Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold187
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: 2169796
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 45208 characters in sequence are not A, C, G, or T
File 8 of 13
Found at i:1044861 original size:17 final size:17
Alignment explanation
Indices: 1044839--1044871 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1044829 AGTTGAGTTT
1044839 AATTTT-GATTTAGATTA
1 AATTTTGGATTT-GATTA
1044856 AATTTTGGATTTGATT
1 AATTTTGGATTTGATT
1044872 TTTGAAGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (17 bp):
AATTTTGGATTTGATTA
Found at i:1045121 original size:2 final size:2
Alignment explanation
Indices: 1045103--1045143 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
1045093 TACAAATAAA
1045103 AT AT -T AT AT -T A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1045142 AT
1 AT
1045144 GTATGTATGA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.08
2 33 0.92
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1045470 original size:3 final size:3
Alignment explanation
Indices: 1045462--1045489 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1045452 ATATAATTTA
1045462 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1045490 TTGTTATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1047482 original size:2 final size:2
Alignment explanation
Indices: 1047475--1047505 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1047465 AAACGTTAGG
*
1047475 AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1047506 AAGGGAGTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1049782 original size:15 final size:14
Alignment explanation
Indices: 1049745--1049811 Score: 55
Period size: 15 Copynumber: 4.6 Consensus size: 14
1049735 TATACCGAAG
*
1049745 GTACTTATGTCAAA
1 GTACTTATGTTAAA
1049759 GTA-TCTATGTTGAAA
1 GTACT-TATGTT-AAA
*
1049774 GTACTTATGTCAAAA
1 GTACTTATGT-TAAA
* * *
1049789 GTACCTGTGCTAAA
1 GTACTTATGTTAAA
1049803 GTACTTATG
1 GTACTTATG
1049812 CCAAAGGTAC
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
13 1 0.02
14 18 0.44
15 21 0.51
16 1 0.02
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (14 bp):
GTACTTATGTTAAA
Found at i:1049805 original size:14 final size:14
Alignment explanation
Indices: 1049771--1049985 Score: 114
Period size: 14 Copynumber: 14.9 Consensus size: 14
1049761 ATCTATGTTG
* *
1049771 AAAGTACTTATGTCA
1 AAAGTACTTGTG-CC
* *
1049786 AAAGTACCTGTGCT
1 AAAGTACTTGTGCC
*
1049800 AAAGTACTTATGCC
1 AAAGTACTTGTGCC
* *
1049814 AAAGGTACCTGTGCT
1 AAA-GTACTTGTGCC
* * * *
1049829 AGAGTACATATGCT
1 AAAGTACTTGTGCC
1049843 AAAGTACTTGTGCC
1 AAAGTACTTGTGCC
*
1049857 AAAGGTACTTATGCC
1 AAA-GTACTTGTGCC
*
1049872 AAAATACTTGTGCC
1 AAAGTACTTGTGCC
* *
1049886 AAAAGTGCCTGTGCC
1 -AAAGTACTTGTGCC
1049901 AAAGTACTTGT--C
1 AAAGTACTTGTGCC
*
1049913 ATAGAGTACTTGTGTCG
1 A-A-AGTACTTGTG-CC
* *
1049930 AAA-TACCTATGCC
1 AAAGTACTTGTGCC
*
1049943 AAAGGTA-TCTGTACC
1 AAA-GTACT-TGTGCC
* *
1049958 GATAGTACTTGTGCT
1 -AAAGTACTTGTGCC
1049973 AAAGGTACTTGTG
1 AAA-GTACTTGTG
1049986 TCGACAGTAC
Statistics
Matches: 151, Mismatches: 35, Indels: 28
0.71 0.16 0.13
Matches are distributed among these distances:
12 2 0.01
13 5 0.03
14 72 0.48
15 67 0.44
16 4 0.03
17 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (14 bp):
AAAGTACTTGTGCC
Found at i:1049879 original size:29 final size:28
Alignment explanation
Indices: 1049745--1049911 Score: 140
Period size: 29 Copynumber: 5.8 Consensus size: 28
1049735 TATACCGAAG
*
1049745 GTACTTATGTCAAAGTATCTATGTTG--AAA
1 GTACTTATGCCAAAGTA-CT-TG-TGCCAAA
* * *
1049774 GTACTTATGTCAAAAGTACCTGTGCTAAA
1 GTACTTATG-CCAAAGTACTTGTGCCAAA
* * *
1049803 GTACTTATGCCAAAGGTACCTGTGCTAGA
1 GTACTTATGCCAAA-GTACTTGTGCCAAA
* *
1049832 GTACATATGCTAAAGTACTTGTGCCAAA
1 GTACTTATGCCAAAGTACTTGTGCCAAA
*
1049860 GGTACTTATGCCAAAATACTTGTGCCAAAA
1 -GTACTTATGCCAAAGTACTTGTGCC-AAA
* * *
1049890 GTGCCTGTGCCAAAGTACTTGT
1 GTACTTATGCCAAAGTACTTGT
1049912 CATAGAGTAC
Statistics
Matches: 115, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
27 2 0.02
28 17 0.15
29 87 0.76
30 9 0.08
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.31
Consensus pattern (28 bp):
GTACTTATGCCAAAGTACTTGTGCCAAA
Found at i:1049907 original size:72 final size:72
Alignment explanation
Indices: 1049771--1049945 Score: 167
Period size: 72 Copynumber: 2.4 Consensus size: 72
1049761 ATCTATGTTG
* * * * * * *
1049771 AAAGTACTTATGTCAAAAGTACCTGTGCTAAAGTACTTATGCCAAAGGTACCTGTGCTAGAGTAC
1 AAAGTACTTATGCCAAAAGTACCTATGCCAAAATACTTATGCCAAAAGTACCTGTGCCAAAGTAC
1049836 ATATGCT
66 ATATGCT
* * * * *
1049843 AAAGTACTTGTGCCAAAGGTACTTATGCCAAAATACTTGTGCCAAAAGTGCCTGTGCCAAAGTAC
1 AAAGTACTTATGCCAAAAGTACCTATGCCAAAATACTTATGCCAAAAGTACCTGTGCCAAAGTAC
1049908 -T-TGTCAT
66 ATATG-C-T
* * * *
1049915 AGAGTACTTGTGTCGAAA-TACCTATGCCAAA
1 AAAGTACTTATGCCAAAAGTACCTATGCCAAA
1049946 GGTATCTGTA
Statistics
Matches: 84, Mismatches: 17, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
70 2 0.02
71 14 0.17
72 68 0.81
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.28
Consensus pattern (72 bp):
AAAGTACTTATGCCAAAAGTACCTATGCCAAAATACTTATGCCAAAAGTACCTGTGCCAAAGTAC
ATATGCT
Found at i:1049995 original size:30 final size:29
Alignment explanation
Indices: 1049786--1050003 Score: 115
Period size: 29 Copynumber: 7.5 Consensus size: 29
1049776 ACTTATGTCA
* * * *
1049786 AAAGTACCTGTGCTAAA-GTACTTATGCC
1 AAAGTACTTGTGCCAAAGGTACTTGTGCG
* * * * * *
1049814 AAAGGTACCTGTGCTAGA-GTACATATGCT
1 AAA-GTACTTGTGCCAAAGGTACTTGTGCG
* *
1049843 AAAGTACTTGTGCCAAAGGTACTTATGCC
1 AAAGTACTTGTGCCAAAGGTACTTGTGCG
* * * * *
1049872 AAAATACTTGTGCCAAAAGTGCCTGTGCC
1 AAAGTACTTGTGCCAAAGGTACTTGTGCG
*
1049901 AAAGTACTTGT--CATAGAGTACTTGTGTCG
1 AAAGTACTTGTGCCAAAG-GTACTTGTG-CG
* * *
1049930 AAA-TACCTATGCCAAAGGTA-TCTGTACCG
1 AAAGTACTTGTGCCAAAGGTACT-TGT-GCG
* *
1049959 ATAGTACTTGTGCTAAAGGTACTTGTGTCG
1 AAAGTACTTGTGCCAAAGGTACTTGTG-CG
* *
1049989 ACAGTACCTGTGCCA
1 AAAGTACTTGTGCCA
1050004 GATGAAGGCT
Statistics
Matches: 148, Mismatches: 31, Indels: 20
0.74 0.16 0.10
Matches are distributed among these distances:
27 3 0.02
28 27 0.18
29 82 0.55
30 35 0.24
31 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (29 bp):
AAAGTACTTGTGCCAAAGGTACTTGTGCG
Found at i:1050278 original size:3 final size:3
Alignment explanation
Indices: 1050270--1050318 Score: 89
Period size: 3 Copynumber: 16.0 Consensus size: 3
1050260 TTAAATGAAT
1050270 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA GTAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA
1050316 TAA
1 TAA
1050319 ATAAATAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 42 0.93
4 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1051191 original size:19 final size:19
Alignment explanation
Indices: 1051167--1051213 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
1051157 TTCTTTCTCT
1051167 AATTTTTTTATGAAATACG
1 AATTTTTTTATGAAATACG
* *
1051186 AA-TTTTTTATGCAATATG
1 AATTTTTTTATGAAATACG
1051204 AATTTTTTTA
1 AATTTTTTTA
1051214 AACAAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 16 0.64
19 9 0.36
ACGTcount: A:0.34, C:0.04, G:0.09, T:0.53
Consensus pattern (19 bp):
AATTTTTTTATGAAATACG
Found at i:1054099 original size:24 final size:24
Alignment explanation
Indices: 1054001--1054114 Score: 72
Period size: 24 Copynumber: 4.8 Consensus size: 24
1053991 CATTTGACAC
* *
1054001 GACTCTTGGAACAT-CTTGGGCAC
1 GACTCTTGGAACATCCTTTGGCAA
* * *
1054024 GACT-TCTAGAACAACCTTTTGCATA
1 GACTCT-TGGAACATCCTTTGGCA-A
* * * *
1054049 -ACTCTTGAAACATCTTTTAGCAT
1 GACTCTTGGAACATCCTTTGGCAA
*
1054072 GACTCGTGGAACATCCTTTGGCAA
1 GACTCTTGGAACATCCTTTGGCAA
* * *
1054096 GACTCCTAGAACATACTTT
1 GACTCTTGGAACATCCTTT
1054115 AGATCAATTT
Statistics
Matches: 67, Mismatches: 19, Indels: 9
0.71 0.20 0.09
Matches are distributed among these distances:
22 1 0.01
23 10 0.15
24 55 0.82
25 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.31
Consensus pattern (24 bp):
GACTCTTGGAACATCCTTTGGCAA
Found at i:1055644 original size:28 final size:28
Alignment explanation
Indices: 1055563--1055644 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
1055553 TTTTGGAGAT
*
1055563 AATAACGAGGTTGGAGTGTTCCCTCG--GA
1 AATAACGAGGTTGGAGT-AT-CCTCGATGA
* * *
1055591 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGAGGTTGGAGTATCCTCGATGA
1055619 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCTCGAT
1055645 TGTAAAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 4 0.09
27 1 0.02
28 40 0.89
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCTCGATGA
Found at i:1055787 original size:51 final size:51
Alignment explanation
Indices: 1055627--1055797 Score: 189
Period size: 51 Copynumber: 3.3 Consensus size: 51
1055617 GAAATAACGA
* * * *
1055627 GGTTGGAGTATCCTCGATTGTAAAAAATTGGTATTTTTAGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGA-AAATAAAATCGG
** * * * * *
1055679 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
1055732 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
1055783 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
1055798 TCAGAAATAA
Statistics
Matches: 96, Mismatches: 21, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
51 39 0.41
52 16 0.17
53 28 0.29
54 13 0.14
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:1055843 original size:27 final size:28
Alignment explanation
Indices: 1055780--1055855 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
1055770 AAAATAAAGT
*
1055780 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
1055808 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
1055835 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
1055856 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:1058337 original size:13 final size:13
Alignment explanation
Indices: 1058319--1058344 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1058309 ACAAAGATCC
1058319 ATGTATCGATACA
1 ATGTATCGATACA
1058332 ATGTATCGATACA
1 ATGTATCGATACA
1058345 CAGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1058340 original size:33 final size:33
Alignment explanation
Indices: 1058298--1058364 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1058288 AAAATTTCCA
***
1058298 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
1058331 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1058364 A
1 A
1058365 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:1058408 original size:19 final size:18
Alignment explanation
Indices: 1058384--1058451 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
1058374 CAGTAGCTAA
1058384 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
1058403 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
1058418 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
1058435 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1058452 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:1058424 original size:13 final size:13
Alignment explanation
Indices: 1058406--1058430 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1058396 ACAATACTTA
1058406 TGTATCGATACAT
1 TGTATCGATACAT
1058419 TGTATCGATACA
1 TGTATCGATACA
1058431 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:1058428 original size:32 final size:32
Alignment explanation
Indices: 1058387--1058449 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1058377 TAGCTAATTA
*
1058387 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
1058419 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
1058450 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:1058531 original size:21 final size:21
Alignment explanation
Indices: 1058507--1058563 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
1058497 CATTTGTAGG
1058507 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
1058528 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
1058549 ATGTATCGATACATT
1 ATGTATCGATACATT
1058564 TATTTATTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.32
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:1061002 original size:21 final size:22
Alignment explanation
Indices: 1060969--1061009 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1060959 AAGAACAACA
1060969 AGAAGAACAAAAAGGGAAAAAG
1 AGAAGAACAAAAAGGGAAAAAG
*
1060991 AGAA-AACTAAAAGGGAAAA
1 AGAAGAACAAAAAGGGAAAA
1061010 TAAGGAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.68, C:0.05, G:0.24, T:0.02
Consensus pattern (22 bp):
AGAAGAACAAAAAGGGAAAAAG
Found at i:1064344 original size:3 final size:3
Alignment explanation
Indices: 1064336--1064365 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
1064326 AAAATTGAAC
1064336 ATT ATT ATT ATT ATT ATT ATTT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT A-TT ATT ATT AT
1064366 AAGAAATTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1065803 original size:2 final size:2
Alignment explanation
Indices: 1065796--1065832 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1065786 CTTGATCTAC
1065796 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1065833 AGAAGAACTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1068673 original size:20 final size:21
Alignment explanation
Indices: 1068630--1068675 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1068620 ATTCAATAAT
1068630 AAATATATAACCAAAATTTCA
1 AAATATATAACCAAAATTTCA
* *
1068651 AAATATCTAA-CAAAACTTTAA
1 AAATATATAACCAAAA-TTTCA
1068672 AAAT
1 AAAT
1068676 TGAAAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.59, C:0.13, G:0.00, T:0.28
Consensus pattern (21 bp):
AAATATATAACCAAAATTTCA
Found at i:1070365 original size:99 final size:99
Alignment explanation
Indices: 1070189--1070387 Score: 281
Period size: 99 Copynumber: 2.0 Consensus size: 99
1070179 AACAAATGTC
* * * * * *
1070189 ATTGCATCTTGATACCTTTGATTCATGTCTTGTGGGCTTCCAACAAAAGATGAAGTTAACATTAT
1 ATTGCATCTTAATACCTTTGATTCAAGTATGGTGGGCCTCCAACAAAAGATGAAGGTAACATTAT
** *
1070254 TCTATGCTCCATGTTCCCTATAATTAGTAATATT
66 TCTACACCCCATGTTCCCTATAATTAGTAATATT
* * *
1070288 ATTGCATCTTAATACCTTTGATTCAAGTATGGTGGGCCTCCAACCAAAGATGATGGTAACATTTT
1 ATTGCATCTTAATACCTTTGATTCAAGTATGGTGGGCCTCCAACAAAAGATGAAGGTAACATTAT
*
1070353 TCTACACCCCATGTTCCTTATAATTAGTAATATT
66 TCTACACCCCATGTTCCCTATAATTAGTAATATT
1070387 A
1 A
1070388 AAAAACTTTT
Statistics
Matches: 87, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
99 87 1.00
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (99 bp):
ATTGCATCTTAATACCTTTGATTCAAGTATGGTGGGCCTCCAACAAAAGATGAAGGTAACATTAT
TCTACACCCCATGTTCCCTATAATTAGTAATATT
Found at i:1071571 original size:2 final size:2
Alignment explanation
Indices: 1071566--1071597 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1071556 GAATTTCAAA
1071566 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1071598 TACATAAGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1073118 original size:13 final size:13
Alignment explanation
Indices: 1073100--1073124 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1073090 CATTTTATGG
1073100 TGTATCGATACAA
1 TGTATCGATACAA
1073113 TGTATCGATACA
1 TGTATCGATACA
1073125 TACTATGTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1073140 original size:32 final size:33
Alignment explanation
Indices: 1073077--1073144 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
1073067 CGTTACAAGC
**
1073077 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
1073110 CAATGTATCGATACATACTAT-GTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
1073142 CAA
1 CAA
1073145 GTTTAGCTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 14 0.42
33 19 0.58
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (33 bp):
CAATGTATCGATACATACTATGGTGTATCGATA
Found at i:1073240 original size:20 final size:20
Alignment explanation
Indices: 1073198--1073247 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1073188 TGTTTTTCAA
*
1073198 GTATCGATACAATGCAACAT
1 GTATCGATACAATGAAACAT
* **
1073218 GTATCGATACAATTAAATGT
1 GTATCGATACAATGAAACAT
1073238 GTATCGATAC
1 GTATCGATAC
1073248 TTTTCAGGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (20 bp):
GTATCGATACAATGAAACAT
Found at i:1075149 original size:21 final size:21
Alignment explanation
Indices: 1075124--1075174 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
1075114 TGAATCAGAA
* *
1075124 GTGTTTTGGTGCAAAATCAAG
1 GTGTTTCGGTGCAAAACCAAG
*
1075145 GTGTTTCGGTGCAAAACCGAG
1 GTGTTTCGGTGCAAAACCAAG
1075166 GTGTTTCGG
1 GTGTTTCGG
1075175 ATGTTCTAAG
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:0.14, G:0.33, T:0.31
Consensus pattern (21 bp):
GTGTTTCGGTGCAAAACCAAG
Found at i:1075898 original size:8 final size:8
Alignment explanation
Indices: 1075882--1075918 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
1075872 TCATTCATTT
*
1075882 ACAACATC
1 ACAAAATC
1075890 ACAAAATC
1 ACAAAATC
1075898 ACAAAAT-
1 ACAAAATC
1075905 -CAAAATC
1 ACAAAATC
1075912 ACAAAAT
1 ACAAAAT
1075919 TTAATCAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
6 6 0.23
8 20 0.77
ACGTcount: A:0.62, C:0.24, G:0.00, T:0.14
Consensus pattern (8 bp):
ACAAAATC
Found at i:1075910 original size:14 final size:14
Alignment explanation
Indices: 1075891--1075918 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1075881 TACAACATCA
1075891 CAAAATCACAAAAT
1 CAAAATCACAAAAT
1075905 CAAAATCACAAAAT
1 CAAAATCACAAAAT
1075919 TTAATCAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.21, G:0.00, T:0.14
Consensus pattern (14 bp):
CAAAATCACAAAAT
Found at i:1081886 original size:13 final size:13
Alignment explanation
Indices: 1081868--1081892 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1081858 CATTTTATGG
1081868 TGTATCGATACAA
1 TGTATCGATACAA
1081881 TGTATCGATACA
1 TGTATCGATACA
1081893 TACTATGTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1081908 original size:32 final size:33
Alignment explanation
Indices: 1081845--1081912 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
1081835 CGTTACAAGC
**
1081845 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
1081878 CAATGTATCGATACATACTAT-GTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
1081910 CAA
1 CAA
1081913 GTTTAGCTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 14 0.42
33 19 0.58
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (33 bp):
CAATGTATCGATACATACTATGGTGTATCGATA
Found at i:1082008 original size:20 final size:20
Alignment explanation
Indices: 1081966--1082015 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1081956 TGTTTTTCAA
*
1081966 GTATCGATACAATGCAACAT
1 GTATCGATACAATGAAACAT
* **
1081986 GTATCGATACAATTAAATGT
1 GTATCGATACAATGAAACAT
1082006 GTATCGATAC
1 GTATCGATAC
1082016 TTTTCAGGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (20 bp):
GTATCGATACAATGAAACAT
Found at i:1082706 original size:21 final size:20
Alignment explanation
Indices: 1082657--1082706 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
1082647 ATATTGATTA
* *
1082657 TAAAGTTAACATATAAGGGC
1 TAAAATTAACATAAAAGGGC
*
1082677 TAAGGATTAACATGAAAAGGGC
1 TAA-AATTAACAT-AAAAGGGC
1082699 TAAAATTA
1 TAAAATTA
1082707 GACACTTTAC
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 3 0.12
21 11 0.46
22 10 0.42
ACGTcount: A:0.48, C:0.08, G:0.20, T:0.24
Consensus pattern (20 bp):
TAAAATTAACATAAAAGGGC
Found at i:1082809 original size:21 final size:21
Alignment explanation
Indices: 1082783--1082826 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1082773 CAGTTACCTT
* *
1082783 GTAACCCCATAATCTCTAGGA
1 GTAACCCCAAAATCTCTAAGA
1082804 GTAACCCCAAAATCTCTAAGA
1 GTAACCCCAAAATCTCTAAGA
1082825 GT
1 GT
1082827 TACAAATATT
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:0.36, C:0.27, G:0.14, T:0.23
Consensus pattern (21 bp):
GTAACCCCAAAATCTCTAAGA
Found at i:1084144 original size:24 final size:24
Alignment explanation
Indices: 1084117--1084163 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
1084107 CATCATGTTC
1084117 AACTATTACAAGAGATGGTAAACT
1 AACTATTACAAGAGATGGTAAACT
*
1084141 AACTATTACAGGAGATGGTAAAC
1 AACTATTACAAGAGATGGTAAAC
1084164 CCTAATGAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.45, C:0.13, G:0.19, T:0.23
Consensus pattern (24 bp):
AACTATTACAAGAGATGGTAAACT
Found at i:1088131 original size:21 final size:21
Alignment explanation
Indices: 1088107--1088146 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1088097 TTTTTGCCAA
*
1088107 AATGTATCGATACATGCCCTT
1 AATGTATCGATACAGGCCCTT
1088128 AATGTATCGATACAGGCCC
1 AATGTATCGATACAGGCCC
1088147 AACGGTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (21 bp):
AATGTATCGATACAGGCCCTT
Found at i:1089728 original size:2 final size:2
Alignment explanation
Indices: 1089723--1089755 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1089713 GAATTTCAAA
1089723 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1089756 TACATAAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1091308 original size:31 final size:31
Alignment explanation
Indices: 1091244--1091308 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
1091234 CGTTACAAGC
**
1091244 CAATGTATCGATACATTTTAATGTGTACGTA
1 CAATGTATCGATACATACTAATGTGTACGTA
*
1091275 CAATGTATCGATACATACT-ATGTGTTCGATA
1 CAATGTATCGATACATACTAATGTGTACG-TA
1091306 CAA
1 CAA
1091309 GTTTAGCTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 8 0.27
31 22 0.73
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Consensus pattern (31 bp):
CAATGTATCGATACATACTAATGTGTACGTA
Found at i:1091404 original size:20 final size:20
Alignment explanation
Indices: 1091362--1091410 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
1091352 GTTTTTTCAA
*
1091362 GTATCGATACAATGCAACAT
1 GTATCGATACAATGAAACAT
* **
1091382 GTATCGATACAATTAAATGT
1 GTATCGATACAATGAAACAT
1091402 GTATCGATA
1 GTATCGATA
1091411 TTTTCAGGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (20 bp):
GTATCGATACAATGAAACAT
Found at i:1093333 original size:22 final size:22
Alignment explanation
Indices: 1093291--1093338 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1093281 ATCAGAAGTG
*
1093291 GTTTTGGTGCAAAATCAAGG-T
1 GTTTTGGTGCAAAACCAAGGTT
*
1093312 GTTTTCGGTGCAAAACCGAGGTT
1 GTTTT-GGTGCAAAACCAAGGTT
1093335 GTTT
1 GTTT
1093339 CGGATGTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 5 0.22
22 13 0.57
23 5 0.22
ACGTcount: A:0.23, C:0.12, G:0.29, T:0.35
Consensus pattern (22 bp):
GTTTTGGTGCAAAACCAAGGTT
Found at i:1100062 original size:32 final size:34
Alignment explanation
Indices: 1099995--1100063 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
1099985 GTTTACAAGC
**
1099995 CAATGTATCATACATTTTATGGTGTTCATCGATA
1 CAATGTATCATACATACTATGGTGTTCATCGATA
1100029 CAATGTATCGATACATACTAT-GTG-T-ATCGATA
1 CAATGTATC-ATACATACTATGGTGTTCATCGATA
1100061 CAA
1 CAA
1100064 GTTTAGCTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 10 0.31
33 1 0.03
34 12 0.38
35 9 0.28
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.36
Consensus pattern (34 bp):
CAATGTATCATACATACTATGGTGTTCATCGATA
Found at i:1100156 original size:20 final size:20
Alignment explanation
Indices: 1100114--1100163 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1100104 ATGTTTTCAA
*
1100114 GTATCGATACAATGCAACAT
1 GTATCGATACAATGAAACAT
* **
1100134 GTATCGATACAATTAAATGT
1 GTATCGATACAATGAAACAT
1100154 GTATCGATAC
1 GTATCGATAC
1100164 TTTTCTCAGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (20 bp):
GTATCGATACAATGAAACAT
Found at i:1100964 original size:20 final size:20
Alignment explanation
Indices: 1100939--1100978 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1100929 TTACCTTGTA
* *
1100939 ACCCCATAATCTCTAGGAGT
1 ACCCCAAAATCTCTAAGAGT
1100959 ACCCCAAAATCTCTAAGAGT
1 ACCCCAAAATCTCTAAGAGT
1100979 TACAAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.35, C:0.30, G:0.12, T:0.23
Consensus pattern (20 bp):
ACCCCAAAATCTCTAAGAGT
Found at i:1102299 original size:25 final size:25
Alignment explanation
Indices: 1102251--1102297 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
1102241 CATCATGTTC
1102251 AACTATTTACAAGAGATGGTAAACT
1 AACTATTTACAAGAGATGGTAAACT
*
1102276 AACTA-TTACAGGAGATGGTAAA
1 AACTATTTACAAGAGATGGTAAA
1102298 ACCCTAATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.45, C:0.11, G:0.19, T:0.26
Consensus pattern (25 bp):
AACTATTTACAAGAGATGGTAAACT
Found at i:1106658 original size:99 final size:99
Alignment explanation
Indices: 1106482--1106680 Score: 274
Period size: 99 Copynumber: 2.0 Consensus size: 99
1106472 AACAAATGTC
* * * * * *
1106482 ATTGCATCTTGATACCTTTGATTCATGTCTTGTGGGCTTCCAACAAAGATGAAAGTTAACATTAT
1 ATTGCATCTTAATACCTTTGATTCAAGTATGGTGGGCCTCCAACAAAGATGAAAGGTAACATTAT
** *
1106547 TCTATGCTCCATGTTCCCTATAATTAGTAATATT
66 TCTACACCCCATGTTCCCTATAATTAGTAATATT
* *
1106581 ATTGCATCTTAATACCTTTGATTCAAGTATGGTGGGCCTCCAACCAAAGATG-ATGGTAACATTT
1 ATTGCATCTTAATACCTTTGATTCAAGTATGGTGGGCCTCCAA-CAAAGATGAAAGGTAACATTA
*
1106645 TTCTACACCCCATGTTCCTTATAATTAGTAATATT
65 TTCTACACCCCATGTTCCCTATAATTAGTAATATT
1106680 A
1 A
1106681 AAAAACTTTT
Statistics
Matches: 87, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
99 79 0.91
100 8 0.09
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (99 bp):
ATTGCATCTTAATACCTTTGATTCAAGTATGGTGGGCCTCCAACAAAGATGAAAGGTAACATTAT
TCTACACCCCATGTTCCCTATAATTAGTAATATT
Found at i:1107854 original size:2 final size:2
Alignment explanation
Indices: 1107849--1107880 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1107839 GAATTTCAAA
1107849 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1107881 TACATAAGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1109406 original size:13 final size:13
Alignment explanation
Indices: 1109388--1109412 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1109378 CATTTTATGG
1109388 TGTATCGATACAA
1 TGTATCGATACAA
1109401 TGTATCGATACA
1 TGTATCGATACA
1109413 TACTATGTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1109427 original size:32 final size:34
Alignment explanation
Indices: 1109364--1109432 Score: 106
Period size: 32 Copynumber: 2.1 Consensus size: 34
1109354 CGTTACAAGC
**
1109364 CAATGTATCCGATACATTTTATGGTGTATCGATA
1 CAATGTATCCGATACATACTATGGTGTATCGATA
1109398 CAATGTAT-CGATACATACTAT-GTGTATCGATA
1 CAATGTATCCGATACATACTATGGTGTATCGATA
1109430 CAA
1 CAA
1109433 GTTTAGCTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 14 0.42
33 11 0.33
34 8 0.24
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (34 bp):
CAATGTATCCGATACATACTATGGTGTATCGATA
Found at i:1111428 original size:21 final size:21
Alignment explanation
Indices: 1111403--1111453 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
1111393 TGAATCAGAA
* *
1111403 GTGTTTTGGTGCAAAATCAAG
1 GTGTTTCGGTGCAAAACCAAG
*
1111424 GTGTTTCGGTGCAAAACCGAG
1 GTGTTTCGGTGCAAAACCAAG
1111445 GTGTTTCGG
1 GTGTTTCGG
1111454 ATGTTCTAAG
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:0.14, G:0.33, T:0.31
Consensus pattern (21 bp):
GTGTTTCGGTGCAAAACCAAG
Found at i:1112179 original size:8 final size:8
Alignment explanation
Indices: 1112163--1112199 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
1112153 TCATTCATTT
*
1112163 ACAACATC
1 ACAAAATC
1112171 ACAAAATC
1 ACAAAATC
1112179 ACAAAAT-
1 ACAAAATC
1112186 -CAAAATC
1 ACAAAATC
1112193 ACAAAAT
1 ACAAAAT
1112200 TTAATCAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
6 6 0.23
8 20 0.77
ACGTcount: A:0.62, C:0.24, G:0.00, T:0.14
Consensus pattern (8 bp):
ACAAAATC
Found at i:1112191 original size:14 final size:14
Alignment explanation
Indices: 1112172--1112199 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1112162 TACAACATCA
1112172 CAAAATCACAAAAT
1 CAAAATCACAAAAT
1112186 CAAAATCACAAAAT
1 CAAAATCACAAAAT
1112200 TTAATCAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.21, G:0.00, T:0.14
Consensus pattern (14 bp):
CAAAATCACAAAAT
Found at i:1118166 original size:13 final size:13
Alignment explanation
Indices: 1118148--1118172 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1118138 CATTTTATGG
1118148 TGTATCGATACAA
1 TGTATCGATACAA
1118161 TGTATCGATACA
1 TGTATCGATACA
1118173 TACTATGTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1118188 original size:32 final size:33
Alignment explanation
Indices: 1118125--1118192 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
1118115 CGTTACAAGC
**
1118125 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
1118158 CAATGTATCGATACATACTAT-GTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
1118190 CAA
1 CAA
1118193 GTTTAGCTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 14 0.42
33 19 0.58
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (33 bp):
CAATGTATCGATACATACTATGGTGTATCGATA
Found at i:1118288 original size:20 final size:20
Alignment explanation
Indices: 1118246--1118295 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1118236 TGTTTTTCAA
*
1118246 GTATCGATACAATGCAACAT
1 GTATCGATACAATGAAACAT
* **
1118266 GTATCGATACAATTAAATGT
1 GTATCGATACAATGAAACAT
1118286 GTATCGATAC
1 GTATCGATAC
1118296 TTTTCAGGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (20 bp):
GTATCGATACAATGAAACAT
Found at i:1118986 original size:21 final size:20
Alignment explanation
Indices: 1118937--1118986 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
1118927 ATATTGATTA
* *
1118937 TAAAGTTAACATATAAGGGC
1 TAAAATTAACATAAAAGGGC
*
1118957 TAAGGATTAACATGAAAAGGGC
1 TAA-AATTAACAT-AAAAGGGC
1118979 TAAAATTA
1 TAAAATTA
1118987 GACACTTTAC
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 3 0.12
21 11 0.46
22 10 0.42
ACGTcount: A:0.48, C:0.08, G:0.20, T:0.24
Consensus pattern (20 bp):
TAAAATTAACATAAAAGGGC
Found at i:1119089 original size:21 final size:21
Alignment explanation
Indices: 1119063--1119106 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1119053 CAGTTACCTT
* *
1119063 GTAACCCCATAATCTCTAGGA
1 GTAACCCCAAAATCTCTAAGA
1119084 GTAACCCCAAAATCTCTAAGA
1 GTAACCCCAAAATCTCTAAGA
1119105 GT
1 GT
1119107 TACAAATATT
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:0.36, C:0.27, G:0.14, T:0.23
Consensus pattern (21 bp):
GTAACCCCAAAATCTCTAAGA
Found at i:1120424 original size:24 final size:24
Alignment explanation
Indices: 1120397--1120443 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
1120387 CATCATGTTC
1120397 AACTATTACAAGAGATGGTAAACT
1 AACTATTACAAGAGATGGTAAACT
*
1120421 AACTATTACAGGAGATGGTAAAC
1 AACTATTACAAGAGATGGTAAAC
1120444 CCTAATGAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.45, C:0.13, G:0.19, T:0.23
Consensus pattern (24 bp):
AACTATTACAAGAGATGGTAAACT
Found at i:1127025 original size:79 final size:76
Alignment explanation
Indices: 1126942--1127404 Score: 409
Period size: 79 Copynumber: 5.9 Consensus size: 76
1126932 TATTTCCAAG
* * *
1126942 GGGATACTCCAACCCTGATTTTATTTCTAAAATACTAATTTTTCATAATCGGAGATATTCCAACC
1 GGGATACTCCAACCCTGATTTTATTTCCAAAACACTAATTTTTCACAATCGG-GATATT-CAACC
*
1127007 TCGTTATTTCTAAA
64 CCGTTATTT-TAAA
* * *
1127021 GGGATACTCCAAACCCTG-TTTTATTTTCAAATCACCT-ATTTTTCACAATCAGGGATGCTTCAA
1 GGGATACTCC-AACCCTGATTTTATTTCCAAAACA-CTAATTTTTCACAATC-GGGAT-ATTCAA
*
1127084 CCCCGTTATTTTTAA
62 CCCCGTTATTTTAAA
* * *
1127099 GGAGATACTCCAA-CCTCGGTTTTATTTCCAAAACACCAA-TTTTCGACAATTTGGGATACTTCA
1 GG-GATACTCCAACCCT-GATTTTATTTCCAAAACACTAATTTTTC-ACAA-TCGGGATA-TTCA
* *
1127162 ACCCCGTTATTTTCGAG
61 ACCCCGTTATTTT-AAA
* *
1127179 GGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAATTTC-GGATACTTCAAC
1 GGGATACTCCAACCCTGATTTTATTTCCAAAACACTAATTTTTCACAA--TCGGGATA-TTCAAC
**
1127243 CCCGTTATTTTCGA
63 CCCGTTATTTTAAA
* * **
1127257 GAGGATACTCCAACCCCGATTTTATTTCCAAAACA-TCGATTTTTCATGATCGGGGATACTTCAA
1 G-GGATACTCCAACCCTGATTTTATTTCCAAAACACT-AATTTTTCACAATC-GGGATA-TTCAA
* * *
1127321 CCCTGTTATTTTCGAG
62 CCCCGTTATTTT-AAA
* * * *
1127337 GGGATACTCCAA-CCTCAGTTTTATTTCCAAAACATTAATTTTTCATAATCGGGGATACTCCAAC
1 GGGATACTCCAACCCTGA-TTTTATTTCCAAAACACTAATTTTTCACAATC-GGGATA-TTCAAC
1127401 CCCG
63 CCCG
1127405 ATTTTATTTC
Statistics
Matches: 327, Mismatches: 35, Indels: 44
0.81 0.09 0.11
Matches are distributed among these distances:
77 5 0.02
78 18 0.06
79 276 0.84
80 28 0.09
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (76 bp):
GGGATACTCCAACCCTGATTTTATTTCCAAAACACTAATTTTTCACAATCGGGATATTCAACCCC
GTTATTTTAAA
Found at i:1127201 original size:158 final size:158
Alignment explanation
Indices: 1126930--1127404 Score: 507
Period size: 158 Copynumber: 3.0 Consensus size: 158
1126920 CTCCCACCTT
* * * * * * *
1126930 GTTATTTCCAAGGGGATACTCCAACCCTGATTTTATTTCTAAAATA-CTAATTTTTCATAATCGG
1 GTTATTTTCAAGAGGATACTCCAACCCCGATTTTATTTCCAAAACATCCAA-TTTTCACAATCGG
* * * * * * *
1126994 AGATA-TTCCAACCTCGTTA-TTTCTAAAGGGATACTCCAAACCCTG-TTTTATTTTCAAATCAC
65 GGATACTT-CAACCCCGTTATTTTC-GAGGGGATACTCC-AACCCCGATTTTATTTCCAAAACAC
*
1127056 CTATTTTTCACAATCAGGGATGCTTCAACCCC
127 CTATTTTTCACAATCAGGGATACTTCAACCCC
* * * **
1127088 GTTATTTTTAAG-GAGATACTCCAACCTCGGTTTTATTTCCAAAACA-CCAATTTTCGACAATTT
1 GTTATTTTCAAGAG-GATACTCCAACCCCGATTTTATTTCCAAAACATCCAATTTTC-ACAATCG
*
1127151 GGGATACTTCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCA
64 GGGATACTTCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCT
***
1127216 ATTTTTCACAATTTCGGATACTTCAACCCC
129 ATTTTTCACAATCAGGGATACTTCAACCCC
* * * **
1127246 GTTATTTTCGAGAGGATACTCCAACCCCGATTTTATTTCCAAAACATCGATTTTTCATGATCGGG
1 GTTATTTTCAAGAGGATACTCCAACCCCGATTTTATTTCCAAAACATCCAATTTTCACAATCGGG
* * *
1127311 GATACTTCAACCCTGTTATTTTCGAGGGGATACTCCAACCTC-AGTTTTATTTCCAAAACA-TTA
66 GATACTTCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGA-TTTTATTTCCAAAACACCT-
* * *
1127374 ATTTTTCATAATCGGGGATACTCCAACCCC
129 ATTTTTCACAATCAGGGATACTTCAACCCC
1127404 G
1 G
1127405 ATTTTATTTC
Statistics
Matches: 266, Mismatches: 42, Indels: 18
0.82 0.13 0.06
Matches are distributed among these distances:
157 13 0.05
158 239 0.90
159 14 0.05
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (158 bp):
GTTATTTTCAAGAGGATACTCCAACCCCGATTTTATTTCCAAAACATCCAATTTTCACAATCGGG
GATACTTCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCTAT
TTTTCACAATCAGGGATACTTCAACCCC
Found at i:1127394 original size:237 final size:237
Alignment explanation
Indices: 1126914--1127404 Score: 589
Period size: 237 Copynumber: 2.1 Consensus size: 237
1126904 TATTTCTGAA
* ** * * * *
1126914 GGGATACTCCCACCTTGTTATTTCCAAGGGGATACTCCAACCCTGATTTTATTTCTAAAATACTA
1 GGGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCA
* * * *
1126979 ATTTTTCATAATCGGAGATATTCCAACCTCGTTATTTCTAAAGGGATACTCCAAACCCTGTTTTA
66 ATTTTTCACAATCGGAGATATTCCAACCCCGTTATTTCGAAAGGGATACTCCAAACCCCGTTTTA
* * * * *
1127044 TTTTCAAATCACCTATTTTTCACAATCAGGGATGCTTCAACCCCGTTATTTTTAAGGAGATACTC
131 TTTCCAAAACACCGATTTTTCACAATCAGGGATACTTCAACCCCGTTATTTTCAAGGAGATACTC
* **
1127109 CAACCTCGGTTTTATTTCCAAAACACCAATTTTCGACAATTT
196 CAACCTCAGTTTTATTTCCAAAACACCAATTTTCGACAATCG
* * *
1127151 GGGATACTTCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCA
1 GGGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCA
*
1127216 ATTTTTCACAATTTC-G-GATACTT-CAACCCCGTTATTTTCGAGA-GGATACTCC-AACCCCGA
66 ATTTTTCACAA--TCGGAGATA-TTCCAACCCCGTTA-TTTCGAAAGGGATACTCCAAACCCCG-
* ** * * * *
1127276 TTTTATTTCCAAAACATCGATTTTTCATGATCGGGGATACTTCAACCCTGTTATTTTCGAGGGGA
126 TTTTATTTCCAAAACACCGATTTTTCACAATCAGGGATACTTCAACCCCGTTATTTTCAAGGAGA
** *
1127341 TACTCCAACCTCAGTTTTATTTCCAAAACATTAATTTTTC-ATAATCG
191 TACTCCAACCTCAGTTTTATTTCCAAAACACCAA-TTTTCGACAATCG
1127388 GGGATACTCCAACCCCG
1 GGGATACTCCAACCCCG
1127405 ATTTTATTTC
Statistics
Matches: 214, Mismatches: 34, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
236 6 0.03
237 192 0.90
238 14 0.07
239 2 0.01
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (237 bp):
GGGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCA
ATTTTTCACAATCGGAGATATTCCAACCCCGTTATTTCGAAAGGGATACTCCAAACCCCGTTTTA
TTTCCAAAACACCGATTTTTCACAATCAGGGATACTTCAACCCCGTTATTTTCAAGGAGATACTC
CAACCTCAGTTTTATTTCCAAAACACCAATTTTCGACAATCG
Found at i:1127398 original size:130 final size:130
Alignment explanation
Indices: 1127259--1127532 Score: 381
Period size: 130 Copynumber: 2.1 Consensus size: 130
1127249 ATTTTCGAGA
* * * *
1127259 GGATACTCCAACCCCGATTTTATTTCCAAAACATCGATTTTTCATGA-TCGGGGATACTTC-AAC
1 GGATACTCCAACCCCGATTTTATTTCCAAAAAATCGATCTTTCA-CATTCGGGGATACTCCGAAC
* * *
1127322 CCTGTTATTTTCGAGGGGATACTCCAACCTCAGTTTTATTTCCAAAACATTAATTTTTCATAATC
65 CC-GTTATTTTCGAGGAGATACTCCAACCTCAGTTTTATTTCCAAAACATCAATTTTTCACAATC
1127387 GG
129 GG
* *
1127389 GGATACTCCAACCCCGATTTTATTTCCAAAAAATTGATCTTTCACATTCGGGGATACTCCGATCC
1 GGATACTCCAACCCCGATTTTATTTCCAAAAAATCGATCTTTCACATTCGGGGATACTCCGAACC
* * * * *
1127454 CGTTATTTTCGAGGAGATACTCCAACCTCGGTTTTATTTCTAAAACATCGATTTTTCACCATTGG
66 CGTTATTTTCGAGGAGATACTCCAACCTCAGTTTTATTTCCAAAACATCAATTTTTCACAATCGG
*
1127519 TGATACTCCAACCC
1 GGATACTCCAACCC
1127533 TGCTATTTCT
Statistics
Matches: 127, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
129 1 0.01
130 122 0.96
131 4 0.03
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (130 bp):
GGATACTCCAACCCCGATTTTATTTCCAAAAAATCGATCTTTCACATTCGGGGATACTCCGAACC
CGTTATTTTCGAGGAGATACTCCAACCTCAGTTTTATTTCCAAAACATCAATTTTTCACAATCGG
Found at i:1127399 original size:51 final size:51
Alignment explanation
Indices: 1127336--1127448 Score: 156
Period size: 51 Copynumber: 2.2 Consensus size: 51
1127326 TTATTTTCGA
* * *
1127336 GGGGATACTCCAACCTCAG-TTTTATTTCCAAAACATTAATTTTTCATAATC
1 GGGGATACTCCAACC-CAGATTTTATTTCCAAAAAATTAATCTTTCACAATC
* * *
1127387 GGGGATACTCCAACCCCGATTTTATTTCCAAAAAATTGATCTTTCACATTC
1 GGGGATACTCCAACCCAGATTTTATTTCCAAAAAATTAATCTTTCACAATC
1127438 GGGGATACTCC
1 GGGGATACTCC
1127449 GATCCCGTTA
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
50 2 0.04
51 53 0.96
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (51 bp):
GGGGATACTCCAACCCAGATTTTATTTCCAAAAAATTAATCTTTCACAATC
Found at i:1127554 original size:79 final size:79
Alignment explanation
Indices: 1127387--1127577 Score: 199
Period size: 79 Copynumber: 2.4 Consensus size: 79
1127377 TTTCATAATC
* * *
1127387 GGGGATACTCCAACCCCGATTTTATTTCCAAAAAATTGATCTTTCACATTCGGGGATACTCCGAT
1 GGGGATACTCCAACCTCGATTTTATTTCCAAAAAATCGATCTTTCACATTCGGGGATACTCCGAA
* *
1127452 CCCGTTATTTTCGA
66 CCCGCTATTTTCAA
* * * * * *
1127466 GGAGATACTCCAACCTCGGTTTTATTTCTAAAACATCGATTTTTCACCATT-GGTGATACTCC-A
1 GGGGATACTCCAACCTCGATTTTATTTCCAAAAAATCGATCTTTCA-CATTCGGGGATACTCCGA
1127529 ACCCTGCTA-TTTCTAA
65 ACCC-GCTATTTTC-AA
* * * *
1127545 GGGGGTACTCCGACCTCGTTTTTATCTCCAAAA
1 GGGGATACTCCAACCTCGATTTTATTTCCAAAA
1127578 TATTAAATTT
Statistics
Matches: 92, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
78 8 0.09
79 80 0.87
80 4 0.04
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.34
Consensus pattern (79 bp):
GGGGATACTCCAACCTCGATTTTATTTCCAAAAAATCGATCTTTCACATTCGGGGATACTCCGAA
CCCGCTATTTTCAA
Found at i:1127577 original size:209 final size:210
Alignment explanation
Indices: 1127178--1127592 Score: 545
Period size: 209 Copynumber: 2.0 Consensus size: 210
1127168 TTATTTTCGA
* * *
1127178 GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAATTTCGGATACTTCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAAAACCAATCTTTCACAATTTCGGATACTCCAAC
**
1127243 CCCGTTATTTTCGAGAGGATACTCCAACCCCGATTTTATTTCCAAAACATCGATTTTTCATGATC
66 CCCGTTATTTTCGAGAGGATACTCCAACCCCGATTTTATTTCCAAAACATCGATTTTTCACCATC
* * * *
1127308 GGGGATACTTCAACCCTGTTATTTTCGAGGGGATACTCCAACCTCAGTTTTATTTCCAAAACATT
131 GGGGATACTCCAACCCTGCTATTTTCAAGGGGATACTCCAACCTCAGTTTTATCTCCAAAACATT
1127373 -AATTTTTCATAATC
196 AAATTTTTCATAATC
*** *
1127387 GGGGATACTCCAACCCCGATTTTATTTCCAAAAAATTGATCTTTCAC-A-TTCGGGGATACTCCG
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAAAACCAATCTTTCACAATTTC--GGATACTCCA
* * * *
1127450 ATCCCGTTATTTTCGAG-GAGATACTCCAACCTCGGTTTTATTTCTAAAACATCGATTTTTCACC
64 ACCCCGTTATTTTCGAGAG-GATACTCCAACCCCGATTTTATTTCCAAAACATCGATTTTTCACC
* * * *
1127514 ATTGGTGATACTCCAACCCTGCTA-TTTCTAAGGGGGTACTCCGACCTC-GTTTTTATCTCCAAA
128 ATCGGGGATACTCCAACCCTGCTATTTTC-AAGGGGATACTCCAACCTCAG-TTTTATCTCCAAA
*
1127577 ATATTAAATTTTTCAT
191 ACATTAAATTTTTCAT
1127593 CAAGAGATGT
Statistics
Matches: 178, Mismatches: 22, Indels: 11
0.84 0.10 0.05
Matches are distributed among these distances:
207 3 0.02
208 7 0.04
209 158 0.89
210 10 0.06
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.35
Consensus pattern (210 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAAAACCAATCTTTCACAATTTCGGATACTCCAAC
CCCGTTATTTTCGAGAGGATACTCCAACCCCGATTTTATTTCCAAAACATCGATTTTTCACCATC
GGGGATACTCCAACCCTGCTATTTTCAAGGGGATACTCCAACCTCAGTTTTATCTCCAAAACATT
AAATTTTTCATAATC
Found at i:1128911 original size:22 final size:21
Alignment explanation
Indices: 1128877--1128921 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
1128867 TAGTTACCTT
* *
1128877 GTAACTCCATAATCTCTAGGA
1 GTAACCCCATAATCTCTAAGA
1128898 GTAACCCCAATAATCTCTAAGA
1 GTAACCCC-ATAATCTCTAAGA
1128920 GT
1 GT
1128922 TACAAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (21 bp):
GTAACCCCATAATCTCTAAGA
Found at i:1130847 original size:43 final size:43
Alignment explanation
Indices: 1130798--1130881 Score: 168
Period size: 43 Copynumber: 2.0 Consensus size: 43
1130788 TTCAAAGATC
1130798 TTGGTTTTCCTGAAGTTTGGTATACTTGGGAACACGAAAACGG
1 TTGGTTTTCCTGAAGTTTGGTATACTTGGGAACACGAAAACGG
1130841 TTGGTTTTCCTGAAGTTTGGTATACTTGGGAACACGAAAAC
1 TTGGTTTTCCTGAAGTTTGGTATACTTGGGAACACGAAAAC
1130882 AGTGAAAGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.33
Consensus pattern (43 bp):
TTGGTTTTCCTGAAGTTTGGTATACTTGGGAACACGAAAACGG
Found at i:1136987 original size:24 final size:24
Alignment explanation
Indices: 1136931--1136987 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
1136921 TGGTTCAATA
*
1136931 ATGGTGTTAATGACAATTGAATCAT
1 ATGGT-TTAATGACAATTGAACCAT
*
1136956 TTGGTTTAATGACAA-TGAACCTAT
1 ATGGTTTAATGACAATTGAACC-AT
*
1136980 ATGTTTTA
1 ATGGTTTA
1136988 CTAATGTGCA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 5 0.19
24 18 0.67
25 4 0.15
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (24 bp):
ATGGTTTAATGACAATTGAACCAT
Found at i:1139001 original size:20 final size:20
Alignment explanation
Indices: 1138976--1139030 Score: 110
Period size: 20 Copynumber: 2.8 Consensus size: 20
1138966 TTTTGACCCA
1138976 AATGTATCGATACATTCTTC
1 AATGTATCGATACATTCTTC
1138996 AATGTATCGATACATTCTTC
1 AATGTATCGATACATTCTTC
1139016 AATGTATCGATACAT
1 AATGTATCGATACAT
1139031 GCAGGCAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (20 bp):
AATGTATCGATACATTCTTC
Found at i:1141444 original size:15 final size:16
Alignment explanation
Indices: 1141424--1141453 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1141414 ATCTGACTCC
1141424 TTATTC-AAAAGAATT
1 TTATTCAAAAAGAATT
1141439 TTATTCAAAAAGAAT
1 TTATTCAAAAAGAAT
1141454 AAGTACCCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.37
Consensus pattern (16 bp):
TTATTCAAAAAGAATT
Found at i:1143649 original size:22 final size:21
Alignment explanation
Indices: 1143618--1143666 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
1143608 TTTTGAAAAG
1143618 AAAA-TTTCTCCCCCTTAATA
1 AAAATTTTCTCCCCCTTAATA
* *
1143638 AAAGATTTTCTCTCCCTTCATA
1 AAA-ATTTTCTCCCCCTTAATA
1143660 AAAATTT
1 AAAATTT
1143667 ATTTTGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 3 0.12
21 5 0.20
22 17 0.68
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.39
Consensus pattern (21 bp):
AAAATTTTCTCCCCCTTAATA
Found at i:1144505 original size:21 final size:21
Alignment explanation
Indices: 1144476--1144518 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
1144466 AGTGGGTGTA
*
1144476 GGAGCTGCCCGATTGCGACCTG
1 GGAGCTG-CCGATCGCGACCTG
1144498 GGAG-TGCCGATCGCGACCTG
1 GGAGCTGCCGATCGCGACCTG
1144518 G
1 G
1144519 AGATGGTTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 14 0.70
21 2 0.10
22 4 0.20
ACGTcount: A:0.14, C:0.30, G:0.40, T:0.16
Consensus pattern (21 bp):
GGAGCTGCCGATCGCGACCTG
Found at i:1144816 original size:20 final size:22
Alignment explanation
Indices: 1144791--1144830 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1144781 TTTGTAGATG
1144791 ATTTTG-A-TGAAAAATAAAGT
1 ATTTTGAAGTGAAAAATAAAGT
1144811 ATTTTGAAGTGAAAAATAAA
1 ATTTTGAAGTGAAAAATAAA
1144831 AAATTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 1 0.06
22 11 0.61
ACGTcount: A:0.53, C:0.00, G:0.15, T:0.33
Consensus pattern (22 bp):
ATTTTGAAGTGAAAAATAAAGT
Found at i:1144836 original size:22 final size:20
Alignment explanation
Indices: 1144791--1144836 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
1144781 TTTGTAGATG
**
1144791 ATTTTGATGAAAAATAAAGT
1 ATTTTGATGAAAAATAAAAA
1144811 ATTTTGAAGTGAAAAATAAAAA
1 ATTTTG-A-TGAAAAATAAAAA
1144833 ATTT
1 ATTT
1144837 AAAAAAGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 6 0.27
21 1 0.05
22 15 0.68
ACGTcount: A:0.52, C:0.00, G:0.13, T:0.35
Consensus pattern (20 bp):
ATTTTGATGAAAAATAAAAA
Found at i:1151181 original size:33 final size:33
Alignment explanation
Indices: 1151137--1151199 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
1151127 TTTGAAGTAA
*
1151137 TGTATCAATACAAT-TCATCATGTATCGATATAT
1 TGTATCAATACAATGT-ACCATGTATCGATATAT
*
1151170 TGTATCGATACAATGTACCATGTATCGATA
1 TGTATCAATACAATGTACCATGTATCGATA
1151200 CAAATAGTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 26 0.96
34 1 0.04
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.37
Consensus pattern (33 bp):
TGTATCAATACAATGTACCATGTATCGATATAT
Found at i:1151275 original size:19 final size:19
Alignment explanation
Indices: 1151231--1151303 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 19
1151221 CTACCAGTTT
**
1151231 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
1151251 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
1151270 CATGTATCGATACAAAGCATA
1 CATGTATCGATACAATG-A-A
1151291 -ATGTATCGATACA
1 CATGTATCGATACA
1151304 TCTGAGTGTG
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
19 18 0.38
20 29 0.60
21 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1151914 original size:20 final size:19
Alignment explanation
Indices: 1151870--1151920 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 19
1151860 ATAATTCTTC
1151870 ATGTATCGATACAATAAAA
1 ATGTATCGATACAATAAAA
*
1151889 ATGTATCGATACAA-AGCAAT
1 ATGTATCGATACAATA--AAA
1151909 ATGTATCGATAC
1 ATGTATCGATAC
1151921 TTCTGGGCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 1 0.03
19 14 0.48
20 14 0.48
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.27
Consensus pattern (19 bp):
ATGTATCGATACAATAAAA
Found at i:1157990 original size:15 final size:16
Alignment explanation
Indices: 1157963--1157996 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1157953 GAGAGTTTCC
1157963 TTTTCTAATTCAACAA
1 TTTTCTAATTCAACAA
*
1157979 TTTTCT-ATTCAAGAA
1 TTTTCTAATTCAACAA
1157994 TTT
1 TTT
1157997 CATTTTCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.32, C:0.15, G:0.03, T:0.50
Consensus pattern (16 bp):
TTTTCTAATTCAACAA
Found at i:1160141 original size:20 final size:20
Alignment explanation
Indices: 1160116--1160192 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
1160106 TACTGCCAGT
*
1160116 TTCATGTATGGATACAATTC
1 TTCATGTATCGATACAATTC
*
1160136 TTCATGTATCGATACAA-TG
1 TTCATGTATCGATACAATTC
**
1160155 AACATGTATCGATACAATTC
1 TTCATGTATCGATACAATTC
*
1160175 TTCATGTATCAATACAAT
1 TTCATGTATCGATACAAT
1160193 GTATTGATAC
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
19 16 0.33
20 32 0.67
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (20 bp):
TTCATGTATCGATACAATTC
Found at i:1160169 original size:39 final size:39
Alignment explanation
Indices: 1160118--1160193 Score: 134
Period size: 39 Copynumber: 1.9 Consensus size: 39
1160108 CTGCCAGTTT
* *
1160118 CATGTATGGATACAATTCTTCATGTATCGATACAATGAA
1 CATGTATCGATACAATTCTTCATGTATCAATACAATGAA
1160157 CATGTATCGATACAATTCTTCATGTATCAATACAATG
1 CATGTATCGATACAATTCTTCATGTATCAATACAATG
1160194 TATTGATACT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (39 bp):
CATGTATCGATACAATTCTTCATGTATCAATACAATGAA
Found at i:1161993 original size:16 final size:16
Alignment explanation
Indices: 1161972--1162002 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1161962 TAGCTCAACC
1161972 TTTTGTTTAAACAAAT
1 TTTTGTTTAAACAAAT
*
1161988 TTTTGTTTGAACAAA
1 TTTTGTTTAAACAAA
1162003 CTTATTCTTT
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:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTTGTTTAAACAAAT
Found at i:1162878 original size:5 final size:5
Alignment explanation
Indices: 1162861--1162890 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
1162851 AATTTAACCA
*
1162861 AAATT AAAAT AAATT AAATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT AAATT
1162891 TTCCTTATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
AAATT
Found at i:1177314 original size:14 final size:14
Alignment explanation
Indices: 1177295--1177323 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1177285 AGTAGTAAAT
1177295 TTATCTTCCAATAA
1 TTATCTTCCAATAA
1177309 TTATCTTCCAATAA
1 TTATCTTCCAATAA
1177323 T
1 T
1177324 GCTAAGCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (14 bp):
TTATCTTCCAATAA
Found at i:1178860 original size:24 final size:24
Alignment explanation
Indices: 1178811--1178860 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
1178801 CATACGTCCA
* *
1178811 TTTATTTAATTTATTTGAATCTAT
1 TTTATTTAATTCATTTGAATCGAT
*
1178835 TTTATTTAATTGCA-TTGGATCGAT
1 TTTATTTAATT-CATTTGAATCGAT
1178859 TT
1 TT
1178861 GAATTTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 21 0.95
25 1 0.05
ACGTcount: A:0.26, C:0.06, G:0.10, T:0.58
Consensus pattern (24 bp):
TTTATTTAATTCATTTGAATCGAT
Found at i:1181559 original size:20 final size:19
Alignment explanation
Indices: 1181534--1181585 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 19
1181524 CGAGATTATT
1181534 TAAATATTTAATTAACTATA
1 TAAATATTTAATTAACTA-A
* *
1181554 TAAATAATTAATTTACTAA
1 TAAATATTTAATTAACTAA
**
1181573 TATCTATTTAATT
1 TAAATATTTAATT
1181586 TAGATTAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (19 bp):
TAAATATTTAATTAACTAA
Found at i:1183471 original size:20 final size:21
Alignment explanation
Indices: 1183448--1183487 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1183438 TTAAATTCTT
*
1183448 TTTTTTTTACTTTT-CTTTTC
1 TTTTTTTTAATTTTCCTTTTC
1183468 TTTTTTTTAATTTTCCTTTT
1 TTTTTTTTAATTTTCCTTTT
1183488 TTATTTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTTTTTTAATTTTCCTTTTC
Found at i:1183498 original size:20 final size:17
Alignment explanation
Indices: 1183443--1183494 Score: 50
Period size: 20 Copynumber: 2.8 Consensus size: 17
1183433 ATTCATTAAA
*
1183443 TTCTTTTTTTTTTACTT
1 TTCTTTTTTTTTTAATT
1183460 TTCTTTTCTTTTTTTTAATT
1 TTC--TT-TTTTTTTTAATT
*
1183480 TTCCTTTTTTATTTA
1 TT-CTTTTTTTTTTA
1183495 TAATCGAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
17 3 0.10
18 8 0.28
19 4 0.14
20 13 0.45
21 1 0.03
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.79
Consensus pattern (17 bp):
TTCTTTTTTTTTTAATT
Found at i:1186261 original size:33 final size:33
Alignment explanation
Indices: 1186224--1186303 Score: 92
Period size: 33 Copynumber: 2.4 Consensus size: 33
1186214 TCAAACAAGC
*
1186224 ATAATATAAATATAAAAATATT-TTAAATTTTAT
1 ATAATATAAATATAAAAAT-TTATTAAAATTTAT
**
1186257 ATAATATAAATA-ATTAATTTATTAAAATTTAT
1 ATAATATAAATATAAAAATTTATTAAAATTTAT
1186289 ATAAATATATAATAT
1 AT-AATATA-AATAT
1186304 TTTAAATATA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
31 2 0.05
32 16 0.40
33 18 0.45
34 4 0.10
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (33 bp):
ATAATATAAATATAAAAATTTATTAAAATTTAT
Found at i:1186265 original size:27 final size:27
Alignment explanation
Indices: 1186227--1186310 Score: 80
Period size: 32 Copynumber: 2.9 Consensus size: 27
1186217 AACAAGCATA
1186227 ATATAAATATAAAAATATTTTAAATTTT
1 ATAT-AATATAAAAATATTTTAAATTTT
*
1186255 ATATAATATAAATAATTAATTTATTAAAATTT
1 ATATAATATAAA-AA-T-A-TT-TTAAATTTT
*
1186287 ATATAA-ATATATAATATTTTAAAT
1 ATATAATATA-AAAATATTTTAAAT
1186311 ATATTTAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 13
0.75 0.05 0.21
Matches are distributed among these distances:
27 13 0.28
28 8 0.17
29 2 0.04
30 2 0.04
31 7 0.15
32 15 0.32
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
ATATAATATAAAAATATTTTAAATTTT
Found at i:1186526 original size:16 final size:17
Alignment explanation
Indices: 1186494--1186554 Score: 56
Period size: 16 Copynumber: 3.7 Consensus size: 17
1186484 TTATATGATC
* *
1186494 ATATTTAT-CATATTTT
1 ATATTTATAAATAATTT
1186510 ATATTTATAAA-AATTT
1 ATATTTATAAATAATTT
*
1186526 A-ATATATAAATAATTT
1 ATATTTATAAATAATTT
*
1186542 TTATTATATAAAT
1 ATATT-TATAAAT
1186555 TTTAAAATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
15 8 0.22
16 18 0.50
17 3 0.08
18 7 0.19
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (17 bp):
ATATTTATAAATAATTT
Found at i:1186596 original size:27 final size:28
Alignment explanation
Indices: 1186566--1186618 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
1186556 TTAAAATATA
*
1186566 TATTTATAATATATTAAT-TAATTATTT
1 TATTCATAATATATTAATATAATTATTT
* *
1186593 TATTCATATTATATTTATATAATTAT
1 TATTCATAATATATTAATATAATTAT
1186619 ACCTAATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 15 0.68
28 7 0.32
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (28 bp):
TATTCATAATATATTAATATAATTATTT
Found at i:1187387 original size:15 final size:15
Alignment explanation
Indices: 1187351--1187392 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
1187341 AGTACAGTAA
*
1187351 AAATTGAAAATT-TT
1 AAATTTAAAATTATT
*
1187365 ATATTTAAAATTATT
1 AAATTTAAAATTATT
*
1187380 AAATTTAATATTA
1 AAATTTAAAATTA
1187393 ATTTTTATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (15 bp):
AAATTTAAAATTATT
Found at i:1188475 original size:6 final size:6
Alignment explanation
Indices: 1188459--1188490 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
1188449 TTAATGTTAA
1188459 AAATTT AAAATTT AAATTT AAATTT AAATTT A
1 AAATTT -AAATTT AAATTT AAATTT AAATTT A
1188491 GTTCGACAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
AAATTT
Found at i:1192096 original size:154 final size:154
Alignment explanation
Indices: 1191914--1192223 Score: 548
Period size: 154 Copynumber: 2.0 Consensus size: 154
1191904 TTCCTCTCTC
**
1191914 CCCAACCCTAATCTCATTAGACTCTATGACATGAACCAAAATATTTTATAATTAATAATTGGGAT
1 CCCAACCCTAATCTCATTAGACTCTATGACATGAACCAAAATATTTTATAATTAATAATTACGAT
1191979 TTCAATCACTAATTTTAAGGATTTTACTATTTTAATGATTGTTGTTATTTTTTTAACAATAATAA
66 TTCAATCACTAATTTTAAGGATTTTACTATTTTAATGATTGTTGTTATTTTTTTAACAATAATAA
1192044 CTTTCAACTACTATTTCAAGTTAA
131 CTTTCAACTACTATTTCAAGTTAA
*
1192068 CCCAACCCTATTCTCATTAGACTCTATGACATGAACCAAAATATTTTATAATTAATAATTACGAT
1 CCCAACCCTAATCTCATTAGACTCTATGACATGAACCAAAATATTTTATAATTAATAATTACGAT
**
1192133 TTCAATCTTTAATTTTAAGGATTTTACTATTTTAATGATTGTTGTTATTTTTTTAACAATAATAA
66 TTCAATCACTAATTTTAAGGATTTTACTATTTTAATGATTGTTGTTATTTTTTTAACAATAATAA
* * *
1192198 TTTTCAATTATTATTTCAAGTTAA
131 CTTTCAACTACTATTTCAAGTTAA
1192222 CC
1 CC
1192224 AAGAAAAAAA
Statistics
Matches: 148, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
154 148 1.00
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.43
Consensus pattern (154 bp):
CCCAACCCTAATCTCATTAGACTCTATGACATGAACCAAAATATTTTATAATTAATAATTACGAT
TTCAATCACTAATTTTAAGGATTTTACTATTTTAATGATTGTTGTTATTTTTTTAACAATAATAA
CTTTCAACTACTATTTCAAGTTAA
Found at i:1198230 original size:20 final size:21
Alignment explanation
Indices: 1198205--1198257 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
1198195 ATCAATACAT
*
1198205 TGTATCGATACATG-ACTA-AA
1 TGTATCGATACATGCA-AAGAA
*
1198225 TGTATCGATACTTGCAAAGAA
1 TGTATCGATACATGCAAAGAA
1198246 TGTATCGATACA
1 TGTATCGATACA
1198258 GGTGATTGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (21 bp):
TGTATCGATACATGCAAAGAA
Found at i:1198324 original size:20 final size:20
Alignment explanation
Indices: 1198299--1198364 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
1198289 CTTAACTGTT
1198299 TGTATCGATACATGACCAAA
1 TGTATCGATACATGACCAAA
1198319 TGTATCGATACAT-------
1 TGTATCGATACATGACCAAA
1198332 TGTATCGATACATGACCAAA
1 TGTATCGATACATGACCAAA
1198352 TGTATCGATACAT
1 TGTATCGATACAT
1198365 TGGCCTGTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 13 0.33
20 26 0.67
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.30
Consensus pattern (20 bp):
TGTATCGATACATGACCAAA
Found at i:1198337 original size:13 final size:13
Alignment explanation
Indices: 1198319--1198344 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1198309 CATGACCAAA
1198319 TGTATCGATACAT
1 TGTATCGATACAT
1198332 TGTATCGATACAT
1 TGTATCGATACAT
1198345 GACCAAATGT
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:1198340 original size:33 final size:33
Alignment explanation
Indices: 1198298--1198366 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
1198288 CCTTAACTGT
1198298 TTGTATCGATACATGACCAAATGTATCGATACA
1 TTGTATCGATACATGACCAAATGTATCGATACA
1198331 TTGTATCGATACATGACCAAATGTATCGATACA
1 TTGTATCGATACATGACCAAATGTATCGATACA
1198364 TTG
1 TTG
1198367 GCCTGTAACG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACATGACCAAATGTATCGATACA
Found at i:1203039 original size:19 final size:19
Alignment explanation
Indices: 1202994--1203068 Score: 105
Period size: 19 Copynumber: 3.8 Consensus size: 19
1202984 CTGCCAGTTT
*
1202994 CATGTATCGATACAATTTGAC
1 CATGTATCGATACAA--TGAA
1203015 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
1203034 CATGTATTGATACAATGAA
1 CATGTATCGATACAATGAA
*
1203053 CATGCATCGATACAAT
1 CATGTATCGATACAAT
1203069 ATATCGATAC
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 35 0.70
21 15 0.30
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1205552 original size:13 final size:13
Alignment explanation
Indices: 1205534--1205562 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1205524 AAATAGTACC
1205534 CAATGTATCGATA
1 CAATGTATCGATA
1205547 CAATGTATCGATA
1 CAATGTATCGATA
1205560 CAA
1 CAA
1205563 GGAATGTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1207685 original size:234 final size:234
Alignment explanation
Indices: 1207276--1207747 Score: 892
Period size: 234 Copynumber: 2.0 Consensus size: 234
1207266 CCTCTTGACT
1207276 ATAACCTTTTGCAACTAGCCTAGCTTTATTTCTAACTATTATTCCATCTTCATCCAACTTATTTC
1 ATAACCTTTTGCAACTAGCCTAGCTTTATTTCTAACTATTATTCCATCTTCATCCAACTTATTTC
1207341 TAAACACCCATTTAGTCCTTATAGTTGGATGATTGTTCGGTCATTTTACCAAAGACCAAACTTTG
66 TAAACACCCATTTAGTCCTTATAGTTGGATGATTGTTCGGTCATTTTACCAAAGACCAAACTTTG
1207406 ATTCTCTCAAATTGATTTAACTCCTCTTGCATAGCCATAATCCAATTTTCATCTAGTAGTGTCTC
131 ATTCTCTCAAATTGATTTAACTCCTCTTGCATAGCCATAATCCAATTTTCATCTAGTAGTGTCTC
1207471 GTCTATGCTTTTAGGTTCTATTTGAGAGAGAAAAGCTAC
196 GTCTATGCTTTTAGGTTCTATTTGAGAGAGAAAAGCTAC
*
1207510 ATAACCTTTTGCAACTAGCCTAGCTTTATTTCTAACTATTATTCCATCTTCCTCCAACTTATTTC
1 ATAACCTTTTGCAACTAGCCTAGCTTTATTTCTAACTATTATTCCATCTTCATCCAACTTATTTC
*
1207575 TAAACACCCATTTAGT-CTCTATAGTTGGATGATTGTTCGGTCTTTTTACCAAAGACCAAACTTT
66 TAAACACCCATTTAGTCCT-TATAGTTGGATGATTGTTCGGTCATTTTACCAAAGACCAAACTTT
* *
1207639 GCTTCTCTCAAATTGATTTAACTCCTCTTGCATAGTCATAATCCAATTTTCATCTAGTAGTGTCT
130 GATTCTCTCAAATTGATTTAACTCCTCTTGCATAGCCATAATCCAATTTTCATCTAGTAGTGTCT
1207704 CGTCTATGCTTTTAGGTTCTATTTGAGAGAGAAAAGCTAC
195 CGTCTATGCTTTTAGGTTCTATTTGAGAGAGAAAAGCTAC
1207744 ATAA
1 ATAA
1207748 TCACAAGTAT
Statistics
Matches: 233, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
233 2 0.01
234 231 0.99
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.39
Consensus pattern (234 bp):
ATAACCTTTTGCAACTAGCCTAGCTTTATTTCTAACTATTATTCCATCTTCATCCAACTTATTTC
TAAACACCCATTTAGTCCTTATAGTTGGATGATTGTTCGGTCATTTTACCAAAGACCAAACTTTG
ATTCTCTCAAATTGATTTAACTCCTCTTGCATAGCCATAATCCAATTTTCATCTAGTAGTGTCTC
GTCTATGCTTTTAGGTTCTATTTGAGAGAGAAAAGCTAC
Found at i:1212063 original size:19 final size:19
Alignment explanation
Indices: 1212018--1212091 Score: 85
Period size: 19 Copynumber: 3.7 Consensus size: 19
1212008 CTGCCAGTTT
* *
1212018 CATGTGTCGATACAATTTGAC
1 CATGTATCGATACAA--TGAA
1212039 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
* *
1212058 CATGTATCGATACAAAGCAG
1 CATGTATCGATACAATG-AA
1212078 CATGTATCGATACA
1 CATGTATCGATACA
1212092 TAGCTTGTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
19 19 0.40
20 15 0.31
21 14 0.29
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1214544 original size:13 final size:13
Alignment explanation
Indices: 1214526--1214563 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
1214516 CAGCATTCTC
* *
1214526 TGTATCGATGCAT
1 TGTATCGATACAG
1214539 TGTATCGATACAG
1 TGTATCGATACAG
1214552 TGTATCGATACA
1 TGTATCGATACA
1214564 AAGGGTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1218070 original size:21 final size:21
Alignment explanation
Indices: 1218037--1218081 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1218027 TTGCAAGTTG
*
1218037 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1218059 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
1218079 AAA
1 AAA
1218082 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1219904 original size:15 final size:15
Alignment explanation
Indices: 1219884--1219914 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1219874 TAAAAATGTC
*
1219884 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1219899 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1219914 C
1 C
1219915 CAAACGAAAT
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:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1222010 original size:13 final size:13
Alignment explanation
Indices: 1221992--1222030 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
1221982 ACATTTTTCT
1221992 TTGTATCGATACA
1 TTGTATCGATACA
1222005 TTGTATCGATACA
1 TTGTATCGATACA
1222018 TTGTATCGATACA
1 TTGTATCGATACA
1222031 GGGTGATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1223876 original size:20 final size:20
Alignment explanation
Indices: 1223838--1223876 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1223828 TGATATGAAT
*
1223838 TACTTGATTAATGGAGAGAA
1 TACTTGATTAAGGGAGAGAA
*
1223858 TACTTGATTAAGGGGGAGA
1 TACTTGATTAAGGGAGAGA
1223877 TTTATTAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.05, G:0.31, T:0.28
Consensus pattern (20 bp):
TACTTGATTAAGGGAGAGAA
Found at i:1224614 original size:13 final size:13
Alignment explanation
Indices: 1224596--1224621 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1224586 TACAGCAAGT
1224596 ATGTATCGATACA
1 ATGTATCGATACA
1224609 ATGTATCGATACA
1 ATGTATCGATACA
1224622 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1227020 original size:20 final size:21
Alignment explanation
Indices: 1226995--1227047 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
1226985 ATCTATACAT
*
1226995 TGTATCGATACATG-ACCA-AA
1 TGTATCGATACATGCA-AAGAA
*
1227015 TGTATCGATACTTGCAAAGAA
1 TGTATCGATACATGCAAAGAA
1227036 TGTATCGATACA
1 TGTATCGATACA
1227048 GGTGATTGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGCAAAGAA
Found at i:1227126 original size:13 final size:13
Alignment explanation
Indices: 1227108--1227133 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1227098 ACATACAAGA
1227108 TGTATCGATACAT
1 TGTATCGATACAT
1227121 TGTATCGATACAT
1 TGTATCGATACAT
1227134 GACCAAATGT
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:1227149 original size:33 final size:32
Alignment explanation
Indices: 1227088--1227155 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 32
1227078 CCTTAACTAT
1227088 TTGTATCGATACATACAAGATGTATCGATACA
1 TTGTATCGATACATACAAGATGTATCGATACA
1227120 TTGTATCGATACATGACCAA-ATGTATCGATACA
1 TTGTATCGATACAT-A-CAAGATGTATCGATACA
1227153 TTG
1 TTG
1227156 ACTTATAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
32 14 0.41
33 17 0.50
34 3 0.09
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (32 bp):
TTGTATCGATACATACAAGATGTATCGATACA
Found at i:1229175 original size:34 final size:34
Alignment explanation
Indices: 1229110--1229175 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 34
1229100 GGTGTTTGTG
*
1229110 GAAAGAATAAGCACAAAGGAATACAATAAGCTTT
1 GAAAGAATAAGCACAAAGGAATACAAAAAGCTTT
*
1229144 GAAAGAATAA-CAACAAA-GAATATATAAAAGCT
1 GAAAGAATAAGC-ACAAAGGAATACA-AAAAGCT
1229176 CTTTGAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 7 0.25
34 21 0.75
ACGTcount: A:0.58, C:0.11, G:0.15, T:0.17
Consensus pattern (34 bp):
GAAAGAATAAGCACAAAGGAATACAAAAAGCTTT
Found at i:1229563 original size:20 final size:19
Alignment explanation
Indices: 1229517--1229566 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
1229507 CTTTTCAAGG
*
1229517 TGTATCGATACTATGAACA
1 TGTATCGATACTAAGAACA
* *
1229536 TTTATCGATACTAAGTAATA
1 TGTATCGATACTAAG-AACA
1229556 TGTATCGATAC
1 TGTATCGATAC
1229567 ATCTGGGTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (19 bp):
TGTATCGATACTAAGAACA
Found at i:1230349 original size:17 final size:17
Alignment explanation
Indices: 1230304--1230351 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
1230294 CCAAAATTTA
* *
1230304 CAAAACAAATTTAT-TT
1 CAAAAAAAATTTCTCTT
1230320 CAAAAAAAATTTCTCTT
1 CAAAAAAAATTTCTCTT
1230337 CAAAAAAAATTTCTC
1 CAAAAAAAATTTCTC
1230352 CCCTTTTTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 12 0.41
17 17 0.59
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (17 bp):
CAAAAAAAATTTCTCTT
Found at i:1230498 original size:17 final size:17
Alignment explanation
Indices: 1230476--1230510 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1230466 TTTATGTAGA
1230476 ATATATTGCATTAATGT
1 ATATATTGCATTAATGT
*
1230493 ATATATTGCATTCATGT
1 ATATATTGCATTAATGT
1230510 A
1 A
1230511 GAAAATACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (17 bp):
ATATATTGCATTAATGT
Found at i:1232291 original size:33 final size:33
Alignment explanation
Indices: 1232226--1232291 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
1232216 AATGGTACCC
* ** *
1232226 ATGTATCGATACAAAGAACTTAATATCGATACA
1 ATGTATCAATACAAAGAACGCAATATCAATACA
* *
1232259 ATGTATCAATACTAAGAACGCAGTATCAATACA
1 ATGTATCAATACAAAGAACGCAATATCAATACA
1232292 TATGGGTTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.45, C:0.17, G:0.12, T:0.26
Consensus pattern (33 bp):
ATGTATCAATACAAAGAACGCAATATCAATACA
Found at i:1234723 original size:80 final size:79
Alignment explanation
Indices: 1234605--1234812 Score: 229
Period size: 80 Copynumber: 2.6 Consensus size: 79
1234595 GAGATAATAA
* * * * * * *
1234605 CGGGGTTGGAGTGTTCCCTTGAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-A
*
1234670 -TTAGAAAAAAAAAAT
65 TTTAG-AAAAAAAAAC
* *
1234685 CGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
* ** * *
1234750 TTTGGGAATAAAGC
66 TTAGAAAAAAAAAC
* * *
1234764 CGGGGTTGGAGTATCCTCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGAT
1234813 GAAATAACAA
Statistics
Matches: 107, Mismatches: 20, Indels: 3
0.82 0.15 0.02
Matches are distributed among these distances:
79 50 0.47
80 57 0.53
ACGTcount: A:0.29, C:0.16, G:0.30, T:0.25
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
TTAGAAAAAAAAAC
Done.