Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold193
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: 3104049
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.32
Warning! 172765 characters in sequence are not A, C, G, or T
File 10 of 18
Found at i:1728899 original size:22 final size:22
Alignment explanation
Indices: 1728864--1728905 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1728854 ACTTATGTGA
*
1728864 TTTTTTAAACAATTTTCTATTT
1 TTTTTTAAACAATTTACTATTT
1728886 TTTTTTGAAA-AATTTACTAT
1 TTTTTT-AAACAATTTACTAT
1728906 AAAATAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.60
Consensus pattern (22 bp):
TTTTTTAAACAATTTACTATTT
Found at i:1729006 original size:14 final size:14
Alignment explanation
Indices: 1728987--1729042 Score: 60
Period size: 14 Copynumber: 3.9 Consensus size: 14
1728977 TTTTATATTT
*
1728987 ATTTTATGTTTAAA
1 ATTTTATATTTAAA
*
1729001 ATTTTA-ATTATTAA
1 ATTTTATATT-TAAA
1729015 ATATTTATAATTTAAA
1 AT-TTTAT-ATTTAAA
1729031 ATTTTATATTTA
1 ATTTTATATTTA
1729043 CATATATATA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
13 2 0.06
14 16 0.46
15 9 0.26
16 5 0.14
17 3 0.09
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (14 bp):
ATTTTATATTTAAA
Found at i:1729029 original size:15 final size:16
Alignment explanation
Indices: 1729011--1729055 Score: 51
Period size: 14 Copynumber: 3.0 Consensus size: 16
1729001 ATTTTAATTA
1729011 TTAAATATTTATA-AT
1 TTAAATATTTATATAT
1729026 TTAAA-ATTT-TATAT
1 TTAAATATTTATATAT
* *
1729040 TTACATATATATATAT
1 TTAAATATTTATATAT
1729056 ATAATAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
13 2 0.08
14 10 0.40
15 8 0.32
16 5 0.20
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAAATATTTATATAT
Found at i:1729191 original size:16 final size:16
Alignment explanation
Indices: 1729170--1729210 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
1729160 TGAAATGACT
1729170 TATCAAAAGATACCAA
1 TATCAAAAGATACCAA
**
1729186 TATCAAAATCTACCAA
1 TATCAAAAGATACCAA
1729202 TATCGAAAA
1 TATC-AAAA
1729211 AAATAATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.54, C:0.20, G:0.05, T:0.22
Consensus pattern (16 bp):
TATCAAAAGATACCAA
Found at i:1730338 original size:18 final size:19
Alignment explanation
Indices: 1730315--1730358 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
1730305 ATTAGAAAAT
*
1730315 TAACAATTC-AAAAAATTA
1 TAACAAATCTAAAAAATTA
*
1730333 TAACAAATCTATAAAATTA
1 TAACAAATCTAAAAAATTA
1730352 -AACAAAT
1 TAACAAAT
1730359 ATTAAAATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.27
Consensus pattern (19 bp):
TAACAAATCTAAAAAATTA
Found at i:1730356 original size:36 final size:37
Alignment explanation
Indices: 1730261--1730356 Score: 94
Period size: 38 Copynumber: 2.6 Consensus size: 37
1730251 TAAATTCAAG
*
1730261 AAAAAAA--AGAAAATCCAAACAATTCAAAAAAGTTTAT
1 AAAAAAATTAGAAAAT-TAAACAATTCAAAAAAG-TTAT
1730298 AAAAAAAATTAGAAAATT-AACAATTCAAAAAA-TTAT
1 -AAAAAAATTAGAAAATTAAACAATTCAAAAAAGTTAT
* *
1730334 -AACAAATCTATAAAATTAAACAA
1 AAAAAAAT-TAGAAAATTAAACAA
1730357 ATATTAAAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
34 6 0.12
35 8 0.16
36 9 0.18
38 21 0.41
40 7 0.14
ACGTcount: A:0.66, C:0.09, G:0.03, T:0.22
Consensus pattern (37 bp):
AAAAAAATTAGAAAATTAAACAATTCAAAAAAGTTAT
Found at i:1730450 original size:24 final size:24
Alignment explanation
Indices: 1730404--1730450 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
1730394 TAAGAAGATA
***
1730404 TTAAAATTTAAAAAAATTTAAATT
1 TTAAAATTTAAAAAAACACAAATT
*
1730428 TTAAAATTTTAAAAAACACAAAT
1 TTAAAATTTAAAAAAACACAAAT
1730451 ATATATATAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (24 bp):
TTAAAATTTAAAAAAACACAAATT
Found at i:1730619 original size:30 final size:30
Alignment explanation
Indices: 1730583--1730642 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
1730573 AAGGAGAAAA
1730583 AGGGGAGGAGGGAGGGCTTCGACGTCAGTC
1 AGGGGAGGAGGGAGGGCTTCGACGTCAGTC
1730613 AGGGGAGGAGGGAGGGCTTCGACGTCAGTC
1 AGGGGAGGAGGGAGGGCTTCGACGTCAGTC
1730643 GGCTATAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.20, C:0.17, G:0.50, T:0.13
Consensus pattern (30 bp):
AGGGGAGGAGGGAGGGCTTCGACGTCAGTC
Found at i:1731219 original size:25 final size:26
Alignment explanation
Indices: 1731185--1731234 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
1731175 GCAGATTTTA
* *
1731185 AATATTTATA-AATTTTAATTAAATT
1 AATAATTATATAATTTAAATTAAATT
1731210 AATAATTATATAATTTAAATTAAAT
1 AATAATTATATAATTTAAATTAAAT
1731235 CATATTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
AATAATTATATAATTTAAATTAAATT
Found at i:1731938 original size:23 final size:23
Alignment explanation
Indices: 1731912--1731982 Score: 89
Period size: 23 Copynumber: 3.3 Consensus size: 23
1731902 ACTTGACTTG
1731912 AATATAATATAAAAAATAAT-TAA
1 AATATAATATAAAAAATAATAT-A
*
1731935 AATATAATATAAAAAATAATATT
1 AATATAATATAAAAAATAATATA
1731958 AATAT-A-AT-AAAAAT-ATATA
1 AATATAATATAAAAAATAATATA
1731977 AATATA
1 AATATA
1731983 TCAATATGTG
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
19 9 0.20
20 6 0.14
21 2 0.05
22 1 0.02
23 25 0.57
24 1 0.02
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (23 bp):
AATATAATATAAAAAATAATATA
Found at i:1731941 original size:11 final size:11
Alignment explanation
Indices: 1731912--1731974 Score: 56
Period size: 11 Copynumber: 5.5 Consensus size: 11
1731902 ACTTGACTTG
1731912 AATATAATATAA
1 AATATAAT-TAA
*
1731924 AAAATAATTAA
1 AATATAATTAA
1731935 AATATAATATAA
1 AATATAAT-TAA
* *
1731947 AAAATAA-TATT
1 AATATAATTA-A
*
1731958 AATATAATAAA
1 AATATAATTAA
1731969 AATATA
1 AATATA
1731975 TAAATATATC
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
10 2 0.05
11 22 0.54
12 17 0.41
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AATATAATTAA
Found at i:1732437 original size:2 final size:2
Alignment explanation
Indices: 1732430--1732474 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1732420 AACTTCTGTA
1732430 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1732472 AT A
1 AT A
1732475 AAGAATGTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1732554 original size:169 final size:171
Alignment explanation
Indices: 1732282--1732594 Score: 567
Period size: 169 Copynumber: 1.8 Consensus size: 171
1732272 AGAGCAGTCA
1732282 ATATATATATATATATATATATAAAGAATGTAAAAATTTTTTAAATTTATGAAAATAATTATTGT
1 ATATATATATATATATATATATAAAGAATGTAAAAATTTTTTAAATTTATGAAAATAATTATTGT
* * * *
1732347 TATTTATTATGATTTTAAATTATTAATAATATTTTTATGATTAATAAAAAGTTATTT-TTTTACA
66 TATTTACTATAATTTTAAATTATTAACAATACTTTTATGATTAATAAAAAGTTATTTCTTTTACA
*
1732411 TGTAAGATAAACTTCTGTAATATATATATATATATATATAT
131 AGTAAGATAAACTTCTGTAATATATATATATATATATATAT
1732452 ATATATATATATATATATATATAAAGAATGTAAAAA-TTTTTAAATTTATGAAAATAATTATTGT
1 ATATATATATATATATATATATAAAGAATGTAAAAATTTTTTAAATTTATGAAAATAATTATTGT
1732516 TATTTACTATAATTTTAAATTATTAACAATACTTTTATGATTAATAAAAAGTTATTTCTTTTACA
66 TATTTACTATAATTTTAAATTATTAACAATACTTTTATGATTAATAAAAAGTTATTTCTTTTACA
1732581 AGTAAGATAAACTT
131 AGTAAGATAAACTT
1732595 AAACATTAAA
Statistics
Matches: 137, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
169 81 0.59
170 56 0.41
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.47
Consensus pattern (171 bp):
ATATATATATATATATATATATAAAGAATGTAAAAATTTTTTAAATTTATGAAAATAATTATTGT
TATTTACTATAATTTTAAATTATTAACAATACTTTTATGATTAATAAAAAGTTATTTCTTTTACA
AGTAAGATAAACTTCTGTAATATATATATATATATATATAT
Found at i:1732858 original size:18 final size:17
Alignment explanation
Indices: 1732834--1732904 Score: 71
Period size: 15 Copynumber: 4.3 Consensus size: 17
1732824 ATAATGTGAT
*
1732834 ATAAT-ATAATTTACTA
1 ATAATAATAATTTAATA
1732850 ATAATATATAAATTTATATA
1 ATAATA-AT-AATTTA-ATA
1732870 ATAATAATAA--TAATA
1 ATAATAATAATTTAATA
1732885 ATAATAATAA--TAATA
1 ATAATAATAATTTAATA
1732900 ATAAT
1 ATAAT
1732905 GTATAAAATA
Statistics
Matches: 50, Mismatches: 1, Indels: 9
0.83 0.02 0.15
Matches are distributed among these distances:
15 23 0.46
16 7 0.14
18 4 0.08
19 8 0.16
20 8 0.16
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (17 bp):
ATAATAATAATTTAATA
Found at i:1732873 original size:3 final size:3
Alignment explanation
Indices: 1732867--1732904 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1732857 ATAAATTTAT
1732867 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1732905 GTATAAAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1732876 original size:16 final size:18
Alignment explanation
Indices: 1732834--1732897 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 18
1732824 ATAATGTGAT
1732834 ATAATATAATTTACTAATA
1 ATAATA-AATTTACTAATA
*
1732853 ATATATAAATTTATATAATA
1 ATA-ATAAATTTA-CTAATA
* *
1732873 ATAAT-AATAATAATAATA
1 ATAATAAAT-TTACTAATA
1732891 ATAATAA
1 ATAATAA
1732898 TAATAATGTA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
18 14 0.36
19 14 0.36
20 11 0.28
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (18 bp):
ATAATAAATTTACTAATA
Found at i:1733052 original size:3 final size:3
Alignment explanation
Indices: 1733007--1733034 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1732997 CAACAACAAC
1733007 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1733035 TGCTTTTATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1738235 original size:7 final size:7
Alignment explanation
Indices: 1738223--1738251 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
1738213 GTAATTACTC
1738223 CCATCAT
1 CCATCAT
1738230 CCATCAT
1 CCATCAT
1738237 CCATCAT
1 CCATCAT
1738244 CCATCAT
1 CCATCAT
1738251 C
1 C
1738252 GTTAGAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.45, G:0.00, T:0.28
Consensus pattern (7 bp):
CCATCAT
Found at i:1739826 original size:16 final size:16
Alignment explanation
Indices: 1739793--1739857 Score: 51
Period size: 16 Copynumber: 3.8 Consensus size: 16
1739783 TAATTAAATC
*
1739793 AAATAAA-TAAACTCAT
1 AAATAAATTAAAAT-AT
1739809 AAATAAATTAAAATAT
1 AAATAAATTAAAATAT
*
1739825 AATTAAATTATCTAAATAT
1 AAATAAATTA---AAATAT
1739844 AATATAAAATTAAA
1 AA-AT-AAATTAAA
1739858 TCAAATTCAC
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
16 18 0.45
17 5 0.12
18 2 0.05
19 8 0.20
20 1 0.03
21 6 0.15
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATAAATTAAAATAT
Found at i:1740423 original size:39 final size:39
Alignment explanation
Indices: 1740366--1740446 Score: 119
Period size: 39 Copynumber: 2.1 Consensus size: 39
1740356 TCAAGTTGCT
*
1740366 TTTTTATGTCCTGCAATGATTATTCAGATGC-CCTTTTTG
1 TTTTTATGTCCAGCAATGATTATTCAGATGCTCC-TTTTG
* *
1740405 TTTTTATGTTCAGTAATGATTATTCAGATGCTCCTTTTG
1 TTTTTATGTCCAGCAATGATTATTCAGATGCTCCTTTTG
1740444 TTT
1 TTT
1740447 ATGAAAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 36 0.95
40 2 0.05
ACGTcount: A:0.19, C:0.15, G:0.15, T:0.52
Consensus pattern (39 bp):
TTTTTATGTCCAGCAATGATTATTCAGATGCTCCTTTTG
Found at i:1740526 original size:2 final size:2
Alignment explanation
Indices: 1740514--1740550 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1740504 CTTCAATTTG
*
1740514 AT AT AT TT 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
1740551 GAAACTAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1740887 original size:13 final size:14
Alignment explanation
Indices: 1740862--1740893 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
1740852 TTCAACCTTG
1740862 AATAAAGATATAAA
1 AATAAAGATATAAA
1740876 AATAAA-ATATAAA
1 AATAAAGATATAAA
1740889 AATAA
1 AATAA
1740894 TAATTAGATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (14 bp):
AATAAAGATATAAA
Found at i:1741646 original size:19 final size:18
Alignment explanation
Indices: 1741607--1741647 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
1741597 ATCAAACAAA
* *
1741607 TATTTTGTTTTTTATTTT
1 TATTTTGTTTTTTAATGT
1741625 TATTTTGTTTTTTTAATGT
1 TATTTTG-TTTTTTAATGT
1741644 TATT
1 TATT
1741648 GTAGCCTACG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (18 bp):
TATTTTGTTTTTTAATGT
Found at i:1743232 original size:15 final size:16
Alignment explanation
Indices: 1743202--1743235 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
1743192 ATTAAAATAT
1743202 TAATATAATTTTTTTAA
1 TAATATAA-TTTTTTAA
1743219 TAATATAA-TTTTTAA
1 TAATATAATTTTTTAA
1743234 TA
1 TA
1743236 TTTATTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TAATATAATTTTTTAA
Found at i:1743316 original size:24 final size:23
Alignment explanation
Indices: 1743232--1743316 Score: 62
Period size: 25 Copynumber: 3.4 Consensus size: 23
1743222 TATAATTTTT
1743232 AATATTTATTTTTGAATATTATTAA
1 AATATTTATTTTT-AA-ATTATTAA
* * ** *
1743257 ACATATATATTTATATTTTAATAA
1 A-ATATTTATTTTTAAATTATTAA
*
1743281 TATAATATTATTTTTAAATTATTAA
1 AAT-AT-TTATTTTTAAATTATTAA
1743306 AATGATTTATT
1 AAT-ATTTATT
1743317 ATTTTAATAA
Statistics
Matches: 44, Mismatches: 13, Indels: 7
0.69 0.20 0.11
Matches are distributed among these distances:
23 2 0.05
24 13 0.30
25 19 0.43
26 10 0.23
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.54
Consensus pattern (23 bp):
AATATTTATTTTTAAATTATTAA
Found at i:1743338 original size:16 final size:17
Alignment explanation
Indices: 1743313--1743344 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1743303 TAAAATGATT
1743313 TATTATTTTAATAAAAA
1 TATTATTTTAATAAAAA
1743330 TATTA-TTTAATAAAA
1 TATTATTTTAATAAAA
1743345 TAATATATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TATTATTTTAATAAAAA
Found at i:1743362 original size:16 final size:16
Alignment explanation
Indices: 1743313--1743346 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
1743303 TAAAATGATT
1743313 TATTATTTTAATAAAAA
1 TATTATTTTAAT-AAAA
1743330 TATTA-TTTAATAAAA
1 TATTATTTTAATAAAA
1743345 TA
1 TA
1743347 ATATATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 6 0.35
17 5 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATTATTTTAATAAAA
Found at i:1743488 original size:45 final size:47
Alignment explanation
Indices: 1743415--1743517 Score: 115
Period size: 45 Copynumber: 2.2 Consensus size: 47
1743405 AAACTGTAAA
* *
1743415 ATAATATTTTAATAATAATTATAATATTTTAAAATATTTAA-A-TAAT
1 ATAATATTTTAATAATAAATATAATATTTT-AAACATTTAATACTAAT
** *
1743461 -TAATATTTTAATAA-AAATAGTGTTATTTTAAGCATTTAATACTAAT
1 ATAATATTTTAATAATAAATA-TAATATTTTAAACATTTAATACTAAT
1743507 ATAATATTTTA
1 ATAATATTTTA
1743518 GAATTAACTA
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
44 12 0.25
45 22 0.46
46 4 0.08
47 10 0.21
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (47 bp):
ATAATATTTTAATAATAAATATAATATTTTAAACATTTAATACTAAT
Found at i:1744625 original size:40 final size:39
Alignment explanation
Indices: 1744570--1744654 Score: 143
Period size: 40 Copynumber: 2.2 Consensus size: 39
1744560 CATTGTAGTG
* *
1744570 TATCATATTCACATGTTTAACGTGCTATGAATTGGAGGTT
1 TATCATATTCACATGTTTAACGTGATATGAATTGCAGG-T
1744610 TATCATATTCACATGTTTAACGTGATATGAATTGCAGGT
1 TATCATATTCACATGTTTAACGTGATATGAATTGCAGGT
1744649 TATCAT
1 TATCAT
1744655 TTTGGTGAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
39 7 0.16
40 36 0.84
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (39 bp):
TATCATATTCACATGTTTAACGTGATATGAATTGCAGGT
Found at i:1752231 original size:13 final size:13
Alignment explanation
Indices: 1752213--1752238 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1752203 CATTTTATGG
1752213 TGTATCGATACAT
1 TGTATCGATACAT
1752226 TGTATCGATACAT
1 TGTATCGATACAT
1752239 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1752235 original size:33 final size:32
Alignment explanation
Indices: 1752193--1752256 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
1752183 TACAAGCTAA
*
1752193 TGTATCGATACAT-TTTATGGTGTATCGATACAT
1 TGTATCGATACATACTT-T-GTGTATCGATACAT
1752226 TGTATCGATACATACTTTGTGTATCGATACA
1 TGTATCGATACATACTTTGTGTATCGATACA
1752257 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 13 0.45
33 14 0.48
34 2 0.07
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (32 bp):
TGTATCGATACATACTTTGTGTATCGATACAT
Found at i:1752316 original size:21 final size:21
Alignment explanation
Indices: 1752290--1752342 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
1752280 CCAATAAGCT
1752290 GTATCGATACATCTTTTTCAA
1 GTATCGATACATCTTTTTCAA
1752311 GTATCGATACATCTTTTTCAA
1 GTATCGATACATCTTTTTCAA
1752332 GTATCGATACA
1 GTATCGATACA
1752343 ATGCAACATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (21 bp):
GTATCGATACATCTTTTTCAA
Found at i:1752368 original size:13 final size:13
Alignment explanation
Indices: 1752350--1752374 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1752340 ACAATGCAAC
1752350 ATGTATCGATACA
1 ATGTATCGATACA
1752363 ATGTATCGATAC
1 ATGTATCGATAC
1752375 TGTGCAACAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1752369 original size:33 final size:33
Alignment explanation
Indices: 1752332--1752397 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
1752322 TCTTTTTCAA
1752332 GTATCGATACAATGCAACATGTATCGATACAAT
1 GTATCGATACAATGCAACATGTATCGATACAAT
**
1752365 GTATCGATACTGTGCAACATGTATCGATACAAT
1 GTATCGATACAATGCAACATGTATCGATACAAT
1752398 TAAATGTGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (33 bp):
GTATCGATACAATGCAACATGTATCGATACAAT
Found at i:1752666 original size:15 final size:15
Alignment explanation
Indices: 1752646--1752684 Score: 69
Period size: 15 Copynumber: 2.5 Consensus size: 15
1752636 ATTTTCGGTT
1752646 TTATTCAATTCTTTG
1 TTATTCAATTCTTTG
1752661 TTATTCAATTCTTTG
1 TTATTCAATTCTTTG
1752676 TTATATCAA
1 TTAT-TCAA
1752685 AACCAAGATC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 19 0.83
16 4 0.17
ACGTcount: A:0.26, C:0.13, G:0.05, T:0.56
Consensus pattern (15 bp):
TTATTCAATTCTTTG
Found at i:1760939 original size:20 final size:21
Alignment explanation
Indices: 1760908--1760946 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
1760898 ATGATTTCCC
1760908 TTGTGAATGTATCGATACAAT
1 TTGTGAATGTATCGATACAAT
1760929 TTGTG-ATGTATCGATACA
1 TTGTGAATGTATCGATACA
1760947 TGCATTTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (21 bp):
TTGTGAATGTATCGATACAAT
Found at i:1761026 original size:13 final size:13
Alignment explanation
Indices: 1761008--1761033 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1760998 CATTTTATGG
1761008 TGTATCGATACAT
1 TGTATCGATACAT
1761021 TGTATCGATACAT
1 TGTATCGATACAT
1761034 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1761030 original size:33 final size:32
Alignment explanation
Indices: 1760988--1761051 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
1760978 TACAAGCCAA
*
1760988 TGTATCGATACAT-TTTATGGTGTATCGATACAT
1 TGTATCGATACATACTT-T-GTGTATCGATACAT
1761021 TGTATCGATACATACTTTGTGTATCGATACA
1 TGTATCGATACATACTTTGTGTATCGATACA
1761052 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 13 0.45
33 14 0.48
34 2 0.07
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (32 bp):
TGTATCGATACATACTTTGTGTATCGATACAT
Found at i:1761142 original size:13 final size:13
Alignment explanation
Indices: 1761124--1761148 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1761114 ACAATGCAAC
1761124 ATGTATCGATACA
1 ATGTATCGATACA
1761137 ATGTATCGATAC
1 ATGTATCGATAC
1761149 TGTGCAACAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1761143 original size:33 final size:33
Alignment explanation
Indices: 1761106--1761171 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
1761096 TATTTTTCAA
1761106 GTATCGATACAATGCAACATGTATCGATACAAT
1 GTATCGATACAATGCAACATGTATCGATACAAT
**
1761139 GTATCGATACTGTGCAACATGTATCGATACAAT
1 GTATCGATACAATGCAACATGTATCGATACAAT
1761172 TAAATGTGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (33 bp):
GTATCGATACAATGCAACATGTATCGATACAAT
Found at i:1761440 original size:15 final size:15
Alignment explanation
Indices: 1761420--1761458 Score: 69
Period size: 15 Copynumber: 2.5 Consensus size: 15
1761410 ATTTTCGGTT
1761420 TTATTCAATTCTTTG
1 TTATTCAATTCTTTG
1761435 TTATTCAATTCTTTG
1 TTATTCAATTCTTTG
1761450 TTATATCAA
1 TTAT-TCAA
1761459 AACCAAGATC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 19 0.83
16 4 0.17
ACGTcount: A:0.26, C:0.13, G:0.05, T:0.56
Consensus pattern (15 bp):
TTATTCAATTCTTTG
Found at i:1763604 original size:33 final size:33
Alignment explanation
Indices: 1763558--1763622 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1763548 TTAGAAGCAA
* *
1763558 TGTATCGATACAAT-TCATCATGTATCGATACAT
1 TGTATCGACACAATGT-ACCATGTATCGATACAT
1763591 TGTATCGACACAATGTACCATGTATCGATACA
1 TGTATCGACACAATGTACCATGTATCGATACA
1763623 AACAGTGGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (33 bp):
TGTATCGACACAATGTACCATGTATCGATACAT
Found at i:1763696 original size:19 final size:19
Alignment explanation
Indices: 1763652--1763707 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
1763642 CTGCCAGTTT
**
1763652 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
*
1763672 CATGTATCAATACAATGAA
1 CATGTATCGATACAATGAA
1763691 CATGTATCGATACAATG
1 CATGTATCGATACAATG
1763708 TATCGATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1763710 original size:13 final size:13
Alignment explanation
Indices: 1763692--1763718 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1763682 TACAATGAAC
1763692 ATGTATCGATACA
1 ATGTATCGATACA
1763705 ATGTATCGATACA
1 ATGTATCGATACA
1763718 A
1 A
1763719 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1771963 original size:19 final size:19
Alignment explanation
Indices: 1771919--1771974 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
1771909 CTGCCGGTTT
* **
1771919 CATGTATCAATACAATTGTC
1 CATGTATCGATACAA-TGAA
1771939 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
1771958 CATGTATCGATACAATG
1 CATGTATCGATACAATG
1771975 TATCGATACA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 19 0.58
20 14 0.42
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1771977 original size:13 final size:13
Alignment explanation
Indices: 1771959--1771985 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1771949 TACAATGAAC
1771959 ATGTATCGATACA
1 ATGTATCGATACA
1771972 ATGTATCGATACA
1 ATGTATCGATACA
1771985 A
1 A
1771986 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1783650 original size:14 final size:12
Alignment explanation
Indices: 1783630--1783701 Score: 67
Period size: 12 Copynumber: 5.8 Consensus size: 12
1783620 ACCTTCTCTT
* *
1783630 CAAAAAAAAGAG
1 CAAAAAAAAAAA
1783642 CAAAAAAAAAAA
1 CAAAAAAAAAAA
1783654 -AGGAAAAAAAAAA
1 CA--AAAAAAAAAA
1783667 -AATAAAAAAAAA
1 CAA-AAAAAAAAA
1783679 CAAAAAAACAAAA
1 CAAAAAAA-AAAA
*
1783692 CAAAGAAAAA
1 CAAAAAAAAA
1783702 GAGAGAAAAG
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
11 2 0.04
12 26 0.50
13 24 0.46
ACGTcount: A:0.85, C:0.07, G:0.07, T:0.01
Consensus pattern (12 bp):
CAAAAAAAAAAA
Found at i:1783666 original size:13 final size:13
Alignment explanation
Indices: 1783631--1783717 Score: 77
Period size: 14 Copynumber: 6.3 Consensus size: 13
1783621 CCTTCTCTTC
*
1783631 AAAAAAAAGAGCAA
1 AAAAAAAAAAG-AA
1783645 AAAAAAAAAAGGAA
1 AAAAAAAAAA-GAA
*
1783659 AAAAAAAAAATAA
1 AAAAAAAAAAGAA
1783672 AAAAAAACAAA-AA
1 AAAAAAA-AAAGAA
*
1783685 AACAAAACAAAGAA
1 AA-AAAAAAAAGAA
*
1783699 AAAGAGAGAAAAGAA
1 AAA-A-AAAAAAGAA
1783714 AAAA
1 AAAA
1783718 CCTACTTAAG
Statistics
Matches: 62, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
13 17 0.27
14 34 0.55
15 11 0.18
ACGTcount: A:0.84, C:0.05, G:0.10, T:0.01
Consensus pattern (13 bp):
AAAAAAAAAAGAA
Found at i:1783668 original size:15 final size:15
Alignment explanation
Indices: 1783631--1783717 Score: 59
Period size: 16 Copynumber: 5.5 Consensus size: 15
1783621 CCTTCTCTTC
*
1783631 AAAAAAAAGAGCAAAA
1 AAAAAAAAG-GAAAAA
1783647 AAAAAAAAGGAAAAA
1 AAAAAAAAGGAAAAA
*
1783662 AAAAAAATA-AAAAAA
1 AAAAAAA-AGGAAAAA
**
1783677 AACAAAAAAACAAAACA
1 AA-AAAAAAGGAAAA-A
* *
1783694 AAGAAAAAGAGAGAAA
1 AAAAAAAAG-GAAAAA
*
1783710 AGAAAAAA
1 AAAAAAAA
1783718 CCTACTTAAG
Statistics
Matches: 57, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
15 20 0.35
16 31 0.54
17 6 0.11
ACGTcount: A:0.84, C:0.05, G:0.10, T:0.01
Consensus pattern (15 bp):
AAAAAAAAGGAAAAA
Found at i:1783717 original size:1 final size:1
Alignment explanation
Indices: 1783643--1783701 Score: 55
Period size: 1 Copynumber: 59.0 Consensus size: 1
1783633 AAAAAAGAGC
** * * * * *
1783643 AAAAAAAAAAAAGGAAAAAAAAAAAATAAAAAAAAACAAAAAAACAAAACAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1783702 GAGAGAAAAG
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.88, C:0.05, G:0.05, T:0.02
Consensus pattern (1 bp):
A
Found at i:1784767 original size:55 final size:55
Alignment explanation
Indices: 1784683--1785288 Score: 815
Period size: 55 Copynumber: 10.9 Consensus size: 55
1784673 TCCGCTTTTT
*
1784683 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCGCCTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTCC
*
1784738 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTCC
**
1784793 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTCC
**
1784848 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTCC
**
1784903 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGTGCCTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTCC
* **
1784958 AGTCCTCAAAGAGCAGGACA-CTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTT
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTCC
* * **
1785013 AGTCCCCGAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTCC
* * ** *
1785068 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTCC
*** * * * *
1785123 AGTCCTCAAAGAGCAGGATGCTTTTTATTTTCAAAGCCTATACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGA--C---ACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTCC
* *
1785184 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTCC
* *
1785239 AGTCCTCAAAGAGCAGGACGCCT-TTCAAAGCCCACACGAGTTGGTGGCAC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCAC
1785289 TTTTTACTCC
Statistics
Matches: 497, Mismatches: 42, Indels: 24
0.88 0.07 0.04
Matches are distributed among these distances:
54 8 0.02
55 433 0.87
56 9 0.02
57 1 0.00
59 1 0.00
60 4 0.01
61 41 0.08
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTCC
Found at i:1785206 original size:26 final size:26
Alignment explanation
Indices: 1785176--1785265 Score: 67
Period size: 26 Copynumber: 3.3 Consensus size: 26
1785166 AAGTTGGTGG
1785176 CACCTTTCAGTCCCCAAAGAGCAGGA
1 CACCTTTCAGTCCCCAAAGAGCAGGA
* * **
1785202 CACCTCTTAAAG-CCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCC-CA-AAG-AGCAGGA
*
1785231 CACCTTTCAGTCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCCCAAAGAGCAGGA
*
1785257 CGCCTTTCA
1 CACCTTTCA
1785266 AAGCCCACAC
Statistics
Matches: 47, Mismatches: 10, Indels: 14
0.66 0.14 0.20
Matches are distributed among these distances:
25 3 0.06
26 16 0.34
27 9 0.19
28 8 0.17
29 8 0.17
30 3 0.06
ACGTcount: A:0.28, C:0.33, G:0.19, T:0.20
Consensus pattern (26 bp):
CACCTTTCAGTCCCCAAAGAGCAGGA
Found at i:1785499 original size:107 final size:108
Alignment explanation
Indices: 1785373--1785600 Score: 422
Period size: 107 Copynumber: 2.1 Consensus size: 108
1785363 TTCCCTTTTT
1785373 CTTTTGTCCTTGGAAAATGGGACGTACTCTTTTTCACTTTGTCCTCAAGAAGCAGGACACTTTCC
1 CTTTT-TCCTTGGAAAATGGGACGTACTCTTTTTCACTTTGTCCTCAAGAAGCAGGACACTTTCC
1785438 TTTTCTTCTCTTCCTTGGTCTTCAAGGAGCAAGACCCATTTC-C
65 TTTTCTTCTCTTCCTTGGTCTTCAAGGAGCAAGACCCATTTCAC
1785481 CTTTTTCCTTGGAAAATGGGACGTACTCTTTTTCACTTTGTCCTCAAGAAGCAGGACACTTTCCT
1 CTTTTTCCTTGGAAAATGGGACGTACTCTTTTTCACTTTGTCCTCAAGAAGCAGGACACTTTCCT
1785546 TTTCTTCTCTTCCTTGGTCTTCAAGGAGCAAGACCCATTTCATC
66 TTTCTTCTCTTCCTTGGTCTTCAAGGAGCAAGACCCATTTCA-C
1785590 CTCTTTTCCTT
1 CT-TTTTCCTT
1785601 TGTCAAGCCT
Statistics
Matches: 117, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
107 101 0.86
108 5 0.04
109 3 0.03
110 8 0.07
ACGTcount: A:0.19, C:0.27, G:0.15, T:0.39
Consensus pattern (108 bp):
CTTTTTCCTTGGAAAATGGGACGTACTCTTTTTCACTTTGTCCTCAAGAAGCAGGACACTTTCCT
TTTCTTCTCTTCCTTGGTCTTCAAGGAGCAAGACCCATTTCAC
Found at i:1786125 original size:27 final size:21
Alignment explanation
Indices: 1786058--1786154 Score: 126
Period size: 21 Copynumber: 4.7 Consensus size: 21
1786048 AAAAATTCCA
1786058 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
1786079 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
***
1786100 AATGTATCGATACATTCACA-
1 AATGTATCGATACATTTGTAG
* *
1786120 AATGTATCGATACA-TTCTACA
1 AATGTATCGATACATTTGTA-G
1786141 AATGTATCGATACA
1 AATGTATCGATACA
1786155 GGGTCCCAAC
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
19 2 0.03
20 14 0.21
21 52 0.76
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.34
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:1786135 original size:41 final size:42
Alignment explanation
Indices: 1786056--1786154 Score: 130
Period size: 41 Copynumber: 2.4 Consensus size: 42
1786046 AAAAAAATTC
*** *
1786056 CAAATGTATCGATACATTTGTAGAATGTATCGATACATTTGTA
1 CAAATGTATCGATACATTCACAGAATGTATCGATACA-TTCTA
*
1786099 -GAATGTATCGATACATTCACA-AATGTATCGATACATTCTA
1 CAAATGTATCGATACATTCACAGAATGTATCGATACATTCTA
1786139 CAAATGTATCGATACA
1 CAAATGTATCGATACA
1786155 GGGTCCCAAC
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
40 4 0.08
41 28 0.57
42 17 0.35
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.33
Consensus pattern (42 bp):
CAAATGTATCGATACATTCACAGAATGTATCGATACATTCTA
Found at i:1786214 original size:19 final size:19
Alignment explanation
Indices: 1786190--1786257 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
1786180 AATTCAACGA
1786190 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1786209 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
1786224 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
1786241 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
1786258 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1786228 original size:32 final size:32
Alignment explanation
Indices: 1786192--1786254 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1786182 TTCAACGATT
*
1786192 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
1786224 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
1786255 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:1786229 original size:13 final size:13
Alignment explanation
Indices: 1786211--1786235 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1786201 ACATAAGTTT
1786211 TGTATCGATACAA
1 TGTATCGATACAA
1786224 TGTATCGATACA
1 TGTATCGATACA
1786236 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1786315 original size:13 final size:13
Alignment explanation
Indices: 1786297--1786322 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1786287 CATTTTTCTG
1786297 TGTATCGATACAT
1 TGTATCGATACAT
1786310 TGTATCGATACAT
1 TGTATCGATACAT
1786323 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1786319 original size:33 final size:33
Alignment explanation
Indices: 1786277--1786343 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1786267 GCCAAGGAAA
***
1786277 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
1786310 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
1786343 T
1 T
1786344 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:1788857 original size:28 final size:27
Alignment explanation
Indices: 1788790--1788858 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 27
1788780 CTTCACAATC
* *
1788790 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
1788817 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
1788845 GGGGATACTCCAAC
1 GGGGATACTCCAAC
1788859 TCCGACTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 21 0.57
28 16 0.43
ACGTcount: A:0.25, C:0.32, G:0.22, T:0.22
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:1788904 original size:51 final size:51
Alignment explanation
Indices: 1788845--1789014 Score: 196
Period size: 51 Copynumber: 3.3 Consensus size: 51
1788835 TTATTTCTGA
* * *
1788845 GGGGATACTCCAACTCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACTCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * * *
1788896 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACTCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
* * *
1788949 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACTCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
1789001 GAGGATACTCCAAC
1 GGGGATACTCCAAC
1789015 CTCGTTATTT
Statistics
Matches: 96, Mismatches: 20, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
51 35 0.36
52 18 0.19
53 32 0.33
54 11 0.11
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (51 bp):
GGGGATACTCCAACTCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:1789034 original size:28 final size:28
Alignment explanation
Indices: 1788998--1789079 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
1788988 ATTTTTCACA
*
1788998 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
1789026 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
*
1789054 --CGAGGGAACACTCCAACCTCGTTATT
1 ATCG-GGG-ATACTCCAACCTCGTTATT
1789080 ATCTCCAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.04
27 3 0.07
28 41 0.89
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Found at i:1792022 original size:13 final size:13
Alignment explanation
Indices: 1792004--1792028 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1791994 CATAAAATGT
1792004 TGTATCGATACAA
1 TGTATCGATACAA
1792017 TGTATCGATACA
1 TGTATCGATACA
1792029 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1792026 original size:33 final size:33
Alignment explanation
Indices: 1791984--1792050 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1791974 TTCAACGATT
1791984 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1792017 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1792050 T
1 T
1792051 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1792111 original size:13 final size:13
Alignment explanation
Indices: 1792093--1792117 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1792083 ATTACTCACA
1792093 TGTATCGATACAT
1 TGTATCGATACAT
1792106 TGTATCGATACA
1 TGTATCGATACA
1792118 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1792182 original size:52 final size:52
Alignment explanation
Indices: 1792126--1792250 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
1792116 CACTGATCTT
*
1792126 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1792178 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1792230 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
1792251 CTTTTCATAT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1795333 original size:3 final size:3
Alignment explanation
Indices: 1795325--1795374 Score: 84
Period size: 3 Copynumber: 16.7 Consensus size: 3
1795315 CGTTACGACA
1795325 ATC ATC ATC A-C TATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC -ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1795370 ATC AT
1 ATC AT
1795375 TTTTGATAGT
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 1 0.02
3 43 0.96
4 1 0.02
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:1798039 original size:30 final size:30
Alignment explanation
Indices: 1797994--1798050 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
1797984 TTTTTAGATT
1797994 TTTAACATATGAGTGATGATTATGATCATG
1 TTTAACATATGAGTGATGATTATGATCATG
* *
1798024 TTTAGCATTTGAGTGATGATTATGATC
1 TTTAACATATGAGTGATGATTATGATC
1798051 TAACTTAGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.30, C:0.07, G:0.21, T:0.42
Consensus pattern (30 bp):
TTTAACATATGAGTGATGATTATGATCATG
Found at i:1799417 original size:34 final size:34
Alignment explanation
Indices: 1799371--1799588 Score: 282
Period size: 34 Copynumber: 6.5 Consensus size: 34
1799361 GTAAAAACAA
*
1799371 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
1799405 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
1799439 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
1799473 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
1799506 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * *
1799540 CCATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
1799573 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
1799589 TCTCCCACTT
Statistics
Matches: 162, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
33 45 0.28
34 115 0.71
35 2 0.01
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:1799485 original size:68 final size:67
Alignment explanation
Indices: 1799370--1799588 Score: 321
Period size: 67 Copynumber: 3.3 Consensus size: 67
1799360 GGTAAAAACA
* * *
1799370 ACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAAA
1 ACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAAA
1799435 TC
66 TC
* * *
1799437 ACCCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCAA
1 A-CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
1799502 ATC
65 ATC
* * * * * *
1799505 TCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACTAAA
1 ACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAAA
1799570 TC
66 TC
1799572 ACCATTTAATCAACAAT
1 ACCATTTAATCAACAAT
1799589 TCTCCCACTT
Statistics
Matches: 135, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
67 74 0.55
68 61 0.45
ACGTcount: A:0.41, C:0.27, G:0.08, T:0.25
Consensus pattern (67 bp):
ACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAAA
TC
Found at i:1803681 original size:19 final size:19
Alignment explanation
Indices: 1803654--1803715 Score: 88
Period size: 19 Copynumber: 3.3 Consensus size: 19
1803644 TCACGTGTAC
* *
1803654 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
1803673 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
**
1803692 AGTACCTATATACGTGAAT
1 AGTACCCGTATACGTGAAT
1803711 AGTAC
1 AGTAC
1803716 ATCGACAACC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:1804067 original size:34 final size:34
Alignment explanation
Indices: 1804021--1804238 Score: 282
Period size: 34 Copynumber: 6.5 Consensus size: 34
1804011 GTAAAAACCA
*
1804021 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
1804055 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
1804089 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
1804123 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
1804156 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * *
1804190 CCATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
1804223 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
1804239 CCAAAGAGAC
Statistics
Matches: 162, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
33 45 0.28
34 115 0.71
35 2 0.01
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:1804135 original size:68 final size:67
Alignment explanation
Indices: 1804019--1804238 Score: 323
Period size: 67 Copynumber: 3.3 Consensus size: 67
1804009 TGGTAAAAAC
* * *
1804019 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
1804084 AT
66 AT
* * *
1804086 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
1804151 AAT
65 AAT
* * * * * *
1804154 CTCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACTAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
1804219 AT
66 AT
1804221 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
1804239 CCAAAGAGAC
Statistics
Matches: 136, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
67 75 0.55
68 61 0.45
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:1806012 original size:16 final size:16
Alignment explanation
Indices: 1805991--1806025 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1805981 CAATTTTTTG
*
1805991 ATTTATTAAATAATGT
1 ATTTATTAAATAATCT
*
1806007 ATTTATTAACTAATCT
1 ATTTATTAAATAATCT
1806023 ATT
1 ATT
1806026 AAAAAACAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.51
Consensus pattern (16 bp):
ATTTATTAAATAATCT
Found at i:1807382 original size:34 final size:33
Alignment explanation
Indices: 1807274--1807384 Score: 97
Period size: 34 Copynumber: 3.5 Consensus size: 33
1807264 GTTTAATTGG
* *
1807274 TATATAATTCTAATACTTATTAAGTGAGAATTAA
1 TATAAAATTATAATAC-TATTAAGTGAGAATTAA
* ** *
1807308 TCTAAAATTAT--TACT-TTAA-T-TTAATTAG
1 TATAAAATTATAATACTATTAAGTGAGAATTAA
* *
1807336 TATATAACTATAATACTAATTAAGTGAGAATTAA
1 TATAAAATTATAATACT-ATTAAGTGAGAATTAA
1807370 TATAAAATTATAATA
1 TATAAAATTATAATA
1807385 ATCCAAATAT
Statistics
Matches: 57, Mismatches: 14, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
28 13 0.23
29 1 0.02
30 8 0.14
31 1 0.02
32 7 0.12
33 1 0.02
34 26 0.46
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.41
Consensus pattern (33 bp):
TATAAAATTATAATACTATTAAGTGAGAATTAA
Found at i:1807488 original size:36 final size:36
Alignment explanation
Indices: 1807447--1807533 Score: 120
Period size: 36 Copynumber: 2.4 Consensus size: 36
1807437 TAATTTTACA
* * *
1807447 ATATATAATATTAACAACACATGATGATTTAAATTT
1 ATATATAATATCAACAACACATGATAATTTAAATAT
* *
1807483 ATATATAATATCAACAACACTTGATAATTTCAATAT
1 ATATATAATATCAACAACACATGATAATTTAAATAT
1807519 ATATATAATTATCAA
1 ATATATAA-TATCAA
1807534 TATATAATTT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 39 0.87
37 6 0.13
ACGTcount: A:0.48, C:0.10, G:0.03, T:0.38
Consensus pattern (36 bp):
ATATATAATATCAACAACACATGATAATTTAAATAT
Found at i:1807535 original size:18 final size:17
Alignment explanation
Indices: 1807506--1807539 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
1807496 ACAACACTTG
1807506 ATAATTTCAATATATAT
1 ATAATTTCAATATATAT
1807523 ATAATTATCAATATATA
1 ATAATT-TCAATATATA
1807540 ATTTTAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAATTTCAATATATAT
Found at i:1811584 original size:52 final size:52
Alignment explanation
Indices: 1811436--1811564 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
1811426 TGAAATATGA
*
1811436 AAATTTGCTTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* *
1811488 AAATTTGCCTGTATGTATCGATACATTTCATAGTGTATCGATACATCTGGGT
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
1811540 AAATTTGCCTGCATGTATTGATACA
1 AAATTTGCCTGCATGTATCGATACA
1811565 AAGATCAGTG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:1811591 original size:13 final size:13
Alignment explanation
Indices: 1811573--1811597 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1811563 CAAAGATCAG
1811573 TGTATCGATACAA
1 TGTATCGATACAA
1811586 TGTATCGATACA
1 TGTATCGATACA
1811598 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1811678 original size:19 final size:19
Alignment explanation
Indices: 1811650--1811714 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 19
1811640 AACGATACAT
*
1811650 TGTATTGATACAAAACTTA
1 TGTATCGATACAAAACTTA
1811669 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
*
1811682 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
1811701 TGTATCGATACAAA
1 TGTATCGATACAAA
1811715 TCATTGAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
16 2 0.05
18 1 0.03
19 23 0.61
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.34
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:1811683 original size:32 final size:32
Alignment explanation
Indices: 1811642--1811712 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
1811632 AGCTTCGTAA
*
1811642 CGATACATTGTATTGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
1811674 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
1811706 CGATACA
1 CGATACA
1811713 AATCATTGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.34
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:1811687 original size:13 final size:13
Alignment explanation
Indices: 1811669--1811693 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1811659 ACAAAACTTA
1811669 TGTATCGATACAT
1 TGTATCGATACAT
1811682 TGTATCGATACA
1 TGTATCGATACA
1811694 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1812728 original size:92 final size:92
Alignment explanation
Indices: 1812461--1813296 Score: 1282
Period size: 92 Copynumber: 9.0 Consensus size: 92
1812451 ATGAGAAGAA
* * **
1812461 TGCCAATGTGCTGATTCAAGGCCAACAACATTGGGTTTTAAAGATGATGATGGTGCCAATATGCT
1 TGCCAATGTGCTGATTCAAGGCCAGCTACATT-GGACTT-AA-A-GATGATGGTGCCAATATGCT
*
1812526 GATTCAAGGCCAGTGATATTGGACTTAAAGATGAAGG
62 GATTCAAGGCCAGCGATATTGGACTT----A--AAGG
* * *
1812563 TGCCAA--TG-TGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGCGCCAATATGCTG
1 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG---ATGGTGCCAATATGCTG
*
1812625 ATTCAAGGCCAGCGATATTAGACTTAAAGG
63 ATTCAAGGCCAGCGATATTGGACTTAAAGG
* * * *
1812655 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGGCTTAAAGATGAGGGTGCCAATATGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGATGGTGCCAATATGCTGATT
**
1812720 CAAGGCCAGCGATATTGGACTTGGAGG
66 CAAGGCCAGCGATATTGGACTTAAAGG
1812747 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGATGGTGCCAATATGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGATGGTGCCAATATGCTGATT
*
1812812 CAAGGCCAGCGATATTAGACTTAAAGG
66 CAAGGCCAGCGATATTGGACTTAAAGG
*
1812839 TGCCAATGTACTGATTCAAGGCCAGCTACATTGGACTTAAAGATGATGGTGCCAATATGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGATGGTGCCAATATGCTGATT
* **
1812904 CAAGGCTAGCGATATTGGACTTGGAGG
66 CAAGGCCAGCGATATTGGACTTAAAGG
*
1812931 TGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGATGGTGCCAATATGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGATGGTGCCAATATGCTGATT
*
1812996 CAAGGCTAGCGATATTGGACTTAAAGG
66 CAAGGCCAGCGATATTGGACTTAAAGG
*
1813023 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGATGGTGCCAATATGCTAATT
1 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGATGGTGCCAATATGCTGATT
1813088 CAAGGCCAGCGATATTGGACTTAAAGG
66 CAAGGCCAGCGATATTGGACTTAAAGG
*
1813115 TGCCAATGTGCTAATTCAAGGCCAGCTACATTGGACTTAAAGATGATGGTGCCAATATGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGATGGTGCCAATATGCTGATT
*
1813180 CAAGGCCAGCGATATTAGACTTAAAGG
66 CAAGGCCAGCGATATTGGACTTAAAGG
* * *
1813207 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGATGCCAATATGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGATGGTGCCAATATGCTGATT
1813272 CAAGGCCAGCGATATTGGACTTAAA
66 CAAGGCCAGCGATATTGGACTTAAA
1813297 AGAAGATGCC
Statistics
Matches: 687, Mismatches: 41, Indels: 22
0.92 0.05 0.03
Matches are distributed among these distances:
92 575 0.84
94 3 0.00
95 37 0.05
96 1 0.00
97 2 0.00
98 42 0.06
99 19 0.03
100 2 0.00
102 6 0.01
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.26
Consensus pattern (92 bp):
TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGATGGTGCCAATATGCTGATT
CAAGGCCAGCGATATTGGACTTAAAGG
Found at i:1813407 original size:65 final size:65
Alignment explanation
Indices: 1813303--1813490 Score: 297
Period size: 65 Copynumber: 2.9 Consensus size: 65
1813293 TAAAAGAAGA
* * * *
1813303 TGCCACCAACTTGTGTGGGCTTTTGAAGAAGGTTGCCACCGACTTGTGTGGGCTTT-AGAGGGGA
1 TGCCACCAACTTGTGTGGGCTTTAGAAAAAGGTTACCACCGACTTGTGTGGGCTTTGAGAAGGG-
1813367 T
65 T
1813368 TGCCACCAACTTGTGTGGGCTTTAGAAAAAGGTTACCACCGACTTGTGTGGGCTTTGAGAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTAGAAAAAGGTTACCACCGACTTGTGTGGGCTTTGAGAAGGGT
* * *
1813433 TGCCACCGACTTGTGTGGGCTTTGGAAAAAGGTTACCACCGACTTATGTGGGCTTTGA
1 TGCCACCAACTTGTGTGGGCTTTAGAAAAAGGTTACCACCGACTTGTGTGGGCTTTGA
1813491 AAAGAAAAAG
Statistics
Matches: 115, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
65 109 0.95
66 6 0.05
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.29
Consensus pattern (65 bp):
TGCCACCAACTTGTGTGGGCTTTAGAAAAAGGTTACCACCGACTTGTGTGGGCTTTGAGAAGGGT
Found at i:1813489 original size:33 final size:32
Alignment explanation
Indices: 1813303--1813493 Score: 240
Period size: 33 Copynumber: 5.9 Consensus size: 32
1813293 TAAAAGAAGA
* *
1813303 TGCCACCAACTTGTGTGGGCTTTTGAAGAAGGT
1 TGCCACCGACTTGTGTGGGC-TTTGAAAAAGGT
* **
1813336 TGCCACCGACTTGTGTGGGCTTT-AGAGGGGAT
1 TGCCACCGACTTGTGTGGGCTTTGAAAAAGG-T
*
1813368 TGCCACCAACTTGTGTGGGCTTTAGAAAAAGGT
1 TGCCACCGACTTGTGTGGGCTTT-GAAAAAGGT
* * *
1813401 TACCACCGACTTGTGTGGGCTTTGAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTGAAAAAGGT
1813433 TGCCACCGACTTGTGTGGGCTTTGGAAAAAGGT
1 TGCCACCGACTTGTGTGGGCTTT-GAAAAAGGT
* *
1813466 TACCACCGACTTATGTGGGCTTTGAAAA
1 TGCCACCGACTTGTGTGGGCTTTGAAAA
1813494 GAAAAAGGTG
Statistics
Matches: 136, Mismatches: 18, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
31 3 0.02
32 60 0.44
33 69 0.51
34 4 0.03
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.28
Consensus pattern (32 bp):
TGCCACCGACTTGTGTGGGCTTTGAAAAAGGT
Found at i:1813549 original size:34 final size:34
Alignment explanation
Indices: 1813494--1813745 Score: 215
Period size: 34 Copynumber: 8.0 Consensus size: 34
1813484 GCTTTGAAAA
*
1813494 GAAAAAG-GTGCCACTGAAGTTGTGGACTTAGAAG
1 GAAAAAGAGTGCCAC-GGAGTTGTGGACTTAGAAG
* *
1813528 GAAAAAGAGTACCACGGAGTTGTGGGCTT-----
1 GAAAAAGAGTGCCACGGAGTTGTGGACTTAGAAG
* *
1813557 --AAAAGGGTGCCACGGAGTTGTGGACTTTGAAG
1 GAAAAAGAGTGCCACGGAGTTGTGGACTTAGAAG
* *
1813589 GAAAAAGAGTGCCACGTAGTTGTGGGCTT-----
1 GAAAAAGAGTGCCACGGAGTTGTGGACTTAGAAG
*
1813618 --AAAAGGGTGCCACGGAGTTGTGGACTT-----
1 GAAAAAGAGTGCCACGGAGTTGTGGACTTAGAAG
* *
1813645 --AAAAGGGTGCCATGGAGTTGTGGACTTAGAAG
1 GAAAAAGAGTGCCACGGAGTTGTGGACTTAGAAG
*
1813677 GAAAAAGAGTGCCACGGAGTTGTGGACTTAGGAG
1 GAAAAAGAGTGCCACGGAGTTGTGGACTTAGAAG
* * *
1813711 GAAAAAGAGTGCCATGGAGTTGTGGGCTTAAAAG
1 GAAAAAGAGTGCCACGGAGTTGTGGACTTAGAAG
1813745 G
1 G
1813746 GTGCCACGGA
Statistics
Matches: 183, Mismatches: 20, Indels: 30
0.79 0.09 0.13
Matches are distributed among these distances:
27 74 0.40
34 103 0.56
35 6 0.03
ACGTcount: A:0.31, C:0.12, G:0.36, T:0.21
Consensus pattern (34 bp):
GAAAAAGAGTGCCACGGAGTTGTGGACTTAGAAG
Found at i:1813569 original size:27 final size:27
Alignment explanation
Indices: 1813530--1813793 Score: 231
Period size: 27 Copynumber: 9.0 Consensus size: 27
1813520 CTTAGAAGGA
* * *
1813530 AAAAGAGTACCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
1813557 AAAAGGGTGCCACGGAGTTGTGGACTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
* * *
1813585 GAAGGAAAAAGAGTGCCACGTAGTTGTGGGCTT
1 ------AAAAGGGTGCCACGGAGTTGTGGACTT
1813618 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
*
1813645 AAAAGGGTGCCATGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
*
1813672 AGAAGGAAAAAGAGTGCCACGGAGTTGTGGACTT
1 -------AAAAGGGTGCCACGGAGTTGTGGACTT
* * *
1813706 AGGAGGAAAAAGAGTGCCATGGAGTTGTGGGCTT
1 -------AAAAGGGTGCCACGGAGTTGTGGACTT
1813740 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
*
1813767 AAAAGGGTGCCATGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
1813794 TGGAGAAAAA
Statistics
Matches: 204, Mismatches: 19, Indels: 28
0.81 0.08 0.11
Matches are distributed among these distances:
27 122 0.60
28 2 0.01
33 2 0.01
34 78 0.38
ACGTcount: A:0.28, C:0.12, G:0.37, T:0.22
Consensus pattern (27 bp):
AAAAGGGTGCCACGGAGTTGTGGACTT
Found at i:1813591 original size:61 final size:61
Alignment explanation
Indices: 1813495--1813772 Score: 327
Period size: 61 Copynumber: 4.5 Consensus size: 61
1813485 CTTTGAAAAG
* * *
1813495 AAAAAGGTGCCACTGAAGTTGTGGACTTAGAAGGAAAAAGAGTACCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCAC-GGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
* *
1813557 AAAAGGGTGCCACGGAGTTGTGGACTTTGAAGGAAAAAGAGTGCCACGTAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
* * *
1813618 AAAAGGGTGCCACGGAGTTGTGGACTT-------AAAAGGGTGCCATGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
* * *
1813672 AGAAGGAAAAAGAGTGCCACGGAGTTGTGGACTTAGGAGGAAAAAGAGTGCCATGGAGTTGTGGG
1 -------AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGG
1813737 CTT
59 CTT
*
1813740 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGG
1 AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGG
1813773 GTGCCATGGA
Statistics
Matches: 187, Mismatches: 15, Indels: 29
0.81 0.06 0.13
Matches are distributed among these distances:
54 23 0.12
61 127 0.68
62 12 0.06
68 25 0.13
ACGTcount: A:0.31, C:0.12, G:0.36, T:0.21
Consensus pattern (61 bp):
AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
Found at i:1813683 original size:122 final size:120
Alignment explanation
Indices: 1813557--1813826 Score: 425
Period size: 122 Copynumber: 2.2 Consensus size: 120
1813547 TTGTGGGCTT
* *
1813557 AAAAGGGTGCCACGGAGTTGTGGACTTTGAAGGAAAAAGAGTGCCACGTAGTTGTGGGCTTAAAA
1 AAAAAGGTGCCACGGAGTTGTGGACTTTGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAA
1813622 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCATGGAGTTGTGGACTTAGAAGG
66 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCATGGAGTTGTGGACTTAGAA-G
* * *
1813678 AAAAAGAGTGCCACGGAGTTGTGGACTTAGGAGGAAAAAGAGTGCCATGGAGTTGTGGGCTTAAA
1 AAAAAG-GTGCCACGGAGTTGTGGACTTTGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAA
* *
1813743 AGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCATGGAGTTGTGGACTTTGGAG
65 AGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCATGGAGTTGTGGACTTAGAAG
* * *
1813799 AAAAA-ATGCCACTGAGTCGTGGACTTTG
1 AAAAAGGTGCCACGGAGTTGTGGACTTTG
1813827 GGACAAAATG
Statistics
Matches: 137, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
119 19 0.14
121 11 0.08
122 107 0.78
ACGTcount: A:0.29, C:0.13, G:0.36, T:0.23
Consensus pattern (120 bp):
AAAAAGGTGCCACGGAGTTGTGGACTTTGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAA
GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCATGGAGTTGTGGACTTAGAAG
Found at i:1813837 original size:30 final size:31
Alignment explanation
Indices: 1813781--1813855 Score: 125
Period size: 30 Copynumber: 2.5 Consensus size: 31
1813771 GGGTGCCATG
*
1813781 GAGTTGTGGACTTTGGAGAAAAAATGCCACT
1 GAGTCGTGGACTTTGGAGAAAAAATGCCACT
*
1813812 GAGTCGTGGACTTTGG-GACAAAATGCCACT
1 GAGTCGTGGACTTTGGAGAAAAAATGCCACT
1813842 GAGTCGTGGACTTT
1 GAGTCGTGGACTTT
1813856 AAGAAGGTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
30 27 0.64
31 15 0.36
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.27
Consensus pattern (31 bp):
GAGTCGTGGACTTTGGAGAAAAAATGCCACT
Found at i:1826067 original size:20 final size:23
Alignment explanation
Indices: 1826030--1826078 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 23
1826020 ATTTGCTTTT
1826030 AAAAAAAGAAAACGAAAAGT-AAA
1 AAAAAAAGAAAAC-AAAAGTGAAA
*
1826053 AAAAAAAG-AAA-AAAATTGAAA
1 AAAAAAAGAAAACAAAAGTGAAA
1826074 AAAAA
1 AAAAA
1826079 TTGAAAAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 5 0.21
21 8 0.33
22 3 0.12
23 8 0.33
ACGTcount: A:0.82, C:0.02, G:0.10, T:0.06
Consensus pattern (23 bp):
AAAAAAAGAAAACAAAAGTGAAA
Found at i:1826075 original size:11 final size:11
Alignment explanation
Indices: 1826061--1826108 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
1826051 AAAAAAAAAG
1826061 AAAAAAATTGA
1 AAAAAAATTGA
1826072 AAAAAAATTGA
1 AAAAAAATTGA
*
1826083 AAAGAAA--GA
1 AAAAAAATTGA
* *
1826092 AAAGAAAGTGA
1 AAAAAAATTGA
1826103 AAAAAA
1 AAAAAA
1826109 TTTATTTAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
9 9 0.27
11 24 0.73
ACGTcount: A:0.75, C:0.00, G:0.15, T:0.10
Consensus pattern (11 bp):
AAAAAAATTGA
Found at i:1826085 original size:20 final size:19
Alignment explanation
Indices: 1826044--1826108 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 19
1826034 AAAGAAAACG
**
1826044 AAAAGTAAAAAAAAAAGAAA
1 AAAAG-AAAAAAAAGTGAAA
*
1826064 AAAATTGAAAAAAAATTGAAA
1 AAAA--GAAAAAAAAGTGAAA
*
1826085 AGAAAGAAAAGAAAGTGAAA
1 A-AAAGAAAAAAAAGTGAAA
1826105 AAAA
1 AAAA
1826109 TTTATTTAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
19 3 0.08
20 18 0.47
21 13 0.34
22 4 0.11
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (19 bp):
AAAAGAAAAAAAAGTGAAA
Found at i:1830470 original size:51 final size:50
Alignment explanation
Indices: 1830344--1830473 Score: 179
Period size: 51 Copynumber: 2.5 Consensus size: 50
1830334 TTTTAACTTG
* * * *
1830344 ATGTATCGATATATTATTCAATGTATCGATACATTTGGGTAAAAAGATAGA
1 ATGTATCGATACATTATAC-ATGTATCCATACATCTGGGTAAAAAGATAGA
* *
1830395 ATGTATCGATACATTGAAAAATGTATCCATACATCTGGGTAAAAAGATAGA
1 ATGTATCGATACATT-ATACATGTATCCATACATCTGGGTAAAAAGATAGA
1830446 ATGTATCGATACATTCATACATGTATCC
1 ATGTATCGATACATT-ATACATGTATCC
1830474 TGAACACGTT
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
51 68 0.99
52 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.32
Consensus pattern (50 bp):
ATGTATCGATACATTATACATGTATCCATACATCTGGGTAAAAAGATAGA
Found at i:1831513 original size:28 final size:28
Alignment explanation
Indices: 1831441--1831911 Score: 550
Period size: 28 Copynumber: 16.5 Consensus size: 28
1831431 CAGTAACTTG
* *
1831441 TGTGGGCTTTGAAAAGAGTTGCCACTAACTT
1 TGTGGGCTTTG-AAAG-GATGCCACTGAC-T
* *
1831472 GTGTGGGCTTTGAAAGGGTGCCACCGACT
1 -TGTGGGCTTTGAAAGGATGCCACTGACT
1831501 TGTGGGCTTTGAAAGGGTATGCCACTGACT
1 TGTGGGCTTTGAAA-GG-ATGCCACTGACT
* *
1831531 TGTGGGCTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
1831559 TGTGGGATTTGAAGGGGTATGCCACTGACT
1 TGTGGGCTTTGAA-AGG-ATGCCACTGACT
*
1831589 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
1831617 TGTGGGATTTGAAGGGGTATGCCACTGACT
1 TGTGGGCTTTGAA-AGG-ATGCCACTGACT
* * *
1831647 TATGGGCTTTGAAAGGGTACCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
1831675 TGTGGGCTTTGAGAGGATGCCACTGAC-
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
1831702 TGTGGCCTTTTG-AAGAGATGCCACTAAGT
1 TGTGGGC-TTTGAAAG-GATGCCACTGACT
1831731 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * *
1831759 TGTGGGCTTTAAAAGGTTGCGACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
1831787 TGTGGGCTTTGGAAGGATGCCACCGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
1831815 TGTGGGCTTTGAAAAGATACCACCGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
1831843 TGTGGGCTTTGAAAGGATGCGACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
1831871 TGTGGGCTTTGAAAGGATGCCATTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
1831899 TATGGGCTTTGAA
1 TGTGGGCTTTGAA
1831912 GAAATGAACG
Statistics
Matches: 376, Mismatches: 53, Indels: 24
0.83 0.12 0.05
Matches are distributed among these distances:
27 8 0.02
28 254 0.68
29 22 0.06
30 77 0.20
31 4 0.01
32 11 0.03
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:1833195 original size:11 final size:11
Alignment explanation
Indices: 1833170--1833246 Score: 74
Period size: 10 Copynumber: 7.4 Consensus size: 11
1833160 TTTTTATCTA
1833170 TTTGTTTTTTG
1 TTTGTTTTTTG
1833181 -TTGTTTTTTG
1 TTTGTTTTTTG
*
1833191 TTTGTTTTTTA
1 TTTGTTTTTTG
1833202 TTT-TTTTTTG
1 TTTGTTTTTTG
*
1833212 -TT-TTTTTTC
1 TTTGTTTTTTG
*
1833221 TTGGTTTTTTTG
1 TTTG-TTTTTTG
*
1833233 TTTCTTTTTT-
1 TTTGTTTTTTG
1833243 TTTG
1 TTTG
1833247 GTATGAAGGA
Statistics
Matches: 54, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
9 8 0.15
10 20 0.37
11 18 0.33
12 8 0.15
ACGTcount: A:0.01, C:0.03, G:0.13, T:0.83
Consensus pattern (11 bp):
TTTGTTTTTTG
Found at i:1833195 original size:21 final size:20
Alignment explanation
Indices: 1833170--1833242 Score: 83
Period size: 21 Copynumber: 3.5 Consensus size: 20
1833160 TTTTTATCTA
1833170 TTTGTTTTTTGTTGTTTTTTG
1 TTTGTTTTTTGTT-TTTTTTG
*
1833191 TTTGTTTTTTATTTTTTTTTG
1 TTTGTTTTTT-GTTTTTTTTG
* *
1833212 TTTTTTTTCTTGGTTTTTTTG
1 TTTGTTTT-TTGTTTTTTTTG
*
1833233 TTTCTTTTTT
1 TTTGTTTTTT
1833243 TTTGGTATGA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
20 2 0.04
21 39 0.87
22 4 0.09
ACGTcount: A:0.01, C:0.03, G:0.12, T:0.84
Consensus pattern (20 bp):
TTTGTTTTTTGTTTTTTTTG
Found at i:1833233 original size:38 final size:37
Alignment explanation
Indices: 1833170--1833245 Score: 93
Period size: 38 Copynumber: 2.0 Consensus size: 37
1833160 TTTTTATCTA
* *
1833170 TTTGTTTTTTGTTGTTTTTTGTTTGTTTTTTATTTTTT
1 TTTGTTTTTTGTTCTTTTTTGTTTGTTTCTT-TTTTTT
1833208 TTTGTTTTTT-TTCTTGGTTTT-TTTGTTTCTTTTTTTT
1 TTTGTTTTTTGTTCTT--TTTTGTTTGTTTCTTTTTTTT
1833245 T
1 T
1833246 GGTATGAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
37 11 0.32
38 19 0.56
39 4 0.12
ACGTcount: A:0.01, C:0.03, G:0.12, T:0.84
Consensus pattern (37 bp):
TTTGTTTTTTGTTCTTTTTTGTTTGTTTCTTTTTTTT
Found at i:1834450 original size:375 final size:375
Alignment explanation
Indices: 1833760--1834506 Score: 1431
Period size: 375 Copynumber: 2.0 Consensus size: 375
1833750 AAAAGGTAGC
*
1833760 TTCTCATGCCAGTCTTTATAAGTCTCGACCATTTTCTCAACTATTCTCTTGATGTTTTTATTGGT
1 TTCTCATGCCAGTCTTTATAAGTCTCGACCATTTTCTCAACTATTCTCTTGATGTTTTTATTGGC
*
1833825 TTCCTCGACTGCCCCATTCATCTTTGGGCGATAAGGGATAAAATTATGATGCTTGATCTTAAACT
66 TGCCTCGACTGCCCCATTCATCTTTGGGCGATAAGGGATAAAATTATGATGCTTGATCTTAAACT
1833890 GAAAATAAATGGCTTGCATCATTTTGTTGTTTAAATTGGTTGCATTATCTATAATGATTTGATTT
131 GAAAATAAATGGCTTGCATCATTTTGTTGTTTAAATTGGTTGCATTATCTATAATGATTTGATTT
* *
1833955 GGGAGGCTGTATCTACAGATGATGTCTCGTTTGACAAACTTACAAACAATTGATCTAGAGACATT
196 GGGAAGCTGTATCTACAGATGATGTCTCGTTTGACAAACTTACAAACAATTAATCTAGAGACATT
1834020 AGCATATGAGGCAGCCTCCACCCATTTGGTGAAATAGTCAATTGCCACCAAGATGAAGTGATGTC
261 AGCATATGAGGCAGCCTCCACCCATTTGGTGAAATAGTCAATTGCCACCAAGATGAAGTGATGTC
1834085 CATTGGAAGCTTTAGGGGTGATTAGCCGGATCACATCCATGCCCCATTTA
326 CATTGGAAGCTTTAGGGGTGATTAGCCGGATCACATCCATGCCCCATTTA
*
1834135 TTCTCATGCCAGTCTTTATAAGTCTCGACCATTTTCTTAACTATTCTCTTGATGTTTTTATTGGC
1 TTCTCATGCCAGTCTTTATAAGTCTCGACCATTTTCTCAACTATTCTCTTGATGTTTTTATTGGC
*
1834200 TGCCTCGACTGCCCCATTCATCTTTGGGCGATAAGGGATAGAATTATGATGCTTGATCTTAAACT
66 TGCCTCGACTGCCCCATTCATCTTTGGGCGATAAGGGATAAAATTATGATGCTTGATCTTAAACT
1834265 GAAAATAAATGGCTTGCATCATTTTGTTGTTTAAATTGGTTGCATTATCTATAATGATTTGATTT
131 GAAAATAAATGGCTTGCATCATTTTGTTGTTTAAATTGGTTGCATTATCTATAATGATTTGATTT
*
1834330 GGGAAGCTGTATCTACAGATGATGTCTCGTTTGACAAACTTACAAACAATTAATCTAGAGATATT
196 GGGAAGCTGTATCTACAGATGATGTCTCGTTTGACAAACTTACAAACAATTAATCTAGAGACATT
1834395 AGCATATGAGGCAGCCTCCACCCATTTGGTGAAATAGTCAATTGCCACCAAGATGAAGTGATGTC
261 AGCATATGAGGCAGCCTCCACCCATTTGGTGAAATAGTCAATTGCCACCAAGATGAAGTGATGTC
1834460 CATTGGAAGCTTTAGGGGTGATTAGCCGGATCACATCCATGCCCCAT
326 CATTGGAAGCTTTAGGGGTGATTAGCCGGATCACATCCATGCCCCAT
1834507 ATTGAGAAGG
Statistics
Matches: 365, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
375 365 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (375 bp):
TTCTCATGCCAGTCTTTATAAGTCTCGACCATTTTCTCAACTATTCTCTTGATGTTTTTATTGGC
TGCCTCGACTGCCCCATTCATCTTTGGGCGATAAGGGATAAAATTATGATGCTTGATCTTAAACT
GAAAATAAATGGCTTGCATCATTTTGTTGTTTAAATTGGTTGCATTATCTATAATGATTTGATTT
GGGAAGCTGTATCTACAGATGATGTCTCGTTTGACAAACTTACAAACAATTAATCTAGAGACATT
AGCATATGAGGCAGCCTCCACCCATTTGGTGAAATAGTCAATTGCCACCAAGATGAAGTGATGTC
CATTGGAAGCTTTAGGGGTGATTAGCCGGATCACATCCATGCCCCATTTA
Found at i:1838920 original size:20 final size:20
Alignment explanation
Indices: 1838895--1838934 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1838885 TAAAGTGGCT
1838895 GCGTTGCTTTGTCTCCTATC
1 GCGTTGCTTTGTCTCCTATC
1838915 GCGTTGCTTTGTCTCCTATC
1 GCGTTGCTTTGTCTCCTATC
1838935 ATGTTAATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.05, C:0.30, G:0.20, T:0.45
Consensus pattern (20 bp):
GCGTTGCTTTGTCTCCTATC
Found at i:1839406 original size:23 final size:23
Alignment explanation
Indices: 1839380--1839427 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
1839370 TCACAGTGGC
1839380 ATTAGGATTGTACCAATGTGGGA
1 ATTAGGATTGTACCAATGTGGGA
*
1839403 ATTAGGATTGTACCATTGTGGGA
1 ATTAGGATTGTACCAATGTGGGA
1839426 AT
1 AT
1839428 GGTGGCTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.29, C:0.08, G:0.29, T:0.33
Consensus pattern (23 bp):
ATTAGGATTGTACCAATGTGGGA
Found at i:1847623 original size:20 final size:20
Alignment explanation
Indices: 1847598--1847674 Score: 93
Period size: 20 Copynumber: 3.9 Consensus size: 20
1847588 GTAAAAAGAT
*
1847598 AGAATGTATCGATTCATTGA
1 AGAATGTATCGATACATTGA
*
1847618 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
* *
1847638 TA-CATTTATCGATACATTGA
1 -AGAATGTATCGATACATTGA
*
1847658 AAAATGTATCGATACAT
1 AGAATGTATCGATACAT
1847675 CTTGGTAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
19 1 0.02
20 46 0.96
21 1 0.02
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:1847694 original size:31 final size:31
Alignment explanation
Indices: 1847658--1847716 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
1847648 GATACATTGA
*
1847658 AAAATGTATCGATACATCTTGGTAAAAAGAT
1 AAAATGTATCGATACATCTGGGTAAAAAGAT
1847689 AAAATGTATCGATACATCTGGGTAAAAA
1 AAAATGTATCGATACATCTGGGTAAAAA
1847717 TGTGACTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.46, C:0.10, G:0.17, T:0.27
Consensus pattern (31 bp):
AAAATGTATCGATACATCTGGGTAAAAAGAT
Found at i:1848836 original size:18 final size:17
Alignment explanation
Indices: 1848815--1848866 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 17
1848805 GATTTAATTC
1848815 ATCTTGTATTTTTATTTT
1 ATCTT-TATTTTTATTTT
1848833 ATCTTTAGTTTAATTATTTT
1 ATCTTTA-TTT--TTATTTT
1848853 A--TTTATTTTTATTT
1 ATCTTTATTTTTATTT
1848867 GAATTGATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
15 6 0.19
17 5 0.16
18 12 0.39
20 8 0.26
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.71
Consensus pattern (17 bp):
ATCTTTATTTTTATTTT
Found at i:1848863 original size:24 final size:25
Alignment explanation
Indices: 1848824--1848871 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
1848814 CATCTTGTAT
1848824 TTTTATTTTATCTTTAGTTT-AATTA
1 TTTTATTTTATCTTTA-TTTGAATTA
*
1848849 TTTTA-TTTATTTTTATTTGAATT
1 TTTTATTTTATCTTTATTTGAATT
1848872 GATAAAAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 3 0.14
24 13 0.62
25 5 0.24
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.71
Consensus pattern (25 bp):
TTTTATTTTATCTTTATTTGAATTA
Found at i:1851652 original size:165 final size:165
Alignment explanation
Indices: 1851433--1851787 Score: 468
Period size: 165 Copynumber: 2.1 Consensus size: 165
1851423 GTGGGGCTTT
* * *
1851433 TTTGTAATTTTAGAAA-TTTAAGGTTTTATTTGAAAATATTGAAAAATATTGTTCCAAGGCTAAA
1 TTTGTAATTTTAAAAAGTTTAAGGTTTTATTTCAAAATATTGAAAAATATTGTTCCAAGACTAAA
* * *
1851497 GGTGATTGGTCGAA-TCTTTGTTGTGA-TTTTAGATGTGCTTTTTGTATTGGTTTTGATATATTT
66 GGTGATTAGTCGAACT-TTTCTTGTGACTTTTAGATGTGATTTTTGTATTGGTTTTGATATATTT
*
1851560 GCTGCTTAATATTGTATTTTAATTACGTA-AAGACTAA
130 GATGCTTAATATTGTATTTTAATTA--TATAAGACTAA
* * * *
1851597 TTTGTAATTTTAAAAAGTTTAACGG-TTTATTTCTAAATATTGAGAAATTTTGTTCCAAGATTAA
1 TTTGTAATTTTAAAAAGTTTAA-GGTTTTATTTCAAAATATTGAAAAATATTGTTCCAAGACTAA
*
1851661 AGGTGATTAGTTGAACTTTTCTTGTGACTTTTAGATGTGATTTTTGTATTGGTTTTGATATATTT
65 AGGTGATTAGTCGAACTTTTCTTGTGACTTTTAGATGTGATTTTTGTATTGGTTTTGATATATTT
* * *
1851726 GATGCTTAATTTTTTATTTTAATTATATAAGACTAG
130 GATGCTTAATATTGTATTTTAATTATATAAGACTAA
* *
1851762 TTTGCAAATTTAGAAAAGTTTGAAGG
1 TTTGTAATTTTA-AAAAGTTT-AAGG
1851788 CCATTGGGAA
Statistics
Matches: 167, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
164 17 0.10
165 77 0.46
166 71 0.43
167 2 0.01
ACGTcount: A:0.30, C:0.06, G:0.17, T:0.47
Consensus pattern (165 bp):
TTTGTAATTTTAAAAAGTTTAAGGTTTTATTTCAAAATATTGAAAAATATTGTTCCAAGACTAAA
GGTGATTAGTCGAACTTTTCTTGTGACTTTTAGATGTGATTTTTGTATTGGTTTTGATATATTTG
ATGCTTAATATTGTATTTTAATTATATAAGACTAA
Found at i:1852868 original size:81 final size:82
Alignment explanation
Indices: 1852771--1852936 Score: 253
Period size: 82 Copynumber: 2.0 Consensus size: 82
1852761 TTCTATGAAA
* *
1852771 TAATAAATTTAAAAAATTA-TTTTAATACATGGAAATTATATTCAAATATTGGATAATAAAACTG
1 TAATAAATTTAAAAAATTATTTTTAATACATGGAAATTATATTCAAATATTGAATAATAAAACTC
* *
1852835 AATGAAAATCAAAATTT
66 AATAAAAATAAAAATTT
* * * *
1852852 TAATAAATTTAGAAAATTATTTTTAATATATGGGAATTGTATTCAAATATTGAATAATAAAACTC
1 TAATAAATTTAAAAAATTATTTTTAATACATGGAAATTATATTCAAATATTGAATAATAAAACTC
1852917 AATAAAAATAAAAATTT
66 AATAAAAATAAAAATTT
1852934 TAA
1 TAA
1852937 GTTAATATGT
Statistics
Matches: 76, Mismatches: 8, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
81 18 0.24
82 58 0.76
ACGTcount: A:0.52, C:0.04, G:0.07, T:0.37
Consensus pattern (82 bp):
TAATAAATTTAAAAAATTATTTTTAATACATGGAAATTATATTCAAATATTGAATAATAAAACTC
AATAAAAATAAAAATTT
Found at i:1855245 original size:21 final size:21
Alignment explanation
Indices: 1855219--1855263 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1855209 AAATTTTCAC
1855219 AAAAGAAGAAAAAGAAAACAA
1 AAAAGAAGAAAAAGAAAACAA
* *
1855240 AAAAGAAGAAGAAGAAAAGAA
1 AAAAGAAGAAAAAGAAAACAA
1855261 AAA
1 AAA
1855264 GAAAATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (21 bp):
AAAAGAAGAAAAAGAAAACAA
Found at i:1855999 original size:13 final size:13
Alignment explanation
Indices: 1855981--1856018 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
1855971 GAGCTATCAA
1855981 AAAAAGAAAAAAG
1 AAAAAGAAAAAAG
1855994 AAAAAG-AAAAAG
1 AAAAAGAAAAAAG
1856006 AAAGAA-AAAAAAG
1 AAA-AAGAAAAAAG
1856019 CTAAAAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 9 0.39
13 14 0.61
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAAG
Found at i:1856005 original size:19 final size:19
Alignment explanation
Indices: 1855981--1856018 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
1855971 GAGCTATCAA
1855981 AAAAAGAAA-AAAGAAAAAG
1 AAAAAGAAAGAAA-AAAAAG
1856000 AAAAAGAAAGAAAAAAAAG
1 AAAAAGAAAGAAAAAAAAG
1856019 CTAAAAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (19 bp):
AAAAAGAAAGAAAAAAAAG
Found at i:1857678 original size:60 final size:59
Alignment explanation
Indices: 1857471--1857722 Score: 229
Period size: 60 Copynumber: 4.2 Consensus size: 59
1857461 TATAGTTGTT
* * * * * **
1857471 TTTAGGTTTTTGGTTTAATCTAGGCCATTTCACTGAGTCTTAGTTTTGCCTAAGTCATTG
1 TTTAGGTTTCTAGTTTTATCCAGGCCATTTCATTGAGTCTTAGTTTCACC-AAGTCATTG
* ** * ** * *
1857531 TTTAGGTTTTTAGTTTCGTCCAAGCCATTTGGTTGAATCTTAGTTTCATCCAAGTCA-TA
1 TTTAGGTTTCTAGTTTTATCCAGGCCATTTCATTGAGTCTTAGTTTCA-CCAAGTCATTG
* * * *
1857590 TTTAGGTTTTTGGTTTTATCCGGGCCATTTCATTGAGTCTTATTTTCACCTAAGTCATTG
1 TTTAGGTTTCTAGTTTTATCCAGGCCATTTCATTGAGTCTTAGTTTCACC-AAGTCATTG
* * ** * *
1857650 CTTAGGTTTCTAGTTTTTTTTAGGCCATTTCATTGAGTCTTGGTTTCTCCAAGTCA-TG
1 TTTAGGTTTCTAGTTTTATCCAGGCCATTTCATTGAGTCTTAGTTTCACCAAGTCATTG
1857708 TTTTAGGTTTCTAGT
1 -TTTAGGTTTCTAGT
1857723 GTTGTCATTT
Statistics
Matches: 155, Mismatches: 33, Indels: 9
0.79 0.17 0.05
Matches are distributed among these distances:
58 4 0.03
59 65 0.42
60 84 0.54
61 2 0.01
ACGTcount: A:0.18, C:0.16, G:0.19, T:0.48
Consensus pattern (59 bp):
TTTAGGTTTCTAGTTTTATCCAGGCCATTTCATTGAGTCTTAGTTTCACCAAGTCATTG
Found at i:1857696 original size:119 final size:119
Alignment explanation
Indices: 1857471--1857717 Score: 309
Period size: 119 Copynumber: 2.1 Consensus size: 119
1857461 TATAGTTGTT
* * *
1857471 TTTAGGTTTTTGGTTTAATCTAGGCCATTTCACTGAGTCTTAGTTTTGCCTAAGTCATTGTTTAG
1 TTTAGGTTTTTGGTTTAATCCAGGCCATTTCACTGAGTCTTAGTTTTACCTAAGTCATTGCTTAG
* **
1857536 GTTTTTAGTTTCGTCCAAGCCATTTGGTTGAATCTTAGTTTCATCCAAGTCAT-A
66 GTTTCTAGTTTCGTCCAAGCCATTTCATTGAATCTTAGTTTC-TCCAAGTCATGA
* * *
1857590 TTTAGGTTTTTGGTTTTATCCGGGCCATTTCATTGAGTCTTA-TTTTCACCTAAGTCATTGCTTA
1 TTTAGGTTTTTGGTTTAATCCAGGCCATTTCACTGAGTCTTAGTTTT-ACCTAAGTCATTGCTTA
** ** * * * *
1857654 GGTTTCTAGTTTTTTTTAGGCCATTTCATTGAGTCTTGGTTTCTCCAAGTCATGT
65 GGTTTCTAGTTTCGTCCAAGCCATTTCATTGAATCTTAGTTTCTCCAAGTCATGA
1857709 TTTAGGTTT
1 TTTAGGTTT
1857718 CTAGTGTTGT
Statistics
Matches: 109, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
118 14 0.13
119 95 0.87
ACGTcount: A:0.18, C:0.16, G:0.19, T:0.48
Consensus pattern (119 bp):
TTTAGGTTTTTGGTTTAATCCAGGCCATTTCACTGAGTCTTAGTTTTACCTAAGTCATTGCTTAG
GTTTCTAGTTTCGTCCAAGCCATTTCATTGAATCTTAGTTTCTCCAAGTCATGA
Found at i:1858294 original size:64 final size:62
Alignment explanation
Indices: 1858133--1858294 Score: 162
Period size: 63 Copynumber: 2.5 Consensus size: 62
1858123 TTTTGCCTTA
* * * * * *
1858133 GTTACTTCTTTGACTATCATGGTTTTGCCTTGGTCAATCTTTCTGATTGAAGGTTCCACCTTG
1 GTTACTTCTTTGACTATCATGGTTTTGCC-TAGTCAATCATTCTGACTGAAAGTTCCACCCTC
* * * * * * *
1858196 GTCACCTCTTTAACTATTATGTTTTTGTCTTAGTCAATCATTCTGACTGAAAGTTCCCTCCCTC
1 GTTACTTCTTTGACTATCATGGTTTTG-CCTAGTCAATCATTCTGACTGAAAGTT-CCACCCTC
*
1858260 GTTACTTCTTTGACTATCAAGGTTTTGCGCTAGTC
1 GTTACTTCTTTGACTATCATGGTTTTGC-CTAGTC
1858295 TTTTCCTTGA
Statistics
Matches: 76, Mismatches: 20, Indels: 5
0.75 0.20 0.05
Matches are distributed among these distances:
63 44 0.58
64 32 0.42
ACGTcount: A:0.18, C:0.23, G:0.16, T:0.43
Consensus pattern (62 bp):
GTTACTTCTTTGACTATCATGGTTTTGCCTAGTCAATCATTCTGACTGAAAGTTCCACCCTC
Found at i:1858511 original size:66 final size:66
Alignment explanation
Indices: 1858441--1858580 Score: 165
Period size: 66 Copynumber: 2.1 Consensus size: 66
1858431 AGTTGACTGT
* * *
1858441 TATGGTTTCACCTTAGCAAACCTTTTTGCTAA-TTACGTTTCGCCATGGTTATCCAAAGTTGGTT
1 TATGGTTTCACCTTAGCAAACATTTTT-CTAACTTACGATTCGCCATGGTCATCCAAAGTTGGTT
1858505 CA
65 CA
** * * * * *
1858507 TATGGTTTCATTTTGGCTAACATTTTTCTAACTTAGGATTCGTCTTGGTCATCCAAAGTTGGTTC
1 TATGGTTTCACCTTAGCAAACATTTTTCTAACTTACGATTCGCCATGGTCATCCAAAGTTGGTTC
*
1858572 G
66 A
1858573 TATGGTTT
1 TATGGTTT
1858581 TGTCTCAGGC
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
65 4 0.06
66 58 0.94
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.43
Consensus pattern (66 bp):
TATGGTTTCACCTTAGCAAACATTTTTCTAACTTACGATTCGCCATGGTCATCCAAAGTTGGTTC
A
Found at i:1858606 original size:66 final size:66
Alignment explanation
Indices: 1858486--1858609 Score: 151
Period size: 66 Copynumber: 1.9 Consensus size: 66
1858476 CGTTTCGCCA
* ** * *
1858486 TGGTTATCCAAAGTTGGTTCATATGGTTTCATTTTGGCTAACATTTTTCTAACTTAGGATTCGTC
1 TGGTCATCCAAAGTTGGTTCATATGGTTTCATTCAGGCTAACATCTTTCCAACTTAGGATTCGTC
1858551 T
66 T
* ** *
1858552 TGGTCATCCAAAGTTGGTTCGTATGGTTTTGTCTCAGGC-AACCTCTTTCCAACTTAGG
1 TGGTCATCCAAAGTTGGTTCATATGGTTTCAT-TCAGGCTAACATCTTTCCAACTTAGG
1858610 TTTTGCCTTA
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
66 44 0.92
67 4 0.08
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (66 bp):
TGGTCATCCAAAGTTGGTTCATATGGTTTCATTCAGGCTAACATCTTTCCAACTTAGGATTCGTC
T
Found at i:1859296 original size:66 final size:64
Alignment explanation
Indices: 1859145--1859398 Score: 214
Period size: 66 Copynumber: 3.9 Consensus size: 64
1859135 TTTCGCCCTA
* * * * *
1859145 ACCAATCCTTTTTTAACTAAGGTTTTGCCTTGGTCACCTTTT-TATGGTCCATATGGTTTTGTCC
1 ACCAA-CCCTTTTTAACTTAGGTTTTGCCTTAGTCACCTTTTGT-TGGTTCATATGGTTTTAT-C
*
1859209 CG
63 CT
* * * *
1859211 ACTAATCCCTTTTCAACTTAGGTTTTGTCTTAGTCACCTTTTGTTGGTTCGTATGGTTTTATCCT
1 ACCAA-CCCTTTTTAACTTAGGTTTTGCCTTAGTCACCTTTTGTTGGTTCATATGGTTTTATCCT
* * * * ** *
1859276 ACCCAACCCTTTTTTGACTTAGGTTTCAG-CTT-GATCACCATTTCTTGGTTGGTATGGTTTCAT
1 A-CCAACCC-TTTTTAACTTAGGTTT-TGCCTTAG-TCACCTTTTGTTGGTTCATATGGTTTTAT
1859339 CCT
62 CCT
**
1859342 AGCCAA--C-TTTGGACTTAGGTTTTGCCTTAGTCACCTTTTGTTGGTTCATATGGTTTT
1 A-CCAACCCTTTTTAACTTAGGTTTTGCCTTAGTCACCTTTTGTTGGTTCATATGGTTTT
1859399 TGTTAGGATC
Statistics
Matches: 155, Mismatches: 26, Indels: 18
0.78 0.13 0.09
Matches are distributed among these distances:
61 1 0.01
62 39 0.25
63 1 0.01
64 1 0.01
65 7 0.05
66 104 0.67
67 2 0.01
ACGTcount: A:0.16, C:0.21, G:0.17, T:0.45
Consensus pattern (64 bp):
ACCAACCCTTTTTAACTTAGGTTTTGCCTTAGTCACCTTTTGTTGGTTCATATGGTTTTATCCT
Found at i:1864714 original size:19 final size:17
Alignment explanation
Indices: 1864689--1864786 Score: 86
Period size: 19 Copynumber: 5.9 Consensus size: 17
1864679 ATTTCAACGA
1864689 TTTGTATCGATACAAAAG
1 TTTGTATCGATAC-AAAG
1864707 TGTTGTATCGATAC-AA-
1 T-TTGTATCGATACAAAG
1864723 --TGTATCGATACATAAG
1 TTTGTATCGATACA-AAG
1864739 TGTTGTATCGATAC-AA-
1 T-TTGTATCGATACAAAG
1864755 --TGTATCGATACATAAG
1 TTTGTATCGATACA-AAG
1864771 TTTTGTATCGATACAA
1 -TTTGTATCGATACAA
1864787 TGTATCGCTA
Statistics
Matches: 67, Mismatches: 0, Indels: 26
0.72 0.00 0.28
Matches are distributed among these distances:
13 22 0.33
15 4 0.06
17 4 0.06
18 2 0.03
19 35 0.52
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (17 bp):
TTTGTATCGATACAAAG
Found at i:1864727 original size:32 final size:32
Alignment explanation
Indices: 1864691--1864793 Score: 188
Period size: 32 Copynumber: 3.2 Consensus size: 32
1864681 TTCAACGATT
*
1864691 TGTATCGATACAAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1864723 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
1864755 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1864787 TGTATCG
1 TGTATCG
1864794 CTACGAAGCT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 69 1.00
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:1864728 original size:13 final size:13
Alignment explanation
Indices: 1864710--1864766 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
1864700 ACAAAAGTGT
1864710 TGTATCGATACAA
1 TGTATCGATACAA
1864723 TGTATCGATACATAA
1 TGTATCGATAC--AA
1864738 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
1864755 TGTATCGATACA
1 TGTATCGATACA
1864767 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Done.