Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008075.1 Hibiscus syriacus cultivar Beakdansim tig00110577_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: 1947163
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 10
Found at i:1175295 original size:21 final size:21
Alignment explanation
Indices: 1175269--1175391 Score: 119
Period size: 21 Copynumber: 6.0 Consensus size: 21
1175259 GATTTACATA
*
1175269 TTCGCAATGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
1175290 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
** * *
1175311 TTCGCATTGCGATTTTTCAAA
1 TTCGCATTGCGATAGTCCAAG
* *
1175332 TTTG--TTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
* *
1175351 TTCGCATTGCGATTTATTCCAAA
1 TTCGCATTGCGA--TAGTCCAAG
1175374 TTCG--TTGCGATAGTCCAA
1 TTCGCATTGCGATAGTCCAA
1175392 AATCGCAACG
Statistics
Matches: 82, Mismatches: 16, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
19 20 0.24
21 52 0.63
23 10 0.12
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.34
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:1175323 original size:42 final size:40
Alignment explanation
Indices: 1175269--1175391 Score: 147
Period size: 42 Copynumber: 3.0 Consensus size: 40
1175259 GATTTACATA
* * *
1175269 TTCGCAATGCGATAGTCCAAGTTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATATTCCAAATTCG--TTGCGATAGTCCAAG
* * * *
1175311 TTCGCATTGCGATTTTTCAAATTTGTTGCGATAGTCGAAG
1 TTCGCATTGCGATATTCCAAATTCGTTGCGATAGTCCAAG
1175351 TTCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCCAA
1 TTCGCATTGCGA--TATTCCAAATTCGTTGCGATAGTCCAA
1175392 AATCGCAACG
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
40 26 0.38
42 42 0.62
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.34
Consensus pattern (40 bp):
TTCGCATTGCGATATTCCAAATTCGTTGCGATAGTCCAAG
Found at i:1175352 original size:40 final size:42
Alignment explanation
Indices: 1175296--1175391 Score: 160
Period size: 40 Copynumber: 2.3 Consensus size: 42
1175286 CAAGTTCGCA
*
1175296 TTGCGATAGTCCAAGTTCGCATTGCGATTT-TT-CAAATTTG
1 TTGCGATAGTCCAAGTTCGCATTGCGATTTATTCCAAATTCG
*
1175336 TTGCGATAGTCGAAGTTCGCATTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCATTGCGATTTATTCCAAATTCG
1175378 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
1175392 AATCGCAACG
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
40 29 0.57
41 2 0.04
42 20 0.39
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCGCATTGCGATTTATTCCAAATTCG
Found at i:1175483 original size:6 final size:6
Alignment explanation
Indices: 1175472--1175496 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1175462 CGTGTCACGT
1175472 ATTACC ATTACC ATTACC ATTACC A
1 ATTACC ATTACC ATTACC ATTACC A
1175497 CGACCACGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (6 bp):
ATTACC
Found at i:1175502 original size:6 final size:6
Alignment explanation
Indices: 1175493--1175529 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
1175483 CATTACCATT
1175493 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
1175530 GGCGAGACGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.35, C:0.49, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1176099 original size:21 final size:21
Alignment explanation
Indices: 1176075--1176155 Score: 76
Period size: 21 Copynumber: 3.9 Consensus size: 21
1176065 TGCAACAAAT
1176075 TTGGAAAATCGCAATGCGAAC
1 TTGGAAAATCGCAATGCGAAC
** *
1176096 TTGGACTATCGCAATGCAAAC
1 TTGGAAAATCGCAATGCGAAC
* **
1176117 TTCGACTATCGCAATGCGAA-
1 TTGGAAAATCGCAATGCGAAC
*
1176137 TAT-GTAAATCGCAATGCGA
1 T-TGGAAAATCGCAATGCGA
1176156 TAGTCGAAGT
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
20 14 0.27
21 37 0.73
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (21 bp):
TTGGAAAATCGCAATGCGAAC
Found at i:1182804 original size:15 final size:15
Alignment explanation
Indices: 1182779--1182814 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1182769 GGATAATTGA
*
1182779 AATAAGGTATGTGAT
1 AATAAGATATGTGAT
*
1182794 TATAAGATATGTGAT
1 AATAAGATATGTGAT
1182809 AATAAG
1 AATAAG
1182815 TTATATGGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.33
Consensus pattern (15 bp):
AATAAGATATGTGAT
Found at i:1183273 original size:30 final size:30
Alignment explanation
Indices: 1183237--1183329 Score: 143
Period size: 30 Copynumber: 3.1 Consensus size: 30
1183227 GTGGTCCTTA
1183237 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
*
1183267 TGGACAGTTACCAAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * *
1183297 TGGATAGTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
1183326 TGGA
1 TGGA
1183330 TAGGTCCTTC
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
29 18 0.31
30 40 0.69
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:1183747 original size:2 final size:2
Alignment explanation
Indices: 1183742--1183870 Score: 192
Period size: 2 Copynumber: 66.0 Consensus size: 2
1183732 ATGTATATGT
* *
1183742 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA -A CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
1183783 CA TA TA TA TA TA TA TA TA TA -A CA TA TA TA TA TA TA TA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1183824 TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1183865 TA TA TA
1 TA TA TA
1183871 ATGTTATATC
Statistics
Matches: 116, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
1 3 0.03
2 113 0.97
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1184563 original size:93 final size:94
Alignment explanation
Indices: 1184435--1184609 Score: 280
Period size: 93 Copynumber: 1.9 Consensus size: 94
1184425 CTAATTGGCC
* * * * *
1184435 TATTAGTTGGTATAAGATATGAAATTTTAGATTTTTTAAATAATGTTTAGAATTTAAATTTTGA-
1 TATTAGTTGGTATAAAAGATGAAATATTAGATTTTTTAAATAATATTTAGAATTTAAAATTTGAT
1184499 ATTATGAATAAAATAAATTAATAAGTAGT
66 ATTATGAATAAAATAAATTAATAAGTAGT
*
1184528 TATTAGTTGTTATAAAAGATGAAATATTAGATTTTTTAAATAATATTTAGAATTTAAAATTTGAT
1 TATTAGTTGGTATAAAAGATGAAATATTAGATTTTTTAAATAATATTTAGAATTTAAAATTTGAT
*
1184593 ATTGTGAATAAAATAAA
66 ATTATGAATAAAATAAA
1184610 ATAAATTATG
Statistics
Matches: 74, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
93 58 0.78
94 16 0.22
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.43
Consensus pattern (94 bp):
TATTAGTTGGTATAAAAGATGAAATATTAGATTTTTTAAATAATATTTAGAATTTAAAATTTGAT
ATTATGAATAAAATAAATTAATAAGTAGT
Found at i:1184858 original size:2 final size:2
Alignment explanation
Indices: 1184851--1184918 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
1184841 ATAATATGTG
1184851 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1184893 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
1184919 CAATTCTTTA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1186068 original size:21 final size:20
Alignment explanation
Indices: 1186044--1186090 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
1186034 TAAAATATCT
1186044 ATTATAAATATTAT-ATTGTAA
1 ATTATAAATATT-TCATT-TAA
*
1186065 ATTAAAAATATTTCATTTAA
1 ATTATAAATATTTCATTTAA
1186085 ATTATA
1 ATTATA
1186091 TTTATATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (20 bp):
ATTATAAATATTTCATTTAA
Found at i:1187520 original size:78 final size:77
Alignment explanation
Indices: 1187378--1187565 Score: 227
Period size: 78 Copynumber: 2.4 Consensus size: 77
1187368 AGCAGGATGT
* ** * *
1187378 TGTAAATAATGTTCCAGCTGGGAATGAGGATAGAAGTGTTGGTGTGAATAATGTAAACAATCCAG
1 TGTAAATAATATTCCAGCTGGGAATGAGGGGAGAAGTGCTGGTGTGAATAATGCAAACAATCCAG
1187443 CA-TAGAAGATAAA
66 CACT-G-AGATAAA
* ** *
1187456 TGTAAATAATATTCCAGCTGGAAATGAGGGGAGAAGTGCTGGTGTGAATTTTGCAAA-AGCTCCA
1 TGTAAATAATATTCCAGCTGGGAATGAGGGGAGAAGTGCTGGTGTGAATAATGCAAACA-ATCCA
1187520 GCACCTGAGATAAA
65 GCA-CTGAGATAAA
* *
1187534 TGTAAATAATTTTCTAGCTGGGAATGAGGGGA
1 TGTAAATAATATTCCAGCTGGGAATGAGGGGA
1187566 AGGGTGTTAG
Statistics
Matches: 95, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
77 1 0.01
78 92 0.97
79 1 0.01
80 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.27, T:0.26
Consensus pattern (77 bp):
TGTAAATAATATTCCAGCTGGGAATGAGGGGAGAAGTGCTGGTGTGAATAATGCAAACAATCCAG
CACTGAGATAAA
Found at i:1199775 original size:44 final size:42
Alignment explanation
Indices: 1199678--1199775 Score: 94
Period size: 44 Copynumber: 2.3 Consensus size: 42
1199668 AGAAATAATG
*
1199678 TATA-TTTTTAATTTTTGAATAATTTACTTTTTATTTTAGTA
1 TATATTTTTTAATTTTTGAATAATTTACTTTTTAATTTAGTA
* **
1199719 T-TATTATATTTAAGTTTTTGAATATTTTTTTATTTTGAATTTA-TA
1 TATATT-T-TTTAA-TTTTTGAATAATTTACT-TTTT-AATTTAGTA
1199764 TATATTTTTTAA
1 TATATTTTTTAA
1199776 AAAAATTAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
40 2 0.04
41 2 0.04
42 1 0.02
43 5 0.11
44 19 0.41
45 8 0.17
46 9 0.20
ACGTcount: A:0.30, C:0.01, G:0.05, T:0.64
Consensus pattern (42 bp):
TATATTTTTTAATTTTTGAATAATTTACTTTTTAATTTAGTA
Found at i:1199833 original size:27 final size:27
Alignment explanation
Indices: 1199803--1199866 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
1199793 TTAAATTTAA
*
1199803 AAAAAATAAATTTGACCCTTAAACTTT
1 AAAAAATAAATTTGACCCTTAAACTTG
* * *
1199830 AAAAAATTAATTTGATCCTTGAACTTG
1 AAAAAATAAATTTGACCCTTAAACTTG
1199857 AAAAAA-AAAT
1 AAAAAATAAAT
1199867 CAATTTAACT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 3 0.09
27 29 0.91
ACGTcount: A:0.52, C:0.11, G:0.06, T:0.31
Consensus pattern (27 bp):
AAAAAATAAATTTGACCCTTAAACTTG
Found at i:1199861 original size:28 final size:27
Alignment explanation
Indices: 1199791--1199863 Score: 83
Period size: 27 Copynumber: 2.6 Consensus size: 27
1199781 TTAAATAAGT
*
1199791 CCTTAAATTTAAAAAAAATAAATTTGAC
1 CCTTAAACTT-AAAAAAATAAATTTGAC
* * *
1199819 CCTTAAACTTTAAAAAATTAATTTGAT
1 CCTTAAACTTAAAAAAATAAATTTGAC
*
1199846 CCTTGAACTTGAAAAAAA
1 CCTTAAACTT-AAAAAAA
1199864 AATCAATTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 23 0.61
28 15 0.39
ACGTcount: A:0.49, C:0.12, G:0.05, T:0.33
Consensus pattern (27 bp):
CCTTAAACTTAAAAAAATAAATTTGAC
Found at i:1200902 original size:20 final size:20
Alignment explanation
Indices: 1200830--1201178 Score: 427
Period size: 20 Copynumber: 17.4 Consensus size: 20
1200820 GATTTTCCAT
* ** *
1200830 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
1200850 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
1200870 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
1200890 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
1200910 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1200930 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1200950 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1200970 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1200990 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1201010 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1201030 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1201050 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
1201070 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1201090 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1201110 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1201130 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1201150 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1201170 AATCACAAC
1 AATCGCAAC
1201179 ACTGAAATTT
Statistics
Matches: 287, Mismatches: 34, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
19 3 0.01
20 281 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1202097 original size:12 final size:12
Alignment explanation
Indices: 1202080--1202104 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1202070 ATATAATCCT
1202080 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1202092 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1202104 G
1 G
1202105 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1204423 original size:20 final size:20
Alignment explanation
Indices: 1204400--1204489 Score: 122
Period size: 20 Copynumber: 4.8 Consensus size: 20
1204390 AAATCCCAAC
1204400 ATGAAAATCGCAATGCGGAA
1 ATGAAAATCGCAATGCGGAA
1204420 ATGAAAATCGCAA--C-G--
1 ATGAAAATCGCAATGCGGAA
*
1204435 A-GAGAATCGCAATGC-GAA
1 ATGAAAATCGCAATGCGGAA
1204453 ATGAAAATCGCAATGCGGAA
1 ATGAAAATCGCAATGCGGAA
1204473 ATGAAAATCGCAATGCG
1 ATGAAAATCGCAATGCG
1204490 TTTATAATTT
Statistics
Matches: 62, Mismatches: 2, Indels: 12
0.82 0.03 0.16
Matches are distributed among these distances:
14 10 0.16
15 1 0.02
16 2 0.03
17 1 0.02
18 2 0.03
19 13 0.21
20 33 0.53
ACGTcount: A:0.44, C:0.17, G:0.24, T:0.14
Consensus pattern (20 bp):
ATGAAAATCGCAATGCGGAA
Found at i:1204433 original size:53 final size:53
Alignment explanation
Indices: 1204372--1204485 Score: 160
Period size: 53 Copynumber: 2.2 Consensus size: 53
1204362 CGGAAAATAC
*
1204372 AATCGCAACGCGA-AAT-GAAAATCCCAACATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACGAGAGAATCG-AAATCCCAA-ATGAAAATCGCAATGCGGAAATGAA
* * *
1204425 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACGAGAGAATCGAAATCCCAAATGAAAATCGCAATGCGGAAATGAA
1204478 AATCGCAA
1 AATCGCAA
1204486 TGCGTTTATA
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
53 45 0.82
54 9 0.16
55 1 0.02
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.13
Consensus pattern (53 bp):
AATCGCAACGAGAGAATCGAAATCCCAAATGAAAATCGCAATGCGGAAATGAA
Found at i:1204459 original size:33 final size:33
Alignment explanation
Indices: 1204372--1204465 Score: 136
Period size: 34 Copynumber: 2.8 Consensus size: 33
1204362 CGGAAAATAC
* *
1204372 AATCGCAACGCGAAATGAAAATCCCAACATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACATGAA
*
1204405 AATCGCAATGCGGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCGCAAC-ATGAA
1204439 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
1204466 TGCGGAAATG
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
33 26 0.46
34 29 0.52
35 1 0.02
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.13
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACATGAA
Found at i:1204542 original size:19 final size:19
Alignment explanation
Indices: 1204518--1204562 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
1204508 GATTATCTCG
1204518 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1204537 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1204556 TTGCGAT
1 TTGCGAT
1204563 AGTCATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1204568 original size:19 final size:19
Alignment explanation
Indices: 1204527--1204570 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
1204517 GTTGCGATTT
**
1204527 TCATTTCGCATTGCGATTT
1 TCATTTCGCATTGCGATAG
1204546 TCATTTCGCATTGCGATAG
1 TCATTTCGCATTGCGATAG
1204565 TCATTT
1 TCATTT
1204571 TTGCCTTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.18, C:0.20, G:0.16, T:0.45
Consensus pattern (19 bp):
TCATTTCGCATTGCGATAG
Found at i:1204688 original size:14 final size:14
Alignment explanation
Indices: 1204669--1204705 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1204659 CATCAATTAC
1204669 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1204683 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1204697 ACAAATCAA
1 ACAAATCAA
1204706 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1206636 original size:20 final size:19
Alignment explanation
Indices: 1206611--1206662 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
1206601 TAGTTTACTT
* *
1206611 TCGCAATACGAAACTTAAAA
1 TCGCAACACGAAAC-CAAAA
*
1206631 TCGCAACGCGAAACCAAAA
1 TCGCAACACGAAACCAAAA
*
1206650 TCGCAACGCGAAA
1 TCGCAACACGAAA
1206663 TGAAATCGCA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.46, C:0.27, G:0.15, T:0.12
Consensus pattern (19 bp):
TCGCAACACGAAACCAAAA
Found at i:1206651 original size:19 final size:18
Alignment explanation
Indices: 1206627--1206744 Score: 72
Period size: 19 Copynumber: 6.8 Consensus size: 18
1206617 TACGAAACTT
1206627 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAA-C
*
1206646 AAAATCGCAACGCGAAAT
1 AAAATCGCAACGCGAAAC
*
1206664 GAAATCGCAA--CG--AC
1 AAAATCGCAACGCGAAAC
* ** *
1206678 AGAATCGCAATACGAAATG
1 AAAATCGCAACGCGAAA-C
1206697 AAAATCGCAA--CG-AA-
1 AAAATCGCAACGCGAAAC
* *
1206711 AGAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAA-C
*
1206730 AAAATCGCAATGCGA
1 AAAATCGCAACGCGA
1206745 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 10, Indels: 20
0.72 0.09 0.18
Matches are distributed among these distances:
14 18 0.23
16 8 0.10
17 4 0.05
18 10 0.13
19 39 0.49
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.10
Consensus pattern (18 bp):
AAAATCGCAACGCGAAAC
Found at i:1206685 original size:14 final size:14
Alignment explanation
Indices: 1206666--1206722 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1206656 CGCGAAATGA
*
1206666 AATCGCAACGACAG
1 AATCGCAACGAAAG
1206680 AATCGCAATACGAAATG
1 AATCGC-A-ACGAAA-G
1206697 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1206713 AATCGCAACG
1 AATCGCAACG
1206723 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
15 1 0.03
16 6 0.16
17 7 0.19
18 1 0.03
19 6 0.16
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1206694 original size:32 final size:33
Alignment explanation
Indices: 1206648--1206739 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
1206638 GCGAAACCAA
*
1206648 AATCGCAACGCGAAATG-AAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
**
1206680 AATCGCAATACGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1206713 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1206740 TGCGATTTTG
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
32 15 0.28
33 39 0.72
ACGTcount: A:0.48, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:1206762 original size:19 final size:19
Alignment explanation
Indices: 1206740--1206867 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
1206730 AAAATCGCAA
1206740 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1206759 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
1206773 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1206792 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
1206806 TGCGATTTTCATTTCGCG-
1 TGCGATTTTGGTTTCGCGT
1206824 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1206843 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
1206863 TGCGA
1 TGCGA
1206868 AAGTAAACTA
Statistics
Matches: 88, Mismatches: 9, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
14 22 0.25
15 1 0.01
16 2 0.02
17 2 0.02
18 18 0.20
19 30 0.34
20 13 0.15
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.45
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:1206782 original size:33 final size:33
Alignment explanation
Indices: 1206740--1206830 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
1206730 AAAATCGCAA
1206740 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
1206773 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
1206806 TGCGATTTTCATTTCGCG-TGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
1206831 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 7 0.13
33 46 0.84
34 2 0.04
ACGTcount: A:0.08, C:0.19, G:0.29, T:0.45
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:1207268 original size:90 final size:93
Alignment explanation
Indices: 1206910--1207556 Score: 1194
Period size: 90 Copynumber: 7.1 Consensus size: 93
1206900 TTGAATGGAT
1206910 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTA-TTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1206974 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1207002 -AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATAC--TTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1207064 AGTTTAGCA-AATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1207091 AAA-TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1207155 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1207183 AAATTTACTTTCAACCAAAAGAC-AAAC-AAGACAAATACTATTTCACAGTGTTAAAG-ATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1207245 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1207273 AAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1207337 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1207365 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACA--GTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1207427 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1207455 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
1207520 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1207548 AAATTTACT
1 AAATTTACT
1207557 AAGCAATCTA
Statistics
Matches: 541, Mismatches: 1, Indels: 25
0.95 0.00 0.04
Matches are distributed among these distances:
89 54 0.10
90 171 0.32
91 136 0.25
92 107 0.20
93 73 0.13
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1207313 original size:182 final size:186
Alignment explanation
Indices: 1206910--1207556 Score: 1194
Period size: 182 Copynumber: 3.5 Consensus size: 186
1206900 TTGAATGGAT
1206910 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTA-TTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1206974 AGTTTAGCAGAATTGGCAGCAACCGAAC-AATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1207038 TAC--TTTCACAGTGTTAAAGAATACACAGTTTAGCA-AATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1207091 AAA-TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1207155 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGAC-AAAC-AAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1207218 TACTATTTCACAGTGTTAAAG-ATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1207273 AAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1207337 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1207402 TA-TATTTCACA--GTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1207455 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
1207520 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
1207557 AAGCAATCTA
Statistics
Matches: 455, Mismatches: 1, Indels: 18
0.96 0.00 0.04
Matches are distributed among these distances:
180 49 0.11
181 79 0.17
182 208 0.46
183 109 0.24
184 10 0.02
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1209288 original size:33 final size:32
Alignment explanation
Indices: 1209245--1209355 Score: 188
Period size: 33 Copynumber: 3.4 Consensus size: 32
1209235 TTTTGGTTGA
1209245 AATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AATGAAAATCGCAACGAGAGAATCGCAACGCG
*
1209277 AGATGACAATCGCAACGAGAGAATCGCAACGCG
1 A-ATGAAAATCGCAACGAGAGAATCGCAACGCG
1209310 AATG-AAATCGCAACGAGAGAATCGCAACGCG
1 AATGAAAATCGCAACGAGAGAATCGCAACGCG
1209341 AAATGAAAATCGCAA
1 -AATGAAAATCGCAA
1209356 TGCGATTTTG
Statistics
Matches: 74, Mismatches: 2, Indels: 5
0.91 0.02 0.06
Matches are distributed among these distances:
31 26 0.35
32 8 0.11
33 40 0.54
ACGTcount: A:0.44, C:0.22, G:0.24, T:0.10
Consensus pattern (32 bp):
AATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:1209289 original size:19 final size:18
Alignment explanation
Indices: 1209250--1209360 Score: 95
Period size: 14 Copynumber: 6.8 Consensus size: 18
1209240 GTTGAAATGA
1209250 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
1209265 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
1209282 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
1209298 -AATCGCAACGCGA-ATG
1 AAATCGCAACGCGAGATG
1209314 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
*
1209329 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
1209346 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
1209361 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 2, Indels: 26
0.74 0.02 0.24
Matches are distributed among these distances:
14 24 0.30
15 5 0.06
16 15 0.19
17 15 0.19
19 20 0.25
ACGTcount: A:0.42, C:0.23, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:1209391 original size:14 final size:14
Alignment explanation
Indices: 1209372--1209426 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1209362 TTTGGTTTCG
1209372 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1209386 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1209405 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1209419 CGTTGCGA
1 CGTTGCGA
1209427 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1209404 original size:33 final size:33
Alignment explanation
Indices: 1209356--1209426 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1209346 AAAATCGCAA
**
1209356 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1209389 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1209422 TGCGA
1 TGCGA
1209427 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:1209434 original size:33 final size:33
Alignment explanation
Indices: 1209367--1209448 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
1209357 GCGATTTTGG
***
1209367 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1209400 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
1209433 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
1209449 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:1209453 original size:20 final size:20
Alignment explanation
Indices: 1209379--1209467 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
1209369 TCGCGTTGCG
1209379 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
1209399 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
1209412 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
1209432 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
1209452 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
1209468 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:1209589 original size:32 final size:32
Alignment explanation
Indices: 1209550--1209618 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
1209540 ACTAACTTGA
*
1209550 AAATCGCAACGAGAGAATAGCAACGCGAAATG
1 AAATCGCAACGACAGAATAGCAACGCGAAATG
* *
1209582 AAATCGCAACGACAGAATCGTAACGCGAAATG
1 AAATCGCAACGACAGAATAGCAACGCGAAATG
1209614 AAATC
1 AAATC
1209619 TAAGTGAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.12
Consensus pattern (32 bp):
AAATCGCAACGACAGAATAGCAACGCGAAATG
Found at i:1209592 original size:18 final size:18
Alignment explanation
Indices: 1209569--1209618 Score: 54
Period size: 16 Copynumber: 3.0 Consensus size: 18
1209559 CGAGAGAATA
1209569 GCAACGCGAAATGAAATC
1 GCAACGCGAAATGAAATC
*
1209587 GCAA--CGACA-G-AATC
1 GCAACGCGAAATGAAATC
*
1209601 GTAACGCGAAATGAAATC
1 GCAACGCGAAATGAAATC
1209619 TAAGTGAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 8
0.69 0.08 0.22
Matches are distributed among these distances:
14 7 0.28
15 1 0.04
16 8 0.32
17 1 0.04
18 8 0.32
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (18 bp):
GCAACGCGAAATGAAATC
Found at i:1209850 original size:22 final size:22
Alignment explanation
Indices: 1209798--1209852 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1209788 TGGTTGTGAG
**
1209798 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
1209820 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
1209842 GGATTTCTTCG
1 GGATTTCTTCG
1209853 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:1210023 original size:20 final size:20
Alignment explanation
Indices: 1209998--1210190 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
1209988 CTTTAAATAT
1209998 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1210018 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1210040 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1210059 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
1210079 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1210099 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1210119 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1210139 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1210159 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1210179 CGCGTTGCGATT
1 CGCGTTGCGATT
1210191 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1210185 original size:60 final size:60
Alignment explanation
Indices: 1209998--1210190 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
1209988 CTTTAAATAT
**
1209998 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
1210059 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
1210119 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
1210179 CGCGTTGCGATT
1 CGCGTTGCGATT
1210191 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:1210271 original size:20 final size:20
Alignment explanation
Indices: 1210246--1210297 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1210236 AAGAATCGCG
*
1210246 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
1210266 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
1210286 TTGCGATTCTGG
1 TTGCGATTCTGG
1210298 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:1212821 original size:2 final size:2
Alignment explanation
Indices: 1212814--1212846 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1212804 ATTTTTAATA
1212814 AT AT AT AT AT A- 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
1212847 CCTTAAAACT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1213224 original size:15 final size:17
Alignment explanation
Indices: 1213198--1213233 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
1213188 ACAAATTACA
1213198 ATATACAATTTA-ATTT
1 ATATACAATTTATATTT
1213214 ATATA-AATTTATATTT
1 ATATACAATTTATATTT
1213230 -TATA
1 ATATA
1213234 TTTTATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATACAATTTATATTT
Found at i:1222067 original size:15 final size:16
Alignment explanation
Indices: 1222029--1222068 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
1222019 TCAGAGCCTC
*
1222029 TGAATCATTCAGCATT
1 TGAATCATTCAGCACT
1222045 TGAATCATTCAGCACT
1 TGAATCATTCAGCACT
1222061 T-AATCATT
1 TGAATCATT
1222069 ATGAAGTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 7 0.30
16 16 0.70
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.38
Consensus pattern (16 bp):
TGAATCATTCAGCACT
Found at i:1222421 original size:4 final size:4
Alignment explanation
Indices: 1222412--1223237 Score: 1473
Period size: 4 Copynumber: 210.0 Consensus size: 4
1222402 ACCTACGGTT
1222412 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * * * * * * * *
1222460 TACA TGCA TGCA TGCA TGCA TGCA TGCA TGCA TGCA TGCA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1222508 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TAC- -ACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1222554 TACA T--A TACA TACA TACA T--A TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1222598 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TAC- -ACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1222644 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TAC-
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1222691 -ACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1222738 TACA TA-A TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1222785 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1222833 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1222881 TACA T--A TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1222927 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1222975 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1223023 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1223071 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1223119 TACA TACA TACA TACA TACA TACA TAC- TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1223166 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1223214 TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA
1223238 CATAATTCCT
Statistics
Matches: 806, Mismatches: 2, Indels: 28
0.96 0.00 0.03
Matches are distributed among these distances:
2 12 0.01
3 6 0.01
4 788 0.98
ACGTcount: A:0.49, C:0.25, G:0.01, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:1223369 original size:18 final size:18
Alignment explanation
Indices: 1223346--1223385 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
1223336 TTGTGTGGGA
1223346 TGAATACTGTAAATACAT
1 TGAATACTGTAAATACAT
1223364 TGAATACTGTAAATACAT
1 TGAATACTGTAAATACAT
1223382 TGAA
1 TGAA
1223386 GCCTCCTTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (18 bp):
TGAATACTGTAAATACAT
Found at i:1235121 original size:19 final size:21
Alignment explanation
Indices: 1235087--1235126 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1235077 TGTATCTTTC
1235087 TCTCTGTTCTTCTTTTTTTTG
1 TCTCTGTTCTTCTTTTTTTTG
1235108 TCTCTGTCTCTT-TTTTTTT
1 TCTCTGT-TCTTCTTTTTTT
1235127 CAGGTTCGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.00, C:0.20, G:0.07, T:0.72
Consensus pattern (21 bp):
TCTCTGTTCTTCTTTTTTTTG
Found at i:1235577 original size:3 final size:3
Alignment explanation
Indices: 1235569--1235645 Score: 145
Period size: 3 Copynumber: 25.7 Consensus size: 3
1235559 AATATATATT
*
1235569 TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1235617 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1235646 TGGGTAAAAA
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1236100 original size:116 final size:116
Alignment explanation
Indices: 1235962--1236354 Score: 607
Period size: 116 Copynumber: 3.4 Consensus size: 116
1235952 TGATAGAATT
* * * *
1235962 ATTGAACAAGTTCTTCTTATTATAAACTTCTTCTTTCTTCTTCAGATGACGAGTTATTCTCATTA
1 ATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTA
*
1236027 TGAACTCTACTTAGCAATGTTGATCTATCAAATGATGAATTCAAGCAAAAG
66 TGAACTCTACTTAGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAG
1236078 ATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTA
1 ATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTA
* * *
1236143 TGAACTCTACCTGGCAATGTCGATCCATCAAATGATGAATTCAAGCAAAAG
66 TGAACTCTACTTAGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAG
1236194 ATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTA
1 ATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTA
* * * *
1236259 TGAACTCTACTTAGC-----TAATCCATCAATTTGATGAATTCAGGTAAAAG
66 TGAACTCTACTTAGCAATGTTGATCCATCAA-ATGATGAATTCAAGCAAAAG
* * *
1236306 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGA
1 ATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA
1236355 TGAATTCAGA
Statistics
Matches: 258, Mismatches: 18, Indels: 6
0.91 0.06 0.02
Matches are distributed among these distances:
111 9 0.03
112 63 0.24
116 186 0.72
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (116 bp):
ATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTA
TGAACTCTACTTAGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAG
Found at i:1236371 original size:65 final size:65
Alignment explanation
Indices: 1236287--1236419 Score: 239
Period size: 65 Copynumber: 2.0 Consensus size: 65
1236277 TCCATCAATT
**
1236287 TGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGA
1 TGATGAATTCAGACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGA
*
1236352 TGATGAATTCAGACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
1 TGATGAATTCAGACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGA
1236417 TGA
1 TGA
1236420 GTTCTTCTCA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.38
Consensus pattern (65 bp):
TGATGAATTCAGACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGA
Found at i:1237366 original size:113 final size:113
Alignment explanation
Indices: 1236352--1237349 Score: 1944
Period size: 113 Copynumber: 8.8 Consensus size: 113
1236342 ATTCTTCAGA
1236352 TGATGAATTCAGACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
1 TGATGAATTCAGACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
1236417 TGAGTTCTTCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCAAG
66 TGAGTTCTTCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCAAG
*
1236465 TTATGAATTCAGACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
1 TGATGAATTCAGACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
*
1236530 TGATTTCTTCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCAAG
66 TGAGTTCTTCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCAAG
1236578 TGATGAATTCAGACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
1 TGATGAATTCAGACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
*
1236643 TGAGTTCTTCTCATTATGAACCTTCTCTGGCAAAATTAATCCATCAAG
66 TGAGTTCTTCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCAAG
*
1236691 TGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
1 TGATGAATTCAGACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
1236756 TGAGTTCTTCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCAAG
66 TGAGTTCTTCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCAAG
1236804 TGATGAATTCAGACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
1 TGATGAATTCAGACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
1236869 TGAGTTCTTCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCAAG
66 TGAGTTCTTCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCAAG
1236917 TGATGAATTCAGACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
1 TGATGAATTCAGACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
1236982 TGAGTTCTTCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCAAG
66 TGAGTTCTTCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCAAG
1237030 TGATGAATTCAGACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
1 TGATGAATTCAGACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
1237095 TGAGTTCTTCTCATTATGAACCTTCTCTGGC-AAAATAATCCATCAAG
66 TGAGTTCTTCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCAAG
*
1237142 TGATGAATTCAGACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGA
1 TGATGAATTCAGACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
1237207 TGAGTTCTTCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCAAG
66 TGAGTTCTTCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCAAG
1237255 TGATGAATTCAGACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
1 TGATGAATTCAGACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
1237320 TGAGTTCTTCTCATTATGAACCTTCTCTGG
66 TGAGTTCTTCTCATTATGAACCTTCTCTGG
1237350 AAATGTCAAT
Statistics
Matches: 874, Mismatches: 10, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
112 111 0.13
113 763 0.87
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.36
Consensus pattern (113 bp):
TGATGAATTCAGACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGA
TGAGTTCTTCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCAAG
Found at i:1238247 original size:83 final size:83
Alignment explanation
Indices: 1238108--1238746 Score: 1091
Period size: 83 Copynumber: 7.7 Consensus size: 83
1238098 GTTCTTACCA
* *
1238108 AACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATT
1238173 CAATGATTGGTTCTGTCC
66 CAATGATTGGTTCTGTCC
* *
1238191 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATTCTATGAGCACATTCATCTTTCAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATT
1238256 CAATGATTGGTTCTGTCC
66 CAATGATTGGTTCTGTCC
* * *
1238274 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATTTTCTAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATT
* * *
1238339 CAATGATTTGTTTTGTCA
66 CAATGATTGGTTCTGTCC
* *
1238357 AACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATT
1238422 CAATGATTGGTTCTGTCC
66 CAATGATTGGTTCTGTCC
*
1238440 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATTCTATGAGCACATTCATCTTCCAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATT
1238505 CAATGATTGGTTCTGTCC
66 CAATGATTGGTTCTGTCC
* *
1238523 AACCAGATCAGCTAACTCAAAGAACACTTCCAGAAGATTCTATGAGCACATTCATCTTCCAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATT
1238588 CAATGATTGGTTCTGTCC
66 CAATGATTGGTTCTGTCC
* *
1238606 AACCAGATCAGCTAACTCAAAGAACACTTCCAGAAGATTCTATGAGCACATTCATCTTCCAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATT
1238671 CAATGATTGGTTCTGTCC
66 CAATGATTGGTTCTGTCC
* *
1238689 AACCAGATCAGATAATTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATTCATCTT
1238747 TCAGTTAATG
Statistics
Matches: 529, Mismatches: 26, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
83 527 1.00
84 2 0.00
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (83 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATT
CAATGATTGGTTCTGTCC
Found at i:1239543 original size:18 final size:19
Alignment explanation
Indices: 1239508--1239544 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1239498 TTCATAGAAG
1239508 AATAAATTGAATTTTCAAA
1 AATAAATTGAATTTTCAAA
1239527 AATAAATTGAA-TTTCAAA
1 AATAAATTGAATTTTCAAA
1239545 TAAAATGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.35
Consensus pattern (19 bp):
AATAAATTGAATTTTCAAA
Found at i:1239547 original size:16 final size:18
Alignment explanation
Indices: 1239508--1239553 Score: 60
Period size: 16 Copynumber: 2.6 Consensus size: 18
1239498 TTCATAGAAG
1239508 AATAAATTGAATTTTCAAA
1 AATAAATTGAATTTTC-AA
1239527 AATAAATTGAA-TTTC-A
1 AATAAATTGAATTTTCAA
*
1239543 AATAAAATGAA
1 AATAAATTGAA
1239554 CTTGAAATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 11 0.42
18 4 0.15
19 11 0.42
ACGTcount: A:0.57, C:0.04, G:0.07, T:0.33
Consensus pattern (18 bp):
AATAAATTGAATTTTCAA
Found at i:1247240 original size:15 final size:16
Alignment explanation
Indices: 1247220--1247252 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1247210 TGAATGATGA
1247220 ATGTATGC-AAAATGT
1 ATGTATGCAAAAATGT
1247235 ATGTATGCAAAAATGT
1 ATGTATGCAAAAATGT
1247251 AT
1 AT
1247253 TGATCCCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.33
Consensus pattern (16 bp):
ATGTATGCAAAAATGT
Found at i:1251279 original size:13 final size:13
Alignment explanation
Indices: 1251235--1251281 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
1251225 CTTTTCTTTG
*
1251235 ATATTGAAAACTAA
1 ATATTTAAAA-TAA
1251249 ATA-TTAAAATAA
1 ATATTTAAAATAA
*
1251261 TTTATTTAAAATAA
1 -ATATTTAAAATAA
1251275 ATATTTA
1 ATATTTA
1251282 TTTATTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 3 0.11
13 13 0.46
14 12 0.43
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (13 bp):
ATATTTAAAATAA
Found at i:1252264 original size:21 final size:20
Alignment explanation
Indices: 1252210--1252276 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 20
1252200 TTTTTCTCGG
*
1252210 TTTTGTCTCTTGTTTCTCTGTAT
1 TTTTGTCTC-TG-TTCTCT-TTT
* *
1252233 CTTTCTCTCTGTTCCTCTTTT
1 TTTTGTCTCTGTT-CTCTTTT
1252254 TTTTGTCTCTG-TCTCTTTT
1 TTTTGTCTCTGTTCTCTTTT
1252273 TTTT
1 TTTT
1252277 TTCAGGTTCG
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
19 11 0.29
20 1 0.03
21 13 0.34
22 6 0.16
23 7 0.18
ACGTcount: A:0.01, C:0.22, G:0.09, T:0.67
Consensus pattern (20 bp):
TTTTGTCTCTGTTCTCTTTT
Found at i:1252729 original size:3 final size:3
Alignment explanation
Indices: 1252721--1252782 Score: 115
Period size: 3 Copynumber: 20.7 Consensus size: 3
1252711 AATATATATT
*
1252721 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1252769 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
1252783 TGGGTAAAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1253601 original size:20 final size:20
Alignment explanation
Indices: 1253576--1253784 Score: 222
Period size: 20 Copynumber: 10.9 Consensus size: 20
1253566 GCGATTTTCC
* *
1253576 GACTATCGCAACGCGAATAT
1 GACTATCGCAACGCGATTCT
1253596 GACTATCGCAACGCGATTCT
1 GACTATCGCAACGCGATTCT
1253616 GACTATCGCAACGCGATTCT
1 GACTATCGCAACGCGATTCT
*
1253636 GACTATCGCAACGAGATTCT
1 GACTATCGCAACGCGATTCT
1253656 GACTATCGCAACGCGATTCT
1 GACTATCGCAACGCGATTCT
* *
1253676 GACTGTCGCAACGCGATGCT
1 GACTATCGCAACGCGATTCT
* *
1253696 GACTATCGTAATGCGA-T-T
1 GACTATCGCAACGCGATTCT
* *
1253714 ---T-TC-AAAGCGCCA-T-T
1 GACTATCGCAA-CGCGATTCT
*
1253728 -ATTATCGCAACGCGATTCT
1 GACTATCGCAACGCGATTCT
* *
1253747 GACTGTCGCAACGCGATGCT
1 GACTATCGCAACGCGATTCT
*
1253767 GACTATCGCAATGCGATT
1 GACTATCGCAACGCGATT
1253785 TTCAAAGCGC
Statistics
Matches: 160, Mismatches: 21, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
13 2 0.01
14 7 0.04
15 1 0.01
16 1 0.01
17 6 0.04
18 4 0.03
19 1 0.01
20 138 0.86
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (20 bp):
GACTATCGCAACGCGATTCT
Found at i:1253780 original size:71 final size:71
Alignment explanation
Indices: 1253659--1253812 Score: 299
Period size: 71 Copynumber: 2.2 Consensus size: 71
1253649 AGATTCTGAC
*
1253659 TATCGCAACGCGATTCTGACTGTCGCAACGCGATGCTGACTATCGTAATGCGATTTTCAAAGCGC
1 TATCGCAACGCGATTCTGACTGTCGCAACGCGATGCTGACTATCGCAATGCGATTTTCAAAGCGC
1253724 CATTAT
66 CATTAT
1253730 TATCGCAACGCGATTCTGACTGTCGCAACGCGATGCTGACTATCGCAATGCGATTTTCAAAGCGC
1 TATCGCAACGCGATTCTGACTGTCGCAACGCGATGCTGACTATCGCAATGCGATTTTCAAAGCGC
1253795 CATTAT
66 CATTAT
1253801 TATCGCAACGCG
1 TATCGCAACGCG
1253813 TATTTTTTTT
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 82 1.00
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (71 bp):
TATCGCAACGCGATTCTGACTGTCGCAACGCGATGCTGACTATCGCAATGCGATTTTCAAAGCGC
CATTAT
Found at i:1254444 original size:20 final size:19
Alignment explanation
Indices: 1254384--1254444 Score: 50
Period size: 20 Copynumber: 3.1 Consensus size: 19
1254374 AACGACAGAA
*
1254384 TCGCAATGCGATTTTAGTT
1 TCGCATTGCGATTTTAGTT
* * * *
1254403 TCGCGTTGCGATAATCATTT
1 TCGCATTGCGAT-TTTAGTT
*
1254423 TCGTATTGCGATTTTAAGTT
1 TCGCATTGCGATTTT-AGTT
1254443 TC
1 TC
1254445 AGAAACTATT
Statistics
Matches: 30, Mismatches: 10, Indels: 3
0.70 0.23 0.07
Matches are distributed among these distances:
19 11 0.37
20 19 0.63
ACGTcount: A:0.20, C:0.16, G:0.20, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTAGTT
Found at i:1256354 original size:20 final size:20
Alignment explanation
Indices: 1256329--1256376 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
1256319 TAGTTTACTT
1256329 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
**
1256349 TCGCAACGCGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
1256369 TCGCAACG
1 TCGCAACG
1256377 AAAGAATCGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.33, C:0.27, G:0.21, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:1256444 original size:20 final size:20
Alignment explanation
Indices: 1256419--1256514 Score: 147
Period size: 20 Copynumber: 4.8 Consensus size: 20
1256409 GCGATTCTCT
* **
1256419 CGTTGCGATAGTTAAATTCG
1 CGTTGCGATAGTCATTTTCG
1256439 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
1256459 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* *
1256479 CATTGCGATAGTCATTTTTG
1 CGTTGCGATAGTCATTTTCG
1256499 CGTTGCGATAGTCATT
1 CGTTGCGATAGTCATT
1256515 CGTGTTGCGA
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 70 1.00
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.40
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:1257106 original size:21 final size:21
Alignment explanation
Indices: 1257015--1257119 Score: 86
Period size: 21 Copynumber: 5.0 Consensus size: 21
1257005 GACTCACCTG
* *
1257015 TCATCGTTCAGGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
1257037 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
1257057 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
1257078 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
1257099 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
1257120 CCAACATTCT
Statistics
Matches: 62, Mismatches: 20, Indels: 3
0.73 0.24 0.04
Matches are distributed among these distances:
20 3 0.05
21 58 0.94
22 1 0.02
ACGTcount: A:0.20, C:0.37, G:0.20, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:1257112 original size:42 final size:42
Alignment explanation
Indices: 1257040--1257122 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
1257030 CCTCCCCTAT
*
1257040 CGTTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCAC
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGT-CCCTCCCAC
* ** *
1257082 CGTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCA
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCA
1257123 ACATTCTAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 33 0.94
43 2 0.06
ACGTcount: A:0.22, C:0.39, G:0.19, T:0.20
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCAC
Found at i:1258530 original size:14 final size:14
Alignment explanation
Indices: 1258511--1258549 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
1258501 TTGCTTGTTT
1258511 AATTGATTTATAAA
1 AATTGATTTATAAA
*
1258525 AATTGATTTCTAAA
1 AATTGATTTATAAA
*
1258539 AGTTGATTTAT
1 AATTGATTTAT
1258550 TTAATATTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46
Consensus pattern (14 bp):
AATTGATTTATAAA
Found at i:1258567 original size:29 final size:28
Alignment explanation
Indices: 1258513--1258567 Score: 65
Period size: 29 Copynumber: 1.9 Consensus size: 28
1258503 GCTTGTTTAA
*
1258513 TTGATTTATAAAAATTGATTTCTAAAAG
1 TTGATTTATAAAAATTGATGTCTAAAAG
* * *
1258541 TTGATTTATTTAATATTGATGTGTAAA
1 TTGATTTA-TAAAAATTGATGTCTAAA
1258568 TAATTCTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 8 0.36
29 14 0.64
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.47
Consensus pattern (28 bp):
TTGATTTATAAAAATTGATGTCTAAAAG
Found at i:1258723 original size:20 final size:20
Alignment explanation
Indices: 1258686--1258724 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1258676 ATGCTAAACT
* *
1258686 CAAAATCACAATGTGAAAGA
1 CAAAATCACAACGCGAAAGA
*
1258706 CAAAATCGCAACGCGAAAG
1 CAAAATCACAACGCGAAAG
1258725 TCAATTCGCG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.51, C:0.21, G:0.18, T:0.10
Consensus pattern (20 bp):
CAAAATCACAACGCGAAAGA
Found at i:1258824 original size:20 final size:20
Alignment explanation
Indices: 1258767--1259044 Score: 218
Period size: 20 Copynumber: 14.8 Consensus size: 20
1258757 GTGATTTTCT
* *
1258767 CGTTGCGATAGTCAAATACC
1 CGTTGCGATAGTCAAATTCG
* *
1258787 CATTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
1258807 CGTTGCGATACTCAAATTCA
1 CGTTGCGATAGTCAAATTCG
*
1258827 CGTTGCGAT--T----TTCT
1 CGTTGCGATAGTCAAATTCG
*
1258841 CGTTGCGATAGTCAAA-TAG
1 CGTTGCGATAGTCAAATTCG
* *
1258860 CCGTTGCGATAATCAAATTTG
1 -CGTTGCGATAGTCAAATTCG
1258881 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
1258901 CGTTGCGATAGACAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
1258921 TGTTGCG--A-T---ATT-G
1 CGTTGCGATAGTCAAATTCG
*
1258934 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
* *
1258954 TGTTGCGATATTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
1258974 CGTTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
* *
1258988 AGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
1259008 CATTGCGATAGTCAAATTAG
1 CGTTGCGATAGTCAAATTCG
*
1259028 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
1259045 GAATGTGTAA
Statistics
Matches: 206, Mismatches: 31, Indels: 42
0.74 0.11 0.15
Matches are distributed among these distances:
13 7 0.03
14 26 0.13
15 1 0.00
16 3 0.01
18 3 0.01
19 4 0.02
20 160 0.78
21 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:1258848 original size:74 final size:74
Alignment explanation
Indices: 1258727--1259044 Score: 286
Period size: 74 Copynumber: 4.3 Consensus size: 74
1258717 CGCGAAAGTC
** * * * *
1258727 AATTCGCGTTGCGATAGTTTAATACGCTTTGTGATTTTCTCGTTGCGATAGTCAAATACCCATTG
1 AATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTAGTTGCGATAGTCAAATACCCATTG
1258792 CGATAATCA
66 CGATAATCA
* * * * *
1258801 AATTCGCGTTGCGATACTCAAATTCACGTTGCGATTTTCTCGTTGCGATAGTCAAATAGCCGTTG
1 AATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTAGTTGCGATAGTCAAATACCCATTG
1258866 CGATAATCA
66 CGATAATCA
* *** * * * ** *
1258875 AATTTGCGTTGCGATAGTCAAATTCGCGTTGCGATAGACAAATT-CG-T-GTTGC-GATATTGCG
1 AATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTAGTTGCGATAG-T-CAAATA-CCCA
*
1258936 TTGCGATAGTCA
63 TTGCGATAATCA
* * * * * *
1258948 TATTCGTGTTGCGATATTCAAATTCGCGTTGCGATTTT-TGAGTTGCGATAATCAAATTCGCATT
1 AATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT-AGTTGCGATAGTCAAATACCCATT
*
1259012 GCGATAGTCA
65 GCGATAATCA
* *
1259022 AATTAGCGTTGCGATATTCAAAT
1 AATTCGCGTTGCGATAGTCAAAT
1259045 GAATGTGTAA
Statistics
Matches: 197, Mismatches: 39, Indels: 16
0.78 0.15 0.06
Matches are distributed among these distances:
71 1 0.01
72 5 0.03
73 50 0.25
74 137 0.70
75 4 0.02
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (74 bp):
AATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTAGTTGCGATAGTCAAATACCCATTG
CGATAATCA
Found at i:1258865 original size:34 final size:34
Alignment explanation
Indices: 1258733--1258869 Score: 114
Period size: 34 Copynumber: 3.9 Consensus size: 34
1258723 AGTCAATTCG
** * * *
1258733 CGTTGCGATAGTTTAATACGCTTTGTGATTTTCT
1 CGTTGCGATAGTCAAATACACGTTGCGATTTTCT
* * *
1258767 CGTTGCGATAGTCAAATACCCATTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATACACGTTGCGAT--T----TTCT
* *
1258807 CGTTGCGATACTCAAATTCACGTTGCGATTTTCT
1 CGTTGCGATAGTCAAATACACGTTGCGATTTTCT
1258841 CGTTGCGATAGTCAAATAGC-CGTTGCGAT
1 CGTTGCGATAGTCAAATA-CACGTTGCGAT
1258870 AATCAAATTT
Statistics
Matches: 83, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
34 52 0.63
35 1 0.01
36 1 0.01
38 1 0.01
40 28 0.34
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.35
Consensus pattern (34 bp):
CGTTGCGATAGTCAAATACACGTTGCGATTTTCT
Found at i:1258939 original size:53 final size:53
Alignment explanation
Indices: 1258878--1259039 Score: 225
Period size: 53 Copynumber: 3.0 Consensus size: 53
1258868 ATAATCAAAT
* *
1258878 TTGCGTTGCGATAGTCAAATTCGCGTTGCGATAGACAAATTCGTGTTGCGATA
1 TTGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATA
* * * *
1258931 TTGCGTTGCGATAGTCATATTCGTGTTGCGATATTCAAATTCGCGTTGCGATTT
1 TTGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGA-TA
* * * *
1258985 TTGAGTTGCGATAATCAAATTCGCATTGCGATAGTCAAATTAGCGTTGCGATA
1 TTGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATA
1259038 TT
1 TT
1259040 CAAATGAATG
Statistics
Matches: 94, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
53 49 0.52
54 45 0.48
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (53 bp):
TTGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATA
Found at i:1258942 original size:33 final size:33
Alignment explanation
Indices: 1258900--1258965 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
1258890 AGTCAAATTC
1258900 GCGTTGCGATAGACAAATTCGTGTTGCGATATT
1 GCGTTGCGATAGACAAATTCGTGTTGCGATATT
* *
1258933 GCGTTGCGATAGTCATATTCGTGTTGCGATATT
1 GCGTTGCGATAGACAAATTCGTGTTGCGATATT
1258966 CAAATTCGCG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.21, C:0.15, G:0.27, T:0.36
Consensus pattern (33 bp):
GCGTTGCGATAGACAAATTCGTGTTGCGATATT
Found at i:1259267 original size:140 final size:140
Alignment explanation
Indices: 1259015--1259284 Score: 504
Period size: 140 Copynumber: 1.9 Consensus size: 140
1259005 TCGCATTGCG
*
1259015 ATAGTCAAATTAGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTAGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
*
1259080 TAGCAATGTTCAAACTTAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
1259145 AGTACACATA
131 AGTACACATA
* *
1259155 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAGCTGAACAGATCA
1 ATAGTCAAATTAGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1259220 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
1259285 TACAACATTT
Statistics
Matches: 126, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 126 1.00
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTAGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AGTACACATA
Found at i:1259367 original size:18 final size:18
Alignment explanation
Indices: 1259344--1259378 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1259334 AAGCCGGTTG
*
1259344 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
1259362 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
1259379 GCCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:1262912 original size:12 final size:12
Alignment explanation
Indices: 1262891--1262924 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1262881 ACCACATTTC
*
1262891 CAATACCAAACA
1 CAATATCAAACA
1262903 CAATATCAAACA
1 CAATATCAAACA
*
1262915 CAATCTCAAA
1 CAATATCAAA
1262925 ACCCATAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:1263100 original size:24 final size:24
Alignment explanation
Indices: 1263049--1263102 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1263039 GTATTCGAAA
*
1263049 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
1263073 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
1263097 TTTGAT
1 TTTGAT
1263103 GATGTGATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:1265392 original size:18 final size:18
Alignment explanation
Indices: 1265369--1265404 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1265359 AAAAAAAAGG
1265369 AAATCAAAATCGCAATCA
1 AAATCAAAATCGCAATCA
*
1265387 AAATCAAAATCTCAATCA
1 AAATCAAAATCGCAATCA
1265405 CATCTGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCGCAATCA
Found at i:1265781 original size:20 final size:20
Alignment explanation
Indices: 1265726--1265784 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 20
1265716 AATAAGCGTT
* *
1265726 GCGATAGTCAAATTCACAAC
1 GCGAAAGTCAAATTCGCAAC
1265746 GCGAAAGTCAAATTCGCAAC
1 GCGAAAGTCAAATTCGCAAC
* *
1265766 GTGAATGTCAAATTCGCAA
1 GCGAAAGTCAAATTCGCAA
1265785 ACCGAAAATC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.20
Consensus pattern (20 bp):
GCGAAAGTCAAATTCGCAAC
Found at i:1266029 original size:47 final size:49
Alignment explanation
Indices: 1265922--1266020 Score: 139
Period size: 52 Copynumber: 2.0 Consensus size: 49
1265912 TTTAGAAACA
*
1265922 ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTT
1 ACAAATCAACTTTTACAAATCAATT--A-AAGCAAAAAAATAAATCTTATTT
*
1265974 ACAAATCAACTTTTACAAATCAATT-AATC-AAAAAATAAATCTTATTT
1 ACAAATCAACTTTTACAAATCAATTAAAGCAAAAAAATAAATCTTATTT
1266021 CCTCATCAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
47 17 0.38
48 3 0.07
52 25 0.56
ACGTcount: A:0.52, C:0.15, G:0.01, T:0.32
Consensus pattern (49 bp):
ACAAATCAACTTTTACAAATCAATTAAAGCAAAAAAATAAATCTTATTT
Found at i:1269689 original size:20 final size:19
Alignment explanation
Indices: 1269651--1269690 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
1269641 AAATCGCAAC
*
1269651 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCACGTT
*
1269670 GCGATTTTCATTTTCACGTT
1 GCGATTTT-AGTTTCACGTT
1269690 G
1 G
1269691 TGAATTTGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.12, C:0.17, G:0.23, T:0.47
Consensus pattern (19 bp):
GCGATTTTAGTTTCACGTT
Found at i:1269996 original size:22 final size:22
Alignment explanation
Indices: 1269959--1270001 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1269949 AGATAGACAG
*
1269959 ATTTCGTCGGAAATGGAGACGA
1 ATTTCGTCAGAAATGGAGACGA
* *
1269981 ATTTCGTCAGAGATGGGGACG
1 ATTTCGTCAGAAATGGAGACG
1270002 GATGTCGCCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.28, C:0.14, G:0.35, T:0.23
Consensus pattern (22 bp):
ATTTCGTCAGAAATGGAGACGA
Found at i:1270185 original size:21 final size:21
Alignment explanation
Indices: 1270141--1270277 Score: 99
Period size: 20 Copynumber: 6.8 Consensus size: 21
1270131 CATTTGACTT
*
1270141 TCGCGTTGCGAATTT-GACTA
1 TCGCGTTGCGAATTTGGAATA
1270161 TCGCGTTGCGAATTTGGAATA
1 TCGCGTTGCGAATTTGGAATA
*** *
1270182 TCGCAAAGCGAATTTGGAAAA
1 TCGCGTTGCGAATTTGGAATA
***
1270203 TCGTAATGCG-ATTT--ACATA
1 TCGCGTTGCGAATTTGGA-ATA
* *
1270222 TTCACGTTGCGAAATTGGAAT-
1 -TCGCGTTGCGAATTTGGAATA
*
1270243 TCGCGTTGCGAATTT-G-AGA
1 TCGCGTTGCGAATTTGGAATA
*
1270262 TCGCGTTACGAATTTG
1 TCGCGTTGCGAATTTG
1270278 TTGGTCATTT
Statistics
Matches: 92, Mismatches: 17, Indels: 16
0.74 0.14 0.13
Matches are distributed among these distances:
18 2 0.02
19 17 0.18
20 38 0.41
21 32 0.35
22 2 0.02
23 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (21 bp):
TCGCGTTGCGAATTTGGAATA
Found at i:1270835 original size:26 final size:26
Alignment explanation
Indices: 1270799--1270854 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
1270789 CGGCTTCCCT
1270799 AGGAGTATTATTCTAATGTTTTAGTA
1 AGGAGTATTATTCTAATGTTTTAGTA
1270825 AGGAGTATTATTCTAATGTTTTAGTA
1 AGGAGTATTATTCTAATGTTTTAGTA
1270851 AGGA
1 AGGA
1270855 CTATGGCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.32, C:0.04, G:0.21, T:0.43
Consensus pattern (26 bp):
AGGAGTATTATTCTAATGTTTTAGTA
Found at i:1272646 original size:3 final size:3
Alignment explanation
Indices: 1272638--1272705 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
1272628 TTTTTATCCA
1272638 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1272686 TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
1272706 ATTTATATTA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1273232 original size:19 final size:19
Alignment explanation
Indices: 1273180--1273245 Score: 64
Period size: 19 Copynumber: 3.5 Consensus size: 19
1273170 AAAAAAAAAA
* *
1273180 AGAAAAAACAGAGAGAAAC
1 AGAAAAAAAAGACAGAAAC
* *
1273199 AGAAAGAAGAGACAGAAAC
1 AGAAAAAAAAGACAGAAAC
*
1273218 AGAAAAAAAATACAGAGAA-
1 AGAAAAAAAAGACAGA-AAC
1273237 A-AAAAAAAA
1 AGAAAAAAAA
1273246 ACAACAAACT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
18 8 0.20
19 30 0.75
20 2 0.05
ACGTcount: A:0.73, C:0.08, G:0.18, T:0.02
Consensus pattern (19 bp):
AGAAAAAAAAGACAGAAAC
Found at i:1286726 original size:52 final size:52
Alignment explanation
Indices: 1286644--1287356 Score: 1381
Period size: 52 Copynumber: 13.7 Consensus size: 52
1286634 GAATATGCCA
1286644 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
1286696 ATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
1286748 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1286800 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1286852 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
1286904 ATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
1286956 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1287008 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1287060 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
1287112 ATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1287164 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1287216 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1287268 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1287320 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
1287357 TGGACAGAAT
Statistics
Matches: 651, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 651 1.00
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (52 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
Found at i:1288438 original size:112 final size:114
Alignment explanation
Indices: 1288029--1288868 Score: 1079
Period size: 116 Copynumber: 7.4 Consensus size: 114
1288019 TCCAGTTAGA
1288029 GTTCATAATGAGAAGAACTCGTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGT
1 GTTCATAATGAGAAGAAC-CGTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGT
* * *
1288094 TCAATCTTTAGCTCAAATCCATCACTTGATGGATCAGCTTTT-CCAGTTAG-A-
65 TCAATCTTTTGCT-GAATTCATCACTTGATGGATCA-CTTTTGCCAG--AGAAG
1288145 GTTCATAATGAGAAGAACTCGTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGT
1 GTTCATAATGAGAAGAAC-CGTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGT
* * * *
1288210 TCAATCTTTAGCTCAAATCCATCACTTGATGAATCAGCTTTT-CCAGTTAG-A-
65 TCAATCTTTTGCT-GAATTCATCACTTGATGGATCA-CTTTTGCCAG--AGAAG
* *
1288261 GTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
1 GTTCATAATGAGAAGAAC-CGTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGT
* * *
1288326 TCAACCTTTTTTCTGAATTCATCACTTGATGGATTA-TTTTGCCAGAGAAG
65 TCAATC-TTTTGCTGAATTCATCACTTGATGGATCACTTTTGCCAGAGAAG
*
1288376 GTTCATAATGAGAAGAA-C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 GTTCATAATGAGAAGAACCGTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
** * *
1288439 CAATCTTTTTTTGAATTCATCACTTGATGGATTATTTTTGCCAGAGAAG
66 CAATCTTTTGCTGAATTCATCACTTGATGGATCACTTTTGCCAGAGAAG
*
1288488 GTTCATAATGAGAAGAA-C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 GTTCATAATGAGAAGAACCGTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
** * *
1288551 CAATCTTTTTTTGAATTCATCACTTGATGGATTATTTTTGCCAGAGAAG
66 CAATCTTTTGCTGAATTCATCACTTGATGGATCACTTTTGCCAGAGAAG
* * * *
1288600 GTTCATAATGAGAAGAA-C-TCATTTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGCT
1 GTTCATAATGAGAAGAACCGTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* *
1288663 CAATCTTTTGCTTGAATTCATCATTTGATGGATCAAC-TTTGCCAG-GTAG
66 CAATCTTTTGC-TGAATTCATCACTTGATGGATC-ACTTTTGCCAGAGAAG
1288712 AGTTCATAATGAGAAGAACTCGTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTG
1 -GTTCATAATGAGAAGAAC-CGTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTG
* * ** *
1288777 TTCAATCTTTTGCTTGAATTCATCATTTGATGGATCA-TCATCCCCAGCAGAAA
64 TTCAATCTTTTGC-TGAATTCATCACTTGATGGATCACT-TTTGCCAG-AGAAG
1288830 GTTCATAATGAGAAGAA-C-TCATCTGAAGAAAG-AGAAGAA
1 GTTCATAATGAGAAGAACCGTCATCTGAAGAAAGAAGAAGAA
1288869 TTTATTCAAT
Statistics
Matches: 678, Mismatches: 31, Indels: 33
0.91 0.04 0.04
Matches are distributed among these distances:
111 28 0.04
112 246 0.36
113 55 0.08
114 20 0.03
115 24 0.04
116 281 0.41
117 22 0.03
118 2 0.00
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.30
Consensus pattern (114 bp):
GTTCATAATGAGAAGAACCGTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
CAATCTTTTGCTGAATTCATCACTTGATGGATCACTTTTGCCAGAGAAG
Found at i:1289012 original size:3 final size:3
Alignment explanation
Indices: 1289004--1289077 Score: 148
Period size: 3 Copynumber: 24.7 Consensus size: 3
1288994 TTTTTATCCA
1289004 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1289052 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
1289078 ATTTATATTA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1289602 original size:19 final size:19
Alignment explanation
Indices: 1289550--1289617 Score: 73
Period size: 19 Copynumber: 3.5 Consensus size: 19
1289540 GAAAAAAAAA
* *
1289550 AGAAAAAACAGAGAGAAAC
1 AGAAAAAAAAGACAGAAAC
* *
1289569 AGAAAGAAGAGACAGAAAC
1 AGAAAAAAAAGACAGAAAC
* *
1289588 AGAAAAAAAATACAGAGAAA
1 AGAAAAAAAAGACAGA-AAC
1289608 AGAAAAAAAA
1 AGAAAAAAAA
1289618 ACAACAAACT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
19 29 0.71
20 12 0.29
ACGTcount: A:0.72, C:0.07, G:0.19, T:0.01
Consensus pattern (19 bp):
AGAAAAAAAAGACAGAAAC
Found at i:1292822 original size:17 final size:17
Alignment explanation
Indices: 1292796--1292830 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1292786 TAAAAAACAT
*
1292796 AAAATATAATTTTTCAA
1 AAAATATAATTTATCAA
*
1292813 AAAATTTAATTTATCAA
1 AAAATATAATTTATCAA
1292830 A
1 A
1292831 TTAAAGTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (17 bp):
AAAATATAATTTATCAA
Found at i:1293943 original size:35 final size:35
Alignment explanation
Indices: 1293870--1293955 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 35
1293860 AAAACAGTCA
* * * *
1293870 TCAATTTCATTTTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
* * * *
1293905 TCAATTTTATTCTAAACCCTAAATTCTAAAATACT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
*
1293940 TCAATTAAATTCTAAA
1 TCAATTTAATTCTAAA
1293956 ATACTTCAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.41, C:0.20, G:0.01, T:0.38
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
Found at i:1293949 original size:21 final size:21
Alignment explanation
Indices: 1293924--1293966 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1293914 TTCTAAACCC
1293924 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
1293945 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
1293966 T
1 T
1293967 TAAGGTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTCTAAAATACTTCAAT
Found at i:1294121 original size:16 final size:18
Alignment explanation
Indices: 1294089--1294121 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
1294079 TATTAATGTA
1294089 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
1294107 TGAAT-ATTT-TATTTT
1 TGAATCATTTATATTTT
1294122 AATAAGAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 4 0.27
18 5 0.33
ACGTcount: A:0.27, C:0.03, G:0.06, T:0.64
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:1294782 original size:128 final size:124
Alignment explanation
Indices: 1294583--1294838 Score: 404
Period size: 128 Copynumber: 2.0 Consensus size: 124
1294573 AATTTTCTTC
* *
1294583 TAATTAGGAGGTGACATGTCACCAATAACACATATCATGATCATGTGTTAACACATGTCAGATCC
1 TAATTAGGAGGTAACATGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGATCC
*
1294648 TGATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATAAA
66 TAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT--CATATAAA
* * * *
1294709 TAATTAGGTGGTAACACGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGAGGTAACA--TGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
*
1294774 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATTATATAAA
64 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATCATATAAA
1294835 TAAT
1 TAAT
1294839 AAAGACTGAA
Statistics
Matches: 120, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
126 25 0.21
128 95 0.79
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.36
Consensus pattern (124 bp):
TAATTAGGAGGTAACATGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGATCC
TAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATCATATAAA
Found at i:1299385 original size:21 final size:22
Alignment explanation
Indices: 1299359--1299400 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1299349 GTGGAGCAGT
*
1299359 AAATTA-AAAAAACTAGAGATC
1 AAATTATAAAAAAATAGAGATC
1299380 AAATTATAAAAAAATAGAGAT
1 AAATTATAAAAAAATAGAGAT
1299401 TTAAAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.64, C:0.05, G:0.10, T:0.21
Consensus pattern (22 bp):
AAATTATAAAAAAATAGAGATC
Found at i:1299407 original size:24 final size:22
Alignment explanation
Indices: 1299359--1299410 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
1299349 GTGGAGCAGT
* *
1299359 AAATTA-AAAAAACTAGAGATC
1 AAATTATAAAAAAATAGAGATA
1299380 AAATTATAAAAAAATAGAGATTTA
1 AAATTATAAAAAAATAGAGA--TA
1299404 AAATTAT
1 AAATTAT
1299411 TTTACGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 6 0.23
22 12 0.46
24 8 0.31
ACGTcount: A:0.62, C:0.04, G:0.08, T:0.27
Consensus pattern (22 bp):
AAATTATAAAAAAATAGAGATA
Found at i:1303830 original size:35 final size:35
Alignment explanation
Indices: 1303778--1303844 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
1303768 TTAATCTCCA
*
1303778 TTCAAATCAAATTGTTAGTATCCATAGTCATAGGT
1 TTCAAATCAAATAGTTAGTATCCATAGTCATAGGT
* * *
1303813 TTCAAATGAAATAGTTAGTGTTCATAGTCATA
1 TTCAAATCAAATAGTTAGTATCCATAGTCATA
1303845 TATTAAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (35 bp):
TTCAAATCAAATAGTTAGTATCCATAGTCATAGGT
Found at i:1304450 original size:13 final size:13
Alignment explanation
Indices: 1304432--1304456 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1304422 TATTTTTGAA
1304432 GAAAACCATAATT
1 GAAAACCATAATT
1304445 GAAAACCATAAT
1 GAAAACCATAAT
1304457 AAATCAAGGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.16, G:0.08, T:0.20
Consensus pattern (13 bp):
GAAAACCATAATT
Found at i:1310244 original size:45 final size:47
Alignment explanation
Indices: 1310178--1310275 Score: 146
Period size: 45 Copynumber: 2.1 Consensus size: 47
1310168 CGTTATTCAC
* *
1310178 AAAAATAAATCCTAACTGCATGATATCTAATTCGCATGC-TTGTTCG
1 AAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCATTATTCG
*
1310224 AAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGCATTTATTCG
1 AAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCA-TTATTCG
1310271 AAAAA
1 AAAAA
1310276 ACGAAAATGA
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
45 27 0.57
46 9 0.19
47 11 0.23
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.30
Consensus pattern (47 bp):
AAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCATTATTCG
Found at i:1317315 original size:14 final size:14
Alignment explanation
Indices: 1317279--1317394 Score: 50
Period size: 14 Copynumber: 8.8 Consensus size: 14
1317269 GAATAGTTTG
1317279 AAAT-AAAATGTAA
1 AAATGAAAATGTAA
** *
1317292 TTATGCAAATGTAA
1 AAATGAAAATGTAA
*
1317306 AAATGAAAATATAA
1 AAATGAAAATGTAA
* *
1317320 ATAT--AAACGTAA
1 AAATGAAAATGTAA
1317332 AAATGAAAA---AA
1 AAATGAAAATGTAA
*
1317343 AGATGCAAAATGT--
1 AAATG-AAAATGTAA
*
1317356 AAATGCAAATGTAA
1 AAATGAAAATGTAA
* **
1317370 ATATGTGAATGTAA
1 AAATGAAAATGTAA
* *
1317384 CAATAAAAATG
1 AAATGAAAATG
1317395 CAAATTGTGC
Statistics
Matches: 72, Mismatches: 22, Indels: 17
0.65 0.20 0.15
Matches are distributed among these distances:
11 6 0.08
12 19 0.26
13 6 0.08
14 41 0.57
ACGTcount: A:0.59, C:0.04, G:0.13, T:0.24
Consensus pattern (14 bp):
AAATGAAAATGTAA
Found at i:1317357 original size:26 final size:27
Alignment explanation
Indices: 1317294--1317358 Score: 68
Period size: 26 Copynumber: 2.5 Consensus size: 27
1317284 AAATGTAATT
1317294 ATGC-AAATGTAAAAATGAAAATATAA
1 ATGCAAAATGTAAAAATGAAAATATAA
*
1317320 AT--ATAAACGTAAAAATGAAAA-A-AA
1 ATGCA-AAATGTAAAAATGAAAATATAA
1317344 GATGCAAAATGTAAA
1 -ATGCAAAATGTAAA
1317359 TGCAAATGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
24 2 0.06
25 3 0.09
26 26 0.81
27 1 0.03
ACGTcount: A:0.63, C:0.05, G:0.12, T:0.20
Consensus pattern (27 bp):
ATGCAAAATGTAAAAATGAAAATATAA
Found at i:1318495 original size:46 final size:49
Alignment explanation
Indices: 1318428--1318518 Score: 127
Period size: 46 Copynumber: 1.9 Consensus size: 49
1318418 AGGTATAAAT
* *
1318428 CCTAACCTCATGCTTTCTAGTTC-CATGC-TTTGTTT-GGAAAAATTAA
1 CCTAACCTCATGATTTCTAGTTCGCATGCATTTATTTAGGAAAAATTAA
1318474 CCTAA-CTGCATGATTTCTAGTTCGCATGCATTTATTTAGGAAAAA
1 CCTAACCT-CATGATTTCTAGTTCGCATGCATTTATTTAGGAAAAA
1318519 GAAAATAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
45 2 0.05
46 19 0.49
47 5 0.13
48 6 0.15
49 7 0.18
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (49 bp):
CCTAACCTCATGATTTCTAGTTCGCATGCATTTATTTAGGAAAAATTAA
Found at i:1321430 original size:3 final size:3
Alignment explanation
Indices: 1321424--1321496 Score: 105
Period size: 3 Copynumber: 24.7 Consensus size: 3
1321414 ATGTATTATT
*
1321424 TAA TAA TAA TAA T-A TAA -CA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1321470 TAA TAA CAA TAA TAA TAAA TAA TAA TA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TA
1321497 TAAGCAAATA
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
2 3 0.05
3 57 0.90
4 3 0.05
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1323764 original size:37 final size:36
Alignment explanation
Indices: 1323689--1323764 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
1323679 TTTTTATATT
*
1323689 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
1323725 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
1323762 TTT
1 TTT
1323765 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:1324968 original size:38 final size:38
Alignment explanation
Indices: 1324925--1325030 Score: 203
Period size: 38 Copynumber: 2.8 Consensus size: 38
1324915 ATGCAAAAGA
1324925 TAATCAAATGGTTGGTTATAACTTTTGGTTTAGGGTTT
1 TAATCAAATGGTTGGTTATAACTTTTGGTTTAGGGTTT
*
1324963 TAATCAAATGGTTGGGTATAACTTTTGGTTTAGGGTTT
1 TAATCAAATGGTTGGTTATAACTTTTGGTTTAGGGTTT
1325001 TAATCAAATGGTTGGTTATAACTTTTGGTT
1 TAATCAAATGGTTGGTTATAACTTTTGGTT
1325031 ATGCTTAAAT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 66 1.00
ACGTcount: A:0.25, C:0.06, G:0.24, T:0.46
Consensus pattern (38 bp):
TAATCAAATGGTTGGTTATAACTTTTGGTTTAGGGTTT
Found at i:1325553 original size:23 final size:23
Alignment explanation
Indices: 1325518--1325565 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1325508 ATCAAGTACA
* *
1325518 ATAATATATTAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCACTTAT
*
1325541 ATAATGTAATAGGTAGCACTTAT
1 ATAATATAATAGGTAGCACTTAT
1325564 AT
1 AT
1325566 TGACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.38
Consensus pattern (23 bp):
ATAATATAATAGGTAGCACTTAT
Found at i:1326451 original size:182 final size:181
Alignment explanation
Indices: 1326141--1326588 Score: 666
Period size: 182 Copynumber: 2.5 Consensus size: 181
1326131 TTTTTACTAT
* * *
1326141 CGGTTTTGTCATTTCGAGATCGATTTTATCATATTTTTATCTGTTATATTATTATGGATCGATAC
1 CGGTTTTGTCATTTCGAGACCG-TTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATAC
* * * * *
1326206 ACTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTATTTTCTTTTAAATTCTAAAAGTGT
65 ATTTTTATAAAGTATCGACACTTTATTAGAGCTATAACTTATTCTCTTTTAAATTCCAAAAGTGT
* * *
1326271 CGATACTTATAATAAAGTATCGACACTGTCAACATATTCGGTAGCTCTTTAC
130 CGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTAC
1326323 CGGTTTTGTCATTTCGAGACCTGTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATAC
1 CGGTTTTGTCATTTCGAGACC-GTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATAC
* *
1326388 ATTTTTATAAAGTATCGACACTTTATTAGAGTTATAACTTCTTCTCTTTTAAATTCCAAAAGTGT
65 ATTTTTATAAAGTATCGACACTTTATTAGAGCTATAACTTATTCTCTTTTAAATTCCAAAAGTGT
1326453 CGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTAC
130 CGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTAC
* * ** * * * * *
1326505 CTGTTTTGTTATTTATAGACCG--TTGTCATTTTTTTACCTTTTTTATTGTTATAGATCGATACA
1 CGGTTTTGTCATTTCGAGACCGTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACA
1326568 TTTTTATAAAGTATCGACACT
66 TTTTTATAAAGTATCGACACT
1326589 ATCAACATAT
Statistics
Matches: 243, Mismatches: 22, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
179 57 0.23
181 1 0.00
182 184 0.76
183 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.44
Consensus pattern (181 bp):
CGGTTTTGTCATTTCGAGACCGTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACA
TTTTTATAAAGTATCGACACTTTATTAGAGCTATAACTTATTCTCTTTTAAATTCCAAAAGTGTC
GATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTAC
Found at i:1326721 original size:113 final size:112
Alignment explanation
Indices: 1326464--1326924 Score: 642
Period size: 112 Copynumber: 4.1 Consensus size: 112
1326454 GATACTTATA
*
1326464 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTTATTTATAGACC-G-
1 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * *
1326527 -TTGTCATTTTTTTACCTTTTTTATTGTTATAGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATAGATCAATACATTTTT
1326573 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
1326638 TTTGTCATTTTTTTTACCTGTTATATTGTTATAGATTAATACATTTTT
66 TTTGTCA-TTTTTTTACCTGTTATATTGTTATAGATCAATACATTTTT
** * * * * *
1326686 ATAAAGTATTAACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTTTTATTTATAGTCCGGT
1 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * * * * *
1326751 TTTATTATTTTTTTACATGTTATATTATTATGGAT-ATATAAATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATAGATCA-ATACATTTTT
* * * *
1326798 ATAAAGTATCGACACTTTCGATATATCCGGTAGCGTTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * *
1326863 TTTGTCATTTTTTTACTTGTTATATTGTTATGGATCAATATATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATAGATCAATACATTTTT
*
1326910 ATAAAATATCGACAC
1 ATAAAGTATCGACAC
1326925 AAACCGACAA
Statistics
Matches: 315, Mismatches: 31, Indels: 9
0.89 0.09 0.03
Matches are distributed among these distances:
109 61 0.19
110 1 0.00
111 1 0.00
112 152 0.48
113 100 0.32
ACGTcount: A:0.26, C:0.14, G:0.13, T:0.47
Consensus pattern (112 bp):
ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACCTGTTATATTGTTATAGATCAATACATTTTT
Found at i:1326852 original size:225 final size:221
Alignment explanation
Indices: 1326464--1326924 Score: 652
Period size: 225 Copynumber: 2.1 Consensus size: 221
1326454 GATACTTATA
*
1326464 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTTATTTATAGACCGTT
1 ATAAAGTATCAACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTTATTTATAGACCGTT
* * * * * * *
1326529 GTCATTTTTTTACCTTTTTTATTGTTATAGATCGATACATTTTTATAAAGTATCGACACTATCAA
66 ATCATTTTTTTACATGTTATATTATTATAGATAGATAAATTTTTATAAAGTATCGACACTATCAA
1326594 CATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTTACCTGT
131 CATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTGTCA-TTTTTTTACCTGT
*
1326659 TATATTGTTATAGATTAATACATTTTT
195 TATATTGTTATAGATCAATACATTTTT
* * * * *
1326686 ATAAAGTATTAACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTTTTATTTATAGTCCGGT
1 ATAAAGTATCAACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTTATTTATAGACC-G-
* * * *
1326751 TTTATTATTTTTTTACATGTTATATTATTATGGATATATAAATTTTTATAAAGTATCGACACTTT
64 -TTATCATTTTTTTACATGTTATATTATTATAGATAGATAAATTTTTATAAAGTATCGACACTAT
* * * *
1326816 CGATATATCCGGTAGCGTTTTACCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACTT
128 CAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACCT
* *
1326881 GTTATATTGTTATGGATCAATATATTTTT
193 GTTATATTGTTATAGATCAATACATTTTT
* *
1326910 ATAAAATATCGACAC
1 ATAAAGTATCAACAC
1326925 AAACCGACAA
Statistics
Matches: 209, Mismatches: 27, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
222 56 0.27
223 1 0.00
224 48 0.23
225 104 0.50
ACGTcount: A:0.26, C:0.14, G:0.13, T:0.47
Consensus pattern (221 bp):
ATAAAGTATCAACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTTATTTATAGACCGTT
ATCATTTTTTTACATGTTATATTATTATAGATAGATAAATTTTTATAAAGTATCGACACTATCAA
CATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACCTGTT
ATATTGTTATAGATCAATACATTTTT
Found at i:1327622 original size:35 final size:35
Alignment explanation
Indices: 1327576--1327644 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
1327566 ATGTCAGTGA
1327576 CTTGATTTGACCCTGCAATTACAAGAAAAATCAAG
1 CTTGATTTGACCCTGCAATTACAAGAAAAATCAAG
*
1327611 CTTGATTTGACCCTGCAATTACAAGAATAATCAA
1 CTTGATTTGACCCTGCAATTACAAGAAAAATCAA
1327645 TCAGTCTGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.28
Consensus pattern (35 bp):
CTTGATTTGACCCTGCAATTACAAGAAAAATCAAG
Found at i:1335678 original size:13 final size:13
Alignment explanation
Indices: 1335660--1335684 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1335650 ATCGGATTTT
1335660 TTTTAACCGGTTA
1 TTTTAACCGGTTA
1335673 TTTTAACCGGTT
1 TTTTAACCGGTT
1335685 TGGAGAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.48
Consensus pattern (13 bp):
TTTTAACCGGTTA
Found at i:1338080 original size:21 final size:21
Alignment explanation
Indices: 1338056--1338095 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1338046 TTTATTTTAT
1338056 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
1338077 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
1338096 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:1338143 original size:33 final size:33
Alignment explanation
Indices: 1338090--1338188 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
1338080 TTTGTTTCAA
1338090 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1338122 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
1338155 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1338188 T
1 T
1338189 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:1338204 original size:27 final size:27
Alignment explanation
Indices: 1338174--1338243 Score: 140
Period size: 27 Copynumber: 2.6 Consensus size: 27
1338164 TTGGAAGTAT
1338174 TTAAGTATTTCAATTATGTTGAGTTAA
1 TTAAGTATTTCAATTATGTTGAGTTAA
1338201 TTAAGTATTTCAATTATGTTGAGTTAA
1 TTAAGTATTTCAATTATGTTGAGTTAA
1338228 TTAAGTATTTCAATTA
1 TTAAGTATTTCAATTA
1338244 AGTATTTGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.34, C:0.04, G:0.13, T:0.49
Consensus pattern (27 bp):
TTAAGTATTTCAATTATGTTGAGTTAA
Found at i:1338244 original size:13 final size:13
Alignment explanation
Indices: 1338174--1338255 Score: 69
Period size: 13 Copynumber: 6.2 Consensus size: 13
1338164 TTGGAAGTAT
1338174 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
1338187 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
1338201 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
1338214 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
1338228 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
1338241 TTAAGTATTTGAA
1 TTAAGTATTTCAA
1338254 TT
1 TT
1338256 TATAGAACTT
Statistics
Matches: 54, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
12 6 0.11
13 28 0.52
14 14 0.26
15 6 0.11
ACGTcount: A:0.34, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:1338478 original size:21 final size:21
Alignment explanation
Indices: 1338454--1338499 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1338444 AGCGTGGGGG
1338454 AATCGGTACCCTCTCATAGGA
1 AATCGGTACCCTCTCATAGGA
** *
1338475 AATCGGTTTCCTCTCATAGGG
1 AATCGGTACCCTCTCATAGGA
1338496 AATC
1 AATC
1338500 AGTTCCCTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (21 bp):
AATCGGTACCCTCTCATAGGA
Done.