Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008724.1 Hibiscus syriacus cultivar Beakdansim tig00111783_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: 5289199
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 23
Found at i:1090795 original size:136 final size:137
Alignment explanation
Indices: 1090635--1090913 Score: 379
Period size: 137 Copynumber: 2.0 Consensus size: 137
1090625 GTCATAGGTG
* * *
1090635 CATTTCTATATACATTTGTATATAATGGTTATCAATCGATTTT-TTTAATGCATATGTTGCATTT
1 CATTTCAACATACATTTGTATATAAAGGTTATCAATCGATTTTGTTTAATGCATATGTTGCATTT
* * *
1090699 TCGTATCA-GTACTATGTGTACTTTCGGCACTA-GATGTGCAA-CAAT-GATATTCATAATGATT
66 TCGTAT-ATGTACTATATGTACTTTCGGCACTATG-TGTG-AATCAATGGA-ATTCATAATAAGT
1090760 TTGTGAATTAC
127 TTGTGAATTAC
* * *
1090771 CATTTCAACATACATTTGTGTATAAAGGTTATCGATCGATTTTGTTTAATGCATATGTTGTATTT
1 CATTTCAACATACATTTGTATATAAAGGTTATCAATCGATTTTGTTTAATGCATATGTTGCATTT
* *
1090836 TTGTATATGTACTATATGTACTTTCGGCACTATGTGTGAATCCATGGAATTCATAATAAGTTTGT
66 TCGTATATGTACTATATGTACTTTCGGCACTATGTGTGAATCAATGGAATTCATAATAAGTTTGT
*
1090901 GAATTTC
131 GAATTAC
1090908 CATTTC
1 CATTTC
1090914 GGCAATTAGG
Statistics
Matches: 126, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
136 41 0.33
137 82 0.65
138 3 0.02
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (137 bp):
CATTTCAACATACATTTGTATATAAAGGTTATCAATCGATTTTGTTTAATGCATATGTTGCATTT
TCGTATATGTACTATATGTACTTTCGGCACTATGTGTGAATCAATGGAATTCATAATAAGTTTGT
GAATTAC
Found at i:1097642 original size:22 final size:22
Alignment explanation
Indices: 1097590--1097650 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 22
1097580 AAAATATGGT
* * *
1097590 ATGATCAGTACCGTGAACAGTA
1 ATGAACAGTACCATGAACAATA
*
1097612 ATGATCAGTACCATGAACAATA
1 ATGAACAGTACCATGAACAATA
* *
1097634 GTGAACAGTGCCATGAA
1 ATGAACAGTACCATGAA
1097651 TGGTGCCGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.21
Consensus pattern (22 bp):
ATGAACAGTACCATGAACAATA
Found at i:1097709 original size:20 final size:20
Alignment explanation
Indices: 1097681--1097720 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1097671 TTCCAGATTG
1097681 CTGCCAGGGAACCGATTCCC
1 CTGCCAGGGAACCGATTCCC
* *
1097701 CTGCTAGGGTACCGATTCCC
1 CTGCCAGGGAACCGATTCCC
1097721 ATACAGTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.38, G:0.25, T:0.20
Consensus pattern (20 bp):
CTGCCAGGGAACCGATTCCC
Found at i:1105440 original size:29 final size:29
Alignment explanation
Indices: 1105407--1105495 Score: 81
Period size: 29 Copynumber: 3.0 Consensus size: 29
1105397 AAATTTTGTC
*
1105407 TAGTGACTAAAATATAAGTTTTGAAAGTT
1 TAGTGACTAAAATATAAATTTTGAAAGTT
* * *
1105436 TAGTGGCTAAAGTATAAACTTTGAAAAGTT
1 TAGTGACTAAAATATAAATTTTG-AAAGTT
* * *
1105466 TAGGGA-TCAAAATTATAATTTTTAAAAGTT
1 TAGTGACT-AAAA-TATAAATTTTGAAAGTT
1105496 ATATATTTTA
Statistics
Matches: 47, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
29 20 0.43
30 19 0.40
31 8 0.17
ACGTcount: A:0.42, C:0.04, G:0.17, T:0.37
Consensus pattern (29 bp):
TAGTGACTAAAATATAAATTTTGAAAGTT
Found at i:1107531 original size:39 final size:39
Alignment explanation
Indices: 1107477--1107567 Score: 182
Period size: 39 Copynumber: 2.3 Consensus size: 39
1107467 CGACAGATGT
1107477 CATTTTCTTCAAATATTTTTTCCTTTAAAGAAACCTGGA
1 CATTTTCTTCAAATATTTTTTCCTTTAAAGAAACCTGGA
1107516 CATTTTCTTCAAATATTTTTTCCTTTAAAGAAACCTGGA
1 CATTTTCTTCAAATATTTTTTCCTTTAAAGAAACCTGGA
1107555 CATTTTCTTCAAA
1 CATTTTCTTCAAA
1107568 GATTCATGTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.31, C:0.19, G:0.07, T:0.44
Consensus pattern (39 bp):
CATTTTCTTCAAATATTTTTTCCTTTAAAGAAACCTGGA
Found at i:1116901 original size:44 final size:44
Alignment explanation
Indices: 1116838--1116928 Score: 173
Period size: 44 Copynumber: 2.1 Consensus size: 44
1116828 TTCAATCACC
1116838 ACCCATTTACATGTTATACTATTTGCACCCAAACTCCAAAATAA
1 ACCCATTTACATGTTATACTATTTGCACCCAAACTCCAAAATAA
*
1116882 ACCCATTTACTTGTTATACTATTTGCACCCAAACTCCAAAATAA
1 ACCCATTTACATGTTATACTATTTGCACCCAAACTCCAAAATAA
1116926 ACC
1 ACC
1116929 TTTCATAAGA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.37, C:0.29, G:0.04, T:0.30
Consensus pattern (44 bp):
ACCCATTTACATGTTATACTATTTGCACCCAAACTCCAAAATAA
Found at i:1118324 original size:22 final size:23
Alignment explanation
Indices: 1118282--1118325 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1118272 ATAAAATGGC
*
1118282 CGACCACCGACAGGTCACTATTT
1 CGACCACCGACAGATCACTATTT
*
1118305 CGACCACCGTC-GATCACTATT
1 CGACCACCGACAGATCACTATT
1118326 CATTAATGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.25, C:0.36, G:0.16, T:0.23
Consensus pattern (23 bp):
CGACCACCGACAGATCACTATTT
Found at i:1119015 original size:3 final size:3
Alignment explanation
Indices: 1119007--1119071 Score: 80
Period size: 3 Copynumber: 22.0 Consensus size: 3
1118997 ATTTTAAAAT
* *
1119007 ATA ATA ATA ATA GTA ATA ATAA ATA ATA ACA ATA ATA AT- ATA ATA
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA
*
1119052 AT- ATA GTA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA
1119072 TATGCAAACT
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
2 4 0.08
3 46 0.87
4 3 0.06
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1119032 original size:22 final size:20
Alignment explanation
Indices: 1119007--1119071 Score: 82
Period size: 19 Copynumber: 3.3 Consensus size: 20
1118997 ATTTTAAAAT
1119007 ATAATAATAATAGTAATAATAA
1 ATAATAAT-ATAGTAATAAT-A
*
1119029 ATAATAACA-A-TAATAAT-
1 ATAATAATATAGTAATAATA
1119046 ATAATAATATAGTAATAATA
1 ATAATAATATAGTAATAATA
1119066 ATAATA
1 ATAATA
1119072 TATGCAAACT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
17 8 0.21
18 1 0.03
19 14 0.37
20 7 0.18
21 1 0.03
22 7 0.18
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (20 bp):
ATAATAATATAGTAATAATA
Found at i:1119342 original size:20 final size:20
Alignment explanation
Indices: 1119314--1119387 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 20
1119304 AAAAAATCCT
*
1119314 ACCCTGAGGTTTTACAGATC
1 ACCCAGAGGTTTTACAGATC
* * *
1119334 ACCCAGAGGATTTATAGATG
1 ACCCAGAGGTTTTACAGATC
* *
1119354 ACCCGGAGGTTTTACAAATC
1 ACCCAGAGGTTTTACAGATC
*
1119374 ACCCAGAGGGTTTA
1 ACCCAGAGGTTTTA
1119388 ATTTTCTAGA
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.26
Consensus pattern (20 bp):
ACCCAGAGGTTTTACAGATC
Found at i:1119531 original size:100 final size:100
Alignment explanation
Indices: 1119398--1119586 Score: 315
Period size: 100 Copynumber: 1.9 Consensus size: 100
1119388 ATTTTCTAGA
* * *
1119398 ACATTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTCATGCGAAAATATTCTACCCTGAGGT
1 ACATTAAATGAGAAACTTTAAAAATCGCTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGGT
*
1119463 TTTACAGATGACCTGGAGGTTTTACAAATCTGTGG
66 TTTACAGATGACCCGGAGGTTTTACAAATCTGTGG
* *
1119498 ACATTAAATGAGAAACTTTAAAAATCGCTTTCTCATTTTCATGTGAAAACATCCTACCTTGAGGT
1 ACATTAAATGAGAAACTTTAAAAATCGCTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGGT
*
1119563 TTTATAGATGACCCGGAGGTTTTA
66 TTTACAGATGACCCGGAGGTTTTA
1119587 TCATCATGCT
Statistics
Matches: 82, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
100 82 1.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (100 bp):
ACATTAAATGAGAAACTTTAAAAATCGCTTTCTCATTTTCATGCGAAAACATCCTACCCTGAGGT
TTTACAGATGACCCGGAGGTTTTACAAATCTGTGG
Found at i:1119628 original size:20 final size:20
Alignment explanation
Indices: 1119558--1119647 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
1119548 ATCCTACCTT
* *
1119558 GAGGTTTTATAGATGACCCG
1 GAGGTTTTACATATGACCCG
*
1119578 GAGGTTTTATCATCATG-CTCG
1 GAGGTTTTA-CAT-ATGACCCG
*
1119599 GAAGG-CTTACATATGACCCG
1 G-AGGTTTTACATATGACCCG
* *
1119619 GAGGTTTTACAAATCACCCG
1 GAGGTTTTACATATGACCCG
*
1119639 GAGGATTTA
1 GAGGTTTTA
1119648 ATTTTCTAGA
Statistics
Matches: 56, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
19 6 0.11
20 36 0.64
21 8 0.14
22 6 0.11
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.29
Consensus pattern (20 bp):
GAGGTTTTACATATGACCCG
Found at i:1119790 original size:99 final size:99
Alignment explanation
Indices: 1119614--1119845 Score: 304
Period size: 99 Copynumber: 2.3 Consensus size: 99
1119604 CTTACATATG
* * * * *
1119614 ACCCGGAGGTTTTACAAATCACCCGGAGGATTTAATTTTCTAGAACATTAAATGAGAAACTTTAA
1 ACCCTGAGGTTTTACAGATGACCCGGAGGTTTTAATTTACTAGAACATTAAATGAGAAACTTTAA
* **
1119679 AAATTGATTTCTCATTTTCTTGCGAAAACATCCT
66 AAATTCATTTCTCATTTTCAGGCGAAAACATCCT
* * * **
1119713 ACCCTGAGGTTTTACAGATGACCCAGAGGTTTTAATTTACTTGAACATTAAATGAGAAATTTTGG
1 ACCCTGAGGTTTTACAGATGACCCGGAGGTTTTAATTTACTAGAACATTAAATGAGAAACTTTAA
* *
1119778 TAA-TCACTTTCTCATTTTCAGGTGAAAACATCCT
66 AAATTCA-TTTCTCATTTTCAGGCGAAAACATCCT
*
1119812 ACCCTGAGGTTTTACAGATGACCTGGAGGTTTTA
1 ACCCTGAGGTTTTACAGATGACCCGGAGGTTTTA
1119846 TAAATTTATG
Statistics
Matches: 115, Mismatches: 17, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
98 2 0.02
99 113 0.98
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (99 bp):
ACCCTGAGGTTTTACAGATGACCCGGAGGTTTTAATTTACTAGAACATTAAATGAGAAACTTTAA
AAATTCATTTCTCATTTTCAGGCGAAAACATCCT
Found at i:1122716 original size:9 final size:9
Alignment explanation
Indices: 1122702--1122756 Score: 62
Period size: 9 Copynumber: 6.4 Consensus size: 9
1122692 AAAAAAAATC
1122702 TTCTTTTTT
1 TTCTTTTTT
1122711 TTC--TTTT
1 TTCTTTTTT
1122718 TTC-TTTTT
1 TTCTTTTTT
*
1122726 TTCTCTTTT
1 TTCTTTTTT
*
1122735 TTCATTTTT
1 TTCTTTTTT
*
1122744 TTCTCTTTT
1 TTCTTTTTT
1122753 TTCT
1 TTCT
1122757 ATGATTGATG
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
7 7 0.18
8 7 0.18
9 25 0.64
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (9 bp):
TTCTTTTTT
Found at i:1122735 original size:18 final size:17
Alignment explanation
Indices: 1122702--1122756 Score: 94
Period size: 18 Copynumber: 3.2 Consensus size: 17
1122692 AAAAAAAATC
1122702 TTCTTTTTTT-TCTTTT
1 TTCTTTTTTTCTCTTTT
1122718 TTCTTTTTTTCTCTTTT
1 TTCTTTTTTTCTCTTTT
1122735 TTCATTTTTTTCTCTTTT
1 TTC-TTTTTTTCTCTTTT
1122753 TTCT
1 TTCT
1122757 ATGATTGATG
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
16 10 0.27
17 10 0.27
18 17 0.46
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (17 bp):
TTCTTTTTTTCTCTTTT
Found at i:1129895 original size:3 final size:3
Alignment explanation
Indices: 1129887--1129948 Score: 63
Period size: 3 Copynumber: 20.0 Consensus size: 3
1129877 ATATTAAAAT
* * *
1129887 ATA ATA ATA ATA GTA ACA ATAA ATA ATA GTA ATA AT- ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA
1129932 CAGTA ATA ATA ATA ATA
1 -A-TA ATA ATA ATA ATA
1129949 TGTGCAAGCT
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
2 2 0.04
3 40 0.82
4 5 0.10
5 2 0.04
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:1129909 original size:25 final size:25
Alignment explanation
Indices: 1129881--1129949 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 25
1129871 ATAAATATAT
1129881 TAAAAT-ATAATAATAATAGTAACAA
1 TAAAATAATAATAATAATA-TAACAA
* *
1129906 T-AAATAATAGTAATAATATAATAA
1 TAAAATAATAATAATAATATAACAA
* *
1129930 TACAGTAATAATAATAATAT
1 TAAAATAATAATAATAATAT
1129950 GTGCAAGCTC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
24 10 0.27
25 27 0.73
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.32
Consensus pattern (25 bp):
TAAAATAATAATAATAATATAACAA
Found at i:1129913 original size:16 final size:17
Alignment explanation
Indices: 1129890--1129931 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
1129880 TTAAAATATA
1129890 ATAATAATAGTAACAAT
1 ATAATAATAGTAACAAT
*
1129907 A-AATAATAGTAATAAT
1 ATAATAATAGTAACAAT
1129923 ATAATAATA
1 ATAATAATA
1129932 CAGTAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (17 bp):
ATAATAATAGTAACAAT
Found at i:1135657 original size:82 final size:82
Alignment explanation
Indices: 1135520--1135684 Score: 285
Period size: 82 Copynumber: 2.0 Consensus size: 82
1135510 ATCAGTTAGG
* * * *
1135520 AAACTATTAATTAGATATTTAAATGAAATATATTAACCAAATCTTGCAAGTATATACAACAACAG
1 AAACTATCAATTAGATATTTAAAAGAAATATATTAACCAAATCTTGAAAATATATACAACAACAG
1135585 AGTAGAAATGACAAACA
66 AGTAGAAATGACAAACA
1135602 AAACTATCAATTAGATATTTAAAAGAAATATATTAACCAAATCTTGAAAATATATACAACAACAG
1 AAACTATCAATTAGATATTTAAAAGAAATATATTAACCAAATCTTGAAAATATATACAACAACAG
*
1135667 AGTAGCAATGACAAACA
66 AGTAGAAATGACAAACA
1135684 A
1 A
1135685 GAATACGGGG
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
82 78 1.00
ACGTcount: A:0.53, C:0.13, G:0.09, T:0.25
Consensus pattern (82 bp):
AAACTATCAATTAGATATTTAAAAGAAATATATTAACCAAATCTTGAAAATATATACAACAACAG
AGTAGAAATGACAAACA
Found at i:1138184 original size:24 final size:24
Alignment explanation
Indices: 1138130--1138186 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
1138120 TAATTGTATA
1138130 TTAG-ATG-TTTTTTTATTAATTC
1 TTAGAATGTTTTTTTTATTAATTC
*
1138152 GTA-AGATGTTTTTTTTATTAATTC
1 TTAGA-ATGTTTTTTTTATTAATTC
1138176 TTAGAATGTTT
1 TTAGAATGTTT
1138187 ATTAATTACG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
22 2 0.07
23 3 0.10
24 23 0.79
25 1 0.03
ACGTcount: A:0.25, C:0.04, G:0.12, T:0.60
Consensus pattern (24 bp):
TTAGAATGTTTTTTTTATTAATTC
Found at i:1142898 original size:65 final size:64
Alignment explanation
Indices: 1142775--1142933 Score: 207
Period size: 65 Copynumber: 2.5 Consensus size: 64
1142765 GCACTAAGAG
* *
1142775 TGCATCGATGCATGAAGTGCATTCGATG-TTTCAAAATAGCCTGAGTGCATCGATGCAT-GTCTT
1 TGCATCGATGCAT-AAATGCATTCGATGTTTTCAAAATAGCCTGAGTGCATCGATGCATGGT-AT
1142838 A
64 A
* *
1142839 TGCATCGATGCATCAAATACATTCGATGTTTTCATAAA-ATCCTGAGTGCATCGATGCATGGTAT
1 TGCATCGATGCAT-AAATGCATTCGATGTTTTCA-AAATAGCCTGAGTGCATCGATGCATGGTAT
*
1142903 G
64 A
1142904 TGCATCGATGCATATAATGCATTCGATGTT
1 TGCATCGATGCATA-AATGCATTCGATGTT
1142934 CAATTTATTC
Statistics
Matches: 84, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
64 26 0.31
65 53 0.63
66 5 0.06
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (64 bp):
TGCATCGATGCATAAATGCATTCGATGTTTTCAAAATAGCCTGAGTGCATCGATGCATGGTATA
Found at i:1150031 original size:44 final size:44
Alignment explanation
Indices: 1149979--1150070 Score: 109
Period size: 44 Copynumber: 2.1 Consensus size: 44
1149969 TGCTTAATGT
*
1149979 ATCGATACA-C-TGAACAGTACATCGATGCA-TCCCTTTGTATGTGC
1 ATCGATACATCATGAACA-TACATCGATGCACT-CC-TTGAATGTGC
* *
1150023 ATCGATACATCATGAAGATGCATCGATGCACTCCTTGAATGTGC
1 ATCGATACATCATGAACATACATCGATGCACTCCTTGAATGTGC
1150067 ATCG
1 ATCG
1150071 TTGCACAAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
44 22 0.52
45 14 0.33
46 6 0.14
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (44 bp):
ATCGATACATCATGAACATACATCGATGCACTCCTTGAATGTGC
Found at i:1150067 original size:23 final size:22
Alignment explanation
Indices: 1149998--1150075 Score: 70
Period size: 23 Copynumber: 3.5 Consensus size: 22
1149988 CTGAACAGTA
*
1149998 CATCGATGCATCCCTTTGTATGTG
1 CATCGATGCAT-CC-TTGAATGTG
* *
1150022 CATCGATACAT-CATGAA-GATG
1 CATCGATGCATCCTTGAATG-TG
1150043 CATCGATGCACTCCTTGAATGTG
1 CATCGATGCA-TCCTTGAATGTG
*
1150066 CATCGTTGCA
1 CATCGATGCA
1150076 CAAAGCCATG
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
20 1 0.02
21 14 0.32
22 2 0.05
23 16 0.36
24 11 0.25
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (22 bp):
CATCGATGCATCCTTGAATGTG
Found at i:1150412 original size:21 final size:21
Alignment explanation
Indices: 1150386--1150425 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1150376 CCCCCTTTGA
*
1150386 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
1150407 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
1150426 TGGGGTTCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:1152719 original size:16 final size:16
Alignment explanation
Indices: 1152694--1152726 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1152684 GTGTGTGTTT
*
1152694 TAAGTGTGTTTTAAAA
1 TAAGTATGTTTTAAAA
1152710 TAAGTATGTTTTAAAA
1 TAAGTATGTTTTAAAA
1152726 T
1 T
1152727 GATAAATGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.45
Consensus pattern (16 bp):
TAAGTATGTTTTAAAA
Found at i:1155219 original size:23 final size:23
Alignment explanation
Indices: 1155187--1155265 Score: 67
Period size: 23 Copynumber: 3.5 Consensus size: 23
1155177 GCATGGCTTT
*
1155187 GTGCAACGATGCACATTCAAGGA
1 GTGCATCGATGCACATTCAAGGA
*
1155210 GTGCATCGATGCATC-TTC-ATGA
1 GTGCATCGATGCA-CATTCAAGGA
* *
1155232 -TGTATCGATGCACATACAAAGG-
1 GTGCATCGATGCACATTC-AAGGA
1155254 GATGCATCGATG
1 G-TGCATCGATG
1155266 TACTGTTCAG
Statistics
Matches: 44, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
20 1 0.02
21 13 0.30
22 3 0.07
23 17 0.39
24 10 0.23
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.24
Consensus pattern (23 bp):
GTGCATCGATGCACATTCAAGGA
Found at i:1161786 original size:35 final size:35
Alignment explanation
Indices: 1161740--1161809 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
1161730 GCCAAGAGTG
*
1161740 ATAGAATTATGAGGAATGCTATCTGGAGTACAGGT
1 ATAGAATTATGAGGAATGCTAGCTGGAGTACAGGT
*
1161775 ATAGAATTATGATGAATGCTAGCTGGAGTACAGGT
1 ATAGAATTATGAGGAATGCTAGCTGGAGTACAGGT
1161810 TGTTTTGCGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.34, C:0.09, G:0.29, T:0.29
Consensus pattern (35 bp):
ATAGAATTATGAGGAATGCTAGCTGGAGTACAGGT
Found at i:1162554 original size:2 final size:2
Alignment explanation
Indices: 1162547--1162574 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1162537 TTACATGTGC
1162547 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1162575 TAACTGCACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1166593 original size:13 final size:13
Alignment explanation
Indices: 1166559--1166613 Score: 69
Period size: 13 Copynumber: 4.3 Consensus size: 13
1166549 AAACTTAATT
*
1166559 AAAATAAAATAAA
1 AAAATACAATAAA
*
1166572 AAAGTACAATAATA
1 AAAATACAATAA-A
1166586 AAAA-ACAATAAA
1 AAAATACAATAAA
1166598 AAAATAC-ATAAA
1 AAAATACAATAAA
1166610 AAAA
1 AAAA
1166614 CTTGAAATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
12 14 0.38
13 19 0.51
14 4 0.11
ACGTcount: A:0.78, C:0.05, G:0.02, T:0.15
Consensus pattern (13 bp):
AAAATACAATAAA
Found at i:1166819 original size:15 final size:16
Alignment explanation
Indices: 1166783--1166824 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
1166773 TATAAACAAC
*
1166783 GACTAAAATGAATAAT
1 GACTAAAATAAATAAT
*
1166799 CA-TAAAA-AAATAAT
1 GACTAAAATAAATAAT
1166813 GACTAAAATAAA
1 GACTAAAATAAA
1166825 ATGAAGTGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
14 7 0.33
15 10 0.48
16 4 0.19
ACGTcount: A:0.64, C:0.07, G:0.07, T:0.21
Consensus pattern (16 bp):
GACTAAAATAAATAAT
Found at i:1166827 original size:14 final size:15
Alignment explanation
Indices: 1166783--1166828 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
1166773 TATAAACAAC
1166783 GACTAAAATGAATAAT
1 GACTAAAAT-AATAAT
* *
1166799 CA-TAAAAAAATAAT
1 GACTAAAATAATAAT
1166813 GACTAAAATAA-AAT
1 GACTAAAATAATAAT
1166827 GA
1 GA
1166829 AGTGTAGGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 12 0.48
16 1 0.04
ACGTcount: A:0.63, C:0.07, G:0.09, T:0.22
Consensus pattern (15 bp):
GACTAAAATAATAAT
Found at i:1167169 original size:110 final size:109
Alignment explanation
Indices: 1167035--1167241 Score: 252
Period size: 110 Copynumber: 1.9 Consensus size: 109
1167025 AAAATAAAAG
* * ** * ** **
1167035 TTAGTAGTTAGCAGAGTCCAAACCATAATAATACGGGTCTTACCCTGAATCGGGTCACCACAAGG
1 TTAGTAATTAACAGAGTCCAAACCATAATAATACGAATCTTACCCCGAATCGAATCA-CACAAAA
*
1167100 TCGAATCGAATAATGCAAACAAATATATAAAAAAAATTAAAAATA
65 TCGAATCGAATAATACAAACAAATATATAAAAAAAATTAAAAATA
** **
1167145 TTAGTAATTAACAGAGTCTGAACCATAATAATTTGAATCTTACCCCGAATCGAATCACACAAAAT
1 TTAGTAATTAACAGAGTCCAAACCATAATAATACGAATCTTACCCCGAATCGAATCACACAAAAT
* * *
1167210 CGAATCGAATACTATAAATAAATATATAAAAA
66 CGAATCGAATAATACAAACAAATATATAAAAA
1167242 TAAAATAAGT
Statistics
Matches: 80, Mismatches: 17, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
109 34 0.43
110 46 0.57
ACGTcount: A:0.46, C:0.17, G:0.13, T:0.25
Consensus pattern (109 bp):
TTAGTAATTAACAGAGTCCAAACCATAATAATACGAATCTTACCCCGAATCGAATCACACAAAAT
CGAATCGAATAATACAAACAAATATATAAAAAAAATTAAAAATA
Found at i:1168246 original size:24 final size:23
Alignment explanation
Indices: 1168206--1168277 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 23
1168196 TCTTAATTTT
* *
1168206 ATTAATATAATTTAATAAATAAA
1 ATTATTATAATTAAATAAATAAA
**
1168229 ATTATTAATAATTAAATATGTAAA
1 ATTATT-ATAATTAAATAAATAAA
*
1168253 ATTATTATATATAAAATAAAATAAA
1 ATTATTATA-ATTAAAT-AAATAAA
1168278 TGTAACCGGA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
23 8 0.21
24 26 0.67
25 5 0.13
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (23 bp):
ATTATTATAATTAAATAAATAAA
Found at i:1168300 original size:16 final size:16
Alignment explanation
Indices: 1168279--1168309 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1168269 TAAAATAAAT
1168279 GTAACCGGATACTCGG
1 GTAACCGGATACTCGG
*
1168295 GTAACCGGGTACTCG
1 GTAACCGGATACTCG
1168310 AAAAAAAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.26, G:0.32, T:0.19
Consensus pattern (16 bp):
GTAACCGGATACTCGG
Found at i:1169032 original size:15 final size:15
Alignment explanation
Indices: 1169009--1169085 Score: 57
Period size: 15 Copynumber: 5.0 Consensus size: 15
1168999 ATCAGATAAC
*
1169009 CAAATGAATACTAAT
1 CAAACGAATACTAAT
1169024 CAAACGAATACTAAT
1 CAAACGAATACTAAT
* * *
1169039 CATTAAAG-ATACCCATT
1 CA--AACGAATA-CTAAT
* **
1169056 TAATTGAATACTAAT
1 CAAACGAATACTAAT
1169071 CAAACGAATACTAAT
1 CAAACGAATACTAAT
1169086 AGGTATGTTC
Statistics
Matches: 46, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
15 33 0.72
16 6 0.13
17 7 0.15
ACGTcount: A:0.49, C:0.17, G:0.06, T:0.27
Consensus pattern (15 bp):
CAAACGAATACTAAT
Found at i:1169613 original size:2 final size:2
Alignment explanation
Indices: 1169559--1169594 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1169549 AAGAATATGA
1169559 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1169595 CAAAGGAGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1169751 original size:43 final size:43
Alignment explanation
Indices: 1169697--1169791 Score: 136
Period size: 43 Copynumber: 2.2 Consensus size: 43
1169687 TTCATTTAAT
* * *
1169697 TAAATGAATATAAAATCTAATTCATATTCGTACGTTTAATAAA
1 TAAATGAATATAAAATATAATTAATATTCATACGTTTAATAAA
* *
1169740 TAAACGAATATAAAATATAATTAATGTTCATACGTTTAATAAA
1 TAAATGAATATAAAATATAATTAATATTCATACGTTTAATAAA
*
1169783 CAAATGAAT
1 TAAATGAAT
1169792 TTCCCGTCGA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.49, C:0.08, G:0.07, T:0.35
Consensus pattern (43 bp):
TAAATGAATATAAAATATAATTAATATTCATACGTTTAATAAA
Found at i:1170156 original size:18 final size:19
Alignment explanation
Indices: 1170119--1170156 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
1170109 CACGGAATGT
*
1170119 AAGATTACTAGTAGGAATAA
1 AAGATTACCAGTA-GAATAA
1170139 AAGATTACCAGT-GAATAA
1 AAGATTACCAGTAGAATAA
1170157 GATTACTGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.50, C:0.08, G:0.18, T:0.24
Consensus pattern (19 bp):
AAGATTACCAGTAGAATAA
Found at i:1172490 original size:31 final size:31
Alignment explanation
Indices: 1172448--1172507 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
1172438 AATAGAAGGA
1172448 AAAAGGGTAAATTACACCATAAGTCATTAGG
1 AAAAGGGTAAATTACACCATAAGTCATTAGG
* *
1172479 AAAATGGTAAATTACACCATGAGTCATTA
1 AAAAGGGTAAATTACACCATAAGTCATTA
1172508 AACTTTACTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.45, C:0.13, G:0.17, T:0.25
Consensus pattern (31 bp):
AAAAGGGTAAATTACACCATAAGTCATTAGG
Found at i:1176062 original size:32 final size:33
Alignment explanation
Indices: 1176024--1176095 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
1176014 CTTTATTTTG
1176024 TTCGGGTCAGGTCAGG-TTTTTTAAGTGTGATA
1 TTCGGGTCAGGTCAGGTTTTTTTAAGTGTGATA
* **
1176056 TTCGGGTCGGGTTTGGTTTTTTTAAGTGTGATA
1 TTCGGGTCAGGTCAGGTTTTTTTAAGTGTGATA
1176089 TTCGGGT
1 TTCGGGT
1176096 TGGGTTTAGG
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
32 13 0.36
33 23 0.64
ACGTcount: A:0.14, C:0.08, G:0.33, T:0.44
Consensus pattern (33 bp):
TTCGGGTCAGGTCAGGTTTTTTTAAGTGTGATA
Found at i:1176082 original size:33 final size:33
Alignment explanation
Indices: 1176040--1176102 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
1176030 TCAGGTCAGG
1176040 TTTTTTAAGTGTGATATTCGGGTCGGGTTTGGT
1 TTTTTTAAGTGTGATATTCGGGTCGGGTTTGGT
*
1176073 TTTTTTAAGTGTGATATTCGGGTTGGGTTT
1 TTTTTTAAGTGTGATATTCGGGTCGGGTTT
1176103 AGGGTGAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.13, C:0.05, G:0.32, T:0.51
Consensus pattern (33 bp):
TTTTTTAAGTGTGATATTCGGGTCGGGTTTGGT
Found at i:1176684 original size:17 final size:18
Alignment explanation
Indices: 1176662--1176708 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
1176652 TATGGAATTG
*
1176662 GATTCCAATTCC-TGACA
1 GATTCCAATTCCTTCACA
1176679 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
1176697 GATTCCAATTCC
1 GATTCCAATTCC
1176709 CTCATAAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 12 0.43
18 16 0.57
ACGTcount: A:0.28, C:0.32, G:0.09, T:0.32
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:1183362 original size:14 final size:14
Alignment explanation
Indices: 1183343--1183382 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1183333 CGAATTCAAT
*
1183343 GAGTTGACTTAGTA-
1 GAGTTGACTCAG-AC
1183357 GAGTTGACTCAGAC
1 GAGTTGACTCAGAC
1183371 GAGTTGACTCAG
1 GAGTTGACTCAG
1183383 TGATTGGACC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 1 0.04
14 23 0.96
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.28
Consensus pattern (14 bp):
GAGTTGACTCAGAC
Found at i:1184547 original size:46 final size:46
Alignment explanation
Indices: 1184489--1184810 Score: 394
Period size: 46 Copynumber: 7.0 Consensus size: 46
1184479 GGTGGACGAC
** *
1184489 TACAACAATAATTCACTGTTTCAATTACTTTTCAGAGGTCATTTAT
1 TACAACAATAATTCACCATTTCAACTACTTTTCAGAGGTCATTTAT
** *
1184535 TACAGTAATAATTCACCGTTTCAACTACTTTTCAGAGGTCATTTAT
1 TACAACAATAATTCACCATTTCAACTACTTTTCAGAGGTCATTTAT
* * * *
1184581 TACAACAATAATTCACCATTTTAGCTA-TTTTTAAAGGTCATTTAT
1 TACAACAATAATTCACCATTTCAACTACTTTTCAGAGGTCATTTAT
* * *
1184626 TACAACAATAATTCACCGTTTCAGCTACTTTTTAGAGGTCATTTAT
1 TACAACAATAATTCACCATTTCAACTACTTTTCAGAGGTCATTTAT
* * **
1184672 TACAGCAATAATTCATCATTTCAACTACTTTTCAGAGACCATTTAT
1 TACAACAATAATTCACCATTTCAACTACTTTTCAGAGGTCATTTAT
* *
1184718 TACAACAATAATTCACTATTTCATCTACTTTTCAGAGGTCATTTAT
1 TACAACAATAATTCACCATTTCAACTACTTTTCAGAGGTCATTTAT
** * * * * * *
1184764 TACAGTAATAATGCATCATTTTAGCTAATTTTCAGAGGTTATTTAT
1 TACAACAATAATTCACCATTTCAACTACTTTTCAGAGGTCATTTAT
1184810 T
1 T
1184811 GTAGTAATAA
Statistics
Matches: 239, Mismatches: 36, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
45 41 0.17
46 198 0.83
ACGTcount: A:0.33, C:0.18, G:0.09, T:0.41
Consensus pattern (46 bp):
TACAACAATAATTCACCATTTCAACTACTTTTCAGAGGTCATTTAT
Found at i:1185592 original size:11 final size:11
Alignment explanation
Indices: 1185576--1185601 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1185566 TTCATGTTAA
1185576 TGTACTAAGTT
1 TGTACTAAGTT
1185587 TGTACTAAGTT
1 TGTACTAAGTT
1185598 TGTA
1 TGTA
1185602 GTTTTGTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.08, G:0.19, T:0.46
Consensus pattern (11 bp):
TGTACTAAGTT
Found at i:1186911 original size:21 final size:21
Alignment explanation
Indices: 1186882--1186924 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1186872 AATATGTAAA
*
1186882 TCACATTGCGATTTTCCGAAT
1 TCACATTGCGATTTTCCAAAT
*
1186903 TCACGTTGCGATTTTCCAAAT
1 TCACATTGCGATTTTCCAAAT
1186924 T
1 T
1186925 TGCAACGCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.40
Consensus pattern (21 bp):
TCACATTGCGATTTTCCAAAT
Found at i:1186966 original size:19 final size:19
Alignment explanation
Indices: 1186942--1186983 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
1186932 CGAATTTGTT
1186942 ATTCGCAACACAAAGTCAA
1 ATTCGCAACACAAAGTCAA
*
1186961 ATTCGCAACACAAAGTTAA
1 ATTCGCAACACAAAGTCAA
1186980 ATTC
1 ATTC
1186984 ACAATGCGCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.45, C:0.24, G:0.10, T:0.21
Consensus pattern (19 bp):
ATTCGCAACACAAAGTCAA
Found at i:1187192 original size:22 final size:22
Alignment explanation
Indices: 1187141--1187192 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
1187131 CTATGGCGTC
*
1187141 ATCCGTCCCCATCTCTGACGAA
1 ATCCGTCTCCATCTCTGACGAA
* *
1187163 ATCCGTCTTCATCTCTGGCGAA
1 ATCCGTCTCCATCTCTGACGAA
1187185 ATCCGTCT
1 ATCCGTCT
1187193 ATCTCCATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.19, C:0.37, G:0.15, T:0.29
Consensus pattern (22 bp):
ATCCGTCTCCATCTCTGACGAA
Found at i:1187558 original size:20 final size:20
Alignment explanation
Indices: 1187535--1187573 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1187525 ACTTAAATTG
1187535 GCAACACGAAAATGAAAATC
1 GCAACACGAAAATGAAAATC
**
1187555 GCAATGCGAAAATGAAAAT
1 GCAACACGAAAATGAAAAT
1187574 TACTTCAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.15, G:0.18, T:0.13
Consensus pattern (20 bp):
GCAACACGAAAATGAAAATC
Found at i:1189097 original size:42 final size:42
Alignment explanation
Indices: 1189009--1189105 Score: 131
Period size: 42 Copynumber: 2.3 Consensus size: 42
1188999 CCCCACTTCA
* * * *
1189009 AGAGCCATCACCTGATCAAGCCGATTCTACAGCTCGACACCC
1 AGAGCCATCACCTGATCAAGCCGATTATACACCTCCACAACC
* * *
1189051 AGAGCCATCACCTGATCGAGCTGATTATACACCTCCACAACG
1 AGAGCCATCACCTGATCAAGCCGATTATACACCTCCACAACC
1189093 AGAGCCATCACCT
1 AGAGCCATCACCT
1189106 ATTCCATCAC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.30, C:0.36, G:0.16, T:0.18
Consensus pattern (42 bp):
AGAGCCATCACCTGATCAAGCCGATTATACACCTCCACAACC
Found at i:1189244 original size:21 final size:21
Alignment explanation
Indices: 1189220--1189269 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
1189210 GTTAGGGGAG
* *
1189220 TTACGTGATGAGGTTAGTGCT
1 TTACGTGAGGAGGTTAGTACT
* *
1189241 TTACTTGAGGAGGTTGGTACT
1 TTACGTGAGGAGGTTAGTACT
1189262 TTACGTGA
1 TTACGTGA
1189270 CGACAATGGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.20, C:0.10, G:0.32, T:0.38
Consensus pattern (21 bp):
TTACGTGAGGAGGTTAGTACT
Found at i:1189442 original size:12 final size:12
Alignment explanation
Indices: 1189425--1189450 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1189415 AATGAGGTTC
1189425 ATACTCTACGCA
1 ATACTCTACGCA
1189437 ATACTCTACGCA
1 ATACTCTACGCA
1189449 AT
1 AT
1189451 GAGGTAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.31, G:0.08, T:0.27
Consensus pattern (12 bp):
ATACTCTACGCA
Found at i:1189745 original size:21 final size:21
Alignment explanation
Indices: 1189713--1189783 Score: 97
Period size: 21 Copynumber: 3.4 Consensus size: 21
1189703 GCCCCCTACT
* *
1189713 TTCAATAGGCCCCTCCCACCA
1 TTCAAGAGGCCCCTCCCACCG
* * *
1189734 TTTAAGAGGCCCCTCTCATCG
1 TTCAAGAGGCCCCTCCCACCG
1189755 TTCAAGAGGCCCCTCCCACCG
1 TTCAAGAGGCCCCTCCCACCG
1189776 TTCAAGAG
1 TTCAAGAG
1189784 CCTGATTCAC
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.23, C:0.39, G:0.17, T:0.21
Consensus pattern (21 bp):
TTCAAGAGGCCCCTCCCACCG
Found at i:1189768 original size:42 final size:39
Alignment explanation
Indices: 1189695--1189783 Score: 115
Period size: 42 Copynumber: 2.2 Consensus size: 39
1189685 CCTGTCATCG
* *
1189695 TTTAAGAGGCCCCCTACTTTCAATAGGCCCCTCCCACCA
1 TTTAAGAGGCCCCCTACGTTCAAGAGGCCCCTCCCACCA
*
1189734 TTTAAGAGGCCCCTCTCATCGTTCAAGAGGCCCCTCCCACCG
1 TTTAAGAGGCCCC-CT-A-CGTTCAAGAGGCCCCTCCCACCA
*
1189776 TTCAAGAG
1 TTTAAGAG
1189784 CCTGATTCAC
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
39 13 0.30
40 2 0.05
41 1 0.02
42 27 0.63
ACGTcount: A:0.22, C:0.38, G:0.17, T:0.22
Consensus pattern (39 bp):
TTTAAGAGGCCCCCTACGTTCAAGAGGCCCCTCCCACCA
Found at i:1197270 original size:24 final size:24
Alignment explanation
Indices: 1197243--1197422 Score: 344
Period size: 24 Copynumber: 7.5 Consensus size: 24
1197233 AACCTCAAGA
1197243 TGGTATCGATACTACTCTATATAG
1 TGGTATCGATACTACTCTATATAG
1197267 TGGTATCGATACTACTCTATATAG
1 TGGTATCGATACTACTCTATATAG
1197291 TGGTATCGATACTACTCTATATAG
1 TGGTATCGATACTACTCTATATAG
1197315 TGGTATCGATACTACTCTATATAG
1 TGGTATCGATACTACTCTATATAG
1197339 TGGTATCGATACTACTCTATATAG
1 TGGTATCGATACTACTCTATATAG
1197363 TGGTATCGATACTACTCTATATAG
1 TGGTATCGATACTACTCTATATAG
1197387 TGGTAT-GATACTACTCTATATAG
1 TGGTATCGATACTACTCTATATAG
*
1197410 TAGTATCGATACT
1 TGGTATCGATACT
1197423 CCTTTAACAG
Statistics
Matches: 154, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
23 22 0.14
24 132 0.86
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (24 bp):
TGGTATCGATACTACTCTATATAG
Found at i:1200908 original size:26 final size:26
Alignment explanation
Indices: 1200878--1201026 Score: 108
Period size: 25 Copynumber: 5.9 Consensus size: 26
1200868 TCTGACGTGG
* *
1200878 CAGTTTCTAGATGGTCTAGTCAGCGA
1 CAGTTTCTAGAAGATCTAGTCAGCGA
1200904 CAGTTTCTAGAAGATCTAGTCAGCG-
1 CAGTTTCTAGAAGATCTAGTCAGCGA
** * *
1200929 CACCTTCTGGAAGATCCAGTCAGCG-
1 CAGTTTCTAGAAGATCTAGTCAGCGA
** *
1200954 CACCTTCTAGAAGATCCAGTCAGCG-
1 CAGTTTCTAGAAGATCTAGTCAGCGA
** * * *
1200979 CACCTTCTGGAAGATCCAATCAGCG-
1 CAGTTTCTAGAAGATCTAGTCAGCGA
** * *
1201004 CACCTTCTGGAAGATCCAGTCAG
1 CAGTTTCTAGAAGATCTAGTCAG
1201027 TGCACCTTCT
Statistics
Matches: 113, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
25 90 0.80
26 23 0.20
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (26 bp):
CAGTTTCTAGAAGATCTAGTCAGCGA
Found at i:1200942 original size:25 final size:25
Alignment explanation
Indices: 1200908--1201043 Score: 227
Period size: 25 Copynumber: 5.4 Consensus size: 25
1200898 CAGCGACAGT
* *
1200908 TTCTAGAAGATCTAGTCAGCGCACC
1 TTCTGGAAGATCCAGTCAGCGCACC
1200933 TTCTGGAAGATCCAGTCAGCGCACC
1 TTCTGGAAGATCCAGTCAGCGCACC
*
1200958 TTCTAGAAGATCCAGTCAGCGCACC
1 TTCTGGAAGATCCAGTCAGCGCACC
*
1200983 TTCTGGAAGATCCAATCAGCGCACC
1 TTCTGGAAGATCCAGTCAGCGCACC
*
1201008 TTCTGGAAGATCCAGTCAGTGCACC
1 TTCTGGAAGATCCAGTCAGCGCACC
1201033 TTCTGGAAGAT
1 TTCTGGAAGAT
1201044 GGACGAGCAA
Statistics
Matches: 104, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 104 1.00
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (25 bp):
TTCTGGAAGATCCAGTCAGCGCACC
Found at i:1221952 original size:46 final size:46
Alignment explanation
Indices: 1221899--1221998 Score: 114
Period size: 46 Copynumber: 2.2 Consensus size: 46
1221889 GCCAATCAGA
1221899 GCATTATTAATACAATAAAT-AACCTCTT-AAAAGTAGCTAAAATGGT
1 GCATTATTAATACAATAAATGAA-CT-TTGAAAAGTAGCTAAAATGGT
** ** *
1221945 GCATTATTGTTGTAATAAATGAACTTTGAAAAGTAGCTGAAATGGT
1 GCATTATTAATACAATAAATGAACTTTGAAAAGTAGCTAAAATGGT
*
1221991 GAATTATT
1 GCATTATT
1221999 GCTGTAATAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
45 2 0.04
46 42 0.91
47 2 0.04
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (46 bp):
GCATTATTAATACAATAAATGAACTTTGAAAAGTAGCTAAAATGGT
Found at i:1221999 original size:46 final size:46
Alignment explanation
Indices: 1221912--1222263 Score: 371
Period size: 46 Copynumber: 7.6 Consensus size: 46
1221902 TTATTAATAC
* * *
1221912 AATAAATAACCTCTTAAAAGTAGCTAAAATGGTGCATTATTGTTGT
1 AATAAATGACCTCTGAAAAGTAGCTAAAATGGTGAATTATTGTTGT
* * * *
1221958 AATAAATGAACTTTGAAAAGTAGCTGAAATGGTGAATTATTGCTGT
1 AATAAATGACCTCTGAAAAGTAGCTAAAATGGTGAATTATTGTTGT
* * * * *
1222004 AATAAATGTCCTCTGAAAAGTAGTTGAAATGATAAATTATTGTTGT
1 AATAAATGACCTCTGAAAAGTAGCTAAAATGGTGAATTATTGTTGT
* * * *** *
1222050 AATAAATGTCCTCTAAAAAGTAGTTAAAATGACAAATTATTATTGT
1 AATAAATGACCTCTGAAAAGTAGCTAAAATGGTGAATTATTGTTGT
* * * * *
1222096 AATAAATGAGCTATGAAAAGTAGCTAAAACGGTGAATTACTGCTGT
1 AATAAATGACCTCTGAAAAGTAGCTAAAATGGTGAATTATTGTTGT
* * * * *
1222142 AATAAATGACCTCAGAAAAATAACTAAAAAGGTGAATTATTGCTGT
1 AATAAATGACCTCTGAAAAGTAGCTAAAATGGTGAATTATTGTTGT
* * * * * *
1222188 AATAATTGGCCTCTGAAAAGTAGTTGAAATGGTAAATTATTGTTTT
1 AATAAATGACCTCTGAAAAGTAGCTAAAATGGTGAATTATTGTTGT
*
1222234 AATAAATGACCTCTAAAAAGTAGCTGAAAA
1 AATAAATGACCTCTGAAAAGTAGCT-AAAA
1222264 GTAGCTGAAA
Statistics
Matches: 252, Mismatches: 53, Indels: 1
0.82 0.17 0.00
Matches are distributed among these distances:
46 249 0.99
47 3 0.01
ACGTcount: A:0.42, C:0.09, G:0.17, T:0.32
Consensus pattern (46 bp):
AATAAATGACCTCTGAAAAGTAGCTAAAATGGTGAATTATTGTTGT
Found at i:1222078 original size:138 final size:138
Alignment explanation
Indices: 1221912--1222262 Score: 414
Period size: 138 Copynumber: 2.5 Consensus size: 138
1221902 TTATTAATAC
* * * ** *
1221912 AATAAATAACCTCTTAAAAGTAGCTAAAATGGTGCATTATTGTTGTAATAAATGAACTTTGAAAA
1 AATAAATGACCTCTAAAAAGTAGTTAAAATGGTAAATTATTGTTGTAATAAATGAACTATGAAAA
* * * * * ** * *
1221977 GTAGCTGAAATGGTGAATTATTGCTGTAATAAATGTCCTCTGAAAAGTAGTTGAAATGATAAATT
66 GTAGCTGAAACGGTGAATTACTGCTGTAATAAATGACCTCAGAAAAATAACTAAAAAGATAAATT
*
1222042 ATTGTTGT
131 ATTGCTGT
* ** * *
1222050 AATAAATGTCCTCTAAAAAGTAGTTAAAATGACAAATTATTATTGTAATAAATGAGCTATGAAAA
1 AATAAATGACCTCTAAAAAGTAGTTAAAATGGTAAATTATTGTTGTAATAAATGAACTATGAAAA
* * *
1222115 GTAGCTAAAACGGTGAATTACTGCTGTAATAAATGACCTCAGAAAAATAACTAAAAAGGTGAATT
66 GTAGCTGAAACGGTGAATTACTGCTGTAATAAATGACCTCAGAAAAATAACTAAAAAGATAAATT
1222180 ATTGCTGT
131 ATTGCTGT
* * * * * * * *
1222188 AATAATTGGCCTCTGAAAAGTAGTTGAAATGGTAAATTATTGTTTTAATAAATGACCTCTAAAAA
1 AATAAATGACCTCTAAAAAGTAGTTAAAATGGTAAATTATTGTTGTAATAAATGAACTATGAAAA
1222253 GTAGCTGAAA
66 GTAGCTGAAA
1222263 AGTAGCTGAA
Statistics
Matches: 177, Mismatches: 36, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
138 177 1.00
ACGTcount: A:0.42, C:0.09, G:0.17, T:0.32
Consensus pattern (138 bp):
AATAAATGACCTCTAAAAAGTAGTTAAAATGGTAAATTATTGTTGTAATAAATGAACTATGAAAA
GTAGCTGAAACGGTGAATTACTGCTGTAATAAATGACCTCAGAAAAATAACTAAAAAGATAAATT
ATTGCTGT
Found at i:1222263 original size:11 final size:11
Alignment explanation
Indices: 1222249--1222273 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1222239 ATGACCTCTA
1222249 AAAAGTAGCTG
1 AAAAGTAGCTG
1222260 AAAAGTAGCTG
1 AAAAGTAGCTG
1222271 AAA
1 AAA
1222274 GATTGAAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.08, G:0.24, T:0.16
Consensus pattern (11 bp):
AAAAGTAGCTG
Found at i:1229049 original size:24 final size:24
Alignment explanation
Indices: 1228970--1229069 Score: 78
Period size: 23 Copynumber: 4.2 Consensus size: 24
1228960 GAGTCAAGGG
*
1228970 TTCTACGTGGTCCTCCAAGA-AAA
1 TTCTACGTGGTCCTCCAGGACAAA
* ** ** * *
1228993 ATCTATATGGTCCTTTAGAAC-AT
1 TTCTACGTGGTCCTCCAGGACAAA
* *
1229016 TTCTACGTGGTCCTTCGGGACAAA
1 TTCTACGTGGTCCTCCAGGACAAA
* *
1229040 TTCTATGTGGTCCTCCAGGATAAA
1 TTCTACGTGGTCCTCCAGGACAAA
1229064 TTCTAC
1 TTCTAC
1229070 TTGGCACTTC
Statistics
Matches: 55, Mismatches: 20, Indels: 3
0.71 0.26 0.04
Matches are distributed among these distances:
23 29 0.53
24 26 0.47
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (24 bp):
TTCTACGTGGTCCTCCAGGACAAA
Found at i:1235718 original size:23 final size:23
Alignment explanation
Indices: 1235685--1235755 Score: 88
Period size: 23 Copynumber: 3.0 Consensus size: 23
1235675 AGTTAAGGGT
* *
1235685 TCTACGCGGTCCTTCGGGACAAA
1 TCTAAGCGGTCCTTCGGGATAAA
* *
1235708 TCTATGTGGTCCTTCGGGATAAA
1 TCTAAGCGGTCCTTCGGGATAAA
*
1235731 TTCTAAGCGGTCCTCCGGGATAAA
1 -TCTAAGCGGTCCTTCGGGATAAA
1235755 T
1 T
1235756 TCTACATGGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
23 21 0.51
24 20 0.49
ACGTcount: A:0.23, C:0.24, G:0.25, T:0.28
Consensus pattern (23 bp):
TCTAAGCGGTCCTTCGGGATAAA
Found at i:1235742 original size:24 final size:24
Alignment explanation
Indices: 1235684--1235759 Score: 100
Period size: 24 Copynumber: 3.2 Consensus size: 24
1235674 GAGTTAAGGG
* *
1235684 TTCTACGCGGTCCTTCGGGACAAA
1 TTCTAAGCGGTCCTTCGGGATAAA
* *
1235708 -TCTATGTGGTCCTTCGGGATAAA
1 TTCTAAGCGGTCCTTCGGGATAAA
*
1235731 TTCTAAGCGGTCCTCCGGGATAAA
1 TTCTAAGCGGTCCTTCGGGATAAA
1235755 TTCTA
1 TTCTA
1235760 CATGGCACTT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 20 0.44
24 25 0.56
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.30
Consensus pattern (24 bp):
TTCTAAGCGGTCCTTCGGGATAAA
Found at i:1245384 original size:64 final size:64
Alignment explanation
Indices: 1245252--1245414 Score: 186
Period size: 64 Copynumber: 2.5 Consensus size: 64
1245242 TGGAACACTT
* * * **
1245252 AGTGCATCGGTGCACCA-AGTGTGCATCGATGCATAAAATGCATTCGATGTTTGAAAATAGCCTG
1 AGTGCATCGATGCA-TAGAGTGTGCATCGATGCATAAAATGCATTCGATGTTTGAAAATAACCCA
* * ** * *
1245316 AGTGCATCGGTGCATTGCTTGTGCATCGATGCATGAAATGCATTCGATGTTTTAATAA-AACCCA
1 AGTGCATCGATGCATAGAGTGTGCATCGATGCATAAAATGCATTCGATGTTTGAA-AATAACCCA
*
1245380 AGTGCATCGATGCATAGAGAGTGCATCGATGCATA
1 AGTGCATCGATGCATAGAGTGTGCATCGATGCATA
1245415 GAGAGTGCAT
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
64 80 0.98
65 2 0.02
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (64 bp):
AGTGCATCGATGCATAGAGTGTGCATCGATGCATAAAATGCATTCGATGTTTGAAAATAACCCA
Found at i:1245404 original size:19 final size:19
Alignment explanation
Indices: 1245380--1245451 Score: 144
Period size: 19 Copynumber: 3.8 Consensus size: 19
1245370 ATAAAACCCA
1245380 AGTGCATCGATGCATAGAG
1 AGTGCATCGATGCATAGAG
1245399 AGTGCATCGATGCATAGAG
1 AGTGCATCGATGCATAGAG
1245418 AGTGCATCGATGCATAGAG
1 AGTGCATCGATGCATAGAG
1245437 AGTGCATCGATGCAT
1 AGTGCATCGATGCAT
1245452 GAAATGCATT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 53 1.00
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.22
Consensus pattern (19 bp):
AGTGCATCGATGCATAGAG
Found at i:1251297 original size:25 final size:25
Alignment explanation
Indices: 1251269--1251345 Score: 69
Period size: 25 Copynumber: 3.3 Consensus size: 25
1251259 TGCTTGCCCT
1251269 TCATGTTGCTTCTGAATCTCAGGAC
1 TCATGTTGCTTCTGAATCTCAGGAC
**
1251294 TCATGTTG---C--AA-C-CATGTCC
1 TCATGTTGCTTCTGAATCTCA-GGAC
*
1251313 TCATGTTGCTTCTGAATCTCAGGAG
1 TCATGTTGCTTCTGAATCTCAGGAC
1251338 TCATGTTG
1 TCATGTTG
1251346 GCAAGCATTA
Statistics
Matches: 39, Mismatches: 5, Indels: 16
0.65 0.08 0.27
Matches are distributed among these distances:
18 2 0.05
19 11 0.28
20 2 0.05
22 2 0.05
24 2 0.05
25 18 0.46
26 2 0.05
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.36
Consensus pattern (25 bp):
TCATGTTGCTTCTGAATCTCAGGAC
Found at i:1258167 original size:23 final size:23
Alignment explanation
Indices: 1258120--1258169 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
1258110 AATAACATAT
**
1258120 TAGGTAGCACTTATATAATGTAA
1 TAGGTAGCACTTATATAATAAAA
*
1258143 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGCACTTATATAATAAAA
1258166 TAGG
1 TAGG
1258170 CATTTAAGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (23 bp):
TAGGTAGCACTTATATAATAAAA
Found at i:1258489 original size:17 final size:17
Alignment explanation
Indices: 1258467--1258499 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1258457 TAATTAACCG
1258467 ATTGTAATTTTACCTAC
1 ATTGTAATTTTACCTAC
1258484 ATTGTAATTTTACCTA
1 ATTGTAATTTTACCTA
1258500 TTATTTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.15, G:0.06, T:0.48
Consensus pattern (17 bp):
ATTGTAATTTTACCTAC
Found at i:1262151 original size:200 final size:201
Alignment explanation
Indices: 1261801--1262814 Score: 1240
Period size: 200 Copynumber: 5.1 Consensus size: 201
1261791 GTAATTTTAA
* * ** * ** * *
1261801 AAAGTATCGACAGAAAAT-TAAAAAGTGTCAACACATTATGTTTACCTATTTTCT-ATTTACACC
1 AAAGTATCGACA-CAAATGTATAAAGTGTTGATACATTATGTAGACCTATTTTCTCA-TAAAACC
* * *
1261864 GGTAAATTTCAACCGGTTACATTGTAAATTGACCTATTACATTATAATTTCTGGTCTCGATGTAT
64 GGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTTCTGGTCTCGATGTTT
* * * *
1261929 TTGGGGTCGATACTTTTTATAAATGTATCGAAACTTTATGCGTGGACATCGTTTGGCAA-TCATT
129 TTGGGATCGATACTTGTTATAAATGTATCGAAACTTTATGCGTGCACATAGTTTGGCAATTCATT
*
1261993 ATGAACAT
194 ATGGACAT
*
1262001 AAAGTATTGACACAAATGTATAAAGT-TTCGATACATTATGTAGACCTATTTTCTCATAAAACCG
1 AAAGTATCGACACAAATGTATAAAGTGTT-GATACATTATGTAGACCTATTTTCTCATAAAACCG
*
1262065 GTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTTTTGGTCTCGATGTTTT
65 GTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTTCTGGTCTCGATGTTTT
* * * *
1262130 TGGGATCGATACTTGTTATAAATGTATCGACATTTTATACGTGCACATAGTTTGGAAATTCATTA
130 TGGGATCGATACTTGTTATAAATGTATCGAAACTTTATGCGTGCACATAGTTTGGCAATTCATTA
1262195 TGGACA-
195 TGGACAT
* * * * * * * *
1262201 AAAGTATCGACACGAATTTAAAAAGAGTCGACACATTATGTTA-ACCTATTTTCT-ATTTACACC
1 AAAGTATCGACACAAATGTATAAAGTGTTGATACATTATG-TAGACCTATTTTCTCA-TAAAACC
* * * * * *
1262264 AGTAAATTTCAACCGGTTACATTGTAAATTGACATATTGCATTATAATTTCTGGTCTCGATGTAT
64 GGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTTCTGGTCTCGATGTTT
* * * * * * *
1262329 TTGGGGTTGATACTTTTTATAAATGTATCGATACTTTATTCGTGGACATCGTTTGGC-ATTCATT
129 TTGGGATCGATACTTGTTATAAATGTATCGAAACTTTATGCGTGCACATAGTTTGGCAATTCATT
1262393 ATGGACAT
194 ATGGACAT
* * * * **
1262401 AAAGTATTGAAACAATTGTATAAAGTGTTAATACATTATGTAGACCTATTTTCTCATAAAAGTGG
1 AAAGTATCGACACAAATGTATAAAGTGTTGATACATTATGTAGACCTATTTTCTCATAAAACCGG
* *
1262466 TAAATTTAAACCGATTACATTGTAAAGTGACCTATTACTTTATAATTT-TCGGTCTCGATGTTTT
66 TAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTTCT-GGTCTCGATGTTTT
*
1262530 TGGGATCGATACTTGTTATAAATGTATCGAAACTTTATGCGTGCACATAGTTTGGGAATTCATTA
130 TGGGATCGATACTTGTTATAAATGTATCGAAACTTTATGCGTGCACATAGTTTGGCAATTCATTA
* *
1262595 TCGACAA
195 TGGACAT
* * *
1262602 AAAGTATCGACACAAATGTATAAAGTGTTGATACATTATGTAGACCTATTTTCTCATGAAACTGA
1 AAAGTATCGACACAAATGTATAAAGTGTTGATACATTATGTAGACCTATTTTCTCATAAAACCGG
* * *
1262667 TAAATTTAAACTGGTTACATTGTAAAGTGACCTATTACATTATAA-TTATGTGTTTCGATGTTTT
66 TAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTTCTG-GTCTCGATGTTTT
* * * * * * * * *
1262731 TAGTATCGACACTTGTTATAAATGTATCGACACTTTGT-CGTGCACTTGGTTTGGAAAATACATT
130 TGGGATCGATACTTGTTATAAATGTATCGAAACTTTATGCGTGCACATAGTTTGG-CAATTCATT
*
1262795 ATGGACAA
194 ATGGACAT
1262803 AAAGTATCGACA
1 AAAGTATCGACA
1262815 TTTGTTAAAT
Statistics
Matches: 698, Mismatches: 101, Indels: 29
0.84 0.12 0.04
Matches are distributed among these distances:
199 23 0.03
200 474 0.68
201 201 0.29
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (201 bp):
AAAGTATCGACACAAATGTATAAAGTGTTGATACATTATGTAGACCTATTTTCTCATAAAACCGG
TAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTTCTGGTCTCGATGTTTTT
GGGATCGATACTTGTTATAAATGTATCGAAACTTTATGCGTGCACATAGTTTGGCAATTCATTAT
GGACAT
Found at i:1262540 original size:400 final size:401
Alignment explanation
Indices: 1261799--1262766 Score: 1428
Period size: 400 Copynumber: 2.4 Consensus size: 401
1261789 GCGTAATTTT
* * *
1261799 AAAAAGTATCGACA-GAAAATTAAAAAGTGTCAACACATTATGTTTACCTATTTTCTATTTACAC
1 AAAAAGTATCGACACG-AATTTAAAAAGTGTCGACACATTATGTTAACCTATTTTCTATTTACAC
*
1261863 CGGTAAATTTCAACCGGTTACATTGTAAATTGACCTATTACATTATAATTTCTGGTCTCGATGTA
65 CAGTAAATTTCAACCGGTTACATTGTAAATTGACCTATTACATTATAATTTCTGGTCTCGATGTA
1261928 TTTGGGGTCGATACTTTTTATAAATGTATCGAAACTTTATGCGTGGACATCGTTTGGCAATCATT
130 TTTGGGGTCGATACTTTTTATAAATGTATCGAAACTTTATGCGTGGACATCGTTTGGCAATCATT
* *
1261993 ATGAACATAAAGTATTGACACAAATGTATAAAGTTTCGATACATTATGTAGACCTATTTTCTCAT
195 ATGAACATAAAGTATTGAAACAAATGTATAAAGTTTCAATACATTATGTAGACCTATTTTCTCAT
* *
1262058 AAAACCGGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTTTTGGTCTCG
260 AAAACCGGTAAATTTAAACCGATTACATTGTAAAGTGACCTATTACATTATAATTTTCGGTCTCG
* *
1262123 ATGTTTTTGGGATCGATACTTGTTATAAATGTATCGACATTTTATACGTGCACATAGTTTGGAAA
325 ATGTTTTTGGGATCGATACTTGTTATAAATGTATCGAAACTTTATACGTGCACATAGTTTGGAAA
*
1262188 TTCATTATGGAC
390 TTCATTATCGAC
*
1262200 -AAAAGTATCGACACGAATTTAAAAAGAGTCGACACATTATGTTAACCTATTTTCTATTTACACC
1 AAAAAGTATCGACACGAATTTAAAAAGTGTCGACACATTATGTTAACCTATTTTCTATTTACACC
* *
1262264 AGTAAATTTCAACCGGTTACATTGTAAATTGACATATTGCATTATAATTTCTGGTCTCGATGTAT
66 AGTAAATTTCAACCGGTTACATTGTAAATTGACCTATTACATTATAATTTCTGGTCTCGATGTAT
* * * *
1262329 TTGGGGTTGATACTTTTTATAAATGTATCGATACTTTATTCGTGGACATCGTTTGGCATTCATTA
131 TTGGGGTCGATACTTTTTATAAATGTATCGAAACTTTATGCGTGGACATCGTTTGGCAATCATTA
* *
1262394 TGGACATAAAGTATTGAAACAATTGTATAAAGTGTT-AATACATTATGTAGACCTATTTTCTCAT
196 TGAACATAAAGTATTGAAACAAATGTATAAAGT-TTCAATACATTATGTAGACCTATTTTCTCAT
** *
1262458 AAAAGTGGTAAATTTAAACCGATTACATTGTAAAGTGACCTATTACTTTATAATTTTCGGTCTCG
260 AAAACCGGTAAATTTAAACCGATTACATTGTAAAGTGACCTATTACATTATAATTTTCGGTCTCG
* *
1262523 ATGTTTTTGGGATCGATACTTGTTATAAATGTATCGAAACTTTATGCGTGCACATAGTTTGGGAA
325 ATGTTTTTGGGATCGATACTTGTTATAAATGTATCGAAACTTTATACGTGCACATAGTTTGGAAA
1262588 TTCATTATCGAC
390 TTCATTATCGAC
* * * * * *
1262600 AAAAAGTATCGACACAAATGTATAAAGTGTTGATACATTATG-TAGACCTATTTTCTCA-TGA-A
1 AAAAAGTATCGACACGAATTTAAAAAGTGTCGACACATTATGTTA-ACCTATTTTCT-ATTTACA
* * * * * * *
1262662 ACTGATAAATTTAAACTGGTTACATTGTAAAGTGACCTATTACATTATAA-TTATGTGTTTCGAT
64 CCAG-TAAATTTCAACCGGTTACATTGTAAATTGACCTATTACATTATAATTTCTG-GTCTCGAT
* * ** * * *
1262726 GTTTTTAGTATCGACACTTGTTATAAATGTATCGACACTTT
127 GTATTTGGGGTCGATACTTTTTATAAATGTATCGAAACTTT
1262767 GTCGTGCACT
Statistics
Matches: 511, Mismatches: 49, Indels: 14
0.89 0.09 0.02
Matches are distributed among these distances:
400 379 0.74
401 131 0.26
402 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.38
Consensus pattern (401 bp):
AAAAAGTATCGACACGAATTTAAAAAGTGTCGACACATTATGTTAACCTATTTTCTATTTACACC
AGTAAATTTCAACCGGTTACATTGTAAATTGACCTATTACATTATAATTTCTGGTCTCGATGTAT
TTGGGGTCGATACTTTTTATAAATGTATCGAAACTTTATGCGTGGACATCGTTTGGCAATCATTA
TGAACATAAAGTATTGAAACAAATGTATAAAGTTTCAATACATTATGTAGACCTATTTTCTCATA
AAACCGGTAAATTTAAACCGATTACATTGTAAAGTGACCTATTACATTATAATTTTCGGTCTCGA
TGTTTTTGGGATCGATACTTGTTATAAATGTATCGAAACTTTATACGTGCACATAGTTTGGAAAT
TCATTATCGAC
Found at i:1267673 original size:18 final size:18
Alignment explanation
Indices: 1267650--1267705 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
1267640 TTTCTATCTC
1267650 CTCATTCTTCTTCTTCTT
1 CTCATTCTTCTTCTTCTT
*
1267668 CTCATTCTCCTTC-TCATT
1 CTCATTCTTCTTCTTC-TT
*
1267686 C-CATTTCTTCTTCTTATT
1 CTCA-TTCTTCTTCTTCTT
1267704 CT
1 CT
1267706 TTTTCTCCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
17 4 0.13
18 26 0.84
19 1 0.03
ACGTcount: A:0.09, C:0.34, G:0.00, T:0.57
Consensus pattern (18 bp):
CTCATTCTTCTTCTTCTT
Found at i:1267710 original size:18 final size:18
Alignment explanation
Indices: 1267654--1267711 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
1267644 TATCTCCTCA
*
1267654 TTCTTCTTCTTCTTCTCA-
1 TTCTTCTTCTTATTCT-AT
* * *
1267672 TTCTCCTTCTCATTCCAT
1 TTCTTCTTCTTATTCTAT
*
1267690 TTCTTCTTCTTATTCTTT
1 TTCTTCTTCTTATTCTAT
1267708 TTCT
1 TTCT
1267712 CCTCCTCCCT
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
17 1 0.03
18 30 0.97
ACGTcount: A:0.07, C:0.31, G:0.00, T:0.62
Consensus pattern (18 bp):
TTCTTCTTCTTATTCTAT
Found at i:1270255 original size:26 final size:25
Alignment explanation
Indices: 1270226--1270282 Score: 64
Period size: 23 Copynumber: 2.3 Consensus size: 25
1270216 ATTATCAAAC
*
1270226 ATAATAACATATTAGGTAGAGCTTAT
1 ATAATAA-ATAATAGGTAGAGCTTAT
* *
1270252 ATAAT--GTAATAGGTAGCGCTTAT
1 ATAATAAATAATAGGTAGAGCTTAT
1270275 ATAATAAA
1 ATAATAAA
1270283 ATAGGCATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
23 20 0.80
26 5 0.20
ACGTcount: A:0.44, C:0.07, G:0.16, T:0.33
Consensus pattern (25 bp):
ATAATAAATAATAGGTAGAGCTTAT
Found at i:1270285 original size:23 final size:23
Alignment explanation
Indices: 1270238--1270287 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
1270228 AATAACATAT
**
1270238 TAGGTAGAGCTTATATAATGTAA
1 TAGGTAGAGCTTATATAATAAAA
*
1270261 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGAGCTTATATAATAAAA
1270284 TAGG
1 TAGG
1270288 CATTTAACTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.06, G:0.22, T:0.32
Consensus pattern (23 bp):
TAGGTAGAGCTTATATAATAAAA
Found at i:1270347 original size:87 final size:87
Alignment explanation
Indices: 1270201--1270363 Score: 281
Period size: 87 Copynumber: 1.9 Consensus size: 87
1270191 TATGTTATAT
*
1270201 CATTTAACCGAAAATATTATCAAACATAATAACATATTAGGTAGAGCTTATATAATGTAATAGGT
1 CATTTAACCGAAAATATTATCAAACACAATAACATATTAGGTAGAGCTTATATAATGTAATAGGT
1270266 AGCGCTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGG
* ** *
1270288 CATTTAACTGAAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
1 CATTTAACCGAAAATATTATCAAACACAATAACATATTAGGTAGAGCTTATATAATGTAATAGGT
1270353 AGCGCTTATAT
66 AGCGCTTATAT
1270364 TGACCTATTT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 71 1.00
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (87 bp):
CATTTAACCGAAAATATTATCAAACACAATAACATATTAGGTAGAGCTTATATAATGTAATAGGT
AGCGCTTATATAATAAAATAGG
Found at i:1270847 original size:187 final size:180
Alignment explanation
Indices: 1270515--1270868 Score: 447
Period size: 180 Copynumber: 1.9 Consensus size: 180
1270505 ACTTTCATTT
* * * *
1270515 TGGAAAAAAGTATCGATACATATTTAAAGAGTGTCGATACATAATGTAGACATATTTTCTAATTA
1 TGGAAAAAAGTATCCATACAAATTTAAAAAGTGTCGATACATAATGTAGACATATTCTCTAATTA
* * * **
1270580 ACTGGTATATTTTTACCGGTTACATGGTAACCCGTTACATAATAATTATCGGTTTCAATGTTTTG
66 ACCGGTATATTTCTACCGGTTACATGGTAACCCATTACATAATAATTATCGGTCACAATGTTTTG
*
1270645 GGATCGATACTTTTTATAAATGTATCGAAAGTTTATGTGTACACCTCGTC
131 GGATCGATACTTTTTATAAATGTATCGAAACTTTATGTGTACACCTCGTC
* * * * * * *
1270695 TGGAGAAATGTATCCATACAAATTTAAAAAGTGTCGATACTTTATGTTGACCTATTCTCTCATTA
1 TGGAAAAAAGTATCCATACAAATTTAAAAAGTGTCGATACATAATGTAGACATATTCTCTAATTA
* * * *
1270760 ACCCGGTATATTTCTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTCACGAT
66 A-CCGGTATATTTCTACCGGTTACATGGT--A---ACCCATTACATAATAATTATCGGTCACAAT
*
1270825 GTTTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATG
125 G-TTTTGGGATCGATACTTTTTATAAATGTATCGAAACTTTATG
1270869 CGTGTCTGTC
Statistics
Matches: 145, Mismatches: 22, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
180 55 0.38
181 24 0.17
183 1 0.01
186 25 0.17
187 40 0.28
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.39
Consensus pattern (180 bp):
TGGAAAAAAGTATCCATACAAATTTAAAAAGTGTCGATACATAATGTAGACATATTCTCTAATTA
ACCGGTATATTTCTACCGGTTACATGGTAACCCATTACATAATAATTATCGGTCACAATGTTTTG
GGATCGATACTTTTTATAAATGTATCGAAACTTTATGTGTACACCTCGTC
Found at i:1275176 original size:199 final size:200
Alignment explanation
Indices: 1274438--1275380 Score: 1236
Period size: 200 Copynumber: 4.7 Consensus size: 200
1274428 ATGATTTTAA
* * * * * * * *
1274438 AAAGTGTCGACACGAATTTAAAAAGTGTCGACACATTATGTTGACCTATTTTCT-ATTTACACCG
1 AAAGTATCGACACAAATGTATAAAGTGTCGATACATTATGTAGACCTATTTTCTCA-TAAAACCG
* * *
1274502 ATAAATTTTAACCGGTTACATTGTAAATTGACCTATTACATTATAATTTTCGGTCTCGATGTATT
65 -TAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTTTCTGTCTCGATGT-TT
* * * *
1274567 TAGGG-TCGATACTTTTTATAAATGT-TCGACACTTTATGCGTGGACATCGTTT-GGCATACATT
128 TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACATAGTTTGGGCATTCATT
1274629 ATGGACAT
193 ATGGACAT
* *
1274637 AAAGTATCGGCACAAACGTATAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCAG
1 AAAGTATCGACACAAATGTATAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACC-G
*
1274702 TAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTTTCGGTCTCGATGTTTTT
65 TAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTTTCTGTCTCGATGTTTTT
* * *
1274767 GGGATTGATACTTGTTATAAATGTATCGACACTTTATGCGTGCACATAGTTTGGGGATTCATTAT
130 GGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACATAGTTTGGGCATTCATTAT
1274832 GGACA-
195 GGACAT
* * * * * * *
1274837 AAAGTATCGACACGAATTTAAAAAGTGTCGACACATTATGTTGACCTATTTTCT-ATTTACACCG
1 AAAGTATCGACACAAATGTATAAAGTGTCGATACATTATGTAGACCTATTTTCTCA-TAAAACCG
* * * *
1274901 ATAAATTTCAACTGGTTACATTGTAAATTGACCTATTACATTATAA-TTTCTGGTCTCGATGTAT
65 -TAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTTTCT-GTCTCGATGTTT
* * * * *
1274965 TTGGGGTCGATACTTTTTATAAATGTATTGACACTTTATGCGTGGACATTGTTT-GGCATTCTTT
128 TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACATAGTTTGGGCATTCATT
1275029 ATGGACAT
193 ATGGACAT
* *
1275037 AAAGTATTGACACAAATGTATAAAGTGTTGATACATTATGTAGACCTATTTTCTCATAAAACCGT
1 AAAGTATCGACACAAATGTATAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGT
* *
1275102 AAATTTAAACCGGTTACATTTTCAAGTGACCTATTACATTATAATTTTCTGTCTCGATGTTTTTG
66 AAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTTTCTGTCTCGATGTTTTTG
* * * * *
1275167 GGATCGATACTTGTTATAAATGTATCGACACTTTATGAGTGCACATAATTTGGGAATTCATTATC
131 GGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACATAGTTTGGGCATTCATTATG
*
1275232 GACAA
196 GACAT
* *
1275237 AAAGTATCGACACAAATGTATAAATTGTCGATACATTATGTAGACCTATTTTCTCATAAAACTAG
1 AAAGTATCGACACAAATGTATAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAAC-CG
* * * * * *
1275302 TAAATTTAAATCGGTTACATTGTAAAGTGACCTATTACATAATAATTATGTGTTTCTATGTTTTT
65 TAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTTTCTGTCTCGATGTTTTT
* * *
1275367 AGTATCGACACTTT
130 GGGATCGATACTTT
1275381 GTCGTGCACT
Statistics
Matches: 648, Mismatches: 83, Indels: 24
0.86 0.11 0.03
Matches are distributed among these distances:
198 6 0.01
199 247 0.38
200 311 0.48
201 84 0.13
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (200 bp):
AAAGTATCGACACAAATGTATAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGT
AAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTTTCTGTCTCGATGTTTTTG
GGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACATAGTTTGGGCATTCATTATG
GACAT
Found at i:1275182 original size:399 final size:399
Alignment explanation
Indices: 1274436--1275348 Score: 1449
Period size: 399 Copynumber: 2.3 Consensus size: 399
1274426 AAATGATTTT
*
1274436 AAAAAGTGTCGACACGAATTTAAAAAGTGTCGACACATTATGTTGACCTATTTTCTATTTACACC
1 AAAAAGTATCGACACGAATTTAAAAAGTGTCGACACATTATGTTGACCTATTTTCTATTTACACC
*
1274501 GATAAATTTTAACCGGTTACATTGTAAATTGACCTATTACATTATAATTTTCGGTCTCGATGTAT
66 GATAAA-TTTAACTGGTTACATTGTAAATTGACCTATTACATTATAATTTTCGGTCTCGATGTAT
1274566 TTAGGGTCGATACTTTTTATAAATGTTCGACACTTTATGCGTGGACATCGTTTGGCATACATTAT
130 TTAGGGTCGATACTTTTTATAAATGTTCGACACTTTATGCGTGGACATCGTTTGGCATACATTAT
*
1274631 GGACATAAAGTATCGGCACAAACGTATAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAA
195 GGACATAAAGTATCGACACAAACGTATAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAA
1274696 AACCAGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTTTCGGTCTCGAT
260 AACCAGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTTTCGGTCTCGAT
* * * *
1274761 GTTTTTGGGATTGATACTTGTTATAAATGTATCGACACTTTATGCGTGCACATAGTTTGGGGATT
325 GTTTTTGGGATCGATACTTGTTATAAATGTATCGACACTTTATGAGTGCACATAATTTGGGAATT
*
1274826 CATTATGGAC
390 CATTATCGAC
1274836 -AAAAGTATCGACACGAATTTAAAAAGTGTCGACACATTATGTTGACCTATTTTCTATTTACACC
1 AAAAAGTATCGACACGAATTTAAAAAGTGTCGACACATTATGTTGACCTATTTTCTATTTACACC
1274900 GATAAATTTCAACTGGTTACATTGTAAATTGACCTATTACATTATAA-TTTCTGGTCTCGATGTA
66 GATAAATTT-AACTGGTTACATTGTAAATTGACCTATTACATTATAATTTTC-GGTCTCGATGTA
* * * * *
1274964 TTTGGGGTCGATACTTTTTATAAATGTATTGACACTTTATGCGTGGACATTGTTTGGCATTCTTT
129 TTTAGGGTCGATACTTTTTATAAATGT-TCGACACTTTATGCGTGGACATCGTTTGGCATACATT
* * *
1275029 ATGGACATAAAGTATTGACACAAATGTATAAAGTGTTGATACATTATGTAGACCTATTTTCTCAT
193 ATGGACATAAAGTATCGACACAAACGTATAAAGTGTCGATACATTATGTAGACCTATTTTCTCAT
* * *
1275094 AAAACC-GTAAATTTAAACCGGTTACATTTTCAAGTGACCTATTACATTATAATTTTCTGTCTCG
258 AAAACCAGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTTTCGGTCTCG
1275158 ATGTTTTTGGGATCGATACTTGTTATAAATGTATCGACACTTTATGAGTGCACATAATTTGGGAA
323 ATGTTTTTGGGATCGATACTTGTTATAAATGTATCGACACTTTATGAGTGCACATAATTTGGGAA
1275223 TTCATTATCGAC
388 TTCATTATCGAC
* * * * * * * *
1275235 AAAAAGTATCGACACAAATGTATAAATTGTCGATACATTATGTAGACCTATTTTCTCA--TAAAA
1 AAAAAGTATCGACACGAATTTAAAAAGTGTCGACACATTATGTTGACCTATTTTCT-ATTTACAC
* * * *
1275298 CTAGTAAATTTAAATCGGTTACATTGTAAAGTGACCTATTACATAATAATT
65 CGA-TAAATTTAACT-GGTTACATTGTAAATTGACCTATTACATTATAATT
1275349 ATGTGTTTCT
Statistics
Matches: 474, Mismatches: 31, Indels: 15
0.91 0.06 0.03
Matches are distributed among these distances:
398 7 0.01
399 278 0.59
400 187 0.39
401 2 0.00
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (399 bp):
AAAAAGTATCGACACGAATTTAAAAAGTGTCGACACATTATGTTGACCTATTTTCTATTTACACC
GATAAATTTAACTGGTTACATTGTAAATTGACCTATTACATTATAATTTTCGGTCTCGATGTATT
TAGGGTCGATACTTTTTATAAATGTTCGACACTTTATGCGTGGACATCGTTTGGCATACATTATG
GACATAAAGTATCGACACAAACGTATAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAA
ACCAGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTTTCGGTCTCGATG
TTTTTGGGATCGATACTTGTTATAAATGTATCGACACTTTATGAGTGCACATAATTTGGGAATTC
ATTATCGAC
Found at i:1275838 original size:30 final size:30
Alignment explanation
Indices: 1275802--1275860 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
1275792 AGTGGAGCAA
*
1275802 AAATTTACATTTAAATTCAAACTCAAATTG
1 AAATTTAAATTTAAATTCAAACTCAAATTG
*
1275832 AAATTTAAATTTAAATTCAAACTCTAATT
1 AAATTTAAATTTAAATTCAAACTCAAATT
1275861 ATAAATGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.39
Consensus pattern (30 bp):
AAATTTAAATTTAAATTCAAACTCAAATTG
Found at i:1278180 original size:19 final size:19
Alignment explanation
Indices: 1278152--1278200 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
1278142 TATTTATACA
*
1278152 ACCTAAAATATCATTTTCT
1 ACCTATAATATCATTTTCT
*
1278171 ACCTATAATATCATTTTTT
1 ACCTATAATATCATTTTCT
1278190 ACCTATAATAT
1 ACCTATAATAT
1278201 TAAATAAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.37, C:0.18, G:0.00, T:0.45
Consensus pattern (19 bp):
ACCTATAATATCATTTTCT
Found at i:1279078 original size:182 final size:182
Alignment explanation
Indices: 1278625--1279280 Score: 951
Period size: 182 Copynumber: 3.6 Consensus size: 182
1278615 TACGCGTACT
* * * * *
1278625 TATTAAAGTATCGACACTTTCAACGTATCCGGTAGCGCTTTACCGGTTTTGTCATTTTGAGACCG
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGTTTTACCAGTTTTGTCATTTCGAGACAG
* * *
1278690 GTTTTGTCATAATTTTACCTGTTATATTTTTATGGATCGATACA-TTTTTTAAAGTATCAACACT
66 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACACT
1278754 TTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
131 TTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* * ** * *
1278806 TAATAAATTATCGACACTTTCAACATATCC-GTTTCTTTTTACCAGTTTTGTCATTTCGAGACAT
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGTTTTACCAGTTTTGTCATTTCGAGACAG
*
1278870 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTTAAGTATCGACACT
66 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACACT
*
1278935 TTATAGGCGCTATAACTTCTTATCTTTTAAATTCCAAAAGTGTCGATACTTA
131 TTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* * * *
1278987 TTTTAAAGTATCGACACTTTCAACATATCCGGTAGTGTTTTACCGGTTTTGTCATTTTGAGACAG
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGTTTTACCAGTTTTGTCATTTCGAGACAG
* ** *** *
1279052 ATTTTGTCATATTTTTAGTTGTTATATTGTTATGGATCGATACATTTACATAAAGTGTCGACACT
66 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACACT
* *
1279117 TTTTAGGCACTATAACTTCTTCTCTTTTAAATT-CAGAAAGTGTCGATACTTA
131 TTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCA-AAAGTGTCGATACTTA
* * * *
1279169 TATTAAATTATCGACACTTTCAACATATTCGGTAGCGTTTTACCAGTTTTGTCATTTCGAGGCCG
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGTTTTACCAGTTTTGTCATTTCGAGACAG
* * *
1279234 GTTTTGTCATATTTTTACCTGTAATATTGCTATGGAGCGATAC-TTTT
66 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTT
1279281 GTCATTTGTA
Statistics
Matches: 420, Mismatches: 52, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
180 68 0.16
181 128 0.30
182 224 0.53
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.43
Consensus pattern (182 bp):
TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGTTTTACCAGTTTTGTCATTTCGAGACAG
GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACACT
TTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
Found at i:1280913 original size:46 final size:46
Alignment explanation
Indices: 1280846--1281062 Score: 389
Period size: 46 Copynumber: 4.7 Consensus size: 46
1280836 TTATTCGTTA
* *
1280846 ATTTTAGTTGTGGTATCCTTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* *
1280892 ATTTTAGTTGTGACATCCTTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
*
1280938 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTGATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
1280984 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
1281030 ATTTTAGTTATGGCATCCTTTCATGCCTTAATG
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATG
1281063 ATAACATATT
Statistics
Matches: 165, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 165 1.00
ACGTcount: A:0.19, C:0.22, G:0.14, T:0.44
Consensus pattern (46 bp):
ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
Found at i:1280915 original size:26 final size:25
Alignment explanation
Indices: 1280876--1281055 Score: 174
Period size: 26 Copynumber: 7.6 Consensus size: 25
1280866 TCATGCCTTA
1280876 ATGCATCCTTTCATGCATTTTAGTT
1 ATGCATCCTTTCATGCATTTTAGTT
* *
1280901 GTGACATCCTTTCATGC--CTTA---
1 ATG-CATCCTTTCATGCATTTTAGTT
1280922 ATGCATCCTTTCATGCATTTTAGTT
1 ATGCATCCTTTCATGCATTTTAGTT
*
1280947 ATGGCATCCTTTCATGC--CTTA---
1 AT-GCATCCTTTCATGCATTTTAGTT
*
1280968 ATGCATCCTTTGATGCATTTTAGTT
1 ATGCATCCTTTCATGCATTTTAGTT
*
1280993 ATGGCATCCTTTCATGC--CTTA---
1 AT-GCATCCTTTCATGCATTTTAGTT
1281014 ATGCATCCTTTCATGCATTTTAGTT
1 ATGCATCCTTTCATGCATTTTAGTT
1281039 ATGGCATCCTTTCATGC
1 AT-GCATCCTTTCATGC
1281056 CTTAATGATA
Statistics
Matches: 126, Mismatches: 10, Indels: 37
0.73 0.06 0.21
Matches are distributed among these distances:
20 40 0.32
21 6 0.05
22 9 0.07
24 9 0.07
25 8 0.06
26 54 0.43
ACGTcount: A:0.19, C:0.23, G:0.14, T:0.43
Consensus pattern (25 bp):
ATGCATCCTTTCATGCATTTTAGTT
Found at i:1287768 original size:46 final size:46
Alignment explanation
Indices: 1287701--1288049 Score: 449
Period size: 46 Copynumber: 7.7 Consensus size: 46
1287691 TTATTTGTTA
* *
1287701 ATTTTAGTTGTGGCATCCTTTCATGCCTTAATGCATCCTTTCATGT
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * *
1287747 ATTTTAGTTATGGCACCCTTTCATGCCCTAATGTATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * * **
1287793 ATTTTAGTTATGGCATGCTTTCATGCCTTAATTCAT--TATTCGTTA
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCT-TTCATGC
** * *
1287838 ATTTTAGTTGCGGCATTCTTTCATTCCTTAATGCATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * *
1287884 ATTTTAGTTATGGCATCCTTTCAT-CCTTAATTCAT--TAT-GTGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * *
1287926 ATTTTACTTATGGCATCCTTTCACGCCTTAATGCATCATTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
1287972 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* *
1288018 ATTTTAGTTGTGGCATTCTTTCATGCCTTAAT
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAAT
1288050 TATAACATAT
Statistics
Matches: 259, Mismatches: 37, Indels: 14
0.84 0.12 0.05
Matches are distributed among these distances:
42 25 0.10
43 12 0.05
44 1 0.00
45 47 0.18
46 173 0.67
47 1 0.00
ACGTcount: A:0.20, C:0.22, G:0.13, T:0.45
Consensus pattern (46 bp):
ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
Found at i:1287961 original size:20 final size:20
Alignment explanation
Indices: 1287938--1288017 Score: 79
Period size: 20 Copynumber: 3.7 Consensus size: 20
1287928 TTTACTTATG
*
1287938 GCATCCTTTCACGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
* *
1287958 GCATCATTTCATGCATTTTAGTTAT
1 GCATCCTTTCATGC--CTTA---AT
1287983 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
1288004 GCATCCTTTCATGC
1 GCATCCTTTCATGC
1288018 ATTTTAGTTG
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
20 26 0.53
21 2 0.04
22 3 0.06
24 3 0.06
25 2 0.04
26 13 0.27
ACGTcount: A:0.20, C:0.28, G:0.12, T:0.40
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:1287994 original size:26 final size:25
Alignment explanation
Indices: 1287923--1288043 Score: 91
Period size: 26 Copynumber: 5.1 Consensus size: 25
1287913 ATTCATTATG
1287923 TGCATTTTACTTATGGCATCCTTTCA
1 TGCATTTTA-TTATGGCATCCTTTCA
* * *
1287949 CGC--CTTA--AT-GCATCATTTCA
1 TGCATTTTATTATGGCATCCTTTCA
1287969 TGCATTTTAGTTATGGCATCCTTTCA
1 TGCATTTTA-TTATGGCATCCTTTCA
*
1287995 TGC--CTTA--AT-GCATCCTTTCA
1 TGCATTTTATTATGGCATCCTTTCA
* *
1288015 TGCATTTTAGTTGTGGCATTCTTTCA
1 TGCATTTTA-TTATGGCATCCTTTCA
1288041 TGC
1 TGC
1288044 CTTAATTATA
Statistics
Matches: 73, Mismatches: 10, Indels: 24
0.68 0.09 0.22
Matches are distributed among these distances:
20 26 0.36
21 4 0.05
22 6 0.08
24 6 0.08
25 3 0.04
26 28 0.38
ACGTcount: A:0.19, C:0.23, G:0.14, T:0.44
Consensus pattern (25 bp):
TGCATTTTATTATGGCATCCTTTCA
Found at i:1289895 original size:70 final size:69
Alignment explanation
Indices: 1289701--1289908 Score: 294
Period size: 69 Copynumber: 3.0 Consensus size: 69
1289691 CAAACACAAA
* * *
1289701 TGTTTCCAGTTCCACTTATATTTAGAAAGGCAACATCATTCCCTTTGCCAAGTAATTAATATTAT
1 TGTTTCCAATTCCACTTATATTTAGAAGGGCAACATCATT-CCTTTCCCAAGTAATTAATATTAT
1289766 ATTAT
65 ATTAT
* *
1289771 TGTTT--AATTCCCACTTTTATTTAGAAGGGCAACATCATTTCCTTTTCCAAGTAATTAATATTA
1 TGTTTCCAATT-CCACTTATATTTAGAAGGGCAACATCA-TTCCTTTCCCAAGTAATTAATATTA
1289834 TATTAT
64 TATTAT
* * *
1289840 TGTTTCCAATTCCACCTATACTTAGAAGGGCAACATCATTCACTTCCCCAAGTAATTAATATTAT
1 TGTTTCCAATTCCACTTATATTTAGAAGGGCAACATCATTC-CTTTCCCAAGTAATTAATATTAT
1289905 ATTA
65 ATTA
1289909 GTGTAAAGTG
Statistics
Matches: 124, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
68 3 0.02
69 61 0.49
70 56 0.45
71 4 0.03
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.40
Consensus pattern (69 bp):
TGTTTCCAATTCCACTTATATTTAGAAGGGCAACATCATTCCTTTCCCAAGTAATTAATATTATA
TTAT
Found at i:1290722 original size:45 final size:45
Alignment explanation
Indices: 1290661--1290897 Score: 366
Period size: 45 Copynumber: 5.3 Consensus size: 45
1290651 TTATTCATTA
* *
1290661 ATTTCATTTATGGCATCCTTTCATGCCTTTTATGCACCATTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* *
1290706 ATTTTATTTATAGCATCCTTTCATGCCTTTAATGCACCGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* *
1290751 ATTTCATTTATGGTATACTTTCATGCCTTTAATGCACCGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* *
1290796 ATTTCATTTATGGCATCCTCTCATGCCTTTAATGCACCGTTATGT
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* ** *
1290841 ATTTAATTTATGGCATCCTAACATGCCTTTAATGCATCGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
1290886 ATTTCATTTATG
1 ATTTCATTTATG
1290898 TAATGAAAAT
Statistics
Matches: 174, Mismatches: 18, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 174 1.00
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (45 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
Found at i:1291430 original size:94 final size:94
Alignment explanation
Indices: 1291264--1291462 Score: 237
Period size: 94 Copynumber: 2.1 Consensus size: 94
1291254 CTTACCATTA
* *
1291264 TATCGATACGT-CTATACTATGGTACAGATACCCCTTTTAGTATCGATACCATTTCTAAATTCTG
1 TATCGATAC-TACTATACTATGGTACAGATACCCCTTTCAGTATCGATACCATTTCTAAATTATG
1291328 TAATTCATGGTATTGATA-TATTTCTCTCAG
65 TAATTCATGGTATTGATACT-TTTCTCTCAG
* * * **
1291358 TATGGATACTACTATACTATGGTACCGATACTCCCTTTCAGTATCGATATCATTT-TGGCATTAT
1 TATCGATACTACTATACTATGGTACAGATAC-CCCTTTCAGTATCGATACCATTTCT-AAATTAT
* *
1291422 AG-AA-TCATGGTATTGATACTTTTCTTTTAG
64 -GTAATTCATGGTATTGATACTTTTCTCTCAG
1291452 TATCGATACTA
1 TATCGATACTA
1291463 ATTGCATCAA
Statistics
Matches: 90, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
93 1 0.01
94 60 0.67
95 28 0.31
96 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.41
Consensus pattern (94 bp):
TATCGATACTACTATACTATGGTACAGATACCCCTTTCAGTATCGATACCATTTCTAAATTATGT
AATTCATGGTATTGATACTTTTCTCTCAG
Found at i:1304071 original size:45 final size:45
Alignment explanation
Indices: 1304020--1304208 Score: 288
Period size: 45 Copynumber: 4.2 Consensus size: 45
1304010 TTTTTCATTA
*
1304020 ATTTCATTTATGTCATCCTTTCATGCCTTTAATGCACCGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* * *
1304065 ATTTCATTTATGGTATCCTTTCATGTCTTTAATGCATCGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* *
1304110 ATTTCATTTATGGCATCATTTCATGCCTTTAATGCACTGTTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
* * * *
1304155 ATTTCATTTATGGCATCCTTTCAAGCATTTAACGCACCATTATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
1304200 ATTTCATTT
1 ATTTCATTT
1304209 GTGTAATGAA
Statistics
Matches: 129, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 129 1.00
ACGTcount: A:0.22, C:0.21, G:0.12, T:0.45
Consensus pattern (45 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGC
Found at i:1306311 original size:18 final size:18
Alignment explanation
Indices: 1306290--1306330 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1306280 AGGCATTTGA
1306290 TCCTCTGGAT-GTGCTTGT
1 TCCTCT-GATCGTGCTTGT
*
1306308 TCCTCTGCTCGTGCTTGT
1 TCCTCTGATCGTGCTTGT
1306326 TCCTC
1 TCCTC
1306331 GTGCTGTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.02, C:0.32, G:0.22, T:0.44
Consensus pattern (18 bp):
TCCTCTGATCGTGCTTGT
Found at i:1307923 original size:21 final size:21
Alignment explanation
Indices: 1307897--1307936 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1307887 CAGAAACCCA
*
1307897 ATGGGGTATCGATTCCCCTAC
1 ATGGGGAATCGATTCCCCTAC
*
1307918 ATGGGGAATCGGTTCCCCT
1 ATGGGGAATCGATTCCCCT
1307937 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.28, G:0.28, T:0.28
Consensus pattern (21 bp):
ATGGGGAATCGATTCCCCTAC
Found at i:1307965 original size:22 final size:23
Alignment explanation
Indices: 1307920--1307980 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
1307910 TCCCCTACAT
1307920 GGGGAATCGGTTCCCCTTCAAAG
1 GGGGAATCGGTTCCCCTTCAAAG
* *
1307943 GGGGAATTGGTTCCCCTTCAAGG
1 GGGGAATCGGTTCCCCTTCAAAG
* *
1307966 GGGGTATCGATTCCC
1 GGGGAATCGGTTCCC
1307981 TCTGCATTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.18, C:0.25, G:0.33, T:0.25
Consensus pattern (23 bp):
GGGGAATCGGTTCCCCTTCAAAG
Found at i:1307981 original size:22 final size:22
Alignment explanation
Indices: 1307899--1307980 Score: 76
Period size: 23 Copynumber: 3.7 Consensus size: 22
1307889 GAAACCCAAT
* * *
1307899 GGGGTATCGATTCCCCTAC-AT
1 GGGGAATCGATTCCCCTTCAAG
*
1307920 GGGGAATCGGTTCCCCTTCAAAG
1 GGGGAATCGATTCCCCTTC-AAG
* *
1307943 GGGGAATTGGTTCCCCTTCAAGG
1 GGGGAATCGATTCCCCTTCAA-G
*
1307966 GGGGTATCGATTCCC
1 GGGGAATCGATTCCC
1307981 TCTGCATTAA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
21 16 0.32
22 2 0.04
23 32 0.64
ACGTcount: A:0.18, C:0.26, G:0.30, T:0.26
Consensus pattern (22 bp):
GGGGAATCGATTCCCCTTCAAG
Found at i:1313581 original size:19 final size:20
Alignment explanation
Indices: 1313559--1313612 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
1313549 AGATTTTGGC
1313559 TTTTTTGGCTTTTTT-TTGT
1 TTTTTTGGCTTTTTTGTTGT
** *
1313578 TTTTTTACCTTTTTTGTTTT
1 TTTTTTGGCTTTTTTGTTGT
1313598 TTTTTTGG-TTTTTTG
1 TTTTTTGGCTTTTTTG
1313613 AAGAAAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 20 0.69
20 9 0.31
ACGTcount: A:0.02, C:0.06, G:0.13, T:0.80
Consensus pattern (20 bp):
TTTTTTGGCTTTTTTGTTGT
Found at i:1313583 original size:28 final size:28
Alignment explanation
Indices: 1313552--1313612 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
1313542 TTTTTTGAGA
* *
1313552 TTTTGGCTTTTTTGGCTTTTTTTTGTTT
1 TTTTGCCTTTTTTGGCTTTTTTTTGGTT
* **
1313580 TTTTACCTTTTTTGTTTTTTTTTTGGTT
1 TTTTGCCTTTTTTGGCTTTTTTTTGGTT
1313608 TTTTG
1 TTTTG
1313613 AAGAAAAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.02, C:0.07, G:0.15, T:0.77
Consensus pattern (28 bp):
TTTTGCCTTTTTTGGCTTTTTTTTGGTT
Found at i:1313986 original size:22 final size:23
Alignment explanation
Indices: 1313942--1313987 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
1313932 TAGGTGCTGG
1313942 AAACAAGATAAGAAATAAGATTA
1 AAACAAGATAAGAAATAAGATTA
1313965 AAACAAGATATAG-AA-AAGATTA
1 AAACAAGATA-AGAAATAAGATTA
1313987 A
1 A
1313988 GGAATTGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 8 0.36
23 12 0.55
24 2 0.09
ACGTcount: A:0.65, C:0.04, G:0.13, T:0.17
Consensus pattern (23 bp):
AAACAAGATAAGAAATAAGATTA
Found at i:1317419 original size:21 final size:21
Alignment explanation
Indices: 1317395--1317436 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1317385 GAGTTTGTTT
*
1317395 TCATTTTTCA-ATTTTGAAACA
1 TCATTTTT-ATATTTTAAAACA
1317416 TCATTTTTATATTTTAAAACA
1 TCATTTTTATATTTTAAAACA
1317437 ATTTCTCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.36, C:0.12, G:0.02, T:0.50
Consensus pattern (21 bp):
TCATTTTTATATTTTAAAACA
Found at i:1323776 original size:21 final size:21
Alignment explanation
Indices: 1323752--1323792 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1323742 GGTAAAAAAT
*
1323752 TACCTAAAACATTATTATTTC
1 TACCTAAAACATTAATATTTC
1323773 TACCTAAAACATTAATATTT
1 TACCTAAAACATTAATATTT
1323793 TTTAACAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.41
Consensus pattern (21 bp):
TACCTAAAACATTAATATTTC
Found at i:1324280 original size:105 final size:105
Alignment explanation
Indices: 1324078--1324390 Score: 522
Period size: 105 Copynumber: 3.0 Consensus size: 105
1324068 AGATAGGAGT
* **
1324078 AAAAGAAATGAAAA-CTTATTATACATCTCTATACTATAAAAATTTAAAACTAAAAAGTTAAATA
1 AAAAGAAAGGAAAATC-TATTATACATCTCTATACTATAAAAATTTAAAACT-TTAAGTTAAATA
1324142 AAAGATATCCTCTAACTTAAAAATCTAAATAAATTAAATTGA
64 AAAGATATCCTCTAACTTAAAAATCTAAATAAATTAAATTGA
* *
1324184 AAAAGAAAGGAAAATCTATTTTACATCTCTATACTATAAAAATTTAAAACTTTTAGTTAAATAAA
1 AAAAGAAAGGAAAATCTATTATACATCTCTATACTATAAAAATTTAAAACTTTAAGTTAAATAAA
1324249 AGATATCCTCTAACTTAAAAATCTAAATAAATTAAATTGA
66 AGATATCCTCTAACTTAAAAATCTAAATAAATTAAATTGA
*
1324289 AAAAGAAAGGAAAATCTATTATACATCT-TATACTATAAAAATTTAAAACTTTCAGTTAAATAAA
1 AAAAGAAAGGAAAATCTATTATACATCTCTATACTATAAAAATTTAAAACTTTAAGTTAAATAAA
* *
1324353 AGATATCCTCTAACTTAAAAATCTAAACAAATTGAATT
66 AGATATCCTCTAACTTAAAAATCTAAATAAATTAAATT
1324391 AATTCCAACT
Statistics
Matches: 197, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
104 71 0.36
105 78 0.40
106 47 0.24
107 1 0.01
ACGTcount: A:0.52, C:0.11, G:0.05, T:0.32
Consensus pattern (105 bp):
AAAAGAAAGGAAAATCTATTATACATCTCTATACTATAAAAATTTAAAACTTTAAGTTAAATAAA
AGATATCCTCTAACTTAAAAATCTAAATAAATTAAATTGA
Found at i:1325162 original size:17 final size:17
Alignment explanation
Indices: 1325140--1325200 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 17
1325130 AAAATATGAA
1325140 TATATTATTTATAAATT
1 TATATTATTTATAAATT
* *
1325157 TATATTTGATTAAATACAA-A
1 TATA-TT-ATT-TATA-AATT
*
1325177 TATATTATTTATGAATT
1 TATATTATTTATAAATT
1325194 TATATTA
1 TATATTA
1325201 AAATTCGAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 10
0.69 0.10 0.20
Matches are distributed among these distances:
16 2 0.06
17 13 0.38
18 5 0.15
19 5 0.15
20 7 0.21
21 2 0.06
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (17 bp):
TATATTATTTATAAATT
Found at i:1325172 original size:37 final size:38
Alignment explanation
Indices: 1325080--1325199 Score: 136
Period size: 37 Copynumber: 3.2 Consensus size: 38
1325070 TATTTAATGG
* * * *
1325080 TTTATATTTAATTAAAATTCAAATATGTTA-TTACAAA
1 TTTATATTTGATTAAAATACAAATATATTATTTATAAA
* ** **
1325117 TTTAAAGGTGATTAAAATATGAATATATTATTTATAAA
1 TTTATATTTGATTAAAATACAAATATATTATTTATAAA
*
1325155 TTTATATTTGATT-AAATACAAATATATTATTTATGAA
1 TTTATATTTGATTAAAATACAAATATATTATTTATAAA
1325192 TTTATATT
1 TTTATATT
1325200 AAAATTCGAA
Statistics
Matches: 67, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
37 51 0.76
38 16 0.24
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (38 bp):
TTTATATTTGATTAAAATACAAATATATTATTTATAAA
Found at i:1325243 original size:31 final size:33
Alignment explanation
Indices: 1325127--1325228 Score: 100
Period size: 37 Copynumber: 3.0 Consensus size: 33
1325117 TTTAAAGGTG
* *
1325127 ATTAAAATAT-GAATATATTATTTATAAATTTAT
1 ATTAAAAT-TCGAATACATTATTTATGAATTTAT
* * *
1325160 ATTTGATTAAATACAAATATATTATTTATGAATTTAT
1 A-TT-A--AAATTCGAATACATTATTTATGAATTTAT
1325197 ATTAAAATTCGAATACATTA-TTATGAATTTAT
1 ATTAAAATTCGAATACATTATTTATGAATTTAT
1325229 TTTTTATTCG
Statistics
Matches: 58, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
32 12 0.21
33 14 0.24
34 2 0.03
35 2 0.03
36 2 0.03
37 26 0.45
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (33 bp):
ATTAAAATTCGAATACATTATTTATGAATTTAT
Found at i:1325885 original size:2 final size:2
Alignment explanation
Indices: 1325867--1325941 Score: 127
Period size: 2 Copynumber: 38.5 Consensus size: 2
1325857 TTATTATAAC
*
1325867 AT AT AT -T AT A- AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1325907 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1325942 GTCCACAGTT
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
1 2 0.03
2 67 0.97
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1331108 original size:17 final size:16
Alignment explanation
Indices: 1331077--1331118 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
1331067 AAAATTACAA
1331077 ATAAAAACATCATTTC
1 ATAAAAACATCATTTC
*
1331093 ATAAAATCATTCATTT-
1 ATAAAAACA-TCATTTC
*
1331109 ATTAAAACAT
1 ATAAAAACAT
1331119 AATCCAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 1 0.05
16 15 0.68
17 6 0.27
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (16 bp):
ATAAAAACATCATTTC
Found at i:1331686 original size:32 final size:32
Alignment explanation
Indices: 1331645--1331729 Score: 82
Period size: 32 Copynumber: 2.7 Consensus size: 32
1331635 ATGTCTTGTA
* * *
1331645 GCCTCAGAGCCTACCCAAGGG-AGTATATTAGG
1 GCCTAAGAGCCTACCCAAGGGAACT-TATCAGG
* ** *
1331677 GCCTGAGAGCCTATACAAGGGAACTTCTCAGG
1 GCCTAAGAGCCTACCCAAGGGAACTTATCAGG
*
1331709 GCCTAAGAGTCTACCCAAGGG
1 GCCTAAGAGCCTACCCAAGGG
1331730 TCACCATAGG
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
32 40 0.95
33 2 0.05
ACGTcount: A:0.28, C:0.26, G:0.28, T:0.18
Consensus pattern (32 bp):
GCCTAAGAGCCTACCCAAGGGAACTTATCAGG
Found at i:1346847 original size:59 final size:59
Alignment explanation
Indices: 1346784--1347223 Score: 353
Period size: 59 Copynumber: 7.5 Consensus size: 59
1346774 TGGCACTATA
* *
1346784 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGAATTTCCATATGGAGCACTGAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATGGAGCACTGAG
*
1346843 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGAGCACTGAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATGGAGCACTGAG
* * * * * * * *
1346902 TCTGCAAAAATGATAAGGAAATCATACTAAATATATGGATTTCTAGATAGG-GCA-TTATA
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGAT-GGAGCACTGA-G
* *** *
1346961 TGTGCTAAAATGGTAAGGAAATCATACTG-GTGTATGGATTTCCAGAAAAAGCACTAAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATGGAGCACTGAG
* * * * * * *
1347019 GGTGCTACAAGGATAAGGAAATCATACT-AATAGTATGGATTTTCATATAGG-GCACTTCA-
1 TGTGCTAAAATGATAAGGAAATCATACTGAGT-GTATGGATTTCCAGAT-GGAGCAC-TGAG
* * * **
1347078 TGTGCTAAAAATGGTAAAGG-AATCATACT-AATGGTATGGA-TTCTCAAATAGG-GCACTTCG
1 TGTGCT-AAAATGAT-AAGGAAATCATACTGAGT-GTATGGATTTC-CAGAT-GGAGCACTGAG
* * * * * *
1347138 TGTGCTAAAATGAGAATGAAATCATATTAAGTATAT-GATATTCCAGATAGAGCACTGAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGAT-TTCCAGATGGAGCACTGAG
* * * * *
1347197 AGTCCTAATATTATAAGGAAATTATAC
1 TGTGCTAAAATGATAAGGAAATCATAC
1347224 GAATTGTATA
Statistics
Matches: 304, Mismatches: 60, Indels: 34
0.76 0.15 0.09
Matches are distributed among these distances:
58 50 0.16
59 200 0.66
60 50 0.16
61 4 0.01
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.29
Consensus pattern (59 bp):
TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATGGAGCACTGAG
Found at i:1346925 original size:118 final size:118
Alignment explanation
Indices: 1346764--1347223 Score: 390
Period size: 118 Copynumber: 3.9 Consensus size: 118
1346754 TATGCATAGT
* * * * *
1346764 GATTTCCGAAT-G-GCACTATA-TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGAATTT
1 GATTTCCAAATGGAGCACTA-AGTGTGCTAAAATGATAAGGAAATCATACTAAATATATGGATTT
*
1346826 CCATAT-GGAGCACTGAGTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATG
65 CCAGATAGG-GCACTGAGTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATG
* * * *
1346880 GATTTCCATATGGAGCACTGAGTCTGCAAAAATGATAAGGAAATCATACTAAATATATGGATTTC
1 GATTTCCAAATGGAGCACTAAGTGTGCTAAAATGATAAGGAAATCATACTAAATATATGGATTTC
* * * *
1346945 TAGATAGGGCA-TTATATGTGCTAAAATGGTAAGGAAATCATACTG-GTGTATG
66 CAGATAGGGCACTGA-GTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATG
** * * *
1346997 GATTTCCAGAA-AAAGCACTAAGGGTGCTACAAGGATAAGGAAATCATACT-AATAGTATGGATT
1 GATTTCCA-AATGGAGCACTAAGTGTGCTAAAATGATAAGGAAATCATACTAAATA-TATGGATT
* * * * *
1347060 TTCATATAGGGCACTTCA-TGTGCTAAAAATGGTAAAGG-AATCATACT-AATGGTATG
64 TCCAGATAGGGCAC-TGAGTGTGCT-AAAATGAT-AAGGAAATCATACTGAGT-GTATG
** * * * *
1347116 GA-TTCTCAAATAGG-GCACTTCGTGTGCTAAAATGAGAATGAAATCATATTAAGTATAT-GATA
1 GATTTC-CAAAT-GGAGCACTAAGTGTGCTAAAATGATAAGGAAATCATACTAAATATATGGAT-
* * * * * *
1347178 TTCCAGATAGAGCACTGAGAGTCCTAATATTATAAGGAAATTATAC
63 TTCCAGATAGGGCACTGAGTGTGCTAAAATGATAAGGAAATCATAC
1347224 GAATTGTATA
Statistics
Matches: 275, Mismatches: 49, Indels: 38
0.76 0.14 0.10
Matches are distributed among these distances:
116 13 0.05
117 78 0.28
118 117 0.43
119 64 0.23
120 3 0.01
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (118 bp):
GATTTCCAAATGGAGCACTAAGTGTGCTAAAATGATAAGGAAATCATACTAAATATATGGATTTC
CAGATAGGGCACTGAGTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATG
Found at i:1347104 original size:177 final size:177
Alignment explanation
Indices: 1346775--1347163 Score: 445
Period size: 177 Copynumber: 2.2 Consensus size: 177
1346765 ATTTCCGAAT
* * * ***
1346775 GGCACTATATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGAATTTCCATATGGAGCACT
1 GGCATTATATGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATGAATTTCCAGAAAAAGCACT
* * * * *
1346840 GAGTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGAGCACTGAGTCT
66 AAGGGTGCTAAAAGGATAAGGAAATCATACTGAATGTATGGATTTCCATATGGAGCACTCAGTCT
*
1346905 GCAAAAATGATAAGGAAATCATACTAAAT-ATATGGATT-TCTAGATAG
131 GCAAAAATGATAAGGAAATCATACT-AATGATATGGATTCTC-AAATAG
*
1346952 GGCATTATATGTGCTAAAATGGTAAGGAAATCATACTG-GTGTATGGATTTCCAGAAAAAGCACT
1 GGCATTATATGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATGAATTTCCAGAAAAAGCACT
* *
1347016 AAGGGTGCTACAAGGATAAGGAAATCATACT-AATAGTATGGATTTTCATATAGG-GCACTTCA-
66 AAGGGTGCTAAAAGGATAAGGAAATCATACTGAAT-GTATGGATTTCCATAT-GGAGCAC-TCAG
* * *
1347078 TGTGCTAAAAATGGTAAAGG-AATCATACTAATGGTATGGATTCTCAAATAG
128 TCTGC-AAAAATGAT-AAGGAAATCATACTAATGATATGGATTCTCAAATAG
** *
1347129 GGCACTT-CGTGTGCTAAAATGAG-AATGAAATCATA
1 GGCA-TTATATGTGCTAAAATG-GTAAGGAAATCATA
1347164 TTAAGTATAT
Statistics
Matches: 182, Mismatches: 21, Indels: 18
0.82 0.10 0.08
Matches are distributed among these distances:
175 2 0.01
176 74 0.41
177 97 0.53
178 9 0.05
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.28
Consensus pattern (177 bp):
GGCATTATATGTGCTAAAATGGTAAGGAAATCATACTGAGTGTATGAATTTCCAGAAAAAGCACT
AAGGGTGCTAAAAGGATAAGGAAATCATACTGAATGTATGGATTTCCATATGGAGCACTCAGTCT
GCAAAAATGATAAGGAAATCATACTAATGATATGGATTCTCAAATAG
Found at i:1347119 original size:60 final size:61
Alignment explanation
Indices: 1346907--1347147 Score: 195
Period size: 60 Copynumber: 4.1 Consensus size: 61
1346897 CTGAGTCTGC
* * *
1346907 AAAAATGAT-AAGGAAATCATACTAAATA-TATGGATT-TCTAGATAGGGCA-TTATATGTGCT
1 AAAAATGGTAAAGGAAATCATACT-AATAGTATGGATTCTC-AAATAGGGCACTT-CATGTGCT
** ** * *
1346967 -AAAATGGT-AAGGAAATCATACTGGT-GTATGGATT-TCCAGAA-AAAGCAC-TAAGGGTGCT
1 AAAAATGGTAAAGGAAATCATACTAATAGTATGGATTCT-CA-AATAGGGCACTTCA-TGTGCT
* * *
1347025 -ACAA-GG-ATAAGGAAATCATACTAATAGTATGGATTTTCATATAGGGCACTTCATGTGCT
1 AAAAATGGTA-AAGGAAATCATACTAATAGTATGGATTCTCAAATAGGGCACTTCATGTGCT
* *
1347084 AAAAATGGTAAAGG-AATCATACTAATGGTATGGATTCTCAAATAGGGCACTTCGTGTGCT
1 AAAAATGGTAAAGGAAATCATACTAATAGTATGGATTCTCAAATAGGGCACTTCATGTGCT
1347144 AAAA
1 AAAA
1347148 TGAGAATGAA
Statistics
Matches: 146, Mismatches: 21, Indels: 28
0.75 0.11 0.14
Matches are distributed among these distances:
57 3 0.02
58 40 0.27
59 44 0.30
60 52 0.36
61 6 0.04
62 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.22, T:0.28
Consensus pattern (61 bp):
AAAAATGGTAAAGGAAATCATACTAATAGTATGGATTCTCAAATAGGGCACTTCATGTGCT
Found at i:1347363 original size:44 final size:44
Alignment explanation
Indices: 1347300--1347688 Score: 533
Period size: 44 Copynumber: 9.0 Consensus size: 44
1347290 TCAGTGATGC
1347300 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
1347344 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
* * *
1347388 AAATTATTGTAAGTATATTGGTAAAATATGCTTACGATCTTATG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
1347432 AAATTATAGTAAGTATATTGGT--AA-AA---TA--AGCTTATG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
* *
1347468 AAATTATAGTAAGTATATTGGTAAAATAAGTTTACGAACTTATG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
*
1347512 AAATTATAGTAAGTATGTTGGTAAAATAAGCTTACGAGCTTATG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
* * *
1347556 GAATAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
* * * *
1347600 GAATAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTAGG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
* * * * * * *
1347644 GATTTAATGGTACGTATATTGTTAAAATAAACTTACGAGTTTATG
1 AAATT-ATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
1347689 GATTAAATGG
Statistics
Matches: 314, Mismatches: 22, Indels: 17
0.89 0.06 0.05
Matches are distributed among these distances:
36 29 0.09
38 4 0.01
39 2 0.01
41 1 0.00
42 4 0.01
44 240 0.76
45 34 0.11
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.35
Consensus pattern (44 bp):
AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
Found at i:1347484 original size:80 final size:80
Alignment explanation
Indices: 1347380--1347633 Score: 328
Period size: 80 Copynumber: 3.1 Consensus size: 80
1347370 TAAGCTTACG
* * *
1347380 AGCTTATGAAATTATTGTAAGTATATTGGTAAAATATGCTTACGATCTTATGAAATTATAGTAAG
1 AGCTTATGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAACTTATGAAATTATAGTAAG
1347445 TATATTGGTAAAATA
66 TATATTGGTAAAATA
*
1347460 AGCTTATGAAATTATAGTAAGTATATTGGTAAAATAAGTTTACGAACTTATGAAATTATAGTAAG
1 AGCTTATGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAACTTATGAAATTATAGTAAG
*
1347525 TATGTTGGTAAAATAAGCTTA
66 TATATTGGT--AA-AA---TA
* * * * * * *
1347546 CGAGCTTATGGAATAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAATGGTA
1 --AGCTTATGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAACTTATGAAATTATAGTA
1347611 AGTATATTGGTAAAATA
64 AGTATATTGGTAAAATA
1347628 AGCTTA
1 AGCTTA
1347634 CGAGCTTAGG
Statistics
Matches: 152, Mismatches: 14, Indels: 16
0.84 0.08 0.09
Matches are distributed among these distances:
80 75 0.49
82 4 0.03
83 2 0.01
85 2 0.01
86 4 0.03
88 65 0.43
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.35
Consensus pattern (80 bp):
AGCTTATGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAACTTATGAAATTATAGTAAG
TATATTGGTAAAATA
Found at i:1347533 original size:124 final size:124
Alignment explanation
Indices: 1347300--1347688 Score: 436
Period size: 124 Copynumber: 3.0 Consensus size: 124
1347290 TCAGTGATGC
1347300 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGAAATTATAGTAAGTATATTGG
1 AAATTATAGTAAGTATATTGGT--AA-AA---TA--AGCTTATGAAATTATAGTAAGTATATTGG
* * * *
1347365 TAAAATAAGCTTACGAGCTTATGAAATTATTGTAAGTATATTGGTAAAATATGCTTACGATCTTA
58 TAAAATAAGCTTACGAACTTATGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
1347430 TG
123 TG
1347432 AAATTATAGTAAGTATATTGGTAAAATAAGCTTATGAAATTATAGTAAGTATATTGGTAAAATAA
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTATGAAATTATAGTAAGTATATTGGTAAAATAA
* *
1347497 GTTTACGAACTTATGAAATTATAGTAAGTATGTTGGTAAAATAAGCTTACGAGCTTATG
66 GCTTACGAACTTATGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
* * * * * *
1347556 GAATAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAATGGTAAGTATATTGG
1 AAATTATAGTAAGTATATTGGT--AA-AA---TA--AGCTTATGAAATTATAGTAAGTATATTGG
* * * * * * * * *
1347621 TAAAATAAGCTTACGAGCTTAGGGATTTAATGGTACGTATATTGTTAAAATAAACTTACGAGTTT
58 TAAAATAAGCTTACGAACTTATGAAATT-ATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTT
1347686 ATG
122 ATG
1347689 GATTAAATGG
Statistics
Matches: 225, Mismatches: 23, Indels: 17
0.85 0.09 0.06
Matches are distributed among these distances:
124 109 0.48
126 4 0.02
127 2 0.01
129 2 0.01
130 4 0.02
132 71 0.32
133 33 0.15
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.35
Consensus pattern (124 bp):
AAATTATAGTAAGTATATTGGTAAAATAAGCTTATGAAATTATAGTAAGTATATTGGTAAAATAA
GCTTACGAACTTATGAAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
Found at i:1347578 original size:168 final size:168
Alignment explanation
Indices: 1347300--1347633 Score: 569
Period size: 168 Copynumber: 2.0 Consensus size: 168
1347290 TCAGTGATGC
*
1347300 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGAAATTATAGTAAGTATATTGG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAACTTATGAAATTATAGTAAGTATATTGG
* * * *
1347365 TAAAATAAGCTTACGAGCTTATGAAATTATTGTAAGTATATTGGTAAAATATGCTTACGATCTTA
66 TAAAATAAGCTTACGAGCTTATGAAATAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
*
1347430 TGAAATTATAGTAAGTATATTGGTAAAATAAGCTTATG
131 TGAAATAATAGTAAGTATATTGGTAAAATAAGCTTATG
* *
1347468 AAATTATAGTAAGTATATTGGTAAAATAAGTTTACGAACTTATGAAATTATAGTAAGTATGTTGG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAACTTATGAAATTATAGTAAGTATATTGG
*
1347533 TAAAATAAGCTTACGAGCTTATGGAATAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
66 TAAAATAAGCTTACGAGCTTATGAAATAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
* *
1347598 TGGAATAATGGTAAGTATATTGGTAAAATAAGCTTA
131 TGAAATAATAGTAAGTATATTGGTAAAATAAGCTTA
1347634 CGAGCTTAGG
Statistics
Matches: 155, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
168 155 1.00
ACGTcount: A:0.41, C:0.06, G:0.19, T:0.35
Consensus pattern (168 bp):
AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAACTTATGAAATTATAGTAAGTATATTGG
TAAAATAAGCTTACGAGCTTATGAAATAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
TGAAATAATAGTAAGTATATTGGTAAAATAAGCTTATG
Found at i:1353107 original size:59 final size:59
Alignment explanation
Indices: 1353044--1353493 Score: 369
Period size: 59 Copynumber: 7.6 Consensus size: 59
1353034 TGGCACTATA
* * * *
1353044 TGTGCTAAAATGATAAGGAAATGATACTGAGTGTATGAATTTCCATATGGAGCACTGAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAATGTATGGATTTCCATATAGAGCACTGAG
*
1353103 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATAGAGCACTGAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAATGTATGGATTTCCATATAGAGCACTGAG
** * * * * * * * *
1353162 TGTGAAAAAATGATAAGGAAATCATATTGAATATATGTATTTTCAAATAGGGCA-TTATA
1 TGTGCTAAAATGATAAGGAAATCATACTGAATGTATGGATTTCCATATAGAGCACTGA-G
* * * * *
1353221 TGTGCTAAAATGGTAAGGAAATCATACTGAATGTATGGATTTCCAGAAAAAGCACTAAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAATGTATGGATTTCCATATAGAGCACTGAG
* * * * * * *
1353280 GGTGCTACAAGGATAAGGAAATCATACT-AATAGTATGGGTTTTCATATAGGGCACTTCA-
1 TGTGCTAAAATGATAAGGAAATCATACTGAAT-GTATGGATTTCCATATAGAGCAC-TGAG
* * * **
1353339 TGTGCTAAAAATGGTAAAGG-AATCATACT-AATGGTATGGA-TTCTCAAATAGGGCACTTCG
1 TGTGCT-AAAATGAT-AAGGAAATCATACTGAAT-GTATGGATTTC-CATATAGAGCACTGAG
* * * * *
1353399 TGTGCTAAAATGAGAATGAAATCATA-TTAA-GTATATGATATTCCAGATAGAGCACTGAG
1 TGTGCTAAAATGATAAGGAAATCATACTGAATGTAT-GGAT-TTCCATATAGAGCACTGAG
* * * * *
1353458 AGTCCTAATATTATAAGGAAATTATAC-GAATTGTAT
1 TGTGCTAAAATGATAAGGAAATCATACTGAA-TGTAT
1353494 AAATTTCCTA
Statistics
Matches: 311, Mismatches: 64, Indels: 30
0.77 0.16 0.07
Matches are distributed among these distances:
57 4 0.01
58 11 0.04
59 241 0.77
60 47 0.15
61 8 0.03
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.30
Consensus pattern (59 bp):
TGTGCTAAAATGATAAGGAAATCATACTGAATGTATGGATTTCCATATAGAGCACTGAG
Found at i:1353445 original size:178 final size:177
Alignment explanation
Indices: 1353043--1353424 Score: 425
Period size: 177 Copynumber: 2.2 Consensus size: 177
1353033 ATGGCACTAT
* * * * * *** * *
1353043 ATGTGCTAAAATGATAAGGAAATGATACTGAGTGTATGAATTTCCATATGGAGCACTGAGTGTGC
1 ATGTGCTAAAATGGTAAGGAAATCATACTGAATGTATGGATTTCCAGAAAAAGCACTAAGGGTGC
* * *
1353108 TAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATAGAGCACTGAGTGTGAAAAAAT
66 TAAAAGGATAAGGAAATCATACTGAATGTATGGATTTCCATATAGAGCACTCAGTGTGAAAAAAT
* * * *
1353173 GATAAGGAAATCATATTGAATATATGTATTTTCAAATAGGGCATTAT
131 GATAAGGAAATCATACTGAATATATGGATTCTCAAATAGGGCATTAC
1353220 ATGTGCTAAAATGGTAAGGAAATCATACTGAATGTATGGATTTCCAGAAAAAGCACTAAGGGTGC
1 ATGTGCTAAAATGGTAAGGAAATCATACTGAATGTATGGATTTCCAGAAAAAGCACTAAGGGTGC
* * * * *
1353285 TACAAGGATAAGGAAATCATACT-AATAGTATGGGTTTTCATATAGGGCACTTCA-TGTGCTAAA
66 TAAAAGGATAAGGAAATCATACTGAAT-GTATGGATTTCCATATAGAGCAC-TCAGTGTG-AAAA
* *
1353348 AATGGTAAAGG-AATCATACT-AATGGTATGGATTCTCAAATAGGGCACTT-C
128 AATGAT-AAGGAAATCATACTGAAT-ATATGGATTCTCAAATAGGGCA-TTAC
* *
1353398 GTGTGCTAAAATGAG-AATGAAATCATA
1 ATGTGCTAAAATG-GTAAGGAAATCATA
1353425 TTAAGTATAT
Statistics
Matches: 172, Mismatches: 26, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
176 2 0.01
177 103 0.60
178 60 0.35
179 7 0.04
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (177 bp):
ATGTGCTAAAATGGTAAGGAAATCATACTGAATGTATGGATTTCCAGAAAAAGCACTAAGGGTGC
TAAAAGGATAAGGAAATCATACTGAATGTATGGATTTCCATATAGAGCACTCAGTGTGAAAAAAT
GATAAGGAAATCATACTGAATATATGGATTCTCAAATAGGGCATTAC
Found at i:1353611 original size:44 final size:44
Alignment explanation
Indices: 1353561--1353913 Score: 508
Period size: 44 Copynumber: 8.0 Consensus size: 44
1353551 TCAATGATGC
1353561 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
* *
1353605 AAATTATAGTAAGTATATTGGTAAAATAACCTTATGAGCTTATG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
*
1353649 AAATTATATTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
* * *
1353693 AAATTATAGTAAGTATATTGGTAAAATAAGTTTACGAACTTATA
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
*
1353737 AAATTATAGTAAGTATGTTGGTAAAATAAGCTTACGAGCTTATG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
* * *
1353781 GAATAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
* * * *
1353825 GAATAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTAAG
1 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
* * * * * * *
1353869 GATTTAATGGTAAGTATATTGTTAAAATAAACTTTCGAGTTTATG
1 AAATT-ATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
1353914 GATTAAATGG
Statistics
Matches: 283, Mismatches: 25, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
44 249 0.88
45 34 0.12
ACGTcount: A:0.40, C:0.06, G:0.18, T:0.35
Consensus pattern (44 bp):
AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
Found at i:1358893 original size:18 final size:18
Alignment explanation
Indices: 1358872--1358915 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1358862 TAGGAGTTCC
1358872 CAACTCAAATAAGATCAA
1 CAACTCAAATAAGATCAA
* *
1358890 CAACTCCAATAAGATGAA
1 CAACTCAAATAAGATCAA
1358908 CAAC-CAAA
1 CAACTCAAA
1358916 GAGGGCAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 3 0.13
18 20 0.87
ACGTcount: A:0.55, C:0.25, G:0.07, T:0.14
Consensus pattern (18 bp):
CAACTCAAATAAGATCAA
Found at i:1359412 original size:13 final size:13
Alignment explanation
Indices: 1359389--1359421 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1359379 TTCCCATTAC
1359389 AGACGTGCATATGA
1 AGAC-TGCATATGA
1359403 AGACTGCATATGA
1 AGACTGCATATGA
1359416 AGACTG
1 AGACTG
1359422 TTCAACTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.36, C:0.15, G:0.27, T:0.21
Consensus pattern (13 bp):
AGACTGCATATGA
Done.