Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008717.1 Hibiscus syriacus cultivar Beakdansim tig00111772_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: 3453450
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 16
Found at i:1627711 original size:19 final size:19
Alignment explanation
Indices: 1627671--1627712 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
1627661 TGATATTTTT
*
1627671 AATTAGTGAATTTGATGTG
1 AATTAGTGAATTTGAAGTG
1627690 AATTAGTGCAATTTGAAG-G
1 AATTAGTG-AATTTGAAGTG
1627709 AATT
1 AATT
1627713 TCCATGTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.36, C:0.02, G:0.24, T:0.38
Consensus pattern (19 bp):
AATTAGTGAATTTGAAGTG
Found at i:1630329 original size:157 final size:157
Alignment explanation
Indices: 1630012--1630305 Score: 534
Period size: 157 Copynumber: 1.9 Consensus size: 157
1630002 TATCAGACTG
*
1630012 TTTAAGTAAAATTTTATTATGGGTTTTGAACTGACAGTTAAATTTATAACTGCTAGTGTATGTAA
1 TTTAAGTAAAATTTTATTATGGGTTTTGAACTGACAGTTAAATTTATAACTACTAGTGTATGTAA
1630077 ATAATATTATTGATCGCAATCGGATTTATACATGTTTAATTTTAATAATATTTTTATATGATATC
66 ATAATATTATTGATCGCAATCGGATTTATACATGTTTAATTTTAATAATATTTTTATATGATATC
* **
1630142 ACATATATAAAAGTTTTATTTATTTTA
131 ACATATATAAAAGTGTTATAAATTTTA
*
1630169 TTTAAGTAAAATTTTATTATGGGTTTTGAACTGACAGTTAAATTTATAACTATTAGTGTATGTAA
1 TTTAAGTAAAATTTTATTATGGGTTTTGAACTGACAGTTAAATTTATAACTACTAGTGTATGTAA
1630234 ATAATATTATTGATCGCAATCGGATTTATACATGTTTAATTTTAATAATATTTTTTATATGATAT
66 ATAATATTATTGATCGCAATCGGATTTATACATGTTTAATTTTAATAATA-TTTTTATATGATAT
1630299 CACATAT
130 CACATAT
1630306 TCTATATGTT
Statistics
Matches: 134, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
157 113 0.84
158 21 0.16
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.46
Consensus pattern (157 bp):
TTTAAGTAAAATTTTATTATGGGTTTTGAACTGACAGTTAAATTTATAACTACTAGTGTATGTAA
ATAATATTATTGATCGCAATCGGATTTATACATGTTTAATTTTAATAATATTTTTATATGATATC
ACATATATAAAAGTGTTATAAATTTTA
Found at i:1641756 original size:18 final size:18
Alignment explanation
Indices: 1641732--1641774 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 18
1641722 AATTTTATAA
1641732 TAATAATAATAATAATAAATT
1 TAATAA-AA-AATAAT-AATT
1641753 TAATAAAAAATAATAATT
1 TAATAAAAAATAATAATT
1641771 TAAT
1 TAAT
1641775 TATATTCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.36
19 6 0.27
20 2 0.09
21 6 0.27
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TAATAAAAAATAATAATT
Found at i:1644028 original size:31 final size:29
Alignment explanation
Indices: 1643988--1644057 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 29
1643978 TTAACGATAC
*
1643988 AGTGGTATAATTGAAACGAAAA-TCAAAGTTT
1 AGTGGTATAATTG--AC-AAAATTAAAAGTTT
*
1644019 AGTGCTATAATTGACAAAATTAAAAGTTT
1 AGTGGTATAATTGACAAAATTAAAAGTTT
1644048 AGTGGTATAA
1 AGTGGTATAA
1644058 ACAATGCAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 4 0.11
29 19 0.54
31 12 0.34
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (29 bp):
AGTGGTATAATTGACAAAATTAAAAGTTT
Found at i:1648697 original size:59 final size:58
Alignment explanation
Indices: 1648605--1648780 Score: 194
Period size: 60 Copynumber: 3.0 Consensus size: 58
1648595 AGATATACGT
* * *
1648605 ATAGTTTGA-GATGAAATTGAAATATTCAAAAAGTTTGGGACCAATTCAGAATGAAGACC
1 ATAGTTTGAGGATGAAATTGAAATATT-TAAAAGTTTGGGACCAATTTAAAATGAAG-CC
* * * **
1648664 ATAGTTTGAGGATGAAAATGAAATGTTTAAAAGTTTGAGGACAAATTTAAAATGATAGTT
1 ATAGTTTGAGGATGAAATTGAAATATTTAAAAGTTTG-GGACCAATTTAAAATGA-AGCC
* *
1648724 ATAGTTT-AGGGATGAAATTAAAATATTTAAAAGTTTAAGGACCAATTTAAAATGAAG
1 ATAGTTTGA-GGATGAAATTGAAATATTTAAAAGTTT-GGGACCAATTTAAAATGAAG
1648781 GTAATACTTT
Statistics
Matches: 99, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
59 21 0.21
60 76 0.77
61 2 0.02
ACGTcount: A:0.44, C:0.05, G:0.20, T:0.31
Consensus pattern (58 bp):
ATAGTTTGAGGATGAAATTGAAATATTTAAAAGTTTGGGACCAATTTAAAATGAAGCC
Found at i:1648716 original size:29 final size:28
Alignment explanation
Indices: 1648684--1648777 Score: 75
Period size: 29 Copynumber: 3.2 Consensus size: 28
1648674 GATGAAAATG
1648684 AAATGTTTAAAAGTTTGAGGACAAATTTA
1 AAATGTTTAAAAGTTT-AGGACAAATTTA
* *
1648713 AAATGATAGTT-ATAGTTTAGGGATGAAA-TTA
1 AAATG-T--TTAAAAGTTTA-GGA-CAAATTTA
* *
1648744 AAATATTTAAAAGTTTAAGGACCAATTTA
1 AAATGTTTAAAAGTTT-AGGACAAATTTA
1648773 AAATG
1 AAATG
1648778 AAGGTAATAC
Statistics
Matches: 50, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
28 4 0.08
29 21 0.42
30 4 0.08
31 16 0.32
32 5 0.10
ACGTcount: A:0.46, C:0.03, G:0.17, T:0.34
Consensus pattern (28 bp):
AAATGTTTAAAAGTTTAGGACAAATTTA
Found at i:1651454 original size:31 final size:31
Alignment explanation
Indices: 1651416--1651485 Score: 113
Period size: 31 Copynumber: 2.3 Consensus size: 31
1651406 CCATTATCGA
*
1651416 CGCAATCGTCCATTTCCTGTTAAATTACGGG
1 CGCAATCGTCCATTTCCCGTTAAATTACGGG
* *
1651447 CGCAATCGTCCGTTTCCCGTTAAATTGCGGG
1 CGCAATCGTCCATTTCCCGTTAAATTACGGG
1651478 CGCAATCG
1 CGCAATCG
1651486 ACCGTGATCG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.20, C:0.29, G:0.23, T:0.29
Consensus pattern (31 bp):
CGCAATCGTCCATTTCCCGTTAAATTACGGG
Found at i:1652989 original size:23 final size:24
Alignment explanation
Indices: 1652953--1652997 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
1652943 ATTTTCTTTT
*
1652953 AAAAAACTCAAAAT-TTTCAAAAAA
1 AAAAAAATCAAAATATTT-AAAAAA
1652977 AAAAAAATC-AAATATTTAAAA
1 AAAAAAATCAAAATATTTAAAA
1652998 TATTTATTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.69, C:0.09, G:0.00, T:0.22
Consensus pattern (24 bp):
AAAAAAATCAAAATATTTAAAAAA
Found at i:1653080 original size:18 final size:18
Alignment explanation
Indices: 1653037--1653080 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
1653027 GATACCGAGT
*
1653037 AGGGAGAAGGGGTACATG
1 AGGGAGAGGGGGTACATG
1653055 AGGGAGAGGGGGTACATG
1 AGGGAGAGGGGGTACATG
1653073 AGGGAGAG
1 AGGGAGAG
1653081 TGTTGAGGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.32, C:0.05, G:0.55, T:0.09
Consensus pattern (18 bp):
AGGGAGAGGGGGTACATG
Found at i:1653393 original size:16 final size:15
Alignment explanation
Indices: 1653372--1653440 Score: 75
Period size: 16 Copynumber: 4.3 Consensus size: 15
1653362 TATTACCCGG
1653372 CCTGTTTTCAACCTGA
1 CCTGTTTT-AACCTGA
*
1653388 CCTGTTATGAACCTGA
1 CCTGTT-TTAACCTGA
1653404 CCTGTTTTTAACCTGA
1 CCTG-TTTTAACCTGA
* *
1653420 TCTGATTTTAGCCTGA
1 CCTG-TTTTAACCTGA
1653436 CCTGT
1 CCTGT
1653441 AAATGATCCG
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
15 1 0.02
16 41 0.91
17 3 0.07
ACGTcount: A:0.19, C:0.26, G:0.16, T:0.39
Consensus pattern (15 bp):
CCTGTTTTAACCTGA
Found at i:1658022 original size:5 final size:5
Alignment explanation
Indices: 1657943--1658019 Score: 120
Period size: 5 Copynumber: 15.2 Consensus size: 5
1657933 AAAAACATTT
1657943 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
*
1657993 TATT- TATTA TTATTA TTATTA TTTTA T
1 TATTA TATTA -TATTA -TATTA TATTA T
1658020 TTTTGTAGGT
Statistics
Matches: 69, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
4 4 0.06
5 54 0.78
6 11 0.16
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TATTA
Found at i:1658118 original size:33 final size:33
Alignment explanation
Indices: 1658071--1658153 Score: 123
Period size: 33 Copynumber: 2.5 Consensus size: 33
1658061 TCAAATAAAT
1658071 CAACATATTTGAGTCCTATTGAAACACTAAAAC
1 CAACATATTTGAGTCCTATTGAAACACTAAAAC
* *
1658104 CAACGTATTTGAGTCCTATTGAAATACTAAAAC
1 CAACATATTTGAGTCCTATTGAAACACTAAAAC
1658137 CGAAGCAT-TTTGAGTCC
1 C-AA-CATATTTGAGTCC
1658154 ACGTAGGACT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
33 32 0.71
34 11 0.24
35 2 0.04
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.29
Consensus pattern (33 bp):
CAACATATTTGAGTCCTATTGAAACACTAAAAC
Found at i:1658542 original size:14 final size:15
Alignment explanation
Indices: 1658509--1658552 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 15
1658499 TTTACATTGT
1658509 TATATA-TATA-T-A
1 TATATATTATATTAA
*
1658521 TATATATTTTATTAA
1 TATATATTATATTAA
1658536 TAT-TATTATATTAA
1 TATATATTATATTAA
1658550 TAT
1 TAT
1658553 CTTTTGTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 6 0.22
13 3 0.11
14 14 0.52
15 4 0.15
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TATATATTATATTAA
Found at i:1662395 original size:110 final size:110
Alignment explanation
Indices: 1662253--1662795 Score: 842
Period size: 110 Copynumber: 5.0 Consensus size: 110
1662243 GATGGTGGTT
* * * *
1662253 GCTCAACTTCACAGCAAAAGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTTATTCAGAGTT
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
* * * * *
1662318 AATTTCAACTTCATAGCGAAGTATATTAGACTCGAGATAATACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* * *
1662363 GCTCAATTTCACAGTGAAGGGGCGGCTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
1662428 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* *
1662473 GCTCAACTTCACAGCGAAGGGGCGACTTACTGTCAACAAACAACTTTTTAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
1662538 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* * *
1662583 GCTCAACTTCACAGCGAAGGGGTGACTGACTGTCAACAAACAACTTTTCAATTTCATTCAGAGGC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
*
1662648 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGATAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* * *
1662693 GCTCAACTTCACAACGAAGGGGCGACTGGCTGTCAACAAACAACTTTCCAG--T--TTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
* * *
1662754 AATTTCAACTTCACGGCGAAGGATATTGGCCTCGAAACAACA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACA
1662796 TATATGTTTG
Statistics
Matches: 400, Mismatches: 33, Indels: 4
0.92 0.08 0.01
Matches are distributed among these distances:
106 46 0.12
108 1 0.00
110 353 0.88
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (110 bp):
GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
Found at i:1663128 original size:84 final size:84
Alignment explanation
Indices: 1662900--1663343 Score: 522
Period size: 85 Copynumber: 5.3 Consensus size: 84
1662890 AAGGGAAATG
* * * * *
1662900 TGCCCACCAAAGACCTTCGAGTTTGACTACGCTCAGC-TCAAAGGCACAACATTTGTAGCATAGT
1 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTTC-AAGGCACATCATTTGCAGCATAGC
*
1662964 TTAAGTCGAGAAAGGTTATC
65 TTAAGTCGAGAAGGGTTATC
* * * *
1662984 TGCCAACTGAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAAC
1 TGCCAAC-CAAAGACCTTCGAGTTCGACTACGCTCAGCTTCAAGGCACATCATTTGCAGCATAGC
1663049 TTAAGTCGAGAAGGGTTATC
65 TTAAGTCGAGAAGGGTTATC
* *
1663069 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTTCAAGACACATCATTTACAGCATAGCT
1 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTTCAAGGCACATCATTTGCAGCATAGCT
* *
1663134 TAAGTCGAGAAGGGCTATT
66 TAAGTCGAGAAGGGTTATC
* * *
1663153 TGCCAACCAAAAGACCTTCGCGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCATCATAGC
1 TGCCAACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTTCAAGGCACATCATTTGCAGCATAGC
*
1663218 TTAAGTCGAGAAGGGCTATC
65 TTAAGTCGAGAAGGGTTATC
* * * * * * * *
1663238 T----ACCAAAGACCCTCGAGTTCGATTACACTCAGCTTTGAGGGCACATCATTTACAACATAAC
1 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TTCAAGGCACATCATTTGCAGCATAGC
* * *
1663299 TCAAGGCTAGAAGGGTTATC
65 TTAAGTCGAGAAGGGTTATC
** *
1663319 TG-TTACCAAAGACCTTCGTGTTCGA
1 TGCCAACCAAAGACCTTCGAGTTCGA
1663344 TCCCATTCAG
Statistics
Matches: 313, Mismatches: 40, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
80 25 0.08
81 41 0.13
84 102 0.33
85 144 0.46
86 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.25
Consensus pattern (84 bp):
TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTTCAAGGCACATCATTTGCAGCATAGCT
TAAGTCGAGAAGGGTTATC
Found at i:1663184 original size:169 final size:168
Alignment explanation
Indices: 1662903--1663296 Score: 535
Period size: 169 Copynumber: 2.4 Consensus size: 168
1662893 GGAAATGTGC
* * ** *
1662903 CCACCAAAGACCTTCGAGTTTGACTACGCTCAGC-TCAAAGGCACAACATTTGTAGCATAGTTTA
1 CCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTTC-AAGGCACATCATTTACAGCATAGCTTA
* ** *
1662967 AGTCGAGAAAGGTTATCTGCCAACTGAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAT
65 AGTCGAGAAAGGCTATCTGCCAACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAC
*
1663032 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG
130 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG
*
1663071 CCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTTCAAGACACATCATTTACAGCATAGCTTA
1 CC-ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTTCAAGGCACATCATTTACAGCATAGCTTA
* * *
1663136 AGTCGAGAAGGGCTATTTGCCAACCAAAAGACCTTCGCGTTCGACTACGCTCAGCTCCAAGGCAC
65 AGTCGAGAAAGGCTATCTGCCAACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAC
* *
1663201 ATCATTTGCATCATAGCTTAAGTCGAGAAGGGCTATCT-
130 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG
* * * * * *
1663239 --ACCAAAGACCCTCGAGTTCGATTACACTCAGCTTTGAGGGCACATCATTTACAACATA
1 CCACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TTCAAGGCACATCATTTACAGCATA
1663297 ACTCAAGGCT
Statistics
Matches: 200, Mismatches: 23, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
165 29 0.14
166 21 0.10
168 2 0.01
169 146 0.73
170 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.24
Consensus pattern (168 bp):
CCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTTCAAGGCACATCATTTACAGCATAGCTTAA
GTCGAGAAAGGCTATCTGCCAACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACA
TCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG
Found at i:1663355 original size:84 final size:81
Alignment explanation
Indices: 1662993--1663355 Score: 198
Period size: 84 Copynumber: 4.4 Consensus size: 81
1662983 CTGCCAACTG
* * ** * * * * * *
1662993 AAAGACCTTCGAGTTCGA-CTACGCTCAGC-TCCAAGGCATATCATTTGCAGCATAACTTAAGTC
1 AAAGACCCTCGAGTTCGATC-ACACTCAGCTTTGAGGGCACATCATTTACAACATAACTCAAGGC
*
1663056 GAGAAGGGTTATCTGCCAACC
65 GAGAAGGGCTATCT----ACC
* * * * * * * * *
1663077 AAAGACCTTCGAGTTCGA-CTACGCTCAGC-TTCAAGACACATCATTTACAGCATAGCTTAAGTC
1 AAAGACCCTCGAGTTCGATC-ACACTCAGCTTTGAGGGCACATCATTTACAACATAACTCAAGGC
*
1663140 GAGAAGGGCTATTTGCCAACC
65 GAGAAGGGCTA--T--CTACC
* * * ** * * * * * *
1663161 AAAAGACCTTCGCGTTCGA-CTACGCTCAGC-TCCAAGGCACATCATTTGCATCATAGCTTAAGT
1 -AAAGACCCTCGAGTTCGATC-ACACTCAGCTTTGAGGGCACATCATTTACAACATAACTCAAGG
1663224 CGAGAAGGGCTATCTACC
64 CGAGAAGGGCTATCTACC
* *
1663242 AAAGACCCTCGAGTTCGATTACACTCAGCTTTGAGGGCACATCATTTACAACATAACTCAAGGCT
1 AAAGACCCTCGAGTTCGATCACACTCAGCTTTGAGGGCACATCATTTACAACATAACTCAAGGCG
*
1663307 AGAAGGGTTATCTGTTACC
66 AGAAGGGCTATC---TACC
* * * *
1663326 AAAGACCTTCGTGTTCGATCCCATTCAGCT
1 AAAGACCCTCGAGTTCGATCACACTCAGCT
1663356 CGAGGGCGTA
Statistics
Matches: 237, Mismatches: 32, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
80 24 0.10
81 41 0.17
83 1 0.00
84 100 0.42
85 69 0.29
86 1 0.00
88 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.25
Consensus pattern (81 bp):
AAAGACCCTCGAGTTCGATCACACTCAGCTTTGAGGGCACATCATTTACAACATAACTCAAGGCG
AGAAGGGCTATCTACC
Found at i:1663701 original size:5 final size:5
Alignment explanation
Indices: 1663691--1663728 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
1663681 AAAAACATTT
1663691 TATTA TATTA TATTA TATTA TATT- TATT- TATT- TATTA T
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA T
1663729 TTTTATTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 12 0.38
5 20 0.62
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (5 bp):
TATTA
Found at i:1663706 original size:10 final size:9
Alignment explanation
Indices: 1663691--1663735 Score: 56
Period size: 10 Copynumber: 4.9 Consensus size: 9
1663681 AAAAACATTT
1663691 TATTATATTA
1 TATT-TATTA
1663701 TATTATATTA
1 TATT-TATTA
1663711 TATTTATT-
1 TATTTATTA
1663719 TATTTATTA
1 TATTTATTA
*
1663728 TTTTTATT
1 TATTTATT
1663736 TTTATTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
8 8 0.24
9 11 0.33
10 14 0.42
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
TATTTATTA
Found at i:1663711 original size:15 final size:14
Alignment explanation
Indices: 1663689--1663735 Score: 62
Period size: 13 Copynumber: 3.4 Consensus size: 14
1663679 ACAAAAACAT
1663689 TTTATTATATTATA
1 TTTATTATATTATA
1663703 TTATATTATATT-TA
1 TT-TATTATATTATA
*
1663717 TTTATT-TATTATT
1 TTTATTATATTATA
1663730 TTTATT
1 TTTATT
1663736 TTTATTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 4 0.13
13 11 0.37
14 6 0.20
15 9 0.30
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTATTATATTATA
Found at i:1663739 original size:15 final size:15
Alignment explanation
Indices: 1663688--1663751 Score: 53
Period size: 17 Copynumber: 4.3 Consensus size: 15
1663678 TACAAAAACA
*
1663688 TTTTATTA-TATTAT
1 TTTTATTATTTTTAT
* *
1663702 ATTATATTATATTTATT
1 -TTTTATTATTTTTA-T
1663719 TATTTATTATTTTTAT
1 T-TTTATTATTTTTAT
1663735 TTTTA-T-TTTTTAT
1 TTTTATTATTTTTAT
1663748 TTTT
1 TTTT
1663752 GTAGGCCCTA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
13 11 0.27
14 1 0.02
15 11 0.27
16 6 0.15
17 12 0.29
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTATTATTTTTAT
Found at i:1663748 original size:13 final size:13
Alignment explanation
Indices: 1663711--1663751 Score: 57
Period size: 13 Copynumber: 3.1 Consensus size: 13
1663701 TATTATATTA
1663711 TATTTATTTATTTAT
1 TATTT-TTTATTT-T
1663726 TA-TTTTTATTTT
1 TATTTTTTATTTT
1663738 TATTTTTTATTTT
1 TATTTTTTATTTT
1663751 T
1 T
1663752 GTAGGCCCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.12
13 18 0.72
14 2 0.08
15 2 0.08
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TATTTTTTATTTT
Found at i:1663750 original size:7 final size:7
Alignment explanation
Indices: 1663711--1663751 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
1663701 TATTATATTA
1663711 TATTTATT
1 TATTT-TT
*
1663719 TATTTAT
1 TATTTTT
1663726 TA-TTTT
1 TATTTTT
1663732 TA-TTTT
1 TATTTTT
1663738 TATTTTT
1 TATTTTT
1663745 TATTTTT
1 TATTTTT
1663752 GTAGGCCCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
6 11 0.37
7 14 0.47
8 5 0.17
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (7 bp):
TATTTTT
Found at i:1663839 original size:33 final size:32
Alignment explanation
Indices: 1663802--1663901 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 32
1663792 GAAAATAAAT
*
1663802 CAACGTATTTGAGTCATATTGAAACACTAAAAC
1 CAACGTATTTGAGTCCTATT-AAACACTAAAAC
1663835 CAACGTATTTGAGTCCTATTAAAACACTAAAAC
1 CAACGTATTTGAGTCCTATT-AAACACTAAAAC
*
1663868 CAACGTATTTGAGTCCTATTAAAGCACTTAAAC
1 CAACGTATTTGAGTCCTATTAAA-CACTAAAAC
1663901 C
1 C
1663902 GAAGCATTTT
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
32 3 0.05
33 60 0.95
ACGTcount: A:0.40, C:0.21, G:0.11, T:0.28
Consensus pattern (32 bp):
CAACGTATTTGAGTCCTATTAAACACTAAAAC
Found at i:1668813 original size:19 final size:19
Alignment explanation
Indices: 1668789--1668859 Score: 142
Period size: 19 Copynumber: 3.7 Consensus size: 19
1668779 ACAAGCCTGA
1668789 GTGCATCGATGCATTGTCT
1 GTGCATCGATGCATTGTCT
1668808 GTGCATCGATGCATTGTCT
1 GTGCATCGATGCATTGTCT
1668827 GTGCATCGATGCATTGTCT
1 GTGCATCGATGCATTGTCT
1668846 GTGCATCGATGCAT
1 GTGCATCGATGCAT
1668860 AAAATGCATT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 52 1.00
ACGTcount: A:0.17, C:0.21, G:0.27, T:0.35
Consensus pattern (19 bp):
GTGCATCGATGCATTGTCT
Found at i:1669767 original size:113 final size:112
Alignment explanation
Indices: 1669569--1669792 Score: 351
Period size: 113 Copynumber: 2.0 Consensus size: 112
1669559 ATTAAACAGT
* * *
1669569 TTATTTAAATCCTAAATAAAGGTAGTCAACAACCTCATACAAGTAATCCGAATGAACAACCAACA
1 TTATTTAAATCCTAAATAAAAGCAGTCAACAACCTCATACAAGCAATCCGAATGAACAACCAACA
*
1669634 ACACAAACAAGGACCACAGAGGAAACAAATTAAACAGTAGCTACAAAA
66 ACAAAAACAAGGACCACAGAGGAAACAAA-TAAACAGTAGCTACAAAA
* *
1669682 TTATTTAAATCCTAAATAAAAGCAG-CTAACAACCTTATACAAGCAATCCGAATGAATAACCAAC
1 TTATTTAAATCCTAAATAAAAGCAGTC-AACAACCTCATACAAGCAATCCGAATGAACAACCAAC
* *
1669746 AACAAAAACAAGGACTACAGAGGAAACAAATCAACAGTAGCTACAAA
65 AACAAAAACAAGGACCACAGAGGAAACAAATAAACAGTAGCTACAAA
1669793 TTAAACAGTT
Statistics
Matches: 102, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
112 17 0.17
113 85 0.83
ACGTcount: A:0.51, C:0.21, G:0.11, T:0.17
Consensus pattern (112 bp):
TTATTTAAATCCTAAATAAAAGCAGTCAACAACCTCATACAAGCAATCCGAATGAACAACCAACA
ACAAAAACAAGGACCACAGAGGAAACAAATAAACAGTAGCTACAAAA
Found at i:1670120 original size:24 final size:24
Alignment explanation
Indices: 1670074--1670120 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
1670064 GTTTGAATTC
* ** *
1670074 AGGTTAGGGTTTAGGTTTGGTTTT
1 AGGTTAGGGTTCAAATTTAGTTTT
1670098 AGGTTAGGGTTCAAATTTAGTTT
1 AGGTTAGGGTTCAAATTTAGTTT
1670121 CAAGTTTTGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.19, C:0.02, G:0.32, T:0.47
Consensus pattern (24 bp):
AGGTTAGGGTTCAAATTTAGTTTT
Found at i:1670128 original size:31 final size:31
Alignment explanation
Indices: 1670093--1670151 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
1670083 TTTAGGTTTG
*
1670093 GTTTTAGG-TTAGGGTTCAAATTTAGTTTCAA
1 GTTTT-GGATTAGGGTTCAAATTCAGTTTCAA
*
1670124 GTTTTGGATTCGGGTTCAAATTCAGTTT
1 GTTTTGGATTAGGGTTCAAATTCAGTTT
1670152 TGGGTTCGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 2 0.08
31 23 0.92
ACGTcount: A:0.22, C:0.08, G:0.24, T:0.46
Consensus pattern (31 bp):
GTTTTGGATTAGGGTTCAAATTCAGTTTCAA
Found at i:1670175 original size:11 final size:11
Alignment explanation
Indices: 1670159--1670185 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1670149 TTTTGGGTTC
1670159 GGGTTTAGTTA
1 GGGTTTAGTTA
1670170 GGGTTTAGTTA
1 GGGTTTAGTTA
1670181 GGGTT
1 GGGTT
1670186 CAGGTTTAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.15, C:0.00, G:0.41, T:0.44
Consensus pattern (11 bp):
GGGTTTAGTTA
Found at i:1670210 original size:6 final size:6
Alignment explanation
Indices: 1670201--1670276 Score: 57
Period size: 6 Copynumber: 12.5 Consensus size: 6
1670191 TTAGGATCGA
* * * *
1670201 GTTTAG GTTTAG G-TTAG GGTCAG GGTTATG ATTTAG GTTTAG GTTTAG
1 GTTTAG GTTTAG GTTTAG GTTTAG GTTTA-G GTTTAG GTTTAG GTTTAG
**
1670249 GTTCGG GTTCTA- GTTTAGG GTTTAG GTT
1 GTTTAG GTT-TAG GTTTA-G GTTTAG GTT
1670277 CAAGTTAGGG
Statistics
Matches: 56, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
5 7 0.12
6 40 0.71
7 9 0.16
ACGTcount: A:0.16, C:0.04, G:0.36, T:0.45
Consensus pattern (6 bp):
GTTTAG
Found at i:1670236 original size:30 final size:29
Alignment explanation
Indices: 1670200--1670276 Score: 93
Period size: 30 Copynumber: 2.6 Consensus size: 29
1670190 TTTAGGATCG
1670200 AGTTTAGGTTTAGGTTAGGGTCAGGGTTAT
1 AGTTTAGGTTTAGGTTAGGGTC-GGGTTAT
* *
1670230 -GATTTAGGTTTAGGTTTAGGTTCGGGTTCT
1 AG-TTTAGGTTTAGG-TTAGGGTCGGGTTAT
1670260 AGTTTAGGGTTTAGGTT
1 AGTTTA-GGTTTAGGTT
1670277 CAAGTTAGGG
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
29 1 0.02
30 24 0.59
31 16 0.39
ACGTcount: A:0.17, C:0.04, G:0.35, T:0.44
Consensus pattern (29 bp):
AGTTTAGGTTTAGGTTAGGGTCGGGTTAT
Found at i:1670967 original size:14 final size:13
Alignment explanation
Indices: 1670943--1671071 Score: 75
Period size: 14 Copynumber: 9.2 Consensus size: 13
1670933 CTATAAAATT
1670943 TTTATTAATTAACTA
1 TTTA-TAATTAA-TA
1670958 TTTATAATTAATA
1 TTTATAATTAATA
1670971 TTATAATAATT-ATA
1 TT-T-ATAATTAATA
1670985 TATTATAATTAATA
1 T-TTATAATTAATA
*
1670999 TTAAT-ATTAATA
1 TTTATAATTAATA
1671011 TAATTA-ATATTAATA
1 T--TTATA-ATTAATA
*
1671026 TTAACTTATATTAATA
1 TTTA--TA-ATTAATA
* *
1671042 TAATATAATTTATAA
1 T-TTATAATTAAT-A
*
1671057 TTTGTAATTAATA
1 TTTATAATTAATA
1671070 TT
1 TT
1671072 AATATAAAAT
Statistics
Matches: 92, Mismatches: 9, Indels: 28
0.71 0.07 0.22
Matches are distributed among these distances:
12 8 0.09
13 18 0.20
14 32 0.35
15 23 0.25
16 10 0.11
17 1 0.01
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.51
Consensus pattern (13 bp):
TTTATAATTAATA
Found at i:1671001 original size:6 final size:6
Alignment explanation
Indices: 1670950--1671107 Score: 68
Period size: 6 Copynumber: 26.3 Consensus size: 6
1670940 ATTTTTATTA
*
1670950 ATTAACT ATTTAT AATTAAT ATTATAAT AATTATAT ATT-AT AATTAAT
1 ATTAA-T ATTAAT -ATTAAT A-T-TAAT -ATTA-AT ATTAAT -ATTAAT
*
1670998 ATTAAT ATTAAT A-T-A- ATTAAT ATTAAT ATTAA- CTT-AT ATTAAT
1 ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT
** * *
1671041 A-TAAT A-TAAT -TT-AT AATTTGT AATTAAT ATTAAT A-TAAA ATATAGT
1 ATTAAT ATTAAT ATTAAT -ATTAAT -ATTAAT ATTAAT ATTAAT AT-TAAT
* *
1671087 CTATAAC ATTAAT ATTAAT AT
1 AT-TAAT ATTAAT ATTAAT AT
1671108 AAACTATATG
Statistics
Matches: 118, Mismatches: 15, Indels: 37
0.69 0.09 0.22
Matches are distributed among these distances:
3 1 0.01
4 5 0.04
5 22 0.19
6 52 0.44
7 30 0.25
8 7 0.06
9 1 0.01
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (6 bp):
ATTAAT
Found at i:1671077 original size:34 final size:33
Alignment explanation
Indices: 1670964--1671078 Score: 117
Period size: 34 Copynumber: 3.3 Consensus size: 33
1670954 ACTATTTATA
* *
1670964 ATTAATATTATAATAA-TTATATATTATAATTAAT
1 ATTAATATAAT-ATAATTTATA-ATTTTAATTAAT
*
1670998 ATTAATATTAATATAATTAATATTAATATTAACTT-AT
1 ATTAATA-TAATATAATT--TA-TAATTTTAA-TTAAT
1671035 ATTAATATAATATAATTTATAATTTGTAATTAAT
1 ATTAATATAATATAATTTATAATTT-TAATTAAT
1671069 ATTAATATAA
1 ATTAATATAA
1671079 AATATAGTCT
Statistics
Matches: 69, Mismatches: 4, Indels: 16
0.78 0.04 0.18
Matches are distributed among these distances:
33 7 0.10
34 28 0.41
35 4 0.06
36 10 0.14
37 16 0.23
38 4 0.06
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.49
Consensus pattern (33 bp):
ATTAATATAATATAATTTATAATTTTAATTAAT
Found at i:1671101 original size:31 final size:30
Alignment explanation
Indices: 1671062--1671127 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 30
1671052 TATAATTTGT
1671062 AATTAATATTAATATAAAATATA-GTCTATA
1 AATTAATATTAATATAAAATATATGT-TATA
*
1671092 ACATTAATATTAATATAAACTATATGTTATA
1 A-ATTAATATTAATATAAAATATATGTTATA
1671123 AATTA
1 AATTA
1671128 TATAGTATAG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
30 5 0.15
31 26 0.79
32 2 0.06
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.41
Consensus pattern (30 bp):
AATTAATATTAATATAAAATATATGTTATA
Found at i:1671102 original size:65 final size:66
Alignment explanation
Indices: 1670964--1671123 Score: 163
Period size: 65 Copynumber: 2.4 Consensus size: 66
1670954 ACTATTTATA
1670964 ATTAATATT-ATAATAATTATATATTATAATTAATATTAATATTAATATAATTAATATTAATATT
1 ATTAATATTAAT-ATAATTATATATTATAATTAATATTAATATTAATATAA-TAATATTAATATT
1671028 AAC
64 AAC
** * *
1671031 -TT-ATATTAATATAA-TATA-ATTTATAATTTGTAATTAATATTAATATAA-AATA-TAGTCTA
1 ATTAATATTAATATAATTATATA-TTATAATTAAT-ATTAATATTAATATAATAATATTAATAT-
1671090 TAAC
63 TAAC
* *
1671094 ATTAATATTAATATAAACTATATGTTATAA
1 ATTAATATTAATAT-AATTATATATTATAA
1671124 ATTATATAGT
Statistics
Matches: 79, Mismatches: 5, Indels: 18
0.77 0.05 0.18
Matches are distributed among these distances:
62 4 0.05
63 9 0.11
64 15 0.19
65 35 0.44
66 6 0.08
67 10 0.13
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (66 bp):
ATTAATATTAATATAATTATATATTATAATTAATATTAATATTAATATAATAATATTAATATTAA
C
Found at i:1671114 original size:24 final size:25
Alignment explanation
Indices: 1671069--1671115 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
1671059 TGTAATTAAT
**
1671069 ATTAATATAAAATATAGTCTATAAC
1 ATTAATATAAAATATAAACTATAAC
*
1671094 ATTAATAT-TAATATAAACTATA
1 ATTAATATAAAATATAAACTATA
1671116 TGTTATAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.38
Consensus pattern (25 bp):
ATTAATATAAAATATAAACTATAAC
Found at i:1671209 original size:15 final size:15
Alignment explanation
Indices: 1671191--1671241 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
1671181 AACTATATAC
1671191 TATATTAATATAAAT
1 TATATTAATATAAAT
*
1671206 TATAGTTAAGAT-AAT
1 TATA-TTAATATAAAT
* *
1671221 TAACATTAATATAAAC
1 T-ATATTAATATAAAT
1671237 TATAT
1 TATAT
1671242 AGTACATTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
15 17 0.61
16 11 0.39
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (15 bp):
TATATTAATATAAAT
Found at i:1671248 original size:22 final size:22
Alignment explanation
Indices: 1671223--1671326 Score: 99
Period size: 22 Copynumber: 4.8 Consensus size: 22
1671213 AAGATAATTA
1671223 ACATTAATATAAACTATATAGT
1 ACATTAATATAAACTATATAGT
1671245 ACATTAATATAAAC--TATAGT
1 ACATTAATATAAACTATATAGT
** * *
1671265 TTATAAATTATATACTATA-AGT
1 ACATTAA-TATAAACTATATAGT
* *
1671287 -TATAAAGTATAAACTATATAGT
1 ACATTAA-TATAAACTATATAGT
*
1671309 ACACTAATATAAACTATA
1 ACATTAATATAAACTATA
1671327 GGTTACATAT
Statistics
Matches: 68, Mismatches: 9, Indels: 10
0.78 0.10 0.11
Matches are distributed among these distances:
20 10 0.15
21 22 0.32
22 31 0.46
23 5 0.07
ACGTcount: A:0.50, C:0.09, G:0.05, T:0.37
Consensus pattern (22 bp):
ACATTAATATAAACTATATAGT
Found at i:1671281 original size:21 final size:20
Alignment explanation
Indices: 1671252--1671304 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
1671242 AGTACATTAA
*
1671252 TATAAACTATAGTTTATAAAT
1 TATAAACTATAG-TTATAAAG
*
1671273 TATATACTATAAGTTATAAAG
1 TATAAACTAT-AGTTATAAAG
1671294 TATAAACTATA
1 TATAAACTATA
1671305 TAGTACACTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 1 0.04
21 25 0.89
22 2 0.07
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.40
Consensus pattern (20 bp):
TATAAACTATAGTTATAAAG
Found at i:1671333 original size:22 final size:21
Alignment explanation
Indices: 1671227--1671339 Score: 85
Period size: 22 Copynumber: 5.3 Consensus size: 21
1671217 TAATTAACAT
1671227 TAATATAAACTATATAG-TACA
1 TAATATAAACTATA-AGTTACA
*
1671248 TTAATATAAACTAT-AGTT-TA
1 -TAATATAAACTATAAGTTACA
* *
1671268 TAAATTATATACTATAAGTTATA
1 T-AA-TATAAACTATAAGTTACA
1671291 -AAGTATAAACTATATAG-TACA
1 TAA-TATAAACTATA-AGTTACA
*
1671312 CTAATATAAACTATAGGTTACA
1 -TAATATAAACTATAAGTTACA
1671334 T-ATATA
1 TAATATA
1671340 GTTTATATAA
Statistics
Matches: 76, Mismatches: 6, Indels: 20
0.75 0.06 0.20
Matches are distributed among these distances:
19 1 0.01
20 10 0.13
21 27 0.36
22 34 0.45
23 4 0.05
ACGTcount: A:0.49, C:0.08, G:0.06, T:0.37
Consensus pattern (21 bp):
TAATATAAACTATAAGTTACA
Found at i:1671360 original size:20 final size:22
Alignment explanation
Indices: 1671337--1671394 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 22
1671327 GGTTACATAT
1671337 ATAGTTTATATA-ACATATA-A
1 ATAGTTTATATATACATATACA
*
1671357 ATAGATTGTATATATACATATACT
1 ATAG-TT-TATATATACATATACA
*
1671381 ATAGGTTATATATA
1 ATAGTTTATATATA
1671395 TATAGTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 4 0.12
21 2 0.06
22 14 0.44
23 8 0.25
24 4 0.12
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (22 bp):
ATAGTTTATATATACATATACA
Found at i:1671372 original size:24 final size:25
Alignment explanation
Indices: 1671343--1671396 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
1671333 ATATATAGTT
*
1671343 TATATAACATATA-AATAGATTGTA
1 TATATAACATATACAATAGATTATA
* *
1671367 TATAT-ACATATACTATAGGTTATA
1 TATATAACATATACAATAGATTATA
1671391 TATATA
1 TATATA
1671397 TAGTTTATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.46, C:0.06, G:0.07, T:0.41
Consensus pattern (25 bp):
TATATAACATATACAATAGATTATA
Found at i:1671398 original size:15 final size:16
Alignment explanation
Indices: 1671374--1671413 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
1671364 GTATATATAC
1671374 ATATACTATAGGTTAT
1 ATATACTATAGGTTAT
*
1671390 ATATA-TATAGTTTAT
1 ATATACTATAGGTTAT
1671405 ATATACTAT
1 ATATACTAT
1671414 GCATAGTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.47
Consensus pattern (16 bp):
ATATACTATAGGTTAT
Found at i:1671455 original size:35 final size:36
Alignment explanation
Indices: 1671416--1671489 Score: 96
Period size: 37 Copynumber: 2.1 Consensus size: 36
1671406 TATACTATGC
*
1671416 ATAGTTT-ATACATACATGTACTATAAGTTACATAT
1 ATAGTTTAATACATACATATACTATAAGTTACATAT
** *
1671451 ATAGTTTACATGTATACATATACTATAGGTTACATAT
1 ATAGTTTA-ATACATACATATACTATAAGTTACATAT
1671488 AT
1 AT
1671490 TAACTATTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 7 0.21
37 26 0.79
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (36 bp):
ATAGTTTAATACATACATATACTATAAGTTACATAT
Found at i:1671467 original size:57 final size:58
Alignment explanation
Indices: 1671321--1671472 Score: 177
Period size: 57 Copynumber: 2.6 Consensus size: 58
1671311 ACTAATATAA
*
1671321 ACTATAGGTTACATATATAGTTTATATA-ACATATAAATAGATTGTATATATACATAT
1 ACTATAGGTTACATATATAGTTTATATATACATATAAATAGATTGTATACATACATAT
* ** *
1671378 ACTATAGGTTATATATATATAGTTTATATATAC-TATGCATAG-TT-TATACATACATGT
1 ACTATAGG-T-TACATATATAGTTTATATATACATATAAATAGATTGTATACATACATAT
* *
1671435 ACTATAAGTTACATATATAGTTTACATGTATACATATA
1 ACTATAGGTTACATATATAGTTT--ATATATACATATA
1671473 CTATAGGTTA
Statistics
Matches: 80, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
55 13 0.16
56 1 0.01
57 33 0.41
58 6 0.08
59 25 0.31
60 2 0.03
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (58 bp):
ACTATAGGTTACATATATAGTTTATATATACATATAAATAGATTGTATACATACATAT
Found at i:1671552 original size:7 final size:7
Alignment explanation
Indices: 1671511--1671562 Score: 61
Period size: 7 Copynumber: 7.6 Consensus size: 7
1671501 TACGTATAGT
1671511 GTTTAGG
1 GTTTAGG
*
1671518 GCTTA-G
1 GTTTAGG
1671524 GTTTAGG
1 GTTTAGG
* *
1671531 TTTTATG
1 GTTTAGG
1671538 GTTTAGG
1 GTTTAGG
1671545 GTTTAGG
1 GTTTAGG
*
1671552 GTATAGG
1 GTTTAGG
1671559 GTTT
1 GTTT
1671563 TTATAAACTA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
6 5 0.14
7 31 0.86
ACGTcount: A:0.15, C:0.02, G:0.37, T:0.46
Consensus pattern (7 bp):
GTTTAGG
Found at i:1671675 original size:20 final size:20
Alignment explanation
Indices: 1671646--1671689 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
1671636 TTATATGGAT
1671646 TATA-TATATATAGTTTATA
1 TATACTATATATAGTTTATA
1671665 TATACTATATATAGTTTATA
1 TATACTATATATAGTTTATA
*
1671685 CATAC
1 TATAC
1671690 ATGTACTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.48
Consensus pattern (20 bp):
TATACTATATATAGTTTATA
Found at i:1671712 original size:35 final size:36
Alignment explanation
Indices: 1671673--1671748 Score: 100
Period size: 37 Copynumber: 2.1 Consensus size: 36
1671663 TATATACTAT
*
1671673 ATATAGTTT-ATACATACATGTACTATAAGTTACAC
1 ATATAGTTTAATACATACATATACTATAAGTTACAC
** *
1671708 ATATAGTTTACATGTATACATATACTATAAGTTACAT
1 ATATAGTTTA-ATACATACATATACTATAAGTTACAC
1671745 ATAT
1 ATAT
1671749 TAACTATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 9 0.26
37 26 0.74
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (36 bp):
ATATAGTTTAATACATACATATACTATAAGTTACAC
Found at i:1671814 original size:16 final size:16
Alignment explanation
Indices: 1671790--1671820 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1671780 TACATATATA
1671790 ATTTATATAAACTATT
1 ATTTATATAAACTATT
*
1671806 ATTTGTATAAACTAT
1 ATTTATATAAACTAT
1671821 ATATGAATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (16 bp):
ATTTATATAAACTATT
Found at i:1671879 original size:14 final size:14
Alignment explanation
Indices: 1671839--1671899 Score: 59
Period size: 14 Copynumber: 4.3 Consensus size: 14
1671829 TATCAAATGT
**
1671839 GTTTATGTTTATAAA
1 GTTTATGTTT-TAGG
* *
1671854 GTTTAGGATTTAGG
1 GTTTATGTTTTAGG
1671868 GTTTATGTTTTAGG
1 GTTTATGTTTTAGG
* *
1671882 GTATATGGTTTAGG
1 GTTTATGTTTTAGG
1671896 GTTT
1 GTTT
1671900 TTAAAAACTA
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
14 29 0.78
15 8 0.22
ACGTcount: A:0.21, C:0.00, G:0.28, T:0.51
Consensus pattern (14 bp):
GTTTATGTTTTAGG
Found at i:1671960 original size:2 final size:2
Alignment explanation
Indices: 1671953--1672314 Score: 122
Period size: 2 Copynumber: 184.0 Consensus size: 2
1671943 TGTTTCTTTA
* *
1671953 AT AT AT AT AT AT AT AT AT AT AT AT ACT -T AT AT -T AGT -T AC AC
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT A-T AT AT AT
* *
1671994 AT AC AT AT AT AT ACT AT AT -T A- AT AT AA AT -T AT A- AT AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
1672033 AA ACT AT AT AT -T TT TT AT AGT TT AT AC AT AT AT AGT TT AT AT
1 AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT
* * * *
1672075 AC AT AC AT AC AT AT AT AT ACT AT AT -T A- AT AT AA AT A- AT AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
1672115 -T TT AT AA ACT AT AT ACT -T TT AT ACT TT AT AC AT AT AT AGT TT
1 AT AT AT AT A-T AT AT A-T AT AT AT A-T AT AT AT AT AT AT A-T AT
* * * * *
1672157 AT AT AC AT AGT TT AT AT AT AT AT AT AGT -T CAC AT AA AC AT A-
1 AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT -AT AT AT AT AT AT
* *
1672198 AT TT TT 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
* * *
1672240 AT CT -T AT A- AT A- AT -T AT AT AGT TT AT A- AT AT AA AT AT AGT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT A-T
* *
1672279 TT AT AT AT AA ACT -T AT AT -T AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
1672315 TTTTTCAATT
Statistics
Matches: 267, Mismatches: 53, Indels: 80
0.67 0.13 0.20
Matches are distributed among these distances:
1 23 0.09
2 227 0.85
3 17 0.06
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1672152 original size:15 final size:14
Alignment explanation
Indices: 1672134--1672180 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
1672124 TATATACTTT
*
1672134 TATACTTTATACATA
1 TATAGTTTATA-ATA
1672149 TATAGTTTAT-ATA
1 TATAGTTTATAATA
*
1672162 CATAGTTTATATATA
1 TATAGTTTATA-ATA
1672177 TATA
1 TATA
1672181 TAGTTCACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 12 0.44
15 15 0.56
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.49
Consensus pattern (14 bp):
TATAGTTTATAATA
Found at i:1672166 original size:13 final size:13
Alignment explanation
Indices: 1672150--1672174 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1672140 TTATACATAT
1672150 ATAGTTTATATAC
1 ATAGTTTATATAC
1672163 ATAGTTTATATA
1 ATAGTTTATATA
1672175 TATATATAGT
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:0.04, G:0.08, T:0.48
Consensus pattern (13 bp):
ATAGTTTATATAC
Found at i:1672180 original size:87 final size:87
Alignment explanation
Indices: 1671992--1672165 Score: 296
Period size: 87 Copynumber: 2.0 Consensus size: 87
1671982 TATTAGTTAC
* * *
1671992 ACATACATATATATACTATATTAATATAAATTATAATATATAAACTATATATTTTTTATAGTTTA
1 ACATACATATATATACTATATTAATATAAATAATAATATATAAACTATATATCTTTTATACTTTA
1672057 TACATATATAGTTTATATACAT
66 TACATATATAGTTTATATACAT
* *
1672079 ACATACATATATATACTATATTAATATAAATAATATTTTATAAACTATATA-CTTTTATACTTTA
1 ACATACATATATATACTATATTAATATAAATAATAATATATAAACTATATATCTTTTATACTTTA
1672143 TACATATATAGTTTATATACAT
66 TACATATATAGTTTATATACAT
1672165 A
1 A
1672166 GTTTATATAT
Statistics
Matches: 82, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
86 34 0.41
87 48 0.59
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (87 bp):
ACATACATATATATACTATATTAATATAAATAATAATATATAAACTATATATCTTTTATACTTTA
TACATATATAGTTTATATACAT
Found at i:1674090 original size:16 final size:16
Alignment explanation
Indices: 1674041--1674090 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
1674031 TTTAAGGACT
1674041 AAATTG-AATAAATATA
1 AAATTGAAATAAAT-TA
* * *
1674057 AAAGTGAAA-GACTTA
1 AAATTGAAATAAATTA
1674072 AAATTGAAATAAATTA
1 AAATTGAAATAAATTA
1674088 AAA
1 AAA
1674091 AAAATGATGA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
15 10 0.38
16 14 0.54
17 2 0.08
ACGTcount: A:0.62, C:0.02, G:0.10, T:0.26
Consensus pattern (16 bp):
AAATTGAAATAAATTA
Found at i:1674223 original size:20 final size:19
Alignment explanation
Indices: 1674200--1674347 Score: 93
Period size: 20 Copynumber: 7.4 Consensus size: 19
1674190 ATAAAGACAA
*
1674200 ATATATAATATATATAGTTT
1 ATATATAATATATATA-TAT
* * * *
1674220 ATATGTAGTTTAT-TAATAA
1 ATATATAATATATAT-ATAT
*
1674239 ACTATGTAATATATATATAT
1 A-TATATAATATATATATAT
1674259 ATATAT-ATATATATATAT
1 ATATATAATATATATATAT
* *
1674277 ATATATAATATAAGATTTAT
1 ATATATAATAT-ATATATAT
* * *
1674297 GTATATAGTTTATATATAT
1 ATATATAATATATATATAT
*
1674316 AGTATATTAAGTACATATATATT
1 A-TATA-TAA-TATATATATA-T
1674339 ATTATATAA
1 A-TATATAA
1674348 ATAGTTTACA
Statistics
Matches: 98, Mismatches: 21, Indels: 16
0.73 0.16 0.12
Matches are distributed among these distances:
18 18 0.18
19 17 0.17
20 43 0.44
21 3 0.03
22 11 0.11
23 6 0.06
ACGTcount: A:0.45, C:0.01, G:0.06, T:0.47
Consensus pattern (19 bp):
ATATATAATATATATATAT
Found at i:1674254 original size:2 final size:2
Alignment explanation
Indices: 1674247--1674346 Score: 86
Period size: 2 Copynumber: 51.5 Consensus size: 2
1674237 AAACTATGTA
1674247 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
1674288 A- AG AT TT AT GT AT AT AGT TT AT AT AT AT AGT AT AT -T A- AGT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT A-T
*
1674328 AC AT AT AT AT -T AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
1674347 AATAGTTTAC
Statistics
Matches: 80, Mismatches: 9, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
1 6 0.08
2 70 0.88
3 4 0.05
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1674433 original size:9 final size:9
Alignment explanation
Indices: 1674419--1674451 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
1674409 GTGTAAACAA
*
1674419 TATATAAAC
1 TATATAAAG
1674428 TATATAAAG
1 TATATAAAG
1674437 TAT-TAAAG
1 TATATAAAG
1674445 TATATAA
1 TATATAA
1674452 TTTATATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.36
Consensus pattern (9 bp):
TATATAAAG
Found at i:1674459 original size:19 final size:19
Alignment explanation
Indices: 1674437--1674491 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 19
1674427 CTATATAAAG
1674437 TATTAAAGTATATAA-TTTA
1 TATTAAA-TATATAAGTTTA
1674456 TATTAATATAATATAAGTTTA
1 TATTAA-AT-ATATAAGTTTA
1674477 TATATAAACTATATA
1 TAT-TAAA-TATATA
1674492 TATATAAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
19 7 0.23
20 7 0.23
21 13 0.42
22 4 0.13
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (19 bp):
TATTAAATATATAAGTTTA
Found at i:1674490 original size:32 final size:31
Alignment explanation
Indices: 1674445--1674548 Score: 88
Period size: 32 Copynumber: 3.3 Consensus size: 31
1674435 AGTATTAAAG
**
1674445 TATATAATTTATATTAATATAATATAAGTTTA
1 TATATAAACTATA-TAATATAATATAAGTTTA
1674477 TATATAAACTATATATATATAA-ACTATA-TTTA
1 TATATAAACTATATA-ATATAATA-TA-AGTTTA
* * *
1674509 TATTATAAACTATATCAT-TATTATAAGCTATA
1 TA-TATAAACTATATAATATAATATAAG-TTTA
1674541 TATATAAA
1 TATATAAA
1674549 TTATGTTTAT
Statistics
Matches: 60, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
30 1 0.02
31 13 0.22
32 33 0.55
33 13 0.22
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (31 bp):
TATATAAACTATATAATATAATATAAGTTTA
Found at i:1674492 original size:28 final size:28
Alignment explanation
Indices: 1674418--1674627 Score: 83
Period size: 28 Copynumber: 7.1 Consensus size: 28
1674408 TGTGTAAACA
*
1674418 ATATATAAACTATATA-AAGTATTAAAGTAT
1 ATATATAAACTATATATAA-TA-T-AAGTTT
* * *
1674448 ATAATTTATATTA-ATATAATATAAGTTT
1 AT-ATATAAACTATATATAATATAAGTTT
1674476 ATATATAAACTATATATATATAAACTATA-TTT
1 ATATATAAACTATATATA-AT--A-TA-AGTTT
* *
1674508 ATATTATAAACTATATCATTATTATAAGCTAT
1 ATA-TATAAACTATAT-A-TAATATAAG-TTT
* * * * *
1674540 ATATATAAATTATGT-TTATATGAACTAT
1 ATATATAAACTATATATAATAT-AAGTTT
* *
1674568 ATATATAAACTATGTAT-ATA-AACTTT
1 ATATATAAACTATATATAATATAAGTTT
*
1674594 ATATGTATAAACTATA-AAAAGTATATAGTTT
1 ATA--TATAAACTATATATAA-TATA-AGTTT
1674625 ATA
1 ATA
1674628 AACTATAATT
Statistics
Matches: 140, Mismatches: 19, Indels: 41
0.70 0.09 0.20
Matches are distributed among these distances:
26 8 0.06
27 8 0.06
28 47 0.34
29 8 0.06
30 9 0.06
31 29 0.21
32 14 0.10
33 13 0.09
34 2 0.01
35 2 0.01
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (28 bp):
ATATATAAACTATATATAATATAAGTTT
Found at i:1674493 original size:15 final size:15
Alignment explanation
Indices: 1674475--1674609 Score: 102
Period size: 15 Copynumber: 9.0 Consensus size: 15
1674465 AATATAAGTT
1674475 TATATATAAACTATA
1 TATATATAAACTATA
1674490 TATATATAAACTATA
1 TATATATAAACTATA
1674505 TTTATATTATAAACTATA
1 --TATA-TATAAACTATA
*
1674523 TCATTATTATAAGC--TA
1 T-A-TA-TATAAACTATA
* *
1674539 TATATATAAATTATG
1 TATATATAAACTATA
* *
1674554 TTTATATGAAC--TA
1 TATATATAAACTATA
1674567 TATATATAAAC--TA
1 TATATATAAACTATA
* *
1674580 TGTATATAAACTTTA
1 TATATATAAACTATA
*
1674595 TATGTATAAACTATA
1 TATATATAAACTATA
1674610 AAAAGTATAT
Statistics
Matches: 97, Mismatches: 14, Indels: 18
0.75 0.11 0.14
Matches are distributed among these distances:
13 27 0.28
14 2 0.02
15 39 0.40
16 4 0.04
17 5 0.05
18 20 0.21
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.44
Consensus pattern (15 bp):
TATATATAAACTATA
Found at i:1674812 original size:9 final size:9
Alignment explanation
Indices: 1674787--1674829 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
1674777 TATAGGTTAT
*
1674787 ATATATATAT
1 ATATATA-AA
1674797 ATATATAAA
1 ATATATAAA
*
1674806 CTATATAAA
1 ATATATAAA
1674815 ATA-ATAAA
1 ATATATAAA
1674823 ATATATA
1 ATATATA
1674830 GTTTATAGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
8 8 0.28
9 14 0.48
10 7 0.24
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (9 bp):
ATATATAAA
Found at i:1675135 original size:2 final size:2
Alignment explanation
Indices: 1675089--1675126 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
1675079 TATGTATAGC
*
1675089 AT AT AT AA ACT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT A
1675127 AACTATATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 32 0.97
3 1 0.03
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1675145 original size:323 final size:330
Alignment explanation
Indices: 1674784--1675453 Score: 958
Period size: 345 Copynumber: 2.0 Consensus size: 330
1674774 ATCTATAGGT
1674784 TATATATATATATATATATAAACTATATAAAATAATAAAATATATAGTTTATAGAAACACTATGC
1 TATATATATATATATATATAAACTATATAAAATAATAAAATATATAGTTTATAGAAACACTATGC
* * *
1674849 ATAAACTA-ATGAAGTAATAAAGTACGTAGTTTATAGAAA-CT-CTAAA-C-CC-T-AAACTATA
66 ATAAACTATATAAAGTAATAAAGTACATAATTTATAGAAACCTACTAAATCACCTTAAAACTATA
* * *
1674907 TATGTATAGACATAGTTGATAATTCATATATAGTTAATATAAACAATAGTTTATATAAATTATAT
131 TATGTATAGACACAATTGATAATTCATATATAGTTAATACAAACAATAGTTTATATAAATTATAT
* * * * * *
1674972 ATGTGACATTAACCTATAGTCTATAAACAATAGTTAATATATGTAACCTATAGTATATGTATGCA
196 ATGTAACATTAACCTATAGTCTATAAACAATAGTTAATACATGTAACATATAATATACGTATACA
1675037 TGTAAACTATATATGTAACTTATAGTACATGTATGTAGAAACTATGTATAGCATATATAAACTAT
261 TGTAAACTATATATGTAACTTATAGTACATGTATGTAGAAACTATGTATAGCATATATAAACTAT
1675102 ATATA
326 ATATA
* * *
1675107 TATATATATATATATATATAAACTATATAAAGTAATAAAGTATATAGTTTGTAGAAACACTATGC
1 TATATATATATATATATATAAACTATATAAAATAATAAAATATATAGTTTATAGAAACACTATGC
*
1675172 ATAAACTATATAAAGTAATAAAGTATATAATTTATAGAAACCCTAAACCCTAAATCTTAAACCTT
66 ATAAACTATATAAAGTAATAAAGTACATAATTTATAGAAA-CCT--A--CTAAATC----ACCTT
* *
1675237 AAACCCAAAACTATATATGTATAGACACAATTTATAATTCATATATAGTTTATACAAACAATAGT
122 ------AAAACTATATATGTATAGACACAATTGATAATTCATATATAGTTAATACAAACAATAGT
* *
1675302 TTATATAAATTATATATGTAACCTTAATCTATAGTCTATAAACAATAGTTAATACATGTAACATA
181 TTATATAAATTATATATGTAACATTAACCTATAGTCTATAAACAATAGTTAATACATGTAACATA
*
1675367 TAATATACGTATACATGTAAACTATATATGTAACTTATAGTACATGTATGTATAAACTATGTATA
246 TAATATACGTATACATGTAAACTATATATGTAACTTATAGTACATGTATGTAGAAACTATGTATA
*
1675432 GTATATATAAACTATATATA
311 GCATATATAAACTATATATA
1675452 TA
1 TA
1675454 ACCTATAGTA
Statistics
Matches: 303, Mismatches: 22, Indels: 22
0.87 0.06 0.06
Matches are distributed among these distances:
323 70 0.23
324 27 0.09
326 2 0.01
331 5 0.02
332 1 0.00
337 2 0.01
338 1 0.00
345 195 0.64
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.36
Consensus pattern (330 bp):
TATATATATATATATATATAAACTATATAAAATAATAAAATATATAGTTTATAGAAACACTATGC
ATAAACTATATAAAGTAATAAAGTACATAATTTATAGAAACCTACTAAATCACCTTAAAACTATA
TATGTATAGACACAATTGATAATTCATATATAGTTAATACAAACAATAGTTTATATAAATTATAT
ATGTAACATTAACCTATAGTCTATAAACAATAGTTAATACATGTAACATATAATATACGTATACA
TGTAAACTATATATGTAACTTATAGTACATGTATGTAGAAACTATGTATAGCATATATAAACTAT
ATATA
Found at i:1675151 original size:48 final size:48
Alignment explanation
Indices: 1675119--1675212 Score: 152
Period size: 48 Copynumber: 2.0 Consensus size: 48
1675109 TATATATATA
* *
1675119 TATATATAAACTATATAAAGTAATAAAGTATATAGTTTGTAGAAACAC
1 TATACATAAACTATATAAAGTAATAAAGTATATAGTTTATAGAAACAC
* *
1675167 TATGCATAAACTATATAAAGTAATAAAGTATATAATTTATAGAAAC
1 TATACATAAACTATATAAAGTAATAAAGTATATAGTTTATAGAAAC
1675213 CCTAAACCCT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.51, C:0.06, G:0.10, T:0.33
Consensus pattern (48 bp):
TATACATAAACTATATAAAGTAATAAAGTATATAGTTTATAGAAACAC
Found at i:1675435 original size:20 final size:20
Alignment explanation
Indices: 1675412--1675451 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1675402 TATAGTACAT
* *
1675412 GTATGTATAAACTATGTATA
1 GTATATATAAACTATATATA
1675432 GTATATATAAACTATATATA
1 GTATATATAAACTATATATA
1675452 TAACCTATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (20 bp):
GTATATATAAACTATATATA
Found at i:1675451 original size:13 final size:13
Alignment explanation
Indices: 1675433--1675466 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
1675423 CTATGTATAG
1675433 TATATATAAACTA
1 TATATATAAACTA
*
1675446 TATATATAACCTA
1 TATATATAAACTA
1675459 TAGTATAT
1 TA-TATAT
1675467 GTATATATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:1675535 original size:59 final size:59
Alignment explanation
Indices: 1675464--1675642 Score: 259
Period size: 59 Copynumber: 2.9 Consensus size: 59
1675454 ACCTATAGTA
*
1675464 TATGTATATATACAATCTATTTATATGTAAACTATATATGCAACCTATAGTATATATAT
1 TATGTATATATACAATCTATTTATATGTAAACTATATATGTAACCTATAGTATATATAT
* *
1675523 TATGTATATATACAATCTATTTATATGTAAACAATATATGTAACCTATCGTATATATAT
1 TATGTATATATACAATCTATTTATATGTAAACTATATATGTAACCTATAGTATATATAT
* * *
1675582 TATGTATATATACAATCTATATATAGTTTATATGAACTATATATGTAACCTATAGTTTATA
1 TATGTATATATACAATCTAT-T-TA---TATGTAAACTATATATGTAACCTATAGTATATA
1675643 AACAATAGTT
Statistics
Matches: 107, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
59 76 0.71
60 1 0.01
61 2 0.02
64 28 0.26
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.43
Consensus pattern (59 bp):
TATGTATATATACAATCTATTTATATGTAAACTATATATGTAACCTATAGTATATATAT
Found at i:1675719 original size:21 final size:21
Alignment explanation
Indices: 1675672--1675712 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1675662 GCATATGTAC
* *
1675672 TATATAGTTTATAACCTATAA
1 TATATAATTTATAAACTATAA
1675693 TATATAATTTATAAACTATA
1 TATATAATTTATAAACTATA
1675713 GTTTATATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.44
Consensus pattern (21 bp):
TATATAATTTATAAACTATAA
Found at i:1675780 original size:15 final size:15
Alignment explanation
Indices: 1675730--1675780 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
1675720 TTAATGTACT
*
1675730 ATATAGTTTATATTA
1 ATATAATTTATATTA
* *
1675745 ATGTTAA-TTATCTTA
1 AT-ATAATTTATATTA
1675760 ACTATAATTTATATTA
1 A-TATAATTTATATTA
1675776 ATATA
1 ATATA
1675781 GTATATAGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
15 17 0.61
16 11 0.39
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (15 bp):
ATATAATTTATATTA
Found at i:1675866 original size:31 final size:31
Alignment explanation
Indices: 1675731--1676041 Score: 176
Period size: 31 Copynumber: 9.8 Consensus size: 31
1675721 TAATGTACTA
* * *
1675731 TATAGTTTATATTAATGTTAATTATCTTAAC
1 TATAGTTTATATTAATATTAATTATATAAAC
* *
1675762 TATAATTTATATTAATATAGTATATAGTTTATAAAC
1 TATAGTTTATATTAATAT--TA-AT--TATATAAAC
* * *
1675798 TATAATTTGTATTAATATAGTAGATAGTTTATAAAC
1 TATAGTTTATATTAATAT--TA-AT--TATATAAAC
* *
1675834 TATAGTTTACATTAATATTAATTATATTAAC
1 TATAGTTTATATTAATATTAATTATATAAAC
* * *
1675865 TACAGTTTATAAACTATACTATATAATT-TATAAAA
1 TATAGTTTAT--A-T-TAATAT-TAATTATATAAAC
* *
1675900 TATAGTTTATATTAATATTAATTTTATAGAC
1 TATAGTTTATATTAATATTAATTATATAAAC
* *
1675931 TATATTTTATATTAATATTAATTA-A-AAAT
1 TATAGTTTATATTAATATTAATTATATAAAC
*** *
1675960 TATAAACTATA--AACTA-T-ATTATATTAA-
1 TATAGTTTATATTAA-TATTAATTATATAAAC
* *
1675987 TATAAGTTAATATTAATATTAATTATA-ATA-
1 TAT-AGTTTATATTAATATTAATTATATAAAC
*
1676017 TATAATTT-TATTAATATTAATTATA
1 TATAGTTTATATTAATATTAATTATA
1676042 AATAGTTTAT
Statistics
Matches: 224, Mismatches: 37, Indels: 41
0.74 0.12 0.14
Matches are distributed among these distances:
26 4 0.02
27 7 0.03
28 25 0.11
29 15 0.07
30 13 0.06
31 69 0.31
32 1 0.00
33 6 0.03
34 5 0.02
35 19 0.08
36 60 0.27
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (31 bp):
TATAGTTTATATTAATATTAATTATATAAAC
Found at i:1675950 original size:88 final size:84
Alignment explanation
Indices: 1675857--1676036 Score: 200
Period size: 88 Copynumber: 2.1 Consensus size: 84
1675847 AATATTAATT
* ** * *
1675857 ATATTAACTACAGTTTATAAACTAT-ACTATATAATTTATAAAATATAGTTTATATTAATATTAA
1 ATATTAACTAAAAATTATAAACTATAACTATATAATAT-TAAAATA-AGTTAATATTAATATTAA
* *
1675921 TTTTATAGACTATATTTTATATTA
64 TTATA-AGA-TATAATTT-TATTA
* * *
1675945 ATATTAATTAAAAATTATAAACTATAAACTATATTATATTAATATAAGTTAATATTAATATTAAT
1 ATATTAACTAAAAATTATAAACTAT-AACTATATAATATTAAAATAAGTTAATATTAATATTAAT
*
1676010 TATAATATATAATTTTATTA
65 TATAAGATATAATTTTATTA
1676030 ATATTAA
1 ATATTAA
1676037 TTATAAATAG
Statistics
Matches: 79, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
85 12 0.15
86 7 0.09
87 2 0.03
88 42 0.53
89 6 0.08
90 10 0.13
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (84 bp):
ATATTAACTAAAAATTATAAACTATAACTATATAATATTAAAATAAGTTAATATTAATATTAATT
ATAAGATATAATTTTATTA
Found at i:1676002 original size:6 final size:6
Alignment explanation
Indices: 1675975--1676037 Score: 50
Period size: 6 Copynumber: 11.3 Consensus size: 6
1675965 ACTATAAACT
*
1675975 ATATT- ATATTA ATA-TA A-GTTA ATATTA ATATTA AT-TATA ATATATA
1 ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATAT-TA ATAT-TA
1676021 AT-TT- -TATTA ATATTA AT
1 ATATTA ATATTA ATATTA AT
1676038 TATAAATAGT
Statistics
Matches: 48, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
3 1 0.02
4 2 0.04
5 13 0.27
6 26 0.54
7 6 0.12
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (6 bp):
ATATTA
Found at i:1676019 original size:41 final size:42
Alignment explanation
Indices: 1675898--1676019 Score: 103
Period size: 41 Copynumber: 2.9 Consensus size: 42
1675888 TAATTTATAA
*
1675898 AATAT-AGTTTATATTAATATTAATTTTATAGACTATATTTTATATT
1 AATATAAGTTAATATTAATATTAA--TTATA-ACTATA--TTATATT
* *
1675944 AATATTAA-TTAA-A--AATTATAAACTATAAACTATATTATATT
1 AATA-TAAGTTAATATTAA-TATTAATTAT-AACTATATTATATT
1675985 AATATAAGTTAATATTAATATTAATTATAA-TATAT
1 AATATAAGTTAATATTAATATTAATTATAACTATAT
1676020 AATTTTATTA
Statistics
Matches: 63, Mismatches: 5, Indels: 21
0.71 0.06 0.24
Matches are distributed among these distances:
40 3 0.05
41 20 0.32
42 3 0.05
43 17 0.27
44 5 0.08
45 5 0.08
46 5 0.08
47 4 0.06
48 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (42 bp):
AATATAAGTTAATATTAATATTAATTATAACTATATTATATT
Found at i:1676029 original size:18 final size:18
Alignment explanation
Indices: 1675939--1676022 Score: 55
Period size: 16 Copynumber: 4.4 Consensus size: 18
1675929 ACTATATTTT
*
1675939 ATATTAATATTAATTAAAA
1 ATATTAATATTAATT-ATA
* * *
1675958 ATTATAAACTATAAACTATATT
1 A-TATTAA-TATTAA-T-TATA
*
1675980 ATATTAATA-TAAGT-TA
1 ATATTAATATTAATTATA
1675996 ATATTAATATTAATTATA
1 ATATTAATATTAATTATA
1676014 ATATATAAT
1 ATAT-TAAT
1676023 TTTATTAATA
Statistics
Matches: 49, Mismatches: 9, Indels: 14
0.68 0.12 0.19
Matches are distributed among these distances:
16 10 0.20
17 5 0.10
18 6 0.12
19 7 0.14
20 7 0.14
21 10 0.20
22 3 0.06
23 1 0.02
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.44
Consensus pattern (18 bp):
ATATTAATATTAATTATA
Found at i:1676050 original size:24 final size:27
Alignment explanation
Indices: 1675977--1676067 Score: 98
Period size: 24 Copynumber: 3.3 Consensus size: 27
1675967 TATAAACTAT
1675977 ATTATATTAATATAAGTTAATATTAATATTA
1 ATTATA-T-ATATAAGTT--TATTAATATTA
*
1676008 ATTATAATATATAATTTTATTAATATTA
1 ATTAT-ATATATAAGTTTATTAATATTA
*
1676036 ATTATA-A-AT-AGTTTATTAATATAA
1 ATTATATATATAAGTTTATTAATATTA
1676060 ATTATATA
1 ATTATATA
1676068 GGGATGAAAT
Statistics
Matches: 55, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
24 19 0.35
25 3 0.05
26 1 0.02
27 1 0.02
28 16 0.29
30 8 0.15
31 6 0.11
32 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.49
Consensus pattern (27 bp):
ATTATATATATAAGTTTATTAATATTA
Found at i:1676818 original size:6 final size:6
Alignment explanation
Indices: 1676801--1676918 Score: 85
Period size: 6 Copynumber: 19.7 Consensus size: 6
1676791 ACCCAACTTG
* * * * * * *
1676801 AACCCTA AACCCA AACCCA AACCTA AATCTA AACCTA AACCCT AACTCG
1 AACCC-A AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA
* * * * * *
1676850 AATCTA AACCCA AACCCA AA-CCA AACCCG AACCCA AATCAA AACCCG
1 AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA
* *
1676897 AACCCA AATCCA AACCCG AACC
1 AACCCA AACCCA AACCCA AACC
1676919 TAAAAAACCC
Statistics
Matches: 86, Mismatches: 24, Indels: 3
0.76 0.21 0.03
Matches are distributed among these distances:
5 5 0.06
6 76 0.88
7 5 0.06
ACGTcount: A:0.47, C:0.41, G:0.03, T:0.09
Consensus pattern (6 bp):
AACCCA
Found at i:1676820 original size:24 final size:24
Alignment explanation
Indices: 1676780--1676870 Score: 96
Period size: 24 Copynumber: 3.8 Consensus size: 24
1676770 CATTTCATCT
1676780 TCTATAACCC-AACCC-AACTTGAA
1 TCTA-AACCCAAACCCAAACTTGAA
* * *
1676803 CCCTAAACCCAAACCCAAACCTAAA
1 -TCTAAACCCAAACCCAAACTTGAA
* * *
1676828 TCTAAACCTAAACCCTAACTCGAA
1 TCTAAACCCAAACCCAAACTTGAA
1676852 TCTAAACCCAAACCCAAAC
1 TCTAAACCCAAACCCAAAC
1676871 CAAACCCGAA
Statistics
Matches: 54, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
23 5 0.09
24 43 0.80
25 6 0.11
ACGTcount: A:0.44, C:0.38, G:0.02, T:0.15
Consensus pattern (24 bp):
TCTAAACCCAAACCCAAACTTGAA
Found at i:1677469 original size:111 final size:113
Alignment explanation
Indices: 1677353--1677562 Score: 334
Period size: 111 Copynumber: 1.9 Consensus size: 113
1677343 GCTATTGTTG
1677353 ATTTGTTTCCTCTGTAGTCCCTGTTTGTGTTGTTGGTTGTTCATTCGGATTGCTTGTAT-A-AGG
1 ATTTGTTTCCTCTGTAGTCCCTGTTTGTGTTGTTGGTTGTTCATTCGGATTGCTTGTATGAGAGG
* *
1677416 TTGTTAGCTGCTTTTATTTAGGATTTAAATAATTTTGTAGCTACTGTA
66 TTGTTAACTGCCTTTATTTAGGATTTAAATAATTTTGTAGCTACTGTA
* * * *
1677464 ATTTGTTTCCTCTGTGGTCCTTGTTTGTGTTGTTGGTTGTTCATTCGGTTTGCTTGTATGAGGTT
1 ATTTGTTTCCTCTGTAGTCCCTGTTTGTGTTGTTGGTTGTTCATTCGGATTGCTTGTATGA-G-A
1677529 GGTTGTTAACTGCCTTTATTTAGGATTTAAATAA
64 GGTTGTTAACTGCCTTTATTTAGGATTTAAATAA
1677563 ACTGTTTAAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
111 56 0.63
112 1 0.01
115 32 0.36
ACGTcount: A:0.16, C:0.11, G:0.23, T:0.50
Consensus pattern (113 bp):
ATTTGTTTCCTCTGTAGTCCCTGTTTGTGTTGTTGGTTGTTCATTCGGATTGCTTGTATGAGAGG
TTGTTAACTGCCTTTATTTAGGATTTAAATAATTTTGTAGCTACTGTA
Found at i:1679976 original size:24 final size:24
Alignment explanation
Indices: 1679944--1680020 Score: 93
Period size: 24 Copynumber: 3.2 Consensus size: 24
1679934 GTAGAAATGT
* *
1679944 TGCCTGCTGTCTATTGC-TGCCTGC
1 TGCCTGCTGCCTACTGCTTG-CTGC
*
1679968 TGCCTGCTGCCTACTGCTTGTTGC
1 TGCCTGCTGCCTACTGCTTGCTGC
* *
1679992 TGCCTGCTGCTTACTGCTTGTTGC
1 TGCCTGCTGCCTACTGCTTGCTGC
1680016 TGCCT
1 TGCCT
1680021 TGTAATTTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
24 46 0.96
25 2 0.04
ACGTcount: A:0.04, C:0.32, G:0.25, T:0.39
Consensus pattern (24 bp):
TGCCTGCTGCCTACTGCTTGCTGC
Found at i:1680009 original size:17 final size:17
Alignment explanation
Indices: 1679944--1680009 Score: 59
Period size: 17 Copynumber: 4.1 Consensus size: 17
1679934 GTAGAAATGT
*
1679944 TGCCTGCTG-TCTATTGC
1 TGCCTGCTGCT-TACTGC
1679961 TGCCTGCTGC---CTGC
1 TGCCTGCTGCTTACTGC
* **
1679975 TGCCTACTGCTTGTTGC
1 TGCCTGCTGCTTACTGC
1679992 TGCCTGCTGCTTACTGC
1 TGCCTGCTGCTTACTGC
1680009 T
1 T
1680010 TGTTGCTGCC
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
14 12 0.31
17 27 0.69
ACGTcount: A:0.05, C:0.33, G:0.24, T:0.38
Consensus pattern (17 bp):
TGCCTGCTGCTTACTGC
Found at i:1680603 original size:23 final size:24
Alignment explanation
Indices: 1680575--1680625 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 24
1680565 TTATTTTTTC
1680575 TTTACATAAATTAAAATATA-TAA
1 TTTACATAAATTAAAATATATTAA
*
1680598 TTTACATAAATTAAACTATATTAA
1 TTTACATAAATTAAAATATATTAA
1680622 TTTA
1 TTTA
1680626 TATTTAATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 19 0.73
24 7 0.27
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (24 bp):
TTTACATAAATTAAAATATATTAA
Found at i:1681094 original size:11 final size:11
Alignment explanation
Indices: 1681063--1681105 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
1681053 TCGGTTTAAT
1681063 TCGGGTTCAGG
1 TCGGGTTCAGG
*
1681074 TC-GTTCTCAGG
1 TCGGGT-TCAGG
1681085 TCGGGTTCAGG
1 TCGGGTTCAGG
*
1681096 TTGGGTTCAG
1 TCGGGTTCAG
1681106 ATCCATAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 2 0.07
11 23 0.85
12 2 0.07
ACGTcount: A:0.09, C:0.19, G:0.40, T:0.33
Consensus pattern (11 bp):
TCGGGTTCAGG
Found at i:1684769 original size:48 final size:48
Alignment explanation
Indices: 1684717--1684808 Score: 116
Period size: 48 Copynumber: 1.9 Consensus size: 48
1684707 TCCGACTTGA
* *
1684717 ATTCTGTTTTGATA-CATGACT-TGAATTTTGTTCTGATTTCTGATCTGG
1 ATTCTGTTATGATATC-T-ACTCTGAATTCTGTTCTGATTTCTGATCTGG
* *
1684765 ATTCTGTTATGATATCTATTCTGAATTCTGTTTTGATTTCTGAT
1 ATTCTGTTATGATATCTACTCTGAATTCTGTTCTGATTTCTGAT
1684809 ATCTCCGTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
47 2 0.05
48 35 0.92
49 1 0.03
ACGTcount: A:0.20, C:0.12, G:0.16, T:0.52
Consensus pattern (48 bp):
ATTCTGTTATGATATCTACTCTGAATTCTGTTCTGATTTCTGATCTGG
Found at i:1684772 original size:24 final size:24
Alignment explanation
Indices: 1684738--1684808 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 24
1684728 ATACATGACT
* *
1684738 TGAATTTTGTTCTGATTTCTGATC
1 TGAATTCTGTTATGATTTCTGATC
* *
1684762 TGGATTCTGTTATGATATCT-ATTC
1 TGAATTCTGTTATGATTTCTGA-TC
*
1684786 TGAATTCTGTTTTGATTTCTGAT
1 TGAATTCTGTTATGATTTCTGAT
1684809 ATCTCCGTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
23 1 0.03
24 36 0.95
25 1 0.03
ACGTcount: A:0.18, C:0.11, G:0.17, T:0.54
Consensus pattern (24 bp):
TGAATTCTGTTATGATTTCTGATC
Found at i:1689812 original size:45 final size:45
Alignment explanation
Indices: 1689763--1689865 Score: 116
Period size: 45 Copynumber: 2.3 Consensus size: 45
1689753 AGTCATAAAG
* * * *
1689763 GACAATAATAAAAAATCAACTTCTCTTTGCGAGAAAGTCAAGGAA
1 GACAACAATAAAAAATCAACTCCACTTCGCGAGAAAGTCAAGGAA
* * * *
1689808 GACAACACTAAAAGATTAACTCCACTTCGCGAGAAAGTCAAGGAG
1 GACAACAATAAAAAATCAACTCCACTTCGCGAGAAAGTCAAGGAA
* *
1689853 GGCAACACTAAAA
1 GACAACAATAAAA
1689866 GATTGACTCT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.46, C:0.19, G:0.17, T:0.17
Consensus pattern (45 bp):
GACAACAATAAAAAATCAACTCCACTTCGCGAGAAAGTCAAGGAA
Found at i:1689887 original size:90 final size:90
Alignment explanation
Indices: 1689792--1690029 Score: 273
Period size: 90 Copynumber: 2.6 Consensus size: 90
1689782 CTTCTCTTTG
* * * * * * *
1689792 CGAGAAAGTCAAGGAA-GACAACACTAAAAGATTAACTCCACTTCGCGAGAAAGTCAAGGAGGGC
1 CGAGAAAGTCAA-GAATGACAATACTGAAAGATTGACTTCTCTTCGTGAGAAAGTCAAGGAAGGC
* * *
1689856 AACACTAAAAGATTGACTCTTCTAT-A
65 AACACTAAAAGATTAAATCATCT-TCA
* * * * * * *
1689882 TGAGAAAGTCCAGAATGACAATATTGAAAGATTGACTTCTCTTCGTAAAAAAGTCGAGGAAGTCA
1 CGAGAAAGTCAAGAATGACAATACTGAAAGATTGACTTCTCTTCGTGAGAAAGTCAAGGAAGGCA
1689947 ACACTAAAAGATTAAATCATCTTCA
66 ACACTAAAAGATTAAATCATCTTCA
* *
1689972 CGAGAAAGTCAAGAATGACAATACTGAACGATTGACTTCTCTTCATGAGAAAGTCAAG
1 CGAGAAAGTCAAGAATGACAATACTGAAAGATTGACTTCTCTTCGTGAGAAAGTCAAG
1690030 AATAACAAAG
Statistics
Matches: 121, Mismatches: 25, Indels: 4
0.81 0.17 0.03
Matches are distributed among these distances:
89 4 0.03
90 117 0.97
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.22
Consensus pattern (90 bp):
CGAGAAAGTCAAGAATGACAATACTGAAAGATTGACTTCTCTTCGTGAGAAAGTCAAGGAAGGCA
ACACTAAAAGATTAAATCATCTTCA
Found at i:1690030 original size:45 final size:45
Alignment explanation
Indices: 1689793--1690037 Score: 194
Period size: 45 Copynumber: 5.4 Consensus size: 45
1689783 TTCTCTTTGC
* * * **
1689793 GAGAAAGTCAAGGAA-GACAACACTAAAAGATTAACTCCACTTCGC
1 GAGAAAGTCAA-GAATGACAACACTAAAAGATTGACTTCTCTTCAT
* * *
1689838 GAGAAAGTCAAGGAGGGCAACACTAAAAGATTGAC-TCTTCTAT-AT
1 GAGAAAGTCAAGAATGACAACACTAAAAGATTGACTTC-TCT-TCAT
* * * * *
1689883 GAGAAAGTCCAGAATGACAATATTGAAAGATTGACTTCTCTTCGT
1 GAGAAAGTCAAGAATGACAACACTAAAAGATTGACTTCTCTTCAT
* * * * ** *
1689928 AAAAAAGTCGAGGAA-GTCAACACTAAAAGATT-AAATCATCTTCAC
1 GAGAAAGTC-AAGAATGACAACACTAAAAGATTGACTTC-TCTTCAT
* * *
1689973 GAGAAAGTCAAGAATGACAATACTGAACGATTGACTTCTCTTCAT
1 GAGAAAGTCAAGAATGACAACACTAAAAGATTGACTTCTCTTCAT
*
1690018 GAGAAAGTCAAGAATAACAA
1 GAGAAAGTCAAGAATGACAA
1690038 AGATCGACTT
Statistics
Matches: 153, Mismatches: 38, Indels: 18
0.73 0.18 0.09
Matches are distributed among these distances:
44 11 0.07
45 133 0.87
46 9 0.06
ACGTcount: A:0.43, C:0.17, G:0.18, T:0.22
Consensus pattern (45 bp):
GAGAAAGTCAAGAATGACAACACTAAAAGATTGACTTCTCTTCAT
Found at i:1690158 original size:122 final size:122
Alignment explanation
Indices: 1689978--1690718 Score: 796
Period size: 122 Copynumber: 6.0 Consensus size: 122
1689968 TTCACGAGAA
* * * * ** * *
1689978 AGTCAAGAATGACAATACTGAACGATTGACTTCTCTTCATGAGAAAGTCAAGAATAACAAAGATC
1 AGTCAAGAAAGAC-A-A-TGAAAGATTGACTCCTCTTCACGAGGGAGCCAAGAATAACAAAGATT
* * * * *
1690043 GACTTCTCTTCACGAGGAAGTCAAAAATAACATTGAAAGATTGGCTCCTTTTAATGATGG
63 GACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGATGG
* * *
1690103 AGTTAAGAAAGACAATGAAAGATTGACTCCTCTTCACGAGGGAGCCAATAATAACAAAGATCGAC
1 AGTCAAGAAAGACAATGAAAGATTGACTCCTCTTCACGAGGGAGCCAAGAATAACAAAGATTGAC
* * * *
1690168 TTCTCTTCACGAGGAAGTCAAGGATAACATTGAAATATTGACTCTTCTTCACGAGGG
66 TTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGATGG
* *
1690225 AGTCAAAAAAGACAATGAAAGATTGACTCCTCTTCACGAGGGAGCCAAGAATAACAAAGATTAAC
1 AGTCAAGAAAGACAATGAAAGATTGACTCCTCTTCACGAGGGAGCCAAGAATAACAAAGATTGAC
* * * *
1690290 TTCTCTTCACGAGGGAGCCAAGAATAAC----AAAGATTAACTTCTCTTCACGA-GG
66 TTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGATGG
* * * *
1690342 AAGTCAAGGATA-ACATTGAAAGATTGACTCTTCTTCACGAGGGAGCCAAGAATAACAAATATTG
1 -AGTCAA-GAAAGACAATGAAAGATTGACTCCTCTTCACGAGGGAGCCAAGAATAACAAAGATTG
* * * * *
1690406 ACTTCTCTTCACAATGAAGTTAAGAATAACATTGAAAGATTTACTCCTCTTCATGATGG
64 ACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGATGG
* * *
1690465 AGTCAAGAAAGACAATGAAATATTGACTCCTCTTCACGAGGGATCCAAGAATAACAAATATTGAC
1 AGTCAAGAAAGACAATGAAAGATTGACTCCTCTTCACGAGGGAGCCAAGAATAACAAAGATTGAC
* * * * * *
1690530 TTCTCTTCATGAGGAAGT-AACGAATAACATTGAAATATTGAATACTCTTCATGAGGG
66 TTCTCTTCACGAGGAAGTCAA-GAATAACATTGAAAGATTGACTCCTCTTCACGATGG
* * * * * * * * * *
1690587 AGTCAGGAATGTCATTGAAAGATCGAATTCTCTTCACGA-GGAGGTCAAGACTAACATTGAAATA
1 AGTCAAGAAAGACAATGAAAGATTGACTCCTCTTCACGAGGGA-GCCAAGAATAAC----AAAGA
** * * *
1690651 TTGACTTCTCTTCGTGAGGAAGTCAAGAATAACATTGAAAGACTGACTCCTCTTCGCGAGGG
61 TTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGATGG
1690713 AGTCAA
1 AGTCAA
1690719 TAATAACAAA
Statistics
Matches: 525, Mismatches: 76, Indels: 29
0.83 0.12 0.05
Matches are distributed among these distances:
117 2 0.00
118 97 0.18
119 2 0.00
121 8 0.02
122 337 0.64
123 3 0.01
124 1 0.00
125 11 0.02
126 62 0.12
127 2 0.00
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (122 bp):
AGTCAAGAAAGACAATGAAAGATTGACTCCTCTTCACGAGGGAGCCAAGAATAACAAAGATTGAC
TTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGATGG
Found at i:1690211 original size:80 final size:80
Alignment explanation
Indices: 1690001--1690813 Score: 640
Period size: 80 Copynumber: 10.1 Consensus size: 80
1689991 AATACTGAAC
* * * * *
1690001 GATTGACTTCTCTTCATGAGAAAGTCAAGAATAAC----AAAGATCGACTTCTCTTCACGAGGAA
1 GATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGAGGGA
*
1690062 GTCAAAAATAACATTGAAA
66 GTCAAGAATAAC----AAA
* * * * * * *
1690081 GATTGGCTCCTTTTAATGATGG-AGTTAAGAA-AGACAATGAAAGATTGACTCCTCTTCACGAGG
1 GATTGACTTCTCTTCACGA-GGAAGTCAAGAATA-ACATTGAAAGATTGACTCCTCTTCACGAGG
* *
1690144 GAGCCAATAATAACAAA
64 GAGTCAAGAATAACAAA
* * * *
1690161 GATCGACTTCTCTTCACGAGGAAGTCAAGGATAACATTGAAATATTGACTCTTCTTCACGAGGGA
1 GATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGAGGGA
*
1690226 GTCAA-AAAAGACAATGAAA
66 GTCAAGAATA-AC----AAA
* * * * *
1690245 GATTGACTCCTCTTCACGAGGGAGCCAAGAATAAC----AAAGATTAACTTCTCTTCACGAGGGA
1 GATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGAGGGA
*
1690306 GCCAAGAATAACAAA
66 GTCAAGAATAACAAA
* * *
1690321 GATTAACTTCTCTTCACGAGGAAGTCAAGGATAACATTGAAAGATTGACTCTTCTTCACGAGGGA
1 GATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGAGGGA
*
1690386 GCCAAGAATAACAAA
66 GTCAAGAATAACAAA
* * * * * * *
1690401 TATTGACTTCTCTTCACAATGAAGTTAAGAATAACATTGAAAGATTTACTCCTCTTCATGATGGA
1 GATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGAGGGA
1690466 GTCAAGAA-AGACAATGAAA
66 GTCAAGAATA-AC----AAA
* * * * * * *
1690485 TATTGACTCCTCTTCACGAGGGA-TCCAAGAATAAC----AAATATTGACTTCTCTTCATGAGGA
1 GATTGACTTCTCTTCACGAGGAAGT-CAAGAATAACATTGAAAGATTGACTCCTCTTCACGAGGG
1690545 AGT-AACGAATAACATTGAAA
65 AGTCAA-GAATAAC----AAA
* * * * * * ** * * *
1690565 TATTGAATACTCTTCATGAGGGAGTCAGGAATGTCATTGAAAGATCGAATTCTCTTCACGA-GGA
1 GATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGAGGGA
*
1690629 GGTCAAGACTAACATTGAAA
66 -GTCAAGAATAAC----AAA
* ** * *
1690649 TATTGACTTCTCTTCGTGAGGAAGTCAAGAATAACATTGAAAGACTGACTCCTCTTCGCGAGGGA
1 GATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGAGGGA
*
1690714 GTCAATAATAACAAA
66 GTCAAGAATAACAAA
* * ** *
1690729 GATTGGCTTCTCTTCACGAGGAACTCAAGAATAACATTGAAAGATTGACTCCTCTAAATGAGGGA
1 GATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGAGGGA
1690794 GTCAAGAATAA-AAA
66 GTCAAGAATAACAAA
1690808 GATTGA
1 GATTGA
1690814 ATTTTCTAGG
Statistics
Matches: 596, Mismatches: 103, Indels: 69
0.78 0.13 0.09
Matches are distributed among these distances:
76 33 0.06
79 17 0.03
80 342 0.57
81 7 0.01
83 3 0.01
84 189 0.32
85 5 0.01
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (80 bp):
GATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGAGGGA
GTCAAGAATAACAAA
Found at i:1690219 original size:42 final size:43
Alignment explanation
Indices: 1689966--1690804 Score: 600
Period size: 42 Copynumber: 20.6 Consensus size: 43
1689956 GATTAAATCA
* * *
1689966 TCTTCACGAGAAAGTCAAGAATGACAATACTGAACGATTGACT-TC
1 TCTTCACGAGGAAGTCAAGAATAAC-AT--TGAAAGATTGACTCTC
* * *
1690011 TCTTCATGAGAAAGTCAAGAATAAC----AAAGATCGACT-TC
1 TCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCTC
* *
1690049 TCTTCACGAGGAAGTCAAAAATAACATTGAAAGATTGGCTC-C
1 TCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCTC
* * * * *
1690091 TTTTAATGATGG-AGTTAAGAA-AGACAATGAAAGATTGACTC-C
1 TCTTCACGA-GGAAGTCAAGAATA-ACATTGAAAGATTGACTCTC
* * * *
1690133 TCTTCACGAGGGAGCCAATAATAAC----AAAGATCGACT-TC
1 TCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCTC
* *
1690171 TCTTCACGAGGAAGTCAAGGATAACATTGAAATATTGACTCT-
1 TCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCTC
* * *
1690213 TCTTCACGAGGGAGTCAA-AAAAGACAATGAAAGATTGACTC-C
1 TCTTCACGAGGAAGTCAAGAATA-ACATTGAAAGATTGACTCTC
* * *
1690255 TCTTCACGAGGGAGCCAAGAATAAC----AAAGATTAACT-TC
1 TCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCTC
* * *
1690293 TCTTCACGAGGGAGCCAAGAATAAC----AAAGATTAACT-TC
1 TCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCTC
*
1690331 TCTTCACGAGGAAGTCAAGGATAACATTGAAAGATTGACTCT-
1 TCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCTC
* * *
1690373 TCTTCACGAGGGAGCCAAGAATAAC----AAATATTGACT-TC
1 TCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCTC
* * * *
1690411 TCTTCACAATGAAGTTAAGAATAACATTGAAAGATTTACTC-C
1 TCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCTC
* * *
1690453 TCTTCATGATGG-AGTCAAGAA-AGACAATGAAATATTGACTC-C
1 TCTTCACGA-GGAAGTCAAGAATA-ACATTGAAAGATTGACTCTC
* *
1690495 TCTTCACGAGGGA-TCCAAGAATAAC----AAATATTGACT-TC
1 TCTTCACGAGGAAGT-CAAGAATAACATTGAAAGATTGACTCTC
* * * *
1690533 TCTTCATGAGGAAGT-AACGAATAACATTGAAATATTGAAT-AC
1 TCTTCACGAGGAAGTCAA-GAATAACATTGAAAGATTGACTCTC
* * * ** * *
1690575 TCTTCATGAGGGAGTCAGGAATGTCATTGAAAGATCGAAT-TC
1 TCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCTC
* * *
1690617 TCTTCACGAGGAGGTCAAGACTAACATTGAAATATTGACT-TC
1 TCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCTC
** *
1690659 TCTTCGTGAGGAAGTCAAGAATAACATTGAAAGACTGACTC-C
1 TCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCTC
* * * *
1690701 TCTTCGCGAGGGAGTCAATAATAAC----AAAGATTGGCT-TC
1 TCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCTC
*
1690739 TCTTCACGAGGAACTCAAGAATAACATTGAAAGATTGACTC-C
1 TCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCTC
** * *
1690781 TCTAAATGAGGGAGTCAAGAATAA
1 TCTTCACGAGGAAGTCAAGAATAA
1690805 AAAGATTGAA
Statistics
Matches: 642, Mismatches: 102, Indels: 103
0.76 0.12 0.12
Matches are distributed among these distances:
37 3 0.00
38 227 0.35
39 1 0.00
41 9 0.01
42 368 0.57
43 11 0.02
45 23 0.04
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (43 bp):
TCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTCTC
Found at i:1691560 original size:41 final size:41
Alignment explanation
Indices: 1691515--1691603 Score: 110
Period size: 42 Copynumber: 2.1 Consensus size: 41
1691505 CGGATGGACT
1691515 GAAGGATTT-ATCATC-TCATTCGAAAGACTTACAGATGACCC
1 GAAGGATTTAATCATCATC--TCGAAAGACTTACAGATGACCC
* *
1691556 GAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCC
1 GAAGGATTTAATCATCAT-CTCGAAAGACTTACAGATGACCC
*
1691598 AAAGGA
1 GAAGGA
1691604 CTTACCATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
41 9 0.21
42 31 0.74
43 1 0.02
44 1 0.02
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (41 bp):
GAAGGATTTAATCATCATCTCGAAAGACTTACAGATGACCC
Found at i:1691733 original size:30 final size:30
Alignment explanation
Indices: 1691697--1691754 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
1691687 TACTAAATGA
*
1691697 GAAACTTTGGAAATCGCTTTCTCATTTTGG
1 GAAACTTTGAAAATCGCTTTCTCATTTTGG
1691727 GAAACTTTGAAAATCGCTTTCTCATTTT
1 GAAACTTTGAAAATCGCTTTCTCATTTT
1691755 CAAATTTATG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.41
Consensus pattern (30 bp):
GAAACTTTGAAAATCGCTTTCTCATTTTGG
Found at i:1693528 original size:21 final size:22
Alignment explanation
Indices: 1693504--1693546 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
1693494 ATATGCAATA
1693504 TATATTATG-CAATGT-ATGATG
1 TATA-TATGTCAATGTAATGATG
*
1693525 TATATATGTGAATGTAATGATG
1 TATATATGTCAATGTAATGATG
1693547 CAATAATGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 9 0.47
22 6 0.32
ACGTcount: A:0.35, C:0.02, G:0.21, T:0.42
Consensus pattern (22 bp):
TATATATGTCAATGTAATGATG
Found at i:1693833 original size:16 final size:16
Alignment explanation
Indices: 1693812--1693847 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
1693802 AAATCAATCC
*
1693812 ACTTGTGATCTATATT
1 ACTTGTGATCCATATT
1693828 ACTTGTGATCCATATT
1 ACTTGTGATCCATATT
1693844 ACTT
1 ACTT
1693848 TCTTGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.25, C:0.17, G:0.11, T:0.47
Consensus pattern (16 bp):
ACTTGTGATCCATATT
Found at i:1694953 original size:46 final size:46
Alignment explanation
Indices: 1694855--1694954 Score: 150
Period size: 46 Copynumber: 2.2 Consensus size: 46
1694845 AATTATAGGG
*
1694855 ATCAAAGATTCTTTTATTATGCTTGATCCAAATCGACCATTACGGC
1 ATCAAAGAATCTTTTATTATGCTTGATCCAAATCGACCATTACGGC
*
1694901 -TACAAAGAATCTTTTATTATGCTTGATCCAAATCGACCATGT-CGTC
1 AT-CAAAGAATCTTTTATTATGCTTGATCCAAATCGACCAT-TACGGC
1694947 ATCAAAGA
1 ATCAAAGA
1694955 GGAGATGGAA
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
45 1 0.02
46 46 0.94
47 2 0.04
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (46 bp):
ATCAAAGAATCTTTTATTATGCTTGATCCAAATCGACCATTACGGC
Found at i:1699955 original size:59 final size:59
Alignment explanation
Indices: 1699847--1699991 Score: 155
Period size: 59 Copynumber: 2.4 Consensus size: 59
1699837 TTCTGATTTG
* * * *
1699847 AAATGTCGTCAATCGAACAATAGGAAATGTTAATCCCTCAACTGGGGCATCGCTGATTCA
1 AAATGTCGTGAATCGAGCAA-AAGAAATGTTAATCCCTCAACTGAGGCATCGCTGATTCA
* * * * * * *
1699907 AAATGTCATGAATCGAGCAAAAGAAATGTTGATCCCTCAAGTGAGGCATTGTTGTTTCG
1 AAATGTCGTGAATCGAGCAAAAGAAATGTTAATCCCTCAACTGAGGCATCGCTGATTCA
* * *
1699966 AAATATCGTGAATCGGGCAATAGAAA
1 AAATGTCGTGAATCGAGCAAAAGAAA
1699992 ATGTGAAAGT
Statistics
Matches: 70, Mismatches: 15, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
59 53 0.76
60 17 0.24
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (59 bp):
AAATGTCGTGAATCGAGCAAAAGAAATGTTAATCCCTCAACTGAGGCATCGCTGATTCA
Found at i:1700115 original size:42 final size:41
Alignment explanation
Indices: 1700023--1700123 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 41
1700013 AGGTCTTGTG
* * *
1700023 GATGGCCCGAAGAACTTATCATCTTACTCGAATGACTTATA
1 GATGGCCCGAAGAACTTAGCATCATACTCGAAAGACTTATA
* * * * * *
1700064 AATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTATT
1 GATGGCCCGAAGAACTT-AGCATCATACTCGAAAGACTTATA
1700106 GATGGCCCGAAGAACTTA
1 GATGGCCCGAAGAACTTA
1700124 CTAATTAAGA
Statistics
Matches: 46, Mismatches: 13, Indels: 2
0.75 0.21 0.03
Matches are distributed among these distances:
41 14 0.30
42 32 0.70
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.26
Consensus pattern (41 bp):
GATGGCCCGAAGAACTTAGCATCATACTCGAAAGACTTATA
Found at i:1700225 original size:58 final size:54
Alignment explanation
Indices: 1700127--1700280 Score: 132
Period size: 58 Copynumber: 2.8 Consensus size: 54
1700117 GAACTTACTA
* * * * * ** *
1700127 ATTAAGAAACCCTTGAAAATCAAGCTCACTTTCGTAAAAAAATTTGTTTACAATTAT
1 ATTAAGAAACCCCTAAAAATTAAGCTTAGTTTC-TTTAAAAATTTATTTACAA--AT
* **
1700184 CATTAAGAAACCCCTAAAAATTAAGCTTAGATTCTTTAAAAA-TTATTTGGAAAT
1 -ATTAAGAAACCCCTAAAAATTAAGCTTAGTTTCTTTAAAAATTTATTTACAAAT
* *
1700238 ATGAAGAAACCCCTAAAAA-TCAGCTTAGTTTCTTTTAAAAATT
1 ATTAAGAAACCCCTAAAAATTAAGCTTAGTTTC-TTTAAAAATT
1700281 CATTGGAAAT
Statistics
Matches: 80, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
52 11 0.14
53 26 0.32
54 3 0.04
56 7 0.09
57 6 0.08
58 27 0.34
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.33
Consensus pattern (54 bp):
ATTAAGAAACCCCTAAAAATTAAGCTTAGTTTCTTTAAAAATTTATTTACAAAT
Found at i:1700255 original size:53 final size:53
Alignment explanation
Indices: 1700188--1700290 Score: 156
Period size: 53 Copynumber: 1.9 Consensus size: 53
1700178 AATTATCATT
1700188 AAGAAACCCCTAAAAATTAAGCTTAGATTC-TTTAAAAATT-ATTTGGAAATATG
1 AAGAAACCCCTAAAAA-TAAGCTTAGATTCTTTTAAAAATTCA-TTGGAAATATG
* *
1700241 AAGAAACCCCTAAAAATCAGCTTAGTTTCTTTTAAAAATTCATTGGAAAT
1 AAGAAACCCCTAAAAATAAGCTTAGATTCTTTTAAAAATTCATTGGAAAT
1700291 CATTATCAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
52 11 0.24
53 34 0.74
54 1 0.02
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.32
Consensus pattern (53 bp):
AAGAAACCCCTAAAAATAAGCTTAGATTCTTTTAAAAATTCATTGGAAATATG
Found at i:1700345 original size:64 final size:58
Alignment explanation
Indices: 1700182--1700392 Score: 220
Period size: 64 Copynumber: 3.6 Consensus size: 58
1700172 GTTTACAATT
* * * * *
1700182 ATCATTAAGAAACCCCTAAAAATTAAGCTTAGATTC-TTTAAAAATT-ATTTGG-AA--
1 ATCATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTTTTAAAAATTCA-TTGGAAATC
* *
1700236 AT-ATGAAGAAACCCCTAAAAATCA-GCTTAGTTTCTTTTAAAAATTCATTGGAAATC
1 ATCATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTTTTAAAAATTCATTGGAAATC
*
1700292 ATTATCAAGAAACCCCTGAAAATCAGGCTTAGCTTTTTTCTTTTATAAAAATTCATTGGAAATC
1 ATCATCAAGAAACCCCTGAAAATCAGGCTTAG----TTTC-TTT-TAAAAATTCATTGGAAATC
* *
1700356 GTCATCAAGAAATCCCTGAAAATCAGGCTTAGTTTCT
1 ATCATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCT
1700393 AAAACACTCG
Statistics
Matches: 136, Mismatches: 8, Indels: 21
0.82 0.05 0.13
Matches are distributed among these distances:
52 9 0.07
53 34 0.25
54 5 0.04
56 2 0.01
57 20 0.15
58 6 0.04
59 1 0.01
60 4 0.03
62 4 0.03
63 3 0.02
64 48 0.35
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (58 bp):
ATCATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTTTTAAAAATTCATTGGAAATC
Found at i:1702494 original size:16 final size:15
Alignment explanation
Indices: 1702473--1702564 Score: 69
Period size: 16 Copynumber: 6.0 Consensus size: 15
1702463 TTGGATATGT
1702473 TTTTTTTTCTTTTCTC
1 TTTTTTTTCTTTT-TC
* *
1702489 TTTTTTTTGTTTTTG
1 TTTTTTTTCTTTTTC
1702504 TTTTTTTTCTTATTTC
1 TTTTTTTTCTT-TTTC
* * * *
1702520 TTTCTTTTGTGTGT-
1 TTTTTTTTCTTTTTC
* * *
1702534 TTTTTTTGCTATATC
1 TTTTTTTTCTTTTTC
1702549 TTTTCTTTTCTTTTTC
1 TTTT-TTTTCTTTTTC
1702565 CTGTCCGTGT
Statistics
Matches: 57, Mismatches: 16, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
14 9 0.16
15 17 0.30
16 31 0.54
ACGTcount: A:0.03, C:0.12, G:0.07, T:0.78
Consensus pattern (15 bp):
TTTTTTTTCTTTTTC
Found at i:1702527 original size:26 final size:26
Alignment explanation
Indices: 1702472--1702539 Score: 68
Period size: 26 Copynumber: 2.5 Consensus size: 26
1702462 GTTGGATATG
* *
1702472 TTTTT-TTTTCTTTTCTCTTTTTTTTG
1 TTTTTGTTTT-TTTTCTCTTTTCTTTC
1702498 TTTTTGTTTTTTTTCT-TATTTCTTTC
1 TTTTTGTTTTTTTTCTCT-TTTCTTTC
1702524 TTTTGTGTGTTTTTTT
1 TTTT-TGT-TTTTTTT
1702540 TGCTATATCT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
25 1 0.03
26 21 0.58
27 7 0.19
28 7 0.19
ACGTcount: A:0.01, C:0.09, G:0.07, T:0.82
Consensus pattern (26 bp):
TTTTTGTTTTTTTTCTCTTTTCTTTC
Found at i:1702539 original size:31 final size:30
Alignment explanation
Indices: 1702472--1702540 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 30
1702462 GTTGGATATG
* *
1702472 TTTTTTTTTCTTTTCTCTTTTTTTTGTTTT
1 TTTTTTTTTCTTTTCTCTTTCTTTTGTTGT
1702502 TGTTTTTTTTCTTATT-TCTTTCTTTTGTGTGT
1 T-TTTTTTTTCTT-TTCTCTTTCTTTTGT-TGT
1702534 TTTTTTT
1 TTTTTTT
1702541 GCTATATCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 1 0.03
31 28 0.82
32 5 0.15
ACGTcount: A:0.01, C:0.09, G:0.07, T:0.83
Consensus pattern (30 bp):
TTTTTTTTTCTTTTCTCTTTCTTTTGTTGT
Found at i:1706348 original size:20 final size:22
Alignment explanation
Indices: 1706325--1706372 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 22
1706315 AAAACTAACT
1706325 AAATAAAACTAA-AAAAAT-T-A
1 AAATAAAAC-AATAAAAATGTAA
1706345 AAAT-AAACAATAAAAATGTAA
1 AAATAAAACAATAAAAATGTAA
1706366 AAATAAA
1 AAATAAA
1706373 TATAAAAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
18 2 0.08
19 10 0.42
20 5 0.21
21 5 0.21
22 2 0.08
ACGTcount: A:0.75, C:0.04, G:0.02, T:0.19
Consensus pattern (22 bp):
AAATAAAACAATAAAAATGTAA
Found at i:1707886 original size:23 final size:24
Alignment explanation
Indices: 1707860--1707911 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
1707850 GTTAGAGTTC
1707860 CGGGTCGGGT-TTGGTTTGGGCCT
1 CGGGTCGGGTCTTGGTTTGGGCCT
*
1707883 CGGGTCGGGTCTTGGTTTGGGCTT
1 CGGGTCGGGTCTTGGTTTGGGCCT
1707907 CGGGT
1 CGGGT
1707912 TTGGGTTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 10 0.37
24 17 0.63
ACGTcount: A:0.00, C:0.17, G:0.48, T:0.35
Consensus pattern (24 bp):
CGGGTCGGGTCTTGGTTTGGGCCT
Found at i:1711796 original size:2 final size:2
Alignment explanation
Indices: 1711789--1711813 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1711779 CATACTAACT
1711789 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1711814 TTTATTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1714502 original size:225 final size:222
Alignment explanation
Indices: 1714112--1714758 Score: 798
Period size: 225 Copynumber: 2.9 Consensus size: 222
1714102 GGTATATTAT
* * * *
1714112 TAATAAATATATCGGTAAGAGG-TTCATGAGCGTACCGATACACATATATG-ATTAGCCTTGGAA
1 TAATAAATGTATCGGTACG-GGATTCGTGAGCGTACCGATACACATATATGAATTAGCCTTCGAA
* * * * * *
1714175 TATGATTTCCCTCCCATTTTTATGAACCCTAATAGTTTAAAAAATGTCATTTGGTATACGCATAC
65 TATGATTTCCC-CCCATTTTTATCAACCCCAACAGTTT-AAAAATGTCATTTGGTGTACGCGTAT
* * * * *
1714240 CGATACTCGTGTAATATGTATCAGTACGAG-ATCATTTAGCTTAAATTCCAGAATGCTCAAACGG
128 CGATACCCGTGTAATACGTATCGGTACG-GTATCATTTAGCCTAAATTCCAGAATGCTCAAATGG
* *
1714304 TACCGATACCTCATTTGTATTGATACCTTAG
192 TACCGATACCTCATATGTATTGATACCATAG
* * * *
1714335 TAATAAATGTATTGGTACGGGATTCGTGAGCGTACTGATACACACATATGAATTAGCCTTTGAAT
1 TAATAAATGTATCGGTACGGGATTCGTGAGCGTACCGATACACATATATGAATTAGCCTTCGAAT
* *
1714400 ATGATTTCCTTCACCCATTTTTATCAACCCCAACAGTTTAAAAATGTCATTTGGTGTATGTGTAT
66 ATGATTTCC--C-CCCATTTTTATCAACCCCAACAGTTTAAAAATGTCATTTGGTGTACGCGTAT
* * ** *
1714465 CGATACCCATGTAATACGTATCGGTACGGTGTCATTTAGCCTAAATTTTAGAAAGCTCAAATGGT
128 CGATACCCGTGTAATACGTATCGGTACGGTATCATTTAGCCTAAATTCCAGAATGCTCAAATGGT
* * *
1714530 ACCGGTACCTCATATGTATTGGTACCATAT
193 ACCGATACCTCATATGTATTGATACCATAG
* * * *
1714560 TAATAAATGTACCAGTACAGGATTCGTGAGCGTACCGATACAC-TGTATGAATTAGCCTTCGAAT
1 TAATAAATGTATCGGTACGGGATTCGTGAGCGTACCGATACACATATATGAATTAGCCTTCGAAT
* ** * *
1714624 ATGATTTCCCCCTATTTTTATCAACTTCAACGGTTTAAATAATGTCATTTGGTGTGCGCGTATCG
66 ATGATTTCCCCCCATTTTTATCAACCCCAACAGTTTAAA-AATGTCATTTGGTGTACGCGTATCG
* * * *
1714689 ATACCCGTATAAAACGTACCGGTACGGTATCATTTAGCCTAAATACCAGAATGCTCAAATGGTAC
130 ATACCCGTGTAATACGTATCGGTACGGTATCATTTAGCCTAAATTCCAGAATGCTCAAATGGTAC
1714754 CGATA
195 CGATA
1714759 TAGGTACGTA
Statistics
Matches: 362, Mismatches: 56, Indels: 13
0.84 0.13 0.03
Matches are distributed among these distances:
221 25 0.07
222 85 0.23
223 41 0.11
224 50 0.14
225 137 0.38
226 24 0.07
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (222 bp):
TAATAAATGTATCGGTACGGGATTCGTGAGCGTACCGATACACATATATGAATTAGCCTTCGAAT
ATGATTTCCCCCCATTTTTATCAACCCCAACAGTTTAAAAATGTCATTTGGTGTACGCGTATCGA
TACCCGTGTAATACGTATCGGTACGGTATCATTTAGCCTAAATTCCAGAATGCTCAAATGGTACC
GATACCTCATATGTATTGATACCATAG
Found at i:1716634 original size:200 final size:203
Alignment explanation
Indices: 1716290--1716693 Score: 778
Period size: 200 Copynumber: 2.0 Consensus size: 203
1716280 ATATTTTTCA
1716290 TGCCTCGACAAAAATTTTCTGCTCACTTCACTTTACAATTTTTATTGACTCGGCCAAACTTTTTC
1 TGCCTCGACAAAAATTTTCTGCTCACTTCACTTTACAATTTTTATTGACTCGGCCAAACTTTTTC
1716355 CATCTTTTTATACCATTTGCCATTGTATATTTTCCTTGTTTATATCATTAAACTTATATACTTAG
66 CATCTTTTTATACCATTTGCCATTGTATATTTTCCTTGTTTATATCATTAAACTTATATACTTAG
1716420 GATTAGTTAGTGACACCTATTCCTAGCTATAGTAATC-TTTAAAAGCCCTCAAATCCCTGT-AGA
131 GATTAGTTAGTGACACCTATTCCTAGCTATAGTAATCTTTTAAAAGCCCTCAAATCCCTGTAAGA
1716483 CGATACTC
196 CGATACTC
1716491 TGCCTCGACAAAAATTTTCTGCTCACTTCAC-TTACAATTTTTATTGACTCGGCCAAACTTTTTC
1 TGCCTCGACAAAAATTTTCTGCTCACTTCACTTTACAATTTTTATTGACTCGGCCAAACTTTTTC
1716555 CATCTTTTTATACCATTTGCCATTGTATATTTTCCTTGTTTATATCATTAAACTTATATACTTAG
66 CATCTTTTTATACCATTTGCCATTGTATATTTTCCTTGTTTATATCATTAAACTTATATACTTAG
1716620 GATTAGTTAGTGACACCTATTCCTAGCTATAGTAATCTTTTAAAAGCCCTCAAATCCCTGTAGAG
131 GATTAGTTAGTGACACCTATTCCTAGCTATAGTAATCTTTTAAAAGCCCTCAAATCCCTGTA-AG
1716685 ACGATACTC
195 ACGATACTC
1716694 ACTCACTACT
Statistics
Matches: 200, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
200 135 0.68
201 54 0.27
203 11 0.05
ACGTcount: A:0.27, C:0.22, G:0.10, T:0.40
Consensus pattern (203 bp):
TGCCTCGACAAAAATTTTCTGCTCACTTCACTTTACAATTTTTATTGACTCGGCCAAACTTTTTC
CATCTTTTTATACCATTTGCCATTGTATATTTTCCTTGTTTATATCATTAAACTTATATACTTAG
GATTAGTTAGTGACACCTATTCCTAGCTATAGTAATCTTTTAAAAGCCCTCAAATCCCTGTAAGA
CGATACTC
Found at i:1719545 original size:40 final size:40
Alignment explanation
Indices: 1719501--1719702 Score: 359
Period size: 40 Copynumber: 5.0 Consensus size: 40
1719491 ACCGTAGTGC
1719501 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1719541 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
1719581 TACACATAAGGTCATGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* *
1719621 TACACATAAGATCATGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* *
1719661 TACACATAAGGTTGTGCCCACCATATACACCTAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1719701 TA
1 TA
1719703 TAAACCTGCA
Statistics
Matches: 156, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 156 1.00
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:1724802 original size:15 final size:15
Alignment explanation
Indices: 1724766--1724814 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
1724756 CACTAGTGAC
*
1724766 GACGACAATGACGGT
1 GACGACAATGACGGG
* *
1724781 GATGACAATGATGGG
1 GACGACAATGACGGG
* *
1724796 GACGACAGTGACGGC
1 GACGACAATGACGGG
1724811 GACG
1 GACG
1724815 GTAGTGATAA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.31, C:0.18, G:0.39, T:0.12
Consensus pattern (15 bp):
GACGACAATGACGGG
Found at i:1725076 original size:16 final size:16
Alignment explanation
Indices: 1725051--1725081 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1725041 ATAATTTAGT
1725051 TTTATGGTGCTCATCG
1 TTTATGGTGCTCATCG
*
1725067 TTTATTGTGCTCATC
1 TTTATGGTGCTCATC
1725082 AACGCTCGAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.19, G:0.19, T:0.48
Consensus pattern (16 bp):
TTTATGGTGCTCATCG
Found at i:1729438 original size:3 final size:3
Alignment explanation
Indices: 1729430--1729464 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
1729420 ATATAATGAT
*
1729430 ATA ATA ATA ATA ATA ATA ATA GTA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1729465 GCGATTTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1734052 original size:3 final size:3
Alignment explanation
Indices: 1734038--1734066 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1734028 ATTAATTATT
1734038 TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1734067 AACTATGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:1734433 original size:135 final size:133
Alignment explanation
Indices: 1734249--1734559 Score: 361
Period size: 135 Copynumber: 2.3 Consensus size: 133
1734239 AAATCAAGAA
* * * * * ** * *
1734249 ACGTTGACTCATTTCATTGTTCTTCATGGAAGATTGAATCTAGGTAGACTTGCTCTACTATCATT
1 ACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGACAGACTTGCTCCACTATCACT
* * * * *
1734314 CGGGGAATGTCAAATCTAGAAAGAGAGAGAGATGTTCCACTTTTTTCTTGAGGGCAAATCAGTTC
66 CAGGGAATATCAAATCTAGAAAGAGAGAGAGATATTCCAC-TTTTTCTTGAGGG-AAATCAGATA
1734379 TAGAG
129 TAGAG
* * * *
1734384 ACTTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGACAGACTTGTTCCACTGTTACT
1 ACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGACAGACTTGCTCCACTATCACT
* * ** * *
1734449 CAGGGAATATCAAATCTTGAAAGAGAGGGATCTATTCCACTTTTTCTTGAGGGAAATTAGATATG
66 CAGGGAATATCAAATCTAGAAAGAGAGAGAGATATTCCACTTTTTCTTGAGGGAAATCAGATATA
*
1734514 GGG
131 GAG
* *
1734517 ACGTTGATTCATTCCACTATTCTTCCGGGAAGATTGAATCGAG
1 ACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAG
1734560 TTCGATTTGT
Statistics
Matches: 148, Mismatches: 28, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
133 50 0.34
134 13 0.09
135 85 0.57
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (133 bp):
ACGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGACAGACTTGCTCCACTATCACT
CAGGGAATATCAAATCTAGAAAGAGAGAGAGATATTCCACTTTTTCTTGAGGGAAATCAGATATA
GAG
Found at i:1735824 original size:7 final size:7
Alignment explanation
Indices: 1735814--1735953 Score: 111
Period size: 7 Copynumber: 19.3 Consensus size: 7
1735804 TAATTTTTTA
1735814 TTTCTTT
1 TTTCTTT
1735821 TTTCTTT
1 TTTCTTT
*
1735828 ATTTTTATCT
1 -TTTCT-T-T
*
1735838 TTTCTCT
1 TTTCTTT
*
1735845 TTTCTCT
1 TTTCTTT
*
1735852 TTTCTCT
1 TTTCTTT
*
1735859 TTTCTCT
1 TTTCTTT
*
1735866 TTTCTAT
1 TTTCTTT
*
1735873 TTTCTAT
1 TTTCTTT
*
1735880 TTTCTAT
1 TTTCTTT
1735887 TTTCTATT
1 TTTCT-TT
1735895 TTCTCTTT
1 TT-TCTTT
*
1735903 TCTCTTT
1 TTTCTTT
*
1735910 TCTCTTT
1 TTTCTTT
*
1735917 TCTCTTT
1 TTTCTTT
1735924 TTTCTTT
1 TTTCTTT
1735931 TTT-TTCT
1 TTTCTT-T
1735938 TTTCTTT
1 TTTCTTT
*
1735945 TTTATTT
1 TTTCTTT
1735952 TT
1 TT
1735954 CATTTTTCAT
Statistics
Matches: 118, Mismatches: 8, Indels: 14
0.84 0.06 0.10
Matches are distributed among these distances:
6 2 0.02
7 95 0.81
8 12 0.10
9 8 0.07
10 1 0.01
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTCTTT
Found at i:1735852 original size:14 final size:14
Alignment explanation
Indices: 1735830--1735931 Score: 150
Period size: 14 Copynumber: 7.3 Consensus size: 14
1735820 TTTTCTTTAT
*
1735830 TTTTATCTTTTCTC
1 TTTTCTCTTTTCTC
1735844 TTTTCTCTTTTCTC
1 TTTTCTCTTTTCTC
*
1735858 TTTTCTCTTTTCTA
1 TTTTCTCTTTTCTC
* *
1735872 TTTTCTATTTTCTA
1 TTTTCTCTTTTCTC
*
1735886 TTTTCTATTTTCTC
1 TTTTCTCTTTTCTC
1735900 TTTTCTCTTTTCTC
1 TTTTCTCTTTTCTC
*
1735914 TTTTCTCTTTTTTC
1 TTTTCTCTTTTCTC
1735928 TTTT
1 TTTT
1735932 TTTTCTTTTC
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 82 1.00
ACGTcount: A:0.05, C:0.22, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTCTCTTTTCTC
Found at i:1735854 original size:21 final size:21
Alignment explanation
Indices: 1735830--1735931 Score: 150
Period size: 21 Copynumber: 4.9 Consensus size: 21
1735820 TTTTCTTTAT
* *
1735830 TTTTATCTTTTCTCTTTTCTC
1 TTTTCTCTTTTCTCTTTTCTA
1735851 TTTTCTCTTTTCTCTTTTCTA
1 TTTTCTCTTTTCTCTTTTCTA
* *
1735872 TTTTCTATTTTCTATTTTCTA
1 TTTTCTCTTTTCTCTTTTCTA
*
1735893 TTTTCTCTTTTCTCTTTTCTC
1 TTTTCTCTTTTCTCTTTTCTA
*
1735914 TTTTCTCTTTTTTCTTTT
1 TTTTCTCTTTTCTCTTTT
1735932 TTTTCTTTTC
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 73 1.00
ACGTcount: A:0.05, C:0.22, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTCTCTTTTCTCTTTTCTA
Done.