Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008756.1 Hibiscus syriacus cultivar Beakdansim tig00111848_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: 4584045
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 21
Found at i:1156973 original size:13 final size:13
Alignment explanation
Indices: 1156957--1156998 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
1156947 GCAATGAGCA
*
1156957 TCATAAATGTGCG
1 TCATAAATGCGCG
*
1156970 TCATAAATGCGTG
1 TCATAAATGCGCG
1156983 TCATAAATGCGCG
1 TCATAAATGCGCG
1156996 TCA
1 TCA
1156999 AAGATTAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (13 bp):
TCATAAATGCGCG
Found at i:1156973 original size:85 final size:85
Alignment explanation
Indices: 1156764--1156977 Score: 220
Period size: 85 Copynumber: 2.5 Consensus size: 85
1156754 AATGACGTGT
** * * * *
1156764 GCTTCAATGACATGCAATGTAAGTCATACATACGTGTCATAAATTTATGACACACAAATTTATGT
1 GCTTCAATGACGCGCAATGTAAGTCATAAATGCGCGTCATAAATTTATGACACACAAATGTATGT
* *
1156829 CAAGCAGATTTATGATAGGG
66 CAAGCAGATTTATGACAGAG
* * * * *
1156849 GCTTCAATGACGCTCAATGTAAGTCATACATGCGTGTCATAAATTTATGACACACAAATGTGTTT
1 GCTTCAATGACGCGCAATGTAAGTCATAAATGCGCGTCATAAATTTATGACACACAAATGTATGT
*
1156914 C-ATCTTA-ATTTATGACAGAG
66 CAAGC--AGATTTATGACAGAG
* *
1156934 GCTTTAATGACGCGCAATG--AGCATCATAAATGTGCGTCATAAAT
1 GCTTCAATGACGCGCAATGTAAG--TCATAAATGCGCGTCATAAAT
1156978 GCGTGTCATA
Statistics
Matches: 110, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
83 2 0.02
84 2 0.02
85 105 0.95
86 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.31
Consensus pattern (85 bp):
GCTTCAATGACGCGCAATGTAAGTCATAAATGCGCGTCATAAATTTATGACACACAAATGTATGT
CAAGCAGATTTATGACAGAG
Found at i:1156978 original size:26 final size:26
Alignment explanation
Indices: 1156949--1156998 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
1156939 AATGACGCGC
*
1156949 AATGAGCATCATAAATGTGCGTCATA
1 AATGAGCATCATAAATGCGCGTCATA
* **
1156975 AATGCGTGTCATAAATGCGCGTCA
1 AATGAGCATCATAAATGCGCGTCA
1156999 AAGATTAATG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (26 bp):
AATGAGCATCATAAATGCGCGTCATA
Found at i:1161156 original size:37 final size:36
Alignment explanation
Indices: 1161091--1161268 Score: 209
Period size: 37 Copynumber: 4.9 Consensus size: 36
1161081 AAAAAAATTC
* *
1161091 AAAACCATATATTATAT-A-TATTTTAAAATGTTTTT
1 AAAACTATATATTATATAAGT-TTTTAAAATGTTTTA
1161126 AAAACTATATATTATATATA-TTTTTCAAAATGTTTTA
1 AAAACTATATATTATATA-AGTTTTT-AAAATGTTTTA
* ** *
1161163 AAAATTATATATTATATAAGTTTTTCAAAACATCTTA
1 AAAACTATATATTATATAAGTTTTT-AAAATGTTTTA
* * *
1161200 AAAACTATATATCATATAAGTTTTTAAAATGATTTC
1 AAAACTATATATTATATAAGTTTTTAAAATGTTTTA
*
1161236 AAAACTATATATTATATAAGTTTTTAAATTGTT
1 AAAACTATATATTATATAAGTTTTTAAAATGTT
1161269 GCCAAATTAT
Statistics
Matches: 123, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
35 16 0.13
36 41 0.33
37 66 0.54
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (36 bp):
AAAACTATATATTATATAAGTTTTTAAAATGTTTTA
Found at i:1167056 original size:8 final size:8
Alignment explanation
Indices: 1167045--1167098 Score: 58
Period size: 8 Copynumber: 6.6 Consensus size: 8
1167035 GAAAACGTGT
1167045 AAATAATA
1 AAATAATA
1167053 AAATAATA
1 AAATAATA
1167061 AAATAATAA
1 AAATAAT-A
1167070 AAATAA-A
1 AAATAATA
*
1167077 TGAATAATAA
1 -AAATAAT-A
1167087 AAATAA-A
1 AAATAATA
1167094 AAATA
1 AAATA
1167099 TAATATACTA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
7 7 0.17
8 20 0.50
9 12 0.30
10 1 0.03
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (8 bp):
AAATAATA
Found at i:1167073 original size:25 final size:26
Alignment explanation
Indices: 1167045--1167105 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 26
1167035 GAAAACGTGT
1167045 AAATAATA-AAATAAT-AAAATAATAA
1 AAATAATATAAATAATAAAAATAA-AA
*
1167070 AAATAA-ATGAATAATAAAAATAAAA
1 AAATAATATAAATAATAAAAATAAAA
1167095 AATATAATATA
1 AA-ATAATATA
1167106 CTATATAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
24 1 0.03
25 16 0.53
26 11 0.37
27 2 0.07
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.25
Consensus pattern (26 bp):
AAATAATATAAATAATAAAAATAAAA
Found at i:1167074 original size:17 final size:16
Alignment explanation
Indices: 1167045--1167098 Score: 74
Period size: 17 Copynumber: 3.3 Consensus size: 16
1167035 GAAAACGTGT
1167045 AAATAAT-AAAATAATA
1 AAATAATAAAAATAA-A
1167061 AAATAATAAAAATAAA
1 AAATAATAAAAATAAA
*
1167077 TGAATAATAAAAATAAA
1 -AAATAATAAAAATAAA
1167094 AAATA
1 AAATA
1167099 TAATATACTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
16 12 0.35
17 22 0.65
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (16 bp):
AAATAATAAAAATAAA
Found at i:1167186 original size:36 final size:35
Alignment explanation
Indices: 1167118--1167407 Score: 150
Period size: 36 Copynumber: 8.2 Consensus size: 35
1167108 ATATAATATA
* * *
1167118 ATATATTTAAAAAAATTTGTTTAAAAAC-TATATAAT
1 ATATATTTAAAAATA-TT-TTCAAAACCATATATAAT
* *
1167154 ATATATTTCAAAAATATTTTCAAACCCATATATTAT
1 ATATATTT-AAAAATATTTTCAAAACCATATATAAT
*
1167190 ATATATTTTAAAATATTTTCAAAA-C-TATAT-AT
1 ATATATTTAAAAATATTTTCAAAACCATATATAAT
* * *
1167222 A-AT-TTTCAAAATGTTTT-AAAATCATATATTATAT
1 ATATATTTAAAAATATTTTCAAAACCATATA-TA-AT
* * * ** * * *
1167256 ATGTTTTTCAAAACGTTTTAAAAACTATATATCAT
1 ATATATTTAAAAATATTTTCAAAACCATATATAAT
* * *
1167291 ATA-AGTTTTCAAAATGA-TTTCAAAACTATATATTAT
1 ATATA--TTTAAAAAT-ATTTTCAAAACCATATATAAT
* * * *
1167327 ATAAGATTT-AAAATGTTTTCAAAACTATATATTAT
1 AT-ATATTTAAAAATATTTTCAAAACCATATATAAT
* * * *
1167362 ATATTATTTTCAAAAACATTTTAAAAACTATATATTAT
1 ATA-TA-TTT-AAAAATATTTTCAAAACCATATATAAT
1167400 ATATATTT
1 ATATATTT
1167408 TTTCAAAATG
Statistics
Matches: 209, Mismatches: 25, Indels: 40
0.76 0.09 0.15
Matches are distributed among these distances:
29 4 0.02
30 13 0.06
31 6 0.03
32 4 0.02
33 5 0.02
34 5 0.02
35 52 0.25
36 75 0.36
37 18 0.09
38 27 0.13
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.44
Consensus pattern (35 bp):
ATATATTTAAAAATATTTTCAAAACCATATATAAT
Found at i:1167394 original size:38 final size:37
Alignment explanation
Indices: 1167215--1167567 Score: 257
Period size: 36 Copynumber: 9.5 Consensus size: 37
1167205 TTTTCAAAAC
* ** *
1167215 TATATATAATTTTCAAAATGTTTTAAAATC-ATATAT
1 TATATATTATTTTCAAAACATTTTAAAAACTATATAT
*
1167251 TATATATGT-TTTTCAAAACGTTTTAAAAACTATATAT
1 TATATAT-TATTTTCAAAACATTTTAAAAACTATATAT
* * *
1167288 CATATA--AGTTTTCAAAATGA-TTTCAAAACTATATAT
1 TATATATTA-TTTTCAAAA-CATTTTAAAAACTATATAT
** ** *
1167324 TATATAAGA-TTT-AAAATGTTTTCAAAACTATATAT
1 TATATATTATTTTCAAAACATTTTAAAAACTATATAT
1167359 TATATATTATTTTCAAAAACATTTTAAAAACTATATAT
1 TATATATTATTTTC-AAAACATTTTAAAAACTATATAT
* * *
1167397 TATATATATTTTTTCAAAATGA-TTTAAAAACTATATAC
1 TATATAT-TATTTTCAAAA-CATTTTAAAAACTATATAT
* **
1167435 TATATA-TATTTCGTTAAAATGTTTTAAAAAC--TATAT
1 TATATATTATTT--TCAAAACATTTTAAAAACTATATAT
* * *
1167471 TATATATATATATATCAAAACACTTTAAAAACCATATAT
1 TATATAT-TAT-TTTCAAAACATTTTAAAAACTATATAT
*
1167510 TATATA--AGTTTTCAAAATATTTTGAAAAA-TATTATAT
1 TATATATTA-TTTTCAAAACATTTT-AAAAACTA-TATAT
1167547 ATATATATATATGTTTCAAAA
1 -TATATAT-TAT-TTTCAAAA
1167568 ATCATTTGCA
Statistics
Matches: 256, Mismatches: 32, Indels: 53
0.75 0.09 0.16
Matches are distributed among these distances:
35 27 0.11
36 88 0.34
37 36 0.14
38 76 0.30
39 19 0.07
40 1 0.00
41 9 0.04
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (37 bp):
TATATATTATTTTCAAAACATTTTAAAAACTATATAT
Found at i:1167592 original size:2 final size:2
Alignment explanation
Indices: 1167581--1167617 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1167571 ATTTGCAAAC
1167581 TA TA -A 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
1167618 AAATATGGAC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1169003 original size:51 final size:51
Alignment explanation
Indices: 1168927--1169029 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
1168917 AAGATGGATT
1168927 ATCTCTTTCAATTGATCAATACAACAAAGCCTTGGAAAAGAATATCATAAC
1 ATCTCTTTCAATTGATCAATACAACAAAGCCTTGGAAAAGAATATCATAAC
1168978 ATCTCTTTCAATTGATCAATACAACAAAGCCTTGGAAAAGAATATCATAAC
1 ATCTCTTTCAATTGATCAATACAACAAAGCCTTGGAAAAGAATATCATAAC
1169029 A
1 A
1169030 GCAACACACT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.44, C:0.19, G:0.10, T:0.27
Consensus pattern (51 bp):
ATCTCTTTCAATTGATCAATACAACAAAGCCTTGGAAAAGAATATCATAAC
Found at i:1170440 original size:68 final size:69
Alignment explanation
Indices: 1170357--1170495 Score: 181
Period size: 68 Copynumber: 2.0 Consensus size: 69
1170347 CAACTAACAA
* * * * * *
1170357 AAGCTCCATAAAACCTACTGCAGCCAAGACGTAG-AAAATCTAGTCTTCTAATTCCATAACTCTT
1 AAGCTCCATAAAACCTACTACAACCAAGACGTAGAAAAACCTAGGCCTCTAATTCCAGAACTCTT
1170421 TACT
66 TACT
* * *
1170425 AAGCTTCATAAAACCTACTACAACCATGACGTAGAAAAACCTAGGCCTCTAATTCTAGAACTCTT
1 AAGCTCCATAAAACCTACTACAACCAAGACGTAGAAAAACCTAGGCCTCTAATTCCAGAACTCTT
*
1170490 TTCT
66 TACT
1170494 AA
1 AA
1170496 ACCAAAGTTC
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
68 30 0.50
69 30 0.50
ACGTcount: A:0.37, C:0.26, G:0.10, T:0.27
Consensus pattern (69 bp):
AAGCTCCATAAAACCTACTACAACCAAGACGTAGAAAAACCTAGGCCTCTAATTCCAGAACTCTT
TACT
Found at i:1172636 original size:21 final size:21
Alignment explanation
Indices: 1172598--1172637 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1172588 ATTTTGTAAA
1172598 TATTATGAATTATCAATATTT
1 TATTATGAATTATCAATATTT
*
1172619 TATTGATGATTTAT-AATAT
1 TATT-ATGAATTATCAATAT
1172638 AATTTAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.53
Consensus pattern (21 bp):
TATTATGAATTATCAATATTT
Found at i:1172763 original size:45 final size:49
Alignment explanation
Indices: 1172678--1172786 Score: 136
Period size: 45 Copynumber: 2.3 Consensus size: 49
1172668 AGGATTGGAT
* *
1172678 TTATTATTTTATTATGAATTAAGATAGATTTAAAATATTATCTTTAGTTTA
1 TTATTATTTTATTAGGAATTAAGA-AGA-TTAAAACATTATCTTTAGTTTA
* *
1172729 TTATTATTTTATTAGGAATTAAG-A-A-T-AAACATTATGTTTCGTTTA
1 TTATTATTTTATTAGGAATTAAGAAGATTAAAACATTATCTTTAGTTTA
1172774 TTATTATTTTATT
1 TTATTATTTTATT
1172787 CAATAGTTAT
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
45 29 0.54
46 1 0.02
48 1 0.02
49 1 0.02
51 22 0.41
ACGTcount: A:0.35, C:0.03, G:0.08, T:0.54
Consensus pattern (49 bp):
TTATTATTTTATTAGGAATTAAGAAGATTAAAACATTATCTTTAGTTTA
Found at i:1177179 original size:77 final size:77
Alignment explanation
Indices: 1177089--1177245 Score: 296
Period size: 77 Copynumber: 2.0 Consensus size: 77
1177079 GATACCTTTA
*
1177089 ATAAATGAATGATATGTGATTTTGATGAAAATGCCCATTGTATGTACACTGAGAATCATTGGTAT
1 ATAAATGAATGATATATGATTTTGATGAAAATGCCCATTGTATGTACACTGAGAATCATTGGTAT
1177154 AATTGGCATGAC
66 AATTGGCATGAC
*
1177166 ATAAATGAATGATATATGATTTTGATGAAAATGCCCATTGTATGTACACTGAGAATCCTTGGTAT
1 ATAAATGAATGATATATGATTTTGATGAAAATGCCCATTGTATGTACACTGAGAATCATTGGTAT
1177231 AATTGGCATGAC
66 AATTGGCATGAC
1177243 ATA
1 ATA
1177246 GAGGTGGGGT
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
77 78 1.00
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.34
Consensus pattern (77 bp):
ATAAATGAATGATATATGATTTTGATGAAAATGCCCATTGTATGTACACTGAGAATCATTGGTAT
AATTGGCATGAC
Found at i:1187415 original size:22 final size:21
Alignment explanation
Indices: 1187370--1187416 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
1187360 TAGTGGTGTG
*
1187370 AATCTCTAAAAAATGAGTTAA
1 AATCTCTAAAAAATGAGCTAA
*
1187391 AATCTCTAAACAAATGAGCTGA
1 AATCTCTAAA-AAATGAGCTAA
1187413 AATC
1 AATC
1187417 ACTTAGGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.49, C:0.15, G:0.11, T:0.26
Consensus pattern (21 bp):
AATCTCTAAAAAATGAGCTAA
Found at i:1188998 original size:17 final size:17
Alignment explanation
Indices: 1188976--1189008 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1188966 AAAACCTTTT
*
1188976 TGTCATGGTGATGCAAA
1 TGTCATGATGATGCAAA
1188993 TGTCATGATGATGCAA
1 TGTCATGATGATGCAA
1189009 GTGGAAGGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.12, G:0.27, T:0.30
Consensus pattern (17 bp):
TGTCATGATGATGCAAA
Found at i:1190438 original size:16 final size:16
Alignment explanation
Indices: 1190417--1190450 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1190407 CGATTAACGG
*
1190417 ATATTATCTAAAAATA
1 ATATTACCTAAAAATA
1190433 ATATTACCTAAAAATA
1 ATATTACCTAAAAATA
1190449 AT
1 AT
1190451 TTAAAATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (16 bp):
ATATTACCTAAAAATA
Found at i:1208931 original size:2 final size:2
Alignment explanation
Indices: 1208919--1208952 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
1208909 CAAAACAAAC
1208919 AT AT CAT 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
1208953 CACGTACTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1210816 original size:52 final size:52
Alignment explanation
Indices: 1210754--1210854 Score: 157
Period size: 52 Copynumber: 1.9 Consensus size: 52
1210744 AGTGAATATT
* ***
1210754 TGTCCCGAAGGACCATTACGTCCTTTAGGACCACTGGATATGTCCCGAATGA
1 TGTCCCGAAGGACCACTACGTCCCGAAGGACCACTGGATATGTCCCGAATGA
*
1210806 TGTCCCGAAGGACCACTACGTCCCGAATGACCACTGGATATGTCCCGAA
1 TGTCCCGAAGGACCACTACGTCCCGAAGGACCACTGGATATGTCCCGAA
1210855 GGACCATTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.26, C:0.30, G:0.23, T:0.22
Consensus pattern (52 bp):
TGTCCCGAAGGACCACTACGTCCCGAAGGACCACTGGATATGTCCCGAATGA
Found at i:1217686 original size:22 final size:22
Alignment explanation
Indices: 1217652--1217752 Score: 120
Period size: 22 Copynumber: 4.8 Consensus size: 22
1217642 GGACCATTAC
*
1217652 GTCCCTAAGGACCACTGGATAT
1 GTCCCGAAGGACCACTGGATAT
* *
1217674 GTCCCGAATGACCACT--ACA-
1 GTCCCGAAGGACCACTGGATAT
1217693 -TCCCGAAGGACCACTGGATAT
1 GTCCCGAAGGACCACTGGATAT
* *
1217714 ATCTCGAAGGACCACTGGATAT
1 GTCCCGAAGGACCACTGGATAT
*
1217736 GTCCTGAAGGACCACTG
1 GTCCCGAAGGACCACTG
1217753 TAACCCTCGA
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
18 14 0.21
20 4 0.06
22 48 0.73
ACGTcount: A:0.29, C:0.29, G:0.23, T:0.20
Consensus pattern (22 bp):
GTCCCGAAGGACCACTGGATAT
Found at i:1217702 original size:40 final size:40
Alignment explanation
Indices: 1217633--1217729 Score: 140
Period size: 40 Copynumber: 2.4 Consensus size: 40
1217623 AGTGAATATT
* * *
1217633 TGTCTCGAAGGACCATTACGTCCCTAAGGACCACTGGATA
1 TGTCTCGAAGGACCACTACATCCCGAAGGACCACTGGATA
* *
1217673 TGTCCCGAATGACCACTACATCCCGAAGGACCACTGGATA
1 TGTCTCGAAGGACCACTACATCCCGAAGGACCACTGGATA
*
1217713 TATCTCGAAGGACCACT
1 TGTCTCGAAGGACCACT
1217730 GGATATGTCC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (40 bp):
TGTCTCGAAGGACCACTACATCCCGAAGGACCACTGGATA
Found at i:1218403 original size:63 final size:63
Alignment explanation
Indices: 1218287--1218449 Score: 166
Period size: 63 Copynumber: 2.6 Consensus size: 63
1218277 GATGCATCCC
* * * *
1218287 TTAAGGGGTGCATCGATGTACTACCTGTGCATCGGTACACAAATCCCATTCGATGT-TTGAATA
1 TTAAGGGGTGCATCGATGCACTACATGTGCATCGATACACAAATCCCAGTCGATGTATT-AATA
* ** ** * *
1218350 TTAAGGGGTGCATCGATGCACTACTTGTGCATCGATACACTGATGGCAGTCGATGTATTTATT
1 TTAAGGGGTGCATCGATGCACTACATGTGCATCGATACACAAATCCCAGTCGATGTATTAATA
* * * *
1218413 TTAAAGGAGTGCATCAATACACTTCATGTGCATCGAT
1 TT-AAGGGGTGCATCGATGCACTACATGTGCATCGAT
1218450 GCACCTTCAA
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
63 52 0.63
64 31 0.37
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (63 bp):
TTAAGGGGTGCATCGATGCACTACATGTGCATCGATACACAAATCCCAGTCGATGTATTAATA
Found at i:1222192 original size:14 final size:14
Alignment explanation
Indices: 1222173--1222210 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
1222163 GGGGCTGTTG
1222173 TGGATGAATATTGA
1 TGGATGAATATTGA
1222187 TGGATGAATATTGA
1 TGGATGAATATTGA
1222201 TGGATGAATA
1 TGGATGAATA
1222211 CTTTTTGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.37, C:0.00, G:0.29, T:0.34
Consensus pattern (14 bp):
TGGATGAATATTGA
Found at i:1223293 original size:64 final size:64
Alignment explanation
Indices: 1223240--1223403 Score: 229
Period size: 65 Copynumber: 2.5 Consensus size: 64
1223230 CGGTGCACCA
*
1223240 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCTGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
** * **
1223304 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
** * *
1223369 AGAATGCATCGGTGCATGGAATGCATTCGATGTTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTT
1223404 CAATTAATTC
Statistics
Matches: 86, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
64 32 0.37
65 54 0.63
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.30
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:1223392 original size:17 final size:19
Alignment explanation
Indices: 1223354--1223400 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
1223344 ATATTCAGAG
1223354 TGCATCGATGCATGGAGAA
1 TGCATCGATGCATGGAGAA
*
1223373 TGCATCGGTGCAT-G-GAA
1 TGCATCGATGCATGGAGAA
1223390 TGCATTCGATG
1 TGCA-TCGATG
1223401 TTTCAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.28
18 6 0.24
19 12 0.48
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCATGGAGAA
Found at i:1223423 original size:65 final size:62
Alignment explanation
Indices: 1223244--1223450 Score: 204
Period size: 65 Copynumber: 3.2 Consensus size: 62
1223234 GCACCAAGTG
* *
1223244 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGC-CTGAGTGCATCGATGCATGGCTTG
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAT-TCACT-AGTGCATCGATGCATGG--AG
1223308 -
62 A
* *
1223308 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCA-GAGTGCATCGATGCATGGAGA
1 TGCATCGATGCATGAAATGCATTCGATG-TTTG-AAA-ATTCACTAGTGCATCGATGCATGGAG-
1223372 A
62 A
* * * * *
1223373 TGCATCGGTGCATGGAATGCATTCGATGTTTCAATTAATTCACTAATGCATCGATGCATGGTTGA
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAA--AATTCACTAGTGCATCGATGCATGG-AGA
*
1223438 TGCATCGGTGCAT
1 TGCATCGATGCAT
1223451 CACCTCAAAT
Statistics
Matches: 122, Mismatches: 11, Indels: 19
0.80 0.07 0.12
Matches are distributed among these distances:
63 3 0.02
64 35 0.29
65 77 0.63
66 5 0.04
67 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.31
Consensus pattern (62 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTGAAAATTCACTAGTGCATCGATGCATGGAGA
Found at i:1223643 original size:20 final size:21
Alignment explanation
Indices: 1223620--1223659 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1223610 GAATCGAATA
1223620 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
1223640 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
1223660 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:1229889 original size:22 final size:21
Alignment explanation
Indices: 1229847--1229886 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1229837 GAGTTTGTTT
*
1229847 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1229868 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1229887 ACAGTTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1231968 original size:65 final size:65
Alignment explanation
Indices: 1231834--1231994 Score: 193
Period size: 65 Copynumber: 2.5 Consensus size: 65
1231824 TGCACCAAGT
* * * *
1231834 GTGCATCGATGCATGAAATGCATTCGATG-TTTGAAATTAGCCTGAGTGCATCGATGCATGGCTT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAATAGCCAGAGTGCATCAATGCATGGCTA
* **
1231898 GTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCAATGCAT-G-TA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAATAGCCAGAGTGCATCAATGCATGGCTA
* * *
1231961 GAATGCATCGGTGCATGGAATGCATTTGATGTTT
1 G--TGCATCGATGCATGAAATGCATTCGATGTTT
1231995 CAATTAATTC
Statistics
Matches: 83, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
63 2 0.02
64 29 0.35
65 52 0.63
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAATAGCCAGAGTGCATCAATGCATGGCTA
Found at i:1232234 original size:20 final size:21
Alignment explanation
Indices: 1232211--1232250 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1232201 GAATCGAATA
1232211 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
1232231 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
1232251 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:1236382 original size:21 final size:22
Alignment explanation
Indices: 1236358--1236407 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
1236348 ACCAATAAAC
*
1236358 AAAATAAGAAAACAA-AAAGAT
1 AAAAGAAGAAAACAATAAAGAT
*
1236379 AAAAGAAGAAATCAATAAAGA-
1 AAAAGAAGAAAACAATAAAGAT
1236400 AACAAGAA
1 AA-AAGAA
1236408 AATAAAGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.74, C:0.06, G:0.12, T:0.08
Consensus pattern (22 bp):
AAAAGAAGAAAACAATAAAGAT
Found at i:1236802 original size:19 final size:20
Alignment explanation
Indices: 1236778--1236825 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
1236768 GCGAATTTGT
1236778 AATTCGCAACACAG-AGTCA
1 AATTCGCAACACAGAAGTCA
*
1236797 AATTCGCAACACTGAAGTCA
1 AATTCGCAACACAGAAGTCA
1236817 AATTCGCAA
1 AATTCGCAA
1236826 TGTGCGTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.42, C:0.25, G:0.15, T:0.19
Consensus pattern (20 bp):
AATTCGCAACACAGAAGTCA
Found at i:1236998 original size:22 final size:22
Alignment explanation
Indices: 1236973--1237019 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1236963 TCACTCTCTA
* * *
1236973 CGGTGACATCCGTCCCCATCTC
1 CGGTGAAATCCATCCCCATATC
1236995 CGGTGAAATCCATCCCCATATC
1 CGGTGAAATCCATCCCCATATC
1237017 CGG
1 CGG
1237020 CGATCCCCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.19, C:0.40, G:0.19, T:0.21
Consensus pattern (22 bp):
CGGTGAAATCCATCCCCATATC
Found at i:1237392 original size:20 final size:20
Alignment explanation
Indices: 1237369--1237407 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1237359 TTTGAAACTT
*
1237369 AAATTTGCAACACGAAAATG
1 AAATTCGCAACACGAAAATG
*
1237389 AAATTCGTAACACGAAAAT
1 AAATTCGCAACACGAAAAT
1237408 CGCTGCGAAT
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:0.51, C:0.15, G:0.13, T:0.21
Consensus pattern (20 bp):
AAATTCGCAACACGAAAATG
Found at i:1238676 original size:16 final size:16
Alignment explanation
Indices: 1238655--1238697 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
1238645 ACTATCCATT
1238655 ACAGAGACTGACACCC
1 ACAGAGACTGACACCC
*
1238671 ACAGAGGCTGACACCC
1 ACAGAGACTGACACCC
* *
1238687 AAAAAGACTGA
1 ACAGAGACTGA
1238698 GCTTGCCACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.42, C:0.30, G:0.21, T:0.07
Consensus pattern (16 bp):
ACAGAGACTGACACCC
Found at i:1238964 original size:21 final size:21
Alignment explanation
Indices: 1238938--1238987 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
1238928 GTTAGGGGAG
* *
1238938 TTACGTGAAGAGGTCAGTGCT
1 TTACGTGAAGAGATCAGTACT
* *
1238959 TTACGTGATGAGATCGGTACT
1 TTACGTGAAGAGATCAGTACT
1238980 TTACGTGA
1 TTACGTGA
1238988 CGACAATGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.24, C:0.14, G:0.30, T:0.32
Consensus pattern (21 bp):
TTACGTGAAGAGATCAGTACT
Found at i:1239383 original size:21 final size:21
Alignment explanation
Indices: 1239359--1239445 Score: 111
Period size: 21 Copynumber: 4.1 Consensus size: 21
1239349 ACCCCGATCA
1239359 CCTATCATCATTCAAGAGGCC
1 CCTATCATCATTCAAGAGGCC
1239380 CCTATCATCATTCAAGAGGCC
1 CCTATCATCATTCAAGAGGCC
* * *
1239401 CCTCTCACCGTTCAAGAGGCC
1 CCTATCATCATTCAAGAGGCC
* ** *
1239422 CCTCTCATTGTTCAAGAGGTC
1 CCTATCATCATTCAAGAGGCC
1239443 CCT
1 CCT
1239446 CCCACCGTTC
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 60 1.00
ACGTcount: A:0.23, C:0.36, G:0.16, T:0.25
Consensus pattern (21 bp):
CCTATCATCATTCAAGAGGCC
Found at i:1239436 original size:42 final size:42
Alignment explanation
Indices: 1239369--1239460 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
1239359 CCTATCATCA
*
1239369 TTCAAGAGGCCCCTATCATCATTCAAGAGGCCCCTCTCACCG
1 TTCAAGAGGCCCCTATCATCATTCAAGAGGCCCCTCCCACCG
* ** *
1239411 TTCAAGAGGCCCCTCTCATTGTTCAAGAGGTCCCTCCCACCG
1 TTCAAGAGGCCCCTATCATCATTCAAGAGGCCCCTCCCACCG
1239453 TTCAAGAG
1 TTCAAGAG
1239461 CCCTATTCAC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TTCAAGAGGCCCCTATCATCATTCAAGAGGCCCCTCCCACCG
Found at i:1239446 original size:21 final size:21
Alignment explanation
Indices: 1239369--1239460 Score: 121
Period size: 21 Copynumber: 4.4 Consensus size: 21
1239359 CCTATCATCA
* * *
1239369 TTCAAGAGGCCCCTATCATCA
1 TTCAAGAGGCCCCTCTCACCG
1239390 TTCAAGAGGCCCCTCTCACCG
1 TTCAAGAGGCCCCTCTCACCG
**
1239411 TTCAAGAGGCCCCTCTCATTG
1 TTCAAGAGGCCCCTCTCACCG
* *
1239432 TTCAAGAGGTCCCTCCCACCG
1 TTCAAGAGGCCCCTCTCACCG
1239453 TTCAAGAG
1 TTCAAGAG
1239461 CCCTATTCAC
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 62 1.00
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (21 bp):
TTCAAGAGGCCCCTCTCACCG
Found at i:1240922 original size:20 final size:20
Alignment explanation
Indices: 1240897--1240957 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
1240887 TTCGCGTTGC
*
1240897 GATTTTTGCGTTGCGAATTT
1 GATTTTCGCGTTGCGAATTT
*
1240917 GATTTTCGCGTTGCAAATTT
1 GATTTTCGCGTTGCGAATTT
*
1240937 GACTTTCGCGTTGCGAATTT
1 GATTTTCGCGTTGCGAATTT
1240957 G
1 G
1240958 TCTTTCGCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.16, C:0.15, G:0.25, T:0.44
Consensus pattern (20 bp):
GATTTTCGCGTTGCGAATTT
Found at i:1240962 original size:20 final size:20
Alignment explanation
Indices: 1240904--1240965 Score: 90
Period size: 20 Copynumber: 3.1 Consensus size: 20
1240894 TGCGATTTTT
1240904 GCGTTGCGAATTTGAT-TTTC
1 GCGTTGCGAATTTG-TCTTTC
* *
1240924 GCGTTGCAAATTTGACTTTC
1 GCGTTGCGAATTTGTCTTTC
1240944 GCGTTGCGAATTTGTCTTTC
1 GCGTTGCGAATTTGTCTTTC
1240964 GC
1 GC
1240966 AACAATCGCA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.15, C:0.19, G:0.24, T:0.42
Consensus pattern (20 bp):
GCGTTGCGAATTTGTCTTTC
Found at i:1240985 original size:29 final size:29
Alignment explanation
Indices: 1240952--1241023 Score: 99
Period size: 29 Copynumber: 2.5 Consensus size: 29
1240942 TCGCGTTGCG
*
1240952 AATTTGTCTTTCGCAACAATCGCAACGCA
1 AATTTGACTTTCGCAACAATCGCAACGCA
* * **
1240981 AATTTGACTTTCGCAATAATCGCAATGTG
1 AATTTGACTTTCGCAACAATCGCAACGCA
1241010 AATTTGACTTTCGC
1 AATTTGACTTTCGC
1241024 GTAGCGAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.33
Consensus pattern (29 bp):
AATTTGACTTTCGCAACAATCGCAACGCA
Found at i:1241032 original size:20 final size:20
Alignment explanation
Indices: 1240999--1241058 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
1240989 TTTCGCAATA
* *
1240999 ATCGCAATGTGAATTTGACT
1 ATCGCAACGCGAATTTGACT
* *
1241019 TTCGCGTA-GCGAATTTGACT
1 ATCGC-AACGCGAATTTGACT
1241039 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
1241059 CAAGTTACTA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
19 1 0.03
20 31 0.94
21 1 0.03
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.32
Consensus pattern (20 bp):
ATCGCAACGCGAATTTGACT
Found at i:1243680 original size:24 final size:24
Alignment explanation
Indices: 1243653--1243699 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
1243643 CAAAATACAA
1243653 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
1243677 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
1243700 AATACTGACT
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:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:1243708 original size:24 final size:24
Alignment explanation
Indices: 1243657--1243708 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
1243647 ATACAAGTAT
** *
1243657 TGACCAAGATCAAAGTTCGGGTAT
1 TGACCAAGATCAAAGTTCGAATAC
*
1243681 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
1243705 TGAC
1 TGAC
1243709 TAGTACTGAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:1244472 original size:14 final size:15
Alignment explanation
Indices: 1244436--1244473 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1244426 GAAATCATTG
1244436 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
1244451 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
1244466 AAAAATTA
1 AAAAATTA
1244474 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:1244658 original size:20 final size:20
Alignment explanation
Indices: 1244633--1244741 Score: 64
Period size: 20 Copynumber: 5.5 Consensus size: 20
1244623 AAATAAAAGT
1244633 TGTTGCGAAATTAAAATTCG
1 TGTTGCGAAATTAAAATTCG
*
1244653 TGTTGCGAATTTGAAAA-TCG
1 TGTTGCGAAATT-AAAATTCG
* * * *
1244673 AGTTGCG-ATTTAGAAAATCT
1 TGTTGCGAAATTA-AAATTCG
** *
1244693 TGTTGCGAAAAGGAAACTT-G
1 TGTTGCG-AAATTAAAATTCG
*
1244713 TGTTGCGAAA-AAGAAATTCG
1 TGTTGCGAAATTA-AAATTCG
*
1244733 CGTTGCGAA
1 TGTTGCGAA
1244742 TTCAGAAATT
Statistics
Matches: 69, Mismatches: 13, Indels: 14
0.72 0.14 0.15
Matches are distributed among these distances:
18 2 0.03
19 14 0.20
20 44 0.64
21 7 0.10
22 2 0.03
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.30
Consensus pattern (20 bp):
TGTTGCGAAATTAAAATTCG
Found at i:1244680 original size:40 final size:41
Alignment explanation
Indices: 1244634--1244886 Score: 143
Period size: 40 Copynumber: 6.3 Consensus size: 41
1244624 AATAAAAGTT
*
1244634 GTTGCGAAATTA-AAATTCGTGTTGCGAATTTGAAAATCGA
1 GTTGCGAAATTAGAAATTCGCGTTGCGAATTTGAAAATCGA
* * ** *** * * *
1244674 GTTGCG-ATTTAGAAAATCTTGTTGCGAAAAGGAAACTTGT
1 GTTGCGAAATTAGAAATTCGCGTTGCGAATTTGAAAATCGA
* * *
1244714 GTTGCGAAA-AAGAAATTCGCGTTGCGAA-TTCAGAAATTGA
1 GTTGCGAAATTAGAAATTCGCGTTGCGAATTTGA-AAATCGA
* ** * *
1244754 GTTGTG-AATT-GAAATTTCATGTTGCGAATTTGGAAATCGC
1 GTTGCGAAATTAGAAA-TTCGCGTTGCGAATTTGAAAATCGA
1244794 GTTGCGAGAA--AGAAATTCGCGTTGCG-A-TTGCAGAAA-CTGA
1 GTTGCGA-AATTAGAAATTCGCGTTGCGAATTTG-A-AAATC-GA
* * * *
1244834 GTTGCGAATTTGGGAAATTCGCGTTGCGAATTTGGAAA-CTGT
1 GTTGCGAAATT-AGAAATTCGCGTTGCGAATTTGAAAATC-GA
1244876 GTTGCGAAATT
1 GTTGCGAAATT
1244887 GGAGTTCACG
Statistics
Matches: 159, Mismatches: 37, Indels: 32
0.70 0.16 0.14
Matches are distributed among these distances:
38 3 0.02
39 14 0.09
40 98 0.62
41 7 0.04
42 33 0.21
43 1 0.01
44 3 0.02
ACGTcount: A:0.31, C:0.11, G:0.26, T:0.31
Consensus pattern (41 bp):
GTTGCGAAATTAGAAATTCGCGTTGCGAATTTGAAAATCGA
Found at i:1244756 original size:80 final size:80
Alignment explanation
Indices: 1244633--1244884 Score: 246
Period size: 80 Copynumber: 3.1 Consensus size: 80
1244623 AAATAAAAGT
* * * * * *
1244633 TGTTGCGAAATTA-AAATTCGTGTTGCGAATT-TGAAAATCGAGTTGCGATTTAGAAAATCTTGT
1 TGTTGCGAAA-AAGAAATTCGCGTTGCGAATTCAG-AAATTGAGTTGCGATTT-GAAATTCATGT
**
1244696 TGCGAA-AAGGAAACTTG
63 TGCGAATTTGGAAACTTG
* *
1244713 TGTTGCGAAAAAGAAATTCGCGTTGCGAATTCAGAAATTGAGTTGTGAATTGAAATTTCATGTTG
1 TGTTGCGAAAAAGAAATTCGCGTTGCGAATTCAGAAATTGAGTTGCGATTTGAAA-TTCATGTTG
*
1244778 CGAATTTGGAAA-TCG
65 CGAATTTGGAAACTTG
* * * **
1244793 CGTTGCGAGAAAGAAATTCGCGTTGCG-ATTGCAGAAACTGAGTTGCGAATTTGGGAAATTCGCG
1 TGTTGCGAAAAAGAAATTCGCGTTGCGAATT-CAGAAATTGAGTTGCG-ATTT--GAAATTCATG
1244857 TTGCGAATTTGGAAAC-TG
62 TTGCGAATTTGGAAACTTG
1244875 TGTTGCGAAA
1 TGTTGCGAAA
1244885 TTGGAGTTCA
Statistics
Matches: 142, Mismatches: 21, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
79 8 0.06
80 93 0.65
81 9 0.06
82 28 0.20
83 4 0.03
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.31
Consensus pattern (80 bp):
TGTTGCGAAAAAGAAATTCGCGTTGCGAATTCAGAAATTGAGTTGCGATTTGAAATTCATGTTGC
GAATTTGGAAACTTG
Found at i:1244757 original size:20 final size:20
Alignment explanation
Indices: 1244724--1244843 Score: 61
Period size: 20 Copynumber: 6.0 Consensus size: 20
1244714 GTTGCGAAAA
*
1244724 AGAAATTCGCGTTGCGAATTC
1 AGAAATT-GAGTTGCGAATTC
*
1244745 AGAAATTGAGTTGTGAATT-
1 AGAAATTGAGTTGCGAATTC
* *
1244764 -GAAATTTCATGTTGCGAATTT
1 AGAAA-TTGA-GTTGCGAATTC
* * * *
1244785 GGAAATCGCGTTGCGAGA--A
1 AGAAATTGAGTTGCGA-ATTC
*
1244804 AGAAATTCGCGTTGCG-ATTGC
1 AGAAATT-GAGTTGCGAATT-C
*
1244825 AGAAACTGAGTTGCGAATT
1 AGAAATTGAGTTGCGAATT
1244844 TGGGAAATTC
Statistics
Matches: 76, Mismatches: 13, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
18 5 0.07
19 8 0.11
20 41 0.54
21 18 0.24
22 4 0.05
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.30
Consensus pattern (20 bp):
AGAAATTGAGTTGCGAATTC
Found at i:1244881 original size:20 final size:20
Alignment explanation
Indices: 1244826--1244889 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
1244816 TGCGATTGCA
1244826 GAAACTGAGTTGCGAATTTGG
1 GAAACTGAGTTGCGAATTT-G
* *
1244847 GAAATTCGCGTTGCGAATTTG
1 GAAACT-GAGTTGCGAATTTG
* *
1244868 GAAACTGTGTTGCGAAATTG
1 GAAACTGAGTTGCGAATTTG
1244888 GA
1 GA
1244890 GTTCACGTTG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
20 14 0.38
21 11 0.30
22 12 0.32
ACGTcount: A:0.28, C:0.11, G:0.31, T:0.30
Consensus pattern (20 bp):
GAAACTGAGTTGCGAATTTG
Found at i:1245940 original size:24 final size:24
Alignment explanation
Indices: 1245908--1245963 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
1245898 GTTTGAGTAT
1245908 GGAGATGACATGATGACGAAGGAA
1 GGAGATGACATGATGACGAAGGAA
* *
1245932 GGAGATGACATGATGAGGAAGGTA
1 GGAGATGACATGATGACGAAGGAA
*
1245956 GAAGATGA
1 GGAGATGA
1245964 TGGTTTATGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.41, C:0.05, G:0.39, T:0.14
Consensus pattern (24 bp):
GGAGATGACATGATGACGAAGGAA
Found at i:1248857 original size:18 final size:20
Alignment explanation
Indices: 1248816--1248857 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
1248806 TTTCATTTTT
*
1248816 TTCTCTCTTTATCTTTCATT
1 TTCTCTCTTTATCTTTCATC
*
1248836 TTCTCTCTTT-T-TTTCCTC
1 TTCTCTCTTTATCTTTCATC
1248854 TTCT
1 TTCT
1248858 TTTGGAGCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 9 0.45
19 1 0.05
20 10 0.50
ACGTcount: A:0.05, C:0.29, G:0.00, T:0.67
Consensus pattern (20 bp):
TTCTCTCTTTATCTTTCATC
Found at i:1249822 original size:3 final size:3
Alignment explanation
Indices: 1249816--1249872 Score: 53
Period size: 3 Copynumber: 18.7 Consensus size: 3
1249806 TCATTTCATT
** * *
1249816 TTA TTA TTA TTA TTA AAA TTA TTA TTA TATA TTA -TA CATA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA -TTA TTA TTA
1249862 TTA TTA TTA TT
1 TTA TTA TTA TT
1249873 TAATAAATAA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
2 2 0.04
3 39 0.85
4 5 0.11
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:1250746 original size:29 final size:29
Alignment explanation
Indices: 1250714--1250770 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
1250704 CTCTCTTTAG
* *
1250714 AGAGAGAACCCATAATAGAAAATGAGGAA
1 AGAGAGAACCCAGAATAGAAAATAAGGAA
1250743 AGAGAGAACCCAGAATAGAAAATAAGGA
1 AGAGAGAACCCAGAATAGAAAATAAGGA
1250771 TAATGGCCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.56, C:0.11, G:0.25, T:0.09
Consensus pattern (29 bp):
AGAGAGAACCCAGAATAGAAAATAAGGAA
Found at i:1252076 original size:16 final size:15
Alignment explanation
Indices: 1252055--1252096 Score: 52
Period size: 13 Copynumber: 2.9 Consensus size: 15
1252045 TTTCAAAATT
1252055 TTTATTACTTATTATA
1 TTTATTA-TTATTATA
1252071 TTTATTA-TA-TATA
1 TTTATTATTATTATA
*
1252084 TTTTTTATTATTA
1 TTTATTATTATTA
1252097 ATGTTTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
13 10 0.43
14 4 0.17
15 2 0.09
16 7 0.30
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTATTATTATTATA
Found at i:1252105 original size:15 final size:16
Alignment explanation
Indices: 1252071--1252107 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1252061 ACTTATTATA
1252071 TTTATTATATATATTT
1 TTTATTATATATATTT
1252087 TTTATTAT-TA-ATGTT
1 TTTATTATATATAT-TT
1252102 TTTATT
1 TTTATT
1252108 TTATTTTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 2 0.10
15 10 0.50
16 8 0.40
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (16 bp):
TTTATTATATATATTT
Found at i:1256405 original size:2 final size:2
Alignment explanation
Indices: 1256393--1256422 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1256383 ATCCTTTCAA
*
1256393 AT AT AT GT 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
1256423 CCCTTGTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1256730 original size:7 final size:8
Alignment explanation
Indices: 1256711--1256747 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
1256701 TCCATCAAAA
1256711 AAAAAAGG
1 AAAAAAGG
1256719 AAAAAAGG
1 AAAAAAGG
**
1256727 AAAAAAAT
1 AAAAAAGG
1256735 AAAAAAGG
1 AAAAAAGG
1256743 AAAAA
1 AAAAA
1256748 TTGAATCAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (8 bp):
AAAAAAGG
Found at i:1260175 original size:75 final size:75
Alignment explanation
Indices: 1260038--1260218 Score: 220
Period size: 75 Copynumber: 2.4 Consensus size: 75
1260028 GGGGGTATGC
* * * *
1260038 TGAAAACCCATTTCAATCAT-AATCAGGAATATTGACGCATTTTGAATGTTCACGTCAACAAATG
1 TGAAAGCCCATTTCAATCATAAAT-TGGAATATTGACGCATTTTGAACGTTCACATCAACAAATG
1260102 CTGGGACATGA
65 CTGGGACATGA
* * *** * *
1260113 TGAAAGTCCATTTCAATCATAAATTGGAATATTGGCGCATTTTGAACGTTTGTATTAGCAAATGC
1 TGAAAGCCCATTTCAATCATAAATTGGAATATTGACGCATTTTGAACGTTCACATCAACAAATGC
* *
1260178 TGGGGCATGT
66 TGGGACATGA
*
1260188 TGAAAGCCCATTTCAATCAGAAATTGGAATA
1 TGAAAGCCCATTTCAATCATAAATTGGAATA
1260219 ACATTTTGAA
Statistics
Matches: 90, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
75 87 0.97
76 3 0.03
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.30
Consensus pattern (75 bp):
TGAAAGCCCATTTCAATCATAAATTGGAATATTGACGCATTTTGAACGTTCACATCAACAAATGC
TGGGACATGA
Found at i:1260268 original size:71 final size:71
Alignment explanation
Indices: 1260075--1260268 Score: 194
Period size: 75 Copynumber: 2.7 Consensus size: 71
1260065 AATATTGACG
* ** * * * *
1260075 CATTTTGAATGTTCACGTCAACAAATGCTGGGACATGA-TGAAAGTCCATTTCAATCATAAATTG
1 CATTTTGAACGTTCATATCAGCAAATGCTGGGGCAT-ATTGAAAGCCCATTTCAATCAGAAATTG
*
1260139 GAATATTGGCG
65 GAATA---G-A
** * *
1260150 CATTTTGAACGTTTGTATTAGCAAATGCTGGGGCATGTTGAAAGCCCATTTCAATCAGAAATTGG
1 CATTTTGAACGTTCATATCAGCAAATGCTGGGGCATATTGAAAGCCCATTTCAATCAGAAATTGG
1260215 AATA-A
66 AATAGA
* *
1260220 CATTTTGAACGTTCATAATCAGTAAATGCTGGGGCATATTGAAGGCCCA
1 CATTTTGAACGTTCAT-ATCAGCAAATGCTGGGGCATATTGAAAGCCCA
1260269 CATCATTATC
Statistics
Matches: 99, Mismatches: 18, Indels: 8
0.79 0.14 0.06
Matches are distributed among these distances:
70 14 0.14
71 28 0.28
75 57 0.58
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.30
Consensus pattern (71 bp):
CATTTTGAACGTTCATATCAGCAAATGCTGGGGCATATTGAAAGCCCATTTCAATCAGAAATTGG
AATAGA
Found at i:1261224 original size:54 final size:54
Alignment explanation
Indices: 1261120--1261224 Score: 140
Period size: 54 Copynumber: 1.9 Consensus size: 54
1261110 ATGAGAAATG
* *
1261120 TGGGCAAAACATATAGGAAAAGATAAATGTGTTGTCAAATATTTTGCGAACATC
1 TGGGCAAAACATACAGGAAAAGATAAATGTGTTGTCAAATATTTTACGAACATC
* * * *
1261174 TGGGCCAAAAC-TACAGGAAAGGATGAATGTGTTGTCAAGTGTTTTACGAAC
1 TGGG-CAAAACATACAGGAAAAGATAAATGTGTTGTCAAATATTTTACGAAC
1261225 CAATTATGGT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
54 38 0.86
55 6 0.14
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (54 bp):
TGGGCAAAACATACAGGAAAAGATAAATGTGTTGTCAAATATTTTACGAACATC
Found at i:1262326 original size:45 final size:45
Alignment explanation
Indices: 1262262--1262533 Score: 476
Period size: 45 Copynumber: 6.1 Consensus size: 45
1262252 CTATTTCCCA
1262262 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1262307 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1262352 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
1262397 CATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAAACTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
1262442 CATCT-TAAACCCTTCAGTGCATGATGTTATCAAAA-CTTGCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTT-CGGGT
*
1262486 CATCTGTAAGCCCTACAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1262531 CAT
1 CAT
1262534 TCATAAGACC
Statistics
Matches: 218, Mismatches: 6, Indels: 6
0.95 0.03 0.03
Matches are distributed among these distances:
43 3 0.01
44 39 0.18
45 173 0.79
46 3 0.01
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.32
Consensus pattern (45 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
Found at i:1262505 original size:134 final size:135
Alignment explanation
Indices: 1262262--1262533 Score: 476
Period size: 134 Copynumber: 2.0 Consensus size: 135
1262252 CTATTTCCCA
* * *
1262262 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAAACTTCGGGTCATCTGTAAACCCTTCAGTG
* *
1262327 CATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTT
66 CATGATGTTATCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCATGATGTTTTCAAAACCTT
1262392 CGGGT
131 CGGGT
1262397 CATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAAACTTCGGGTCATCT-TAAACCCTTCAGTG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAAACTTCGGGTCATCTGTAAACCCTTCAGTG
1262461 CATGATGTTATCAAAA-CTTGCGGGTCATCTGTAAGCCCTACAGTGCATGATGTTTTCAAAACCT
66 CATGATGTTATCAAAACCTT-CGGGTCATCTGTAAGCCCTACAGTGCATGATGTTTTCAAAACCT
1262525 TCGGGT
130 TCGGGT
1262531 CAT
1 CAT
1262534 TCATAAGACC
Statistics
Matches: 131, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
133 3 0.02
134 80 0.61
135 48 0.37
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.32
Consensus pattern (135 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAAACTTCGGGTCATCTGTAAACCCTTCAGTG
CATGATGTTATCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCATGATGTTTTCAAAACCTT
CGGGT
Found at i:1262699 original size:3 final size:3
Alignment explanation
Indices: 1262693--1262761 Score: 77
Period size: 3 Copynumber: 22.7 Consensus size: 3
1262683 TCATTTCATT
** *
1262693 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA ATA TTA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
*
1262739 -TA CATA TTA TTA TTA TTA TTA TT
1 TTA -TTA TTA TTA TTA TTA TTA TT
1262762 TAATAAATAA
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
2 2 0.04
3 49 0.88
4 5 0.09
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:1263864 original size:45 final size:45
Alignment explanation
Indices: 1263810--1263955 Score: 283
Period size: 45 Copynumber: 3.2 Consensus size: 45
1263800 TTAAATTGTA
1263810 ATTTAGTCACTGCATATACTTATAAATATTTAAGATAAATAACCT
1 ATTTAGTCACTGCATATACTTATAAATATTTAAGATAAATAACCT
1263855 ATTTAGTCACTGCATATACTTATAAATATTTAAGATAAATAACCT
1 ATTTAGTCACTGCATATACTTATAAATATTTAAGATAAATAACCT
1263900 ATTTAGTCACTGCATATACTTATAAATATTTAAGATAAATAACCT
1 ATTTAGTCACTGCATATACTTATAAATATTTAAGATAAATAACCT
*
1263945 ATTTAGCCACT
1 ATTTAGTCACT
1263956 ATTAATTTTA
Statistics
Matches: 100, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
45 100 1.00
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.38
Consensus pattern (45 bp):
ATTTAGTCACTGCATATACTTATAAATATTTAAGATAAATAACCT
Found at i:1264239 original size:16 final size:16
Alignment explanation
Indices: 1264215--1264246 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1264205 TTCAATATAT
*
1264215 TTAATTATTATTATTA
1 TTAAGTATTATTATTA
1264231 TTAAGTATTATTATTA
1 TTAAGTATTATTATTA
1264247 GGTCATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
TTAAGTATTATTATTA
Found at i:1264465 original size:2 final size:2
Alignment explanation
Indices: 1264458--1264491 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1264448 ATATCTTATT
1264458 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1264492 TTTCTTAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1269352 original size:30 final size:31
Alignment explanation
Indices: 1269289--1269355 Score: 127
Period size: 31 Copynumber: 2.2 Consensus size: 31
1269279 ATGCTTCAAA
1269289 TAGGTTTAATTGATCTACCCTTGAATGGGGG
1 TAGGTTTAATTGATCTACCCTTGAATGGGGG
1269320 TAGGTTTAATTGATCTACCCTTGAAT-GGGG
1 TAGGTTTAATTGATCTACCCTTGAATGGGGG
1269350 TAGGTT
1 TAGGTT
1269356 GATGGTCAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 10 0.28
31 26 0.72
ACGTcount: A:0.22, C:0.12, G:0.28, T:0.37
Consensus pattern (31 bp):
TAGGTTTAATTGATCTACCCTTGAATGGGGG
Found at i:1272909 original size:23 final size:21
Alignment explanation
Indices: 1272883--1272924 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
1272873 ATAGACTGAG
*
1272883 TTAGTGTTGTTGTTTATGGTTAT
1 TTAGGGTTGTT-TTT-TGGTTAT
1272906 TTAGGGTTGTTTTTTGGTT
1 TTAGGGTTGTTTTTTGGTT
1272925 TTCTTTTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 3 0.17
23 10 0.56
ACGTcount: A:0.10, C:0.00, G:0.29, T:0.62
Consensus pattern (21 bp):
TTAGGGTTGTTTTTTGGTTAT
Found at i:1277807 original size:24 final size:25
Alignment explanation
Indices: 1277780--1277839 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 25
1277770 TTAAATCAAT
1277780 TTTTAATAATTTAA-TT-TTGTAATA
1 TTTTAATAATTTAATTTATTG-AATA
*
1277804 TTTTTAT-ATTTAATTTATTGAATA
1 TTTTAATAATTTAATTTATTGAATA
*
1277828 TCTTAATAATTT
1 TTTTAATAATTT
1277840 TTTATATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 6 0.20
24 17 0.57
25 7 0.23
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (25 bp):
TTTTAATAATTTAATTTATTGAATA
Found at i:1277877 original size:43 final size:47
Alignment explanation
Indices: 1277770--1277877 Score: 111
Period size: 43 Copynumber: 2.4 Consensus size: 47
1277760 AATGTAATCC
* *
1277770 TTAAATCAATTTTTAATAATTTAATTTTGTAATATTTTTATATTTAAT
1 TTAAATTAATTTTTAATAATTT-ATTTTATAATATTTTTATATTTAAT
* *
1277818 TT--ATTGAATATCTTAATAA-TT-TTTTAT-AT-TTTTTATATTTGAT
1 TTAAATT-AAT-TTTTAATAATTTATTTTATAATATTTTTATATTTAAT
1277861 TTAAATTAATTTTTAAT
1 TTAAATTAATTTTTAAT
1277878 TTTTAAAAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
43 21 0.41
44 5 0.10
45 8 0.16
46 2 0.04
47 5 0.10
48 10 0.20
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (47 bp):
TTAAATTAATTTTTAATAATTTATTTTATAATATTTTTATATTTAAT
Found at i:1279617 original size:20 final size:20
Alignment explanation
Indices: 1279589--1279658 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
1279579 TACTGAAAGG
1279589 GGTATCGATACTATGAGGAA
1 GGTATCGATACTATGAGGAA
* * ** *
1279609 GGCATCGATACCAAAAGG-G
1 GGTATCGATACTATGAGGAA
*
1279628 GGTATCGATACTATGAGAAA
1 GGTATCGATACTATGAGGAA
1279648 GGTATCGATAC
1 GGTATCGATAC
1279659 CATTGATAAC
Statistics
Matches: 38, Mismatches: 11, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
19 13 0.34
20 25 0.66
ACGTcount: A:0.36, C:0.14, G:0.29, T:0.21
Consensus pattern (20 bp):
GGTATCGATACTATGAGGAA
Found at i:1279730 original size:22 final size:22
Alignment explanation
Indices: 1279697--1279778 Score: 98
Period size: 22 Copynumber: 3.9 Consensus size: 22
1279687 CGATATCGTA
1279697 ATAGAA-TATCGATACCATAGT
1 ATAGAAGTATCGATACCATAGT
*
1279718 ATAGTAGTATCGATACCAT-G-
1 ATAGAAGTATCGATACCATAGT
* ** *
1279738 GTAGGGGTATCGATACCAAAGT
1 ATAGAAGTATCGATACCATAGT
1279760 ATAGAAGTATCGATACCAT
1 ATAGAAGTATCGATACCAT
1279779 GGTAGGTGTA
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
20 15 0.31
21 7 0.14
22 27 0.55
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.27
Consensus pattern (22 bp):
ATAGAAGTATCGATACCATAGT
Found at i:1279749 original size:20 final size:20
Alignment explanation
Indices: 1279703--1279795 Score: 78
Period size: 20 Copynumber: 4.5 Consensus size: 20
1279693 CGTAATAGAA
* *
1279703 TATCGATACCATAGTATAGTAG
1 TATCGATACCAT-G-GTAGGAG
*
1279725 TATCGATACCATGGTAGGGG
1 TATCGATACCATGGTAGGAG
* * *
1279745 TATCGATACCAAAGTATAGAAG
1 TATCGATACC-ATG-GTAGGAG
*
1279767 TATCGATACCATGGTAGGTG
1 TATCGATACCATGGTAGGAG
*
1279787 TACCGATAC
1 TATCGATAC
1279796 TATTGAGCCA
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
20 26 0.46
21 5 0.09
22 26 0.46
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (20 bp):
TATCGATACCATGGTAGGAG
Found at i:1279753 original size:42 final size:42
Alignment explanation
Indices: 1279703--1279795 Score: 150
Period size: 42 Copynumber: 2.2 Consensus size: 42
1279693 CGTAATAGAA
* *
1279703 TATCGATACCATAGTATAGTAGTATCGATACCATGGTAGGGG
1 TATCGATACCAAAGTATAGAAGTATCGATACCATGGTAGGGG
*
1279745 TATCGATACCAAAGTATAGAAGTATCGATACCATGGTAGGTG
1 TATCGATACCAAAGTATAGAAGTATCGATACCATGGTAGGGG
*
1279787 TACCGATAC
1 TATCGATAC
1279796 TATTGAGCCA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (42 bp):
TATCGATACCAAAGTATAGAAGTATCGATACCATGGTAGGGG
Found at i:1280162 original size:56 final size:56
Alignment explanation
Indices: 1280099--1280551 Score: 703
Period size: 56 Copynumber: 8.1 Consensus size: 56
1280089 TATGGTGATC
* * * * *
1280099 TCCGTATGGGCACTTTGTGTGAAAAAACTAACAAAATCATAATAATTTTATGAATT
1 TCCGTATGGGCACTTTGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATT
*
1280155 TTCGTAT-GGCACTTTGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATT
1 TCCGTATGGGCACTTTGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATT
*
1280210 TCCGTATGGGCACTTTGTGTGTAAAAACTAAGAAATTCATAATGAGTTTATGAATT
1 TCCGTATGGGCACTTTGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATT
* *
1280266 TCAGTATGGGCACTTTGTGTGCCAAAACTAAGAAATTCATAATGAGTTTATGAATT
1 TCCGTATGGGCACTTTGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATT
* * *
1280322 TCCGTATGGGCACTTTGTGTGCAAAAACTAAGAAATTCATAGTGAGTTTATAAATA
1 TCCGTATGGGCACTTTGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATT
* * *
1280378 CCCGTATGGGCACTTTGAGTGCAAAAAATAAGAAATTCATAATGAGTTTATGAATT
1 TCCGTATGGGCACTTTGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATT
* ** *
1280434 TCCATATGGGCACCGTGTGTGCAAAAACTAAGAAATTCATAATAAGTTTATGAATT
1 TCCGTATGGGCACTTTGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATT
* *
1280490 TCCGTATGGACACTTTGTGTGCAAAAACTAAGAAATTCATAATGAATTT-TGAATT
1 TCCGTATGGGCACTTTGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATT
1280545 TCCGTAT
1 TCCGTAT
1280552 TGGAAGGGTG
Statistics
Matches: 361, Mismatches: 35, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
55 62 0.17
56 299 0.83
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.34
Consensus pattern (56 bp):
TCCGTATGGGCACTTTGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAATT
Found at i:1285479 original size:20 final size:20
Alignment explanation
Indices: 1285454--1285504 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
1285444 ACCCAGACTT
1285454 GGTATTGATACCCTACAGGG
1 GGTATTGATACCCTACAGGG
1285474 GGTATTGATACCCTACAGGG
1 GGTATTGATACCCTACAGGG
*
1285494 GGTATCGATAC
1 GGTATTGATAC
1285505 TACTTTAAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.25
Consensus pattern (20 bp):
GGTATTGATACCCTACAGGG
Found at i:1286071 original size:22 final size:22
Alignment explanation
Indices: 1286041--1286107 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 22
1286031 AGTCGAGGGT
*
1286041 TACATAGGTCATTCGGGACATA
1 TACATAGGTCCTTCGGGACATA
* * *
1286063 TACACAGGTCCTTCAGTACATA
1 TACATAGGTCCTTCGGGACATA
*
1286085 TGCATAGGTCCTTCGGGACATA
1 TACATAGGTCCTTCGGGACATA
1286107 T
1 T
1286108 TTCACATGCC
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.28
Consensus pattern (22 bp):
TACATAGGTCCTTCGGGACATA
Found at i:1290316 original size:22 final size:22
Alignment explanation
Indices: 1290273--1290336 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
1290263 GTTACATAGG
* *
1290273 CCTTCAGGACATATACACAGGT
1 CCTTCGGGACATATTCACAGGT
* *
1290295 TCTTCGGGACATATTCATAGGT
1 CCTTCGGGACATATTCACAGGT
*
1290317 CCTTCGGGATATATTTCACA
1 CCTTCGGGACATA-TTCACA
1290337 TGCCACTCAG
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
22 29 0.85
23 5 0.15
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (22 bp):
CCTTCGGGACATATTCACAGGT
Found at i:1291017 original size:16 final size:17
Alignment explanation
Indices: 1290990--1291022 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1290980 TTTTTAGTAA
1290990 CTTTGTAAAAGTAAATG
1 CTTTGTAAAAGTAAATG
*
1291007 CTTTG-AAAAGTCAATG
1 CTTTGTAAAAGTAAATG
1291023 TGACACCTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.33
Consensus pattern (17 bp):
CTTTGTAAAAGTAAATG
Found at i:1293712 original size:22 final size:21
Alignment explanation
Indices: 1293681--1293762 Score: 85
Period size: 22 Copynumber: 3.9 Consensus size: 21
1293671 TGATACCGTA
* *
1293681 ATAGATTATCGGTACCATAGT
1 ATAGAGTATCGATACCATAGT
*
1293702 ATAGTAGTATCGATACCATGGT
1 ATAG-AGTATCGATACCATAGT
* *
1293724 AGAG-GTATCAATACCATAGT
1 ATAGAGTATCGATACCATAGT
*
1293744 ATAAAAGTATCGATACCAT
1 AT-AGAGTATCGATACCAT
1293763 GGTAGGGGTA
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
20 15 0.31
21 5 0.10
22 29 0.59
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (21 bp):
ATAGAGTATCGATACCATAGT
Found at i:1293737 original size:20 final size:20
Alignment explanation
Indices: 1293708--1293779 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
1293698 TAGTATAGTA
1293708 GTATCGATACCATGGTAGAG
1 GTATCGATACCATGGTAGAG
* * * *
1293728 GTATCAATACCATAGTATAAAA
1 GTATCGATACCAT-G-GTAGAG
*
1293750 GTATCGATACCATGGTAGGG
1 GTATCGATACCATGGTAGAG
*
1293770 GTACCGATAC
1 GTATCGATAC
1293780 AATTGAGCCA
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
20 23 0.57
21 2 0.05
22 15 0.38
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.25
Consensus pattern (20 bp):
GTATCGATACCATGGTAGAG
Found at i:1293740 original size:42 final size:42
Alignment explanation
Indices: 1293693--1293772 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
1293683 AGATTATCGG
**
1293693 TACCATAGTATAGTAGTATCGATACCATGGTAGAGGTATCAA
1 TACCATAGTATAAAAGTATCGATACCATGGTAGAGGTATCAA
*
1293735 TACCATAGTATAAAAGTATCGATACCATGGTAGGGGTA
1 TACCATAGTATAAAAGTATCGATACCATGGTAGAGGTA
1293773 CCGATACAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (42 bp):
TACCATAGTATAAAAGTATCGATACCATGGTAGAGGTATCAA
Found at i:1304157 original size:56 final size:56
Alignment explanation
Indices: 1303856--1304149 Score: 419
Period size: 56 Copynumber: 5.2 Consensus size: 56
1303846 TGTATGGTGA
*
1303856 TTTCTGTATGGGTACTTTGTGTGCAAAAACTAAAAAATTCATAATAAGTTTATGAAT
1 TTTC-GTATGGGTACTTTGTGTGCAAAAACTAAGAAATTCATAATAAGTTTATGAAT
* * * *
1303913 TTCCGTATGGGCACTTTGTGTGCAAAAACCAAGAAATTCATAGTAAGTTTATGAAT
1 TTTCGTATGGGTACTTTGTGTGCAAAAACTAAGAAATTCATAATAAGTTTATGAAT
** * * *
1303969 TTTCGTATGGGTACTTTGTGTATAATAACTAAGAAATTCATAATGACTTTATGAAT
1 TTTCGTATGGGTACTTTGTGTGCAAAAACTAAGAAATTCATAATAAGTTTATGAAT
*
1304025 TTTCGTAT-GGTCATTTTGTGTGCAAAAACTAAGAAATTCATAATAAGTTTATGAAT
1 TTTCGTATGGGT-ACTTTGTGTGCAAAAACTAAGAAATTCATAATAAGTTTATGAAT
* * *
1304081 TTCCGTATGGGCACTTTGTGTGCAAAAACTAAGAAATTCATAATGAGTTTATGAAT
1 TTTCGTATGGGTACTTTGTGTGCAAAAACTAAGAAATTCATAATAAGTTTATGAAT
* *
1304137 TTTTGTATTGGTA
1 TTTCGTATGGGTA
1304150 GGGTGTGTAA
Statistics
Matches: 207, Mismatches: 28, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
55 3 0.01
56 199 0.96
57 5 0.02
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (56 bp):
TTTCGTATGGGTACTTTGTGTGCAAAAACTAAGAAATTCATAATAAGTTTATGAAT
Found at i:1306343 original size:2 final size:2
Alignment explanation
Indices: 1306336--1306371 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1306326 AAGTTAAGCC
1306336 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1306372 TAATATACGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1306428 original size:25 final size:25
Alignment explanation
Indices: 1306400--1306447 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
1306390 TATATTTAAA
*
1306400 CTTATTATACAAACATTAAAAATAT
1 CTTATTATACAAAAATTAAAAATAT
1306425 CTTATTATACAAAAATTAAAAAT
1 CTTATTATACAAAAATTAAAAAT
1306448 TAAAATAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.35
Consensus pattern (25 bp):
CTTATTATACAAAAATTAAAAATAT
Found at i:1306953 original size:30 final size:30
Alignment explanation
Indices: 1306900--1306989 Score: 85
Period size: 31 Copynumber: 2.9 Consensus size: 30
1306890 ACTTGACCCG
* *
1306900 TAAATTTTAGACATAATAT-TAATTTGAGC-T
1 TAAATTTT--ACATAAAATATAATTTGACCAT
*
1306930 TAAATTTTACATAAAATACTAATTTAACCAT
1 TAAATTTTACATAAAATA-TAATTTGACCAT
* *
1306961 TAAACTTTATATAAAATATCAATTTGACC
1 TAAATTTTACATAAAATAT-AATTTGACC
1306990 TTTGAATCCA
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
28 8 0.16
30 17 0.34
31 25 0.50
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.40
Consensus pattern (30 bp):
TAAATTTTACATAAAATATAATTTGACCAT
Found at i:1309768 original size:2 final size:2
Alignment explanation
Indices: 1309761--1309801 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1309751 TTTGAGTGTT
1309761 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1309802 GCTTTACGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1325708 original size:21 final size:22
Alignment explanation
Indices: 1325684--1325727 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
1325674 ATCATCAACC
1325684 CAATCAATCC-AACTTGATCCT
1 CAATCAATCCAAACTTGATCCT
1325705 CAATCAATCCAAACTTGATCCT
1 CAATCAATCCAAACTTGATCCT
1325727 C
1 C
1325728 GAGCCCACAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.34, C:0.34, G:0.05, T:0.27
Consensus pattern (22 bp):
CAATCAATCCAAACTTGATCCT
Found at i:1325846 original size:210 final size:213
Alignment explanation
Indices: 1325584--1326011 Score: 826
Period size: 210 Copynumber: 2.0 Consensus size: 213
1325574 AAATTTTCAA
1325584 ACACCTCTACATACACTTCAAAAAGCCTTTCCCTTATTTCGTGTTCCAAACCTACCAACAAAAAT
1 ACACCTCTACATACACTTCAAAAAGCCTTTCCCTTATTTCGTGTTCCAAACCTACCAACAAAAAT
1325649 ATTTGTTGCAAAACGTTTGTCCACAATCATCAACCCAATCAATCC-AACTTGATCCTCAATCAAT
66 ATTTGTTGCAAAACGTTTGTCCACAATCATCAACCCAATCAATCCAAACTTGATCCTCAATCAAT
1325713 CCAAACTTGATCCTCGAGCCCACACGCATCTTCATTGGCTACT-CC-CACACGAAAGGGCTATAA
131 CCAAACTTGATCCTCGAGCCCACACGCATCTTCATTGGCTACTCCCTCACACGAAAGGGCTATAA
1325776 GTGTTACTCACAAACCTT
196 GTGTTACTCACAAACCTT
1325794 ACACCTCTACATACACTTCAAAAAGCCTTTCCCTTATTTCGTGTTCCAAACCTACCAACAAAAAT
1 ACACCTCTACATACACTTCAAAAAGCCTTTCCCTTATTTCGTGTTCCAAACCTACCAACAAAAAT
1325859 ATTTGTTGCAAAACGTTTGTCCACAATCATCAACCCAATCAATCCAAACTTGATCCTCAATCAAT
66 ATTTGTTGCAAAACGTTTGTCCACAATCATCAACCCAATCAATCCAAACTTGATCCTCAATCAAT
1325924 CCAAACTTGATCCTCGAGCCCACACGCATCTTCATTGGCTACTCCCTCACACGAAAGGGCTATAA
131 CCAAACTTGATCCTCGAGCCCACACGCATCTTCATTGGCTACTCCCTCACACGAAAGGGCTATAA
*
1325989 GTGTTACTCACCAACCTT
196 GTGTTACTCACAAACCTT
1326007 ACACC
1 ACACC
1326012 GAATGTTTGT
Statistics
Matches: 214, Mismatches: 1, Indels: 3
0.98 0.00 0.01
Matches are distributed among these distances:
210 110 0.51
211 62 0.29
212 2 0.01
213 40 0.19
ACGTcount: A:0.32, C:0.32, G:0.09, T:0.26
Consensus pattern (213 bp):
ACACCTCTACATACACTTCAAAAAGCCTTTCCCTTATTTCGTGTTCCAAACCTACCAACAAAAAT
ATTTGTTGCAAAACGTTTGTCCACAATCATCAACCCAATCAATCCAAACTTGATCCTCAATCAAT
CCAAACTTGATCCTCGAGCCCACACGCATCTTCATTGGCTACTCCCTCACACGAAAGGGCTATAA
GTGTTACTCACAAACCTT
Found at i:1325919 original size:22 final size:22
Alignment explanation
Indices: 1325894--1325938 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1325884 ATCATCAACC
1325894 CAATCAATCCAAACTTGATCCT
1 CAATCAATCCAAACTTGATCCT
1325916 CAATCAATCCAAACTTGATCCT
1 CAATCAATCCAAACTTGATCCT
1325938 C
1 C
1325939 GAGCCCACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.33, G:0.04, T:0.27
Consensus pattern (22 bp):
CAATCAATCCAAACTTGATCCT
Found at i:1326399 original size:9 final size:9
Alignment explanation
Indices: 1326385--1326411 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
1326375 GGGATTTAAG
1326385 AAGGGGAAA
1 AAGGGGAAA
1326394 AAGGGGAAA
1 AAGGGGAAA
1326403 AAGGGGAAA
1 AAGGGGAAA
1326412 GTTAAAGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (9 bp):
AAGGGGAAA
Found at i:1328052 original size:65 final size:64
Alignment explanation
Indices: 1327939--1328094 Score: 174
Period size: 65 Copynumber: 2.4 Consensus size: 64
1327929 TACACTAGGG
* * *
1327939 GTGCATCGGTACACT-AATTACATTCGATGTTTCAAAAGAGCTAGGAGTGCATCAATGCATGGTC
1 GTGCATCGGTACA-TAAAATGCATTCGATGTTTCAAAAGAGCTAAGAGTGCATCAATGCATGG-C
1328003 T
64 T
* *
1328004 GTGCATCGGTACATAAAATGCATTCGATGTTTCAATAA-A-TTCAAGAGTGCATCGATGCATGGC
1 GTGCATCGGTACATAAAATGCATTCGATGTTTCAA-AAGAGCT-AAGAGTGCATCAATGCATGGC
1328067 T
64 T
* * * *
1328068 ATACATCAGTACACAAAATGCATTCGA
1 GTGCATCGGTACATAAAATGCATTCGA
1328095 AATAGGGGTG
Statistics
Matches: 79, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
64 27 0.34
65 50 0.63
66 2 0.03
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (64 bp):
GTGCATCGGTACATAAAATGCATTCGATGTTTCAAAAGAGCTAAGAGTGCATCAATGCATGGCT
Found at i:1328488 original size:13 final size:13
Alignment explanation
Indices: 1328470--1328494 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1328460 CATCACTATA
1328470 ACATATTAGGGAG
1 ACATATTAGGGAG
1328483 ACATATTAGGGA
1 ACATATTAGGGA
1328495 AGTGCATTTA
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:0.40, C:0.08, G:0.28, T:0.24
Consensus pattern (13 bp):
ACATATTAGGGAG
Found at i:1328840 original size:45 final size:45
Alignment explanation
Indices: 1328720--1329125 Score: 352
Period size: 45 Copynumber: 9.0 Consensus size: 45
1328710 ATAAAAAGTT
* * * * *
1328720 AAATGTATAACAATGCATAATTGTCATGAAAGGATG-TCATAAATG
1 AAATGCATAACAGTGCATTATCGGCATGAAAGGATGCT-ATAAATG
* * * *
1328765 AAAATGTATAACAATGCATAATCGACATGAAAGGATGCTATAAATG
1 -AAATGCATAACAGTGCATTATCGGCATGAAAGGATGCTATAAATG
* * * *
1328811 AAATGCATAACAGTACATTATCGGAATGAAAAGATGCCATAAATG
1 AAATGCATAACAGTGCATTATCGGCATGAAAGGATGCTATAAATG
* ** * * * **
1328856 AAATGTATAATGGTGTATTATCGACATAAAATAATG-TCATAAATG
1 AAATGCATAACAGTGCATTATCGGCATGAAAGGATGCT-ATAAATG
* * *
1328901 AAATGCATAACAATGCATTATTGGCATGAAATGATG-TCATAAATG
1 AAATGCATAACAGTGCATTATCGGCATGAAAGGATGCT-ATAAATG
* * *
1328946 AAATGCATAAC-GATGCATTATCGGCATAAAAAGATGCCATAAATG
1 AAATGCATAACAG-TGCATTATCGGCATGAAAGGATGCTATAAATG
* * *
1328991 AAATGTATAACAGTGCATTATCGGCATGAAATGATGTTATAAATG
1 AAATGCATAACAGTGCATTATCGGCATGAAAGGATGCTATAAATG
* * * * * * *
1329036 AAATACAGAACGGTGCATTATTGGCATAAAAGGATGCCATAAATAA
1 AAATGCATAACAGTGCATTATCGGCATGAAAGGATGCTATAAAT-G
** ** *
1329082 AAATGCATAATTGTGCATTATATGCATGAAACGATGCTATAAAT
1 AAATGCATAACAGTGCATTATCGGCATGAAAGGATGCTATAAAT
1329126 AAAAATAAAA
Statistics
Matches: 295, Mismatches: 59, Indels: 12
0.81 0.16 0.03
Matches are distributed among these distances:
45 217 0.74
46 77 0.26
47 1 0.00
ACGTcount: A:0.44, C:0.11, G:0.18, T:0.27
Consensus pattern (45 bp):
AAATGCATAACAGTGCATTATCGGCATGAAAGGATGCTATAAATG
Found at i:1328965 original size:135 final size:134
Alignment explanation
Indices: 1328720--1329091 Score: 431
Period size: 135 Copynumber: 2.7 Consensus size: 134
1328710 ATAAAAAGTT
* * * * * ** * *
1328720 AAATGTATAACAATGCATAATTGTCATGAAAGGATGTCATAAATGAAAATGTATAACAATGCATA
1 AAATGTATAACAGTGCATTATCGACATAAAATAATGTCATAAATG-AAATGCATAACAATGCATT
* * *
1328785 ATCGACATGAAAGGATGCTATAAATGAAATGCATAACAGTACATTATCGGAATGAAAAGATGCCA
65 ATTGGCATGAAAGGATGC-ATAAATGAAATGCATAACAGTACATTATCGGAATAAAAAGATGCCA
1328850 TAAATG
129 TAAATG
** *
1328856 AAATGTATAATGGTGTATTATCGACATAAAATAATGTCATAAATGAAATGCATAACAATGCATTA
1 AAATGTATAACAGTGCATTATCGACATAAAATAATGTCATAAATGAAATGCATAACAATGCATTA
* * *
1328921 TTGGCATGAAATGATGTCATAAATGAAATGCATAAC-GATGCATTATCGGCATAAAAAGATGCCA
66 TTGGCATGAAAGGATG-CATAAATGAAATGCATAACAG-TACATTATCGGAATAAAAAGATGCCA
1328985 TAAATG
129 TAAATG
* * * * * * **
1328991 AAATGTATAACAGTGCATTATCGGCATGAAATGATGTTATAAATGAAATACAGAACGGTGCATTA
1 AAATGTATAACAGTGCATTATCGACATAAAATAATGTCATAAATGAAATGCATAACAATGCATTA
* *
1329056 TTGGCATAAAAGGATGCCATAAATAAAAATGCATAA
66 TTGGCATGAAAGGATG-CATAAAT-GAAATGCATAA
1329092 TTGTGCATTA
Statistics
Matches: 200, Mismatches: 33, Indels: 6
0.84 0.14 0.03
Matches are distributed among these distances:
134 1 0.00
135 153 0.76
136 46 0.23
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.26
Consensus pattern (134 bp):
AAATGTATAACAGTGCATTATCGACATAAAATAATGTCATAAATGAAATGCATAACAATGCATTA
TTGGCATGAAAGGATGCATAAATGAAATGCATAACAGTACATTATCGGAATAAAAAGATGCCATA
AATG
Found at i:1330215 original size:16 final size:16
Alignment explanation
Indices: 1330173--1330204 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
1330163 AGATGGTGGG
1330173 AGAGAGA-AAA-TAAA
1 AGAGAGATAAATTAAA
1330187 AGAGAGATAAATTAAA
1 AGAGAGATAAATTAAA
1330203 AG
1 AG
1330205 GGAATATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 3 0.19
16 6 0.38
ACGTcount: A:0.66, C:0.00, G:0.22, T:0.12
Consensus pattern (16 bp):
AGAGAGATAAATTAAA
Found at i:1344501 original size:31 final size:31
Alignment explanation
Indices: 1344466--1344524 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
1344456 GCTTAATGCG
1344466 TTTAGTACCTAAACAATAAATTTTATCACAT
1 TTTAGTACCTAAACAATAAATTTTATCACAT
** *
1344497 TTTAGTACCTAAACTTTTAATTTTATCA
1 TTTAGTACCTAAACAATAAATTTTATCA
1344525 AAATCATACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.37, C:0.15, G:0.03, T:0.44
Consensus pattern (31 bp):
TTTAGTACCTAAACAATAAATTTTATCACAT
Found at i:1344579 original size:39 final size:39
Alignment explanation
Indices: 1344536--1344629 Score: 188
Period size: 39 Copynumber: 2.4 Consensus size: 39
1344526 AATCATACTT
1344536 AAATTTTAATTTTTGTTATATTTTAATACCTACCGTTAA
1 AAATTTTAATTTTTGTTATATTTTAATACCTACCGTTAA
1344575 AAATTTTAATTTTTGTTATATTTTAATACCTACCGTTAA
1 AAATTTTAATTTTTGTTATATTTTAATACCTACCGTTAA
1344614 AAATTTTAATTTTTGT
1 AAATTTTAATTTTTGT
1344630 GTGGTTTTCA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 55 1.00
ACGTcount: A:0.33, C:0.09, G:0.05, T:0.53
Consensus pattern (39 bp):
AAATTTTAATTTTTGTTATATTTTAATACCTACCGTTAA
Found at i:1344580 original size:22 final size:22
Alignment explanation
Indices: 1344555--1344623 Score: 67
Period size: 22 Copynumber: 3.4 Consensus size: 22
1344545 TTTTTGTTAT
1344555 ATTTTAATACCTACCGTTAAAA
1 ATTTTAATACCTACCGTTAAAA
*** *
1344577 ATTTTAAT---TTTTGTT--AT
1 ATTTTAATACCTACCGTTAAAA
1344594 ATTTTAATACCTACCGTTAAAA
1 ATTTTAATACCTACCGTTAAAA
1344616 ATTTTAAT
1 ATTTTAAT
1344624 TTTTGTGTGG
Statistics
Matches: 34, Mismatches: 8, Indels: 10
0.65 0.15 0.19
Matches are distributed among these distances:
17 9 0.26
19 4 0.12
20 4 0.12
22 17 0.50
ACGTcount: A:0.36, C:0.12, G:0.04, T:0.48
Consensus pattern (22 bp):
ATTTTAATACCTACCGTTAAAA
Found at i:1346131 original size:22 final size:22
Alignment explanation
Indices: 1346106--1346154 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
1346096 ATTAATTGGA
1346106 TTTTAAAAAATAAATAAA-ATAT
1 TTTTAAAAAAT-AATAAATATAT
* * *
1346128 TTTTATAATATTATAAATATAT
1 TTTTAAAAAATAATAAATATAT
1346150 TTTTA
1 TTTTA
1346155 TAACTATACT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTTAAAAAATAATAAATATAT
Found at i:1346155 original size:14 final size:15
Alignment explanation
Indices: 1346138--1346170 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1346128 TTTTATAATA
1346138 TTATAAATATA-TTT
1 TTATAAATATACTTT
*
1346152 TTATAACTATACTTT
1 TTATAAATATACTTT
1346167 TTAT
1 TTAT
1346171 TAAAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (15 bp):
TTATAAATATACTTT
Found at i:1348019 original size:100 final size:100
Alignment explanation
Indices: 1347846--1348045 Score: 391
Period size: 100 Copynumber: 2.0 Consensus size: 100
1347836 GGGGGAACTG
*
1347846 AAGTAGGCGAAGACTCAAGTGAATGGCAGCTTTGTCACTGTCATCTTTATCCTGCCCTTACAAGG
1 AAGTAGGCGAAGACTCAAGTGAATGGCAGCTTTGGCACTGTCATCTTTATCCTGCCCTTACAAGG
1347911 TATGCATGTTTTCTGTTGCTCATATCATGAAAGAA
66 TATGCATGTTTTCTGTTGCTCATATCATGAAAGAA
1347946 AAGTAGGCGAAGACTCAAGTGAATGGCAGCTTTGGCACTGTCATCTTTATCCTGCCCTTACAAGG
1 AAGTAGGCGAAGACTCAAGTGAATGGCAGCTTTGGCACTGTCATCTTTATCCTGCCCTTACAAGG
1348011 TATGCATGTTTTCTGTTGCTCATATCATGAAAGAA
66 TATGCATGTTTTCTGTTGCTCATATCATGAAAGAA
1348046 GAGCTTTCGT
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
100 99 1.00
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (100 bp):
AAGTAGGCGAAGACTCAAGTGAATGGCAGCTTTGGCACTGTCATCTTTATCCTGCCCTTACAAGG
TATGCATGTTTTCTGTTGCTCATATCATGAAAGAA
Found at i:1350322 original size:13 final size:13
Alignment explanation
Indices: 1350301--1350355 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
1350291 AAGTTCGATA
*
1350301 AATTCAAATACTT
1 AATTGAAATACTT
1350314 AATTGAAATACTT
1 AATTGAAATACTT
* *
1350327 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
1350341 AATTGAAATACTT
1 AATTGAAATACTT
1350354 AA
1 AA
1350356 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:1350409 original size:73 final size:73
Alignment explanation
Indices: 1350290--1350461 Score: 326
Period size: 73 Copynumber: 2.4 Consensus size: 73
1350280 CATCAAACCT
* *
1350290 CAAGTTCGATAAATTCAAATACTTAATTGAAATACTTAATTAACTCAACATAATTGAAATACTTA
1 CAAGTTTGATAAATTCAAATACTTAATTGAAATAATTAATTAACTCAACATAATTGAAATACTTA
1350355 AATACTTC
66 AATACTTC
1350363 CAAGTTTGATAAATTCAAATACTTAATTGAAATAATTAATTAACTCAACATAATTGAAATACTTA
1 CAAGTTTGATAAATTCAAATACTTAATTGAAATAATTAATTAACTCAACATAATTGAAATACTTA
1350428 AATACTTC
66 AATACTTC
1350436 CAAGTTTGATAAATTCAAATACTTAA
1 CAAGTTTGATAAATTCAAATACTTAA
1350462 AAACTTCCAA
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
73 97 1.00
ACGTcount: A:0.46, C:0.13, G:0.06, T:0.35
Consensus pattern (73 bp):
CAAGTTTGATAAATTCAAATACTTAATTGAAATAATTAATTAACTCAACATAATTGAAATACTTA
AATACTTC
Found at i:1350510 original size:32 final size:33
Alignment explanation
Indices: 1350414--1350512 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
1350404 AACTCAACAT
* * *
1350414 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1350447 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1350480 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1350512 A
1 A
1350513 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:1350531 original size:21 final size:21
Alignment explanation
Indices: 1350507--1350548 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1350497 ACTTCAAGTT
1350507 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
1350528 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
1350549 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:1352854 original size:24 final size:24
Alignment explanation
Indices: 1352827--1352880 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
1352817 TTAAACCCAG
* *
1352827 ACCGGATTTTTTTTCC-GGATAAAA
1 ACCGG-TTTTTTATCCAGGAAAAAA
*
1352851 ACCGGTTTTTTATCCAGTAAAAAA
1 ACCGGTTTTTTATCCAGGAAAAAA
1352875 ACCGGT
1 ACCGGT
1352881 CTAGGTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 9 0.35
24 17 0.65
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (24 bp):
ACCGGTTTTTTATCCAGGAAAAAA
Found at i:1360722 original size:7 final size:7
Alignment explanation
Indices: 1360710--1360798 Score: 58
Period size: 7 Copynumber: 12.1 Consensus size: 7
1360700 CAAAGCAAAG
1360710 AGAAAAA
1 AGAAAAA
1360717 AG--AAA
1 AGAAAAA
1360722 AGAAAAA
1 AGAAAAA
*
1360729 AGCAAAA
1 AGAAAAA
*
1360736 AGCAAAA
1 AGAAAAA
1360743 AGCAAAGAGA
1 AG-AAA-A-A
*
1360753 ACAAAAA
1 AGAAAAA
1360760 AGAAAAA
1 AGAAAAA
*
1360767 A-ACACAA
1 AGA-AAAA
1360774 AGAAAAAA
1 AG-AAAAA
1360782 AGAAAAA
1 AGAAAAA
1360789 GAGAGAAAA
1 -AGA-AAAA
1360798 A
1 A
1360799 ATGACAAGAA
Statistics
Matches: 66, Mismatches: 6, Indels: 19
0.73 0.07 0.21
Matches are distributed among these distances:
5 5 0.08
6 1 0.02
7 37 0.56
8 12 0.18
9 9 0.14
10 2 0.03
ACGTcount: A:0.78, C:0.07, G:0.16, T:0.00
Consensus pattern (7 bp):
AGAAAAA
Found at i:1360723 original size:14 final size:14
Alignment explanation
Indices: 1360701--1360798 Score: 66
Period size: 14 Copynumber: 7.2 Consensus size: 14
1360691 AGATCAAATC
*
1360701 AAAGCAAAGAGAAA
1 AAAGAAAAGAGAAA
1360715 AAAG-AAA-AGAAA
1 AAAGAAAAGAGAAA
*
1360727 AAAGCAAAA-AGCAA
1 AAAG-AAAAGAGAAA
*
1360741 AAAGCAAAGAG-AA
1 AAAGAAAAGAGAAA
*
1360754 CAA-AAAAGA-AAA
1 AAAGAAAAGAGAAA
*
1360766 AAACACAAAGA-AAA
1 AAAGA-AAAGAGAAA
1360780 AAAGAAAAAGAGAGAA
1 AAAG-AAAAGAGA-AA
1360796 AAA
1 AAA
1360799 ATGACAAGAA
Statistics
Matches: 69, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
12 18 0.26
13 11 0.16
14 33 0.48
15 2 0.03
16 5 0.07
ACGTcount: A:0.77, C:0.07, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAGAAAAGAGAAA
Found at i:1360730 original size:26 final size:26
Alignment explanation
Indices: 1360701--1360781 Score: 78
Period size: 26 Copynumber: 3.1 Consensus size: 26
1360691 AGATCAAATC
1360701 AAAGCAAAGAGAAAAAAGAAAAGAAA
1 AAAGCAAAGAGAAAAAAGAAAAGAAA
* * *
1360727 AAAGCAAAAAGCAAAAAGCAAAGAGAAC
1 AAAGCAAAGAGAAAAAAG-AAA-AGAAA
*
1360755 AAA--AAAGA-AAAAAACACAAAGAAA
1 AAAGCAAAGAGAAAAAAGA-AAAGAAA
1360779 AAA
1 AAA
1360782 AGAAAAAGAG
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
24 8 0.18
25 7 0.16
26 20 0.44
27 3 0.07
28 7 0.16
ACGTcount: A:0.77, C:0.09, G:0.15, T:0.00
Consensus pattern (26 bp):
AAAGCAAAGAGAAAAAAGAAAAGAAA
Found at i:1360750 original size:31 final size:30
Alignment explanation
Indices: 1360715--1360799 Score: 91
Period size: 31 Copynumber: 2.8 Consensus size: 30
1360705 CAAAGAGAAA
* *
1360715 AAAGAAAAGAAAAAAGCAAAAAGCAAAAAG
1 AAAGAAAAGAAAAAAGAAAAAAACAAAAAG
* * *
1360745 CAAAGAGAACAAAAAAGAAAAAAACACAAAG
1 -AAAGAAAAGAAAAAAGAAAAAAACAAAAAG
1360776 AAA-AAAAGAAAAAGAGAGAAAAAA
1 AAAGAAAAGAAAAA-AGA-AAAAAA
1360800 TGACAAGAAG
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
29 8 0.18
30 6 0.13
31 31 0.69
ACGTcount: A:0.78, C:0.07, G:0.15, T:0.00
Consensus pattern (30 bp):
AAAGAAAAGAAAAAAGAAAAAAACAAAAAG
Found at i:1361720 original size:26 final size:23
Alignment explanation
Indices: 1361662--1361728 Score: 64
Period size: 25 Copynumber: 2.7 Consensus size: 23
1361652 GAAAGGGGCA
1361662 ATATTTTTTCAAAAGTTTTTTATT
1 ATATTTTTTCAAAA-TTTTTTATT
* *
1361686 AAACATTTTTCAAAATTCTTTTAATT
1 ATA-TTTTTTCAAAATT-TTTT-ATT
1361712 GATATTTTTT-AAAATTT
1 -ATATTTTTTCAAAATTT
1361729 AGAAAATAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
24 5 0.14
25 20 0.57
26 8 0.23
27 2 0.06
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.57
Consensus pattern (23 bp):
ATATTTTTTCAAAATTTTTTATT
Found at i:1374051 original size:56 final size:55
Alignment explanation
Indices: 1373985--1374094 Score: 130
Period size: 55 Copynumber: 2.0 Consensus size: 55
1373975 TATTGTAAAA
* *
1373985 CACACGAAGTGCCCTATACAGAAATTCATCAACTCATGATGAATTCTGTGAATATG
1 CACACAAAGTG-CCTATACAGAAATTCATAAACTCATGATGAATTCTGTGAATATG
* ** ** * *
1374041 CACACAAAGTGCCTGTATGGTGATTCATAAACTTATGATTAATTCTGTGAATAT
1 CACACAAAGTGCCTATACAGAAATTCATAAACTCATGATGAATTCTGTGAATAT
1374095 ACATACATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
55 35 0.78
56 10 0.22
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (55 bp):
CACACAAAGTGCCTATACAGAAATTCATAAACTCATGATGAATTCTGTGAATATG
Found at i:1374085 original size:55 final size:55
Alignment explanation
Indices: 1374008--1374328 Score: 311
Period size: 55 Copynumber: 5.8 Consensus size: 55
1373998 CTATACAGAA
* * *
1374008 ATTCATCAACTCATGATGAATTCTGTGAATATGCACACAAAGTGCCTGTATGGTG
1 ATTCATCAACTTATGATGAATTCTGTGATTATGCACACAAAGTGCCTGTACGGTG
* * * * * * *
1374063 ATTCATAAACTTATGATTAATTCTGTGAATATACATACATGAAGCGCATGTACGGTG
1 ATTCATCAACTTATGATGAATTCTGTGATTATGCACACA--AAGTGCCTGTACGGTG
* * * ** * * * *
1374120 ATTTATCAACTAATGAAGAATTCCATGATTATGCAAACGAAGTACCTGTATGGTG
1 ATTCATCAACTTATGATGAATTCTGTGATTATGCACACAAAGTGCCTGTACGGTG
* * ** * * *
1374175 ATTCATCAACTTATGATGAATTTTGTGATTATTCACATGAAGTGCCAGTACGATT
1 ATTCATCAACTTATGATGAATTCTGTGATTATGCACACAAAGTGCCTGTACGGTG
* * * *
1374230 ATTCATCAACTTATGATTAATTCCT-TGATTACGCACACAAAGTACCTGTACAGTG
1 ATTCATCAACTTATGATGAATT-CTGTGATTATGCACACAAAGTGCCTGTACGGTG
* * *
1374285 ATTCATCAACTTATGATGAATTCCGTGATTATGTACACGAAGTG
1 ATTCATCAACTTATGATGAATTCTGTGATTATGCACACAAAGTG
1374329 TGTGTAGTAC
Statistics
Matches: 208, Mismatches: 54, Indels: 8
0.77 0.20 0.03
Matches are distributed among these distances:
54 1 0.00
55 165 0.79
56 1 0.00
57 41 0.20
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (55 bp):
ATTCATCAACTTATGATGAATTCTGTGATTATGCACACAAAGTGCCTGTACGGTG
Found at i:1374273 original size:110 final size:111
Alignment explanation
Indices: 1374008--1374316 Score: 372
Period size: 110 Copynumber: 2.8 Consensus size: 111
1373998 CTATACAGAA
* * * *
1374008 ATTCATCAACTCATGATGAATT-CTGTGAATATGCACACAAAGTGCCTGTATGGTGATTCATAAA
1 ATTCATCAACTAATGATGAATTCCT-TGATTATGCACACAAAGTACCTGTATGGTGATTCATCAA
* * *
1374072 CTTATGATTAATTCTGTGAATATACATACATGAAGCGCATGTACGGTG
65 CTTATGATGAATTCTGTGATTATACA-ACATGAAGCGCATGTACGATG
* * * * *
1374120 ATTTATCAACTAATGAAGAATTCCATGATTATGCAAACGAAGTACCTGTATGGTGATTCATCAAC
1 ATTCATCAACTAATGATGAATTCCTTGATTATGCACACAAAGTACCTGTATGGTGATTCATCAAC
* * * *
1374185 TTATGATGAATTTTGTGATTATTC-ACATGAAGTGCCA-GTACGATT
66 TTATGATGAATTCTGTGATTATACAACATGAAGCG-CATGTACGATG
* * * **
1374230 ATTCATCAACTTATGATTAATTCCTTGATTACGCACACAAAGTACCTGTACAGTGATTCATCAAC
1 ATTCATCAACTAATGATGAATTCCTTGATTATGCACACAAAGTACCTGTATGGTGATTCATCAAC
*
1374295 TTATGATGAATTCCGTGATTAT
66 TTATGATGAATTCTGTGATTAT
1374317 GTACACGAAG
Statistics
Matches: 167, Mismatches: 28, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
110 90 0.54
111 2 0.01
112 74 0.44
113 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Consensus pattern (111 bp):
ATTCATCAACTAATGATGAATTCCTTGATTATGCACACAAAGTACCTGTATGGTGATTCATCAAC
TTATGATGAATTCTGTGATTATACAACATGAAGCGCATGTACGATG
Found at i:1374415 original size:2 final size:2
Alignment explanation
Indices: 1374363--1374402 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1374353 TATCGATGCA
1374363 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1374403 TTTAACAATA
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):
AT
Found at i:1376834 original size:19 final size:22
Alignment explanation
Indices: 1376810--1376864 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
1376800 AATCTAAATT
*
1376810 GGGTATCGATACC-TA-GA-AG
1 GGGTATCGATACCATATCATAG
*
1376829 GGGTATCGGTACCATATCATAG
1 GGGTATCGATACCATATCATAG
1376851 GGGTATCGATACCA
1 GGGTATCGATACCA
1376865 GGTTATATAG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 12 0.40
20 2 0.07
21 1 0.03
22 15 0.50
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (22 bp):
GGGTATCGATACCATATCATAG
Done.