Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008180.1 Hibiscus syriacus cultivar Beakdansim tig00110777_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: 2670214
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 14
Found at i:1081262 original size:22 final size:22
Alignment explanation
Indices: 1081200--1081265 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 22
1081190 CATATAAAAT
*
1081200 TAAATTATAAATAAACAATGAC
1 TAAAATATAAATAAACAATGAC
1081222 TAAAATAT--AT-AA-AAT---
1 TAAAATATAAATAAACAATGAC
1081237 TAAAATATAAATAAACAATGAC
1 TAAAATATAAATAAACAATGAC
1081259 TAAAATA
1 TAAAATA
1081266 AATAAAATTA
Statistics
Matches: 36, Mismatches: 1, Indels: 14
0.71 0.02 0.27
Matches are distributed among these distances:
15 8 0.22
17 2 0.06
18 5 0.14
19 5 0.14
20 2 0.06
22 14 0.39
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.27
Consensus pattern (22 bp):
TAAAATATAAATAAACAATGAC
Found at i:1081268 original size:20 final size:20
Alignment explanation
Indices: 1081206--1081271 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
1081196 AAATTAAATT
1081206 ATAAATAAACAATGACTAAA
1 ATAAATAAACAATGACTAAA
* *
1081226 ATATAT-AA-AATTA--AAA
1 ATAAATAAACAATGACTAAA
1081242 TATAAATAAACAATGACTAAA
1 -ATAAATAAACAATGACTAAA
1081263 ATAAATAAA
1 ATAAATAAA
1081272 ATTAAAAAGT
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
16 3 0.08
17 5 0.14
18 6 0.16
19 6 0.16
20 14 0.38
21 3 0.08
ACGTcount: A:0.67, C:0.06, G:0.03, T:0.24
Consensus pattern (20 bp):
ATAAATAAACAATGACTAAA
Found at i:1081279 original size:16 final size:16
Alignment explanation
Indices: 1081223--1081303 Score: 56
Period size: 19 Copynumber: 4.6 Consensus size: 16
1081213 AACAATGACT
*
1081223 AAAATATATAAAATTA
1 AAAATAAATAAAATTA
*
1081239 AAATATAAATAAACAATGA
1 AAA-ATAAAT-AA-AATTA
1081258 CTAAAATAAATAAAATTA
1 --AAAATAAATAAAATTA
1081276 AAAAGT-AATAAAACTTGTA
1 AAAA-TAAATAAAA--T-TA
1081295 AAAATAAAT
1 AAAATAAAT
1081304 GAAAGTAGTG
Statistics
Matches: 52, Mismatches: 3, Indels: 17
0.72 0.04 0.24
Matches are distributed among these distances:
16 14 0.27
17 6 0.12
18 8 0.15
19 15 0.29
20 6 0.12
21 3 0.06
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.26
Consensus pattern (16 bp):
AAAATAAATAAAATTA
Found at i:1082560 original size:3 final size:3
Alignment explanation
Indices: 1082552--1082626 Score: 82
Period size: 3 Copynumber: 25.0 Consensus size: 3
1082542 TTATTTATTA
*
1082552 AAT AAT AAT AAT AAT AAT ATAT ATAT AAT AAT AAT AAT AAT AAT GAT
1 AAT AAT AAT AAT AAT AAT A-AT A-AT AAT AAT AAT AAT AAT AAT AAT
* * *
1082599 AAA AAT AAA AAT AA- AA- AAT AAA AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1082627 TTTAATGAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
2 4 0.06
3 51 0.82
4 7 0.11
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:1082617 original size:13 final size:13
Alignment explanation
Indices: 1082599--1082625 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1082589 TAATAATGAT
1082599 AAAAATAAAAATA
1 AAAAATAAAAATA
1082612 AAAAATAAAAATA
1 AAAAATAAAAATA
1082625 A
1 A
1082626 TTTTAATGAA
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAATAAAAATA
Found at i:1082870 original size:73 final size:73
Alignment explanation
Indices: 1082752--1083301 Score: 786
Period size: 73 Copynumber: 7.5 Consensus size: 73
1082742 GATGGAAATG
* * *
1082752 TTGAAAACATTC-TGCCCAG-AGGTCTTA-TGAATGACCCTGAGGCTTTAATATCAAAAAGCTCC
1 TTGAAAACA-TCATGCACAGTAGGTCTTACAG-ATGACCCTGAGGCTTTAAAATCAAAAAGCTCC
*
1082814 TGAAGGCTTT
64 CGAAGGCTTT
1082824 TTGAAAACATCATGCACAGTAGGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCG
1 TTGAAAACATCATGCACAGTAGGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCG
1082889 AAGGCTTTTT
66 AAGGC--TTT
* * * * * *
1082899 TTTAAAACATCATGCACTGTAGGTCTTATAGATGACCCTAAGGTTTTAAGATCAAAAAGCTCCCG
1 TTGAAAACATCATGCACAGTAGGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCG
1082964 AAGGCTTT
66 AAGGCTTT
* * *
1082972 TTGAAAACATCATGCACTA-TAGGTCTTACAGATGACCCTGAGGATTTAAGATCAAAAAGCTCCT
1 TTGAAAACATCATGCAC-AGTAGGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCC
1083036 GAAGGCTTT
65 GAAGGCTTT
* * *
1083045 TTGAGAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAGAATCAAAAAGCTCCCG
1 TTGAAAACATCATGCACAGTAGGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCG
1083110 AAGGCTTT
66 AAGGCTTT
*
1083118 TTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCG
1 TTGAAAACATCATGCACAGTAGGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCG
*
1083183 AAGGTTTT
66 AAGGCTTT
*
1083191 TTGAAAACATCATGCACTA-TAGGTTTTACAGATGACCCTGAGGCTTTAAAAAATATCAAAAAGC
1 TTGAAAACATCATGCAC-AGTAGGTCTTACAGATGACCCTGAGGCTTT---AAA-ATCAAAAAGC
1083255 TCCCGAAGGCTTT
61 TCCCGAAGGCTTT
* *
1083268 TTGAAAACATCATGCACTGTAGGTCTTATAGATG
1 TTGAAAACATCATGCACAGTAGGTCTTACAGATG
1083302 TGGGAAATAA
Statistics
Matches: 434, Mismatches: 31, Indels: 21
0.89 0.06 0.04
Matches are distributed among these distances:
71 2 0.00
72 15 0.03
73 294 0.68
74 1 0.00
75 67 0.15
76 3 0.01
77 52 0.12
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (73 bp):
TTGAAAACATCATGCACAGTAGGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCG
AAGGCTTT
Found at i:1083990 original size:22 final size:22
Alignment explanation
Indices: 1083962--1084016 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
1083952 AATAAAGTGT
*
1083962 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAAAATCTA
1083984 TCATCTTTGAAAAGAAAATCTA
1 TCATCTTTGAAAAGAAAATCTA
1084006 TCATCTTTGAA
1 TCATCTTTGAA
1084017 GAGTGTAGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAAAATCTA
Found at i:1094523 original size:140 final size:141
Alignment explanation
Indices: 1094257--1094549 Score: 304
Period size: 140 Copynumber: 2.1 Consensus size: 141
1094247 TCTATTAATT
* * *
1094257 TATATAT-ATATAT-AAATAAGATATTTATTTATTTAGAAATATCAGAAAATGACTTCTAGGTGC
1 TATATATAATTTATAAAATAAAATATTTATTTATTTAGAAATATCAGAAAATGACATCTAGGTGC
* * * *
1094320 TTTAAGACAACTCTTTTCTTAATATAAAAAAATAAATAAATATTAATAAAACATTTATCTAAAAA
66 TTTAAGACAACTCCTTTCTTAATATAAAAAAATAAATAAAAAATAATAAAACATTAATCTAAAAA
1094385 TAA-TTA-AAA
131 TAATTTATAAA
* *
1094394 TATATATAATTTATAAAAGTAAAATATTTATTTATTTA-ATGATATCA-AAAATGGACATCTAGT
1 TATATATAATTTATAAAA-TAAAATATTTATTTATTTAGA-AATATCAGAAAAT-GACATCTAGG
** * * * *
1094457 TGCTTTAAGACTGC-CCTTTCTTAATATTAAAAAATAAATATTAAAACATGATTAAA-A-TAATT
63 TGCTTTAAGACAACTCCTTTCTTAATATAAAAAAATAAATA--AAAA-ATAATAAAACATTAATC
*
1094519 TAAAAGTAATTTATAAA
125 TAAAAATAATTTATAAA
1094536 -AT-TA-AATTTATAAA
1 TATATATAATTTATAAA
1094550 TAGGATTTTA
Statistics
Matches: 130, Mismatches: 16, Indels: 18
0.79 0.10 0.11
Matches are distributed among these distances:
137 7 0.05
138 5 0.04
139 43 0.33
140 57 0.44
141 9 0.07
142 9 0.07
ACGTcount: A:0.49, C:0.07, G:0.06, T:0.38
Consensus pattern (141 bp):
TATATATAATTTATAAAATAAAATATTTATTTATTTAGAAATATCAGAAAATGACATCTAGGTGC
TTTAAGACAACTCCTTTCTTAATATAAAAAAATAAATAAAAAATAATAAAACATTAATCTAAAAA
TAATTTATAAA
Found at i:1094660 original size:22 final size:21
Alignment explanation
Indices: 1094626--1094668 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
1094616 ATATAATAAT
1094626 AACAATAATAATTAAATATATA
1 AACAATAATAATTAAA-ATATA
1094648 AACATATAA-AATTAAAATATA
1 AACA-ATAATAATTAAAATATA
1094669 GATAAACAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (21 bp):
AACAATAATAATTAAAATATA
Found at i:1094665 original size:23 final size:22
Alignment explanation
Indices: 1094626--1094680 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 22
1094616 ATATAATAAT
1094626 AACAATAATAATTAAATATATA
1 AACAATAATAATTAAATATATA
1094648 AACATATAA-AATTAAAATATAGATA
1 AACA-ATAATAATT-AAATAT--ATA
1094673 AACAATAA
1 AACAATAA
1094681 CTAAAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
22 8 0.28
23 10 0.34
24 4 0.14
25 7 0.24
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.27
Consensus pattern (22 bp):
AACAATAATAATTAAATATATA
Found at i:1096025 original size:16 final size:16
Alignment explanation
Indices: 1095984--1096019 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1095974 ATATATGTAT
*
1095984 ATAATAATGA-TAAAA
1 ATAATAATAATTAAAA
1095999 ATAATAATAATTAAAA
1 ATAATAATAATTAAAA
1096015 ATAAT
1 ATAAT
1096020 TTTAATGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (16 bp):
ATAATAATAATTAAAA
Found at i:1096524 original size:30 final size:28
Alignment explanation
Indices: 1096501--1096555 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
1096491 CGGTGATCGG
1096501 TATATTTATCGATCTAACACCGGTCAGAT
1 TATATTTATCGATCTAACACCGGT-AGAT
* *
1096530 TATATTTTTCGATCTAACACCCGTAG
1 TATATTTATCGATCTAACACCGGTAG
1096556 CAGTAAAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (28 bp):
TATATTTATCGATCTAACACCGGTAGAT
Found at i:1096687 original size:50 final size:50
Alignment explanation
Indices: 1096581--1096687 Score: 115
Period size: 50 Copynumber: 2.1 Consensus size: 50
1096571 CCTGAACCAT
* * * * *
1096581 GCTATACGCTGATTTGGCACCACGTGGGTATAGCGCGCCCCCTGCCCCGC
1 GCTATACGCTGATCTGCCACCACGTAGGTATAGCGCACCCCCTGACCCGC
* * * * *
1096631 GATATACGGTGATCTGCCGCCACGTAGGTATAGTGCACCCCCTGATCCGC
1 GCTATACGCTGATCTGCCACCACGTAGGTATAGCGCACCCCCTGACCCGC
*
1096681 TCTATAC
1 GCTATAC
1096688 CTGGGTATCT
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.18, C:0.35, G:0.25, T:0.22
Consensus pattern (50 bp):
GCTATACGCTGATCTGCCACCACGTAGGTATAGCGCACCCCCTGACCCGC
Found at i:1097167 original size:100 final size:101
Alignment explanation
Indices: 1097013--1097218 Score: 387
Period size: 100 Copynumber: 2.0 Consensus size: 101
1097003 TTAGTAATAT
1097013 TTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAAATATCTCGACACTTTGCTGATA
1 TTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAAATATCTCGACACTTTGCTGATA
1097078 CGAT-ACATTTTAACGTTTTAATTTAATTTAAATTA
66 CGATAACATTTTAACGTTTTAATTTAATTTAAATTA
1097113 TTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAAATATCTCGACACTTTGCTGATA
1 TTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAAATATCTCGACACTTTGCTGATA
* *
1097178 CGGTAACATTTTAATGTTTTAATTTAATTTAAATTA
66 CGATAACATTTTAACGTTTTAATTTAATTTAAATTA
1097214 TTAGT
1 TTAGT
1097219 AATAATTAGT
Statistics
Matches: 103, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
100 68 0.66
101 35 0.34
ACGTcount: A:0.34, C:0.08, G:0.12, T:0.46
Consensus pattern (101 bp):
TTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAAATATCTCGACACTTTGCTGATA
CGATAACATTTTAACGTTTTAATTTAATTTAAATTA
Found at i:1098796 original size:18 final size:18
Alignment explanation
Indices: 1098773--1098810 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1098763 ACAGTAGCCA
1098773 CCGCAACCATATATGATG
1 CCGCAACCATATATGATG
1098791 CCGCAACCATATATGATG
1 CCGCAACCATATATGATG
1098809 CC
1 CC
1098811 ACCATCGTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.21
Consensus pattern (18 bp):
CCGCAACCATATATGATG
Found at i:1103122 original size:50 final size:50
Alignment explanation
Indices: 1103004--1103130 Score: 148
Period size: 50 Copynumber: 2.5 Consensus size: 50
1102994 CCCTACGTGG
* *
1103004 CATATAGCGCGGATCAGGGGGCGCGCTATACCCACATGGCACCAGATCAC
1 CATATAGCGCGGATCAGGGGGCGCGCTATACCCACATGGCACCAAATCAA
* * * **
1103054 CGTATATCGCGGGA-CAGGGGGCGCGCTATACCCACGTGGTGCCAAATCAA
1 CATATAGCGC-GGATCAGGGGGCGCGCTATACCCACATGGCACCAAATCAA
* * *
1103104 CATATAGCGCAGTTCAGGGGTCGCGCT
1 CATATAGCGCGGATCAGGGGGCGCGCT
1103131 TTACTGCTAC
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
49 1 0.02
50 59 0.94
51 3 0.05
ACGTcount: A:0.24, C:0.29, G:0.31, T:0.17
Consensus pattern (50 bp):
CATATAGCGCGGATCAGGGGGCGCGCTATACCCACATGGCACCAAATCAA
Found at i:1104774 original size:103 final size:103
Alignment explanation
Indices: 1104595--1104820 Score: 373
Period size: 103 Copynumber: 2.2 Consensus size: 103
1104585 GTAGAGGGTC
*
1104595 TATGTGGTCCTTAGGGACATATATGTATTCTTTGGAATATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTAGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
*
1104660 TTAATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTAATCCTTGGCATATGTATATGATTATTAAGGAATGA
*
1104698 TATGTGGTCTTTCA-GGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATA
1 TATGTGGTCCTT-AGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATA
*
1104762 CTTGATCCTTGGCATATGTATATGATTATTAAGGAATGA
65 CTTAATCCTTGGCATATGTATATGATTATTAAGGAATGA
* * *
1104801 CATGTAGTCCTTATGGACAT
1 TATGTGGTCCTTAGGGACAT
1104821 TATTATATGG
Statistics
Matches: 114, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
102 1 0.01
103 112 0.98
104 1 0.01
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTAGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
TTAATCCTTGGCATATGTATATGATTATTAAGGAATGA
Found at i:1104862 original size:23 final size:23
Alignment explanation
Indices: 1104828--1104891 Score: 103
Period size: 23 Copynumber: 2.8 Consensus size: 23
1104818 CATTATTATA
1104828 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
*
1104851 TGGCACTCCGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
1104874 TGGCACTTA-GGTGCAATT
1 TGGCAC-TACGGTGCAATT
1104892 ATATGAGCTG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 37 0.97
24 1 0.03
ACGTcount: A:0.20, C:0.25, G:0.27, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:1111083 original size:64 final size:63
Alignment explanation
Indices: 1110998--1111158 Score: 182
Period size: 64 Copynumber: 2.5 Consensus size: 63
1110988 TTGTTTAAGG
* * * * *
1110998 TGCATCGATGCACATGCAGTGCATCGATGCAT-TAATTTAAAAAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCAA-TTAAAAA-AAAACATCGAATAAGATTTA
* * *
1111062 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAAGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCAT-CCAATTAAAAAAAAACATCGAATAAGATTTA
*
1111126 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
1111159 ACCTCCATTA
Statistics
Matches: 84, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
63 1 0.01
64 61 0.73
65 21 0.25
66 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (63 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCAATTAAAAAAAAACATCGAATAAGATTTA
Found at i:1111798 original size:103 final size:103
Alignment explanation
Indices: 1111619--1111836 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
1111609 GTAGATGGTC
* *
1111619 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAATATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1111684 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
1111722 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1111787 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
1111825 TATGTAGTCCTT
1 TATGTGGTCCTT
1111837 ATGGACATTA
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:1111886 original size:23 final size:23
Alignment explanation
Indices: 1111853--1111915 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 23
1111843 ATTATTATAT
1111853 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
1111876 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
1111899 GGCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
1111916 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 35 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:1115503 original size:16 final size:16
Alignment explanation
Indices: 1115482--1115513 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1115472 AATCAAATAT
1115482 TATATTTTTGAATTTA
1 TATATTTTTGAATTTA
1115498 TATATTTTTGAATTTA
1 TATATTTTTGAATTTA
1115514 ATGGAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.62
Consensus pattern (16 bp):
TATATTTTTGAATTTA
Found at i:1120589 original size:21 final size:21
Alignment explanation
Indices: 1120527--1120582 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
1120517 TTCTGGGTTG
1120527 TGTGCATCGATGCATCTTCAA
1 TGTGCATCGATGCATCTTCAA
1120548 TGTGCATCGATGCATCTTCAA
1 TGTGCATCGATGCATCTTCAA
* *
1120569 TGTGTATTGATGCA
1 TGTGCATCGATGCA
1120583 CTCTCAAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (21 bp):
TGTGCATCGATGCATCTTCAA
Found at i:1122232 original size:23 final size:23
Alignment explanation
Indices: 1122198--1122261 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
1122188 ACATCTTATA
1122198 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTTCGGTGCATTTCTACG
* * *
1122221 TGGCACTACGGTACAATTCTACG
1 TGGCACTTCGGTGCATTTCTACG
1122244 TGGCACTTCGGTGCATTT
1 TGGCACTTCGGTGCATTT
1122262 ATATGAGCTG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.33
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:1125428 original size:27 final size:28
Alignment explanation
Indices: 1125374--1125429 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
1125364 AATTTTAATA
*
1125374 AAAATTATTAATTTATATATATATAAAT
1 AAAATTATTAATTTATATATATAGAAAT
* * *
1125402 AAAA-TATTTATTTATTTATTTAGAAAT
1 AAAATTATTAATTTATATATATAGAAAT
1125429 A
1 A
1125430 TCAGAAAAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (28 bp):
AAAATTATTAATTTATATATATAGAAAT
Found at i:1125535 original size:27 final size:30
Alignment explanation
Indices: 1125470--1125536 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 30
1125460 AACTCTTTCC
1125470 TTAATATTAAAAAATAAATAAATATTAAAACA
1 TTAAT-TT-AAAAATAAATAAATATTAAAACA
* *
1125502 TTTATTTAAAAAT-AAT-AAT-TTAAAATA
1 TTAATTTAAAAATAAATAAATATTAAAACA
1125529 TTAATTTA
1 TTAATTTA
1125537 TTTAAAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
27 14 0.44
28 3 0.09
29 3 0.09
30 6 0.19
31 2 0.06
32 4 0.12
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (30 bp):
TTAATTTAAAAATAAATAAATATTAAAACA
Found at i:1125696 original size:2 final size:2
Alignment explanation
Indices: 1125685--1125720 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
1125675 AAATAAATAA
*
1125685 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1125721 ATAATAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1125829 original size:27 final size:25
Alignment explanation
Indices: 1125760--1125844 Score: 71
Period size: 27 Copynumber: 3.1 Consensus size: 25
1125750 ATATACTGAA
* *
1125760 AATAAACATATAAAATTAAAACAAT
1 AATAAACATAAAAAATTAAAACTAT
* *
1125785 AAGAAAAATAAATGAAATTAAAACTAT
1 AATAAACATAAA--AAATTAAAACTAT
1125812 AATATTAACATAAAAAATAATAAAACTAGT
1 AATA--AACATAAAAAAT--TAAAACTA-T
1125842 AAT
1 AAT
1125845 TAAATGAAAG
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
25 9 0.19
27 19 0.40
29 15 0.32
30 4 0.09
ACGTcount: A:0.66, C:0.06, G:0.04, T:0.25
Consensus pattern (25 bp):
AATAAACATAAAAAATTAAAACTAT
Found at i:1127249 original size:3 final size:3
Alignment explanation
Indices: 1127241--1127306 Score: 64
Period size: 3 Copynumber: 22.3 Consensus size: 3
1127231 TTTATTTATT
* *
1127241 TAA TAA TAA AAA TAA TAA -AA T-A TAA TAA TTAA TAT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA
** *
1127285 TAA TTT TAA TAA TAA TGA TAA T
1 TAA TAA TAA TAA TAA TAA TAA T
1127307 GAAATGAAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
2 4 0.08
3 43 0.86
4 3 0.06
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:1128382 original size:18 final size:18
Alignment explanation
Indices: 1128359--1128456 Score: 95
Period size: 18 Copynumber: 5.9 Consensus size: 18
1128349 ATATAACACA
*
1128359 TATGTCCCTAAGGACCAC
1 TATGTCCCGAAGGACCAC
1128377 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
* *
1128395 -ATAT----AA-CA-CA-
1 TATGTCCCGAAGGACCAC
1128405 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
* *
1128423 TATGTCCCGAGGGACCGC
1 TATGTCCCGAAGGACCAC
1128441 TATGTCCCGAAGGACC
1 TATGTCCCGAAGGACC
1128457 GCGTAGACCC
Statistics
Matches: 64, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
11 5 0.08
12 1 0.02
13 2 0.03
15 2 0.03
16 1 0.02
17 5 0.08
18 48 0.75
ACGTcount: A:0.29, C:0.32, G:0.21, T:0.18
Consensus pattern (18 bp):
TATGTCCCGAAGGACCAC
Found at i:1128403 original size:46 final size:46
Alignment explanation
Indices: 1128313--1128438 Score: 191
Period size: 46 Copynumber: 2.7 Consensus size: 46
1128303 ACATAGAATT
*
1128313 TGTCCATAAGGACCACATAGATGTCCCGAA-GACCACATATAACACATA
1 TGTCCCTAAGGACCAC-T--ATGTCCCGAAGGACCACATATAACACATA
1128361 TGTCCCTAAGGACCACTATGTCCCGAAGGACCACATATAACACATA
1 TGTCCCTAAGGACCACTATGTCCCGAAGGACCACATATAACACATA
* *
1128407 TGTCCCGAAGGACCACTATGTCCCGAGGGACC
1 TGTCCCTAAGGACCACTATGTCCCGAAGGACC
1128439 GCTATGTCCC
Statistics
Matches: 74, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
45 10 0.14
46 48 0.65
47 1 0.01
48 15 0.20
ACGTcount: A:0.33, C:0.30, G:0.18, T:0.18
Consensus pattern (46 bp):
TGTCCCTAAGGACCACTATGTCCCGAAGGACCACATATAACACATA
Found at i:1129929 original size:10 final size:10
Alignment explanation
Indices: 1129914--1129968 Score: 56
Period size: 10 Copynumber: 5.3 Consensus size: 10
1129904 CTTGGTGTTT
1129914 TAAGCTTATA
1 TAAGCTTATA
* *
1129924 TAAGCTTTCTT
1 TAAGC-TTATA
1129935 TAAGCTTATA
1 TAAGCTTATA
* *
1129945 TAAGCTTTCTT
1 TAAGC-TTATA
1129956 TAAGCTTATA
1 TAAGCTTATA
1129966 TAA
1 TAA
1129969 TACTCAAAGA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
10 19 0.54
11 16 0.46
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.45
Consensus pattern (10 bp):
TAAGCTTATA
Found at i:1129938 original size:21 final size:21
Alignment explanation
Indices: 1129912--1129968 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
1129902 CTCTTGGTGT
1129912 TTTAAGCTTATATAAGCTTTC
1 TTTAAGCTTATATAAGCTTTC
1129933 TTTAAGCTTATATAAGCTTTC
1 TTTAAGCTTATATAAGCTTTC
1129954 TTTAAGCTTATATAA
1 TTTAAGCTTATATAA
1129969 TACTCAAAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.32, C:0.12, G:0.09, T:0.47
Consensus pattern (21 bp):
TTTAAGCTTATATAAGCTTTC
Found at i:1129940 original size:11 final size:11
Alignment explanation
Indices: 1129924--1129962 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
1129914 TAAGCTTATA
1129924 TAAGCTTTCTT
1 TAAGCTTTCTT
* *
1129935 TAAGC-TTATA
1 TAAGCTTTCTT
1129945 TAAGCTTTCTT
1 TAAGCTTTCTT
1129956 TAAGCTT
1 TAAGCTT
1129963 ATATAATACT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.26, C:0.15, G:0.10, T:0.49
Consensus pattern (11 bp):
TAAGCTTTCTT
Found at i:1132811 original size:18 final size:18
Alignment explanation
Indices: 1132788--1132823 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1132778 ATATAACACA
1132788 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
1132806 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
1132824 GTAGACCCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.33, G:0.22, T:0.17
Consensus pattern (18 bp):
TATGTCCCGAAGGACCAC
Found at i:1134305 original size:21 final size:21
Alignment explanation
Indices: 1134280--1134336 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
1134270 CTCTTGGTGT
* *
1134280 TTTAAGTTTCTATAAGCTTTC
1 TTTAAGCTTATATAAGCTTTC
1134301 TTTAAGCTTATATAAGCTTTC
1 TTTAAGCTTATATAAGCTTTC
1134322 TTTAAGCTTATATAA
1 TTTAAGCTTATATAA
1134337 TACTCAAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.49
Consensus pattern (21 bp):
TTTAAGCTTATATAAGCTTTC
Found at i:1134306 original size:11 final size:11
Alignment explanation
Indices: 1134280--1134330 Score: 61
Period size: 11 Copynumber: 4.8 Consensus size: 11
1134270 CTCTTGGTGT
1134280 TTTAAG-TTTC
1 TTTAAGCTTTC
*
1134290 TATAAGCTTTC
1 TTTAAGCTTTC
*
1134301 TTTAAGC-TTA
1 TTTAAGCTTTC
*
1134311 TATAAGCTTTC
1 TTTAAGCTTTC
1134322 TTTAAGCTT
1 TTTAAGCTT
1134331 ATATAATACT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
10 13 0.39
11 20 0.61
ACGTcount: A:0.25, C:0.14, G:0.10, T:0.51
Consensus pattern (11 bp):
TTTAAGCTTTC
Found at i:1136853 original size:15 final size:15
Alignment explanation
Indices: 1136819--1136860 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
1136809 AATAAAAAAA
1136819 TAATATATAATTAATAT
1 TAATA-ATAA-TAATAT
*
1136836 TAATAATAATAATTT
1 TAATAATAATAATAT
1136851 TAATAATAAT
1 TAATAATAAT
1136861 GATAATGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 15 0.62
16 4 0.17
17 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TAATAATAATAATAT
Found at i:1137201 original size:45 final size:46
Alignment explanation
Indices: 1137120--1137229 Score: 132
Period size: 45 Copynumber: 2.4 Consensus size: 46
1137110 TCAAAAGGCT
* * **
1137120 CCCGAAGGCTTTTTAAAAACATCCTGCACTGCAGGGCTTACGGATGA
1 CCCGAAGGC-TTTTAAAAACATCATGCACTGAAGGGCTTAAAGATGA
* *
1137167 CCCGAAGG-TTTTGAAACCATCATGCACTGAAGGGCTTAAAGATGA
1 CCCGAAGGCTTTTAAAAACATCATGCACTGAAGGGCTTAAAGATGA
* *
1137212 CCCAAAGGCTTTAAAAAA
1 CCCGAAGGCTTTTAAAAA
1137230 TATCTAAAAG
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
45 38 0.73
46 6 0.12
47 8 0.15
ACGTcount: A:0.34, C:0.23, G:0.22, T:0.22
Consensus pattern (46 bp):
CCCGAAGGCTTTTAAAAACATCATGCACTGAAGGGCTTAAAGATGA
Found at i:1137254 original size:121 final size:121
Alignment explanation
Indices: 1137018--1137651 Score: 980
Period size: 121 Copynumber: 5.2 Consensus size: 121
1137008 GAGGTCCTAT
* * * * * * *
1137018 CATCTTGCACTGTAGGTCTTGCAGATGACCCGAAGTTTTTGAAAGCATCATGCACTGAAGGGATT
1 CATCCTGCACTGCAGGGCTTACGGATGACCCGAAGGTTTTGAAAGCATCATGCACTGAAGGGCTT
* * *
1137083 ACAGATGACCCTAAGGCTTTGAAAATATCAAAAGGCTCCCGAAGGCTTTTTAAAAA
66 ACAGATGACCCGAAGGCTTTGAAAATATCAAAAAGCTCCCGAAGGCTTTTTGAAAA
*
1137139 CATCCTGCACTGCAGGGCTTACGGATGACCCGAAGGTTTTGAAACCATCATGCACTGAAGGGCTT
1 CATCCTGCACTGCAGGGCTTACGGATGACCCGAAGGTTTTGAAAGCATCATGCACTGAAGGGCTT
* * * * * *
1137204 AAAGATGACCCAAAGGCTTTAAAAAATATCTAAAAGCTCCCGAAGGTTTTTTTTAAAA
66 ACAGATGACCCGAAGGCTTT-GAAAATATCAAAAAGCTCCCGAAGG-CTTTTTGAAAA
1137262 CATCCTGCACTGCAGGGCTTACGGATGACCCGAAGGTTTTGAAAGCATCATGCACTGAAGGGCTT
1 CATCCTGCACTGCAGGGCTTACGGATGACCCGAAGGTTTTGAAAGCATCATGCACTGAAGGGCTT
1137327 ACAGATGACCCGAAGGCTTTGAAAATATCAAAAAGCTCCCGAAGGCTTTTTGAAAA
66 ACAGATGACCCGAAGGCTTTGAAAATATCAAAAAGCTCCCGAAGGCTTTTTGAAAA
* *
1137383 CATCCTGCACTACAGGGCTTACGGATGACCAGAAGGTTTTGAAAGCATCATGCACTGAAGGGCTT
1 CATCCTGCACTGCAGGGCTTACGGATGACCCGAAGGTTTTGAAAGCATCATGCACTGAAGGGCTT
*
1137448 ACAGATGACCTGAAGGCTTTGAAAATATCAAAAAGCTCCCGAAGGCTTTTTGAAAA
66 ACAGATGACCCGAAGGCTTTGAAAATATCAAAAAGCTCCCGAAGGCTTTTTGAAAA
* * * *
1137504 CATCCTGCACTGCAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGATT
1 CATCCTGCACTGCAGGGCTTACGGATGACCCGAAGGTTTTGAAAGCATCATGCACTGAAGGGCTT
* * *
1137569 ACAAATGACCCGAAGGCTTTGAAAATATAAAAAACCTCCCGAAGGCTTTTTGAAAA
66 ACAGATGACCCGAAGGCTTTGAAAATATCAAAAAGCTCCCGAAGGCTTTTTGAAAA
* * *
1137625 CATCTTGCACTACAGGTCTTACGGATG
1 CATCCTGCACTGCAGGGCTTACGGATG
1137652 GTGGGAAATA
Statistics
Matches: 473, Mismatches: 38, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
121 337 0.71
122 45 0.10
123 91 0.19
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.24
Consensus pattern (121 bp):
CATCCTGCACTGCAGGGCTTACGGATGACCCGAAGGTTTTGAAAGCATCATGCACTGAAGGGCTT
ACAGATGACCCGAAGGCTTTGAAAATATCAAAAAGCTCCCGAAGGCTTTTTGAAAA
Found at i:1137324 original size:45 final size:45
Alignment explanation
Indices: 1137253--1137356 Score: 145
Period size: 45 Copynumber: 2.3 Consensus size: 45
1137243 CCGAAGGTTT
* * * *
1137253 TTTTTAAAACATCCTGCACTGCAGGGCTTACGGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
*
1137298 TTTTGAAAGCATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
* *
1137343 CTTTGAAAATATCA
1 TTTTGAAAACATCA
1137357 AAAAGCTCCC
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (45 bp):
TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
Found at i:1137437 original size:45 final size:45
Alignment explanation
Indices: 1137374--1137477 Score: 138
Period size: 45 Copynumber: 2.3 Consensus size: 45
1137364 CCCGAAGGCT
* *
1137374 TTTTGAAAACATCCTGCACT-ACAGGGCTTACGGATGACCAGAAGG
1 TTTTGAAAACATCATGCACTGA-AGGGCTTACAGATGACCAGAAGG
* *
1137419 TTTTGAAAGCATCATGCACTGAAGGGCTTACAGATGACCTGAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCAGAAGG
* *
1137464 CTTTGAAAATATCA
1 TTTTGAAAACATCA
1137478 AAAAGCTCCC
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
45 50 0.98
46 1 0.02
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (45 bp):
TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCAGAAGG
Found at i:1137456 original size:244 final size:242
Alignment explanation
Indices: 1137018--1137651 Score: 1007
Period size: 244 Copynumber: 2.6 Consensus size: 242
1137008 GAGGTCCTAT
* * * * *
1137018 CATCTTGCACTGTAGGTCTTGCAGATGACCCGAAGTTTTTGAAAGCATCATGCACTGAAGGGATT
1 CATCCTGCACTGCAGGTCTTACGGATGACCCGAAGGTTTTGAAAGCATCATGCACTGAAGGGATT
* * *
1137083 ACAGATGACCCTAAGGCTTTGAAAATATCAAAAGGCTCCCGAAGGCTTTTTAAAAACATCCTGCA
66 ACAGATGACCCGAAGGCTTTGAAAATATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCA
* *
1137148 CTGCAGGGCTTACGGATGACCCGAAGGTTTTGAAACCATCATGCACTGAAGGGCTTAAAGATGAC
131 CTACAGGGCTTACGGATGACCAGAAGGTTTTGAAACCATCATGCACTGAAGGGCTTAAAGATGAC
* * *
1137213 CCAAAGGCTTTAAAAAATATCTAAAAGCTCCCGAAGGTTTTTTTTAAAA
196 CCAAAGGCTTT-AAAAATATCAAAAAGCTCCCGAAGG-CTTTTTGAAAA
* *
1137262 CATCCTGCACTGCAGGGCTTACGGATGACCCGAAGGTTTTGAAAGCATCATGCACTGAAGGGCTT
1 CATCCTGCACTGCAGGTCTTACGGATGACCCGAAGGTTTTGAAAGCATCATGCACTGAAGGGATT
1137327 ACAGATGACCCGAAGGCTTTGAAAATATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCA
66 ACAGATGACCCGAAGGCTTTGAAAATATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCA
* *
1137392 CTACAGGGCTTACGGATGACCAGAAGGTTTTGAAAGCATCATGCACTGAAGGGCTTACAGATGAC
131 CTACAGGGCTTACGGATGACCAGAAGGTTTTGAAACCATCATGCACTGAAGGGCTTAAAGATGAC
** *
1137457 CTGAAGGCTTTGAAAATATCAAAAAGCTCCCGAAGGCTTTTTGAAAA
196 CCAAAGGCTTTAAAAATATCAAAAAGCTCCCGAAGGCTTTTTGAAAA
* *
1137504 CATCCTGCACTGCAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGATT
1 CATCCTGCACTGCAGGTCTTACGGATGACCCGAAGGTTTTGAAAGCATCATGCACTGAAGGGATT
* * * *
1137569 ACAAATGACCCGAAGGCTTTGAAAATATAAAAAACCTCCCGAAGGCTTTTTGAAAACATCTTGCA
66 ACAGATGACCCGAAGGCTTTGAAAATATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCA
*
1137634 CTACAGGTCTTACGGATG
131 CTACAGGGCTTACGGATG
1137652 GTGGGAAATA
Statistics
Matches: 361, Mismatches: 29, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
242 148 0.41
243 23 0.06
244 190 0.53
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.24
Consensus pattern (242 bp):
CATCCTGCACTGCAGGTCTTACGGATGACCCGAAGGTTTTGAAAGCATCATGCACTGAAGGGATT
ACAGATGACCCGAAGGCTTTGAAAATATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCCTGCA
CTACAGGGCTTACGGATGACCAGAAGGTTTTGAAACCATCATGCACTGAAGGGCTTAAAGATGAC
CCAAAGGCTTTAAAAATATCAAAAAGCTCCCGAAGGCTTTTTGAAAA
Found at i:1137551 original size:45 final size:45
Alignment explanation
Indices: 1137485--1137593 Score: 128
Period size: 45 Copynumber: 2.4 Consensus size: 45
1137475 TCAAAAAGCT
* * ** ***
1137485 CCCGAAGGCTTTTTGAAAACATCCTGCACTGCAGGTCTTATGGATGA
1 CCCGAAGG--TTTTGAAAACATCATGCACTGAAGGGATTACAAATGA
1137532 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGATTACAAATGA
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGATTACAAATGA
*
1137577 CCCGAAGGCTTTGAAAA
1 CCCGAAGGTTTTGAAAA
1137594 TATAAAAAAC
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
45 46 0.85
47 8 0.15
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (45 bp):
CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGATTACAAATGA
Found at i:1138347 original size:22 final size:22
Alignment explanation
Indices: 1138322--1138376 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
1138312 CATAAAGCTT
1138322 TCATCTTTGAAAAGAGAATCCA
1 TCATCTTTGAAAAGAGAATCCA
* *
1138344 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCCA
1138366 TCATCTTTGAA
1 TCATCTTTGAA
1138377 GAGTATGGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCCA
Found at i:1139744 original size:75 final size:74
Alignment explanation
Indices: 1139648--1139890 Score: 280
Period size: 75 Copynumber: 3.3 Consensus size: 74
1139638 TGTTTCACTA
* * *
1139648 TTTTCATGCATGCCCCTATATTTGTTGATATGAACATTCAAAATACATCAACATTCCTGATTCTA
1 TTTTCA-GCATGCCCCAATATTTGTTGATATGAACATTCAAAAT-CATCAATATTCCTGATTCTG
1139713 ATTGAAATGGG
64 ATTGAAATGGG
* * * *
1139724 CTTTCAGCATGCCCCAATATTTGTTGATATGAACGTTCAAAAT-GT---TATTCC-AATTTCTGA
1 TTTTCAGCATGCCCCAATATTTGTTGATATGAACATTCAAAATCATCAATATTCCTGA-TTCTGA
1139784 TTGAAATGGG
65 TTGAAATGGG
* * ** * *
1139794 TTTTCAGTATGCCCCAACATTTGTTGACGTGAACATTCAAAATGCTTCAATATTCCTGATTATGA
1 TTTTCAGCATGCCCCAATATTTGTTGATATGAACATTCAAAAT-CATCAATATTCCTGATTCTGA
1139859 TTGAAATGGG
65 TTGAAATGGG
* *
1139869 TTTTCAACATACCCCAATATTT
1 TTTTCAGCATGCCCCAATATTT
1139891 TCTTCTTATT
Statistics
Matches: 140, Mismatches: 20, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
69 1 0.01
70 57 0.41
72 1 0.01
73 1 0.01
75 74 0.53
76 6 0.04
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (74 bp):
TTTTCAGCATGCCCCAATATTTGTTGATATGAACATTCAAAATCATCAATATTCCTGATTCTGAT
TGAAATGGG
Found at i:1142775 original size:29 final size:29
Alignment explanation
Indices: 1142743--1142798 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
1142733 GAAATGGTTG
*
1142743 TTATGCTCATCTTGTAGAGATACTTTTCA
1 TTATGCTCATCTCGTAGAGATACTTTTCA
1142772 TTATGCTCATCTCGTAGAGATACTTTT
1 TTATGCTCATCTCGTAGAGATACTTTT
1142799 TGTTTCCAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.23, C:0.18, G:0.14, T:0.45
Consensus pattern (29 bp):
TTATGCTCATCTCGTAGAGATACTTTTCA
Found at i:1143309 original size:7 final size:8
Alignment explanation
Indices: 1143298--1143337 Score: 62
Period size: 8 Copynumber: 4.8 Consensus size: 8
1143288 TTTTTTCATT
1143298 TTTTTTCC
1 TTTTTTCC
1143306 TTTTTTCC
1 TTTTTTCC
1143314 TTTTTTCC
1 TTTTTTCC
1143322 TTTTTTTTCC
1 --TTTTTTCC
1143332 TTTTTT
1 TTTTTT
1143338 TTCTTCTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
8 22 0.73
10 8 0.27
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTTTCC
Found at i:1143317 original size:26 final size:26
Alignment explanation
Indices: 1143288--1143337 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
1143278 TTTTGATTCA
1143288 TTTTTTCATTTTTTTTCCTTTTTTCC
1 TTTTTTCATTTTTTTTCCTTTTTTCC
*
1143314 TTTTTTCCTTTTTTTTCCTTTTTT
1 TTTTTTCATTTTTTTTCCTTTTTT
1143338 TTCTTCTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (26 bp):
TTTTTTCATTTTTTTTCCTTTTTTCC
Found at i:1143328 original size:10 final size:10
Alignment explanation
Indices: 1143288--1143340 Score: 69
Period size: 10 Copynumber: 5.7 Consensus size: 10
1143278 TTTTGATTCA
*
1143288 TTTTTTCATT
1 TTTTTTCCTT
1143298 TTTTTTCC--
1 TTTTTTCCTT
1143306 TTTTTTCC--
1 TTTTTTCCTT
1143314 TTTTTTCCTT
1 TTTTTTCCTT
1143324 TTTTTTCCTT
1 TTTTTTCCTT
1143334 TTTTTTC
1 TTTTTTC
1143341 TTCTTCAAGT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
8 16 0.40
10 24 0.60
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTTTCCTT
Found at i:1143328 original size:18 final size:16
Alignment explanation
Indices: 1143298--1143337 Score: 62
Period size: 18 Copynumber: 2.4 Consensus size: 16
1143288 TTTTTTCATT
1143298 TTTTTTCCTTTTTTCC
1 TTTTTTCCTTTTTTCC
1143314 TTTTTTCCTTTTTTTTCC
1 TTTTTTCC--TTTTTTCC
1143332 TTTTTT
1 TTTTTT
1143338 TTCTTCTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 8 0.36
18 14 0.64
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTTTCCTTTTTTCC
Found at i:1148208 original size:21 final size:22
Alignment explanation
Indices: 1148173--1148217 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
1148163 TTCCAGATTG
1148173 CTAAGAGGGAACCGATTCCCCC
1 CTAAGAGGGAACCGATTCCCCC
*
1148195 CTAAG-GGGTACCGATTCCCCC
1 CTAAGAGGGAACCGATTCCCCC
1148216 CT
1 CT
1148218 GAATGGTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.22, C:0.38, G:0.22, T:0.18
Consensus pattern (22 bp):
CTAAGAGGGAACCGATTCCCCC
Found at i:1154036 original size:20 final size:20
Alignment explanation
Indices: 1154011--1154048 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1154001 TTTTGGTGCA
1154011 GAGGGAATCGATACCCCCAT
1 GAGGGAATCGATACCCCCAT
*
1154031 GAGGGAATCGATTCCCCC
1 GAGGGAATCGATACCCCC
1154049 TTTGAAGGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.32, G:0.26, T:0.16
Consensus pattern (20 bp):
GAGGGAATCGATACCCCCAT
Found at i:1158873 original size:27 final size:30
Alignment explanation
Indices: 1158816--1158878 Score: 87
Period size: 27 Copynumber: 2.2 Consensus size: 30
1158806 CTTTCCTTAA
*
1158816 TATTAAAAAATAAATAAATATTAAAACATT
1 TATTTAAAAATAAATAAATATTAAAACATT
*
1158846 TATTTAAAAAT-AAT-AAT-TTAAAATATT
1 TATTTAAAAATAAATAAATATTAAAACATT
1158873 TATTTA
1 TATTTA
1158879 TTTAAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
27 15 0.48
28 3 0.10
29 3 0.10
30 10 0.32
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (30 bp):
TATTTAAAAATAAATAAATATTAAAACATT
Found at i:1160765 original size:2 final size:2
Alignment explanation
Indices: 1160758--1160790 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1160748 TTTGGTCTGT
1160758 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1160791 TCTGTAGTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1162709 original size:24 final size:24
Alignment explanation
Indices: 1162681--1162741 Score: 122
Period size: 24 Copynumber: 2.5 Consensus size: 24
1162671 TATTCTTTCA
1162681 CTTCAATCGAGCTCGAATTTCAGG
1 CTTCAATCGAGCTCGAATTTCAGG
1162705 CTTCAATCGAGCTCGAATTTCAGG
1 CTTCAATCGAGCTCGAATTTCAGG
1162729 CTTCAATCGAGCT
1 CTTCAATCGAGCT
1162742 TCTAAATTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.30
Consensus pattern (24 bp):
CTTCAATCGAGCTCGAATTTCAGG
Found at i:1163009 original size:30 final size:30
Alignment explanation
Indices: 1162973--1163048 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 30
1162963 ACATAACCGA
* ** * *
1162973 CGGTTCACACTGGTTTTATCAGTTTTCAGC
1 CGGTTCACACCGGTTTTAGAAATTCTCAGC
1163003 CGGTTCACACCGGTTTTAGAAATTCTCAGC
1 CGGTTCACACCGGTTTTAGAAATTCTCAGC
*
1163033 CGGTTC-TACCGGTTTT
1 CGGTTCACACCGGTTTT
1163049 CAACCGGTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 9 0.22
30 31 0.77
ACGTcount: A:0.17, C:0.25, G:0.21, T:0.37
Consensus pattern (30 bp):
CGGTTCACACCGGTTTTAGAAATTCTCAGC
Found at i:1168768 original size:19 final size:17
Alignment explanation
Indices: 1168726--1168769 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
1168716 TCATGAATGA
*
1168726 GATTATATGGTTGTTAT
1 GATTATATGGTTATTAT
*
1168743 TATTATATGTGTTATATAT
1 GATTATATG-GTTAT-TAT
1168762 GATTATAT
1 GATTATAT
1168770 ATTTTACATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 8 0.36
18 4 0.18
19 10 0.45
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (17 bp):
GATTATATGGTTATTAT
Found at i:1174013 original size:23 final size:23
Alignment explanation
Indices: 1173987--1174054 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 23
1173977 CATATTATAT
*
1173987 GGCACTTTGGTACATTTCTACGC
1 GGCACTTTGGTGCATTTCTACGC
* * **
1174010 GGCACTATGGTGCAATTCTACAT
1 GGCACTTTGGTGCATTTCTACGC
* *
1174033 GGCACTTTAGTGCATTTATACG
1 GGCACTTTGGTGCATTTCTACG
1174055 AGCTGTGGTG
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.34
Consensus pattern (23 bp):
GGCACTTTGGTGCATTTCTACGC
Found at i:1174203 original size:23 final size:23
Alignment explanation
Indices: 1174177--1174220 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
1174167 CCTGCTTTGC
1174177 TATGTGAAATGTAATATATGTTA
1 TATGTGAAATGTAATATATGTTA
1174200 TATGTGAAATGTAATATATGT
1 TATGTGAAATGTAATATATGT
1174221 CAAATATAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.43
Consensus pattern (23 bp):
TATGTGAAATGTAATATATGTTA
Found at i:1176836 original size:75 final size:76
Alignment explanation
Indices: 1176750--1176921 Score: 242
Period size: 75 Copynumber: 2.3 Consensus size: 76
1176740 TTATGAGATG
* * * * *
1176750 GGGGGTATCGGTAACTC-CTGGGGGGTATCGGTACCCTCTGAGCAATCTGTTATTTCTCAGAGCT
1 GGGGGTATCGGTAACCCTCTGGGGGGTATCAGTACCCTCCGAGCAATCTATTATTTCTCAGAGCC
* *
1176814 AGATCTTATAT
66 AAATCTTACAT
* *
1176825 GGGGGTATCGGT-ACCCTCTTGGGGGTATCAGTACCCTCCGAGCAATCTATTATTTCTCGGAGCC
1 GGGGGTATCGGTAACCCTCTGGGGGGTATCAGTACCCTCCGAGCAATCTATTATTTCTCAGAGCC
1176889 AAATCTTACAT
66 AAATCTTACAT
1176900 GGGGGTATCGGT-ACCCTCTGGG
1 GGGGGTATCGGTAACCCTCTGGG
1176922 CAATCTGGTT
Statistics
Matches: 86, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
74 3 0.03
75 83 0.97
ACGTcount: A:0.19, C:0.23, G:0.28, T:0.30
Consensus pattern (76 bp):
GGGGGTATCGGTAACCCTCTGGGGGGTATCAGTACCCTCCGAGCAATCTATTATTTCTCAGAGCC
AAATCTTACAT
Found at i:1176849 original size:20 final size:20
Alignment explanation
Indices: 1176824--1176862 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1176814 AGATCTTATA
*
1176824 TGGGGGTATCGGTACCCTCT
1 TGGGGGTATCAGTACCCTCT
1176844 TGGGGGTATCAGTACCCTC
1 TGGGGGTATCAGTACCCTC
1176863 CGAGCAATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.26, G:0.33, T:0.28
Consensus pattern (20 bp):
TGGGGGTATCAGTACCCTCT
Found at i:1177597 original size:14 final size:15
Alignment explanation
Indices: 1177565--1177597 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1177555 TTAACAATTC
1177565 AAAGTTCTAAATCCG
1 AAAGTTCTAAATCCG
1177580 -AAGTTCTAAAT-CG
1 AAAGTTCTAAATCCG
1177593 AAAGT
1 AAAGT
1177598 AGGCAAGGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 2 0.12
14 15 0.88
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.27
Consensus pattern (15 bp):
AAAGTTCTAAATCCG
Found at i:1180190 original size:14 final size:15
Alignment explanation
Indices: 1180171--1180204 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
1180161 CAACAACTAA
1180171 CCGCTGAAATGT-TT
1 CCGCTGAAATGTATT
1180185 CCGCTGAAATGTATT
1 CCGCTGAAATGTATT
1180200 CCGCT
1 CCGCT
1180205 TCAGTGGTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (15 bp):
CCGCTGAAATGTATT
Found at i:1183457 original size:22 final size:21
Alignment explanation
Indices: 1183415--1183454 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1183405 AAGACTATTT
1183415 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
1183436 TCATTTTT-ATATTTTGAAA
1 TCATTTTTCA-ATTTTGAAA
1183455 ATAAAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:1185395 original size:21 final size:21
Alignment explanation
Indices: 1185369--1185432 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
1185359 ATTATGAGAT
*
1185369 GGGGGTATTGGTACCTTCTGG
1 GGGGGTATTGGTACCTCCTGG
*
1185390 GGGGGTTTTGGTACCTCCT-G
1 GGGGGTATTGGTACCTCCTGG
1185410 GGGGGTATTGGTACCTCCTGG
1 GGGGGTATTGGTACCTCCTGG
1185431 GG
1 GG
1185433 CTTATCGGTA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
20 19 0.49
21 20 0.51
ACGTcount: A:0.08, C:0.17, G:0.44, T:0.31
Consensus pattern (21 bp):
GGGGGTATTGGTACCTCCTGG
Found at i:1185412 original size:20 final size:20
Alignment explanation
Indices: 1185369--1185432 Score: 101
Period size: 20 Copynumber: 3.1 Consensus size: 20
1185359 ATTATGAGAT
*
1185369 GGGGGTATTGGTACCTTCTGG
1 GGGGGTATTGGTACCTCCT-G
*
1185390 GGGGGTTTTGGTACCTCCTG
1 GGGGGTATTGGTACCTCCTG
1185410 GGGGGTATTGGTACCTCCTG
1 GGGGGTATTGGTACCTCCTG
1185430 GGG
1 GGG
1185433 CTTATCGGTA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
20 23 0.57
21 17 0.43
ACGTcount: A:0.08, C:0.17, G:0.44, T:0.31
Consensus pattern (20 bp):
GGGGGTATTGGTACCTCCTG
Found at i:1185442 original size:20 final size:20
Alignment explanation
Indices: 1185368--1185444 Score: 66
Period size: 20 Copynumber: 3.9 Consensus size: 20
1185358 CATTATGAGA
* *
1185368 TGGGG-GTATTGGTACCTTC
1 TGGGGCGTATCGGTACCTCC
* * *
1185387 TGGGGGGGTTTTGGTACCTCC
1 T-GGGGCGTATCGGTACCTCC
* *
1185408 TGGGGGGTATTGGTACCTCC
1 TGGGGCGTATCGGTACCTCC
*
1185428 TGGGGCTTATCGGTACC
1 TGGGGCGTATCGGTACC
1185445 CTCCGAGCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
19 1 0.02
20 36 0.72
21 13 0.26
ACGTcount: A:0.09, C:0.19, G:0.39, T:0.32
Consensus pattern (20 bp):
TGGGGCGTATCGGTACCTCC
Found at i:1185601 original size:19 final size:20
Alignment explanation
Indices: 1185561--1185602 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
1185551 AATCTTACAT
1185561 GGGGTATCAGTACCCTCTTG
1 GGGGTATCAGTACCCTCTTG
1185581 GGGGTATCAGTACCCTC-TG
1 GGGGTATCAGTACCCTCTTG
1185600 GGG
1 GGG
1185603 AATCTGGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.14, C:0.24, G:0.36, T:0.26
Consensus pattern (20 bp):
GGGGTATCAGTACCCTCTTG
Found at i:1187225 original size:13 final size:13
Alignment explanation
Indices: 1187207--1187255 Score: 50
Period size: 12 Copynumber: 3.9 Consensus size: 13
1187197 CTTAGCATGT
1187207 TTAAAAATAAAAC
1 TTAAAAATAAAAC
1187220 TT-AAAATAAAA-
1 TTAAAAATAAAAC
*
1187231 -TGAAAATGAAAAC
1 TTAAAAAT-AAAAC
*
1187244 TTAAAAAGAAAA
1 TTAAAAATAAAA
1187256 GAAAAAAGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
10 1 0.03
11 5 0.17
12 13 0.43
13 6 0.20
14 5 0.17
ACGTcount: A:0.69, C:0.04, G:0.06, T:0.20
Consensus pattern (13 bp):
TTAAAAATAAAAC
Found at i:1187227 original size:12 final size:12
Alignment explanation
Indices: 1187210--1187249 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
1187200 AGCATGTTTA
1187210 AAAATAAAACTT
1 AAAATAAAACTT
*
1187222 AAAATAAAA-TG
1 AAAATAAAACTT
1187233 AAAATGAAAACTT
1 AAAAT-AAAACTT
1187246 AAAA
1 AAAA
1187250 AGAAAAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 6 0.25
12 13 0.54
13 5 0.21
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.20
Consensus pattern (12 bp):
AAAATAAAACTT
Found at i:1187259 original size:24 final size:23
Alignment explanation
Indices: 1187210--1187260 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
1187200 AGCATGTTTA
*
1187210 AAAATAAAACTTAAAATAAAATG
1 AAAATAAAACTTAAAATAAAAAG
1187233 AAAATGAAAACTTAAAA-AGAAAAG
1 AAAAT-AAAACTTAAAATA-AAAAG
1187257 AAAA
1 AAAA
1187261 AAGAGAACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.73, C:0.04, G:0.08, T:0.16
Consensus pattern (23 bp):
AAAATAAAACTTAAAATAAAAAG
Found at i:1191077 original size:17 final size:17
Alignment explanation
Indices: 1191064--1191098 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1191054 GAGAGGCATT
1191064 ACATTAGTAGAGGCACC
1 ACATTAGTAGAGGCACC
1191081 ACATTAGTAGAGGCACC
1 ACATTAGTAGAGGCACC
1191098 A
1 A
1191099 AGATCACACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (17 bp):
ACATTAGTAGAGGCACC
Found at i:1193511 original size:22 final size:22
Alignment explanation
Indices: 1193486--1193530 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1193476 GTTTCAATAA
1193486 CTACTAATTTTGATCTCAATTC
1 CTACTAATTTTGATCTCAATTC
1193508 CTACTAATTTTGATCTCAATTC
1 CTACTAATTTTGATCTCAATTC
1193530 C
1 C
1193531 CTCTTGGCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.24, G:0.04, T:0.44
Consensus pattern (22 bp):
CTACTAATTTTGATCTCAATTC
Found at i:1193832 original size:13 final size:13
Alignment explanation
Indices: 1193814--1193863 Score: 59
Period size: 12 Copynumber: 3.9 Consensus size: 13
1193804 CTTAGAATGT
1193814 TTAAAAATAAAAC
1 TTAAAAATAAAAC
1193827 TT-AAAATAAAA-
1 TTAAAAATAAAAC
*
1193838 ATAAAAATGAAAAC
1 TTAAAAAT-AAAAC
*
1193852 TTAAAAAGAAAA
1 TTAAAAATAAAA
1193864 GAGAGAACTT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
11 1 0.03
12 14 0.45
13 10 0.32
14 6 0.19
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.20
Consensus pattern (13 bp):
TTAAAAATAAAAC
Found at i:1193850 original size:18 final size:18
Alignment explanation
Indices: 1193815--1193850 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1193805 TTAGAATGTT
* *
1193815 TAAAAATAAAACTTAAAA
1 TAAAAATAAAAATGAAAA
1193833 TAAAAATAAAAATGAAAA
1 TAAAAATAAAAATGAAAA
1193851 CTTAAAAAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (18 bp):
TAAAAATAAAAATGAAAA
Found at i:1194776 original size:12 final size:12
Alignment explanation
Indices: 1194759--1194786 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1194749 GAGGAATTTC
1194759 AAAAAAAAATGA
1 AAAAAAAAATGA
1194771 AAAAAAAAATGA
1 AAAAAAAAATGA
1194783 AAAA
1 AAAA
1194787 CGAAAAAAAG
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:0.86, C:0.00, G:0.07, T:0.07
Consensus pattern (12 bp):
AAAAAAAAATGA
Found at i:1195642 original size:20 final size:20
Alignment explanation
Indices: 1195617--1195678 Score: 94
Period size: 19 Copynumber: 3.2 Consensus size: 20
1195607 AAAGTTATAT
1195617 TTTTCTTTCATCTTTTTTAC
1 TTTTCTTTCATCTTTTTTAC
1195637 TTTTCTTTCATC-TTTTTAC
1 TTTTCTTTCATCTTTTTTAC
*
1195656 TTTTCTTTCAT-TATTTT-C
1 TTTTCTTTCATCTTTTTTAC
1195674 TTTTC
1 TTTTC
1195679 GCAATGATAA
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
18 6 0.15
19 22 0.55
20 12 0.30
ACGTcount: A:0.10, C:0.19, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTCTTTCATCTTTTTTAC
Found at i:1195802 original size:18 final size:18
Alignment explanation
Indices: 1195779--1195813 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1195769 AACGCGCTTC
1195779 ACATCTTCAAAGTTCTTA
1 ACATCTTCAAAGTTCTTA
*
1195797 ACATCTTTAAAGTTCTT
1 ACATCTTCAAAGTTCTT
1195814 TCTTGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.20, G:0.06, T:0.43
Consensus pattern (18 bp):
ACATCTTCAAAGTTCTTA
Found at i:1198793 original size:23 final size:23
Alignment explanation
Indices: 1198767--1198833 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
1198757 ACCATGTCCG
* *
1198767 GTTCATTTAATATTCACGAACAT
1 GTTCATTTAACATTCACAAACAT
*
1198790 GTTCGTTTAACATTCACAAACAT
1 GTTCATTTAACATTCACAAACAT
* * *
1198813 ATTCATTTAACGTTAACAAAC
1 GTTCATTTAACATTCACAAAC
1198834 TTCTTTACTT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.36
Consensus pattern (23 bp):
GTTCATTTAACATTCACAAACAT
Found at i:1199226 original size:87 final size:87
Alignment explanation
Indices: 1199080--1199240 Score: 268
Period size: 87 Copynumber: 1.9 Consensus size: 87
1199070 ATAAACTATA
* * *
1199080 TTATCATGTGTTCAATTTAATCCATACATTTATCAATATTTAAAATGTAAAAAGATAAAAGGAAA
1 TTATCATGTGTTCAATTTAATCCATACATTCACCAATAGTTAAAATGTAAAAAGATAAAAGGAAA
1199145 AAGAGAATTTGAACTCCAAAAT
66 AAGAGAATTTGAACTCCAAAAT
* * *
1199167 TTATCATGTGTTCAATTTAGTCCTTATATTCACCAATAGTTAAAATGTAAAAAGATAAAAGGAAA
1 TTATCATGTGTTCAATTTAATCCATACATTCACCAATAGTTAAAATGTAAAAAGATAAAAGGAAA
1199232 AAGAGAATT
66 AAGAGAATT
1199241 GGGTAAACAA
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 68 1.00
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.32
Consensus pattern (87 bp):
TTATCATGTGTTCAATTTAATCCATACATTCACCAATAGTTAAAATGTAAAAAGATAAAAGGAAA
AAGAGAATTTGAACTCCAAAAT
Found at i:1202816 original size:45 final size:45
Alignment explanation
Indices: 1202763--1202883 Score: 134
Period size: 45 Copynumber: 2.7 Consensus size: 45
1202753 ATGTCTCATC
* *
1202763 ACCATGACCATGAGGACGATCACCACCACCACCATCATGACCATG
1 ACCATGACCATGAGGAAGATCACCACCACCACCACCATGACCATG
* ** * * * *
1202808 ACCATGACCATAAGGAAGAGGACGATCATCATCACCATGACCATG
1 ACCATGACCATGAGGAAGATCACCACCACCACCACCATGACCATG
* * *
1202853 ACCTTGACCACGAGGAAGATCATCACCACCA
1 ACCATGACCATGAGGAAGATCACCACCACCA
1202884 TAAAGAGGGA
Statistics
Matches: 58, Mismatches: 18, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
45 58 1.00
ACGTcount: A:0.36, C:0.33, G:0.17, T:0.14
Consensus pattern (45 bp):
ACCATGACCATGAGGAAGATCACCACCACCACCACCATGACCATG
Found at i:1202868 original size:39 final size:39
Alignment explanation
Indices: 1202795--1202884 Score: 108
Period size: 39 Copynumber: 2.3 Consensus size: 39
1202785 CCACCACCAC
* ** *
1202795 CATCATGACCATGACCATGACCATAAGGAAGAGGACGAT
1 CATCATCACCATGACCATGACCATAACCAAGAGGAAGAT
* * *
1202834 CATCATCACCATGACCATGACCTTGACCACGAGGAAGAT
1 CATCATCACCATGACCATGACCATAACCAAGAGGAAGAT
*
1202873 CATCACCACCAT
1 CATCATCACCAT
1202885 AAAGAGGGAC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.36, C:0.30, G:0.18, T:0.17
Consensus pattern (39 bp):
CATCATCACCATGACCATGACCATAACCAAGAGGAAGAT
Found at i:1212530 original size:19 final size:19
Alignment explanation
Indices: 1212471--1212517 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
1212461 TAGGGGAATG
***
1212471 AAAAATATATTTTTAATA-
1 AAAAATATATTAAAAATAT
1212489 AAAAATATATTAAAAATAT
1 AAAAATATATTAAAAATAT
1212508 AAAAATATAT
1 AAAAATATAT
1212518 AATAATTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 15 0.60
19 10 0.40
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAAATATATTAAAAATAT
Found at i:1219723 original size:14 final size:14
Alignment explanation
Indices: 1219704--1219742 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
1219694 AATTTTAAAA
1219704 TAAAAATATATTT-T
1 TAAAAATA-ATTTAT
1219718 TAAAAATAATTTAT
1 TAAAAATAATTTAT
1219732 TATAAAATAAT
1 TA-AAAATAAT
1219743 ATAAGATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.17
14 11 0.48
15 8 0.35
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TAAAAATAATTTAT
Found at i:1221407 original size:66 final size:63
Alignment explanation
Indices: 1221266--1221476 Score: 198
Period size: 66 Copynumber: 3.3 Consensus size: 63
1221256 TTTTTCAGAG
* * * *
1221266 TGATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGA-ATTAAATTG-AACATTGAATGC
1 TGATGCATCGATGCA-CAGT-CATGCATCGATGCACTCAGGATATT---TTGAAACATCGAATGC
1221328 ATT
61 ATT
* *
1221331 TCATGCATCGATGCACA-TACCATGCATCGATGCACTGAGGAT-TTTATGAAAAACATCGAATGC
1 TGATGCATCGATGCACAGT--CATGCATCGATGCACTCAGGATATTT-TG--AAACATCGAATGC
1221394 ATT
61 ATT
* * * *
1221397 TGATGTATCGATGCACCAGTCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCA-CAGTCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
1221461 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
1221477 TCTTAGTGCA
Statistics
Matches: 124, Mismatches: 12, Indels: 22
0.78 0.08 0.14
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 47 0.38
65 18 0.15
66 48 0.39
67 5 0.04
68 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (63 bp):
TGATGCATCGATGCACAGTCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
Found at i:1221476 original size:17 final size:19
Alignment explanation
Indices: 1221448--1221496 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1221438 TATTTTGAAA
1221448 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
1221466 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
1221485 CACCGATGCACT
1 CATCGATGCACT
1221497 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:1228947 original size:21 final size:21
Alignment explanation
Indices: 1228905--1228948 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1228895 ACCCCGGGAG
*
1228905 CTAGCTCTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCTCCTC
* *
1228926 CTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
1228947 CT
1 CT
1228949 CCTCCTCCGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.41, G:0.16, T:0.34
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Found at i:1229545 original size:13 final size:13
Alignment explanation
Indices: 1229527--1229551 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1229517 ACCATGTCAC
1229527 ATTGATTATGAAT
1 ATTGATTATGAAT
1229540 ATTGATTATGAA
1 ATTGATTATGAA
1229552 ACCAATGGCT
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:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (13 bp):
ATTGATTATGAAT
Found at i:1229732 original size:28 final size:28
Alignment explanation
Indices: 1229701--1229764 Score: 119
Period size: 28 Copynumber: 2.3 Consensus size: 28
1229691 GAAGTGTGTT
*
1229701 AAGTGTTAAAATGTTTTTAAAAGGGGAG
1 AAGTGTTAAAATGTTTTTAAAAGAGGAG
1229729 AAGTGTTAAAATGTTTTTAAAAGAGGAG
1 AAGTGTTAAAATGTTTTTAAAAGAGGAG
1229757 AAGTGTTA
1 AAGTGTTA
1229765 TAGTAAGGGG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.41, C:0.00, G:0.27, T:0.33
Consensus pattern (28 bp):
AAGTGTTAAAATGTTTTTAAAAGAGGAG
Found at i:1230180 original size:19 final size:19
Alignment explanation
Indices: 1230156--1230208 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
1230146 GAATGTTTTT
1230156 CATGCATCGATGCACATAC
1 CATGCATCGATGCACATAC
*
1230175 CATGCATCGATGCACATGC
1 CATGCATCGATGCACATAC
*
1230194 CATTCATCGATGCAC
1 CATGCATCGATGCAC
1230209 TGAGGATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.23
Consensus pattern (19 bp):
CATGCATCGATGCACATAC
Found at i:1230339 original size:17 final size:19
Alignment explanation
Indices: 1230311--1230359 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1230301 TATTTTGAAA
1230311 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
1230329 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
1230348 CACCGATGCACT
1 CATCGATGCACT
1230360 AAGGGTCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:1231435 original size:42 final size:42
Alignment explanation
Indices: 1231372--1231466 Score: 163
Period size: 42 Copynumber: 2.3 Consensus size: 42
1231362 TTCCCCGAAA
*
1231372 TCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTT
1 TCCCGTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATGTTT
*
1231414 TCCCGTGTTTGTTTCATGTAATTCGTTTTCCGAAAAATGTTT
1 TCCCGTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATGTTT
*
1231456 TCCAGTGTTTG
1 TCCCGTGTTTG
1231467 GTTGGAGGAA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.17, C:0.18, G:0.19, T:0.46
Consensus pattern (42 bp):
TCCCGTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATGTTT
Found at i:1231708 original size:21 final size:23
Alignment explanation
Indices: 1231682--1231731 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 23
1231672 TAATTATTAA
1231682 AATATTTAAAAT-ATATT-TATT
1 AATATTTAAAATAATATTATATT
*
1231703 AATATTTATAATAATATTATATT
1 AATATTTAAAATAATATTATATT
1231726 -ATATTT
1 AATATTT
1231732 TAATATTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 11 0.42
22 11 0.42
23 4 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
AATATTTAAAATAATATTATATT
Found at i:1231717 original size:12 final size:12
Alignment explanation
Indices: 1231682--1231736 Score: 50
Period size: 11 Copynumber: 5.1 Consensus size: 12
1231672 TAATTATTAA
*
1231682 AATATTTAAAAT
1 AATATTTATAAT
1231694 -ATATTTAT--T
1 AATATTTATAAT
1231703 AATATTTATAAT
1 AATATTTATAAT
1231715 AATA-TTAT-AT
1 AATATTTATAAT
*
1231725 TATATTT-TAAT
1 AATATTTATAAT
1231736 A
1 A
1231737 TTATAATAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 11
0.71 0.06 0.22
Matches are distributed among these distances:
9 1 0.03
10 14 0.40
11 15 0.43
12 5 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
AATATTTATAAT
Found at i:1231727 original size:26 final size:25
Alignment explanation
Indices: 1231665--1231727 Score: 71
Period size: 23 Copynumber: 2.6 Consensus size: 25
1231655 ATTTTAATCA
1231665 AAAATATTA-ATTATTAAAATATTT
1 AAAATATTATATTATTAAAATATTT
*
1231689 AAAATA-TAT-TTATTAATAT-TTAT
1 AAAATATTATATTATTAAAATATT-T
1231712 AATAATATTATATTAT
1 AA-AATATTATATTAT
1231728 ATTTTAATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 14 0.42
24 10 0.30
25 3 0.09
26 4 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
AAAATATTATATTATTAAAATATTT
Found at i:1231834 original size:54 final size:55
Alignment explanation
Indices: 1231776--1231892 Score: 127
Period size: 54 Copynumber: 2.2 Consensus size: 55
1231766 TAATATAAGA
*** * *
1231776 TATTATATTTTCATTTTAATAATATATAATAAATTATTAA-AA-ATTTATATTATT
1 TATTATATTTTCATAGAAATAATAT-TAATAAATTATTAATAAGAATAATATTATT
*
1231830 TATTA-A-TTTCATAGAAATAATATTATTAAATTATTAATAATGAATAATATTATT
1 TATTATATTTTCATAGAAATAATATTAATAAATTATTAATAA-GAATAATATTATT
1231884 TA-TATATTT
1 TATTATATTT
1231893 AATATTAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
51 13 0.25
52 16 0.31
53 3 0.06
54 18 0.35
55 2 0.04
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (55 bp):
TATTATATTTTCATAGAAATAATATTAATAAATTATTAATAAGAATAATATTATT
Found at i:1231883 original size:19 final size:18
Alignment explanation
Indices: 1231859--1231927 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 18
1231849 ATATTATTAA
1231859 ATTATTAATAATGAATAAT
1 ATTATTAATAAT-AATAAT
* *
1231878 ATTATTTAT-ATATTTAAT
1 ATTATTAATAATA-ATAAT
1231896 ATTAATATAATAATCTAATAAT
1 ATT-AT-TAATAA--TAATAAT
1231918 ATT-TTAATAA
1 ATTATTAATAA
1231928 AGATATTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
17 1 0.03
18 9 0.22
19 16 0.40
20 4 0.10
21 1 0.03
22 7 0.17
23 2 0.05
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (18 bp):
ATTATTAATAATAATAAT
Found at i:1231902 original size:27 final size:27
Alignment explanation
Indices: 1231822--1231907 Score: 70
Period size: 27 Copynumber: 3.1 Consensus size: 27
1231812 TTAAAAATTT
* *
1231822 ATATTATTTAT-TAATTTCATAGAAATA
1 ATATTATTTATAT-ATTTAATATAAATA
* *
1231849 ATATTA-TTAAAT-TATTAATAATGAATA
1 ATATTATTTATATAT-TTAAT-ATAAATA
1231876 ATATTATTTATATATTTAATATTAATATA
1 ATATTATTTATATATTTAATA-TAA-ATA
1231905 ATA
1 ATA
1231908 ATCTAATAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
25 1 0.02
26 7 0.15
27 19 0.41
28 12 0.26
29 7 0.15
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (27 bp):
ATATTATTTATATATTTAATATAAATA
Found at i:1232075 original size:26 final size:27
Alignment explanation
Indices: 1232046--1232096 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
1232036 ATTATAAAAA
*
1232046 TAATA-TTTAATAATAAATAA-ATTATT
1 TAATATTTTAAAAAT-AATAATATTATT
1232072 TAATATTTTAAAAATAATAATATTA
1 TAATATTTTAAAAATAATAATATTA
1232097 AGTTTTATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
TAATATTTTAAAAATAATAATATTATT
Found at i:1232568 original size:81 final size:81
Alignment explanation
Indices: 1232428--1232941 Score: 644
Period size: 81 Copynumber: 6.4 Consensus size: 81
1232418 ATGATTATGC
* * * * *
1232428 CAAAGGCACAATTAGACCATTAATCTTTCACTCAAAGGTATTTAACCTTTCATCTAACTGTCATA
1 CAAATGCACAACTAGGCCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATA
* * *
1232493 ATTGACATATTTATAT
66 ATTGACACATTTCTGT
*
1232509 CAAATGCACAACTAGGCGATTAATCTTTTACTCAAAGGTA-TTAACCTTTTCATCTAACTGGCAT
1 CAAATGCACAACTAGGCCATTAATCTTTTACTCAAAGGTATTTAACC-TTTCATCTAACTGGCAT
* *
1232573 AATTGACACCTTTCTTT
65 AATTGACACATTTCTGT
** * *
1232590 CAAATGCACAGGTAGACCATTAATCTTTTACTCAAAGGTATTTAACCTTCCATCTAACTGGCATA
1 CAAATGCACAACTAGGCCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATA
1232655 ATTGACACATTTCTGT
66 ATTGACACATTTCTGT
** * ** * **
1232671 CAAATGCACAGTTAGGTCATTAATCTTTTACTCAAAGAAATTTAACATTTCATCTAACTACCATA
1 CAAATGCACAACTAGGCCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATA
*
1232736 ATTGGCACATTTCTGT
66 ATTGACACATTTCTGT
* * **
1232752 CAAATGCACAACTAGGCCATTAATC-ATTA---AAAGGTATTTAACCTTTCATTTAACTAACATA
1 CAAATGCACAACTAGGCCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATA
* * * *
1232813 ATTTACACCTTTATAT
66 ATTGACACATTTCTGT
*
1232829 CAAATGCACAACTAGGCCATTAATCTTTTACTCAAAGGTATTTAACC-TTCAATCTAAATGGCAT
1 CAAATGCACAACTAGGCCATTAATCTTTTACTCAAAGGTATTTAACCTTTC-ATCTAACTGGCAT
*
1232893 AATTGACTCATTTCTGT
65 AATTGACACATTTCTGT
* *
1232910 CAAATGCACATCTAGGTCATTAATCTTTTACT
1 CAAATGCACAACTAGGCCATTAATCTTTTACT
1232942 TTAAATCATA
Statistics
Matches: 373, Mismatches: 53, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
77 63 0.17
78 3 0.01
80 12 0.03
81 289 0.77
82 6 0.02
ACGTcount: A:0.34, C:0.21, G:0.10, T:0.35
Consensus pattern (81 bp):
CAAATGCACAACTAGGCCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATA
ATTGACACATTTCTGT
Found at i:1232893 original size:239 final size:241
Alignment explanation
Indices: 1232445--1232941 Score: 714
Period size: 239 Copynumber: 2.1 Consensus size: 241
1232435 ACAATTAGAC
* ** * ** *
1232445 CATTAATCTTTCACTCAAAGGTATTTAACCTTTCATCTAACTGTCATAATTGACATATTTATATC
1 CATTAATCTTTTACTCAAAGAAATTTAACATTTCATCTAACTACCATAATTGACACATTTATATC
* * **
1232510 AAATGCACAACTAGGCGATTAATCTTTTACTCAAAGGTATTAACCTTTTCATCTAACTGGCATAA
66 AAATGCACAACTAGGCCATTAATCTATTA--CAAAGGTATTAACCTTTTCATCTAACTAACATAA
* * **
1232575 TTGACACCTTTCTTTCAAATGCACAGGTAGACCATTAATCTTTTACTCAAAGGTATTTAACCTTC
129 TTGACACCTTTATATCAAATGCACAACTAGACCATTAATCTTTTACTCAAAGGTATTTAACCTTC
* *
1232640 CATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGT-TAGGT
194 AATCTAAATGGCATAATTGACACATTTCTGTCAAATGCACA-TCTAGGT
* * *
1232688 CATTAATCTTTTACTCAAAGAAATTTAACATTTCATCTAACTACCATAATTGGCACATTTCTGTC
1 CATTAATCTTTTACTCAAAGAAATTTAACATTTCATCTAACTACCATAATTGACACATTTATATC
*
1232753 AAATGCACAACTAGGCCATTAATC-ATTA-AAAGGTATTTAACC-TTTCATTTAACTAACATAAT
66 AAATGCACAACTAGGCCATTAATCTATTACAAAGGTA-TTAACCTTTTCATCTAACTAACATAAT
* *
1232815 TTACACCTTTATATCAAATGCACAACTAGGCCATTAATCTTTTACTCAAAGGTATTTAACCTTCA
130 TGACACCTTTATATCAAATGCACAACTAGACCATTAATCTTTTACTCAAAGGTATTTAACCTTCA
*
1232880 ATCTAAATGGCATAATTGACTCATTTCTGTCAAATGCACATCTAGGT
195 ATCTAAATGGCATAATTGACACATTTCTGTCAAATGCACATCTAGGT
1232927 CATTAATCTTTTACT
1 CATTAATCTTTTACT
1232942 TTAAATCATA
Statistics
Matches: 228, Mismatches: 24, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
238 1 0.00
239 140 0.61
240 6 0.03
242 3 0.01
243 78 0.34
ACGTcount: A:0.34, C:0.21, G:0.10, T:0.36
Consensus pattern (241 bp):
CATTAATCTTTTACTCAAAGAAATTTAACATTTCATCTAACTACCATAATTGACACATTTATATC
AAATGCACAACTAGGCCATTAATCTATTACAAAGGTATTAACCTTTTCATCTAACTAACATAATT
GACACCTTTATATCAAATGCACAACTAGACCATTAATCTTTTACTCAAAGGTATTTAACCTTCAA
TCTAAATGGCATAATTGACACATTTCTGTCAAATGCACATCTAGGT
Found at i:1233489 original size:34 final size:32
Alignment explanation
Indices: 1233436--1233505 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
1233426 ACCTTACAAC
*
1233436 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
1233468 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
1233502 TCCC
1 TCCC
1233506 CTTTATAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:1233816 original size:21 final size:21
Alignment explanation
Indices: 1233790--1233831 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1233780 CCAGAATGGG
*
1233790 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1233811 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1233832 ATATTCAAAT
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:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:1234062 original size:29 final size:31
Alignment explanation
Indices: 1234030--1234089 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
1234020 AAATTTTGAA
*
1234030 TAAATTCAA-TTAAGTCCAAATA-CATTTTG
1 TAAATTCAATTTAAGTCCAAAAACCATTTTG
1234059 TAAATTCAATTTAAGTCCAAAAACCATTTTG
1 TAAATTCAATTTAAGTCCAAAAACCATTTTG
1234090 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 9 0.32
30 12 0.43
31 7 0.25
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.37
Consensus pattern (31 bp):
TAAATTCAATTTAAGTCCAAAAACCATTTTG
Found at i:1240482 original size:33 final size:33
Alignment explanation
Indices: 1240407--1240537 Score: 111
Period size: 37 Copynumber: 3.7 Consensus size: 33
1240397 TTTAACTTTC
* *
1240407 ACACATGCATAATATCTATCTATAATATATACATGTAC
1 ACACATGCAGAATATCTATC--T-ATATATACA-G-AT
*
1240445 ACACATGCAAAATATCTATCTATATATACAGAT
1 ACACATGCAGAATATCTATCTATATATACAGAT
* *
1240478 ACACATATATGCAGAATATCTATCTATTTAT-CTATAT
1 ACAC----ATGCAGAATATCTATCTATATATAC-AGAT
*
1240515 ACACATGTAGAATATCTATCTAT
1 ACACATGCAGAATATCTATCTAT
1240538 CAATATATAC
Statistics
Matches: 82, Mismatches: 6, Indels: 15
0.80 0.06 0.15
Matches are distributed among these distances:
33 23 0.28
34 1 0.01
35 9 0.11
36 2 0.02
37 28 0.34
38 19 0.23
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (33 bp):
ACACATGCAGAATATCTATCTATATATACAGAT
Found at i:1240490 original size:37 final size:38
Alignment explanation
Indices: 1240406--1240504 Score: 119
Period size: 37 Copynumber: 2.6 Consensus size: 38
1240396 ATTTAACTTT
* * **
1240406 CACACATGCATAATATCTATCTATAATATATACATGTA
1 CACACATGCAAAATATCTATCTATAATATACACATACA
*
1240444 CACACATGCAAAATATCTATCTAT-ATATACAGATACA
1 CACACATGCAAAATATCTATCTATAATATACACATACA
* * *
1240481 CATATATGCAGAATATCTATCTAT
1 CACACATGCAAAATATCTATCTAT
1240505 TTATCTATAT
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
37 30 0.57
38 23 0.43
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.32
Consensus pattern (38 bp):
CACACATGCAAAATATCTATCTATAATATACACATACA
Found at i:1240530 original size:29 final size:29
Alignment explanation
Indices: 1240498--1240554 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
1240488 GCAGAATATC
* *
1240498 TATCTATTTATCTATATACACATGTAGAA
1 TATCTATCTATCAATATACACATGTAGAA
*
1240527 TATCTATCTATCAATATATACATGTAGA
1 TATCTATCTATCAATATACACATGTAGA
1240555 CATACGTGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.40
Consensus pattern (29 bp):
TATCTATCTATCAATATACACATGTAGAA
Found at i:1240861 original size:166 final size:160
Alignment explanation
Indices: 1240572--1240876 Score: 463
Period size: 166 Copynumber: 1.9 Consensus size: 160
1240562 GCAAAATATT
* *
1240572 TATCAATACATATATTAGATAGTTATACTAATAAATTTTCTCTAATAAAGACTTGATAAAATAAT
1 TATCAATACAAATATTAGATAGTTATACTAATAAATTATCTCTAATAAAGACTTGATAAAATAAT
* *
1240637 AGTAGTAATAGTAGAGAAGTTTAGGATGAAAAAATTCGATTTGACTCGATATAATATTATAATCA
66 AGTAGTAATAGTAGAGAAGTTTAGGATGAAAAAATTCAATTTGACTCAATATAATATTATAATCA
1240702 T-TCCTTATAAGGGATAATTACAATAAAATC
131 TCT-CTTATAAGGGATAATTACAATAAAATC
*
1240732 TATCAATACAAATATTAGATAGTTCTACT-ATAAATTATCTCTAATAAAGA-TTGATAAAATAAT
1 TATCAATACAAATATTAGATAGTTATACTAATAAATTATCTCTAATAAAGACTTGATAAAATAAT
1240795 AGTAGTAATACTAACAGTAGAGAAGTTTAGGATGAAAAAAAATTCAATTTGACTCAATATAATAT
66 AGTAGT-A-A-T---AGTAGAGAAGTTTAGGATG--AAAAAATTCAATTTGACTCAATATAATAT
1240860 TATAATCATCTCTTATA
123 TATAATCATCTCTTATA
1240877 TATTAAGGGA
Statistics
Matches: 131, Mismatches: 5, Indels: 12
0.89 0.03 0.08
Matches are distributed among these distances:
158 19 0.15
159 21 0.16
160 28 0.21
161 1 0.01
164 19 0.15
166 42 0.32
167 1 0.01
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.35
Consensus pattern (160 bp):
TATCAATACAAATATTAGATAGTTATACTAATAAATTATCTCTAATAAAGACTTGATAAAATAAT
AGTAGTAATAGTAGAGAAGTTTAGGATGAAAAAATTCAATTTGACTCAATATAATATTATAATCA
TCTCTTATAAGGGATAATTACAATAAAATC
Found at i:1242772 original size:47 final size:47
Alignment explanation
Indices: 1242699--1242789 Score: 139
Period size: 47 Copynumber: 1.9 Consensus size: 47
1242689 ACAATAGAAG
* * *
1242699 AACCCAGAAAAACTGAAATTATATTCTCTTAATCTAACCCTCTTTAA
1 AACCCAGAAAAACTGAAATAACATTCTCTTAATCTAACACTCTTTAA
1242746 AACCCAG-AAAACTGAAATCAACATTCTCTTAATCTAACACTCTT
1 AACCCAGAAAAACTGAAAT-AACATTCTCTTAATCTAACACTCTT
1242790 CTGGGATACT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
46 11 0.28
47 29 0.73
ACGTcount: A:0.41, C:0.25, G:0.04, T:0.30
Consensus pattern (47 bp):
AACCCAGAAAAACTGAAATAACATTCTCTTAATCTAACACTCTTTAA
Found at i:1245749 original size:29 final size:29
Alignment explanation
Indices: 1245707--1245771 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
1245697 ATCGAACCAA
* *
1245707 AATTTATTTGAAAATTATTAACCGTACCG
1 AATTAATTTGAAAATTATTAACCGAACCG
*
1245736 AATTAATTTGAAAATTATTAACCGAATCG
1 AATTAATTTGAAAATTATTAACCGAACCG
1245765 AATTAAT
1 AATTAAT
1245772 CAGTTTTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (29 bp):
AATTAATTTGAAAATTATTAACCGAACCG
Found at i:1245840 original size:127 final size:125
Alignment explanation
Indices: 1245607--1246021 Score: 559
Period size: 127 Copynumber: 3.4 Consensus size: 125
1245597 ATCGAACCAA
* * *
1245607 AATTTATTTGAAAATTATTAACCGAACCGAATTAATCAAAATTTTTTAATTATTAATCAAAGCAA
1 AATTAATTTGAAAATTATTAACCGAA-CGAATTAATC--AGTTTTTTAATTATTAATCGAAGCAA
*
1245672 AAATTTGGTTAATTGGGTTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGTACCG
63 AAATTTGGTTAATT-GGTTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCG
1245736 AATTAATTTGAAAATTATTAACCGAATCGAATTAATCAGTTTTTTAATTATTAATCGAAGCAAAA
1 AATTAATTTGAAAATTATTAACCGAA-CGAATTAATCAGTTTTTTAATTATTAATCGAAGCAAAA
*
1245801 ATTTGGTTAATTCGGCTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCG
65 ATTTGGTTAATT-GGTTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCG
*
1245863 AATTAATTTGAAAATTATTAA-C---CG----AAT---TTTTTTAATTTTTAATCGGAA-C-AAA
1 AATTAATTTGAAAATTATTAACCGAACGAATTAATCAGTTTTTTAATTATTAATC-GAAGCAAAA
* * *
1245915 ATTCGGTTAATTGATTTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACTGAACCG
65 ATTTGGTTAATTG-GTTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCG
* *
1245977 AATTAATTTGAAAATTATTAACCGAACTGAATTAAACGGTTTTTT
1 AATTAATTTGAAAATTATTAACCGAAC-GAATTAATCAGTTTTTT
1246022 TAAACCATTA
Statistics
Matches: 259, Mismatches: 13, Indels: 31
0.85 0.04 0.10
Matches are distributed among these distances:
113 1 0.00
114 80 0.31
115 18 0.07
116 3 0.01
118 4 0.02
119 1 0.00
122 2 0.01
123 2 0.01
126 7 0.03
127 106 0.41
129 35 0.14
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37
Consensus pattern (125 bp):
AATTAATTTGAAAATTATTAACCGAACGAATTAATCAGTTTTTTAATTATTAATCGAAGCAAAAA
TTTGGTTAATTGGTTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCG
Found at i:1245857 original size:227 final size:233
Alignment explanation
Indices: 1245455--1246021 Score: 686
Period size: 241 Copynumber: 2.4 Consensus size: 233
1245445 AAAGAAAAAA
* * **
1245455 TTCGGTTAATTGAACCAAAATTTATCTGAAAATTATTAACCGAACTAAATTAATTTG-AAATTAT
1 TTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCGAATTAATTTGAAAATTAT
*** * * **
1245519 TAAATAAACTGAATTAACCGATTTTTAATTATTAATTGAATTAATCGAAGCAAAGGTTCAGTTAA
66 TAACCGAACTGAATTAAAC-A--GTT--TT-TTAATT-AATTAATCGAAGCAAAAATTCAGTTAA
1245584 TTCGGCTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCG-AA-TT-A-ATCA
124 TTCGGCTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCGAAATTTAATATCA
* *
1245645 A-AA-TTTTTTAATTATTAATC-AAAGCAAAAATTTGGTTAATTGGG
189 ACAATTTTTTTAATTATTAATCGAAA-C-AAAATTCGGTTAATTGAG
*
1245689 TTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGTACCGAATTAATTTGAAAATTAT
1 TTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCGAATTAATTTGAAAATTAT
* **
1245754 TAACCGAA-TCGAATTAATCAGTTTTTTAATT-ATTAATCGAAGCAAAAATTTGGTTAATTCGGC
66 TAACCGAACT-GAATTAAACAGTTTTTTAATTAATTAATCGAAGCAAAAATTCAGTTAATTCGGC
*
1245817 TCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCGAATTAATTTGAAAATTATT
130 TCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCG-A--AATTT---AA-TATC
* * *
1245882 AACCGAATTTTTTTAATTTTTAATCGGAACAAAATTCGGTTAATTGAT
188 AA-C-AATTTTTTTAATTATTAATCGAAACAAAATTCGGTTAATTGAG
*
1245930 TTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACTGAACCGAATTAATTTGAAAATTAT
1 TTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCGAATTAATTTGAAAATTAT
*
1245995 TAACCGAACTGAATTAAACGGTTTTTT
66 TAACCGAACTGAATTAAACAGTTTTTT
1246022 TAAACCATTA
Statistics
Matches: 290, Mismatches: 24, Indels: 31
0.84 0.07 0.09
Matches are distributed among these distances:
227 74 0.26
229 6 0.02
230 2 0.01
231 2 0.01
232 4 0.01
234 54 0.19
235 20 0.07
236 1 0.00
238 4 0.01
241 103 0.36
242 18 0.06
243 2 0.01
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.37
Consensus pattern (233 bp):
TTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCGAATTAATTTGAAAATTAT
TAACCGAACTGAATTAAACAGTTTTTTAATTAATTAATCGAAGCAAAAATTCAGTTAATTCGGCT
CGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCGAAATTTAATATCAACAATTT
TTTTAATTATTAATCGAAACAAAATTCGGTTAATTGAG
Found at i:1245985 original size:29 final size:29
Alignment explanation
Indices: 1245948--1246011 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
1245938 ATCGAACCAA
* *
1245948 AATTTATTTGAAAATTATTAACTGAACCG
1 AATTAATTTGAAAATTATTAACCGAACCG
*
1245977 AATTAATTTGAAAATTATTAACCGAACTG
1 AATTAATTTGAAAATTATTAACCGAACCG
1246006 AATTAA
1 AATTAA
1246012 ACGGTTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (29 bp):
AATTAATTTGAAAATTATTAACCGAACCG
Found at i:1246587 original size:30 final size:30
Alignment explanation
Indices: 1246553--1246615 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
1246543 AGAATATGTA
*
1246553 AATATTAAGGACCAAATGTATAATAATGCC
1 AATATTAAGGACCAAATATATAATAATGCC
* *
1246583 AATATTAAGGATCAAATATATAATTATGCC
1 AATATTAAGGACCAAATATATAATAATGCC
1246613 AAT
1 AAT
1246616 TTATTAACGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.48, C:0.11, G:0.11, T:0.30
Consensus pattern (30 bp):
AATATTAAGGACCAAATATATAATAATGCC
Found at i:1247177 original size:3 final size:3
Alignment explanation
Indices: 1247165--1247225 Score: 58
Period size: 3 Copynumber: 21.3 Consensus size: 3
1247155 GTCACTAAAA
* * *
1247165 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT -CT ATG A-T ATG A-T
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1247209 ATTT ATT ATT ATT ATT A
1 A-TT ATT ATT ATT ATT A
1247226 AAAAGAATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
2 5 0.11
3 40 0.85
4 2 0.04
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:1261732 original size:22 final size:23
Alignment explanation
Indices: 1261707--1261750 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1261697 CACCACAGCT
*
1261707 CGTATAAATGCA-CAAAGTGCCG
1 CGTAGAAATGCACCAAAGTGCCG
*
1261729 CGTAGAATTGCACCAAAGTGCC
1 CGTAGAAATGCACCAAAGTGCC
1261751 ATAAAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.34, C:0.25, G:0.23, T:0.18
Consensus pattern (23 bp):
CGTAGAAATGCACCAAAGTGCCG
Found at i:1270605 original size:210 final size:209
Alignment explanation
Indices: 1270361--1271018 Score: 938
Period size: 211 Copynumber: 3.1 Consensus size: 209
1270351 AATAAAAAAG
* * *
1270361 TACAAATAAAAAATTAAATAA--ACAACATACATTGATGAGGAATCAAATCGAAATAATTTTAAA
1 TACAAATAAAAATTTAAATAATTAAAACATACATTGATGAGGGATCAAATCGAAATAATTTTAAA
1270424 TTGTGAGGTTGAAATTAATACAAAAAATACTAAATTATA-TCCATTTAAAAAGTTCTGGGCCAAT
66 TTGTGAGGTTGAAATTAATACAAAAAATACTAAATTATACT-CATTTAAAAAGTTCTGGGCCAAT
* *
1270488 TAAAAAATAGAAATAAATAATAAGTATG-GATCAATTTCAGTTGCAAAAAAATTTGGAGGATTAA
130 TAAAAAATAGAAATAAATAATAAGTATGTG-TCAATTTCAGATGCAAAAAAATTTGGAGGACTAA
1270552 ATTGAATATATGAAAT
194 ATTGAATATATGAAAT
*
1270568 TACAAATAAAAATTTAAATAAATTAAAACATACATTGATGAGGGATCAAATTGAAATAATTTTAA
1 TACAAATAAAAATTTAAAT-AATTAAAACATACATTGATGAGGGATCAAATCGAAATAATTTTAA
*
1270633 ATTGTGAGGTTGAAATTAATACAAAAAAGTATTAAATTATACTCATTTAAAAAGTTAC-GGGCCA
65 ATTGTGAGGTTGAAATTAATACAAAAAA-TACTAAATTATACTCATTTAAAAAGTT-CTGGGCCA
* * *
1270697 ATTAAAAAATAGAAATAAGTAATAAGCATGTGTCAATTTCAGATGCAAATAAATTTGGAGGACTA
128 ATTAAAAAATAGAAATAAATAATAAGTATGTGTCAATTTCAGATGCAAAAAAATTTGGAGGACTA
1270762 AA-T-AATGAATATGAAAT
193 AATTGAAT--ATATGAAAT
** *
1270779 TACAAATAAAAATTTAAATAATT-AAACAATACACATTGATGAGGGATTGAATCAAAATAATTTT
1 TACAAATAAAAATTTAAATAATTAAAAC-AT--ACATTGATGAGGGATCAAATCGAAATAATTTT
* * * * *
1270843 AAATTTTGAGGTTGAAATTAATACAAAAAGTACTAAGTTAAACTCATTTAAAAAGTTATGGGCC-
63 AAATTGTGAGGTTGAAATTAATACAAAAAATACTAAATTATACTCATTTAAAAAGTTCTGGGCCA
*
1270907 ATTAAAAAATAGAAATAAATAATAAGTATGTGTCAATTTCAGATGCTAAGAAAATTTGGAGGACT
128 ATTAAAAAATAGAAATAAATAATAAGTATGTGTCAATTTCAGATGC-AAAAAAATTTGGAGGACT
*
1270972 AAATTGAACAAATATGAAAT
192 AAATTG-A-ATATATGAAAT
*
1270992 TAAAAATAAAAATTTAAATAAATTAAA
1 TACAAATAAAAATTTAAAT-AATTAAA
1271019 CAACACAAAG
Statistics
Matches: 405, Mismatches: 26, Indels: 32
0.87 0.06 0.07
Matches are distributed among these distances:
207 18 0.04
208 2 0.00
209 7 0.02
210 117 0.29
211 166 0.41
212 60 0.15
213 27 0.07
214 5 0.01
215 3 0.01
ACGTcount: A:0.50, C:0.07, G:0.13, T:0.30
Consensus pattern (209 bp):
TACAAATAAAAATTTAAATAATTAAAACATACATTGATGAGGGATCAAATCGAAATAATTTTAAA
TTGTGAGGTTGAAATTAATACAAAAAATACTAAATTATACTCATTTAAAAAGTTCTGGGCCAATT
AAAAAATAGAAATAAATAATAAGTATGTGTCAATTTCAGATGCAAAAAAATTTGGAGGACTAAAT
TGAATATATGAAAT
Found at i:1271111 original size:2 final size:2
Alignment explanation
Indices: 1271106--1271215 Score: 89
Period size: 2 Copynumber: 53.5 Consensus size: 2
1271096 TAAAACACTA
* *
1271106 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT TT AT AT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
* * * *
1271149 AGT AT AT GT AT -T AT AT AT AA AA ACT AT AT AGT TT AT AT AT AT
1 A-T AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT
* *
1271191 AT AT AT -T AT GT AT AA ACT AT AT AT A
1 AT AT AT AT AT AT AT AT A-T AT AT AT A
1271216 CCATGTATAA
Statistics
Matches: 87, Mismatches: 14, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
1 2 0.02
2 80 0.92
3 5 0.06
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1271190 original size:35 final size:34
Alignment explanation
Indices: 1271106--1271215 Score: 116
Period size: 35 Copynumber: 3.2 Consensus size: 34
1271096 TAAAACACTA
*
1271106 ATATATATATATATATATA-TATATATATATACT
1 ATATATATATATATATATATTATATATATAAACT
* * * *
1271139 TTATATATAAAGTATATGTATTATATATAAAAACT
1 ATATATATATA-TATATATATTATATATATAAACT
* *
1271174 ATATAGTTTATATATATATA-TATTATGTATAAACT
1 ATATA-TATATATATATATATTA-TATATATAAACT
1271209 ATATATA
1 ATATATA
1271216 CCATGTATAA
Statistics
Matches: 61, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
33 9 0.15
34 10 0.16
35 38 0.62
36 4 0.07
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (34 bp):
ATATATATATATATATATATTATATATATAAACT
Done.