Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A10
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: 110302803
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1825971 characters in sequence are not A, C, G, or T
File 189 of 343
Found at i:62691295 original size:27 final size:27
Alignment explanation
Indices: 62691256--62691313 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
62691246 TAGTTGAACT
* *
62691256 ATGGCAAAGTGATAAAGTGTGCCAAAC
1 ATGGAAAAATGATAAAGTGTGCCAAAC
*
62691283 ATGGAAAAATGATAAAGTGTGCCAAAT
1 ATGGAAAAATGATAAAGTGTGCCAAAC
62691310 ATGG
1 ATGG
62691314 CAAAGTGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.43, C:0.10, G:0.26, T:0.21
Consensus pattern (27 bp):
ATGGAAAAATGATAAAGTGTGCCAAAC
Found at i:62697192 original size:17 final size:17
Alignment explanation
Indices: 62697170--62697209 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
62697160 TCATAGTCTC
62697170 TATCAGTTTTAATACAG
1 TATCAGTTTTAATACAG
*
62697187 TATCAG-TTTACTACAG
1 TATCAGTTTTAATACAG
*
62697203 TTTCAGT
1 TATCAGT
62697210 ATACACTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42
Consensus pattern (17 bp):
TATCAGTTTTAATACAG
Found at i:62711099 original size:40 final size:40
Alignment explanation
Indices: 62711039--62711166 Score: 204
Period size: 40 Copynumber: 3.2 Consensus size: 40
62711029 CGGATGAGAA
* * * *
62711039 CCGGACTAAGATCTGAAGGCATTCGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
62711079 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
*
62711119 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
62711159 CC-GGCTAA
1 CCGGGCTAA
62711167 ATCCTGAAGA
Statistics
Matches: 83, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 6 0.07
40 77 0.93
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
Found at i:62719022 original size:40 final size:40
Alignment explanation
Indices: 62718943--62719109 Score: 223
Period size: 40 Copynumber: 4.2 Consensus size: 40
62718933 TCGATGATAA
* * * *
62718943 CCGGACTAAGATCCGAAGGCATTCGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* * * *
62718983 CCGGGCTATGTCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-TTATAT
*
62719023 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
62719063 CC-GGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
62719102 CC-GGCTAA
1 CCGGGCTAA
62719110 ATCTTGCTGT
Statistics
Matches: 111, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
39 46 0.41
40 63 0.57
41 2 0.02
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
Found at i:62732440 original size:18 final size:16
Alignment explanation
Indices: 62732404--62732436 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
62732394 TCAAATTGGG
62732404 ATTAAGTGTTTCTAAA
1 ATTAAGTGTTTCTAAA
*
62732420 ATTAAGTTTTTCTAAA
1 ATTAAGTGTTTCTAAA
62732436 A
1 A
62732437 AATTGTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.09, T:0.45
Consensus pattern (16 bp):
ATTAAGTGTTTCTAAA
Found at i:62732826 original size:19 final size:19
Alignment explanation
Indices: 62732804--62732840 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
62732794 ACCATTGTCA
62732804 CCCACCGTAATCAAATTTT
1 CCCACCGTAATCAAATTTT
**
62732823 CCCATTGTAATCAAATTT
1 CCCACCGTAATCAAATTT
62732841 GTTATTAATT
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:0.32, C:0.27, G:0.05, T:0.35
Consensus pattern (19 bp):
CCCACCGTAATCAAATTTT
Found at i:62734568 original size:43 final size:41
Alignment explanation
Indices: 62734520--62734610 Score: 121
Period size: 43 Copynumber: 2.2 Consensus size: 41
62734510 TGATTTCATG
*
62734520 TAAGACCATGTCTGGGACATTGGCATCAATATGA-GATTACGTA
1 TAAGACCATGTCTGGGAAATTGGCATC-ATAT-ACGATT-CGTA
* *
62734563 TAAGACCATGTTTGGGAAATTGGCATCGTATACGATTCGTA
1 TAAGACCATGTCTGGGAAATTGGCATCATATACGATTCGTA
62734604 TAAGACC
1 TAAGACC
62734611 CTATTTGGGA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
41 12 0.27
42 7 0.16
43 25 0.57
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (41 bp):
TAAGACCATGTCTGGGAAATTGGCATCATATACGATTCGTA
Found at i:62737284 original size:47 final size:47
Alignment explanation
Indices: 62737230--62737608 Score: 589
Period size: 47 Copynumber: 8.1 Consensus size: 47
62737220 TTAGGATTTT
** * *
62737230 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
62737277 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
62737324 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGGCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
62737371 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
62737418 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
62737465 ATGTGATGAATGTGAACATGCATATATGTTATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
62737512 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCAGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * * * * *
62737559 ATGTGATGAACGTGGGA-GTGTATATATGTGGTAAAGCCGAATGGCTA
1 ATGTGATGAATGT-GAACATGCATATATGTGATAAGGCCGAATGGCCA
62737606 ATG
1 ATG
62737609 CGAAATGTGT
Statistics
Matches: 312, Mismatches: 19, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
47 310 0.99
48 2 0.01
ACGTcount: A:0.34, C:0.11, G:0.29, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:62737424 original size:22 final size:22
Alignment explanation
Indices: 62737397--62737471 Score: 57
Period size: 22 Copynumber: 3.3 Consensus size: 22
62737387 CATGCATATG
62737397 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* *
62737419 TGTGATGAATG-TGAACAT-G-CATA
1 TGTGAT-AAGGCCG-A-ATGGCCA-A
62737442 TGTGTGATAAGGCCGAATGGCCAA
1 --TGTGATAAGGCCGAATGGCCAA
62737466 TGTGAT
1 TGTGAT
62737472 GAATGTGAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 18
0.65 0.06 0.29
Matches are distributed among these distances:
22 15 0.38
23 8 0.20
24 8 0.20
25 9 0.22
ACGTcount: A:0.31, C:0.13, G:0.31, T:0.25
Consensus pattern (22 bp):
TGTGATAAGGCCGAATGGCCAA
Found at i:62737638 original size:46 final size:46
Alignment explanation
Indices: 62737582--62737764 Score: 276
Period size: 46 Copynumber: 4.0 Consensus size: 46
62737572 GGGAGTGTAT
* **
62737582 ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
1 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACATGTATGAGATGG
62737628 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACATGTATGAGATGG
1 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACATGTATGAGATGG
* *
62737674 ATATGAGGTAAAGCCGAATGGCTAATGCAAAACGTGTATGAGATGG
1 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACATGTATGAGATGG
* * * * *
62737720 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGATG
1 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACATGTATGAGATG
62737765 TGTATATATA
Statistics
Matches: 125, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 125 1.00
ACGTcount: A:0.36, C:0.09, G:0.31, T:0.25
Consensus pattern (46 bp):
ATATGAGGTAAAGCCGAATGGCTAATGCGAAACATGTATGAGATGG
Found at i:62742685 original size:39 final size:39
Alignment explanation
Indices: 62742600--62742686 Score: 129
Period size: 39 Copynumber: 2.2 Consensus size: 39
62742590 CCGGCAATTA
* **
62742600 GCCTGCTAGGTATAAACCTGAACTTATCACCGGCATGAG
1 GCCTGCTAGGTATAAACCTGAACTTATCACCAGCACAAG
* *
62742639 GCTTGCTAGGTATAAACTTGAACTTATCACCAGCACAAG
1 GCCTGCTAGGTATAAACCTGAACTTATCACCAGCACAAG
62742678 GCCTGCTAG
1 GCCTGCTAG
62742687 ACATTAAGTC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (39 bp):
GCCTGCTAGGTATAAACCTGAACTTATCACCAGCACAAG
Found at i:62761583 original size:47 final size:47
Alignment explanation
Indices: 62761520--62761823 Score: 437
Period size: 47 Copynumber: 6.4 Consensus size: 47
62761510 CCCTTCGGGA
* * *
62761520 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCACTCGGC
* * *
62761567 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCACTCGGC
* *
62761614 CTTATCTCATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCACTCGGC
* * *
62761661 CTTATCACATATATACACTTTCACATTCATCACGTTGGTCACTCGAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCACTCGGC
* *
62761708 CCTATCACATATATACACTTTCACATTCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCACTCGGC
* *
62761755 CCTATCACATATATATATACTTTCACATTCATCACATTGGCCACTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCACTCGGC
* *
62761804 CCTATCACATATATATACTT
1 CTTATCACATATATACACTT
62761824 GTACATCAAT
Statistics
Matches: 238, Mismatches: 17, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
47 193 0.81
49 45 0.19
ACGTcount: A:0.28, C:0.30, G:0.08, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCACTCGGC
Found at i:62767348 original size:47 final size:47
Alignment explanation
Indices: 62767285--62767588 Score: 437
Period size: 47 Copynumber: 6.4 Consensus size: 47
62767275 CCCTTCGGGA
* * *
62767285 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCACTCGGC
* * *
62767332 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCACTCGGC
* *
62767379 CTTATCTCATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCACTCGGC
* * *
62767426 CTTATCACATATATACACTTTCACATTCATCACGTTGGTCACTCGAC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCACTCGGC
* *
62767473 CCTATCACATATATACACTTTCACATTCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCACTCGGC
* *
62767520 CCTATCACATATATATATACTTTCACATTCATCACATTGGCCACTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCACTCGGC
* *
62767569 CCTATCACATATATATACTT
1 CTTATCACATATATACACTT
62767589 GTACATCAAT
Statistics
Matches: 238, Mismatches: 17, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
47 193 0.81
49 45 0.19
ACGTcount: A:0.28, C:0.30, G:0.08, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCACTCGGC
Found at i:62772624 original size:23 final size:22
Alignment explanation
Indices: 62772582--62772646 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 22
62772572 AATTTAGCCA
*
62772582 TTTATTTTTA-TTGTACTTTTATT
1 TTTATTTTTAGTT-TAATTTT-TT
62772605 TTTATTTTTAGTTTAATTTTTT
1 TTTATTTTTAGTTTAATTTTTT
*
62772627 TTCTAATTTTT-GTTTTATTT
1 TT-T-ATTTTTAGTTTAATTT
62772647 GCTTCTGGCA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
22 4 0.11
23 25 0.68
24 8 0.22
ACGTcount: A:0.17, C:0.03, G:0.05, T:0.75
Consensus pattern (22 bp):
TTTATTTTTAGTTTAATTTTTT
Found at i:62773833 original size:22 final size:23
Alignment explanation
Indices: 62773791--62773834 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
62773781 GTTTTCATTG
**
62773791 AAAACCTTTCTTAAAATAAAAGA
1 AAAACCTTAATTAAAATAAAAGA
*
62773814 AAAACCTTAATTAAAAAAAAA
1 AAAACCTTAATTAAAATAAAA
62773835 CCCTTTCAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.64, C:0.11, G:0.02, T:0.23
Consensus pattern (23 bp):
AAAACCTTAATTAAAATAAAAGA
Found at i:62774922 original size:29 final size:29
Alignment explanation
Indices: 62774865--62774995 Score: 176
Period size: 29 Copynumber: 4.6 Consensus size: 29
62774855 TACCTGTATC
* *
62774865 TGGCCCATTAAGCCC-AATCA-TTTTCATA
1 TGGCCCATTAGGCCCAAATCACATTT-ATA
* *
62774893 TGGCCCATTAGGCCCAAATCACCTATATA
1 TGGCCCATTAGGCCCAAATCACATTTATA
*
62774922 TGGCTCATTAGGCCCAAATCACATTTATA
1 TGGCCCATTAGGCCCAAATCACATTTATA
*
62774951 TGGCCCGTTAGGCCCAAATCACATTTATA
1 TGGCCCATTAGGCCCAAATCACATTTATA
*
62774980 TGGCCCGTTAGGCCCA
1 TGGCCCATTAGGCCCA
62774996 GTCACATACA
Statistics
Matches: 93, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
28 14 0.15
29 77 0.83
30 2 0.02
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.27
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACATTTATA
Found at i:62775090 original size:17 final size:18
Alignment explanation
Indices: 62775068--62775101 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
62775058 TGCCTATTAT
62775068 GGGCCCA-ATAGCCTATC
1 GGGCCCATATAGCCTATC
*
62775085 GGGCCCATTTAGCCTAT
1 GGGCCCATATAGCCTAT
62775102 TTTGGCCCGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.21, C:0.32, G:0.24, T:0.24
Consensus pattern (18 bp):
GGGCCCATATAGCCTATC
Found at i:62775239 original size:16 final size:16
Alignment explanation
Indices: 62775189--62775231 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
62775179 TAGCCAAACA
62775189 TTTGGCTTTTCGGTAT
1 TTTGGCTTTTCGGTAT
* *
62775205 TTCGGCTTTTCGGCAT
1 TTTGGCTTTTCGGTAT
62775221 TTTGGCTTTTC
1 TTTGGCTTTTC
62775232 AGTTTTTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.05, C:0.19, G:0.23, T:0.53
Consensus pattern (16 bp):
TTTGGCTTTTCGGTAT
Found at i:62778740 original size:5 final size:5
Alignment explanation
Indices: 62778730--62778777 Score: 55
Period size: 5 Copynumber: 9.8 Consensus size: 5
62778720 AAGTAACCCC
* *
62778730 TTTTA TTTTA TTTTA TTTTA -TTTA TTATTA -TTTC TTATA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT-TTA TTTTA TTTTA TTTTA TTTT
62778778 CTTATTTTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
4 6 0.17
5 27 0.75
6 3 0.08
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:62778755 original size:9 final size:9
Alignment explanation
Indices: 62778731--62778794 Score: 51
Period size: 10 Copynumber: 6.9 Consensus size: 9
62778721 AGTAACCCCT
62778731 TTTATTTTA
1 TTTATTTTA
62778740 TTTTATTTTA
1 -TTTATTTTA
62778750 TTTATTATTA
1 TTTATT-TTA
* *
62778760 TTTCTTATA
1 TTTATTTTA
62778769 TTTTATTTT-
1 -TTTATTTTA
*
62778778 CTTATTTT-
1 TTTATTTTA
62778786 TCTTATTTT
1 T-TTATTTT
62778795 TCTTATACTT
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
8 7 0.16
9 15 0.33
10 23 0.51
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTATTTTA
Found at i:62778778 original size:15 final size:16
Alignment explanation
Indices: 62778738--62778801 Score: 55
Period size: 15 Copynumber: 4.1 Consensus size: 16
62778728 CCTTTTATTT
*
62778738 TATT-TTATTTTATT-
1 TATTATTATTTTCTTA
62778752 TATTATTA-TTTCTTA
1 TATTATTATTTTCTTA
62778767 TATT-TTATTTTCTTA
1 TATTATTATTTTCTTA
* *
62778782 TTTTTCTTATTTTTCTTA
1 -TATTATTA-TTTTCTTA
62778800 TA
1 TA
62778802 CTTAGATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
14 12 0.29
15 14 0.34
16 3 0.07
17 4 0.10
18 8 0.20
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.73
Consensus pattern (16 bp):
TATTATTATTTTCTTA
Found at i:62778795 original size:9 final size:9
Alignment explanation
Indices: 62778754--62778800 Score: 55
Period size: 9 Copynumber: 5.4 Consensus size: 9
62778744 ATTTTATTTA
62778754 TTATTATTTC
1 TTATT-TTTC
*
62778764 TTA-TATT-
1 TTATTTTTC
62778771 TTA-TTTTC
1 TTATTTTTC
62778779 TTATTTTTC
1 TTATTTTTC
62778788 TTATTTTTC
1 TTATTTTTC
62778797 TTAT
1 TTAT
62778801 ACTTAGATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
7 6 0.18
8 5 0.15
9 19 0.58
10 3 0.09
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (9 bp):
TTATTTTTC
Found at i:62778805 original size:24 final size:25
Alignment explanation
Indices: 62778743--62778805 Score: 78
Period size: 24 Copynumber: 2.6 Consensus size: 25
62778733 TATTTTATTT
62778743 TATTTTATTTA-TTATTATTTCTTA
1 TATTTTATTTACTTATTATTTCTTA
*
62778767 TATTTTATTTTCTTATT-TTTCTTA
1 TATTTTATTTACTTATTATTTCTTA
*
62778791 T-TTTTCTTATACTTA
1 TATTTTATT-TACTTA
62778806 GATTTTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 6 0.18
24 23 0.68
25 5 0.15
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.71
Consensus pattern (25 bp):
TATTTTATTTACTTATTATTTCTTA
Found at i:62778942 original size:12 final size:12
Alignment explanation
Indices: 62778906--62778947 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
62778896 TATCTTTGAG
62778906 TTTATTATT-TTT
1 TTTATT-TTATTT
*
62778918 TTCATTTTA-TT
1 TTTATTTTATTT
62778929 TTTATTTTATTT
1 TTTATTTTATTT
62778941 TTTATTT
1 TTTATTT
62778948 ATCTTTCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 12 0.46
12 14 0.54
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTATTTTATTT
Found at i:62780889 original size:42 final size:43
Alignment explanation
Indices: 62780783--62780893 Score: 134
Period size: 43 Copynumber: 2.6 Consensus size: 43
62780773 ATGTACAATG
* * *
62780783 CCAATGTCCCAAACGTGGTCTTACATGTAATCAAATATCGATA
1 CCAATGTCCCAAACATGGTCTTACACGAAATCAAATATCGATA
* * * *
62780826 CCACTGTCCCAAATAGGGTCTTACACGAAATCAAATAT-GATG
1 CCAATGTCCCAAACATGGTCTTACACGAAATCAAATATCGATA
* *
62780868 TCAATGTCCCAAACATTGTCTTACAC
1 CCAATGTCCCAAACATGGTCTTACAC
62780894 ATAAATCATA
Statistics
Matches: 56, Mismatches: 12, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
42 24 0.43
43 32 0.57
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.27
Consensus pattern (43 bp):
CCAATGTCCCAAACATGGTCTTACACGAAATCAAATATCGATA
Found at i:62782871 original size:18 final size:18
Alignment explanation
Indices: 62782848--62782882 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
62782838 TTATTGTTAA
62782848 AAAAATCAAA-AAATAAAG
1 AAAAAT-AAAGAAATAAAG
62782866 AAAAATAAAGAAATAAA
1 AAAAATAAAGAAATAAA
62782883 AAATATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.80, C:0.03, G:0.06, T:0.11
Consensus pattern (18 bp):
AAAAATAAAGAAATAAAG
Found at i:62785298 original size:6 final size:6
Alignment explanation
Indices: 62785283--62785332 Score: 66
Period size: 6 Copynumber: 8.2 Consensus size: 6
62785273 TTGATGAGTA
*
62785283 TTTTATT TTTTAT TTTT-T TTATTTT TTTTAT TTTTAT TTTTAT TTTTAT
1 TTTTA-T TTTTAT TTTTAT TT-TTAT TTTTAT TTTTAT TTTTAT TTTTAT
62785332 T
1 T
62785333 GGTATCTTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
5 3 0.08
6 29 0.73
7 8 0.20
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTAT
Found at i:62785302 original size:9 final size:9
Alignment explanation
Indices: 62785288--62785332 Score: 65
Period size: 9 Copynumber: 5.0 Consensus size: 9
62785278 GAGTATTTTA
62785288 TTTTTTATT
1 TTTTTTATT
62785297 TTTTTTATT
1 TTTTTTATT
62785306 TTTTTTATT
1 TTTTTTATT
62785315 TTTATTT-TT
1 TTT-TTTATT
*
62785324 ATTTTTATT
1 TTTTTTATT
62785333 GGTATCTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
8 3 0.09
9 27 0.82
10 3 0.09
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (9 bp):
TTTTTTATT
Found at i:62785926 original size:71 final size:72
Alignment explanation
Indices: 62785845--62785987 Score: 270
Period size: 72 Copynumber: 2.0 Consensus size: 72
62785835 TGGGGACATT
62785845 TCTAGGATGAGCTTTACT-AAAAAAACGACATATGAAAAGCTTTTACCAAAATATCTAATGATTT
1 TCTAGGATGAGCTTTACTAAAAAAAACGACATATGAAAAGCTTTTACCAAAATATCTAATGATTT
62785909 ACCCATA
66 ACCCATA
*
62785916 TCTAGGATGAGCTTTACTAAAAAAAACGACATATGAAAAGCTTTTTCCAAAATATCTAATGATTT
1 TCTAGGATGAGCTTTACTAAAAAAAACGACATATGAAAAGCTTTTACCAAAATATCTAATGATTT
62785981 ACCCATA
66 ACCCATA
62785988 AAAATATTGA
Statistics
Matches: 70, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
71 18 0.26
72 52 0.74
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.30
Consensus pattern (72 bp):
TCTAGGATGAGCTTTACTAAAAAAAACGACATATGAAAAGCTTTTACCAAAATATCTAATGATTT
ACCCATA
Found at i:62789515 original size:18 final size:17
Alignment explanation
Indices: 62789478--62789516 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
62789468 AATAAAATGA
*
62789478 TTTTTTGAAAATGATAG
1 TTTTTTGAAAATAATAG
*
62789495 TTTTTCTGAAAATAATTG
1 TTTTT-TGAAAATAATAG
62789513 TTTT
1 TTTT
62789517 CAAGAAGACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.31, C:0.03, G:0.13, T:0.54
Consensus pattern (17 bp):
TTTTTTGAAAATAATAG
Found at i:62791641 original size:13 final size:13
Alignment explanation
Indices: 62791623--62791649 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
62791613 GGCACATGCT
62791623 CGTGTGGCCAGCC
1 CGTGTGGCCAGCC
62791636 CGTGTGGCCAGCC
1 CGTGTGGCCAGCC
62791649 C
1 C
62791650 ATGGGGAATT
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:0.07, C:0.41, G:0.37, T:0.15
Consensus pattern (13 bp):
CGTGTGGCCAGCC
Found at i:62793726 original size:19 final size:19
Alignment explanation
Indices: 62793682--62793726 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
62793672 TCCCTCTTTC
*
62793682 TTTCTTTTTCTTTATTCTA
1 TTTCTTTTTATTTATTCTA
*
62793701 TTTCTTTTTATTT-TTTTA
1 TTTCTTTTTATTTATTCTA
62793719 TTTACTTT
1 TTT-CTTT
62793727 AATTATTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTCTTTTTATTTATTCTA
Found at i:62793747 original size:16 final size:17
Alignment explanation
Indices: 62793726--62793768 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
62793716 TTATTTACTT
62793726 TAATTATTATATTATA-
1 TAATTATTATATTATAG
* *
62793742 TTATTATTATATTTTAG
1 TAATTATTATATTATAG
62793759 TAATTATTAT
1 TAATTATTAT
62793769 TTACTTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
TAATTATTATATTATAG
Found at i:62794186 original size:49 final size:49
Alignment explanation
Indices: 62794129--62794257 Score: 170
Period size: 49 Copynumber: 2.6 Consensus size: 49
62794119 GTTATGTGTT
* *
62794129 AGTGTAAGACCTATCTGGGACATGGCATCGACAC-CGATAGATGAGAGCC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGAC-CTCGATAGATGAAAGCC
* * **
62794178 AGTGTAAGACCTGTCTGGGACATGGCATCGGCCTCGATATATGAAAGTT
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATAGATGAAAGCC
* *
62794227 AGTGTAAGACCTGTCTAGGACACGGCATCGA
1 AGTGTAAGACCTGTCTGGGACATGGCATCGA
62794258 ATTTAATGTG
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
48 1 0.01
49 69 0.99
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.22
Consensus pattern (49 bp):
AGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATAGATGAAAGCC
Found at i:62795490 original size:20 final size:21
Alignment explanation
Indices: 62795451--62795490 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
62795441 GTCATAATGG
62795451 CCATACAGGCATGTTGCCCTT
1 CCATACAGGCATGTTGCCCTT
* *
62795472 CCATACGGGCGTG-TGCCCT
1 CCATACAGGCATGTTGCCCT
62795491 ACTTCAAGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.15, C:0.35, G:0.25, T:0.25
Consensus pattern (21 bp):
CCATACAGGCATGTTGCCCTT
Found at i:62799747 original size:20 final size:21
Alignment explanation
Indices: 62799722--62799761 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
62799712 CTCATGAAAT
62799722 AGGGC-ACACGCCCGTGTGGA
1 AGGGCAACACGCCCGTGTGGA
62799742 AGGGCAACACGCCCGTGTGG
1 AGGGCAACACGCCCGTGTGG
62799762 TCATTATAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.20, C:0.30, G:0.40, T:0.10
Consensus pattern (21 bp):
AGGGCAACACGCCCGTGTGGA
Found at i:62804597 original size:12 final size:12
Alignment explanation
Indices: 62804580--62804612 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
62804570 GATGCCACAC
62804580 GGCCGTGTGGCT-
1 GGCCGTGTGG-TA
62804592 GGCCGTGTGGTA
1 GGCCGTGTGGTA
62804604 GGCCGTGTG
1 GGCCGTGTG
62804613 CGACACACAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 1 0.05
12 19 0.95
ACGTcount: A:0.03, C:0.21, G:0.52, T:0.24
Consensus pattern (12 bp):
GGCCGTGTGGTA
Found at i:62807783 original size:14 final size:15
Alignment explanation
Indices: 62807766--62807795 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
62807756 ATTTTTGTTC
62807766 ATATA-TTTAAAACT
1 ATATATTTTAAAACT
62807780 ATATATTTTAAAACT
1 ATATATTTTAAAACT
62807795 A
1 A
62807796 GAGCAAGCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (15 bp):
ATATATTTTAAAACT
Found at i:62808338 original size:27 final size:28
Alignment explanation
Indices: 62808299--62808353 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
62808289 TAACCCAAAT
* * *
62808299 AATATACTCATTATTACTCAAA-CTCAA
1 AATAAACTAATTATAACTCAAATCTCAA
62808326 AATAAACTAATTATAACTCAAATCTCAA
1 AATAAACTAATTATAACTCAAATCTCAA
62808354 GTTCAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 19 0.79
28 5 0.21
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (28 bp):
AATAAACTAATTATAACTCAAATCTCAA
Found at i:62808882 original size:14 final size:14
Alignment explanation
Indices: 62808863--62808906 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
62808853 ATAATCTATA
62808863 ATATATTAA-TAGTT
1 ATATATTAATTA-TT
62808877 ATATATTAATTATT
1 ATATATTAATTATT
*
62808891 ATATATTATTTATT
1 ATATATTAATTATT
62808905 AT
1 AT
62808907 TGTACTAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
14 26 0.93
15 2 0.07
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (14 bp):
ATATATTAATTATT
Found at i:62808897 original size:7 final size:7
Alignment explanation
Indices: 62808836--62808906 Score: 56
Period size: 7 Copynumber: 10.0 Consensus size: 7
62808826 ATATCATGTA
62808836 ATATTAT
1 ATATTAT
*
62808843 ATATTTT
1 ATATTAT
*
62808850 ATTATAAT
1 A-TATTAT
* *
62808858 CTATAAT
1 ATATTAT
62808865 ATATTA-
1 ATATTAT
62808871 ATAGTTAT
1 ATA-TTAT
62808879 ATATTA-
1 ATATTAT
62808885 ATTATTAT
1 A-TATTAT
62808893 ATATTAT
1 ATATTAT
*
62808900 TTATTAT
1 ATATTAT
62808907 TGTACTAGTT
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
6 4 0.08
7 40 0.77
8 8 0.15
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (7 bp):
ATATTAT
Found at i:62808905 original size:35 final size:35
Alignment explanation
Indices: 62808822--62808905 Score: 89
Period size: 35 Copynumber: 2.3 Consensus size: 35
62808812 GATTAAACAT
* *
62808822 TATAATATCATGTAATATTATATATTTTATTATAATC
1 TATAATAT-AT-TAATATTATATATTTAATTATAATA
*
62808859 TATAATATATTAATAGTTATATA-TTAATTATTATA
1 TATAATATATTAATA-TTATATATTTAATTATAATA
* *
62808894 TATTATTTATTA
1 TATAATATATTA
62808906 TTGTACTAGT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
35 24 0.59
36 9 0.22
37 8 0.20
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (35 bp):
TATAATATATTAATATTATATATTTAATTATAATA
Found at i:62823955 original size:46 final size:46
Alignment explanation
Indices: 62823905--62824075 Score: 206
Period size: 46 Copynumber: 3.7 Consensus size: 46
62823895 GTTGAGCATT
62823905 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC
* * * *
62823951 CGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGGCATC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G--TC
* *
62823998 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC
*
62824044 CGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
62824076 GGGACGGGTT
Statistics
Matches: 105, Mismatches: 11, Indels: 18
0.78 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 59 0.56
47 29 0.28
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC
Found at i:62824064 original size:93 final size:93
Alignment explanation
Indices: 62823900--62824070 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
62823890 GGATGGTTGA
* * *
62823900 GCATTCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
62823965 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
*
62823993 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
62824058 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
62824071 ACTTAGGGAC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:62829287 original size:11 final size:11
Alignment explanation
Indices: 62829271--62829315 Score: 63
Period size: 11 Copynumber: 4.1 Consensus size: 11
62829261 TTCATCCATT
*
62829271 GTTTTTTGTTG
1 GTTTTTTCTTG
*
62829282 GTTTTTTCTTT
1 GTTTTTTCTTG
*
62829293 GTTTTTTGTTG
1 GTTTTTTCTTG
62829304 GTTTTTTCTTG
1 GTTTTTTCTTG
62829315 G
1 G
62829316 CAACCTTGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.00, C:0.04, G:0.22, T:0.73
Consensus pattern (11 bp):
GTTTTTTCTTG
Found at i:62829295 original size:22 final size:22
Alignment explanation
Indices: 62829269--62829313 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
62829259 TCTTCATCCA
62829269 TTGTTTTTTGTTGGTTTTTTCT
1 TTGTTTTTTGTTGGTTTTTTCT
62829291 TTGTTTTTTGTTGGTTTTTTCT
1 TTGTTTTTTGTTGGTTTTTTCT
62829313 T
1 T
62829314 GGCAACCTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.00, C:0.04, G:0.18, T:0.78
Consensus pattern (22 bp):
TTGTTTTTTGTTGGTTTTTTCT
Found at i:62829684 original size:12 final size:12
Alignment explanation
Indices: 62829667--62829700 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
62829657 CTGACCTGCC
62829667 TATATTAATTTT
1 TATATTAATTTT
62829679 TATATT-ATTTT
1 TATATTAATTTT
62829690 TATA-TAATTTT
1 TATATTAATTTT
62829701 AAAATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.05
11 14 0.67
12 6 0.29
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TATATTAATTTT
Found at i:62829869 original size:30 final size:30
Alignment explanation
Indices: 62829825--62829887 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
62829815 ACTTAACAAG
62829825 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* * *
62829855 CAAATGTCTTTAAAATAATAACAAAATTGA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
62829885 CAA
1 CAA
62829888 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.56, C:0.14, G:0.05, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:62829941 original size:11 final size:11
Alignment explanation
Indices: 62829923--62829962 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
62829913 ACAATAACAA
62829923 CAAAATAATAG
1 CAAAATAATAG
*
62829934 CAACATAATAG
1 CAAAATAATAG
*
62829945 TAAAATAATAG
1 CAAAATAATAG
62829956 CAAAATA
1 CAAAATA
62829963 GGGAGAAAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.62, C:0.10, G:0.07, T:0.20
Consensus pattern (11 bp):
CAAAATAATAG
Found at i:62829941 original size:22 final size:22
Alignment explanation
Indices: 62829916--62829958 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
62829906 TATCCAAACA
62829916 ATAACAACAAAATAATAGCAAC
1 ATAACAACAAAATAATAGCAAC
* **
62829938 ATAATAGTAAAATAATAGCAA
1 ATAACAACAAAATAATAGCAA
62829959 AATAGGGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.63, C:0.12, G:0.07, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATAATAGCAAC
Found at i:62830954 original size:11 final size:11
Alignment explanation
Indices: 62830938--62830963 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
62830928 TTATATATTT
62830938 AACCGATAAGC
1 AACCGATAAGC
62830949 AACCGATAAGC
1 AACCGATAAGC
62830960 AACC
1 AACC
62830964 TAAGCTCTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (11 bp):
AACCGATAAGC
Found at i:62833013 original size:16 final size:16
Alignment explanation
Indices: 62832979--62833012 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
62832969 CCACTTTTGG
*
62832979 TTTCACTAACCTAATT
1 TTTCACTAACCCAATT
62832995 TTTC-CTAACCCAATT
1 TTTCACTAACCCAATT
62833010 TTT
1 TTT
62833013 TGGATGTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTCACTAACCCAATT
Found at i:62838358 original size:17 final size:17
Alignment explanation
Indices: 62838336--62838371 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
62838326 AAGCCAAAGT
* *
62838336 AACTTTTATTCAGGAAC
1 AACTTTCATTCAAGAAC
62838353 AACTTTCATTCAAGAAC
1 AACTTTCATTCAAGAAC
62838370 AA
1 AA
62838372 TCATCGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (17 bp):
AACTTTCATTCAAGAAC
Found at i:62851030 original size:21 final size:21
Alignment explanation
Indices: 62851004--62851082 Score: 56
Period size: 21 Copynumber: 3.9 Consensus size: 21
62850994 CTTTACAGCA
62851004 CATTATGGATAAACCACTCAT
1 CATTATGGATAAACCACTCAT
* **
62851025 CATTATGTATGTACCA--C-T
1 CATTATGGATAAACCACTCAT
* *
62851043 CGTTGTGGATAAACCACTCAT
1 CATTATGGATAAACCACTCAT
* * **
62851064 CCTTGTGGATGTACCACTC
1 CATTATGGATAAACCACTC
62851083 GTTGTGGATA
Statistics
Matches: 44, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
18 12 0.27
19 1 0.02
20 1 0.02
21 30 0.68
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (21 bp):
CATTATGGATAAACCACTCAT
Found at i:62851060 original size:18 final size:18
Alignment explanation
Indices: 62851037--62851099 Score: 72
Period size: 18 Copynumber: 3.3 Consensus size: 18
62851027 TTATGTATGT
62851037 ACCACTCGTTGTGGATAA
1 ACCACTCGTTGTGGATAA
* **
62851055 ACCACTCATCCTTGTGGATGT
1 ACCA--C-TCGTTGTGGATAA
62851076 ACCACTCGTTGTGGATAA
1 ACCACTCGTTGTGGATAA
62851094 ACCACT
1 ACCACT
62851100 AATAATAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
18 20 0.56
19 1 0.03
20 1 0.03
21 14 0.39
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (18 bp):
ACCACTCGTTGTGGATAA
Found at i:62851063 original size:39 final size:39
Alignment explanation
Indices: 62851009--62851099 Score: 155
Period size: 39 Copynumber: 2.3 Consensus size: 39
62850999 CAGCACATTA
*
62851009 TGGATAAACCACTCATCATTATGTATGTACCACTCGTTG
1 TGGATAAACCACTCATCATTATGGATGTACCACTCGTTG
* *
62851048 TGGATAAACCACTCATCCTTGTGGATGTACCACTCGTTG
1 TGGATAAACCACTCATCATTATGGATGTACCACTCGTTG
62851087 TGGATAAACCACT
1 TGGATAAACCACT
62851100 AATAATAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 49 1.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (39 bp):
TGGATAAACCACTCATCATTATGGATGTACCACTCGTTG
Found at i:62851757 original size:43 final size:43
Alignment explanation
Indices: 62851685--62851769 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 43
62851675 AGCTATTAAT
*
62851685 ACGGTGTGGATAAACCAATCAATGATGCAGATAA-ACTGCTCAA
1 ACGGTGTGGATAAACCAATCAAAGATGCAGATAATA-TGCTCAA
* *
62851728 ACGGTGTGGATAAGCCACTCAACAG-TGCAGATAATATGCTCA
1 ACGGTGTGGATAAACCAATCAA-AGATGCAGATAATATGCTCA
62851770 CACTTCCTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
43 35 0.95
44 2 0.05
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.21
Consensus pattern (43 bp):
ACGGTGTGGATAAACCAATCAAAGATGCAGATAATATGCTCAA
Found at i:62859535 original size:40 final size:40
Alignment explanation
Indices: 62859401--62859623 Score: 262
Period size: 40 Copynumber: 5.7 Consensus size: 40
62859391 TTGAATGATG
* * * *
62859401 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
62859441 TCCGGACTAAGAT--CGAAGGCATTT-TGCGAGATACTAATT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAA-A
*
62859480 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
62859519 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
62859559 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
62859600 -CCGGGCTATGT-CCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
62859624 AACGAGGAGC
Statistics
Matches: 160, Mismatches: 15, Indels: 17
0.83 0.08 0.09
Matches are distributed among these distances:
38 5 0.03
39 53 0.33
40 99 0.62
41 3 0.02
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:62859575 original size:80 final size:79
Alignment explanation
Indices: 62859401--62859623 Score: 249
Period size: 79 Copynumber: 2.8 Consensus size: 79
62859391 TTGAATGATG
* * * * * *
62859401 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CGAAGGCATT
1 TCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTATAACCGGGCTAAG-TCCGAAGGCATT
*
62859464 T-TGCGAGATACTAATT
63 TGTGCGAGATACTAATA
*
62859480 TCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTA-AATCCGGGTTAAGTCCCGAAGGCATTT
1 TCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTATAA-CCGGGCTAAGT-CCGAAGGCATTT
*
62859544 GTGCGAGTTACTAA-A
64 GTGCGAGATACTAATA
* * *
62859559 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCGAAGGCATTTG
1 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTATAACCGGGCTAAGTCCGAAGGCATTTG
62859624 AACGAGGAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
77 2 0.02
78 23 0.19
79 51 0.41
80 46 0.37
81 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (79 bp):
TCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTATAACCGGGCTAAGTCCGAAGGCATTTGT
GCGAGATACTAATA
Found at i:62866650 original size:39 final size:40
Alignment explanation
Indices: 62866543--62866766 Score: 260
Period size: 40 Copynumber: 5.7 Consensus size: 40
62866533 TTGAATGATG
* * * *
62866543 TCCGGGCTAAGT-CCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * *
62866582 TCCGGACTAAGAT-CCAAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
62866622 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
62866661 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
62866701 TCCGGGTTAAGTCCCGAAAGCATTTATGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
62866742 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
62866767 AACGAGGAGC
Statistics
Matches: 159, Mismatches: 21, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
39 43 0.27
40 107 0.67
41 9 0.06
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:62866784 original size:80 final size:79
Alignment explanation
Indices: 62866581--62866789 Score: 203
Period size: 80 Copynumber: 2.6 Consensus size: 79
62866571 AAGTGACCAT
* * ** * * *
62866581 ATCCGGACTAAGAT-CCAAAGGCATTTGTGCGAGAT-ACTAATTCCGGGCTAAGCCCGAAGGCAT
1 ATCCGGGCTAAG-TCCCGAAGGCATTTGAACGAG-TGACTAAATCCGGGTTAAGCCCGAAAGCAT
*
62866644 TGGTGCGAGTTACTAA
64 TGATGCGAGTTACTAA
* ** *
62866660 ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAAGCATT
1 ATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAG-CCCGAAAGCATT
*
62866725 TATGCGAGTTACTATA
65 GATGCGAGTTACTA-A
* *
62866741 A-CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAA
1 ATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGA-CTAAATCCGGGTTAA
62866790 ATTCCGAAGG
Statistics
Matches: 111, Mismatches: 14, Indels: 10
0.82 0.10 0.07
Matches are distributed among these distances:
78 2 0.02
79 50 0.45
80 57 0.51
81 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (79 bp):
ATCCGGGCTAAGTCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAGCCCGAAAGCATTG
ATGCGAGTTACTAA
Found at i:62869827 original size:53 final size:53
Alignment explanation
Indices: 62869628--62869834 Score: 180
Period size: 53 Copynumber: 3.8 Consensus size: 53
62869618 ATTAGGATTT
* * * * *
62869628 AAGGATACCAAGTAAGACCATGCCAAGGCATGACATTGGTAAGTTTAACAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGACAATGGTAAG-TTCATAAGGC
* * ** * * * * *
62869682 AAGGAAATCATGTAAGACCATGTTAAGACATGGCATTGATAAACTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGACAATGGT-AAGTTC-ATAAGGC
* * * * * *
62869737 AAAGATCCCATGTAAGACCGTGCCAAGGCATGGCAATGGTGAGTTCATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGACAATGGTAAGTTCATAAGGC
* * *
62869790 AAGGATACCACGTAAGACTATGTCAAGACATGACAATGGTAAGTT
1 AAGGATACCATGTAAGACCATGCCAAGACATGACAATGGTAAGTT
62869835 TAAAAAGGAA
Statistics
Matches: 117, Mismatches: 34, Indels: 5
0.75 0.22 0.03
Matches are distributed among these distances:
53 43 0.37
54 36 0.31
55 38 0.32
ACGTcount: A:0.38, C:0.17, G:0.24, T:0.21
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGACAATGGTAAGTTCATAAGGC
Found at i:62875201 original size:8 final size:8
Alignment explanation
Indices: 62875188--62875224 Score: 65
Period size: 8 Copynumber: 4.6 Consensus size: 8
62875178 CTATTTCAAA
62875188 AAAAAAAG
1 AAAAAAAG
62875196 AAAAAAAG
1 AAAAAAAG
*
62875204 AAAAAGAG
1 AAAAAAAG
62875212 AAAAAAAG
1 AAAAAAAG
62875220 AAAAA
1 AAAAA
62875225 TGGAGATGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:62876301 original size:87 final size:85
Alignment explanation
Indices: 62876155--62876360 Score: 267
Period size: 87 Copynumber: 2.4 Consensus size: 85
62876145 AAATTCAGCG
*
62876155 CCTTAATCCCCTAAGCAGTAGAGTAACAGG-CTAAAATTACAGATCTTATCTCCCCAAGCAGTAG
1 CCTTAATCCCCTAAGCAGTAGGGTAACAGGTCTAAAATTACAGATCTTATCTCCCCAAGCAGTAG
62876219 CGGAACAGATC-AACGATGACTCA
66 CGGAACAGATCGAA-GATG---CA
* * * *
62876242 CCTTAATCCCCTAAGCAATAGGGTAACAGGTC-AAAATTGCGGATCTTATCTCCCTAAGCAGTAG
1 CCTTAATCCCCTAAGCAGTAGGGTAACAGGTCTAAAATTACAGATCTTATCTCCCCAAGCAGTAG
* * *
62876306 TGGAGCAGATCGAAGATGCG
66 CGGAACAGATCGAAGATGCA
*
62876326 CCTTAAACCCCTAAGCAGTAGGGTAACAGGT-TAAA
1 CCTTAATCCCCTAAGCAGTAGGGTAACAGGTCTAAA
62876361 GTATAGCAGA
Statistics
Matches: 106, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
84 33 0.31
87 70 0.66
88 3 0.03
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.21
Consensus pattern (85 bp):
CCTTAATCCCCTAAGCAGTAGGGTAACAGGTCTAAAATTACAGATCTTATCTCCCCAAGCAGTAG
CGGAACAGATCGAAGATGCA
Found at i:62877044 original size:288 final size:289
Alignment explanation
Indices: 62876392--62877044 Score: 1085
Period size: 289 Copynumber: 2.3 Consensus size: 289
62876382 GGTGCTCACG
* * *
62876392 CTGAAGCAGATCCAAGATGATTTGGCATTCTTGTGTTTACAAGGAACAAATCGATA-ACATAACA
1 CTGAAGTAGATCCAAGATGATTTGGCATTCTTGTGTTTACAAGGAACAAATC-AAAGACATAGCA
* *
62876456 GATTTGACTCTGAGATGTTCTCAAACAAATCCAAGATGATTTGGTATCCTTGTGTTTGCAAGGAA
65 GATTTGACTCTCAGATGTTCACAAACAAATCCAAGATGATTTGGTATCCTTGTGTTTGCAAGGAA
*
62876521 CAAATCGAACACATAGCTGATTTGGCTTTCAAGTGTTTACACTGAAGCAAATCTAAGATTATTTG
130 CAAATCGAACACATAGCTGATTTGGCTTTCAAGTGTTTACACTGAAGCAAATCTAAGATGATTTG
* * * *
62876586 GCATCTCTACATTGTTAGAGAACAAATCAAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACG
195 GCATATCTACATTGTCAGAGAACAAATCAAAGTTTGGCGTCTCCATATCCGACAGAGGGCAGACG
*
62876651 CATGGCATATCTAACCTTCAGATGTTTATA
260 CATGGCAGATCTAACCTTCAGATGTTTATA
* * *
62876681 CTGAAGTAGATCCAAGATGATTTGGTATTCTTGTGTTTACAAGGAACAAATCGAGGACATAGCAG
1 CTGAAGTAGATCCAAGATGATTTGGCATTCTTGTGTTTACAAGGAACAAATCAAAGACATAGCAG
62876746 ATTTGACTCTCAGATGTTCACAAACAAATCCAAGATGATTTGGTATCCTTGTGTTTGCAAGGAAC
66 ATTTGACTCTCAGATGTTCACAAACAAATCCAAGATGATTTGGTATCCTTGTGTTTGCAAGGAAC
* *
62876811 AAATCGAACACATTGCTGATTTGGCTTTCACGTGTTTACACTGAAGCAAATCTAAGATGATTTGG
131 AAATCGAACACATAGCTGATTTGGCTTTCAAGTGTTTACACTGAAGCAAATCTAAGATGATTTGG
** * *
62876876 CATATCTGTATTGTCAGATAAC-AATCGAAGTTTGGCGTCTCCATATCCGACAGAGGGCAGACGC
196 CATATCTACATTGTCAGAGAACAAATCAAAGTTTGGCGTCTCCATATCCGACAGAGGGCAGACGC
62876940 ATGGCAGATCTAACCTTCAGATGTTTATA
261 ATGGCAGATCTAACCTTCAGATGTTTATA
* *
62876969 CTGAAGTAGATCCTAGATGATTTGGCATTCTTATGTTTACAAGGAACAAATCAAAGACATAGCAG
1 CTGAAGTAGATCCAAGATGATTTGGCATTCTTGTGTTTACAAGGAACAAATCAAAGACATAGCAG
62877034 ATTTGACTCTC
66 ATTTGACTCTC
62877045 GAGGTCCTCA
Statistics
Matches: 338, Mismatches: 25, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
288 138 0.41
289 200 0.59
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (289 bp):
CTGAAGTAGATCCAAGATGATTTGGCATTCTTGTGTTTACAAGGAACAAATCAAAGACATAGCAG
ATTTGACTCTCAGATGTTCACAAACAAATCCAAGATGATTTGGTATCCTTGTGTTTGCAAGGAAC
AAATCGAACACATAGCTGATTTGGCTTTCAAGTGTTTACACTGAAGCAAATCTAAGATGATTTGG
CATATCTACATTGTCAGAGAACAAATCAAAGTTTGGCGTCTCCATATCCGACAGAGGGCAGACGC
ATGGCAGATCTAACCTTCAGATGTTTATA
Found at i:62878833 original size:24 final size:23
Alignment explanation
Indices: 62878806--62878880 Score: 57
Period size: 24 Copynumber: 3.1 Consensus size: 23
62878796 ATGAATATCA
62878806 ATCCTGTAATATTATATTTATATT
1 ATCCT-TAATATTATATTTATATT
62878830 ATCCATT-ATATTATTATTATATATTTT
1 ATCC-TTAATATTA-TATT-TATA--TT
*
62878857 AT-CTATAAAATTATATTT-TATT
1 ATCCT-TAATATTATATTTATATT
62878879 AT
1 AT
62878881 ATATTTCCTT
Statistics
Matches: 43, Mismatches: 1, Indels: 16
0.72 0.02 0.27
Matches are distributed among these distances:
22 4 0.09
23 6 0.14
24 11 0.26
25 7 0.16
26 6 0.14
27 9 0.21
ACGTcount: A:0.36, C:0.07, G:0.01, T:0.56
Consensus pattern (23 bp):
ATCCTTAATATTATATTTATATT
Found at i:62885002 original size:8 final size:8
Alignment explanation
Indices: 62884989--62885025 Score: 65
Period size: 8 Copynumber: 4.6 Consensus size: 8
62884979 TATTTCGAAA
62884989 AAAAAAAG
1 AAAAAAAG
62884997 AAAAAAAG
1 AAAAAAAG
*
62885005 AAAAAGAG
1 AAAAAAAG
62885013 AAAAAAAG
1 AAAAAAAG
62885021 AAAAA
1 AAAAA
62885026 TGGAGAGGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:62886013 original size:43 final size:43
Alignment explanation
Indices: 62885966--62886108 Score: 141
Period size: 43 Copynumber: 3.3 Consensus size: 43
62885956 CGCCTTAATC
62885966 CCCTAAGCAGTAGGGTAACAGG-CTAAAATTACAGATCTTATCT
1 CCCTAAGCAGTAGGGTAACAGGTC-AAAATTACAGATCTTATCT
* * * * * *
62886009 CCCTAAACAGTAGCGG-AACAGATCAACGATGACTTG-CCTTAATC-
1 CCCTAAGCAGTAG-GGTAACAGGTCAA-AATTAC-AGATCTT-ATCT
* *
62886053 CCCTAAGCAGTAGGGTAACAGGTCAAAATTGCGGATCTTATCT
1 CCCTAAGCAGTAGGGTAACAGGTCAAAATTACAGATCTTATCT
62886096 CCCTAAGCAGTAG
1 CCCTAAGCAGTAG
62886109 TGGAGCAGAT
Statistics
Matches: 79, Mismatches: 13, Indels: 16
0.73 0.12 0.15
Matches are distributed among these distances:
42 4 0.05
43 40 0.51
44 31 0.39
45 4 0.05
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (43 bp):
CCCTAAGCAGTAGGGTAACAGGTCAAAATTACAGATCTTATCT
Found at i:62886107 original size:87 final size:85
Alignment explanation
Indices: 62885955--62886163 Score: 291
Period size: 87 Copynumber: 2.5 Consensus size: 85
62885945 ACAAAATTCA
62885955 GCGCCTTAATCCCCTAAGCAGTAGGGTAACAGG-CTAAAATTACAGATCTTATCTCCCTAAACAG
1 GCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTCTAAAATTACAGATCTTATCTCCCTAAACAG
62886019 TAGCGGAACAGATC-AACGAT
66 TAGCGGAACAGATCGAA-GAT
* * *
62886039 GACTTGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTC-AAAATTGCGGATCTTATCTCCCTAAG
1 G-C--GCCTTAATCCCCTAAGCAGTAGGGTAACAGGTCTAAAATTACAGATCTTATCTCCCTAAA
* *
62886103 CAGTAGTGGAGCAGATCGAAGAT
63 CAGTAGCGGAACAGATCGAAGAT
* *
62886126 GCGCCTTAACCCCCTAAGTAGTAGGGTAACAGGT-TAAA
1 GCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTCTAAA
62886164 CTATAGCAGA
Statistics
Matches: 112, Mismatches: 7, Indels: 12
0.85 0.05 0.09
Matches are distributed among these distances:
84 34 0.30
85 1 0.01
86 1 0.01
87 73 0.65
88 3 0.03
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.22
Consensus pattern (85 bp):
GCGCCTTAATCCCCTAAGCAGTAGGGTAACAGGTCTAAAATTACAGATCTTATCTCCCTAAACAG
TAGCGGAACAGATCGAAGAT
Found at i:62888491 original size:12 final size:12
Alignment explanation
Indices: 62888469--62888549 Score: 66
Period size: 12 Copynumber: 7.0 Consensus size: 12
62888459 TATTATCCAT
62888469 TATATTATTATTA
1 TATATT-TTATTA
62888482 TATATTTTATCTA
1 TATATTTTAT-TA
*
62888495 TA-A---AATTA
1 TATATTTTATTA
62888503 T--ATTTTATTA
1 TATATTTTATTA
62888513 TATATTTTATTA
1 TATATTTTATTA
**
62888525 TATATTTCCTTA
1 TATATTTTATTA
62888537 TATTATTTTATTA
1 TA-TATTTTATTA
62888550 AAATTATGTA
Statistics
Matches: 55, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
7 1 0.02
8 3 0.05
9 2 0.04
10 5 0.09
12 26 0.47
13 18 0.33
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (12 bp):
TATATTTTATTA
Found at i:62888511 original size:31 final size:31
Alignment explanation
Indices: 62888467--62888526 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 31
62888457 TATATTATCC
62888467 ATTATATTATTATTATATATTTTATCTATAAA
1 ATTATATTATTATTATATATTTTAT-TATAAA
62888499 ATTATATT-TTATTATATATTTTATTATA
1 ATTATATTATTATTATATATTTTATTATA
62888527 TATTTCCTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 4 0.14
31 16 0.57
32 8 0.29
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (31 bp):
ATTATATTATTATTATATATTTTATTATAAA
Found at i:62888522 original size:19 final size:19
Alignment explanation
Indices: 62888471--62888522 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
62888461 TTATCCATTA
*
62888471 TATTAT-TATTATATATTT
1 TATTATATATTTTATATTT
**
62888489 TATCTATA-AAATTATATTT
1 TAT-TATATATTTTATATTT
62888508 TATTATATATTTTAT
1 TATTATATATTTTAT
62888523 TATATATTTC
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
18 7 0.27
19 19 0.73
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTATATATTTTATATTT
Found at i:62888538 original size:34 final size:35
Alignment explanation
Indices: 62888447--62888547 Score: 99
Period size: 31 Copynumber: 3.0 Consensus size: 35
62888437 CAATCATGTA
*
62888447 ATATTATATT-TATATTATCCATTATATTATTATTAT
1 ATATTTTATTATATATT-TCC-TTATATTATTATTAT
**
62888483 ATATTTTATCTATA-A---AATTATATT-TTATTAT
1 ATATTTTAT-TATATATTTCCTTATATTATTATTAT
62888514 ATATTTTATTATATATTTCCTTATATTATT-TTAT
1 ATATTTTATTATATATTTCCTTATATTATTATTAT
62888548 TAAAATTATG
Statistics
Matches: 53, Mismatches: 5, Indels: 16
0.72 0.07 0.22
Matches are distributed among these distances:
30 4 0.08
31 17 0.32
32 7 0.13
34 11 0.21
35 2 0.04
36 8 0.15
37 2 0.04
38 2 0.04
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (35 bp):
ATATTTTATTATATATTTCCTTATATTATTATTAT
Found at i:62888667 original size:16 final size:15
Alignment explanation
Indices: 62888646--62888680 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
62888636 TTATAGTATC
62888646 TATATTACATTTATAT
1 TATATTACATTTA-AT
*
62888662 TATATTATATTTAAT
1 TATATTACATTTAAT
62888677 TATA
1 TATA
62888681 AATTATTCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (15 bp):
TATATTACATTTAAT
Found at i:62893783 original size:53 final size:53
Alignment explanation
Indices: 62893590--62893793 Score: 165
Period size: 53 Copynumber: 3.8 Consensus size: 53
62893580 AGGGTTTAAG
* * * * * * * * *
62893590 GATACCAAGTAAGACCATGCAAAGGCATGACATTGGTAAGTTTTACAAGGCAAG
1 GATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAG-TTCATAACGCAAA
* * * * * * *
62893644 GAAATCATGTAAGACCATGCCAAGACATTGCATTGATAAACTACTATAACGCAAA
1 GATACCATGTAAGACCATGCCAAGACATGGCAATGGT-AAGTTC-ATAACGCAAA
* * * * * *
62893699 GATCCCATGTAAGACCGTGCCAAGGCATGGCAATGGTGAGTTCATAAGGCAAG
1 GATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAACGCAAA
* *
62893752 GATACCATGTAAGATCATGTCAAGACATGGCAATGGTAAGTT
1 GATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTT
62893794 TAAAAAGGAA
Statistics
Matches: 115, Mismatches: 33, Indels: 5
0.75 0.22 0.03
Matches are distributed among these distances:
53 44 0.38
54 33 0.29
55 38 0.33
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (53 bp):
GATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAACGCAAA
Found at i:62899749 original size:9 final size:9
Alignment explanation
Indices: 62899709--62899910 Score: 74
Period size: 9 Copynumber: 21.6 Consensus size: 9
62899699 CGATAATTTT
62899709 TTTTTATAA
1 TTTTTATAA
* *
62899718 ATTTTATAT
1 TTTTTATAA
* *
62899727 TTCTTTACAT
1 TT-TTTATAA
62899737 TTTTTATAA
1 TTTTTATAA
*
62899746 TTTTCTTATGA
1 -TTT-TTATAA
62899757 -TTTTATAAA
1 TTTTTAT-AA
*
62899766 ATTTTATAA
1 TTTTTATAA
*
62899775 TTTTTTTCTATA
1 --TTTTTATA-A
*
62899787 TTTCTAT-A
1 TTTTTATAA
62899795 TATTTTAT-A
1 T-TTTTATAA
*
62899804 TATTTTATGA
1 T-TTTTATAA
*
62899814 TTTTTCTAA
1 TTTTTATAA
62899823 TTTTTAATAA
1 TTTTT-ATAA
**
62899833 AATTTA-AA
1 TTTTTATAA
*
62899841 TATTTTAT-T
1 T-TTTTATAA
62899850 TTTTTATTAAA
1 TTTTTA-T-AA
* *
62899861 ATTTAATAA
1 TTTTTATAA
62899870 TTTTTATAA
1 TTTTTATAA
*
62899879 TTTTTATTGA
1 TTTTTA-TAA
*
62899889 TTTTTAT-T
1 TTTTTATAA
*
62899897 TTTTTATCA
1 TTTTTATAA
62899906 TTTTT
1 TTTTT
62899911 TGTCACATGT
Statistics
Matches: 146, Mismatches: 29, Indels: 36
0.69 0.14 0.17
Matches are distributed among these distances:
8 20 0.14
9 71 0.49
10 39 0.27
11 15 0.10
12 1 0.01
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.65
Consensus pattern (9 bp):
TTTTTATAA
Found at i:62905418 original size:24 final size:25
Alignment explanation
Indices: 62905385--62905450 Score: 82
Period size: 24 Copynumber: 2.7 Consensus size: 25
62905375 ATGAGTTGAC
* *
62905385 ATATGACACTATGTGTGCG-GTTTA
1 ATATGGCACTATGTGTGCGAGTGTA
*
62905409 CTATGGCACTATGTGTGCGAGTGTA
1 ATATGGCACTATGTGTGCGAGTGTA
*
62905434 AT-TAGCACTATGTGTGC
1 ATATGGCACTATGTGTGC
62905451 AAATACGGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
24 31 0.86
25 5 0.14
ACGTcount: A:0.23, C:0.15, G:0.27, T:0.35
Consensus pattern (25 bp):
ATATGGCACTATGTGTGCGAGTGTA
Found at i:62913405 original size:24 final size:24
Alignment explanation
Indices: 62913373--62913433 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
62913363 AAAATCCAAT
* * *
62913373 GCACTATGTGTGCG-GTTTACTATG
1 GCACTATGTGTGCGAGTGTAAT-TA
62913397 GCACTATGTGTGCGAGTGTAATTA
1 GCACTATGTGTGCGAGTGTAATTA
62913421 GCACTATGTGTGC
1 GCACTATGTGTGC
62913434 AAATACGGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 28 0.85
25 5 0.15
ACGTcount: A:0.20, C:0.16, G:0.30, T:0.34
Consensus pattern (24 bp):
GCACTATGTGTGCGAGTGTAATTA
Found at i:62915371 original size:24 final size:24
Alignment explanation
Indices: 62915344--62915489 Score: 116
Period size: 24 Copynumber: 6.1 Consensus size: 24
62915334 AGGCACCCTC
* *
62915344 GAATACACCACAAAGACATTTACA
1 GAATACACCACAAAGGCACTTACA
* *
62915368 GAATACACCAGAAAGGCACTTATA
1 GAATACACCACAAAGGCACTTACA
*
62915392 GAATACACCACAAAGGCAGTTACA
1 GAATACACCACAAAGGCACTTACA
** *
62915416 -AATTATGCCACAAAGGCACTAACA
1 GAA-TACACCACAAAGGCACTTACA
* ** * * * *
62915440 TAATATGCCATAAA-ACAATTATA
1 GAATACACCACAAAGGCACTTACA
*
62915463 GAGTACACCACAAAGGGCACTTACA
1 GAATACACCACAAA-GGCACTTACA
62915488 GA
1 GA
62915490 GTATGCCATG
Statistics
Matches: 94, Mismatches: 24, Indels: 7
0.75 0.19 0.06
Matches are distributed among these distances:
23 16 0.17
24 68 0.72
25 10 0.11
ACGTcount: A:0.47, C:0.23, G:0.14, T:0.17
Consensus pattern (24 bp):
GAATACACCACAAAGGCACTTACA
Found at i:62920081 original size:20 final size:20
Alignment explanation
Indices: 62920019--62920316 Score: 123
Period size: 19 Copynumber: 15.0 Consensus size: 20
62920009 AATTTTTATC
62920019 ATATATTTTTATTATATA-T
1 ATATATTTTTATTATATATT
*
62920038 AT-TATTTATTCTGT-TATATT
1 ATATATTT-TTAT-TATATATT
*
62920058 -TATATTTTTATTATATGTT
1 ATATATTTTTATTATATATT
62920077 ATATATTTTTATTATATATT
1 ATATATTTTTATTATATATT
* *
62920097 ATTTA-TTTTACTATAT-TT
1 ATATATTTTTATTATATATT
* *
62920115 TTATATTATTATTAT-TATT
1 ATATATTTTTATTATATATT
*
62920134 AT-TA-TTTTATATATTCCTTATT
1 ATATATTTTTAT-TA-T--ATATT
*
62920156 ATATTATATTTCATTATATTTTATCT
1 ATA-TAT-TTTTATTATA---TAT-T
* *
62920182 ACATATTTTTATTACATA-T
1 ATATATTTTTATTATATATT
62920201 -TATA-TTTTATTATATATT
1 ATATATTTTTATTATATATT
* *
62920219 AT-TCA---TTATAATATCTT
1 ATAT-ATTTTTATTATATATT
* *
62920236 -TCTTTCTTTTA-TATATATT
1 ATATAT-TTTTATTATATATT
* **
62920255 ATATCATATACATT-T-TATT
1 ATAT-ATTTTTATTATATATT
*
62920274 ATATATTTTTATATTATTTATT
1 ATATA-TTTT-TATTATATATT
*
62920296 ATATGATTTATATTATATATT
1 ATAT-ATTTTTATTATATATT
62920317 TTATTTGTAA
Statistics
Matches: 208, Mismatches: 34, Indels: 72
0.66 0.11 0.23
Matches are distributed among these distances:
16 1 0.00
17 27 0.13
18 22 0.11
19 58 0.28
20 40 0.19
21 15 0.07
22 17 0.08
23 1 0.00
24 11 0.05
25 8 0.04
26 8 0.04
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.63
Consensus pattern (20 bp):
ATATATTTTTATTATATATT
Found at i:62920100 original size:36 final size:36
Alignment explanation
Indices: 62920010--62920316 Score: 144
Period size: 36 Copynumber: 8.4 Consensus size: 36
62920000 TTTTTTAAAA
* *
62920010 ATTTTTATCATATATT-TTTATTA-TATATATTATTT
1 ATTTTTATTATATATTATTT-TTATTATATATTATAT
* *
62920045 ATTCTGTTA-TATTTA-TATTTTTATTATATGTTATAT
1 ATT-T-TTATTATATATTATTTTTATTATATATTATAT
*
62920081 ATTTTTATTATATATTA--TTTATT-T-TACTATAT
1 ATTTTTATTATATATTATTTTTATTATATATTATAT
*
62920113 -TTTTATATTAT-TATTATTATTATTAT-T-TTATAT
1 ATTTT-TATTATATATTATTTTTATTATATATTATAT
* * *
62920146 ATTCCTTATTATAT-TATATTTCATTA-TATTTTATCTACAT
1 ATT-TTTATTATATAT-TATTT--TTATTA-TATAT-TATAT
*
62920186 ATTTTTATTACATATTATATTTTATTATATATTAT-T
1 ATTTTTATTATATATTAT-TTTTATTATATATTATAT
* * * * *
62920222 CATTATAATATCTTTCT-TTCTTTTATATATATTATATCATAT
1 -ATT-T-TTAT-TATATATTATTTT-TAT-TA-TATATTATAT
* * *
62920264 ACATTTTATTATATATT-TTTATATTATTTATTATAT
1 A-TTTTTATTATATATTATTTTTATTATATATTATAT
*
62920300 GATTTATATTATATATT
1 -ATTTTTATTATATATT
62920317 TTATTTGTAA
Statistics
Matches: 207, Mismatches: 31, Indels: 67
0.68 0.10 0.22
Matches are distributed among these distances:
31 9 0.04
32 12 0.06
33 11 0.05
34 20 0.10
35 19 0.09
36 47 0.23
37 15 0.07
38 15 0.07
39 29 0.14
40 19 0.09
41 9 0.04
42 2 0.01
ACGTcount: A:0.31, C:0.05, G:0.01, T:0.63
Consensus pattern (36 bp):
ATTTTTATTATATATTATTTTTATTATATATTATAT
Found at i:62920112 original size:56 final size:54
Alignment explanation
Indices: 62920019--62920220 Score: 173
Period size: 52 Copynumber: 3.7 Consensus size: 54
62920009 AATTTTTATC
* *
62920019 ATATATTTTTATTATATATATTATTTATTCTGTTATATTTATATTTTTATTATATGTT
1 ATATATTTTTA-T-TATATATTATTTATTTTATTATATTTATA-TTTTATTATAT-TT
* * *
62920077 ATATATTTTTATTATATATTATTTATTTTACTATATTTTTATATTATTAT-TATT
1 ATATATTTTTATTATATATTATTTATTTTATTATATTTATATTTTATTATAT-TT
* ** * * * * *
62920131 AT-TATTATT-TTATATATTCCTTATTATATTATATTT-CATTATATTTTATCT
1 ATATATTTTTATTATATATTATTTATTTTATTATATTTATATTTTATTATATTT
* *
62920182 ACATATTTTTATTACATATTA--TATTTTATTATATATTAT
1 ATATATTTTTATTATATATTATTTATTTTATTATAT-TTAT
62920221 TCATTATAAT
Statistics
Matches: 117, Mismatches: 22, Indels: 15
0.76 0.14 0.10
Matches are distributed among these distances:
51 21 0.18
52 32 0.27
53 14 0.12
54 5 0.04
55 8 0.07
56 25 0.21
57 1 0.01
58 11 0.09
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (54 bp):
ATATATTTTTATTATATATTATTTATTTTATTATATTTATATTTTATTATATTT
Found at i:62920118 original size:58 final size:57
Alignment explanation
Indices: 62920014--62920141 Score: 154
Period size: 58 Copynumber: 2.2 Consensus size: 57
62920004 TTAAAAATTT
* * * *
62920014 TTATCATATATTTTTATTATATATATTATTTATTCTGTTATATTTATATTTTTATTA
1 TTATTATATATTTTTATTATATATATTATTTATACTGATATATTTATATTATTATTA
* *
62920071 TATGTTATATATTTTTATTATATATTATTTATTT-TACT-ATATTTTTATATTATTATTA
1 T-TATTATATATTTTTATTATATA-TA-TTATTTATACTGATATATTTATATTATTATTA
62920129 TTATTAT-TATTTT
1 TTATTATATATTTT
62920142 ATATATTCCT
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
56 6 0.10
57 6 0.10
58 38 0.62
59 5 0.08
60 6 0.10
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (57 bp):
TTATTATATATTTTTATTATATATATTATTTATACTGATATATTTATATTATTATTA
Found at i:62920139 original size:108 final size:103
Alignment explanation
Indices: 62920022--62920215 Score: 226
Period size: 108 Copynumber: 1.8 Consensus size: 103
62920012 TTTTATCATA
* * * * * * * *
62920022 TATTTTTATTATATATATTATTTATTCTGTTATATTTATATTTTTATTATATGTTATATATTTTT
1 TATTATTATTATATATATTACTTATTATATTATATTT-CA-TTATATTATAT-CTACATATTTTT
*
62920087 ATTATATATTATTTATTTTACTATATTTTTATATTATTATTAT
63 ATTACATATTA--TATTTTACTATATTTTTATATTATTATTAT
* * *
62920130 TATTATTATTTTATATATTCCTTATTATATTATATTTCATTATATTTTATCTACATATTTTTATT
1 TATTATTATTATATATATTACTTATTATATTATATTTCATTATATTATATCTACATATTTTTATT
*
62920195 ACATATTATATTTTATTATAT
66 ACATATTATATTTTACTATAT
62920216 ATTATTCATT
Statistics
Matches: 73, Mismatches: 13, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
103 12 0.16
105 20 0.27
106 9 0.12
107 1 0.01
108 31 0.42
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.64
Consensus pattern (103 bp):
TATTATTATTATATATATTACTTATTATATTATATTTCATTATATTATATCTACATATTTTTATT
ACATATTATATTTTACTATATTTTTATATTATTATTAT
Found at i:62920144 original size:52 final size:53
Alignment explanation
Indices: 62920014--62920179 Score: 149
Period size: 56 Copynumber: 3.1 Consensus size: 53
62920004 TTAAAAATTT
* * * * * *
62920014 TTATCATA-TATTTTTATTATATATATTATTTATTCTGTTATATTTATATTTTTA
1 TTAT-ATATTATTATTATTTTATATATTATTTATTATATTATATTTTTA-TATTA
* * * *
62920068 TTATATGTTATATATTTTTATTATATATTATTTATTTTACTATATTTTTATATTA
1 TTATATATTAT-TATTATT-TTATATATTATTTATTATATTATATTTTTATATTA
**
62920123 TTAT-TATTATTATTATTTTATATATTCCTTATTATATTATATTTCATTATATT-
1 TTATATATTATTATTATTTTATATATTATTTATTATATTATATTT--TTATATTA
62920176 TTAT
1 TTAT
62920180 CTACATATTT
Statistics
Matches: 92, Mismatches: 15, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
52 23 0.25
53 12 0.13
54 19 0.21
55 13 0.14
56 25 0.27
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (53 bp):
TTATATATTATTATTATTTTATATATTATTTATTATATTATATTTTTATATTA
Found at i:62920194 original size:67 final size:64
Alignment explanation
Indices: 62920053--62920215 Score: 157
Period size: 67 Copynumber: 2.5 Consensus size: 64
62920043 TTATTCTGTT
* * * * * * **
62920053 ATATTTATATTTTTATTATATGTTATATATTTTTATTATATATTATTTATTTTACTATATTTTT
1 ATATTTTTATTATTATTATATTTTATATATTCTTATTATATATTATTTATTATACTATATCTAC
* * *
62920117 ATATTATTATTATTATTATTATTTTATATATTCCTTATTATAT-TATATTTCATTATATTTTATC
1 ATATTTTTATTATTATTA-TATTTTATATATT-CTTATTATATAT-TATTT-ATTATACTATATC
62920181 TAC
62 TAC
*
62920184 ATATTTTTATTACATATTATATTTTATTATAT
1 ATATTTTTATTA-TTATTATATTTTA-TATAT
62920216 ATTATTCATT
Statistics
Matches: 80, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
64 15 0.19
65 13 0.16
66 14 0.17
67 28 0.35
68 10 0.12
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (64 bp):
ATATTTTTATTATTATTATATTTTATATATTCTTATTATATATTATTTATTATACTATATCTAC
Found at i:62920210 original size:17 final size:17
Alignment explanation
Indices: 62920168--62920220 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
62920158 ATTATATTTC
62920168 ATTATATTTTATCTAC--
1 ATTATATTTTAT-TACAT
62920184 A-TAT-TTTTATTACAT
1 ATTATATTTTATTACAT
*
62920199 ATTATATTTTATTATAT
1 ATTATATTTTATTACAT
62920216 ATTAT
1 ATTAT
62920221 TCATTATAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
13 3 0.09
14 6 0.19
15 4 0.12
16 4 0.12
17 15 0.47
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTATATTTTATTACAT
Found at i:62920211 original size:10 final size:10
Alignment explanation
Indices: 62920028--62920321 Score: 102
Period size: 9 Copynumber: 30.7 Consensus size: 10
62920018 CATATATTTT
62920028 TATTA-TATA
1 TATTATTATA
62920037 TATTATT-TA
1 TATTATTATA
*
62920046 T-TCTGTTATA
1 TAT-TATTATA
62920056 T-TTA-TAT-
1 TATTATTATA
*
62920063 TTTTATTATA
1 TATTATTATA
*
62920073 TGTTA-TATA
1 TATTATTATA
62920082 T-TT-TTAT-
1 TATTATTATA
*
62920089 TATATATTATT
1 TAT-TATTATA
62920100 TATT-TTACTA
1 TATTATTA-TA
62920110 TATT-TT-TA
1 TATTATTATA
62920118 TATTATTAT-
1 TATTATTATA
62920127 TATTATTAT-
1 TATTATTATA
62920136 TATT-TTATA
1 TATTATTATA
*
62920145 TATTCCTTAT-
1 TATT-ATTATA
62920155 TA-TATTATA
1 TATTATTATA
62920164 T-TTCATTATA
1 TATT-ATTATA
* *
62920174 TTTTATCTACA
1 TATTAT-TATA
*
62920185 TATTTTTAT-
1 TATTATTATA
*
62920194 TACATATTATA
1 TA-TTATTATA
*
62920205 TTTTATTATA
1 TATTATTATA
62920215 TATTATTCATTA
1 TATTATT-A-TA
* * *
62920227 TAATATCTTTC
1 TATTAT-TATA
* *
62920238 T-TTCTTTTA
1 TATTATTATA
62920247 TATATATTATA
1 TAT-TATTATA
*
62920258 TCA-TA-TACA
1 T-ATTATTATA
*
62920267 TTTTATTATA
1 TATTATTATA
62920277 TATT-TT-TA
1 TATTATTATA
62920285 TATTATTTATTA
1 TATTA-TTA-TA
*
62920297 TATGATT-TA
1 TATTATTATA
62920306 TATTA-TATA
1 TATTATTATA
*
62920315 TTTTATT
1 TATTATT
62920322 TGTAAATTAT
Statistics
Matches: 218, Mismatches: 29, Indels: 75
0.68 0.09 0.23
Matches are distributed among these distances:
7 2 0.01
8 34 0.16
9 72 0.33
10 67 0.31
11 28 0.13
12 14 0.06
13 1 0.00
ACGTcount: A:0.31, C:0.05, G:0.01, T:0.63
Consensus pattern (10 bp):
TATTATTATA
Found at i:62920311 original size:14 final size:12
Alignment explanation
Indices: 62920012--62920321 Score: 107
Period size: 12 Copynumber: 24.6 Consensus size: 12
62920002 TTTTAAAAAT
*
62920012 TTTTATCATATA
1 TTTTATTATATA
62920024 TTTTTATTATATA
1 -TTTTATTATATA
*
62920037 TATTATT-TAT-
1 TTTTATTATATA
*
62920047 TCTGTTA-TATTTA
1 T-T-TTATTATATA
62920060 TATTT-TTATTATA
1 T-TTTATTA-TATA
*
62920073 TGTTA-TATAT-
1 TTTTATTATATA
62920083 TTTTATTATATA
1 TTTTATTATATA
*
62920095 TTATTTATTTTACTA
1 -T-TTTATTATA-TA
62920110 TATTT-TTATATTA
1 T-TTTATTATA-TA
62920123 TTATTATTAT-TA
1 TT-TTATTATATA
62920135 TTATT-TTATATA
1 TT-TTATTATATA
62920147 TTCCTTATTATATTA
1 TT--TTATTATA-TA
62920162 TATTTCA-T-TATA
1 T-TTT-ATTATATA
*
62920174 TTTTATCTACATA
1 TTTTAT-TATATA
62920187 TTTTTATTACATATTATA
1 -TTTTA-T---TA-TATA
62920205 TTTTATTATATA
1 TTTTATTATATA
62920217 TTATTCATTATAATA
1 TT-TT-ATTAT-ATA
* *
62920232 TCTTT-CT-T-TC
1 T-TTTATTATATA
62920242 TTTTA-TATATA
1 TTTTATTATATA
* *
62920253 TTATATCATATACA
1 TTTTAT--TATATA
62920267 TTTTATTATATA
1 TTTTATTATATA
62920279 -TTT-TTATAT-
1 TTTTATTATATA
62920288 TATTTATTATATGA
1 T-TTTATTATAT-A
62920302 TTTATATTATATA
1 TTT-TATTATATA
62920315 TTTTATT
1 TTTTATT
62920322 TGTAAATTAT
Statistics
Matches: 231, Mismatches: 22, Indels: 89
0.68 0.06 0.26
Matches are distributed among these distances:
9 4 0.02
10 15 0.06
11 30 0.13
12 57 0.25
13 45 0.19
14 54 0.23
15 13 0.06
16 3 0.01
17 7 0.03
18 3 0.01
ACGTcount: A:0.31, C:0.05, G:0.01, T:0.63
Consensus pattern (12 bp):
TTTTATTATATA
Found at i:62920311 original size:21 final size:21
Alignment explanation
Indices: 62920020--62920148 Score: 77
Period size: 20 Copynumber: 6.6 Consensus size: 21
62920010 ATTTTTATCA
*
62920020 TATATT-TTTATTATATATAT
1 TATATTATTTATTATATATTT
*
62920040 TAT-TTATTCT-GT-TATA-TT
1 TATATTATT-TATTATATATTT
* *
62920058 TATATT-TTTATTATATGTTA
1 TATATTATTTATTATATATTT
62920078 TATATT-TTTATTATATA--T
1 TATATTATTTATTATATATTT
*
62920096 TAT-TTATTTTACTATAT-TTT
1 TATATTA-TTTATTATATATTT
62920116 TATATTA-TTATTAT-TATTAT
1 TATATTATTTATTATATATT-T
* *
62920136 TATTTTATATATT
1 TATATTATTTATT
62920149 CCTTATTATA
Statistics
Matches: 84, Mismatches: 11, Indels: 27
0.69 0.09 0.22
Matches are distributed among these distances:
17 3 0.04
18 11 0.13
19 28 0.33
20 34 0.40
21 8 0.10
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (21 bp):
TATATTATTTATTATATATTT
Found at i:62920331 original size:34 final size:35
Alignment explanation
Indices: 62920266--62920331 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
62920256 TATCATATAC
**
62920266 ATTTTATTATATATTTTTATATTATTTATTATATG
1 ATTTTATTATATATTTTTATATTATAAATTATATG
*
62920301 ATTTATATTATATA-TTTTAT-TTGTAAATTAT
1 ATTT-TATTATATATTTTTATATTATAAATTAT
62920332 GTTATACACT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 8 0.30
35 10 0.37
36 9 0.33
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (35 bp):
ATTTTATTATATATTTTTATATTATAAATTATATG
Found at i:62922115 original size:18 final size:19
Alignment explanation
Indices: 62922077--62922119 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
62922067 AAAAATGATT
**
62922077 TAAAATGTTCATAAAGTTC
1 TAAAATGTTCATAAAAATC
62922096 TAAAATGTTC-TAAAAATC
1 TAAAATGTTCATAAAAATC
62922114 TAAAAT
1 TAAAAT
62922120 TTGAAACAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.35
Consensus pattern (19 bp):
TAAAATGTTCATAAAAATC
Found at i:62927443 original size:38 final size:38
Alignment explanation
Indices: 62927387--62927466 Score: 117
Period size: 38 Copynumber: 2.1 Consensus size: 38
62927377 GATGTGTATT
* *
62927387 CGGGTTAAATCCCGCAGGCTTCA-TGCTGGTATTATATC
1 CGGGATAAATCCCGCAGGCCT-AGTGCTGGTATTATATC
*
62927425 CGGGATAAATCCCGCAGGCCTAGTGCTGGTATTATATT
1 CGGGATAAATCCCGCAGGCCTAGTGCTGGTATTATATC
62927463 CGGG
1 CGGG
62927467 CCTTCGTGCC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 1 0.03
38 37 0.97
ACGTcount: A:0.21, C:0.23, G:0.28, T:0.29
Consensus pattern (38 bp):
CGGGATAAATCCCGCAGGCCTAGTGCTGGTATTATATC
Found at i:62927513 original size:43 final size:43
Alignment explanation
Indices: 62927438--62927622 Score: 257
Period size: 43 Copynumber: 4.3 Consensus size: 43
62927428 GATAAATCCC
* * *
62927438 GCAGGCCTAGTGCTGGT-AT-TATATTCGGGCCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
62927479 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* *
62927522 GCAGGCTTTGTGCTGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* * **
62927565 GCAGGCTTCGTGTCGGTGATGTGTATTCGGGCCTTCGTATCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* *
62927608 GCAGGCGTAATGCCG
1 GCAGGCTTAGTGCCG
62927623 ATGAAATGAT
Statistics
Matches: 128, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
41 15 0.12
42 2 0.02
43 111 0.87
ACGTcount: A:0.12, C:0.23, G:0.34, T:0.31
Consensus pattern (43 bp):
GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
Found at i:62928010 original size:45 final size:42
Alignment explanation
Indices: 62927943--62928050 Score: 110
Period size: 45 Copynumber: 2.5 Consensus size: 42
62927933 TTGACTTGAT
* * * *
62927943 TATTCGGACCTTTGAGCTTAGCAAACTATAATGCTGGTGAGATAC
1 TATTCGGGCCTTCGAGCCTAGCAAACTATAATGCCGGT--GA-AC
**
62927988 TATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAAC
1 TATTCGGGCCTTCGAGCCTAGCAAACTATAATGCCGGTGAAC
62928030 TGATATCGGGCC-TCGAGCCTA
1 T-AT-TCGGGCCTTCGAGCCTA
62928051 ACAGGCGAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
42 3 0.05
43 13 0.24
44 7 0.13
45 32 0.58
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (42 bp):
TATTCGGGCCTTCGAGCCTAGCAAACTATAATGCCGGTGAAC
Found at i:62929306 original size:21 final size:21
Alignment explanation
Indices: 62929265--62929306 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
62929255 TTCGATCAAA
* *
62929265 TCGAATTGAGTGAGATGGAAT
1 TCGAATTGAATGAGATCGAAT
62929286 TCGAATTGAATCGA-ATCGAAT
1 TCGAATTGAAT-GAGATCGAAT
62929307 ATATTTGTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.36, C:0.10, G:0.26, T:0.29
Consensus pattern (21 bp):
TCGAATTGAATGAGATCGAAT
Found at i:62932223 original size:96 final size:94
Alignment explanation
Indices: 62932113--62932404 Score: 398
Period size: 96 Copynumber: 3.1 Consensus size: 94
62932103 ATTAAAAATT
* *
62932113 AATTAATATAATAGTACAGGTACATCAACATAAATTAAACAAAAAAAAGTATGTTAAATTACATT
1 AATTAATATAATAGTACA-GTACATCAGCATAAATTAAACAAAAAAAAGTATGTTAAACTACATT
62932178 TCAAACTTTAAAGTTAGTTAATTGAAGCCTA
65 T-AAACTTTAAAGTTAGTTAATTGAAGCCTA
* *
62932209 AATTAATATAATAGTAC---A-AT-AGCATAAATTAAACAAAAAAAAGTTTGTTAAGCTACCATT
1 AATTAATATAATAGTACAGTACATCAGCATAAATTAAACAAAAAAAAGTATGTTAAACTA-CATT
*
62932269 TAAAATTTAAAGTTAGTTAATTGAAGCCTA
65 TAAACTTTAAAGTTAGTTAATTGAAGCCTA
* * * *
62932299 AATTAATATAATAGTACAAGTACAACAGGATAAATTAGAA-AAAAAACAGTATGTTAAACTATAG
1 AATTAATATAATAGTAC-AGTACATCAGCATAAATTA-AACAAAAAAAAGTATGTTAAACTACA-
*
62932363 TTTAAACTTTAAAGTTAGTTAATTGAAGGCTA
63 TTTAAACTTTAAAGTTAGTTAATTGAAGCCTA
62932395 AATTAATATA
1 AATTAATATA
62932405 CAACAGCATA
Statistics
Matches: 174, Mismatches: 13, Indels: 18
0.85 0.06 0.09
Matches are distributed among these distances:
90 76 0.44
91 7 0.04
92 1 0.01
94 1 0.01
95 2 0.01
96 85 0.49
97 2 0.01
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.32
Consensus pattern (94 bp):
AATTAATATAATAGTACAGTACATCAGCATAAATTAAACAAAAAAAAGTATGTTAAACTACATTT
AAACTTTAAAGTTAGTTAATTGAAGCCTA
Found at i:62932628 original size:17 final size:17
Alignment explanation
Indices: 62932606--62932654 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
62932596 TTTTCTCTAT
*
62932606 TAATATTACGTTATTAC
1 TAATATTACATTATTAC
* *
62932623 TAATATTATATTATTAT
1 TAATATTACATTATTAC
62932640 TAATATTACATTATT
1 TAATATTACATTATT
62932655 GCTTTGGGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.53
Consensus pattern (17 bp):
TAATATTACATTATTAC
Found at i:62934461 original size:268 final size:269
Alignment explanation
Indices: 62933983--62934522 Score: 830
Period size: 268 Copynumber: 2.0 Consensus size: 269
62933973 CTAGGTTGTC
* * *
62933983 TTATATTGTGACTAATCAAGTCCTTGACCGGTTAGGTTATTAGACAAACATTGCTAGATAGCCGT
1 TTATATTGTGACTAATCAAGTCCTTGACCGATTAGGTCATTAGACAAACATTGCTAAATAGCCGT
* * * *
62934048 TGAAACACCCCGATGCTCAACTCGATCGTCGGGTACGAGCTACAGGGATAAACGTTCATTTTCAG
66 TGAAACACCCCGATACTCAACCCGATCATCGGGTACGAGCTACAGGGATAAACATTCATTTTCAG
62934113 AGCAACTATGATAAAATTATATTCGATTTAAAATCATTGAACATTCAAATATAAGTAAAACATGT
131 AGCAACTATGATAAAATTATATTCGATTTAAAATCATTGAACATTCAAATATAAGTAAAACATGT
* * * *
62934178 GTATAATACAATACGTAATCTTTTTCAGGTTTTATACGACCTTACGAAAGATCTAATGCTAACCC
196 GTATAATACAATACGTAATCATATTCAGGTTTTATACAACCTTACGAAAGATCTAATGCAAACCC
*
62934243 GAGGTCGAA
261 GAGGTCAAA
*
62934252 TTATATTGTGACTAATCAAGTCCTTGACCGATTAGGTCGTTAGACAAACATTGCTAAATAGCCGT
1 TTATATTGTGACTAATCAAGTCCTTGACCGATTAGGTCATTAGACAAACATTGCTAAATAGCCGT
** * * * * *
62934317 TGAAACACCTTGATATTCGACCCGATCATC-GGTCCGAGCTATAGGGATCAACATTCATTTTCAG
66 TGAAACACCCCGATACTCAACCCGATCATCGGGTACGAGCTACAGGGATAAACATTCATTTTCAG
* * **
62934381 AGCAACTATGATCAAATTATATTTGATTTAAAATCATTGAACATTCAAATATAAGTAAAATGTGT
131 AGCAACTATGATAAAATTATATTCGATTTAAAATCATTGAACATTCAAATATAAGTAAAACATGT
* * *
62934446 GTATAATGCAATACGTAATCATATTCAGGTTTTATACAACCTTACGAAAGCTCTAATGCAAACCT
196 GTATAATACAATACGTAATCATATTCAGGTTTTATACAACCTTACGAAAGATCTAATGCAAACCC
62934511 GAGGTCAAA
261 GAGGTCAAA
62934520 TTA
1 TTA
62934523 AGACCAAATT
Statistics
Matches: 244, Mismatches: 27, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
268 160 0.66
269 84 0.34
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (269 bp):
TTATATTGTGACTAATCAAGTCCTTGACCGATTAGGTCATTAGACAAACATTGCTAAATAGCCGT
TGAAACACCCCGATACTCAACCCGATCATCGGGTACGAGCTACAGGGATAAACATTCATTTTCAG
AGCAACTATGATAAAATTATATTCGATTTAAAATCATTGAACATTCAAATATAAGTAAAACATGT
GTATAATACAATACGTAATCATATTCAGGTTTTATACAACCTTACGAAAGATCTAATGCAAACCC
GAGGTCAAA
Found at i:62937362 original size:44 final size:41
Alignment explanation
Indices: 62937307--62937425 Score: 123
Period size: 44 Copynumber: 2.8 Consensus size: 41
62937297 ATCTGAGATA
* *
62937307 TCGTGTAAGACCGTGTCTGGGACACAGGCCTCG-ATTTGAGATT
1 TCGTGTAAGACC-TGTCTGGGACACAGGCATCGTATCT--GATT
* *
62937350 TATGTGTAAGACCATGTCTGGGACATAGGCATCGTATCTGATT
1 T-CGTGTAAGACC-TGTCTGGGACACAGGCATCGTATCTGATT
* *
62937393 TCGTGTAAGATCCTGTCTGGGACAGAGACATCG
1 TCGTGTAAGA-CCTGTCTGGGACACAGGCATCG
62937426 ATATTGAATT
Statistics
Matches: 65, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
42 26 0.40
43 8 0.12
44 28 0.43
45 3 0.05
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.29
Consensus pattern (41 bp):
TCGTGTAAGACCTGTCTGGGACACAGGCATCGTATCTGATT
Found at i:62937410 original size:42 final size:41
Alignment explanation
Indices: 62937307--62937458 Score: 128
Period size: 43 Copynumber: 3.6 Consensus size: 41
62937297 ATCTGAGATA
* *
62937307 TCGTGTAAGACCGTGTCTGGGACACAGGCCTCG-ATTTGAGATT
1 TCGTGTAAGACCATGTCTGGGACACAGGCATCGTA-TT--GATT
* *
62937350 TATGTGTAAGACCATGTCTGGGACATAGGCATCGTATCTGATT
1 T-CGTGTAAGACCATGTCTGGGACACAGGCATCGTAT-TGATT
* *
62937393 TCGTGTAAGATCC-TGTCTGGGACAGAGACATCGATATTGAATT
1 TCGTGTAAGA-CCATGTCTGGGACACAGGCATCG-TATTG-ATT
* * * *
62937436 ACATGTAAGATCACGTCTGGGAC
1 TCGTGTAAGACCATGTCTGGGAC
62937459 GTCAACATTG
Statistics
Matches: 91, Mismatches: 11, Indels: 14
0.78 0.09 0.12
Matches are distributed among these distances:
42 29 0.32
43 31 0.34
44 29 0.32
45 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (41 bp):
TCGTGTAAGACCATGTCTGGGACACAGGCATCGTATTGATT
Found at i:62937456 original size:43 final size:42
Alignment explanation
Indices: 62937354--62937458 Score: 115
Period size: 42 Copynumber: 2.5 Consensus size: 42
62937344 GAGATTTATG
* * * * * *
62937354 TGTAAGACCATGTCTGGGACATAGGCATCGTATCTGATTTCG
1 TGTAAGATCACGTCTGGGACAGAGACATCGTATCTGATTACA
62937396 TGTAAGATC-CTGTCTGGGACAGAGACATCGATAT-TGAATTACA
1 TGTAAGATCAC-GTCTGGGACAGAGACATCG-TATCTG-ATTACA
62937439 TGTAAGATCACGTCTGGGAC
1 TGTAAGATCACGTCTGGGAC
62937459 GTCAACATTG
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
42 27 0.51
43 25 0.47
44 1 0.02
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.29
Consensus pattern (42 bp):
TGTAAGATCACGTCTGGGACAGAGACATCGTATCTGATTACA
Found at i:62942088 original size:13 final size:13
Alignment explanation
Indices: 62942062--62942135 Score: 67
Period size: 13 Copynumber: 5.6 Consensus size: 13
62942052 AAATATTTAG
*
62942062 ATGAAATTGTTAT
1 ATGAAATGGTTAT
*
62942075 ATGAAATGGATAT
1 ATGAAATGGTTAT
*
62942088 ATGAAATGCTTAT
1 ATGAAATGGTTAT
* * *
62942101 TTGGAAATAGATAT
1 AT-GAAATGGTTAT
**
62942115 ATGAACCGGTTAT
1 ATGAAATGGTTAT
62942128 ATGAAATG
1 ATGAAATG
62942136 TTTAAACGAA
Statistics
Matches: 45, Mismatches: 15, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
13 36 0.80
14 9 0.20
ACGTcount: A:0.41, C:0.04, G:0.20, T:0.35
Consensus pattern (13 bp):
ATGAAATGGTTAT
Found at i:62955538 original size:43 final size:43
Alignment explanation
Indices: 62955490--62955596 Score: 142
Period size: 43 Copynumber: 2.5 Consensus size: 43
62955480 ACTTTCGAGG
* * **
62955490 TGTGATTTCGTGTAAGACCATGTCTGGGACATTGGCATCGATT
1 TGTGATTACGTGTAAGACCATGTCTGAGACAAAGGCATCGATT
* *
62955533 TGTGATTACGTGTAAGACCCTGTCTGAGACAAAGGCATCGGTT
1 TGTGATTACGTGTAAGACCATGTCTGAGACAAAGGCATCGATT
* *
62955576 TGTGATAACATGTAAGACCAT
1 TGTGATTACGTGTAAGACCAT
62955597 ATTTGGGATA
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 55 1.00
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (43 bp):
TGTGATTACGTGTAAGACCATGTCTGAGACAAAGGCATCGATT
Found at i:62958410 original size:43 final size:42
Alignment explanation
Indices: 62958362--62958507 Score: 166
Period size: 43 Copynumber: 3.4 Consensus size: 42
62958352 ATCAGATATA
* * * *
62958362 GTCTTACATGTTATCACGTATCGATGCCACTATCCCAGACAGG
1 GTCTTACATGTAATCAC-TATCGATGCCAATGTCCCAGACATG
*** * *
62958405 GTCTTACACAAAATCGATTAACGATGCCAATGTCCCAGACATG
1 GTCTTACATGTAATC-ACTATCGATGCCAATGTCCCAGACATG
* *
62958448 GTCTTACATGTAATCACAATACAATGCCAATGTCCCAGACATG
1 GTCTTACATGTAATCACTAT-CGATGCCAATGTCCCAGACATG
62958491 GTCTTACATGTAATCAC
1 GTCTTACATGTAATCAC
62958508 ATCTCAATAA
Statistics
Matches: 85, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
42 2 0.02
43 82 0.96
44 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.27
Consensus pattern (42 bp):
GTCTTACATGTAATCACTATCGATGCCAATGTCCCAGACATG
Found at i:62960123 original size:26 final size:26
Alignment explanation
Indices: 62960051--62960124 Score: 78
Period size: 26 Copynumber: 2.7 Consensus size: 26
62960041 GGAGGACATG
*
62960051 TTAGTTGTTAACCACTTTGTGGCCAC
1 TTAGTTGTTAACCAGTTTGTGGCCAC
62960077 TAGTAGGGTATGTTAACCAGTTTGGTGGCCA-
1 T--TA--GT-TGTTAACCAGTTT-GTGGCCAC
62960108 TTAGTTGTTAACCAGTT
1 TTAGTTGTTAACCAGTT
62960125 GGCGAGAGTA
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
26 13 0.32
27 2 0.05
28 2 0.05
29 2 0.05
30 2 0.05
31 13 0.32
32 7 0.17
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.38
Consensus pattern (26 bp):
TTAGTTGTTAACCAGTTTGTGGCCAC
Found at i:62962389 original size:43 final size:42
Alignment explanation
Indices: 62962323--62962475 Score: 189
Period size: 42 Copynumber: 3.6 Consensus size: 42
62962313 TAACATACCA
* ** *
62962323 ATGCCATATCCCAGTTATGGTCTTACATGGGATCTCGTATCG
1 ATGCCATATCCCAGATATGGTCTTACATGAAATCTCATATCG
* * * *
62962365 ATGCCAATAGCCCAGCTATTGTCTTACACGAAATCTCATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACATGAAATCTCATATCG
* * *
62962408 ATGCCATATCTCAGATATGGTCTTACATGAAGTCTCATATAG
1 ATGCCATATCCCAGATATGGTCTTACATGAAATCTCATATCG
*
62962450 ATGCCATATCCCAAATATGGTCTTAC
1 ATGCCATATCCCAGATATGGTCTTAC
62962476 GCATAGTCTT
Statistics
Matches: 94, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
42 59 0.63
43 35 0.37
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.31
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACATGAAATCTCATATCG
Found at i:62966977 original size:23 final size:24
Alignment explanation
Indices: 62966947--62967012 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 24
62966937 ATATTAAGTC
*
62966947 CGCACACTCAGTGCTAATC-AACT
1 CGCACACTTAGTGCTAATCAAACT
62966970 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGC----TAATCAAACT
62966998 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
62967013 GAACAATTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
23 13 0.35
24 1 0.03
27 5 0.14
28 18 0.49
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.26
Consensus pattern (24 bp):
CGCACACTTAGTGCTAATCAAACT
Found at i:62967000 original size:28 final size:28
Alignment explanation
Indices: 62966961--62967040 Score: 101
Period size: 28 Copynumber: 2.9 Consensus size: 28
62966951 CACTCAGTGC
62966961 TAATC-AACTCGCACACTTAGTGCT-ATA
1 TAATCAAACTCGCACACTTAGTGCTGA-A
62966988 TAATCAAACTCGCACACTTAGTGCTGAA
1 TAATCAAACTCGCACACTTAGTGCTGAA
* * *
62967016 CAATTTAAACCCGCACACTTAGTGC
1 TAA-TCAAACTCGCACACTTAGTGC
62967041 CAATCTCATG
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
27 5 0.11
28 22 0.47
29 20 0.43
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26
Consensus pattern (28 bp):
TAATCAAACTCGCACACTTAGTGCTGAA
Found at i:62969108 original size:27 final size:27
Alignment explanation
Indices: 62969032--62969113 Score: 94
Period size: 27 Copynumber: 3.0 Consensus size: 27
62969022 AGAATTTGCT
* * *
62969032 ACAAAGGCTCTTCTTTCAGAGTCCT-CC
1 ACAAAGGATTTTCTTTCAGAG-CTTACC
*
62969059 ATAAAGGATTTTCTTTCAGAGCTTACC
1 ACAAAGGATTTTCTTTCAGAGCTTACC
* *
62969086 ACAAAGGGTTTTCTTTCAGAGCTCACC
1 ACAAAGGATTTTCTTTCAGAGCTTACC
62969113 A
1 A
62969114 TAAATGTAAC
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 2 0.04
27 45 0.96
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.32
Consensus pattern (27 bp):
ACAAAGGATTTTCTTTCAGAGCTTACC
Found at i:62970981 original size:28 final size:26
Alignment explanation
Indices: 62970917--62970982 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 26
62970907 AACAAAGTTG
62970917 CTAATAACAGTAAACGTGGCAAAGCCA
1 CTAAT-ACAGTAAACGTGGCAAAGCCA
* *
62970944 TTAGA-GCAGTAATTACGTGGCAAAGCCA
1 CTA-ATACAGTAA--ACGTGGCAAAGCCA
62970972 CTAATACAGTA
1 CTAATACAGTA
62970983 CTTCCTCCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
26 6 0.19
27 3 0.10
28 22 0.71
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.20
Consensus pattern (26 bp):
CTAATACAGTAAACGTGGCAAAGCCA
Found at i:62975987 original size:16 final size:16
Alignment explanation
Indices: 62975966--62976005 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
62975956 TCATAGTTTT
*
62975966 TTTTGTACTAAAACTG
1 TTTTGTACTAAAACTA
62975982 TTTTGTACTAAAACTA
1 TTTTGTACTAAAACTA
62975998 TTTTGTAC
1 TTTTGTAC
62976006 AGTAGCTGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.47
Consensus pattern (16 bp):
TTTTGTACTAAAACTA
Found at i:62978416 original size:16 final size:15
Alignment explanation
Indices: 62978395--62978424 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
62978385 ATTTTGGTAT
62978395 ACATGATATGATATGC
1 ACATGATATG-TATGC
62978411 ACATGATATGTATG
1 ACATGATATGTATG
62978425 ATATGCACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.33
Consensus pattern (15 bp):
ACATGATATGTATGC
Found at i:62978527 original size:26 final size:25
Alignment explanation
Indices: 62978487--62978568 Score: 105
Period size: 25 Copynumber: 3.3 Consensus size: 25
62978477 GAAGTGAAAG
* *
62978487 AAGGGC-TATGCCCCAGTTTATCGAA
1 AAGGGCTTTTGCCCCAGTTCATC-AA
62978512 AAGGGCTTTTGCCCCAGTTCATCAA
1 AAGGGCTTTTGCCCCAGTTCATCAA
*
62978537 AAGGGCTTTTGCCCCAGTT-ATTAA
1 AAGGGCTTTTGCCCCAGTTCATCAA
62978561 AAGAGGCT
1 AAG-GGCT
62978569 AGGCCTCCAG
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
24 7 0.13
25 31 0.60
26 14 0.27
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (25 bp):
AAGGGCTTTTGCCCCAGTTCATCAA
Found at i:62978812 original size:31 final size:31
Alignment explanation
Indices: 62978777--62978867 Score: 103
Period size: 38 Copynumber: 2.7 Consensus size: 31
62978767 CGTTTACAGT
62978777 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
62978808 AAAGGCTTCGACCCAGTGTTATGAAATATGAAATATGA
1 AAAGGCTTCGGCCCA--G---T--AATATGAAATATGA
62978846 AAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTAATATG
62978868 CTAAGATGGA
Statistics
Matches: 51, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
30 5 0.10
31 14 0.27
33 2 0.04
36 2 0.04
38 28 0.55
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.24
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:62979143 original size:23 final size:24
Alignment explanation
Indices: 62979116--62979166 Score: 95
Period size: 23 Copynumber: 2.2 Consensus size: 24
62979106 AATAAGGCCA
62979116 TTTTAACTTTATTATTTTTCTTT-
1 TTTTAACTTTATTATTTTTCTTTC
62979139 TTTTAACTTTATTATTTTTCTTTC
1 TTTTAACTTTATTATTTTTCTTTC
62979163 TTTT
1 TTTT
62979167 TTGGAACTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 23 0.85
24 4 0.15
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.75
Consensus pattern (24 bp):
TTTTAACTTTATTATTTTTCTTTC
Found at i:62979181 original size:28 final size:25
Alignment explanation
Indices: 62979123--62979183 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 25
62979113 CCATTTTAAC
* *
62979123 TTTATTATTTTTCTTTTTTTAACTT
1 TTTATTTTTTTTCTTTTTTGAACTT
62979148 TATTATTTTTCTTTCTTTTTTGGAACTAT
1 T-TTATTTTT-TTTCTTTTTT-GAACT-T
62979177 TTTATTT
1 TTTATTT
62979184 CTAATAACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
25 1 0.03
26 7 0.23
27 10 0.33
28 10 0.33
29 2 0.07
ACGTcount: A:0.16, C:0.08, G:0.03, T:0.72
Consensus pattern (25 bp):
TTTATTTTTTTTCTTTTTTGAACTT
Found at i:62986540 original size:16 final size:15
Alignment explanation
Indices: 62986519--62986548 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
62986509 ATTTTGGTAT
62986519 ACATGATATGATATGC
1 ACATGATATG-TATGC
62986535 ACATGATATGTATG
1 ACATGATATGTATG
62986549 ATATGCACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.33
Consensus pattern (15 bp):
ACATGATATGTATGC
Found at i:62986637 original size:25 final size:25
Alignment explanation
Indices: 62986609--62986679 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 25
62986599 AGGAAGTGCA
62986609 AAAAGGGC-TATGCCCCAGTTTAAC
1 AAAAGGGCTTATGCCCCAGTTTAAC
* *
62986633 GAAAAGGGCTTTTGCCCCAGTTTATC
1 -AAAAGGGCTTATGCCCCAGTTTAAC
* * *
62986659 AAAAGGACTTTTGCCCTAGTT
1 AAAAGGGCTTATGCCCCAGTT
62986680 ATTAAAAGAG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
25 27 0.66
26 14 0.34
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (25 bp):
AAAAGGGCTTATGCCCCAGTTTAAC
Found at i:62986686 original size:24 final size:25
Alignment explanation
Indices: 62986619--62986687 Score: 86
Period size: 25 Copynumber: 2.8 Consensus size: 25
62986609 AAAAGGGCTA
* *
62986619 TGCCCCAGTTTAACGAAAAGGGCTTT
1 TGCCCCAGTTTATC-AAAAGGACTTT
62986645 TGCCCCAGTTTATCAAAAGGACTTT
1 TGCCCCAGTTTATCAAAAGGACTTT
* *
62986670 TGCCCTAG-TTATTAAAAG
1 TGCCCCAGTTTATCAAAAG
62986688 AGGCAAGGCC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
24 9 0.23
25 17 0.44
26 13 0.33
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (25 bp):
TGCCCCAGTTTATCAAAAGGACTTT
Done.