Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold30
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: 2650045
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.30
Warning! 144233 characters in sequence are not A, C, G, or T
File 8 of 17
Found at i:1118282 original size:30 final size:33
Alignment explanation
Indices: 1118247--1118308 Score: 94
Period size: 30 Copynumber: 2.0 Consensus size: 33
1118237 TCAATCTACA
1118247 TTTTTTCTTTTT-ATTTTATG-CTTT-TTTTTG
1 TTTTTTCTTTTTCATTTTATGTCTTTCTTTTTG
*
1118277 TTTTTTCTTTTTCATTTTGTGTCTTTCTTTTT
1 TTTTTTCTTTTTCATTTTATGTCTTTCTTTTT
1118309 TTCATCTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 12 0.43
31 7 0.25
32 4 0.14
33 5 0.18
ACGTcount: A:0.05, C:0.10, G:0.06, T:0.79
Consensus pattern (33 bp):
TTTTTTCTTTTTCATTTTATGTCTTTCTTTTTG
Found at i:1118317 original size:31 final size:30
Alignment explanation
Indices: 1118252--1118319 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 30
1118242 CTACATTTTT
* **
1118252 TCTTTTTATTTTATGCTTTTTTTTGTTTTT
1 TCTTTTTATTTTATGCTTTCTTTTGTTTCA
*
1118282 TCTTTTTCATTTTGTGTCTTTCTTTT-TTTCA
1 TCTTTTT-ATTTTATG-CTTTCTTTTGTTTCA
1118313 TCTTTTT
1 TCTTTTT
1118320 TTCTTTTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 7 0.22
31 17 0.53
32 8 0.25
ACGTcount: A:0.06, C:0.12, G:0.06, T:0.76
Consensus pattern (30 bp):
TCTTTTTATTTTATGCTTTCTTTTGTTTCA
Found at i:1122550 original size:52 final size:52
Alignment explanation
Indices: 1122472--1122600 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
1122462 CGAAATATGA
* *
1122472 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTACATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
*
1122524 AAATTTGCCTACATGTATCGATACATTTTATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTACATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
1122576 AAATTTGCCTACATGTATCGATACA
1 AAATTTGCCTACATGTATCGATACA
1122601 AAGATTAGTG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTACATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
Found at i:1122610 original size:52 final size:52
Alignment explanation
Indices: 1122472--1122620 Score: 203
Period size: 52 Copynumber: 2.9 Consensus size: 52
1122462 CGAAATATGA
* * *
1122472 AAATTTGCCTGCATGTATCGATACATTTCA-TAGTGTATCGATACATCTGGGC
1 AAATTTGCCTACATGTATCGATACA-ATCATTAGTGTATCGATACATCTAGGC
**
1122524 AAATTTGCCTACATGTATCGATAC-ATTTTATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTACATGTATCGATACAATCAT-TAGTGTATCGATACATCTAGGC
**
1122576 AAATTTGCCTACATGTATCGATACAAAGATTAGTGTATCGATACA
1 AAATTTGCCTACATGTATCGATACAATCATTAGTGTATCGATACA
1122621 ATGTATCGAT
Statistics
Matches: 86, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
50 1 0.01
52 83 0.97
53 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTACATGTATCGATACAATCATTAGTGTATCGATACATCTAGGC
Found at i:1122627 original size:13 final size:13
Alignment explanation
Indices: 1122609--1122633 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1122599 CAAAGATTAG
1122609 TGTATCGATACAA
1 TGTATCGATACAA
1122622 TGTATCGATACA
1 TGTATCGATACA
1122634 GTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1122719 original size:32 final size:33
Alignment explanation
Indices: 1122674--1122739 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 33
1122664 AGTAGCTTAA
*
1122674 ATTGTATCGATACAAAAC-TTATGTATCGATAC
1 ATTGTATCAATACAAAACTTTATGTATCGATAC
*
1122706 ATTGTATCAATACAACACTTTATGTATCGATAC
1 ATTGTATCAATACAAAACTTTATGTATCGATAC
1122739 A
1 A
1122740 AATCGTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 16 0.52
33 15 0.48
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.35
Consensus pattern (33 bp):
ATTGTATCAATACAAAACTTTATGTATCGATAC
Found at i:1124892 original size:13 final size:13
Alignment explanation
Indices: 1124874--1124898 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1124864 CTTATTCATT
1124874 TTTATTTAATTTA
1 TTTATTTAATTTA
1124887 TTTATTTAATTT
1 TTTATTTAATTT
1124899 TACTTTGGTT
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTATTTAATTTA
Found at i:1125393 original size:34 final size:35
Alignment explanation
Indices: 1125330--1125396 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
1125320 TTGTGAAGGT
* *
1125330 ATAAGCACAAAGGAATACAAATGAGCTTTGAAAGA
1 ATAAGAACAAAGGAATACAAAAGAGCTTTGAAAGA
**
1125365 ATAAGAACAAA-GAATACAAAAGCTCTTTGAAA
1 ATAAGAACAAAGGAATACAAAAGAGCTTTGAAA
1125397 TGTAGAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 18 0.64
35 10 0.36
ACGTcount: A:0.54, C:0.12, G:0.16, T:0.18
Consensus pattern (35 bp):
ATAAGAACAAAGGAATACAAAAGAGCTTTGAAAGA
Found at i:1125689 original size:20 final size:20
Alignment explanation
Indices: 1125647--1125701 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
1125637 GTTGGGCTCA
* *
1125647 ATGTATTGATACATTTCACC
1 ATGTATTGATACAATCCACC
**
1125667 ATGTATTGATACAATCCTTC
1 ATGTATTGATACAATCCACC
*
1125687 ATGTATCGATACAAT
1 ATGTATTGATACAAT
1125702 GTGAGTTTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (20 bp):
ATGTATTGATACAATCCACC
Found at i:1127478 original size:34 final size:35
Alignment explanation
Indices: 1127440--1127506 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
1127430 CCTTACAACA
1127440 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
1127474 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
1127507 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:1127982 original size:13 final size:13
Alignment explanation
Indices: 1127964--1127989 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1127954 CAATTTTTTG
1127964 TGTATCGATACAT
1 TGTATCGATACAT
1127977 TGTATCGATACAT
1 TGTATCGATACAT
1127990 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1128001 original size:32 final size:33
Alignment explanation
Indices: 1127944--1128007 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1127934 TATAAGCCAA
**
1127944 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
1127977 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
1128008 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:1128680 original size:40 final size:41
Alignment explanation
Indices: 1128634--1128724 Score: 116
Period size: 39 Copynumber: 2.3 Consensus size: 41
1128624 TTTTCTTTCT
*
1128634 CCCTTAATTAAAG-TAATTTTAACAAATTTGTACATTCTCC
1 CCCTTAATTAAAGATAATTTTAACAAATTTATACATTCTCC
* *
1128674 CCCTTAA-T-AAGATAATTTTAGCAAATTTATGCATTCTCC
1 CCCTTAATTAAAGATAATTTTAACAAATTTATACATTCTCC
* *
1128713 CCTTTTATTAAA
1 CCCTTAATTAAA
1128725 AAAAATCTCC
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
38 3 0.07
39 30 0.70
40 8 0.19
41 2 0.05
ACGTcount: A:0.34, C:0.20, G:0.05, T:0.41
Consensus pattern (41 bp):
CCCTTAATTAAAGATAATTTTAACAAATTTATACATTCTCC
Found at i:1129171 original size:20 final size:21
Alignment explanation
Indices: 1129130--1129173 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1129120 GTTTATGCAG
1129130 GTTCTCCCCCTTAATACGAAA
1 GTTCTCCCCCTTAATACGAAA
* *
1129151 GTTCTTCCCTTTAATAC-AAA
1 GTTCTCCCCCTTAATACGAAA
1129171 GTT
1 GTT
1129174 TATACAAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.27, C:0.27, G:0.09, T:0.36
Consensus pattern (21 bp):
GTTCTCCCCCTTAATACGAAA
Found at i:1130233 original size:23 final size:24
Alignment explanation
Indices: 1130188--1130234 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1130178 CAAAGAATTG
*
1130188 AACACAAATTCAATGAAGCACAAA
1 AACACAAATTCAATGAAGAACAAA
1130212 AACACAAA-TCAATTGAA-AACAAA
1 AACACAAATTCAA-TGAAGAACAAA
1130235 TTTTCAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.62, C:0.19, G:0.06, T:0.13
Consensus pattern (24 bp):
AACACAAATTCAATGAAGAACAAA
Found at i:1131268 original size:84 final size:84
Alignment explanation
Indices: 1131113--1131277 Score: 192
Period size: 84 Copynumber: 2.0 Consensus size: 84
1131103 CATTTTCCAC
* * * *
1131113 TTGCAACTCATTTCTTTTCTCCTCTAATCCATTTATTTTCTTTTTAAAAGAATTATTTTCTAAAC
1 TTGCAACTCATTTCTATTCTCCTCTAATCCACTTAATTTCTTTTTAAAAGAATTATTCTCTAAAC
1131178 TCATTGATTTACTTTCATT
66 TCATTGATTTACTTTCATT
* * *
1131197 TTGCAACTC-TTTCATATTCTTCTCTAATTCACTTAATTTC-TTTT-CAAGAATATCATTCTCTA
1 TTGCAACTCATTTC-TATTCTCCTCTAATCCACTTAATTTCTTTTTAAAAGAAT-T-ATTCTCTA
* * *
1131259 CACTTATTGATTTATTTTC
63 AACTCATTGATTTACTTTC
1131278 TTCTTTGAGT
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
82 6 0.09
83 9 0.13
84 53 0.78
ACGTcount: A:0.25, C:0.20, G:0.04, T:0.52
Consensus pattern (84 bp):
TTGCAACTCATTTCTATTCTCCTCTAATCCACTTAATTTCTTTTTAAAAGAATTATTCTCTAAAC
TCATTGATTTACTTTCATT
Found at i:1134015 original size:13 final size:13
Alignment explanation
Indices: 1133997--1134022 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1133987 CAATTTTTTG
1133997 TGTATCGATACAT
1 TGTATCGATACAT
1134010 TGTATCGATACAT
1 TGTATCGATACAT
1134023 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1134034 original size:32 final size:33
Alignment explanation
Indices: 1133977--1134040 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1133967 TATAAGCCAA
**
1133977 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
1134010 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
1134041 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:1134783 original size:49 final size:49
Alignment explanation
Indices: 1134574--1134929 Score: 395
Period size: 48 Copynumber: 7.3 Consensus size: 49
1134564 ACACCATAAA
* * * *
1134574 ATGCTGATTCAAGGCCAGCGATATTAGACTTAAAGGTGCCAAAGGCGCCAAT
1 ATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG---AAGGTGCCAAT
* *
1134626 ATGCTGATTCAAGGCCGGCGATATTGGACTTAAAGATGAA-GTGCCAAT
1 ATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAAT
* * *
1134674 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA-CAAGGTGCCAAT
1 ATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAAT
* *
1134722 ATGCTGATTCAAGGCCAGCTATATTGGGCTTAAAGGTGAAGGTGCCAAT
1 ATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAAT
*
1134771 ATGCTAATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGCCAAT
1 ATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAAT
* * * *
1134814 GTGCTGATTCAAGGCCGGCTAGATTGGACTTAAAGATGAAGGTACCAAT
1 ATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAAT
* * * ** * * *
1134863 GTGCCGATTCAAGGCCAACTATATTGGGTTTAAAAGATAAAGGCGCTAAT
1 ATGCTGATTCAAGGCCAGCTATATTGGACTT-AAAGATGAAGGTGCCAAT
*
1134913 ATGCTGGTTCAAGGCCA
1 ATGCTGATTCAAGGCCA
1134930 ACGATATCAG
Statistics
Matches: 260, Mismatches: 35, Indels: 20
0.83 0.11 0.06
Matches are distributed among these distances:
43 38 0.15
47 3 0.01
48 79 0.30
49 77 0.30
50 28 0.11
52 35 0.13
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (49 bp):
ATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAAT
Found at i:1134846 original size:92 final size:93
Alignment explanation
Indices: 1134614--1134898 Score: 385
Period size: 92 Copynumber: 3.0 Consensus size: 93
1134604 TAAAGGTGCC
* *
1134614 AAAGGCGCCAATATGCTGATTCAAGGCCGGCGATATTGGACTTAAAGATGAA-GTGCCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCGGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
*
1134678 TGATTCAAGGCCAGCTACATTGGACTTAAA
66 TGATTCAAGGCCAGCTATATTGGACTT--A
* * * *
1134708 GACAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAAGGTGAAGGTGCCAATAT
1 -A-AAGGTGCCAATATGCTGATTCAAGGCCGGCTATATTGGACTTAAAGATGAAGGTGCCAATGT
*
1134773 GCTAATTCAAGGCCAGCTATATTGGACTT-
64 GCTGATTCAAGGCCAGCTATATTGGACTTA
* * *
1134802 AAAGGTGCCAATGTGCTGATTCAAGGCCGGCTAGATTGGACTTAAAGATGAAGGTACCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCGGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
* * **
1134867 CGATTCAAGGCCAACTATATTGGGTTTA
66 TGATTCAAGGCCAGCTATATTGGACTTA
1134895 AAAG
1 AAAG
1134899 ATAAAGGCGC
Statistics
Matches: 167, Mismatches: 20, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
92 79 0.47
93 5 0.03
95 1 0.01
96 46 0.28
97 36 0.22
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (93 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCGGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
TGATTCAAGGCCAGCTATATTGGACTTA
Found at i:1135023 original size:28 final size:28
Alignment explanation
Indices: 1134966--1135117 Score: 189
Period size: 28 Copynumber: 5.3 Consensus size: 28
1134956 CACCAACTTG
** *
1134966 TGTGGGCTTTTGAAAGGTTTGCGTC-AACT
1 TGTGGGCTTTT-AAAGG-TTGCCACTGACT
* *
1134995 TGTGTGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
*
1135023 TGTGGGCTTTTAAAGATTGCCACTGACT
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
1135051 TGTGGGCTTTTAAAGGTTGCCACTGACT
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
* *
1135079 TGTGGGCTTTTGAAAAGGGTGCCACTAACT
1 TGTGGGCTTTT--AAAGGTTGCCACTGACT
1135109 TGTGGGCTT
1 TGTGGGCTT
1135118 AAAAGGAAAA
Statistics
Matches: 109, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
27 5 0.05
28 70 0.64
29 10 0.09
30 24 0.22
ACGTcount: A:0.18, C:0.16, G:0.30, T:0.36
Consensus pattern (28 bp):
TGTGGGCTTTTAAAGGTTGCCACTGACT
Found at i:1135120 original size:84 final size:84
Alignment explanation
Indices: 1134966--1135122 Score: 201
Period size: 86 Copynumber: 1.8 Consensus size: 84
1134956 CACCAACTTG
** * * *
1134966 TGTGGGCTTTTGAAAGGTTTGCGTCAACTTGTGTGCTTTTGAAGGTTGCCACTGACTTGTGGGCT
1 TGTGGGCTTTTGAAAGGTTTGCCACAACTTGTGGGCTTTTGAAGGGTGCCACTAACTTGTGGGC-
1135031 TTTAAAGATTGCCACTGACT
65 TTTAAAGATTGCCACTGACT
*
1135051 TGTGGGCTTTT-AAAGG-TTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGG
1 TGTGGGCTTTTGAAAGGTTTGCCAC-AACTTGTGGGCTTTTG--AAGGGTGCCACTAACTTGTGG
*
1135114 GCTTAAAAG
63 GCTTTAAAG
1135123 GAAAAAGAGT
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
83 5 0.08
84 19 0.31
85 17 0.27
86 21 0.34
ACGTcount: A:0.20, C:0.16, G:0.29, T:0.35
Consensus pattern (84 bp):
TGTGGGCTTTTGAAAGGTTTGCCACAACTTGTGGGCTTTTGAAGGGTGCCACTAACTTGTGGGCT
TTAAAGATTGCCACTGACT
Found at i:1135146 original size:34 final size:35
Alignment explanation
Indices: 1135108--1135182 Score: 107
Period size: 35 Copynumber: 2.2 Consensus size: 35
1135098 TGCCACTAAC
* *
1135108 TTGTGGGCTTA-AAAGGAAAAAGAGTGCTACGGAG
1 TTGTGGGCTTACAAAAGAAAAAGAGTGCCACGGAG
* *
1135142 TTGTGAGCTTACAAAAGAAAAAGAGTGCCATGGAG
1 TTGTGGGCTTACAAAAGAAAAAGAGTGCCACGGAG
1135177 TTGTGG
1 TTGTGG
1135183 ACTTTGGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
34 10 0.29
35 25 0.71
ACGTcount: A:0.35, C:0.09, G:0.33, T:0.23
Consensus pattern (35 bp):
TTGTGGGCTTACAAAAGAAAAAGAGTGCCACGGAG
Found at i:1135209 original size:29 final size:29
Alignment explanation
Indices: 1135160--1135331 Score: 197
Period size: 29 Copynumber: 5.9 Consensus size: 29
1135150 TTACAAAAGA
* *
1135160 AAAAGAGTGCCA-TGGAGTTGTGGACTTTGG
1 AAAAGA-TGCCACT-GACTTGTGGGCTTTGG
* *
1135190 AAAAGATGCCACCGACTTGTGGGCTTCGG
1 AAAAGATGCCACTGACTTGTGGGCTTTGG
* *
1135219 AAAAGGGTGCCACTGATTTGTGGGCTTT-G
1 AAAA-GATGCCACTGACTTGTGGGCTTTGG
* * * *
1135248 -AAGGTTGCCACTGACTTGTGGACTTTGA
1 AAAAGATGCCACTGACTTGTGGGCTTTGG
*
1135276 AAAAGATGCCACTGACTTGTGGGCTTTGA
1 AAAAGATGCCACTGACTTGTGGGCTTTGG
1135305 AAAAGATGCCACTGACTTGTGGGCTTT
1 AAAAGATGCCACTGACTTGTGGGCTTT
1135332 TGAAGGGTGA
Statistics
Matches: 122, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
27 20 0.16
28 2 0.02
29 75 0.61
30 25 0.20
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.28
Consensus pattern (29 bp):
AAAAGATGCCACTGACTTGTGGGCTTTGG
Found at i:1135334 original size:86 final size:86
Alignment explanation
Indices: 1135177--1135337 Score: 252
Period size: 86 Copynumber: 1.9 Consensus size: 86
1135167 TGCCATGGAG
* * * *
1135177 TTGTGGACTTTGGAAAAGATGCCACCGACTTGTGGGCTTCGGAAAAGGGTGCCACTGATTTGTGG
1 TTGTGGACTTTGAAAAAGATGCCACCGACTTGTGGGCTTCGGAAAAAGATGCCACTGACTTGTGG
1135242 GCTTTGAAGGTTGCCACTGAC
66 GCTTTGAAGGTTGCCACTGAC
* *
1135263 TTGTGGACTTTGAAAAAGATGCCACTGACTTGTGGGCTT-TGAAAAAGATGCCACTGACTTGTGG
1 TTGTGGACTTTGAAAAAGATGCCACCGACTTGTGGGCTTCGGAAAAAGATGCCACTGACTTGTGG
1135327 GCTTTTGAAGG
66 GC-TTTGAAGG
1135338 GTGAGGAATG
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
85 23 0.34
86 45 0.66
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (86 bp):
TTGTGGACTTTGAAAAAGATGCCACCGACTTGTGGGCTTCGGAAAAAGATGCCACTGACTTGTGG
GCTTTGAAGGTTGCCACTGAC
Found at i:1136787 original size:16 final size:15
Alignment explanation
Indices: 1136768--1136808 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
1136758 ATCCGGACCC
1136768 TTTTTGTTGTTGTTTT
1 TTTTTGTT-TTGTTTT
1136784 TTTTTGTTTTGTTTT
1 TTTTTGTTTTGTTTT
*
1136799 TTTTTCTTTT
1 TTTTTGTTTT
1136809 TTCTGTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 16 0.67
16 8 0.33
ACGTcount: A:0.00, C:0.02, G:0.12, T:0.85
Consensus pattern (15 bp):
TTTTTGTTTTGTTTT
Found at i:1136826 original size:24 final size:24
Alignment explanation
Indices: 1136781--1136826 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
1136771 TTGTTGTTGT
* *
1136781 TTTTTTTTGTTTTGTTTTTTTTTC
1 TTTTTTCTGTTTTGTTTATTTTTC
1136805 TTTTTTCTGTTTAT-TTTATTTT
1 TTTTTTCTGTTT-TGTTTATTTT
1136827 ATTTTATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 18 0.95
25 1 0.05
ACGTcount: A:0.04, C:0.04, G:0.07, T:0.85
Consensus pattern (24 bp):
TTTTTTCTGTTTTGTTTATTTTTC
Found at i:1136827 original size:10 final size:10
Alignment explanation
Indices: 1136814--1136845 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
1136804 CTTTTTTCTG
1136814 TTTATTTTAT
1 TTTATTTTAT
1136824 TTTATTTTAT
1 TTTATTTTAT
1136834 TTTATTTT-T
1 TTTATTTTAT
1136843 TTT
1 TTT
1136846 GTGGAGGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTATTTTAT
Found at i:1136834 original size:15 final size:14
Alignment explanation
Indices: 1136781--1136845 Score: 62
Period size: 14 Copynumber: 4.6 Consensus size: 14
1136771 TTGTTGTTGT
* *
1136781 TTTTTTTTGTTTTG
1 TTTTTTTTATTTTA
1136795 TTTTTTTT-TCTTT-
1 TTTTTTTTAT-TTTA
*
1136808 TTTCTGTTTATTTTA
1 TTT-TTTTTATTTTA
1136823 TTTTATTTTATTTTA
1 TTTT-TTTTATTTTA
1136838 TTTTTTTT
1 TTTTTTTT
1136846 GTGGAGGATG
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
13 4 0.09
14 23 0.52
15 17 0.39
ACGTcount: A:0.08, C:0.03, G:0.05, T:0.85
Consensus pattern (14 bp):
TTTTTTTTATTTTA
Found at i:1147217 original size:46 final size:46
Alignment explanation
Indices: 1147150--1147240 Score: 146
Period size: 46 Copynumber: 2.0 Consensus size: 46
1147140 GCACCCTGAG
* *
1147150 TCTAGGCCCATCGCGGGTTTGGAAAATTGGGTTTGATTTGGTGGAA
1 TCTAGGCCCATCGCGGGTTTGGAAAATCGGGTTTGATTCGGTGGAA
**
1147196 TCTAGGCCCATCGCGGGTTTGGCGAATCGGGTTTGATTCGGTGGA
1 TCTAGGCCCATCGCGGGTTTGGAAAATCGGGTTTGATTCGGTGGA
1147241 TGTATTTCCC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.16, C:0.16, G:0.36, T:0.31
Consensus pattern (46 bp):
TCTAGGCCCATCGCGGGTTTGGAAAATCGGGTTTGATTCGGTGGAA
Found at i:1149878 original size:20 final size:20
Alignment explanation
Indices: 1149853--1149900 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
1149843 TGGAGGTGCT
**
1149853 AAACATGCTGTAAATGCATG
1 AAACATGCTCAAAATGCATG
1149873 AAACATAGCTCAAAATGCATG
1 AAACAT-GCTCAAAATGCATG
*
1149894 AATCATG
1 AAACATG
1149901 GGCTGTTAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.23
Consensus pattern (20 bp):
AAACATGCTCAAAATGCATG
Found at i:1150813 original size:52 final size:53
Alignment explanation
Indices: 1150735--1150866 Score: 230
Period size: 52 Copynumber: 2.5 Consensus size: 53
1150725 CCCGAAATAT
*
1150735 GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATTGATACATCT-GG
1 GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGG
*
1150787 GAAAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTAGG
1 GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGG
*
1150840 GCAAATTTGCCTGCATGTATCGATACA
1 GAAAATTTGCCTGCATGTATCGATACA
1150867 AAGATCAGTG
Statistics
Matches: 76, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
52 48 0.63
53 28 0.37
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35
Consensus pattern (53 bp):
GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGG
Found at i:1150981 original size:32 final size:33
Alignment explanation
Indices: 1150940--1151001 Score: 108
Period size: 32 Copynumber: 1.9 Consensus size: 33
1150930 AGTAGCTTAA
1150940 ATTGTATCGATACAAAAC-TTATGTATCGAGAC
1 ATTGTATCGATACAAAACTTTATGTATCGAGAC
*
1150972 ATTGTATCGATACAACACTTTATGTATCGA
1 ATTGTATCGATACAAAACTTTATGTATCGA
1151002 TACAAATCGT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAACTTTATGTATCGAGAC
Found at i:1153271 original size:13 final size:13
Alignment explanation
Indices: 1153253--1153277 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1153243 CTTATTCATT
1153253 TTTATTTAATTTA
1 TTTATTTAATTTA
1153266 TTTATTTAATTT
1 TTTATTTAATTT
1153278 TACTTTGGTT
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTATTTAATTTA
Found at i:1154052 original size:20 final size:20
Alignment explanation
Indices: 1154027--1154081 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
1154017 GTTGGGCTCA
* *
1154027 ATGTATCGATACATTTCACC
1 ATGTATCGATACAATCCACC
* **
1154047 ATGTATTGATACAATCCTTC
1 ATGTATCGATACAATCCACC
1154067 ATGTATCGATACAAT
1 ATGTATCGATACAAT
1154082 GTGAGTTTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACAATCCACC
Found at i:1164582 original size:33 final size:32
Alignment explanation
Indices: 1164540--1164603 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
1164530 CACACCCAGA
*
1164540 TGTATCGATACATATTGCTTGGTATTGATACAT
1 TGTATCGATACATATT-CTTGGTATCGATACAT
* *
1164573 TGTATCGATACATGTTCTTTGTATCGATACA
1 TGTATCGATACATATTCTTGGTATCGATACA
1164604 CCACAAAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.42
Consensus pattern (32 bp):
TGTATCGATACATATTCTTGGTATCGATACAT
Found at i:1165745 original size:9 final size:9
Alignment explanation
Indices: 1165733--1165774 Score: 50
Period size: 9 Copynumber: 4.4 Consensus size: 9
1165723 TTTCTCTCTT
1165733 TTTTTTCTC
1 TTTTTTCTC
1165742 TTTTCTT-TC
1 TTTT-TTCTC
1165751 TTTTCTTTCTC
1 -TTT-TTTCTC
1165762 TTTTTTCTC
1 TTTTTTCTC
1165771 TTTT
1 TTTT
1165775 CTTTTTTCAG
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
9 16 0.55
10 10 0.34
11 3 0.10
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTTCTC
Found at i:1165747 original size:20 final size:20
Alignment explanation
Indices: 1165722--1165779 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
1165712 TGTATTCTAA
1165722 TTTTCTCTCTTTTTTTTCTC
1 TTTTCTCTCTTTTTTTTCTC
* *
1165742 TTTTCTTTCTTTTCTTTCTC
1 TTTTCTCTCTTTTTTTTCTC
*
1165762 TTTTTTCTCTTTTCTTTT
1 TTTTCTCTCTTTT-TTTT
1165780 TTCAGCTGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 29 0.91
21 3 0.09
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTTCTCTCTTTTTTTTCTC
Found at i:1165765 original size:29 final size:29
Alignment explanation
Indices: 1165722--1165778 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
1165712 TGTATTCTAA
*
1165722 TTTTCTCTCTTTTTTTTCTCTTTTCTTTC
1 TTTTCTCTCTCTTTTTTCTCTTTTCTTTC
*
1165751 TTTTCTTTCTCTTTTTTCTCTTTTCTTT
1 TTTTCTCTCTCTTTTTTCTCTTTTCTTT
1165779 TTTCAGCTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (29 bp):
TTTTCTCTCTCTTTTTTCTCTTTTCTTTC
Found at i:1166126 original size:21 final size:21
Alignment explanation
Indices: 1166083--1166127 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1166073 CATATAAAAT
**
1166083 AAATTAATAAAATTAAATTTA
1 AAATTAATAAAATTAAAACTA
*
1166104 AAATTAATAAAGTTAAAACTA
1 AAATTAATAAAATTAAAACTA
1166125 AAA
1 AAA
1166128 ACTAATTCTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (21 bp):
AAATTAATAAAATTAAAACTA
Found at i:1166560 original size:164 final size:165
Alignment explanation
Indices: 1166366--1166728 Score: 473
Period size: 164 Copynumber: 2.2 Consensus size: 165
1166356 TATGGAGTAA
* * * *
1166366 AAAACTTGGTTTTTCGAAAATAGAAAAATTTCAAGGAAAAATTGAAAAACTCATGAAAATGAAAG
1 AAAACTTCGTATTCCGAAAATAGAAAAATTTCAAAGAAAAATTGAAAAACTCATGAAAATGAAAG
* *
1166431 AATTTTTGAAAACTAATTTACTATGAAATAAAAAATAATTTTTGATGAATTTTAAAAATTAAAAA
66 AATTTTTGAAAACTAATTTAATATGAAATAAAAAATAATATTTGATGAATTTTAAAAATTAAAAA
1166496 CCA-AAAACAATCC-CCCAAAAAAATTACAGAGG-AG
131 CCATAAAA-AATCCTCCCAAAAAAATTAC-GAGGTAG
* * *
1166530 AAAACTTCGTATTCCGAAAATTGGAAAATTTCAAAGAAAAATTGAAAAACTCATGAAAATGAATG
1 AAAACTTCGTATTCCGAAAATAGAAAAATTTCAAAGAAAAATTGAAAAACTCATGAAAATGAAAG
* * * ** *
1166595 AATTTTTTAGAACTAATTTAATATGAATTAAATGATAATATTTGATGACTTTTAAAAATTAAAAA
66 AATTTTTGAAAACTAATTTAATATGAAATAAAAAATAATATTTGATGAATTTTAAAAATTAAAAA
* * *
1166660 CCATGAAAAATCCTCTCGAAAAAATTACGAGGTAG
131 CCATAAAAAATCCTCCCAAAAAAATTACGAGGTAG
* * * *
1166695 AAAACTCCATATTGTCG-AAATAGAAAAAGTTCAA
1 AAAACTTCGTATT-CCGAAAATAGAAAAATTTCAA
1166729 GTAAAAAATG
Statistics
Matches: 171, Mismatches: 24, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
164 127 0.74
165 42 0.25
166 2 0.01
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.28
Consensus pattern (165 bp):
AAAACTTCGTATTCCGAAAATAGAAAAATTTCAAAGAAAAATTGAAAAACTCATGAAAATGAAAG
AATTTTTGAAAACTAATTTAATATGAAATAAAAAATAATATTTGATGAATTTTAAAAATTAAAAA
CCATAAAAAATCCTCCCAAAAAAATTACGAGGTAG
Found at i:1174775 original size:13 final size:13
Alignment explanation
Indices: 1174756--1174786 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1174746 ACAATTCATC
1174756 ATGTATCGATACA
1 ATGTATCGATACA
*
1174769 TTGTATCGATACA
1 ATGTATCGATACA
1174782 ATGTA
1 ATGTA
1174787 CCATGTATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1174781 original size:33 final size:33
Alignment explanation
Indices: 1174737--1174801 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
1174727 TTAGAAGCAA
* *
1174737 TGTATCCATACAAT-TCATCATGTATCGATACAT
1 TGTATCCATACAATGT-ACCATGTATCAATACAT
*
1174770 TGTATCGATACAATGTACCATGTATCAATACA
1 TGTATCCATACAATGTACCATGTATCAATACA
1174802 AACAGTGGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.34
Consensus pattern (33 bp):
TGTATCCATACAATGTACCATGTATCAATACAT
Found at i:1174876 original size:19 final size:19
Alignment explanation
Indices: 1174831--1174886 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
1174821 CTGCCAGTTT
**
1174831 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
1174851 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
* * *
1174870 TATGTATTGGTACAATG
1 CATGTATCGATACAATG
1174887 TATCGATACA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1177210 original size:180 final size:180
Alignment explanation
Indices: 1176809--1177332 Score: 761
Period size: 180 Copynumber: 2.9 Consensus size: 180
1176799 GACTACACAA
* * *
1176809 TTTTTAAAAAATATTAATTTTAGGG-AAACTAAATTTTTCTAAATTTTTAAATTTAACTTTTAAA
1 TTTTTAAAAAATATTAA-TTT-GGGAAAACCAAATTTTTCTAAATTCTTAAATTTAACTTCT-AA
* ** ** *
1176873 TTTTGAAAATTATGTTTCATACCGGACGGAAAATCAAGGGATACAAAAGGTGTTAAAAAAATTTT
63 TTTTGAAAATTATGTTTCGTACCCAACAAAAAATCAAGGGATACGAAAGGTGTT-AAAAAATTTT
1176938 CATACCCCTACGGAAAACCATAGGGATATGAAAACATAAACGACCTCATATTCT
127 CATACCCCTACGGAAAACCATAGGGATATGAAAACATAAACGACCTCATATTCT
* * * *
1176992 TTTTT--TAAATATTAATTTAGGAAAACCGAATCTTTCTAAATTCTTAAATTTAACTTCTAATTT
1 TTTTTAAAAAATATTAATTTGGGAAAACCAAATTTTTCTAAATTCTTAAATTTAACTTCTAATTT
** *
1177055 CAAAAATTATGTTTCGTACCCAACAAAAAATCAGGGGATACGAAAGGTGTTAAAAAATTTTCATA
66 TGAAAATTATGTTTCGTACCCAACAAAAAATCAAGGGATACGAAAGGTGTTAAAAAATTTTCATA
* * *
1177120 CCTCAACAGAAAACCATAGGGATATGAAAACATAAACGACCTCATATT-T
131 CCCCTACGGAAAACCATAGGGATATGAAAACATAAACGACCTCATATTCT
1177169 TTTTTAAAAAAATATTAATTTGGGAAAACCAAATTTTTCTAAATTCTTAAATTTAACTTCTAATT
1 TTTTT-AAAAAATATTAATTTGGGAAAACCAAATTTTTCTAAATTCTTAAATTTAACTTCTAATT
*
1177234 TTGAAAATTATGTTTCGTACCCAACAGAAAAACCAAGGGATACGAAAGGTGTT-AAAAATTTTCA
65 TTGAAAATTATGTTTCGTACCCAACA-AAAAATCAAGGGATACGAAAGGTGTTAAAAAATTTTCA
* *
1177298 TACCCCTACGGAAAATCATAGGAATATGAAAACAT
129 TACCCCTACGGAAAACCATAGGGATATGAAAACAT
1177333 GACTCGAGTG
Statistics
Matches: 304, Mismatches: 32, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
177 6 0.02
178 59 0.19
179 49 0.16
180 152 0.50
181 33 0.11
183 5 0.02
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.33
Consensus pattern (180 bp):
TTTTTAAAAAATATTAATTTGGGAAAACCAAATTTTTCTAAATTCTTAAATTTAACTTCTAATTT
TGAAAATTATGTTTCGTACCCAACAAAAAATCAAGGGATACGAAAGGTGTTAAAAAATTTTCATA
CCCCTACGGAAAACCATAGGGATATGAAAACATAAACGACCTCATATTCT
Found at i:1178835 original size:25 final size:26
Alignment explanation
Indices: 1178792--1178853 Score: 92
Period size: 25 Copynumber: 2.5 Consensus size: 26
1178782 TTCGTTGGTG
1178792 TCTTCATTGC-TGCAACTTAATTGCT
1 TCTTCATTGCATGCAACTTAATTGCT
* *
1178817 TTTTCATTGCAT-CAGCTTAATTGCT
1 TCTTCATTGCATGCAACTTAATTGCT
1178842 TCTTCATTGCAT
1 TCTTCATTGCAT
1178854 TATTTCAACT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
25 32 0.97
26 1 0.03
ACGTcount: A:0.19, C:0.23, G:0.11, T:0.47
Consensus pattern (26 bp):
TCTTCATTGCATGCAACTTAATTGCT
Found at i:1179025 original size:14 final size:14
Alignment explanation
Indices: 1179002--1179070 Score: 59
Period size: 14 Copynumber: 4.9 Consensus size: 14
1178992 GGCGTGAAAC
*
1179002 ATGCACGAAATGTA
1 ATGCATGAAATGTA
*
1179016 ATGCATGAAATGAA
1 ATGCATGAAATGTA
* * *
1179030 CATTACGTGAAATG-C
1 -A-TGCATGAAATGTA
*
1179045 ATGCATGAAAAGTA
1 ATGCATGAAATGTA
1179059 ATGCATGAAATG
1 ATGCATGAAATG
1179071 AAAATTACGT
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
13 8 0.19
14 24 0.57
15 1 0.02
16 9 0.21
ACGTcount: A:0.43, C:0.12, G:0.22, T:0.23
Consensus pattern (14 bp):
ATGCATGAAATGTA
Found at i:1179043 original size:25 final size:24
Alignment explanation
Indices: 1179015--1179098 Score: 83
Period size: 25 Copynumber: 3.7 Consensus size: 24
1179005 CACGAAATGT
1179015 AATGCATGAAATGAACATTACGTGA
1 AATGCATGAAATGAA-ATTACGTGA
*
1179040 AATGCATG-CATGAAA--A-GT--
1 AATGCATGAAATGAAATTACGTGA
1179058 AATGCATGAAATGAAAATTACGTGA
1 AATGCATGAAATG-AAATTACGTGA
*
1179083 AATGCATG-CATGAAAT
1 AATGCATGAAATGAAAT
1179099 GCATGAAAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
18 8 0.16
19 3 0.06
20 5 0.10
21 1 0.02
22 1 0.02
23 7 0.14
24 8 0.16
25 16 0.33
ACGTcount: A:0.45, C:0.11, G:0.20, T:0.24
Consensus pattern (24 bp):
AATGCATGAAATGAAATTACGTGA
Found at i:1179048 original size:43 final size:43
Alignment explanation
Indices: 1178994--1179099 Score: 171
Period size: 43 Copynumber: 2.5 Consensus size: 43
1178984 GAACTCATGG
* *
1178994 CGTGAAA--CATGCACGAAATGTAATGCATGAAATGAACATTA
1 CGTGAAATGCATGCATGAAATGTAATGCATGAAATGAAAATTA
*
1179035 CGTGAAATGCATGCATGAAAAGTAATGCATGAAATGAAAATTA
1 CGTGAAATGCATGCATGAAATGTAATGCATGAAATGAAAATTA
1179078 CGTGAAATGCATGCATGAAATG
1 CGTGAAATGCATGCATGAAATG
1179100 CATGAAAATA
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
41 7 0.12
43 52 0.88
ACGTcount: A:0.43, C:0.12, G:0.22, T:0.23
Consensus pattern (43 bp):
CGTGAAATGCATGCATGAAATGTAATGCATGAAATGAAAATTA
Found at i:1179168 original size:10 final size:9
Alignment explanation
Indices: 1179148--1179203 Score: 51
Period size: 10 Copynumber: 5.7 Consensus size: 9
1179138 TAATTCGGGT
1179148 TTTTTCTTTA
1 TTTTT-TTTA
1179158 TTTTTTATTA
1 TTTTTT-TTA
1179168 TTATTTTTTA
1 TT-TTTTTTA
1179178 TATACTTTTTTA
1 T-T--TTTTTTA
1179190 -TTTTTTTA
1 TTTTTTTTA
1179198 TTTTTT
1 TTTTTT
1179204 ATAAATGTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
8 7 0.17
9 6 0.15
10 15 0.38
11 5 0.12
12 7 0.17
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:1181362 original size:23 final size:23
Alignment explanation
Indices: 1181336--1181384 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
1181326 AACCAAGATT
1181336 TTCAATTTCTTTTCCATGATCAC
1 TTCAATTTCTTTTCCATGATCAC
*
1181359 TTCAATTTCTTTTTCATGATCAC
1 TTCAATTTCTTTTCCATGATCAC
1181382 TTC
1 TTC
1181385 TTATACTAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.20, C:0.24, G:0.04, T:0.51
Consensus pattern (23 bp):
TTCAATTTCTTTTCCATGATCAC
Found at i:1184818 original size:63 final size:63
Alignment explanation
Indices: 1184714--1184874 Score: 232
Period size: 63 Copynumber: 2.6 Consensus size: 63
1184704 ACATGCTTCT
* ** * *
1184714 ATGTATCGATACAATTCATAATGTATCGATACAATGCATTTGATATTCTAGCCGTTGGGCTCA
1 ATGTATCAATACAATTCACCATGTATCGATACAATGCATTTGAAATTCTAGCCGTTGAGCTCA
* * * *
1184777 ATGTATCAATATAATTTACCATGTATCGATACAATGTATTTGAAATTCTAGCTGTTGAGCTCA
1 ATGTATCAATACAATTCACCATGTATCGATACAATGCATTTGAAATTCTAGCCGTTGAGCTCA
*
1184840 ATGTATCGATACAATTCACCATGTATCGATACAAT
1 ATGTATCAATACAATTCACCATGTATCGATACAAT
1184875 TCAATTATAA
Statistics
Matches: 86, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
63 86 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (63 bp):
ATGTATCAATACAATTCACCATGTATCGATACAATGCATTTGAAATTCTAGCCGTTGAGCTCA
Found at i:1184865 original size:20 final size:20
Alignment explanation
Indices: 1184840--1184877 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1184830 GTTGAGCTCA
1184840 ATGTATCGATACAATTCACC
1 ATGTATCGATACAATTCACC
1184860 ATGTATCGATACAATTCA
1 ATGTATCGATACAATTCA
1184878 ATTATAAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.32
Consensus pattern (20 bp):
ATGTATCGATACAATTCACC
Found at i:1186736 original size:167 final size:166
Alignment explanation
Indices: 1186542--1187324 Score: 825
Period size: 167 Copynumber: 4.7 Consensus size: 166
1186532 CATTACTTTT
** * *
1186542 AATTCATCAAACCTTATTATTTATTTCATAGTAAATTAGTATTCAAAAATTCCTTCATTTTCATT
1 AATTCATCAAATATTATTATTTATTTCATATTAAATTAGTTTTCAAAAATTCCTTCATTTTCATT
* *
1186607 AGTTTTTGAATTTTTTCCTTAAAATTTCCTTTTTTTCTAAATACGAAGTTTTTTACTCTGTAAAT
66 AGTTTTTG-ATTTTTTCCTTAAAATTTCCTTTTTTTCGAAATACGAAGTTTTCTACTCTGTAAAT
*
1186672 TTTTTTGGGGAGATTTTTCTTAGTTTTTAATTTTTTA
130 TTTTTTGGGGAGATTTTTCTTAGTTTTTAATTTTTAA
* * * * *
1186709 AATTCATAAAATATTATTATATATTTCATATTAAATCAGTTTTTAAAAATTCCTTCATTTTCGTT
1 AATTCATCAAATATTATTATTTATTTCATATTAAATTAGTTTTCAAAAATTCCTTCATTTTCATT
* * * *
1186774 AGTTTTTGATTTTTTTCTTCAAATTTCTCTCTTTTT-GAAATA-TAGAGTTTTCTACTCTGTAAA
66 AGTTTTTGATTTTTTCCTTAAAATTTC-CTTTTTTTCGAAATACGA-AGTTTTCTACTCTGTAAA
*** * *
1186837 TTTTTCCAAGGG-GATTTTTCTTGGTTTTTAA-ATTTAA
129 TTTTT-TTGGGGAGATTTTTCTTAGTTTTTAATTTTTAA
* *
1186874 AATTCATCAAATATTATTATTTATTTCATATTAAATTATTTTTCAAAAATTCCTTCATTTTCACT
1 AATTCATCAAATATTATTATTTATTTCATATTAAATTAGTTTTCAAAAATTCCTTCATTTTCATT
* * * * * *
1186939 AGTTTTTGATTTTTTCCTTGAAATTTTCTTGTTTTCAAAATACGAAATTTTCCT-CTCCGTAAAT
66 AGTTTTTGATTTTTTCCTTAAAATTTCCTTTTTTTCGAAATACGAAGTTTT-CTACTCTGTAAAT
**
1187003 TTTTTTAGGGTGA-ATTTTTCTCTTTTTTTTAATTTTTAA
130 TTTTTT-GGG-GAGATTTTTCT-TAGTTTTTAATTTTTAA
* * * * ** * *
1187042 AATTCAT-AAATATTATTATTTATTTTATGTTTAATTATTTTTCAAAAATTTATTTATTTTCATG
1 AATTCATCAAATATTATTATTTATTTCATATTAAATTAGTTTTCAAAAATTCCTTCATTTTCATT
* * *** * * * * *
1187106 AGTTTTTAAATTTTTTCCTTAAAATTTTC-TTGCATGGAAATATGAGGTTTTCTAATC-GTAATT
66 AGTTTTT-GATTTTTTCCTTAAAATTTCCTTTTTTTCGAAATACGAAGTTTTCTACTCTGTAAAT
1187169 TTTTTTGGCGGAG--TTTTCTTAGTTTTTAATTTTTAA
130 TTTTTTGG-GGAGATTTTTCTTAGTTTTTAATTTTTAA
* * ** * * * *
1187205 AATCCATCAGATATTATTATTTATTTCATATTAAATCCGTTTTCAAAAATTCATTCCTATTCATG
1 AATTCATCAAATATTATTATTTATTTCATATTAAATTAGTTTTCAAAAATTCCTTCATTTTCATT
* * * *
1187270 ACTTTTTGATTTTTTCCTTGAAA-TTCTCTTTTTTTCGAAAAACTGAATTTTTCTA
66 AGTTTTTGATTTTTTCCTTAAAATTTC-CTTTTTTTCGAAATAC-GAAGTTTTCTA
1187325 TTCCATAAAT
Statistics
Matches: 507, Mismatches: 90, Indels: 40
0.80 0.14 0.06
Matches are distributed among these distances:
162 2 0.00
163 36 0.07
164 72 0.14
165 125 0.25
166 88 0.17
167 153 0.30
168 31 0.06
ACGTcount: A:0.28, C:0.11, G:0.08, T:0.53
Consensus pattern (166 bp):
AATTCATCAAATATTATTATTTATTTCATATTAAATTAGTTTTCAAAAATTCCTTCATTTTCATT
AGTTTTTGATTTTTTCCTTAAAATTTCCTTTTTTTCGAAATACGAAGTTTTCTACTCTGTAAATT
TTTTTGGGGAGATTTTTCTTAGTTTTTAATTTTTAA
Found at i:1187148 original size:332 final size:329
Alignment explanation
Indices: 1186542--1187334 Score: 913
Period size: 332 Copynumber: 2.4 Consensus size: 329
1186532 CATTACTTTT
** * *
1186542 AATTCATCAAACCTTATTATTTATTTCATAGTAAATTAGTATTCAAAAATTCCTTCATTTTCATT
1 AATTCATCAAATATTATTATTTATTTCATATTAAATTAGTTTTCAAAAATTCCTTCATTTTCA-T
* * * * * *
1186607 AGTTTTTGAATTTTTTCCTTAAAATTTCCTTTTTTTCTAAATACGAAGTTTTTTACTCTGTAAAT
65 AGTTTTTG-ATTTTTTCCTTGAAATTTTCTTTTTTTCAAAATACGAAATTTTCTACTCCGTAAAT
*
1186672 TTTTTTGGGGAGATTTTTCTTAGTTTTTAATTTTTTAAATTCATAAAATATTATTATATATTTCA
129 TTTTTTGGGGAGATTTTTCTTAGTTTTTAATTTTTAAAATTCATAAAATATTATTATATATTTCA
* * * * * *
1186737 TATTAAATCAGTTTTTAAAAATTCCTTCATTTTCGTTAGTTTTTGATTTTTTTCTTCAAATTTCT
194 TATTAAATCAGTTTTTAAAAATTCATTCATTTTCATGAGTTTTTAATTTTTTCCTTAAAATTTCT
** * * * *
1186802 CTCTTTTTGAAATAT-AGAGTTTTCTACTCTGTAAATTTTTCCAAGG-GGATTTTTCTTGGTTTT
259 CTCTCATGGAAATATGAG-GTTTTCTAATC-GT-AATTTTT-CAAGGCGGAGTTTTCTTAGTTTT
1186865 TAA-ATTTAA
320 TAATATTTAA
*
1186874 AATTCATCAAATATTATTATTTATTTCATATTAAATTATTTTTCAAAAATTCCTTCATTTTCACT
1 AATTCATCAAATATTATTATTTATTTCATATTAAATTAGTTTTCAAAAATTCCTTCATTTTCA-T
*
1186939 AGTTTTTGATTTTTTCCTTGAAATTTTCTTGTTTTCAAAATACGAAATTTTCCT-CTCCGTAAAT
65 AGTTTTTGATTTTTTCCTTGAAATTTTCTTTTTTTCAAAATACGAAATTTT-CTACTCCGTAAAT
** *
1187003 TTTTTTAGGGTGA-ATTTTTCTCTTTTTTTTAATTTTTAAAATTCAT-AAATATTATTATTTATT
129 TTTTTT-GGG-GAGATTTTTCT-TAGTTTTTAATTTTTAAAATTCATAAAATATTATTATATATT
* * * * * *
1187066 TTATGTTTAATTA-TTTTTCAAAAATTTATTTATTTTCATGAGTTTTTAAATTTTTTCCTTAAAA
191 TCATATTAAATCAGTTTTT-AAAAATTCATTCATTTTCATGAGTTTTT-AATTTTTTCCTTAAAA
***
1187130 TTT-TCT-TGCATGGAAATATGAGGTTTTCTAATCGTAATTTTTTTTGGCGGAGTTTTCTTAGTT
254 TTTCTCTCT-CATGGAAATATGAGGTTTTCTAATCGTAATTTTTCAAGGCGGAGTTTTCTTAGTT
*
1187193 TTTAATTTTTAA
318 TTTAATATTTAA
* * ** * * *
1187205 AATCCATCAGATATTATTATTTATTTCATATTAAATCCGTTTTCAAAAATTCATTCCTATTCATG
1 AATTCATCAAATATTATTATTTATTTCATATTAAATTAGTTTTCAAAAATTCCTTCATTTTCAT-
* * * * *
1187270 ACTTTTTGATTTTTTCCTTGAAATTCTCTTTTTTTCGAAAA-ACTGAATTTTTCTATTCCATAAA
65 AGTTTTTGATTTTTTCCTTGAAATTTTCTTTTTTTC-AAAATAC-GAAATTTTCTACTCCGTAAA
1187334 T
128 T
1187335 ATTTCCAAGG
Statistics
Matches: 394, Mismatches: 53, Indels: 28
0.83 0.11 0.06
Matches are distributed among these distances:
329 2 0.01
330 26 0.07
331 158 0.40
332 167 0.42
333 41 0.10
ACGTcount: A:0.28, C:0.11, G:0.08, T:0.53
Consensus pattern (329 bp):
AATTCATCAAATATTATTATTTATTTCATATTAAATTAGTTTTCAAAAATTCCTTCATTTTCATA
GTTTTTGATTTTTTCCTTGAAATTTTCTTTTTTTCAAAATACGAAATTTTCTACTCCGTAAATTT
TTTTGGGGAGATTTTTCTTAGTTTTTAATTTTTAAAATTCATAAAATATTATTATATATTTCATA
TTAAATCAGTTTTTAAAAATTCATTCATTTTCATGAGTTTTTAATTTTTTCCTTAAAATTTCTCT
CTCATGGAAATATGAGGTTTTCTAATCGTAATTTTTCAAGGCGGAGTTTTCTTAGTTTTTAATAT
TTAA
Found at i:1188230 original size:33 final size:33
Alignment explanation
Indices: 1188188--1188250 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
1188178 TGGGACAATG
* **
1188188 TATCGATACAATTTGTTATGTATCGATACATTA
1 TATCGATACAATGTGCCATGTATCGATACATTA
1188221 TATCGATACAATGTGCCATGTATCGATACA
1 TATCGATACAATGTGCCATGTATCGATACA
1188251 AACAGTGCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (33 bp):
TATCGATACAATGTGCCATGTATCGATACATTA
Found at i:1188326 original size:19 final size:20
Alignment explanation
Indices: 1188280--1188333 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 20
1188270 CTGCCAGTTT
*
1188280 CATGTATCGATACAATTGTA
1 CATGTATCGATACAATTGAA
*
1188300 CGTGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
1188319 CATGTATCGATACAA
1 CATGTATCGATACAA
1188334 AGCATTATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:1188345 original size:20 final size:19
Alignment explanation
Indices: 1188280--1188350 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
1188270 CTGCCAGTTT
* *
1188280 CATGTATCGATACAATTGTA
1 CATGTATCGATACAA-AGAA
* *
1188300 CGTGTATCGATACAATGAA
1 CATGTATCGATACAAAGAA
*
1188319 CATGTATCGATACAAAGCAT
1 CATGTATCGATACAAAG-AA
*
1188339 TATGTATCGATA
1 CATGTATCGATA
1188351 TATCTGGATA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
19 18 0.41
20 26 0.59
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (19 bp):
CATGTATCGATACAAAGAA
Found at i:1189196 original size:20 final size:20
Alignment explanation
Indices: 1189173--1189277 Score: 84
Period size: 20 Copynumber: 4.7 Consensus size: 20
1189163 AAGTACCCAG
1189173 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
1189193 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
1189213 ATGTATCGATACATTCTGTCTTTTTACGCA
1 ATGTATCGATACA-------TTTTT---CA
1189243 GATGTATCGATACATTTTTCA
1 -ATGTATCGATACATTTTTCA
1189264 ATGTATCGATACAT
1 ATGTATCGATACAT
1189278 CTAGTTAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 22
0.71 0.06 0.23
Matches are distributed among these distances:
20 44 0.65
21 2 0.03
24 5 0.07
27 3 0.04
30 1 0.01
31 13 0.19
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1192756 original size:77 final size:77
Alignment explanation
Indices: 1192660--1192839 Score: 292
Period size: 77 Copynumber: 2.3 Consensus size: 77
1192650 GTTTTAAAGT
*
1192660 TCTCC-CCTTTGATAAAATAATAAAGGCTCTCTTAAGGAAAAATTTCTCCCCCTTTTTGTTATTT
1 TCTCCTCC-TTGATAAAATAATAAAGGCTCTCTTAAGAAAAAATTTCTCCCCCTTTTTGTTATTT
1192724 CTCCCTAAAAATA
65 CTCCCTAAAAATA
*
1192737 TCTCCTCCTTGATAAAATAATAAAGGCTCTCTTAAGAAAAAATTTCTCCCTCTTTTTGTTATTTC
1 TCTCCTCCTTGATAAAATAATAAAGGCTCTCTTAAGAAAAAATTTCTCCCCCTTTTTGTTATTTC
* *
1192802 TCCCTTAAAATT
66 TCCCTAAAAATA
1192814 TCT-CTCCCTTGATAAAATAATAAAGG
1 TCTCCT-CCTTGATAAAATAATAAAGG
1192840 TAGAAATTTA
Statistics
Matches: 97, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
76 2 0.02
77 93 0.96
78 2 0.02
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.38
Consensus pattern (77 bp):
TCTCCTCCTTGATAAAATAATAAAGGCTCTCTTAAGAAAAAATTTCTCCCCCTTTTTGTTATTTC
TCCCTAAAAATA
Found at i:1193841 original size:13 final size:13
Alignment explanation
Indices: 1193823--1193848 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1193813 TACACAAAGT
1193823 ATGTATCGATACA
1 ATGTATCGATACA
1193836 ATGTATCGATACA
1 ATGTATCGATACA
1193849 CCAAAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1193935 original size:20 final size:22
Alignment explanation
Indices: 1193904--1193947 Score: 74
Period size: 20 Copynumber: 2.1 Consensus size: 22
1193894 ACTATATTTT
1193904 CAAATATGTATCGATACA-TCA
1 CAAATATGTATCGATACATTCA
1193925 CAAAT-TGTATCGATACATTCA
1 CAAATATGTATCGATACATTCA
1193946 CA
1 CA
1193948 CGGAAAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (22 bp):
CAAATATGTATCGATACATTCA
Found at i:1201929 original size:15 final size:15
Alignment explanation
Indices: 1201911--1201941 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1201901 TGAGTCAACT
1201911 TCATCATTATCTTCA
1 TCATCATTATCTTCA
1201926 TCATCATTATCTTCA
1 TCATCATTATCTTCA
1201941 T
1 T
1201942 TATCTTTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (15 bp):
TCATCATTATCTTCA
Found at i:1203584 original size:33 final size:33
Alignment explanation
Indices: 1203542--1203606 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
1203532 TTTGGGACAA
* **
1203542 TGTATCGATACAATTTGTTATGTATCAATACAT
1 TGTATCGATACAATGTGCCATGTATCAATACAT
1203575 TGTATCGATACAATGTGCCATGTATCAATACA
1 TGTATCGATACAATGTGCCATGTATCAATACA
1203607 AACAATGGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (33 bp):
TGTATCGATACAATGTGCCATGTATCAATACAT
Found at i:1204234 original size:20 final size:20
Alignment explanation
Indices: 1204211--1204250 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1204201 ACTAGTTTGT
1204211 TGGAAACTAGTGTAGTTAGC
1 TGGAAACTAGTGTAGTTAGC
1204231 TGGAAACTAGTGTAGTTAGC
1 TGGAAACTAGTGTAGTTAGC
1204251 CTCCAATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.10, G:0.30, T:0.30
Consensus pattern (20 bp):
TGGAAACTAGTGTAGTTAGC
Found at i:1204548 original size:20 final size:20
Alignment explanation
Indices: 1204524--1204569 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1204514 AAACTAAGCA
1204524 AAAAAAG-GAAAAAAAAGAAAG
1 AAAAAAGAG-AAAAAAA-AAAG
*
1204545 AAAAAAGAGAAAAAAACAAG
1 AAAAAAGAGAAAAAAAAAAG
1204565 AAAAA
1 AAAAA
1204570 TAGCAAAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 8 0.35
21 14 0.61
22 1 0.04
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (20 bp):
AAAAAAGAGAAAAAAAAAAG
Found at i:1206200 original size:13 final size:13
Alignment explanation
Indices: 1206182--1206241 Score: 69
Period size: 13 Copynumber: 5.1 Consensus size: 13
1206172 ACATTATGCT
1206182 TTGTATCGATACA
1 TTGTATCGATACA
1206195 TTGTATCGATACA
1 TTGTATCGATACA
*
1206208 -TG-A---AGA-A
1 TTGTATCGATACA
1206215 TTGTATCGATACA
1 TTGTATCGATACA
1206228 TTGTATCGATACA
1 TTGTATCGATACA
1206241 T
1 T
1206242 GAAGAATTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
7 1 0.03
8 4 0.10
9 1 0.03
11 1 0.03
12 4 0.10
13 28 0.72
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1206207 original size:33 final size:33
Alignment explanation
Indices: 1206182--1206258 Score: 154
Period size: 33 Copynumber: 2.3 Consensus size: 33
1206172 ACATTATGCT
1206182 TTGTATCGATACATTGTATCGATACATGAAGAA
1 TTGTATCGATACATTGTATCGATACATGAAGAA
1206215 TTGTATCGATACATTGTATCGATACATGAAGAA
1 TTGTATCGATACATTGTATCGATACATGAAGAA
1206248 TTGTATCGATA
1 TTGTATCGATA
1206259 TATTATGCCC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (33 bp):
TTGTATCGATACATTGTATCGATACATGAAGAA
Found at i:1206219 original size:20 final size:20
Alignment explanation
Indices: 1206194--1206258 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
1206184 GTATCGATAC
1206194 ATTGTATCGATACATGAAGA
1 ATTGTATCGATACATGAAGA
1206214 ATTGTATCGATAC-------
1 ATTGTATCGATACATGAAGA
1206227 ATTGTATCGATACATGAAGA
1 ATTGTATCGATACATGAAGA
1206247 ATTGTATCGATA
1 ATTGTATCGATA
1206259 TATTATGCCC
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 13 0.34
20 25 0.66
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (20 bp):
ATTGTATCGATACATGAAGA
Found at i:1208242 original size:10 final size:10
Alignment explanation
Indices: 1208227--1208282 Score: 51
Period size: 10 Copynumber: 5.6 Consensus size: 10
1208217 TCTTTCACGT
1208227 TTTTTTTGAA
1 TTTTTTTGAA
**
1208237 TTTTTTT-CT
1 TTTTTTTGAA
**
1208246 TTTATTTTTTA
1 TTT-TTTTGAA
*
1208257 TTTTTTTGGA
1 TTTTTTTGAA
1208267 TTTTTTTGAA
1 TTTTTTTGAA
1208277 TTTTTT
1 TTTTTT
1208283 AAATTATTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
9 3 0.08
10 31 0.84
11 3 0.08
ACGTcount: A:0.12, C:0.02, G:0.07, T:0.79
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:1208881 original size:42 final size:42
Alignment explanation
Indices: 1208781--1210587 Score: 959
Period size: 42 Copynumber: 42.7 Consensus size: 42
1208771 AAGAAAAGAT
* * *
1208781 TCTCCCGGGTCAAAGCCAACAGGCAGAC-TGAGGGAT-AGGAAAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTA--GATGAGG-AAG
* * * *
1208824 TCTCCAAGGCCAAAGCCAACAGGCAGACTTTAGATGAGGTAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTAGATGAGGAAG
* * * * * *
1208866 TCTCTAGGGTCAAAGCCAACAAGAAGGCTTTAGATGAGGTAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTAGATGAGGAAG
* * * * *
1208908 TATCCAAGGTCAAAGCCGACAGGTAGAC-TAAGGGAT-AGGAAAC
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTA--GATGAGG-AAG
* *
1208951 TCTCCAGGGTCAAAGCCAACAGGCAGACTTTAGATGAGGCAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTAGATGAGGAAG
* * * ***
1208993 TCTCCAAGGTCAAAGCCGACAGGAAGTCTGCGGGAT-AGGAAAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACT-TTAGATGAGG-AAG
* * * * * *
1209036 TCTCTAAGGTCAAGGCCAACAAGCAGACTTTAGATGAGGCAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTAGATGAGGAAG
* * * * **
1209078 TTTCCAGGGTCAAAGTCGACAGGCAAAC-TAAGGGGTAGGAAAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTAGATG-AGG-AAG
* * * *
1209121 TCTCTAAGGTCAAAGCCAACAGGCAGACTTTAGAT-AAGACAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTAGATGAGGA-AG
* * *
1209163 TCTCTAGGGTCAAAGCCGATAGGCAGAC-TAAGGGAT-AGGAAAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTA--GATGAGG-AAG
* * * *
1209206 TGTCCAAGGTCAAAGCC-ACCAAGCAGACTTTAGATGAGGTAG
1 TCTCCAGGGTCAAAGCCGA-CAGGCAGACTTTAGATGAGGAAG
* * * * * * * *
1209248 TCTCTAGGGTCAAAGCTGACAAGTAGAC-TAAGGGTG-GAAAAC
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTA-GATGAG-GAAG
* * * * *
1209290 TCTTCAGGGTCAGAGCCGACAGGTAGACTTTAGAT-AAGACAA
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTAGATGAGGA-AG
* * * * * * *
1209332 TCTCCAAGGTCAAAGCCAAGAAGCAGAC-TAAG-GGTAGAAAAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTAGATG-AG-GAAG
**
1209374 TCTCCAGGGTCAAAGCCGACAGGCAGACTGAAGGAT-AGGAAAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTA-GATGAGG-AAG
* * * *
1209417 TCTCCACGGTCAAAGCCAACAAGCAGACTTTAGATGAGGCAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTAGATGAGGAAG
* * * * *
1209459 TCTCTAGGGTCAAAACTGATAGGCAGAC-TAAGGGAT-AGGAAAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTA--GATGAGG-AAG
* * *
1209502 TCTCTAGGGTCAAAGCCGACAGGCAGA-ATGAGGGAT-AGGAAAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTA--GATGAGG-AAG
* * * * * *
1209545 TCTCTAAGATCAAAGTCGACAGGCAAACTTTAGATGAGGCAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTAGATGAGGAAG
* *
1209587 TCTCCAGGGTCAAAGCCGACAAGCAGAC-TAAGGGAT-AGGAAAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTA--GATGAGG-AAG
* *
1209630 TCTCCAAGGTCAAAGCCGACAGGCAAACTTTAGAT-AGGGCAA-
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTAGATGA-GG-AAG
* * * * *
1209672 TCTTCAGAGTCAAAACCGATAGGCAGACTTTAGATAAGGCAA-
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTAGATGAGG-AAG
** * * * * *
1209714 TCT-CTTGGTCAAATCCGACAGGTAGAC-TAAG-GGTAGAAAAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTAGATG-AG-GAAG
* * * **
1209755 TCTCCAGGGTCAAAGCTGACAGACAGAC-TAAGGGGTAGGAAAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTAGATG-AGG-AAG
* * *
1209798 TCTCTAGGGTCAAAGCCAACAGGTAGACTTTAGATGA-GACAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTAGATGAGGA-AG
* * *
1209840 TCTCTAGGGTCAAAGCCGATAGGCAGAC-TGAGGGAT-AGGAAAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTA--GATGAGG-AAG
* * * *
1209883 TGTCCAAGGTCAAAGCC-ACCAGGCAGACTTTAGATGAAGTAG
1 TCTCCAGGGTCAAAGCCGA-CAGGCAGACTTTAGATGAGGAAG
* * * * * * * *
1209925 TCTCTAGGGTCAAAGCTGACAAGTAGAC-TAAGGGTG-GAAAAC
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTA-GATGAG-GAAG
** * * *
1209967 TCTTTAGGGTCAGAGCCGACAGGTAGACTTTAGAT-AAGACAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTAGATGAGGA-AG
* * * * * *
1210009 TCTCCAAGGTCAAAGTCGACAAGCAGAC-TAAG-GGTAGAAAAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTAGATG-AG-GAAG
* * *
1210051 TCTCCAAGGTCAAAGCCGATAGGCAGAC-TGAGGGAT-AGGAAAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTA--GATGAGG-AAG
* * * * *
1210094 TCTCCACGGTCAAAGCCAACAAGCAAACTTTAGATGAGGCAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTAGATGAGGAAG
* * *
1210136 TCTCCAGGGTCAAAACCGATAGGCAGAC-TAAGGGAT-AGGAAAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTA--GATGAGG-AAG
* *
1210179 TCTCCAGGGTCAAAGCCGACAGGCAGA-ATGAGGGAT-AGGAAAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTA--GATGAGG-AAG
* * * * *
1210222 TCTCTAAGATCAAAGCCGACAGGCAAACTTTAGATGAGGCAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTAGATGAGGAAG
* *
1210264 TCTCCAGGGTCAAAGCCGACAAGCAGAC-TGAGGGAT-AGGAAAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTA--GATGAGG-AAG
* *
1210307 TCTCCAGGGTCAAAGCCGATAGGCAGACTTTAGAT-AGGGCAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTAGATGA-GGAAG
* * * * *
1210349 TCTTCAGAGTCAAAACCGATAGGCAGACTTTAGATAAGGCAA-
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTAGATGAGG-AAG
** * * * * * * *
1210391 TCTCTTGGGTCAAATCCAACAGGTAGA-GTAAG-GGTAGAAAAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTAGATG-AG-GAAG
* *
1210433 TCTCCAGGGTCAAAGCCAATAGGCAGACTTTAGATGAGGCAA-
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTAGATGAGG-AAG
* * * * * *
1210475 TCTCCAAGGTCAAATCCGACAAGCAGAC-TAAG-GGTAGAAAAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTAGATG-AG-GAAG
*
1210517 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTAGAT-AGGGCAG
1 TCTCCAGGGTCAAAGCCGACAGGCAGACTTTAGATGA-GGAAG
*
1210559 TCTCCAGGGCCAAAGCCGACAGGCAGACT
1 TCTCCAGGGTCAAAGCCGACAGGCAGACT
1210588 GAAGTAGGAA
Statistics
Matches: 1347, Mismatches: 316, Indels: 203
0.72 0.17 0.11
Matches are distributed among these distances:
40 8 0.01
41 68 0.05
42 738 0.55
43 503 0.37
44 30 0.02
ACGTcount: A:0.35, C:0.20, G:0.28, T:0.17
Consensus pattern (42 bp):
TCTCCAGGGTCAAAGCCGACAGGCAGACTTTAGATGAGGAAG
Found at i:1208955 original size:127 final size:126
Alignment explanation
Indices: 1208788--1210587 Score: 554
Period size: 127 Copynumber: 14.2 Consensus size: 126
1208778 GATTCTCCCG
* *
1208788 GGTCAAAGCCAACAGGCAGACTGAGGGATAGGAAAGTCTCCAAGGCCAAAGCCAACAGGCAGACT
1 GGTCAAAGCCAACAGGCAGACTAAGGGATAGGAAAGTCTCCAAGGTCAAAGCCAACAGGCAGACT
* * * * * *
1208853 TTAGATGAGGTAGTCTCTAGGGTCAAAGCCAACAAGAAGGCTTTAGATGAGGTAGTATCCAA
66 TTAGATGAGGTAGTCTCTAAGGTCAAAGCCAACAGGAAGACTTTAGAT-AGGAAGTCTCTAA
* * * *
1208915 GGTCAAAGCCGACAGGTAGACTAAGGGATAGGAAACTCTCCAGGGTCAAAGCCAACAGGCAGACT
1 GGTCAAAGCCAACAGGCAGACTAAGGGATAGGAAAGTCTCCAAGGTCAAAGCCAACAGGCAGACT
* * * * ***
1208980 TTAGATGAGGCAGTCTCCAAGGTCAAAGCCGACAGGAAGTCTGCGGGATAGGAAAGTCTCTAA
66 TTAGATGAGGTAGTCTCTAAGGTCAAAGCCAACAGGAAGACT-TTAGATAGG-AAGTCTCTAA
* * * * * * * * *
1209043 GGTCAAGGCCAACAAGCAGACTTTA--GATGAGG-CAGTTTCCAGGGTCAAAGTCGACAGGCAAA
1 GGTCAAAGCCAACAGGCAGAC-TAAGGGAT-AGGAAAGTCTCCAAGGTCAAAGCCAACAGGCAGA
* ** * * *
1209105 C-TAAGGGGTAGGAAAGTCTCTAAGGTCAAAGCCAACAGGCAGACTTTAGATAAGACAGTCTCTA
64 CTTTAGATG-AGG-TAGTCTCTAAGGTCAAAGCCAACAGGAAGACTTTAGATAGGA-AGTCTCTA
*
1209169 G
126 A
* * * * *
1209170 GGTCAAAGCCGATAGGCAGACTAAGGGATAGGAAAGTGTCCAAGGTCAAAGCCACCAAGCAGACT
1 GGTCAAAGCCAACAGGCAGACTAAGGGATAGGAAAGTCTCCAAGGTCAAAGCCAACAGGCAGACT
* ** * * * * ** *
1209235 TTAGATGAGGTAGTCTCTAGGGTCAAAGCTGACAAGTAGAC-TAAGGGT-GGAAAACTCTTCAG
66 TTAGATGAGGTAGTCTCTAAGGTCAAAGCCAACAGGAAGACTTTA-GATAGGAAGTCTC-T-AA
* * * * * * *
1209297 GGTCAGAGCCGACAGGTAGACTTTA--GATAAGACAA-TCTCCAAGGTCAAAGCCAAGAAGCAGA
1 GGTCAAAGCCAACAGGCAGAC-TAAGGGATAGGA-AAGTCTCCAAGGTCAAAGCCAACAGGCAGA
* * ** * * * * ** *
1209359 C-TAAG-GGTAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAAGGATAGGAAAGTCTCC
64 CTTTAGATG-AG-GTAGTCTCTAAGGTCAAAGCCAACAGGAAGACTTTA-GATAGG-AAGTCTCT
*
1209422 AC
125 AA
* * * * * * ** *
1209424 GGTCAAAGCCAACAAGCAGACTTTA--GATGAGG-CAGTCTCTAGGGTCAAAACTGATAGGCAGA
1 GGTCAAAGCCAACAGGCAGAC-TAAGGGAT-AGGAAAGTCTCCAAGGTCAAAGCCAACAGGCAGA
* * * * * * *
1209486 C-TAAGGGAT-AGGAAAGTCTCTAGGGTCAAAGCCGACAGGCAGA-ATGAGGGATAGGAAAGTCT
64 CTTTA--GATGAGG-TAGTCTCTAAGGTCAAAGCCAACAGGAAGACTTTA--GATAGG-AAGTCT
1209548 CTAA
123 CTAA
* * * * * * * * *
1209552 GATCAAAGTCGACAGGCAAACTTTA--GATGAGG-CAGTCTCCAGGGTCAAAGCCGACAAGCAGA
1 GGTCAAAGCCAACAGGCAGAC-TAAGGGAT-AGGAAAGTCTCCAAGGTCAAAGCCAACAGGCAGA
* * * *
1209614 C-TAAGGGAT-AGGAAAGTCTCCAAGGTCAAAGCCGACAGGCAA-ACTTTAGATAGGGCAA-TCT
64 CTTTA--GATGAGG-TAGTCTCTAAGGTCAAAGCCAACAGG-AAGACTTTAGATA-GG-AAGTCT
*
1209675 -TCA
123 CTAA
* * * * * ** * * *
1209678 GAGTCAAAACCGATAGGCAGACTTTA--GATAAGGCAA-TCT-CTTGGTCAAATCCGACAGGTAG
1 G-GTCAAAGCCAACAGGCAGAC-TAAGGGAT-AGGAAAGTCTCCAAGGTCAAAGCCAACAGGCAG
* * ** * * ** * *
1209739 AC-TAAG-GGTAGAAAAGTCTCCAGGGTCAAAGCTGACA-GACAGAC-TAAGGGGTAGGAAAGTC
63 ACTTTAGATG-AG-GTAGTCTCTAAGGTCAAAGCCAACAGGA-AGACTTTA--GATAGG-AAGTC
*
1209800 TCTAG
122 TCTAA
* * * * * * *
1209805 GGTCAAAGCCAACAGGTAGACTTTA--GAT-GAGACAGTCTCTAGGGTCAAAGCCGATAGGCAGA
1 GGTCAAAGCCAACAGGCAGAC-TAAGGGATAG-GAAAGTCTCCAAGGTCAAAGCCAACAGGCAGA
* * * * * * * *
1209867 C-TGAGGGAT-AGGAAAGTGTCCAAGGTCAAAGCCACCAGGCAGACTTTAGATGAAGTAGTCTCT
64 CTTTA--GATGAGG-TAGTCTCTAAGGTCAAAGCCAACAGGAAGACTTTAGAT-AGGAAGTCTCT
*
1209930 AG
125 AA
** * * * ** * * * *
1209932 GGTCAAAGCTGACAAGTAGACTAAGGG-T-GGAAAACTCTTTAGGGTCAGAGCCGACAGGTAGAC
1 GGTCAAAGCCAACAGGCAGACTAAGGGATAGG-AAAGTCTCCAAGGTCAAAGCCAACAGGCAGAC
* ** * * * * * * * * *
1209995 TTTAGATAAGACAGTCTCCAAGGTCAAAGTCGACAAGCAGAC-TAAGGGTAGAAAAGTCTCCAA
65 TTTAGATGAGGTAGTCTCTAAGGTCAAAGCCAACAGGAAGACTTTA-GATAG-GAAGTCTCTAA
* * * * * *
1210058 GGTCAAAGCCGATAGGCAGACTGAGGGATAGGAAAGTCTCCACGGTCAAAGCCAACAAGCAAACT
1 GGTCAAAGCCAACAGGCAGACTAAGGGATAGGAAAGTCTCCAAGGTCAAAGCCAACAGGCAGACT
* * * * * * * * * *
1210123 TTAGATGAGGCAGTCTCCAGGGTCAAAACCGATAGGCAGAC-TAAGGGATAGGAAAGTCTCCAG
66 TTAGATGAGGTAGTCTCTAAGGTCAAAGCCAACAGGAAGACTTTA--GATAGG-AAGTCTCTAA
* * * * * * *
1210186 GGTCAAAGCCGACAGGCAGAATGAGGGATAGGAAAGTCTCTAAGATCAAAGCCGACAGGCAAACT
1 GGTCAAAGCCAACAGGCAGACTAAGGGATAGGAAAGTCTCCAAGGTCAAAGCCAACAGGCAGACT
* * * * * * * * *
1210251 TTAGATGAGGCAGTCTCCAGGGTCAAAGCCGACAAGCAGAC-TGAGGGATAGGAAAGTCTCCAG
66 TTAGATGAGGTAGTCTCTAAGGTCAAAGCCAACAGGAAGACTTTA--GATAGG-AAGTCTCTAA
* * * ** * * * *
1210314 GGTCAAAGCCGATAGGCAGACTTTA--GATAGGGCAGTCTTC-AGAGTCAAAACCGATAGGCAGA
1 GGTCAAAGCCAACAGGCAGAC-TAAGGGATAGGAAAGTCTCCAAG-GTCAAAGCCAACAGGCAGA
* * * ** * * * * * * * *
1210376 CTTTAGATAAGGCAATCTCTTGGGTCAAATCCAACAGGTAGA-GTAAGGGTAGAAAAGTCTCCAG
64 CTTTAGATGAGGTAGTCTCTAAGGTCAAAGCCAACAGGAAGACTTTA-GATAG-GAAGTCTCTAA
* * * * * *
1210440 GGTCAAAGCCAATAGGCAGACTTTA--GATGAGGCAA-TCTCCAAGGTCAAATCCGACAAGCAGA
1 GGTCAAAGCCAACAGGCAGAC-TAAGGGAT-AGGAAAGTCTCCAAGGTCAAAGCCAACAGGCAGA
* * ** * * * * * *
1210502 C-TAAG-GGTAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTTAGATAGGGCAGTCTCCA
64 CTTTAGATG-AG-GTAGTCTCTAAGGTCAAAGCCAACAGGAAGACTTTAGATA-GGAAGTCTCTA
*
1210565 G
126 A
* *
1210566 GGCCAAAGCCGACAGGCAGACT
1 GGTCAAAGCCAACAGGCAGACT
1210588 GAAGTAGGAA
Statistics
Matches: 1317, Mismatches: 283, Indels: 148
0.75 0.16 0.08
Matches are distributed among these distances:
123 1 0.00
124 7 0.01
125 50 0.04
126 307 0.23
127 515 0.39
128 416 0.32
129 21 0.02
ACGTcount: A:0.35, C:0.20, G:0.28, T:0.17
Consensus pattern (126 bp):
GGTCAAAGCCAACAGGCAGACTAAGGGATAGGAAAGTCTCCAAGGTCAAAGCCAACAGGCAGACT
TTAGATGAGGTAGTCTCTAAGGTCAAAGCCAACAGGAAGACTTTAGATAGGAAGTCTCTAA
Found at i:1208964 original size:85 final size:85
Alignment explanation
Indices: 1208788--1210377 Score: 1228
Period size: 85 Copynumber: 18.8 Consensus size: 85
1208778 GATTCTCCCG
* * * * *
1208788 GGTCAAAGCCAACAGGCAGAC-TGAGGGAT-AGGAAAGTCTCCAAGGCCAAAGCCAACAGGCAGA
1 GGTCAAAGCCAACAGGCAGACTTTA--GATGAGG-CAGTCTCCAGGGTCAAAGCCGACAGGCAGA
* * * *
1208851 CTTTA--GATGAGG-TAGTCTCTAG
63 C-TAAGGGAT-AGGAAAGTCTCCAA
* * * * * * *
1208873 GGTCAAAGCCAACAAGAAGGCTTTAGATGAGGTAGTATCCAAGGTCAAAGCCGACAGGTAGACTA
1 GGTCAAAGCCAACAGGCAGACTTTAGATGAGGCAGTCTCCAGGGTCAAAGCCGACAGGCAGACTA
* *
1208938 AGGGATAGGAAACTCTCCAG
66 AGGGATAGGAAAGTCTCCAA
* * * *
1208958 GGTCAAAGCCAACAGGCAGACTTTAGATGAGGCAGTCTCCAAGGTCAAAGCCGACAGGAAGTCTG
1 GGTCAAAGCCAACAGGCAGACTTTAGATGAGGCAGTCTCCAGGGTCAAAGCCGACAGGCAGACTA
* *
1209023 CGGGATAGGAAAGTCTCTAA
66 AGGGATAGGAAAGTCTCCAA
* * * * *
1209043 GGTCAAGGCCAACAAGCAGACTTTAGATGAGGCAGTTTCCAGGGTCAAAGTCGACAGGCAAACTA
1 GGTCAAAGCCAACAGGCAGACTTTAGATGAGGCAGTCTCCAGGGTCAAAGCCGACAGGCAGACTA
* *
1209108 AGGGGTAGGAAAGTCTCTAA
66 AGGGATAGGAAAGTCTCCAA
* * * *
1209128 GGTCAAAGCCAACAGGCAGACTTTAGATAAGACAGTCTCTAGGGTCAAAGCCGATAGGCAGACTA
1 GGTCAAAGCCAACAGGCAGACTTTAGATGAGGCAGTCTCCAGGGTCAAAGCCGACAGGCAGACTA
*
1209193 AGGGATAGGAAAGTGTCCAA
66 AGGGATAGGAAAGTCTCCAA
* * * * * * *
1209213 GGTCAAAGCCACCAAGCAGACTTTAGATGAGGTAGTCTCTAGGGTCAAAGCTGACAAGTAGACTA
1 GGTCAAAGCCAACAGGCAGACTTTAGATGAGGCAGTCTCCAGGGTCAAAGCCGACAGGCAGACTA
* * *
1209278 AGGG-T-GGAAAACTCTTCAG
66 AGGGATAGG-AAAGTCTCCAA
* * * * * * * * * *
1209297 GGTCAGAGCCGACAGGTAGACTTTAGATAAGACAATCTCCAAGGTCAAAGCCAAGAAGCAGACTA
1 GGTCAAAGCCAACAGGCAGACTTTAGATGAGGCAGTCTCCAGGGTCAAAGCCGACAGGCAGACTA
* *
1209362 AGGG-TAGAAAAGTCTCCAG
66 AGGGATAGGAAAGTCTCCAA
* ** * * * *
1209381 GGTCAAAGCCGACAGGCAGACTGAAGGAT-AGGAAAGTCTCCACGGTCAAAGCCAACAAGCAGAC
1 GGTCAAAGCCAACAGGCAGACTTTA-GATGAGG-CAGTCTCCAGGGTCAAAGCCGACAGGCAGAC
* * * *
1209445 TTTA--GATGAGG-CAGTCTCTAG
64 -TAAGGGAT-AGGAAAGTCTCCAA
* ** * * * *
1209466 GGTCAAAACTGATAGGCAGAC-TAAGGGAT-AGGAAAGTCTCTAGGGTCAAAGCCGACAGGCAGA
1 GGTCAAAGCCAACAGGCAGACTTTA--GATGAGG-CAGTCTCCAGGGTCAAAGCCGACAGGCAGA
* * *
1209529 ATGAGGGATAGGAAAGTCTCTAA
63 CTAAGGGATAGGAAAGTCTCCAA
* * * * *
1209552 GATCAAAGTCGACAGGCAAACTTTAGATGAGGCAGTCTCCAGGGTCAAAGCCGACAAGCAGACTA
1 GGTCAAAGCCAACAGGCAGACTTTAGATGAGGCAGTCTCCAGGGTCAAAGCCGACAGGCAGACTA
1209617 AGGGATAGGAAAGTCTCCAA
66 AGGGATAGGAAAGTCTCCAA
* * * * * * *
1209637 GGTCAAAGCCGACAGGCAAACTTTAGAT-AGGGCAATCTTCAGAGTCAAAACCGATAGGCAGACT
1 GGTCAAAGCCAACAGGCAGACTTTAGATGA-GGCAGTCTCCAGGGTCAAAGCCGACAGGCAGAC-
* * **
1209701 TTA--GATAAGGCAA-TCT-CTT
64 TAAGGGAT-AGGAAAGTCTCCAA
* * * * * ** * *
1209720 GGTCAAATCCGACAGGTAGAC-TAAG-GGTAGAAAAGTCTCCAGGGTCAAAGCTGACAGACAGAC
1 GGTCAAAGCCAACAGGCAGACTTTAGATG-AG-GCAGTCTCCAGGGTCAAAGCCGACAGGCAGAC
* * *
1209783 TAAGGGGTAGGAAAGTCTCTAG
64 TAAGGGATAGGAAAGTCTCCAA
* * * * *
1209805 GGTCAAAGCCAACAGGTAGACTTTAGATGAGACAGTCTCTAGGGTCAAAGCCGATAGGCAGACTG
1 GGTCAAAGCCAACAGGCAGACTTTAGATGAGGCAGTCTCCAGGGTCAAAGCCGACAGGCAGACTA
*
1209870 AGGGATAGGAAAGTGTCCAA
66 AGGGATAGGAAAGTCTCCAA
* * * * * * *
1209890 GGTCAAAGCCACCAGGCAGACTTTAGATGAAGTAGTCTCTAGGGTCAAAGCTGACAAGTAGACTA
1 GGTCAAAGCCAACAGGCAGACTTTAGATGAGGCAGTCTCCAGGGTCAAAGCCGACAGGCAGACTA
* ** *
1209955 AGGG-T-GGAAAACTCTTTAG
66 AGGGATAGG-AAAGTCTCCAA
* * * * * * * *
1209974 GGTCAGAGCCGACAGGTAGACTTTAGATAAGACAGTCTCCAAGGTCAAAGTCGACAAGCAGACTA
1 GGTCAAAGCCAACAGGCAGACTTTAGATGAGGCAGTCTCCAGGGTCAAAGCCGACAGGCAGACTA
*
1210039 AGGG-TAGAAAAGTCTCCAA
66 AGGGATAGGAAAGTCTCCAA
* * * * * * * *
1210058 GGTCAAAGCCGATAGGCAGAC-TGAGGGAT-AGGAAAGTCTCCACGGTCAAAGCCAACAAGCAAA
1 GGTCAAAGCCAACAGGCAGACTTTA--GATGAGG-CAGTCTCCAGGGTCAAAGCCGACAGGCAGA
* * *
1210121 CTTTA--GATGAGG-CAGTCTCCAG
63 C-TAAGGGAT-AGGAAAGTCTCCAA
* * * * *
1210143 GGTCAAAACCGATAGGCAGAC-TAAGGGAT-AGGAAAGTCTCCAGGGTCAAAGCCGACAGGCAGA
1 GGTCAAAGCCAACAGGCAGACTTTA--GATGAGG-CAGTCTCCAGGGTCAAAGCCGACAGGCAGA
* * *
1210206 ATGAGGGATAGGAAAGTCTCTAA
63 CTAAGGGATAGGAAAGTCTCCAA
* * * * *
1210229 GATCAAAGCCGACAGGCAAACTTTAGATGAGGCAGTCTCCAGGGTCAAAGCCGACAAGCAGACTG
1 GGTCAAAGCCAACAGGCAGACTTTAGATGAGGCAGTCTCCAGGGTCAAAGCCGACAGGCAGACTA
*
1210294 AGGGATAGGAAAGTCTCCAG
66 AGGGATAGGAAAGTCTCCAA
* * * * * *
1210314 GGTCAAAGCCGATAGGCAGACTTTAGAT-AGGGCAGTCTTCAGAGTCAAAACCGATAGGCAGACT
1 GGTCAAAGCCAACAGGCAGACTTTAGATGA-GGCAGTCTCCAGGGTCAAAGCCGACAGGCAGACT
1210378 TTAGATAAGG
Statistics
Matches: 1222, Mismatches: 239, Indels: 88
0.79 0.15 0.06
Matches are distributed among these distances:
82 6 0.00
83 56 0.05
84 239 0.20
85 840 0.69
86 76 0.06
87 5 0.00
ACGTcount: A:0.35, C:0.20, G:0.28, T:0.17
Consensus pattern (85 bp):
GGTCAAAGCCAACAGGCAGACTTTAGATGAGGCAGTCTCCAGGGTCAAAGCCGACAGGCAGACTA
AGGGATAGGAAAGTCTCCAA
Found at i:1210445 original size:84 final size:84
Alignment explanation
Indices: 1210051--1210587 Score: 323
Period size: 85 Copynumber: 6.3 Consensus size: 84
1210041 GGTAGAAAAG
* * * * * * * * * *
1210051 TCTCCAAGGTCAAAGCCGATAGGCAGACTGAGGGATAGGAAAGTCTCCACGGTCAAAGCCAACAA
1 TCTCCAAGGTCAAATCCAACAAGCAGACTAAGGG-TAGAAAAGTCTCCAGGGTCAAAGCCGATAG
* * *
1210116 GCAAACTTTAGATGAGGCAG
65 GCAGACTTTAGATAAGGCAA
* * * * * * *
1210136 TCTCCAGGGTCAAAACCGATAGGCAGACTAAGGGATAGGAAAGTCTCCAGGGTCAAAGCCGACAG
1 TCTCCAAGGTCAAATCCAACAAGCAGACTAAGGG-TAGAAAAGTCTCCAGGGTCAAAGCCGATAG
* * *
1210201 GCAGA-ATGAGGGAT-AGGAAA
65 GCAGACTTTA--GATAAGGCAA
* * * * * * * * ** *
1210221 GTCTCTAAGATCAAAGCCGACAGGCAAACTTTA-GAT-GAGGCAGTCTCCAGGGTCAAAGCCGAC
1 -TCTCCAAGGTCAAATCCAACAAGCAGAC-TAAGGGTAGA-AAAGTCTCCAGGGTCAAAGCCGAT
* * *
1210284 AAGCAGAC-TGAGGGAT-AGGAAA
63 AGGCAGACTTTA--GATAAGGCAA
* * * * * * * *** * * *
1210306 GTCTCCAGGGTCAAAGCCGATAGGCAGACTTTA-GATAGGGCAGTCTTCAGAGTCAAAACCGATA
1 -TCTCCAAGGTCAAATCCAACAAGCAGAC-TAAGGGTAGAAAAGTCTCCAGGGTCAAAGCCGATA
1210370 GGCAGACTTTAGATAAGGCAA
64 GGCAGACTTTAGATAAGGCAA
*** * * * *
1210391 TCTCTTGGGTCAAATCCAACAGGTAGAGTAAGGGTAGAAAAGTCTCCAGGGTCAAAGCCAATAGG
1 TCTCCAAGGTCAAATCCAACAAGCAGACTAAGGGTAGAAAAGTCTCCAGGGTCAAAGCCGATAGG
*
1210456 CAGACTTTAGATGAGGCAA
66 CAGACTTTAGATAAGGCAA
* *
1210475 TCTCCAAGGTCAAATCCGACAAGCAGACTAAGGGTAGAAAAGTCTCCAGGGTCAAAGCCGACAGG
1 TCTCCAAGGTCAAATCCAACAAGCAGACTAAGGGTAGAAAAGTCTCCAGGGTCAAAGCCGATAGG
* *
1210540 CAGACTTTAGATAGGGCAG
66 CAGACTTTAGATAAGGCAA
* * * * *
1210559 TCTCCAGGGCCAAAGCCGACAGGCAGACT
1 TCTCCAAGGTCAAATCCAACAAGCAGACT
1210588 GAAGTAGGAA
Statistics
Matches: 373, Mismatches: 69, Indels: 21
0.81 0.15 0.05
Matches are distributed among these distances:
83 2 0.01
84 167 0.45
85 173 0.46
86 29 0.08
87 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.28, T:0.16
Consensus pattern (84 bp):
TCTCCAAGGTCAAATCCAACAAGCAGACTAAGGGTAGAAAAGTCTCCAGGGTCAAAGCCGATAGG
CAGACTTTAGATAAGGCAA
Found at i:1210528 original size:677 final size:678
Alignment explanation
Indices: 1208781--1210545 Score: 2534
Period size: 677 Copynumber: 2.6 Consensus size: 678
1208771 AAGAAAAGAT
* * * * * * * *
1208781 TCTCCCGGGTCAAAGCCAACAGGCAGACTGAGGGATAGGAAAGTCTCCAAGGCCAAAGCCAACAG
1 TCTCCAGGGTCAAAACCGATAGGCAGACTAAGGGATAGGAAAGTCTCCAGGGTCAAAGCCGACAG
* * * * * * * * *
1208846 GCAGACTTTA--GATGAGG-TAGTCTCTAGGGTCAAAGCCAACAAG-AAGGCTTTAGATGAGGTA
66 GCAGA-ATGAGGGAT-AGGAAAGTCTCTAAGATCAAAGCCGACAGGCAA-ACTTTAGATGAGGCA
* * * * * *
1208907 GTATCCAAGGTCAAAGCCGACAGGTAGACTAAGGGATAGGAAACTCTCCAGGGTCAAAGCCAACA
128 GTCTCCAGGGTCAAAGCCGACAAGCAGACTAAGGGATAGGAAAGTCTCCAGGGTCAAAGCCGACA
* * * * * *** *
1208972 GGCAGACTTTAGAT-GAGGCAGTCTCCA-AGGTCAAAGCCGACAGGAAGTCTGCGGGAT-AGGAA
193 GGCAGACTTTAGATAG-GGCAGTCTTCAGA-GTCAAAACCGATAGGCAGACT-TTAGATAAGGCA
* ** * * * * ** * *
1209034 AGTCTCTAAGGTCAAGGCCAACAAGCAGACTTTA-GAT-GAGGCAGTTTCCAGGGTCAAAGTCGA
255 A-TCTCT-TGGTCAAATCCAACAGGTAGAC-TAAGGGTAGA-AAAGTCTCCAGGGTCAAAGCCGA
*
1209097 CAGGCAAACTAAGGGGTAGGAAAGTCTCTAAGGTCAAAGCCAACAGGCAGACTTTAGATA-AGAC
316 CAGGCAGACTAAGGGGTAGGAAAGTCTCTAAGGTCAAAGCCAACAGGCAGACTTTAGATAGAGAC
1209161 AGTCTCTAGGGTCAAAGCCGATAGGCAGACTAAGGGATAGGAAAGTGTCCAAGGTCAAAGCCACC
381 AGTCTCTAGGGTCAAAGCCGATAGGCAGACTAAGGGATAGGAAAGTGTCCAAGGTCAAAGCCACC
*
1209226 AAGCAGACTTTAGATGAGGTAGTCTCTAGGGTCAAAGCTGACAAGTAGACTAAGGGTGGAAAACT
446 AAGCAGACTTTAGATGAAGTAGTCTCTAGGGTCAAAGCTGACAAGTAGACTAAGGGTGGAAAACT
*
1209291 CTTCAGGGTCAGAGCCGACAGGTAGACTTTAGATAAGACAATCTCCAAGGTCAAAGCCAAGAAGC
511 CTTCAGGGTCAGAGCCGACAGGTAGACTTTAGATAAGACAATCTCCAAGGTCAAAGCCAACAAGC
*
1209356 AGACTAAGGGTAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTGAAGGATAGGAAAGTCTC
576 AGACTAAGGGTAGAAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGATAGGAAAGTCTC
*
1209421 CACGGTCAAAGCCAACAAGCAGACTTTAGATGAGGCAG
641 CACGGTCAAAGCCAACAAGCAAACTTTAGATGAGGCAG
* * *
1209459 TCTCTAGGGTCAAAACTGATAGGCAGACTAAGGGATAGGAAAGTCTCTAGGGTCAAAGCCGACAG
1 TCTCCAGGGTCAAAACCGATAGGCAGACTAAGGGATAGGAAAGTCTCCAGGGTCAAAGCCGACAG
*
1209524 GCAGAATGAGGGATAGGAAAGTCTCTAAGATCAAAGTCGACAGGCAAACTTTAGATGAGGCAGTC
66 GCAGAATGAGGGATAGGAAAGTCTCTAAGATCAAAGCCGACAGGCAAACTTTAGATGAGGCAGTC
*
1209589 TCCAGGGTCAAAGCCGACAAGCAGACTAAGGGATAGGAAAGTCTCCAAGGTCAAAGCCGACAGGC
131 TCCAGGGTCAAAGCCGACAAGCAGACTAAGGGATAGGAAAGTCTCCAGGGTCAAAGCCGACAGGC
* *
1209654 AAACTTTAGATAGGGCAATCTTCAGAGTCAAAACCGATAGGCAGACTTTAGATAAGGCAATCTCT
196 AGACTTTAGATAGGGCAGTCTTCAGAGTCAAAACCGATAGGCAGACTTTAGATAAGGCAATCTCT
* * *
1209719 TGGTCAAATCCGACAGGTAGACTAAGGGTAGAAAAGTCTCCAGGGTCAAAGCTGACAGACAGACT
261 TGGTCAAATCCAACAGGTAGACTAAGGGTAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACT
* *
1209784 AAGGGGTAGGAAAGTCTCTAGGGTCAAAGCCAACAGGTAGACTTTAGAT-GAGACAGTCTCTAGG
326 AAGGGGTAGGAAAGTCTCTAAGGTCAAAGCCAACAGGCAGACTTTAGATAGAGACAGTCTCTAGG
* *
1209848 GTCAAAGCCGATAGGCAGACTGAGGGATAGGAAAGTGTCCAAGGTCAAAGCCACCAGGCAGACTT
391 GTCAAAGCCGATAGGCAGACTAAGGGATAGGAAAGTGTCCAAGGTCAAAGCCACCAAGCAGACTT
*
1209913 TAGATGAAGTAGTCTCTAGGGTCAAAGCTGACAAGTAGACTAAGGGTGGAAAACTCTTTAGGGTC
456 TAGATGAAGTAGTCTCTAGGGTCAAAGCTGACAAGTAGACTAAGGGTGGAAAACTCTTCAGGGTC
* * *
1209978 AGAGCCGACAGGTAGACTTTAGATAAGACAGTCTCCAAGGTCAAAGTCGACAAGCAGACTAAGGG
521 AGAGCCGACAGGTAGACTTTAGATAAGACAATCTCCAAGGTCAAAGCCAACAAGCAGACTAAGGG
* *
1210043 TAGAAAAGTCTCCAAGGTCAAAGCCGATAGGCAGACTGAGGGATAGGAAAGTCTCCACGGTCAAA
586 TAGAAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGATAGGAAAGTCTCCACGGTCAAA
1210108 GCCAACAAGCAAACTTTAGATGAGGCAG
651 GCCAACAAGCAAACTTTAGATGAGGCAG
1210136 TCTCCAGGGTCAAAACCGATAGGCAGACTAAGGGATAGGAAAGTCTCCAGGGTCAAAGCCGACAG
1 TCTCCAGGGTCAAAACCGATAGGCAGACTAAGGGATAGGAAAGTCTCCAGGGTCAAAGCCGACAG
1210201 GCAGAATGAGGGATAGGAAAGTCTCTAAGATCAAAGCCGACAGGCAAACTTTAGATGAGGCAGTC
66 GCAGAATGAGGGATAGGAAAGTCTCTAAGATCAAAGCCGACAGGCAAACTTTAGATGAGGCAGTC
* *
1210266 TCCAGGGTCAAAGCCGACAAGCAGACTGAGGGATAGGAAAGTCTCCAGGGTCAAAGCCGATAGGC
131 TCCAGGGTCAAAGCCGACAAGCAGACTAAGGGATAGGAAAGTCTCCAGGGTCAAAGCCGACAGGC
1210331 AGACTTTAGATAGGGCAGTCTTCAGAGTCAAAACCGATAGGCAGACTTTAGATAAGGCAATCTCT
196 AGACTTTAGATAGGGCAGTCTTCAGAGTCAAAACCGATAGGCAGACTTTAGATAAGGCAATCTCT
* * *
1210396 TGGGTCAAATCCAACAGGTAGAGTAAGGGTAGAAAAGTCTCCAGGGTCAAAGCCAATAGGCAGAC
261 T-GGTCAAATCCAACAGGTAGACTAAGGGTAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGAC
* ** * * * * * * * * *
1210461 TTTAGATG-AGGCAA-TCTCCAAGGTCAAATCCGACAAGCAGAC-TAAGGGTAGA-AAAGTCTCC
325 -TAAGGGGTAGGAAAGTCTCTAAGGTCAAAGCCAACAGGCAGACTTTA-GATAGAGACAGTCTCT
*
1210522 AGGGTCAAAGCCGACAGGCAGACT
388 AGGGTCAAAGCCGATAGGCAGACT
1210546 TTAGATAGGG
Statistics
Matches: 975, Mismatches: 98, Indels: 29
0.88 0.09 0.03
Matches are distributed among these distances:
676 4 0.00
677 689 0.71
678 136 0.14
679 142 0.15
680 4 0.00
ACGTcount: A:0.35, C:0.20, G:0.28, T:0.17
Consensus pattern (678 bp):
TCTCCAGGGTCAAAACCGATAGGCAGACTAAGGGATAGGAAAGTCTCCAGGGTCAAAGCCGACAG
GCAGAATGAGGGATAGGAAAGTCTCTAAGATCAAAGCCGACAGGCAAACTTTAGATGAGGCAGTC
TCCAGGGTCAAAGCCGACAAGCAGACTAAGGGATAGGAAAGTCTCCAGGGTCAAAGCCGACAGGC
AGACTTTAGATAGGGCAGTCTTCAGAGTCAAAACCGATAGGCAGACTTTAGATAAGGCAATCTCT
TGGTCAAATCCAACAGGTAGACTAAGGGTAGAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACT
AAGGGGTAGGAAAGTCTCTAAGGTCAAAGCCAACAGGCAGACTTTAGATAGAGACAGTCTCTAGG
GTCAAAGCCGATAGGCAGACTAAGGGATAGGAAAGTGTCCAAGGTCAAAGCCACCAAGCAGACTT
TAGATGAAGTAGTCTCTAGGGTCAAAGCTGACAAGTAGACTAAGGGTGGAAAACTCTTCAGGGTC
AGAGCCGACAGGTAGACTTTAGATAAGACAATCTCCAAGGTCAAAGCCAACAAGCAGACTAAGGG
TAGAAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAAGGATAGGAAAGTCTCCACGGTCAAA
GCCAACAAGCAAACTTTAGATGAGGCAG
Found at i:1219063 original size:22 final size:23
Alignment explanation
Indices: 1219033--1219077 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
1219023 ATTCTTATTA
*
1219033 ATTAAGAAAATATTG-ATGAATG
1 ATTAAGAAAATAATGAATGAATG
*
1219055 ATTATGAAAATAATGAATGAATG
1 ATTAAGAAAATAATGAATGAATG
1219078 TCATGAATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.51, C:0.00, G:0.18, T:0.31
Consensus pattern (23 bp):
ATTAAGAAAATAATGAATGAATG
Found at i:1219083 original size:22 final size:22
Alignment explanation
Indices: 1219038--1219084 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
1219028 TATTAATTAA
* *
1219038 GAAAATATTGATGAATGATTAT
1 GAAAATAATGATGAATGATCAT
1219060 GAAAATAATGAATGAATG-TCAT
1 GAAAATAATG-ATGAATGATCAT
1219082 GAA
1 GAA
1219085 TCTGAATGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.49, C:0.02, G:0.19, T:0.30
Consensus pattern (22 bp):
GAAAATAATGATGAATGATCAT
Found at i:1224310 original size:16 final size:16
Alignment explanation
Indices: 1224279--1224313 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1224269 TATAAGAATT
**
1224279 TCAACAAAATTTAGCA
1 TCAACAAAATCAAGCA
1224295 TCAACAAAATCAAGCA
1 TCAACAAAATCAAGCA
1224311 TCA
1 TCA
1224314 CACCTCTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.23, G:0.06, T:0.20
Consensus pattern (16 bp):
TCAACAAAATCAAGCA
Found at i:1225642 original size:30 final size:30
Alignment explanation
Indices: 1225601--1225659 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
1225591 ATGAAAGCAA
1225601 ATGCAATGAAATGAACATATGAAATGCATGT
1 ATGCAATGAAATGAACATATG-AATGCATGT
* *
1225632 ATGC-ATGAAATGATCATATGCATGCATG
1 ATGCAATGAAATGAACATATGAATGCATG
1225660 AACCATGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 7 0.27
30 15 0.58
31 4 0.15
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (30 bp):
ATGCAATGAAATGAACATATGAATGCATGT
Found at i:1225800 original size:16 final size:17
Alignment explanation
Indices: 1225775--1225812 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1225765 TTTTTTCGAC
*
1225775 TTTTTTATTTCTTT-GA
1 TTTTTGATTTCTTTGGA
*
1225791 TTTTTGATTTTTTTGGA
1 TTTTTGATTTCTTTGGA
1225808 TTTTT
1 TTTTT
1225813 TTTGAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.11, C:0.03, G:0.11, T:0.76
Consensus pattern (17 bp):
TTTTTGATTTCTTTGGA
Found at i:1226782 original size:19 final size:19
Alignment explanation
Indices: 1226738--1226793 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
1226728 TTGCCAGTTT
* **
1226738 CATGTATCAATACAATTGTC
1 CATGTATCGATACAA-TGAA
1226758 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
1226777 CATGTATTGATACAATG
1 CATGTATCGATACAATG
1226794 TATCGATACA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1229186 original size:20 final size:21
Alignment explanation
Indices: 1229156--1229201 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
1229146 CTGTTTTTGT
1229156 TGAAGATTTTG-A-TGAAAAA
1 TGAAGATTTTGAAGTGAAAAA
1229175 TGAAGTATTTTGAAGTGAAAAA
1 TGAAG-ATTTTGAAGTGAAAAA
1229197 T-AAGA
1 TGAAGA
1229202 AATTTGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 5 0.21
20 7 0.29
21 4 0.17
22 8 0.33
ACGTcount: A:0.48, C:0.00, G:0.22, T:0.30
Consensus pattern (21 bp):
TGAAGATTTTGAAGTGAAAAA
Found at i:1229206 original size:22 final size:20
Alignment explanation
Indices: 1229156--1229234 Score: 58
Period size: 21 Copynumber: 3.9 Consensus size: 20
1229146 CTGTTTTTGT
1229156 TGAAG-ATTTTGATGAAAAA
1 TGAAGAATTTTGATGAAAAA
*
1229175 TGAAGTATTTTGAAGTGAAAAA
1 TGAAGAATTTTG-A-TGAAAAA
*
1229197 T-AAGAAATTTGA--AAAAGA
1 TGAAGAATTTTGATGAAAA-A
*
1229215 TTTGATGAATTTTGATGAAA
1 --TGAAGAATTTTGATGAAA
1229235 GGATGTTAGG
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
17 4 0.09
18 1 0.02
19 5 0.11
20 8 0.17
21 18 0.38
22 8 0.17
23 3 0.06
ACGTcount: A:0.47, C:0.00, G:0.20, T:0.33
Consensus pattern (20 bp):
TGAAGAATTTTGATGAAAAA
Found at i:1229207 original size:21 final size:22
Alignment explanation
Indices: 1229168--1229209 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1229158 AAGATTTTGA
* *
1229168 TGAAAAATGAAGTATTTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
1229190 TGAAAAAT-AAGAAATTTGAA
1 TGAAAAATGAAGAAATTTGAA
1229210 AAAGATTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.52, C:0.00, G:0.19, T:0.29
Consensus pattern (22 bp):
TGAAAAATGAAGAAATTTGAAG
Found at i:1235642 original size:20 final size:20
Alignment explanation
Indices: 1235596--1235646 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1235586 GTTAGAAACA
* *
1235596 ATGTATCTATACAATTCATC
1 ATGTATCGATACAATTCACC
*
1235616 ATATATCGATACAATGT-ACC
1 ATGTATCGATACAAT-TCACC
1235636 ATGTATCGATA
1 ATGTATCGATA
1235647 TAAACAGTGG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 25 0.96
21 1 0.04
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACAATTCACC
Found at i:1237908 original size:20 final size:20
Alignment explanation
Indices: 1237883--1237922 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1237873 GCTGTCCCGC
1237883 TTTATAATGTATCGATACAT
1 TTTATAATGTATCGATACAT
1237903 TTTATAATGTATCGATACAT
1 TTTATAATGTATCGATACAT
1237923 CTGGGCAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (20 bp):
TTTATAATGTATCGATACAT
Found at i:1238047 original size:13 final size:13
Alignment explanation
Indices: 1238029--1238053 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1238019 AAAAAAAATA
1238029 TGTATCGATACAT
1 TGTATCGATACAT
1238042 TGTATCGATACA
1 TGTATCGATACA
1238054 ACACTTTATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1239123 original size:49 final size:49
Alignment explanation
Indices: 1238959--1239376 Score: 484
Period size: 49 Copynumber: 8.7 Consensus size: 49
1238949 AAAATGATGT
* *
1238959 CAATGTGCTGATTCAAAGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
* *
1239011 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
1239054 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * * *
1239103 CAATATGCTGATTCAAGGCCAGCGATATCGGGCTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
1239146 CAATGTGCTGATTCAAGGCCAGCTACATTGGTCTTAAACATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * * *
1239195 CAATATGCCGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
1239244 CAATGTGCTGAGTCAAGGCTAGCTACATTGGACTTAAAGGTG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
1239292 CAATGTGTTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
1239341 CAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
1239377 GAAGGGTTGC
Statistics
Matches: 313, Mismatches: 40, Indels: 29
0.82 0.10 0.08
Matches are distributed among these distances:
43 76 0.24
45 1 0.00
47 2 0.01
48 46 0.15
49 157 0.50
52 31 0.10
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
Found at i:1239148 original size:92 final size:94
Alignment explanation
Indices: 1238959--1239376 Score: 522
Period size: 92 Copynumber: 4.4 Consensus size: 94
1238949 AAAATGATGT
* *
1238959 CAATGTGCTGATTCAAAGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTGATT
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGCCAATATGCTGATT
1239024 CAAGGCCAGCTATATTGGACTT-A-AAGGTGC
63 CAAGGCCAGCTATATTGGACTTAAGAAGGTGC
*
1239054 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
* * *
1239119 GGCCAGCGATATCGGGCTT-A-AAGGTGC
66 GGCCAGCTATATTGGACTTAAGAAGGTGC
* * * *
1239146 CAATGTGCTGATTCAAGGCCAGCTACATTGGTCTTAAACATAAAGGTGCCAATATGCCGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
1239211 GGCCAGCTATATTGGACTTAATGGTGAAGGTGC
66 GGCCAGCTATATTGGACTTAA----GAAGGTGC
* * * * * *
1239244 CAATGTGCTGAGTCAAGGCTAGCTACATTGGACTTAAAGGTG-AGGTGCCAATGTGTTGAGTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
*
1239308 GGCCAGCTACATTGGACTTAAAGATGAAGGTGC
66 GGCCAGCTATATTGGACTT--A-A-GAAGGTGC
* * *
1239341 CAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
1239377 GAAGGGTTGC
Statistics
Matches: 284, Mismatches: 30, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
92 122 0.43
93 1 0.00
94 1 0.00
95 39 0.14
97 76 0.27
98 43 0.15
99 1 0.00
100 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (94 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
GGCCAGCTATATTGGACTTAAGAAGGTGC
Found at i:1239403 original size:30 final size:32
Alignment explanation
Indices: 1239369--1239487 Score: 163
Period size: 33 Copynumber: 3.7 Consensus size: 32
1239359 CCAGCTATAT
1239369 TGGGC-TTAGAAG-GGTTGCCACCGACTTGTG
1 TGGGCTTTAGAAGAGGTTGCCACCGACTTGTG
*
1239399 TGGGCTTTAGAGAGTGGTTGCCACCGACTTGTG
1 TGGGCTTTAGA-AGAGGTTGCCACCGACTTGTG
* *
1239432 TGGGCTTTGGAAGAAGATTGCCACCGACTTGTG
1 TGGGCTTTAGAAG-AGGTTGCCACCGACTTGTG
1239465 TGGGCTTTAGAAGAAGG-TGCCAC
1 TGGGCTTTAGAAG-AGGTTGCCAC
1239488 GGAGTCGTGG
Statistics
Matches: 80, Mismatches: 5, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
30 5 0.06
31 5 0.06
32 10 0.12
33 60 0.75
ACGTcount: A:0.19, C:0.18, G:0.35, T:0.27
Consensus pattern (32 bp):
TGGGCTTTAGAAGAGGTTGCCACCGACTTGTG
Found at i:1239546 original size:34 final size:33
Alignment explanation
Indices: 1239481--1239571 Score: 130
Period size: 33 Copynumber: 2.8 Consensus size: 33
1239471 TTAGAAGAAG
* *
1239481 GTGCCACGGAGTCGTGGACTTAAAAGGAAAAGA
1 GTGCCACGGAGTTGTGGGCTTAAAAGGAAAAGA
* *
1239514 GTGCCACGTAGTTGTGGGCTTTAAAGGAAAA-A
1 GTGCCACGGAGTTGTGGGCTTAAAAGGAAAAGA
1239546 GATGCCACGGAGTTGTGGGCTTAAAA
1 G-TGCCACGGAGTTGTGGGCTTAAAA
1239572 TGGTGCCACA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
32 2 0.04
33 49 0.96
ACGTcount: A:0.32, C:0.14, G:0.33, T:0.21
Consensus pattern (33 bp):
GTGCCACGGAGTTGTGGGCTTAAAAGGAAAAGA
Found at i:1239579 original size:27 final size:27
Alignment explanation
Indices: 1239548--1239621 Score: 112
Period size: 27 Copynumber: 2.7 Consensus size: 27
1239538 AGGAAAAAGA
*
1239548 TGCCACGGAGTTGTGGGCTTAAAATGG
1 TGCCACGGAGTTGTGGGCTTAAAAGGG
* * *
1239575 TGCCACAGAGTTGTGGACTTAAACGGG
1 TGCCACGGAGTTGTGGGCTTAAAAGGG
1239602 TGCCACGGAGTTGTGGGCTT
1 TGCCACGGAGTTGTGGGCTT
1239622 TAAGAAGGAG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.20, C:0.18, G:0.36, T:0.26
Consensus pattern (27 bp):
TGCCACGGAGTTGTGGGCTTAAAAGGG
Found at i:1240646 original size:23 final size:22
Alignment explanation
Indices: 1240620--1240680 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 22
1240610 CTTCTTCTTC
1240620 TTCTTTTTTTTTTGTTTGTTTGT
1 TTCTTTTTTTTTTGTTT-TTTGT
*
1240643 TTCTTTTTTTTTTCCTTTTTTGT
1 TTCTTTTTTTTTT-GTTTTTTGT
1240666 TT-TGTTTCTTTTTTG
1 TTCT-TTT-TTTTTTG
1240681 GAAAAGAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
22 1 0.03
23 23 0.70
24 9 0.27
ACGTcount: A:0.00, C:0.08, G:0.10, T:0.82
Consensus pattern (22 bp):
TTCTTTTTTTTTTGTTTTTTGT
Found at i:1240655 original size:28 final size:28
Alignment explanation
Indices: 1240617--1240679 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
1240607 CTTCTTCTTC
*
1240617 TTCTTCTTTTTTTT--TTGTTTG-TTTGT
1 TTCTT-TTTTTTTTCCTTTTTTGTTTTGT
1240643 TTCTTTTTTTTTTCCTTTTTTGTTTTGT
1 TTCTTTTTTTTTTCCTTTTTTGTTTTGT
1240671 TTCTTTTTT
1 TTCTTTTTT
1240680 GGAAAAGAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
25 8 0.24
26 5 0.15
27 6 0.18
28 14 0.42
ACGTcount: A:0.00, C:0.10, G:0.08, T:0.83
Consensus pattern (28 bp):
TTCTTTTTTTTTTCCTTTTTTGTTTTGT
Found at i:1240668 original size:17 final size:16
Alignment explanation
Indices: 1240627--1240680 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
1240617 TTCTTCTTTT
*
1240627 TTTTTTG-TTTGTTTG
1 TTTTTTGTTTTGTTTC
1240642 TTTCTTT-TTTT-TTTCC
1 TTT-TTTGTTTTGTTT-C
1240658 TTTTTTGTTTTGTTTC
1 TTTTTTGTTTTGTTTC
1240674 TTTTTTG
1 TTTTTTG
1240681 GAAAAGAACA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
15 9 0.27
16 21 0.64
17 3 0.09
ACGTcount: A:0.00, C:0.07, G:0.11, T:0.81
Consensus pattern (16 bp):
TTTTTTGTTTTGTTTC
Found at i:1240948 original size:11 final size:11
Alignment explanation
Indices: 1240934--1240973 Score: 57
Period size: 10 Copynumber: 3.7 Consensus size: 11
1240924 TTGTTCTGTT
1240934 TTTTTTTTGTG
1 TTTTTTTTGTG
1240945 TTTTGTTTTGT-
1 TTTT-TTTTGTG
1240956 TTTTTTTT-TG
1 TTTTTTTTGTG
1240966 TTTTTTTT
1 TTTTTTTT
1240974 TTTACTTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 1 0.04
10 12 0.44
11 8 0.30
12 6 0.22
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (11 bp):
TTTTTTTTGTG
Found at i:1240960 original size:21 final size:21
Alignment explanation
Indices: 1240934--1240974 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1240924 TTGTTCTGTT
1240934 TTTTTTTTGTGTTTTGTTTTG
1 TTTTTTTTGTGTTTTGTTTTG
* *
1240955 TTTTTTTTTTGTTTTTTTTT
1 TTTTTTTTGTGTTTTGTTTT
1240975 TTACTTTTGT
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:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (21 bp):
TTTTTTTTGTGTTTTGTTTTG
Found at i:1240974 original size:11 final size:11
Alignment explanation
Indices: 1240920--1240975 Score: 76
Period size: 11 Copynumber: 4.9 Consensus size: 11
1240910 CCTTTACACC
*
1240920 TTTTTTGTTCTG
1 TTTTTT-TTTTG
1240932 TTTTTTTTTTG
1 TTTTTTTTTTG
*
1240943 TGTTTTGTTTTG
1 T-TTTTTTTTTG
1240955 TTTTTTTTTTG
1 TTTTTTTTTTG
1240966 TTTTTTTTTT
1 TTTTTTTTTT
1240976 TACTTTTGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
11 24 0.60
12 16 0.40
ACGTcount: A:0.00, C:0.02, G:0.12, T:0.86
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:1240976 original size:23 final size:23
Alignment explanation
Indices: 1240920--1240976 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
1240910 CCTTTACACC
*
1240920 TTTTTTGTTCTGTTTTTTTTTTG
1 TTTTTTGTTTTGTTTTTTTTTTG
*
1240943 TGTTTTGTTTTGTTTTTTTTTTG
1 TTTTTTGTTTTGTTTTTTTTTTG
*
1240966 TTTTTTTTTTT
1 TTTTTTGTTTT
1240977 ACTTTTGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.00, C:0.02, G:0.12, T:0.86
Consensus pattern (23 bp):
TTTTTTGTTTTGTTTTTTTTTTG
Found at i:1240982 original size:23 final size:23
Alignment explanation
Indices: 1240936--1240994 Score: 50
Period size: 23 Copynumber: 2.6 Consensus size: 23
1240926 GTTCTGTTTT
1240936 TTTTTTG-TGTTTTGTTTTGTTTT
1 TTTTTTGTTGTTTTGTTTTG-TTT
* **
1240959 TTTTTTGTT-TTTTTTTTTACTT
1 TTTTTTGTTGTTTTGTTTTGTTT
*
1240981 TTGTTTGTGTGTTT
1 TTTTTTGT-TGTTT
1240995 ACTTTTGGCT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
22 9 0.31
23 16 0.55
24 4 0.14
ACGTcount: A:0.02, C:0.02, G:0.15, T:0.81
Consensus pattern (23 bp):
TTTTTTGTTGTTTTGTTTTGTTT
Found at i:1240983 original size:34 final size:35
Alignment explanation
Indices: 1240920--1240986 Score: 93
Period size: 34 Copynumber: 1.9 Consensus size: 35
1240910 CCTTTACACC
*
1240920 TTTTTTGTTCTGTTTTTTTTTTGTGTTTTGTTTTG
1 TTTTTTGTTCTGTTTTTTTTTTGTCTTTTGTTTTG
*
1240955 TTTTTT-TTTTGTTTTTTTTTT-TACTTTTGTTT
1 TTTTTTGTTCTGTTTTTTTTTTGT-CTTTTGTTT
1240987 GTGTGTTTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 1 0.03
34 22 0.76
35 6 0.21
ACGTcount: A:0.01, C:0.03, G:0.12, T:0.84
Consensus pattern (35 bp):
TTTTTTGTTCTGTTTTTTTTTTGTCTTTTGTTTTG
Found at i:1247938 original size:52 final size:52
Alignment explanation
Indices: 1247853--1247977 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
1247843 ATATGAAAAG
* *
1247853 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
1247905 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
1247957 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
1247978 AAGATCAGTG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:1247990 original size:52 final size:51
Alignment explanation
Indices: 1247853--1247997 Score: 211
Period size: 52 Copynumber: 2.8 Consensus size: 51
1247843 ATATGAAAAG
*
1247853 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
1247905 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
1247957 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
1247998 ATGTATCGAT
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 83 0.98
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:1248004 original size:13 final size:13
Alignment explanation
Indices: 1247986--1248010 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1247976 CAAAGATCAG
1247986 TGTATCGATACAA
1 TGTATCGATACAA
1247999 TGTATCGATACA
1 TGTATCGATACA
1248011 TGTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1248079 original size:20 final size:20
Alignment explanation
Indices: 1248050--1248107 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1248040 GCAGTAGCTT
1248050 AAAT-TGTATCGATACAAAA
1 AAATATGTATCGATACAAAA
*
1248069 AAATATGTATCGATACAACA
1 AAATATGTATCGATACAAAA
***
1248089 TTTTATGTATCGATACAAA
1 AAATATGTATCGATACAAA
1248108 TCATTGAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.31
Consensus pattern (20 bp):
AAATATGTATCGATACAAAA
Found at i:1248949 original size:155 final size:155
Alignment explanation
Indices: 1248706--1249090 Score: 463
Period size: 155 Copynumber: 2.5 Consensus size: 155
1248696 ACATCTATAG
* *
1248706 ATCCTTTTTAAGTCCTTTAAGGGC-ATTGGGCACTTTTACGTCGAAGGTATCTCC-TAGGGGCAT
1 ATCCTTTTTAAATCCTTT-AGGGCTATTGGGTACTTTTACGTCGAAGGTATC-CCTTAGGGGCAT
* ** * * * * * * * *
1248769 TCTGGTAATTTTTTAGAATCGAGTCCTAGGTTGTCACTAGGTTTGCTTTTATGCCGAAGGTAGAT
64 TTTCATAATTTTCTAGAACCAAGTCCTAAGTTGCCACCAAGTCTGCTTTTATGCCGAAGGTAGAT
* * *
1248834 ATTTAGTATAGGTTCATCCCTTTTAAA
129 ATTTAGGATAGGTTCATCCCATTCAAA
* *
1248861 ATCCTTTTTAAATCCTTTAGGGCTATCGTGTACTTTTACGTCGAAGGTATCCCTTAGGGGCATTT
1 ATCCTTTTTAAATCCTTTAGGGCTATTGGGTACTTTTACGTCGAAGGTATCCCTTAGGGGCATTT
*
1248926 TCATAATTTTCTAGAACCAAGTCCTAAGTTGCCACCAAGTCTGCTTTTATGCCGATGGTAGATAT
66 TCATAATTTTCTAGAACCAAGTCCTAAGTTGCCACCAAGTCTGCTTTTATGCCGAAGGTAGATAT
* **
1248991 TTAGGATATGTTCATCCCATTCATG
131 TTAGGATAGGTTCATCCCATTCAAA
* * * * *
1249016 ATCCTTTTTAACTCTTTTAGGGGTATTGGGTACTTTT-CTGTCAAAGGTAT-CCTCTAGGGACAT
1 ATCCTTTTTAAATCCTTTAGGGCTATTGGGTACTTTTAC-GTCGAAGGTATCCCT-TAGGGGCAT
1249079 TTTCATAATTTT
64 TTTCATAATTTT
1249091 TTTAAATTTA
Statistics
Matches: 197, Mismatches: 29, Indels: 8
0.84 0.12 0.03
Matches are distributed among these distances:
154 11 0.06
155 186 0.94
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.39
Consensus pattern (155 bp):
ATCCTTTTTAAATCCTTTAGGGCTATTGGGTACTTTTACGTCGAAGGTATCCCTTAGGGGCATTT
TCATAATTTTCTAGAACCAAGTCCTAAGTTGCCACCAAGTCTGCTTTTATGCCGAAGGTAGATAT
TTAGGATAGGTTCATCCCATTCAAA
Found at i:1250496 original size:156 final size:155
Alignment explanation
Indices: 1250218--1250717 Score: 551
Period size: 156 Copynumber: 3.3 Consensus size: 155
1250208 CAGTTCTAGG
* * ** * *
1250218 AAAACTACGAAAATGCCTATGGGGTATACCTTAAATATGAAAGTATCCCA-G-TAACCCTAATGG
1 AAAATTACGAAAATGCCT-TGAGGTATACCTTTGACATAAAAGTAT--CATGATAACCCTAATGG
* *
1250281 ACACTAAAATGATCATAAATGGGATAAACCTATCCTAAATGCACACCTTCGACATAAAAGCATTT
63 ACACTAAAATGATCATAAATGGGATAAACCTATCCTAAATGCACACTTTTGACATAAAAGCATTT
*
1250346 CGGTGACAACCTAAGACTCTATTCAAGA
128 CGGTGACAACCTAAGACTCGATTCAAGA
* *
1250374 AAAATTACGAAAATGCCTTCGAAGTATACCTTTGACATAAAAGTATC-TCGATAACACTAATGGA
1 AAAATTACGAAAATGCCTT-GAGGTATACCTTTGACATAAAAGTATCAT-GATAACCCTAATGGA
* ** * * * *
1250438 TACTAAGGTGATCATAAATGGGATAAACCTATCCTAAATGCACACTTTTGTCAAAAAAGCGTTCC
64 CACTAAAATGATCATAAATGGGATAAACCTATCCTAAATGCACACTTTTGACATAAAAGCATTTC
** * ** *
1250503 AATGACAACCTAAGACTCGGTTTTAGG
129 GGTGACAACCTAAGACTCGATTCAAGA
* * *
1250530 AAAA-TAC-----T-CCTAG-GGTATA-CTTTCAACATAAAAGTATCATGATAACCCTTATGGAC
1 AAAATTACGAAAATGCCTTGAGGTATACCTTT-GACATAAAAGTATCATGATAACCCTAATGGAC
* * *
1250586 ACTAAAATGATCATAAATGAGATAAACCTATCCCAAATGCACACTTTTGACATAAAAGCATCTCG
65 ACTAAAATGATCATAAATGGGATAAACCTATCCTAAATGCACACTTTTGACATAAAAGCATTTCG
1250651 GTGACAACCTAAGACTCGATTCAA-A
130 GTGACAACCTAAGACTCGATTCAAGA
*
1250676 AAAATTACGAAAATGCCCTT-AGGTATACCTTCGACATGAAAA
1 AAAATTACGAAAATG-CCTTGAGGTATACCTTTGACAT-AAAA
1250718 TACCCAAAAG
Statistics
Matches: 279, Mismatches: 48, Indels: 35
0.77 0.13 0.10
Matches are distributed among these distances:
146 8 0.03
147 109 0.39
148 2 0.01
149 3 0.01
150 1 0.00
152 1 0.00
154 14 0.05
155 12 0.04
156 129 0.46
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.25
Consensus pattern (155 bp):
AAAATTACGAAAATGCCTTGAGGTATACCTTTGACATAAAAGTATCATGATAACCCTAATGGACA
CTAAAATGATCATAAATGGGATAAACCTATCCTAAATGCACACTTTTGACATAAAAGCATTTCGG
TGACAACCTAAGACTCGATTCAAGA
Found at i:1251467 original size:165 final size:164
Alignment explanation
Indices: 1251249--1251982 Score: 873
Period size: 165 Copynumber: 4.5 Consensus size: 164
1251239 AGTCAAAAAG
* *
1251249 AAGATTCGGCCAAGTAACATTGGCCTTGGAACAAAATTTTCAATATTTACACTTAAATCTCTAAA
1 AAGATTCGGCCAAGT-ACTTTGGCCTTAGAACAAAATTTTCAATATTTACACTTAAATCTCTAAA
* *
1251314 CTTTTTAAAATTACAAATT-GATCCAC-ACAAAAATT-AAAGCACAAAATTAAATATCAAACATA
65 CTTTCTAAAATTATAAATTAG-TCC-CTA-AAAAATTCAAA-CACAAAATTAAATATCAAACATA
**
1251376 TTGAAATCCACACAAAAATCTGATCCAAAAATTACAAGA
126 TCAAAATCCACACAAAAATCTGATCCAAAAATTACAAGA
* * * *
1251415 AAGATTTGGCCAAGTACTTTGGCCTTGGAACAAAATTTTCAATATTTACACTTAAATTTCTGAAC
1 AAGATTCGGCCAAGTACTTTGGCCTTAGAACAAAATTTTCAATATTTACACTTAAATCTCTAAAC
* * * *
1251480 TTTCTAAAATTATAAATTGGTCCCTATATAATTTAAAACACAAAATTAAATATCAAACATATCAA
66 TTTCTAAAATTATAAATTAGTCCCTA-AAAAATTCAAACACAAAATTAAATATCAAACATATCAA
* *
1251545 AATCCACACAAAAGTTTGATCCAAAAATTACAAGA
130 AATCCACACAAAAATCTGATCCAAAAATTACAAGA
* *
1251580 AATATTCGGCCAAGTACTTTTGGCGTTAGAACAAAATTTTCAATATTTACACTTAAAT-TCCTAA
1 AAGATTCGGCCAAGTAC-TTTGGCCTTAGAACAAAATTTTCAATATTTACACTTAAATCT-CTAA
* *
1251644 ACTTTCTAAAATTATAAATTAGTCCCTATATAATTCAAACACAAAATTAAATATCAAACATATCA
64 ACTTTCTAAAATTATAAATTAGTCCCTAAAAAATTCAAACACAAAATTAAATATCAAACATATCA
* * * **
1251709 AAATACACAAAAAAAT-TAGATCAAAAAATTACAACT
129 AAATCCACACAAAAATCT-GATCCAAAAATTACAAGA
* * *
1251745 AAGATTCGGCC---T--TTTGGCCTTAGAACAAAATTTTCAATACTTACACTCAAATCTCTGAAC
1 AAGATTCGGCCAAGTACTTTGGCCTTAGAACAAAATTTTCAATATTTACACTTAAATCTCTAAAC
* *
1251805 TTTCTAAAATTATAAATTAGTCCCTATATAATTCAAACACAAAATTAAATATCGAAA-ATATCAA
66 TTTCTAAAATTATAAATTAGTCCCTAAAAAATTCAAACACAAAATTAAATATC-AAACATATCAA
* * * *
1251869 AATCAACACAAAAATCAGATCTAAAAATTAAAAGA
130 AATCCACACAAAAATCTGATCCAAAAATTACAAGA
* ** * * * **
1251904 AAGATTTGGCCAACCACCTTTGGCC-TATGAACAAATTTTTTCAATATTTACAAATTTACCCT-T
1 AAGATTCGGCCAAGTA-CTTTGGCCTTA-GAACAAA-ATTTTCAATATTTAC-ACTTAAATCTCT
1251967 AAACTTTCTAAAATTA
62 AAACTTTCTAAAATTA
1251983 CAAAAAACCC
Statistics
Matches: 497, Mismatches: 53, Indels: 36
0.85 0.09 0.06
Matches are distributed among these distances:
159 138 0.28
160 4 0.01
162 1 0.00
164 4 0.01
165 230 0.46
166 115 0.23
167 5 0.01
ACGTcount: A:0.45, C:0.17, G:0.07, T:0.30
Consensus pattern (164 bp):
AAGATTCGGCCAAGTACTTTGGCCTTAGAACAAAATTTTCAATATTTACACTTAAATCTCTAAAC
TTTCTAAAATTATAAATTAGTCCCTAAAAAATTCAAACACAAAATTAAATATCAAACATATCAAA
ATCCACACAAAAATCTGATCCAAAAATTACAAGA
Found at i:1253110 original size:22 final size:23
Alignment explanation
Indices: 1253072--1253116 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
1253062 TTACAATAAA
* *
1253072 ATTTTACATAATCAATTTAATTT
1 ATTTTACATAATAAATTCAATTT
1253095 ATTTTA-ATAATAAATTCAATTT
1 ATTTTACATAATAAATTCAATTT
1253117 TAATATCCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (23 bp):
ATTTTACATAATAAATTCAATTT
Found at i:1253631 original size:154 final size:152
Alignment explanation
Indices: 1253208--1253648 Score: 507
Period size: 154 Copynumber: 2.9 Consensus size: 152
1253198 TATTATATGA
* * *
1253208 AAAAAATGC-AAAACTCATAACATAAATTGAATTTTCACAAACTATTTAATATGAATTTAATGAA
1 AAAAAATTCTAAAACTCATAAAATAAATTGAATTTTCA-AAACTATTTAATATGAATTAAAT-AA
* * * * * * * **
1253272 -AATATTT-AATAAATTTTAAAAATTTTAAACTGAGAAAAATCCA-ACCAAAGAAATATATGGAG
64 TAATATTTGAA-GAATTTTAGAAATTATAAATTTAGAAAAAT-CATATCAAAGAAATTTACAGAG
* *
1253334 TA-AAAACTCTGTATCTTGGTAATAG
127 TAGAAAACTCTGCATCTTGATAATAG
* * * *
1253359 AAAAAATTCTAAAACTCGTAAAATAAATTAAATTTTTCAAAATTAATTTAATATGAATTAAACAA
1 AAAAAATTCTAAAACTCATAAAATAAATTGAA-TTTTCAAAACT-ATTTAATATGAATTAAATAA
* * ** * *
1253424 TAATATGTGAAGAATTTTTGAAATTATAAATTTAGAAAAATCAT-TCTGGAGAAATTTACAAAGG
64 TAATATTTGAAGAATTTTAGAAATTATAAATTTAGAAAAATCATATC-AAAGAAATTTACAGAGT
*
1253488 AGAAAACTCTGCATTTTGATAATAG
128 AGAAAACTCTGCATCTTGATAATAG
* *
1253513 AAAAAATTTTAAAACTCATAAAATGAATTGAAGTTTTCAAAACTGATTTAATATGAATTAAATAA
1 AAAAAATTCTAAAACTCATAAAATAAATTGAA-TTTTCAAAACT-ATTTAATATGAATTAAATAA
*
1253578 TAATATTTGAAGAATTTTAGAAATTATAAATTTAGAAAAATCTTATCAAAGAAATTTACAGAGTA
64 TAATATTTGAAGAATTTTAGAAATTATAAATTTAGAAAAATCATATCAAAGAAATTTACAGAGTA
1253643 GAAAAC
129 GAAAAC
1253649 CACATATTTT
Statistics
Matches: 241, Mismatches: 40, Indels: 15
0.81 0.14 0.05
Matches are distributed among these distances:
151 8 0.03
152 28 0.12
153 63 0.26
154 140 0.58
155 2 0.01
ACGTcount: A:0.50, C:0.08, G:0.10, T:0.33
Consensus pattern (152 bp):
AAAAAATTCTAAAACTCATAAAATAAATTGAATTTTCAAAACTATTTAATATGAATTAAATAATA
ATATTTGAAGAATTTTAGAAATTATAAATTTAGAAAAATCATATCAAAGAAATTTACAGAGTAGA
AAACTCTGCATCTTGATAATAG
Found at i:1263866 original size:24 final size:25
Alignment explanation
Indices: 1263825--1263877 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
1263815 GTATGTACTT
1263825 AAAAAATAAATCAATTAA-AATATA
1 AAAAAATAAATCAATTAAGAATATA
* *
1263849 AAAAAAT-AATGCAGTTAAGAATGTA
1 AAAAAATAAAT-CAATTAAGAATATA
1263874 AAAA
1 AAAA
1263878 GAAATAAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 3 0.12
24 13 0.52
25 9 0.36
ACGTcount: A:0.66, C:0.04, G:0.08, T:0.23
Consensus pattern (25 bp):
AAAAAATAAATCAATTAAGAATATA
Found at i:1265344 original size:2 final size:2
Alignment explanation
Indices: 1265337--1265374 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
1265327 GTTTGGCTTT
* *
1265337 TA TA TA TA TT TA TA TA TA TA TA TA TA TA TA AA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1265375 GGTTTTAGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1268534 original size:15 final size:15
Alignment explanation
Indices: 1268514--1268546 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1268504 CTTTCACTTT
*
1268514 TCAACATTTTGGGAA
1 TCAACATTTTAGGAA
1268529 TCAACATTTTAGGAA
1 TCAACATTTTAGGAA
1268544 TCA
1 TCA
1268547 TAATTGAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (15 bp):
TCAACATTTTAGGAA
Found at i:1271881 original size:13 final size:13
Alignment explanation
Indices: 1271863--1271889 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1271853 ATAGTTACCC
1271863 ATGTATCGATACA
1 ATGTATCGATACA
1271876 ATGTATCGATACA
1 ATGTATCGATACA
1271889 A
1 A
1271890 GGAATGTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1278054 original size:13 final size:13
Alignment explanation
Indices: 1278036--1278065 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1278026 ACAATTCATC
1278036 ATGTATCGATATA
1 ATGTATCGATATA
1278049 ATGTATCGATATA
1 ATGTATCGATATA
1278062 ATGT
1 ATGT
1278066 CCTATGTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.40
Consensus pattern (13 bp):
ATGTATCGATATA
Found at i:1278054 original size:33 final size:33
Alignment explanation
Indices: 1278015--1278079 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1278005 CGTTATAAGC
1278015 AATGTATCGATACAAT-TCATCATGTATCGATAT
1 AATGTATCGATACAATGTCAT-ATGTATCGATAT
* *
1278048 AATGTATCGATATAATGTCCTATGTATCGATA
1 AATGTATCGATACAATGTCATATGTATCGATA
1278080 CAAATAGTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 26 0.90
34 3 0.10
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (33 bp):
AATGTATCGATACAATGTCATATGTATCGATAT
Found at i:1281868 original size:2 final size:2
Alignment explanation
Indices: 1281861--1281896 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1281851 AATATACCAC
1281861 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1281897 GAGGTAAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1296883 original size:27 final size:27
Alignment explanation
Indices: 1296853--1296908 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
1296843 AAAATCATTC
*
1296853 AAATA-AAAAATAATTAATATATTATAT
1 AAATATAAAAATAATTAAAAT-TTATAT
* *
1296880 AAATATTAAAATTATTAAAATTTATAT
1 AAATATAAAAATAATTAAAATTTATAT
1296907 AA
1 AA
1296909 TAATTAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 13 0.52
28 12 0.48
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (27 bp):
AAATATAAAAATAATTAAAATTTATAT
Found at i:1296932 original size:18 final size:19
Alignment explanation
Indices: 1296892--1296938 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
1296882 ATATTAAAAT
*
1296892 TATTAAAATTTATATAATA
1 TATTAAAATTTATACAATA
*
1296911 -ATTAATATTTAT-CAATA
1 TATTAAAATTTATACAATA
1296928 TATTAAAATTT
1 TATTAAAATTT
1296939 TTTAAAATCT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 4 0.17
18 20 0.83
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
TATTAAAATTTATACAATA
Found at i:1297155 original size:19 final size:19
Alignment explanation
Indices: 1297128--1297164 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1297118 TATGTATATA
*
1297128 TATACAAATTGAAAATTAT
1 TATAAAAATTGAAAATTAT
*
1297147 TATAAAAATTTAAAATTA
1 TATAAAAATTGAAAATTA
1297165 AAGATATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (19 bp):
TATAAAAATTGAAAATTAT
Done.