Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008259.1 Hibiscus syriacus cultivar Beakdansim tig00110912_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: 2373650
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 11
Found at i:1090756 original size:16 final size:16
Alignment explanation
Indices: 1090735--1090770 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
1090725 ACTAGAATTT
1090735 TGGAGACTAATGAATA
1 TGGAGACTAATGAATA
1090751 TGGAGACTAATGAATA
1 TGGAGACTAATGAATA
1090767 TGGA
1 TGGA
1090771 CCCAAAAGAA
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:0.42, C:0.06, G:0.28, T:0.25
Consensus pattern (16 bp):
TGGAGACTAATGAATA
Found at i:1094032 original size:44 final size:43
Alignment explanation
Indices: 1093945--1094037 Score: 114
Period size: 44 Copynumber: 2.1 Consensus size: 43
1093935 TTGTGCAACA
* * * * * *
1093945 TGCATCGATACACTAGAGGGTGTACTGATGCATCCCTTGAATG
1 TGCATCAATACACCAGAAGGTGCACCGATGCATCCCTTAAATG
*
1093988 TGCATCAATACACCATGAAGGTGCACCGATGCATTCCTTAAATG
1 TGCATCAATACACCA-GAAGGTGCACCGATGCATCCCTTAAATG
1094032 TGCATC
1 TGCATC
1094038 GATGCACTCT
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
43 13 0.31
44 29 0.69
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.27
Consensus pattern (43 bp):
TGCATCAATACACCAGAAGGTGCACCGATGCATCCCTTAAATG
Found at i:1099153 original size:13 final size:14
Alignment explanation
Indices: 1099135--1099163 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1099125 CATATGTAAC
1099135 TTAAGTA-ATTTAA
1 TTAAGTACATTTAA
1099148 TTAAGTACATTTAA
1 TTAAGTACATTTAA
1099162 TT
1 TT
1099164 TAAGGTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.48
Consensus pattern (14 bp):
TTAAGTACATTTAA
Found at i:1100938 original size:19 final size:19
Alignment explanation
Indices: 1100914--1100953 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1100904 GATCAGAATT
1100914 AAGAAAATCAAA-TTAAAAA
1 AAGAAAAT-AAAGTTAAAAA
1100933 AAGAAAATAAAGTTTAAAAA
1 AAGAAAATAAAG-TTAAAAA
1100953 A
1 A
1100954 CATGAGAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.16
19 8 0.42
20 8 0.42
ACGTcount: A:0.72, C:0.03, G:0.07, T:0.17
Consensus pattern (19 bp):
AAGAAAATAAAGTTAAAAA
Found at i:1102556 original size:85 final size:85
Alignment explanation
Indices: 1102446--1102640 Score: 248
Period size: 85 Copynumber: 2.3 Consensus size: 85
1102436 ATGCAATTTG
* * ** * *
1102446 TAATCAATGGTTGATGTGCTCCTTTCTCTGAAGGATGCCAAATCGACGAACGCTCTTGATTC-TT
1 TAATCAATGGTTGATATGCTCCTTTCTCTAAAACATGCCAAATCGAAGAACGATCTTGA-TCATT
* *
1102510 TCTCTAAAAGACACCAAGTTA
65 TCTCTAAAAGACACAAAGTCA
* *
1102531 TAATCAGTGGTTGATCTGCTCCTTTCTCTAAAACATGCCAAATCGAAGAACGATCTTGATCATTT
1 TAATCAATGGTTGATATGCTCCTTTCTCTAAAACATGCCAAATCGAAGAACGATCTTGATCATTT
* **
1102596 CTCTGAAAGATGCAAAGTCA
66 CTCTAAAAGACACAAAGTCA
*
1102616 TAATAAATGGTTGATATGCTCCTTT
1 TAATCAATGGTTGATATGCTCCTTT
1102641 TTATTAAGGA
Statistics
Matches: 94, Mismatches: 15, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
84 2 0.02
85 92 0.98
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.33
Consensus pattern (85 bp):
TAATCAATGGTTGATATGCTCCTTTCTCTAAAACATGCCAAATCGAAGAACGATCTTGATCATTT
CTCTAAAAGACACAAAGTCA
Found at i:1102917 original size:48 final size:48
Alignment explanation
Indices: 1102846--1102942 Score: 149
Period size: 48 Copynumber: 2.0 Consensus size: 48
1102836 TGGTTTATTC
* * * *
1102846 ATCCATTATCTTCAATAATGAGATGAATCTTCAAAATCCTGCTAAGAA
1 ATCCACTATATTCAACAATGAGATGAATCTTCAAAATCCTACTAAGAA
*
1102894 ATCCACTATATTCAACAATGAGATGAATCTTCGAAATCCTACTAAGAA
1 ATCCACTATATTCAACAATGAGATGAATCTTCAAAATCCTACTAAGAA
1102942 A
1 A
1102943 CTTACATGAT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (48 bp):
ATCCACTATATTCAACAATGAGATGAATCTTCAAAATCCTACTAAGAA
Found at i:1106865 original size:65 final size:65
Alignment explanation
Indices: 1106732--1106891 Score: 211
Period size: 65 Copynumber: 2.5 Consensus size: 65
1106722 TGCACTAAGA
* *
1106732 GTGCATCGATGCATGAAATGCATTCGATG-TTTCAAAATAGCCAGAGTGCATTGATGCATGGCTG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTCAAAATAGCCAGAGTGCATCGATGCATAGCTG
* *
1106796 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-A-CTCTGAGTGCATCGATGCATAG-
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTCA-AAATAGC-CAGAGTGCATCGATGCATAGC
*
1106858 TAT
64 T-G
*
1106861 GTGCATCGATGCATGGAATGCATTCGATGTT
1 GTGCATCGATGCATGAAATGCATTCGATGTT
1106892 CAATTTATTC
Statistics
Matches: 85, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
64 30 0.35
65 52 0.61
66 3 0.04
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTTCAAAATAGCCAGAGTGCATCGATGCATAGCTG
Found at i:1106930 original size:65 final size:64
Alignment explanation
Indices: 1106732--1106933 Score: 209
Period size: 65 Copynumber: 3.1 Consensus size: 64
1106722 TGCACTAAGA
* * * *
1106732 GTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATAGCCA-GAGTGCATTGATGCATGGCTG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTC-AATTAACCATGAGTGCATCGATGCATGGTTG
* * *
1106796 GTGCATCGATGCATCAAATGCATTCGATGTTTTC-ATAAAACTC-TGAGTGCATCGATGCATAGT
1 GTGCATCGATGCATGAAATGCATTCGATG-TTTCAAT-TAAC-CATGAGTGCATCGATGCATGGT
1106859 AT-
63 -TG
* *
1106861 GTGCATCGATGCATGGAATGCATTCGATG-TTCAATTTATTCCATG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAA-TTA-ACCATGAGTGCATCGATGCATGG-T
1106924 TG
63 TG
1106926 GTGCATCG
1 GTGCATCG
1106934 GCGCATCACT
Statistics
Matches: 115, Mismatches: 12, Indels: 21
0.78 0.08 0.14
Matches are distributed among these distances:
63 4 0.03
64 49 0.43
65 61 0.53
66 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAACCATGAGTGCATCGATGCATGGTTG
Found at i:1107409 original size:2 final size:2
Alignment explanation
Indices: 1107402--1107430 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1107392 TAGCCAATTG
1107402 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1107431 GCTTAAGCTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1109655 original size:21 final size:22
Alignment explanation
Indices: 1109600--1109680 Score: 92
Period size: 23 Copynumber: 3.6 Consensus size: 22
1109590 CATGGCCTTG
1109600 TGCATCGATGCACATTCAAGGCA
1 TGCATCGATGCACATTCAAGG-A
* * *
1109623 TGCATCGGTGCACCTTCATGG-
1 TGCATCGATGCACATTCAAGGA
*
1109644 TGTATCGATGCACATTCAAAGGGA
1 TGCATCGATGCACATTC-AA-GGA
1109668 TGCATCGATGCAC
1 TGCATCGATGCAC
1109681 TGTTAACTGT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
21 14 0.30
22 1 0.02
23 20 0.43
24 12 0.26
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.25
Consensus pattern (22 bp):
TGCATCGATGCACATTCAAGGA
Found at i:1109692 original size:44 final size:44
Alignment explanation
Indices: 1109603--1109699 Score: 117
Period size: 44 Copynumber: 2.2 Consensus size: 44
1109593 GGCCTTGTGC
* **
1109603 ATCGATGCACATTCAAGGCATGCATCGGTGCACCTTCATGGTGT
1 ATCGATGCACATTCAAGGCATGCATCGATGCACCTTCATACTGT
* *
1109647 ATCGATGCACATTCAAAGGGATGCATCGATGCA-CTGTTA-ACTGT
1 ATCGATGCACATTC-AAGGCATGCATCGATGCACCT-TCATACTGT
1109691 ATCGATGCA
1 ATCGATGCA
1109700 TGAAGCACAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
44 28 0.61
45 18 0.39
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.27
Consensus pattern (44 bp):
ATCGATGCACATTCAAGGCATGCATCGATGCACCTTCATACTGT
Found at i:1115631 original size:65 final size:65
Alignment explanation
Indices: 1115498--1115705 Score: 214
Period size: 65 Copynumber: 3.2 Consensus size: 65
1115488 TGCACTAAGA
* *
1115498 GTGCATCGATGCATGAAATGCATTCAATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGGTG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTCAAAATAGCCAGAGTGCATCGATGCATGAGTG
* *
1115562 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-A-CTCCGAGTGCATCGATGCAT-AG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTCA-AAATAGC-CAGAGTGCATCGATGCATGAG
*
1115624 TAT
64 T-G
* ** *
1115627 GTGCATCGATGCATGGAATGCATTCGATG--TTCAATTTATTCCATG-GTGCATCGATGCATGGA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTCAAAATA-GCCA-GAGTGCATCGATGCAT-GA
*
1115689 TTG
63 GTG
*
1115692 GTGCATCGGTGCAT
1 GTGCATCGATGCAT
1115706 CACTTTGAAA
Statistics
Matches: 121, Mismatches: 13, Indels: 19
0.79 0.08 0.12
Matches are distributed among these distances:
62 1 0.01
63 5 0.04
64 45 0.37
65 65 0.54
66 5 0.04
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTTCAAAATAGCCAGAGTGCATCGATGCATGAGTG
Found at i:1116500 original size:40 final size:40
Alignment explanation
Indices: 1116445--1116522 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 40
1116435 ATTGATTAAG
* *
1116445 CACTTCGGTGCATATGGTGGGCACGACCTTATGTGTAATA
1 CACTTCAGTGCATATGGTGGGCACGACCTTATGCGTAATA
1116485 CACTTCAGTGCATATGGTGGGCACGACCTTATGCGTAA
1 CACTTCAGTGCATATGGTGGGCACGACCTTATGCGTAA
1116523 GCATTACGAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (40 bp):
CACTTCAGTGCATATGGTGGGCACGACCTTATGCGTAATA
Found at i:1116559 original size:24 final size:24
Alignment explanation
Indices: 1116527--1116577 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
1116517 GCGTAAGCAT
1116527 TACGACACATATATTTGACTCGAA
1 TACGACACATATATTTGACTCGAA
*
1116551 TACGGCACATATATTTGACTCGAA
1 TACGACACATATATTTGACTCGAA
1116575 TAC
1 TAC
1116578 CCAGGGTCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (24 bp):
TACGACACATATATTTGACTCGAA
Found at i:1120526 original size:20 final size:20
Alignment explanation
Indices: 1120501--1120541 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1120491 CACATTTTAA
1120501 AATGATGGAAAATAATATGG
1 AATGATGGAAAATAATATGG
1120521 AATGATGGAAAATAATATGG
1 AATGATGGAAAATAATATGG
1120541 A
1 A
1120542 GCATTGGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.24, T:0.24
Consensus pattern (20 bp):
AATGATGGAAAATAATATGG
Found at i:1122767 original size:40 final size:40
Alignment explanation
Indices: 1122710--1122828 Score: 211
Period size: 40 Copynumber: 3.0 Consensus size: 40
1122700 TATCGATTAA
*
1122710 GCACTTTGGTGTATATGGTGGGCACGACCTTATGTGTAAT
1 GCACTTCGGTGTATATGGTGGGCACGACCTTATGTGTAAT
*
1122750 GCACTTCGGTGTGTATGGTGGGCACGACCTTATGTGTAAT
1 GCACTTCGGTGTATATGGTGGGCACGACCTTATGTGTAAT
*
1122790 GCACTTCGGTGCATATGGTGGGCACGACCTTATGTGTAA
1 GCACTTCGGTGTATATGGTGGGCACGACCTTATGTGTAA
1122829 GCGCTATTGT
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 75 1.00
ACGTcount: A:0.19, C:0.18, G:0.31, T:0.32
Consensus pattern (40 bp):
GCACTTCGGTGTATATGGTGGGCACGACCTTATGTGTAAT
Found at i:1123895 original size:13 final size:13
Alignment explanation
Indices: 1123877--1123908 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1123867 AGATAATAAA
*
1123877 AGATCAATGGGTT
1 AGATCAATGGGCT
1123890 AGATCAATGGGCT
1 AGATCAATGGGCT
1123903 AGATCA
1 AGATCA
1123909 TTCCCTAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.34, C:0.12, G:0.28, T:0.25
Consensus pattern (13 bp):
AGATCAATGGGCT
Found at i:1126936 original size:10 final size:10
Alignment explanation
Indices: 1126897--1126946 Score: 55
Period size: 10 Copynumber: 5.0 Consensus size: 10
1126887 TTCATCACAC
1126897 CAAATTCTCT
1 CAAATTCTCT
*
1126907 CAATTTCTCT
1 CAAATTCTCT
*
1126917 CAACTTCTCT
1 CAAATTCTCT
*
1126927 CAAATACTCT
1 CAAATTCTCT
* *
1126937 TATATTCTCT
1 CAAATTCTCT
1126947 GTTTAAGGTA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.26, C:0.30, G:0.00, T:0.44
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:1127022 original size:17 final size:18
Alignment explanation
Indices: 1126985--1127023 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1126975 ATATTTTGTA
1126985 TTTAATTTATGTAAGTAT
1 TTTAATTTATGTAAGTAT
*
1127003 TTTAATTTATTTAA-TAT
1 TTTAATTTATGTAAGTAT
1127020 TTTA
1 TTTA
1127024 CTTATATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (18 bp):
TTTAATTTATGTAAGTAT
Found at i:1128140 original size:20 final size:22
Alignment explanation
Indices: 1128117--1128156 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1128107 TGTTGTATAT
1128117 AGCTG-TTGGGGATG-TTTTGG
1 AGCTGTTTGGGGATGATTTTGG
1128137 AGCTGTTTGGGGATGATTTT
1 AGCTGTTTGGGGATGATTTT
1128157 TTTACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.05, G:0.40, T:0.42
Consensus pattern (22 bp):
AGCTGTTTGGGGATGATTTTGG
Found at i:1128306 original size:41 final size:41
Alignment explanation
Indices: 1128261--1128342 Score: 114
Period size: 41 Copynumber: 2.0 Consensus size: 41
1128251 TAGCCGTTGT
* *
1128261 AGCCTTCG-TGCATGGATGCACATCAA-GATGCATCGATGCAC
1 AGCCTT-GATGCATCGATGCACA-AAATGATGCATCGATGCAC
1128302 AGCCTTGATGCATCGATGCACAAAATGATGCATCGATGCAC
1 AGCCTTGATGCATCGATGCACAAAATGATGCATCGATGCAC
1128343 TAATTGCATT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
40 3 0.08
41 34 0.92
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.22
Consensus pattern (41 bp):
AGCCTTGATGCATCGATGCACAAAATGATGCATCGATGCAC
Found at i:1128313 original size:21 final size:20
Alignment explanation
Indices: 1128269--1128342 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
1128259 GTAGCCTTCG
* *
1128269 TGCATGGATGCACATCAA-GA
1 TGCATCGATGCACA-AAATGA
***
1128289 TGCATCGATGCACAGCCTTGA
1 TGCATCGATGCACA-AAATGA
1128310 TGCATCGATGCACAAAATGA
1 TGCATCGATGCACAAAATGA
1128330 TGCATCGATGCAC
1 TGCATCGATGCAC
1128343 TAATTGCATT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
20 30 0.65
21 16 0.35
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.22
Consensus pattern (20 bp):
TGCATCGATGCACAAAATGA
Found at i:1128432 original size:21 final size:21
Alignment explanation
Indices: 1128363--1128461 Score: 114
Period size: 21 Copynumber: 4.7 Consensus size: 21
1128353 CGGTGTTTGA
*
1128363 GTGCATGGATGCACTGCA-TG
1 GTGCATGGATGCACTGCAGGG
*
1128383 GTGCATCGATGCACT--AGTGTAG
1 GTGCATGGATGCACTGCAG-G--G
1128405 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
* *
1128426 ATGCATGGATGCATTGCAGGG
1 GTGCATGGATGCACTGCAGGG
1128447 GTGCATGGATGCACT
1 GTGCATGGATGCACT
1128462 TTGACACCCT
Statistics
Matches: 66, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
18 1 0.02
20 14 0.21
21 33 0.50
22 15 0.23
23 1 0.02
24 2 0.03
ACGTcount: A:0.21, C:0.18, G:0.36, T:0.24
Consensus pattern (21 bp):
GTGCATGGATGCACTGCAGGG
Found at i:1128588 original size:30 final size:30
Alignment explanation
Indices: 1128541--1128600 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
1128531 AAACTTTGAA
*
1128541 TAAATTCAGTTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
1128570 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
1128601 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 10 0.36
30 11 0.39
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:1132010 original size:21 final size:20
Alignment explanation
Indices: 1131941--1132039 Score: 110
Period size: 21 Copynumber: 4.8 Consensus size: 20
1131931 CGATGTTTGA
* *
1131941 GTGCATGGATGCACTACATG
1 GTGCATGGATGCACTGCAGG
*
1131961 GTGCATCGATGCACTAGTGCA-G
1 GTGCATGGATGCAC---TGCAGG
1131983 GTGCATGGATGCACTGCAGG
1 GTGCATGGATGCACTGCAGG
*
1132003 GATGCATGGATGCATTGCAGGG
1 G-TGCATGGATGCACTGCA-GG
1132025 GTGCATGGATGCACT
1 GTGCATGGATGCACT
1132040 TTGACACCTT
Statistics
Matches: 68, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
19 4 0.06
20 15 0.22
21 29 0.43
22 17 0.25
23 3 0.04
ACGTcount: A:0.22, C:0.19, G:0.35, T:0.23
Consensus pattern (20 bp):
GTGCATGGATGCACTGCAGG
Found at i:1132165 original size:30 final size:30
Alignment explanation
Indices: 1132118--1132177 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
1132108 AAACTATGAA
1132118 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
1132147 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
1132178 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:1133716 original size:13 final size:13
Alignment explanation
Indices: 1133698--1133722 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1133688 AGGAGGAAGA
1133698 TGACGACGACGAC
1 TGACGACGACGAC
1133711 TGACGACGACGA
1 TGACGACGACGA
1133723 TGATGGTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.28, G:0.32, T:0.08
Consensus pattern (13 bp):
TGACGACGACGAC
Found at i:1134043 original size:34 final size:34
Alignment explanation
Indices: 1133963--1134044 Score: 98
Period size: 34 Copynumber: 2.4 Consensus size: 34
1133953 TTCAGTTAAT
1133963 TTTGTTTA-TTACCATTTAATATCAGTTATTGTAA
1 TTTGTTTATTTACCATTTAATATCA-TTATTGTAA
1133997 TTTGGTTATATTTACCATTTAATA-C-TTATTGTAA
1 TTT-GTT-TATTTACCATTTAATATCATTATTGTAA
1134031 GTTTGTTGTATTTA
1 -TTTGTT-TATTTA
1134045 AAATTATTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
34 21 0.49
35 6 0.14
36 3 0.07
37 13 0.30
ACGTcount: A:0.27, C:0.07, G:0.11, T:0.55
Consensus pattern (34 bp):
TTTGTTTATTTACCATTTAATATCATTATTGTAA
Found at i:1137689 original size:49 final size:51
Alignment explanation
Indices: 1137628--1137739 Score: 133
Period size: 53 Copynumber: 2.2 Consensus size: 51
1137618 GGTACCTACA
*
1137628 CCGCGCCT-TATATAATTATATC-AG-TTAAAGGTATGACGCGGCCCCTG-C
1 CCGCG-CTATATATAATTATATCAAGATTAAAGGTAAGACGCGGCCCCTGAC
* *
1137676 CCTGCGCTATATATAATTATGTCAGAGAATTAAAGGTAAGGCGCGGCCCCTGAC
1 CC-GCGCTATATATAATTATATCA-AG-ATTAAAGGTAAGACGCGGCCCCTGAC
1137730 CCGCGCTATA
1 CCGCGCTATA
1137740 CCCTACGTGG
Statistics
Matches: 54, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
48 4 0.07
49 16 0.30
51 2 0.04
53 29 0.54
54 3 0.06
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (51 bp):
CCGCGCTATATATAATTATATCAAGATTAAAGGTAAGACGCGGCCCCTGAC
Found at i:1143563 original size:7 final size:7
Alignment explanation
Indices: 1143553--1143616 Score: 78
Period size: 7 Copynumber: 9.0 Consensus size: 7
1143543 AAAAAATGAG
1143553 TAATAAA
1 TAATAAA
1143560 TAATAAA
1 TAATAAA
*
1143567 TAATAAT
1 TAATAAA
1143574 TAA-AAA
1 TAATAAA
1143580 TAA-AAA
1 TAATAAA
1143586 TAATAAAA
1 TAAT-AAA
1143594 TAATAAA
1 TAATAAA
1143601 TAATAATA
1 TAATAA-A
1143609 TATATAAA
1 TA-ATAAA
1143617 AAATCATTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
6 11 0.22
7 25 0.49
8 11 0.22
9 4 0.08
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
TAATAAA
Found at i:1143564 original size:3 final size:3
Alignment explanation
Indices: 1143553--1143608 Score: 51
Period size: 3 Copynumber: 17.7 Consensus size: 3
1143543 AAAAAATGAG
* *
1143553 TAA TAAA TAA TAAA TAA TAA TTAA AAA TAA AAA TAA TAA -AA TAA TAAA
1 TAA T-AA TAA T-AA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA T-AA
1143601 TAA TAA TA
1 TAA TAA TA
1143609 TATATAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
2 2 0.05
3 30 0.68
4 12 0.27
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:1143657 original size:38 final size:37
Alignment explanation
Indices: 1143615--1143982 Score: 280
Period size: 37 Copynumber: 9.8 Consensus size: 37
1143605 AATATATATA
*
1143615 AAAAATCATTTTTAAAACCATATATTATATATGATTTT-
1 AAAAAT-ATTTTTAAAACTATATATTATATAT-ATTTTC
* *
1143653 AAAAAT-TGTTTTCAAAACCATATAATATATATATTTTTTC
1 AAAAATAT-TTTT-AAAACTATAT-AT-TATATATATTTTC
1143693 AAAAAT-TGTTTTAAAACTATA-A--ATATATATTTTC
1 AAAAATAT-TTTTAAAACTATATATTATATATATTTTC
* * *
1143727 AAAAATATTTTCAAAACTATATATTATATACATTTTT
1 AAAAATATTTTTAAAACTATATATTATATATATTTTC
*
1143764 AAAAATATTTTCAAAAACTATATATTATATATATATTT-
1 AAAAATATTTT-TAAAACTATATATTATATATAT-TTTC
** *
1143802 TTAAATTTTTTTCAAAAACTATATATTATATATATGTTTTC
1 AAAAATATTTTT--AAAACTATATATTATATATA--TTTTC
* * *
1143843 AAAAA-A-TTTCAATACTATATAATATATATATTTTC
1 AAAAATATTTTTAAAACTATATATTATATATATTTTC
***
1143878 GAAAACCGTTTTTCAAAACTATATA--ATATATATTTTC
1 -AAAAATATTTTT-AAAACTATATATTATATATATTTTC
*
1143915 AAAAATCGA-TTTTAAAA-TATATA-T-TATATGTTTTC
1 AAAAAT--ATTTTTAAAACTATATATTATATATATTTTC
* *
1143950 AAAAATCGTTCTCTAAAAACTATATATTATATA
1 AAAAAT-ATT-T-TTAAAACTATATATTATATA
1143983 AACCCCAGAC
Statistics
Matches: 272, Mismatches: 29, Indels: 56
0.76 0.08 0.16
Matches are distributed among these distances:
34 29 0.11
35 30 0.11
36 14 0.05
37 65 0.24
38 53 0.19
39 51 0.19
40 26 0.10
41 4 0.01
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (37 bp):
AAAAATATTTTTAAAACTATATATTATATATATTTTC
Found at i:1143736 original size:12 final size:12
Alignment explanation
Indices: 1143719--1143780 Score: 54
Period size: 12 Copynumber: 5.1 Consensus size: 12
1143709 CTATAAATAT
1143719 ATATTTTCAAAA
1 ATATTTTCAAAA
1143731 ATATTTTCAAAA
1 ATATTTTCAAAA
* * *
1143743 CTATATATT-ATAT
1 --ATATTTTCAAAA
* *
1143756 ACATTTTTAAAA
1 ATATTTTCAAAA
1143768 ATATTTTCAAAA
1 ATATTTTCAAAA
1143780 A
1 A
1143781 CTATATATTA
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
11 5 0.13
12 25 0.66
13 2 0.05
14 6 0.16
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (12 bp):
ATATTTTCAAAA
Found at i:1144758 original size:85 final size:84
Alignment explanation
Indices: 1144560--1144793 Score: 353
Period size: 85 Copynumber: 2.8 Consensus size: 84
1144550 ATATGTCATC
* *
1144560 GAGCTGAAT-AGAATCGAACTCGACAGTTTTTTTATTGACAGATAGCCCTTCTCGCCTTGAGCTA
1 GAGCTGAATGA-AATCGAACTCGA-AG-GTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTA
*
1144624 TGTTGTAAATTTGATATGCCTT
63 TGCTGTAAATTTGATATGCCTT
* * *
1144646 GAGCTAAATGAAATCTAACTCGGAGGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
1 GAGCTGAATGAAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
*
1144711 TGTAAATTTGTTATGGCCTT
66 TGTAAATTTGATAT-GCCTT
*
1144731 GAGCTGAATGAAATCGAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTAT
1 GAGCTGAATGAAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTAT
1144794 ACCGTAATAG
Statistics
Matches: 135, Mismatches: 11, Indels: 5
0.89 0.07 0.03
Matches are distributed among these distances:
84 50 0.37
85 66 0.49
86 18 0.13
87 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.34
Consensus pattern (84 bp):
GAGCTGAATGAAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
TGTAAATTTGATATGCCTT
Found at i:1149281 original size:22 final size:23
Alignment explanation
Indices: 1149242--1149285 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1149232 GTAAAAATGT
1149242 TAAAAAAAAGAAAGAAAATAAAA
1 TAAAAAAAAGAAAGAAAATAAAA
1149265 TAAAAAAAATG-AA-AAAATAAA
1 TAAAAAAAA-GAAAGAAAATAAA
1149286 TTTTTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 8 0.40
23 11 0.55
24 1 0.05
ACGTcount: A:0.82, C:0.00, G:0.07, T:0.11
Consensus pattern (23 bp):
TAAAAAAAAGAAAGAAAATAAAA
Found at i:1150656 original size:38 final size:37
Alignment explanation
Indices: 1150614--1151040 Score: 334
Period size: 38 Copynumber: 11.5 Consensus size: 37
1150604 AATCATTTTT
1150614 AAAACTATATATTATATATGATTTTAAAAATTGTTTTCA
1 AAAACTATATATTATATAT-ATTTTAAAAA-TGTTTTCA
*
1150653 AAACCATATAATATCTATATATATATATTTTCAAAAATTGTTTT--
1 AAA--A-CT-ATA--TAT-TATATATATTTT-AAAAA-TGTTTTCA
*
1150697 AAAACTATATA--ATATATATTTTCAAAA------C-
1 AAAACTATATATTATATATATTTTAAAAATGTTTTCA
* * * * *
1150725 TATA-TAT-TA-TATACAT-TTTCAAAAATATTTTCA
1 AAAACTATATATTATATATATTTTAAAAATGTTTTCA
* *
1150758 AAAACTATATATTATATATATTTTTTCAAAATGTTTTCT
1 AAAACTATATATTATATATA--TTTTAAAAATGTTTTCA
*
1150797 AAAACTATATATTATATACATTTTCAAAAATGTTTTCA
1 AAAACTATATATTATATATATTTT-AAAAATGTTTTCA
*
1150835 AAAACTATATATTATATATATTTTCAAAATGTTTTCA
1 AAAACTATATATTATATATATTTTAAAAATGTTTTCA
*
1150872 AAAACTATATATTATATATATTTTTAAAAATGTTTTCG
1 AAAACTATATATTATATATA-TTTTAAAAATGTTTTCA
* ** *
1150910 AAAACTATATATTATATATTTGTTTTCAAATTTTTTC-
1 AAAACTATATATTATATATAT-TTTAAAAATGTTTTCA
**
1150947 AAAACTATATA--ATATATATTTTCGAAAACCGTTTTCAA
1 AAAACTATATATTATATATATTTT--AAAAATGTTTTC-A
* * *
1150985 AAAAGTATATATTATATAT-TTTCAAAAATCGTTCTCTA
1 AAAACTATATATTATATATATTTTAAAAAT-GTTTTC-A
*
1151023 AAAATTATATATTATATA
1 AAAACTATATATTATATA
1151041 AACCCTGAAC
Statistics
Matches: 316, Mismatches: 39, Indels: 67
0.75 0.09 0.16
Matches are distributed among these distances:
26 9 0.03
27 8 0.03
28 2 0.01
32 1 0.00
33 2 0.01
34 10 0.03
35 20 0.06
36 13 0.04
37 52 0.16
38 115 0.36
39 38 0.12
40 9 0.03
41 2 0.01
42 2 0.01
43 3 0.01
44 3 0.01
45 8 0.03
46 19 0.06
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.45
Consensus pattern (37 bp):
AAAACTATATATTATATATATTTTAAAAATGTTTTCA
Found at i:1150707 original size:45 final size:47
Alignment explanation
Indices: 1150621--1150711 Score: 143
Period size: 45 Copynumber: 2.0 Consensus size: 47
1150611 TTTAAAACTA
1150621 TATATTATATATGATTTTAAAAATTGTTTTCAAAACCATATAATATC
1 TATATTATATATGATTTTAAAAATTGTTTTCAAAACCATATAATATC
*
1150668 TATA-TATATAT-ATTTTCAAAAATTGTTTT-AAAACTATATAATAT
1 TATATTATATATGATTTT-AAAAATTGTTTTCAAAACCATATAATAT
1150712 ATATTTTCAA
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
45 19 0.45
46 19 0.45
47 4 0.10
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (47 bp):
TATATTATATATGATTTTAAAAATTGTTTTCAAAACCATATAATATC
Found at i:1150724 original size:23 final size:24
Alignment explanation
Indices: 1150693--1150748 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 24
1150683 TCAAAAATTG
*
1150693 TTTT-AAAACTATATA-ATATATA
1 TTTTCAAAACTATATATATATACA
1150715 TTTTCAAAACTATATATTATATACA
1 TTTTCAAAACTATATA-TATATACA
1150740 TTTTCAAAA
1 TTTTCAAAA
1150749 ATATTTTCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 4 0.13
23 11 0.37
25 15 0.50
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTTCAAAACTATATATATATACA
Found at i:1150735 original size:21 final size:22
Alignment explanation
Indices: 1150693--1150737 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
1150683 TCAAAAATTG
1150693 TTTTAAAACTATATAATATATA
1 TTTTAAAACTATATAATATATA
*
1150715 TTTTCAAAACTATATATTATATA
1 TTTT-AAAACTATATAATATATA
1150738 CATTTTCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (22 bp):
TTTTAAAACTATATAATATATA
Found at i:1150819 original size:77 final size:76
Alignment explanation
Indices: 1150715--1151003 Score: 410
Period size: 75 Copynumber: 3.8 Consensus size: 76
1150705 ATAATATATA
*
1150715 TTTTCAAAACTATATATTATATACATTTTCAAAAATATTTTCAAAAACTATATATTATATATATT
1 TTTTCAAAACTATATATTATATACATTTTCAAAAATGTTTTCAAAAACTATATATTATATATATT
1150780 TTTTCAAAATG
66 TTTTCAAAATG
1150791 TTTTCTAAAACTATATATTATATACATTTTCAAAAATGTTTTCAAAAACTATATATTATATATA-
1 TTTTC-AAAACTATATATTATATACATTTTCAAAAATGTTTTCAAAAACTATATATTATATATAT
1150855 -TTTTCAAAATG
65 TTTTTCAAAATG
* * *
1150866 TTTTCAAAAACTATATATTATATATATTTTTAAAAATGTTTTCGAAAACTATATATTATATAT-T
1 TTTTC-AAAACTATATATTATATACATTTTCAAAAATGTTTTCAAAAACTATATATTATATATAT
*
1150930 TGTTTTC-AAATT
65 T-TTTTCAAAATG
* ** *
1150942 TTTTCAAAACTATATA--ATATATATTTTCGAAAACCGTTTTCAAAAAAGTATATATTATATAT
1 TTTTCAAAACTATATATTATATACATTTTC-AAAAATGTTTTC-AAAAACTATATATTATATAT
1151004 TTTCAAAAAT
Statistics
Matches: 196, Mismatches: 11, Indels: 13
0.89 0.05 0.06
Matches are distributed among these distances:
73 11 0.06
74 10 0.05
75 99 0.51
76 14 0.07
77 62 0.32
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.46
Consensus pattern (76 bp):
TTTTCAAAACTATATATTATATACATTTTCAAAAATGTTTTCAAAAACTATATATTATATATATT
TTTTCAAAATG
Found at i:1150863 original size:75 final size:74
Alignment explanation
Indices: 1150715--1151040 Score: 401
Period size: 75 Copynumber: 4.3 Consensus size: 74
1150705 ATAATATATA
*
1150715 TTTTCAAAACTATATATTATATACATTTTCAAAAATATTTTCAAAAACTATATATTATATATATT
1 TTTTCAAAACTATATATTATATACATTTTCAAAAATGTTTTCAAAAACTATATATTATATATA--
1150780 TTTTCAAAATG
64 TTTTCAAAATG
1150791 TTTTCTAAAACTATATATTATATACATTTTCAAAAATGTTTTCAAAAACTATATATTATATATAT
1 TTTTC-AAAACTATATATTATATACATTTTCAAAAATGTTTTCAAAAACTATATATTATATATAT
1150856 TTTCAAAATG
65 TTTCAAAATG
* * *
1150866 TTTTCAAAAACTATATATTATATATATTTTTAAAAATGTTTTCGAAAACTATATATTATATATTT
1 TTTTC-AAAACTATATATTATATACATTTTCAAAAATGTTTTCAAAAACTATATATTATATA--T
* *
1150931 GTTTTC-AAATT
63 ATTTTCAAAATG
* ** *
1150942 TTTTCAAAACTATATA--ATATATATTTTCGAAAACCGTTTTCAAAAAAGTATATA-T-TATATA
1 TTTTCAAAACTATATATTATATACATTTTC-AAAAATGTTTTC-AAAAACTATATATTATATATA
1151003 TTTTCAAAAATCG
64 TTTTC-AAAAT-G
* *
1151016 TTCTCTAAAAATTATATATTATATA
1 TT-T-TCAAAACTATATATTATATA
1151041 AACCCTGAAC
Statistics
Matches: 222, Mismatches: 16, Indels: 22
0.85 0.06 0.08
Matches are distributed among these distances:
71 6 0.03
73 19 0.09
74 13 0.06
75 91 0.41
76 25 0.11
77 63 0.28
78 5 0.02
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.46
Consensus pattern (74 bp):
TTTTCAAAACTATATATTATATACATTTTCAAAAATGTTTTCAAAAACTATATATTATATATATT
TTCAAAATG
Found at i:1152122 original size:17 final size:18
Alignment explanation
Indices: 1152095--1152132 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
1152085 TACTTTAAAG
1152095 TTTAGAAAGTTTCAAATT
1 TTTAGAAAGTTTCAAATT
1152113 TTTA-AAAGTTTCAAATT
1 TTTAGAAAGTTTCAAATT
1152130 TTT
1 TTT
1152133 TTTAAAAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.50
Consensus pattern (18 bp):
TTTAGAAAGTTTCAAATT
Found at i:1152136 original size:20 final size:20
Alignment explanation
Indices: 1152095--1152164 Score: 76
Period size: 21 Copynumber: 3.6 Consensus size: 20
1152085 TACTTTAAAG
1152095 TTTAGAAAGTTTCAAA---TT
1 TTTA-AAAGTTTCAAATTTTT
1152113 TTTAAAAGTTTCAAATTTTT
1 TTTAAAAGTTTCAAATTTTT
* *
1152133 TTTAAAAGTTTTGAAATTTTC
1 TTTAAAAG-TTTCAAATTTTT
1152154 TTTAAAA-TTTC
1 TTTAAAAGTTTC
1152165 GAAAATTTGA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
17 11 0.24
18 4 0.09
19 3 0.07
20 10 0.22
21 17 0.38
ACGTcount: A:0.36, C:0.06, G:0.07, T:0.51
Consensus pattern (20 bp):
TTTAAAAGTTTCAAATTTTT
Found at i:1152172 original size:21 final size:21
Alignment explanation
Indices: 1152113--1152168 Score: 80
Period size: 20 Copynumber: 2.8 Consensus size: 21
1152103 GTTTCAAATT
*
1152113 TTTAAAAGTTTC-AAATTTTT
1 TTTAAAAGTTTCGAAATTTTC
*
1152133 TTTAAAAGTTTTGAAATTTTC
1 TTTAAAAGTTTCGAAATTTTC
1152154 TTTAAAA-TTTCGAAA
1 TTTAAAAGTTTCGAAA
1152169 ATTTGAGTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 18 0.56
21 14 0.44
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (21 bp):
TTTAAAAGTTTCGAAATTTTC
Found at i:1152367 original size:30 final size:30
Alignment explanation
Indices: 1152303--1152368 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
1152293 TCAATTAATT
* *
1152303 AAAACATATAAAAAAGTTTTCAAACAACTA
1 AAAAAATATAAAAAAATTTTCAAACAACTA
* *
1152333 AAAAAATATAAAAAAATTATTCCAACAA-TC
1 AAAAAATATAAAAAAATT-TTCAAACAACTA
1152363 AAAAAA
1 AAAAAA
1152369 CAAATAGAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 23 0.74
31 8 0.26
ACGTcount: A:0.65, C:0.12, G:0.02, T:0.21
Consensus pattern (30 bp):
AAAAAATATAAAAAAATTTTCAAACAACTA
Found at i:1153342 original size:29 final size:28
Alignment explanation
Indices: 1153296--1153370 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 28
1153286 GATATTATTT
* *
1153296 TAATTTATGAAAAGTTTTGTCCTTGATTG
1 TAATTTAT-AAAAATTTTGACCTTGATTG
* * *
1153325 TAATTTATAAAACATTTTGACTTTTATTT
1 TAATTTATAAAA-ATTTTGACCTTGATTG
1153354 TAATTTATAAAAATTTT
1 TAATTTATAAAAATTTT
1153371 AGGTTTTTGT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
28 9 0.22
29 31 0.77
ACGTcount: A:0.35, C:0.05, G:0.08, T:0.52
Consensus pattern (28 bp):
TAATTTATAAAAATTTTGACCTTGATTG
Found at i:1153378 original size:29 final size:28
Alignment explanation
Indices: 1153290--1153378 Score: 81
Period size: 29 Copynumber: 3.1 Consensus size: 28
1153280 ATTACAGATA
* *
1153290 TTATTTTAATTTATGAAAAGTTTT-GTCCT
1 TTATTTTAATTTAT-AAAAATTTTGGT-TT
* * **
1153319 TGATTGTAATTTATAAAACATTTTGACTT
1 TTATTTTAATTTATAAAA-ATTTTGGTTT
1153348 TTATTTTAATTTATAAAAATTTTAGGTTT
1 TTATTTTAATTTATAAAAATTTT-GGTTT
1153377 TT
1 TT
1153379 GTTGAAACTT
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
28 9 0.19
29 38 0.81
ACGTcount: A:0.31, C:0.04, G:0.09, T:0.55
Consensus pattern (28 bp):
TTATTTTAATTTATAAAAATTTTGGTTT
Found at i:1158834 original size:73 final size:75
Alignment explanation
Indices: 1158687--1158834 Score: 201
Period size: 76 Copynumber: 2.0 Consensus size: 75
1158677 CATTTTAAAT
* * ****
1158687 TTAGGATTTTTAGTTTGATTATTTTATTATTATTTTATTTATTTCTTAGTAATTAGTTATTTACA
1 TTAGGATTTTTAGTTTGATTATATCATTATTATTTTATTTAGGAATTAGTAATTA-TTATTTACA
1158752 TAGAACTCTCA
65 TAGAACTCTCA
* *
1158763 TTAGGATTTTTAGTTTGATTATATCATTATT-TTTTATTTAGGAATTAGTTATT-TTATTTACTT
1 TTAGGATTTTTAGTTTGATTATATCATTATTATTTTATTTAGGAATTAGTAATTATTATTTACAT
1158826 AGAACTCTC
66 AGAACTCTC
1158835 GGGTTATAGA
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
73 18 0.28
75 17 0.27
76 29 0.45
ACGTcount: A:0.27, C:0.07, G:0.10, T:0.56
Consensus pattern (75 bp):
TTAGGATTTTTAGTTTGATTATATCATTATTATTTTATTTAGGAATTAGTAATTATTATTTACAT
AGAACTCTCA
Found at i:1158954 original size:18 final size:18
Alignment explanation
Indices: 1158915--1158955 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
1158905 TGAAGTTCTC
1158915 CTTTT-TTTCATATCTTT
1 CTTTTCTTTCATATCTTT
*
1158932 TTTTTCTTTCATAAT-TTT
1 CTTTTCTTTCAT-ATCTTT
1158950 CTTTTC
1 CTTTTC
1158956 ACAATGCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 4 0.20
18 14 0.70
19 2 0.10
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.71
Consensus pattern (18 bp):
CTTTTCTTTCATATCTTT
Found at i:1165068 original size:90 final size:90
Alignment explanation
Indices: 1164953--1165130 Score: 284
Period size: 90 Copynumber: 2.0 Consensus size: 90
1164943 TAATTCCGAA
* * * * *
1164953 TATTTAATTTTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATTAT
1 TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCCAATATGAT
1165018 TAGGGTAACCTGGATATAAAAGGAT
66 TAGGGTAACCTGGATATAAAAGGAT
*
1165043 TATTAAATTTCAATTAATTAAATATAGATTTAATTATTTTGAAATAATAAAAACCCCAATATGAT
1 TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCCAATATGAT
* *
1165108 TAGGGTAACTTGGCTATAAAAGG
66 TAGGGTAACCTGGATATAAAAGG
1165131 GTGTGTTAGG
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 80 1.00
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.38
Consensus pattern (90 bp):
TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCCAATATGAT
TAGGGTAACCTGGATATAAAAGGAT
Found at i:1171788 original size:90 final size:90
Alignment explanation
Indices: 1171689--1171854 Score: 287
Period size: 90 Copynumber: 1.8 Consensus size: 90
1171679 ATTTAATTTT
* *
1171689 AATTAATTAAATATATATTTAATTAATTTGAAATAATAAAATCTCTAATATGATTAGGGTAACCT
1 AATTAATTAAATATATATTTAATTAATTTGAAATAATAAAAACCCTAATATGATTAGGGTAACCT
1171754 GGATATAAAAGGATTATTAAATTCC
66 GGATATAAAAGGATTATTAAATTCC
* *
1171779 AATTAATTAAATATATATTTAATTATTTTGAAATAATAAAAACCCTAATATGATTAGGGTAACTT
1 AATTAATTAAATATATATTTAATTAATTTGAAATAATAAAAACCCTAATATGATTAGGGTAACCT
*
1171844 GGCTATAAAAG
66 GGATATAAAAG
1171855 AGTATGTTAG
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
90 71 1.00
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.37
Consensus pattern (90 bp):
AATTAATTAAATATATATTTAATTAATTTGAAATAATAAAAACCCTAATATGATTAGGGTAACCT
GGATATAAAAGGATTATTAAATTCC
Found at i:1177164 original size:20 final size:21
Alignment explanation
Indices: 1177139--1177183 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
1177129 ATTTTAACGT
1177139 AATTGATATTC-ATTTT-AAAC
1 AATTGATA-TCAATTTTCAAAC
1177159 AATTGATATCAATTTTCAAAC
1 AATTGATATCAATTTTCAAAC
1177180 AATT
1 AATT
1177184 TGATTTTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 2 0.09
20 13 0.57
21 8 0.35
ACGTcount: A:0.42, C:0.11, G:0.04, T:0.42
Consensus pattern (21 bp):
AATTGATATCAATTTTCAAAC
Found at i:1180490 original size:20 final size:21
Alignment explanation
Indices: 1180465--1180546 Score: 71
Period size: 21 Copynumber: 3.9 Consensus size: 21
1180455 TTTTGGTGCA
1180465 GAGGGAATCGA-TCCCCCCAT
1 GAGGGAATCGATTCCCCCCAT
**
1180485 GAGGGAA-CTGATTCCCCCTTT
1 GAGGGAATC-GATTCCCCCCAT
1180506 GAAGGGGAATCGATTCCCCCCA-
1 G-A-GGGAATCGATTCCCCCCAT
* *
1180528 CAGGAGAATCGATACCCCC
1 GAGG-GAATCGATTCCCCC
1180547 ATGGGGTTCT
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
19 1 0.02
20 11 0.22
21 22 0.44
22 1 0.02
23 14 0.28
24 1 0.02
ACGTcount: A:0.26, C:0.33, G:0.24, T:0.17
Consensus pattern (21 bp):
GAGGGAATCGATTCCCCCCAT
Found at i:1185126 original size:28 final size:28
Alignment explanation
Indices: 1185086--1185144 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
1185076 AGTGTGGCAA
*
1185086 ATGCACAGAGGTGCTAGCTTAATTATTG
1 ATGCACAGAGGTGCTAGCTTAATGATTG
* *
1185114 ATGCCCAGAGGTGCTAGGTTAATGATTG
1 ATGCACAGAGGTGCTAGCTTAATGATTG
1185142 ATG
1 ATG
1185145 ACCAAAGATG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.31
Consensus pattern (28 bp):
ATGCACAGAGGTGCTAGCTTAATGATTG
Found at i:1185156 original size:28 final size:28
Alignment explanation
Indices: 1185097--1185156 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
1185087 TGCACAGAGG
* * * *
1185097 TGCTAGCTTAATTATTGATGCCCAGAGG
1 TGCTAGCTTAATGATTGATGACCAAAGA
*
1185125 TGCTAGGTTAATGATTGATGACCAAAGA
1 TGCTAGCTTAATGATTGATGACCAAAGA
1185153 TGCT
1 TGCT
1185157 CAATTGTTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (28 bp):
TGCTAGCTTAATGATTGATGACCAAAGA
Found at i:1185318 original size:57 final size:57
Alignment explanation
Indices: 1185257--1185475 Score: 318
Period size: 57 Copynumber: 3.8 Consensus size: 57
1185247 CTAGATTGAA
*
1185257 GCACAGAGGTACCTA-ATCTAAGATTGATGCACAGAGGTGCTCAATCATTTTTTTAAT
1 GCACAGAGGTACC-AGATCTAAGATTGATGCACAGAGGTGCTCAATCATTTCTTTAAT
*
1185314 GCACAGAGGTACCTA-ATCTAAGATTGATGCACAGAGGTGCTCAATCATCTCTTTAAT
1 GCACAGAGGTACC-AGATCTAAGATTGATGCACAGAGGTGCTCAATCATTTCTTTAAT
* * *
1185371 GCACAGAGGTTCCAGTTCAAAGATTGATGCACAGAGGTGCTCAATCATTTCTTTAAT
1 GCACAGAGGTACCAGATCTAAGATTGATGCACAGAGGTGCTCAATCATTTCTTTAAT
* * *
1185428 GCACAGAGGTGCCAGGTCCT-AGATTGAAGCACAGAGGTGCTCAATCAT
1 GCACAGAGGTACCAGAT-CTAAGATTGATGCACAGAGGTGCTCAATCAT
1185476 CCCAAAGCAC
Statistics
Matches: 150, Mismatches: 10, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
56 1 0.01
57 148 0.99
58 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (57 bp):
GCACAGAGGTACCAGATCTAAGATTGATGCACAGAGGTGCTCAATCATTTCTTTAAT
Found at i:1185322 original size:29 final size:29
Alignment explanation
Indices: 1185198--1185475 Score: 153
Period size: 28 Copynumber: 9.8 Consensus size: 29
1185188 TCAAAGATTG
* *
1185198 ATGCACAGAGGTGCTCAAACATTTCTTTA
1 ATGCACAGAGGTGCTCAATCATATCTTTA
* * ** *
1185227 ATGCACAGAGGTGC-CAGGTCCTAGATTGA
1 ATGCACAGAGGTGCTCA-ATCATATCTTTA
* *** *
1185256 A-GCACAGAGGTAC-CTAATC-TAAGATTG
1 ATGCACAGAGGTGCTC-AATCATATCTTTA
* *
1185283 ATGCACAGAGGTGCTCAATCATTTTTTTA
1 ATGCACAGAGGTGCTCAATCATATCTTTA
* *** *
1185312 ATGCACAGAGGTAC-CTAATC-TAAGATTG
1 ATGCACAGAGGTGCTC-AATCATATCTTTA
*
1185340 ATGCACAGAGGTGCTCAATCATCTCTTTA
1 ATGCACAGAGGTGCTCAATCATATCTTTA
* * *** *
1185369 ATGCACAGAGGTTC-CAGTTCA-AAGATTG
1 ATGCACAGAGGTGCTCA-ATCATATCTTTA
*
1185397 ATGCACAGAGGTGCTCAATCATTTCTTTA
1 ATGCACAGAGGTGCTCAATCATATCTTTA
* * ** *
1185426 ATGCACAGAGGTGC-CAGGTCCTAGATTGA
1 ATGCACAGAGGTGCTCA-ATCATATCTTTA
1185455 A-GCACAGAGGTGCTCAATCAT
1 ATGCACAGAGGTGCTCAATCAT
1185476 CCCAAAGCAC
Statistics
Matches: 182, Mismatches: 54, Indels: 27
0.69 0.21 0.10
Matches are distributed among these distances:
27 4 0.02
28 89 0.49
29 89 0.49
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (29 bp):
ATGCACAGAGGTGCTCAATCATATCTTTA
Found at i:1185338 original size:85 final size:85
Alignment explanation
Indices: 1185191--1185351 Score: 245
Period size: 85 Copynumber: 1.9 Consensus size: 85
1185181 TGTTATTTCA
* *
1185191 AAGATTGATGCACAGAGGTGCTCAAACATTTCTTTAATGCACAGAGGTGCCAGGTCCTAGATTGA
1 AAGATTGATGCACAGAGGTGCTCAAACATTTCTTTAATGCACAGAGGTACCAGATCCTAGATTGA
1185256 AGCACAGAGGTACCTAATCT
66 AGCACAGAGGTACCTAATCT
* *
1185276 AAGATTGATGCACAGAGGTGCTCAATCATTTTTTTAATGCACAGAGGTACCTA-AT-CTAAGATT
1 AAGATTGATGCACAGAGGTGCTCAAACATTTCTTTAATGCACAGAGGTACC-AGATCCT-AGATT
*
1185339 GATGCACAGAGGT
64 GAAGCACAGAGGT
1185352 GCTCAATCAT
Statistics
Matches: 69, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
84 2 0.03
85 66 0.96
86 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (85 bp):
AAGATTGATGCACAGAGGTGCTCAAACATTTCTTTAATGCACAGAGGTACCAGATCCTAGATTGA
AGCACAGAGGTACCTAATCT
Found at i:1192842 original size:7 final size:7
Alignment explanation
Indices: 1192832--1192865 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
1192822 TTTCTTTTAC
1192832 ACATTAT
1 ACATTAT
1192839 ACATTAT
1 ACATTAT
*
1192846 GCATTAT
1 ACATTAT
*
1192853 ACATTTT
1 ACATTAT
1192860 ACATTA
1 ACATTA
1192866 ATATTATTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.44
Consensus pattern (7 bp):
ACATTAT
Found at i:1193690 original size:2 final size:2
Alignment explanation
Indices: 1193685--1193735 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
1193675 TCTCTCTCTC
* *
1193685 TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA GA 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
1193727 TA TA T- TA TA
1 TA TA TA TA TA
1193736 AACAATGTTG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1200810 original size:81 final size:81
Alignment explanation
Indices: 1200714--1200973 Score: 274
Period size: 81 Copynumber: 3.2 Consensus size: 81
1200704 TTACCCAAAT
* * * * * * *** *
1200714 GTATTTAGCCTTTCATCTAACTTTCATATTTGACACATTTCTGTCAAATGCACAACGAGTCCATT
1 GTATTTAACCATTCATCTAACTGTCATAATTGACACCTTTCTGCCAAATGCACAGTTAGGCCATT
1200779 ATTCATTTACTCAATA
66 ATTCATTTACTCAATA
* * * * * *
1200795 GTGTTTAACTATTCATCCAACTGTCATAATTGA-ACCTTTATGCCAAATGTAGAGTTAGGCCATT
1 GTATTTAACCATTCATCTAACTGTCATAATTGACACCTTTCTGCCAAATGCACAGTTAGGCCATT
*
1200859 ATT-ATTTTACTCAA-C
66 ATTCA-TTTACTCAATA
* * *
1200874 GATATTTAACCATTCATATAACTGGCATAATTGACACCTTTCTACCAAATGCACAGTTAGGCCAT
1 G-TATTTAACCATTCATCTAACTGTCATAATTGACACCTTTCTGCCAAATGCACAGTTAGGCCAT
* *
1200939 TATTCTTTTACTCAATG
65 TATTCATTTACTCAATA
*
1200956 GTATTTAACCGTTCATCT
1 GTATTTAACCATTCATCT
1200974 TTTACTCAAC
Statistics
Matches: 144, Mismatches: 30, Indels: 10
0.78 0.16 0.05
Matches are distributed among these distances:
79 2 0.01
80 61 0.42
81 80 0.56
82 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (81 bp):
GTATTTAACCATTCATCTAACTGTCATAATTGACACCTTTCTGCCAAATGCACAGTTAGGCCATT
ATTCATTTACTCAATA
Found at i:1200991 original size:29 final size:29
Alignment explanation
Indices: 1200942--1201002 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
1200932 AGGCCATTAT
**
1200942 TCTTTTACTCAATGGTATTTAACCGTTCA
1 TCTTTTACTCAACAGTATTTAACCGTTCA
*
1200971 TCTTTTACTCAACAGTGTTTAACCGTTCA
1 TCTTTTACTCAACAGTATTTAACCGTTCA
1201000 TCT
1 TCT
1201003 AACTGACATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.44
Consensus pattern (29 bp):
TCTTTTACTCAACAGTATTTAACCGTTCA
Found at i:1201058 original size:110 final size:110
Alignment explanation
Indices: 1200863--1201083 Score: 327
Period size: 110 Copynumber: 2.0 Consensus size: 110
1200853 GCCATTATTA
* * *
1200863 TTTTACTCAACGATATTTAACCATTCATATAACTGGCATAATTGACACCTTTCTACCAAATGCAC
1 TTTTACTCAACGATATTTAACCATTCATATAACTGACATAATTGACACCTCTCTAACAAATGCAC
* * ***
1200928 AGTTAGGCCATTATTCTTTTACTCAATGGTATTTAACCGTTCATC
66 AGTTAGACCATTATTATTTTACTCAACAATATTTAACCGTTCATC
* * *
1200973 TTTTACTCAAC-AGTGTTTAACCGTTCATCTAACTGACATAATTGACACCTCTCTAACAAATGCA
1 TTTTACTCAACGA-TATTTAACCATTCATATAACTGACATAATTGACACCTCTCTAACAAATGCA
1201037 CAGTTAGACCATTATTATTTTACTCAACAATATTTAACCGTTCATC
65 CAGTTAGACCATTATTATTTTACTCAACAATATTTAACCGTTCATC
1201083 T
1 T
1201084 AACTGGCATA
Statistics
Matches: 99, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
109 1 0.01
110 98 0.99
ACGTcount: A:0.31, C:0.23, G:0.09, T:0.37
Consensus pattern (110 bp):
TTTTACTCAACGATATTTAACCATTCATATAACTGACATAATTGACACCTCTCTAACAAATGCAC
AGTTAGACCATTATTATTTTACTCAACAATATTTAACCGTTCATC
Found at i:1201115 original size:191 final size:190
Alignment explanation
Indices: 1200784--1201164 Score: 573
Period size: 191 Copynumber: 2.0 Consensus size: 190
1200774 CCATTATTCA
* * * * ** * *
1200784 TTTACTCAATAGTGTTTAACTATTCATCCAACTGTCATAATTGAACCTTTATGCCAAATGTAGAG
1 TTTACTCAACAGTGTTTAACCATTCATCCAACTGACATAATTGAACCTCTATAACAAATGCACAG
* *
1200849 TTAGGCCATTATTATTTTACTCAACGATATTTAACCATTCATATAACTGGCATAATTGACACCTT
66 TTAGACCATTATTATTTTACTCAACAATATTTAACCATTCATATAACTGGCATAATTGACACCTT
* * * *
1200914 TCTACCAAATGCACAGTTAGGCCATTATTCTTTTACTCAATGGTATTTAACCGTTCATCT
131 TATACCAAATGCAAAGTTAGGCCATTATTCTTTCACTCAACGGTATTTAACCGTTCATCT
* * *
1200974 TTTACTCAACAGTGTTTAACCGTTCATCTAACTGACATAATTGACACCTCTCTAACAAATGCACA
1 TTTACTCAACAGTGTTTAACCATTCATCCAACTGACATAATTGA-ACCTCTATAACAAATGCACA
* *
1201039 GTTAGACCATTATTATTTTACTCAACAATATTTAACCGTTCATCTAACTGGCATAATTGACACCT
65 GTTAGACCATTATTATTTTACTCAACAATATTTAACCATTCATATAACTGGCATAATTGACACCT
*
1201104 TTATGCCAAATGCAAAGTTAGGCCATTATTCTTTCACTCAACGGTATTTAACCGTTCATCT
130 TTATACCAAATGCAAAGTTAGGCCATTATTCTTTCACTCAACGGTATTTAACCGTTCATCT
1201165 AACTGGCATA
Statistics
Matches: 170, Mismatches: 20, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
190 39 0.23
191 131 0.77
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (190 bp):
TTTACTCAACAGTGTTTAACCATTCATCCAACTGACATAATTGAACCTCTATAACAAATGCACAG
TTAGACCATTATTATTTTACTCAACAATATTTAACCATTCATATAACTGGCATAATTGACACCTT
TATACCAAATGCAAAGTTAGGCCATTATTCTTTCACTCAACGGTATTTAACCGTTCATCT
Found at i:1201232 original size:80 final size:81
Alignment explanation
Indices: 1200971--1201265 Score: 432
Period size: 81 Copynumber: 3.7 Consensus size: 81
1200961 TAACCGTTCA
* * * * **
1200971 TCTTTTACTCAAC-AGTGTTTAACCGTTCATCTAACTGACATAATTGACACCTCTCTAACAAATG
1 TCTTTTACTCAACGA-TATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTATGCCAAATG
1201035 CACAGTTAGACCATTAT
65 CACAGTTAGACCATTAT
* *
1201052 TATTTTACTCAACAATATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTATGCCAAATGC
1 TCTTTTACTCAACGATATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTATGCCAAATGC
* *
1201117 AAAGTTAGGCCATTAT
66 ACAGTTAGACCATTAT
* *
1201133 TCTTTCACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACA-CTTTATGCCAAATGC
1 TCTTTTACTCAACGATATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTATGCCAAATGC
1201197 ACAGTTAGACCATTAT
66 ACAGTTAGACCATTAT
* * *
1201213 TCTTTTACTCAATGATATTTAACCGTTCATCTAATTGGCATAAATGACACCTT
1 TCTTTTACTCAACGATATTTAACCGTTCATCTAACTGGCATAATTGACACCTT
1201266 CCTATCAAAT
Statistics
Matches: 192, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
80 73 0.38
81 118 0.61
82 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.35
Consensus pattern (81 bp):
TCTTTTACTCAACGATATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTATGCCAAATGC
ACAGTTAGACCATTAT
Found at i:1201243 original size:161 final size:162
Alignment explanation
Indices: 1200971--1201265 Score: 466
Period size: 161 Copynumber: 1.8 Consensus size: 162
1200961 TAACCGTTCA
* * *
1200971 TCTTTTACTCAACAGTGTTTAACCGTTCATCTAACTGACATAATTGACACCTCTCTAACAAATGC
1 TCTTTCACTCAACAGTATTTAACCGTTCATCTAACTGACATAATTGACACCTCTATAACAAATGC
*
1201036 ACAGTTAGACCATTATTATTTTACTCAACAATATTTAACCGTTCATCTAACTGGCATAATTGACA
66 ACAGTTAGACCATTATTATTTTACTCAACAATATTTAACCGTTCATCTAACTGGCATAAATGACA
1201101 CCTTTATGCCAAATGCAAAGTTAGGCCATTAT
131 CCTTTATGCCAAATGCAAAGTTAGGCCATTAT
* * * **
1201133 TCTTTCACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACA-CTTTATGCCAAATGC
1 TCTTTCACTCAACAGTATTTAACCGTTCATCTAACTGACATAATTGACACCTCTATAACAAATGC
* ** *
1201197 ACAGTTAGACCATTATTCTTTTACTCAATGATATTTAACCGTTCATCTAATTGGCATAAATGACA
66 ACAGTTAGACCATTATTATTTTACTCAACAATATTTAACCGTTCATCTAACTGGCATAAATGACA
1201262 CCTT
131 CCTT
1201266 CCTATCAAAT
Statistics
Matches: 120, Mismatches: 13, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
161 75 0.62
162 45 0.38
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.35
Consensus pattern (162 bp):
TCTTTCACTCAACAGTATTTAACCGTTCATCTAACTGACATAATTGACACCTCTATAACAAATGC
ACAGTTAGACCATTATTATTTTACTCAACAATATTTAACCGTTCATCTAACTGGCATAAATGACA
CCTTTATGCCAAATGCAAAGTTAGGCCATTAT
Found at i:1201558 original size:68 final size:68
Alignment explanation
Indices: 1201238--1201557 Score: 392
Period size: 68 Copynumber: 4.7 Consensus size: 68
1201228 TATTTAACCG
* * * * * * * *
1201238 TTCATCTAATTGGCATAAATGACACCTTCCTATCAAATGCATAGCTAGGCCTGAAA-GTACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
*
1201302 TCT
66 CCT
* * * * *
1201305 TTTATATAAATGGCATAAATGATACATTTCTGTCAAATGCACAGTTAGACCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
*
1201370 ACT
66 CCT
* * *
1201373 TTCATCTAACTGGTATAAATGACTCATTTCTGTCAAATGCACAGTTAGGCTTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
*
1201438 CAT
66 CCT
* * *
1201441 TTTATCTAACTGGCATAAATGACACCA-TTCTGTCAAATGAACAGTTAGGTCTCAAAGGCACTTA
1 TTCATCTAACTGGCATAAATGACA-CATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTA
*
1201505 TCCT
65 GCCT
* *
1201509 TTCATCTAACTGGCATAAATGACATATTTCTGTCAAATGCATAGTTAGG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGG
1201558 TATATTAATC
Statistics
Matches: 215, Mismatches: 35, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
67 46 0.21
68 167 0.78
69 2 0.01
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:1212703 original size:18 final size:18
Alignment explanation
Indices: 1212680--1212724 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
1212670 TAGTTTGATT
1212680 AATGAACTAACATTATTC
1 AATGAACTAACATTATTC
*
1212698 AATGAACTAACTTTATTC
1 AATGAACTAACATTATTC
1212716 AATGAACTA
1 AATGAACTA
1212725 GATGCATGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (18 bp):
AATGAACTAACATTATTC
Found at i:1214694 original size:16 final size:16
Alignment explanation
Indices: 1214673--1214704 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1214663 CCTCTTTAAA
*
1214673 TTTTTTTTTTCTTTTT
1 TTTTTTTTTTATTTTT
1214689 TTTTTTTTTTATTTTT
1 TTTTTTTTTTATTTTT
1214705 GATTTTTTTA
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:0.03, C:0.03, G:0.00, T:0.94
Consensus pattern (16 bp):
TTTTTTTTTTATTTTT
Found at i:1214703 original size:15 final size:15
Alignment explanation
Indices: 1214673--1214714 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
1214663 CCTCTTTAAA
*
1214673 TTTTTTTTTTCT-TT
1 TTTTTTTTTTTTATT
1214687 TTTTTTTTTTTTATT
1 TTTTTTTTTTTTATT
**
1214702 TTTGATTTTTTTA
1 TTTTTTTTTTTTA
1214715 CTAATATGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.07, C:0.02, G:0.02, T:0.88
Consensus pattern (15 bp):
TTTTTTTTTTTTATT
Found at i:1214710 original size:16 final size:16
Alignment explanation
Indices: 1214675--1214713 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1214665 TCTTTAAATT
* **
1214675 TTTTTTTTCTTTTTTT
1 TTTTTTTTATTTTTGA
1214691 TTTTTTTTATTTTTGA
1 TTTTTTTTATTTTTGA
1214707 TTTTTTT
1 TTTTTTT
1214714 ACTAATATGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.05, C:0.03, G:0.03, T:0.90
Consensus pattern (16 bp):
TTTTTTTTATTTTTGA
Found at i:1216238 original size:18 final size:18
Alignment explanation
Indices: 1216210--1216259 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
1216200 AGAGTTAGTT
1216210 TTATT-AATGAACTAAAA
1 TTATTCAATGAACTAAAA
**
1216227 TTATTCAATGAACTAACT
1 TTATTCAATGAACTAAAA
1216245 TTATTCAATGAACTA
1 TTATTCAATGAACTA
1216260 GATGCATGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 5 0.17
18 25 0.83
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (18 bp):
TTATTCAATGAACTAAAA
Found at i:1217801 original size:16 final size:16
Alignment explanation
Indices: 1217780--1217810 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1217770 TGATTCAAAT
1217780 TCTACAAAGGATTTTC
1 TCTACAAAGGATTTTC
1217796 TCTACAAAGGATTTT
1 TCTACAAAGGATTTT
1217811 ATCAGGAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (16 bp):
TCTACAAAGGATTTTC
Found at i:1219863 original size:33 final size:33
Alignment explanation
Indices: 1219825--1219891 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
1219815 TTATCATCTT
1219825 TGACAATAAGTATAACAATGAACATGTATATCA
1 TGACAATAAGTATAACAATGAACATGTATATCA
1219858 TGACAATAAGTATAACAATGAACATGTATATCA
1 TGACAATAAGTATAACAATGAACATGTATATCA
1219891 T
1 T
1219892 CATATCAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.28
Consensus pattern (33 bp):
TGACAATAAGTATAACAATGAACATGTATATCA
Found at i:1220381 original size:15 final size:15
Alignment explanation
Indices: 1220357--1220396 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1220347 TTGTTAGGAT
1220357 AGTTTCCTCATG-GA
1 AGTTTCCTCATGTGA
1220371 AGTTCTCCTCATGTGA
1 AGTT-TCCTCATGTGA
*
1220387 TGTTTCCTCA
1 AGTTTCCTCA
1220397 GGGTCCTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 4 0.17
15 14 0.61
16 5 0.22
ACGTcount: A:0.17, C:0.25, G:0.17, T:0.40
Consensus pattern (15 bp):
AGTTTCCTCATGTGA
Found at i:1221607 original size:46 final size:46
Alignment explanation
Indices: 1221535--1221626 Score: 114
Period size: 46 Copynumber: 2.0 Consensus size: 46
1221525 AGGGTTTTGT
*
1221535 GCTAACACTTCAACGACCGCACGTTTTTCAGCCATTGGATCTGGCC
1 GCTAACACTTCAACGACCGCACGTTTTCCAGCCATTGGATCTGGCC
* * * **
1221581 GCTAACACTTCAAC-AGTCGTATGTTTTCCAGCTGTTGGATCTGGCC
1 GCTAACACTTCAACGA-CCGCACGTTTTCCAGCCATTGGATCTGGCC
1221627 AGATCCAACG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
45 1 0.03
46 38 0.97
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (46 bp):
GCTAACACTTCAACGACCGCACGTTTTCCAGCCATTGGATCTGGCC
Found at i:1222342 original size:20 final size:20
Alignment explanation
Indices: 1222295--1222365 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
1222285 GCGATTTTCC
1222295 GACTATCGCAATGCGAATAT
1 GACTATCGCAATGCGAATAT
* *
1222315 GTA-AATCGCAATGCGAGTAT
1 G-ACTATCGCAATGCGAATAT
* * *
1222335 GACTATCGCAAAGCGATTCT
1 GACTATCGCAATGCGAATAT
1222355 GACTATCGCAA
1 GACTATCGCAA
1222366 CGAGATTCTG
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
19 1 0.02
20 41 0.95
21 1 0.02
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (20 bp):
GACTATCGCAATGCGAATAT
Found at i:1222372 original size:20 final size:20
Alignment explanation
Indices: 1222319--1222432 Score: 120
Period size: 20 Copynumber: 5.7 Consensus size: 20
1222309 GAATATGTAA
* * *
1222319 ATCGCAATGCGAGTATGACT
1 ATCGCAACGCGATTCTGACT
*
1222339 ATCGCAAAGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* *
1222359 ATCGCAACGAGATTCTGACC
1 ATCGCAACGCGATTCTGACT
*
1222379 ATCGCAACGTGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* * *
1222399 GTCGCAACGCGATGCTGTCT
1 ATCGCAACGCGATTCTGACT
* *
1222419 ATCACAATGCGATT
1 ATCGCAACGCGATT
1222433 TTCAAAGCGC
Statistics
Matches: 78, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 78 1.00
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:1222629 original size:22 final size:22
Alignment explanation
Indices: 1222604--1222646 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1222594 AGGCGACATC
1222604 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
1222626 GTCCCCATCTCCGACGAAATC
1 GTCCCCATCTCCGACGAAATC
1222647 CGTCTATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.26, C:0.42, G:0.14, T:0.19
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:1223055 original size:19 final size:19
Alignment explanation
Indices: 1223031--1223074 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
1223021 AGAATCGTAA
1223031 TGCGATTTT-AGTTTCGCAT
1 TGCGATTTTCA-TTTCGCAT
*
1223050 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCAT
1223069 TGCGAT
1 TGCGAT
1223075 AGTCAAATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 22 0.96
20 1 0.04
ACGTcount: A:0.14, C:0.18, G:0.23, T:0.45
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCAT
Found at i:1223120 original size:20 final size:20
Alignment explanation
Indices: 1223031--1223137 Score: 92
Period size: 20 Copynumber: 5.5 Consensus size: 20
1223021 AGAATCGTAA
* *
1223031 TGCGATTTT-AGTTTCGCAT
1 TGCGATTTTCATTTTCGCGT
1223050 TGCGATTTTCA-TTTCGCGT
1 TGCGATTTTCATTTTCGCGT
** **
1223069 TGCGATAGTCAAATTCGCGT
1 TGCGATTTTCATTTTCGCGT
* ** *
1223089 TGCAATAGTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
* *
1223109 TGCGATTTTCATTTTTGTGT
1 TGCGATTTTCATTTTCGCGT
1223129 TGCGATTTT
1 TGCGATTTT
1223138 AAGTTTCAGA
Statistics
Matches: 74, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
19 25 0.34
20 49 0.66
ACGTcount: A:0.16, C:0.16, G:0.21, T:0.47
Consensus pattern (20 bp):
TGCGATTTTCATTTTCGCGT
Found at i:1224893 original size:18 final size:18
Alignment explanation
Indices: 1224870--1224919 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
1224860 TTTACTCGTA
1224870 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
1224888 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
1224906 ATTTCACTTAGATT
1 ATTTCACTTAGATT
1224920 GCTTAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.42
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:1225098 original size:20 final size:20
Alignment explanation
Indices: 1225069--1225133 Score: 103
Period size: 20 Copynumber: 3.2 Consensus size: 20
1225059 TTTACTTTCA
1225069 CAACGCGAAAATGACTATCG
1 CAACGCGAAAATGACTATCG
*
1225089 CAATGCGAAAATGACTATCG
1 CAACGCGAAAATGACTATCG
**
1225109 CAACGCGAATTTGACTATCG
1 CAACGCGAAAATGACTATCG
1225129 CAACG
1 CAACG
1225134 AAAGAATCGC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.18
Consensus pattern (20 bp):
CAACGCGAAAATGACTATCG
Found at i:1225229 original size:20 final size:20
Alignment explanation
Indices: 1225175--1225230 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
1225165 GCGATTCTCT
**
1225175 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
1225195 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
1225215 CGTTACGATAGTCATT
1 CGTTGCGATAGTCATT
1225231 CGTGCTGCGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:1225822 original size:21 final size:20
Alignment explanation
Indices: 1225727--1225834 Score: 74
Period size: 21 Copynumber: 5.2 Consensus size: 20
1225717 GCCCGACTCA
1225727 CCTGTCATCGTTCAAGAGG-
1 CCTGTCATCGTTCAAGAGGC
**
1225746 CCTCCCCTATCGTTCAAGAGGC
1 CCT-GTC-ATCGTTCAAGAGGC
* ** *
1225768 CCTTATCATCCCTCAAGAGTCC
1 CC-TGTCATCGTTCAAGAG-GC
* *
1225790 CCTGCCACCGTTCAAGAGGC
1 CCTGTCATCGTTCAAGAGGC
*
1225810 CACTGTCATCGTTGAAGAGGTC
1 C-CTGTCATCGTTCAAGAGG-C
1225832 CCT
1 CCT
1225835 CCCAACATTC
Statistics
Matches: 66, Mismatches: 16, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
19 3 0.05
20 3 0.05
21 51 0.77
22 8 0.12
23 1 0.02
ACGTcount: A:0.20, C:0.35, G:0.20, T:0.24
Consensus pattern (20 bp):
CCTGTCATCGTTCAAGAGGC
Found at i:1227105 original size:18 final size:18
Alignment explanation
Indices: 1227082--1227116 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1227072 AAGCCGGTTG
*
1227082 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
1227100 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
1227117 GCCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:1229388 original size:24 final size:24
Alignment explanation
Indices: 1229354--1229407 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1229344 CTGAAACATC
1229354 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1229378 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1229402 ATCAAA
1 ATCAAA
1229408 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1230269 original size:20 final size:20
Alignment explanation
Indices: 1230236--1230356 Score: 111
Period size: 20 Copynumber: 6.0 Consensus size: 20
1230226 GTGTTGTGAC
*
1230236 AGTCAGAATCGCATTGCGAT
1 AGTCATAATCGCATTGCGAT
*
1230256 AGTCATAATTGCATTGCGAT
1 AGTCATAATCGCATTGCGAT
* *
1230276 -TTACATATTCGCATTGCGAT
1 AGT-CATAATCGCATTGCGAT
* *
1230296 -TTACATATTCGCATTGCGAT
1 AGT-CATAATCGCATTGCGAT
* *
1230316 AGTCAGAAAATCGCAATGCGAT
1 AGTC--ATAATCGCATTGCGAT
*
1230338 AGTCAGAATCGCATTGCGA
1 AGTCATAATCGCATTGCGA
1230357 ATCTGGAAAC
Statistics
Matches: 86, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
19 1 0.01
20 67 0.78
21 1 0.01
22 17 0.20
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.30
Consensus pattern (20 bp):
AGTCATAATCGCATTGCGAT
Found at i:1230335 original size:22 final size:22
Alignment explanation
Indices: 1230304--1230345 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1230294 ATTTACATAT
*
1230304 TCGCATTGCGATAGTCAGAAAA
1 TCGCAATGCGATAGTCAGAAAA
1230326 TCGCAATGCGATAGTCAGAA
1 TCGCAATGCGATAGTCAGAA
1230346 TCGCATTGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.21
Consensus pattern (22 bp):
TCGCAATGCGATAGTCAGAAAA
Found at i:1233320 original size:55 final size:55
Alignment explanation
Indices: 1233251--1233360 Score: 193
Period size: 55 Copynumber: 2.0 Consensus size: 55
1233241 TTATTTTATT
* *
1233251 TTTCAAAAGTTTGTGAGTTTCTTCTCACAAGTAACACGTGCATTTGCATACCACG
1 TTTCAAAAGTTTGTGAGTTTCTTCTCACAAGCAACACGCGCATTTGCATACCACG
*
1233306 TTTCAAAAGTTTGTGAGTTTCTTCTCACAAGCGACACGCGCATTTGCATACCACG
1 TTTCAAAAGTTTGTGAGTTTCTTCTCACAAGCAACACGCGCATTTGCATACCACG
1233361 AGCTTTCTAC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (55 bp):
TTTCAAAAGTTTGTGAGTTTCTTCTCACAAGCAACACGCGCATTTGCATACCACG
Found at i:1235968 original size:30 final size:30
Alignment explanation
Indices: 1235934--1236022 Score: 133
Period size: 30 Copynumber: 3.0 Consensus size: 30
1235924 GGGACCATGT
1235934 GCTGCTGCAGCTGATTCTGTTAGACCACGC
1 GCTGCTGCAGCTGATTCTGTTAGACCACGC
*
1235964 GCTGCTGCAGCTGATTCTGTTGGACCACGC
1 GCTGCTGCAGCTGATTCTGTTAGACCACGC
* * * *
1235994 CCTGTTGTAGCTGATTCTGCTAGACCACG
1 GCTGCTGCAGCTGATTCTGTTAGACCACG
1236023 ACATACTGCA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.16, C:0.29, G:0.27, T:0.28
Consensus pattern (30 bp):
GCTGCTGCAGCTGATTCTGTTAGACCACGC
Found at i:1250947 original size:21 final size:21
Alignment explanation
Indices: 1250921--1250965 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1250911 AAAAATGGGT
* *
1250921 TATTTATTCTAACATGCAAAC
1 TATTTATCCTAACATGAAAAC
1250942 TATTTATCCTAACATGAAAAC
1 TATTTATCCTAACATGAAAAC
1250963 TAT
1 TAT
1250966 ATAATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.38
Consensus pattern (21 bp):
TATTTATCCTAACATGAAAAC
Found at i:1250983 original size:18 final size:18
Alignment explanation
Indices: 1250960--1250996 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1250950 CTAACATGAA
*
1250960 AACTATATAATATATACT
1 AACTATATAATATAAACT
*
1250978 AACTATGTAATATAAACT
1 AACTATATAATATAAACT
1250996 A
1 A
1250997 TGTCATATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.03, T:0.35
Consensus pattern (18 bp):
AACTATATAATATAAACT
Found at i:1251060 original size:17 final size:18
Alignment explanation
Indices: 1251025--1251060 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
1251015 ATATCTAATG
1251025 TAATATGCAATACTATTTA
1 TAATATGCAATA-TATTTA
1251044 TAATATGCAAT-TATTTA
1 TAATATGCAATATATTTA
1251061 ATATGAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
19 11 0.65
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (18 bp):
TAATATGCAATATATTTA
Found at i:1251209 original size:18 final size:17
Alignment explanation
Indices: 1251186--1251220 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1251176 TTATCTAAAC
*
1251186 TATATATTGTATTCATAT
1 TATATATTATATT-ATAT
1251204 TATATATTATATTATAT
1 TATATATTATATTATAT
1251221 ATGGCCACAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (17 bp):
TATATATTATATTATAT
Found at i:1252577 original size:11 final size:10
Alignment explanation
Indices: 1252536--1252588 Score: 51
Period size: 10 Copynumber: 5.6 Consensus size: 10
1252526 CTTTGTTTTT
1252536 TTTTTCTTC-
1 TTTTTCTTCA
*
1252545 TTCTTCTTC-
1 TTTTTCTTCA
1252554 -TTTTCTTTC-
1 TTTTTC-TTCA
1252563 TTTTTCTTCA
1 TTTTTCTTCA
*
1252573 TTTTTCTTTA
1 TTTTTCTTCA
1252583 TTTTTC
1 TTTTTC
1252589 ACTTTTCTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
8 4 0.11
9 14 0.37
10 20 0.53
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTTTCTTCA
Found at i:1252587 original size:21 final size:21
Alignment explanation
Indices: 1252533--1252588 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
1252523 TCACTTTGTT
* * *
1252533 TTTTTTTTCTTCTTCTTCTTC
1 TTTTCTTTCTTTTTCTTCATC
1252554 TTTTCTTTCTTTTTCTTCAT-
1 TTTTCTTTCTTTTTCTTCATC
*
1252574 TTTTCTTTATTTTTC
1 TTTTCTTTCTTTTTC
1252589 ACTTTTCTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTTCTTTCTTTTTCTTCATC
Found at i:1253315 original size:12 final size:12
Alignment explanation
Indices: 1253298--1253338 Score: 59
Period size: 11 Copynumber: 3.6 Consensus size: 12
1253288 CCCATTTTCA
1253298 TTTTCTTATTAT
1 TTTTCTTATTAT
1253310 TTTTCTTATTA-
1 TTTTCTTATTAT
*
1253321 TTTTCTT-TTTT
1 TTTTCTTATTAT
1253332 TTTTCTT
1 TTTTCTT
1253339 TTTTTCAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 2 0.07
11 14 0.52
12 11 0.41
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTCTTATTAT
Found at i:1253341 original size:12 final size:11
Alignment explanation
Indices: 1253298--1253343 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
1253288 CCCATTTTCA
*
1253298 TTTTCTTATTAT
1 TTTTCTT-TTTT
* *
1253310 TTTTCTTATTA
1 TTTTCTTTTTT
1253321 TTTTCTTTTTT
1 TTTTCTTTTTT
1253332 TTTTCTTTTTT
1 TTTTCTTTTTT
1253343 T
1 T
1253344 CAAGAATAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
11 22 0.76
12 7 0.24
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:1270794 original size:25 final size:24
Alignment explanation
Indices: 1270756--1270808 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
1270746 TAGTGGCAAT
* * *
1270756 CTTCTTGTGTCCATTGCACTGCAGC
1 CTTCTTATGACCATTACACTGCA-C
1270781 CTTCTTATGACCATTACACTGCAC
1 CTTCTTATGACCATTACACTGCAC
1270805 CTTC
1 CTTC
1270809 AATTAGTGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.17, C:0.34, G:0.13, T:0.36
Consensus pattern (24 bp):
CTTCTTATGACCATTACACTGCAC
Found at i:1276519 original size:55 final size:55
Alignment explanation
Indices: 1276482--1276705 Score: 227
Period size: 55 Copynumber: 4.1 Consensus size: 55
1276472 CCGATATGGT
*
1276482 AATTCACAAACTCATTATGAATTTTGTAGGGTTGCACACATAGTATCAATAAGGA
1 AATTCACAAACTCATTATGAATTTTGTAGGGTTGCACACATAGTACCAATAAGGA
* * * * * * *
1276537 AATTCATAAACTCGTTATGAATTTTTTAAGGTTGCACACACAGTACCAATACGAA
1 AATTCACAAACTCATTATGAATTTTGTAGGGTTGCACACATAGTACCAATAAGGA
* ** * * ***
1276592 AATTCATAAACTCATTACAAATTTCGT-GAGGTTGCACATATAGTACCAATACCAA
1 AATTCACAAACTCATTATGAATTTTGTAG-GGTTGCACACATAGTACCAATAAGGA
* * * * *
1276647 AATACATAAACTCATTATGAATTTCGT-GAGGTTGCATACATAGTGCCAATAAGGA
1 AATTCACAAACTCATTATGAATTTTGTAG-GGTTGCACACATAGTACCAATAAGGA
1276702 AATT
1 AATT
1276706 GCAACATATA
Statistics
Matches: 141, Mismatches: 27, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
55 141 1.00
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (55 bp):
AATTCACAAACTCATTATGAATTTTGTAGGGTTGCACACATAGTACCAATAAGGA
Found at i:1276705 original size:110 final size:110
Alignment explanation
Indices: 1276435--1276705 Score: 276
Period size: 110 Copynumber: 2.5 Consensus size: 110
1276425 TGAATATTTC
* * * * * * *
1276435 AACTCATTATAAATTTCGTG-GTTTTGCACACGTAGAGCCGATATGGTAATTCACAAACTCATTA
1 AACTCATTATGAATTTCGTGAG-GTTGCACACATAGTGCCAATAAGGAAATTCACAAACTCATTA
** * * ** *
1276499 TGAATTTTGTAGGGTTGCACACATAGTATCAATAAGGAAATTCATA
65 CAAATTTCGTAGGGTTGCACACATAGTACCAATAACAAAATACATA
* ** * * * * * *
1276545 AACTCGTTATGAATTTTTTAAGGTTGCACACACAGTACCAATACGAAAATTCATAAACTCATTAC
1 AACTCATTATGAATTTCGTGAGGTTGCACACATAGTGCCAATAAGGAAATTCACAAACTCATTAC
* *
1276610 AAATTTCGT-GAGGTTGCACATATAGTACCAATACCAAAATACATA
66 AAATTTCGTAG-GGTTGCACACATAGTACCAATAACAAAATACATA
*
1276655 AACTCATTATGAATTTCGTGAGGTTGCATACATAGTGCCAATAAGGAAATT
1 AACTCATTATGAATTTCGTGAGGTTGCACACATAGTGCCAATAAGGAAATT
1276706 GCAACATATA
Statistics
Matches: 126, Mismatches: 33, Indels: 4
0.77 0.20 0.02
Matches are distributed among these distances:
109 1 0.01
110 124 0.98
111 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (110 bp):
AACTCATTATGAATTTCGTGAGGTTGCACACATAGTGCCAATAAGGAAATTCACAAACTCATTAC
AAATTTCGTAGGGTTGCACACATAGTACCAATAACAAAATACATA
Found at i:1280050 original size:20 final size:20
Alignment explanation
Indices: 1280011--1280053 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1280001 GTTACTAGCA
**
1280011 TATCCAATATACTTGTCATT
1 TATCCAATATACTTACCATT
*
1280031 TATCCCATATACTTACCATT
1 TATCCAATATACTTACCATT
1280051 TAT
1 TAT
1280054 TATCATAAGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.23, G:0.02, T:0.44
Consensus pattern (20 bp):
TATCCAATATACTTACCATT
Found at i:1280145 original size:24 final size:24
Alignment explanation
Indices: 1280072--1280146 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
1280062 GCTTGTAAGC
*
1280072 TTATTTTACCGATATACTTACCAT
1 TTATTTTACCGATATACTTATCAT
* *
1280096 TTA--TTACC-ATA-AGC-TAGTAAGC
1 TTATTTTACCGATATA-CTTA-TCA-T
1280118 TTATTTTACCGATATACTTATCAT
1 TTATTTTACCGATATACTTATCAT
1280142 TTATT
1 TTATT
1280147 CCATAAGCTC
Statistics
Matches: 38, Mismatches: 5, Indels: 16
0.64 0.08 0.27
Matches are distributed among these distances:
20 3 0.08
21 5 0.13
22 8 0.21
24 13 0.34
25 6 0.16
26 3 0.08
ACGTcount: A:0.31, C:0.17, G:0.07, T:0.45
Consensus pattern (24 bp):
TTATTTTACCGATATACTTATCAT
Found at i:1280169 original size:45 final size:45
Alignment explanation
Indices: 1280037--1280302 Score: 417
Period size: 45 Copynumber: 5.9 Consensus size: 45
1280027 CATTTATCCC
* * *
1280037 ATATACTTACCATTTATTATCATAAGCTTGTAAGCTTATTTTACCG
1 ATATACTTACCATTTATT-CCATAAGCTCGTAAGCTTATTTTACCA
* *
1280083 ATATACTTACCATTTATTACCATAAGCTAGTAAGCTTATTTTACCG
1 ATATACTTACCATTTATT-CCATAAGCTCGTAAGCTTATTTTACCA
* *
1280129 ATATACTTATCATTTATTCCATAAGCTCGTAAGCTAATTTTACCA
1 ATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCA
*
1280174 ATATACTTACCATTTATTCCATAAGCTCATAAGCTTATTTTACCA
1 ATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCA
*
1280219 ATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACTA
1 ATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCA
*
1280264 ATATACTTGCCA-TTATTCCATAAGCTCGTAAGCTTATTT
1 ATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
1280303 GCCAGTTTTT
Statistics
Matches: 208, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
44 27 0.13
45 120 0.58
46 61 0.29
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.41
Consensus pattern (45 bp):
ATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCA
Found at i:1286654 original size:13 final size:13
Alignment explanation
Indices: 1286636--1286663 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1286626 TTTACATCTC
1286636 TTAATCGCAACCA
1 TTAATCGCAACCA
1286649 TTAATCGCAACCA
1 TTAATCGCAACCA
1286662 TT
1 TT
1286664 GCTAATATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.29
Consensus pattern (13 bp):
TTAATCGCAACCA
Found at i:1288440 original size:45 final size:45
Alignment explanation
Indices: 1288355--1288619 Score: 397
Period size: 45 Copynumber: 5.9 Consensus size: 45
1288345 TATTTATCCC
* * * *
1288355 ATATACTTACCATTTATTACCATAACCTTGTAAGCTTATTTTATCG
1 ATATACTTACCATTTATT-CCATAAGCTCGTAAGCTTATTTTACCA
* * *
1288401 ATATACTAACCATTTATTCCATAAGCTCATAAGTTTATTTTACCA
1 ATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCA
*
1288446 ATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTGCCA
1 ATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCA
*
1288491 ATATACTTACCATTTATTCCATAAGCTCATAAGCTTATTTTACCA
1 ATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCA
* *
1288536 ATATACTTACCATTTATCCCATAAGTTCGTAAGCTTATTTTACCA
1 ATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCA
* *
1288581 ATATATTTGCCA-TTATTCCATAAGCTCGTAAGCTTATTT
1 ATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
1288620 GCCAGTTATT
Statistics
Matches: 199, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
44 25 0.13
45 157 0.79
46 17 0.09
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.41
Consensus pattern (45 bp):
ATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCA
Found at i:1292491 original size:14 final size:14
Alignment explanation
Indices: 1292472--1292498 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1292462 ATTATATTTA
1292472 CCTCTTACTCAATT
1 CCTCTTACTCAATT
1292486 CCTCTTACTCAAT
1 CCTCTTACTCAAT
1292499 CAACAATGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.37, G:0.00, T:0.41
Consensus pattern (14 bp):
CCTCTTACTCAATT
Found at i:1293697 original size:20 final size:20
Alignment explanation
Indices: 1293668--1293710 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1293658 GTTACTAGCA
* *
1293668 TATCCAATATTCTTGTCATT
1 TATCCAATATACTTGCCATT
*
1293688 TATCCCATATACTTGCCATT
1 TATCCAATATACTTGCCATT
1293708 TAT
1 TAT
1293711 TACCATAAGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.26, C:0.23, G:0.05, T:0.47
Consensus pattern (20 bp):
TATCCAATATACTTGCCATT
Found at i:1293778 original size:45 final size:45
Alignment explanation
Indices: 1293694--1293958 Score: 433
Period size: 45 Copynumber: 5.9 Consensus size: 45
1293684 CATTTATCCC
* * *
1293694 ATATACTTGCCATTTATTACCATAAGCTTGTAAGCTTATTTTACCG
1 ATATACTTACCATTTATT-CCATAAGCTCGTAAGCTTATTTTACCA
* *
1293740 ATATACTTACCATTTATTACATAAGCTCGTAAGTTTATTTTACCA
1 ATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCA
*
1293785 ATATACTTACAATTTATTCCATAAGCTCGTAAGCTTATTTTACCA
1 ATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCA
1293830 ATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCA
1 ATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCA
*
1293875 ATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTTCCA
1 ATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCA
* *
1293920 ATATACTTGCCA-TAATTCCATAAGCTCGTAAGCTTATTT
1 ATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
1293959 GCCAGTTTTT
Statistics
Matches: 207, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
44 26 0.13
45 164 0.79
46 17 0.08
ACGTcount: A:0.31, C:0.20, G:0.08, T:0.41
Consensus pattern (45 bp):
ATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCA
Found at i:1293919 original size:24 final size:25
Alignment explanation
Indices: 1293796--1293919 Score: 71
Period size: 25 Copynumber: 5.4 Consensus size: 25
1293786 TATACTTACA
1293796 ATTTATTCCATAAGCTCGTAAGCTT
1 ATTTATTCCATAAGCTCGTAAGCTT
* *
1293821 ATTT-TACCAATATA-CT--T-A-C-C
1 ATTTATTCC-ATA-AGCTCGTAAGCTT
1293841 ATTTATTCCATAAGCTCGTAAGCTT
1 ATTTATTCCATAAGCTCGTAAGCTT
* *
1293866 ATTT-TACCAATATA-CT--T-A-C-C
1 ATTTATTCC-ATA-AGCTCGTAAGCTT
1293886 ATTTATTCCATAAGCTCGTAAGCTT
1 ATTTATTCCATAAGCTCGTAAGCTT
1293911 ATTT-TTCCA
1 ATTTATTCCA
1293920 ATATACTTGC
Statistics
Matches: 73, Mismatches: 8, Indels: 37
0.62 0.07 0.31
Matches are distributed among these distances:
19 2 0.03
20 18 0.25
21 8 0.11
22 4 0.05
23 4 0.05
24 13 0.18
25 22 0.30
26 2 0.03
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.41
Consensus pattern (25 bp):
ATTTATTCCATAAGCTCGTAAGCTT
Found at i:1299857 original size:55 final size:55
Alignment explanation
Indices: 1299793--1300146 Score: 505
Period size: 55 Copynumber: 6.4 Consensus size: 55
1299783 GAGGTTTTGT
* * * * * *
1299793 ACACGTAGTGCCAATACAGTAATTCAAAAACTCATTATTAATTACGTGGGGTTGC
1 ACACATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCGTGAGGTTGC
* * *
1299848 ACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTTGTGGGGTTGC
1 ACACATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCGTGAGGTTGC
* * * *
1299903 ACACATAATGCCAATACAGAAATTCATAAACTCGTTATGAATTTCATAAGGTTGC
1 ACACATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCGTGAGGTTGC
* *
1299958 ACACATAGTGCCAATAC-GAAAATTTATAAACTCATTATGAATTTCATGAGGTTGC
1 ACACATAGTGCCAATACAG-AAATTCATAAACTCATTATGAATTTCGTGAGGTTGC
*
1300013 ACACATAGTGCCAATACAGAAATTCATAAATTCATTATGAATTTCGTGAGGTTGC
1 ACACATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCGTGAGGTTGC
*
1300068 ACACATAGTGCCAATAC-GAAAATTCATAAACTCATTATGAATTTCGTGAGATTGC
1 ACACATAGTGCCAATACAG-AAATTCATAAACTCATTATGAATTTCGTGAGGTTGC
* *
1300123 ACGCATAGTGCCAATATAGAAATT
1 ACACATAGTGCCAATACAGAAATT
1300147 GCAACATATA
Statistics
Matches: 270, Mismatches: 25, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
54 2 0.01
55 266 0.99
56 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (55 bp):
ACACATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTTCGTGAGGTTGC
Found at i:1312948 original size:12 final size:12
Alignment explanation
Indices: 1312912--1312954 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
1312902 AAACCAGAAG
1312912 AAAAATGAGAGAA
1 AAAAATGAGAG-A
*
1312925 AGCAAAAGGAGAGA
1 A--AAAATGAGAGA
1312939 AAAAATGAGAGA
1 AAAAATGAGAGA
1312951 AAAA
1 AAAA
1312955 CAAAAAGAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 14 0.54
13 1 0.04
14 2 0.08
15 9 0.35
ACGTcount: A:0.67, C:0.02, G:0.26, T:0.05
Consensus pattern (12 bp):
AAAAATGAGAGA
Found at i:1318195 original size:65 final size:66
Alignment explanation
Indices: 1318018--1318198 Score: 190
Period size: 65 Copynumber: 2.7 Consensus size: 66
1318008 CTTTTGAAAA
* * * * * * * *
1318018 AAATATTTGAGTTTGTTTCCTTTGAAATAAAGTTTAGTCTCTCTTGACATAGTTTCTATTGAAAC
1 AAATCTTTGAG-TCGTTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGACAGTTTATATTGAAAC
1318083 ACT
64 ACT
* * * *
1318086 TAA-CTTTGAGTCGTTTTCCTTGAAACGAATTTTGTCTCCCTTGAGACAGTTTATCA-TGAAACA
1 AAATCTTTGAGTCGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTAT-ATTGAAACA
1318149 C-
65 CT
1318150 AAATCTTTGAGATCGTTTCCCTTGAAACAAATTTTGTCT-TCTTGAGACA
1 AAATCTTTGAG-TCGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
1318199 ACTTCTCTTG
Statistics
Matches: 94, Mismatches: 16, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
64 2 0.02
65 44 0.47
66 40 0.43
67 6 0.06
68 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.40
Consensus pattern (66 bp):
AAATCTTTGAGTCGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTATATTGAAACAC
T
Found at i:1318607 original size:134 final size:132
Alignment explanation
Indices: 1318249--1318608 Score: 383
Period size: 134 Copynumber: 2.7 Consensus size: 132
1318239 ACCATTATCC
* * * * *
1318249 CTAAAGATGGCCTACCGTCCTCATCGCGTA-GAACCGTGTCATCCCCCGACCAGACCTCCTCATC
1 CTAAAGATGACCGAACGTCCTCATCACATAGGAACCGTGTCATCCCCCGACCAGACCTCCTCATC
* * ** *
1318313 ACGTAGGAGTCGTGTCAGCCC-TA-ATAACCAGCCGTCCTCATCACGTAGGAACTGTGTTATCAT
66 ACGTAGGAGCCGTGTCACCCCTTAGATAACCAGCCGTCCTCATCACGTAGGAACCATGTTATCAC
1318376 CT
131 CT
* * * *
1318378 CTAAAGATGGCCTACCGTCCTCATCACATAGGAACCATGTCATCCCCCGACCAGACCT-CTACAT
1 CTAAAGATGACCGAACGTCCTCATCACATAGGAACCGTGTCATCCCCCGACCAGACCTCCT-CAT
* *
1318442 CACGCAGGAGCCGTGTCACCCCTT-GATAACCAGCCGTCCTCATCGCGTAGGAACCATGTTATCA
65 CACGTAGGAGCCGTGTCACCCCTTAGATAACCAGCCGTCCTCATCACGTAGGAACCATGTTATCA
1318506 CCCTT
130 -CC-T
* * * ** * * **
1318511 ACTAAAGATGACCAGAAC-TCTTCATCACGTATGAGTCGTGTCATCCACCGATCAGATATCCTCA
1 -CTAAAGATGACC-GAACGTCCTCATCACATAGGAACCGTGTCATCCCCCGACCAGACCTCCTCA
* *
1318575 TCATGTAGGAGCCGTGTCA-CCCTTAGACAACCAG
64 TCACGTAGGAGCCGTGTCACCCCTTAGATAACCAG
1318609 AACTCTTCAT
Statistics
Matches: 195, Mismatches: 26, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
129 30 0.15
130 48 0.25
131 37 0.19
132 1 0.01
133 6 0.03
134 69 0.35
135 4 0.02
ACGTcount: A:0.26, C:0.34, G:0.18, T:0.23
Consensus pattern (132 bp):
CTAAAGATGACCGAACGTCCTCATCACATAGGAACCGTGTCATCCCCCGACCAGACCTCCTCATC
ACGTAGGAGCCGTGTCACCCCTTAGATAACCAGCCGTCCTCATCACGTAGGAACCATGTTATCAC
CT
Found at i:1319163 original size:30 final size:28
Alignment explanation
Indices: 1319123--1319225 Score: 98
Period size: 30 Copynumber: 3.5 Consensus size: 28
1319113 TTAGACCTTG
* *
1319123 AATTTCTGTTTATATTATTTTAGTTCTTTA
1 AATTTTTGTTT-T-TTATTTTAGTCCTTTA
*
1319153 AATTTTTGTTTTTGTTATTTTAGTCCCTTA
1 AATTTTTG-TTTT-TTATTTTAGTCCTTTA
* *
1319183 AGTTTTTATTTTTCTATTTTAGTCCTTTA
1 AATTTTTGTTTTT-TATTTTAGTCCTTTA
* *
1319212 AATGTCTGTTTTTT
1 AATTTTTGTTTTTT
1319226 CTATTTAATC
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
28 2 0.03
29 27 0.45
30 28 0.47
31 3 0.05
ACGTcount: A:0.18, C:0.09, G:0.09, T:0.64
Consensus pattern (28 bp):
AATTTTTGTTTTTTATTTTAGTCCTTTA
Found at i:1319200 original size:29 final size:29
Alignment explanation
Indices: 1319138--1319253 Score: 92
Period size: 30 Copynumber: 4.0 Consensus size: 29
1319128 CTGTTTATAT
* * * * *
1319138 TATTTTAGTTCTTTAAATTTTTGTTTTTGT
1 TATTTTAGTCCCTTAAGTTTTTATTTTT-C
1319168 TATTTTAGTCCCTTAAGTTTTTATTTTTC
1 TATTTTAGTCCCTTAAGTTTTTATTTTTC
* * *
1319197 TATTTTAGTCCTTTAAATGTCTGT-TTTTTC
1 TATTTTAGTCCCTT-AA-GTTTTTATTTTTC
* * *
1319227 TA-TTTAATCCCTTCAGTTTCTATTTTT
1 TATTTTAGTCCCTTAAGTTTTTATTTTT
1319254 TTTCTATTTT
Statistics
Matches: 70, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
27 4 0.06
28 6 0.09
29 22 0.31
30 34 0.49
31 4 0.06
ACGTcount: A:0.17, C:0.12, G:0.08, T:0.63
Consensus pattern (29 bp):
TATTTTAGTCCCTTAAGTTTTTATTTTTC
Found at i:1319201 original size:59 final size:58
Alignment explanation
Indices: 1319138--1319253 Score: 153
Period size: 59 Copynumber: 2.0 Consensus size: 58
1319128 CTGTTTATAT
* * * * *
1319138 TATTTTAGTTCTTTAAATTTTTGTTTTTGT-TATTTTAGTCCCTTAAGTTTTTATTTTTC
1 TATTTTAGTCCTTTAAATGTCTGTTTTT-TCTA-TTTAATCCCTTAAGTTTCTATTTTTC
*
1319197 TATTTTAGTCCTTTAAATGTCTGTTTTTTCTATTTAATCCCTTCAGTTTCTATTTTT
1 TATTTTAGTCCTTTAAATGTCTGTTTTTTCTATTTAATCCCTTAAGTTTCTATTTTT
1319254 TTTCTATTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
58 23 0.46
59 27 0.54
ACGTcount: A:0.17, C:0.12, G:0.08, T:0.63
Consensus pattern (58 bp):
TATTTTAGTCCTTTAAATGTCTGTTTTTTCTATTTAATCCCTTAAGTTTCTATTTTTC
Found at i:1319227 original size:30 final size:30
Alignment explanation
Indices: 1319138--1319231 Score: 104
Period size: 30 Copynumber: 3.2 Consensus size: 30
1319128 CTGTTTATAT
* *
1319138 TATTTTAGTTCTTTAAATTTTTGTTTTTGT-
1 TATTTTAGTCCTTTAAATGTTTGTTTTT-TC
* *
1319168 TATTTTAGTCCCTT-AA-GTTTTTATTTTTC
1 TATTTTAGTCCTTTAAATGTTTGT-TTTTTC
*
1319197 TATTTTAGTCCTTTAAATGTCTGTTTTTTC
1 TATTTTAGTCCTTTAAATGTTTGTTTTTTC
1319227 TATTT
1 TATTT
1319232 AATCCCTTCA
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
28 5 0.09
29 19 0.36
30 25 0.47
31 4 0.08
ACGTcount: A:0.17, C:0.10, G:0.09, T:0.65
Consensus pattern (30 bp):
TATTTTAGTCCTTTAAATGTTTGTTTTTTC
Found at i:1319254 original size:29 final size:30
Alignment explanation
Indices: 1319168--1319317 Score: 108
Period size: 29 Copynumber: 5.0 Consensus size: 30
1319158 TTGTTTTTGT
*
1319168 TATTTTAGTCCCTTAAGTTTTTA-TTTTTC
1 TATTTTAGTCCCTTAAGTTTCTATTTTTTC
* * * *
1319197 TATTTTAGTCCTTTAAATGTCTGTTTTTTC
1 TATTTTAGTCCCTTAAGTTTCTATTTTTTC
* *
1319227 TA-TTTAATCCCTTCAGTTTCTATTTTTTTTC
1 TATTTTAGTCCCTTAAGTTTCTA--TTTTTTC
* * * * * *
1319258 TATTTTGGACCTTTAAATTCCTATTTGTAT-
1 TATTTTAGTCCCTTAAGTTTCTATTT-TTTC
* * *
1319288 TATTTTGGTCCTTTTAGTTTCTATTTTTTC
1 TATTTTAGTCCCTTAAGTTTCTATTTTTTC
1319318 ATTATGGTCC
Statistics
Matches: 91, Mismatches: 24, Indels: 11
0.72 0.19 0.09
Matches are distributed among these distances:
29 34 0.37
30 33 0.36
31 11 0.12
32 13 0.14
ACGTcount: A:0.17, C:0.15, G:0.08, T:0.61
Consensus pattern (30 bp):
TATTTTAGTCCCTTAAGTTTCTATTTTTTC
Done.