Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008208.1 Hibiscus syriacus cultivar Beakdansim tig00110830_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: 2533913
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 8
Found at i:1948723 original size:19 final size:20
Alignment explanation
Indices: 1948695--1948734 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
1948685 GGATAATAAT
1948695 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
1948715 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
1948734 A
1 A
1948735 GGATGGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:1950585 original size:23 final size:23
Alignment explanation
Indices: 1950554--1950605 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
1950544 CACCATCTTC
*
1950554 CATCTCCATTATCACGCCTATAT
1 CATCACCATTATCACGCCTATAT
*
1950577 CATCACCATTATCACGCCTTTAT
1 CATCACCATTATCACGCCTATAT
1950600 CATCAC
1 CATCAC
1950606 TATAGTCCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.27, C:0.37, G:0.04, T:0.33
Consensus pattern (23 bp):
CATCACCATTATCACGCCTATAT
Found at i:1950630 original size:36 final size:36
Alignment explanation
Indices: 1950577--1950679 Score: 134
Period size: 36 Copynumber: 2.9 Consensus size: 36
1950567 ACGCCTATAT
* *
1950577 CATCACCATTATCACGCCTTTATCATCACTATAGTC
1 CATCACCATTATCACGCCTATATCATCACCATAGTC
* * *
1950613 CATCTCCATTATTACGCCTATATCATCACCATATTC
1 CATCACCATTATCACGCCTATATCATCACCATAGTC
* * *
1950649 CACCACCATTATCACGTCTATATTATCACCA
1 CATCACCATTATCACGCCTATATCATCACCA
1950680 ACTTATAAAT
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 57 1.00
ACGTcount: A:0.29, C:0.34, G:0.04, T:0.33
Consensus pattern (36 bp):
CATCACCATTATCACGCCTATATCATCACCATAGTC
Found at i:1951157 original size:14 final size:15
Alignment explanation
Indices: 1951123--1951169 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
1951113 AACTTGGAGT
1951123 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
1951138 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
1951152 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
1951169 G
1 G
1951170 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:1956335 original size:13 final size:13
Alignment explanation
Indices: 1956313--1956342 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1956303 ACTAAACACC
1956313 TTTC-ACATACCT
1 TTTCAACATACCT
1956325 TTTCAACATACCT
1 TTTCAACATACCT
1956338 TTTCA
1 TTTCA
1956343 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:1959519 original size:10 final size:10
Alignment explanation
Indices: 1959504--1959559 Score: 60
Period size: 10 Copynumber: 5.7 Consensus size: 10
1959494 TTTTTTTTTC
1959504 AAAAAAACAA
1 AAAAAAACAA
1959514 AAAAAAAC-A
1 AAAAAAACAA
**
1959523 AAAAAGGCAA
1 AAAAAAACAA
***
1959533 AAAAAAAGGC
1 AAAAAAACAA
1959543 AAAAAAACAA
1 AAAAAAACAA
1959553 AAAAAAA
1 AAAAAAA
1959560 GAGCCAAAAA
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
9 7 0.20
10 28 0.80
ACGTcount: A:0.84, C:0.09, G:0.07, T:0.00
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:1959535 original size:20 final size:20
Alignment explanation
Indices: 1959503--1959561 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
1959493 TTTTTTTTTT
1959503 CAAAAAAAC-AAAAAAAA-A
1 CAAAAAAACAAAAAAAAAGA
* *
1959521 CAAAAAAGGCAAAAAAAAAGG
1 CAAAAAA-ACAAAAAAAAAGA
1959542 CAAAAAAACAAAAAAAAAGA
1 CAAAAAAACAAAAAAAAAGA
1959562 GCCAAAAAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
18 7 0.21
19 1 0.03
20 19 0.56
21 7 0.21
ACGTcount: A:0.81, C:0.10, G:0.08, T:0.00
Consensus pattern (20 bp):
CAAAAAAACAAAAAAAAAGA
Found at i:1959536 original size:11 final size:12
Alignment explanation
Indices: 1959522--1959549 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1959512 AAAAAAAAAC
1959522 AAAAAAGGCAAA
1 AAAAAAGGCAAA
1959534 AAAAAAGGCAAA
1 AAAAAAGGCAAA
1959546 AAAA
1 AAAA
1959550 CAAAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.79, C:0.07, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAAAGGCAAA
Found at i:1959538 original size:13 final size:13
Alignment explanation
Indices: 1959517--1959549 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
1959507 AAAACAAAAA
1959517 AAAACAAAAAAGGC
1 AAAA-AAAAAAGGC
1959531 -AAAAAAAAAGGC
1 AAAAAAAAAAGGC
1959543 AAAAAAA
1 AAAAAAA
1959550 CAAAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 9 0.50
13 9 0.50
ACGTcount: A:0.79, C:0.09, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAGGC
Found at i:1959538 original size:21 final size:21
Alignment explanation
Indices: 1959512--1959577 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
1959502 TCAAAAAAAC
*
1959512 AAAAAAAAACAAAAAAGGCAA
1 AAAAAAAAACAAAAAAGACAA
**
1959533 AAAAAAAGGCAAAAAA-ACAA
1 AAAAAAAAACAAAAAAGACAA
* *
1959553 AAAAAAAGAGCCAAAAAAGCCAA
1 AAAAAAA-A-ACAAAAAAGACAA
1959576 AA
1 AA
1959578 TTTCAAAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
20 10 0.28
21 14 0.39
22 7 0.19
23 5 0.14
ACGTcount: A:0.77, C:0.12, G:0.11, T:0.00
Consensus pattern (21 bp):
AAAAAAAAACAAAAAAGACAA
Found at i:1959568 original size:20 final size:20
Alignment explanation
Indices: 1959503--1959570 Score: 86
Period size: 21 Copynumber: 3.4 Consensus size: 20
1959493 TTTTTTTTTT
1959503 CAAAAAAACAAAAAAAAA--
1 CAAAAAAACAAAAAAAAAGG
*
1959521 CAAAAAAGGCAAAAAAAAAGG
1 CAAAAAA-ACAAAAAAAAAGG
1959542 CAAAAAAACAAAAAAAAAGAG
1 CAAAAAAACAAAAAAAAAG-G
*
1959563 CCAAAAAA
1 CAAAAAAA
1959571 GCCAAAATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
18 7 0.16
19 10 0.23
20 11 0.26
21 15 0.35
ACGTcount: A:0.79, C:0.12, G:0.09, T:0.00
Consensus pattern (20 bp):
CAAAAAAACAAAAAAAAAGG
Found at i:1971295 original size:13 final size:12
Alignment explanation
Indices: 1971277--1971338 Score: 58
Period size: 13 Copynumber: 5.2 Consensus size: 12
1971267 ATACTATATG
1971277 TCCATCACCATCT
1 TCCATCACCAT-T
1971290 TCCATCACCATT
1 TCCATCACCATT
* *
1971302 T-CA-CGCCTATA
1 TCCATCACC-ATT
1971313 T-CATCACCATCT
1 TCCATCACCAT-T
1971325 TCCATCACCATT
1 TCCATCACCATT
1971337 TC
1 TC
1971339 ATGCCTATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
10 3 0.07
11 9 0.22
12 9 0.22
13 20 0.49
ACGTcount: A:0.24, C:0.42, G:0.02, T:0.32
Consensus pattern (12 bp):
TCCATCACCATT
Found at i:1971319 original size:35 final size:35
Alignment explanation
Indices: 1971279--1971358 Score: 151
Period size: 35 Copynumber: 2.3 Consensus size: 35
1971269 ACTATATGTC
1971279 CATCACCATCTTCCATCACCATTTCACGCCTATAT
1 CATCACCATCTTCCATCACCATTTCACGCCTATAT
*
1971314 CATCACCATCTTCCATCACCATTTCATGCCTATAT
1 CATCACCATCTTCCATCACCATTTCACGCCTATAT
1971349 CATCACCATC
1 CATCACCATC
1971359 CCTTAACCAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.26, C:0.40, G:0.03, T:0.31
Consensus pattern (35 bp):
CATCACCATCTTCCATCACCATTTCACGCCTATAT
Found at i:1971519 original size:15 final size:16
Alignment explanation
Indices: 1971496--1971539 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
1971486 TTGATAACAT
*
1971496 TTCTATCCATTT-CAA
1 TTCTTTCCATTTCCAA
*
1971511 TTCTTTCCATTTCCAT
1 TTCTTTCCATTTCCAA
1971527 TTCCTTTCCATTT
1 TT-CTTTCCATTT
1971540 ATTAATTATC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 11 0.44
16 4 0.16
17 10 0.40
ACGTcount: A:0.16, C:0.30, G:0.00, T:0.55
Consensus pattern (16 bp):
TTCTTTCCATTTCCAA
Found at i:1972011 original size:16 final size:16
Alignment explanation
Indices: 1971972--1972024 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 16
1971962 GAGTTGTAAG
1971972 TTATCTTCATTTTCTTA
1 TTAT-TTCATTTTCTTA
*
1971989 CTATTTCATTTTCTTA
1 TTATTTCATTTTCTTA
*
1972005 TTCTTTCATCTTTTCTTA
1 TTATTTCA--TTTTCTTA
1972023 TT
1 TT
1972025 TACTACATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
16 18 0.58
17 3 0.10
18 10 0.32
ACGTcount: A:0.15, C:0.19, G:0.00, T:0.66
Consensus pattern (16 bp):
TTATTTCATTTTCTTA
Found at i:1975060 original size:35 final size:36
Alignment explanation
Indices: 1975009--1975082 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 36
1974999 ATAAGATACT
*
1975009 ATCTGTCCATCACCATTTCACACCTATATTATCACC
1 ATCTGTCCATCACCATTTCACACCTATATCATCACC
*
1975045 ATCT-TCCATCACCATTTCACGCCTATATCATCACC
1 ATCTGTCCATCACCATTTCACACCTATATCATCACC
1975080 ATC
1 ATC
1975083 CCTTAACCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
35 32 0.89
36 4 0.11
ACGTcount: A:0.27, C:0.38, G:0.03, T:0.32
Consensus pattern (36 bp):
ATCTGTCCATCACCATTTCACACCTATATCATCACC
Found at i:1989376 original size:15 final size:15
Alignment explanation
Indices: 1989356--1989401 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 15
1989346 TTTGATATCA
1989356 TTTCTTTCCATTTCC
1 TTTCTTTCCATTTCC
1989371 TTTCTTAT-CATTTCC
1 TTTCTT-TCCATTTCC
1989386 TTTCTTCTTCCATTTC
1 TTTC-T-TTCCATTTC
1989402 TTATTTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 17 0.63
16 3 0.11
17 7 0.26
ACGTcount: A:0.09, C:0.30, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTCTTTCCATTTCC
Found at i:1993065 original size:15 final size:15
Alignment explanation
Indices: 1993045--1993090 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 15
1993035 TTTGATATCA
1993045 TTTCTTTCCATTTCC
1 TTTCTTTCCATTTCC
1993060 TTTCTTAT-CATTTCC
1 TTTCTT-TCCATTTCC
1993075 TTTCTTCTTCCATTTC
1 TTTC-T-TTCCATTTC
1993091 TTATTTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 17 0.63
16 3 0.11
17 7 0.26
ACGTcount: A:0.09, C:0.30, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTCTTTCCATTTCC
Found at i:1993962 original size:178 final size:181
Alignment explanation
Indices: 1993676--1994012 Score: 653
Period size: 178 Copynumber: 1.9 Consensus size: 181
1993666 CTACACCATC
1993676 TCCATAAACATTTTCATCACCATTAAAGCATCCTTTCATCACCAACAATATAATCATCCATTCCT
1 TCCATAAACATTTTCATCACCATTAAAGCATCCTTTCATCACCAACAATATAATCATCCATTCCT
1993741 CATCATTGGAGGTCAAATTCATCAACAAATTAAAGGATACTTCTTTATCAATTATGCATGCACTT
66 CATCATTGGAGGTCAAATTCATCAACAAATTAAAGGATACTTCTTTATCAATTATGCATGCACTT
1993806 TGATAACATTTTTTCCTTTCATCTTTTCATTATTTCATTTCTTTCTAATTT
131 TGATAACATTTTTTCCTTTCATCTTTTCATTATTTCATTTCTTTCTAATTT
1993857 TCCATAAACATTTTCATCACCATTAAAGCATCCTTTCATCACCAACAATATAATCATCCATT-C-
1 TCCATAAACATTTTCATCACCATTAAAGCATCCTTTCATCACCAACAATATAATCATCCATTCCT
1993920 C-TCATTGGAGGTCAAATTCATCAACAAATTAAAGGATACTTCTTTATCAATTATGCATGCACTT
66 CATCATTGGAGGTCAAATTCATCAACAAATTAAAGGATACTTCTTTATCAATTATGCATGCACTT
1993984 TGATAACATTTTTTCCTTTCATCTTTTCA
131 TGATAACATTTTTTCCTTTCATCTTTTCA
1994013 AACAACATGG
Statistics
Matches: 156, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
178 92 0.59
179 1 0.01
180 1 0.01
181 62 0.40
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.39
Consensus pattern (181 bp):
TCCATAAACATTTTCATCACCATTAAAGCATCCTTTCATCACCAACAATATAATCATCCATTCCT
CATCATTGGAGGTCAAATTCATCAACAAATTAAAGGATACTTCTTTATCAATTATGCATGCACTT
TGATAACATTTTTTCCTTTCATCTTTTCATTATTTCATTTCTTTCTAATTT
Found at i:2002513 original size:15 final size:15
Alignment explanation
Indices: 2002493--2002538 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 15
2002483 TTTGATATCA
2002493 TTTCTTTCCATTTCC
1 TTTCTTTCCATTTCC
2002508 TTTCTTAT-CATTTCC
1 TTTCTT-TCCATTTCC
2002523 TTTCTTCTTCCATTTC
1 TTTC-T-TTCCATTTC
2002539 TTATTTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 17 0.63
16 3 0.11
17 7 0.26
ACGTcount: A:0.09, C:0.30, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTCTTTCCATTTCC
Found at i:2004416 original size:15 final size:15
Alignment explanation
Indices: 2004398--2004427 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2004388 TCATTCTTTC
*
2004398 CATTTTCTTTCTTAT
1 CATTTCCTTTCTTAT
2004413 CATTTCCTTTCTTAT
1 CATTTCCTTTCTTAT
2004428 TCCATTTCTT
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:0.13, C:0.23, G:0.00, T:0.63
Consensus pattern (15 bp):
CATTTCCTTTCTTAT
Found at i:2007552 original size:13 final size:12
Alignment explanation
Indices: 2007533--2007597 Score: 57
Period size: 13 Copynumber: 5.4 Consensus size: 12
2007523 ATATGGGCGT
2007533 GATATGGTGATG
1 GATATGGTGATG
2007545 GAATATGGTGAT-
1 G-ATATGGTGATG
*
2007557 GATATAGGCG-T-
1 GATAT-GGTGATG
2007568 GATAATGGTGATG
1 GAT-ATGGTGATG
2007581 GACTATGGTGAT-
1 GA-TATGGTGATG
2007593 GATAT
1 GATAT
2007598 AGGCGTGATA
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
11 14 0.31
12 10 0.22
13 20 0.44
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.35, T:0.32
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:2007588 original size:36 final size:36
Alignment explanation
Indices: 2007515--2007619 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
2007505 ATTTATAAGT
* * *
2007515 TGGTGATAATATGGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
2007550 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
2007586 TGGTGATGATATAGGCGTGATAATGATGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
2007620 AGATTGTATC
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 19 0.29
36 46 0.71
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:2012079 original size:13 final size:12
Alignment explanation
Indices: 2012060--2012145 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
2012050 ATATGGGCGT
2012060 GATATGGTGATG
1 GATATGGTGATG
2012072 GAATATGGTGAT-
1 G-ATATGGTGATG
*
2012084 GATATAGGCG-T-
1 GATAT-GGTGATG
2012095 GATAATGGTGATG
1 GAT-ATGGTGATG
2012108 GACTATGGTGAT-
1 GA-TATGGTGATG
*
2012120 GATATAGGCG-T-
1 GATAT-GGTGATG
2012131 GATAATGGTGATG
1 GAT-ATGGTGATG
2012144 GA
1 GA
2012146 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:2012115 original size:36 final size:36
Alignment explanation
Indices: 2012042--2012146 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
2012032 ATTTATAAGT
* * *
2012042 TGGTGATAATATGGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
2012077 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
2012113 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
2012147 AGATTGTATC
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 19 0.29
36 47 0.71
ACGTcount: A:0.28, C:0.05, G:0.37, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:2018525 original size:23 final size:24
Alignment explanation
Indices: 2018497--2018549 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
2018487 AAAATCCGCA
*
2018497 AAGAAAATCAAAGTACTC-AAAAG
1 AAGAAAATCAAAGCACTCAAAAAG
* *
2018520 AAGAAAATTACAGCACTCAAAAAG
1 AAGAAAATCAAAGCACTCAAAAAG
2018544 AAGAAA
1 AAGAAA
2018550 GAAAAGCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 15 0.58
24 11 0.42
ACGTcount: A:0.62, C:0.13, G:0.13, T:0.11
Consensus pattern (24 bp):
AAGAAAATCAAAGCACTCAAAAAG
Found at i:2018557 original size:23 final size:22
Alignment explanation
Indices: 2018497--2018557 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 22
2018487 AAAATCCGCA
*
2018497 AAGAAAATCAAAGTACTCAAAAG
1 AAGAAAAT-AAAGCACTCAAAAG
*
2018520 AAGAAAATTACAGCACTCAAAAAG
1 AAGAAAA-TAAAGCACTC-AAAAG
2018544 AAGAAAGA-AAAGCA
1 AAGAAA-ATAAAGCA
2018558 AAGAAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
23 19 0.59
24 12 0.38
25 1 0.03
ACGTcount: A:0.62, C:0.13, G:0.15, T:0.10
Consensus pattern (22 bp):
AAGAAAATAAAGCACTCAAAAG
Found at i:2041205 original size:19 final size:19
Alignment explanation
Indices: 2041181--2041246 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
2041171 TTGGAGTGCA
*
2041181 AAAAGAAGACAAAAATCAG
1 AAAAGAAGACAAAAATAAG
*
2041200 AAAAGAAGAGAAAAATAAG
1 AAAAGAAGACAAAAATAAG
* *
2041219 AAAAGAAGAAAAGAAGAAAAG
1 AAAAGAAGACAA-AA-ATAAG
2041240 AAAAGAA
1 AAAAGAA
2041247 AAAGAGAAGT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 28 0.68
20 2 0.05
21 11 0.27
ACGTcount: A:0.74, C:0.03, G:0.20, T:0.03
Consensus pattern (19 bp):
AAAAGAAGACAAAAATAAG
Found at i:2041211 original size:5 final size:5
Alignment explanation
Indices: 2041198--2041248 Score: 52
Period size: 5 Copynumber: 10.2 Consensus size: 5
2041188 GACAAAAATC
* *
2041198 AGAAA AGAAG AGAAA A-ATA AGAAA AGAAGA A-AAGA AGAAA AGAAA AGAAA
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAA-A AGAA-A AGAAA AGAAA AGAAA
2041248 A
1 A
2041249 AGAGAAGTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
4 3 0.08
5 32 0.82
6 4 0.10
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (5 bp):
AGAAA
Found at i:2041222 original size:8 final size:8
Alignment explanation
Indices: 2041211--2041241 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
2041201 AAAGAAGAGA
*
2041211 AAAATAAG
1 AAAAGAAG
2041219 AAAAGAAG
1 AAAAGAAG
2041227 AAAAGAAG
1 AAAAGAAG
2041235 AAAAGAA
1 AAAAGAA
2041242 AAGAAAAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.03
Consensus pattern (8 bp):
AAAAGAAG
Found at i:2041251 original size:16 final size:16
Alignment explanation
Indices: 2041181--2041251 Score: 63
Period size: 16 Copynumber: 4.1 Consensus size: 16
2041171 TTGGAGTGCA
2041181 AAAAGAAGACAAAAATCAG
1 AAAAGAAGA-AAAAA--AG
2041200 AAAAGAAGAGAAAAATAAG
1 AAAAG-A-AGAAAAA-AAG
*
2041219 AAAAGAAGAAAAGAAG
1 AAAAGAAGAAAAAAAG
2041235 AAAAGAA-AAGAAAAAG
1 AAAAGAAGAA-AAAAAG
2041251 A
1 A
2041252 GAAGTTCAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
15 2 0.04
16 16 0.35
17 6 0.13
18 1 0.02
19 12 0.26
20 5 0.11
21 4 0.09
ACGTcount: A:0.75, C:0.03, G:0.20, T:0.03
Consensus pattern (16 bp):
AAAAGAAGAAAAAAAG
Found at i:2041251 original size:27 final size:27
Alignment explanation
Indices: 2041198--2041248 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
2041188 GACAAAAATC
2041198 AGAAAAGAAGAGAAAAATAAGAAAAGA
1 AGAAAAGAAGAGAAAAATAAGAAAAGA
2041225 AGAAAAGAAGA-AAAGAA-AAGAAAA
1 AGAAAAGAAGAGAAA-AATAAGAAAA
2041249 AGAGAAGTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (27 bp):
AGAAAAGAAGAGAAAAATAAGAAAAGA
Found at i:2046857 original size:198 final size:194
Alignment explanation
Indices: 2046503--2046858 Score: 622
Period size: 198 Copynumber: 1.8 Consensus size: 194
2046493 TATTTATTTC
2046503 ATTTCATTCTTATTATTTATTTTCATTACTTATATTATTACCCTTTATTAAGTCCATTATTAAAC
1 ATTTCATTCTTATTATTTATTTTCATTACTTATATTATTACCCTTTATTAAGTCCATTATTAAAC
*
2046568 ATATTTTCTTATCTTATTTTGCAGCCCAAACTTATAAATTCGAGGACATCAATACTTGTCAATCC
66 ATATTTTCTTATCTTATTTTGCAGCCCAAACTTATAAATTCAAGGACATCAATACTTGTCAATCC
*
2046633 TAGATCGGGACACAATAAGGCTATCTACTCTTCTCACCAAAGTATATAGATTCGCCTTACATCA
131 TAAATCGGGACACAATAAGGCTATCTACTCTTCTCACCAAAGTATATAGATTCGCCTTACATCA
* *
2046697 ATTTCATTCTTATTATTTCTTTTTCATTACTTATATTATTATCCCCTTTATTAATTCCATTATTA
1 ATTTCATTCTTATTATTT-ATTTTCATTACTTATATTATTA--CCCTTTATTAAGTCCATTATTA
* *
2046762 ATCATTATTTTCTTATCTTATTTTGCAGTCCAAACTTATAAATTCAAGGACATCAATACTTGTCA
63 AACA-TATTTTCTTATCTTATTTTGCAGCCCAAACTTATAAATTCAAGGACATCAATACTTGTCA
2046827 ATCCTAAATCGGGACACAATAAGGCTATCTAC
127 ATCCTAAATCGGGACACAATAAGGCTATCTAC
2046859 ATCTATTCCA
Statistics
Matches: 152, Mismatches: 6, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
194 18 0.12
195 21 0.14
197 24 0.16
198 89 0.59
ACGTcount: A:0.31, C:0.20, G:0.07, T:0.42
Consensus pattern (194 bp):
ATTTCATTCTTATTATTTATTTTCATTACTTATATTATTACCCTTTATTAAGTCCATTATTAAAC
ATATTTTCTTATCTTATTTTGCAGCCCAAACTTATAAATTCAAGGACATCAATACTTGTCAATCC
TAAATCGGGACACAATAAGGCTATCTACTCTTCTCACCAAAGTATATAGATTCGCCTTACATCA
Found at i:2047302 original size:36 final size:36
Alignment explanation
Indices: 2047261--2047409 Score: 208
Period size: 36 Copynumber: 4.1 Consensus size: 36
2047251 ATTTATAAGT
* * * *
2047261 TGGTGATAATATGGGCGTGATAATGGTGGTGGAATA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
* *
2047297 TGGTGACGATATAGGCGTGATAATGGAGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
* * *
2047333 TGGTGATGATAAAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
*
2047369 TGGTGATGATATAGGCGTGATAATGGAGATGGAAGA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
2047405 TGGTG
1 TGGTG
2047410 TTGGATAGAT
Statistics
Matches: 100, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 100 1.00
ACGTcount: A:0.30, C:0.05, G:0.38, T:0.28
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
Found at i:2047399 original size:23 final size:23
Alignment explanation
Indices: 2047304--2047399 Score: 56
Period size: 25 Copynumber: 4.0 Consensus size: 23
2047294 ATATGGTGAC
2047304 GATATAGGCGTGATAATGGAGAT
1 GATATAGGCGTGATAATGGAGAT
* * *
2047327 GGACTAT-GGTGATGATAAAGGCG-T
1 -GA-TATAGGCG-TGATAATGGAGAT
* *
2047351 GATA-ATG-GTGATGGACTATGGTGAT
1 GATATAGGCGTGAT--A--ATGGAGAT
2047376 GATATAGGCGTGATAATGGAGAT
1 GATATAGGCGTGATAATGGAGAT
2047399 G
1 G
2047400 GAAGATGGTG
Statistics
Matches: 54, Mismatches: 8, Indels: 21
0.65 0.10 0.25
Matches are distributed among these distances:
20 4 0.07
21 1 0.02
22 4 0.07
23 10 0.19
24 10 0.19
25 18 0.33
26 2 0.04
27 5 0.09
ACGTcount: A:0.31, C:0.05, G:0.36, T:0.27
Consensus pattern (23 bp):
GATATAGGCGTGATAATGGAGAT
Found at i:2051330 original size:36 final size:36
Alignment explanation
Indices: 2051277--2051425 Score: 208
Period size: 36 Copynumber: 4.1 Consensus size: 36
2051267 ATTTATAAGT
* * * *
2051277 TGGTGATAATATGGGCGTGATAATGGTGGTGGAATA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
* *
2051313 TGGTGACGATATAGGCGTGATAATGGAGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
* * *
2051349 TGGTGATGATAAAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
*
2051385 TGGTGATGATATAGGCGTGATAATGGAGATGGAAGA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
2051421 TGGTG
1 TGGTG
2051426 TTGGACAGAT
Statistics
Matches: 100, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 100 1.00
ACGTcount: A:0.30, C:0.05, G:0.38, T:0.28
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
Found at i:2051415 original size:23 final size:23
Alignment explanation
Indices: 2051320--2051415 Score: 56
Period size: 25 Copynumber: 4.0 Consensus size: 23
2051310 ATATGGTGAC
2051320 GATATAGGCGTGATAATGGAGAT
1 GATATAGGCGTGATAATGGAGAT
* * *
2051343 GGACTAT-GGTGATGATAAAGGCG-T
1 -GA-TATAGGCG-TGATAATGGAGAT
* *
2051367 GATA-ATG-GTGATGGACTATGGTGAT
1 GATATAGGCGTGAT--A--ATGGAGAT
2051392 GATATAGGCGTGATAATGGAGAT
1 GATATAGGCGTGATAATGGAGAT
2051415 G
1 G
2051416 GAAGATGGTG
Statistics
Matches: 54, Mismatches: 8, Indels: 21
0.65 0.10 0.25
Matches are distributed among these distances:
20 4 0.07
21 1 0.02
22 4 0.07
23 10 0.19
24 10 0.19
25 18 0.33
26 2 0.04
27 5 0.09
ACGTcount: A:0.31, C:0.05, G:0.36, T:0.27
Consensus pattern (23 bp):
GATATAGGCGTGATAATGGAGAT
Found at i:2054025 original size:19 final size:19
Alignment explanation
Indices: 2053989--2054026 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2053979 AATAAAAAGC
*
2053989 AACAAGAAAGAAGAAAAAA
1 AACAAGAAAGAAAAAAAAA
2054008 AACAA-AAAGAAAAGAAAAA
1 AACAAGAAAGAAAA-AAAAA
2054027 GACTCCTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.82, C:0.05, G:0.13, T:0.00
Consensus pattern (19 bp):
AACAAGAAAGAAAAAAAAA
Found at i:2054113 original size:25 final size:24
Alignment explanation
Indices: 2054057--2054106 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2054047 AGTGCAAAAG
* *
2054057 AAAGAAAAGAAAAAGAAGAATCAA
1 AAAGCAAAGAAAAAGAAGAAACAA
2054081 AAAGCAAAGAAAAA-AATGAAACAA
1 AAAGCAAAGAAAAAGAA-GAAACAA
2054105 AA
1 AA
2054107 TTGCAAATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 2 0.09
24 21 0.91
ACGTcount: A:0.76, C:0.06, G:0.14, T:0.04
Consensus pattern (24 bp):
AAAGCAAAGAAAAAGAAGAAACAA
Found at i:2060428 original size:16 final size:17
Alignment explanation
Indices: 2060409--2060441 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2060399 CTTTTTCTTT
2060409 TCTTTTC-TTCTTTTTG
1 TCTTTTCTTTCTTTTTG
2060425 TCTTTTCTTTCTTTTTG
1 TCTTTTCTTTCTTTTTG
2060442 CACTCCAATT
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:0.00, C:0.18, G:0.06, T:0.76
Consensus pattern (17 bp):
TCTTTTCTTTCTTTTTG
Found at i:2060428 original size:21 final size:21
Alignment explanation
Indices: 2060394--2060434 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2060384 TCTTTTTGAA
2060394 CTTCTCTTTTTCTTTTCTTTT
1 CTTCTCTTTTTCTTTTCTTTT
2060415 CTTCT-TTTTGTCTTTTCTTT
1 CTTCTCTTTT-TCTTTTCTTT
2060435 CTTTTTGCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (21 bp):
CTTCTCTTTTTCTTTTCTTTT
Found at i:2065147 original size:13 final size:12
Alignment explanation
Indices: 2065131--2065178 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 12
2065121 GTGCAAAAAG
2065131 AAAAGAAAAGACA
1 AAAAGAAAAGA-A
2065144 AAAAGAAAA-AA
1 AAAAGAAAAGAA
2065155 AAATCAGAAAAGAA
1 AAA--AGAAAAGAA
2065169 GAAAAGAAAA
1 -AAAAGAAAA
2065179 AGAAGTTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
11 4 0.13
12 1 0.03
13 21 0.68
14 2 0.06
15 3 0.10
ACGTcount: A:0.79, C:0.04, G:0.15, T:0.02
Consensus pattern (12 bp):
AAAAGAAAAGAA
Found at i:2070367 original size:19 final size:19
Alignment explanation
Indices: 2070345--2070382 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
2070335 CTTTATTTCA
2070345 TTTCATT-CTTATTATTATT
1 TTTCATTACTTA-TATTATT
2070364 TTTCATTACTTATATTATT
1 TTTCATTACTTATATTATT
2070383 ATCCCCTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTCATTACTTATATTATT
Found at i:2074977 original size:8 final size:8
Alignment explanation
Indices: 2074966--2075005 Score: 55
Period size: 8 Copynumber: 4.9 Consensus size: 8
2074956 TCTTTTTCTT
2074966 TTCTTTTC
1 TTCTTTTC
2074974 TTCTTTTC
1 TTCTTTTC
2074982 TTCTTTT-
1 TTCTTTTC
2074989 TGTCTTTTC
1 T-TCTTTTC
2074998 TTTCTTTT
1 -TTCTTTT
2075006 TGCACTCCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
7 1 0.03
8 21 0.72
9 6 0.21
10 1 0.03
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.78
Consensus pattern (8 bp):
TTCTTTTC
Found at i:2074985 original size:16 final size:17
Alignment explanation
Indices: 2074959--2075007 Score: 66
Period size: 16 Copynumber: 2.9 Consensus size: 17
2074949 GAACTTCTCT
2074959 TTTTCTTTTCTTTTCT-TC
1 TTTTC-TTTCTTTT-TGTC
2074977 TTTTC-TTCTTTTTGTC
1 TTTTCTTTCTTTTTGTC
2074993 TTTTCTTTCTTTTTG
1 TTTTCTTTCTTTTTG
2075008 CACTCCAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
15 1 0.03
16 14 0.48
17 9 0.31
18 5 0.17
ACGTcount: A:0.00, C:0.18, G:0.04, T:0.78
Consensus pattern (17 bp):
TTTTCTTTCTTTTTGTC
Found at i:2075308 original size:19 final size:20
Alignment explanation
Indices: 2075269--2075304 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 20
2075259 GGGTAATAAT
2075269 ATAAGTAATGAAAATAAATA
1 ATAAGTAATGAAAATAAATA
2075289 ATAAG-AATG-AAATAAA
1 ATAAGTAATGAAAATAAA
2075305 ATAAATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.44
19 4 0.25
20 5 0.31
ACGTcount: A:0.67, C:0.00, G:0.11, T:0.22
Consensus pattern (20 bp):
ATAAGTAATGAAAATAAATA
Found at i:2084369 original size:23 final size:24
Alignment explanation
Indices: 2084338--2084441 Score: 67
Period size: 25 Copynumber: 4.4 Consensus size: 24
2084328 CACCATCTTC
*
2084338 CATCTCCATTATCA-CGCCTATAT
1 CATCACCATTATCATCGCCTATAT
*
2084361 CATCACCA-TAGTCCATCACC-ATTAT
1 CATCACCATTA-T-CATCGCCTA-TAT
* * *
2084386 CA-CGCCTTTATCATC-ACTATAGT
1 CATCACCATTATCATCGCCTATA-T
*
2084409 CCATCTCCATTATCA-CGCCTATAT
1 -CATCACCATTATCATCGCCTATAT
2084433 CATCACCAT
1 CATCACCAT
2084442 ATTCCACCAC
Statistics
Matches: 62, Mismatches: 9, Indels: 20
0.68 0.10 0.22
Matches are distributed among these distances:
22 5 0.08
23 22 0.35
24 11 0.18
25 24 0.39
ACGTcount: A:0.28, C:0.36, G:0.05, T:0.32
Consensus pattern (24 bp):
CATCACCATTATCATCGCCTATAT
Found at i:2084376 original size:36 final size:36
Alignment explanation
Indices: 2084336--2084476 Score: 219
Period size: 36 Copynumber: 3.9 Consensus size: 36
2084326 AACACCATCT
*
2084336 TCCATCTCCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
* *
2084372 TCCATCACCATTATCACGCCTTTATCATCACTATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
* *
2084408 TCCATCTCCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
* *
2084444 TCCACCACCATTATCACGCCTATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
2084477 ACTTATAAAT
Statistics
Matches: 95, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 95 1.00
ACGTcount: A:0.28, C:0.36, G:0.04, T:0.31
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAG
Found at i:2084453 original size:72 final size:72
Alignment explanation
Indices: 2084336--2084474 Score: 242
Period size: 72 Copynumber: 1.9 Consensus size: 72
2084326 AACACCATCT
* *
2084336 TCCATCTCCATTATCACGCCTATATCATCACCATAGTCCATCACCATTATCACGCCTTTATCATC
1 TCCATCTCCATTATCACGCCTATATCATCACCATAGTCCACCACCATTATCACGCCTATATCATC
2084401 ACTATAG
66 ACTATAG
* *
2084408 TCCATCTCCATTATCACGCCTATATCATCACCATATTCCACCACCATTATCACGCCTATATTATC
1 TCCATCTCCATTATCACGCCTATATCATCACCATAGTCCACCACCATTATCACGCCTATATCATC
2084473 AC
66 AC
2084475 CAACTTATAA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 63 1.00
ACGTcount: A:0.28, C:0.36, G:0.04, T:0.32
Consensus pattern (72 bp):
TCCATCTCCATTATCACGCCTATATCATCACCATAGTCCACCACCATTATCACGCCTATATCATC
ACTATAG
Found at i:2084636 original size:15 final size:15
Alignment explanation
Indices: 2084616--2084650 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
2084606 TCTTTGATAA
2084616 CTATTCTATCCATTT
1 CTATTCTATCCATTT
*
2084631 CTATTCTTTCCATTT
1 CTATTCTATCCATTT
2084646 CTATT
1 CTATT
2084651 TCATTTCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.17, C:0.26, G:0.00, T:0.57
Consensus pattern (15 bp):
CTATTCTATCCATTT
Found at i:2084892 original size:12 final size:11
Alignment explanation
Indices: 2084872--2084899 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
2084862 GAGAAAGAAT
2084872 AAAAGAAAAAA
1 AAAAGAAAAAA
2084883 AAAAGAAAAAA
1 AAAAGAAAAAA
2084894 AAAAGA
1 AAAAGA
2084900 CTCCTACAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAA
Found at i:2088422 original size:13 final size:13
Alignment explanation
Indices: 2088400--2088429 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2088390 ACTAAACACC
2088400 TTTC-ACATACCT
1 TTTCAACATACCT
2088412 TTTCAACATACCT
1 TTTCAACATACCT
2088425 TTTCA
1 TTTCA
2088430 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:2095679 original size:23 final size:23
Alignment explanation
Indices: 2095648--2095751 Score: 63
Period size: 25 Copynumber: 4.4 Consensus size: 23
2095638 CACCATCTTC
*
2095648 CATCTCCATTATCACGCCTATAT
1 CATCACCATTATCACGCCTATAT
*
2095671 CATCACCATAGTCCATCACG-AT-TAT
1 CATCACCAT--T--ATCACGCCTATAT
* * *
2095696 CA-CGCCTTTATCATC-ACTATAGT
1 CATCACCATTATCA-CGCCTATA-T
*
2095719 CCATCTCCATTATCACGCCTATAT
1 -CATCACCATTATCACGCCTATAT
2095743 CATCACCAT
1 CATCACCAT
2095752 ATTCCACCAC
Statistics
Matches: 61, Mismatches: 9, Indels: 22
0.66 0.10 0.24
Matches are distributed among these distances:
20 4 0.07
21 2 0.03
22 3 0.05
23 17 0.28
24 8 0.13
25 20 0.33
26 1 0.02
27 6 0.10
ACGTcount: A:0.28, C:0.35, G:0.06, T:0.32
Consensus pattern (23 bp):
CATCACCATTATCACGCCTATAT
Found at i:2095686 original size:36 final size:36
Alignment explanation
Indices: 2095646--2095786 Score: 210
Period size: 36 Copynumber: 3.9 Consensus size: 36
2095636 AACACCATCT
*
2095646 TCCATCTCCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
* * *
2095682 TCCATCACGATTATCACGCCTTTATCATCACTATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
* *
2095718 TCCATCTCCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
* *
2095754 TCCACCACCATTATCACGCCTATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
2095787 ACTTATAAAT
Statistics
Matches: 93, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 93 1.00
ACGTcount: A:0.28, C:0.35, G:0.05, T:0.31
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAG
Found at i:2095767 original size:72 final size:72
Alignment explanation
Indices: 2095646--2095784 Score: 233
Period size: 72 Copynumber: 1.9 Consensus size: 72
2095636 AACACCATCT
* * *
2095646 TCCATCTCCATTATCACGCCTATATCATCACCATAGTCCATCACGATTATCACGCCTTTATCATC
1 TCCATCTCCATTATCACGCCTATATCATCACCATAGTCCACCACCATTATCACGCCTATATCATC
2095711 ACTATAG
66 ACTATAG
* *
2095718 TCCATCTCCATTATCACGCCTATATCATCACCATATTCCACCACCATTATCACGCCTATATTATC
1 TCCATCTCCATTATCACGCCTATATCATCACCATAGTCCACCACCATTATCACGCCTATATCATC
2095783 AC
66 AC
2095785 CAACTTATAA
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 62 1.00
ACGTcount: A:0.28, C:0.35, G:0.05, T:0.32
Consensus pattern (72 bp):
TCCATCTCCATTATCACGCCTATATCATCACCATAGTCCACCACCATTATCACGCCTATATCATC
ACTATAG
Found at i:2097575 original size:15 final size:15
Alignment explanation
Indices: 2097555--2097587 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2097545 TAAGAAATGA
2097555 AATTGAAATGGAAAG
1 AATTGAAATGGAAAG
*
2097570 AATTGAAATGGATAG
1 AATTGAAATGGAAAG
2097585 AAT
1 AAT
2097588 AGTTATCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (15 bp):
AATTGAAATGGAAAG
Found at i:2097771 original size:36 final size:36
Alignment explanation
Indices: 2097729--2097877 Score: 217
Period size: 36 Copynumber: 4.1 Consensus size: 36
2097719 ATTTATAAGT
* * *
2097729 TGGTGATAATATAGGCGTGATAATGGTGGTGGAATA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
*
2097765 TGGTGATGATATAGGCGTGATAATGGAGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
* * * *
2097801 TAGTGATGATAAAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
*
2097837 TGGTGATGATATAGGCGTGATAATGGAGATGGAAGA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
2097873 TGGTG
1 TGGTG
2097878 TTGGACAGAT
Statistics
Matches: 101, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 101 1.00
ACGTcount: A:0.31, C:0.04, G:0.37, T:0.28
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
Found at i:2097795 original size:23 final size:22
Alignment explanation
Indices: 2097764--2097867 Score: 59
Period size: 25 Copynumber: 4.4 Consensus size: 22
2097754 GTGGTGGAAT
*
2097764 ATGGTGATGATATAGGCGTGATA
1 ATGGAGATGATATAGG-GTGATA
*
2097787 ATGGAGATGGACTATAGTGATGATA
1 ATGGAGAT-GA-TATAG-GGTGATA
* * *
2097812 AAGGCG-TGATA-ATGGTGATGGA
1 ATGGAGATGATATAGGGTGAT--A
*
2097834 CTATGGTGATGATATAGGCGTGATA
1 --ATGGAGATGATATAGG-GTGATA
2097859 ATGGAGATG
1 ATGGAGATG
2097868 GAAGATGGTG
Statistics
Matches: 61, Mismatches: 10, Indels: 20
0.67 0.11 0.22
Matches are distributed among these distances:
20 5 0.08
21 1 0.02
22 3 0.05
23 17 0.28
24 7 0.11
25 20 0.33
26 3 0.05
27 5 0.08
ACGTcount: A:0.32, C:0.05, G:0.36, T:0.28
Consensus pattern (22 bp):
ATGGAGATGATATAGGGTGATA
Found at i:2097848 original size:72 final size:72
Alignment explanation
Indices: 2097731--2097869 Score: 242
Period size: 72 Copynumber: 1.9 Consensus size: 72
2097721 TTATAAGTTG
* *
2097731 GTGATAATATAGGCGTGATAATGGTGGTGGAATATGGTGATGATATAGGCGTGATAATGGAGATG
1 GTGATAATAAAGGCGTGATAATGGTGATGGAATATGGTGATGATATAGGCGTGATAATGGAGATG
2097796 GACTATA
66 GACTATA
* *
2097803 GTGATGATAAAGGCGTGATAATGGTGATGGACTATGGTGATGATATAGGCGTGATAATGGAGATG
1 GTGATAATAAAGGCGTGATAATGGTGATGGAATATGGTGATGATATAGGCGTGATAATGGAGATG
2097868 GA
66 GA
2097870 AGATGGTGTT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 63 1.00
ACGTcount: A:0.32, C:0.04, G:0.36, T:0.28
Consensus pattern (72 bp):
GTGATAATAAAGGCGTGATAATGGTGATGGAATATGGTGATGATATAGGCGTGATAATGGAGATG
GACTATA
Found at i:2101617 original size:36 final size:36
Alignment explanation
Indices: 2101576--2101724 Score: 208
Period size: 36 Copynumber: 4.1 Consensus size: 36
2101566 ATTTATAAGT
* * *
2101576 TGGTGATAATATAGGCGTGATAATGGTGGTGGAATA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
*
2101612 TGGTGATGATATAGGCGTGATAATGGAGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
* * * *
2101648 TAGTGATGATAAAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
* *
2101684 TGGTGATGATATAGGCGCGATAATGGAGATGGAAGA
1 TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
2101720 TGGTG
1 TGGTG
2101725 TTGGACAGAT
Statistics
Matches: 100, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 100 1.00
ACGTcount: A:0.31, C:0.05, G:0.37, T:0.28
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGAGATGGAATA
Found at i:2101695 original size:72 final size:72
Alignment explanation
Indices: 2101578--2101716 Score: 233
Period size: 72 Copynumber: 1.9 Consensus size: 72
2101568 TTATAAGTTG
* * *
2101578 GTGATAATATAGGCGTGATAATGGTGGTGGAATATGGTGATGATATAGGCGTGATAATGGAGATG
1 GTGATAATAAAGGCGTGATAATGGTGATGGAATATGGTGATGATATAGGCGCGATAATGGAGATG
2101643 GACTATA
66 GACTATA
* *
2101650 GTGATGATAAAGGCGTGATAATGGTGATGGACTATGGTGATGATATAGGCGCGATAATGGAGATG
1 GTGATAATAAAGGCGTGATAATGGTGATGGAATATGGTGATGATATAGGCGCGATAATGGAGATG
2101715 GA
66 GA
2101717 AGATGGTGTT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 62 1.00
ACGTcount: A:0.32, C:0.05, G:0.36, T:0.27
Consensus pattern (72 bp):
GTGATAATAAAGGCGTGATAATGGTGATGGAATATGGTGATGATATAGGCGCGATAATGGAGATG
GACTATA
Found at i:2107744 original size:19 final size:19
Alignment explanation
Indices: 2107720--2107760 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
2107710 GATGTAGGAG
* *
2107720 TTTTTCTTTTCTTTTTGTT
1 TTTTTCTTCTCTTTTTATT
2107739 TTTTTCTTCTCTTTTTATT
1 TTTTTCTTCTCTTTTTATT
2107758 TTT
1 TTT
2107761 GTTGCATCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.02, C:0.12, G:0.02, T:0.83
Consensus pattern (19 bp):
TTTTTCTTCTCTTTTTATT
Found at i:2114019 original size:2 final size:2
Alignment explanation
Indices: 2114012--2114046 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
2114002 TTGATATCTT
*
2114012 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2114047 GTTATAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2118096 original size:13 final size:11
Alignment explanation
Indices: 2118055--2118139 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
2118045 ACAATATGTC
2118055 CATCACCATTAT
1 CATCACCA-TAT
*
2118067 CATGC-CTATAT
1 CAT-CACCATAT
2118078 CATCACCATAGT
1 CATCACCATA-T
2118090 CCATCACCATTAT
1 -CATCACCA-TAT
*
2118103 CA-CGCCTATAT
1 CATCACC-ATAT
2118114 CATCACCATATT
1 CATCACCATA-T
2118126 CCATCACCATAT
1 -CATCACCATAT
2118138 CA
1 CA
2118140 CGCCCATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
10 1 0.02
11 23 0.38
12 14 0.23
13 20 0.33
14 2 0.03
ACGTcount: A:0.32, C:0.35, G:0.04, T:0.29
Consensus pattern (11 bp):
CATCACCATAT
Found at i:2118099 original size:36 final size:36
Alignment explanation
Indices: 2118052--2118156 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
2118042 GATACAATAT
*
2118052 GTCCATCACCATTATCATGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
2118088 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
2118124 TTCCATCACCA-TATCACGCCCATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
2118157 ACTTATAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 20 0.31
36 45 0.69
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:2120762 original size:2 final size:2
Alignment explanation
Indices: 2120755--2120802 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
2120745 TGACAACAGA
2120755 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
2120797 AT AT AT
1 AT AT AT
2120803 GTTGGTGATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2124206 original size:17 final size:17
Alignment explanation
Indices: 2124181--2124220 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
2124171 GTATGTTGTT
*
2124181 CATTAAAGCATGCATTG
1 CATTTAAGCATGCATTG
* *
2124198 CATTTAAGCATGTATTT
1 CATTTAAGCATGCATTG
2124215 CATTTA
1 CATTTA
2124221 GGGAAGTAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (17 bp):
CATTTAAGCATGCATTG
Found at i:2126681 original size:19 final size:19
Alignment explanation
Indices: 2126657--2126708 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 19
2126647 GAAGAAGAAA
2126657 TGAGAGTTGAAAAAGAC-AT
1 TGAGAGTTGAAAAA-ACAAT
2126676 TGAGAGAATTGAAAAAACAAT
1 TGAGAG--TTGAAAAAACAAT
2126697 TGAGAG-TGAAAA
1 TGAGAGTTGAAAA
2126709 TGAGCATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
18 6 0.20
19 6 0.20
20 2 0.07
21 16 0.53
ACGTcount: A:0.52, C:0.04, G:0.25, T:0.19
Consensus pattern (19 bp):
TGAGAGTTGAAAAAACAAT
Found at i:2126682 original size:21 final size:21
Alignment explanation
Indices: 2126658--2126702 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
2126648 AAGAAGAAAT
*
2126658 GAGAGTTGAAAAAGAC-ATTGA
1 GAGAATTGAAAAA-ACAATTGA
2126679 GAGAATTGAAAAAACAATTGA
1 GAGAATTGAAAAAACAATTGA
2126700 GAG
1 GAG
2126703 TGAAAATGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.51, C:0.04, G:0.27, T:0.18
Consensus pattern (21 bp):
GAGAATTGAAAAAACAATTGA
Found at i:2128057 original size:18 final size:18
Alignment explanation
Indices: 2128034--2128075 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
2128024 ATGCATTTAG
2128034 TTCATTGAATAAAGTTAT
1 TTCATTGAATAAAGTTAT
*
2128052 TTCATTGAATAATGTTAT
1 TTCATTGAATAAAGTTAT
2128070 TTCATT
1 TTCATT
2128076 AATCAAACTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (18 bp):
TTCATTGAATAAAGTTAT
Found at i:2130225 original size:13 final size:14
Alignment explanation
Indices: 2130202--2130230 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2130192 ATAAGATACT
2130202 ATCTGTCCATCACC
1 ATCTGTCCATCACC
2130216 ATCT-TCCATCACC
1 ATCTGTCCATCACC
2130229 AT
1 AT
2130231 TTAACGCCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.24, C:0.41, G:0.03, T:0.31
Consensus pattern (14 bp):
ATCTGTCCATCACC
Found at i:2130255 original size:35 final size:35
Alignment explanation
Indices: 2130209--2130288 Score: 133
Period size: 35 Copynumber: 2.3 Consensus size: 35
2130199 ACTATCTGTC
* *
2130209 CATCACCATCTTCCATCACCATTTAACGCCTATAT
1 CATCACCATCTTCCATCACCATATAACGCCTACAT
*
2130244 CATCACCATCTTCCATCACCATATCACGCCTACAT
1 CATCACCATCTTCCATCACCATATAACGCCTACAT
2130279 CATCACCATC
1 CATCACCATC
2130289 CCTTATCCAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.29, C:0.41, G:0.03, T:0.28
Consensus pattern (35 bp):
CATCACCATCTTCCATCACCATATAACGCCTACAT
Found at i:2131017 original size:17 final size:17
Alignment explanation
Indices: 2130992--2131024 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2130982 ATTCTACCTC
2130992 TACCATAACCATTTCTA
1 TACCATAACCATTTCTA
*
2131009 TACCCTAACCATTTCT
1 TACCATAACCATTTCT
2131025 TTTAAGCCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.36
Consensus pattern (17 bp):
TACCATAACCATTTCTA
Found at i:2132077 original size:17 final size:17
Alignment explanation
Indices: 2132055--2132098 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
2132045 ACACAAGGTG
*
2132055 GGATGAATTTGGCCAAA
1 GGATGAATTCGGCCAAA
2132072 GGATGAATTCGGCCAAA
1 GGATGAATTCGGCCAAA
*
2132089 GGATGTATTC
1 GGATGAATTC
2132099 CATTAAAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.32, C:0.14, G:0.30, T:0.25
Consensus pattern (17 bp):
GGATGAATTCGGCCAAA
Found at i:2136316 original size:13 final size:13
Alignment explanation
Indices: 2136298--2136322 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2136288 GATACTATAT
2136298 TTCCATCACCATC
1 TTCCATCACCATC
2136311 TTCCATCACCAT
1 TTCCATCACCAT
2136323 TTCACGCCTA
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:0.24, C:0.44, G:0.00, T:0.32
Consensus pattern (13 bp):
TTCCATCACCATC
Found at i:2139015 original size:15 final size:17
Alignment explanation
Indices: 2138992--2139025 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
2138982 TTAATATATG
2138992 TTTAGTTTATTA-TTAT
1 TTTAGTTTATTAGTTAT
2139008 TTTA-TTTATTAGTTAT
1 TTTAGTTTATTAGTTAT
2139024 TT
1 TT
2139026 AGGACCTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (17 bp):
TTTAGTTTATTAGTTAT
Found at i:2139836 original size:9 final size:8
Alignment explanation
Indices: 2139776--2139835 Score: 66
Period size: 8 Copynumber: 7.0 Consensus size: 8
2139766 ATTTTGTTTT
2139776 CAAAAAAA
1 CAAAAAAA
2139784 CAAAAAAAA
1 C-AAAAAAA
2139793 CAAAAAAAA
1 C-AAAAAAA
2139802 GGCAAAAAAA
1 --CAAAAAAA
**
2139812 CAAAAAGG
1 CAAAAAAA
2139820 CAAAAAAA
1 CAAAAAAA
2139828 CAAAAAAA
1 CAAAAAAA
2139836 AAGCCAAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
8 21 0.47
9 16 0.36
10 7 0.16
11 1 0.02
ACGTcount: A:0.82, C:0.12, G:0.07, T:0.00
Consensus pattern (8 bp):
CAAAAAAA
Found at i:2139848 original size:10 final size:10
Alignment explanation
Indices: 2139776--2139854 Score: 55
Period size: 10 Copynumber: 8.5 Consensus size: 10
2139766 ATTTTGTTTT
2139776 CAAAAAAA--
1 CAAAAAAAGC
*
2139784 CAAAAAAAAC
1 CAAAAAAAGC
* *
2139794 AAAAAAAAGG
1 CAAAAAAAGC
2139804 CAAAAAAA--
1 CAAAAAAAGC
*
2139812 C--AAAAAGG
1 CAAAAAAAGC
2139820 CAAAAAAA-C
1 CAAAAAAAGC
*
2139829 AAAAAAAAAGC
1 -CAAAAAAAGC
2139840 CAAAAAAAGC
1 CAAAAAAAGC
2139850 CAAAA
1 CAAAA
2139855 TTTCAAAAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
6 5 0.09
8 10 0.18
10 40 0.71
11 1 0.02
ACGTcount: A:0.78, C:0.14, G:0.08, T:0.00
Consensus pattern (10 bp):
CAAAAAAAGC
Found at i:2143751 original size:15 final size:17
Alignment explanation
Indices: 2143728--2143761 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
2143718 TTAATATATG
2143728 TTTAGTTTATTA-TTAT
1 TTTAGTTTATTAGTTAT
2143744 TTTA-TTTATTAGTTAT
1 TTTAGTTTATTAGTTAT
2143760 TT
1 TT
2143762 AGGACCTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (17 bp):
TTTAGTTTATTAGTTAT
Found at i:2145882 original size:24 final size:25
Alignment explanation
Indices: 2145845--2145892 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
2145835 ACCTATTTTT
* *
2145845 GATGAGGAACCTGAA-AAAATGCAA
1 GATGAAGAAACTGAAGAAAATGCAA
2145869 GATGAAGAAACTGAAGAAAATGCA
1 GATGAAGAAACTGAAGAAAATGCA
2145893 TATCATGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.52, C:0.10, G:0.25, T:0.12
Consensus pattern (25 bp):
GATGAAGAAACTGAAGAAAATGCAA
Found at i:2149569 original size:36 final size:36
Alignment explanation
Indices: 2149522--2149661 Score: 208
Period size: 36 Copynumber: 3.9 Consensus size: 36
2149512 CTGTCCAACA
*
2149522 CCATCTCCATTATCACGCCTATATCATCACCATAGT
1 CCATCACCATTATCACGCCTATATCATCACCATAGT
*
2149558 CCATCACCATTATCACGCCTTTATCATCACCATAGT
1 CCATCACCATTATCACGCCTATATCATCACCATAGT
* * *
2149594 CCATCTCCATTATCACGCCTATATCGTCACCATATT
1 CCATCACCATTATCACGCCTATATCATCACCATAGT
* * *
2149630 CCACCACCATTATCACGCCCATATTATCACCA
1 CCATCACCATTATCACGCCTATATCATCACCA
2149662 ACTTATAAAT
Statistics
Matches: 93, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 93 1.00
ACGTcount: A:0.28, C:0.38, G:0.05, T:0.29
Consensus pattern (36 bp):
CCATCACCATTATCACGCCTATATCATCACCATAGT
Found at i:2153434 original size:19 final size:20
Alignment explanation
Indices: 2153373--2153436 Score: 73
Period size: 19 Copynumber: 3.4 Consensus size: 20
2153363 ATTGGAGTGC
* *
2153373 AAAAAGAAGACAAAAATCA-
1 AAAAAGAAGAGAAAAATAAG
2153392 AAAAAGAAGAGAAAAATAAG
1 AAAAAGAAGAGAAAAATAAG
2153412 -AAAAGAAGA-AAAGAA-AAG
1 AAAAAGAAGAGAAA-AATAAG
2153430 AAAAAGA
1 AAAAAGA
2153437 GAAGTTCAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
18 6 0.15
19 34 0.85
ACGTcount: A:0.77, C:0.03, G:0.17, T:0.03
Consensus pattern (20 bp):
AAAAAGAAGAGAAAAATAAG
Found at i:2153439 original size:13 final size:12
Alignment explanation
Indices: 2153391--2153439 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 12
2153381 GACAAAAATC
*
2153391 AAAAAAGAAGAG
1 AAAAAAGAAAAG
2153403 AAAAATAAGAAAAG
1 -AAAA-AAGAAAAG
2153417 AAGAAAAGAAAAG
1 AA-AAAAGAAAAG
2153430 AAAAAGAGAA
1 AAAAA-AGAA
2153440 GTTCAAAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
12 3 0.09
13 20 0.62
14 9 0.28
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (12 bp):
AAAAAAGAAAAG
Found at i:2167566 original size:13 final size:13
Alignment explanation
Indices: 2167548--2167574 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2167538 ATAATGCAAT
2167548 TGACATGATAACA
1 TGACATGATAACA
2167561 TGACATGATAACA
1 TGACATGATAACA
2167574 T
1 T
2167575 AAGTAAGGAA
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:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (13 bp):
TGACATGATAACA
Found at i:2170459 original size:18 final size:17
Alignment explanation
Indices: 2170438--2170507 Score: 70
Period size: 18 Copynumber: 4.0 Consensus size: 17
2170428 AGTATCACCT
2170438 TTCATTCAA-TAAAGCTAG
1 TTCATT-AATTAAA-CTAG
*
2170456 TTCACTAATTAAACTAG
1 TTCATTAATTAAACTAG
* * *
2170473 TTCATCCATTTAAACTGG
1 TTCAT-TAATTAAACTAG
2170491 TTCATTAATTAAACTAG
1 TTCATTAATTAAACTAG
2170508 CTCTTTATAT
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
17 19 0.45
18 23 0.55
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (17 bp):
TTCATTAATTAAACTAG
Found at i:2172599 original size:8 final size:8
Alignment explanation
Indices: 2172586--2172632 Score: 60
Period size: 8 Copynumber: 5.8 Consensus size: 8
2172576 TAACAACAAC
*
2172586 AAAAAAGA
1 AAAAAATA
2172594 AAAAAATA
1 AAAAAATA
2172602 CAAAAAGA-A
1 -AAAAA-ATA
2172611 AAAAAATA
1 AAAAAATA
2172619 AAAAAATA
1 AAAAAATA
2172627 AAAAAA
1 AAAAAA
2172633 AAGAAAGTGA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
7 1 0.03
8 27 0.77
9 6 0.17
10 1 0.03
ACGTcount: A:0.87, C:0.02, G:0.04, T:0.06
Consensus pattern (8 bp):
AAAAAATA
Found at i:2172633 original size:17 final size:17
Alignment explanation
Indices: 2172586--2172633 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
2172576 TAACAACAAC
2172586 AAAAAAG-AAAAAAATA
1 AAAAAAGAAAAAAAATA
*
2172602 CAAAAAGAAAAAAAATA
1 AAAAAAGAAAAAAAATA
*
2172619 AAAAAATAAAAAAAA
1 AAAAAAGAAAAAAAA
2172634 AGAAAGTGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 6 0.21
17 22 0.79
ACGTcount: A:0.88, C:0.02, G:0.04, T:0.06
Consensus pattern (17 bp):
AAAAAAGAAAAAAAATA
Found at i:2172706 original size:23 final size:24
Alignment explanation
Indices: 2172677--2172725 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
2172667 AAAATCAGAA
*
2172677 AAGAAA-TTAAAGCACTCCAAAAG
1 AAGAAATTTAAAGCACTCAAAAAG
**
2172700 AAGAAATTTCCAGCACTCAAAAAG
1 AAGAAATTTAAAGCACTCAAAAAG
2172724 AA
1 AA
2172726 AAAAAACAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.55, C:0.18, G:0.12, T:0.14
Consensus pattern (24 bp):
AAGAAATTTAAAGCACTCAAAAAG
Found at i:2172753 original size:12 final size:13
Alignment explanation
Indices: 2172720--2172757 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
2172710 CAGCACTCAA
* *
2172720 AAAGAAAAAAAAC
1 AAAGAAAAGAAAG
2172733 AAAGAAAAGAAAG
1 AAAGAAAAGAAAG
2172746 AAAG-AAAGAAAG
1 AAAGAAAAGAAAG
2172758 TTGAAGCACT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 8 0.35
13 15 0.65
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (13 bp):
AAAGAAAAGAAAG
Found at i:2173335 original size:13 final size:13
Alignment explanation
Indices: 2173317--2173386 Score: 69
Period size: 13 Copynumber: 5.6 Consensus size: 13
2173307 ATTTATAAGT
2173317 TGGTGATGGAATA
1 TGGTGATGGAATA
2173330 TGGTGATGGAATA
1 TGGTGATGGAATA
2173343 TGGTGAT-G-ATA
1 TGGTGATGGAATA
*
2173354 TAGGCG-T-G-ATAA
1 T-GGTGATGGAAT-A
*
2173366 TGGTGATGGACTA
1 TGGTGATGGAATA
2173379 TGGTGATG
1 TGGTGATG
2173387 ATATAGGCGT
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
11 11 0.22
12 7 0.14
13 30 0.61
14 1 0.02
ACGTcount: A:0.27, C:0.03, G:0.39, T:0.31
Consensus pattern (13 bp):
TGGTGATGGAATA
Found at i:2173412 original size:36 final size:36
Alignment explanation
Indices: 2173329--2173412 Score: 159
Period size: 36 Copynumber: 2.3 Consensus size: 36
2173319 GTGATGGAAT
*
2173329 ATGGTGATGGAATATGGTGATGATATAGGCGTGATA
1 ATGGTGATGGACTATGGTGATGATATAGGCGTGATA
2173365 ATGGTGATGGACTATGGTGATGATATAGGCGTGATA
1 ATGGTGATGGACTATGGTGATGATATAGGCGTGATA
2173401 ATGGTGATGGAC
1 ATGGTGATGGAC
2173413 AGATTGTATC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.29, C:0.05, G:0.37, T:0.30
Consensus pattern (36 bp):
ATGGTGATGGACTATGGTGATGATATAGGCGTGATA
Found at i:2173800 original size:19 final size:20
Alignment explanation
Indices: 2173753--2173803 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
2173743 GAAACCCCTT
**
2173753 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
2173773 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
2173792 TGAAGATACATG
1 TGAAAATACATG
2173804 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:2177451 original size:13 final size:13
Alignment explanation
Indices: 2177433--2177502 Score: 69
Period size: 13 Copynumber: 5.6 Consensus size: 13
2177423 ATTTATAAGT
2177433 TGGTGATGGAATA
1 TGGTGATGGAATA
2177446 TGGTGATGGAATA
1 TGGTGATGGAATA
2177459 TGGTGAT-G-ATA
1 TGGTGATGGAATA
*
2177470 TAGGCG-T-G-ATAA
1 T-GGTGATGGAAT-A
*
2177482 TGGTGATGGACTA
1 TGGTGATGGAATA
2177495 TGGTGATG
1 TGGTGATG
2177503 ATATAGGCGT
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
11 11 0.22
12 7 0.14
13 30 0.61
14 1 0.02
ACGTcount: A:0.27, C:0.03, G:0.39, T:0.31
Consensus pattern (13 bp):
TGGTGATGGAATA
Found at i:2177528 original size:36 final size:36
Alignment explanation
Indices: 2177445--2177528 Score: 159
Period size: 36 Copynumber: 2.3 Consensus size: 36
2177435 GTGATGGAAT
*
2177445 ATGGTGATGGAATATGGTGATGATATAGGCGTGATA
1 ATGGTGATGGACTATGGTGATGATATAGGCGTGATA
2177481 ATGGTGATGGACTATGGTGATGATATAGGCGTGATA
1 ATGGTGATGGACTATGGTGATGATATAGGCGTGATA
2177517 ATGGTGATGGAC
1 ATGGTGATGGAC
2177529 AGATTGTATC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.29, C:0.05, G:0.37, T:0.30
Consensus pattern (36 bp):
ATGGTGATGGACTATGGTGATGATATAGGCGTGATA
Found at i:2179648 original size:24 final size:24
Alignment explanation
Indices: 2179609--2179681 Score: 128
Period size: 24 Copynumber: 3.0 Consensus size: 24
2179599 CTTTCTTTTC
2179609 TTCTTCTTTTTGAGTGCTTGAATTT
1 TTCTTC-TTTTGAGTGCTTGAATTT
2179634 TTCTTCTTTTGAGTGCTTGAATTT
1 TTCTTCTTTTGAGTGCTTGAATTT
*
2179658 TTCTTCTTTTGAGTGCTTTAATTT
1 TTCTTCTTTTGAGTGCTTGAATTT
2179682 CTTTGCTGGA
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
24 41 0.87
25 6 0.13
ACGTcount: A:0.12, C:0.12, G:0.15, T:0.60
Consensus pattern (24 bp):
TTCTTCTTTTGAGTGCTTGAATTT
Found at i:2189678 original size:27 final size:26
Alignment explanation
Indices: 2189639--2189691 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
2189629 ATGGAAAGGT
* *
2189639 AGAAGAAAGGATTCAAGGAAATGAAA
1 AGAAGAAAAGATTCAAGGAAAGGAAA
*
2189665 AGAAGGAAAAGATTTAAGGAAAGGAAA
1 AGAA-GAAAAGATTCAAGGAAAGGAAA
2189692 TGAAAGTAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.58, C:0.02, G:0.28, T:0.11
Consensus pattern (26 bp):
AGAAGAAAAGATTCAAGGAAAGGAAA
Found at i:2200838 original size:20 final size:19
Alignment explanation
Indices: 2200815--2200852 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2200805 AAATTTTGGC
2200815 TTTTTTGGCTCTTTTTTTTG
1 TTTTTTGGC-CTTTTTTTTG
*
2200835 TTTTTTTGCCTTTTTTTT
1 TTTTTTGGCCTTTTTTTT
2200853 TTTGCCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.00, C:0.11, G:0.11, T:0.79
Consensus pattern (19 bp):
TTTTTTGGCCTTTTTTTTG
Found at i:2200852 original size:14 final size:14
Alignment explanation
Indices: 2200830--2200870 Score: 64
Period size: 14 Copynumber: 2.8 Consensus size: 14
2200820 TGGCTCTTTT
2200830 TTTTGTTTTTTTGCC
1 TTTT-TTTTTTTGCC
2200845 TTTTTTTTTTTGCC
1 TTTTTTTTTTTGCC
2200859 TTTTTTTGTTTT
1 TTTTTTT-TTTT
2200871 TTTGAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 17 0.68
15 8 0.32
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.80
Consensus pattern (14 bp):
TTTTTTTTTTTGCC
Found at i:2200853 original size:20 final size:21
Alignment explanation
Indices: 2200815--2200854 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2200805 AAATTTTGGC
*
2200815 TTTTTTGGCTCTTTTTTTTGT
1 TTTTTTGCCTCTTTTTTTTGT
*
2200836 TTTTTTGCCTTTTTTTTTT
1 TTTTTTGCCTCTTTTTTTT
2200855 TGCCTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.80
Consensus pattern (21 bp):
TTTTTTGCCTCTTTTTTTTGT
Found at i:2200855 original size:22 final size:21
Alignment explanation
Indices: 2200808--2200873 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 21
2200798 TTTTTTGAAA
* * * *
2200808 TTTTGGCTTTTTTGGCTCTTT
1 TTTTTGCTTTTTTTGTTTTTT
2200829 TTTTTG-TTTTTTTGCCTTTTTT
1 TTTTTGCTTTTTTTG--TTTTTT
2200851 TTTTTGCCTTTTTTTGTTTTTT
1 TTTTTG-CTTTTTTTGTTTTTT
2200873 T
1 T
2200874 GAAAAAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
20 7 0.19
21 5 0.14
22 17 0.46
24 8 0.22
ACGTcount: A:0.00, C:0.11, G:0.12, T:0.77
Consensus pattern (21 bp):
TTTTTGCTTTTTTTGTTTTTT
Found at i:2206328 original size:24 final size:25
Alignment explanation
Indices: 2206282--2206329 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
2206272 CACCATGATA
* * *
2206282 TGCATTTTCTTCAGTTTCTTCATCT
1 TGCATTGTCTTCAGGTTCCTCATCT
2206307 TGCATTGT-TTCAGGTTCCTCATC
1 TGCATTGTCTTCAGGTTCCTCATC
2206330 AAAAATAGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.12, C:0.25, G:0.12, T:0.50
Consensus pattern (25 bp):
TGCATTGTCTTCAGGTTCCTCATCT
Found at i:2216285 original size:19 final size:20
Alignment explanation
Indices: 2216249--2216289 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
2216239 AACCCCTTTA
*
2216249 AAAATACATTATTTTTAATG
1 AAAATACATTAATTTTAATG
2216269 AAAATACA-TAATTTTAATG
1 AAAATACATTAATTTTAATG
2216288 AA
1 AA
2216290 GATAAATGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39
Consensus pattern (20 bp):
AAAATACATTAATTTTAATG
Found at i:2218221 original size:21 final size:20
Alignment explanation
Indices: 2218195--2218233 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
2218185 ATGGATAATT
2218195 AAGAAAGGAAATGGAAATGGA
1 AAGAAAGGAAAT-GAAATGGA
*
2218216 AAGAAATGAAATGAAATG
1 AAGAAAGGAAATGAAATG
2218234 CATAGAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.59, C:0.00, G:0.28, T:0.13
Consensus pattern (20 bp):
AAGAAAGGAAATGAAATGGA
Found at i:2218233 original size:20 final size:21
Alignment explanation
Indices: 2218195--2218243 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
2218185 ATGGATAATT
* *
2218195 AAGAAAGGAAATGGAAATGGA
1 AAGAAATGAAATGGAAATGCA
2218216 AAGAAATGAAAT-GAAATGCA
1 AAGAAATGAAATGGAAATGCA
*
2218236 TAGAAATG
1 AAGAAATG
2218244 TTATCAAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.57, C:0.02, G:0.27, T:0.14
Consensus pattern (21 bp):
AAGAAATGAAATGGAAATGCA
Found at i:2220267 original size:123 final size:123
Alignment explanation
Indices: 2220097--2220344 Score: 379
Period size: 123 Copynumber: 2.0 Consensus size: 123
2220087 GAAGGGGAGG
*
2220097 ATGATGTGATCCTGTCTAGCTCCAACTTTATCCATAACTTGATCACACCATGGAGATTACTAAAA
1 ATGATGTGATCCTGTCTAGCTCCAAATTTATCCATAACTTGATCACACCATGGAGATTACTAAAA
* * * *
2220162 GCTGATTTTAAGGGAGTTCTTCCTTACTTTATCTTATATTTACTTATTTATGGACTAT
66 GCTGATTCTAAGGGAGTTCTACCGTACTTTATCTTATATTTACTTATTTATGCACTAT
* * * * * *
2220220 ATGATGTGATCCTGTCTAGCTCCAAATTTCTCCATGATTTGATCACACCATGGAGGTTATTCAAA
1 ATGATGTGATCCTGTCTAGCTCCAAATTTATCCATAACTTGATCACACCATGGAGATTACTAAAA
* *
2220285 TCTGGTTCTAAGGGAGTTCTACCGTACTTTATCTTATATTTACTTATTTATGCACTAT
66 GCTGATTCTAAGGGAGTTCTACCGTACTTTATCTTATATTTACTTATTTATGCACTAT
2220343 AT
1 AT
2220345 ATTATTATAA
Statistics
Matches: 112, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
123 112 1.00
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.40
Consensus pattern (123 bp):
ATGATGTGATCCTGTCTAGCTCCAAATTTATCCATAACTTGATCACACCATGGAGATTACTAAAA
GCTGATTCTAAGGGAGTTCTACCGTACTTTATCTTATATTTACTTATTTATGCACTAT
Found at i:2224253 original size:47 final size:47
Alignment explanation
Indices: 2224183--2224275 Score: 132
Period size: 47 Copynumber: 2.0 Consensus size: 47
2224173 TTGGTGCTTA
*
2224183 AGTGGAGACAAACACCTTGCTTTGCTGGTCATGCACATGGGCTGTTT
1 AGTGGAGACAAACACCTTGCTTTGCTGGTCACGCACATGGGCTGTTT
* * * * *
2224230 AGTGGAGATAAGCATCTTTCTTTGCTGGTCACGCACATGGGGTGTT
1 AGTGGAGACAAACACCTTGCTTTGCTGGTCACGCACATGGGCTGTT
2224276 CTTTGAGTGC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
47 40 1.00
ACGTcount: A:0.20, C:0.19, G:0.29, T:0.31
Consensus pattern (47 bp):
AGTGGAGACAAACACCTTGCTTTGCTGGTCACGCACATGGGCTGTTT
Found at i:2226760 original size:30 final size:30
Alignment explanation
Indices: 2226725--2226819 Score: 95
Period size: 30 Copynumber: 3.2 Consensus size: 30
2226715 GCTATTTGTG
2226725 AGCTGTTTGTGTCTCCCAAATGCTCCACCA
1 AGCTGTTTGTGTCTCCCAAATGCTCCACCA
* * *
2226755 AGCTGTTTGTCT-TCCAAAATTCTCC-CCTA
1 AGCTGTTTGTGTCTCCCAAATGCTCCACC-A
* * * * *
2226784 AGTTGTATGTGTCTTCCAAATGCTTCATCA
1 AGCTGTTTGTGTCTCCCAAATGCTCCACCA
2226814 AGCTGT
1 AGCTGT
2226820 CCCAATGTGT
Statistics
Matches: 50, Mismatches: 12, Indels: 6
0.74 0.18 0.09
Matches are distributed among these distances:
28 2 0.04
29 21 0.42
30 26 0.52
31 1 0.02
ACGTcount: A:0.21, C:0.27, G:0.16, T:0.36
Consensus pattern (30 bp):
AGCTGTTTGTGTCTCCCAAATGCTCCACCA
Found at i:2232935 original size:16 final size:16
Alignment explanation
Indices: 2232914--2232950 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
2232904 GTTGCGGAAT
2232914 TGATGGAAGAGATGGA
1 TGATGGAAGAGATGGA
2232930 TGATGGAAGAGATGGA
1 TGATGGAAGAGATGGA
2232946 TGATG
1 TGATG
2232951 TTGATGATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.43, T:0.22
Consensus pattern (16 bp):
TGATGGAAGAGATGGA
Found at i:2237155 original size:8 final size:8
Alignment explanation
Indices: 2237144--2237183 Score: 55
Period size: 8 Copynumber: 4.9 Consensus size: 8
2237134 TCTTTTTCTT
2237144 TTCTTTTC
1 TTCTTTTC
2237152 TTCTTTTC
1 TTCTTTTC
2237160 TTCTTTT-
1 TTCTTTTC
2237167 TGTCTTTTC
1 T-TCTTTTC
2237176 TTTCTTTT
1 -TTCTTTT
2237184 TGCACTCCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
7 1 0.03
8 21 0.72
9 6 0.21
10 1 0.03
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.78
Consensus pattern (8 bp):
TTCTTTTC
Found at i:2237163 original size:16 final size:17
Alignment explanation
Indices: 2237137--2237185 Score: 66
Period size: 16 Copynumber: 2.9 Consensus size: 17
2237127 GAACTTCTCT
2237137 TTTTCTTTTCTTTTCT-TC
1 TTTTC-TTTCTTTT-TGTC
2237155 TTTTC-TTCTTTTTGTC
1 TTTTCTTTCTTTTTGTC
2237171 TTTTCTTTCTTTTTG
1 TTTTCTTTCTTTTTG
2237186 CACTCCAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
15 1 0.03
16 14 0.48
17 9 0.31
18 5 0.17
ACGTcount: A:0.00, C:0.18, G:0.04, T:0.78
Consensus pattern (17 bp):
TTTTCTTTCTTTTTGTC
Found at i:2240782 original size:15 final size:15
Alignment explanation
Indices: 2240764--2240793 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2240754 TCCATTTCTT
2240764 ATATATATTTTCCGC
1 ATATATATTTTCCGC
2240779 ATATATATTTTCCGC
1 ATATATATTTTCCGC
2240794 TGCCATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.20, G:0.07, T:0.47
Consensus pattern (15 bp):
ATATATATTTTCCGC
Found at i:2245244 original size:34 final size:34
Alignment explanation
Indices: 2245201--2245266 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
2245191 CTTTTAATGT
*
2245201 CTCTTTTCTGTCTCCTCTTCTGATCTCACACGGA
1 CTCTTTTCTGTCTCCCCTTCTGATCTCACACGGA
2245235 CTCTTTTCTGTCTCCCCTTCTGATCTCACACG
1 CTCTTTTCTGTCTCCCCTTCTGATCTCACACG
2245267 CTCAATATGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.11, C:0.38, G:0.11, T:0.41
Consensus pattern (34 bp):
CTCTTTTCTGTCTCCCCTTCTGATCTCACACGGA
Found at i:2246858 original size:13 final size:12
Alignment explanation
Indices: 2246839--2246924 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
2246829 TTATTGGCGT
2246839 GATATGGTGATG
1 GATATGGTGATG
2246851 GAATATGGTGAT-
1 G-ATATGGTGATG
*
2246863 GATATAGGCG-T-
1 GATAT-GGTGATG
2246874 GATAATGGTGATG
1 GAT-ATGGTGATG
2246887 GACTATGGTGAT-
1 GA-TATGGTGATG
*
2246899 GATATAGGCG-T-
1 GATAT-GGTGATG
2246910 GATAATGGTGATG
1 GAT-ATGGTGATG
2246923 GA
1 GA
2246925 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:2246894 original size:36 final size:36
Alignment explanation
Indices: 2246824--2246925 Score: 170
Period size: 36 Copynumber: 2.9 Consensus size: 36
2246814 AATGGAAGGA
* * *
2246824 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
2246859 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
2246895 TGATGATATAGGCGTGATAATGGTGATGGAC
1 TGATGATATAGGCGTGATAATGGTGATGGAC
2246926 AGATTGTATC
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 16 0.25
36 47 0.75
ACGTcount: A:0.26, C:0.05, G:0.36, T:0.32
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGACTATGG
Found at i:2250943 original size:36 final size:36
Alignment explanation
Indices: 2250903--2251007 Score: 165
Period size: 36 Copynumber: 2.9 Consensus size: 36
2250893 AAAACCATCT
*
2250903 TCCATCTCCATTATCACGTCTATATCATCACCATAG
1 TCCATCTCCATTATCACGCCTATATCATCACCATAG
* * *
2250939 TCCATCACCATTATCACGCCTTTATCATCACTATAG
1 TCCATCTCCATTATCACGCCTATATCATCACCATAG
*
2250975 TCCATCTCCATTATCACGCCTATATTATCACCA
1 TCCATCTCCATTATCACGCCTATATCATCACCA
2251008 ACTTATAAAT
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 61 1.00
ACGTcount: A:0.28, C:0.34, G:0.05, T:0.33
Consensus pattern (36 bp):
TCCATCTCCATTATCACGCCTATATCATCACCATAG
Found at i:2251644 original size:16 final size:15
Alignment explanation
Indices: 2251618--2251669 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
2251608 GAGTTGTAAG
2251618 TTATC-TTCATTTTT
1 TTATCTTTCATTTTT
*
2251632 TTATCATTTCATTTCT
1 TTATC-TTTCATTTTT
2251648 TTATTCTTTCATCTTTT
1 TTA-TCTTTCAT-TTTT
2251665 CTTAT
1 -TTAT
2251670 TTCATTACCA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
14 5 0.16
16 17 0.55
17 6 0.19
18 3 0.10
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATCTTTCATTTTT
Found at i:2255000 original size:36 final size:36
Alignment explanation
Indices: 2254953--2255050 Score: 160
Period size: 36 Copynumber: 2.7 Consensus size: 36
2254943 CATCTTCCAT
2254953 CCATTATCACGCCTATATCATCACCATAGTCCATCA
1 CCATTATCACGCCTATATCATCACCATAGTCCATCA
* * *
2254989 CCATTATCACGCCTTTATCATCACTATAGTCCATCT
1 CCATTATCACGCCTATATCATCACCATAGTCCATCA
*
2255025 CCATTATCACGCCTATATTATCACCA
1 CCATTATCACGCCTATATCATCACCA
2255051 ACTTATAATT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 56 1.00
ACGTcount: A:0.29, C:0.35, G:0.05, T:0.32
Consensus pattern (36 bp):
CCATTATCACGCCTATATCATCACCATAGTCCATCA
Found at i:2257527 original size:40 final size:40
Alignment explanation
Indices: 2257478--2257558 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
2257468 AATGAATGTT
2257478 CATCCATTTAAGTGAATACATCT-TCATAGCCGAATTCATC
1 CATCCATTTAAGTGAATA-ATCTCTCATAGCCGAATTCATC
2257518 CATCCATTTAAGTGAATAATCTCTCATAGCCGAATTCATC
1 CATCCATTTAAGTGAATAATCTCTCATAGCCGAATTCATC
2257558 C
1 C
2257559 TCTCTTGATG
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
39 4 0.10
40 36 0.90
ACGTcount: A:0.32, C:0.26, G:0.10, T:0.32
Consensus pattern (40 bp):
CATCCATTTAAGTGAATAATCTCTCATAGCCGAATTCATC
Found at i:2263170 original size:34 final size:34
Alignment explanation
Indices: 2263127--2263192 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
2263117 CTTTTAATGT
*
2263127 CTCTTTTCTGTCTCCTCTTCTGATCTCACACGGA
1 CTCTTTTCTGTCTCCCCTTCTGATCTCACACGGA
2263161 CTCTTTTCTGTCTCCCCTTCTGATCTCACACG
1 CTCTTTTCTGTCTCCCCTTCTGATCTCACACG
2263193 CTCAATATGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.11, C:0.38, G:0.11, T:0.41
Consensus pattern (34 bp):
CTCTTTTCTGTCTCCCCTTCTGATCTCACACGGA
Found at i:2264837 original size:36 final size:36
Alignment explanation
Indices: 2264767--2264868 Score: 161
Period size: 36 Copynumber: 2.9 Consensus size: 36
2264757 AATGGAAGGA
* * *
2264767 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
*
2264802 TGATGATTTAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
2264838 TGATGATATAGGCGTGATAATGGTGATGGAC
1 TGATGATATAGGCGTGATAATGGTGATGGAC
2264869 AGATTGTATC
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
35 15 0.25
36 46 0.75
ACGTcount: A:0.25, C:0.05, G:0.36, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGACTATGG
Done.