Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005349.1 Hibiscus syriacus cultivar Beakdansim tig00012136_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: 1796274
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
File 7 of 8
Found at i:1408852 original size:11 final size:11
Alignment explanation
Indices: 1408836--1408862 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1408826 GCCAAACTAC
1408836 CAATGGCCATA
1 CAATGGCCATA
1408847 CAATGGCCATA
1 CAATGGCCATA
1408858 CAATG
1 CAATG
1408863 AACGTAGCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.19
Consensus pattern (11 bp):
CAATGGCCATA
Found at i:1410069 original size:30 final size:30
Alignment explanation
Indices: 1410021--1410085 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
1410011 TAATAGTTAG
* * *
1410021 ATTACTATTTTATGTAAATTTTA-AGGTCAA
1 ATTAATATTTTATCTAAA-TTCAGAGGTCAA
*
1410051 ATTAATATTTTGTCTAAATTCAGAGGTCAA
1 ATTAATATTTTATCTAAATTCAGAGGTCAA
1410081 ATTAA
1 ATTAA
1410086 AGTTTAACCA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 3 0.10
30 27 0.90
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (30 bp):
ATTAATATTTTATCTAAATTCAGAGGTCAA
Found at i:1413155 original size:57 final size:57
Alignment explanation
Indices: 1412928--1413157 Score: 273
Period size: 57 Copynumber: 4.0 Consensus size: 57
1412918 AACCATACAA
* * * * * * * *
1412928 CCCCGTCACGAACAGTAAGACTCTCAATAAAAAGCCAAAGAACCTGCAAGTATT-TAA
1 CCCCGTCACGAACAATAAGGCTCTCAACACAAAGCCGAGGAACCTACAAGTATTCT-T
* * *
1412985 CCCCGTCACGAACAATAAGGCTCTCAGCGCAAAGCTGAGGAACCTACAAGTATTCTT
1 CCCCGTCACGAACAATAAGGCTCTCAACACAAAGCCGAGGAACCTACAAGTATTCTT
* * * * **
1413042 CTCTGTCACGAACAGTAAGGCTCTCAGCACAAATTCGAGGAACCTACAAGTATTCTT
1 CCCCGTCACGAACAATAAGGCTCTCAACACAAAGCCGAGGAACCTACAAGTATTCTT
* *
1413099 CCCCGTCACGAACAATAAGGCCCTCAACACAAACCCGAGGAACCTACAAGTATTCTT
1 CCCCGTCACGAACAATAAGGCTCTCAACACAAAGCCGAGGAACCTACAAGTATTCTT
1413156 CC
1 CC
1413158 TCCAACTATA
Statistics
Matches: 147, Mismatches: 25, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
57 146 0.99
58 1 0.01
ACGTcount: A:0.35, C:0.30, G:0.16, T:0.19
Consensus pattern (57 bp):
CCCCGTCACGAACAATAAGGCTCTCAACACAAAGCCGAGGAACCTACAAGTATTCTT
Found at i:1413238 original size:24 final size:24
Alignment explanation
Indices: 1413211--1413274 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 24
1413201 TATATCAAAA
*
1413211 ATCAAAACATAATTCAGGTCAAGT
1 ATCAAAACAGAATTCAGGTCAAGT
* * * * *
1413235 ATCAGATCAGAATCCATGTCAGGT
1 ATCAAAACAGAATTCAGGTCAAGT
*
1413259 ATCATAACAGAATTCA
1 ATCAAAACAGAATTCA
1413275 AATAAAAAAT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGGTCAAGT
Found at i:1414342 original size:16 final size:16
Alignment explanation
Indices: 1414321--1414354 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1414311 GTTTGGTAAT
1414321 ATTCTAGGTCATTCCC
1 ATTCTAGGTCATTCCC
1414337 ATTCTAGGTCATTCCC
1 ATTCTAGGTCATTCCC
1414353 AT
1 AT
1414355 ATGATCTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.21, C:0.29, G:0.12, T:0.38
Consensus pattern (16 bp):
ATTCTAGGTCATTCCC
Found at i:1415529 original size:27 final size:27
Alignment explanation
Indices: 1415499--1415560 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
1415489 GTCAAAGTTC
1415499 TGGTCAACAGTGGTCAACGCCGATCAA
1 TGGTCAACAGTGGTCAACGCCGATCAA
1415526 TGGTCAACAGTGGTCAACGCCGATCAA
1 TGGTCAACAGTGGTCAACGCCGATCAA
1415553 TGGTCAAC
1 TGGTCAAC
1415561 GCAGGTCAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.29, C:0.26, G:0.26, T:0.19
Consensus pattern (27 bp):
TGGTCAACAGTGGTCAACGCCGATCAA
Found at i:1415556 original size:17 final size:17
Alignment explanation
Indices: 1415536--1415577 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
1415526 TGGTCAACAG
*
1415536 TGGTCAACGCCGATCAA
1 TGGTCAACGCAGATCAA
*
1415553 TGGTCAACGCAGGTCAA
1 TGGTCAACGCAGATCAA
*
1415570 CGGTCAAC
1 TGGTCAAC
1415578 AGTCGATCGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.17
Consensus pattern (17 bp):
TGGTCAACGCAGATCAA
Found at i:1415567 original size:27 final size:27
Alignment explanation
Indices: 1415499--1415571 Score: 112
Period size: 27 Copynumber: 2.7 Consensus size: 27
1415489 GTCAAAGTTC
*
1415499 TGGTCAACAGTGGTCAACGCCGATCAA
1 TGGTCAACAGAGGTCAACGCCGATCAA
*
1415526 TGGTCAACAGTGGTCAACGCCGATCAA
1 TGGTCAACAGAGGTCAACGCCGATCAA
1415553 TGGTCAAC-GCAGGTCAACG
1 TGGTCAACAG-AGGTCAACG
1415572 GTCAACAGTC
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
26 1 0.02
27 43 0.98
ACGTcount: A:0.29, C:0.26, G:0.27, T:0.18
Consensus pattern (27 bp):
TGGTCAACAGAGGTCAACGCCGATCAA
Found at i:1421637 original size:22 final size:24
Alignment explanation
Indices: 1421612--1421660 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 24
1421602 GGATTTTTTA
1421612 TTATTTAA-AATT-AATTAAATAT
1 TTATTTAATAATTGAATTAAATAT
1421634 TTATTTAATTAATTGGAATTAAATAT
1 TTATTTAA-TAATT-GAATTAAATAT
1421660 T
1 T
1421661 CGAGATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.35
24 4 0.17
26 11 0.48
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (24 bp):
TTATTTAATAATTGAATTAAATAT
Found at i:1434089 original size:17 final size:16
Alignment explanation
Indices: 1434060--1434092 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
1434050 TGAAAAAAAA
1434060 CAAATAAAATAATAAC
1 CAAATAAAATAATAAC
1434076 CAAATAATAATAATAAC
1 CAAATAA-AATAATAAC
1434093 AGAAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.67, C:0.12, G:0.00, T:0.21
Consensus pattern (16 bp):
CAAATAAAATAATAAC
Found at i:1435633 original size:16 final size:16
Alignment explanation
Indices: 1435606--1435651 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
1435596 ATTTTTCTAC
1435606 CTAT-ATTATTATTAA
1 CTATAATTATTATTAA
*
1435621 -TATATTATATTA-TAA
1 CTATAAT-TATTATTAA
1435636 CTATAATTATTATTAA
1 CTATAATTATTATTAA
1435652 ACCAATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
14 3 0.12
15 9 0.36
16 13 0.52
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.52
Consensus pattern (16 bp):
CTATAATTATTATTAA
Found at i:1437444 original size:24 final size:23
Alignment explanation
Indices: 1437406--1437455 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
1437396 GCCCAAACCG
1437406 AACCGAACCCGACCCGAAACCCA
1 AACCGAACCCGACCCGAAACCCA
* **
1437429 AACCGAGACTCGACCCGAGGCCCA
1 AACCGA-ACCCGACCCGAAACCCA
1437453 AAC
1 AAC
1437456 TAAGCCTAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 6 0.26
24 17 0.74
ACGTcount: A:0.36, C:0.44, G:0.18, T:0.02
Consensus pattern (23 bp):
AACCGAACCCGACCCGAAACCCA
Found at i:1450556 original size:240 final size:240
Alignment explanation
Indices: 1449973--1450822 Score: 1060
Period size: 240 Copynumber: 3.6 Consensus size: 240
1449963 ATTTTCATGG
* * *
1449973 GTTTCTTGA-TTAGTAAGTCCTTCAGGCCATCAGTAAGTCATTCAAGCATGATATTTAAATCCTT
1 GTTTCTT-ACTTAGTAAGTCATTCAGGCCATCAGTAAGTCTTTCAAGCATGATGTTTAAATCCTT
** * * *
1450037 TTGGTCATC---AAGTCTTTCAAGCAAGATGATAAGTCCTTT-GGACTATCCATAAGTCCTTTAT
65 CGGGTCATCTATAAGTCTTTCAAGCAAGATGATAAGTCCTTTGGGTC-ATCCATAAGACCTTCAT
* * * *
1450098 GCAGGATGTTTTCACCTGATATTTGAAAAACGAGAAAGCGATTTCCAAAG-TTCTCATTTAAATA
129 GCAGGATGTTTTCACATGATTTTTG-AAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATC
* *
1450162 TTTTCTAAAAG-CTGACATTTCTGAAAAGTAAGAAAATGATTTCCAAA
193 TTTTCTAAAAGACTGACTTTTCTGAAAAGTAAGAAAAAGATTTCCAAA
* * ** * * *
1450209 GTTTCATAC-TAGTAAGTCCTTTGGGCCATCAGTAAGTCTTTCAAGCATGATTTTTAAATCATCC
1 GTTTCTTACTTAGTAAGTCATTCAGGCCATCAGTAAGTCTTTCAAGCATGATGTTTAAATCCTTC
* **
1450273 GGGTCATCTATAAGTCTTTTCAA-CAAGATGATAAGTCCTTTGGGTCATCCATAAGACCTTGACC
66 GGGTCATCTATAAGTC-TTTCAAGCAAGATGATAAGTCCTTTGGGTCATCCATAAGACCTTCATG
* *
1450337 CAAGATGTTTTCACATGATTTTTGAAAATGAGAAAGCGATTTCCAGAGTTTCTCATTTAAATCTT
130 CAGGATGTTTTCACATGATTTTTGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATCTT
* *
1450402 TTC-AGAAAGACTGGCTTTTCTGAAAAGTAAGAAAAAGATTTCTAAA
195 TTCTA-AAAGACTGACTTTTCTGAAAAGTAAGAAAAAGATTTCCAAA
* * *
1450448 GTTTCTTACTTAGTAAGTCATTCGGGCCATCAATAAGTTTTTCTAAG-ATGATGTTTAAATCCTT
1 GTTTCTTACTTAGTAAGTCATTCAGGCCATCAGTAAGTCTTTC-AAGCATGATGTTTAAATCCTT
* * *
1450512 CGGGTCATCAATAAGTCTTTCAAGCAAGATGATAAGTACTTTGGGTCATCCATAAGACCTCCATG
65 CGGGTCATCTATAAGTCTTTCAAGCAAGATGATAAGTCCTTTGGGTCATCCATAAGACCTTCATG
* * *
1450577 CAGGATGTTTTCACATGATTTTCGAAAATGAGAAAGCGATTTCCAAATTTTCTCATTTAAACCTT
130 CAGGATGTTTTCACATGATTTTTGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATCTT
* * **
1450642 TTCTAAAA-ATTGATTTTTCTTGAAAAGTAAGAAAGCGATTTCCAAA
195 TTCTAAAAGACTGACTTTTC-TGAAAAGTAAGAAAAAGATTTCCAAA
* * **
1450688 GTTTCTTACTTAGTAAGTCATTCAGGACACCAGTAAGTCTTTTGAGCATGATGTTTAAATCCTTC
1 GTTTCTTACTTAGTAAGTCATTCAGGCCATCAGTAAGTCTTTCAAGCATGATGTTTAAATCCTTC
* ** * * * **
1450753 GGGTAATCTATAAGTCTTTCGTGCAAGATGATAAGT-CTTTCTGGTCATCTATAAGGCCTTCGGG
66 GGGTCATCTATAAGTCTTTCAAGCAAGATGATAAGTCCTTT-GGGTCATCCATAAGACCTTCATG
1450817 CAGGAT
130 CAGGAT
1450823 ATTTCTAAAT
Statistics
Matches: 532, Mismatches: 66, Indels: 28
0.85 0.11 0.04
Matches are distributed among these distances:
235 56 0.11
236 6 0.01
237 23 0.04
238 80 0.15
239 69 0.13
240 294 0.55
241 4 0.01
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (240 bp):
GTTTCTTACTTAGTAAGTCATTCAGGCCATCAGTAAGTCTTTCAAGCATGATGTTTAAATCCTTC
GGGTCATCTATAAGTCTTTCAAGCAAGATGATAAGTCCTTTGGGTCATCCATAAGACCTTCATGC
AGGATGTTTTCACATGATTTTTGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATCTTT
TCTAAAAGACTGACTTTTCTGAAAAGTAAGAAAAAGATTTCCAAA
Found at i:1452953 original size:10 final size:9
Alignment explanation
Indices: 1452919--1452952 Score: 50
Period size: 10 Copynumber: 3.6 Consensus size: 9
1452909 AAATATATGT
1452919 TATAATATA
1 TATAATATA
1452928 TATATATATA
1 TATA-ATATA
1452938 TATAACTATA
1 TATAA-TATA
1452948 TATAA
1 TATAA
1452953 CAAGTGTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 5 0.22
10 18 0.78
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (9 bp):
TATAATATA
Found at i:1464080 original size:5 final size:5
Alignment explanation
Indices: 1464070--1464115 Score: 56
Period size: 5 Copynumber: 8.8 Consensus size: 5
1464060 AGTAAAACAT
* *
1464070 AATAA AATAAA AATAA AATAA CATAA CATAA AATTAA AATAA AATA
1 AATAA AAT-AA AATAA AATAA AATAA AATAA AA-TAA AATAA AATA
1464116 TTAATATTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
5 27 0.73
6 10 0.27
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (5 bp):
AATAA
Found at i:1464095 original size:21 final size:21
Alignment explanation
Indices: 1464071--1464111 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1464061 GTAAAACATA
1464071 ATAAAATAAAAATAAAATAAC
1 ATAAAATAAAAATAAAATAAC
* *
1464092 ATAACATAAAATTAAAATAA
1 ATAAAATAAAAATAAAATAA
1464112 AATATTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (21 bp):
ATAAAATAAAAATAAAATAAC
Found at i:1464339 original size:2 final size:2
Alignment explanation
Indices: 1464332--1464386 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
1464322 ACCAAACGTG
1464332 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1464374 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
1464387 GGGACATATG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1465559 original size:3 final size:3
Alignment explanation
Indices: 1465551--1465715 Score: 107
Period size: 3 Copynumber: 51.7 Consensus size: 3
1465541 TAGTATTTTA
* * * * * *
1465551 AAT AAT AAT AAC AAT AAGC ACT ACT AAG AAT TAAT AAC AAT AAGT AAT
1 AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT -AAT AAT AAT AA-T AAT
* * *
1465599 AAT AAT AAT AAT AAT AAT AAAT ACT GAT AAC AAT AAAT AAT AAT AATT
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT -AAT AAT AAT AA-T
* * *
1465647 AAT ATTT ATT AAT -AT TAT CAAT AAT AAAT AAT AAT AAT AAT AAT AACT
1 AAT A-AT AAT AAT AAT AAT -AAT AAT -AAT AAT AAT AAT AAT AAT AA-T
*
1465695 AAT AAT AACC AAT AAT AAT AA
1 AAT AAT AA-T AAT AAT AAT AA
1465716 CAAGTTTTGG
Statistics
Matches: 129, Mismatches: 21, Indels: 24
0.74 0.12 0.14
Matches are distributed among these distances:
2 2 0.02
3 99 0.77
4 28 0.22
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1465621 original size:10 final size:10
Alignment explanation
Indices: 1465583--1465712 Score: 81
Period size: 10 Copynumber: 13.1 Consensus size: 10
1465573 ACTAAGAATT
*
1465583 AATAACAATA
1 AATAATAATA
*
1465593 AGTAATAAT-
1 AATAATAATA
1465602 AATAATAAT-
1 AATAATAATA
1465611 AATAATAAATA
1 AATAAT-AATA
* *
1465622 CTGATAACAATA
1 --AATAATAATA
1465634 AATAATAATA
1 AATAATAATA
* * *
1465644 ATTAATATTT
1 AATAATAATA
*
1465654 ATTAAT-AT-
1 AATAATAATA
*
1465662 TATCAATAATA
1 AAT-AATAATA
1465673 AATAATAAT-
1 AATAATAATA
1465682 AATAATAATA
1 AATAATAATA
*
1465692 ACTAATAATA
1 AATAATAATA
**
1465702 ACCAATAATA
1 AATAATAATA
1465712 A
1 A
1465713 TAACAAGTTT
Statistics
Matches: 96, Mismatches: 16, Indels: 16
0.75 0.12 0.12
Matches are distributed among these distances:
8 1 0.01
9 27 0.28
10 58 0.60
11 2 0.02
12 4 0.04
13 4 0.04
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (10 bp):
AATAATAATA
Found at i:1465698 original size:29 final size:28
Alignment explanation
Indices: 1465589--1465715 Score: 116
Period size: 29 Copynumber: 4.5 Consensus size: 28
1465579 AATTAATAAC
1465589 AATAAGTAATAATAATAATAATAATAATA
1 AATAA-TAATAATAATAATAATAATAATA
* * *
1465618 AATACTGATAACAAT-A-AATAATAATA
1 AATAATAATAATAATAATAATAATAATA
* * * *
1465644 ATTAATATTTATTAAT-ATTATCAATAATA
1 AATAATA-ATAATAATAATAAT-AATAATA
1465673 AATAATAATAATAATAATAACTAATAATA
1 AATAATAATAATAATAATAA-TAATAATA
**
1465702 ACCAATAATAATAA
1 AATAATAATAATAA
1465716 CAAGTTTTGG
Statistics
Matches: 77, Mismatches: 16, Indels: 10
0.75 0.16 0.10
Matches are distributed among these distances:
26 14 0.18
27 7 0.09
28 16 0.21
29 39 0.51
30 1 0.01
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.33
Consensus pattern (28 bp):
AATAATAATAATAATAATAATAATAATA
Found at i:1465714 original size:13 final size:12
Alignment explanation
Indices: 1465551--1465718 Score: 81
Period size: 13 Copynumber: 13.2 Consensus size: 12
1465541 TAGTATTTTA
1465551 AATAATAATAAC
1 AATAATAATAAC
* *
1465563 AATAAGCACT-AC
1 AATAA-TAATAAC
*
1465575 TAAGAATTAATAAC
1 -AATAA-TAATAAC
*
1465589 AATAAGTAATAAT
1 AATAA-TAATAAC
*
1465602 AATAATAATAAT
1 AATAATAATAAC
1465614 AATAAATACTGATAAC
1 AAT-AATA---ATAAC
*
1465630 AAT-A-AATAAT
1 AATAATAATAAC
**
1465640 AATAATTAATATTT
1 AATAA-TAATA-AC
* * *
1465654 ATTAATATTATC
1 AATAATAATAAC
*
1465666 AATAATAAATAAT
1 AATAAT-AATAAC
*
1465679 AATAATAATAAT
1 AATAATAATAAC
1465691 AACTAATAATAACC
1 AA-TAATAATAA-C
1465705 AATAATAATAAC
1 AATAATAATAAC
1465717 AA
1 AA
1465719 GTTTTGGACA
Statistics
Matches: 122, Mismatches: 20, Indels: 28
0.72 0.12 0.16
Matches are distributed among these distances:
10 7 0.06
11 1 0.01
12 34 0.28
13 63 0.52
14 10 0.08
16 7 0.06
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.30
Consensus pattern (12 bp):
AATAATAATAAC
Found at i:1466348 original size:60 final size:60
Alignment explanation
Indices: 1466243--1466360 Score: 148
Period size: 60 Copynumber: 2.0 Consensus size: 60
1466233 AATTGATCAT
*** * *
1466243 TTTATAACTTTTAATAGTTGGGAGACTTAACGAAACAACAACCTATAGTTGAAGGACCAC
1 TTTATAACTTTTAATAAACGAGAGACTTAACGAAACAACAACCTATAATTGAAGGACCAC
* * *
1466303 TTTATAACTTTTAATAAACGAGAGACTTAAC-AAAGTAACACCCTATAATTGAGGGACC
1 TTTATAACTTTTAATAAACGAGAGACTTAACGAAA-CAACAACCTATAATTGAAGGACC
1466361 GGGACCATTT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 3 0.06
60 46 0.94
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (60 bp):
TTTATAACTTTTAATAAACGAGAGACTTAACGAAACAACAACCTATAATTGAAGGACCAC
Found at i:1468156 original size:3 final size:3
Alignment explanation
Indices: 1468136--1468256 Score: 83
Period size: 3 Copynumber: 41.0 Consensus size: 3
1468126 TTTCATCTAT
* * *
1468136 TTA TTA GTA TTA -TA TTA TTA TTG TTA TT- TTA TTTA TTA TTG TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
* *
1468180 TT- TTA TTTA TTA TTG TTA TTA TT- TTA -TA TTA -TA TTA TTTA CTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
* * * *
1468223 CTA TTA ATA TTA TTA TTAA TAA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA
1468257 CATATCACAG
Statistics
Matches: 92, Mismatches: 16, Indels: 20
0.72 0.12 0.16
Matches are distributed among these distances:
2 12 0.13
3 69 0.75
4 11 0.12
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1468171 original size:18 final size:18
Alignment explanation
Indices: 1468145--1468199 Score: 101
Period size: 18 Copynumber: 3.0 Consensus size: 18
1468135 TTTATTAGTA
1468145 TTATATTATTATTGTTATT
1 TTAT-TTATTATTGTTATT
1468164 TTATTTATTATTGTTATT
1 TTATTTATTATTGTTATT
1468182 TTATTTATTATTGTTATT
1 TTATTTATTATTGTTATT
1468200 ATTTTATATT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 32 0.89
19 4 0.11
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (18 bp):
TTATTTATTATTGTTATT
Found at i:1469524 original size:15 final size:16
Alignment explanation
Indices: 1469497--1469527 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1469487 AAATCCTAAT
1469497 TATAAATTTAATTTTA
1 TATAAATTTAATTTTA
1469513 TATAAA-TTAATTTTA
1 TATAAATTTAATTTTA
1469528 AAATTATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TATAAATTTAATTTTA
Found at i:1477353 original size:44 final size:45
Alignment explanation
Indices: 1477303--1477389 Score: 122
Period size: 46 Copynumber: 1.9 Consensus size: 45
1477293 TTACCATTTA
1477303 TCCATAAGCTCGTAAG-TATTTTACCAAAATACATACCATTAAAT
1 TCCATAAGCTCGTAAGCTATTTTACCAAAATACATACCATTAAAT
* * * *
1477347 TCCATAAGCTCGTAAGCTTATTTTTCCAATATACTTGCCATTA
1 TCCATAAGCTCGTAAGC-TATTTTACCAAAATACATACCATTA
1477390 CGTAAGCTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
44 16 0.43
46 21 0.57
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.36
Consensus pattern (45 bp):
TCCATAAGCTCGTAAGCTATTTTACCAAAATACATACCATTAAAT
Found at i:1477458 original size:40 final size:41
Alignment explanation
Indices: 1477409--1477489 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 41
1477399 ATAAGTATTA
1477409 TTTGCATGGTTACCATTTATTAACCAATAAACATAATCCAT
1 TTTGCATGGTTACCATTTATTAACCAATAAACATAATCCAT
1477450 TTTG-ATGGTTACCATTTATTAACCAATAAACATAATCCAT
1 TTTGCATGGTTACCATTTATTAACCAATAAACATAATCCAT
1477490 AGCCAATAGC
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 36 0.90
41 4 0.10
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37
Consensus pattern (41 bp):
TTTGCATGGTTACCATTTATTAACCAATAAACATAATCCAT
Found at i:1478809 original size:24 final size:24
Alignment explanation
Indices: 1478778--1478827 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
1478768 TATGAACACA
*
1478778 ATATATAAAAGTAACCTCCAAATT
1 ATATATAAAAGGAACCTCCAAATT
1478802 ATATATAAAAGGAACCTCCAAATT
1 ATATATAAAAGGAACCTCCAAATT
1478826 AT
1 AT
1478828 TTTTATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.16, G:0.06, T:0.28
Consensus pattern (24 bp):
ATATATAAAAGGAACCTCCAAATT
Found at i:1488378 original size:54 final size:53
Alignment explanation
Indices: 1488292--1488394 Score: 143
Period size: 54 Copynumber: 1.9 Consensus size: 53
1488282 CAAACATCTG
* * * *
1488292 TGCAGAAGCCACAGGAATGATGAATATGTTGTCAAATGTATTACGAACCTTTA
1 TGCAGAAACCACAGAAATGATGAACATATTGTCAAATGTATTACGAACCTTTA
* *
1488345 TGCAGAAACCACAAGAAATGATGAACGTATTGTCAAATGTTTTACGAACC
1 TGCAGAAACCAC-AGAAATGATGAACATATTGTCAAATGTATTACGAACC
1488395 AATGATTATA
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
53 11 0.26
54 32 0.74
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (53 bp):
TGCAGAAACCACAGAAATGATGAACATATTGTCAAATGTATTACGAACCTTTA
Found at i:1489357 original size:113 final size:112
Alignment explanation
Indices: 1489152--1489493 Score: 490
Period size: 113 Copynumber: 3.0 Consensus size: 112
1489142 TAGCAAAGAT
* * *
1489152 TCGAATCCATCACTCGATAGATCAACAATGCCAGGTAGAGTTCGTAATGAGAAGAACTCATCTGA
1 TCGAATTCATCACTCGATGGATCAACATTGCCAGGTAGAGTTCGTAATGAGAAGAACTCATCTGA
1489217 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCATTTGC
66 AG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCATTTGC
*** *
1489265 TTTCATTCATCACTCGATGGATCAACATTGCCAGGTAGAGTTCGTAATGAGAAGAGCTCATCTGA
1 TCGAATTCATCACTCGATGGATCAACATTGCCAGGTAGAGTTCGTAATGAGAAGAACTCATCTGA
*
1489330 AGAGGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
66 AGA-GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCATTTGC
* * * * * * *
1489378 TCGAATTCATCACTTGATGGATCAACTTTTCCAGAG-AAAGTTCATAATTAGAAGAACTCATCTA
1 TCGAATTCATCACTCGATGGATCAACATTGCCAG-GTAGAGTTCGTAATGAGAAGAACTCATCTG
*
1489442 AAGAGGAAGAAGAAGTTCATAATGGGAAGAACTTGTTCAA-CATTTTGC
65 AAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCA-TTTGC
1489490 TCGA
1 TCGA
1489494 CGCTATCACA
Statistics
Matches: 205, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
111 1 0.00
112 45 0.22
113 158 0.77
114 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (112 bp):
TCGAATTCATCACTCGATGGATCAACATTGCCAGGTAGAGTTCGTAATGAGAAGAACTCATCTGA
AGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCATTTGC
Found at i:1489560 original size:122 final size:122
Alignment explanation
Indices: 1489398--1489836 Score: 353
Period size: 122 Copynumber: 3.5 Consensus size: 122
1489388 CACTTGATGG
* * * *
1489398 ATCAACTTTTCCAGAGAAAGTTCATAATTAGAAGAACTCATCTAAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGA-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATA
* **
1489463 ATGGGAAGAACTTGTTCAACATTTTGCTCGACGCTATCACAGAAAGAGAATGATCAAC
65 ATGAGAAGAACTTGTTCAACATTTTGCTCGATACTATCACAGAAAGAGAATGATCAAC
** * * *
1489521 ATCAACATTTCCAGAAGTGTTCGTAATGAGAAGAACTCATCTGAAGAAGAATAAGAGGTTCATAA
1 ATCAACATTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAA
* * * * * ** * * * *
1489586 TAAGAATAATTTTTTCAACTTTGCCTTAATTCAATACATATGA-AGCCAAATTAACAAT-ACCTC
66 TGAGAAGAACTTGTTCAACATT---TT-GCTCGATAC-TATCACAG--AAA--GAGAATGA--TC
*
1489649 TTTTGAAG
120 -----AAC
* * * *
1489657 ATCAGCATTTCCAGAAAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCGTA
1 ATCAACATTTCCAG-AAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATA
* * * * *
1489722 ATGAGAAGAGCTTGTTCAACATTTTGCTTGATTCTATCACAGAAGGAG-ATAGATCATC
65 ATGAGAAGAACTTGTTCAACATTTTGCTCGATACTATCACAGAAAGAGAAT-GATCAAC
* ** *
1489780 ATCAATATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAATAAGAAGAA
1 ATCAACATTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAA
1489837 CTTGTTCAAC
Statistics
Matches: 239, Mismatches: 57, Indels: 41
0.71 0.17 0.12
Matches are distributed among these distances:
122 96 0.40
123 27 0.11
125 2 0.01
126 6 0.03
127 4 0.02
128 7 0.03
129 2 0.01
130 5 0.02
131 4 0.02
132 4 0.02
133 6 0.03
134 2 0.01
136 15 0.06
137 59 0.25
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (122 bp):
ATCAACATTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAA
TGAGAAGAACTTGTTCAACATTTTGCTCGATACTATCACAGAAAGAGAATGATCAAC
Found at i:1490146 original size:3 final size:3
Alignment explanation
Indices: 1490126--1490228 Score: 81
Period size: 3 Copynumber: 35.0 Consensus size: 3
1490116 TTTCATCCAT
* *
1490126 TTA TTA GTA TTA -TA TTA TTA TTG TTA TT- TTA TTTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
* * *
1490170 TTA TT- TTA -TA TTA -TA TTA TTTA CTA CTA TTA ATA TTA TTA TTAA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TT-A
* *
1490214 TAA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA
1490229 CATATCACAA
Statistics
Matches: 80, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
2 10 0.12
3 62 0.77
4 8 0.10
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:1490200 original size:31 final size:32
Alignment explanation
Indices: 1490124--1490210 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 32
1490114 TTTTTCATCC
* * * *
1490124 ATTTATTAGTATT-ATATTATTATTGTTATTTT
1 ATTTACTACTATTAATATTATTA-TATTATATT
* * *
1490156 ATTTATTATTATTATTATT-TTATATTATATT
1 ATTTACTACTATTAATATTATTATATTATATT
1490187 ATTTACTACTATTAATATTATTAT
1 ATTTACTACTATTAATATTATTAT
1490211 TAATAAATAT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
31 23 0.50
32 19 0.41
33 4 0.09
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (32 bp):
ATTTACTACTATTAATATTATTATATTATATT
Found at i:1498734 original size:3 final size:3
Alignment explanation
Indices: 1498721--1498784 Score: 87
Period size: 3 Copynumber: 21.7 Consensus size: 3
1498711 GTACCCTGAA
*
1498721 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAAT AGT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT
*
1498766 GAT AAT -AT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
1498785 ATTATAACCC
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
2 4 0.07
3 47 0.87
4 3 0.06
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1499249 original size:133 final size:133
Alignment explanation
Indices: 1498969--1499401 Score: 537
Period size: 133 Copynumber: 3.2 Consensus size: 133
1498959 ACATTGACTG
* * *
1498969 ATTCTACTGTTCCTCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTCACTCAGGGAATAT
1 ATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTTACTCAGGGAATAT
* * * * ** *
1499034 CAAATCTTGAAAGAGACGGATCTGTTATATTTCTTATTGAGGGAAAATTTGATCTAGGGACT-TT
66 CAAATCTTGAAA-AGAAGGATCTGTTTTGTTTCTTCTTGAGGGAAAATCAGATCTGGGGA-TGTT
1499098 GATTC
129 GATTC
* * * * * *
1499103 ACTCCACTTTTCTTTAGGGAAGATTGAATCGAGGTAGACTTGTTCAAGTGTTACTTAGGGAATAT
1 ATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTTACTCAGGGAATAT
* * * *
1499168 TAAACCTTGAAAAGAGGGATCTGTTTTGCTTCTTCTTGAGGGAAAATCAGATCTGGGGATGTTGA
66 CAAATCTTGAAAAGAAGGATCTGTTTTGTTTCTTCTTGAGGGAAAATCAGATCTGGGGATGTTGA
*
1499233 TTT
131 TTC
* *
1499236 ATTCCACTGTTCTTCAGGGAAGATTAAATCGAGGTAGAGTTGTTCCACTGTTACTCAGGGAATAT
1 ATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTTACTCAGGGAATAT
* * * * * *
1499301 CAAATCTTGAAAAGAAGGATATATTTCGTTTCTTCTTAAGGGAAAAATCAGATTTGGGTATGTTG
66 CAAATCTTGAAAAGAAGGATCTGTTTTGTTTCTTCTTGAGGG-AAAATCAGATCTGGGGATGTTG
1499366 ATTC
130 ATTC
* * *
1499370 ATTCCACCGCTCTTCA-GGAAAATTGAATCGAG
1 ATTCCACTGTTCTTCAGGGAAGATTGAATCGAG
1499402 TTTGATTCAC
Statistics
Matches: 254, Mismatches: 43, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
132 1 0.00
133 150 0.59
134 103 0.41
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.34
Consensus pattern (133 bp):
ATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTTACTCAGGGAATAT
CAAATCTTGAAAAGAAGGATCTGTTTTGTTTCTTCTTGAGGGAAAATCAGATCTGGGGATGTTGA
TTC
Found at i:1500078 original size:230 final size:230
Alignment explanation
Indices: 1499725--1500172 Score: 612
Period size: 230 Copynumber: 1.9 Consensus size: 230
1499715 AAATCATGCA
** * * * *
1499725 AAAACATCCTACCTGAAGGACTTGTGGATGGCCCGAATGACTTATCATCTTGTTCGAAAGGATTA
1 AAAACATCCTACCTGAAGGACTTACGGATGGCACGAAGGACTTATCATCTTGCTCGAAAAGATTA
* * * * *
1499790 TAGATGACCTGAAGGATTTAAGCATCATGCTTGAAAGACTTACTAATGGCCTGAAGGACTTACCA
66 CAGATGACCTGAAGGATTTAAGCATCACGCTCGAAAGACTTACTAATGACCCGAAGGACTTACC-
*
1499855 AATTTAGG-AATAATTTACTAGGTAAGAAAATTTCCTTAGTTTTCAAAAAATTCAATTTTAAGAT
130 AATTTAGGAAATAATTTACTAGGTAAGAAAATTTCCTTACTTTTCAAAAAATTCAATTTTAAGAT
*
1499919 TTAAATGAGAAACTTTTCTTATTTGAGAGACATGTG
195 TTAAATGAGAAACATTTCTTATTTGAGAGACATGTG
* * *
1499955 AAAACATCCTAGCTGAAGGTCTTACGGATTGCACGAAGGACTTATCATCTTGCTC-AAAAGACTT
1 AAAACATCCTACCTGAAGGACTTACGGATGGCACGAAGGACTTATCATCTTGCTCGAAAAGA-TT
* * *
1500019 ACATATGACCTGAAGGATTTAAGCATCACGCTCGAAAGACTTACTGATTACCCGAAGGACTTACC
65 ACAGATGACCTGAAGGATTTAAGCATCACGCTCGAAAGACTTACTAATGACCCGAAGGACTTACC
* * * * * * * *
1500084 AATTTTGGAAATAGTTTACTAGGTAAGAAACTTTTCTTACTTTTCAAATATTTCGATTTTCAGAT
130 AATTTAGGAAATAATTTACTAGGTAAGAAAATTTCCTTACTTTTCAAAAAATTCAATTTTAAGAT
*
1500149 TTAAATGGGAAACATTTCTTATTT
195 TTAAATGAGAAACATTTCTTATTT
1500173 TTTAATTTAT
Statistics
Matches: 188, Mismatches: 28, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
229 12 0.06
230 176 0.94
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (230 bp):
AAAACATCCTACCTGAAGGACTTACGGATGGCACGAAGGACTTATCATCTTGCTCGAAAAGATTA
CAGATGACCTGAAGGATTTAAGCATCACGCTCGAAAGACTTACTAATGACCCGAAGGACTTACCA
ATTTAGGAAATAATTTACTAGGTAAGAAAATTTCCTTACTTTTCAAAAAATTCAATTTTAAGATT
TAAATGAGAAACATTTCTTATTTGAGAGACATGTG
Found at i:1504962 original size:65 final size:65
Alignment explanation
Indices: 1504886--1505027 Score: 275
Period size: 65 Copynumber: 2.2 Consensus size: 65
1504876 GTGATGTGAA
*
1504886 GGTATCGATACTAATAGGAAGGTATCGATACTGTAATTGAAATCTAATTTCTAGAAGGCCAGAAT
1 GGTATCAATACTAATAGGAAGGTATCGATACTGTAATTGAAATCTAATTTCTAGAAGGCCAGAAT
1504951 GGTATCAATACTAATAGGAAGGTATCGATACTGTAATTGAAATCTAATTTCTAGAAGGCCAGAAT
1 GGTATCAATACTAATAGGAAGGTATCGATACTGTAATTGAAATCTAATTTCTAGAAGGCCAGAAT
1505016 GGTATCAATACT
1 GGTATCAATACT
1505028 GAAGTGGGTA
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
65 76 1.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (65 bp):
GGTATCAATACTAATAGGAAGGTATCGATACTGTAATTGAAATCTAATTTCTAGAAGGCCAGAAT
Found at i:1508789 original size:16 final size:17
Alignment explanation
Indices: 1508768--1508801 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1508758 AGGTATCACA
1508768 TTGACTT-TTCAAAACT
1 TTGACTTGTTCAAAACT
*
1508784 TTGACTTGTTGAAAACT
1 TTGACTTGTTCAAAACT
1508801 T
1 T
1508802 ATTGAAAATT
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:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (17 bp):
TTGACTTGTTCAAAACT
Found at i:1509400 original size:22 final size:22
Alignment explanation
Indices: 1509361--1509415 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
1509351 CACCAAAGTG
* *
1509361 CCACATA-TTTGTCCCGAAGGA
1 CCACATAGTTTTTCCCGAAAGA
1509382 CCACATAGTTTTTCCCGAAAGA
1 CCACATAGTTTTTCCCGAAAGA
1509404 CCACATAGTTTT
1 CCACATAGTTTT
1509416 AAACTGAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 7 0.23
22 24 0.77
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (22 bp):
CCACATAGTTTTTCCCGAAAGA
Found at i:1516239 original size:23 final size:23
Alignment explanation
Indices: 1516185--1516269 Score: 91
Period size: 23 Copynumber: 3.7 Consensus size: 23
1516175 ACAGTTTTCG
*
1516185 CCCGAAGGACCACATAGGTTTTT
1 CCCGAAGGACCACATAGGTTTGT
*
1516208 CCCTG-AGGATCACATAGGTTTGT
1 CCC-GAAGGACCACATAGGTTTGT
* ** * *
1516231 CTCGAAGGACTGCATAGTTTTAT
1 CCCGAAGGACCACATAGGTTTGT
1516254 CCCGAAGGACCACATA
1 CCCGAAGGACCACATA
1516270 AGACCCTCAA
Statistics
Matches: 49, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
22 1 0.02
23 47 0.96
24 1 0.02
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.26
Consensus pattern (23 bp):
CCCGAAGGACCACATAGGTTTGT
Found at i:1517954 original size:29 final size:29
Alignment explanation
Indices: 1517899--1517954 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
1517889 CCGTTGATCG
* * * *
1517899 GGTGACATTTTAGTAATTATTTTGAAACT
1 GGTGACATATTAGGAATTAATTCGAAACT
*
1517928 GGTGACATATTGGGAATTAATTCGAAA
1 GGTGACATATTAGGAATTAATTCGAAA
1517955 AGGGTACTAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.34, C:0.07, G:0.21, T:0.38
Consensus pattern (29 bp):
GGTGACATATTAGGAATTAATTCGAAACT
Found at i:1518019 original size:28 final size:27
Alignment explanation
Indices: 1517963--1518119 Score: 126
Period size: 28 Copynumber: 5.8 Consensus size: 27
1517953 AAAGGGTACT
*
1517963 ATTTTCATAATTTTTT--AAAAATG-C
1 ATTTTCGTAATTTTTTGAAAAAATGAC
1517987 TATTTTCGTAATTTTGTTGAAAAAATGAC
1 -ATTTTCGTAATTTT-TTGAAAAAATGAC
* * **
1518016 ATTTTAGTAAATATTTTGAAAAGGGTG-C
1 ATTTTCGT-AATTTTTTGAAAA-AATGAC
* * *
1518044 TATTTTTGAAATTTTTT-AAAAAATGAT
1 -ATTTTCGTAATTTTTTGAAAAAATGAC
*
1518071 ATTTTCGTAATTTTTTGAAAAAATTAC
1 ATTTTCGTAATTTTTTGAAAAAATGAC
* *
1518098 ATTTTAGTAAATATTTTGAAAA
1 ATTTTCGT-AATTTTTTGAAAA
1518120 TGGTGCTATA
Statistics
Matches: 105, Mismatches: 17, Indels: 17
0.76 0.12 0.12
Matches are distributed among these distances:
25 13 0.12
26 18 0.17
27 19 0.18
28 41 0.39
29 14 0.13
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.46
Consensus pattern (27 bp):
ATTTTCGTAATTTTTTGAAAAAATGAC
Found at i:1518047 original size:82 final size:82
Alignment explanation
Indices: 1517951--1518171 Score: 293
Period size: 82 Copynumber: 2.6 Consensus size: 82
1517941 GAATTAATTC
* *
1517951 GAAAAGGGTACTATTTTCATAATTTTTTAAAAATGCTATTTTCGTAATTTTGTTGAAAAAATGAC
1 GAAAAGGGTGCTATTTTGATAATTTTTTAAAAATGCTATTTTCGTAATTTTGTTGAAAAAATGAC
1518016 ATTTTAGTAAATATTTT
66 ATTTTAGTAAATATTTT
* *
1518033 GAAAAGGGTGCTATTTTTGA-AATTTTTTAAAAAATGATATTTTCGTAATTTT-TTGAAAAAATT
1 GAAAAGGGTGCTA-TTTTGATAATTTTTT-AAAAATGCTATTTTCGTAATTTTGTTGAAAAAATG
1518096 ACATTTTAGTAAATATTTT
64 ACATTTTAGTAAATATTTT
* * * * *
1518115 GAAAATGGTGCTATATTGGTAATTAATTTTAAAATGGTGCTATTTTCATAATTTTGT
1 GAAAAGGGTGCTATTTTGATAATT--TTTTAAAA--ATGCTATTTTCGTAATTTTGT
1518172 AAATATATAT
Statistics
Matches: 121, Mismatches: 10, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
81 4 0.03
82 65 0.54
83 31 0.26
84 4 0.03
85 16 0.13
86 1 0.01
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.46
Consensus pattern (82 bp):
GAAAAGGGTGCTATTTTGATAATTTTTTAAAAATGCTATTTTCGTAATTTTGTTGAAAAAATGAC
ATTTTAGTAAATATTTT
Found at i:1518166 original size:29 final size:30
Alignment explanation
Indices: 1518110--1518167 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
1518100 TTTAGTAAAT
**
1518110 ATTTTGAAAATGGTGCTATATTGGTAATTA
1 ATTTTGAAAATGGTGCTATATTCATAATTA
*
1518140 ATTTT-AAAATGGTGCTATTTTCATAATT
1 ATTTTGAAAATGGTGCTATATTCATAATT
1518168 TTGTAAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.33, C:0.05, G:0.16, T:0.47
Consensus pattern (30 bp):
ATTTTGAAAATGGTGCTATATTCATAATTA
Found at i:1519179 original size:42 final size:42
Alignment explanation
Indices: 1519120--1519249 Score: 206
Period size: 42 Copynumber: 3.1 Consensus size: 42
1519110 TATCAGGTCT
1519120 CTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTCCCAAGTCC
1 CTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTCCCAAGTCC
* ** *
1519162 CTTTGCTGTGTGTGAAGGTAAGCCTTACAGTTTATCAGGTCC
1 CTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTCCCAAGTCC
* *
1519204 CTTTGCTTTGTGCGAAGGTAAGCCTTACAGTTTCCCATGTCC
1 CTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTCCCAAGTCC
1519246 CTTT
1 CTTT
1519250 AATGTGTGTA
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 79 1.00
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (42 bp):
CTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTCCCAAGTCC
Found at i:1519256 original size:84 final size:84
Alignment explanation
Indices: 1519109--1519278 Score: 261
Period size: 84 Copynumber: 2.0 Consensus size: 84
1519099 GAAGGAAGTA
* **
1519109 TTATCAGGTCTCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTCCCAAGTCCCTTTGCTGTGTG
1 TTATCAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTCCCAAGTCCCTTTAATGTGTG
*
1519174 TGAAGG-TAAGCCTTACAGT
66 T-AAGGATAAACCTTACAGT
* *
1519193 TTATCAGGTCCCTTTGCTTTGTGCGAAGGTAAGCCTTACAGTTTCCCATGTCCCTTTAATGTGTG
1 TTATCAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTCCCAAGTCCCTTTAATGTGTG
*
1519258 TAAGGATAAACCTTATAGT
66 TAAGGATAAACCTTACAGT
1519277 TT
1 TT
1519279 TCCTAGACTC
Statistics
Matches: 78, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
83 4 0.05
84 74 0.95
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (84 bp):
TTATCAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTCCCAAGTCCCTTTAATGTGTG
TAAGGATAAACCTTACAGT
Found at i:1519272 original size:42 final size:41
Alignment explanation
Indices: 1519120--1519278 Score: 183
Period size: 42 Copynumber: 3.8 Consensus size: 41
1519110 TATCAGGTCT
*
1519120 CTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTCCCAAGTCC
1 CTTTGCTGTGTG-TAAGGTAAGCCTTACAGTTTCCCAAGTCC
** *
1519162 CTTTGCTGTGTGTGAAGGTAAGCCTTACAGTTTATCAGGTCC
1 CTTTGCTGTGTGT-AAGGTAAGCCTTACAGTTTCCCAAGTCC
* * *
1519204 CTTTGCTTTGTGCGAAGGTAAGCCTTACAGTTTCCCATGTCC
1 CTTTGCTGTGTG-TAAGGTAAGCCTTACAGTTTCCCAAGTCC
** * *
1519246 CTTTAATGTGTGTAAGGATAAACCTTATAGTTT
1 CTTTGCTGTGTGTAAGG-TAAGCCTTACAGTTT
1519279 TCCTAGACTC
Statistics
Matches: 99, Mismatches: 15, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
41 4 0.04
42 95 0.96
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.36
Consensus pattern (41 bp):
CTTTGCTGTGTGTAAGGTAAGCCTTACAGTTTCCCAAGTCC
Found at i:1525444 original size:18 final size:18
Alignment explanation
Indices: 1525421--1525475 Score: 92
Period size: 18 Copynumber: 3.1 Consensus size: 18
1525411 TTGACCGGTT
*
1525421 CCGACCTGACCCGTTGAC
1 CCGACCCGACCCGTTGAC
1525439 CCGACCCGACCCGTTGAC
1 CCGACCCGACCCGTTGAC
*
1525457 CCGACCCGAACCGTTGAC
1 CCGACCCGACCCGTTGAC
1525475 C
1 C
1525476 GTTGAACGGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.18, C:0.47, G:0.22, T:0.13
Consensus pattern (18 bp):
CCGACCCGACCCGTTGAC
Found at i:1525539 original size:29 final size:29
Alignment explanation
Indices: 1525488--1525544 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
1525478 TGAACGGGTG
* * * * *
1525488 ACATTTTAGTAATTATTTTGAAACTGGTT
1 ACATATTAGGAATTAATTCGAAAATGGTT
1525517 ACATATTAGGAATTAATTCGAAAATGGT
1 ACATATTAGGAATTAATTCGAAAATGGT
1525545 GTTATTTTTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.37, C:0.07, G:0.16, T:0.40
Consensus pattern (29 bp):
ACATATTAGGAATTAATTCGAAAATGGTT
Found at i:1525583 original size:26 final size:28
Alignment explanation
Indices: 1525544--1525623 Score: 92
Period size: 28 Copynumber: 2.9 Consensus size: 28
1525534 TCGAAAATGG
*
1525544 TGTTATTTTTGTAA-TTTTTT-AAAAAA
1 TGTTATTTTCGTAATTTTTTTGAAAAAA
1525570 TGTTATTTTCGTAATTTTTTTGAAAAAA
1 TGTTATTTTCGTAATTTTTTTGAAAAAA
** * * *
1525598 TGACATTTTAGTAAATATTTTGAAAA
1 TGTTATTTTCGTAATTTTTTTGAAAA
1525624 TGGTGCTATA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
26 13 0.28
27 6 0.13
28 27 0.59
ACGTcount: A:0.36, C:0.03, G:0.10, T:0.51
Consensus pattern (28 bp):
TGTTATTTTCGTAATTTTTTTGAAAAAA
Found at i:1525670 original size:29 final size:30
Alignment explanation
Indices: 1525614--1525671 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
1525604 TTTAGTAAAT
*
1525614 ATTTTGAAAATGGTGCTATATTGGTAATTA
1 ATTTTGAAAATGGTGCTATATTCGTAATTA
* * *
1525644 ATTTT-AAAATGGTGTTATTTTCTTAATT
1 ATTTTGAAAATGGTGCTATATTCGTAATT
1525672 TTGTAATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.31, C:0.03, G:0.16, T:0.50
Consensus pattern (30 bp):
ATTTTGAAAATGGTGCTATATTCGTAATTA
Found at i:1526487 original size:29 final size:29
Alignment explanation
Indices: 1526451--1526508 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
1526441 CATATTTAAT
1526451 GTATTAATTATCGTTTTTACTCCAATGCA
1 GTATTAATTATCGTTTTTACTCCAATGCA
1526480 GTATTAATTATCGTTTTTACTCCAATGCA
1 GTATTAATTATCGTTTTTACTCCAATGCA
1526509 TACATGTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.17, G:0.10, T:0.45
Consensus pattern (29 bp):
GTATTAATTATCGTTTTTACTCCAATGCA
Found at i:1526615 original size:42 final size:42
Alignment explanation
Indices: 1526556--1526721 Score: 253
Period size: 42 Copynumber: 4.0 Consensus size: 42
1526546 GAAGTATTAT
1526556 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTCC
1 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTCC
**
1526598 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTAT
1 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTCC
* * *
1526640 CAGGTCCCTTTGCTGTGTACGAAGGTATGCCTTATAGTTTCC
1 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTCC
* *
1526682 CAGGTCCCTTTGCTATGTGC-AAGGATAAACCTTACAGTTT
1 CAGGTCCCTTTGCTGTGTGCGAAGG-TAAGCCTTACAGTTT
1526722 TCCTAGGCTC
Statistics
Matches: 111, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
41 4 0.04
42 107 0.96
ACGTcount: A:0.19, C:0.23, G:0.24, T:0.33
Consensus pattern (42 bp):
CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTCC
Found at i:1526693 original size:84 final size:84
Alignment explanation
Indices: 1526552--1526721 Score: 279
Period size: 84 Copynumber: 2.0 Consensus size: 84
1526542 GAAGGAAGTA
* *
1526552 TTATCAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTCCCAGGTCCCTTTGCTGTGTG
1 TTATCAGGTCCCTTTGCTGTGTACGAAGGTAAGCCTTACAGTTTCCCAGGTCCCTTTGCTATGTG
*
1526617 CGAAGG-TAAGCCTTACAGT
66 C-AAGGATAAACCTTACAGT
* *
1526636 TTATCAGGTCCCTTTGCTGTGTACGAAGGTATGCCTTATAGTTTCCCAGGTCCCTTTGCTATGTG
1 TTATCAGGTCCCTTTGCTGTGTACGAAGGTAAGCCTTACAGTTTCCCAGGTCCCTTTGCTATGTG
1526701 CAAGGATAAACCTTACAGT
66 CAAGGATAAACCTTACAGT
1526720 TT
1 TT
1526722 TCCTAGGCTC
Statistics
Matches: 80, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
83 4 0.05
84 76 0.95
ACGTcount: A:0.19, C:0.23, G:0.24, T:0.34
Consensus pattern (84 bp):
TTATCAGGTCCCTTTGCTGTGTACGAAGGTAAGCCTTACAGTTTCCCAGGTCCCTTTGCTATGTG
CAAGGATAAACCTTACAGT
Found at i:1530416 original size:15 final size:15
Alignment explanation
Indices: 1530365--1530405 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
1530355 AAAATGATAT
*
1530365 GTGAATATGTT-TAA
1 GTGAAAATGTTCTAA
*
1530379 ATGAAAATGTTCTAA
1 GTGAAAATGTTCTAA
1530394 GTGAAAATGTTC
1 GTGAAAATGTTC
1530406 AACTTGAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
14 9 0.39
15 14 0.61
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.37
Consensus pattern (15 bp):
GTGAAAATGTTCTAA
Found at i:1530618 original size:22 final size:22
Alignment explanation
Indices: 1530558--1530647 Score: 90
Period size: 23 Copynumber: 3.9 Consensus size: 22
1530548 CTACGCGATT
*
1530558 CTTCGGGACATATCTATGTGGTC
1 CTTC-GGACAAATCTATGTGGTC
* * **
1530581 CTTAGGGACAATTCTACATGGTC
1 CTT-CGGACAAATCTATGTGGTC
1530604 CTTCGGACAAATCTATGTGGTC
1 CTTCGGACAAATCTATGTGGTC
*
1530626 CTTTGGAACAAATTCTATGTGG
1 CTTCGG-ACAAA-TCTATGTGG
1530648 CACTTTGGTA
Statistics
Matches: 54, Mismatches: 10, Indels: 5
0.78 0.14 0.07
Matches are distributed among these distances:
22 20 0.37
23 25 0.46
24 9 0.17
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.33
Consensus pattern (22 bp):
CTTCGGACAAATCTATGTGGTC
Found at i:1532994 original size:21 final size:21
Alignment explanation
Indices: 1532965--1533041 Score: 59
Period size: 21 Copynumber: 3.5 Consensus size: 21
1532955 TGCATTTTCA
*
1532965 TTTATTGCATCCTTTCATGCC
1 TTTAATGCATCCTTTCATGCC
* *
1532986 TTTAATGCA-CCGTT-ATGCAT
1 TTTAATGCATCCTTTCATGC-C
1533006 TTTCATTTATGGCATCCTTTCATGCC
1 TTT-A---AT-GCATCCTTTCATGCC
1533032 TTTAATGCAT
1 TTTAATGCAT
1533042 AATTATTCAT
Statistics
Matches: 43, Mismatches: 5, Indels: 16
0.67 0.08 0.25
Matches are distributed among these distances:
19 4 0.09
20 7 0.16
21 13 0.30
22 2 0.05
24 2 0.05
25 4 0.09
26 7 0.16
27 4 0.09
ACGTcount: A:0.19, C:0.23, G:0.12, T:0.45
Consensus pattern (21 bp):
TTTAATGCATCCTTTCATGCC
Found at i:1533021 original size:46 final size:46
Alignment explanation
Indices: 1532950--1533091 Score: 178
Period size: 46 Copynumber: 3.1 Consensus size: 46
1532940 TTCCATACAT
*
1532950 CGTTATGCATTTTCATTTATTGCATCCTTTCATGCCTTTAATGCAC
1 CGTTATGCATTTTCATTTATAGCATCCTTTCATGCCTTTAATGCAC
* *
1532996 CGTTATGCATTTTCATTTATGGCATCCTTTCATGCCTTTAATGCAT
1 CGTTATGCATTTTCATTTATAGCATCCTTTCATGCCTTTAATGCAC
** * * ** *
1533042 AATTATTCATTTT-ATTTACAAAATCCTTTCATGACTTTAATGCAC
1 CGTTATGCATTTTCATTTATAGCATCCTTTCATGCCTTTAATGCAC
*
1533087 TGTTA
1 CGTTA
1533092 ATGCCACCGT
Statistics
Matches: 83, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
45 29 0.35
46 54 0.65
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.46
Consensus pattern (46 bp):
CGTTATGCATTTTCATTTATAGCATCCTTTCATGCCTTTAATGCAC
Found at i:1539623 original size:45 final size:45
Alignment explanation
Indices: 1539502--1539638 Score: 211
Period size: 46 Copynumber: 3.0 Consensus size: 45
1539492 GATGATAGTT
1539502 GCATCATTTATTGCCTTTAATGCACCGTTATGCATTTTCATTTATG
1 GCATCATTTA-TGCCTTTAATGCACCGTTATGCATTTTCATTTATG
1539548 GCATCATTTCATGCCTTTAATGCACCGTTATGCATTTTCATTTATG
1 GCATCATTT-ATGCCTTTAATGCACCGTTATGCATTTTCATTTATG
* * **
1539594 GTATCCTTTATGCCTTTAATGCATTGTTATGCATTTTTCATTTAT
1 GCATCATTTATGCCTTTAATGCACCGTTATGCA-TTTTCATTTAT
1539639 TCATTCATTT
Statistics
Matches: 85, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
45 22 0.26
46 62 0.73
47 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.12, T:0.47
Consensus pattern (45 bp):
GCATCATTTATGCCTTTAATGCACCGTTATGCATTTTCATTTATG
Found at i:1542280 original size:22 final size:21
Alignment explanation
Indices: 1542246--1542305 Score: 84
Period size: 22 Copynumber: 2.8 Consensus size: 21
1542236 ATCCTCTCTC
*
1542246 TACCCTAAACCCAAATCTAAA
1 TACCCTAACCCCAAATCTAAA
1542267 TACCACTAACCCCAAATCTAAA
1 TACC-CTAACCCCAAATCTAAA
*
1542289 CACCCCTAACCCCAAAT
1 TA-CCCTAACCCCAAAT
1542306 ACCCTCCAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
21 4 0.11
22 29 0.83
23 2 0.06
ACGTcount: A:0.43, C:0.40, G:0.00, T:0.17
Consensus pattern (21 bp):
TACCCTAACCCCAAATCTAAA
Found at i:1543110 original size:3 final size:3
Alignment explanation
Indices: 1543097--1543161 Score: 66
Period size: 3 Copynumber: 22.7 Consensus size: 3
1543087 GTCCCCTGTA
* *
1543097 AAT AA- AAT AAT AAT AA- AA- AAT AAT ATT AAT AAAT AAT TAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
*
1543140 AAT GAT AAT -AT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
1543162 ATTCTGACCG
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
2 8 0.15
3 41 0.79
4 3 0.06
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1543118 original size:13 final size:13
Alignment explanation
Indices: 1543100--1543161 Score: 54
Period size: 13 Copynumber: 4.8 Consensus size: 13
1543090 CCCTGTAAAT
1543100 AAAATAATAATAA
1 AAAATAATAATAA
*
1543113 AAAATAATATTAA
1 AAAATAATAATAA
* *
1543126 TAAATAATTAT-A
1 AAAATAATAATAA
* *
1543138 ATAATGATAATATA
1 AAAATAATAATA-A
*
1543152 ATAATAATAA
1 AAAATAATAA
1543162 ATTCTGACCG
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
12 8 0.21
13 20 0.53
14 10 0.26
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (13 bp):
AAAATAATAATAA
Found at i:1543120 original size:10 final size:11
Alignment explanation
Indices: 1543097--1543158 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
1543087 GTCCCCTGTA
1543097 AATAAAATAAT
1 AATAAAATAAT
1543108 AATAAAA-AAT
1 AATAAAATAAT
*
1543118 AATATTAATAAAT
1 AATA-AAAT-AAT
*
1543131 AATTATAATAAT
1 AA-TAAAATAAT
* *
1543143 GATAATATAAT
1 AATAAAATAAT
1543154 AATAA
1 AATAA
1543159 TAAATTCTGA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
10 7 0.17
11 20 0.48
12 4 0.10
13 9 0.21
14 2 0.05
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:1547027 original size:4 final size:4
Alignment explanation
Indices: 1547020--1547074 Score: 110
Period size: 4 Copynumber: 13.8 Consensus size: 4
1547010 TATATATATA
1547020 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1547068 TATG TAT
1 TATG TAT
1547075 ATGAAGATCC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 51 1.00
ACGTcount: A:0.25, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:1553674 original size:12 final size:12
Alignment explanation
Indices: 1553657--1553681 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1553647 GTCGAGGGAG
1553657 TCGACTCAAACT
1 TCGACTCAAACT
1553669 TCGACTCAAACT
1 TCGACTCAAACT
1553681 T
1 T
1553682 GAAAATTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.32, G:0.08, T:0.28
Consensus pattern (12 bp):
TCGACTCAAACT
Found at i:1557731 original size:24 final size:24
Alignment explanation
Indices: 1557696--1557741 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
1557686 GCATGATATG
1557696 GTACATAAATGTTTTATACATCGT
1 GTACATAAATGTTTTATACATCGT
*
1557720 GTACATAGATGTTTTATACATC
1 GTACATAAATGTTTTATACATC
1557742 ATATGGAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (24 bp):
GTACATAAATGTTTTATACATCGT
Found at i:1564821 original size:24 final size:24
Alignment explanation
Indices: 1564789--1564834 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
1564779 GCCTGATATG
1564789 GTACATAGATGTTTTATACATCGT
1 GTACATAGATGTTTTATACATCGT
1564813 GTACATAGATGTTTTATACATC
1 GTACATAGATGTTTTATACATC
1564835 ATATGGAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.41
Consensus pattern (24 bp):
GTACATAGATGTTTTATACATCGT
Found at i:1568977 original size:20 final size:20
Alignment explanation
Indices: 1568952--1568990 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1568942 AGGATAATGA
1568952 AAACAAACAAATAA-AATAAT
1 AAAC-AACAAATAATAATAAT
*
1568972 AAACAACTAATAATAATAA
1 AAACAACAAATAATAATAA
1568991 CAAAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.72, C:0.10, G:0.00, T:0.18
Consensus pattern (20 bp):
AAACAACAAATAATAATAAT
Found at i:1568988 original size:17 final size:16
Alignment explanation
Indices: 1568956--1568999 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
1568946 TAATGAAAAC
1568956 AAACAAATAAAATAAT
1 AAACAAATAAAATAAT
*
1568972 AAACAACTAATAATAAT
1 AAACAAATAA-AATAAT
1568989 -AACAAA-AAAAT
1 AAACAAATAAAAT
1569000 TAAAACACGT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 3 0.12
15 2 0.08
16 14 0.56
17 6 0.24
ACGTcount: A:0.73, C:0.09, G:0.00, T:0.18
Consensus pattern (16 bp):
AAACAAATAAAATAAT
Found at i:1575752 original size:21 final size:21
Alignment explanation
Indices: 1575728--1575767 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1575718 ATGATTATAG
1575728 ATATATTATTATTA-TTATTAA
1 ATATATTATT-TTACTTATTAA
1575749 ATATATTATTTTACTTATT
1 ATATATTATTTTACTTATT
1575768 TTAAAATACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATATTATTTTACTTATTAA
Found at i:1580536 original size:24 final size:24
Alignment explanation
Indices: 1580509--1580620 Score: 79
Period size: 24 Copynumber: 4.6 Consensus size: 24
1580499 AAATCCTAAT
1580509 TAAAATACTTAAAACTATTTAAAC
1 TAAAATACTTAAAACTATTTAAAC
* * ** *
1580533 TAAAATACCTAAAACAAAGATAAAA
1 TAAAATACTTAAAAC-TATTTAAAC
* *
1580558 TAAAATAATATCTTAAATC-A--T-AAT
1 T--AA-AATA-CTTAAAACTATTTAAAC
1580582 TAAAATACTTAAAACTATTTAAAC
1 TAAAATACTTAAAACTATTTAAAC
*
1580606 TAAAATACATAAAAC
1 TAAAATACTTAAAAC
1580621 AAATATAAGA
Statistics
Matches: 68, Mismatches: 11, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
20 7 0.10
21 5 0.07
22 2 0.03
23 1 0.01
24 33 0.49
25 7 0.10
27 3 0.04
28 4 0.06
29 6 0.09
ACGTcount: A:0.59, C:0.12, G:0.01, T:0.29
Consensus pattern (24 bp):
TAAAATACTTAAAACTATTTAAAC
Found at i:1580647 original size:73 final size:73
Alignment explanation
Indices: 1580499--1580647 Score: 246
Period size: 73 Copynumber: 2.0 Consensus size: 73
1580489 ATAAATAAAC
* *
1580499 AAATCCTAATTAAAATACTTAAAACTATTTAAACTAAAATACCTAAAACAAAGATAAAATAAAAT
1 AAATCATAATTAAAATACTTAAAACTATTTAAACTAAAATACATAAAACAAAGATAAAATAAAAT
1580564 AATATCTT
66 AATATCTT
* *
1580572 AAATCATAATTAAAATACTTAAAACTATTTAAACTAAAATACATAAAACAAATATAAGATAAATA
1 AAATCATAATTAAAATACTTAAAACTATTTAAACTAAAATACATAAAACAAAGATAAAATAAA-A
1580637 TAATAT-TT
65 TAATATCTT
1580645 AAA
1 AAA
1580648 AGAATATCCT
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
73 64 0.90
74 7 0.10
ACGTcount: A:0.59, C:0.10, G:0.01, T:0.30
Consensus pattern (73 bp):
AAATCATAATTAAAATACTTAAAACTATTTAAACTAAAATACATAAAACAAAGATAAAATAAAAT
AATATCTT
Found at i:1582095 original size:13 final size:13
Alignment explanation
Indices: 1582077--1582103 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1582067 TTACATACGC
1582077 GCATATGAAGACT
1 GCATATGAAGACT
1582090 GCATATGAAGACT
1 GCATATGAAGACT
1582103 G
1 G
1582104 TTCAACGATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (13 bp):
GCATATGAAGACT
Found at i:1587087 original size:2 final size:2
Alignment explanation
Indices: 1587082--1587114 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1587072 ACAAAAAATA
1587082 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1587115 TATTTATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1588606 original size:87 final size:87
Alignment explanation
Indices: 1588486--1588661 Score: 280
Period size: 87 Copynumber: 2.0 Consensus size: 87
1588476 AGTTCATGGT
* * *
1588486 GGGGTTCGAAATAAACAAGCACAAAGCATGTTTTATCTGTTCCTTACAACTCAAATAACAAAATA
1 GGGGATCGAAATAAACAAGCACAAAGCAAGTTTTATCTGTTCCTTACAACCCAAATAACAAAATA
* *
1588551 TGAAAGCAAAGAACTAGGGGAA
66 TGAAAGAAAAGAACTAAGGGAA
* * *
1588573 GGGGATCGAAATAAACAAGCACAAAGCAAGTTTTATCTGTTCCTTACAACCCAAGTGATAAAATA
1 GGGGATCGAAATAAACAAGCACAAAGCAAGTTTTATCTGTTCCTTACAACCCAAATAACAAAATA
1588638 TGAAAGAAAAGAACTAAGGGAA
66 TGAAAGAAAAGAACTAAGGGAA
1588660 GG
1 GG
1588662 AGGAAAAGCC
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 81 1.00
ACGTcount: A:0.44, C:0.15, G:0.20, T:0.20
Consensus pattern (87 bp):
GGGGATCGAAATAAACAAGCACAAAGCAAGTTTTATCTGTTCCTTACAACCCAAATAACAAAATA
TGAAAGAAAAGAACTAAGGGAA
Found at i:1591503 original size:12 final size:12
Alignment explanation
Indices: 1591484--1591516 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1591474 CAAATATTAG
1591484 AAAC-AATAAAT
1 AAACAAATAAAT
*
1591495 AAATAAATAAAT
1 AAACAAATAAAT
1591507 AAACAAATAA
1 AAACAAATAA
1591517 TGGTTTGAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 3 0.16
12 16 0.84
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (12 bp):
AAACAAATAAAT
Found at i:1594540 original size:47 final size:47
Alignment explanation
Indices: 1594446--1594605 Score: 254
Period size: 47 Copynumber: 3.5 Consensus size: 47
1594436 GTTAATATGC
* * * * *
1594446 AAATAAGCTTATGAGCTTACGGAA--T-AATGGCAAGTATATTGGAA
1 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1594490 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1594537 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1594584 AAATAAGCTTACGAGCTTATGG
1 AAATAAGCTTACGAGCTTATGG
1594606 GATAAATTGT
Statistics
Matches: 108, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
44 22 0.20
46 1 0.01
47 85 0.79
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.33
Consensus pattern (47 bp):
AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
Found at i:1600946 original size:47 final size:47
Alignment explanation
Indices: 1600852--1601011 Score: 236
Period size: 47 Copynumber: 3.5 Consensus size: 47
1600842 GTTAATATGC
* * * * *
1600852 AAATAAGCTTATGAGCTTACGGAA--T-AATGGCAAGTATATTGGAA
1 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
*
1600896 AAATAAGCTTTCGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
*
1600943 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGTTA
1 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1600990 AAATAAGCTTACGAGCTTATGG
1 AAATAAGCTTACGAGCTTATGG
1601012 GATAAATTGT
Statistics
Matches: 105, Mismatches: 8, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
44 21 0.20
46 1 0.01
47 83 0.79
ACGTcount: A:0.37, C:0.08, G:0.21, T:0.34
Consensus pattern (47 bp):
AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
Found at i:1602639 original size:140 final size:140
Alignment explanation
Indices: 1602387--1602946 Score: 653
Period size: 140 Copynumber: 4.0 Consensus size: 140
1602377 TTTAGGTAAA
* * * * * * **
1602387 TTTGGAAACAACACGGTTCCTACATTATGACGAAGTCTGGTTATCTAAGGATGACG-TTGTCCCT
1 TTTGGAGACAACACGGTTCTTACGTGATGAGGAAGTATGGTTATCTAAGGATGACGCTACT-CCT
* * * * *
1602451 ACTTGATGAGGAGATCGGATCTGTGGATGACATTGTTCCTACATGATGAGGACGTCTAGCCATCT
65 ACGTGATGAAGAGATCGGGTCGGTGGATGACATTGTTCCTACGTGATGAGGACGTCTAGCCATCT
*
1602516 TTAAGGATAAT
130 TTAGGGATAAT
*
1602527 TTTGGAGACAACACGGTTCTTACGTGATGAGGAAGTATGGTTATCTAAGGATGACACTACTCCTA
1 TTTGGAGACAACACGGTTCTTACGTGATGAGGAAGTATGGTTATCTAAGGATGACGCTACTCCTA
* * * * * *
1602592 CATGATGAAGAGATCGGGTCGGTGGATGATATTTTTCCTACGTGATGAAGACGTCTAGCAATATT
66 CGTGATGAAGAGATCGGGTCGGTGGATGACATTGTTCCTACGTGATGAGGACGTCTAGCCATCTT
1602657 TAGGGATAAT
131 TAGGGATAAT
* * * * * * * *
1602667 TTGGGAGACGACACGATTCTTACGTGCTGAGAAAGTATGGTTATCTAAGGATGACGTTGCTTCTA
1 TTTGGAGACAACACGGTTCTTACGTGATGAGGAAGTATGGTTATCTAAGGATGACGCTACTCCTA
* * * * * *
1602732 CGTGATGAGGAGATCGGGTCGGTGTATGACATTGTTCCTATGTGATGAGGATGTCTATCCATTTT
66 CGTGATGAAGAGATCGGGTCGGTGGATGACATTGTTCCTACGTGATGAGGACGTCTAGCCATCTT
*
1602797 TATGGATAA-
131 TAGGGATAAT
* ** *
1602806 -ATGGAGACAACAAAGTTACTATA--TGATGAGGAAGTCTGGTTATCTAAGGATGACGCTACTCC
1 TTTGGAGACAACACGGTT-CT-TACGTGATGAGGAAGTATGGTTATCTAAGGATGACGCTACTCC
* * * * *
1602868 TATGTGATGAAGAGATCTGGTTGGTGGATGACATTGTTCCTACGTGATAAGGACGTCTAACCATC
64 TACGTGATGAAGAGATCGGGTCGGTGGATGACATTGTTCCTACGTGATGAGGACGTCTAGCCATC
1602933 TTTAGGGATAAT
129 TTTAGGGATAAT
1602945 TT
1 TT
1602947 ATTTTAAGAT
Statistics
Matches: 350, Mismatches: 65, Indels: 10
0.82 0.15 0.02
Matches are distributed among these distances:
138 109 0.31
139 2 0.01
140 237 0.68
141 2 0.01
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (140 bp):
TTTGGAGACAACACGGTTCTTACGTGATGAGGAAGTATGGTTATCTAAGGATGACGCTACTCCTA
CGTGATGAAGAGATCGGGTCGGTGGATGACATTGTTCCTACGTGATGAGGACGTCTAGCCATCTT
TAGGGATAAT
Found at i:1602869 original size:278 final size:278
Alignment explanation
Indices: 1602419--1602946 Score: 740
Period size: 278 Copynumber: 1.9 Consensus size: 278
1602409 CATTATGACG
* * *
1602419 AAGTCTGGTTATCTAAGGATGACGTTGTCCCTACTTGATGAGGAGATCGGATCTGTGGATGACAT
1 AAGTATGGTTATCTAAGGATGACGTTGTCCCTACGTGATGAGGAGATCGGATCGGTGGATGACAT
* **
1602484 TGTTCCTACATGATGAGGACGTCTAGCCATCTTTAAGGATAATTTTGGAGACAACACGGTTCTTA
66 TGTTCCTACATGATGAGGACGTCTAGCCATCTTTAAGGATAA-TATGGAGACAACAAAGTTCTTA
1602549 CGTGATGAGGAAGTATGGTTATCTAAGGATGACACTACTCCTACATGATGAAGAGATCGGGTCGG
130 C-TGATGAGGAAGTATGGTTATCTAAGGATGACACTACTCCTACATGATGAAGAGATCGGGTCGG
* * *
1602614 TGGATGATATTTTTCCTACGTGATGAA-GACGTCTAGCAATATTTAGGGATAATTTGGGAGACGA
194 TGGATGACATTGTTCCTACGTGAT-AAGGACGTCTAACAATATTTAGGGATAATTTGGGAGACGA
1602678 CACGATTCTTACGTGCTGAGA
258 CACGATTCTTACGTGCTGAGA
* * *
1602699 AAGTATGGTTATCTAAGGATGACGTTG-CTTCTACGTGATGAGGAGATCGGGTCGGTGTATGACA
1 AAGTATGGTTATCTAAGGATGACGTTGTC-CCTACGTGATGAGGAGATCGGATCGGTGGATGACA
** * * * *
1602763 TTGTTCCTATGTGATGAGGATGTCTATCCATTTTTATGGATAA-ATGGAGACAACAAAGTTACTA
65 TTGTTCCTACATGATGAGGACGTCTAGCCATCTTTAAGGATAATATGGAGACAACAAAGTT-CT-
* * ** * *
1602827 TA-TGATGAGGAAGTCTGGTTATCTAAGGATGACGCTACTCCTATGTGATGAAGAGATCTGGTTG
128 TACTGATGAGGAAGTATGGTTATCTAAGGATGACACTACTCCTACATGATGAAGAGATCGGGTCG
* *
1602891 GTGGATGACATTGTTCCTACGTGATAAGGACGTCTAACCATCTTTAGGGATAATTT
193 GTGGATGACATTGTTCCTACGTGATAAGGACGTCTAACAATATTTAGGGATAATTT
1602947 ATTTTAAGAT
Statistics
Matches: 218, Mismatches: 26, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
277 2 0.01
278 118 0.54
279 3 0.01
280 95 0.44
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (278 bp):
AAGTATGGTTATCTAAGGATGACGTTGTCCCTACGTGATGAGGAGATCGGATCGGTGGATGACAT
TGTTCCTACATGATGAGGACGTCTAGCCATCTTTAAGGATAATATGGAGACAACAAAGTTCTTAC
TGATGAGGAAGTATGGTTATCTAAGGATGACACTACTCCTACATGATGAAGAGATCGGGTCGGTG
GATGACATTGTTCCTACGTGATAAGGACGTCTAACAATATTTAGGGATAATTTGGGAGACGACAC
GATTCTTACGTGCTGAGA
Found at i:1603135 original size:37 final size:36
Alignment explanation
Indices: 1603093--1603179 Score: 111
Period size: 37 Copynumber: 2.4 Consensus size: 36
1603083 TGAGAAAGAT
*
1603093 TGTCTCAAGTGAGACGAAATTTATTTTTAAGAGAAAC
1 TGTCTCAAGTGAGACAAAATTTATTTTTAAGA-AAAC
* *
1603130 TGTCTCAAGCGAGACAAAATTTGTTTTTAAGAAAAC
1 TGTCTCAAGTGAGACAAAATTTATTTTTAAGAAAAC
** *
1603166 AATATCAAGTGAGA
1 TGTCTCAAGTGAGA
1603180 TCAATTATGT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
36 14 0.33
37 29 0.67
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.30
Consensus pattern (36 bp):
TGTCTCAAGTGAGACAAAATTTATTTTTAAGAAAAC
Found at i:1603442 original size:36 final size:36
Alignment explanation
Indices: 1603395--1603508 Score: 122
Period size: 36 Copynumber: 3.1 Consensus size: 36
1603385 TCTCAAGGGA
*
1603395 AAATGGTCTCAAGCGAGAAGAAATTTGTTTTGAGAG
1 AAATTGTCTCAAGCGAGAAGAAATTTGTTTTGAGAG
* *
1603431 AAATTGTCTCAAGCGAGACA-AAATTTATTTTTAGAG
1 AAATTGTCTCAAGCGAGA-AGAAATTTGTTTTGAGAG
** * * *
1603467 AAAATTAACTCAAGTGAGATGAAACTTTGTTTCGAGAG
1 -AAATTGTCTCAAGCGAGAAGAAA-TTTGTTTTGAGAG
1603505 AAAT
1 AAAT
1603509 AATCTCAAAG
Statistics
Matches: 64, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
36 31 0.48
37 23 0.36
38 10 0.16
ACGTcount: A:0.39, C:0.10, G:0.21, T:0.30
Consensus pattern (36 bp):
AAATTGTCTCAAGCGAGAAGAAATTTGTTTTGAGAG
Found at i:1605859 original size:16 final size:16
Alignment explanation
Indices: 1605838--1605902 Score: 53
Period size: 18 Copynumber: 3.8 Consensus size: 16
1605828 ATCTGTTATG
1605838 TTTC-TTCTTTTCTTTC
1 TTTCTTTCTTTT-TTTC
1605854 TTTCTTTCTTTATTTTTC
1 TTTCTTTC-TT-TTTTTC
*
1605872 TTCTCTTTGCTTTTTCTC
1 TT-TCTTT-CTTTTTTTC
1605890 TTTGC-TTCTTTTT
1 TTT-CTTTCTTTTT
1605903 CCTTTGATTT
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
16 10 0.24
17 6 0.14
18 16 0.38
19 9 0.21
20 1 0.02
ACGTcount: A:0.02, C:0.22, G:0.03, T:0.74
Consensus pattern (16 bp):
TTTCTTTCTTTTTTTC
Found at i:1605903 original size:16 final size:16
Alignment explanation
Indices: 1605881--1605918 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
1605871 CTTCTCTTTG
*
1605881 CTTTTTCTCTTTGCTT
1 CTTTTTCTCTTTGATT
1605897 CTTTTTC-CTTTGATT
1 CTTTTTCTCTTTGATT
1605912 -TTTTTCT
1 CTTTTTCT
1605919 TTTTTCTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 6 0.30
15 7 0.35
16 7 0.35
ACGTcount: A:0.03, C:0.21, G:0.05, T:0.71
Consensus pattern (16 bp):
CTTTTTCTCTTTGATT
Found at i:1605928 original size:20 final size:20
Alignment explanation
Indices: 1605895--1605934 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1605885 TTCTCTTTGC
1605895 TTCTTTTTCCTTTGATTTTT
1 TTCTTTTTCCTTTGATTTTT
*
1605915 TTCTTTTTTCTTTGATTTTT
1 TTCTTTTTCCTTTGATTTTT
1605935 CTCTATGCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.05, C:0.12, G:0.05, T:0.78
Consensus pattern (20 bp):
TTCTTTTTCCTTTGATTTTT
Found at i:1605934 original size:13 final size:13
Alignment explanation
Indices: 1605845--1605920 Score: 64
Period size: 13 Copynumber: 5.6 Consensus size: 13
1605835 ATGTTTCTTC
1605845 TTTTCTTT-CTTT
1 TTTTCTTTGCTTT
* **
1605857 CTTTCTTTATTTT
1 TTTTCTTTGCTTT
1605870 TCTTCTCTTTGCTTT
1 T-TT-TCTTTGCTTT
*
1605885 TTCTCTTTGCTTCT
1 TTTTCTTTGCTT-T
*
1605899 TTTTCCTTTGATTT
1 TTTT-CTTTGCTTT
1605913 TTTTCTTT
1 TTTTCTTT
1605921 TTTCTTTGAT
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
12 7 0.14
13 16 0.31
14 12 0.24
15 16 0.31
ACGTcount: A:0.03, C:0.20, G:0.04, T:0.74
Consensus pattern (13 bp):
TTTTCTTTGCTTT
Found at i:1608737 original size:47 final size:43
Alignment explanation
Indices: 1608684--1608793 Score: 157
Period size: 47 Copynumber: 2.5 Consensus size: 43
1608674 CATTTATCCT
*
1608684 ATAAGCTCGTAAGCTTATTTTACCAAAATACTTGCCATTTAAATTCC
1 ATAAGCTCATAAGCTTATTTTACCAAAATACTTGCCA-TT--ATT-C
* *
1608731 ATAAGCTCATAAGCTTATTTTATCAATATACTTGCCATTATTC
1 ATAAGCTCATAAGCTTATTTTACCAAAATACTTGCCATTATTC
1608774 ATAAGCTCATAAGCTTATTT
1 ATAAGCTCATAAGCTTATTT
1608794 GCATACTTAC
Statistics
Matches: 60, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
43 21 0.35
44 3 0.05
46 2 0.03
47 34 0.57
ACGTcount: A:0.34, C:0.19, G:0.08, T:0.39
Consensus pattern (43 bp):
ATAAGCTCATAAGCTTATTTTACCAAAATACTTGCCATTATTC
Found at i:1613854 original size:43 final size:46
Alignment explanation
Indices: 1613735--1613858 Score: 157
Period size: 47 Copynumber: 2.8 Consensus size: 46
1613725 ATAAAATCCA
** *
1613735 TTACCATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAAAATAC
1 TTACCATTTAATTTCATAAGCTCATAAGCTTATTTTACCAAAATAC
* *
1613780 TTACCATTTAAATTTCATAAGCTCATAAGCTTATTTTATCAATATAC
1 TTACCATTT-AATTTCATAAGCTCATAAGCTTATTTTACCAAAATAC
*
1613827 TTGCCA-TT-A-TTCATAAGCTCATAAGCTTATTT
1 TTACCATTTAATTTCATAAGCTCATAAGCTTATTT
1613859 GCATACTTAC
Statistics
Matches: 71, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
43 23 0.32
44 1 0.01
45 9 0.13
46 2 0.03
47 36 0.51
ACGTcount: A:0.33, C:0.20, G:0.06, T:0.40
Consensus pattern (46 bp):
TTACCATTTAATTTCATAAGCTCATAAGCTTATTTTACCAAAATAC
Found at i:1618249 original size:16 final size:15
Alignment explanation
Indices: 1618225--1618258 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
1618215 AAAGAAAATA
*
1618225 AAAAGGCATAAATTT
1 AAAAGGCATAAAGTT
1618240 AAAAGTGCATAAAGTT
1 AAAAG-GCATAAAGTT
1618256 AAA
1 AAA
1618259 TAATGAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.56, C:0.06, G:0.15, T:0.24
Consensus pattern (15 bp):
AAAAGGCATAAAGTT
Found at i:1619654 original size:59 final size:59
Alignment explanation
Indices: 1619562--1619752 Score: 314
Period size: 59 Copynumber: 3.3 Consensus size: 59
1619552 AGATTGTTGA
*
1619562 TAAATAGTTTTAAAAGAGTTACTAATATGTAATTAATTTCGGTTATGGTGGTATTTTTG
1 TAAATAGTTTTAAAAGAGTGACTAATATGTAATTAATTTCGGTTATGGTGGTATTTTTG
*
1619621 TAAATAGTTTTAAAAGAGTGACTAATACGTAATTAATTTCGGTTATGGTGGTATTTTTG
1 TAAATAGTTTTAAAAGAGTGACTAATATGTAATTAATTTCGGTTATGGTGGTATTTTTG
* * *
1619680 CAAATTGTTTTAAAAGAGTGACTAATATGTAATTAATTTCGGTTAT-GTGGTATTTTCG
1 TAAATAGTTTTAAAAGAGTGACTAATATGTAATTAATTTCGGTTATGGTGGTATTTTTG
1619738 TAAATA-TTGTTAAAA
1 TAAATAGTT-TTAAAA
1619753 AGGTGTTAGT
Statistics
Matches: 123, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
57 2 0.02
58 21 0.17
59 100 0.81
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.43
Consensus pattern (59 bp):
TAAATAGTTTTAAAAGAGTGACTAATATGTAATTAATTTCGGTTATGGTGGTATTTTTG
Found at i:1619766 original size:29 final size:29
Alignment explanation
Indices: 1619733--1619894 Score: 242
Period size: 29 Copynumber: 5.7 Consensus size: 29
1619723 TATGTGGTAT
1619733 TTTCGTAAATATTGTTAAAAAGGTGTTAG
1 TTTCGTAAATATTGTTAAAAAGGTGTTAG
1619762 TTTCGTAAATATTGTTAAAAAGGTGTTAG
1 TTTCGTAAATATTGTTAAAAAGGTGTTAG
*
1619791 TTTCGTAAATATTGTTAAGAAGGTGTTAG
1 TTTCGTAAATATTGTTAAAAAGGTGTTAG
* *
1619820 TTTCCTAGATATTGTT---AAGGTGTTAG
1 TTTCGTAAATATTGTTAAAAAGGTGTTAG
* *
1619846 CTTCGTAAATATTGTTAAAAA-TTGTTAG
1 TTTCGTAAATATTGTTAAAAAGGTGTTAG
*
1619874 TTTCGTAAATATTTTTAAAAA
1 TTTCGTAAATATTGTTAAAAA
1619895 AAAGTTTCGT
Statistics
Matches: 121, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
26 23 0.19
28 25 0.21
29 73 0.60
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (29 bp):
TTTCGTAAATATTGTTAAAAAGGTGTTAG
Found at i:1623950 original size:59 final size:58
Alignment explanation
Indices: 1623878--1624068 Score: 303
Period size: 59 Copynumber: 3.3 Consensus size: 58
1623868 AGATTGTTGA
* *
1623878 TAAATAGTTTTAAAAGAGTGACTAATATGTAATTAATTTTGGTTATGGTGGTATTTTTG
1 TAAATAGTTTTAAAAGAGTGACTAATACGTAATTAATTTCGGTTAT-GTGGTATTTTTG
* *
1623937 TAAATAGCTTTAAAAGAATGACTAATACGTAATTAATTTCGGTTATAGTGGTATTTTTG
1 TAAATAGTTTTAAAAGAGTGACTAATACGTAATTAATTTCGGTTAT-GTGGTATTTTTG
*
1623996 TAAATAGTTTTAAAAGAGTGACTAATACGTAATTAACTTCGGTTATGTGGTATTTTTG
1 TAAATAGTTTTAAAAGAGTGACTAATACGTAATTAATTTCGGTTATGTGGTATTTTTG
1624054 TAAATA-TTGTTAAAA
1 TAAATAGTT-TTAAAA
1624069 AGGTGTTAGT
Statistics
Matches: 123, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
57 2 0.02
58 24 0.20
59 97 0.79
ACGTcount: A:0.35, C:0.05, G:0.18, T:0.42
Consensus pattern (58 bp):
TAAATAGTTTTAAAAGAGTGACTAATACGTAATTAATTTCGGTTATGTGGTATTTTTG
Found at i:1624095 original size:29 final size:29
Alignment explanation
Indices: 1624053--1624183 Score: 192
Period size: 29 Copynumber: 4.6 Consensus size: 29
1624043 TGGTATTTTT
1624053 GTAAATATTGTTAAAAAGGTGTTAGTTTC
1 GTAAATATTGTTAAAAAGGTGTTAGTTTC
* *
1624082 GTAAATACTGTTAAAAAGGCGTTAGTTTC
1 GTAAATATTGTTAAAAAGGTGTTAGTTTC
* *
1624111 GTAAATATTGTTAAGATGGTGTTAGTTTC
1 GTAAATATTGTTAAAAAGGTGTTAGTTTC
*
1624140 GTAAATATTGTTAAAAA-TTGTTAGTTTC
1 GTAAATATTGTTAAAAAGGTGTTAGTTTC
* *
1624168 ATAAATATTTTTAAAA
1 GTAAATATTGTTAAAA
1624184 TTATGTTAGT
Statistics
Matches: 91, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
28 24 0.26
29 67 0.74
ACGTcount: A:0.36, C:0.05, G:0.18, T:0.42
Consensus pattern (29 bp):
GTAAATATTGTTAAAAAGGTGTTAGTTTC
Found at i:1624191 original size:57 final size:58
Alignment explanation
Indices: 1624054--1624200 Score: 197
Period size: 58 Copynumber: 2.6 Consensus size: 58
1624044 GGTATTTTTG
* *
1624054 TAAATATTGTTAAAAAGGTGTTAGTTTCGTAAATACTGTTAAAAAGGCGTTAGTTTCG
1 TAAATATTGTTAAAATGGTGTTAGTTTCGTAAATACTGTTAAAAAGGCGTTAGTTTCA
* * **
1624112 TAAATATTGTTAAGATGGTGTTAGTTTCGTAAATATTGTTAAAAA-TTGTTAGTTTCA
1 TAAATATTGTTAAAATGGTGTTAGTTTCGTAAATACTGTTAAAAAGGCGTTAGTTTCA
* ** *
1624169 TAAATATTTTTAAAATTATGTTAGTTTTGTAA
1 TAAATATTGTTAAAATGGTGTTAGTTTCGTAA
1624201 TTAATTTATG
Statistics
Matches: 78, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
57 36 0.46
58 42 0.54
ACGTcount: A:0.35, C:0.04, G:0.17, T:0.44
Consensus pattern (58 bp):
TAAATATTGTTAAAATGGTGTTAGTTTCGTAAATACTGTTAAAAAGGCGTTAGTTTCA
Found at i:1624230 original size:86 final size:87
Alignment explanation
Indices: 1624046--1624230 Score: 194
Period size: 86 Copynumber: 2.1 Consensus size: 87
1624036 GGTTATGTGG
* * *
1624046 TATTTTTGTAAATATTGTTAAAAAGGTGTTAGTTTCGTAAATACTGTTAAAAAGGCGTTAGTTTC
1 TATTTTAGTAAATATTGTTAAAAAGGTGTTAGTTTCATAAATACTGTTAAAAAGACGTTAGTTTC
* * *
1624111 GTAAATATTGTTAAGATGGTGT
66 GTAAATAATGTTAAGAAGGTGC
* * * * * ** * *
1624133 TAGTTTCGTAAATATTGTTAAAAA-TTGTTAGTTTCATAAATATTTTTAAAATTATGTTAGTTTT
1 TATTTTAGTAAATATTGTTAAAAAGGTGTTAGTTTCATAAATACTGTTAAAAAGACGTTAGTTTC
* *
1624197 GTAATTAAT-TTATGTAAGGTGC
66 GTAAATAATGTTAAG-AAGGTGC
1624219 TATTTTAGTAAA
1 TATTTTAGTAAA
1624231 AGTTGACAGT
Statistics
Matches: 79, Mismatches: 18, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
85 4 0.05
86 53 0.67
87 22 0.28
ACGTcount: A:0.34, C:0.04, G:0.17, T:0.46
Consensus pattern (87 bp):
TATTTTAGTAAATATTGTTAAAAAGGTGTTAGTTTCATAAATACTGTTAAAAAGACGTTAGTTTC
GTAAATAATGTTAAGAAGGTGC
Found at i:1628781 original size:2 final size:2
Alignment explanation
Indices: 1628774--1628810 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1628764 TATTTAAACA
1628774 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1628811 CAAGTGTCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1630593 original size:15 final size:15
Alignment explanation
Indices: 1630573--1630602 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1630563 TTTCGTTGCA
1630573 TTTGCATATGCATTT
1 TTTGCATATGCATTT
*
1630588 TTTGCATTTGCATTT
1 TTTGCATATGCATTT
1630603 ACCTTTACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.13, G:0.13, T:0.57
Consensus pattern (15 bp):
TTTGCATATGCATTT
Found at i:1630950 original size:24 final size:24
Alignment explanation
Indices: 1630922--1630973 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
1630912 AGGACAAAGG
* *
1630922 AAGAGGCTTCTATGCAATGGGGAA
1 AAGAGGCTTCTATGAAAAGGGGAA
1630946 AAGAGGCTTCTATGAAAAGGGGAA
1 AAGAGGCTTCTATGAAAAGGGGAA
1630970 AAGA
1 AAGA
1630974 ACTTGACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.40, C:0.10, G:0.33, T:0.17
Consensus pattern (24 bp):
AAGAGGCTTCTATGAAAAGGGGAA
Found at i:1635454 original size:18 final size:19
Alignment explanation
Indices: 1635427--1635462 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1635417 AAACAAAATC
*
1635427 GAAGATATGAG-CGATGAG
1 GAAGAAATGAGACGATGAG
1635445 GAAGAAATGAGACGATGA
1 GAAGAAATGAGACGATGA
1635463 ACTGAACAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.44, C:0.06, G:0.36, T:0.14
Consensus pattern (19 bp):
GAAGAAATGAGACGATGAG
Found at i:1641735 original size:2 final size:2
Alignment explanation
Indices: 1641728--1641756 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1641718 AAGGCGATTG
1641728 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1641757 ATAAAGTTAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1644275 original size:257 final size:255
Alignment explanation
Indices: 1643550--1644351 Score: 934
Period size: 257 Copynumber: 3.1 Consensus size: 255
1643540 TTCTTACTTA
* * * * * *
1643550 GTAAGTCCTTCGGGCCATCAGTATGTCTTTTGAGAATGAAGATTAAATCCTTTGGGTTATCTG-C
1 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTTAGGTTATATGTC
* ** * * *
1643614 AAGTCTTTCAAGTAAGATGATAAGTCCTTTGGACCATCTATAAGACCTACGAAAAAGGGTGTTTT
66 -AGTCTTTCAAGCAAGATGATAAGT-CTTTGGGTCATCTATAAGACCTTCG-AGAAGGATGTTTT
*
1643679 TACATGAATTTGAAAAATGAGAAACTGATTTTCAAAGTTTCTCATTTAGTATTTTTCATAAAA-T
128 CACATGAATTTGAAAAATGAGAAAC-GATTTTCAAAGTTTCTCATTTAGTA-TTTTCA-AAAAGT
* * * ** *
1643743 GAAATTTTTGAAAAGTAAGAAAGTGATTTCCAATGTTTATTTCCCGGTAAACTATTTCCAAAATC
190 GAAATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATT
1643808 G
255 G
* * * *
1643809 GTAAGT-CTGTAGGGCTATCAGTAAGTCTTTCGAGCATTATGATT-AATCCTTCAGGTTATATGT
1 GTAAGTCCT-TCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTTAGGTTATATGT
* * * * * * * *
1643872 AAGTCTTTCGAGCAATATAATAAGTCTTTCAGGTCATTTATAAGACCTTC-ATGCATGATGTTTT
65 CAGTCTTTCAAGCAAGATGATAAGTCTTT-GGGTCATCTATAAGACCTTCGA-GAAGGATGTTTT
* * * * *
1643936 CACATGAGTTTGAAAAATGAGAAAAC-AGTTTTCATAGTTTCACCTTTAGTATTTTCAGAAAGTG
128 CACATGAATTTGAAAAATGAG-AAACGA-TTTTCAAAGTTTCTCATTTAGTATTTTCAAAAAGTG
*
1644000 GAATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTG
191 AAATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTG
* * * *
1644065 GTAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTTTGGTCATTTGTC
1 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTTAGGTTATATGTC
* * ** * *
1644130 AGTCATTCTAGCAAGATGATAAGTCATTTGGGTCATCCGTAAGACCTTCGGGTAGGATGTTTTCA
66 AGTCTTTCAAGCAAGATGATAAGTC-TTTGGGTCATCTATAAGACCTTCGAGAAGGATGTTTTCA
* *
1644195 TATGAATTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAGTATTTTCAAAAAGTGAAA
130 CATGAATTTGAAAAATGAGAAA-CGATTTTCAAAGTTTCTCATTTAGTATTTTCAAAAAGTGAAA
** *
1644260 TTTTTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTA-CTCAGTAAACTATTTGCAAAATTG
194 TTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCT-AGTAAACTATTTCCAAAATTG
** *
1644322 GTAAGTTTTTCGGGCCATCAGGAAGTCTTT
1 GTAAGTCCTTCGGGCCATCAGTAAGTCTTT
1644352 TGACATACGT
Statistics
Matches: 457, Mismatches: 72, Indels: 30
0.82 0.13 0.05
Matches are distributed among these distances:
255 3 0.01
256 110 0.24
257 250 0.55
258 60 0.13
259 34 0.07
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (255 bp):
GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTTAGGTTATATGTC
AGTCTTTCAAGCAAGATGATAAGTCTTTGGGTCATCTATAAGACCTTCGAGAAGGATGTTTTCAC
ATGAATTTGAAAAATGAGAAACGATTTTCAAAGTTTCTCATTTAGTATTTTCAAAAAGTGAAATT
TTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTG
Found at i:1644611 original size:45 final size:45
Alignment explanation
Indices: 1644547--1644783 Score: 278
Period size: 45 Copynumber: 5.2 Consensus size: 45
1644537 TTTTGGTGTT
*
1644547 ATTCTTGACTTTCTTGTGAAGAGAAGTCAATCTTTTAGTGTTGTC
1 ATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTTAGTGTTGTC
* *
1644592 -TTCCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGTTTTTC
1 ATT-CTTGACTTTCTCGTGAAGAGAAGTCAATCTTTTAGTG-TTGTC
* * *
1644638 CTTCTTGACTTTCTCGTGAAGAGAAGTCAATATTTTAATGTTGTC
1 ATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTTAGTGTTGTC
* * * * * *
1644683 ATTCTTAACTTTTTCATGAAGAGGATTCAATCATTTAGTGTTGTC
1 ATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTTAGTGTTGTC
* * ** * *
1644728 ATTCTTGATTTTCTCATGAAGAGAAGTTGACCTTTTAGTGATGTC
1 ATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTTAGTGTTGTC
*
1644773 ATTCTTAACTT
1 ATTCTTGACTT
1644784 GACTTTTTCC
Statistics
Matches: 161, Mismatches: 28, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
44 2 0.01
45 119 0.74
46 38 0.24
47 2 0.01
ACGTcount: A:0.23, C:0.15, G:0.18, T:0.44
Consensus pattern (45 bp):
ATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTTAGTGTTGTC
Found at i:1644680 original size:91 final size:90
Alignment explanation
Indices: 1644524--1644783 Score: 294
Period size: 91 Copynumber: 2.9 Consensus size: 90
1644514 ACAGATAGAT
* * * * *
1644524 AGAGGAGTCAAT-ATTT--TGGTGTTATTCTTGACTTTCTTGTGAAGAGAAGTCAATCTTTTAGT
1 AGAGGAGTCAATCATTTAGTGTTGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAATATTTTAAT
* *
1644586 GTTGTC-TTCCTTGACTTTCTCGTGA
66 GTTGTCATT-CTTAACTTTCTCATGA
* * *
1644611 AGAGGAGTCAATCTTTTAGTGTTTTTCCTTCTTGACTTTCTCGTGAAGAGAAGTCAATATTTTAA
1 AGAGGAGTCAATCATTTAGTG-TTGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAATATTTTAA
*
1644676 TGTTGTCATTCTTAACTTTTTCATGA
65 TGTTGTCATTCTTAACTTTCTCATGA
* * * ** ** *
1644702 AGAGGATTCAATCATTTAGTGTTGTCATTCTTGATTTTCTCATGAAGAGAAGTTGACCTTTTAGT
1 AGAGGAGTCAATCATTTAGTGTTGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAATATTTTAAT
*
1644767 GATGTCATTCTTAACTT
66 GTTGTCATTCTTAACTT
1644784 GACTTTTTCC
Statistics
Matches: 145, Mismatches: 23, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
87 12 0.08
88 3 0.02
90 53 0.37
91 75 0.52
92 2 0.01
ACGTcount: A:0.23, C:0.14, G:0.19, T:0.44
Consensus pattern (90 bp):
AGAGGAGTCAATCATTTAGTGTTGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAATATTTTAAT
GTTGTCATTCTTAACTTTCTCATGA
Found at i:1644835 original size:51 final size:51
Alignment explanation
Indices: 1644774--1644894 Score: 179
Period size: 51 Copynumber: 2.4 Consensus size: 51
1644764 AGTGATGTCA
* *
1644774 TTCTTAACTTGACTTTTTCCCAGAGAGGACTCAACTTTTTAATAGTATCAT
1 TTCTTAACTTGACTTTCTCCCAGAGAGGACTCAACTTTTCAATAGTATCAT
* * *
1644825 TTCTTAACTTGACTTTCTCGCGGAGAGGAGTCAACTTTTCAATAGTATCAT
1 TTCTTAACTTGACTTTCTCCCAGAGAGGACTCAACTTTTCAATAGTATCAT
* *
1644876 TCCTTAACTTGACTCTCTC
1 TTCTTAACTTGACTTTCTC
1644895 GTGTAGAGAA
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 63 1.00
ACGTcount: A:0.25, C:0.22, G:0.13, T:0.40
Consensus pattern (51 bp):
TTCTTAACTTGACTTTCTCCCAGAGAGGACTCAACTTTTCAATAGTATCAT
Found at i:1644916 original size:51 final size:51
Alignment explanation
Indices: 1644771--1644919 Score: 158
Period size: 51 Copynumber: 2.9 Consensus size: 51
1644761 TTTAGTGATG
* * * * * * *
1644771 TCATT-CTTAACTTGACTTTTTCCCAGAGAGGACTCAACTTTTTAATAGTA
1 TCATTCCTTAACTTGACTCTCTCGCGGAGAGAAGTCAACTTTTCAATAGTA
* * *
1644821 TCATTTCTTAACTTGACTTTCTCGCGGAGAGGAGTCAACTTTTCAATAGTA
1 TCATTCCTTAACTTGACTCTCTCGCGGAGAGAAGTCAACTTTTCAATAGTA
* * *
1644872 TCATTCCTTAACTTGACTCTCTCGTGTAGAGAAGTTAA-TCTTTCAATA
1 TCATTCCTTAACTTGACTCTCTCGCGGAGAGAAGTCAACT-TTTCAATA
1644920 ATGTTATCTT
Statistics
Matches: 86, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
50 6 0.07
51 80 0.93
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (51 bp):
TCATTCCTTAACTTGACTCTCTCGCGGAGAGAAGTCAACTTTTCAATAGTA
Found at i:1646005 original size:268 final size:268
Alignment explanation
Indices: 1645527--1646071 Score: 727
Period size: 268 Copynumber: 2.0 Consensus size: 268
1645517 AAATAAGAGG
* * *
1645527 AGCAAATCACATTCAATTCAATCTTCCCTTAAGAGCAACGAGGTGGATCAAAATTTCCTCAAGTC
1 AGCAAATCACATTCAATTCAATCTTCCCTGAAGAGCAACGAAGTGGATCAAAATTTCATCAAGTC
* * * * *
1645592 TGATATCCCCTAAAGAGTAGTGGGGAATGTTCCTCTTCTTCCAGATTTGGTTTTCCTTAAGAACC
66 TGATATCCCCTAAAGAGTAGTGGGGAATATTCCTCTTCTTCCAGATTTGGTATTACTAAAGAACA
* *** * * *
1645657 ACAAAGAAAATCACGTTCGATTCAATCTTGTTTGAAGAGTAATGAAGTGGATAAAAATTTCCTTA
131 ACAAAGAAAATCAAGTTCGATTCAATCTTCCCTGAAGAGCAACGAAGTGGATAAAAATTTCCTCA
* *
1645722 AGTCTGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTTTCAGATTTGGTATTCCTGAAG
196 AGTCTGATATCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTTTAAGATTTGGTATTCCTGAAG
1645787 AGTAGCGA
261 AGTAGCGA
* * * * *
1645795 AGCAAATTACATTTAATTCAATCTTCCCTGAAGAGCAACGAAGTGGATCAAAGTTTTATCTAGTC
1 AGCAAATCACATTCAATTCAATCTTCCCTGAAGAGCAACGAAGTGGATCAAAATTTCATCAAGTC
* * * * ** *
1645860 TGATCTCCCCTAAAGAGTAGTGGAGTAA-ATTCTTTTTCTTTTAGATTTGGTATTACTAAAGAGC
66 TGATATCCCCTAAAGAGTAGTGG-GGAATATTCCTCTTCTTCCAGATTTGGTATTACTAAAGAAC
* * *
1645924 AACAAA-ACAAATCAAGTTCGATT-AAGTCTTCCCTGAAGAGCAACGAAGTTGATCAAAATTTTC
130 AACAAAGA-AAATCAAGTTCGATTCAA-TCTTCCCTGAAGAGCAACGAAGTGGATAAAAATTTCC
*
1645987 TCAAGTCTGATATCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTTTAAGATTTGGTCTTCCTG
193 TCAAGTCTGATATCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTTTAAGATTTGGTATTCCTG
*
1646052 AAGAGTAGTGA
258 AAGAGTAGCGA
*
1646063 AGTAAATCA
1 AGCAAATCA
1646072 AGCTGGATTC
Statistics
Matches: 238, Mismatches: 36, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
267 3 0.01
268 232 0.97
269 3 0.01
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (268 bp):
AGCAAATCACATTCAATTCAATCTTCCCTGAAGAGCAACGAAGTGGATCAAAATTTCATCAAGTC
TGATATCCCCTAAAGAGTAGTGGGGAATATTCCTCTTCTTCCAGATTTGGTATTACTAAAGAACA
ACAAAGAAAATCAAGTTCGATTCAATCTTCCCTGAAGAGCAACGAAGTGGATAAAAATTTCCTCA
AGTCTGATATCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTTTAAGATTTGGTATTCCTGAAG
AGTAGCGA
Found at i:1646070 original size:134 final size:134
Alignment explanation
Indices: 1645527--1646099 Score: 607
Period size: 134 Copynumber: 4.3 Consensus size: 134
1645517 AAATAAGAGG
* * *
1645527 AGCAAATCACA-TTCAATTCAATCTTCCCTTAAGAGCAACGAGGTGGATCAAAATTTCCTCAAGT
1 AGCAAATCA-AGTTCGATTCAATCTTCCCTGAAGAGCAACGAAGTGGATCAAAATTTCCTCAAGT
* * * * * *
1645591 CTGATATCCCCTAAAGAGTAGTGGGGAATG-TTCCTCTTCTTCCAGATTTGGTTTTCCTTAAGAA
65 CTGATATCCCCTAAAGAGTAGTGGAGCA-GATTCTTCTTCTTTCAGATTTGGTATTCCTGAAG-A
*
1645655 CCA-CAA
128 GCAGCAA
* * *** * * * *
1645661 AGAAAATCACGTTCGATTCAATCTTGTTTGAAGAGTAATGAAGTGGATAAAAATTTCCTTAAGTC
1 AGCAAATCAAGTTCGATTCAATCTTCCCTGAAGAGCAACGAAGTGGATCAAAATTTCCTCAAGTC
* *
1645726 TGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTTTCAGATTTGGTATTCCTGAAGAGTA
66 TGATATCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTTTCAGATTTGGTATTCCTGAAGAGCA
*
1645791 GCGA
131 GCAA
* ** * ** *
1645795 AGCAAATTACA-TTTAATTCAATCTTCCCTGAAGAGCAACGAAGTGGATCAAAGTTTTATCTAGT
1 AGCAAATCA-AGTTCGATTCAATCTTCCCTGAAGAGCAACGAAGTGGATCAAAATTTCCTCAAGT
* * * * * * *
1645859 CTGATCTCCCCTAAAGAGTAGTGGAGTAAATTCTTTTTCTTTTAGATTTGGTATTACTAAAGAGC
65 CTGATATCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTTTCAGATTTGGTATTCCTGAAGAGC
*
1645924 AACAA
130 AGCAA
* * *
1645929 AACAAATCAAGTTCGATT-AAGTCTTCCCTGAAGAGCAACGAAGTTGATCAAAATTTTCTCAAGT
1 AGCAAATCAAGTTCGATTCAA-TCTTCCCTGAAGAGCAACGAAGTGGATCAAAATTTCCTCAAGT
* * *
1645993 CTGATATCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTTTAAGATTTGGTCTTCCTGAAGAGT
65 CTGATATCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTTTCAGATTTGGTATTCCTGAAGAGC
**
1646058 AGTGA
130 AGCAA
* * * * * *
1646063 AGTAAATCAAGCTGGATTCCATCTCCCCTCAAGAGCA
1 AGCAAATCAAGTTCGATTCAATCTTCCCTGAAGAGCA
1646100 TCATAGTGAA
Statistics
Matches: 358, Mismatches: 74, Indels: 14
0.80 0.17 0.03
Matches are distributed among these distances:
133 6 0.02
134 351 0.98
135 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (134 bp):
AGCAAATCAAGTTCGATTCAATCTTCCCTGAAGAGCAACGAAGTGGATCAAAATTTCCTCAAGTC
TGATATCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTTTCAGATTTGGTATTCCTGAAGAGCA
GCAA
Found at i:1647095 original size:27 final size:27
Alignment explanation
Indices: 1647051--1647114 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
1647041 GATGGGATTA
*
1647051 AAAAAAACTAAGAACATTCA-CGGACAT
1 AAAAAAACTAAGAACATTCATC-AACAT
* *
1647078 AAAAAAAC-AGAGAGCATTTATCAACAT
1 AAAAAAACTA-AGAACATTCATCAACAT
1647105 AAAAAAACTA
1 AAAAAAACTA
1647115 GATAGAACCA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
26 1 0.03
27 28 0.90
28 2 0.06
ACGTcount: A:0.59, C:0.16, G:0.09, T:0.16
Consensus pattern (27 bp):
AAAAAAACTAAGAACATTCATCAACAT
Found at i:1649482 original size:56 final size:56
Alignment explanation
Indices: 1649365--1649574 Score: 219
Period size: 56 Copynumber: 3.8 Consensus size: 56
1649355 TTAAATAAGT
* ** *** * * *
1649365 TTTTAAAGAAACTAAGAATGATTTTCAAAAGTTCCTTAACGA-T-TTTCCATTGAA
1 TTTTAAAGAAGCTAAGCCTGATTTTCAGGGGTTTCTTAATGATTATTTCCAATGAA
*
1649419 TTTTAAAGAAGCTTAGCCTGATTTTCAGGGGTTTTCTT-ATGATTATTTCCAATGAA
1 TTTTAAAGAAGCTAAGCCTGATTTTCAGGGG-TTTCTTAATGATTATTTCCAATGAA
* * * *
1649475 TTTTAAAGAAGCTAATCTTGATTTTCAGGGGTTTCTTGATGATTATTTCCAAAAGAA
1 TTTTAAAGAAGCTAAGCCTGATTTTCAGGGGTTTCTTAATGATTATTTCC-AATGAA
* * * *
1649532 TTTTAAAGAAACTAAGCCTAATTTTTAGGTGTTTCTTAATGAT
1 TTTTAAAGAAGCTAAGCCTGATTTTCAGGGGTTTCTTAATGAT
1649575 AACTGTAAAC
Statistics
Matches: 130, Mismatches: 21, Indels: 7
0.82 0.13 0.04
Matches are distributed among these distances:
54 27 0.21
55 12 0.09
56 50 0.38
57 41 0.32
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.41
Consensus pattern (56 bp):
TTTTAAAGAAGCTAAGCCTGATTTTCAGGGGTTTCTTAATGATTATTTCCAATGAA
Found at i:1649739 original size:41 final size:42
Alignment explanation
Indices: 1649633--1649739 Score: 128
Period size: 42 Copynumber: 2.6 Consensus size: 42
1649623 TCTTGATACG
* * *
1649633 TAAGTCCTTCGGGCCAT-CAGTAAGTCTTTCAATCAAGATGTT
1 TAAGTCCTTCGGGCCATCCA-TAAGTCTTTCAAACAAAATGTA
* * *
1649675 TAAATCCTTCGGGTCATCTATAAGTCTTTCAAACAAAATG-A
1 TAAGTCCTTCGGGCCATCCATAAGTCTTTCAAACAAAATGTA
*
1649716 TAAGTCGTTCGGGCCATCCATAAG
1 TAAGTCCTTCGGGCCATCCATAAG
1649740 ACCTTCAGGT
Statistics
Matches: 54, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
41 20 0.37
42 33 0.61
43 1 0.02
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (42 bp):
TAAGTCCTTCGGGCCATCCATAAGTCTTTCAAACAAAATGTA
Found at i:1650076 original size:240 final size:239
Alignment explanation
Indices: 1649632--1650714 Score: 1343
Period size: 240 Copynumber: 4.6 Consensus size: 239
1649622 TTCTTGATAC
* * *
1649632 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCAATCAAGATGTTTAAATCCTTCGGGTCATCTATA
1 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTATA
* * * * * * *
1649697 AGTCTTTCAAACAAAATGATAAGTCGTTCGGGCCATCCATAAGACCTTCAGGTAGGATGTTTTCA
66 AGTCTTTTAAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAAGATGTTTTCA
* * * * *
1649762 CATGATTTTCGAAAAATGAGAAAGTTATTTCCAAAGTTTCACTTTTACATCTTTTCTGAAAACTG
131 CATGATTTTCG-AAAATGAGAAAGTGATTTCCAAAGTTTCTCATTTAAATCTTTTCTGAAAATTG
* * *
1649827 ACATTTCTGAAAAGTAAGAAAACGATTTACAAAGTTTCATACTTA
195 ACTTTTCTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACTTA
* * *
1649872 GTAAGTCCTTCAGGCCATCAGTAAGCCTTTCGAGCATGATGTTTAAATCCTACGGGTCATCTATA
1 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTATA
* * *
1649937 AGT-TATTTGAGCAAGACGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTC
66 AGTCT-TTTAAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAAGATGTTTTC
* *
1650001 ACATGATTTT-GAAAATGAGCAAGTAAATTTCCAAAGTTTCTCATTTAAATCTTTTCTGAAAATA
130 ACATGATTTTCGAAAATGAGAAAGT-GATTTCCAAAGTTTCTCATTTAAATCTTTTCTGAAAAT-
*
1650065 TGACTTTTCTGAAAAGTAAGAAAATGATTTCCAAAGTTTCTTACTTA
193 TGACTTTTCTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACTTA
** * *
1650112 GTAAGTCCTTCGGGATATTAGTAAGTCTTTCAAGCATGATGTTTAAATCCTTCGGGTCATCTATA
1 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTATA
* * **
1650177 AGTGTTTTAAGCAAGATGATAAGTACTTCGGGCCATCCATAAGACCTTTAGGCAAGATGTTTTCA
66 AGTCTTTTAAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAAGATGTTTTCA
*
1650242 CATGATTTTCGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATCTTTTCTGAAAGACTT
131 CATGATTTTCGAAAATGAGAAAGTGATTTCCAAAGTTTCTCATTTAAATCTTTTCTGAAA-A-TT
*
1650307 -ACTTTTCTGAAAAGTAAGAAAACTATTTCCAAAGTTTCTTACTTA
194 GACTTTTCTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACTTA
* * *
1650352 GTAAGTCTTTCGGGCCATCAGTAAGTAC-TTCGAGCATGATGTCTAAATCGTTCGGG---TC---
1 GTAAGTCCTTCGGGCCATCAGTAAGT-CTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTAT
*
1650410 -A------T---C----T-ATAAGTCCTTCGGGTCATCCATAAGACCTTCGGGCAAGATGTTTTC
65 AAGTCTTTTAAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAAGATGTTTTC
* *
1650460 ACATGATTTTTTGAAAATGAGAAAGTGATTTCCAAAGTTTCTCATTTAAACCTTTTCTGAAAATT
130 ACATGA-TTTTCGAAAATGAGAAAGTGATTTCCAAAGTTTCTCATTTAAATCTTTTCTGAAAATT
* * * *
1650525 GATTTTTCTTGGAAAGTAAGAAAGCGATTTCAAAAGTTTCTTACTTA
194 GACTTTTC-TGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACTTA
* * * * * ** *
1650572 GTAAGTCCTTCAGGCCATCAGTAAGTCTTTTGAACATGATATGTAAATATTTCAGGTCATCTATA
1 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTATA
** * * * * * *
1650637 AGTCTTTCGAGTAAGATGATATGTCTTTCGGGCCATCCATAAGGCCTTCGGGCATGATGTTTCCA
66 AGTCTTTTAAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAAGATGTTTTCA
1650702 CATGATTTTCGAA
131 CATGATTTTCGAA
1650715 GAGTAAGAAA
Statistics
Matches: 731, Mismatches: 79, Indels: 66
0.83 0.09 0.08
Matches are distributed among these distances:
218 2 0.00
219 56 0.08
220 132 0.18
223 2 0.00
224 1 0.00
227 2 0.00
233 1 0.00
237 2 0.00
238 12 0.02
239 35 0.05
240 423 0.58
241 62 0.08
242 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (239 bp):
GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTATA
AGTCTTTTAAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCAAGATGTTTTCA
CATGATTTTCGAAAATGAGAAAGTGATTTCCAAAGTTTCTCATTTAAATCTTTTCTGAAAATTGA
CTTTTCTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTACTTA
Found at i:1650427 original size:20 final size:20
Alignment explanation
Indices: 1650402--1650447 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1650392 GTCTAAATCG
* *
1650402 TTCGGGTCATCTATAAGTCC
1 TTCGGGTCATCCATAAGACC
1650422 TTCGGGTCATCCATAAGACC
1 TTCGGGTCATCCATAAGACC
1650442 TTCGGG
1 TTCGGG
1650448 CAAGATGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.26, G:0.24, T:0.30
Consensus pattern (20 bp):
TTCGGGTCATCCATAAGACC
Found at i:1650517 original size:220 final size:219
Alignment explanation
Indices: 1650195--1650645 Score: 647
Period size: 220 Copynumber: 2.1 Consensus size: 219
1650185 AAGCAAGATG
* *
1650195 ATAAGTACTTCGGGCCATCCATAAGACCTTTAGGCAAGATGTTTTCACATGATTTTCGAAAATGA
1 ATAAGTCCTTCGGGCCATCCATAAGACCTTCAGGCAAGATGTTTTCACATGATTTTCGAAAATGA
*
1650260 GAAAGCGATTTCCAAAGTTTCTCATTTAAATCTTTTCTGAAAGACTT-ACTTTTC-TGAAAAGTA
66 GAAAGCGATTTCCAAAGTTTCTCATTTAAACCTTTTCTGAAA-A-TTGACTTTTCTTGAAAAGTA
* * * * *
1650323 AGAAAACTATTTCCAAAGTTTCTTACTTAGTAAGTCTTTCGGGCCATCAGTAAGTAC-TTCGAGC
129 AGAAAACGATTTCAAAAGTTTCTTACTTAGTAAGTCCTTCAGGCCATCAGTAAGT-CTTTCGAAC
* * *
1650387 ATGATGTCTAAATCGTTCGGGTCATCT
193 ATGATATCTAAATAGTTCAGGTCATCT
* * *
1650414 ATAAGTCCTTCGGGTCATCCATAAGACCTTCGGGCAAGATGTTTTCACATGATTTTTTGAAAATG
1 ATAAGTCCTTCGGGCCATCCATAAGACCTTCAGGCAAGATGTTTTCACATGA-TTTTCGAAAATG
* * *
1650479 AGAAAGTGATTTCCAAAGTTTCTCATTTAAACCTTTTCTGAAAATTGATTTTTCTTGGAAAGTAA
65 AGAAAGCGATTTCCAAAGTTTCTCATTTAAACCTTTTCTGAAAATTGACTTTTCTTGAAAAGTAA
* *
1650544 GAAAGCGATTTCAAAAGTTTCTTACTTAGTAAGTCCTTCAGGCCATCAGTAAGTCTTTTGAACAT
130 GAAAACGATTTCAAAAGTTTCTTACTTAGTAAGTCCTTCAGGCCATCAGTAAGTCTTTCGAACAT
* *
1650609 GATATGTAAATATTTCAGGTCATCT
195 GATATCTAAATAGTTCAGGTCATCT
*
1650634 ATAAGTCTTTCG
1 ATAAGTCCTTCG
1650646 AGTAAGATGA
Statistics
Matches: 206, Mismatches: 22, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
218 2 0.01
219 56 0.27
220 148 0.72
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (219 bp):
ATAAGTCCTTCGGGCCATCCATAAGACCTTCAGGCAAGATGTTTTCACATGATTTTCGAAAATGA
GAAAGCGATTTCCAAAGTTTCTCATTTAAACCTTTTCTGAAAATTGACTTTTCTTGAAAAGTAAG
AAAACGATTTCAAAAGTTTCTTACTTAGTAAGTCCTTCAGGCCATCAGTAAGTCTTTCGAACATG
ATATCTAAATAGTTCAGGTCATCT
Found at i:1652807 original size:2 final size:2
Alignment explanation
Indices: 1652800--1652827 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1652790 GCATGTGTTA
1652800 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
1652828 TATGTTCGCT
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:1660475 original size:2 final size:2
Alignment explanation
Indices: 1660468--1660511 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1660458 CAAATATTAA
*
1660468 AT AT AT AT AT AC 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
1660510 AT
1 AT
1660512 TTAGAGTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1662064 original size:3 final size:3
Alignment explanation
Indices: 1662056--1662121 Score: 89
Period size: 3 Copynumber: 22.0 Consensus size: 3
1662046 ATTTTTTATT
* * *
1662056 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TGTA TAT TAA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
1662101 TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
1662122 AAGCAAAATG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
2 2 0.04
3 51 0.93
4 2 0.04
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1662457 original size:95 final size:96
Alignment explanation
Indices: 1662287--1662486 Score: 341
Period size: 95 Copynumber: 2.1 Consensus size: 96
1662277 AATGGCCCTA
*
1662287 AGGTCTTATCATCTTGCTATGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTC
1 AGGTCTTATCATCTTGCTATGTAGGTCTTACAGATGACCCAGAGGCTTTAAATATCAAAAAGCTC
*
1662352 CCGAAGGCTTTTTGAAAACAACCTGCACTGT
66 CCGAAGGCTTTTTGAAAACAACATGCACTGT
*
1662383 AGGTCTTATCATCTTTC-ACTGTAGGTCTTACAGATGA-CCAGAGGCTTTAAATATCAAAAAGCT
1 AGGTCTTATCATCTTGCTA-TGTAGGTCTTACAGATGACCCAGAGGCTTTAAATATCAAAAAGCT
*
1662446 CCCGAAGGCTTTTTGAAAACATCATGCACTGT
65 CCCGAAGGCTTTTTGAAAACAACATGCACTGT
1662478 AGGTCTTAT
1 AGGTCTTAT
1662487 GGATGGCCTT
Statistics
Matches: 99, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
95 65 0.66
96 34 0.34
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.31
Consensus pattern (96 bp):
AGGTCTTATCATCTTGCTATGTAGGTCTTACAGATGACCCAGAGGCTTTAAATATCAAAAAGCTC
CCGAAGGCTTTTTGAAAACAACATGCACTGT
Found at i:1662590 original size:116 final size:116
Alignment explanation
Indices: 1662383--1662950 Score: 931
Period size: 116 Copynumber: 4.9 Consensus size: 116
1662373 CCTGCACTGT
* * *
1662383 AGGTCTTATCATCTTTCACTGTAGGTCTTACAGATGA-CCAGAGGCTTTAAATATCAAAAAGCTC
1 AGGTCTTATCATCTTGCACTATAGGTCTTACAGATGACCCGGAGGCTTTAAATATCAAAAAGCTC
* *
1662447 CCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTATGGATGGCCTTG
66 CCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGGCCCTG
* *
1662498 AGGTCTTATCATCTTGCATTATAGGTCTTACAGATAACCCGGAGGCTTTAAATATCAAAAAGCTC
1 AGGTCTTATCATCTTGCACTATAGGTCTTACAGATGACCCGGAGGCTTTAAATATCAAAAAGCTC
*
1662563 CCGAAGGCTTTTTGAAAACATCCTGCACTATAGGTCTTATGGATGGCCCTG
66 CCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGGCCCTG
* **
1662614 AGGTCTTATCAGCTTGCACTATAGGTCTTATGGATGACCCGGAGGCTTTAAATATCAAAAAGCTC
1 AGGTCTTATCATCTTGCACTATAGGTCTTACAGATGACCCGGAGGCTTTAAATATCAAAAAGCTC
* *
1662679 CCGAAGGCTTTTTGAAAACAACTTGCACTGTAGGTCTTATGGATGGCCCTG
66 CCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGGCCCTG
* *
1662730 AGGTCTTATCATCTTGTACTGTAGGTCTTACAGATGACCCGGAGGCTTTAAATATCAAAAAGCTC
1 AGGTCTTATCATCTTGCACTATAGGTCTTACAGATGACCCGGAGGCTTTAAATATCAAAAAGCTC
* * * *
1662795 CCGAAGACTTTTTGAAAACATCCTGTACTGTAGGTCTTATGGATGGTCATG
66 CCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGGCCCTG
*
1662846 AGGTCTTATCATCTTGCACTATAGGTCTTACAGATGACCCAGAGGCTTTAAATATCAAAAAGCTC
1 AGGTCTTATCATCTTGCACTATAGGTCTTACAGATGACCCGGAGGCTTTAAATATCAAAAAGCTC
* *
1662911 TCGAAGGCTCTTTGAAAACATCCTGCACTGTAGGTCTTAT
66 CCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTAT
1662951 AAATGACCCG
Statistics
Matches: 418, Mismatches: 34, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
115 33 0.08
116 385 0.92
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (116 bp):
AGGTCTTATCATCTTGCACTATAGGTCTTACAGATGACCCGGAGGCTTTAAATATCAAAAAGCTC
CCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGGCCCTG
Found at i:1662981 original size:74 final size:74
Alignment explanation
Indices: 1662855--1663024 Score: 250
Period size: 74 Copynumber: 2.3 Consensus size: 74
1662845 GAGGTCTTAT
* * * * *
1662855 CATCTTGCACTATAGGTCTTACAGATGACCCAGAGGCTTTAAATATCAAAAAGCTCTCGAAGGCT
1 CATCATGCACTGTAGGTCTTATAAATGACCCAGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
1662920 CTTTGAAAA
66 CTTTGAAAA
* * *
1662929 CATCCTGCACTGTAGGTCTTATAAATGACCCGGATGCTTTAAATATCAAAAAGCTCCCGAAGGCT
1 CATCATGCACTGTAGGTCTTATAAATGACCCAGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
*
1662994 TTTTGAAAA
66 CTTTGAAAA
*
1663003 CTTCATGCACTGTAGGTCTTAT
1 CATCATGCACTGTAGGTCTTAT
1663025 GGATGTGGGA
Statistics
Matches: 86, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
74 86 1.00
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (74 bp):
CATCATGCACTGTAGGTCTTATAAATGACCCAGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
CTTTGAAAA
Found at i:1663704 original size:22 final size:22
Alignment explanation
Indices: 1663681--1663757 Score: 109
Period size: 22 Copynumber: 3.5 Consensus size: 22
1663671 TAAAGCTTTT
* *
1663681 ATCTTTGAAAATAGAATCTATT
1 ATCTTTGAAGATAGAATCTATC
* *
1663703 ATCTTTGAAGAGAGAAGCTATC
1 ATCTTTGAAGATAGAATCTATC
1663725 ATCTTTGAAGATAGAATCTATC
1 ATCTTTGAAGATAGAATCTATC
*
1663747 ATATTTGAAGA
1 ATCTTTGAAGA
1663758 ATGTAGATGT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
ATCTTTGAAGATAGAATCTATC
Done.