Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008428.1 Hibiscus syriacus cultivar Beakdansim tig00111213_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: 6915314
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 30
Found at i:1134629 original size:35 final size:35
Alignment explanation
Indices: 1134573--1134647 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
1134563 TTCATGTTCA
1134573 AAATTCCAAAACACTTCAATTACATTCTAAACCCT
1 AAATTCCAAAACACTTCAATTACATTCTAAACCCT
* * * *
1134608 AAATTCTAAAATACTTTAATTATATTCTAAACCCT
1 AAATTCCAAAACACTTCAATTACATTCTAAACCCT
1134643 AAATT
1 AAATT
1134648 AAAGTATTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (35 bp):
AAATTCCAAAACACTTCAATTACATTCTAAACCCT
Found at i:1134691 original size:35 final size:35
Alignment explanation
Indices: 1134643--1134717 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 35
1134633 TCTAAACCCT
1134643 AAATTAAAGTATTTTAGAATTTAGGGTTTAAAATG
1 AAATTAAAGTATTTTAGAATTTAGGGTTTAAAATG
* * * * *
1134678 TAATTAAATTATTTTGGAATTTGGGGTTTAGAATG
1 AAATTAAAGTATTTTAGAATTTAGGGTTTAAAATG
1134713 AAATT
1 AAATT
1134718 GAAGACTATG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.39, C:0.00, G:0.19, T:0.43
Consensus pattern (35 bp):
AAATTAAAGTATTTTAGAATTTAGGGTTTAAAATG
Found at i:1135221 original size:87 final size:87
Alignment explanation
Indices: 1135075--1135237 Score: 290
Period size: 87 Copynumber: 1.9 Consensus size: 87
1135065 TATGTTATAT
1135075 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
1 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
1135140 AGAGCTTATATAATAAAATAGG
66 AGAGCTTATATAATAAAATAGG
* * *
1135162 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATTTAATGTAATAGGT
1 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
*
1135227 AGCGCTTATAT
66 AGAGCTTATAT
1135238 TGACCTATTT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (87 bp):
TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
AGAGCTTATATAATAAAATAGG
Found at i:1136112 original size:23 final size:23
Alignment explanation
Indices: 1136082--1136154 Score: 137
Period size: 23 Copynumber: 3.2 Consensus size: 23
1136072 ATACTTTACA
1136082 ATATAAGCGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
1136105 ATATAAGCGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
1136128 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
1136151 ATAT
1 ATAT
1136155 TTTTATCTAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.36, C:0.22, G:0.08, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:1137412 original size:34 final size:34
Alignment explanation
Indices: 1137369--1137436 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
1137359 AGGCTAGAGT
1137369 CTTAGTTACTGCAACAAATACAAACGATCAGTGG
1 CTTAGTTACTGCAACAAATACAAACGATCAGTGG
1137403 CTTAGTTACTGCAACAAATACAAACGATCAGTGG
1 CTTAGTTACTGCAACAAATACAAACGATCAGTGG
1137437 GTTATAAGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (34 bp):
CTTAGTTACTGCAACAAATACAAACGATCAGTGG
Found at i:1141174 original size:20 final size:19
Alignment explanation
Indices: 1141128--1141174 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1141118 TCCAGTAGCA
1141128 TTTTACCGGTTTCATCATT
1 TTTTACCGGTTTCATCATT
* *
1141147 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTCATCAT-T
1141168 TTTTACC
1 TTTTACC
1141175 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.19, C:0.19, G:0.11, T:0.51
Consensus pattern (19 bp):
TTTTACCGGTTTCATCATT
Found at i:1141290 original size:182 final size:181
Alignment explanation
Indices: 1140914--1141386 Score: 712
Period size: 182 Copynumber: 2.6 Consensus size: 181
1140904 GTACTTATGC
1140914 AAGTATCGACACTTTCAATATATCCGGTAGCATTTTACCGGTTTTATCATTTTGATACCGGTTTT
1 AAGTATCGACACTTTCAATATATCCGGTAGCATTTTACCGGTTTTATCATTTTGATACCGGTTTT
* * * *
1140979 ATAATATTTTTACATATTATATCGTTATGGATCGATACATTTTTTTTAAAGTATCGACACTTTAT
66 ATCATATTTTTACCTGTTATATCGTTGTGGATCGATACA-TTTTTTTAAAGTATCGACACTTTAT
* * * * *
1141044 AGGCGTTAAAACTGCTTCTTTTTTAAATTCACAAAGTGTCGATCCTTATAAA
130 AGGCGCTAAAACTGATTCTCTTTTAAATTAACAAAGTGTAGATCCTTATAAA
* *
1141096 AAGTATCGACACTTTCAATATATCCAGTAGCATTTTACCGGTTTCATCATTTTGATACCGGTTTT
1 AAGTATCGACACTTTCAATATATCCGGTAGCATTTTACCGGTTTTATCATTTTGATACCGGTTTT
*
1141161 ATCATATTTTTACCTGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACTTTATA
66 ATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTTTAAAGTATCGACACTTTATA
* *
1141226 GGCGCTAAAACTGATTCTCTTTTAAATTAACGAAGTGTAGATCCTTATATTA
131 GGCGCTAAAACTGATTCTCTTTTAAATTAACAAAGTGTAGATCCTTATA-AA
* * * * * ** *
1141278 AAGTACCGACACTTTAAATATATCTGGTACCGTTTTACCGGTTTTATCATTTCAATACCGATTTT
1 AAGTATCGACACTTTCAATATATCCGGTAGCATTTTACCGGTTTTATCATTTTGATACCGGTTTT
* *
1141343 GTCATAGTTTTACCTGTTATATCGTTGTGGATCGATACATTTTT
66 ATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTT
1141387 AATTTGGATC
Statistics
Matches: 263, Mismatches: 27, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
181 69 0.26
182 194 0.74
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (181 bp):
AAGTATCGACACTTTCAATATATCCGGTAGCATTTTACCGGTTTTATCATTTTGATACCGGTTTT
ATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTTTAAAGTATCGACACTTTATA
GGCGCTAAAACTGATTCTCTTTTAAATTAACAAAGTGTAGATCCTTATAAA
Found at i:1143568 original size:15 final size:15
Alignment explanation
Indices: 1143548--1143581 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1143538 CCGATCTGCT
1143548 TATTGTGAATTCAGA
1 TATTGTGAATTCAGA
*
1143563 TATTGTGGATTCAGA
1 TATTGTGAATTCAGA
1143578 TATT
1 TATT
1143582 ATAATTACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.29, C:0.06, G:0.21, T:0.44
Consensus pattern (15 bp):
TATTGTGAATTCAGA
Found at i:1149413 original size:64 final size:60
Alignment explanation
Indices: 1149340--1149560 Score: 203
Period size: 64 Copynumber: 3.5 Consensus size: 60
1149330 TGTTTGAATG
** *
1149340 TGCACCGATGCATTGGTAATGCATCGATGCACTCTTTTAAAATAAATACATCGAATGCAATTCA
1 TGCACCGATGCATAAGTAGTGCATCGATGCA-TC--TTAAAAT-AATACATCGAATGCAATTCA
* *
1149404 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAGTGAA-ACATCGAATGCAA-TCG
1 TGCACCGATGCATAAGTAGTGCATCGATGCAT--C-TTAA-AAT-AATACATCGAATGCAATTC-
*
1149467 G
60 A
* * * * * * *
1149468 TGCATCGATGCATAAGGAGTGCATCGATGCATCTCAGCAATAATACATCGAATACATTTTA
1 TGCACCGATGCATAAGTAGTGCATCGATGCATCTTA-AAATAATACATCGAATGCAATTCA
*
1149529 TGCACCGATGCATCAGTAGTGCATCGATGCAT
1 TGCACCGATGCATAAGTAGTGCATCGATGCAT
1149561 ACCTTCATTA
Statistics
Matches: 131, Mismatches: 19, Indels: 17
0.78 0.11 0.10
Matches are distributed among these distances:
60 2 0.02
61 44 0.34
62 2 0.02
63 3 0.02
64 75 0.57
65 5 0.04
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (60 bp):
TGCACCGATGCATAAGTAGTGCATCGATGCATCTTAAAATAATACATCGAATGCAATTCA
Found at i:1149639 original size:56 final size:58
Alignment explanation
Indices: 1149553--1149667 Score: 216
Period size: 56 Copynumber: 2.0 Consensus size: 58
1149543 AGTAGTGCAT
1149553 CGATGCATACCTTCATTAAAAGATGAAATTGAC-TTT-TCTTGGTCTAAAGAGTGAAC
1 CGATGCATACCTTCATTAAAAGATGAAATTGACTTTTCTCTTGGTCTAAAGAGTGAAC
1149609 CGATGCATACCTTCATTAAAAGATGAAATTGACTTTTCTCTTGGTCTAAAGAGTGAAC
1 CGATGCATACCTTCATTAAAAGATGAAATTGACTTTTCTCTTGGTCTAAAGAGTGAAC
1149667 C
1 C
1149668 ATTAGAGTAT
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
56 33 0.58
57 3 0.05
58 21 0.37
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Consensus pattern (58 bp):
CGATGCATACCTTCATTAAAAGATGAAATTGACTTTTCTCTTGGTCTAAAGAGTGAAC
Found at i:1150151 original size:16 final size:16
Alignment explanation
Indices: 1150130--1150214 Score: 56
Period size: 16 Copynumber: 5.4 Consensus size: 16
1150120 TCGAGGGTTT
1150130 ACATATGTTTAAAGGC
1 ACATATGTTTAAAGGC
**
1150146 ACATATG---AACAGTTT
1 ACATATGTTTAA-AG-GC
1150161 ACATATGTTTAAAGGC
1 ACATATGTTTAAAGGC
**
1150177 ACATATG---AACAGTTT
1 ACATATGTTTAA-AG-GC
1150192 ACATATGTTTAAAGGC
1 ACATATGTTTAAAGGC
1150208 ACATATG
1 ACATATG
1150215 AACAGTTTAT
Statistics
Matches: 51, Mismatches: 8, Indels: 20
0.65 0.10 0.25
Matches are distributed among these distances:
13 4 0.08
14 4 0.08
15 14 0.27
16 21 0.41
17 4 0.08
18 4 0.08
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (16 bp):
ACATATGTTTAAAGGC
Found at i:1150164 original size:31 final size:31
Alignment explanation
Indices: 1150126--1150223 Score: 196
Period size: 31 Copynumber: 3.2 Consensus size: 31
1150116 AGAGTCGAGG
1150126 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
1150157 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
1150188 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
1150219 GTTTA
1 GTTTA
1150224 TATTGTGACC
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 67 1.00
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (31 bp):
GTTTACATATGTTTAAAGGCACATATGAACA
Found at i:1153436 original size:64 final size:64
Alignment explanation
Indices: 1153302--1153480 Score: 200
Period size: 64 Copynumber: 2.8 Consensus size: 64
1153292 TTTTAAATAA
* ** *
1153302 ATACATCGAATGCAATTCATGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAGTG
1 ATACATCGAATGCAATTCATGCATCGATGCATAAGGAGTGCATCGATGCATCCCAGCAATAATG
* * *
1153366 AAACATCGAATGCAA-TCGGTGCATCGATGCATAAGGAGTGCATCGATGCATCTCAGCAATAAT-
1 ATACATCGAATGCAATTC-ATGCATCGATGCATAAGGAGTGCATCGATGCATCCCAGCAATAATG
* * * * * * *
1153429 ACTACATCGAATACATTTTATGCACCGATGCATCAGTAGTGCATCGTTGCAT
1 A-TACATCGAATGCAATTCATGCATCGATGCATAAGGAGTGCATCGATGCAT
1153481 ACCTTCATTA
Statistics
Matches: 96, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
63 3 0.03
64 92 0.96
65 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (64 bp):
ATACATCGAATGCAATTCATGCATCGATGCATAAGGAGTGCATCGATGCATCCCAGCAATAATG
Found at i:1154022 original size:31 final size:31
Alignment explanation
Indices: 1153984--1154205 Score: 399
Period size: 31 Copynumber: 7.2 Consensus size: 31
1153974 AGAGTCGAGG
1153984 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
1154015 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
1154046 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
*
1154077 GTTTCCATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
* *
1154108 GTCTAAATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
*
1154139 GTTTATATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
*
1154170 GTCTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
1154201 GTTTA
1 GTTTA
1154206 TATTGTGACC
Statistics
Matches: 182, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 182 1.00
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.32
Consensus pattern (31 bp):
GTTTACATATGTTTAAAGGCACATATGAACA
Found at i:1154927 original size:29 final size:30
Alignment explanation
Indices: 1154851--1154927 Score: 68
Period size: 29 Copynumber: 2.6 Consensus size: 30
1154841 GAAAGATTTT
* **
1154851 AGTTTTTTAGAGTTTTTTTGTAATTTCATTAA
1 AGTTTTTTA-A-TTTTTTTGTAAATAAATTAA
* * *
1154883 AATTTTTT-GTTATTTTGTAAATAAATT-A
1 AGTTTTTTAATTTTTTTGTAAATAAATTAA
1154911 AGTTTTTTAATTTTTTT
1 AGTTTTTTAATTTTTTT
1154928 ATTTTTTAAT
Statistics
Matches: 35, Mismatches: 9, Indels: 5
0.71 0.18 0.10
Matches are distributed among these distances:
28 8 0.23
29 20 0.57
32 7 0.20
ACGTcount: A:0.27, C:0.01, G:0.09, T:0.62
Consensus pattern (30 bp):
AGTTTTTTAATTTTTTTGTAAATAAATTAA
Found at i:1165796 original size:32 final size:33
Alignment explanation
Indices: 1165742--1165805 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1165732 AATTTAAAAA
*
1165742 AACATATTTTTTTAAATAAAAATTTCAAAAATT
1 AACATATTTCTTTAAATAAAAATTTCAAAAATT
* *
1165775 AACATA-TTCTTTAATTCAAAATTTCAAAAAT
1 AACATATTTCTTTAAATAAAAATTTCAAAAAT
1165806 AAATTTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 22 0.79
33 6 0.21
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (33 bp):
AACATATTTCTTTAAATAAAAATTTCAAAAATT
Found at i:1165827 original size:16 final size:16
Alignment explanation
Indices: 1165787--1165829 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 16
1165777 CATATTCTTT
* *
1165787 AATTCAAAATTTCAAA
1 AATTCAAATTTTAAAA
1165803 AA-T-AAATTTTAAAA
1 AATTCAAATTTTAAAA
1165817 AATTCAAATTTTA
1 AATTCAAATTTTA
1165830 TATACTACAC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 11 0.48
15 2 0.09
16 10 0.43
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (16 bp):
AATTCAAATTTTAAAA
Found at i:1165891 original size:10 final size:9
Alignment explanation
Indices: 1165852--1165881 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
1165842 AATATTAAGG
1165852 AAAATTTCAA
1 AAAATTT-AA
1165862 AAAATTTAA
1 AAAATTTAA
1165871 AAAATTTAA
1 AAAATTTAA
1165880 AA
1 AA
1165882 TTTATAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 13 0.65
10 7 0.35
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (9 bp):
AAAATTTAA
Found at i:1166002 original size:16 final size:17
Alignment explanation
Indices: 1165980--1166025 Score: 67
Period size: 16 Copynumber: 2.8 Consensus size: 17
1165970 GAATGAAAAT
*
1165980 TTTTTAATTAAATTTTA
1 TTTTTAATTAAATGTTA
*
1165997 -TTTTAATTAAAAGTTA
1 TTTTTAATTAAATGTTA
1166013 TTTTTAATTAAAT
1 TTTTTAATTAAAT
1166026 AGTTTCATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (17 bp):
TTTTTAATTAAATGTTA
Found at i:1166057 original size:17 final size:17
Alignment explanation
Indices: 1166035--1166067 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1166025 TAGTTTCATT
1166035 TTTGTTTACATATTTTA
1 TTTGTTTACATATTTTA
1166052 TTTGTTTACATATTTT
1 TTTGTTTACATATTTT
1166068 TCAAAGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.06, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTGTTTACATATTTTA
Found at i:1170397 original size:31 final size:30
Alignment explanation
Indices: 1170359--1170447 Score: 99
Period size: 31 Copynumber: 2.9 Consensus size: 30
1170349 TAAGGCGACC
* *
1170359 CTTGGGTAGGCTCTGCGGCCCCGAGATCTTT
1 CTTGGGTAGGCTCT-CGGCCCCAAGATCCTT
* *
1170390 CTTGGGTAGGC-CCCATGGCCCCAAGAACCTT
1 CTTGGGTAGGCTCTC--GGCCCCAAGATCCTT
1170421 CTTGGGTAGGCTCTCAGGCCCCAAGAT
1 CTTGGGTAGGCTCTC-GGCCCCAAGAT
1170448 GTTCCCTTAG
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
29 1 0.02
30 1 0.02
31 44 0.92
32 2 0.04
ACGTcount: A:0.16, C:0.31, G:0.29, T:0.24
Consensus pattern (30 bp):
CTTGGGTAGGCTCTCGGCCCCAAGATCCTT
Found at i:1170600 original size:2 final size:2
Alignment explanation
Indices: 1170593--1170641 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1170583 TTTAAAACGT
1170593 TA 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 TA
1170635 TA TA TA T
1 TA TA TA T
1170642 CTTTTCATTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1188327 original size:14 final size:14
Alignment explanation
Indices: 1188308--1188342 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
1188298 ATATGTTAAG
1188308 GCAAGTAAATATGT
1 GCAAGTAAATATGT
1188322 GCAAGTAAATATGT
1 GCAAGTAAATATGT
1188336 GCAAGTA
1 GCAAGTA
1188343 TACACAATCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.43, C:0.09, G:0.23, T:0.26
Consensus pattern (14 bp):
GCAAGTAAATATGT
Found at i:1194311 original size:21 final size:23
Alignment explanation
Indices: 1194267--1194313 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
1194257 TCACTTTATT
*
1194267 ATTTGTATGTTTAAAATTGGATA
1 ATTTGTATGTTTAAAATTGAATA
*
1194290 ATTT-TAT-TTTAAAATTTAATA
1 ATTTGTATGTTTAAAATTGAATA
1194311 ATT
1 ATT
1194314 AAGTCATCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 15 0.68
22 3 0.14
23 4 0.18
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (23 bp):
ATTTGTATGTTTAAAATTGAATA
Found at i:1194882 original size:21 final size:22
Alignment explanation
Indices: 1194856--1194897 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1194846 AGTATGAAAA
* *
1194856 ATAAATA-CATATATTTGTTTT
1 ATAAATATAATATAATTGTTTT
1194877 ATAAATATAATATAATTGTTT
1 ATAAATATAATATAATTGTTT
1194898 GAGTTTAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (22 bp):
ATAAATATAATATAATTGTTTT
Found at i:1197946 original size:14 final size:15
Alignment explanation
Indices: 1197911--1197954 Score: 72
Period size: 14 Copynumber: 2.9 Consensus size: 15
1197901 TAGTATTGTT
1197911 TGTAGAAAACAGACTG
1 TGTAGAAAACAGAC-G
1197927 TGTAGAAAACAGAC-
1 TGTAGAAAACAGACG
1197941 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
1197955 AAGTCTGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 14 0.50
16 14 0.50
ACGTcount: A:0.48, C:0.14, G:0.23, T:0.16
Consensus pattern (15 bp):
TGTAGAAAACAGACG
Found at i:1199358 original size:16 final size:16
Alignment explanation
Indices: 1199337--1199368 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1199327 AGTAGCCTCT
1199337 TGGTAACCATCATTAC
1 TGGTAACCATCATTAC
1199353 TGGTAACCATCATTAC
1 TGGTAACCATCATTAC
1199369 CTTCTGTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.31
Consensus pattern (16 bp):
TGGTAACCATCATTAC
Found at i:1199750 original size:51 final size:51
Alignment explanation
Indices: 1199674--1199774 Score: 193
Period size: 51 Copynumber: 2.0 Consensus size: 51
1199664 TAAGGAAAGG
*
1199674 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGTTGAAATTCCTTGTAACTA
1 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACTA
1199725 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACT
1 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACT
1199775 CTCCCCCTAA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.31
Consensus pattern (51 bp):
ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACTA
Found at i:1215669 original size:21 final size:22
Alignment explanation
Indices: 1215640--1215681 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1215630 ACAAGACAGG
*
1215640 ACCAGAGATAGTGATGATGATT
1 ACCAGAGATAGGGATGATGATT
*
1215662 ACCA-AGATAGGGATTATGAT
1 ACCAGAGATAGGGATGATGAT
1215682 GTTACAGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.38, C:0.10, G:0.26, T:0.26
Consensus pattern (22 bp):
ACCAGAGATAGGGATGATGATT
Found at i:1222450 original size:112 final size:112
Alignment explanation
Indices: 1222253--1222477 Score: 450
Period size: 112 Copynumber: 2.0 Consensus size: 112
1222243 GAGTTAGGGA
1222253 TTCGACAGGGCTTCTTCAGTCTTTCCCCAATATTTGGCGGCCGACTAGCATCGGTGGTTGGCTGG
1 TTCGACAGGGCTTCTTCAGTCTTTCCCCAATATTTGGCGGCCGACTAGCATCGGTGGTTGGCTGG
1222318 GGTATTACAATTCTCCTCTCCTTAAAAGAGATTTCATCCTTGAAATT
66 GGTATTACAATTCTCCTCTCCTTAAAAGAGATTTCATCCTTGAAATT
1222365 TTCGACAGGGCTTCTTCAGTCTTTCCCCAATATTTGGCGGCCGACTAGCATCGGTGGTTGGCTGG
1 TTCGACAGGGCTTCTTCAGTCTTTCCCCAATATTTGGCGGCCGACTAGCATCGGTGGTTGGCTGG
1222430 GGTATTACAATTCTCCTCTCCTTAAAAGAGATTTCATCCTTGAAATT
66 GGTATTACAATTCTCCTCTCCTTAAAAGAGATTTCATCCTTGAAATT
1222477 T
1 T
1222478 ACTTAAATCA
Statistics
Matches: 113, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
112 113 1.00
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.34
Consensus pattern (112 bp):
TTCGACAGGGCTTCTTCAGTCTTTCCCCAATATTTGGCGGCCGACTAGCATCGGTGGTTGGCTGG
GGTATTACAATTCTCCTCTCCTTAAAAGAGATTTCATCCTTGAAATT
Found at i:1226191 original size:2 final size:2
Alignment explanation
Indices: 1226184--1226257 Score: 148
Period size: 2 Copynumber: 37.0 Consensus size: 2
1226174 TATGGAGATA
1226184 AT 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 AT
1226226 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
1226258 CAAGGAAGCA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1228946 original size:15 final size:15
Alignment explanation
Indices: 1228904--1228950 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
1228894 CTATGAGTAT
* *
1228904 ATGTTATAAGTGAAT
1 ATGTTATACGTGAAA
*
1228919 ATGTTATATGTGAAA
1 ATGTTATACGTGAAA
*
1228934 ATGTTTTACGTGAAA
1 ATGTTATACGTGAAA
1228949 AT
1 AT
1228951 ATCTATGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.38, C:0.02, G:0.19, T:0.40
Consensus pattern (15 bp):
ATGTTATACGTGAAA
Found at i:1230755 original size:67 final size:67
Alignment explanation
Indices: 1230647--1230780 Score: 196
Period size: 67 Copynumber: 2.0 Consensus size: 67
1230637 CCTTAGGTCC
* * *
1230647 ATAAGGAATTACCAATCGATGTTGAACCTATACAAGGAATTACAAGCAGTGACTGAACCTGCGAG
1 ATAAGGAATTACCAATCGATGTTGAACCAATACAAGGAATTACAAGCAATGACTGAACCTGCCAG
1230712 AG
66 AG
* * * * *
1230714 ATAAGGAATTATCAGTCGGTGTTGAACCAATACAAGGAATTACCAGCAATGATTGAACCTGCCAG
1 ATAAGGAATTACCAATCGATGTTGAACCAATACAAGGAATTACAAGCAATGACTGAACCTGCCAG
1230779 AG
66 AG
1230781 TCTTCAGTCA
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
67 59 1.00
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (67 bp):
ATAAGGAATTACCAATCGATGTTGAACCAATACAAGGAATTACAAGCAATGACTGAACCTGCCAG
AG
Found at i:1234027 original size:14 final size:14
Alignment explanation
Indices: 1233990--1234029 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
1233980 TCAAAGTTAA
1233990 CGAGTTGACTCAGT
1 CGAGTTGACTCAGT
*
1234004 -GAGTTGACTCGGT
1 CGAGTTGACTCAGT
*
1234017 CGAGTTAACTCAG
1 CGAGTTGACTCAG
1234030 AGACTAGACT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.28
Consensus pattern (14 bp):
CGAGTTGACTCAGT
Found at i:1235631 original size:17 final size:16
Alignment explanation
Indices: 1235609--1235642 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1235599 TAAAAACAGT
1235609 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
1235626 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
1235642 A
1 A
1235643 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:1239832 original size:15 final size:16
Alignment explanation
Indices: 1239799--1239838 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
1239789 AATTAATTAC
*
1239799 AAAATAAAA-TAAAAT
1 AAAATAAAACTAAAAG
1239814 AAAATAAAACT-AAAG
1 AAAATAAAACTAAAAG
1239829 AAAA-AAAACT
1 AAAATAAAACT
1239839 TGAATGTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 6 0.26
15 16 0.70
16 1 0.04
ACGTcount: A:0.78, C:0.05, G:0.03, T:0.15
Consensus pattern (16 bp):
AAAATAAAACTAAAAG
Found at i:1245864 original size:17 final size:16
Alignment explanation
Indices: 1245842--1245875 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1245832 TAAAAACAAT
1245842 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
1245859 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
1245875 A
1 A
1245876 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:1247269 original size:15 final size:15
Alignment explanation
Indices: 1247249--1247278 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1247239 TAATTTATGG
1247249 GAGTCATTGGCTAAT
1 GAGTCATTGGCTAAT
1247264 GAGTCATTGGCTAAT
1 GAGTCATTGGCTAAT
1247279 CATAGGAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (15 bp):
GAGTCATTGGCTAAT
Found at i:1251477 original size:21 final size:21
Alignment explanation
Indices: 1251453--1251493 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1251443 GTGTTATCAG
*
1251453 TAATATAAAATTATACACAAA
1 TAATATAAAAGTATACACAAA
* *
1251474 TAATGTGAAAGTATACACAA
1 TAATATAAAAGTATACACAA
1251494 TCGCTCAAGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.56, C:0.10, G:0.07, T:0.27
Consensus pattern (21 bp):
TAATATAAAAGTATACACAAA
Found at i:1256142 original size:24 final size:25
Alignment explanation
Indices: 1256114--1256192 Score: 75
Period size: 25 Copynumber: 3.4 Consensus size: 25
1256104 GCAAGTGTAT
1256114 TGGTA-AAATAAGCTTACGAGCTTA
1 TGGTACAAATAAGCTTACGAGCTTA
*
1256138 TGGTACAAAT--G-GTA--AG-TATA
1 TGGTACAAATAAGCTTACGAGCT-TA
1256158 TTGGTA-AAATAAGCTTACGAGCTTA
1 -TGGTACAAATAAGCTTACGAGCTTA
1256183 TGGTACAAAT
1 TGGTACAAAT
1256193 GGTAAGTATT
Statistics
Matches: 43, Mismatches: 2, Indels: 19
0.67 0.03 0.30
Matches are distributed among these distances:
19 1 0.02
20 8 0.19
21 5 0.12
22 3 0.07
23 3 0.07
24 10 0.23
25 12 0.28
26 1 0.02
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30
Consensus pattern (25 bp):
TGGTACAAATAAGCTTACGAGCTTA
Found at i:1256160 original size:45 final size:45
Alignment explanation
Indices: 1256100--1256228 Score: 222
Period size: 45 Copynumber: 2.9 Consensus size: 45
1256090 GTTATGGAAT
* *
1256100 AATGGCAAGTGTATTGGTAAAATAAGCTTACGAGCTTATGGTACA
1 AATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGTACA
1256145 AATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGTACA
1 AATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGTACA
* *
1256190 AATGGTAAGTATTTTGGTAAAATAAGCTTACGAGGTTAT
1 AATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTAT
1256229 AGTTAATAAA
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 80 1.00
ACGTcount: A:0.36, C:0.09, G:0.23, T:0.32
Consensus pattern (45 bp):
AATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGTACA
Found at i:1256903 original size:17 final size:17
Alignment explanation
Indices: 1256878--1256917 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1256868 GTATATTATT
*
1256878 CATTAAAGCATGCATTG
1 CATTTAAGCATGCATTG
* *
1256895 CATTTAAGCATGTATTT
1 CATTTAAGCATGCATTG
1256912 CATTTA
1 CATTTA
1256918 GGCAAGTAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (17 bp):
CATTTAAGCATGCATTG
Found at i:1256944 original size:17 final size:17
Alignment explanation
Indices: 1256895--1256982 Score: 54
Period size: 17 Copynumber: 5.2 Consensus size: 17
1256885 GCATGCATTG
* * *
1256895 CATTTAAGCATGTATTT
1 CATTTATGCATCTAGTT
* **
1256912 CATTTAGGCAAGTAGTT
1 CATTTATGCATCTAGTT
1256929 CATTTATGCATCTAGTT
1 CATTTATGCATCTAGTT
* * *
1256946 -ATTTAAT-AAACTACTT
1 CATTT-ATGCATCTAGTT
* *
1256962 CATTCATGCATTTAGTT
1 CATTTATGCATCTAGTT
1256979 CATT
1 CATT
1256983 GAATAAAGTT
Statistics
Matches: 54, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
16 12 0.22
17 42 0.78
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.44
Consensus pattern (17 bp):
CATTTATGCATCTAGTT
Found at i:1256996 original size:18 final size:18
Alignment explanation
Indices: 1256973--1257018 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
1256963 ATTCATGCAT
1256973 TTAGTTCATTGAATAAAG
1 TTAGTTCATTGAATAAAG
*
1256991 TTAGTTCATTGAATAATG
1 TTAGTTCATTGAATAAAG
*
1257009 TTATTTCATT
1 TTAGTTCATT
1257019 AATCAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.48
Consensus pattern (18 bp):
TTAGTTCATTGAATAAAG
Found at i:1265918 original size:14 final size:14
Alignment explanation
Indices: 1265887--1265937 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 14
1265877 TTATGTTATT
1265887 TTAAATT-T-ATAA
1 TTAAATTATGATAA
*
1265899 TAAAATTATGATAA
1 TTAAATTATGATAA
1265913 TTAAATTATTATGATAA
1 TT-AA--ATTATGATAA
1265930 TTAAATTA
1 TTAAATTA
1265938 ATATGATTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
12 6 0.19
13 1 0.03
14 9 0.28
15 2 0.06
16 2 0.06
17 12 0.38
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (14 bp):
TTAAATTATGATAA
Found at i:1265925 original size:17 final size:17
Alignment explanation
Indices: 1265903--1265944 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
1265893 TTATAATAAA
1265903 ATTATGATAATTAAATT
1 ATTATGATAATTAAATT
1265920 ATTATGATAATTAAATT
1 ATTATGATAATTAAATT
*
1265937 AATATGAT
1 ATTATGAT
1265945 TACTCTTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (17 bp):
ATTATGATAATTAAATT
Found at i:1265976 original size:51 final size:52
Alignment explanation
Indices: 1265914--1266011 Score: 171
Period size: 51 Copynumber: 1.9 Consensus size: 52
1265904 TTATGATAAT
*
1265914 TAAATTATTATGATAATTAAATTAATATGATTAC-TCTTTGAAATTTTATCA
1 TAAATTATTATGATAATCAAATTAATATGATTACTTCTTTGAAATTTTATCA
*
1265965 TAAATTATTATGATAATCAAATTAATATGATTACTTTTTTGAAATTT
1 TAAATTATTATGATAATCAAATTAATATGATTACTTCTTTGAAATTT
1266012 AATTTTATAT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
51 33 0.75
52 11 0.25
ACGTcount: A:0.41, C:0.05, G:0.06, T:0.48
Consensus pattern (52 bp):
TAAATTATTATGATAATCAAATTAATATGATTACTTCTTTGAAATTTTATCA
Found at i:1269621 original size:28 final size:28
Alignment explanation
Indices: 1269562--1269621 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
1269552 ATAAACTATT
* *
1269562 TATAATTAATATTAAAATAATTATATAT
1 TATAATTAATATTAAAATAATTATAAAA
* *
1269590 TATAATTAGTATTAATACTAA-TATAAAA
1 TATAATTAATATTAA-AATAATTATAAAA
1269618 TATA
1 TATA
1269622 GTCTATAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 23 0.85
29 4 0.15
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (28 bp):
TATAATTAATATTAAAATAATTATAAAA
Found at i:1269643 original size:31 final size:31
Alignment explanation
Indices: 1269600--1269661 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
1269590 TATAATTAGT
1269600 ATTAATACTAATATAAAATATA-GTCTATAAA
1 ATTAATACTAATATAAAATATATGT-TATAAA
* *
1269631 ATTAATATTAATATAAACTATATGTTATAAA
1 ATTAATACTAATATAAAATATATGTTATAAA
1269662 TTATATAGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 26 0.93
32 2 0.07
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (31 bp):
ATTAATACTAATATAAAATATATGTTATAAA
Found at i:1269673 original size:21 final size:21
Alignment explanation
Indices: 1269642--1269805 Score: 88
Period size: 21 Copynumber: 7.6 Consensus size: 21
1269632 TTAATATTAA
*
1269642 TATAAACTATATGTTATAAAT
1 TATATACTATATGTTATAAAT
* *
1269663 TATATAGTATA-GTTTATAAAC
1 TATATACTATATG-TTATAAAT
1269684 TATATACTATAT-TAATATAAAT
1 TATATACTATATGT--TATAAAT
* * *
1269706 TATAGTTACAATA-ATTA-ACAT
1 TATA--TACTATATGTTATAAAT
*
1269727 TAATATAAACTATATAGTATATTAA-
1 T-ATAT--ACTATAT-GT-TATAAAT
*
1269752 TATAAACTATA-GTTTATAAAT
1 TATATACTATATG-TTATAAAT
* *
1269773 TATATACTATAGGTTATAAAG
1 TATATACTATATGTTATAAAT
*
1269794 TATAAACTATAT
1 TATATACTATAT
1269806 AGTACATTAA
Statistics
Matches: 109, Mismatches: 17, Indels: 34
0.68 0.11 0.21
Matches are distributed among these distances:
20 9 0.08
21 58 0.53
22 27 0.25
24 11 0.10
25 3 0.03
26 1 0.01
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.41
Consensus pattern (21 bp):
TATATACTATATGTTATAAAT
Found at i:1269709 original size:22 final size:21
Alignment explanation
Indices: 1269631--1269783 Score: 66
Period size: 22 Copynumber: 7.0 Consensus size: 21
1269621 AGTCTATAAA
* *
1269631 ATTAATATTAATATAAACTAT
1 ATTAATATAAATATATACTAT
* * *
1269652 ATGTTATA-AATTATATAGTAT
1 AT-TAATATAAATATATACTAT
1269673 AGTT--TATAAACTATATACTAT
1 A-TTAATATAAA-TATATACTAT
*
1269694 ATTAATATAAATTATAGTTACAAT
1 ATTAATATAAA-TATA--TACTAT
* * *
1269718 AATTAACATTAATATAAACTAT
1 -ATTAATATAAATATATACTAT
* *
1269740 A-TAGTATATTAATATAAACTAT
1 ATTA--ATATAAATATATACTAT
1269762 AGTT--TATAAATTATATACTAT
1 A-TTAATATAAA-TATATACTAT
1269783 A
1 A
1269784 GGTTATAAAG
Statistics
Matches: 102, Mismatches: 16, Indels: 28
0.70 0.11 0.19
Matches are distributed among these distances:
19 2 0.02
20 11 0.11
21 34 0.33
22 36 0.35
24 10 0.10
25 9 0.09
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.42
Consensus pattern (21 bp):
ATTAATATAAATATATACTAT
Found at i:1269722 original size:88 final size:89
Alignment explanation
Indices: 1269608--1269783 Score: 250
Period size: 88 Copynumber: 2.0 Consensus size: 89
1269598 GTATTAATAC
* * * *
1269608 TAATATAAAATATAGTCTATAAAATTAATATTAATATAAACTATAT-GT-TATAAATTATATAGT
1 TAATATAAAATATAGTCTACAAAATTAACATTAATATAAACTATATAGTATATAAA-TATAAACT
1269671 ATAGTTTATAAACTATATACTATAT
65 ATAGTTTATAAACTATATACTATAT
* *
1269696 TAATATAAATTATAGT-TACAATAATTAACATTAATATAAACTATATAGTATATTAATATAAACT
1 TAATATAAAATATAGTCTACAA-AATTAACATTAATATAAACTATATAGTATATAAATATAAACT
*
1269760 ATAGTTTATAAATTATATACTATA
65 ATAGTTTATAAACTATATACTATA
1269784 GGTTATAAAG
Statistics
Matches: 78, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
87 4 0.05
88 38 0.49
89 31 0.40
90 5 0.06
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.41
Consensus pattern (89 bp):
TAATATAAAATATAGTCTACAAAATTAACATTAATATAAACTATATAGTATATAAATATAAACTA
TAGTTTATAAACTATATACTATAT
Found at i:1269898 original size:24 final size:23
Alignment explanation
Indices: 1269857--1269910 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
1269847 ATATACAGTT
*
1269857 TATATA-ACATATAAATAGATTG
1 TATATATACATATAAATAGATTA
* *
1269879 TATATATACATATACTATAGGTTA
1 TATATATACATATA-AATAGATTA
1269903 TATATATA
1 TATATATA
1269911 TAGTTTGTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 6 0.22
23 7 0.26
24 14 0.52
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.41
Consensus pattern (23 bp):
TATATATACATATAAATAGATTA
Found at i:1269939 original size:15 final size:15
Alignment explanation
Indices: 1269888--1269941 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
1269878 GTATATATAC
*
1269888 ATATACTATAGGTTAT
1 ATATAC-ATAGTTTAT
* *
1269904 ATATATATAGTTTGT
1 ATATACATAGTTTAT
1269919 ATATACATAGTTTAT
1 ATATACATAGTTTAT
*
1269934 ACATACAT
1 ATATACAT
1269942 GTACTATAAG
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
15 27 0.84
16 5 0.16
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.44
Consensus pattern (15 bp):
ATATACATAGTTTAT
Found at i:1270053 original size:28 final size:30
Alignment explanation
Indices: 1270021--1270082 Score: 85
Period size: 28 Copynumber: 2.1 Consensus size: 30
1270011 ATGCATATTG
*
1270021 TTTAGGGTTTAGGG-TTTA-AAGATTATA-A
1 TTTAGGATTTAGGGTTTTATAA-ATTATATA
1270049 TTTAGGATTTAGGGTTTTATAAATTATATA
1 TTTAGGATTTAGGGTTTTATAAATTATATA
1270079 TTTA
1 TTTA
1270083 TTATTTTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 13 0.43
29 10 0.33
30 7 0.23
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.48
Consensus pattern (30 bp):
TTTAGGATTTAGGGTTTTATAAATTATATA
Found at i:1270155 original size:2 final size:2
Alignment explanation
Indices: 1270117--1270143 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1270107 TGTTTCTGTA
1270117 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 A
1270144 CATTCTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1270263 original size:4 final size:4
Alignment explanation
Indices: 1270254--1270312 Score: 100
Period size: 4 Copynumber: 14.8 Consensus size: 4
1270244 TATAGTTTAT
* *
1270254 ATAC ATAC ATAC ATAC ATAC ATAC ATAT ATAC ATAT ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1270302 ATAC ATAC ATA
1 ATAC ATAC ATA
1270313 TATATATACT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 51 1.00
ACGTcount: A:0.51, C:0.20, G:0.00, T:0.29
Consensus pattern (4 bp):
ATAC
Found at i:1270321 original size:12 final size:12
Alignment explanation
Indices: 1270251--1270326 Score: 100
Period size: 12 Copynumber: 6.4 Consensus size: 12
1270241 ATTTATAGTT
1270251 TATATACATACA
1 TATATACATACA
*
1270263 TACATACATACA
1 TATATACATACA
* *
1270275 TACATATATACA
1 TATATACATACA
1270287 TATATACATACA
1 TATATACATACA
*
1270299 TACATACATACA
1 TATATACATACA
*
1270311 TATATATATAC-
1 TATATACATACA
1270322 TATAT
1 TATAT
1270327 TAATATAAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
11 5 0.09
12 52 0.91
ACGTcount: A:0.49, C:0.17, G:0.00, T:0.34
Consensus pattern (12 bp):
TATATACATACA
Found at i:1270402 original size:13 final size:13
Alignment explanation
Indices: 1270362--1270447 Score: 58
Period size: 13 Copynumber: 6.8 Consensus size: 13
1270352 ATATACTTTT
*
1270362 TATAGTTTATATAA
1 TATAGTATATA-AA
1270376 T-TAGTATA-AAA
1 TATAGTATATAAA
1270387 TATAGTATATAAA
1 TATAGTATATAAA
1270400 TATA-TATAGT--A
1 TATAGTATA-TAAA
*
1270411 TATA-AATATAAA
1 TATAGTATATAAA
* * *
1270423 CTATAATTTATATA
1 -TATAGTATATAAA
1270437 TATAGTATATA
1 TATAGTATATA
1270448 CTATATAAAG
Statistics
Matches: 58, Mismatches: 7, Indels: 15
0.73 0.09 0.19
Matches are distributed among these distances:
10 1 0.02
11 11 0.19
12 13 0.22
13 27 0.47
14 6 0.10
ACGTcount: A:0.50, C:0.01, G:0.06, T:0.43
Consensus pattern (13 bp):
TATAGTATATAAA
Found at i:1270447 original size:133 final size:133
Alignment explanation
Indices: 1270183--1270423 Score: 296
Period size: 133 Copynumber: 1.8 Consensus size: 133
1270173 ACAACATGGA
*
1270183 ATATACTATATTAATATAAATTATAATTTATAAACTACATATTTTATATAGTTTATACATTTATA
1 ATATACTATATTAATATAAATTATAATTTATAAACTACATATTTTATATAGTTTATACATATATA
* * * *
1270248 GTTTATATACATACATACATACATACATACATATATACATATATACATACATACATACATACATA
66 G-TTATATAAATACATACATAAATACATACATATATAAATATAAACATACATACATACATACATA
1270313 TA-T
130 TACT
* * *
1270316 ATATACTATATTAATATAAATTATATTTTATAAACTATATACTTTT-TATAGTTTATATA-AT-T
1 ATATACTATATTAATATAAATTATAATTTATAAACTACATA-TTTTATATAGTTTATACATATAT
* * * *
1270378 AG-TATA-AAATATAGTATATAAATATATATAGTATATAAATATAAAC
65 AGTTATATAAATACA-TACATAAATACATACA-TATATAAATATAAAC
1270424 TATAATTTAT
Statistics
Matches: 93, Mismatches: 12, Indels: 9
0.82 0.11 0.08
Matches are distributed among these distances:
128 5 0.05
129 16 0.17
130 13 0.14
131 3 0.03
132 1 0.01
133 51 0.55
134 4 0.04
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.42
Consensus pattern (133 bp):
ATATACTATATTAATATAAATTATAATTTATAAACTACATATTTTATATAGTTTATACATATATA
GTTATATAAATACATACATAAATACATACATATATAAATATAAACATACATACATACATACATAT
ACT
Found at i:1270467 original size:2 final size:2
Alignment explanation
Indices: 1270278--1270454 Score: 55
Period size: 2 Copynumber: 87.5 Consensus size: 2
1270268 ACATACATAC
* * * * * *
1270278 AT AT AT AC AT AT AT AC AT AC AT AC AT AC AT AC AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
1270320 ACT AT AT -T A- AT AT AA AT -T AT AT -T TT AT AA ACT AT AT ACT
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T
* * * * *
1270359 TT TT AT AGT TT AT AT A- AT -T AGT AT A- AA AT AT AGT AT AT AA
1 AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT
* * *
1270399 AT AT AT AT AGT AT AT AA AT AT AA ACT AT A- AT TT AT AT AT AT AGT
1 AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT A-T
1270443 AT AT ACT AT AT A
1 AT AT A-T AT AT A
1270455 AAGAGTTTAT
Statistics
Matches: 127, Mismatches: 30, Indels: 36
0.66 0.16 0.19
Matches are distributed among these distances:
1 8 0.06
2 103 0.81
3 16 0.13
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (2 bp):
AT
Found at i:1270534 original size:13 final size:13
Alignment explanation
Indices: 1270516--1270540 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1270506 TATACTTTAC
1270516 ATAGTTTATATAT
1 ATAGTTTATATAT
1270529 ATAGTTTATATA
1 ATAGTTTATATA
1270541 GTTTATACAT
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:0.00, G:0.08, T:0.52
Consensus pattern (13 bp):
ATAGTTTATATAT
Found at i:1270552 original size:13 final size:12
Alignment explanation
Indices: 1270516--1270592 Score: 50
Period size: 11 Copynumber: 7.1 Consensus size: 12
1270506 TATACTTTAC
1270516 ATAGTTTATATAT
1 ATAGTTTATA-AT
1270529 ATAG-TT-T-AT
1 ATAGTTTATAAT
1270538 ATAGTTTATACAT
1 ATAGTTTATA-AT
1270551 ATAG--TATAAGT
1 ATAGTTTATAA-T
1270562 -TAGTTTAT-AT
1 ATAGTTTATAAT
1270572 -T-GTTTAT-AT
1 ATAGTTTATAAT
1270581 ATAGTTTA-AAT
1 ATAGTTTATAAT
1270592 A
1 A
1270593 CTACTATATA
Statistics
Matches: 54, Mismatches: 0, Indels: 22
0.71 0.00 0.29
Matches are distributed among these distances:
9 14 0.26
10 9 0.17
11 16 0.30
12 5 0.09
13 10 0.19
ACGTcount: A:0.38, C:0.01, G:0.10, T:0.51
Consensus pattern (12 bp):
ATAGTTTATAAT
Found at i:1270554 original size:22 final size:22
Alignment explanation
Indices: 1270505--1270555 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
1270495 TATGTAAAAT
* *
1270505 ATATACTTTACATAGTTTATAT
1 ATATAGTTTACATAGTTTATAC
*
1270527 ATATAGTTTATATAGTTTATAC
1 ATATAGTTTACATAGTTTATAC
1270549 ATATAGT
1 ATATAGT
1270556 ATAAGTTAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.37, C:0.06, G:0.08, T:0.49
Consensus pattern (22 bp):
ATATAGTTTACATAGTTTATAC
Found at i:1273437 original size:106 final size:106
Alignment explanation
Indices: 1273316--1273757 Score: 509
Period size: 106 Copynumber: 4.3 Consensus size: 106
1273306 ATATCCTCAA
* * * *
1273316 CTGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTGTTTGTTGACAGTCAGCCCCCCCTTCACC
1 CTGTGAAGTTGAAATTGGTTCTGAAACTGGGAAATTATTTGTTGACAGTCAGCCGCCCCTTCGCC
* * * *
1273381 ATGAAGTTGAGCTTGTGTTGTCTTGAGTCCAATGTCCTTCG
66 GTGAAGTTGAGCTTGTGCTATCTTGAGTCCAATATCCTTCG
* * *
1273422 CTGTGAAGTTGAAATTGGATCTGAAACTGGGGAATTATTTGTTGACAGTCAGCCGCCCCTTCGCT
1 CTGTGAAGTTGAAATTGGTTCTGAAACTGGGAAATTATTTGTTGACAGTCAGCCGCCCCTTCGCC
* *
1273487 GTGAAGTTGAGCTTGTGCTGTCTTGAGTCTAATA----TC-
66 GTGAAGTTGAGCTTGTGCTATCTTGAGTCCAATATCCTTCG
** * * * *
1273523 C--TG-AGTTGAAATTGACTCTGAAA----G---TTATTTGTAGATAATCAGCCGCCCCTTCGTC
1 CTGTGAAGTTGAAATTGGTTCTGAAACTGGGAAATTATTTGTTGACAGTCAGCCGCCCCTTCGCC
* * *
1273578 GTGAAGTTGAGCTTGTGTTATCTTGGGACCAATATCCTTCG
66 GTGAAGTTGAGCTTGTGCTATCTTGAGTCCAATATCCTTCG
* * * *
1273619 CTGTGAAGTTGAAATTGGTTCTGAAATTAGGAAATTATTTGTTGAAAGTCAGCCGCCCCTTCGCT
1 CTGTGAAGTTGAAATTGGTTCTGAAACTGGGAAATTATTTGTTGACAGTCAGCCGCCCCTTCGCC
1273684 GTGAAGTTGAGCTTGTGCTATCTTGAGTCCAATATCCTTCG
66 GTGAAGTTGAGCTTGTGCTATCTTGAGTCCAATATCCTTCG
* * * *
1273725 TTGTGAAGTTGCAATTGGCTCTGAAATTGGGAA
1 CTGTGAAGTTGAAATTGGTTCTGAAACTGGGAA
1273758 GCCCCTTCGT
Statistics
Matches: 284, Mismatches: 37, Indels: 30
0.81 0.11 0.09
Matches are distributed among these distances:
91 55 0.19
94 1 0.00
95 2 0.01
96 1 0.00
98 20 0.07
99 20 0.07
101 1 0.00
102 2 0.01
103 1 0.00
106 181 0.64
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
CTGTGAAGTTGAAATTGGTTCTGAAACTGGGAAATTATTTGTTGACAGTCAGCCGCCCCTTCGCC
GTGAAGTTGAGCTTGTGCTATCTTGAGTCCAATATCCTTCG
Found at i:1273710 original size:197 final size:197
Alignment explanation
Indices: 1273364--1273721 Score: 581
Period size: 197 Copynumber: 1.8 Consensus size: 197
1273354 TTGTTGACAG
* * *
1273364 TCAGCCCCCCCTTCACCATGAAGTTGAGCTTGTGTTGTCTTGAGTCCAATGTCCTTCGCTGTGAA
1 TCAGCCCCCCCTTCACCATGAAGTTGAGCTTGTGTTATCTTGAGACCAATATCCTTCGCTGTGAA
* * *
1273429 GTTGAAATTGGATCTGAAACTGGGGAATTATTTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGT
66 GTTGAAATTGGATCTGAAACTAGGAAATTATTTGTTGAAAGTCAGCCGCCCCTTCGCTGTGAAGT
* *
1273494 TGAGCTTGTGCTGTCTTGAGTCTAATATCCTGAGTTGAAATTGACTCTGAAAGTTATTTGTAGAT
131 TGAGCTTGTGCTATCTTGAGTCCAATATCCTGAGTTGAAATTGACTCTGAAAGTTATTTGTAGAT
1273559 AA
196 AA
* ** * *
1273561 TCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTATCTTGGGACCAATATCCTTCGCTGTGAA
1 TCAGCCCCCCCTTCACCATGAAGTTGAGCTTGTGTTATCTTGAGACCAATATCCTTCGCTGTGAA
* *
1273626 GTTGAAATTGGTTCTGAAATTAGGAAATTATTTGTTGAAAGTCAGCCGCCCCTTCGCTGTGAAGT
66 GTTGAAATTGGATCTGAAACTAGGAAATTATTTGTTGAAAGTCAGCCGCCCCTTCGCTGTGAAGT
1273691 TGAGCTTGTGCTATCTTGAGTCCAATATCCT
131 TGAGCTTGTGCTATCTTGAGTCCAATATCCT
1273722 TCGTTGTGAA
Statistics
Matches: 146, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
197 146 1.00
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (197 bp):
TCAGCCCCCCCTTCACCATGAAGTTGAGCTTGTGTTATCTTGAGACCAATATCCTTCGCTGTGAA
GTTGAAATTGGATCTGAAACTAGGAAATTATTTGTTGAAAGTCAGCCGCCCCTTCGCTGTGAAGT
TGAGCTTGTGCTATCTTGAGTCCAATATCCTGAGTTGAAATTGACTCTGAAAGTTATTTGTAGAT
AA
Found at i:1274851 original size:21 final size:21
Alignment explanation
Indices: 1274826--1274869 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1274816 TGAACCCACC
*
1274826 TTATTTTCTTT-TCTTTTTCTT
1 TTATTTT-TTTCTCTTTTCCTT
1274847 TTATTTTTTTCTCTTTTCCTT
1 TTATTTTTTTCTCTTTTCCTT
1274868 TT
1 TT
1274870 TCTCTCTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.80
Consensus pattern (21 bp):
TTATTTTTTTCTCTTTTCCTT
Found at i:1274869 original size:14 final size:13
Alignment explanation
Indices: 1274832--1274883 Score: 54
Period size: 14 Copynumber: 4.0 Consensus size: 13
1274822 CACCTTATTT
1274832 TCTTTTCTTTTTC
1 TCTTTTCTTTTTC
*
1274845 T-TTTATTTTTTTC
1 TCTTT-TCTTTTTC
1274858 TCTTTTCCTTTTTC
1 TCTTTT-CTTTTTC
*
1274872 TCTCTT-TTTTTC
1 TCTTTTCTTTTTC
1274884 AACTTAGGAC
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
12 9 0.27
13 10 0.30
14 14 0.42
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (13 bp):
TCTTTTCTTTTTC
Found at i:1274869 original size:16 final size:15
Alignment explanation
Indices: 1274829--1274879 Score: 57
Period size: 16 Copynumber: 3.3 Consensus size: 15
1274819 ACCCACCTTA
*
1274829 TTTTCTTTTCTTTTTC
1 TTTTCTTTT-TTTCTC
*
1274845 TTTTATTTTTTTCTC
1 TTTTCTTTTTTTCTC
*
1274860 TTTTCCTTTTTCTCTC
1 TTTT-CTTTTTTTCTC
1274876 TTTT
1 TTTT
1274880 TTTCAACTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
15 9 0.30
16 21 0.70
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTCTTTTTTTCTC
Found at i:1274880 original size:27 final size:26
Alignment explanation
Indices: 1274832--1274883 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1274822 CACCTTATTT
*
1274832 TCTTTTCTTTTTCTTTTATTTTTTTC
1 TCTTTTCTTTTTCTTCTATTTTTTTC
*
1274858 TCTTTTCCTTTTTC-TCTCTTTTTTTC
1 TCTTTT-CTTTTTCTTCTATTTTTTTC
1274884 AACTTAGGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 16 0.70
27 7 0.30
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (26 bp):
TCTTTTCTTTTTCTTCTATTTTTTTC
Found at i:1278453 original size:13 final size:13
Alignment explanation
Indices: 1278437--1278471 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
1278427 AAGAGAAATG
1278437 GAAATGAAGTGCT
1 GAAATGAAGTGCT
1278450 GAAATGAAGTGCT
1 GAAATGAAGTGCT
1278463 GAAATGAAG
1 GAAATGAAG
1278472 AAATAGACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.43, C:0.06, G:0.31, T:0.20
Consensus pattern (13 bp):
GAAATGAAGTGCT
Found at i:1281932 original size:24 final size:23
Alignment explanation
Indices: 1281905--1281957 Score: 54
Period size: 24 Copynumber: 2.2 Consensus size: 23
1281895 TAGTTAATAC
*
1281905 AAATGTAA-AAACATGGAAAATATA
1 AAATGAAACAAACAT-G-AAATATA
*
1281929 AAATAAAAACAAACATGAAATATA
1 AAAT-GAAACAAACATGAAATATA
1281953 AAATG
1 AAATG
1281958 CAAGAAATGC
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
24 15 0.62
25 3 0.12
26 6 0.25
ACGTcount: A:0.66, C:0.06, G:0.09, T:0.19
Consensus pattern (23 bp):
AAATGAAACAAACATGAAATATA
Found at i:1286792 original size:17 final size:17
Alignment explanation
Indices: 1286754--1286854 Score: 73
Period size: 18 Copynumber: 5.8 Consensus size: 17
1286744 ATTAATAAAC
1286754 TATATAATTTATACAATA
1 TATATAATTTATA-AATA
* *
1286772 TATATTATTTATAATTA
1 TATATAATTTATAAATA
*
1286789 TATATAATATAT-AA-A
1 TATATAATTTATAAATA
**
1286804 TATA-AATTGTATAGTTTA
1 TATATAATT-TATA-AATA
*
1286822 TATATAATTTATATATAAA
1 TATATAATTTATA-A-ATA
1286841 CTATATAATTTATA
1 -TATATAATTTATA
1286855 TTAATAAACT
Statistics
Matches: 64, Mismatches: 12, Indels: 12
0.73 0.14 0.14
Matches are distributed among these distances:
14 3 0.05
15 8 0.12
16 1 0.02
17 13 0.20
18 21 0.33
19 5 0.08
20 13 0.20
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (17 bp):
TATATAATTTATAAATA
Found at i:1286836 original size:20 final size:20
Alignment explanation
Indices: 1286724--1286908 Score: 103
Period size: 22 Copynumber: 9.7 Consensus size: 20
1286714 TCATATATTA
*
1286724 ATATAAACTATATAGTTTAT
1 ATATAAACTATATAATTTAT
1286744 ATTAATAAACTATATAA-TT-T
1 A-T-ATAAACTATATAATTTAT
*
1286764 ATA-CAA-TATAT-A-TTAT
1 ATATAAACTATATAATTTAT
* * *
1286780 TTAT-AATTATAT-A-TAAT
1 ATATAAACTATATAATTTAT
1286797 ATATAAA-TATA-AATTGTAT
1 ATATAAACTATATAATT-TAT
*
1286816 AGT-T-TA-TATATAATTTAT
1 A-TATAAACTATATAATTTAT
1286834 ATATAAACTATATAATTTAT
1 ATATAAACTATATAATTTAT
* *
1286854 ATTAATAAACTATGTAGTTTAT
1 A-T-ATAAACTATATAATTTAT
** * *
1286876 ATAT-AGTTAAATAATTCAT
1 ATATAAACTATATAATTTAT
1286895 ATATAAACTATATA
1 ATATAAACTATATA
1286909 GTATTATAGT
Statistics
Matches: 129, Mismatches: 19, Indels: 34
0.71 0.10 0.19
Matches are distributed among these distances:
15 3 0.02
16 10 0.08
17 20 0.16
18 14 0.11
19 23 0.18
20 25 0.19
21 5 0.04
22 29 0.22
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (20 bp):
ATATAAACTATATAATTTAT
Found at i:1286838 original size:31 final size:33
Alignment explanation
Indices: 1286754--1286860 Score: 96
Period size: 31 Copynumber: 3.3 Consensus size: 33
1286744 ATTAATAAAC
* * *
1286754 TATATAATTTATACAATATATATTATTTATAA-TTA
1 TATATAATATATA-AATATAAACTA--TATAATTTA
* * *
1286789 TATATAATATATAAATATAAATTGTATAGTTTA
1 TATATAATATATAAATATAAACTATATAATTTA
*
1286822 TATATAAT-T-TATATATAAACTATATAATTTA
1 TATATAATATATAAATATAAACTATATAATTTA
1286853 TAT-TAATA
1 TATATAATA
1286861 AACTATGTAG
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
30 4 0.06
31 21 0.34
32 5 0.08
33 11 0.18
34 9 0.15
35 12 0.19
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (33 bp):
TATATAATATATAAATATAAACTATATAATTTA
Found at i:1286973 original size:29 final size:28
Alignment explanation
Indices: 1286903--1286979 Score: 95
Period size: 28 Copynumber: 2.7 Consensus size: 28
1286893 ATATATAAAC
*
1286903 TATATAGTATTATA-GTTTATACATGGTA
1 TATATAGT-TTATATATTTATACATGGTA
1286931 TATATAGTTTATATATTTATACAT-GTA
1 TATATAGTTTATATATTTATACATGGTA
*
1286958 TATATATTTATAATATATTTAT
1 TATATAGTT-T-ATATATTTAT
1286980 TATATAATTA
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
27 16 0.36
28 18 0.41
29 10 0.23
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.52
Consensus pattern (28 bp):
TATATAGTTTATATATTTATACATGGTA
Found at i:1287448 original size:185 final size:183
Alignment explanation
Indices: 1287212--1287581 Score: 543
Period size: 185 Copynumber: 2.0 Consensus size: 183
1287202 TATTTTTAAT
* * * *
1287212 TGACCCATAATTTTTTAAATGGGTATAATTTAGTTCTTTTTTGTATTAATTTAAACCTCACAATT
1 TGACCCATAACTTTTAAAATGAGTATAATTTAGTACTTTTTTGTATTAATTTAAACCTCACAATT
1287277 TAAAATTAATTTGATTTGATCCCTCTCAATGTGTGTGTTTAATTTATTTAAA-TTTAATTTATAA
66 TAAAATTAATTTGATTTGATCCCT-T---TGTGT-TGTTTAATTTATTTAAATTTTAATTTATAA
1287341 TTTCATATTTGT-TCAATTTAGTCCTT-AAAAT-TATTTGCATATGAAATTGACCCATAC
126 TTTCATATTTGTAT-AATTTAGT-CTTCAAAATATATTTGCATATGAAATTGACCCATAC
1287398 TGACCCATAACTTTTAAAATGAGTATAATTTAGTAC-TTTTTGTATTAATTTAAACCTCACAATT
1 TGACCCATAACTTTTAAAATGAGTATAATTTAGTACTTTTTTGTATTAATTTAAACCTCACAATT
* * *
1287462 TAAAATTATTTTGATTTGATCCCTTTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCA
66 TAAAATTAATTTGATTTGATCCCTTTGTGTTGTTTAATTTATTTAAATTTTAATTTATAATTTCA
* * *
1287527 TATTTGTATAATTTTGTCTTCCAAATTATATTTGCATCTGAAATTGACCCATAC
131 TATTTGTATAATTTAGTCTT-CAAAATATATTTGCATATGAAATTGACCCATAC
1287581 T
1 T
1287582 TATTACTTAT
Statistics
Matches: 169, Mismatches: 10, Indels: 13
0.88 0.05 0.07
Matches are distributed among these distances:
180 20 0.12
181 34 0.20
182 5 0.03
183 26 0.15
184 1 0.01
185 51 0.30
186 32 0.19
ACGTcount: A:0.31, C:0.12, G:0.09, T:0.48
Consensus pattern (183 bp):
TGACCCATAACTTTTAAAATGAGTATAATTTAGTACTTTTTTGTATTAATTTAAACCTCACAATT
TAAAATTAATTTGATTTGATCCCTTTGTGTTGTTTAATTTATTTAAATTTTAATTTATAATTTCA
TATTTGTATAATTTAGTCTTCAAAATATATTTGCATATGAAATTGACCCATAC
Found at i:1288202 original size:26 final size:25
Alignment explanation
Indices: 1288166--1288215 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
1288156 AAGCATCAAA
* *
1288166 TTTACCTGACTTGACATGTATCCGAT
1 TTTACCCGACTTGACA-GGATCCGAT
1288192 TTTACCCGACTTGACAGGATCCGA
1 TTTACCCGACTTGACAGGATCCGA
1288216 CTGAAACCTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (25 bp):
TTTACCCGACTTGACAGGATCCGAT
Found at i:1290402 original size:2 final size:2
Alignment explanation
Indices: 1290397--1290440 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1290387 ATAAAATTTA
1290397 AT 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 AT
1290439 AT
1 AT
1290441 CAAATTTATC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1292432 original size:16 final size:15
Alignment explanation
Indices: 1292405--1292435 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
1292395 ATTTTTTTCC
1292405 AAATATTAAATAATA
1 AAATATTAAATAATA
1292420 AAATATATAAATAATA
1 AAATAT-TAAATAATA
1292436 TTAATAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AAATATTAAATAATA
Found at i:1293418 original size:21 final size:21
Alignment explanation
Indices: 1293370--1293421 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
1293360 ATTTATCGTG
*
1293370 ATTGCGACCGTCGCGGAAGCT
1 ATTGCGGCCGTCGCGGAAGCT
* **
1293391 ATTGCGGCTGTCGCGGACTCT
1 ATTGCGGCCGTCGCGGAAGCT
1293412 ATTGCGGCCG
1 ATTGCGGCCG
1293422 CCGCTGATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.13, C:0.29, G:0.35, T:0.23
Consensus pattern (21 bp):
ATTGCGGCCGTCGCGGAAGCT
Found at i:1297619 original size:41 final size:41
Alignment explanation
Indices: 1297562--1297640 Score: 149
Period size: 41 Copynumber: 1.9 Consensus size: 41
1297552 CCCTTTATCC
1297562 TGGTCAAATTGTTAGCAACCAAAGTTGATTTGTTATTCTTT
1 TGGTCAAATTGTTAGCAACCAAAGTTGATTTGTTATTCTTT
*
1297603 TGGTCAAATTGTTAGCAATCAAAGTTGATTTGTTATTC
1 TGGTCAAATTGTTAGCAACCAAAGTTGATTTGTTATTC
1297641 CTTGTGGAGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.28, C:0.11, G:0.18, T:0.43
Consensus pattern (41 bp):
TGGTCAAATTGTTAGCAACCAAAGTTGATTTGTTATTCTTT
Found at i:1303202 original size:2 final size:2
Alignment explanation
Indices: 1303195--1303223 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1303185 TAATGCAAAA
1303195 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1303224 TTGTAGCGGA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1308294 original size:55 final size:55
Alignment explanation
Indices: 1308235--1308645 Score: 410
Period size: 55 Copynumber: 7.5 Consensus size: 55
1308225 ATGACGAGCA
1308235 TGCTCCCTATTCCTTCA-AGAAGTATA-AGACTCGAACAATCTTCATA-AAACGTGTC
1 TGCTCCCTATTCCTTCAGAG-AGTATAGA-ACTCGAACAATCTTCA-ACAAACGTGTC
* * * *
1308290 TGCTCCCTATTCATTCAGGGAGTATA-AGACTCGAACAATCTTCAGCAAATGTGTC
1 TGCTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAAACGTGTC
* * * * *
1308345 TGCTCCCTATTCATTCAGGGAGTATA-AGACTCAAACAATCTTCAATAAACAG-ATC
1 TGCTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAAAC-GTGTC
* * * *
1308400 TGCTCCCTATTCGTTCAGGGAGTATAGAAC-CTGAACAGTCTTCATA-AAACGGGTC
1 TGCTCCCTATTCCTTCAGAGAGTATAGAACTC-GAACAATCTTCA-ACAAACGTGTC
* * * * * * *
1308455 CGCTCTCTATTTCTTCAGAGAGTATAGAACTCGAATAGTCTTCAATAAACGGGT-
1 TGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTC
* **
1308509 TCGCTCCCTATT-CTATCAGAGAGTATAGAACTCGAACAATATTCAACAAACAAGTC
1 T-GCTCCCTATTCCT-TCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTC
* * * *
1308565 TGCTCTCTATTCTTTCAGAGAGTATAGAACTCGAACAATCTTCAACGAACTTGTC
1 TGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTC
*
1308620 CGCTCCCTATTCCTTCAGAGAGTATA
1 TGCTCCCTATTCCTTCAGAGAGTATA
1308646 TGACTCAATC
Statistics
Matches: 307, Mismatches: 36, Indels: 26
0.83 0.10 0.07
Matches are distributed among these distances:
54 5 0.02
55 295 0.96
56 7 0.02
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (55 bp):
TGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTC
Found at i:1308489 original size:165 final size:165
Alignment explanation
Indices: 1308235--1308666 Score: 467
Period size: 165 Copynumber: 2.6 Consensus size: 165
1308225 ATGACGAGCA
* * *
1308235 TGCTCCCTATTCCTTCAAGAAGTATA-AGACTCGAACAATCTTCATAAAACGTGTCTGCTCCCTA
1 TGCTCCCTATTCCTTCAGGGAGTATAGA-ACTCGAACAATCTTCATAAAACGTGTCCGCTCCCTA
* * * *
1308299 -TTCATTCAGGGAGTATAAGACTCGAACAATCTTCAGCAAATGTG-TCTGCTCCCTATTC-ATTC
65 TTTC-TTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGGGTTC-GCTCCCTATTCTA-TC
* * *
1308361 AGGGAGTATA-AGACTCAAACAATCTTCAATAAAC-AGATC
127 AGAGAGTATAGA-ACTCAAACAATATTCAACAAACAAG-TC
* * * *
1308400 TGCTCCCTATTCGTTCAGGGAGTATAGAAC-CTGAACAGTCTTCATAAAACGGGTCCGCTCTCTA
1 TGCTCCCTATTCCTTCAGGGAGTATAGAACTC-GAACAATCTTCATAAAACGTGTCCGCTCCCTA
* * *
1308464 TTTCTTCAGAGAGTAT-AGAACTCGAATAGTCTTCAATAAACGGGTTCGCTCCCTATTCTATCAG
65 TTTCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAAACGGGTTCGCTCCCTATTCTATCAG
*
1308528 AGAGTATAGAACTCGAACAATATTCAACAAACAAGTC
129 AGAGTATAGAACTCAAACAATATTCAACAAACAAGTC
* * * * *
1308565 TGCTCTCTATTCTTTCAGAGAGTATAGAACTCGAACAATCTTCA-ACGAACTTGTCCGCTCCCTA
1 TGCTCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCATA-AAACGTGTCCGCTCCCTA
* *
1308629 TTCCTTCAGAGAGTATATGACT----CAATCTTCAACAAACG
65 TTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACG
1308667 AGTTTGCTTC
Statistics
Matches: 225, Mismatches: 31, Indels: 26
0.80 0.11 0.09
Matches are distributed among these distances:
161 13 0.06
164 4 0.02
165 196 0.87
166 12 0.05
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (165 bp):
TGCTCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCATAAAACGTGTCCGCTCCCTAT
TTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGGGTTCGCTCCCTATTCTATCAGAG
AGTATAGAACTCAAACAATATTCAACAAACAAGTC
Found at i:1310110 original size:44 final size:44
Alignment explanation
Indices: 1310038--1310138 Score: 109
Period size: 44 Copynumber: 2.3 Consensus size: 44
1310028 TATTTTTTCA
* * **
1310038 TTTTTCTCTTTTTGTTTTTCTCTTTCATTTTTACCCATTTTC-C-AT
1 TTTTTTTCTTTTCGTTTTTCTCCATCATTTTT--CC-TTTTCTCAAT
1310083 TTTTTTTCTTTTCGTTTTT-TCCATCATTTTTCCTTTTCTCAAT
1 TTTTTTTCTTTTCGTTTTTCTCCATCATTTTTCCTTTTCTCAAT
1310126 TTTCTTTTCTTTT
1 TTT-TTTTCTTTT
1310139 TTTTCTTCTT
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
41 5 0.10
42 3 0.06
43 5 0.10
44 19 0.39
45 17 0.35
ACGTcount: A:0.08, C:0.21, G:0.02, T:0.69
Consensus pattern (44 bp):
TTTTTTTCTTTTCGTTTTTCTCCATCATTTTTCCTTTTCTCAAT
Found at i:1310140 original size:28 final size:27
Alignment explanation
Indices: 1310109--1310169 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
1310099 TTTTCCATCA
* *
1310109 TTTTTCCTT-TTCTCAATTTTCTTTTCTT
1 TTTTTCCTTCTTCTC-ATTTT-TATTATT
*
1310137 TTTTTTCTTCTTCTCATTTTTATTATT
1 TTTTTCCTTCTTCTCATTTTTATTATT
1310164 TTTTTC
1 TTTTTC
1310170 ATTCATTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
27 10 0.36
28 13 0.46
29 5 0.18
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (27 bp):
TTTTTCCTTCTTCTCATTTTTATTATT
Found at i:1310156 original size:15 final size:14
Alignment explanation
Indices: 1310106--1310157 Score: 59
Period size: 15 Copynumber: 3.6 Consensus size: 14
1310096 GTTTTTTCCA
1310106 TCATTTTTCCTTTTC
1 TCATTTTT-CTTTTC
*
1310121 TCAATTTTCTTTTC
1 TCATTTTTCTTTTC
**
1310135 TTTTTTTTCTTCTTC
1 TCATTTTTCTT-TTC
1310150 TCATTTTT
1 TCATTTTT
1310158 ATTATTTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
14 14 0.47
15 16 0.53
ACGTcount: A:0.08, C:0.21, G:0.00, T:0.71
Consensus pattern (14 bp):
TCATTTTTCTTTTC
Found at i:1310178 original size:11 final size:12
Alignment explanation
Indices: 1310163--1310195 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
1310153 TTTTTATTAT
1310163 TTTTTTCATTCA
1 TTTTTTCATTCA
*
1310175 TTTTTT-TTTCA
1 TTTTTTCATTCA
1310186 TTTTTTCATT
1 TTTTTTCATT
1310196 TACTCTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTTTCATTCA
Found at i:1319893 original size:45 final size:45
Alignment explanation
Indices: 1319826--1319976 Score: 248
Period size: 45 Copynumber: 3.3 Consensus size: 45
1319816 CCATGCTTTG
*
1319826 TTATTCACAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGC
1 TTATTCA-AAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGC
1319873 TTATTCAAAAAATAAACCTAACCGCATGATATCTAGTTCGCATGC
1 TTATTCAAAAAATAAACCTAACCGCATGATATCTAGTTCGCATGC
1319918 TTATTCAAAAAATAAACCTAACCGCATGATATCTAGTTCGCATGC
1 TTATTCAAAAAATAAACCTAACCGCATGATATCTAGTTCGCATGC
*
1319963 ATTTATTCGAAAAA
1 --TTATTCAAAAAA
1319977 CGAAAATAAA
Statistics
Matches: 100, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
45 73 0.73
46 9 0.09
47 18 0.18
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.30
Consensus pattern (45 bp):
TTATTCAAAAAATAAACCTAACCGCATGATATCTAGTTCGCATGC
Found at i:1324479 original size:13 final size:15
Alignment explanation
Indices: 1324453--1324485 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1324443 AATGAATTAA
1324453 ATTTTCTGGAAAAT-
1 ATTTTCTGGAAAATC
1324467 ATTTTCT-GAAAATC
1 ATTTTCTGGAAAATC
1324481 ATTTT
1 ATTTT
1324486 ACAATGTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.48
Consensus pattern (15 bp):
ATTTTCTGGAAAATC
Found at i:1324747 original size:32 final size:32
Alignment explanation
Indices: 1324657--1324747 Score: 91
Period size: 32 Copynumber: 2.8 Consensus size: 32
1324647 CAATATCATT
1324657 AAAAATATTAATATTATT-ATAT-TTTATTAAA
1 AAAAATATT-ATATTATTAATATATTTATTAAA
1324688 ATAAAATATTATAATTATTTTAA-ATATTTATT-AA
1 A-AAAATATTAT-ATTA--TTAATATATTTATTAAA
*
1324722 AAAAATAATATATTATTAAGTATATT
1 AAAAATATTATATTATTAA-TATATT
1324748 ACTTACTTGT
Statistics
Matches: 51, Mismatches: 1, Indels: 15
0.76 0.01 0.22
Matches are distributed among these distances:
30 4 0.08
31 3 0.06
32 21 0.41
33 9 0.18
34 7 0.14
35 7 0.14
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (32 bp):
AAAAATATTATATTATTAATATATTTATTAAA
Found at i:1325030 original size:27 final size:25
Alignment explanation
Indices: 1324983--1325034 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 25
1324973 TTAATATTTT
1324983 TATTAAAATAATACTAAAAATAATA
1 TATTAAAATAATACTAAAAATAATA
1325008 TATTAATAATAAATA-TATAAAATAATA
1 TATTAA-AAT-AATACTA-AAAATAATA
1325035 ATGTTTTGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 6 0.25
26 5 0.21
27 13 0.54
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (25 bp):
TATTAAAATAATACTAAAAATAATA
Found at i:1338004 original size:174 final size:174
Alignment explanation
Indices: 1337706--1338037 Score: 488
Period size: 174 Copynumber: 1.9 Consensus size: 174
1337696 AACATTCGGC
** * *
1337706 CCTGATTGATTTACAGCAAGTAAACCTCTAGCCTTACATTTTCTCTTGTCGGTCACCCCAGCAAT
1 CCTGATTGAGCTACAGCAAGTAAACCTCTAGCCTTACATTTTCTCTTGTCGGTAACCCCAGAAAT
* *
1337771 GAGATGGCCAGCACTGTAACAGGCAGGAGTTGTTGCCATGGTTGCAGTAGACTGAATCTCGGGAG
66 GAGATGACCAGCACTGTAACAGGCAGGAGTTGTTGCCATGGTTGCAGTAGACCGAATCTCGGGAG
* *
1337836 AAAATGAAGCTTGCAGGGGTGGTGTTTTGGTCTCATCATTGGGT
131 AAAACGAAGCCTGCAGGGGTGGTGTTTTGGTCTCATCATTGGGT
* *
1337880 CCTGATTGAGCTACAGCAAGTACACCTCTAG-CTCTACATTTTCTCTTGTCGGTAACCCCGGAAA
1 CCTGATTGAGCTACAGCAAGTAAACCTCTAGCCT-TACATTTTCTCTTGTCGGTAACCCCAGAAA
* * * * * *
1337944 TGATATGACCGGCAGC-GTAACAGGCAGGAGTTTTTGTCATGGTTGCCGTCGACCGAATCTCGGG
65 TGAGATGACCAGCA-CTGTAACAGGCAGGAGTTGTTGCCATGGTTGCAGTAGACCGAATCTCGGG
1338008 AGAAAACGAAGCCTGCAGGGGTGGTGTTTT
129 AGAAAACGAAGCCTGCAGGGGTGGTGTTTT
1338038 AGTGTTCGGT
Statistics
Matches: 140, Mismatches: 16, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
173 2 0.01
174 137 0.98
175 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.27
Consensus pattern (174 bp):
CCTGATTGAGCTACAGCAAGTAAACCTCTAGCCTTACATTTTCTCTTGTCGGTAACCCCAGAAAT
GAGATGACCAGCACTGTAACAGGCAGGAGTTGTTGCCATGGTTGCAGTAGACCGAATCTCGGGAG
AAAACGAAGCCTGCAGGGGTGGTGTTTTGGTCTCATCATTGGGT
Found at i:1341454 original size:2 final size:2
Alignment explanation
Indices: 1341447--1341486 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1341437 GAAAAATACA
1341447 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
1341487 TGAAGAGACT
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:1342381 original size:55 final size:55
Alignment explanation
Indices: 1342297--1342406 Score: 202
Period size: 55 Copynumber: 2.0 Consensus size: 55
1342287 GTAGTGTGTG
* *
1342297 ATAAACTCCATTTTTTCTGAACCTTAAAAGAAAGCATCTGCATTGTTTGCTTAGT
1 ATAAACTCCATTTTTTCTCAACCTTAAAAGAAAGCATCTGCATTGTGTGCTTAGT
1342352 ATAAACTCCATTTTTTCTCAACCTTAAAAGAAAGCATCTGCATTGTGTGCTTAGT
1 ATAAACTCCATTTTTTCTCAACCTTAAAAGAAAGCATCTGCATTGTGTGCTTAGT
1342407 TTTCCTAGAC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (55 bp):
ATAAACTCCATTTTTTCTCAACCTTAAAAGAAAGCATCTGCATTGTGTGCTTAGT
Found at i:1366352 original size:3 final size:3
Alignment explanation
Indices: 1366339--1366371 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
1366329 TCGAGATGGG
1366339 ATC AT- ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1366372 AAATTCATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.36, C:0.30, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:1369032 original size:16 final size:16
Alignment explanation
Indices: 1369011--1369046 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
1369001 GAAGAAGAAT
1369011 AGGGGATAGAGAGGCA
1 AGGGGATAGAGAGGCA
1369027 AGGGGATAGAGAGGCA
1 AGGGGATAGAGAGGCA
1369043 AGGG
1 AGGG
1369047 TTAGGGATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.36, C:0.06, G:0.53, T:0.06
Consensus pattern (16 bp):
AGGGGATAGAGAGGCA
Found at i:1382799 original size:22 final size:22
Alignment explanation
Indices: 1382768--1382839 Score: 110
Period size: 22 Copynumber: 3.3 Consensus size: 22
1382758 CTGAGTGGCA
1382768 TATGAAATTTGTCCCGAAGGACC
1 TATG-AATTTGTCCCGAAGGACC
*
1382791 TGTGAATTTGTCCCGAAGGACC
1 TATGAATTTGTCCCGAAGGACC
*
1382813 TATG-AGTTGTCCCGAAGGACC
1 TATGAATTTGTCCCGAAGGACC
1382834 TATGAA
1 TATGAA
1382840 ACCCTCGACT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
21 20 0.44
22 22 0.49
23 3 0.07
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (22 bp):
TATGAATTTGTCCCGAAGGACC
Found at i:1382824 original size:21 final size:21
Alignment explanation
Indices: 1382776--1382838 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
1382766 CATATGAAAT
* *
1382776 TTGTCCCGAAGGACCTGTGAAT
1 TTGTCCCGAAGGACCTATG-AG
1382798 TTGTCCCGAAGGACCTATGAG
1 TTGTCCCGAAGGACCTATGAG
1382819 TTGTCCCGAAGGACCTATGA
1 TTGTCCCGAAGGACCTATGA
1382839 AACCCTCGAC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
21 21 0.54
22 18 0.46
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGAG
Found at i:1384315 original size:64 final size:64
Alignment explanation
Indices: 1384215--1384375 Score: 209
Period size: 64 Copynumber: 2.5 Consensus size: 64
1384205 TAATGAAGGT
* * *
1384215 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTGTATTT-AATGG
1 ATGCATCGATGCACTACA-TATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAAT--
*
1384278 GG
63 GC
* *
1384280 ATGCATCGATGCACTACTTATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTACATATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATGC
* *
1384344 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACTACATATGCATCGATGCA
1384376 CCTTAAACAA
Statistics
Matches: 85, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 57 0.67
65 25 0.29
66 3 0.04
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACATATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATGC
Found at i:1388267 original size:22 final size:22
Alignment explanation
Indices: 1388236--1388307 Score: 92
Period size: 22 Copynumber: 3.3 Consensus size: 22
1388226 CTGAGTGGCA
1388236 TATGAAATTTGTCCCGAAGGACC
1 TATG-AATTTGTCCCGAAGGACC
* * *
1388259 TGTGAATTTGACCTGAAGGACC
1 TATGAATTTGTCCCGAAGGACC
*
1388281 TATG-AGTTGTCCCGAAGGACC
1 TATGAATTTGTCCCGAAGGACC
1388302 TATGAA
1 TATGAA
1388308 ACCCTCGACT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
21 18 0.44
22 20 0.49
23 3 0.07
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.26
Consensus pattern (22 bp):
TATGAATTTGTCCCGAAGGACC
Found at i:1388299 original size:21 final size:21
Alignment explanation
Indices: 1388244--1388306 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
1388234 CATATGAAAT
* *
1388244 TTGTCCCGAAGGACCTGTGAAT
1 TTGTCCCGAAGGACCTATG-AG
* *
1388266 TTGACCTGAAGGACCTATGAG
1 TTGTCCCGAAGGACCTATGAG
1388287 TTGTCCCGAAGGACCTATGA
1 TTGTCCCGAAGGACCTATGA
1388307 AACCCTCGAC
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
21 19 0.54
22 16 0.46
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGAG
Found at i:1389813 original size:64 final size:63
Alignment explanation
Indices: 1389676--1389836 Score: 198
Period size: 64 Copynumber: 2.5 Consensus size: 63
1389666 TAATGAAGGT
* * * *
1389676 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAATGGGG
1 ATGCATCGATGCACTACA-TATGCATCGATGCATAAATCATATTCGATGTTTCTATTTAAT-GGC
* * *
1389741 ATGAATCGATGCACTACTTATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAAT-TC
1 ATGCATCGATGCACTACATATGCATCGATGCATAAATCATATTCGATG-TTTCTATTT-AATGGC
* *
1389805 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACTACATATGCATCGATGCA
1389837 CCTTAAACAA
Statistics
Matches: 83, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
64 56 0.67
65 24 0.29
66 3 0.04
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTACATATGCATCGATGCATAAATCATATTCGATGTTTCTATTTAATGGC
Found at i:1401514 original size:90 final size:88
Alignment explanation
Indices: 1401361--1401534 Score: 276
Period size: 90 Copynumber: 2.0 Consensus size: 88
1401351 CCTAACACAC
* * * *
1401361 CCTTTTATAGCCAAGTTACCCTAGTCATTTAGGGTTTTTATTATTTCAAATTAATTAAGTCTATA
1 CCTTTTATAGCCAAGTTACCCTAATCATTCAGGGATTTTATTATTTCAAATTAATTAAATCTATA
*
1401426 TTTAATTAATTAGAATTTAATAAT
66 TTTAATTAATT-GAAATTAATAAT
*
1401450 CCTTTTATATCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCAT-TCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1401515 ATTTAATTAATTGAAATTAA
65 ATTTAATTAATTGAAATTAA
1401535 ATATTCAGGA
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
89 33 0.42
90 45 0.58
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.45
Consensus pattern (88 bp):
CCTTTTATAGCCAAGTTACCCTAATCATTCAGGGATTTTATTATTTCAAATTAATTAAATCTATA
TTTAATTAATTGAAATTAATAAT
Found at i:1412467 original size:3 final size:3
Alignment explanation
Indices: 1412459--1412498 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
1412449 GTGACTCTAG
1412459 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1412499 TATATATAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1413079 original size:23 final size:22
Alignment explanation
Indices: 1413039--1413084 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
1413029 ATGTTGTAAT
*
1413039 AAATTATAGAAATTAGTGTAAAG
1 AAATTATAGAAATAAGTG-AAAG
1413062 AAATTATATG-AATAAGTGAAAG
1 AAATTATA-GAAATAAGTGAAAG
1413084 A
1 A
1413085 GTAAAATAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 5 0.24
23 15 0.71
24 1 0.05
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.28
Consensus pattern (22 bp):
AAATTATAGAAATAAGTGAAAG
Found at i:1413223 original size:28 final size:29
Alignment explanation
Indices: 1413170--1413227 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
1413160 ACAAGAATCT
1413170 ATATGATATGACCTATGAGATCATATGAA
1 ATATGATATGACCTATGAGATCATATGAA
* * *
1413199 ATATTATATGA-CTATGTGATTATATGAA
1 ATATGATATGACCTATGAGATCATATGAA
1413227 A
1 A
1413228 AAGAAATACA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.41, C:0.07, G:0.16, T:0.36
Consensus pattern (29 bp):
ATATGATATGACCTATGAGATCATATGAA
Found at i:1413634 original size:23 final size:23
Alignment explanation
Indices: 1413599--1413666 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
1413589 AATCTTATAT
* *
1413599 GGCACTTCAGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTATACGC
* * *
1413622 GGCACTACGGTGCAATTATACGT
1 GGCACTTCGGTGCATTTATACGC
*
1413645 GGTACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTATACG
1413667 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.21, C:0.24, G:0.25, T:0.31
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTATACGC
Found at i:1423113 original size:28 final size:29
Alignment explanation
Indices: 1423060--1423117 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
1423050 ATAAGAATCT
1423060 ATATGATATGACCTATGAGATCATATGAA
1 ATATGATATGACCTATGAGATCATATGAA
* * *
1423089 ATATTATATGA-CTATGTGATTATATGAA
1 ATATGATATGACCTATGAGATCATATGAA
1423117 A
1 A
1423118 ACGAAATACA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.41, C:0.07, G:0.16, T:0.36
Consensus pattern (29 bp):
ATATGATATGACCTATGAGATCATATGAA
Found at i:1423524 original size:23 final size:23
Alignment explanation
Indices: 1423489--1423556 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
1423479 AATCTTATAT
* *
1423489 GGCACTTCAGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTATACGC
* * *
1423512 GGCACTACGGTGCAATTATACGT
1 GGCACTTCGGTGCATTTATACGC
1423535 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTATACG
1423557 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTATACGC
Found at i:1427082 original size:21 final size:21
Alignment explanation
Indices: 1427040--1427082 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1427030 TTTCTAGACT
* * *
1427040 AGGGGAATCGGTACCCATTCA
1 AGGGGAAACGATACCCACTCA
*
1427061 AGGGGAAACGATACCCCCTCA
1 AGGGGAAACGATACCCACTCA
1427082 A
1 A
1427083 ACGAACCAGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.28, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAAACGATACCCACTCA
Found at i:1427647 original size:22 final size:22
Alignment explanation
Indices: 1427622--1427667 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
1427612 GTCATTATGA
*
1427622 TATATAAGAATGAAATGTAAGC
1 TATATAAGAATAAAATGTAAGC
1427644 TATATAAGAATAAAATGTAAGC
1 TATATAAGAATAAAATGTAAGC
1427666 TA
1 TA
1427668 CACATAAGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.52, C:0.04, G:0.15, T:0.28
Consensus pattern (22 bp):
TATATAAGAATAAAATGTAAGC
Found at i:1427777 original size:2 final size:2
Alignment explanation
Indices: 1427770--1427830 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
1427760 AATAATAATA
1427770 AT 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 AT
1427812 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
1427831 AATTAGGGGA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1428547 original size:28 final size:29
Alignment explanation
Indices: 1428494--1428551 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
1428484 ATAAGAATCT
1428494 ATATGATATGACCTATGAGATCATATGAA
1 ATATGATATGACCTATGAGATCATATGAA
* * *
1428523 ATATTATATGA-CTATGTGATTATATGAA
1 ATATGATATGACCTATGAGATCATATGAA
1428551 A
1 A
1428552 AAGAAATACA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.41, C:0.07, G:0.16, T:0.36
Consensus pattern (29 bp):
ATATGATATGACCTATGAGATCATATGAA
Found at i:1428990 original size:23 final size:23
Alignment explanation
Indices: 1428922--1428990 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
1428912 CAATCTTAAA
*
1428922 TGGCACTTCAGTGCATTTCTACG
1 TGGCACTTCGGTGCATTTCTACG
* *
1428945 CGGCACTAT-GGTGCAATTCTACG
1 TGGCACT-TCGGTGCATTTCTACG
* *
1428968 TGGCACTTCGGTACATTTATACG
1 TGGCACTTCGGTGCATTTCTACG
1428991 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
22 1 0.03
23 35 0.95
24 1 0.03
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.32
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:1432523 original size:21 final size:21
Alignment explanation
Indices: 1432481--1432523 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1432471 TTTATGGACT
* * *
1432481 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
1432502 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
1432523 A
1 A
1432524 ACGAACCAGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:1433187 original size:3 final size:3
Alignment explanation
Indices: 1433179--1433206 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1433169 GTGACTCTAG
1433179 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1433207 TATATAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1433929 original size:28 final size:29
Alignment explanation
Indices: 1433876--1433933 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
1433866 ATAAGAATCT
1433876 ATATGATATGACCTATGAGATCATATGAA
1 ATATGATATGACCTATGAGATCATATGAA
* * *
1433905 ATATTATATGA-CTATGTGATTATATGAA
1 ATATGATATGACCTATGAGATCATATGAA
1433933 A
1 A
1433934 AAGAAATACA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.41, C:0.07, G:0.16, T:0.36
Consensus pattern (29 bp):
ATATGATATGACCTATGAGATCATATGAA
Found at i:1434335 original size:23 final size:23
Alignment explanation
Indices: 1434267--1434335 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
1434257 CAATCTTATA
* *
1434267 TGGCACTTCAGTGTATTTCTACG
1 TGGCACTTCGGTGCATTTCTACG
** * *
1434290 CAGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCATTTCTACG
*
1434313 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCATTTCTACG
1434336 AGCTGTGGTG
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.32
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Done.