Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004123.1 Hibiscus syriacus cultivar Beakdansim tig00009023_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: 1596068
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 9
Found at i:1093535 original size:21 final size:21
Alignment explanation
Indices: 1093509--1093576 Score: 109
Period size: 21 Copynumber: 3.2 Consensus size: 21
1093499 GATTTACGTA
* *
1093509 TTCGCATTGCGGTAGTCCAAG
1 TTCGCATTGCGATAGTCGAAG
*
1093530 TTCGCATTGTGATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAG
1093551 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAG
1093572 TTCGC
1 TTCGC
1093577 GTTGAGATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.31
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCGAAG
Found at i:1093713 original size:6 final size:6
Alignment explanation
Indices: 1093702--1093751 Score: 93
Period size: 6 Copynumber: 8.5 Consensus size: 6
1093692 GACACGTATT
1093702 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1093749 ACC
1 ACC
1093752 CGAGACGAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.11
6 39 0.89
ACGTcount: A:0.32, C:0.52, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1093760 original size:5 final size:5
Alignment explanation
Indices: 1093752--1093783 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
1093742 CGACCCGACC
1093752 CGAGA CGAGA CGAGA CGAGA CGAGA CG-GA CGA
1 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CGA
1093784 CGGCGGCGGC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.38, C:0.22, G:0.41, T:0.00
Consensus pattern (5 bp):
CGAGA
Found at i:1094433 original size:21 final size:21
Alignment explanation
Indices: 1094407--1094543 Score: 147
Period size: 21 Copynumber: 6.6 Consensus size: 21
1094397 TTTGGAATAA
*
1094407 ATCGCAACGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
*
1094428 ATCGCAATGCGAACTTGGACT
1 ATCGCAATGCGAACTTCGACT
*
1094449 ATCGCAATGCGAA-TAT-GTA-A
1 ATCGCAATGCGAACT-TCG-ACT
* *
1094469 ATCGTAATGCGATA-GTCGACT
1 ATCGCAATGCGA-ACTTCGACT
*
1094490 ATCGCAATGCGAACTTGGACT
1 ATCGCAATGCGAACTTCGACT
*
1094511 ATCGCAACGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
*
1094532 ATCGCATTGCGA
1 ATCGCAATGCGA
1094544 TTTACATATT
Statistics
Matches: 97, Mismatches: 13, Indels: 12
0.80 0.11 0.10
Matches are distributed among these distances:
20 16 0.16
21 81 0.84
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (21 bp):
ATCGCAATGCGAACTTCGACT
Found at i:1094581 original size:21 final size:21
Alignment explanation
Indices: 1094552--1094602 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
1094542 GATTTACATA
1094552 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
1094573 TTTGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
1094594 TTCGCATTG
1 TTCGCATTG
1094603 TGAATCTGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:1094901 original size:16 final size:16
Alignment explanation
Indices: 1094876--1094906 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1094866 CTCTCTTCAC
1094876 TCATTCTCTTTCTTTT
1 TCATTCTCTTTCTTTT
*
1094892 TCATTTTCTTTCTTT
1 TCATTCTCTTTCTTT
1094907 CATATAACAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.06, C:0.23, G:0.00, T:0.71
Consensus pattern (16 bp):
TCATTCTCTTTCTTTT
Found at i:1096076 original size:3 final size:3
Alignment explanation
Indices: 1096068--1096098 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1096058 TATATAATTA
*
1096068 AAT AAT AAT AAT ATT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1096099 TATTAAAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:1096927 original size:18 final size:17
Alignment explanation
Indices: 1096874--1096927 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 17
1096864 TTGTTTCCAT
1096874 TTTATTTTATATTAGTCA
1 TTTATTTTA-ATTAGTCA
*
1096892 -CTATTTTAA-TATGTCA
1 TTTATTTTAATTA-GTCA
1096908 TTTATTTTAATGTAGTCA
1 TTTATTTTAAT-TAGTCA
1096926 TT
1 TT
1096928 GATCTTTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
15 2 0.07
16 5 0.17
17 15 0.50
18 6 0.20
19 2 0.07
ACGTcount: A:0.28, C:0.07, G:0.07, T:0.57
Consensus pattern (17 bp):
TTTATTTTAATTAGTCA
Found at i:1099987 original size:3 final size:3
Alignment explanation
Indices: 1099981--1100051 Score: 65
Period size: 3 Copynumber: 23.7 Consensus size: 3
1099971 AAATTATTAA
* ** * *
1099981 AAT AAT AAT AAT AAT AAT AAAT AAC GTT GAA- AAT TAT TA- AAT AAT
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT -AAT AAT AAT AAT AAT AAT
1100026 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
1100052 ATAACGTTGA
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
2 3 0.05
3 50 0.89
4 3 0.05
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1102496 original size:60 final size:60
Alignment explanation
Indices: 1102431--1102568 Score: 181
Period size: 60 Copynumber: 2.3 Consensus size: 60
1102421 TTGAGTAACC
* ** * *
1102431 ATTTTATAACTTTTAATAGTCGAGAAACTTAATTAAATAAT-TTTATATAGTCAA-AAAATT
1 ATTTTATAACTTTTAATAGTCAAGAAACTTAACAAAATAATATTT-TATAAT-AAGAAAACT
*
1102491 ATTTTATAACTTTTAATAGTCAATAAACTTAACAAAATAATATTTTATAATAAGAAAACT
1 ATTTTATAACTTTTAATAGTCAAGAAACTTAACAAAATAATATTTTATAATAAGAAAACT
*
1102551 ATTTTGTAACTTTTAATA
1 ATTTTATAACTTTTAATA
1102569 TTTAAAACTT
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
59 2 0.03
60 64 0.93
61 3 0.04
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.42
Consensus pattern (60 bp):
ATTTTATAACTTTTAATAGTCAAGAAACTTAACAAAATAATATTTTATAATAAGAAAACT
Found at i:1102509 original size:29 final size:30
Alignment explanation
Indices: 1102431--1102522 Score: 98
Period size: 30 Copynumber: 3.0 Consensus size: 30
1102421 TTGAGTAACC
* *
1102431 ATTTTATAACTTTTAATAGTCGAGAAACTTA
1 ATTTTATAACTTTTAATAGTC-AAAAAATTA
**
1102462 ATTAAATAA-TTTTATATAGTCAAAAAATT-
1 ATTTTATAACTTTTA-ATAGTCAAAAAATTA
*
1102491 ATTTTATAACTTTTAATAGTCAATAAACTTA
1 ATTTTATAACTTTTAATAGTCAA-AAAATTA
1102522 A
1 A
1102523 CAAAATAATA
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
29 15 0.30
30 21 0.42
31 14 0.28
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (30 bp):
ATTTTATAACTTTTAATAGTCAAAAAATTA
Found at i:1106025 original size:31 final size:31
Alignment explanation
Indices: 1105987--1106050 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
1105977 TTACGTCAGA
* * *
1105987 GACCATATTATAAACGGACTAAATGTTGAGG
1 GACCATATTACAAACAGACTAAATATTGAGG
* *
1106018 GACCATATTGCAAATAGACTAAATATTGAGG
1 GACCATATTACAAACAGACTAAATATTGAGG
1106049 GA
1 GA
1106051 TGATATTGTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.41, C:0.12, G:0.22, T:0.25
Consensus pattern (31 bp):
GACCATATTACAAACAGACTAAATATTGAGG
Found at i:1107564 original size:31 final size:31
Alignment explanation
Indices: 1107529--1107589 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
1107519 TATAATCTCC
*
1107529 CAACATTTAGTCCGTTTGTAATATGGTCCCT
1 CAACATTTAGTCCGTTTATAATATGGTCCCT
1107560 CAACATTTAGTCCGTTTATAATATGGTCCC
1 CAACATTTAGTCCGTTTATAATATGGTCCC
1107590 CGACGTAACT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.38
Consensus pattern (31 bp):
CAACATTTAGTCCGTTTATAATATGGTCCCT
Found at i:1108768 original size:16 final size:17
Alignment explanation
Indices: 1108736--1108768 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1108726 AAGAATCTAA
*
1108736 ATTATTTAAAAATTATT
1 ATTATTTAAAAAGTATT
1108753 ATTATTT-AAAAGTATT
1 ATTATTTAAAAAGTATT
1108769 TAACGGTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (17 bp):
ATTATTTAAAAAGTATT
Found at i:1109112 original size:2 final size:2
Alignment explanation
Indices: 1109107--1109134 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1109097 ATCCAAAACA
1109107 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
1109135 TAAAAATTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1111780 original size:29 final size:29
Alignment explanation
Indices: 1111694--1111773 Score: 142
Period size: 29 Copynumber: 2.8 Consensus size: 29
1111684 CGCCATAGGA
*
1111694 CGCCATGCAATCCAGGCGACATTGGAGGT
1 CGCCATGCAATCCAGGCGACCTTGGAGGT
1111723 CGCCATGCAATCCAGGCGACCTTGGAGGT
1 CGCCATGCAATCCAGGCGACCTTGGAGGT
*
1111752 CGCCATGCAATCCGGGCGACCT
1 CGCCATGCAATCCAGGCGACCT
1111774 CCAAGGTATA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.21, C:0.33, G:0.30, T:0.16
Consensus pattern (29 bp):
CGCCATGCAATCCAGGCGACCTTGGAGGT
Found at i:1112408 original size:21 final size:21
Alignment explanation
Indices: 1112383--1112426 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1112373 AATCTAGTTA
1112383 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
1112404 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
1112425 AT
1 AT
1112427 ATTATATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:1112462 original size:28 final size:28
Alignment explanation
Indices: 1112396--1112462 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 28
1112386 AGTTTGTTAG
* *
1112396 TATAAATTATTAGTTTGTTAGTTTAAGT
1 TATATATTATTAGTTTATTAGTTTAAGT
1112424 TATAT-TATATTAGTTTATTAGTTTAAGT
1 TATATAT-TATTAGTTTATTAGTTTAAGT
1112452 TATATATTATT
1 TATATATTATT
1112463 TATATAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 1 0.03
28 33 0.94
29 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (28 bp):
TATATATTATTAGTTTATTAGTTTAAGT
Found at i:1116213 original size:26 final size:25
Alignment explanation
Indices: 1116184--1116491 Score: 193
Period size: 26 Copynumber: 12.5 Consensus size: 25
1116174 TTTGATGATT
1116184 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTT-ATAATAATCATTA
*
1116210 TAGTAATGATTGATAATAATCATTA
1 TAGTAATGATTTATAATAATCATTA
*
1116235 TAATAATGATTTAGTAATAATCATTA
1 TAGTAATGATTTA-TAATAATCATTA
** *
1116261 TAAAAATGA-TT-TAATAATGATT-
1 TAGTAATGATTTATAATAATCATTA
* * *
1116283 TA--AAT-ATTTAATGATTTGATGATT-
1 TAGTAATGATTT-AT-A-ATAATCATTA
1116307 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTT-ATAATAATCATTA
1116333 TAGTAATGATTTAGTAATAATCATTA
1 TAGTAATGATTTA-TAATAATCATTA
** *
1116359 TAAAAATGA-TT-TAATAATGATT-
1 TAGTAATGATTTATAATAATCATTA
* * *
1116381 TA--AAT-ATTTAATGATTTGATGATT-
1 TAGTAATGATTT-AT-A-ATAATCATTA
1116405 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTT-ATAATAATCATTA
* *
1116431 TAAT-ATGATTTTATAATAATTATTA
1 TAGTAATGA-TTTATAATAATCATTA
* * *
1116456 T-GTTATTATTTAGTAATTAT--TTA
1 TAGTAATGATTTA-TAATAATCATTA
*
1116479 TAATAATGATTTA
1 TAGTAATGATTTA
1116492 ATACTAATTA
Statistics
Matches: 230, Mismatches: 28, Indels: 50
0.75 0.09 0.16
Matches are distributed among these distances:
19 2 0.01
20 10 0.04
22 6 0.03
23 26 0.11
24 31 0.13
25 67 0.29
26 76 0.33
27 12 0.05
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (25 bp):
TAGTAATGATTTATAATAATCATTA
Found at i:1116340 original size:98 final size:98
Alignment explanation
Indices: 1116210--1116456 Score: 446
Period size: 98 Copynumber: 2.5 Consensus size: 98
1116200 ATAATCATTA
1116210 TAGTAATGA-TTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAAAAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAAAAATGATTTA
1116274 ATAATGATTTAAATATTTAATGATTTGATGATT
66 ATAATGATTTAAATATTTAATGATTTGATGATT
*
1116307 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTAGTAATAATCATTATAAAAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAAAAATGATTTA
1116372 ATAATGATTTAAATATTTAATGATTTGATGATT
66 ATAATGATTTAAATATTTAATGATTTGATGATT
*
1116405 TAGTAATGATTTGATAATAATCATTATAAT-ATGATTTTA-TAATAATTATTAT
1 TAGTAATGATTTGATAATAATCATTATAATAATGA-TTTAGTAATAATCATTAT
1116457 GTTATTATTT
Statistics
Matches: 145, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
97 25 0.17
98 120 0.83
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (98 bp):
TAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAAAAATGATTTA
ATAATGATTTAAATATTTAATGATTTGATGATT
Found at i:1116405 original size:61 final size:60
Alignment explanation
Indices: 1116301--1116494 Score: 189
Period size: 61 Copynumber: 3.2 Consensus size: 60
1116291 TAATGATTTG
* * * * * *
1116301 ATGATTTAGTAATGATTTGATAATAATCATTATAGTAATGATTTAGTAATAATCATTATAAAA
1 ATGATTTAATAATGATTTTATAATAATTATGAT-GTTATGATTTAGTAATAAT--TTATAATA
* *
1116364 ATGATTTAATAATGA-TTTA-AATATTTAATGAT-TTGATGATTTAGTAATGATTTGATAATA
1 ATGATTTAATAATGATTTTATAATAATT-ATGATGTT-ATGATTTAGTAATAATTT-ATAATA
* * * *
1116424 ATCATTATAAT-ATGATTTTATAATAATTATTATGTTATTATTTAGTAATTATTTATAATA
1 ATGATT-TAATAATGATTTTATAATAATTATGATGTTATGATTTAGTAATAATTTATAATA
1116484 ATGATTTAATA
1 ATGATTTAATA
1116495 CTAATTATTT
Statistics
Matches: 109, Mismatches: 14, Indels: 19
0.77 0.10 0.13
Matches are distributed among these distances:
59 6 0.06
60 26 0.24
61 48 0.44
62 15 0.14
63 14 0.13
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.47
Consensus pattern (60 bp):
ATGATTTAATAATGATTTTATAATAATTATGATGTTATGATTTAGTAATAATTTATAATA
Found at i:1116422 original size:11 final size:11
Alignment explanation
Indices: 1116178--1116350 Score: 51
Period size: 12 Copynumber: 15.2 Consensus size: 11
1116168 TAATGATTTG
1116178 ATGATTTAGTA
1 ATGATTTAGTA
*
1116189 ATGATTTGATAATA
1 ATGA-TT--TAGTA
*
1116203 ATCATTATAGTA
1 ATGATT-TAGTA
*
1116215 ATGATTGATAATA
1 ATGATT--TAGTA
* *
1116228 ATCATTATAATA
1 ATGATT-TAGTA
1116240 ATGATTTAGTA
1 ATGATTTAGTA
*
1116251 ATAATCATTA-TAAAA
1 ATGAT--TTAGT---A
*
1116266 ATGATTTAATA
1 ATGATTTAGTA
1116277 ATGATTTA--A
1 ATGATTTAGTA
1116286 AT-A-TT--TA
1 ATGATTTAGTA
1116293 ATGATTT-G--
1 ATGATTTAGTA
1116301 ATGATTTAGTA
1 ATGATTTAGTA
*
1116312 ATGATTTGATAATA
1 ATGA-TT--TAGTA
*
1116326 ATCATTATAGTA
1 ATGATT-TAGTA
1116338 ATGATTTAGTA
1 ATGATTTAGTA
1116349 AT
1 AT
1116351 AATCATTATA
Statistics
Matches: 128, Mismatches: 14, Indels: 40
0.70 0.08 0.22
Matches are distributed among these distances:
7 5 0.04
8 9 0.07
9 6 0.05
11 32 0.25
12 36 0.28
13 20 0.16
14 15 0.12
15 5 0.04
ACGTcount: A:0.43, C:0.02, G:0.12, T:0.43
Consensus pattern (11 bp):
ATGATTTAGTA
Found at i:1116466 original size:25 final size:25
Alignment explanation
Indices: 1116189--1116456 Score: 138
Period size: 25 Copynumber: 10.9 Consensus size: 25
1116179 TGATTTAGTA
*
1116189 ATGATTTGATAATAATCATTATAGT
1 ATGATTTGATAATAATCATTATAAT
1116214 AATGA-TTGATAATAATCATTATAAT
1 -ATGATTTGATAATAATCATTATAAT
*
1116239 AATGATTT-AGTAATAATCATTATAAAA
1 -ATGATTTGA-TAATAATCATTAT-AAT
*
1116266 ATGA-TT--TAATAATGATT-TAA-
1 ATGATTTGATAATAATCATTATAAT
* * * * *
1116286 AT-ATTTAATGATTTGATGATT-TAGT
1 ATGATTTGAT-A-ATAATCATTATAAT
*
1116311 AATGATTTGATAATAATCATTATAGT
1 -ATGATTTGATAATAATCATTATAAT
*
1116337 AATGATTT-AGTAATAATCATTATAAAA
1 -ATGATTTGA-TAATAATCATTAT-AAT
*
1116364 ATGA-TT--TAATAATGATT-TAA-
1 ATGATTTGATAATAATCATTATAAT
* * * * *
1116384 AT-ATTTAATGATTTGATGATT-TAGT
1 ATGATTTGAT-A-ATAATCATTATAAT
1116409 AATGATTTGATAATAATCATTATAAT
1 -ATGATTTGATAATAATCATTATAAT
* *
1116435 ATGATTTTATAATAATTATTAT
1 ATGATTTGATAATAATCATTAT
1116457 GTTATTATTT
Statistics
Matches: 196, Mismatches: 23, Indels: 47
0.74 0.09 0.18
Matches are distributed among these distances:
19 2 0.01
20 8 0.04
21 4 0.02
22 4 0.02
23 22 0.11
24 18 0.09
25 62 0.32
26 61 0.31
27 15 0.08
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.44
Consensus pattern (25 bp):
ATGATTTGATAATAATCATTATAAT
Found at i:1116504 original size:14 final size:13
Alignment explanation
Indices: 1116469--1116511 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
1116459 TATTATTTAG
*
1116469 TAATTATTTATAA
1 TAATTATTTATAC
*
1116482 TAATGATTTAATAC
1 TAATTATTT-ATAC
1116496 TAATTATTTGATAC
1 TAATTATTT-ATAC
1116510 TA
1 TA
1116512 GTAATGATTG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
13 8 0.32
14 17 0.68
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.49
Consensus pattern (13 bp):
TAATTATTTATAC
Found at i:1118948 original size:46 final size:48
Alignment explanation
Indices: 1118871--1118961 Score: 134
Period size: 46 Copynumber: 1.9 Consensus size: 48
1118861 CAACAAACAA
1118871 ATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTTTTT
1 ATATAACTTAACTATTTAACTAACACAAACTAATT-AATAATTTTTTTT
* *
1118920 ATATAAC-TAACTA-TTAAC-AATACAAACTAATTAATTATTTTT
1 ATATAACTTAACTATTTAACTAACACAAACTAATTAATAATTTTT
1118962 AACTATATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
45 9 0.22
46 13 0.32
47 5 0.12
48 6 0.15
49 7 0.17
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (48 bp):
ATATAACTTAACTATTTAACTAACACAAACTAATTAATAATTTTTTTT
Found at i:1118969 original size:46 final size:48
Alignment explanation
Indices: 1118871--1118974 Score: 133
Period size: 46 Copynumber: 2.2 Consensus size: 48
1118861 CAACAAACAA
**
1118871 ATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTTTTT
1 ATATAAC-TAACTATTTAACTAACACAAACTAATTAAATAATTTTTACT
* *
1118920 ATATAACTAACTA-TTAAC-AATACAAACTAATT-AATTATTTTTAACT
1 ATATAACTAACTATTTAACTAACACAAACTAATTAAATAATTTTT-ACT
1118966 ATATAACTA
1 ATATAACTA
1118975 TCAAACATAT
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
45 9 0.18
46 23 0.46
47 5 0.10
48 6 0.12
49 7 0.14
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.40
Consensus pattern (48 bp):
ATATAACTAACTATTTAACTAACACAAACTAATTAAATAATTTTTACT
Found at i:1119029 original size:40 final size:39
Alignment explanation
Indices: 1118943--1119029 Score: 95
Period size: 40 Copynumber: 2.2 Consensus size: 39
1118933 TTAACAATAC
*
1118943 AAACTAATTAATTATTTTTAACTATATAACTATCAAACAT
1 AAACTAATTAATAATTTTTAACTATATAACTAT-AAACAT
* * * *
1118983 ATACTAATTAAATAATTTTTAATTATGTATACTAT-AACTT
1 AAACTAATT-AATAATTTTTAACTATATA-ACTATAAACAT
1119023 AAACTAA
1 AAACTAA
1119030 CAATCATATA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
40 18 0.46
41 16 0.41
42 5 0.13
ACGTcount: A:0.47, C:0.10, G:0.01, T:0.41
Consensus pattern (39 bp):
AAACTAATTAATAATTTTTAACTATATAACTATAAACAT
Found at i:1119193 original size:21 final size:21
Alignment explanation
Indices: 1119163--1119221 Score: 93
Period size: 21 Copynumber: 2.9 Consensus size: 21
1119153 CCCTTTCTTC
1119163 TTCTTACTTTCCTTTCTCCCT
1 TTCTTACTTTCCTTTCTCCCT
*
1119184 TTCTTCCTTTCCTTTCTCCCT
1 TTCTTACTTTCCTTTCTCCCT
*
1119205 TTCTTTCTTT-CTTTCTC
1 TTCTTACTTTCCTTTCTC
1119222 GGCTGCAATC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 7 0.19
21 29 0.81
ACGTcount: A:0.02, C:0.37, G:0.00, T:0.61
Consensus pattern (21 bp):
TTCTTACTTTCCTTTCTCCCT
Found at i:1119254 original size:23 final size:23
Alignment explanation
Indices: 1119224--1119269 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1119214 TCTTTCTCGG
1119224 CTGCAATCTCTTCTCCCTTTCTT
1 CTGCAATCTCTTCTCCCTTTCTT
1119247 CTGCAATCTCTTCTCCCTTTCTT
1 CTGCAATCTCTTCTCCCTTTCTT
1119270 TCTTTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.09, C:0.39, G:0.04, T:0.48
Consensus pattern (23 bp):
CTGCAATCTCTTCTCCCTTTCTT
Found at i:1119381 original size:18 final size:18
Alignment explanation
Indices: 1119358--1119392 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1119348 GTACCAATAA
1119358 TCAAATGGTTCACATGCC
1 TCAAATGGTTCACATGCC
1119376 TCAAATGGTTCACATGC
1 TCAAATGGTTCACATGC
1119393 ATGCATTGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (18 bp):
TCAAATGGTTCACATGCC
Found at i:1119447 original size:37 final size:37
Alignment explanation
Indices: 1119397--1119471 Score: 134
Period size: 37 Copynumber: 2.0 Consensus size: 37
1119387 ACATGCATGC
1119397 ATTGGGAGGTGTAGGC-ATGCAGCGGGGGAGCACGTGA
1 ATTGGGAGGTGTAGGCAATGCAGC-GGGGAGCACGTGA
1119434 ATTGGGAGGTGTAGGCAATGCAGCGGGGAGCACGTGA
1 ATTGGGAGGTGTAGGCAATGCAGCGGGGAGCACGTGA
1119471 A
1 A
1119472 GGAATCTATG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
37 30 0.81
38 7 0.19
ACGTcount: A:0.24, C:0.13, G:0.47, T:0.16
Consensus pattern (37 bp):
ATTGGGAGGTGTAGGCAATGCAGCGGGGAGCACGTGA
Found at i:1119554 original size:29 final size:29
Alignment explanation
Indices: 1119521--1119658 Score: 242
Period size: 29 Copynumber: 4.8 Consensus size: 29
1119511 GATGGAATGG
1119521 CGCCGGGACTACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
1119550 CGCCGGGACTACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
1119579 CGCCGGGACTACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
1119608 CGCCGGGACTACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
* *
1119637 CGCCTAGG-CTGCATGGCGACCT
1 CGCC-GGGACTACATGGCGACCT
1119659 CTCTATTCCT
Statistics
Matches: 106, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
29 104 0.98
30 2 0.02
ACGTcount: A:0.22, C:0.32, G:0.31, T:0.14
Consensus pattern (29 bp):
CGCCGGGACTACATGGCGACCTACAAGGT
Found at i:1119731 original size:28 final size:28
Alignment explanation
Indices: 1119691--1119856 Score: 188
Period size: 28 Copynumber: 5.6 Consensus size: 28
1119681 TATGGCTCGT
1119691 TGCATGCTCCCCATTGGCTCTCTATTCC
1 TGCATGCTCCCCATTGGCTCTCTATTCC
* *
1119719 TGCATGCTCCCCATTGGCTCGTATATGGCTCGT
1 TGCATGCTCCCCATTGGCTC-TCTAT---TC-C
1119752 TGCATGCTCCCCATTGGCTCTCTATTCC
1 TGCATGCTCCCCATTGGCTCTCTATTCC
* * * *
1119780 TGCATGCTCCCCGTGGGCTCGTATATGGCTCGT
1 TGCATGCTCCCCATTGGCTC-TCTAT---TC-C
1119813 TGCATGCTCCCCATTGGCTCTCTATTCC
1 TGCATGCTCCCCATTGGCTCTCTATTCC
1119841 TGCATGCTCCCCATTG
1 TGCATGCTCCCCATTG
1119857 CCTCGTTGCA
Statistics
Matches: 116, Mismatches: 12, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
28 54 0.47
29 12 0.10
32 12 0.10
33 38 0.33
ACGTcount: A:0.11, C:0.36, G:0.20, T:0.34
Consensus pattern (28 bp):
TGCATGCTCCCCATTGGCTCTCTATTCC
Found at i:1119747 original size:61 final size:61
Alignment explanation
Indices: 1119672--1119862 Score: 355
Period size: 61 Copynumber: 3.1 Consensus size: 61
1119662 TATTCCTGCA
1119672 TGGCTCGTATATGGCTCGTTGCATGCTCCCCATTGGCTCTCTATTCCTGCATGCTCCCCAT
1 TGGCTCGTATATGGCTCGTTGCATGCTCCCCATTGGCTCTCTATTCCTGCATGCTCCCCAT
*
1119733 TGGCTCGTATATGGCTCGTTGCATGCTCCCCATTGGCTCTCTATTCCTGCATGCTCCCCGT
1 TGGCTCGTATATGGCTCGTTGCATGCTCCCCATTGGCTCTCTATTCCTGCATGCTCCCCAT
*
1119794 GGGCTCGTATATGGCTCGTTGCATGCTCCCCATTGGCTCTCTATTCCTGCATGCTCCCCAT
1 TGGCTCGTATATGGCTCGTTGCATGCTCCCCATTGGCTCTCTATTCCTGCATGCTCCCCAT
*
1119855 TGCCTCGT
1 TGGCTCGT
1119863 TGCATCCTCC
Statistics
Matches: 125, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
61 125 1.00
ACGTcount: A:0.10, C:0.35, G:0.21, T:0.34
Consensus pattern (61 bp):
TGGCTCGTATATGGCTCGTTGCATGCTCCCCATTGGCTCTCTATTCCTGCATGCTCCCCAT
Found at i:1119830 original size:22 final size:22
Alignment explanation
Indices: 1119805--1119884 Score: 79
Period size: 22 Copynumber: 3.4 Consensus size: 22
1119795 GGCTCGTATA
1119805 TGGCTCGTTGCATGCTCCCCAT
1 TGGCTCGTTGCATGCTCCCCAT
*
1119827 TGGCTCTCTATTCCTGCATGCTCCCCAT
1 TGG--CTC--GT--TGCATGCTCCCCAT
* *
1119855 TGCCTCGTTGCATCCTCCCCAT
1 TGGCTCGTTGCATGCTCCCCAT
1119877 TGGCTCGT
1 TGGCTCGT
1119885 ATGACTCGTA
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
22 23 0.49
24 4 0.09
26 4 0.09
28 16 0.34
ACGTcount: A:0.09, C:0.39, G:0.19, T:0.34
Consensus pattern (22 bp):
TGGCTCGTTGCATGCTCCCCAT
Found at i:1119903 original size:11 final size:11
Alignment explanation
Indices: 1119884--1119917 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
1119874 CATTGGCTCG
*
1119884 TATGACTCGTA
1 TATGGCTCGTA
1119895 TATGGCTCGTA
1 TATGGCTCGTA
1119906 TATGGCTCGTA
1 TATGGCTCGTA
1119917 T
1 T
1119918 GTCACCCTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.38
Consensus pattern (11 bp):
TATGGCTCGTA
Found at i:1122141 original size:2 final size:2
Alignment explanation
Indices: 1122134--1122169 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1122124 TTTTTATAGT
1122134 TA TA TA TA TA TA TA 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
1122170 ATTGAAATTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1125396 original size:12 final size:12
Alignment explanation
Indices: 1125379--1125405 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1125369 ACATTAAACA
1125379 AATATTAAAATT
1 AATATTAAAATT
1125391 AATATTAAAATT
1 AATATTAAAATT
1125403 AAT
1 AAT
1125406 CATTTTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
AATATTAAAATT
Found at i:1130201 original size:65 final size:63
Alignment explanation
Indices: 1130093--1130284 Score: 192
Period size: 65 Copynumber: 3.0 Consensus size: 63
1130083 TGATTAACCA
* ** *
1130093 ATCCATGCATCGATGCAC-CATGGAATAAATTG-AACATCGAATGCATTTCATGCACCGATGCAC
1 ATCCATGCATCGATGCACTCA--GAGTATTTTGAAACATCGAATGCATTTCATGCATCGATGCAC
* * * *
1130156 ATACTATGCATCGATGCACTCAGAGT-TTTATGAAAACATCAAATGCATTTGATACATCGATGCT
1 AT-CCATGCATCGATGCACTCAGAGTATTT-TG-AAACATCGAATGCATTTCATGCATCGATGC-
*
1130220 CC
62 AC
* * * *
1130222 ATCCATGTATCGATGCACTCTGGGTATTTTGAAACAACGAATGCATTTCATGCATCGATGCAC
1 ATCCATGCATCGATGCACTCAGAGTATTTTGAAACATCGAATGCATTTCATGCATCGATGCAC
1130285 CATTATAAAG
Statistics
Matches: 104, Mismatches: 18, Indels: 14
0.76 0.13 0.10
Matches are distributed among these distances:
62 1 0.01
63 8 0.08
64 41 0.39
65 48 0.46
66 6 0.06
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (63 bp):
ATCCATGCATCGATGCACTCAGAGTATTTTGAAACATCGAATGCATTTCATGCATCGATGCAC
Found at i:1132099 original size:65 final size:62
Alignment explanation
Indices: 1132021--1132200 Score: 202
Period size: 65 Copynumber: 2.8 Consensus size: 62
1132011 GAATAAATTG
*
1132021 AACATCGAATGCATTTCATGCACCGATGCATATACTATGCATCGATGCACTCAGAG-T-TTTATG
1 AACATCGAATGCATTTCATGCATCGATGCA-AT-CTATGCATCGATGCACTCAG-GCTATTT-TG
1132084 AA
62 -A
* * * *
1132086 AACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTCATGCATCGATGCA--ATCTATGCATCGATGCACTCAGGCTATTTTGA
* *
1132150 AACATCGAATGTATTTCATGCATCGATGCACTCTTAGTGCATCGATGCACT
1 AACATCGAATGCATTTCATGCATCGATGCAATC-TA-TGCATCGATGCACT
1132201 AAGGGTCCAA
Statistics
Matches: 99, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 44 0.44
65 49 0.49
66 4 0.04
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.29
Consensus pattern (62 bp):
AACATCGAATGCATTTCATGCATCGATGCAATCTATGCATCGATGCACTCAGGCTATTTTGA
Found at i:1140158 original size:65 final size:63
Alignment explanation
Indices: 1140041--1140248 Score: 215
Period size: 65 Copynumber: 3.2 Consensus size: 63
1140031 TTTCAGAGTG
* * * **
1140041 ATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGGAATAAATTG-AACATCGAATGCATT
1 ATGCATCGATGCA-CAA-CTATGCATCGATGCACTCA--GACTATTTTGAAACATCGAATGCATT
1140104 TC
62 TC
* * *
1140106 ATGCACCGATGCACATACTATGCATCGATGCACTCAGAGT-TTTATGAAAACATTGAATGCATTT
1 ATGCATCGATGCACA-ACTATGCATCGATGCACTCAGACTATTT-TG-AAACATCGAATGCATTT
*
1140170 G
63 C
***
1140171 ATGCATCGATGCACCAACTATGCATCGATGCACTCTTCCTATTTTGAAACATCGAATGCATTTC
1 ATGCATCGATGCA-CAACTATGCATCGATGCACTCAGACTATTTTGAAACATCGAATGCATTTC
1140235 ATGCATCGATGCAC
1 ATGCATCGATGCAC
1140249 TCTTAGTGCA
Statistics
Matches: 123, Mismatches: 13, Indels: 16
0.81 0.09 0.11
Matches are distributed among these distances:
62 1 0.01
63 6 0.05
64 46 0.37
65 65 0.53
66 5 0.04
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (63 bp):
ATGCATCGATGCACAACTATGCATCGATGCACTCAGACTATTTTGAAACATCGAATGCATTTC
Found at i:1141213 original size:26 final size:26
Alignment explanation
Indices: 1141177--1141230 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
1141167 CCAAACGGTT
1141177 GCACGGGTTGAACATCGGGCTTATGG
1 GCACGGGTTGAACATCGGGCTTATGG
1141203 GCACGGGTTGAACATCGGGCTTATGG
1 GCACGGGTTGAACATCGGGCTTATGG
1141229 GC
1 GC
1141231 TCGGTTGTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.19, C:0.20, G:0.39, T:0.22
Consensus pattern (26 bp):
GCACGGGTTGAACATCGGGCTTATGG
Found at i:1141674 original size:55 final size:55
Alignment explanation
Indices: 1141605--1141976 Score: 449
Period size: 55 Copynumber: 6.7 Consensus size: 55
1141595 TTCGAAAAAC
* *
1141605 GTGTCTGCTCCCTATTCTTTCAGGGAATATAGGACTCGAACAATCTTCAGCAAAT
1 GTGTCCGCTCCCTATTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAGCAAAT
* * * *
1141660 -TGGTCCGCTTCCTATTTTTTCAGGGAGTATAGGACTCAAACAATATTCAGCAAAT
1 GT-GTCCGCTCCCTATTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAGCAAAT
* * * *
1141715 GCGTCCGGCTCCCTATTCTTTCATGGAGTATAGGACTCGAAACAATCTTCAACAAAC
1 GTGTCC-GCTCCCTATTCTTTCAGGGAGTATAGGACTCG-AACAATCTTCAGCAAAT
* * * * *
1141772 GTGTCCACTCCCTATTCTTTCAGAGAGTATAGGACTCAAACAATCTTTAGCAAAC
1 GTGTCCGCTCCCTATTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAGCAAAT
** * *
1141827 GTGTTTGCTCCCTATTCTTTCAAGGAGTATAGGACTCGAGCAATCTTCAGCAAAT
1 GTGTCCGCTCCCTATTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAGCAAAT
* *** *
1141882 GTCTTTACTCCCTATTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAACAAAT
1 GTGTCCGCTCCCTATTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAGCAAAT
* ** * *
1141937 GTATTTGCGCCCTATTCTTTCAGAGAGTATAGGACTCGAA
1 GTGTCCGCTCCCTATTCTTTCAGGGAGTATAGGACTCGAA
1141977 ATTGATTTGC
Statistics
Matches: 274, Mismatches: 39, Indels: 8
0.85 0.12 0.02
Matches are distributed among these distances:
54 1 0.00
55 198 0.72
56 56 0.20
57 19 0.07
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (55 bp):
GTGTCCGCTCCCTATTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAGCAAAT
Found at i:1142206 original size:37 final size:37
Alignment explanation
Indices: 1141977--1142206 Score: 173
Period size: 37 Copynumber: 6.1 Consensus size: 37
1141967 AGGACTCGAA
1141977 ATTGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAG
1 ATTGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAG
* *
1142014 ATTAATTTGCATT-ACTACTCTTTCGTGAAGGCTTAAG
1 ATTGATTTGC-TTCACTACTCTTCCGTGAAGGCTTAAG
* * ** ** * * *
1142051 A-CGGTCCGGATGACTTATCATCTTACTCG-GAAGCCTTACTG
1 ATTGATTTGCTTCAC-TA-C-TCTT-C-CGTGAAGGCTTA-AG
** * *
1142092 A-TGGCTTGCTTCACTACTCTGT-CATGAAGACTTAAG
1 ATTGATTTGCTTCACTACTCT-TCCGTGAAGGCTTAAG
* * * *
1142128 ATTGATTTTCTTTACTACTCTTCTGTGAAGGCTTAAA
1 ATTGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAG
*
1142165 ATTGATTTGCTTCACTGCTCTTCCGTGAAGGCTTAAG
1 ATTGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAG
1142202 ATTGA
1 ATTGA
1142207 CTTTCCCCAA
Statistics
Matches: 146, Mismatches: 35, Indels: 24
0.71 0.17 0.12
Matches are distributed among these distances:
35 1 0.01
36 8 0.05
37 105 0.72
38 6 0.04
39 6 0.04
40 10 0.07
41 10 0.07
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.37
Consensus pattern (37 bp):
ATTGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAG
Found at i:1144835 original size:99 final size:99
Alignment explanation
Indices: 1144664--1144852 Score: 288
Period size: 99 Copynumber: 1.9 Consensus size: 99
1144654 TGTAATTTGT
* * ** * * *
1144664 CTTTATCAGGTTAGTTGAATCTTATCCATAAAGCTGGGGCGTTTAACCAATTATTTTAGAGGGAC
1 CTTTATCAGGCTAGCTGAATCTTATCCATAAAGCCAGGGCGTTTAACCAATTACTCTAAAGGGAC
*
1144729 AACTCAAGCTTTATTGTATATATATTATAATCAC
66 AACTCAAGCTTTATTGTATACATATTATAATCAC
* *
1144763 CTTTATCAGGCTAGCTGAATCTTATCCATAAAGCCATGGCGTTTAACCAATTGCTCTAAAGGGAC
1 CTTTATCAGGCTAGCTGAATCTTATCCATAAAGCCAGGGCGTTTAACCAATTACTCTAAAGGGAC
1144828 AACTCAAGCTTTATTGTATACATAT
66 AACTCAAGCTTTATTGTATACATAT
1144853 AATATTATAA
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
99 80 1.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (99 bp):
CTTTATCAGGCTAGCTGAATCTTATCCATAAAGCCAGGGCGTTTAACCAATTACTCTAAAGGGAC
AACTCAAGCTTTATTGTATACATATTATAATCAC
Found at i:1154812 original size:35 final size:34
Alignment explanation
Indices: 1154765--1154840 Score: 82
Period size: 35 Copynumber: 2.2 Consensus size: 34
1154755 AACACAATCC
1154765 TCAATTTAATTCTAAATCC-CAAATTCCAAAATAAT
1 TCAA-TTAATTCTAAA-CCTCAAATTCCAAAATAAT
* * * *
1154800 TCAATTACATTCTGAACCTTAAATTCTAAAATACT
1 TCAATTA-ATTCTAAACCTCAAATTCCAAAATAAT
1154835 TCAATT
1 TCAATT
1154841 TAGGGTTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
34 5 0.14
35 30 0.86
ACGTcount: A:0.42, C:0.20, G:0.01, T:0.37
Consensus pattern (34 bp):
TCAATTAATTCTAAACCTCAAATTCCAAAATAAT
Found at i:1157784 original size:30 final size:30
Alignment explanation
Indices: 1157748--1157805 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
1157738 TAATAAATGG
*
1157748 AGGGAATTAAACTTGGGTCTCATGAGATGT
1 AGGGAATTAAACTTGGATCTCATGAGATGT
1157778 AGGGAATTAAACTTGGATCTCATGAGAT
1 AGGGAATTAAACTTGGATCTCATGAGAT
1157806 ATTTGAGTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.33, C:0.10, G:0.28, T:0.29
Consensus pattern (30 bp):
AGGGAATTAAACTTGGATCTCATGAGATGT
Found at i:1159633 original size:13 final size:14
Alignment explanation
Indices: 1159615--1159643 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1159605 ACATTTGCTA
1159615 ATGTTTC-CACAAG
1 ATGTTTCTCACAAG
1159628 ATGTTTCTCACAAG
1 ATGTTTCTCACAAG
1159642 AT
1 AT
1159644 TCAAGCTCCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (14 bp):
ATGTTTCTCACAAG
Found at i:1159875 original size:58 final size:59
Alignment explanation
Indices: 1159795--1159960 Score: 248
Period size: 58 Copynumber: 2.8 Consensus size: 59
1159785 TACACAAATG
* *
1159795 GTCCCCCGACTATAGGGTGTTGCTTTATTGAGTCCCATC-ACTATTAAAAGTTAT-AAAGG
1 GTCCCCC-ACTATAGGGAGTTGCTTTATTGAGT-CCATCGACTATTAAAAGTTATGAAAGA
* * *
1159854 GTCCTCCATTATAGGGAGTTGCTTTATTGAGTCC-TCGACTATTAAAAGTTATGAAATA
1 GTCCCCCACTATAGGGAGTTGCTTTATTGAGTCCATCGACTATTAAAAGTTATGAAAGA
1159912 GTCCCCCACTATAGGGAGTTGCTTTATTGAGTCCATCGACTATTAAAAG
1 GTCCCCCACTATAGGGAGTTGCTTTATTGAGTCCATCGACTATTAAAAG
1159961 CTACAAAAGA
Statistics
Matches: 97, Mismatches: 7, Indels: 6
0.88 0.06 0.05
Matches are distributed among these distances:
56 2 0.02
57 17 0.18
58 58 0.60
59 20 0.21
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (59 bp):
GTCCCCCACTATAGGGAGTTGCTTTATTGAGTCCATCGACTATTAAAAGTTATGAAAGA
Found at i:1161498 original size:153 final size:153
Alignment explanation
Indices: 1161297--1161602 Score: 612
Period size: 153 Copynumber: 2.0 Consensus size: 153
1161287 ATTGTTTTCT
1161297 ACACATAATTAATGTTTACTGTGTTTATATTAAATAAAAAAACATTTTCAAAGAGACACATCTGA
1 ACACATAATTAATGTTTACTGTGTTTATATTAAATAAAAAAACATTTTCAAAGAGACACATCTGA
1161362 AATCATATAATTGAAAAAACTCGTAACTTGACTCATCAAAGATTCATATTTGAATATGAATATAA
66 AATCATATAATTGAAAAAACTCGTAACTTGACTCATCAAAGATTCATATTTGAATATGAATATAA
1161427 AAATATAATTTTTAAATACATAA
131 AAATATAATTTTTAAATACATAA
1161450 ACACATAATTAATGTTTACTGTGTTTATATTAAATAAAAAAACATTTTCAAAGAGACACATCTGA
1 ACACATAATTAATGTTTACTGTGTTTATATTAAATAAAAAAACATTTTCAAAGAGACACATCTGA
1161515 AATCATATAATTGAAAAAACTCGTAACTTGACTCATCAAAGATTCATATTTGAATATGAATATAA
66 AATCATATAATTGAAAAAACTCGTAACTTGACTCATCAAAGATTCATATTTGAATATGAATATAA
1161580 AAATATAATTTTTAAATACATAA
131 AAATATAATTTTTAAATACATAA
1161603 GGAAATGATA
Statistics
Matches: 153, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
153 153 1.00
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.34
Consensus pattern (153 bp):
ACACATAATTAATGTTTACTGTGTTTATATTAAATAAAAAAACATTTTCAAAGAGACACATCTGA
AATCATATAATTGAAAAAACTCGTAACTTGACTCATCAAAGATTCATATTTGAATATGAATATAA
AAATATAATTTTTAAATACATAA
Found at i:1163444 original size:29 final size:28
Alignment explanation
Indices: 1163412--1163506 Score: 109
Period size: 29 Copynumber: 3.3 Consensus size: 28
1163402 AAAAATCTTA
*
1163412 AAATTATAATAAAGATATAAACTTTTTGG
1 AAATTATAATAAAGATA-AAACTTTTTAG
** * *
1163441 AAATTATAATAGGGAAAAAACTTTTTAA
1 AAATTATAATAAAGATAAAACTTTTTAG
* *
1163469 AAATTATAGTAAAGGATAAAACTTTGTAG
1 AAATTATAATAAA-GATAAAACTTTTTAG
1163498 AAATTATAA
1 AAATTATAA
1163507 CCCTCTATGT
Statistics
Matches: 53, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
28 19 0.36
29 34 0.64
ACGTcount: A:0.52, C:0.03, G:0.12, T:0.34
Consensus pattern (28 bp):
AAATTATAATAAAGATAAAACTTTTTAG
Found at i:1164934 original size:23 final size:23
Alignment explanation
Indices: 1164890--1164934 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1164880 CTCTATTCAA
*
1164890 TGAAAAATAGTTAAGTCTTTTCT
1 TGAAAAATAGTTAAGTCATTTCT
*
1164913 TGAAAAATAGTTAATTCATTTC
1 TGAAAAATAGTTAAGTCATTTC
1164935 ACCCAATAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (23 bp):
TGAAAAATAGTTAAGTCATTTCT
Found at i:1170200 original size:23 final size:23
Alignment explanation
Indices: 1170174--1170223 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
1170164 AACATCTCTA
* *
1170174 TTCATGAAAAATAGTTAAGTCTT
1 TTCATCAAAAATAGTTAAGTCAT
* *
1170197 TTCATCAAAAGTAGTTAATTCAT
1 TTCATCAAAAATAGTTAAGTCAT
1170220 TTCA
1 TTCA
1170224 CCCAAAAAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (23 bp):
TTCATCAAAAATAGTTAAGTCAT
Found at i:1171222 original size:3 final size:3
Alignment explanation
Indices: 1171214--1171287 Score: 55
Period size: 3 Copynumber: 24.7 Consensus size: 3
1171204 TTCGAGTTGA
* * *
1171214 TAT TAT TA- TAT TAT TAT TAT TAT ATAT AAT TAT ATGT TA- TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT -TAT TAT TAT TAT
* *
1171259 TAT TAT TAT ATAT TAA TAT TGT TA- TAT TA
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TA
1171288 CAAGCCCAAT
Statistics
Matches: 56, Mismatches: 9, Indels: 12
0.73 0.12 0.16
Matches are distributed among these distances:
2 6 0.11
3 42 0.75
4 8 0.14
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:1171226 original size:8 final size:8
Alignment explanation
Indices: 1171213--1171287 Score: 61
Period size: 8 Copynumber: 9.8 Consensus size: 8
1171203 ATTCGAGTTG
1171213 ATATTATT
1 ATATTATT
1171221 ATATTATT
1 ATATTATT
1171229 ATTATTA-T
1 A-TATTATT
*
1171237 ATATAATT
1 ATATTATT
*
1171245 ATA-TGTT
1 ATATTATT
*
1171252 ATACTA-T
1 ATATTATT
1171259 -TATTATT
1 ATATTATT
1171266 ATA-TATT
1 ATATTATT
*
1171273 AATATTGTT
1 -ATATTATT
1171282 ATATTA
1 ATATTA
1171288 CAAGCCCAAT
Statistics
Matches: 53, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
6 4 0.08
7 15 0.28
8 26 0.49
9 8 0.15
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (8 bp):
ATATTATT
Found at i:1171254 original size:31 final size:30
Alignment explanation
Indices: 1171213--1171287 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 30
1171203 ATTCGAGTTG
*
1171213 ATATTATTATATTATTATTATTATATA-TA
1 ATATTGTTATATTATTATTATTATATATTA
*
1171242 ATTATATGTTATACTATTATTATTATATATTA
1 A-TAT-TGTTATATTATTATTATTATATATTA
1171274 ATATTGTTATATTA
1 ATATTGTTATATTA
1171288 CAAGCCCAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
29 1 0.03
30 12 0.30
31 24 0.60
32 3 0.08
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (30 bp):
ATATTGTTATATTATTATTATTATATATTA
Found at i:1171386 original size:25 final size:26
Alignment explanation
Indices: 1171342--1171433 Score: 125
Period size: 25 Copynumber: 3.6 Consensus size: 26
1171332 GAAGGTCCAG
* *
1171342 ACCCGAGCAGGCCCAAAACCAGTTCA
1 ACCCGAGCAAGCCCAGAACCAGTTCA
1171368 ACCCGAG-AAGCCCAGAACCAGTTCA
1 ACCCGAGCAAGCCCAGAACCAGTTCA
* * *
1171393 ACCCAAGCAGGCCCAGAACCCGTTCA
1 ACCCGAGCAAGCCCAGAACCAGTTCA
1171419 ACCCGAG-AAGCCCAG
1 ACCCGAGCAAGCCCAG
1171434 GACCCGAAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
25 29 0.50
26 29 0.50
ACGTcount: A:0.34, C:0.39, G:0.21, T:0.07
Consensus pattern (26 bp):
ACCCGAGCAAGCCCAGAACCAGTTCA
Found at i:1173311 original size:19 final size:19
Alignment explanation
Indices: 1173287--1173325 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1173277 TCGAATGCAT
1173287 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
1173306 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
1173325 T
1 T
1173326 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:1173342 original size:65 final size:64
Alignment explanation
Indices: 1173224--1173431 Score: 208
Period size: 65 Copynumber: 3.2 Consensus size: 64
1173214 TATTCAAAGG
* * *
1173224 CATGCACCGATGCA-TCAGTCCATGCATCGATGCATCTATGAAT-TAATT-GAACATCGAATGCA
1 CATGCACCGATGCACTC--TCCATGCATCGATGCA-CTCTGAATAT-TTTCAAACATCGAATGCA
*
1173286 TTC
62 TTT
1173289 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTC-AAACATCGAATGCATTT
* * *** * **
1173354 GATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTCAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATA-TTTTCAAACATCGAATGCATTT
* *
1173418 TATGCATCGATGCA
1 CATGCACCGATGCA
1173432 TCATTAGTGC
Statistics
Matches: 125, Mismatches: 13, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
63 9 0.07
64 51 0.41
65 63 0.50
66 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (64 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTT
Found at i:1174039 original size:65 final size:65
Alignment explanation
Indices: 1173901--1174033 Score: 205
Period size: 67 Copynumber: 2.0 Consensus size: 65
1173891 AGGAATTTGT
****
1173901 TGGAAAATCCTTAGTGTGGATAGCTAGGTAGGGACGTAGACTTTGTTTGAGAAAGTCGAATTTGT
1 TGGAAAATCCTTAGTGTGGATAGCTAGGTAGGGACGTAGACTTTGTTTGAGAAAGTCGAATCCAC
1173966 TGGAAAATCCTTAGTGTGGATAGCTAAGGTAGTGGACGTAGACTTTGTTTGAGAAAGTCGAA-CC
1 TGGAAAATCCTTAGTGTGGATAGCT-AGGTAG-GGACGTAGACTTTGTTTGAGAAAGTCGAATCC
1174030 AC
64 AC
1174032 TG
1 TG
1174034 TAAATCACTG
Statistics
Matches: 62, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
65 25 0.40
66 8 0.13
67 29 0.47
ACGTcount: A:0.29, C:0.11, G:0.30, T:0.30
Consensus pattern (65 bp):
TGGAAAATCCTTAGTGTGGATAGCTAGGTAGGGACGTAGACTTTGTTTGAGAAAGTCGAATCCAC
Found at i:1180737 original size:127 final size:130
Alignment explanation
Indices: 1180510--1180767 Score: 495
Period size: 127 Copynumber: 2.0 Consensus size: 130
1180500 CTAGCAATTT
1180510 GTTTATCAAACTCGGCCTAGATGTCTCCCTTGACAATCCTATCCCGCTCCAAAACCCAATCAATA
1 GTTTATCAAACTCGGCCTAGATGTCTCCCTTGACAATCCTATCCCGCTCCAAAACCCAATCAATA
1180575 TCACATCCTTAAAGAAATCGGATTAGAAATTGGATGAG-A-ATCGGACTATGGTCTTTTCGACCC
66 TCACATCCTTAAAGAAATCGGATTAGAAATTGGATGAGAACATCGGACTATGGTCTTTTCGACCC
1180638 GTTTATCAAACTCGGCCTAGATGTCTCCCTTGACAATCCTA-CCCGCTCCAAAACCCAATCAATA
1 GTTTATCAAACTCGGCCTAGATGTCTCCCTTGACAATCCTATCCCGCTCCAAAACCCAATCAATA
1180702 TCACATCCTTAAAGAAATCGGATTAGAAATTGGATGAGAACATCGGACTATGGTCTTTTCGACCC
66 TCACATCCTTAAAGAAATCGGATTAGAAATTGGATGAGAACATCGGACTATGGTCTTTTCGACCC
1180767 G
1 G
1180768 GTAAGCAAAC
Statistics
Matches: 128, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
127 61 0.48
128 42 0.33
129 25 0.20
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.27
Consensus pattern (130 bp):
GTTTATCAAACTCGGCCTAGATGTCTCCCTTGACAATCCTATCCCGCTCCAAAACCCAATCAATA
TCACATCCTTAAAGAAATCGGATTAGAAATTGGATGAGAACATCGGACTATGGTCTTTTCGACCC
Found at i:1180827 original size:21 final size:21
Alignment explanation
Indices: 1180785--1180828 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1180775 AACCCCGGAG
*
1180785 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
1180806 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
1180827 CT
1 CT
1180829 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:1181443 original size:30 final size:29
Alignment explanation
Indices: 1181407--1181471 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
1181397 ATTTAACAAA
*
1181407 AAGGGGAGAAAATTTAAGATGTGCTATAGT
1 AAGGGGAGAAAATTT-AGATGTGCAATAGT
* * *
1181437 AAGGGGAGTAAGTTTTGATGTGCAATAGT
1 AAGGGGAGAAAATTTAGATGTGCAATAGT
1181466 AAGGGG
1 AAGGGG
1181472 GAGTAAGTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 18 0.58
30 13 0.42
ACGTcount: A:0.35, C:0.03, G:0.35, T:0.26
Consensus pattern (29 bp):
AAGGGGAGAAAATTTAGATGTGCAATAGT
Found at i:1181464 original size:29 final size:30
Alignment explanation
Indices: 1181424--1181482 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
1181414 GAAAATTTAA
*
1181424 GATGTGCTATAGTAA-GGGGAGTAAGTTTT
1 GATGTGCAATAGTAAGGGGGAGTAAGTTTT
1181453 GATGTGCAATAGTAAGGGGGAGTAAGTTTT
1 GATGTGCAATAGTAAGGGGGAGTAAGTTTT
1181483 TCAAAATCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 14 0.50
30 14 0.50
ACGTcount: A:0.29, C:0.03, G:0.36, T:0.32
Consensus pattern (30 bp):
GATGTGCAATAGTAAGGGGGAGTAAGTTTT
Found at i:1181899 original size:19 final size:19
Alignment explanation
Indices: 1181863--1181932 Score: 108
Period size: 19 Copynumber: 3.7 Consensus size: 19
1181853 ATTAATTGAA
1181863 CATCGAATGCA-T-TCCATG
1 CATCG-ATGCACTCTCCATG
*
1181881 CACCGATGCACTCTCCATG
1 CATCGATGCACTCTCCATG
1181900 CATCGATGCACTCTCCATG
1 CATCGATGCACTCTCCATG
1181919 CATCGATGCACTCT
1 CATCGATGCACTCT
1181933 GAATATTTTC
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
17 5 0.10
18 5 0.10
19 38 0.79
ACGTcount: A:0.23, C:0.36, G:0.16, T:0.26
Consensus pattern (19 bp):
CATCGATGCACTCTCCATG
Found at i:1181953 original size:84 final size:83
Alignment explanation
Indices: 1181812--1181994 Score: 212
Period size: 84 Copynumber: 2.2 Consensus size: 83
1181802 TATTCAAAGG
*
1181812 CATGCATCGATGCA-TCAGTCCATGCATCGATGCATCGATGAATTAATTGAACATCGAATGCATT
1 CATGCATCGATGCACTCA-TCCATGCATCGATGCATC-ATGAATTAATTAAACATCGAATGCATT
***
1181876 CCATGCACCGATGCACTCTC
64 CCATGCACCGATGCACAAGC
*
1181896 CATGCATCGATGCACTC-TCCATGCATCGATGCACTC-TGAA-TATTTTCAAAACATCGAATGCA
1 CATGCATCGATGCACTCATCCATGCATCGATGCA-TCATGAATTA-ATT--AAACATCGAATGCA
** *
1181958 TTTGATGCATCGATGCACAAGC
62 TTCCATGCACCGATGCACAAGC
1181980 CATGCATCGATGCAC
1 CATGCATCGATGCAC
1181995 CAGGCTATTT
Statistics
Matches: 86, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
81 2 0.02
82 6 0.07
83 16 0.19
84 60 0.70
85 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.26
Consensus pattern (83 bp):
CATGCATCGATGCACTCATCCATGCATCGATGCATCATGAATTAATTAAACATCGAATGCATTCC
ATGCACCGATGCACAAGC
Found at i:1182037 original size:64 final size:65
Alignment explanation
Indices: 1181897--1182038 Score: 198
Period size: 65 Copynumber: 2.2 Consensus size: 65
1181887 TGCACTCTCC
*** *
1181897 ATGCATCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTTG
1 ATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAAAACATCGAATGCATTTG
**
1181962 ATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTC-AAACATCGAATGCATTT
1 ATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATA-TTTTCAAAACATCGAATGCATTT
*
1182025 T
65 G
1182026 ATGCATCGATGCA
1 ATGCATCGATGCA
1182039 TCCTTAGTGC
Statistics
Matches: 69, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
64 34 0.49
65 35 0.51
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.29
Consensus pattern (65 bp):
ATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAAAACATCGAATGCATTTG
Found at i:1183070 original size:31 final size:31
Alignment explanation
Indices: 1183032--1183156 Score: 171
Period size: 31 Copynumber: 4.0 Consensus size: 31
1183022 CCCGAAGGAC
* * * *
1183032 CAGTCCATA-GATTCCGAAGAACCTATGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
1183063 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1183094 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* * *
1183125 CATTCCATATGTCCCAAAGAACATAAGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1183156 C
1 C
1183157 CCTCGACCCT
Statistics
Matches: 86, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 85 0.99
32 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1183767 original size:36 final size:37
Alignment explanation
Indices: 1183720--1183792 Score: 112
Period size: 36 Copynumber: 2.0 Consensus size: 37
1183710 TTTCATTTAG
**
1183720 GGGGAATCGATACCACCCC-AGGGGGAATTTGTTCCC
1 GGGGAATCGATACCACCCCAAGGGGGAAACTGTTCCC
*
1183756 GGGGAATCGATACCCCCCCAAGGGGGAAACTGTTCCC
1 GGGGAATCGATACCACCCCAAGGGGGAAACTGTTCCC
1183793 CTTGTACATA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 18 0.55
37 15 0.45
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.16
Consensus pattern (37 bp):
GGGGAATCGATACCACCCCAAGGGGGAAACTGTTCCC
Found at i:1186102 original size:31 final size:30
Alignment explanation
Indices: 1186027--1186084 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
1186017 TCAATCTTGA
1186027 GGTGGAATTTGAAAGGTCCCAAAACCTTAG
1 GGTGGAATTTGAAAGGTCCCAAAACCTTAG
1186057 GGTGGAATTTGAAAGGTCCCAAAACCTT
1 GGTGGAATTTGAAAGGTCCCAAAACCTT
1186085 GGGGGACTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (30 bp):
GGTGGAATTTGAAAGGTCCCAAAACCTTAG
Found at i:1188760 original size:32 final size:33
Alignment explanation
Indices: 1188718--1188780 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
1188708 CAATTACATG
1188718 AATTTCTTAAAATACA-TT-AAAAATTTAATTTT
1 AATTTCTT-AAATACATTTCAAAAATTTAATTTT
* *
1188750 AATTTTTTAAATAGATTTCAAAAATTTAATT
1 AATTTCTTAAATACATTTCAAAAATTTAATT
1188781 GAAGTGTCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 6 0.22
32 9 0.33
33 12 0.44
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.48
Consensus pattern (33 bp):
AATTTCTTAAATACATTTCAAAAATTTAATTTT
Found at i:1189142 original size:2 final size:2
Alignment explanation
Indices: 1189135--1189160 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1189125 TTTCACACCA
1189135 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
1189161 TGATTAAGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1189873 original size:23 final size:23
Alignment explanation
Indices: 1189847--1189923 Score: 102
Period size: 23 Copynumber: 3.3 Consensus size: 23
1189837 TCGAAGGACA
1189847 GCGTAGAATTTTTCC-AAATGACC
1 GCGTAGAA-TTTTCCTAAATGACC
*
1189870 GCGTAGAATTTTCCTGAATGACC
1 GCGTAGAATTTTCCTAAATGACC
* * *
1189893 ACATAGAATTTTCCTAAAGGACC
1 GCGTAGAATTTTCCTAAATGACC
1189916 GCGTAGAA
1 GCGTAGAA
1189924 CCCTCACTCT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
22 6 0.13
23 40 0.87
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.27
Consensus pattern (23 bp):
GCGTAGAATTTTCCTAAATGACC
Found at i:1190110 original size:57 final size:57
Alignment explanation
Indices: 1190028--1190173 Score: 179
Period size: 57 Copynumber: 2.6 Consensus size: 57
1190018 TATTATTTCT
* * * *
1190028 CATAAAACATATACTCATAATATTTCCCATAGCATTACCCAAATTTA-TATTTATTCA
1 CATAAAACATATACTCATAACATTTCACATAGCATTACCC-AACTTAGCATTTATTCA
* * *
1190085 CATAAAACA-ATTACTCATAGCATTTCATATAGCATTACTCAACTTAGCATTTATTCA
1 CATAAAACATA-TACTCATAACATTTCACATAGCATTACCCAACTTAGCATTTATTCA
* *
1190142 CATAGAACATATACTCATAATATTTCACATAG
1 CATAAAACATATACTCATAACATTTCACATAG
1190174 AATATATATA
Statistics
Matches: 75, Mismatches: 11, Indels: 6
0.82 0.12 0.07
Matches are distributed among these distances:
56 6 0.08
57 68 0.91
58 1 0.01
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.35
Consensus pattern (57 bp):
CATAAAACATATACTCATAACATTTCACATAGCATTACCCAACTTAGCATTTATTCA
Found at i:1196352 original size:19 final size:21
Alignment explanation
Indices: 1196312--1196351 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1196302 CCTTCTTCGG
1196312 ATATTATCCTTTCATTTCCCC
1 ATATTATCCTTTCATTTCCCC
1196333 ATATT-TCC-TTCACTTTCCC
1 ATATTATCCTTTCA-TTTCCC
1196352 AATACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 9 0.50
21 5 0.28
ACGTcount: A:0.17, C:0.35, G:0.00, T:0.47
Consensus pattern (21 bp):
ATATTATCCTTTCATTTCCCC
Found at i:1196650 original size:22 final size:22
Alignment explanation
Indices: 1196622--1196665 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1196612 AAATCCAACA
1196622 CCGGTGCTTCGGGTATTTCCTC
1 CCGGTGCTTCGGGTATTTCCTC
1196644 CCGGTGCTTCGGGTATTTCCTC
1 CCGGTGCTTCGGGTATTTCCTC
1196666 TGGTGTAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.05, C:0.32, G:0.27, T:0.36
Consensus pattern (22 bp):
CCGGTGCTTCGGGTATTTCCTC
Found at i:1199502 original size:18 final size:19
Alignment explanation
Indices: 1199479--1199535 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 19
1199469 CCAATAATCC
1199479 TATTCC-CTGGTAATCTTT
1 TATTCCACTGGTAATCTTT
1199497 TATTCCTACTGGTAATCTTT
1 TATTCC-ACTGGTAATCTTT
* *
1199517 GATTTCCACTAGTAATCTT
1 TA-TTCCACTGGTAATCTT
1199536 ACATTTCGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.18
20 24 0.71
21 4 0.12
ACGTcount: A:0.21, C:0.21, G:0.11, T:0.47
Consensus pattern (19 bp):
TATTCCACTGGTAATCTTT
Found at i:1201752 original size:20 final size:20
Alignment explanation
Indices: 1201704--1201795 Score: 105
Period size: 20 Copynumber: 4.6 Consensus size: 20
1201694 TGCAATTTTC
*
1201704 TGACTATCGCAATGCGAATA
1 TGACTATCGCAATGCGATTA
*
1201724 TGTA-AATCGCAATGCGATTA
1 TG-ACTATCGCAATGCGATTA
* *
1201744 TGACTATCGTAATGCGATTC
1 TGACTATCGCAATGCGATTA
* *
1201764 TGACTATCGCAACGCGATTC
1 TGACTATCGCAATGCGATTA
*
1201784 TGACTGTCGCAA
1 TGACTATCGCAA
1201796 CACTGAATTT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
19 1 0.02
20 60 0.97
21 1 0.02
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (20 bp):
TGACTATCGCAATGCGATTA
Found at i:1204334 original size:3 final size:3
Alignment explanation
Indices: 1204328--1204387 Score: 77
Period size: 3 Copynumber: 20.0 Consensus size: 3
1204318 TTACCCATTT
* * *
1204328 TTA TTA TTA TTA TTA CTA TAA TTA TTA TTA TTA TAA TTA TTA -TA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
1204376 TTA TTA TTA TTA
1 TTA TTA TTA TTA
1204388 AAAAATAATT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
2 2 0.04
3 44 0.90
4 3 0.06
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:1205915 original size:23 final size:26
Alignment explanation
Indices: 1205883--1205932 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 26
1205873 CCTTTTCTGA
*
1205883 TATTTCTAAATA-A-ATAAA-TATTT
1 TATTTATAAATATATATAAATTATTT
1205906 TATTTATAAATATATATAAATTATTT
1 TATTTATAAATATATATAAATTATTT
1205932 T
1 T
1205933 TTCTCATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 1 0.04
25 5 0.22
26 6 0.26
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (26 bp):
TATTTATAAATATATATAAATTATTT
Found at i:1214567 original size:25 final size:25
Alignment explanation
Indices: 1214533--1214583 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
1214523 CATCGTTAGT
1214533 GGTGTATCAATTGCGAGGAGAATGG
1 GGTGTATCAATTGCGAGGAGAATGG
1214558 GGTGTATCAATTGCGAGGAGAATGG
1 GGTGTATCAATTGCGAGGAGAATGG
1214583 G
1 G
1214584 AAACAAAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.08, G:0.41, T:0.24
Consensus pattern (25 bp):
GGTGTATCAATTGCGAGGAGAATGG
Found at i:1216090 original size:11 final size:11
Alignment explanation
Indices: 1216074--1216104 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1216064 ATTATGCTTG
1216074 AAGAAAAAAAA
1 AAGAAAAAAAA
*
1216085 AAGAAACAAAA
1 AAGAAAAAAAA
1216096 AAGAAAAAA
1 AAGAAAAAA
1216105 GGGGGTCAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.87, C:0.03, G:0.10, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:1217653 original size:93 final size:93
Alignment explanation
Indices: 1217488--1217763 Score: 455
Period size: 93 Copynumber: 3.0 Consensus size: 93
1217478 ACAAGTGCCA
* * *
1217488 TGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATG-AACCCCA
1 TGTGCTCATAACATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACA
*
1217552 AAACCCAATCATTTAACTTGAAAGATGAG
66 AAA-CCAATCATTGAACTTGAAAGATGAG
1217581 TGTGCTCATAACATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACA
1 TGTGCTCATAACATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACA
* *
1217646 GAACCAATCATTGGACTTGAAAGATGAG
66 AAACCAATCATTGAACTTGAAAGATGAG
1217674 TGTGCTCATAACATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACA
1 TGTGCTCATAACATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACA
* * *
1217739 TAATCAATCATTGAATTTGAAAGAT
66 AAACCAATCATTGAACTTGAAAGAT
1217764 TAATGTGACC
Statistics
Matches: 172, Mismatches: 10, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
93 164 0.95
94 8 0.05
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (93 bp):
TGTGCTCATAACATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTTGGTATGAAACCACA
AAACCAATCATTGAACTTGAAAGATGAG
Found at i:1218770 original size:115 final size:115
Alignment explanation
Indices: 1218563--1219338 Score: 753
Period size: 113 Copynumber: 7.0 Consensus size: 115
1218553 TAGCAAAGAT
* * *** *
1218563 TCAAATCCATCATTTGATGGATCAGCTTTTCCAAAAAAAGTTCATAATGAGAAGAA--CTCATCT
1 TCAAATCCATCATTTGATGGATCAACTATTCCAGGTAGAGTTCATAATGAGAAGAACTCTCATCT
* *
1218626 GAAGAAGGAAGAAGAAGTTTATAATGAGAAGAATTTGTTCAACCTTTTGT
66 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * **
1218676 TTAAATTCATCATTTGATGGATTAAC-ATTGAAGGTAGAGTTCATAATGAGAAGAACTCATCATC
1 TCAAATCCATCATTTGATGGATCAACTATTCCAGGTAGAGTTCATAATGAGAAGAACTC-TCATC
* * *
1218740 TGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTATTCAACCTTTCGC
65 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * ** * *
1218791 TCAAATCCATCATTTGA-AGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAA-AA-ACTCATCT
1 TCAAATCCATCATTTGATGGATCAACTATTCCAGGTAGAGTTCATAATGAGAAGAACTCTCATCT
*
1218853 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTT-TT-----TGTT--
66 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *
1218895 T-AAATTCATCATTTGATGGATTAAC-ATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCAT
1 TCAAATCCATCATTTGATGGATCAACTATT-CCAGGTAGAGTTCATAATGAGAAGAACTC-TCAT
*
1218958 CTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
64 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * *
1219010 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGTTTGAGTTCATAATGAGAAGAACT-T-ATCT
1 TCAAATCCATCATTTGATGGATCAACTATTCCAGGTAGAGTTCATAATGAGAAGAACTCTCATCT
1219073 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA-CTTTTGGC
66 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-GC
* * * *
1219123 TCAAATCTATCACTTGATGGATC-AGTTTTCCA-G-AGAAGTTCATAATGAGAAGAA--CTCATC
1 TCAAATCCATCATTTGATGGATCAACTATTCCAGGTAG-AGTTCATAATGAGAAGAACTCTCATC
* ** *
1219183 TGAAGAA-G-A-AA-AAGTTCACAATGAGAAGAGCTTATTCAACCTTTTTGC
65 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACC-TTTTGC
* ** * * * *
1219231 AT-AATTTTATCA---CA-GCATCAACCT-TTCCAGAG-AAAGTTCATAATGAGAAGAA--CTCG
1 -TCAAATCCATCATTTGATGGATCAA-CTATTCCAG-GTAGAGTTCATAATGAGAAGAACTCTCA
* * ** *
1219287 TCTGAAAAAGAAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTTG
63 TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
1219339 AATGACTCTA
Statistics
Matches: 560, Mismatches: 69, Indels: 72
0.80 0.10 0.10
Matches are distributed among these distances:
103 16 0.03
104 30 0.05
105 9 0.02
106 33 0.06
107 67 0.12
108 16 0.03
109 13 0.02
110 32 0.06
111 30 0.05
112 75 0.13
113 94 0.17
114 9 0.02
115 87 0.16
116 47 0.08
117 2 0.00
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (115 bp):
TCAAATCCATCATTTGATGGATCAACTATTCCAGGTAGAGTTCATAATGAGAAGAACTCTCATCT
GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:1219208 original size:220 final size:223
Alignment explanation
Indices: 1218563--1219321 Score: 910
Period size: 219 Copynumber: 3.4 Consensus size: 223
1218553 TAGCAAAGAT
*
1218563 TCAAATCCATCATTTGATGGATCAGCTTTTCCAAAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATTTGA-GGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
*
1218628 AGAAGGAAGAAGAAGTTTATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTCATCATTTGA
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA-CTTTTG--TAAATTCATCATTTGA
* **
1218693 TGGATTAACA-TTGAAGGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAGAAGAA
127 TGGA-TAAAATTTCCAGGTAGAGTTCATAATGAGAAGAAC-CATCATCTGAAGAAGGAAGAAGAA
*
1218757 ATTCATAATGAGAAGAATTTATTCAACCTTTCGC
190 ATTCATAATGAGAAGAATTTATTCAACCTTTTGC
* *
1218791 TCAAATCCATCATTTGAAGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAAAACTCATCTGAA
1 TCAAATCCATCATTTGAGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAA
*
1218856 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTT-TT----TGTT-TAAATTCATCATTTGATGGA
66 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTGTAAATTCATCATTTGATGGA
* *
1218915 TTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAGAAGAAATTC
131 -TAAAATTTCCAGGTAGAGTTCATAATGAGAAGAAC-CATCATCTGAAGAAGGAAGAAGAAATTC
*
1218980 ATAATGAGAAGAATTTGTTCAACCTTTTGC
194 ATAATGAGAAGAATTTATTCAACCTTTTGC
**** *
1219010 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGTTTGAGTTCATAATGAGAAGAACTTATCTGA
1 TCAAATCCATCATTTGA-GGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
*
1219075 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTGGCTCAAA-TCTATCACTTG
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTT-G-T-AAATTC-ATCATTTG
* **
1219139 ATGGATCAGTTTTCCA-G-AGAAGTTCATAATGAGAAGAA-C-TCATCTGAAGAA-G-A-AA-AA
126 ATGGATAAAATTTCCAGGTAG-AGTTCATAATGAGAAGAACCATCATCTGAAGAAGGAAGAAGAA
* * **
1219196 GTTCACAATGAGAAGAGCTTATTCAACCTTTTTGC
190 ATTCATAATGAGAAGAATTTATTCAACC-TTTTGC
* ** * * * * * *
1219231 AT-AATTTTATCA---CAGCATCAACCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCGTCTGA
1 -TCAAATCCATCATTTGAGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
* *
1219292 AAAAGAAAGAAGAAGTTCATAATGAGAAGA
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGA
1219322 GCTTATTCAA
Statistics
Matches: 473, Mismatches: 43, Indels: 41
0.85 0.08 0.07
Matches are distributed among these distances:
217 66 0.14
218 27 0.06
219 100 0.21
220 99 0.21
221 20 0.04
222 2 0.00
223 1 0.00
224 12 0.03
225 4 0.01
226 4 0.01
227 96 0.20
228 27 0.06
229 15 0.03
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (223 bp):
TCAAATCCATCATTTGAGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAA
GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTGTAAATTCATCATTTGATGGA
TAAAATTTCCAGGTAGAGTTCATAATGAGAAGAACCATCATCTGAAGAAGGAAGAAGAAATTCAT
AATGAGAAGAATTTATTCAACCTTTTGC
Found at i:1219560 original size:3 final size:3
Alignment explanation
Indices: 1219554--1219616 Score: 74
Period size: 3 Copynumber: 21.0 Consensus size: 3
1219544 TTACCCATTT
* * * *
1219554 TTA TTA TTA TTA TTA CTA TAA TTA TTA TTA TTA TAA TTA TTA -TA CATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
1219602 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
1219617 AAAAATAATT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
2 2 0.04
3 47 0.92
4 2 0.04
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:1221187 original size:23 final size:26
Alignment explanation
Indices: 1221155--1221204 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 26
1221145 CATTTTCTGA
*
1221155 TATTTCTAAATA-A-ATAAA-TATTT
1 TATTTATAAATATATATAAATTATTT
1221178 TATTTATAAATATATATAAATTATTT
1 TATTTATAAATATATATAAATTATTT
1221204 T
1 T
1221205 TTCTCATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 1 0.04
25 5 0.22
26 6 0.26
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (26 bp):
TATTTATAAATATATATAAATTATTT
Found at i:1223468 original size:22 final size:22
Alignment explanation
Indices: 1223440--1223482 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1223430 GAATCCAACA
1223440 CCGGTGCTTCGGGTATTTCCTC
1 CCGGTGCTTCGGGTATTTCCTC
1223462 CCGGTGCTTCGGGTATTTCCT
1 CCGGTGCTTCGGGTATTTCCT
1223483 TGGTGTAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.05, C:0.30, G:0.28, T:0.37
Consensus pattern (22 bp):
CCGGTGCTTCGGGTATTTCCTC
Found at i:1225757 original size:101 final size:101
Alignment explanation
Indices: 1225582--1225783 Score: 404
Period size: 101 Copynumber: 2.0 Consensus size: 101
1225572 TGCTTTGGCC
1225582 ATTGTTGTGTAAAGATGATAAGTTTTATGCTATCATAACATTATCTGGTAAAGACATGAAAAGGT
1 ATTGTTGTGTAAAGATGATAAGTTTTATGCTATCATAACATTATCTGGTAAAGACATGAAAAGGT
1225647 ACGATTGATGGAATGAAATTATTCCCAAATTGCCAA
66 ACGATTGATGGAATGAAATTATTCCCAAATTGCCAA
1225683 ATTGTTGTGTAAAGATGATAAGTTTTATGCTATCATAACATTATCTGGTAAAGACATGAAAAGGT
1 ATTGTTGTGTAAAGATGATAAGTTTTATGCTATCATAACATTATCTGGTAAAGACATGAAAAGGT
1225748 ACGATTGATGGAATGAAATTATTCCCAAATTGCCAA
66 ACGATTGATGGAATGAAATTATTCCCAAATTGCCAA
1225784 CCTTCTTGAC
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 101 1.00
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.33
Consensus pattern (101 bp):
ATTGTTGTGTAAAGATGATAAGTTTTATGCTATCATAACATTATCTGGTAAAGACATGAAAAGGT
ACGATTGATGGAATGAAATTATTCCCAAATTGCCAA
Found at i:1227648 original size:19 final size:19
Alignment explanation
Indices: 1227612--1227649 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1227602 ATAAATAATT
*
1227612 TTTATTTAAACATTTAGAA
1 TTTATTTAAACATATAGAA
1227631 TTTACTTTAAA-ATATAGAA
1 TTTA-TTTAAACATATAGAA
1227650 CAAGGACAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (19 bp):
TTTATTTAAACATATAGAA
Found at i:1227796 original size:20 final size:20
Alignment explanation
Indices: 1227767--1227821 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
1227757 AGTAATCCTA
*
1227767 TTCC-CTGGTAATCTTTTA-
1 TTCCACTGGTAATCTTTGAT
1227785 TTCTCACTGGTAATCTTTGAT
1 TTC-CACTGGTAATCTTTGAT
*
1227806 TTCCACTAGTAATCTT
1 TTCCACTGGTAATCTT
1227822 ACATTTCGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 3 0.09
19 1 0.03
20 25 0.78
21 3 0.09
ACGTcount: A:0.20, C:0.22, G:0.11, T:0.47
Consensus pattern (20 bp):
TTCCACTGGTAATCTTTGAT
Found at i:1227827 original size:20 final size:20
Alignment explanation
Indices: 1227789--1227828 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1227779 CTTTTATTCT
* **
1227789 CACTGGTAATCTTTGATTTC
1 CACTAGTAATCTTACATTTC
1227809 CACTAGTAATCTTACATTTC
1 CACTAGTAATCTTACATTTC
1227829 GTGAATCAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.25, C:0.23, G:0.10, T:0.42
Consensus pattern (20 bp):
CACTAGTAATCTTACATTTC
Found at i:1230400 original size:148 final size:150
Alignment explanation
Indices: 1230241--1230541 Score: 563
Period size: 148 Copynumber: 2.0 Consensus size: 150
1230231 CTGTTGACTC
1230241 TTTTTTTCTTGCTTTTATGAACTGTGCTTTGCAGATTAAACGAGTATAATTCTTTGTTAAAATCA
1 TTTTTTTCTTGCTTTTATGAACTGTGCTTTGCAGATTAAACGAGTATAATTCTTTGTTAAAATCA
*
1230306 TTGAAAATACATCG-GAATCTTTA-TTTCGAAATT-AACGAACTGATTGCCGCAAAGGTTTGATT
66 TTGAAAAGACATCGTGAATCTTTATTTTCGAAATTAAACGAACTGATTGCCGCAAAGG-TTGATT
1230368 TCTTTCTCTTTGATGGATTTT
130 TCTTTCTCTTTGATGGATTTT
1230389 TTTTTTTCTTGCTTTTATGAACTGTGCTTTGCAGATTAAACGAGTATAATTCTTTGTTAAAATCA
1 TTTTTTTCTTGCTTTTATGAACTGTGCTTTGCAGATTAAACGAGTATAATTCTTTGTTAAAATCA
1230454 TTGAAAAGACATCGTGAATCTTTATTTTCGAAATTAAACGAACTGATTGCCGCAAAGGTTGATTT
66 TTGAAAAGACATCGTGAATCTTTATTTTCGAAATTAAACGAACTGATTGCCGCAAAGGTTGATTT
1230519 CTTTCTCTTTGATGGATTTT
131 CTTTCTCTTTGATGGATTTT
1230539 TTT
1 TTT
1230542 ATCAATGTTT
Statistics
Matches: 149, Mismatches: 1, Indels: 4
0.97 0.01 0.03
Matches are distributed among these distances:
148 78 0.52
149 9 0.06
150 40 0.27
151 22 0.15
ACGTcount: A:0.27, C:0.13, G:0.16, T:0.44
Consensus pattern (150 bp):
TTTTTTTCTTGCTTTTATGAACTGTGCTTTGCAGATTAAACGAGTATAATTCTTTGTTAAAATCA
TTGAAAAGACATCGTGAATCTTTATTTTCGAAATTAAACGAACTGATTGCCGCAAAGGTTGATTT
CTTTCTCTTTGATGGATTTT
Found at i:1237400 original size:29 final size:29
Alignment explanation
Indices: 1237368--1237433 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
1237358 GTTTATTATT
1237368 AAAATATTATT-TTATAATTTTA-TAAATAA
1 AAAATATTATTATTAT-ATTTTATTAAAT-A
**
1237397 AAAATAAGATTATTATATTTTATTAAATA
1 AAAATATTATTATTATATTTTATTAAATA
1237426 AAAATATT
1 AAAATATT
1237434 GTAAATTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
29 22 0.71
30 9 0.29
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (29 bp):
AAAATATTATTATTATATTTTATTAAATA
Found at i:1237464 original size:21 final size:21
Alignment explanation
Indices: 1237435--1237502 Score: 77
Period size: 21 Copynumber: 3.2 Consensus size: 21
1237425 AAAAATATTG
*
1237435 TAAATTATATTAATTATTTAT
1 TAAATTATATCAATTATTTAT
*
1237456 TAAAATATA-CATATTATATTAT
1 TAAATTATATCA-ATTAT-TTAT
*
1237478 T-AATTATATCAATTACTTAT
1 TAAATTATATCAATTATTTAT
1237498 TAAAT
1 TAAAT
1237503 AATAATATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 6 0.15
21 26 0.67
22 7 0.18
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (21 bp):
TAAATTATATCAATTATTTAT
Found at i:1237665 original size:20 final size:20
Alignment explanation
Indices: 1237642--1237714 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
1237632 GTTTCCAGAT
* *
1237642 TCGCAACGTGATTTTGACTA
1 TCGCAACGCGATTATGACTA
*
1237662 TCGCAACGCGATAAT-ACATAA
1 TCGCAACGCGATTATGAC-T-A
*
1237683 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTATGACTA
1237703 TCGCAACGCGAT
1 TCGCAACGCGAT
1237715 AATACAAAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
19 2 0.04
20 26 0.58
21 15 0.33
22 2 0.04
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATTATGACTA
Found at i:1237687 original size:21 final size:21
Alignment explanation
Indices: 1237661--1237735 Score: 91
Period size: 21 Copynumber: 3.6 Consensus size: 21
1237651 GATTTTGACT
1237661 ATCGCAACGCGATAATACATA
1 ATCGCAACGCGATAATACATA
**
1237682 ATCGCAACGCGATTCTGAC-T-
1 ATCGCAACGCGATAAT-ACATA
*
1237702 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATAATACATA
*
1237723 ATCGCAATGCGAT
1 ATCGCAACGCGAT
1237736 TTTCAAAGCG
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
19 2 0.04
20 14 0.31
21 27 0.60
22 2 0.04
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGATAATACATA
Found at i:1237690 original size:41 final size:41
Alignment explanation
Indices: 1237642--1237738 Score: 158
Period size: 41 Copynumber: 2.4 Consensus size: 41
1237632 GTTTCCAGAT
* *
1237642 TCGCAACGTGATTTTGACTATCGCAACGCGATAATACATAA
1 TCGCAACGCGATTTTGACTATCGCAACGCGATAATACAAAA
*
1237683 TCGCAACGCGATTCTGACTATCGCAACGCGATAATACAAAA
1 TCGCAACGCGATTTTGACTATCGCAACGCGATAATACAAAA
*
1237724 TCGCAATGCGATTTT
1 TCGCAACGCGATTTT
1237739 CAAAGCGCGA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.26
Consensus pattern (41 bp):
TCGCAACGCGATTTTGACTATCGCAACGCGATAATACAAAA
Found at i:1237904 original size:22 final size:22
Alignment explanation
Indices: 1237879--1237971 Score: 163
Period size: 22 Copynumber: 4.3 Consensus size: 22
1237869 CTACGGCGAC
1237879 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
1237901 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
1237923 ATCCGTCCCCATCT-CGACGAA
1 ATCCGTCCCCATCTCCGACGAA
*
1237944 ATCC-TCCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGACGAA
1237965 ATCCGTC
1 ATCCGTC
1237972 TATCTCCATC
Statistics
Matches: 68, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
20 9 0.13
21 21 0.31
22 38 0.56
ACGTcount: A:0.22, C:0.45, G:0.14, T:0.19
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:1237965 original size:42 final size:44
Alignment explanation
Indices: 1237872--1237971 Score: 168
Period size: 42 Copynumber: 2.3 Consensus size: 44
1237862 TCACTCTCTA
*
1237872 CGGCGACATCCGTCCCCATCTCCGACGAAATCCGTCCCCATCTC
1 CGGCGAAATCCGTCCCCATCTCCGACGAAATCCGTCCCCATCTC
*
1237916 CGACGAAATCCGTCCCCATCT-CGACGAAATCC-TCCCCATCTC
1 CGGCGAAATCCGTCCCCATCTCCGACGAAATCCGTCCCCATCTC
1237958 CGGCGAAATCCGTC
1 CGGCGAAATCCGTC
1237972 TATCTCCATC
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
42 23 0.43
43 11 0.21
44 19 0.36
ACGTcount: A:0.21, C:0.45, G:0.16, T:0.18
Consensus pattern (44 bp):
CGGCGAAATCCGTCCCCATCTCCGACGAAATCCGTCCCCATCTC
Found at i:1238367 original size:20 final size:20
Alignment explanation
Indices: 1238342--1238439 Score: 82
Period size: 20 Copynumber: 5.2 Consensus size: 20
1238332 AAAATCGCAA
1238342 CGATAGTCAAATTCGCGTTG
1 CGATAGTCAAATTCGCGTTG
** *
1238362 CGATAGTCATTTTCGTGTTG
1 CGATAGTCAAATTCGCGTTG
*
1238382 CGAT--T---A-TCTCGTTG
1 CGATAGTCAAATTCGCGTTG
1238396 CGATAGTCAAATTCGCGTTG
1 CGATAGTCAAATTCGCGTTG
* ** *
1238416 TGATAGTCATTTTCGTGTTG
1 CGATAGTCAAATTCGCGTTG
1238436 CGAT
1 CGAT
1238440 TTTAAGTTTC
Statistics
Matches: 60, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
14 10 0.17
16 1 0.02
18 1 0.02
19 1 0.02
20 47 0.78
ACGTcount: A:0.19, C:0.17, G:0.24, T:0.39
Consensus pattern (20 bp):
CGATAGTCAAATTCGCGTTG
Found at i:1240366 original size:20 final size:20
Alignment explanation
Indices: 1240343--1240391 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1240333 CGAAACTTAA
1240343 ATCGCAACGCGGAA-ATGACT
1 ATCGCAACGC-GAAGATGACT
*
1240363 ATCGCAACGCGAAGTTGACT
1 ATCGCAACGCGAAGATGACT
1240383 ATCGCAACG
1 ATCGCAACG
1240392 GGATAATCGC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 3 0.11
20 24 0.89
ACGTcount: A:0.33, C:0.27, G:0.24, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAGATGACT
Found at i:1240480 original size:19 final size:19
Alignment explanation
Indices: 1240458--1240499 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
1240448 CTATCGCAAC
1240458 GCGAATTTAGTTTCGCGTT
1 GCGAATTTAGTTTCGCGTT
* *
1240477 GCGATTTTGGTTTCGCGTT
1 GCGAATTTAGTTTCGCGTT
1240496 GCGA
1 GCGA
1240500 TTTTTATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.12, C:0.17, G:0.31, T:0.40
Consensus pattern (19 bp):
GCGAATTTAGTTTCGCGTT
Found at i:1240500 original size:19 final size:19
Alignment explanation
Indices: 1240467--1240503 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1240457 CGCGAATTTA
1240467 GTTTCGCGTTGCGATTTTG
1 GTTTCGCGTTGCGATTTTG
1240486 GTTTCGCGTTGCGATTTT
1 GTTTCGCGTTGCGATTTT
1240504 TATTTAGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.05, C:0.16, G:0.30, T:0.49
Consensus pattern (19 bp):
GTTTCGCGTTGCGATTTTG
Found at i:1240516 original size:19 final size:19
Alignment explanation
Indices: 1240475--1240520 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1240465 TAGTTTCGCG
* * *
1240475 TTGCGATTTTGGTTTCGCG
1 TTGCGATTTTGATTTAGCA
*
1240494 TTGCGATTTTTATTTAGCA
1 TTGCGATTTTGATTTAGCA
1240513 TTGCGATT
1 TTGCGATT
1240521 ATCCCGTTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.13, C:0.13, G:0.24, T:0.50
Consensus pattern (19 bp):
TTGCGATTTTGATTTAGCA
Found at i:1240574 original size:20 final size:20
Alignment explanation
Indices: 1240551--1240593 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1240541 TTCGCATTGC
1240551 GATAGTCATTTCCGCGTTGT
1 GATAGTCATTTCCGCGTTGT
**
1240571 GATAGTCATTTTTGCGTTGT
1 GATAGTCATTTCCGCGTTGT
1240591 GAT
1 GAT
1240594 TTAAGTTTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.16, C:0.14, G:0.26, T:0.44
Consensus pattern (20 bp):
GATAGTCATTTCCGCGTTGT
Found at i:1241151 original size:21 final size:21
Alignment explanation
Indices: 1241127--1241196 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
1241117 TTATCATCCC
1241127 TCAAGAGTCCCCTTCCACCGT
1 TCAAGAGTCCCCTTCCACCGT
* *
1241148 TCAAGAGGCCCCTGT-CATCGT
1 TCAAGAGTCCCCT-TCCACCGT
* * *
1241169 TGAAGAGGT-CCCTCCCACCAT
1 TCAAGA-GTCCCCTTCCACCGT
1241190 TCAAGAG
1 TCAAGAG
1241197 CCCGATTCAT
Statistics
Matches: 38, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
20 1 0.03
21 35 0.92
22 2 0.05
ACGTcount: A:0.23, C:0.36, G:0.20, T:0.21
Consensus pattern (21 bp):
TCAAGAGTCCCCTTCCACCGT
Found at i:1241175 original size:42 final size:42
Alignment explanation
Indices: 1241103--1241196 Score: 109
Period size: 42 Copynumber: 2.2 Consensus size: 42
1241093 CACCTGTCAT
* *
1241103 CGTTCAAGAGGCCCTTATCATCCCTCAAGA-GTCCCCTTCCAC
1 CGTTCAAGAGGCCCCTATCATCCCTCAAGAGGT-CCCTCCCAC
* ** *
1241145 CGTTCAAGAGGCCCCTGTCATCGTTGAAGAGGTCCCTCCCAC
1 CGTTCAAGAGGCCCCTATCATCCCTCAAGAGGTCCCTCCCAC
*
1241187 CATTCAAGAG
1 CGTTCAAGAG
1241197 CCCGATTCAT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
42 42 0.95
43 2 0.05
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.22
Consensus pattern (42 bp):
CGTTCAAGAGGCCCCTATCATCCCTCAAGAGGTCCCTCCCAC
Found at i:1242605 original size:15 final size:14
Alignment explanation
Indices: 1242570--1242617 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
1242560 TTGCTTGTTT
1242570 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
1242584 AATTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
1242599 TATTGATGTGTAAA
1 AATTGATTTGTAAA
1242613 TAATT
1 -AATT
1242618 CTTATTTGTG
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
14 13 0.48
15 14 0.52
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.48
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:1242754 original size:20 final size:21
Alignment explanation
Indices: 1242716--1242773 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 21
1242706 AGGTACACTT
*
1242716 TCGCAATGCTAAA-CTCAAAA
1 TCGCAATGCGAAAGCTCAAAA
*
1242736 TTGCAATGCGAAAGC-CAAAA
1 TCGCAATGCGAAAGCTCAAAA
*
1242756 TCGCAACGCGAAAG-TCAA
1 TCGCAATGCGAAAGCTCAA
1242774 TTCGCGTTGC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.43, C:0.24, G:0.17, T:0.16
Consensus pattern (21 bp):
TCGCAATGCGAAAGCTCAAAA
Found at i:1242837 original size:20 final size:20
Alignment explanation
Indices: 1242812--1242900 Score: 126
Period size: 20 Copynumber: 4.5 Consensus size: 20
1242802 ACGATTTTCT
* *
1242812 CGTTGCGATAGTCAAATACC
1 CGTTGCGATAGTCAAATTCA
*
1242832 CGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCA
*
1242852 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCA
1242872 CGTTGCGATAGTCAAATT-A
1 CGTTGCGATAGTCAAATTCA
1242891 GCGTTGCGAT
1 -CGTTGCGAT
1242901 TTTTACATTG
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.29
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCA
Found at i:1242901 original size:94 final size:93
Alignment explanation
Indices: 1242763--1242934 Score: 231
Period size: 94 Copynumber: 1.8 Consensus size: 93
1242753 AAATCGCAAC
* * *
1242763 GCGAAAGTCAATTCGCGTTGCAATAGTCTAATACGCTTTACGATTTTCT-CGTTGCGATAGTCAA
1 GCGAAAGTCAATTCGCGTTGCAATAGTCAAATACGCGTTACGATTTT-TACATTGCGATAGTCAA
1242827 ATACCCGTTGCGATAATCAAATTCACGTT
65 ATACCCGTTGCGATAATCAAATTCACGTT
* * *
1242856 GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTA-GCGTTGCGATTTTTACATTGCGATAGTCA
1 GCGAAAGTC-AATTCGCGTTGCAATAGTCAAA-TACGCGTTACGATTTTTACATTGCGATAGTCA
* *
1242920 AATTCGCGTTGCGAT
64 AATACCCGTTGCGAT
1242935 TTTTGAGTTG
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
93 9 0.13
94 57 0.84
95 2 0.03
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.33
Consensus pattern (93 bp):
GCGAAAGTCAATTCGCGTTGCAATAGTCAAATACGCGTTACGATTTTTACATTGCGATAGTCAAA
TACCCGTTGCGATAATCAAATTCACGTT
Found at i:1242917 original size:34 final size:34
Alignment explanation
Indices: 1242874--1242968 Score: 138
Period size: 34 Copynumber: 2.8 Consensus size: 34
1242864 CAAATTCGCG
*
1242874 TTGCGATAGTCAAATTAGCGTTGCGATTTTT-ACA
1 TTGCGATAGTCAAATTCGCGTTGCGATTTTTGA-A
*
1242908 TTGCGATAGTCAAATTCGCGTTGCGATTTTTGAG
1 TTGCGATAGTCAAATTCGCGTTGCGATTTTTGAA
* *
1242942 TTGCAATAATCAAATTCGCGTTGCGAT
1 TTGCGATAGTCAAATTCGCGTTGCGAT
1242969 ATTCAAATGA
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
34 55 0.98
35 1 0.02
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (34 bp):
TTGCGATAGTCAAATTCGCGTTGCGATTTTTGAA
Found at i:1243203 original size:140 final size:140
Alignment explanation
Indices: 1242946--1243229 Score: 523
Period size: 140 Copynumber: 2.0 Consensus size: 140
1242936 TTTGAGTTGC
*
1242946 AATAATCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATC
1 AATAATCAAATTCGCGTTACGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATC
1243011 ATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATA
66 ATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATA
1243076 AAATACACAT
131 AAATACACAT
* *
1243086 AATAGTCAAATTCGCGTTACGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATC
1 AATAATCAAATTCGCGTTACGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATC
* *
1243151 ATAGCAATGTTTAAACTCAAGTTACTAATACATGTCTAACTGAAAATGTTAAAAGTTTACACATA
66 ATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATA
1243216 AAATACACAT
131 AAATACACAT
1243226 AATA
1 AATA
1243230 CAACATTTGC
Statistics
Matches: 139, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 139 1.00
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (140 bp):
AATAATCAAATTCGCGTTACGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATC
ATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATA
AAATACACAT
Found at i:1243310 original size:18 final size:18
Alignment explanation
Indices: 1243287--1243321 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1243277 AAGCCGGTTG
*
1243287 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
1243305 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
1243322 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:1245612 original size:24 final size:24
Alignment explanation
Indices: 1245578--1245631 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1245568 CTGAAACATC
1245578 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1245602 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1245626 ATCAAA
1 ATCAAA
1245632 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1246444 original size:20 final size:20
Alignment explanation
Indices: 1246419--1246525 Score: 126
Period size: 20 Copynumber: 5.3 Consensus size: 20
1246409 GAAATTCAGT
*
1246419 GTTGCGACAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
*
1246439 GTTGCGATAGTCAGAATCAC
1 GTTGCGATAGTCAGAATCGC
1246459 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
* * * *
1246479 GTTGCGAT-TTACATATTCGT
1 GTTGCGATAGT-CAGAATCGC
* *
1246499 ATTGCGATAGTCAAAATCGC
1 GTTGCGATAGTCAGAATCGC
1246519 GTTGCGA
1 GTTGCGA
1246526 ATCTGGAAAC
Statistics
Matches: 72, Mismatches: 13, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
19 1 0.01
20 70 0.97
21 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:1246563 original size:20 final size:19
Alignment explanation
Indices: 1246540--1246585 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1246530 GGAAACTGAT
* *
1246540 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
1246560 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
1246579 TTGCGAT
1 TTGCGAT
1246586 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:1246575 original size:19 final size:19
Alignment explanation
Indices: 1246551--1246587 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1246541 TGCGATACTG
*
1246551 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
1246570 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
1246588 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:1246908 original size:17 final size:16
Alignment explanation
Indices: 1246888--1246919 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1246878 TTAAAAGTAT
1246888 TAATAAATATATTTTAA
1 TAATAAATAT-TTTTAA
1246905 TAATAAATATTTTTA
1 TAATAAATATTTTTA
1246920 TTAAAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TAATAAATATTTTTAA
Done.