA
1 TTATAATAAGTCATGTAACTTGGTGAATAGACTTA
1567388 ATTTTTAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.37
Consensus pattern (35 bp):
TTATAATAAGTCATGTAACTTGGTGAATAGACTTA
Found at i:1567912 original size:3 final size:3
Alignment explanation
Indices: 1567904--1567934 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1567894 ATGATAATAT
1567904 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1567935 CTCAGATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1570251 original size:59 final size:58
Alignment explanation
Indices: 1570174--1570413 Score: 243
Period size: 59 Copynumber: 4.1 Consensus size: 58
1570164 CTAACTTGAG
* * *
1570174 TATGAC-ACATAAGGTCATGCCCACCATCTGAACTAGTTATACTTTAGTGCAGTCCCGAA
1 TATGACAACA-AA-GTCATGCCCACCATATGCACTAGTTATACTTTAGTGCAATCCCGAA
* * * *
1570233 TATGACATACAAAGTCATGCCCACTATTTGCACTAGATATACTTTAGTGTAATCCCGAA
1 TATGACA-ACAAAGTCATGCCCACCATATGCACTAGTTATACTTTAGTGCAATCCCGAA
* * * **
1570292 CATGAC-ACATAAGGTCGTGCCCACCATATGCACTAGTTATACTTTAGTGTAATCCATAA
1 TATGACAACA-AA-GTCATGCCCACCATATGCACTAGTTATACTTTAGTGCAATCCCGAA
* * ** *
1570351 TATGA-AACATAAGGTCGTACTTACCATATGCACTAGTTATACTTTAGTGCAATCTCGAA
1 TATGACAACA-AA-GTCATGCCCACCATATGCACTAGTTATACTTTAGTGCAATCCCGAA
1570410 TATG
1 TATG
1570414 CATCCTACTG
Statistics
Matches: 155, Mismatches: 21, Indels: 10
0.83 0.11 0.05
Matches are distributed among these distances:
57 3 0.02
58 2 0.01
59 145 0.94
60 2 0.01
61 3 0.02
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (58 bp):
TATGACAACAAAGTCATGCCCACCATATGCACTAGTTATACTTTAGTGCAATCCCGAA
Found at i:1570383 original size:118 final size:118
Alignment explanation
Indices: 1570175--1570409 Score: 294
Period size: 118 Copynumber: 2.0 Consensus size: 118
1570165 TAACTTGAGT
* * *
1570175 ATGACACATAAGGTCATGCCCACCATCTGAACTAGTTATACTTTAGTGCAGTCCCGAATATGACA
1 ATGACACATAAGGTCATGCCCACCATATGAACTAGTTATACTTTAGTGCAATCCAGAATATGACA
* * * *
1570240 TACAAAGTCATGCCCACTATTTGCACTAGATATACTTTAGTGTAATCCCGAAC
66 TACAAAGTCATACCCACCATATGCACTAGATATACTTTAGTGCAATCCCGAAC
* * * *
1570293 ATGACACATAAGGTCGTGCCCACCATATGCACTAGTTATACTTTAGTGTAATCCATAATATGA-A
1 ATGACACATAAGGTCATGCCCACCATATGAACTAGTTATACTTTAGTGCAATCCAGAATATGACA
* ** * *
1570357 -ACATAAGGTCGTACTTACCATATGCACTAGTTATACTTTAGTGCAATCTCGAA
66 TACA-AA-GTCATACCCACCATATGCACTAGATATACTTTAGTGCAATCCCGAA
1570410 TATGCATCCT
Statistics
Matches: 99, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
116 3 0.03
117 3 0.03
118 93 0.94
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (118 bp):
ATGACACATAAGGTCATGCCCACCATATGAACTAGTTATACTTTAGTGCAATCCAGAATATGACA
TACAAAGTCATACCCACCATATGCACTAGATATACTTTAGTGCAATCCCGAAC
Found at i:1576003 original size:59 final size:59
Alignment explanation
Indices: 1575909--1576063 Score: 220
Period size: 59 Copynumber: 2.6 Consensus size: 59
1575899 CTAACTTGAG
* * * *
1575909 TATGACACATAAGGTCATGCCCACCATCTGAACTAGCTATACTTTAGTGCAGTCCCGAA
1 TATGACACATAAGGTCATGCCCACCATATGCACTAGATATACTTTAGTGCAATCCCGAA
* * * * *
1575968 TATGACATATAAAGTCATGCCCACTATTTGCACTAGATATACTTTAGTGTAATCCCGAA
1 TATGACACATAAGGTCATGCCCACCATATGCACTAGATATACTTTAGTGCAATCCCGAA
*
1576027 TATGACACATAAGGTCGTGCCCACCATATGCACTAGA
1 TATGACACATAAGGTCATGCCCACCATATGCACTAGA
1576064 ATTTTAATTT
Statistics
Matches: 83, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
59 83 1.00
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (59 bp):
TATGACACATAAGGTCATGCCCACCATATGCACTAGATATACTTTAGTGCAATCCCGAA
Found at i:1577107 original size:59 final size:59
Alignment explanation
Indices: 1577028--1577208 Score: 238
Period size: 59 Copynumber: 3.1 Consensus size: 59
1577018 CTAACTCAAG
* * * * **
1577028 TATGACACATAAGGTCGTGCCCAACATCTGCACTAATTATAATTTAGTGCAGTCATGAA
1 TATGACACATAAGGTCGTGCCCAACATATGCACTAGTTATACTTTAGTGCAATCACAAA
* * * *
1577087 TATGACACATAAGGTTGTGCCCACCATATGCACTAGTTATACTTTAATGCAATCCCAAA
1 TATGACACATAAGGTCGTGCCCAACATATGCACTAGTTATACTTTAGTGCAATCACAAA
* *
1577146 TATGACACATAAGGTCGTGCCC-ACAATATACACTAGTTATACTTTAGTGCAATCCCAAA
1 TATGACACATAAGGTCGTGCCCAAC-ATATGCACTAGTTATACTTTAGTGCAATCACAAA
1577205 TATG
1 TATG
1577209 CAACCTGCTA
Statistics
Matches: 107, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
58 1 0.01
59 106 0.99
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (59 bp):
TATGACACATAAGGTCGTGCCCAACATATGCACTAGTTATACTTTAGTGCAATCACAAA
Found at i:1580227 original size:35 final size:35
Alignment explanation
Indices: 1580188--1580257 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
1580178 TTGATGCTAT
*
1580188 TTATAATAAGTCATGTCATTTGGTGAATAGACTTA
1 TTATAATAAGTCATGTCACTTGGTGAATAGACTTA
*
1580223 TTATAATAAGTCATGTCACTTGGTGAATGGACTTA
1 TTATAATAAGTCATGTCACTTGGTGAATAGACTTA
1580258 ATTTTTAGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.39
Consensus pattern (35 bp):
TTATAATAAGTCATGTCACTTGGTGAATAGACTTA
Found at i:1580776 original size:3 final size:3
Alignment explanation
Indices: 1580770--1580808 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1580760 AGAATAATAA
1580770 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1580809 CTCGGATTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1581359 original size:120 final size:120
Alignment explanation
Indices: 1581154--1581379 Score: 267
Period size: 120 Copynumber: 1.9 Consensus size: 120
1581144 CAAGTCTCGT
* * * ** * *
1581154 AGCTATGAGTTCGTATGAGAACTTTAAACACAACTATGTCTTTCATAAATTTTTTGTGGGTGGTT
1 AGCTATGAGTTCGTAGGAGAACTTTAAACACAACTAAGTCTTTCATAAAATGGTAGTGGGTAGTT
*
1581219 TAATTAGAAGAATAAAAAGAAAAAGAATAAGAAAAAGATAAAATTCAAGTCCCAC
66 TAATTAGAAGAATAAAAAGAAAAAGAAGAAGAAAAAGATAAAATTCAAGTCCCAC
* * *
1581274 AGCTATGAGTTTGTAGGATAACTTTAAAC-CAAGCTAAGTCTTTTATAAAATGGTAGTGGGTAGT
1 AGCTATGAGTTCGTAGGAGAACTTTAAACACAA-CTAAGTCTTTCATAAAATGGTAGTGGGTAGT
* * *
1581338 TTAA-TAGGATGAAATAGAAGAAGAAGAAGAAGAAGAAGAAGA
65 TTAATTA-GAAG-AATA-AA-AAGAAAAAGAAGAAGAAAAAGA
1581380 AGAAGAAGAA
Statistics
Matches: 87, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
119 5 0.06
120 57 0.66
121 4 0.05
122 2 0.02
123 19 0.22
ACGTcount: A:0.43, C:0.08, G:0.21, T:0.27
Consensus pattern (120 bp):
AGCTATGAGTTCGTAGGAGAACTTTAAACACAACTAAGTCTTTCATAAAATGGTAGTGGGTAGTT
TAATTAGAAGAATAAAAAGAAAAAGAAGAAGAAAAAGATAAAATTCAAGTCCCAC
Found at i:1581361 original size:3 final size:3
Alignment explanation
Indices: 1581353--1581389 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1581343 AGGATGAAAT
1581353 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1581390 ATTTAATTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1588083 original size:15 final size:15
Alignment explanation
Indices: 1588063--1588093 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1588053 TTTAATTTTA
1588063 ATTGTAATTTATGTC
1 ATTGTAATTTATGTC
1588078 ATTGTAATTTATGTC
1 ATTGTAATTTATGTC
1588093 A
1 A
1588094 ATGCAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.06, G:0.13, T:0.52
Consensus pattern (15 bp):
ATTGTAATTTATGTC
Found at i:1588471 original size:22 final size:22
Alignment explanation
Indices: 1588431--1588472 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1588421 TTGGTGCTGG
*
1588431 AAACAAGATAGAAATAAGATTA
1 AAACAAGATAGAAAAAAGATTA
1588453 AAACAAGATA-AAGAAAAGAT
1 AAACAAGATAGAA-AAAAGAT
1588473 AAATGAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.67, C:0.05, G:0.14, T:0.14
Consensus pattern (22 bp):
AAACAAGATAGAAAAAAGATTA
Found at i:1588884 original size:15 final size:17
Alignment explanation
Indices: 1588859--1588895 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1588849 TAAAGGTTCT
*
1588859 AAATAACTAATGAA-TA
1 AAATAACTAATAAACTA
1588875 AAATAA-TAATAAACTA
1 AAATAACTAATAAACTA
1588891 AAATA
1 AAATA
1588896 TCTCAACTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (17 bp):
AAATAACTAATAAACTA
Found at i:1591769 original size:21 final size:21
Alignment explanation
Indices: 1591745--1591789 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
1591735 CTCCTTACAG
1591745 AACTAGGTGTCACTCTTCCCC
1 AACTAGGTGTCACTCTTCCCC
1591766 AACTAGGTGTCACTCTTCCCC
1 AACTAGGTGTCACTCTTCCCC
1591787 AAC
1 AAC
1591790 AACCAGTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.38, G:0.13, T:0.27
Consensus pattern (21 bp):
AACTAGGTGTCACTCTTCCCC
Found at i:1595844 original size:24 final size:24
Alignment explanation
Indices: 1595803--1595848 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
1595793 ATCAAAAGTA
1595803 TTAGCATTAACAACATCAACATTT
1 TTAGCATTAACAACATCAACATTT
*
1595827 TTAGCATTATA-AATATCAACAT
1 TTAGCATTA-ACAACATCAACAT
1595849 CAGAAGGCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 19 0.95
25 1 0.05
ACGTcount: A:0.43, C:0.17, G:0.04, T:0.35
Consensus pattern (24 bp):
TTAGCATTAACAACATCAACATTT
Found at i:1596494 original size:18 final size:18
Alignment explanation
Indices: 1596471--1596515 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
1596461 TATTTAACAA
*
1596471 ATTGAAGAATATATTGAT
1 ATTGAAGAATAGATTGAT
1596489 ATTGAAGAATAGATTGAT
1 ATTGAAGAATAGATTGAT
1596507 ATTGAAGAA
1 ATTGAAGAA
1596516 GAAAAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.20, T:0.33
Consensus pattern (18 bp):
ATTGAAGAATAGATTGAT
Found at i:1596929 original size:21 final size:21
Alignment explanation
Indices: 1596900--1597138 Score: 242
Period size: 21 Copynumber: 11.5 Consensus size: 21
1596890 TTCCAGATTT
*
1596900 GCAACGCGAACTTCGACTATC
1 GCAATGCGAACTTCGACTATC
1596921 GCAATGCGAACTTCGACTATC
1 GCAATGCGAACTTCGACTATC
* *
1596942 GCAATGCAAACTTGGACTATC
1 GCAATGCGAACTTCGACTATC
* *
1596963 GCAATGTGAA-TAT-GTA-AATC
1 GCAATGCGAACT-TCG-ACTATC
*
1596983 GCAATGCGATA-GTCGACTATC
1 GCAATGCGA-ACTTCGACTATC
* *
1597004 ACAATGCGAACTTGGACTATC
1 GCAATGCGAACTTCGACTATC
*
1597025 GCAACGCGAACTTCGACTATC
1 GCAATGCGAACTTCGACTATC
*
1597046 GCAATGCGAACTTGGACTATC
1 GCAATGCGAACTTCGACTATC
*
1597067 GCAACGCGAACTTCGACTATC
1 GCAATGCGAACTTCGACTATC
*
1597088 GCAATGCGAA-TAT-GTA-AATC
1 GCAATGCGAACT-TCG-ACTATC
*
1597108 GCAATGCGATA-GTCGACTATC
1 GCAATGCGA-ACTTCGACTATC
*
1597129 TCAATGCGAA
1 GCAATGCGAA
1597139 TATGTAATTC
Statistics
Matches: 183, Mismatches: 24, Indels: 23
0.80 0.10 0.10
Matches are distributed among these distances:
20 33 0.18
21 150 0.82
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.23
Consensus pattern (21 bp):
GCAATGCGAACTTCGACTATC
Found at i:1597110 original size:20 final size:20
Alignment explanation
Indices: 1597085--1597157 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
1597075 AACTTCGACT
1597085 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
1597105 ATCGCAATGCG-ATA-GTCGACT
1 ATCGCAATGCGAATATGT--A-A
*
1597126 ATCTCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
* *
1597146 TTCGCATTGCGA
1 ATCGCAATGCGA
1597158 TAGTCCAAGT
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
18 2 0.05
19 3 0.07
20 21 0.50
21 11 0.26
22 3 0.07
23 2 0.05
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:1597122 original size:125 final size:125
Alignment explanation
Indices: 1596900--1597138 Score: 424
Period size: 125 Copynumber: 1.9 Consensus size: 125
1596890 TTCCAGATTT
* *
1596900 GCAACGCGAACTTCGACTATCGCAATGCGAACTTCGACTATCGCAATGCAAACTTGGACTATCGC
1 GCAACGCGAACTTCGACTATCGCAATGCGAACTTCGACTATCGCAACGCAAACTTCGACTATCGC
*
1596965 AATGTGAATATGTAAATCGCAATGCGATAGTCGACTATCACAATGCGAACTTGGACTATC
66 AATGCGAATATGTAAATCGCAATGCGATAGTCGACTATCACAATGCGAACTTGGACTATC
* *
1597025 GCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAACGCGAACTTCGACTATCGC
1 GCAACGCGAACTTCGACTATCGCAATGCGAACTTCGACTATCGCAACGCAAACTTCGACTATCGC
*
1597090 AATGCGAATATGTAAATCGCAATGCGATAGTCGACTATCTCAATGCGAA
66 AATGCGAATATGTAAATCGCAATGCGATAGTCGACTATCACAATGCGAA
1597139 TATGTAATTC
Statistics
Matches: 108, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
125 108 1.00
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.23
Consensus pattern (125 bp):
GCAACGCGAACTTCGACTATCGCAATGCGAACTTCGACTATCGCAACGCAAACTTCGACTATCGC
AATGCGAATATGTAAATCGCAATGCGATAGTCGACTATCACAATGCGAACTTGGACTATC
Found at i:1597178 original size:41 final size:41
Alignment explanation
Indices: 1596957--1597162 Score: 177
Period size: 42 Copynumber: 5.0 Consensus size: 41
1596947 GCAAACTTGG
* *
1596957 ACTATCGCAATGTGAATATGTAAATCGCAATGCGATAGTCG
1 ACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCA
* * * * * *
1596998 ACTATCACAATGCGAACT-TGGACTATCGCAACGCGA-ACTTCG
1 ACTATCGCAATGCGAA-TATGTA-AATCGCAATGCGATA-GTCA
* * * * *
1597040 ACTATCGCAATGCGAACT-TGGACTATCGCAACGCGA-ACTTCG
1 ACTATCGCAATGCGAA-TATGTA-AATCGCAATGCGATA-GTCA
*
1597082 ACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCG
1 ACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCA
* * *
1597123 ACTATCTCAATGCGAATATGTAATTCGCATTGCGATAGTC
1 ACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
1597163 CAAGTTCGCA
Statistics
Matches: 146, Mismatches: 14, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
41 70 0.48
42 76 0.52
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (41 bp):
ACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCA
Found at i:1597193 original size:23 final size:21
Alignment explanation
Indices: 1597144--1597214 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
1597134 GCGAATATGT
1597144 AATTCGCATTGCGATAGTCCA
1 AATTCGCATTGCGATAGTCCA
* *
1597165 AGTTCGCATTGCGATTTATTCCA
1 AATTCGCATTGCGA--TAGTCCA
*
1597188 AATTCG--TTGTGATAGTCCA
1 AATTCGCATTGCGATAGTCCA
*
1597207 AAATCGCA
1 AATTCGCA
1597215 ACGACTGGTG
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
19 11 0.28
21 18 0.45
23 11 0.28
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.32
Consensus pattern (21 bp):
AATTCGCATTGCGATAGTCCA
Found at i:1597833 original size:6 final size:6
Alignment explanation
Indices: 1597822--1597855 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
1597812 GTCTCGTCTT
1597822 TGGTCG TGGTCG TGGTCG TGGTCG TGGTCG TGGT
1 TGGTCG TGGTCG TGGTCG TGGTCG TGGTCG TGGT
1597856 AATACGTGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.15, G:0.50, T:0.35
Consensus pattern (6 bp):
TGGTCG
Found at i:1598014 original size:21 final size:21
Alignment explanation
Indices: 1597982--1598186 Score: 301
Period size: 21 Copynumber: 9.8 Consensus size: 21
1597972 AATCGCAACG
*
1597982 CGAACTTCGCATTGCGATAGT
1 CGAAGTTCGCATTGCGATAGT
* *
1598003 CG-ACTATCGCATTGCGAT-TT
1 CGAAGT-TCGCATTGCGATAGT
*
1598023 AC-ATA-TTCTCATTGCGATAGT
1 -CGA-AGTTCGCATTGCGATAGT
*
1598044 CGAATTTCGCATTGCGATAGT
1 CGAAGTTCGCATTGCGATAGT
1598065 CGAAGTTCGCATTGCGATAGT
1 CGAAGTTCGCATTGCGATAGT
1598086 CGAAGTTCGCATTGCGATAGT
1 CGAAGTTCGCATTGCGATAGT
1598107 CGAAGTTCGCATTGCGATAGT
1 CGAAGTTCGCATTGCGATAGT
1598128 CGAAGTTCGCATTGCGATAGT
1 CGAAGTTCGCATTGCGATAGT
*
1598149 CCAAGTTCGCATTGCGATAGT
1 CGAAGTTCGCATTGCGATAGT
1598170 CGAAGTTCGCATTGCGA
1 CGAAGTTCGCATTGCGA
1598187 ATCTGGAAAC
Statistics
Matches: 170, Mismatches: 7, Indels: 14
0.89 0.04 0.07
Matches are distributed among these distances:
20 17 0.10
21 152 0.89
22 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (21 bp):
CGAAGTTCGCATTGCGATAGT
Found at i:1598422 original size:2 final size:2
Alignment explanation
Indices: 1598400--1598446 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
1598390 CCAATTAAAC
* *
1598400 AT AT AT AA AT AT AA AT A- 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
1598441 AT AT AT
1 AT AT AT
1598447 TACAAATAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1601102 original size:17 final size:16
Alignment explanation
Indices: 1601073--1601120 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
1601063 ATATTTTGTT
1601073 TTTAATTTATTTAAGTA
1 TTTAATTTATTTAA-TA
1601090 TTTACATTT-TTTAATA
1 TTTA-ATTTATTTAATA
* *
1601106 TTTTATTTAATTAAT
1 TTTAATTTATTTAAT
1601121 TTTTTATGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 4 0.15
16 10 0.37
17 9 0.33
18 4 0.15
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (16 bp):
TTTAATTTATTTAATA
Found at i:1603515 original size:35 final size:32
Alignment explanation
Indices: 1603476--1603560 Score: 80
Period size: 35 Copynumber: 2.4 Consensus size: 32
1603466 GTATTTTGGT
1603476 TAATTTTGTTTATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTTATTACCATTTAATA-C--TTATTG
* *
1603511 TAATTTGTGTATCATTTATCATTTAATACTTATTG
1 TAATTT-TGT-TTA-TTACCATTTAATACTTATTG
*
1603546 TAAGTTTGTTGTATT
1 TAATTTTGTT-TATT
1603561 TAAAATTATA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
33 3 0.07
34 4 0.10
35 17 0.40
36 3 0.07
37 3 0.07
38 12 0.29
ACGTcount: A:0.27, C:0.07, G:0.11, T:0.55
Consensus pattern (32 bp):
TAATTTTGTTTATTACCATTTAATACTTATTG
Found at i:1606367 original size:54 final size:54
Alignment explanation
Indices: 1606300--1607170 Score: 725
Period size: 54 Copynumber: 16.2 Consensus size: 54
1606290 GATGCACGCG
* * * *
1606300 TAGTGCTTATACGGTCGTTCATCAACACATGATGAATTTCGTGGGTCGCACACA
1 TAGTGCCTAAACGGTTGTTCATCAACACATGATGAATTTCGTGGGTTGCACACA
** * * * * *
1606354 TAGTGCCTCTACGGTTGTTCATCATCTCATGATGAATTCCGTGGATTACACACA
1 TAGTGCCTAAACGGTTGTTCATCAACACATGATGAATTTCGTGGGTTGCACACA
** * * * * * *
1606408 TAGTGCCTGTACGGTTGTTCATCATCTCATGATAAATTTCGTAGGTTGAATACA
1 TAGTGCCTAAACGGTTGTTCATCAACACATGATGAATTTCGTGGGTTGCACACA
* ** * * * *
1606462 TAGTGCTTGTACGGTTGTTCAACATCTCATGATGAA-TTCTGTAGGTTGCACACA
1 TAGTGCCTAAACGGTTGTTCATCAACACATGATGAATTTC-GTGGGTTGCACACA
* ** * *
1606516 TAGTGTCTGTACGGTTGTTCATCAACTCATGATGAATTTCGTGAGTTGCACACA
1 TAGTGCCTAAACGGTTGTTCATCAACACATGATGAATTTCGTGGGTTGCACACA
* * * * *
1606570 AAGTG-CTGAAACGATTGTTCATCAACATATGATGAATTCCTTGGGTTGCACACA
1 TAGTGCCT-AAACGGTTGTTCATCAACACATGATGAATTTCGTGGGTTGCACACA
* * * *
1606624 TAGTGCCGATACGGTTGTTCATCATCTCATGATGAATTAT-GTGGGTTGCACACA
1 TAGTGCCTAAACGGTTGTTCATCAACACATGATGAATT-TCGTGGGTTGCACACA
* ** * * * * *
1606678 TAGTGCTTGTATGCTTGTTCATCATCTCATGATGAATTTCGTAGGTTGCACACA
1 TAGTGCCTAAACGGTTGTTCATCAACACATGATGAATTTCGTGGGTTGCACACA
** ** * * *
1606732 TAGTGCCTGTACGGTTACTCATCAACTCATGATGAATTTTGTGAGTTGCACACA
1 TAGTGCCTAAACGGTTGTTCATCAACACATGATGAATTTCGTGGGTTGCACACA
* * * * * * *
1606786 AAGTG-CTGAAACAGTTGTTCATCAACATATGATGAGTTCCGTGAGTTGCATACA
1 TAGTGCCT-AAACGGTTGTTCATCAACACATGATGAATTTCGTGGGTTGCACACA
* * * * * * *
1606840 TGGTGCCAAAATGGTT-TTCCATCAACATATAATGAATTCCGTGAGTT--ACACA
1 TAGTGCCTAAACGGTTGTT-CATCAACACATGATGAATTTCGTGGGTTGCACACA
* * * * * *
1606892 CAGTTCCGAAACGGTTGTTCATCAACATATGATGAATTCCGTGAGTTGCACACA
1 TAGTGCCTAAACGGTTGTTCATCAACACATGATGAATTTCGTGGGTTGCACACA
* * * * *
1606946 TAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCCGTGAGTTGCACATA
1 TAGTGCCTAAACGGTTGTTCATCAACACATGATGAATTTCGTGGGTTGCACACA
* * * * * *
1607000 TAGTGTCGAAATGGTTGTTCATCAACATATGATGAATTTCGTGAGTTGCACCCA
1 TAGTGCCTAAACGGTTGTTCATCAACACATGATGAATTTCGTGGGTTGCACACA
* * * * *
1607054 TAGTGCCAAAACAGTTGTTCATTAACATATGATGAA-TTC-TGCGAGTTTCACACA
1 TAGTGCCTAAACGGTTGTTCATCAACACATGATGAATTTCGTG-G-GTTGCACACA
* * * * ** * *
1607108 TAGTGCCAAAACGATTGTTCATCAACATATGATGAATTCCGTGAATTACACACT
1 TAGTGCCTAAACGGTTGTTCATCAACACATGATGAATTTCGTGGGTTGCACACA
1607162 TAGTGCCTA
1 TAGTGCCTA
1607171 TTTGGTAATC
Statistics
Matches: 689, Mismatches: 112, Indels: 32
0.83 0.13 0.04
Matches are distributed among these distances:
52 44 0.06
53 15 0.02
54 621 0.90
55 7 0.01
56 2 0.00
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.32
Consensus pattern (54 bp):
TAGTGCCTAAACGGTTGTTCATCAACACATGATGAATTTCGTGGGTTGCACACA
Found at i:1607368 original size:23 final size:23
Alignment explanation
Indices: 1607342--1607391 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
1607332 GATTACGATC
1607342 TATACAAGCATCCATTAAAGACA
1 TATACAAGCATCCATTAAAGACA
* *
1607365 TATATATGCATCCATTAAAGACA
1 TATACAAGCATCCATTAAAGACA
1607388 TATA
1 TATA
1607392 TCATACTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.46, C:0.18, G:0.08, T:0.28
Consensus pattern (23 bp):
TATACAAGCATCCATTAAAGACA
Found at i:1607392 original size:23 final size:23
Alignment explanation
Indices: 1607349--1607392 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
1607339 ATCTATACAA
1607349 GCATCCATTAAAGACATATATAT
1 GCATCCATTAAAGACATATATAT
1607372 GCATCCATTAAAGACATATAT
1 GCATCCATTAAAGACATATAT
1607393 CATACTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.30
Consensus pattern (23 bp):
GCATCCATTAAAGACATATATAT
Found at i:1612660 original size:54 final size:54
Alignment explanation
Indices: 1612578--1613453 Score: 1077
Period size: 54 Copynumber: 16.3 Consensus size: 54
1612568 TTTAATAAGA
* * * * * *
1612578 TGCACACGTAGTGCCTATAA-GGTCGTTCATCAACACATGATGAATTCTTTGGGT
1 TGCACACATAGTGCCGA-AACGGTTGTTCATCAACATATGATGAATTCTGTGAGT
* * * * * *
1612632 TGCATACATAGTGCCTG-TACGGTTGTTCATTATC-TCATGATGATTTCCGT-AGGT
1 TGCACACATAGTGCC-GAAACGGTTGTTCATCAACAT-ATGATGAATTCTGTGA-GT
** *
1612686 TGCACACATAGTGTTTG-TACGGTTGTTCATCAACATATGATGAATTC-GTGAGT
1 TGCACACATAGTG-CCGAAACGGTTGTTCATCAACATATGATGAATTCTGTGAGT
* * * * * * *
1612739 TGTAGACAGAGTGCCTAAACAGTTTTTCATCAACATATGATGAATTCCGTGAGT
1 TGCACACATAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCTGTGAGT
* *
1612793 TGCACACATAGTGCCGAAACGGTTGTTCAT-TA-ATATGATGAATTCCGTGAGT
1 TGCACACATAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCTGTGAGT
*
1612845 TGCATACATAGTGCCGAAACGGTTGTTCATCAACATATGATGAATT-TCGTGAGT
1 TGCACACATAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCT-GTGAGT
* * * * * * *
1612899 TGCATACATAGTGTCGAAACGATTGTTAATCAATATATGATGAATTCTATGGGT
1 TGCACACATAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCTGTGAGT
* * * * *
1612953 TTCACACATAGTACCAAAACGGTTGTTCATCAACATATGATGAATTCCGTGAAT
1 TGCACACATAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCTGTGAGT
** * * ** *
1613007 TAAACATATAGTGCCGAAATGGTTGTTCATCAACATATGATGAATTCCATGAAT
1 TGCACACATAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCTGTGAGT
*
1613061 TGCACACATAGTGCCAAAACGGTTGTTCATCAACATATGATGAATTCTGTGAGT
1 TGCACACATAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCTGTGAGT
* *
1613115 TGCACACATAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCCGTAAGT
1 TGCACACATAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCTGTGAGT
1613169 TGCACACATAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCTGTGAGT
1 TGCACACATAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCTGTGAGT
1613223 TGCACACATAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCTGTGAGT
1 TGCACACATAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCTGTGAGT
**
1613277 TGCACACATAGTGTTGAAACGGTTGTTCATCAACATATGATGAATTCTGTGAGT
1 TGCACACATAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCTGTGAGT
* * * * *
1613331 TGCACACATAGTGCTGAAATGGATGTTCATCAACATATGATGAATTCCGTTAGT
1 TGCACACATAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCTGTGAGT
* * * * * *
1613385 TGCGCATATAGTGCCGAAATGGTTGTTCATCAACATATGAGGAATTCCGTGAAT
1 TGCACACATAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCTGTGAGT
* *
1613439 AGCACACTTAGTGCC
1 TGCACACATAGTGCC
1613454 TATTTGGTAA
Statistics
Matches: 716, Mismatches: 93, Indels: 26
0.86 0.11 0.03
Matches are distributed among these distances:
52 49 0.07
53 44 0.06
54 621 0.87
55 2 0.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (54 bp):
TGCACACATAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCTGTGAGT
Found at i:1617602 original size:33 final size:35
Alignment explanation
Indices: 1617537--1617613 Score: 113
Period size: 33 Copynumber: 2.3 Consensus size: 35
1617527 TAATTTGATT
*
1617537 AATGAACTAAGTTTATTCAATGAACTAAATGCATG
1 AATGAACTAAGTTTATTAAATGAACTAAATGCATG
* *
1617572 AATGAAGT-AGTTTATTAAAT-AACTAGATGCATG
1 AATGAACTAAGTTTATTAAATGAACTAAATGCATG
1617605 AATGAACTA
1 AATGAACTA
1617614 CTTCCCTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
33 19 0.51
34 11 0.30
35 7 0.19
ACGTcount: A:0.44, C:0.09, G:0.16, T:0.31
Consensus pattern (35 bp):
AATGAACTAAGTTTATTAAATGAACTAAATGCATG
Found at i:1617624 original size:33 final size:33
Alignment explanation
Indices: 1617559--1617624 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
1617549 TTATTCAATG
* * * *
1617559 AACTAAATGCATGAATGAAGTAGTTTATTAAAT
1 AACTAAATGCATGAATGAACTACTTCACTAAAT
* *
1617592 AACTAGATGCATGAATGAACTACTTCCCTAAAT
1 AACTAAATGCATGAATGAACTACTTCACTAAAT
1617625 GAAATACATG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (33 bp):
AACTAAATGCATGAATGAACTACTTCACTAAAT
Found at i:1617640 original size:17 final size:17
Alignment explanation
Indices: 1617620--1617672 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
1617610 ACTACTTCCC
*
1617620 TAAATGAAATACATGCT
1 TAAATGAAATACATACT
* *
1617637 TAAATGCAATGCATACT
1 TAAATGAAATACATACT
*
1617654 TTAATGAACA-ACATACT
1 TAAATGAA-ATACATACT
1617671 TA
1 TA
1617673 TTAAATGCAA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
17 27 0.96
18 1 0.04
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.30
Consensus pattern (17 bp):
TAAATGAAATACATACT
Found at i:1619706 original size:20 final size:20
Alignment explanation
Indices: 1619667--1619708 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1619657 ATATCAAATA
*
1619667 TAATAAATAATATTATTTAT
1 TAATAAATAATAATATTTAT
1619687 TAATAAATAATTAATA-TTAT
1 TAATAAATAA-TAATATTTAT
1619707 TA
1 TA
1619709 TTTTTGAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TAATAAATAATAATATTTAT
Found at i:1619936 original size:15 final size:15
Alignment explanation
Indices: 1619916--1619949 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1619906 GTAATTATAC
1619916 TATTAAAAATAAGAA
1 TATTAAAAATAAGAA
*
1619931 TATT-AAAATTAGAA
1 TATTAAAAATAAGAA
1619945 TATTA
1 TATTA
1619950 TATTATATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (15 bp):
TATTAAAAATAAGAA
Found at i:1619987 original size:22 final size:24
Alignment explanation
Indices: 1619953--1619997 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
1619943 AATATTATAT
1619953 TATATTCTATAAAT-TATTAATAAA
1 TATATTCTATAAATAT-TTAATAAA
1619977 TATATT-T-TAAATATTTAATAA
1 TATATTCTATAAATATTTAATAA
1619998 TTTAATAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 12 0.60
23 2 0.10
24 6 0.30
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (24 bp):
TATATTCTATAAATATTTAATAAA
Found at i:1622091 original size:31 final size:31
Alignment explanation
Indices: 1622056--1622159 Score: 91
Period size: 31 Copynumber: 3.2 Consensus size: 31
1622046 CAGTCGGTGT
*
1622056 TGAACCTATTCAAGGAATTACCAACAGCGAC
1 TGAACCTATACAAGGAATTACCAACAGCGAC
* * ** **
1622087 TGAACCTGCCAGAGATAGGAATTACCAATTGTTAC
1 TGAACCT---ATACA-AGGAATTACCAACAGCGAC
* *
1622122 TGAACCTATACAAGGAATTACCACCAGCGAG
1 TGAACCTATACAAGGAATTACCAACAGCGAC
1622153 TGAACCT
1 TGAACCT
1622160 GCCAGAGTCT
Statistics
Matches: 54, Mismatches: 15, Indels: 8
0.70 0.19 0.10
Matches are distributed among these distances:
31 27 0.50
32 3 0.06
34 2 0.04
35 22 0.41
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (31 bp):
TGAACCTATACAAGGAATTACCAACAGCGAC
Found at i:1622109 original size:35 final size:34
Alignment explanation
Indices: 1622067--1622166 Score: 98
Period size: 35 Copynumber: 3.0 Consensus size: 34
1622057 GAACCTATTC
1622067 AAGGAATTACCAACAGCGACTGAACCTGCCAGAG
1 AAGGAATTACCAACAGCGACTGAACCTGCCAGAG
** ** * *
1622101 ATAGGAATTACCAATTGTTACTGAACCT---ATAC
1 A-AGGAATTACCAACAGCGACTGAACCTGCCAGAG
* *
1622133 AAGGAATTACCACCAGCGAGTGAACCTGCCAGAG
1 AAGGAATTACCAACAGCGACTGAACCTGCCAGAG
1622167 TCTTCATACC
Statistics
Matches: 48, Mismatches: 14, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
31 20 0.42
32 3 0.06
34 3 0.06
35 22 0.46
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.18
Consensus pattern (34 bp):
AAGGAATTACCAACAGCGACTGAACCTGCCAGAG
Found at i:1624668 original size:24 final size:24
Alignment explanation
Indices: 1624639--1624688 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1624629 TGGTGGTTGA
*
1624639 TTTAATGGT-TGTTTAAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
1624663 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
1624687 TT
1 TT
1624689 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.26, C:0.02, G:0.12, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:1632717 original size:48 final size:48
Alignment explanation
Indices: 1632626--1632717 Score: 132
Period size: 48 Copynumber: 1.9 Consensus size: 48
1632616 TCCCAAATTT
** * *
1632626 TTAACTTTTTTCTTTTCTCTTTCTTTATTCATTTTTTTCTCTTTCATG
1 TTAACTTTTACCTTTTCTCTTTCTTTATTCATCTTCTTCTCTTTCATG
1632674 TTAACTTTTACCTTTTCTCTTTCTTTCATTCATCTTCTT-TCTTT
1 TTAACTTTTACCTTTTCTCTTTCTTT-ATTCATCTTCTTCTCTTT
1632718 GTTATTTCTC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
48 29 0.74
49 10 0.26
ACGTcount: A:0.11, C:0.22, G:0.01, T:0.66
Consensus pattern (48 bp):
TTAACTTTTACCTTTTCTCTTTCTTTATTCATCTTCTTCTCTTTCATG
Found at i:1635999 original size:24 final size:24
Alignment explanation
Indices: 1635970--1636019 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1635960 TGGTGGTTGA
*
1635970 TTTAATGGT-TGTTTAAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
1635994 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
1636018 TT
1 TT
1636020 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.26, C:0.02, G:0.12, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:1642815 original size:23 final size:24
Alignment explanation
Indices: 1642776--1642827 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
1642766 CAACAGTCAA
* * *
1642776 TGACT-GGTCAACGGTCAATGGGT
1 TGACTCGGTCAACAGTCAACGAGT
1642799 TGACTCGGTCAA-AGTCAACGAGT
1 TGACTCGGTCAACAGTCAACGAGT
1642822 TGACTC
1 TGACTC
1642828 AGTGACTGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (24 bp):
TGACTCGGTCAACAGTCAACGAGT
Found at i:1645008 original size:22 final size:23
Alignment explanation
Indices: 1644983--1645028 Score: 85
Period size: 22 Copynumber: 2.0 Consensus size: 23
1644973 AATTTATTAC
1644983 TTTTGAAGCTTTAATGGA-AAAA
1 TTTTGAAGCTTTAATGGAGAAAA
1645005 TTTTGAAGCTTTAATGGAGAAAA
1 TTTTGAAGCTTTAATGGAGAAAA
1645028 T
1 T
1645029 AAAATTTACT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.39, C:0.04, G:0.20, T:0.37
Consensus pattern (23 bp):
TTTTGAAGCTTTAATGGAGAAAA
Found at i:1645098 original size:17 final size:19
Alignment explanation
Indices: 1645059--1645099 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
1645049 TCAACGTTTG
1645059 TATAGTTTACCCTGTGTTA
1 TATAGTTTACCCTGTGTTA
1645078 TATAGTTTACCCTGTGTTA
1 TATAGTTTACCCTGTGTTA
1645097 TAT
1 TAT
1645100 TACTTATTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.22, C:0.15, G:0.15, T:0.49
Consensus pattern (19 bp):
TATAGTTTACCCTGTGTTA
Done.