Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 208 of 208
Found at i:63840878 original size:3 final size:3
Alignment explanation
Indices: 63840870--63840917 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
63840860 TTGTACTAAC
63840870 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
63840918 TAAATTTTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:63841274 original size:27 final size:27
Alignment explanation
Indices: 63841201--63841278 Score: 120
Period size: 27 Copynumber: 2.9 Consensus size: 27
63841191 ATAACACGAG
** *
63841201 TGGTGCCGCCAACAGGGAACCCTTGTT
1 TGGTGCCGCCAACAGGGTTCCCTTCTT
63841228 TGGTGCCGCCAACAGGGTTCCCTTCTT
1 TGGTGCCGCCAACAGGGTTCCCTTCTT
*
63841255 TGGTGCCGCCAACAGTGTTCCCTT
1 TGGTGCCGCCAACAGGGTTCCCTT
63841279 GACCCAGGGA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.14, C:0.32, G:0.27, T:0.27
Consensus pattern (27 bp):
TGGTGCCGCCAACAGGGTTCCCTTCTT
Found at i:63841375 original size:28 final size:29
Alignment explanation
Indices: 63841338--63841408 Score: 110
Period size: 28 Copynumber: 2.5 Consensus size: 29
63841328 TGGTTTTTTT
*
63841338 TATATATTTTGGTAAATAAAAAAAAT-TA
1 TATATATTTTGGTAAATAAAAAAAATGCA
63841366 TATATATTTTGGTAAATAAAAAAAATGCA
1 TATATATTTTGGTAAATAAAAAAAATGCA
*
63841395 TA-ACATTTTGGTAA
1 TATATATTTTGGTAA
63841409 TTTTTTATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
28 37 0.93
29 3 0.08
ACGTcount: A:0.49, C:0.03, G:0.10, T:0.38
Consensus pattern (29 bp):
TATATATTTTGGTAAATAAAAAAAATGCA
Found at i:63856789 original size:44 final size:42
Alignment explanation
Indices: 63856740--63856823 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
63856730 ATATCCTCCC
63856740 ATATCTGAAAATAGAAAAATAAAAATCAAACTAAAGGGAAAAGA
1 ATATCTGAAAATAGAAAAA-AAAAA-CAAACTAAAGGGAAAAGA
** * * *
63856784 ATATCTTCAATTTGATAAAAAAAACAAACTAAAGGGAAAA
1 ATATCTGAAAATAGAAAAAAAAAACAAACTAAAGGGAAAA
63856824 AATGAGGAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 16 0.46
43 5 0.14
44 14 0.40
ACGTcount: A:0.61, C:0.08, G:0.12, T:0.19
Consensus pattern (42 bp):
ATATCTGAAAATAGAAAAAAAAAACAAACTAAAGGGAAAAGA
Found at i:63869611 original size:39 final size:41
Alignment explanation
Indices: 63869552--63869633 Score: 116
Period size: 41 Copynumber: 2.0 Consensus size: 41
63869542 TCATCAGAGA
63869552 AACACAACATTCAG-AAAA-ACAGATTACACAA-CTACAATC
1 AACACAACATTCAGAAAAACACAGATTACACAATC-ACAATC
* *
63869591 AACATAACATTCAGAAAAACACAGATTATACAATCACAATC
1 AACACAACATTCAGAAAAACACAGATTACACAATCACAATC
63869632 AA
1 AA
63869634 TCCAGGTCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
39 13 0.34
40 4 0.11
41 20 0.53
42 1 0.03
ACGTcount: A:0.55, C:0.23, G:0.05, T:0.17
Consensus pattern (41 bp):
AACACAACATTCAGAAAAACACAGATTACACAATCACAATC
Found at i:63870457 original size:20 final size:21
Alignment explanation
Indices: 63870429--63870467 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
63870419 TCATGAATAA
63870429 AAAGCAAAAGAT-TCTTTTCT
1 AAAGCAAAAGATATCTTTTCT
*
63870449 AAAGTAAAAGATATCTTTT
1 AAAGCAAAAGATATCTTTT
63870468 TTTTATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (21 bp):
AAAGCAAAAGATATCTTTTCT
Found at i:63870796 original size:19 final size:20
Alignment explanation
Indices: 63870772--63870810 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
63870762 CTAAAACAGC
*
63870772 AAACAAAAAATTTTA-AAGA
1 AAACAAAAAAATTTAGAAGA
63870791 AAACAAAAAAATTTAGAAGA
1 AAACAAAAAAATTTAGAAGA
63870811 GAACCAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.69, C:0.05, G:0.08, T:0.18
Consensus pattern (20 bp):
AAACAAAAAAATTTAGAAGA
Found at i:63873352 original size:36 final size:37
Alignment explanation
Indices: 63873312--63873394 Score: 123
Period size: 36 Copynumber: 2.3 Consensus size: 37
63873302 TTTGCTTTGC
**
63873312 TTCTTGCTCTCCTTCTTTTGCTTGA-TTTTTTTTTCA
1 TTCTTGCTCTCCGACTTTTGCTTGATTTTTTTTTTCA
*
63873348 TTCTTGCTCTTCGACTTTTGCTTGATTTTTTTTTTCA
1 TTCTTGCTCTCCGACTTTTGCTTGATTTTTTTTTTCA
*
63873385 TTCTTCCTCT
1 TTCTTGCTCT
63873395 ATTGCAAAGG
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
36 22 0.52
37 20 0.48
ACGTcount: A:0.06, C:0.23, G:0.08, T:0.63
Consensus pattern (37 bp):
TTCTTGCTCTCCGACTTTTGCTTGATTTTTTTTTTCA
Found at i:63881037 original size:13 final size:13
Alignment explanation
Indices: 63881019--63881044 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
63881009 CCTCTCCCTC
63881019 TTTTTTTCTTTTT
1 TTTTTTTCTTTTT
63881032 TTTTTTTCTTTTT
1 TTTTTTTCTTTTT
63881045 AAGTTTATCT
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (13 bp):
TTTTTTTCTTTTT
Found at i:63886710 original size:23 final size:23
Alignment explanation
Indices: 63886660--63886715 Score: 87
Period size: 22 Copynumber: 2.5 Consensus size: 23
63886650 ATCGGAATAG
*
63886660 AGTTAACATTTATTGTTTAAAAA
1 AGTTAACATTTATTATTTAAAAA
63886683 A-TTAACATTTATTATTTAAAAA
1 AGTTAACATTTATTATTTAAAAA
*
63886705 AGTTAATATTT
1 AGTTAACATTT
63886716 TTAAAGTCCT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 21 0.70
23 9 0.30
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (23 bp):
AGTTAACATTTATTATTTAAAAA
Found at i:63888860 original size:20 final size:20
Alignment explanation
Indices: 63888835--63888872 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
63888825 TAACGATAAT
*
63888835 ATCAATTAAATTAATATTTA
1 ATCAATTAAATAAATATTTA
*
63888855 ATCAATTAGATAAATATT
1 ATCAATTAAATAAATATT
63888873 AAAGAAACAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (20 bp):
ATCAATTAAATAAATATTTA
Found at i:63890202 original size:4 final size:4
Alignment explanation
Indices: 63890193--63890263 Score: 74
Period size: 4 Copynumber: 18.0 Consensus size: 4
63890183 TGCCATCACA
* * * *
63890193 ACAT ACAT ACAT -CAA ACAT CACA- ACAT ACAT ACAT GCAT CCAT CCAT
1 ACAT ACAT ACAT ACAT ACAT -ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
63890240 CCAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT
63890264 CAAACACCAG
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
3 5 0.08
4 51 0.86
5 3 0.05
ACGTcount: A:0.45, C:0.31, G:0.01, T:0.23
Consensus pattern (4 bp):
ACAT
Found at i:63891577 original size:3 final size:3
Alignment explanation
Indices: 63891569--63891598 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
63891559 GTTGTTCGCT
63891569 TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
63891599 AATTGAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:63894250 original size:6 final size:6
Alignment explanation
Indices: 63894216--63894249 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
63894206 CAATTATCAA
*
63894216 AATACT AATACT AATACT AATACT AATAAT AATA
1 AATACT AATACT AATACT AATACT AATACT AATA
63894250 AAAGAAAGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (6 bp):
AATACT
Found at i:63903513 original size:16 final size:15
Alignment explanation
Indices: 63903490--63903547 Score: 53
Period size: 16 Copynumber: 3.7 Consensus size: 15
63903480 AAAGAGAATA
63903490 TATTTTCTTTCTTTC
1 TATTTTCTTTCTTTC
* *
63903505 TATTTTTCTAGTCATTC
1 TA-TTTTCT-TTCTTTC
* *
63903522 GATTTTCTATCTTTC
1 TATTTTCTTTCTTTC
63903537 TAATTTTCTTT
1 T-ATTTTCTTT
63903548 AATGTAAAAC
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
15 7 0.21
16 20 0.61
17 6 0.18
ACGTcount: A:0.14, C:0.17, G:0.03, T:0.66
Consensus pattern (15 bp):
TATTTTCTTTCTTTC
Found at i:63912704 original size:2 final size:2
Alignment explanation
Indices: 63912697--63912728 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
63912687 TCTTAATTTA
*
63912697 CT CT CT CT CT CT AT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
63912729 ATATAAAGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.03, C:0.47, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:63920338 original size:19 final size:19
Alignment explanation
Indices: 63920314--63920352 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
63920304 TATTCTTCTC
63920314 AGGTAAATCAATTTCCTTT
1 AGGTAAATCAATTTCCTTT
63920333 AGGTAAATCAATTTCCTTT
1 AGGTAAATCAATTTCCTTT
63920352 A
1 A
63920353 TGTTATTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.41
Consensus pattern (19 bp):
AGGTAAATCAATTTCCTTT
Found at i:63925643 original size:94 final size:96
Alignment explanation
Indices: 63925521--63925714 Score: 268
Period size: 94 Copynumber: 2.0 Consensus size: 96
63925511 TAGAGCATGT
* * *
63925521 ATTAACTCATATATTTTTCAACCGTTTC-ATTGTAGCTATAATTCATTTTTTAACCTTATTCTTA
1 ATTAACTCATATATTTTTCAACCGTTTCAATTGCAACTACAATT-ATTTTTTAACCTTATTCTTA
63925585 TTAGTATATGAAGTTGTAGGACTATATGATTC
65 TTAGTATATGAAGTTGTAGGACTATATGATTC
** * * * * *
63925617 ATTAACTCATA-A-TTTTCATTCTTTTCAATTGCAATTGCAATTGTTTTTTGACCTTATTCTTAT
1 ATTAACTCATATATTTTTCAACCGTTTCAATTGCAACTACAATTATTTTTTAACCTTATTCTTAT
63925680 TAGTATATGAAGTTGTAGGACTATATGATTC
66 TAGTATATGAAGTTGTAGGACTATATGATTC
63925711 ATTA
1 ATTA
63925715 GAGAAGGGAA
Statistics
Matches: 87, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
94 65 0.75
95 11 0.13
96 11 0.13
ACGTcount: A:0.29, C:0.13, G:0.11, T:0.47
Consensus pattern (96 bp):
ATTAACTCATATATTTTTCAACCGTTTCAATTGCAACTACAATTATTTTTTAACCTTATTCTTAT
TAGTATATGAAGTTGTAGGACTATATGATTC
Found at i:63948545 original size:13 final size:13
Alignment explanation
Indices: 63948527--63948553 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
63948517 ATATATAGAT
63948527 GCACATTTAATTG
1 GCACATTTAATTG
63948540 GCACATTTAATTG
1 GCACATTTAATTG
63948553 G
1 G
63948554 TGAAGTTTTA
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:0.30, C:0.15, G:0.19, T:0.37
Consensus pattern (13 bp):
GCACATTTAATTG
Found at i:63958185 original size:22 final size:22
Alignment explanation
Indices: 63958157--63958309 Score: 225
Period size: 22 Copynumber: 7.0 Consensus size: 22
63958147 TGTTGATAGT
*
63958157 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
63958179 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
63958201 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
* * * **
63958223 ACGAACTAAACCCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
**
63958245 ACGTACTAAGCTCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
*
63958267 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
63958289 ACGTACTAAGCTCTCATGTTT
1 ACGTACTAAGCTCTCATGTTT
63958310 GAACAATAAA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTA
Found at i:63966361 original size:32 final size:32
Alignment explanation
Indices: 63966323--63966414 Score: 148
Period size: 32 Copynumber: 2.9 Consensus size: 32
63966313 AAATGGTTAT
* *
63966323 TGAATTATTCAAAAGTTTTTATTCAAGTCAAC
1 TGAATTATTCGAAAGCTTTTATTCAAGTCAAC
*
63966355 TGAATTATTCGAAAGCTTTTATTCAAGTCAAT
1 TGAATTATTCGAAAGCTTTTATTCAAGTCAAC
*
63966387 TGAATTATTCGAAAGCTTTTATTTAAGT
1 TGAATTATTCGAAAGCTTTTATTCAAGT
63966415 TTTTTTAAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 56 1.00
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.42
Consensus pattern (32 bp):
TGAATTATTCGAAAGCTTTTATTCAAGTCAAC
Found at i:63974771 original size:104 final size:104
Alignment explanation
Indices: 63974587--63974794 Score: 326
Period size: 104 Copynumber: 2.0 Consensus size: 104
63974577 ATTTGTAAGA
* * * * *
63974587 AATAGGGGCAAATTCTATTGAAGATACGTTAATTTCATCAAAAAATCATACAATCATTTGATTTA
1 AATAGGGACAAACTCTATGGAAGATACGTTAATTTCATCAAAAAATCATACAACCATTTGATTCA
*
63974652 ACAATAAATTAATTGCTTGATTTGTAAGAAATATTTAGT
66 ACAATAAATTAATTGCTTGATTAGTAAGAAATATTTAGT
*
63974691 AATAGGGACAAACTCTATGGAAGATACGTTAATTTCATCAAAAAATCATACGACCATTTGATTCA
1 AATAGGGACAAACTCTATGGAAGATACGTTAATTTCATCAAAAAATCATACAACCATTTGATTCA
* * *
63974756 ATAATAAATTCATTGCTTGATTAGTAAGAAATCTTTAGT
66 ACAATAAATTAATTGCTTGATTAGTAAGAAATATTTAGT
63974795 CCCTACTAAA
Statistics
Matches: 94, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
104 94 1.00
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.35
Consensus pattern (104 bp):
AATAGGGACAAACTCTATGGAAGATACGTTAATTTCATCAAAAAATCATACAACCATTTGATTCA
ACAATAAATTAATTGCTTGATTAGTAAGAAATATTTAGT
Found at i:63997149 original size:16 final size:18
Alignment explanation
Indices: 63997128--63997165 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
63997118 TAAGGATACA
63997128 ATTTTAT-TATTT-TAAT
1 ATTTTATGTATTTATAAT
63997144 ATTTTATGTATTTATAAT
1 ATTTTATGTATTTATAAT
63997162 ATTT
1 ATTT
63997166 AAATGATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 7 0.35
17 5 0.25
18 8 0.40
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (18 bp):
ATTTTATGTATTTATAAT
Found at i:63997803 original size:24 final size:24
Alignment explanation
Indices: 63997770--63997820 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
63997760 GTGATAAATG
63997770 TTTGAATTGAGGAATGTTTGAATA
1 TTTGAATTGAGGAATGTTTGAATA
*
63997794 TTTGATTTGAGGAATGTTTGAATA
1 TTTGAATTGAGGAATGTTTGAATA
63997818 TTT
1 TTT
63997821 CAGTTTGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (24 bp):
TTTGAATTGAGGAATGTTTGAATA
Found at i:64001205 original size:16 final size:18
Alignment explanation
Indices: 64001184--64001221 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
64001174 TAAGGATACA
64001184 ATTTTAT-TATTT-TAAT
1 ATTTTATGTATTTATAAT
64001200 ATTTTATGTATTTATAAT
1 ATTTTATGTATTTATAAT
64001218 ATTT
1 ATTT
64001222 AAATGATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 7 0.35
17 5 0.25
18 8 0.40
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (18 bp):
ATTTTATGTATTTATAAT
Found at i:64003297 original size:31 final size:31
Alignment explanation
Indices: 64003237--64003297 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
64003227 CATTCTAGTG
**
64003237 ACTTAAATCAAAACTTTCGAATAGTTCAATC
1 ACTTAAATCAAAACTTTCGAATAACTCAATC
* *
64003268 ACTTAAATGAAAATTTTCGAATAACTCAAT
1 ACTTAAATCAAAACTTTCGAATAACTCAAT
64003298 GACCATTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (31 bp):
ACTTAAATCAAAACTTTCGAATAACTCAATC
Found at i:64007685 original size:21 final size:21
Alignment explanation
Indices: 64007659--64007704 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
64007649 TCACAAATTC
* *
64007659 AAATTT-TATTATTATTTTATT
1 AAATTTGTATT-TTAATTTATA
64007680 AAATTTGTATTTTAATTTATA
1 AAATTTGTATTTTAATTTATA
64007701 AAAT
1 AAAT
64007705 GTAAAAGGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
AAATTTGTATTTTAATTTATA
Found at i:64009717 original size:20 final size:19
Alignment explanation
Indices: 64009690--64009728 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
64009680 AATTTTAAAA
* *
64009690 TATTTTTAAAATATATTTT
1 TATTTTTTAAATAAATTTT
64009709 TATTTTTTAAATAAATTTT
1 TATTTTTTAAATAAATTTT
64009728 T
1 T
64009729 GGTGTTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TATTTTTTAAATAAATTTT
Found at i:64009727 original size:32 final size:31
Alignment explanation
Indices: 64009665--64009728 Score: 85
Period size: 30 Copynumber: 2.0 Consensus size: 31
64009655 CCGAATATAA
*
64009665 TAAATATATATTTTTAATTTTAAAATATTTT
1 TAAATATATATTTTTAATTTTAAAAAATTTT
*
64009696 TAAA-ATATATTTTTATTTTTTAAATAAATTTT
1 TAAATATATATTTTTA-ATTTTAAA-AAATTTT
64009728 T
1 T
64009729 GGTGTTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 11 0.38
31 11 0.38
32 7 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (31 bp):
TAAATATATATTTTTAATTTTAAAAAATTTT
Found at i:64010375 original size:15 final size:16
Alignment explanation
Indices: 64010355--64010386 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
64010345 GACCAGGCCG
64010355 AAATATT-TTAAAAAT
1 AAATATTATTAAAAAT
64010370 AAATATTATTAAAAAT
1 AAATATTATTAAAAAT
64010386 A
1 A
64010387 TTTTAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATATTATTAAAAAT
Found at i:64010428 original size:19 final size:21
Alignment explanation
Indices: 64010380--64010430 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 21
64010370 AAATATTATT
64010380 AAAAATATT-TTAAAATTGTA
1 AAAAATATTATTAAAATTGTA
*
64010400 AAAAAAATTATTAAAA-TG-A
1 AAAAATATTATTAAAATTGTA
*
64010419 TAAAATATTATT
1 AAAAATATTATT
64010431 TAATTTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 11 0.41
20 10 0.37
21 6 0.22
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (21 bp):
AAAAATATTATTAAAATTGTA
Found at i:64010779 original size:29 final size:27
Alignment explanation
Indices: 64010735--64010799 Score: 67
Period size: 29 Copynumber: 2.3 Consensus size: 27
64010725 AATTATTTGT
* *
64010735 ATTTTTTAATAATTTTTCCAATTTTATA
1 ATTTTTT-ATAATTTTTACAATTTTAAA
*
64010763 ATTTTTTATAACTTTTTTATAATTTTAAA
1 ATTTTTTATAA--TTTTTACAATTTTAAA
*
64010792 ATATTTTA
1 ATTTTTTA
64010800 AACAACCTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
27 4 0.13
28 7 0.23
29 20 0.65
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.62
Consensus pattern (27 bp):
ATTTTTTATAATTTTTACAATTTTAAA
Found at i:64010780 original size:11 final size:10
Alignment explanation
Indices: 64010756--64010788 Score: 57
Period size: 10 Copynumber: 3.2 Consensus size: 10
64010746 ATTTTTCCAA
64010756 TTTTATAATT
1 TTTTATAATT
64010766 TTTTATAACTT
1 TTTTATAA-TT
64010777 TTTTATAATT
1 TTTTATAATT
64010787 TT
1 TT
64010789 AAAATATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (10 bp):
TTTTATAATT
Found at i:64010852 original size:18 final size:18
Alignment explanation
Indices: 64010807--64010853 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
64010797 TTAAACAACC
64010807 TTTAACAATTTAAATATT
1 TTTAACAATTTAAATATT
* *
64010825 TTTAATAATTTAAATCTAT
1 TTTAACAATTTAAATAT-T
64010844 TTT-ACAATTT
1 TTTAACAATTT
64010854 TTATATATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 21 0.84
19 4 0.16
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTAACAATTTAAATATT
Found at i:64015030 original size:30 final size:30
Alignment explanation
Indices: 64014994--64015056 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
64014984 TTGATGTGTG
*
64014994 TAAATTATATTAAAGAGAACAAATAAATAT
1 TAAATTATATTAAAGAGAACAAACAAATAT
64015024 TAAATTATATTAAAGAGAACAAACAAATAT
1 TAAATTATATTAAAGAGAACAAACAAATAT
64015054 TAA
1 TAA
64015057 GAATTTAGTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.60, C:0.05, G:0.06, T:0.29
Consensus pattern (30 bp):
TAAATTATATTAAAGAGAACAAACAAATAT
Found at i:64022680 original size:12 final size:12
Alignment explanation
Indices: 64022663--64022688 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
64022653 AAACAAACAT
64022663 ATTCATGAATAC
1 ATTCATGAATAC
64022675 ATTCATGAATAC
1 ATTCATGAATAC
64022687 AT
1 AT
64022689 AAGTGAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (12 bp):
ATTCATGAATAC
Found at i:64026659 original size:5 final size:6
Alignment explanation
Indices: 64026623--64026668 Score: 60
Period size: 6 Copynumber: 8.0 Consensus size: 6
64026613 AACGCCGTAT
* *
64026623 CTTTTG CTTTTG CTTTTG CTTTTA CTTTTT CTTTT- CTTTT- CTTTTG
1 CTTTTG CTTTTG CTTTTG CTTTTG CTTTTG CTTTTG CTTTTG CTTTTG
64026669 ATAAAGCAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
5 10 0.27
6 27 0.73
ACGTcount: A:0.02, C:0.17, G:0.09, T:0.72
Consensus pattern (6 bp):
CTTTTG
Found at i:64036044 original size:5 final size:5
Alignment explanation
Indices: 64036034--64036061 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
64036024 AACGCCTCCA
64036034 TTCTC TTCTC TTCTC TTCTC TTCTC TTC
1 TTCTC TTCTC TTCTC TTCTC TTCTC TTC
64036062 AAGAAACACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (5 bp):
TTCTC
Found at i:64038430 original size:14 final size:15
Alignment explanation
Indices: 64038399--64038485 Score: 51
Period size: 14 Copynumber: 6.0 Consensus size: 15
64038389 AAACATAAAA
**
64038399 TAAAAATATAATTGT
1 TAAAAATATAATAAT
64038414 TAAAAA-ATAATAAT
1 TAAAAATATAATAAT
*
64038428 TAAACATA-AATAAATT
1 TAAAAATATAAT-AA-T
* *
64038444 TATTAAGTATAAT--T
1 TA-AAAATATAATAAT
*
64038458 TAATAATA-AATAAT
1 TAAAAATATAATAAT
64038472 T-AAAATATAATAAT
1 TAAAAATATAATAAT
64038486 ACAATTTAAA
Statistics
Matches: 54, Mismatches: 10, Indels: 17
0.67 0.12 0.21
Matches are distributed among these distances:
12 3 0.06
13 8 0.15
14 25 0.46
15 9 0.17
16 3 0.06
17 3 0.06
18 3 0.06
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (15 bp):
TAAAAATATAATAAT
Found at i:64042627 original size:50 final size:50
Alignment explanation
Indices: 64042512--64042760 Score: 282
Period size: 50 Copynumber: 4.8 Consensus size: 50
64042502 GATAATAACA
* * ** * *
64042512 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCATCTCGG
* *
64042563 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
64042613 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
64042663 TGCCCATGCCATTTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* * *
64042718 ATGCCAATGTCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
64042761 TTACCCAAAT
Statistics
Matches: 168, Mismatches: 24, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
50 93 0.55
51 33 0.20
53 2 0.01
54 1 0.01
55 2 0.01
56 37 0.22
ACGTcount: A:0.20, C:0.29, G:0.23, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:64042698 original size:100 final size:104
Alignment explanation
Indices: 64042511--64042760 Score: 337
Period size: 100 Copynumber: 2.4 Consensus size: 104
64042501 TGATAATAAC
** * *
64042511 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGGTGCCCATGCCATG
* *
64042576 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* * *
64042613 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTGCCCATGCCATTT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCATGCCATGT
64042677 CCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
66 CCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* * *
64042718 ATGCCAATGTCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
64042761 TTACCCAAAT
Statistics
Matches: 130, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
100 49 0.38
101 36 0.28
103 3 0.02
104 1 0.01
105 2 0.02
106 39 0.30
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.27
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:64042876 original size:13 final size:13
Alignment explanation
Indices: 64042855--64042886 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
64042845 GCTTGGATCA
*
64042855 TCATCAAATAAAT
1 TCATAAAATAAAT
64042868 TCATAAAATAAAT
1 TCATAAAATAAAT
64042881 TCATAA
1 TCATAA
64042887 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:64043133 original size:30 final size:30
Alignment explanation
Indices: 64043098--64043155 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
64043088 CCTCGACTCT
*
64043098 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
64043128 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
64043156 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:64049217 original size:12 final size:14
Alignment explanation
Indices: 64049188--64049219 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
64049178 AACAAACGAA
64049188 AAAAATTAGAATTT
1 AAAAATTAGAATTT
64049202 AAAAATTA-AA-TT
1 AAAAATTAGAATTT
64049214 AAAAAT
1 AAAAAT
64049220 AAAAATATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.44
13 2 0.11
14 8 0.44
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (14 bp):
AAAAATTAGAATTT
Found at i:64050150 original size:30 final size:30
Alignment explanation
Indices: 64050115--64050181 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
64050105 TAAACTTCAA
64050115 AGAAATCAAAAGGAGATCTTCAATCTTAAT
1 AGAAATCAAAAGGAGATCTTCAATCTTAAT
*
64050145 AGAAATTAAAAGGAGATCTTCAATCTTAAT
1 AGAAATCAAAAGGAGATCTTCAATCTTAAT
64050175 AGAAATC
1 AGAAATC
64050182 TGCTTTAGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.48, C:0.12, G:0.13, T:0.27
Consensus pattern (30 bp):
AGAAATCAAAAGGAGATCTTCAATCTTAAT
Found at i:64058058 original size:20 final size:20
Alignment explanation
Indices: 64058033--64058073 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
64058023 TCAAGTATCC
*
64058033 ACCATCATTGGTAA-ATTACT
1 ACCATC-TTGGAAAGATTACT
64058053 ACCATCTTGGAAAGATTACT
1 ACCATCTTGGAAAGATTACT
64058073 A
1 A
64058074 AAGGTATTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.32
Consensus pattern (20 bp):
ACCATCTTGGAAAGATTACT
Found at i:64060071 original size:15 final size:16
Alignment explanation
Indices: 64060051--64060085 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
64060041 ACAAAGAACG
64060051 AAGATTGTCCAATAA-
1 AAGATTGTCCAATAAT
64060066 AAGATTGTCCAATAAT
1 AAGATTGTCCAATAAT
64060082 AAGA
1 AAGA
64060086 AGCTTATTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.49, C:0.11, G:0.14, T:0.26
Consensus pattern (16 bp):
AAGATTGTCCAATAAT
Found at i:64068162 original size:11 final size:11
Alignment explanation
Indices: 64068146--64068184 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
64068136 TCTTTTAATA
*
64068146 TTCTCTCATAT
1 TTCTCTCAAAT
*
64068157 TTCTCTTAAAT
1 TTCTCTCAAAT
64068168 TTCTCTCAAAT
1 TTCTCTCAAAT
*
64068179 TCCTCT
1 TTCTCT
64068185 TAAAGCTCTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.21, C:0.28, G:0.00, T:0.51
Consensus pattern (11 bp):
TTCTCTCAAAT
Found at i:64068165 original size:22 final size:22
Alignment explanation
Indices: 64068146--64068188 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
64068136 TCTTTTAATA
* *
64068146 TTCTCTCATATTTCTCTTAAAT
1 TTCTCTCAAATTCCTCTTAAAT
64068168 TTCTCTCAAATTCCTCTTAAA
1 TTCTCTCAAATTCCTCTTAAA
64068189 GCTCTCTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.49
Consensus pattern (22 bp):
TTCTCTCAAATTCCTCTTAAAT
Found at i:64068194 original size:22 final size:22
Alignment explanation
Indices: 64068147--64068195 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
64068137 CTTTTAATAT
* * **
64068147 TCTCTCATATTTCTCTTAAATT
1 TCTCTCAAATTCCTCTTAAAGC
64068169 TCTCTCAAATTCCTCTTAAAGC
1 TCTCTCAAATTCCTCTTAAAGC
64068191 TCTCT
1 TCTCT
64068196 TTAATTTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.29, G:0.02, T:0.47
Consensus pattern (22 bp):
TCTCTCAAATTCCTCTTAAAGC
Found at i:64069895 original size:30 final size:30
Alignment explanation
Indices: 64069861--64069971 Score: 125
Period size: 30 Copynumber: 3.7 Consensus size: 30
64069851 TGACAACACA
* * *
64069861 GGCCCATCAATAGCGCCCACACAATTACTC
1 GGCCCATCAACAGCACCCACACAATCACTC
* *
64069891 GGCCCATCAACAACGCCCACACAATCACTC
1 GGCCCATCAACAGCACCCACACAATCACTC
* *
64069921 GGCCCATCAACAGTACCCATACAATCAC-C
1 GGCCCATCAACAGCACCCACACAATCACTC
* *
64069950 AGGCCCAACAATAGCACCCACA
1 -GGCCCATCAACAGCACCCACA
64069972 ACACAACCTT
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
29 1 0.01
30 68 0.99
ACGTcount: A:0.34, C:0.42, G:0.12, T:0.12
Consensus pattern (30 bp):
GGCCCATCAACAGCACCCACACAATCACTC
Found at i:64070024 original size:18 final size:18
Alignment explanation
Indices: 64070001--64070043 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
64069991 TGCCAAGTGC
*
64070001 GTATCCTAGCCCTTTTAT
1 GTATCCTAGCCCTTATAT
64070019 GTATCCTAGCCCTTATAT
1 GTATCCTAGCCCTTATAT
*
64070037 GTTTCCT
1 GTATCCT
64070044 TTTTCTAGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.28, G:0.12, T:0.44
Consensus pattern (18 bp):
GTATCCTAGCCCTTATAT
Found at i:64070927 original size:117 final size:116
Alignment explanation
Indices: 64070451--64070948 Score: 915
Period size: 116 Copynumber: 4.3 Consensus size: 116
64070441 TTGTATAAAC
* *
64070451 ATTTTGAATATTTTTATATTATTTCATGTAATAAAATAGAAGGTTGTTTTGAATAAAGTAATTGT
1 ATTTTGAATATTTTTATATTATTTCATGTAATAAAATAAAAGATTGTTTTGAATAAAGTAATTGT
*
64070516 AATTTACTTTTATATTTTTAATAAAATAGAAATTCTTTTAAATAAGACAAT
66 AATTTAATTTTATATTTTTAATAAAATAGAAATTCTTTTAAATAAGACAAT
64070567 ATTTTGAATATTTTTATATTATTTCATGTAATAAAATAAAAGATTGTTTTGAATAAAGTAATTGT
1 ATTTTGAATATTTTTATATTATTTCATGTAATAAAATAAAAGATTGTTTTGAATAAAGTAATTGT
64070632 AATTTAATTTTATATTTTTAATAAAATAGAAATTCTTTTAAATAAGACAAT
66 AATTTAATTTTATATTTTTAATAAAATAGAAATTCTTTTAAATAAGACAAT
*
64070683 ATTTTGAATATTTTTATATTATTTCATGTAATAAAATAAAAGATTGTTTTGAATAAAGTAACTGT
1 ATTTTGAATATTTTTATATTATTTCATGTAATAAAATAAAAGATTGTTTTGAATAAAGTAATTGT
*
64070748 AATTTACTTTTATATTTTTAATAAAATAGAAATTCTTTTAAATAAGACAAT
66 AATTTAATTTTATATTTTTAATAAAATAGAAATTCTTTTAAATAAGACAAT
* *
64070799 ATTTTTAATATTTCTATATTATTTCATGTAATAAAATAAAAGATTGTTTTGAATAAAGTAATTGT
1 ATTTTGAATATTTTTATATTATTTCATGTAATAAAATAAAAGATTGTTTTGAATAAAGTAATTGT
*
64070864 AATTATAATTTTATATTTTTAATAAAATAGAAATTCTTTTAAATAGGACAAT
66 AATT-TAATTTTATATTTTTAATAAAATAGAAATTCTTTTAAATAAGACAAT
64070916 ATTTTGAATATTTTTATATTATTTCATGTAATA
1 ATTTTGAATATTTTTATATTATTTCATGTAATA
64070949 GGACCGGTGG
Statistics
Matches: 369, Mismatches: 12, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
116 293 0.79
117 76 0.21
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (116 bp):
ATTTTGAATATTTTTATATTATTTCATGTAATAAAATAAAAGATTGTTTTGAATAAAGTAATTGT
AATTTAATTTTATATTTTTAATAAAATAGAAATTCTTTTAAATAAGACAAT
Found at i:64073437 original size:31 final size:31
Alignment explanation
Indices: 64073402--64073463 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
64073392 TAAAAAATAA
64073402 ACTATAATTATAATTGCAATTGTAATTTAAG
1 ACTATAATTATAATTGCAATTGTAATTTAAG
64073433 ACTATAATTATAATTGCAATTGTAATTTAAG
1 ACTATAATTATAATTGCAATTGTAATTTAAG
64073464 TAATAAATGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (31 bp):
ACTATAATTATAATTGCAATTGTAATTTAAG
Found at i:64076882 original size:3 final size:3
Alignment explanation
Indices: 64076876--64076914 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
64076866 TATTATTATT
* *
64076876 ATC ATC ATC ATC ATC ATC ATC ATT ATC AGC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
64076915 TGATGGAGAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.33, C:0.31, G:0.03, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:64082176 original size:78 final size:78
Alignment explanation
Indices: 64082047--64082197 Score: 248
Period size: 78 Copynumber: 1.9 Consensus size: 78
64082037 CTCATATTCT
* * *
64082047 ACCATTAAACCATGATCCCTTGATCTCACCGGCTGGGAGAGTCGGTGATCATGTTGATAATGATC
1 ACCATTAAACCATGATCCCTTGATCTCACCAGCTAGGAGAGTCGGTGATCATGTTGATAACGATC
64082112 ACCATGGAGTTCG
66 ACCATGGAGTTCG
* * *
64082125 ACCATTAAACCATGATCCCTTGATCTCATCAGCTAGGAGAGTTGGTGATCATGTTGATAGCGATC
1 ACCATTAAACCATGATCCCTTGATCTCACCAGCTAGGAGAGTCGGTGATCATGTTGATAACGATC
64082190 ACCATGGA
66 ACCATGGA
64082198 CTTTGTGTAC
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
78 67 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (78 bp):
ACCATTAAACCATGATCCCTTGATCTCACCAGCTAGGAGAGTCGGTGATCATGTTGATAACGATC
ACCATGGAGTTCG
Found at i:64089420 original size:44 final size:45
Alignment explanation
Indices: 64089357--64089446 Score: 173
Period size: 44 Copynumber: 2.0 Consensus size: 45
64089347 AATGAAGTTT
64089357 ATGCTGTTGTTATATAGCACATAATGCCC-TTTTTTCTAAGGTTA
1 ATGCTGTTGTTATATAGCACATAATGCCCTTTTTTTCTAAGGTTA
64089401 ATGCTGTTGTTATATAGCACATAATGCCCTTTTTTTCTAAGGTTA
1 ATGCTGTTGTTATATAGCACATAATGCCCTTTTTTTCTAAGGTTA
64089446 A
1 A
64089447 AGTTGTAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 29 0.64
45 16 0.36
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.43
Consensus pattern (45 bp):
ATGCTGTTGTTATATAGCACATAATGCCCTTTTTTTCTAAGGTTA
Found at i:64103692 original size:10 final size:10
Alignment explanation
Indices: 64103658--64103692 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
64103648 GTTGCCTGCC
64103658 AAATATATAA
1 AAATATATAA
*
64103668 AAAAATATTAA
1 AAATATA-TAA
64103679 AAATATATAA
1 AAATATATAA
64103689 AAAT
1 AAAT
64103693 CATAGAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
AAATATATAA
Found at i:64109697 original size:21 final size:22
Alignment explanation
Indices: 64109671--64109718 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
64109661 TTTCTCTTTA
*
64109671 GGTTTTAGGTTTCCGG-TTAGG
1 GGTTTTAGGTTCCCGGATTAGG
*
64109692 GGTTTTAGGTTCCCGGATTGGG
1 GGTTTTAGGTTCCCGGATTAGG
64109714 GGTTT
1 GGTTT
64109719 GGGGGTTGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.08, C:0.10, G:0.40, T:0.42
Consensus pattern (22 bp):
GGTTTTAGGTTCCCGGATTAGG
Found at i:64109751 original size:30 final size:30
Alignment explanation
Indices: 64109712--64109787 Score: 116
Period size: 30 Copynumber: 2.5 Consensus size: 30
64109702 TCCCGGATTG
* * *
64109712 GGGGTTTGGGGGTTGGGGGTTGGAGTTTTA
1 GGGGCTTGGGGCTTGGGGCTTGGAGTTTTA
*
64109742 GGGGCTTGGGGCTTGGGGCTTGGGGTTTTA
1 GGGGCTTGGGGCTTGGGGCTTGGAGTTTTA
64109772 GGGGCTTGGGGCTTGG
1 GGGGCTTGGGGCTTGG
64109788 TTCTTTTACT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.04, C:0.07, G:0.57, T:0.33
Consensus pattern (30 bp):
GGGGCTTGGGGCTTGGGGCTTGGAGTTTTA
Found at i:64109752 original size:7 final size:7
Alignment explanation
Indices: 64109742--64109787 Score: 65
Period size: 7 Copynumber: 6.3 Consensus size: 7
64109732 TGGAGTTTTA
64109742 GGGGCTT
1 GGGGCTT
64109749 GGGGCTT
1 GGGGCTT
64109756 GGGGCTT
1 GGGGCTT
*
64109763 GGGGTTTT
1 GGGG-CTT
64109771 AGGGGCTT
1 -GGGGCTT
64109779 GGGGCTT
1 GGGGCTT
64109786 GG
1 GG
64109788 TTCTTTTACT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
7 27 0.77
8 4 0.11
9 4 0.11
ACGTcount: A:0.02, C:0.11, G:0.57, T:0.30
Consensus pattern (7 bp):
GGGGCTT
Found at i:64109966 original size:25 final size:25
Alignment explanation
Indices: 64109938--64109985 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
64109928 TTCTTCTTTG
*
64109938 TTTAAATTTTGTTTATTTTTCTTGC
1 TTTAAATTTTGTTTATTTATCTTGC
* *
64109963 TTTAATTTTTGTTTCTTTATCTT
1 TTTAAATTTTGTTTATTTATCTT
64109986 TGATCTAAGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.15, C:0.08, G:0.06, T:0.71
Consensus pattern (25 bp):
TTTAAATTTTGTTTATTTATCTTGC
Found at i:64112890 original size:79 final size:80
Alignment explanation
Indices: 64112759--64112920 Score: 290
Period size: 79 Copynumber: 2.0 Consensus size: 80
64112749 TGAAGCTTTC
* *
64112759 AAGTTCATAATCCGTTAAATTAATGAATGGAGGGCTTTAAACAAAGCCAACAATTG-TTCGGGTT
1 AAGTTAATAATCCGTTAAACTAATGAATGGAGGGCTTTAAACAAAGCCAACAATTGTTTCGGGTT
*
64112823 TACCTATTTGTTATA
66 TACCTATTTATTATA
64112838 AAGTTAATAATCCGTTAAACTAATGAATGGAGGGCTTTAAACAAAGCCAACAATTGTTTCGGGTT
1 AAGTTAATAATCCGTTAAACTAATGAATGGAGGGCTTTAAACAAAGCCAACAATTGTTTCGGGTT
64112903 TACCTATTTATTATA
66 TACCTATTTATTATA
64112918 AAG
1 AAG
64112921 CTGATTTTGT
Statistics
Matches: 79, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
79 54 0.68
80 25 0.32
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (80 bp):
AAGTTAATAATCCGTTAAACTAATGAATGGAGGGCTTTAAACAAAGCCAACAATTGTTTCGGGTT
TACCTATTTATTATA
Found at i:64113189 original size:21 final size:21
Alignment explanation
Indices: 64113165--64113204 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
64113155 GAATTTTAGC
64113165 TGACCGGTTCGGCTGTTTTGG
1 TGACCGGTTCGGCTGTTTTGG
* *
64113186 TGACCGGTTCTGTTGTTTT
1 TGACCGGTTCGGCTGTTTT
64113205 ATGAACCCGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.05, C:0.17, G:0.33, T:0.45
Consensus pattern (21 bp):
TGACCGGTTCGGCTGTTTTGG
Found at i:64113301 original size:31 final size:31
Alignment explanation
Indices: 64113235--64113320 Score: 93
Period size: 31 Copynumber: 2.7 Consensus size: 31
64113225 CTCTCGCGCT
* * *
64113235 TATCCCGGTCGGGGATATCCTATTATGCGTT
1 TATCCCGGTCGGGGATATCCCATAATGCGTG
*
64113266 TATCCCGGTCGGGGATATCCCATAAT-AGTGG
1 TATCCCGGTCGGGGATATCCCATAATGCGT-G
* *
64113297 TATCCCGGCTTGGGTATATCCCAT
1 TATCCCGG-TCGGGGATATCCCAT
64113321 TGCAGGGATA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
30 2 0.04
31 32 0.68
32 13 0.28
ACGTcount: A:0.19, C:0.24, G:0.26, T:0.31
Consensus pattern (31 bp):
TATCCCGGTCGGGGATATCCCATAATGCGTG
Found at i:64114328 original size:15 final size:15
Alignment explanation
Indices: 64114310--64114340 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
64114300 CAAGAAATTC
*
64114310 CTATCCTTGCATTGG
1 CTATCCTTGAATTGG
64114325 CTATCCTTGAATTGG
1 CTATCCTTGAATTGG
64114340 C
1 C
64114341 CTGTTTGGAG
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:0.16, C:0.26, G:0.19, T:0.39
Consensus pattern (15 bp):
CTATCCTTGAATTGG
Found at i:64123290 original size:31 final size:30
Alignment explanation
Indices: 64123215--64123291 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 30
64123205 GGAGGGATAT
64123215 TTCGGGGATATCCCAAGCTGAATTAAGCTA
1 TTCGGGGATATCCCAAGCTGAATTAAGCTA
* * * *
64123245 TATCGCGGAAATCCCAA-CTGGATTTAAGGTA
1 T-TCGGGGATATCCCAAGCT-GAATTAAGCTA
64123276 TTCGGAGGATATCCCA
1 TTCGG-GGATATCCCA
64123292 TCCAAATCCC
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
30 6 0.16
31 32 0.84
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (30 bp):
TTCGGGGATATCCCAAGCTGAATTAAGCTA
Found at i:64123473 original size:32 final size:32
Alignment explanation
Indices: 64123422--64123491 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
64123412 TATTCCACGG
*
64123422 ATATCCCGGTTTAGGTTTATTCCATTCTATGC
1 ATATCCCGATTTAGGTTTATTCCATTCTATGC
* *
64123454 ATATCCCGATTT-GGATTTATTCTATTCTTTGC
1 ATATCCCGATTTAGG-TTTATTCCATTCTATGC
64123486 ATATCC
1 ATATCC
64123492 AGGCTTGGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 2 0.06
32 32 0.94
ACGTcount: A:0.20, C:0.21, G:0.13, T:0.46
Consensus pattern (32 bp):
ATATCCCGATTTAGGTTTATTCCATTCTATGC
Found at i:64123517 original size:7 final size:7
Alignment explanation
Indices: 64123498--64123657 Score: 105
Period size: 7 Copynumber: 22.9 Consensus size: 7
64123488 ATCCAGGCTT
64123498 GGGTTTAA
1 GGGTTT-A
64123506 GGGTTTA
1 GGGTTTA
64123513 GGGTTT-
1 GGGTTTA
64123519 GGGTTTA
1 GGGTTTA
*
64123526 GGGTTTG
1 GGGTTTA
64123533 GGGTTTTA
1 GGG-TTTA
64123541 GGGTTTA
1 GGGTTTA
*
64123548 GGGTTGA
1 GGGTTTA
*
64123555 -GG-TTC
1 GGGTTTA
* *
64123560 GGGGTTC
1 GGGTTTA
* **
64123567 GGGGTGG
1 GGGTTTA
*
64123574 GGGTTTC
1 GGGTTTA
*
64123581 GGGTTTG
1 GGGTTTA
64123588 GGGTTT-
1 GGGTTTA
*
64123594 GGGTTTC
1 GGGTTTA
*
64123601 GGGTTTG
1 GGGTTTA
64123608 GGGTTTA
1 GGGTTTA
*
64123615 CGGGTTTG
1 -GGGTTTA
64123623 GGGTTT-
1 GGGTTTA
64123629 GGGTTTA
1 GGGTTTA
*
64123636 GTGTTTTA
1 G-GGTTTA
*
64123644 GGGGTTTC
1 -GGGTTTA
64123652 GGGTTT
1 GGGTTT
64123658 TGGGNNNNNN
Statistics
Matches: 126, Mismatches: 17, Indels: 19
0.78 0.10 0.12
Matches are distributed among these distances:
5 1 0.01
6 22 0.17
7 75 0.60
8 27 0.21
9 1 0.01
ACGTcount: A:0.06, C:0.04, G:0.48, T:0.42
Consensus pattern (7 bp):
GGGTTTA
Found at i:64123524 original size:13 final size:14
Alignment explanation
Indices: 64123498--64123657 Score: 105
Period size: 13 Copynumber: 11.4 Consensus size: 14
64123488 ATCCAGGCTT
64123498 GGGTTTAAGGGTTTA
1 GGGTTT-AGGGTTTA
64123513 GGGTTT-GGGTTTA
1 GGGTTTAGGGTTTA
*
64123526 GGGTTTGGGGTTTTA
1 GGGTTTAGGG-TTTA
*
64123541 GGGTTTAGGGTTGA
1 GGGTTTAGGGTTTA
* * *
64123555 -GG-TTCGGGGTTC
1 GGGTTTAGGGTTTA
* ** *
64123567 GGGGTGGGGGTTTC
1 GGGTTTAGGGTTTA
*
64123581 GGGTTTGGGGTTT-
1 GGGTTTAGGGTTTA
* *
64123594 GGGTTTCGGGTTTG
1 GGGTTTAGGGTTTA
*
64123608 GGGTTTACGGGTTTG
1 GGGTTTA-GGGTTTA
64123623 GGGTTT-GGGTTTA
1 GGGTTTAGGGTTTA
* *
64123636 GTGTTTTAGGGGTTTC
1 G-GGTTTA-GGGTTTA
64123652 GGGTTT
1 GGGTTT
64123658 TGGGNNNNNN
Statistics
Matches: 119, Mismatches: 17, Indels: 18
0.77 0.11 0.12
Matches are distributed among these distances:
12 6 0.05
13 36 0.30
14 34 0.29
15 36 0.30
16 7 0.06
ACGTcount: A:0.06, C:0.04, G:0.48, T:0.42
Consensus pattern (14 bp):
GGGTTTAGGGTTTA
Found at i:64123544 original size:35 final size:35
Alignment explanation
Indices: 64123498--64123650 Score: 130
Period size: 35 Copynumber: 4.2 Consensus size: 35
64123488 ATCCAGGCTT
*
64123498 GGGTTTAAGGGTTTAGGGTTTGGGTTTAGGGTTTG
1 GGGTTTTAGGGTTTAGGGTTTGGGTTTAGGGTTTG
**
64123533 GGGTTTTAGGGTTTAGGG-TTGAGGTTCGGGGTTCGGGGTG
1 GGGTTTTAGGGTTTAGGGTTTG-GGTTTAGGGTT-----TG
* * * *
64123573 GGGGTTTCGGGTTTGGGGTTTGGGTTTCGGGTTTG
1 GGGTTTTAGGGTTTAGGGTTTGGGTTTAGGGTTTG
* *
64123608 GGG-TTTACGGGTTTGGGGTTTGGGTTTAGTGTTTTAG
1 GGGTTTTA-GGGTTTAGGGTTTGGGTTTAG-GGTTT-G
64123645 GGGTTT
1 GGGTTT
64123651 CGGGTTTTGG
Statistics
Matches: 96, Mismatches: 11, Indels: 19
0.76 0.09 0.15
Matches are distributed among these distances:
34 6 0.06
35 51 0.53
36 4 0.04
37 4 0.04
38 2 0.02
40 26 0.27
41 3 0.03
ACGTcount: A:0.07, C:0.03, G:0.48, T:0.42
Consensus pattern (35 bp):
GGGTTTTAGGGTTTAGGGTTTGGGTTTAGGGTTTG
Found at i:64123643 original size:29 final size:28
Alignment explanation
Indices: 64123574--64123657 Score: 82
Period size: 29 Copynumber: 3.0 Consensus size: 28
64123564 TTCGGGGTGG
* *
64123574 GGGTTTCGGGTTT-GGGGTTTGGGTTTC
1 GGGTTTGGGGTTTACGGGTTTGGGTTTC
64123601 GGGTTTGGGGTTTACGGGTTTGGGGTTT-
1 GGGTTTGGGGTTTACGGGTTT-GGGTTTC
* * *
64123629 GGGTTTAGTGTTTTAGGGGTTTCGGGTTT
1 GGGTTT-GGGGTTTACGGGTTT-GGGTTT
64123658 TGGGNNNNNN
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
27 12 0.25
28 12 0.25
29 24 0.50
ACGTcount: A:0.04, C:0.05, G:0.46, T:0.45
Consensus pattern (28 bp):
GGGTTTGGGGTTTACGGGTTTGGGTTTC
Found at i:64140238 original size:31 final size:32
Alignment explanation
Indices: 64140203--64140284 Score: 80
Period size: 31 Copynumber: 2.6 Consensus size: 32
64140193 CTGTTGGAGG
64140203 GCTATTTCGGGGATATCCCAAAC-TGAATTAA
1 GCTATTTCGGGGATATCCCAAACTTGAATTAA
* * * * *
64140234 GCTATATCGCGGAAATTCC-AACTTGATTTAA
1 GCTATTTCGGGGATATCCCAAACTTGAATTAA
*
64140265 GGTA-TTCTGGGGATATCCCA
1 GCTATTTC-GGGGATATCCCA
64140285 TCCAAATCGC
Statistics
Matches: 38, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
30 5 0.13
31 33 0.87
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (32 bp):
GCTATTTCGGGGATATCCCAAACTTGAATTAA
Done.