Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold187
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: 2169796
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 45208 characters in sequence are not A, C, G, or T
File 3 of 13
Found at i:315921 original size:157 final size:155
Alignment explanation
Indices: 315699--316444 Score: 618
Period size: 156 Copynumber: 4.8 Consensus size: 155
315689 ACCAAGTCTG
* **
315699 CTTTTATGCCAAAGATGGGTATTTGGGATAGATTCATCCCATCTATAATCTTTTTTAAGTCTTTT
1 CTTTTATGCCAAAGATGGGTATTTAGGATAGATTCATCCCATCTATAATCCCTTTTAAGTCTTTT
** * * * *
315764 AGAGGTATCTTATACTTCTAAGTCTTAAGGTATCCCTTAGAGGCATTTTCGTAATTTTTTTAAAA
66 AG-GGTATCAGACACTTCTAAGTC-GAAGGTATCCCCTAGAGGCATTTTCATAATTTTTTTAAAA
*
315829 TCGAGTCCTAGGTTGTCACTAGGTCCA
129 TCAAGTCCTAGGTTGTCACTAGGTCCA
* * *
315856 CTTTTATACCAAATATGGGTATTTAGGATAGATTCATCCCATCTATAATCCCTTTTAAGTATTTT
1 CTTTTATGCCAAAGATGGGTATTTAGGATAGATTCATCCCATCTATAATCCCTTTTAAGTCTTTT
* * * *
315921 AGGAGTATCAGACACTTCTAAGCCGAAGGTATCCCCTATG-GGCATTTTCATAATTTTATCAGAA
66 AGG-GTATCAGACACTTCTAAGTCGAAGGTATCCCCTA-GAGGCATTTTCATAATTTTTTTAAAA
* * * *
315985 CCAAGTCTTAGGTTGTCATTGGGTCCA
129 TCAAGTCCTAGGTTGTCACTAGGTCCA
* ** * * ** *
316012 CTTATATGCTGAAGGTGGGTACTTAGGATA-AGTTCATCCCATCTATAATCTTTTTTAAGTCCTT
1 CTTTTATGCCAAAGATGGGTATTTAGGATAGA-TTCATCCCATCTATAATCCCTTTTAAGTCTTT
* * * *
316076 TAGGGATATCAGACACTTCTAAGTCGAAGGTATCCCGTAAAGCCATTTTCATAATTTTTTTCATA
65 TAGGG-TATCAGACACTTCTAAGTCGAAGGTATCCCCTAGAGGCATTTTCATAATTTTTTT-AAA
* * * **
316141 ATCAAGTCCTAGGTTATCACCAAGTCTG
128 ATCAAGTCCTAGGTTGTCACTAGGTCCA
* * *
316169 TTTTTATGCCAAA-AGTGTGTATTTAAGATATG-TTCATCCCATCTATAAT-CCTTTTAAAGT-T
1 CTTTTATGCCAAAGA-TGGGTATTTAGGATA-GATTCATCCCATCTATAATCCCTTTT-AAGTCT
* * * * * * * *
316230 ATTTAGGGGTATTAGGCACTTCTAAGTTGAAGGTA-CCCTTTAGGGGTATTTTTATAATTTTTTC
63 -TTTA-GGGTATCAGACACTTCTAAGTCGAAGGTATCCC-CTAGAGGCATTTTCATAATTTTTTT
* * * * * ** *
316294 AGAA-CTGAGTCTTAGGTTATCACCATAT-CG
125 AAAATC-AAGTCCTAGGTTGTCACTAGGTCCA
** * * * * * *
316324 CTTTTATATCGAAGGTGGGTGTTTAGGATA-AGGTCATCCCATCTATAAT-ACTTTGTAAGTCCT
1 CTTTTATGCCAAAGATGGGTATTTAGGATAGA-TTCATCCCATCTATAATCCCTTT-TAAGTCTT
* * *
316387 TTAGGGGGATC-GAGCACTTCTAAGTCGAAGTTA-CCCTCTAAAGGCATTTTCATAATTT
64 TTA-GGGTATCAGA-CACTTCTAAGTCGAAGGTATCCC-CTAGAGGCATTTTCATAATTT
316445 CTAGAATCGA
Statistics
Matches: 473, Mismatches: 96, Indels: 42
0.77 0.16 0.07
Matches are distributed among these distances:
154 1 0.00
155 96 0.20
156 187 0.40
157 186 0.39
158 3 0.01
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (155 bp):
CTTTTATGCCAAAGATGGGTATTTAGGATAGATTCATCCCATCTATAATCCCTTTTAAGTCTTTT
AGGGTATCAGACACTTCTAAGTCGAAGGTATCCCCTAGAGGCATTTTCATAATTTTTTTAAAATC
AAGTCCTAGGTTGTCACTAGGTCCA
Found at i:316207 original size:313 final size:309
Alignment explanation
Indices: 315714--316444 Score: 814
Period size: 313 Copynumber: 2.3 Consensus size: 309
315704 ATGCCAAAGA
* * * *
315714 TGGGTATTTGGGAT-AGATTCATCCCATCTATAATCTTTTTTAAGTCTTTTAGAGGTATCTTATA
1 TGGGTATTTAGGATAAG-TTCATCCCATCTATAATCTTTTTTAAGTCCTTTAG-GGTATC-GACA
* * * * *
315778 CTTCTAAGTCTTAAGGTATCCCTTAGAGGCATTTTCGTAATTTTTTTAAAATCGAGTCCTAGGTT
63 CTTCTAAGTC-GAAGGTATCCCCTAAAGGCATTTTCATAATTTTTTTAAAATCAAGTCCTAGGTT
* * * *
315843 GTCACTAGGTCCACTTTTATACCAAATATGGGTATTTAGGATAGATTCATCCCATCTATAATCCC
127 ATCACCAAGTCCACTTTTATACCAAATATGGGTATTTAAGATAGATTCATCCCATCTATAAT-CC
*
315908 TTTT-AAG-TATTTTAGGAGTATCAGACACTTCTAAGCCGAAGGTATCCC-CTATGGGCATTTTC
191 TTTTAAAGTTA-TTTAGGAGTATCAGACACTTCTAAGCCGAAGGTA-CCCTCTAGGGGCATTTTC
* *** *
315970 ATAATTTTATCAGAACCAAGTCTTAGGTTGTCATTGGGTC-CACTTATATGCTGAAGG
254 ATAATTTTATCAGAACCAAGTCTTAGGTTATCACCAGATCGCACTTATAT-C-GAAGG
*
316027 TGGGTACTTAGGATAAGTTCATCCCATCTATAATCTTTTTTAAGTCCTTTAGGGATATCAGACAC
1 TGGGTATTTAGGATAAGTTCATCCCATCTATAATCTTTTTTAAGTCCTTTAGGG-TATC-GACAC
* * *
316092 TTCTAAGTCGAAGGTATCCCGTAAAGCCATTTTCATAATTTTTTTCATAATCAAGTCCTAGGTTA
64 TTCTAAGTCGAAGGTATCCCCTAAAGGCATTTTCATAATTTTTTT-AAAATCAAGTCCTAGGTTA
*** * *
316157 TCACCAAGTCTGTTTTTATGCCAAA-AGTGTGTATTTAAGATATG-TTCATCCCATCTATAATCC
128 TCACCAAGTCCACTTTTATACCAAATA-TGGGTATTTAAGATA-GATTCATCCCATCTATAATCC
* * * ** * * *
316220 TTTTAAAGTTATTTAGGGGTATTAGGCACTTCTAAGTTGAAGGTACCCTTTAGGGGTATTTTTAT
191 TTTTAAAGTTATTTAGGAGTATCAGACACTTCTAAGCCGAAGGTACCCTCTAGGGGCATTTTCAT
* ** * **
316285 AATTTTTTCAGAACTGAGTCTTAGGTTATCACCATATCGCTTTTATATCGAAGG
256 AATTTTATCAGAACCAAGTCTTAGGTTATCACCAGATCGCACTTATATCGAAGG
* * * *
316339 TGGGTGTTTAGGATAAGGTCATCCCATCTATAATAC-TTTGTAAGTCCTTTAGGGGGATCGAGCA
1 TGGGTATTTAGGATAAGTTCATCCCATCTATAAT-CTTTTTTAAGTCCTTTA-GGGTATCGA-CA
*
316403 CTTCTAAGTCGAAGTTA-CCCTCTAAAGGCATTTTCATAATTT
63 CTTCTAAGTCGAAGGTATCCC-CTAAAGGCATTTTCATAATTT
316445 CTAGAATCGA
Statistics
Matches: 355, Mismatches: 50, Indels: 27
0.82 0.12 0.06
Matches are distributed among these distances:
311 5 0.01
312 133 0.37
313 205 0.58
314 12 0.03
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (309 bp):
TGGGTATTTAGGATAAGTTCATCCCATCTATAATCTTTTTTAAGTCCTTTAGGGTATCGACACTT
CTAAGTCGAAGGTATCCCCTAAAGGCATTTTCATAATTTTTTTAAAATCAAGTCCTAGGTTATCA
CCAAGTCCACTTTTATACCAAATATGGGTATTTAAGATAGATTCATCCCATCTATAATCCTTTTA
AAGTTATTTAGGAGTATCAGACACTTCTAAGCCGAAGGTACCCTCTAGGGGCATTTTCATAATTT
TATCAGAACCAAGTCTTAGGTTATCACCAGATCGCACTTATATCGAAGG
Found at i:316404 original size:155 final size:154
Alignment explanation
Indices: 315689--316444 Score: 550
Period size: 157 Copynumber: 4.8 Consensus size: 154
315679 TTAAGTTGTT
** * * *
315689 ACCAAGTCTGCTTTTATGCCAAAGATGGGTATTTGGGAT-AGATTCATCCCATCTATAATCTTTT
1 ACCAAGTCTGCTTTTATATCGAAGGTGGGTATTTAGGATAAG-TTCATCCCATCTATAATC--TT
* * * * * * *
315753 TTAAGTCTTTTAGAGGTATCTTA-TACTTCTAAGTCTTAAGGTATCCCT-TAGAGGCATTTTCGT
63 TTAAGTCCTTTAGGGGTATC--AGCACTTCTAAGTC-GAAGGTA-CCCTGTAAAGCCATTTTCAT
* * *
315816 AATTTTTTT-AAAATCGAGTCCTAGGTTGTC
124 AATTTTTTTCAGAATCAAGTCCTAGGTTATC
* * ** * * **
315846 ACTAGGTCCACTTTTATACCAAATATGGGTATTTAGGAT-AGATTCATCCCATCTATAATCCCTT
1 ACCAAGTCTGCTTTTATATCGAAGGTGGGTATTTAGGATAAG-TTCATCCCATCTATAAT--CTT
** * * * ** *
315910 TTAAGTATTTTAGGAGTATCAGACACTTCTAAGCCGAAGGTATCCC-CTATGGGCATTTTCATAA
63 TTAAGTCCTTTAGGGGTATCAG-CACTTCTAAGTCGAAGGTA-CCCTGTAAAGCCATTTTCATAA
* * * *
315974 -TTTTATCAGAACCAAGTCTTAGGTTGTC
126 TTTTTTTCAGAATCAAGTCCTAGGTTATC
**** ** *
316002 ATTGGGTC--CACTTATATGCTGAAGGTGGGTACTTAGGATAAGTTCATCCCATCTATAATCTTT
1 ACCAAGTCTGCTTTTATAT-C-GAAGGTGGGTATTTAGGATAAGTTCATCCCATCTATAATC--T
*
316065 TTTAAGTCCTTTAGGGATATCAGACACTTCTAAGTCGAAGGTATCCC-GTAAAGCCATTTTCATA
62 TTTAAGTCCTTTAGGGGTATCAG-CACTTCTAAGTCGAAGGTA-CCCTGTAAAGCCATTTTCATA
*
316129 ATTTTTTTCATAATCAAGTCCTAGGTTATC
125 ATTTTTTTCAGAATCAAGTCCTAGGTTATC
* ** * * * * *
316159 ACCAAGTCTGTTTTTATGCCAAAAGTGTGTATTTAAGATATGTTCATCCCATCTATAATCCTTTT
1 ACCAAGTCTGCTTTTATATCGAAGGTGGGTATTTAGGATAAGTTCATCCCATCTATAAT-CTTTT
** * * * ** ** *
316224 AAAGTTATTTAGGGGTATTAGGCACTTCTAAGTTGAAGGTACCCTTTAGGGGTATTTTTATAA-T
65 -AAGTCCTTTAGGGGTATCA-GCACTTCTAAGTCGAAGGTACCCTGTAAAGCCATTTTCATAATT
* *
316288 TTTTTCAGAA-CTGAGTCTTAGGTTATC
128 TTTTTCAGAATC-AAGTCCTAGGTTATC
* *
316315 ACCATA-TC-GCTTTTATATCGAAGGTGGGTGTTTAGGATAAGGTCATCCCATCTATAATACTTT
1 ACCA-AGTCTGCTTTTATATCGAAGGTGGGTATTTAGGATAAGTTCATCCCATCTATAAT-CTTT
* * * *
316378 GTAAGTCCTTTAGGGGGATCGAGCACTTCTAAGTCGAAGTTACCCTCTAAAGGCATTTTCATAAT
64 -TAAGTCCTTTAGGGGTATC-AGCACTTCTAAGTCGAAGGTACCCTGTAAAGCCATTTTCATAAT
316443 TT
127 TT
316445 CTAGAATCGA
Statistics
Matches: 481, Mismatches: 95, Indels: 47
0.77 0.15 0.08
Matches are distributed among these distances:
154 7 0.01
155 101 0.21
156 176 0.37
157 189 0.39
158 3 0.01
159 5 0.01
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (154 bp):
ACCAAGTCTGCTTTTATATCGAAGGTGGGTATTTAGGATAAGTTCATCCCATCTATAATCTTTTA
AGTCCTTTAGGGGTATCAGCACTTCTAAGTCGAAGGTACCCTGTAAAGCCATTTTCATAATTTTT
TTCAGAATCAAGTCCTAGGTTATC
Found at i:318061 original size:13 final size:13
Alignment explanation
Indices: 318043--318068 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
318033 CAACATGCTT
318043 TGTATCGATACAA
1 TGTATCGATACAA
318056 TGTATCGATACAA
1 TGTATCGATACAA
318069 AATCATTGTA
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):
TGTATCGATACAA
Found at i:318064 original size:33 final size:32
Alignment explanation
Indices: 318022--318086 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 32
318012 ACACATCCAG
* *
318022 ATGTATCGATACAACATGCTTTGTATCGATACA
1 ATGTATCGATACAAAAT-CATTGTATCGATACA
318055 ATGTATCGATACAAAATCATTGTATCGATACA
1 ATGTATCGATACAAAATCATTGTATCGATACA
318087 CACTCAATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 14 0.47
33 16 0.53
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (32 bp):
ATGTATCGATACAAAATCATTGTATCGATACA
Found at i:318080 original size:19 final size:20
Alignment explanation
Indices: 318056--318106 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
318046 ATCGATACAA
318056 TGTATCGATACAAAATC-AT
1 TGTATCGATACAAAATCAAT
* *
318075 TGTATCGATACACACTCAAT
1 TGTATCGATACAAAATCAAT
318095 TGTATCGATACA
1 TGTATCGATACA
318107 TGAAACTGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.31
Consensus pattern (20 bp):
TGTATCGATACAAAATCAAT
Found at i:318170 original size:13 final size:13
Alignment explanation
Indices: 318152--318182 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
318142 CGATACATGG
*
318152 TACATTGTATCGA
1 TACATTGCATCGA
318165 TACATTGCATCGA
1 TACATTGCATCGA
318178 TACAT
1 TACAT
318183 AGTGAAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGCATCGA
Found at i:319752 original size:9 final size:9
Alignment explanation
Indices: 319725--319772 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 9
319715 TTAACCATCA
*
319725 AAGATAATG
1 AAGATGATG
**
319734 AAGAAAATG
1 AAGATGATG
319743 AAGATGATG
1 AAGATGATG
*
319752 ATGATGATG
1 AAGATGATG
*
319761 ATGATGATG
1 AAGATGATG
319770 AAG
1 AAG
319773 TTGACACAGA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.48, C:0.00, G:0.29, T:0.23
Consensus pattern (9 bp):
AAGATGATG
Found at i:319753 original size:3 final size:3
Alignment explanation
Indices: 319740--319770 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
319730 AATGAAGAAA
*
319740 ATG AAG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
319771 AGTTGACACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.32, T:0.29
Consensus pattern (3 bp):
ATG
Found at i:326204 original size:34 final size:34
Alignment explanation
Indices: 326166--326231 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
326156 TAAATTTGTT
326166 AGGATAACAAAAAGGGGGAATAGTTAATAAGGTC
1 AGGATAACAAAAAGGGGGAATAGTTAATAAGGTC
* *
326200 AGGATAACAAAAAGGGGGAGTAGTTACTAAGG
1 AGGATAACAAAAAGGGGGAATAGTTAATAAGG
326232 GGAATACTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.45, C:0.06, G:0.32, T:0.17
Consensus pattern (34 bp):
AGGATAACAAAAAGGGGGAATAGTTAATAAGGTC
Found at i:326948 original size:20 final size:19
Alignment explanation
Indices: 326903--326956 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
326893 TGTATCAATA
***
326903 CATTGTATCGATACATGTT
1 CATTGTATCGATACACACT
326922 CATTGTATCGATACACACT
1 CATTGTATCGATACACACT
*
326941 CAATTGTATGGATACA
1 C-ATTGTATCGATACA
326957 TGAAACTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (19 bp):
CATTGTATCGATACACACT
Found at i:327021 original size:13 final size:13
Alignment explanation
Indices: 327003--327046 Score: 79
Period size: 13 Copynumber: 3.4 Consensus size: 13
326993 CGATACATGG
327003 TACATTGTATTGA
1 TACATTGTATTGA
327016 TACATTGTATTGA
1 TACATTGTATTGA
*
327029 TACATTGTATCGA
1 TACATTGTATTGA
327042 TACAT
1 TACAT
327047 ATTGAAAAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (13 bp):
TACATTGTATTGA
Found at i:332689 original size:17 final size:17
Alignment explanation
Indices: 332669--332701 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
332659 TAGCTGTAAG
332669 TCTTTCTTTTTTCTCTC
1 TCTTTCTTTTTTCTCTC
*
332686 TCTTTTTTTTTTCTCT
1 TCTTTCTTTTTTCTCT
332702 TTGGCTAAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (17 bp):
TCTTTCTTTTTTCTCTC
Found at i:334312 original size:68 final size:68
Alignment explanation
Indices: 334107--334312 Score: 200
Period size: 68 Copynumber: 3.0 Consensus size: 68
334097 AAGCGTTTTA
* * * * * * *
334107 CTCTTTGAGGACTGAAG-TAGGTAGATGCTACTAGCTTGTTTGGGCTTTGAGATGGGTAAGCATC
1 CTCTTTCAGGAGTGAGGATAGGTAGGTGCCACTAGCTTGTGTGGGCTTTGAGATAGGTAAGCATC
*
334171 CTA
66 CTG
* * * * * * * * *
334174 CTCTTTGAGGATTGAGGGTAGGTAGGTGTCA-TCGACTTGTGTGGGCTTTAAGGTAGGTAAACGT
1 CTCTTTCAGGAGTGAGGATAGGTAGGTGCCACTAG-CTTGTGTGGGCTTTGAGATAGGTAAGCAT
334238 CCTG
65 CCTG
* * *
334242 CTCTTTCCGGAGTGAGGATAGGTGGGTGCCACTAGCTTGTGTGAGCTTTGAGATAGGTAAGCATC
1 CTCTTTCAGGAGTGAGGATAGGTAGGTGCCACTAGCTTGTGTGGGCTTTGAGATAGGTAAGCATC
*
334307 TTG
66 CTG
334310 CTC
1 CTC
334313 CTTAAGGACT
Statistics
Matches: 110, Mismatches: 26, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
67 17 0.15
68 91 0.83
69 2 0.02
ACGTcount: A:0.20, C:0.16, G:0.33, T:0.32
Consensus pattern (68 bp):
CTCTTTCAGGAGTGAGGATAGGTAGGTGCCACTAGCTTGTGTGGGCTTTGAGATAGGTAAGCATC
CTG
Found at i:335470 original size:20 final size:20
Alignment explanation
Indices: 335447--335499 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
335437 ATACCTAGAT
335447 GTATTGATACATTTTGCTTA
1 GTATTGATACATTTTGCTTA
335467 GTATTGATACATTTTGCTTA
1 GTATTGATACATTTTGCTTA
335487 GTATTGATACATT
1 GTATTGATACATT
335500 GTATCGATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.09, G:0.15, T:0.49
Consensus pattern (20 bp):
GTATTGATACATTTTGCTTA
Found at i:335585 original size:20 final size:20
Alignment explanation
Indices: 335560--335645 Score: 71
Period size: 20 Copynumber: 4.7 Consensus size: 20
335550 CACTATTCAT
335560 GTATCGATACATTGTGAATA
1 GTATCGATACATTGTGAATA
* *
335580 GTATCGATACA---TCACT-
1 GTATCGATACATTGTGAATA
* **
335596 GT-TC-AT-CACTGTTCATA
1 GTATCGATACATTGTGAATA
335613 -TATCGATACATTGTGAATA
1 GTATCGATACATTGTGAATA
335632 GTATCGATACATTG
1 GTATCGATACATTG
335646 AGTCCAACGG
Statistics
Matches: 50, Mismatches: 8, Indels: 16
0.68 0.11 0.22
Matches are distributed among these distances:
13 2 0.04
14 2 0.04
15 2 0.04
16 5 0.10
17 5 0.10
18 2 0.04
19 8 0.16
20 24 0.48
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.36
Consensus pattern (20 bp):
GTATCGATACATTGTGAATA
Found at i:335617 original size:52 final size:52
Alignment explanation
Indices: 335539--335643 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 52
335529 AATCTCATTT
*
335539 TCACTATTCATCACTATTCATGTATCGATACATTGTGAATAGTATCGATACA
1 TCACTATTCATCACTATTCATATATCGATACATTGTGAATAGTATCGATACA
* *
335591 TCACTGTTCATCACTGTTCATATATCGATACATTGTGAATAGTATCGATACA
1 TCACTATTCATCACTATTCATATATCGATACATTGTGAATAGTATCGATACA
335643 T
1 T
335644 TGAGTCCAAC
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.37
Consensus pattern (52 bp):
TCACTATTCATCACTATTCATATATCGATACATTGTGAATAGTATCGATACA
Found at i:336125 original size:36 final size:33
Alignment explanation
Indices: 336080--336172 Score: 109
Period size: 36 Copynumber: 2.8 Consensus size: 33
336070 CGAAGTGATT
336080 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGGG
1 GAGAGGTTCTATCTTAG-CTTTGAAAAAGATA-GG
* *
336115 AGAGAGGTTCTATCATAGCTCGTG-AAAAGATAGG
1 -GAGAGGTTCTATCTTAGCT-TTGAAAAAGATAGG
*
336149 GAG-GTTTCTATCTTAGCTTTGAAA
1 GAGAGGTTCTATCTTAGCTTTGAAA
336173 GATAGTGTTG
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
31 2 0.04
32 15 0.30
33 3 0.06
34 2 0.04
35 10 0.20
36 18 0.36
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.30
Consensus pattern (33 bp):
GAGAGGTTCTATCTTAGCTTTGAAAAAGATAGG
Found at i:336516 original size:29 final size:29
Alignment explanation
Indices: 336463--336529 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 29
336453 GATGGAAAGT
336463 ATAAAACTAACCCTAAAAAGCTCTAAAATGC
1 ATAAAA-TAA-CCTAAAAAGCTCTAAAATGC
* * *
336494 ATGAAATAACCTAAATAGGTCTAAAATGC
1 ATAAAATAACCTAAAAAGCTCTAAAATGC
336523 ATAAAAT
1 ATAAAAT
336530 TGCATAATGG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 24 0.75
30 3 0.09
31 5 0.16
ACGTcount: A:0.52, C:0.16, G:0.09, T:0.22
Consensus pattern (29 bp):
ATAAAATAACCTAAAAAGCTCTAAAATGC
Found at i:336750 original size:17 final size:17
Alignment explanation
Indices: 336728--336760 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
336718 GATGTTAACA
336728 AAATAATAAAA-TAAAAT
1 AAATAA-AAAATTAAAAT
336745 AAATAAAAAATTAAAA
1 AAATAAAAAATTAAAA
336761 ATTAAAAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (17 bp):
AAATAAAAAATTAAAAT
Found at i:337275 original size:52 final size:52
Alignment explanation
Indices: 337201--337318 Score: 200
Period size: 52 Copynumber: 2.3 Consensus size: 52
337191 TGAATAGTAC
*
337201 ATGTATGGATACATTCTATTTTTTTTACCCAGATGTATCGATACATTTTTCA
1 ATGTATCGATACATTCTATTTTTTTTACCCAGATGTATCGATACATTTTTCA
* * *
337253 ATGTATCGATGCATTTTGTTTTTTTTACCCAGATGTATCGATACATTTTTCA
1 ATGTATCGATACATTCTATTTTTTTTACCCAGATGTATCGATACATTTTTCA
337305 ATGTATCGATACAT
1 ATGTATCGATACAT
337319 CTAGTTAATT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 61 1.00
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.46
Consensus pattern (52 bp):
ATGTATCGATACATTCTATTTTTTTTACCCAGATGTATCGATACATTTTTCA
Found at i:340260 original size:20 final size:19
Alignment explanation
Indices: 340235--340307 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 19
340225 CTGCCGGTTT
**
340235 CATGTATCGATACAATTGTG
1 CATGTATCGATACAA-TGAA
340255 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
340274 CATGTATCGATACAAAGCATA
1 CATGTATCGATACAATG-A-A
340295 -ATGTATCGATACA
1 CATGTATCGATACA
340308 TTCTAGGGTT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
19 18 0.38
20 29 0.60
21 1 0.02
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:342719 original size:13 final size:13
Alignment explanation
Indices: 342701--342725 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
342691 TAGTAGCTTA
342701 TGTATCGATACAT
1 TGTATCGATACAT
342714 TGTATCGATACA
1 TGTATCGATACA
342726 ATATATTAAT
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:346884 original size:18 final size:18
Alignment explanation
Indices: 346861--346900 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
346851 ACAGATTTTG
346861 ATTTATTTTCTTCCTTTA
1 ATTTATTTTCTTCCTTTA
346879 ATTTATTTTCTTCCTTTA
1 ATTTATTTTCTTCCTTTA
346897 ATTT
1 ATTT
346901 TAAAAATGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.17, C:0.15, G:0.00, T:0.68
Consensus pattern (18 bp):
ATTTATTTTCTTCCTTTA
Found at i:347322 original size:15 final size:15
Alignment explanation
Indices: 347304--347338 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
347294 CGAGTCAACT
347304 TCATCATTATCATCA
1 TCATCATTATCATCA
*
347319 TCATCATTATCTTCA
1 TCATCATTATCATCA
347334 TCATC
1 TCATC
347339 TTTGATGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (15 bp):
TCATCATTATCATCA
Found at i:348960 original size:13 final size:13
Alignment explanation
Indices: 348942--348966 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
348932 CAATTCTTCA
348942 TGTATCGATACAT
1 TGTATCGATACAT
348955 TGTATCGATACA
1 TGTATCGATACA
348967 ATGTGCCATG
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:348968 original size:33 final size:33
Alignment explanation
Indices: 348922--348986 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
348912 TTTAGGACAA
348922 TGTATCGACACAAT-T-CTTCATGTATCGATACAT
1 TGTATCGACACAATGTGC--CATGTATCGATACAT
*
348955 TGTATCGATACAATGTGCCATGTATCGATACA
1 TGTATCGACACAATGTGCCATGTATCGATACA
348987 AACAGTGGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 27 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (33 bp):
TGTATCGACACAATGTGCCATGTATCGATACAT
Found at i:349039 original size:20 final size:19
Alignment explanation
Indices: 349014--349069 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
349004 TACTACCAGT
*
349014 TTCATGTATCGATATAATTG
1 TTCATGTATCGATACAA-TG
349034 TTCATGTATCGATACAATG
1 TTCATGTATCGATACAATG
**
349053 AACATGTATCGATACAA
1 TTCATGTATCGATACAA
349070 AGCATAATGT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (19 bp):
TTCATGTATCGATACAATG
Found at i:350844 original size:58 final size:57
Alignment explanation
Indices: 350458--351028 Score: 370
Period size: 57 Copynumber: 9.9 Consensus size: 57
350448 GCGACAACCC
* * * * * * * * *
350458 TAAATCATGAAAAATTACTAAAGTGGTCCCAAAAAGCATGAAATTACATTATAGTTCA
1 TAAATCATG-AAAATAACTAAAATGATGCTAAAATGCATGAAATTACATAATAGTCCT
* * * * *
350516 TAAATCATGGAAAATGATTAAAATGATCCTCAAATGTA-GAAATTATC-TAATAGT-CT
1 TAAATCAT-GAAAATAACTAAAATGATGCTAAAATGCATGAAATTA-CATAATAGTCCT
* * *
350572 CTAATTCATGTAAAATGACTAAAAT-A-GCCTTAAAATGCATGAAATTATATAAATAGTCCT
1 -TAAATCATG-AAAATAACTAAAATGATG-C-TAAAATGCATGAAATTACAT-AATAGTCCT
* * * * * * * *
350632 TAAATTATGCAGAATGACCAAAATGGTGCTAAAAATGCATGAAATTGCATTATA-ACC-
1 TAAATCATG-AAAATAACTAAAATGATGCT-AAAATGCATGAAATTACATAATAGTCCT
* * * *
350689 T--CTCATAAAAAATGACTAAAGT-A-GCCTTAAAATGCATG-AATTGACATAATAGTCC-
1 TAAATCAT-GAAAATAACTAAAATGATG-C-TAAAATGCATGAAATT-ACATAATAGTCCT
* * * *
350744 TAAATCGTGAAAAATGATTAAAATGACT-CTAAAATGCATGAAATTACATAATAGTTCT
1 TAAATCATG-AAAATAACTAAAATGA-TGCTAAAATGCATGAAATTACATAATAGTCCT
* * * **
350802 TAAACCATAGAAAATAAGTAAAATTG-TGCTAAAATGCATGAAATTATATAATAACCCT
1 TAAATCAT-GAAAATAACTAAAA-TGATGCTAAAATGCATGAAATTACATAATAGTCCT
* * * * **
350860 TAAATCATGGAAATGAC-AAAACTGA-CCTAAAAATG-AGTAAAATTATGTAATAGTCCT
1 TAAATCATGAAAATAACTAAAA-TGATGCT-AAAATGCA-TGAAATTACATAATAGTCCT
* **
350917 TAAATCATGAAAAATAACTAAAATGATGCTAACATGCATGAAATTACATAATAACCCT
1 TAAATCATG-AAAATAACTAAAATGATGCTAAAATGCATGAAATTACATAATAGTCCT
*
350975 TAAATCATGAAAATGACTAAAATGAT-CTTAAAATGCATGAAATTACATAATAGT
1 TAAATCATGAAAATAACTAAAATGATGC-TAAAATGCATGAAATTACATAATAGT
351029 AACTAATATG
Statistics
Matches: 403, Mismatches: 73, Indels: 75
0.73 0.13 0.14
Matches are distributed among these distances:
53 5 0.01
54 17 0.04
55 18 0.04
56 14 0.03
57 155 0.38
58 133 0.33
59 40 0.10
60 20 0.05
61 1 0.00
ACGTcount: A:0.47, C:0.13, G:0.12, T:0.29
Consensus pattern (57 bp):
TAAATCATGAAAATAACTAAAATGATGCTAAAATGCATGAAATTACATAATAGTCCT
Found at i:350853 original size:115 final size:114
Alignment explanation
Indices: 350458--351028 Score: 374
Period size: 115 Copynumber: 5.0 Consensus size: 114
350448 GCGACAACCC
* * * * * * * * *** *
350458 TAAATCATGAAAAATTACTAAAGTGGTCCCAAAAAGCATGAAATTACATTATAGTTCATAAATCA
1 TAAACCATGAAAAATAACTAAAATGATGCTAAAATGCATGAAATTACATAATAACCCTTAAATCA
* *
350523 TGGAAAATGATTAAAATGA-TCCTCAAATGTA-GAAATTATC-TAATAGT-CT
66 T-GAAAATGA-TAAAATGACT-CTAAAATGCATGAAATTA-CATAATAGTCCT
** * * * **
350572 CTAATTCATGTAAAATGACTAAAAT-A-GCCTTAAAATGCATGAAATTATATAAATAGTCCTTAA
1 -TAAACCATGAAAAATAACTAAAATGATG-C-TAAAATGCATGAAATTACAT-AATAACCCTTAA
* * * * * * *
350635 ATTATGCAGAATGACCAAAATG-GTGCTAAAAATGCATGAAATTGCATTATA-ACC-
62 ATCATG-AAAATGA-TAAAATGACT-CT-AAAATGCATGAAATTACATAATAGTCCT
* * * **
350689 T---CTCATAAAAAATGACTAAAGT-A-GCCTTAAAATGCATG-AATTGACATAATAGTCC-TAA
1 TAAAC-CATGAAAAATAACTAAAATGATG-C-TAAAATGCATGAAATT-ACATAATAACCCTTAA
* *
350747 ATCGTGAAAAATGATTAAAATGACTCTAAAATGCATGAAATTACATAATAGTTCT
62 ATCATG-AAAATGA-TAAAATGACTCTAAAATGCATGAAATTACATAATAGTCCT
* *
350802 TAAACCAT-AGAAAATAAGTAAAATTG-TGCTAAAATGCATGAAATTATATAATAACCCTTAAAT
1 TAAACCATGA-AAAATAACTAAAA-TGATGCTAAAATGCATGAAATTACATAATAACCCTTAAAT
* * * **
350865 CATGGAAATGACAAAACTGAC-CTAAAAATG-AGTAAAATTATGTAATAGTCCT
64 CATGAAAATGATAAAA-TGACTCT-AAAATGCA-TGAAATTACATAATAGTCCT
* *
350917 TAAATCATGAAAAATAACTAAAATGATGCTAACATGCATGAAATTACATAATAACCCTTAAATCA
1 TAAACCATGAAAAATAACTAAAATGATGCTAAAATGCATGAAATTACATAATAACCCTTAAATCA
350982 TGAAAATGACTAAAATGA-TCTTAAAATGCATGAAATTACATAATAGT
66 TGAAAATGA-TAAAATGACTC-TAAAATGCATGAAATTACATAATAGT
351029 AACTAATATG
Statistics
Matches: 364, Mismatches: 60, Indels: 64
0.75 0.12 0.13
Matches are distributed among these distances:
111 21 0.06
112 22 0.06
113 14 0.04
114 46 0.13
115 191 0.52
116 51 0.14
117 8 0.02
118 11 0.03
ACGTcount: A:0.47, C:0.13, G:0.12, T:0.29
Consensus pattern (114 bp):
TAAACCATGAAAAATAACTAAAATGATGCTAAAATGCATGAAATTACATAATAACCCTTAAATCA
TGAAAATGATAAAATGACTCTAAAATGCATGAAATTACATAATAGTCCT
Found at i:353042 original size:20 final size:21
Alignment explanation
Indices: 352998--353046 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 21
352988 TTTTAGAGTT
352998 AATAGATGTTTTTCAAGCATAAA
1 AATA-ATGTTTTTCAAG-ATAAA
353021 AATAATGTTTTTCAAG-TAAA
1 AATAATGTTTTTCAAGATAAA
353041 AATAAT
1 AATAAT
353047 TCAGAGTATC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.38
22 12 0.46
23 4 0.15
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (21 bp):
AATAATGTTTTTCAAGATAAA
Found at i:353152 original size:20 final size:21
Alignment explanation
Indices: 353115--353153 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
353105 AGGTCAAAAC
* *
353115 CCTAGAATGTCTCTATACACA
1 CCTAGAATGTATCGATACACA
353136 CCTAG-ATGTATCGATACA
1 CCTAGAATGTATCGATACA
353154 TGTTGCTAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.33, C:0.26, G:0.13, T:0.28
Consensus pattern (21 bp):
CCTAGAATGTATCGATACACA
Found at i:353187 original size:19 final size:20
Alignment explanation
Indices: 353143--353192 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
353133 ACACCTAGAT
353143 GTATCGATACATGTTGCTAA
1 GTATCGATACATGTTGCTAA
**
353163 GTATCGATACATGTT-CTTG
1 GTATCGATACATGTTGCTAA
353182 GTATCGATACA
1 GTATCGATACA
353193 CCTTGAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (20 bp):
GTATCGATACATGTTGCTAA
Found at i:355338 original size:21 final size:21
Alignment explanation
Indices: 355313--355353 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
355303 TAATACTCTT
* *
355313 GAAAAGAAATTAAATGAGTTG
1 GAAAAAAAAATAAATGAGTTG
*
355334 GAAAAAAAAATAAGTGAGTT
1 GAAAAAAAAATAAATGAGTT
355354 ACAAAATGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.22, T:0.22
Consensus pattern (21 bp):
GAAAAAAAAATAAATGAGTTG
Found at i:359969 original size:51 final size:52
Alignment explanation
Indices: 359888--359994 Score: 153
Period size: 51 Copynumber: 2.1 Consensus size: 52
359878 TCTGGGAAGA
* * *
359888 AAATGTATTGATACATTTTTCATTGCATCGATACATTCTAGGTTTTTGACCC
1 AAATATATTGATACATTATTCATTGCATCGATACATTATAGGTTTTTGACCC
* * *
359940 AAATATATTGATGC-TTATTCATTGTATCGATACATTATGGGTTTTTGACCC
1 AAATATATTGATACATTATTCATTGCATCGATACATTATAGGTTTTTGACCC
359991 AAAT
1 AAAT
359995 GTGTCTATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
51 37 0.76
52 12 0.24
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.42
Consensus pattern (52 bp):
AAATATATTGATACATTATTCATTGCATCGATACATTATAGGTTTTTGACCC
Found at i:360526 original size:53 final size:52
Alignment explanation
Indices: 360456--360560 Score: 174
Period size: 53 Copynumber: 2.0 Consensus size: 52
360446 ACCTTCTCCT
* * *
360456 AGCAATCTTAACTTCCCTTAATAGCTTAAACACTCAGCAAACACAAATTCCC
1 AGCAATCTTAACTTCCCTTAACAGCTCAAACACTCAACAAACACAAATTCCC
360508 AGCAATCCTTAACTTCCCTTAACAGCTCAAACACTCAACAAACACAAATTCCC
1 AGCAAT-CTTAACTTCCCTTAACAGCTCAAACACTCAACAAACACAAATTCCC
360561 GTAGTTCCCC
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
52 6 0.12
53 43 0.88
ACGTcount: A:0.39, C:0.33, G:0.05, T:0.23
Consensus pattern (52 bp):
AGCAATCTTAACTTCCCTTAACAGCTCAAACACTCAACAAACACAAATTCCC
Found at i:368410 original size:19 final size:20
Alignment explanation
Indices: 368364--368417 Score: 74
Period size: 21 Copynumber: 2.7 Consensus size: 20
368354 TTTCAACAAT
368364 TTGTATCGATACAAATAGTA
1 TTGTATCGATACAAATAGTA
* *
368384 TATGTATCGATACATA-AGTG
1 T-TGTATCGATACAAATAGTA
368404 TTGTATCGATACAA
1 TTGTATCGATACAA
368418 TGTATCGCTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 12 0.40
20 5 0.17
21 13 0.43
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (20 bp):
TTGTATCGATACAAATAGTA
Found at i:382401 original size:14 final size:13
Alignment explanation
Indices: 382379--382510 Score: 90
Period size: 14 Copynumber: 9.9 Consensus size: 13
382369 CGTCATTCGC
382379 AAAAAA-AAAAAA
1 AAAAAACAAAAAA
* *
382391 ATAAAACAAAAGAC
1 AAAAAACAAAA-AA
* * *
382405 AAAAAATAGAGACA
1 AAAAAACA-AAAAA
382419 AAAAAACAAAAACA
1 AAAAAACAAAAA-A
*
382433 AAAAAACAACAAAC
1 AAAAAACAA-AAAA
382447 AAAAAACAAAAAA
1 AAAAAACAAAAAA
*
382460 AAAGAGAC--AAAA
1 AAA-AAACAAAAAA
*
382472 AACAAACAAAAAA
1 AAAAAACAAAAAA
* *
382485 CAAAAAGAAAAAA
1 AAAAAACAAAAAA
*
382498 ATAACAACAAAAA
1 A-AAAAACAAAAA
382511 GGGTTCGGAT
Statistics
Matches: 90, Mismatches: 21, Indels: 16
0.71 0.17 0.13
Matches are distributed among these distances:
11 3 0.03
12 11 0.12
13 26 0.29
14 45 0.50
15 5 0.06
ACGTcount: A:0.82, C:0.11, G:0.05, T:0.02
Consensus pattern (13 bp):
AAAAAACAAAAAA
Found at i:382410 original size:21 final size:20
Alignment explanation
Indices: 382378--382498 Score: 102
Period size: 21 Copynumber: 6.0 Consensus size: 20
382368 TCGTCATTCG
*
382378 CAAAAAA-AAAAAAATAAAA
1 CAAAAAACAAAAAAAAAAAA
* * * *
382397 CAAAAGACAAAAAATAGAGA
1 CAAAAAACAAAAAAAAAAAA
382417 CAAAAAAACAAAAACAAAAAAA
1 C-AAAAAACAAAAA-AAAAAAA
* *
382439 CAACAAACAAAAAACAAAAA
1 CAAAAAACAAAAAAAAAAAA
* * * *
382459 -AAAAGAGACAAAAAACAAA
1 CAAAAAACAAAAAAAAAAAA
382478 CAAAAAACAAAAAGAAAAAAA
1 CAAAAAACAAAAA-AAAAAAA
382499 TAACAACAAA
Statistics
Matches: 76, Mismatches: 21, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
19 19 0.25
20 24 0.32
21 28 0.37
22 5 0.07
ACGTcount: A:0.82, C:0.12, G:0.05, T:0.02
Consensus pattern (20 bp):
CAAAAAACAAAAAAAAAAAA
Found at i:382425 original size:28 final size:26
Alignment explanation
Indices: 382393--382504 Score: 99
Period size: 25 Copynumber: 4.3 Consensus size: 26
382383 AAAAAAAAAT
382393 AAAACAAAAGACAAAAAATAGAGACAAA
1 AAAACAAAA-ACAAAAAA-AGAGACAAA
*
382421 AAAACAAAAACAAAAAAACA-ACAAA
1 AAAACAAAAACAAAAAAAGAGACAAA
*
382446 CAAAA-AACAA-AAAAAAAGAGAC-AA
1 -AAAACAAAAACAAAAAAAGAGACAAA
* *
382470 AAAACAAACAA-AAAACAAAAAGAAAAA
1 AAAACAAA-AACAAAA-AAAGAGACAAA
382497 AATAACAA
1 AA-AACAA
382505 CAAAAAGGGT
Statistics
Matches: 71, Mismatches: 6, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
23 4 0.06
24 12 0.17
25 17 0.24
26 12 0.17
27 12 0.17
28 14 0.20
ACGTcount: A:0.80, C:0.12, G:0.05, T:0.02
Consensus pattern (26 bp):
AAAACAAAAACAAAAAAAGAGACAAA
Found at i:382495 original size:11 final size:10
Alignment explanation
Indices: 382378--382510 Score: 85
Period size: 11 Copynumber: 12.6 Consensus size: 10
382368 TCGTCATTCG
382378 CAAAAAAAAA
1 CAAAAAAAAA
*
382388 -AAAATAAAA
1 CAAAAAAAAA
382397 CAAAAGACAAAA
1 CAAAA-A-AAAA
382409 -AATAGAGACAAAA
1 CAA-A-A-A-AAAA
*
382422 -AAACAAAAA
1 CAAAAAAAAA
382431 CAAAAAAACAA
1 CAAAAAAA-AA
382442 CAAACAAAAAA
1 CAAA-AAAAAA
382453 CAAAAAAAAA
1 CAAAAAAAAA
* *
382463 GAGACAAAAAA
1 CA-AAAAAAAA
382474 CAAACAAAAAA
1 CAAA-AAAAAA
382485 CAAAAAGAAAA
1 CAAAAA-AAAA
* *
382496 -AAATAACAA
1 CAAAAAAAAA
382505 CAAAAA
1 CAAAAA
382511 GGGTTCGGAT
Statistics
Matches: 100, Mismatches: 11, Indels: 24
0.74 0.08 0.18
Matches are distributed among these distances:
9 15 0.15
10 29 0.29
11 36 0.36
12 10 0.10
13 10 0.10
ACGTcount: A:0.81, C:0.12, G:0.05, T:0.02
Consensus pattern (10 bp):
CAAAAAAAAA
Found at i:382504 original size:49 final size:47
Alignment explanation
Indices: 382379--382510 Score: 142
Period size: 49 Copynumber: 2.7 Consensus size: 47
382369 CGTCATTCGC
* *
382379 AAAAAAAAAAAAATAAAACAAAAGAC-AAAAAATAGAGACAAAAAAACA
1 AAAAAAAAAAAAACAAAA-AAAA-ACAAAAAAAAAGAGACAAAAAAACA
382427 AAAACAAAAAAACAACAAACAAAAAACAAAAAAAAAGAGAC-AAAAAACA
1 AAAA-AAAAAAA-AACAAA-AAAAAACAAAAAAAAAGAGACAAAAAAACA
* *
382476 AACAAAAAACAAAAAGAAAAAAATAACAACAAAAA
1 AA-AAAAAA-AAAAACAAAAAAA-AACAAAAAAAA
382511 GGGTTCGGAT
Statistics
Matches: 73, Mismatches: 4, Indels: 13
0.81 0.04 0.14
Matches are distributed among these distances:
48 8 0.11
49 38 0.52
50 26 0.36
51 1 0.01
ACGTcount: A:0.82, C:0.11, G:0.05, T:0.02
Consensus pattern (47 bp):
AAAAAAAAAAAAACAAAAAAAAACAAAAAAAAAGAGACAAAAAAACA
Found at i:382510 original size:1 final size:1
Alignment explanation
Indices: 382379--382498 Score: 51
Period size: 1 Copynumber: 120.0 Consensus size: 1
382369 CGTCATTCGC
* * * * * * * * * * * *
382379 AAAAAAAAAAAAATAAAACAAAAGACAAAAAATAGAGACAAAAAAACAAAAACAAAAAAACAACA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * * * *
382444 AACAAAAAACAAAAAAAAAGAGACAAAAAACAAACAAAAAACAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
382499 TAACAACAAA
Statistics
Matches: 77, Mismatches: 42, Indels: 0
0.65 0.35 0.00
Matches are distributed among these distances:
1 77 1.00
ACGTcount: A:0.82, C:0.11, G:0.05, T:0.02
Consensus pattern (1 bp):
A
Found at i:382510 original size:28 final size:28
Alignment explanation
Indices: 382423--382510 Score: 97
Period size: 32 Copynumber: 3.0 Consensus size: 28
382413 GAGACAAAAA
* *
382423 AACAAAAACAAAAAAACAACAAACAAAA
1 AACAAAAAGAAAAAAATAACAAACAAAA
* *
382451 AACAAAAAAAAAGAGACAAAAAACAAACAAAA
1 AAC-AAAAAGAA-A-A-AAATAACAAACAAAA
382483 AACAAAAAGAAAAAAATAAC-AACAAAA
1 AACAAAAAGAAAAAAATAACAAACAAAA
382510 A
1 A
382511 GGGTTCGGAT
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
27 8 0.15
28 9 0.17
29 8 0.15
30 2 0.04
31 8 0.15
32 17 0.33
ACGTcount: A:0.82, C:0.14, G:0.03, T:0.01
Consensus pattern (28 bp):
AACAAAAAGAAAAAAATAACAAACAAAA
Found at i:387870 original size:15 final size:15
Alignment explanation
Indices: 387850--387880 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
387840 TAAAAATGTC
*
387850 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
387865 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
387880 C
1 C
387881 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:390117 original size:20 final size:19
Alignment explanation
Indices: 390076--390118 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
390066 ATCTTTTACA
390076 AAATACTTGTTTTTCACTTC
1 AAATACTTGTTTTTCAC-TC
390096 AAATCACTTCGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
390116 AAA
1 AAA
390119 ACCAGCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.30, C:0.21, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Found at i:394627 original size:21 final size:21
Alignment explanation
Indices: 394571--394629 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
394561 CACCAAATGT
* *
394571 TTTCT-AGTTAAGTATAATTGT
1 TTTCTAAGTTAA-AATAATTGA
394592 TTTC-AAGGATTAAAATAATTGA
1 TTTCTAA-G-TTAAAATAATTGA
394614 TTTCTAAGTTAAAATA
1 TTTCTAAGTTAAAATA
394630 TATCAAAGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
21 13 0.41
22 13 0.41
23 6 0.19
ACGTcount: A:0.39, C:0.05, G:0.12, T:0.44
Consensus pattern (21 bp):
TTTCTAAGTTAAAATAATTGA
Found at i:394848 original size:13 final size:13
Alignment explanation
Indices: 394830--394855 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
394820 TACACCAAGT
394830 ATGTATCGATACA
1 ATGTATCGATACA
394843 ATGTATCGATACA
1 ATGTATCGATACA
394856 CAAAAAATTG
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:394853 original size:32 final size:33
Alignment explanation
Indices: 394812--394875 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
394802 TAGCCAAACT
* **
394812 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
394844 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
394876 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:395831 original size:37 final size:37
Alignment explanation
Indices: 395790--395874 Score: 161
Period size: 37 Copynumber: 2.3 Consensus size: 37
395780 TGCCACAATC
395790 ATGCATTTGTGACATTCATAACATTTCATTTTGCATG
1 ATGCATTTGTGACATTCATAACATTTCATTTTGCATG
*
395827 ATGCATTTATGACATTCATAACATTTCATTTTGCATG
1 ATGCATTTGTGACATTCATAACATTTCATTTTGCATG
395864 ATGCATTTGTG
1 ATGCATTTGTG
395875 CTTCATCTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (37 bp):
ATGCATTTGTGACATTCATAACATTTCATTTTGCATG
Found at i:396396 original size:28 final size:28
Alignment explanation
Indices: 396239--396625 Score: 412
Period size: 28 Copynumber: 13.7 Consensus size: 28
396229 CCTCACCTTC
*
396239 CAAATCCCACAAGTCAGTGGCACCCTTTT
1 CAAAGCCCACAAGTCAGTGGCA-CCTTTT
* *
396268 AAAAGCCCACAAGTTAGTGGCACCCTTTT
1 CAAAGCCCACAAGTCAGTGGCA-CCTTTT
* *
396297 AAAAGCCCACAAGTTAGTGGCACCCTTTT
1 CAAAGCCCACAAGTCAGTGGCA-CCTTTT
* **
396326 CAAAGCCCATAAGTCAGTGGCATTTTTT
1 CAAAGCCCACAAGTCAGTGGCACCTTTT
* * *
396354 CAAAAGCACATAAGTCAGCGGCACCTTTT
1 C-AAAGCCCACAAGTCAGTGGCACCTTTT
* *
396383 CAAAGCCCACAAGTCAGTGGTATCTTTT
1 CAAAGCCCACAAGTCAGTGGCACCTTTT
*
396411 CAAAGCCCACAAGTCAGTGGCATCTTTT
1 CAAAGCCCACAAGTCAGTGGCACCTTTT
*
396439 CAAAGCCCACAAGTCAGTGGCAACC--CT
1 CAAAGCCCACAAGTCAGTGGC-ACCTTTT
*
396466 CAAAAGCCCACAAGTCAATGGCAACC--TT
1 C-AAAGCCCACAAGTCAGTGGC-ACCTTTT
*
396494 CAGAAGCCCACAAGTCAGTGGCATCTTTT
1 CA-AAGCCCACAAGTCAGTGGCACCTTTT
* *
396523 CTAAGCCCACGAGTCAGTGGCAACC-TTT
1 CAAAGCCCACAAGTCAGTGGC-ACCTTTT
* *
396551 -AGAAGCCCATAAGTTAGTGGCACCTTTT
1 CA-AAGCCCACAAGTCAGTGGCACCTTTT
396579 CAAAGCCCACAAGTCAGTGGCAGCC--TT
1 CAAAGCCCACAAGTCAGTGGCA-CCTTTT
* *
396606 CAAAGCCCATAAGGCAGTGG
1 CAAAGCCCACAAGTCAGTGG
396626 TAACCTTCAA
Statistics
Matches: 312, Mismatches: 35, Indels: 24
0.84 0.09 0.06
Matches are distributed among these distances:
27 28 0.09
28 176 0.56
29 108 0.35
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (28 bp):
CAAAGCCCACAAGTCAGTGGCACCTTTT
Found at i:396501 original size:84 final size:84
Alignment explanation
Indices: 396233--396673 Score: 444
Period size: 84 Copynumber: 5.2 Consensus size: 84
396223 AGAATTCCTC
* * * * * * *
396233 ACCTTCCAAATCCCACAAGTCAGTGGCACCCTTTTAAAAGCCCACAAGTTAGTGGCACCCTTTTA
1 ACCTTTCAAAGCCCACAAGTCAGTGGCA-TCTTTTCAAAGCCCACAAGTCAGTGGCAACC-TTCA
*
396298 AAAGCCCACAAGTTAGTGGCA
64 AAAGCCCACAAGTCAGTGGCA
* * * * * *
396319 CCCTTTTCAAAGCCCATAAGTCAGTGGCATTTTTTCAAAAGCACATAAGTCAGCGGC-ACCTTTT
1 ACC-TTTCAAAGCCCACAAGTCAGTGGCATCTTTTC-AAAGCCCACAAGTCAGTGGCAACC--TT
*
396383 C-AAAGCCCACAAGTCAGTGGTA
62 CAAAAGCCCACAAGTCAGTGGCA
* * *
396405 TCTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCAACCCTCAAA
1 ACCTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCAACCTTCAAA
*
396470 AGCCCACAAGTCAATGGCA
66 AGCCCACAAGTCAGTGGCA
* * * *
396489 ACC-TTCAGAAGCCCACAAGTCAGTGGCATCTTTTCTAAGCCCACGAGTCAGTGGCAACCTTTAG
1 ACCTTTCA-AAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCAACCTTCAA
* *
396553 AAGCCCATAAGTTAGTGGC-
65 AAGCCCACAAGTCAGTGGCA
* * * * *
396572 ACCTTTTCAAAGCCCACAAGTCAGTGGCAGC-CTTCAAAGCCCATAAGGCAGTGGTAACCTTCAA
1 ACC-TTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCAACCTTCAA
* **
396636 AAGCACACAAGTTGGT-GCA
65 AAGCCCACAAGTCAGTGGCA
*
396655 ACCCTTGCAAAAGCCCACA
1 A-CCTTTC-AAAGCCCACA
396674 CGAGTTGGTG
Statistics
Matches: 296, Mismatches: 48, Indels: 24
0.80 0.13 0.07
Matches are distributed among these distances:
82 2 0.01
83 51 0.17
84 137 0.46
85 37 0.12
86 28 0.09
87 41 0.14
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (84 bp):
ACCTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCAACCTTCAAA
AGCCCACAAGTCAGTGGCA
Found at i:396747 original size:43 final size:45
Alignment explanation
Indices: 396695--396917 Score: 256
Period size: 43 Copynumber: 4.9 Consensus size: 45
396685 CATCTTCTTC
396695 TAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCA-C-CTT
1 TAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCACTT
* * * *
396738 TAAGTCCAATGTTGCTGGCCTTGATTCAACACATTGGCACCTTCATCTT
1 TAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCA-C--CA-CTT
*
396787 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-C-CTT
1 TAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCACTT
* *
396830 TAAGTCCAATGTTGCTGGCCTTAAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCA-C--CA-CTT
** *
396879 TAAGTCCAATATCACTAGCCTTGAATCAGCATATTGGCA
1 TAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCA
396918 TCCGTAACAT
Statistics
Matches: 151, Mismatches: 17, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
43 74 0.49
45 1 0.01
47 2 0.01
49 74 0.49
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (45 bp):
TAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCACTT
Found at i:396866 original size:92 final size:92
Alignment explanation
Indices: 396690--396917 Score: 384
Period size: 92 Copynumber: 2.5 Consensus size: 92
396680 GGTGGCATCT
*
396690 TCTTCTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTTAAGTCCAATGTTGCTG
1 TCTT-TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTAAGTCCAATGTTGCTG
* *
396755 GCCTTGATTCAACACATTGGCACCTTCA
65 GCCTTAAATCAACACATTGGCACCTTCA
396783 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTAAGTCCAATGTTGCTGG
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTAAGTCCAATGTTGCTGG
* *
396848 CCTTAAATCAGCATATTGGCACCTTCA
66 CCTTAAATCAACACATTGGCACCTTCA
* *
396875 TCTTTAAGTCCAATATCACTAGCCTTGAATCAGCATATTGGCA
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
396918 TCCGTAACAT
Statistics
Matches: 128, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
92 124 0.97
93 4 0.03
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (92 bp):
TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTAAGTCCAATGTTGCTGG
CCTTAAATCAACACATTGGCACCTTCA
Found at i:397043 original size:104 final size:102
Alignment explanation
Indices: 396827--397077 Score: 231
Period size: 104 Copynumber: 2.5 Consensus size: 102
396817 ATATTGGCAC
* * * *
396827 CTTTAAGTCCAATGTTGCTGGCCTTAAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATC
1 CTTTAAGCCCAATGTCGCTGGCCTTAAATCAGCACATTGGCACCTTCATCTTCAAGTCCAATATC
* * *
396892 ACTAGCCTTGAATCAGCATATTGGCATCCGTAACATT
66 ACTAGCCGTGAATCAGCACATTGACATCCGTAACATT
* * * * *
396929 CCTTAA-CCCAATGTCGTTGGCCTTGAATCAGCACATTGGCATTCTTCTCATCTTCAAGTCTAAT
1 CTTTAAGCCCAATGTCGCTGGCCTTAAATCAGCACATTGGCA--CCT-TCATCTTCAAGTCCAAT
* * * * * *
396993 GTCGCT-GACCGTGAATCAGCACGTTGACATTCTTTACA-T
63 ATCACTAG-CCGTGAATCAGCACATTGACATCCGTAACATT
* * * *
397032 CTTTAAGCCCAATATCACTGGTCC-TCAATCAGCATATTGGCACCTT
1 CTTTAAGCCCAATGTCGCTGG-CCTTAAATCAGCACATTGGCACCTT
397078 TATCACTCTT
Statistics
Matches: 118, Mismatches: 25, Indels: 13
0.76 0.16 0.08
Matches are distributed among these distances:
101 31 0.26
102 7 0.06
103 9 0.08
104 69 0.58
105 2 0.02
ACGTcount: A:0.25, C:0.27, G:0.15, T:0.33
Consensus pattern (102 bp):
CTTTAAGCCCAATGTCGCTGGCCTTAAATCAGCACATTGGCACCTTCATCTTCAAGTCCAATATC
ACTAGCCGTGAATCAGCACATTGACATCCGTAACATT
Found at i:404276 original size:19 final size:19
Alignment explanation
Indices: 404252--404318 Score: 74
Period size: 19 Copynumber: 3.8 Consensus size: 19
404242 ATTCAACGAT
404252 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
404271 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
*
404285 -TGTATCGACACATAAGTG
1 TTGTATCGATACATAAGTG
*
404303 TTGTATTGATACATAA
1 TTGTATCGATACATAA
404319 TTAGCTACTG
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
13 10 0.26
15 2 0.05
17 2 0.05
19 25 0.64
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:404289 original size:32 final size:32
Alignment explanation
Indices: 404253--404315 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
404243 TTCAACGATT
*
404253 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGACACATAAGTGTTGTATCGATACAA
*
404285 TGTATCGACACATAAGTGTTGTATTGATACA
1 TGTATCGACACATAAGTGTTGTATCGATACA
404316 TAATTAGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (32 bp):
TGTATCGACACATAAGTGTTGTATCGATACAA
Found at i:404377 original size:13 final size:13
Alignment explanation
Indices: 404359--404383 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
404349 ATTACTTAAA
404359 TGTATCGATACAT
1 TGTATCGATACAT
404372 TGTATCGATACA
1 TGTATCGATACA
404384 CTGATCTTTG
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:404435 original size:52 final size:52
Alignment explanation
Indices: 404400--404517 Score: 218
Period size: 52 Copynumber: 2.3 Consensus size: 52
404390 TTTGTATCGG
404400 TACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAATGTATCAA
1 TACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAATGTATCAA
* *
404452 TACATGCAGGCAAATTTGCCCAGATGTATCGATACACCATGAAATGTATCGA
1 TACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAATGTATCAA
404504 TACATGCAGGCAAA
1 TACATGCAGGCAAA
404518 ATTTCATATT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 64 1.00
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (52 bp):
TACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAATGTATCAA
Found at i:414869 original size:15 final size:15
Alignment explanation
Indices: 414849--414883 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
414839 TGCATCCCTG
414849 GTTCATTCCTTCCAT
1 GTTCATTCCTTCCAT
*
414864 GTTCATTTCTTCCAT
1 GTTCATTCCTTCCAT
*
414879 ATTCA
1 GTTCA
414884 CATCCTCATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.17, C:0.29, G:0.06, T:0.49
Consensus pattern (15 bp):
GTTCATTCCTTCCAT
Found at i:416329 original size:51 final size:52
Alignment explanation
Indices: 416252--416406 Score: 195
Period size: 51 Copynumber: 3.0 Consensus size: 52
416242 TTCATCGATG
* * *
416252 TTTTTATTTCTAAAACACCGATTTTTCACTGTCAGGGATACTCCAACCCCGA
1 TTTTTATTTCTAAAACACCAATTTTTCACTATCAGGGATACTCTAACCCCGA
* **
416304 -TTTTATTTCTAAAACACCAATTTTTCACAATCAGGGATACTCTAACCCTAA
1 TTTTTATTTCTAAAACACCAATTTTTCACTATCAGGGATACTCTAACCCCGA
* * ** *
416355 TTTTTATTCCAAAAACATTGATTTTTTCACTATCAGGGATACTCTAACCCCG
1 TTTTTATTTCTAAAACA-CCAATTTTTCACTATCAGGGATACTCTAACCCCG
416407 TTACTTTCGT
Statistics
Matches: 87, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
51 45 0.52
52 14 0.16
53 28 0.32
ACGTcount: A:0.30, C:0.25, G:0.09, T:0.36
Consensus pattern (52 bp):
TTTTTATTTCTAAAACACCAATTTTTCACTATCAGGGATACTCTAACCCCGA
Found at i:416501 original size:80 final size:81
Alignment explanation
Indices: 416337--416511 Score: 199
Period size: 80 Copynumber: 2.2 Consensus size: 81
416327 TTCACAATCA
* * * * *
416337 GGGATACTCTAACCCTAATTTTTATTCCAAAAACATTGATTTTTTCACTATCAGGGATACTCTAA
1 GGGATACTCTAACCCTAAGTTTTATTCCAAAAACATCGAATTTTCCACTATCAGGGATACTCCAA
* *
416402 CCCCGTTACTTTCGTG
66 CCCCATTACTTTCGAG
* ** * *
416418 GGGATATTCTAACCCT-AGTTTTATTCTTAAAACATCGAATTTTCCATTATCATGGATACTCCAA
1 GGGATACTCTAACCCTAAGTTTTATTCCAAAAACATCGAATTTTCCACTATCAGGGATACTCCAA
* * *
416482 CCTCATTATTTTTGAG
66 CCCCATTACTTTCGAG
*
416498 GGGATACTCCAACC
1 GGGATACTCTAACC
416512 TCGTTATTTT
Statistics
Matches: 77, Mismatches: 17, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
80 62 0.81
81 15 0.19
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.37
Consensus pattern (81 bp):
GGGATACTCTAACCCTAAGTTTTATTCCAAAAACATCGAATTTTCCACTATCAGGGATACTCCAA
CCCCATTACTTTCGAG
Found at i:416511 original size:28 final size:28
Alignment explanation
Indices: 416471--416568 Score: 178
Period size: 28 Copynumber: 3.5 Consensus size: 28
416461 CCATTATCAT
*
416471 GGATACTCCAACCTCATTATTTTTGAGG
1 GGATACTCCAACCTCATTATTTTCGAGG
*
416499 GGATACTCCAACCTCGTTATTTTCGAGG
1 GGATACTCCAACCTCATTATTTTCGAGG
416527 GGATACTCCAACCTCATTATTTTCGAGG
1 GGATACTCCAACCTCATTATTTTCGAGG
416555 GGATACTCCAACCT
1 GGATACTCCAACCT
416569 TGATTTTATT
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 67 1.00
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (28 bp):
GGATACTCCAACCTCATTATTTTCGAGG
Found at i:416616 original size:79 final size:78
Alignment explanation
Indices: 416525--417124 Score: 594
Period size: 79 Copynumber: 7.6 Consensus size: 78
416515 TTATTTTCGA
*
416525 GGGGATACTCCAACCTCATTATTTTCGAGGGGATACTCCAACCTTGATTTTATTTTCAAAACATC
1 GGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCTTGATTTTA-TTTCAAAACATC
416590 GATTTTCCACAATC
65 GATTTTCCACAATC
* * * * * ** *
416604 GGGGATATTCCAACCCCGTTATTTCCAAGGGGATACTCTAACCCCGATTTTATTTCTAGAACATC
1 GGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCTTGATTTTATTTC-AAAACATC
* * *
416669 AATTTTTCATAATC
65 GATTTTCCACAATC
* * * *
416683 GGGGATACTCCAACCCCTTTATTTTCGAGGGGATACTCTAACCCTGATTTTATTTCTAAAACACC
1 GGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCTTGATTTTATTTC-AAAACATC
*
416748 GATATTTTTCCATAATC
65 G--A-TTTTCCACAATC
* * *** * *
416765 AGGGATACTCTAACCATGTTA-TTTCTGAGGGGATACTCCAACCTCGATTTTATTTCTGAAACAT
1 GGGGATACTCCAACCCCATTATTTTC-GAGGGGATACTCCAACCTTGATTTTATTTC-AAAACAT
* *
416829 AGATTTTCCACAAAC
64 CGATTTTCCACAATC
* * **
416844 GGGGATACTCTAACCCCATTATTTTCGAGAGGATACTCCAACCTTGATTTTATTTTTGAAACATC
1 GGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCTTGATTTTA-TTTCAAAACATC
* *
416909 GATTTTTCACAATT
65 GATTTTCCACAATC
* * *
416923 GGGGATACTCCAACCCTATTATTTTTGATGGGATACTCCAACTCTT-ATTTTATTTCCAAAACAT
1 GGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAAC-CTTGATTTTATTT-CAAAACAT
* **
416987 TGATTTTTTACAATC
64 CGATTTTCCACAATC
* ** * * *
417002 GGGGATACTCCAACCTCC-TTATTTTTGAGGGGATAACTCTGACCTCGTTTTTATTTCCAAACAT
1 GGGGATACTCCAACC-CCATTATTTTCGAGGGGAT-ACTCCAACCTTGATTTTATTTCAAAACAT
* *
417066 CGATTTTCTACCATTC
64 CGATTTTCCA-CAATC
** * * *
417082 ACGGATACTCTAACCCCGTTATTTTTGAGGGGATACTCCAACC
1 GGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACC
417125 CCATTTTTAT
Statistics
Matches: 437, Mismatches: 70, Indels: 28
0.82 0.13 0.05
Matches are distributed among these distances:
78 7 0.02
79 306 0.70
80 58 0.13
81 5 0.01
82 61 0.14
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.35
Consensus pattern (78 bp):
GGGGATACTCCAACCCCATTATTTTCGAGGGGATACTCCAACCTTGATTTTATTTCAAAACATCG
ATTTTCCACAATC
Found at i:416836 original size:240 final size:237
Alignment explanation
Indices: 416526--417131 Score: 713
Period size: 240 Copynumber: 2.5 Consensus size: 237
416516 TATTTTCGAG
* *
416526 GGGATACTCCAACCTCATTATTT-TCGAGGGGATACTCCAACCTTGATTTTATTT-TCAAAACAT
1 GGGATACTCCAACCTCCTTATTTCT-GAGGGGATACTCCAACCTCGATTTTATTTCT-AAAACAT
* * * * *
416589 CGATTTTCCACAATCGGGGATATTCCAACCCCGTTATTTCCAAGGGGATACTCTAACCCCGATTT
64 CGATTTTCCACAATCGGGGATACTCTAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTT
*
416654 TATTTCTAG-AACATCAATTTTTCATAATCGGGGATACTCCAACCCCT-TTATTTTCGAGGGGAT
129 TATTT-TAGAAACATCAATTTTTCACAATCGGGGATACTCCAA-CCCTATTATTTTCGAGGGGAT
* * *
416717 ACTCTAACCCTGATTTTATTTCTAAAACACCGATATTTTTCCATAATCA
192 ACTCCAACCCTGATTTTATTTCCAAAACACCGAT-TTTTT--ACAATCA
* * * *
416766 GGGATACTCTAACCAT-GTTATTTCTGAGGGGATACTCCAACCTCGATTTTATTTCTGAAACATA
1 GGGATACTCCAACC-TCCTTATTTCTGAGGGGATACTCCAACCTCGATTTTATTTCTAAAACATC
* * * **
416830 GATTTTCCACAAACGGGGATACTCTAACCCCATTATTTTCGAGAGGATACTCCAACCTTGATTTT
65 GATTTTCCACAATCGGGGATACTCTAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTT
* * * * *
416895 ATTTTTGAAACATCGATTTTTCACAATTGGGGATACTCCAACCCTATTATTTTTGATGGGATACT
130 ATTTTAGAAACATCAATTTTTCACAATCGGGGATACTCCAACCCTATTATTTTCGAGGGGATACT
* * ** *
416960 CCAACTCTTATTTTATTTCCAAAACATTGATTTTTTACAATCG
195 CCAACCCTGATTTTATTTCCAAAACACCGATTTTTTACAATCA
* ** * *
417003 GGGATACTCCAACCTCCTTATTTTTGAGGGGATAACTCTGACCTCGTTTTTATTTC-CAAACATC
1 GGGATACTCCAACCTCCTTATTTCTGAGGGGAT-ACTCCAACCTCGATTTTATTTCTAAAACATC
* * ** *
417067 GATTTTCTACCATTCACGGATACTCTAACCCCGTTATTTTTGAGGGGATACTCCAACCCC-ATTT
65 GATTTTCCA-CAATCGGGGATACTCTAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTT
417131 T
129 T
417132 TATCTCTAAA
Statistics
Matches: 311, Mismatches: 47, Indels: 19
0.82 0.12 0.05
Matches are distributed among these distances:
236 1 0.00
237 52 0.17
238 60 0.19
239 11 0.04
240 184 0.59
241 3 0.01
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (237 bp):
GGGATACTCCAACCTCCTTATTTCTGAGGGGATACTCCAACCTCGATTTTATTTCTAAAACATCG
ATTTTCCACAATCGGGGATACTCTAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTA
TTTTAGAAACATCAATTTTTCACAATCGGGGATACTCCAACCCTATTATTTTCGAGGGGATACTC
CAACCCTGATTTTATTTCCAAAACACCGATTTTTTACAATCA
Found at i:416885 original size:319 final size:317
Alignment explanation
Indices: 416525--417124 Score: 812
Period size: 319 Copynumber: 1.9 Consensus size: 317
416515 TTATTTTCGA
* *
416525 GGGGATACTCCAACCTCATTATTTTCGAGGGGATACTCCAACCTTGATTTTATTTTCAAAACATC
1 GGGGATACTCCAACCCCATTATTTTCGAGAGGATACTCCAACCTTGATTTTATTTTCAAAACATC
* * *
416590 GATTTTCCACAATCGGGGATATTCCAACCCCGTTATTTCCAAGGGGATACTCTAACCCCGATTTT
66 GATTTTCCACAATCGGGGATACTCCAACCCCATTATTTCCAAGGGGATACTCCAACCCCGATTTT
* * *
416655 ATTTCTAGAACATCAATTTTTCATAATCGGGGATACTCCAACC-CCTTTATTTTCGAGGGGAT-A
131 ATTTCCAAAACATCAATTTTTCACAATCGGGGATACTCCAACCTCC-TTATTTTCGAGGGGATAA
* *
416718 CTCTAACC-CTGATTTTATTTCTAAAACACCGATATTT-TTCCATAATCAGGGATACTCTAACCA
195 CTCTAACCTC-GATTTTATTTC-AAAACACCGAT-TTTCTACCAT--TCACGGATACTCTAACCA
*
416781 TGTTATTTCTGAGGGGATACTCCAACCTCGATTTTATTTCTGAAACATAGATTTTCCACAAAC
255 CGTTATTTCTGAGGGGATACTCCAACCTCGATTTTATTTCTGAAACATAGATTTTCCACAAAC
* **
416844 GGGGATACTCTAACCCCATTATTTTCGAGAGGATACTCCAACCTTGATTTTATTTTTGAAACATC
1 GGGGATACTCCAACCCCATTATTTTCGAGAGGATACTCCAACCTTGATTTTATTTTCAAAACATC
* * * *** * * **
416909 GATTTTTCACAATTGGGGATACTCCAACCCTATTATTTTTGATGGGATACTCCAACTCTTATTTT
66 GATTTTCCACAATCGGGGATACTCCAACCCCATTATTTCCAAGGGGATACTCCAACCCCGATTTT
** * *
416974 ATTTCCAAAACATTGATTTTTTACAATCGGGGATACTCCAACCTCCTTATTTTTGAGGGGATAAC
131 ATTTCCAAAACATCAATTTTTCACAATCGGGGATACTCCAACCTCCTTATTTTCGAGGGGATAAC
* * * * *
417039 TCTGACCTCGTTTTTATTTCCAAACATCGATTTTCTACCATTCACGGATACTCTAACCCCGTTAT
196 TCTAACCTCGATTTTATTTCAAAACACCGATTTTCTACCATTCACGGATACTCTAACCACGTTAT
*
417104 TTTTGAGGGGATACTCCAACC
261 TTCTGAGGGGATACTCCAACC
417125 CCATTTTTAT
Statistics
Matches: 243, Mismatches: 34, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
317 41 0.17
318 3 0.01
319 178 0.73
320 20 0.08
321 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.35
Consensus pattern (317 bp):
GGGGATACTCCAACCCCATTATTTTCGAGAGGATACTCCAACCTTGATTTTATTTTCAAAACATC
GATTTTCCACAATCGGGGATACTCCAACCCCATTATTTCCAAGGGGATACTCCAACCCCGATTTT
ATTTCCAAAACATCAATTTTTCACAATCGGGGATACTCCAACCTCCTTATTTTCGAGGGGATAAC
TCTAACCTCGATTTTATTTCAAAACACCGATTTTCTACCATTCACGGATACTCTAACCACGTTAT
TTCTGAGGGGATACTCCAACCTCGATTTTATTTCTGAAACATAGATTTTCCACAAAC
Found at i:417744 original size:13 final size:13
Alignment explanation
Indices: 417726--417751 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
417716 TACACCAAGT
417726 ATGTATCGATACA
1 ATGTATCGATACA
417739 ATGTATCGATACA
1 ATGTATCGATACA
417752 TTGGCTTGTA
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:422667 original size:20 final size:20
Alignment explanation
Indices: 422642--422691 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
422632 AAGGAAATAT
422642 ATCGATACATTATTCAATGC
1 ATCGATACATTATTCAATGC
*
422662 ATCGATACATTATTCAATGT
1 ATCGATACATTATTCAATGC
422682 ATCGATACAT
1 ATCGATACAT
422692 GCAGGCAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (20 bp):
ATCGATACATTATTCAATGC
Found at i:427594 original size:27 final size:27
Alignment explanation
Indices: 427564--427628 Score: 112
Period size: 27 Copynumber: 2.4 Consensus size: 27
427554 GTCTGTAAGC
*
427564 CTAATGAAGCTAGTAAGCTAGTTCCAG
1 CTAAAGAAGCTAGTAAGCTAGTTCCAG
427591 CTAAAGAAGCTAGTAAGCTAGTTCCAG
1 CTAAAGAAGCTAGTAAGCTAGTTCCAG
*
427618 CTAAAAAAGCT
1 CTAAAGAAGCT
427629 TGTACCATGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.23
Consensus pattern (27 bp):
CTAAAGAAGCTAGTAAGCTAGTTCCAG
Found at i:427733 original size:55 final size:55
Alignment explanation
Indices: 427596--427797 Score: 154
Period size: 55 Copynumber: 3.7 Consensus size: 55
427586 TCCAGCTAAA
* * ** ** *
427596 GAAGCTAGTAAGCTAGTTCCAGCTAAAAAAG-CTTGTACCATGAGTCAAGCCCAAT
1 GAAGCTAGTAGGCTAGTTCCAACTAAATTAGAC-CATACCAAGAGTCAAGCCCAAT
* * *
427651 GATGCTAGTAGGCTAGTTCCTACTAAATTAGACCATACCAAGAGTTAAGCCCAAT
1 GAAGCTAGTAGGCTAGTTCCAACTAAATTAGACCATACCAAGAGTCAAGCCCAAT
* * * * ** * ** *
427706 GAAGTTAGTAGGCTTGTTCCAACTAAATTGGCCCATATTAAAAACCAAGCCTAAT
1 GAAGCTAGTAGGCTAGTTCCAACTAAATTAGACCATACCAAGAGTCAAGCCCAAT
* * * * * *
427761 GAAGCGAGTAAGATAATTCTAACTAAATTAGCCCATA
1 GAAGCTAGTAGGCTAGTTCCAACTAAATTAGACCATA
427798 TCGTGAACTA
Statistics
Matches: 115, Mismatches: 31, Indels: 2
0.78 0.21 0.01
Matches are distributed among these distances:
55 114 0.99
56 1 0.01
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (55 bp):
GAAGCTAGTAGGCTAGTTCCAACTAAATTAGACCATACCAAGAGTCAAGCCCAAT
Found at i:427950 original size:54 final size:54
Alignment explanation
Indices: 427882--428072 Score: 247
Period size: 54 Copynumber: 3.5 Consensus size: 54
427872 GGTGGTACGT
* * ** * *
427882 TAGTTCTAGCTAGTTGGCTCATACCAAGAGTTAAGCCTGATGACATTGTTAGGC
1 TAGTTCTAGCTAGTTGGCCCATACCAAGAGTCAAGCCCAATGACACTGGTAGGC
* * * * *
427936 TAATTGTAACTAGTTGGCCCATATCGAGAGTCAAGCCCAATGACACTGGTAGGC
1 TAGTTCTAGCTAGTTGGCCCATACCAAGAGTCAAGCCCAATGACACTGGTAGGC
* * *
427990 TAGTTCTAGCTAGTTGGCCCATATCGAGAGTCAAGCCCAATGACACTGGTAGCC
1 TAGTTCTAGCTAGTTGGCCCATACCAAGAGTCAAGCCCAATGACACTGGTAGGC
*
428044 TAGTTCTAGCTAGTTGGCCCATACTAAGA
1 TAGTTCTAGCTAGTTGGCCCATACCAAGA
428073 ATTAAACACA
Statistics
Matches: 119, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 119 1.00
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (54 bp):
TAGTTCTAGCTAGTTGGCCCATACCAAGAGTCAAGCCCAATGACACTGGTAGGC
Found at i:428542 original size:21 final size:21
Alignment explanation
Indices: 428509--428549 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
428499 CTAAGTAAAA
428509 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
428530 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
428550 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:428614 original size:20 final size:19
Alignment explanation
Indices: 428589--428659 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
428579 ACCCTGAAAA
428589 GTATCGATACACATTTAAAT
1 GTATCGATACACA-TTAAAT
* **
428609 GTATCGATACAAATTGCAT
1 GTATCGATACACATTAAAT
**
428628 AGTATCGATACACACAAATAT
1 -GTATCGATACACATTAA-AT
428649 GTATCGATACA
1 GTATCGATACA
428660 GGACATTGGC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.10
20 35 0.85
21 2 0.05
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.30
Consensus pattern (19 bp):
GTATCGATACACATTAAAT
Found at i:428712 original size:53 final size:53
Alignment explanation
Indices: 428629--428807 Score: 287
Period size: 53 Copynumber: 3.5 Consensus size: 53
428619 AAATTGCATA
428629 GTATCGATACACACAAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
1 GTATCGATACACA-AAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
* *
428683 GTATCGATACACACAATATGTATCGATACAGGTCATTGGCAGTAGCCAAATTT
1 GTATCGATACACAAAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
*
428736 GTATCGATACACAAAATATGTATCGAT-----ACATTGGAAGTAGCCAAATTT
1 GTATCGATACACAAAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
428784 GTATCGATACACAAAATATGTATC
1 GTATCGATACACAAAATATGTATC
428808 ACCTTCATGT
Statistics
Matches: 120, Mismatches: 5, Indels: 6
0.92 0.04 0.05
Matches are distributed among these distances:
48 43 0.36
53 64 0.53
54 13 0.11
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.28
Consensus pattern (53 bp):
GTATCGATACACAAAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
Found at i:428842 original size:9 final size:9
Alignment explanation
Indices: 428828--428855 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
428818 ATCGATACAT
428828 CACTGTTCA
1 CACTGTTCA
428837 CACTGTTCA
1 CACTGTTCA
428846 CACTGTTCA
1 CACTGTTCA
428855 C
1 C
428856 GTATCACTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.21, C:0.36, G:0.11, T:0.32
Consensus pattern (9 bp):
CACTGTTCA
Found at i:428940 original size:13 final size:13
Alignment explanation
Indices: 428922--428947 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
428912 ACATATTTGT
428922 GTGTATCGATACA
1 GTGTATCGATACA
428935 GTGTATCGATACA
1 GTGTATCGATACA
428948 TCATAAACAG
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:0.23, T:0.31
Consensus pattern (13 bp):
GTGTATCGATACA
Found at i:429481 original size:34 final size:35
Alignment explanation
Indices: 429418--429484 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
429408 CTAAGTGATT
429418 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
429454 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
429485 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:432381 original size:34 final size:35
Alignment explanation
Indices: 432343--432410 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
432333 TAACTTACAG
*
432343 CCCTATCTTTT-CGAAGGCTAAGATAGAACCTCTT
1 CCCTATCTTTTACAAAGGCTAAGATAGAACCTCTT
*
432377 CCCTATTTTTTACAAAGGCTAAGATAGAACCTCT
1 CCCTATCTTTTACAAAGGCTAAGATAGAACCTCT
432411 CAATCACTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 10 0.32
35 21 0.68
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.32
Consensus pattern (35 bp):
CCCTATCTTTTACAAAGGCTAAGATAGAACCTCTT
Found at i:433240 original size:13 final size:13
Alignment explanation
Indices: 433222--433246 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
433212 TAGCCAAACT
433222 TGTATCGATACAA
1 TGTATCGATACAA
433235 TGTATCGATACA
1 TGTATCGATACA
433247 CAAAAAATTG
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:435503 original size:21 final size:21
Alignment explanation
Indices: 435470--435514 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
435460 TTGCAAGTTG
*
435470 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
435492 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
435512 AAA
1 AAA
435515 ATTAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:437338 original size:15 final size:15
Alignment explanation
Indices: 437318--437348 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
437308 TAAAAATGTC
*
437318 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
437333 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
437348 C
1 C
437349 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:439436 original size:13 final size:13
Alignment explanation
Indices: 439418--439456 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
439408 ACATTTTTCT
439418 TTGTATCGATACA
1 TTGTATCGATACA
439431 TTGTATCGATACA
1 TTGTATCGATACA
*
439444 CTGTATCGATACA
1 TTGTATCGATACA
439457 GGAGGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:439620 original size:20 final size:19
Alignment explanation
Indices: 439579--439621 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
439569 ATCTTTTACA
439579 AAATACTTGTTTTTCACTTC
1 AAATACTTGTTTTTCAC-TC
439599 AAATCACTTCGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
439619 AAA
1 AAA
439622 ACCAGCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.30, C:0.21, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Found at i:439939 original size:21 final size:20
Alignment explanation
Indices: 439891--439931 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
439881 CCCCTAGGTA
* *
439891 GCACTACCAGGTCGCGACCG
1 GCACTCCCAGGTCGCAACCG
439911 GCACTCCCAGGTCGCAACCG
1 GCACTCCCAGGTCGCAACCG
439931 G
1 G
439932 GCAGTCCCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.20, C:0.41, G:0.29, T:0.10
Consensus pattern (20 bp):
GCACTCCCAGGTCGCAACCG
Found at i:442020 original size:13 final size:13
Alignment explanation
Indices: 442002--442027 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
441992 TACAGCAAGT
442002 ATGTATCGATACA
1 ATGTATCGATACA
442015 ATGTATCGATACA
1 ATGTATCGATACA
442028 CAAAAAATTG
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:443870 original size:21 final size:24
Alignment explanation
Indices: 443825--443870 Score: 71
Period size: 21 Copynumber: 2.0 Consensus size: 24
443815 AAAAATCATA
443825 AATCATATAAAAGAATGAGAAATG
1 AATCATATAAAAGAATGAGAAATG
443849 AATCAT-TAAAA-AATGA-AAATG
1 AATCATATAAAAGAATGAGAAATG
443870 A
1 A
443871 TAATAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 6 0.27
22 5 0.23
23 5 0.23
24 6 0.27
ACGTcount: A:0.61, C:0.04, G:0.13, T:0.22
Consensus pattern (24 bp):
AATCATATAAAAGAATGAGAAATG
Found at i:451146 original size:21 final size:20
Alignment explanation
Indices: 451120--451172 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
451110 TCACTGTGCA
* *
451120 TGTATCAATACATACTTGAAT
1 TGTATCGATACATA-GTGAAT
*
451141 TGTATCGATAC-TAGTGCAT
1 TGTATCGATACATAGTGAAT
451160 TGTATCGATACAT
1 TGTATCGATACAT
451173 TGAGCCCAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 15 0.54
20 3 0.11
21 10 0.36
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (20 bp):
TGTATCGATACATAGTGAAT
Found at i:460686 original size:34 final size:35
Alignment explanation
Indices: 460643--460710 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
460633 AACCTTAAAA
460643 CCCTATCTTTT-CAAAGGCTAAGATAAAACCTCTT
1 CCCTATCTTTTACAAAGGCTAAGATAAAACCTCTT
* *
460677 CCCTATCTTTTACAGAGGCTAAGATAGAACCTCT
1 CCCTATCTTTTACAAAGGCTAAGATAAAACCTCT
460711 CAATCACTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 11 0.35
35 20 0.65
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.31
Consensus pattern (35 bp):
CCCTATCTTTTACAAAGGCTAAGATAAAACCTCTT
Found at i:461188 original size:21 final size:20
Alignment explanation
Indices: 461142--461188 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
461132 GTTGGGCCAC
***
461142 ATGTATCGATACAATTCTTG
1 ATGTATCGATACAATTCAAA
461162 ATGTATCGATACAATTCAAAA
1 ATGTATCGATACAATTC-AAA
461183 ATGTAT
1 ATGTAT
461189 AGTGGTAGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACAATTCAAA
Found at i:462716 original size:13 final size:13
Alignment explanation
Indices: 462698--462722 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
462688 AATTATGACA
462698 AAATAAATAAAAT
1 AAATAAATAAAAT
462711 AAATAAATAAAA
1 AAATAAATAAAA
462723 CTATGCATTG
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAATAAATAAAAT
Found at i:464967 original size:65 final size:65
Alignment explanation
Indices: 464852--465296 Score: 298
Period size: 66 Copynumber: 6.8 Consensus size: 65
464842 TTAAGGTGAG
* * * * * *
464852 ACCTAAGTCGAAAGGAAGTTGATTGAGGCGAAACCGTCACATCAAATAAAAGGTGACTAGGGATA
1 ACCTAAGTCTAAAGGAGGTTGACT-AGGTGAAACCATCACATCAACTAAAAGGTGACTAGGGATA
464917 A
65 A
* * *** *
464918 ACCTAA-TTTAAAGTGAGGTTGACTAGGTAAAACCATCACATCAACTAAAAGACAACTAAGGCA-
1 ACCTAAGTCTAAAG-GAGGTTGACTAGGTGAAACCATCACATCAACTAAAAGGTGACT-AGGGAT
*
464981 AT
64 AA
* * ** ** **
464983 ACCTAAGTCGAAAAGAGGTTGA-TAAGGTGAAATAATCATGTCAACTAAAAGGTGACTAGGGCGA
1 ACCTAAGTCTAAAGGAGGTTGACT-AGGTGAAACCATCACATCAACTAAAAGGTGACTAGGGATA
465047 A
65 A
* * * *
465048 ACCTAAGTCAAAAGG-GGATTGACTAGGATGAAACCAAT-ACAATTAAC-AAATGGCGACTA-GG
1 ACCTAAGTCTAAAGGAGG-TTGACTAGG-TGAAACC-ATCAC-ATCAACTAAAAGGTGACTAGGG
*
465109 ACAAA
62 A-TAA
* * *
465114 ACCTAAGTCTAAAGGAGATTGCCTAGGGTGAAACCATCACATCAACTAAAAGGTGAC-AAGGATG
1 ACCTAAGTCTAAAGGAGGTTGACTA-GGTGAAACCATCACATCAACTAAAAGGTGACTAGGGAT-
465178 AA
64 AA
* * * * * * * *
465180 ATCTAAGTCAAAAAGAGGTTGACCAAGGGGAAACCATCACGTCAACTAAAAGGTGACCAGAGCA-
1 ACCTAAGTCTAAAGGAGGTTGA-CTAGGTGAAACCATCACATCAACTAAAAGGTGACTAG-GGAT
*
465244 AG
64 AA
* * * * *
465246 ACATAGGT-TGAAAGGAGGTTGACCAAGGTGAAACCATCACGTTAACTAAAA
1 ACCTAAGTCT-AAAGGAGGTTGA-CTAGGTGAAACCATCACATCAACTAAAA
465297 TCTTATTGAG
Statistics
Matches: 295, Mismatches: 63, Indels: 42
0.74 0.16 0.10
Matches are distributed among these distances:
64 6 0.02
65 102 0.35
66 173 0.59
67 12 0.04
68 2 0.01
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.18
Consensus pattern (65 bp):
ACCTAAGTCTAAAGGAGGTTGACTAGGTGAAACCATCACATCAACTAAAAGGTGACTAGGGATAA
Found at i:465237 original size:34 final size:34
Alignment explanation
Indices: 465138--465238 Score: 95
Period size: 34 Copynumber: 3.0 Consensus size: 34
465128 GAGATTGCCT
*
465138 AGGGTGAAACCATCACATCAACTAAAAGGTGA-CA
1 AGGG-GAAACCATCACGTCAACTAAAAGGTGACCA
* * *
465172 AGGATGAAATC-T-AAGTCAA--AAAGAGGTTGACCA
1 AGG-GGAAACCATCACGTCAACTAAA-AGG-TGACCA
465205 AGGGGAAACCATCACGTCAACTAAAAGGTGACCA
1 AGGGGAAACCATCACGTCAACTAAAAGGTGACCA
465239 GAGCAAGACA
Statistics
Matches: 52, Mismatches: 7, Indels: 16
0.69 0.09 0.21
Matches are distributed among these distances:
30 3 0.06
31 3 0.06
32 13 0.25
33 7 0.13
34 20 0.38
35 3 0.06
36 3 0.06
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.15
Consensus pattern (34 bp):
AGGGGAAACCATCACGTCAACTAAAAGGTGACCA
Found at i:465505 original size:19 final size:19
Alignment explanation
Indices: 465481--465535 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
465471 GATAAGGAAC
465481 TTACATGACTTTATTCTAT
1 TTACATGACTTTATTCTAT
* **
465500 TTACAT-A--TGA-TGAAT
1 TTACATGACTTTATTCTAT
465515 TTACATGACTTTATTCTAT
1 TTACATGACTTTATTCTAT
465534 TT
1 TT
465536 GAAATTAAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 8
0.65 0.15 0.20
Matches are distributed among these distances:
15 9 0.35
16 3 0.12
18 3 0.12
19 11 0.42
ACGTcount: A:0.29, C:0.13, G:0.07, T:0.51
Consensus pattern (19 bp):
TTACATGACTTTATTCTAT
Found at i:466646 original size:13 final size:13
Alignment explanation
Indices: 466628--466652 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
466618 ATTTTGCTTA
466628 GTATCGATACATT
1 GTATCGATACATT
466641 GTATCGATACAT
1 GTATCGATACAT
466653 GTTTATTGTA
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):
GTATCGATACATT
Found at i:466662 original size:19 final size:17
Alignment explanation
Indices: 466638--466689 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 17
466628 GTATCGATAC
466638 ATTGTATCGATACAT-G
1 ATTGTATCGATACATAG
*
466654 TTTATTGTATCGATAGATAG
1 ---ATTGTATCGATACATAG
466674 ATTGTATCGATACATA
1 ATTGTATCGATACATA
466690 AAACTGGTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 15 0.50
19 14 0.47
20 1 0.03
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (17 bp):
ATTGTATCGATACATAG
Found at i:466748 original size:22 final size:22
Alignment explanation
Indices: 466720--466773 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
466710 ACACTTTTAA
*
466720 ATCGATACATTACTATTCATGT
1 ATCGATACATCACTATTCATGT
* *
466742 ATCGATACATCATTGTTCATGT
1 ATCGATACATCACTATTCATGT
466764 ATCGATACAT
1 ATCGATACAT
466774 GTGAATAGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (22 bp):
ATCGATACATCACTATTCATGT
Found at i:468643 original size:21 final size:21
Alignment explanation
Indices: 468619--468677 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
468609 TAATATTCTT
* *
468619 GAAAAGAAATTAAGTGAATTA
1 GAAAAGAAAATAAATGAATTA
468640 GAAAAGAAAATAAATGAATTA
1 GAAAAGAAAATAAATGAATTA
** *
468661 GAGGAGAAAAGAAATGA
1 GAAAAGAAAATAAATGA
468678 GTTGCAAGTG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.61, C:0.00, G:0.22, T:0.17
Consensus pattern (21 bp):
GAAAAGAAAATAAATGAATTA
Found at i:471980 original size:13 final size:13
Alignment explanation
Indices: 471962--471987 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
471952 ACATTTTGGG
471962 ATGTATCGATACA
1 ATGTATCGATACA
471975 ATGTATCGATACA
1 ATGTATCGATACA
471988 TATTGTGTGT
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:471982 original size:33 final size:32
Alignment explanation
Indices: 471940--472007 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
471930 CGTTACAAGC
*
471940 CAATGTATCGATACATTTTGGGATGTATCGATA
1 CAATGTATCGATACATATTGGG-TGTATCGATA
*
471973 CAATGTATCGATACATATTGTGTGTATCGATA
1 CAATGTATCGATACATATTGGGTGTATCGATA
472005 CAA
1 CAA
472008 ACAGTTAAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATATTGGGTGTATCGATA
Found at i:472095 original size:20 final size:21
Alignment explanation
Indices: 472045--472100 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
472035 ACTGCCAATC
*
472045 ACATGTATCGATACATTCTTT
1 ACATGTATCGATACATTCTGT
*
472066 ACAAGTATCGATACATT-TGGT
1 ACATGTATCGATACATTCT-GT
472087 -CATGTATCGATACA
1 ACATGTATCGATACA
472101 ATGTATCGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (21 bp):
ACATGTATCGATACATTCTGT
Found at i:472106 original size:13 final size:13
Alignment explanation
Indices: 472088--472112 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
472078 ACATTTGGTC
472088 ATGTATCGATACA
1 ATGTATCGATACA
472101 ATGTATCGATAC
1 ATGTATCGATAC
472113 TGTGCATTAT
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):
ATGTATCGATACA
Found at i:474596 original size:13 final size:13
Alignment explanation
Indices: 474578--474615 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
474568 ATAATCCCTT
*
474578 TGTATCGATACAC
1 TGTATCGATACAA
474591 TGTATCGATACAA
1 TGTATCGATACAA
474604 TGTATCGATACA
1 TGTATCGATACA
474616 GAGAATGCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:474831 original size:8 final size:8
Alignment explanation
Indices: 474818--474843 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
474808 AACATCAATC
474818 ATCACAAA
1 ATCACAAA
474826 ATCACAAA
1 ATCACAAA
474834 ATCACAAA
1 ATCACAAA
474842 AT
1 AT
474844 TTAATCAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (8 bp):
ATCACAAA
Found at i:480731 original size:13 final size:13
Alignment explanation
Indices: 480713--480738 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
480703 ACATTTTGGG
480713 ATGTATCGATACA
1 ATGTATCGATACA
480726 ATGTATCGATACA
1 ATGTATCGATACA
480739 TATTGTGTGT
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:480733 original size:33 final size:32
Alignment explanation
Indices: 480691--480758 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
480681 CGTTACAAGC
*
480691 CAATGTATCGATACATTTTGGGATGTATCGATA
1 CAATGTATCGATACATATTGGG-TGTATCGATA
* *
480724 CAATGTATCGATACATATTGTGTGTATCTATA
1 CAATGTATCGATACATATTGGGTGTATCGATA
480756 CAA
1 CAA
480759 ACAGTTAAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 12 0.38
33 20 0.62
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (32 bp):
CAATGTATCGATACATATTGGGTGTATCGATA
Found at i:481401 original size:20 final size:19
Alignment explanation
Indices: 481357--481408 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
481347 GTGTCGATAT
* **
481357 ATTGTATCGATACATGTTT
1 ATTGTATCGATACATATGG
481376 ATTGTATCGATACATCATGG
1 ATTGTATCGATACAT-ATGG
*
481396 ATTGTATCTATAC
1 ATTGTATCGATAC
481409 GTAAAATTAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.42
Consensus pattern (19 bp):
ATTGTATCGATACATATGG
Found at i:481473 original size:22 final size:22
Alignment explanation
Indices: 481445--481492 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
481435 CTTTTAAATT
* *
481445 GATACATTATTGTTCATGTATC
1 GATACATCACTGTTCATGTATC
481467 GATACATCACTGTTCATGTATC
1 GATACATCACTGTTCATGTATC
481489 GATA
1 GATA
481493 TATGTGAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.40
Consensus pattern (22 bp):
GATACATCACTGTTCATGTATC
Found at i:486145 original size:16 final size:16
Alignment explanation
Indices: 486120--486168 Score: 71
Period size: 16 Copynumber: 3.1 Consensus size: 16
486110 TGAAAAAGTT
486120 CGAACTCGAAAGAACC
1 CGAACTCGAAAGAACC
*
486136 CGAACCCGAAAGAACC
1 CGAACTCGAAAGAACC
* *
486152 TGAACTCGAGAGAACC
1 CGAACTCGAAAGAACC
486168 C
1 C
486169 AAAGTCAAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.41, C:0.33, G:0.20, T:0.06
Consensus pattern (16 bp):
CGAACTCGAAAGAACC
Found at i:486651 original size:16 final size:15
Alignment explanation
Indices: 486630--486659 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
486620 ATGTTACATT
486630 TAGAATAGCAATATAG
1 TAGAATAG-AATATAG
486646 TAGAATAGAATATA
1 TAGAATAGAATATA
486660 AAGTTAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.53, C:0.03, G:0.17, T:0.27
Consensus pattern (15 bp):
TAGAATAGAATATAG
Found at i:487600 original size:32 final size:31
Alignment explanation
Indices: 487564--487655 Score: 85
Period size: 32 Copynumber: 2.9 Consensus size: 31
487554 CTGACCTGAA
*
487564 CCCAAACCCGAATAAGCTCAAACTCGGATAAG
1 CCCAAACCCGAA-AAGCTCAAACTCGAATAAG
** ** * *
487596 CCCAAACTGGAGAAAGCTTGAACTCAAATAAT
1 CCCAAACCCGA-AAAGCTCAAACTCGAATAAG
*
487628 CCCGAACCCGAAAAAGCTCAAACTCGAA
1 CCCAAACCCG-AAAAGCTCAAACTCGAA
487656 AGAGCTCGAA
Statistics
Matches: 45, Mismatches: 13, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
32 43 0.96
33 2 0.04
ACGTcount: A:0.42, C:0.29, G:0.15, T:0.13
Consensus pattern (31 bp):
CCCAAACCCGAAAAGCTCAAACTCGAATAAG
Found at i:487603 original size:16 final size:16
Alignment explanation
Indices: 487564--487603 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
487554 CTGACCTGAA
*
487564 CCCAAACCCGAATAAG
1 CCCAAACTCGAATAAG
* *
487580 CTCAAACTCGGATAAG
1 CCCAAACTCGAATAAG
487596 CCCAAACT
1 CCCAAACT
487604 GGAGAAAGCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.40, C:0.35, G:0.12, T:0.12
Consensus pattern (16 bp):
CCCAAACTCGAATAAG
Found at i:490853 original size:70 final size:70
Alignment explanation
Indices: 490740--490887 Score: 224
Period size: 70 Copynumber: 2.1 Consensus size: 70
490730 TTGCATCATT
* * *
490740 GTATCATTCAAGTACAACTAGATATTCATTTAATGCCATCCATAACTTGAGGTATATCTCAGACA
1 GTATCATTCAAGTACAACCAAATACTCATTTAATGCCATCCATAACTTGAGGTATATCTCAGACA
**
490805 TTTGC
66 TTTAA
* * *
490810 GTATCATTCAAGTACAGCCAAATGCTCATTTAATGCCATCCATAACTTGAGGTGTATCTCAGACA
1 GTATCATTCAAGTACAACCAAATACTCATTTAATGCCATCCATAACTTGAGGTATATCTCAGACA
490875 TTTAA
66 TTTAA
490880 GTATCATT
1 GTATCATT
490888 TCAATAGCCT
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (70 bp):
GTATCATTCAAGTACAACCAAATACTCATTTAATGCCATCCATAACTTGAGGTATATCTCAGACA
TTTAA
Found at i:496106 original size:19 final size:19
Alignment explanation
Indices: 496078--496115 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
496068 TTAAAATGAG
*
496078 AAAATGATATATTTGAAAT
1 AAAATAATATATTTGAAAT
496097 AAAATAATATATTTGAAAT
1 AAAATAATATATTTGAAAT
496116 TATACCATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (19 bp):
AAAATAATATATTTGAAAT
Found at i:497915 original size:20 final size:19
Alignment explanation
Indices: 497872--497915 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
497862 CTTTTCAAGG
* *
497872 TGTATCGATACTATGAACA
1 TGTATCGATACAAAGAACA
*
497891 TGTATCGATACAAAGCAATA
1 TGTATCGATACAAAG-AACA
497911 TGTAT
1 TGTAT
497916 TAATATATCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (19 bp):
TGTATCGATACAAAGAACA
Found at i:509589 original size:23 final size:23
Alignment explanation
Indices: 509512--509602 Score: 100
Period size: 23 Copynumber: 4.1 Consensus size: 23
509502 ACTGTCTACA
509512 TTTGCT-TTT-TTTTTTCTTTG-
1 TTTGCTGTTTCTTTTTTCTTTGC
* *
509532 TTTGCTGTTTCAATTTTGCTTTGC
1 TTTGCTGTTTC-TTTTTTCTTTGC
*
509556 -TTGCTATTTCTTTTTTCTTTGC
1 TTTGCTGTTTCTTTTTTCTTTGC
* *
509578 TTTGCTGTTTCTTCTTTCCTTGC
1 TTTGCTGTTTCTTTTTTCTTTGC
509601 TT
1 TT
509603 ACTATTTTAG
Statistics
Matches: 58, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
20 6 0.10
21 3 0.05
22 10 0.17
23 39 0.67
ACGTcount: A:0.03, C:0.18, G:0.12, T:0.67
Consensus pattern (23 bp):
TTTGCTGTTTCTTTTTTCTTTGC
Found at i:509601 original size:45 final size:43
Alignment explanation
Indices: 509513--509610 Score: 119
Period size: 45 Copynumber: 2.2 Consensus size: 43
509503 CTGTCTACAT
*
509513 TTGCT-TTTTTTTTTCTTTGTTTGCTGTTTCAATTTTGCTTTGC
1 TTGCTATTTTTTTTTCTTTGTTTGCTGTTTC-ATTTTGCCTTGC
*
509556 TTGCTATTTCTTTTTTCTTTGCTTTGCTGTTTC-TTCTTTCCTTGC
1 TTGCTATTT-TTTTTTCTTTG-TTTGCTGTTTCATT-TTGCCTTGC
*
509601 TTACTATTTT
1 TTGCTATTTT
509611 AGTTTTGCTT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
43 5 0.10
44 6 0.12
45 26 0.54
46 11 0.23
ACGTcount: A:0.05, C:0.17, G:0.11, T:0.66
Consensus pattern (43 bp):
TTGCTATTTTTTTTTCTTTGTTTGCTGTTTCATTTTGCCTTGC
Found at i:510503 original size:23 final size:23
Alignment explanation
Indices: 510460--510503 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
510450 ATAAGTATAA
*
510460 ATGTTTTTAAAGATAAAAATCAT
1 ATGTTTTTAAAGAAAAAAATCAT
510483 ATGTTTTT-AAGAAAAATAATC
1 ATGTTTTTAAAGAAAAA-AATC
510504 CAAATTATCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.48, C:0.05, G:0.09, T:0.39
Consensus pattern (23 bp):
ATGTTTTTAAAGAAAAAAATCAT
Found at i:516353 original size:20 final size:20
Alignment explanation
Indices: 516328--516373 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
516318 GAAAACTATT
*
516328 GATACACATTTAAATGTATC
1 GATACACATTGAAATGTATC
* * *
516348 GATACAGATTGCATTGTATC
1 GATACACATTGAAATGTATC
516368 GATACA
1 GATACA
516374 TTGTATCGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (20 bp):
GATACACATTGAAATGTATC
Found at i:516377 original size:13 final size:13
Alignment explanation
Indices: 516359--516387 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
516349 ATACAGATTG
516359 CATTGTATCGATA
1 CATTGTATCGATA
516372 CATTGTATCGATA
1 CATTGTATCGATA
516385 CAT
1 CAT
516388 GACCAAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:516420 original size:21 final size:20
Alignment explanation
Indices: 516375--516427 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
516365 ATCGATACAT
**
516375 TGTATCGATACATGACCAAA
1 TGTATCGATACATGAAAAAA
*
516395 TGTATCGATACTTGAAAAATA
1 TGTATCGATACATGAAAAA-A
*
516416 TGTATCGCTACA
1 TGTATCGATACA
516428 GGTCATTGGC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (20 bp):
TGTATCGATACATGAAAAAA
Done.