Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007858.1 Hibiscus syriacus cultivar Beakdansim tig00110220_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 969818
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:749437 original size:13 final size:13
Alignment explanation
Indices: 749419--749443 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
749409 TATAAACAGT
749419 TAATCAAATCAGA
1 TAATCAAATCAGA
749432 TAATCAAATCAG
1 TAATCAAATCAG
749444 CCAGATCAAA
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:0.52, C:0.16, G:0.08, T:0.24
Consensus pattern (13 bp):
TAATCAAATCAGA
Found at i:750726 original size:2 final size:2
Alignment explanation
Indices: 750719--750747 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
750709 ACAGAAAGTA
750719 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 A
750748 AAGGGAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:752994 original size:16 final size:19
Alignment explanation
Indices: 752959--752995 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
752949 GAACTGGATC
752959 TAAAATAATATATTTATTA
1 TAAAATAATATATTTATTA
* *
752978 TAAAATATTATTTTTATT
1 TAAAATAATATATTTATT
752996 TAATAAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TAAAATAATATATTTATTA
Found at i:764602 original size:18 final size:18
Alignment explanation
Indices: 764579--764639 Score: 113
Period size: 18 Copynumber: 3.4 Consensus size: 18
764569 GCAACGGAAA
*
764579 CCGAAGGCGAAGGATGCT
1 CCGAAGGCGAAGGATCCT
764597 CCGAAGGCGAAGGATCCT
1 CCGAAGGCGAAGGATCCT
764615 CCGAAGGCGAAGGATCCT
1 CCGAAGGCGAAGGATCCT
764633 CCGAAGG
1 CCGAAGG
764640 TGGAGAAAGA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.28, C:0.26, G:0.36, T:0.10
Consensus pattern (18 bp):
CCGAAGGCGAAGGATCCT
Found at i:765097 original size:35 final size:35
Alignment explanation
Indices: 765058--765131 Score: 121
Period size: 35 Copynumber: 2.1 Consensus size: 35
765048 GCATGGATCG
* *
765058 AATTCGATTAAATATCATTTTTAAGCTTCAAACTT
1 AATTCGATTAAATATCATTTTTAAGATTCAAAATT
*
765093 AATTCGATTAAATATTATTTTTAAGATTCAAAATT
1 AATTCGATTAAATATCATTTTTAAGATTCAAAATT
765128 AATT
1 AATT
765132 TGAAATGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (35 bp):
AATTCGATTAAATATCATTTTTAAGATTCAAAATT
Found at i:768424 original size:16 final size:17
Alignment explanation
Indices: 768388--768431 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
768378 TTTATGAGGA
*
768388 AATTGAAATTTGTGAAGG
1 AATTGAAATCTGT-AAGG
768406 AATTGAAATCTGT-AGG
1 AATTGAAATCTGTAAGG
*
768422 AATTGGAATC
1 AATTGAAATC
768432 AAATTCCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 12 0.50
18 12 0.50
ACGTcount: A:0.39, C:0.05, G:0.25, T:0.32
Consensus pattern (17 bp):
AATTGAAATCTGTAAGG
Found at i:769275 original size:32 final size:33
Alignment explanation
Indices: 769206--769281 Score: 136
Period size: 33 Copynumber: 2.3 Consensus size: 33
769196 CCCGAACCCG
769206 ACCCGACCCGACCCGAATATCACACTAAAAAAA
1 ACCCGACCCGACCCGAATATCACACTAAAAAAA
*
769239 ACCCGACCCGACCCGAATATCACACT-TAAAAA
1 ACCCGACCCGACCCGAATATCACACTAAAAAAA
769271 ACCCGACCCGA
1 ACCCGACCCGA
769282 ACAAAATAAG
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
32 16 0.38
33 26 0.62
ACGTcount: A:0.41, C:0.39, G:0.11, T:0.09
Consensus pattern (33 bp):
ACCCGACCCGACCCGAATATCACACTAAAAAAA
Found at i:770414 original size:16 final size:16
Alignment explanation
Indices: 770393--770437 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
770383 CACAAATAAT
*
770393 AAACAACAACAAAAGC
1 AAACAAAAACAAAAGC
* *
770409 AAACAAAAAAAAAAGT
1 AAACAAAAACAAAAGC
*
770425 AAAGAAAAACAAA
1 AAACAAAAACAAA
770438 CAAATTACAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.78, C:0.13, G:0.07, T:0.02
Consensus pattern (16 bp):
AAACAAAAACAAAAGC
Found at i:771858 original size:2 final size:2
Alignment explanation
Indices: 771851--771884 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
771841 TGGACTTCTA
771851 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
771885 TAAAATTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:772405 original size:35 final size:35
Alignment explanation
Indices: 772359--772430 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
772349 AATAGTCCTA
*
772359 AATTTCATTCTAAACCCCAAATTCCAAAATAATTC
1 AATTACATTCTAAACCCCAAATTCCAAAATAATTC
* *
772394 AATTACATTCTAAACCCCAAATTCTAAAATACTTC
1 AATTACATTCTAAACCCCAAATTCCAAAATAATTC
772429 AA
1 AA
772431 AATAATATTG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (35 bp):
AATTACATTCTAAACCCCAAATTCCAAAATAATTC
Found at i:773018 original size:35 final size:35
Alignment explanation
Indices: 772970--773039 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
772960 TATTATTTTG
* *
772970 ATTATTTTGGAATTTGGGGTTTAGAATGTAATTGA
1 ATTATTTTGGAATTTGAGGTTTAGAATGAAATTGA
*
773005 ATTATTTTTGAATTTGAGGTTTAGAATGAAATTGA
1 ATTATTTTGGAATTTGAGGTTTAGAATGAAATTGA
773040 GGACTATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (35 bp):
ATTATTTTGGAATTTGAGGTTTAGAATGAAATTGA
Found at i:773375 original size:19 final size:18
Alignment explanation
Indices: 773332--773384 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
773322 TTTTTGTCAA
* *
773332 TTTTTAA-TGTATTTTTG
1 TTTTTAATTTTATTTTGG
773349 TTTTTAATTTTATTTTGG
1 TTTTTAATTTTATTTTGG
773367 TTATTTAATTTTAATTTT
1 TT-TTTAATTTT-ATTTT
773385 TTTCAATATG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
17 7 0.23
18 10 0.32
19 9 0.29
20 5 0.16
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.72
Consensus pattern (18 bp):
TTTTTAATTTTATTTTGG
Found at i:775278 original size:15 final size:15
Alignment explanation
Indices: 775258--775286 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
775248 GCTTGTAGTG
775258 AAGCTCCTTAATCAC
1 AAGCTCCTTAATCAC
775273 AAGCTCCTTAATCA
1 AAGCTCCTTAATCA
775287 GCGGAAGGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.31, G:0.07, T:0.28
Consensus pattern (15 bp):
AAGCTCCTTAATCAC
Found at i:780349 original size:37 final size:37
Alignment explanation
Indices: 780308--780383 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
780298 TTTGAATGAA
780308 TAAATGGAAATAGAGGATAAGTTCAAGCAATTTACAG
1 TAAATGGAAATAGAGGATAAGTTCAAGCAATTTACAG
780345 TAAATGGAAATAGAGGATAAGTTCAAGCAATTTACAG
1 TAAATGGAAATAGAGGATAAGTTCAAGCAATTTACAG
780382 TA
1 TA
780384 TGTGGAGGAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.46, C:0.08, G:0.21, T:0.25
Consensus pattern (37 bp):
TAAATGGAAATAGAGGATAAGTTCAAGCAATTTACAG
Found at i:793206 original size:26 final size:24
Alignment explanation
Indices: 793166--793220 Score: 74
Period size: 26 Copynumber: 2.2 Consensus size: 24
793156 CAAAGGGCTC
*
793166 GTTCGTTCATTTACGTTCGATTATAT
1 GTTCGTTCATGTACGTTC-ATT-TAT
*
793192 GTTCGTTTATGTACGTTCATTTAT
1 GTTCGTTCATGTACGTTCATTTAT
793216 GTTCG
1 GTTCG
793221 AACAGATGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 8 0.30
25 3 0.11
26 16 0.59
ACGTcount: A:0.16, C:0.15, G:0.18, T:0.51
Consensus pattern (24 bp):
GTTCGTTCATGTACGTTCATTTAT
Found at i:793553 original size:14 final size:14
Alignment explanation
Indices: 793521--793565 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
793511 TGTTTGTTTA
* *
793521 TGTTCATTTAT-TA
1 TGTTCGTTTATGTT
793534 TGTTCGTTTATGTT
1 TGTTCGTTTATGTT
*
793548 TGTTCGTTTGTGTT
1 TGTTCGTTTATGTT
793562 TGTT
1 TGTT
793566 TATGTTCGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
13 10 0.36
14 18 0.64
ACGTcount: A:0.09, C:0.07, G:0.20, T:0.64
Consensus pattern (14 bp):
TGTTCGTTTATGTT
Found at i:793566 original size:24 final size:24
Alignment explanation
Indices: 793488--793592 Score: 110
Period size: 23 Copynumber: 4.5 Consensus size: 24
793478 ATGTTTGTGT
*
793488 TGTTCGTTTATGTACGTT--TATTG
1 TGTTCGTTTATGTTCGTTCGT-TTG
* * *
793511 TGTTTGTTTATGTTCATT--TATTA
1 TGTTCGTTTATGTTCGTTCGT-TTG
*
793534 TGTTCGTTTATGTTTGTTCGTTTG
1 TGTTCGTTTATGTTCGTTCGTTTG
*
793558 TGTTTGTTTATGTTCGTTCGTTTG
1 TGTTCGTTTATGTTCGTTCGTTTG
793582 TGTTCGTTTAT
1 TGTTCGTTTAT
793593 CATTTAAATG
Statistics
Matches: 69, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
23 34 0.49
24 34 0.49
25 1 0.01
ACGTcount: A:0.10, C:0.08, G:0.21, T:0.62
Consensus pattern (24 bp):
TGTTCGTTTATGTTCGTTCGTTTG
Found at i:793580 original size:14 final size:14
Alignment explanation
Indices: 793535--793589 Score: 55
Period size: 14 Copynumber: 4.2 Consensus size: 14
793525 CATTTATTAT
*
793535 GTTCGTTTATGTTT
1 GTTCGTTTATGTTC
793549 GTTCG-TT-TG-T-
1 GTTCGTTTATGTTC
*
793559 GTTTGTTTATGTTC
1 GTTCGTTTATGTTC
*
793573 GTTCGTTTGTGTTC
1 GTTCGTTTATGTTC
793587 GTT
1 GTT
793590 TATCATTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
10 4 0.12
11 3 0.09
12 4 0.12
13 3 0.09
14 20 0.59
ACGTcount: A:0.04, C:0.09, G:0.25, T:0.62
Consensus pattern (14 bp):
GTTCGTTTATGTTC
Found at i:798265 original size:19 final size:19
Alignment explanation
Indices: 798241--798277 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
798231 AAAAACGTGT
798241 TGTTGCGATAGTGAAAAAG
1 TGTTGCGATAGTGAAAAAG
798260 TGTTGCGATAGTGAAAAA
1 TGTTGCGATAGTGAAAAA
798278 TCCAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.30, T:0.27
Consensus pattern (19 bp):
TGTTGCGATAGTGAAAAAG
Found at i:798646 original size:41 final size:41
Alignment explanation
Indices: 798589--798700 Score: 197
Period size: 41 Copynumber: 2.7 Consensus size: 41
798579 GGTTCGTGGT
*
798589 CGTTGCGATTTTGTATTAACGCGTTGCGATAGTCAGAATCG
1 CGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGAATCG
*
798630 CGTTGCGATTTTGTATTATCGAGTTGCGATAGTCAGAATCG
1 CGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGAATCG
*
798671 CGTTGCGATTCTGTATTATCGCGTTGCGAT
1 CGTTGCGATTTTGTATTATCGCGTTGCGAT
798701 TTTGTATTAT
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 67 1.00
ACGTcount: A:0.20, C:0.17, G:0.27, T:0.37
Consensus pattern (41 bp):
CGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGAATCG
Found at i:798692 original size:62 final size:62
Alignment explanation
Indices: 798626--798762 Score: 247
Period size: 62 Copynumber: 2.2 Consensus size: 62
798616 GATAGTCAGA
798626 ATCGCGTTGCGATTTTGTATTATCGAGTTGCGATAGTCAGAATCGCGTTGCGATTCTGTATT
1 ATCGCGTTGCGATTTTGTATTATCGAGTTGCGATAGTCAGAATCGCGTTGCGATTCTGTATT
* * *
798688 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGAATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATTTTGTATTATCGAGTTGCGATAGTCAGAATCGCGTTGCGATTCTGTATT
798750 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
798763 AGTCAGAATC
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 72 1.00
ACGTcount: A:0.18, C:0.17, G:0.26, T:0.39
Consensus pattern (62 bp):
ATCGCGTTGCGATTTTGTATTATCGAGTTGCGATAGTCAGAATCGCGTTGCGATTCTGTATT
Found at i:798768 original size:103 final size:103
Alignment explanation
Indices: 798589--798783 Score: 363
Period size: 103 Copynumber: 1.9 Consensus size: 103
798579 GGTTCGTGGT
798589 CGTTGCGATTTTGTATTAACGCGTTGCGATAGTCAGAATCGCGTTGCGATTTTGTATTATCGAGT
1 CGTTGCGATTTTGTATTAACGCGTTGCGATAGTCAGAATCGCGTTGCGATTTTGTATTATCGAGT
798654 TGCGATAGTCAGAATCGCGTTGCGATTCTGTATTATCG
66 TGCGATAGTCAGAATCGCGTTGCGATTCTGTATTATCG
* * *
798692 CGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGAATCTCGTTGCGATTTTGTATTATCGCGT
1 CGTTGCGATTTTGTATTAACGCGTTGCGATAGTCAGAATCGCGTTGCGATTTTGTATTATCGAGT
798757 TGCGATAGTCAGAATCGCGTTGCGATT
66 TGCGATAGTCAGAATCGCGTTGCGATT
798784 TACATATTCG
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 89 1.00
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.37
Consensus pattern (103 bp):
CGTTGCGATTTTGTATTAACGCGTTGCGATAGTCAGAATCGCGTTGCGATTTTGTATTATCGAGT
TGCGATAGTCAGAATCGCGTTGCGATTCTGTATTATCG
Found at i:798813 original size:40 final size:41
Alignment explanation
Indices: 798688--798821 Score: 200
Period size: 41 Copynumber: 3.3 Consensus size: 41
798678 ATTCTGTATT
798688 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGA
*
798729 ATCTCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGA
** * *
798770 ATCGCGTTGCGA-TTTACA-TATTCGCATTGCGATAGTCAAA
1 ATCGCGTTGCGATTTTGTATTA-TCGCGTTGCGATAGTCAGA
798810 ATCGCGTTGCGA
1 ATCGCGTTGCGA
798822 ATCTGGAAAC
Statistics
Matches: 86, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
39 2 0.02
40 33 0.38
41 51 0.59
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.35
Consensus pattern (41 bp):
ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGA
Found at i:798943 original size:20 final size:21
Alignment explanation
Indices: 798888--798952 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
798878 GCAATTTTCT
*
798888 AAAATCGCAACGCGAATTTGG
1 AAAATCGCAACGCGAATATGG
* *
798909 AAAATCACAATGCGAATAT-G
1 AAAATCGCAACGCGAATATGG
* *
798929 TAAATCGCAACGCGAATCTGG
1 AAAATCGCAACGCGAATATGG
798950 AAA
1 AAA
798953 CTGATTTGCG
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 16 0.46
21 19 0.54
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.18
Consensus pattern (21 bp):
AAAATCGCAACGCGAATATGG
Found at i:798981 original size:20 final size:19
Alignment explanation
Indices: 798958--799003 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
798948 GGAAACTGAT
* *
798958 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
798978 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
798997 TTGCGAT
1 TTGCGAT
799004 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:798993 original size:19 final size:19
Alignment explanation
Indices: 798969--799005 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
798959 TGCGATACTG
*
798969 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
798988 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
799006 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:801136 original size:3 final size:3
Alignment explanation
Indices: 801128--801157 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
801118 TGATTTGATA
801128 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
801158 ATAAGATTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:801908 original size:13 final size:13
Alignment explanation
Indices: 801886--801921 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
801876 ATTTAAATCT
801886 ATTTTT-AATTTA
1 ATTTTTCAATTTA
801898 ATTTTTCAATTTA
1 ATTTTTCAATTTA
801911 ATTTTTCAATT
1 ATTTTTCAATT
801922 AGGACTTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 6 0.26
13 17 0.74
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (13 bp):
ATTTTTCAATTTA
Found at i:804392 original size:14 final size:13
Alignment explanation
Indices: 804373--804410 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
804363 GTTAAATGAC
804373 TATTTTAGTAATAT
1 TATTTTA-TAATAT
804387 TATTTTA-AATAT
1 TATTTTATAATAT
*
804399 TATGTTATAATA
1 TATTTTATAATA
804411 ATAATTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 11 0.50
13 4 0.18
14 7 0.32
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (13 bp):
TATTTTATAATAT
Found at i:818210 original size:17 final size:18
Alignment explanation
Indices: 818173--818215 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
818163 ACAAGTCTTG
*
818173 TAAATAAATAATATAGAT
1 TAAATAAATAAAATAGAT
*
818191 TAAATAAA-AAAATTGAT
1 TAAATAAATAAAATAGAT
818208 TAAA-AAAT
1 TAAATAAAT
818216 TTATGATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 3 0.14
17 11 0.50
18 8 0.36
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (18 bp):
TAAATAAATAAAATAGAT
Found at i:821151 original size:26 final size:26
Alignment explanation
Indices: 821101--821151 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
821091 CCGAAATTTT
* * * *
821101 TTAAATTTTTTTAATTTATATAAAAA
1 TTAAATGTTTTTAATTAAAAGAAAAA
821127 TTAAATGTTTTTAATTAAAAGAAAA
1 TTAAATGTTTTTAATTAAAAGAAAA
821152 TTTATAATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (26 bp):
TTAAATGTTTTTAATTAAAAGAAAAA
Found at i:821447 original size:186 final size:183
Alignment explanation
Indices: 821134--821504 Score: 604
Period size: 186 Copynumber: 2.0 Consensus size: 183
821124 AAATTAAATG
*
821134 TTTTTAATTAAAAGAAAATTTATAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAG
1 TTTTTAATTAAAAGAAAATTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAG
*
821199 ATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGATCTTAAATTATTAATT-
66 ATAAATATTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGATCTTAAATTATTAATTG
* * *
821263 AGGTTTTAAATGGTTTGGGCTGAGCCTATATGTTATATATATAATATATTTAATAT
131 A-GTTTTAAATGGTTTGGACTAAGCCCATATGTTATATATAT--TATATTTAATAT
*
821319 TTTTTAATTAAAA-AAACAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTT
1 TTTTTAATTAAAAGAAA-A-TTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTC
*
821383 ATATAAA-ATTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAA
64 AGATAAATATTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATT-GATCTTAAATTATTAA
821447 TTGAGTTTTAAATGGTTTGGACTAAGCCCATATGTTATATATATTATATTTAATAT
128 TTGAGTTTTAAATGGTTTGGACTAAGCCCATATGTTATATATATTATATTTAATAT
821503 TT
1 TT
821505 AAAATTTAAT
Statistics
Matches: 175, Mismatches: 7, Indels: 9
0.92 0.04 0.05
Matches are distributed among these distances:
184 17 0.10
185 53 0.30
186 104 0.59
187 1 0.01
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (183 bp):
TTTTTAATTAAAAGAAAATTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAG
ATAAATATTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGATCTTAAATTATTAATTG
AGTTTTAAATGGTTTGGACTAAGCCCATATGTTATATATATTATATTTAATAT
Found at i:822316 original size:2 final size:2
Alignment explanation
Indices: 822309--822333 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
822299 ACTTTTCTTG
822309 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
822334 CCCACTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:839420 original size:37 final size:36
Alignment explanation
Indices: 839345--839420 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
839335 TTTTTATATT
*
839345 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
839381 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
839418 TTT
1 TTT
839421 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:839602 original size:20 final size:20
Alignment explanation
Indices: 839566--839603 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
839556 ATCCTATTCC
**
839566 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
839586 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
839604 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:839834 original size:17 final size:17
Alignment explanation
Indices: 839814--839852 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
839804 TTAAATTTTT
839814 TTCTTTAAAAAATATCA
1 TTCTTTAAAAAATATCA
839831 TTCTTTAAAAAATATCA
1 TTCTTTAAAAAATATCA
839848 TTCTT
1 TTCTT
839853 ATGTCATTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.41, C:0.13, G:0.00, T:0.46
Consensus pattern (17 bp):
TTCTTTAAAAAATATCA
Found at i:841725 original size:21 final size:21
Alignment explanation
Indices: 841687--841726 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
841677 AAAAAATTAT
*
841687 CTAAAACACTATTATTTTTAC
1 CTAAAACACTAATATTTTTAC
* *
841708 CTAAAACATTAATGTTTTT
1 CTAAAACACTAATATTTTT
841727 TAACATTTCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.45
Consensus pattern (21 bp):
CTAAAACACTAATATTTTTAC
Found at i:841819 original size:81 final size:81
Alignment explanation
Indices: 841728--841878 Score: 232
Period size: 81 Copynumber: 1.9 Consensus size: 81
841718 AATGTTTTTT
* * *
841728 AACATTTCTGGTAAAGTGTCCAATATTAATATTTCCGGTAGAAAA-AATAATATTTTAGGTAATG
1 AACATTTCTGGTAAAATGTCCAATAATAATATTTCCGGTA-AAAATAATAATATTTTAGATAATG
841792 TTTTACCGTATATGTTA
65 TTTTACCGTATATGTTA
* * *
841809 AACATTTCTGGTAAAATGTCCAATAATAATATTTTCGGTAAAAATAATAATGTTTTAGATAATTT
1 AACATTTCTGGTAAAATGTCCAATAATAATATTTCCGGTAAAAATAATAATATTTTAGATAATGT
841874 TTTAC
66 TTTAC
841879 AGGAAATGTT
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
80 4 0.06
81 59 0.94
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (81 bp):
AACATTTCTGGTAAAATGTCCAATAATAATATTTCCGGTAAAAATAATAATATTTTAGATAATGT
TTTACCGTATATGTTA
Found at i:860452 original size:29 final size:29
Alignment explanation
Indices: 860409--860486 Score: 111
Period size: 29 Copynumber: 2.7 Consensus size: 29
860399 TAAATTGATA
*
860409 TCATTGCTTATATCATTTAAGTAAAAATG
1 TCATTGCTTACATCATTTAAGTAAAAATG
* **
860438 TCATTGCTTGCATCATTTAAGTAATGATG
1 TCATTGCTTACATCATTTAAGTAAAAATG
860467 TCATTGCTTACATCAATTTA
1 TCATTGCTTACATC-ATTTA
860487 GTTAGGTGAG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 38 0.88
30 5 0.12
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (29 bp):
TCATTGCTTACATCATTTAAGTAAAAATG
Found at i:863916 original size:108 final size:108
Alignment explanation
Indices: 863697--863893 Score: 295
Period size: 108 Copynumber: 1.8 Consensus size: 108
863687 TGTTTCGGGG
* * * *
863697 ATTTTTAATCAGACAAATGAATTATTCATTTGCATTTAGTAACAAATTATTGATAGCAACTCTAT
1 ATTTTTAATCAAACAAATGAATTATTCATTTACATTTAGCAACAAATTATTGATAACAACTCTAT
** * *
863762 TTAATTAAATATTCCTAAAACTTCTCTGGATAATGAATTATTA
66 TTAATTAAATATTCCTAAAACAACTCAGGATAATGAATTAATA
* * *
863805 ATTTTTAATCAAACAAATGAATTATTCATTTATATTTAGCAACAAATTATTGATAATAACTTTAT
1 ATTTTTAATCAAACAAATGAATTATTCATTTACATTTAGCAACAAATTATTGATAACAACTCTAT
863870 TTAATTAAATATTCCTAAAACAAC
66 TTAATTAAATATTCCTAAAACAAC
863894 CAAGTTTAAG
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
108 80 1.00
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.41
Consensus pattern (108 bp):
ATTTTTAATCAAACAAATGAATTATTCATTTACATTTAGCAACAAATTATTGATAACAACTCTAT
TTAATTAAATATTCCTAAAACAACTCAGGATAATGAATTAATA
Found at i:865130 original size:39 final size:39
Alignment explanation
Indices: 865087--865164 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
865077 TATTGTTAAA
865087 TTATAT-TACATTAATATGTTAATATATTTAAATAATTAC
1 TTATATAT-CATTAATATGTTAATATATTTAAATAATTAC
** *
865126 TTATATATTTTTTATATGTTAATATATTTAAATAATTAC
1 TTATATATCATTAATATGTTAATATATTTAAATAATTAC
865165 ATTAGGTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
39 34 0.97
40 1 0.03
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.53
Consensus pattern (39 bp):
TTATATATCATTAATATGTTAATATATTTAAATAATTAC
Found at i:877205 original size:21 final size:20
Alignment explanation
Indices: 877177--877219 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
877167 AATAAATCAG
877177 AAATAAAAGGAAAAAAAAAC
1 AAATAAAAGGAAAAAAAAAC
* *
877197 AAATCAAAAGGAGAAAATAAC
1 AAAT-AAAAGGAAAAAAAAAC
877218 AA
1 AA
877220 TAATAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.74, C:0.07, G:0.12, T:0.07
Consensus pattern (20 bp):
AAATAAAAGGAAAAAAAAAC
Found at i:878554 original size:4 final size:4
Alignment explanation
Indices: 878541--878608 Score: 59
Period size: 4 Copynumber: 17.0 Consensus size: 4
878531 GACCTGAAAC
* *
878541 AAAT -AAT AAAT AAAT AAAT GAAA- AAAA AAGAA AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AA-AT AAAT AAAT AAAT AAAT
** *
878589 AAAT GGAT AAAT TAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT
878609 TAATTAAAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
3 6 0.11
4 40 0.75
5 7 0.13
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:878714 original size:35 final size:35
Alignment explanation
Indices: 878644--878928 Score: 255
Period size: 35 Copynumber: 8.1 Consensus size: 35
878634 CAATATATAC
* *
878644 TTTTAAAAAAATAATTTTCAAAAC--TATAATATA
1 TTTTTAAAAACTAATTTTCAAAACTATATAATATA
878677 TTTTTAAAAACTAATTTTCAAAACTATATAATATA
1 TTTTTAAAAACTAATTTTCAAAACTATATAATATA
878712 TTTTTAAAAACTAATTTTCAAAACTATAT-ATATA
1 TTTTTAAAAACTAATTTTCAAAACTATATAATATA
*
878746 TATTTTAAAAACTAATTTTCAAAATTATATAATATA
1 T-TTTTAAAAACTAATTTTCAAAACTATATAATATA
* * * **
878782 TATTTAGAAACTAATTTTCAAAATTATAT-ATACG
1 TTTTTAAAAACTAATTTTCAAAACTATATAATATA
* * *
878816 TTTTTCAAAA-T-GTTTTTAAAAGCTATATATTATATA
1 TTTTTAAAAACTAATTTTCAAAA-CTATATA--ATATA
** * *
878852 TACTTAAAAA-AAAGTTTTCAAAACAATATAATATGTA
1 TTTTTAAAAACTAA-TTTTCAAAACTATATAATA--TA
* * * *
878889 TTTTCAAAAA-T-GTTTTCAAAAATTATATATTATA
1 TTTTTAAAAACTAATTTTC-AAAACTATATAATATA
878923 TATTTT
1 T-TTTT
878929 CGAAATATTT
Statistics
Matches: 207, Mismatches: 31, Indels: 26
0.78 0.12 0.10
Matches are distributed among these distances:
32 8 0.04
33 28 0.14
34 19 0.09
35 102 0.49
36 27 0.13
37 15 0.07
38 8 0.04
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (35 bp):
TTTTTAAAAACTAATTTTCAAAACTATATAATATA
Found at i:878798 original size:105 final size:99
Alignment explanation
Indices: 878612--878891 Score: 285
Period size: 105 Copynumber: 2.7 Consensus size: 99
878602 AATAAATTAA
* *
878612 TTAAAAAC-ATTTTAAAACTATACAATATATACTTTTAAAAAAATAATTTTCAAAACTATAATAT
1 TTAAAAACTATTTTAAAACTATA-TATATATA-TTTT--AAAAATAATTTTCAAAAATATAATAT
* *
878676 ATTTTTAAAAACTAATTTTCAAAACTATATAATATATTT
62 ATATTTAAAAACTAATTTTCAAAACTATAT-ATACATTT
878715 TTAAAAACTAATTTTCAAAACTATATATATATATTTTAAAAACTAATTTTCAAAATTATATAATA
1 TTAAAAACT-ATTTT-AAAACTATATATATATATTTTAAAAA-TAATTTTCAAAA--ATATAATA
* * *
878780 TATATTTAGAAACTAATTTTCAAAATTATATATACGTTT
61 TATATTTAAAAACTAATTTTCAAAACTATATATACATTT
* * * *
878819 TTCAAAA-TGTTTTTAAAAGCTATATATTATATATACTTAAAAAAAAGTTTTCAAAACAATATAA
1 TTAAAAACT-ATTTTAAAA-CTATATA-TATATAT-TTTAAAAATAA-TTTTC-AAA-AATATAA
*
878883 TATGTATTT
59 TATATATTT
878892 TCAAAAATGT
Statistics
Matches: 152, Mismatches: 13, Indels: 22
0.81 0.07 0.12
Matches are distributed among these distances:
102 9 0.06
103 32 0.21
104 25 0.16
105 73 0.48
106 12 0.08
107 1 0.01
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (99 bp):
TTAAAAACTATTTTAAAACTATATATATATATTTTAAAAATAATTTTCAAAAATATAATATATAT
TTAAAAACTAATTTTCAAAACTATATATACATTT
Found at i:879714 original size:81 final size:81
Alignment explanation
Indices: 879614--880263 Score: 644
Period size: 81 Copynumber: 7.9 Consensus size: 81
879604 AAGTTGAATA
* * *
879614 TAATCGAACTCGAAGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTG
*
879679 CCCTCGAAGCTGAGTG
66 CCCTTGAAGCTGAGTG
* * *
879695 TAATCGAACTTGGGGGTCTTTGGCAGATAGCTCTTCTCGACTTAAGCTATACTGCAAATGATGTG
1 TAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTG
*
879760 -CCTTGGAGCTGAGTG
66 CCCTTGAAGCTGAGTG
* * * * * * * *
879775 TAGTCGAACTCGAAGGTCTTGGTGGGCAGATAGCCCTTCTGGCCTTGAGCTATGCTGTAAATAAT
1 TAATCGAACTCGAGGGTCTT--T-GGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGAT
*
879840 ATGCCCTTGAAGCTGAGTG
63 GTGCCCTTGAAGCTGAGTG
** * ** * *
879859 TAATCGAACTTAAGGGTCTTTAGTTGGCAGATAACCCTTCTTAACTTGAGTTATACTGCAAATGA
1 TAATCGAACTCGAGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGA
**
879924 TGTG-CCTTCGAAGCTGAACG
62 TGTGCCCTT-GAAGCTGAGTG
* * *
879944 TAGTCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTTGACTTAAGCTATTCTGCAAATGATGTG
1 TAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTG
* *
880009 -CCTTGGAGCTGAGCG
66 CCCTTGAAGCTGAGTG
* * * * * * * * * *
880024 TAGTCGAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGAT
1 TAATCGAACTCGAGGGTCTTT-G-G-CAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGAT
*
880089 ATGCCCTTGAAGCTGAGTG
63 GTGCCCTTGAAGCTGAGTG
** * * *
880108 TAATCGAA-TTAAGGGTCTTTAGTTGGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGA
1 TAATCGAACTCGAGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGA
**
880172 TGTG-CCTTCGAAGCTGAACG
62 TGTGCCCTT-GAAGCTGAGTG
* * *
880192 TAGTCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATATG
1 TAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTG
*
880257 CCTTTGA
66 CCCTTGA
880264 GCGTAGTCGA
Statistics
Matches: 471, Mismatches: 78, Indels: 40
0.80 0.13 0.07
Matches are distributed among these distances:
80 57 0.12
81 148 0.31
82 5 0.01
83 83 0.18
84 104 0.22
85 68 0.14
86 3 0.01
87 2 0.00
88 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.30
Consensus pattern (81 bp):
TAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTG
CCCTTGAAGCTGAGTG
Found at i:880237 original size:248 final size:249
Alignment explanation
Indices: 879636--880331 Score: 1118
Period size: 249 Copynumber: 2.8 Consensus size: 249
879626 AAGGTCTTTA
* * * * * ** *
879636 GCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
1 GCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCG
* * * *
879701 AACTTGGGGGTCTTTGGCAGATAGCTCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGG
66 AACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGG
* * * * * *
879766 AGCTGAGTGTAGTCGAACTCGAAGGTC-TTGGTGGGCAGATAGCCCTTCTGGCCTTGAGCTATGC
131 AGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGT-GACAGATAACCCTTCTAGCCTTGAGTTATGC
*
879830 TGTAAATAATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTG
195 TGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTG
* *
879885 GCAGATAACCCTTCTTAACTTGAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCG
1 GCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCG
*
879950 AACTCGAGGGTCTTTGGCAGATAGCCCTTCTTGACTTAAGCTATTCTGCAAATGATGTGCCTTGG
66 AACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGG
880015 AGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCT
131 AGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCT
880080 GTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAA-TTAAGGGTCTTTAGTTG
196 GTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTG
880133 GCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCG
1 GCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCG
*
880198 AACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATATGCCTT--
66 AACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGG
*
880261 ---TGAGCGTAGTCGAACTCAAAGGTCTTTGGTGACAAATAACCCTTCTAGCCTTGAGTTATGCT
131 AGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCT
880323 GTAAATGAT
196 GTAAATGAT
880332 TTGTTTAAAA
Statistics
Matches: 419, Mismatches: 27, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
243 70 0.17
248 141 0.34
249 203 0.48
250 5 0.01
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.30
Consensus pattern (249 bp):
GCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCG
AACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGG
AGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCT
GTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTAGTTG
Found at i:885409 original size:21 final size:20
Alignment explanation
Indices: 885381--885423 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
885371 AATAAATCAG
885381 AAATAAAAGGAAAAAAAAAC
1 AAATAAAAGGAAAAAAAAAC
* *
885401 AAATCAAAAGGAGAAAATAAC
1 AAAT-AAAAGGAAAAAAAAAC
885422 AA
1 AA
885424 TAATAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.74, C:0.07, G:0.12, T:0.07
Consensus pattern (20 bp):
AAATAAAAGGAAAAAAAAAC
Found at i:886762 original size:4 final size:4
Alignment explanation
Indices: 886749--886816 Score: 59
Period size: 4 Copynumber: 17.0 Consensus size: 4
886739 GACCTGAAAC
* *
886749 AAAT -AAT AAAT AAAT AAAT GAAA- AAAA AAGAA AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AA-AT AAAT AAAT AAAT AAAT
** *
886797 AAAT GGAT AAAT TAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT
886817 TAATTAAAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
3 6 0.11
4 40 0.75
5 7 0.13
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:886886 original size:73 final size:69
Alignment explanation
Indices: 886820--887143 Score: 278
Period size: 73 Copynumber: 4.5 Consensus size: 69
886810 AATAAATTAA
* *
886820 TTAAAAAC-ATTTTTAAAACTATACAATATATACTTTTAAAAAAAATAATTTTCAAAACTATATA
1 TTAAAAACAATTTTCAAAACTATATAATATATA--TTT--AAAAAATAATTTTCAAAACTATATA
886884 ATATATTT
62 ATATATTT
* *
886892 TTAAAAACTAATTTTCAAAACTATATAATATATTTTTAAAAACTAATTTTCAAAACTATATAATA
1 TTAAAAAC-AATTTTCAAAACTATATAATATATATTTAAAAAATAATTTTCAAAACTATAT-A-A
886957 TATATATT
63 TATAT-TT
* * * *
886965 TTAAAAACTAATTTTCAAAATTATATAATATATATTTAGAAACTAATTTTCAAAATTATAT-ATA
1 TTAAAAAC-AATTTTCAAAACTATATAATATATATTTAAAAAATAATTTTCAAAACTATATAATA
**
887029 CGTTT
65 TATTT
* ** * * * *
887034 TTCAAAA-TGTTTTTAAAAGCTATATATTATATATACTTAAAAAAAAAGTTTTCAAAACAATATA
1 TTAAAAACAATTTTCAAAA-CTATATA--ATATATATTTAAAAAATAA-TTTTCAAAACTATATA
887098 ATATGTATTT
62 ATA--TATTT
* ** * *
887108 TCAAAAA-TGTTTTCAAAAATTATATATTATATATTT
1 TTAAAAACAATTTTC-AAAACTATATAATATATATTT
887144 TCGAAATATT
Statistics
Matches: 210, Mismatches: 29, Indels: 26
0.79 0.11 0.10
Matches are distributed among these distances:
67 8 0.04
68 6 0.03
69 8 0.04
70 42 0.20
71 14 0.07
72 28 0.13
73 59 0.28
74 41 0.20
75 4 0.02
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.42
Consensus pattern (69 bp):
TTAAAAACAATTTTCAAAACTATATAATATATATTTAAAAAATAATTTTCAAAACTATATAATAT
ATTT
Found at i:886905 original size:35 final size:35
Alignment explanation
Indices: 886820--887144 Score: 277
Period size: 35 Copynumber: 9.1 Consensus size: 35
886810 AATAAATTAA
* *
886820 TTAAAAAC--ATTTTTAAAACTATACAATATATACTT
1 TTAAAAACTAATTTTCAAAACTATATAATATAT--TT
*
886855 TTAAAAAAAATAATTTTCAAAACTATATAATATATTT
1 TT--AAAAACTAATTTTCAAAACTATATAATATATTT
886892 TTAAAAACTAATTTTCAAAACTATATAATATATTT
1 TTAAAAACTAATTTTCAAAACTATATAATATATTT
886927 TTAAAAACTAATTTTCAAAACTATATAATATATATATT
1 TTAAAAACTAATTTTCAAAACTATAT-A-ATATAT-TT
* *
886965 TTAAAAACTAATTTTCAAAATTATATAATATATAT
1 TTAAAAACTAATTTTCAAAACTATATAATATATTT
* * **
887000 TTAGAAACTAATTTTCAAAATTATAT-ATACGTTT
1 TTAAAAACTAATTTTCAAAACTATATAATATATTT
* * * **
887034 TTCAAAA-T-GTTTTTAAAAGCTATATATTATATATAC
1 TTAAAAACTAATTTTCAAAA-CTATATA--ATATATTT
** *
887070 TTAAAAAAAAAGTTTTCAAAACAATATAATATGTATTT
1 TTAAAAACTAA-TTTTCAAAACTATATAATA--TATTT
* * * *
887108 TCAAAAA-T-GTTTTCAAAAATTATATATTATATATT
1 TTAAAAACTAATTTTC-AAAACTATATAATATAT-TT
887143 TT
1 TT
887145 CGAAATATTT
Statistics
Matches: 239, Mismatches: 33, Indels: 36
0.78 0.11 0.12
Matches are distributed among these distances:
32 8 0.03
33 6 0.03
34 13 0.05
35 94 0.39
36 31 0.13
37 16 0.07
38 42 0.18
39 29 0.12
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.42
Consensus pattern (35 bp):
TTAAAAACTAATTTTCAAAACTATATAATATATTT
Found at i:886911 original size:13 final size:13
Alignment explanation
Indices: 886890--886984 Score: 51
Period size: 13 Copynumber: 7.6 Consensus size: 13
886880 TATAATATAT
886890 TTTTAAAAACTAA
1 TTTTAAAAACTAA
*
886903 TTTTCAAAACT-A
1 TTTTAAAAACTAA
* * *
886915 -TAT-AATA-TAT
1 TTTTAAAAACTAA
886925 TTTTAAAAACTAA
1 TTTTAAAAACTAA
*
886938 TTTTCAAAACT-A
1 TTTTAAAAACTAA
* *
886950 -TATAATATA-TATA
1 TTTTAA-AAACTA-A
886963 TTTTAAAAACTAA
1 TTTTAAAAACTAA
886976 TTTTCAAAA
1 TTTT-AAAA
886985 TTATATAATA
Statistics
Matches: 59, Mismatches: 13, Indels: 19
0.65 0.14 0.21
Matches are distributed among these distances:
9 1 0.02
10 3 0.05
11 8 0.14
12 7 0.12
13 30 0.51
14 10 0.17
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.42
Consensus pattern (13 bp):
TTTTAAAAACTAA
Found at i:887008 original size:108 final size:106
Alignment explanation
Indices: 886820--887107 Score: 341
Period size: 108 Copynumber: 2.7 Consensus size: 106
886810 AATAAATTAA
* *
886820 TTAAAAAC-ATTTTTAAAACTATACAATATATACT-TTTAAAAAAAATAATTTTCAAAACTATAT
1 TTAAAAACTATTTTTAAAACTATATAATATATA-TATTT-TAAAAAATAATTTTCAAAACTATAT
* *
886883 AATATATTTTTAAAAACTAATTTTCAAAACTATATAATATATTT
64 AATATATATTTAAAAACTAATTTTCAAAACTATAT-ATACATTT
* * *
886927 TTAAAAACTAATTTTCAAAACTATATAATATATATATTTTAAAAACTAATTTTCAAAATTATATA
1 TTAAAAACT-ATTTTTAAAACTATATAATATATATATTTTAAAAAATAATTTTCAAAACTATATA
* * *
886992 ATATATATTTAGAAACTAATTTTCAAAATTATATATACGTTT
65 ATATATATTTAAAAACTAATTTTCAAAACTATATATACATTT
* * * * * *
887034 TTCAAAA-TGTTTTTAAAAGCTATATATTATATATA-CTTAAAAAAAAAGTTTTCAAAACAATAT
1 TTAAAAACTATTTTTAAAA-CTATATAATATATATATTTTAAAAAATAA-TTTTCAAAACTATAT
*
887097 AATATGTATTT
64 AATATATATTT
887108 TCAAAAATGT
Statistics
Matches: 156, Mismatches: 20, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
105 17 0.11
106 39 0.25
107 20 0.13
108 55 0.35
109 25 0.16
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.42
Consensus pattern (106 bp):
TTAAAAACTATTTTTAAAACTATATAATATATATATTTTAAAAAATAATTTTCAAAACTATATAA
TATATATTTAAAAACTAATTTTCAAAACTATATATACATTT
Found at i:888017 original size:2 final size:2
Alignment explanation
Indices: 888010--888049 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
888000 TTAATGTATT
888010 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
888050 ACGAGATTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:889298 original size:2 final size:2
Alignment explanation
Indices: 889291--889320 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
889281 AAATTGAATC
889291 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
889321 GATTCTTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:889469 original size:21 final size:23
Alignment explanation
Indices: 889425--889472 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
889415 CGTATAATTA
*
889425 TAAATTAATTAAAAATTTAAAGG
1 TAAATTAATTAAAAATTAAAAGG
*
889448 TAAATT-ATTTAAAA-TAAAAGG
1 TAAATTAATTAAAAATTAAAAGG
889469 TAAA
1 TAAA
889473 CTGTAAATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 10 0.43
22 7 0.30
23 6 0.26
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.33
Consensus pattern (23 bp):
TAAATTAATTAAAAATTAAAAGG
Found at i:890566 original size:21 final size:22
Alignment explanation
Indices: 890540--890590 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
890530 GGTCATTGAC
*
890540 ATAATTTACTTTT-TATTTTAA
1 ATAATTTACTTTTAAATTTTAA
890561 ATAATTTACTTTTAAATTTTAA
1 ATAATTTACTTTTAAATTTTAA
*
890583 CTAATTTA
1 ATAATTTA
890591 TAATTAAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 13 0.48
22 14 0.52
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (22 bp):
ATAATTTACTTTTAAATTTTAA
Found at i:890597 original size:22 final size:22
Alignment explanation
Indices: 890540--890598 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
890530 GGTCATTGAC
**
890540 ATAATTTACT-TTTTATTTTAA
1 ATAATTTACTATTAAATTTTAA
*
890561 ATAATTTACTTTTAAATTTTAA
1 ATAATTTACTATTAAATTTTAA
*
890583 CTAATTTA-TAATTAAA
1 ATAATTTACT-ATTAAA
890599 CTTGACTCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 11 0.34
22 21 0.66
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (22 bp):
ATAATTTACTATTAAATTTTAA
Found at i:891593 original size:35 final size:35
Alignment explanation
Indices: 891554--891626 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
891544 AAACTTTTAA
891554 ACAGGTCAGGCCTAAATAAAAGCCTTTGACAGGCC
1 ACAGGTCAGGCCTAAATAAAAGCCTTTGACAGGCC
891589 ACAGGTCAGGCCTAAATAAAAGCCTTTGACAGGCC
1 ACAGGTCAGGCCTAAATAAAAGCCTTTGACAGGCC
891624 ACA
1 ACA
891627 TGCCAGGCTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.26, G:0.22, T:0.16
Consensus pattern (35 bp):
ACAGGTCAGGCCTAAATAAAAGCCTTTGACAGGCC
Found at i:892052 original size:5 final size:5
Alignment explanation
Indices: 892042--892069 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
892032 TGCCAAAGGA
892042 AAAAG AAAAG AAAAG AAAAG AAAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAA
892070 GGATGGACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:894246 original size:15 final size:15
Alignment explanation
Indices: 894226--894255 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
894216 TGTCTGTCTG
*
894226 GGGTGCTGCTGGTTC
1 GGGTGCCGCTGGTTC
894241 GGGTGCCGCTGGTTC
1 GGGTGCCGCTGGTTC
894256 CATTGGCAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.23, G:0.47, T:0.30
Consensus pattern (15 bp):
GGGTGCCGCTGGTTC
Found at i:900978 original size:50 final size:51
Alignment explanation
Indices: 900853--900978 Score: 134
Period size: 50 Copynumber: 2.5 Consensus size: 51
900843 GTAGCAGTAA
* * * * * *
900853 AGCGAGCCCCCTGAACCGC-TCTATACGCTGATTTGGCGCCACGTTGGTAT
1 AGCGCGCCCCCTGATCCGCGTATATACGCTGATCTGGCGCAACGTGGGTAT
** *
900903 AGCGCATCCCCTG-TCC-CGTGATATACGGTGATCTGGCGCAACGTGGGTAT
1 AGCGCGCCCCCTGATCCGCGT-ATATACGCTGATCTGGCGCAACGTGGGTAT
900953 AGCGCGCCCCCTGATCCGCGT-TATAC
1 AGCGCGCCCCCTGATCCGCGTATATAC
900979 ATGGGTATCT
Statistics
Matches: 61, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
48 1 0.02
49 3 0.05
50 51 0.84
51 3 0.05
52 3 0.05
ACGTcount: A:0.17, C:0.33, G:0.27, T:0.23
Consensus pattern (51 bp):
AGCGCGCCCCCTGATCCGCGTATATACGCTGATCTGGCGCAACGTGGGTAT
Found at i:901115 original size:10 final size:10
Alignment explanation
Indices: 901100--901140 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
901090 TTCTATCACA
901100 TCAAATTCTC
1 TCAAATTCTC
901110 TCAAATTCTC
1 TCAAATTCTC
901120 T-AAATTTCTC
1 TCAAA-TTCTC
*
901130 TCAAATACTC
1 TCAAATTCTC
901140 T
1 T
901141 ATCTTTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 22 0.79
11 3 0.11
ACGTcount: A:0.32, C:0.27, G:0.00, T:0.41
Consensus pattern (10 bp):
TCAAATTCTC
Found at i:901461 original size:111 final size:111
Alignment explanation
Indices: 901267--901599 Score: 567
Period size: 111 Copynumber: 3.0 Consensus size: 111
901257 TGGAAATCAT
* * *
901267 ATATCTCTACACTTTGTTGATACGGTAACATTTTAACGGTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
901332 TATTTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
901378 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* *
901443 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAAAAATAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
* * *
901489 ATATCTTGATACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* *
901554 TAATTAGTTGATTTATTTAATGCATGATCATTAGAGTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
901600 TTTTTGTAAT
Statistics
Matches: 209, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
111 209 1.00
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.44
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:904522 original size:51 final size:51
Alignment explanation
Indices: 904462--904575 Score: 183
Period size: 51 Copynumber: 2.2 Consensus size: 51
904452 CCCCTACGTG
904462 GCGTATAGCGCGGAGCAGGGGGCGCGCTATACCCCACGTGTAACCCAATCA
1 GCGTATAGCGCGGAGCAGGGGGCGCGCTATACCCCACGTGTAACCCAATCA
* * * *
904513 GCGTATAGCGTGGAGCAGGGGGTGCGTTATACCCCACGTGTAACCCAGTCA
1 GCGTATAGCGCGGAGCAGGGGGCGCGCTATACCCCACGTGTAACCCAATCA
*
904564 GCGTATAACGCG
1 GCGTATAGCGCG
904576 ATACAGGGGA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 57 1.00
ACGTcount: A:0.23, C:0.28, G:0.32, T:0.17
Consensus pattern (51 bp):
GCGTATAGCGCGGAGCAGGGGGCGCGCTATACCCCACGTGTAACCCAATCA
Found at i:904583 original size:51 final size:51
Alignment explanation
Indices: 904477--904602 Score: 148
Period size: 51 Copynumber: 2.5 Consensus size: 51
904467 TAGCGCGGAG
* * *
904477 CAGGGGGCGCGCTATACCCCACGTGTAACCCAATCAGCGTATAGCGTGGAG
1 CAGGGGGCGCGCTATACCCCACGTGTAACCCAATCAGCGTATAACGTCGAA
* * *
904528 CAGGGGGTGCGTTATACCCCACGTGTAACCCAGTCAGCGTATAACG-CGATA
1 CAGGGGGCGCGCTATACCCCACGTGTAACCCAATCAGCGTATAACGTCGA-A
* * *
904579 CA-GGGGAGAGCTATACTCCACGTG
1 CAGGGGGCGCGCTATACCCCACGTG
904603 ACGCCAAATC
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
50 20 0.31
51 44 0.69
ACGTcount: A:0.25, C:0.28, G:0.30, T:0.17
Consensus pattern (51 bp):
CAGGGGGCGCGCTATACCCCACGTGTAACCCAATCAGCGTATAACGTCGAA
Found at i:907297 original size:21 final size:22
Alignment explanation
Indices: 907264--907308 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
907254 AAGATTTTTT
907264 TATTTTTATATTATT-AAAATA
1 TATTTTTATATTATTAAAAATA
907285 TATTCTTTA-ATTATTAAAAATA
1 TATT-TTTATATTATTAAAAATA
907307 TA
1 TA
907309 AAATTATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TATTTTTATATTATTAAAAATA
Found at i:907315 original size:17 final size:18
Alignment explanation
Indices: 907293--907326 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
907283 TATATTCTTT
907293 AATTATTA-AAAATATAA
1 AATTATTATAAAATATAA
907310 AATTATTATAAAATATA
1 AATTATTATAAAATATA
907327 TTAATTTAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTATTATAAAATATAA
Found at i:915874 original size:2 final size:2
Alignment explanation
Indices: 915867--915899 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
915857 ACTAGCAACA
915867 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 A
915900 AACGGTGAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:917126 original size:2 final size:2
Alignment explanation
Indices: 917108--917169 Score: 101
Period size: 2 Copynumber: 32.0 Consensus size: 2
917098 AGCACATTAG
*
917108 TA TA TA T- TA CA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
917148 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
917170 ACTAACTATA
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
1 2 0.04
2 54 0.96
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:917546 original size:21 final size:21
Alignment explanation
Indices: 917520--917559 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
917510 CATCGGGCTT
917520 CAACACCCTCACCATCTCCCC
1 CAACACCCTCACCATCTCCCC
*
917541 CAACACCCTCACCCTCTCC
1 CAACACCCTCACCATCTCC
917560 GCCGCCGCCT
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:0.23, C:0.62, G:0.00, T:0.15
Consensus pattern (21 bp):
CAACACCCTCACCATCTCCCC
Found at i:919311 original size:29 final size:28
Alignment explanation
Indices: 919269--919352 Score: 107
Period size: 29 Copynumber: 2.9 Consensus size: 28
919259 AGCAACGTGG
919269 GTAGGTCT-CCAGGGAATCCCAGCGACATT
1 GTAGGT-TGCCAGGG-ATCCCAGCGACATT
919298 GTAGGTTGCCAGGGCATCCCAGCGACATT
1 GTAGGTTGCCAGGG-ATCCCAGCGACATT
* *
919327 GTAGGTCGCCAAGGGATCCCAACGAC
1 GTAGGTTGCC-AGGGATCCCAGCGAC
919353 CTATGCCTTC
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
28 1 0.02
29 45 0.90
30 4 0.08
ACGTcount: A:0.24, C:0.29, G:0.30, T:0.18
Consensus pattern (28 bp):
GTAGGTTGCCAGGGATCCCAGCGACATT
Found at i:919443 original size:15 final size:15
Alignment explanation
Indices: 919423--919455 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
919413 CACGATCATT
919423 CTCATGCACACGACC
1 CTCATGCACACGACC
919438 CTCATGCACACGACC
1 CTCATGCACACGACC
919453 CTC
1 CTC
919456 CTGAGCAGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.48, G:0.12, T:0.15
Consensus pattern (15 bp):
CTCATGCACACGACC
Found at i:923765 original size:117 final size:112
Alignment explanation
Indices: 923551--923843 Score: 393
Period size: 117 Copynumber: 2.6 Consensus size: 112
923541 AAGCGTTGGA
923551 TTGAACAAGTTCTTCTCATTATGAACTTCTTCT-CTCTTGTTGGATGAGTTCTTCTCATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTC-T-TTGGATGAGTTCTTCTCATTATGAA
923615 CTCTTCACTGAAAATGTTGATCCACCTCCTTCTGTGATGAAATCAAACCAAGG
64 CTCTTCACTGAAAATGTTGATCCACCTCCTTCTGTGATGAAAT-AAA--AA-G
923668 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTTGGATGAGTTCTTCTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTC-TCCTCTTTGGATGAGTTCTTCTCATTATGAAC
* * * * **
923733 TCTTCACTGAAAATGTTGATCCATCTCTTTCTGTGATGGACTTGAAAG
65 TCTTCACTGAAAATGTTGATCCACCTCCTTCTGTGATGAAATAAAAAG
* *
923781 --GAACAAGTTCTTCTCATTATAAAC-T-TTC-CC-CTTTAGGACGAGTTCTTCTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTCTTT-GGATGAGTTCTTCTCATTATGAAC
923840 TCTT
65 TCTT
923844 AATTAAAAAT
Statistics
Matches: 165, Mismatches: 8, Indels: 16
0.87 0.04 0.08
Matches are distributed among these distances:
106 4 0.02
107 29 0.18
109 3 0.02
110 1 0.01
111 23 0.14
113 1 0.01
114 2 0.01
116 1 0.01
117 96 0.58
118 2 0.01
119 3 0.02
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.40
Consensus pattern (112 bp):
TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTCTTTGGATGAGTTCTTCTCATTATGAACT
CTTCACTGAAAATGTTGATCCACCTCCTTCTGTGATGAAATAAAAAG
Found at i:924281 original size:334 final size:334
Alignment explanation
Indices: 923667--924322 Score: 992
Period size: 334 Copynumber: 2.0 Consensus size: 334
923657 TCAAACCAAG
* * * * *
923667 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTTGGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAAATTATTCTTCCTCGTTGGATGAATTCTTCTCATTATAAA
* *
923732 CTCTTCACTGAAAATGTTGATCCATCTCTTTCTGTGATGGACTTGAAAGGAACAAGTTCTTCTCA
66 CTCTCCACTGAAAATGTTAATCCATCTCTTTCTGTGATGGACTTGAAAGGAACAAGTTCTTCTCA
*
923797 TTATAAACTTTCCCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTAATTAAAAATGTCAATCC
131 TTATAAACTTTCCCCTTTAGGACGAGTTCTTCTCATTATGAACTATTAATTAAAAATGTCAATCC
* * *
923862 CTCAAGCGAGGTGTCACTGATTCAAAATGTCGTGAATCGAGTGATAGGTCGAACAAACTCTTCTC
196 CTCAAGCGAGGTGTCACTGATTCAAAACGCCATGAATCGAGTGATAGGTCGAACAAACTCTTCTC
*
923927 ATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTCTCCATTGGAAACAC
261 ATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATAAACTCTCCATTGGAAACAC
923992 TAATGCGAA
326 TAATGCGAA
* * *
924001 GTTGGACAAGTTTTTCTCATTATGAAATTATTC-TCTCTCGTTGGATGAATTCTTCTTATTATAA
1 GTTGAACAAGTTCTTCTCATTATGAAATTATTCTTC-CTCGTTGGATGAATTCTTCTCATTATAA
* * * * *
924065 ACTCTCCATTGGAAATTTTAATCCATCTCTTTCTTTGATGGATTTGAAAGGAACAAGTTCTTCTC
65 ACTCTCCACTGAAAATGTTAATCCATCTCTTTCTGTGATGGACTTGAAAGGAACAAGTTCTTCTC
* * * ** **
924130 ATTATGAACTTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTATT-CTCTGGAAATGTTGAT
130 ATTATAAACTTTCCCCTTTAGGACGAGTTCTTCTCATTATGAACTATTAAT-TAAAAATGTCAAT
* * **
924194 CCCTCAAGCGAGGTGTCACTGATTCGAAACGCCATGAATCGAGTGATAGGTCGAATAGGCTCTTC
194 CCCTCAAGCGAGGTGTCACTGATTCAAAACGCCATGAATCGAGTGATAGGTCGAACAAACTCTTC
*
924259 TCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATAAACTCTTCATTGGAAA
259 TCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATAAACTCTCCATTGGAAA
924323 TGTTGATCAA
Statistics
Matches: 288, Mismatches: 32, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
333 3 0.01
334 285 0.99
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (334 bp):
GTTGAACAAGTTCTTCTCATTATGAAATTATTCTTCCTCGTTGGATGAATTCTTCTCATTATAAA
CTCTCCACTGAAAATGTTAATCCATCTCTTTCTGTGATGGACTTGAAAGGAACAAGTTCTTCTCA
TTATAAACTTTCCCCTTTAGGACGAGTTCTTCTCATTATGAACTATTAATTAAAAATGTCAATCC
CTCAAGCGAGGTGTCACTGATTCAAAACGCCATGAATCGAGTGATAGGTCGAACAAACTCTTCTC
ATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATAAACTCTCCATTGGAAACAC
TAATGCGAA
Found at i:925244 original size:20 final size:20
Alignment explanation
Indices: 925204--925244 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
925194 CCTTTTTCTA
* *
925204 TTTTTCTTTTTTTTCTCTTT
1 TTTTTCTTCTTTTTATCTTT
925224 TTTTTCTTCTTTTTAT-TTT
1 TTTTTCTTCTTTTTATCTTT
925243 TT
1 TT
925245 CATTTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.85
Consensus pattern (20 bp):
TTTTTCTTCTTTTTATCTTT
Found at i:925253 original size:11 final size:11
Alignment explanation
Indices: 925204--925254 Score: 57
Period size: 11 Copynumber: 4.4 Consensus size: 11
925194 CCTTTTTCTA
925204 TTTTTCTTTTT
1 TTTTTCTTTTT
*
925215 TTTCTCTTTTT
1 TTTTTCTTTTT
925226 TTTCTTCTTTTTAT
1 TTT-TTC-TTTT-T
*
925240 TTTTTCATTTT
1 TTTTTCTTTTT
925251 TTTT
1 TTTT
925255 CAAGCATAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
11 18 0.53
12 5 0.15
13 7 0.21
14 4 0.12
ACGTcount: A:0.04, C:0.12, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:941158 original size:15 final size:15
Alignment explanation
Indices: 941103--941158 Score: 55
Period size: 15 Copynumber: 3.8 Consensus size: 15
941093 TACACTATTG
*
941103 TTAA-ATTATATTAGG
1 TTAAGATTATATTA-A
*
941118 TTAATATT-TA-TAA
1 TTAAGATTATATTAA
941131 TTAAGACTTATATTAA
1 TTAAGA-TTATATTAA
941147 TTAAGATTATAT
1 TTAAGATTATAT
941159 ATTTTTGATA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
13 5 0.14
14 4 0.11
15 14 0.40
16 12 0.34
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (15 bp):
TTAAGATTATATTAA
Found at i:941957 original size:14 final size:15
Alignment explanation
Indices: 941940--941970 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
941930 TTTAAAAAAT
941940 ATTTTA-TAAATATG
1 ATTTTAGTAAATATG
941954 ATTTTAGTAAATATG
1 ATTTTAGTAAATATG
941969 AT
1 AT
941971 GAGGCAAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (15 bp):
ATTTTAGTAAATATG
Found at i:953346 original size:17 final size:18
Alignment explanation
Indices: 953315--953349 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
953305 AGAAAAGTCA
*
953315 AGAAAGGGGGGCTGATGG
1 AGAAAGGGGGCCTGATGG
953333 AGAAA-GGGGCCTGATGG
1 AGAAAGGGGGCCTGATGG
953350 GTCAAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.29, C:0.09, G:0.51, T:0.11
Consensus pattern (18 bp):
AGAAAGGGGGCCTGATGG
Found at i:956705 original size:14 final size:16
Alignment explanation
Indices: 956673--956713 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 16
956663 GTCATAATGT
*
956673 AAAAAAGACTATATCC
1 AAAAAATACTATATCC
956689 AAAAAATAC-ATAT-C
1 AAAAAATACTATATCC
*
956703 AAATAATACTA
1 AAAAAATACTA
956714 GGATAAGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 9 0.41
15 5 0.23
16 8 0.36
ACGTcount: A:0.61, C:0.15, G:0.02, T:0.22
Consensus pattern (16 bp):
AAAAAATACTATATCC
Found at i:956939 original size:59 final size:58
Alignment explanation
Indices: 956824--956945 Score: 145
Period size: 59 Copynumber: 2.1 Consensus size: 58
956814 ATGTGACTAT
* * * * ** *
956824 TTTGTAACTTTTAATAGTCAGGGACTCAACAAAGCAACGCCTTATAGTTAAAGGACCA
1 TTTGTAACTTTCAATAATCAGGAACTCAACAAAGCAACACCGCATAATTAAAGGACCA
* **
956882 CTTTGTAACTTTCAATAATCAGGAACTCAACAAAGCAATACCGCATAATTAGGGGACCA
1 -TTTGTAACTTTCAATAATCAGGAACTCAACAAAGCAACACCGCATAATTAAAGGACCA
956941 TTTGT
1 TTTGT
956946 GTACTTTACC
Statistics
Matches: 53, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
58 5 0.09
59 48 0.91
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (58 bp):
TTTGTAACTTTCAATAATCAGGAACTCAACAAAGCAACACCGCATAATTAAAGGACCA
Done.