Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold110
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: 1159294
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
File 6 of 6
Found at i:913466 original size:42 final size:42
Alignment explanation
Indices: 913407--913516 Score: 166
Period size: 42 Copynumber: 2.6 Consensus size: 42
913397 TAGCCCTCAA
* *
913407 AGAGAAAGAAGAGATAGGAGGGATGATAGAAGGAGAGATAGG
1 AGAGATAGTAGAGATAGGAGGGATGATAGAAGGAGAGATAGG
* *
913449 AGAGATAGTAGAGATAGGAAGGATGATAGGAGGAGAGATAGG
1 AGAGATAGTAGAGATAGGAGGGATGATAGAAGGAGAGATAGG
* *
913491 AGAGATAATAGAGAGAGGAGGGATGA
1 AGAGATAGTAGAGATAGGAGGGATGA
913517 CAAGAGGAGG
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 61 1.00
ACGTcount: A:0.45, C:0.00, G:0.43, T:0.12
Consensus pattern (42 bp):
AGAGATAGTAGAGATAGGAGGGATGATAGAAGGAGAGATAGG
Found at i:913489 original size:24 final size:23
Alignment explanation
Indices: 913416--913507 Score: 81
Period size: 24 Copynumber: 4.2 Consensus size: 23
913406 AAGAGAAAGA
*
913416 AGAGATAGGAGGGATGATAGAAGG
1 AGAGATAGGAAGGATGATAG-AGG
*
913440 AGAGATAGG-A-GA-GAT--AGT
1 AGAGATAGGAAGGATGATAGAGG
913458 AGAGATAGGAAGGATGATAGGAGG
1 AGAGATAGGAAGGATGATA-GAGG
*
913482 AGAGATAGG-AGAGATAATAGA-G
1 AGAGATAGGAAG-GATGATAGAGG
913504 AGAG
1 AGAG
913508 GAGGGATGAC
Statistics
Matches: 57, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
18 11 0.19
19 1 0.02
20 2 0.04
21 6 0.11
22 7 0.12
23 4 0.07
24 26 0.46
ACGTcount: A:0.45, C:0.00, G:0.42, T:0.13
Consensus pattern (23 bp):
AGAGATAGGAAGGATGATAGAGG
Found at i:926121 original size:24 final size:24
Alignment explanation
Indices: 926088--926173 Score: 94
Period size: 24 Copynumber: 3.8 Consensus size: 24
926078 AAGAGAAAGA
*
926088 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
926112 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
926130 AGAGACAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
926154 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
926174 AGAGAGGAGG
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
18 12 0.24
20 2 0.04
21 6 0.12
22 2 0.04
24 29 0.57
ACGTcount: A:0.42, C:0.03, G:0.45, T:0.09
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:926135 original size:18 final size:18
Alignment explanation
Indices: 926112--926182 Score: 61
Period size: 18 Copynumber: 3.6 Consensus size: 18
926102 TGATAGGAGG
926112 AGAGACAGGAGAGATAGT
1 AGAGACAGGAGAGATAGT
*
926130 AGAGACAGGAGGGATGATAGGAGG
1 AGAGACAGGA--GA-GAT---AGT
*
926154 AGAGACAGGAGAGATAAT
1 AGAGACAGGAGAGATAGT
*
926172 AGAGAGAGGAG
1 AGAGACAGGAG
926183 GGATGACAGG
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
18 21 0.49
20 2 0.05
21 6 0.14
22 2 0.05
24 12 0.28
ACGTcount: A:0.44, C:0.04, G:0.44, T:0.08
Consensus pattern (18 bp):
AGAGACAGGAGAGATAGT
Found at i:926140 original size:42 final size:42
Alignment explanation
Indices: 926079--926197 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
926069 TAGCCCTCAA
* *
926079 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
926121 AGAGATAGTAGAGACAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
926163 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
926198 GAGAGAAGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.43, C:0.03, G:0.46, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:940667 original size:42 final size:42
Alignment explanation
Indices: 940612--940730 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
940602 TTCTTCTCTC
* *
940612 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
940654 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
940696 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
940731 TTGAGGGCTA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.08, C:0.46, G:0.03, T:0.43
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:940671 original size:12 final size:11
Alignment explanation
Indices: 940645--940720 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
940635 TCTATTATCT
*
940645 CTCCTGTCTCTC
1 CTCCTATCTC-C
940657 CTCCTATCATCC
1 CTCCTATC-TCC
940669 CTCCTATCT--
1 CTCCTATCTCC
*
940678 CTACTATCT--
1 CTCCTATCTCC
*
940687 CTCCTGTCTCTC
1 CTCCTATCTC-C
940699 CTCCTATCATCC
1 CTCCTATC-TCC
*
940711 CTCCTCTCTC
1 CTCCTATCTC
940721 TTCTTTCTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 3 0.06
12 31 0.58
13 4 0.08
ACGTcount: A:0.09, C:0.49, G:0.03, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:940672 original size:24 final size:24
Alignment explanation
Indices: 940636--940721 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
940626 CCTCCTCTCT
* *
940636 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
940660 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
940681 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
940702 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
940722 TCTTTCTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 4 0.08
20 5 0.10
21 14 0.29
22 5 0.10
24 21 0.43
ACGTcount: A:0.10, C:0.45, G:0.02, T:0.42
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:940696 original size:18 final size:18
Alignment explanation
Indices: 940627--940697 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
940617 CCTGTCATCC
* *
940627 CTCCTCTCTCTATTATCT
1 CTCCTGTCTCTACTATCT
*
940645 CTCCTGTCTCTCCTCCTATCAT
1 CTCCTG--TCT-CTACTATC-T
*
940667 CCCTCCTATCTCTACTATCT
1 --CTCCTGTCTCTACTATCT
940687 CTCCTGTCTCT
1 CTCCTGTCTCT
940698 CCTCCTATCA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
18 15 0.37
20 4 0.10
21 13 0.32
22 4 0.10
24 5 0.12
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.44
Consensus pattern (18 bp):
CTCCTGTCTCTACTATCT
Found at i:956077 original size:42 final size:42
Alignment explanation
Indices: 956022--956140 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
956012 TTCTTCTCTC
* *
956022 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
956064 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
956106 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
956141 TTGAGGGCTA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.08, C:0.46, G:0.03, T:0.43
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:956081 original size:12 final size:11
Alignment explanation
Indices: 956055--956130 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
956045 TCTATTATCT
*
956055 CTCCTGTCTCTC
1 CTCCTATCTC-C
956067 CTCCTATCATCC
1 CTCCTATC-TCC
956079 CTCCTATCT--
1 CTCCTATCTCC
*
956088 CTACTATCT--
1 CTCCTATCTCC
*
956097 CTCCTGTCTCTC
1 CTCCTATCTC-C
956109 CTCCTATCATCC
1 CTCCTATC-TCC
*
956121 CTCCTCTCTC
1 CTCCTATCTC
956131 TTCTTTCTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 3 0.06
12 31 0.58
13 4 0.08
ACGTcount: A:0.09, C:0.49, G:0.03, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:956082 original size:24 final size:24
Alignment explanation
Indices: 956046--956131 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
956036 CCTCCTCTCT
* *
956046 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
956070 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
956091 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
956112 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
956132 TCTTTCTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 4 0.08
20 5 0.10
21 14 0.29
22 5 0.10
24 21 0.43
ACGTcount: A:0.10, C:0.45, G:0.02, T:0.42
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:956106 original size:18 final size:18
Alignment explanation
Indices: 956037--956107 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
956027 CCTGTCATCC
* *
956037 CTCCTCTCTCTATTATCT
1 CTCCTGTCTCTACTATCT
*
956055 CTCCTGTCTCTCCTCCTATCAT
1 CTCCTG--TCT-CTACTATC-T
*
956077 CCCTCCTATCTCTACTATCT
1 --CTCCTGTCTCTACTATCT
956097 CTCCTGTCTCT
1 CTCCTGTCTCT
956108 CCTCCTATCA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
18 15 0.37
20 4 0.10
21 13 0.32
22 4 0.10
24 5 0.12
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.44
Consensus pattern (18 bp):
CTCCTGTCTCTACTATCT
Found at i:959404 original size:12 final size:11
Alignment explanation
Indices: 959382--959457 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
959372 AGAGAAAGAA
*
959382 GAGAGAGGAGG
1 GAGATAGGAGG
959393 GATGATAGGAGG
1 GA-GATAGGAGG
*
959405 AGAGACAGGA--
1 -GAGATAGGAGG
*
959415 GAGATAGTA--
1 GAGATAGGAGG
959424 GAGATAGGAGG
1 GAGATAGGAGG
959435 GATGATAGGAGG
1 GA-GATAGGAGG
*
959447 AGAGACAGGAG
1 -GAGATAGGAG
959458 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:959414 original size:24 final size:24
Alignment explanation
Indices: 959381--959466 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
959371 AAGAGAAAGA
*
959381 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
959405 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
959423 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
959447 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
959467 AGAGAGGAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:959433 original size:42 final size:42
Alignment explanation
Indices: 959372--959490 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
959362 TAGCCCTCAA
* *
959372 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
959414 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
959456 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
959491 GAGAGAAGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.43, C:0.03, G:0.46, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:970404 original size:24 final size:24
Alignment explanation
Indices: 970379--970456 Score: 78
Period size: 24 Copynumber: 3.5 Consensus size: 24
970369 GAAGAGAGAT
*
970379 GAGGGATGATAGGAGGAGAGACAT
1 GAGGGATGATAGGAGGAGAGACAG
* *
970403 GA--GA-GAT---AGTAGAGATAG
1 GAGGGATGATAGGAGGAGAGACAG
970421 GAGGGATGATAGGAGGAGAGACAG
1 GAGGGATGATAGGAGGAGAGACAG
*
970445 GAGGGATAATAG
1 GAGGGATGATAG
970457 AGAGAGGAGG
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
18 10 0.24
20 2 0.05
21 6 0.14
22 2 0.05
24 22 0.52
ACGTcount: A:0.40, C:0.03, G:0.45, T:0.13
Consensus pattern (24 bp):
GAGGGATGATAGGAGGAGAGACAG
Found at i:970425 original size:42 final size:42
Alignment explanation
Indices: 970371--970477 Score: 160
Period size: 42 Copynumber: 2.5 Consensus size: 42
970361 AAGAGAAAGA
* * *
970371 AGAGAGATGAGGGATGATAGGAGGAGAGACATGAGAGATAGT
1 AGAGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
* *
970413 AGAGATAGGAGGGATGATAGGAGGAGAGACAGGAGGGATAAT
1 AGAGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
*
970455 AGAGAGAGGAGGGATGACAGGAG
1 AGAGAGAGGAGGGATGATAGGAG
970478 AAGAAGAGAA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 58 1.00
ACGTcount: A:0.40, C:0.03, G:0.46, T:0.11
Consensus pattern (42 bp):
AGAGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
Found at i:983624 original size:223 final size:219
Alignment explanation
Indices: 983231--983671 Score: 679
Period size: 223 Copynumber: 2.0 Consensus size: 219
983221 AACGTCAAGG
*
983231 ATAAAAAAGTCACCTAAAGAGCCCTGTCGGTGTTCCCTTAGTCAATTGTATATAGATGTAGAGAC
1 ATAAAAAAGTCACCTAAAGAGCCCTGTCGGTGTTCCCTTAGTCAATTATATATAGATGTAGAGAC
* * *
983296 TACACTTGTGTACCGCTCTTGGGATTATGGGGAAGTACCAGTTATGCTTCTCTATTGGTATTGAG
66 TACACTTGTGTACCGCTCTTGGGATTATGGGGAAGTACCAGTTATGCTCCACTATTAGTATTGAG
* * *
983361 TCAGTTCCAGGGCCATCAATTCATCCTGTTCTTTGAAGACTTGGGACATTGGGATTT-TGAAATG
131 TCAGTTCCAGGGCCATCAATTCATCCCGTTCTTCGAAGACTTGCGACATTGGGATTTATG--AT-
983425 GAGAGCCCAATTATAAAGCAAAAGTCTAC
193 --GAGCCCAATTATAAAGCAAAAGTCTAC
** *
983454 ATAAAAAAGTCACCTGGAGAGCCTTGTCGGTGTTCCCTTAGTCAATTATATATAGATGTAGAGAC
1 ATAAAAAAGTCACCTAAAGAGCCCTGTCGGTGTTCCCTTAGTCAATTATATATAGATGTAGAGAC
* *
983519 TACACTTGTGTACCGTTTTTGGGATTATGGGGAAGTACCAGTTATGCTCCACTATTAGTATTGAG
66 TACACTTGTGTACCGCTCTTGGGATTATGGGGAAGTACCAGTTATGCTCCACTATTAGTATTGAG
* * *
983584 TCAGTTCCAGTGTCAGT-AATTCATCCCGTTCTTCGAAGACTTGCGATATTGGGATTTATGATGA
131 TCAGTTCCAGGGCCA-TCAATTCATCCCGTTCTTCGAAGACTTGCGACATTGGGATTTATGATGA
983648 GCCCAATTATAAAGCAAAAGTCTA
195 GCCCAATTATAAAGCAAAAGTCTA
983672 GATAGCTTTT
Statistics
Matches: 201, Mismatches: 15, Indels: 8
0.90 0.07 0.04
Matches are distributed among these distances:
219 26 0.13
222 2 0.01
223 170 0.85
224 3 0.01
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (219 bp):
ATAAAAAAGTCACCTAAAGAGCCCTGTCGGTGTTCCCTTAGTCAATTATATATAGATGTAGAGAC
TACACTTGTGTACCGCTCTTGGGATTATGGGGAAGTACCAGTTATGCTCCACTATTAGTATTGAG
TCAGTTCCAGGGCCATCAATTCATCCCGTTCTTCGAAGACTTGCGACATTGGGATTTATGATGAG
CCCAATTATAAAGCAAAAGTCTAC
Found at i:988963 original size:9 final size:9
Alignment explanation
Indices: 988951--989011 Score: 74
Period size: 9 Copynumber: 7.1 Consensus size: 9
988941 CTCTCTCTAT
988951 TATCTCTCC
1 TATCTCTCC
988960 TATCTCTCC
1 TATCTCTCC
*
988969 T-TCTAT-C
1 TATCTCTCC
*
988976 -ATCCCTCC
1 TATCTCTCC
*
988984 TATCTCTAC
1 TATCTCTCC
988993 TATCTCTCC
1 TATCTCTCC
989002 TATCTCTCC
1 TATCTCTCC
989011 T
1 T
989012 CCTATCATCC
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
7 4 0.09
8 5 0.12
9 34 0.79
ACGTcount: A:0.13, C:0.43, G:0.00, T:0.44
Consensus pattern (9 bp):
TATCTCTCC
Found at i:988965 original size:18 final size:18
Alignment explanation
Indices: 988938--989008 Score: 61
Period size: 18 Copynumber: 3.6 Consensus size: 18
988928 CCTGTCATCA
*
988938 CTCCTCTCTCTATTATCT
1 CTCCTATCTCTATTATCT
*
988956 CTCCTATCTCTCCTTCTATCAT
1 CTCCTATCTCT--AT-TATC-T
*
988978 CCCTCCTATCTCTACTATCT
1 --CTCCTATCTCTATTATCT
988998 CTCCTATCTCT
1 CTCCTATCTCT
989009 CCTCCTATCA
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
18 21 0.49
20 2 0.05
21 8 0.19
22 1 0.02
24 11 0.26
ACGTcount: A:0.13, C:0.42, G:0.00, T:0.45
Consensus pattern (18 bp):
CTCCTATCTCTATTATCT
Found at i:988969 original size:42 final size:42
Alignment explanation
Indices: 988922--989030 Score: 155
Period size: 42 Copynumber: 2.6 Consensus size: 42
988912 CTTCTTCTCT
* * *
988922 TCTCCTCCTGTCATCACTCCTCTCTCTATTATCTCTCCTATC
1 TCTCCTCCTATCATCACTCCTATCTCTACTATCTCTCCTATC
* *
988964 TCTCCTTCTATCATCCCTCCTATCTCTACTATCTCTCCTATC
1 TCTCCTCCTATCATCACTCCTATCTCTACTATCTCTCCTATC
* *
989006 TCTCCTCCTATCATCCCTCTTATCT
1 TCTCCTCCTATCATCACTCCTATCT
989031 ATTCTTTCTC
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 60 1.00
ACGTcount: A:0.13, C:0.43, G:0.01, T:0.43
Consensus pattern (42 bp):
TCTCCTCCTATCATCACTCCTATCTCTACTATCTCTCCTATC
Found at i:988983 original size:24 final size:24
Alignment explanation
Indices: 988946--989030 Score: 83
Period size: 24 Copynumber: 3.8 Consensus size: 24
988936 CACTCCTCTC
* *
988946 TCTATTATCTCTCCTATCTCTCCT
1 TCTATCATCCCTCCTATCTCTCCT
988970 TCTATCATCCCTCCTA--TCT-CT
1 TCTATCATCCCTCCTATCTCTCCT
*
988991 ACTATC-T--CTCCTATCTCTCCT
1 TCTATCATCCCTCCTATCTCTCCT
* *
989012 CCTATCATCCCTCTTATCT
1 TCTATCATCCCTCCTATCT
989031 ATTCTTTCTC
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
18 6 0.12
20 4 0.08
21 14 0.28
22 4 0.08
24 22 0.44
ACGTcount: A:0.14, C:0.41, G:0.00, T:0.45
Consensus pattern (24 bp):
TCTATCATCCCTCCTATCTCTCCT
Found at i:994147 original size:79 final size:79
Alignment explanation
Indices: 994011--994214 Score: 230
Period size: 79 Copynumber: 2.6 Consensus size: 79
994001 GAGATAATAA
* * * * * ** * *
994011 CGGGGTTGGAGTGTTCCCTTGAAAATAACGAGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAAT-A
*
994076 -TTAGAAAAAAAAAT
65 TTTAGAAAAAAAAAC
*
994090 CGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
* ** * *
994155 TTTGGGAATAAAGC
66 TTAGAAAAAAAAAC
* *
994169 CGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCC
994215 GATGAAATAA
Statistics
Matches: 105, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
78 1 0.01
79 104 0.99
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.24
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
TTAGAAAAAAAAAC
Found at i:994209 original size:28 final size:28
Alignment explanation
Indices: 994169--994240 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
994159 GGAATAAAGC
** *
994169 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
994197 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
994225 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
994241 TCGACTGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:994436 original size:51 final size:51
Alignment explanation
Indices: 994228--994449 Score: 203
Period size: 52 Copynumber: 4.3 Consensus size: 51
994218 GAAATAACGA
* * * ** *
994228 GGTTGGAGTATCCTCGACTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATCAGTA-TTTTGGAAATAAAACCGG
* * * * * * *
994280 AGTTGGAGTATCCCTGATTAAAGGAAAA-CTGGTGTTTTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT-ATGAAAAATC-AGTATTTTGGAAATAAAACCGG
* * * * * *
994332 GGTTGGAGTATCCCCGATTGTGGAAAAATTACTGTTTTAGCAATAAAACCGG
1 GGTTGGAGTATCCCCGATTAT-GAAAAATCAGTATTTTGGAAATAAAACCGG
* **
994384 GGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATCAGTATTTTGGAAATAAAACCGG
994435 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
994450 TCAGAAATAA
Statistics
Matches: 136, Mismatches: 30, Indels: 9
0.78 0.17 0.05
Matches are distributed among these distances:
51 38 0.28
52 90 0.66
53 8 0.06
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATCAGTATTTTGGAAATAAAACCGG
Found at i:994522 original size:82 final size:79
Alignment explanation
Indices: 994381--994531 Score: 203
Period size: 82 Copynumber: 1.9 Consensus size: 79
994371 GCAATAAAAC
* **
994381 CGGGGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAATCGAAGTTGGAGTAT
994446 CCCCTCAGAAATAA
66 CCCCTCAGAAATAA
* *** *
994460 CGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGAAGTTGGAG
1 CGGGGTTGGAGTATCCCCGATTATGAA-AAA-T-CAATATTTTGGAAATAAAATCGAAGTTGGAG
994525 TATCCCC
63 TATCCCC
994532 GATTATAGAA
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
79 26 0.43
80 3 0.05
81 1 0.02
82 31 0.51
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAATCGAAGTTGGAGTAT
CCCCTCAGAAATAA
Found at i:994532 original size:54 final size:51
Alignment explanation
Indices: 994464--994594 Score: 165
Period size: 51 Copynumber: 2.5 Consensus size: 51
994454 AAATAACGGG
* *
994464 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGAA
1 GTTGGAGTATCCCCGATTGTG-AGAAATTAGTG--TTTTGAAAATAAAATCGAA
* *
994518 GTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAG-AAATTAGTGTTTTGAAAATAAAATCGAA
*
994569 GTTGGAATATCCCCGATTGTGGAGAA
1 GTTGGAGTATCCCCGATTGT-GAGAA
994595 TTGAGAAACT
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
51 35 0.51
52 4 0.06
53 10 0.15
54 19 0.28
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.31
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGAGAAATTAGTGTTTTGAAAATAAAATCGAA
Found at i:994573 original size:133 final size:131
Alignment explanation
Indices: 994329--994582 Score: 332
Period size: 133 Copynumber: 1.9 Consensus size: 131
994319 AAAATAAAAC
* **
994329 CGGGGTTGGAGTATCCCCGATTGTGGAAAAATTACTGTTTTAGCAATAAAACCGGGGTTGGAGTA
1 CGGGGTTGGAGTATCCCCGATTGTGGAAAAATTACTGTTTTAGAAATAAAACCGAAGTTGGAGTA
* * * *
994394 TCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGGGGTTGGAGTATCCCCTCAGAAATA
66 TCCCCGATTATGAAAAATCAATATTTTGAAAATAAAATCGGAGTTGGAATATCCCCTCAGAAATA
994459 A
131 A
** * *
994460 CGGGGTTGGAGTATCCCCGATTGT-GAAGAAATTGGTGTTTTTTGGAAATAAAATCGAAGTTGGA
1 CGGGGTTGGAGTATCCCCGATTGTGGAA-AAATTACTG--TTTTAGAAATAAAACCGAAGTTGGA
* * *
994524 GTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCC
63 GTATCCCCGATTATGA-AAAATCAATATTTTGAAAATAAAATCGGAGTTGGAATATCCCC
994583 GATTGTGGAG
Statistics
Matches: 105, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
130 3 0.03
131 31 0.30
132 1 0.01
133 70 0.67
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (131 bp):
CGGGGTTGGAGTATCCCCGATTGTGGAAAAATTACTGTTTTAGAAATAAAACCGAAGTTGGAGTA
TCCCCGATTATGAAAAATCAATATTTTGAAAATAAAATCGGAGTTGGAATATCCCCTCAGAAATA
A
Found at i:996980 original size:33 final size:33
Alignment explanation
Indices: 996935--997001 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
996925 AAAATTTCCA
***
996935 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
* *
996968 AATGTATTGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
997001 A
1 A
997002 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:997045 original size:19 final size:18
Alignment explanation
Indices: 997021--997088 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
997011 CAGTAGCTAA
997021 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
997040 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
997055 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
997072 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
997089 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:997061 original size:13 final size:13
Alignment explanation
Indices: 997043--997067 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
997033 ACAATACTTA
997043 TGTATCGATACAT
1 TGTATCGATACAT
997056 TGTATCGATACA
1 TGTATCGATACA
997068 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:997065 original size:32 final size:32
Alignment explanation
Indices: 997024--997086 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
997014 TAGCTAATTA
*
997024 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
997056 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
997087 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:997149 original size:21 final size:21
Alignment explanation
Indices: 997123--997199 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
997113 CGTTGGACCC
* *
997123 TGTATCGATACATTTGTA-GAA
1 TGTATCGATACA-TTCTACAAA
* *
997144 TGTATCGATATATTCCACAAA
1 TGTATCGATACATTCTACAAA
997165 TGTATCGATACATTCTACAAA
1 TGTATCGATACATTCTACAAA
997186 TGTATCGATACATT
1 TGTATCGATACATT
997200 TGAATTTTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 3 0.06
21 46 0.94
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTCTACAAA
Found at i:998513 original size:60 final size:59
Alignment explanation
Indices: 997904--999014 Score: 1196
Period size: 55 Copynumber: 19.3 Consensus size: 59
997894 ATAAAGCGTA
* * * *
997904 TCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTT----G-AAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
** * *
997959 TCCTGCTCTTTGAGGACTGGAAAATGCCA-CAACTTGTGTGGGC-TT---CG-AAAGGGG
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* ** * *
998013 TCCTGCTCTTTGGGGACTGAAAAATGCCACCAACTTGTGTGGGC-TT---CG-AAAGGGG
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * ** * *
998068 TCCTGCTCTTTGGGGATTGAAAAATGCCACCAACTTGTGTGGGC-TT---CG-AAAGGGG
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * *
998123 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAA-AAAAAGCA
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCG
*
998183 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* *
998242 TACC-GCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAATGCG
1 T-CCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* ** *
998301 TCCTACTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTT----G-AAAGGGG
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* ** * *
998356 TCCTGCTCTTTGGGGACTGAAAAATGCCACCAACTTGTGTGGGC-TT---CG-AAAGGGG
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * * *
998411 TCCTGCTCTTTGGGGACTGAAAGGTGCTACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCG
*
998472 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* *
998531 TACC-GCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAATGCG
1 T-CCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* **
998590 TCCCGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTT-----AAAAGGCG
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * * *
998645 TCCTACTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAGGCG
* * *
998706 TCCTGCTCTTTGAGGACTGAAGCTGCCACCAACTTGGGTAGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
* * *
998765 TCCCGCTCTTTGAGGACTGGAGGTGCCACCAACTTGTGGGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
** *
998824 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAGGCG
*
998885 TCCTGCTCTTTGAGGACTGGGAA-GTGCCACCAACTTGTGTGGGCTTT-----AAAAGGTG
1 TCCTGCTCTTTGAGGACT--GAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
*
998940 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCA
1 TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAGGCG
999000 TCCTGCTCTTTGAGG
1 TCCTGCTCTTTGAGG
999015 GCTAAAAAGT
Statistics
Matches: 937, Mismatches: 80, Indels: 73
0.86 0.07 0.07
Matches are distributed among these distances:
53 6 0.01
54 72 0.08
55 315 0.34
56 5 0.01
58 8 0.01
59 259 0.28
60 175 0.19
61 94 0.10
62 3 0.00
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.26
Consensus pattern (59 bp):
TCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCG
Found at i:998680 original size:234 final size:229
Alignment explanation
Indices: 997904--999022 Score: 1291
Period size: 234 Copynumber: 4.9 Consensus size: 229
997894 ATAAAGCGTA
* * *
997904 TCCTGCTCTTTGAGGACT-AAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGTGTCCTGCTCT
1 TCCTGCTCTTTGAGGACTGAAAAA-TGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCT
* * * *
997968 TTGAGGACTGGAAA-ATGCCA-CAACTTGTGTGGGCTTCG-AAAG----GGGTCCTGCTCTTTGG
65 TTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAGCGTCCTGCTCTTTGA
** * * * *
998026 GGACTGAAAAATGCCACCAACTTGTGTGGGC-TT---CG-AAAGGGGTCCTGCTCTTTGGGGATT
129 GGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCTGCTCTTTGAGGACT
* *
998086 GAAAAATGCCACCAACTTGTGTGGGC-TTCGAAAGGGG
193 -AAAAATGCCACCAACTTGTGTGGGCTTTAGAAAGGCG
* ** * *
998123 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAAAAAAGCATCCTG
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTT-----AAAAGGCGTCCTG
*
998188 CTCTTTGAGGACTG-AAGGTGCCACCAACTTGGGTGGGCTTT-AAAAGAAAAGGCGTACC-GCTC
61 CTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAA-GCGT-CCTGCTC
* * *
998250 TTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAATGCGTCCTACTCTTTGAG
124 TTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCTGCTCTTTGAG
*
998315 GACTGAAAAATGCCACCAACTTGTGTGGGCTTT-GAAAGGGG
189 GACT-AAAAATGCCACCAACTTGTGTGGGCTTTAGAAAGGCG
* ** *
998356 TCCTGCTCTTTGGGGACTGAAAAATGCCACCAACTTGTGTGGGCTTCGAAAGGGGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCTT
* * *
998421 TGGGGACTGAAAGGTGCTACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAG
66 TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAG-AAAAGCGTCCTGCTCTTTGAG
*
998486 GACTGAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCGTACC-GCTCTTTGAGGACTA
130 GACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGT-CCTGCTCTTTGAGGACTA
** *
998550 AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAATGCG
194 AAAATGCCACCAACTTGTGTGGGCTTT---AG-AAAGGCG
* *
998590 TCCCGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTACTCTT
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCTT
* *
998655 TGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAG
66 TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAG-AAAAGCGTCCTGCTCTTTGAG
* * * * **
998720 GACTGAAGCTGCCACCAACTTGGGTAGGCTTTAAAAGAAAAGGCGTCCCGCTCTTTGAGGACTGG
130 GACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTAA
** *
998785 AGGTGCCACCAACTTGTGGGGGCTTTAAAAGAAAAGGCG
195 AAATGCCACCAACTTGTGTGGGCTTT---AG-AAAGGCG
998824 TCCTGCTCTTTGAGGACT-AGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCC
1 TCCTGCTCTTTGAGGACTGA-AAAATGCCACCAACTTGTGTGGGCTTT---A--A-AAGGCGTCC
* *
998888 TGCTCTTTGAGGACTGGGAA-GTGCCACCAACTTGTGTGGGCTTT-AAAAG----GTGTCCTGCT
59 TGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAGCGTCCTGCT
*
998947 CTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCATCCTGCTCTTTG
123 CTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAA-GAAAAGGCGTCCTGCTCTTTG
*
999012 AGGGCTAAAAA
187 AGGACTAAAAA
999023 GTGGAAGGAG
Statistics
Matches: 789, Mismatches: 70, Indels: 66
0.85 0.08 0.07
Matches are distributed among these distances:
219 39 0.05
220 3 0.00
222 2 0.00
223 6 0.01
224 41 0.05
228 44 0.06
229 71 0.09
230 76 0.10
231 6 0.01
232 1 0.00
233 102 0.13
234 317 0.40
235 25 0.03
237 1 0.00
239 6 0.01
240 46 0.06
241 3 0.00
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (229 bp):
TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTGCTCTT
TGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAGCGTCCTGCTCTTTGAGG
ACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAAGGCGTCCTGCTCTTTGAGGACTAAA
AATGCCACCAACTTGTGTGGGCTTTAGAAAGGCG
Found at i:1000033 original size:11 final size:10
Alignment explanation
Indices: 1000015--1000053 Score: 53
Period size: 11 Copynumber: 3.8 Consensus size: 10
1000005 CTTTGTTTTG
1000015 TTTTTTTGTT
1 TTTTTTTGTT
1000025 TTGTTTTTG-T
1 TT-TTTTTGTT
1000035 TTTTTTTGCTT
1 TTTTTTTG-TT
1000046 TTTTTTTG
1 TTTTTTTG
1000054 AAGAGAAGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 6 0.23
10 5 0.19
11 15 0.58
ACGTcount: A:0.00, C:0.03, G:0.13, T:0.85
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:1000039 original size:13 final size:13
Alignment explanation
Indices: 1000001--1000032 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
999991 TTTTCTCTCT
1000001 TTTTCTTTGTTTTG
1 TTTT-TTTGTTTTG
1000015 TTTTTTTGTTTTG
1 TTTTTTTGTTTTG
1000028 TTTTT
1 TTTTT
1000033 GTTTTTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.78
14 4 0.22
ACGTcount: A:0.00, C:0.03, G:0.12, T:0.84
Consensus pattern (13 bp):
TTTTTTTGTTTTG
Found at i:1008329 original size:9 final size:9
Alignment explanation
Indices: 1008317--1008377 Score: 56
Period size: 9 Copynumber: 7.1 Consensus size: 9
1008307 CTTTCTCTAT
1008317 TATCTCTCC
1 TATCTCTCC
1008326 TATCTCTCC
1 TATCTCTCC
* *
1008335 T-CCTAT-C
1 TATCTCTCC
*
1008342 -ATCCCTCC
1 TATCTCTCC
*
1008350 TATCTCTAC
1 TATCTCTCC
1008359 TATCTCTCC
1 TATCTCTCC
*
1008368 TGTCTCTCC
1 TATCTCTCC
1008377 T
1 T
1008378 CCTATCATCC
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
7 3 0.08
8 4 0.10
9 33 0.82
ACGTcount: A:0.11, C:0.44, G:0.02, T:0.43
Consensus pattern (9 bp):
TATCTCTCC
Found at i:1008337 original size:12 final size:12
Alignment explanation
Indices: 1008322--1008356 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
1008312 TCTATTATCT
1008322 CTCCTATCTCTC
1 CTCCTATCTCTC
1008334 CTCCTATCATC-C
1 CTCCTATC-TCTC
1008346 CTCCTATCTCT
1 CTCCTATCTCT
1008357 ACTATCTCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.10
12 17 0.81
13 2 0.10
ACGTcount: A:0.11, C:0.49, G:0.00, T:0.40
Consensus pattern (12 bp):
CTCCTATCTCTC
Found at i:1008345 original size:42 final size:42
Alignment explanation
Indices: 1008289--1008407 Score: 175
Period size: 42 Copynumber: 2.8 Consensus size: 42
1008279 TTCTTCTCTC
* * *
1008289 CTCCTCCTGTCATCCCTCCTTTCTCTATTATCTCTCCTATCT
1 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATCT
*
1008331 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATCT
* * *
1008373 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCT
1008408 TTGAGGGCTA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.09, C:0.45, G:0.02, T:0.44
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATCT
Found at i:1008349 original size:24 final size:24
Alignment explanation
Indices: 1008313--1008398 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
1008303 CCTCCTTTCT
* *
1008313 CTATTATCTCTCCTATCTCTCCTC
1 CTATCATCCCTCCTATCTCTCCTC
*
1008337 CTATCATCCCTCCTA--TCT-CTA
1 CTATCATCCCTCCTATCTCTCCTC
*
1008358 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTATCTCTCCTC
*
1008379 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTATCTCT
1008399 TCTTTCTCTT
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
18 5 0.10
20 4 0.08
21 14 0.28
22 4 0.08
24 23 0.46
ACGTcount: A:0.12, C:0.45, G:0.01, T:0.42
Consensus pattern (24 bp):
CTATCATCCCTCCTATCTCTCCTC
Found at i:1013977 original size:18 final size:18
Alignment explanation
Indices: 1013954--1014061 Score: 58
Period size: 21 Copynumber: 5.3 Consensus size: 18
1013944 ATCTTCTTCT
1013954 CTCCTCCTCCTATCATCC
1 CTCCTCCTCCTATCATCC
*
1013972 CTCCT-CTCTCTATTATCTCTC
1 CTCCTCCTC-CTATCA--TC-C
1013993 CTGTCTCTCCTCCTATCATCC
1 C--TC-CTCCTCCTATCATCC
*
1014014 CTCCTATCTCTACTATC-TCTC
1 CTCC--TC-CTCCTATCATC-C
1014035 CTGTCTCTCCTCCTATCATCC
1 C--TC-CTCCTCCTATCATCC
1014056 CTCCTC
1 CTCCTC
1014062 TCTCTTCTTT
Statistics
Matches: 70, Mismatches: 4, Indels: 32
0.66 0.04 0.30
Matches are distributed among these distances:
17 3 0.04
18 14 0.20
19 4 0.06
20 6 0.09
21 22 0.31
22 6 0.09
23 4 0.06
24 8 0.11
25 3 0.04
ACGTcount: A:0.10, C:0.48, G:0.02, T:0.40
Consensus pattern (18 bp):
CTCCTCCTCCTATCATCC
Found at i:1014003 original size:42 final size:42
Alignment explanation
Indices: 1013957--1014075 Score: 202
Period size: 42 Copynumber: 2.8 Consensus size: 42
1013947 TTCTTCTCTC
*
1013957 CTCCTCCTATCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
1013999 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
1014041 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
1014076 TTGAGGGCTA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.09, C:0.46, G:0.02, T:0.43
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:1014016 original size:12 final size:11
Alignment explanation
Indices: 1013990--1014065 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
1013980 TCTATTATCT
*
1013990 CTCCTGTCTCTC
1 CTCCTATCTC-C
1014002 CTCCTATCATCC
1 CTCCTATC-TCC
1014014 CTCCTATCT--
1 CTCCTATCTCC
*
1014023 CTACTATCT--
1 CTCCTATCTCC
*
1014032 CTCCTGTCTCTC
1 CTCCTATCTC-C
1014044 CTCCTATCATCC
1 CTCCTATC-TCC
*
1014056 CTCCTCTCTC
1 CTCCTATCTC
1014066 TTCTTTCTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 3 0.06
12 31 0.58
13 4 0.08
ACGTcount: A:0.09, C:0.49, G:0.03, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:1016103 original size:728 final size:729
Alignment explanation
Indices: 1014994--1016418 Score: 2609
Period size: 728 Copynumber: 2.0 Consensus size: 729
1014984 TGATACCAAT
* *
1014994 TGATGACAACCATGAACCAAGGTTGCCTAAATAATGATCTTGAGATGGATTTCTAACAATAAACA
1 TGATGACAACCATGAACCAAGGTTGCCTAAATAATGATCTTAAGATGGATCTCTAACAATAAACA
1015059 GAATTATTGATGCAAGAACAGAAATTGAAAGAAGCAGAAAAAAAATAACAAAATGGAATAGATTA
66 GAATTATTGATGCAAGAACAGAAATTGAAAGAAGCAGAAAAAAAATAACAAAATGGAATAGATTA
*
1015124 GAGATGGAGGATGGCGCCACAATCACAAGATTGATAAGCCAAAAGGAATGATCGCCACAAGAGTC
131 GAGATGAAGGATGGCGCCACAATCACAAGATTGATAAGCCAAAAGGAATGATCGCCACAAGAGTC
1015189 TTGGCCTCTTGATAAGATCCAGAAAAATTGGCTCACTCAAGAACCTAAGAATCACACTCTCACAC
196 TTGGCCTCTTGATAAGATCCAGAAAAATTGGCTCACTCAAGAACCTAAGAATCACACTCTCACAC
*
1015254 AAAATGTGTTTAATCTGCAAATATGAATGTCTGCCCCCTCCAAATCTATTTACAAGAGCTTATAT
261 AAAATGTGTTTAATCTGCAAATATCAATGTCTGCCCCCTCCAAATCTATTTACAAGAGCTTATAT
1015319 ATGCCCTCATAAGCCATAGTTAACACAAACCCTAAGGGGATTATTATGCTAACAAGCCCAACTCT
326 ATGCCCTCATAAGCCATAGTTAACACAAACCCTAAGGGGATTATTATGCTAACAAGCCCAACTCT
1015384 TACTTAAACCCAAATAACAAGTTTTTATGCTAAATAAAGCCCAAAGCAAGTCACAACCAGCAGGC
391 TACTTAAACCCAAATAACAAGTTTTTATGCTAAATAAAGCCCAAAGCAAGTCACAACCAGCAGGC
*
1015449 CCTTTATTACAAAATAACCCAAGTCCTAATTGAATCCATTGGAGCCCATATCTTCCAAATATATG
456 CCTTTATTACAAAATAACCCAAGTCCTAATTCAATCCATTGGAGCCCATATCTTCCAAATATATG
* *
1015514 CAATTAACTAGCTTGGGCTCTTCTAACTCCAGATTGGGTCTACTTTCAAATAGGCCAGCAACCAT
521 CAATTAACTAGCTTGGGCTCCTCTAACTCCAAATTGGGTCTACTTTCAAATAGGCCAGCAACCAT
* *
1015579 CTTCTCTAGGTCTTCCTTTATCCTCTTTGCCTTTGCCCTCGTTATTGGTCCTTGAAATCCTTCCA
586 CTTCTCTAGGTCTTCCTTTATCCTCTTTGCCTTTGCCCTCGTCATTGGTCCTTGAAACCCTTCCA
* * *
1015644 ACGCCTTCAGGTCTTTGTCTTCAATGGACCTTCCTTGGTTTTCATCAGATCATGATAAGAACCAA
651 ACGCCTTCAGGTCATTGTATTCAATGGACCTTCCTTGGATTTCATCAGATCATGATAAGAACCAA
1015709 GCAAGGTCTATTGA
716 GCAAGGTCTATTGA
*
1015723 TGATGACAACCATGAACCAAGGTTGCCTAAATAATGATCTTAAGATGGATCTCTAACAATAAATA
1 TGATGACAACCATGAACCAAGGTTGCCTAAATAATGATCTTAAGATGGATCTCTAACAATAAACA
*
1015788 GAATTATTGATGCAAGAACAGAAATTGAAAGAAGCAG-AAAAAAATAACAAAATTGAATAGATTA
66 GAATTATTGATGCAAGAACAGAAATTGAAAGAAGCAGAAAAAAAATAACAAAATGGAATAGATTA
1015852 GAGATGAAGGATGGCGCCACAATCACAAGATTGATAAGCCAAAAGGAATGATCGCCACAAGAGTC
131 GAGATGAAGGATGGCGCCACAATCACAAGATTGATAAGCCAAAAGGAATGATCGCCACAAGAGTC
* * *
1015917 TTTGCCTCTTTATAAGATCCAGAAAAATTGGCTCACTCAAGAACCTAAGAATCACACTCTCACCC
196 TTGGCCTCTTGATAAGATCCAGAAAAATTGGCTCACTCAAGAACCTAAGAATCACACTCTCACAC
* *
1015982 AAAATGTGTTTAATCTGCAAATATCAATGTCTGCCTCCTCCAAATCTGTTTACAAGAGCTTATAT
261 AAAATGTGTTTAATCTGCAAATATCAATGTCTGCCCCCTCCAAATCTATTTACAAGAGCTTATAT
* *
1016047 ATGCCCTCATAAGCCATAGTTAACACAAACCCTAAGGGGCTTATTATGTTAACAAGCCCAACTCT
326 ATGCCCTCATAAGCCATAGTTAACACAAACCCTAAGGGGATTATTATGCTAACAAGCCCAACTCT
*
1016112 TAGTTAAACCCAAATAACAAGTTTTTATGCTAAATAAAGCCCAAAGCAAGTCACAACCAGCAGGC
391 TACTTAAACCCAAATAACAAGTTTTTATGCTAAATAAAGCCCAAAGCAAGTCACAACCAGCAGGC
*
1016177 CTTTTATTACAAAATAACCCAAGTCCTAATTCAATCCATTGGAGCCCATATCTTCCAAATATATG
456 CCTTTATTACAAAATAACCCAAGTCCTAATTCAATCCATTGGAGCCCATATCTTCCAAATATATG
1016242 CAATTAACTAGCTTGGGCTCCTCTAACTCCAAATTGGGTCTACTTTCAAATAGGCCAGCAACCAT
521 CAATTAACTAGCTTGGGCTCCTCTAACTCCAAATTGGGTCTACTTTCAAATAGGCCAGCAACCAT
*
1016307 CTTCTCTAGGTCTTCCTTTATCCTCTTTGCCTTTGCCCTCGTCATTGGTCCTTGAAGCCCTTCCA
586 CTTCTCTAGGTCTTCCTTTATCCTCTTTGCCTTTGCCCTCGTCATTGGTCCTTGAAACCCTTCCA
* *
1016372 ATGCCTTCAGGTCATTGTATTCAATGGACCTTGCTTGGATTTCATCA
651 ACGCCTTCAGGTCATTGTATTCAATGGACCTTCCTTGGATTTCATCA
1016419 ACCCCTCCTT
Statistics
Matches: 670, Mismatches: 26, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
728 571 0.85
729 99 0.15
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (729 bp):
TGATGACAACCATGAACCAAGGTTGCCTAAATAATGATCTTAAGATGGATCTCTAACAATAAACA
GAATTATTGATGCAAGAACAGAAATTGAAAGAAGCAGAAAAAAAATAACAAAATGGAATAGATTA
GAGATGAAGGATGGCGCCACAATCACAAGATTGATAAGCCAAAAGGAATGATCGCCACAAGAGTC
TTGGCCTCTTGATAAGATCCAGAAAAATTGGCTCACTCAAGAACCTAAGAATCACACTCTCACAC
AAAATGTGTTTAATCTGCAAATATCAATGTCTGCCCCCTCCAAATCTATTTACAAGAGCTTATAT
ATGCCCTCATAAGCCATAGTTAACACAAACCCTAAGGGGATTATTATGCTAACAAGCCCAACTCT
TACTTAAACCCAAATAACAAGTTTTTATGCTAAATAAAGCCCAAAGCAAGTCACAACCAGCAGGC
CCTTTATTACAAAATAACCCAAGTCCTAATTCAATCCATTGGAGCCCATATCTTCCAAATATATG
CAATTAACTAGCTTGGGCTCCTCTAACTCCAAATTGGGTCTACTTTCAAATAGGCCAGCAACCAT
CTTCTCTAGGTCTTCCTTTATCCTCTTTGCCTTTGCCCTCGTCATTGGTCCTTGAAACCCTTCCA
ACGCCTTCAGGTCATTGTATTCAATGGACCTTCCTTGGATTTCATCAGATCATGATAAGAACCAA
GCAAGGTCTATTGA
Found at i:1020715 original size:42 final size:42
Alignment explanation
Indices: 1020662--1020777 Score: 160
Period size: 42 Copynumber: 2.8 Consensus size: 42
1020652 TTCTCTCCTT
* * * *
1020662 CTCCTGTCATCCCTCCTCTCTCTATTATCTCTTCTATCTCTC
1 CTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATCTCTC
*
1020704 TTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATCTCTC
1 CTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATCTCTC
* * *
1020746 CTCTTATCATCCCTCCTATCTCTTCTTTCTCT
1 CTCCTATCATCCCTCCTATCTCTACTATCTCT
1020778 TTGAGGGCTA
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.11, C:0.42, G:0.01, T:0.46
Consensus pattern (42 bp):
CTCCTATCATCCCTCCTATCTCTACTATCTCTCCTATCTCTC
Found at i:1020745 original size:9 final size:9
Alignment explanation
Indices: 1020716--1020747 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
1020706 CCTATCATCC
1020716 CTCCTATCT
1 CTCCTATCT
*
1020725 CTACTATCT
1 CTCCTATCT
1020734 CTCCTATCT
1 CTCCTATCT
1020743 CTCCT
1 CTCCT
1020748 CTTATCATCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.12, C:0.44, G:0.00, T:0.44
Consensus pattern (9 bp):
CTCCTATCT
Found at i:1024637 original size:12 final size:11
Alignment explanation
Indices: 1024618--1024689 Score: 62
Period size: 12 Copynumber: 6.5 Consensus size: 11
1024608 AGAGAAAAAA
1024618 GAGATAGGAGG
1 GAGATAGGAGG
1024629 GATGATAGGAGG
1 GA-GATAGGAGG
*
1024641 AGAGATCGGA--
1 -GAGATAGGAGG
*
1024651 GAGATAGTA--
1 GAGATAGGAGG
1024660 GAGATAGGAGG
1 GAGATAGGAGG
1024671 GATGATAGGAGG
1 GA-GATAGGAGG
1024683 AGAGATA
1 -GAGATA
1024690 ATAGAGAGAG
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
9 15 0.29
11 4 0.08
12 28 0.55
13 4 0.08
ACGTcount: A:0.39, C:0.01, G:0.46, T:0.14
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:1024685 original size:33 final size:33
Alignment explanation
Indices: 1024648--1024720 Score: 119
Period size: 33 Copynumber: 2.2 Consensus size: 33
1024638 AGGAGAGATC
* * *
1024648 GGAGAGATAGTAGAGATAGGAGGGATGATAGGA
1 GGAGAGATAATAGAGAGAGGAGGGATGACAGGA
1024681 GGAGAGATAATAGAGAGAGGAGGGATGACAGGA
1 GGAGAGATAATAGAGAGAGGAGGGATGACAGGA
1024714 GGAGAGA
1 GGAGAGA
1024721 AGAAGATGGA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.41, C:0.01, G:0.47, T:0.11
Consensus pattern (33 bp):
GGAGAGATAATAGAGAGAGGAGGGATGACAGGA
Found at i:1024696 original size:42 final size:42
Alignment explanation
Indices: 1024617--1024696 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
1024607 AAGAGAAAAA
**
1024617 AGAGATAGGAGGGATGATAGGAGGAGAGATCGGAGAGATAGT
1 AGAGATAGGAGGGATGATAGGAGGAGAGATAAGAGAGATAGT
*
1024659 AGAGATAGGAGGGATGATAGGAGGAGAGATAATAGAGA
1 AGAGATAGGAGGGATGATAGGAGGAGAGATAAGAGAGA
1024697 GAGGAGGGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.41, C:0.01, G:0.44, T:0.14
Consensus pattern (42 bp):
AGAGATAGGAGGGATGATAGGAGGAGAGATAAGAGAGATAGT
Found at i:1024702 original size:18 final size:18
Alignment explanation
Indices: 1024648--1024702 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
1024638 AGGAGAGATC
* *
1024648 GGAGAGATAGTAGAGATA
1 GGAGAGATAATAGAGAGA
* *
1024666 GGAGGGATGAT--AG-GA
1 GGAGAGATAATAGAGAGA
1024681 GGAGAGATAATAGAGAGA
1 GGAGAGATAATAGAGAGA
1024699 GGAG
1 GGAG
1024703 GGATGACAGG
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
15 10 0.36
16 2 0.07
17 2 0.07
18 14 0.50
ACGTcount: A:0.42, C:0.00, G:0.45, T:0.13
Consensus pattern (18 bp):
GGAGAGATAATAGAGAGA
Found at i:1027863 original size:18 final size:18
Alignment explanation
Indices: 1027842--1027912 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
1027832 TGATAGGAGG
1027842 AGAGACAGGAGAGATAGT
1 AGAGACAGGAGAGATAGT
* *
1027860 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGA--GA-GAT---AGT
*
1027884 AGAGACAGGAGAGATAAT
1 AGAGACAGGAGAGATAGT
*
1027902 AGAGAGAGGAG
1 AGAGACAGGAG
1027913 GGATGACAGG
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
18 20 0.49
20 2 0.05
21 6 0.15
22 2 0.05
24 11 0.27
ACGTcount: A:0.44, C:0.03, G:0.44, T:0.10
Consensus pattern (18 bp):
AGAGACAGGAGAGATAGT
Found at i:1027873 original size:42 final size:42
Alignment explanation
Indices: 1027809--1027927 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
1027799 TAGCCCTCAA
* * *
1027809 AGAGAAAGAAGAGAGAGAAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
1027851 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
1027893 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
1027928 GAGAGAAGAA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.44, C:0.03, G:0.45, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:1033436 original size:21 final size:21
Alignment explanation
Indices: 1033410--1033458 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
1033400 ATATTTTGAG
*
1033410 TTTCTTCATTTTGTGAGAACT
1 TTTCTTCATTTTGTAAGAACT
1033431 TTTCTTCATTTTGTAAGAACT
1 TTTCTTCATTTTGTAAGAACT
1033452 TCTTCTT
1 T-TTCTT
1033459 GGTTCTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 21 0.81
22 5 0.19
ACGTcount: A:0.18, C:0.16, G:0.10, T:0.55
Consensus pattern (21 bp):
TTTCTTCATTTTGTAAGAACT
Found at i:1033802 original size:16 final size:16
Alignment explanation
Indices: 1033778--1033809 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1033768 TGTATCTTAA
1033778 TAAGAAACTTTGATTC
1 TAAGAAACTTTGATTC
*
1033794 TAAGGAACTTTGATTC
1 TAAGAAACTTTGATTC
1033810 CTTATTCCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (16 bp):
TAAGAAACTTTGATTC
Found at i:1033855 original size:48 final size:49
Alignment explanation
Indices: 1033782--1033915 Score: 198
Period size: 48 Copynumber: 2.8 Consensus size: 49
1033772 TCTTAATAAG
* *
1033782 AAACTTTGATTCTAAGGAACTTTGATTCCTTATTCCTTATTTGAGGGAT
1 AAACTTTGATTCTAAGGAACTTTGATTCCTTATTCCTTATTAGAGGGAC
* * * * *
1033831 GAACTTTCATTC-AAGGAAGTTTGATACCTTAATCCTTATTAGAGGGAC
1 AAACTTTGATTCTAAGGAACTTTGATTCCTTATTCCTTATTAGAGGGAC
1033879 AAACTTTGATTCTAAGGAACTTTGATTCCTTATTCCT
1 AAACTTTGATTCTAAGGAACTTTGATTCCTTATTCCT
1033916 AGAATGTGCT
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
48 41 0.57
49 31 0.43
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (49 bp):
AAACTTTGATTCTAAGGAACTTTGATTCCTTATTCCTTATTAGAGGGAC
Found at i:1039679 original size:42 final size:42
Alignment explanation
Indices: 1039624--1039742 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
1039614 TTCTTCTCTC
* *
1039624 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
1039666 CTCTTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
1039708 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
1039743 TTGAGGGCTA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.08, C:0.45, G:0.03, T:0.44
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:1039708 original size:18 final size:18
Alignment explanation
Indices: 1039639--1039709 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
1039629 CCTGTCATCC
* *
1039639 CTCCTCTCTCTATTATCT
1 CTCCTGTCTCTACTATCT
*
1039657 CTCCTGTCTCTCTTCCTATCAT
1 CTCCTG--TCTC-TACTATC-T
*
1039679 CCCTCCTATCTCTACTATCT
1 --CTCCTGTCTCTACTATCT
1039699 CTCCTGTCTCT
1 CTCCTGTCTCT
1039710 CCTCCTATCA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
18 15 0.37
20 5 0.12
21 11 0.27
22 5 0.12
24 5 0.12
ACGTcount: A:0.10, C:0.42, G:0.03, T:0.45
Consensus pattern (18 bp):
CTCCTGTCTCTACTATCT
Found at i:1039727 original size:24 final size:24
Alignment explanation
Indices: 1039648--1039733 Score: 76
Period size: 24 Copynumber: 3.8 Consensus size: 24
1039638 CCTCCTCTCT
* * *
1039648 CTATTATCTCTCCTGTCTCTCTTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
1039672 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
1039693 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
1039714 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
1039734 TCTTTCTCTT
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
18 4 0.08
20 5 0.10
21 13 0.27
22 5 0.10
24 21 0.44
ACGTcount: A:0.10, C:0.44, G:0.02, T:0.43
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:1050285 original size:21 final size:21
Alignment explanation
Indices: 1050259--1050307 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
1050249 ATATTTTGAG
*
1050259 TTTCTTCATTTTGTGAGAACT
1 TTTCTTCATTTTGTAAGAACT
1050280 TTTCTTCATTTTGTAAGAACT
1 TTTCTTCATTTTGTAAGAACT
1050301 TCTTCTT
1 T-TTCTT
1050308 GGTTCTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 21 0.81
22 5 0.19
ACGTcount: A:0.18, C:0.16, G:0.10, T:0.55
Consensus pattern (21 bp):
TTTCTTCATTTTGTAAGAACT
Found at i:1050651 original size:16 final size:16
Alignment explanation
Indices: 1050627--1050658 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1050617 TGTATCTTAA
1050627 TAAGAAACTTTGATTC
1 TAAGAAACTTTGATTC
*
1050643 TAAGGAACTTTGATTC
1 TAAGAAACTTTGATTC
1050659 CTTATTCCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (16 bp):
TAAGAAACTTTGATTC
Found at i:1050704 original size:48 final size:49
Alignment explanation
Indices: 1050631--1050764 Score: 198
Period size: 48 Copynumber: 2.8 Consensus size: 49
1050621 TCTTAATAAG
* *
1050631 AAACTTTGATTCTAAGGAACTTTGATTCCTTATTCCTTATTTGAGGGAT
1 AAACTTTGATTCTAAGGAACTTTGATTCCTTATTCCTTATTAGAGGGAC
* * * * *
1050680 GAACTTTCATTC-AAGGAAGTTTGATACCTTAATCCTTATTAGAGGGAC
1 AAACTTTGATTCTAAGGAACTTTGATTCCTTATTCCTTATTAGAGGGAC
1050728 AAACTTTGATTCTAAGGAACTTTGATTCCTTATTCCT
1 AAACTTTGATTCTAAGGAACTTTGATTCCTTATTCCT
1050765 AGAATGTGCT
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
48 41 0.57
49 31 0.43
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (49 bp):
AAACTTTGATTCTAAGGAACTTTGATTCCTTATTCCTTATTAGAGGGAC
Found at i:1056529 original size:42 final size:42
Alignment explanation
Indices: 1056474--1056592 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
1056464 TTCTTCTCTC
* *
1056474 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
1056516 CTCTTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
1056558 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
1056593 TTGAGGGCTA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.08, C:0.45, G:0.03, T:0.44
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:1056558 original size:18 final size:18
Alignment explanation
Indices: 1056489--1056559 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
1056479 CCTGTCATCC
* *
1056489 CTCCTCTCTCTATTATCT
1 CTCCTGTCTCTACTATCT
*
1056507 CTCCTGTCTCTCTTCCTATCAT
1 CTCCTG--TCTC-TACTATC-T
*
1056529 CCCTCCTATCTCTACTATCT
1 --CTCCTGTCTCTACTATCT
1056549 CTCCTGTCTCT
1 CTCCTGTCTCT
1056560 CCTCCTATCA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
18 15 0.37
20 5 0.12
21 11 0.27
22 5 0.12
24 5 0.12
ACGTcount: A:0.10, C:0.42, G:0.03, T:0.45
Consensus pattern (18 bp):
CTCCTGTCTCTACTATCT
Found at i:1056577 original size:24 final size:24
Alignment explanation
Indices: 1056498--1056583 Score: 76
Period size: 24 Copynumber: 3.8 Consensus size: 24
1056488 CCTCCTCTCT
* * *
1056498 CTATTATCTCTCCTGTCTCTCTTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
1056522 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
1056543 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
1056564 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
1056584 TCTTTCTCTT
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
18 4 0.08
20 5 0.10
21 13 0.27
22 5 0.10
24 21 0.44
ACGTcount: A:0.10, C:0.44, G:0.02, T:0.43
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:1061572 original size:12 final size:11
Alignment explanation
Indices: 1061550--1061625 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
1061540 AGAGAAAGAA
*
1061550 GAGAGAGGAGG
1 GAGATAGGAGG
1061561 GATGATAGGAGG
1 GA-GATAGGAGG
*
1061573 AGAGACAGGA--
1 -GAGATAGGAGG
*
1061583 GAGATAGTA--
1 GAGATAGGAGG
1061592 GAGATAGGAGG
1 GAGATAGGAGG
1061603 GATGATAGGAGG
1 GA-GATAGGAGG
*
1061615 AGAGACAGGAG
1 -GAGATAGGAG
1061626 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:1061582 original size:24 final size:24
Alignment explanation
Indices: 1061549--1061634 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
1061539 AAGAGAAAGA
*
1061549 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
1061573 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
1061591 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
1061615 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
1061635 AGAGAGGAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:1061601 original size:42 final size:42
Alignment explanation
Indices: 1061540--1061658 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
1061530 TAGCCCTCAA
* *
1061540 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
1061582 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
1061624 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
1061659 GAGAGAAGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.43, C:0.03, G:0.46, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:1067168 original size:21 final size:21
Alignment explanation
Indices: 1067142--1067190 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
1067132 ATATTTTGAG
*
1067142 TTTCTTCATTTTGTGAGAACT
1 TTTCTTCATTTTGTAAGAACT
1067163 TTTCTTCATTTTGTAAGAACT
1 TTTCTTCATTTTGTAAGAACT
1067184 TCTTCTT
1 T-TTCTT
1067191 GGTTCTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 21 0.81
22 5 0.19
ACGTcount: A:0.18, C:0.16, G:0.10, T:0.55
Consensus pattern (21 bp):
TTTCTTCATTTTGTAAGAACT
Found at i:1067534 original size:16 final size:16
Alignment explanation
Indices: 1067510--1067541 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1067500 TGTATCTTAA
1067510 TAAGAAACTTTGATTC
1 TAAGAAACTTTGATTC
*
1067526 TAAGGAACTTTGATTC
1 TAAGAAACTTTGATTC
1067542 CTTATTCCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (16 bp):
TAAGAAACTTTGATTC
Found at i:1067587 original size:48 final size:49
Alignment explanation
Indices: 1067514--1067647 Score: 198
Period size: 48 Copynumber: 2.8 Consensus size: 49
1067504 TCTTAATAAG
* *
1067514 AAACTTTGATTCTAAGGAACTTTGATTCCTTATTCCTTATTTGAGGGAT
1 AAACTTTGATTCTAAGGAACTTTGATTCCTTATTCCTTATTAGAGGGAC
* * * * *
1067563 GAACTTTCATTC-AAGGAAGTTTGATACCTTAATCCTTATTAGAGGGAC
1 AAACTTTGATTCTAAGGAACTTTGATTCCTTATTCCTTATTAGAGGGAC
1067611 AAACTTTGATTCTAAGGAACTTTGATTCCTTATTCCT
1 AAACTTTGATTCTAAGGAACTTTGATTCCTTATTCCT
1067648 AGAATGTGCT
Statistics
Matches: 72, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
48 41 0.57
49 31 0.43
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (49 bp):
AAACTTTGATTCTAAGGAACTTTGATTCCTTATTCCTTATTAGAGGGAC
Found at i:1073410 original size:42 final size:42
Alignment explanation
Indices: 1073355--1073473 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
1073345 TTCTTCTCTC
* *
1073355 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
1073397 CTCTTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
1073439 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
1073474 TTGAGGGCTA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.08, C:0.45, G:0.03, T:0.44
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:1073439 original size:18 final size:18
Alignment explanation
Indices: 1073370--1073440 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
1073360 CCTGTCATCC
* *
1073370 CTCCTCTCTCTATTATCT
1 CTCCTGTCTCTACTATCT
*
1073388 CTCCTGTCTCTCTTCCTATCAT
1 CTCCTG--TCTC-TACTATC-T
*
1073410 CCCTCCTATCTCTACTATCT
1 --CTCCTGTCTCTACTATCT
1073430 CTCCTGTCTCT
1 CTCCTGTCTCT
1073441 CCTCCTATCA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
18 15 0.37
20 5 0.12
21 11 0.27
22 5 0.12
24 5 0.12
ACGTcount: A:0.10, C:0.42, G:0.03, T:0.45
Consensus pattern (18 bp):
CTCCTGTCTCTACTATCT
Found at i:1073458 original size:24 final size:24
Alignment explanation
Indices: 1073379--1073464 Score: 76
Period size: 24 Copynumber: 3.8 Consensus size: 24
1073369 CCTCCTCTCT
* * *
1073379 CTATTATCTCTCCTGTCTCTCTTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
1073403 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
1073424 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
1073445 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
1073465 TCTTTCTCTT
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
18 4 0.08
20 5 0.10
21 13 0.27
22 5 0.10
24 21 0.44
ACGTcount: A:0.10, C:0.44, G:0.02, T:0.43
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:1077829 original size:12 final size:11
Alignment explanation
Indices: 1077810--1077876 Score: 66
Period size: 12 Copynumber: 5.9 Consensus size: 11
1077800 AGAGAAAGAA
1077810 GAGATAGGAGG
1 GAGATAGGAGG
1077821 GATGATAGGAGG
1 GA-GATAGGAGG
*
1077833 AGAGATAGTA--
1 -GAGATAGGAGG
1077843 GAGATAGGAGG
1 GAGATAGGAGG
*
1077854 GATGATAAGAGG
1 GA-GATAGGAGG
1077866 AGAGATAGGAG
1 -GAGATAGGAG
1077877 AGATAATAGA
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
9 8 0.17
11 4 0.09
12 30 0.65
13 4 0.09
ACGTcount: A:0.40, C:0.00, G:0.46, T:0.13
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:1077837 original size:33 final size:33
Alignment explanation
Indices: 1077800--1077881 Score: 128
Period size: 33 Copynumber: 2.5 Consensus size: 33
1077790 TAGCCCTCAA
* *
1077800 AGAGAAAGAAGAGATAGGAGGGATGATAGGAGG
1 AGAGATAGAAGAGATAGGAGGGATGATAAGAGG
*
1077833 AGAGATAGTAGAGATAGGAGGGATGATAAGAGG
1 AGAGATAGAAGAGATAGGAGGGATGATAAGAGG
*
1077866 AGAGATAGGAGAGATA
1 AGAGATAGAAGAGATA
1077882 ATAGAGAGAG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.45, C:0.00, G:0.43, T:0.12
Consensus pattern (33 bp):
AGAGATAGAAGAGATAGGAGGGATGATAAGAGG
Found at i:1077876 original size:42 final size:42
Alignment explanation
Indices: 1077830--1077909 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 42
1077820 GGATGATAGG
* *
1077830 AGGAGAGATAGTAGAGATAGGAGGGATGATAAGAGGAGAGAT
1 AGGAGAGATAATAGAGAGAGGAGGGATGATAAGAGGAGAGAT
1077872 AGGAGAGATAATAGAGAGAGGAGGGATGATAAGAGGAG
1 AGGAGAGATAATAGAGAGAGGAGGGATGATAAGAGGAG
1077910 GAGAGAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.44, C:0.00, G:0.44, T:0.12
Consensus pattern (42 bp):
AGGAGAGATAATAGAGAGAGGAGGGATGATAAGAGGAGAGAT
Found at i:1077893 original size:18 final size:18
Alignment explanation
Indices: 1077829--1077915 Score: 59
Period size: 18 Copynumber: 4.5 Consensus size: 18
1077819 GGGATGATAG
*
1077829 GAGGAGAGATAGTAGAGA
1 GAGGAGAGATAATAGAGA
* *
1077847 TAGGAGGGATGATAAGAGGAGA
1 GAGGA--GA-GATAATA-GAGA
1077869 GATAGGAGAGATAATAGAGA
1 G--AGGAGAGATAATAGAGA
* *
1077889 GAGGAGGGATGATA-AGA
1 GAGGAGAGATAATAGAGA
1077906 GGAGGAGAGA
1 -GAGGAGAGA
1077916 AAAAGATGGA
Statistics
Matches: 54, Mismatches: 8, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
17 3 0.06
18 23 0.43
20 7 0.13
21 11 0.20
22 6 0.11
24 4 0.07
ACGTcount: A:0.44, C:0.00, G:0.45, T:0.11
Consensus pattern (18 bp):
GAGGAGAGATAATAGAGA
Found at i:1077902 original size:21 final size:21
Alignment explanation
Indices: 1077827--1077903 Score: 70
Period size: 21 Copynumber: 3.7 Consensus size: 21
1077817 GAGGGATGAT
* *
1077827 AGGAGGAGAGATAGTAGAGAT
1 AGGAGGAGAGATAATAGAGAG
*
1077848 AGGAGG-GATGATAAGAG-GAG
1 AGGAGGAGA-GATAATAGAGAG
*
1077868 AGATAGGAGAGATAATAGAGAG
1 AG-GAGGAGAGATAATAGAGAG
1077890 AGGAGG-GATGATAA
1 AGGAGGAGA-GATAA
1077904 GAGGAGGAGA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
20 8 0.18
21 30 0.67
22 7 0.16
ACGTcount: A:0.44, C:0.00, G:0.43, T:0.13
Consensus pattern (21 bp):
AGGAGGAGAGATAATAGAGAG
Found at i:1083518 original size:21 final size:21
Alignment explanation
Indices: 1083477--1083520 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1083467 CTCTCCTTTA
* *
1083477 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
1083498 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
1083519 TC
1 TC
1083521 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:1085345 original size:13 final size:13
Alignment explanation
Indices: 1085327--1085351 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1085317 ATAATCACCC
1085327 TGTATCGATACAT
1 TGTATCGATACAT
1085340 TGTATCGATACA
1 TGTATCGATACA
1085352 AAGAAAAATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1087431 original size:15 final size:15
Alignment explanation
Indices: 1087411--1087441 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1087401 ATTTCGTTTG
*
1087411 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1087426 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1087441 G
1 G
1087442 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1089274 original size:21 final size:21
Alignment explanation
Indices: 1089245--1089289 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1089235 AAGTTTTCAT
*
1089245 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1089265 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1089287 TTT
1 TTT
1089290 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1091534 original size:13 final size:13
Alignment explanation
Indices: 1091516--1091541 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1091506 CAATTTTTTG
1091516 TGTATCGATACAT
1 TGTATCGATACAT
1091529 TGTATCGATACAT
1 TGTATCGATACAT
1091542 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1093052 original size:161 final size:160
Alignment explanation
Indices: 1092737--1093057 Score: 518
Period size: 160 Copynumber: 2.0 Consensus size: 160
1092727 AAAGAGGGGT
* *
1092737 TGATGATAACCAAGGAAGGTCCATTGAAGACAAAGACCTAAAGGCGTTGGAAAGGTTTCAAGGAC
1 TGATGAAAACCAAGGAAGGTCCATTGAAGACAAAGACCTAAAGGCGTTGGAAAGGTTTCAAAGAC
* * * *
1092802 CAATGACGAGGGCAAAGGCAAAAGGATAAGGGAAGACTTAGAGAAGATGGTTGCAGCCCTATTTG
66 CAATAACGAAGGCAAAGGCAAAAGGATAAAGGAAGACCTAGAGAAGATGGTTGCAGCCCTATTTG
1092867 AAAGTAGACCCAACTTGGAGTTAGAAGAGC
131 AAAGTAGACCCAACTTGGAGTTAGAAGAGC
* *
1092897 TGATGAAAACCAAGGAAGGTCCGTTGAAGACAAAGACCTGAAGGCGTTGG-AAGGATTTCAAAGA
1 TGATGAAAACCAAGGAAGGTCCATTGAAGACAAAGACCTAAAGGCGTTGGAAAGG-TTTCAAAGA
* *
1092961 CCAATAACGAAGGCAAAGGCAAAGAGGATAAAGGAAGACCTAGAGAAGATGGTTGCTGGCCTATT
65 CCAATAACGAAGGCAAAGGCAAA-AGGATAAAGGAAGACCTAGAGAAGATGGTTGCAGCCCTATT
*
1093026 TGAAAGTAGACCCAATTTGGAGTTAGAAGAGC
129 TGAAAGTAGACCCAACTTGGAGTTAGAAGAGC
1093058 CCAAGCTAGT
Statistics
Matches: 148, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
159 4 0.03
160 76 0.51
161 68 0.46
ACGTcount: A:0.39, C:0.15, G:0.29, T:0.17
Consensus pattern (160 bp):
TGATGAAAACCAAGGAAGGTCCATTGAAGACAAAGACCTAAAGGCGTTGGAAAGGTTTCAAAGAC
CAATAACGAAGGCAAAGGCAAAAGGATAAAGGAAGACCTAGAGAAGATGGTTGCAGCCCTATTTG
AAAGTAGACCCAACTTGGAGTTAGAAGAGC
Found at i:1094813 original size:18 final size:18
Alignment explanation
Indices: 1094792--1094862 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
1094782 TGATAAGAGG
1094792 AGAGACAGGAGAGATAGT
1 AGAGACAGGAGAGATAGT
* *
1094810 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGA--GA-GAT---AGT
*
1094834 AGAGACAGGAGAGATAAT
1 AGAGACAGGAGAGATAGT
*
1094852 AGAGAGAGGAG
1 AGAGACAGGAG
1094863 GGATGACAGG
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
18 20 0.49
20 2 0.05
21 6 0.15
22 2 0.05
24 11 0.27
ACGTcount: A:0.44, C:0.03, G:0.44, T:0.10
Consensus pattern (18 bp):
AGAGACAGGAGAGATAGT
Found at i:1094823 original size:42 final size:42
Alignment explanation
Indices: 1094759--1094877 Score: 175
Period size: 42 Copynumber: 2.8 Consensus size: 42
1094749 TAGCCCTCAA
* * * *
1094759 AGAGAAAGAAGAGAGAGAAGGGATGATAAGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
1094801 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
1094843 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
1094878 GAGAGAAGAA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.45, C:0.03, G:0.45, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:1100732 original size:155 final size:150
Alignment explanation
Indices: 1100360--1100779 Score: 426
Period size: 149 Copynumber: 2.8 Consensus size: 150
1100350 ATCTCTAATT
* *
1100360 AGATTGTTATGAGAATCCATGTTTG-CATTATTTGAGGGATGAACTTTGATTTTAAGGAAAATGA
1 AGATTATTATGAGAATCCATGTTTGTC-TTATTTGAGGGATGAACTTTGATTATAA-GAAAATGA
* * *
1100424 TGGGAAGAAAAGCTTTTCTAAGGAAACCAAAGCACTAATATGGTGTATCCCAATGAGGAAAATGT
64 TGGGAA-AAAAGCTTTTCT--TGAAACCAAAGCATTAATATCGTGTATCCCAATGAGGAAAATGT
*
1100489 ATGTTGTCCAATCACAAAAAAATGG
126 ATGTTGTCCAATCACAAAAAAATAG
* * * * *
1100514 AGA-TA-CA--AGAGTCCAT-TTTGTCTCATTTGAGGGATAAACTTTGATTATAGAGAAAATGGT
1 AGATTATTATGAGAATCCATGTTTGTCTTATTTGAGGGATGAACTTTGATTATA-AGAAAATGAT
*
1100574 GGGAAAAAAGCTTTTCTTGAAACCAAAGCATTAATATCATGTATCCCAAT-AGGAGAACATGTTT
65 GGGAAAAAAGCTTTTCTTGAAACCAAAGCATTAATATCGTGTATCCCAATGAGGA-AA-ATG--T
* * *
1100638 TTGTTGGT-CAATTATAAAAACAATAG
126 ATGTT-GTCCAATCACAAAAA-AATAG
* * * * *
1100664 AGATTATTATGACAAAT-CATGTTTGTCTTGTTTTAGGGATGAACTTAGATTCTAAGTAAAATGA
1 AGATTATTATGA-GAATCCATGTTTGTCTTATTTGAGGGATGAACTTTGATTATAAG-AAAATGA
* * *
1100728 TGGGAAAAAAGCTTTTCTTGGGAAACCAAAGCATCAACATTGTGTATCCCAA
64 TGGGAAAAAAGCTTTTCTT--GAAACCAAAGCATTAATATCGTGTATCCCAA
1100780 GGATAAGAAT
Statistics
Matches: 220, Mismatches: 29, Indels: 31
0.79 0.10 0.11
Matches are distributed among these distances:
145 4 0.02
146 31 0.14
147 3 0.01
148 12 0.05
149 56 0.25
150 19 0.09
151 2 0.01
152 2 0.01
153 1 0.00
154 9 0.04
155 54 0.25
157 27 0.12
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (150 bp):
AGATTATTATGAGAATCCATGTTTGTCTTATTTGAGGGATGAACTTTGATTATAAGAAAATGATG
GGAAAAAAGCTTTTCTTGAAACCAAAGCATTAATATCGTGTATCCCAATGAGGAAAATGTATGTT
GTCCAATCACAAAAAAATAG
Found at i:1109908 original size:30 final size:30
Alignment explanation
Indices: 1109874--1109953 Score: 126
Period size: 30 Copynumber: 2.7 Consensus size: 30
1109864 TTCTCTCCTC
* *
1109874 CTCCTGTCATC-CCTCCTCTCTCTATTATCT
1 CTCCTGTC-TCTCCTCCTATCTCTACTATCT
1109904 CTCCTGTCTCTCCTCCTATCTCTACTATCT
1 CTCCTGTCTCTCCTCCTATCTCTACTATCT
1109934 CTCCTGTCTCTCCTCCTATC
1 CTCCTGTCTCTCCTCCTATC
1109954 ATCCCTCCTG
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
29 2 0.04
30 45 0.96
ACGTcount: A:0.09, C:0.45, G:0.04, T:0.42
Consensus pattern (30 bp):
CTCCTGTCTCTCCTCCTATCTCTACTATCT
Found at i:1109925 original size:21 final size:21
Alignment explanation
Indices: 1109899--1109938 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1109889 CTCTCTCTAT
* *
1109899 TATCTCTCCTGTCTCTCCTCC
1 TATCTCTACTATCTCTCCTCC
1109920 TATCTCTACTATCTCTCCT
1 TATCTCTACTATCTCTCCT
1109939 GTCTCTCCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.42, G:0.03, T:0.45
Consensus pattern (21 bp):
TATCTCTACTATCTCTCCTCC
Found at i:1111300 original size:24 final size:24
Alignment explanation
Indices: 1111273--1111360 Score: 71
Period size: 24 Copynumber: 3.9 Consensus size: 24
1111263 TCTCTCCTCC
* *
1111273 TCCTGTCATCCCTCCTGTCTCTCT
1 TCCTATCATCCCTCCTATCTCTCT
*
1111297 TCCTATCATCCCTTCTA--TCTC-
1 TCCTATCATCCCTCCTATCTCTCT
* * *
1111318 TACTATC-T--CTCCGATCTCTCC
1 TCCTATCATCCCTCCTATCTCTCT
*
1111339 TCCTATCATCCCTCCTCTCTCT
1 TCCTATCATCCCTCCTATCTCT
1111361 TCTTTCTCTT
Statistics
Matches: 49, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
18 4 0.08
20 5 0.10
21 12 0.24
22 5 0.10
24 23 0.47
ACGTcount: A:0.10, C:0.45, G:0.03, T:0.41
Consensus pattern (24 bp):
TCCTATCATCCCTCCTATCTCTCT
Found at i:1111349 original size:42 final size:42
Alignment explanation
Indices: 1111290--1111369 Score: 115
Period size: 42 Copynumber: 1.9 Consensus size: 42
1111280 ATCCCTCCTG
* *
1111290 TCTCTCTTCCTATCATCCCTTCTATCTCTACTATCTCTCCGA
1 TCTCTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCGA
* * *
1111332 TCTCTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 TCTCTCCTCCTATCATCCCTCCTATCTCTACTATCTCT
1111370 TTGAGGGCTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.10, C:0.44, G:0.01, T:0.45
Consensus pattern (42 bp):
TCTCTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCGA
Found at i:1113035 original size:16 final size:16
Alignment explanation
Indices: 1113014--1113049 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
1113004 GGGAGAGTAC
1113014 TCCTCCCTCACCTAAG
1 TCCTCCCTCACCTAAG
*
1113030 TCCTCCGTCACCTAAG
1 TCCTCCCTCACCTAAG
1113046 TCCT
1 TCCT
1113050 TGGCTGTTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.17, C:0.47, G:0.08, T:0.28
Consensus pattern (16 bp):
TCCTCCCTCACCTAAG
Found at i:1113246 original size:12 final size:11
Alignment explanation
Indices: 1113229--1113299 Score: 51
Period size: 12 Copynumber: 6.5 Consensus size: 11
1113219 AAGAATTGAG
1113229 AGGAGGGATGAT
1 AGGAGGGA-GAT
*
1113241 AGGAGGAGAGAC
1 AGGAGG-GAGAT
1113253 AGGA--GAGAT
1 AGGAGGGAGAT
*
1113262 AGTA--GAGAT
1 AGGAGGGAGAT
1113271 AGGAGGGATGAT
1 AGGAGGGA-GAT
*
1113283 AGGAGGAGAGAC
1 AGGAGG-GAGAT
1113295 AGGAG
1 AGGAG
1113300 AGATAATAGA
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
9 15 0.31
11 2 0.04
12 28 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.48, T:0.10
Consensus pattern (11 bp):
AGGAGGGAGAT
Found at i:1113276 original size:42 final size:42
Alignment explanation
Indices: 1113226--1113332 Score: 187
Period size: 42 Copynumber: 2.5 Consensus size: 42
1113216 AGAAAGAATT
*
1113226 GAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAGTAGA
1 GAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAATAGA
*
1113268 GATAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAATAGA
1 GAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAATAGA
*
1113310 GAGAGGAGGGATGACAGGAGGAG
1 GAGAGGAGGGATGATAGGAGGAG
1113333 GAGAGAAGAG
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 61 1.00
ACGTcount: A:0.40, C:0.03, G:0.48, T:0.09
Consensus pattern (42 bp):
GAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAATAGA
Found at i:1123376 original size:42 final size:42
Alignment explanation
Indices: 1123322--1123431 Score: 184
Period size: 42 Copynumber: 2.6 Consensus size: 42
1123312 AAGAGAAAGA
* *
1123322 AGAGAGACGAGGGATGATAGGAGGAGAGACAGGAGAGATAGT
1 AGAGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
*
1123364 AGAGATAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
1 AGAGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
*
1123406 AGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGAGAGGAGGGATGATAGGAGGAG
1123432 GAGAGAAGAA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.41, C:0.04, G:0.46, T:0.09
Consensus pattern (42 bp):
AGAGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
Found at i:1128963 original size:26 final size:26
Alignment explanation
Indices: 1128934--1128998 Score: 130
Period size: 26 Copynumber: 2.5 Consensus size: 26
1128924 AAAGCCAATT
1128934 TTGAGTGAAACACGAGTGAACATCTA
1 TTGAGTGAAACACGAGTGAACATCTA
1128960 TTGAGTGAAACACGAGTGAACATCTA
1 TTGAGTGAAACACGAGTGAACATCTA
1128986 TTGAGTGAAACAC
1 TTGAGTGAAACAC
1128999 TTAGCGAGTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (26 bp):
TTGAGTGAAACACGAGTGAACATCTA
Found at i:1128967 original size:15 final size:15
Alignment explanation
Indices: 1128947--1128994 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
1128937 AGTGAAACAC
1128947 GAGTGAACATCTATT
1 GAGTGAACATCTATT
*
1128962 GAGTGAA-A-C-A-C
1 GAGTGAACATCTATT
1128973 GAGTGAACATCTATT
1 GAGTGAACATCTATT
1128988 GAGTGAA
1 GAGTGAA
1128995 ACACTTAGCG
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
11 7 0.26
12 2 0.07
13 2 0.07
14 2 0.07
15 14 0.52
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25
Consensus pattern (15 bp):
GAGTGAACATCTATT
Found at i:1135545 original size:12 final size:11
Alignment explanation
Indices: 1135493--1135559 Score: 57
Period size: 12 Copynumber: 5.9 Consensus size: 11
1135483 AGAGAAAGAA
*
1135493 GAGACAGAAGG
1 GAGATAGAAGG
*
1135504 GATGATAGGAGG
1 GA-GATAGAAGG
*
1135516 AGAGATAGTA--
1 -GAGATAGAAGG
1135526 GAGATAGAAGG
1 GAGATAGAAGG
1135537 GATGATAGAAGG
1 GA-GATAGAAGG
1135549 AGAGATAGAAG
1 -GAGATAGAAG
1135560 AGATATGGGG
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
9 8 0.17
11 4 0.09
12 30 0.65
13 4 0.09
ACGTcount: A:0.45, C:0.01, G:0.42, T:0.12
Consensus pattern (11 bp):
GAGATAGAAGG
Found at i:1135563 original size:33 final size:33
Alignment explanation
Indices: 1135483--1135564 Score: 128
Period size: 33 Copynumber: 2.5 Consensus size: 33
1135473 TAGCCCTCAA
* * *
1135483 AGAGAAAGAAGAGACAGAAGGGATGATAGGAGG
1 AGAGATAGAAGAGATAGAAGGGATGATAGAAGG
*
1135516 AGAGATAGTAGAGATAGAAGGGATGATAGAAGG
1 AGAGATAGAAGAGATAGAAGGGATGATAGAAGG
1135549 AGAGATAGAAGAGATA
1 AGAGATAGAAGAGATA
1135565 TGGGGAAATG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.49, C:0.01, G:0.39, T:0.11
Consensus pattern (33 bp):
AGAGATAGAAGAGATAGAAGGGATGATAGAAGG
Found at i:1145482 original size:13 final size:13
Alignment explanation
Indices: 1145464--1145489 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1145454 CAATTTTTTG
1145464 TGTATCGATACAT
1 TGTATCGATACAT
1145477 TGTATCGATACAT
1 TGTATCGATACAT
1145490 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1146239 original size:21 final size:21
Alignment explanation
Indices: 1146198--1146241 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1146188 CTCCCCTTTA
* *
1146198 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
1146219 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
1146240 TC
1 TC
1146242 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:1148069 original size:13 final size:13
Alignment explanation
Indices: 1148047--1148085 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1148037 ATAATCACCC
*
1148047 TGTATGGATACAA
1 TGTATCGATACAA
1148060 TGTATCGATACAA
1 TGTATCGATACAA
1148073 TGTATCGATACAA
1 TGTATCGATACAA
1148086 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1150176 original size:15 final size:15
Alignment explanation
Indices: 1150156--1150186 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1150146 ATTTCGTTTG
*
1150156 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1150171 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1150186 G
1 G
1150187 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1152019 original size:21 final size:21
Alignment explanation
Indices: 1151990--1152034 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1151980 AAGTTTTCAT
*
1151990 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1152010 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1152032 TTT
1 TTT
1152035 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1154270 original size:13 final size:13
Alignment explanation
Indices: 1154252--1154277 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1154242 CAATTTTTTG
1154252 TGTATCGATACAT
1 TGTATCGATACAT
1154265 TGTATCGATACAT
1 TGTATCGATACAT
1154278 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1155027 original size:21 final size:21
Alignment explanation
Indices: 1154986--1155029 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1154976 CTCCCCTTTA
* *
1154986 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
1155007 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
1155028 TC
1 TC
1155030 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:1155046 original size:25 final size:25
Alignment explanation
Indices: 1155018--1155069 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
1155008 CTCCCCCTTA
1155018 ATCAAGTAATTCATATCAAAAATTT
1 ATCAAGTAATTCATATCAAAAATTT
1155043 ATCAAGTAATTCATATCAAAAATTT
1 ATCAAGTAATTCATATCAAAAATTT
1155068 AT
1 AT
1155070 TTGCACATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.48, C:0.12, G:0.04, T:0.37
Consensus pattern (25 bp):
ATCAAGTAATTCATATCAAAAATTT
Found at i:1155061 original size:14 final size:14
Alignment explanation
Indices: 1155018--1155061 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
1155008 CTCCCCCTTA
1155018 ATCAAGTAATTCAT
1 ATCAAGTAATTCAT
*
1155032 ATCAA-AAATT--T
1 ATCAAGTAATTCAT
1155043 ATCAAGTAATTCAT
1 ATCAAGTAATTCAT
1155057 ATCAA
1 ATCAA
1155062 AAATTTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
11 6 0.24
12 4 0.16
13 4 0.16
14 11 0.44
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.34
Consensus pattern (14 bp):
ATCAAGTAATTCAT
Found at i:1156882 original size:13 final size:13
Alignment explanation
Indices: 1156860--1156898 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1156850 ATAATCACCC
*
1156860 TGTATGGATACAA
1 TGTATCGATACAA
1156873 TGTATCGATACAA
1 TGTATCGATACAA
1156886 TGTATCGATACAA
1 TGTATCGATACAA
1156899 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1158987 original size:15 final size:15
Alignment explanation
Indices: 1158967--1158997 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1158957 AATTTCGTTG
*
1158967 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1158982 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1158997 G
1 G
1158998 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Done.