Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 183 of 193
Found at i:57123265 original size:2 final size:2
Alignment explanation
Indices: 57123258--57123282 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
57123248 ATATCATCTA
57123258 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 A
57123283 ATGCTGCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:57128280 original size:17 final size:16
Alignment explanation
Indices: 57128239--57128281 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 16
57128229 TTTTTAATGA
57128239 AATAA-AAAT-ATTTT
1 AATAATAAATCATTTT
*
57128253 AATAATTAATCATTTT
1 AATAATAAATCATTTT
57128269 AATTAATAAATCA
1 AA-TAATAAATCA
57128282 AACTTATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 5 0.21
15 3 0.12
16 7 0.29
17 9 0.38
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (16 bp):
AATAATAAATCATTTT
Found at i:57133851 original size:7 final size:7
Alignment explanation
Indices: 57133840--57133874 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
57133830 ACCCTTTTCA
*
57133840 TTGCCAA
1 TTGCCAC
57133847 TTGCCAC
1 TTGCCAC
57133854 TTGCCAC
1 TTGCCAC
57133861 TTGCCAC
1 TTGCCAC
57133868 TTGCCAC
1 TTGCCAC
57133875 CTATATCTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.17, C:0.40, G:0.14, T:0.29
Consensus pattern (7 bp):
TTGCCAC
Found at i:57140799 original size:17 final size:18
Alignment explanation
Indices: 57140759--57140799 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
57140749 AAAATATGAG
57140759 TAAAAACGCTTATTTTAC
1 TAAAAACGCTTATTTTAC
57140777 TAAAAACGCTTATTTTAC
1 TAAAAACGCTTATTTTAC
57140795 TAAAA
1 TAAAA
57140800 TTAAACACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.37
Consensus pattern (18 bp):
TAAAAACGCTTATTTTAC
Found at i:57144113 original size:29 final size:30
Alignment explanation
Indices: 57144067--57144134 Score: 75
Period size: 31 Copynumber: 2.3 Consensus size: 30
57144057 CAATTAGAGT
*
57144067 TTCATGTGGATAACTG-CATCAAATCAAAA
1 TTCATGTAGATAACTGACATCAAATCAAAA
* * * *
57144096 TTCATGTATATAATTGCACATTAAATCAAAG
1 TTCATGTAGATAACTG-ACATCAAATCAAAA
57144127 TTCATGTA
1 TTCATGTA
57144135 AAATTTTAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 13 0.41
31 19 0.59
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.34
Consensus pattern (30 bp):
TTCATGTAGATAACTGACATCAAATCAAAA
Found at i:57144360 original size:24 final size:24
Alignment explanation
Indices: 57144316--57144369 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
57144306 CCGAACAAAT
* **
57144316 TAAAAGATTTAATATTTTAAAAAA
1 TAAAATATTTAATATAATAAAAAA
**
57144340 TAAAATATTTAATATAATAAAGTA
1 TAAAATATTTAATATAATAAAAAA
57144364 TAAAAT
1 TAAAAT
57144370 CAATAATAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (24 bp):
TAAAATATTTAATATAATAAAAAA
Found at i:57147879 original size:6 final size:7
Alignment explanation
Indices: 57147864--57147888 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
57147854 TTGCCTCAGG
57147864 AAAATAA
1 AAAATAA
57147871 AAAATAA
1 AAAATAA
57147878 AAAATAA
1 AAAATAA
57147885 AAAA
1 AAAA
57147889 AATCCTTGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAATAA
Found at i:57162645 original size:9 final size:9
Alignment explanation
Indices: 57162631--57162655 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
57162621 CTATTAGTAT
57162631 ACATTTCTC
1 ACATTTCTC
57162640 ACATTTCTC
1 ACATTTCTC
57162649 ACATTTC
1 ACATTTC
57162656 CTTCTCTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.32, G:0.00, T:0.44
Consensus pattern (9 bp):
ACATTTCTC
Found at i:57163861 original size:24 final size:24
Alignment explanation
Indices: 57163829--57163874 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
57163819 TAATTTAACT
* *
57163829 TAATCGAACATGTTCATGAACATA
1 TAATCGAACATATTCACGAACATA
*
57163853 TAATTGAACATATTCACGAACA
1 TAATCGAACATATTCACGAACA
57163875 ATGTTAATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.28
Consensus pattern (24 bp):
TAATCGAACATATTCACGAACATA
Found at i:57165776 original size:9 final size:9
Alignment explanation
Indices: 57165759--57165797 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
57165749 TGAATTTCAC
57165759 AATTCGAAT
1 AATTCGAAT
*
57165768 AACTCGAAT
1 AATTCGAAT
*
57165777 AATTCTAAT
1 AATTCGAAT
57165786 AATTCGAAT
1 AATTCGAAT
57165795 AAT
1 AAT
57165798 AAATTGGTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.13, G:0.08, T:0.33
Consensus pattern (9 bp):
AATTCGAAT
Found at i:57165912 original size:19 final size:19
Alignment explanation
Indices: 57165865--57165915 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 19
57165855 TCTCTCTCAA
* *
57165865 CAAAAATTACAAAAAAAAT
1 CAAAATTTATAAAAAAAAT
*
57165884 CAAAATATTTATAAAAAAATT
1 C-AAA-ATTTATAAAAAAAAT
57165905 CAAAATTTATA
1 CAAAATTTATA
57165916 TTTTAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 8 0.30
20 6 0.22
21 13 0.48
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (19 bp):
CAAAATTTATAAAAAAAAT
Found at i:57169366 original size:22 final size:22
Alignment explanation
Indices: 57169339--57169382 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
57169329 TAATTAAAAA
57169339 TTTTATTGT-ATTAAATATTAAT
1 TTTTATTGTAATTAAAT-TTAAT
*
57169361 TTTTATTTTAATTAAATTTAAT
1 TTTTATTGTAATTAAATTTAAT
57169383 AATAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
TTTTATTGTAATTAAATTTAAT
Found at i:57171169 original size:24 final size:26
Alignment explanation
Indices: 57171129--57171178 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
57171119 AACATCAAAC
**
57171129 GAACATGTTCATGAAC-ATA-TAATT
1 GAACATGTTCACAAACAATATTAATT
57171153 GAACATGTTCACAAACAATATTAATT
1 GAACATGTTCACAAACAATATTAATT
57171179 AATAATAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 14 0.64
25 3 0.14
26 5 0.23
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (26 bp):
GAACATGTTCACAAACAATATTAATT
Found at i:57177932 original size:16 final size:16
Alignment explanation
Indices: 57177913--57177961 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
57177903 ATGATAGGGT
57177913 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
57177929 ATTATTTTTAT-ATT-
1 ATTATTTTGATAATTA
*
57177943 A-TATTTTGGTAATTA
1 ATTATTTTGATAATTA
57177958 ATTA
1 ATTA
57177962 GCTAAGTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
13 7 0.26
14 4 0.15
15 4 0.15
16 12 0.44
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:57178282 original size:46 final size:46
Alignment explanation
Indices: 57178230--57178372 Score: 113
Period size: 46 Copynumber: 3.2 Consensus size: 46
57178220 TTACTAACTA
57178230 ATTTTTTTAAACATTATTAAATTTTAAATCAATAAATATGAACAAT
1 ATTTTTTTAAACATTATTAAATTTTAAATCAATAAATATGAACAAT
* ** * *
57178276 A-TTTTTT--AC-TTATT-ACTACTAACAACAAAATAAA-AT-TACTAACT
1 ATTTTTTTAAACATTATTAAATTTTAA-ATC--AATAAATATGAAC-AA-T
*
57178320 AATTTTTTTAAACATTATTAAA-TTTAAATTAATAAATATGAACAAT
1 -ATTTTTTTAAACATTATTAAATTTTAAATCAATAAATATGAACAAT
*
57178366 GTTTTTT
1 ATTTTTT
57178373 ACTTACTACT
Statistics
Matches: 72, Mismatches: 12, Indels: 27
0.65 0.11 0.24
Matches are distributed among these distances:
41 5 0.07
42 9 0.12
43 6 0.08
44 7 0.10
45 13 0.18
46 14 0.19
47 4 0.06
48 5 0.07
49 8 0.11
50 1 0.01
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.44
Consensus pattern (46 bp):
ATTTTTTTAAACATTATTAAATTTTAAATCAATAAATATGAACAAT
Found at i:57178411 original size:93 final size:94
Alignment explanation
Indices: 57178156--57178506 Score: 556
Period size: 93 Copynumber: 3.8 Consensus size: 94
57178146 TATATTATTT
57178156 TTTTAAATCAATAAATATGAACAATATTTTTTACTTACTACTACTTACTAACAACAAAATAAAAT
1 TTTTAAATCAATAAATATGAACAATATTTTTTACTTACTACTAC-TACTAACAACAAAATAAAAT
57178221 TACTAACTAATTTTTTTAAACATTATTAAA
65 TACTAACTAATTTTTTTAAACATTATTAAA
57178251 TTTTAAATCAATAAATATGAACAATATTTTTTACTTA-T--TACTACTAACAACAAAATAAAATT
1 TTTTAAATCAATAAATATGAACAATATTTTTTACTTACTACTACTACTAACAACAAAATAAAATT
57178313 ACTAACTAATTTTTTTAAACATTATTAAA
66 ACTAACTAATTTTTTTAAACATTATTAAA
* *
57178342 -TTTAAATTAATAAATATGAACAATGTTTTTTACTTACTACTACTACTAACAACAAAATAAAATT
1 TTTTAAATCAATAAATATGAACAATATTTTTTACTTACTACTACTACTAACAACAAAATAAAATT
*** *
57178406 ACTAACTAGCA-AAATTTAAATATTATTAAA
66 ACTAACTA--ATTTTTTTAAACATTATTAAA
57178436 TTTTAAATCAATAAATATGAACAATA-TTTTT--TTACTTACTACTACTAACAACAAAATAAAAT
1 TTTTAAATCAATAAATATGAACAATATTTTTTACTTAC-TACTACTACTAACAACAAAATAAAAT
57178498 TACTAACTA
65 TACTAACTA
57178507 GCAAAATTAA
Statistics
Matches: 241, Mismatches: 8, Indels: 16
0.91 0.03 0.06
Matches are distributed among these distances:
90 34 0.14
91 51 0.21
92 7 0.03
93 67 0.28
94 21 0.09
95 61 0.25
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (94 bp):
TTTTAAATCAATAAATATGAACAATATTTTTTACTTACTACTACTACTAACAACAAAATAAAATT
ACTAACTAATTTTTTTAAACATTATTAAA
Found at i:57178503 original size:20 final size:21
Alignment explanation
Indices: 57178478--57178520 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
57178468 TACTTACTAC
57178478 TACTAAC-AACAAAATAAAAT
1 TACTAACTAACAAAATAAAAT
* *
57178498 TACTAACTAGCAAAATTAAAT
1 TACTAACTAACAAAATAAAAT
57178519 TA
1 TA
57178521 AAGTAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (21 bp):
TACTAACTAACAAAATAAAAT
Found at i:57179369 original size:22 final size:21
Alignment explanation
Indices: 57179312--57179369 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 21
57179302 AACTTTAGTG
* *
57179312 ATAATATTGTAAAAATAAAAACT
1 ATAA-ATT-TAAATATAAAAAAT
*
57179335 ATGAATTTCAAATATAAAATAAT
1 ATAAATTT-AAATATAAAA-AAT
57179358 ATAAATTTAAAT
1 ATAAATTTAAAT
57179370 TCAAACTCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
21 1 0.03
22 16 0.55
23 12 0.41
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.34
Consensus pattern (21 bp):
ATAAATTTAAATATAAAAAAT
Found at i:57183496 original size:20 final size:19
Alignment explanation
Indices: 57183418--57183497 Score: 54
Period size: 19 Copynumber: 3.8 Consensus size: 19
57183408 ACTTATTAAA
*
57183418 ATTAAAATTAGTATAAAAATA
1 ATTAAAATTA-T-TAAAAATT
*
57183439 ATTAAAAGAAGTTATAAAAAATT
1 ATT--AA-AA-TTATTAAAAATT
*
57183462 ATTAAAATTAATAAAAATGT
1 ATTAAAATTATTAAAAAT-T
57183482 -TTAAAATTTATTAAAA
1 ATTAAAA-TTATTAAAA
57183498 GCCACGCTAG
Statistics
Matches: 48, Mismatches: 5, Indels: 13
0.73 0.08 0.20
Matches are distributed among these distances:
19 15 0.31
20 11 0.23
21 5 0.10
23 11 0.23
24 3 0.06
25 3 0.06
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (19 bp):
ATTAAAATTATTAAAAATT
Found at i:57186230 original size:23 final size:22
Alignment explanation
Indices: 57186204--57186293 Score: 99
Period size: 23 Copynumber: 4.0 Consensus size: 22
57186194 TTACCGTTCA
57186204 GCACTGTGTGTGCTTACTGTTT
1 GCACTGTGTGTGCTTACTGTTT
* *
57186226 CGCACTTTGTGTGCCTACTGATTT
1 -GCACTGTGTGTGCTTACTG-TTT
* * * * *
57186250 GCGCTATGTGCGCCTACTGATT
1 GCACTGTGTGTGCTTACTGTTT
57186272 GCACTGTGTGTGCTTACTGTTT
1 GCACTGTGTGTGCTTACTGTTT
57186294 CCCCAGCACT
Statistics
Matches: 55, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
22 19 0.35
23 33 0.60
24 3 0.05
ACGTcount: A:0.11, C:0.22, G:0.26, T:0.41
Consensus pattern (22 bp):
GCACTGTGTGTGCTTACTGTTT
Found at i:57187813 original size:22 final size:23
Alignment explanation
Indices: 57187778--57187827 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
57187768 AATGAAATCA
*
57187778 TAAATACACGAGCA-CATAAGTGC
1 TAAATACAAGAGCATCA-AAGTGC
*
57187801 TAAAT-CAAGAGCATCAAAGTGT
1 TAAATACAAGAGCATCAAAGTGC
57187823 TAAAT
1 TAAAT
57187828 TTCACGAGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 17 0.71
23 7 0.29
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.22
Consensus pattern (23 bp):
TAAATACAAGAGCATCAAAGTGC
Found at i:57190495 original size:15 final size:14
Alignment explanation
Indices: 57190450--57190494 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
57190440 ATAACTTATA
57190450 TTCAACACTTAATTT
1 TTCAACACTT-ATTT
* *
57190465 TTCAATATTTATTT
1 TTCAACACTTATTT
57190479 TTCAACACTTATTT
1 TTCAACACTTATTT
57190493 TT
1 TT
57190495 TATTCTTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
14 18 0.69
15 8 0.31
ACGTcount: A:0.29, C:0.16, G:0.00, T:0.56
Consensus pattern (14 bp):
TTCAACACTTATTT
Found at i:57190546 original size:17 final size:17
Alignment explanation
Indices: 57190524--57190557 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
57190514 TTTTCAATCT
57190524 ATCAAAGAAATTGAAAA
1 ATCAAAGAAATTGAAAA
**
57190541 ATCAAATCAATTGAAAA
1 ATCAAAGAAATTGAAAA
57190558 TCATGTTTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.62, C:0.09, G:0.09, T:0.21
Consensus pattern (17 bp):
ATCAAAGAAATTGAAAA
Found at i:57190894 original size:14 final size:13
Alignment explanation
Indices: 57190852--57190907 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
57190842 ATATATAAAA
57190852 TAATTTT-ATAACT
1 TAATTTTCA-AACT
* * *
57190865 TAAATTTGATACT
1 TAATTTTCAAACT
57190878 TAATTTTCAACACT
1 TAATTTTCAA-ACT
57190892 TAAATTTTCAAACT
1 T-AATTTTCAAACT
57190906 TA
1 TA
57190908 TTACACTTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
13 17 0.49
14 9 0.26
15 9 0.26
ACGTcount: A:0.39, C:0.12, G:0.02, T:0.46
Consensus pattern (13 bp):
TAATTTTCAAACT
Found at i:57190899 original size:15 final size:14
Alignment explanation
Indices: 57190861--57190907 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
57190851 ATAATTTTAT
*
57190861 AACTTAAA-TTTGA
1 AACTTAAATTTTCA
*
57190874 TACTT-AATTTTCA
1 AACTTAAATTTTCA
57190887 ACACTTAAATTTTCA
1 A-ACTTAAATTTTCA
57190902 AACTTA
1 AACTTA
57190908 TTACACTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 2 0.07
13 8 0.29
14 9 0.32
15 9 0.32
ACGTcount: A:0.40, C:0.15, G:0.02, T:0.43
Consensus pattern (14 bp):
AACTTAAATTTTCA
Found at i:57196385 original size:22 final size:21
Alignment explanation
Indices: 57196322--57196406 Score: 97
Period size: 20 Copynumber: 4.1 Consensus size: 21
57196312 CTTTTATCGA
*
57196322 TACTTCT-CAAAAGGTACTTG
1 TACTTCTCCCAAAGGTACTTG
*
57196342 TACTTCT-CCAAAGGTACCTG
1 TACTTCTCCCAAAGGTACTTG
57196362 TACTTCTCCCATGAA-GTACTTG
1 TACTTCTCCCA--AAGGTACTTG
*
57196384 TACTTCT-CCAAAGGTATTTG
1 TACTTCTCCCAAAGGTACTTG
57196404 TAC
1 TAC
57196407 CACTACTTTA
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
19 2 0.04
20 34 0.60
21 6 0.11
22 13 0.23
23 2 0.04
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.35
Consensus pattern (21 bp):
TACTTCTCCCAAAGGTACTTG
Found at i:57197169 original size:13 final size:13
Alignment explanation
Indices: 57197151--57197176 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
57197141 TTTGGCCCAA
57197151 AAAATATTTTTTT
1 AAAATATTTTTTT
57197164 AAAATATTTTTTT
1 AAAATATTTTTTT
57197177 TGTCTCAAAA
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
AAAATATTTTTTT
Found at i:57198344 original size:2 final size:2
Alignment explanation
Indices: 57198337--57198363 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
57198327 CTGTTCCAGA
57198337 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
57198364 ATGGAAACCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:57221311 original size:13 final size:13
Alignment explanation
Indices: 57221293--57221319 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
57221283 TTTTCATACT
57221293 AACTTTATAAATC
1 AACTTTATAAATC
57221306 AACTTTATAAATC
1 AACTTTATAAATC
57221319 A
1 A
57221320 TTCATTCATA
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:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (13 bp):
AACTTTATAAATC
Found at i:57222674 original size:29 final size:30
Alignment explanation
Indices: 57222626--57222706 Score: 101
Period size: 31 Copynumber: 2.7 Consensus size: 30
57222616 GAATTAGATC
* *
57222626 AAATCAAAATTTCATTTATAAAATTGCACA-
1 AAATCAAAGTTT-ATGTATAAAATTGCACAT
*
57222656 AAATCAAAGTTTATGTATAGAATTGCACATT
1 AAATCAAAGTTTATGTATAAAATTGCACA-T
*
57222687 AAATCAAAGTTCATGTATAA
1 AAATCAAAGTTTATGTATAA
57222707 TTTTATGATT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
29 15 0.34
30 11 0.25
31 18 0.41
ACGTcount: A:0.47, C:0.11, G:0.09, T:0.33
Consensus pattern (30 bp):
AAATCAAAGTTTATGTATAAAATTGCACAT
Found at i:57222708 original size:29 final size:28
Alignment explanation
Indices: 57222626--57222706 Score: 90
Period size: 29 Copynumber: 2.7 Consensus size: 28
57222616 GAATTAGATC
* *
57222626 AAATCAAAATTTCATTTATAAAATTGCACA
1 AAATC-AAAGTTCATGTAT-AAATTGCACA
*
57222656 AAATCAAAGTTTATGTATAGAATTGCACA
1 AAATCAAAGTTCATGTATA-AATTGCACA
57222685 TTAAATCAAAGTTCATGTATAA
1 --AAATCAAAGTTCATGTATAA
57222707 TTTTATGATT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
28 1 0.02
29 19 0.43
30 6 0.14
31 18 0.41
ACGTcount: A:0.47, C:0.11, G:0.09, T:0.33
Consensus pattern (28 bp):
AAATCAAAGTTCATGTATAAATTGCACA
Found at i:57222987 original size:10 final size:10
Alignment explanation
Indices: 57222927--57222988 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
57222917 AAATATATCC
*
57222927 ATAATTTTTC
1 ATAATTTTTT
57222937 ATAATTTTTT
1 ATAATTTTTT
*
57222947 ACAATTTTTCT
1 ATAATTTTT-T
*
57222958 ATGATTTTTGT
1 ATAATTTTT-T
**
57222969 AGTTTTTTTTT
1 A-TAATTTTTT
57222980 ATAATTTTT
1 ATAATTTTT
57222989 ATTAGAAAAG
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
10 23 0.56
11 12 0.29
12 6 0.15
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (10 bp):
ATAATTTTTT
Found at i:57229660 original size:21 final size:22
Alignment explanation
Indices: 57229636--57229681 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
57229626 GAAAATATTG
57229636 ATTTGATAGTC-AATTCAATTA
1 ATTTGATAGTCTAATTCAATTA
*
57229657 ATTTTATAGTCTAATTCAATTA
1 ATTTGATAGTCTAATTCAATTA
57229679 ATT
1 ATT
57229682 CGAGGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.48
Consensus pattern (22 bp):
ATTTGATAGTCTAATTCAATTA
Found at i:57234599 original size:48 final size:48
Alignment explanation
Indices: 57234523--57234616 Score: 143
Period size: 48 Copynumber: 2.0 Consensus size: 48
57234513 ATTGAAAAAT
*
57234523 GAAGTTGAAGGGCCCGATGTTGGCGCAATATATCCCATTAATTTTAAC
1 GAAGTTGAAGGGCCCGATGGTGGCGCAATATATCCCATTAATTTTAAC
* * * *
57234571 GAAGTTGAAGGGCCTGATGGTGGTGCAATATATCCCCTTAGTTTTA
1 GAAGTTGAAGGGCCCGATGGTGGCGCAATATATCCCATTAATTTTA
57234617 GACTTATGTA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.31
Consensus pattern (48 bp):
GAAGTTGAAGGGCCCGATGGTGGCGCAATATATCCCATTAATTTTAAC
Found at i:57237891 original size:12 final size:12
Alignment explanation
Indices: 57237874--57237912 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
57237864 GGTTTTGACT
57237874 AAGGGAAGGGGA
1 AAGGGAAGGGGA
*
57237886 AAGGGAAAGGGA
1 AAGGGAAGGGGA
57237898 AAGGGAAAGGGGA
1 AAGGG-AAGGGGA
57237911 AA
1 AA
57237913 ATTTTGTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 16 0.67
13 8 0.33
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (12 bp):
AAGGGAAGGGGA
Found at i:57237912 original size:7 final size:6
Alignment explanation
Indices: 57237874--57237908 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
57237864 GGTTTTGACT
*
57237874 AAGGGA AGGGGA AAGGGA AAGGGA AAGGGA AAGGG
1 AAGGGA AAGGGA AAGGGA AAGGGA AAGGGA AAGGG
57237909 GAAAATTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (6 bp):
AAGGGA
Found at i:57238752 original size:32 final size:32
Alignment explanation
Indices: 57238716--57238835 Score: 84
Period size: 32 Copynumber: 3.6 Consensus size: 32
57238706 TAATCACTTT
57238716 AATATTAAATTAATATAATACTTATCAAGATA
1 AATATTAAATTAATATAATACTTATCAAGATA
* * * * *
57238748 AATATTAGATTAAATTTAATA-TTAATATAATCACTTT
1 AATATTAAATT-AATATAATACTT-AT-CAA-GA--TA
*
57238785 AATATTAAATTAATA-AATAC-TATCAAGACA
1 AATATTAAATTAATATAATACTTATCAAGATA
* *
57238815 AGTATTAAATTTAATTTAATA
1 AATATTAAA-TTAATATAATA
57238836 TTAAATTTAT
Statistics
Matches: 66, Mismatches: 13, Indels: 18
0.68 0.13 0.19
Matches are distributed among these distances:
30 8 0.12
31 5 0.08
32 17 0.26
33 12 0.18
34 4 0.06
35 6 0.09
36 3 0.05
37 11 0.17
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (32 bp):
AATATTAAATTAATATAATACTTATCAAGATA
Found at i:57238838 original size:67 final size:69
Alignment explanation
Indices: 57238706--57238839 Score: 218
Period size: 67 Copynumber: 2.0 Consensus size: 69
57238696 TGGTTAAACT
* *
57238706 TAATCACTTTAATATTAAATTAATATAATACTTATCAAGATAAATATTAGATTAAATTTAATATT
1 TAATCACTTTAATATTAAATTAATATAATACTTATCAAGACAAATATTAAATTAAATTTAATATT
57238771 AATA
66 AATA
* *
57238775 TAATCACTTTAATATTAAATTAATA-AATAC-TATCAAGACAAGTATTAAATTTAATTTAATATT
1 TAATCACTTTAATATTAAATTAATATAATACTTATCAAGACAAATATTAAATTAAATTTAATATT
57238838 AA
66 AA
57238840 ATTTATTAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
67 31 0.51
68 5 0.08
69 25 0.41
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (69 bp):
TAATCACTTTAATATTAAATTAATATAATACTTATCAAGACAAATATTAAATTAAATTTAATATT
AATA
Found at i:57239433 original size:20 final size:20
Alignment explanation
Indices: 57239408--57239447 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
57239398 CTCTCATGAC
57239408 TGCCTAATTTAATTCCACAT
1 TGCCTAATTTAATTCCACAT
57239428 TGCCTAATTTAATTCCACAT
1 TGCCTAATTTAATTCCACAT
57239448 CGAATAAATT
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:0.30, C:0.25, G:0.05, T:0.40
Consensus pattern (20 bp):
TGCCTAATTTAATTCCACAT
Found at i:57239459 original size:20 final size:20
Alignment explanation
Indices: 57239416--57239459 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
57239406 ACTGCCTAAT
* ** *
57239416 TTAATTCCACATTGCCTAAT
1 TTAATTCCACATCGAATAAA
57239436 TTAATTCCACATCGAATAAA
1 TTAATTCCACATCGAATAAA
57239456 TTAA
1 TTAA
57239460 ATCAATTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.20, G:0.05, T:0.36
Consensus pattern (20 bp):
TTAATTCCACATCGAATAAA
Found at i:57240025 original size:16 final size:16
Alignment explanation
Indices: 57239986--57240025 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
57239976 GTTGCTAGTA
*
57239986 AAGTCATGCCATATAC
1 AAGTCATGCCATACAC
**
57240002 AAACCATGCCATACAC
1 AAGTCATGCCATACAC
57240018 AAGTCATG
1 AAGTCATG
57240026 TACCCAATAT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.40, C:0.28, G:0.12, T:0.20
Consensus pattern (16 bp):
AAGTCATGCCATACAC
Found at i:57241049 original size:57 final size:58
Alignment explanation
Indices: 57240942--57241102 Score: 173
Period size: 57 Copynumber: 2.8 Consensus size: 58
57240932 ATCCCGATTG
* * * * * *
57240942 TTGAAGATATGCCTCAGCTTTGTTGATAGCCCAAAGGATTCACAGAGGGGCTCGAATA
1 TTGAAGATATGCCTCACCTTCGTTGAGAGCCCAAAGGATTCACAAAGGGGCCCAAATA
** * ** *
57241000 TTGAAGATATGCCTCATATTCGTT-AGAGCCCAAAGGGTTTTCAAAGGGGCCCAAATG
1 TTGAAGATATGCCTCACCTTCGTTGAGAGCCCAAAGGATTCACAAAGGGGCCCAAATA
**
57241057 TCAAAGATATGCCTCACCTTCGTTGAGAGCCCAAA-GAGTTCACAAA
1 TTGAAGATATGCCTCACCTTCGTTGAGAGCCCAAAGGA-TTCACAAA
57241103 AAAGCTTAAA
Statistics
Matches: 83, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
57 46 0.55
58 37 0.45
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (58 bp):
TTGAAGATATGCCTCACCTTCGTTGAGAGCCCAAAGGATTCACAAAGGGGCCCAAATA
Found at i:57243799 original size:2 final size:2
Alignment explanation
Indices: 57243792--57243839 Score: 71
Period size: 2 Copynumber: 24.0 Consensus size: 2
57243782 CACCGCCCAC
57243792 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G- GCA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G-A GA GA
*
57243834 CA GA GA
1 GA GA GA
57243840 AGGGGAAAGC
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 1 0.02
2 40 0.95
3 1 0.02
ACGTcount: A:0.48, C:0.04, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:57245876 original size:17 final size:18
Alignment explanation
Indices: 57245854--57245887 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
57245844 TGGTTTCACC
57245854 TTTTA-TCTTTAGTTTAT
1 TTTTATTCTTTAGTTTAT
*
57245871 TTTTATTCTTTATTTTA
1 TTTTATTCTTTAGTTTA
57245888 GAAATTCAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.74
Consensus pattern (18 bp):
TTTTATTCTTTAGTTTAT
Found at i:57248307 original size:24 final size:24
Alignment explanation
Indices: 57248280--57248327 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
57248270 GGTCTATGCA
*
57248280 ATTTCATGGATAGCAAAAAACCAG
1 ATTTAATGGATAGCAAAAAACCAG
*
57248304 ATTTAATGGATGGCAAAAAACCAG
1 ATTTAATGGATAGCAAAAAACCAG
57248328 TTTTGCTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.46, C:0.15, G:0.19, T:0.21
Consensus pattern (24 bp):
ATTTAATGGATAGCAAAAAACCAG
Found at i:57256321 original size:14 final size:15
Alignment explanation
Indices: 57256297--57256326 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
57256287 TACTTTCTTT
57256297 TTCTCTTTTCTTTAA
1 TTCTCTTTTCTTTAA
57256312 TTCT-TTTTCTTTAA
1 TTCTCTTTTCTTTAA
57256326 T
1 T
57256327 AACAAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (15 bp):
TTCTCTTTTCTTTAA
Found at i:57257959 original size:30 final size:29
Alignment explanation
Indices: 57257923--57257983 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
57257913 GTCAGTGATT
57257923 TGTA-AAAATTAAATC-AAA-TAAAATTCAA
1 TGTATAAAATTAAA-CAAAATTAAAATTC-A
*
57257951 TGTATAAAATTACACAAAATTAAAATTCA
1 TGTATAAAATTAAACAAAATTAAAATTCA
57257980 TGTA
1 TGTA
57257984 GAACCTTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 5 0.17
29 16 0.55
30 8 0.28
ACGTcount: A:0.56, C:0.08, G:0.05, T:0.31
Consensus pattern (29 bp):
TGTATAAAATTAAACAAAATTAAAATTCA
Found at i:57259031 original size:19 final size:19
Alignment explanation
Indices: 57259007--57259048 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
57258997 TTTTTAAAAC
*
57259007 ATTTTA-AATATGTTTTATT
1 ATTTTATAATAT-TTTTATA
57259026 ATTTTATAATATTTTTATA
1 ATTTTATAATATTTTTATA
57259045 ATTT
1 ATTT
57259049 ATTAGAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
ATTTTATAATATTTTTATA
Found at i:57262899 original size:14 final size:14
Alignment explanation
Indices: 57262876--57262905 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
57262866 TATTCAGAGG
*
57262876 TTGTTGTTAGTTGA
1 TTGTTATTAGTTGA
57262890 TTGTTATTAGTTGA
1 TTGTTATTAGTTGA
57262904 TT
1 TT
57262906 ATATCAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.00, G:0.23, T:0.60
Consensus pattern (14 bp):
TTGTTATTAGTTGA
Found at i:57266583 original size:23 final size:23
Alignment explanation
Indices: 57266557--57266667 Score: 125
Period size: 23 Copynumber: 4.8 Consensus size: 23
57266547 TTAATGTTCA
**
57266557 CGAACATGTTCATTTAAC-TTAAT
1 CGAACATGTTCA-CGAACATTAAT
*
57266580 CGAACATGTTCACGAGCATTAAT
1 CGAACATGTTCACGAACATTAAT
*
57266603 CGAACATGTTCACGAACAATAAT
1 CGAACATGTTCACGAACATTAAT
*
57266626 CGAACATGTTCATGAACATATAAT
1 CGAACATGTTCACGAACAT-TAAT
* * *
57266650 TGAATACGTTCACGAACA
1 CGAACATGTTCACGAACA
57266668 ATATTAATGA
Statistics
Matches: 75, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
22 2 0.03
23 55 0.73
24 18 0.24
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.28
Consensus pattern (23 bp):
CGAACATGTTCACGAACATTAAT
Found at i:57266678 original size:25 final size:24
Alignment explanation
Indices: 57266587--57266680 Score: 77
Period size: 23 Copynumber: 4.0 Consensus size: 24
57266577 AATCGAACAT
* * * *
57266587 GTTCACGAGCAT-TAATCGAACAT
1 GTTCACGAACATATAATTGAATAC
* * *
57266610 GTTCACGAACA-ATAATCGAACAT
1 GTTCACGAACATATAATTGAATAC
*
57266633 GTTCATGAACATATAATTGAATAC
1 GTTCACGAACATATAATTGAATAC
57266657 GTTCACGAACAATATTAA-TGAATA
1 GTTCACGAAC-ATA-TAATTGAATA
57266681 ATAAACAAAC
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
23 31 0.51
24 18 0.30
25 9 0.15
26 3 0.05
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (24 bp):
GTTCACGAACATATAATTGAATAC
Found at i:57266692 original size:4 final size:4
Alignment explanation
Indices: 57266683--57266708 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
57266673 AATGAATAAT
57266683 AAAC AAAC AAAC AAAC AAAC AAAC AA
1 AAAC AAAC AAAC AAAC AAAC AAAC AA
57266709 TAAAGACATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.23, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:57266793 original size:24 final size:24
Alignment explanation
Indices: 57266766--57266823 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
57266756 TCATTAATAA
**
57266766 ATAAACGAGTTAATAAACGAGCTT
1 ATAAACGAGCCAATAAACGAGCTT
57266790 ATAAACGAGCCAATAAACGAGCTT
1 ATAAACGAGCCAATAAACGAGCTT
*
57266814 TTAAACGAGC
1 ATAAACGAGC
57266824 TTGTTCGTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.45, C:0.17, G:0.17, T:0.21
Consensus pattern (24 bp):
ATAAACGAGCCAATAAACGAGCTT
Found at i:57266825 original size:12 final size:12
Alignment explanation
Indices: 57266766--57266825 Score: 77
Period size: 12 Copynumber: 5.0 Consensus size: 12
57266756 TCATTAATAA
57266766 ATAAACGAG-TT
1 ATAAACGAGCTT
57266777 AATAAACGAGCTT
1 -ATAAACGAGCTT
**
57266790 ATAAACGAGCCA
1 ATAAACGAGCTT
57266802 ATAAACGAGCTT
1 ATAAACGAGCTT
*
57266814 TTAAACGAGCTT
1 ATAAACGAGCTT
57266826 GTTCGTGAAC
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
12 40 0.95
13 2 0.05
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23
Consensus pattern (12 bp):
ATAAACGAGCTT
Found at i:57267087 original size:49 final size:50
Alignment explanation
Indices: 57267031--57267145 Score: 135
Period size: 50 Copynumber: 2.3 Consensus size: 50
57267021 TAAATGTAAA
* * *
57267031 ATATTTATATAAAATATAATATCTGAAC-AAAC-AATATAAACAAATATTT
1 ATATTTATATAAAACACAATATCTAAACAAAACAAAT-TAAACAAATATTT
* * * *
57267080 ATGTTTATGTAAAACACCATATCTAAACAAAACAAATTAAATAAATATTT
1 ATATTTATATAAAACACAATATCTAAACAAAACAAATTAAACAAATATTT
*
57267130 ATATTTATTTAAAACA
1 ATATTTATATAAAACA
57267146 TTAGATCTGA
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
49 22 0.40
50 30 0.55
51 3 0.05
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.35
Consensus pattern (50 bp):
ATATTTATATAAAACACAATATCTAAACAAAACAAATTAAACAAATATTT
Found at i:57267445 original size:13 final size:13
Alignment explanation
Indices: 57267427--57267454 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
57267417 TGTGTTGTAA
57267427 AGAATTCAAGCTT
1 AGAATTCAAGCTT
57267440 AGAATTCAAGCTT
1 AGAATTCAAGCTT
57267453 AG
1 AG
57267455 TCATTCTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (13 bp):
AGAATTCAAGCTT
Found at i:57268489 original size:30 final size:30
Alignment explanation
Indices: 57268453--57268509 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
57268443 CGAAATACGT
57268453 AAATTTTATCTCAAAATTCTT-GAGTTTCAA
1 AAATTTTATCTCAAAATT-TTCGAGTTTCAA
*
57268483 AAATTTTATTTCAAAATTTTCGAGTTT
1 AAATTTTATCTCAAAATTTTCGAGTTT
57268510 AAAGTTAGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 2 0.08
30 23 0.92
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.47
Consensus pattern (30 bp):
AAATTTTATCTCAAAATTTTCGAGTTTCAA
Found at i:57268496 original size:14 final size:13
Alignment explanation
Indices: 57268453--57268502 Score: 55
Period size: 13 Copynumber: 3.5 Consensus size: 13
57268443 CGAAATACGT
*
57268453 AAATTTTATCTCA
1 AAATTTTATTTCA
57268466 AAATTCTTGAGTTTCAA
1 AAATT-TT-A-TTTC-A
57268483 AAATTTTATTTCA
1 AAATTTTATTTCA
57268496 AAATTTT
1 AAATTTT
57268503 CGAGTTTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
13 13 0.41
14 6 0.19
15 2 0.06
16 5 0.16
17 6 0.19
ACGTcount: A:0.38, C:0.10, G:0.04, T:0.48
Consensus pattern (13 bp):
AAATTTTATTTCA
Found at i:57268888 original size:17 final size:17
Alignment explanation
Indices: 57268868--57268911 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
57268858 AGTTGTTAGA
57268868 TATTATTATATTTTAA-T
1 TATTATTAT-TTTTAAGT
57268885 TATTAATTATTTTTAAGT
1 TATT-ATTATTTTTAAGT
*
57268903 TAATATTAT
1 TATTATTAT
57268912 GATAAAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (17 bp):
TATTATTATTTTTAAGT
Found at i:57274385 original size:6 final size:6
Alignment explanation
Indices: 57274370--57274420 Score: 57
Period size: 6 Copynumber: 8.5 Consensus size: 6
57274360 GGGTGATTTG
* * * * *
57274370 GAGGAA GAGGAG GAGGAA GAAGAA GAAGAG GAGGAA GAGGAA GAAGAA
1 GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA
57274418 GAG
1 GAG
57274421 CAGATTGAAG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (6 bp):
GAGGAA
Found at i:57274400 original size:18 final size:18
Alignment explanation
Indices: 57274373--57274438 Score: 71
Period size: 18 Copynumber: 3.7 Consensus size: 18
57274363 TGATTTGGAG
*
57274373 GAAGAGGAGGAGGAAGAA
1 GAAGAAGAGGAGGAAGAA
*
57274391 GAAGAAGAGGAGGAAGAG
1 GAAGAAGAGGAGGAAGAA
* * *
57274409 GAAGAAGAAGA-GCAGATT
1 GAAGAAGAGGAGGAAGA-A
57274427 GAAGAAGAGGAG
1 GAAGAAGAGGAG
57274439 TTGGAGGATG
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
17 4 0.10
18 36 0.90
ACGTcount: A:0.50, C:0.02, G:0.45, T:0.03
Consensus pattern (18 bp):
GAAGAAGAGGAGGAAGAA
Found at i:57274434 original size:21 final size:21
Alignment explanation
Indices: 57274373--57274423 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
57274363 TGATTTGGAG
* *
57274373 GAAGAGGAGGAGGAAGAAGAA
1 GAAGAGCAGGAAGAAGAAGAA
* *
57274394 GAAGAGGAGGAAGAGGAAGAA
1 GAAGAGCAGGAAGAAGAAGAA
57274415 GAAGAGCAG
1 GAAGAGCAG
57274424 ATTGAAGAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.51, C:0.02, G:0.47, T:0.00
Consensus pattern (21 bp):
GAAGAGCAGGAAGAAGAAGAA
Found at i:57275683 original size:9 final size:9
Alignment explanation
Indices: 57275669--57275694 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
57275659 TTCATCCATC
57275669 ATCATCATT
1 ATCATCATT
57275678 ATCATCATT
1 ATCATCATT
57275687 ATCATCAT
1 ATCATCAT
57275695 CATAATAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (9 bp):
ATCATCATT
Found at i:57275995 original size:4 final size:4
Alignment explanation
Indices: 57275986--57276010 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
57275976 CAATGGAAGA
57275986 TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG T
57276011 TTCTTGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:57276484 original size:12 final size:12
Alignment explanation
Indices: 57276467--57276491 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
57276457 TTTGCCGATT
57276467 GGTAATGAGACC
1 GGTAATGAGACC
57276479 GGTAATGAGACC
1 GGTAATGAGACC
57276491 G
1 G
57276492 ATTGTCCTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.36, T:0.16
Consensus pattern (12 bp):
GGTAATGAGACC
Found at i:57280079 original size:32 final size:33
Alignment explanation
Indices: 57280017--57280083 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
57280007 AAAAGTCAAC
* * *
57280017 TTTTCAAAAAAATATGAAAAGTAATCATAATTT
1 TTTTAAAAAAAAAATCAAAAGTAATCATAATTT
57280050 TTTTAAAAAAAAAATCAAAA-TAAAT-ATAATTT
1 TTTTAAAAAAAAAATCAAAAGT-AATCATAATTT
57280082 TT
1 TT
57280084 GGATAATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
32 10 0.33
33 20 0.67
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.37
Consensus pattern (33 bp):
TTTTAAAAAAAAAATCAAAAGTAATCATAATTT
Found at i:57281277 original size:21 final size:20
Alignment explanation
Indices: 57281228--57281277 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
57281218 CGTATTTAAG
*
57281228 GGTTTAGGATTTAAGGTCTC
1 GGTTTAGGATTTAAGGTCTA
* *
57281248 GAGTATAGGATTTAAGGTTTTA
1 G-GTTTAGGATTTAAGG-TCTA
57281270 GGTTTAGG
1 GGTTTAGG
57281278 GTTTTAATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 1 0.04
21 20 0.83
22 3 0.12
ACGTcount: A:0.24, C:0.04, G:0.32, T:0.40
Consensus pattern (20 bp):
GGTTTAGGATTTAAGGTCTA
Found at i:57283127 original size:94 final size:94
Alignment explanation
Indices: 57282904--57283444 Score: 876
Period size: 94 Copynumber: 5.8 Consensus size: 94
57282894 TTAATTTTGC
*
57282904 TAGTTAGTAATTTTATTTTATTGTTAG---TAGTAGTAAGTAAAAAATATTGTTCATATTTATTG
1 TAGTTAGTAATTTTATTTTGTTGTTAGTAATAGTAGTAAGTAAAAAATATTGTTCATATTTATTG
*** *
57282966 ATTTAAAATTTAATAATGTTTAAATTTTAC
66 ATTTAAAATTTAATAATGTTTAAA-AAAAT
* *
57282996 TAGTTAGTAATTTTATTTTGTTGTTAGTAGTAGTAGTAAGTAAAAAAATATTGTTTATATTTATT
1 TAGTTAGTAATTTTATTTTGTTGTTAGTAATAGTAGTAAGT-AAAAAATATTGTTCATATTTATT
*
57283061 GATTT-AAATTTAATAATGTTTAAAAAATT
65 GATTTAAAATTTAATAATGTTTAAAAAAAT
* * * *
57283090 TAATTAGTAATTTTATTTTGTTGTTAGTAATAATAGTAAGTAAAAAATATTTTTTATATTTATTG
1 TAGTTAGTAATTTTATTTTGTTGTTAGTAATAGTAGTAAGTAAAAAATATTGTTCATATTTATTG
57283155 ATTTAAAATTTAATAATGTTTAAAAAAAT
66 ATTTAAAATTTAATAATGTTTAAAAAAAT
* *
57283184 TAGTTAGTAATTTTATTTTGTTGTTAGTAATAGTAGTAAGTAAAAAATATTATTTATATTTATTG
1 TAGTTAGTAATTTTATTTTGTTGTTAGTAATAGTAGTAAGTAAAAAATATTGTTCATATTTATTG
57283249 ATTTAAAATTTAATAATGTTTAAAAAAAT
66 ATTTAAAATTTAATAATGTTTAAAAAAAT
*
57283278 TAGTTAGTAATTTTATTTTGTTGTTAGTAGTAGTAGTAAGTAAAAAATATTGTTCATATTT-TTG
1 TAGTTAGTAATTTTATTTTGTTGTTAGTAATAGTAGTAAGTAAAAAATATTGTTCATATTTATTG
*
57283342 ATTTAAAATTTAATAATATTTAAAAAAAT
66 ATTTAAAATTTAATAATGTTTAAAAAAAT
57283371 TAGTTAGTAATTTTATTTTGTTGTTAGTAAGTAGTAGTAAGTAAAAAATATTGTTCATATTTATT
1 TAGTTAGTAATTTTATTTTGTTGTTAGTAA-TAGTAGTAAGTAAAAAATATTGTTCATATTTATT
57283436 GATTTAAAA
65 GATTTAAAA
57283445 AAATAATATA
Statistics
Matches: 422, Mismatches: 20, Indels: 11
0.93 0.04 0.02
Matches are distributed among these distances:
92 26 0.06
93 87 0.21
94 241 0.57
95 41 0.10
96 27 0.06
ACGTcount: A:0.39, C:0.01, G:0.11, T:0.48
Consensus pattern (94 bp):
TAGTTAGTAATTTTATTTTGTTGTTAGTAATAGTAGTAAGTAAAAAATATTGTTCATATTTATTG
ATTTAAAATTTAATAATGTTTAAAAAAAT
Found at i:57283684 original size:16 final size:16
Alignment explanation
Indices: 57283639--57283688 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
57283629 TAAACCTAGC
*
57283639 TAATTAATTACCAAAA
1 TAATTAATTATCAAAA
*
57283655 T-A-TAA-TATAAAAAA
1 TAATTAATTAT-CAAAA
57283669 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
57283685 TAAT
1 TAAT
57283689 ACCCCAATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 2 0.07
16 12 0.44
17 3 0.11
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Found at i:57283755 original size:30 final size:30
Alignment explanation
Indices: 57283721--57283822 Score: 73
Period size: 30 Copynumber: 3.4 Consensus size: 30
57283711 AAATGGTACA
57283721 AAATAAATATTTATTTTGTACCATTTTAGT
1 AAATAAATATTTATTTTGTACCATTTTAGT
* ** * * * * *
57283751 AAAT-AGT-GGTGTGTGGATACTATTTTGGT
1 AAATAAATATTTATTTTG-TACCATTTTAGT
* * *
57283780 ATATAAAAATATATTTTGTACCATTTTAGT
1 AAATAAATATTTATTTTGTACCATTTTAGT
57283810 AAATAATATATTT
1 AAATAA-ATATTT
57283823 TTGGTATTTA
Statistics
Matches: 47, Mismatches: 21, Indels: 7
0.63 0.28 0.09
Matches are distributed among these distances:
28 4 0.09
29 15 0.32
30 20 0.43
31 8 0.17
ACGTcount: A:0.36, C:0.05, G:0.13, T:0.46
Consensus pattern (30 bp):
AAATAAATATTTATTTTGTACCATTTTAGT
Found at i:57285576 original size:15 final size:15
Alignment explanation
Indices: 57285556--57285586 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
57285546 GCAACAAGGA
57285556 GAGGAGGAAGAAGAG
1 GAGGAGGAAGAAGAG
*
57285571 GAGGAGGAGGAAGAG
1 GAGGAGGAAGAAGAG
57285586 G
1 G
57285587 CATTGGATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.58, T:0.00
Consensus pattern (15 bp):
GAGGAGGAAGAAGAG
Found at i:57285713 original size:21 final size:21
Alignment explanation
Indices: 57285687--57285733 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
57285677 ACGAGCCACC
*
57285687 GCAATACTTTACTCCTCTC-GG
1 GCAATACTCTACTCCTC-CGGG
57285708 GCAATACTCTACTCCTCCGGG
1 GCAATACTCTACTCCTCCGGG
57285729 GCAAT
1 GCAAT
57285734 TGAACCCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.21, C:0.34, G:0.17, T:0.28
Consensus pattern (21 bp):
GCAATACTCTACTCCTCCGGG
Found at i:57288859 original size:4 final size:4
Alignment explanation
Indices: 57288840--57288890 Score: 59
Period size: 4 Copynumber: 12.2 Consensus size: 4
57288830 AACACATTAC
*
57288840 CTTT CTTT CCTCT CTTT CTTT CTTT CTTT CTTT CTTT CCTCTT -TTT CTTT
1 CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTTT CTTT -CT-TT CTTT CTTT
57288890 C
1 C
57288891 CCGTTTTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
3 2 0.05
4 32 0.78
5 5 0.12
6 2 0.05
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (4 bp):
CTTT
Found at i:57288898 original size:13 final size:13
Alignment explanation
Indices: 57288841--57288891 Score: 57
Period size: 13 Copynumber: 3.7 Consensus size: 13
57288831 ACACATTACC
*
57288841 TTTCTTTCCTCTC
1 TTTCTTTCCTCTT
*
57288854 TTTCTTTCTTTCTTT
1 TTTCTTTC-CTC-TT
57288869 CTTTCTTTCCTCTT
1 -TTTCTTTCCTCTT
57288883 TTTCTTTCC
1 TTTCTTTCC
57288892 CGTTTTTTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
13 17 0.53
14 4 0.12
15 3 0.09
16 8 0.25
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTCTTTCCTCTT
Found at i:57289090 original size:27 final size:27
Alignment explanation
Indices: 57289060--57289116 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
57289050 ACACCCCTTA
57289060 GTGCCGCCACTTGATATTCCTCCATTG
1 GTGCCGCCACTTGATATTCCTCCATTG
*
57289087 GTGCCGCCACTTGATGTTCCTCCATTG
1 GTGCCGCCACTTGATATTCCTCCATTG
57289114 GTG
1 GTG
57289117 TCAGGTATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.12, C:0.32, G:0.23, T:0.33
Consensus pattern (27 bp):
GTGCCGCCACTTGATATTCCTCCATTG
Found at i:57298209 original size:17 final size:17
Alignment explanation
Indices: 57298177--57298210 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
57298167 TAAGTGTTTG
* *
57298177 AATAAATATTTTTAATT
1 AATAAATAATTATAATT
57298194 AATAAATAATTATAATT
1 AATAAATAATTATAATT
57298211 GTGAGTGATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AATAAATAATTATAATT
Found at i:57299340 original size:1 final size:1
Alignment explanation
Indices: 57299334--57299359 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
57299324 TCTTCATCTG
57299334 CCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCC
57299360 AAAAAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:57301627 original size:39 final size:39
Alignment explanation
Indices: 57301584--57301660 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 39
57301574 ATTAATATTA
*
57301584 TTTTTATATTATTGATATATTTCTATTTTATTTATTTCC
1 TTTTTATATTATTGATATATTTCTATTTCATTTATTTCC
* *
57301623 TTTTTATATTATTTATCTATTTCTATTTCATTTATTTC
1 TTTTTATATTATTGATATATTTCTATTTCATTTATTTC
57301661 ATTTGCACTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.22, C:0.09, G:0.01, T:0.68
Consensus pattern (39 bp):
TTTTTATATTATTGATATATTTCTATTTCATTTATTTCC
Found at i:57301636 original size:20 final size:19
Alignment explanation
Indices: 57301515--57301657 Score: 80
Period size: 20 Copynumber: 7.4 Consensus size: 19
57301505 GCTACAGGAT
57301515 TTATTTATATA-TTTTATTAA
1 TTATTTATATATTTTTA-T-A
*
57301535 TTTTTTATATA-TTTTAT-
1 TTATTTATATATTTTTATA
* ***
57301552 TTA-TAATATATTAGAATA
1 TTATTTATATATTTTTATA
57301570 TTATATTAATATTATTTTTATA
1 TTAT-TT-ATA-TATTTTTATA
* * *
57301592 TTATTGATATATTTCTATT
1 TTATTTATATATTTTTATA
* *
57301611 TTATTTATTTCCTTTTTATA
1 TTATTTATAT-ATTTTTATA
* *
57301631 TTATTTATCTATTTCTAT-
1 TTATTTATATATTTTTATA
57301649 TTCATTTAT
1 TT-ATTTAT
57301658 TTCATTTGCA
Statistics
Matches: 94, Mismatches: 21, Indels: 17
0.71 0.16 0.13
Matches are distributed among these distances:
16 6 0.06
17 5 0.05
18 5 0.05
19 29 0.31
20 34 0.36
21 4 0.04
22 11 0.12
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.64
Consensus pattern (19 bp):
TTATTTATATATTTTTATA
Found at i:57303099 original size:27 final size:27
Alignment explanation
Indices: 57303069--57303127 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
57303059 GTATTTATGA
* *
57303069 TCCTGACAGACTGCCCCGTGTTTAACG
1 TCCTGACAAACTACCCCGTGTTTAACG
* **
57303096 TCCTGGCAAACTACCTTGTGTTTAACG
1 TCCTGACAAACTACCCCGTGTTTAACG
57303123 TCCTG
1 TCCTG
57303128 GTGACTACCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.19, C:0.31, G:0.20, T:0.31
Consensus pattern (27 bp):
TCCTGACAAACTACCCCGTGTTTAACG
Found at i:57303143 original size:26 final size:27
Alignment explanation
Indices: 57303087--57303146 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
57303077 GACTGCCCCG
**
57303087 TGTTTAACGTCCTGGCAAACTACCTTG
1 TGTTTAACGTCCTGGCAAACTACCTCA
**
57303114 TGTTTAACGTCCTGG-TGACTACCTCA
1 TGTTTAACGTCCTGGCAAACTACCTCA
57303140 TGTTTAA
1 TGTTTAA
57303147 TTTCCCAGCG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 14 0.48
27 15 0.52
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.37
Consensus pattern (27 bp):
TGTTTAACGTCCTGGCAAACTACCTCA
Found at i:57307273 original size:3 final size:3
Alignment explanation
Indices: 57307265--57307290 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
57307255 ATTAAAACTA
57307265 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
57307291 ACCTAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:57312197 original size:10 final size:11
Alignment explanation
Indices: 57312175--57312205 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
57312165 TTTTGACTTT
57312175 GAAAAATTATA
1 GAAAAATTATA
57312186 GAAAAATT-TA
1 GAAAAATTATA
57312196 GAAAAATTAT
1 GAAAAATTAT
57312206 TAGAGACTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.61, C:0.00, G:0.10, T:0.29
Consensus pattern (11 bp):
GAAAAATTATA
Found at i:57317171 original size:23 final size:23
Alignment explanation
Indices: 57316999--57317159 Score: 166
Period size: 23 Copynumber: 6.9 Consensus size: 23
57316989 CGAAGTACTT
57316999 AACAGTAAGCACAC-AAGTGCTGGGGA
1 AACAGTAAGCACACAAAGTGC----GA
*
57317025 AACAGTAAGCACACACAGTGC-A
1 AACAGTAAGCACACAAAGTGCGA
* * * * *
57317047 ATCAGTAGGCGCACATAGCGC-A
1 AACAGTAAGCACACAAAGTGCGA
* *
57317069 AATCAGTAGGCACACGAAGTGCGA
1 AA-CAGTAAGCACACAAAGTGCGA
*
57317093 AACAGTAGGCACACAAAGTGCGA
1 AACAGTAAGCACACAAAGTGCGA
57317116 AACAGTAAGCACACAAAGTGCGA
1 AACAGTAAGCACACAAAGTGCGA
*
57317139 AACAGTAAGCACACACAGTGC
1 AACAGTAAGCACACAAAGTGC
57317160 TGAACGGTAA
Statistics
Matches: 118, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
22 19 0.16
23 77 0.65
24 3 0.03
26 14 0.12
27 5 0.04
ACGTcount: A:0.41, C:0.24, G:0.25, T:0.11
Consensus pattern (23 bp):
AACAGTAAGCACACAAAGTGCGA
Found at i:57320069 original size:14 final size:14
Alignment explanation
Indices: 57320052--57320081 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
57320042 AAAATAAAAA
57320052 AAATATAAAAAATT
1 AAATATAAAAAATT
57320066 AAATATAAAAAATT
1 AAATATAAAAAATT
57320080 AA
1 AA
57320082 GAAAAAATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
AAATATAAAAAATT
Found at i:57320070 original size:23 final size:23
Alignment explanation
Indices: 57320043--57320086 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
57320033 AACTAGAATA
57320043 AAATAAAAAAAATATAA-AAAATT
1 AAATAAAAAAAAT-TAAGAAAATT
*
57320066 AAATATAAAAAATTAAGAAAA
1 AAATAAAAAAAATTAAGAAAA
57320087 AATACCAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.20
Consensus pattern (23 bp):
AAATAAAAAAAATTAAGAAAATT
Found at i:57320208 original size:16 final size:16
Alignment explanation
Indices: 57320185--57320256 Score: 117
Period size: 16 Copynumber: 4.5 Consensus size: 16
57320175 CGTTTGGTTC
57320185 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
57320201 GGTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
* *
57320217 ACTGTAATGGAATATA
1 GCTGTAATGGAATAGA
57320233 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
57320249 GCTGTAAT
1 GCTGTAAT
57320257 CAGTAATTCA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.38, C:0.06, G:0.29, T:0.28
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:57320310 original size:39 final size:39
Alignment explanation
Indices: 57320267--57320342 Score: 102
Period size: 39 Copynumber: 1.9 Consensus size: 39
57320257 CAGTAATTCA
57320267 ATTCTT-TGGTTGATTGGAATGGAATAGA-GCTGTAATAAT
1 ATTCTTGTGGTTGATT-GAATGGAAT-GATGCTGTAATAAT
* *
57320306 ATTCTTGTGTTTGGTTGAATGGAATGATGCTGTAATA
1 ATTCTTGTGGTTGATTGAATGGAATGATGCTGTAATA
57320343 GCATAAGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
38 2 0.06
39 24 0.73
40 7 0.21
ACGTcount: A:0.28, C:0.05, G:0.26, T:0.41
Consensus pattern (39 bp):
ATTCTTGTGGTTGATTGAATGGAATGATGCTGTAATAAT
Found at i:57320492 original size:57 final size:59
Alignment explanation
Indices: 57320426--57320562 Score: 181
Period size: 57 Copynumber: 2.3 Consensus size: 59
57320416 AATTTTAATG
* * *
57320426 ATTATTATTAAATATAATTTAATAAAATATTAAT-TTATTTAATTAT-A-TTTTAACATA
1 ATTATTATTAAATATAATTTAATAAAATAAT-ATGTAATTTAATAATAATTTTTAACATA
* *
57320483 ATTATTATTAAATACAATTTAATAAAATAATATGTAATTTAATAATAATTTTTAATATA
1 ATTATTATTAAATATAATTTAATAAAATAATATGTAATTTAATAATAATTTTTAACATA
57320542 ATTATTATTAAAATATGAATT
1 ATTATTATT-AAATAT-AATT
57320563 AGTAAAAATT
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
56 2 0.03
57 39 0.57
58 1 0.01
59 18 0.26
60 5 0.07
61 4 0.06
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (59 bp):
ATTATTATTAAATATAATTTAATAAAATAATATGTAATTTAATAATAATTTTTAACATA
Found at i:57324897 original size:26 final size:26
Alignment explanation
Indices: 57324861--57324916 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
57324851 CATTAACTAT
57324861 ATCTGGATCTTAGGCCTATCCTTTAC
1 ATCTGGATCTTAGGCCTATCCTTTAC
57324887 ATCTGGATCTTAGGCCTATCCTTTAC
1 ATCTGGATCTTAGGCCTATCCTTTAC
57324913 ATCT
1 ATCT
57324917 TCCTCTTGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.20, C:0.27, G:0.14, T:0.39
Consensus pattern (26 bp):
ATCTGGATCTTAGGCCTATCCTTTAC
Found at i:57326261 original size:15 final size:15
Alignment explanation
Indices: 57326237--57326276 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
57326227 AGAAAAAAGC
*
57326237 CAAAATAGAGAGTAT
1 CAAAACAGAGAGTAT
57326252 CAAAACAGAGAGTAT
1 CAAAACAGAGAGTAT
57326267 CAAAACAGAG
1 CAAAACAGAG
57326277 GGAGAGCTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.55, C:0.12, G:0.20, T:0.12
Consensus pattern (15 bp):
CAAAACAGAGAGTAT
Found at i:57326792 original size:6 final size:6
Alignment explanation
Indices: 57326781--57326831 Score: 84
Period size: 6 Copynumber: 8.5 Consensus size: 6
57326771 ATAAATAATT
* *
57326781 ATTTTA ATTTTA ATTTCA ATTTCA ATTTCA ATTTCA ATTTCA ATTTCA
1 ATTTCA ATTTCA ATTTCA ATTTCA ATTTCA ATTTCA ATTTCA ATTTCA
57326829 ATT
1 ATT
57326832 GTTAAAAGAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.55
Consensus pattern (6 bp):
ATTTCA
Found at i:57327601 original size:29 final size:31
Alignment explanation
Indices: 57327552--57327615 Score: 71
Period size: 29 Copynumber: 2.1 Consensus size: 31
57327542 TATATAATTG
*
57327552 TATACATAAATTTTAATTTTG-TAT-ATTTT
1 TATACATAAAATTTAATTTTGATATGATTTT
* *
57327581 TATACATGAAAATTTGA-TTTGATTTGATTTT
1 TATACAT-AAAATTTAATTTTGATATGATTTT
57327612 TATA
1 TATA
57327616 AATTATTAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 11 0.38
30 9 0.31
31 9 0.31
ACGTcount: A:0.34, C:0.03, G:0.08, T:0.55
Consensus pattern (31 bp):
TATACATAAAATTTAATTTTGATATGATTTT
Found at i:57328362 original size:21 final size:21
Alignment explanation
Indices: 57328337--57328378 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
57328327 TATATATACG
*
57328337 AAAAAGTCTAAAAAGTTGAAT
1 AAAAAGTCGAAAAAGTTGAAT
57328358 AAAAAGTCGAAAAAGTTGAAT
1 AAAAAGTCGAAAAAGTTGAAT
57328379 GTTAAAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.57, C:0.05, G:0.17, T:0.21
Consensus pattern (21 bp):
AAAAAGTCGAAAAAGTTGAAT
Found at i:57329128 original size:20 final size:20
Alignment explanation
Indices: 57329090--57329128 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
57329080 GAAGGGCCAA
* **
57329090 ATAAATTATTATATCTTTTG
1 ATAAATTATTAGAAATTTTG
57329110 ATAAATTATTAGAAATTTT
1 ATAAATTATTAGAAATTTT
57329129 TTACTATCAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (20 bp):
ATAAATTATTAGAAATTTTG
Found at i:57334781 original size:20 final size:20
Alignment explanation
Indices: 57334718--57334808 Score: 85
Period size: 20 Copynumber: 4.5 Consensus size: 20
57334708 GCCTGGAGCT
* *
57334718 ATTTTGACTTGTTTAAAAAAC
1 ATTTTGACTTGGTT-AAAATC
** *
57334739 ATTTTGAAGT-GTTAAAATG
1 ATTTTGACTTGGTTAAAATC
* *
57334758 ATTTTGACTTGGTTCAAATT
1 ATTTTGACTTGGTTAAAATC
*
57334778 ATTTTGACTTGTTTAAAATC
1 ATTTTGACTTGGTTAAAATC
*
57334798 ATTTTAACTTG
1 ATTTTGACTTG
57334809 ATTTTAAAAT
Statistics
Matches: 56, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
19 12 0.21
20 36 0.64
21 8 0.14
ACGTcount: A:0.32, C:0.08, G:0.13, T:0.47
Consensus pattern (20 bp):
ATTTTGACTTGGTTAAAATC
Found at i:57335099 original size:18 final size:18
Alignment explanation
Indices: 57335076--57335118 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
57335066 AAATAAAATT
57335076 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
57335094 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
57335112 TTAATTA
1 TTAATTA
57335119 CAACTGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:57336132 original size:18 final size:19
Alignment explanation
Indices: 57336092--57336136 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
57336082 TAAAATTTTA
57336092 AAAATATTAAAATTAAAAC
1 AAAATATTAAAATTAAAAC
*
57336111 AAAAT-TTATAAA-TAAAAT
1 AAAATATTA-AAATTAAAAC
57336129 AAAATATT
1 AAAATATT
57336137 TATTAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAATATTAAAATTAAAAC
Found at i:57336261 original size:8 final size:9
Alignment explanation
Indices: 57336243--57336290 Score: 53
Period size: 9 Copynumber: 5.2 Consensus size: 9
57336233 TTAATTAAAG
57336243 TTTTATAAT
1 TTTTATAAT
57336252 TTTTAT-AT
1 TTTTATAAT
57336260 TTTTATGATAT
1 TTTTAT-A-AT
*
57336271 TTTAATAAT
1 TTTTATAAT
*
57336280 TTTTAAAAT
1 TTTTATAAT
57336289 TT
1 TT
57336291 AAAATGATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
8 8 0.24
9 17 0.52
10 1 0.03
11 7 0.21
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (9 bp):
TTTTATAAT
Found at i:57337999 original size:13 final size:13
Alignment explanation
Indices: 57337981--57338005 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57337971 GAACAAACAC
57337981 TTTCTCTTGAAAA
1 TTTCTCTTGAAAA
57337994 TTTCTCTTGAAA
1 TTTCTCTTGAAA
57338006 GGATTTCCAA
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:0.28, C:0.16, G:0.08, T:0.48
Consensus pattern (13 bp):
TTTCTCTTGAAAA
Found at i:57340712 original size:26 final size:27
Alignment explanation
Indices: 57340662--57340715 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 27
57340652 ACATACAAAG
57340662 AAAATTAATTAACTAACTCATTTTAATA
1 AAAATTAATTAAC-AACTCATTTTAATA
57340690 AAAATTAAATTAA-AA-TCATTTTAATA
1 AAAATT-AATTAACAACTCATTTTAATA
57340716 CACATGACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 11 0.44
27 2 0.08
28 6 0.24
29 6 0.24
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (27 bp):
AAAATTAATTAACAACTCATTTTAATA
Found at i:57350890 original size:39 final size:39
Alignment explanation
Indices: 57350847--57351080 Score: 172
Period size: 39 Copynumber: 5.9 Consensus size: 39
57350837 TGAAGGTGCC
57350847 ATAGGTGGTGGTGCTGGTGGTAATGATGCAGTTCTATGA
1 ATAGGTGGTGGTGCTGGTGGTAATGATGCAGTTCTATGA
* ** * *
57350886 ATAGGAGGTGGTGGGGGTGGTAATGATGCACTTCCA-G-
1 ATAGGTGGTGGTGCTGGTGGTAATGATGCAGTTCTATGA
* * ** * * ** *
57350923 GT-GGTGGAGGTGGCAT--TGGTCCTGATTCTGTTGAAGGTGCC
1 ATAGGTGGTGGT-GC-TGGTGGTAATGATGCAGTTCTA--TG-A
*
57350964 ATAGTTGGTGGTGCTGGTGGTAATGATGCAGTTCTATGA
1 ATAGGTGGTGGTGCTGGTGGTAATGATGCAGTTCTATGA
*
57351003 ATAGGAGGTGGTGGTGCTGGTGGTAATGATGCAGTTCTAAGA
1 AT---AGGTGGTGGTGCTGGTGGTAATGATGCAGTTCTATGA
* ** * *
57351045 ATAGGAGGTGGTGGGGGTGGTAACGATGCACTTCTA
1 ATAGGTGGTGGTGCTGGTGGTAATGATGCAGTTCTA
57351081 GGTACAGGAG
Statistics
Matches: 148, Mismatches: 34, Indels: 26
0.71 0.16 0.12
Matches are distributed among these distances:
36 19 0.13
37 2 0.01
38 1 0.01
39 63 0.43
40 3 0.02
41 3 0.02
42 57 0.39
ACGTcount: A:0.20, C:0.10, G:0.40, T:0.30
Consensus pattern (39 bp):
ATAGGTGGTGGTGCTGGTGGTAATGATGCAGTTCTATGA
Found at i:57350895 original size:42 final size:41
Alignment explanation
Indices: 57350849--57351097 Score: 180
Period size: 42 Copynumber: 6.2 Consensus size: 41
57350839 AAGGTGCCAT
57350849 AGGTGGTGGTGCTGGTGGTAATGATGCAGTTCTATGAATAGG
1 AGGTGGTGG-GCTGGTGGTAATGATGCAGTTCTATGAATAGG
* * *
57350891 AGGTGGTGGG--GGTGGTAATGATGCACTTCCA-G-GT-GG
1 AGGTGGTGGGCTGGTGGTAATGATGCAGTTCTATGAATAGG
* * ** * * ** * *
57350927 TGGAGGT-GGCAT--TGGTCCTGATTCTGTTGAAGGTGCCATAGT
1 AGGTGGTGGGC-TGGTGGTAATGATGCAGTTCTA--TG-AATAGG
*
57350969 TGGTGGT--GCTGGTGGTAATGATGCAGTTCTATGAATAGG
1 AGGTGGTGGGCTGGTGGTAATGATGCAGTTCTATGAATAGG
*
57351008 AGGTGGTGGTGCTGGTGGTAATGATGCAGTTCTAAGAATAGG
1 AGGTGGTGG-GCTGGTGGTAATGATGCAGTTCTATGAATAGG
* * * * *
57351050 AGGTGGTGGG--GGTGGTAACGATGCACTTCTAGGTACAGG
1 AGGTGGTGGGCTGGTGGTAATGATGCAGTTCTATGAATAGG
57351089 AGGTGGTGG
1 AGGTGGTGG
57351098 TGGTAAACCT
Statistics
Matches: 163, Mismatches: 30, Indels: 31
0.73 0.13 0.14
Matches are distributed among these distances:
35 2 0.01
36 19 0.12
37 1 0.01
38 1 0.01
39 63 0.39
40 3 0.02
41 5 0.03
42 69 0.42
ACGTcount: A:0.20, C:0.10, G:0.42, T:0.29
Consensus pattern (41 bp):
AGGTGGTGGGCTGGTGGTAATGATGCAGTTCTATGAATAGG
Found at i:57350947 original size:117 final size:119
Alignment explanation
Indices: 57350805--57351035 Score: 403
Period size: 117 Copynumber: 1.9 Consensus size: 119
57350795 TCCGGGTATT
* *
57350805 GGTGGTGGCGGTGGCATTGGTCCTGATCCTTTTGAAGGTGCCATAGGTGGTGGTGCTGGTGGTAA
1 GGTGGTGGAGGTGGCATTGGTCCTGATCCTGTTGAAGGTGCCATAGGTGGTGGTGCTGGTGGTAA
57350870 TGATGCAGTTCTATGAATAGGAGGTGGTGG-G-GGTGGTAATGATGCACTTCCA
66 TGATGCAGTTCTATGAATAGGAGGTGGTGGTGCGGTGGTAATGATGCACTTCCA
* *
57350922 GGTGGTGGAGGTGGCATTGGTCCTGATTCTGTTGAAGGTGCCATAGTTGGTGGTGCTGGTGGTAA
1 GGTGGTGGAGGTGGCATTGGTCCTGATCCTGTTGAAGGTGCCATAGGTGGTGGTGCTGGTGGTAA
57350987 TGATGCAGTTCTATGAATAGGAGGTGGTGGTGCTGGTGGTAATGATGCA
66 TGATGCAGTTCTATGAATAGGAGGTGGTGGTGC-GGTGGTAATGATGCA
57351036 GTTCTAAGAA
Statistics
Matches: 107, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
117 91 0.85
118 1 0.01
120 15 0.14
ACGTcount: A:0.17, C:0.11, G:0.41, T:0.31
Consensus pattern (119 bp):
GGTGGTGGAGGTGGCATTGGTCCTGATCCTGTTGAAGGTGCCATAGGTGGTGGTGCTGGTGGTAA
TGATGCAGTTCTATGAATAGGAGGTGGTGGTGCGGTGGTAATGATGCACTTCCA
Found at i:57351101 original size:36 final size:36
Alignment explanation
Indices: 57351015--57351103 Score: 97
Period size: 39 Copynumber: 2.4 Consensus size: 36
57351005 AGGAGGTGGT
* * * *
57351015 GGTGCTGGTGGTAATGATGCAGTTCTAAGAATAGGA
1 GGTGGTGGTGGTAACGATGCACTTCTAAGAACAGGA
* *
57351051 GGTGGTGGGGGTGGTAACGATGCACTTCTAGGTACAGGA
1 GGTGGT---GGTGGTAACGATGCACTTCTAAGAACAGGA
57351090 GGTGGTGGTGGTAA
1 GGTGGTGGTGGTAA
57351104 ACCTGGTGGC
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
36 13 0.30
39 31 0.70
ACGTcount: A:0.22, C:0.09, G:0.43, T:0.26
Consensus pattern (36 bp):
GGTGGTGGTGGTAACGATGCACTTCTAAGAACAGGA
Found at i:57352938 original size:2 final size:2
Alignment explanation
Indices: 57352926--57352954 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
57352916 TTTTCCCTGC
57352926 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
57352955 TTGAAAATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:57354956 original size:18 final size:19
Alignment explanation
Indices: 57354916--57354959 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
57354906 AAACATTCTT
* *
57354916 TAAAAATTTCATAAAATTA
1 TAAAATTTTCATAAAATCA
*
57354935 TAAAATTTTC-TAAAATCC
1 TAAAATTTTCATAAAATCA
57354953 TAAAATT
1 TAAAATT
57354960 CCAAACAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (19 bp):
TAAAATTTTCATAAAATCA
Found at i:57355112 original size:18 final size:20
Alignment explanation
Indices: 57355091--57355139 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 20
57355081 ATTTTATAAA
*
57355091 TTTTAATATTTTTGA-G-TT
1 TTTTAATATTTTTAATGATT
**
57355109 TTTTTTTATTTTTAATGATT
1 TTTTAATATTTTTAATGATT
57355129 TTTTAA-ATTTT
1 TTTTAATATTTT
57355140 AAGTATTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
18 12 0.50
19 6 0.25
20 6 0.25
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.71
Consensus pattern (20 bp):
TTTTAATATTTTTAATGATT
Found at i:57359794 original size:17 final size:17
Alignment explanation
Indices: 57359772--57359834 Score: 65
Period size: 17 Copynumber: 3.6 Consensus size: 17
57359762 AATAAAAAAA
57359772 TATAATTTTATAATTTT
1 TATAATTTTATAATTTT
* *
57359789 TATAATTTTTTATTTTT
1 TATAATTTTATAATTTT
*
57359806 TTTGAATTTTAAATAATTTT
1 TAT-AATTTT--ATAATTTT
57359826 TA-AATTTTA
1 TATAATTTTA
57359835 GAAGGGCTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
16 1 0.03
17 17 0.46
18 12 0.32
20 7 0.19
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (17 bp):
TATAATTTTATAATTTT
Found at i:57359798 original size:18 final size:18
Alignment explanation
Indices: 57359772--57359833 Score: 58
Period size: 18 Copynumber: 3.5 Consensus size: 18
57359762 AATAAAAAAA
57359772 TATAA-TTTTATAATTTT
1 TATAATTTTTATAATTTT
*
57359789 TATAATTTTT-TATTTTT
1 TATAATTTTTATAATTTT
* *
57359806 TTTGAATTTTAAATAATTTT
1 TAT-AATTTT-TATAATTTT
57359826 TA-AATTTT
1 TATAATTTT
57359834 AGAAGGGCTT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
17 13 0.36
18 16 0.44
20 7 0.19
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (18 bp):
TATAATTTTTATAATTTT
Found at i:57360384 original size:19 final size:22
Alignment explanation
Indices: 57360348--57360389 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
57360338 CAATCTGCGT
57360348 ATACATAATAAGAATTAA-AAA
1 ATACATAATAAGAATTAATAAA
57360369 ATACATAA-AA-AATTAATAAA
1 ATACATAATAAGAATTAATAAA
57360389 A
1 A
57360390 ATTTAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 6 0.30
21 8 0.40
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (22 bp):
ATACATAATAAGAATTAATAAA
Found at i:57360554 original size:22 final size:22
Alignment explanation
Indices: 57360527--57360571 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
57360517 AAGATTAAAG
*
57360527 ATCAAAGTGAAC-AAAAAATTAA
1 ATCAAAGTG-ACTAAAAAAATAA
*
57360549 ATCAAATTGACTAAAAAAATAA
1 ATCAAAGTGACTAAAAAAATAA
57360571 A
1 A
57360572 AGTTGAGAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 2 0.10
22 18 0.90
ACGTcount: A:0.64, C:0.09, G:0.07, T:0.20
Consensus pattern (22 bp):
ATCAAAGTGACTAAAAAAATAA
Found at i:57364500 original size:50 final size:49
Alignment explanation
Indices: 57364375--57364715 Score: 243
Period size: 50 Copynumber: 6.9 Consensus size: 49
57364365 GGCTACAATG
* * * * * *
57364375 TCTTCGTGGTACTAGATTCGTCATTACGGCTTAAATCTTTCCCTTCA-T-
1 TCTTC-TGGTACTGGATTCGCCGTTGCGACTTAAATCTTTCCCTCCATTA
* * * *
57364423 GCTTCTGAGGTACAAGG-TTCGCCGTTGCGACTTAAACCCTTCCCTCCATTA
1 TCTTCT--GGTAC-TGGATTCGCCGTTGCGACTTAAATCTTTCCCTCCATTA
* * *
57364474 TCTTCATGGTACTGGATTCACCGTTGCGGCTTAAATCTTTCCCTTCA-T-
1 TCTTC-TGGTACTGGATTCGCCGTTGCGACTTAAATCTTTCCCTCCATTA
* * *
57364522 GCTTCTGAGGTA-TAAGG-TTCGCCATTGCGACTTAAACCTTTCCCTCCATTA
1 TCTTCT--GGTACT--GGATTCGCCGTTGCGACTTAAATCTTTCCCTCCATTA
* * *
57364573 TCTTCGTAGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCA-T-
1 TCTTC-TGGTACTGGATTCGCCGTTGCGACTTAAATCTTTCCCTCCATTA
* * * * *
57364621 GCTTCTGAGGTACACGG-TTCGCCGTTGTGACTTAAATCTTTCCCTCTATCA
1 TCTTCT--GGTAC-TGGATTCGCCGTTGCGACTTAAATCTTTCCCTCCATTA
* * *
57364672 TCTTCGTGGTACTAGATTCACCGTTGCGGCTTAAATCTTTCCCT
1 TCTTC-TGGTACTGGATTCGCCGTTGCGACTTAAATCTTTCCCT
57364716 TCATGCTTTG
Statistics
Matches: 227, Mismatches: 43, Indels: 44
0.72 0.14 0.14
Matches are distributed among these distances:
47 3 0.01
48 13 0.06
49 97 0.43
50 98 0.43
51 13 0.06
52 3 0.01
ACGTcount: A:0.18, C:0.28, G:0.18, T:0.37
Consensus pattern (49 bp):
TCTTCTGGTACTGGATTCGCCGTTGCGACTTAAATCTTTCCCTCCATTA
Found at i:57364550 original size:99 final size:99
Alignment explanation
Indices: 57364375--57364723 Score: 545
Period size: 99 Copynumber: 3.5 Consensus size: 99
57364365 GGCTACAATG
* ** * *
57364375 TCTTCGTGGTACTAGATTCGTCATTACGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGG
1 TCTTCGTGGTACTGGATTCACCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGG
*
57364440 TTCGCCGTTGCGACTTAAACCCTTCCCTCCATTA
66 TTCGCCGTTGCGACTTAAACCTTTCCCTCCATTA
* *
57364474 TCTTCATGGTACTGGATTCACCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTATAAGG
1 TCTTCGTGGTACTGGATTCACCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGG
*
57364539 TTCGCCATTGCGACTTAAACCTTTCCCTCCATTA
66 TTCGCCGTTGCGACTTAAACCTTTCCCTCCATTA
* * *
57364573 TCTTCGTAGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACACGG
1 TCTTCGTGGTACTGGATTCACCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGG
* * * *
57364638 TTCGCCGTTGTGACTTAAATCTTTCCCTCTATCA
66 TTCGCCGTTGCGACTTAAACCTTTCCCTCCATTA
*
57364672 TCTTCGTGGTACTAGATTCACCGTTGCGGCTTAAATCTTTCCCTTCATGCTT
1 TCTTCGTGGTACTGGATTCACCGTTGCGGCTTAAATCTTTCCCTTCATGCTT
57364724 TGTGGTAATG
Statistics
Matches: 228, Mismatches: 22, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
99 228 1.00
ACGTcount: A:0.18, C:0.28, G:0.18, T:0.37
Consensus pattern (99 bp):
TCTTCGTGGTACTGGATTCACCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGG
TTCGCCGTTGCGACTTAAACCTTTCCCTCCATTA
Found at i:57378496 original size:15 final size:16
Alignment explanation
Indices: 57378476--57378520 Score: 72
Period size: 17 Copynumber: 2.7 Consensus size: 16
57378466 AATATATATA
57378476 TTTTTTTGTTGCTGGTT
1 TTTTTTTGTTGCTGG-T
57378493 TTTTTGTTGTTGCTGGT
1 TTTTT-TTGTTGCTGGT
57378510 TTTTTTTGTTG
1 TTTTTTTGTTG
57378521 TTTTGGTGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.22
17 11 0.41
18 10 0.37
ACGTcount: A:0.00, C:0.04, G:0.24, T:0.71
Consensus pattern (16 bp):
TTTTTTTGTTGCTGGT
Found at i:57378497 original size:18 final size:18
Alignment explanation
Indices: 57378476--57378522 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
57378466 AATATATATA
57378476 TTTTTTTGTTGCTGGTTT
1 TTTTTTTGTTGCTGGTTT
*
57378494 TTTTGTTGTTGCTGGTTT
1 TTTTTTTGTTGCTGGTTT
57378512 TTTTTGTTGTT
1 TTTTT-TTGTT
57378523 TTGGTGCTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 21 0.81
19 5 0.19
ACGTcount: A:0.00, C:0.04, G:0.23, T:0.72
Consensus pattern (18 bp):
TTTTTTTGTTGCTGGTTT
Found at i:57378527 original size:18 final size:19
Alignment explanation
Indices: 57378476--57378522 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
57378466 AATATATATA
57378476 TTTTT-TTGTTGCTGG-TT
1 TTTTTGTTGTTGCTGGTTT
57378493 TTTTTGTTGTTGCTGGTTT
1 TTTTTGTTGTTGCTGGTTT
57378512 TTTTTGTTGTT
1 TTTTTGTTGTT
57378523 TTGGTGCTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 5 0.18
18 10 0.36
19 13 0.46
ACGTcount: A:0.00, C:0.04, G:0.23, T:0.72
Consensus pattern (19 bp):
TTTTTGTTGTTGCTGGTTT
Found at i:57378547 original size:23 final size:24
Alignment explanation
Indices: 57378503--57378547 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
57378493 TTTTTGTTGT
* * *
57378503 TGCTGGTTTTTTTTGTTGTTTTGG
1 TGCTGGTTTTTGTTATTATTTTGG
57378527 TGCT-GTTTTTGTTATTATTTT
1 TGCTGGTTTTTGTTATTATTTT
57378548 TATTGTTTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 14 0.78
24 4 0.22
ACGTcount: A:0.04, C:0.04, G:0.22, T:0.69
Consensus pattern (24 bp):
TGCTGGTTTTTGTTATTATTTTGG
Found at i:57378556 original size:20 final size:20
Alignment explanation
Indices: 57378533--57378574 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
57378523 TTGGTGCTGT
57378533 TTTTGTTATTATTTTTATTG
1 TTTTGTTATTATTTTTATTG
* *
57378553 TTTTGTTGTTGTTTTTATTG
1 TTTTGTTATTATTTTTATTG
57378573 TT
1 TT
57378575 GTTTTGCTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.10, C:0.00, G:0.14, T:0.76
Consensus pattern (20 bp):
TTTTGTTATTATTTTTATTG
Found at i:57378561 original size:23 final size:22
Alignment explanation
Indices: 57378535--57378636 Score: 82
Period size: 23 Copynumber: 4.5 Consensus size: 22
57378525 GGTGCTGTTT
57378535 TTGTTATTATTTTTATTGTTTTG
1 TTGTTATT-TTTTTATTGTTTTG
* *
57378558 TTGTTGTTTTTATTGTTGTTTTG
1 TTGTTATTTTT-TTATTGTTTTG
* *
57378581 CTGTTATTTTTGCTATTGTTTTG
1 TTGTTATTTTT-TTATTGTTTTG
* * * *
57378604 --GTTATAGTTTTTGTTGCTTGG
1 TTGTTAT-TTTTTTATTGTTTTG
57378625 TTGTTATTTTTT
1 TTGTTATTTTTT
57378637 ATGCGTTTTT
Statistics
Matches: 62, Mismatches: 13, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
21 12 0.19
22 10 0.16
23 40 0.65
ACGTcount: A:0.09, C:0.03, G:0.19, T:0.70
Consensus pattern (22 bp):
TTGTTATTTTTTTATTGTTTTG
Done.