Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008275.1 Hibiscus syriacus cultivar Beakdansim tig00110933_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: 1991061
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 8
Found at i:1259709 original size:24 final size:23
Alignment explanation
Indices: 1259648--1259710 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 23
1259638 AAGACATAAG
* *
1259648 AAACATGTCATAAGAGCAGAGAA
1 AAACTTGTCATAAAAGCAGAGAA
* *
1259671 AAAATGTGTCATAAAAGTAGAGAA
1 AAACT-TGTCATAAAAGCAGAGAA
1259695 AAACTTGTCACTAAAA
1 AAACTTGTCA-TAAAA
1259711 CAAAAATTCT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
23 8 0.24
24 25 0.76
ACGTcount: A:0.52, C:0.11, G:0.17, T:0.19
Consensus pattern (23 bp):
AAACTTGTCATAAAAGCAGAGAA
Found at i:1259952 original size:27 final size:26
Alignment explanation
Indices: 1259915--1259968 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 26
1259905 AAGGTGGAAT
1259915 ACCCCATTAGCCATTGTTTCTACAAA
1 ACCCCATTAGCCATTGTTTCTACAAA
1259941 ACCCACATTAGCCATTGTTTCTACAAA
1 ACCC-CATTAGCCATTGTTTCTACAAA
1259968 A
1 A
1259969 TGAAAGCTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 4 0.15
27 23 0.85
ACGTcount: A:0.33, C:0.30, G:0.07, T:0.30
Consensus pattern (26 bp):
ACCCCATTAGCCATTGTTTCTACAAA
Found at i:1260162 original size:58 final size:59
Alignment explanation
Indices: 1260061--1260181 Score: 145
Period size: 58 Copynumber: 2.1 Consensus size: 59
1260051 TTCAAATTGT
* * * ** *
1260061 TCCTTAAATTTTTAAATATTTTAATTTCATCATTAAACTATGAC-TCATTCTAAATTAG
1 TCCTCAAATTTTTAAACAATTTAATTTCATCACCAAACCATGACATCATTCTAAATTAG
* * *
1260119 TCCTCAAATTTTTGAACAATTTAATTTCATCCCCAAACCATGACATTCATTCTAAATTGG
1 TCCTCAAATTTTTAAACAATTTAATTTCATCACCAAACCATGACA-TCATTCTAAATTAG
1260179 TCC
1 TCC
1260182 CTAAACTTTT
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
58 36 0.69
60 16 0.31
ACGTcount: A:0.34, C:0.20, G:0.05, T:0.41
Consensus pattern (59 bp):
TCCTCAAATTTTTAAACAATTTAATTTCATCACCAAACCATGACATCATTCTAAATTAG
Found at i:1260467 original size:60 final size:60
Alignment explanation
Indices: 1260403--1260520 Score: 146
Period size: 60 Copynumber: 2.0 Consensus size: 60
1260393 TTAAGTATGT
* * * * * *
1260403 AATTAGAATGTTCAAAAGTTTAAGCACTAATTTAAAATGAGAGTCATTGTTTATGGATGA
1 AATTAAAATATTCAAAAGTTTAAGAACCAATTTAAAATGAGAGTCATAGTTTAGGGATGA
* * * *
1260463 AATTAAAATATTTAAAAGTTTAATAACCAATTTAAAATTAGAGTTATAGTTTAGGGAT
1 AATTAAAATATTCAAAAGTTTAAGAACCAATTTAAAATGAGAGTCATAGTTTAGGGAT
1260521 ATATGATGCG
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.43, C:0.05, G:0.15, T:0.36
Consensus pattern (60 bp):
AATTAAAATATTCAAAAGTTTAAGAACCAATTTAAAATGAGAGTCATAGTTTAGGGATGA
Found at i:1261060 original size:29 final size:26
Alignment explanation
Indices: 1261007--1261061 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
1260997 TCTTCCAAAT
* *
1261007 TATTTTAAATTCATCTTCTCCTAAAA
1 TATTATAAATTCATCTTCTCATAAAA
1261033 TATTATAAATTCATCATTCTAGCATAAAA
1 TATTATAAATTCATC-TTCT--CATAAAA
1261062 GCATATGCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 14 0.58
27 4 0.17
29 6 0.25
ACGTcount: A:0.40, C:0.16, G:0.02, T:0.42
Consensus pattern (26 bp):
TATTATAAATTCATCTTCTCATAAAA
Found at i:1265329 original size:20 final size:20
Alignment explanation
Indices: 1265304--1265342 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1265294 ATTTACTACA
* *
1265304 TTAATTATTACTTTTGTTTC
1 TTAATTATCAATTTTGTTTC
1265324 TTAATTATCAATTTTGTTT
1 TTAATTATCAATTTTGTTT
1265343 TGTTTTGGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.08, G:0.05, T:0.64
Consensus pattern (20 bp):
TTAATTATCAATTTTGTTTC
Found at i:1275640 original size:13 final size:13
Alignment explanation
Indices: 1275624--1275657 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1275614 GAACTTAAAA
*
1275624 TTAAAGTTTAATG
1 TTAAAATTTAATG
1275637 TTAAAATTTAATG
1 TTAAAATTTAATG
*
1275650 ATAAAATT
1 TTAAAATT
1275658 AATAAAAACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (13 bp):
TTAAAATTTAATG
Found at i:1286599 original size:20 final size:20
Alignment explanation
Indices: 1286574--1286611 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1286564 TTTTTGATTA
* *
1286574 ATTTTTTATTTTTAAAAATT
1 ATTTTTTAATATTAAAAATT
1286594 ATTTTTTAATATTAAAAA
1 ATTTTTTAATATTAAAAA
1286612 AATATATCAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTTTTTAATATTAAAAATT
Found at i:1286611 original size:21 final size:20
Alignment explanation
Indices: 1286574--1286612 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1286564 TTTTTGATTA
* *
1286574 ATTTTTTATTTTTAAAAATT
1 ATTTTTTATATTAAAAAATT
1286594 ATTTTTTAATATTAAAAAA
1 ATTTTTT-ATATTAAAAAA
1286613 ATATATCAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTTTTTATATTAAAAAATT
Found at i:1287297 original size:28 final size:28
Alignment explanation
Indices: 1287237--1287301 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
1287227 AGTTCCAAAC
*
1287237 TCCTAATAATTTGAAAATTTGCAAAGAA
1 TCCTAATAATTTGAAAATTTACAAAGAA
* * *
1287265 CCCTAGTAATTTGAAAATTTACAAGGAA
1 TCCTAATAATTTGAAAATTTACAAAGAA
1287293 TCCTAATAA
1 TCCTAATAA
1287302 CTTATAGTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.31
Consensus pattern (28 bp):
TCCTAATAATTTGAAAATTTACAAAGAA
Found at i:1288214 original size:24 final size:25
Alignment explanation
Indices: 1288187--1288236 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
1288177 ATAAGGTATT
*
1288187 TAATAATTTTT-TTAAAATTTACAG
1 TAATAATTTTTGTAAAAATTTACAG
1288211 TAATAATTTTTGTAAAAATTTACAG
1 TAATAATTTTTGTAAAAATTTACAG
1288236 T
1 T
1288237 GACAATGTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (25 bp):
TAATAATTTTTGTAAAAATTTACAG
Found at i:1289319 original size:2 final size:2
Alignment explanation
Indices: 1289308--1289352 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
1289298 GATCCAGGTG
*
1289308 TC TC -C TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC TC T-
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1289348 TC TC T
1 TC TC T
1289353 TTTTCTTTGA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:1291589 original size:22 final size:22
Alignment explanation
Indices: 1291563--1291604 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
1291553 ATTTCCTGGT
1291563 TATTTGTTTGACTTTTATGCAC
1 TATTTGTTTGACTTTTATGCAC
1291585 TATTTGTTTGACTTTTATGC
1 TATTTGTTTGACTTTTATGC
1291605 GTTGCTTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.17, C:0.12, G:0.14, T:0.57
Consensus pattern (22 bp):
TATTTGTTTGACTTTTATGCAC
Found at i:1305564 original size:2 final size:2
Alignment explanation
Indices: 1305557--1305592 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1305547 TAATAGTCTA
1305557 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1305593 GTGTACGGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1305939 original size:18 final size:18
Alignment explanation
Indices: 1305918--1305952 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1305908 CCTCCGAAAC
*
1305918 CACCTACACCTACACCAG
1 CACCTACACCCACACCAG
*
1305936 CACCTGCACCCACACCA
1 CACCTACACCCACACCA
1305953 AAACCAAAGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.54, G:0.06, T:0.09
Consensus pattern (18 bp):
CACCTACACCCACACCAG
Found at i:1305988 original size:18 final size:18
Alignment explanation
Indices: 1305967--1306080 Score: 65
Period size: 18 Copynumber: 6.5 Consensus size: 18
1305957 CAAAGCCAGA
1305967 ACCGACACCAAAACCAAC
1 ACCGACACCAAAACCAAC
* **
1305985 ACCGGCACCAACTCCAAC
1 ACCGACACCAAAACCAAC
* * *
1306003 ACC-AGCTCC---TCCAGC
1 ACCGA-CACCAAAACCAAC
*
1306018 ACCGATACCAAAACCAAC
1 ACCGACACCAAAACCAAC
* ** *
1306036 ACCGGCACCAGCACCAAT
1 ACCGACACCAAAACCAAC
* *
1306054 ACCGACACCGAAACCTAC
1 ACCGACACCAAAACCAAC
*
1306072 ACCAACACC
1 ACCGACACC
1306081 GGCGCCAACA
Statistics
Matches: 69, Mismatches: 22, Indels: 10
0.68 0.22 0.10
Matches are distributed among these distances:
15 10 0.14
16 1 0.01
18 58 0.84
ACGTcount: A:0.39, C:0.46, G:0.10, T:0.05
Consensus pattern (18 bp):
ACCGACACCAAAACCAAC
Found at i:1308039 original size:18 final size:18
Alignment explanation
Indices: 1308016--1308079 Score: 83
Period size: 18 Copynumber: 3.6 Consensus size: 18
1308006 AGCTAAAGGA
* *
1308016 ACCCGAGAAGCCGAAAGC
1 ACCCGAAAAGCCCAAAGC
*
1308034 ACCCGAAAAGCCCAAAGT
1 ACCCGAAAAGCCCAAAGC
1308052 ACCCGAAAAGCCCAAAGC
1 ACCCGAAAAGCCCAAAGC
* *
1308070 TCCCTAAAAG
1 ACCCGAAAAG
1308080 TCGAAGGAGG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.42, C:0.34, G:0.19, T:0.05
Consensus pattern (18 bp):
ACCCGAAAAGCCCAAAGC
Found at i:1308496 original size:17 final size:18
Alignment explanation
Indices: 1308463--1308509 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
1308453 TAATTTTGCC
* *
1308463 ACCGAAGGAATCTG-AAA
1 ACCGAAAGAACCTGAAAA
*
1308480 ACCTAAAGAACCTGAAAA
1 ACCGAAAGAACCTGAAAA
1308498 ACCGAAAGAACC
1 ACCGAAAGAACC
1308510 ACTGGCTCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.51, C:0.23, G:0.17, T:0.09
Consensus pattern (18 bp):
ACCGAAAGAACCTGAAAA
Found at i:1309609 original size:37 final size:37
Alignment explanation
Indices: 1309556--1309630 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
1309546 GGTCCCTAAA
* *
1309556 ATATTTAAGACTAAATTGTAAAATATCAAAATTTATC
1 ATATTTAAGACGAAATTCTAAAATATCAAAATTTATC
1309593 ATATTTAAGACGAAATTCTAAAATATCAAAATTTATC
1 ATATTTAAGACGAAATTCTAAAATATCAAAATTTATC
1309630 A
1 A
1309631 AAATCCAAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.36
Consensus pattern (37 bp):
ATATTTAAGACGAAATTCTAAAATATCAAAATTTATC
Found at i:1310961 original size:20 final size:20
Alignment explanation
Indices: 1310936--1310976 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1310926 CCATCATCAT
1310936 CCTATGATTCTTCTTTTAAC
1 CCTATGATTCTTCTTTTAAC
1310956 CCTATGATTCTTCTTTTAAC
1 CCTATGATTCTTCTTTTAAC
1310976 C
1 C
1310977 ATTACAAACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.27, G:0.05, T:0.49
Consensus pattern (20 bp):
CCTATGATTCTTCTTTTAAC
Found at i:1311525 original size:4 final size:4
Alignment explanation
Indices: 1311516--1311789 Score: 539
Period size: 4 Copynumber: 68.5 Consensus size: 4
1311506 TTCAGTAATT
*
1311516 CATA CATA CATA CATA CATA CATA TATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1311564 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1311612 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1311660 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1311708 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1311756 CATA CATA CATA CATA CATA CATA CATA CATA CA
1 CATA CATA CATA CATA CATA CATA CATA CATA CA
1311790 GACAGACAAA
Statistics
Matches: 268, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
4 268 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:1321124 original size:18 final size:19
Alignment explanation
Indices: 1321089--1321125 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1321079 CACGGAATGT
1321089 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
1321109 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
1321126 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:1321297 original size:15 final size:15
Alignment explanation
Indices: 1321279--1321309 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1321269 AAATTCTAAA
1321279 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
1321294 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
1321309 T
1 T
1321310 CTATTTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:1326841 original size:17 final size:18
Alignment explanation
Indices: 1326816--1326853 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1326806 TAATACAAAA
1326816 AAAACATAT-AAAATTAT
1 AAAACATATGAAAATTAT
* *
1326833 AAAATATATGAAAATTTT
1 AAAACATATGAAAATTAT
1326851 AAA
1 AAA
1326854 TTTTTAGGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (18 bp):
AAAACATATGAAAATTAT
Found at i:1336080 original size:13 final size:13
Alignment explanation
Indices: 1336062--1336087 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1336052 AATCGCCTTC
1336062 GCCTTTGCAGTAT
1 GCCTTTGCAGTAT
1336075 GCCTTTGCAGTAT
1 GCCTTTGCAGTAT
1336088 CCAATTTGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.38
Consensus pattern (13 bp):
GCCTTTGCAGTAT
Found at i:1337044 original size:2 final size:2
Alignment explanation
Indices: 1337037--1337086 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1337027 TTTCACCCAC
1337037 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1337079 AT AT AT AT
1 AT AT AT AT
1337087 TATGGGAGTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1339961 original size:27 final size:27
Alignment explanation
Indices: 1339924--1339975 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
1339914 ATAACTTATA
1339924 TTTTCTCTTAA-GTTTTGAAAAGTTAGT
1 TTTTCTCTTAATGTTTT-AAAAGTTAGT
* *
1339951 TTTTTTCTTAATGTTTTAGAAGTTA
1 TTTTCTCTTAATGTTTTAAAAGTTA
1339976 ATCTTATAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 17 0.77
28 5 0.23
ACGTcount: A:0.25, C:0.06, G:0.13, T:0.56
Consensus pattern (27 bp):
TTTTCTCTTAATGTTTTAAAAGTTAGT
Found at i:1347383 original size:60 final size:60
Alignment explanation
Indices: 1347259--1347397 Score: 147
Period size: 60 Copynumber: 2.3 Consensus size: 60
1347249 AAAATGTTCA
** * * *** * * *
1347259 AAAAGTTTGGAGACTAATTTAGAATGAATGTCATAGTTTGGGGATAGAATTGGCATGTTC
1 AAAAGTTTTAAGACTAATTTAGAATGAAGGTAATAGTTTAAAGATAGAAATGGAATATTC
*
1347319 AAAAGTTTTAAGACTAATTTAGAATGAAGGTAATAGTTTAAAGAT-GAAAATGGAATATTT
1 AAAAGTTTTAAGACTAATTTAGAATGAAGGTAATAGTTTAAAGATAG-AAATGGAATATTC
1347379 AAAAG-TTTAGAGACTAATT
1 AAAAGTTTTA-AGACTAATT
1347398 AAAATTAAAA
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
59 5 0.08
60 61 0.92
ACGTcount: A:0.41, C:0.04, G:0.22, T:0.33
Consensus pattern (60 bp):
AAAAGTTTTAAGACTAATTTAGAATGAAGGTAATAGTTTAAAGATAGAAATGGAATATTC
Found at i:1349524 original size:15 final size:15
Alignment explanation
Indices: 1349490--1349535 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 15
1349480 AGAATAACAA
1349490 TAAAAACTAAAACTTATT
1 TAAAAA-TAAAA--TATT
1349508 TAAAAATAAAATATT
1 TAAAAATAAAATATT
1349523 TAAAAATAAAATA
1 TAAAAATAAAATA
1349536 AAATAGTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 17 0.61
17 5 0.18
18 6 0.21
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.30
Consensus pattern (15 bp):
TAAAAATAAAATATT
Found at i:1353349 original size:21 final size:21
Alignment explanation
Indices: 1353323--1353385 Score: 80
Period size: 19 Copynumber: 3.2 Consensus size: 21
1353313 TTAGGGGTGG
1353323 TTTAGATATTATAATATGTAC
1 TTTAGATATTATAATATGTAC
* *
1353344 TTTAGAAATTTTAATA--TAC
1 TTTAGATATTATAATATGTAC
1353363 TTTAGATATTAT-ATATGTA-
1 TTTAGATATTATAATATGTAC
1353382 TTTA
1 TTTA
1353386 TTGACCTATG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
18 3 0.08
19 17 0.47
20 2 0.06
21 14 0.39
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (21 bp):
TTTAGATATTATAATATGTAC
Found at i:1355657 original size:22 final size:21
Alignment explanation
Indices: 1355623--1355672 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
1355613 ATAATTATTT
1355623 AAAAA-ATTAAATAAAAATACC
1 AAAAACATTAAATAAAAA-ACC
* *
1355644 AAAAACATTTAATAAAAAACT
1 AAAAACATTAAATAAAAAACC
1355665 AAAAACAT
1 AAAAACAT
1355673 CCCCCACACC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 15 0.58
22 11 0.42
ACGTcount: A:0.70, C:0.10, G:0.00, T:0.20
Consensus pattern (21 bp):
AAAAACATTAAATAAAAAACC
Found at i:1356047 original size:27 final size:27
Alignment explanation
Indices: 1356014--1356123 Score: 220
Period size: 27 Copynumber: 4.1 Consensus size: 27
1356004 AACTATTCAT
1356014 ATAATGTTCATTTTTGTTCATTTATTA
1 ATAATGTTCATTTTTGTTCATTTATTA
1356041 ATAATGTTCATTTTTGTTCATTTATTA
1 ATAATGTTCATTTTTGTTCATTTATTA
1356068 ATAATGTTCATTTTTGTTCATTTATTA
1 ATAATGTTCATTTTTGTTCATTTATTA
1356095 ATAATGTTCATTTTTGTTCATTTATTA
1 ATAATGTTCATTTTTGTTCATTTATTA
1356122 AT
1 AT
1356124 CTAAATAAAC
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 83 1.00
ACGTcount: A:0.26, C:0.07, G:0.07, T:0.59
Consensus pattern (27 bp):
ATAATGTTCATTTTTGTTCATTTATTA
Found at i:1356050 original size:17 final size:17
Alignment explanation
Indices: 1356028--1356107 Score: 62
Period size: 17 Copynumber: 5.5 Consensus size: 17
1356018 TGTTCATTTT
1356028 TGTTCATTTATTAATAA
1 TGTTCATTTATTAATAA
1356045 TGTTCA--T-TT--T--
1 TGTTCATTTATTAATAA
1356055 TGTTCATTTATTAATAA
1 TGTTCATTTATTAATAA
1356072 TGTTCA--T-TT--T--
1 TGTTCATTTATTAATAA
1356082 TGTTCATTTATTAATAA
1 TGTTCATTTATTAATAA
1356099 TGTTCATTT
1 TGTTCATTT
1356108 TTGTTCATTT
Statistics
Matches: 49, Mismatches: 0, Indels: 28
0.64 0.00 0.36
Matches are distributed among these distances:
10 12 0.24
12 4 0.08
13 4 0.08
14 4 0.08
15 4 0.08
17 21 0.43
ACGTcount: A:0.26, C:0.07, G:0.07, T:0.59
Consensus pattern (17 bp):
TGTTCATTTATTAATAA
Found at i:1356250 original size:24 final size:24
Alignment explanation
Indices: 1356218--1356264 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1356208 TCACGAAAAA
*
1356218 ACTCATTTATAAGTTTGTTTATTG
1 ACTCATTTATAAGCTTGTTTATTG
*
1356242 ACTCGTTTATAAGCTTGTTTATT
1 ACTCATTTATAAGCTTGTTTATT
1356265 CAATTCTCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.23, C:0.11, G:0.13, T:0.53
Consensus pattern (24 bp):
ACTCATTTATAAGCTTGTTTATTG
Found at i:1357021 original size:25 final size:25
Alignment explanation
Indices: 1356987--1357036 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1356977 TTTTTTAACG
1356987 AAAAAATGACGAGTTTGGAACATAT
1 AAAAAATGACGAGTTTGGAACATAT
1357012 AAAAAATGACGAGTTTGGAACATAT
1 AAAAAATGACGAGTTTGGAACATAT
1357037 GAACAGTCGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.48, C:0.08, G:0.20, T:0.24
Consensus pattern (25 bp):
AAAAAATGACGAGTTTGGAACATAT
Found at i:1373107 original size:2 final size:2
Alignment explanation
Indices: 1373100--1373133 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1373090 TATACTTTCA
1373100 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1373134 TAAGTTAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1377570 original size:84 final size:87
Alignment explanation
Indices: 1377428--1377648 Score: 349
Period size: 85 Copynumber: 2.6 Consensus size: 87
1377418 CTTGAATGTG
* *
1377428 TGACGATATTCATCAACTATGCAATAGACCTTACAAGATAACATATGATAGTTCAGTAGGA-TGC
1 TGACGATATACATCAACTATGCACTAGACCTTACAAGATAACATATGATAGTTCAGTAGGATTGC
*
1377492 TTTTGGACATTACCAC-AACCA
66 TCTTGGACATTACCACGAACCA
* *
1377513 TGACGACATGCATCAACTATGCACTAGACC-TACAAGATAACATATGATAGTTCAGTAGGATTGC
1 TGACGATATACATCAACTATGCACTAGACCTTACAAGATAACATATGATAGTTCAGTAGGATTGC
*
1377577 TCTTGGACATTACCACTGGACCA
66 TCTTGGACATTACCAC-GAACCA
*
1377600 CGACGATATACATCAACTATGCACTAGACCTTACAAGATAACATATGAT
1 TGACGATATACATCAACTATGCACTAGACCTTACAAGATAACATATGAT
1377649 GATAGTTTAT
Statistics
Matches: 124, Mismatches: 8, Indels: 5
0.91 0.06 0.04
Matches are distributed among these distances:
84 30 0.24
85 45 0.36
87 31 0.25
88 18 0.15
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (87 bp):
TGACGATATACATCAACTATGCACTAGACCTTACAAGATAACATATGATAGTTCAGTAGGATTGC
TCTTGGACATTACCACGAACCA
Found at i:1378948 original size:37 final size:37
Alignment explanation
Indices: 1378901--1378974 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
1378891 TTTCAATTCC
1378901 AAGACGGATTTAAATTTATAAAATTTAAATAATTAAA
1 AAGACGGATTTAAATTTATAAAATTTAAATAATTAAA
*
1378938 AAGATGGATTTAAATTTATAAAATTTAAATAATTAAA
1 AAGACGGATTTAAATTTATAAAATTTAAATAATTAAA
1378975 TAATAAATCA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.54, C:0.01, G:0.08, T:0.36
Consensus pattern (37 bp):
AAGACGGATTTAAATTTATAAAATTTAAATAATTAAA
Found at i:1379582 original size:2 final size:2
Alignment explanation
Indices: 1379575--1379603 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1379565 CCGGTAAGTG
1379575 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1379604 GACGGTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1384626 original size:14 final size:15
Alignment explanation
Indices: 1384607--1384644 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
1384597 TTTCGGTTTG
*
1384607 AAAAAAATCG-ATTT
1 AAAAAAATCGAATAT
1384621 AAAAAAA-CGAATAT
1 AAAAAAATCGAATAT
1384635 AAAAAAATCG
1 AAAAAAATCG
1384645 GTTTGTAGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 2 0.10
14 17 0.81
15 2 0.10
ACGTcount: A:0.66, C:0.08, G:0.08, T:0.18
Consensus pattern (15 bp):
AAAAAAATCGAATAT
Found at i:1387361 original size:31 final size:31
Alignment explanation
Indices: 1387309--1387373 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
1387299 AATTCTTTTA
* * * *
1387309 TTAGTCCTTATACTATGTATAATTTATGTAT
1 TTAGCCCTTATACTATATATAAATTATATAT
*
1387340 TTAGCCCTTATATTATATATAAATTATATAT
1 TTAGCCCTTATACTATATATAAATTATATAT
1387371 TTA
1 TTA
1387374 ATCTTTATAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.51
Consensus pattern (31 bp):
TTAGCCCTTATACTATATATAAATTATATAT
Found at i:1392912 original size:21 final size:21
Alignment explanation
Indices: 1392887--1392964 Score: 104
Period size: 21 Copynumber: 3.8 Consensus size: 21
1392877 AAAACGAAAT
*
1392887 TCGCGTTGCGATTTTGGAGAA
1 TCGCGTTGCGAATTTGGAGAA
*
1392908 TCGCGTTGCGAATTT-GAAAA
1 TCGCGTTGCGAATTTGGAGAA
* *
1392928 CCGCGTTGCGATTTTGGAGAA
1 TCGCGTTGCGAATTTGGAGAA
*
1392949 TTGCGTTGCGAATTTG
1 TCGCGTTGCGAATTTG
1392965 AAAACTGTGT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
20 17 0.35
21 31 0.65
ACGTcount: A:0.21, C:0.15, G:0.31, T:0.33
Consensus pattern (21 bp):
TCGCGTTGCGAATTTGGAGAA
Found at i:1392913 original size:91 final size:89
Alignment explanation
Indices: 1392744--1392927 Score: 325
Period size: 91 Copynumber: 2.0 Consensus size: 89
1392734 AAATAACAAA
*
1392744 AAAATCTGAGTTGCGTGTTTACCTATATCGGTAATTAGCGCGAAAACGAAATTCGCGTTGCGATT
1 AAAATCTGAGTTGCGTGTTTACCTATATCAGTAATTAGCGCGAAAACGAAATTCGCGTTGCGATT
1392809 TTGGAGAATCGCGTTGCGAATTT-
66 TTGGAGAATCGCGTTGCGAATTTG
1392832 AAAATCTGAGTTGCGTGTTTACCTATATCAGTAATTAGCGTTACGAAAACGAAATTCGCGTTGCG
1 AAAATCTGAGTTGCGTGTTTACCTATATCAGTAATTAGCG---CGAAAACGAAATTCGCGTTGCG
1392897 ATTTTGGAGAATCGCGTTGCGAATTTG
63 ATTTTGGAGAATCGCGTTGCGAATTTG
1392924 AAAA
1 AAAA
1392928 CCGCGTTGCG
Statistics
Matches: 91, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
88 39 0.43
91 48 0.53
92 4 0.04
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (89 bp):
AAAATCTGAGTTGCGTGTTTACCTATATCAGTAATTAGCGCGAAAACGAAATTCGCGTTGCGATT
TTGGAGAATCGCGTTGCGAATTTG
Found at i:1392933 original size:41 final size:41
Alignment explanation
Indices: 1392888--1392979 Score: 157
Period size: 41 Copynumber: 2.2 Consensus size: 41
1392878 AAACGAAATT
1392888 CGCGTTGCGATTTTGGAGAATCGCGTTGCGAATTTGAAAAC
1 CGCGTTGCGATTTTGGAGAATCGCGTTGCGAATTTGAAAAC
*
1392929 CGCGTTGCGATTTTGGAGAATTGCGTTGCGAATTTGAAAAC
1 CGCGTTGCGATTTTGGAGAATCGCGTTGCGAATTTGAAAAC
* *
1392970 TGTGTTGCGA
1 CGCGTTGCGA
1392980 AACTGGTGTT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.32
Consensus pattern (41 bp):
CGCGTTGCGATTTTGGAGAATCGCGTTGCGAATTTGAAAAC
Found at i:1392934 original size:20 final size:21
Alignment explanation
Indices: 1392888--1392980 Score: 91
Period size: 20 Copynumber: 4.5 Consensus size: 21
1392878 AAACGAAATT
* * *
1392888 CGCGTTGCGATTTTGGAGAAT
1 CGCGTTGCGAATTTGGAAAAC
1392909 CGCGTTGCGAATTT-GAAAAC
1 CGCGTTGCGAATTTGGAAAAC
* * *
1392929 CGCGTTGCGATTTTGGAGAAT
1 CGCGTTGCGAATTTGGAAAAC
*
1392950 TGCGTTGCGAATTT-GAAAAC
1 CGCGTTGCGAATTTGGAAAAC
* *
1392970 TGTGTTGCGAA
1 CGCGTTGCGAA
1392981 ACTGGTGTTC
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
20 31 0.52
21 29 0.48
ACGTcount: A:0.24, C:0.15, G:0.30, T:0.31
Consensus pattern (21 bp):
CGCGTTGCGAATTTGGAAAAC
Found at i:1395096 original size:26 final size:26
Alignment explanation
Indices: 1395030--1395096 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 26
1395020 ATTAGTTAGA
* *
1395030 ATATAATTATAAA-AATACTATTATT
1 ATATAATTATAAATAAAACTATCATT
* * *
1395055 ATTTAGAATAT-TATAAAACTATCATT
1 ATATA-ATTATAAATAAAACTATCATT
1395081 ATATAATTATAAATAA
1 ATATAATTATAAATAA
1395097 TACAGCCTCA
Statistics
Matches: 31, Mismatches: 8, Indels: 5
0.70 0.18 0.11
Matches are distributed among these distances:
25 9 0.29
26 22 0.71
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.42
Consensus pattern (26 bp):
ATATAATTATAAATAAAACTATCATT
Found at i:1395195 original size:28 final size:29
Alignment explanation
Indices: 1395163--1395230 Score: 88
Period size: 28 Copynumber: 2.4 Consensus size: 29
1395153 AATGGTTTGG
* *
1395163 CTATGAGCCTATGTAAATTCAGCATG-GA
1 CTATGAGCCTATATAAATCCAGCATGTGA
*
1395191 CTATGAGCCTATATAAATCCAGCCTGTGA
1 CTATGAGCCTATATAAATCCAGCATGTGA
1395220 --ATGAGCCTATA
1 CTATGAGCCTATA
1395231 GAAAGAAAGG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 11 0.31
28 23 0.64
29 2 0.06
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (29 bp):
CTATGAGCCTATATAAATCCAGCATGTGA
Found at i:1395786 original size:2 final size:2
Alignment explanation
Indices: 1395775--1395822 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
1395765 TCATGTCTTC
1395775 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1395816 TA TA TA T
1 TA TA TA T
1395823 TAGAATTTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1397256 original size:20 final size:20
Alignment explanation
Indices: 1397227--1397264 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1397217 GGTTCGCATG
*
1397227 TATTTAAAATTTGATTCACC
1 TATTTAAAATATGATTCACC
*
1397247 TATTTTAAATATGATTCA
1 TATTTAAAATATGATTCA
1397265 AAGTCAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (20 bp):
TATTTAAAATATGATTCACC
Found at i:1406007 original size:29 final size:29
Alignment explanation
Indices: 1405965--1406053 Score: 115
Period size: 29 Copynumber: 3.1 Consensus size: 29
1405955 GTACCGGGGT
*
1405965 AGGTCGCCATGCACGCCCGGCGACCTACC
1 AGGTCGCCATGCACGCCCAGCGACCTACC
* ***
1405994 AGGTTGCCATGCACGCCCAGCGACCTGGT
1 AGGTCGCCATGCACGCCCAGCGACCTACC
* *
1406023 AGGTCGCCATGCATGCCCTGCGACCTACC
1 AGGTCGCCATGCACGCCCAGCGACCTACC
1406052 AG
1 AG
1406054 CCAACGACCT
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.18, C:0.39, G:0.28, T:0.15
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCAGCGACCTACC
Found at i:1406083 original size:10 final size:10
Alignment explanation
Indices: 1406068--1406093 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1406058 CGACCTCCAT
1406068 GCCCATGCAC
1 GCCCATGCAC
1406078 GCCCATGCAC
1 GCCCATGCAC
1406088 GCCCAT
1 GCCCAT
1406094 CTCGCCAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.50, G:0.19, T:0.12
Consensus pattern (10 bp):
GCCCATGCAC
Found at i:1406131 original size:33 final size:33
Alignment explanation
Indices: 1406082--1406180 Score: 180
Period size: 33 Copynumber: 3.0 Consensus size: 33
1406072 ATGCACGCCC
* *
1406082 ATGCACGCCCATCTCGCCAAAGGTCACCATGCA
1 ATGCACGTCCAGCTCGCCAAAGGTCACCATGCA
1406115 ATGCACGTCCAGCTCGCCAAAGGTCACCATGCA
1 ATGCACGTCCAGCTCGCCAAAGGTCACCATGCA
1406148 ATGCACGTCCAGCTCGCCAAAGGTCACCATGCA
1 ATGCACGTCCAGCTCGCCAAAGGTCACCATGCA
1406181 GTCCATGCTT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 64 1.00
ACGTcount: A:0.27, C:0.37, G:0.20, T:0.15
Consensus pattern (33 bp):
ATGCACGTCCAGCTCGCCAAAGGTCACCATGCA
Found at i:1406391 original size:12 final size:11
Alignment explanation
Indices: 1406371--1406406 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
1406361 GAAATCAACT
1406371 GCATTATTGCA
1 GCATTATTGCA
*
1406382 GCACTTATTGCT
1 GCA-TTATTGCA
1406394 GCATTATTGCA
1 GCATTATTGCA
1406405 GC
1 GC
1406407 CCGTGAACGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.36
Consensus pattern (11 bp):
GCATTATTGCA
Found at i:1406753 original size:27 final size:29
Alignment explanation
Indices: 1406690--1406753 Score: 73
Period size: 27 Copynumber: 2.3 Consensus size: 29
1406680 ATATATAAAA
1406690 AAATAATTAATTAGTGTGTTAGTTAGTCT
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
* *
1406719 --ATATTTAATTAGTTTG-TAGTTAGT-T
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
*
1406744 AAATAGTTAA
1 AAATAATTAA
1406754 GTTATATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
25 1 0.03
26 8 0.27
27 21 0.70
ACGTcount: A:0.36, C:0.02, G:0.16, T:0.47
Consensus pattern (29 bp):
AAATAATTAATTAGTGTGTTAGTTAGTCT
Found at i:1406847 original size:34 final size:36
Alignment explanation
Indices: 1406778--1406848 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 36
1406768 GTTGAATTTA
1406778 TATTATATAAAAAATTAGTTTATTAGTAGTTTAAGTT
1 TATTATATAAAAAATTAGTTTATTA-TAGTTTAAGTT
1406815 TATTATAATAAAAAA-TAGTTTA-T-TAGTTTAAGTT
1 TATTAT-ATAAAAAATTAGTTTATTATAGTTTAAGTT
1406849 ATAAAAGAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
34 11 0.33
36 1 0.03
37 13 0.39
38 8 0.24
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (36 bp):
TATTATATAAAAAATTAGTTTATTATAGTTTAAGTT
Found at i:1406970 original size:21 final size:21
Alignment explanation
Indices: 1406945--1406984 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1406935 GTTAATTAGT
1406945 TTGTTAGTTTAAGTTATATTA
1 TTGTTAGTTTAAGTTATATTA
1406966 TTGTTAGTTTAAGTTATAT
1 TTGTTAGTTTAAGTTATAT
1406985 CATATAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (21 bp):
TTGTTAGTTTAAGTTATATTA
Found at i:1407221 original size:30 final size:30
Alignment explanation
Indices: 1407153--1407226 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 30
1407143 ATGAGTTAAT
* *
1407153 TAGTTTTTTAGTAGTAAATTATAATTAAAAA
1 TAGTTTATTAGT-TTAAATTATAATTAAAAA
*
1407184 TCA-TTTATTAGTTTAATTTAT-ATTAAAGAA
1 T-AGTTTATTAGTTTAAATTATAATTAAA-AA
1407214 TAGTTTATTAGTT
1 TAGTTTATTAGTT
1407227 GTTTAAGGGA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
29 7 0.19
30 20 0.54
31 9 0.24
32 1 0.03
ACGTcount: A:0.39, C:0.01, G:0.09, T:0.50
Consensus pattern (30 bp):
TAGTTTATTAGTTTAAATTATAATTAAAAA
Found at i:1409137 original size:26 final size:25
Alignment explanation
Indices: 1409107--1409164 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 25
1409097 AATTTTTTAT
*
1409107 ATAATCTAATATAATTAAACTAACAA
1 ATAATATAATA-AATTAAACTAACAA
*
1409133 ATAATATAATAACTTAAACTAACAA
1 ATAATATAATAAATTAAACTAACAA
1409158 ACTAATA
1 A-TAATA
1409165 ATTTATACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 14 0.48
26 15 0.52
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (25 bp):
ATAATATAATAAATTAAACTAACAA
Found at i:1409138 original size:21 final size:22
Alignment explanation
Indices: 1409112--1409192 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 22
1409102 TTTATATAAT
1409112 CTAATATAATTAAACTAACAAA
1 CTAATATAATTAAACTAACAAA
1409134 -TAATATAATAACTTAAACTAACAAA
1 CT-A-AT-ATAA-TTAAACTAACAAA
* *
1409159 CTAATA-ATTTATACTAACAAA
1 CTAATATAATTAAACTAACAAA
*
1409180 CTAAT-TAACTAAA
1 CTAATATAATTAAA
1409193 TTTCTGTTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 13
0.73 0.08 0.20
Matches are distributed among these distances:
21 22 0.46
22 2 0.04
23 3 0.06
24 6 0.12
25 14 0.29
26 1 0.02
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.30
Consensus pattern (22 bp):
CTAATATAATTAAACTAACAAA
Found at i:1414535 original size:16 final size:16
Alignment explanation
Indices: 1414514--1414545 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1414504 ACTAGGTAAC
1414514 AAATACATTTTAATTT
1 AAATACATTTTAATTT
1414530 AAATACATTTTAATTT
1 AAATACATTTTAATTT
1414546 GACATATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (16 bp):
AAATACATTTTAATTT
Found at i:1418075 original size:20 final size:20
Alignment explanation
Indices: 1418050--1418102 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
1418040 GGGGGAACAA
1418050 ATTCCCCCCCAGGAGTACAG
1 ATTCCCCCCCAGGAGTACAG
* *
1418070 ATT-CCCCCCAGTGGGTACCG
1 ATTCCCCCCCAG-GAGTACAG
1418090 ATTCCCCCCCAGG
1 ATTCCCCCCCAGG
1418103 GGGTACCGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 8 0.28
20 13 0.45
21 8 0.28
ACGTcount: A:0.19, C:0.43, G:0.21, T:0.17
Consensus pattern (20 bp):
ATTCCCCCCCAGGAGTACAG
Found at i:1418106 original size:21 final size:21
Alignment explanation
Indices: 1418050--1418113 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
1418040 GGGGGAACAA
* *
1418050 ATTCCCCCCCA-GGAGTACAG
1 ATTCCCCCCCAGGGGGTACCG
*
1418070 ATT-CCCCCCAGTGGGTACCG
1 ATTCCCCCCCAGGGGGTACCG
1418090 ATTCCCCCCCAGGGGGTACCG
1 ATTCCCCCCCAGGGGGTACCG
1418111 ATT
1 ATT
1418114 GCACTTAGGG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
19 7 0.18
20 12 0.32
21 19 0.50
ACGTcount: A:0.19, C:0.39, G:0.23, T:0.19
Consensus pattern (21 bp):
ATTCCCCCCCAGGGGGTACCG
Found at i:1421451 original size:26 final size:26
Alignment explanation
Indices: 1421416--1421482 Score: 134
Period size: 26 Copynumber: 2.6 Consensus size: 26
1421406 GGAGGTCAAT
1421416 ACGACGCCGTTTTGGAACTAAACGGG
1 ACGACGCCGTTTTGGAACTAAACGGG
1421442 ACGACGCCGTTTTGGAACTAAACGGG
1 ACGACGCCGTTTTGGAACTAAACGGG
1421468 ACGACGCCGTTTTGG
1 ACGACGCCGTTTTGG
1421483 CGTACGAGAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.24, C:0.24, G:0.31, T:0.21
Consensus pattern (26 bp):
ACGACGCCGTTTTGGAACTAAACGGG
Found at i:1423893 original size:109 final size:108
Alignment explanation
Indices: 1423658--1424176 Score: 586
Period size: 109 Copynumber: 4.8 Consensus size: 108
1423648 CAAACTTGTA
1423658 TGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTAT
1 TGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTAT
*
1423723 TTCTTCAGAGAGTATAAGACCCATAATCTTCATCAATCGCATC
66 TTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCATC
*
1423766 TGCCCCCTATTTCTTCAGAGAGTATAAGA-TCCGAACAATCTTCAATGATTGCGTCTGCCCCCTT
1 TGCCCCCTATTTCTTCAGAGAGTATAAGACT-CGAACAATCTTCAACGATTGCGTCTGCCCCC-T
* *
1423830 TTTTCTTCGGAGAGTATAAGACCCACAATCTTCATCAATCGCATC
64 ATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCATC
*
1423875 TGTCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTAT
1 TGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTAT
* **
1423940 TTCTTCAGAGAGTATAAGACCCACAATCTTCAACAATCGGGT-
66 TTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCATC
** * * * * ** * * *
1423982 TCGTTCCCTCTTTCTCCAGGGAGTAT-AGAACTCGAA-AATCTTTTGAA--AACGTGTATGCTCC
1 T-GCCCCCTATTTCTTCAGAGAGTATAAG-ACTCGAACAATC--TTCAACGATTGCGTCTGCCCC
* * * * **
1424043 CTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTC
62 CTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGCATC
* * * * * * * * *
1424092 TACTCCCTA-TTCTTTCAGAGAGTATGAGACTCAAATAATCTTCAACAATCGTGTCTGCTCCCTA
1 TGCCCCCTATTTC-TTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTA
1424156 -TTCTTTCAGAGAGTATAAGAC
65 TTTC-TTCAGAGAGTATAAGAC
1424177 TCGAACAAAC
Statistics
Matches: 359, Mismatches: 36, Indels: 30
0.84 0.08 0.07
Matches are distributed among these distances:
107 39 0.11
108 134 0.37
109 147 0.41
110 39 0.11
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.31
Consensus pattern (108 bp):
TGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTAT
TTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCATC
Found at i:1424077 original size:217 final size:215
Alignment explanation
Indices: 1423563--1424242 Score: 687
Period size: 217 Copynumber: 3.1 Consensus size: 215
1423553 TTATTCTTTT
* * ** * *
1423563 CAGGGAGTATAGAATTCAATAAATCTTCAGAAAATGGGTTCGCTCCCTATTTCTTCAGAGGGTAT
1 CAGGGAGTATAGAACTCGA-AAATCTTTTGAAAATGCGTT-GCTCCCTATTTCTTCAGAGAGTAT
* * * * *
1423628 AAGACTTGAATC-ATCTTCAACAAACTTGTATGCCCCCTATTTCTTCAGAGAGTATAAGACTCGA
64 AAGACTCGAA-CAATCTTCAACAATCGTGTCTGACCCCTATTTCTTCAGAGAGTATAAGACTCGA
* *
1423692 ACAATCTTCAACGATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCATAATCTTCATC
128 ACAATCTTCAACGATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCAAC
** ** *
1423757 AATCGCATCTGCCCCCTATTTCTT
193 AATCGGGTC-GTTCCCTATTTCTC
* * * * * * *
1423781 CAGAGAGTATAAGATC-CGAACAATC--TTCAATGATTGCGTCTGCCCCCTTTTTTCTTCGGAGA
1 CAGGGAGTAT-AGAACTCGAA-AATCTTTTGAA--AATGCGT-TGCTCCC-TATTTCTTCAGAGA
* * ** *
1423843 GTATAAGAC-C-CACAATCTTCATCAATCGCATCTGTCCCCTATTTCTTCAGAGAGTATAAGACT
60 GTATAAGACTCGAACAATCTTCAACAATCGTGTCTGACCCCTATTTCTTCAGAGAGTATAAGACT
1423906 CGAACAATCTTCAACGATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTC
125 CGAACAATCTTCAACGATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTC
*
1423971 AACAATCGGGTTCGTTCCCTCTTTCTC
190 AACAATCGGG-TCGTTCCCTATTTCTC
* * * *
1423998 CAGGGAGTATAGAACTCGAAAATCTTTTGAAAACGTGTATGCTCCCTATTCCTTCAGAGAGTATG
1 CAGGGAGTATAGAACTCGAAAATCTTTTGAAAATGCGT-TGCTCCCTATTTCTTCAGAGAGTATA
* *
1424063 AGACTCGAACAATCTTCAACAATCGTGTCT-ACTCCCTA-TTCTTTCAGAGAGTATGAGACTCAA
65 AGACTCGAACAATCTTCAACAATCGTGTCTGAC-CCCTATTTC-TTCAGAGAGTATAAGACTCGA
* * * * * * *
1424126 ATAATCTTCAACAATCGTGTCTGCTCCCTA-TTCTTTCAGAGAGTATAAGACTCGAACAAACTTC
128 ACAATCTTCAACGATTGCGTCTGCCCCCTATTTC-TTCAGAGAGTATAAGAC-C-CACAATCTTC
1424190 AACAATCGGGTC-TACTCCCTATTTCTC
190 AACAATCGGGTCGT--TCCCTATTTCTC
* * * *
1424217 TAGGGATTATGGAACTCGAACATCTT
1 CAGGGAGTATAGAACTCGAAAATCTT
1424243 CTTCTTACAG
Statistics
Matches: 381, Mismatches: 61, Indels: 39
0.79 0.13 0.08
Matches are distributed among these distances:
215 19 0.05
216 29 0.08
217 224 0.59
218 34 0.09
219 75 0.20
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.31
Consensus pattern (215 bp):
CAGGGAGTATAGAACTCGAAAATCTTTTGAAAATGCGTTGCTCCCTATTTCTTCAGAGAGTATAA
GACTCGAACAATCTTCAACAATCGTGTCTGACCCCTATTTCTTCAGAGAGTATAAGACTCGAACA
ATCTTCAACGATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCAACAAT
CGGGTCGTTCCCTATTTCTC
Found at i:1424195 original size:55 final size:55
Alignment explanation
Indices: 1423604--1424215 Score: 599
Period size: 55 Copynumber: 11.2 Consensus size: 55
1423594 AAATGGGTTC
* * * ** *
1423604 GCTCCCTATTTCTTCAGAGGGTATAAGACTTGAATC-ATCTTCAACAAACTTGTAT
1 GCTCCCTATTTCTTCAGAGAGTATAAGACTCGAA-CAATCTTCAACAATCGCGTCT
* * *
1423659 GCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCT
1 GCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCT
* * * * *
1423714 GCCCCCTATTTCTTCAGAGAGTATAAGAC-C-CATAATCTTCATCAATCGCATCT
1 GCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCT
* ** *
1423767 GCCCCCTATTTCTTCAGAGAGTATAAGA-TCCGAACAATCTTCAATGATTGCGTCT
1 GCTCCCTATTTCTTCAGAGAGTATAAGACT-CGAACAATCTTCAACAATCGCGTCT
* * * * * *
1423822 GCCCCCTTTTTTCTTCGGAGAGTATAAGAC-C-CACAATCTTCATCAATCGCATCT
1 GCTCCC-TATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCT
* *
1423876 G-TCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCT
1 GCT-CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCT
* * *
1423931 GCCCCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTCAACAATCGGGT-T
1 GCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCT
* * * * * * *
1423983 CGTTCCCTCTTTCTCCAGGGAGTAT-AGAACTCGAA-AATCTTTTGAA-AA-CGTGTAT
1 -GCTCCCTATTTCTTCAGAGAGTATAAG-ACTCGAACAATC--TTCAACAATCGCGTCT
* * *
1424038 GCTCCCTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCT
1 GCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCT
* * * * *
1424093 ACTCCCTA-TTCTTTCAGAGAGTATGAGACTCAAATAATCTTCAACAATCGTGTCT
1 GCTCCCTATTTC-TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCT
* *
1424148 GCTCCCTA-TTCTTTCAGAGAGTATAAGACTCGAACAAACTTCAACAATCGGGTCT
1 GCTCCCTATTTC-TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCT
*
1424203 ACTCCCTATTTCT
1 GCTCCCTATTTCT
1424216 CTAGGGATTA
Statistics
Matches: 465, Mismatches: 69, Indels: 46
0.80 0.12 0.08
Matches are distributed among these distances:
52 3 0.01
53 108 0.23
54 65 0.14
55 262 0.56
56 27 0.06
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (55 bp):
GCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCT
Found at i:1424238 original size:55 final size:55
Alignment explanation
Indices: 1423489--1424212 Score: 381
Period size: 55 Copynumber: 13.3 Consensus size: 55
1423479 TGGAAAAAAC
** *
1423489 GTCTACTCCCTATTCTTTCAGAGAGTAT-AGGACTCGATTAATCTTCAATC-AGCGT
1 GTCTACTCCCTATTCTTTCAGAGAGTATGA-GACTCGAACAATCTTCAA-CAATCGT
* * * * * * * *
1423544 -ACTTGCTCCTTATTCTTTTCAGGGAGTAT-AGAATTC-AATAAATCTTCAGAAAAT-GG
1 GTC-TACTCCCTATTC-TTTCAGAGAGTATGAG-ACTCGAA-CAATCTTCA-ACAATCGT
* * * * * *
1423600 GT-TCGCTCCCTATT-TCTTCAGAGGGTATAAGACTTGAATC-ATCTTCAACAAACTT
1 GTCT-ACTCCCTATTCT-TTCAGAGAGTATGAGACTCGAA-CAATCTTCAACAATCGT
* * * * * * *
1423655 GTATGCCCCCTATT-TCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGC
1 GTCTACTCCCTATTCT-TTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGT
* * * * * * *
1423710 GTCTGCCCCCTATT-TCTTCAGAGAGTATAAGAC-C-CATAATCTTCATCAATCGC
1 GTCTACTCCCTATTCT-TTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGT
* * * * ** * *
1423763 ATCTGCCCCCTATT-TCTTCAGAGAGTATAAGA-TCCGAACAATCTTCAATGATTGC
1 GTCTACTCCCTATTCT-TTCAGAGAGTATGAGACT-CGAACAATCTTCAACAATCGT
* * * * * * * * *
1423818 GTCTGCCCCCTTTTTTCTTCGGAGAGTATAAGAC-C-CACAATCTTCATCAATCGC
1 GTCTACTCCCTATTCT-TTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGT
* * * * * *
1423872 ATCT-GTCCCCTATT-TCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGC
1 GTCTACT-CCCTATTCT-TTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGT
* * * * *
1423927 GTCTGCCCCCTATT-TCTTCAGAGAGTATAAGAC-C-CACAATCTTCAACAATCGG
1 GTCTACTCCCTATTCT-TTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGT
* * * *
1423980 GT-T-CGTTCCCTCTT-TCTCCAGGGAGTAT-AGAACTCGAA-AATCTTTTGAA-AA-CGT
1 GTCTAC--TCCCTATTCT-TTCAGAGAGTATGAG-ACTCGAACAATC--TTCAACAATCGT
* * *
1424034 GTATGCTCCCTATTCCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGT
1 GTCTACTCCCTATTCTTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGT
* *
1424089 GTCTACTCCCTATTCTTTCAGAGAGTATGAGACTCAAATAATCTTCAACAATCGT
1 GTCTACTCCCTATTCTTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGT
* * * *
1424144 GTCTGCTCCCTATTCTTTCAGAGAGTATAAGACTCGAACAAACTTCAACAATCGG
1 GTCTACTCCCTATTCTTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGT
1424199 GTCTACTCCCTATT
1 GTCTACTCCCTATT
1424213 TCTCTAGGGA
Statistics
Matches: 542, Mismatches: 90, Indels: 74
0.77 0.13 0.10
Matches are distributed among these distances:
51 1 0.00
52 3 0.01
53 104 0.19
54 68 0.13
55 302 0.56
56 62 0.11
57 2 0.00
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.31
Consensus pattern (55 bp):
GTCTACTCCCTATTCTTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGT
Found at i:1424624 original size:164 final size:155
Alignment explanation
Indices: 1424204--1425238 Score: 1057
Period size: 155 Copynumber: 6.5 Consensus size: 155
1424194 ATCGGGTCTA
* * * ** * *
1424204 CTCCCTATTTCTCTAGGGATTATGGAACTCGAACATCTTCTTCTTACAGGTTTGCTCCCTCTTTC
1 CTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATATTCTTCAAACGGGTTCGCTCCCTCTTTC
* * * ** *
1424269 TCTAGGGAGTATAGAACTTGAATAATCTTCTGTAAGCGAATT--C-CCTTTTTCTTTAAGGAGTA
66 TCTAGGGAGTATAGAACTCGAA-CATCTTC---AAACGGGTTCGCTCCTCTTTC-TTAAGGAGTA
* * *
1424331 TAGAACTCGAATAATCTTTTGGAAACGGGTTTG
126 TAGAACTCGAACAATC--TT-CAAACGGGTTCG
* * * * * ** *
1424364 CTCCCTCTTTCTTTCAGGAAGTATAGAACTCGAATGATCTTCTGAAAACGGGCTCGCTCCCTCTT
1 CTCCCTCTTTCTCT-AGGGAGTATGGAACTCGAA-CATATTCTTCAAACGGGTTCGCTCCCTCTT
* * **
1424429 TCT-TCAGGGAGTATAGAACTCGAATATCTTCTTATTACGGGTTCGCTTCGCTCTTTCTCCAGGA
64 TCTCT-AGGGAGTATAGAACTCGAACATCTTC--A-AACGGGTTCGC-TC-CTCTTTCTTAAGG-
1424493 AGTATAGAACTCGAACAATCTTCTGAAAACGGGTTCG
122 AGTATAGAACTCGAACAATCTTC---AAACGGGTTCG
*
1424530 CTCCCTCTTTCT-TCAGGGAGTATGGAACTCGAACATATTCTTCAAACGGGTTCGCTCCCCCTTT
1 CTCCCTCTTTCTCT-AGGGAGTATGGAACTCGAACATATTCTTCAAACGGGTTCGCTCCCTCTTT
* ** **
1424594 CTCTAGGGAGTATAGAACTCGAGCATCTTCTTCTTACGGGTTCGCTTCGCTCTTTCTCCAGGAAG
65 CTCTAGGGAGTATAGAACTCGA--A-CATCTTCAAACGGGTTCGC-TC-CTCTTTCTTAAGG-AG
1424659 TATAGAACTCGAACAATCTTCTGAAAACGGGTTCG
124 TATAGAACTCGAACAATCTTC---AAACGGGTTCG
*
1424694 CTCCCTCTTTCT-TCAGGGAGTATGGAACTCGAACATATTCTTCAAACGGGTTCGCTCCCCCTTT
1 CTCCCTCTTTCTCT-AGGGAGTATGGAACTCGAACATATTCTTCAAACGGGTTCGCTCCCTCTTT
* *
1424758 CTCTAGGGAGTATAGAACTCGAGCATCTTCAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATA
65 CTCTAGGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCT-CCTCTTTC-TTAAGGAGTATA
* *
1424823 GAACTCGAA-TATCTTCACACGGGTTCG
128 GAACTCGAACAATCTTCAAACGGGTTCG
* **
1424850 CTCCCTCTTTCTCTAGGGAGTATGGAACTC-AGACAT-CTCTTCAAACGGGTTCGCTCATTCTTT
1 CTCCCTCTTTCTCTAGGGAGTATGGAACTCGA-ACATATTCTTCAAACGGGTTCGCTCCCTCTTT
* * *
1424913 CTTTAAGGAGTATGGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATA
65 CTCTAGGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCC-TCTTTC-TTAAGGAGTATA
*
1424978 GAACTCG--CATATCTTCACACGGGTTCG
128 GAACTCGAACA-ATCTTCAAACGGGTTCG
* * *
1425005 CTCCTTCTTTCTCTAGGGAGTATGGAACTC-AGACAT-CTCTTCAAACGGGTTCGCTCCTTCTTT
1 CTCCCTCTTTCTCTAGGGAGTATGGAACTCGA-ACATATTCTTCAAACGGGTTCGCTCCCTCTTT
* * *
1425068 CTTTAAGGAGTATGGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATA
65 CTCTAGGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCC-TCTTTC-TTAAGGAGTATA
*
1425133 GAACTCG--CATATCTTCACACGGGTTCG
128 GAACTCGAACA-ATCTTCAAACGGGTTCG
* *
1425160 CTCCTTCTTTCTCTAGGGAGTATAGAACTCGAAC--A-TCTTCAAACGGGTTCGCTCCCTC--TC
1 CTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATATTCTTCAAACGGGTTCGCTCCCTCTTTC
*
1425220 TCTAGGGAGTATGGAACTC
66 TCTAGGGAGTATAGAACTC
1425239 AAATAATCTT
Statistics
Matches: 787, Mismatches: 62, Indels: 61
0.86 0.07 0.07
Matches are distributed among these distances:
151 19 0.02
153 22 0.03
154 2 0.00
155 289 0.37
156 43 0.05
157 1 0.00
159 6 0.01
160 37 0.05
161 47 0.06
162 43 0.05
163 1 0.00
164 199 0.25
165 25 0.03
166 48 0.06
167 5 0.01
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.33
Consensus pattern (155 bp):
CTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATATTCTTCAAACGGGTTCGCTCCCTCTTTC
TCTAGGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTCTTTCTTAAGGAGTATAGAA
CTCGAACAATCTTCAAACGGGTTCG
Found at i:1424809 original size:51 final size:51
Alignment explanation
Indices: 1424204--1425238 Score: 967
Period size: 51 Copynumber: 19.6 Consensus size: 51
1424194 ATCGGGTCTA
* * * ** * *
1424204 CTCCCTATTTCTCTAGGGATTATGGAACTCGAACATCTTCTTCTTACAGGTTTG
1 CTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACA---TCTTCAAACGGGTTCG
* * * **
1424258 CTCCCTCTTTCTCTAGGGAGTATAGAACTTGAATAATCTTCTGTAA-GCGAAT--
1 CTCCCTCTTTCTCTAGGGAGTATAGAACTCGAA-CATCTTC--AAACG-GGTTCG
* * * * * *
1424310 -TCCCTTTTTCTTTAAGGAGTATAGAACTCGAATAATCTTTTGGAAACGGGTTTG
1 CTCCCTCTTTCTCTAGGGAGTATAGAACTCGAA-CATC--TT-CAAACGGGTTCG
* * * *
1424364 CTCCCTCTTTCTTTCAGGAAGTATAGAACTCGAATGATCTTCTGAAAACGGGCTCG
1 CTCCCTCTTTCTCT-AGGGAGTATAGAACTCGAA-CATCTTC---AAACGGGTTCG
* *
1424420 CTCCCTCTTTCT-TCAGGGAGTATAGAACTCGAATATCTTCTTATTACGGGTTCG
1 CTCCCTCTTTCTCT-AGGGAGTATAGAACTCGAACATCTTC--A-AACGGGTTCG
* * *
1424474 CTTCGCTCTTTCTCCAGGAAGTATAGAACTCGAACAATCTTCTGAAAACGGGTTCG
1 C-TCCCTCTTTCTCTAGGGAGTATAGAACTCGAAC-ATCTTC---AAACGGGTTCG
*
1424530 CTCCCTCTTTCT-TCAGGGAGTATGGAACTCGAACATATTCTTCAAACGGGTTCG
1 CTCCCTCTTTCTCT-AGGGAGTATAGAACTCGAAC--A-TCTTCAAACGGGTTCG
* * **
1424584 CTCCCCCTTTCTCTAGGGAGTATAGAACTCGAGCATCTTCTTCTTACGGGTTCG
1 CTCCCTCTTTCTCTAGGGAGTATAGAACTCGA--A-CATCTTCAAACGGGTTCG
* * *
1424638 CTTCGCTCTTTCTCCAGGAAGTATAGAACTCGAACAATCTTCTGAAAACGGGTTCG
1 C-TCCCTCTTTCTCTAGGGAGTATAGAACTCGAAC-ATCTTC---AAACGGGTTCG
*
1424694 CTCCCTCTTTCT-TCAGGGAGTATGGAACTCGAACATATTCTTCAAACGGGTTCG
1 CTCCCTCTTTCTCT-AGGGAGTATAGAACTCGAAC--A-TCTTCAAACGGGTTCG
* *
1424748 CTCCCCCTTTCTCTAGGGAGTATAGAACTCGAGCATCTTCAAACGGGTTCG
1 CTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCAAACGGGTTCG
* * *
1424799 CTCCCTCTTTCTTTAGGGAGTATAGAACTCGAATATCTTCACACGGGTTCG
1 CTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCAAACGGGTTCG
*
1424850 CTCCCTCTTTCTCTAGGGAGTATGGAACTC-AGACATCTCTTCAAACGGGTTCG
1 CTCCCTCTTTCTCTAGGGAGTATAGAACTCGA-ACA--TCTTCAAACGGGTTCG
** * * *
1424903 CTCATTCTTTCTTTAAGGAGTATGGAACTCGAACATCTTCAAACGGGTTCG
1 CTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCAAACGGGTTCG
* * * * * *
1424954 CTCCTTCTTTCTTTAAGGAGTATAGAACTCGCATATCTTCACACGGGTTCG
1 CTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCAAACGGGTTCG
* *
1425005 CTCCTTCTTTCTCTAGGGAGTATGGAACTC-AGACATCTCTTCAAACGGGTTCG
1 CTCCCTCTTTCTCTAGGGAGTATAGAACTCGA-ACA--TCTTCAAACGGGTTCG
* * * *
1425058 CTCCTTCTTTCTTTAAGGAGTATGGAACTCGAACATCTTCAAACGGGTTCG
1 CTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCAAACGGGTTCG
* * * * * *
1425109 CTCCTTCTTTCTTTAAGGAGTATAGAACTCGCATATCTTCACACGGGTTCG
1 CTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCAAACGGGTTCG
*
1425160 CTCCTTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCAAACGGGTTCG
1 CTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCAAACGGGTTCG
*
1425211 CTCCCTC--TCTCTAGGGAGTATGGAACTC
1 CTCCCTCTTTCTCTAGGGAGTATAGAACTC
1425239 AAATAATCTT
Statistics
Matches: 838, Mismatches: 99, Indels: 93
0.81 0.10 0.09
Matches are distributed among these distances:
49 20 0.02
50 1 0.00
51 331 0.39
52 11 0.01
53 100 0.12
54 146 0.17
55 146 0.17
56 71 0.08
57 12 0.01
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.33
Consensus pattern (51 bp):
CTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCAAACGGGTTCG
Found at i:1425495 original size:36 final size:36
Alignment explanation
Indices: 1425469--1425624 Score: 222
Period size: 36 Copynumber: 4.3 Consensus size: 36
1425459 ACTACTTTTT
* *
1425469 GGTGAAGACTTAAGATGGTTTGCTTCACTACTCTCT
1 GGTGAAGACTTAAGATGGTTTGCTTCACTATTCTCC
*
1425505 GGTGAAGACTTATGATGGTTTGCTTCACTATTCTCC
1 GGTGAAGACTTAAGATGGTTTGCTTCACTATTCTCC
* * * *
1425541 GGTGAAGGCTTCAGATTGATTGCTTCACTATTCTCC
1 GGTGAAGACTTAAGATGGTTTGCTTCACTATTCTCC
* *
1425577 GGTGAAGGCTTCAGATGGTTTGCTTCACTATTCTCC
1 GGTGAAGACTTAAGATGGTTTGCTTCACTATTCTCC
*
1425613 GGTGAAGGCTTA
1 GGTGAAGACTTA
1425625 GGATTGACTT
Statistics
Matches: 109, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 109 1.00
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (36 bp):
GGTGAAGACTTAAGATGGTTTGCTTCACTATTCTCC
Found at i:1432903 original size:26 final size:26
Alignment explanation
Indices: 1432868--1432934 Score: 134
Period size: 26 Copynumber: 2.6 Consensus size: 26
1432858 GGAGGTCAAT
1432868 ACGACGCCGTTTTGGAACTAAACGGG
1 ACGACGCCGTTTTGGAACTAAACGGG
1432894 ACGACGCCGTTTTGGAACTAAACGGG
1 ACGACGCCGTTTTGGAACTAAACGGG
1432920 ACGACGCCGTTTTGG
1 ACGACGCCGTTTTGG
1432935 CGTACGAGAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.24, C:0.24, G:0.31, T:0.21
Consensus pattern (26 bp):
ACGACGCCGTTTTGGAACTAAACGGG
Found at i:1435623 original size:2 final size:2
Alignment explanation
Indices: 1435618--1435652 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1435608 TATTTTACTG
1435618 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1435653 TAGGATTTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1442950 original size:32 final size:31
Alignment explanation
Indices: 1442895--1442980 Score: 95
Period size: 33 Copynumber: 2.7 Consensus size: 31
1442885 TTATATATTT
1442895 TTGAATTTTTTTAC-TTTATATTC-TTTTTGTA
1 TTGAA-TTTTTTACTTTTA-ATTCTTTTTTGTA
*
1442926 TTGAATTTTATTCACTTTTAATTCTTTTTTTTA
1 TTGAATTTT-TT-ACTTTTAATTCTTTTTTGTA
*
1442959 TTGCATTTTTATACTTTTAATT
1 TTGAATTTTT-TACTTTTAATT
1442981 ACAATTGATA
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
30 4 0.08
31 7 0.15
32 17 0.35
33 20 0.42
ACGTcount: A:0.21, C:0.08, G:0.05, T:0.66
Consensus pattern (31 bp):
TTGAATTTTTTACTTTTAATTCTTTTTTGTA
Found at i:1442975 original size:23 final size:23
Alignment explanation
Indices: 1442931--1442976 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1442921 TTGTATTGAA
*
1442931 TTTTATTCACTTTTAATTCTTTT
1 TTTTATTCACTTTTAATACTTTT
*
1442954 TTTTATTGCA-TTTTTATACTTTT
1 TTTTATT-CACTTTTAATACTTTT
1442977 AATTACAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.17, C:0.11, G:0.02, T:0.70
Consensus pattern (23 bp):
TTTTATTCACTTTTAATACTTTT
Found at i:1443039 original size:11 final size:10
Alignment explanation
Indices: 1443018--1443075 Score: 55
Period size: 10 Copynumber: 5.6 Consensus size: 10
1443008 TTCATTTTTT
1443018 TAAAAATCAA
1 TAAAAATCAA
1443028 TAAAAATGCAA
1 TAAAAAT-CAA
1443039 TAAAAAAT-AA
1 T-AAAAATCAA
* *
1443049 TTAAAAGCGAA
1 TAAAAATC-AA
*
1443060 TAAAATTCAA
1 TAAAAATCAA
1443070 TAAAAA
1 TAAAAA
1443076 CGCCAACTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 4 0.11
10 17 0.45
11 11 0.29
12 6 0.16
ACGTcount: A:0.67, C:0.07, G:0.05, T:0.21
Consensus pattern (10 bp):
TAAAAATCAA
Found at i:1443044 original size:21 final size:21
Alignment explanation
Indices: 1443018--1443075 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
1443008 TTCATTTTTT
1443018 TAAAAATCAATAAAAATGC-AA
1 TAAAAATCAATAAAAA-GCGAA
*
1443039 TAAAAAAT-AATTAAAAGCGAA
1 T-AAAAATCAATAAAAAGCGAA
*
1443060 TAAAATTCAATAAAAA
1 TAAAAATCAATAAAAA
1443076 CGCCAACTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 7 0.23
21 18 0.58
22 6 0.19
ACGTcount: A:0.67, C:0.07, G:0.05, T:0.21
Consensus pattern (21 bp):
TAAAAATCAATAAAAAGCGAA
Found at i:1443906 original size:11 final size:11
Alignment explanation
Indices: 1443892--1443933 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
1443882 AAAAGAGTTT
1443892 TAAATTAATAA
1 TAAATTAATAA
**
1443903 TAAATTAAGTTT
1 TAAATTAA-TAA
1443915 TAAATTAATAA
1 TAAATTAATAA
1443926 TAAATTAA
1 TAAATTAA
1443934 GTTATTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
11 17 0.65
12 9 0.35
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (11 bp):
TAAATTAATAA
Found at i:1443915 original size:23 final size:23
Alignment explanation
Indices: 1443887--1443936 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
1443877 ATTTTAAAAG
1443887 AGTTTTAAATTAATAATAAATTA
1 AGTTTTAAATTAATAATAAATTA
1443910 AGTTTTAAATTAATAATAAATTA
1 AGTTTTAAATTAATAATAAATTA
1443933 AGTT
1 AGTT
1443937 ATTATATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (23 bp):
AGTTTTAAATTAATAATAAATTA
Found at i:1444817 original size:30 final size:30
Alignment explanation
Indices: 1444783--1444839 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
1444773 ATCCCCCAAC
1444783 ATTTAGT-TCGTTTGCAATATGGTCCCCACT
1 ATTTAGTCT-GTTTGCAATATGGTCCCCACT
1444813 ATTTAGTCTGTTTGCAATATGGTCCCC
1 ATTTAGTCTGTTTGCAATATGGTCCCC
1444840 GACCGTTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.40
Consensus pattern (30 bp):
ATTTAGTCTGTTTGCAATATGGTCCCCACT
Found at i:1449506 original size:2 final size:2
Alignment explanation
Indices: 1449499--1449526 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1449489 AAAACAGAAC
1449499 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1449527 GAAATTTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1462678 original size:2 final size:2
Alignment explanation
Indices: 1462671--1462700 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1462661 ATTCAACTTT
1462671 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1462701 GATAAAGTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1465953 original size:35 final size:35
Alignment explanation
Indices: 1465914--1466025 Score: 161
Period size: 35 Copynumber: 3.2 Consensus size: 35
1465904 AAAACAATCC
*
1465914 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCTAAAATAAT
* * *
1465949 TCAATTTCACTCTAAACTCTAAATTCTAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCTAAAATAAT
** *
1465984 TCAATTAAATTCTAAACCCCAAATTCTAAAATACT
1 TCAATTTCATTCTAAACCCCAAATTCTAAAATAAT
1466019 TCAATTT
1 TCAATTT
1466026 AAGGTTTAGA
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 66 1.00
ACGTcount: A:0.43, C:0.22, G:0.00, T:0.35
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCTAAAATAAT
Found at i:1468133 original size:35 final size:35
Alignment explanation
Indices: 1468085--1468194 Score: 157
Period size: 35 Copynumber: 3.1 Consensus size: 35
1468075 TCTAAACCTT
* * * *
1468085 AAATTGAAGTATTTTAGAATTTGGGGTTTAGATTT
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
* *
1468120 TAATTGAATTATTTTGGAATTTAGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
*
1468155 AAATTGAATTACTTTGGAATTTGGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
1468190 AAATT
1 AAATT
1468195 AAGGACTATT
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 66 1.00
ACGTcount: A:0.33, C:0.01, G:0.23, T:0.44
Consensus pattern (35 bp):
AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
Found at i:1471335 original size:27 final size:27
Alignment explanation
Indices: 1471305--1471392 Score: 88
Period size: 32 Copynumber: 3.1 Consensus size: 27
1471295 TGATATTTTT
*
1471305 ATATTATTAATTTTATTTTAATAAATAA
1 ATATTAATAATTTTATTTTAATAAAT-A
1471333 TATAATTAATAATATATTATTTTAATAATATA
1 -AT-ATTAATAAT-T-TTATTTTAATAA-ATA
**
1471365 ATA-TAATAAACTTATTTTAATAAATA
1 ATATTAATAATTTTATTTTAATAAATA
1471391 AT
1 AT
1471393 GAATATGGTT
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
26 5 0.10
27 12 0.23
29 8 0.15
30 9 0.17
31 3 0.06
32 13 0.25
33 2 0.04
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (27 bp):
ATATTAATAATTTTATTTTAATAAATA
Found at i:1471343 original size:16 final size:17
Alignment explanation
Indices: 1471322--1471371 Score: 68
Period size: 16 Copynumber: 3.1 Consensus size: 17
1471312 TAATTTTATT
1471322 TTAATAA-ATAATATAA
1 TTAATAATATAATATAA
* *
1471338 TTAATAATATATTAT-T
1 TTAATAATATAATATAA
1471354 TTAATAATATAATATAA
1 TTAATAATATAATATAA
1471371 T
1 T
1471372 AAACTTATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
16 21 0.75
17 7 0.25
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TTAATAATATAATATAA
Found at i:1471363 original size:28 final size:26
Alignment explanation
Indices: 1471328--1471397 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 26
1471318 TATTTTAATA
1471328 AATAATATAATTAATAATATATTATTTT
1 AATAATATAATTAATAA-A-ATTATTTT
*
1471356 AATAATATAATATAATAAACTTATTTT
1 AATAATATAAT-TAATAAAATTATTTT
*
1471383 AATAA-ATAATGAATA
1 AATAATATAATTAATA
1471398 TGGTTTATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
25 4 0.10
26 5 0.13
27 12 0.31
28 12 0.31
29 6 0.15
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (26 bp):
AATAATATAATTAATAAAATTATTTT
Found at i:1479357 original size:2 final size:2
Alignment explanation
Indices: 1479342--1479381 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
1479332 ATTAATCAAT
1479342 TA TA -A TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1479381 T
1 T
1479382 TTTCATACTA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 32 0.91
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1480563 original size:21 final size:19
Alignment explanation
Indices: 1480537--1480583 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1480527 CATGACAAGA
*
1480537 GGAATCATTGTTTGAATAGTT
1 GGAATCATCGTTT--ATAGTT
*
1480558 GGAATCATCGTTTTTAGTT
1 GGAATCATCGTTTATAGTT
1480577 GGAATCA
1 GGAATCA
1480584 ATAAGTCGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 12 0.50
21 12 0.50
ACGTcount: A:0.28, C:0.09, G:0.23, T:0.40
Consensus pattern (19 bp):
GGAATCATCGTTTATAGTT
Found at i:1481397 original size:29 final size:29
Alignment explanation
Indices: 1481330--1481409 Score: 76
Period size: 29 Copynumber: 2.7 Consensus size: 29
1481320 TTAAGGGTCA
1481330 AATTAATATTTCATCTAAAATTTAGGATT
1 AATTAATATTTCATCTAAAATTTAGGATT
*
1481359 AAGTTGATATTT-ATCT-AAATTTGAGG-TT
1 AA-TTAATATTTCATCTAAAATTT-AGGATT
**
1481387 CATATTAATATTTTGTCTAAAAT
1 -A-ATTAATATTTCATCTAAAAT
1481410 GTAAGGGATA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
28 8 0.19
29 18 0.43
30 12 0.29
31 4 0.10
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.46
Consensus pattern (29 bp):
AATTAATATTTCATCTAAAATTTAGGATT
Found at i:1494121 original size:84 final size:85
Alignment explanation
Indices: 1493978--1494138 Score: 243
Period size: 84 Copynumber: 1.9 Consensus size: 85
1493968 TATATATTTG
* * *
1493978 TTTTTTCCCAGTGAATATATCCTTATTTTTTACTATTAATCTCAATCTTTAGTTACTCAAATTCA
1 TTTTTTCCCAGTGAATATATCCTCATTTTCTACTATTAATCTCAATATTTAGTTACTCAAATTCA
*
1494043 ACGATCCTAAAATATTTAAA
66 ACGATACTAAAATATTTAAA
* * * *
1494063 TTTTTT-CCAGTGAATATATTCTCGTTTTCTACTATTAATCTCAATATTTTGTTTCTCAAATTCA
1 TTTTTTCCCAGTGAATATATCCTCATTTTCTACTATTAATCTCAATATTTAGTTACTCAAATTCA
1494127 ACGATACTAAAA
66 ACGATACTAAAA
1494139 ATATGTACTT
Statistics
Matches: 68, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
84 62 0.91
85 6 0.09
ACGTcount: A:0.32, C:0.17, G:0.06, T:0.45
Consensus pattern (85 bp):
TTTTTTCCCAGTGAATATATCCTCATTTTCTACTATTAATCTCAATATTTAGTTACTCAAATTCA
ACGATACTAAAATATTTAAA
Found at i:1495763 original size:39 final size:39
Alignment explanation
Indices: 1495709--1495786 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
1495699 GAATGTGTAA
1495709 TTCCAATAGTTGCAAGAAGGTATTTTCCATCTCAAGAGT
1 TTCCAATAGTTGCAAGAAGGTATTTTCCATCTCAAGAGT
1495748 TTCCAATAGTTGCAAGAAGGTATTTTCCATCTCAAGAGT
1 TTCCAATAGTTGCAAGAAGGTATTTTCCATCTCAAGAGT
1495787 AGGCATTTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (39 bp):
TTCCAATAGTTGCAAGAAGGTATTTTCCATCTCAAGAGT
Found at i:1500671 original size:30 final size:30
Alignment explanation
Indices: 1500619--1500689 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
1500609 ATTCTTGTTA
* *
1500619 TATATGCATATTATTTTCTATTAATTTTAT
1 TATATGTATATTATTTTCTATTAATATTAT
* *
1500649 TATATGTATATGT-TTTTTTATTAGTATTAT
1 TATATGTATAT-TATTTTCTATTAATATTAT
*
1500679 TATATATATAT
1 TATATGTATAT
1500690 ATATATATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 34 0.97
31 1 0.03
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.61
Consensus pattern (30 bp):
TATATGTATATTATTTTCTATTAATATTAT
Found at i:1500684 original size:2 final size:2
Alignment explanation
Indices: 1500679--1500728 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
1500669 TTAGTATTAT
1500679 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1500720 TT TA TA TA T
1 TA TA TA TA T
1500729 TTCCTATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:1500852 original size:21 final size:20
Alignment explanation
Indices: 1500813--1500881 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 20
1500803 TATATATATA
1500813 TATATATTTTA-C-TTT-TT
1 TATATATTTTATCATTTATT
1500830 TATATATTTTACTCATTTATT
1 TATATATTTTA-TCATTTATT
* *
1500851 TATCTATTTTTAT-ATTTATC
1 TATATA-TTTTATCATTTATT
1500871 T-TATATTTTAT
1 TATATATTTTAT
1500882 GTTTTTATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
17 11 0.25
18 6 0.14
19 4 0.09
20 10 0.23
21 8 0.18
22 5 0.11
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (20 bp):
TATATATTTTATCATTTATT
Found at i:1500868 original size:16 final size:18
Alignment explanation
Indices: 1500847--1500881 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
1500837 TTTACTCATT
1500847 TATTTATC-TAT-TTTTA
1 TATTTATCTTATATTTTA
1500863 TATTTATCTTATATTTTA
1 TATTTATCTTATATTTTA
1500881 T
1 T
1500882 GTTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.69
Consensus pattern (18 bp):
TATTTATCTTATATTTTA
Found at i:1501016 original size:16 final size:16
Alignment explanation
Indices: 1500978--1501016 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
1500968 TTATTGTTTT
1500978 TTTATTTTATATTCTA
1 TTTATTTTATATTCTA
*
1500994 TTCATTTTATATT-TA
1 TTTATTTTATATTCTA
1501009 CTTTATTT
1 -TTTATTT
1501017 CTTACTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 2 0.10
16 18 0.90
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTATTTTATATTCTA
Found at i:1504089 original size:21 final size:22
Alignment explanation
Indices: 1504067--1504127 Score: 79
Period size: 22 Copynumber: 2.7 Consensus size: 22
1504057 AAAAAAGGGC
1504067 AAAAAGAAAAAAAAAAGAAGCA
1 AAAAAGAAAAAAAAAAGAAGCA
* *
1504089 AAAAAGGAAAAAACAAGAA-CA
1 AAAAAGAAAAAAAAAAGAAGCA
1504110 AAAAAGAAAGAACAAAAA
1 AAAAAGAAA-AA-AAAAA
1504128 TAAAAAAGGG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 10 0.30
22 19 0.58
23 4 0.12
ACGTcount: A:0.80, C:0.07, G:0.13, T:0.00
Consensus pattern (22 bp):
AAAAAGAAAAAAAAAAGAAGCA
Found at i:1504092 original size:22 final size:21
Alignment explanation
Indices: 1504067--1504135 Score: 77
Period size: 22 Copynumber: 3.3 Consensus size: 21
1504057 AAAAAAGGGC
1504067 AAAAAGAAAAAAAAAAGAAGCA
1 AAAAAGAAAAAAAAAAGAA-CA
* *
1504089 AAAAAGGAAAAAACAAGAACA
1 AAAAAGAAAAAAAAAAGAACA
* * *
1504110 AAAAAGAAAGAACAAA-AATA
1 AAAAAGAAAAAAAAAAGAACA
1504130 AAAAAG
1 AAAAAG
1504136 GGAACAAAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 9 0.22
21 14 0.35
22 17 0.43
ACGTcount: A:0.80, C:0.06, G:0.13, T:0.01
Consensus pattern (21 bp):
AAAAAGAAAAAAAAAAGAACA
Found at i:1504132 original size:20 final size:20
Alignment explanation
Indices: 1504067--1504135 Score: 75
Period size: 20 Copynumber: 3.3 Consensus size: 20
1504057 AAAAAAGGGC
*
1504067 AAAAAGAAAAAAAAAAGAAGCA
1 AAAAAGAAAAAACAAA-AA-CA
*
1504089 AAAAAGGAAAAAACAAGAACA
1 AAAAA-GAAAAAACAAAAACA
* *
1504110 AAAAAGAAAGAACAAAAATA
1 AAAAAGAAAAAACAAAAACA
1504130 AAAAAG
1 AAAAAG
1504136 GGAACAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
20 18 0.44
21 7 0.17
22 7 0.17
23 9 0.22
ACGTcount: A:0.80, C:0.06, G:0.13, T:0.01
Consensus pattern (20 bp):
AAAAAGAAAAAACAAAAACA
Found at i:1505679 original size:36 final size:36
Alignment explanation
Indices: 1505632--1505736 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
1505622 GTGCTCATCA
1505632 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
*
1505668 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAACT
*
1505705 TTGTCTCCCTTGAGACAGTTTCTCC-TGAAACA
1 TTGTCTCTCTTGAGACAGTTTC-CCTTGAAACA
1505737 TAAACATTGA
Statistics
Matches: 65, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
36 32 0.49
37 31 0.48
38 2 0.03
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (36 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
Found at i:1505717 original size:37 final size:37
Alignment explanation
Indices: 1505632--1505741 Score: 170
Period size: 37 Copynumber: 3.0 Consensus size: 37
1505622 GTGCTCATCA
1505632 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
*
1505668 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
*
1505705 TTGTCTCCCTTGAGACAGTTTCTCC-TGAAACATAAAC
1 TTGTCTCTCTTGAGACAGTTTC-CCTTGAAACA-AAAC
1505742 ATTGAAAACA
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
36 31 0.46
37 32 0.47
38 5 0.07
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.35
Consensus pattern (37 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
Found at i:1505806 original size:36 final size:36
Alignment explanation
Indices: 1505751--1505820 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
1505741 CATTGAAAAC
** *
1505751 ATTTCCCTAGAAATGAATTTCGTCTCTCTTGAGATA
1 ATTTCCCTAGAAACAAATTTCGTCTCCCTTGAGATA
* *
1505787 ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGA
1 ATTTCCCTAGAAACAAATTTCGTCTCCCTTGAGA
1505821 CAGCTTCTCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (36 bp):
ATTTCCCTAGAAACAAATTTCGTCTCCCTTGAGATA
Found at i:1505833 original size:36 final size:36
Alignment explanation
Indices: 1505766--1505837 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
1505756 CCTAGAAATG
* * *
1505766 AATTTCGTCTCTCTTGAGATAATTTCCCTTGAAACA
1 AATTTCGTCTCCCTTGAGACAACTTCCCTTGAAACA
* * *
1505802 AATTTTGTCTCCCTTGAGACAGCTTCTCTTGAAACA
1 AATTTCGTCTCCCTTGAGACAACTTCCCTTGAAACA
1505838 CAAAACCTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (36 bp):
AATTTCGTCTCCCTTGAGACAACTTCCCTTGAAACA
Found at i:1505928 original size:67 final size:67
Alignment explanation
Indices: 1505779--1505937 Score: 223
Period size: 67 Copynumber: 2.4 Consensus size: 67
1505769 TTCGTCTCTC
** *
1505779 TTGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGCTTCTCTTGAAACACAAAAC
1 TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCATGAGACAGCTTCTCTTGAAACACAAAAC
1505844 CT
66 CT
* * *
1505846 TTGAGATTGTTTCCCTCGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAAT
1 TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCATGAGACAGCTTCTCTTGAAACACAAAAC
1505911 CT
66 CT
*
1505913 TTGA-ATT-TATCTCCCTTAAAACAAA
1 TTGAGATTGT-T-TCCCTTGAAACAAA
1505938 ATTTCGTTTC
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
65 1 0.01
66 4 0.05
67 77 0.94
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.34
Consensus pattern (67 bp):
TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCATGAGACAGCTTCTCTTGAAACACAAAAC
CT
Found at i:1507020 original size:100 final size:103
Alignment explanation
Indices: 1506771--1507833 Score: 1528
Period size: 100 Copynumber: 10.3 Consensus size: 103
1506761 GCCATCCGCG
* * * * * *
1506771 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
1506836 GGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
63 GGGACCGCTGCTTGTCAAC-AACAACTT-TCAA-TTCAGAGCCA
*
1506880 ATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
**
1506945 ACCGCTGCTTGTCAACAA-AA-TTTC-ATTCAGATTCA
66 ACCGCTGCTTGTCAACAACAACTTTCAATTCAGAGCCA
*
1506980 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
1507045 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTT-TCAAT-TCAGAGCCA
*
1507085 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1507150 ACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTT-CAAT-TCAGAGCCA
1507190 ATTTCAACTT--C-ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1507252 ACCGCTGCTTGTCAACAA-AA-TTTC-ATTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTTCAATTCAGAGCCA
* *
1507287 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
1507352 ACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCTA
66 ACCGCTGCTTGTCAACAACAACTTT-CAAT-TCAGAGCCA
1507392 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1507457 ACCGCTGCTTGTCAACAA-AA-TTTC-ATTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTTCAATTCAGAGCCA
* *
1507492 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * *
1507557 ACCGCTGTTTGTCAACAACAACTTCCCAATCCCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTT-TCAAT-TCAGAGCCA
* *
1507597 ATTTCAACTTCACAACGAAAGATATTGCACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
**
1507662 ACCGCTGCTTGTCAACAA-AA-TTTC-ATTCAGATTCA
66 ACCGCTGCTTGTCAACAACAACTTTCAATTCAGAGCCA
* * *
1507697 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * **
1507762 ACGGCTGGTTGTCAACAAACAA-TTTCCCGGTTCCAGAGCCA
66 ACCGCTGCTTGTCAAC-AACAACTTT--CAATT-CAGAGCCA
* *
1507803 ATTTCAACTTCACTACGGAGGATATTGGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
1507834 TGGAACAATG
Statistics
Matches: 875, Mismatches: 54, Indels: 53
0.89 0.05 0.05
Matches are distributed among these distances:
97 19 0.02
98 2 0.00
99 2 0.00
100 326 0.37
101 15 0.02
102 84 0.10
103 11 0.01
104 13 0.01
105 296 0.34
106 83 0.09
107 3 0.00
109 21 0.02
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.22
Consensus pattern (103 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTTCAATTCAGAGCCA
Found at i:1507160 original size:205 final size:204
Alignment explanation
Indices: 1506771--1507833 Score: 1577
Period size: 205 Copynumber: 5.1 Consensus size: 204
1506761 GCCATCCGCG
* * * * *
1506771 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCAC-ACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* * *
1506836 GGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAAG
62 GGGACCGCTGCTTGTCAAC-AA-AA-TT-TC-A-TTCAGAGCCAATTTCAACTTCACAACGAAGG
*
1506901 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA
121 ATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAA
**
1506965 -TTT-C-AT-TCAGATTCA
186 CTTTCCAATCTCAGAGCCA
1506980 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACA-CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
1507045 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
65 ACCGCTGCTTGTCAACAA-AA-TT-TC-AT-TCAGAGCCAATTTCAACTTCACAACGAAGGATAT
1507110 TGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTT
125 TGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTT
1507175 CCAATCTCAGAGCCA
190 CCAATCTCAGAGCCA
1507190 ATTTCAACTT--CACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGA
1 ATTTCAACTTCACACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGA
*
1507253 CCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACT
66 CCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
1507318 CCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAATC
131 CCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAATC
*
1507383 TCAGAGCTA
196 TCAGAGCCA
1507392 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCAC-ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
1507457 ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
65 ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
* *
1507522 TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGTTTGTCAACAACAACTTCCCAAT
130 TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAAT
*
1507587 CCCAGAGCCA
195 CTCAGAGCCA
* *
1507597 ATTTCAACTTCACAACGAAAGATATTGCACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCAC-ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
**
1507662 ACCGCTGCTTGTCAACAAAATTTCATTCAGATTCAATTTCAACTTCACAACGAAGGATATTGGAC
65 ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
* ** * * * *
1507727 TCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAA-TTTCCCG
130 TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTT-CCA
*
1507791 GT-TCCAGAGCCA
193 ATCT-CAGAGCCA
*
1507803 ATTTCAACTTCACTACGGAGGATATTGGACT
1 ATTTCAACTTCAC-ACGAAGGATATTGGACT
1507834 TGGAACAATG
Statistics
Matches: 803, Mismatches: 38, Indels: 29
0.92 0.04 0.03
Matches are distributed among these distances:
202 122 0.15
203 2 0.00
204 3 0.00
205 463 0.58
206 96 0.12
207 73 0.09
208 4 0.00
209 23 0.03
210 17 0.02
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.22
Consensus pattern (204 bp):
ATTTCAACTTCACACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGA
CCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
CCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAATC
TCAGAGCCA
Found at i:1508876 original size:34 final size:33
Alignment explanation
Indices: 1508804--1508900 Score: 99
Period size: 34 Copynumber: 2.9 Consensus size: 33
1508794 TTTTTCCTAC
* *
1508804 TTTATT-ATTCTTGTTATATATGCATAT-TATTT
1 TTTATTAATT-TTATTATATATGTATATATATTT
* *
1508836 TCTATTAATTTTATTATATATGTATATATGTTTT
1 TTTATTAATTTTATTATATATGTATATAT-ATTT
* * *
1508870 TTTATTAGTGTTATTATATATATATATATAT
1 TTTATTAATTTTATTATATATGTATATATAT
1508901 ATATTATTTA
Statistics
Matches: 53, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
32 20 0.38
33 5 0.09
34 28 0.53
ACGTcount: A:0.30, C:0.03, G:0.06, T:0.61
Consensus pattern (33 bp):
TTTATTAATTTTATTATATATGTATATATATTT
Found at i:1509061 original size:17 final size:16
Alignment explanation
Indices: 1509029--1509062 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1509019 TTTACTCATT
*
1509029 TATTTATCTATTTTTA
1 TATTTATCTATATTTA
1509045 TATTTATCCTATATTTA
1 TATTTAT-CTATATTTA
1509062 T
1 T
1509063 GTTTTTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTTATCTATATTTA
Found at i:1512852 original size:19 final size:19
Alignment explanation
Indices: 1512828--1512877 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 19
1512818 AATTTTAAAT
1512828 AATTATAATTCATTTTTAG-
1 AATTATAATT-ATTTTTAGA
*
1512847 AATTATAAAATTATTTTTTGA
1 AATTAT--AATTATTTTTAGA
1512868 AATTATAATT
1 AATTATAATT
1512878 TTATATAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 10 0.37
20 7 0.26
21 10 0.37
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (19 bp):
AATTATAATTATTTTTAGA
Found at i:1512862 original size:20 final size:22
Alignment explanation
Indices: 1512834--1512875 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1512824 AAATAATTAT
1512834 AATTCATTTTTAG-AATTATAA
1 AATTCATTTTTAGAAATTATAA
*
1512855 AATT-ATTTTTTGAAATTATAA
1 AATTCATTTTTAGAAATTATAA
1512876 TTTTATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (22 bp):
AATTCATTTTTAGAAATTATAA
Found at i:1512881 original size:21 final size:19
Alignment explanation
Indices: 1512828--1512878 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
1512818 AATTTTAAAT
*
1512828 AATTATAATTCATTTTTAG
1 AATTATAATTTATTTTTAG
* *
1512847 AATTATAAAATTATTTTTTG
1 AATTAT-AATTTATTTTTAG
1512867 AAATTATAATTT
1 -AATTATAATTT
1512879 TATATAACTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 6 0.23
20 14 0.54
21 6 0.23
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (19 bp):
AATTATAATTTATTTTTAG
Found at i:1513139 original size:31 final size:31
Alignment explanation
Indices: 1513072--1513139 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
1513062 CAGTTACGTC
* ** *
1513072 GGGGACCATATTGTAAACAGACTAAATGTTG
1 GGGGATCATATTCCAAACAGACTAAATATTG
* *
1513103 GGGGATCATATTCCAAATAGACTAAATATTT
1 GGGGATCATATTCCAAACAGACTAAATATTG
1513134 GGGGAT
1 GGGGAT
1513140 GGTATTACAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (31 bp):
GGGGATCATATTCCAAACAGACTAAATATTG
Found at i:1518010 original size:55 final size:54
Alignment explanation
Indices: 1517926--1518036 Score: 168
Period size: 55 Copynumber: 2.0 Consensus size: 54
1517916 GTAAATACTT
*
1517926 AATATTTTTATATTATCATTAAAAGTATTTAAAATTTAATTTCATTATCATTTTA
1 AATATTTTTATATTATCATTAAAAGTATTT-AAATTTAATTTCATTATAATTTTA
* * * *
1517981 AATATTTTTGTATTATCATTTAAAGTATTTAAATTTAATTTCGTTGTAATTTTA
1 AATATTTTTATATTATCATTAAAAGTATTTAAATTTAATTTCATTATAATTTTA
1518035 AA
1 AA
1518037 GTTAACACGT
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
54 23 0.45
55 28 0.55
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.53
Consensus pattern (54 bp):
AATATTTTTATATTATCATTAAAAGTATTTAAATTTAATTTCATTATAATTTTA
Found at i:1523004 original size:95 final size:95
Alignment explanation
Indices: 1522841--1523020 Score: 360
Period size: 95 Copynumber: 1.9 Consensus size: 95
1522831 AGGTCGCAAA
1522841 GCCTTCAAGATCCCTTGCTGCGCCAATAGATCCTTCACCCTCGTTTGCCATAATCCGAAGTTACC
1 GCCTTCAAGATCCCTTGCTGCGCCAATAGATCCTTCACCCTCGTTTGCCATAATCCGAAGTTACC
1522906 CTGACCATCGAATTTCGCGACTTCGAATTT
66 CTGACCATCGAATTTCGCGACTTCGAATTT
1522936 GCCTTCAAGATCCCTTGCTGCGCCAATAGATCCTTCACCCTCGTTTGCCATAATCCGAAGTTACC
1 GCCTTCAAGATCCCTTGCTGCGCCAATAGATCCTTCACCCTCGTTTGCCATAATCCGAAGTTACC
1523001 CTGACCATCGAATTTCGCGA
66 CTGACCATCGAATTTCGCGA
1523021 TGTGCTTACG
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 85 1.00
ACGTcount: A:0.22, C:0.33, G:0.16, T:0.28
Consensus pattern (95 bp):
GCCTTCAAGATCCCTTGCTGCGCCAATAGATCCTTCACCCTCGTTTGCCATAATCCGAAGTTACC
CTGACCATCGAATTTCGCGACTTCGAATTT
Found at i:1524182 original size:17 final size:18
Alignment explanation
Indices: 1524142--1524182 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
1524132 AGAATATTAA
1524142 AATAAA-TAATAAAATAT
1 AATAAATTAATAAAATAT
*
1524159 AAT-AATTATTAAAA-AT
1 AATAAATTAATAAAATAT
1524175 AATAAATT
1 AATAAATT
1524183 TTACATACAG
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AATAAATTAATAAAATAT
Found at i:1524832 original size:60 final size:60
Alignment explanation
Indices: 1524723--1524847 Score: 144
Period size: 60 Copynumber: 2.1 Consensus size: 60
1524713 TTCGAGTGAT
* * * *
1524723 CATTTTATAACTTTTAATAATCGAGTGATTCAACAAAATAATACCCTATAGTCAGTTGAC
1 CATTTTATAACTTTTAATAATCGAATGACTCAACAAAACAATACCCTATAGTCAGTAGAC
* * * * * *
1524783 CATTTTATAATTTTTAATAGTCGGAAT-ACTCAATAAAACAATTCTCTATAGTCGGTAGAC
1 CATTTTATAACTTTTAATAATC-GAATGACTCAACAAAACAATACCCTATAGTCAGTAGAC
1524843 CATTT
1 CATTT
1524848 ATTTACTTAA
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
60 51 0.94
61 3 0.06
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (60 bp):
CATTTTATAACTTTTAATAATCGAATGACTCAACAAAACAATACCCTATAGTCAGTAGAC
Found at i:1525346 original size:20 final size:20
Alignment explanation
Indices: 1525314--1525369 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
1525304 ACTTCGACTA
*
1525314 TCGCATTGCGATTTACATA-T
1 TCGCGTTGCGATTTACA-AGT
* *
1525334 TCGCGTTGTGATTTTCCAAGT
1 TCGCGTTGCGA-TTTACAAGT
1525355 TCGCGTTGCGATTTA
1 TCGCGTTGCGATTTA
1525370 TTCCAAATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (20 bp):
TCGCGTTGCGATTTACAAGT
Found at i:1526159 original size:6 final size:6
Alignment explanation
Indices: 1526148--1526174 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1526138 TCTCGTCTCG
1526148 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1526175 AATACGTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:1526321 original size:21 final size:21
Alignment explanation
Indices: 1526295--1526404 Score: 102
Period size: 21 Copynumber: 5.3 Consensus size: 21
1526285 TGGAATAAAC
*
1526295 CGCAACGCGAACTTCGACTAT
1 CGCAACGCGAACTTAGACTAT
*
1526316 CCCAA--CGAACTTAGACTAT
1 CGCAACGCGAACTTAGACTAT
* *
1526335 CGTAACGCGAACTTGGACTAT
1 CGCAACGCGAACTTAGACTAT
* * *
1526356 CGCAA--CGAATTTGGAATAAAT
1 CGCAACGCGAACTTAGACT--AT
*
1526377 CGCAACGCGAACTTGGACTAT
1 CGCAACGCGAACTTAGACTAT
1526398 CGCAACG
1 CGCAACG
1526405 AATTTGGAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 12
0.77 0.11 0.13
Matches are distributed among these distances:
19 26 0.36
21 37 0.51
23 10 0.14
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (21 bp):
CGCAACGCGAACTTAGACTAT
Found at i:1526393 original size:42 final size:42
Alignment explanation
Indices: 1526265--1526413 Score: 212
Period size: 42 Copynumber: 3.6 Consensus size: 42
1526255 CGTTGCGATT
* *
1526265 TTGGACTATTGCAACGAATTTGGAATAAACCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* * * * * *
1526307 TTCGACTATCCCAACGAACTTAGACT--ATCGTAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1526347 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1526389 TTGGACTATCGCAACGAATTTGGAA
1 TTGGACTATCGCAACGAATTTGGAA
1526414 AATCGCGTTG
Statistics
Matches: 91, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
40 33 0.36
42 58 0.64
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (42 bp):
TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
Done.